pax_global_header00006660000000000000000000000064147506254550014527gustar00rootroot0000000000000052 comment=6b4e1364003b3134eeecb86def6604c45ae751a9 pysam-0.23.0/000077500000000000000000000000001475062545500127425ustar00rootroot00000000000000pysam-0.23.0/.cirrus.yml000066400000000000000000000040311475062545500150500ustar00rootroot00000000000000build_wheels_task: only_if: $CIRRUS_BRANCH =~ "release/.*" || $CIRRUS_TAG =~ "v0\..*" matrix: - compute_engine_instance: image_project: cirrus-images image: family/docker-builder-arm64 architecture: arm64 platform: linux matrix: - name: Build ARM Linux py3.6-9 wheels env: CIBW_BUILD: "cp36-* cp37-* cp38-* cp39-*" - name: Build ARM Linux py3.10-13 wheels env: CIBW_BUILD: "cp310-* cp311-* cp312-* cp313-*" - name: Build ARM macOS wheels macos_instance: image: ghcr.io/cirruslabs/macos-sonoma-base:latest env: CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-*" alias: build_wheels env: CIRRUS_CLONE_DEPTH: 1 VENV: $HOME/relenv PATH: $VENV/bin:$PATH CIBW_SKIP: "*-musllinux_*" CIBW_BUILD_VERBOSITY: 1 # Avoid linking with non-system library libdeflate.dylib CIBW_ENVIRONMENT_MACOS: HTSLIB_CONFIGURE_OPTIONS="--without-libdeflate" CIBW_MANYLINUX_AARCH64_IMAGE: manylinux_2_28 install_script: | python3 -m venv $VENV pip3 install cibuildwheel==2.22.0 build_script: | cibuildwheel wheels_artifacts: path: wheelhouse/*.whl upload_pypi_task: only_if: $CIRRUS_BRANCH =~ "release/.*" || $CIRRUS_TAG =~ "v0\..*" depends_on: build_wheels name: Publish ARM wheels container: image: python:latest env: CIRRUS_CLONE_DEPTH: 1 API_BASEURL: https://api.cirrus-ci.com/v1 TWINE_USERNAME: __token__ install_script: | python3 -m pip install twine get_artifacts_script: | curl -sSLO $API_BASEURL/artifact/build/$CIRRUS_BUILD_ID/wheels.zip unzip -q wheels.zip upload_script: | case "$CIRRUS_TAG" in v0.*) export TWINE_REPOSITORY=pypi TWINE_PASSWORD=$PYPI_TOKEN ;; *) export TWINE_REPOSITORY=testpypi TWINE_PASSWORD=$TESTPYPI_TOKEN ;; esac echo Uploading wheels to $TWINE_REPOSITORY... python3 -m twine check wheelhouse/*.whl python3 -m twine upload --disable-progress-bar wheelhouse/*.whl pysam-0.23.0/AUTHORS000066400000000000000000000025341475062545500140160ustar00rootroot00000000000000Many people have contributed to pysam. The list of GitHub contributors is the best place to get a full list of authors and their contributions. The list and summary below is a out-of-date and represents the earlier stages of the project. List of contributors: Andreas Heger, Tildon Grant Belgard, Florian Finkernagel, Leo Goodstadt, Martin Goodson all contributed code to pysam. John Marshall has been looking after pysam and its community for several years, as well as making many code contributions and improving the engineering of pysam. Kevin B. Jacobs implemented a Cython wrapper for the VCF/BCF reader/writer in htslib. Gerton Lunter provided a validating VCF parser. Marcel Martin implemented Python 3 compatibility and added type hints. Ben Schiller contributed a Windows compatible clone. The sources in the directory samtools are from the samtools project: http://samtools.sourceforge.net/. All of these are available under the MIT licence. The attributions for this code are as follows: Heng Li from the Sanger Institute wrote most of the initial source code of SAMtools and various converters. Bob Handsaker from the Broad Institute is a major contributor to the SAM/BAM specification. He designed and implemented the BGZF format, the underlying indexable compression format for the BAM format. BGZF does not support arithmetic between file offsets. pysam-0.23.0/COPYING000066400000000000000000000020751475062545500140010ustar00rootroot00000000000000The MIT License Copyright (c) 2008-2009 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.pysam-0.23.0/Containerfile000066400000000000000000000004621475062545500154510ustar00rootroot00000000000000FROM ubi8:latest RUN yum update \ && yum install -y python3-pip python3-devel pigz \ && cd /usr/local/bin \ && ln -s /usr/bin/python3 python \ && pip3 --no-cache-dir install --upgrade pip \ && yum clean all \ && echo "system packages installed" RUN python -m pip install pysam WORKDIR /opt/ pysam-0.23.0/INSTALL000066400000000000000000000064601475062545500140010ustar00rootroot00000000000000An online version of the installation instructions can be found here: http://pysam.readthedocs.io/en/latest/installation.html ================ Installing pysam ================ Pysam can be installed through conda_, PyPI_ and from the repository. The recommended way to install pysam is through conda/bioconda. Conda installation ================== To install pysam in your current conda_ environment, type:: conda config --add channels r conda config --add channels bioconda conda install pysam This will install pysam from the bioconda_ channel and automatically makes sure that dependencies are installed. Also, compilation flags will be set automatically, which will potentially save a lot of trouble on OS X. PyPI installation ================= Pysam provides a python interface to the functionality contained within the htslib_ C library. There are two ways that these two can be combined, ``builtin`` and ``external``. Builtin ------- The typical installation will be through PyPI_:: pip install pysam This will compile the ``builtin`` htslib source code within pysam. htslib_ can be configured at compilation to turn on additional features such support using encrypted configurations, enable plugins, and more. See the htslib_ project for more information on these. Pysam will attempt to configure htslib_ to turn on some advanced features. If these fail, for example due to missing library dependencies (`libcurl`, `libcrypto`), it will fall back to conservative defaults. Options can be passed to the configure script explicitly by setting the environment variable `HTSLIB_CONFIGURE_OPTIONS`. For example:: export HTSLIB_CONFIGURE_OPTIONS=--enable-plugins pip install pysam External -------- pysam can be combined with an externally installed htslib_ library. This is a good way to avoid duplication of libraries. To link against an externally installed library, set the environment variables `HTSLIB_LIBRARY_DIR` and `HTSLIB_INCLUDE_DIR` before installing:: export HTSLIB_LIBRARY_DIR=/usr/local/lib export HTSLIB_INCLUDE_DIR=/usr/local/include pip install pysam Note that the location of the file :file:`libhts.so` needs to be known to the linker once you run pysam, for example by setting the environment-varirable `LD_LIBRARY_PATH`. Note that generally the pysam and htslib version need to be compatible. See the release notes for more information. Installation from repository ============================ pysam depends on cython_ to provide the connectivity to the htslib_ C library. The installation of the source tarball (:file:`.tar.gz`) contains pre-built C-files and cython needs not be present during installation. However, when installing from the repository, cython needs to be installed beforehand. To install from repository, type:: python setup.py install For compilation options, see the section on PyPI installation above. Requirements ============ Depending on the installation method, requirements for building pysam differ. When installing through conda_, dependencies will be resolved by the package manager. The pip_ installation and installation from source require a C compiler and its standard libraries as well as all requirements for building htslib. Htslib requirements are listed in the htslib/INSTALL file. Installing from the repository will require cython_ to be installed. pysam-0.23.0/MANIFEST.in000066400000000000000000000024121475062545500144770ustar00rootroot00000000000000# # Use .add_data_files and .add_data_dir methods in a appropriate # setup.py files to include non-python files such as documentation, # data, etc files to distribution. Avoid using MANIFEST.in for that. # include MANIFEST.in include COPYING include NEWS include INSTALL include KNOWN_BUGS include THANKS include requirements-dev.txt include pysam/libc*.pxd include pysam/libc*.pyx include pysam/libc*.c include pysam/*.c include pysam/*.h exclude pysam/config.py include win32/*.[ch] # exclude tests from sdist tarball as they require additional data prune tests/ # samtools include samtools/LICENSE samtools/README samtools/lz4/LICENSE recursive-include samtools *.[ch] include samtools/version.sh exclude samtools/*config*.h # bcftools include bcftools/LICENSE bcftools/README include bcftools/*.[ch] include bcftools/version.sh exclude bcftools/*config*.h # htslib include htslib/LICENSE htslib/README recursive-include htslib *.[ch] exclude htslib/*config*.h include htslib/configure.ac htslib/m4/*.m4 htslib/*.in include htslib/configure htslib/config.guess htslib/config.sub htslib/version.sh include htslib/Makefile htslib/*.mk exclude htslib/config.mk htslib/htscodecs.mk # documentation include doc/*.py doc/*.rst include doc/Makefile doc/make.bat doc/requirements-rtd.txt pysam-0.23.0/NEWS000066400000000000000000001157571475062545500134610ustar00rootroot00000000000000.. An online version of the release history can be found here: .. http://pysam.readthedocs.io/en/latest/release.html Release 0.23.0 ============== .. rubric:: 5 February 2025 This pysam release wraps htslib/samtools/bcftools 1.21 (PR #1310). It has been tested with Python versions 3.6 through 3.13, and wheels are available via PyPI_ for all of those Python versions. Python versions 3.6 through 3.8 are end-of-life; particularly if you use pysam with one of these versions, please vote in the version survey at issue #1230. This is expected to be the last release supporting Python 3.6 and 3.7. Bugs fixed: * Fix :func:`pysam.samtools.command(save_stdout=filename) <.samtools.command>` redirection of output to a file. (#677, reported by Haowen Zhang and analysed by Youri Hoogstrate) * Reinstate HTTPS/S3/GCS support in pre-built Linux wheels when used on Debian and Ubuntu: these wheels now work around the discrepancy between Red Hat and Debian CA Certificate file locations. (#1257, #1268, reported by Daisie Huang and Li Tai Fang) * Calling :meth:`.VariantHeader.new_record` repeatedly with the same :obj:`samples` object now sets GT correctly every time. (#1308, reported by Arthur Gymer) * Correct the exception produced when :meth:`.AlignedSegment.set_tags` is used with an invalid value type. (#1233, PR #1235, reported by Weisheng Wu and Marcus Stoiber) * Many type hinting corrections. (#1298, #1316, PR #1296, PR #1306, PR #1313, PR #1315, thanks to Victor Epain, Arthur Gymer, @mshunjan, and Matt Stone) * The undocumented :func:`!pysam.samtools.import_` alias for invoking ``samtools import`` has been removed; use :func:`pysam.samtools.fqimport() <.samtools.command>` instead. * Corrections to several test data files to account for HTSlib 1.20 and later's improved validity checking. (#1291, reported by David Seifert; etc) New functionality: * :meth:`.AlignedSegment.get_aligned_pairs` now optionally returns the associated CIGAR operator in each position tuple. (#1292, PR #1294, thanks to Lara Fuhrmann and Ivan Blagoev Topolsky) * New :meth:`AlignmentFile.flush() <.HTSFile.flush>` and :meth:`VariantFile.flush() <.HTSFile.flush>` methods for flushing buffered output to streams. (#1299, requested by @blex-max) * Improved :class:`str() ` for :class:`.AlignedSegment` now displays reference sequence names when they are available and uses ``#N`` only when necessary. (#1318, requested by Liu) * Implement :func:`repr` for :class:`.AlignedSegment` so that it displays the most useful fields. (PR #1267, thanks to Marcel Martin) * Pysam's tests can now run in parallel. (#1284, reported by Yuri Victorovich) Documentation improvements: * More complete documentation of invoking SAMtools and BCFtools subcommands via Pysam. (#1096, #1241, PR #1261, PR #1275, #1323, et al, reported by Seung-been "Steven" Lee, Robert Baldwin, Michael Hall, Indraniel Das, and @shokrofont) * Use the Pysam names for CIGAR operators rather than internal C names. (#1255, reported by Ilya Shlyakhter) * Mention :meth:`AlignmentFile.fetch("*") <.AlignmentFile.fetch>` in the FAQ entry on fetching unmapped reads. (#424, reported by Ben Weisburd) Release 0.22.1 ============== .. rubric:: 24 April 2024 Bugfix release, which still wraps htslib/samtools/bcftools 1.18. Bugs fixed: * Preserve all header field tags defined in the SAM specification (notably TP) in :meth:`.AlignmentHeader.from_dict` and :meth:`.AlignmentHeader.to_dict`. (#1237, PR #1238, thanks to Tim Fennell and Nils Homer) * Adjust HTSlib's Makefile so that ``make distclean`` no longer tries to rebuild the htscodecs configury. (PR #1247, reported by Nicola Soranzo) * Reinstate S3 support in pre-built Linux wheels: support for this protocol was inadvertently omitted from the pre-built 0.22.0 wheels on Linux. (#1249, #1277, etc varying circumstances; likely it is this that was reported by Mathew Baines, Benjamin Sargsyan, et al) * Add missing :attr:`.AlignedSegment.is_mapped` etc properties to type stubs. (PR #1273, thanks to Matt Stone) * Fix off-by-one NamedTupleProxy, :class:`.asBed`, etc array bounds check. (#1279, reported by Dan Bolser) * Make pysam's klib headers compatible with C++. (reported by Martin Grigorov) Release 0.22.0 ============== .. rubric:: 5 October 2023 This pysam release wraps htslib/samtools/bcftools 1.18 (PR #1208). It has been tested with Python versions 3.6 through 3.12, and wheels are available via PyPI_ for all of those Python versions. Python versions 3.6 and 3.7 are end-of-life; particularly if you use pysam with either of these versions, please vote in the version survey at issue #1230. The final pysam release that supported Python 2.7 was v0.20.0. Bugs fixed: * Remove Cython from runtime dependencies. (PR #1186, thanks to Nicola Soranzo, also reported by Arya Massarat in PR #1194) * Miscellaneous dependency improvements. (PR #1216, #1217, PR #1218, PR #1219, thanks to Martin Larralde and Arthur Vigil) * Suppress spurious "Could not retrieve index file" message when opening an AlignmentFile. (#939, #1214, reported by ChengYong Tham and Sebastian Röner) * Propagate SAM parsing errors encounted in :meth:`.AlignedSegment.fromstring`. (#1196, reported by DV Klopfenstein) * Accept invalid MD:A tagged fields produced by HTSeq instead of crashing in :meth:`AlignedSegment.get_aligned_pairs(with_seq=True) <.AlignedSegment.get_aligned_pairs>`. (#1226, reported by Isaac Vock) * Fix multiarch macOS CI builds by removing brewed liblzma. (#1205, reported by Till Hartmann) * Fix :attr:`.VariantRecordSample.alleles` type hint. (#1179, reported by David Seifert) New functionality: * Add optional :meth:`HTSFile.seek(..., whence) <.HTSFile.seek>` parameter and clarify which functions use libc.SEEK_SET vs io.SEEK_SET. (#1185, requested by luyulin) * File handling improvements in samtools & bcftools commands. (should improve #1193 and #1195, reported by Rob Bierman and Sam Chorlton) * Improve :class:`.FastxFile` performance. (PR #1227, thanks to Fabian Klötzl and Valentyn Bezshapkin) * Improve the accuracy of type hints for :class:`.AlignmentFile` iteration. (#1184, PR #1189, reported by @PikalaxALT) Documentation improvements: * Clarify that :meth:`.AlignedSegment.get_aligned_pairs` results are 0-based. (#1180, reported by Nick Semenkovich) * Clarify :meth:`.AlignedSegment.get_reference_positions` documentation. (#836, #838, reported by Liang Ou and Nick Stoler) * Clarify that installation via pip usually uses a wheel, and that configuring the build via $HTSLIB_CONFIGURE_OPTIONS etc only applies when installing from an sdist. (#1086, reported by Layne Sadler) A message from pysam's founder, Andreas Heger: As many of you will have noticed, John Marshall has been effectively maintaining pysam and supporting users over the last few years. I, Andreas, am very grateful for the countless hours he has contributed. Unfortunately, I will not be able to contribute much in the near and intermediate future. To keep pysam going, John has kindly agreed to continue maintaining and supporting pysam as the principal developer of pysam. I am very happy to know that pysam is in good hands and want to thank again John and the wider pysam community for their suggestions, bug reports, code contributions and general support. Thank you Andreas for all your work over the years and the solid foundations that pysam enjoys and the useful functionality it provides. Release 0.21.0 ============== .. rubric:: 2 April 2023 This release wraps htslib/samtools/bcftools version 1.17. Pysam is now compatible with Python 3.11. We have removed Python 2.x support. Pysam is tested with Python versions 3.6 to 3.11. * [#1175] VariantHeader.new_record: set start/stop before alleles * [#1173] Add multiple build improvements in htscodecs on multi-arch macOS * [#1148] Ignore CIGAR-less reads in find_introns. * [#1172] Add new `samtools cram-size` and `samtools reset` commands * [#1169] Fix CRAM index-related crash when using the musl C standard library. * [#1168] Add a minimal pyproject.toml for PEP517. * [#1158] Fix type hints and add FastqProxy type hints. * [#1147] Py3.11 compatibility, get shared object suffix from EXT_SUFFIX. * [#1143] Add mypy symbols for samtools and bcftools. * [#1155] Fix pysam.index() when using recent `samtools index` options. * [#1151] Test suite py3.11 compatibility, work around failing test case. * [#1149] MacOS universal build compatibility. * [#1146] Fix build when CFLAGS/etc environment variables are set. Release 0.20.0 ============== .. rubric:: 29 October 2022 This release wraps htslib/bcftools version 1.16 and samtools version 1.16.1. * [#1113] Full compatibility with setuptools v62.1.0's build directory name changes * [#1121] Build-time symbol check portability improved * [#1122] Fix setting sample genotype using .alleles property * [#1128] Fix test suite failure when using a libdeflate-enabled samtools Many additional type hints have been provided by the community, thanks! Release 0.19.1 ============== .. rubric:: 27 May 2022 This release wraps htslib/samtools/bcftools version 1.15.1. * [#1104] add an add_samples() method to quickly add multiple samples to VCF. Release 0.19.0 ============== .. rubric:: 30 March 2022 This release wraps htslib/samtools/bcftools version 1.15. * [#1085] Improve getopt()/getopt_long() resetting when running samtools/bcftools commands * [#1078] Support BAM_CPAD in get_aligned_pairs * [#1063] Run flake8 and fix some linting issues * [#1088] Add AlignedSegment is_mapped/mate_is_mapped/is_forward/mate_is_forward properties * Write an absent AlignedSegment.qual as all-bytes-0xff * Fix BGZFile.read() behaviour near or at EOF * First API for the htslib modified bases interface Release 0.18.0 ============== .. rubric:: 17 November 2021 This release wraps htslib/samtools/bcftools version 1.14. * [#1048] and [#1060], clarify documentation of index statistics with CRAM files * Prevent "retval may be used uninitialised" warning. * Add new "samples" subcommand to pysam/samtools.py * Introduce TupleProxyIterator iterator object class Release 0.17.0 ============== .. rubric:: 30 September 2021 This release wraps htslib/samtools/bcftools version 1.13. Corresponding to new samtools commands, `pysam.samtools` now has additional functions `ampliconclip`, `ampliconstats`, `fqimport`, and `version`. Bugs fixed: * [#447] The maximum QNAME length is fully restored to 254 * [#506, #958, #1000] Don't crash the Python interpreter on ``pysam.bcftools.*()`` errors * [#603] count_coverage: ignore reads that have no SEQ field * [#928] Fix ``pysam.bcftools.mpileup()`` segmentation fault * [#983] Add win32/\*.[ch] to MANIFEST.in * [#994] Raise exception in ``get_tid()`` if header could not be parsed * [#995] Choose TBI/CSI in ``tabix_index()`` via both min_shift and csi * [#996] ``AlignmentFile.fetch()`` now works with large chromosomes longer than 2\ :sup:`29` bases * [#1019] Fix Sphinx documentation generation by avoiding Python 2 ``ur'string'`` syntax * [#1035] Improved handling of file iteration errors * [#1038] ``tabix_index()`` no longer leaks file descriptors * [#1040] ``print(aligned_segment)`` now prints the correct TLEN value (it also now prints RNAME/RNEXT more clearly and prints POS/PNEXT 1-based) * *setup.py* longer uses ``setup(use_2to3)`` for compatibility with setuptools >= v58.0.0 New facilities: * [PR #963] Additional VCF classes are exposed to pysam programmers * [#998, PR #1001] Add ``get/set_encoding_error_handler()`` to control UTF-8 conversion * [PR #1012] Running ``python setup.py sdist`` now automatically runs cythonize * Running tests with ``pytest`` now automatically runs ``make`` to generate test data Documentation improvements: * [#726] Clarify get_forward_sequence/get_forward_qualities documentation * [#865] Improved example * [#968] ``get_index_statstics`` parameters * [#986] Clarify ``VariantFile.fetch`` start/stop region parameters are 0-based and half-open. * [#990] Corrected ``PileupColumn.get_query_sequences`` documentation * [#999] Fix documentation for ``AlignmentFile.get_reference_length()`` * [#1002] Document the default min_base_quality for ``pileup()`` Release 0.16.0 ============== .. rubric:: 8 June 2020 This release wraps htslib/bcftools version 1.10.2 and samtools version 1.10. The following bugs reported against pysam are fixed due to this: * [#447] Writing out QNAME longer than 251 characters corrupts BAM * [#640, #734, #843] Setting VariantRecord pos or stop raises error * [#738, #919] FastxFile truncates concatenated plain gzip compressed files Additional bugfixes: * [#840] Pileup doesn't work on python3 when `index_filename` is used * [#886] FastqProxy raises ValueError when instantiated from python * [#904] VariantFile.fetch() throws ValueError on files with no records * [#909] Fix incorrect quoting in VariantFile contig records * [#915, #916] Implement pileup() for unindexed files and/or SAM files Backwards incompatible changes: * The `samtools import` command was removed in samtools 1.10, so pysam no longer exports a `samimport` function. Use `pysam.view()` instead. Release 0.15.4 ============== Bugfix release. Principal reason for release is to update cython version in order to fix pip install pysam with python 3.8. * [#879] Fix add_meta function in libcbcf.pyx, so meta-information lines in header added with this function have double-quoting rules in accordance to rules specified in VCF4.2 and VCF4.3 specifications * [#863] Force arg to bytes to support non-ASCII encoding * [#875] Bump minimum Cython version * [#868] Prevent segfault on Python 2.7 AlignedSegment.compare(other=None) * [#867] Fix wheel building on TravisCI * [#863] Force arg to bytes to support non-ASCII encoding * [#799] disambiguate interpretation of bcf_read return code * [#841] Fix silent truncation of FASTQ with bad q strings * [#846] Prevent segmentation fault on ID, when handling malformed records * [#829] Run configure with the correct CC/CFLAGS/LDFLAGS env vars Release 0.15.3 ============== Bugfix release. * [#824] allow reading of UTF-8 encoded text in VCF/BCF files. * [#780] close all filehandles before opening new ones in pysam_dispatch * [#773] do not cache VariantRecord.id to avoid memory leak * [#781] default of multiple_iterators=True is changed to False for CRAM files. * [#825] fix collections.abc import * [#825] use bcf_hdr_format instead of bcf_hdr_fmt_text, fix memcpy bug when setting FORMAT fields. * [#804] Use HTSlib's kstring_t, which reallocates and enlarges its memory as needed, rather than a fixed-size char buffer. * [#814] Build wheels and upload them to PyPI * [#755] Allow passing flags and arguments to index methods * [#763] Strip \0 in header check * [#761] Test Tabix index contents, not the compression Release 0.15.2 ============== Bugfix release. * [#746] catch pileup itorator out-of-scope segfaults * [#747] fix faixd fetch with region * [#748] increase max_pos to (1<<31)-1 * [#645] Add missing macOS stub files in `MANIFEST.in`, @SoapZA * [#737] Fix bug in get_aligned_pairs, @bkohrn Release 0.15.1 ============== Bugfix release. * [#716] raise ValueError if tid is out of range when writing * [#697] release version using cython 0.28.5 for python 3.7 compatibility Release 0.15.0 ============== This release wraps htslib/samtools/bcftools version 1.9. * [#673] permit dash in chromosome name of region string * [#656] Support `text` when opening a SAM file for writing * [#658] return None in get_forward_sequence if sequence not in record * [#683] allow lower case bases in MD tags * Ensure that = and X CIGAR ops are treated the same as M Release 0.14.1 ============== This is mostly a bugfix release, though bcftools has now also been upgraded to 1.7.0. * [#621] Add a warning to count_coverage when an alignment has an empty QUAL field * [#635] Speed-up of AlignedSegment.find_intro() * treat border case of all bases in pileup column below quality score * [#634] Fix access to pileup reference_sequence Release 0.14.0 ============== This release wraps htslib/samtools versions 1.7.0. * SAM/BAM/CRAM headers are now managed by a separate AlignmentHeader class. * AlignmentFile.header.as_dict() returns an ordered dictionary. * Use "stop" instead of "end" to ensure consistency to VariantFile. The end designations have been kept for backwards compatibility. * [#611] and [#293] CRAM repeated fetch now works, each iterator reloads index if multiple_iterators=True * [#608] pysam now wraps htslib 1.7 and samtools 1.7. * [#580] reference_name and next_reference_name can now be set to "*" (will be converted to None to indicate an unmapped location) * [#302] providing no coordinate to count_coverage will not count from start/end of contig. * [#325] @SQ records will be automatically added to header if they are absent from text section of header. * [#529] add get_forward_sequence() and get_forward_qualities() methods * [#577] add from_string() and to_dict()/from_dict() methods to AlignedSegment. Rename tostring() to to_string() throughout for consistency * [#589] return None from build_alignment_sequence if no MD tag is set * [#528] add PileupColumn.__len__ method Backwards incompatible changes: * AlignmentFile.header now returns an AlignmentHeader object. Use AlignmentFile.header.to_dict() to get the dictionary as previously. Most dictionary accessor methods (keys(), values(), __getitem__, ...) have been implemented to ensure some level of backwards compatibility when only reading. The rationale for this change is to have consistency between AlignmentFile and VariantFile. * AlignmentFile and FastaFile now raise IOError instead of OSError Medium term we plan to have a 1.0 release. The pysam interface has grown over the years and the API is cluttered with deprecated names (Samfile, getrname(), gettid(), ...). To work towards this, the next release (0.15.0) will yield DeprecationWarnings for any parts of the API that are considered obsolete and will not be in 1.0. Once 1.0 has been reached, we will use semantic versioning. Release 0.13.0 =============== This release wraps htslib/samtools/bcftools versions 1.6.0 and contains a series of bugfixes. * [#544] reading header from remote TabixFiles now works. * [#531] add missing tag types H and A. A python float will now be added as 'f' type instead of 'd' type. * [#543] use FastaFile instead of Fastafile in pileup. * [#546] set is_modified flag in setAttribute so updated attributes are output. * [#537] allow tabix index files to be created in a custom location. * [#530] add get_index_statistics() method Release 0.12.0.1 ================ Bugfix release to solve compilation issue due to missinge bcftools/config.h file. Release 0.12.0 ============== This release wraps htslib/samtools/bcftools versions 1.5.0 and contains a series of bugfixes. * [#473] A new FastxRecord class that can be instantiated from class and modified in-place. Replaces PersistentFastqProxy. * [#521] In AligmentFile, Simplify file detection logic and allow remote index files * Removed attempts to guess data and index file names; this is magic left to htslib. * Removed file existence check prior to opening files with htslib * Better error checking after opening files that raise the appropriate error (IOError for when errno is set, ValueError otherwise for backward compatibility). * Report IO errors when loading an index by name. * Allow remote indices (tested using S3 signed URLs). * Document filepath_index and make it an alias for index_filename. * Added a require_index parameter to AlignmentFile * [#526] handle unset ref when creating new records * [#513] fix bcf_translate to skip deleted FORMAT fields to avoid segfaults * [#516] expose IO errors via IOError exceptions * [#487] add tabix line_skip, remove 'pileup' preset * add FastxRecord, replaces PersistentFastqProxy (still present for backwards compatibility) * [#496] upgrade to htslib/samtools/bcftools versions 1.5 * add start/stop to AlignmentFile.fetch() to be consistent with VariantFile.fetch(). "end" is kept for backwards compatibility. * [#512] add get_index_statistics() method to AlignmentFile. Upcoming changes: In the next release we are plannig to separate the header information from AlignmentFile into a separate class AlignmentHeader. This layout is similar to VariantFile/VariantHeader. With this change we will ensure that an AlignedSegment record will be linked to a header so that chromosome names can be automatically translated from the numeric representation. As a consequence, the way new AlignedSegment records are created will need to change as the constructor requires a header:: header = pysam.AlignmentHeader( reference_names=["chr1", "chr2"], reference_lengths=[1000, 1000]) read = pysam.AlignedSegment(header) This will affect all code that instantiates AlignedSegment objects directly. We have not yet merged to allow users to provide feed-back. The pull-request is here: https://github.com/pysam-developers/pysam/pull/518 Please comment on github. Release 0.11.2.2 ================ Bugfix release to address two issues: * Changes in 0.11.2.1 broke the GTF/GFF3 parser. Corrected and more tests have been added. * [#479] Correct VariantRecord edge cases described in issue Release 0.11.2.1 ================ Release to fix release tar-ball containing 0.11.1 pre-compiled C-files. Release 0.11.2 ============== This release wraps htslib/samtools/bcfools versions 1.4.1 in response to a security fix in these libraries. Additionally the following issues have been fixed: * [#452] add GFF3 support for tabix parsers * [#461] Multiple fixes related to VariantRecordInfo and handling of INFO/END * [#447] limit query name to 251 characters (only partially addresses issue) VariantFile and related object fixes * Restore VariantFile.\_\_dealloc\_\_ * Correct handling of bcf_str_missing in bcf_array_to_object and bcf_object_to_array * Added update() and pop() methods to some dict-like proxy objects * scalar INFO entries could not be set again after being deleted * VariantRecordInfo.__delitem__ now allows unset flags to be deleted without raising a KeyError * Multiple other fixes for VariantRecordInfo methods * INFO/END is now accessible only via VariantRecord.stop and VariantRecord.rlen. Even if present behind the scenes, it is no longer accessible via VariantRecordInfo. * Add argument to issue a warning instead of an exception if input appears to be truncated Other features and fixes: * Make AlignmentFile \_\_dealloc\_\_ and close more stringent * Add argument AlignmentFile to issue a warning instead of an exception if input appears to be truncated Release 0.11.1 ============== Bugfix release * [#440] add deprecated 'always' option to infer_query_length for backwards compatibility. Release 0.11.0 ============== This release wraps the latest versions of htslib/samtools/bcftools and implements a few bugfixes. * [#413] Wrap HTSlib/Samtools/BCFtools 1.4 * [#422] Fix missing pysam.sort.usage() message * [#411] Fix BGZfile initialization bug * [#412] Add seek support for BGZFile * [#395] Make BGZfile iterable * [#433] Correct getQueryEnd * [#419] Export SAM enums such as pysam.CMATCH * [#415] Fix access by tid in AlignmentFile.fetch() * [#405] Writing SAM now outputs a header by default. * [#332] split infer_query_length(always) into infer_query_length and infer_read_length Release 0.10.0 ============== This release implements further functionality in the VariantFile API and includes several bugfixes: * treat special case -c option in samtools view outputs to stdout even if -o given, fixes #315 * permit reading BAM files with CSI index, closes #370 * raise Error if query name exceeds maximum length, fixes #373 * new method to compute hash value for AlignedSegment * AlignmentFile, VariantFile and TabixFile all inherit from HTSFile * Avoid segfault by detecting out of range reference_id and next_reference in AlignedSegment.tostring * Issue #355: Implement streams using file descriptors for VariantFile * upgrade to htslib 1.3.2 * fix compilation with musl libc * Issue #316, #360: Rename all Cython modules to have lib as a prefix * Issue #332, hardclipped bases in cigar included by pysam.AlignedSegment.infer_query_length() * Added support for Python 3.6 filename encoding protocol * Issue #371, fix incorrect parsing of scalar INFO and FORMAT fields in VariantRecord * Issue #331, fix failure in VariantFile.reset() method * Issue #314, add VariantHeader.new_record(), VariantFile.new_record() and VariantRecord.copy() methods to create new VariantRecord objects * Added VariantRecordFilter.add() method to allow setting new VariantRecord filters * Preliminary (potentially unsafe) support for removing and altering header metadata * Many minor fixes and improvements to VariantFile and related objects Please note that all internal cython extensions now have a lib prefix to facilitate linking against pysam extension modules. Any user cython extensions using cimport to import pysam definitions will need changes, for example:: cimport pysam.csamtools will become:: cimport pysam.libcsamtools Release 0.9.1 ============= This is a bugfix release addressing some installation problems in pysam 0.9.0, in particular: * patch included htslib to work with older libcurl versions, fixes #262. * do not require cython for python 3 install, fixes #260 * FastaFile does not accept filepath_index any more, see #270 * add AlignedSegment.get_cigar_stats method. * py3 bugfix in VariantFile.subset_samples, fixes #272 * add missing sysconfig import, fixes #278 * do not redirect stdout, but instead write to a separately created file. This should resolve issues when pysam is used in notebooks or other environments that redirect stdout. * wrap htslib-1.3.1, samtools-1.3.1 and bcftools-1.3.1 * use bgzf throughout instead of gzip * allow specifying a fasta reference for CRAM file when opening for both read and write, fixes #280 Release 0.9.0 ============= Overview -------- The 0.9.0 release upgrades htslib to htslib 1.3 and numerous other enhancements and bugfixes. See below for a detailed list. `Htslib 1.3 `_ comes with additional capabilities for remote file access which depend on the presence of optional system libraries. As a consequence, the installation script :file:`setup.py` has become more complex. For an overview, see :ref:`installation`. We have tested installation on linux and OS X, but could not capture all variations. It is possible that a 0.9.1 release might follow soon addressing installation issues. The :py:class:`~.pysam.VariantFile` class provides access to :term:`vcf` and :term:`bcf` formatted files. The class is certainly usable and interface is reaching completion, but the API and the functionality is subject to change. Detailed release notes ---------------------- * upgrade to htslib 1.3 * python 3 compatibility tested throughout. * added a first set of bcftools commands in the pysam.bcftools submodule. * samtools commands are now in the pysam.samtools module. For backwards compatibility they are still imported into the pysam namespace. * samtools/bcftools return stdout as a single (byte) string. As output can be binary (VCF.gz, BAM) this is necessary to ensure py2/py3 compatibility. To replicate the previous behaviour in py2.7, use:: pysam.samtools.view(self.filename).splitlines(True) * get_tags() returns the tag type as a character, not an integer (#214) * TabixFile now raises ValueError on indices created by tabix <1.0 (#206) * improve OSX installation and develop mode * FastxIterator now handles empty sequences (#204) * TabixFile.isremote is not TabixFile.is_remote in line with AlignmentFile * AlignmentFile.count() has extra optional argument read_callback * setup.py has been changed to: * install a single builtin htslib library. Previously, each pysam module contained its own version. This reduces compilation time and code bloat. * run configure for the builtin htslib library in order to detect optional libraries such as libcurl. Configure behaviour can be controlled by setting the environment variable HTSLIB_CONFIGURE_OPTIONS. * get_reference_sequence() now returns the reference sequence and not something looking like it. This bug had effects on get_aligned_pairs(with_seq=True), see #225. If you have relied on on get_aligned_pairs(with_seq=True) in pysam-0.8.4, please check your results. * improved autodetection of file formats in AlignmentFile and VariantFile. Release 0.8.4 ============= This release contains numerous bugfixes and a first implementation of a pythonic interface to VCF/BCF files. Note that this code is still incomplete and preliminary, but does offer a nearly complete immutable Pythonic interface to VCF/BCF metadata and data with reading and writing capability. Potential isses when upgrading from v0.8.3: * binary tags are now returned as python arrays * renamed several methods for pep8 compatibility, old names still retained for backwards compatibility, but should be considered deprecated. * gettid() is now get_tid() * getrname() is now get_reference_name() * parseRegion() is now parse_region() * some methods have changed for pep8 compatibility without the old names being present: * fromQualityString() is now qualitystring_to_array() * toQualityString() is now qualities_to_qualitystring() * faidx now returns strings and not binary strings in py3. * The cython components have been broken up into smaller files with more specific content. This will affect users using the cython interfaces. Edited list of commit log changes: * fixes AlignmentFile.check_index to return True * add RG/PM header tag - closes #179 * add with_seq option to get_aligned_pairs * use char * inside reconsituteReferenceSequence * add soft clipping for get_reference_sequence * add get_reference_sequence * queryEnd now computes length from cigar string if no sequence present, closes #176 * tolerate missing space at end of gtf files, closes #162 * do not raise Error when receiving output on stderr * add docu about fetching without index, closes #170 * FastaFile and FastxFile now return strings in python3, closes #173 * py3 compat: relative -> absolute imports. * add reference_name and next_reference_name attributes to AlignedSegment * add function signatures to cvcf cython. Added note about other VCF code. * add context manager functions to FastaFile * add reference_name and next_reference_name attributes to AlignedSegment * PileupColumn also gets a reference_name attribute. * add context manager functions to FastaFile * TabixFile.header for remote files raises AttributeError, fixes #157 * add context manager interface to TabixFile, closes #165 * change ctypedef enum to typedef enum for cython 0.23 * add function signatures to cvcf cython, also added note about other VCF code * remove exception for custom upper-case header record tags. * rename VALID_HEADER_FIELDS to KNOWN_HEADER_FIELDS * fix header record tag parsing for custom tags. * use cython.str in count_coverage, fixes #141 * avoid maketrans (issues with python3) * refactoring: AlignedSegment now in separate module * do not execute remote tests if URL not available * fix the unmapped count, incl reads with no SQ group * add raw output to tags * added write access for binary tags * bugfix in call to resize * implemented writing of binary tags from arrays * implemented convert_binary_tag to use arrays * add special cases for reads that are unmapped or whose mates are unmapped. * rename TabProxies to ctabixproxies * remove underscores from utility functions * move utility methods into cutils * remove callback argument to fetch - closes #128 * avoid calling close in dealloc * add unit tests for File object opening * change AlignmentFile.open to filepath_or_object * implement copy.copy, close #65 * add chaching of array attributes in AlignedSegment, closes #121 * add export of Fastafile * remove superfluous pysam_dispatch * use persist option in FastqFile * get_tag: expose tag type if requested with `with_value_type` * fix to allow reading vcf record info via tabix-based vcf reader * add pFastqProxy and pFastqFile objects to make it possible to work with multiple fastq records per file handle, unlike FastqProxy/FastqFile. * release GIL around htslib IO operations * More work on read/write support, API improvements * add `phased` property on `VariantRecordSample` * add mutable properties to VariantRecord * BCF fixes and start of read/write support * VariantHeaderRecord objects now act like mappings for attributes. * add VariantHeader.alts dict from alt ID->Record. * Bug fix to strong representation of structured header records. * VariantHeader is now mutable Release 0.8.3 ============= * samtools command now accept the "catch_stdout" option. * get_aligned_pairs now works for soft-clipped reads. * query_position is now None when a PileupRead is not aligned to a particular position. * AlignedSegments are now comparable and hashable. Release 0.8.2.1 =============== * Installation bugfix release. Release 0.8.2 ============= * Pysam now wraps htslib 1.2.1 and samtools version 1.2. * Added CRAM file support to pysam. * New alignment info interface. * opt() and setTag are deprecated, use get_tag() and set_tag() instead. * added has_tag() * tags is deprecated, use get_tags() and set_tags() instead. * FastqFile is now FastxFile to reflect that the latter permits iteration over both fastq- and fasta-formatted files. * A Cython wrapper for htslib VCF/BCF reader/writer. The wrapper provides a nearly complete Pythonic interface to VCF/BCF metadata with reading and writing capability. However, the interface is still incomplete and preliminary and lacks capability to mutate the resulting data. Release 0.8.1 ============= * Pysam now wraps htslib and samtools versions 1.1. * Bugfixes, most notable: * issue #43: uncompressed BAM output * issue #42: skip tests requiring network if none available * issue #19: multiple iterators can now be made to work on the same tabix file * issue #24: All strings returned from/passed to the pysam API are now unicode in python 3 * issue #5: type guessing for lists of integers fixed * API changes for consistency. The old API is still present, but deprecated. In particular: * Tabixfile -> TabixFile * Fastafile -> FastaFile * Fastqfile -> FastqFile * Samfile -> AlignmentFile * AlignedRead -> AlignedSegment * qname -> query_name * tid -> reference_id * pos -> reference_start * mapq -> mapping_quality * rnext -> next_reference_id * pnext -> next_reference_start * cigar -> cigartuples * cigarstring -> cigarstring * tlen -> template_length * seq -> query_sequence * qual -> query_qualities, now returns array * qqual -> query_alignment_qualities, now returns array * tags -> tags * alen -> reference_length, reference is always "alignment", so removed * aend -> reference_end * rlen -> query_length * query -> query_alignment_sequence * qstart -> query_alignment_start * qend -> query_alignment_end * qlen -> query_alignment_length * mrnm -> next_reference_id * mpos -> next_reference_start * rname -> reference_id * isize -> template_length * blocks -> get_blocks() * aligned_pairs -> get_aligned_pairs() * inferred_length -> infer_query_length() * positions -> get_reference_positions() * overlap() -> get_overlap() * All strings are now passed to or received from the pysam API as strings, no more bytes. Other changes: * AlignmentFile.fetch(reopen) option is now multiple_iterators. The default changed to not reopen a file unless requested by the user. * FastaFile.getReferenceLength is now FastaFile.get_reference_length Backwards incompatible changes * Empty cigarstring now returns None (instead of '') * Empty cigar now returns None (instead of []) * When using the extension classes in cython modules, AlignedRead needs to be substituted with AlignedSegment. * fancy_str() has been removed * qual, qqual now return arrays Release 0.8.0 ============= * Disabled features * IteratorColumn.setMask() disabled as htslib does not implement this functionality? * Not implemented yet: * reading SAM files without header Tabix files between version 0.7.8 and 0.8.0 are not compatible and need to be re-indexed. While version 0.7.8 and 0.8.0 should be mostly compatible, there are some notable exceptions: * tabix iterators will fail if there are comments in the middle or the end of a file. * tabix raises always ValueError for invalid intervals. Previously, different types of errors were raised (KeyError, IndexError, ValueError) depending on the type of invalid intervals (missing chromosome, out-of-range, malformatted interval). Release 0.7.8 ============= * added AlignedRead.setTag method * added AlignedRead.blocks * unsetting CIGAR strings is now possible * empty CIGAR string returns empty list * added reopen flag to Samfile.fetch() * various bugfixes Release 0.7.7 ============= * added Fastafile.references, .nreferences and .lengths * tabix_iterator now uses kseq.h for python 2.7 Release 0.7.6 ============= * added inferred_length property * issue 122: MACOSX getline missing, now it works? * seq and qual can be set None * added Fastqfile Release 0.7.5 ============= * switch to samtools 0.1.19 * issue 122: MACOSX getline missing * issue 130: clean up tempfiles * various other bugfixes Release 0.7.4 ============= * further bugfixes to setup.py and package layout Release 0.7.3 ============= * further bugfixes to setup.py * upgraded distribute_setup.py to 0.6.34 Release 0.7.2 ============= * bugfix in installer - failed when cython not present * changed installation locations of shared libraries Release 0.7.1 ============= * bugfix: missing PP tag PG records in header * added pre-built .c files to distribution Release 0.7 =========== * switch to tabix 0.2.6 * added cigarstring field * python3 compatibility * added B tag handling * added check_sq and check_header options to Samfile.__init__ * added lazy GTF parsing to tabix * reworked support for VCF format parsing * bugfixes Release 0.6 =========== * switch to samtools 0.1.18 * various bugfixes * removed references to deprecated 'samtools pileup' functionality * AlignedRead.tags now returns an empty list if there are no tags. * added pnext, rnext and tlen Release 0.5 =========== * switch to samtools 0.1.16 and tabix 0.2.5 * improved tabix parsing, added vcf support * re-organized code to permit linking against pysam * various bugfixes * added Samfile.positions and Samfile.overlap Release 0.4 =========== * switch to samtools 0.1.12a and tabix 0.2.3 * added snp and indel calling. * switch from pyrex to cython * changed handling of samtools stderr * various bugfixes * added Samfile.count and Samfile.mate * deprecated AlignedRead.rname, added AlignedRead.tid Release 0.3 =========== * switch to samtools 0.1.8 * added support for tabix files * numerous bugfixes including * permit simultaneous iterators on the same file * working access to remote files pysam-0.23.0/README.rst000066400000000000000000000036131475062545500144340ustar00rootroot00000000000000===== Pysam ===== |build-status| |docs| Pysam is a python module for reading and manipulating files in the SAM/BAM format. The SAM/BAM format is a way to store efficiently large numbers of alignments (`Li 2009`_), such as those routinely created by next-generation sequencing methods. Pysam is a lightweight wrapper of the samtools_ C-API. Pysam also includes an interface for tabix_. If you are using the conda packaging manager (e.g. miniconda or anaconda), you can install pysam from the `bioconda channel `_:: conda config --add channels defaults conda config --add channels conda-forge conda config --add channels bioconda conda install pysam Installation through bioconda is the recommended way to install pysam as it resolves non-python dependencies and uses pre-configured compilation options. Especially for OS X this will potentially save a lot of trouble. The current version of pysam wraps 3rd-party code from htslib-1.21, samtools-1.21, and bcftools-1.21. Pysam is available through `PyPI `_. To install, type:: pip install pysam Pysam documentation is available `here `_ Questions and comments are very welcome and should be sent to the `pysam user group `_ .. _samtools: http://samtools.sourceforge.net/ .. _tabix: http://samtools.sourceforge.net/tabix.shtml .. _Li 2009: http://www.ncbi.nlm.nih.gov/pubmed/19505943 .. |build-status| image:: https://github.com/pysam-developers/pysam/actions/workflows/ci.yaml/badge.svg :alt: build status :scale: 100% :target: https://github.com/pysam-developers/pysam/actions/workflows/ci.yaml .. |docs| image:: https://readthedocs.org/projects/pysam/badge/?version=latest :alt: Documentation Status :scale: 100% :target: https://pysam.readthedocs.org/en/latest/?badge=latest pysam-0.23.0/bcftools/000077500000000000000000000000001475062545500145555ustar00rootroot00000000000000pysam-0.23.0/bcftools/HMM.c000066400000000000000000000435111475062545500153460ustar00rootroot00000000000000/* The MIT License Copyright (c) 2014-2017 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include "HMM.h" typedef struct { int nstates; // number of hmm's states uint32_t snap_at_pos; // snapshot at this position, 0 when inactive double *vit_prob; // viterbi probabilities, NULL for uniform probs double *fwd_prob; // transition probabilities double *bwd_prob; // transition probabilities } snapshot_t; struct _hmm_t { int nstates; // number of states double *vprob, *vprob_tmp; // viterbi probs [nstates] uint8_t *vpath; // viterbi path [nstates*nvpath] double *bwd, *bwd_tmp; // bwd probs [nstates] double *fwd; // fwd probs [nstates*(nfwd+1)] int nvpath, nfwd; int ntprob_arr; // number of pre-calculated tprob matrices double *curr_tprob, *tmp; // Temporary arrays; curr_tprob is short lived, valid only for // one site (that is, one step of Viterbi algorithm) double *tprob_arr; // Array of transition matrices, precalculated to ntprob_arr // positions. The first matrix is the initial tprob matrix // set by hmm_init() or hmm_set_tprob() set_tprob_f set_tprob; // Optional user function to set / modify transition probabilities // at each site (one step of Viterbi algorithm) void *set_tprob_data; snapshot_t init, state; // Initial and current state probs. Set state from snapshot if prev_snap_pos!=0 or from init otherwise snapshot_t *snapshot; // snapshot->snap_at_pos .. request a snapshot at this position // hmm->state.snap_at_pos .. the current state comes from snapshot made at this position }; uint8_t *hmm_get_viterbi_path(hmm_t *hmm) { return hmm->vpath; } double *hmm_get_tprob(hmm_t *hmm) { return hmm->tprob_arr; } int hmm_get_nstates(hmm_t *hmm) { return hmm->nstates; } double *hmm_get_fwd_bwd_prob(hmm_t *hmm) { return hmm->fwd; } static inline void multiply_matrix(int n, double *a, double *b, double *dst, double *tmp) { double *out = dst; if ( a==dst || b==dst ) out = tmp; int i,j,k; for (i=0; iinit.snap_at_pos = hmm->state.snap_at_pos = 0; if ( !hmm->init.vit_prob ) hmm->init.vit_prob = (double*) malloc(sizeof(double)*hmm->nstates); if ( !hmm->init.fwd_prob ) hmm->init.fwd_prob = (double*) malloc(sizeof(double)*hmm->nstates); if ( !hmm->init.bwd_prob ) hmm->init.bwd_prob = (double*) malloc(sizeof(double)*hmm->nstates); if ( !hmm->state.vit_prob ) hmm->state.vit_prob = (double*) malloc(sizeof(double)*hmm->nstates); if ( !hmm->state.fwd_prob ) hmm->state.fwd_prob = (double*) malloc(sizeof(double)*hmm->nstates); if ( !hmm->state.bwd_prob ) hmm->state.bwd_prob = (double*) malloc(sizeof(double)*hmm->nstates); int i; if ( probs ) { memcpy(hmm->init.vit_prob,probs,sizeof(double)*hmm->nstates); double sum = 0; for (i=0; instates; i++) sum += hmm->init.vit_prob[i]; for (i=0; instates; i++) hmm->init.vit_prob[i] /= sum; } else for (i=0; instates; i++) hmm->init.vit_prob[i] = 1./hmm->nstates; memcpy(hmm->init.fwd_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates); // these remain unchanged memcpy(hmm->init.bwd_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates); memcpy(hmm->state.vit_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates); // can be changed by snapshotting memcpy(hmm->state.fwd_prob,hmm->init.fwd_prob,sizeof(double)*hmm->nstates); memcpy(hmm->state.bwd_prob,hmm->init.bwd_prob,sizeof(double)*hmm->nstates); } hmm_t *hmm_init(int nstates, double *tprob, int ntprob) { hmm_t *hmm = (hmm_t*) calloc(1,sizeof(hmm_t)); hmm->nstates = nstates; hmm->curr_tprob = (double*) malloc(sizeof(double)*nstates*nstates); hmm->tmp = (double*) malloc(sizeof(double)*nstates*nstates); hmm_set_tprob(hmm, tprob, ntprob); hmm_init_states(hmm, NULL); return hmm; } void *hmm_snapshot(hmm_t *hmm, void *_snapshot, uint32_t pos) { snapshot_t *snapshot = (snapshot_t*) _snapshot; if ( snapshot && snapshot->nstates!=hmm->nstates ) { free(snapshot); snapshot = NULL; } if ( !snapshot ) { // Allocate the snapshot as a single memory block so that it can be // free()-ed by the user. So make sure the arrays are aligned.. size_t str_size = sizeof(snapshot_t); size_t dbl_size = sizeof(double); size_t pad_size = (dbl_size - str_size % dbl_size) % dbl_size; uint8_t *mem = (uint8_t*) malloc(str_size + pad_size + dbl_size*2*hmm->nstates); snapshot = (snapshot_t*) mem; snapshot->nstates = hmm->nstates; snapshot->vit_prob = (double*) (mem + str_size + pad_size); snapshot->fwd_prob = snapshot->vit_prob + hmm->nstates; } snapshot->snap_at_pos = pos; hmm->snapshot = snapshot; return snapshot; } void hmm_restore(hmm_t *hmm, void *_snapshot) { snapshot_t *snapshot = (snapshot_t*) _snapshot; if ( !snapshot || !snapshot->snap_at_pos ) { hmm->state.snap_at_pos = 0; memcpy(hmm->state.vit_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates); memcpy(hmm->state.fwd_prob,hmm->init.fwd_prob,sizeof(double)*hmm->nstates); } else { hmm->state.snap_at_pos = snapshot->snap_at_pos; memcpy(hmm->state.vit_prob,snapshot->vit_prob,sizeof(double)*hmm->nstates); memcpy(hmm->state.fwd_prob,snapshot->fwd_prob,sizeof(double)*hmm->nstates); } } void hmm_reset(hmm_t *hmm, void *_snapshot) { snapshot_t *snapshot = (snapshot_t*) _snapshot; if ( snapshot ) snapshot->snap_at_pos = 0; hmm->state.snap_at_pos = 0; memcpy(hmm->state.vit_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates); memcpy(hmm->state.fwd_prob,hmm->init.fwd_prob,sizeof(double)*hmm->nstates); } void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob) { hmm->ntprob_arr = ntprob; if ( ntprob<=0 ) ntprob = 1; if ( !hmm->tprob_arr ) hmm->tprob_arr = (double*) malloc(sizeof(double)*hmm->nstates*hmm->nstates*ntprob); memcpy(hmm->tprob_arr,tprob,sizeof(double)*hmm->nstates*hmm->nstates); int i; for (i=1; instates, hmm->tprob_arr, hmm->tprob_arr+(i-1)*hmm->nstates*hmm->nstates, hmm->tprob_arr+i*hmm->nstates*hmm->nstates, hmm->tmp); } void hmm_set_tprob_func(hmm_t *hmm, set_tprob_f set_tprob, void *data) { hmm->set_tprob = set_tprob; hmm->set_tprob_data = data; } static void _set_tprob(hmm_t *hmm, int pos_diff) { assert( pos_diff>=0 ); int i, n; n = hmm->ntprob_arr ? pos_diff % hmm->ntprob_arr : 0; // n-th precalculated matrix memcpy(hmm->curr_tprob, hmm->tprob_arr+n*hmm->nstates*hmm->nstates, sizeof(*hmm->curr_tprob)*hmm->nstates*hmm->nstates); if ( hmm->ntprob_arr > 0 ) { n = pos_diff / hmm->ntprob_arr; // number of full blocks to jump for (i=0; instates, hmm->tprob_arr+(hmm->ntprob_arr-1)*hmm->nstates*hmm->nstates, hmm->curr_tprob, hmm->curr_tprob, hmm->tmp); } } void hmm_run_viterbi(hmm_t *hmm, int n, double *eprobs, uint32_t *sites) { // Init arrays when run for the first time if ( hmm->nvpath < n ) { hmm->nvpath = n; hmm->vpath = (uint8_t*) realloc(hmm->vpath, sizeof(uint8_t)*hmm->nvpath*hmm->nstates); } if ( !hmm->vprob ) { hmm->vprob = (double*) malloc(sizeof(double)*hmm->nstates); hmm->vprob_tmp = (double*) malloc(sizeof(double)*hmm->nstates); } // Init all states with equal likelihood int i,j, nstates = hmm->nstates; memcpy(hmm->vprob, hmm->state.vit_prob, sizeof(*hmm->state.vit_prob)*nstates); uint32_t prev_pos = hmm->state.snap_at_pos ? hmm->state.snap_at_pos : sites[0]; // Run Viterbi for (i=0; ivpath[i*nstates]; double *eprob = &eprobs[i*nstates]; int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1; _set_tprob(hmm, pos_diff); if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob); prev_pos = sites[i]; double vnorm = 0; for (j=0; jvprob[k] * MAT(hmm->curr_tprob,hmm->nstates,j,k); if ( vmax < pval ) { vmax = pval; k_vmax = k; } } vpath[j] = k_vmax; hmm->vprob_tmp[j] = vmax * eprob[j]; vnorm += hmm->vprob_tmp[j]; } for (j=0; jvprob_tmp[j] /= vnorm; double *tmp = hmm->vprob; hmm->vprob = hmm->vprob_tmp; hmm->vprob_tmp = tmp; if ( hmm->snapshot && sites[i]==hmm->snapshot->snap_at_pos ) memcpy(hmm->snapshot->vit_prob, hmm->vprob, sizeof(*hmm->vprob)*nstates); } // Find the most likely state int iptr = 0; for (i=1; ivprob[iptr] < hmm->vprob[i] ) iptr = i; // Trace back the Viterbi path, we are reusing vpath for storing the states (vpath[i*nstates]) for (i=n-1; i>=0; i--) { assert( iptrvpath[i*nstates + iptr]vpath[i*nstates + iptr]; hmm->vpath[i*nstates] = iptr; // reusing the array for different purpose here } } void hmm_run_fwd_bwd(hmm_t *hmm, int n, double *eprobs, uint32_t *sites) { // Init arrays when run for the first time if ( hmm->nfwd < n ) { hmm->nfwd = n; hmm->fwd = (double*) realloc(hmm->fwd, sizeof(double)*(hmm->nfwd+1)*hmm->nstates); } if ( !hmm->bwd ) { hmm->bwd = (double*) malloc(sizeof(double)*hmm->nstates); hmm->bwd_tmp = (double*) malloc(sizeof(double)*hmm->nstates); } int i,j,k, nstates = hmm->nstates; memcpy(hmm->fwd, hmm->state.fwd_prob, sizeof(*hmm->state.fwd_prob)*nstates); memcpy(hmm->bwd, hmm->state.bwd_prob, sizeof(*hmm->state.bwd_prob)*nstates); uint32_t prev_pos = hmm->state.snap_at_pos ? hmm->state.snap_at_pos : sites[0]; // Run fwd for (i=0; ifwd[i*nstates]; double *fwd = &hmm->fwd[(i+1)*nstates]; double *eprob = &eprobs[i*nstates]; int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1; _set_tprob(hmm, pos_diff); if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob); prev_pos = sites[i]; double norm = 0; for (j=0; jcurr_tprob,hmm->nstates,j,k); fwd[j] = pval * eprob[j]; norm += fwd[j]; } for (j=0; jsnapshot && sites[i]==hmm->snapshot->snap_at_pos ) memcpy(hmm->snapshot->fwd_prob, fwd, sizeof(*fwd)*nstates); } // Run bwd double *bwd = hmm->bwd, *bwd_tmp = hmm->bwd_tmp; prev_pos = sites[n-1]; for (i=0; ifwd[(n-i)*nstates]; double *eprob = &eprobs[(n-i-1)*nstates]; int pos_diff = sites[n-i-1] == prev_pos ? 0 : prev_pos - sites[n-i-1] - 1; _set_tprob(hmm, pos_diff); if ( hmm->set_tprob ) hmm->set_tprob(hmm, sites[n-i-1], prev_pos, hmm->set_tprob_data, hmm->curr_tprob); prev_pos = sites[n-i-1]; double bwd_norm = 0; for (j=0; jcurr_tprob,hmm->nstates,k,j); bwd_tmp[j] = pval; bwd_norm += pval; } double norm = 0; for (j=0; jnfwd < n ) { hmm->nfwd = n; hmm->fwd = (double*) realloc(hmm->fwd, sizeof(double)*(hmm->nfwd+1)*hmm->nstates); } if ( !hmm->bwd ) { hmm->bwd = (double*) malloc(sizeof(double)*hmm->nstates); hmm->bwd_tmp = (double*) malloc(sizeof(double)*hmm->nstates); } // Init all states with equal likelihood int i,j,k, nstates = hmm->nstates; memcpy(hmm->fwd, hmm->state.fwd_prob, sizeof(*hmm->state.fwd_prob)*nstates); memcpy(hmm->bwd, hmm->state.bwd_prob, sizeof(*hmm->state.bwd_prob)*nstates); uint32_t prev_pos = hmm->state.snap_at_pos ? hmm->state.snap_at_pos : sites[0]; // New transition matrix: temporary values double *tmp_xi = (double*) calloc(nstates*nstates,sizeof(double)); double *tmp_gamma = (double*) calloc(nstates,sizeof(double)); double *fwd_bwd = (double*) malloc(sizeof(double)*nstates); // Run fwd for (i=0; ifwd[i*nstates]; double *fwd = &hmm->fwd[(i+1)*nstates]; double *eprob = &eprobs[i*nstates]; int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1; _set_tprob(hmm, pos_diff); if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob); prev_pos = sites[i]; double norm = 0; for (j=0; jcurr_tprob,hmm->nstates,j,k); fwd[j] = pval * eprob[j]; norm += fwd[j]; } for (j=0; jbwd, *bwd_tmp = hmm->bwd_tmp; prev_pos = sites[n-1]; for (i=0; ifwd[(n-i)*nstates]; double *eprob = &eprobs[(n-i-1)*nstates]; int pos_diff = sites[n-i-1] == prev_pos ? 0 : prev_pos - sites[n-i-1] - 1; _set_tprob(hmm, pos_diff); if ( hmm->set_tprob ) hmm->set_tprob(hmm, sites[n-i-1], prev_pos, hmm->set_tprob_data, hmm->curr_tprob); prev_pos = sites[n-i-1]; double bwd_norm = 0; for (j=0; jcurr_tprob,hmm->nstates,k,j); bwd_tmp[j] = pval; bwd_norm += pval; } double norm = 0; for (j=0; jtprob_arr,hmm->nstates,k,j)*eprob[k] / norm; } } for (j=0; jcurr_tprob,nstates,k,j) = MAT(tmp_xi,nstates,k,j) / tmp_gamma[j]; norm += MAT(hmm->curr_tprob,nstates,k,j); } for (k=0; kcurr_tprob,nstates,k,j) /= norm; } free(tmp_gamma); free(tmp_xi); free(fwd_bwd); return hmm->curr_tprob; } void hmm_destroy(hmm_t *hmm) { free(hmm->init.vit_prob); free(hmm->init.fwd_prob); free(hmm->init.bwd_prob); free(hmm->state.vit_prob); free(hmm->state.fwd_prob); free(hmm->state.bwd_prob); free(hmm->vprob); free(hmm->vprob_tmp); free(hmm->vpath); free(hmm->curr_tprob); free(hmm->tmp); free(hmm->tprob_arr); free(hmm->fwd); free(hmm->bwd); free(hmm->bwd_tmp); free(hmm); } pysam-0.23.0/bcftools/HMM.c.pysam.c000066400000000000000000000435461475062545500167270ustar00rootroot00000000000000#include "bcftools.pysam.h" /* The MIT License Copyright (c) 2014-2017 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include "HMM.h" typedef struct { int nstates; // number of hmm's states uint32_t snap_at_pos; // snapshot at this position, 0 when inactive double *vit_prob; // viterbi probabilities, NULL for uniform probs double *fwd_prob; // transition probabilities double *bwd_prob; // transition probabilities } snapshot_t; struct _hmm_t { int nstates; // number of states double *vprob, *vprob_tmp; // viterbi probs [nstates] uint8_t *vpath; // viterbi path [nstates*nvpath] double *bwd, *bwd_tmp; // bwd probs [nstates] double *fwd; // fwd probs [nstates*(nfwd+1)] int nvpath, nfwd; int ntprob_arr; // number of pre-calculated tprob matrices double *curr_tprob, *tmp; // Temporary arrays; curr_tprob is short lived, valid only for // one site (that is, one step of Viterbi algorithm) double *tprob_arr; // Array of transition matrices, precalculated to ntprob_arr // positions. The first matrix is the initial tprob matrix // set by hmm_init() or hmm_set_tprob() set_tprob_f set_tprob; // Optional user function to set / modify transition probabilities // at each site (one step of Viterbi algorithm) void *set_tprob_data; snapshot_t init, state; // Initial and current state probs. Set state from snapshot if prev_snap_pos!=0 or from init otherwise snapshot_t *snapshot; // snapshot->snap_at_pos .. request a snapshot at this position // hmm->state.snap_at_pos .. the current state comes from snapshot made at this position }; uint8_t *hmm_get_viterbi_path(hmm_t *hmm) { return hmm->vpath; } double *hmm_get_tprob(hmm_t *hmm) { return hmm->tprob_arr; } int hmm_get_nstates(hmm_t *hmm) { return hmm->nstates; } double *hmm_get_fwd_bwd_prob(hmm_t *hmm) { return hmm->fwd; } static inline void multiply_matrix(int n, double *a, double *b, double *dst, double *tmp) { double *out = dst; if ( a==dst || b==dst ) out = tmp; int i,j,k; for (i=0; iinit.snap_at_pos = hmm->state.snap_at_pos = 0; if ( !hmm->init.vit_prob ) hmm->init.vit_prob = (double*) malloc(sizeof(double)*hmm->nstates); if ( !hmm->init.fwd_prob ) hmm->init.fwd_prob = (double*) malloc(sizeof(double)*hmm->nstates); if ( !hmm->init.bwd_prob ) hmm->init.bwd_prob = (double*) malloc(sizeof(double)*hmm->nstates); if ( !hmm->state.vit_prob ) hmm->state.vit_prob = (double*) malloc(sizeof(double)*hmm->nstates); if ( !hmm->state.fwd_prob ) hmm->state.fwd_prob = (double*) malloc(sizeof(double)*hmm->nstates); if ( !hmm->state.bwd_prob ) hmm->state.bwd_prob = (double*) malloc(sizeof(double)*hmm->nstates); int i; if ( probs ) { memcpy(hmm->init.vit_prob,probs,sizeof(double)*hmm->nstates); double sum = 0; for (i=0; instates; i++) sum += hmm->init.vit_prob[i]; for (i=0; instates; i++) hmm->init.vit_prob[i] /= sum; } else for (i=0; instates; i++) hmm->init.vit_prob[i] = 1./hmm->nstates; memcpy(hmm->init.fwd_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates); // these remain unchanged memcpy(hmm->init.bwd_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates); memcpy(hmm->state.vit_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates); // can be changed by snapshotting memcpy(hmm->state.fwd_prob,hmm->init.fwd_prob,sizeof(double)*hmm->nstates); memcpy(hmm->state.bwd_prob,hmm->init.bwd_prob,sizeof(double)*hmm->nstates); } hmm_t *hmm_init(int nstates, double *tprob, int ntprob) { hmm_t *hmm = (hmm_t*) calloc(1,sizeof(hmm_t)); hmm->nstates = nstates; hmm->curr_tprob = (double*) malloc(sizeof(double)*nstates*nstates); hmm->tmp = (double*) malloc(sizeof(double)*nstates*nstates); hmm_set_tprob(hmm, tprob, ntprob); hmm_init_states(hmm, NULL); return hmm; } void *hmm_snapshot(hmm_t *hmm, void *_snapshot, uint32_t pos) { snapshot_t *snapshot = (snapshot_t*) _snapshot; if ( snapshot && snapshot->nstates!=hmm->nstates ) { free(snapshot); snapshot = NULL; } if ( !snapshot ) { // Allocate the snapshot as a single memory block so that it can be // free()-ed by the user. So make sure the arrays are aligned.. size_t str_size = sizeof(snapshot_t); size_t dbl_size = sizeof(double); size_t pad_size = (dbl_size - str_size % dbl_size) % dbl_size; uint8_t *mem = (uint8_t*) malloc(str_size + pad_size + dbl_size*2*hmm->nstates); snapshot = (snapshot_t*) mem; snapshot->nstates = hmm->nstates; snapshot->vit_prob = (double*) (mem + str_size + pad_size); snapshot->fwd_prob = snapshot->vit_prob + hmm->nstates; } snapshot->snap_at_pos = pos; hmm->snapshot = snapshot; return snapshot; } void hmm_restore(hmm_t *hmm, void *_snapshot) { snapshot_t *snapshot = (snapshot_t*) _snapshot; if ( !snapshot || !snapshot->snap_at_pos ) { hmm->state.snap_at_pos = 0; memcpy(hmm->state.vit_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates); memcpy(hmm->state.fwd_prob,hmm->init.fwd_prob,sizeof(double)*hmm->nstates); } else { hmm->state.snap_at_pos = snapshot->snap_at_pos; memcpy(hmm->state.vit_prob,snapshot->vit_prob,sizeof(double)*hmm->nstates); memcpy(hmm->state.fwd_prob,snapshot->fwd_prob,sizeof(double)*hmm->nstates); } } void hmm_reset(hmm_t *hmm, void *_snapshot) { snapshot_t *snapshot = (snapshot_t*) _snapshot; if ( snapshot ) snapshot->snap_at_pos = 0; hmm->state.snap_at_pos = 0; memcpy(hmm->state.vit_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates); memcpy(hmm->state.fwd_prob,hmm->init.fwd_prob,sizeof(double)*hmm->nstates); } void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob) { hmm->ntprob_arr = ntprob; if ( ntprob<=0 ) ntprob = 1; if ( !hmm->tprob_arr ) hmm->tprob_arr = (double*) malloc(sizeof(double)*hmm->nstates*hmm->nstates*ntprob); memcpy(hmm->tprob_arr,tprob,sizeof(double)*hmm->nstates*hmm->nstates); int i; for (i=1; instates, hmm->tprob_arr, hmm->tprob_arr+(i-1)*hmm->nstates*hmm->nstates, hmm->tprob_arr+i*hmm->nstates*hmm->nstates, hmm->tmp); } void hmm_set_tprob_func(hmm_t *hmm, set_tprob_f set_tprob, void *data) { hmm->set_tprob = set_tprob; hmm->set_tprob_data = data; } static void _set_tprob(hmm_t *hmm, int pos_diff) { assert( pos_diff>=0 ); int i, n; n = hmm->ntprob_arr ? pos_diff % hmm->ntprob_arr : 0; // n-th precalculated matrix memcpy(hmm->curr_tprob, hmm->tprob_arr+n*hmm->nstates*hmm->nstates, sizeof(*hmm->curr_tprob)*hmm->nstates*hmm->nstates); if ( hmm->ntprob_arr > 0 ) { n = pos_diff / hmm->ntprob_arr; // number of full blocks to jump for (i=0; instates, hmm->tprob_arr+(hmm->ntprob_arr-1)*hmm->nstates*hmm->nstates, hmm->curr_tprob, hmm->curr_tprob, hmm->tmp); } } void hmm_run_viterbi(hmm_t *hmm, int n, double *eprobs, uint32_t *sites) { // Init arrays when run for the first time if ( hmm->nvpath < n ) { hmm->nvpath = n; hmm->vpath = (uint8_t*) realloc(hmm->vpath, sizeof(uint8_t)*hmm->nvpath*hmm->nstates); } if ( !hmm->vprob ) { hmm->vprob = (double*) malloc(sizeof(double)*hmm->nstates); hmm->vprob_tmp = (double*) malloc(sizeof(double)*hmm->nstates); } // Init all states with equal likelihood int i,j, nstates = hmm->nstates; memcpy(hmm->vprob, hmm->state.vit_prob, sizeof(*hmm->state.vit_prob)*nstates); uint32_t prev_pos = hmm->state.snap_at_pos ? hmm->state.snap_at_pos : sites[0]; // Run Viterbi for (i=0; ivpath[i*nstates]; double *eprob = &eprobs[i*nstates]; int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1; _set_tprob(hmm, pos_diff); if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob); prev_pos = sites[i]; double vnorm = 0; for (j=0; jvprob[k] * MAT(hmm->curr_tprob,hmm->nstates,j,k); if ( vmax < pval ) { vmax = pval; k_vmax = k; } } vpath[j] = k_vmax; hmm->vprob_tmp[j] = vmax * eprob[j]; vnorm += hmm->vprob_tmp[j]; } for (j=0; jvprob_tmp[j] /= vnorm; double *tmp = hmm->vprob; hmm->vprob = hmm->vprob_tmp; hmm->vprob_tmp = tmp; if ( hmm->snapshot && sites[i]==hmm->snapshot->snap_at_pos ) memcpy(hmm->snapshot->vit_prob, hmm->vprob, sizeof(*hmm->vprob)*nstates); } // Find the most likely state int iptr = 0; for (i=1; ivprob[iptr] < hmm->vprob[i] ) iptr = i; // Trace back the Viterbi path, we are reusing vpath for storing the states (vpath[i*nstates]) for (i=n-1; i>=0; i--) { assert( iptrvpath[i*nstates + iptr]vpath[i*nstates + iptr]; hmm->vpath[i*nstates] = iptr; // reusing the array for different purpose here } } void hmm_run_fwd_bwd(hmm_t *hmm, int n, double *eprobs, uint32_t *sites) { // Init arrays when run for the first time if ( hmm->nfwd < n ) { hmm->nfwd = n; hmm->fwd = (double*) realloc(hmm->fwd, sizeof(double)*(hmm->nfwd+1)*hmm->nstates); } if ( !hmm->bwd ) { hmm->bwd = (double*) malloc(sizeof(double)*hmm->nstates); hmm->bwd_tmp = (double*) malloc(sizeof(double)*hmm->nstates); } int i,j,k, nstates = hmm->nstates; memcpy(hmm->fwd, hmm->state.fwd_prob, sizeof(*hmm->state.fwd_prob)*nstates); memcpy(hmm->bwd, hmm->state.bwd_prob, sizeof(*hmm->state.bwd_prob)*nstates); uint32_t prev_pos = hmm->state.snap_at_pos ? hmm->state.snap_at_pos : sites[0]; // Run fwd for (i=0; ifwd[i*nstates]; double *fwd = &hmm->fwd[(i+1)*nstates]; double *eprob = &eprobs[i*nstates]; int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1; _set_tprob(hmm, pos_diff); if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob); prev_pos = sites[i]; double norm = 0; for (j=0; jcurr_tprob,hmm->nstates,j,k); fwd[j] = pval * eprob[j]; norm += fwd[j]; } for (j=0; jsnapshot && sites[i]==hmm->snapshot->snap_at_pos ) memcpy(hmm->snapshot->fwd_prob, fwd, sizeof(*fwd)*nstates); } // Run bwd double *bwd = hmm->bwd, *bwd_tmp = hmm->bwd_tmp; prev_pos = sites[n-1]; for (i=0; ifwd[(n-i)*nstates]; double *eprob = &eprobs[(n-i-1)*nstates]; int pos_diff = sites[n-i-1] == prev_pos ? 0 : prev_pos - sites[n-i-1] - 1; _set_tprob(hmm, pos_diff); if ( hmm->set_tprob ) hmm->set_tprob(hmm, sites[n-i-1], prev_pos, hmm->set_tprob_data, hmm->curr_tprob); prev_pos = sites[n-i-1]; double bwd_norm = 0; for (j=0; jcurr_tprob,hmm->nstates,k,j); bwd_tmp[j] = pval; bwd_norm += pval; } double norm = 0; for (j=0; jnfwd < n ) { hmm->nfwd = n; hmm->fwd = (double*) realloc(hmm->fwd, sizeof(double)*(hmm->nfwd+1)*hmm->nstates); } if ( !hmm->bwd ) { hmm->bwd = (double*) malloc(sizeof(double)*hmm->nstates); hmm->bwd_tmp = (double*) malloc(sizeof(double)*hmm->nstates); } // Init all states with equal likelihood int i,j,k, nstates = hmm->nstates; memcpy(hmm->fwd, hmm->state.fwd_prob, sizeof(*hmm->state.fwd_prob)*nstates); memcpy(hmm->bwd, hmm->state.bwd_prob, sizeof(*hmm->state.bwd_prob)*nstates); uint32_t prev_pos = hmm->state.snap_at_pos ? hmm->state.snap_at_pos : sites[0]; // New transition matrix: temporary values double *tmp_xi = (double*) calloc(nstates*nstates,sizeof(double)); double *tmp_gamma = (double*) calloc(nstates,sizeof(double)); double *fwd_bwd = (double*) malloc(sizeof(double)*nstates); // Run fwd for (i=0; ifwd[i*nstates]; double *fwd = &hmm->fwd[(i+1)*nstates]; double *eprob = &eprobs[i*nstates]; int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1; _set_tprob(hmm, pos_diff); if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob); prev_pos = sites[i]; double norm = 0; for (j=0; jcurr_tprob,hmm->nstates,j,k); fwd[j] = pval * eprob[j]; norm += fwd[j]; } for (j=0; jbwd, *bwd_tmp = hmm->bwd_tmp; prev_pos = sites[n-1]; for (i=0; ifwd[(n-i)*nstates]; double *eprob = &eprobs[(n-i-1)*nstates]; int pos_diff = sites[n-i-1] == prev_pos ? 0 : prev_pos - sites[n-i-1] - 1; _set_tprob(hmm, pos_diff); if ( hmm->set_tprob ) hmm->set_tprob(hmm, sites[n-i-1], prev_pos, hmm->set_tprob_data, hmm->curr_tprob); prev_pos = sites[n-i-1]; double bwd_norm = 0; for (j=0; jcurr_tprob,hmm->nstates,k,j); bwd_tmp[j] = pval; bwd_norm += pval; } double norm = 0; for (j=0; jtprob_arr,hmm->nstates,k,j)*eprob[k] / norm; } } for (j=0; jcurr_tprob,nstates,k,j) = MAT(tmp_xi,nstates,k,j) / tmp_gamma[j]; norm += MAT(hmm->curr_tprob,nstates,k,j); } for (k=0; kcurr_tprob,nstates,k,j) /= norm; } free(tmp_gamma); free(tmp_xi); free(fwd_bwd); return hmm->curr_tprob; } void hmm_destroy(hmm_t *hmm) { free(hmm->init.vit_prob); free(hmm->init.fwd_prob); free(hmm->init.bwd_prob); free(hmm->state.vit_prob); free(hmm->state.fwd_prob); free(hmm->state.bwd_prob); free(hmm->vprob); free(hmm->vprob_tmp); free(hmm->vpath); free(hmm->curr_tprob); free(hmm->tmp); free(hmm->tprob_arr); free(hmm->fwd); free(hmm->bwd); free(hmm->bwd_tmp); free(hmm); } pysam-0.23.0/bcftools/HMM.h000066400000000000000000000116361475062545500153560ustar00rootroot00000000000000/* The MIT License Copyright (c) 2014-2016 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef __HMM_H__ #define __HMM_H__ #define MAT(matrix,ndim,i,j) (matrix)[(ndim)*(i)+(j)] // P(i|j), that is, transition j->i typedef struct _hmm_t hmm_t; typedef void (*set_tprob_f) (hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob); /** * hmm_init() - initialize HMM * @nstates: number of states * @tprob: transition probabilities matrix (nstates x nstates), for elements ordering * see the MAT macro above. * @ntprob: number of precalculated tprob matrices or 0 for constant probs, independent * of distance */ hmm_t *hmm_init(int nstates, double *tprob, int ntprob); void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob); #define HMM_VIT 1 #define HMM_FWD 2 #define HMM_BWD 4 /** * hmm_init_states() - initial state probabilities * @probs: initial state probabilities or NULL to reset to default * * If uncalled, all states are initialized with the same likelihood */ void hmm_init_states(hmm_t *hmm, double *probs); /** * hmm_snapshot() - take the model's snapshot, intended for sliding HMM * @snapshot: NULL or snapshot returned by previous hmm_snapshot() call, must be free()-ed by the caller * @pos: take the snapshot at this position * * If both restore() and snapshot() are needed, restore() must be called first. */ void *hmm_snapshot(hmm_t *hmm, void *snapshot, uint32_t pos); /** * hmm_restore() - restore model's snapshot, intended for sliding HMM * @snapshot: snapshot returned by hmm_snapshot() call or NULL to reset * @isite: take the snapshot at i-th step * * If both restore() and snapshot() are needed, restore() must be called first. */ void hmm_restore(hmm_t *hmm, void *snapshot); void hmm_reset(hmm_t *hmm, void *snapshot); /** * hmm_get_tprob() - return the array of transition matrices, precalculated * to ntprob positions. The first matrix is the initial tprob matrix * set by hmm_init() or hmm_set_tprob() */ double *hmm_get_tprob(hmm_t *hmm); int hmm_get_nstates(hmm_t *hmm); /** * hmm_set_tprob_func() - custom setter of transition probabilities */ void hmm_set_tprob_func(hmm_t *hmm, set_tprob_f set_tprob, void *data); /** * hmm_run_viterbi() - run Viterbi algorithm * @nsites: number of sites * @eprob: emission probabilities for each site and state (nsites x nstates) * @sites: list of positions * * When done, hmm->vpath[] contains the calculated Viterbi path. The states * are indexed starting from 0, a state at i-th site can be accessed as * vpath[nstates*i]. */ void hmm_run_viterbi(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites); /** * hmm_get_viterbi_path() - the viterbi path: state at ith site is the * (nstates*isite)-th element */ uint8_t *hmm_get_viterbi_path(hmm_t *hmm); /** * hmm_run_fwd_bwd() - run the forward-backward algorithm * @nsites: number of sites * @eprob: emission probabilities for each site and state (nsites x nstates) * @sites: list of positions */ void hmm_run_fwd_bwd(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites); /** * hmm_get_fwd_bwd_prob() - the probability of i-th state at j-th site can * be accessed as fwd_bwd[j*nstates+i]. */ double *hmm_get_fwd_bwd_prob(hmm_t *hmm); /** * hmm_run_baum_welch() - run one iteration of Baum-Welch algorithm * @nsites: number of sites * @eprob: emission probabilities for each site and state (nsites x nstates) * @sites: list of positions * * Same as hmm_run_fwd_bwd, in addition a pointer to a matrix with the new * transition probabilities is returned. In this version, emission * probabilities are not updated. */ double *hmm_run_baum_welch(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites); void hmm_destroy(hmm_t *hmm); #endif pysam-0.23.0/bcftools/LICENSE000066400000000000000000001201511475062545500155620ustar00rootroot00000000000000This software is available to you under a choice of one of two licenses. You may chose to be licensed under the terms of the MIT/Expat license or the GNU General Public License (GPL), both included below. If compiled with the GNU Scientific Library (which is optional and disabled by default as explained in the INSTALL document), the use of this software is governed by the GPL license. ----------------------------------------------------------------------------- The MIT/Expat License Copyright (C) 2012-2024 Genome Research Ltd. 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Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see . The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read . ----------------------------------------------------------------------------- LICENSE FOR VariantKey (https://github.com/tecnickcom/variantkey) The MIT License Copyright (c) 2017-2018 GENOMICS plc Copyright (c) 2018-2023 Nicola Asuni - Tecnick.com Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ----------------------------------------------------------------------------- LICENSE for utlist.h Copyright (c) 2007-2014, Troy D. Hanson http://troydhanson.github.com/uthash/ All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ----------------------------------------------------------------------------- License for edlib.[ch] The MIT License (MIT) Copyright (c) 2014 Martin Šošić Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. pysam-0.23.0/bcftools/README000066400000000000000000000042201475062545500154330ustar00rootroot00000000000000BCFtools implements utilities for variant calling (in conjunction with SAMtools) and manipulating VCF and BCF files. The program is intended to replace the Perl-based tools from vcftools. See INSTALL for building and installation instructions. Please cite this paper when using BCFtools for your publications: Twelve years of SAMtools and BCFtools Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008 @article{10.1093/gigascience/giab008, author = {Danecek, Petr and Bonfield, James K and Liddle, Jennifer and Marshall, John and Ohan, Valeriu and Pollard, Martin O and Whitwham, Andrew and Keane, Thomas and McCarthy, Shane A and Davies, Robert M and Li, Heng}, title = "{Twelve years of SAMtools and BCFtools}", journal = {GigaScience}, volume = {10}, number = {2}, year = {2021}, month = {02}, abstract = "{SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines.Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed \\>1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.}", issn = {2047-217X}, doi = {10.1093/gigascience/giab008}, url = {https://doi.org/10.1093/gigascience/giab008}, note = {giab008}, eprint = {https://academic.oup.com/gigascience/article-pdf/10/2/giab008/36332246/giab008.pdf}, } pysam-0.23.0/bcftools/abuf.c000066400000000000000000001014251475062545500156410ustar00rootroot00000000000000/* The MIT License Copyright (c) 2021-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include "bcftools.h" #include "abuf.h" #include "rbuf.h" typedef enum { M_FIRST, M_SUM } merge_rule_t; typedef struct { kstring_t ref, alt; int ial; // the index of the original ALT allele, 1-based int beg, end; // 0-based inclusive offsets to ref,alt int plen; // the ref,alt prefix length, eg plen=1 for C>CA } atom_t; typedef struct { bcf1_t *rec; int nori, nout; // number of ALTs in the input, and VCF rows on output uint8_t *tbl; // nori columns, nout rows; indicates allele contribution to output rows, see "The atomization works as follows" below uint8_t *overlaps; // is the star allele needed for this variant? atom_t **atoms; int matoms, mtbl, moverlaps; char *info_tag; } split_t; struct _abuf_t { abuf_opt_t mode; split_t split; atom_t *atoms; int natoms, matoms; const bcf_hdr_t *hdr; bcf_hdr_t *out_hdr; bcf1_t **vcf; // dimensions stored in rbuf rbuf_t rbuf; kstring_t tmps; void *tmp, *tmp2; int32_t *gt, *tmpi; int ngt, mgt, ntmpi, mtmpi, mtmp, mtmp2; int star_allele; }; abuf_t *abuf_init(const bcf_hdr_t *hdr, abuf_opt_t mode) { if ( mode!=SPLIT ) error("todo\n"); abuf_t *buf = (abuf_t*) calloc(1,sizeof(abuf_t)); buf->hdr = hdr; buf->out_hdr = (bcf_hdr_t*) hdr; buf->mode = mode; buf->star_allele = 1; rbuf_init(&buf->rbuf, 0); return buf; } void abuf_destroy(abuf_t *buf) { int i; for (i=0; imatoms; i++) { free(buf->atoms[i].ref.s); free(buf->atoms[i].alt.s); } free(buf->atoms); free(buf->split.atoms); free(buf->split.overlaps); free(buf->split.tbl); for (i=0; irbuf.m; i++) if ( buf->vcf[i] ) bcf_destroy(buf->vcf[i]); free(buf->vcf); free(buf->gt); free(buf->tmpi); free(buf->tmp); free(buf->tmp2); free(buf->tmps.s); free(buf); } void abuf_set(abuf_t *buf, abuf_opt_t key, void *value) { if ( key==BCF_HDR ) { buf->out_hdr = *((bcf_hdr_t**)value); return; } if ( key==INFO_TAG ) { buf->split.info_tag = *((char**)value); bcf_hdr_printf(buf->out_hdr,"##INFO=",buf->split.info_tag); return; } if ( key==STAR_ALLELE ) { buf->star_allele = *((int*)value); return; } } /* Split alleles into primitivs, e.g. CC>TT becomes C>T,C>T GCGT>GTGA becomes C>T,T>A There is no sequence alignment, just trimming and hungry matching from left side. */ static void _atomize_allele(abuf_t *buf, bcf1_t *rec, int ial) { // Trim identical sequence from right char *ref = rec->d.allele[0]; char *alt = rec->d.allele[ial]; int rlen = strlen(ref); int alen = strlen(alt); while ( rlen>1 && alen>1 && ref[rlen-1]==alt[alen-1] ) rlen--, alen--; int Mlen = rlen > alen ? rlen : alen; atom_t *atom = NULL; int i; for (i=0; ialt); if ( refb!='-' ) { kputc(refb, &atom->ref); atom->end++; } continue; } buf->natoms++; hts_expand0(atom_t,buf->natoms,buf->matoms,buf->atoms); atom = &buf->atoms[buf->natoms-1]; atom->ref.l = 0; atom->alt.l = 0; kputc(refb, &atom->ref); kputc(altb, &atom->alt); atom->beg = atom->end = i; atom->ial = ial; if ( rlen!=alen && (i+1>=rlen || i+1>=alen) ) // the next base is an indel combined with SNV, e.g. C>GGG? { buf->natoms++; hts_expand0(atom_t,buf->natoms,buf->matoms,buf->atoms); atom = &buf->atoms[buf->natoms-1]; atom->ref.l = 0; atom->alt.l = 0; kputc(refb, &atom->ref); kputc(refb, &atom->alt); atom->beg = atom->end = i; atom->ial = ial; atom->plen = 1; } continue; } if ( i+1>=rlen || i+1>=alen ) // is the next base an indel? { buf->natoms++; hts_expand0(atom_t,buf->natoms,buf->matoms,buf->atoms); atom = &buf->atoms[buf->natoms-1]; atom->ref.l = 0; atom->alt.l = 0; kputc(refb, &atom->ref); kputc(altb, &atom->alt); atom->beg = atom->end = i; atom->ial = ial; } } } static int _atoms_inconsistent(const atom_t *a, const atom_t *b) { if ( a->beg < b->beg ) return -1; if ( a->beg > b->beg ) return 1; int rcmp = strcasecmp(a->ref.s,b->ref.s); if ( rcmp ) return rcmp; return strcasecmp(a->alt.s,b->alt.s); } // returns // 0 .. identical beg,ref,alt // 1 .. non-overlapping variants, but record may overlap (A>AT vs A>C) // 2 .. overlapping (conflicting) variants static int _atoms_overlap(const atom_t *a, const atom_t *b) { if ( a->beg < b->beg ) return 2; if ( a->beg > b->beg ) return 2; // consider SNV followed by DEL as not overlapping // CC > C a.plen=1 (ref,alt prefix len=1) // C > T b.plen=0 (ref,alt prefix len=0) if ( a->plen && a->plen >= b->ref.l ) return 1; if ( b->plen && b->plen >= a->ref.l ) return 1; int rcmp = strcasecmp(a->ref.s,b->ref.s); if ( rcmp ) return 2; // consider SNV followed by INS as not overlapping // A > AT a.plen=1 (ref,alt prefix len=1) // A > C b.plen=0 (ref,alt prefix len=0) if ( a->plen && a->plen >= b->alt.l ) return 1; if ( b->plen && b->plen >= a->alt.l ) return 1; rcmp = strcasecmp(a->alt.s,b->alt.s); if ( rcmp ) return 2; return 0; } /* For reproducibility of tests on different platforms, we need to guarantee the same order of identical atoms originating from different source ALTs. Even though they are consistent, different values can be picked for VCF annotations as currently the values from the one that comes first are used. */ static int _cmp_atoms(const void *aptr, const void *bptr) { const atom_t *a = (const atom_t*) aptr; const atom_t *b = (const atom_t*) bptr; int rcmp = _atoms_inconsistent(a,b); if ( rcmp ) return rcmp; if ( a->ial < b->ial ) return -1; if ( a->ial > b->ial ) return 1; return 0; } static void _split_table_init(abuf_t *buf, bcf1_t *rec, int natoms) { buf->split.rec = rec; buf->split.nori = rec->n_allele - 1; buf->split.nout = 0; hts_expand(uint8_t,buf->split.nori*natoms,buf->split.mtbl,buf->split.tbl); hts_expand(atom_t*,natoms,buf->split.matoms,buf->split.atoms); hts_expand(uint8_t,natoms,buf->split.moverlaps,buf->split.overlaps); memset(buf->split.overlaps,0,sizeof(*buf->split.overlaps)*natoms); } static void _split_table_new(abuf_t *buf, atom_t *atom) { int i, iout = buf->split.nout++; buf->split.atoms[iout] = atom; uint8_t *ptr = buf->split.tbl + iout*buf->split.nori; for (i=0; isplit.nori; i++) ptr[i] = 0; ptr[atom->ial-1] = 1; } static void _split_table_overlap(abuf_t *buf, int iout, atom_t *atom) { uint8_t *ptr = buf->split.tbl + iout*buf->split.nori; int olap = _atoms_overlap(atom,buf->split.atoms[iout]); ptr[atom->ial-1] = olap > 1 ? 2 : 1; // The test test/atomize.split.5.vcf shows why we sometimes can and sometimes // cannot remove the star allele like this // buf->split.overlaps[iout] = olap > 1 ? 1 : 0; // I forgot the details of the code, so don't immediately see // if this could be made smarter buf->split.overlaps[iout] = 1; } #if 0 static void _split_table_print(abuf_t *buf) { int i,j; for (i=0; isplit.nout; i++) { atom_t *atom = buf->split.atoms[i]; uint8_t *ptr = buf->split.tbl + i*buf->split.nori; fprintf(stderr,"%d\t%s\t%s",(int)buf->split.rec->pos+1+atom->beg,atom->ref.s,atom->alt.s); for (j=0; jsplit.nori; j++) fprintf(stderr,"\t%d",(int)ptr[j]); fprintf(stderr,"\n"); } } static void _split_table_print_atoms(abuf_t *buf) { int i; for (i=0; inatoms; i++) { atom_t *atom = &buf->atoms[i]; fprintf(stderr,"atom%d %p: ialt=%d %s>%s %d-%d\n",i,atom,atom->ial,atom->ref.s,atom->alt.s,atom->beg,atom->end); } } #endif static inline uint8_t _has_star_allele(abuf_t *buf, int iout) { if ( !buf->star_allele ) return 0; return buf->split.overlaps[iout]; } static inline int _split_table_get_ial(abuf_t *buf, int irow, int ial) { if ( !ial ) return ial; return buf->split.tbl[irow*buf->split.nori + ial - 1]; } static void _split_table_set_chrom_qual(abuf_t *buf) { int iout,j; bcf1_t *rec = buf->split.rec; for (iout=0; ioutsplit.nout; iout++) { rbuf_expand0(&buf->rbuf, bcf1_t*, buf->rbuf.n+1, buf->vcf); j = rbuf_append(&buf->rbuf); if ( !buf->vcf[j] ) buf->vcf[j] = bcf_init1(); bcf1_t *out = buf->vcf[j]; bcf_clear1(out); atom_t *atom = buf->split.atoms[iout]; out->rid = rec->rid; out->pos = rec->pos + atom->beg; bcf_update_id(buf->out_hdr, out, rec->d.id); const char *als[3]; als[0] = atom->ref.s; als[1] = atom->alt.s; als[2] = "*"; int nals = _has_star_allele(buf,iout) ? 3 : 2; bcf_update_alleles(buf->out_hdr, out, als, nals); if ( bcf_float_is_missing(rec->qual) ) bcf_float_set_missing(out->qual); else out->qual = rec->qual; bcf_update_filter(buf->out_hdr, out, rec->d.flt, rec->d.n_flt); } } int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst); static void _split_table_set_info(abuf_t *buf, bcf_info_t *info, merge_rule_t mode) { const char *tag = bcf_hdr_int2id(buf->hdr,BCF_DT_ID,info->key); int type = bcf_hdr_id2type(buf->hdr,BCF_HL_INFO,info->key); int len = bcf_hdr_id2length(buf->hdr,BCF_HL_INFO,info->key); if ( len==BCF_VL_G ) return; // todo: Number=G INFO tags if ( type==BCF_HT_LONG ) return; // todo: 64bit integers bcf1_t *rec = buf->split.rec; int mtmp = ( type==BCF_HT_INT || type==BCF_HT_REAL ) ? buf->mtmp/4 : buf->mtmp; int nval = bcf_get_info_values(buf->hdr,rec,tag,&buf->tmp,&mtmp,type); if ( type==BCF_HT_INT || type==BCF_HT_REAL ) buf->mtmp = mtmp*4; // Check for incorrect number of values. Note this check does not consider all values missing // and will remove annotations that don't pass. if ( type==BCF_HT_INT || type==BCF_HT_REAL ) { if ( (len==BCF_VL_A && nval != rec->n_allele - 1) || (len==BCF_VL_R && nval != rec->n_allele) ) return; } if ( buf->mtmp2 < buf->mtmp ) { buf->tmp2 = realloc(buf->tmp2, buf->mtmp); if ( !buf->tmp2 ) error("Failed to alloc %d bytes\n", buf->mtmp); buf->mtmp2 = buf->mtmp; } const int num_size = 4; assert( num_size==sizeof(int32_t) && num_size==sizeof(float) ); int32_t missing = bcf_int32_missing; void *missing_ptr = (void*)&missing; if ( type==BCF_HT_REAL ) bcf_float_set_missing(*((float*)missing_ptr)); int32_t vector_end = bcf_int32_vector_end; void *vector_end_ptr = (void*)&vector_end; if ( type==BCF_HT_REAL ) bcf_float_set_vector_end(*((float*)vector_end_ptr)); int iout,i; for (iout=0; ioutsplit.nout; iout++) { bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,iout)]; int star_allele = _has_star_allele(buf,iout); int ret = 0; if ( len==BCF_VL_FIXED || len==BCF_VL_VAR ) ret = bcf_update_info(buf->out_hdr, out, tag, type==BCF_HT_FLAG ? NULL : buf->tmp, nval, type); else if ( len==BCF_VL_A && type!=BCF_HT_STR ) { int iori = buf->split.atoms[iout]->ial - 1; assert( ioritmp+num_size*iori,num_size) ) memcpy(buf->tmp2,missing_ptr,num_size); else memcpy(buf->tmp2,buf->tmp+num_size*iori,num_size); if ( star_allele ) memcpy(buf->tmp2+num_size,missing_ptr,num_size); ret = bcf_update_info(buf->out_hdr, out, tag, buf->tmp2, 1 + star_allele, type); } else if ( len==BCF_VL_A && type==BCF_HT_STR ) { int iori = buf->split.atoms[iout]->ial - 1; kstring_t dst; dst.l = 0; dst.m = buf->mtmp2; dst.s = (char*)buf->tmp2; kputc('.',&dst); if ( star_allele ) kputs(",.",&dst); copy_string_field(buf->tmp, iori, nval, &dst, 0); if ( star_allele ) copy_string_field(".", 0, 1, &dst, 1); buf->mtmp2 = dst.m; buf->tmp2 = dst.s; ret = bcf_update_info(buf->out_hdr, out, tag, buf->tmp2, dst.l, type); } else if ( len==BCF_VL_R && type!=BCF_HT_STR ) { memcpy(buf->tmp2,buf->tmp,num_size); // REF contributes to all records int iori = buf->split.atoms[iout]->ial; assert( iorisplit.nori ); if ( !memcmp(vector_end_ptr,buf->tmp+num_size*iori,num_size) ) memcpy(buf->tmp2+num_size,missing_ptr,num_size); else memcpy(buf->tmp2+num_size,buf->tmp+num_size*iori,num_size); if ( type==BCF_HT_INT && mode==M_SUM ) { uint8_t *tbl = buf->split.tbl + iout*buf->split.nori; for (i=iori; isplit.nori; i++) { if ( tbl[i]==1 ) ((int32_t*)buf->tmp2)[1] += ((int32_t*)buf->tmp)[i+1]; } } if ( star_allele ) memcpy(buf->tmp2+2*num_size,missing_ptr,num_size); ret = bcf_update_info(buf->out_hdr, out, tag, buf->tmp2, 2 + star_allele, type); } else if ( len==BCF_VL_R && type==BCF_HT_STR ) { int iori = buf->split.atoms[iout]->ial - 1; kstring_t dst; dst.l = 0; dst.m = buf->mtmp2; dst.s = (char*)buf->tmp2; kputs(".,.",&dst); if ( star_allele ) kputs(",.",&dst); copy_string_field(buf->tmp, 0, nval, &dst, 0); copy_string_field(buf->tmp, iori+1, nval, &dst, 1); if ( star_allele ) copy_string_field(".", 0, 1, &dst, 2); buf->mtmp2 = dst.m; buf->tmp2 = dst.s; ret = bcf_update_info(buf->out_hdr, out, tag, buf->tmp2, dst.l, type); } if ( ret!=0 ) error("An error occurred while updating INFO/%s (errcode=%d)\n",tag,ret); } } static void _split_table_set_history(abuf_t *buf) { int i,j,ret; bcf1_t *rec = buf->split.rec; // Don't update if the tag already exists. This is to prevent -a from overwriting -m int m = 0; char *tmp = NULL; ret = bcf_get_info_string(buf->hdr,rec,buf->split.info_tag,&tmp,&m); free(tmp); if ( ret>0 ) return; buf->tmps.l = 0; ksprintf(&buf->tmps,"%s|%"PRIhts_pos"|%s|",bcf_seqname(buf->hdr,rec),rec->pos+1,rec->d.allele[0]); for (i=1; in_allele; i++) { kputs(rec->d.allele[i],&buf->tmps); if ( i+1n_allele ) kputc(',',&buf->tmps); else kputc(',',&buf->tmps); } int len = buf->tmps.l; buf->tmps.s[buf->tmps.l-1] = '|'; for (i=0; isplit.nout; i++) { buf->tmps.l = len; bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,i)]; uint8_t *ptr = buf->split.tbl + i*buf->split.nori; for (j=0; jsplit.nori; j++) { if ( ptr[j]!=1 ) continue; kputw(j+1,&buf->tmps); kputc(',',&buf->tmps); } buf->tmps.s[--buf->tmps.l] = 0; if ( (ret=bcf_update_info_string(buf->out_hdr, out, buf->split.info_tag, buf->tmps.s))!=0 ) error("An error occurred while updating INFO/%s (errcode=%d)\n",buf->split.info_tag,ret); } } static void _split_table_set_gt(abuf_t *buf) { int nsmpl = bcf_hdr_nsamples(buf->hdr); if ( !nsmpl ) return; bcf1_t *rec = buf->split.rec; buf->ngt = bcf_get_genotypes(buf->hdr, rec, &buf->gt, &buf->mgt); if ( buf->ngt<=0 ) return; else hts_expand(int32_t,buf->ngt,buf->mtmpi,buf->tmpi); int iout,i,j; for (iout=0; ioutsplit.nout; iout++) { bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,iout)]; int star_allele = _has_star_allele(buf,iout); int max_ploidy = buf->ngt/nsmpl; int32_t *src = buf->gt, *dst = buf->tmpi; for (i=0; i=rec->n_allele ) error("Out-of-bounds genotypes at %s:%"PRIhts_pos"\n",bcf_seqname(buf->hdr,rec),rec->pos+1); int ial = _split_table_get_ial(buf,iout,iori); if ( ial==2 && !star_allele ) { dst[j] = bcf_gt_missing; if ( bcf_gt_is_phased(src[j]) ) dst[j] |= 1; } else dst[j] = bcf_gt_is_phased(src[j]) ? bcf_gt_phased(ial) : bcf_gt_unphased(ial); } src += max_ploidy; dst += max_ploidy; } bcf_update_genotypes(buf->out_hdr,out,buf->tmpi,buf->ngt); } } static void _split_table_set_format(abuf_t *buf, bcf_fmt_t *fmt, merge_rule_t mode) { int nsmpl = bcf_hdr_nsamples(buf->hdr); if ( !nsmpl ) return; const char *tag = bcf_hdr_int2id(buf->hdr,BCF_DT_ID,fmt->id); if ( tag[0]=='G' && tag[1]=='T' && !tag[2] ) // FORMAT/GT { _split_table_set_gt(buf); return; } int type = bcf_hdr_id2type(buf->hdr,BCF_HL_FMT,fmt->id); int len = bcf_hdr_id2length(buf->hdr,BCF_HL_FMT,fmt->id); if ( type==BCF_HT_STR && len==BCF_VL_G ) return; // possible todo: Number=G for strings if ( type==BCF_HT_LONG ) return; // todo: 64bit integers const int num_size = 4; assert( num_size==sizeof(int32_t) && num_size==sizeof(float) ); int32_t missing = bcf_int32_missing; void *missing_ptr = (void*)&missing; if ( type==BCF_HT_REAL ) bcf_float_set_missing(*((float*)missing_ptr)); int32_t vector_end = bcf_int32_vector_end; void *vector_end_ptr = (void*)&vector_end; if ( type==BCF_HT_REAL ) bcf_float_set_vector_end(*((float*)vector_end_ptr)); bcf1_t *rec = buf->split.rec; int mtmp = ( type==BCF_HT_INT || type==BCF_HT_REAL ) ? buf->mtmp/num_size : buf->mtmp; // number of items int nval = bcf_get_format_values(buf->hdr,rec,tag,&buf->tmp,&mtmp,type); if ( type==BCF_HT_INT || type==BCF_HT_REAL ) buf->mtmp = mtmp*num_size; // number of bytes if ( type==BCF_HT_INT || type==BCF_HT_REAL ) { if ( len==BCF_VL_G && nval!=nsmpl*rec->n_allele && nval!=nsmpl*rec->n_allele*(rec->n_allele+1)/2 ) return; // not haploid nor diploid // Check for incorrect number of values. Note this check does not consider all values missing // and will remove annotations that don't pass. if ( (len==BCF_VL_A && nval != nsmpl*(rec->n_allele - 1)) || (len==BCF_VL_R && nval != nsmpl*rec->n_allele) ) return; } // Increase buffer size to accommodate star allele int nval1 = nval / nsmpl; mtmp = buf->mtmp; if ( type==BCF_HT_INT || type==BCF_HT_REAL ) { if ( (len==BCF_VL_A || len==BCF_VL_R) && mtmp < num_size*nsmpl*(nval1+1) ) mtmp = num_size*nsmpl*(nval1+1); // +1 for the possibility of the star allele else if ( len==BCF_VL_G && mtmp < num_size*nsmpl*(nval1+3) ) mtmp = num_size*nsmpl*(nval1+3); } else if ( type==BCF_HT_STR ) { if ( (len==BCF_VL_A || len==BCF_VL_R) && mtmp < nsmpl*(nval1+2) ) mtmp = nsmpl*(nval1+2); // +2 for the possibility of the star allele, ",." else if ( len==BCF_VL_G && mtmp < nsmpl*(nval1+6) ) mtmp = nsmpl*(nval1+6); } if ( buf->mtmp2 < mtmp ) { buf->tmp2 = realloc(buf->tmp2, mtmp); if ( !buf->tmp2 ) error("Failed to alloc %d bytes\n", mtmp); buf->mtmp2 = mtmp; } int iout, i, j; for (iout=0; ioutsplit.nout; iout++) { int star_allele = _has_star_allele(buf,iout); bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,iout)]; int ret = 0; if ( len==BCF_VL_FIXED || len==BCF_VL_VAR ) ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp, nval, type); else if ( len==BCF_VL_A && type!=BCF_HT_STR ) { int iori = buf->split.atoms[iout]->ial - 1; assert( ioritmp + nval1*num_size*i; void *dst = buf->tmp2 + num_size*i*(star_allele+1); if ( !memcmp(vector_end_ptr,src+iori*num_size,num_size) ) memcpy(dst,missing_ptr,num_size); else memcpy(dst,src+iori*num_size,num_size); if ( star_allele ) memcpy(dst+num_size,missing_ptr,num_size); } ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp2, nsmpl*(star_allele+1), type); } else if ( (len==BCF_VL_A || len==BCF_VL_R) && type==BCF_HT_STR ) { int ioff = len==BCF_VL_R ? 1 : 0; int iori = buf->split.atoms[iout]->ial - 1; int nval1_dst = star_allele ? nval1 + 2 : nval1; memset(buf->tmp2,0,nval1_dst*nsmpl); for (i=0; itmp2 + nval1_dst*i; kputc_('.',&dst); if ( star_allele ) kputsn_(",.",2,&dst); if ( len==BCF_VL_R ) { kputsn_(",.",2,&dst); copy_string_field(buf->tmp+nval1*i, 0, nval1, &dst, 0); } copy_string_field(buf->tmp+nval1*i, iori+ioff, nval1, &dst, 0+ioff); if ( star_allele ) copy_string_field(".", 0, 1, &dst, 1+ioff); } ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp2, nval1_dst*nsmpl, type); } else if ( len==BCF_VL_R && type!=BCF_HT_STR ) { int iori = buf->split.atoms[iout]->ial; assert( iori<=nval ); for (i=0; itmp + nval1*num_size*i; void *dst = buf->tmp2 + num_size*i*(star_allele+2); memcpy(dst,src,num_size); memcpy(dst+num_size,src+iori*num_size,num_size); if ( type==BCF_HT_INT && mode==M_SUM ) { uint8_t *tbl = buf->split.tbl + iout*buf->split.nori; for (j=iori; jsplit.nori; j++) if ( tbl[j]==1 ) ((int32_t*)dst)[1] += ((int32_t*)src)[j+1]; } if ( star_allele ) memcpy(dst+num_size*2,missing_ptr,num_size); } ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp2, nsmpl*(star_allele+2), type); } else if ( len==BCF_VL_G && type!=BCF_HT_STR ) { int iori = buf->split.atoms[iout]->ial; int i01 = bcf_alleles2gt(0,iori); int i11 = bcf_alleles2gt(iori,iori); assert( ioritmp + i*nval1; \ type_t *dst = (type_t*)buf->tmp2 + i*3*(1+star_allele); \ int n=0; /* determine ploidy of this genotype */ \ while ( ntmp + i*nval1; \ memcpy(dst++,src,sizeof(type)); \ int nmiss = 0, nend = 0; \ if ( n==rec->n_allele ) /* haploid */ \ { \ memcpy(dst++,src+iori,sizeof(type)); \ if ( star_allele ) { nmiss = 1; nend = 3; } \ else nend = 1; \ } \ else if ( n==nval1 ) \ { \ memcpy(dst++,src+i01,sizeof(type)); \ memcpy(dst++,src+i11,sizeof(type)); \ if ( star_allele ) nmiss = 3; \ } \ else if ( n==1 && is_missing ) \ { \ if ( star_allele ) nend = 5; \ else nend = 2; \ } \ else \ error("Incorrect number of values at %s:%"PRIhts_pos" .. tag=FORMAT/%s Number=G nAlleles=%d nValues=%d, %d-th sample\n", \ bcf_seqname(buf->hdr,rec),rec->pos+1,tag,rec->n_allele,n,i+1); \ for (j=0; jout_hdr, out, tag, buf->tmp2, 3*(1+star_allele)*nsmpl, type); } if ( ret!=0 ) error("An error occurred while updating FORMAT/%s (errcode=%d)\n",tag,ret); } } static inline int _is_acgtn(char *seq) { while ( *seq ) { char c = toupper(*seq); if ( c!='A' && c!='C' && c!='G' && c!='T' && c!='N' ) return 0; seq++; } return 1; } /* The atomization works as follows: - Atomize each alternate allele separately by leaving out sequence identical to the reference. No alignment is performed, just greedy trimming of the end, then from left. This operation returns a list of atoms (atom_t) which carry fragments of REF,ALT and their positions as 0-based offsets to the original REF allele - Sort atoms by POS, REF and ALT. Each unique atom (POS+REF+ALT) forms a new VCF record, each with a single ALT. - For each new VCF record determine how to translate the original allele index (iori) to this new record: - 1: the original allele matches the atom - 0: the original allele does not overlap this atom or the overlapping part matches the REF allele - 2 (or equivalently "."): there is a mismatch between the original allele and the atom The mapping is encoded in a table with columns corresponding to the original ALTs and rows to the new POS+ALTs (atoms). The table is initialized to 0, then we set 1's for matching atoms and 2's for overlapping mismatching atoms. Note that different ALT alleles can result in the same atom (the same output line) and this code does not know how to reconcile possibly conflicting VCF annotations. This could be improved and merge logic provided, similarly to `merge -l`. For example, the allelic depths (AD) should be summed for the same atomized output allele. However, this level of complexity is not addressed in this initial draft. Higher priority for now is to provide the inverse "join" operation. Update 2021-04-09: Tags QS,AD are now automatically incremented as they should be, for both INFO and FORMAT. Note that the code will fail on missing values (todo) and it needs to be generalized and made customizable. */ void _abuf_split(abuf_t *buf, bcf1_t *rec) { int i,j; if ( rec->n_allele < 2 ) { rbuf_expand0(&buf->rbuf, bcf1_t*, buf->rbuf.n+1, buf->vcf); int j = rbuf_append(&buf->rbuf); if ( buf->vcf[j] ) bcf_destroy(buf->vcf[j]); buf->vcf[j] = bcf_dup(rec); return; } for (i=0; in_allele; i++) { if ( _is_acgtn(rec->d.allele[i]) ) continue; rbuf_expand0(&buf->rbuf, bcf1_t*, buf->rbuf.n+1, buf->vcf); int j = rbuf_append(&buf->rbuf); if ( buf->vcf[j] ) bcf_destroy(buf->vcf[j]); buf->vcf[j] = bcf_dup(rec); return; } buf->natoms = 0; for (i=1; in_allele; i++) _atomize_allele(buf,rec,i); qsort(buf->atoms,buf->natoms,sizeof(*buf->atoms),_cmp_atoms); _split_table_init(buf,rec,buf->natoms); for (i=0; inatoms; i++) { if ( i && _atoms_inconsistent(&buf->atoms[i-1],&buf->atoms[i])==0 ) continue; _split_table_new(buf, &buf->atoms[i]); // add a new unique output atom } for (i=0; inatoms; i++) { // Looping over sorted list of all atoms with possible duplicates from different source ALT alleles atom_t *atom = &buf->atoms[i]; for (j=0; jsplit.nout; j++) { atom_t *out = buf->split.atoms[j]; if ( atom == out ) continue; // table already set to 1 if ( atom->beg > out->end ) continue; // cannot overlap this output atom if ( atom->end < out->beg ) break; // this atom is ahead of all subsequent output records _split_table_overlap(buf, j, atom); } } // _split_table_print(buf); // _split_table_print_atoms(buf); assert( !buf->rbuf.n ); // all records should be flushed first in the SPLIT mode // Create the output records, transferring all annotations: // CHROM-QUAL _split_table_set_chrom_qual(buf); // INFO for (i=0; in_info; i++) { // this implementation of merging rules is temporary: generalize and made customizable through the API merge_rule_t mode = M_FIRST; const char *tag = bcf_hdr_int2id(buf->hdr,BCF_DT_ID,rec->d.info[i].key); if ( !strcmp(tag,"QS") || !strcmp(tag,"AD") ) mode = M_SUM; _split_table_set_info(buf, &rec->d.info[i], mode); } // Set INFO tag showing the original record if ( buf->split.info_tag ) _split_table_set_history(buf); // FORMAT for (i=0; in_fmt; i++) { // this implementation of merging rules is temporary: generalize and made customizable through the API merge_rule_t mode = M_FIRST; const char *tag = bcf_hdr_int2id(buf->hdr,BCF_DT_ID,rec->d.fmt[i].id); if ( !strcmp(tag,"QS") || !strcmp(tag,"AD") ) mode = M_SUM; _split_table_set_format(buf, &rec->d.fmt[i], mode); } // Check that at least one FORMAT field was added, if not, the number of samples must be set manually for (i=0; isplit.nout; i++) { bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,i)]; if ( !out->n_sample ) out->n_sample = rec->n_sample; } } void abuf_push(abuf_t *buf, bcf1_t *rec) { bcf_unpack(rec, BCF_UN_ALL); if ( buf->mode==SPLIT ) _abuf_split(buf,rec); } bcf1_t *abuf_flush(abuf_t *buf, int flush_all) { int i; if ( buf->rbuf.n==0 ) return NULL; if ( flush_all ) goto ret; ret: i = rbuf_shift(&buf->rbuf); return buf->vcf[i]; } pysam-0.23.0/bcftools/abuf.c.pysam.c000066400000000000000000001015261475062545500172140ustar00rootroot00000000000000#include "bcftools.pysam.h" /* The MIT License Copyright (c) 2021-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include "bcftools.h" #include "abuf.h" #include "rbuf.h" typedef enum { M_FIRST, M_SUM } merge_rule_t; typedef struct { kstring_t ref, alt; int ial; // the index of the original ALT allele, 1-based int beg, end; // 0-based inclusive offsets to ref,alt int plen; // the ref,alt prefix length, eg plen=1 for C>CA } atom_t; typedef struct { bcf1_t *rec; int nori, nout; // number of ALTs in the input, and VCF rows on output uint8_t *tbl; // nori columns, nout rows; indicates allele contribution to output rows, see "The atomization works as follows" below uint8_t *overlaps; // is the star allele needed for this variant? atom_t **atoms; int matoms, mtbl, moverlaps; char *info_tag; } split_t; struct _abuf_t { abuf_opt_t mode; split_t split; atom_t *atoms; int natoms, matoms; const bcf_hdr_t *hdr; bcf_hdr_t *out_hdr; bcf1_t **vcf; // dimensions stored in rbuf rbuf_t rbuf; kstring_t tmps; void *tmp, *tmp2; int32_t *gt, *tmpi; int ngt, mgt, ntmpi, mtmpi, mtmp, mtmp2; int star_allele; }; abuf_t *abuf_init(const bcf_hdr_t *hdr, abuf_opt_t mode) { if ( mode!=SPLIT ) error("todo\n"); abuf_t *buf = (abuf_t*) calloc(1,sizeof(abuf_t)); buf->hdr = hdr; buf->out_hdr = (bcf_hdr_t*) hdr; buf->mode = mode; buf->star_allele = 1; rbuf_init(&buf->rbuf, 0); return buf; } void abuf_destroy(abuf_t *buf) { int i; for (i=0; imatoms; i++) { free(buf->atoms[i].ref.s); free(buf->atoms[i].alt.s); } free(buf->atoms); free(buf->split.atoms); free(buf->split.overlaps); free(buf->split.tbl); for (i=0; irbuf.m; i++) if ( buf->vcf[i] ) bcf_destroy(buf->vcf[i]); free(buf->vcf); free(buf->gt); free(buf->tmpi); free(buf->tmp); free(buf->tmp2); free(buf->tmps.s); free(buf); } void abuf_set(abuf_t *buf, abuf_opt_t key, void *value) { if ( key==BCF_HDR ) { buf->out_hdr = *((bcf_hdr_t**)value); return; } if ( key==INFO_TAG ) { buf->split.info_tag = *((char**)value); bcf_hdr_printf(buf->out_hdr,"##INFO=",buf->split.info_tag); return; } if ( key==STAR_ALLELE ) { buf->star_allele = *((int*)value); return; } } /* Split alleles into primitivs, e.g. CC>TT becomes C>T,C>T GCGT>GTGA becomes C>T,T>A There is no sequence alignment, just trimming and hungry matching from left side. */ static void _atomize_allele(abuf_t *buf, bcf1_t *rec, int ial) { // Trim identical sequence from right char *ref = rec->d.allele[0]; char *alt = rec->d.allele[ial]; int rlen = strlen(ref); int alen = strlen(alt); while ( rlen>1 && alen>1 && ref[rlen-1]==alt[alen-1] ) rlen--, alen--; int Mlen = rlen > alen ? rlen : alen; atom_t *atom = NULL; int i; for (i=0; ialt); if ( refb!='-' ) { kputc(refb, &atom->ref); atom->end++; } continue; } buf->natoms++; hts_expand0(atom_t,buf->natoms,buf->matoms,buf->atoms); atom = &buf->atoms[buf->natoms-1]; atom->ref.l = 0; atom->alt.l = 0; kputc(refb, &atom->ref); kputc(altb, &atom->alt); atom->beg = atom->end = i; atom->ial = ial; if ( rlen!=alen && (i+1>=rlen || i+1>=alen) ) // the next base is an indel combined with SNV, e.g. C>GGG? { buf->natoms++; hts_expand0(atom_t,buf->natoms,buf->matoms,buf->atoms); atom = &buf->atoms[buf->natoms-1]; atom->ref.l = 0; atom->alt.l = 0; kputc(refb, &atom->ref); kputc(refb, &atom->alt); atom->beg = atom->end = i; atom->ial = ial; atom->plen = 1; } continue; } if ( i+1>=rlen || i+1>=alen ) // is the next base an indel? { buf->natoms++; hts_expand0(atom_t,buf->natoms,buf->matoms,buf->atoms); atom = &buf->atoms[buf->natoms-1]; atom->ref.l = 0; atom->alt.l = 0; kputc(refb, &atom->ref); kputc(altb, &atom->alt); atom->beg = atom->end = i; atom->ial = ial; } } } static int _atoms_inconsistent(const atom_t *a, const atom_t *b) { if ( a->beg < b->beg ) return -1; if ( a->beg > b->beg ) return 1; int rcmp = strcasecmp(a->ref.s,b->ref.s); if ( rcmp ) return rcmp; return strcasecmp(a->alt.s,b->alt.s); } // returns // 0 .. identical beg,ref,alt // 1 .. non-overlapping variants, but record may overlap (A>AT vs A>C) // 2 .. overlapping (conflicting) variants static int _atoms_overlap(const atom_t *a, const atom_t *b) { if ( a->beg < b->beg ) return 2; if ( a->beg > b->beg ) return 2; // consider SNV followed by DEL as not overlapping // CC > C a.plen=1 (ref,alt prefix len=1) // C > T b.plen=0 (ref,alt prefix len=0) if ( a->plen && a->plen >= b->ref.l ) return 1; if ( b->plen && b->plen >= a->ref.l ) return 1; int rcmp = strcasecmp(a->ref.s,b->ref.s); if ( rcmp ) return 2; // consider SNV followed by INS as not overlapping // A > AT a.plen=1 (ref,alt prefix len=1) // A > C b.plen=0 (ref,alt prefix len=0) if ( a->plen && a->plen >= b->alt.l ) return 1; if ( b->plen && b->plen >= a->alt.l ) return 1; rcmp = strcasecmp(a->alt.s,b->alt.s); if ( rcmp ) return 2; return 0; } /* For reproducibility of tests on different platforms, we need to guarantee the same order of identical atoms originating from different source ALTs. Even though they are consistent, different values can be picked for VCF annotations as currently the values from the one that comes first are used. */ static int _cmp_atoms(const void *aptr, const void *bptr) { const atom_t *a = (const atom_t*) aptr; const atom_t *b = (const atom_t*) bptr; int rcmp = _atoms_inconsistent(a,b); if ( rcmp ) return rcmp; if ( a->ial < b->ial ) return -1; if ( a->ial > b->ial ) return 1; return 0; } static void _split_table_init(abuf_t *buf, bcf1_t *rec, int natoms) { buf->split.rec = rec; buf->split.nori = rec->n_allele - 1; buf->split.nout = 0; hts_expand(uint8_t,buf->split.nori*natoms,buf->split.mtbl,buf->split.tbl); hts_expand(atom_t*,natoms,buf->split.matoms,buf->split.atoms); hts_expand(uint8_t,natoms,buf->split.moverlaps,buf->split.overlaps); memset(buf->split.overlaps,0,sizeof(*buf->split.overlaps)*natoms); } static void _split_table_new(abuf_t *buf, atom_t *atom) { int i, iout = buf->split.nout++; buf->split.atoms[iout] = atom; uint8_t *ptr = buf->split.tbl + iout*buf->split.nori; for (i=0; isplit.nori; i++) ptr[i] = 0; ptr[atom->ial-1] = 1; } static void _split_table_overlap(abuf_t *buf, int iout, atom_t *atom) { uint8_t *ptr = buf->split.tbl + iout*buf->split.nori; int olap = _atoms_overlap(atom,buf->split.atoms[iout]); ptr[atom->ial-1] = olap > 1 ? 2 : 1; // The test test/atomize.split.5.vcf shows why we sometimes can and sometimes // cannot remove the star allele like this // buf->split.overlaps[iout] = olap > 1 ? 1 : 0; // I forgot the details of the code, so don't immediately see // if this could be made smarter buf->split.overlaps[iout] = 1; } #if 0 static void _split_table_print(abuf_t *buf) { int i,j; for (i=0; isplit.nout; i++) { atom_t *atom = buf->split.atoms[i]; uint8_t *ptr = buf->split.tbl + i*buf->split.nori; fprintf(bcftools_stderr,"%d\t%s\t%s",(int)buf->split.rec->pos+1+atom->beg,atom->ref.s,atom->alt.s); for (j=0; jsplit.nori; j++) fprintf(bcftools_stderr,"\t%d",(int)ptr[j]); fprintf(bcftools_stderr,"\n"); } } static void _split_table_print_atoms(abuf_t *buf) { int i; for (i=0; inatoms; i++) { atom_t *atom = &buf->atoms[i]; fprintf(bcftools_stderr,"atom%d %p: ialt=%d %s>%s %d-%d\n",i,atom,atom->ial,atom->ref.s,atom->alt.s,atom->beg,atom->end); } } #endif static inline uint8_t _has_star_allele(abuf_t *buf, int iout) { if ( !buf->star_allele ) return 0; return buf->split.overlaps[iout]; } static inline int _split_table_get_ial(abuf_t *buf, int irow, int ial) { if ( !ial ) return ial; return buf->split.tbl[irow*buf->split.nori + ial - 1]; } static void _split_table_set_chrom_qual(abuf_t *buf) { int iout,j; bcf1_t *rec = buf->split.rec; for (iout=0; ioutsplit.nout; iout++) { rbuf_expand0(&buf->rbuf, bcf1_t*, buf->rbuf.n+1, buf->vcf); j = rbuf_append(&buf->rbuf); if ( !buf->vcf[j] ) buf->vcf[j] = bcf_init1(); bcf1_t *out = buf->vcf[j]; bcf_clear1(out); atom_t *atom = buf->split.atoms[iout]; out->rid = rec->rid; out->pos = rec->pos + atom->beg; bcf_update_id(buf->out_hdr, out, rec->d.id); const char *als[3]; als[0] = atom->ref.s; als[1] = atom->alt.s; als[2] = "*"; int nals = _has_star_allele(buf,iout) ? 3 : 2; bcf_update_alleles(buf->out_hdr, out, als, nals); if ( bcf_float_is_missing(rec->qual) ) bcf_float_set_missing(out->qual); else out->qual = rec->qual; bcf_update_filter(buf->out_hdr, out, rec->d.flt, rec->d.n_flt); } } int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst); static void _split_table_set_info(abuf_t *buf, bcf_info_t *info, merge_rule_t mode) { const char *tag = bcf_hdr_int2id(buf->hdr,BCF_DT_ID,info->key); int type = bcf_hdr_id2type(buf->hdr,BCF_HL_INFO,info->key); int len = bcf_hdr_id2length(buf->hdr,BCF_HL_INFO,info->key); if ( len==BCF_VL_G ) return; // todo: Number=G INFO tags if ( type==BCF_HT_LONG ) return; // todo: 64bit integers bcf1_t *rec = buf->split.rec; int mtmp = ( type==BCF_HT_INT || type==BCF_HT_REAL ) ? buf->mtmp/4 : buf->mtmp; int nval = bcf_get_info_values(buf->hdr,rec,tag,&buf->tmp,&mtmp,type); if ( type==BCF_HT_INT || type==BCF_HT_REAL ) buf->mtmp = mtmp*4; // Check for incorrect number of values. Note this check does not consider all values missing // and will remove annotations that don't pass. if ( type==BCF_HT_INT || type==BCF_HT_REAL ) { if ( (len==BCF_VL_A && nval != rec->n_allele - 1) || (len==BCF_VL_R && nval != rec->n_allele) ) return; } if ( buf->mtmp2 < buf->mtmp ) { buf->tmp2 = realloc(buf->tmp2, buf->mtmp); if ( !buf->tmp2 ) error("Failed to alloc %d bytes\n", buf->mtmp); buf->mtmp2 = buf->mtmp; } const int num_size = 4; assert( num_size==sizeof(int32_t) && num_size==sizeof(float) ); int32_t missing = bcf_int32_missing; void *missing_ptr = (void*)&missing; if ( type==BCF_HT_REAL ) bcf_float_set_missing(*((float*)missing_ptr)); int32_t vector_end = bcf_int32_vector_end; void *vector_end_ptr = (void*)&vector_end; if ( type==BCF_HT_REAL ) bcf_float_set_vector_end(*((float*)vector_end_ptr)); int iout,i; for (iout=0; ioutsplit.nout; iout++) { bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,iout)]; int star_allele = _has_star_allele(buf,iout); int ret = 0; if ( len==BCF_VL_FIXED || len==BCF_VL_VAR ) ret = bcf_update_info(buf->out_hdr, out, tag, type==BCF_HT_FLAG ? NULL : buf->tmp, nval, type); else if ( len==BCF_VL_A && type!=BCF_HT_STR ) { int iori = buf->split.atoms[iout]->ial - 1; assert( ioritmp+num_size*iori,num_size) ) memcpy(buf->tmp2,missing_ptr,num_size); else memcpy(buf->tmp2,buf->tmp+num_size*iori,num_size); if ( star_allele ) memcpy(buf->tmp2+num_size,missing_ptr,num_size); ret = bcf_update_info(buf->out_hdr, out, tag, buf->tmp2, 1 + star_allele, type); } else if ( len==BCF_VL_A && type==BCF_HT_STR ) { int iori = buf->split.atoms[iout]->ial - 1; kstring_t dst; dst.l = 0; dst.m = buf->mtmp2; dst.s = (char*)buf->tmp2; kputc('.',&dst); if ( star_allele ) kputs(",.",&dst); copy_string_field(buf->tmp, iori, nval, &dst, 0); if ( star_allele ) copy_string_field(".", 0, 1, &dst, 1); buf->mtmp2 = dst.m; buf->tmp2 = dst.s; ret = bcf_update_info(buf->out_hdr, out, tag, buf->tmp2, dst.l, type); } else if ( len==BCF_VL_R && type!=BCF_HT_STR ) { memcpy(buf->tmp2,buf->tmp,num_size); // REF contributes to all records int iori = buf->split.atoms[iout]->ial; assert( iorisplit.nori ); if ( !memcmp(vector_end_ptr,buf->tmp+num_size*iori,num_size) ) memcpy(buf->tmp2+num_size,missing_ptr,num_size); else memcpy(buf->tmp2+num_size,buf->tmp+num_size*iori,num_size); if ( type==BCF_HT_INT && mode==M_SUM ) { uint8_t *tbl = buf->split.tbl + iout*buf->split.nori; for (i=iori; isplit.nori; i++) { if ( tbl[i]==1 ) ((int32_t*)buf->tmp2)[1] += ((int32_t*)buf->tmp)[i+1]; } } if ( star_allele ) memcpy(buf->tmp2+2*num_size,missing_ptr,num_size); ret = bcf_update_info(buf->out_hdr, out, tag, buf->tmp2, 2 + star_allele, type); } else if ( len==BCF_VL_R && type==BCF_HT_STR ) { int iori = buf->split.atoms[iout]->ial - 1; kstring_t dst; dst.l = 0; dst.m = buf->mtmp2; dst.s = (char*)buf->tmp2; kputs(".,.",&dst); if ( star_allele ) kputs(",.",&dst); copy_string_field(buf->tmp, 0, nval, &dst, 0); copy_string_field(buf->tmp, iori+1, nval, &dst, 1); if ( star_allele ) copy_string_field(".", 0, 1, &dst, 2); buf->mtmp2 = dst.m; buf->tmp2 = dst.s; ret = bcf_update_info(buf->out_hdr, out, tag, buf->tmp2, dst.l, type); } if ( ret!=0 ) error("An error occurred while updating INFO/%s (errcode=%d)\n",tag,ret); } } static void _split_table_set_history(abuf_t *buf) { int i,j,ret; bcf1_t *rec = buf->split.rec; // Don't update if the tag already exists. This is to prevent -a from overwriting -m int m = 0; char *tmp = NULL; ret = bcf_get_info_string(buf->hdr,rec,buf->split.info_tag,&tmp,&m); free(tmp); if ( ret>0 ) return; buf->tmps.l = 0; ksprintf(&buf->tmps,"%s|%"PRIhts_pos"|%s|",bcf_seqname(buf->hdr,rec),rec->pos+1,rec->d.allele[0]); for (i=1; in_allele; i++) { kputs(rec->d.allele[i],&buf->tmps); if ( i+1n_allele ) kputc(',',&buf->tmps); else kputc(',',&buf->tmps); } int len = buf->tmps.l; buf->tmps.s[buf->tmps.l-1] = '|'; for (i=0; isplit.nout; i++) { buf->tmps.l = len; bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,i)]; uint8_t *ptr = buf->split.tbl + i*buf->split.nori; for (j=0; jsplit.nori; j++) { if ( ptr[j]!=1 ) continue; kputw(j+1,&buf->tmps); kputc(',',&buf->tmps); } buf->tmps.s[--buf->tmps.l] = 0; if ( (ret=bcf_update_info_string(buf->out_hdr, out, buf->split.info_tag, buf->tmps.s))!=0 ) error("An error occurred while updating INFO/%s (errcode=%d)\n",buf->split.info_tag,ret); } } static void _split_table_set_gt(abuf_t *buf) { int nsmpl = bcf_hdr_nsamples(buf->hdr); if ( !nsmpl ) return; bcf1_t *rec = buf->split.rec; buf->ngt = bcf_get_genotypes(buf->hdr, rec, &buf->gt, &buf->mgt); if ( buf->ngt<=0 ) return; else hts_expand(int32_t,buf->ngt,buf->mtmpi,buf->tmpi); int iout,i,j; for (iout=0; ioutsplit.nout; iout++) { bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,iout)]; int star_allele = _has_star_allele(buf,iout); int max_ploidy = buf->ngt/nsmpl; int32_t *src = buf->gt, *dst = buf->tmpi; for (i=0; i=rec->n_allele ) error("Out-of-bounds genotypes at %s:%"PRIhts_pos"\n",bcf_seqname(buf->hdr,rec),rec->pos+1); int ial = _split_table_get_ial(buf,iout,iori); if ( ial==2 && !star_allele ) { dst[j] = bcf_gt_missing; if ( bcf_gt_is_phased(src[j]) ) dst[j] |= 1; } else dst[j] = bcf_gt_is_phased(src[j]) ? bcf_gt_phased(ial) : bcf_gt_unphased(ial); } src += max_ploidy; dst += max_ploidy; } bcf_update_genotypes(buf->out_hdr,out,buf->tmpi,buf->ngt); } } static void _split_table_set_format(abuf_t *buf, bcf_fmt_t *fmt, merge_rule_t mode) { int nsmpl = bcf_hdr_nsamples(buf->hdr); if ( !nsmpl ) return; const char *tag = bcf_hdr_int2id(buf->hdr,BCF_DT_ID,fmt->id); if ( tag[0]=='G' && tag[1]=='T' && !tag[2] ) // FORMAT/GT { _split_table_set_gt(buf); return; } int type = bcf_hdr_id2type(buf->hdr,BCF_HL_FMT,fmt->id); int len = bcf_hdr_id2length(buf->hdr,BCF_HL_FMT,fmt->id); if ( type==BCF_HT_STR && len==BCF_VL_G ) return; // possible todo: Number=G for strings if ( type==BCF_HT_LONG ) return; // todo: 64bit integers const int num_size = 4; assert( num_size==sizeof(int32_t) && num_size==sizeof(float) ); int32_t missing = bcf_int32_missing; void *missing_ptr = (void*)&missing; if ( type==BCF_HT_REAL ) bcf_float_set_missing(*((float*)missing_ptr)); int32_t vector_end = bcf_int32_vector_end; void *vector_end_ptr = (void*)&vector_end; if ( type==BCF_HT_REAL ) bcf_float_set_vector_end(*((float*)vector_end_ptr)); bcf1_t *rec = buf->split.rec; int mtmp = ( type==BCF_HT_INT || type==BCF_HT_REAL ) ? buf->mtmp/num_size : buf->mtmp; // number of items int nval = bcf_get_format_values(buf->hdr,rec,tag,&buf->tmp,&mtmp,type); if ( type==BCF_HT_INT || type==BCF_HT_REAL ) buf->mtmp = mtmp*num_size; // number of bytes if ( type==BCF_HT_INT || type==BCF_HT_REAL ) { if ( len==BCF_VL_G && nval!=nsmpl*rec->n_allele && nval!=nsmpl*rec->n_allele*(rec->n_allele+1)/2 ) return; // not haploid nor diploid // Check for incorrect number of values. Note this check does not consider all values missing // and will remove annotations that don't pass. if ( (len==BCF_VL_A && nval != nsmpl*(rec->n_allele - 1)) || (len==BCF_VL_R && nval != nsmpl*rec->n_allele) ) return; } // Increase buffer size to accommodate star allele int nval1 = nval / nsmpl; mtmp = buf->mtmp; if ( type==BCF_HT_INT || type==BCF_HT_REAL ) { if ( (len==BCF_VL_A || len==BCF_VL_R) && mtmp < num_size*nsmpl*(nval1+1) ) mtmp = num_size*nsmpl*(nval1+1); // +1 for the possibility of the star allele else if ( len==BCF_VL_G && mtmp < num_size*nsmpl*(nval1+3) ) mtmp = num_size*nsmpl*(nval1+3); } else if ( type==BCF_HT_STR ) { if ( (len==BCF_VL_A || len==BCF_VL_R) && mtmp < nsmpl*(nval1+2) ) mtmp = nsmpl*(nval1+2); // +2 for the possibility of the star allele, ",." else if ( len==BCF_VL_G && mtmp < nsmpl*(nval1+6) ) mtmp = nsmpl*(nval1+6); } if ( buf->mtmp2 < mtmp ) { buf->tmp2 = realloc(buf->tmp2, mtmp); if ( !buf->tmp2 ) error("Failed to alloc %d bytes\n", mtmp); buf->mtmp2 = mtmp; } int iout, i, j; for (iout=0; ioutsplit.nout; iout++) { int star_allele = _has_star_allele(buf,iout); bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,iout)]; int ret = 0; if ( len==BCF_VL_FIXED || len==BCF_VL_VAR ) ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp, nval, type); else if ( len==BCF_VL_A && type!=BCF_HT_STR ) { int iori = buf->split.atoms[iout]->ial - 1; assert( ioritmp + nval1*num_size*i; void *dst = buf->tmp2 + num_size*i*(star_allele+1); if ( !memcmp(vector_end_ptr,src+iori*num_size,num_size) ) memcpy(dst,missing_ptr,num_size); else memcpy(dst,src+iori*num_size,num_size); if ( star_allele ) memcpy(dst+num_size,missing_ptr,num_size); } ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp2, nsmpl*(star_allele+1), type); } else if ( (len==BCF_VL_A || len==BCF_VL_R) && type==BCF_HT_STR ) { int ioff = len==BCF_VL_R ? 1 : 0; int iori = buf->split.atoms[iout]->ial - 1; int nval1_dst = star_allele ? nval1 + 2 : nval1; memset(buf->tmp2,0,nval1_dst*nsmpl); for (i=0; itmp2 + nval1_dst*i; kputc_('.',&dst); if ( star_allele ) kputsn_(",.",2,&dst); if ( len==BCF_VL_R ) { kputsn_(",.",2,&dst); copy_string_field(buf->tmp+nval1*i, 0, nval1, &dst, 0); } copy_string_field(buf->tmp+nval1*i, iori+ioff, nval1, &dst, 0+ioff); if ( star_allele ) copy_string_field(".", 0, 1, &dst, 1+ioff); } ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp2, nval1_dst*nsmpl, type); } else if ( len==BCF_VL_R && type!=BCF_HT_STR ) { int iori = buf->split.atoms[iout]->ial; assert( iori<=nval ); for (i=0; itmp + nval1*num_size*i; void *dst = buf->tmp2 + num_size*i*(star_allele+2); memcpy(dst,src,num_size); memcpy(dst+num_size,src+iori*num_size,num_size); if ( type==BCF_HT_INT && mode==M_SUM ) { uint8_t *tbl = buf->split.tbl + iout*buf->split.nori; for (j=iori; jsplit.nori; j++) if ( tbl[j]==1 ) ((int32_t*)dst)[1] += ((int32_t*)src)[j+1]; } if ( star_allele ) memcpy(dst+num_size*2,missing_ptr,num_size); } ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp2, nsmpl*(star_allele+2), type); } else if ( len==BCF_VL_G && type!=BCF_HT_STR ) { int iori = buf->split.atoms[iout]->ial; int i01 = bcf_alleles2gt(0,iori); int i11 = bcf_alleles2gt(iori,iori); assert( ioritmp + i*nval1; \ type_t *dst = (type_t*)buf->tmp2 + i*3*(1+star_allele); \ int n=0; /* determine ploidy of this genotype */ \ while ( ntmp + i*nval1; \ memcpy(dst++,src,sizeof(type)); \ int nmiss = 0, nend = 0; \ if ( n==rec->n_allele ) /* haploid */ \ { \ memcpy(dst++,src+iori,sizeof(type)); \ if ( star_allele ) { nmiss = 1; nend = 3; } \ else nend = 1; \ } \ else if ( n==nval1 ) \ { \ memcpy(dst++,src+i01,sizeof(type)); \ memcpy(dst++,src+i11,sizeof(type)); \ if ( star_allele ) nmiss = 3; \ } \ else if ( n==1 && is_missing ) \ { \ if ( star_allele ) nend = 5; \ else nend = 2; \ } \ else \ error("Incorrect number of values at %s:%"PRIhts_pos" .. tag=FORMAT/%s Number=G nAlleles=%d nValues=%d, %d-th sample\n", \ bcf_seqname(buf->hdr,rec),rec->pos+1,tag,rec->n_allele,n,i+1); \ for (j=0; jout_hdr, out, tag, buf->tmp2, 3*(1+star_allele)*nsmpl, type); } if ( ret!=0 ) error("An error occurred while updating FORMAT/%s (errcode=%d)\n",tag,ret); } } static inline int _is_acgtn(char *seq) { while ( *seq ) { char c = toupper(*seq); if ( c!='A' && c!='C' && c!='G' && c!='T' && c!='N' ) return 0; seq++; } return 1; } /* The atomization works as follows: - Atomize each alternate allele separately by leaving out sequence identical to the reference. No alignment is performed, just greedy trimming of the end, then from left. This operation returns a list of atoms (atom_t) which carry fragments of REF,ALT and their positions as 0-based offsets to the original REF allele - Sort atoms by POS, REF and ALT. Each unique atom (POS+REF+ALT) forms a new VCF record, each with a single ALT. - For each new VCF record determine how to translate the original allele index (iori) to this new record: - 1: the original allele matches the atom - 0: the original allele does not overlap this atom or the overlapping part matches the REF allele - 2 (or equivalently "."): there is a mismatch between the original allele and the atom The mapping is encoded in a table with columns corresponding to the original ALTs and rows to the new POS+ALTs (atoms). The table is initialized to 0, then we set 1's for matching atoms and 2's for overlapping mismatching atoms. Note that different ALT alleles can result in the same atom (the same output line) and this code does not know how to reconcile possibly conflicting VCF annotations. This could be improved and merge logic provided, similarly to `merge -l`. For example, the allelic depths (AD) should be summed for the same atomized output allele. However, this level of complexity is not addressed in this initial draft. Higher priority for now is to provide the inverse "join" operation. Update 2021-04-09: Tags QS,AD are now automatically incremented as they should be, for both INFO and FORMAT. Note that the code will fail on missing values (todo) and it needs to be generalized and made customizable. */ void _abuf_split(abuf_t *buf, bcf1_t *rec) { int i,j; if ( rec->n_allele < 2 ) { rbuf_expand0(&buf->rbuf, bcf1_t*, buf->rbuf.n+1, buf->vcf); int j = rbuf_append(&buf->rbuf); if ( buf->vcf[j] ) bcf_destroy(buf->vcf[j]); buf->vcf[j] = bcf_dup(rec); return; } for (i=0; in_allele; i++) { if ( _is_acgtn(rec->d.allele[i]) ) continue; rbuf_expand0(&buf->rbuf, bcf1_t*, buf->rbuf.n+1, buf->vcf); int j = rbuf_append(&buf->rbuf); if ( buf->vcf[j] ) bcf_destroy(buf->vcf[j]); buf->vcf[j] = bcf_dup(rec); return; } buf->natoms = 0; for (i=1; in_allele; i++) _atomize_allele(buf,rec,i); qsort(buf->atoms,buf->natoms,sizeof(*buf->atoms),_cmp_atoms); _split_table_init(buf,rec,buf->natoms); for (i=0; inatoms; i++) { if ( i && _atoms_inconsistent(&buf->atoms[i-1],&buf->atoms[i])==0 ) continue; _split_table_new(buf, &buf->atoms[i]); // add a new unique output atom } for (i=0; inatoms; i++) { // Looping over sorted list of all atoms with possible duplicates from different source ALT alleles atom_t *atom = &buf->atoms[i]; for (j=0; jsplit.nout; j++) { atom_t *out = buf->split.atoms[j]; if ( atom == out ) continue; // table already set to 1 if ( atom->beg > out->end ) continue; // cannot overlap this output atom if ( atom->end < out->beg ) break; // this atom is ahead of all subsequent output records _split_table_overlap(buf, j, atom); } } // _split_table_print(buf); // _split_table_print_atoms(buf); assert( !buf->rbuf.n ); // all records should be flushed first in the SPLIT mode // Create the output records, transferring all annotations: // CHROM-QUAL _split_table_set_chrom_qual(buf); // INFO for (i=0; in_info; i++) { // this implementation of merging rules is temporary: generalize and made customizable through the API merge_rule_t mode = M_FIRST; const char *tag = bcf_hdr_int2id(buf->hdr,BCF_DT_ID,rec->d.info[i].key); if ( !strcmp(tag,"QS") || !strcmp(tag,"AD") ) mode = M_SUM; _split_table_set_info(buf, &rec->d.info[i], mode); } // Set INFO tag showing the original record if ( buf->split.info_tag ) _split_table_set_history(buf); // FORMAT for (i=0; in_fmt; i++) { // this implementation of merging rules is temporary: generalize and made customizable through the API merge_rule_t mode = M_FIRST; const char *tag = bcf_hdr_int2id(buf->hdr,BCF_DT_ID,rec->d.fmt[i].id); if ( !strcmp(tag,"QS") || !strcmp(tag,"AD") ) mode = M_SUM; _split_table_set_format(buf, &rec->d.fmt[i], mode); } // Check that at least one FORMAT field was added, if not, the number of samples must be set manually for (i=0; isplit.nout; i++) { bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,i)]; if ( !out->n_sample ) out->n_sample = rec->n_sample; } } void abuf_push(abuf_t *buf, bcf1_t *rec) { bcf_unpack(rec, BCF_UN_ALL); if ( buf->mode==SPLIT ) _abuf_split(buf,rec); } bcf1_t *abuf_flush(abuf_t *buf, int flush_all) { int i; if ( buf->rbuf.n==0 ) return NULL; if ( flush_all ) goto ret; ret: i = rbuf_shift(&buf->rbuf); return buf->vcf[i]; } pysam-0.23.0/bcftools/abuf.h000066400000000000000000000047311475062545500156500ustar00rootroot00000000000000/* The MIT License Copyright (c) 2021 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Atomize/deatomize complex variants */ #ifndef __ABUF_H__ #define __ABUF_H__ #include typedef struct _abuf_t abuf_t; // Modes of operation typedef enum { NONE, // mode of operation, to be passed to abuf_init SPLIT, JOIN, BCF_HDR, // should the records be annotated, a writable bcf header is required INFO_TAG, // set BCF_HDR first STAR_ALLELE // 1: use STAR allele (the default), 0: set overlaps to missing } abuf_opt_t; #define abuf_set_opt(buf,type,key,value) { type tmp = value; abuf_set(buf, key, (void*)&tmp); } void abuf_set(abuf_t *buf, abuf_opt_t key, void *value); /* * abuf_init() - init buffer * @win: number of sites (>0) or bp (<0) */ abuf_t *abuf_init(const bcf_hdr_t *hdr, abuf_opt_t mode); void abuf_destroy(abuf_t *buf); /* * abuf_push() - Push a new site for analysis */ void abuf_push(abuf_t *buf, bcf1_t *rec); /* * abuf_flush() - Return next buffered record * @flush_all: Set to 1 if no more overlapping records are coming (e.g. end of chromosome or end of file), * the buffer can be emptied. * return: The next atomized/deatomized VCF record or NULL if no record is ready. The returned * structure will be cleaned by abuf. */ bcf1_t *abuf_flush(abuf_t *buf, int flush_all); #endif pysam-0.23.0/bcftools/bam2bcf.c000066400000000000000000001444611475062545500162270ustar00rootroot00000000000000/* bam2bcf.c -- variant calling. Copyright (C) 2010-2012 Broad Institute. Copyright (C) 2012-2024 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include "bam2bcf.h" extern void ks_introsort_uint32_t(size_t n, uint32_t a[]); #define CALL_DEFTHETA 0.83 #define DEF_MAPQ 20 #define CAP_DIST 25 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ, int max_baseQ, int delta_baseQ) { bcf_callaux_t *bca; if (theta <= 0.) theta = CALL_DEFTHETA; bca = (bcf_callaux_t*) calloc(1, sizeof(bcf_callaux_t)); bca->capQ = 60; bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100; bca->min_baseQ = min_baseQ; bca->max_baseQ = max_baseQ; bca->delta_baseQ = delta_baseQ; bca->e = errmod_init(1. - theta); bca->min_frac = 0.002; bca->min_support = 1; bca->per_sample_flt = 0; bca->npos = 100; bca->ref_pos = (int*) malloc(bca->npos*sizeof(int)); bca->alt_pos = (int*) malloc(bca->npos*sizeof(int)); bca->iref_pos= (int*) malloc(bca->npos*sizeof(int)); bca->ialt_pos= (int*) malloc(bca->npos*sizeof(int)); bca->nqual = 60; bca->ref_mq = (int*) malloc(bca->nqual*sizeof(int)); bca->alt_mq = (int*) malloc(bca->nqual*sizeof(int)); bca->iref_mq = (int*) malloc(bca->nqual*sizeof(int)); bca->ialt_mq = (int*) malloc(bca->nqual*sizeof(int)); bca->ref_bq = (int*) malloc(bca->nqual*sizeof(int)); bca->alt_bq = (int*) malloc(bca->nqual*sizeof(int)); bca->fwd_mqs = (int*) malloc(bca->nqual*sizeof(int)); bca->rev_mqs = (int*) malloc(bca->nqual*sizeof(int)); return bca; } void bcf_iaux_destroy(bcf_callaux_t *bca); void bcf_call_destroy(bcf_callaux_t *bca) { if (bca == 0) return; bcf_iaux_destroy(bca); errmod_destroy(bca->e); if (bca->npos) { free(bca->ref_pos); free(bca->alt_pos); free(bca->iref_pos); free(bca->ialt_pos); bca->npos = 0; } free(bca->ref_mq); free(bca->alt_mq); free(bca->iref_mq); free(bca->ialt_mq); free(bca->ref_bq); free(bca->alt_bq); free(bca->fwd_mqs); free(bca->rev_mqs); bca->nqual = 0; free(bca->bases); free(bca->inscns); free(bca); } static int get_aux_nm(const bam_pileup1_t *p, int32_t qpos, int is_ref) { int64_t nm; const bam_pileup_cd *cd = &p->cd; if ( PLP_NM(cd) == -1 ) return -1; if ( PLP_NM(cd) == PLP_NM_UNSET ) { // todo: make this localized to be useful for long reads as well bam1_t *rec = p->b; uint8_t *nm_tag = bam_aux_get(rec, "NM"); if ( !nm_tag ) { PLP_NM(cd) = -1; return -1; } nm = bam_aux2i(nm_tag); // Count indels as single events, not as the number of inserted/deleted // bases (which is what NM does). Add soft clips as mismatches. int i; for (i=0; i < rec->core.n_cigar; i++) { int val = bam_get_cigar(rec)[i] & BAM_CIGAR_MASK; if ( val==BAM_CSOFT_CLIP ) { nm += bam_get_cigar(rec)[i] >> BAM_CIGAR_SHIFT; } else if ( val==BAM_CINS || val==BAM_CDEL ) { val = bam_get_cigar(rec)[i] >> BAM_CIGAR_SHIFT; if ( val > 1 ) nm -= val - 1; } } PLP_NM(cd) = nm; } else nm = PLP_NM(cd); // Take into account MNPs, 2% of de novo SNVs appear within 20bp of another de novo SNV // http://www.genome.org/cgi/doi/10.1101/gr.239756.118 nm -= is_ref ? 1 : 2; if ( nm < 0 ) nm = 0; if ( nm >= B2B_N_NM ) nm = B2B_N_NM - 1; return nm; } // position in the sequence with respect to the aligned part of the read static int get_position(const bam_pileup1_t *p, int *len, int *sc_len, int *sc_dist) { int i, j, edist = p->qpos + 1; int sc_left = 0, sc_right = 0; int sc_left_dist = -1, sc_right_dist = -1; // left end for (i = 0; i < p->b->core.n_cigar; i++) { int cig = bam_get_cigar(p->b)[i] & BAM_CIGAR_MASK; if (cig == BAM_CHARD_CLIP) continue; else if (cig == BAM_CSOFT_CLIP) sc_left += bam_get_cigar(p->b)[i] >> BAM_CIGAR_SHIFT; else break; } if (sc_left) sc_left_dist = p->qpos+1 - sc_left; edist -= sc_left; // right end for (j = p->b->core.n_cigar-1; j >= i; j--) { int cig = bam_get_cigar(p->b)[j] & BAM_CIGAR_MASK; if (cig == BAM_CHARD_CLIP) continue; else if (cig == BAM_CSOFT_CLIP) sc_right += bam_get_cigar(p->b)[j] >> BAM_CIGAR_SHIFT; else break; } if (sc_right) sc_right_dist = p->b->core.l_qseq - sc_right - p->qpos; // Distance to nearest soft-clips and length of that clip. if (sc_left_dist >= 0) { if (sc_right_dist < 0 || sc_left_dist < sc_right_dist) { *sc_len = sc_left; *sc_dist = sc_left_dist; } } else if (sc_right_dist >= 0) { *sc_len = sc_right; *sc_dist = sc_right_dist; } else { *sc_len = 0; *sc_dist = 0; } *len = p->b->core.l_qseq - sc_left - sc_right; return edist; } void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call) { memset(bca->ref_pos,0,sizeof(int)*bca->npos); memset(bca->alt_pos,0,sizeof(int)*bca->npos); memset(bca->iref_pos,0,sizeof(int)*bca->npos); memset(bca->ialt_pos,0,sizeof(int)*bca->npos); memset(bca->ref_mq,0,sizeof(int)*bca->nqual); memset(bca->alt_mq,0,sizeof(int)*bca->nqual); memset(bca->iref_mq,0,sizeof(int)*bca->nqual); memset(bca->ialt_mq,0,sizeof(int)*bca->nqual); memset(bca->ref_bq,0,sizeof(int)*bca->nqual); memset(bca->alt_bq,0,sizeof(int)*bca->nqual); memset(bca->fwd_mqs,0,sizeof(int)*bca->nqual); memset(bca->rev_mqs,0,sizeof(int)*bca->nqual); if ( call->ADF ) memset(call->ADF,0,sizeof(int32_t)*(call->n+1)*B2B_MAX_ALLELES); if ( call->ADR ) memset(call->ADR,0,sizeof(int32_t)*(call->n+1)*B2B_MAX_ALLELES); if ( call->SCR ) memset(call->SCR,0,sizeof(*call->SCR)*(call->n+1)); if ( call->SCR ) memset(call->SCR,0,sizeof(*call->SCR)*(call->n+1)); if ( bca->fmt_flag&B2B_FMT_NMBZ ) { memset(call->ref_nm,0,sizeof(*call->ref_nm)*(call->n+1)*B2B_N_NM); memset(call->alt_nm,0,sizeof(*call->alt_nm)*(call->n+1)*B2B_N_NM); } else { memset(call->ref_nm,0,sizeof(*call->ref_nm)*B2B_N_NM); memset(call->alt_nm,0,sizeof(*call->alt_nm)*B2B_N_NM); } memset(call->QS,0,sizeof(*call->QS)*call->n*B2B_MAX_ALLELES); memset(bca->ref_scl, 0, 100*sizeof(int)); memset(bca->alt_scl, 0, 100*sizeof(int)); memset(bca->iref_scl, 0, 100*sizeof(int)); memset(bca->ialt_scl, 0, 100*sizeof(int)); int i; for (i=0; i<2; i++) bca->nnm[i] = 0; for (i=0; i<2; i++) bca->nm[i] = 0; } /* Notes: - Called from bam_plcmd.c by mpileup. Amongst other things, sets the bcf_callret1_t.QS frequencies which are carried over via bcf_call_combine and bcf_call2bcf to the output BCF as the INFO/QS and FMT/QS annotations. Later it's used for multiallelic calling by `call -m`, `call -mG` and `+trio-dnm`. - ref_base is the 4-bit representation of the reference base. It is negative if we are looking at an indel. */ /* * This function is called once for each sample. * _n is number of pilesups pl contributing reads to this sample * pl is pointer to array of _n pileups (one pileup per read) * ref_base is the 4-bit representation of the reference base. It is negative if we are looking at an indel. * bca is the settings to perform calls across all samples * r is the returned value of the call */ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r) { int i, n, ref4, is_indel, ori_depth = 0; #ifdef GLF_DEBUG fprintf(stderr, "Call GLFGEN\n"); #endif // clean from previous run r->ori_depth = 0; r->mq0 = 0; memset(r->anno,0,sizeof(double)*16); memset(r->p,0,sizeof(float)*25); r->SCR = 0; if (ref_base >= 0) { ref4 = seq_nt16_int[ref_base]; is_indel = 0; } else ref4 = 4, is_indel = 1; if (_n == 0) return -1; // enlarge the bases array if necessary if (bca->max_bases < _n) { bca->max_bases = _n; kroundup32(bca->max_bases); bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases); } // Detect if indel occurs anywhere in this sample int indel_in_sample = 0; if (bca->edlib) { for (i = n = 0; i < _n; ++i) { const bam_pileup1_t *p = pl + i; if (p->indel) indel_in_sample = 1; } } // fill the bases array double nqual_over_60 = bca->nqual / 60.0; int ADR_ref_missed[4] = {0}; int ADF_ref_missed[4] = {0}; for (i = n = 0; i < _n; ++i) { const bam_pileup1_t *p = pl + i; int b; // the base or indel type int q; // the base or indel quality used to calculate PL int seqQ; // used to cap the indel quality given the sequence context int mapQ; // to cap the quality for low MQ reads int baseQ; // used only for supporting INFO annotations int is_diff; // is this base or indel type different from the reference int min_dist; // distance from the end, used for tail distance bias if ( bca->fmt_flag&(B2B_INFO_SCR|B2B_FMT_SCR) && PLP_HAS_SOFT_CLIP(&p->cd) ) r->SCR++; if (p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue; // The meaning of the indel related variables: // is_indel .. is this position currently tested for an indel // p->is_del .. is the current base a deletion in this read (unrelated to the tested indel) // p->indel .. is there an indel starting after this position (i.e. does this read have the tested indel) if (p->is_del && !is_indel) continue; // not testing an indel and the read has a spanning deletion int inm = -1; ++ori_depth; if (is_indel) // testing an indel position { b = p->aux>>16&0x3f; // indel type seqQ = q = (p->aux & 0xff); // mp2 + builtin indel-bias if (bca->edlib) { if (indel_in_sample) { seqQ = q = (p->aux & 0xff); // mp2 + builtin indel-bias } else if (p->aux & 0xff) { // An indel in another sample, but not this. So just use // basic sequence confidences. q = bam_get_qual(p->b)[p->qpos]; if (q > bca->max_baseQ) q = bca->max_baseQ; seqQ = 99; } } if ( !bca->indels_v20 && !bca->edlib ) { /* This heuristics was introduced by e4e161068 and claims to fix #1446. However, we obtain correct result on the provided test case even when this code is commented out, so this may not be needed anymore. Leaving it in only for backward compatibility for now. See mpileup-tests homdel-issue-1446 and CHM1_CHM13_2.45x-1-1701408 which work only when this code is disabled. */ if (p->indel == 0 && (q < _n/2 || _n > 20)) { // high quality indel calls without p->indel set aren't // particularly indicative of being a good REF match either, // at least not in low coverage. So require solid coverage // before we start utilising such quals. b = 0; q = (int)bam_get_qual(p->b)[p->qpos]; seqQ = (3*seqQ + 2*q)/8; } if (_n > 20 && seqQ > 40) seqQ = 40; } is_diff = b ? 1 : 0; if ( bca->fmt_flag&(B2B_FMT_NMBZ|B2B_INFO_NMBZ|B2B_INFO_NM) ) { inm = get_aux_nm(p,p->qpos,is_diff?0:1); if ( inm>=0 ) { bca->nnm[is_diff]++; bca->nm[is_diff] += inm; } } #ifdef GLF_DEBUG fprintf(stderr, "GLF %s\t%d\t%d\n", bam_get_qname(p->b), bca->indel_types[b], q); #endif if (q < bca->min_baseQ) { if (!p->indel && b < 4) // not an indel read { if (bam_is_rev(p->b)) ADR_ref_missed[b]++; else ADF_ref_missed[b]++; } continue; } #ifndef MIN #define MIN(a,b) ((a)<(b)?(a):(b)) #endif #ifndef MAX #define MAX(a,b) ((a)>(b)?(a):(b)) #endif #if 1 // TEST 6 if (bca->edlib) { // Deeper data should rely more heavily on counts of data // than quality, as quality can be unreliable and prone to // miscalculations through BAQ, STR analysis, etc. // So we put a cap on how good seqQ can be. // // Is it simply the equivalent of increasing -F filter? // Not quite, as the latter removes many real variants upfront. // This calls them and then post-adjusts quality, potentially // dropping it later or changing genotype. So we still get // calls, but lower qual. seqQ = MIN(seqQ, bca->seqQ_offset-(MIN(20,_n)*5)); if (indel_in_sample && p->indel == 0 && b != 0) { // This read doesn't contain an indel in CIGAR, but it // is assigned to an indel now (b != 0), These are // reads we've corrected with realignment, but they're // also enriched for FPs so at high depth we reduce their // confidence and let the depth do the talking. If it's // real and deep, then we don't need every read aligning. // We also reduce base quality too to reflect the // chance of our realignment being incorrect. seqQ = MIN(seqQ, seqQ/2 + 5); // q2p5 // Finally reduce indel quality. // This is a blend of indelQ and base QUAL. q = MIN((int)bam_get_qual(p->b)[p->qpos]/4+10, q/4+1); } } #endif // Note baseQ changes some output fields such as I16, but has no // significant affect on "call". baseQ = p->aux>>8&0xff; } else { b = bam_seqi(bam_get_seq(p->b), p->qpos); // base b = seq_nt16_int[b? b : ref_base]; // b is the 2-bit base // Lowest of this and neighbour quality values uint8_t *qual = bam_get_qual(p->b); q = qual[p->qpos]; if (p->qpos > 0 && q > qual[p->qpos-1]+bca->delta_baseQ) q = qual[p->qpos-1]+bca->delta_baseQ; if (p->qpos+1 < p->b->core.l_qseq && q > qual[p->qpos+1]+bca->delta_baseQ) q = qual[p->qpos+1]+bca->delta_baseQ; if (q < bca->min_baseQ) continue; if (q > bca->max_baseQ) q = bca->max_baseQ; baseQ = q; seqQ = 99; is_diff = (ref4 < 4 && b == ref4)? 0 : 1; if ( bca->fmt_flag&(B2B_FMT_NMBZ|B2B_INFO_NMBZ|B2B_INFO_NM) ) { inm = get_aux_nm(p,p->qpos,is_diff?0:1); if ( inm>=0 ) { bca->nnm[is_diff]++; bca->nm[is_diff] += inm; } } } mapQ = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255 if ( !mapQ ) r->mq0++; #ifdef GLF_DEBUG fprintf(stderr, "GLF2 %s\t%d\t%d\t%d,%d\n", bam_get_qname(p->b), b, q, seqQ, mapQ); #endif if (q > seqQ) q = seqQ; mapQ = mapQ < bca->capQ? mapQ : bca->capQ; if (q > mapQ) q = mapQ; if (q > 63) q = 63; if (q < 4) q = 4; // MQ=0 reads count as BQ=4 bca->bases[n++] = q<<5 | (int)bam_is_rev(p->b)<<4 | b; //if (is_indel) fprintf(stderr,"xx:base,q,strand\t%d\t%d\t%d\n",b,q,bam_is_rev(p->b)?0:1); // collect annotations if (b < 4) { r->QS[b] += q; if ( r->ADF ) { if ( bam_is_rev(p->b) ) r->ADR[b]++; else r->ADF[b]++; } } ++r->anno[0<<2|is_diff<<1|bam_is_rev(p->b)]; min_dist = p->b->core.l_qseq - 1 - p->qpos; if (min_dist > p->qpos) min_dist = p->qpos; if (min_dist > CAP_DIST) min_dist = CAP_DIST; r->anno[1<<2|is_diff<<1|0] += baseQ; r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ; r->anno[2<<2|is_diff<<1|0] += mapQ; r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ; r->anno[3<<2|is_diff<<1|0] += min_dist; r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist; // collect for bias tests if ( baseQ > 59 ) baseQ = 59; if ( mapQ > 59 ) mapQ = 59; int len, epos = 0, sc_len = 0, sc_dist = 0; if ( bca->fmt_flag & (B2B_INFO_RPBZ|B2B_INFO_VDB|B2B_INFO_SCBZ) ) { int pos = get_position(p, &len, &sc_len, &sc_dist); epos = (double)pos/(len+1) * (bca->npos - 1); if (sc_len) { sc_len = 15.0*sc_len / (sc_dist+1); if (sc_len > 99) sc_len = 99; } assert( epos>=0 && eposnpos ); assert( sc_len>=0 && sc_lennpos ); } int imq = mapQ * nqual_over_60; int ibq = baseQ * nqual_over_60; if ( bam_is_rev(p->b) ) bca->rev_mqs[imq]++; else bca->fwd_mqs[imq]++; if ( !is_diff ) { bca->ref_pos[epos]++; bca->ref_bq[ibq]++; bca->ref_mq[imq]++; bca->ref_scl[sc_len]++; if ( inm>=0 ) { bca->ref_nm[inm]++; if ( r->ref_nm ) r->ref_nm[inm]++; } } else { bca->alt_pos[epos]++; bca->alt_bq[ibq]++; bca->alt_mq[imq]++; bca->alt_scl[sc_len]++; if ( inm>=0 ) { bca->alt_nm[inm]++; if ( r->alt_nm ) r->alt_nm[inm]++; } } } // Compensate for AD not being counted on low quality REF indel matches. if ( r->ADF && bca->ambig_reads==B2B_INC_AD0 ) { for (i=0; i<4; i++) { r->ADR[0] += ADR_ref_missed[i]; r->ADF[0] += ADF_ref_missed[i]; } } else if ( r->ADF && bca->ambig_reads==B2B_INC_AD ) { int dp = 0, dp_ambig = 0; for (i=0; i<4; i++) dp += r->ADR[i]; for (i=0; i<4; i++) dp_ambig += ADR_ref_missed[i]; if ( dp ) for (i=0; i<4; i++) r->ADR[i] += lroundf((float)dp_ambig * r->ADR[i]/dp); dp = 0, dp_ambig = 0; for (i=0; i<4; i++) dp += r->ADF[i]; for (i=0; i<4; i++) dp_ambig += ADF_ref_missed[i]; if ( dp ) for (i=0; i<4; i++) r->ADF[i] += lroundf((float)dp_ambig * r->ADF[i]/dp); } // Else consider downgrading bca->bases[] scores by AD vs AD_ref_missed // ratios. This is detrimental on Illumina, but beneficial on PacBio CCS. // It's possibly related to the homopolyer error likelihoods or overall // Indel accuracy. Maybe tie this in to the -h option? r->ori_depth = ori_depth; // glfgen errmod_cal(bca->e, n, 5, bca->bases, r->p); // calculate PL of each genotype // TODO: account for the number of unassigned reads. If depth is 50, // but AD is 5,7 then it may look like a variant but it probably // should be low quality. return n; } /* * calc_vdb() - returns value between zero (most biased) and one (no bias) * on success, or HUGE_VAL when VDB cannot be calculated because * of insufficient depth (<2x) * * Variant Distance Bias tests if the variant bases are positioned within the * reads with sufficient randomness. Unlike other tests, it looks only at * variant reads and therefore gives different kind of information than Read * Position Bias for instance. VDB was developed for detecting artefacts in * RNA-seq calls where reads from spliced transcripts span splice site * boundaries. The current implementation differs somewhat from the original * version described in supplementary material of PMID:22524474, but the idea * remains the same. (Here the random variable tested is the average distance * from the averaged position, not the average pairwise distance.) * * For coverage of 2x, the calculation is exact but is approximated for the * rest. The result is most accurate between 4-200x. For 3x or >200x, the * reported values are slightly more favourable than those of a true random * distribution. */ double calc_vdb(int *pos, int npos) { // Note well: the parameters were obtained by fitting to simulated data of // 100bp reads. This assumes rescaling to 100bp in bcf_call_glfgen(). const int readlen = 100; assert( npos==readlen ); #define nparam 15 const float param[nparam][3] = { {3,0.079,18}, {4,0.09,19.8}, {5,0.1,20.5}, {6,0.11,21.5}, {7,0.125,21.6}, {8,0.135,22}, {9,0.14,22.2}, {10,0.153,22.3}, {15,0.19,22.8}, {20,0.22,23.2}, {30,0.26,23.4}, {40,0.29,23.5}, {50,0.35,23.65}, {100,0.5,23.7}, {200,0.7,23.7} }; int i, dp = 0; float mean_pos = 0, mean_diff = 0; for (i=0; i=200 ) i = nparam; // shortcut for big depths else { for (i=0; i=dp ) break; } float pshift, pscale; if ( i==nparam ) { // the depth is too high, go with 200x pscale = param[nparam-1][1]; pshift = param[nparam-1][2]; } else if ( i>0 && param[i][0]!=dp ) { // linear interpolation of parameters pscale = (param[i-1][1] + param[i][1])*0.5; pshift = (param[i-1][2] + param[i][2])*0.5; } else { pscale = param[i][1]; pshift = param[i][2]; } return 0.5*kf_erfc(-(mean_diff-pshift)*pscale); } double calc_chisq_bias(int *a, int *b, int n) { int na = 0, nb = 0, i, ndf = n; for (i=0; i= 2 && m >= 2); return (n < 8 && m < 8 && U < 50) ? mw[n-2][m-2][U] : mann_whitney_1947_(n,m,U); } double mann_whitney_1947_cdf(int n, int m, int U) { int i; double sum = 0; for (i=0; i<=U; i++) sum += mann_whitney_1947(n,m,i); return sum; } double calc_mwu_bias_cdf(int *a, int *b, int n) { int na = 0, nb = 0, i; double U = 0; //double ties = 0; for (i=0; i=8 && nb>=8 and reasonable if na<8 or nb<8 if ( na>=8 || nb>=8 ) { double mean = ((double)na*nb)*0.5; // Correction for ties: // double N = na+nb; // double var2 = (N*N-1)*N-ties; // if ( var2==0 ) return 1.0; // var2 *= ((double)na*nb)/N/(N-1)/12.0; // No correction for ties: double var2 = ((double)na*nb)*(na+nb+1)/12.0; double z = (U_min - mean)/sqrt(2*var2); // z is N(0,1) return 2.0 - kf_erfc(z); // which is 1 + erf(z) } // Exact calculation double pval = 2*mann_whitney_1947_cdf(na,nb,U_min); return pval>1 ? 1 : pval; } double calc_mwu_bias(int *a, int *b, int n, int left) { int na = 0, nb = 0, i; double U = 0; // double ties = 0; for (i=0; i mean) return 1; // for MQB which is asymmetrical if ( na==2 || nb==2 ) { // Linear approximation return U>mean ? (2.0*mean-U)/mean : U/mean; } // Correction for ties: // double N = na+nb; // double var2 = (N*N-1)*N-ties; // if ( var2==0 ) return 1.0; // var2 *= ((double)na*nb)/N/(N-1)/12.0; // No correction for ties: double var2 = ((double)na*nb)*(na+nb+1)/12.0; if ( na>=8 || nb>=8 ) { // Normal approximation, very good for na>=8 && nb>=8 and reasonable if na<8 or nb<8 return exp(-0.5*(U-mean)*(U-mean)/var2); } // Exact calculation return mann_whitney_1947(na,nb,U) * sqrt(2*M_PI*var2); } // A Z-score version of the above function. // // See "Normal approximation and tie correction" at // https://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U_test // // The Z score is the number of standard deviations above or below the mean // with 0 being equality of the two distributions and +ve/-ve from there. // // This is a more robust score to filter on. double calc_mwu_biasZ(int *a, int *b, int n, int left_only, int do_Z) { int i; int64_t t; // Optimisation for (i = 0; i < n; i++) if (b[i]) break; int b_empty = (i == n); // Count equal (e), less-than (l) and greater-than (g) permutations. int e = 0, l = 0, na = 0, nb = 0; if (b_empty) { for (t = 0, i = n-1; i >= 0; i--) { na += a[i]; t += (a[i]*a[i]-1)*a[i]; // adjustment score for ties } } else { for (t = 0, i = n-1; i >= 0; i--) { // Combinations of a[i] and b[j] for i==j e += a[i]*b[i]; // nb is running total of b[i+1]..b[n-1]. // Therefore a[i]*nb is the number of combinations of a[i] and b[j] // for all i < j. l += a[i]*nb; // a= 0 ? 0.5 : -0.5)) / sd; // gatk method? return (U - m) / sqrt(var2); } // Else U score, which can be asymmetric for some data types. if (left_only && U > m) return HUGE_VAL; // one-sided, +ve bias is OK, -ve is not. if (na >= 8 || nb >= 8) { // Normal approximation, very good for na>=8 && nb>=8 and // reasonable if na<8 or nb<8 return exp(-0.5*(U-m)*(U-m)/var2); } // Exact calculation if (na==1 || nb == 1) return mann_whitney_1947_(na, nb, U) * sqrt(2*M_PI*var2); else return mann_whitney_1947(na, nb, U) * sqrt(2*M_PI*var2); } static inline double logsumexp2(double a, double b) { if ( a>b ) return log(1 + exp(b-a)) + a; else return log(1 + exp(a-b)) + b; } void calc_SegBias(const bcf_callret1_t *bcr, bcf_call_t *call) { call->seg_bias = HUGE_VAL; if ( !bcr ) return; int nr = call->anno[2] + call->anno[3]; // number of observed non-reference reads if ( !nr ) return; int avg_dp = (call->anno[0] + call->anno[1] + nr) / call->n; // average depth double M = floor((double)nr / avg_dp + 0.5); // an approximate number of variants samples in the population if ( M>call->n ) M = call->n; // clamp M at the number of samples else if ( M==0 ) M = 1; double f = M / 2. / call->n; // allele frequency double p = (double) nr / call->n; // number of variant reads per sample expected if variant not real (poisson) double q = (double) nr / M; // number of variant reads per sample expected if variant is real (poisson) double sum = 0; const double log2 = log(2.0); // fprintf(stderr,"M=%.1f p=%e q=%e f=%f dp=%d\n",M,p,q,f,avg_dp); int i; for (i=0; in; i++) { int oi = bcr[i].anno[2] + bcr[i].anno[3]; // observed number of non-ref reads double tmp; if ( oi ) { // tmp = log(f) + oi*log(q/p) - q + log(2*(1-f) + f*pow(2,oi)*exp(-q)) + p; // this can under/overflow tmp = logsumexp2(log(2*(1-f)), log(f) + oi*log2 - q); tmp += log(f) + oi*log(q/p) - q + p; } else tmp = log(2*f*(1-f)*exp(-q) + f*f*exp(-2*q) + (1-f)*(1-f)) + p; sum += tmp; // fprintf(stderr,"oi=%d %e\n", oi,tmp); } call->seg_bias = sum; } /** * bcf_call_combine() - sets the PL array and VDB, RPB annotations, finds the top two alleles * @n: number of samples * @calls: each sample's calls * @bca: auxiliary data structure for holding temporary values * @ref_base: the reference base * @call: filled with the annotations * * Combines calls across the various samples being studied * 1. For each allele at each base across all samples the quality is summed so * you end up with a set of quality sums for each allele present 2. The quality * sums are sorted. * 3. Using the sorted quality sums we now create the allele ordering array * A\subN. This is done by doing the following: * a) If the reference allele is known it always comes first, otherwise N * comes first. * b) Then the rest of the alleles are output in descending order of quality * sum (which we already know the qsum array was sorted). Any allelles with * qsum 0 will be excluded. * 4. Using the allele ordering array we create the genotype ordering array. * In the worst case with an unknown reference this will be: A0/A0 A1/A0 A1/A1 * A2/A0 A2/A1 A2/A2 A3/A0 A3/A1 A3/A2 A3/A3 A4/A0 A4/A1 A4/A2 A4/A3 A4/A4 * 5. The genotype ordering array is then used to extract data from the error * model 5*5 matrix and is used to produce a Phread likelihood array for each * sample. */ int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call) { int ref4, i, j; float qsum[B2B_MAX_ALLELES] = {0,0,0,0,0}; if (ref_base >= 0) { call->ori_ref = ref4 = seq_nt16_int[ref_base]; if (ref4 > 4) ref4 = 4; } else call->ori_ref = -1, ref4 = 0; // calculate qsum, this is done by summing normalized qsum across all samples, // to account for differences in coverage for (i = 0; i < n; ++i) { float sum = 0; for (j = 0; j < 4; ++j) sum += calls[i].QS[j]; if ( sum ) for (j = 0; j < 4; j++) qsum[j] += (float)calls[i].QS[j] / sum; } // sort qsum in ascending order (insertion sort) float *ptr[5], *tmp; for (i=0; i<5; i++) ptr[i] = &qsum[i]; for (i=1; i<4; i++) for (j=i; j>0 && *ptr[j] < *ptr[j-1]; j--) tmp = ptr[j], ptr[j] = ptr[j-1], ptr[j-1] = tmp; // Set the reference allele and alternative allele(s) for (i=0; i<5; i++) call->a[i] = -1; for (i=0; iqsum[i] = 0; call->unseen = -1; call->a[0] = ref4; for (i=3, j=1; i>=0; i--) // i: alleles sorted by QS; j, a[j]: output allele ordering { int ipos = ptr[i] - qsum; // position in sorted qsum array if ( ipos==ref4 ) call->qsum[0] = qsum[ipos]; // REF's qsum else { if ( !qsum[ipos] ) break; // qsum is 0, this and consequent alleles are not seen in the pileup call->qsum[j] = qsum[ipos]; call->a[j++] = ipos; } } if (ref_base >= 0) { // for SNPs, find the "unseen" base if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0) call->unseen = j, call->a[j++] = ptr[i] - qsum; call->n_alleles = j; } else { call->n_alleles = j; if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything } int has_alt = (call->n_alleles==2 && call->unseen!=-1) ? 0 : 1; /* * Set the phread likelihood array (call->PL) This array is 15 entries long * for each sample because that is size of an upper or lower triangle of a * worst case 5x5 matrix of possible genotypes. This worst case matrix will * occur when all 4 possible alleles are present and the reference allele * is unknown. The sides of the matrix will correspond to the reference * allele (if known) followed by the alleles present in descending order of * quality sum */ { int x, g[15], z; double sum_min = 0.; x = call->n_alleles * (call->n_alleles + 1) / 2; // get the possible genotypes // this is done by creating an ordered list of locations g for call (allele a, allele b) in the genotype likelihood matrix for (i = z = 0; i < call->n_alleles; ++i) { for (j = 0; j <= i; ++j) { g[z++] = call->a[j] * 5 + call->a[i]; } } // for each sample calculate the PL for (i = 0; i < n; ++i) { int32_t *PL = call->PL + x * i; const bcf_callret1_t *r = calls + i; float min = FLT_MAX; for (j = 0; j < x; ++j) { if (min > r->p[g[j]]) min = r->p[g[j]]; } sum_min += min; for (j = 0; j < x; ++j) { int y; y = (int)(r->p[g[j]] - min + .499); if (y > 255) y = 255; PL[j] = y; } } if ( call->DP4 ) { for (i=0; iDP4[4*i] = calls[i].anno[0]; call->DP4[4*i+1] = calls[i].anno[1]; call->DP4[4*i+2] = calls[i].anno[2]; call->DP4[4*i+3] = calls[i].anno[3]; } } if ( call->SCR ) { for (i=0; iSCR[0] += calls[i].SCR; call->SCR[1+i] = calls[i].SCR; } } if ( call->ADF ) { assert( call->n_alleles<=B2B_MAX_ALLELES ); // this is always true for SNPs and so far for indels as well // reorder ADR,ADF to match the allele ordering at this site int32_t tmp[B2B_MAX_ALLELES]; int32_t *adr = call->ADR + B2B_MAX_ALLELES, *adr_out = call->ADR + B2B_MAX_ALLELES; int32_t *adf = call->ADF + B2B_MAX_ALLELES, *adf_out = call->ADF + B2B_MAX_ALLELES; int32_t *adr_tot = call->ADR; // the first bin stores total counts per site int32_t *adf_tot = call->ADF; for (i=0; in_alleles; j++) { tmp[j] = adr[ call->a[j] ]; adr_tot[j] += tmp[j]; } for (j=0; jn_alleles; j++) adr_out[j] = tmp[j]; for (j=0; jn_alleles; j++) { tmp[j] = adf[ call->a[j] ]; adf_tot[j] += tmp[j]; } for (j=0; jn_alleles; j++) adf_out[j] = tmp[j]; adf_out += call->n_alleles; adr_out += call->n_alleles; adr += B2B_MAX_ALLELES; adf += B2B_MAX_ALLELES; } } if ( bca->fmt_flag & B2B_FMT_QS ) { assert( call->n_alleles<=B2B_MAX_ALLELES ); // this is always true for SNPs and so far for indels as well // reorder QS to match the allele ordering at this site int32_t tmp[B2B_MAX_ALLELES]; int32_t *qs = call->QS, *qs_out = call->QS; for (i=0; in_alleles; j++) tmp[j] = qs[ call->a[j] ]; for (j=0; jn_alleles; j++) qs_out[j] = tmp[j] < BCF_MAX_BT_INT32 ? tmp[j] : BCF_MAX_BT_INT32; qs_out += call->n_alleles; qs += B2B_MAX_ALLELES; } } // if (ref_base < 0) fprintf(stderr, "%d,%d,%f,%d\n", call->n_alleles, x, sum_min, call->unseen); // fprintf(stderr,"sum_min=%f\n",sum_min); call->shift = (int)(sum_min + .499); } // combine annotations memset(call->anno, 0, 16 * sizeof(double)); call->ori_depth = 0; call->depth = 0; call->mq0 = 0; for (i = 0; i < n; ++i) { call->depth += calls[i].anno[0] + calls[i].anno[1] + calls[i].anno[2] + calls[i].anno[3]; call->ori_depth += calls[i].ori_depth; call->mq0 += calls[i].mq0; for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j]; } // No need to calculate MWU tests when there is no ALT allele, this should speed up things slightly if ( !has_alt ) return 0; if ( bca->fmt_flag & B2B_INFO_FS ) { double left,right,two; call->strand_bias = kt_fisher_exact(call->anno[0], call->anno[1], call->anno[2], call->anno[3], &left, &right, &two); } if ( bca->fmt_flag & B2B_INFO_SGB ) calc_SegBias(calls, call); // calc_chisq_bias("XPOS", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_pos, bca->alt_pos, bca->npos); // calc_chisq_bias("XMQ", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_mq, bca->alt_mq, bca->nqual); // calc_chisq_bias("XBQ", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_bq, bca->alt_bq, bca->nqual); // U z-normalised as +/- number of standard deviations from mean. if (call->ori_ref < 0) { // indel if ( bca->fmt_flag & B2B_INFO_RPBZ ) call->mwu_pos = calc_mwu_biasZ(bca->iref_pos, bca->ialt_pos, bca->npos, 0, 1); if ( bca->fmt_flag & B2B_INFO_MQBZ ) call->mwu_mq = calc_mwu_biasZ(bca->iref_mq, bca->ialt_mq, bca->nqual,1,1); if ( bca->fmt_flag & B2B_INFO_SCBZ ) call->mwu_sc = calc_mwu_biasZ(bca->iref_scl, bca->ialt_scl, 100, 0,1); } else { if ( bca->fmt_flag & B2B_INFO_RPBZ ) call->mwu_pos = calc_mwu_biasZ(bca->ref_pos, bca->alt_pos, bca->npos, 0, 1); if ( bca->fmt_flag & B2B_INFO_MQBZ ) call->mwu_mq = calc_mwu_biasZ(bca->ref_mq, bca->alt_mq, bca->nqual,1,1); if ( bca->fmt_flag & B2B_INFO_BQBZ ) call->mwu_bq = calc_mwu_biasZ(bca->ref_bq, bca->alt_bq, bca->nqual,0,1); if ( bca->fmt_flag & B2B_INFO_MQSBZ ) call->mwu_mqs = calc_mwu_biasZ(bca->fwd_mqs, bca->rev_mqs, bca->nqual,0,1); if ( bca->fmt_flag & B2B_INFO_SCBZ ) call->mwu_sc = calc_mwu_biasZ(bca->ref_scl, bca->alt_scl, 100, 0,1); } if ( bca->fmt_flag & B2B_INFO_NMBZ ) call->mwu_nm[0] = calc_mwu_biasZ(bca->ref_nm, bca->alt_nm, B2B_N_NM,0,1); if ( bca->fmt_flag & B2B_FMT_NMBZ ) { for (i=0; imwu_nm[i+1] = val!=HUGE_VAL ? val : 0; } } if ( bca->fmt_flag & B2B_INFO_VDB ) call->vdb = calc_vdb(bca->alt_pos, bca->npos); return 0; } int bcf_call2bcf(bcf_call_t *bc, bcf1_t *rec, bcf_callret1_t *bcr, int fmt_flag, const bcf_callaux_t *bca, const char *ref) { extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two); int i, j, nals = 1, has_alt = 0; bcf_hdr_t *hdr = bc->bcf_hdr; rec->rid = bc->tid; rec->pos = bc->pos; rec->qual = 0; bc->tmp.l = 0; if (bc->ori_ref < 0) // indel { // REF kputc(ref[bc->pos], &bc->tmp); for (j = 0; j < bca->indelreg; ++j) kputc(ref[bc->pos+1+j], &bc->tmp); // ALT for (i=1; i<4; i++) { if (bc->a[i] < 0) break; kputc(',', &bc->tmp); kputc(ref[bc->pos], &bc->tmp); if (bca->indel_types[bc->a[i]] < 0) { // deletion for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j) kputc(ref[bc->pos+1+j], &bc->tmp); } else { // insertion; cannot be a reference unless a bug char *inscns = &bca->inscns[bc->a[i] * bca->maxins]; for (j = 0; j < bca->indel_types[bc->a[i]]; ++j) kputc("ACGTN"[(int)inscns[j]], &bc->tmp); for (j = 0; j < bca->indelreg; ++j) kputc(ref[bc->pos+1+j], &bc->tmp); } nals++; has_alt = 1; } } else // SNP { kputc("ACGTN"[bc->ori_ref], &bc->tmp); for (i=1; i<5; i++) { if (bc->a[i] < 0) break; kputc(',', &bc->tmp); if ( bc->unseen==i ) kputs("<*>", &bc->tmp); else { kputc("ACGT"[bc->a[i]], &bc->tmp); has_alt = 1; } nals++; } } bcf_update_alleles_str(hdr, rec, bc->tmp.s); bc->tmp.l = 0; // INFO if ( bc->ori_ref < 0 ) { bcf_update_info_flag(hdr, rec, "INDEL", NULL, 1); uint32_t idv = bca->max_support; if ( fmt_flag&B2B_INFO_IMF) { float max_frac; // Recompute IDV and IMF based on alignment results for more // accurate counts, but only when in new "--indels-cns" mode. if (bc->ADF && bc->ADR && bca->edlib) { int max_ad = 0; for (int k = 1; k < rec->n_allele; k++) { if (max_ad < bc->ADF[k] + bc->ADR[k]) max_ad = bc->ADF[k] + bc->ADR[k]; } max_frac = (double)(max_ad) / bc->ori_depth; idv = max_ad; } else { max_frac = bca->max_frac; } // Copied here to maintain order for consistency of "make check" if ( fmt_flag&B2B_INFO_IDV ) bcf_update_info_int32(hdr, rec, "IDV", &idv, 1); bcf_update_info_float(hdr, rec, "IMF", &max_frac, 1); } else { if ( fmt_flag&B2B_INFO_IDV ) bcf_update_info_int32(hdr, rec, "IDV", &idv, 1); } } bcf_update_info_int32(hdr, rec, "DP", &bc->ori_depth, 1); if ( fmt_flag&B2B_INFO_ADF ) bcf_update_info_int32(hdr, rec, "ADF", bc->ADF, rec->n_allele); if ( fmt_flag&B2B_INFO_ADR ) bcf_update_info_int32(hdr, rec, "ADR", bc->ADR, rec->n_allele); if ( fmt_flag&(B2B_INFO_AD|B2B_INFO_DPR) ) { for (i=0; in_allele; i++) bc->ADF[i] += bc->ADR[i]; if ( fmt_flag&B2B_INFO_AD ) bcf_update_info_int32(hdr, rec, "AD", bc->ADF, rec->n_allele); if ( fmt_flag&B2B_INFO_DPR ) bcf_update_info_int32(hdr, rec, "DPR", bc->ADF, rec->n_allele); } if ( fmt_flag&B2B_INFO_SCR ) bcf_update_info_int32(hdr, rec, "SCR", bc->SCR, 1); float tmpf[16]; for (i=0; i<16; i++) tmpf[i] = bc->anno[i]; bcf_update_info_float(hdr, rec, "I16", tmpf, 16); bcf_update_info_float(hdr, rec, "QS", bc->qsum, nals); if ( has_alt ) { if ( fmt_flag&B2B_INFO_MIN_PL_SUM ) bcf_update_info_int32(hdr, rec, "MIN_PL_SUM", &bc->shift, 1); if ( fmt_flag&B2B_INFO_VDB && bc->vdb != HUGE_VAL ) bcf_update_info_float(hdr, rec, "VDB", &bc->vdb, 1); if ( fmt_flag&B2B_INFO_SGB && bc->seg_bias != HUGE_VAL ) bcf_update_info_float(hdr, rec, "SGB", &bc->seg_bias, 1); if ( fmt_flag&B2B_INFO_NM && (bca->nnm[0] || bca->nnm[1]) ) { for (i=0; i<2; i++) bc->nm[i] = bca->nnm[i] ? bca->nm[i]/bca->nnm[i] : 0; bcf_update_info_float(hdr, rec, "NM", bc->nm, 2); } if ( fmt_flag&B2B_INFO_RPBZ && bc->mwu_pos != HUGE_VAL ) bcf_update_info_float(hdr, rec, "RPBZ", &bc->mwu_pos, 1); if ( fmt_flag&B2B_INFO_MQBZ && bc->mwu_mq != HUGE_VAL ) bcf_update_info_float(hdr, rec, "MQBZ", &bc->mwu_mq, 1); if ( fmt_flag&B2B_INFO_MQSBZ && bc->mwu_mqs != HUGE_VAL ) bcf_update_info_float(hdr, rec, "MQSBZ", &bc->mwu_mqs, 1); if ( fmt_flag&B2B_INFO_BQBZ && bc->mwu_bq != HUGE_VAL ) bcf_update_info_float(hdr, rec, "BQBZ", &bc->mwu_bq, 1); if ( fmt_flag&B2B_INFO_NMBZ && bc->mwu_nm[0] != HUGE_VAL ) bcf_update_info_float(hdr, rec, "NMBZ", bc->mwu_nm, 1); if ( fmt_flag&B2B_INFO_SCBZ && bc->mwu_sc != HUGE_VAL ) bcf_update_info_float(hdr, rec, "SCBZ", &bc->mwu_sc, 1); if ( fmt_flag&B2B_INFO_FS && bc->strand_bias != HUGE_VAL ) bcf_update_info_float(hdr, rec, "FS", &bc->strand_bias, 1); } tmpf[0] = bc->ori_depth ? (float)bc->mq0/bc->ori_depth : 0; if ( fmt_flag&B2B_INFO_MQ0F ) bcf_update_info_float(hdr, rec, "MQ0F", tmpf, 1); // FORMAT rec->n_sample = bc->n; bcf_update_format_int32(hdr, rec, "PL", bc->PL, nals*(nals+1)/2 * rec->n_sample); if ( fmt_flag&B2B_FMT_DP ) { int32_t *ptr = (int32_t*) bc->fmt_arr; for (i=0; in; i++) ptr[i] = bc->DP4[4*i] + bc->DP4[4*i+1] + bc->DP4[4*i+2] + bc->DP4[4*i+3]; bcf_update_format_int32(hdr, rec, "DP", bc->fmt_arr, rec->n_sample); } if ( fmt_flag&B2B_FMT_DV ) { int32_t *ptr = (int32_t*) bc->fmt_arr; for (i=0; in; i++) ptr[i] = bc->DP4[4*i+2] + bc->DP4[4*i+3]; bcf_update_format_int32(hdr, rec, "DV", bc->fmt_arr, rec->n_sample); } if ( fmt_flag&B2B_FMT_SP ) { int32_t *ptr = (int32_t*) bc->fmt_arr; for (i=0; in; i++) { int fwd_ref = bc->DP4[4*i], rev_ref = bc->DP4[4*i+1], fwd_alt = bc->DP4[4*i+2], rev_alt = bc->DP4[4*i+3]; if ( fwd_ref+rev_ref<2 || fwd_alt+rev_alt<2 || fwd_ref+fwd_alt<2 || rev_ref+rev_alt<2 ) ptr[i] = 0; else { double left, right, two; kt_fisher_exact(fwd_ref, rev_ref, fwd_alt, rev_alt, &left, &right, &two); int32_t x = (int)(-4.343 * log(two) + .499); if (x > 255) x = 255; ptr[i] = x; } } bcf_update_format_int32(hdr, rec, "SP", bc->fmt_arr, rec->n_sample); } if ( fmt_flag&B2B_FMT_DP4 ) bcf_update_format_int32(hdr, rec, "DP4", bc->DP4, rec->n_sample*4); if ( fmt_flag&B2B_FMT_ADF ) bcf_update_format_int32(hdr, rec, "ADF", bc->ADF+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele); if ( fmt_flag&B2B_FMT_ADR ) bcf_update_format_int32(hdr, rec, "ADR", bc->ADR+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele); if ( fmt_flag&(B2B_FMT_AD|B2B_FMT_DPR) ) { for (i=0; in_sample*rec->n_allele; i++) bc->ADF[B2B_MAX_ALLELES+i] += bc->ADR[B2B_MAX_ALLELES+i]; if ( fmt_flag&B2B_FMT_AD ) bcf_update_format_int32(hdr, rec, "AD", bc->ADF+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele); if ( fmt_flag&B2B_FMT_DPR ) bcf_update_format_int32(hdr, rec, "DPR", bc->ADF+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele); } if ( fmt_flag&B2B_FMT_SCR ) bcf_update_format_int32(hdr, rec, "SCR", bc->SCR+1, rec->n_sample); if ( fmt_flag&B2B_FMT_QS ) bcf_update_format_int32(hdr, rec, "QS", bc->QS, rec->n_sample*rec->n_allele); if ( has_alt ) { if ( fmt_flag&B2B_FMT_NMBZ ) bcf_update_format_float(hdr, rec, "NMBZ", bc->mwu_nm+1, rec->n_sample); } return 0; } pysam-0.23.0/bcftools/bam2bcf.c.pysam.c000066400000000000000000001446261475062545500176030ustar00rootroot00000000000000#include "bcftools.pysam.h" /* bam2bcf.c -- variant calling. Copyright (C) 2010-2012 Broad Institute. Copyright (C) 2012-2024 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include "bam2bcf.h" extern void ks_introsort_uint32_t(size_t n, uint32_t a[]); #define CALL_DEFTHETA 0.83 #define DEF_MAPQ 20 #define CAP_DIST 25 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ, int max_baseQ, int delta_baseQ) { bcf_callaux_t *bca; if (theta <= 0.) theta = CALL_DEFTHETA; bca = (bcf_callaux_t*) calloc(1, sizeof(bcf_callaux_t)); bca->capQ = 60; bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100; bca->min_baseQ = min_baseQ; bca->max_baseQ = max_baseQ; bca->delta_baseQ = delta_baseQ; bca->e = errmod_init(1. - theta); bca->min_frac = 0.002; bca->min_support = 1; bca->per_sample_flt = 0; bca->npos = 100; bca->ref_pos = (int*) malloc(bca->npos*sizeof(int)); bca->alt_pos = (int*) malloc(bca->npos*sizeof(int)); bca->iref_pos= (int*) malloc(bca->npos*sizeof(int)); bca->ialt_pos= (int*) malloc(bca->npos*sizeof(int)); bca->nqual = 60; bca->ref_mq = (int*) malloc(bca->nqual*sizeof(int)); bca->alt_mq = (int*) malloc(bca->nqual*sizeof(int)); bca->iref_mq = (int*) malloc(bca->nqual*sizeof(int)); bca->ialt_mq = (int*) malloc(bca->nqual*sizeof(int)); bca->ref_bq = (int*) malloc(bca->nqual*sizeof(int)); bca->alt_bq = (int*) malloc(bca->nqual*sizeof(int)); bca->fwd_mqs = (int*) malloc(bca->nqual*sizeof(int)); bca->rev_mqs = (int*) malloc(bca->nqual*sizeof(int)); return bca; } void bcf_iaux_destroy(bcf_callaux_t *bca); void bcf_call_destroy(bcf_callaux_t *bca) { if (bca == 0) return; bcf_iaux_destroy(bca); errmod_destroy(bca->e); if (bca->npos) { free(bca->ref_pos); free(bca->alt_pos); free(bca->iref_pos); free(bca->ialt_pos); bca->npos = 0; } free(bca->ref_mq); free(bca->alt_mq); free(bca->iref_mq); free(bca->ialt_mq); free(bca->ref_bq); free(bca->alt_bq); free(bca->fwd_mqs); free(bca->rev_mqs); bca->nqual = 0; free(bca->bases); free(bca->inscns); free(bca); } static int get_aux_nm(const bam_pileup1_t *p, int32_t qpos, int is_ref) { int64_t nm; const bam_pileup_cd *cd = &p->cd; if ( PLP_NM(cd) == -1 ) return -1; if ( PLP_NM(cd) == PLP_NM_UNSET ) { // todo: make this localized to be useful for long reads as well bam1_t *rec = p->b; uint8_t *nm_tag = bam_aux_get(rec, "NM"); if ( !nm_tag ) { PLP_NM(cd) = -1; return -1; } nm = bam_aux2i(nm_tag); // Count indels as single events, not as the number of inserted/deleted // bases (which is what NM does). Add soft clips as mismatches. int i; for (i=0; i < rec->core.n_cigar; i++) { int val = bam_get_cigar(rec)[i] & BAM_CIGAR_MASK; if ( val==BAM_CSOFT_CLIP ) { nm += bam_get_cigar(rec)[i] >> BAM_CIGAR_SHIFT; } else if ( val==BAM_CINS || val==BAM_CDEL ) { val = bam_get_cigar(rec)[i] >> BAM_CIGAR_SHIFT; if ( val > 1 ) nm -= val - 1; } } PLP_NM(cd) = nm; } else nm = PLP_NM(cd); // Take into account MNPs, 2% of de novo SNVs appear within 20bp of another de novo SNV // http://www.genome.org/cgi/doi/10.1101/gr.239756.118 nm -= is_ref ? 1 : 2; if ( nm < 0 ) nm = 0; if ( nm >= B2B_N_NM ) nm = B2B_N_NM - 1; return nm; } // position in the sequence with respect to the aligned part of the read static int get_position(const bam_pileup1_t *p, int *len, int *sc_len, int *sc_dist) { int i, j, edist = p->qpos + 1; int sc_left = 0, sc_right = 0; int sc_left_dist = -1, sc_right_dist = -1; // left end for (i = 0; i < p->b->core.n_cigar; i++) { int cig = bam_get_cigar(p->b)[i] & BAM_CIGAR_MASK; if (cig == BAM_CHARD_CLIP) continue; else if (cig == BAM_CSOFT_CLIP) sc_left += bam_get_cigar(p->b)[i] >> BAM_CIGAR_SHIFT; else break; } if (sc_left) sc_left_dist = p->qpos+1 - sc_left; edist -= sc_left; // right end for (j = p->b->core.n_cigar-1; j >= i; j--) { int cig = bam_get_cigar(p->b)[j] & BAM_CIGAR_MASK; if (cig == BAM_CHARD_CLIP) continue; else if (cig == BAM_CSOFT_CLIP) sc_right += bam_get_cigar(p->b)[j] >> BAM_CIGAR_SHIFT; else break; } if (sc_right) sc_right_dist = p->b->core.l_qseq - sc_right - p->qpos; // Distance to nearest soft-clips and length of that clip. if (sc_left_dist >= 0) { if (sc_right_dist < 0 || sc_left_dist < sc_right_dist) { *sc_len = sc_left; *sc_dist = sc_left_dist; } } else if (sc_right_dist >= 0) { *sc_len = sc_right; *sc_dist = sc_right_dist; } else { *sc_len = 0; *sc_dist = 0; } *len = p->b->core.l_qseq - sc_left - sc_right; return edist; } void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call) { memset(bca->ref_pos,0,sizeof(int)*bca->npos); memset(bca->alt_pos,0,sizeof(int)*bca->npos); memset(bca->iref_pos,0,sizeof(int)*bca->npos); memset(bca->ialt_pos,0,sizeof(int)*bca->npos); memset(bca->ref_mq,0,sizeof(int)*bca->nqual); memset(bca->alt_mq,0,sizeof(int)*bca->nqual); memset(bca->iref_mq,0,sizeof(int)*bca->nqual); memset(bca->ialt_mq,0,sizeof(int)*bca->nqual); memset(bca->ref_bq,0,sizeof(int)*bca->nqual); memset(bca->alt_bq,0,sizeof(int)*bca->nqual); memset(bca->fwd_mqs,0,sizeof(int)*bca->nqual); memset(bca->rev_mqs,0,sizeof(int)*bca->nqual); if ( call->ADF ) memset(call->ADF,0,sizeof(int32_t)*(call->n+1)*B2B_MAX_ALLELES); if ( call->ADR ) memset(call->ADR,0,sizeof(int32_t)*(call->n+1)*B2B_MAX_ALLELES); if ( call->SCR ) memset(call->SCR,0,sizeof(*call->SCR)*(call->n+1)); if ( call->SCR ) memset(call->SCR,0,sizeof(*call->SCR)*(call->n+1)); if ( bca->fmt_flag&B2B_FMT_NMBZ ) { memset(call->ref_nm,0,sizeof(*call->ref_nm)*(call->n+1)*B2B_N_NM); memset(call->alt_nm,0,sizeof(*call->alt_nm)*(call->n+1)*B2B_N_NM); } else { memset(call->ref_nm,0,sizeof(*call->ref_nm)*B2B_N_NM); memset(call->alt_nm,0,sizeof(*call->alt_nm)*B2B_N_NM); } memset(call->QS,0,sizeof(*call->QS)*call->n*B2B_MAX_ALLELES); memset(bca->ref_scl, 0, 100*sizeof(int)); memset(bca->alt_scl, 0, 100*sizeof(int)); memset(bca->iref_scl, 0, 100*sizeof(int)); memset(bca->ialt_scl, 0, 100*sizeof(int)); int i; for (i=0; i<2; i++) bca->nnm[i] = 0; for (i=0; i<2; i++) bca->nm[i] = 0; } /* Notes: - Called from bam_plcmd.c by mpileup. Amongst other things, sets the bcf_callret1_t.QS frequencies which are carried over via bcf_call_combine and bcf_call2bcf to the output BCF as the INFO/QS and FMT/QS annotations. Later it's used for multiallelic calling by `call -m`, `call -mG` and `+trio-dnm`. - ref_base is the 4-bit representation of the reference base. It is negative if we are looking at an indel. */ /* * This function is called once for each sample. * _n is number of pilesups pl contributing reads to this sample * pl is pointer to array of _n pileups (one pileup per read) * ref_base is the 4-bit representation of the reference base. It is negative if we are looking at an indel. * bca is the settings to perform calls across all samples * r is the returned value of the call */ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r) { int i, n, ref4, is_indel, ori_depth = 0; #ifdef GLF_DEBUG fprintf(bcftools_stderr, "Call GLFGEN\n"); #endif // clean from previous run r->ori_depth = 0; r->mq0 = 0; memset(r->anno,0,sizeof(double)*16); memset(r->p,0,sizeof(float)*25); r->SCR = 0; if (ref_base >= 0) { ref4 = seq_nt16_int[ref_base]; is_indel = 0; } else ref4 = 4, is_indel = 1; if (_n == 0) return -1; // enlarge the bases array if necessary if (bca->max_bases < _n) { bca->max_bases = _n; kroundup32(bca->max_bases); bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases); } // Detect if indel occurs anywhere in this sample int indel_in_sample = 0; if (bca->edlib) { for (i = n = 0; i < _n; ++i) { const bam_pileup1_t *p = pl + i; if (p->indel) indel_in_sample = 1; } } // fill the bases array double nqual_over_60 = bca->nqual / 60.0; int ADR_ref_missed[4] = {0}; int ADF_ref_missed[4] = {0}; for (i = n = 0; i < _n; ++i) { const bam_pileup1_t *p = pl + i; int b; // the base or indel type int q; // the base or indel quality used to calculate PL int seqQ; // used to cap the indel quality given the sequence context int mapQ; // to cap the quality for low MQ reads int baseQ; // used only for supporting INFO annotations int is_diff; // is this base or indel type different from the reference int min_dist; // distance from the end, used for tail distance bias if ( bca->fmt_flag&(B2B_INFO_SCR|B2B_FMT_SCR) && PLP_HAS_SOFT_CLIP(&p->cd) ) r->SCR++; if (p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue; // The meaning of the indel related variables: // is_indel .. is this position currently tested for an indel // p->is_del .. is the current base a deletion in this read (unrelated to the tested indel) // p->indel .. is there an indel starting after this position (i.e. does this read have the tested indel) if (p->is_del && !is_indel) continue; // not testing an indel and the read has a spanning deletion int inm = -1; ++ori_depth; if (is_indel) // testing an indel position { b = p->aux>>16&0x3f; // indel type seqQ = q = (p->aux & 0xff); // mp2 + builtin indel-bias if (bca->edlib) { if (indel_in_sample) { seqQ = q = (p->aux & 0xff); // mp2 + builtin indel-bias } else if (p->aux & 0xff) { // An indel in another sample, but not this. So just use // basic sequence confidences. q = bam_get_qual(p->b)[p->qpos]; if (q > bca->max_baseQ) q = bca->max_baseQ; seqQ = 99; } } if ( !bca->indels_v20 && !bca->edlib ) { /* This heuristics was introduced by e4e161068 and claims to fix #1446. However, we obtain correct result on the provided test case even when this code is commented out, so this may not be needed anymore. Leaving it in only for backward compatibility for now. See mpileup-tests homdel-issue-1446 and CHM1_CHM13_2.45x-1-1701408 which work only when this code is disabled. */ if (p->indel == 0 && (q < _n/2 || _n > 20)) { // high quality indel calls without p->indel set aren't // particularly indicative of being a good REF match either, // at least not in low coverage. So require solid coverage // before we start utilising such quals. b = 0; q = (int)bam_get_qual(p->b)[p->qpos]; seqQ = (3*seqQ + 2*q)/8; } if (_n > 20 && seqQ > 40) seqQ = 40; } is_diff = b ? 1 : 0; if ( bca->fmt_flag&(B2B_FMT_NMBZ|B2B_INFO_NMBZ|B2B_INFO_NM) ) { inm = get_aux_nm(p,p->qpos,is_diff?0:1); if ( inm>=0 ) { bca->nnm[is_diff]++; bca->nm[is_diff] += inm; } } #ifdef GLF_DEBUG fprintf(bcftools_stderr, "GLF %s\t%d\t%d\n", bam_get_qname(p->b), bca->indel_types[b], q); #endif if (q < bca->min_baseQ) { if (!p->indel && b < 4) // not an indel read { if (bam_is_rev(p->b)) ADR_ref_missed[b]++; else ADF_ref_missed[b]++; } continue; } #ifndef MIN #define MIN(a,b) ((a)<(b)?(a):(b)) #endif #ifndef MAX #define MAX(a,b) ((a)>(b)?(a):(b)) #endif #if 1 // TEST 6 if (bca->edlib) { // Deeper data should rely more heavily on counts of data // than quality, as quality can be unreliable and prone to // miscalculations through BAQ, STR analysis, etc. // So we put a cap on how good seqQ can be. // // Is it simply the equivalent of increasing -F filter? // Not quite, as the latter removes many real variants upfront. // This calls them and then post-adjusts quality, potentially // dropping it later or changing genotype. So we still get // calls, but lower qual. seqQ = MIN(seqQ, bca->seqQ_offset-(MIN(20,_n)*5)); if (indel_in_sample && p->indel == 0 && b != 0) { // This read doesn't contain an indel in CIGAR, but it // is assigned to an indel now (b != 0), These are // reads we've corrected with realignment, but they're // also enriched for FPs so at high depth we reduce their // confidence and let the depth do the talking. If it's // real and deep, then we don't need every read aligning. // We also reduce base quality too to reflect the // chance of our realignment being incorrect. seqQ = MIN(seqQ, seqQ/2 + 5); // q2p5 // Finally reduce indel quality. // This is a blend of indelQ and base QUAL. q = MIN((int)bam_get_qual(p->b)[p->qpos]/4+10, q/4+1); } } #endif // Note baseQ changes some output fields such as I16, but has no // significant affect on "call". baseQ = p->aux>>8&0xff; } else { b = bam_seqi(bam_get_seq(p->b), p->qpos); // base b = seq_nt16_int[b? b : ref_base]; // b is the 2-bit base // Lowest of this and neighbour quality values uint8_t *qual = bam_get_qual(p->b); q = qual[p->qpos]; if (p->qpos > 0 && q > qual[p->qpos-1]+bca->delta_baseQ) q = qual[p->qpos-1]+bca->delta_baseQ; if (p->qpos+1 < p->b->core.l_qseq && q > qual[p->qpos+1]+bca->delta_baseQ) q = qual[p->qpos+1]+bca->delta_baseQ; if (q < bca->min_baseQ) continue; if (q > bca->max_baseQ) q = bca->max_baseQ; baseQ = q; seqQ = 99; is_diff = (ref4 < 4 && b == ref4)? 0 : 1; if ( bca->fmt_flag&(B2B_FMT_NMBZ|B2B_INFO_NMBZ|B2B_INFO_NM) ) { inm = get_aux_nm(p,p->qpos,is_diff?0:1); if ( inm>=0 ) { bca->nnm[is_diff]++; bca->nm[is_diff] += inm; } } } mapQ = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255 if ( !mapQ ) r->mq0++; #ifdef GLF_DEBUG fprintf(bcftools_stderr, "GLF2 %s\t%d\t%d\t%d,%d\n", bam_get_qname(p->b), b, q, seqQ, mapQ); #endif if (q > seqQ) q = seqQ; mapQ = mapQ < bca->capQ? mapQ : bca->capQ; if (q > mapQ) q = mapQ; if (q > 63) q = 63; if (q < 4) q = 4; // MQ=0 reads count as BQ=4 bca->bases[n++] = q<<5 | (int)bam_is_rev(p->b)<<4 | b; //if (is_indel) fprintf(bcftools_stderr,"xx:base,q,strand\t%d\t%d\t%d\n",b,q,bam_is_rev(p->b)?0:1); // collect annotations if (b < 4) { r->QS[b] += q; if ( r->ADF ) { if ( bam_is_rev(p->b) ) r->ADR[b]++; else r->ADF[b]++; } } ++r->anno[0<<2|is_diff<<1|bam_is_rev(p->b)]; min_dist = p->b->core.l_qseq - 1 - p->qpos; if (min_dist > p->qpos) min_dist = p->qpos; if (min_dist > CAP_DIST) min_dist = CAP_DIST; r->anno[1<<2|is_diff<<1|0] += baseQ; r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ; r->anno[2<<2|is_diff<<1|0] += mapQ; r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ; r->anno[3<<2|is_diff<<1|0] += min_dist; r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist; // collect for bias tests if ( baseQ > 59 ) baseQ = 59; if ( mapQ > 59 ) mapQ = 59; int len, epos = 0, sc_len = 0, sc_dist = 0; if ( bca->fmt_flag & (B2B_INFO_RPBZ|B2B_INFO_VDB|B2B_INFO_SCBZ) ) { int pos = get_position(p, &len, &sc_len, &sc_dist); epos = (double)pos/(len+1) * (bca->npos - 1); if (sc_len) { sc_len = 15.0*sc_len / (sc_dist+1); if (sc_len > 99) sc_len = 99; } assert( epos>=0 && eposnpos ); assert( sc_len>=0 && sc_lennpos ); } int imq = mapQ * nqual_over_60; int ibq = baseQ * nqual_over_60; if ( bam_is_rev(p->b) ) bca->rev_mqs[imq]++; else bca->fwd_mqs[imq]++; if ( !is_diff ) { bca->ref_pos[epos]++; bca->ref_bq[ibq]++; bca->ref_mq[imq]++; bca->ref_scl[sc_len]++; if ( inm>=0 ) { bca->ref_nm[inm]++; if ( r->ref_nm ) r->ref_nm[inm]++; } } else { bca->alt_pos[epos]++; bca->alt_bq[ibq]++; bca->alt_mq[imq]++; bca->alt_scl[sc_len]++; if ( inm>=0 ) { bca->alt_nm[inm]++; if ( r->alt_nm ) r->alt_nm[inm]++; } } } // Compensate for AD not being counted on low quality REF indel matches. if ( r->ADF && bca->ambig_reads==B2B_INC_AD0 ) { for (i=0; i<4; i++) { r->ADR[0] += ADR_ref_missed[i]; r->ADF[0] += ADF_ref_missed[i]; } } else if ( r->ADF && bca->ambig_reads==B2B_INC_AD ) { int dp = 0, dp_ambig = 0; for (i=0; i<4; i++) dp += r->ADR[i]; for (i=0; i<4; i++) dp_ambig += ADR_ref_missed[i]; if ( dp ) for (i=0; i<4; i++) r->ADR[i] += lroundf((float)dp_ambig * r->ADR[i]/dp); dp = 0, dp_ambig = 0; for (i=0; i<4; i++) dp += r->ADF[i]; for (i=0; i<4; i++) dp_ambig += ADF_ref_missed[i]; if ( dp ) for (i=0; i<4; i++) r->ADF[i] += lroundf((float)dp_ambig * r->ADF[i]/dp); } // Else consider downgrading bca->bases[] scores by AD vs AD_ref_missed // ratios. This is detrimental on Illumina, but beneficial on PacBio CCS. // It's possibly related to the homopolyer error likelihoods or overall // Indel accuracy. Maybe tie this in to the -h option? r->ori_depth = ori_depth; // glfgen errmod_cal(bca->e, n, 5, bca->bases, r->p); // calculate PL of each genotype // TODO: account for the number of unassigned reads. If depth is 50, // but AD is 5,7 then it may look like a variant but it probably // should be low quality. return n; } /* * calc_vdb() - returns value between zero (most biased) and one (no bias) * on success, or HUGE_VAL when VDB cannot be calculated because * of insufficient depth (<2x) * * Variant Distance Bias tests if the variant bases are positioned within the * reads with sufficient randomness. Unlike other tests, it looks only at * variant reads and therefore gives different kind of information than Read * Position Bias for instance. VDB was developed for detecting artefacts in * RNA-seq calls where reads from spliced transcripts span splice site * boundaries. The current implementation differs somewhat from the original * version described in supplementary material of PMID:22524474, but the idea * remains the same. (Here the random variable tested is the average distance * from the averaged position, not the average pairwise distance.) * * For coverage of 2x, the calculation is exact but is approximated for the * rest. The result is most accurate between 4-200x. For 3x or >200x, the * reported values are slightly more favourable than those of a true random * distribution. */ double calc_vdb(int *pos, int npos) { // Note well: the parameters were obtained by fitting to simulated data of // 100bp reads. This assumes rescaling to 100bp in bcf_call_glfgen(). const int readlen = 100; assert( npos==readlen ); #define nparam 15 const float param[nparam][3] = { {3,0.079,18}, {4,0.09,19.8}, {5,0.1,20.5}, {6,0.11,21.5}, {7,0.125,21.6}, {8,0.135,22}, {9,0.14,22.2}, {10,0.153,22.3}, {15,0.19,22.8}, {20,0.22,23.2}, {30,0.26,23.4}, {40,0.29,23.5}, {50,0.35,23.65}, {100,0.5,23.7}, {200,0.7,23.7} }; int i, dp = 0; float mean_pos = 0, mean_diff = 0; for (i=0; i=200 ) i = nparam; // shortcut for big depths else { for (i=0; i=dp ) break; } float pshift, pscale; if ( i==nparam ) { // the depth is too high, go with 200x pscale = param[nparam-1][1]; pshift = param[nparam-1][2]; } else if ( i>0 && param[i][0]!=dp ) { // linear interpolation of parameters pscale = (param[i-1][1] + param[i][1])*0.5; pshift = (param[i-1][2] + param[i][2])*0.5; } else { pscale = param[i][1]; pshift = param[i][2]; } return 0.5*kf_erfc(-(mean_diff-pshift)*pscale); } double calc_chisq_bias(int *a, int *b, int n) { int na = 0, nb = 0, i, ndf = n; for (i=0; i= 2 && m >= 2); return (n < 8 && m < 8 && U < 50) ? mw[n-2][m-2][U] : mann_whitney_1947_(n,m,U); } double mann_whitney_1947_cdf(int n, int m, int U) { int i; double sum = 0; for (i=0; i<=U; i++) sum += mann_whitney_1947(n,m,i); return sum; } double calc_mwu_bias_cdf(int *a, int *b, int n) { int na = 0, nb = 0, i; double U = 0; //double ties = 0; for (i=0; i=8 && nb>=8 and reasonable if na<8 or nb<8 if ( na>=8 || nb>=8 ) { double mean = ((double)na*nb)*0.5; // Correction for ties: // double N = na+nb; // double var2 = (N*N-1)*N-ties; // if ( var2==0 ) return 1.0; // var2 *= ((double)na*nb)/N/(N-1)/12.0; // No correction for ties: double var2 = ((double)na*nb)*(na+nb+1)/12.0; double z = (U_min - mean)/sqrt(2*var2); // z is N(0,1) return 2.0 - kf_erfc(z); // which is 1 + erf(z) } // Exact calculation double pval = 2*mann_whitney_1947_cdf(na,nb,U_min); return pval>1 ? 1 : pval; } double calc_mwu_bias(int *a, int *b, int n, int left) { int na = 0, nb = 0, i; double U = 0; // double ties = 0; for (i=0; i mean) return 1; // for MQB which is asymmetrical if ( na==2 || nb==2 ) { // Linear approximation return U>mean ? (2.0*mean-U)/mean : U/mean; } // Correction for ties: // double N = na+nb; // double var2 = (N*N-1)*N-ties; // if ( var2==0 ) return 1.0; // var2 *= ((double)na*nb)/N/(N-1)/12.0; // No correction for ties: double var2 = ((double)na*nb)*(na+nb+1)/12.0; if ( na>=8 || nb>=8 ) { // Normal approximation, very good for na>=8 && nb>=8 and reasonable if na<8 or nb<8 return exp(-0.5*(U-mean)*(U-mean)/var2); } // Exact calculation return mann_whitney_1947(na,nb,U) * sqrt(2*M_PI*var2); } // A Z-score version of the above function. // // See "Normal approximation and tie correction" at // https://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U_test // // The Z score is the number of standard deviations above or below the mean // with 0 being equality of the two distributions and +ve/-ve from there. // // This is a more robust score to filter on. double calc_mwu_biasZ(int *a, int *b, int n, int left_only, int do_Z) { int i; int64_t t; // Optimisation for (i = 0; i < n; i++) if (b[i]) break; int b_empty = (i == n); // Count equal (e), less-than (l) and greater-than (g) permutations. int e = 0, l = 0, na = 0, nb = 0; if (b_empty) { for (t = 0, i = n-1; i >= 0; i--) { na += a[i]; t += (a[i]*a[i]-1)*a[i]; // adjustment score for ties } } else { for (t = 0, i = n-1; i >= 0; i--) { // Combinations of a[i] and b[j] for i==j e += a[i]*b[i]; // nb is running total of b[i+1]..b[n-1]. // Therefore a[i]*nb is the number of combinations of a[i] and b[j] // for all i < j. l += a[i]*nb; // a= 0 ? 0.5 : -0.5)) / sd; // gatk method? return (U - m) / sqrt(var2); } // Else U score, which can be asymmetric for some data types. if (left_only && U > m) return HUGE_VAL; // one-sided, +ve bias is OK, -ve is not. if (na >= 8 || nb >= 8) { // Normal approximation, very good for na>=8 && nb>=8 and // reasonable if na<8 or nb<8 return exp(-0.5*(U-m)*(U-m)/var2); } // Exact calculation if (na==1 || nb == 1) return mann_whitney_1947_(na, nb, U) * sqrt(2*M_PI*var2); else return mann_whitney_1947(na, nb, U) * sqrt(2*M_PI*var2); } static inline double logsumexp2(double a, double b) { if ( a>b ) return log(1 + exp(b-a)) + a; else return log(1 + exp(a-b)) + b; } void calc_SegBias(const bcf_callret1_t *bcr, bcf_call_t *call) { call->seg_bias = HUGE_VAL; if ( !bcr ) return; int nr = call->anno[2] + call->anno[3]; // number of observed non-reference reads if ( !nr ) return; int avg_dp = (call->anno[0] + call->anno[1] + nr) / call->n; // average depth double M = floor((double)nr / avg_dp + 0.5); // an approximate number of variants samples in the population if ( M>call->n ) M = call->n; // clamp M at the number of samples else if ( M==0 ) M = 1; double f = M / 2. / call->n; // allele frequency double p = (double) nr / call->n; // number of variant reads per sample expected if variant not real (poisson) double q = (double) nr / M; // number of variant reads per sample expected if variant is real (poisson) double sum = 0; const double log2 = log(2.0); // fprintf(bcftools_stderr,"M=%.1f p=%e q=%e f=%f dp=%d\n",M,p,q,f,avg_dp); int i; for (i=0; in; i++) { int oi = bcr[i].anno[2] + bcr[i].anno[3]; // observed number of non-ref reads double tmp; if ( oi ) { // tmp = log(f) + oi*log(q/p) - q + log(2*(1-f) + f*pow(2,oi)*exp(-q)) + p; // this can under/overflow tmp = logsumexp2(log(2*(1-f)), log(f) + oi*log2 - q); tmp += log(f) + oi*log(q/p) - q + p; } else tmp = log(2*f*(1-f)*exp(-q) + f*f*exp(-2*q) + (1-f)*(1-f)) + p; sum += tmp; // fprintf(bcftools_stderr,"oi=%d %e\n", oi,tmp); } call->seg_bias = sum; } /** * bcf_call_combine() - sets the PL array and VDB, RPB annotations, finds the top two alleles * @n: number of samples * @calls: each sample's calls * @bca: auxiliary data structure for holding temporary values * @ref_base: the reference base * @call: filled with the annotations * * Combines calls across the various samples being studied * 1. For each allele at each base across all samples the quality is summed so * you end up with a set of quality sums for each allele present 2. The quality * sums are sorted. * 3. Using the sorted quality sums we now create the allele ordering array * A\subN. This is done by doing the following: * a) If the reference allele is known it always comes first, otherwise N * comes first. * b) Then the rest of the alleles are output in descending order of quality * sum (which we already know the qsum array was sorted). Any allelles with * qsum 0 will be excluded. * 4. Using the allele ordering array we create the genotype ordering array. * In the worst case with an unknown reference this will be: A0/A0 A1/A0 A1/A1 * A2/A0 A2/A1 A2/A2 A3/A0 A3/A1 A3/A2 A3/A3 A4/A0 A4/A1 A4/A2 A4/A3 A4/A4 * 5. The genotype ordering array is then used to extract data from the error * model 5*5 matrix and is used to produce a Phread likelihood array for each * sample. */ int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call) { int ref4, i, j; float qsum[B2B_MAX_ALLELES] = {0,0,0,0,0}; if (ref_base >= 0) { call->ori_ref = ref4 = seq_nt16_int[ref_base]; if (ref4 > 4) ref4 = 4; } else call->ori_ref = -1, ref4 = 0; // calculate qsum, this is done by summing normalized qsum across all samples, // to account for differences in coverage for (i = 0; i < n; ++i) { float sum = 0; for (j = 0; j < 4; ++j) sum += calls[i].QS[j]; if ( sum ) for (j = 0; j < 4; j++) qsum[j] += (float)calls[i].QS[j] / sum; } // sort qsum in ascending order (insertion sort) float *ptr[5], *tmp; for (i=0; i<5; i++) ptr[i] = &qsum[i]; for (i=1; i<4; i++) for (j=i; j>0 && *ptr[j] < *ptr[j-1]; j--) tmp = ptr[j], ptr[j] = ptr[j-1], ptr[j-1] = tmp; // Set the reference allele and alternative allele(s) for (i=0; i<5; i++) call->a[i] = -1; for (i=0; iqsum[i] = 0; call->unseen = -1; call->a[0] = ref4; for (i=3, j=1; i>=0; i--) // i: alleles sorted by QS; j, a[j]: output allele ordering { int ipos = ptr[i] - qsum; // position in sorted qsum array if ( ipos==ref4 ) call->qsum[0] = qsum[ipos]; // REF's qsum else { if ( !qsum[ipos] ) break; // qsum is 0, this and consequent alleles are not seen in the pileup call->qsum[j] = qsum[ipos]; call->a[j++] = ipos; } } if (ref_base >= 0) { // for SNPs, find the "unseen" base if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0) call->unseen = j, call->a[j++] = ptr[i] - qsum; call->n_alleles = j; } else { call->n_alleles = j; if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything } int has_alt = (call->n_alleles==2 && call->unseen!=-1) ? 0 : 1; /* * Set the phread likelihood array (call->PL) This array is 15 entries long * for each sample because that is size of an upper or lower triangle of a * worst case 5x5 matrix of possible genotypes. This worst case matrix will * occur when all 4 possible alleles are present and the reference allele * is unknown. The sides of the matrix will correspond to the reference * allele (if known) followed by the alleles present in descending order of * quality sum */ { int x, g[15], z; double sum_min = 0.; x = call->n_alleles * (call->n_alleles + 1) / 2; // get the possible genotypes // this is done by creating an ordered list of locations g for call (allele a, allele b) in the genotype likelihood matrix for (i = z = 0; i < call->n_alleles; ++i) { for (j = 0; j <= i; ++j) { g[z++] = call->a[j] * 5 + call->a[i]; } } // for each sample calculate the PL for (i = 0; i < n; ++i) { int32_t *PL = call->PL + x * i; const bcf_callret1_t *r = calls + i; float min = FLT_MAX; for (j = 0; j < x; ++j) { if (min > r->p[g[j]]) min = r->p[g[j]]; } sum_min += min; for (j = 0; j < x; ++j) { int y; y = (int)(r->p[g[j]] - min + .499); if (y > 255) y = 255; PL[j] = y; } } if ( call->DP4 ) { for (i=0; iDP4[4*i] = calls[i].anno[0]; call->DP4[4*i+1] = calls[i].anno[1]; call->DP4[4*i+2] = calls[i].anno[2]; call->DP4[4*i+3] = calls[i].anno[3]; } } if ( call->SCR ) { for (i=0; iSCR[0] += calls[i].SCR; call->SCR[1+i] = calls[i].SCR; } } if ( call->ADF ) { assert( call->n_alleles<=B2B_MAX_ALLELES ); // this is always true for SNPs and so far for indels as well // reorder ADR,ADF to match the allele ordering at this site int32_t tmp[B2B_MAX_ALLELES]; int32_t *adr = call->ADR + B2B_MAX_ALLELES, *adr_out = call->ADR + B2B_MAX_ALLELES; int32_t *adf = call->ADF + B2B_MAX_ALLELES, *adf_out = call->ADF + B2B_MAX_ALLELES; int32_t *adr_tot = call->ADR; // the first bin stores total counts per site int32_t *adf_tot = call->ADF; for (i=0; in_alleles; j++) { tmp[j] = adr[ call->a[j] ]; adr_tot[j] += tmp[j]; } for (j=0; jn_alleles; j++) adr_out[j] = tmp[j]; for (j=0; jn_alleles; j++) { tmp[j] = adf[ call->a[j] ]; adf_tot[j] += tmp[j]; } for (j=0; jn_alleles; j++) adf_out[j] = tmp[j]; adf_out += call->n_alleles; adr_out += call->n_alleles; adr += B2B_MAX_ALLELES; adf += B2B_MAX_ALLELES; } } if ( bca->fmt_flag & B2B_FMT_QS ) { assert( call->n_alleles<=B2B_MAX_ALLELES ); // this is always true for SNPs and so far for indels as well // reorder QS to match the allele ordering at this site int32_t tmp[B2B_MAX_ALLELES]; int32_t *qs = call->QS, *qs_out = call->QS; for (i=0; in_alleles; j++) tmp[j] = qs[ call->a[j] ]; for (j=0; jn_alleles; j++) qs_out[j] = tmp[j] < BCF_MAX_BT_INT32 ? tmp[j] : BCF_MAX_BT_INT32; qs_out += call->n_alleles; qs += B2B_MAX_ALLELES; } } // if (ref_base < 0) fprintf(bcftools_stderr, "%d,%d,%f,%d\n", call->n_alleles, x, sum_min, call->unseen); // fprintf(bcftools_stderr,"sum_min=%f\n",sum_min); call->shift = (int)(sum_min + .499); } // combine annotations memset(call->anno, 0, 16 * sizeof(double)); call->ori_depth = 0; call->depth = 0; call->mq0 = 0; for (i = 0; i < n; ++i) { call->depth += calls[i].anno[0] + calls[i].anno[1] + calls[i].anno[2] + calls[i].anno[3]; call->ori_depth += calls[i].ori_depth; call->mq0 += calls[i].mq0; for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j]; } // No need to calculate MWU tests when there is no ALT allele, this should speed up things slightly if ( !has_alt ) return 0; if ( bca->fmt_flag & B2B_INFO_FS ) { double left,right,two; call->strand_bias = kt_fisher_exact(call->anno[0], call->anno[1], call->anno[2], call->anno[3], &left, &right, &two); } if ( bca->fmt_flag & B2B_INFO_SGB ) calc_SegBias(calls, call); // calc_chisq_bias("XPOS", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_pos, bca->alt_pos, bca->npos); // calc_chisq_bias("XMQ", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_mq, bca->alt_mq, bca->nqual); // calc_chisq_bias("XBQ", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_bq, bca->alt_bq, bca->nqual); // U z-normalised as +/- number of standard deviations from mean. if (call->ori_ref < 0) { // indel if ( bca->fmt_flag & B2B_INFO_RPBZ ) call->mwu_pos = calc_mwu_biasZ(bca->iref_pos, bca->ialt_pos, bca->npos, 0, 1); if ( bca->fmt_flag & B2B_INFO_MQBZ ) call->mwu_mq = calc_mwu_biasZ(bca->iref_mq, bca->ialt_mq, bca->nqual,1,1); if ( bca->fmt_flag & B2B_INFO_SCBZ ) call->mwu_sc = calc_mwu_biasZ(bca->iref_scl, bca->ialt_scl, 100, 0,1); } else { if ( bca->fmt_flag & B2B_INFO_RPBZ ) call->mwu_pos = calc_mwu_biasZ(bca->ref_pos, bca->alt_pos, bca->npos, 0, 1); if ( bca->fmt_flag & B2B_INFO_MQBZ ) call->mwu_mq = calc_mwu_biasZ(bca->ref_mq, bca->alt_mq, bca->nqual,1,1); if ( bca->fmt_flag & B2B_INFO_BQBZ ) call->mwu_bq = calc_mwu_biasZ(bca->ref_bq, bca->alt_bq, bca->nqual,0,1); if ( bca->fmt_flag & B2B_INFO_MQSBZ ) call->mwu_mqs = calc_mwu_biasZ(bca->fwd_mqs, bca->rev_mqs, bca->nqual,0,1); if ( bca->fmt_flag & B2B_INFO_SCBZ ) call->mwu_sc = calc_mwu_biasZ(bca->ref_scl, bca->alt_scl, 100, 0,1); } if ( bca->fmt_flag & B2B_INFO_NMBZ ) call->mwu_nm[0] = calc_mwu_biasZ(bca->ref_nm, bca->alt_nm, B2B_N_NM,0,1); if ( bca->fmt_flag & B2B_FMT_NMBZ ) { for (i=0; imwu_nm[i+1] = val!=HUGE_VAL ? val : 0; } } if ( bca->fmt_flag & B2B_INFO_VDB ) call->vdb = calc_vdb(bca->alt_pos, bca->npos); return 0; } int bcf_call2bcf(bcf_call_t *bc, bcf1_t *rec, bcf_callret1_t *bcr, int fmt_flag, const bcf_callaux_t *bca, const char *ref) { extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two); int i, j, nals = 1, has_alt = 0; bcf_hdr_t *hdr = bc->bcf_hdr; rec->rid = bc->tid; rec->pos = bc->pos; rec->qual = 0; bc->tmp.l = 0; if (bc->ori_ref < 0) // indel { // REF kputc(ref[bc->pos], &bc->tmp); for (j = 0; j < bca->indelreg; ++j) kputc(ref[bc->pos+1+j], &bc->tmp); // ALT for (i=1; i<4; i++) { if (bc->a[i] < 0) break; kputc(',', &bc->tmp); kputc(ref[bc->pos], &bc->tmp); if (bca->indel_types[bc->a[i]] < 0) { // deletion for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j) kputc(ref[bc->pos+1+j], &bc->tmp); } else { // insertion; cannot be a reference unless a bug char *inscns = &bca->inscns[bc->a[i] * bca->maxins]; for (j = 0; j < bca->indel_types[bc->a[i]]; ++j) kputc("ACGTN"[(int)inscns[j]], &bc->tmp); for (j = 0; j < bca->indelreg; ++j) kputc(ref[bc->pos+1+j], &bc->tmp); } nals++; has_alt = 1; } } else // SNP { kputc("ACGTN"[bc->ori_ref], &bc->tmp); for (i=1; i<5; i++) { if (bc->a[i] < 0) break; kputc(',', &bc->tmp); if ( bc->unseen==i ) kputs("<*>", &bc->tmp); else { kputc("ACGT"[bc->a[i]], &bc->tmp); has_alt = 1; } nals++; } } bcf_update_alleles_str(hdr, rec, bc->tmp.s); bc->tmp.l = 0; // INFO if ( bc->ori_ref < 0 ) { bcf_update_info_flag(hdr, rec, "INDEL", NULL, 1); uint32_t idv = bca->max_support; if ( fmt_flag&B2B_INFO_IMF) { float max_frac; // Recompute IDV and IMF based on alignment results for more // accurate counts, but only when in new "--indels-cns" mode. if (bc->ADF && bc->ADR && bca->edlib) { int max_ad = 0; for (int k = 1; k < rec->n_allele; k++) { if (max_ad < bc->ADF[k] + bc->ADR[k]) max_ad = bc->ADF[k] + bc->ADR[k]; } max_frac = (double)(max_ad) / bc->ori_depth; idv = max_ad; } else { max_frac = bca->max_frac; } // Copied here to maintain order for consistency of "make check" if ( fmt_flag&B2B_INFO_IDV ) bcf_update_info_int32(hdr, rec, "IDV", &idv, 1); bcf_update_info_float(hdr, rec, "IMF", &max_frac, 1); } else { if ( fmt_flag&B2B_INFO_IDV ) bcf_update_info_int32(hdr, rec, "IDV", &idv, 1); } } bcf_update_info_int32(hdr, rec, "DP", &bc->ori_depth, 1); if ( fmt_flag&B2B_INFO_ADF ) bcf_update_info_int32(hdr, rec, "ADF", bc->ADF, rec->n_allele); if ( fmt_flag&B2B_INFO_ADR ) bcf_update_info_int32(hdr, rec, "ADR", bc->ADR, rec->n_allele); if ( fmt_flag&(B2B_INFO_AD|B2B_INFO_DPR) ) { for (i=0; in_allele; i++) bc->ADF[i] += bc->ADR[i]; if ( fmt_flag&B2B_INFO_AD ) bcf_update_info_int32(hdr, rec, "AD", bc->ADF, rec->n_allele); if ( fmt_flag&B2B_INFO_DPR ) bcf_update_info_int32(hdr, rec, "DPR", bc->ADF, rec->n_allele); } if ( fmt_flag&B2B_INFO_SCR ) bcf_update_info_int32(hdr, rec, "SCR", bc->SCR, 1); float tmpf[16]; for (i=0; i<16; i++) tmpf[i] = bc->anno[i]; bcf_update_info_float(hdr, rec, "I16", tmpf, 16); bcf_update_info_float(hdr, rec, "QS", bc->qsum, nals); if ( has_alt ) { if ( fmt_flag&B2B_INFO_MIN_PL_SUM ) bcf_update_info_int32(hdr, rec, "MIN_PL_SUM", &bc->shift, 1); if ( fmt_flag&B2B_INFO_VDB && bc->vdb != HUGE_VAL ) bcf_update_info_float(hdr, rec, "VDB", &bc->vdb, 1); if ( fmt_flag&B2B_INFO_SGB && bc->seg_bias != HUGE_VAL ) bcf_update_info_float(hdr, rec, "SGB", &bc->seg_bias, 1); if ( fmt_flag&B2B_INFO_NM && (bca->nnm[0] || bca->nnm[1]) ) { for (i=0; i<2; i++) bc->nm[i] = bca->nnm[i] ? bca->nm[i]/bca->nnm[i] : 0; bcf_update_info_float(hdr, rec, "NM", bc->nm, 2); } if ( fmt_flag&B2B_INFO_RPBZ && bc->mwu_pos != HUGE_VAL ) bcf_update_info_float(hdr, rec, "RPBZ", &bc->mwu_pos, 1); if ( fmt_flag&B2B_INFO_MQBZ && bc->mwu_mq != HUGE_VAL ) bcf_update_info_float(hdr, rec, "MQBZ", &bc->mwu_mq, 1); if ( fmt_flag&B2B_INFO_MQSBZ && bc->mwu_mqs != HUGE_VAL ) bcf_update_info_float(hdr, rec, "MQSBZ", &bc->mwu_mqs, 1); if ( fmt_flag&B2B_INFO_BQBZ && bc->mwu_bq != HUGE_VAL ) bcf_update_info_float(hdr, rec, "BQBZ", &bc->mwu_bq, 1); if ( fmt_flag&B2B_INFO_NMBZ && bc->mwu_nm[0] != HUGE_VAL ) bcf_update_info_float(hdr, rec, "NMBZ", bc->mwu_nm, 1); if ( fmt_flag&B2B_INFO_SCBZ && bc->mwu_sc != HUGE_VAL ) bcf_update_info_float(hdr, rec, "SCBZ", &bc->mwu_sc, 1); if ( fmt_flag&B2B_INFO_FS && bc->strand_bias != HUGE_VAL ) bcf_update_info_float(hdr, rec, "FS", &bc->strand_bias, 1); } tmpf[0] = bc->ori_depth ? (float)bc->mq0/bc->ori_depth : 0; if ( fmt_flag&B2B_INFO_MQ0F ) bcf_update_info_float(hdr, rec, "MQ0F", tmpf, 1); // FORMAT rec->n_sample = bc->n; bcf_update_format_int32(hdr, rec, "PL", bc->PL, nals*(nals+1)/2 * rec->n_sample); if ( fmt_flag&B2B_FMT_DP ) { int32_t *ptr = (int32_t*) bc->fmt_arr; for (i=0; in; i++) ptr[i] = bc->DP4[4*i] + bc->DP4[4*i+1] + bc->DP4[4*i+2] + bc->DP4[4*i+3]; bcf_update_format_int32(hdr, rec, "DP", bc->fmt_arr, rec->n_sample); } if ( fmt_flag&B2B_FMT_DV ) { int32_t *ptr = (int32_t*) bc->fmt_arr; for (i=0; in; i++) ptr[i] = bc->DP4[4*i+2] + bc->DP4[4*i+3]; bcf_update_format_int32(hdr, rec, "DV", bc->fmt_arr, rec->n_sample); } if ( fmt_flag&B2B_FMT_SP ) { int32_t *ptr = (int32_t*) bc->fmt_arr; for (i=0; in; i++) { int fwd_ref = bc->DP4[4*i], rev_ref = bc->DP4[4*i+1], fwd_alt = bc->DP4[4*i+2], rev_alt = bc->DP4[4*i+3]; if ( fwd_ref+rev_ref<2 || fwd_alt+rev_alt<2 || fwd_ref+fwd_alt<2 || rev_ref+rev_alt<2 ) ptr[i] = 0; else { double left, right, two; kt_fisher_exact(fwd_ref, rev_ref, fwd_alt, rev_alt, &left, &right, &two); int32_t x = (int)(-4.343 * log(two) + .499); if (x > 255) x = 255; ptr[i] = x; } } bcf_update_format_int32(hdr, rec, "SP", bc->fmt_arr, rec->n_sample); } if ( fmt_flag&B2B_FMT_DP4 ) bcf_update_format_int32(hdr, rec, "DP4", bc->DP4, rec->n_sample*4); if ( fmt_flag&B2B_FMT_ADF ) bcf_update_format_int32(hdr, rec, "ADF", bc->ADF+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele); if ( fmt_flag&B2B_FMT_ADR ) bcf_update_format_int32(hdr, rec, "ADR", bc->ADR+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele); if ( fmt_flag&(B2B_FMT_AD|B2B_FMT_DPR) ) { for (i=0; in_sample*rec->n_allele; i++) bc->ADF[B2B_MAX_ALLELES+i] += bc->ADR[B2B_MAX_ALLELES+i]; if ( fmt_flag&B2B_FMT_AD ) bcf_update_format_int32(hdr, rec, "AD", bc->ADF+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele); if ( fmt_flag&B2B_FMT_DPR ) bcf_update_format_int32(hdr, rec, "DPR", bc->ADF+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele); } if ( fmt_flag&B2B_FMT_SCR ) bcf_update_format_int32(hdr, rec, "SCR", bc->SCR+1, rec->n_sample); if ( fmt_flag&B2B_FMT_QS ) bcf_update_format_int32(hdr, rec, "QS", bc->QS, rec->n_sample*rec->n_allele); if ( has_alt ) { if ( fmt_flag&B2B_FMT_NMBZ ) bcf_update_format_float(hdr, rec, "NMBZ", bc->mwu_nm+1, rec->n_sample); } return 0; } pysam-0.23.0/bcftools/bam2bcf.h000066400000000000000000000224011475062545500162210ustar00rootroot00000000000000/* bam2bcf.h -- variant calling. Copyright (C) 2010-2012 Broad Institute. Copyright (C) 2012-2022 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef BAM2BCF_H #define BAM2BCF_H #include #include #include /** * A simplified version of Mann-Whitney U-test is calculated * by default (no CDF) because it is faster and seems to work * better in machine learning filtering. When enabled by setting * CDF_MWU_TESTS, additional annotations will appear on mpileup's * output (RPB2 in addition to RPB, etc.). */ #ifndef CDF_MWU_TESTS #define CDF_MWU_TESTS 0 #endif #define B2B_INDEL_NULL 10000 #define B2B_FMT_DP (1<<0) #define B2B_FMT_SP (1<<1) #define B2B_FMT_DV (1<<2) #define B2B_FMT_DP4 (1<<3) #define B2B_FMT_DPR (1<<4) #define B2B_INFO_DPR (1<<5) #define B2B_FMT_AD (1<<6) #define B2B_FMT_ADF (1<<7) #define B2B_FMT_ADR (1<<8) #define B2B_INFO_AD (1<<9) #define B2B_INFO_ADF (1<<10) #define B2B_INFO_ADR (1<<11) #define B2B_INFO_SCR (1<<12) #define B2B_FMT_SCR (1<<13) #define B2B_INFO_VDB (1<<14) #define B2B_FMT_QS (1<<15) #define B2B_FMT_NMBZ (1<<16) // per-sample NMBZ #define B2B_INFO_NMBZ (1<<17) #define B2B_INFO_BQBZ (1<<18) #define B2B_INFO_MQBZ (1<<19) #define B2B_INFO_MQSBZ (1<<20) #define B2B_INFO_RPBZ (1<<21) #define B2B_INFO_SCBZ (1<<22) #define B2B_INFO_SGB (1<<23) #define B2B_INFO_MIN_PL_SUM (1<<24) #define B2B_INFO_NM (1<<25) #define B2B_INFO_MQ0F (1<<26) #define B2B_INFO_IDV (1<<27) #define B2B_INFO_IMF (1<<28) #define B2B_INFO_FS (1<<29) #define B2B_MAX_ALLELES 5 #define B2B_N_NM 32 // number of NMBZ bins, i.e. max number of mismatches #define B2B_DROP 0 #define B2B_INC_AD 1 #define B2B_INC_AD0 2 // Pileup "client data" for each read to cache per-read information #define PLP_CD(x) ((plp_cd_t*)((x)->p)) #define PLP_HAS_SOFT_CLIP(cd) (PLP_CD(cd)->i & 1) #define PLP_HAS_INDEL(cd) (PLP_CD(cd)->i & 2) #define PLP_IS_REALN(cd) (PLP_CD(cd)->i & 4) #define PLP_SAMPLE_ID(cd) (PLP_CD(cd)->i >> 3) #define PLP_QLEN(cd) (PLP_CD(cd)->qlen) #define PLP_NM(cd) (PLP_CD(cd)->nm) #define PLP_NM_UNSET -2 #define PLP_SET_SOFT_CLIP(cd) (PLP_CD(cd)->i |= 1) #define PLP_SET_INDEL(cd) (PLP_CD(cd)->i |= 2) #define PLP_SET_REALN(cd) (PLP_CD(cd)->i |= 4) #define PLP_SET_SAMPLE_ID(cd,n) (PLP_CD(cd)->i |= (n)<<3) typedef struct { int64_t i; // used to store sample id and flags for presence of soft-clip and indel uint32_t qlen; // cached output of bam_cigar2qlen(), 0 if unset int nm; // -2 PLP_NM_UNSET; -1 not available; >=0 NM value computed by get_aux_nm() } plp_cd_t; typedef struct __bcf_callaux_t { int fmt_flag, ambig_reads; int capQ, min_baseQ, max_baseQ, delta_baseQ; int openQ, extQ, tandemQ; // for indels uint32_t min_support, max_support; // for collecting indel candidates double min_frac; // for collecting indel candidates float max_frac; // for collecting indel candidates int per_sample_flt; // indel filtering strategy int *ref_pos, *alt_pos, npos, *ref_mq, *alt_mq, *ref_bq, *alt_bq, *fwd_mqs, *rev_mqs, nqual; // for bias tests int *iref_pos, *ialt_pos, *iref_mq, *ialt_mq; // for indels int ref_scl[100], alt_scl[100]; // soft-clip length bias; SNP int iref_scl[100], ialt_scl[100]; // soft-clip length bias; INDEL // for internal uses int max_bases; int indel_types[4]; // indel lengths int indel_win_size, indels_v20, edlib; int seqQ_offset; // edlib mode, seqQ=MIN(seqQ, offset - MIN(20,depth)*5); int maxins, indelreg, poly_mqual; int read_len; char *inscns; uint16_t *bases; // 5bit: unused, 6:quality, 1:is_rev, 4:2-bit base or indel allele (index to bcf_callaux_t.indel_types) errmod_t *e; void *rghash; float indel_bias; // adjusts indel score threshold; lower => call more. float del_bias; // (-.9 < x < .9) error profile; >0 => more del, <0 => more ins float vs_ref; // 0 to 1. 0: score vs next-best. 1: score vs ref int32_t *ref_nm, *alt_nm; // pointers to bcf_call_t.{ref_nm,alt_nm} unsigned int nnm[2]; // number of nm observations float nm[2]; // cumulative count of mismatches in ref and alt reads void *iaux; // auxiliary structure for --indels-2.0 calling char *chr; // current chromosome } bcf_callaux_t; // per-sample values typedef struct { uint32_t ori_depth; // ori_depth = anno[0..3] but before --min-BQ is applied unsigned int mq0; int32_t *ADF, *ADR, SCR, *QS; // FMT/QS int32_t *ref_nm, *alt_nm; // The fields are: // depth fwd .. ref (0) and non-ref (2) // depth rev .. ref (1) and non-ref (3) // baseQ .. ref (4) and non-ref (6) // baseQ^2 .. ref (5) and non-ref (7) // mapQ .. ref (8) and non-ref (10) // mapQ^2 .. ref (9) and non-ref (11) // minDist .. ref (12) and non-ref (14) // minDist^2 .. ref (13) and non-ref (15) // Note that this probably needs a more thorough fix: int types in // bcf_call_t do overflow with high-coverage data, such as exomes, and // BCFv2 supports only floats which may not suffice. double anno[16]; float p[25]; // phred-scaled likelihood of each genotype } bcf_callret1_t; // values for all samples typedef struct { int tid, pos; bcf_hdr_t *bcf_hdr; int a[5]; // alleles: ref, alt, alt2, alt3 float qsum[B2B_MAX_ALLELES]; // INFO/QS tag int n, n_alleles, ori_ref, unseen; int32_t shift; // shift is the sum of min_PL before normalization to 0 across all samples int n_supp; // number of supporting non-reference reads double anno[16]; unsigned int depth, ori_depth, mq0; int32_t *PL, *DP4, *ADR, *ADF, *SCR, *QS, *ref_nm, *alt_nm; uint8_t *fmt_arr; float vdb; // variant distance bias float mwu_pos, mwu_mq, mwu_bq, mwu_mqs, mwu_sc, *mwu_nm, nm[2]; float seg_bias; float strand_bias; // phred-scaled fisher-exact test kstring_t tmp; } bcf_call_t; #ifdef __cplusplus extern "C" { #endif bcf_callaux_t *bcf_call_init(double theta, int min_baseQ, int max_baseQ, int delta_baseQ); void bcf_call_destroy(bcf_callaux_t *bca); int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r); int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call); int bcf_call2bcf(bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag, const bcf_callaux_t *bca, const char *ref); int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref); int bcf_iaux_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref); int bcf_edlib_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, int ref_len); void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call); int bcf_cgp_l_run(const char *ref, int pos); int est_indelreg(int pos, const char *ref, int l, char *ins4); /* ---------------------------------------------------------------------- * Shared between bam2bcf_indel.c and bam2bcf_edlib.c */ // Take a reference position tpos and convert to a query position (returned). // This uses the CIGAR string plus alignment c->pos to do the mapping. // // *_tpos is returned as tpos if query overlaps tpos, but for deletions // it'll be either the start (is_left) or end (!is_left) ref position. int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int is_left, int32_t *_tpos); // Identify spft-clip length, position in seq, and clipped seq len void get_pos(const bcf_callaux_t *bca, bam_pileup1_t *p, int *sc_len_r, int *slen_r, int *epos_r, int *end); // Compute the consensus for this sample 's', minus indels which // get added later. char *bcf_cgp_calc_cons(int n, int *n_plp, bam_pileup1_t **plp, int pos, int *types, int n_types, int max_ins, int s); #ifdef __cplusplus } #endif #endif pysam-0.23.0/bcftools/bam2bcf_edlib.c000066400000000000000000002034221475062545500173570ustar00rootroot00000000000000/* bam2bcf_indel.c -- indel caller. Copyright (C) 2010, 2011 Broad Institute. Copyright (C) 2012-2014,2016-2017, 2021-2024 Genome Research Ltd. Author: Heng Li Petr Danecek James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ // Show consensus //#define CONS_DEBUG // Show alignments to consensus //#define ALIGN_DEBUG #include #include #include #include #include #include #include #include "bam2bcf.h" #include "str_finder.h" #include // Is there no way to share these between the 3 implementations? KSORT_INIT_STATIC_GENERIC(uint32_t) #define MINUS_CONST 0x10000000 #define MAX_TYPES 64 #ifndef MIN # define MIN(a,b) ((a)<(b)?(a):(b)) #endif #ifndef ABS # define ABS(a) ((a)<0?-(a):(a)) #endif #ifndef MAX # define MAX(a,b) ((a)>(b)?(a):(b)) #endif // l is the relative gap length and l_run is the length of the homopolymer // on the reference. // // Larger seqQ is good, so increasing tandemQ calls more indels, // and longer l_run means fewer calls. It is capped later at 255. // For short l_runs, the qual is simply based on size of indel // larger ones being considered more likely to be real. // Longer indels get assigned a score based on the relative indel size // to homopolymer, where l_run base will have already been verified by // the caller to ensure it's compatible. static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run, int str_len) { int q, qh; // Short indels are more likely sequencing error than large ones. // So "seqQ" scales with size of observation "l". // // Note openQ and extQ are error likelihoods in Phred scale. Hence high // openQ means we're very unlikely to miscall an indel. // Ie it's not the open/ext "costs" normally used in alignment; more the reverse. // // We use MIN(q,qh) below, so we can remove the q component by specifying // a large -o parameter in mpileup. q = bca->openQ + bca->extQ * (abs(l) - 1); // Orig method; best with Illumina (high openQ) // qh = bca->tandemQ * (double)abs(l) / l_run + .499; // Penalise longer homopolymers quadratically more, but boost shorter ones. // Best with CCS (low openQ) //qh = 2 * bca->tandemQ * pow((double)abs(l) / l_run, 1.5) + .499; // (l/l_run)^1.26 for openQ=25 or ^1 for openQ=40. // double openQ = MIN(40, bca->openQ); // qh = (30/openQ) * bca->tandemQ // * pow((double)abs(l) / l_run, 1/sqrt(openQ/40)) + .499; // Linear scaled on openQ too qh = bca->tandemQ * (double)abs(l) / l_run + .499; // Generic maybe ? // power = 1/sqrt(MIN(40,bca->openQ)/40.); // qh = ... * pow((double)abs(l)/l_run, power) // bam2bcf.c caps has "if q>seqQ) q=seqQ" so it caps base qual 'q'. // A 1bp indel would therefore have a maximum qual it could be considered based // on open+ext. Hence why openQ is phred score indicating if the base is real // or an over/under-call. (high openQ means high trust in base) return q < qh? q : qh; } // Part of bcf_call_gap_prep. // // Scans the pileup to identify all the different sizes of indels // present. // types[] returned is sorted by size, from smallest (maybe negative) to largest. // // Returns types and fills out n_types_r, max_rd_len_r and ref_type_r, // or NULL on error. static int *bcf_cgp_find_types(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, int *max_rd_len_r, int *n_types_r, int *ref_type_r, int *N_r) { int i, j, t, s, N, m, max_rd_len, n_types; int n_alt = 0, n_tot = 0, indel_support_ok = 0; uint32_t *aux; int *types; // N is the total number of reads for (s = N = 0; s < n; ++s) N += n_plp[s]; bca->max_support = bca->max_frac = 0; aux = (uint32_t*) calloc(N + 1, 4); if (!aux) return NULL; m = max_rd_len = 0; aux[m++] = MINUS_CONST; // zero indel is always a type (REF) // Fill out aux[] array with all the non-zero indel sizes. // Also tally number with indels (n_alt) and total (n_tot). for (s = 0; s < n; ++s) { int na = 0, nt = 0; for (i = 0; i < n_plp[s]; ++i) { const bam_pileup1_t *p = plp[s] + i; ++nt; if (p->indel != 0) { ++na; aux[m++] = MINUS_CONST + p->indel; } // FIXME: cache me in pileup struct. j = bam_cigar2qlen(p->b->core.n_cigar, bam_get_cigar(p->b)); if (j > max_rd_len) max_rd_len = j; } double frac = (double)na/nt; if ( !indel_support_ok && na >= bca->min_support && frac >= bca->min_frac ) indel_support_ok = 1; if ( na > bca->max_support && frac > 0 ) bca->max_support = na, bca->max_frac = frac; n_alt += na; n_tot += nt; } // Sort aux[] and dedup ks_introsort(uint32_t, m, aux); for (i = 1, n_types = 1; i < m; ++i) if (aux[i] != aux[i-1]) ++n_types; // Taking totals makes it hard to call rare indels (IMF filter) if ( !bca->per_sample_flt ) indel_support_ok = ( (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support ) ? 0 : 1; if ( n_types == 1 || !indel_support_ok ) { // then skip free(aux); return NULL; } // Bail out if we have far too many types of indel if (n_types >= MAX_TYPES) { free(aux); // TODO revisit how/whether to control printing this warning if (hts_verbose >= 2) fprintf(stderr, "[%s] excessive INDEL alleles at position %d. " "Skip the position.\n", __func__, pos + 1); return NULL; } // To prevent long stretches of N's to be mistaken for indels // (sometimes thousands of bases), check the number of N's in the // sequence and skip places where half or more reference bases are Ns. int nN=0, i_end = pos + (2*bca->indel_win_size < max_rd_len ?2*bca->indel_win_size : max_rd_len); for (i=pos; i(i-pos) ) { free(aux); return NULL; } // Finally fill out the types[] array detailing the size of insertion // or deletion. types = (int*)calloc(n_types, sizeof(int)); if (!types) { free(aux); return NULL; } t = 0; for (i = 0; i < m; ++i) { int sz = (int32_t)(aux[i] - MINUS_CONST); int j; for (j = i+1; j < m; j++) if (aux[j] != aux[i]) break; if (sz == 0 || (j-i >= bca->min_support && // Note, doesn't handle bca->per_sample_flt yet (bca->per_sample_flt || (double)(j-i) / n_tot >= bca->min_frac))) types[t++] = sz; i = j-1; } free(aux); if (t <= 1) { free(types); return NULL; } n_types = t; // Find reference type; types[?] == 0) for (t = 0; t < n_types; ++t) if (types[t] == 0) break; *ref_type_r = t; *n_types_r = n_types; *max_rd_len_r = max_rd_len; *N_r = N; return types; } // Increment ins["str"] and freq["str"] #define NI 100 // number of alternative insertion sequences // Could use a hash table too, but expectation is a tiny number of alternatives typedef struct { char *str[NI]; int len[NI]; int freq[NI]; } str_freq; static int bcf_cgp_append_cons(str_freq *sf, char *str, int len, int freq) { int j; for (j = 0; j < NI && sf->str[j]; j++) { if (sf->len[j] == len && memcmp(sf->str[j], str, len) == 0) break; } if (j >= NI) return 0; // too many choices; discard sf->freq[j]+=freq; if (!sf->str[j]) { // new insertion if (!(sf->str[j] = malloc(len+1))) return -1; memcpy(sf->str[j], str, len); sf->len[j] = len; } return 0; } /* * Compute the consensus for a specific indel type at pos. * * left_shift is the number of inserted(+) or deleted(-) bases added to * the consensus before we get to pos. This is necessary so the alignment * band is correct as it's expected to start at left/right edges in * sync * * We accumulate into several buffers for counting base types: * cons_base - consensus of data with p->indel == type, bases or gap * ref_base - consensus of data with p->indel != type, bases or gap * cons_ins - consensus of data with p->indel == type, insertions * ref_ins - consensus of data with p->indel == type, bases or gap * * The purpose of cons_ins vs cons_base is if we have very low * coverage due to nearly all reads being another type, then we can * still get a robust consensus using the other data. If we don't * have shallow data, then we'll not use as much of ref_base as we may * have correlated variants. * * Eg: * REF: AGCTATGAGGCTGATA * SEQ: AGGTAGGAGGGTGATA (x1) * SEQ: AGCTACGAGG*TGATA (x24) * SEQ: AGCTACTAGG*TGATA (x24) * * Cons for no-del is Cs not Gs. Cannot trust it, so use N if shallow. * CON: AGCTACNAGGGTGATA * * There are still some problems in cons_ins vs ref_ins assignment. * We sometimes seem multiple similar-length insertions added at * different locations. Ideally we'd like to consider these as all * the same insertion if the size is the same and it's comparable seq. */ #define MAX_INS 8192 static char **bcf_cgp_consensus(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, int ref_len, int left, int right, int sample, int type, int biggest_del, int *left_shift, int *right_shift, int *band, int *tcon_len, int *cpos_pos, int pos_l, int pos_r) { // Map ASCII ACGTN* to 012345 static uint8_t base6[256] = { 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,5,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, //A C G *^ T 4,0,4,1,4,4,4,2, 4,4,4,4,4,4,4,4, 4,4,4,4,3,3,4,4, 4,4,4,4,4,4,4,4, 4,0,4,1,4,4,4,2, 4,4,4,4,4,4,4,4, 4,4,4,4,3,3,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, }; // single base or del int (*cons_base)[6] = calloc(right - left + 1, sizeof(*cons_base)); // multi-base insertions str_freq *cons_ins = calloc(right - left + 1, sizeof(*cons_ins)); // non-indel ref for all reads on this sample, rather than those just // matching type. We use this for handling the case where we have a // homozygous deletion being studied, but with 1 or 2 reads misaligned // and containing a base there. // // Eg if the type[]=0 consensus is made up of a very small sample size, // which is also enriched for highly error prone data. We can use // the other reads from type[] != 0 to flesh out the consensus and // improve accuracy. int (*ref_base)[6] = calloc(right - left + 1, sizeof(*ref_base)); str_freq *ref_ins = calloc(right - left + 1, sizeof(*ref_ins)); int i, j, k, s = sample; char **cons = NULL; if (!cons_base || !cons_ins || !ref_base || !ref_ins) goto err; //-------------------------------------------------- // Accumulate sequences into cons_base and cons_ins arrays int local_band_max = 0; // maximum absolute deviation from diagonal int total_span_str = 0; int type_depth = 0; for (i = 0; i < n_plp[s]; i++) { const bam_pileup1_t *p = plp[s] + i; bam1_t *b = p->b; int x = b->core.pos; // ref coordinate int y = 0; // seq coordinate uint32_t *cigar = bam_get_cigar(b); uint8_t *seq = bam_get_seq(b); int local_band = 0; // current deviation from diagonal for (k = 0; k < b->core.n_cigar; ++k) { int op = cigar[k] & BAM_CIGAR_MASK; int len = cigar[k] >> BAM_CIGAR_SHIFT; int base; int skip_to = 0; switch(op) { case BAM_CSOFT_CLIP: y += len; break; case BAM_CMATCH: case BAM_CEQUAL: case BAM_CDIFF: { // Can short-cut this with j_start and j_end based on // x+len and left,right for (j = 0; j < len; j++, x++, y++) { if (x < left) continue; if (x >= right) break; base = bam_seqi(seq, y); if (p->indel == type) // Convert 4-bit base ambig code to 0,1,2,3,4 range cons_base[x-left][seq_nt16_int[base]]++; else if (x != pos+1) // indel being assessed question ref_base[x-left][seq_nt16_int[base]]++; } break; } case BAM_CINS: { if (x >= left && x < right) { local_band += p->indel; if (local_band_max < local_band) local_band_max = local_band; } char ins[MAX_INS]; for (j = 0; j < len; j++, y++) { if (x < left) continue; if (x >= right) break; base = bam_seqi(seq, y); if (j < MAX_INS) ins[j] = seq_nt16_int[base]; } // Insertions come before a ref match. // 5I 5M is IIIIIM M M M M events, not // {IIIII,M} M M M M choice. So we need to include the // next match in our sequence when choosing the consensus. if (x >= left && x < right) { int ilen = jindel == type /*&& x == pos+1*/) { // Assume any ins of the same size is the same ins. // (This rescues misaligned insertions.) if (bcf_cgp_append_cons(&cons_ins[x-left], ins, ilen, 1) < 0) goto err; type_depth += (x == pos+1); } else if (x != pos+1){ if (bcf_cgp_append_cons(&ref_ins[x-left], ins, ilen, 1) < 0) goto err; } } break; } case BAM_CDEL: if (x >= left && x < right) { local_band += p->indel; if (local_band_max < -local_band) local_band_max = -local_band; } // Maybe not perfect for I/D combos, but likely sufficient. for (j = 0; j < len; j++, x++) { if (x < left) continue; if (x >= right) break; if ((p->indel == type && !p->is_del) || // starts here (p->indel == 0 && p->is_del && len == -type)) { // left cons_base[x-left][5]++; type_depth += (x == pos+1); } else if (x+len <= pos+1 || (skip_to && x > skip_to)) ref_base[x-left][5]++; else if (x <= pos && x+len > pos+1) { // we have a deletion which overlaps pos, but // isn't the same "type". We don't wish to // include these as they may bias the // evaluation by confirming against a // secondary consensus produced with the other // deletion. We set a marker for how long to // skip adding to ref_base. if (x > skip_to) skip_to = x+len; } } break; } } if (b->core.pos <= pos_l && x >= pos_r) total_span_str++; // Also track the biggest deviation +/- from diagonal. We use // this band observation in our BAQ alignment step. if (*band < local_band_max) *band = local_band_max; } //-------------------------------------------------- // Expand cons_base to include depth from ref_base/ref_ins // Caveat: except at pos itself, where true ref is used if type != 0 #if 1 // TEST 1 // We could retest this heuristic further maybe. for (i = 0; i < right-left; i++) { // Total observed depth int t = cons_base[i][0] + cons_base[i][1] + cons_base[i][2] + cons_base[i][3] + cons_base[i][4] + cons_base[i][5]; for (j = 0; j < NI; j++) { if (!cons_ins[i].str[j]) break; t += cons_ins[i].freq[j]; } // Similarly for depth on the non-ALT calls (NB: not necessarily // REF as maybe it's other ALTs). int r = ref_base[i][0] + ref_base[i][1] + ref_base[i][2] + ref_base[i][3] + ref_base[i][4] + ref_base[i][5]; for (j = 0; j < NI; j++) { if (!ref_ins[i].str[j]) break; r += ref_ins[i].freq[j]; } // When evaluating this particular indel, we don't want to // penalise alignments by SNP errors elsewhere. This can // happen when we have low depth for a particular 'type'. // // So add in a little data from ref_base/ref_ins. double rfract = (r - t*2)*.75 / (r+1); if (rfract < 1.01 / (r+1e-10)) rfract = 1.01 / (r+1e-10); // low depth compensation // if (rfract > 0.2) // rfract = 0.2; // TODO: consider limiting rfract so we never drown out the // signal. We want to use the remaining data only to correct // for sequencing errors in low depth alleles. If we get // conflicts, it's better to use N than to change a base // incase that variant is genuine. if (i+left >= pos+1 && i+left < pos+1-biggest_del) { // We're overlapping the current indel region, so // we don't wish to bring in evidence from the other // "type" data as it'll harm calling. continue; } else { // Otherwise add in a portion of other data to // boost low population numbers. cons_base[i][0] += rfract * ref_base[i][0]; cons_base[i][1] += rfract * ref_base[i][1]; cons_base[i][2] += rfract * ref_base[i][2]; cons_base[i][3] += rfract * ref_base[i][3]; cons_base[i][4] += rfract * ref_base[i][4]; cons_base[i][5] += rfract * ref_base[i][5]; } // Similarly for insertions too; consider a different rfract here? for (j = 0; j < NI; j++) { if (!ref_ins[i].str[j]) break; if (bcf_cgp_append_cons(&cons_ins[i], ref_ins[i].str[j], ref_ins[i].len[j], rfract * ref_ins[i].freq[j]) < 0) goto err; } } #endif //-------------------------------------------------- // Allocate consensus buffer, to worst case length int max_len = right-left; for (i = 0; i < right-left; i++) { if (!cons_ins[i].str[0]) continue; int ins = 0; for (j = 0; j < NI; j++) { if (!cons_ins[i].str[j]) break; if (cons_ins[i].str[j] && ins < cons_ins[i].len[j]) ins = cons_ins[i].len[j]; } max_len += ins; } max_len += MAX(0, type); // incase type inserted bases never occur cons = malloc((max_len+1)*2 + sizeof(char *)*2); if (!cons) goto err; cons[0] = (char *)&cons[2]; cons[1] = cons[0] + max_len+1; //-------------------------------------------------- // Merge insertions where they are the same length but different // sequences. // NB: we could just index by length and have accumulators for each, // instead of storing separately and merging later (here). // Ie str_freq.str is [NI][5] instead. for (i = 0; i < right-left; i++) { int ins[MAX_INS][5]; for (j = 0; j < NI; j++) { if (!cons_ins[i].str[j]) break; if (cons_ins[i].freq[j] == 0) continue; // already merged int l; for (l = 0; l < cons_ins[i].len[j]; l++) { // Append to relevant frequency counter, zero all others ins[l][0] = ins[l][1] = ins[l][2] = ins[l][3] = ins[l][4] = 0; uint8_t b = cons_ins[i].str[j][l]; ins[l][b] = cons_ins[i].freq[j]; } // Merge other insertions of the same length to ins[] counters for (k = j+1; k < NI; k++) { if (!cons_ins[i].str[k]) break; if (cons_ins[i].len[k] != cons_ins[i].len[j]) continue; if (cons_ins[i].freq[k] == 0) continue; // redundant? // Merge str[j] and str[k] for (l = 0; l < cons_ins[i].len[k]; l++) { uint8_t b = cons_ins[i].str[k][l]; ins[l][b] += cons_ins[i].freq[k]; } cons_ins[i].freq[j] += cons_ins[i].freq[k]; cons_ins[i].freq[k] = 0; } // Now replace ins[j] with the consensus insertion of this len. for (l = 0; l < cons_ins[i].len[j]; l++) { int max_v = 0, base = 0; int tot = ins[l][0] + ins[l][1] + ins[l][2] + ins[l][3] + ins[l][4]; if (max_v < ins[l][0]) max_v = ins[l][0], base = 0; if (max_v < ins[l][1]) max_v = ins[l][1], base = 1; if (max_v < ins[l][2]) max_v = ins[l][2], base = 2; if (max_v < ins[l][3]) max_v = ins[l][3], base = 3; if (max_v < ins[l][4]) max_v = ins[l][4], base = 4; cons_ins[i].str[j][l] = (max_v > 0.6*tot) ? base : 4; } } } #define CONS_CUTOFF .40 // % needed for base vs N #define CONS_CUTOFF_DEL .35 // % to include any het del #define CONS_CUTOFF2 .80 // % needed for gap in cons[1] #define CONS_CUTOFF_INC .35 // % to include any insertion cons[0] #define CONS_CUTOFF_INC2 .80 // % to include any insertion cons[1] HOM #define CONS_CUTOFF_INS .60 // and then 60% needed for it to be bases vs N //-------------------------------------------------- // Walk through the frequency arrays to call the consensus. // We produce cons[0] and cons[1]. Both include strongly // homozygous indels. Both also include the indel at 'pos'. // However for heterozygous indels we call the most likely event // for cons[0] and the less-likely alternative in cons[1]. // TODO: a proper phase analysis so multiple events end up // combining together into the correct consensus. *left_shift = 0; *right_shift = 0; int cnum; // Het call filled out in cnum==0 (+ve or -ve). // Used in cnum==1 to do the opposite of whichever way we did before. int heti[MAX_INS] = {0}, hetd[MAX_INS] = {0}; *cpos_pos = -1; for (cnum = 0; cnum < 2; cnum++) { for (i = k = 0; i < right-left; i++) { // Location in consensus matching the indel itself if (i >= pos-left+1 && *cpos_pos == -1) *cpos_pos = k; int max_v = 0, max_v2 = 0, max_j = 4, max_j2 = 4, tot = 0; for (j = 0; j < 6; j++) { // Top 2 consensus calls if (max_v < cons_base[i][j]) { max_v2 = max_v, max_j2 = max_j; max_v = cons_base[i][j], max_j = j; } else if (max_v2 < cons_base[i][j]) { max_v2 = cons_base[i][j], max_j2 = j; } tot += cons_base[i][j]; } // +INS int max_v_ins = 0, max_j_ins = 0; int tot_ins = 0; for (j = 0; j < NI; j++) { if (i+left==pos+1) if (type > 0 && i+left == pos+1 && cons_ins[i].len[j] < type && j == 0) { cons_ins[i].str[j] = realloc(cons_ins[i].str[j], type); if (!cons_ins[i].str[j]) goto err; memset(cons_ins[i].str[j] + cons_ins[i].len[j], 4, type - cons_ins[i].len[j]); cons_ins[i].len[j] = type; } if (!cons_ins[i].str[j]) break; if (cons_ins[i].freq[j] == 0) continue; // previously merged if (max_v_ins < cons_ins[i].freq[j]) //if (i != pos-left+1 || cons_ins[i].len[j] == type) max_v_ins = cons_ins[i].freq[j], max_j_ins = j; tot_ins += cons_ins[i].freq[j]; } // NB: tot is based on next matching base, so it includes // everything with or without the insertion. int tot_sum = tot; int always_ins = (i == pos-left+1 && type>0) || // current eval max_v_ins > CONS_CUTOFF_INC2*tot_sum;// HOM int het_ins = 0; if (!always_ins && max_v_ins >= bca->min_support) { // Candidate HET ins. if (cnum == 0) { het_ins = max_v_ins > CONS_CUTOFF_INC * tot_sum; if (i < MAX_INS) heti[i] = het_ins ? 1 : (max_v_ins > .3*tot_sum ? -1:0); } else { // HET but uncalled before het_ins = i < MAX_INS ? (heti[i] == -1) : 0; } } if (always_ins || het_ins) { if (max_v_ins > CONS_CUTOFF_INS*tot_ins) { // Insert bases for (j = 0; j < cons_ins[i].len[max_j_ins]; j++) { if (cnum == 0) { if (k < pos-left+*left_shift) (*left_shift)++; else (*right_shift)++; } cons[cnum][k++] = cons_ins[i].str[max_j_ins][j]; } } else { for (j = 0; j < cons_ins[i].len[max_j_ins]; j++) cons[cnum][k++] = 4; // 'N'; } } // Call deletions & bases int always_del = (type < 0 && i > pos-left && i <= pos-left-type) || cons_base[i][5] > CONS_CUTOFF2 * tot; // HOM del int het_del = 0; if (!always_del && cons_base[i][5] >= bca->min_support) { // Candidate HET del. if (cnum == 0) { int tot2 = tot; if (i > pos-left && i <= pos-left-biggest_del) tot2 = total_span_str - type_depth; het_del = cons_base[i][5] >= CONS_CUTOFF_DEL * tot2; if (i < MAX_INS) { if (i > pos-left && i <= pos-left-biggest_del) hetd[i] = 0; else hetd[i] = het_del ? 1 : (cons_base[i][5] >= .3 * tot2 ? -1 : 0); } } else { // HET del uncalled on cnum 0 het_del = i < MAX_INS ? (hetd[i] == -1) : 0; if (max_j == 5 && het_del == 0) { max_v = max_v2; max_j = max_j2; } } } if (always_del || het_del) { // Deletion if (k < pos-left+*left_shift) (*left_shift)--; else (*right_shift)++; } else { // Finally the easy case - a non-indel base or an N if (max_v > CONS_CUTOFF*tot) cons[cnum][k++] = max_j; // "ACGTN*" else if (max_v > 0) cons[cnum][k++] = 4; // 'N'; else { cons[cnum][k] = left+k < ref_len ? base6[(uint8_t)ref[left+k]] : 4; k++; } } } tcon_len[cnum] = k; } // TODO: replace by io_lib's string pool for rapid tidying. // For now this isn't the bottleneck though. for (i = 0; i < right-left; i++) { for (j = 0; j < NI; j++) { if (cons_ins[i].str[j]) free(cons_ins[i].str[j]); if (ref_ins[i].str[j]) free(ref_ins[i].str[j]); } } err: free(cons_base); free(ref_base); free(cons_ins); free(ref_ins); return cons; } // A rename of bcf_cgp_calc_cons from bam2bcf_indel.c // // Compute the insertion consensus for this sample 's' via a basic // majority rule. // // TODO: merge this into bcf_cgp_consensus as another return value? static char *bcf_cgp_calc_ins_cons(int n, int *n_plp, bam_pileup1_t **plp, int pos, int *types, int n_types, int max_ins, int s) { return bcf_cgp_calc_cons(n, n_plp, plp, pos, types, n_types, max_ins, s); } #define MAX(a,b) ((a)>(b)?(a):(b)) #define MIN(a,b) ((a)<(b)?(a):(b)) // Compile with LIBS="-L. -ldl -ledlib" CLD=g++ // This is faster than ksw and BAQ, meaning we can use larger --indel-size and // get a more accurate context, improving alignments further. This *may* // compensate for reduced sensitivity. #include "edlib.h" int edlib_glocal(uint8_t *ref, int l_ref, uint8_t *query, int l_query, double m, double del_bias) { EdlibAlignConfig cfg = edlibNewAlignConfig( //ABS(type)+ABS(l_ref-l_query)+10, -1, // k; use small positive for faster alignment EDLIB_MODE_HW, // mode #ifdef ALIGN_DEBUG EDLIB_TASK_PATH, #else EDLIB_TASK_LOC, #endif NULL, // additionalEqualities 0); // additionalEqualitiesLength EdlibAlignResult r = edlibAlign((char *)query, l_query, (char *)ref, l_ref, cfg); if (r.status != EDLIB_STATUS_OK || r.numLocations < 1 || !r.endLocations || !r.startLocations) { edlibFreeAlignResult(r); return INT_MAX; } #ifdef ALIGN_DEBUG // NB: Needs linking against the C++ libedlib.a as our cut-down C // implementation misses the alignment generation code. { int i, j = 0, pt = r.startLocations[0], pq = 0; char line1[80]; char line2[80]; char line3[80]; for (i = 0; i < r.alignmentLength && pt < r.endLocations[0]; i++) { int n; switch (n = r.alignment[i]) { case 0: // match case 3: // mismatch line1[j] = "ACGTN"[ref[pt++]]; line2[j] = "ACGTN"[query[pq++]]; line3[j] = " x"[n==3]; break; case 2: // insertion to ref line1[j] = "ACGTN"[ref[pt++]]; line2[j] = '-'; line3[j] = '-'; break; case 1: // insertion to query line1[j] = '-'; line2[j] = "ACGTN"[query[pq++]]; line3[j] = '+'; break; } if (++j == sizeof(line1)) { fprintf(stderr, "%.*s\n", j, line1); fprintf(stderr, "%.*s\n", j, line2); fprintf(stderr, "%.*s\n", j, line3); j = 0; } } if (j) { fprintf(stderr, "%.*s\n", j, line1); fprintf(stderr, "%.*s\n", j, line2); fprintf(stderr, "%.*s\n", j, line3); } } #endif // Aligned target length minus query length is an indication of the number // of insertions and/or deletions. // // For CIGAR 10M1I10M t_len > l_query ("AC" / "ATC") // For CIGAR 10M1D10M t_len < l_query ("ATC" / "AC") // Hence t_len-l_query is -ve for net insertions and +ve for net deletions. // If we compute nins and ndel directly via walking though EDLIB_TASK_PATH // we'll see t_len-l_query == ndel-nins. // // If a technology has a significantly higher chance of making deletion // errors than insertion errors, then we would view deletions as less // indicative of this sequence not coming from this candidate allele than // if it had insertion (as the deletions are more likely to be errors // rather than real, relative to the insertions). Hence we can skew the // score by the net delta of num_del - num_ins. // // Note this is an approximation that doesn't account for multiple // insertions and deletions within the same sequence, but it is much faster // as it doesn't require EDLIB_TASK_PATH to be computed. // // Given editDistance is +1 for every mismatch, insertion and deletion, // provided the t_len-l_query multiplier < 1 then this is always +ve. int t_len = *r.endLocations - *r.startLocations + 1; int score = m*(r.editDistance - del_bias*(t_len - l_query)); edlibFreeAlignResult(r); return score; } // Part of bcf_call_gap_prep. // // Realign using BAQ to get an alignment score of a single read vs // a haplotype consensus. TODO: replace BAQ with something more robust. // // There are many coordinates, so let's explain them. // - left, right, tbeg, tend, r_start and r_end are in aligned reference // coordinates. // left/right start from pos +/- indel_win_size. // r_start/r_end are the BAM first and last mapped coord on the reference. // tbeg and tend are the intersection of the two. // - qbeg and qend are in BAM sequence coordinates // - qpos is in sequence coordinates, relative to qbeg. // // To see what this means, we have illustrations with coordinates // above the seqs in reference space and below the seqs in BAM seq space. // // Overlap left: // tbeg tend // r_start left pos r_end right // REF :..............|--------------------#------:--------------|... // SEQ :..............|--------------------#------| // 0 qbeg qpos qend // // Overlap right: // r_start tend // left tbeg pos right r_end // REF ...|--------------:-----#---------------------|...........: // SEQ |-----#---------------------|...........: // qbeg qpos qend // 0 // // The "-" sequence is the bit passed in. // Ie ref2 spans left..right and query spans qbeg..qend. // We need to adjust ref2 therefore to tbeg..tend. // // Fills out score // Returns 0 on success, // <0 on error static int bcf_cgp_align_score(bam_pileup1_t *p, bcf_callaux_t *bca, int type, int band, uint8_t *ref1, uint8_t *ref2, uint8_t *query, int r_start, int r_end, int tbeg, int tend1, int tend2, int left, int right, int qbeg, int qend, int pos, int qpos, int max_deletion, double qavg, double del_bias, int *score, int *str_len1_p, int *str_len2_p) { int atype = abs(type); int l, sc1, sc2; // Trim poly_Ns at ends of ref. // This helps to keep len(ref) and len(query) similar, to reduce // band size and reduce the chance of -ve BAQ scores. for (l = 0; l < tend1-tbeg && l < tend2-tbeg; l++) if (ref1[l + tbeg-left] != 4 || ref2[l + tbeg-left] != 4) break; if (l > atype) tbeg += l-atype; for (l = tend1-tbeg-1; l >= 0; l--) if (ref1[l + tbeg-left] != 4) break; l = tend1-tbeg-1 - l; if (l > atype) tend1 -= l-atype; for (l = tend2-tbeg-1; l >= 0; l--) if (ref2[l + tbeg-left] != 4) break; l = tend2-tbeg-1 - l; if (l > atype) { tend2 -= l-atype; } // The bottom 8 bits are length-normalised score while // the top bits are unnormalised. // // Try original cons and new cons and pick best. // This doesn't reduce FN much (infact maybe adds very slightly), // but it does reduce GT errors and is a slight reduction to FP. double mm = 30; // a const average qual for now. Could tune sc2 = edlib_glocal(ref2 + tbeg - left, tend2 - tbeg, query, qend - qbeg, mm, del_bias); if (tend1 != tend2 || memcmp((char *)ref1 + tbeg - left, (char *)ref2 + tbeg - left, tend1 - tbeg) != 0) sc1 = edlib_glocal(ref1 + tbeg - left, tend1 - tbeg, query, qend - qbeg, mm, del_bias); else sc1 = INT_MAX; // skip // Find the best of the two alignments if (sc1 < 0 && sc2 < 0) { *score = 0xffffff; return 0; } if (sc1 < 0) { // sc2 is already correct } else if (sc2 < 0) { sc2 = sc1; } else { // sc1 and sc2 both pass, so use best if (sc2 > sc1) sc2 = sc1; } // Sc is overall alignment score, in top 24 bits (SeqQ). It's based // purely on the scores for the whole alignment. // We also have a separate indel score in bottom 8 bits (IndelQ). // This is a function of all sorts of attributes of the candidate indel // itself, such as STR length and the presence of poor quality bases. // Used for adjusting indelQ below. Lower l is more likely to call // (--FN, ++FP). (NB CLI --indel_bias is 1/indel_bias var). // Starts as average score per base, and then adjusted based on seq // complexity / quality. l = .5*(100. * sc2 / (qend - qbeg) + .499); *score = (sc2<<8) | (int)MIN(255, l * bca->indel_bias * .5); return 0; } // Part of bcf_call_gap_prep. // // Returns n_alt on success // -1 on failure // TODO: almost identical to bam2bcf_indel.c's copy, so we could share // the code and add a check on bca->edlib. static int bcf_cgp_compute_indelQ(int n, int *n_plp, bam_pileup1_t **plp, bcf_callaux_t *bca, char *inscns, int l_run, int max_ins, int ref_type, int *types, int n_types, double qavg, int *score, int str_len1, int str_len2) { // FIXME: n_types has a maximum; no need to alloc - use a #define? int sc[MAX_TYPES], sumq[MAX_TYPES], s, i, j, t, K, n_alt, tmp; memset(sumq, 0, n_types * sizeof(int)); int sum_indelQ1[100] = {0}; // n int sum_indelQ2[100] = {0}; // n // Confusing variable naming and bit usage. // // score[] is low 8 bits normalised (by len) alignment score // top 24 bits full alignment score // This gets cast into "sct"; mnemonic score-per-indel-type. // // sc = (score<<6) | type (index to types[] array for indel size) // So sc>>14 = score>>(14-6) = score>>8. Ie full alignment score for (s = K = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i, ++K) { bam_pileup1_t *p = plp[s] + i; // Labelling is confusing here. // sct is short for score. // sc is score + t(type) // Why aren't these variable names reversed? int *sct = &score[K*n_types], seqQ, indelQ1=0, indelQ2=0, indelQ=0; for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t; for (t = 1; t < n_types; ++t) // insertion sort for (j = t; j > 0 && sc[j] < sc[j-1]; --j) tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp; #ifdef ALIGN_DEBUG fprintf(stderr, "READ %s\tscores ", bam_get_qname(p->b)); for (t = 0; t < n_types; ++t) { fprintf(stderr, "%+2d/%-3d ", types[sc[t]&0x3f], sc[t]>>14); } #endif /* errmod_cal() assumes that if the call is wrong, the * likelihoods of other events are equal. This is about * right for substitutions, but is not desired for * indels. To reuse errmod_cal(), I have to make * compromise for multi-allelic indels. */ if ((sc[0]&0x3f) == ref_type) { // sc >> 14 is the total score. It's been shifted by 8 // from normalised score and 6 from type. // &0x3f is type number // Best call is REF. Compare vs best indel indelQ = (sc[1]>>14) - (sc[0]>>14); seqQ = est_seqQ(bca, types[sc[1]&0x3f], l_run, str_len1); } else { // look for the reference type for (t = 0; t < n_types; ++t) { if ((sc[t]&0x3f) == ref_type) break; } indelQ = indelQ1 = (sc[t]>>14) - (sc[0]>>14); // fprintf(stderr, "IndelQ = %d: %d-%d", // indelQ, (sc[t]>>14), (sc[0]>>14)); // Best call is non-ref, compare vs next best non-ref, // or ref if it's just 2 choices (most common case). for (t = 1; t < n_types; t++) if ((sc[t]&0x3f) == ref_type) continue; else break; if (t == n_types) t--; // it's ref, but it'll do as next best. indelQ2 = (sc[t]>>14) - (sc[0]>>14); seqQ = est_seqQ(bca, types[sc[0]&0x3f], l_run, str_len1); #if 1 // TEST 3 indelQ = bca->vs_ref*indelQ1 + (1-bca->vs_ref)*indelQ2; #endif } // So we lower qual in some, but raise the average to keep FN/FP // ratios up. // Is this key diff for PacBio old vs new HiFi? indelQ /= bca->indel_bias*0.5; indelQ1 /= bca->indel_bias*0.5; // Or maybe just *2 if bca->poly_mqual and be done with it? // Or perhaps adjust the MIN(qavg/20, ...) to MIN(qavg/10) ? // Skew SeqQ and IndelQ based on a portion of the minimum quality // found within a homopolymer. This is useful where the quality // values are a bit mutable and move around in such data, but less // so on clocked sequencing technologies. // // Enabling this causes lots of GT errors on Illumina. // However on PacBio it's key to removal of false positives. // ONT and UG seem somewhere inbetween. if (bca->poly_mqual) { // TEST 4 int qpos = p->qpos, l; uint8_t *seq = bam_get_seq(p->b); uint8_t *qual = bam_get_qual(p->b); int min_q = qual[qpos]; // scan homopolymer left char baseL = bam_seqi(seq, qpos+1 < p->b->core.l_qseq ? qpos+1 : qpos); for (l = qpos; l >= 0; l--) { if (bam_seqi(seq, l) != baseL) break; if (min_q > qual[l]) min_q = qual[l]; } // scan homo-polymer right (including site of indel) char base = bam_seqi(seq, qpos+1); for (l = qpos+1; l < p->b->core.l_qseq; l++) { if (min_q > qual[l]) min_q = qual[l]; if (bam_seqi(seq, l) != base) break; } // We reduce -h so homopolymers get reduced likelihood of being // called, but then optionally increase or decrease from there // based on base quality. Hence lack of low quality bases in // homopolymer will rescue the score back again, reducing FNs. // The score factors here may also be machine specific, but for // now these work well (tuned on PB HiFi). seqQ += MIN(qavg/20, min_q - qavg/10); indelQ += MIN(qavg/20, min_q - qavg/5); indelQ1+= MIN(qavg/20, min_q - qavg/5); if (seqQ < 0) seqQ = 0; if (indelQ < 0) indelQ = 0; if (indelQ1< 0) indelQ1= 0; } // This is the length-normalised score from bcf_cgp_align_score tmp = sc[0]>>6 & 0xff; // reduce indelQ // high score = bad, low score = good; flip for indelQ // low normalised scores leave indelQ unmodified // high normalised scores set indelQ to 0 // inbetween scores have a linear scale from indelQ to 0 // Altering the MAGIC value below (originally 111, but chosen for unknown // reasons) is comparable to altering --indel-bias. #define TMP_MAGIC 255.0 indelQ = tmp > TMP_MAGIC? 0 : (int)((1. - tmp/TMP_MAGIC) * indelQ + .499); indelQ1= tmp > TMP_MAGIC? 0 : (int)((1. - tmp/TMP_MAGIC) * indelQ1+ .499); indelQ = MIN(indelQ, 255); indelQ1 = MIN(indelQ1, 255); // Doesn't really help accuracy, but permits -h to take // affect still. if (indelQ > seqQ) indelQ = seqQ; if (indelQ > 255) indelQ = 255; if (indelQ1> 255) indelQ1= 255; if (seqQ > 255) seqQ = 255; // Use 22 bits in total. // 0-7 IndelQ // 8-15 SeqQ // 16-22 Score-per-base p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ; sumq[sc[0]&0x3f] += indelQ; #ifdef ALIGN_DEBUG fprintf(stderr, "\t%d\t%d\n", indelQ, seqQ); #endif // Experiment in p->aux vs sumq. // One gives likelihood of an indel being here, while the other // is likelihood of a specific genotype? But which is which? sum_indelQ1[s] += indelQ1; sum_indelQ2[s] += indelQ; } } // Determine bca->indel_types[] and bca->inscns. // Sumq[0] is always reference. // Sumq[1] is best non-ref (and maybe better than ref) bca->maxins = max_ins; bca->inscns = (char*) realloc(bca->inscns, bca->maxins * 4); if (bca->maxins && !bca->inscns) return -1; for (t = 0; t < n_types; ++t) sumq[t] = sumq[t]<<6 | t; for (t = 1; t < n_types; ++t) // insertion sort for (j = t; j > 0 && sumq[j] > sumq[j-1]; --j) tmp = sumq[j], sumq[j] = sumq[j-1], sumq[j-1] = tmp; for (t = 0; t < n_types; ++t) // look for the reference type if ((sumq[t]&0x3f) == ref_type) break; if (t) { // then move the reference type to the first tmp = sumq[t]; for (; t > 0; --t) sumq[t] = sumq[t-1]; sumq[0] = tmp; } for (t = 0; t < 4; ++t) bca->indel_types[t] = B2B_INDEL_NULL; for (t = 0; t < 4 && t < n_types; ++t) { bca->indel_types[t] = types[sumq[t]&0x3f]; #ifdef ALIGN_DEBUG fprintf(stderr, "TYPE %+2d %d\n", types[t], sumq[t]>>6); #endif if (bca->maxins) // potentially an insertion memcpy(&bca->inscns[t * bca->maxins], &inscns[(sumq[t]&0x3f) * max_ins], bca->maxins); } // Update p->aux. // If per-alignment type isn't found, then indelQ/seqQ is 0, // otherwise unchanged. for (s = n_alt = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i) { bam_pileup1_t *p = plp[s] + i; int x = types[p->aux>>16&0x3f]; for (j = 0; j < 4; ++j) if (x == bca->indel_types[j]) break; p->aux = j<<16 | (j == 4? 0 : (p->aux&0xffff)); if ((p->aux>>16&0x3f) > 0) ++n_alt; #ifdef ALIGN_DEBUG fprintf(stderr, "FIN %s\t%d\t%d\t%d\n", bam_get_qname(p->b), (p->aux>>16)&0x3f, bca->indel_types[(p->aux>>16)&0x3f], p->aux&0xff); #endif } } return n_alt; } /* FIXME: with high number of samples, do we handle IMF correctly? Is it fraction of indels across entire data set, or just fraction for this specific sample? Needs to check bca->per_sample_flt (--per-sample-mF) opt. */ /* notes: - n .. number of samples - the routine sets bam_pileup1_t.aux of each read as follows: - 6: unused - 6: the call; index to bcf_callaux_t.indel_types .. (aux>>16)&0x3f - 8: estimated sequence quality .. (aux>>8)&0xff - 8: indel quality .. aux&0xff */ int bcf_edlib_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, int ref_len) { if (ref == 0 || bca == 0) return -1; int i, s, t, n_types, *types = NULL, max_rd_len, left, right, max_ins; int *score = NULL; int N, K, l_run, ref_type, n_alt = -1; char *inscns = NULL, *query = NULL; // determine if there is a gap for (s = N = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i) if (plp[s][i].indel != 0) break; if (i < n_plp[s]) break; } if (s == n) // there is no indel at this position. return -1; // Find average base quality over this region double qavg = 30, qsum = 0, qcount = 0; int qmax = 0; for (s = 0; s < n; s++) { for (i = 0; i < n_plp[s]; i++) { #define QWIN 50 bam_pileup1_t *p = plp[s] + i; int kstart = p->qpos - QWIN > 0 ? p->qpos - QWIN : 0; int kend = p->qpos + QWIN < p->b->core.l_qseq ? p->qpos + QWIN : p->b->core.l_qseq; uint8_t *qual = bam_get_qual(p->b); int k; for (k = kstart; k < kend; k++) { qsum += qual[k]; qcount++; if (qmax < qual[k]) qmax = qual[k]; } } } qavg = (qsum+1) / (qcount+1); // find out how many types of indels are present types = bcf_cgp_find_types(n, n_plp, plp, pos, bca, ref, &max_rd_len, &n_types, &ref_type, &N); if (!types) goto err; // calculate left and right boundary, based on type size for a bit more // speed. int max_indel = 20*MAX(ABS(types[0]), ABS(types[n_types-1])) + bca->indel_win_size/4; if (max_indel > bca->indel_win_size) max_indel = bca->indel_win_size; left = pos > max_indel ? pos - max_indel : 0; right = pos + max_indel; int del_size = types[0]<0 ? -types[0] : 0; right += del_size; // in case the alignments stand out the reference for (i = pos; i < right; ++i) if (ref[i] == 0) break; right = i; // compute the likelihood given each type of indel for each read max_ins = types[n_types - 1]; // max_ins is at least 0 // The length of the homopolymer run around the current position l_run = bcf_cgp_l_run(ref, pos); int l_run_base = seq_nt16_table[(uint8_t)ref[pos+1]]; int l_run_ins = 0; // construct the consensus sequence (minus indels, which are added later) if (max_ins > 0) { // TODO: replace filling inscns[] with calc_consensus return // so the merges of the insertion consensus for type[t] is // reported directly. (It may need adjustment to avoid N) inscns = bcf_cgp_calc_ins_cons(n, n_plp, plp, pos, types, n_types, max_ins, s); if (!inscns) return -1; } query = (char*) calloc(right - left + max_rd_len + max_ins + 2, 1); score = (int*) calloc(N * n_types, sizeof(int)); bca->indelreg = 0; double nqual_over_60 = bca->nqual / 60.0; int biggest_del = 0; int biggest_ins = 0; for (t = 0; t < n_types; t++) { if (biggest_del > types[t]) biggest_del = types[t]; if (biggest_ins < types[t]) biggest_ins = types[t]; } int band = biggest_ins - biggest_del; // NB del is -ve // Find left & right extents of STR covering pos, from ref int pos_l = pos, pos_r = pos; { rep_ele *reps, *elt, *tmp; int pstart = MAX(0, pos-30); int pmid = pos-pstart; int pend = MIN(ref_len, pos+30); reps = find_STR((char *)&ref[pstart], pend-pstart, 0); DL_FOREACH_SAFE(reps, elt, tmp) { if (elt->end >= pmid && elt->start <= pmid) { if (pos_l > pstart + elt->start) pos_l = pstart + elt->start; if (pos_r < pstart + elt->end) pos_r = pstart + elt->end; } DL_DELETE(reps, elt); free(elt); } } int str_len1 = l_run, str_len2 = l_run/4; for (t = 0; t < n_types; ++t) { int l, ir; // Compute indelreg. This is the context in the reference. Eg: // // REF: AG--TTTC Inscns is "TT". // SEQ: AGTTTTTC Indelreg is 3; next 3 "TTT" bases // // => GTTT GTTTTT is call. if (types[t] == 0) ir = 0; else if (types[t] > 0) ir = est_indelreg(pos, ref, types[t], &inscns[t*max_ins]); else ir = est_indelreg(pos, ref, -types[t], 0); if (ir > bca->indelreg) bca->indelreg = ir; // Realignment score, computed via BAQ for (s = K = 0; s < n; ++s) { char **tcons; int left_shift, right_shift; int tcon_len[2]; int cpos_pos; tcons = bcf_cgp_consensus(n, n_plp, plp, pos, bca, ref, ref_len, left, right, s, types[t], biggest_del, &left_shift, &right_shift, &band, tcon_len, &cpos_pos, pos_l, pos_r); // TODO: Consensus for a deletion shouldn't match the // consensus for type 0. Eg consider // vv vv // REF: AATGTGTGAACAA REF: AATGTG--AACAA // T0: AATGTG--AACAA T0: AATGTG--AACAA // T-2: AA--TGTGAATAA T-2: AA--TGTGAATAA: // // On left: both T0 and T-2 are the same length, as it's // just a deletion that moved. We may end up assigning // reads to an indel allele based on the SNP they have and // not the actual indel. // There *is* a deletion here though, but only 1. How do // we call it once only? Need to replace entire region // with a reassembly. // // On right: T0 and T-2 have same length again, but there // isn't an indel as it's ins+del vs del+ins. They're // also the same length as the REF for this region. // Hence likelihood of this variant existing is tied in // with their equal and high similarity with/to the ref. // // We could do an alignment of tcons[0] and tcons[1] and check // whether their differences are consistent with (ie the // hamming distance is at least ABS(types[t]/2). I don't think // it'll rescue many FPs though. #ifdef CONS_DEBUG { int j; for (j = 0; j < 2; j++) { int k; fprintf(stderr, "Cons%d @ %d %4d/%4d ", j, pos, types[t], left_shift); for (k = 0; k < tcon_len[j]; k++) { if (k == cpos_pos) putc('#', stderr); putc("ACGTN"[(uint8_t)tcons[j][k]], stderr); } putc('\n', stderr); } } #endif // Scan for base-runs in the insertion. // We use this to avoid over-correction in est_seqQ when the // insertion is not part of the neighbouring homopolymer. int k = tcons[0][cpos_pos], j; for (j = 0; j < types[t]; j++) if (tcons[0][cpos_pos+j] != k) break; if (j && j == types[t]) l_run_ins |= "\x1\x2\x4\x8\xf"[k]; // ACGTN if (types[t] < 0) l_run_ins |= 0xff; // align each read to consensus(es) for (i = 0; i < n_plp[s]; ++i, ++K) { bam_pileup1_t *p = plp[s] + i; // Some basic ref vs alt stats. int imq = p->b->core.qual > 59 ? 59 : p->b->core.qual; imq *= nqual_over_60; int sc_len, slen, epos, sc_end; // Only need to gather stats on one type, as it's // identical calculation for all the subsequent ones // and we're sharing the same stats array if (t == 0) { // Gather stats for INFO field to aid filtering. // mq and sc_len not very helpful for filtering, but could // help in assigning a better QUAL value. // // Pos is slightly useful. // Base qual can be useful, but need qual prior to BAQ? // May need to cache orig quals in aux tag so we can fetch // them even after mpileup step. get_pos(bca, p, &sc_len, &slen, &epos, &sc_end); assert(imq >= 0 && imq < bca->nqual); assert(epos >= 0 && epos < bca->npos); assert(sc_len >= 0 && sc_len < 100); if (p->indel) { bca->ialt_mq[imq]++; bca->ialt_scl[sc_len]++; bca->ialt_pos[epos]++; } else { bca->iref_mq[imq]++; bca->iref_scl[sc_len]++; bca->iref_pos[epos]++; } } int qbeg, qpos, qend, tbeg, tend, kk; uint8_t *seq = bam_get_seq(p->b); uint32_t *cigar = bam_get_cigar(p->b); if (p->b->core.flag & BAM_FUNMAP) continue; // FIXME: the following loop should be better moved outside; // nonetheless, realignment should be much slower anyway. for (kk = 0; kk < p->b->core.n_cigar; ++kk) if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP) break; if (kk < p->b->core.n_cigar) continue; // determine the start and end of sequences for alignment int left2 = left, right2 = right; int min_win_size = MAX(-biggest_del, biggest_ins); min_win_size += ABS(left_shift) + ABS(right_shift); { rep_ele *reps, *elt, *tmp; reps = find_STR(tcons[0], tcon_len[0], 0); //int max_str = 0; int tot_str = 0; DL_FOREACH_SAFE(reps, elt, tmp) { // if (max_str < elt->end - elt->start) // max_str = elt->end - elt->start; tot_str += elt->end - elt->start; DL_DELETE(reps, elt); free(elt); } // Ideally max_str should be enough, but it's still not // sufficient in longer range some repeats. //min_win_size += max_str; min_win_size += tot_str; } min_win_size += 10; // TEST 8 if (p->b->core.l_qseq > 1000) { // long read data needs less context. It also tends to // have many more candidate indels to investigate so // speed here matters more. if (pos - left >= min_win_size) left2 = MAX(left2, pos - min_win_size); if (right-pos >= min_win_size) right2 = MIN(right2, pos + min_win_size); } // Genomic coords for first and last base of query // alignment. This is only used in bcf_cgp_align_score // for computing scores by looking for the proximity // of STRs with the end of the query alignment. int r_start = p->b->core.pos; int r_end = bam_cigar2rlen(p->b->core.n_cigar, bam_get_cigar(p->b)); r_end += -1 + r_start; // Map left2/right2 genomic coordinates to qbeg/qend // query coordinates. The query may not span the // entire left/right region, so this also returns the // equivalent genomic coords for qbeg/qend in tbeg/tend. qbeg = tpos2qpos(&p->b->core, bam_get_cigar(p->b), left2, 0, &tbeg); qpos = tpos2qpos(&p->b->core, bam_get_cigar(p->b), pos, 0, &tend) - qbeg; qend = tpos2qpos(&p->b->core, bam_get_cigar(p->b), right2, 1, &tend); int old_tend = tend; int old_tbeg = tbeg; // write the query sequence for (l = qbeg; l < qend; ++l) query[l - qbeg] = seq_nt16_int[bam_seqi(seq, l)]; // tbeg and tend are the genomic locations equivalent // to qbeg and qend on the sequence. // These may being entirely within our left/right // coordinates over which we've computed the // consensus, or overlapping to left/right. // // We know an estimation of band, plus biggest indel, // so we can trim tbeg/tend to a smaller region if we // wish here. This speeds up BAQ scoring. int wband = band + MAX(-biggest_del, biggest_ins)*2 + 20; int tend1 = left + tcon_len[0] - (left2-left); int tend2 = left + tcon_len[1] - (left2-left); tend1 = MIN(tend1, old_tend + wband); tend2 = MIN(tend2, old_tend + wband); tbeg = MAX(left2, old_tbeg - wband); // do realignment; this is the bottleneck. // // Note low score = good, high score = bad. if (tend1 > tbeg && tend2 > tbeg) { //fprintf(stderr, "Num %d\n", i); if (bcf_cgp_align_score(p, bca, types[t], band, (uint8_t *)tcons[0] + left2-left, (uint8_t *)tcons[1] + left2-left, (uint8_t *)query, r_start, r_end, tbeg, tend1, tend2, left2, left + tcon_len[0], qbeg, qend, pos,qpos, -biggest_del, qavg, bca->del_bias, &score[K*n_types + t], &str_len1, &str_len2) < 0) { goto err; } #ifdef ALIGN_DEBUG fprintf(stderr, "type %d %x / %x\t%s\n", types[t], score[K*n_types + t] >> 8, score[K*n_types + t] & 0xff, bam_get_qname(p->b)); #endif } else { // place holder large cost for reads that cover the // region entirely within a deletion (thus tend < tbeg). score[K*n_types + t] = 0xffffff; } } free(tcons); } } // compute indelQ if (!(l_run_base & l_run_ins)) l_run = 1; // different base type in ins to flanking region. n_alt = bcf_cgp_compute_indelQ(n, n_plp, plp, bca, inscns, l_run, max_ins, ref_type, types, n_types, qavg, score, str_len1, str_len2); err: // free free(query); free(score); free(types); free(inscns); return n_alt > 0? 0 : -1; } pysam-0.23.0/bcftools/bam2bcf_edlib.c.pysam.c000066400000000000000000002037321475062545500207340ustar00rootroot00000000000000#include "bcftools.pysam.h" /* bam2bcf_indel.c -- indel caller. Copyright (C) 2010, 2011 Broad Institute. Copyright (C) 2012-2014,2016-2017, 2021-2024 Genome Research Ltd. Author: Heng Li Petr Danecek James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ // Show consensus //#define CONS_DEBUG // Show alignments to consensus //#define ALIGN_DEBUG #include #include #include #include #include #include #include #include "bam2bcf.h" #include "str_finder.h" #include // Is there no way to share these between the 3 implementations? KSORT_INIT_STATIC_GENERIC(uint32_t) #define MINUS_CONST 0x10000000 #define MAX_TYPES 64 #ifndef MIN # define MIN(a,b) ((a)<(b)?(a):(b)) #endif #ifndef ABS # define ABS(a) ((a)<0?-(a):(a)) #endif #ifndef MAX # define MAX(a,b) ((a)>(b)?(a):(b)) #endif // l is the relative gap length and l_run is the length of the homopolymer // on the reference. // // Larger seqQ is good, so increasing tandemQ calls more indels, // and longer l_run means fewer calls. It is capped later at 255. // For short l_runs, the qual is simply based on size of indel // larger ones being considered more likely to be real. // Longer indels get assigned a score based on the relative indel size // to homopolymer, where l_run base will have already been verified by // the caller to ensure it's compatible. static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run, int str_len) { int q, qh; // Short indels are more likely sequencing error than large ones. // So "seqQ" scales with size of observation "l". // // Note openQ and extQ are error likelihoods in Phred scale. Hence high // openQ means we're very unlikely to miscall an indel. // Ie it's not the open/ext "costs" normally used in alignment; more the reverse. // // We use MIN(q,qh) below, so we can remove the q component by specifying // a large -o parameter in mpileup. q = bca->openQ + bca->extQ * (abs(l) - 1); // Orig method; best with Illumina (high openQ) // qh = bca->tandemQ * (double)abs(l) / l_run + .499; // Penalise longer homopolymers quadratically more, but boost shorter ones. // Best with CCS (low openQ) //qh = 2 * bca->tandemQ * pow((double)abs(l) / l_run, 1.5) + .499; // (l/l_run)^1.26 for openQ=25 or ^1 for openQ=40. // double openQ = MIN(40, bca->openQ); // qh = (30/openQ) * bca->tandemQ // * pow((double)abs(l) / l_run, 1/sqrt(openQ/40)) + .499; // Linear scaled on openQ too qh = bca->tandemQ * (double)abs(l) / l_run + .499; // Generic maybe ? // power = 1/sqrt(MIN(40,bca->openQ)/40.); // qh = ... * pow((double)abs(l)/l_run, power) // bam2bcf.c caps has "if q>seqQ) q=seqQ" so it caps base qual 'q'. // A 1bp indel would therefore have a maximum qual it could be considered based // on open+ext. Hence why openQ is phred score indicating if the base is real // or an over/under-call. (high openQ means high trust in base) return q < qh? q : qh; } // Part of bcf_call_gap_prep. // // Scans the pileup to identify all the different sizes of indels // present. // types[] returned is sorted by size, from smallest (maybe negative) to largest. // // Returns types and fills out n_types_r, max_rd_len_r and ref_type_r, // or NULL on error. static int *bcf_cgp_find_types(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, int *max_rd_len_r, int *n_types_r, int *ref_type_r, int *N_r) { int i, j, t, s, N, m, max_rd_len, n_types; int n_alt = 0, n_tot = 0, indel_support_ok = 0; uint32_t *aux; int *types; // N is the total number of reads for (s = N = 0; s < n; ++s) N += n_plp[s]; bca->max_support = bca->max_frac = 0; aux = (uint32_t*) calloc(N + 1, 4); if (!aux) return NULL; m = max_rd_len = 0; aux[m++] = MINUS_CONST; // zero indel is always a type (REF) // Fill out aux[] array with all the non-zero indel sizes. // Also tally number with indels (n_alt) and total (n_tot). for (s = 0; s < n; ++s) { int na = 0, nt = 0; for (i = 0; i < n_plp[s]; ++i) { const bam_pileup1_t *p = plp[s] + i; ++nt; if (p->indel != 0) { ++na; aux[m++] = MINUS_CONST + p->indel; } // FIXME: cache me in pileup struct. j = bam_cigar2qlen(p->b->core.n_cigar, bam_get_cigar(p->b)); if (j > max_rd_len) max_rd_len = j; } double frac = (double)na/nt; if ( !indel_support_ok && na >= bca->min_support && frac >= bca->min_frac ) indel_support_ok = 1; if ( na > bca->max_support && frac > 0 ) bca->max_support = na, bca->max_frac = frac; n_alt += na; n_tot += nt; } // Sort aux[] and dedup ks_introsort(uint32_t, m, aux); for (i = 1, n_types = 1; i < m; ++i) if (aux[i] != aux[i-1]) ++n_types; // Taking totals makes it hard to call rare indels (IMF filter) if ( !bca->per_sample_flt ) indel_support_ok = ( (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support ) ? 0 : 1; if ( n_types == 1 || !indel_support_ok ) { // then skip free(aux); return NULL; } // Bail out if we have far too many types of indel if (n_types >= MAX_TYPES) { free(aux); // TODO revisit how/whether to control printing this warning if (hts_verbose >= 2) fprintf(bcftools_stderr, "[%s] excessive INDEL alleles at position %d. " "Skip the position.\n", __func__, pos + 1); return NULL; } // To prevent long stretches of N's to be mistaken for indels // (sometimes thousands of bases), check the number of N's in the // sequence and skip places where half or more reference bases are Ns. int nN=0, i_end = pos + (2*bca->indel_win_size < max_rd_len ?2*bca->indel_win_size : max_rd_len); for (i=pos; i(i-pos) ) { free(aux); return NULL; } // Finally fill out the types[] array detailing the size of insertion // or deletion. types = (int*)calloc(n_types, sizeof(int)); if (!types) { free(aux); return NULL; } t = 0; for (i = 0; i < m; ++i) { int sz = (int32_t)(aux[i] - MINUS_CONST); int j; for (j = i+1; j < m; j++) if (aux[j] != aux[i]) break; if (sz == 0 || (j-i >= bca->min_support && // Note, doesn't handle bca->per_sample_flt yet (bca->per_sample_flt || (double)(j-i) / n_tot >= bca->min_frac))) types[t++] = sz; i = j-1; } free(aux); if (t <= 1) { free(types); return NULL; } n_types = t; // Find reference type; types[?] == 0) for (t = 0; t < n_types; ++t) if (types[t] == 0) break; *ref_type_r = t; *n_types_r = n_types; *max_rd_len_r = max_rd_len; *N_r = N; return types; } // Increment ins["str"] and freq["str"] #define NI 100 // number of alternative insertion sequences // Could use a hash table too, but expectation is a tiny number of alternatives typedef struct { char *str[NI]; int len[NI]; int freq[NI]; } str_freq; static int bcf_cgp_append_cons(str_freq *sf, char *str, int len, int freq) { int j; for (j = 0; j < NI && sf->str[j]; j++) { if (sf->len[j] == len && memcmp(sf->str[j], str, len) == 0) break; } if (j >= NI) return 0; // too many choices; discard sf->freq[j]+=freq; if (!sf->str[j]) { // new insertion if (!(sf->str[j] = malloc(len+1))) return -1; memcpy(sf->str[j], str, len); sf->len[j] = len; } return 0; } /* * Compute the consensus for a specific indel type at pos. * * left_shift is the number of inserted(+) or deleted(-) bases added to * the consensus before we get to pos. This is necessary so the alignment * band is correct as it's expected to start at left/right edges in * sync * * We accumulate into several buffers for counting base types: * cons_base - consensus of data with p->indel == type, bases or gap * ref_base - consensus of data with p->indel != type, bases or gap * cons_ins - consensus of data with p->indel == type, insertions * ref_ins - consensus of data with p->indel == type, bases or gap * * The purpose of cons_ins vs cons_base is if we have very low * coverage due to nearly all reads being another type, then we can * still get a robust consensus using the other data. If we don't * have shallow data, then we'll not use as much of ref_base as we may * have correlated variants. * * Eg: * REF: AGCTATGAGGCTGATA * SEQ: AGGTAGGAGGGTGATA (x1) * SEQ: AGCTACGAGG*TGATA (x24) * SEQ: AGCTACTAGG*TGATA (x24) * * Cons for no-del is Cs not Gs. Cannot trust it, so use N if shallow. * CON: AGCTACNAGGGTGATA * * There are still some problems in cons_ins vs ref_ins assignment. * We sometimes seem multiple similar-length insertions added at * different locations. Ideally we'd like to consider these as all * the same insertion if the size is the same and it's comparable seq. */ #define MAX_INS 8192 static char **bcf_cgp_consensus(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, int ref_len, int left, int right, int sample, int type, int biggest_del, int *left_shift, int *right_shift, int *band, int *tcon_len, int *cpos_pos, int pos_l, int pos_r) { // Map ASCII ACGTN* to 012345 static uint8_t base6[256] = { 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,5,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, //A C G *^ T 4,0,4,1,4,4,4,2, 4,4,4,4,4,4,4,4, 4,4,4,4,3,3,4,4, 4,4,4,4,4,4,4,4, 4,0,4,1,4,4,4,2, 4,4,4,4,4,4,4,4, 4,4,4,4,3,3,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4, }; // single base or del int (*cons_base)[6] = calloc(right - left + 1, sizeof(*cons_base)); // multi-base insertions str_freq *cons_ins = calloc(right - left + 1, sizeof(*cons_ins)); // non-indel ref for all reads on this sample, rather than those just // matching type. We use this for handling the case where we have a // homozygous deletion being studied, but with 1 or 2 reads misaligned // and containing a base there. // // Eg if the type[]=0 consensus is made up of a very small sample size, // which is also enriched for highly error prone data. We can use // the other reads from type[] != 0 to flesh out the consensus and // improve accuracy. int (*ref_base)[6] = calloc(right - left + 1, sizeof(*ref_base)); str_freq *ref_ins = calloc(right - left + 1, sizeof(*ref_ins)); int i, j, k, s = sample; char **cons = NULL; if (!cons_base || !cons_ins || !ref_base || !ref_ins) goto err; //-------------------------------------------------- // Accumulate sequences into cons_base and cons_ins arrays int local_band_max = 0; // maximum absolute deviation from diagonal int total_span_str = 0; int type_depth = 0; for (i = 0; i < n_plp[s]; i++) { const bam_pileup1_t *p = plp[s] + i; bam1_t *b = p->b; int x = b->core.pos; // ref coordinate int y = 0; // seq coordinate uint32_t *cigar = bam_get_cigar(b); uint8_t *seq = bam_get_seq(b); int local_band = 0; // current deviation from diagonal for (k = 0; k < b->core.n_cigar; ++k) { int op = cigar[k] & BAM_CIGAR_MASK; int len = cigar[k] >> BAM_CIGAR_SHIFT; int base; int skip_to = 0; switch(op) { case BAM_CSOFT_CLIP: y += len; break; case BAM_CMATCH: case BAM_CEQUAL: case BAM_CDIFF: { // Can short-cut this with j_start and j_end based on // x+len and left,right for (j = 0; j < len; j++, x++, y++) { if (x < left) continue; if (x >= right) break; base = bam_seqi(seq, y); if (p->indel == type) // Convert 4-bit base ambig code to 0,1,2,3,4 range cons_base[x-left][seq_nt16_int[base]]++; else if (x != pos+1) // indel being assessed question ref_base[x-left][seq_nt16_int[base]]++; } break; } case BAM_CINS: { if (x >= left && x < right) { local_band += p->indel; if (local_band_max < local_band) local_band_max = local_band; } char ins[MAX_INS]; for (j = 0; j < len; j++, y++) { if (x < left) continue; if (x >= right) break; base = bam_seqi(seq, y); if (j < MAX_INS) ins[j] = seq_nt16_int[base]; } // Insertions come before a ref match. // 5I 5M is IIIIIM M M M M events, not // {IIIII,M} M M M M choice. So we need to include the // next match in our sequence when choosing the consensus. if (x >= left && x < right) { int ilen = jindel == type /*&& x == pos+1*/) { // Assume any ins of the same size is the same ins. // (This rescues misaligned insertions.) if (bcf_cgp_append_cons(&cons_ins[x-left], ins, ilen, 1) < 0) goto err; type_depth += (x == pos+1); } else if (x != pos+1){ if (bcf_cgp_append_cons(&ref_ins[x-left], ins, ilen, 1) < 0) goto err; } } break; } case BAM_CDEL: if (x >= left && x < right) { local_band += p->indel; if (local_band_max < -local_band) local_band_max = -local_band; } // Maybe not perfect for I/D combos, but likely sufficient. for (j = 0; j < len; j++, x++) { if (x < left) continue; if (x >= right) break; if ((p->indel == type && !p->is_del) || // starts here (p->indel == 0 && p->is_del && len == -type)) { // left cons_base[x-left][5]++; type_depth += (x == pos+1); } else if (x+len <= pos+1 || (skip_to && x > skip_to)) ref_base[x-left][5]++; else if (x <= pos && x+len > pos+1) { // we have a deletion which overlaps pos, but // isn't the same "type". We don't wish to // include these as they may bias the // evaluation by confirming against a // secondary consensus produced with the other // deletion. We set a marker for how long to // skip adding to ref_base. if (x > skip_to) skip_to = x+len; } } break; } } if (b->core.pos <= pos_l && x >= pos_r) total_span_str++; // Also track the biggest deviation +/- from diagonal. We use // this band observation in our BAQ alignment step. if (*band < local_band_max) *band = local_band_max; } //-------------------------------------------------- // Expand cons_base to include depth from ref_base/ref_ins // Caveat: except at pos itself, where true ref is used if type != 0 #if 1 // TEST 1 // We could retest this heuristic further maybe. for (i = 0; i < right-left; i++) { // Total observed depth int t = cons_base[i][0] + cons_base[i][1] + cons_base[i][2] + cons_base[i][3] + cons_base[i][4] + cons_base[i][5]; for (j = 0; j < NI; j++) { if (!cons_ins[i].str[j]) break; t += cons_ins[i].freq[j]; } // Similarly for depth on the non-ALT calls (NB: not necessarily // REF as maybe it's other ALTs). int r = ref_base[i][0] + ref_base[i][1] + ref_base[i][2] + ref_base[i][3] + ref_base[i][4] + ref_base[i][5]; for (j = 0; j < NI; j++) { if (!ref_ins[i].str[j]) break; r += ref_ins[i].freq[j]; } // When evaluating this particular indel, we don't want to // penalise alignments by SNP errors elsewhere. This can // happen when we have low depth for a particular 'type'. // // So add in a little data from ref_base/ref_ins. double rfract = (r - t*2)*.75 / (r+1); if (rfract < 1.01 / (r+1e-10)) rfract = 1.01 / (r+1e-10); // low depth compensation // if (rfract > 0.2) // rfract = 0.2; // TODO: consider limiting rfract so we never drown out the // signal. We want to use the remaining data only to correct // for sequencing errors in low depth alleles. If we get // conflicts, it's better to use N than to change a base // incase that variant is genuine. if (i+left >= pos+1 && i+left < pos+1-biggest_del) { // We're overlapping the current indel region, so // we don't wish to bring in evidence from the other // "type" data as it'll harm calling. continue; } else { // Otherwise add in a portion of other data to // boost low population numbers. cons_base[i][0] += rfract * ref_base[i][0]; cons_base[i][1] += rfract * ref_base[i][1]; cons_base[i][2] += rfract * ref_base[i][2]; cons_base[i][3] += rfract * ref_base[i][3]; cons_base[i][4] += rfract * ref_base[i][4]; cons_base[i][5] += rfract * ref_base[i][5]; } // Similarly for insertions too; consider a different rfract here? for (j = 0; j < NI; j++) { if (!ref_ins[i].str[j]) break; if (bcf_cgp_append_cons(&cons_ins[i], ref_ins[i].str[j], ref_ins[i].len[j], rfract * ref_ins[i].freq[j]) < 0) goto err; } } #endif //-------------------------------------------------- // Allocate consensus buffer, to worst case length int max_len = right-left; for (i = 0; i < right-left; i++) { if (!cons_ins[i].str[0]) continue; int ins = 0; for (j = 0; j < NI; j++) { if (!cons_ins[i].str[j]) break; if (cons_ins[i].str[j] && ins < cons_ins[i].len[j]) ins = cons_ins[i].len[j]; } max_len += ins; } max_len += MAX(0, type); // incase type inserted bases never occur cons = malloc((max_len+1)*2 + sizeof(char *)*2); if (!cons) goto err; cons[0] = (char *)&cons[2]; cons[1] = cons[0] + max_len+1; //-------------------------------------------------- // Merge insertions where they are the same length but different // sequences. // NB: we could just index by length and have accumulators for each, // instead of storing separately and merging later (here). // Ie str_freq.str is [NI][5] instead. for (i = 0; i < right-left; i++) { int ins[MAX_INS][5]; for (j = 0; j < NI; j++) { if (!cons_ins[i].str[j]) break; if (cons_ins[i].freq[j] == 0) continue; // already merged int l; for (l = 0; l < cons_ins[i].len[j]; l++) { // Append to relevant frequency counter, zero all others ins[l][0] = ins[l][1] = ins[l][2] = ins[l][3] = ins[l][4] = 0; uint8_t b = cons_ins[i].str[j][l]; ins[l][b] = cons_ins[i].freq[j]; } // Merge other insertions of the same length to ins[] counters for (k = j+1; k < NI; k++) { if (!cons_ins[i].str[k]) break; if (cons_ins[i].len[k] != cons_ins[i].len[j]) continue; if (cons_ins[i].freq[k] == 0) continue; // redundant? // Merge str[j] and str[k] for (l = 0; l < cons_ins[i].len[k]; l++) { uint8_t b = cons_ins[i].str[k][l]; ins[l][b] += cons_ins[i].freq[k]; } cons_ins[i].freq[j] += cons_ins[i].freq[k]; cons_ins[i].freq[k] = 0; } // Now replace ins[j] with the consensus insertion of this len. for (l = 0; l < cons_ins[i].len[j]; l++) { int max_v = 0, base = 0; int tot = ins[l][0] + ins[l][1] + ins[l][2] + ins[l][3] + ins[l][4]; if (max_v < ins[l][0]) max_v = ins[l][0], base = 0; if (max_v < ins[l][1]) max_v = ins[l][1], base = 1; if (max_v < ins[l][2]) max_v = ins[l][2], base = 2; if (max_v < ins[l][3]) max_v = ins[l][3], base = 3; if (max_v < ins[l][4]) max_v = ins[l][4], base = 4; cons_ins[i].str[j][l] = (max_v > 0.6*tot) ? base : 4; } } } #define CONS_CUTOFF .40 // % needed for base vs N #define CONS_CUTOFF_DEL .35 // % to include any het del #define CONS_CUTOFF2 .80 // % needed for gap in cons[1] #define CONS_CUTOFF_INC .35 // % to include any insertion cons[0] #define CONS_CUTOFF_INC2 .80 // % to include any insertion cons[1] HOM #define CONS_CUTOFF_INS .60 // and then 60% needed for it to be bases vs N //-------------------------------------------------- // Walk through the frequency arrays to call the consensus. // We produce cons[0] and cons[1]. Both include strongly // homozygous indels. Both also include the indel at 'pos'. // However for heterozygous indels we call the most likely event // for cons[0] and the less-likely alternative in cons[1]. // TODO: a proper phase analysis so multiple events end up // combining together into the correct consensus. *left_shift = 0; *right_shift = 0; int cnum; // Het call filled out in cnum==0 (+ve or -ve). // Used in cnum==1 to do the opposite of whichever way we did before. int heti[MAX_INS] = {0}, hetd[MAX_INS] = {0}; *cpos_pos = -1; for (cnum = 0; cnum < 2; cnum++) { for (i = k = 0; i < right-left; i++) { // Location in consensus matching the indel itself if (i >= pos-left+1 && *cpos_pos == -1) *cpos_pos = k; int max_v = 0, max_v2 = 0, max_j = 4, max_j2 = 4, tot = 0; for (j = 0; j < 6; j++) { // Top 2 consensus calls if (max_v < cons_base[i][j]) { max_v2 = max_v, max_j2 = max_j; max_v = cons_base[i][j], max_j = j; } else if (max_v2 < cons_base[i][j]) { max_v2 = cons_base[i][j], max_j2 = j; } tot += cons_base[i][j]; } // +INS int max_v_ins = 0, max_j_ins = 0; int tot_ins = 0; for (j = 0; j < NI; j++) { if (i+left==pos+1) if (type > 0 && i+left == pos+1 && cons_ins[i].len[j] < type && j == 0) { cons_ins[i].str[j] = realloc(cons_ins[i].str[j], type); if (!cons_ins[i].str[j]) goto err; memset(cons_ins[i].str[j] + cons_ins[i].len[j], 4, type - cons_ins[i].len[j]); cons_ins[i].len[j] = type; } if (!cons_ins[i].str[j]) break; if (cons_ins[i].freq[j] == 0) continue; // previously merged if (max_v_ins < cons_ins[i].freq[j]) //if (i != pos-left+1 || cons_ins[i].len[j] == type) max_v_ins = cons_ins[i].freq[j], max_j_ins = j; tot_ins += cons_ins[i].freq[j]; } // NB: tot is based on next matching base, so it includes // everything with or without the insertion. int tot_sum = tot; int always_ins = (i == pos-left+1 && type>0) || // current eval max_v_ins > CONS_CUTOFF_INC2*tot_sum;// HOM int het_ins = 0; if (!always_ins && max_v_ins >= bca->min_support) { // Candidate HET ins. if (cnum == 0) { het_ins = max_v_ins > CONS_CUTOFF_INC * tot_sum; if (i < MAX_INS) heti[i] = het_ins ? 1 : (max_v_ins > .3*tot_sum ? -1:0); } else { // HET but uncalled before het_ins = i < MAX_INS ? (heti[i] == -1) : 0; } } if (always_ins || het_ins) { if (max_v_ins > CONS_CUTOFF_INS*tot_ins) { // Insert bases for (j = 0; j < cons_ins[i].len[max_j_ins]; j++) { if (cnum == 0) { if (k < pos-left+*left_shift) (*left_shift)++; else (*right_shift)++; } cons[cnum][k++] = cons_ins[i].str[max_j_ins][j]; } } else { for (j = 0; j < cons_ins[i].len[max_j_ins]; j++) cons[cnum][k++] = 4; // 'N'; } } // Call deletions & bases int always_del = (type < 0 && i > pos-left && i <= pos-left-type) || cons_base[i][5] > CONS_CUTOFF2 * tot; // HOM del int het_del = 0; if (!always_del && cons_base[i][5] >= bca->min_support) { // Candidate HET del. if (cnum == 0) { int tot2 = tot; if (i > pos-left && i <= pos-left-biggest_del) tot2 = total_span_str - type_depth; het_del = cons_base[i][5] >= CONS_CUTOFF_DEL * tot2; if (i < MAX_INS) { if (i > pos-left && i <= pos-left-biggest_del) hetd[i] = 0; else hetd[i] = het_del ? 1 : (cons_base[i][5] >= .3 * tot2 ? -1 : 0); } } else { // HET del uncalled on cnum 0 het_del = i < MAX_INS ? (hetd[i] == -1) : 0; if (max_j == 5 && het_del == 0) { max_v = max_v2; max_j = max_j2; } } } if (always_del || het_del) { // Deletion if (k < pos-left+*left_shift) (*left_shift)--; else (*right_shift)++; } else { // Finally the easy case - a non-indel base or an N if (max_v > CONS_CUTOFF*tot) cons[cnum][k++] = max_j; // "ACGTN*" else if (max_v > 0) cons[cnum][k++] = 4; // 'N'; else { cons[cnum][k] = left+k < ref_len ? base6[(uint8_t)ref[left+k]] : 4; k++; } } } tcon_len[cnum] = k; } // TODO: replace by io_lib's string pool for rapid tidying. // For now this isn't the bottleneck though. for (i = 0; i < right-left; i++) { for (j = 0; j < NI; j++) { if (cons_ins[i].str[j]) free(cons_ins[i].str[j]); if (ref_ins[i].str[j]) free(ref_ins[i].str[j]); } } err: free(cons_base); free(ref_base); free(cons_ins); free(ref_ins); return cons; } // A rename of bcf_cgp_calc_cons from bam2bcf_indel.c // // Compute the insertion consensus for this sample 's' via a basic // majority rule. // // TODO: merge this into bcf_cgp_consensus as another return value? static char *bcf_cgp_calc_ins_cons(int n, int *n_plp, bam_pileup1_t **plp, int pos, int *types, int n_types, int max_ins, int s) { return bcf_cgp_calc_cons(n, n_plp, plp, pos, types, n_types, max_ins, s); } #define MAX(a,b) ((a)>(b)?(a):(b)) #define MIN(a,b) ((a)<(b)?(a):(b)) // Compile with LIBS="-L. -ldl -ledlib" CLD=g++ // This is faster than ksw and BAQ, meaning we can use larger --indel-size and // get a more accurate context, improving alignments further. This *may* // compensate for reduced sensitivity. #include "edlib.h" int edlib_glocal(uint8_t *ref, int l_ref, uint8_t *query, int l_query, double m, double del_bias) { EdlibAlignConfig cfg = edlibNewAlignConfig( //ABS(type)+ABS(l_ref-l_query)+10, -1, // k; use small positive for faster alignment EDLIB_MODE_HW, // mode #ifdef ALIGN_DEBUG EDLIB_TASK_PATH, #else EDLIB_TASK_LOC, #endif NULL, // additionalEqualities 0); // additionalEqualitiesLength EdlibAlignResult r = edlibAlign((char *)query, l_query, (char *)ref, l_ref, cfg); if (r.status != EDLIB_STATUS_OK || r.numLocations < 1 || !r.endLocations || !r.startLocations) { edlibFreeAlignResult(r); return INT_MAX; } #ifdef ALIGN_DEBUG // NB: Needs linking against the C++ libedlib.a as our cut-down C // implementation misses the alignment generation code. { int i, j = 0, pt = r.startLocations[0], pq = 0; char line1[80]; char line2[80]; char line3[80]; for (i = 0; i < r.alignmentLength && pt < r.endLocations[0]; i++) { int n; switch (n = r.alignment[i]) { case 0: // match case 3: // mismatch line1[j] = "ACGTN"[ref[pt++]]; line2[j] = "ACGTN"[query[pq++]]; line3[j] = " x"[n==3]; break; case 2: // insertion to ref line1[j] = "ACGTN"[ref[pt++]]; line2[j] = '-'; line3[j] = '-'; break; case 1: // insertion to query line1[j] = '-'; line2[j] = "ACGTN"[query[pq++]]; line3[j] = '+'; break; } if (++j == sizeof(line1)) { fprintf(bcftools_stderr, "%.*s\n", j, line1); fprintf(bcftools_stderr, "%.*s\n", j, line2); fprintf(bcftools_stderr, "%.*s\n", j, line3); j = 0; } } if (j) { fprintf(bcftools_stderr, "%.*s\n", j, line1); fprintf(bcftools_stderr, "%.*s\n", j, line2); fprintf(bcftools_stderr, "%.*s\n", j, line3); } } #endif // Aligned target length minus query length is an indication of the number // of insertions and/or deletions. // // For CIGAR 10M1I10M t_len > l_query ("AC" / "ATC") // For CIGAR 10M1D10M t_len < l_query ("ATC" / "AC") // Hence t_len-l_query is -ve for net insertions and +ve for net deletions. // If we compute nins and ndel directly via walking though EDLIB_TASK_PATH // we'll see t_len-l_query == ndel-nins. // // If a technology has a significantly higher chance of making deletion // errors than insertion errors, then we would view deletions as less // indicative of this sequence not coming from this candidate allele than // if it had insertion (as the deletions are more likely to be errors // rather than real, relative to the insertions). Hence we can skew the // score by the net delta of num_del - num_ins. // // Note this is an approximation that doesn't account for multiple // insertions and deletions within the same sequence, but it is much faster // as it doesn't require EDLIB_TASK_PATH to be computed. // // Given editDistance is +1 for every mismatch, insertion and deletion, // provided the t_len-l_query multiplier < 1 then this is always +ve. int t_len = *r.endLocations - *r.startLocations + 1; int score = m*(r.editDistance - del_bias*(t_len - l_query)); edlibFreeAlignResult(r); return score; } // Part of bcf_call_gap_prep. // // Realign using BAQ to get an alignment score of a single read vs // a haplotype consensus. TODO: replace BAQ with something more robust. // // There are many coordinates, so let's explain them. // - left, right, tbeg, tend, r_start and r_end are in aligned reference // coordinates. // left/right start from pos +/- indel_win_size. // r_start/r_end are the BAM first and last mapped coord on the reference. // tbeg and tend are the intersection of the two. // - qbeg and qend are in BAM sequence coordinates // - qpos is in sequence coordinates, relative to qbeg. // // To see what this means, we have illustrations with coordinates // above the seqs in reference space and below the seqs in BAM seq space. // // Overlap left: // tbeg tend // r_start left pos r_end right // REF :..............|--------------------#------:--------------|... // SEQ :..............|--------------------#------| // 0 qbeg qpos qend // // Overlap right: // r_start tend // left tbeg pos right r_end // REF ...|--------------:-----#---------------------|...........: // SEQ |-----#---------------------|...........: // qbeg qpos qend // 0 // // The "-" sequence is the bit passed in. // Ie ref2 spans left..right and query spans qbeg..qend. // We need to adjust ref2 therefore to tbeg..tend. // // Fills out score // Returns 0 on success, // <0 on error static int bcf_cgp_align_score(bam_pileup1_t *p, bcf_callaux_t *bca, int type, int band, uint8_t *ref1, uint8_t *ref2, uint8_t *query, int r_start, int r_end, int tbeg, int tend1, int tend2, int left, int right, int qbeg, int qend, int pos, int qpos, int max_deletion, double qavg, double del_bias, int *score, int *str_len1_p, int *str_len2_p) { int atype = abs(type); int l, sc1, sc2; // Trim poly_Ns at ends of ref. // This helps to keep len(ref) and len(query) similar, to reduce // band size and reduce the chance of -ve BAQ scores. for (l = 0; l < tend1-tbeg && l < tend2-tbeg; l++) if (ref1[l + tbeg-left] != 4 || ref2[l + tbeg-left] != 4) break; if (l > atype) tbeg += l-atype; for (l = tend1-tbeg-1; l >= 0; l--) if (ref1[l + tbeg-left] != 4) break; l = tend1-tbeg-1 - l; if (l > atype) tend1 -= l-atype; for (l = tend2-tbeg-1; l >= 0; l--) if (ref2[l + tbeg-left] != 4) break; l = tend2-tbeg-1 - l; if (l > atype) { tend2 -= l-atype; } // The bottom 8 bits are length-normalised score while // the top bits are unnormalised. // // Try original cons and new cons and pick best. // This doesn't reduce FN much (infact maybe adds very slightly), // but it does reduce GT errors and is a slight reduction to FP. double mm = 30; // a const average qual for now. Could tune sc2 = edlib_glocal(ref2 + tbeg - left, tend2 - tbeg, query, qend - qbeg, mm, del_bias); if (tend1 != tend2 || memcmp((char *)ref1 + tbeg - left, (char *)ref2 + tbeg - left, tend1 - tbeg) != 0) sc1 = edlib_glocal(ref1 + tbeg - left, tend1 - tbeg, query, qend - qbeg, mm, del_bias); else sc1 = INT_MAX; // skip // Find the best of the two alignments if (sc1 < 0 && sc2 < 0) { *score = 0xffffff; return 0; } if (sc1 < 0) { // sc2 is already correct } else if (sc2 < 0) { sc2 = sc1; } else { // sc1 and sc2 both pass, so use best if (sc2 > sc1) sc2 = sc1; } // Sc is overall alignment score, in top 24 bits (SeqQ). It's based // purely on the scores for the whole alignment. // We also have a separate indel score in bottom 8 bits (IndelQ). // This is a function of all sorts of attributes of the candidate indel // itself, such as STR length and the presence of poor quality bases. // Used for adjusting indelQ below. Lower l is more likely to call // (--FN, ++FP). (NB CLI --indel_bias is 1/indel_bias var). // Starts as average score per base, and then adjusted based on seq // complexity / quality. l = .5*(100. * sc2 / (qend - qbeg) + .499); *score = (sc2<<8) | (int)MIN(255, l * bca->indel_bias * .5); return 0; } // Part of bcf_call_gap_prep. // // Returns n_alt on success // -1 on failure // TODO: almost identical to bam2bcf_indel.c's copy, so we could share // the code and add a check on bca->edlib. static int bcf_cgp_compute_indelQ(int n, int *n_plp, bam_pileup1_t **plp, bcf_callaux_t *bca, char *inscns, int l_run, int max_ins, int ref_type, int *types, int n_types, double qavg, int *score, int str_len1, int str_len2) { // FIXME: n_types has a maximum; no need to alloc - use a #define? int sc[MAX_TYPES], sumq[MAX_TYPES], s, i, j, t, K, n_alt, tmp; memset(sumq, 0, n_types * sizeof(int)); int sum_indelQ1[100] = {0}; // n int sum_indelQ2[100] = {0}; // n // Confusing variable naming and bit usage. // // score[] is low 8 bits normalised (by len) alignment score // top 24 bits full alignment score // This gets cast into "sct"; mnemonic score-per-indel-type. // // sc = (score<<6) | type (index to types[] array for indel size) // So sc>>14 = score>>(14-6) = score>>8. Ie full alignment score for (s = K = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i, ++K) { bam_pileup1_t *p = plp[s] + i; // Labelling is confusing here. // sct is short for score. // sc is score + t(type) // Why aren't these variable names reversed? int *sct = &score[K*n_types], seqQ, indelQ1=0, indelQ2=0, indelQ=0; for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t; for (t = 1; t < n_types; ++t) // insertion sort for (j = t; j > 0 && sc[j] < sc[j-1]; --j) tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp; #ifdef ALIGN_DEBUG fprintf(bcftools_stderr, "READ %s\tscores ", bam_get_qname(p->b)); for (t = 0; t < n_types; ++t) { fprintf(bcftools_stderr, "%+2d/%-3d ", types[sc[t]&0x3f], sc[t]>>14); } #endif /* errmod_cal() assumes that if the call is wrong, the * likelihoods of other events are equal. This is about * right for substitutions, but is not desired for * indels. To reuse errmod_cal(), I have to make * compromise for multi-allelic indels. */ if ((sc[0]&0x3f) == ref_type) { // sc >> 14 is the total score. It's been shifted by 8 // from normalised score and 6 from type. // &0x3f is type number // Best call is REF. Compare vs best indel indelQ = (sc[1]>>14) - (sc[0]>>14); seqQ = est_seqQ(bca, types[sc[1]&0x3f], l_run, str_len1); } else { // look for the reference type for (t = 0; t < n_types; ++t) { if ((sc[t]&0x3f) == ref_type) break; } indelQ = indelQ1 = (sc[t]>>14) - (sc[0]>>14); // fprintf(bcftools_stderr, "IndelQ = %d: %d-%d", // indelQ, (sc[t]>>14), (sc[0]>>14)); // Best call is non-ref, compare vs next best non-ref, // or ref if it's just 2 choices (most common case). for (t = 1; t < n_types; t++) if ((sc[t]&0x3f) == ref_type) continue; else break; if (t == n_types) t--; // it's ref, but it'll do as next best. indelQ2 = (sc[t]>>14) - (sc[0]>>14); seqQ = est_seqQ(bca, types[sc[0]&0x3f], l_run, str_len1); #if 1 // TEST 3 indelQ = bca->vs_ref*indelQ1 + (1-bca->vs_ref)*indelQ2; #endif } // So we lower qual in some, but raise the average to keep FN/FP // ratios up. // Is this key diff for PacBio old vs new HiFi? indelQ /= bca->indel_bias*0.5; indelQ1 /= bca->indel_bias*0.5; // Or maybe just *2 if bca->poly_mqual and be done with it? // Or perhaps adjust the MIN(qavg/20, ...) to MIN(qavg/10) ? // Skew SeqQ and IndelQ based on a portion of the minimum quality // found within a homopolymer. This is useful where the quality // values are a bit mutable and move around in such data, but less // so on clocked sequencing technologies. // // Enabling this causes lots of GT errors on Illumina. // However on PacBio it's key to removal of false positives. // ONT and UG seem somewhere inbetween. if (bca->poly_mqual) { // TEST 4 int qpos = p->qpos, l; uint8_t *seq = bam_get_seq(p->b); uint8_t *qual = bam_get_qual(p->b); int min_q = qual[qpos]; // scan homopolymer left char baseL = bam_seqi(seq, qpos+1 < p->b->core.l_qseq ? qpos+1 : qpos); for (l = qpos; l >= 0; l--) { if (bam_seqi(seq, l) != baseL) break; if (min_q > qual[l]) min_q = qual[l]; } // scan homo-polymer right (including site of indel) char base = bam_seqi(seq, qpos+1); for (l = qpos+1; l < p->b->core.l_qseq; l++) { if (min_q > qual[l]) min_q = qual[l]; if (bam_seqi(seq, l) != base) break; } // We reduce -h so homopolymers get reduced likelihood of being // called, but then optionally increase or decrease from there // based on base quality. Hence lack of low quality bases in // homopolymer will rescue the score back again, reducing FNs. // The score factors here may also be machine specific, but for // now these work well (tuned on PB HiFi). seqQ += MIN(qavg/20, min_q - qavg/10); indelQ += MIN(qavg/20, min_q - qavg/5); indelQ1+= MIN(qavg/20, min_q - qavg/5); if (seqQ < 0) seqQ = 0; if (indelQ < 0) indelQ = 0; if (indelQ1< 0) indelQ1= 0; } // This is the length-normalised score from bcf_cgp_align_score tmp = sc[0]>>6 & 0xff; // reduce indelQ // high score = bad, low score = good; flip for indelQ // low normalised scores leave indelQ unmodified // high normalised scores set indelQ to 0 // inbetween scores have a linear scale from indelQ to 0 // Altering the MAGIC value below (originally 111, but chosen for unknown // reasons) is comparable to altering --indel-bias. #define TMP_MAGIC 255.0 indelQ = tmp > TMP_MAGIC? 0 : (int)((1. - tmp/TMP_MAGIC) * indelQ + .499); indelQ1= tmp > TMP_MAGIC? 0 : (int)((1. - tmp/TMP_MAGIC) * indelQ1+ .499); indelQ = MIN(indelQ, 255); indelQ1 = MIN(indelQ1, 255); // Doesn't really help accuracy, but permits -h to take // affect still. if (indelQ > seqQ) indelQ = seqQ; if (indelQ > 255) indelQ = 255; if (indelQ1> 255) indelQ1= 255; if (seqQ > 255) seqQ = 255; // Use 22 bits in total. // 0-7 IndelQ // 8-15 SeqQ // 16-22 Score-per-base p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ; sumq[sc[0]&0x3f] += indelQ; #ifdef ALIGN_DEBUG fprintf(bcftools_stderr, "\t%d\t%d\n", indelQ, seqQ); #endif // Experiment in p->aux vs sumq. // One gives likelihood of an indel being here, while the other // is likelihood of a specific genotype? But which is which? sum_indelQ1[s] += indelQ1; sum_indelQ2[s] += indelQ; } } // Determine bca->indel_types[] and bca->inscns. // Sumq[0] is always reference. // Sumq[1] is best non-ref (and maybe better than ref) bca->maxins = max_ins; bca->inscns = (char*) realloc(bca->inscns, bca->maxins * 4); if (bca->maxins && !bca->inscns) return -1; for (t = 0; t < n_types; ++t) sumq[t] = sumq[t]<<6 | t; for (t = 1; t < n_types; ++t) // insertion sort for (j = t; j > 0 && sumq[j] > sumq[j-1]; --j) tmp = sumq[j], sumq[j] = sumq[j-1], sumq[j-1] = tmp; for (t = 0; t < n_types; ++t) // look for the reference type if ((sumq[t]&0x3f) == ref_type) break; if (t) { // then move the reference type to the first tmp = sumq[t]; for (; t > 0; --t) sumq[t] = sumq[t-1]; sumq[0] = tmp; } for (t = 0; t < 4; ++t) bca->indel_types[t] = B2B_INDEL_NULL; for (t = 0; t < 4 && t < n_types; ++t) { bca->indel_types[t] = types[sumq[t]&0x3f]; #ifdef ALIGN_DEBUG fprintf(bcftools_stderr, "TYPE %+2d %d\n", types[t], sumq[t]>>6); #endif if (bca->maxins) // potentially an insertion memcpy(&bca->inscns[t * bca->maxins], &inscns[(sumq[t]&0x3f) * max_ins], bca->maxins); } // Update p->aux. // If per-alignment type isn't found, then indelQ/seqQ is 0, // otherwise unchanged. for (s = n_alt = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i) { bam_pileup1_t *p = plp[s] + i; int x = types[p->aux>>16&0x3f]; for (j = 0; j < 4; ++j) if (x == bca->indel_types[j]) break; p->aux = j<<16 | (j == 4? 0 : (p->aux&0xffff)); if ((p->aux>>16&0x3f) > 0) ++n_alt; #ifdef ALIGN_DEBUG fprintf(bcftools_stderr, "FIN %s\t%d\t%d\t%d\n", bam_get_qname(p->b), (p->aux>>16)&0x3f, bca->indel_types[(p->aux>>16)&0x3f], p->aux&0xff); #endif } } return n_alt; } /* FIXME: with high number of samples, do we handle IMF correctly? Is it fraction of indels across entire data set, or just fraction for this specific sample? Needs to check bca->per_sample_flt (--per-sample-mF) opt. */ /* notes: - n .. number of samples - the routine sets bam_pileup1_t.aux of each read as follows: - 6: unused - 6: the call; index to bcf_callaux_t.indel_types .. (aux>>16)&0x3f - 8: estimated sequence quality .. (aux>>8)&0xff - 8: indel quality .. aux&0xff */ int bcf_edlib_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, int ref_len) { if (ref == 0 || bca == 0) return -1; int i, s, t, n_types, *types = NULL, max_rd_len, left, right, max_ins; int *score = NULL; int N, K, l_run, ref_type, n_alt = -1; char *inscns = NULL, *query = NULL; // determine if there is a gap for (s = N = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i) if (plp[s][i].indel != 0) break; if (i < n_plp[s]) break; } if (s == n) // there is no indel at this position. return -1; // Find average base quality over this region double qavg = 30, qsum = 0, qcount = 0; int qmax = 0; for (s = 0; s < n; s++) { for (i = 0; i < n_plp[s]; i++) { #define QWIN 50 bam_pileup1_t *p = plp[s] + i; int kstart = p->qpos - QWIN > 0 ? p->qpos - QWIN : 0; int kend = p->qpos + QWIN < p->b->core.l_qseq ? p->qpos + QWIN : p->b->core.l_qseq; uint8_t *qual = bam_get_qual(p->b); int k; for (k = kstart; k < kend; k++) { qsum += qual[k]; qcount++; if (qmax < qual[k]) qmax = qual[k]; } } } qavg = (qsum+1) / (qcount+1); // find out how many types of indels are present types = bcf_cgp_find_types(n, n_plp, plp, pos, bca, ref, &max_rd_len, &n_types, &ref_type, &N); if (!types) goto err; // calculate left and right boundary, based on type size for a bit more // speed. int max_indel = 20*MAX(ABS(types[0]), ABS(types[n_types-1])) + bca->indel_win_size/4; if (max_indel > bca->indel_win_size) max_indel = bca->indel_win_size; left = pos > max_indel ? pos - max_indel : 0; right = pos + max_indel; int del_size = types[0]<0 ? -types[0] : 0; right += del_size; // in case the alignments stand out the reference for (i = pos; i < right; ++i) if (ref[i] == 0) break; right = i; // compute the likelihood given each type of indel for each read max_ins = types[n_types - 1]; // max_ins is at least 0 // The length of the homopolymer run around the current position l_run = bcf_cgp_l_run(ref, pos); int l_run_base = seq_nt16_table[(uint8_t)ref[pos+1]]; int l_run_ins = 0; // construct the consensus sequence (minus indels, which are added later) if (max_ins > 0) { // TODO: replace filling inscns[] with calc_consensus return // so the merges of the insertion consensus for type[t] is // reported directly. (It may need adjustment to avoid N) inscns = bcf_cgp_calc_ins_cons(n, n_plp, plp, pos, types, n_types, max_ins, s); if (!inscns) return -1; } query = (char*) calloc(right - left + max_rd_len + max_ins + 2, 1); score = (int*) calloc(N * n_types, sizeof(int)); bca->indelreg = 0; double nqual_over_60 = bca->nqual / 60.0; int biggest_del = 0; int biggest_ins = 0; for (t = 0; t < n_types; t++) { if (biggest_del > types[t]) biggest_del = types[t]; if (biggest_ins < types[t]) biggest_ins = types[t]; } int band = biggest_ins - biggest_del; // NB del is -ve // Find left & right extents of STR covering pos, from ref int pos_l = pos, pos_r = pos; { rep_ele *reps, *elt, *tmp; int pstart = MAX(0, pos-30); int pmid = pos-pstart; int pend = MIN(ref_len, pos+30); reps = find_STR((char *)&ref[pstart], pend-pstart, 0); DL_FOREACH_SAFE(reps, elt, tmp) { if (elt->end >= pmid && elt->start <= pmid) { if (pos_l > pstart + elt->start) pos_l = pstart + elt->start; if (pos_r < pstart + elt->end) pos_r = pstart + elt->end; } DL_DELETE(reps, elt); free(elt); } } int str_len1 = l_run, str_len2 = l_run/4; for (t = 0; t < n_types; ++t) { int l, ir; // Compute indelreg. This is the context in the reference. Eg: // // REF: AG--TTTC Inscns is "TT". // SEQ: AGTTTTTC Indelreg is 3; next 3 "TTT" bases // // => GTTT GTTTTT is call. if (types[t] == 0) ir = 0; else if (types[t] > 0) ir = est_indelreg(pos, ref, types[t], &inscns[t*max_ins]); else ir = est_indelreg(pos, ref, -types[t], 0); if (ir > bca->indelreg) bca->indelreg = ir; // Realignment score, computed via BAQ for (s = K = 0; s < n; ++s) { char **tcons; int left_shift, right_shift; int tcon_len[2]; int cpos_pos; tcons = bcf_cgp_consensus(n, n_plp, plp, pos, bca, ref, ref_len, left, right, s, types[t], biggest_del, &left_shift, &right_shift, &band, tcon_len, &cpos_pos, pos_l, pos_r); // TODO: Consensus for a deletion shouldn't match the // consensus for type 0. Eg consider // vv vv // REF: AATGTGTGAACAA REF: AATGTG--AACAA // T0: AATGTG--AACAA T0: AATGTG--AACAA // T-2: AA--TGTGAATAA T-2: AA--TGTGAATAA: // // On left: both T0 and T-2 are the same length, as it's // just a deletion that moved. We may end up assigning // reads to an indel allele based on the SNP they have and // not the actual indel. // There *is* a deletion here though, but only 1. How do // we call it once only? Need to replace entire region // with a reassembly. // // On right: T0 and T-2 have same length again, but there // isn't an indel as it's ins+del vs del+ins. They're // also the same length as the REF for this region. // Hence likelihood of this variant existing is tied in // with their equal and high similarity with/to the ref. // // We could do an alignment of tcons[0] and tcons[1] and check // whether their differences are consistent with (ie the // hamming distance is at least ABS(types[t]/2). I don't think // it'll rescue many FPs though. #ifdef CONS_DEBUG { int j; for (j = 0; j < 2; j++) { int k; fprintf(bcftools_stderr, "Cons%d @ %d %4d/%4d ", j, pos, types[t], left_shift); for (k = 0; k < tcon_len[j]; k++) { if (k == cpos_pos) putc('#', bcftools_stderr); putc("ACGTN"[(uint8_t)tcons[j][k]], bcftools_stderr); } putc('\n', bcftools_stderr); } } #endif // Scan for base-runs in the insertion. // We use this to avoid over-correction in est_seqQ when the // insertion is not part of the neighbouring homopolymer. int k = tcons[0][cpos_pos], j; for (j = 0; j < types[t]; j++) if (tcons[0][cpos_pos+j] != k) break; if (j && j == types[t]) l_run_ins |= "\x1\x2\x4\x8\xf"[k]; // ACGTN if (types[t] < 0) l_run_ins |= 0xff; // align each read to consensus(es) for (i = 0; i < n_plp[s]; ++i, ++K) { bam_pileup1_t *p = plp[s] + i; // Some basic ref vs alt stats. int imq = p->b->core.qual > 59 ? 59 : p->b->core.qual; imq *= nqual_over_60; int sc_len, slen, epos, sc_end; // Only need to gather stats on one type, as it's // identical calculation for all the subsequent ones // and we're sharing the same stats array if (t == 0) { // Gather stats for INFO field to aid filtering. // mq and sc_len not very helpful for filtering, but could // help in assigning a better QUAL value. // // Pos is slightly useful. // Base qual can be useful, but need qual prior to BAQ? // May need to cache orig quals in aux tag so we can fetch // them even after mpileup step. get_pos(bca, p, &sc_len, &slen, &epos, &sc_end); assert(imq >= 0 && imq < bca->nqual); assert(epos >= 0 && epos < bca->npos); assert(sc_len >= 0 && sc_len < 100); if (p->indel) { bca->ialt_mq[imq]++; bca->ialt_scl[sc_len]++; bca->ialt_pos[epos]++; } else { bca->iref_mq[imq]++; bca->iref_scl[sc_len]++; bca->iref_pos[epos]++; } } int qbeg, qpos, qend, tbeg, tend, kk; uint8_t *seq = bam_get_seq(p->b); uint32_t *cigar = bam_get_cigar(p->b); if (p->b->core.flag & BAM_FUNMAP) continue; // FIXME: the following loop should be better moved outside; // nonetheless, realignment should be much slower anyway. for (kk = 0; kk < p->b->core.n_cigar; ++kk) if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP) break; if (kk < p->b->core.n_cigar) continue; // determine the start and end of sequences for alignment int left2 = left, right2 = right; int min_win_size = MAX(-biggest_del, biggest_ins); min_win_size += ABS(left_shift) + ABS(right_shift); { rep_ele *reps, *elt, *tmp; reps = find_STR(tcons[0], tcon_len[0], 0); //int max_str = 0; int tot_str = 0; DL_FOREACH_SAFE(reps, elt, tmp) { // if (max_str < elt->end - elt->start) // max_str = elt->end - elt->start; tot_str += elt->end - elt->start; DL_DELETE(reps, elt); free(elt); } // Ideally max_str should be enough, but it's still not // sufficient in longer range some repeats. //min_win_size += max_str; min_win_size += tot_str; } min_win_size += 10; // TEST 8 if (p->b->core.l_qseq > 1000) { // long read data needs less context. It also tends to // have many more candidate indels to investigate so // speed here matters more. if (pos - left >= min_win_size) left2 = MAX(left2, pos - min_win_size); if (right-pos >= min_win_size) right2 = MIN(right2, pos + min_win_size); } // Genomic coords for first and last base of query // alignment. This is only used in bcf_cgp_align_score // for computing scores by looking for the proximity // of STRs with the end of the query alignment. int r_start = p->b->core.pos; int r_end = bam_cigar2rlen(p->b->core.n_cigar, bam_get_cigar(p->b)); r_end += -1 + r_start; // Map left2/right2 genomic coordinates to qbeg/qend // query coordinates. The query may not span the // entire left/right region, so this also returns the // equivalent genomic coords for qbeg/qend in tbeg/tend. qbeg = tpos2qpos(&p->b->core, bam_get_cigar(p->b), left2, 0, &tbeg); qpos = tpos2qpos(&p->b->core, bam_get_cigar(p->b), pos, 0, &tend) - qbeg; qend = tpos2qpos(&p->b->core, bam_get_cigar(p->b), right2, 1, &tend); int old_tend = tend; int old_tbeg = tbeg; // write the query sequence for (l = qbeg; l < qend; ++l) query[l - qbeg] = seq_nt16_int[bam_seqi(seq, l)]; // tbeg and tend are the genomic locations equivalent // to qbeg and qend on the sequence. // These may being entirely within our left/right // coordinates over which we've computed the // consensus, or overlapping to left/right. // // We know an estimation of band, plus biggest indel, // so we can trim tbeg/tend to a smaller region if we // wish here. This speeds up BAQ scoring. int wband = band + MAX(-biggest_del, biggest_ins)*2 + 20; int tend1 = left + tcon_len[0] - (left2-left); int tend2 = left + tcon_len[1] - (left2-left); tend1 = MIN(tend1, old_tend + wband); tend2 = MIN(tend2, old_tend + wband); tbeg = MAX(left2, old_tbeg - wband); // do realignment; this is the bottleneck. // // Note low score = good, high score = bad. if (tend1 > tbeg && tend2 > tbeg) { //fprintf(bcftools_stderr, "Num %d\n", i); if (bcf_cgp_align_score(p, bca, types[t], band, (uint8_t *)tcons[0] + left2-left, (uint8_t *)tcons[1] + left2-left, (uint8_t *)query, r_start, r_end, tbeg, tend1, tend2, left2, left + tcon_len[0], qbeg, qend, pos,qpos, -biggest_del, qavg, bca->del_bias, &score[K*n_types + t], &str_len1, &str_len2) < 0) { goto err; } #ifdef ALIGN_DEBUG fprintf(bcftools_stderr, "type %d %x / %x\t%s\n", types[t], score[K*n_types + t] >> 8, score[K*n_types + t] & 0xff, bam_get_qname(p->b)); #endif } else { // place holder large cost for reads that cover the // region entirely within a deletion (thus tend < tbeg). score[K*n_types + t] = 0xffffff; } } free(tcons); } } // compute indelQ if (!(l_run_base & l_run_ins)) l_run = 1; // different base type in ins to flanking region. n_alt = bcf_cgp_compute_indelQ(n, n_plp, plp, bca, inscns, l_run, max_ins, ref_type, types, n_types, qavg, score, str_len1, str_len2); err: // free free(query); free(score); free(types); free(inscns); return n_alt > 0? 0 : -1; } pysam-0.23.0/bcftools/bam2bcf_iaux.c000066400000000000000000000673731475062545500172630ustar00rootroot00000000000000/* bam2bcf_iaux.c -- modified indel caller Copyright (C) 2022 Genome Research Ltd. Author: pd3@sanger, jkb Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE */ #include #include #include #include #include #include #include #include "bcftools.h" #include "bam2bcf.h" #include "read_consensus.h" #include "cigar_state.h" #include KSORT_INIT_STATIC_GENERIC(uint32_t) #ifndef DEBUG_ALN #define DEBUG_ALN 0 #endif #define MAX_TYPES 64 typedef struct { int pos; // current position char *chr; // current chromosome int nsmpl; // number of samples int *nplp; // per-sample number of reads bam_pileup1_t **plp; // per-sample reads bcf_callaux_t *bca; // auxiliary bam2bcf structure const char *ref; // reference genome (ASCII) uint32_t *uitmp; // temporary unsigned int array char *inscns; // insertions consensus "ACGTN"[itype*max_ins_len+i] int muitmp, minscns; // size of uitmp, inscns int iref_type, ntypes, types[MAX_TYPES]; // indel types int max_ins_len; // largest insertion int left, right; // consensus sequence boundaries, 0-based fa ref coordinates read_cns_t *rcns; // read consensus cns_seq_t *cns_seq; // array of consensus sequences int *cns_pos; // array of relative pos indexes within cns_seq sequences uint8_t *ref_seq, *qry_seq; // reference and query sequence to align int nref_seq, nqry_seq; // the allocated size of ref_seq and qry_seq uint8_t *qual; int nqual; int *read_scores, // read scores for each indel type [ntypes*iread+itype] mread_scores, ref_qual[MAX_TYPES], // refseq quality at pos for each indel type in the context of homopolymer runs sum_qual[MAX_TYPES]; // qual contributions to each indel type from all reads } indel_aux_t; #if DEBUG_ALN static void debug_print_types(indel_aux_t *iaux) { int i,j; fprintf(stderr,"types at %s:%d ntypes=%d... ",iaux->chr,iaux->pos+1,iaux->ntypes); for (i=0; intypes; i++) { fprintf(stderr," type%d=",i); if ( iaux->types[i]<=0 ) { if ( i==iaux->iref_type ) fprintf(stderr,"%d(ref)",iaux->types[i]); else fprintf(stderr,"%d",iaux->types[i]); continue; } char *cns = &iaux->inscns[i*iaux->max_ins_len]; for (j=0; jtypes[i]; j++) fprintf(stderr,"%c","ACGTN"[(int)cns[j]]); } fprintf(stderr,"\n"); } #else #define debug_print_types(iaux) #endif void bcf_iaux_destroy(bcf_callaux_t *bca) { if ( !bca->iaux ) return; indel_aux_t *iaux = (indel_aux_t*)bca->iaux; free(iaux->uitmp); free(iaux->inscns); free(iaux->ref_seq); free(iaux->qry_seq); free(iaux->qual); free(iaux->read_scores); rcns_destroy(iaux->rcns); free(iaux); } static void iaux_init_sequence_context(indel_aux_t *iaux) { // Calculate left and right boundary. The array types is sorted in ascending order, the first // element is the largest deletion (if a deletion present) iaux->left = iaux->pos > iaux->bca->indel_win_size ? iaux->pos - iaux->bca->indel_win_size : 0; iaux->right = iaux->pos + iaux->bca->indel_win_size; if ( iaux->types[0] < 0 ) iaux->right -= iaux->types[0]; // extend by the largest deletion length // In case the alignments stand out the reference int i; for (i=iaux->pos; iright; i++) if ( !iaux->ref[i] ) break; iaux->right = i; // Sequence quality in the context of homopolymers for each indel type int l_run = bcf_cgp_l_run(iaux->ref, iaux->pos); // The length of the homopolymer run around the current position for (i=0; intypes; i++) { int l = iaux->types[i]; // This is the original est_seqQ() code. FIXME: check if the inserted sequence is consistent with the homopolymer run int q = iaux->bca->openQ + iaux->bca->extQ * (abs(l) - 1); int qh = l_run >= 3? (int)(iaux->bca->tandemQ * (double)abs(l) / l_run + .499) : 1000; if ( q > qh ) q = qh; iaux->ref_qual[i] = q < 255 ? q : 255; } // Determine the indel region, this makes the difference between e.g. T>TA vs TA>TAA iaux->bca->indelreg = 0; for (i=0; intypes; i++) { if ( !iaux->types[i] ) continue; int ireg; if ( iaux->types[i] > 0 ) ireg = est_indelreg(iaux->pos, iaux->ref, iaux->types[i], &iaux->inscns[i*iaux->max_ins_len]); else ireg = est_indelreg(iaux->pos, iaux->ref, -iaux->types[i], 0); if ( ireg > iaux->bca->indelreg ) iaux->bca->indelreg = ireg; } } static int iaux_init_scores(indel_aux_t *iaux, int ismpl) { int n = iaux->nplp[ismpl] * iaux->ntypes; if ( iaux->mread_scores < n ) { int *tmp = (int*) realloc(iaux->read_scores,n*sizeof(int)); if ( !tmp ) return -1; iaux->mread_scores = n; iaux->read_scores = tmp; } memset(iaux->read_scores,0,n); return 0; } static int _have_indel_reads(indel_aux_t *iaux) { int i,j; for (i=0; insmpl; i++) { for (j=0; jnplp[i]; j++) if ( iaux->plp[i][j].indel ) return 1; } return 0; } // For insertions only their sizes were collected so far. Now go through the reads and // create consensus sequence for each insert, therefore note that there can be only one // sequence per insertion length static int iaux_init_ins_types(indel_aux_t *iaux) { if ( !iaux->max_ins_len ) return 0; uint32_t *aux; int naux = 5 * iaux->ntypes * iaux->max_ins_len; if ( iaux->muitmp < naux ) { aux = (uint32_t*) realloc(iaux->uitmp,naux*sizeof(*aux)); if ( !aux ) return -1; iaux->uitmp = aux; iaux->muitmp = naux; } else aux = iaux->uitmp; memset(aux,0,naux*sizeof(*aux)); // count the number of occurrences of each base at each position for each type of insertion int t,s,i,j; for (t=0; tntypes; t++) { if ( iaux->types[t] <= 0) continue; for (s=0; snsmpl; s++) { for (i=0; inplp[s]; i++) { bam_pileup1_t *plp = iaux->plp[s] + i; if ( plp->indel != iaux->types[t] ) continue; uint8_t *seq = bam_get_seq(plp->b); for (j=0; jindel; j++) { int c = seq_nt16_int[bam_seqi(seq, plp->qpos+j+1)]; assert(c<5); aux[5*(t*iaux->max_ins_len+j) + c]++; } } } } char *cns; int ncns = iaux->ntypes * iaux->max_ins_len; if ( iaux->minscns < ncns ) { cns = (char*) realloc(iaux->inscns,naux*sizeof(*aux)); if ( !cns ) return -1; iaux->inscns = cns; iaux->minscns = ncns; } else cns = iaux->inscns; memset(aux,0,ncns*sizeof(*cns)); // use the majority rule to construct the consensus for (t=0; tntypes; t++) { for (i=0; itypes[t]; i++) // this naturally includes only insertions { uint32_t *tmp = &aux[5*(t*iaux->max_ins_len+i)], max = tmp[0], max_j = 0; for (j=1; j<5; j++) if ( max < tmp[j] ) max = tmp[j], max_j = j; cns[t*iaux->max_ins_len + i] = max ? max_j : 4; if ( max_j==4 ) { iaux->types[t] = 0; break; } // discard insertions which contain N's } } return 0; } #define MINUS_CONST 0x10000000 static int iaux_init_types(indel_aux_t *iaux) { if ( !_have_indel_reads(iaux) ) return 0; iaux->bca->max_support = 0; memset(iaux->sum_qual,0,MAX_TYPES*sizeof(*iaux->sum_qual)); int i,j, nreads = 0; for (i=0; insmpl; i++) nreads += iaux->nplp[i]; uint32_t *aux; if ( iaux->muitmp < nreads+1 ) { aux = (uint32_t*) realloc(iaux->uitmp,(nreads+1)*sizeof(*iaux->uitmp)); if ( !aux ) return -1; iaux->uitmp = aux; iaux->muitmp = nreads+1; } else aux = iaux->uitmp; memset(aux,0,(nreads+1)*sizeof(*aux)); int naux = 0, indel_support_ok = 0, n_alt = 0, n_tot = 0; int max_rd_len = 0; // max sequence length that includes ref+del bases // Fill out aux[] array with all the non-zero indel sizes. This is an unsorted list with as many // entries as there are reads aux[naux++] = MINUS_CONST; // zero indel is always a type (REF) for (i=0; insmpl; i++) { int nalt = naux, ntot = 0; // per sample values for (j=0; jnplp[i]; j++) { const bam_pileup1_t *plp = iaux->plp[i] + j; ntot++; if ( plp->indel ) aux[naux++] = MINUS_CONST + plp->indel; if ( !PLP_QLEN(&plp->cd) ) PLP_QLEN(&plp->cd) = bam_cigar2qlen(plp->b->core.n_cigar, bam_get_cigar(plp->b)); if ( PLP_QLEN(&plp->cd) > max_rd_len ) max_rd_len = PLP_QLEN(&plp->cd); } nalt = naux - nalt; if ( iaux->bca->per_sample_flt ) { double frac = (double)nalt/naux; if ( nalt >= iaux->bca->min_support && frac >= iaux->bca->min_frac ) indel_support_ok = 1; if ( nalt > iaux->bca->max_support && frac > 0 ) iaux->bca->max_support = nalt, iaux->bca->max_frac = frac; } else { n_alt += nalt; n_tot += ntot; } } // Check if the minimum required number of indel reads has been observed if ( !iaux->bca->per_sample_flt && n_alt >= iaux->bca->min_support && (double)n_alt/n_tot >= iaux->bca->min_frac ) indel_support_ok = 1; if ( naux==1 || !indel_support_ok ) return 0; // To prevent long stretches of N's to be mistaken for indels (sometimes thousands of bases), check the number of N's in the // sequence and skip places where half or more reference bases in the sequence that follows pos are Ns int nN = 0, i_end = iaux->pos + (iaux->bca->indel_win_size < max_rd_len ? iaux->bca->indel_win_size : max_rd_len); for (i=iaux->pos; iref[i]; i++) if ( iaux->ref[i] == 'N' ) nN++; if ( 2*nN > i - iaux->pos ) return -1; // Sort aux[] and dedup indel types int n_types = 1; ks_introsort(uint32_t, naux, aux); for (i=1; i= MAX_TYPES ) { static int warned = 0; if ( !warned ) { fprintf(stderr, "Warning: excessive number of INDEL alleles at %s:%d, skipping. (This warning is printed only once)\n",iaux->chr,iaux->pos+1); warned = 1; } return -1; } // Fill out the types[] array detailing the size of insertion or deletion. iaux->ntypes = 0; iaux->max_ins_len = 0; for (i=0; iiref_type = iaux->ntypes; } else { if ( j-i >= iaux->bca->min_support ) is_ok = 1; // What is the best way to handle the -pmF options: // - consider only sites where a single indel type passes the -mF threshold, as opposed to all indel types cumulatively // - once a site passes, include all indel types in the evaluation, as opposed to considering only the strong candidates // In this implementation sites are selected by counting reads from all indel types cumulatively and all indel types // are considered. // Uncomment the following condition to consider only strong indel candidates once the site has been selected // if ( !iaux->bca->per_sample_flt && (double)(j-i) / n_tot < iaux->bca->min_frac ) is_ok = 0; } if ( is_ok ) { iaux->types[iaux->ntypes++] = isize; if ( isize > 0 && isize > iaux->max_ins_len ) iaux->max_ins_len = isize; } i = j-1; } if ( iaux->ntypes <= 1 ) return 0; // Init insertion types, including their sequence if ( iaux_init_ins_types(iaux) < 0 ) return -1; iaux_init_sequence_context(iaux); return iaux->ntypes; } #undef MINUS_CONST static int iaux_set_consensus(indel_aux_t *iaux, int ismpl) { if ( !iaux->rcns ) iaux->rcns = rcns_init(iaux->pos, iaux->left, iaux->right); else rcns_reset(iaux->rcns, iaux->pos, iaux->left, iaux->right); rcns_set_reads(iaux->rcns, iaux->plp[ismpl], iaux->nplp[ismpl]); iaux->cns_seq = rcns_get_consensus(iaux->rcns, iaux->ref + iaux->left); // todo: // rcns should also collect localized number of mismatches as a substitute // for uninformative MQ. This would not affect calling but would help with // filtering return 0; } #if 0 // Finds the smallest index in the seq_pos array holding value equal to pos, or if there is no // such value, the largest index with value smaller than pos. Starts at initial guess ioff. // This could use a binary search but the assumption is that the initial guess is indel-size close // to the actual coordinate. // // TODO: remove this function and seq_pos from cns creation as it seems unnecessary static int find_ref_offset(hts_pos_t pos, hts_pos_t *seq_pos, int nseq_pos, int ioff) { if ( ioff<0 ) ioff = 0; else if ( ioff >= nseq_pos ) ioff = nseq_pos - 1; if ( seq_pos[ioff] < pos ) { while ( ioff+1 < nseq_pos && seq_pos[ioff] < pos ) ioff++; if ( seq_pos[ioff] > pos ) ioff--; return ioff; } while ( ioff > 0 && seq_pos[ioff-1] >= pos ) ioff--; return ioff; } #endif static int iaux_align_read(indel_aux_t *iaux, bam1_t *bam, uint8_t *ref_seq, int nref_seq) { if ( bam->core.flag & BAM_FUNMAP ) return 1; // skip unmapped reads // Trim both ref and qry to the window of interest hts_pos_t ref_beg = iaux->left; // fa ref coordinates hts_pos_t ref_end = iaux->right < ref_beg + nref_seq ? iaux->right : ref_beg + nref_seq - 1; cigar_state_t cigar; cstate_init(&cigar,bam); int qry_off1, qry_off2, ref_off1, ref_off2; if ( ref_beg > bam->core.pos ) { // the read needs trimming from left qry_off1 = cstate_seek_fwd(&cigar, &ref_beg, 1); ref_off1 = ref_beg - iaux->left; if ( ref_beg + (bam->core.l_qseq - qry_off1) > ref_end ) { // the read needs trimming from right qry_off2 = ref_end - ref_beg + qry_off1; ref_off2 = ref_end - iaux->left; } else { // the ref template needs trimming from right qry_off2 = bam->core.l_qseq - 1; ref_off2 = ref_off1 + qry_off2 - qry_off1; } } else { // the ref template needs trimming from left qry_off1 = 0; ref_off1 = bam->core.pos - ref_beg; if ( bam->core.pos + bam->core.l_qseq - 1 > ref_end ) { // the read needs trimming from right ref_off2 = ref_end - iaux->left; qry_off2 = ref_off2 - ref_off1; } else { // the ref template needs trimming from right qry_off2 = bam->core.l_qseq - 1; ref_off2 = ref_off1 + qry_off2 - qry_off1; } } //fprintf(stderr,"xtrim: %s .. left,right=%d,%d rbeg,end=%d,%d qpos=%d qlen=%d qoff=%d,%d roff=%d,%d rlen=%d\n",bam_get_qname(bam),iaux->left,iaux->right,(int)ref_beg,(int)ref_end,(int)bam->core.pos,bam->core.l_qseq, qry_off1,qry_off2,ref_off1,ref_off2,nref_seq); assert( qry_off1<=qry_off2 ); assert( qry_off1>=0 && qry_off1core.l_qseq ); assert( qry_off2>=0 && qry_off2core.l_qseq ); assert( ref_off1<=ref_off2 ); assert( ref_off1>=0 && ref_off1=0 && ref_off2nqry_seq < qlen ) { uint8_t *tmp = (uint8_t*) realloc(iaux->qry_seq, qlen); if ( !tmp ) return -1; // critical error iaux->qry_seq = tmp; iaux->nqry_seq = qlen; } uint8_t *seq = bam_get_seq(bam); for (i=qry_off1; i<=qry_off2; i++) iaux->qry_seq[i-qry_off1] = seq_nt16_int[bam_seqi(seq,i)]; // prepare qualities, either BQ or BAQ qualities (ZQ) if ( iaux->nqual < qlen ) { uint8_t *tmp = (uint8_t*) realloc(iaux->qual, qlen); if ( !tmp ) return -1; // critical error iaux->qual = tmp; iaux->nqual = qlen; } uint8_t *qual = iaux->qual; const uint8_t *qq = bam_get_qual(bam); const uint8_t *bq = (uint8_t*)bam_aux_get(bam, "ZQ"); if ( bq ) bq++; // skip type for (i=qry_off1; i<=qry_off2; i++) { int j = i - qry_off1; qual[j] = bq ? qq[i] + (bq[i] - 64) : qq[i]; if ( qual[j] > 30 ) qual[j] = 30; if ( qual[j] < 7 ) qual[j] = 7; } // Illumina probaln_par_t apf = { 1e-4, 1e-2, 10 }; // align int score = probaln_glocal(ref_seq + ref_off1, rlen, iaux->qry_seq, qlen, qual, &apf, 0, 0); int adj_score = (int)(100. * score / qlen + .499) * iaux->bca->indel_bias; #if DEBUG_ALN fprintf(stderr,"aln: %d/%d\t%s\n\tref: ",score,adj_score,bam_get_qname(bam)); for (i=0; iqry_seq[i]]); fprintf(stderr,"\n\tqual: "); for (i=0; i 255 ) adj_score = 255; return score<<8 | adj_score; } // Score all reads for this sample and indel type using the up to two consensus sequence templates. // On output sets iaux->read_scores[iread*ntypes+itype] = (raw_score<<8 | length_adjusted_score) static int iaux_score_reads(indel_aux_t *iaux, int ismpl, int itype) { int i; cns_seq_t *cns = iaux->cns_seq; while ( cns->nseq ) { // Resize buffers if necessary int ref_len = cns->nseq + iaux->types[itype]; if ( iaux->nref_seq < ref_len ) { uint8_t *ref_buf = (uint8_t*) realloc(iaux->ref_seq,sizeof(uint8_t)*ref_len); if ( !ref_buf ) return -1; iaux->ref_seq = ref_buf; iaux->nref_seq = ref_len; } // Apply the indel and create the template ref sequence... memcpy(iaux->ref_seq,cns->seq,(cns->ipos+1)*sizeof(*iaux->ref_seq)); if ( iaux->types[itype] < 0 ) // deletion memcpy(iaux->ref_seq + cns->ipos + 1, cns->seq + cns->ipos + 1 - iaux->types[itype], (cns->nseq - cns->ipos - 1 + iaux->types[itype])*sizeof(*iaux->ref_seq)); else { char *ins = &iaux->inscns[itype*iaux->max_ins_len]; for (i=0; itypes[itype]; i++) iaux->ref_seq[cns->ipos+1+i] = ins[i]; memcpy(iaux->ref_seq + cns->ipos + 1 + iaux->types[itype], cns->seq + 1 + cns->ipos, (cns->nseq - cns->ipos - 1)*sizeof(*iaux->ref_seq)); } #if DEBUG_ALN fprintf(stderr,"template %d, type %d, sample %d: ",cns==iaux->cns_seq?0:1,itype,ismpl); for (i=0; iref_seq[i]]); fprintf(stderr,"\n"); #endif // Align and score reads for (i=0; inplp[ismpl]; i++) { const bam_pileup1_t *plp = iaux->plp[ismpl] + i; int aln_score = iaux_align_read(iaux, plp->b, iaux->ref_seq, ref_len); int *score = &iaux->read_scores[i*iaux->ntypes+itype]; if ( cns==iaux->cns_seq || *score > aln_score ) *score = aln_score; } cns++; } return 0; } // Determines indel quality for each read and populates 22 bits of pileup aux field with // three integers as follows // plp->aux = indel_type << 16 | seqQ << 8 | indelQ static int iaux_eval_scored_reads(indel_aux_t *iaux, int ismpl) { int i,j; for (i=0; inplp[ismpl]; i++) { bam_pileup1_t *plp = iaux->plp[ismpl] + i; // Find the best indel type and the ref type, their scores difference is the indel quality int *score = &iaux->read_scores[i*iaux->ntypes]; int alt_score = INT_MAX, alt_j = 0; for (j=0; jiref_type; j++) if ( alt_score > score[j] ) alt_score = score[j], alt_j = j; for (j=iaux->iref_type+1; jntypes; j++) if ( alt_score > score[j] ) alt_score = score[j], alt_j = j; int ref_score = score[iaux->iref_type]; int sc0, sc1, j0; if ( alt_score < ref_score ) sc0 = alt_score, sc1 = ref_score, j0 = alt_j; else sc0 = ref_score, sc1 = alt_score, j0 = iaux->iref_type; int indelQ = (sc1>>8) - (sc0>>8); // low=bad, high=good int seqQ = iaux->ref_qual[alt_j]; // Reduce indelQ. High length-normalized alignment scores (i.e. bad alignments) // lower the quality more (e.g. gnuplot> plot [0:111] (1-x/111.)*255) int len_normQ = sc0 & 0xff; // length-normalized score of the best match (ref or alt) int adj_indelQ; // final indelQ used in calling if ( len_normQ > 111 ) { // In the original code reads matching badly to any indel type or reference had indelQ set to 0 // here and thus would be effectively removed from calling. This leads to problems when there are // many soft clipped reads and a few good matching indel reads (see noisy-softclips.bam in // mpileup-tests). Only the few good quality indel reads would become visible to the caller and // the indel would be called with high quality. Here we change the logic to make the badly matching // reads low quality reference reads. The threshold was set to make the test case still be called // as an indel, but with very low quality. // // Original code: // adj_indelQ = 0; // adj_indelQ = 12; j0 = iaux->iref_type; } else adj_indelQ = (int)((1. - len_normQ/111.) * indelQ + .499); #if DEBUG_ALN // Prints the selected indel type (itype); adjusted indelQ which will be used if bigger than seqQ; // raw indelQ; length-normalized indelQ and sequence context quality; ref and best alt indel type // and their raw and length-normalized scores fprintf(stderr,"itype=%d adj_indelQ=%d\trawQ=%d\tlen_normQ=%d\tseqQ=%d\tref:%d=%d/%d alt:%d=%d/%d)\t%s\n", j0,adj_indelQ,indelQ,len_normQ,seqQ,iaux->iref_type,ref_score>>8,ref_score&0xff,alt_j,alt_score>>8,alt_score&0xff,bam_get_qname(plp->b)); #endif if ( adj_indelQ > seqQ ) adj_indelQ = seqQ; // seqQ already capped at 255 plp->aux = j0<<16 | seqQ<<8 | adj_indelQ; // use 22 bits in total iaux->sum_qual[j0] += adj_indelQ; } return 0; } // Find the best indel types, include the ref type plus maximum three alternate indel alleles. static int iaux_eval_best_indels(indel_aux_t *iaux) { bcf_callaux_t *bca = iaux->bca; bca->maxins = iaux->max_ins_len; bca->inscns = (char*) realloc(bca->inscns, bca->maxins * 4); if ( bca->maxins && !bca->inscns ) return -1; // insertion sort, descending, high-quality indels come first int i,j,t, tmp, *sumq = iaux->sum_qual, ntypes = iaux->ntypes; for (t=0; t0 && sumq[j] > sumq[j-1]; j--) tmp = sumq[j], sumq[j] = sumq[j-1], sumq[j-1] = tmp; for (t=0; tiref_type ) break; if ( t ) { // move the reference type to the first tmp = sumq[t]; for (; t>0; t--) sumq[t] = sumq[t-1]; sumq[0] = tmp; } // Initialize bca's structures and create a mapping between old and new types int old2new_type[MAX_TYPES]; for (t=0; tntypes; t++) { int itype = sumq[t] & 0x3f; old2new_type[itype] = t; if ( t>=4 ) continue; bca->indel_types[t] = iaux->types[itype]; if ( bca->indel_types[t] <= 0 ) continue; memcpy(&bca->inscns[t*bca->maxins], &iaux->inscns[itype*iaux->max_ins_len], bca->maxins); } // Update indel type in plp->aux for all reads int ismpl, n_alt = 0; for (ismpl=0; ismplnsmpl; ismpl++) { for (i=0; inplp[ismpl]; i++) { bam_pileup1_t *plp = iaux->plp[ismpl] + i; int itype_old = (plp->aux >> 16) & 0x3f; int itype_new = old2new_type[itype_old]; plp->aux = itype_new<<16 | (itype_new>=4 ? 0 : (plp->aux & 0xffff)); if ( itype_new>0 ) n_alt++; } } return n_alt; } /* notes: - n .. number of samples - the routine sets bam_pileup1_t.aux (27 bits) of each read as follows: - 5: unused - 6: the call; index to bcf_callaux_t.indel_types .. (aux>>16)&0x3f - 8: estimated sequence quality .. (aux>>8)&0xff - 8: indel quality .. aux&0xff */ int bcf_iaux_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref) { assert(!(ref == 0 || bca == 0)); // can this ever happen? when? if (ref == 0 || bca == 0) return -1; if ( !bca->iaux ) bca->iaux = calloc(1,sizeof(indel_aux_t)); indel_aux_t *iaux = bca->iaux; iaux->nsmpl = n; iaux->nplp = n_plp; iaux->plp = plp; iaux->bca = bca; iaux->ref = ref; iaux->pos = pos; iaux->chr = bca->chr; // Check if there is an indel at this position and if yes, find all indel types and determine // window boundaries. todo: We want this information cached so that for long reads we don't keep // redoing the whole analysis again and again int ntypes = iaux_init_types(iaux); if ( ntypes<=0 ) return -1; debug_print_types(iaux); // Create two template consensus sequences for each sample (assuming max diploid organism). // Then apply each indel type on top of the templates, realign every read and remember score int i,j; for (i=0; insmpl; i++) { iaux_set_consensus(iaux, i); iaux_init_scores(iaux, i); for (j=0; j 0 ? 0 : -1; } pysam-0.23.0/bcftools/bam2bcf_iaux.c.pysam.c000066400000000000000000000677031475062545500206310ustar00rootroot00000000000000#include "bcftools.pysam.h" /* bam2bcf_iaux.c -- modified indel caller Copyright (C) 2022 Genome Research Ltd. Author: pd3@sanger, jkb Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE */ #include #include #include #include #include #include #include #include "bcftools.h" #include "bam2bcf.h" #include "read_consensus.h" #include "cigar_state.h" #include KSORT_INIT_STATIC_GENERIC(uint32_t) #ifndef DEBUG_ALN #define DEBUG_ALN 0 #endif #define MAX_TYPES 64 typedef struct { int pos; // current position char *chr; // current chromosome int nsmpl; // number of samples int *nplp; // per-sample number of reads bam_pileup1_t **plp; // per-sample reads bcf_callaux_t *bca; // auxiliary bam2bcf structure const char *ref; // reference genome (ASCII) uint32_t *uitmp; // temporary unsigned int array char *inscns; // insertions consensus "ACGTN"[itype*max_ins_len+i] int muitmp, minscns; // size of uitmp, inscns int iref_type, ntypes, types[MAX_TYPES]; // indel types int max_ins_len; // largest insertion int left, right; // consensus sequence boundaries, 0-based fa ref coordinates read_cns_t *rcns; // read consensus cns_seq_t *cns_seq; // array of consensus sequences int *cns_pos; // array of relative pos indexes within cns_seq sequences uint8_t *ref_seq, *qry_seq; // reference and query sequence to align int nref_seq, nqry_seq; // the allocated size of ref_seq and qry_seq uint8_t *qual; int nqual; int *read_scores, // read scores for each indel type [ntypes*iread+itype] mread_scores, ref_qual[MAX_TYPES], // refseq quality at pos for each indel type in the context of homopolymer runs sum_qual[MAX_TYPES]; // qual contributions to each indel type from all reads } indel_aux_t; #if DEBUG_ALN static void debug_print_types(indel_aux_t *iaux) { int i,j; fprintf(bcftools_stderr,"types at %s:%d ntypes=%d... ",iaux->chr,iaux->pos+1,iaux->ntypes); for (i=0; intypes; i++) { fprintf(bcftools_stderr," type%d=",i); if ( iaux->types[i]<=0 ) { if ( i==iaux->iref_type ) fprintf(bcftools_stderr,"%d(ref)",iaux->types[i]); else fprintf(bcftools_stderr,"%d",iaux->types[i]); continue; } char *cns = &iaux->inscns[i*iaux->max_ins_len]; for (j=0; jtypes[i]; j++) fprintf(bcftools_stderr,"%c","ACGTN"[(int)cns[j]]); } fprintf(bcftools_stderr,"\n"); } #else #define debug_print_types(iaux) #endif void bcf_iaux_destroy(bcf_callaux_t *bca) { if ( !bca->iaux ) return; indel_aux_t *iaux = (indel_aux_t*)bca->iaux; free(iaux->uitmp); free(iaux->inscns); free(iaux->ref_seq); free(iaux->qry_seq); free(iaux->qual); free(iaux->read_scores); rcns_destroy(iaux->rcns); free(iaux); } static void iaux_init_sequence_context(indel_aux_t *iaux) { // Calculate left and right boundary. The array types is sorted in ascending order, the first // element is the largest deletion (if a deletion present) iaux->left = iaux->pos > iaux->bca->indel_win_size ? iaux->pos - iaux->bca->indel_win_size : 0; iaux->right = iaux->pos + iaux->bca->indel_win_size; if ( iaux->types[0] < 0 ) iaux->right -= iaux->types[0]; // extend by the largest deletion length // In case the alignments stand out the reference int i; for (i=iaux->pos; iright; i++) if ( !iaux->ref[i] ) break; iaux->right = i; // Sequence quality in the context of homopolymers for each indel type int l_run = bcf_cgp_l_run(iaux->ref, iaux->pos); // The length of the homopolymer run around the current position for (i=0; intypes; i++) { int l = iaux->types[i]; // This is the original est_seqQ() code. FIXME: check if the inserted sequence is consistent with the homopolymer run int q = iaux->bca->openQ + iaux->bca->extQ * (abs(l) - 1); int qh = l_run >= 3? (int)(iaux->bca->tandemQ * (double)abs(l) / l_run + .499) : 1000; if ( q > qh ) q = qh; iaux->ref_qual[i] = q < 255 ? q : 255; } // Determine the indel region, this makes the difference between e.g. T>TA vs TA>TAA iaux->bca->indelreg = 0; for (i=0; intypes; i++) { if ( !iaux->types[i] ) continue; int ireg; if ( iaux->types[i] > 0 ) ireg = est_indelreg(iaux->pos, iaux->ref, iaux->types[i], &iaux->inscns[i*iaux->max_ins_len]); else ireg = est_indelreg(iaux->pos, iaux->ref, -iaux->types[i], 0); if ( ireg > iaux->bca->indelreg ) iaux->bca->indelreg = ireg; } } static int iaux_init_scores(indel_aux_t *iaux, int ismpl) { int n = iaux->nplp[ismpl] * iaux->ntypes; if ( iaux->mread_scores < n ) { int *tmp = (int*) realloc(iaux->read_scores,n*sizeof(int)); if ( !tmp ) return -1; iaux->mread_scores = n; iaux->read_scores = tmp; } memset(iaux->read_scores,0,n); return 0; } static int _have_indel_reads(indel_aux_t *iaux) { int i,j; for (i=0; insmpl; i++) { for (j=0; jnplp[i]; j++) if ( iaux->plp[i][j].indel ) return 1; } return 0; } // For insertions only their sizes were collected so far. Now go through the reads and // create consensus sequence for each insert, therefore note that there can be only one // sequence per insertion length static int iaux_init_ins_types(indel_aux_t *iaux) { if ( !iaux->max_ins_len ) return 0; uint32_t *aux; int naux = 5 * iaux->ntypes * iaux->max_ins_len; if ( iaux->muitmp < naux ) { aux = (uint32_t*) realloc(iaux->uitmp,naux*sizeof(*aux)); if ( !aux ) return -1; iaux->uitmp = aux; iaux->muitmp = naux; } else aux = iaux->uitmp; memset(aux,0,naux*sizeof(*aux)); // count the number of occurrences of each base at each position for each type of insertion int t,s,i,j; for (t=0; tntypes; t++) { if ( iaux->types[t] <= 0) continue; for (s=0; snsmpl; s++) { for (i=0; inplp[s]; i++) { bam_pileup1_t *plp = iaux->plp[s] + i; if ( plp->indel != iaux->types[t] ) continue; uint8_t *seq = bam_get_seq(plp->b); for (j=0; jindel; j++) { int c = seq_nt16_int[bam_seqi(seq, plp->qpos+j+1)]; assert(c<5); aux[5*(t*iaux->max_ins_len+j) + c]++; } } } } char *cns; int ncns = iaux->ntypes * iaux->max_ins_len; if ( iaux->minscns < ncns ) { cns = (char*) realloc(iaux->inscns,naux*sizeof(*aux)); if ( !cns ) return -1; iaux->inscns = cns; iaux->minscns = ncns; } else cns = iaux->inscns; memset(aux,0,ncns*sizeof(*cns)); // use the majority rule to construct the consensus for (t=0; tntypes; t++) { for (i=0; itypes[t]; i++) // this naturally includes only insertions { uint32_t *tmp = &aux[5*(t*iaux->max_ins_len+i)], max = tmp[0], max_j = 0; for (j=1; j<5; j++) if ( max < tmp[j] ) max = tmp[j], max_j = j; cns[t*iaux->max_ins_len + i] = max ? max_j : 4; if ( max_j==4 ) { iaux->types[t] = 0; break; } // discard insertions which contain N's } } return 0; } #define MINUS_CONST 0x10000000 static int iaux_init_types(indel_aux_t *iaux) { if ( !_have_indel_reads(iaux) ) return 0; iaux->bca->max_support = 0; memset(iaux->sum_qual,0,MAX_TYPES*sizeof(*iaux->sum_qual)); int i,j, nreads = 0; for (i=0; insmpl; i++) nreads += iaux->nplp[i]; uint32_t *aux; if ( iaux->muitmp < nreads+1 ) { aux = (uint32_t*) realloc(iaux->uitmp,(nreads+1)*sizeof(*iaux->uitmp)); if ( !aux ) return -1; iaux->uitmp = aux; iaux->muitmp = nreads+1; } else aux = iaux->uitmp; memset(aux,0,(nreads+1)*sizeof(*aux)); int naux = 0, indel_support_ok = 0, n_alt = 0, n_tot = 0; int max_rd_len = 0; // max sequence length that includes ref+del bases // Fill out aux[] array with all the non-zero indel sizes. This is an unsorted list with as many // entries as there are reads aux[naux++] = MINUS_CONST; // zero indel is always a type (REF) for (i=0; insmpl; i++) { int nalt = naux, ntot = 0; // per sample values for (j=0; jnplp[i]; j++) { const bam_pileup1_t *plp = iaux->plp[i] + j; ntot++; if ( plp->indel ) aux[naux++] = MINUS_CONST + plp->indel; if ( !PLP_QLEN(&plp->cd) ) PLP_QLEN(&plp->cd) = bam_cigar2qlen(plp->b->core.n_cigar, bam_get_cigar(plp->b)); if ( PLP_QLEN(&plp->cd) > max_rd_len ) max_rd_len = PLP_QLEN(&plp->cd); } nalt = naux - nalt; if ( iaux->bca->per_sample_flt ) { double frac = (double)nalt/naux; if ( nalt >= iaux->bca->min_support && frac >= iaux->bca->min_frac ) indel_support_ok = 1; if ( nalt > iaux->bca->max_support && frac > 0 ) iaux->bca->max_support = nalt, iaux->bca->max_frac = frac; } else { n_alt += nalt; n_tot += ntot; } } // Check if the minimum required number of indel reads has been observed if ( !iaux->bca->per_sample_flt && n_alt >= iaux->bca->min_support && (double)n_alt/n_tot >= iaux->bca->min_frac ) indel_support_ok = 1; if ( naux==1 || !indel_support_ok ) return 0; // To prevent long stretches of N's to be mistaken for indels (sometimes thousands of bases), check the number of N's in the // sequence and skip places where half or more reference bases in the sequence that follows pos are Ns int nN = 0, i_end = iaux->pos + (iaux->bca->indel_win_size < max_rd_len ? iaux->bca->indel_win_size : max_rd_len); for (i=iaux->pos; iref[i]; i++) if ( iaux->ref[i] == 'N' ) nN++; if ( 2*nN > i - iaux->pos ) return -1; // Sort aux[] and dedup indel types int n_types = 1; ks_introsort(uint32_t, naux, aux); for (i=1; i= MAX_TYPES ) { static int warned = 0; if ( !warned ) { fprintf(bcftools_stderr, "Warning: excessive number of INDEL alleles at %s:%d, skipping. (This warning is printed only once)\n",iaux->chr,iaux->pos+1); warned = 1; } return -1; } // Fill out the types[] array detailing the size of insertion or deletion. iaux->ntypes = 0; iaux->max_ins_len = 0; for (i=0; iiref_type = iaux->ntypes; } else { if ( j-i >= iaux->bca->min_support ) is_ok = 1; // What is the best way to handle the -pmF options: // - consider only sites where a single indel type passes the -mF threshold, as opposed to all indel types cumulatively // - once a site passes, include all indel types in the evaluation, as opposed to considering only the strong candidates // In this implementation sites are selected by counting reads from all indel types cumulatively and all indel types // are considered. // Uncomment the following condition to consider only strong indel candidates once the site has been selected // if ( !iaux->bca->per_sample_flt && (double)(j-i) / n_tot < iaux->bca->min_frac ) is_ok = 0; } if ( is_ok ) { iaux->types[iaux->ntypes++] = isize; if ( isize > 0 && isize > iaux->max_ins_len ) iaux->max_ins_len = isize; } i = j-1; } if ( iaux->ntypes <= 1 ) return 0; // Init insertion types, including their sequence if ( iaux_init_ins_types(iaux) < 0 ) return -1; iaux_init_sequence_context(iaux); return iaux->ntypes; } #undef MINUS_CONST static int iaux_set_consensus(indel_aux_t *iaux, int ismpl) { if ( !iaux->rcns ) iaux->rcns = rcns_init(iaux->pos, iaux->left, iaux->right); else rcns_reset(iaux->rcns, iaux->pos, iaux->left, iaux->right); rcns_set_reads(iaux->rcns, iaux->plp[ismpl], iaux->nplp[ismpl]); iaux->cns_seq = rcns_get_consensus(iaux->rcns, iaux->ref + iaux->left); // todo: // rcns should also collect localized number of mismatches as a substitute // for uninformative MQ. This would not affect calling but would help with // filtering return 0; } #if 0 // Finds the smallest index in the seq_pos array holding value equal to pos, or if there is no // such value, the largest index with value smaller than pos. Starts at initial guess ioff. // This could use a binary search but the assumption is that the initial guess is indel-size close // to the actual coordinate. // // TODO: remove this function and seq_pos from cns creation as it seems unnecessary static int find_ref_offset(hts_pos_t pos, hts_pos_t *seq_pos, int nseq_pos, int ioff) { if ( ioff<0 ) ioff = 0; else if ( ioff >= nseq_pos ) ioff = nseq_pos - 1; if ( seq_pos[ioff] < pos ) { while ( ioff+1 < nseq_pos && seq_pos[ioff] < pos ) ioff++; if ( seq_pos[ioff] > pos ) ioff--; return ioff; } while ( ioff > 0 && seq_pos[ioff-1] >= pos ) ioff--; return ioff; } #endif static int iaux_align_read(indel_aux_t *iaux, bam1_t *bam, uint8_t *ref_seq, int nref_seq) { if ( bam->core.flag & BAM_FUNMAP ) return 1; // skip unmapped reads // Trim both ref and qry to the window of interest hts_pos_t ref_beg = iaux->left; // fa ref coordinates hts_pos_t ref_end = iaux->right < ref_beg + nref_seq ? iaux->right : ref_beg + nref_seq - 1; cigar_state_t cigar; cstate_init(&cigar,bam); int qry_off1, qry_off2, ref_off1, ref_off2; if ( ref_beg > bam->core.pos ) { // the read needs trimming from left qry_off1 = cstate_seek_fwd(&cigar, &ref_beg, 1); ref_off1 = ref_beg - iaux->left; if ( ref_beg + (bam->core.l_qseq - qry_off1) > ref_end ) { // the read needs trimming from right qry_off2 = ref_end - ref_beg + qry_off1; ref_off2 = ref_end - iaux->left; } else { // the ref template needs trimming from right qry_off2 = bam->core.l_qseq - 1; ref_off2 = ref_off1 + qry_off2 - qry_off1; } } else { // the ref template needs trimming from left qry_off1 = 0; ref_off1 = bam->core.pos - ref_beg; if ( bam->core.pos + bam->core.l_qseq - 1 > ref_end ) { // the read needs trimming from right ref_off2 = ref_end - iaux->left; qry_off2 = ref_off2 - ref_off1; } else { // the ref template needs trimming from right qry_off2 = bam->core.l_qseq - 1; ref_off2 = ref_off1 + qry_off2 - qry_off1; } } //fprintf(bcftools_stderr,"xtrim: %s .. left,right=%d,%d rbeg,end=%d,%d qpos=%d qlen=%d qoff=%d,%d roff=%d,%d rlen=%d\n",bam_get_qname(bam),iaux->left,iaux->right,(int)ref_beg,(int)ref_end,(int)bam->core.pos,bam->core.l_qseq, qry_off1,qry_off2,ref_off1,ref_off2,nref_seq); assert( qry_off1<=qry_off2 ); assert( qry_off1>=0 && qry_off1core.l_qseq ); assert( qry_off2>=0 && qry_off2core.l_qseq ); assert( ref_off1<=ref_off2 ); assert( ref_off1>=0 && ref_off1=0 && ref_off2nqry_seq < qlen ) { uint8_t *tmp = (uint8_t*) realloc(iaux->qry_seq, qlen); if ( !tmp ) return -1; // critical error iaux->qry_seq = tmp; iaux->nqry_seq = qlen; } uint8_t *seq = bam_get_seq(bam); for (i=qry_off1; i<=qry_off2; i++) iaux->qry_seq[i-qry_off1] = seq_nt16_int[bam_seqi(seq,i)]; // prepare qualities, either BQ or BAQ qualities (ZQ) if ( iaux->nqual < qlen ) { uint8_t *tmp = (uint8_t*) realloc(iaux->qual, qlen); if ( !tmp ) return -1; // critical error iaux->qual = tmp; iaux->nqual = qlen; } uint8_t *qual = iaux->qual; const uint8_t *qq = bam_get_qual(bam); const uint8_t *bq = (uint8_t*)bam_aux_get(bam, "ZQ"); if ( bq ) bq++; // skip type for (i=qry_off1; i<=qry_off2; i++) { int j = i - qry_off1; qual[j] = bq ? qq[i] + (bq[i] - 64) : qq[i]; if ( qual[j] > 30 ) qual[j] = 30; if ( qual[j] < 7 ) qual[j] = 7; } // Illumina probaln_par_t apf = { 1e-4, 1e-2, 10 }; // align int score = probaln_glocal(ref_seq + ref_off1, rlen, iaux->qry_seq, qlen, qual, &apf, 0, 0); int adj_score = (int)(100. * score / qlen + .499) * iaux->bca->indel_bias; #if DEBUG_ALN fprintf(bcftools_stderr,"aln: %d/%d\t%s\n\tref: ",score,adj_score,bam_get_qname(bam)); for (i=0; iqry_seq[i]]); fprintf(bcftools_stderr,"\n\tqual: "); for (i=0; i 255 ) adj_score = 255; return score<<8 | adj_score; } // Score all reads for this sample and indel type using the up to two consensus sequence templates. // On output sets iaux->read_scores[iread*ntypes+itype] = (raw_score<<8 | length_adjusted_score) static int iaux_score_reads(indel_aux_t *iaux, int ismpl, int itype) { int i; cns_seq_t *cns = iaux->cns_seq; while ( cns->nseq ) { // Resize buffers if necessary int ref_len = cns->nseq + iaux->types[itype]; if ( iaux->nref_seq < ref_len ) { uint8_t *ref_buf = (uint8_t*) realloc(iaux->ref_seq,sizeof(uint8_t)*ref_len); if ( !ref_buf ) return -1; iaux->ref_seq = ref_buf; iaux->nref_seq = ref_len; } // Apply the indel and create the template ref sequence... memcpy(iaux->ref_seq,cns->seq,(cns->ipos+1)*sizeof(*iaux->ref_seq)); if ( iaux->types[itype] < 0 ) // deletion memcpy(iaux->ref_seq + cns->ipos + 1, cns->seq + cns->ipos + 1 - iaux->types[itype], (cns->nseq - cns->ipos - 1 + iaux->types[itype])*sizeof(*iaux->ref_seq)); else { char *ins = &iaux->inscns[itype*iaux->max_ins_len]; for (i=0; itypes[itype]; i++) iaux->ref_seq[cns->ipos+1+i] = ins[i]; memcpy(iaux->ref_seq + cns->ipos + 1 + iaux->types[itype], cns->seq + 1 + cns->ipos, (cns->nseq - cns->ipos - 1)*sizeof(*iaux->ref_seq)); } #if DEBUG_ALN fprintf(bcftools_stderr,"template %d, type %d, sample %d: ",cns==iaux->cns_seq?0:1,itype,ismpl); for (i=0; iref_seq[i]]); fprintf(bcftools_stderr,"\n"); #endif // Align and score reads for (i=0; inplp[ismpl]; i++) { const bam_pileup1_t *plp = iaux->plp[ismpl] + i; int aln_score = iaux_align_read(iaux, plp->b, iaux->ref_seq, ref_len); int *score = &iaux->read_scores[i*iaux->ntypes+itype]; if ( cns==iaux->cns_seq || *score > aln_score ) *score = aln_score; } cns++; } return 0; } // Determines indel quality for each read and populates 22 bits of pileup aux field with // three integers as follows // plp->aux = indel_type << 16 | seqQ << 8 | indelQ static int iaux_eval_scored_reads(indel_aux_t *iaux, int ismpl) { int i,j; for (i=0; inplp[ismpl]; i++) { bam_pileup1_t *plp = iaux->plp[ismpl] + i; // Find the best indel type and the ref type, their scores difference is the indel quality int *score = &iaux->read_scores[i*iaux->ntypes]; int alt_score = INT_MAX, alt_j = 0; for (j=0; jiref_type; j++) if ( alt_score > score[j] ) alt_score = score[j], alt_j = j; for (j=iaux->iref_type+1; jntypes; j++) if ( alt_score > score[j] ) alt_score = score[j], alt_j = j; int ref_score = score[iaux->iref_type]; int sc0, sc1, j0; if ( alt_score < ref_score ) sc0 = alt_score, sc1 = ref_score, j0 = alt_j; else sc0 = ref_score, sc1 = alt_score, j0 = iaux->iref_type; int indelQ = (sc1>>8) - (sc0>>8); // low=bad, high=good int seqQ = iaux->ref_qual[alt_j]; // Reduce indelQ. High length-normalized alignment scores (i.e. bad alignments) // lower the quality more (e.g. gnuplot> plot [0:111] (1-x/111.)*255) int len_normQ = sc0 & 0xff; // length-normalized score of the best match (ref or alt) int adj_indelQ; // final indelQ used in calling if ( len_normQ > 111 ) { // In the original code reads matching badly to any indel type or reference had indelQ set to 0 // here and thus would be effectively removed from calling. This leads to problems when there are // many soft clipped reads and a few good matching indel reads (see noisy-softclips.bam in // mpileup-tests). Only the few good quality indel reads would become visible to the caller and // the indel would be called with high quality. Here we change the logic to make the badly matching // reads low quality reference reads. The threshold was set to make the test case still be called // as an indel, but with very low quality. // // Original code: // adj_indelQ = 0; // adj_indelQ = 12; j0 = iaux->iref_type; } else adj_indelQ = (int)((1. - len_normQ/111.) * indelQ + .499); #if DEBUG_ALN // Prints the selected indel type (itype); adjusted indelQ which will be used if bigger than seqQ; // raw indelQ; length-normalized indelQ and sequence context quality; ref and best alt indel type // and their raw and length-normalized scores fprintf(bcftools_stderr,"itype=%d adj_indelQ=%d\trawQ=%d\tlen_normQ=%d\tseqQ=%d\tref:%d=%d/%d alt:%d=%d/%d)\t%s\n", j0,adj_indelQ,indelQ,len_normQ,seqQ,iaux->iref_type,ref_score>>8,ref_score&0xff,alt_j,alt_score>>8,alt_score&0xff,bam_get_qname(plp->b)); #endif if ( adj_indelQ > seqQ ) adj_indelQ = seqQ; // seqQ already capped at 255 plp->aux = j0<<16 | seqQ<<8 | adj_indelQ; // use 22 bits in total iaux->sum_qual[j0] += adj_indelQ; } return 0; } // Find the best indel types, include the ref type plus maximum three alternate indel alleles. static int iaux_eval_best_indels(indel_aux_t *iaux) { bcf_callaux_t *bca = iaux->bca; bca->maxins = iaux->max_ins_len; bca->inscns = (char*) realloc(bca->inscns, bca->maxins * 4); if ( bca->maxins && !bca->inscns ) return -1; // insertion sort, descending, high-quality indels come first int i,j,t, tmp, *sumq = iaux->sum_qual, ntypes = iaux->ntypes; for (t=0; t0 && sumq[j] > sumq[j-1]; j--) tmp = sumq[j], sumq[j] = sumq[j-1], sumq[j-1] = tmp; for (t=0; tiref_type ) break; if ( t ) { // move the reference type to the first tmp = sumq[t]; for (; t>0; t--) sumq[t] = sumq[t-1]; sumq[0] = tmp; } // Initialize bca's structures and create a mapping between old and new types int old2new_type[MAX_TYPES]; for (t=0; tntypes; t++) { int itype = sumq[t] & 0x3f; old2new_type[itype] = t; if ( t>=4 ) continue; bca->indel_types[t] = iaux->types[itype]; if ( bca->indel_types[t] <= 0 ) continue; memcpy(&bca->inscns[t*bca->maxins], &iaux->inscns[itype*iaux->max_ins_len], bca->maxins); } // Update indel type in plp->aux for all reads int ismpl, n_alt = 0; for (ismpl=0; ismplnsmpl; ismpl++) { for (i=0; inplp[ismpl]; i++) { bam_pileup1_t *plp = iaux->plp[ismpl] + i; int itype_old = (plp->aux >> 16) & 0x3f; int itype_new = old2new_type[itype_old]; plp->aux = itype_new<<16 | (itype_new>=4 ? 0 : (plp->aux & 0xffff)); if ( itype_new>0 ) n_alt++; } } return n_alt; } /* notes: - n .. number of samples - the routine sets bam_pileup1_t.aux (27 bits) of each read as follows: - 5: unused - 6: the call; index to bcf_callaux_t.indel_types .. (aux>>16)&0x3f - 8: estimated sequence quality .. (aux>>8)&0xff - 8: indel quality .. aux&0xff */ int bcf_iaux_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref) { assert(!(ref == 0 || bca == 0)); // can this ever happen? when? if (ref == 0 || bca == 0) return -1; if ( !bca->iaux ) bca->iaux = calloc(1,sizeof(indel_aux_t)); indel_aux_t *iaux = bca->iaux; iaux->nsmpl = n; iaux->nplp = n_plp; iaux->plp = plp; iaux->bca = bca; iaux->ref = ref; iaux->pos = pos; iaux->chr = bca->chr; // Check if there is an indel at this position and if yes, find all indel types and determine // window boundaries. todo: We want this information cached so that for long reads we don't keep // redoing the whole analysis again and again int ntypes = iaux_init_types(iaux); if ( ntypes<=0 ) return -1; debug_print_types(iaux); // Create two template consensus sequences for each sample (assuming max diploid organism). // Then apply each indel type on top of the templates, realign every read and remember score int i,j; for (i=0; insmpl; i++) { iaux_set_consensus(iaux, i); iaux_init_scores(iaux, i); for (j=0; j 0 ? 0 : -1; } pysam-0.23.0/bcftools/bam2bcf_indel.c000066400000000000000000001041571475062545500174000ustar00rootroot00000000000000/* bam2bcf_indel.c -- indel caller. Copyright (C) 2010, 2011 Broad Institute. Copyright (C) 2012-2014,2016-2017, 2021 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "bam2bcf.h" #include "str_finder.h" #include KSORT_INIT_GENERIC(uint32_t) #define MINUS_CONST 0x10000000 #define MAX_TYPES 64 // Take a reference position tpos and convert to a query position (returned). // This uses the CIGAR string plus alignment c->pos to do the mapping. // // *_tpos is returned as tpos if query overlaps tpos, but for deletions // it'll be either the start (is_left) or end (!is_left) ref position. int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int is_left, int32_t *_tpos) { // x = pos in ref, y = pos in query seq int k, x = c->pos, y = 0, last_y = 0; *_tpos = c->pos; for (k = 0; k < c->n_cigar; ++k) { int op = cigar[k] & BAM_CIGAR_MASK; int l = cigar[k] >> BAM_CIGAR_SHIFT; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { if (c->pos > tpos) return y; if (x + l > tpos) { *_tpos = tpos; return y + (tpos - x); } x += l; y += l; last_y = y; } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l; else if (op == BAM_CDEL || op == BAM_CREF_SKIP) { if (x + l > tpos) { *_tpos = is_left? x : x + l; return y; } x += l; } } *_tpos = x; return last_y; } // FIXME: check if the inserted sequence is consistent with the homopolymer run // l is the relative gap length and l_run is the length of the homopolymer on the reference static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run) { int q, qh; q = bca->openQ + bca->extQ * (abs(l) - 1); qh = l_run >= 3? (int)(bca->tandemQ * (double)abs(l) / l_run + .499) : 1000; return q < qh? q : qh; } inline int est_indelreg(int pos, const char *ref, int l, char *ins4) { int i, j, max = 0, max_i = pos, score = 0; l = abs(l); for (i = pos + 1, j = 0; ref[i]; ++i, ++j) { if (ins4) score += (toupper(ref[i]) != "ACGTN"[(int)ins4[j%l]])? -10 : 1; else score += (toupper(ref[i]) != toupper(ref[pos+1+j%l]))? -10 : 1; if (score < 0) break; if (max < score) max = score, max_i = i; } return max_i - pos; } // Identify spft-clip length, position in seq, and clipped seq len void get_pos(const bcf_callaux_t *bca, bam_pileup1_t *p, int *sc_len_r, int *slen_r, int *epos_r, int *end) { bam1_t *b = p->b; int sc_len = 0, sc_dist = -1, at_left = 1; int epos = p->qpos, slen = b->core.l_qseq; int k; uint32_t *cigar = bam_get_cigar(b); *end = -1; for (k = 0; k < b->core.n_cigar; k++) { int op = bam_cigar_op(cigar[k]); if (op == BAM_CSOFT_CLIP) { slen -= bam_cigar_oplen(cigar[k]); if (at_left) { // left end sc_len += bam_cigar_oplen(cigar[k]); epos -= sc_len; // don't count SC in seq pos sc_dist = epos; *end = 0; } else { // right end int srlen = bam_cigar_oplen(cigar[k]); int rd = b->core.l_qseq - srlen - p->qpos; if (sc_dist < 0 || sc_dist > rd) { // closer to right end than left // FIXME: compensate for indel length too? sc_dist = rd; sc_len = srlen; *end = 1; } } } else if (op != BAM_CHARD_CLIP) { at_left = 0; } } if (p->indel > 0 && slen - (epos+p->indel) < epos) epos += p->indel-1; // end of insertion, if near end of seq // slen is now length of sequence minus soft-clips and // epos is position of indel in seq minus left-clip. *epos_r = (double)epos / (slen+1) * bca->npos; if (sc_len) { // scale importance of clip by distance to closest end *sc_len_r = 15.0*sc_len / (sc_dist+1); if (*sc_len_r > 99) *sc_len_r = 99; } else { *sc_len_r = 0; } *slen_r = slen; } // Part of bcf_call_gap_prep. // // Scans the pileup to identify all the different sizes of indels // present. // types[] returned is sorted by size, from smallest (maybe negative) to largest. // // Returns types and fills out n_types_r, max_rd_len_r and ref_type_r, // or NULL on error. static int *bcf_cgp_find_types(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, int *max_rd_len_r, int *n_types_r, int *ref_type_r, int *N_r) { int i, j, t, s, N, m, max_rd_len, n_types; int n_alt = 0, n_tot = 0, indel_support_ok = 0; uint32_t *aux; int *types; // N is the total number of reads for (s = N = 0; s < n; ++s) N += n_plp[s]; bca->max_support = bca->max_frac = 0; aux = (uint32_t*) calloc(N + 1, 4); if (!aux) return NULL; m = max_rd_len = 0; aux[m++] = MINUS_CONST; // zero indel is always a type (REF) // Fill out aux[] array with all the non-zero indel sizes. // Also tally number with indels (n_alt) and total (n_tot). for (s = 0; s < n; ++s) { int na = 0, nt = 0; for (i = 0; i < n_plp[s]; ++i) { const bam_pileup1_t *p = plp[s] + i; ++nt; if (p->indel != 0) { ++na; aux[m++] = MINUS_CONST + p->indel; } // FIXME: cache me in pileup struct. j = bam_cigar2qlen(p->b->core.n_cigar, bam_get_cigar(p->b)); if (j > max_rd_len) max_rd_len = j; } double frac = (double)na/nt; if ( !indel_support_ok && na >= bca->min_support && frac >= bca->min_frac ) indel_support_ok = 1; if ( na > bca->max_support && frac > 0 ) bca->max_support = na, bca->max_frac = frac; n_alt += na; n_tot += nt; } // Sort aux[] and dedup ks_introsort(uint32_t, m, aux); for (i = 1, n_types = 1; i < m; ++i) if (aux[i] != aux[i-1]) ++n_types; // Taking totals makes it hard to call rare indels (IMF filter) if ( !bca->per_sample_flt ) indel_support_ok = ( (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support ) ? 0 : 1; if ( n_types == 1 || !indel_support_ok ) { // then skip free(aux); return NULL; } // Bail out if we have far too many types of indel if (n_types >= MAX_TYPES) { free(aux); // TODO revisit how/whether to control printing this warning if (hts_verbose >= 2) fprintf(stderr, "[%s] excessive INDEL alleles at position %d. " "Skip the position.\n", __func__, pos + 1); return NULL; } // To prevent long stretches of N's to be mistaken for indels // (sometimes thousands of bases), check the number of N's in the // sequence and skip places where half or more reference bases are Ns. int nN=0, i_end = pos + (2*bca->indel_win_size < max_rd_len ?2*bca->indel_win_size : max_rd_len); for (i=pos; i(i-pos) ) { free(aux); return NULL; } // Finally fill out the types[] array detailing the size of insertion // or deletion. types = (int*)calloc(n_types, sizeof(int)); if (!types) { free(aux); return NULL; } t = 0; types[t++] = aux[0] - MINUS_CONST; for (i = 1; i < m; ++i) if (aux[i] != aux[i-1]) types[t++] = aux[i] - MINUS_CONST; free(aux); // Find reference type; types[?] == 0) for (t = 0; t < n_types; ++t) if (types[t] == 0) break; *ref_type_r = t; *n_types_r = n_types; *max_rd_len_r = max_rd_len; *N_r = N; return types; } // Part of bcf_call_gap_prep. // // Construct per-sample consensus. // // Returns an array of consensus seqs, // or NULL on failure. static char **bcf_cgp_ref_sample(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, int left, int right) { int i, k, s, L = right - left + 1, max_i, max2_i; char **ref_sample; // returned uint32_t *cns = NULL, max, max2; char *ref0 = NULL, *r; ref_sample = (char**) calloc(n, sizeof(char*)); cns = (uint32_t*) calloc(L, 4); ref0 = (char*) calloc(L, 1); if (!ref_sample || !cns || !ref0) { n = 0; goto err; } // Convert ref ASCII to 0-15. for (i = 0; i < right - left; ++i) ref0[i] = seq_nt16_table[(int)ref[i+left]]; // NB: one consensus per sample 'n', not per indel type. // FIXME: consider fixing this. We should compute alignments vs // types, not vs samples? Or types/sample combined? for (s = 0; s < n; ++s) { r = ref_sample[s] = (char*) calloc(L, 1); if (!r) { n = s-1; goto err; } memset(cns, 0, sizeof(int) * L); // collect ref and non-ref counts in cns for (i = 0; i < n_plp[s]; ++i) { bam_pileup1_t *p = plp[s] + i; bam1_t *b = p->b; uint32_t *cigar = bam_get_cigar(b); uint8_t *seq = bam_get_seq(b); int x = b->core.pos, y = 0; // TODO: pileup exposes pileup_ind, but we also need e.g. // pileup_len to know how much of the current CIGAR op-len // we've used (or have remaining). If we had that, we // could start at p->qpos without having to scan through // the entire CIGAR string until we find it. // // Without it about all we could do is have a side channel // to cache the last known coords. Messy, so punt for now. // This is no longer the bottle neck until we get to 1000s of // CIGAR ops. for (k = 0; k < b->core.n_cigar; ++k) { int op = cigar[k]&0xf; int j, l = cigar[k]>>4; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { if (x + l >= left) { j = left - x > 0 ? left - x : 0; int j_end = right - x < l ? right - x : l; for (; j < j_end; j++) // Append to cns. Note this is ref coords, // so insertions aren't in cns and deletions // will have lower coverage. // FIXME: want true consensus (with ins) per // type, so we can independently compare each // seq to each consensus and see which it // matches best, so we get proper GT analysis. cns[x+j-left] += (bam_seqi(seq, y+j) == ref0[x+j-left]) ? 1 // REF : (1<<16); // ALT } x += l; y += l; } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) { x += l; } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) { y += l; } if (x > right) break; } } // Determine a sample specific reference. for (i = 0; i < right - left; ++i) r[i] = ref0[i]; // Find deepest and 2nd deepest ALT region (max & max2). max = max2 = 0; max_i = max2_i = -1; for (i = 0; i < right - left; ++i) { if (cns[i]>>16 >= max>>16) max2 = max, max2_i = max_i, max = cns[i], max_i = i; else if (cns[i]>>16 >= max2>>16) max2 = cns[i], max2_i = i; } // Masks mismatches present in at least 70% of the reads with 'N'. // This code is nREF/(nREF+n_ALT) >= 70% for deepest region. // The effect is that at least 30% of bases differing to REF will // use "N" in consensus, so we don't penalise ALT or REF when // aligning against it. (A poor man IUPAC code) // // Why is it only done in two loci at most? if ((double)(max&0xffff) / ((max&0xffff) + (max>>16)) >= 0.7) max_i = -1; if ((double)(max2&0xffff) / ((max2&0xffff) + (max2>>16)) >= 0.7) max2_i = -1; if (max_i >= 0) r[max_i] = 15; if (max2_i >= 0) r[max2_i] = 15; //for (i = 0; i < right - left; ++i) // fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], stderr); //fputc('\n', stderr); } free(ref0); free(cns); return ref_sample; err: free(ref0); free(cns); if (ref_sample) { for (s = 0; s < n; s++) free(ref_sample[s]); free(ref_sample); } return NULL; } // The length of the homopolymer run around the current position int bcf_cgp_l_run(const char *ref, int pos) { int i, l_run; int c = seq_nt16_table[(int)ref[pos + 1]]; if (c == 15) { l_run = 1; } else { for (i = pos + 2; ref[i]; ++i) if (seq_nt16_table[(int)ref[i]] != c) break; l_run = i; for (i = pos; i >= 0; --i) if (seq_nt16_table[(int)ref[i]] != c) break; l_run -= i + 1; } return l_run; } // Compute the consensus for this sample 's', minus indels which // get added later. char *bcf_cgp_calc_cons(int n, int *n_plp, bam_pileup1_t **plp, int pos, int *types, int n_types, int max_ins, int s) { int i, j, t, k; int *inscns_aux = (int*)calloc(5 * n_types * max_ins, sizeof(int)); if (!inscns_aux) return NULL; // Count the number of occurrences of each base at each position for // each type of insertion. for (t = 0; t < n_types; ++t) { if (types[t] > 0) { for (s = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i) { bam_pileup1_t *p = plp[s] + i; if (p->indel == types[t]) { uint8_t *seq = bam_get_seq(p->b); for (k = 1; k <= p->indel; ++k) { int c = seq_nt16_int[bam_seqi(seq, p->qpos + k)]; assert(c<5); ++inscns_aux[(t*max_ins+(k-1))*5 + c]; } } } } } } // Use the majority rule to construct the consensus char *inscns = (char *)calloc(n_types * max_ins, 1); for (t = 0; t < n_types; ++t) { for (j = 0; j < types[t]; ++j) { int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*5]; for (k = 0; k < 5; ++k) if (ia[k] > max) max = ia[k], max_k = k; inscns[t*max_ins + j] = max ? max_k : 4; if (max_k == 4) { // discard insertions which contain N's types[t] = 0; break; } } } free(inscns_aux); return inscns; } #ifndef MIN # define MIN(a,b) ((a)<(b)?(a):(b)) #endif // Part of bcf_call_gap_prep. // // Realign using BAQ to get an alignment score of a single read vs // a haplotype consensus. // // Fills out score // Returns 0 on success, // <0 on error static int bcf_cgp_align_score(bam_pileup1_t *p, bcf_callaux_t *bca, int type, uint8_t *ref2, uint8_t *query, int r_start, int r_end, int long_read, int tbeg, int tend, int left, int right, int qbeg, int qend, int qpos, int max_deletion, int *score) { // Illumina probaln_par_t apf = { 1e-4, 1e-2, 10 }; // Parameters that work better on PacBio CCS 15k. // We should consider querying the header and RG PU field. // See also htslib/realn.c:sam_prob_realn() if (long_read) { apf.d = 1e-3; apf.e = 1e-1; } type = abs(type); apf.bw = type + 3; int l, sc; const uint8_t *qual = bam_get_qual(p->b), *bq; uint8_t *qq; // Get segment of quality, either ZQ tag or if absent QUAL. if (!(qq = (uint8_t*) calloc(qend - qbeg, 1))) return -1; bq = (uint8_t*)bam_aux_get(p->b, "ZQ"); if (bq) ++bq; // skip type for (l = qbeg; l < qend; ++l) { int qval = bq? qual[l] + (bq[l] - 64) : qual[l]; if (qval > 30) qval = 30; if (qval < 7) qval = 7; qq[l - qbeg] = qval; } // The bottom 8 bits are length-normalised score while // the top bits are unnormalised. sc = probaln_glocal(ref2 + tbeg - left, tend - tbeg + type, query, qend - qbeg, qq, &apf, 0, 0); if (sc < 0) { *score = 0xffffff; free(qq); return 0; } // used for adjusting indelQ below l = (int)(100. * sc / (qend - qbeg) + .499) * bca->indel_bias; *score = sc<<8 | MIN(255, l); rep_ele *reps, *elt, *tmp; uint8_t *seg = ref2 + tbeg - left; int seg_len = tend - tbeg + type; // Note: although seg moves (tbeg varies), ref2 is reused many times // so we could factor out some find_STR calls. However it's not the // bottleneck for now. // FIXME: need to make this work on IUPAC. reps = find_STR((char *)seg, seg_len, 0); int iscore = 0; // Identify STRs in ref covering the indel up to // (or close to) the end of the sequence. // Those having an indel and right at the sequence // end do not confirm the total length of indel // size. Specifically a *lack* of indel at the // end, where we know indels occur in other // sequences, is a possible reference bias. // // This is emphasised further if the sequence ends with // soft clipping. DL_FOREACH_SAFE(reps, elt, tmp) { if (elt->start <= qpos && elt->end >= qpos) { iscore += (elt->end-elt->start) / elt->rep_len; // c if (elt->start+tbeg <= r_start || elt->end+tbeg >= r_end) iscore += 2*(elt->end-elt->start); } DL_DELETE(reps, elt); free(elt); } // Apply STR score to existing indelQ l = (*score&0xff)*.8 + iscore*2; *score = (*score & ~0xff) | MIN(255, l); free(qq); return 0; } // Part of bcf_call_gap_prep. // // Returns n_alt on success // -1 on failure static int bcf_cgp_compute_indelQ(int n, int *n_plp, bam_pileup1_t **plp, bcf_callaux_t *bca, char *inscns, int l_run, int max_ins, int ref_type, int *types, int n_types, int *score) { // FIXME: n_types has a maximum; no need to alloc - use a #define? int sc[MAX_TYPES], sumq[MAX_TYPES], s, i, j, t, K, n_alt, tmp; memset(sumq, 0, n_types * sizeof(int)); for (s = K = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i, ++K) { bam_pileup1_t *p = plp[s] + i; int *sct = &score[K*n_types], seqQ, indelQ; for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t; for (t = 1; t < n_types; ++t) // insertion sort for (j = t; j > 0 && sc[j] < sc[j-1]; --j) tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp; /* errmod_cal() assumes that if the call is wrong, the * likelihoods of other events are equal. This is about * right for substitutions, but is not desired for * indels. To reuse errmod_cal(), I have to make * compromise for multi-allelic indels. */ if ((sc[0]&0x3f) == ref_type) { indelQ = (sc[1]>>14) - (sc[0]>>14); seqQ = est_seqQ(bca, types[sc[1]&0x3f], l_run); } else { for (t = 0; t < n_types; ++t) // look for the reference type if ((sc[t]&0x3f) == ref_type) break; indelQ = (sc[t]>>14) - (sc[0]>>14); seqQ = est_seqQ(bca, types[sc[0]&0x3f], l_run); } tmp = sc[0]>>6 & 0xff; // reduce indelQ indelQ = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ + .499); // Doesn't really help accuracy, but permits -h to take // affect still. if (indelQ > seqQ) indelQ = seqQ; if (indelQ > 255) indelQ = 255; if (seqQ > 255) seqQ = 255; p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ; // use 22 bits in total sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ; // fprintf(stderr, "pos=%d read=%d:%d name=%s call=%d indelQ=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ, seqQ); } } // determine bca->indel_types[] and bca->inscns bca->maxins = max_ins; bca->inscns = (char*) realloc(bca->inscns, bca->maxins * 4); if (bca->maxins && !bca->inscns) return -1; for (t = 0; t < n_types; ++t) sumq[t] = sumq[t]<<6 | t; for (t = 1; t < n_types; ++t) // insertion sort for (j = t; j > 0 && sumq[j] > sumq[j-1]; --j) tmp = sumq[j], sumq[j] = sumq[j-1], sumq[j-1] = tmp; for (t = 0; t < n_types; ++t) // look for the reference type if ((sumq[t]&0x3f) == ref_type) break; if (t) { // then move the reference type to the first tmp = sumq[t]; for (; t > 0; --t) sumq[t] = sumq[t-1]; sumq[0] = tmp; } for (t = 0; t < 4; ++t) bca->indel_types[t] = B2B_INDEL_NULL; for (t = 0; t < 4 && t < n_types; ++t) { bca->indel_types[t] = types[sumq[t]&0x3f]; if (bca->maxins) memcpy(&bca->inscns[t * bca->maxins], &inscns[(sumq[t]&0x3f) * max_ins], bca->maxins); } // update p->aux for (s = n_alt = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i) { bam_pileup1_t *p = plp[s] + i; int x = types[p->aux>>16&0x3f]; for (j = 0; j < 4; ++j) if (x == bca->indel_types[j]) break; p->aux = j<<16 | (j == 4? 0 : (p->aux&0xffff)); if ((p->aux>>16&0x3f) > 0) ++n_alt; //fprintf(stderr, "X pos=%d read=%d:%d name=%s call=%d type=%d seqQ=%d indelQ=%d\n", pos, s, i, bam_get_qname(p->b), (p->aux>>16)&0x3f, bca->indel_types[(p->aux>>16)&0x3f], (p->aux>>8)&0xff, p->aux&0xff); } } return n_alt; } /* FIXME: with high number of samples, do we handle IMF correctly? Is it fraction of indels across entire data set, or just fraction for this specific sample? Needs to check bca->per_sample_flt (--per-sample-mF) opt. */ /* notes: - n .. number of samples - the routine sets bam_pileup1_t.aux of each read as follows: - 6: unused - 6: the call; index to bcf_callaux_t.indel_types .. (aux>>16)&0x3f - 8: estimated sequence quality .. (aux>>8)&0xff - 8: indel quality .. aux&0xff */ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref) { if (ref == 0 || bca == 0) return -1; int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins; int *score, max_ref2; int N, K, l_run, ref_type, n_alt; char *inscns = 0, *ref2, *query, **ref_sample; // determine if there is a gap for (s = N = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i) if (plp[s][i].indel != 0) break; if (i < n_plp[s]) break; } if (s == n) // there is no indel at this position. return -1; // find out how many types of indels are present types = bcf_cgp_find_types(n, n_plp, plp, pos, bca, ref, &max_rd_len, &n_types, &ref_type, &N); if (!types) return -1; // calculate left and right boundary left = pos > bca->indel_win_size ? pos - bca->indel_win_size : 0; right = pos + bca->indel_win_size; if (types[0] < 0) right -= types[0]; // in case the alignments stand out the reference for (i = pos; i < right; ++i) if (ref[i] == 0) break; right = i; /* The following call fixes a long-existing flaw in the INDEL * calling model: the interference of nearby SNPs. However, it also * reduces the power because sometimes, substitutions caused by * indels are not distinguishable from true mutations. Multiple * sequence realignment helps to increase the power. * * Masks mismatches present in at least 70% of the reads with 'N'. */ ref_sample = bcf_cgp_ref_sample(n, n_plp, plp, pos, bca, ref, left, right); // The length of the homopolymer run around the current position l_run = bcf_cgp_l_run(ref, pos); // construct the consensus sequence (minus indels, which are added later) max_ins = types[n_types - 1]; // max_ins is at least 0 if (max_ins > 0) { inscns = bcf_cgp_calc_cons(n, n_plp, plp, pos, types, n_types, max_ins, s); if (!inscns) return -1; } // compute the likelihood given each type of indel for each read max_ref2 = right - left + 2 + 2 * (max_ins > -types[0]? max_ins : -types[0]); ref2 = (char*) calloc(max_ref2, 1); query = (char*) calloc(right - left + max_rd_len + max_ins + 2, 1); score = (int*) calloc(N * n_types, sizeof(int)); bca->indelreg = 0; double nqual_over_60 = bca->nqual / 60.0; for (t = 0; t < n_types; ++t) { int l, ir; // compute indelreg if (types[t] == 0) ir = 0; else if (types[t] > 0) ir = est_indelreg(pos, ref, types[t], &inscns[t*max_ins]); else ir = est_indelreg(pos, ref, -types[t], 0); if (ir > bca->indelreg) bca->indelreg = ir; // Identify max deletion length int max_deletion = 0; for (s = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i, ++K) { bam_pileup1_t *p = plp[s] + i; if (max_deletion < -p->indel) max_deletion = -p->indel; } } // Realignment score, computed via BAQ for (s = K = 0; s < n; ++s) { // Construct ref2 from ref_sample, inscns and indels. // This is now the true sample consensus (possibly prepended // and appended with reference if sample data doesn't span // the full length). for (k = 0, j = left; j <= pos; ++j) ref2[k++] = seq_nt16_int[(int)ref_sample[s][j-left]]; if (types[t] <= 0) j += -types[t]; else for (l = 0; l < types[t]; ++l) ref2[k++] = inscns[t*max_ins + l]; for (; j < right && ref[j]; ++j) ref2[k++] = seq_nt16_int[(int)ref_sample[s][j-left]]; for (; k < max_ref2; ++k) ref2[k] = 4; if (right > j) right = j; // align each read to ref2 for (i = 0; i < n_plp[s]; ++i, ++K) { bam_pileup1_t *p = plp[s] + i; // Some basic ref vs alt stats. int imq = p->b->core.qual > 59 ? 59 : p->b->core.qual; imq *= nqual_over_60; int sc_len, slen, epos, sc_end; // Only need to gather stats on one type, as it's // identical calculation for all the subsequent ones // and we're sharing the same stats array if (t == 0) { // Gather stats for INFO field to aid filtering. // mq and sc_len not very helpful for filtering, but could // help in assigning a better QUAL value. // // Pos is slightly useful. // Base qual can be useful, but need qual prior to BAQ? // May need to cache orig quals in aux tag so we can fetch // them even after mpileup step. get_pos(bca, p, &sc_len, &slen, &epos, &sc_end); assert(imq >= 0 && imq < bca->nqual); assert(epos >= 0 && epos < bca->npos); assert(sc_len >= 0 && sc_len < 100); if (p->indel) { bca->ialt_mq[imq]++; bca->ialt_scl[sc_len]++; bca->ialt_pos[epos]++; } else { bca->iref_mq[imq]++; bca->iref_scl[sc_len]++; bca->iref_pos[epos]++; } } int qbeg, qpos, qend, tbeg, tend, kk; uint8_t *seq = bam_get_seq(p->b); uint32_t *cigar = bam_get_cigar(p->b); if (p->b->core.flag & BAM_FUNMAP) continue; // FIXME: the following loop should be better moved outside; // nonetheless, realignment should be much slower anyway. for (kk = 0; kk < p->b->core.n_cigar; ++kk) if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP) break; if (kk < p->b->core.n_cigar) continue; // determine the start and end of sequences for alignment // FIXME: loops over CIGAR multiple times int left2 = left, right2 = right; if (p->b->core.l_qseq > 1000) { // long read data needs less context. It also tends to // have many more candidate indels to investigate so // speed here matters more. if (pos - left >= bca->indel_win_size) left2 += bca->indel_win_size/2; if (right-pos >= bca->indel_win_size) right2 -= bca->indel_win_size/2; } int r_start = p->b->core.pos; int r_end = bam_cigar2rlen(p->b->core.n_cigar, bam_get_cigar(p->b)) -1 + r_start; qbeg = tpos2qpos(&p->b->core, bam_get_cigar(p->b), left2, 0, &tbeg); qpos = tpos2qpos(&p->b->core, bam_get_cigar(p->b), pos, 0, &tend) - qbeg; qend = tpos2qpos(&p->b->core, bam_get_cigar(p->b), right2, 1, &tend); if (types[t] < 0) { int l = -types[t]; tbeg = tbeg - l > left? tbeg - l : left; } // write the query sequence for (l = qbeg; l < qend; ++l) query[l - qbeg] = seq_nt16_int[bam_seqi(seq, l)]; // A fudge for now. Consider checking SAM header for // RG platform field. int long_read = p->b->core.l_qseq > 1000; // do realignment; this is the bottleneck if (tend > tbeg) { if (bcf_cgp_align_score(p, bca, types[t], (uint8_t *)ref2 + left2-left, (uint8_t *)query, r_start, r_end, long_read, tbeg, tend, left2, right2, qbeg, qend, qpos, max_deletion, &score[K*n_types + t]) < 0) { score[K*n_types + t] = 0xffffff; return -1; } } else { // place holder large cost for reads that cover the // region entirely within a deletion (thus tend < tbeg). score[K*n_types + t] = 0xffffff; } #if 0 for (l = 0; l < tend - tbeg + abs(types[t]); ++l) fputc("ACGTN"[(int)ref2[tbeg-left+l]], stderr); fputc('\n', stderr); for (l = 0; l < qend - qbeg; ++l) fputc("ACGTN"[(int)query[l]], stderr); fputc('\n', stderr); fprintf(stderr, "pos=%d type=%d read=%d:%d name=%s " "qbeg=%d tbeg=%d score=%d\n", pos, types[t], s, i, bam_get_qname(p->b), qbeg, tbeg, score[K*n_types + t]); #endif } } } // compute indelQ n_alt = bcf_cgp_compute_indelQ(n, n_plp, plp, bca, inscns, l_run, max_ins, ref_type, types, n_types, score); // free free(ref2); free(query); free(score); for (i = 0; i < n; ++i) free(ref_sample[i]); free(ref_sample); free(types); free(inscns); return n_alt > 0? 0 : -1; } pysam-0.23.0/bcftools/bam2bcf_indel.c.pysam.c000066400000000000000000001043461475062545500207510ustar00rootroot00000000000000#include "bcftools.pysam.h" /* bam2bcf_indel.c -- indel caller. Copyright (C) 2010, 2011 Broad Institute. Copyright (C) 2012-2014,2016-2017, 2021 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "bam2bcf.h" #include "str_finder.h" #include KSORT_INIT_GENERIC(uint32_t) #define MINUS_CONST 0x10000000 #define MAX_TYPES 64 // Take a reference position tpos and convert to a query position (returned). // This uses the CIGAR string plus alignment c->pos to do the mapping. // // *_tpos is returned as tpos if query overlaps tpos, but for deletions // it'll be either the start (is_left) or end (!is_left) ref position. int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int is_left, int32_t *_tpos) { // x = pos in ref, y = pos in query seq int k, x = c->pos, y = 0, last_y = 0; *_tpos = c->pos; for (k = 0; k < c->n_cigar; ++k) { int op = cigar[k] & BAM_CIGAR_MASK; int l = cigar[k] >> BAM_CIGAR_SHIFT; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { if (c->pos > tpos) return y; if (x + l > tpos) { *_tpos = tpos; return y + (tpos - x); } x += l; y += l; last_y = y; } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l; else if (op == BAM_CDEL || op == BAM_CREF_SKIP) { if (x + l > tpos) { *_tpos = is_left? x : x + l; return y; } x += l; } } *_tpos = x; return last_y; } // FIXME: check if the inserted sequence is consistent with the homopolymer run // l is the relative gap length and l_run is the length of the homopolymer on the reference static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run) { int q, qh; q = bca->openQ + bca->extQ * (abs(l) - 1); qh = l_run >= 3? (int)(bca->tandemQ * (double)abs(l) / l_run + .499) : 1000; return q < qh? q : qh; } inline int est_indelreg(int pos, const char *ref, int l, char *ins4) { int i, j, max = 0, max_i = pos, score = 0; l = abs(l); for (i = pos + 1, j = 0; ref[i]; ++i, ++j) { if (ins4) score += (toupper(ref[i]) != "ACGTN"[(int)ins4[j%l]])? -10 : 1; else score += (toupper(ref[i]) != toupper(ref[pos+1+j%l]))? -10 : 1; if (score < 0) break; if (max < score) max = score, max_i = i; } return max_i - pos; } // Identify spft-clip length, position in seq, and clipped seq len void get_pos(const bcf_callaux_t *bca, bam_pileup1_t *p, int *sc_len_r, int *slen_r, int *epos_r, int *end) { bam1_t *b = p->b; int sc_len = 0, sc_dist = -1, at_left = 1; int epos = p->qpos, slen = b->core.l_qseq; int k; uint32_t *cigar = bam_get_cigar(b); *end = -1; for (k = 0; k < b->core.n_cigar; k++) { int op = bam_cigar_op(cigar[k]); if (op == BAM_CSOFT_CLIP) { slen -= bam_cigar_oplen(cigar[k]); if (at_left) { // left end sc_len += bam_cigar_oplen(cigar[k]); epos -= sc_len; // don't count SC in seq pos sc_dist = epos; *end = 0; } else { // right end int srlen = bam_cigar_oplen(cigar[k]); int rd = b->core.l_qseq - srlen - p->qpos; if (sc_dist < 0 || sc_dist > rd) { // closer to right end than left // FIXME: compensate for indel length too? sc_dist = rd; sc_len = srlen; *end = 1; } } } else if (op != BAM_CHARD_CLIP) { at_left = 0; } } if (p->indel > 0 && slen - (epos+p->indel) < epos) epos += p->indel-1; // end of insertion, if near end of seq // slen is now length of sequence minus soft-clips and // epos is position of indel in seq minus left-clip. *epos_r = (double)epos / (slen+1) * bca->npos; if (sc_len) { // scale importance of clip by distance to closest end *sc_len_r = 15.0*sc_len / (sc_dist+1); if (*sc_len_r > 99) *sc_len_r = 99; } else { *sc_len_r = 0; } *slen_r = slen; } // Part of bcf_call_gap_prep. // // Scans the pileup to identify all the different sizes of indels // present. // types[] returned is sorted by size, from smallest (maybe negative) to largest. // // Returns types and fills out n_types_r, max_rd_len_r and ref_type_r, // or NULL on error. static int *bcf_cgp_find_types(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, int *max_rd_len_r, int *n_types_r, int *ref_type_r, int *N_r) { int i, j, t, s, N, m, max_rd_len, n_types; int n_alt = 0, n_tot = 0, indel_support_ok = 0; uint32_t *aux; int *types; // N is the total number of reads for (s = N = 0; s < n; ++s) N += n_plp[s]; bca->max_support = bca->max_frac = 0; aux = (uint32_t*) calloc(N + 1, 4); if (!aux) return NULL; m = max_rd_len = 0; aux[m++] = MINUS_CONST; // zero indel is always a type (REF) // Fill out aux[] array with all the non-zero indel sizes. // Also tally number with indels (n_alt) and total (n_tot). for (s = 0; s < n; ++s) { int na = 0, nt = 0; for (i = 0; i < n_plp[s]; ++i) { const bam_pileup1_t *p = plp[s] + i; ++nt; if (p->indel != 0) { ++na; aux[m++] = MINUS_CONST + p->indel; } // FIXME: cache me in pileup struct. j = bam_cigar2qlen(p->b->core.n_cigar, bam_get_cigar(p->b)); if (j > max_rd_len) max_rd_len = j; } double frac = (double)na/nt; if ( !indel_support_ok && na >= bca->min_support && frac >= bca->min_frac ) indel_support_ok = 1; if ( na > bca->max_support && frac > 0 ) bca->max_support = na, bca->max_frac = frac; n_alt += na; n_tot += nt; } // Sort aux[] and dedup ks_introsort(uint32_t, m, aux); for (i = 1, n_types = 1; i < m; ++i) if (aux[i] != aux[i-1]) ++n_types; // Taking totals makes it hard to call rare indels (IMF filter) if ( !bca->per_sample_flt ) indel_support_ok = ( (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support ) ? 0 : 1; if ( n_types == 1 || !indel_support_ok ) { // then skip free(aux); return NULL; } // Bail out if we have far too many types of indel if (n_types >= MAX_TYPES) { free(aux); // TODO revisit how/whether to control printing this warning if (hts_verbose >= 2) fprintf(bcftools_stderr, "[%s] excessive INDEL alleles at position %d. " "Skip the position.\n", __func__, pos + 1); return NULL; } // To prevent long stretches of N's to be mistaken for indels // (sometimes thousands of bases), check the number of N's in the // sequence and skip places where half or more reference bases are Ns. int nN=0, i_end = pos + (2*bca->indel_win_size < max_rd_len ?2*bca->indel_win_size : max_rd_len); for (i=pos; i(i-pos) ) { free(aux); return NULL; } // Finally fill out the types[] array detailing the size of insertion // or deletion. types = (int*)calloc(n_types, sizeof(int)); if (!types) { free(aux); return NULL; } t = 0; types[t++] = aux[0] - MINUS_CONST; for (i = 1; i < m; ++i) if (aux[i] != aux[i-1]) types[t++] = aux[i] - MINUS_CONST; free(aux); // Find reference type; types[?] == 0) for (t = 0; t < n_types; ++t) if (types[t] == 0) break; *ref_type_r = t; *n_types_r = n_types; *max_rd_len_r = max_rd_len; *N_r = N; return types; } // Part of bcf_call_gap_prep. // // Construct per-sample consensus. // // Returns an array of consensus seqs, // or NULL on failure. static char **bcf_cgp_ref_sample(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, int left, int right) { int i, k, s, L = right - left + 1, max_i, max2_i; char **ref_sample; // returned uint32_t *cns = NULL, max, max2; char *ref0 = NULL, *r; ref_sample = (char**) calloc(n, sizeof(char*)); cns = (uint32_t*) calloc(L, 4); ref0 = (char*) calloc(L, 1); if (!ref_sample || !cns || !ref0) { n = 0; goto err; } // Convert ref ASCII to 0-15. for (i = 0; i < right - left; ++i) ref0[i] = seq_nt16_table[(int)ref[i+left]]; // NB: one consensus per sample 'n', not per indel type. // FIXME: consider fixing this. We should compute alignments vs // types, not vs samples? Or types/sample combined? for (s = 0; s < n; ++s) { r = ref_sample[s] = (char*) calloc(L, 1); if (!r) { n = s-1; goto err; } memset(cns, 0, sizeof(int) * L); // collect ref and non-ref counts in cns for (i = 0; i < n_plp[s]; ++i) { bam_pileup1_t *p = plp[s] + i; bam1_t *b = p->b; uint32_t *cigar = bam_get_cigar(b); uint8_t *seq = bam_get_seq(b); int x = b->core.pos, y = 0; // TODO: pileup exposes pileup_ind, but we also need e.g. // pileup_len to know how much of the current CIGAR op-len // we've used (or have remaining). If we had that, we // could start at p->qpos without having to scan through // the entire CIGAR string until we find it. // // Without it about all we could do is have a side channel // to cache the last known coords. Messy, so punt for now. // This is no longer the bottle neck until we get to 1000s of // CIGAR ops. for (k = 0; k < b->core.n_cigar; ++k) { int op = cigar[k]&0xf; int j, l = cigar[k]>>4; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { if (x + l >= left) { j = left - x > 0 ? left - x : 0; int j_end = right - x < l ? right - x : l; for (; j < j_end; j++) // Append to cns. Note this is ref coords, // so insertions aren't in cns and deletions // will have lower coverage. // FIXME: want true consensus (with ins) per // type, so we can independently compare each // seq to each consensus and see which it // matches best, so we get proper GT analysis. cns[x+j-left] += (bam_seqi(seq, y+j) == ref0[x+j-left]) ? 1 // REF : (1<<16); // ALT } x += l; y += l; } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) { x += l; } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) { y += l; } if (x > right) break; } } // Determine a sample specific reference. for (i = 0; i < right - left; ++i) r[i] = ref0[i]; // Find deepest and 2nd deepest ALT region (max & max2). max = max2 = 0; max_i = max2_i = -1; for (i = 0; i < right - left; ++i) { if (cns[i]>>16 >= max>>16) max2 = max, max2_i = max_i, max = cns[i], max_i = i; else if (cns[i]>>16 >= max2>>16) max2 = cns[i], max2_i = i; } // Masks mismatches present in at least 70% of the reads with 'N'. // This code is nREF/(nREF+n_ALT) >= 70% for deepest region. // The effect is that at least 30% of bases differing to REF will // use "N" in consensus, so we don't penalise ALT or REF when // aligning against it. (A poor man IUPAC code) // // Why is it only done in two loci at most? if ((double)(max&0xffff) / ((max&0xffff) + (max>>16)) >= 0.7) max_i = -1; if ((double)(max2&0xffff) / ((max2&0xffff) + (max2>>16)) >= 0.7) max2_i = -1; if (max_i >= 0) r[max_i] = 15; if (max2_i >= 0) r[max2_i] = 15; //for (i = 0; i < right - left; ++i) // fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], bcftools_stderr); //fputc('\n', bcftools_stderr); } free(ref0); free(cns); return ref_sample; err: free(ref0); free(cns); if (ref_sample) { for (s = 0; s < n; s++) free(ref_sample[s]); free(ref_sample); } return NULL; } // The length of the homopolymer run around the current position int bcf_cgp_l_run(const char *ref, int pos) { int i, l_run; int c = seq_nt16_table[(int)ref[pos + 1]]; if (c == 15) { l_run = 1; } else { for (i = pos + 2; ref[i]; ++i) if (seq_nt16_table[(int)ref[i]] != c) break; l_run = i; for (i = pos; i >= 0; --i) if (seq_nt16_table[(int)ref[i]] != c) break; l_run -= i + 1; } return l_run; } // Compute the consensus for this sample 's', minus indels which // get added later. char *bcf_cgp_calc_cons(int n, int *n_plp, bam_pileup1_t **plp, int pos, int *types, int n_types, int max_ins, int s) { int i, j, t, k; int *inscns_aux = (int*)calloc(5 * n_types * max_ins, sizeof(int)); if (!inscns_aux) return NULL; // Count the number of occurrences of each base at each position for // each type of insertion. for (t = 0; t < n_types; ++t) { if (types[t] > 0) { for (s = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i) { bam_pileup1_t *p = plp[s] + i; if (p->indel == types[t]) { uint8_t *seq = bam_get_seq(p->b); for (k = 1; k <= p->indel; ++k) { int c = seq_nt16_int[bam_seqi(seq, p->qpos + k)]; assert(c<5); ++inscns_aux[(t*max_ins+(k-1))*5 + c]; } } } } } } // Use the majority rule to construct the consensus char *inscns = (char *)calloc(n_types * max_ins, 1); for (t = 0; t < n_types; ++t) { for (j = 0; j < types[t]; ++j) { int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*5]; for (k = 0; k < 5; ++k) if (ia[k] > max) max = ia[k], max_k = k; inscns[t*max_ins + j] = max ? max_k : 4; if (max_k == 4) { // discard insertions which contain N's types[t] = 0; break; } } } free(inscns_aux); return inscns; } #ifndef MIN # define MIN(a,b) ((a)<(b)?(a):(b)) #endif // Part of bcf_call_gap_prep. // // Realign using BAQ to get an alignment score of a single read vs // a haplotype consensus. // // Fills out score // Returns 0 on success, // <0 on error static int bcf_cgp_align_score(bam_pileup1_t *p, bcf_callaux_t *bca, int type, uint8_t *ref2, uint8_t *query, int r_start, int r_end, int long_read, int tbeg, int tend, int left, int right, int qbeg, int qend, int qpos, int max_deletion, int *score) { // Illumina probaln_par_t apf = { 1e-4, 1e-2, 10 }; // Parameters that work better on PacBio CCS 15k. // We should consider querying the header and RG PU field. // See also htslib/realn.c:sam_prob_realn() if (long_read) { apf.d = 1e-3; apf.e = 1e-1; } type = abs(type); apf.bw = type + 3; int l, sc; const uint8_t *qual = bam_get_qual(p->b), *bq; uint8_t *qq; // Get segment of quality, either ZQ tag or if absent QUAL. if (!(qq = (uint8_t*) calloc(qend - qbeg, 1))) return -1; bq = (uint8_t*)bam_aux_get(p->b, "ZQ"); if (bq) ++bq; // skip type for (l = qbeg; l < qend; ++l) { int qval = bq? qual[l] + (bq[l] - 64) : qual[l]; if (qval > 30) qval = 30; if (qval < 7) qval = 7; qq[l - qbeg] = qval; } // The bottom 8 bits are length-normalised score while // the top bits are unnormalised. sc = probaln_glocal(ref2 + tbeg - left, tend - tbeg + type, query, qend - qbeg, qq, &apf, 0, 0); if (sc < 0) { *score = 0xffffff; free(qq); return 0; } // used for adjusting indelQ below l = (int)(100. * sc / (qend - qbeg) + .499) * bca->indel_bias; *score = sc<<8 | MIN(255, l); rep_ele *reps, *elt, *tmp; uint8_t *seg = ref2 + tbeg - left; int seg_len = tend - tbeg + type; // Note: although seg moves (tbeg varies), ref2 is reused many times // so we could factor out some find_STR calls. However it's not the // bottleneck for now. // FIXME: need to make this work on IUPAC. reps = find_STR((char *)seg, seg_len, 0); int iscore = 0; // Identify STRs in ref covering the indel up to // (or close to) the end of the sequence. // Those having an indel and right at the sequence // end do not confirm the total length of indel // size. Specifically a *lack* of indel at the // end, where we know indels occur in other // sequences, is a possible reference bias. // // This is emphasised further if the sequence ends with // soft clipping. DL_FOREACH_SAFE(reps, elt, tmp) { if (elt->start <= qpos && elt->end >= qpos) { iscore += (elt->end-elt->start) / elt->rep_len; // c if (elt->start+tbeg <= r_start || elt->end+tbeg >= r_end) iscore += 2*(elt->end-elt->start); } DL_DELETE(reps, elt); free(elt); } // Apply STR score to existing indelQ l = (*score&0xff)*.8 + iscore*2; *score = (*score & ~0xff) | MIN(255, l); free(qq); return 0; } // Part of bcf_call_gap_prep. // // Returns n_alt on success // -1 on failure static int bcf_cgp_compute_indelQ(int n, int *n_plp, bam_pileup1_t **plp, bcf_callaux_t *bca, char *inscns, int l_run, int max_ins, int ref_type, int *types, int n_types, int *score) { // FIXME: n_types has a maximum; no need to alloc - use a #define? int sc[MAX_TYPES], sumq[MAX_TYPES], s, i, j, t, K, n_alt, tmp; memset(sumq, 0, n_types * sizeof(int)); for (s = K = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i, ++K) { bam_pileup1_t *p = plp[s] + i; int *sct = &score[K*n_types], seqQ, indelQ; for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t; for (t = 1; t < n_types; ++t) // insertion sort for (j = t; j > 0 && sc[j] < sc[j-1]; --j) tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp; /* errmod_cal() assumes that if the call is wrong, the * likelihoods of other events are equal. This is about * right for substitutions, but is not desired for * indels. To reuse errmod_cal(), I have to make * compromise for multi-allelic indels. */ if ((sc[0]&0x3f) == ref_type) { indelQ = (sc[1]>>14) - (sc[0]>>14); seqQ = est_seqQ(bca, types[sc[1]&0x3f], l_run); } else { for (t = 0; t < n_types; ++t) // look for the reference type if ((sc[t]&0x3f) == ref_type) break; indelQ = (sc[t]>>14) - (sc[0]>>14); seqQ = est_seqQ(bca, types[sc[0]&0x3f], l_run); } tmp = sc[0]>>6 & 0xff; // reduce indelQ indelQ = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ + .499); // Doesn't really help accuracy, but permits -h to take // affect still. if (indelQ > seqQ) indelQ = seqQ; if (indelQ > 255) indelQ = 255; if (seqQ > 255) seqQ = 255; p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ; // use 22 bits in total sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ; // fprintf(bcftools_stderr, "pos=%d read=%d:%d name=%s call=%d indelQ=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ, seqQ); } } // determine bca->indel_types[] and bca->inscns bca->maxins = max_ins; bca->inscns = (char*) realloc(bca->inscns, bca->maxins * 4); if (bca->maxins && !bca->inscns) return -1; for (t = 0; t < n_types; ++t) sumq[t] = sumq[t]<<6 | t; for (t = 1; t < n_types; ++t) // insertion sort for (j = t; j > 0 && sumq[j] > sumq[j-1]; --j) tmp = sumq[j], sumq[j] = sumq[j-1], sumq[j-1] = tmp; for (t = 0; t < n_types; ++t) // look for the reference type if ((sumq[t]&0x3f) == ref_type) break; if (t) { // then move the reference type to the first tmp = sumq[t]; for (; t > 0; --t) sumq[t] = sumq[t-1]; sumq[0] = tmp; } for (t = 0; t < 4; ++t) bca->indel_types[t] = B2B_INDEL_NULL; for (t = 0; t < 4 && t < n_types; ++t) { bca->indel_types[t] = types[sumq[t]&0x3f]; if (bca->maxins) memcpy(&bca->inscns[t * bca->maxins], &inscns[(sumq[t]&0x3f) * max_ins], bca->maxins); } // update p->aux for (s = n_alt = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i) { bam_pileup1_t *p = plp[s] + i; int x = types[p->aux>>16&0x3f]; for (j = 0; j < 4; ++j) if (x == bca->indel_types[j]) break; p->aux = j<<16 | (j == 4? 0 : (p->aux&0xffff)); if ((p->aux>>16&0x3f) > 0) ++n_alt; //fprintf(bcftools_stderr, "X pos=%d read=%d:%d name=%s call=%d type=%d seqQ=%d indelQ=%d\n", pos, s, i, bam_get_qname(p->b), (p->aux>>16)&0x3f, bca->indel_types[(p->aux>>16)&0x3f], (p->aux>>8)&0xff, p->aux&0xff); } } return n_alt; } /* FIXME: with high number of samples, do we handle IMF correctly? Is it fraction of indels across entire data set, or just fraction for this specific sample? Needs to check bca->per_sample_flt (--per-sample-mF) opt. */ /* notes: - n .. number of samples - the routine sets bam_pileup1_t.aux of each read as follows: - 6: unused - 6: the call; index to bcf_callaux_t.indel_types .. (aux>>16)&0x3f - 8: estimated sequence quality .. (aux>>8)&0xff - 8: indel quality .. aux&0xff */ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref) { if (ref == 0 || bca == 0) return -1; int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins; int *score, max_ref2; int N, K, l_run, ref_type, n_alt; char *inscns = 0, *ref2, *query, **ref_sample; // determine if there is a gap for (s = N = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i) if (plp[s][i].indel != 0) break; if (i < n_plp[s]) break; } if (s == n) // there is no indel at this position. return -1; // find out how many types of indels are present types = bcf_cgp_find_types(n, n_plp, plp, pos, bca, ref, &max_rd_len, &n_types, &ref_type, &N); if (!types) return -1; // calculate left and right boundary left = pos > bca->indel_win_size ? pos - bca->indel_win_size : 0; right = pos + bca->indel_win_size; if (types[0] < 0) right -= types[0]; // in case the alignments stand out the reference for (i = pos; i < right; ++i) if (ref[i] == 0) break; right = i; /* The following call fixes a long-existing flaw in the INDEL * calling model: the interference of nearby SNPs. However, it also * reduces the power because sometimes, substitutions caused by * indels are not distinguishable from true mutations. Multiple * sequence realignment helps to increase the power. * * Masks mismatches present in at least 70% of the reads with 'N'. */ ref_sample = bcf_cgp_ref_sample(n, n_plp, plp, pos, bca, ref, left, right); // The length of the homopolymer run around the current position l_run = bcf_cgp_l_run(ref, pos); // construct the consensus sequence (minus indels, which are added later) max_ins = types[n_types - 1]; // max_ins is at least 0 if (max_ins > 0) { inscns = bcf_cgp_calc_cons(n, n_plp, plp, pos, types, n_types, max_ins, s); if (!inscns) return -1; } // compute the likelihood given each type of indel for each read max_ref2 = right - left + 2 + 2 * (max_ins > -types[0]? max_ins : -types[0]); ref2 = (char*) calloc(max_ref2, 1); query = (char*) calloc(right - left + max_rd_len + max_ins + 2, 1); score = (int*) calloc(N * n_types, sizeof(int)); bca->indelreg = 0; double nqual_over_60 = bca->nqual / 60.0; for (t = 0; t < n_types; ++t) { int l, ir; // compute indelreg if (types[t] == 0) ir = 0; else if (types[t] > 0) ir = est_indelreg(pos, ref, types[t], &inscns[t*max_ins]); else ir = est_indelreg(pos, ref, -types[t], 0); if (ir > bca->indelreg) bca->indelreg = ir; // Identify max deletion length int max_deletion = 0; for (s = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i, ++K) { bam_pileup1_t *p = plp[s] + i; if (max_deletion < -p->indel) max_deletion = -p->indel; } } // Realignment score, computed via BAQ for (s = K = 0; s < n; ++s) { // Construct ref2 from ref_sample, inscns and indels. // This is now the true sample consensus (possibly prepended // and appended with reference if sample data doesn't span // the full length). for (k = 0, j = left; j <= pos; ++j) ref2[k++] = seq_nt16_int[(int)ref_sample[s][j-left]]; if (types[t] <= 0) j += -types[t]; else for (l = 0; l < types[t]; ++l) ref2[k++] = inscns[t*max_ins + l]; for (; j < right && ref[j]; ++j) ref2[k++] = seq_nt16_int[(int)ref_sample[s][j-left]]; for (; k < max_ref2; ++k) ref2[k] = 4; if (right > j) right = j; // align each read to ref2 for (i = 0; i < n_plp[s]; ++i, ++K) { bam_pileup1_t *p = plp[s] + i; // Some basic ref vs alt stats. int imq = p->b->core.qual > 59 ? 59 : p->b->core.qual; imq *= nqual_over_60; int sc_len, slen, epos, sc_end; // Only need to gather stats on one type, as it's // identical calculation for all the subsequent ones // and we're sharing the same stats array if (t == 0) { // Gather stats for INFO field to aid filtering. // mq and sc_len not very helpful for filtering, but could // help in assigning a better QUAL value. // // Pos is slightly useful. // Base qual can be useful, but need qual prior to BAQ? // May need to cache orig quals in aux tag so we can fetch // them even after mpileup step. get_pos(bca, p, &sc_len, &slen, &epos, &sc_end); assert(imq >= 0 && imq < bca->nqual); assert(epos >= 0 && epos < bca->npos); assert(sc_len >= 0 && sc_len < 100); if (p->indel) { bca->ialt_mq[imq]++; bca->ialt_scl[sc_len]++; bca->ialt_pos[epos]++; } else { bca->iref_mq[imq]++; bca->iref_scl[sc_len]++; bca->iref_pos[epos]++; } } int qbeg, qpos, qend, tbeg, tend, kk; uint8_t *seq = bam_get_seq(p->b); uint32_t *cigar = bam_get_cigar(p->b); if (p->b->core.flag & BAM_FUNMAP) continue; // FIXME: the following loop should be better moved outside; // nonetheless, realignment should be much slower anyway. for (kk = 0; kk < p->b->core.n_cigar; ++kk) if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP) break; if (kk < p->b->core.n_cigar) continue; // determine the start and end of sequences for alignment // FIXME: loops over CIGAR multiple times int left2 = left, right2 = right; if (p->b->core.l_qseq > 1000) { // long read data needs less context. It also tends to // have many more candidate indels to investigate so // speed here matters more. if (pos - left >= bca->indel_win_size) left2 += bca->indel_win_size/2; if (right-pos >= bca->indel_win_size) right2 -= bca->indel_win_size/2; } int r_start = p->b->core.pos; int r_end = bam_cigar2rlen(p->b->core.n_cigar, bam_get_cigar(p->b)) -1 + r_start; qbeg = tpos2qpos(&p->b->core, bam_get_cigar(p->b), left2, 0, &tbeg); qpos = tpos2qpos(&p->b->core, bam_get_cigar(p->b), pos, 0, &tend) - qbeg; qend = tpos2qpos(&p->b->core, bam_get_cigar(p->b), right2, 1, &tend); if (types[t] < 0) { int l = -types[t]; tbeg = tbeg - l > left? tbeg - l : left; } // write the query sequence for (l = qbeg; l < qend; ++l) query[l - qbeg] = seq_nt16_int[bam_seqi(seq, l)]; // A fudge for now. Consider checking SAM header for // RG platform field. int long_read = p->b->core.l_qseq > 1000; // do realignment; this is the bottleneck if (tend > tbeg) { if (bcf_cgp_align_score(p, bca, types[t], (uint8_t *)ref2 + left2-left, (uint8_t *)query, r_start, r_end, long_read, tbeg, tend, left2, right2, qbeg, qend, qpos, max_deletion, &score[K*n_types + t]) < 0) { score[K*n_types + t] = 0xffffff; return -1; } } else { // place holder large cost for reads that cover the // region entirely within a deletion (thus tend < tbeg). score[K*n_types + t] = 0xffffff; } #if 0 for (l = 0; l < tend - tbeg + abs(types[t]); ++l) fputc("ACGTN"[(int)ref2[tbeg-left+l]], bcftools_stderr); fputc('\n', bcftools_stderr); for (l = 0; l < qend - qbeg; ++l) fputc("ACGTN"[(int)query[l]], bcftools_stderr); fputc('\n', bcftools_stderr); fprintf(bcftools_stderr, "pos=%d type=%d read=%d:%d name=%s " "qbeg=%d tbeg=%d score=%d\n", pos, types[t], s, i, bam_get_qname(p->b), qbeg, tbeg, score[K*n_types + t]); #endif } } } // compute indelQ n_alt = bcf_cgp_compute_indelQ(n, n_plp, plp, bca, inscns, l_run, max_ins, ref_type, types, n_types, score); // free free(ref2); free(query); free(score); for (i = 0; i < n; ++i) free(ref_sample[i]); free(ref_sample); free(types); free(inscns); return n_alt > 0? 0 : -1; } pysam-0.23.0/bcftools/bam_sample.c000066400000000000000000000326261475062545500170320ustar00rootroot00000000000000/* bam_sample.c -- group data by sample. Copyright (C) 2010, 2011 Broad Institute. Copyright (C) 2013, 2016-2022 Genome Research Ltd. Author: Heng Li , Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "bam_sample.h" #include "bcftools.h" typedef struct { char *fname; void *rg2idx; // hash: read group name to BCF output sample index. Maintained by bsmpl_add_readgroup int default_idx; // default BCF output sample index, set only when all readgroups are treated as one sample } file_t; struct _bam_smpl_t { kstring_t tmp; file_t *files; int ignore_rg, nsmpl, nfiles; char **smpl; // list of BCF output sample names. Maintained by bsmpl_add_readgroup void *sample_list; // hash: BAM input sample name to BCF output sample name. This is the -s/-S list int sample_logic; // the -s/-S logic, 1: include, 0: exclude void *rg_list; // hash: BAM/rg_id to sample name or */rg_id for global ids. This is the -G list int rg_logic; // the -G logic, 1: include, 0: exclude void *name2idx; // hash: BCF output sample name to BCF output sample index. Maintained by bsmpl_add_readgroup }; bam_smpl_t *bam_smpl_init(void) { bam_smpl_t *bsmpl; bsmpl = (bam_smpl_t*) calloc(1, sizeof(bam_smpl_t)); bsmpl->name2idx = khash_str2int_init(); return bsmpl; } void bam_smpl_destroy(bam_smpl_t *bsmpl) { if ( !bsmpl ) return; if ( bsmpl->name2idx ) khash_str2int_destroy_free(bsmpl->name2idx); if ( bsmpl->sample_list ) khash_str2str_destroy_free_all(bsmpl->sample_list); if ( bsmpl->rg_list ) khash_str2str_destroy_free_all(bsmpl->rg_list); int i; for (i=0; infiles; i++) { file_t *file = &bsmpl->files[i]; if ( file->rg2idx ) khash_str2int_destroy_free(file->rg2idx); free(file->fname); } free(bsmpl->smpl); free(bsmpl->files); free(bsmpl->tmp.s); free(bsmpl); } void bam_smpl_ignore_readgroups(bam_smpl_t* bsmpl) { bsmpl->ignore_rg = 1; } static void bsmpl_add_readgroup(bam_smpl_t *bsmpl, file_t *file, const char *rg_id, const char *smpl_name) { int ismpl = -1; if ( smpl_name ) { if ( khash_str2int_get(bsmpl->name2idx,smpl_name,&ismpl) < 0 ) { // new sample bsmpl->nsmpl++; bsmpl->smpl = (char**) realloc(bsmpl->smpl,sizeof(char*)*bsmpl->nsmpl); bsmpl->smpl[bsmpl->nsmpl-1] = strdup(smpl_name); ismpl = khash_str2int_inc(bsmpl->name2idx,bsmpl->smpl[bsmpl->nsmpl-1]); } } if ( !strcmp("*",rg_id) ) { // all read groups in the bam treated as the same sample file->default_idx = ismpl; return; } if ( !file->rg2idx ) file->rg2idx = khash_str2int_init(); if ( khash_str2int_has_key(file->rg2idx,rg_id) ) return; // duplicate @RG:ID khash_str2int_set(file->rg2idx, strdup(rg_id), ismpl); } static int bsmpl_keep_readgroup(bam_smpl_t *bsmpl, file_t *file, const char *rg_id, const char **smpl_name) { char *rg_smpl = khash_str2str_get(bsmpl->rg_list,rg_id); // unique read group present in one bam only if ( !rg_smpl ) { // read group specific to this bam bsmpl->tmp.l = 0; ksprintf(&bsmpl->tmp,"%s\t%s",rg_id,file->fname); rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s); } if ( !rg_smpl ) { // any read group in this file? bsmpl->tmp.l = 0; ksprintf(&bsmpl->tmp,"*\t%s",file->fname); rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s); } if ( !rg_smpl && bsmpl->rg_logic ) return 0; if ( rg_smpl && !bsmpl->rg_logic ) return 0; if ( rg_smpl && rg_smpl[0]!='\t' ) *smpl_name = rg_smpl; // rename the sample return 1; } /* The logic of this function is a bit complicated because we want to work also with broken bams containing read groups that are not listed in the header. The desired behavior is as follows: - when -G is given, read groups which are not listed in the header must be given explicitly using the "?" symbol in -G. Otherwise: - if the bam has no header, all reads in the file are assigned to a single sample named after the file - if there is at least one sample defined in the header, reads with no read group id or with a read group id not listed in the header are assigned to the first sample encountered in the header */ int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname) { bsmpl->nfiles++; bsmpl->files = (file_t*) realloc(bsmpl->files,bsmpl->nfiles*sizeof(file_t)); file_t *file = &bsmpl->files[bsmpl->nfiles-1]; memset(file,0,sizeof(file_t)); file->fname = strdup(fname); file->default_idx = -1; if ( bsmpl->ignore_rg || !bam_hdr ) { // The option --ignore-RG is set or there is no BAM header: use the file name as the sample name bsmpl_add_readgroup(bsmpl,file,"*",file->fname); return bsmpl->nfiles-1; } void *bam_smpls = khash_str2int_init(); int first_smpl = -1, nskipped = 0; const char *p = bam_hdr, *q, *r; while (p != NULL && (q = strstr(p, "@RG")) != 0) { char *eol = strchr(q + 3, '\n'); if (q > bam_hdr && *(q - 1) != '\n') { // @RG must be at start of line p = eol; continue; } p = q + 3; if ((q = strstr(p, "\tID:")) != 0) q += 4; if ((r = strstr(p, "\tSM:")) != 0) r += 4; if (r && q) { char *u, *v; int ioq, ior; for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u); for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v); ioq = *u; ior = *v; *u = *v = '\0'; // q now points to a null terminated read group id // r points to a null terminated sample name if ( !strcmp("*",q) || !strcmp("?",q) ) error("Error: the read group IDs \"*\" and \"?\" have a special meaning in the mpileup code. Please fix the code or the bam: %s\n", fname); int accept_rg = 1; if ( bsmpl->sample_list ) { // restrict samples based on the -s/-S options char *name = khash_str2str_get(bsmpl->sample_list,r); if ( bsmpl->sample_logic==0 ) accept_rg = name ? 0 : 1; else if ( !name ) accept_rg = 0; else r = name; } if ( accept_rg && bsmpl->rg_list ) { // restrict readgroups based on the -G option, possibly renaming the sample accept_rg = bsmpl_keep_readgroup(bsmpl,file,q,&r); } if ( accept_rg ) bsmpl_add_readgroup(bsmpl,file,q,r); else { bsmpl_add_readgroup(bsmpl,file,q,NULL); // ignore this RG but note that it was seen in the header nskipped++; } if ( first_smpl<0 ) khash_str2int_get(bsmpl->name2idx,r,&first_smpl); if ( !khash_str2int_has_key(bam_smpls,r) ) khash_str2int_inc(bam_smpls,strdup(r)); *u = ioq; *v = ior; } else break; p = eol; } int nsmpls = khash_str2int_size(bam_smpls); khash_str2int_destroy_free(bam_smpls); const char *smpl_name = NULL; int accept_null_rg = 1; if ( bsmpl->rg_list && !bsmpl_keep_readgroup(bsmpl,file,"?",&smpl_name) ) accept_null_rg = 0; if ( bsmpl->sample_list && first_smpl==-1 ) accept_null_rg = 0; if ( !accept_null_rg && first_smpl==-1 ) { // no suitable read group is available in this bam: ignore the whole file. free(file->fname); if ( file->rg2idx ) khash_str2int_destroy_free(file->rg2idx); bsmpl->nfiles--; return -1; } if ( !accept_null_rg ) return bsmpl->nfiles-1; if ( nsmpls==1 && !nskipped ) { file->default_idx = first_smpl; return bsmpl->nfiles-1; } if ( !smpl_name ) smpl_name = first_smpl==-1 ? file->fname : bsmpl->smpl[first_smpl]; bsmpl_add_readgroup(bsmpl,file,"?",smpl_name); return bsmpl->nfiles-1; } const char **bam_smpl_get_samples(bam_smpl_t *bsmpl, int *nsmpl) { *nsmpl = bsmpl->nsmpl; return (const char**)bsmpl->smpl; } int bam_smpl_get_sample_id(bam_smpl_t *bsmpl, int bam_id, bam1_t *bam_rec) { file_t *file = &bsmpl->files[bam_id]; if ( file->default_idx >= 0 ) return file->default_idx; char *aux_rg = (char*) bam_aux_get(bam_rec, "RG"); aux_rg = aux_rg ? aux_rg+1 : "?"; int rg_id; if ( khash_str2int_get(file->rg2idx, aux_rg, &rg_id)==0 ) return rg_id; if ( khash_str2int_get(file->rg2idx, "?", &rg_id)==0 ) return rg_id; return -1; } int bam_smpl_add_samples(bam_smpl_t *bsmpl, char *list, int is_file) { if ( list[0]!='^' ) bsmpl->sample_logic = 1; else list++; int i, nsamples = 0; char **samples = hts_readlist(list, is_file, &nsamples); if ( !samples || !nsamples ) return 0; kstring_t ori = {0,0,0}; kstring_t ren = {0,0,0}; bsmpl->sample_list = khash_str2str_init(); for (i=0; isample_list,strdup(ori.s),strdup(ren.l?ren.s:ori.s)); free(samples[i]); } free(samples); free(ori.s); free(ren.s); return nsamples; } int bam_smpl_add_readgroups(bam_smpl_t *bsmpl, char *list, int is_file) { if ( list[0]!='^' ) bsmpl->rg_logic = 1; else list++; int i, nrows = 0; char **rows = hts_readlist(list, is_file, &nrows); if ( !rows || !nrows ) return 0; kstring_t fld1 = {0,0,0}; kstring_t fld2 = {0,0,0}; kstring_t fld3 = {0,0,0}; bsmpl->rg_list = khash_str2str_init(); for (i=0; irg_list,fld1.s); if ( !value ) khash_str2str_set(bsmpl->rg_list,strdup(fld1.s),strdup(fld2.l?fld2.s:"\t")); else if ( strcmp(value,fld2.l?fld2.s:"\t") ) error("Error: The read group \"%s\" was assigned to two different samples: \"%s\" and \"%s\"\n", fld1.s,value,fld2.l?fld2.s:"\t"); free(rows[i]); } free(rows); free(fld1.s); free(fld2.s); free(fld3.s); return nrows; } pysam-0.23.0/bcftools/bam_sample.c.pysam.c000066400000000000000000000326631475062545500204040ustar00rootroot00000000000000#include "bcftools.pysam.h" /* bam_sample.c -- group data by sample. Copyright (C) 2010, 2011 Broad Institute. Copyright (C) 2013, 2016-2022 Genome Research Ltd. Author: Heng Li , Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "bam_sample.h" #include "bcftools.h" typedef struct { char *fname; void *rg2idx; // hash: read group name to BCF output sample index. Maintained by bsmpl_add_readgroup int default_idx; // default BCF output sample index, set only when all readgroups are treated as one sample } file_t; struct _bam_smpl_t { kstring_t tmp; file_t *files; int ignore_rg, nsmpl, nfiles; char **smpl; // list of BCF output sample names. Maintained by bsmpl_add_readgroup void *sample_list; // hash: BAM input sample name to BCF output sample name. This is the -s/-S list int sample_logic; // the -s/-S logic, 1: include, 0: exclude void *rg_list; // hash: BAM/rg_id to sample name or */rg_id for global ids. This is the -G list int rg_logic; // the -G logic, 1: include, 0: exclude void *name2idx; // hash: BCF output sample name to BCF output sample index. Maintained by bsmpl_add_readgroup }; bam_smpl_t *bam_smpl_init(void) { bam_smpl_t *bsmpl; bsmpl = (bam_smpl_t*) calloc(1, sizeof(bam_smpl_t)); bsmpl->name2idx = khash_str2int_init(); return bsmpl; } void bam_smpl_destroy(bam_smpl_t *bsmpl) { if ( !bsmpl ) return; if ( bsmpl->name2idx ) khash_str2int_destroy_free(bsmpl->name2idx); if ( bsmpl->sample_list ) khash_str2str_destroy_free_all(bsmpl->sample_list); if ( bsmpl->rg_list ) khash_str2str_destroy_free_all(bsmpl->rg_list); int i; for (i=0; infiles; i++) { file_t *file = &bsmpl->files[i]; if ( file->rg2idx ) khash_str2int_destroy_free(file->rg2idx); free(file->fname); } free(bsmpl->smpl); free(bsmpl->files); free(bsmpl->tmp.s); free(bsmpl); } void bam_smpl_ignore_readgroups(bam_smpl_t* bsmpl) { bsmpl->ignore_rg = 1; } static void bsmpl_add_readgroup(bam_smpl_t *bsmpl, file_t *file, const char *rg_id, const char *smpl_name) { int ismpl = -1; if ( smpl_name ) { if ( khash_str2int_get(bsmpl->name2idx,smpl_name,&ismpl) < 0 ) { // new sample bsmpl->nsmpl++; bsmpl->smpl = (char**) realloc(bsmpl->smpl,sizeof(char*)*bsmpl->nsmpl); bsmpl->smpl[bsmpl->nsmpl-1] = strdup(smpl_name); ismpl = khash_str2int_inc(bsmpl->name2idx,bsmpl->smpl[bsmpl->nsmpl-1]); } } if ( !strcmp("*",rg_id) ) { // all read groups in the bam treated as the same sample file->default_idx = ismpl; return; } if ( !file->rg2idx ) file->rg2idx = khash_str2int_init(); if ( khash_str2int_has_key(file->rg2idx,rg_id) ) return; // duplicate @RG:ID khash_str2int_set(file->rg2idx, strdup(rg_id), ismpl); } static int bsmpl_keep_readgroup(bam_smpl_t *bsmpl, file_t *file, const char *rg_id, const char **smpl_name) { char *rg_smpl = khash_str2str_get(bsmpl->rg_list,rg_id); // unique read group present in one bam only if ( !rg_smpl ) { // read group specific to this bam bsmpl->tmp.l = 0; ksprintf(&bsmpl->tmp,"%s\t%s",rg_id,file->fname); rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s); } if ( !rg_smpl ) { // any read group in this file? bsmpl->tmp.l = 0; ksprintf(&bsmpl->tmp,"*\t%s",file->fname); rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s); } if ( !rg_smpl && bsmpl->rg_logic ) return 0; if ( rg_smpl && !bsmpl->rg_logic ) return 0; if ( rg_smpl && rg_smpl[0]!='\t' ) *smpl_name = rg_smpl; // rename the sample return 1; } /* The logic of this function is a bit complicated because we want to work also with broken bams containing read groups that are not listed in the header. The desired behavior is as follows: - when -G is given, read groups which are not listed in the header must be given explicitly using the "?" symbol in -G. Otherwise: - if the bam has no header, all reads in the file are assigned to a single sample named after the file - if there is at least one sample defined in the header, reads with no read group id or with a read group id not listed in the header are assigned to the first sample encountered in the header */ int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname) { bsmpl->nfiles++; bsmpl->files = (file_t*) realloc(bsmpl->files,bsmpl->nfiles*sizeof(file_t)); file_t *file = &bsmpl->files[bsmpl->nfiles-1]; memset(file,0,sizeof(file_t)); file->fname = strdup(fname); file->default_idx = -1; if ( bsmpl->ignore_rg || !bam_hdr ) { // The option --ignore-RG is set or there is no BAM header: use the file name as the sample name bsmpl_add_readgroup(bsmpl,file,"*",file->fname); return bsmpl->nfiles-1; } void *bam_smpls = khash_str2int_init(); int first_smpl = -1, nskipped = 0; const char *p = bam_hdr, *q, *r; while (p != NULL && (q = strstr(p, "@RG")) != 0) { char *eol = strchr(q + 3, '\n'); if (q > bam_hdr && *(q - 1) != '\n') { // @RG must be at start of line p = eol; continue; } p = q + 3; if ((q = strstr(p, "\tID:")) != 0) q += 4; if ((r = strstr(p, "\tSM:")) != 0) r += 4; if (r && q) { char *u, *v; int ioq, ior; for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u); for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v); ioq = *u; ior = *v; *u = *v = '\0'; // q now points to a null terminated read group id // r points to a null terminated sample name if ( !strcmp("*",q) || !strcmp("?",q) ) error("Error: the read group IDs \"*\" and \"?\" have a special meaning in the mpileup code. Please fix the code or the bam: %s\n", fname); int accept_rg = 1; if ( bsmpl->sample_list ) { // restrict samples based on the -s/-S options char *name = khash_str2str_get(bsmpl->sample_list,r); if ( bsmpl->sample_logic==0 ) accept_rg = name ? 0 : 1; else if ( !name ) accept_rg = 0; else r = name; } if ( accept_rg && bsmpl->rg_list ) { // restrict readgroups based on the -G option, possibly renaming the sample accept_rg = bsmpl_keep_readgroup(bsmpl,file,q,&r); } if ( accept_rg ) bsmpl_add_readgroup(bsmpl,file,q,r); else { bsmpl_add_readgroup(bsmpl,file,q,NULL); // ignore this RG but note that it was seen in the header nskipped++; } if ( first_smpl<0 ) khash_str2int_get(bsmpl->name2idx,r,&first_smpl); if ( !khash_str2int_has_key(bam_smpls,r) ) khash_str2int_inc(bam_smpls,strdup(r)); *u = ioq; *v = ior; } else break; p = eol; } int nsmpls = khash_str2int_size(bam_smpls); khash_str2int_destroy_free(bam_smpls); const char *smpl_name = NULL; int accept_null_rg = 1; if ( bsmpl->rg_list && !bsmpl_keep_readgroup(bsmpl,file,"?",&smpl_name) ) accept_null_rg = 0; if ( bsmpl->sample_list && first_smpl==-1 ) accept_null_rg = 0; if ( !accept_null_rg && first_smpl==-1 ) { // no suitable read group is available in this bam: ignore the whole file. free(file->fname); if ( file->rg2idx ) khash_str2int_destroy_free(file->rg2idx); bsmpl->nfiles--; return -1; } if ( !accept_null_rg ) return bsmpl->nfiles-1; if ( nsmpls==1 && !nskipped ) { file->default_idx = first_smpl; return bsmpl->nfiles-1; } if ( !smpl_name ) smpl_name = first_smpl==-1 ? file->fname : bsmpl->smpl[first_smpl]; bsmpl_add_readgroup(bsmpl,file,"?",smpl_name); return bsmpl->nfiles-1; } const char **bam_smpl_get_samples(bam_smpl_t *bsmpl, int *nsmpl) { *nsmpl = bsmpl->nsmpl; return (const char**)bsmpl->smpl; } int bam_smpl_get_sample_id(bam_smpl_t *bsmpl, int bam_id, bam1_t *bam_rec) { file_t *file = &bsmpl->files[bam_id]; if ( file->default_idx >= 0 ) return file->default_idx; char *aux_rg = (char*) bam_aux_get(bam_rec, "RG"); aux_rg = aux_rg ? aux_rg+1 : "?"; int rg_id; if ( khash_str2int_get(file->rg2idx, aux_rg, &rg_id)==0 ) return rg_id; if ( khash_str2int_get(file->rg2idx, "?", &rg_id)==0 ) return rg_id; return -1; } int bam_smpl_add_samples(bam_smpl_t *bsmpl, char *list, int is_file) { if ( list[0]!='^' ) bsmpl->sample_logic = 1; else list++; int i, nsamples = 0; char **samples = hts_readlist(list, is_file, &nsamples); if ( !samples || !nsamples ) return 0; kstring_t ori = {0,0,0}; kstring_t ren = {0,0,0}; bsmpl->sample_list = khash_str2str_init(); for (i=0; isample_list,strdup(ori.s),strdup(ren.l?ren.s:ori.s)); free(samples[i]); } free(samples); free(ori.s); free(ren.s); return nsamples; } int bam_smpl_add_readgroups(bam_smpl_t *bsmpl, char *list, int is_file) { if ( list[0]!='^' ) bsmpl->rg_logic = 1; else list++; int i, nrows = 0; char **rows = hts_readlist(list, is_file, &nrows); if ( !rows || !nrows ) return 0; kstring_t fld1 = {0,0,0}; kstring_t fld2 = {0,0,0}; kstring_t fld3 = {0,0,0}; bsmpl->rg_list = khash_str2str_init(); for (i=0; irg_list,fld1.s); if ( !value ) khash_str2str_set(bsmpl->rg_list,strdup(fld1.s),strdup(fld2.l?fld2.s:"\t")); else if ( strcmp(value,fld2.l?fld2.s:"\t") ) error("Error: The read group \"%s\" was assigned to two different samples: \"%s\" and \"%s\"\n", fld1.s,value,fld2.l?fld2.s:"\t"); free(rows[i]); } free(rows); free(fld1.s); free(fld2.s); free(fld3.s); return nrows; } pysam-0.23.0/bcftools/bam_sample.h000066400000000000000000000037561475062545500170410ustar00rootroot00000000000000/* bam_sample.h -- group data by sample. Copyright (C) 2010 Broad Institute. Copyright (C) 2016 Genome Research Ltd. Author: Heng Li , Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef BAM_SAMPLE_H #define BAM_SAMPLE_H #include typedef struct _bam_smpl_t bam_smpl_t; bam_smpl_t *bam_smpl_init(void); int bam_smpl_add_samples(bam_smpl_t *bsmpl, char *list, int is_file); int bam_smpl_add_readgroups(bam_smpl_t *bsmpl, char *list, int is_file); void bam_smpl_ignore_readgroups(bam_smpl_t* bsmpl); // The above should be called only before bams are added. Returns the BAM id // to be passed to bam_smpl_get_sample_id() later. It is safe to assume // sequential numbering, starting from 0. // int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname); const char **bam_smpl_get_samples(bam_smpl_t *bsmpl, int *nsmpl); int bam_smpl_get_sample_id(bam_smpl_t *bsmpl, int bam_id, bam1_t *bam_rec); void bam_smpl_destroy(bam_smpl_t *bsmpl); #endif pysam-0.23.0/bcftools/bcftools.h000066400000000000000000000147301475062545500165460ustar00rootroot00000000000000/* bcftools.h -- utility function declarations. Copyright (C) 2013-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef BCFTOOLS_H #define BCFTOOLS_H #include #include #include #include #include #include #define FT_TAB_TEXT 0 // custom tab-delimited text file #define FT_GZ 1 #define FT_VCF 2 #define FT_VCF_GZ (FT_GZ|FT_VCF) #define FT_BCF (1<<2) #define FT_BCF_GZ (FT_GZ|FT_BCF) #define FT_STDIN (1<<3) char *bcftools_version(void); /// Report an error and exit -1 void error(const char *format, ...) HTS_NORETURN HTS_FORMAT(HTS_PRINTF_FMT, 1, 2); /// Report an error and exit -1. If errno != 0, appends strerror(errno). // Note: unlike error() above, the message should not end with "\n" as a // newline will be added by the function. void error_errno(const char *format, ...) HTS_NORETURN HTS_FORMAT(HTS_PRINTF_FMT, 1, 2); // For on the fly index creation with --write-index int init_index2(htsFile *fh, bcf_hdr_t *hdr, const char *fname, char **idx_fname, int idx_fmt); int init_index(htsFile *fh, bcf_hdr_t *hdr, const char *fname, char **idx_fname); // Used to set args->write_index in CLI. // It will be true if set correctly. // Note due to HTS_FMT_CSI being zero we have to use an additional bit. int write_index_parse(char *arg); void bcf_hdr_append_version(bcf_hdr_t *hdr, int argc, char **argv, const char *cmd); const char *hts_bcf_wmode(int file_type); const char *hts_bcf_wmode2(int file_type, const char *fname); void set_wmode(char dst[8], int file_type, const char *fname, int compression_level); // clevel: 0-9 with or zb type, -1 unset char *init_tmp_prefix(const char *prefix); int read_AF(bcf_sr_regions_t *tgt, bcf1_t *line, double *alt_freq); int parse_overlap_option(const char *arg); // Default sort order: chr,pos,alleles int cmp_bcf_pos(const void *aptr, const void *bptr); int cmp_bcf_pos_ref_alt(const void *aptr, const void *bptr); static inline int iupac2bitmask(char iupac) { const int A = 1; const int C = 2; const int G = 4; const int T = 8; if ( iupac >= 97 ) iupac -= 32; if ( iupac == 'A' ) return A; if ( iupac == 'C' ) return C; if ( iupac == 'G' ) return G; if ( iupac == 'T' ) return T; if ( iupac == 'M' ) return A|C; if ( iupac == 'R' ) return A|G; if ( iupac == 'W' ) return A|T; if ( iupac == 'S' ) return C|G; if ( iupac == 'Y' ) return C|T; if ( iupac == 'K' ) return G|T; if ( iupac == 'V' ) return A|C|G; if ( iupac == 'H' ) return A|C|T; if ( iupac == 'D' ) return A|G|T; if ( iupac == 'B' ) return C|G|T; if ( iupac == 'N' ) return A|C|G|T; return -1; } static inline char bitmask2iupac(int bitmask) { const char iupac[16] = {'.','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N'}; if ( bitmask <= 0 || bitmask > 15 ) return 0; return iupac[bitmask]; } static inline int iupac_consistent(char iupac, char nt) { static const char iupac_mask[90] = { 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,14,2, 13,0,0,4,11,0,0,12,0,3,15,0,0,0,5,6,8,0,7,9,0,10 }; if ( iupac > 89 ) return 0; if ( nt > 90 ) nt -= 32; // lowercase if ( nt=='A' ) nt = 1; else if ( nt=='C' ) nt = 2; else if ( nt=='G' ) nt = 4; else if ( nt=='T' ) nt = 8; return iupac_mask[(int)iupac] & nt ? 1 : 0; } static inline char nt_to_upper(char nt) { if ( nt < 97 ) return nt; return nt - 32; } static inline double phred_score(double prob) { if ( prob==0 ) return 99; prob = -4.3429*log(prob); return prob>99 ? 99 : prob; } static inline double calc_binom_two_sided(int na, int nb, double aprob) { if ( !na && !nb ) return -1; if ( na==nb ) return 1; // kfunc.h implements kf_betai, which is the regularized beta function P(X<=k/N;p) = I_{1-p}(N-k,k+1) double prob = na > nb ? 2 * kf_betai(na, nb+1, aprob) : 2 * kf_betai(nb, na+1, aprob); if ( prob > 1 ) prob = 1; // this can happen, machine precision error, eg. kf_betai(1,0,0.5) return prob; } static inline double calc_binom_one_sided(int na, int nb, double aprob, int ge) { return ge ? kf_betai(na, nb + 1, aprob) : kf_betai(nb, na + 1, 1 - aprob); } static const uint64_t bcf_double_missing = 0x7ff0000000000001; static const uint64_t bcf_double_vector_end = 0x7ff0000000000002; static inline void bcf_double_set(double *ptr, uint64_t value) { union { uint64_t i; double d; } u; u.i = value; *ptr = u.d; } static inline int bcf_double_test(double d, uint64_t value) { union { uint64_t i; double d; } u; u.d = d; return u.i==value ? 1 : 0; } #define bcf_double_set_vector_end(x) bcf_double_set(&(x),bcf_double_vector_end) #define bcf_double_set_missing(x) bcf_double_set(&(x),bcf_double_missing) #define bcf_double_is_vector_end(x) bcf_double_test((x),bcf_double_vector_end) #define bcf_double_is_missing(x) bcf_double_test((x),bcf_double_missing) #define bcf_double_is_missing_or_vector_end(x) (bcf_double_test((x),bcf_double_missing) || bcf_double_test((x),bcf_double_vector_end)) static inline int get_unseen_allele(bcf1_t *line) { int i; for (i=1; in_allele; i++) { if ( !strcmp(line->d.allele[i],"<*>") ) return i; if ( !strcmp(line->d.allele[i],"") ) return i; if ( !strcmp(line->d.allele[i],"") ) return i; } return 0; } #endif pysam-0.23.0/bcftools/bcftools.pysam.c000066400000000000000000000030651475062545500176700ustar00rootroot00000000000000#include #include #include #include #include #include #include "bcftools.pysam.h" FILE * bcftools_stderr = NULL; FILE * bcftools_stdout = NULL; const char * bcftools_stdout_fn = NULL; FILE * bcftools_set_stderr(int fd) { if (bcftools_stderr != NULL) fclose(bcftools_stderr); bcftools_stderr = fdopen(fd, "w"); return bcftools_stderr; } void bcftools_close_stderr(void) { fclose(bcftools_stderr); bcftools_stderr = NULL; } FILE * bcftools_set_stdout(int fd) { if (bcftools_stdout != NULL) fclose(bcftools_stdout); bcftools_stdout = fdopen(fd, "w"); if (bcftools_stdout == NULL) { fprintf(bcftools_stderr, "could not set stdout to fd %i", fd); } return bcftools_stdout; } void bcftools_set_stdout_fn(const char *fn) { bcftools_stdout_fn = fn; } void bcftools_close_stdout(void) { fclose(bcftools_stdout); bcftools_stdout = NULL; } int bcftools_puts(const char *s) { if (fputs(s, bcftools_stdout) == EOF) return EOF; return putc('\n', bcftools_stdout); } static jmp_buf bcftools_jmpbuf; static int bcftools_status = 0; int bcftools_dispatch(int argc, char *argv[]) { /* Reset getopt()/getopt_long() processing. */ #if defined __GLIBC__ optind = 0; #elif defined _OPTRESET || defined _OPTRESET_DECLARED optreset = optind = 1; #else optind = 1; #endif if (setjmp(bcftools_jmpbuf) == 0) return bcftools_main(argc, argv); else return bcftools_status; } void bcftools_exit(int status) { bcftools_status = status; longjmp(bcftools_jmpbuf, 1); } pysam-0.23.0/bcftools/bcftools.pysam.h000066400000000000000000000035241475062545500176750ustar00rootroot00000000000000#ifndef bcftools_PYSAM_H #define bcftools_PYSAM_H #include #ifndef __has_attribute #define __has_attribute(attribute) 0 #endif #ifndef PYSAM_NORETURN #if __has_attribute(__noreturn__) || __GNUC__ >= 3 #define PYSAM_NORETURN __attribute__((__noreturn__)) #else #define PYSAM_NORETURN #endif #endif extern FILE * bcftools_stderr; extern FILE * bcftools_stdout; extern const char * bcftools_stdout_fn; /*! set pysam standard error to point to file descriptor Setting the stderr will close the previous stderr. */ FILE * bcftools_set_stderr(int fd); /*! set pysam standard output to point to file descriptor Setting the stdout will close the previous stdout. */ FILE * bcftools_set_stdout(int fd); /*! set pysam standard output to point to filename */ void bcftools_set_stdout_fn(const char * fn); /*! close pysam standard error and set to NULL */ void bcftools_close_stderr(void); /*! close pysam standard output and set to NULL */ void bcftools_close_stdout(void); int bcftools_puts(const char *s); int bcftools_dispatch(int argc, char *argv[]); void PYSAM_NORETURN bcftools_exit(int status); extern int bcftools_main(int argc, char *argv[]); /* Define these only in samtools/bcftools C source, not Cython code. */ #if !(defined CYTHON_ABI || defined CYTHON_HEX_VERSION) /*! Several non-static function names are used in both samtools and bcftools. Both libcsamtools.so and libcbcftools.so are loaded simultaneously, leading to collisions and wrong functions being called. #define these names so the actual symbol names include distinct prefixes to avoid collisions. */ #define main_consensus bcftools_main_consensus #define main_reheader bcftools_main_reheader #define bam_smpl_init bcftools_bam_smpl_init #define bam_smpl_destroy bcftools_bam_smpl_destroy #define read_file_list bcftools_read_file_list #endif #endif pysam-0.23.0/bcftools/bin.c000066400000000000000000000066151475062545500155010ustar00rootroot00000000000000/* The MIT License Copyright (c) 2016-2022 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include "bcftools.h" #include "bin.h" struct _bin_t { float *bins; int nbins; }; bin_t *bin_init(const char *list_def, float min, float max) { bin_t *bin = (bin_t*) calloc(1,sizeof(bin_t)); // a comma indicates a list, otherwise a file int is_file = strchr(list_def,',') ? 0 : 1; int i, nlist; char **list = hts_readlist(list_def, is_file, &nlist); if ( !list ) error("Error: failed to read %s\n",list_def); bin->nbins = nlist; bin->bins = (float*) malloc(sizeof(float)*nlist); for (i=0; ibins[i] = strtod(list[i],&tmp); if ( *tmp ) error("Could not parse %s: %s\n", list_def, list[i]); if ( min!=max && (bin->bins[i]bins[i]>max) ) error("Expected values from the interval [%f,%f], found %s\n", min, max, list[i]); free(list[i]); } free(list); if ( min!=max ) { // make sure we've got both boundaries: min,max. assert( nlist>1 ); float max_err = (bin->bins[1] - bin->bins[0])*1e-6; if ( fabs(bin->bins[0] - min) > max_err ) { bin->bins = (float*) realloc(bin->bins, (++bin->nbins)*sizeof(float)); memmove(bin->bins+1, bin->bins, sizeof(float)*(bin->nbins-1)); bin->bins[0] = min; } if ( fabs(bin->bins[bin->nbins-1] - max) > max_err ) { bin->bins = (float*) realloc(bin->bins, (++bin->nbins)*sizeof(float)); bin->bins[bin->nbins-1] = max; } } return bin; } void bin_destroy(bin_t *bin) { free(bin->bins); free(bin); } int bin_get_size(bin_t *bin) { return bin->nbins; } float bin_get_value(bin_t *bin, int idx) { return bin->bins[idx]; } int bin_get_idx(bin_t *bin, float value) { if ( bin->bins[bin->nbins-1] < value ) return bin->nbins-1; // Binary search in half-closed,half-open intervals [) int imin = 0, imax = bin->nbins - 2; while ( iminbins[i] ) imax = i - 1; else if ( value > bin->bins[i] ) imin = i + 1; else return i; } if ( bin->bins[imax] <= value ) return imax; return imin - 1; } pysam-0.23.0/bcftools/bin.c.pysam.c000066400000000000000000000066521475062545500170530ustar00rootroot00000000000000#include "bcftools.pysam.h" /* The MIT License Copyright (c) 2016-2022 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include "bcftools.h" #include "bin.h" struct _bin_t { float *bins; int nbins; }; bin_t *bin_init(const char *list_def, float min, float max) { bin_t *bin = (bin_t*) calloc(1,sizeof(bin_t)); // a comma indicates a list, otherwise a file int is_file = strchr(list_def,',') ? 0 : 1; int i, nlist; char **list = hts_readlist(list_def, is_file, &nlist); if ( !list ) error("Error: failed to read %s\n",list_def); bin->nbins = nlist; bin->bins = (float*) malloc(sizeof(float)*nlist); for (i=0; ibins[i] = strtod(list[i],&tmp); if ( *tmp ) error("Could not parse %s: %s\n", list_def, list[i]); if ( min!=max && (bin->bins[i]bins[i]>max) ) error("Expected values from the interval [%f,%f], found %s\n", min, max, list[i]); free(list[i]); } free(list); if ( min!=max ) { // make sure we've got both boundaries: min,max. assert( nlist>1 ); float max_err = (bin->bins[1] - bin->bins[0])*1e-6; if ( fabs(bin->bins[0] - min) > max_err ) { bin->bins = (float*) realloc(bin->bins, (++bin->nbins)*sizeof(float)); memmove(bin->bins+1, bin->bins, sizeof(float)*(bin->nbins-1)); bin->bins[0] = min; } if ( fabs(bin->bins[bin->nbins-1] - max) > max_err ) { bin->bins = (float*) realloc(bin->bins, (++bin->nbins)*sizeof(float)); bin->bins[bin->nbins-1] = max; } } return bin; } void bin_destroy(bin_t *bin) { free(bin->bins); free(bin); } int bin_get_size(bin_t *bin) { return bin->nbins; } float bin_get_value(bin_t *bin, int idx) { return bin->bins[idx]; } int bin_get_idx(bin_t *bin, float value) { if ( bin->bins[bin->nbins-1] < value ) return bin->nbins-1; // Binary search in half-closed,half-open intervals [) int imin = 0, imax = bin->nbins - 2; while ( iminbins[i] ) imax = i - 1; else if ( value > bin->bins[i] ) imin = i + 1; else return i; } if ( bin->bins[imax] <= value ) return imax; return imin - 1; } pysam-0.23.0/bcftools/bin.h000066400000000000000000000042141475062545500154770ustar00rootroot00000000000000/* The MIT License Copyright (c) 2016 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Simple binning of float values into predefined bins */ #ifndef __BIN_H__ #define __BIN_H__ #include typedef struct _bin_t bin_t; /* * bin_init() - init bins * @list: list of half-open intervals [). If the list does not contain commas, * it is interpreted as a file name. * @min,max: extreme values. This is for user convenience so that well-known * extremes can be left out from the list. Ignored if min=max */ bin_t *bin_init(const char *list, float min, float max); void bin_destroy(bin_t *bin); /* * bin_get_size() - number of boundaries, subtract 1 to get the number of bins */ int bin_get_size(bin_t *bin); /* bin_get_idx() - find the bin index which corresponds to the value (binary search) Returns the bin index 0 <= idx <= size-2 or -1,size-1 for out of range values. */ int bin_get_idx(bin_t *bin, float value); /* bin_get_value() - get the i-th boundary value, i=0,..,size-1 */ float bin_get_value(bin_t *bin, int ith); #endif pysam-0.23.0/bcftools/call.h000066400000000000000000000123251475062545500156440ustar00rootroot00000000000000/* call.h -- variant calling declarations. Copyright (C) 2013-2015, 2019-2020 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef __CALL_H__ #define __CALL_H__ #include #include #include "vcmp.h" #define CALL_KEEPALT 1 #define CALL_VARONLY (1<<1) #define CALL_CONSTR_TRIO (1<<2) #define CALL_CONSTR_ALLELES (1<<3) #define CALL_KEEP_UNSEEN (1<<4) #define CALL_FMT_PV4 (1<<5) #define CALL_FMT_GQ (1<<6) #define CALL_FMT_GP (1<<7) #define FATHER 0 #define MOTHER 1 #define CHILD 2 typedef struct { char *name; int sample[3]; // father, mother, child int type; // see FTYPE_* definitions in mcall.c } family_t; // For the single-sample and grouped -G calling typedef struct { double ref_lk, max_lk, lk_sum; float *qsum; // QS(quality sum) values int nqsum; uint32_t *smpl, nsmpl; uint32_t nals, als; } smpl_grp_t; // For the `-C alleles -i` constrained calling typedef struct { uint32_t n:31, used:1; char **allele; } tgt_als_t; typedef struct _ccall_t ccall_t; typedef struct { // mcall only int npdg; int *als_map, nals_map; // mapping from full set of alleles to trimmed set of alleles (old -> new) int *pl_map, npl_map; // same as above for PLs, but reverse (new -> old) char **als; // array to hold the trimmed set of alleles to appear on output int nals; // size of the als array int als_new, nals_new; // bitmask with final alleles and their number family_t *fams; // list of families and samples for trio calling int nfams, mfams; int ntrio[5][5]; // possible trio genotype combinations and their counts; first idx: uint16_t *trio[5][5]; // family type, second index: allele count (2-4, first two are unused) double *GLs; float *GPs; // FORMAT/GP: posterior probabilities int32_t *GQs, *ADs; // FORMAT/GQ: genotype qualities; AD: allelic depth for -G int32_t *itmp; // temporary int array, used for new PLs with CALL_CONSTR_ALLELES int n_itmp, nGPs, nADs; vcmp_t *vcmp; double trio_Pm_SNPs, trio_Pm_del, trio_Pm_ins; // P(mendelian) for trio calling, see mcall_call_trio_genotypes() int32_t *ugts, *cgts; // unconstraind and constrained GTs uint32_t output_tags; char *prior_AN, *prior_AC; // reference panel AF tags (AF=AC/AN) tgt_als_t *tgt_als; // for CALL_CONSTR_ALLELES char *sample_groups; // for single-sample or grouped calling with -G char *sample_groups_tag; // for -G [AD|QS:] smpl_grp_t *smpl_grp; int nsmpl_grp; // ccall only double indel_frac, min_perm_p, min_lrt; double prior_type, pref; int ngrp1_samples, n_perm; char *prior_file; ccall_t *cdat; // shared bcf_srs_t *srs; // BCF synced readers holding target alleles for CALL_CONSTR_ALLELES bcf1_t *rec; bcf_hdr_t *hdr; uint32_t flag; // One or more of the CALL_* flags defined above uint8_t *ploidy, all_diploid, unseen; double pl2p[256]; // PL to 10^(-PL/10) table int32_t *PLs; // VCF PL likelihoods (rw) int nPLs, mPLs, nac; int32_t *gts, *ac; // GTs and AC (w) double *pdg; // PLs converted to P(D|G) float *anno16; int n16; // see anno[16] in bam2bcf.h double theta; // prior } call_t; void error(const char *format, ...); /* * call() - return -1 value on critical error; -2 to skip the site; or the number of alleles on success */ int mcall(call_t *call, bcf1_t *rec); // multiallic and rare-variant calling model int ccall(call_t *call, bcf1_t *rec); // the default consensus calling model int qcall(call_t *call, bcf1_t *rec); // QCall output void mcall_init(call_t *call); void ccall_init(call_t *call); void qcall_init(call_t *call); void mcall_destroy(call_t *call); void ccall_destroy(call_t *call); void qcall_destroy(call_t *call); void call_init_pl2p(call_t *call); uint32_t *call_trio_prep(int is_x, int is_son); void init_allele_trimming_maps(call_t *call, int nals_ori, int als_out); void mcall_trim_and_update_numberR(call_t *call, bcf1_t *rec, int nals_ori, int nals_new); #endif pysam-0.23.0/bcftools/ccall.c000066400000000000000000000316041475062545500160030ustar00rootroot00000000000000/* ccall.c -- consensus variant calling. Copyright (C) 2013-2014 Genome Research Ltd. Portions copyright (C) 2010 Broad Institute. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include "call.h" #include "kmin.h" #include "prob1.h" // Most of the original -c calling was moved to bcftools as it was // and its data structures were wrapped into the ccal_t to make it // functional quickly. This is not the desired state. struct _ccall_t { bcf_p1aux_t *p1; }; void ccall_init(call_t *call) { call->cdat = (ccall_t*) calloc(1,sizeof(ccall_t)); call_init_pl2p(call); call->cdat->p1 = bcf_p1_init(bcf_hdr_nsamples(call->hdr), call->ploidy); call->gts = (int*) calloc(bcf_hdr_nsamples(call->hdr)*2,sizeof(int)); // assuming at most diploid everywhere call->nals_map = 5; call->als_map = (int*) malloc(sizeof(int)*call->nals_map); bcf_hdr_append(call->hdr,"##FORMAT="); if ( call->output_tags & CALL_FMT_GQ ) { bcf_hdr_append(call->hdr,"##FORMAT="); call->GQs = (int32_t*) malloc(sizeof(int32_t)*bcf_hdr_nsamples(call->hdr)); } if ( call->output_tags & CALL_FMT_GP ) error("Sorry, -f GP is not supported with -c\n"); bcf_hdr_append(call->hdr,"##INFO="); // Todo: groups not migrated to 'bcftools call' yet bcf_hdr_append(call->hdr,"##INFO="); bcf_hdr_append(call->hdr,"##INFO="); bcf_hdr_append(call->hdr,"##INFO=\n"); bcf_hdr_append(call->hdr,"##INFO=\n"); bcf_hdr_append(call->hdr,"##INFO=\n"); bcf_hdr_append(call->hdr,"##INFO=\n"); bcf_hdr_append(call->hdr,"##INFO=\n"); // bcf_hdr_append(call->hdr,); // bcf_hdr_append(call->hdr,); bcf_hdr_append(call->hdr,"##INFO="); return; } void ccall_destroy(call_t *call) { free(call->itmp); free(call->als_map); free(call->gts); free(call->anno16); free(call->PLs); free(call->GQs); free(call->pdg); bcf_p1_destroy(call->cdat->p1); free(call->cdat); return; } // Inits P(D|G): convert PLs from log space, only two alleles (three PLs) are used. // NB: The original samtools calling code uses pdgs in reverse order (AA comes // first, RR last), while the -m calling model uses the canonical order. static void set_pdg3(double *pl2p, int *PLs, double *pdg, int n_smpl, int n_gt) { int i; for (i=0; ip[0] = a->p[1] = a->p[2] = a->p[3] = 1.; for (i=0; i<4; i++) a->d[i] = anno[i]; a->depth = anno[0] + anno[1] + anno[2] + anno[3]; a->is_tested = (anno[0] + anno[1] > 0 && anno[2] + anno[3] > 0); if (a->depth == 0) return -1; a->mq = (int)(sqrt((anno[9] + anno[11]) / a->depth) + .499); kt_fisher_exact(anno[0], anno[1], anno[2], anno[3], &left, &right, &a->p[0]); for (i = 1; i < 4; ++i) a->p[i] = ttest(anno[0] + anno[1], anno[2] + anno[3], anno+4*i); return 0; } int test16(float *anno16, anno16_t *a) { a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.; a->d[0] = a->d[1] = a->d[2] = a->d[3] = 0.; a->mq = a->depth = a->is_tested = 0; return test16_core(anno16, a); } static int update_bcf1(call_t *call, bcf1_t *rec, const bcf_p1rst_t *pr, double em[10]) { int has_I16, is_var; float fq, r; anno16_t a; float tmpf[4], tmpi; bcf_get_info_float(call->hdr, rec, "I16", &call->anno16, &call->n16); has_I16 = test16(call->anno16, &a) >= 0? 1 : 0; // print EM if (em[0] >= 0) { tmpf[0] = 1 - em[0]; bcf_update_info_float(call->hdr, rec, "AF1", tmpf, 1); } if (em[4] >= 0 && em[4] <= 0.05) { tmpf[0] = em[3]; tmpf[1] = em[2]; tmpf[2] = em[1]; tmpf[3] = em[4]; bcf_update_info_float(call->hdr, rec, "G3", tmpf, 3); bcf_update_info_float(call->hdr, rec, "HWE", &tmpf[3], 1); } if (em[5] >= 0 && em[6] >= 0) { tmpf[0] = 1 - em[5]; tmpf[1] = 1 - em[6]; bcf_update_info_float(call->hdr, rec, "AF2", tmpf, 2); } if (em[7] >= 0) { tmpf[0] = em[7]; bcf_update_info_float(call->hdr, rec, "LRT", tmpf, 1); } if (em[8] >= 0) { tmpf[0] = em[8]; bcf_update_info_float(call->hdr, rec, "LRT2", tmpf, 1); } bcf_p1aux_t *p1 = call->cdat->p1; if (p1->cons_llr > 0) { tmpi = p1->cons_llr; bcf_update_info_int32(call->hdr, rec, "CLR", &tmpi, 1); // todo: trio calling with -c if (p1->cons_gt > 0) { char tmp[4]; tmp[0] = p1->cons_gt&0xff; tmp[1] = p1->cons_gt>>8&0xff; tmp[2] = p1->cons_gt>>16&0xff; tmp[3] = 0; bcf_update_info_string(call->hdr, rec, "UGT", tmp); tmp[0] = p1->cons_gt>>32&0xff; tmp[1] = p1->cons_gt>>40&0xff; tmp[2] = p1->cons_gt>>48&0xff; bcf_update_info_string(call->hdr, rec, "CGT", tmp); } } is_var = (pr->p_ref < call->pref); r = is_var? pr->p_ref : pr->p_var; bcf_update_info_int32(call->hdr, rec, "AC1", &pr->ac, 1); int32_t dp[4]; dp[0] = call->anno16[0]; dp[1] = call->anno16[1]; dp[2] = call->anno16[2]; dp[3] = call->anno16[3]; bcf_update_info_int32(call->hdr, rec, "DP4", dp, 4); bcf_update_info_int32(call->hdr, rec, "MQ", &a.mq, 1); fq = pr->p_ref_folded < 0.5? -4.343 * log(pr->p_ref_folded) : 4.343 * log(pr->p_var_folded); if (fq < -999) fq = -999; if (fq > 999) fq = 999; bcf_update_info_float(call->hdr, rec, "FQ", &fq, 1); assert( pr->cmp[0]<0 ); // todo // if (pr->cmp[0] >= 0.) { // two sample groups // int i, q[3]; // for (i = 1; i < 3; ++i) { // double x = pr->cmp[i] + pr->cmp[0]/2.; // q[i] = x == 0? 255 : (int)(-4.343 * log(x) + .499); // if (q[i] > 255) q[i] = 255; // } // if (pr->perm_rank >= 0) ksprintf(&s, "PR=%d;", pr->perm_rank); // // ksprintf(&s, "PCHI2=%.3g;PC2=%d,%d;", q[1], q[2], pr->p_chi2); // } if (has_I16 && a.is_tested) { int i; for (i=0; i<4; i++) tmpf[i] = a.p[i]; bcf_update_info_float(call->hdr, rec, "PV4", tmpf, 4); } bcf_update_info_int32(call->hdr, rec, "I16", NULL, 0); // remove I16 tag bcf_update_info_int32(call->hdr, rec, "QS", NULL, 0); // remove QS tag rec->qual = r < 1e-100? 999 : -4.343 * log(r); if (rec->qual > 999) rec->qual = 999; // Remove unused alleles int nals_ori = rec->n_allele, nals = !is_var && !(call->flag & CALL_KEEPALT) ? 1 : pr->rank0 < 2? 2 : pr->rank0+1; if ( call->flag & CALL_KEEPALT && call->unseen==nals-1 ) nals--; if ( nalsn_allele ) { bcf_update_alleles(call->hdr, rec, (const char**)rec->d.allele, nals); // Update PLs int npls_src = call->nPLs / rec->n_sample, npls_dst = nals*(nals+1)/2; int *pls_src = call->PLs - npls_src, *pls_dst = call->PLs - npls_dst; int isample, i; for (isample = 0; isample < rec->n_sample; isample++) { pls_src += npls_src; pls_dst += npls_dst; if ( !call->ploidy || call->ploidy[isample]==2 ) { for (i=0; ihdr, rec, "PL", call->PLs, npls_dst*rec->n_sample); } // Call genotypes int i; for (i=0; in_sample; i++) { int x = ( is_var || call->output_tags & CALL_FMT_GQ ) ? bcf_p1_call_gt(p1, pr->f_exp, i, is_var) : 2; int gt = x&3; if ( !call->ploidy || call->ploidy[i]==2 ) { if ( gt==1 ) { call->gts[2*i] = bcf_gt_unphased(0); call->gts[2*i+1] = bcf_gt_unphased(1); } else if ( gt==0 ) { call->gts[2*i] = bcf_gt_unphased(1); call->gts[2*i+1] = bcf_gt_unphased(1); } else { call->gts[2*i] = bcf_gt_unphased(0); call->gts[2*i+1] = bcf_gt_unphased(0); } if ( call->output_tags & CALL_FMT_GQ ) call->GQs[i] = x>>2; } else { if ( gt==0 ) call->gts[2*i] = bcf_gt_unphased(1); else call->gts[2*i] = bcf_gt_unphased(0); call->gts[2*i+1] = bcf_int32_vector_end; if ( call->output_tags & CALL_FMT_GQ ) call->GQs[i] = bcf_int32_missing; } } bcf_update_genotypes(call->hdr, rec, call->gts, rec->n_sample*2); if ( call->output_tags & CALL_FMT_GQ ) bcf_update_format_int32(call->hdr, rec, "GQ", call->GQs, rec->n_sample); // trim Number=R tags int out_als = 0; for (i=0; ihdr); // Get the genotype likelihoods int nals = rec->n_allele; call->nPLs = bcf_get_format_int32(call->hdr, rec, "PL", &call->PLs, &call->mPLs); if ( call->nPLs!=nsmpl*nals*(nals+1)/2 && call->nPLs!=nsmpl*nals ) // diploid+haploid or haploid only error("Wrong number of PL fields? nals=%d npl=%d\n", nals,call->nPLs); // Convert PLs to probabilities, only first two alleles are considered int ngts = nals*(nals+1)/2; hts_expand(double, 3*nsmpl, call->npdg, call->pdg); set_pdg3(call->pl2p, call->PLs, call->pdg, nsmpl, ngts); double em[10] = {-1.,-1.,-1.,-1.,-1.,-1.,-1.,-1.,-1.,-1.}; int ret = bcf_em1(call, rec, call->ngrp1_samples, 0x1ff, em); bcf_p1rst_t pr; int do_contrast = (em[7] >= 0 && em[7] < call->min_lrt) ? 1 : 0; ret = bcf_p1_cal(call, rec, do_contrast, call->cdat->p1, &pr); if (pr.p_ref >= call->pref && (call->flag & CALL_VARONLY)) return 0; if (ret >= 0) ret = update_bcf1(call, rec, &pr, em); return ret; } pysam-0.23.0/bcftools/ccall.c.pysam.c000066400000000000000000000316411475062545500173550ustar00rootroot00000000000000#include "bcftools.pysam.h" /* ccall.c -- consensus variant calling. Copyright (C) 2013-2014 Genome Research Ltd. Portions copyright (C) 2010 Broad Institute. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include "call.h" #include "kmin.h" #include "prob1.h" // Most of the original -c calling was moved to bcftools as it was // and its data structures were wrapped into the ccal_t to make it // functional quickly. This is not the desired state. struct _ccall_t { bcf_p1aux_t *p1; }; void ccall_init(call_t *call) { call->cdat = (ccall_t*) calloc(1,sizeof(ccall_t)); call_init_pl2p(call); call->cdat->p1 = bcf_p1_init(bcf_hdr_nsamples(call->hdr), call->ploidy); call->gts = (int*) calloc(bcf_hdr_nsamples(call->hdr)*2,sizeof(int)); // assuming at most diploid everywhere call->nals_map = 5; call->als_map = (int*) malloc(sizeof(int)*call->nals_map); bcf_hdr_append(call->hdr,"##FORMAT="); if ( call->output_tags & CALL_FMT_GQ ) { bcf_hdr_append(call->hdr,"##FORMAT="); call->GQs = (int32_t*) malloc(sizeof(int32_t)*bcf_hdr_nsamples(call->hdr)); } if ( call->output_tags & CALL_FMT_GP ) error("Sorry, -f GP is not supported with -c\n"); bcf_hdr_append(call->hdr,"##INFO="); // Todo: groups not migrated to 'bcftools call' yet bcf_hdr_append(call->hdr,"##INFO="); bcf_hdr_append(call->hdr,"##INFO="); bcf_hdr_append(call->hdr,"##INFO=\n"); bcf_hdr_append(call->hdr,"##INFO=\n"); bcf_hdr_append(call->hdr,"##INFO=\n"); bcf_hdr_append(call->hdr,"##INFO=\n"); bcf_hdr_append(call->hdr,"##INFO=\n"); // bcf_hdr_append(call->hdr,); // bcf_hdr_append(call->hdr,); bcf_hdr_append(call->hdr,"##INFO="); return; } void ccall_destroy(call_t *call) { free(call->itmp); free(call->als_map); free(call->gts); free(call->anno16); free(call->PLs); free(call->GQs); free(call->pdg); bcf_p1_destroy(call->cdat->p1); free(call->cdat); return; } // Inits P(D|G): convert PLs from log space, only two alleles (three PLs) are used. // NB: The original samtools calling code uses pdgs in reverse order (AA comes // first, RR last), while the -m calling model uses the canonical order. static void set_pdg3(double *pl2p, int *PLs, double *pdg, int n_smpl, int n_gt) { int i; for (i=0; ip[0] = a->p[1] = a->p[2] = a->p[3] = 1.; for (i=0; i<4; i++) a->d[i] = anno[i]; a->depth = anno[0] + anno[1] + anno[2] + anno[3]; a->is_tested = (anno[0] + anno[1] > 0 && anno[2] + anno[3] > 0); if (a->depth == 0) return -1; a->mq = (int)(sqrt((anno[9] + anno[11]) / a->depth) + .499); kt_fisher_exact(anno[0], anno[1], anno[2], anno[3], &left, &right, &a->p[0]); for (i = 1; i < 4; ++i) a->p[i] = ttest(anno[0] + anno[1], anno[2] + anno[3], anno+4*i); return 0; } int test16(float *anno16, anno16_t *a) { a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.; a->d[0] = a->d[1] = a->d[2] = a->d[3] = 0.; a->mq = a->depth = a->is_tested = 0; return test16_core(anno16, a); } static int update_bcf1(call_t *call, bcf1_t *rec, const bcf_p1rst_t *pr, double em[10]) { int has_I16, is_var; float fq, r; anno16_t a; float tmpf[4], tmpi; bcf_get_info_float(call->hdr, rec, "I16", &call->anno16, &call->n16); has_I16 = test16(call->anno16, &a) >= 0? 1 : 0; // print EM if (em[0] >= 0) { tmpf[0] = 1 - em[0]; bcf_update_info_float(call->hdr, rec, "AF1", tmpf, 1); } if (em[4] >= 0 && em[4] <= 0.05) { tmpf[0] = em[3]; tmpf[1] = em[2]; tmpf[2] = em[1]; tmpf[3] = em[4]; bcf_update_info_float(call->hdr, rec, "G3", tmpf, 3); bcf_update_info_float(call->hdr, rec, "HWE", &tmpf[3], 1); } if (em[5] >= 0 && em[6] >= 0) { tmpf[0] = 1 - em[5]; tmpf[1] = 1 - em[6]; bcf_update_info_float(call->hdr, rec, "AF2", tmpf, 2); } if (em[7] >= 0) { tmpf[0] = em[7]; bcf_update_info_float(call->hdr, rec, "LRT", tmpf, 1); } if (em[8] >= 0) { tmpf[0] = em[8]; bcf_update_info_float(call->hdr, rec, "LRT2", tmpf, 1); } bcf_p1aux_t *p1 = call->cdat->p1; if (p1->cons_llr > 0) { tmpi = p1->cons_llr; bcf_update_info_int32(call->hdr, rec, "CLR", &tmpi, 1); // todo: trio calling with -c if (p1->cons_gt > 0) { char tmp[4]; tmp[0] = p1->cons_gt&0xff; tmp[1] = p1->cons_gt>>8&0xff; tmp[2] = p1->cons_gt>>16&0xff; tmp[3] = 0; bcf_update_info_string(call->hdr, rec, "UGT", tmp); tmp[0] = p1->cons_gt>>32&0xff; tmp[1] = p1->cons_gt>>40&0xff; tmp[2] = p1->cons_gt>>48&0xff; bcf_update_info_string(call->hdr, rec, "CGT", tmp); } } is_var = (pr->p_ref < call->pref); r = is_var? pr->p_ref : pr->p_var; bcf_update_info_int32(call->hdr, rec, "AC1", &pr->ac, 1); int32_t dp[4]; dp[0] = call->anno16[0]; dp[1] = call->anno16[1]; dp[2] = call->anno16[2]; dp[3] = call->anno16[3]; bcf_update_info_int32(call->hdr, rec, "DP4", dp, 4); bcf_update_info_int32(call->hdr, rec, "MQ", &a.mq, 1); fq = pr->p_ref_folded < 0.5? -4.343 * log(pr->p_ref_folded) : 4.343 * log(pr->p_var_folded); if (fq < -999) fq = -999; if (fq > 999) fq = 999; bcf_update_info_float(call->hdr, rec, "FQ", &fq, 1); assert( pr->cmp[0]<0 ); // todo // if (pr->cmp[0] >= 0.) { // two sample groups // int i, q[3]; // for (i = 1; i < 3; ++i) { // double x = pr->cmp[i] + pr->cmp[0]/2.; // q[i] = x == 0? 255 : (int)(-4.343 * log(x) + .499); // if (q[i] > 255) q[i] = 255; // } // if (pr->perm_rank >= 0) ksprintf(&s, "PR=%d;", pr->perm_rank); // // ksprintf(&s, "PCHI2=%.3g;PC2=%d,%d;", q[1], q[2], pr->p_chi2); // } if (has_I16 && a.is_tested) { int i; for (i=0; i<4; i++) tmpf[i] = a.p[i]; bcf_update_info_float(call->hdr, rec, "PV4", tmpf, 4); } bcf_update_info_int32(call->hdr, rec, "I16", NULL, 0); // remove I16 tag bcf_update_info_int32(call->hdr, rec, "QS", NULL, 0); // remove QS tag rec->qual = r < 1e-100? 999 : -4.343 * log(r); if (rec->qual > 999) rec->qual = 999; // Remove unused alleles int nals_ori = rec->n_allele, nals = !is_var && !(call->flag & CALL_KEEPALT) ? 1 : pr->rank0 < 2? 2 : pr->rank0+1; if ( call->flag & CALL_KEEPALT && call->unseen==nals-1 ) nals--; if ( nalsn_allele ) { bcf_update_alleles(call->hdr, rec, (const char**)rec->d.allele, nals); // Update PLs int npls_src = call->nPLs / rec->n_sample, npls_dst = nals*(nals+1)/2; int *pls_src = call->PLs - npls_src, *pls_dst = call->PLs - npls_dst; int isample, i; for (isample = 0; isample < rec->n_sample; isample++) { pls_src += npls_src; pls_dst += npls_dst; if ( !call->ploidy || call->ploidy[isample]==2 ) { for (i=0; ihdr, rec, "PL", call->PLs, npls_dst*rec->n_sample); } // Call genotypes int i; for (i=0; in_sample; i++) { int x = ( is_var || call->output_tags & CALL_FMT_GQ ) ? bcf_p1_call_gt(p1, pr->f_exp, i, is_var) : 2; int gt = x&3; if ( !call->ploidy || call->ploidy[i]==2 ) { if ( gt==1 ) { call->gts[2*i] = bcf_gt_unphased(0); call->gts[2*i+1] = bcf_gt_unphased(1); } else if ( gt==0 ) { call->gts[2*i] = bcf_gt_unphased(1); call->gts[2*i+1] = bcf_gt_unphased(1); } else { call->gts[2*i] = bcf_gt_unphased(0); call->gts[2*i+1] = bcf_gt_unphased(0); } if ( call->output_tags & CALL_FMT_GQ ) call->GQs[i] = x>>2; } else { if ( gt==0 ) call->gts[2*i] = bcf_gt_unphased(1); else call->gts[2*i] = bcf_gt_unphased(0); call->gts[2*i+1] = bcf_int32_vector_end; if ( call->output_tags & CALL_FMT_GQ ) call->GQs[i] = bcf_int32_missing; } } bcf_update_genotypes(call->hdr, rec, call->gts, rec->n_sample*2); if ( call->output_tags & CALL_FMT_GQ ) bcf_update_format_int32(call->hdr, rec, "GQ", call->GQs, rec->n_sample); // trim Number=R tags int out_als = 0; for (i=0; ihdr); // Get the genotype likelihoods int nals = rec->n_allele; call->nPLs = bcf_get_format_int32(call->hdr, rec, "PL", &call->PLs, &call->mPLs); if ( call->nPLs!=nsmpl*nals*(nals+1)/2 && call->nPLs!=nsmpl*nals ) // diploid+haploid or haploid only error("Wrong number of PL fields? nals=%d npl=%d\n", nals,call->nPLs); // Convert PLs to probabilities, only first two alleles are considered int ngts = nals*(nals+1)/2; hts_expand(double, 3*nsmpl, call->npdg, call->pdg); set_pdg3(call->pl2p, call->PLs, call->pdg, nsmpl, ngts); double em[10] = {-1.,-1.,-1.,-1.,-1.,-1.,-1.,-1.,-1.,-1.}; int ret = bcf_em1(call, rec, call->ngrp1_samples, 0x1ff, em); bcf_p1rst_t pr; int do_contrast = (em[7] >= 0 && em[7] < call->min_lrt) ? 1 : 0; ret = bcf_p1_cal(call, rec, do_contrast, call->cdat->p1, &pr); if (pr.p_ref >= call->pref && (call->flag & CALL_VARONLY)) return 0; if (ret >= 0) ret = update_bcf1(call, rec, &pr, em); return ret; } pysam-0.23.0/bcftools/cigar_state.h000066400000000000000000000151201475062545500172120ustar00rootroot00000000000000/* cigar_state.h -- API for efficient parsing of CIGAR strings Copyright (C) 2022 Genome Research Ltd. Author: pd3@sanger Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef CIGAR_STATE_H #define CIGAR_STATE_H #include #include #include typedef struct { bam1_t *bam; uint32_t *cigar; uint8_t *seq; int ncig; int icig; // position in the cigar string int iseq; // the cigar[icigar] operation refers to &seq[iseq] hts_pos_t ref_pos; // reference coordinate, corresponds to iseq; points to // the first base after the read when consumed } cigar_state_t; static inline void cstate_init(cigar_state_t *cs, bam1_t *bam) { cs->bam = bam; cs->cigar = bam_get_cigar(bam); cs->seq = bam_get_seq(bam); cs->ncig = bam->core.n_cigar; cs->icig = 0; cs->iseq = 0; cs->ref_pos = bam->core.pos; } /** * cstate_seek_fwd() - Move in the cigar forward to find query index that * matches the reference position. * * When the position is not contained within the sequence, either because there * is a deletion or there is no overlap, the behavior is controlled by the value * of trim_left: * - read starts after: qry_beg > pos && trim_left=1 .. returns 0 and sets pos to qry_beg * - read starts after: qry_beg > pos && trim_left=0 .. returns -1 * - read ends before: qry_end < pos && trim_left=1 .. returns -2 * - read ends before: qry_end < pos && trim_left=0 .. returns qry_len-1 and sets pos to qry_end * - pos inside a deletion && trim_left=1 .. returns position after the deletion * - pos inside a deletion && trim_left=0 .. returns position before the deletion */ static inline int cstate_seek_fwd(cigar_state_t *cs, hts_pos_t *pos_ptr, int trim_left) { hts_pos_t pos = *pos_ptr; while ( cs->ref_pos <= pos ) { if ( cs->icig >= cs->ncig ) // the read ends before pos { if ( trim_left ) return -2; *pos_ptr = cs->ref_pos - 1; return cs->iseq - 1; } int op = cs->cigar[cs->icig] & BAM_CIGAR_MASK; int len = cs->cigar[cs->icig] >> BAM_CIGAR_SHIFT; if ( op==BAM_CMATCH || op==BAM_CEQUAL || op==BAM_CDIFF ) { if ( cs->ref_pos + len > pos ) return pos - cs->ref_pos + cs->iseq; // the cigar op overlaps pos cs->ref_pos += len; cs->iseq += len; cs->icig++; continue; } if ( op==BAM_CINS || op==BAM_CSOFT_CLIP ) { cs->iseq += len; cs->icig++; continue; } if ( op==BAM_CDEL || op==BAM_CREF_SKIP ) { if ( cs->ref_pos + len > pos ) { // The deletion overlaps the position. NB: assuming del is never the first or last op *pos_ptr = trim_left ? cs->ref_pos + len : cs->ref_pos - 1; return trim_left ? cs->iseq : cs->iseq - 1; } cs->ref_pos += len; cs->icig++; continue; } if ( op==BAM_CHARD_CLIP || op==BAM_CPAD ) { cs->icig++; continue; } error("FIXME: not ready for CIGAR operator %d\n",op); } // the read starts after pos if ( trim_left ) { *pos_ptr = cs->bam->core.pos; return 0; } return -1; } /** * cstate_seek_op_fwd() - Move in the cigar forward to find query index that * matches the seek operator and the reference position. * * In order to match a deletion, pass the position of the first deleted base. * In order to match an insertion, pass the reference coordinate of the base * after the inserted sequence. * * Returns the index to the query sequence cs->seq * on success; -1 when there is no such matching position but the cigar * is still not entirely consumed (e.g. a deletion or a soft-clip); -2 * when there is no overlap (i.e. the read ends before the position). */ static inline int cstate_seek_op_fwd(cigar_state_t *cs, hts_pos_t pos, int seek_op, int *oplen) { while ( cs->ref_pos <= pos ) { if ( cs->icig >= cs->ncig ) return -2; int op = cs->cigar[cs->icig] & BAM_CIGAR_MASK; int len = cs->cigar[cs->icig] >> BAM_CIGAR_SHIFT; if ( op==BAM_CMATCH || op==BAM_CEQUAL || op==BAM_CDIFF ) { if ( cs->ref_pos + len <= pos ) { cs->ref_pos += len; cs->iseq += len; cs->icig++; continue; } if ( seek_op==BAM_CMATCH ) return pos - cs->ref_pos + cs->iseq; return -1; } if ( op==BAM_CINS || op==BAM_CSOFT_CLIP ) { if ( cs->ref_pos == pos && seek_op==op ) { if ( oplen ) *oplen = len; return cs->iseq; } if ( cs->ref_pos >= pos ) return -1; cs->iseq += len; cs->icig++; continue; } if ( op==BAM_CDEL || op==BAM_CREF_SKIP ) { if ( cs->ref_pos == pos && seek_op==op ) { if ( oplen ) *oplen = len; return cs->iseq; } if ( cs->ref_pos >= pos ) return -1; cs->ref_pos += len; cs->icig++; continue; } if ( op==BAM_CHARD_CLIP || op==BAM_CPAD ) { cs->icig++; continue; } error("FIXME: not ready for CIGAR operator %d\n",op); } return cs->icig < cs->ncig ? -1 : -2; } #endif pysam-0.23.0/bcftools/cols.c000066400000000000000000000064131475062545500156650ustar00rootroot00000000000000/* Copyright (C) 2019 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include "cols.h" cols_t *cols_split(const char *line, cols_t *cols, char delim) { if ( !cols ) cols = (cols_t*) calloc(1,sizeof(cols_t)); if ( cols->rmme ) free(cols->rmme); cols->n = 0; cols->rmme = strdup(line); char *ss = cols->rmme; while (1) { char *se = ss; while ( *se && *se!=delim ) se++; char tmp = *se; *se = 0; cols->n++; if ( cols->n > cols->m ) { cols->m += 10; cols->off = (char**) realloc(cols->off, sizeof(*cols->off)*cols->m); } cols->off[ cols->n - 1 ] = ss; if ( !tmp ) break; ss = se + 1; } return cols; } void cols_append(cols_t *cols, char *str) { if ( cols->rmme ) { size_t str_len = strlen(str); size_t lst_len = strlen(cols->off[ cols->n - 1 ]); size_t tot_len = 2 + str_len + lst_len + (cols->off[ cols->n - 1 ] - cols->rmme); cols_t *tmp_cols = (cols_t*)calloc(1,sizeof(cols_t)); tmp_cols->rmme = (char*) calloc(tot_len,1); tmp_cols->off = (char**) calloc(cols->n+1,sizeof(*tmp_cols->off)); char *ptr = tmp_cols->rmme; int i; for (i=0; in; i++) { size_t len = strlen(cols->off[i]); memcpy(ptr, cols->off[i], len); tmp_cols->off[i] = ptr; ptr += len + 1; } memcpy(ptr, str, str_len); tmp_cols->off[i] = ptr; free(cols->off); free(cols->rmme); cols->rmme = tmp_cols->rmme; cols->off = tmp_cols->off; cols->n = cols->n+1; cols->m = cols->n; free(tmp_cols); return; } cols->n++; if ( cols->n > cols->m ) { cols->m++; cols->off = (char**) realloc(cols->off,sizeof(*cols->off)*cols->m); } cols->off[cols->n-1] = str; } void cols_clear(cols_t *cols) { if ( !cols ) return; free(cols->rmme); free(cols->off); cols->rmme = NULL; cols->off = NULL; } void cols_destroy(cols_t *cols) { if ( !cols ) return; cols_clear(cols); free(cols); } pysam-0.23.0/bcftools/cols.c.pysam.c000066400000000000000000000064501475062545500172370ustar00rootroot00000000000000#include "bcftools.pysam.h" /* Copyright (C) 2019 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include "cols.h" cols_t *cols_split(const char *line, cols_t *cols, char delim) { if ( !cols ) cols = (cols_t*) calloc(1,sizeof(cols_t)); if ( cols->rmme ) free(cols->rmme); cols->n = 0; cols->rmme = strdup(line); char *ss = cols->rmme; while (1) { char *se = ss; while ( *se && *se!=delim ) se++; char tmp = *se; *se = 0; cols->n++; if ( cols->n > cols->m ) { cols->m += 10; cols->off = (char**) realloc(cols->off, sizeof(*cols->off)*cols->m); } cols->off[ cols->n - 1 ] = ss; if ( !tmp ) break; ss = se + 1; } return cols; } void cols_append(cols_t *cols, char *str) { if ( cols->rmme ) { size_t str_len = strlen(str); size_t lst_len = strlen(cols->off[ cols->n - 1 ]); size_t tot_len = 2 + str_len + lst_len + (cols->off[ cols->n - 1 ] - cols->rmme); cols_t *tmp_cols = (cols_t*)calloc(1,sizeof(cols_t)); tmp_cols->rmme = (char*) calloc(tot_len,1); tmp_cols->off = (char**) calloc(cols->n+1,sizeof(*tmp_cols->off)); char *ptr = tmp_cols->rmme; int i; for (i=0; in; i++) { size_t len = strlen(cols->off[i]); memcpy(ptr, cols->off[i], len); tmp_cols->off[i] = ptr; ptr += len + 1; } memcpy(ptr, str, str_len); tmp_cols->off[i] = ptr; free(cols->off); free(cols->rmme); cols->rmme = tmp_cols->rmme; cols->off = tmp_cols->off; cols->n = cols->n+1; cols->m = cols->n; free(tmp_cols); return; } cols->n++; if ( cols->n > cols->m ) { cols->m++; cols->off = (char**) realloc(cols->off,sizeof(*cols->off)*cols->m); } cols->off[cols->n-1] = str; } void cols_clear(cols_t *cols) { if ( !cols ) return; free(cols->rmme); free(cols->off); cols->rmme = NULL; cols->off = NULL; } void cols_destroy(cols_t *cols) { if ( !cols ) return; cols_clear(cols); free(cols); } pysam-0.23.0/bcftools/cols.h000066400000000000000000000034201475062545500156650ustar00rootroot00000000000000/* Copyright (C) 2019 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef __COLS_H__ #define __COLS_H__ #include typedef struct { int n,m; char **off, *rmme; } cols_t; /* cols_split() can be called repeatedly to split new strings, memory is allocated and deallocated automatically */ cols_t *cols_split(const char *line, cols_t *cols, char delim); /* Although cols_append() can be combined with cols_split(), it is much slower and the string must exist throughout the life of cols unless initialized with cols_split(). */ void cols_append(cols_t *cols, char *str); void cols_clear(cols_t *cols); void cols_destroy(cols_t *cols); #endif pysam-0.23.0/bcftools/consensus.c000066400000000000000000001510621475062545500167460ustar00rootroot00000000000000/* The MIT License Copyright (c) 2014-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "regidx.h" #include "bcftools.h" #include "rbuf.h" #include "filter.h" #include "smpl_ilist.h" // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 #define PICK_REF 1 #define PICK_ALT 2 #define PICK_LONG 4 #define PICK_SHORT 8 #define PICK_IUPAC 16 #define TO_UPPER 1 #define TO_LOWER 2 typedef struct { int num; // number of ungapped blocks in this chain int *block_lengths; // length of the ungapped blocks in this chain int *ref_gaps; // length of the gaps on the reference sequence between blocks int *alt_gaps; // length of the gaps on the alternative sequence between blocks int ori_pos; int ref_last_block_ori; // start position on the reference sequence of the following ungapped block (0-based) int alt_last_block_ori; // start position on the alternative sequence of the following ungapped block (0-based) } chain_t; #define MASK_LC 1 #define MASK_UC 2 #define MASK_SKIP(x) (((x)->with!=MASK_LC && (x)->with!=MASK_UC) ? 1 : 0) typedef struct { char *fname, with; regidx_t *idx; regitr_t *itr; } mask_t; typedef struct { kstring_t fa_buf; // buffered reference sequence int fa_ori_pos; // start position of the fa_buffer (wrt original sequence) int fa_frz_pos; // protected position to avoid conflicting variants (last pos for SNPs/ins) int fa_mod_off; // position difference of fa_frz_pos in the ori and modified sequence (ins positive) int fa_frz_mod; // the fa_buf offset of the protected fa_frz_pos position, includes the modified sequence int fa_end_pos; // region's end position in the original sequence int fa_length; // region's length in the original sequence (in case end_pos not provided in the FASTA header) int fa_case; // output upper case or lower case: TO_UPPER|TO_LOWER int fa_src_pos; // last genomic coordinate read from the input fasta (0-based) char prev_base; // this is only to validate the REF allele in the VCF - the modified fa_buf cannot be used for inserts following deletions, see 600#issuecomment-383186778 int prev_base_pos; // the position of prev_base int prev_is_insert; rbuf_t vcf_rbuf; bcf1_t **vcf_buf; int nvcf_buf, rid; char *chr, *chr_prefix; mask_t *mask; int nmask; int chain_id; // chain_id, to provide a unique ID to each chain in the chain output chain_t *chain; // chain structure to store the sequence of ungapped blocks between the ref and alt sequences // Note that the chain is re-initialised for each chromosome/seq_region filter_t *filter; char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE bcf_srs_t *files; bcf_hdr_t *hdr; FILE *fp_out; FILE *fp_chain; char **argv; int argc, output_iupac, iupac_GTs, haplotype, allele, isample, napplied; uint8_t *iupac_bitmask, *iupac_als; int miupac_bitmask, miupac_als, regions_overlap; char *fname, *ref_fname, *sample, *sample_fname, *output_fname, *mask_fname, *chain_fname, missing_allele, absent_allele; char mark_del, mark_ins, mark_snv; smpl_ilist_t *smpl; } args_t; static void destroy_chain(chain_t *chain) { if ( !chain ) return; free(chain->ref_gaps); free(chain->alt_gaps); free(chain->block_lengths); free(chain); } static chain_t* init_chain(chain_t *chain, int ref_ori_pos) { if ( chain ) destroy_chain(chain); chain = (chain_t*) calloc(1,sizeof(chain_t)); chain->num = 0; chain->block_lengths = NULL; chain->ref_gaps = NULL; chain->alt_gaps = NULL; chain->ori_pos = ref_ori_pos; chain->ref_last_block_ori = ref_ori_pos; chain->alt_last_block_ori = ref_ori_pos; return chain; } static void print_chain(args_t *args) { /* Example chain format (see: https://genome.ucsc.edu/goldenPath/help/chain.html): chain 1 500 + 480 500 1 501 + 480 501 1 12 3 1 1 0 3 484 chain line is: - chain - score (sum of the length of ungapped block in this case) - ref_seqname (from the fasta header, parsed by htslib) - ref_seqlength (from the fasta header) - ref_strand (+ or -; always + for bcf-consensus) - ref_start (as defined in the fasta header) - ref_end (as defined in the fasta header) - alt_seqname (same as ref_seqname as bcf-consensus only considers SNPs and indels) - alt_seqlength (adjusted to match the length of the alt sequence) - alt_strand (+ or -; always + for bcf-consensus) - alt_start (same as ref_start, as no edits are recorded/applied before that position) - alt_end (adjusted to match the length of the alt sequence) - chain_num (just an auto-increment id) the other (sorted) lines are: - length of the ungapped alignment block - gap on the ref sequence between this and the next block (all but the last line) - gap on the alt sequence between this and the next block (all but the last line) */ chain_t *chain = args->chain; int n = chain->num; int ref_end_pos = args->fa_length + chain->ori_pos; int last_block_size = ref_end_pos - chain->ref_last_block_ori; int alt_end_pos = chain->alt_last_block_ori + last_block_size; int score = 0; for (n=0; nnum; n++) { score += chain->block_lengths[n]; } score += last_block_size; fprintf(args->fp_chain, "chain %d %s %d + %d %d %s %d + %d %d %d\n", score, args->chr, ref_end_pos, chain->ori_pos, ref_end_pos, args->chr, alt_end_pos, chain->ori_pos, alt_end_pos, ++args->chain_id); for (n=0; nnum; n++) { fprintf(args->fp_chain, "%d %d %d\n", chain->block_lengths[n], chain->ref_gaps[n], chain->alt_gaps[n]); } fprintf(args->fp_chain, "%d\n\n", last_block_size); } static void push_chain_gap(chain_t *chain, int ref_start, int ref_len, int alt_start, int alt_len) { // fprintf(stderr, "push_chain_gap(chain=%p, ref_start=%d, ref_len=%d, alt_start=%d, alt_len=%d)\n", chain, ref_start, ref_len, alt_start, alt_len); int num = chain->num; if (num && ref_start <= chain->ref_last_block_ori) { // In case this variant is back-to-back with the previous one chain->ref_last_block_ori = ref_start + ref_len; chain->alt_last_block_ori = alt_start + alt_len; chain->ref_gaps[num-1] += ref_len; chain->alt_gaps[num-1] += alt_len; } else { // Extend the ungapped blocks, store the gap length chain->block_lengths = (int*) realloc(chain->block_lengths, (num + 1) * sizeof(int)); chain->ref_gaps = (int*) realloc(chain->ref_gaps, (num + 1) * sizeof(int)); chain->alt_gaps = (int*) realloc(chain->alt_gaps, (num + 1) * sizeof(int)); chain->block_lengths[num] = ref_start - chain->ref_last_block_ori; chain->ref_gaps[num] = ref_len; chain->alt_gaps[num] = alt_len; // Update the start positions of the next block chain->ref_last_block_ori = ref_start + ref_len; chain->alt_last_block_ori = alt_start + alt_len; // Increment the number of ungapped blocks chain->num++; } } static void init_data(args_t *args) { args->files = bcf_sr_init(); args->files->require_index = 1; if ( !bcf_sr_add_reader(args->files,args->fname) ) error("Failed to read from %s: %s\n", !strcmp("-",args->fname)?"standard input":args->fname, bcf_sr_strerror(args->files->errnum)); args->hdr = args->files->readers[0].header; args->isample = -1; if ( !args->sample ) { args->smpl = smpl_ilist_init(args->hdr,NULL,0,SMPL_NONE|SMPL_VERBOSE); if ( !args->smpl->n ) { smpl_ilist_destroy(args->smpl); args->smpl = NULL; } } else if ( args->sample && strcmp("-",args->sample) ) { args->smpl = smpl_ilist_init(args->hdr,args->sample,0,SMPL_NONE|SMPL_VERBOSE); if ( args->smpl && !args->smpl->n ) error("No matching sample found\n"); } else if ( args->sample_fname ) { args->smpl = smpl_ilist_init(args->hdr,args->sample_fname,1,SMPL_NONE|SMPL_VERBOSE); if ( args->smpl && !args->smpl->n ) error("No matching sample found\n"); } if ( args->smpl ) { if ( args->haplotype || args->allele ) { if ( args->smpl->n > 1 ) error("Too many samples, only one can be used with -H; check the -s,-S options\n"); args->isample = args->smpl->idx[0]; } else { args->iupac_GTs = 1; if ( args->smpl->n==1 ) fprintf(stderr,"Note: applying IUPAC codes based on FORMAT/GT in sample %s\n",bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->smpl->idx[0])); else fprintf(stderr,"Note: applying IUPAC codes based on FORMAT/GT in %d samples\n",args->smpl->n); } } else if ( args->output_iupac ) fprintf(stderr,"Note: applying IUPAC codes based on REF,ALT%s\n",bcf_hdr_nsamples(args->hdr)?", ignoring samples":""); else fprintf(stderr,"Note: applying REF,ALT variants%s\n",bcf_hdr_nsamples(args->hdr)?", ignoring samples":""); int i; for (i=0; inmask; i++) { mask_t *mask = &args->mask[i]; mask->idx = regidx_init(mask->fname,NULL,NULL,0,NULL); if ( !mask->idx ) error("Failed to initialize mask regions\n"); mask->itr = regitr_init(mask->idx); } // In case we want to store the chains if ( args->chain_fname ) { args->fp_chain = fopen(args->chain_fname,"w"); if ( ! args->fp_chain ) error("Failed to create %s: %s\n", args->chain_fname, strerror(errno)); args->chain_id = 0; } rbuf_init(&args->vcf_rbuf, 100); args->vcf_buf = (bcf1_t**) calloc(args->vcf_rbuf.m, sizeof(bcf1_t*)); if ( args->output_fname ) { args->fp_out = fopen(args->output_fname,"w"); if ( ! args->fp_out ) error("Failed to create %s: %s\n", args->output_fname, strerror(errno)); } else args->fp_out = stdout; if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); args->rid = -1; } static void add_mask(args_t *args, char *fname) { args->nmask++; args->mask = (mask_t*)realloc(args->mask,args->nmask*sizeof(*args->mask)); mask_t *mask = &args->mask[args->nmask-1]; mask->fname = fname; mask->with = 'N'; } static void add_mask_with(args_t *args, char *with) { if ( !args->nmask ) error("The --mask-with option must follow --mask\n"); mask_t *mask = &args->mask[args->nmask-1]; if ( !strcasecmp(with,"uc") ) mask->with = MASK_UC; else if ( !strcasecmp(with,"lc") ) mask->with = MASK_LC; else if ( strlen(with)!=1 ) error("Expected \"lc\", \"uc\", or a single character with the --mask-with option\n"); else mask->with = *with; } static void destroy_data(args_t *args) { free(args->iupac_als); free(args->iupac_bitmask); if (args->filter) filter_destroy(args->filter); if ( args->smpl ) smpl_ilist_destroy(args->smpl); bcf_sr_destroy(args->files); int i; for (i=0; ivcf_rbuf.m; i++) if ( args->vcf_buf[i] ) bcf_destroy1(args->vcf_buf[i]); free(args->vcf_buf); free(args->fa_buf.s); free(args->chr); for (i=0; inmask; i++) { mask_t *mask = &args->mask[i]; regidx_destroy(mask->idx); regitr_destroy(mask->itr); } free(args->mask); if ( args->chain_fname ) if ( fclose(args->fp_chain) ) error("Close failed: %s\n", args->chain_fname); if ( fclose(args->fp_out) ) error("Close failed: %s\n", args->output_fname); destroy_chain(args->chain); } static void init_region(args_t *args, char *line) { char *ss, *se = line; while ( *se && !isspace(*se) && *se!=':' ) se++; hts_pos_t from = 0, to = 0; char tmp = 0, *tmp_ptr = NULL; if ( *se ) { tmp = *se; *se = 0; tmp_ptr = se; ss = ++se; from = strtol(ss,&se,10); if ( ss==se || !*se || *se!='-' ) from = 0; else { from--; ss = ++se; to = strtol(ss,&se,10); if ( ss==se || (*se && !isspace(*se)) ) { from = 0; to = 0; } else to--; } } free(args->chr); args->chr = strdup(line); args->rid = bcf_hdr_name2id(args->hdr,line); if ( args->rid<0 ) fprintf(stderr,"Warning: Sequence \"%s\" not in %s\n", line,args->fname); args->prev_base_pos = -1; args->fa_buf.l = 0; args->fa_length = 0; args->fa_end_pos = to; // 0-based args->fa_ori_pos = from; // 0-based args->fa_src_pos = from; // 0-based args->fa_mod_off = 0; args->fa_frz_pos = -1; args->fa_frz_mod = -1; args->fa_case = -1; args->vcf_rbuf.n = 0; // bcf_sr_set_regions accepts 1-based coordinates kstring_t str = {0,0,0}; if ( !from ) from = 1; else from++; #ifndef MAX_CSI_COOR #define MAX_CSI_COOR ((1LL << (14 + 30)) - 1) #endif if ( to==0 ) to = MAX_CSI_COOR - 1; else to++; ksprintf(&str,"%s:%"PRIhts_pos"-%"PRIhts_pos,line,from,to); bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap); bcf_sr_set_regions(args->files,str.s,0); free(str.s); if ( tmp_ptr ) *tmp_ptr = tmp; fprintf(args->fp_out,">%s%s\n",args->chr_prefix?args->chr_prefix:"",line); if ( args->chain_fname ) args->chain = init_chain(args->chain, args->fa_ori_pos); } static bcf1_t **next_vcf_line(args_t *args) { if ( args->vcf_rbuf.n ) { int i = rbuf_shift(&args->vcf_rbuf); return &args->vcf_buf[i]; } while ( bcf_sr_next_line(args->files) ) { if ( args->filter ) { int is_ok = filter_test(args->filter, bcf_sr_get_line(args->files,0), NULL); if ( args->filter_logic & FLT_EXCLUDE ) is_ok = is_ok ? 0 : 1; if ( !is_ok ) continue; } return &args->files->readers[0].buffer[0]; } return NULL; } static void unread_vcf_line(args_t *args, bcf1_t **rec_ptr) { bcf1_t *rec = *rec_ptr; if ( args->vcf_rbuf.n >= args->vcf_rbuf.m ) error("FIXME: too many overlapping records near %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); // Insert the new record in the buffer. The line would be overwritten in // the next bcf_sr_next_line call, therefore we need to swap it with an // unused one int i = rbuf_append(&args->vcf_rbuf); if ( !args->vcf_buf[i] ) args->vcf_buf[i] = bcf_init1(); bcf1_t *tmp = rec; *rec_ptr = args->vcf_buf[i]; args->vcf_buf[i] = tmp; } static void flush_fa_buffer(args_t *args, int len) { if ( !args->fa_buf.l ) return; int nwr = 0; while ( nwr + 60 <= args->fa_buf.l ) { if ( fwrite(args->fa_buf.s+nwr,1,60,args->fp_out) != 60 ) error("Could not write: %s\n", args->output_fname); if ( fwrite("\n",1,1,args->fp_out) != 1 ) error("Could not write: %s\n", args->output_fname); nwr += 60; } if ( nwr ) args->fa_ori_pos += nwr; args->fa_frz_mod -= nwr; if ( len ) { // not finished on this chr yet and the buffer cannot be emptied completely if ( nwr && nwr < args->fa_buf.l ) memmove(args->fa_buf.s,args->fa_buf.s+nwr,args->fa_buf.l-nwr); args->fa_buf.l -= nwr; return; } // empty the whole buffer if ( nwr == args->fa_buf.l ) { args->fa_buf.l = 0; return; } if ( fwrite(args->fa_buf.s+nwr,1,args->fa_buf.l - nwr,args->fp_out) != args->fa_buf.l - nwr ) error("Could not write: %s\n", args->output_fname); if ( fwrite("\n",1,1,args->fp_out) != 1 ) error("Could not write: %s\n", args->output_fname); args->fa_ori_pos += args->fa_buf.l - nwr - args->fa_mod_off; args->fa_mod_off = 0; args->fa_buf.l = 0; } static void apply_absent(args_t *args, hts_pos_t pos) { if ( !args->fa_buf.l || pos <= args->fa_frz_pos + 1 || pos <= args->fa_ori_pos ) return; int ie = pos && pos - args->fa_ori_pos + args->fa_mod_off < args->fa_buf.l ? pos - args->fa_ori_pos + args->fa_mod_off : args->fa_buf.l; int ib = args->fa_frz_mod < 0 ? 0 : args->fa_frz_mod; int i; for (i=ib; ifa_buf.s[i] = args->absent_allele; } static void freeze_ref(args_t *args, bcf1_t *rec) { if ( args->fa_frz_pos >= rec->pos + rec->rlen - 1 ) return; args->fa_frz_pos = rec->pos + rec->rlen - 1; args->fa_frz_mod = rec->pos - args->fa_ori_pos + args->fa_mod_off + rec->rlen; } static char *mark_del(char *ref, int rlen, char *alt, int mark) { char *out = malloc(rlen+1); int i; if ( alt ) { int nalt = strlen(alt); for (i=0; i { int nref = strlen(ref); for (i=0; in_allele, &args->miupac_als, &args->iupac_als, 0); for (i=0; imiupac_als; i++) args->iupac_als[i] = 0; } static int iupac_add_gt(args_t *args, bcf1_t *rec, uint8_t *gt, int ngt) { int i, is_set = 0; for (i=0; i= rec->n_allele ) error("Invalid VCF, too few ALT alleles at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); args->iupac_als[ial] = 1; is_set = 1; } return is_set; } static int iupac_set_allele(args_t *args, bcf1_t *rec) { int i,j, max_len = 0, alt_len = 0, ialt = -1, fallback_alt = -1; for (i=0; in_allele; i++) { if ( !args->iupac_als[i] ) continue; if ( fallback_alt <=0 ) fallback_alt = i; int l = strlen(rec->d.allele[i]); for (j=0; jd.allele[i][j]) < 0 ) break; if ( jmax_len ) { hts_resize(uint8_t, l, &args->miupac_bitmask, &args->iupac_bitmask, HTS_RESIZE_CLEAR); for (j=max_len; jiupac_bitmask[j] = 0; max_len = l; } if ( i>0 && l>alt_len ) { alt_len = l; ialt = i; } for (j=0; jiupac_bitmask[j] |= iupac2bitmask(rec->d.allele[i][j]); } if ( alt_len > 0 ) { for (j=0; jd.allele[ialt][j] = bitmask2iupac(args->iupac_bitmask[j]); return ialt; } if ( fallback_alt >= 0 ) return fallback_alt; return ialt; } static void apply_variant(args_t *args, bcf1_t *rec) { static int warned_haplotype = 0; if ( args->absent_allele ) apply_absent(args, rec->pos); if ( rec->n_allele==1 && !args->missing_allele && !args->absent_allele ) { return; } int i,j; if ( args->mask ) { char *chr = (char*)bcf_hdr_id2name(args->hdr,args->rid); int start = rec->pos; int end = rec->pos + rec->rlen - 1; for (i=0; inmask; i++) { mask_t *mask = &args->mask[i]; if ( MASK_SKIP(mask) && regidx_overlap(mask->idx, chr,start,end,NULL) ) return; } } int ialt = 1; // the alternate allele if ( args->iupac_GTs ) { bcf_unpack(rec, BCF_UN_FMT); bcf_fmt_t *fmt = bcf_get_fmt(args->hdr, rec, "GT"); if ( !fmt ) return; if ( fmt->type!=BCF_BT_INT8 ) error("Todo: GT field represented with BCF_BT_INT8, too many alleles at %s:%"PRId64"?\n",bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); ialt = -1; int is_set = 0; iupac_init(args,rec); for (i=0; ismpl->n; i++) { uint8_t *ptr = fmt->p + fmt->size*args->smpl->idx[i]; is_set += iupac_add_gt(args, rec, ptr, fmt->n); } if ( !is_set && !args->missing_allele ) return; if ( is_set ) ialt = iupac_set_allele(args, rec); } else if ( args->isample >= 0 ) { bcf_unpack(rec, BCF_UN_FMT); bcf_fmt_t *fmt = bcf_get_fmt(args->hdr, rec, "GT"); if ( !fmt ) return; if ( fmt->type!=BCF_BT_INT8 ) error("Todo: GT field represented with BCF_BT_INT8, too many alleles at %s:%"PRId64"?\n",bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); uint8_t *ptr = fmt->p + fmt->size*args->isample; enum { use_hap, use_iupac, pick_one } action = use_hap; if ( args->allele==PICK_IUPAC ) { if ( !args->haplotype ) action = use_iupac; if ( !bcf_gt_is_phased(ptr[0]) && !bcf_gt_is_phased(ptr[fmt->n-1]) ) action = use_iupac; } else if ( args->output_iupac ) action = use_iupac; else if ( !args->haplotype ) action = pick_one; if ( action==use_hap ) { if ( args->haplotype > fmt->n ) { if ( bcf_gt_is_missing(ptr[fmt->n-1]) || bcf_gt_is_missing(ptr[0]) ) { if ( !args->missing_allele ) return; ialt = -1; } else { if ( !warned_haplotype ) { fprintf(stderr, "Can't apply %d-th haplotype at %s:%"PRId64". (This warning is printed only once.)\n", args->haplotype,bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); warned_haplotype = 1; } return; } } else { ialt = (int8_t)ptr[args->haplotype-1]; if ( bcf_gt_is_missing(ialt) || ialt==bcf_int8_vector_end ) { if ( !args->missing_allele ) return; ialt = -1; } else ialt = bcf_gt_allele(ialt); } } else if ( action==use_iupac ) { ialt = -1; iupac_init(args,rec); int is_set = iupac_add_gt(args, rec, ptr, fmt->n); if ( !is_set && !args->missing_allele ) return; if ( is_set ) ialt = iupac_set_allele(args, rec); } else { int is_hom = 1; for (i=0; in; i++) { if ( bcf_gt_is_missing(ptr[i]) ) { if ( !args->missing_allele ) return; // ignore missing or half-missing genotypes ialt = -1; break; } if ( ptr[i]==(uint8_t)bcf_int8_vector_end ) break; ialt = bcf_gt_allele(ptr[i]); if ( i>0 && ialt!=bcf_gt_allele(ptr[i-1]) ) { is_hom = 0; break; } } if ( !is_hom ) { int prev_len = 0, jalt; for (i=0; in; i++) { if ( ptr[i]==(uint8_t)bcf_int8_vector_end ) break; jalt = bcf_gt_allele(ptr[i]); if ( rec->n_allele <= jalt ) error("Broken VCF, too few alts at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); if ( args->allele & (PICK_LONG|PICK_SHORT) ) { int len = jalt==0 ? rec->rlen : strlen(rec->d.allele[jalt]); if ( i==0 ) ialt = jalt, prev_len = len; else if ( len == prev_len ) { if ( args->allele & PICK_REF && jalt==0 ) ialt = jalt, prev_len = len; else if ( args->allele & PICK_ALT && ialt==0 ) ialt = jalt, prev_len = len; } else if ( args->allele & PICK_LONG && len > prev_len ) ialt = jalt, prev_len = len; else if ( args->allele & PICK_SHORT && len < prev_len ) ialt = jalt, prev_len = len; } else { if ( args->allele & PICK_REF && jalt==0 ) ialt = jalt; else if ( args->allele & PICK_ALT && ialt==0 ) ialt = jalt; } } } } if ( !ialt ) { // ref allele if ( args->absent_allele ) freeze_ref(args,rec); return; } if ( rec->n_allele <= ialt ) error("Broken VCF, too few alts at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); } else if ( args->output_iupac && rec->n_allele>1 ) { int ialt, alen = 0, mlen = 0; for (i=0; in_allele; i++) { int l = strlen(rec->d.allele[i]); for (j=0; jd.allele[i][j]) < 0 ) break; if ( j mlen ) { hts_expand(uint8_t,l,args->miupac_bitmask,args->iupac_bitmask); for (j=mlen; jiupac_bitmask[j] = 0; mlen = l; } if ( i>0 && l>alen ) { alen = l; ialt = i; } for (j=0; jiupac_bitmask[j] |= iupac2bitmask(rec->d.allele[i][j]); } if ( alen > 0 ) for (j=0; jd.allele[ialt][j] = bitmask2iupac(args->iupac_bitmask[j]); else ialt = 1; } if ( rec->n_allele==1 && ialt!=-1 ) { // non-missing reference if ( args->absent_allele ) freeze_ref(args,rec); return; } if ( ialt==-1 ) { char alleles[4]; alleles[0] = rec->d.allele[0][0]; alleles[1] = ','; alleles[2] = args->missing_allele; alleles[3] = 0; bcf_update_alleles_str(args->hdr, rec, alleles); ialt = 1; } // For some variant types POS+REF refer to the base *before* the event; in such case set trim_beg int trim_beg = 0; int var_type = bcf_get_variant_type(rec,ialt); int var_len = rec->d.var[ialt].n; if ( var_type & VCF_INDEL ) { // normally indel starts one base after, but not if the first base of the fa reference is deleted if ( rec->d.allele[0][0] == rec->d.allele[ialt][0] ) trim_beg = 1; else trim_beg = 0; } else if ( (var_type & VCF_OTHER) && !strcasecmp(rec->d.allele[ialt],"") ) { trim_beg = 1; var_len = 1 - rec->rlen; } else if ( (var_type & VCF_OTHER) && !strncasecmp(rec->d.allele[ialt],"pos <= args->fa_frz_pos && rec->pos + rec->rlen - 1 > args->fa_frz_pos ) { // Applying the reference allele which overlaps a previous deletion. If we are here, it // means it goes beyond the freezed position, hence the record can be trimmed and moved // forward int ntrim = args->fa_frz_pos - rec->pos + 1; int nref = strlen(rec->d.allele[0]); assert( ntrim < nref ); rec->pos += ntrim; rec->rlen -= ntrim; memmove(rec->d.allele[0],rec->d.allele[0]+ntrim,nref-ntrim); rec->d.allele[0][nref-ntrim] = 0; } if ( rec->pos <= args->fa_frz_pos ) { // Can be still OK iff this is an insertion (and which does not follow another insertion, see #888). // This still may not be enough for more complicated cases with multiple duplicate positions // and other types in between. In such case let the user normalize the VCF and remove duplicates. int overlap = 0; if ( rec->pos < args->fa_frz_pos || !trim_beg || var_len==0 || args->prev_is_insert ) overlap = 1; if ( overlap ) { fprintf(stderr,"The site %s:%"PRId64" overlaps with another variant, skipping...\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); return; } } char *ref_allele = rec->d.allele[0]; char *alt_allele = rec->d.allele[ialt]; int rmme_alt = 0; int len_diff = 0, alen = 0; int idx = rec->pos - args->fa_ori_pos + args->fa_mod_off; // position of the variant within the modified fasta sequence if ( idx<0 ) { if ( alt_allele[0]=='<' ) // symbolic allele { rec->pos -= idx + 1; rec->rlen += idx + 1; idx = -1; } else if ( strlen(ref_allele) < -idx ) // the ref allele is shorter but overlaps the fa sequence? This should never happen { assert(0); fprintf(stderr,"Warning: ignoring overlapping variant starting at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); return; } else if ( strlen(alt_allele) > -idx ) // the ref allele overlaps the fa and so does the alt allele { rec->pos -= idx; rec->rlen += idx; ref_allele -= idx; alt_allele -= idx; idx = 0; } else // the ref allele overlaps the fa but alt allele does not: trim to leave one base before { rec->pos -= idx + 1; rec->rlen += idx + 1; ref_allele -= idx + 1; alt_allele += strlen(alt_allele) - 1; idx = -1; } } if ( rec->rlen > args->fa_buf.l - idx ) { rec->rlen = args->fa_buf.l - idx; if ( alt_allele[0]!='<' ) { alen = strlen(alt_allele); if ( alen > rec->rlen ) { fprintf(stderr,"Warning: trimming variant \"%s\" starting at %s:%"PRId64"\n", alt_allele,bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); alt_allele[rec->rlen] = 0; } } } // the variant is beyond the available fasta sequence if ( idx>0 && idx>=args->fa_buf.l ) return; // sanity check the reference base if ( alt_allele[0]=='<' ) { // TODO: symbolic deletions probably need more work above with PICK_SHORT|PICK_LONG if ( strcasecmp(alt_allele,"") && strcasecmp(alt_allele,"<*>") && strcasecmp(alt_allele,"") ) error("Symbolic alleles other than , <*> or are currently not supported, e.g. \"%s\" at %s:%"PRId64".\n" "Please use filtering expressions to exclude such sites, for example by running with: -e 'ALT~\"<.*>\"'\n", alt_allele,bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); if ( !strcasecmp(alt_allele,"") ) { static int multibase_ref_del_warned = 0; if ( ref_allele[1]!=0 && !multibase_ref_del_warned ) { fprintf(stderr, "Warning: one REF base is expected with , assuming the actual deletion starts at POS+1 at %s:%"PRId64".\n" " (This warning is printed only once.)\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); multibase_ref_del_warned = 1; } if ( args->mark_del ) // insert dashes instead of delete sequence { alt_allele = mark_del(ref_allele, rec->rlen, NULL, args->mark_del); alen = rec->rlen; len_diff = 0; rmme_alt = 1; } else { len_diff = 1-rec->rlen; alt_allele = ref_allele; // according to VCF spec, the first REF base must precede the event alen = 1; } } else { // <*> or .. gVCF, evidence for the reference allele throughout the whole block freeze_ref(args,rec); return; } } else if ( idx>=0 && strncasecmp(ref_allele,args->fa_buf.s+idx,rec->rlen) ) { // This is hacky, handle a special case: if SNP or an insert follows a deletion (AAC>A, C>CAA), // the reference base in fa_buf is lost and the check fails. We do not keep a buffer // with the original sequence as it should not be necessary, we should encounter max // one base overlap int fail = 1; if ( args->prev_base_pos==rec->pos && toupper(ref_allele[0])==toupper(args->prev_base) ) { if ( rec->rlen==1 ) fail = 0; else if ( !strncasecmp(ref_allele+1,args->fa_buf.s+idx+1,rec->rlen-1) ) fail = 0; } if ( fail ) { char tmp = 0; if ( args->fa_buf.l - idx > rec->rlen ) { tmp = args->fa_buf.s[idx+rec->rlen]; args->fa_buf.s[idx+rec->rlen] = 0; } error( "The fasta sequence does not match the REF allele at %s:%"PRId64":\n" " REF .vcf: [%s]\n" " ALT .vcf: [%s]\n" " REF .fa : [%s]%c%s\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1, ref_allele, alt_allele, args->fa_buf.s+idx, tmp?tmp:' ',tmp?args->fa_buf.s+idx+rec->rlen+1:"" ); } alen = strlen(alt_allele); len_diff = alen - rec->rlen; if ( args->mark_del && len_diff<0 ) { alt_allele = mark_del(ref_allele, rec->rlen, alt_allele, args->mark_del); alen = rec->rlen; len_diff = 0; rmme_alt = 1; } } else { alen = strlen(alt_allele); len_diff = alen - rec->rlen; if ( args->mark_del && len_diff<0 ) { alt_allele = mark_del(ref_allele, rec->rlen, alt_allele, args->mark_del); alen = rec->rlen; len_diff = 0; rmme_alt = 1; } } int safe_idx = idx<0 ? 0 : idx; // idx can be negative in case of overlapping deletion args->fa_case = toupper(args->fa_buf.s[safe_idx])==args->fa_buf.s[safe_idx] ? TO_UPPER : TO_LOWER; if ( args->fa_case==TO_UPPER ) for (i=0; imark_ins && len_diff>0 ) mark_ins(ref_allele, alt_allele, args->mark_ins); if ( args->mark_snv ) mark_snv(ref_allele, alt_allele, args->mark_snv); if ( len_diff <= 0 ) { // deletion or same size event assert( args->fa_buf.l >= idx+rec->rlen ); args->prev_base = args->fa_buf.s[idx+rec->rlen-1]; args->prev_base_pos = rec->pos + rec->rlen - 1; args->prev_is_insert = 0; args->fa_frz_mod = idx + alen; for (i=trim_beg; ifa_buf.s[idx+i] = alt_allele[i]; if ( len_diff ) memmove(args->fa_buf.s+idx+alen,args->fa_buf.s+idx+rec->rlen,args->fa_buf.l-idx-rec->rlen); } else { args->prev_is_insert = 1; args->prev_base_pos = rec->pos; // insertion ks_resize(&args->fa_buf, args->fa_buf.l + len_diff); memmove(args->fa_buf.s + idx + rec->rlen + len_diff, args->fa_buf.s + idx + rec->rlen, args->fa_buf.l - idx - rec->rlen); // This can get tricky, make sure the bases unchanged by the insertion do not overwrite preceding variants. // For example, here we want to get TAA: // POS REF ALT // 1 C T // 1 C CAA int ibeg = 0; while ( ibegpos + ibeg <= args->prev_base_pos ) ibeg++; for (i=ibeg; ifa_buf.s[idx+i] = alt_allele[i]; args->fa_frz_mod = idx + alen - ibeg + 1; } if (args->chain && len_diff != 0) { // If first nucleotide of both REF and ALT are the same... (indels typically include the nucleotide before the variant) if ( strncasecmp(ref_allele,alt_allele,1) == 0) { // ...extend the block by 1 bp: start is 1 bp further and alleles are 1 bp shorter push_chain_gap(args->chain, rec->pos + 1, rec->rlen - 1, rec->pos + 1 + args->fa_mod_off, alen - 1); } else { // otherwise, just the coordinates of the variant as given push_chain_gap(args->chain, rec->pos, rec->rlen, rec->pos + args->fa_mod_off, alen); } } args->fa_buf.l += len_diff; args->fa_mod_off += len_diff; args->fa_frz_pos = rec->pos + rec->rlen - 1; args->napplied++; if ( rmme_alt ) free(alt_allele); } static void mask_region(args_t *args, char *seq, int len) { int start = args->fa_src_pos - len; int end = args->fa_src_pos; int i; for (i=0; inmask; i++) { mask_t *mask = &args->mask[i]; if ( !regidx_overlap(mask->idx, args->chr,start,end, mask->itr) ) continue; int idx_start, idx_end, j; while ( regitr_overlap(mask->itr) ) { idx_start = mask->itr->beg - start; idx_end = mask->itr->end - start; if ( idx_start < 0 ) idx_start = 0; if ( idx_end >= len ) idx_end = len - 1; if ( mask->with==MASK_UC ) for (j=idx_start; j<=idx_end; j++) seq[j] = toupper(seq[j]); else if ( mask->with==MASK_LC ) for (j=idx_start; j<=idx_end; j++) seq[j] = tolower(seq[j]); else for (j=idx_start; j<=idx_end; j++) seq[j] = mask->with; } } } static void consensus(args_t *args) { BGZF *fasta = bgzf_open(args->ref_fname, "r"); if ( !fasta ) error("Error reading %s\n", args->ref_fname); kstring_t str = {0,0,0}; while ( bgzf_getline(fasta, '\n', &str) > 0 ) { if ( str.s[0]=='>' ) { // new sequence encountered if ( args->chain ) print_chain(args); // apply all cached variants and variants that might have been missed because of short fasta (see test/consensus.9.*) bcf1_t **rec_ptr = NULL; while ( args->rid>=0 && (rec_ptr = next_vcf_line(args)) ) { bcf1_t *rec = *rec_ptr; if ( rec->rid!=args->rid || ( args->fa_end_pos && rec->pos > args->fa_end_pos ) ) break; apply_variant(args, rec); } if ( args->absent_allele ) { int pos = 0; if ( args->vcf_rbuf.n && args->vcf_buf[args->vcf_rbuf.f]->rid==args->rid ) pos = args->vcf_buf[args->vcf_rbuf.f]->pos; apply_absent(args, pos); } flush_fa_buffer(args, 0); init_region(args, str.s+1); continue; } args->fa_length += str.l; args->fa_src_pos += str.l; // determine if uppercase or lowercase is used in this fasta file if ( args->fa_case==-1 ) args->fa_case = toupper(str.s[0])==str.s[0] ? 1 : 0; if ( args->mask ) mask_region(args, str.s, str.l); kputs(str.s, &args->fa_buf); bcf1_t **rec_ptr = NULL; while ( args->rid>=0 && (rec_ptr = next_vcf_line(args)) ) { bcf1_t *rec = *rec_ptr; // still the same chr and the same region? if not, fasta buf can be flushed if ( rec->rid!=args->rid || ( args->fa_end_pos && rec->pos > args->fa_end_pos ) ) { // save the vcf record until next time and flush unread_vcf_line(args, rec_ptr); rec_ptr = NULL; break; } // is the vcf record well beyond cached fasta buffer? if yes, the buf can be flushed if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off <= rec->pos ) { unread_vcf_line(args, rec_ptr); rec_ptr = NULL; break; } // is the cached fasta buffer full enough? if not, read more fasta, no flushing if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off < rec->pos + rec->rlen ) { unread_vcf_line(args, rec_ptr); break; } apply_variant(args, rec); } if ( !rec_ptr ) { if ( args->absent_allele ) apply_absent(args, args->fa_ori_pos - args->fa_mod_off + args->fa_buf.l); flush_fa_buffer(args, 60); } } bcf1_t **rec_ptr = NULL; while ( args->rid>=0 && (rec_ptr = next_vcf_line(args)) ) { bcf1_t *rec = *rec_ptr; if ( rec->rid!=args->rid ) break; if ( args->fa_end_pos && rec->pos > args->fa_end_pos ) break; if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off <= rec->pos ) break; apply_variant(args, rec); } if (args->chain) print_chain(args); if ( args->absent_allele ) apply_absent(args, HTS_POS_MAX); flush_fa_buffer(args, 0); bgzf_close(fasta); free(str.s); fprintf(stderr,"Applied %d variants\n", args->napplied); } static void usage(args_t *args) { fprintf(stderr, "\n"); fprintf(stderr, "About: Create consensus sequence by applying VCF variants to a reference fasta\n"); fprintf(stderr, " file. By default, the program will apply all ALT variants. Using the\n"); fprintf(stderr, " --samples (and, optionally, --haplotype) option will apply genotype\n"); fprintf(stderr, " (or haplotype) calls from FORMAT/GT. The program ignores allelic depth\n"); fprintf(stderr, " information, such as INFO/AD or FORMAT/AD.\n"); fprintf(stderr, "Usage: bcftools consensus [OPTIONS] \n"); fprintf(stderr, "Options:\n"); fprintf(stderr, " -c, --chain FILE Write a chain file for liftover\n"); fprintf(stderr, " -a, --absent CHAR Replace positions absent from VCF with CHAR\n"); fprintf(stderr, " -e, --exclude EXPR Exclude sites for which the expression is true (see man page for details)\n"); fprintf(stderr, " -f, --fasta-ref FILE Reference sequence in fasta format\n"); fprintf(stderr, " -H, --haplotype WHICH Choose which allele to use from the FORMAT/GT field, note\n"); fprintf(stderr, " the codes are case-insensitive:\n"); fprintf(stderr, " N: N={1,2,3,..} is the index of the allele from GT, regardless of phasing (e.g. \"2\")\n"); fprintf(stderr, " R: REF allele in het genotypes\n"); fprintf(stderr, " A: ALT allele\n"); fprintf(stderr, " I: IUPAC code for all genotypes\n"); fprintf(stderr, " LR,LA: longer allele and REF/ALT if equal length\n"); fprintf(stderr, " SR,SA: shorter allele and REF/ALT if equal length\n"); fprintf(stderr, " NpIu: index of the allele for phased and IUPAC code for unphased GTs (e.g. \"2pIu\")\n"); fprintf(stderr, " -i, --include EXPR Select sites for which the expression is true (see man page for details)\n"); fprintf(stderr, " -I, --iupac-codes Output IUPAC codes based on FORMAT/GT, use -s/-S to subset samples\n"); fprintf(stderr, " --mark-del CHAR Instead of removing sequence, insert character CHAR for deletions\n"); fprintf(stderr, " --mark-ins uc|lc|CHAR Highlight insertions in uppercase (uc), lowercase (lc), or use CHAR, leaving the rest as is\n"); fprintf(stderr, " --mark-snv uc|lc|CHAR Highlight substitutions in uppercase (uc), lowercase (lc), or use CHAR, leaving the rest as is\n"); fprintf(stderr, " -m, --mask FILE Replace regions according to the next --mask-with option. The default is --mask-with N\n"); fprintf(stderr, " --mask-with CHAR|uc|lc Replace with CHAR (skips overlapping variants); change to uppercase (uc) or lowercase (lc)\n"); fprintf(stderr, " -M, --missing CHAR Output CHAR instead of skipping a missing genotype \"./.\"\n"); fprintf(stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(stderr, " -p, --prefix STRING Prefix to add to output sequence names\n"); fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " -s, --samples LIST Comma-separated list of samples to include, \"-\" to ignore samples and use REF,ALT\n"); fprintf(stderr, " -S, --samples-file FILE File of samples to include\n"); fprintf(stderr, "Examples:\n"); fprintf(stderr, " # Get the consensus for one region. The fasta header lines are then expected\n"); fprintf(stderr, " # in the form \">chr:from-to\".\n"); fprintf(stderr, " samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz > out.fa\n"); fprintf(stderr, "\n"); fprintf(stderr, " # See also http://samtools.github.io/bcftools/howtos/consensus-sequence.html\n"); fprintf(stderr, "\n"); exit(1); } int main_consensus(int argc, char *argv[]) { args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->regions_overlap = 1; static struct option loptions[] = { {"mark-del",required_argument,NULL,1}, {"mark-ins",required_argument,NULL,2}, {"mark-snv",required_argument,NULL,3}, {"mask-with",1,0,4}, {"exclude",required_argument,NULL,'e'}, {"include",required_argument,NULL,'i'}, {"sample",1,0,'s'}, {"samples",1,0,'s'}, {"samples-file",1,0,'S'}, {"iupac-codes",0,0,'I'}, {"haplotype",1,0,'H'}, {"output",1,0,'o'}, {"fasta-ref",1,0,'f'}, {"mask",1,0,'m'}, {"missing",1,0,'M'}, {"absent",1,0,'a'}, {"chain",1,0,'c'}, {"prefix",required_argument,0,'p'}, {"regions-overlap",required_argument,0,5}, {0,0,0,0} }; int c; while ((c = getopt_long(argc, argv, "h?s:S:1Ii:e:H:f:o:m:c:M:p:a:",loptions,NULL)) >= 0) { switch (c) { case 1 : args->mark_del = optarg[0]; break; case 2 : if ( !strcasecmp(optarg,"uc") ) args->mark_ins = TO_UPPER; else if ( !strcasecmp(optarg,"lc") ) args->mark_ins = TO_LOWER; else if ( !optarg[1] && optarg[0]>32 && optarg[0]<127 ) args->mark_ins = optarg[0]; else error("The argument is not recognised: --mark-ins %s\n",optarg); break; case 3 : if ( !strcasecmp(optarg,"uc") ) args->mark_snv = TO_UPPER; else if ( !strcasecmp(optarg,"lc") ) args->mark_snv = TO_LOWER; else if ( !optarg[1] && optarg[0]>32 && optarg[0]<127 ) args->mark_snv = optarg[0]; else error("The argument is not recognised: --mark-snv %s\n",optarg); break; case 5 : args->regions_overlap = parse_overlap_option(optarg); if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 'p': args->chr_prefix = optarg; break; case 's': args->sample = optarg; break; case 'S': args->sample_fname = optarg; break; case 'o': args->output_fname = optarg; break; case 'I': args->output_iupac = 1; break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'f': args->ref_fname = optarg; break; case 'm': add_mask(args,optarg); break; case 4 : add_mask_with(args,optarg); break; case 'a': args->absent_allele = optarg[0]; if ( optarg[1]!=0 ) error("Expected single character with -a, got \"%s\"\n", optarg); break; case 'M': args->missing_allele = optarg[0]; if ( optarg[1]!=0 ) error("Expected single character with -M, got \"%s\"\n", optarg); break; case 'c': args->chain_fname = optarg; break; case 'H': if ( !strcasecmp(optarg,"R") ) args->allele |= PICK_REF; else if ( !strcasecmp(optarg,"A") ) args->allele |= PICK_ALT; else if ( !strcasecmp(optarg,"L") ) args->allele |= PICK_LONG|PICK_REF; else if ( !strcasecmp(optarg,"S") ) args->allele |= PICK_SHORT|PICK_REF; else if ( !strcasecmp(optarg,"LR") ) args->allele |= PICK_LONG|PICK_REF; else if ( !strcasecmp(optarg,"LA") ) args->allele |= PICK_LONG|PICK_ALT; else if ( !strcasecmp(optarg,"SR") ) args->allele |= PICK_SHORT|PICK_REF; else if ( !strcasecmp(optarg,"SA") ) args->allele |= PICK_SHORT|PICK_ALT; else if ( !strcasecmp(optarg,"I") ) args->allele |= PICK_IUPAC; else if ( !strcasecmp(optarg,"1pIu") ) args->allele |= PICK_IUPAC, args->haplotype = 1; else if ( !strcasecmp(optarg,"2pIu") ) args->allele |= PICK_IUPAC, args->haplotype = 2; else { char *tmp; args->haplotype = strtol(optarg, &tmp, 10); if ( tmp==optarg || (*tmp && strcasecmp(tmp,"pIu")) ) error("Error: Could not parse \"--haplotype %s\", expected number of number followed with \"pIu\"\n", optarg); if ( *tmp ) args->allele |= PICK_IUPAC; if ( args->haplotype <=0 ) error("Error: Expected positive integer with --haplotype\n"); } break; default: usage(args); break; } } if ( optind>=argc ) usage(args); args->fname = argv[optind]; if ( !args->ref_fname && !isatty(fileno((FILE *)stdin)) ) args->ref_fname = "-"; if ( !args->ref_fname ) usage(args); init_data(args); consensus(args); destroy_data(args); free(args); return 0; } pysam-0.23.0/bcftools/consensus.c.pysam.c000066400000000000000000001520761475062545500203250ustar00rootroot00000000000000#include "bcftools.pysam.h" /* The MIT License Copyright (c) 2014-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "regidx.h" #include "bcftools.h" #include "rbuf.h" #include "filter.h" #include "smpl_ilist.h" // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 #define PICK_REF 1 #define PICK_ALT 2 #define PICK_LONG 4 #define PICK_SHORT 8 #define PICK_IUPAC 16 #define TO_UPPER 1 #define TO_LOWER 2 typedef struct { int num; // number of ungapped blocks in this chain int *block_lengths; // length of the ungapped blocks in this chain int *ref_gaps; // length of the gaps on the reference sequence between blocks int *alt_gaps; // length of the gaps on the alternative sequence between blocks int ori_pos; int ref_last_block_ori; // start position on the reference sequence of the following ungapped block (0-based) int alt_last_block_ori; // start position on the alternative sequence of the following ungapped block (0-based) } chain_t; #define MASK_LC 1 #define MASK_UC 2 #define MASK_SKIP(x) (((x)->with!=MASK_LC && (x)->with!=MASK_UC) ? 1 : 0) typedef struct { char *fname, with; regidx_t *idx; regitr_t *itr; } mask_t; typedef struct { kstring_t fa_buf; // buffered reference sequence int fa_ori_pos; // start position of the fa_buffer (wrt original sequence) int fa_frz_pos; // protected position to avoid conflicting variants (last pos for SNPs/ins) int fa_mod_off; // position difference of fa_frz_pos in the ori and modified sequence (ins positive) int fa_frz_mod; // the fa_buf offset of the protected fa_frz_pos position, includes the modified sequence int fa_end_pos; // region's end position in the original sequence int fa_length; // region's length in the original sequence (in case end_pos not provided in the FASTA header) int fa_case; // output upper case or lower case: TO_UPPER|TO_LOWER int fa_src_pos; // last genomic coordinate read from the input fasta (0-based) char prev_base; // this is only to validate the REF allele in the VCF - the modified fa_buf cannot be used for inserts following deletions, see 600#issuecomment-383186778 int prev_base_pos; // the position of prev_base int prev_is_insert; rbuf_t vcf_rbuf; bcf1_t **vcf_buf; int nvcf_buf, rid; char *chr, *chr_prefix; mask_t *mask; int nmask; int chain_id; // chain_id, to provide a unique ID to each chain in the chain output chain_t *chain; // chain structure to store the sequence of ungapped blocks between the ref and alt sequences // Note that the chain is re-initialised for each chromosome/seq_region filter_t *filter; char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE bcf_srs_t *files; bcf_hdr_t *hdr; FILE *fp_out; FILE *fp_chain; char **argv; int argc, output_iupac, iupac_GTs, haplotype, allele, isample, napplied; uint8_t *iupac_bitmask, *iupac_als; int miupac_bitmask, miupac_als, regions_overlap; char *fname, *ref_fname, *sample, *sample_fname, *output_fname, *mask_fname, *chain_fname, missing_allele, absent_allele; char mark_del, mark_ins, mark_snv; smpl_ilist_t *smpl; } args_t; static void destroy_chain(chain_t *chain) { if ( !chain ) return; free(chain->ref_gaps); free(chain->alt_gaps); free(chain->block_lengths); free(chain); } static chain_t* init_chain(chain_t *chain, int ref_ori_pos) { if ( chain ) destroy_chain(chain); chain = (chain_t*) calloc(1,sizeof(chain_t)); chain->num = 0; chain->block_lengths = NULL; chain->ref_gaps = NULL; chain->alt_gaps = NULL; chain->ori_pos = ref_ori_pos; chain->ref_last_block_ori = ref_ori_pos; chain->alt_last_block_ori = ref_ori_pos; return chain; } static void print_chain(args_t *args) { /* Example chain format (see: https://genome.ucsc.edu/goldenPath/help/chain.html): chain 1 500 + 480 500 1 501 + 480 501 1 12 3 1 1 0 3 484 chain line is: - chain - score (sum of the length of ungapped block in this case) - ref_seqname (from the fasta header, parsed by htslib) - ref_seqlength (from the fasta header) - ref_strand (+ or -; always + for bcf-consensus) - ref_start (as defined in the fasta header) - ref_end (as defined in the fasta header) - alt_seqname (same as ref_seqname as bcf-consensus only considers SNPs and indels) - alt_seqlength (adjusted to match the length of the alt sequence) - alt_strand (+ or -; always + for bcf-consensus) - alt_start (same as ref_start, as no edits are recorded/applied before that position) - alt_end (adjusted to match the length of the alt sequence) - chain_num (just an auto-increment id) the other (sorted) lines are: - length of the ungapped alignment block - gap on the ref sequence between this and the next block (all but the last line) - gap on the alt sequence between this and the next block (all but the last line) */ chain_t *chain = args->chain; int n = chain->num; int ref_end_pos = args->fa_length + chain->ori_pos; int last_block_size = ref_end_pos - chain->ref_last_block_ori; int alt_end_pos = chain->alt_last_block_ori + last_block_size; int score = 0; for (n=0; nnum; n++) { score += chain->block_lengths[n]; } score += last_block_size; fprintf(args->fp_chain, "chain %d %s %d + %d %d %s %d + %d %d %d\n", score, args->chr, ref_end_pos, chain->ori_pos, ref_end_pos, args->chr, alt_end_pos, chain->ori_pos, alt_end_pos, ++args->chain_id); for (n=0; nnum; n++) { fprintf(args->fp_chain, "%d %d %d\n", chain->block_lengths[n], chain->ref_gaps[n], chain->alt_gaps[n]); } fprintf(args->fp_chain, "%d\n\n", last_block_size); } static void push_chain_gap(chain_t *chain, int ref_start, int ref_len, int alt_start, int alt_len) { // fprintf(bcftools_stderr, "push_chain_gap(chain=%p, ref_start=%d, ref_len=%d, alt_start=%d, alt_len=%d)\n", chain, ref_start, ref_len, alt_start, alt_len); int num = chain->num; if (num && ref_start <= chain->ref_last_block_ori) { // In case this variant is back-to-back with the previous one chain->ref_last_block_ori = ref_start + ref_len; chain->alt_last_block_ori = alt_start + alt_len; chain->ref_gaps[num-1] += ref_len; chain->alt_gaps[num-1] += alt_len; } else { // Extend the ungapped blocks, store the gap length chain->block_lengths = (int*) realloc(chain->block_lengths, (num + 1) * sizeof(int)); chain->ref_gaps = (int*) realloc(chain->ref_gaps, (num + 1) * sizeof(int)); chain->alt_gaps = (int*) realloc(chain->alt_gaps, (num + 1) * sizeof(int)); chain->block_lengths[num] = ref_start - chain->ref_last_block_ori; chain->ref_gaps[num] = ref_len; chain->alt_gaps[num] = alt_len; // Update the start positions of the next block chain->ref_last_block_ori = ref_start + ref_len; chain->alt_last_block_ori = alt_start + alt_len; // Increment the number of ungapped blocks chain->num++; } } static void init_data(args_t *args) { args->files = bcf_sr_init(); args->files->require_index = 1; if ( !bcf_sr_add_reader(args->files,args->fname) ) error("Failed to read from %s: %s\n", !strcmp("-",args->fname)?"standard input":args->fname, bcf_sr_strerror(args->files->errnum)); args->hdr = args->files->readers[0].header; args->isample = -1; if ( !args->sample ) { args->smpl = smpl_ilist_init(args->hdr,NULL,0,SMPL_NONE|SMPL_VERBOSE); if ( !args->smpl->n ) { smpl_ilist_destroy(args->smpl); args->smpl = NULL; } } else if ( args->sample && strcmp("-",args->sample) ) { args->smpl = smpl_ilist_init(args->hdr,args->sample,0,SMPL_NONE|SMPL_VERBOSE); if ( args->smpl && !args->smpl->n ) error("No matching sample found\n"); } else if ( args->sample_fname ) { args->smpl = smpl_ilist_init(args->hdr,args->sample_fname,1,SMPL_NONE|SMPL_VERBOSE); if ( args->smpl && !args->smpl->n ) error("No matching sample found\n"); } if ( args->smpl ) { if ( args->haplotype || args->allele ) { if ( args->smpl->n > 1 ) error("Too many samples, only one can be used with -H; check the -s,-S options\n"); args->isample = args->smpl->idx[0]; } else { args->iupac_GTs = 1; if ( args->smpl->n==1 ) fprintf(bcftools_stderr,"Note: applying IUPAC codes based on FORMAT/GT in sample %s\n",bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->smpl->idx[0])); else fprintf(bcftools_stderr,"Note: applying IUPAC codes based on FORMAT/GT in %d samples\n",args->smpl->n); } } else if ( args->output_iupac ) fprintf(bcftools_stderr,"Note: applying IUPAC codes based on REF,ALT%s\n",bcf_hdr_nsamples(args->hdr)?", ignoring samples":""); else fprintf(bcftools_stderr,"Note: applying REF,ALT variants%s\n",bcf_hdr_nsamples(args->hdr)?", ignoring samples":""); int i; for (i=0; inmask; i++) { mask_t *mask = &args->mask[i]; mask->idx = regidx_init(mask->fname,NULL,NULL,0,NULL); if ( !mask->idx ) error("Failed to initialize mask regions\n"); mask->itr = regitr_init(mask->idx); } // In case we want to store the chains if ( args->chain_fname ) { args->fp_chain = fopen(args->chain_fname,"w"); if ( ! args->fp_chain ) error("Failed to create %s: %s\n", args->chain_fname, strerror(errno)); args->chain_id = 0; } rbuf_init(&args->vcf_rbuf, 100); args->vcf_buf = (bcf1_t**) calloc(args->vcf_rbuf.m, sizeof(bcf1_t*)); if ( args->output_fname ) { args->fp_out = fopen(args->output_fname,"w"); if ( ! args->fp_out ) error("Failed to create %s: %s\n", args->output_fname, strerror(errno)); } else args->fp_out = bcftools_stdout; if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); args->rid = -1; } static void add_mask(args_t *args, char *fname) { args->nmask++; args->mask = (mask_t*)realloc(args->mask,args->nmask*sizeof(*args->mask)); mask_t *mask = &args->mask[args->nmask-1]; mask->fname = fname; mask->with = 'N'; } static void add_mask_with(args_t *args, char *with) { if ( !args->nmask ) error("The --mask-with option must follow --mask\n"); mask_t *mask = &args->mask[args->nmask-1]; if ( !strcasecmp(with,"uc") ) mask->with = MASK_UC; else if ( !strcasecmp(with,"lc") ) mask->with = MASK_LC; else if ( strlen(with)!=1 ) error("Expected \"lc\", \"uc\", or a single character with the --mask-with option\n"); else mask->with = *with; } static void destroy_data(args_t *args) { free(args->iupac_als); free(args->iupac_bitmask); if (args->filter) filter_destroy(args->filter); if ( args->smpl ) smpl_ilist_destroy(args->smpl); bcf_sr_destroy(args->files); int i; for (i=0; ivcf_rbuf.m; i++) if ( args->vcf_buf[i] ) bcf_destroy1(args->vcf_buf[i]); free(args->vcf_buf); free(args->fa_buf.s); free(args->chr); for (i=0; inmask; i++) { mask_t *mask = &args->mask[i]; regidx_destroy(mask->idx); regitr_destroy(mask->itr); } free(args->mask); if ( args->chain_fname ) if ( fclose(args->fp_chain) ) error("Close failed: %s\n", args->chain_fname); if ( fclose(args->fp_out) ) error("Close failed: %s\n", args->output_fname); destroy_chain(args->chain); } static void init_region(args_t *args, char *line) { char *ss, *se = line; while ( *se && !isspace(*se) && *se!=':' ) se++; hts_pos_t from = 0, to = 0; char tmp = 0, *tmp_ptr = NULL; if ( *se ) { tmp = *se; *se = 0; tmp_ptr = se; ss = ++se; from = strtol(ss,&se,10); if ( ss==se || !*se || *se!='-' ) from = 0; else { from--; ss = ++se; to = strtol(ss,&se,10); if ( ss==se || (*se && !isspace(*se)) ) { from = 0; to = 0; } else to--; } } free(args->chr); args->chr = strdup(line); args->rid = bcf_hdr_name2id(args->hdr,line); if ( args->rid<0 ) fprintf(bcftools_stderr,"Warning: Sequence \"%s\" not in %s\n", line,args->fname); args->prev_base_pos = -1; args->fa_buf.l = 0; args->fa_length = 0; args->fa_end_pos = to; // 0-based args->fa_ori_pos = from; // 0-based args->fa_src_pos = from; // 0-based args->fa_mod_off = 0; args->fa_frz_pos = -1; args->fa_frz_mod = -1; args->fa_case = -1; args->vcf_rbuf.n = 0; // bcf_sr_set_regions accepts 1-based coordinates kstring_t str = {0,0,0}; if ( !from ) from = 1; else from++; #ifndef MAX_CSI_COOR #define MAX_CSI_COOR ((1LL << (14 + 30)) - 1) #endif if ( to==0 ) to = MAX_CSI_COOR - 1; else to++; ksprintf(&str,"%s:%"PRIhts_pos"-%"PRIhts_pos,line,from,to); bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap); bcf_sr_set_regions(args->files,str.s,0); free(str.s); if ( tmp_ptr ) *tmp_ptr = tmp; fprintf(args->fp_out,">%s%s\n",args->chr_prefix?args->chr_prefix:"",line); if ( args->chain_fname ) args->chain = init_chain(args->chain, args->fa_ori_pos); } static bcf1_t **next_vcf_line(args_t *args) { if ( args->vcf_rbuf.n ) { int i = rbuf_shift(&args->vcf_rbuf); return &args->vcf_buf[i]; } while ( bcf_sr_next_line(args->files) ) { if ( args->filter ) { int is_ok = filter_test(args->filter, bcf_sr_get_line(args->files,0), NULL); if ( args->filter_logic & FLT_EXCLUDE ) is_ok = is_ok ? 0 : 1; if ( !is_ok ) continue; } return &args->files->readers[0].buffer[0]; } return NULL; } static void unread_vcf_line(args_t *args, bcf1_t **rec_ptr) { bcf1_t *rec = *rec_ptr; if ( args->vcf_rbuf.n >= args->vcf_rbuf.m ) error("FIXME: too many overlapping records near %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); // Insert the new record in the buffer. The line would be overwritten in // the next bcf_sr_next_line call, therefore we need to swap it with an // unused one int i = rbuf_append(&args->vcf_rbuf); if ( !args->vcf_buf[i] ) args->vcf_buf[i] = bcf_init1(); bcf1_t *tmp = rec; *rec_ptr = args->vcf_buf[i]; args->vcf_buf[i] = tmp; } static void flush_fa_buffer(args_t *args, int len) { if ( !args->fa_buf.l ) return; int nwr = 0; while ( nwr + 60 <= args->fa_buf.l ) { if ( fwrite(args->fa_buf.s+nwr,1,60,args->fp_out) != 60 ) error("Could not write: %s\n", args->output_fname); if ( fwrite("\n",1,1,args->fp_out) != 1 ) error("Could not write: %s\n", args->output_fname); nwr += 60; } if ( nwr ) args->fa_ori_pos += nwr; args->fa_frz_mod -= nwr; if ( len ) { // not finished on this chr yet and the buffer cannot be emptied completely if ( nwr && nwr < args->fa_buf.l ) memmove(args->fa_buf.s,args->fa_buf.s+nwr,args->fa_buf.l-nwr); args->fa_buf.l -= nwr; return; } // empty the whole buffer if ( nwr == args->fa_buf.l ) { args->fa_buf.l = 0; return; } if ( fwrite(args->fa_buf.s+nwr,1,args->fa_buf.l - nwr,args->fp_out) != args->fa_buf.l - nwr ) error("Could not write: %s\n", args->output_fname); if ( fwrite("\n",1,1,args->fp_out) != 1 ) error("Could not write: %s\n", args->output_fname); args->fa_ori_pos += args->fa_buf.l - nwr - args->fa_mod_off; args->fa_mod_off = 0; args->fa_buf.l = 0; } static void apply_absent(args_t *args, hts_pos_t pos) { if ( !args->fa_buf.l || pos <= args->fa_frz_pos + 1 || pos <= args->fa_ori_pos ) return; int ie = pos && pos - args->fa_ori_pos + args->fa_mod_off < args->fa_buf.l ? pos - args->fa_ori_pos + args->fa_mod_off : args->fa_buf.l; int ib = args->fa_frz_mod < 0 ? 0 : args->fa_frz_mod; int i; for (i=ib; ifa_buf.s[i] = args->absent_allele; } static void freeze_ref(args_t *args, bcf1_t *rec) { if ( args->fa_frz_pos >= rec->pos + rec->rlen - 1 ) return; args->fa_frz_pos = rec->pos + rec->rlen - 1; args->fa_frz_mod = rec->pos - args->fa_ori_pos + args->fa_mod_off + rec->rlen; } static char *mark_del(char *ref, int rlen, char *alt, int mark) { char *out = malloc(rlen+1); int i; if ( alt ) { int nalt = strlen(alt); for (i=0; i { int nref = strlen(ref); for (i=0; in_allele, &args->miupac_als, &args->iupac_als, 0); for (i=0; imiupac_als; i++) args->iupac_als[i] = 0; } static int iupac_add_gt(args_t *args, bcf1_t *rec, uint8_t *gt, int ngt) { int i, is_set = 0; for (i=0; i= rec->n_allele ) error("Invalid VCF, too few ALT alleles at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); args->iupac_als[ial] = 1; is_set = 1; } return is_set; } static int iupac_set_allele(args_t *args, bcf1_t *rec) { int i,j, max_len = 0, alt_len = 0, ialt = -1, fallback_alt = -1; for (i=0; in_allele; i++) { if ( !args->iupac_als[i] ) continue; if ( fallback_alt <=0 ) fallback_alt = i; int l = strlen(rec->d.allele[i]); for (j=0; jd.allele[i][j]) < 0 ) break; if ( jmax_len ) { hts_resize(uint8_t, l, &args->miupac_bitmask, &args->iupac_bitmask, HTS_RESIZE_CLEAR); for (j=max_len; jiupac_bitmask[j] = 0; max_len = l; } if ( i>0 && l>alt_len ) { alt_len = l; ialt = i; } for (j=0; jiupac_bitmask[j] |= iupac2bitmask(rec->d.allele[i][j]); } if ( alt_len > 0 ) { for (j=0; jd.allele[ialt][j] = bitmask2iupac(args->iupac_bitmask[j]); return ialt; } if ( fallback_alt >= 0 ) return fallback_alt; return ialt; } static void apply_variant(args_t *args, bcf1_t *rec) { static int warned_haplotype = 0; if ( args->absent_allele ) apply_absent(args, rec->pos); if ( rec->n_allele==1 && !args->missing_allele && !args->absent_allele ) { return; } int i,j; if ( args->mask ) { char *chr = (char*)bcf_hdr_id2name(args->hdr,args->rid); int start = rec->pos; int end = rec->pos + rec->rlen - 1; for (i=0; inmask; i++) { mask_t *mask = &args->mask[i]; if ( MASK_SKIP(mask) && regidx_overlap(mask->idx, chr,start,end,NULL) ) return; } } int ialt = 1; // the alternate allele if ( args->iupac_GTs ) { bcf_unpack(rec, BCF_UN_FMT); bcf_fmt_t *fmt = bcf_get_fmt(args->hdr, rec, "GT"); if ( !fmt ) return; if ( fmt->type!=BCF_BT_INT8 ) error("Todo: GT field represented with BCF_BT_INT8, too many alleles at %s:%"PRId64"?\n",bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); ialt = -1; int is_set = 0; iupac_init(args,rec); for (i=0; ismpl->n; i++) { uint8_t *ptr = fmt->p + fmt->size*args->smpl->idx[i]; is_set += iupac_add_gt(args, rec, ptr, fmt->n); } if ( !is_set && !args->missing_allele ) return; if ( is_set ) ialt = iupac_set_allele(args, rec); } else if ( args->isample >= 0 ) { bcf_unpack(rec, BCF_UN_FMT); bcf_fmt_t *fmt = bcf_get_fmt(args->hdr, rec, "GT"); if ( !fmt ) return; if ( fmt->type!=BCF_BT_INT8 ) error("Todo: GT field represented with BCF_BT_INT8, too many alleles at %s:%"PRId64"?\n",bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); uint8_t *ptr = fmt->p + fmt->size*args->isample; enum { use_hap, use_iupac, pick_one } action = use_hap; if ( args->allele==PICK_IUPAC ) { if ( !args->haplotype ) action = use_iupac; if ( !bcf_gt_is_phased(ptr[0]) && !bcf_gt_is_phased(ptr[fmt->n-1]) ) action = use_iupac; } else if ( args->output_iupac ) action = use_iupac; else if ( !args->haplotype ) action = pick_one; if ( action==use_hap ) { if ( args->haplotype > fmt->n ) { if ( bcf_gt_is_missing(ptr[fmt->n-1]) || bcf_gt_is_missing(ptr[0]) ) { if ( !args->missing_allele ) return; ialt = -1; } else { if ( !warned_haplotype ) { fprintf(bcftools_stderr, "Can't apply %d-th haplotype at %s:%"PRId64". (This warning is printed only once.)\n", args->haplotype,bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); warned_haplotype = 1; } return; } } else { ialt = (int8_t)ptr[args->haplotype-1]; if ( bcf_gt_is_missing(ialt) || ialt==bcf_int8_vector_end ) { if ( !args->missing_allele ) return; ialt = -1; } else ialt = bcf_gt_allele(ialt); } } else if ( action==use_iupac ) { ialt = -1; iupac_init(args,rec); int is_set = iupac_add_gt(args, rec, ptr, fmt->n); if ( !is_set && !args->missing_allele ) return; if ( is_set ) ialt = iupac_set_allele(args, rec); } else { int is_hom = 1; for (i=0; in; i++) { if ( bcf_gt_is_missing(ptr[i]) ) { if ( !args->missing_allele ) return; // ignore missing or half-missing genotypes ialt = -1; break; } if ( ptr[i]==(uint8_t)bcf_int8_vector_end ) break; ialt = bcf_gt_allele(ptr[i]); if ( i>0 && ialt!=bcf_gt_allele(ptr[i-1]) ) { is_hom = 0; break; } } if ( !is_hom ) { int prev_len = 0, jalt; for (i=0; in; i++) { if ( ptr[i]==(uint8_t)bcf_int8_vector_end ) break; jalt = bcf_gt_allele(ptr[i]); if ( rec->n_allele <= jalt ) error("Broken VCF, too few alts at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); if ( args->allele & (PICK_LONG|PICK_SHORT) ) { int len = jalt==0 ? rec->rlen : strlen(rec->d.allele[jalt]); if ( i==0 ) ialt = jalt, prev_len = len; else if ( len == prev_len ) { if ( args->allele & PICK_REF && jalt==0 ) ialt = jalt, prev_len = len; else if ( args->allele & PICK_ALT && ialt==0 ) ialt = jalt, prev_len = len; } else if ( args->allele & PICK_LONG && len > prev_len ) ialt = jalt, prev_len = len; else if ( args->allele & PICK_SHORT && len < prev_len ) ialt = jalt, prev_len = len; } else { if ( args->allele & PICK_REF && jalt==0 ) ialt = jalt; else if ( args->allele & PICK_ALT && ialt==0 ) ialt = jalt; } } } } if ( !ialt ) { // ref allele if ( args->absent_allele ) freeze_ref(args,rec); return; } if ( rec->n_allele <= ialt ) error("Broken VCF, too few alts at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); } else if ( args->output_iupac && rec->n_allele>1 ) { int ialt, alen = 0, mlen = 0; for (i=0; in_allele; i++) { int l = strlen(rec->d.allele[i]); for (j=0; jd.allele[i][j]) < 0 ) break; if ( j mlen ) { hts_expand(uint8_t,l,args->miupac_bitmask,args->iupac_bitmask); for (j=mlen; jiupac_bitmask[j] = 0; mlen = l; } if ( i>0 && l>alen ) { alen = l; ialt = i; } for (j=0; jiupac_bitmask[j] |= iupac2bitmask(rec->d.allele[i][j]); } if ( alen > 0 ) for (j=0; jd.allele[ialt][j] = bitmask2iupac(args->iupac_bitmask[j]); else ialt = 1; } if ( rec->n_allele==1 && ialt!=-1 ) { // non-missing reference if ( args->absent_allele ) freeze_ref(args,rec); return; } if ( ialt==-1 ) { char alleles[4]; alleles[0] = rec->d.allele[0][0]; alleles[1] = ','; alleles[2] = args->missing_allele; alleles[3] = 0; bcf_update_alleles_str(args->hdr, rec, alleles); ialt = 1; } // For some variant types POS+REF refer to the base *before* the event; in such case set trim_beg int trim_beg = 0; int var_type = bcf_get_variant_type(rec,ialt); int var_len = rec->d.var[ialt].n; if ( var_type & VCF_INDEL ) { // normally indel starts one base after, but not if the first base of the fa reference is deleted if ( rec->d.allele[0][0] == rec->d.allele[ialt][0] ) trim_beg = 1; else trim_beg = 0; } else if ( (var_type & VCF_OTHER) && !strcasecmp(rec->d.allele[ialt],"") ) { trim_beg = 1; var_len = 1 - rec->rlen; } else if ( (var_type & VCF_OTHER) && !strncasecmp(rec->d.allele[ialt],"pos <= args->fa_frz_pos && rec->pos + rec->rlen - 1 > args->fa_frz_pos ) { // Applying the reference allele which overlaps a previous deletion. If we are here, it // means it goes beyond the freezed position, hence the record can be trimmed and moved // forward int ntrim = args->fa_frz_pos - rec->pos + 1; int nref = strlen(rec->d.allele[0]); assert( ntrim < nref ); rec->pos += ntrim; rec->rlen -= ntrim; memmove(rec->d.allele[0],rec->d.allele[0]+ntrim,nref-ntrim); rec->d.allele[0][nref-ntrim] = 0; } if ( rec->pos <= args->fa_frz_pos ) { // Can be still OK iff this is an insertion (and which does not follow another insertion, see #888). // This still may not be enough for more complicated cases with multiple duplicate positions // and other types in between. In such case let the user normalize the VCF and remove duplicates. int overlap = 0; if ( rec->pos < args->fa_frz_pos || !trim_beg || var_len==0 || args->prev_is_insert ) overlap = 1; if ( overlap ) { fprintf(bcftools_stderr,"The site %s:%"PRId64" overlaps with another variant, skipping...\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); return; } } char *ref_allele = rec->d.allele[0]; char *alt_allele = rec->d.allele[ialt]; int rmme_alt = 0; int len_diff = 0, alen = 0; int idx = rec->pos - args->fa_ori_pos + args->fa_mod_off; // position of the variant within the modified fasta sequence if ( idx<0 ) { if ( alt_allele[0]=='<' ) // symbolic allele { rec->pos -= idx + 1; rec->rlen += idx + 1; idx = -1; } else if ( strlen(ref_allele) < -idx ) // the ref allele is shorter but overlaps the fa sequence? This should never happen { assert(0); fprintf(bcftools_stderr,"Warning: ignoring overlapping variant starting at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); return; } else if ( strlen(alt_allele) > -idx ) // the ref allele overlaps the fa and so does the alt allele { rec->pos -= idx; rec->rlen += idx; ref_allele -= idx; alt_allele -= idx; idx = 0; } else // the ref allele overlaps the fa but alt allele does not: trim to leave one base before { rec->pos -= idx + 1; rec->rlen += idx + 1; ref_allele -= idx + 1; alt_allele += strlen(alt_allele) - 1; idx = -1; } } if ( rec->rlen > args->fa_buf.l - idx ) { rec->rlen = args->fa_buf.l - idx; if ( alt_allele[0]!='<' ) { alen = strlen(alt_allele); if ( alen > rec->rlen ) { fprintf(bcftools_stderr,"Warning: trimming variant \"%s\" starting at %s:%"PRId64"\n", alt_allele,bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); alt_allele[rec->rlen] = 0; } } } // the variant is beyond the available fasta sequence if ( idx>0 && idx>=args->fa_buf.l ) return; // sanity check the reference base if ( alt_allele[0]=='<' ) { // TODO: symbolic deletions probably need more work above with PICK_SHORT|PICK_LONG if ( strcasecmp(alt_allele,"") && strcasecmp(alt_allele,"<*>") && strcasecmp(alt_allele,"") ) error("Symbolic alleles other than , <*> or are currently not supported, e.g. \"%s\" at %s:%"PRId64".\n" "Please use filtering expressions to exclude such sites, for example by running with: -e 'ALT~\"<.*>\"'\n", alt_allele,bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); if ( !strcasecmp(alt_allele,"") ) { static int multibase_ref_del_warned = 0; if ( ref_allele[1]!=0 && !multibase_ref_del_warned ) { fprintf(bcftools_stderr, "Warning: one REF base is expected with , assuming the actual deletion starts at POS+1 at %s:%"PRId64".\n" " (This warning is printed only once.)\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); multibase_ref_del_warned = 1; } if ( args->mark_del ) // insert dashes instead of delete sequence { alt_allele = mark_del(ref_allele, rec->rlen, NULL, args->mark_del); alen = rec->rlen; len_diff = 0; rmme_alt = 1; } else { len_diff = 1-rec->rlen; alt_allele = ref_allele; // according to VCF spec, the first REF base must precede the event alen = 1; } } else { // <*> or .. gVCF, evidence for the reference allele throughout the whole block freeze_ref(args,rec); return; } } else if ( idx>=0 && strncasecmp(ref_allele,args->fa_buf.s+idx,rec->rlen) ) { // This is hacky, handle a special case: if SNP or an insert follows a deletion (AAC>A, C>CAA), // the reference base in fa_buf is lost and the check fails. We do not keep a buffer // with the original sequence as it should not be necessary, we should encounter max // one base overlap int fail = 1; if ( args->prev_base_pos==rec->pos && toupper(ref_allele[0])==toupper(args->prev_base) ) { if ( rec->rlen==1 ) fail = 0; else if ( !strncasecmp(ref_allele+1,args->fa_buf.s+idx+1,rec->rlen-1) ) fail = 0; } if ( fail ) { char tmp = 0; if ( args->fa_buf.l - idx > rec->rlen ) { tmp = args->fa_buf.s[idx+rec->rlen]; args->fa_buf.s[idx+rec->rlen] = 0; } error( "The fasta sequence does not match the REF allele at %s:%"PRId64":\n" " REF .vcf: [%s]\n" " ALT .vcf: [%s]\n" " REF .fa : [%s]%c%s\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1, ref_allele, alt_allele, args->fa_buf.s+idx, tmp?tmp:' ',tmp?args->fa_buf.s+idx+rec->rlen+1:"" ); } alen = strlen(alt_allele); len_diff = alen - rec->rlen; if ( args->mark_del && len_diff<0 ) { alt_allele = mark_del(ref_allele, rec->rlen, alt_allele, args->mark_del); alen = rec->rlen; len_diff = 0; rmme_alt = 1; } } else { alen = strlen(alt_allele); len_diff = alen - rec->rlen; if ( args->mark_del && len_diff<0 ) { alt_allele = mark_del(ref_allele, rec->rlen, alt_allele, args->mark_del); alen = rec->rlen; len_diff = 0; rmme_alt = 1; } } int safe_idx = idx<0 ? 0 : idx; // idx can be negative in case of overlapping deletion args->fa_case = toupper(args->fa_buf.s[safe_idx])==args->fa_buf.s[safe_idx] ? TO_UPPER : TO_LOWER; if ( args->fa_case==TO_UPPER ) for (i=0; imark_ins && len_diff>0 ) mark_ins(ref_allele, alt_allele, args->mark_ins); if ( args->mark_snv ) mark_snv(ref_allele, alt_allele, args->mark_snv); if ( len_diff <= 0 ) { // deletion or same size event assert( args->fa_buf.l >= idx+rec->rlen ); args->prev_base = args->fa_buf.s[idx+rec->rlen-1]; args->prev_base_pos = rec->pos + rec->rlen - 1; args->prev_is_insert = 0; args->fa_frz_mod = idx + alen; for (i=trim_beg; ifa_buf.s[idx+i] = alt_allele[i]; if ( len_diff ) memmove(args->fa_buf.s+idx+alen,args->fa_buf.s+idx+rec->rlen,args->fa_buf.l-idx-rec->rlen); } else { args->prev_is_insert = 1; args->prev_base_pos = rec->pos; // insertion ks_resize(&args->fa_buf, args->fa_buf.l + len_diff); memmove(args->fa_buf.s + idx + rec->rlen + len_diff, args->fa_buf.s + idx + rec->rlen, args->fa_buf.l - idx - rec->rlen); // This can get tricky, make sure the bases unchanged by the insertion do not overwrite preceding variants. // For example, here we want to get TAA: // POS REF ALT // 1 C T // 1 C CAA int ibeg = 0; while ( ibegpos + ibeg <= args->prev_base_pos ) ibeg++; for (i=ibeg; ifa_buf.s[idx+i] = alt_allele[i]; args->fa_frz_mod = idx + alen - ibeg + 1; } if (args->chain && len_diff != 0) { // If first nucleotide of both REF and ALT are the same... (indels typically include the nucleotide before the variant) if ( strncasecmp(ref_allele,alt_allele,1) == 0) { // ...extend the block by 1 bp: start is 1 bp further and alleles are 1 bp shorter push_chain_gap(args->chain, rec->pos + 1, rec->rlen - 1, rec->pos + 1 + args->fa_mod_off, alen - 1); } else { // otherwise, just the coordinates of the variant as given push_chain_gap(args->chain, rec->pos, rec->rlen, rec->pos + args->fa_mod_off, alen); } } args->fa_buf.l += len_diff; args->fa_mod_off += len_diff; args->fa_frz_pos = rec->pos + rec->rlen - 1; args->napplied++; if ( rmme_alt ) free(alt_allele); } static void mask_region(args_t *args, char *seq, int len) { int start = args->fa_src_pos - len; int end = args->fa_src_pos; int i; for (i=0; inmask; i++) { mask_t *mask = &args->mask[i]; if ( !regidx_overlap(mask->idx, args->chr,start,end, mask->itr) ) continue; int idx_start, idx_end, j; while ( regitr_overlap(mask->itr) ) { idx_start = mask->itr->beg - start; idx_end = mask->itr->end - start; if ( idx_start < 0 ) idx_start = 0; if ( idx_end >= len ) idx_end = len - 1; if ( mask->with==MASK_UC ) for (j=idx_start; j<=idx_end; j++) seq[j] = toupper(seq[j]); else if ( mask->with==MASK_LC ) for (j=idx_start; j<=idx_end; j++) seq[j] = tolower(seq[j]); else for (j=idx_start; j<=idx_end; j++) seq[j] = mask->with; } } } static void consensus(args_t *args) { BGZF *fasta = bgzf_open(args->ref_fname, "r"); if ( !fasta ) error("Error reading %s\n", args->ref_fname); kstring_t str = {0,0,0}; while ( bgzf_getline(fasta, '\n', &str) > 0 ) { if ( str.s[0]=='>' ) { // new sequence encountered if ( args->chain ) print_chain(args); // apply all cached variants and variants that might have been missed because of short fasta (see test/consensus.9.*) bcf1_t **rec_ptr = NULL; while ( args->rid>=0 && (rec_ptr = next_vcf_line(args)) ) { bcf1_t *rec = *rec_ptr; if ( rec->rid!=args->rid || ( args->fa_end_pos && rec->pos > args->fa_end_pos ) ) break; apply_variant(args, rec); } if ( args->absent_allele ) { int pos = 0; if ( args->vcf_rbuf.n && args->vcf_buf[args->vcf_rbuf.f]->rid==args->rid ) pos = args->vcf_buf[args->vcf_rbuf.f]->pos; apply_absent(args, pos); } flush_fa_buffer(args, 0); init_region(args, str.s+1); continue; } args->fa_length += str.l; args->fa_src_pos += str.l; // determine if uppercase or lowercase is used in this fasta file if ( args->fa_case==-1 ) args->fa_case = toupper(str.s[0])==str.s[0] ? 1 : 0; if ( args->mask ) mask_region(args, str.s, str.l); kputs(str.s, &args->fa_buf); bcf1_t **rec_ptr = NULL; while ( args->rid>=0 && (rec_ptr = next_vcf_line(args)) ) { bcf1_t *rec = *rec_ptr; // still the same chr and the same region? if not, fasta buf can be flushed if ( rec->rid!=args->rid || ( args->fa_end_pos && rec->pos > args->fa_end_pos ) ) { // save the vcf record until next time and flush unread_vcf_line(args, rec_ptr); rec_ptr = NULL; break; } // is the vcf record well beyond cached fasta buffer? if yes, the buf can be flushed if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off <= rec->pos ) { unread_vcf_line(args, rec_ptr); rec_ptr = NULL; break; } // is the cached fasta buffer full enough? if not, read more fasta, no flushing if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off < rec->pos + rec->rlen ) { unread_vcf_line(args, rec_ptr); break; } apply_variant(args, rec); } if ( !rec_ptr ) { if ( args->absent_allele ) apply_absent(args, args->fa_ori_pos - args->fa_mod_off + args->fa_buf.l); flush_fa_buffer(args, 60); } } bcf1_t **rec_ptr = NULL; while ( args->rid>=0 && (rec_ptr = next_vcf_line(args)) ) { bcf1_t *rec = *rec_ptr; if ( rec->rid!=args->rid ) break; if ( args->fa_end_pos && rec->pos > args->fa_end_pos ) break; if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off <= rec->pos ) break; apply_variant(args, rec); } if (args->chain) print_chain(args); if ( args->absent_allele ) apply_absent(args, HTS_POS_MAX); flush_fa_buffer(args, 0); bgzf_close(fasta); free(str.s); fprintf(bcftools_stderr,"Applied %d variants\n", args->napplied); } static void usage(args_t *args) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: Create consensus sequence by applying VCF variants to a reference fasta\n"); fprintf(bcftools_stderr, " file. By default, the program will apply all ALT variants. Using the\n"); fprintf(bcftools_stderr, " --samples (and, optionally, --haplotype) option will apply genotype\n"); fprintf(bcftools_stderr, " (or haplotype) calls from FORMAT/GT. The program ignores allelic depth\n"); fprintf(bcftools_stderr, " information, such as INFO/AD or FORMAT/AD.\n"); fprintf(bcftools_stderr, "Usage: bcftools consensus [OPTIONS] \n"); fprintf(bcftools_stderr, "Options:\n"); fprintf(bcftools_stderr, " -c, --chain FILE Write a chain file for liftover\n"); fprintf(bcftools_stderr, " -a, --absent CHAR Replace positions absent from VCF with CHAR\n"); fprintf(bcftools_stderr, " -e, --exclude EXPR Exclude sites for which the expression is true (see man page for details)\n"); fprintf(bcftools_stderr, " -f, --fasta-ref FILE Reference sequence in fasta format\n"); fprintf(bcftools_stderr, " -H, --haplotype WHICH Choose which allele to use from the FORMAT/GT field, note\n"); fprintf(bcftools_stderr, " the codes are case-insensitive:\n"); fprintf(bcftools_stderr, " N: N={1,2,3,..} is the index of the allele from GT, regardless of phasing (e.g. \"2\")\n"); fprintf(bcftools_stderr, " R: REF allele in het genotypes\n"); fprintf(bcftools_stderr, " A: ALT allele\n"); fprintf(bcftools_stderr, " I: IUPAC code for all genotypes\n"); fprintf(bcftools_stderr, " LR,LA: longer allele and REF/ALT if equal length\n"); fprintf(bcftools_stderr, " SR,SA: shorter allele and REF/ALT if equal length\n"); fprintf(bcftools_stderr, " NpIu: index of the allele for phased and IUPAC code for unphased GTs (e.g. \"2pIu\")\n"); fprintf(bcftools_stderr, " -i, --include EXPR Select sites for which the expression is true (see man page for details)\n"); fprintf(bcftools_stderr, " -I, --iupac-codes Output IUPAC codes based on FORMAT/GT, use -s/-S to subset samples\n"); fprintf(bcftools_stderr, " --mark-del CHAR Instead of removing sequence, insert character CHAR for deletions\n"); fprintf(bcftools_stderr, " --mark-ins uc|lc|CHAR Highlight insertions in uppercase (uc), lowercase (lc), or use CHAR, leaving the rest as is\n"); fprintf(bcftools_stderr, " --mark-snv uc|lc|CHAR Highlight substitutions in uppercase (uc), lowercase (lc), or use CHAR, leaving the rest as is\n"); fprintf(bcftools_stderr, " -m, --mask FILE Replace regions according to the next --mask-with option. The default is --mask-with N\n"); fprintf(bcftools_stderr, " --mask-with CHAR|uc|lc Replace with CHAR (skips overlapping variants); change to uppercase (uc) or lowercase (lc)\n"); fprintf(bcftools_stderr, " -M, --missing CHAR Output CHAR instead of skipping a missing genotype \"./.\"\n"); fprintf(bcftools_stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(bcftools_stderr, " -p, --prefix STRING Prefix to add to output sequence names\n"); fprintf(bcftools_stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " -s, --samples LIST Comma-separated list of samples to include, \"-\" to ignore samples and use REF,ALT\n"); fprintf(bcftools_stderr, " -S, --samples-file FILE File of samples to include\n"); fprintf(bcftools_stderr, "Examples:\n"); fprintf(bcftools_stderr, " # Get the consensus for one region. The fasta header lines are then expected\n"); fprintf(bcftools_stderr, " # in the form \">chr:from-to\".\n"); fprintf(bcftools_stderr, " samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz > out.fa\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, " # See also http://samtools.github.io/bcftools/howtos/consensus-sequence.html\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int main_consensus(int argc, char *argv[]) { args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->regions_overlap = 1; static struct option loptions[] = { {"mark-del",required_argument,NULL,1}, {"mark-ins",required_argument,NULL,2}, {"mark-snv",required_argument,NULL,3}, {"mask-with",1,0,4}, {"exclude",required_argument,NULL,'e'}, {"include",required_argument,NULL,'i'}, {"sample",1,0,'s'}, {"samples",1,0,'s'}, {"samples-file",1,0,'S'}, {"iupac-codes",0,0,'I'}, {"haplotype",1,0,'H'}, {"output",1,0,'o'}, {"fasta-ref",1,0,'f'}, {"mask",1,0,'m'}, {"missing",1,0,'M'}, {"absent",1,0,'a'}, {"chain",1,0,'c'}, {"prefix",required_argument,0,'p'}, {"regions-overlap",required_argument,0,5}, {0,0,0,0} }; int c; while ((c = getopt_long(argc, argv, "h?s:S:1Ii:e:H:f:o:m:c:M:p:a:",loptions,NULL)) >= 0) { switch (c) { case 1 : args->mark_del = optarg[0]; break; case 2 : if ( !strcasecmp(optarg,"uc") ) args->mark_ins = TO_UPPER; else if ( !strcasecmp(optarg,"lc") ) args->mark_ins = TO_LOWER; else if ( !optarg[1] && optarg[0]>32 && optarg[0]<127 ) args->mark_ins = optarg[0]; else error("The argument is not recognised: --mark-ins %s\n",optarg); break; case 3 : if ( !strcasecmp(optarg,"uc") ) args->mark_snv = TO_UPPER; else if ( !strcasecmp(optarg,"lc") ) args->mark_snv = TO_LOWER; else if ( !optarg[1] && optarg[0]>32 && optarg[0]<127 ) args->mark_snv = optarg[0]; else error("The argument is not recognised: --mark-snv %s\n",optarg); break; case 5 : args->regions_overlap = parse_overlap_option(optarg); if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 'p': args->chr_prefix = optarg; break; case 's': args->sample = optarg; break; case 'S': args->sample_fname = optarg; break; case 'o': args->output_fname = optarg; break; case 'I': args->output_iupac = 1; break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'f': args->ref_fname = optarg; break; case 'm': add_mask(args,optarg); break; case 4 : add_mask_with(args,optarg); break; case 'a': args->absent_allele = optarg[0]; if ( optarg[1]!=0 ) error("Expected single character with -a, got \"%s\"\n", optarg); break; case 'M': args->missing_allele = optarg[0]; if ( optarg[1]!=0 ) error("Expected single character with -M, got \"%s\"\n", optarg); break; case 'c': args->chain_fname = optarg; break; case 'H': if ( !strcasecmp(optarg,"R") ) args->allele |= PICK_REF; else if ( !strcasecmp(optarg,"A") ) args->allele |= PICK_ALT; else if ( !strcasecmp(optarg,"L") ) args->allele |= PICK_LONG|PICK_REF; else if ( !strcasecmp(optarg,"S") ) args->allele |= PICK_SHORT|PICK_REF; else if ( !strcasecmp(optarg,"LR") ) args->allele |= PICK_LONG|PICK_REF; else if ( !strcasecmp(optarg,"LA") ) args->allele |= PICK_LONG|PICK_ALT; else if ( !strcasecmp(optarg,"SR") ) args->allele |= PICK_SHORT|PICK_REF; else if ( !strcasecmp(optarg,"SA") ) args->allele |= PICK_SHORT|PICK_ALT; else if ( !strcasecmp(optarg,"I") ) args->allele |= PICK_IUPAC; else if ( !strcasecmp(optarg,"1pIu") ) args->allele |= PICK_IUPAC, args->haplotype = 1; else if ( !strcasecmp(optarg,"2pIu") ) args->allele |= PICK_IUPAC, args->haplotype = 2; else { char *tmp; args->haplotype = strtol(optarg, &tmp, 10); if ( tmp==optarg || (*tmp && strcasecmp(tmp,"pIu")) ) error("Error: Could not parse \"--haplotype %s\", expected number of number followed with \"pIu\"\n", optarg); if ( *tmp ) args->allele |= PICK_IUPAC; if ( args->haplotype <=0 ) error("Error: Expected positive integer with --haplotype\n"); } break; default: usage(args); break; } } if ( optind>=argc ) usage(args); args->fname = argv[optind]; if ( !args->ref_fname && !isatty(fileno((FILE *)stdin)) ) args->ref_fname = "-"; if ( !args->ref_fname ) usage(args); init_data(args); consensus(args); destroy_data(args); free(args); return 0; } pysam-0.23.0/bcftools/convert.c000066400000000000000000002071101475062545500164020ustar00rootroot00000000000000/* convert.c -- functions for converting between VCF/BCF and related formats. Copyright (C) 2013-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #define __STDC_FORMAT_MACROS #include #include #include #include #include #include #include #include #include "bcftools.h" #include "variantkey.h" #include "convert.h" #include "filter.h" #define T_CHROM 1 #define T_POS 2 #define T_ID 3 #define T_REF 4 #define T_ALT 5 #define T_QUAL 6 #define T_FILTER 7 #define T_INFO 8 #define T_FORMAT 9 #define T_SAMPLE 10 #define T_SEP 11 #define T_IS_TS 12 #define T_TYPE 13 #define T_MASK 14 #define T_GT 15 #define T_TGT 16 #define T_LINE 17 #define T_CHROM_POS_ID 18 // not publicly advertised #define T_GT_TO_PROB3 19 // not publicly advertised #define T_PL_TO_PROB3 20 // not publicly advertised #define T_GP_TO_PROB3 21 // not publicly advertised #define T_FIRST_ALT 22 // not publicly advertised #define T_IUPAC_GT 23 #define T_GT_TO_HAP 24 // not publicly advertised #define T_GT_TO_HAP2 25 // not publicly advertised #define T_TBCSQ 26 #define T_END 27 #define T_POS0 28 #define T_END0 29 #define T_RSX 30 // RSID HEX #define T_VKX 31 // VARIANTKEY HEX #define T_PBINOM 32 #define T_NPASS 33 typedef struct _fmt_t { int type, id, is_gt_field, ready, subscript; char *key; bcf_fmt_t *fmt; void *usr; // user data (optional) void (*handler)(convert_t *, bcf1_t *, struct _fmt_t *, int, kstring_t *); void (*destroy)(void*); // clean user data (optional) } fmt_t; struct _convert_t { fmt_t *fmt; int nfmt, mfmt; int nsamples, *samples; bcf_hdr_t *header; int max_unpack; char *format_str; bcf_srs_t *readers; // required only for %MASK int nreaders; void *dat; int ndat; char *undef_info_tag; void *used_tags_hash; char **used_tags_list; char *print_filtered; int nused_tags; int allow_undef_tags; int force_newline; int header_samples; int no_hdr_indices; uint8_t **subset_samples; }; typedef struct { kstring_t hap1,hap2; char **str; int n, m; } bcsq_t; static void process_chrom(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(convert->header->id[BCF_DT_CTG][line->rid].key, str); } static void process_pos(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos+1, str); } static void process_pos0(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos, str); } static void process_end(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos+line->rlen, str); } static void process_end0(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos+line->rlen-1, str); } static void process_id(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(line->d.id, str); } static void process_ref(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(line->d.allele[0], str); } static void process_alt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int i; if ( line->n_allele==1 ) { kputc('.', str); return; } if ( fmt->subscript>=0 ) { if ( line->n_allele > fmt->subscript+1 ) kputs(line->d.allele[fmt->subscript+1], str); else kputc('.', str); return; } for (i=1; in_allele; i++) { if ( i>1 ) kputc(',', str); kputs(line->d.allele[i], str); } } static void process_first_alt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( line->n_allele==1 ) kputc('.', str); else kputs(line->d.allele[1], str); } static void process_qual(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( bcf_float_is_missing(line->qual) ) kputc('.', str); else kputd(line->qual, str); } static void process_filter(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int i; if ( line->d.n_flt ) { for (i=0; id.n_flt; i++) { if (i) kputc(';', str); kputs(convert->header->id[BCF_DT_ID][line->d.flt[i]].key, str); } } else kputc('.', str); } static inline int32_t bcf_array_ivalue(uint8_t *bcf_array, int type, int idx) { if ( type==BCF_BT_INT8 ) { int8_t val = le_to_i8(&bcf_array[idx * sizeof(val)]); if ( val==bcf_int8_missing ) return bcf_int32_missing; if ( val==bcf_int8_vector_end ) return bcf_int32_vector_end; return val; } if ( type==BCF_BT_INT16 ) { int16_t val = le_to_i16(&bcf_array[idx * sizeof(val)]); if ( val==bcf_int16_missing ) return bcf_int32_missing; if ( val==bcf_int16_vector_end ) return bcf_int32_vector_end; return val; } return le_to_i32(&bcf_array[idx * sizeof(int32_t)]); } static inline void _copy_field(char *src, uint32_t len, int idx, kstring_t *str) { int n = 0, ibeg = 0; while ( src[ibeg] && ibegibeg ) kputsn(src+ibeg, iend-ibeg, str); else kputc('.', str); } static void process_info(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int i; if ( !fmt->key ) // the whole INFO column { int first = 1; for (i=0; in_info; i++) { bcf_info_t *inf = &line->d.info[i]; if ( !inf->vptr ) continue; if ( !first ) kputc(';', str); first = 0; if ( inf->key >= convert->header->n[BCF_DT_ID] ) continue; kputs(convert->header->id[BCF_DT_ID][inf->key].key, str); if ( inf->len <= 0 ) continue; kputc('=', str); if ( inf->len == 1 ) { switch (inf->type) { case BCF_BT_INT8: if ( inf->v1.i==bcf_int8_missing ) kputc('.', str); else kputw(inf->v1.i, str); break; case BCF_BT_INT16: if ( inf->v1.i==bcf_int16_missing ) kputc('.', str); else kputw(inf->v1.i, str); break; case BCF_BT_INT32: if ( inf->v1.i==bcf_int32_missing ) kputc('.', str); else kputw(inf->v1.i, str); break; case BCF_BT_FLOAT: if ( bcf_float_is_missing(inf->v1.f) ) kputc('.', str); else kputd(inf->v1.f, str); break; case BCF_BT_CHAR: kputc(inf->v1.i, str); break; default: error("Unexpected type %d", inf->type); break; } } else bcf_fmt_array(str, inf->len, inf->type, inf->vptr); } if ( first ) kputc('.', str); return; } if ( fmt->id<0 ) { kputc('.', str); return; } for (i=0; in_info; i++) if ( line->d.info[i].key == fmt->id ) break; // output "." if the tag is not present if ( i==line->n_info ) { kputc('.', str); return; } bcf_info_t *info = &line->d.info[i]; // if this is a flag, output 1 if ( info->len <=0 ) { kputc('1', str); return; } if ( info->len == 1 ) { switch (info->type) { case BCF_BT_INT8: if ( info->v1.i==bcf_int8_missing ) kputc('.', str); else kputw(info->v1.i, str); break; case BCF_BT_INT16: if ( info->v1.i==bcf_int16_missing ) kputc('.', str); else kputw(info->v1.i, str); break; case BCF_BT_INT32: if ( info->v1.i==bcf_int32_missing ) kputc('.', str); else kputw(info->v1.i, str); break; case BCF_BT_FLOAT: if ( bcf_float_is_missing(info->v1.f) ) kputc('.', str); else kputd(info->v1.f, str); break; case BCF_BT_CHAR: kputc(info->v1.i, str); break; default: fprintf(stderr,"todo: type %d\n", info->type); exit(1); break; } } else if ( fmt->subscript >=0 ) { if ( info->len <= fmt->subscript ) { kputc('.', str); return; } #define BRANCH(type_t, convert, is_missing, is_vector_end, kprint) { \ type_t val = convert(&info->vptr[fmt->subscript * sizeof(type_t)]); \ if ( is_missing || is_vector_end ) kputc('.',str); \ else kprint; \ } switch (info->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, kputw(val, str)); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, kputw(val, str)); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, val==bcf_int32_missing, val==bcf_int32_vector_end, kputw(val, str)); break; case BCF_BT_FLOAT: BRANCH(float, le_to_float, bcf_float_is_missing(val), bcf_float_is_vector_end(val), kputd(val, str)); break; case BCF_BT_CHAR: _copy_field((char*)info->vptr, info->vptr_len, fmt->subscript, str); break; default: fprintf(stderr,"todo: type %d\n", info->type); exit(1); break; } #undef BRANCH } else bcf_fmt_array(str, info->len, info->type, info->vptr); } static void init_format(convert_t *convert, bcf1_t *line, fmt_t *fmt) { fmt->id = bcf_hdr_id2int(convert->header, BCF_DT_ID, fmt->key); if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,fmt->id) ) fmt->id = -1; fmt->fmt = NULL; if ( fmt->id >= 0 ) { int i; for (i=0; i<(int)line->n_fmt; i++) if ( line->d.fmt[i].id==fmt->id ) { fmt->fmt = &line->d.fmt[i]; break; } } else if ( !convert->allow_undef_tags ) error("Error: no such tag defined in the VCF header: FORMAT/%s\n", fmt->key); fmt->ready = 1; } static void process_complete_format(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( convert->nsamples ) { int i,j; if ( line->n_fmt) { int gt_i = -1; bcf_fmt_t *fmt = line->d.fmt; int first = 1; for (i=0; i<(int)line->n_fmt; i++) { if ( !fmt[i].p || fmt[i].id<0 ) continue; if ( !first ) kputc(':', str); first = 0; kputs(convert->header->id[BCF_DT_ID][fmt[i].id].key, str); if ( strcmp(convert->header->id[BCF_DT_ID][fmt[i].id].key, "GT") == 0) gt_i = i; } if ( first ) kputc('.', str); for (j=0; jnsamples; j++) { kputc('\t', str); first = 1; for (i=0; i<(int)line->n_fmt; i++) { bcf_fmt_t *f = &fmt[i]; if ( !f->p ) continue; if ( !first ) kputc(':', str); first = 0; if (gt_i == i) bcf_format_gt(f,convert->samples[j],str); else bcf_fmt_array(str, f->n, f->type, f->p + convert->samples[j] * f->size); } if ( first ) kputc('.', str); } } else for (j=0; j<=line->n_sample; j++) kputs("\t.", str); } else kputc('.',str); } static void process_format(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( !fmt->ready ) init_format(convert, line, fmt); if ( fmt->fmt==NULL ) { kputc('.', str); return; } else if ( fmt->subscript >=0 ) { if ( fmt->fmt->n <= fmt->subscript ) { kputc('.', str); return; } if ( fmt->fmt->type == BCF_BT_FLOAT ) { uint8_t *ptr = fmt->fmt->p + isample*fmt->fmt->size; float val = le_to_float(&ptr[fmt->subscript * sizeof(float)]); if ( bcf_float_is_missing(val) || bcf_float_is_vector_end(val) ) kputc('.', str); else kputd(val, str); } else if ( fmt->fmt->type != BCF_BT_CHAR ) { int32_t ival = bcf_array_ivalue(fmt->fmt->p+isample*fmt->fmt->size,fmt->fmt->type,fmt->subscript); if ( ival==bcf_int32_missing || ival==bcf_int32_vector_end ) kputc('.', str); else kputw(ival, str); } else if ( fmt->fmt->type == BCF_BT_CHAR ) _copy_field((char*)(fmt->fmt->p + isample*fmt->fmt->size), fmt->fmt->size, fmt->subscript, str); else error("TODO: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt->fmt->type); } else bcf_fmt_array(str, fmt->fmt->n, fmt->fmt->type, fmt->fmt->p + isample*fmt->fmt->size); } static void process_gt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( !fmt->ready ) init_format(convert, line, fmt); if ( fmt->fmt==NULL ) { kputc('.', str); return; } bcf_format_gt(fmt->fmt, isample, str); } static void process_tgt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( !fmt->ready ) init_format(convert, line, fmt); if ( fmt->fmt==NULL ) { kputc('.', str); return; } assert( fmt->fmt->type==BCF_BT_INT8 ); int l; int8_t *x = (int8_t*)(fmt->fmt->p + isample*fmt->fmt->size); // FIXME: does not work with n_alt >= 64 for (l = 0; l < fmt->fmt->n && x[l] != bcf_int8_vector_end; ++l) { if (l) kputc("/|"[x[l]&1], str); if (x[l]>>1) { int ial = (x[l]>>1) - 1; kputs(line->d.allele[ial], str); } else kputc('.', str); } if (l == 0) kputc('.', str); } static void destroy_tbcsq(void *usr) { if ( !usr ) return; bcsq_t *csq = (bcsq_t*) usr; free(csq->hap1.s); free(csq->hap2.s); if ( csq->n ) free(csq->str[0]); free(csq->str); free(csq); } static void process_tbcsq(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( !fmt->ready ) { init_format(convert, line, fmt); bcsq_t *csq; if ( fmt->usr ) { csq = (bcsq_t*) fmt->usr; if ( csq->n ) free(csq->str[0]); csq->n = 0; } else csq = (bcsq_t*) calloc(1,sizeof(bcsq_t)); fmt->usr = csq; int i=0, len = 0; char *tmp = NULL; if ( bcf_get_info_string(convert->header,line,fmt->key,&tmp,&len)<0 ) { csq->n = 0; return; } do { csq->n++; hts_expand(char*, csq->n, csq->m, csq->str); csq->str[ csq->n-1 ] = tmp + i; while ( iusr; if ( fmt->fmt==NULL || !csq->n ) return; csq->hap1.l = 0; csq->hap2.l = 0; int mask = fmt->subscript==0 ? 3 : 1; // merge both haplotypes if subscript==0 #define BRANCH(type_t, convert, nbits) { \ uint8_t *x = fmt->fmt->p + isample*fmt->fmt->size; \ int i,j; \ if ( fmt->subscript<=0 || fmt->subscript==1 ) \ { \ for (j=0; j < fmt->fmt->n; j++) \ { \ type_t val = convert(&x[j * sizeof(type_t)]); \ if ( !val ) continue; \ for (i=0; istr[(j*30+i)/2], &csq->hap1); kputc_(',', &csq->hap1); } \ } \ } \ if ( fmt->subscript<0 || fmt->subscript==2 ) \ { \ for (j=0; j < fmt->fmt->n; j++) \ { \ type_t val = convert(&x[j * sizeof(type_t)]); \ if ( !val ) continue; \ for (i=1; istr[(j*30+i)/2], &csq->hap2); kputc_(',', &csq->hap2); } \ } \ } \ } switch (fmt->fmt->type) { case BCF_BT_INT8: BRANCH(uint8_t, le_to_u8, 8); break; case BCF_BT_INT16: BRANCH(uint16_t, le_to_u16, 16); break; case BCF_BT_INT32: BRANCH(uint32_t, le_to_u32, 30); break; // 2 bits unused to account for the reserved BCF values default: error("Unexpected type: %d\n", fmt->fmt->type); exit(1); break; } #undef BRANCH if ( !csq->hap1.l && !csq->hap2.l ) return; if ( csq->hap1.l ) csq->hap1.s[--csq->hap1.l] = 0; if ( csq->hap2.l ) csq->hap2.s[--csq->hap2.l] = 0; if ( fmt->subscript<0 ) { kputs(csq->hap1.l?csq->hap1.s:".", str); kputc_('\t', str); kputs(csq->hap2.l?csq->hap2.s:".", str); } else if ( fmt->subscript<2 ) kputs(csq->hap1.l?csq->hap1.s:".", str); else kputs(csq->hap2.l?csq->hap2.s:".", str); } static void init_format_iupac(convert_t *convert, bcf1_t *line, fmt_t *fmt) { init_format(convert, line, fmt); if ( fmt->fmt==NULL ) return; // Init mapping between alleles and IUPAC table hts_expand(uint8_t, line->n_allele, convert->ndat, convert->dat); int8_t *dat = (int8_t*)convert->dat; int i; for (i=0; in_allele; i++) { if ( line->d.allele[i][1] ) dat[i] = -1; else { switch (line->d.allele[i][0]) { case 'A': dat[i] = 0; break; case 'C': dat[i] = 1; break; case 'G': dat[i] = 2; break; case 'T': dat[i] = 3; break; case 'a': dat[i] = 0; break; case 'c': dat[i] = 1; break; case 'g': dat[i] = 2; break; case 't': dat[i] = 3; break; default: dat[i] = -1; } } } } static void process_iupac_gt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( !fmt->ready ) init_format_iupac(convert, line, fmt); if ( fmt->fmt==NULL ) { kputc('.', str); return; } assert( fmt->fmt->type==BCF_BT_INT8 ); static const char iupac[4][4] = { {'A','M','R','W'},{'M','C','S','Y'},{'R','S','G','K'},{'W','Y','K','T'} }; int8_t *dat = (int8_t*)convert->dat; int8_t *x = (int8_t*)(fmt->fmt->p + isample*fmt->fmt->size); // FIXME: does not work with n_alt >= 64 int l = 0; while ( lfmt->n && x[l]!=bcf_int8_vector_end && x[l]!=bcf_int8_missing ) l++; if ( l==2 ) { // diploid int ia = (x[0]>>1) - 1, ib = (x[1]>>1) - 1; if ( ia>=0 && ian_allele && ib>=0 && ibn_allele && dat[ia]>=0 && dat[ib]>=0 ) { kputc(iupac[dat[ia]][dat[ib]], str); return; } } for (l = 0; l < fmt->fmt->n && x[l] != bcf_int8_vector_end; ++l) { if (l) kputc("/|"[x[l]&1], str); if (x[l]>>1) { int ial = (x[l]>>1) - 1; kputs(line->d.allele[ial], str); } else kputc('.', str); } if (l == 0) kputc('.', str); } static void process_sample(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(convert->header->samples[isample], str); } static void process_sep(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if (fmt->key) kputs(fmt->key, str); } static void process_is_ts(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int is_ts = 0; if ( bcf_get_variant_types(line) & (VCF_SNP|VCF_MNP) ) is_ts = abs(bcf_acgt2int(*line->d.allele[0])-bcf_acgt2int(*line->d.allele[1])) == 2 ? 1 : 0; kputc(is_ts ? '1' : '0', str); } static void process_type(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int line_type = bcf_get_variant_types(line); int i = 0; if ( line_type == VCF_REF ) { kputs("REF", str); i++; } if ( line_type & VCF_SNP ) { if (i) kputc(',',str); kputs("SNP", str); i++; } if ( line_type & VCF_MNP ) { if (i) kputc(',',str); kputs("MNP", str); i++; } if ( line_type & VCF_INDEL ) { if (i) kputc(',',str); kputs("INDEL", str); i++; } if ( line_type & VCF_OTHER ) { if (i) kputc(',',str); kputs("OTHER", str); i++; } if ( line_type & VCF_BND ) { if (i) kputc(',',str); kputs("BND", str); i++; } if ( line_type & VCF_OVERLAP ) { if (i) kputc(',',str); kputs("OVERLAP", str); i++; } } static void process_line(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { vcf_format1(convert->header, line, str); if ( str->s[str->l-1]=='\n' ) str->l--; } static void process_chrom_pos_id(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( line->d.id[0]!='.' || line->d.id[1] ) { // ID is present kputs(line->d.id, str); } else { // use CHROM:POS instead of ID kputs(convert->header->id[BCF_DT_CTG][line->rid].key, str); kputc(':', str); kputw(line->pos+1, str); } } static void process_gt_to_prob3(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int m,n,i; m = convert->ndat / sizeof(int32_t); n = bcf_get_genotypes(convert->header,line,&convert->dat,&m); convert->ndat = m * sizeof(int32_t); if ( n<=0 ) { // Throw an error or silently proceed? // // for (i=0; insamples; i++) kputs(" 0.33 0.33 0.33", str); // return; error("Error parsing GT tag at %s:%"PRId64"\n", bcf_seqname(convert->header,line),(int64_t) line->pos+1); } n /= convert->nsamples; for (i=0; insamples; i++) { int32_t *ptr = (int32_t*)convert->dat + i*n; int j; for (j=0; jndat / sizeof(int32_t); n = bcf_get_format_int32(convert->header,line,"PL",&convert->dat,&m); convert->ndat = m * sizeof(int32_t); if ( n<=0 ) { // Throw an error or silently proceed? // // for (i=0; insamples; i++) kputs(" 0.33 0.33 0.33", str); // return; error("Error parsing PL tag at %s:%"PRId64"\n", bcf_seqname(convert->header,line),(int64_t) line->pos+1); } n /= convert->nsamples; for (i=0; insamples; i++) { int32_t *ptr = (int32_t*)convert->dat + i*n; int j; float sum = 0; for (j=0; jn_allele ) { // haploid kputc(' ',str); ksprintf(str,"%f",pow(10,-0.1*ptr[0])/sum); kputs(" 0 ", str); ksprintf(str,"%f",pow(10,-0.1*ptr[1])/sum); } else { // diploid kputc(' ',str); ksprintf(str,"%f",pow(10,-0.1*ptr[0])/sum); kputc(' ',str); ksprintf(str,"%f",pow(10,-0.1*ptr[1])/sum); kputc(' ',str); ksprintf(str,"%f",pow(10,-0.1*ptr[2])/sum); } } } static void process_gp_to_prob3(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int m,n,i; m = convert->ndat / sizeof(float); n = bcf_get_format_float(convert->header,line,"GP",&convert->dat,&m); convert->ndat = m * sizeof(float); if ( n<=0 ) { // Throw an error or silently proceed? // // for (i=0; insamples; i++) kputs(" 0.33 0.33 0.33", str); // return; error("Error parsing GP tag at %s:%"PRId64"\n", bcf_seqname(convert->header,line),(int64_t) line->pos+1); } n /= convert->nsamples; for (i=0; insamples; i++) { float *ptr = (float*)convert->dat + i*n; int j; for (j=0; j1 ) error("[%s:%"PRId64":%f] GP value outside range [0,1]; bcftools convert expects the VCF4.3+ spec for the GP field encoding genotype posterior probabilities", bcf_seqname(convert->header,line),(int64_t) line->pos+1,ptr[j]); } if ( j==line->n_allele ) ksprintf(str," %f %f %f",ptr[0],0.,ptr[1]); // haploid else ksprintf(str," %f %f %f",ptr[0],ptr[1],ptr[2]); // diploid } } static void process_gt_to_hap(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { // https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#-known_haps_g // File containing known haplotypes for the study cohort. The format // is the same as the output format from IMPUTE2's -phase option: // five header columns (as in the -g file) followed by two columns // (haplotypes) per individual. Allowed values in the haplotype // columns are 0, 1, and ?. // If your study dataset is fully phased, you can replace the -g file // with a -known_haps_g file. This will cause IMPUTE2 to perform // haploid imputation, although it will still report diploid imputation // probabilities in the main output file. If any genotypes are missing, // they can be marked as '? ?' (two question marks separated by one // space) in the input file. (The program does not allow just one // allele from a diploid genotype to be missing.) If the reference // panels are also phased, IMPUTE2 will perform a single, fast // imputation step rather than its standard MCMC module this is how // the program imputes into pre-phased GWAS haplotypes. // The -known_haps_g file can also be used to specify study // genotypes that are "partially" phased, in the sense that some // genotypes are phased relative to a fixed reference point while // others are not. We anticipate that this will be most useful when // trying to phase resequencing data onto a scaffold of known // haplotypes. To mark a known genotype as unphased, place an // asterisk immediately after each allele, with no space between // the allele (0/1) and the asterisk (*); e.g., "0* 1*" for a // heterozygous genotype of unknown phase. int i, gt_id = bcf_hdr_id2int(convert->header, BCF_DT_ID, "GT"); if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,gt_id) ) error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1); if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT); bcf_fmt_t *fmt_gt = NULL; for (i=0; in_fmt; i++) if ( line->d.fmt[i].id==gt_id ) { fmt_gt = &line->d.fmt[i]; break; } if ( !fmt_gt ) error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1); // Alloc all memory in advance to avoid kput routines. The biggest allowed allele index is 99 if ( line->n_allele > 100 ) error("Too many alleles (%d) at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1); if ( ks_resize(str, str->l+convert->nsamples*8) != 0 ) error("Could not alloc %" PRIu64 " bytes\n", (uint64_t)(str->l + convert->nsamples*8)); if ( fmt_gt->type!=BCF_BT_INT8 ) // todo: use BRANCH_INT if the VCF is valid error("Uh, too many alleles (%d) or redundant BCF representation at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1); if ( fmt_gt->n!=1 && fmt_gt->n!=2 ) error("Uh, ploidy of %d not supported, see %s:%"PRId64"\n", fmt_gt->n, bcf_seqname(convert->header, line),(int64_t) line->pos+1); int8_t *ptr = ((int8_t*) fmt_gt->p) - fmt_gt->n; for (i=0; insamples; i++) { ptr += fmt_gt->n; if ( fmt_gt->n==1 ) // haploid genotypes { if ( ptr[0]==2 ) /* 0 */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' '; } else if ( ptr[0]==bcf_int8_missing ) /* . */ { str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' '; } else if ( ptr[0]==4 ) /* 1 */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' '; } else { kputw(bcf_gt_allele(ptr[0]),str); str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' '; } } else if ( ptr[0]==2 ) { if ( ptr[1]==3 ) /* 0|0 */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' '; } else if ( ptr[1]==5 ) /* 0|1 */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' '; } else if ( ptr[1]==bcf_int8_vector_end ) /* 0 */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' '; } else if ( ptr[1]==2 ) /* 0/0 */ { str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; } else if ( ptr[1]==4 ) /* 0/1 */ { str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; } else if ( bcf_gt_is_missing(ptr[1]) ) /* 0/. */ { str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' '; } else if ( bcf_gt_is_phased(ptr[1]) ) /* 0|x */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); str->s[str->l++] = ' '; } else /* 0/x */ { str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); str->s[str->l++] = '*'; str->s[str->l++] = ' '; } } else if ( ptr[0]==4 ) { if ( ptr[1]==3 ) /* 1|0 */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' '; } else if ( ptr[1]==5 ) /* 1|1 */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' '; } else if ( ptr[1]==bcf_int8_vector_end ) /* 1 */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' '; } else if ( ptr[1]==2 ) /* 1/0 */ { str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; } else if ( ptr[1]==4 ) /* 1/1 */ { str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; } else if ( bcf_gt_is_missing(ptr[1]) ) /* 1/. */ { str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' '; } else if ( bcf_gt_is_phased(ptr[1]) ) /* 1|x */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); str->s[str->l++] = ' '; } else /* 1/x */ { str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); str->s[str->l++] = '*'; str->s[str->l++] = ' '; } } else if ( bcf_gt_is_missing(ptr[0]) ) { if ( ptr[1]==bcf_int8_vector_end ) { str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' '; } else { str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' '; } } else if ( ptr[1]==bcf_int8_vector_end ) { /* use REF for something else than first ALT */ str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' '; } else { kputw(bcf_gt_allele(ptr[0]),str); if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*'; str->s[str->l++] = ' '; } } str->s[--str->l] = 0; // delete the last space } static void process_gt_to_hap2(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { // same as process_gt_to_hap but converts haploid genotypes into diploid int i, gt_id = bcf_hdr_id2int(convert->header, BCF_DT_ID, "GT"); if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,gt_id) ) error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1); if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT); bcf_fmt_t *fmt_gt = NULL; for (i=0; in_fmt; i++) if ( line->d.fmt[i].id==gt_id ) { fmt_gt = &line->d.fmt[i]; break; } if ( !fmt_gt ) error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1); // Alloc all memory in advance to avoid kput routines. The biggest allowed allele index is 99 if ( line->n_allele > 100 ) error("Too many alleles (%d) at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1); if ( ks_resize(str, str->l+convert->nsamples*8) != 0 ) error("Could not alloc %" PRIu64 " bytes\n", (uint64_t)(str->l + convert->nsamples*8)); if ( fmt_gt->type!=BCF_BT_INT8 ) // todo: use BRANCH_INT if the VCF is valid error("Uh, too many alleles (%d) or redundant BCF representation at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1); int8_t *ptr = ((int8_t*) fmt_gt->p) - fmt_gt->n; for (i=0; insamples; i++) { ptr += fmt_gt->n; if ( ptr[0]==2 ) { if ( ptr[1]==3 ) /* 0|0 */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' '; } else if ( ptr[1]==5 ) /* 0|1 */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' '; } else if ( ptr[1]==bcf_int8_vector_end ) /* 0 -> 0|0 */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' '; } else if ( ptr[1]==2 ) /* 0/0 */ { str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; } else if ( ptr[1]==4 ) /* 0/1 */ { str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; } else if ( bcf_gt_is_missing(ptr[1]) ) /* 0/. */ { str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' '; } else if ( bcf_gt_is_phased(ptr[1]) ) /* 0|x */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); str->s[str->l++] = ' '; } else /* 0/x */ { str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); str->s[str->l++] = '*'; str->s[str->l++] = ' '; } } else if ( ptr[0]==4 ) { if ( ptr[1]==3 ) /* 1|0 */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' '; } else if ( ptr[1]==5 ) /* 1|1 */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' '; } else if ( ptr[1]==bcf_int8_vector_end ) /* 1 -> 1|1 */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' '; } else if ( ptr[1]==2 ) /* 1/0 */ { str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; } else if ( ptr[1]==4 ) /* 1/1 */ { str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; } else if ( bcf_gt_is_missing(ptr[1]) ) /* 1/. */ { str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' '; } else if ( bcf_gt_is_phased(ptr[1]) ) /* 1|x */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); str->s[str->l++] = ' '; } else /* 1/x */ { str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); str->s[str->l++] = '*'; str->s[str->l++] = ' '; } } else if ( bcf_gt_is_missing(ptr[0]) ) { str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' '; } else if ( ptr[1]==bcf_int8_vector_end ) { /* use REF for something else than first ALT */ str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' '; } else { kputw(bcf_gt_allele(ptr[0]),str); if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*'; str->s[str->l++] = ' '; } } str->s[--str->l] = 0; // delete the last space } static void process_rsid_hex(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { char *ptr = line->d.id; ptr += 2; // remove 'rs' ksprintf(str, "%08" PRIx32 "", (uint32_t)strtoul(ptr, NULL, 10)); } static void process_variantkey_hex(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { const char *alt = NULL; size_t sizealt = 0; if ( line->n_allele>1 ) { alt = line->d.allele[1]; sizealt = strlen(line->d.allele[1]); } uint64_t vk = variantkey( convert->header->id[BCF_DT_CTG][line->rid].key, strlen(convert->header->id[BCF_DT_CTG][line->rid].key), line->pos, line->d.allele[0], strlen(line->d.allele[0]), alt, sizealt); ksprintf(str, "%016" PRIx64 "", vk); } static void process_npass(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int i, nsmpl = 0; filter_t *flt = (filter_t*) fmt->usr; const uint8_t *smpl; filter_test(flt,line,&smpl); for (i=0; insamples; i++) if ( smpl[i] ) nsmpl++; kputd(nsmpl, str); } static void destroy_npass(void *usr) { filter_destroy((filter_t*)usr); } static void process_pbinom(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int i; if ( !fmt->ready ) { fmt->fmt = NULL; // AD fmt->usr = NULL; // GT for (i=0; i<(int)line->n_fmt; i++) if ( line->d.fmt[i].id==fmt->id ) { fmt->fmt = &line->d.fmt[i]; break; } // Check that the first field is GT int gt_id = bcf_hdr_id2int(convert->header, BCF_DT_ID, "GT"); if ( !bcf_hdr_idinfo_exists(convert->header, BCF_HL_FMT, fmt->id) ) error("Error: FORMAT/GT is not defined in the header\n"); for (i=0; i<(int)line->n_fmt; i++) if ( line->d.fmt[i].id==gt_id ) { fmt->usr = &line->d.fmt[i]; break; } // it should always be first according to VCF spec, but... if ( fmt->usr && line->d.fmt[i].type!=BCF_BT_INT8 ) // skip sites with many alleles fmt->usr = NULL; fmt->ready = 1; } bcf_fmt_t *gt_fmt = (bcf_fmt_t*) fmt->usr; if ( !fmt->fmt || !gt_fmt || gt_fmt->n!=2 ) goto invalid; int n[2] = {0,0}; int8_t *gt = (int8_t*)(gt_fmt->p + isample*gt_fmt->size); for (i=0; i<2; i++) { if ( bcf_gt_is_missing(gt[i]) || gt[i] == bcf_int8_vector_end ) goto invalid; int al = bcf_gt_allele(gt[i]); if ( al > line->n_allele || al >= fmt->fmt->n ) goto invalid; #define BRANCH(type_t, convert, missing, vector_end) { \ type_t val = convert(&fmt->fmt->p[(al + isample*fmt->fmt->n)*sizeof(type_t)]); \ if ( val==missing || val==vector_end ) goto invalid; \ else n[i] = val; \ } switch (fmt->fmt->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, bcf_int8_missing, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, bcf_int16_missing, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, bcf_int32_missing, bcf_int32_vector_end); break; default: goto invalid; break; } #undef BRANCH } if ( n[0]==n[1] ) kputc(n[0]==0 ? '.':'0', str); else { double pval = calc_binom_two_sided(n[0],n[1],0.5); // convrt to phred if ( pval>=1 ) pval = 0; else pval = -4.34294481903*log(pval); kputd(pval, str); } return; invalid: kputc('.', str); } static void _used_tags_add(convert_t *convert, int type, char *key) { kstring_t str = {0,0,0}; ksprintf(&str,"%s/%s",type==T_INFO?"INFO":"FORMAT",key); khash_str2int_inc(convert->used_tags_hash,str.s); convert->nused_tags++; convert->used_tags_list = (char**)realloc(convert->used_tags_list,sizeof(*convert->used_tags_list)*convert->nused_tags); convert->used_tags_list[convert->nused_tags-1] = str.s; } #define _SET_NON_FORMAT_TAGS(function,key,...) \ if ( !strcmp("CHROM",key) ) { function(__VA_ARGS__, T_CHROM); } \ else if ( !strcmp("POS",key) ) { function(__VA_ARGS__, T_POS); } \ else if ( !strcmp("POS0",key) ) { function(__VA_ARGS__, T_POS0); } \ else if ( !strcmp("END",key) ) { function(__VA_ARGS__, T_END); } \ else if ( !strcmp("END0",key) ) { function(__VA_ARGS__, T_END0); } \ else if ( !strcmp("ID",key) ) { function(__VA_ARGS__, T_ID); } \ else if ( !strcmp("REF",key) ) { function(__VA_ARGS__, T_REF); } \ else if ( !strcmp("FIRST_ALT",key) ) { function(__VA_ARGS__, T_FIRST_ALT); } \ else if ( !strcmp("QUAL",key) ) { function(__VA_ARGS__, T_QUAL); } \ else if ( !strcmp("TYPE",key) ) { function(__VA_ARGS__, T_TYPE); } \ else if ( !strcmp("FILTER",key) ) { function(__VA_ARGS__, T_FILTER); } \ else if ( !strcmp("IS_TS",key) ) { function(__VA_ARGS__, T_IS_TS); } \ else if ( !strcmp("MASK",key) ) { function(__VA_ARGS__, T_MASK); } \ else if ( !strcmp("LINE",key) ) { function(__VA_ARGS__, T_LINE); } static void set_type(fmt_t *fmt, int type) { fmt->type = type; } static fmt_t *register_tag(convert_t *convert, char *key, int is_gtf, int type) { convert->nfmt++; if ( convert->nfmt > convert->mfmt ) { convert->mfmt += 10; convert->fmt = (fmt_t*) realloc(convert->fmt, convert->mfmt*sizeof(fmt_t)); } fmt_t *fmt = &convert->fmt[ convert->nfmt-1 ]; fmt->type = type; fmt->key = key ? strdup(key) : NULL; fmt->is_gt_field = is_gtf; fmt->subscript = -1; fmt->usr = NULL; fmt->destroy = NULL; // Allow non-format tags, such as CHROM, INFO, etc., to appear amongst the format tags. if ( key ) { int id = bcf_hdr_id2int(convert->header, BCF_DT_ID, key); if ( fmt->type==T_FORMAT && !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,id) ) { _SET_NON_FORMAT_TAGS(set_type,key,fmt) else if ( !strcmp("ALT",key) ) { fmt->type = T_ALT; } else if ( !strcmp("_CHROM_POS_ID",key) ) { fmt->type = T_CHROM_POS_ID; } else if ( !strcmp("RSX",key) ) { fmt->type = T_RSX; } else if ( !strcmp("VKX",key) ) { fmt->type = T_VKX; } else if ( id>=0 && bcf_hdr_idinfo_exists(convert->header,BCF_HL_INFO,id) ) { fmt->type = T_INFO; _used_tags_add(convert,T_INFO,key); } } else if ( fmt->type==T_PBINOM ) { fmt->id = bcf_hdr_id2int(convert->header, BCF_DT_ID, fmt->key); if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT, fmt->id) ) error("No such FORMAT tag defined in the header: %s\n", fmt->key); _used_tags_add(convert,T_FORMAT,key); } else if ( fmt->type==T_NPASS ) { filter_t *flt = filter_init(convert->header,key); convert->max_unpack |= filter_max_unpack(flt); fmt->usr = (void*) flt; } } switch (fmt->type) { case T_FIRST_ALT: fmt->handler = &process_first_alt; break; case T_CHROM_POS_ID: fmt->handler = &process_chrom_pos_id; break; case T_GT_TO_PROB3: fmt->handler = &process_gt_to_prob3; break; case T_PL_TO_PROB3: fmt->handler = &process_pl_to_prob3; break; case T_GP_TO_PROB3: fmt->handler = &process_gp_to_prob3; break; case T_CHROM: fmt->handler = &process_chrom; break; case T_POS: fmt->handler = &process_pos; break; case T_POS0: fmt->handler = &process_pos0; break; case T_END: fmt->handler = &process_end; convert->max_unpack |= BCF_UN_INFO; break; case T_END0: fmt->handler = &process_end0; convert->max_unpack |= BCF_UN_INFO; break; case T_ID: fmt->handler = &process_id; break; case T_REF: fmt->handler = &process_ref; break; case T_ALT: fmt->handler = &process_alt; break; case T_QUAL: fmt->handler = &process_qual; break; case T_FILTER: fmt->handler = &process_filter; convert->max_unpack |= BCF_UN_FLT; break; case T_INFO: fmt->handler = &process_info; convert->max_unpack |= BCF_UN_INFO; break; case T_FORMAT: fmt->handler = fmt->key ? &process_format : &process_complete_format; convert->max_unpack |= BCF_UN_FMT; break; case T_SAMPLE: fmt->handler = &process_sample; break; case T_SEP: fmt->handler = &process_sep; break; case T_IS_TS: fmt->handler = &process_is_ts; break; case T_TYPE: fmt->handler = &process_type; break; case T_MASK: fmt->handler = NULL; break; case T_GT: fmt->handler = &process_gt; convert->max_unpack |= BCF_UN_FMT; break; case T_TGT: fmt->handler = &process_tgt; convert->max_unpack |= BCF_UN_FMT; break; case T_IUPAC_GT: fmt->handler = &process_iupac_gt; convert->max_unpack |= BCF_UN_FMT; break; case T_GT_TO_HAP: fmt->handler = &process_gt_to_hap; convert->max_unpack |= BCF_UN_FMT; break; case T_GT_TO_HAP2: fmt->handler = &process_gt_to_hap2; convert->max_unpack |= BCF_UN_FMT; break; case T_TBCSQ: fmt->handler = &process_tbcsq; fmt->destroy = &destroy_tbcsq; convert->max_unpack |= BCF_UN_FMT; break; case T_LINE: fmt->handler = &process_line; convert->max_unpack |= BCF_UN_FMT; break; case T_RSX: fmt->handler = &process_rsid_hex; break; case T_VKX: fmt->handler = &process_variantkey_hex; break; case T_PBINOM: fmt->handler = &process_pbinom; convert->max_unpack |= BCF_UN_FMT; break; case T_NPASS: fmt->handler = &process_npass; fmt->destroy = &destroy_npass; break; default: error("TODO: handler for type %d\n", fmt->type); } if ( key && fmt->type==T_INFO ) { fmt->id = bcf_hdr_id2int(convert->header, BCF_DT_ID, key); if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_INFO,fmt->id) ) { fmt->id = -1; convert->undef_info_tag = strdup(key); } } return fmt; } static int parse_subscript(char **p) { char *q = *p; if ( *q!='{' ) return -1; q++; while ( *q && *q!='}' && isdigit(*q) ) q++; if ( *q!='}' ) return -1; int idx = atoi((*p)+1); *p = q+1; return idx; } static char *parse_tag(convert_t *convert, char *p, int is_gtf) { char *q = ++p; while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++; kstring_t str = {0,0,0}; if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str); kputsn(p, q-p, &str); if ( is_gtf ) { if ( !strcmp(str.s, "SAMPLE") ) register_tag(convert, "SAMPLE", is_gtf, T_SAMPLE); else if ( !strcmp(str.s, "GT") ) register_tag(convert, "GT", is_gtf, T_GT); else if ( !strcmp(str.s, "TGT") ) register_tag(convert, "GT", is_gtf, T_TGT); else if ( !strcmp(str.s, "TBCSQ") ) { fmt_t *fmt = register_tag(convert, "BCSQ", is_gtf, T_TBCSQ); fmt->subscript = parse_subscript(&q); if ( fmt->subscript==-1 ) { if ( !strncmp(q,"{*}",3) ) { fmt->subscript = 0; q += 3; } } else fmt->subscript++; } else if ( !strcmp(str.s, "IUPACGT") ) register_tag(convert, "GT", is_gtf, T_IUPAC_GT); else if ( !strcmp(str.s, "INFO") ) { if ( *q!='/' ) { int id = bcf_hdr_id2int(convert->header, BCF_DT_ID, str.s); if ( bcf_hdr_idinfo_exists(convert->header,BCF_HL_INFO,id) ) error("Could not parse format string \"%s\". Did you mean %%INFO/%s?\n", convert->format_str,str.s); else error("Could not parse format string: %s\n", convert->format_str); } p = ++q; str.l = 0; while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++; if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str); kputsn(p, q-p, &str); fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_INFO); fmt->subscript = parse_subscript(&q); _used_tags_add(convert,T_INFO,str.s); } else if ( !strcmp(str.s,"PBINOM") ) { if ( *q!='(' ) error("Could not parse the expression: %s\n", convert->format_str); p = ++q; str.l = 0; while ( *q && *q!=')' ) q++; if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str); kputsn(p, q-p, &str); register_tag(convert, str.s, is_gtf, T_PBINOM); q++; } else if ( !strcmp(str.s,"N_PASS") ) error("N_PASS() must be placed outside the square brackets\n"); else { fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_FORMAT); fmt->subscript = parse_subscript(&q); } } else { _SET_NON_FORMAT_TAGS(register_tag, str.s, convert, str.s, is_gtf) else if ( !strcmp(str.s, "ALT") ) { fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_ALT); fmt->subscript = parse_subscript(&q); } else if ( !strcmp(str.s, "_CHROM_POS_ID") ) register_tag(convert, str.s, is_gtf, T_CHROM_POS_ID); else if ( !strcmp(str.s, "_GT_TO_PROB3") ) register_tag(convert, str.s, is_gtf, T_GT_TO_PROB3); else if ( !strcmp(str.s, "_PL_TO_PROB3") ) register_tag(convert, str.s, is_gtf, T_PL_TO_PROB3); else if ( !strcmp(str.s, "_GP_TO_PROB3") ) register_tag(convert, str.s, is_gtf, T_GP_TO_PROB3); else if ( !strcmp(str.s, "_GT_TO_HAP") ) register_tag(convert, str.s, is_gtf, T_GT_TO_HAP); else if ( !strcmp(str.s, "_GT_TO_HAP2") ) register_tag(convert, str.s, is_gtf, T_GT_TO_HAP2); else if ( !strcmp(str.s, "RSX") ) register_tag(convert, str.s, is_gtf, T_RSX); else if ( !strcmp(str.s, "VKX") ) register_tag(convert, str.s, is_gtf, T_VKX); else if ( !strcmp(str.s,"PBINOM") ) error("Error: PBINOM() is currently supported only with FORMAT tags. (todo)\n"); else if ( !strcmp(str.s, "INFO") ) { if ( *q=='/' ) { p = ++q; str.l = 0; while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++; if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str); kputsn(p, q-p, &str); fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_INFO); fmt->subscript = parse_subscript(&q); _used_tags_add(convert,T_INFO,str.s); } else register_tag(convert, NULL, is_gtf, T_INFO); // the whole INFO } else if ( !strcmp(str.s, "FORMAT") ) register_tag(convert, NULL, 0, T_FORMAT); else if ( !strcmp(str.s,"N_PASS") ) { if ( *q!='(' ) error("Could not parse the expression: %s\n", convert->format_str); p = ++q; str.l = 0; int nopen = 1; while ( *q && nopen ) { if ( *q=='(' ) nopen++; else if ( *q==')' ) nopen--; q++; } if ( q-p==0 || nopen ) error("Could not parse format string: %s\n", convert->format_str); kputsn(p, q-p-1, &str); register_tag(convert, str.s, is_gtf, T_NPASS); } else { fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_INFO); fmt->subscript = parse_subscript(&q); _used_tags_add(convert,T_INFO,str.s); } } free(str.s); return q; } static char *parse_sep(convert_t *convert, char *p, int is_gtf) { char *q = p; kstring_t str = {0,0,0}; while ( *q && *q!='[' && *q!=']' && *q!='%' ) { if ( *q=='\\' ) { q++; if ( *q=='n' ) kputc('\n', &str); else if ( *q=='t' ) kputc('\t', &str); else kputc(*q, &str); } else kputc(*q, &str); q++; } if ( !str.l ) error("Could not parse format string: %s\n", convert->format_str); register_tag(convert, str.s, is_gtf, T_SEP); free(str.s); return q; } convert_t *convert_init(bcf_hdr_t *hdr, int *samples, int nsamples, const char *format_str) { convert_t *convert = (convert_t*) calloc(1,sizeof(convert_t)); convert->header = hdr; convert->format_str = strdup(format_str); convert->max_unpack = BCF_UN_STR; convert->used_tags_hash = khash_str2int_init(); int i, is_gtf = 0; char *p = convert->format_str; while ( *p ) { //fprintf(stderr,"<%s>\n", p); switch (*p) { case '[': is_gtf = 1; p++; break; case ']': is_gtf = 0; register_tag(convert, NULL, 0, T_SEP); p++; break; case '%': p = parse_tag(convert, p, is_gtf); break; default: p = parse_sep(convert, p, is_gtf); break; } } if ( is_gtf ) error("Could not parse the format string, missing the square bracket \"]\": %s\n", convert->format_str); if ( nsamples ) { convert->nsamples = nsamples; convert->samples = (int*) malloc(sizeof(int)*nsamples); for (i=0; insamples; i++) convert->samples[i] = samples[i]; } else { convert->nsamples = bcf_hdr_nsamples(convert->header); convert->samples = (int*) malloc(sizeof(int)*convert->nsamples); for (i=0; insamples; i++) convert->samples[i] = i; } return convert; } void convert_destroy(convert_t *convert) { int i; for (i=0; infmt; i++) { if ( convert->fmt[i].destroy ) convert->fmt[i].destroy(convert->fmt[i].usr); free(convert->fmt[i].key); } if ( convert->nused_tags ) { for (i=0; inused_tags; i++) free(convert->used_tags_list[i]); free(convert->used_tags_list); } khash_str2int_destroy(convert->used_tags_hash); free(convert->print_filtered); free(convert->fmt); free(convert->undef_info_tag); free(convert->dat); free(convert->samples); free(convert->format_str); free(convert); } int convert_header(convert_t *convert, kstring_t *str) { int i, icol = 0, l_ori = str->l; bcf_hdr_t *hdr = convert->header; // Suppress the header output if LINE is present for (i=0; infmt; i++) if ( convert->fmt[i].type == T_LINE ) break; if ( i!=convert->nfmt ) return str->l - l_ori; // Header formatting becomes problematic when the formatting expression contains a newline. // Simple cases like // -f'[%CHROM %POS %SAMPLE\n]' // can be handled quite easily with has_fmt_newline. Note this will not work if multiple newlines // are present. int has_fmt_newline = 0; kputc('#', str); for (i=0; infmt; i++) { // Genotype fields if ( convert->fmt[i].is_gt_field ) { int j = i, js, k; while ( convert->fmt[j].is_gt_field ) j++; for (js=0; jsnsamples; js++) { int ks = convert->samples[js]; for (k=i; kfmt[k].type == T_SEP ) { if ( convert->fmt[k].key ) { char *tmp = convert->fmt[k].key; while ( *tmp ) { if ( *tmp=='\n' ) has_fmt_newline = 1; else kputc(*tmp,str); tmp++; } } } else if ( convert->header_samples ) { icol++; if ( !convert->no_hdr_indices ) ksprintf(str,"[%d]",icol); ksprintf(str,"%s:%s", hdr->samples[ks], convert->fmt[k].key); } else { icol++; if ( !convert->no_hdr_indices ) ksprintf(str,"[%d]",icol); ksprintf(str,"%s", convert->fmt[k].key); } } if ( has_fmt_newline ) { if ( !convert->header_samples ) break; // this is unfortunate: the formatting expression breaks the per-sample output into separate lines, // therefore including a sample name in the header makes no sense anymore convert->header_samples = 0; str->l = l_ori; return convert_header(convert, str); } } i = j-1; continue; } // Fixed fields if ( convert->fmt[i].type == T_SEP ) { if ( convert->fmt[i].key ) kputs(convert->fmt[i].key, str); continue; } icol++; if ( !convert->no_hdr_indices ) ksprintf(str,"[%d]",icol); ksprintf(str,"%s", convert->fmt[i].key); } if ( has_fmt_newline ) kputc('\n',str); return str->l - l_ori; } int convert_line(convert_t *convert, bcf1_t *line, kstring_t *str) { if ( !convert->allow_undef_tags && convert->undef_info_tag ) { kstring_t msg = {0,0,0}; ksprintf(&msg,"Error: no such tag defined in the VCF header: INFO/%s", convert->undef_info_tag); int hdr_id = bcf_hdr_id2int(convert->header,BCF_DT_ID,convert->undef_info_tag); if ( hdr_id>=0 && bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,hdr_id) ) ksprintf(&msg,". FORMAT fields must be enclosed in square brackets, e.g. \"[ %%%s]\"", convert->undef_info_tag); error("%s\n", msg.s); } int l_ori = str->l; bcf_unpack(line, convert->max_unpack); int i, ir; str->l = 0; for (i=0; infmt; i++) { // Genotype fields. if ( convert->fmt[i].is_gt_field ) { int j = i, js, k; while ( jnfmt && convert->fmt[j].is_gt_field ) { convert->fmt[j].ready = 0; j++; } for (js=0; jsnsamples; js++) { // Skip samples when filtering was requested int ks = convert->samples[js]; if ( convert->subset_samples && *convert->subset_samples && !(*convert->subset_samples)[ks] ) { if ( !convert->print_filtered ) continue; for (k=i; kfmt[k].type==T_SEP ) convert->fmt[k].handler(convert, line, &convert->fmt[k], ks, str); else kputs(convert->print_filtered, str); continue; } // Here comes a hack designed for TBCSQ. When running on large files, // such as 1000GP, there are too many empty fields in the output and // it's very very slow. Therefore in case the handler does not add // anything to the string, we trim all genotype fields enclosed in square // brackets here. This may be changed in future, time will show... size_t l_start = str->l; for (k=i; kfmt[k].type == T_MASK ) { for (ir=0; irnreaders; ir++) kputc(bcf_sr_has_line(convert->readers,ir)?'1':'0', str); } else if ( convert->fmt[k].handler ) { size_t l = str->l; convert->fmt[k].handler(convert, line, &convert->fmt[k], ks, str); if ( l==str->l ) { str->l = l_start; break; } // only TBCSQ does this } } } i = j-1; continue; } // Fixed fields if ( convert->fmt[i].type == T_MASK ) { for (ir=0; irnreaders; ir++) kputc(bcf_sr_has_line(convert->readers,ir)?'1':'0', str); } else if ( convert->fmt[i].handler ) convert->fmt[i].handler(convert, line, &convert->fmt[i], -1, str); } return str->l - l_ori; } static void force_newline_(convert_t *convert) { int i, has_newline = 0; for (i=0; infmt; i++) { if ( !convert->fmt[i].key ) continue; char *tmp = convert->fmt[i].key; while (*tmp) { if ( *tmp=='\n' ) { has_newline = 1; break; } tmp++; } if ( has_newline ) break; } if ( has_newline ) return; // A newline is not present, force it. But where to add it? Always at the end. // // Briefly, in 1.18, we considered the following automatic behavior, which for // per-site output it would add it at the end of the expression and for per-sample // output it would add it inside the square brackets: // -f'%CHROM[ %SAMPLE]\n' // -f'[%CHROM %SAMPLE\n]' // // However, this is an annoyance for users, as it is not entirely clear what // will happen unless one understands the internals well (#1969) register_tag(convert, "\n", 0, T_SEP); } int convert_set_option(convert_t *convert, enum convert_option opt, ...) { int ret = 0; va_list args; va_start(args, opt); switch (opt) { case allow_undef_tags: convert->allow_undef_tags = va_arg(args, int); break; case subset_samples: convert->subset_samples = va_arg(args, uint8_t**); break; case header_samples: convert->header_samples = va_arg(args, int); break; case print_filtered: convert->print_filtered = strdup(va_arg(args, char*)); break; case force_newline: convert->force_newline = va_arg(args, int); if ( convert->force_newline ) force_newline_(convert); break; case no_hdr_indices: convert->no_hdr_indices = va_arg(args, int); break; default: ret = -1; } va_end(args); return ret; } int convert_max_unpack(convert_t *convert) { return convert->max_unpack; } int convert_is_tag_used(convert_t *convert, char *tag) { return khash_str2int_has_key(convert->used_tags_hash, tag); } const char **convert_list_used_tags(convert_t *convert, int *ntags) { *ntags = convert->nused_tags; return (const char **)convert->used_tags_list; } pysam-0.23.0/bcftools/convert.c.pysam.c000066400000000000000000002072331475062545500177610ustar00rootroot00000000000000#include "bcftools.pysam.h" /* convert.c -- functions for converting between VCF/BCF and related formats. Copyright (C) 2013-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #define __STDC_FORMAT_MACROS #include #include #include #include #include #include #include #include #include "bcftools.h" #include "variantkey.h" #include "convert.h" #include "filter.h" #define T_CHROM 1 #define T_POS 2 #define T_ID 3 #define T_REF 4 #define T_ALT 5 #define T_QUAL 6 #define T_FILTER 7 #define T_INFO 8 #define T_FORMAT 9 #define T_SAMPLE 10 #define T_SEP 11 #define T_IS_TS 12 #define T_TYPE 13 #define T_MASK 14 #define T_GT 15 #define T_TGT 16 #define T_LINE 17 #define T_CHROM_POS_ID 18 // not publicly advertised #define T_GT_TO_PROB3 19 // not publicly advertised #define T_PL_TO_PROB3 20 // not publicly advertised #define T_GP_TO_PROB3 21 // not publicly advertised #define T_FIRST_ALT 22 // not publicly advertised #define T_IUPAC_GT 23 #define T_GT_TO_HAP 24 // not publicly advertised #define T_GT_TO_HAP2 25 // not publicly advertised #define T_TBCSQ 26 #define T_END 27 #define T_POS0 28 #define T_END0 29 #define T_RSX 30 // RSID HEX #define T_VKX 31 // VARIANTKEY HEX #define T_PBINOM 32 #define T_NPASS 33 typedef struct _fmt_t { int type, id, is_gt_field, ready, subscript; char *key; bcf_fmt_t *fmt; void *usr; // user data (optional) void (*handler)(convert_t *, bcf1_t *, struct _fmt_t *, int, kstring_t *); void (*destroy)(void*); // clean user data (optional) } fmt_t; struct _convert_t { fmt_t *fmt; int nfmt, mfmt; int nsamples, *samples; bcf_hdr_t *header; int max_unpack; char *format_str; bcf_srs_t *readers; // required only for %MASK int nreaders; void *dat; int ndat; char *undef_info_tag; void *used_tags_hash; char **used_tags_list; char *print_filtered; int nused_tags; int allow_undef_tags; int force_newline; int header_samples; int no_hdr_indices; uint8_t **subset_samples; }; typedef struct { kstring_t hap1,hap2; char **str; int n, m; } bcsq_t; static void process_chrom(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(convert->header->id[BCF_DT_CTG][line->rid].key, str); } static void process_pos(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos+1, str); } static void process_pos0(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos, str); } static void process_end(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos+line->rlen, str); } static void process_end0(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos+line->rlen-1, str); } static void process_id(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(line->d.id, str); } static void process_ref(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(line->d.allele[0], str); } static void process_alt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int i; if ( line->n_allele==1 ) { kputc('.', str); return; } if ( fmt->subscript>=0 ) { if ( line->n_allele > fmt->subscript+1 ) kputs(line->d.allele[fmt->subscript+1], str); else kputc('.', str); return; } for (i=1; in_allele; i++) { if ( i>1 ) kputc(',', str); kputs(line->d.allele[i], str); } } static void process_first_alt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( line->n_allele==1 ) kputc('.', str); else kputs(line->d.allele[1], str); } static void process_qual(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( bcf_float_is_missing(line->qual) ) kputc('.', str); else kputd(line->qual, str); } static void process_filter(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int i; if ( line->d.n_flt ) { for (i=0; id.n_flt; i++) { if (i) kputc(';', str); kputs(convert->header->id[BCF_DT_ID][line->d.flt[i]].key, str); } } else kputc('.', str); } static inline int32_t bcf_array_ivalue(uint8_t *bcf_array, int type, int idx) { if ( type==BCF_BT_INT8 ) { int8_t val = le_to_i8(&bcf_array[idx * sizeof(val)]); if ( val==bcf_int8_missing ) return bcf_int32_missing; if ( val==bcf_int8_vector_end ) return bcf_int32_vector_end; return val; } if ( type==BCF_BT_INT16 ) { int16_t val = le_to_i16(&bcf_array[idx * sizeof(val)]); if ( val==bcf_int16_missing ) return bcf_int32_missing; if ( val==bcf_int16_vector_end ) return bcf_int32_vector_end; return val; } return le_to_i32(&bcf_array[idx * sizeof(int32_t)]); } static inline void _copy_field(char *src, uint32_t len, int idx, kstring_t *str) { int n = 0, ibeg = 0; while ( src[ibeg] && ibegibeg ) kputsn(src+ibeg, iend-ibeg, str); else kputc('.', str); } static void process_info(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int i; if ( !fmt->key ) // the whole INFO column { int first = 1; for (i=0; in_info; i++) { bcf_info_t *inf = &line->d.info[i]; if ( !inf->vptr ) continue; if ( !first ) kputc(';', str); first = 0; if ( inf->key >= convert->header->n[BCF_DT_ID] ) continue; kputs(convert->header->id[BCF_DT_ID][inf->key].key, str); if ( inf->len <= 0 ) continue; kputc('=', str); if ( inf->len == 1 ) { switch (inf->type) { case BCF_BT_INT8: if ( inf->v1.i==bcf_int8_missing ) kputc('.', str); else kputw(inf->v1.i, str); break; case BCF_BT_INT16: if ( inf->v1.i==bcf_int16_missing ) kputc('.', str); else kputw(inf->v1.i, str); break; case BCF_BT_INT32: if ( inf->v1.i==bcf_int32_missing ) kputc('.', str); else kputw(inf->v1.i, str); break; case BCF_BT_FLOAT: if ( bcf_float_is_missing(inf->v1.f) ) kputc('.', str); else kputd(inf->v1.f, str); break; case BCF_BT_CHAR: kputc(inf->v1.i, str); break; default: error("Unexpected type %d", inf->type); break; } } else bcf_fmt_array(str, inf->len, inf->type, inf->vptr); } if ( first ) kputc('.', str); return; } if ( fmt->id<0 ) { kputc('.', str); return; } for (i=0; in_info; i++) if ( line->d.info[i].key == fmt->id ) break; // output "." if the tag is not present if ( i==line->n_info ) { kputc('.', str); return; } bcf_info_t *info = &line->d.info[i]; // if this is a flag, output 1 if ( info->len <=0 ) { kputc('1', str); return; } if ( info->len == 1 ) { switch (info->type) { case BCF_BT_INT8: if ( info->v1.i==bcf_int8_missing ) kputc('.', str); else kputw(info->v1.i, str); break; case BCF_BT_INT16: if ( info->v1.i==bcf_int16_missing ) kputc('.', str); else kputw(info->v1.i, str); break; case BCF_BT_INT32: if ( info->v1.i==bcf_int32_missing ) kputc('.', str); else kputw(info->v1.i, str); break; case BCF_BT_FLOAT: if ( bcf_float_is_missing(info->v1.f) ) kputc('.', str); else kputd(info->v1.f, str); break; case BCF_BT_CHAR: kputc(info->v1.i, str); break; default: fprintf(bcftools_stderr,"todo: type %d\n", info->type); bcftools_exit(1); break; } } else if ( fmt->subscript >=0 ) { if ( info->len <= fmt->subscript ) { kputc('.', str); return; } #define BRANCH(type_t, convert, is_missing, is_vector_end, kprint) { \ type_t val = convert(&info->vptr[fmt->subscript * sizeof(type_t)]); \ if ( is_missing || is_vector_end ) kputc('.',str); \ else kprint; \ } switch (info->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, kputw(val, str)); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, kputw(val, str)); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, val==bcf_int32_missing, val==bcf_int32_vector_end, kputw(val, str)); break; case BCF_BT_FLOAT: BRANCH(float, le_to_float, bcf_float_is_missing(val), bcf_float_is_vector_end(val), kputd(val, str)); break; case BCF_BT_CHAR: _copy_field((char*)info->vptr, info->vptr_len, fmt->subscript, str); break; default: fprintf(bcftools_stderr,"todo: type %d\n", info->type); bcftools_exit(1); break; } #undef BRANCH } else bcf_fmt_array(str, info->len, info->type, info->vptr); } static void init_format(convert_t *convert, bcf1_t *line, fmt_t *fmt) { fmt->id = bcf_hdr_id2int(convert->header, BCF_DT_ID, fmt->key); if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,fmt->id) ) fmt->id = -1; fmt->fmt = NULL; if ( fmt->id >= 0 ) { int i; for (i=0; i<(int)line->n_fmt; i++) if ( line->d.fmt[i].id==fmt->id ) { fmt->fmt = &line->d.fmt[i]; break; } } else if ( !convert->allow_undef_tags ) error("Error: no such tag defined in the VCF header: FORMAT/%s\n", fmt->key); fmt->ready = 1; } static void process_complete_format(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( convert->nsamples ) { int i,j; if ( line->n_fmt) { int gt_i = -1; bcf_fmt_t *fmt = line->d.fmt; int first = 1; for (i=0; i<(int)line->n_fmt; i++) { if ( !fmt[i].p || fmt[i].id<0 ) continue; if ( !first ) kputc(':', str); first = 0; kputs(convert->header->id[BCF_DT_ID][fmt[i].id].key, str); if ( strcmp(convert->header->id[BCF_DT_ID][fmt[i].id].key, "GT") == 0) gt_i = i; } if ( first ) kputc('.', str); for (j=0; jnsamples; j++) { kputc('\t', str); first = 1; for (i=0; i<(int)line->n_fmt; i++) { bcf_fmt_t *f = &fmt[i]; if ( !f->p ) continue; if ( !first ) kputc(':', str); first = 0; if (gt_i == i) bcf_format_gt(f,convert->samples[j],str); else bcf_fmt_array(str, f->n, f->type, f->p + convert->samples[j] * f->size); } if ( first ) kputc('.', str); } } else for (j=0; j<=line->n_sample; j++) kputs("\t.", str); } else kputc('.',str); } static void process_format(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( !fmt->ready ) init_format(convert, line, fmt); if ( fmt->fmt==NULL ) { kputc('.', str); return; } else if ( fmt->subscript >=0 ) { if ( fmt->fmt->n <= fmt->subscript ) { kputc('.', str); return; } if ( fmt->fmt->type == BCF_BT_FLOAT ) { uint8_t *ptr = fmt->fmt->p + isample*fmt->fmt->size; float val = le_to_float(&ptr[fmt->subscript * sizeof(float)]); if ( bcf_float_is_missing(val) || bcf_float_is_vector_end(val) ) kputc('.', str); else kputd(val, str); } else if ( fmt->fmt->type != BCF_BT_CHAR ) { int32_t ival = bcf_array_ivalue(fmt->fmt->p+isample*fmt->fmt->size,fmt->fmt->type,fmt->subscript); if ( ival==bcf_int32_missing || ival==bcf_int32_vector_end ) kputc('.', str); else kputw(ival, str); } else if ( fmt->fmt->type == BCF_BT_CHAR ) _copy_field((char*)(fmt->fmt->p + isample*fmt->fmt->size), fmt->fmt->size, fmt->subscript, str); else error("TODO: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt->fmt->type); } else bcf_fmt_array(str, fmt->fmt->n, fmt->fmt->type, fmt->fmt->p + isample*fmt->fmt->size); } static void process_gt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( !fmt->ready ) init_format(convert, line, fmt); if ( fmt->fmt==NULL ) { kputc('.', str); return; } bcf_format_gt(fmt->fmt, isample, str); } static void process_tgt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( !fmt->ready ) init_format(convert, line, fmt); if ( fmt->fmt==NULL ) { kputc('.', str); return; } assert( fmt->fmt->type==BCF_BT_INT8 ); int l; int8_t *x = (int8_t*)(fmt->fmt->p + isample*fmt->fmt->size); // FIXME: does not work with n_alt >= 64 for (l = 0; l < fmt->fmt->n && x[l] != bcf_int8_vector_end; ++l) { if (l) kputc("/|"[x[l]&1], str); if (x[l]>>1) { int ial = (x[l]>>1) - 1; kputs(line->d.allele[ial], str); } else kputc('.', str); } if (l == 0) kputc('.', str); } static void destroy_tbcsq(void *usr) { if ( !usr ) return; bcsq_t *csq = (bcsq_t*) usr; free(csq->hap1.s); free(csq->hap2.s); if ( csq->n ) free(csq->str[0]); free(csq->str); free(csq); } static void process_tbcsq(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( !fmt->ready ) { init_format(convert, line, fmt); bcsq_t *csq; if ( fmt->usr ) { csq = (bcsq_t*) fmt->usr; if ( csq->n ) free(csq->str[0]); csq->n = 0; } else csq = (bcsq_t*) calloc(1,sizeof(bcsq_t)); fmt->usr = csq; int i=0, len = 0; char *tmp = NULL; if ( bcf_get_info_string(convert->header,line,fmt->key,&tmp,&len)<0 ) { csq->n = 0; return; } do { csq->n++; hts_expand(char*, csq->n, csq->m, csq->str); csq->str[ csq->n-1 ] = tmp + i; while ( iusr; if ( fmt->fmt==NULL || !csq->n ) return; csq->hap1.l = 0; csq->hap2.l = 0; int mask = fmt->subscript==0 ? 3 : 1; // merge both haplotypes if subscript==0 #define BRANCH(type_t, convert, nbits) { \ uint8_t *x = fmt->fmt->p + isample*fmt->fmt->size; \ int i,j; \ if ( fmt->subscript<=0 || fmt->subscript==1 ) \ { \ for (j=0; j < fmt->fmt->n; j++) \ { \ type_t val = convert(&x[j * sizeof(type_t)]); \ if ( !val ) continue; \ for (i=0; istr[(j*30+i)/2], &csq->hap1); kputc_(',', &csq->hap1); } \ } \ } \ if ( fmt->subscript<0 || fmt->subscript==2 ) \ { \ for (j=0; j < fmt->fmt->n; j++) \ { \ type_t val = convert(&x[j * sizeof(type_t)]); \ if ( !val ) continue; \ for (i=1; istr[(j*30+i)/2], &csq->hap2); kputc_(',', &csq->hap2); } \ } \ } \ } switch (fmt->fmt->type) { case BCF_BT_INT8: BRANCH(uint8_t, le_to_u8, 8); break; case BCF_BT_INT16: BRANCH(uint16_t, le_to_u16, 16); break; case BCF_BT_INT32: BRANCH(uint32_t, le_to_u32, 30); break; // 2 bits unused to account for the reserved BCF values default: error("Unexpected type: %d\n", fmt->fmt->type); bcftools_exit(1); break; } #undef BRANCH if ( !csq->hap1.l && !csq->hap2.l ) return; if ( csq->hap1.l ) csq->hap1.s[--csq->hap1.l] = 0; if ( csq->hap2.l ) csq->hap2.s[--csq->hap2.l] = 0; if ( fmt->subscript<0 ) { kputs(csq->hap1.l?csq->hap1.s:".", str); kputc_('\t', str); kputs(csq->hap2.l?csq->hap2.s:".", str); } else if ( fmt->subscript<2 ) kputs(csq->hap1.l?csq->hap1.s:".", str); else kputs(csq->hap2.l?csq->hap2.s:".", str); } static void init_format_iupac(convert_t *convert, bcf1_t *line, fmt_t *fmt) { init_format(convert, line, fmt); if ( fmt->fmt==NULL ) return; // Init mapping between alleles and IUPAC table hts_expand(uint8_t, line->n_allele, convert->ndat, convert->dat); int8_t *dat = (int8_t*)convert->dat; int i; for (i=0; in_allele; i++) { if ( line->d.allele[i][1] ) dat[i] = -1; else { switch (line->d.allele[i][0]) { case 'A': dat[i] = 0; break; case 'C': dat[i] = 1; break; case 'G': dat[i] = 2; break; case 'T': dat[i] = 3; break; case 'a': dat[i] = 0; break; case 'c': dat[i] = 1; break; case 'g': dat[i] = 2; break; case 't': dat[i] = 3; break; default: dat[i] = -1; } } } } static void process_iupac_gt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( !fmt->ready ) init_format_iupac(convert, line, fmt); if ( fmt->fmt==NULL ) { kputc('.', str); return; } assert( fmt->fmt->type==BCF_BT_INT8 ); static const char iupac[4][4] = { {'A','M','R','W'},{'M','C','S','Y'},{'R','S','G','K'},{'W','Y','K','T'} }; int8_t *dat = (int8_t*)convert->dat; int8_t *x = (int8_t*)(fmt->fmt->p + isample*fmt->fmt->size); // FIXME: does not work with n_alt >= 64 int l = 0; while ( lfmt->n && x[l]!=bcf_int8_vector_end && x[l]!=bcf_int8_missing ) l++; if ( l==2 ) { // diploid int ia = (x[0]>>1) - 1, ib = (x[1]>>1) - 1; if ( ia>=0 && ian_allele && ib>=0 && ibn_allele && dat[ia]>=0 && dat[ib]>=0 ) { kputc(iupac[dat[ia]][dat[ib]], str); return; } } for (l = 0; l < fmt->fmt->n && x[l] != bcf_int8_vector_end; ++l) { if (l) kputc("/|"[x[l]&1], str); if (x[l]>>1) { int ial = (x[l]>>1) - 1; kputs(line->d.allele[ial], str); } else kputc('.', str); } if (l == 0) kputc('.', str); } static void process_sample(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(convert->header->samples[isample], str); } static void process_sep(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if (fmt->key) kputs(fmt->key, str); } static void process_is_ts(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int is_ts = 0; if ( bcf_get_variant_types(line) & (VCF_SNP|VCF_MNP) ) is_ts = abs(bcf_acgt2int(*line->d.allele[0])-bcf_acgt2int(*line->d.allele[1])) == 2 ? 1 : 0; kputc(is_ts ? '1' : '0', str); } static void process_type(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int line_type = bcf_get_variant_types(line); int i = 0; if ( line_type == VCF_REF ) { kputs("REF", str); i++; } if ( line_type & VCF_SNP ) { if (i) kputc(',',str); kputs("SNP", str); i++; } if ( line_type & VCF_MNP ) { if (i) kputc(',',str); kputs("MNP", str); i++; } if ( line_type & VCF_INDEL ) { if (i) kputc(',',str); kputs("INDEL", str); i++; } if ( line_type & VCF_OTHER ) { if (i) kputc(',',str); kputs("OTHER", str); i++; } if ( line_type & VCF_BND ) { if (i) kputc(',',str); kputs("BND", str); i++; } if ( line_type & VCF_OVERLAP ) { if (i) kputc(',',str); kputs("OVERLAP", str); i++; } } static void process_line(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { vcf_format1(convert->header, line, str); if ( str->s[str->l-1]=='\n' ) str->l--; } static void process_chrom_pos_id(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if ( line->d.id[0]!='.' || line->d.id[1] ) { // ID is present kputs(line->d.id, str); } else { // use CHROM:POS instead of ID kputs(convert->header->id[BCF_DT_CTG][line->rid].key, str); kputc(':', str); kputw(line->pos+1, str); } } static void process_gt_to_prob3(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int m,n,i; m = convert->ndat / sizeof(int32_t); n = bcf_get_genotypes(convert->header,line,&convert->dat,&m); convert->ndat = m * sizeof(int32_t); if ( n<=0 ) { // Throw an error or silently proceed? // // for (i=0; insamples; i++) kputs(" 0.33 0.33 0.33", str); // return; error("Error parsing GT tag at %s:%"PRId64"\n", bcf_seqname(convert->header,line),(int64_t) line->pos+1); } n /= convert->nsamples; for (i=0; insamples; i++) { int32_t *ptr = (int32_t*)convert->dat + i*n; int j; for (j=0; jndat / sizeof(int32_t); n = bcf_get_format_int32(convert->header,line,"PL",&convert->dat,&m); convert->ndat = m * sizeof(int32_t); if ( n<=0 ) { // Throw an error or silently proceed? // // for (i=0; insamples; i++) kputs(" 0.33 0.33 0.33", str); // return; error("Error parsing PL tag at %s:%"PRId64"\n", bcf_seqname(convert->header,line),(int64_t) line->pos+1); } n /= convert->nsamples; for (i=0; insamples; i++) { int32_t *ptr = (int32_t*)convert->dat + i*n; int j; float sum = 0; for (j=0; jn_allele ) { // haploid kputc(' ',str); ksprintf(str,"%f",pow(10,-0.1*ptr[0])/sum); kputs(" 0 ", str); ksprintf(str,"%f",pow(10,-0.1*ptr[1])/sum); } else { // diploid kputc(' ',str); ksprintf(str,"%f",pow(10,-0.1*ptr[0])/sum); kputc(' ',str); ksprintf(str,"%f",pow(10,-0.1*ptr[1])/sum); kputc(' ',str); ksprintf(str,"%f",pow(10,-0.1*ptr[2])/sum); } } } static void process_gp_to_prob3(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int m,n,i; m = convert->ndat / sizeof(float); n = bcf_get_format_float(convert->header,line,"GP",&convert->dat,&m); convert->ndat = m * sizeof(float); if ( n<=0 ) { // Throw an error or silently proceed? // // for (i=0; insamples; i++) kputs(" 0.33 0.33 0.33", str); // return; error("Error parsing GP tag at %s:%"PRId64"\n", bcf_seqname(convert->header,line),(int64_t) line->pos+1); } n /= convert->nsamples; for (i=0; insamples; i++) { float *ptr = (float*)convert->dat + i*n; int j; for (j=0; j1 ) error("[%s:%"PRId64":%f] GP value outside range [0,1]; bcftools convert expects the VCF4.3+ spec for the GP field encoding genotype posterior probabilities", bcf_seqname(convert->header,line),(int64_t) line->pos+1,ptr[j]); } if ( j==line->n_allele ) ksprintf(str," %f %f %f",ptr[0],0.,ptr[1]); // haploid else ksprintf(str," %f %f %f",ptr[0],ptr[1],ptr[2]); // diploid } } static void process_gt_to_hap(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { // https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#-known_haps_g // File containing known haplotypes for the study cohort. The format // is the same as the output format from IMPUTE2's -phase option: // five header columns (as in the -g file) followed by two columns // (haplotypes) per individual. Allowed values in the haplotype // columns are 0, 1, and ?. // If your study dataset is fully phased, you can replace the -g file // with a -known_haps_g file. This will cause IMPUTE2 to perform // haploid imputation, although it will still report diploid imputation // probabilities in the main output file. If any genotypes are missing, // they can be marked as '? ?' (two question marks separated by one // space) in the input file. (The program does not allow just one // allele from a diploid genotype to be missing.) If the reference // panels are also phased, IMPUTE2 will perform a single, fast // imputation step rather than its standard MCMC module this is how // the program imputes into pre-phased GWAS haplotypes. // The -known_haps_g file can also be used to specify study // genotypes that are "partially" phased, in the sense that some // genotypes are phased relative to a fixed reference point while // others are not. We anticipate that this will be most useful when // trying to phase resequencing data onto a scaffold of known // haplotypes. To mark a known genotype as unphased, place an // asterisk immediately after each allele, with no space between // the allele (0/1) and the asterisk (*); e.g., "0* 1*" for a // heterozygous genotype of unknown phase. int i, gt_id = bcf_hdr_id2int(convert->header, BCF_DT_ID, "GT"); if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,gt_id) ) error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1); if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT); bcf_fmt_t *fmt_gt = NULL; for (i=0; in_fmt; i++) if ( line->d.fmt[i].id==gt_id ) { fmt_gt = &line->d.fmt[i]; break; } if ( !fmt_gt ) error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1); // Alloc all memory in advance to avoid kput routines. The biggest allowed allele index is 99 if ( line->n_allele > 100 ) error("Too many alleles (%d) at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1); if ( ks_resize(str, str->l+convert->nsamples*8) != 0 ) error("Could not alloc %" PRIu64 " bytes\n", (uint64_t)(str->l + convert->nsamples*8)); if ( fmt_gt->type!=BCF_BT_INT8 ) // todo: use BRANCH_INT if the VCF is valid error("Uh, too many alleles (%d) or redundant BCF representation at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1); if ( fmt_gt->n!=1 && fmt_gt->n!=2 ) error("Uh, ploidy of %d not supported, see %s:%"PRId64"\n", fmt_gt->n, bcf_seqname(convert->header, line),(int64_t) line->pos+1); int8_t *ptr = ((int8_t*) fmt_gt->p) - fmt_gt->n; for (i=0; insamples; i++) { ptr += fmt_gt->n; if ( fmt_gt->n==1 ) // haploid genotypes { if ( ptr[0]==2 ) /* 0 */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' '; } else if ( ptr[0]==bcf_int8_missing ) /* . */ { str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' '; } else if ( ptr[0]==4 ) /* 1 */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' '; } else { kputw(bcf_gt_allele(ptr[0]),str); str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' '; } } else if ( ptr[0]==2 ) { if ( ptr[1]==3 ) /* 0|0 */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' '; } else if ( ptr[1]==5 ) /* 0|1 */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' '; } else if ( ptr[1]==bcf_int8_vector_end ) /* 0 */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' '; } else if ( ptr[1]==2 ) /* 0/0 */ { str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; } else if ( ptr[1]==4 ) /* 0/1 */ { str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; } else if ( bcf_gt_is_missing(ptr[1]) ) /* 0/. */ { str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' '; } else if ( bcf_gt_is_phased(ptr[1]) ) /* 0|x */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); str->s[str->l++] = ' '; } else /* 0/x */ { str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); str->s[str->l++] = '*'; str->s[str->l++] = ' '; } } else if ( ptr[0]==4 ) { if ( ptr[1]==3 ) /* 1|0 */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' '; } else if ( ptr[1]==5 ) /* 1|1 */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' '; } else if ( ptr[1]==bcf_int8_vector_end ) /* 1 */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' '; } else if ( ptr[1]==2 ) /* 1/0 */ { str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; } else if ( ptr[1]==4 ) /* 1/1 */ { str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; } else if ( bcf_gt_is_missing(ptr[1]) ) /* 1/. */ { str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' '; } else if ( bcf_gt_is_phased(ptr[1]) ) /* 1|x */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); str->s[str->l++] = ' '; } else /* 1/x */ { str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); str->s[str->l++] = '*'; str->s[str->l++] = ' '; } } else if ( bcf_gt_is_missing(ptr[0]) ) { if ( ptr[1]==bcf_int8_vector_end ) { str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' '; } else { str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' '; } } else if ( ptr[1]==bcf_int8_vector_end ) { /* use REF for something else than first ALT */ str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' '; } else { kputw(bcf_gt_allele(ptr[0]),str); if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*'; str->s[str->l++] = ' '; } } str->s[--str->l] = 0; // delete the last space } static void process_gt_to_hap2(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { // same as process_gt_to_hap but converts haploid genotypes into diploid int i, gt_id = bcf_hdr_id2int(convert->header, BCF_DT_ID, "GT"); if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,gt_id) ) error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1); if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT); bcf_fmt_t *fmt_gt = NULL; for (i=0; in_fmt; i++) if ( line->d.fmt[i].id==gt_id ) { fmt_gt = &line->d.fmt[i]; break; } if ( !fmt_gt ) error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1); // Alloc all memory in advance to avoid kput routines. The biggest allowed allele index is 99 if ( line->n_allele > 100 ) error("Too many alleles (%d) at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1); if ( ks_resize(str, str->l+convert->nsamples*8) != 0 ) error("Could not alloc %" PRIu64 " bytes\n", (uint64_t)(str->l + convert->nsamples*8)); if ( fmt_gt->type!=BCF_BT_INT8 ) // todo: use BRANCH_INT if the VCF is valid error("Uh, too many alleles (%d) or redundant BCF representation at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1); int8_t *ptr = ((int8_t*) fmt_gt->p) - fmt_gt->n; for (i=0; insamples; i++) { ptr += fmt_gt->n; if ( ptr[0]==2 ) { if ( ptr[1]==3 ) /* 0|0 */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' '; } else if ( ptr[1]==5 ) /* 0|1 */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' '; } else if ( ptr[1]==bcf_int8_vector_end ) /* 0 -> 0|0 */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' '; } else if ( ptr[1]==2 ) /* 0/0 */ { str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; } else if ( ptr[1]==4 ) /* 0/1 */ { str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; } else if ( bcf_gt_is_missing(ptr[1]) ) /* 0/. */ { str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' '; } else if ( bcf_gt_is_phased(ptr[1]) ) /* 0|x */ { str->s[str->l++] = '0'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); str->s[str->l++] = ' '; } else /* 0/x */ { str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); str->s[str->l++] = '*'; str->s[str->l++] = ' '; } } else if ( ptr[0]==4 ) { if ( ptr[1]==3 ) /* 1|0 */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' '; } else if ( ptr[1]==5 ) /* 1|1 */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' '; } else if ( ptr[1]==bcf_int8_vector_end ) /* 1 -> 1|1 */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' '; } else if ( ptr[1]==2 ) /* 1/0 */ { str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; } else if ( ptr[1]==4 ) /* 1/1 */ { str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; } else if ( bcf_gt_is_missing(ptr[1]) ) /* 1/. */ { str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' '; } else if ( bcf_gt_is_phased(ptr[1]) ) /* 1|x */ { str->s[str->l++] = '1'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); str->s[str->l++] = ' '; } else /* 1/x */ { str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); str->s[str->l++] = '*'; str->s[str->l++] = ' '; } } else if ( bcf_gt_is_missing(ptr[0]) ) { str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' '; } else if ( ptr[1]==bcf_int8_vector_end ) { /* use REF for something else than first ALT */ str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' '; } else { kputw(bcf_gt_allele(ptr[0]),str); if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*'; str->s[str->l++] = ' '; kputw(bcf_gt_allele(ptr[1]),str); if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*'; str->s[str->l++] = ' '; } } str->s[--str->l] = 0; // delete the last space } static void process_rsid_hex(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { char *ptr = line->d.id; ptr += 2; // remove 'rs' ksprintf(str, "%08" PRIx32 "", (uint32_t)strtoul(ptr, NULL, 10)); } static void process_variantkey_hex(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { const char *alt = NULL; size_t sizealt = 0; if ( line->n_allele>1 ) { alt = line->d.allele[1]; sizealt = strlen(line->d.allele[1]); } uint64_t vk = variantkey( convert->header->id[BCF_DT_CTG][line->rid].key, strlen(convert->header->id[BCF_DT_CTG][line->rid].key), line->pos, line->d.allele[0], strlen(line->d.allele[0]), alt, sizealt); ksprintf(str, "%016" PRIx64 "", vk); } static void process_npass(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int i, nsmpl = 0; filter_t *flt = (filter_t*) fmt->usr; const uint8_t *smpl; filter_test(flt,line,&smpl); for (i=0; insamples; i++) if ( smpl[i] ) nsmpl++; kputd(nsmpl, str); } static void destroy_npass(void *usr) { filter_destroy((filter_t*)usr); } static void process_pbinom(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { int i; if ( !fmt->ready ) { fmt->fmt = NULL; // AD fmt->usr = NULL; // GT for (i=0; i<(int)line->n_fmt; i++) if ( line->d.fmt[i].id==fmt->id ) { fmt->fmt = &line->d.fmt[i]; break; } // Check that the first field is GT int gt_id = bcf_hdr_id2int(convert->header, BCF_DT_ID, "GT"); if ( !bcf_hdr_idinfo_exists(convert->header, BCF_HL_FMT, fmt->id) ) error("Error: FORMAT/GT is not defined in the header\n"); for (i=0; i<(int)line->n_fmt; i++) if ( line->d.fmt[i].id==gt_id ) { fmt->usr = &line->d.fmt[i]; break; } // it should always be first according to VCF spec, but... if ( fmt->usr && line->d.fmt[i].type!=BCF_BT_INT8 ) // skip sites with many alleles fmt->usr = NULL; fmt->ready = 1; } bcf_fmt_t *gt_fmt = (bcf_fmt_t*) fmt->usr; if ( !fmt->fmt || !gt_fmt || gt_fmt->n!=2 ) goto invalid; int n[2] = {0,0}; int8_t *gt = (int8_t*)(gt_fmt->p + isample*gt_fmt->size); for (i=0; i<2; i++) { if ( bcf_gt_is_missing(gt[i]) || gt[i] == bcf_int8_vector_end ) goto invalid; int al = bcf_gt_allele(gt[i]); if ( al > line->n_allele || al >= fmt->fmt->n ) goto invalid; #define BRANCH(type_t, convert, missing, vector_end) { \ type_t val = convert(&fmt->fmt->p[(al + isample*fmt->fmt->n)*sizeof(type_t)]); \ if ( val==missing || val==vector_end ) goto invalid; \ else n[i] = val; \ } switch (fmt->fmt->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, bcf_int8_missing, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, bcf_int16_missing, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, bcf_int32_missing, bcf_int32_vector_end); break; default: goto invalid; break; } #undef BRANCH } if ( n[0]==n[1] ) kputc(n[0]==0 ? '.':'0', str); else { double pval = calc_binom_two_sided(n[0],n[1],0.5); // convrt to phred if ( pval>=1 ) pval = 0; else pval = -4.34294481903*log(pval); kputd(pval, str); } return; invalid: kputc('.', str); } static void _used_tags_add(convert_t *convert, int type, char *key) { kstring_t str = {0,0,0}; ksprintf(&str,"%s/%s",type==T_INFO?"INFO":"FORMAT",key); khash_str2int_inc(convert->used_tags_hash,str.s); convert->nused_tags++; convert->used_tags_list = (char**)realloc(convert->used_tags_list,sizeof(*convert->used_tags_list)*convert->nused_tags); convert->used_tags_list[convert->nused_tags-1] = str.s; } #define _SET_NON_FORMAT_TAGS(function,key,...) \ if ( !strcmp("CHROM",key) ) { function(__VA_ARGS__, T_CHROM); } \ else if ( !strcmp("POS",key) ) { function(__VA_ARGS__, T_POS); } \ else if ( !strcmp("POS0",key) ) { function(__VA_ARGS__, T_POS0); } \ else if ( !strcmp("END",key) ) { function(__VA_ARGS__, T_END); } \ else if ( !strcmp("END0",key) ) { function(__VA_ARGS__, T_END0); } \ else if ( !strcmp("ID",key) ) { function(__VA_ARGS__, T_ID); } \ else if ( !strcmp("REF",key) ) { function(__VA_ARGS__, T_REF); } \ else if ( !strcmp("FIRST_ALT",key) ) { function(__VA_ARGS__, T_FIRST_ALT); } \ else if ( !strcmp("QUAL",key) ) { function(__VA_ARGS__, T_QUAL); } \ else if ( !strcmp("TYPE",key) ) { function(__VA_ARGS__, T_TYPE); } \ else if ( !strcmp("FILTER",key) ) { function(__VA_ARGS__, T_FILTER); } \ else if ( !strcmp("IS_TS",key) ) { function(__VA_ARGS__, T_IS_TS); } \ else if ( !strcmp("MASK",key) ) { function(__VA_ARGS__, T_MASK); } \ else if ( !strcmp("LINE",key) ) { function(__VA_ARGS__, T_LINE); } static void set_type(fmt_t *fmt, int type) { fmt->type = type; } static fmt_t *register_tag(convert_t *convert, char *key, int is_gtf, int type) { convert->nfmt++; if ( convert->nfmt > convert->mfmt ) { convert->mfmt += 10; convert->fmt = (fmt_t*) realloc(convert->fmt, convert->mfmt*sizeof(fmt_t)); } fmt_t *fmt = &convert->fmt[ convert->nfmt-1 ]; fmt->type = type; fmt->key = key ? strdup(key) : NULL; fmt->is_gt_field = is_gtf; fmt->subscript = -1; fmt->usr = NULL; fmt->destroy = NULL; // Allow non-format tags, such as CHROM, INFO, etc., to appear amongst the format tags. if ( key ) { int id = bcf_hdr_id2int(convert->header, BCF_DT_ID, key); if ( fmt->type==T_FORMAT && !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,id) ) { _SET_NON_FORMAT_TAGS(set_type,key,fmt) else if ( !strcmp("ALT",key) ) { fmt->type = T_ALT; } else if ( !strcmp("_CHROM_POS_ID",key) ) { fmt->type = T_CHROM_POS_ID; } else if ( !strcmp("RSX",key) ) { fmt->type = T_RSX; } else if ( !strcmp("VKX",key) ) { fmt->type = T_VKX; } else if ( id>=0 && bcf_hdr_idinfo_exists(convert->header,BCF_HL_INFO,id) ) { fmt->type = T_INFO; _used_tags_add(convert,T_INFO,key); } } else if ( fmt->type==T_PBINOM ) { fmt->id = bcf_hdr_id2int(convert->header, BCF_DT_ID, fmt->key); if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT, fmt->id) ) error("No such FORMAT tag defined in the header: %s\n", fmt->key); _used_tags_add(convert,T_FORMAT,key); } else if ( fmt->type==T_NPASS ) { filter_t *flt = filter_init(convert->header,key); convert->max_unpack |= filter_max_unpack(flt); fmt->usr = (void*) flt; } } switch (fmt->type) { case T_FIRST_ALT: fmt->handler = &process_first_alt; break; case T_CHROM_POS_ID: fmt->handler = &process_chrom_pos_id; break; case T_GT_TO_PROB3: fmt->handler = &process_gt_to_prob3; break; case T_PL_TO_PROB3: fmt->handler = &process_pl_to_prob3; break; case T_GP_TO_PROB3: fmt->handler = &process_gp_to_prob3; break; case T_CHROM: fmt->handler = &process_chrom; break; case T_POS: fmt->handler = &process_pos; break; case T_POS0: fmt->handler = &process_pos0; break; case T_END: fmt->handler = &process_end; convert->max_unpack |= BCF_UN_INFO; break; case T_END0: fmt->handler = &process_end0; convert->max_unpack |= BCF_UN_INFO; break; case T_ID: fmt->handler = &process_id; break; case T_REF: fmt->handler = &process_ref; break; case T_ALT: fmt->handler = &process_alt; break; case T_QUAL: fmt->handler = &process_qual; break; case T_FILTER: fmt->handler = &process_filter; convert->max_unpack |= BCF_UN_FLT; break; case T_INFO: fmt->handler = &process_info; convert->max_unpack |= BCF_UN_INFO; break; case T_FORMAT: fmt->handler = fmt->key ? &process_format : &process_complete_format; convert->max_unpack |= BCF_UN_FMT; break; case T_SAMPLE: fmt->handler = &process_sample; break; case T_SEP: fmt->handler = &process_sep; break; case T_IS_TS: fmt->handler = &process_is_ts; break; case T_TYPE: fmt->handler = &process_type; break; case T_MASK: fmt->handler = NULL; break; case T_GT: fmt->handler = &process_gt; convert->max_unpack |= BCF_UN_FMT; break; case T_TGT: fmt->handler = &process_tgt; convert->max_unpack |= BCF_UN_FMT; break; case T_IUPAC_GT: fmt->handler = &process_iupac_gt; convert->max_unpack |= BCF_UN_FMT; break; case T_GT_TO_HAP: fmt->handler = &process_gt_to_hap; convert->max_unpack |= BCF_UN_FMT; break; case T_GT_TO_HAP2: fmt->handler = &process_gt_to_hap2; convert->max_unpack |= BCF_UN_FMT; break; case T_TBCSQ: fmt->handler = &process_tbcsq; fmt->destroy = &destroy_tbcsq; convert->max_unpack |= BCF_UN_FMT; break; case T_LINE: fmt->handler = &process_line; convert->max_unpack |= BCF_UN_FMT; break; case T_RSX: fmt->handler = &process_rsid_hex; break; case T_VKX: fmt->handler = &process_variantkey_hex; break; case T_PBINOM: fmt->handler = &process_pbinom; convert->max_unpack |= BCF_UN_FMT; break; case T_NPASS: fmt->handler = &process_npass; fmt->destroy = &destroy_npass; break; default: error("TODO: handler for type %d\n", fmt->type); } if ( key && fmt->type==T_INFO ) { fmt->id = bcf_hdr_id2int(convert->header, BCF_DT_ID, key); if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_INFO,fmt->id) ) { fmt->id = -1; convert->undef_info_tag = strdup(key); } } return fmt; } static int parse_subscript(char **p) { char *q = *p; if ( *q!='{' ) return -1; q++; while ( *q && *q!='}' && isdigit(*q) ) q++; if ( *q!='}' ) return -1; int idx = atoi((*p)+1); *p = q+1; return idx; } static char *parse_tag(convert_t *convert, char *p, int is_gtf) { char *q = ++p; while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++; kstring_t str = {0,0,0}; if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str); kputsn(p, q-p, &str); if ( is_gtf ) { if ( !strcmp(str.s, "SAMPLE") ) register_tag(convert, "SAMPLE", is_gtf, T_SAMPLE); else if ( !strcmp(str.s, "GT") ) register_tag(convert, "GT", is_gtf, T_GT); else if ( !strcmp(str.s, "TGT") ) register_tag(convert, "GT", is_gtf, T_TGT); else if ( !strcmp(str.s, "TBCSQ") ) { fmt_t *fmt = register_tag(convert, "BCSQ", is_gtf, T_TBCSQ); fmt->subscript = parse_subscript(&q); if ( fmt->subscript==-1 ) { if ( !strncmp(q,"{*}",3) ) { fmt->subscript = 0; q += 3; } } else fmt->subscript++; } else if ( !strcmp(str.s, "IUPACGT") ) register_tag(convert, "GT", is_gtf, T_IUPAC_GT); else if ( !strcmp(str.s, "INFO") ) { if ( *q!='/' ) { int id = bcf_hdr_id2int(convert->header, BCF_DT_ID, str.s); if ( bcf_hdr_idinfo_exists(convert->header,BCF_HL_INFO,id) ) error("Could not parse format string \"%s\". Did you mean %%INFO/%s?\n", convert->format_str,str.s); else error("Could not parse format string: %s\n", convert->format_str); } p = ++q; str.l = 0; while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++; if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str); kputsn(p, q-p, &str); fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_INFO); fmt->subscript = parse_subscript(&q); _used_tags_add(convert,T_INFO,str.s); } else if ( !strcmp(str.s,"PBINOM") ) { if ( *q!='(' ) error("Could not parse the expression: %s\n", convert->format_str); p = ++q; str.l = 0; while ( *q && *q!=')' ) q++; if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str); kputsn(p, q-p, &str); register_tag(convert, str.s, is_gtf, T_PBINOM); q++; } else if ( !strcmp(str.s,"N_PASS") ) error("N_PASS() must be placed outside the square brackets\n"); else { fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_FORMAT); fmt->subscript = parse_subscript(&q); } } else { _SET_NON_FORMAT_TAGS(register_tag, str.s, convert, str.s, is_gtf) else if ( !strcmp(str.s, "ALT") ) { fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_ALT); fmt->subscript = parse_subscript(&q); } else if ( !strcmp(str.s, "_CHROM_POS_ID") ) register_tag(convert, str.s, is_gtf, T_CHROM_POS_ID); else if ( !strcmp(str.s, "_GT_TO_PROB3") ) register_tag(convert, str.s, is_gtf, T_GT_TO_PROB3); else if ( !strcmp(str.s, "_PL_TO_PROB3") ) register_tag(convert, str.s, is_gtf, T_PL_TO_PROB3); else if ( !strcmp(str.s, "_GP_TO_PROB3") ) register_tag(convert, str.s, is_gtf, T_GP_TO_PROB3); else if ( !strcmp(str.s, "_GT_TO_HAP") ) register_tag(convert, str.s, is_gtf, T_GT_TO_HAP); else if ( !strcmp(str.s, "_GT_TO_HAP2") ) register_tag(convert, str.s, is_gtf, T_GT_TO_HAP2); else if ( !strcmp(str.s, "RSX") ) register_tag(convert, str.s, is_gtf, T_RSX); else if ( !strcmp(str.s, "VKX") ) register_tag(convert, str.s, is_gtf, T_VKX); else if ( !strcmp(str.s,"PBINOM") ) error("Error: PBINOM() is currently supported only with FORMAT tags. (todo)\n"); else if ( !strcmp(str.s, "INFO") ) { if ( *q=='/' ) { p = ++q; str.l = 0; while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++; if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str); kputsn(p, q-p, &str); fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_INFO); fmt->subscript = parse_subscript(&q); _used_tags_add(convert,T_INFO,str.s); } else register_tag(convert, NULL, is_gtf, T_INFO); // the whole INFO } else if ( !strcmp(str.s, "FORMAT") ) register_tag(convert, NULL, 0, T_FORMAT); else if ( !strcmp(str.s,"N_PASS") ) { if ( *q!='(' ) error("Could not parse the expression: %s\n", convert->format_str); p = ++q; str.l = 0; int nopen = 1; while ( *q && nopen ) { if ( *q=='(' ) nopen++; else if ( *q==')' ) nopen--; q++; } if ( q-p==0 || nopen ) error("Could not parse format string: %s\n", convert->format_str); kputsn(p, q-p-1, &str); register_tag(convert, str.s, is_gtf, T_NPASS); } else { fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_INFO); fmt->subscript = parse_subscript(&q); _used_tags_add(convert,T_INFO,str.s); } } free(str.s); return q; } static char *parse_sep(convert_t *convert, char *p, int is_gtf) { char *q = p; kstring_t str = {0,0,0}; while ( *q && *q!='[' && *q!=']' && *q!='%' ) { if ( *q=='\\' ) { q++; if ( *q=='n' ) kputc('\n', &str); else if ( *q=='t' ) kputc('\t', &str); else kputc(*q, &str); } else kputc(*q, &str); q++; } if ( !str.l ) error("Could not parse format string: %s\n", convert->format_str); register_tag(convert, str.s, is_gtf, T_SEP); free(str.s); return q; } convert_t *convert_init(bcf_hdr_t *hdr, int *samples, int nsamples, const char *format_str) { convert_t *convert = (convert_t*) calloc(1,sizeof(convert_t)); convert->header = hdr; convert->format_str = strdup(format_str); convert->max_unpack = BCF_UN_STR; convert->used_tags_hash = khash_str2int_init(); int i, is_gtf = 0; char *p = convert->format_str; while ( *p ) { //fprintf(bcftools_stderr,"<%s>\n", p); switch (*p) { case '[': is_gtf = 1; p++; break; case ']': is_gtf = 0; register_tag(convert, NULL, 0, T_SEP); p++; break; case '%': p = parse_tag(convert, p, is_gtf); break; default: p = parse_sep(convert, p, is_gtf); break; } } if ( is_gtf ) error("Could not parse the format string, missing the square bracket \"]\": %s\n", convert->format_str); if ( nsamples ) { convert->nsamples = nsamples; convert->samples = (int*) malloc(sizeof(int)*nsamples); for (i=0; insamples; i++) convert->samples[i] = samples[i]; } else { convert->nsamples = bcf_hdr_nsamples(convert->header); convert->samples = (int*) malloc(sizeof(int)*convert->nsamples); for (i=0; insamples; i++) convert->samples[i] = i; } return convert; } void convert_destroy(convert_t *convert) { int i; for (i=0; infmt; i++) { if ( convert->fmt[i].destroy ) convert->fmt[i].destroy(convert->fmt[i].usr); free(convert->fmt[i].key); } if ( convert->nused_tags ) { for (i=0; inused_tags; i++) free(convert->used_tags_list[i]); free(convert->used_tags_list); } khash_str2int_destroy(convert->used_tags_hash); free(convert->print_filtered); free(convert->fmt); free(convert->undef_info_tag); free(convert->dat); free(convert->samples); free(convert->format_str); free(convert); } int convert_header(convert_t *convert, kstring_t *str) { int i, icol = 0, l_ori = str->l; bcf_hdr_t *hdr = convert->header; // Suppress the header output if LINE is present for (i=0; infmt; i++) if ( convert->fmt[i].type == T_LINE ) break; if ( i!=convert->nfmt ) return str->l - l_ori; // Header formatting becomes problematic when the formatting expression contains a newline. // Simple cases like // -f'[%CHROM %POS %SAMPLE\n]' // can be handled quite easily with has_fmt_newline. Note this will not work if multiple newlines // are present. int has_fmt_newline = 0; kputc('#', str); for (i=0; infmt; i++) { // Genotype fields if ( convert->fmt[i].is_gt_field ) { int j = i, js, k; while ( convert->fmt[j].is_gt_field ) j++; for (js=0; jsnsamples; js++) { int ks = convert->samples[js]; for (k=i; kfmt[k].type == T_SEP ) { if ( convert->fmt[k].key ) { char *tmp = convert->fmt[k].key; while ( *tmp ) { if ( *tmp=='\n' ) has_fmt_newline = 1; else kputc(*tmp,str); tmp++; } } } else if ( convert->header_samples ) { icol++; if ( !convert->no_hdr_indices ) ksprintf(str,"[%d]",icol); ksprintf(str,"%s:%s", hdr->samples[ks], convert->fmt[k].key); } else { icol++; if ( !convert->no_hdr_indices ) ksprintf(str,"[%d]",icol); ksprintf(str,"%s", convert->fmt[k].key); } } if ( has_fmt_newline ) { if ( !convert->header_samples ) break; // this is unfortunate: the formatting expression breaks the per-sample output into separate lines, // therefore including a sample name in the header makes no sense anymore convert->header_samples = 0; str->l = l_ori; return convert_header(convert, str); } } i = j-1; continue; } // Fixed fields if ( convert->fmt[i].type == T_SEP ) { if ( convert->fmt[i].key ) kputs(convert->fmt[i].key, str); continue; } icol++; if ( !convert->no_hdr_indices ) ksprintf(str,"[%d]",icol); ksprintf(str,"%s", convert->fmt[i].key); } if ( has_fmt_newline ) kputc('\n',str); return str->l - l_ori; } int convert_line(convert_t *convert, bcf1_t *line, kstring_t *str) { if ( !convert->allow_undef_tags && convert->undef_info_tag ) { kstring_t msg = {0,0,0}; ksprintf(&msg,"Error: no such tag defined in the VCF header: INFO/%s", convert->undef_info_tag); int hdr_id = bcf_hdr_id2int(convert->header,BCF_DT_ID,convert->undef_info_tag); if ( hdr_id>=0 && bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,hdr_id) ) ksprintf(&msg,". FORMAT fields must be enclosed in square brackets, e.g. \"[ %%%s]\"", convert->undef_info_tag); error("%s\n", msg.s); } int l_ori = str->l; bcf_unpack(line, convert->max_unpack); int i, ir; str->l = 0; for (i=0; infmt; i++) { // Genotype fields. if ( convert->fmt[i].is_gt_field ) { int j = i, js, k; while ( jnfmt && convert->fmt[j].is_gt_field ) { convert->fmt[j].ready = 0; j++; } for (js=0; jsnsamples; js++) { // Skip samples when filtering was requested int ks = convert->samples[js]; if ( convert->subset_samples && *convert->subset_samples && !(*convert->subset_samples)[ks] ) { if ( !convert->print_filtered ) continue; for (k=i; kfmt[k].type==T_SEP ) convert->fmt[k].handler(convert, line, &convert->fmt[k], ks, str); else kputs(convert->print_filtered, str); continue; } // Here comes a hack designed for TBCSQ. When running on large files, // such as 1000GP, there are too many empty fields in the output and // it's very very slow. Therefore in case the handler does not add // anything to the string, we trim all genotype fields enclosed in square // brackets here. This may be changed in future, time will show... size_t l_start = str->l; for (k=i; kfmt[k].type == T_MASK ) { for (ir=0; irnreaders; ir++) kputc(bcf_sr_has_line(convert->readers,ir)?'1':'0', str); } else if ( convert->fmt[k].handler ) { size_t l = str->l; convert->fmt[k].handler(convert, line, &convert->fmt[k], ks, str); if ( l==str->l ) { str->l = l_start; break; } // only TBCSQ does this } } } i = j-1; continue; } // Fixed fields if ( convert->fmt[i].type == T_MASK ) { for (ir=0; irnreaders; ir++) kputc(bcf_sr_has_line(convert->readers,ir)?'1':'0', str); } else if ( convert->fmt[i].handler ) convert->fmt[i].handler(convert, line, &convert->fmt[i], -1, str); } return str->l - l_ori; } static void force_newline_(convert_t *convert) { int i, has_newline = 0; for (i=0; infmt; i++) { if ( !convert->fmt[i].key ) continue; char *tmp = convert->fmt[i].key; while (*tmp) { if ( *tmp=='\n' ) { has_newline = 1; break; } tmp++; } if ( has_newline ) break; } if ( has_newline ) return; // A newline is not present, force it. But where to add it? Always at the end. // // Briefly, in 1.18, we considered the following automatic behavior, which for // per-site output it would add it at the end of the expression and for per-sample // output it would add it inside the square brackets: // -f'%CHROM[ %SAMPLE]\n' // -f'[%CHROM %SAMPLE\n]' // // However, this is an annoyance for users, as it is not entirely clear what // will happen unless one understands the internals well (#1969) register_tag(convert, "\n", 0, T_SEP); } int convert_set_option(convert_t *convert, enum convert_option opt, ...) { int ret = 0; va_list args; va_start(args, opt); switch (opt) { case allow_undef_tags: convert->allow_undef_tags = va_arg(args, int); break; case subset_samples: convert->subset_samples = va_arg(args, uint8_t**); break; case header_samples: convert->header_samples = va_arg(args, int); break; case print_filtered: convert->print_filtered = strdup(va_arg(args, char*)); break; case force_newline: convert->force_newline = va_arg(args, int); if ( convert->force_newline ) force_newline_(convert); break; case no_hdr_indices: convert->no_hdr_indices = va_arg(args, int); break; default: ret = -1; } va_end(args); return ret; } int convert_max_unpack(convert_t *convert) { return convert->max_unpack; } int convert_is_tag_used(convert_t *convert, char *tag) { return khash_str2int_has_key(convert->used_tags_hash, tag); } const char **convert_list_used_tags(convert_t *convert, int *ntags) { *ntags = convert->nused_tags; return (const char **)convert->used_tags_list; } pysam-0.23.0/bcftools/convert.h000066400000000000000000000046761475062545500164230ustar00rootroot00000000000000/* convert.h -- functions for converting between VCF/BCF and related formats. Copyright (C) 2014-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef __CONVERT_H__ #define __CONVERT_H__ #include typedef struct _convert_t convert_t; enum convert_option { allow_undef_tags, // see `bcftools query --allow-undef-tags`, throws an error if tag is not defined otherwise subset_samples, // in bracketed expressions (e.g. [ %GT]) consider only marked samples header_samples, // include sample name in bracketed tags (e.g. SAMPLE1:GT SAMPLE2:GT for [ %GT]) force_newline, // automatically insert a newline when not part of the formatting expression print_filtered, // print the provided string instead of discarding samples not included in subset_samples no_hdr_indices, // drop column indices when printing header, i.e. "#CHROM", not "#[1]CHROM" }; convert_t *convert_init(bcf_hdr_t *hdr, int *samples, int nsamples, const char *str); void convert_destroy(convert_t *convert); int convert_set_option(convert_t *convert, enum convert_option opt, ...); int convert_header(convert_t *convert, kstring_t *str); int convert_line(convert_t *convert, bcf1_t *rec, kstring_t *str); int convert_max_unpack(convert_t *convert); int convert_is_tag_used(convert_t *convert, char *tag); const char **convert_list_used_tags(convert_t *convert, int *ntags); #endif pysam-0.23.0/bcftools/csq.c000066400000000000000000004346321475062545500155230ustar00rootroot00000000000000/* The MIT License Copyright (c) 2016-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Things that would be nice to have - dynamic N_REF_PAD - for stop-lost events (also in frameshifts) report the number of truncated aa's - memory could be greatly reduced by indexing gff (but it is quite compact already) - deletions that go beyond transcript boundaries are not checked at sequence level - alloc tscript->ref in hap_finalize, introduce fa_off_beg:16,fa_off_end:16 - see test/csq/ENST00000573314/insertion-overlap.vcf #1476288882 Read about transcript types here http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html https://www.gencodegenes.org/pages/biotypes.html List of supported biotypes antisense IG_C_gene IG_D_gene IG_J_gene IG_LV_gene IG_V_gene lincRNA lncRNA .. generic term for 3prime_overlapping_ncRNA, antisense, bidirectional_promoter_lncRNA, lincRNA, macro_lncRNA, non_coding, processed_transcript, sense_intronic, sense_overlapping macro_lncRNA miRNA misc_RNA Mt_rRNA Mt_tRNA polymorphic_pseudogene processed_transcript protein_coding, mRNA ribozyme rRNA sRNA scRNA scaRNA sense_intronic sense_overlapping snRNA snoRNA TR_C_gene TR_D_gene TR_J_gene TR_V_gene The gff parsing logic We collect features such by combining gff lines A,B,C as follows: A .. gene line with a supported biotype A.ID=~/^gene:/ B .. transcript line referencing A with supported biotype B.ID=~/^transcript:/ && B.Parent=~/^gene:A.ID/ C .. corresponding CDS, exon, and UTR lines: C[3] in {"CDS","exon","three_prime_UTR","five_prime_UTR"} && C.Parent=~/^transcript:B.ID/ For coding biotypes ("protein_coding" or "polymorphic_pseudogene") the complete chain link C -> B -> A is required. For the rest, link B -> A suffices. The supported consequence types, sorted by impact: splice_acceptor_variant .. end region of an intron changed (2bp at the 3' end of an intron) splice_donor_variant .. start region of an intron changed (2bp at the 5' end of an intron) stop_gained .. DNA sequence variant resulting in a stop codon frameshift_variant .. number of inserted/deleted bases not a multiple of three, disrupted translational frame stop_lost .. elongated transcript, stop codon changed start_lost .. the first codon changed inframe_altering .. combination of indels leading to unchanged reading frame and length inframe_insertion .. inserted coding sequence, unchanged reading frame inframe_deletion .. deleted coding sequence, unchanged reading frame missense_variant .. amino acid (aa) change, unchanged length splice_region_variant .. change within 1-3 bases of the exon or 3-8 bases of the intron synonymous_variant .. DNA sequence variant resulting in no amino acid change stop_retained_variant .. different stop codon start_retained_variant .. start codon retained by indel realignment non_coding_variant .. variant in non-coding sequence, such as RNA gene 5_prime_UTR_variant 3_prime_UTR_variant intron_variant .. reported only if none of the above intergenic_variant .. reported only if none of the above The annotation algorithm. The algorithm checks if the variant falls in a region of a supported type. The search is performed in the following order, until a match is found: 1. idx_cds(gf_cds_t) - lookup CDS by position, create haplotypes, call consequences 2. idx_utr(gf_utr_t) - check UTR hits 3. idx_exon(gf_exon_t) - check for splice variants 4. idx_tscript(tscript_t) - check for intronic variants, RNAs, etc. These regidx indexes are created by parsing a gff3 file as follows: 1. create the array "ftr" of all UTR, CDS, exons. This will be processed later and pruned based on transcript types we want to keep. In the same go, create the hash "id2tr" of transcripts to keep (based on biotype) which maps from transcript_id to a transcript. At the same time also build the hash "gid2gene" which maps from gene_id to gf_gene_t pointer. 2. build "idx_cds", "idx_tscript", "idx_utr" and "idx_exon" indexes. Use only features from "ftr" which are present in "id2tr". 3. clean data that won't be needed anymore: ftr, id2tr, gid2gene. Data structures. idx_cds, idx_utr, idx_exon, idx_tscript: as described above, regidx structures for fast lookup of exons/transcripts overlapping a region, the payload is a pointer to tscript.cds */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "filter.h" #include "regidx.h" #include "kheap.h" #include "smpl_ilist.h" #include "rbuf.h" #include "gff.h" #ifndef __FUNCTION__ # define __FUNCTION__ __func__ #endif // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 #define N_REF_PAD 10 // number of bases to avoid boundary effects // How to treat phased/unphased genotypes #define PHASE_REQUIRE 0 // --phase r #define PHASE_MERGE 1 // --phase m #define PHASE_AS_IS 2 // --phase a #define PHASE_SKIP 3 // --phase s #define PHASE_NON_REF 4 // --phase R #define PHASE_DROP_GT 5 // --samples - // Node types in the haplotype tree #define HAP_CDS 0 #define HAP_ROOT 1 #define HAP_SSS 2 // start/stop/splice #define CSQ_PRINTED_UPSTREAM (1<<0) #define CSQ_SYNONYMOUS_VARIANT (1<<1) #define CSQ_MISSENSE_VARIANT (1<<2) #define CSQ_STOP_LOST (1<<3) #define CSQ_STOP_GAINED (1<<4) #define CSQ_INFRAME_DELETION (1<<5) #define CSQ_INFRAME_INSERTION (1<<6) #define CSQ_FRAMESHIFT_VARIANT (1<<7) #define CSQ_SPLICE_ACCEPTOR (1<<8) #define CSQ_SPLICE_DONOR (1<<9) #define CSQ_START_LOST (1<<10) #define CSQ_SPLICE_REGION (1<<11) #define CSQ_STOP_RETAINED (1<<12) #define CSQ_UTR5 (1<<13) #define CSQ_UTR3 (1<<14) #define CSQ_NON_CODING (1<<15) #define CSQ_INTRON (1<<16) //#define CSQ_INTERGENIC (1<<17) #define CSQ_INFRAME_ALTERING (1<<18) #define CSQ_UPSTREAM_STOP (1<<19) // adds * in front of the csq string #define CSQ_INCOMPLETE_CDS (1<<20) // to remove START/STOP in incomplete CDS, see ENSG00000173376/synon.vcf #define CSQ_CODING_SEQUENCE (1<<21) // cannot tell exactly what it is, but it does affect the coding sequence #define CSQ_ELONGATION (1<<22) // symbolic insertion #define CSQ_START_RETAINED (1<<23) // Haplotype-aware consequences, printed in one vcf record only, the rest has a reference @12345 #define CSQ_COMPOUND (CSQ_SYNONYMOUS_VARIANT|CSQ_MISSENSE_VARIANT|CSQ_STOP_LOST|CSQ_STOP_GAINED| \ CSQ_INFRAME_DELETION|CSQ_INFRAME_INSERTION|CSQ_FRAMESHIFT_VARIANT| \ CSQ_START_LOST|CSQ_STOP_RETAINED|CSQ_INFRAME_ALTERING|CSQ_INCOMPLETE_CDS| \ CSQ_UPSTREAM_STOP|CSQ_START_RETAINED) #define CSQ_START_STOP (CSQ_STOP_LOST|CSQ_STOP_GAINED|CSQ_STOP_RETAINED|CSQ_START_LOST|CSQ_START_RETAINED) #define CSQ_PRN_STRAND(csq) ((csq)&CSQ_COMPOUND && !((csq)&(CSQ_SPLICE_ACCEPTOR|CSQ_SPLICE_DONOR|CSQ_SPLICE_REGION))) #define CSQ_PRN_TSCRIPT (~(CSQ_INTRON|CSQ_NON_CODING)) #define CSQ_PRN_NMD (~(CSQ_INTRON|CSQ_NON_CODING)) #define CSQ_PRN_BIOTYPE CSQ_NON_CODING // see kput_vcsq() const char *csq_strings[] = { NULL, "synonymous", "missense", "stop_lost", "stop_gained", "inframe_deletion", "inframe_insertion", "frameshift", "splice_acceptor", "splice_donor", "start_lost", "splice_region", "stop_retained", "5_prime_utr", "3_prime_utr", "non_coding", "intron", "intergenic", "inframe_altering", NULL, NULL, "coding_sequence", "feature_elongation", "start_retained" }; /* Structures related to VCF output: vcsq_t information required to assemble consequence lines such as "inframe_deletion|XYZ|ENST01|+|5TY>5I|121ACG>A+124TA>T" vrec_t single VCF record and csq tied to this record. (Haplotype can have multiple consequences in several VCF records. Each record can have multiple consequences from multiple haplotypes.) csq_t a top-level consequence tied to a haplotype vbuf_t pos2vbuf VCF records with the same position clustered together for a fast lookup via pos2vbuf */ typedef struct _vbuf_t vbuf_t; typedef struct _vcsq_t vcsq_t; struct _vcsq_t { uint32_t strand:1, type:31; // one of CSQ_* types uint32_t trid; uint32_t vcf_ial; uint32_t biotype; // one of GF_* types char *gene; // gene name bcf1_t *ref; // if type&CSQ_PRINTED_UPSTREAM, ref consequence "@1234" kstring_t vstr; // variant string, eg 5TY>5I|121ACG>A+124TA>T }; typedef struct { bcf1_t *line; uint32_t *fmt_bm; // bitmask of sample consequences with first/second haplotype interleaved uint32_t nfmt:4, // the bitmask size (the number of integers per sample) nvcsq:28, mvcsq; vcsq_t *vcsq; // there can be multiple consequences for a single VCF record } vrec_t; typedef struct { uint32_t pos; vrec_t *vrec; // vcf line that this csq is tied to; needed when printing haplotypes (hap_stage_vcf) int idx; // 0-based index of the csq at the VCF line, for FMT/BCSQ vcsq_t type; } csq_t; struct _vbuf_t { vrec_t **vrec; // buffer of VCF lines with the same position int n, m; uint32_t keep_until; // the maximum transcript end position }; KHASH_MAP_INIT_INT(pos2vbuf, vbuf_t*) /* Structures related to haplotype-aware consequences in coding regions hap_node_t node of a haplotype tree. Each transcript has one tree tscript_t despite its general name, it is intended for coding transcripts only hap_t hstack_t for traversal of the haplotype tree and braking combined consequences into independent parts */ typedef struct _hap_node_t hap_node_t; struct _hap_node_t { char *seq; // cds segment [parent_node,this_node) char *var; // variant "ref>alt" uint32_t type:2, // HAP_ROOT or HAP_CDS csq:30; // this node's consequence int dlen; // alt minus ref length: <0 del, >0 ins, 0 substitution uint32_t rbeg; // variant's VCF position (0-based, inclusive) int32_t rlen; // variant's rlen; alen=rlen+dlen; fake for non CDS types uint32_t sbeg; // variant's position on the spliced reference transcript (0-based, inclusive, N_REF_PAD not included) uint32_t icds; // which exon does this node's variant overlaps hap_node_t **child, *prev; // children haplotypes and previous coding node int nchild, mchild; bcf1_t *cur_rec, *rec; // current VCF record and node's VCF record int vcf_ial; // which VCF allele generated this node uint32_t nend; // number of haplotypes ending in this node int *cur_child, mcur_child; // mapping from the allele to the currently active child csq_t *csq_list; // list of haplotype's consequences, broken by position (each corresponds to a VCF record) int ncsq_list, mcsq_list; }; #define TSCRIPT_AUX(x) ((tscript_t*)(x)->aux) typedef struct { char *ref; // reference sequence, padded with N_REF_PAD bases on both ends char *sref; // spliced reference sequence, padded with N_REF_PAD bases on both ends hap_node_t *root; // root of the haplotype tree hap_node_t **hap; // pointer to haplotype leaves, two for each sample int nhap, nsref; // number of haplotypes and length of sref, including 2*N_REF_PAD } tscript_t; static inline int cmp_tscript(gf_tscript_t **a, gf_tscript_t **b) { return ( (*a)->end < (*b)->end ) ? 1 : 0; } KHEAP_INIT(trhp, gf_tscript_t*, cmp_tscript) typedef khp_trhp_t tr_heap_t; typedef struct { hap_node_t *node; // current node int ichild; // current child in the active node int dlen; // total dlen, from the root to the active node size_t slen; // total sequence length, from the root to the active node } hstack_t; typedef struct { int mstack; hstack_t *stack; gf_tscript_t *tr; // tr->ref: spliced transcript on ref strand kstring_t sseq; // spliced haplotype sequence on ref strand kstring_t tseq; // the variable part of translated haplotype transcript, coding strand kstring_t tref; // the variable part of translated reference transcript, coding strand uint32_t sbeg; // stack's sbeg, for cases first node's type is HAP_SSS int upstream_stop; } hap_t; typedef struct _args_t { // the main regidx lookups, from chr:beg-end to overlapping features and // index iterator gff_t *gff; regidx_t *idx_cds, *idx_utr, *idx_exon, *idx_tscript; regitr_t *itr; // text tab-delimited output (out) or vcf/bcf output (out_fh) FILE *out; htsFile *out_fh; char *index_fn; int write_index; char *dump_gff; // vcf bcf_srs_t *sr; bcf_hdr_t *hdr; int hdr_nsmpl; // actual number of samples in the vcf, for bcf_update_format_values() // include or exclude sites which match the filters filter_t *filter; char *filter_str; int filter_logic; // FLT_INCLUDE or FLT_EXCLUDE // samples to process int sample_is_file; char *sample_list; smpl_ilist_t *smpl; char *outdir, **argv, *fa_fname, *gff_fname, *output_fname; char *bcsq_tag; int argc, output_type, clevel; int phase, verbosity, local_csq, record_cmd_line; int ncsq2_max, nfmt_bcsq; // maximum number of csq per site that can be accessed from FORMAT/BCSQ (*2 and 1 bit skipped to avoid BCF missing values) int ncsq2_small_warned; int brief_predictions; int unify_chr_names; char *chr_name; int mchr_name; struct { int unknown_chr,unknown_tscript_biotype,unknown_strand,unknown_phase,duplicate_id; int unknown_cds_phase,incomplete_cds,wrong_phase,overlapping_cds; } warned; int rid; // current chromosome tr_heap_t *active_tr; // heap of active transcripts for quick flushing hap_t *hap; // transcript haplotype recursion vbuf_t **vcf_buf; // buffered VCF lines to annotate with CSQ and flush rbuf_t vcf_rbuf; // round buffer indexes to vcf_buf kh_pos2vbuf_t *pos2vbuf; // fast lookup of buffered lines by position gf_tscript_t **rm_tr; // buffer of transcripts to clean int nrm_tr, mrm_tr; csq_t *csq_buf; // pool of csq not managed by hap_node_t, i.e. non-CDS csqs int ncsq_buf, mcsq_buf; int force; // force run under various conditions. Currently only to skip out-of-phase transcripts int n_threads; // extra compression/decompression threads faidx_t *fai; kstring_t str, str2; int32_t *gt_arr, mgt_arr; } args_t; // AAA, AAC, ... const char *gencode = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF"; const uint8_t nt4[] = { 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,0,4,1, 4,4,4,2, 4,4,4,4, 4,4,4,4, 4,4,4,4, 3,4,4,4, 4,4,4,4, 4,4,4,4, 4,0,4,1, 4,4,4,2, 4,4,4,4, 4,4,4,4, 4,4,4,4, 3 }; const uint8_t cnt4[] = { 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,3,4,2, 4,4,4,1, 4,4,4,4, 4,4,4,4, 4,4,4,4, 0,4,4,4, 4,4,4,4, 4,4,4,4, 4,3,4,2, 4,4,4,1, 4,4,4,4, 4,4,4,4, 4,4,4,4, 0 }; #define dna2aa(x) gencode[ nt4[(uint8_t)(x)[0]]<<4 | nt4[(uint8_t)(x)[1]]<<2 | nt4[(uint8_t)(x)[2]] ] #define cdna2aa(x) gencode[ cnt4[(uint8_t)(x)[2]]<<4 | cnt4[(uint8_t)(x)[1]]<<2 | cnt4[(uint8_t)(x)[0]] ] static inline int ncsq2_to_nfmt(int ncsq2) { return 1 + (ncsq2 - 1) / 30; } static inline void icsq2_to_bit(int icsq2, int *ival, int *ibit) { *ival = icsq2 / 30; *ibit = icsq2 % 30; } void init_data(args_t *args) { args->nfmt_bcsq = ncsq2_to_nfmt(args->ncsq2_max); args->fai = fai_load(args->fa_fname); if ( !args->fai ) error("Failed to load the fai index: %s\n", args->fa_fname); args->gff = gff_init(args->gff_fname); gff_set(args->gff,verbosity,args->verbosity); gff_set(args->gff,strip_chr_names,args->unify_chr_names); gff_set(args->gff,force_out_of_phase,args->force); gff_set(args->gff,dump_fname,args->dump_gff); gff_parse(args->gff); args->idx_cds = gff_get(args->gff,idx_cds); args->idx_utr = gff_get(args->gff,idx_utr); args->idx_exon = gff_get(args->gff,idx_exon); args->idx_tscript = gff_get(args->gff,idx_tscript); args->itr = regitr_init(NULL); args->rid = -1; if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); args->pos2vbuf = kh_init(pos2vbuf); args->active_tr = khp_init(trhp); args->hap = (hap_t*) calloc(1,sizeof(hap_t)); // init samples if ( !bcf_hdr_nsamples(args->hdr) ) args->phase = PHASE_DROP_GT; if ( args->sample_list && !strcmp("-",args->sample_list) ) { // ignore all samples if ( args->output_type==FT_TAB_TEXT ) { // significant speedup for plain VCFs if (bcf_hdr_set_samples(args->hdr,NULL,0) < 0) error_errno("[%s] Couldn't build sample filter", __func__); } args->phase = PHASE_DROP_GT; } else args->smpl = smpl_ilist_init(args->hdr, args->sample_list, args->sample_is_file, SMPL_STRICT); args->hdr_nsmpl = args->phase==PHASE_DROP_GT ? 0 : bcf_hdr_nsamples(args->hdr); if ( args->output_type==FT_TAB_TEXT ) { args->out = args->output_fname ? fopen(args->output_fname,"w") : stdout; if ( !args->out ) error("Failed to write to %s: %s\n", !strcmp("-",args->output_fname)?"standard output":args->output_fname,strerror(errno)); fprintf(args->out,"# This file was produced by: bcftools +csq(%s+htslib-%s)\n", bcftools_version(),hts_version()); fprintf(args->out,"# The command line was:\tbcftools +%s", args->argv[0]); int i; for (i=1; iargc; i++) fprintf(args->out," %s",args->argv[i]); fprintf(args->out,"\n"); fprintf(args->out,"# LOG\t[2]Message\n"); fprintf(args->out,"# CSQ"); i = 1; fprintf(args->out,"\t[%d]Sample", ++i); fprintf(args->out,"\t[%d]Haplotype", ++i); fprintf(args->out,"\t[%d]Chromosome", ++i); fprintf(args->out,"\t[%d]Position", ++i); fprintf(args->out,"\t[%d]Consequence", ++i); fprintf(args->out,"\n"); } else { char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( args->out_fh == NULL ) error("[%s] Error: cannot write to %s: %s\n", __func__,args->output_fname? args->output_fname : "standard output", strerror(errno)); if ( args->n_threads > 0) hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->sr->p); if ( args->record_cmd_line ) bcf_hdr_append_version(args->hdr,args->argc,args->argv,"bcftools/csq"); bcf_hdr_printf(args->hdr,"##INFO=",args->bcsq_tag, args->local_csq ? "Local" : "Haplotype-aware"); if ( args->hdr_nsmpl ) bcf_hdr_printf(args->hdr,"##FORMAT=",args->bcsq_tag); if ( bcf_hdr_write(args->out_fh, args->hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname?args->output_fname:"standard output"); if ( init_index2(args->out_fh,args->hdr,args->output_fname, &args->index_fn, args->write_index) < 0 ) error("Error: failed to initialise index for %s\n",args->output_fname); } if ( args->verbosity > 0 ) fprintf(stderr,"Calling...\n"); } void destroy_data(args_t *args) { if ( args->ncsq2_small_warned ) fprintf(stderr, "Note: Some samples had too many consequences to be represented in %d bytes. If you need to record them all,\n" " the limit can be increased by running with `--ncsq %d`.\n",ncsq2_to_nfmt(args->ncsq2_max)/8,1+args->ncsq2_small_warned/2); regitr_destroy(args->itr); gff_destroy(args->gff); if ( args->filter ) filter_destroy(args->filter); khp_destroy(trhp,args->active_tr); kh_destroy(pos2vbuf,args->pos2vbuf); if ( args->smpl ) smpl_ilist_destroy(args->smpl); int i,j,ret; if ( args->out_fh ) { if ( args->write_index ) { if ( bcf_idx_save(args->out_fh)<0 ) { if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } ret = hts_close(args->out_fh); } else ret = fclose(args->out); if ( ret ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"stdout"); for (i=0; ivcf_rbuf.m; i++) { vbuf_t *vbuf = args->vcf_buf[i]; if ( !vbuf ) continue; for (j=0; jm; j++) { if ( !vbuf->vrec[j] ) continue; if ( vbuf->vrec[j]->line ) bcf_destroy(vbuf->vrec[j]->line); free(vbuf->vrec[j]->fmt_bm); free(vbuf->vrec[j]->vcsq); free(vbuf->vrec[j]); } free(vbuf->vrec); free(vbuf); } free(args->vcf_buf); free(args->rm_tr); free(args->csq_buf); free(args->hap->stack); free(args->hap->sseq.s); free(args->hap->tseq.s); free(args->hap->tref.s); free(args->hap); fai_destroy(args->fai); free(args->gt_arr); free(args->str.s); free(args->str2.s); free(args->chr_name); } /* The splice_* functions are for consequences around splice sites: start,stop,splice_* */ #define SPLICE_VAR_REF 0 // ref: ACGT>ACGT, csq not applicable, skip completely #define SPLICE_OUTSIDE 1 // splice acceptor or similar; csq set and is done, does not overlap the region #define SPLICE_INSIDE 2 // overlaps coding region; csq can be set but coding prediction is needed #define SPLICE_OVERLAP 3 // indel overlaps region boundary, csq set but could not determine csq typedef struct { gf_tscript_t *tr; struct { int32_t pos, rlen, alen, ial; char *ref, *alt; bcf1_t *rec; } vcf; uint16_t check_acceptor:1, // check distance from exon start (fwd) or end (rev) check_start:1, // this is the first coding exon (relative to transcript orientation), check first (fwd) or last (rev) codon check_stop:1, // this is the last coding exon (relative to transcript orientation), check last (fwd) or first (rev) codon check_donor:1, // as with check_acceptor check_region_beg:1, // do/don't check for splices at this end, eg. in the first or last exon check_region_end:1, // check_utr:1, // check splice sites (acceptor/donor/region_*) only if not in utr set_refalt:1; // set kref,kalt, if set, check also for synonymous events uint32_t csq; int tbeg, tend; // number of trimmed bases from beg and end of ref,alt allele uint32_t ref_beg, // ref coordinates with spurious bases removed, ACC>AC can become AC>A or CC>C, whichever gives ref_end; // a more conservative csq (the first and last base in kref.s) kstring_t kref, kalt; // trimmed alleles, set only with SPLICE_OLAP } splice_t; void splice_init(splice_t *splice, bcf1_t *rec) { memset(splice,0,sizeof(*splice)); splice->vcf.rec = rec; splice->vcf.pos = rec->pos; splice->vcf.rlen = rec->rlen; splice->vcf.ref = rec->d.allele[0]; splice->csq = 0; } static inline void splice_build_hap(splice_t *splice, uint32_t beg, int len) { // len>0 .. beg is the first base, del filled from right // len<0 .. beg is the last base, del filled from left int rlen, alen, rbeg, abeg; // first base to include (ref coordinates) if ( len<0 ) { rlen = alen = -len; rbeg = beg - rlen + 1; int dlen = splice->vcf.alen - splice->vcf.rlen; if ( dlen<0 && beg < splice->ref_end ) // incomplete del, beg is in the middle dlen += splice->ref_end - beg; abeg = rbeg + dlen; } else { rbeg = abeg = beg; rlen = alen = len; // check for incomplete del as above?? } #define XDBG 0 #if XDBG fprintf(stderr,"build_hap: rbeg=%d + %d abeg=%d \n",rbeg,rlen,abeg); #endif splice->kref.l = 0; splice->kalt.l = 0; // add the part before vcf.ref, in the vcf.ref and after vcf.ref int roff; // how many vcf.ref bases already used if ( rbeg < splice->vcf.pos ) { assert( splice->tr->beg <= rbeg ); // this can be extended thanks to N_REF_PAD kputsn(TSCRIPT_AUX(splice->tr)->ref + N_REF_PAD + rbeg - splice->tr->beg, splice->vcf.pos - rbeg, &splice->kref); roff = 0; } else roff = rbeg - splice->vcf.pos; #if XDBG fprintf(stderr,"r1: %s roff=%d\n",splice->kref.s,roff); #endif if ( roff < splice->vcf.rlen && splice->kref.l < rlen ) { int len = splice->vcf.rlen - roff; // len still available in vcf.ref if ( len > rlen - splice->kref.l ) len = rlen - splice->kref.l; // how much of ref allele is still needed kputsn(splice->vcf.ref + roff, len, &splice->kref); } #if XDBG fprintf(stderr,"r2: %s\n",splice->kref.s); #endif uint32_t end = splice->vcf.pos + splice->vcf.rlen; // position just after the ref allele if ( splice->kref.l < rlen ) { if ( end + rlen - splice->kref.l - 1 > splice->tr->end ) // trim, the requested sequence is too long (could be extended, see N_REF_PAD) rlen -= end + rlen - splice->kref.l - 1 - splice->tr->end; if ( splice->kref.l < rlen ) kputsn(TSCRIPT_AUX(splice->tr)->ref + N_REF_PAD + end - splice->tr->beg, rlen - splice->kref.l, &splice->kref); } #if XDBG fprintf(stderr,"r3: %s\n",splice->kref.s); #endif int aoff; if ( abeg < splice->vcf.pos ) { assert( splice->tr->beg <= abeg ); kputsn(TSCRIPT_AUX(splice->tr)->ref + N_REF_PAD + abeg - splice->tr->beg, splice->vcf.pos - abeg, &splice->kalt); aoff = 0; } else aoff = abeg - splice->vcf.pos; #if XDBG fprintf(stderr,"a1: %s aoff=%d\n",splice->kalt.s,aoff); #endif if ( aoff < splice->vcf.alen && splice->kalt.l < alen ) { int len = splice->vcf.alen - aoff; // len still available in vcf.alt if ( len > alen - splice->kalt.l ) len = alen - splice->kalt.l; // how much of alt allele is still needed kputsn(splice->vcf.alt + aoff, len, &splice->kalt); aoff -= len; } if ( aoff < 0 ) aoff = 0; else aoff--; #if XDBG fprintf(stderr,"a2: %s aoff=%d\n",splice->kalt.s,aoff); #endif end = splice->vcf.pos + splice->vcf.rlen; // position just after the ref allele if ( splice->kalt.l < alen ) { if ( end + alen + aoff - splice->kalt.l - 1 > splice->tr->end ) // trim, the requested sequence is too long alen -= end + alen + aoff - splice->kalt.l - 1 - splice->tr->end; if ( alen > 0 && alen > splice->kalt.l ) kputsn(TSCRIPT_AUX(splice->tr)->ref + aoff + N_REF_PAD + end - splice->tr->beg, alen - splice->kalt.l, &splice->kalt); } #if XDBG fprintf(stderr,"a3: %s\n",splice->kalt.s); fprintf(stderr," [%s]\n [%s]\n\n",splice->kref.s,splice->kalt.s); #endif } void csq_stage(args_t *args, csq_t *csq, bcf1_t *rec); static inline int csq_stage_utr(args_t *args, regitr_t *itr, bcf1_t *rec, uint32_t trid, uint32_t type, int ial) { while ( regitr_overlap(itr) ) { gf_utr_t *utr = regitr_payload(itr, gf_utr_t*); gf_tscript_t *tr = utr->tr; if ( tr->id != trid ) continue; csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.type = (utr->which==prime5 ? CSQ_UTR5 : CSQ_UTR3) | type; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.vcf_ial = ial; csq.type.gene = tr->gene->name; csq_stage(args, &csq, rec); return csq.type.type; } return 0; } static inline void csq_stage_splice(args_t *args, bcf1_t *rec, gf_tscript_t *tr, uint32_t type, int ial) { #if XDBG fprintf(stderr,"csq_stage_splice %d: type=%d\n",(int)rec->pos+1,type); #endif if ( !type ) return; csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.type = type; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.vcf_ial = ial; csq.type.gene = tr->gene->name; csq_stage(args, &csq, rec); } static inline const char *drop_chr_prefix(args_t *args, const char *chr) { if ( !args->unify_chr_names ) return chr; if ( !strncasecmp("chr",chr,3) ) return chr+3; return chr; } static inline const char *add_chr_prefix(args_t *args, const char *chr) { if ( !args->unify_chr_names ) return chr; int len = strlen(chr); hts_expand(char,len+4,args->mchr_name,args->chr_name); memcpy(args->chr_name,"chr",3); memcpy(args->chr_name+3,chr,len+1); return args->chr_name; } static inline int splice_csq_ins(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end) { // coordinates that matter for consequences, eg AC>ACG trimmed to C>CG, 1bp // before and after the inserted bases if ( splice->tbeg || splice->vcf.ref[0]!=splice->vcf.alt[0] ) { splice->ref_beg = splice->vcf.pos + splice->tbeg - 1; splice->ref_end = splice->vcf.pos + splice->vcf.rlen - splice->tend; } else { if ( splice->tend ) splice->tend--; splice->ref_beg = splice->vcf.pos; splice->ref_end = splice->vcf.pos + splice->vcf.rlen - splice->tend; } #if XDBG fprintf(stderr,"ins: %s>%s .. ex=%d,%d beg,end=%d,%d tbeg,tend=%d,%d check_utr=%d start,stop,beg,end=%d,%d,%d,%d\n", splice->vcf.ref,splice->vcf.alt,ex_beg,ex_end,splice->ref_beg,splice->ref_end,splice->tbeg,splice->tend,splice->check_utr,splice->check_start,splice->check_stop,splice->check_region_beg,splice->check_region_end); #endif int ret; if ( splice->ref_beg >= ex_end ) // fully outside, beyond the exon { if ( splice->check_utr ) { regitr_t *itr = regitr_init(NULL); const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,splice->vcf.rec)); if ( regidx_overlap(args->idx_utr,chr,splice->ref_beg+1,splice->ref_beg+1, itr) ) // adjacent utr { ret = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial); if ( ret!=0 ) { regitr_destroy(itr); return SPLICE_OUTSIDE; // overlaps utr } } regitr_destroy(itr); } if ( !splice->check_region_end ) return SPLICE_OUTSIDE; char *ref = NULL, *alt = NULL; if ( splice->set_refalt ) // seq identity is checked only when tr->ref is available { splice_build_hap(splice, ex_end+1, N_SPLICE_REGION_INTRON); ref = splice->kref.s, alt = splice->kalt.s; } if ( splice->ref_beg < ex_end + N_SPLICE_REGION_INTRON && splice->ref_end > ex_end + N_SPLICE_DONOR ) { splice->csq |= CSQ_SPLICE_REGION; if ( ref && !strncmp(ref,alt,N_SPLICE_REGION_INTRON) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT; } if ( splice->ref_beg < ex_end + N_SPLICE_DONOR ) { if ( splice->check_donor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_DONOR; if ( splice->check_acceptor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_ACCEPTOR; if ( ref && !strncmp(ref,alt,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT; } csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial); return SPLICE_OUTSIDE; } if ( splice->ref_end < ex_beg || (splice->ref_end == ex_beg && !splice->check_region_beg) ) // fully outside, before the exon { if ( splice->check_utr ) { regitr_t *itr = regitr_init(NULL); const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,splice->vcf.rec)); if ( regidx_overlap(args->idx_utr,chr,splice->ref_end-1,splice->ref_end-1, itr) ) // adjacent utr { ret = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial); if ( ret!=0 ) { regitr_destroy(itr); return SPLICE_OUTSIDE; // overlaps utr } } regitr_destroy(itr); } if ( !splice->check_region_beg ) return SPLICE_OUTSIDE; char *ref = NULL, *alt = NULL; if ( splice->set_refalt ) // seq identity is checked only when tr->ref is available { splice_build_hap(splice, ex_beg - N_SPLICE_REGION_INTRON, N_SPLICE_REGION_INTRON); ref = splice->kref.s, alt = splice->kalt.s; } if ( splice->ref_end > ex_beg - N_SPLICE_REGION_INTRON && splice->ref_beg < ex_beg - N_SPLICE_DONOR ) { splice->csq |= CSQ_SPLICE_REGION; if ( ref && !strncmp(ref,alt,N_SPLICE_REGION_INTRON) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT; } if ( splice->ref_end > ex_beg - N_SPLICE_DONOR ) { if ( splice->check_donor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_DONOR; if ( splice->check_acceptor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_ACCEPTOR; if ( ref && !strncmp(ref+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,alt+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT; } csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial); return SPLICE_OUTSIDE; } // overlaps the exon or inside the exon // possible todo: find better alignment for frameshifting variants? if ( splice->ref_beg <= ex_beg + 2 ) // in the first 3bp { if ( splice->check_region_beg ) splice->csq |= CSQ_SPLICE_REGION; if ( splice->tr->strand==STRAND_FWD ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; } else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; } } if ( splice->ref_end > ex_end - 2 ) { if ( splice->check_region_end ) splice->csq |= CSQ_SPLICE_REGION; if ( splice->tr->strand==STRAND_REV ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; } else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; } } if ( splice->set_refalt ) { // Make sure the variant will not end up left aligned to avoid overlapping vcf records // splice_build_hap(splice, splice->ref_beg, splice->vcf.alen - splice->tend - splice->tbeg + 1); // splice->vcf.rlen -= splice->tbeg + splice->tend - 1; // if ( splice->kref.l > splice->vcf.rlen ) { splice->kref.l = splice->vcf.rlen; splice->kref.s[splice->kref.l] = 0; } if ( splice->ref_beg < splice->vcf.pos ) // this must have been caused by too much trimming from right { int dlen = splice->vcf.pos - splice->ref_beg; assert( dlen==1 ); splice->tbeg += dlen; if ( splice->tbeg + splice->tend == splice->vcf.rlen ) splice->tend -= dlen; splice->ref_beg = splice->vcf.pos; } if ( splice->ref_end==ex_beg ) splice->tend--; // prevent zero-length ref allele splice_build_hap(splice, splice->ref_beg, splice->vcf.alen - splice->tend - splice->tbeg + 1); splice->vcf.rlen -= splice->tbeg + splice->tend - 1; if ( splice->kref.l > splice->vcf.rlen ) { splice->kref.l = splice->vcf.rlen; splice->kref.s[splice->kref.l] = 0; } } csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial); return SPLICE_INSIDE; } int shifted_del_synonymous(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end) { static int small_ref_padding_warned = 0; gf_tscript_t *tr = splice->tr; // We know the VCF record overlaps the exon, but does it overlap the start codon? if ( tr->strand==STRAND_REV && splice->vcf.pos + splice->vcf.rlen + 2 <= ex_end ) return 0; if ( tr->strand==STRAND_FWD && splice->vcf.pos >= ex_beg + 3 ) return 0; #if XDBG fprintf(stderr,"shifted_del_synonymous: %d-%d %s\n",ex_beg,ex_end, tr->strand==STRAND_FWD?"fwd":(tr->strand==STRAND_REV?"rev":"unk")); fprintf(stderr," %d .. %s > %s\n",splice->vcf.pos+1,splice->vcf.ref,splice->vcf.alt); #endif // is there enough ref sequence for the extension? All coordinates are 0-based int ref_len = strlen(splice->vcf.ref); int alt_len = strlen(splice->vcf.alt); assert( ref_len > alt_len ); int ndel = ref_len - alt_len; if ( tr->strand==STRAND_REV ) { int32_t vcf_ref_end = splice->vcf.pos + ref_len - 1; // end pos of the VCF REF allele int32_t tr_ref_end = splice->tr->end + N_REF_PAD; // the end pos of accessible cached ref seq if ( vcf_ref_end + ndel > tr_ref_end ) { if ( !small_ref_padding_warned ) { fprintf(stderr,"Warning: Could not verify synonymous start/stop at %s:%d due to small N_REF_PAD. (Improve me?)\n",bcf_seqname(args->hdr,splice->vcf.rec),splice->vcf.pos+1); small_ref_padding_warned = 1; } return 0; } char *ptr_vcf = splice->vcf.ref + alt_len; // the first deleted base in the VCF REF allele char *ptr_ref = TSCRIPT_AUX(splice->tr)->ref + N_REF_PAD + (vcf_ref_end + 1 - splice->tr->beg); // the first ref base after the ndel bases deleted #if XDBG fprintf(stderr,"vcf: %s\nref: %s\n",ptr_vcf,ptr_ref); #endif int i = 0; while ( ptr_vcf[i] && ptr_vcf[i]==ptr_ref[i] ) i++; if ( ptr_vcf[i] ) return 0; // the deleted sequence cannot be replaced } else if ( tr->strand==STRAND_FWD ) { // STRAND_FWD int32_t vcf_block_beg = splice->vcf.pos + ref_len - 2*ndel; // the position of the first base of the ref block that could potentially replace the deletion if ( vcf_block_beg < 0 ) return 0; #if XDBG fprintf(stderr,"vcf_block_beg: %d\n",vcf_block_beg+1); #endif if ( N_REF_PAD + vcf_block_beg < ex_beg ) { if ( !small_ref_padding_warned ) { fprintf(stderr,"Warning: Could not verify synonymous start/stop at %s:%d due to small N_REF_PAD. (Improve me?)\n",bcf_seqname(args->hdr,splice->vcf.rec),splice->vcf.pos+1); small_ref_padding_warned = 1; } return 0; } char *ptr_vcf = splice->vcf.ref + alt_len; // the first deleted base in the VCF REF allele char *ptr_ref = TSCRIPT_AUX(splice->tr)->ref + N_REF_PAD + vcf_block_beg - splice->tr->beg; // the replacement ref block #if XDBG fprintf(stderr,"vcf: %s\nref: %s\n",ptr_vcf,ptr_ref); #endif int i = 0; while ( ptr_vcf[i] && ptr_vcf[i]==ptr_ref[i] ) i++; if ( ptr_vcf[i] ) return 0; // the deleted sequence cannot be replaced } return 1; } static inline int splice_csq_del(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end) { if ( splice->check_start ) { // check for synonymous start // test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.txt // test/csq/ENST00000368801.2/start-lost.txt // test/csq/ENST00000318249.2/synonymous-start-lost.txt int is_synonymous = shifted_del_synonymous(args, splice, ex_beg, ex_end); if ( is_synonymous ) { splice->csq |= CSQ_START_RETAINED; return SPLICE_OVERLAP; } } // coordinates that matter for consequences, eg AC>ACG trimmed to C>CG splice->ref_beg = splice->vcf.pos + splice->tbeg - 1; // 1b before the deleted base splice->ref_end = splice->vcf.pos + splice->vcf.rlen - splice->tend - 1; // the last deleted base #if XDBG fprintf(stderr,"splice_csq_del: %s>%s .. ex=%d,%d beg,end=%d,%d tbeg,tend=%d,%d check_utr=%d start,stop,beg,end=%d,%d,%d,%d\n", splice->vcf.ref,splice->vcf.alt,ex_beg,ex_end,splice->ref_beg,splice->ref_end,splice->tbeg,splice->tend,splice->check_utr,splice->check_start,splice->check_stop,splice->check_region_beg,splice->check_region_end); #endif if ( splice->ref_beg + 1 < ex_beg ) // the part before the exon; ref_beg is off by -1 { if ( splice->check_region_beg ) { int csq = 0; if ( splice->check_utr ) { regitr_t *itr = regitr_init(NULL); const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,splice->vcf.rec)); if ( regidx_overlap(args->idx_utr,chr,splice->ref_beg,ex_beg-1, itr) ) // adjacent utr csq = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial); regitr_destroy(itr); } if ( !csq ) { char *ref = NULL, *alt = NULL; if ( splice->set_refalt ) // seq identity is checked only when tr->ref is available { // filling from the left does not work for ENST00000341065/frame3.vcf // CAG.GTGGCCAG CAG.GTGGCCAG // CA-.--GGCCAG vs CAG.---GCCAG // splice_build_hap(splice, ex_beg-1, -N_SPLICE_REGION_INTRON); // // filling from the right: splice_build_hap(splice, ex_beg - N_SPLICE_REGION_INTRON, N_SPLICE_REGION_INTRON); ref = splice->kref.s, alt = splice->kalt.s; } if ( splice->ref_end >= ex_beg - N_SPLICE_REGION_INTRON && splice->ref_beg < ex_beg - N_SPLICE_DONOR ) { splice->csq |= CSQ_SPLICE_REGION; if ( ref && alt && !strncmp(ref,alt,N_SPLICE_REGION_INTRON) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT; } if ( splice->ref_end >= ex_beg - N_SPLICE_DONOR ) { if ( splice->check_donor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_DONOR; if ( splice->check_acceptor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_ACCEPTOR; if ( ref && alt && !strncmp(ref+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,alt+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT; } } } if ( splice->ref_end >= ex_beg ) { splice->tbeg = splice->ref_beg - splice->vcf.pos + 1; splice->ref_beg = ex_beg - 1; if ( splice->tbeg + splice->tend == splice->vcf.alen ) { // the deletion overlaps ex_beg and cannot be easily realigned to the right if ( !splice->tend ) { splice->csq |= CSQ_CODING_SEQUENCE; return SPLICE_OVERLAP; } splice->tend--; } } } if ( ex_end < splice->ref_end ) // the part after the exon { if ( splice->check_region_end ) { int csq = 0; if ( splice->check_utr ) { regitr_t *itr = regitr_init(NULL); const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,splice->vcf.rec)); if ( regidx_overlap(args->idx_utr,chr,ex_end+1,splice->ref_end, itr) ) // adjacent utr csq = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial); regitr_destroy(itr); } if ( !csq ) { char *ref = NULL, *alt = NULL; if ( splice->set_refalt ) // seq identity is checked only when tr->ref is available { splice_build_hap(splice, ex_end+1, N_SPLICE_REGION_INTRON); // ref,alt positioned at the first intron base ref = splice->kref.s, alt = splice->kalt.s; } if ( splice->ref_beg < ex_end + N_SPLICE_REGION_INTRON && splice->ref_end > ex_end + N_SPLICE_DONOR ) { splice->csq |= CSQ_SPLICE_REGION; if ( ref && alt && !strncmp(ref,alt,N_SPLICE_REGION_INTRON) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT; } if ( splice->ref_beg < ex_end + N_SPLICE_DONOR ) { if ( splice->check_donor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_DONOR; if ( splice->check_acceptor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_ACCEPTOR; if ( ref && alt && !strncmp(ref+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,alt+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT; } } } if ( splice->ref_beg < ex_end ) { splice->tend = splice->vcf.rlen - (splice->ref_end - splice->vcf.pos + 1); splice->ref_end = ex_end; } } if ( splice->ref_end < ex_beg || splice->ref_beg >= ex_end ) { csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial); return SPLICE_OUTSIDE; } if ( splice->ref_beg < ex_beg + 2 ) // ref_beg is off by -1 { if ( splice->check_region_beg ) splice->csq |= CSQ_SPLICE_REGION; if ( splice->tr->strand==STRAND_FWD ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; } else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; } } if ( splice->ref_end > ex_end - 3 ) { if ( splice->check_region_end ) splice->csq |= CSQ_SPLICE_REGION; if ( splice->tr->strand==STRAND_REV ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; } else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; } } if ( splice->set_refalt ) { if ( splice->tbeg>0 ) splice->tbeg--; //why is this? if ( splice->vcf.rlen > splice->tbeg + splice->tend && splice->vcf.alen > splice->tbeg + splice->tend ) { splice->vcf.rlen -= splice->tbeg + splice->tend; splice->vcf.alen -= splice->tbeg + splice->tend; } splice->kref.l = 0; kputsn(splice->vcf.ref + splice->tbeg, splice->vcf.rlen, &splice->kref); splice->kalt.l = 0; kputsn(splice->vcf.alt + splice->tbeg, splice->vcf.alen, &splice->kalt); if ( (splice->ref_beg+1 < ex_beg && splice->ref_end >= ex_beg) || (splice->ref_beg+1 < ex_end && splice->ref_end >= ex_end) ) // ouch, ugly ENST00000409523/long-overlapping-del.vcf { int ref_beg = splice->ref_beg + splice->kalt.l - 1; // 0 for AAA>A, 1 for AAA>AC if ( ref_beg < splice->ref_end ) splice->csq |= (splice->ref_end - ref_beg)%3 ? CSQ_FRAMESHIFT_VARIANT : CSQ_INFRAME_DELETION; return SPLICE_OVERLAP; } } csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial); return SPLICE_INSIDE; } static inline int splice_csq_mnp(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end) { // not a real variant, can be ignored: eg ACGT>ACGT if ( splice->tbeg + splice->tend == splice->vcf.rlen ) return SPLICE_VAR_REF; splice->ref_beg = splice->vcf.pos + splice->tbeg; splice->ref_end = splice->vcf.pos + splice->vcf.rlen - splice->tend - 1; #if XDBG fprintf(stderr,"mnp: %s>%s .. ex=%d,%d beg,end=%d,%d tbeg,tend=%d,%d check_utr=%d start,stop,beg,end=%d,%d,%d,%d\n", splice->vcf.ref,splice->vcf.alt,ex_beg,ex_end,splice->ref_beg,splice->ref_end,splice->tbeg,splice->tend,splice->check_utr,splice->check_start,splice->check_stop,splice->check_region_beg,splice->check_region_end); #endif if ( splice->ref_beg < ex_beg ) // the part before the exon { if ( splice->check_region_beg ) { int csq = 0; if ( splice->check_utr ) { regitr_t *itr = regitr_init(NULL); const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,splice->vcf.rec)); if ( regidx_overlap(args->idx_utr,chr,splice->ref_beg,ex_beg-1, itr) ) // adjacent utr csq = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial); regitr_destroy(itr); } if ( !csq ) { if ( splice->ref_end >= ex_beg - N_SPLICE_REGION_INTRON && splice->ref_beg < ex_beg - N_SPLICE_DONOR ) splice->csq |= CSQ_SPLICE_REGION; if ( splice->ref_end >= ex_beg - N_SPLICE_DONOR ) { if ( splice->check_donor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_DONOR; if ( splice->check_acceptor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_ACCEPTOR; } } } if ( splice->ref_end >= ex_beg ) { splice->tbeg = splice->ref_beg - splice->vcf.pos; splice->ref_beg = ex_beg; } } if ( ex_end < splice->ref_end ) // the part after the exon { if ( splice->check_region_end ) { int csq = 0; if ( splice->check_utr ) { regitr_t *itr = regitr_init(NULL); const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,splice->vcf.rec)); if ( regidx_overlap(args->idx_utr,chr,ex_end+1,splice->ref_end, itr) ) // adjacent utr csq = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial); regitr_destroy(itr); } if ( !csq ) { if ( splice->ref_beg <= ex_end + N_SPLICE_REGION_INTRON && splice->ref_end > ex_end + N_SPLICE_DONOR ) splice->csq |= CSQ_SPLICE_REGION; if ( splice->ref_beg <= ex_end + N_SPLICE_DONOR ) { if ( splice->check_donor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_DONOR; if ( splice->check_acceptor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_ACCEPTOR; } } } if ( splice->ref_beg <= ex_end ) { splice->tend = splice->vcf.rlen - (splice->ref_end - splice->vcf.pos + 1); splice->ref_end = ex_end; } } if ( splice->ref_end < ex_beg || splice->ref_beg > ex_end ) { csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial); return SPLICE_OUTSIDE; } if ( splice->ref_beg < ex_beg + 3 ) { if ( splice->check_region_beg ) splice->csq |= CSQ_SPLICE_REGION; if ( splice->tr->strand==STRAND_FWD ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; } else if ( splice->tr->strand==STRAND_REV ) { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; } } if ( splice->ref_end > ex_end - 3 ) { if ( splice->check_region_end ) splice->csq |= CSQ_SPLICE_REGION; if ( splice->tr->strand==STRAND_REV ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; } else if ( splice->tr->strand==STRAND_FWD ) { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; } } if ( splice->set_refalt ) { splice->vcf.rlen -= splice->tbeg + splice->tend; splice->kref.l = 0; kputsn(splice->vcf.ref + splice->tbeg, splice->vcf.rlen, &splice->kref); splice->kalt.l = 0; kputsn(splice->vcf.alt + splice->tbeg, splice->vcf.rlen, &splice->kalt); } csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial); return SPLICE_INSIDE; } static inline int splice_csq(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end) { splice->vcf.alen = strlen(splice->vcf.alt); int rlen1 = splice->vcf.rlen - 1, alen1 = splice->vcf.alen - 1, i = 0; splice->tbeg = 0, splice->tend = 0; // trim from the right, then from the left while ( i<=rlen1 && i<=alen1 ) { if ( splice->vcf.ref[rlen1-i] != splice->vcf.alt[alen1-i] ) break; i++; } splice->tend = i; rlen1 -= i, alen1 -= i, i = 0; while ( i<=rlen1 && i<=alen1 ) { if ( splice->vcf.ref[i] != splice->vcf.alt[i] ) break; i++; } splice->tbeg = i; // The mnp, ins and del code was split into near-identical functions for clarity and debugging; // possible todo: generalize once stable if ( splice->vcf.rlen==splice->vcf.alen ) return splice_csq_mnp(args, splice, ex_beg, ex_end); if ( splice->vcf.rlen < splice->vcf.alen ) return splice_csq_ins(args, splice, ex_beg, ex_end); if ( splice->vcf.rlen > splice->vcf.alen ) return splice_csq_del(args, splice, ex_beg, ex_end); return 0; } // return value: 0 added, 1 overlapping variant, 2 silent discard (intronic,alt=ref) int hap_init(args_t *args, hap_node_t *parent, hap_node_t *child, gf_cds_t *cds, bcf1_t *rec, int ial) { int i; kstring_t str = {0,0,0}; gf_tscript_t *tr = cds->tr; child->icds = cds->icds; // index of cds in the tscript's list of exons child->vcf_ial = ial; splice_t splice; splice_init(&splice, rec); splice.tr = tr; splice.vcf.ial = ial; splice.vcf.alt = rec->d.allele[ial]; splice.check_acceptor = splice.check_donor = splice.set_refalt = splice.check_utr = 1; if ( !(tr->trim & TRIM_5PRIME) ) { if ( tr->strand==STRAND_FWD ) { if ( child->icds==0 ) splice.check_start = 1; } else if ( tr->strand==STRAND_REV ) { if ( child->icds==tr->ncds-1 ) splice.check_start = 1; } } if ( !(tr->trim & TRIM_3PRIME) ) { if ( tr->strand==STRAND_FWD ) { if ( child->icds==tr->ncds-1 ) splice.check_stop = 1; } else if ( tr->strand==STRAND_REV ) { if ( child->icds==0 ) splice.check_stop = 1; } } if ( splice.check_start ) // do not check starts in incomplete CDS, defined as not starting with M { if ( tr->strand==STRAND_FWD ) { if ( dna2aa(TSCRIPT_AUX(tr)->ref+N_REF_PAD+cds->beg-tr->beg) != 'M' ) splice.check_start = 0; } else if ( tr->strand==STRAND_REV ) { if ( cdna2aa(TSCRIPT_AUX(tr)->ref+N_REF_PAD+cds->beg-tr->beg+cds->len-3) != 'M' ) splice.check_start = 0; } } if ( child->icds!=0 ) splice.check_region_beg = 1; if ( child->icds!=tr->ncds-1 ) splice.check_region_end = 1; #if XDBG fprintf(stderr,"\nhap_init: %d [%s][%s] check start:%d,stop:%d\n",splice.vcf.pos+1,splice.vcf.ref,splice.vcf.alt,splice.check_start,splice.check_stop); #endif int ret = splice_csq(args, &splice, cds->beg, cds->beg + cds->len - 1); #if XDBG fprintf(stderr,"cds splice_csq: %d [%s][%s] .. beg,end=%d %d, ret=%d, csq=%d\n\n",splice.vcf.pos+1,splice.kref.s,splice.kalt.s,splice.ref_beg+1,splice.ref_end+1,ret,splice.csq); #endif if ( ret==SPLICE_VAR_REF ) return 2; // not a variant, eg REF=CA ALT=CA if ( ret==SPLICE_OUTSIDE || ret==SPLICE_OVERLAP || splice.csq==CSQ_START_LOST ) // not a coding csq { free(splice.kref.s); free(splice.kalt.s); if ( !splice.csq ) return 2; // fully intronic, no csq // splice_region/acceptor/donor child->seq = NULL; child->sbeg = 0; child->rbeg = rec->pos; child->rlen = 0; child->dlen = 0; kputs(rec->d.allele[0],&str); kputc('>',&str); kputs(rec->d.allele[ial],&str); child->var = str.s; child->type = HAP_SSS; child->csq = splice.csq; child->rec = rec; return 0; } if ( splice.csq & CSQ_SYNONYMOUS_VARIANT ) splice.csq &= ~CSQ_SYNONYMOUS_VARIANT; // synonymous&splice,frame could become synonymous&frame,splice int dbeg = 0; if ( splice.ref_beg < cds->beg ) { // The vcf record overlaps the exon boundary, but the variant itself // should fit inside since we are here. This will need more work. // #1475227917 dbeg = cds->beg - splice.ref_beg; splice.kref.l -= dbeg; splice.ref_beg = cds->beg; assert( dbeg <= splice.kalt.l ); } assert( parent->type!=HAP_SSS ); if ( parent->type==HAP_CDS ) { i = parent->icds; if ( i!=cds->icds ) { // the variant is on a new exon, finish up the previous int len = tr->cds[i]->len - parent->rbeg - parent->rlen + tr->cds[i]->beg; if ( len > 0 ) kputsn_(TSCRIPT_AUX(tr)->ref + N_REF_PAD + parent->rbeg + parent->rlen - tr->beg, len, &str); } // append any skipped non-variant exons while ( ++i < cds->icds ) kputsn_(TSCRIPT_AUX(tr)->ref + N_REF_PAD + tr->cds[i]->beg - tr->beg, tr->cds[i]->len, &str); if ( parent->icds==child->icds ) { int len = splice.ref_beg - parent->rbeg - parent->rlen; if ( len < 0 ) // overlapping variants { free(str.s); free(splice.kref.s); free(splice.kalt.s); return 1; } kputsn_(TSCRIPT_AUX(tr)->ref + N_REF_PAD + parent->rbeg + parent->rlen - tr->beg, len, &str); } else kputsn_(TSCRIPT_AUX(tr)->ref + N_REF_PAD + cds->beg - tr->beg, splice.ref_beg - cds->beg, &str); } kputs(splice.kalt.s + dbeg, &str); child->seq = str.s; child->sbeg = cds->pos + (splice.ref_beg - cds->beg); child->rbeg = splice.ref_beg; child->rlen = splice.kref.l; child->type = HAP_CDS; child->prev = parent; child->rec = rec; child->csq = splice.csq; // set vlen and the "ref>alt" string { int rlen = strlen(rec->d.allele[0]); int alen = strlen(rec->d.allele[ial]); child->dlen = alen - rlen; child->var = (char*) malloc(rlen+alen+2); memcpy(child->var,rec->d.allele[0],rlen); child->var[rlen] = '>'; memcpy(child->var+rlen+1,rec->d.allele[ial],alen); child->var[rlen+alen+1] = 0; } // yuck, the whole CDS is modified/deleted, not ready for this, todo. if ( child->rbeg + child->rlen > cds->beg + cds->len ) { child->type = HAP_SSS; if ( !child->csq ) child->csq |= CSQ_CODING_SEQUENCE; // hack, specifically for ENST00000390520/deletion-overlap.vcf } free(splice.kref.s); free(splice.kalt.s); return 0; } void hap_destroy(hap_node_t *hap) { int i; for (i=0; inchild; i++) if ( hap->child[i] ) hap_destroy(hap->child[i]); for (i=0; imcsq_list; i++) free(hap->csq_list[i].type.vstr.s); free(hap->csq_list); free(hap->child); free(hap->cur_child); free(hap->seq); free(hap->var); free(hap); } /* ref: spliced reference and its length (ref.l) seq: part of the spliced query transcript on the reference strand to translate, its length (seq.l) and the total length of the complete transcript (seq.m) sbeg: seq offset within the spliced query transcript rbeg: seq offset within ref, 0-based rend: last base of seq within ref, plus one. If seq does not contain indels, it is rend=rbeg+seq->l strand: coding strand - 0:rev, 1:fwd tseq: translated sequence (aa) fill: frameshift, fill until the end (strand=fwd) or from the start (strand=rev) */ void cds_translate(kstring_t *_ref, kstring_t *_seq, uint32_t sbeg, uint32_t rbeg, uint32_t rend, int strand, kstring_t *tseq, int fill) { #if XDBG fprintf(stderr,"\ntranslate: %d %d %d fill=%d seq.l=%d\n",sbeg,rbeg,rend,fill,(int)_seq->l); #endif char tmp[3], *codon, *end; int i, len, npad; kstring_t ref = *_ref; kstring_t seq = *_seq; tseq->l = 0; if ( !seq.l ) { kputc('?', tseq); return; } #define DBG 0 #if DBG fprintf(stderr,"translate: sbeg,rbeg,rend=%d %d %d fill=%d seq.l=%d\n",sbeg,rbeg,rend,fill,(int)_seq->l); fprintf(stderr," ref: l=%d %s\n", (int)ref.l,ref.s); fprintf(stderr," seq: l=%d m=%d ", (int)seq.l,(int)seq.m); for (i=0; i1 fprintf(stderr," npad: %d\n",npad); #endif assert( npad<=rbeg ); for (i=0; i1 fprintf(stderr,"\t i=%d\n", i); #endif if ( i==3 ) { kputc_(dna2aa(tmp), tseq); #if DBG>1 fprintf(stderr,"[1]%c%c%c\n",tmp[0],tmp[1],tmp[2]); #endif codon = seq.s + 3 - npad; // next codon end = codon + len - 1 - (len % 3); // last position of a valid codon while ( codon < end ) { kputc_(dna2aa(codon), tseq); #if DBG>1 fprintf(stderr,"[2]%c%c%c\n",codon[0],codon[1],codon[2]); #endif codon += 3; } end = seq.s + seq.l - 1; for (i=0; codon+i<=end; i++) tmp[i] = codon[i]; } // right padding codon = ref.s + rend + N_REF_PAD; if ( i>0 ) { #if DBG>1 if(i==1)fprintf(stderr,"[3]%c\n",tmp[0]); if(i==2)fprintf(stderr,"[3]%c%c\n",tmp[0],tmp[1]); #endif for (; i<3; i++) { tmp[i] = *codon; codon++; } kputc_(dna2aa(tmp), tseq); #if DBG>1 fprintf(stderr,"[4]%c%c%c\n",tmp[0],tmp[1],tmp[2]); #endif } if ( fill!=0 ) { end = ref.s + ref.l - N_REF_PAD; while ( codon+3 <= end ) { kputc_(dna2aa(codon), tseq); #if DBG>1 fprintf(stderr,"[5]%c%c%c\t%c\n",codon[0],codon[1],codon[2],dna2aa(codon)); #endif codon += 3; } } } else if ( strand==STRAND_REV ) { // right padding - number of bases to take from ref npad = (seq.m - (sbeg + seq.l)) % 3; #if DBG>1 fprintf(stderr," npad: %d\n",npad); #endif if ( !(npad>=0 && sbeg+seq.l+npad<=seq.m) ) fprintf(stderr,"sbeg=%d seq.l=%d seq.m=%d npad=%d\n",sbeg,(int)seq.l,(int)seq.m,npad); assert( npad>=0 && sbeg+seq.l+npad<=seq.m ); // todo: first codon on the rev strand if ( npad==2 ) { tmp[1] = ref.s[rend+N_REF_PAD]; tmp[2] = ref.s[rend+N_REF_PAD+1]; i = 0; } else if ( npad==1 ) { tmp[2] = ref.s[rend+N_REF_PAD]; i = 1; } else i = 2; end = seq.s + seq.l; for (; i>=0 && end>seq.s; i--) tmp[i] = *(--end); #if DBG>1 fprintf(stderr,"\t i=%d\n", i); if(i==1)fprintf(stderr,"[0] %c\n",tmp[2]); if(i==0)fprintf(stderr,"[0] %c%c\n",tmp[1],tmp[2]); #endif if ( i==-1 ) { #if DBG>1 fprintf(stderr,"[1]%c%c%c\t%c\n",tmp[0],tmp[1],tmp[2], cdna2aa(tmp)); #endif kputc_(cdna2aa(tmp), tseq); codon = end - 3; while ( codon >= seq.s ) { kputc_(cdna2aa(codon), tseq); #if DBG>1 fprintf(stderr,"[2]%c%c%c\t%c\n",codon[0],codon[1],codon[2], cdna2aa(codon)); #endif codon -= 3; } if ( seq.s-codon==2 ) { tmp[2] = seq.s[0]; i = 1; } else if ( seq.s-codon==1 ) { tmp[1] = seq.s[0]; tmp[2] = seq.s[1]; i = 0; } else i = -1; #if DBG>1 if(i==1)fprintf(stderr,"[3] %c\n",tmp[2]); if(i==0)fprintf(stderr,"[3] %c%c\n",tmp[1],tmp[2]); #endif } // left padding end = ref.s + N_REF_PAD + rbeg; if ( i>=0 ) { for (; i>=0 && end>=ref.s; i--) tmp[i] = *(--end); kputc_(cdna2aa(tmp), tseq); #if DBG>1 fprintf(stderr,"[4]%c%c%c\t%c\n",tmp[0],tmp[1],tmp[2],cdna2aa(tmp)); #endif } if ( fill!=0 ) { codon = end - 3; while ( codon >= ref.s + N_REF_PAD ) { kputc_(cdna2aa(codon), tseq); #if DBG>1 fprintf(stderr,"[5]%c%c%c\t%c\n",codon[0],codon[1],codon[2],cdna2aa(codon)); #endif codon -= 3; } } } else error("Should not happen: %d\n", strand); kputc_(0,tseq); tseq->l--; #if DBG fprintf(stderr," tseq: %s\n", tseq->s); #endif } void tscript_splice_ref(gf_tscript_t *tr) { int i, len = 0; for (i=0; incds; i++) len += tr->cds[i]->len; TSCRIPT_AUX(tr)->nsref = len + 2*N_REF_PAD; TSCRIPT_AUX(tr)->sref = (char*) malloc(len + 1 + 2*N_REF_PAD); len = 0; memcpy(TSCRIPT_AUX(tr)->sref, TSCRIPT_AUX(tr)->ref + tr->cds[0]->beg - tr->beg, N_REF_PAD); len += N_REF_PAD; for (i=0; incds; i++) { memcpy(TSCRIPT_AUX(tr)->sref + len, TSCRIPT_AUX(tr)->ref + N_REF_PAD + tr->cds[i]->beg - tr->beg, tr->cds[i]->len); len += tr->cds[i]->len; } memcpy(TSCRIPT_AUX(tr)->sref + len, TSCRIPT_AUX(tr)->ref + N_REF_PAD + tr->cds[tr->ncds-1]->beg - tr->beg, N_REF_PAD); len += N_REF_PAD; TSCRIPT_AUX(tr)->sref[len] = 0; } // returns: 0 if consequence was added, 1 if it already exists or could not be added int csq_push(args_t *args, csq_t *csq, bcf1_t *rec) { #if XDBG fprintf(stderr,"csq_push: %d .. %d\n",(int)rec->pos+1,csq->type.type); #endif khint_t k = kh_get(pos2vbuf, args->pos2vbuf, (int)csq->pos); vbuf_t *vbuf = (k == kh_end(args->pos2vbuf)) ? NULL : kh_val(args->pos2vbuf, k); if ( !vbuf ) error("This should not happen. %s:%d %s\n",bcf_seqname(args->hdr,rec),csq->pos+1,csq->type.vstr.s); int i; for (i=0; in; i++) if ( vbuf->vrec[i]->line==rec ) break; if ( i==vbuf->n ) error("This should not happen.. %s:%d %s\n", bcf_seqname(args->hdr,rec),csq->pos+1,csq->type.vstr.s); vrec_t *vrec = vbuf->vrec[i]; // if the variant overlaps donor/acceptor and also splice region, report only donor/acceptor if ( csq->type.type & CSQ_SPLICE_REGION && csq->type.type & (CSQ_SPLICE_DONOR|CSQ_SPLICE_ACCEPTOR) ) csq->type.type &= ~CSQ_SPLICE_REGION; if ( csq->type.type & CSQ_PRINTED_UPSTREAM ) { for (i=0; invcsq; i++) { // Same as below, to avoid records like // 3630 .. @3632,stop_lost|AL627309.1|ENST00000423372|protein_coding|- // 3632 .. stop_lost|AL627309.1|ENST00000423372|protein_coding|-|260*>260G|3630T>A+3632A>C if ( csq->type.type&CSQ_START_STOP && vrec->vcsq[i].type&CSQ_START_STOP ) { vrec->vcsq[i] = csq->type; goto exit_duplicate; } if ( !(vrec->vcsq[i].type & CSQ_PRINTED_UPSTREAM) ) continue; if ( csq->type.ref != vrec->vcsq[i].ref ) continue; goto exit_duplicate; } } else if ( csq->type.type & CSQ_COMPOUND ) { for (i=0; invcsq; i++) { if ( csq->type.trid != vrec->vcsq[i].trid && (csq->type.type|vrec->vcsq[i].type)&CSQ_PRN_TSCRIPT ) continue; if ( csq->type.biotype != vrec->vcsq[i].biotype ) continue; if ( csq->type.gene != vrec->vcsq[i].gene ) continue; if ( csq->type.vcf_ial != vrec->vcsq[i].vcf_ial ) continue; if ( (csq->type.type&CSQ_UPSTREAM_STOP)^(vrec->vcsq[i].type&CSQ_UPSTREAM_STOP) ) continue; // both must or mustn't have upstream_stop if ( csq->type.vstr.s || vrec->vcsq[i].vstr.s ) { // This is a bit hacky, but we want a simpler and more predictable output. The splice_csq() function // can trigger stop/start events based on indel overlap, then another stop/start event can be triggered // from add_csq() or test_cds_local() based on sequence comparison, and on output we could find two // consequences: // stop_lost|AL627309.1|ENST00000423372|protein_coding|- // stop_lost&inframe_insertion|AL627309.1|ENST00000423372|protein_coding|-|260*>260CL|3630T>TAAA if ( !csq->type.vstr.s || !vrec->vcsq[i].vstr.s ) { if ( csq->type.type&CSQ_START_STOP && vrec->vcsq[i].type&CSQ_START_STOP ) { vrec->vcsq[i].type |= csq->type.type; // remove stop_lost&synonymous if stop_retained set if ( vrec->vcsq[i].type&CSQ_STOP_RETAINED ) vrec->vcsq[i].type &= ~(CSQ_STOP_LOST|CSQ_SYNONYMOUS_VARIANT); if ( !vrec->vcsq[i].vstr.s ) vrec->vcsq[i].vstr = csq->type.vstr; goto exit_duplicate; } continue; } if ( strcmp(csq->type.vstr.s,vrec->vcsq[i].vstr.s) ) continue; } vrec->vcsq[i].type |= csq->type.type; goto exit_duplicate; } } else { for (i=0; invcsq; i++) { if ( csq->type.trid != vrec->vcsq[i].trid && (csq->type.type|vrec->vcsq[i].type)&CSQ_PRN_TSCRIPT) continue; if ( csq->type.biotype != vrec->vcsq[i].biotype ) continue; if ( !(vrec->vcsq[i].type & CSQ_COMPOUND) ) { vrec->vcsq[i].type |= csq->type.type; goto exit_duplicate; } if ( vrec->vcsq[i].type==(vrec->vcsq[i].type|csq->type.type) ) goto exit_duplicate; } } // no such csq yet in this vcf record csq->vrec = vrec; csq->idx = vrec->nvcsq++; hts_expand0(vcsq_t, vrec->nvcsq, vrec->mvcsq, vrec->vcsq); vrec->vcsq[i] = csq->type; return 0; exit_duplicate: csq->vrec = vrec; csq->idx = i; return 1; } // soff .. position of the variant within the trimmed query transcript // sbeg .. position of the variant within the query transcript // rbeg .. position on the reference transcript (if there are no indels, then rbeg=send) // rpos .. VCF position #define node2soff(i) (hap->stack[i].slen - (hap->stack[i].node->rlen + hap->stack[i].node->dlen)) #define node2sbeg(i) (hap->sbeg + node2soff(i)) #define node2send(i) (hap->sbeg + hap->stack[i].slen) #define node2rbeg(i) (hap->stack[i].node->sbeg) #define node2rend(i) (hap->stack[i].node->sbeg + hap->stack[i].node->rlen) #define node2rpos(i) (hap->stack[i].node->rec->pos) void kput_vcsq(args_t *args, vcsq_t *csq, kstring_t *str) { // Remove start/stop from incomplete CDS, but only if there is another // consequence as something must be reported if ( csq->type & CSQ_INCOMPLETE_CDS && (csq->type & ~(CSQ_START_STOP|CSQ_INCOMPLETE_CDS|CSQ_UPSTREAM_STOP)) ) csq->type &= ~(CSQ_START_STOP|CSQ_INCOMPLETE_CDS); // Remove missense from start/stops if ( csq->type & CSQ_START_STOP && csq->type & CSQ_MISSENSE_VARIANT ) csq->type &= ~CSQ_MISSENSE_VARIANT; if ( csq->type & CSQ_PRINTED_UPSTREAM && csq->ref ) { kputc_('@',str); kputw(csq->ref->pos+1, str); return; } if ( csq->type & CSQ_UPSTREAM_STOP ) kputc_('*',str); int has_csq = 0, i, n = sizeof(csq_strings)/sizeof(char*); for (i=1; itype&(1<type&(1<biotype==GF_NMD) && (csq->type & CSQ_PRN_NMD) ) { if ( has_csq ) kputc_('&',str); // just in case, this should always be true kputs("NMD_transcript",str); } kputc_('|', str); if ( csq->gene ) kputs(csq->gene , str); kputc_('|', str); // if ( csq->type & CSQ_PRN_TSCRIPT ) kputs(args->tscript_ids.str[csq->trid], str); if ( csq->type & CSQ_PRN_TSCRIPT ) kputs(gff_id2string(args->gff,transcript,csq->trid), str); kputc_('|', str); kputs(gf_type2gff_string(csq->biotype), str); if ( CSQ_PRN_STRAND(csq->type) || csq->vstr.l ) kputs(csq->strand==STRAND_FWD ? "|+" : (csq->strand==STRAND_REV ? "|-" : "|."), str); if ( csq->vstr.l ) kputs(csq->vstr.s, str); } void kprint_aa_prediction(args_t *args, int beg, kstring_t *aa, kstring_t *str) { if ( !args->brief_predictions || (int)aa->l - args->brief_predictions < 3 ) kputs(aa->s, str); else { int i, len = aa->l; if ( aa->s[len-1]=='*' ) len--; for (i=0; ibrief_predictions; i++) kputc(aa->s[i], str); kputs("..", str); kputw(beg+len, str); } } void hap_add_csq(args_t *args, hap_t *hap, hap_node_t *node, int tlen, int ibeg, int iend, int dlen, int indel) { int i; gf_tscript_t *tr = hap->tr; assert( tr->strand==STRAND_FWD || tr->strand==STRAND_REV ); int ref_node = tr->strand==STRAND_FWD ? ibeg : iend; int icsq = node->ncsq_list++; hts_expand0(csq_t,node->ncsq_list,node->mcsq_list,node->csq_list); csq_t *csq = &node->csq_list[icsq]; csq->pos = hap->stack[ref_node].node->rec->pos; csq->type.trid = tr->id; csq->type.vcf_ial = node->vcf_ial; csq->type.gene = tr->gene->name; csq->type.strand = tr->strand; csq->type.biotype = tr->type; // only now we see the translated sequence and can determine if the stop/start changes are real int rm_csq = 0; csq->type.type = 0; for (i=ibeg; i<=iend; i++) csq->type.type |= hap->stack[i].node->csq & CSQ_COMPOUND; if ( dlen==0 && indel ) csq->type.type |= CSQ_INFRAME_ALTERING; int has_upstream_stop = hap->upstream_stop; if ( hap->stack[ibeg].node->type != HAP_SSS ) { // check for truncating stops for (i=0; itref.l; i++) if ( hap->tref.s[i]=='*' ) break; if ( i!=hap->tref.l ) { hap->tref.l = i+1; hap->tref.s[i+1] = 0; } for (i=0; itseq.l; i++) if ( hap->tseq.s[i]=='*' ) break; if ( i!=hap->tseq.l ) { hap->tseq.l = i+1; hap->tseq.s[i+1] = 0; hap->upstream_stop = 1; } if ( csq->type.type & CSQ_STOP_LOST ) { if ( hap->tref.s[hap->tref.l-1]=='*' && hap->tref.s[hap->tref.l-1] == hap->tseq.s[hap->tseq.l-1] ) { rm_csq |= CSQ_STOP_LOST; csq->type.type |= CSQ_STOP_RETAINED; } else if ( hap->tref.s[hap->tref.l-1]!='*' ) { // This is CDS 3' incomplete ENSG00000173376/synon.vcf, can also be missense // We observe in real data a change to a stop, ENST00000528237/retained-stop-incomplete-cds.vcf if ( hap->tseq.s[hap->tseq.l-1] == '*' ) { rm_csq |= CSQ_STOP_GAINED; csq->type.type |= CSQ_STOP_RETAINED; } else csq->type.type |= CSQ_INCOMPLETE_CDS; } } if ( csq->type.type & CSQ_START_LOST && hap->tref.s[0]!='M' ) { rm_csq |= CSQ_START_LOST; csq->type.type &= ~CSQ_START_LOST; } if ( dlen!=0 ) { if ( dlen%3 ) csq->type.type |= CSQ_FRAMESHIFT_VARIANT; else if ( dlen<0 ) csq->type.type |= CSQ_INFRAME_DELETION; else csq->type.type |= CSQ_INFRAME_INSERTION; if ( hap->tref.s[hap->tref.l-1]!='*' && hap->tseq.s[hap->tseq.l-1]=='*' ) csq->type.type |= CSQ_STOP_GAINED; } else { int aa_change = 0; for (i=0; itref.l; i++) { if ( hap->tref.s[i] == hap->tseq.s[i] ) continue; aa_change = 1; if ( hap->tref.s[i] == '*' ) csq->type.type |= CSQ_STOP_LOST; else if ( hap->tseq.s[i] == '*' ) csq->type.type |= CSQ_STOP_GAINED; else csq->type.type |= CSQ_MISSENSE_VARIANT; } if ( !aa_change ) csq->type.type |= CSQ_SYNONYMOUS_VARIANT; } } // Check if compound inframe variants are real inframes, or if the stop codon occurs before the frameshift can be restored if ( ibeg!=iend && (csq->type.type & (CSQ_INFRAME_DELETION|CSQ_INFRAME_INSERTION|CSQ_INFRAME_ALTERING)) && hap->tseq.s[hap->tseq.l-1]=='*' ) { rm_csq |= CSQ_INFRAME_DELETION | CSQ_INFRAME_INSERTION | CSQ_INFRAME_ALTERING; csq->type.type |= CSQ_FRAMESHIFT_VARIANT | CSQ_STOP_GAINED; } if ( has_upstream_stop ) csq->type.type |= CSQ_UPSTREAM_STOP; csq->type.type &= ~rm_csq; if ( hap->stack[ibeg].node->type == HAP_SSS ) { node->csq_list[icsq].type.type |= hap->stack[ibeg].node->csq & ~rm_csq; node->csq_list[icsq].type.ref = hap->stack[ibeg].node->rec; node->csq_list[icsq].type.biotype = tr->type; csq_push(args, node->csq_list+icsq, hap->stack[ibeg].node->rec); return; } kstring_t str = node->csq_list[icsq].type.vstr; str.l = 0; // create the aa variant string int aa_rbeg = tr->strand==STRAND_FWD ? node2rbeg(ibeg)/3+1 : (TSCRIPT_AUX(hap->tr)->nsref - 2*N_REF_PAD - node2rend(iend))/3+1; int aa_sbeg = tr->strand==STRAND_FWD ? node2sbeg(ibeg)/3+1 : (tlen - node2send(iend))/3+1; kputc_('|', &str); kputw(aa_rbeg, &str); kprint_aa_prediction(args,aa_rbeg,&hap->tref,&str); if ( !(csq->type.type & CSQ_SYNONYMOUS_VARIANT) ) { kputc_('>', &str); kputw(aa_sbeg, &str); kprint_aa_prediction(args,aa_sbeg,&hap->tseq,&str); } kputc_('|', &str); // create the dna variant string and, in case of combined variants, // insert silent CSQ_PRINTED_UPSTREAM variants for (i=ibeg; i<=iend; i++) { if ( i>ibeg ) kputc_('+', &str); kputw(node2rpos(i)+1, &str); kputs(hap->stack[i].node->var, &str); } node->csq_list[icsq].type.vstr = str; csq_push(args, node->csq_list+icsq, hap->stack[ref_node].node->rec); for (i=ibeg; i<=iend; i++) { // csq are printed at one position only for combined variants, the rest is // silent and references the first if ( hap->stack[i].node->csq & ~CSQ_COMPOUND ) { node->ncsq_list++; hts_expand0(csq_t,node->ncsq_list,node->mcsq_list,node->csq_list); csq_t *tmp_csq = &node->csq_list[node->ncsq_list - 1]; tmp_csq->pos = hap->stack[i].node->rec->pos; tmp_csq->type.trid = tr->id; //??tmp_csq->type.vcf_ial = node->vcf_ial; .. this should not be needed for non-compound variants tmp_csq->type.gene = tr->gene->name; tmp_csq->type.strand = tr->strand; tmp_csq->type.type = hap->stack[i].node->csq & ~CSQ_COMPOUND & ~rm_csq; tmp_csq->type.biotype = tr->type; tmp_csq->type.vstr.l = 0; kputs(str.s,&tmp_csq->type.vstr); csq_push(args, tmp_csq, hap->stack[i].node->rec); } if ( i!=ref_node && (node->csq_list[icsq].type.type & CSQ_COMPOUND || !(hap->stack[i].node->csq & ~CSQ_COMPOUND)) ) { node->ncsq_list++; hts_expand0(csq_t,node->ncsq_list,node->mcsq_list,node->csq_list); csq_t *tmp_csq = &node->csq_list[node->ncsq_list - 1]; tmp_csq->pos = hap->stack[i].node->rec->pos; tmp_csq->type.trid = tr->id; //??tmp_csq->type.vcf_ial = node->vcf_ial; .. this should not be needed for non-compound variants tmp_csq->type.gene = tr->gene->name; tmp_csq->type.strand = tr->strand; tmp_csq->type.type = CSQ_PRINTED_UPSTREAM | hap->stack[i].node->csq; tmp_csq->type.biotype = tr->type; tmp_csq->type.ref = hap->stack[ref_node].node->rec; tmp_csq->type.vstr.l = 0; csq_push(args, tmp_csq, hap->stack[i].node->rec); } } } void hap_finalize(args_t *args, hap_t *hap) { gf_tscript_t *tr = hap->tr; if ( !TSCRIPT_AUX(tr)->sref ) tscript_splice_ref(tr); kstring_t sref; sref.s = TSCRIPT_AUX(tr)->sref; sref.l = TSCRIPT_AUX(tr)->nsref; sref.m = sref.l; int istack = 0; hts_expand(hstack_t,1,hap->mstack,hap->stack); hap->sseq.l = 0; hap->tseq.l = 0; hap->stack[0].node = TSCRIPT_AUX(tr)->root; hap->stack[0].ichild = -1; hap->stack[0].slen = 0; hap->stack[0].dlen = 0; while ( istack>=0 ) { hstack_t *stack = &hap->stack[istack]; hap_node_t *node = hap->stack[istack].node; while ( ++hap->stack[istack].ichild < node->nchild ) { if ( node->child[stack->ichild] ) break; } if ( stack->ichild == node->nchild ) { istack--; continue; } node = node->child[stack->ichild]; istack++; hts_expand(hstack_t,istack+1,hap->mstack,hap->stack); stack = &hap->stack[istack-1]; hap->stack[istack].node = node; hap->stack[istack].ichild = -1; hap->sseq.l = stack->slen; if ( node->type==HAP_CDS ) kputs(node->seq, &hap->sseq); hap->stack[istack].slen = hap->sseq.l; hap->stack[istack].dlen = hap->stack[istack-1].dlen + node->dlen; if ( !node->nend ) continue; // not a leaf node // The spliced sequence has been built for the current haplotype and stored // in hap->sseq. Now we break it and output as independent parts kstring_t sseq; sseq.m = sref.m - 2*N_REF_PAD + hap->stack[istack].dlen; // total length of the spliced query transcript hap->upstream_stop = 0; int i = 1, dlen = 0, ibeg, indel = 0; hap->sbeg = hap->stack[i].node->sbeg; assert( hap->stack[istack].node->type != HAP_SSS ); if ( tr->strand==STRAND_FWD ) { i = 0, ibeg = -1; while ( ++i <= istack ) { assert( hap->stack[i].node->type != HAP_SSS ); dlen += hap->stack[i].node->dlen; if ( hap->stack[i].node->dlen ) indel = 1; // This condition extends compound variants. if ( istack[i].node->dlen > 0 ) icur += hap->stack[i].node->dlen; else if ( hap->stack[i].node->dlen < 0 ) icur++; if ( icur/3 == inext/3 ) // in the same codon, can't be flushed yet { if ( ibeg==-1 ) ibeg = i; continue; } } if ( ibeg<0 ) ibeg = i; int ioff = node2soff(ibeg); int icur = node2sbeg(ibeg); int rbeg = node2rbeg(ibeg); int rend = node2rend(i); int fill = dlen%3; // alt if ( hap->sseq.l ) { sseq.l = hap->stack[i].slen - ioff; sseq.s = hap->sseq.s + ioff; } else // splice site overlap, see #1475227917 sseq.l = fill = 0; cds_translate(&sref, &sseq, icur,rbeg,rend, tr->strand, &hap->tseq, fill); // ref sseq.l = node2rend(i) - rbeg; sseq.s = sref.s + N_REF_PAD + rbeg; sseq.m = sref.m - 2*N_REF_PAD; cds_translate(&sref, &sseq, rbeg,rbeg,rend, tr->strand, &hap->tref, fill); sseq.m = sref.m - 2*N_REF_PAD + hap->stack[istack].dlen; hap_add_csq(args,hap,node,0, ibeg,i,dlen,indel); ibeg = -1; dlen = 0; indel = 0; } } else if ( tr->strand==STRAND_REV ) { i = istack + 1, ibeg = -1; while ( --i > 0 ) { assert ( hap->stack[i].node->type != HAP_SSS ); dlen += hap->stack[i].node->dlen; if ( hap->stack[i].node->dlen ) indel = 1; if ( i>1 ) { if ( dlen%3 ) { if ( ibeg==-1 ) ibeg = i; continue; } // the last base of the current variant vs the first base of the next // variant: are they in the same codon? (reverse strand) int icur = sseq.m - 1 - node2sbeg(i); int inext = sseq.m - 1 - node2sbeg(i-1); if ( hap->stack[i].node->dlen > 0 ) icur += hap->stack[i].node->dlen - 1; else if ( hap->stack[i].node->dlen < 0 ) icur -= hap->stack[i].node->dlen; if ( hap->stack[i-1].node->dlen > 0 ) inext -= hap->stack[i-1].node->dlen; if ( icur/3 == inext/3 ) { if ( ibeg==-1 ) ibeg = i; continue; } } if ( ibeg<0 ) ibeg = i; int ioff = node2soff(i); int icur = node2sbeg(i); int rbeg = node2rbeg(i); int rend = node2rend(ibeg); int fill = dlen%3; // alt if ( hap->sseq.l ) { sseq.l = hap->stack[ibeg].slen - ioff; sseq.s = hap->sseq.s + ioff; } else // splice site overlap, see #1475227917 sseq.l = fill = 0; cds_translate(&sref, &sseq, icur,rbeg,rend, tr->strand, &hap->tseq, fill); // ref sseq.l = node2rend(ibeg) - rbeg; sseq.s = sref.s + N_REF_PAD + rbeg; sseq.m = sref.m - 2*N_REF_PAD; cds_translate(&sref, &sseq, rbeg,rbeg,rend, tr->strand, &hap->tref, fill); sseq.m = sref.m - 2*N_REF_PAD + hap->stack[istack].dlen; hap_add_csq(args,hap,node,sseq.m, i,ibeg,dlen,indel); ibeg = -1; dlen = 0; indel = 0; } } } } static inline void csq_print_text(args_t *args, csq_t *csq, int ismpl, int ihap) { if ( csq->type.type & CSQ_PRINTED_UPSTREAM ) return; char *smpl = ismpl >= 0 ? args->hdr->samples[ismpl] : "-"; const char *chr = bcf_hdr_id2name(args->hdr,args->rid); fprintf(args->out,"CSQ\t%s\t", smpl); if ( ihap>0 ) fprintf(args->out,"%d", ihap); else fprintf(args->out,"-"); args->str.l = 0; kput_vcsq(args, &csq->type, &args->str); fprintf(args->out,"\t%s\t%d\t%s\n",chr,csq->pos+1,args->str.s); } static inline void hap_print_text(args_t *args, gf_tscript_t *tr, int ismpl, int ihap, hap_node_t *node) { if ( !node || !node->ncsq_list ) return; char *smpl = ismpl >= 0 ? args->hdr->samples[ismpl] : "-"; const char *chr = bcf_hdr_id2name(args->hdr,args->rid); int i; for (i=0; incsq_list; i++) { csq_t *csq = node->csq_list + i; if ( csq->type.type & CSQ_PRINTED_UPSTREAM ) continue; assert( csq->type.vstr.l ); fprintf(args->out,"CSQ\t%s\t", smpl); if ( ihap>0 ) fprintf(args->out,"%d", ihap); else fprintf(args->out,"-"); args->str.l = 0; kput_vcsq(args, &csq->type, &args->str); fprintf(args->out,"\t%s\t%d\t%s\n",chr,csq->pos+1,args->str.s); } } static inline void hap_stage_vcf(args_t *args, gf_tscript_t *tr, int ismpl, int ihap, hap_node_t *node) { if ( !node || !node->ncsq_list || ismpl<0 ) return; int i; for (i=0; incsq_list; i++) { csq_t *csq = node->csq_list + i; vrec_t *vrec = csq->vrec; int icsq2 = 2*csq->idx + ihap; if ( icsq2 >= args->ncsq2_max ) // more than ncsq2_max consequences, so can't fit it in FMT { if ( args->verbosity && (!args->ncsq2_small_warned || args->verbosity > 1) ) { fprintf(stderr, "Warning: Too many consequences for sample %s at %s:%"PRId64", keeping the first %d and skipping the rest.\n", args->hdr->samples[ismpl],bcf_hdr_id2name(args->hdr,args->rid),(int64_t) vrec->line->pos+1,csq->idx); if ( !args->ncsq2_small_warned ) fprintf(stderr," The limit can be increased by setting the --ncsq parameter. This warning is printed only once.\n"); } if ( args->ncsq2_small_warned < icsq2 ) args->ncsq2_small_warned = icsq2; break; } int ival, ibit; icsq2_to_bit(icsq2, &ival,&ibit); if ( vrec->nfmt < 1 + ival ) vrec->nfmt = 1 + ival; vrec->fmt_bm[ismpl*args->nfmt_bcsq + ival] |= 1 << ibit; } } void hap_flush(args_t *args, uint32_t pos) { int i,j; tr_heap_t *heap = args->active_tr; while ( heap->ndat && heap->dat[0]->end<=pos ) { gf_tscript_t *tr = heap->dat[0]; khp_delete(trhp, heap); args->hap->tr = tr; if ( TSCRIPT_AUX(tr)->root && TSCRIPT_AUX(tr)->root->nchild ) // normal, non-localized calling { hap_finalize(args, args->hap); if ( args->output_type==FT_TAB_TEXT ) // plain text output, not a vcf { if ( args->phase==PHASE_DROP_GT ) hap_print_text(args, tr, -1,0, TSCRIPT_AUX(tr)->hap[0]); else { for (i=0; ismpl->n; i++) { for (j=0; j<2; j++) hap_print_text(args, tr, args->smpl->idx[i],j+1, TSCRIPT_AUX(tr)->hap[i*2+j]); } } } else if ( args->phase!=PHASE_DROP_GT ) { for (i=0; ismpl->n; i++) { for (j=0; j<2; j++) hap_stage_vcf(args, tr, args->smpl->idx[i],j, TSCRIPT_AUX(tr)->hap[i*2+j]); } } } // mark the transcript for deletion. Cannot delete it immediately because // by-position VCF output will need them when flushed by vcf_buf_push args->nrm_tr++; hts_expand(gf_tscript_t*,args->nrm_tr,args->mrm_tr,args->rm_tr); args->rm_tr[args->nrm_tr-1] = tr; } } #define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; } vbuf_t *vbuf_push(args_t *args, bcf1_t **rec_ptr) { int i; assert(rec_ptr); bcf1_t *rec = *rec_ptr; // check for duplicate records i = args->vcf_rbuf.n ? rbuf_last(&args->vcf_rbuf) : -1; if ( i<0 || args->vcf_buf[i]->vrec[0]->line->pos!=rec->pos ) { // vcf record with a new pos rbuf_expand0(&args->vcf_rbuf, vbuf_t*, args->vcf_rbuf.n+1, args->vcf_buf); i = rbuf_append(&args->vcf_rbuf); if ( !args->vcf_buf[i] ) args->vcf_buf[i] = (vbuf_t*) calloc(1,sizeof(vbuf_t)); args->vcf_buf[i]->n = 0; args->vcf_buf[i]->keep_until = 0; } vbuf_t *vbuf = args->vcf_buf[i]; vbuf->n++; hts_expand0(vrec_t*, vbuf->n, vbuf->m, vbuf->vrec); if ( !vbuf->vrec[vbuf->n - 1] ) vbuf->vrec[vbuf->n - 1] = (vrec_t*) calloc(1,sizeof(vrec_t)); vrec_t *vrec = vbuf->vrec[vbuf->n - 1]; if ( args->phase!=PHASE_DROP_GT && args->smpl->n ) { if ( !vrec->fmt_bm ) vrec->fmt_bm = (uint32_t*) calloc(args->hdr_nsmpl,sizeof(*vrec->fmt_bm) * args->nfmt_bcsq); else memset(vrec->fmt_bm,0,args->hdr_nsmpl*sizeof(*vrec->fmt_bm) * args->nfmt_bcsq); } if ( !vrec->line ) vrec->line = bcf_init1(); SWAP(bcf1_t*, (*rec_ptr), vrec->line); int ret; khint_t k = kh_put(pos2vbuf, args->pos2vbuf, (int)rec->pos, &ret); kh_val(args->pos2vbuf,k) = vbuf; return vbuf; } void vbuf_flush(args_t *args, uint32_t pos) { int i,j; while ( args->vcf_rbuf.n ) { vbuf_t *vbuf; if ( !args->local_csq && args->active_tr->ndat ) { // check if the first active transcript starts beyond the first buffered VCF record, // cannot output buffered VCF lines (args.vbuf) until the active transcripts are gone vbuf = args->vcf_buf[ args->vcf_rbuf.f ]; if ( vbuf->keep_until > pos ) break; assert( vbuf->n ); } i = rbuf_shift(&args->vcf_rbuf); assert( i>=0 ); vbuf = args->vcf_buf[i]; int pos = vbuf->n ? vbuf->vrec[0]->line->pos : -1; for (i=0; in; i++) { vrec_t *vrec = vbuf->vrec[i]; if ( !args->out_fh ) // not a VCF output { vrec->nvcsq = 0; continue; } if ( !vrec->nvcsq ) { if ( bcf_write(args->out_fh, args->hdr, vrec->line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname?args->output_fname:"standard output"); int save_pos = vrec->line->pos; bcf_empty(vrec->line); vrec->line->pos = save_pos; // this is necessary for compound variants continue; } args->str.l = 0; kput_vcsq(args, &vrec->vcsq[0], &args->str); for (j=1; jnvcsq; j++) { kputc_(',', &args->str); kput_vcsq(args, &vrec->vcsq[j], &args->str); } bcf_update_info_string(args->hdr, vrec->line, args->bcsq_tag, args->str.s); if ( args->hdr_nsmpl ) { if ( vrec->nfmt < args->nfmt_bcsq ) for (j=1; jhdr_nsmpl; j++) memmove(&vrec->fmt_bm[j*vrec->nfmt], &vrec->fmt_bm[j*args->nfmt_bcsq], vrec->nfmt*sizeof(*vrec->fmt_bm)); bcf_update_format_int32(args->hdr, vrec->line, args->bcsq_tag, vrec->fmt_bm, args->hdr_nsmpl*vrec->nfmt); } vrec->nvcsq = 0; if ( bcf_write(args->out_fh, args->hdr, vrec->line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname?args->output_fname:"standard output"); int save_pos = vrec->line->pos; bcf_empty(vrec->line); vrec->line->pos = save_pos; } if ( pos!=-1 ) { khint_t k = kh_get(pos2vbuf, args->pos2vbuf, pos); if ( k != kh_end(args->pos2vbuf) ) kh_del(pos2vbuf, args->pos2vbuf, k); } vbuf->n = 0; } if ( args->active_tr->ndat ) return; for (i=0; inrm_tr; i++) { gf_tscript_t *tr = args->rm_tr[i]; tscript_t *aux = TSCRIPT_AUX(tr); if ( aux->root ) hap_destroy(aux->root); aux->root = NULL; free(aux->hap); free(aux->ref); free(aux->sref); free(aux); tr->aux = NULL; } args->nrm_tr = 0; args->ncsq_buf = 0; } void tscript_init_ref(args_t *args, gf_tscript_t *tr, const char *chr) { int i, len; int pad_beg = tr->beg >= N_REF_PAD ? N_REF_PAD : tr->beg; const char *tmp_chr = chr; if ( !faidx_has_seq(args->fai,tmp_chr) ) { tmp_chr = drop_chr_prefix(args,chr); if ( !faidx_has_seq(args->fai,tmp_chr) ) tmp_chr = add_chr_prefix(args,chr); } TSCRIPT_AUX(tr)->ref = faidx_fetch_seq(args->fai, tmp_chr, tr->beg - pad_beg, tr->end + N_REF_PAD, &len); if ( !TSCRIPT_AUX(tr)->ref ) error("faidx_fetch_seq failed %s:%d-%d\n", chr,tr->beg+1,tr->end+1); int pad_end = len - (tr->end - tr->beg + 1 + pad_beg); if ( pad_beg + pad_end != 2*N_REF_PAD ) { char *ref = (char*) malloc(tr->end - tr->beg + 1 + 2*N_REF_PAD + 1); for (i=0; i < N_REF_PAD - pad_beg; i++) ref[i] = 'N'; memcpy(ref+i, TSCRIPT_AUX(tr)->ref, len); len += i; for (i=0; i < N_REF_PAD - pad_end; i++) ref[i+len] = 'N'; ref[i+len] = 0; free(TSCRIPT_AUX(tr)->ref); TSCRIPT_AUX(tr)->ref = ref; } } static void sanity_check_ref(args_t *args, gf_tscript_t *tr, bcf1_t *rec) { int vbeg = 0; int rbeg = rec->pos - tr->beg + N_REF_PAD; if ( rbeg < 0 ) { vbeg += abs(rbeg); rbeg = 0; } char *ref = TSCRIPT_AUX(tr)->ref + rbeg; char *vcf = rec->d.allele[0] + vbeg; assert( vcf - rec->d.allele[0] < strlen(rec->d.allele[0]) && ref - TSCRIPT_AUX(tr)->ref < tr->end - tr->beg + 2*N_REF_PAD ); int i = 0; while ( ref[i] && vcf[i] ) { if ( ref[i]!=vcf[i] && toupper(ref[i])!=toupper(vcf[i]) ) error("Error: the fasta reference does not match the VCF REF allele at %s:%"PRId64" .. fasta=%c vcf=%c\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+vbeg+1,ref[i],vcf[i]); i++; } } int test_cds_local(args_t *args, bcf1_t *rec) { int i,j, ret = 0; const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,rec)); // note that the off-by-one extension of rlen is deliberate to account for insertions if ( !regidx_overlap(args->idx_cds,chr,rec->pos,rec->pos+rec->rlen, args->itr) ) return 0; // structures to fake the normal test_cds machinery hap_node_t root, node; root.type = HAP_ROOT; kstring_t *tref = &args->hap->tref, *tseq = &args->hap->tseq; while ( regitr_overlap(args->itr) ) { gf_cds_t *cds = regitr_payload(args->itr,gf_cds_t*); gf_tscript_t *tr = cds->tr; if ( !GF_is_coding(tr->type) ) continue; ret = 1; if ( !TSCRIPT_AUX(tr) ) { tr->aux = calloc(sizeof(tscript_t),1); tscript_init_ref(args, tr, chr); tscript_splice_ref(tr); khp_insert(trhp, args->active_tr, &tr); // only to clean the reference afterwards } sanity_check_ref(args, tr, rec); kstring_t sref; sref.s = TSCRIPT_AUX(tr)->sref; sref.l = TSCRIPT_AUX(tr)->nsref; sref.m = sref.l; for (i=1; in_allele; i++) { if ( rec->d.allele[i][0]=='<' || rec->d.allele[i][0]=='*' ) { continue; } if ( hap_init(args, &root, &node, cds, rec, i)!=0 ) continue; csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.vcf_ial = i; csq.type.gene = tr->gene->name; int csq_type = node.csq; // code repetition: it would be nice to reuse the code from hap_add_csq, needs refactoring though if ( node.type == HAP_SSS ) { csq.type.type = csq_type; csq_stage(args, &csq, rec); } else { kstring_t sseq; sseq.m = sref.m - 2*N_REF_PAD + node.dlen; sseq.s = node.seq; int alen = sseq.l = strlen(sseq.s); int fill = node.dlen%3 && alen ? 1 : 0; // see #1475227917 cds_translate(&sref, &sseq, node.sbeg,node.sbeg,node.sbeg+node.rlen, tr->strand, tseq, fill); sseq.m = sref.m - 2*N_REF_PAD; sseq.s = sref.s + N_REF_PAD + node.sbeg; sseq.l = node.rlen; cds_translate(&sref, &sseq, node.sbeg,node.sbeg,node.sbeg+node.rlen, tr->strand, tref, fill); // check for truncating stops for (j=0; jl; j++) if ( tref->s[j]=='*' ) break; if ( j!=tref->l ) { tref->l = j+1; tref->s[j+1] = 0; } for (j=0; jl; j++) if ( tseq->s[j]=='*' ) break; if ( j!=tseq->l ) { tseq->l = j+1; tseq->s[j+1] = 0; } if ( csq_type & CSQ_STOP_LOST ) { if ( tref->s[tref->l-1]=='*' && tref->s[tref->l-1] == tseq->s[tseq->l-1] ) { csq_type &= ~CSQ_STOP_LOST; csq_type |= CSQ_STOP_RETAINED; } else if (tref->s[tref->l-1]!='*' ) { // This is CDS 3' incomplete ENSG00000173376/synon.vcf, can also be missense // We observe in real data a change to a stop, ENST00000528237/retained-stop-incomplete-cds.vcf if ( tseq->s[tseq->l-1] == '*' ) { csq_type &= ~CSQ_STOP_GAINED; csq_type |= CSQ_STOP_RETAINED; } else csq_type |= CSQ_INCOMPLETE_CDS; } } if ( csq_type & CSQ_START_LOST && tref->s[0]!='M' ) csq_type &= ~CSQ_START_LOST; if ( node.dlen!=0 ) { if ( node.dlen%3 ) csq_type |= CSQ_FRAMESHIFT_VARIANT; else if ( node.dlen<0 ) csq_type |= CSQ_INFRAME_DELETION; else csq_type |= CSQ_INFRAME_INSERTION; if ( tref->s[tref->l-1]!='*' && tseq->s[tseq->l-1]=='*' ) csq_type |= CSQ_STOP_GAINED; } else { int aa_change = 0; for (j=0; jl; j++) { if ( tref->s[j] == tseq->s[j] ) continue; aa_change = 1; if ( tref->s[j] == '*' ) csq_type |= CSQ_STOP_LOST; else if ( tseq->s[j] == '*' ) csq_type |= CSQ_STOP_GAINED; else csq_type |= CSQ_MISSENSE_VARIANT; } if ( !aa_change ) csq_type |= CSQ_SYNONYMOUS_VARIANT; } if ( csq_type & CSQ_COMPOUND ) { // create the aa variant string kstring_t str = {0,0,0}; int aa_rbeg = tr->strand==STRAND_FWD ? node.sbeg/3+1 : (TSCRIPT_AUX(tr)->nsref - 2*N_REF_PAD - node.sbeg - node.rlen)/3+1; int aa_sbeg = tr->strand==STRAND_FWD ? node.sbeg/3+1 : (TSCRIPT_AUX(tr)->nsref - 2*N_REF_PAD + node.dlen - node.sbeg - alen)/3+1; kputc_('|', &str); kputw(aa_rbeg, &str); kprint_aa_prediction(args,aa_rbeg,tref,&str); if ( !(csq_type & CSQ_SYNONYMOUS_VARIANT) ) { kputc_('>', &str); kputw(aa_sbeg, &str); kprint_aa_prediction(args,aa_sbeg,tseq,&str); } kputc_('|', &str); kputw(rec->pos+1, &str); kputs(node.var, &str); csq.type.vstr = str; csq.type.type = csq_type & CSQ_COMPOUND; csq_stage(args, &csq, rec); // all this only to clean vstr when vrec is flushed if ( !TSCRIPT_AUX(tr)->root ) TSCRIPT_AUX(tr)->root = (hap_node_t*) calloc(1,sizeof(hap_node_t)); TSCRIPT_AUX(tr)->root->ncsq_list++; hts_expand0(csq_t,TSCRIPT_AUX(tr)->root->ncsq_list,TSCRIPT_AUX(tr)->root->mcsq_list,TSCRIPT_AUX(tr)->root->csq_list); csq_t *rm_csq = TSCRIPT_AUX(tr)->root->csq_list + TSCRIPT_AUX(tr)->root->ncsq_list - 1; rm_csq->type.vstr = str; } if ( csq_type & ~CSQ_COMPOUND ) { csq.type.type = csq_type & ~CSQ_COMPOUND; csq.type.vstr.l = 0; csq_stage(args, &csq, rec); } } free(node.seq); free(node.var); } } return ret; } int test_cds(args_t *args, bcf1_t *rec, vbuf_t *vbuf) { static int overlaps_warned = 0, multiploid_warned = 0; int i, ret = 0, hap_ret; const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,rec)); // note that the off-by-one extension of rlen is deliberate to account for insertions if ( !regidx_overlap(args->idx_cds,chr,rec->pos,rec->pos+rec->rlen, args->itr) ) return 0; while ( regitr_overlap(args->itr) ) { gf_cds_t *cds = regitr_payload(args->itr,gf_cds_t*); gf_tscript_t *tr = cds->tr; if ( !GF_is_coding(tr->type) ) continue; if ( vbuf->keep_until < tr->end ) vbuf->keep_until = tr->end; ret = 1; if ( !TSCRIPT_AUX(tr) ) { // initialize the transcript and its haplotype tree, fetch the reference sequence tr->aux = calloc(sizeof(tscript_t),1); tscript_init_ref(args, tr, chr); TSCRIPT_AUX(tr)->root = (hap_node_t*) calloc(1,sizeof(hap_node_t)); TSCRIPT_AUX(tr)->nhap = args->phase==PHASE_DROP_GT ? 1 : 2*args->smpl->n; // maximum ploidy = diploid TSCRIPT_AUX(tr)->hap = (hap_node_t**) malloc(TSCRIPT_AUX(tr)->nhap*sizeof(hap_node_t*)); for (i=0; inhap; i++) TSCRIPT_AUX(tr)->hap[i] = NULL; TSCRIPT_AUX(tr)->root->nend = TSCRIPT_AUX(tr)->nhap; TSCRIPT_AUX(tr)->root->type = HAP_ROOT; khp_insert(trhp, args->active_tr, &tr); } sanity_check_ref(args, tr, rec); if ( args->phase==PHASE_DROP_GT ) { if ( rec->d.allele[1][0]=='<' || rec->d.allele[1][0]=='*' ) { continue; } hap_node_t *parent = TSCRIPT_AUX(tr)->hap[0] ? TSCRIPT_AUX(tr)->hap[0] : TSCRIPT_AUX(tr)->root; hap_node_t *child = (hap_node_t*)calloc(1,sizeof(hap_node_t)); hap_ret = hap_init(args, parent, child, cds, rec, 1); if ( hap_ret!=0 ) { // overlapping or intron variant, cannot apply if ( hap_ret==1 ) { if ( args->verbosity && (!overlaps_warned || args->verbosity > 1) ) { fprintf(stderr, "Warning: Skipping overlapping variants at %s:%"PRId64"\t%s>%s.\n", chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]); if ( !overlaps_warned ) fprintf(stderr," This message is printed only once, the verbosity can be increased with `--verbose 2`\n"); overlaps_warned = 1; } if ( args->out ) fprintf(args->out,"LOG\tWarning: Skipping overlapping variants at %s:%"PRId64"\t%s>%s\n", chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]); } else ret = 1; // prevent reporting as intron in test_tscript hap_destroy(child); continue; } if ( child->type==HAP_SSS ) { csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.vcf_ial = 1; csq.type.gene = tr->gene->name; csq.type.type = child->csq; csq_stage(args, &csq, rec); hap_destroy(child); ret = 1; continue; } parent->nend--; parent->nchild = 1; parent->mchild = 1; parent->child = (hap_node_t**) malloc(sizeof(hap_node_t*)); parent->child[0] = child; TSCRIPT_AUX(tr)->hap[0] = child; TSCRIPT_AUX(tr)->hap[0]->nend = 1; continue; } // apply the VCF variants and extend the haplotype tree int j, ismpl, ihap, ngts = bcf_get_genotypes(args->hdr, rec, &args->gt_arr, &args->mgt_arr); ngts /= bcf_hdr_nsamples(args->hdr); if ( ngts!=1 && ngts!=2 ) { if ( args->verbosity && (!multiploid_warned || args->verbosity > 1) ) { fprintf(stderr, "Warning: Skipping site with non-diploid/non-haploid genotypes at %s:%"PRId64"\t%s>%s.\n", chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]); if ( !multiploid_warned ) fprintf(stderr," This message is printed only once, the verbosity can be increased with `--verbose 2`\n"); multiploid_warned = 1; } if ( args->out ) fprintf(args->out,"LOG\tWarning: Skipping site with non-diploid/non-haploid genotypes at %s:%"PRId64"\t%s>%s\n", chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]); continue; } for (ismpl=0; ismplsmpl->n; ismpl++) { int32_t *gt = args->gt_arr + args->smpl->idx[ismpl]*ngts; if ( gt[0]==bcf_gt_missing ) continue; if ( ngts>1 && gt[1]!=bcf_gt_missing && gt[1]!=bcf_int32_vector_end && bcf_gt_allele(gt[0])!=bcf_gt_allele(gt[1]) ) { if ( args->phase==PHASE_MERGE ) { if ( !bcf_gt_allele(gt[0]) ) gt[0] = gt[1]; } if ( !bcf_gt_is_phased(gt[0]) && !bcf_gt_is_phased(gt[1]) ) { if ( args->phase==PHASE_REQUIRE ) error("Unphased heterozygous genotype at %s:%"PRId64", sample %s. See the --phase option.\n", chr,(int64_t) rec->pos+1,args->hdr->samples[args->smpl->idx[ismpl]]); if ( args->phase==PHASE_SKIP ) continue; if ( args->phase==PHASE_NON_REF ) { if ( !bcf_gt_allele(gt[0]) ) gt[0] = gt[1]; else if ( !bcf_gt_allele(gt[1]) ) gt[1] = gt[0]; } } } for (ihap=0; ihapn_allele ); if ( rec->d.allele[ial][0]=='<' || rec->d.allele[ial][0]=='*' ) { continue; } hap_node_t *parent = TSCRIPT_AUX(tr)->hap[i] ? TSCRIPT_AUX(tr)->hap[i] : TSCRIPT_AUX(tr)->root; if ( parent->cur_rec==rec && parent->cur_child[ial]>=0 ) { // this haplotype has been seen in another sample TSCRIPT_AUX(tr)->hap[i] = parent->child[ parent->cur_child[ial] ]; TSCRIPT_AUX(tr)->hap[i]->nend++; parent->nend--; continue; } hap_node_t *child = (hap_node_t*)calloc(1,sizeof(hap_node_t)); hap_ret = hap_init(args, parent, child, cds, rec, ial); if ( hap_ret!=0 ) { // overlapping or intron variant, cannot apply if ( hap_ret==1 ) { if ( args->verbosity && (!overlaps_warned || args->verbosity > 1) ) { fprintf(stderr, "Warning: Skipping overlapping variants at %s:%"PRId64", sample %s\t%s>%s.\n", chr,(int64_t) rec->pos+1,args->hdr->samples[args->smpl->idx[ismpl]],rec->d.allele[0],rec->d.allele[ial]); if ( !overlaps_warned ) fprintf(stderr," This message is printed only once, the verbosity can be increased with `--verbose 2`\n"); overlaps_warned = 1; } if ( args->out ) fprintf(args->out,"LOG\tWarning: Skipping overlapping variants at %s:%"PRId64", sample %s\t%s>%s\n", chr,(int64_t) rec->pos+1,args->hdr->samples[args->smpl->idx[ismpl]],rec->d.allele[0],rec->d.allele[ial]); } hap_destroy(child); continue; } if ( child->type==HAP_SSS ) { csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.vcf_ial = ial; csq.type.gene = tr->gene->name; csq.type.type = child->csq; csq_stage(args, &csq, rec); hap_destroy(child); continue; } if ( parent->cur_rec!=rec ) { hts_expand(int,rec->n_allele,parent->mcur_child,parent->cur_child); for (j=0; jn_allele; j++) parent->cur_child[j] = -1; parent->cur_rec = rec; } j = parent->nchild++; hts_expand0(hap_node_t*,parent->nchild,parent->mchild,parent->child); parent->cur_child[ial] = j; parent->child[j] = child; TSCRIPT_AUX(tr)->hap[i] = child; TSCRIPT_AUX(tr)->hap[i]->nend++; parent->nend--; } } } return ret; } void csq_stage(args_t *args, csq_t *csq, bcf1_t *rec) { // known issues: tab output leads to unsorted output. This is because // coding haplotypes are printed in one go and buffering is not used // with tab output. VCF output is OK though. if ( csq_push(args, csq, rec)!=0 && args->phase==PHASE_DROP_GT ) return; // the consequence already exists int i,j,ngt = 0; if ( args->phase!=PHASE_DROP_GT ) { ngt = bcf_get_genotypes(args->hdr, rec, &args->gt_arr, &args->mgt_arr); if ( ngt>0 ) ngt /= bcf_hdr_nsamples(args->hdr); } if ( ngt<=0 ) { if ( args->output_type==FT_TAB_TEXT ) csq_print_text(args, csq, -1,0); return; } assert( ngt<=2 ); if ( args->output_type==FT_TAB_TEXT ) { for (i=0; ismpl->n; i++) { int32_t *gt = args->gt_arr + args->smpl->idx[i]*ngt; for (j=0; jtype.vcf_ial ) continue; csq_print_text(args, csq, args->smpl->idx[i],j+1); } } return; } vrec_t *vrec = csq->vrec; for (i=0; ismpl->n; i++) { int32_t *gt = args->gt_arr + args->smpl->idx[i]*ngt; for (j=0; jtype.vcf_ial ) continue; int icsq2 = 2*csq->idx + j; if ( icsq2 >= args->ncsq2_max ) // more than ncsq_max consequences, so can't fit it in FMT { int ismpl = args->smpl->idx[i]; if ( args->verbosity && (!args->ncsq2_small_warned || args->verbosity > 1) ) { fprintf(stderr, "Warning: Too many consequences for sample %s at %s:%"PRId64", keeping the first %d and skipping the rest.\n", args->hdr->samples[ismpl],bcf_hdr_id2name(args->hdr,args->rid),(int64_t) vrec->line->pos+1,icsq2+1); if ( !args->ncsq2_small_warned ) fprintf(stderr," The limit can be increased by setting the --ncsq parameter. This warning is printed only once.\n"); args->ncsq2_small_warned = 1; } if ( args->ncsq2_small_warned < icsq2 ) args->ncsq2_small_warned = icsq2; break; } int ival, ibit; icsq2_to_bit(icsq2, &ival,&ibit); if ( vrec->nfmt < 1 + ival ) vrec->nfmt = 1 + ival; vrec->fmt_bm[i*args->nfmt_bcsq + ival] |= 1 << ibit; } } } int test_utr(args_t *args, bcf1_t *rec) { const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,rec)); // note that the off-by-one extension of rlen is deliberate to account for insertions if ( !regidx_overlap(args->idx_utr,chr,rec->pos,rec->pos+rec->rlen, args->itr) ) return 0; splice_t splice; splice_init(&splice, rec); int i, ret = 0; while ( regitr_overlap(args->itr) ) { gf_utr_t *utr = regitr_payload(args->itr, gf_utr_t*); gf_tscript_t *tr = splice.tr = utr->tr; for (i=1; in_allele; i++) { if ( rec->d.allele[i][0]=='<' || rec->d.allele[i][0]=='*' ) { continue; } splice.vcf.alt = rec->d.allele[i]; splice.csq = 0; int splice_ret = splice_csq(args, &splice, utr->beg, utr->end); if ( splice_ret!=SPLICE_INSIDE && splice_ret!=SPLICE_OVERLAP ) continue; csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.type = utr->which==prime5 ? CSQ_UTR5 : CSQ_UTR3; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.vcf_ial = i; csq.type.gene = tr->gene->name; csq_stage(args, &csq, rec); ret = 1; } } assert(!splice.kref.s); assert(!splice.kalt.s); return ret; } int test_splice(args_t *args, bcf1_t *rec) { const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,rec)); if ( !regidx_overlap(args->idx_exon,chr,rec->pos,rec->pos + rec->rlen, args->itr) ) return 0; splice_t splice; splice_init(&splice, rec); splice.check_acceptor = splice.check_donor = 1; int i, ret = 0; while ( regitr_overlap(args->itr) ) { gf_exon_t *exon = regitr_payload(args->itr, gf_exon_t*); splice.tr = exon->tr; if ( !splice.tr->ncds ) continue; // not a coding transcript, no interest in splice sites splice.check_region_beg = splice.tr->beg==exon->beg ? 0 : 1; splice.check_region_end = splice.tr->end==exon->end ? 0 : 1; for (i=1; in_allele; i++) { if ( rec->d.allele[1][0]=='<' || rec->d.allele[1][0]=='*' ) { continue; } splice.vcf.alt = rec->d.allele[i]; splice.csq = 0; splice_csq(args, &splice, exon->beg, exon->end); if ( splice.csq ) ret = 1; } } free(splice.kref.s); free(splice.kalt.s); return ret; } int test_tscript(args_t *args, bcf1_t *rec) { const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,rec)); if ( !regidx_overlap(args->idx_tscript,chr,rec->pos,rec->pos+rec->rlen, args->itr) ) return 0; splice_t splice; splice_init(&splice, rec); int i, ret = 0; while ( regitr_overlap(args->itr) ) { gf_tscript_t *tr = splice.tr = regitr_payload(args->itr, gf_tscript_t*); for (i=1; in_allele; i++) { if ( rec->d.allele[i][0]=='<' || rec->d.allele[i][0]=='*' ) { continue; } splice.vcf.alt = rec->d.allele[i]; splice.csq = 0; int splice_ret = splice_csq(args, &splice, tr->beg, tr->end); if ( splice_ret!=SPLICE_INSIDE && splice_ret!=SPLICE_OVERLAP ) continue; // SPLICE_OUTSIDE or SPLICE_REF csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.type = GF_is_coding(tr->type) ? CSQ_INTRON : CSQ_NON_CODING; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.gene = tr->gene->name; csq_stage(args, &csq, rec); ret = 1; } } assert(!splice.kref.s); assert(!splice.kalt.s); return ret; } void test_symbolic_alt(args_t *args, bcf1_t *rec) { static int warned = 0; if ( args->verbosity && (!warned && args->verbosity > 0) ) { fprintf(stderr,"Warning: The support for symbolic ALT insertions is experimental.\n"); warned = 1; } const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,rec)); // only insertions atm int beg = rec->pos + 1; int end = beg; int csq_class = CSQ_ELONGATION; int hit = 0; if ( regidx_overlap(args->idx_cds,chr,beg,end, args->itr) ) { while ( regitr_overlap(args->itr) ) { csq_t csq; memset(&csq, 0, sizeof(csq_t)); gf_cds_t *cds = regitr_payload(args->itr,gf_cds_t*); gf_tscript_t *tr = cds->tr; csq.type.type = (GF_is_coding(tr->type) ? CSQ_CODING_SEQUENCE : CSQ_NON_CODING) | csq_class; csq.pos = rec->pos; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.gene = tr->gene->name; csq_stage(args, &csq, rec); hit = 1; } } if ( regidx_overlap(args->idx_utr,chr,beg,end, args->itr) ) { while ( regitr_overlap(args->itr) ) { csq_t csq; memset(&csq, 0, sizeof(csq_t)); gf_utr_t *utr = regitr_payload(args->itr, gf_utr_t*); gf_tscript_t *tr = utr->tr; csq.type.type = (utr->which==prime5 ? CSQ_UTR5 : CSQ_UTR3) | csq_class; csq.pos = rec->pos; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.gene = tr->gene->name; csq_stage(args, &csq, rec); hit = 1; } } if ( regidx_overlap(args->idx_exon,chr,beg,end, args->itr) ) { splice_t splice; splice_init(&splice, rec); splice.check_acceptor = splice.check_donor = 1; while ( regitr_overlap(args->itr) ) { gf_exon_t *exon = regitr_payload(args->itr, gf_exon_t*); splice.tr = exon->tr; if ( !splice.tr->ncds ) continue; // not a coding transcript, no interest in splice sites splice.check_region_beg = splice.tr->beg==exon->beg ? 0 : 1; splice.check_region_end = splice.tr->end==exon->end ? 0 : 1; splice.vcf.alt = rec->d.allele[1]; splice.csq = csq_class; splice_csq(args, &splice, exon->beg, exon->end); if ( splice.csq ) hit = 1; } } if ( !hit && regidx_overlap(args->idx_tscript,chr,beg,end, args->itr) ) { splice_t splice; splice_init(&splice, rec); while ( regitr_overlap(args->itr) ) { csq_t csq; memset(&csq, 0, sizeof(csq_t)); gf_tscript_t *tr = splice.tr = regitr_payload(args->itr, gf_tscript_t*); splice.vcf.alt = rec->d.allele[1]; splice.csq = csq_class; int splice_ret = splice_csq(args, &splice, tr->beg, tr->end); if ( splice_ret!=SPLICE_INSIDE && splice_ret!=SPLICE_OVERLAP ) continue; // SPLICE_OUTSIDE or SPLICE_REF csq.type.type = (GF_is_coding(tr->type) ? CSQ_INTRON : CSQ_NON_CODING) | csq_class; csq.pos = rec->pos; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.gene = tr->gene->name; csq_stage(args, &csq, rec); } } } void debug_print_buffers(args_t *args, int pos) { int i,j; fprintf(stderr,"debug_print_buffers at %d\n", pos); fprintf(stderr,"vbufs:\n"); for (i=0; ivcf_rbuf.n; i++) { int k = rbuf_kth(&args->vcf_rbuf, i); vbuf_t *vbuf = args->vcf_buf[k]; fprintf(stderr,"\tvbuf %d:\n", i); for (j=0; jn; j++) { vrec_t *vrec = vbuf->vrec[j]; fprintf(stderr,"\t\t%"PRId64" .. nvcsq=%d\n", (int64_t) vrec->line->pos+1, vrec->nvcsq); } } fprintf(stderr,"pos2vbuf:"); khint_t k; for (k = 0; k < kh_end(args->pos2vbuf); ++k) if (kh_exist(args->pos2vbuf, k)) fprintf(stderr," %d",1+(int)kh_key(args->pos2vbuf, k)); fprintf(stderr,"\n"); fprintf(stderr,"active_tr: %d\n", args->active_tr->ndat); } static void process(args_t *args, bcf1_t **rec_ptr) { if ( !rec_ptr ) { hap_flush(args, REGIDX_MAX); vbuf_flush(args, REGIDX_MAX); return; } bcf1_t *rec = *rec_ptr; static int32_t prev_rid = -1, prev_pos = -1; if ( prev_rid!=rec->rid ) { prev_rid = rec->rid; prev_pos = rec->pos; // Common error is to use different naming conventions in the fasta and the VCF (e.g. X vs chrX). // Perform a simple sanity check (that does not catch much), the chromosome must be present in the // reference file if ( !faidx_has_seq(args->fai,bcf_seqname(args->hdr,rec)) ) { if ( !faidx_has_seq(args->fai,drop_chr_prefix(args,bcf_seqname(args->hdr,rec))) && !faidx_has_seq(args->fai,add_chr_prefix(args,bcf_seqname(args->hdr,rec))) ) error("Error: the chromosome \"%s\" is not present in %s\n",bcf_seqname(args->hdr,rec),args->fa_fname); } } if ( prev_pos > rec->pos ) error("Error: The file is not sorted, %s:%d comes before %s:%"PRId64"\n",bcf_seqname(args->hdr,rec),prev_pos+1,bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); int call_csq = 1; if ( rec->n_allele < 2 ) call_csq = 0; // no alternate allele else if ( rec->n_allele==2 && (rec->d.allele[1][0]=='*' || rec->d.allele[1][1]=='*') ) call_csq = 0; // gVCF, not an alt allele else if ( rec->d.allele[1][0]=='<' ) { if ( strncmp("d.allele[1], 4) ) call_csq = 0; // only is supported at the moment } if ( call_csq && args->filter ) { call_csq = filter_test(args->filter, rec, NULL); if ( args->filter_logic==FLT_EXCLUDE ) call_csq = call_csq ? 0 : 1; } if ( !call_csq ) { if ( !args->out_fh ) return; // not a VCF output vbuf_push(args, rec_ptr); hap_flush(args, rec->pos-1); vbuf_flush(args, rec->pos-1); return; } if ( args->rid != rec->rid ) { hap_flush(args, REGIDX_MAX); vbuf_flush(args, REGIDX_MAX); } args->rid = rec->rid; vbuf_t *vbuf = vbuf_push(args, rec_ptr); if ( rec->d.allele[1][0]!='<' ) { int hit = args->local_csq ? test_cds_local(args, rec) : test_cds(args, rec, vbuf); hit += test_utr(args, rec); hit += test_splice(args, rec); if ( !hit ) test_tscript(args, rec); } else test_symbolic_alt(args, rec); if ( rec->pos > 0 ) { hap_flush(args, rec->pos-1); vbuf_flush(args, rec->pos-1); } return; } static const char *usage(void) { return "\n" "About: Haplotype-aware consequence caller.\n" "Usage: bcftools csq [OPTIONS] in.vcf\n" "\n" "Required options:\n" " -f, --fasta-ref FILE Reference file in fasta format\n" " -g, --gff-annot FILE GFF3 annotation file\n" "\n" "CSQ options:\n" " -B, --trim-protein-seq INT Abbreviate protein-changing predictions to max INT aminoacids\n" " -c, --custom-tag STRING Use this tag instead of the default BCSQ\n" " -l, --local-csq Localized predictions, consider only one VCF record at a time\n" " -n, --ncsq INT Maximum number of per-haplotype consequences to consider for each site [15]\n" " -p, --phase a|m|r|R|s How to handle unphased heterozygous genotypes: [r]\n" " a: take GTs as is, create haplotypes regardless of phase (0/1 -> 0|1)\n" " m: merge *all* GTs into a single haplotype (0/1 -> 1, 1/2 -> 1)\n" " r: require phased GTs, throw an error on unphased het GTs\n" " R: create non-reference haplotypes if possible (0/1 -> 1|1, 1/2 -> 1|2)\n" " s: skip unphased hets\n" "GFF options:\n" " --dump-gff FILE.gz Dump the parsed GFF file (for debugging purposes)\n" " --force Run even if some sanity checks fail\n" " --unify-chr-names 1|0 Automatically unify chromosome naming (e.g. chrX vs X) in GFF, fasta, and VCF [1]\n" "General options:\n" " -e, --exclude EXPR Exclude sites for which the expression is true\n" " -i, --include EXPR Select sites for which the expression is true\n" " --no-version Do not append version and command line to the header\n" " -o, --output FILE Write output to a file [standard output]\n" " -O, --output-type b|u|z|v|t[0-9] b: compressed BCF, u: uncompressed BCF, z: compressed VCF\n" " v: uncompressed VCF, t: plain tab-delimited text output, 0-9: compression level [v]\n" " -r, --regions REGION Restrict to comma-separated list of regions\n" " -R, --regions-file FILE Restrict to regions listed in a file\n" " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n" " -s, --samples -|LIST Samples to include or \"-\" to apply all variants and ignore samples\n" " -S, --samples-file FILE Samples to include\n" " -t, --targets REGION Similar to -r but streams rather than index-jumps\n" " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n" " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n" " --threads INT Use multithreading with worker threads [0]\n" " -v, --verbose INT Verbosity level 0-2 [1]\n" " -W, --write-index[=FMT] Automatically index the output files [off]\n" "\n" "Example:\n" " bcftools csq -f hs37d5.fa -g Homo_sapiens.GRCh37.87.gff3.gz in.vcf\n" "\n" " # GFF3 annotation files can be downloaded from Ensembl. e.g. for human:\n" " http://ftp.ensembl.org/pub/current_gff3/homo_sapiens/\n" " http://ftp.ensembl.org/pub/grch37/current/gff3/homo_sapiens/\n" "\n"; } int main_csq(int argc, char *argv[]) { args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->output_type = FT_VCF; args->bcsq_tag = "BCSQ"; args->ncsq2_max = 2*(16-1); // 1 bit is reserved for BCF missing values args->verbosity = 1; args->record_cmd_line = 1; args->clevel = -1; args->unify_chr_names = 1; static struct option loptions[] = { {"force",0,0,1}, {"threads",required_argument,NULL,2}, {"help",0,0,'h'}, {"ncsq",1,0,'n'}, {"brief-predictions",no_argument,0,'b'}, {"trim-protein-seq",required_argument,0,'B'}, {"custom-tag",1,0,'c'}, {"local-csq",0,0,'l'}, {"gff-annot",1,0,'g'}, {"fasta-ref",1,0,'f'}, {"include",1,0,'i'}, {"exclude",1,0,'e'}, {"output",1,0,'o'}, {"output-type",1,NULL,'O'}, {"phase",1,0,'p'}, {"quiet",0,0,'q'}, {"verbose",1,0,'v'}, {"regions",1,0,'r'}, {"regions-file",1,0,'R'}, {"regions-overlap",required_argument,NULL,4}, {"samples",1,0,'s'}, {"samples-file",1,0,'S'}, {"targets",1,0,'t'}, {"targets-file",1,0,'T'}, {"targets-overlap",required_argument,NULL,5}, {"no-version",no_argument,NULL,3}, {"write-index",optional_argument,NULL,'W'}, {"dump-gff",required_argument,NULL,7}, {"unify-chr-names",required_argument,NULL,8}, {0,0,0,0} }; int c, targets_is_file = 0, regions_is_file = 0; int regions_overlap = 1; int targets_overlap = 0; char *targets_list = NULL, *regions_list = NULL, *tmp; while ((c = getopt_long(argc, argv, "?hr:R:t:T:i:e:f:o:O:g:s:S:p:qc:ln:bB:v:W::",loptions,NULL)) >= 0) { switch (c) { case 1 : args->force = 1; break; case 2 : args->n_threads = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --threads %s\n", optarg); break; case 3 : args->record_cmd_line = 0; break; case 'b': args->brief_predictions = 1; fprintf(stderr,"Warning: The -b option will be removed in future versions. Please use -B 1 instead.\n"); break; case 'B': args->brief_predictions = strtol(optarg,&tmp,10); if ( *tmp || args->brief_predictions<1 ) error("Could not parse argument: --trim-protein-seq %s\n", optarg); break; case 'l': args->local_csq = 1; break; case 'c': args->bcsq_tag = optarg; break; case 'q': error("Error: the -q option has been deprecated, use -v, --verbose instead.\n"); break; case 'v': args->verbosity = atoi(optarg); if ( args->verbosity<0 || args->verbosity>2 ) error("Error: expected integer 0-2 with -v, --verbose\n"); break; case 'p': switch (optarg[0]) { case 'a': args->phase = PHASE_AS_IS; break; case 'm': args->phase = PHASE_MERGE; break; case 'r': args->phase = PHASE_REQUIRE; break; case 'R': args->phase = PHASE_NON_REF; break; case 's': args->phase = PHASE_SKIP; break; default: error("The -p code \"%s\" not recognised\n", optarg); } break; case 'f': args->fa_fname = optarg; break; case 'g': args->gff_fname = optarg; break; case 'n': args->ncsq2_max = 2 * atoi(optarg); if ( args->ncsq2_max <= 0 ) error("Expected positive integer with -n, got %s\n", optarg); break; case 'o': args->output_fname = optarg; break; case 'O': switch (optarg[0]) { case 't': args->output_type = FT_TAB_TEXT; break; case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --output-type %s\n", optarg+1); } break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'r': regions_list = optarg; break; case 'R': regions_list = optarg; regions_is_file = 1; break; case 's': args->sample_list = optarg; break; case 'S': args->sample_list = optarg; args->sample_is_file = 1; break; case 't': targets_list = optarg; break; case 'T': targets_list = optarg; targets_is_file = 1; break; case 4 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 5 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 7 : args->dump_gff = optarg; break; case 8 : if ( !strcmp(optarg,"0") ) args->unify_chr_names = 0; else if ( !strcmp(optarg,"1") ) args->unify_chr_names = 1; else error("Could not parse: --unify-chr-names %s\n",optarg); break; case 'h': case '?': error("%s",usage()); default: error("The option not recognised: %s\n\n", optarg); break; } } char *fname = NULL; if ( optind==argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else error("%s", usage()); } else fname = argv[optind]; if ( argc - optind>1 ) error("%s", usage()); if ( !args->fa_fname ) error("Missing the --fasta-ref option\n"); if ( !args->gff_fname ) error("Missing the --gff option\n"); args->sr = bcf_sr_init(); if ( targets_list ) { bcf_sr_set_opt(args->sr,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->sr, targets_list, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", targets_list); } if ( regions_list ) { bcf_sr_set_opt(args->sr,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->sr, regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", regions_list); } if ( bcf_sr_set_threads(args->sr, args->n_threads)<0 ) error("Failed to create %d extra threads\n", args->n_threads); if ( !bcf_sr_add_reader(args->sr, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->sr->errnum)); args->hdr = bcf_sr_get_header(args->sr,0); init_data(args); while ( bcf_sr_next_line(args->sr) ) { process(args, &args->sr->readers[0].buffer[0]); } process(args,NULL); destroy_data(args); bcf_sr_destroy(args->sr); free(args); return 0; } pysam-0.23.0/bcftools/csq.c.pysam.c000066400000000000000000004361321475062545500170710ustar00rootroot00000000000000#include "bcftools.pysam.h" /* The MIT License Copyright (c) 2016-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Things that would be nice to have - dynamic N_REF_PAD - for stop-lost events (also in frameshifts) report the number of truncated aa's - memory could be greatly reduced by indexing gff (but it is quite compact already) - deletions that go beyond transcript boundaries are not checked at sequence level - alloc tscript->ref in hap_finalize, introduce fa_off_beg:16,fa_off_end:16 - see test/csq/ENST00000573314/insertion-overlap.vcf #1476288882 Read about transcript types here http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html https://www.gencodegenes.org/pages/biotypes.html List of supported biotypes antisense IG_C_gene IG_D_gene IG_J_gene IG_LV_gene IG_V_gene lincRNA lncRNA .. generic term for 3prime_overlapping_ncRNA, antisense, bidirectional_promoter_lncRNA, lincRNA, macro_lncRNA, non_coding, processed_transcript, sense_intronic, sense_overlapping macro_lncRNA miRNA misc_RNA Mt_rRNA Mt_tRNA polymorphic_pseudogene processed_transcript protein_coding, mRNA ribozyme rRNA sRNA scRNA scaRNA sense_intronic sense_overlapping snRNA snoRNA TR_C_gene TR_D_gene TR_J_gene TR_V_gene The gff parsing logic We collect features such by combining gff lines A,B,C as follows: A .. gene line with a supported biotype A.ID=~/^gene:/ B .. transcript line referencing A with supported biotype B.ID=~/^transcript:/ && B.Parent=~/^gene:A.ID/ C .. corresponding CDS, exon, and UTR lines: C[3] in {"CDS","exon","three_prime_UTR","five_prime_UTR"} && C.Parent=~/^transcript:B.ID/ For coding biotypes ("protein_coding" or "polymorphic_pseudogene") the complete chain link C -> B -> A is required. For the rest, link B -> A suffices. The supported consequence types, sorted by impact: splice_acceptor_variant .. end region of an intron changed (2bp at the 3' end of an intron) splice_donor_variant .. start region of an intron changed (2bp at the 5' end of an intron) stop_gained .. DNA sequence variant resulting in a stop codon frameshift_variant .. number of inserted/deleted bases not a multiple of three, disrupted translational frame stop_lost .. elongated transcript, stop codon changed start_lost .. the first codon changed inframe_altering .. combination of indels leading to unchanged reading frame and length inframe_insertion .. inserted coding sequence, unchanged reading frame inframe_deletion .. deleted coding sequence, unchanged reading frame missense_variant .. amino acid (aa) change, unchanged length splice_region_variant .. change within 1-3 bases of the exon or 3-8 bases of the intron synonymous_variant .. DNA sequence variant resulting in no amino acid change stop_retained_variant .. different stop codon start_retained_variant .. start codon retained by indel realignment non_coding_variant .. variant in non-coding sequence, such as RNA gene 5_prime_UTR_variant 3_prime_UTR_variant intron_variant .. reported only if none of the above intergenic_variant .. reported only if none of the above The annotation algorithm. The algorithm checks if the variant falls in a region of a supported type. The search is performed in the following order, until a match is found: 1. idx_cds(gf_cds_t) - lookup CDS by position, create haplotypes, call consequences 2. idx_utr(gf_utr_t) - check UTR hits 3. idx_exon(gf_exon_t) - check for splice variants 4. idx_tscript(tscript_t) - check for intronic variants, RNAs, etc. These regidx indexes are created by parsing a gff3 file as follows: 1. create the array "ftr" of all UTR, CDS, exons. This will be processed later and pruned based on transcript types we want to keep. In the same go, create the hash "id2tr" of transcripts to keep (based on biotype) which maps from transcript_id to a transcript. At the same time also build the hash "gid2gene" which maps from gene_id to gf_gene_t pointer. 2. build "idx_cds", "idx_tscript", "idx_utr" and "idx_exon" indexes. Use only features from "ftr" which are present in "id2tr". 3. clean data that won't be needed anymore: ftr, id2tr, gid2gene. Data structures. idx_cds, idx_utr, idx_exon, idx_tscript: as described above, regidx structures for fast lookup of exons/transcripts overlapping a region, the payload is a pointer to tscript.cds */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "filter.h" #include "regidx.h" #include "kheap.h" #include "smpl_ilist.h" #include "rbuf.h" #include "gff.h" #ifndef __FUNCTION__ # define __FUNCTION__ __func__ #endif // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 #define N_REF_PAD 10 // number of bases to avoid boundary effects // How to treat phased/unphased genotypes #define PHASE_REQUIRE 0 // --phase r #define PHASE_MERGE 1 // --phase m #define PHASE_AS_IS 2 // --phase a #define PHASE_SKIP 3 // --phase s #define PHASE_NON_REF 4 // --phase R #define PHASE_DROP_GT 5 // --samples - // Node types in the haplotype tree #define HAP_CDS 0 #define HAP_ROOT 1 #define HAP_SSS 2 // start/stop/splice #define CSQ_PRINTED_UPSTREAM (1<<0) #define CSQ_SYNONYMOUS_VARIANT (1<<1) #define CSQ_MISSENSE_VARIANT (1<<2) #define CSQ_STOP_LOST (1<<3) #define CSQ_STOP_GAINED (1<<4) #define CSQ_INFRAME_DELETION (1<<5) #define CSQ_INFRAME_INSERTION (1<<6) #define CSQ_FRAMESHIFT_VARIANT (1<<7) #define CSQ_SPLICE_ACCEPTOR (1<<8) #define CSQ_SPLICE_DONOR (1<<9) #define CSQ_START_LOST (1<<10) #define CSQ_SPLICE_REGION (1<<11) #define CSQ_STOP_RETAINED (1<<12) #define CSQ_UTR5 (1<<13) #define CSQ_UTR3 (1<<14) #define CSQ_NON_CODING (1<<15) #define CSQ_INTRON (1<<16) //#define CSQ_INTERGENIC (1<<17) #define CSQ_INFRAME_ALTERING (1<<18) #define CSQ_UPSTREAM_STOP (1<<19) // adds * in front of the csq string #define CSQ_INCOMPLETE_CDS (1<<20) // to remove START/STOP in incomplete CDS, see ENSG00000173376/synon.vcf #define CSQ_CODING_SEQUENCE (1<<21) // cannot tell exactly what it is, but it does affect the coding sequence #define CSQ_ELONGATION (1<<22) // symbolic insertion #define CSQ_START_RETAINED (1<<23) // Haplotype-aware consequences, printed in one vcf record only, the rest has a reference @12345 #define CSQ_COMPOUND (CSQ_SYNONYMOUS_VARIANT|CSQ_MISSENSE_VARIANT|CSQ_STOP_LOST|CSQ_STOP_GAINED| \ CSQ_INFRAME_DELETION|CSQ_INFRAME_INSERTION|CSQ_FRAMESHIFT_VARIANT| \ CSQ_START_LOST|CSQ_STOP_RETAINED|CSQ_INFRAME_ALTERING|CSQ_INCOMPLETE_CDS| \ CSQ_UPSTREAM_STOP|CSQ_START_RETAINED) #define CSQ_START_STOP (CSQ_STOP_LOST|CSQ_STOP_GAINED|CSQ_STOP_RETAINED|CSQ_START_LOST|CSQ_START_RETAINED) #define CSQ_PRN_STRAND(csq) ((csq)&CSQ_COMPOUND && !((csq)&(CSQ_SPLICE_ACCEPTOR|CSQ_SPLICE_DONOR|CSQ_SPLICE_REGION))) #define CSQ_PRN_TSCRIPT (~(CSQ_INTRON|CSQ_NON_CODING)) #define CSQ_PRN_NMD (~(CSQ_INTRON|CSQ_NON_CODING)) #define CSQ_PRN_BIOTYPE CSQ_NON_CODING // see kput_vcsq() const char *csq_strings[] = { NULL, "synonymous", "missense", "stop_lost", "stop_gained", "inframe_deletion", "inframe_insertion", "frameshift", "splice_acceptor", "splice_donor", "start_lost", "splice_region", "stop_retained", "5_prime_utr", "3_prime_utr", "non_coding", "intron", "intergenic", "inframe_altering", NULL, NULL, "coding_sequence", "feature_elongation", "start_retained" }; /* Structures related to VCF output: vcsq_t information required to assemble consequence lines such as "inframe_deletion|XYZ|ENST01|+|5TY>5I|121ACG>A+124TA>T" vrec_t single VCF record and csq tied to this record. (Haplotype can have multiple consequences in several VCF records. Each record can have multiple consequences from multiple haplotypes.) csq_t a top-level consequence tied to a haplotype vbuf_t pos2vbuf VCF records with the same position clustered together for a fast lookup via pos2vbuf */ typedef struct _vbuf_t vbuf_t; typedef struct _vcsq_t vcsq_t; struct _vcsq_t { uint32_t strand:1, type:31; // one of CSQ_* types uint32_t trid; uint32_t vcf_ial; uint32_t biotype; // one of GF_* types char *gene; // gene name bcf1_t *ref; // if type&CSQ_PRINTED_UPSTREAM, ref consequence "@1234" kstring_t vstr; // variant string, eg 5TY>5I|121ACG>A+124TA>T }; typedef struct { bcf1_t *line; uint32_t *fmt_bm; // bitmask of sample consequences with first/second haplotype interleaved uint32_t nfmt:4, // the bitmask size (the number of integers per sample) nvcsq:28, mvcsq; vcsq_t *vcsq; // there can be multiple consequences for a single VCF record } vrec_t; typedef struct { uint32_t pos; vrec_t *vrec; // vcf line that this csq is tied to; needed when printing haplotypes (hap_stage_vcf) int idx; // 0-based index of the csq at the VCF line, for FMT/BCSQ vcsq_t type; } csq_t; struct _vbuf_t { vrec_t **vrec; // buffer of VCF lines with the same position int n, m; uint32_t keep_until; // the maximum transcript end position }; KHASH_MAP_INIT_INT(pos2vbuf, vbuf_t*) /* Structures related to haplotype-aware consequences in coding regions hap_node_t node of a haplotype tree. Each transcript has one tree tscript_t despite its general name, it is intended for coding transcripts only hap_t hstack_t for traversal of the haplotype tree and braking combined consequences into independent parts */ typedef struct _hap_node_t hap_node_t; struct _hap_node_t { char *seq; // cds segment [parent_node,this_node) char *var; // variant "ref>alt" uint32_t type:2, // HAP_ROOT or HAP_CDS csq:30; // this node's consequence int dlen; // alt minus ref length: <0 del, >0 ins, 0 substitution uint32_t rbeg; // variant's VCF position (0-based, inclusive) int32_t rlen; // variant's rlen; alen=rlen+dlen; fake for non CDS types uint32_t sbeg; // variant's position on the spliced reference transcript (0-based, inclusive, N_REF_PAD not included) uint32_t icds; // which exon does this node's variant overlaps hap_node_t **child, *prev; // children haplotypes and previous coding node int nchild, mchild; bcf1_t *cur_rec, *rec; // current VCF record and node's VCF record int vcf_ial; // which VCF allele generated this node uint32_t nend; // number of haplotypes ending in this node int *cur_child, mcur_child; // mapping from the allele to the currently active child csq_t *csq_list; // list of haplotype's consequences, broken by position (each corresponds to a VCF record) int ncsq_list, mcsq_list; }; #define TSCRIPT_AUX(x) ((tscript_t*)(x)->aux) typedef struct { char *ref; // reference sequence, padded with N_REF_PAD bases on both ends char *sref; // spliced reference sequence, padded with N_REF_PAD bases on both ends hap_node_t *root; // root of the haplotype tree hap_node_t **hap; // pointer to haplotype leaves, two for each sample int nhap, nsref; // number of haplotypes and length of sref, including 2*N_REF_PAD } tscript_t; static inline int cmp_tscript(gf_tscript_t **a, gf_tscript_t **b) { return ( (*a)->end < (*b)->end ) ? 1 : 0; } KHEAP_INIT(trhp, gf_tscript_t*, cmp_tscript) typedef khp_trhp_t tr_heap_t; typedef struct { hap_node_t *node; // current node int ichild; // current child in the active node int dlen; // total dlen, from the root to the active node size_t slen; // total sequence length, from the root to the active node } hstack_t; typedef struct { int mstack; hstack_t *stack; gf_tscript_t *tr; // tr->ref: spliced transcript on ref strand kstring_t sseq; // spliced haplotype sequence on ref strand kstring_t tseq; // the variable part of translated haplotype transcript, coding strand kstring_t tref; // the variable part of translated reference transcript, coding strand uint32_t sbeg; // stack's sbeg, for cases first node's type is HAP_SSS int upstream_stop; } hap_t; typedef struct _args_t { // the main regidx lookups, from chr:beg-end to overlapping features and // index iterator gff_t *gff; regidx_t *idx_cds, *idx_utr, *idx_exon, *idx_tscript; regitr_t *itr; // text tab-delimited output (out) or vcf/bcf output (out_fh) FILE *out; htsFile *out_fh; char *index_fn; int write_index; char *dump_gff; // vcf bcf_srs_t *sr; bcf_hdr_t *hdr; int hdr_nsmpl; // actual number of samples in the vcf, for bcf_update_format_values() // include or exclude sites which match the filters filter_t *filter; char *filter_str; int filter_logic; // FLT_INCLUDE or FLT_EXCLUDE // samples to process int sample_is_file; char *sample_list; smpl_ilist_t *smpl; char *outdir, **argv, *fa_fname, *gff_fname, *output_fname; char *bcsq_tag; int argc, output_type, clevel; int phase, verbosity, local_csq, record_cmd_line; int ncsq2_max, nfmt_bcsq; // maximum number of csq per site that can be accessed from FORMAT/BCSQ (*2 and 1 bit skipped to avoid BCF missing values) int ncsq2_small_warned; int brief_predictions; int unify_chr_names; char *chr_name; int mchr_name; struct { int unknown_chr,unknown_tscript_biotype,unknown_strand,unknown_phase,duplicate_id; int unknown_cds_phase,incomplete_cds,wrong_phase,overlapping_cds; } warned; int rid; // current chromosome tr_heap_t *active_tr; // heap of active transcripts for quick flushing hap_t *hap; // transcript haplotype recursion vbuf_t **vcf_buf; // buffered VCF lines to annotate with CSQ and flush rbuf_t vcf_rbuf; // round buffer indexes to vcf_buf kh_pos2vbuf_t *pos2vbuf; // fast lookup of buffered lines by position gf_tscript_t **rm_tr; // buffer of transcripts to clean int nrm_tr, mrm_tr; csq_t *csq_buf; // pool of csq not managed by hap_node_t, i.e. non-CDS csqs int ncsq_buf, mcsq_buf; int force; // force run under various conditions. Currently only to skip out-of-phase transcripts int n_threads; // extra compression/decompression threads faidx_t *fai; kstring_t str, str2; int32_t *gt_arr, mgt_arr; } args_t; // AAA, AAC, ... const char *gencode = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF"; const uint8_t nt4[] = { 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,0,4,1, 4,4,4,2, 4,4,4,4, 4,4,4,4, 4,4,4,4, 3,4,4,4, 4,4,4,4, 4,4,4,4, 4,0,4,1, 4,4,4,2, 4,4,4,4, 4,4,4,4, 4,4,4,4, 3 }; const uint8_t cnt4[] = { 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,3,4,2, 4,4,4,1, 4,4,4,4, 4,4,4,4, 4,4,4,4, 0,4,4,4, 4,4,4,4, 4,4,4,4, 4,3,4,2, 4,4,4,1, 4,4,4,4, 4,4,4,4, 4,4,4,4, 0 }; #define dna2aa(x) gencode[ nt4[(uint8_t)(x)[0]]<<4 | nt4[(uint8_t)(x)[1]]<<2 | nt4[(uint8_t)(x)[2]] ] #define cdna2aa(x) gencode[ cnt4[(uint8_t)(x)[2]]<<4 | cnt4[(uint8_t)(x)[1]]<<2 | cnt4[(uint8_t)(x)[0]] ] static inline int ncsq2_to_nfmt(int ncsq2) { return 1 + (ncsq2 - 1) / 30; } static inline void icsq2_to_bit(int icsq2, int *ival, int *ibit) { *ival = icsq2 / 30; *ibit = icsq2 % 30; } void init_data(args_t *args) { args->nfmt_bcsq = ncsq2_to_nfmt(args->ncsq2_max); args->fai = fai_load(args->fa_fname); if ( !args->fai ) error("Failed to load the fai index: %s\n", args->fa_fname); args->gff = gff_init(args->gff_fname); gff_set(args->gff,verbosity,args->verbosity); gff_set(args->gff,strip_chr_names,args->unify_chr_names); gff_set(args->gff,force_out_of_phase,args->force); gff_set(args->gff,dump_fname,args->dump_gff); gff_parse(args->gff); args->idx_cds = gff_get(args->gff,idx_cds); args->idx_utr = gff_get(args->gff,idx_utr); args->idx_exon = gff_get(args->gff,idx_exon); args->idx_tscript = gff_get(args->gff,idx_tscript); args->itr = regitr_init(NULL); args->rid = -1; if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); args->pos2vbuf = kh_init(pos2vbuf); args->active_tr = khp_init(trhp); args->hap = (hap_t*) calloc(1,sizeof(hap_t)); // init samples if ( !bcf_hdr_nsamples(args->hdr) ) args->phase = PHASE_DROP_GT; if ( args->sample_list && !strcmp("-",args->sample_list) ) { // ignore all samples if ( args->output_type==FT_TAB_TEXT ) { // significant speedup for plain VCFs if (bcf_hdr_set_samples(args->hdr,NULL,0) < 0) error_errno("[%s] Couldn't build sample filter", __func__); } args->phase = PHASE_DROP_GT; } else args->smpl = smpl_ilist_init(args->hdr, args->sample_list, args->sample_is_file, SMPL_STRICT); args->hdr_nsmpl = args->phase==PHASE_DROP_GT ? 0 : bcf_hdr_nsamples(args->hdr); if ( args->output_type==FT_TAB_TEXT ) { args->out = args->output_fname ? fopen(args->output_fname,"w") : bcftools_stdout; if ( !args->out ) error("Failed to write to %s: %s\n", !strcmp("-",args->output_fname)?"standard output":args->output_fname,strerror(errno)); fprintf(args->out,"# This file was produced by: bcftools +csq(%s+htslib-%s)\n", bcftools_version(),hts_version()); fprintf(args->out,"# The command line was:\tbcftools +%s", args->argv[0]); int i; for (i=1; iargc; i++) fprintf(args->out," %s",args->argv[i]); fprintf(args->out,"\n"); fprintf(args->out,"# LOG\t[2]Message\n"); fprintf(args->out,"# CSQ"); i = 1; fprintf(args->out,"\t[%d]Sample", ++i); fprintf(args->out,"\t[%d]Haplotype", ++i); fprintf(args->out,"\t[%d]Chromosome", ++i); fprintf(args->out,"\t[%d]Position", ++i); fprintf(args->out,"\t[%d]Consequence", ++i); fprintf(args->out,"\n"); } else { char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( args->out_fh == NULL ) error("[%s] Error: cannot write to %s: %s\n", __func__,args->output_fname? args->output_fname : "standard output", strerror(errno)); if ( args->n_threads > 0) hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->sr->p); if ( args->record_cmd_line ) bcf_hdr_append_version(args->hdr,args->argc,args->argv,"bcftools/csq"); bcf_hdr_printf(args->hdr,"##INFO=",args->bcsq_tag, args->local_csq ? "Local" : "Haplotype-aware"); if ( args->hdr_nsmpl ) bcf_hdr_printf(args->hdr,"##FORMAT=",args->bcsq_tag); if ( bcf_hdr_write(args->out_fh, args->hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname?args->output_fname:"standard output"); if ( init_index2(args->out_fh,args->hdr,args->output_fname, &args->index_fn, args->write_index) < 0 ) error("Error: failed to initialise index for %s\n",args->output_fname); } if ( args->verbosity > 0 ) fprintf(bcftools_stderr,"Calling...\n"); } void destroy_data(args_t *args) { if ( args->ncsq2_small_warned ) fprintf(bcftools_stderr, "Note: Some samples had too many consequences to be represented in %d bytes. If you need to record them all,\n" " the limit can be increased by running with `--ncsq %d`.\n",ncsq2_to_nfmt(args->ncsq2_max)/8,1+args->ncsq2_small_warned/2); regitr_destroy(args->itr); gff_destroy(args->gff); if ( args->filter ) filter_destroy(args->filter); khp_destroy(trhp,args->active_tr); kh_destroy(pos2vbuf,args->pos2vbuf); if ( args->smpl ) smpl_ilist_destroy(args->smpl); int i,j,ret; if ( args->out_fh ) { if ( args->write_index ) { if ( bcf_idx_save(args->out_fh)<0 ) { if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"bcftools_stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } ret = hts_close(args->out_fh); } else ret = fclose(args->out); if ( ret ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"bcftools_stdout"); for (i=0; ivcf_rbuf.m; i++) { vbuf_t *vbuf = args->vcf_buf[i]; if ( !vbuf ) continue; for (j=0; jm; j++) { if ( !vbuf->vrec[j] ) continue; if ( vbuf->vrec[j]->line ) bcf_destroy(vbuf->vrec[j]->line); free(vbuf->vrec[j]->fmt_bm); free(vbuf->vrec[j]->vcsq); free(vbuf->vrec[j]); } free(vbuf->vrec); free(vbuf); } free(args->vcf_buf); free(args->rm_tr); free(args->csq_buf); free(args->hap->stack); free(args->hap->sseq.s); free(args->hap->tseq.s); free(args->hap->tref.s); free(args->hap); fai_destroy(args->fai); free(args->gt_arr); free(args->str.s); free(args->str2.s); free(args->chr_name); } /* The splice_* functions are for consequences around splice sites: start,stop,splice_* */ #define SPLICE_VAR_REF 0 // ref: ACGT>ACGT, csq not applicable, skip completely #define SPLICE_OUTSIDE 1 // splice acceptor or similar; csq set and is done, does not overlap the region #define SPLICE_INSIDE 2 // overlaps coding region; csq can be set but coding prediction is needed #define SPLICE_OVERLAP 3 // indel overlaps region boundary, csq set but could not determine csq typedef struct { gf_tscript_t *tr; struct { int32_t pos, rlen, alen, ial; char *ref, *alt; bcf1_t *rec; } vcf; uint16_t check_acceptor:1, // check distance from exon start (fwd) or end (rev) check_start:1, // this is the first coding exon (relative to transcript orientation), check first (fwd) or last (rev) codon check_stop:1, // this is the last coding exon (relative to transcript orientation), check last (fwd) or first (rev) codon check_donor:1, // as with check_acceptor check_region_beg:1, // do/don't check for splices at this end, eg. in the first or last exon check_region_end:1, // check_utr:1, // check splice sites (acceptor/donor/region_*) only if not in utr set_refalt:1; // set kref,kalt, if set, check also for synonymous events uint32_t csq; int tbeg, tend; // number of trimmed bases from beg and end of ref,alt allele uint32_t ref_beg, // ref coordinates with spurious bases removed, ACC>AC can become AC>A or CC>C, whichever gives ref_end; // a more conservative csq (the first and last base in kref.s) kstring_t kref, kalt; // trimmed alleles, set only with SPLICE_OLAP } splice_t; void splice_init(splice_t *splice, bcf1_t *rec) { memset(splice,0,sizeof(*splice)); splice->vcf.rec = rec; splice->vcf.pos = rec->pos; splice->vcf.rlen = rec->rlen; splice->vcf.ref = rec->d.allele[0]; splice->csq = 0; } static inline void splice_build_hap(splice_t *splice, uint32_t beg, int len) { // len>0 .. beg is the first base, del filled from right // len<0 .. beg is the last base, del filled from left int rlen, alen, rbeg, abeg; // first base to include (ref coordinates) if ( len<0 ) { rlen = alen = -len; rbeg = beg - rlen + 1; int dlen = splice->vcf.alen - splice->vcf.rlen; if ( dlen<0 && beg < splice->ref_end ) // incomplete del, beg is in the middle dlen += splice->ref_end - beg; abeg = rbeg + dlen; } else { rbeg = abeg = beg; rlen = alen = len; // check for incomplete del as above?? } #define XDBG 0 #if XDBG fprintf(bcftools_stderr,"build_hap: rbeg=%d + %d abeg=%d \n",rbeg,rlen,abeg); #endif splice->kref.l = 0; splice->kalt.l = 0; // add the part before vcf.ref, in the vcf.ref and after vcf.ref int roff; // how many vcf.ref bases already used if ( rbeg < splice->vcf.pos ) { assert( splice->tr->beg <= rbeg ); // this can be extended thanks to N_REF_PAD kputsn(TSCRIPT_AUX(splice->tr)->ref + N_REF_PAD + rbeg - splice->tr->beg, splice->vcf.pos - rbeg, &splice->kref); roff = 0; } else roff = rbeg - splice->vcf.pos; #if XDBG fprintf(bcftools_stderr,"r1: %s roff=%d\n",splice->kref.s,roff); #endif if ( roff < splice->vcf.rlen && splice->kref.l < rlen ) { int len = splice->vcf.rlen - roff; // len still available in vcf.ref if ( len > rlen - splice->kref.l ) len = rlen - splice->kref.l; // how much of ref allele is still needed kputsn(splice->vcf.ref + roff, len, &splice->kref); } #if XDBG fprintf(bcftools_stderr,"r2: %s\n",splice->kref.s); #endif uint32_t end = splice->vcf.pos + splice->vcf.rlen; // position just after the ref allele if ( splice->kref.l < rlen ) { if ( end + rlen - splice->kref.l - 1 > splice->tr->end ) // trim, the requested sequence is too long (could be extended, see N_REF_PAD) rlen -= end + rlen - splice->kref.l - 1 - splice->tr->end; if ( splice->kref.l < rlen ) kputsn(TSCRIPT_AUX(splice->tr)->ref + N_REF_PAD + end - splice->tr->beg, rlen - splice->kref.l, &splice->kref); } #if XDBG fprintf(bcftools_stderr,"r3: %s\n",splice->kref.s); #endif int aoff; if ( abeg < splice->vcf.pos ) { assert( splice->tr->beg <= abeg ); kputsn(TSCRIPT_AUX(splice->tr)->ref + N_REF_PAD + abeg - splice->tr->beg, splice->vcf.pos - abeg, &splice->kalt); aoff = 0; } else aoff = abeg - splice->vcf.pos; #if XDBG fprintf(bcftools_stderr,"a1: %s aoff=%d\n",splice->kalt.s,aoff); #endif if ( aoff < splice->vcf.alen && splice->kalt.l < alen ) { int len = splice->vcf.alen - aoff; // len still available in vcf.alt if ( len > alen - splice->kalt.l ) len = alen - splice->kalt.l; // how much of alt allele is still needed kputsn(splice->vcf.alt + aoff, len, &splice->kalt); aoff -= len; } if ( aoff < 0 ) aoff = 0; else aoff--; #if XDBG fprintf(bcftools_stderr,"a2: %s aoff=%d\n",splice->kalt.s,aoff); #endif end = splice->vcf.pos + splice->vcf.rlen; // position just after the ref allele if ( splice->kalt.l < alen ) { if ( end + alen + aoff - splice->kalt.l - 1 > splice->tr->end ) // trim, the requested sequence is too long alen -= end + alen + aoff - splice->kalt.l - 1 - splice->tr->end; if ( alen > 0 && alen > splice->kalt.l ) kputsn(TSCRIPT_AUX(splice->tr)->ref + aoff + N_REF_PAD + end - splice->tr->beg, alen - splice->kalt.l, &splice->kalt); } #if XDBG fprintf(bcftools_stderr,"a3: %s\n",splice->kalt.s); fprintf(bcftools_stderr," [%s]\n [%s]\n\n",splice->kref.s,splice->kalt.s); #endif } void csq_stage(args_t *args, csq_t *csq, bcf1_t *rec); static inline int csq_stage_utr(args_t *args, regitr_t *itr, bcf1_t *rec, uint32_t trid, uint32_t type, int ial) { while ( regitr_overlap(itr) ) { gf_utr_t *utr = regitr_payload(itr, gf_utr_t*); gf_tscript_t *tr = utr->tr; if ( tr->id != trid ) continue; csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.type = (utr->which==prime5 ? CSQ_UTR5 : CSQ_UTR3) | type; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.vcf_ial = ial; csq.type.gene = tr->gene->name; csq_stage(args, &csq, rec); return csq.type.type; } return 0; } static inline void csq_stage_splice(args_t *args, bcf1_t *rec, gf_tscript_t *tr, uint32_t type, int ial) { #if XDBG fprintf(bcftools_stderr,"csq_stage_splice %d: type=%d\n",(int)rec->pos+1,type); #endif if ( !type ) return; csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.type = type; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.vcf_ial = ial; csq.type.gene = tr->gene->name; csq_stage(args, &csq, rec); } static inline const char *drop_chr_prefix(args_t *args, const char *chr) { if ( !args->unify_chr_names ) return chr; if ( !strncasecmp("chr",chr,3) ) return chr+3; return chr; } static inline const char *add_chr_prefix(args_t *args, const char *chr) { if ( !args->unify_chr_names ) return chr; int len = strlen(chr); hts_expand(char,len+4,args->mchr_name,args->chr_name); memcpy(args->chr_name,"chr",3); memcpy(args->chr_name+3,chr,len+1); return args->chr_name; } static inline int splice_csq_ins(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end) { // coordinates that matter for consequences, eg AC>ACG trimmed to C>CG, 1bp // before and after the inserted bases if ( splice->tbeg || splice->vcf.ref[0]!=splice->vcf.alt[0] ) { splice->ref_beg = splice->vcf.pos + splice->tbeg - 1; splice->ref_end = splice->vcf.pos + splice->vcf.rlen - splice->tend; } else { if ( splice->tend ) splice->tend--; splice->ref_beg = splice->vcf.pos; splice->ref_end = splice->vcf.pos + splice->vcf.rlen - splice->tend; } #if XDBG fprintf(bcftools_stderr,"ins: %s>%s .. ex=%d,%d beg,end=%d,%d tbeg,tend=%d,%d check_utr=%d start,stop,beg,end=%d,%d,%d,%d\n", splice->vcf.ref,splice->vcf.alt,ex_beg,ex_end,splice->ref_beg,splice->ref_end,splice->tbeg,splice->tend,splice->check_utr,splice->check_start,splice->check_stop,splice->check_region_beg,splice->check_region_end); #endif int ret; if ( splice->ref_beg >= ex_end ) // fully outside, beyond the exon { if ( splice->check_utr ) { regitr_t *itr = regitr_init(NULL); const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,splice->vcf.rec)); if ( regidx_overlap(args->idx_utr,chr,splice->ref_beg+1,splice->ref_beg+1, itr) ) // adjacent utr { ret = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial); if ( ret!=0 ) { regitr_destroy(itr); return SPLICE_OUTSIDE; // overlaps utr } } regitr_destroy(itr); } if ( !splice->check_region_end ) return SPLICE_OUTSIDE; char *ref = NULL, *alt = NULL; if ( splice->set_refalt ) // seq identity is checked only when tr->ref is available { splice_build_hap(splice, ex_end+1, N_SPLICE_REGION_INTRON); ref = splice->kref.s, alt = splice->kalt.s; } if ( splice->ref_beg < ex_end + N_SPLICE_REGION_INTRON && splice->ref_end > ex_end + N_SPLICE_DONOR ) { splice->csq |= CSQ_SPLICE_REGION; if ( ref && !strncmp(ref,alt,N_SPLICE_REGION_INTRON) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT; } if ( splice->ref_beg < ex_end + N_SPLICE_DONOR ) { if ( splice->check_donor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_DONOR; if ( splice->check_acceptor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_ACCEPTOR; if ( ref && !strncmp(ref,alt,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT; } csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial); return SPLICE_OUTSIDE; } if ( splice->ref_end < ex_beg || (splice->ref_end == ex_beg && !splice->check_region_beg) ) // fully outside, before the exon { if ( splice->check_utr ) { regitr_t *itr = regitr_init(NULL); const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,splice->vcf.rec)); if ( regidx_overlap(args->idx_utr,chr,splice->ref_end-1,splice->ref_end-1, itr) ) // adjacent utr { ret = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial); if ( ret!=0 ) { regitr_destroy(itr); return SPLICE_OUTSIDE; // overlaps utr } } regitr_destroy(itr); } if ( !splice->check_region_beg ) return SPLICE_OUTSIDE; char *ref = NULL, *alt = NULL; if ( splice->set_refalt ) // seq identity is checked only when tr->ref is available { splice_build_hap(splice, ex_beg - N_SPLICE_REGION_INTRON, N_SPLICE_REGION_INTRON); ref = splice->kref.s, alt = splice->kalt.s; } if ( splice->ref_end > ex_beg - N_SPLICE_REGION_INTRON && splice->ref_beg < ex_beg - N_SPLICE_DONOR ) { splice->csq |= CSQ_SPLICE_REGION; if ( ref && !strncmp(ref,alt,N_SPLICE_REGION_INTRON) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT; } if ( splice->ref_end > ex_beg - N_SPLICE_DONOR ) { if ( splice->check_donor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_DONOR; if ( splice->check_acceptor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_ACCEPTOR; if ( ref && !strncmp(ref+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,alt+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT; } csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial); return SPLICE_OUTSIDE; } // overlaps the exon or inside the exon // possible todo: find better alignment for frameshifting variants? if ( splice->ref_beg <= ex_beg + 2 ) // in the first 3bp { if ( splice->check_region_beg ) splice->csq |= CSQ_SPLICE_REGION; if ( splice->tr->strand==STRAND_FWD ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; } else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; } } if ( splice->ref_end > ex_end - 2 ) { if ( splice->check_region_end ) splice->csq |= CSQ_SPLICE_REGION; if ( splice->tr->strand==STRAND_REV ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; } else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; } } if ( splice->set_refalt ) { // Make sure the variant will not end up left aligned to avoid overlapping vcf records // splice_build_hap(splice, splice->ref_beg, splice->vcf.alen - splice->tend - splice->tbeg + 1); // splice->vcf.rlen -= splice->tbeg + splice->tend - 1; // if ( splice->kref.l > splice->vcf.rlen ) { splice->kref.l = splice->vcf.rlen; splice->kref.s[splice->kref.l] = 0; } if ( splice->ref_beg < splice->vcf.pos ) // this must have been caused by too much trimming from right { int dlen = splice->vcf.pos - splice->ref_beg; assert( dlen==1 ); splice->tbeg += dlen; if ( splice->tbeg + splice->tend == splice->vcf.rlen ) splice->tend -= dlen; splice->ref_beg = splice->vcf.pos; } if ( splice->ref_end==ex_beg ) splice->tend--; // prevent zero-length ref allele splice_build_hap(splice, splice->ref_beg, splice->vcf.alen - splice->tend - splice->tbeg + 1); splice->vcf.rlen -= splice->tbeg + splice->tend - 1; if ( splice->kref.l > splice->vcf.rlen ) { splice->kref.l = splice->vcf.rlen; splice->kref.s[splice->kref.l] = 0; } } csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial); return SPLICE_INSIDE; } int shifted_del_synonymous(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end) { static int small_ref_padding_warned = 0; gf_tscript_t *tr = splice->tr; // We know the VCF record overlaps the exon, but does it overlap the start codon? if ( tr->strand==STRAND_REV && splice->vcf.pos + splice->vcf.rlen + 2 <= ex_end ) return 0; if ( tr->strand==STRAND_FWD && splice->vcf.pos >= ex_beg + 3 ) return 0; #if XDBG fprintf(bcftools_stderr,"shifted_del_synonymous: %d-%d %s\n",ex_beg,ex_end, tr->strand==STRAND_FWD?"fwd":(tr->strand==STRAND_REV?"rev":"unk")); fprintf(bcftools_stderr," %d .. %s > %s\n",splice->vcf.pos+1,splice->vcf.ref,splice->vcf.alt); #endif // is there enough ref sequence for the extension? All coordinates are 0-based int ref_len = strlen(splice->vcf.ref); int alt_len = strlen(splice->vcf.alt); assert( ref_len > alt_len ); int ndel = ref_len - alt_len; if ( tr->strand==STRAND_REV ) { int32_t vcf_ref_end = splice->vcf.pos + ref_len - 1; // end pos of the VCF REF allele int32_t tr_ref_end = splice->tr->end + N_REF_PAD; // the end pos of accessible cached ref seq if ( vcf_ref_end + ndel > tr_ref_end ) { if ( !small_ref_padding_warned ) { fprintf(bcftools_stderr,"Warning: Could not verify synonymous start/stop at %s:%d due to small N_REF_PAD. (Improve me?)\n",bcf_seqname(args->hdr,splice->vcf.rec),splice->vcf.pos+1); small_ref_padding_warned = 1; } return 0; } char *ptr_vcf = splice->vcf.ref + alt_len; // the first deleted base in the VCF REF allele char *ptr_ref = TSCRIPT_AUX(splice->tr)->ref + N_REF_PAD + (vcf_ref_end + 1 - splice->tr->beg); // the first ref base after the ndel bases deleted #if XDBG fprintf(bcftools_stderr,"vcf: %s\nref: %s\n",ptr_vcf,ptr_ref); #endif int i = 0; while ( ptr_vcf[i] && ptr_vcf[i]==ptr_ref[i] ) i++; if ( ptr_vcf[i] ) return 0; // the deleted sequence cannot be replaced } else if ( tr->strand==STRAND_FWD ) { // STRAND_FWD int32_t vcf_block_beg = splice->vcf.pos + ref_len - 2*ndel; // the position of the first base of the ref block that could potentially replace the deletion if ( vcf_block_beg < 0 ) return 0; #if XDBG fprintf(bcftools_stderr,"vcf_block_beg: %d\n",vcf_block_beg+1); #endif if ( N_REF_PAD + vcf_block_beg < ex_beg ) { if ( !small_ref_padding_warned ) { fprintf(bcftools_stderr,"Warning: Could not verify synonymous start/stop at %s:%d due to small N_REF_PAD. (Improve me?)\n",bcf_seqname(args->hdr,splice->vcf.rec),splice->vcf.pos+1); small_ref_padding_warned = 1; } return 0; } char *ptr_vcf = splice->vcf.ref + alt_len; // the first deleted base in the VCF REF allele char *ptr_ref = TSCRIPT_AUX(splice->tr)->ref + N_REF_PAD + vcf_block_beg - splice->tr->beg; // the replacement ref block #if XDBG fprintf(bcftools_stderr,"vcf: %s\nref: %s\n",ptr_vcf,ptr_ref); #endif int i = 0; while ( ptr_vcf[i] && ptr_vcf[i]==ptr_ref[i] ) i++; if ( ptr_vcf[i] ) return 0; // the deleted sequence cannot be replaced } return 1; } static inline int splice_csq_del(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end) { if ( splice->check_start ) { // check for synonymous start // test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.txt // test/csq/ENST00000368801.2/start-lost.txt // test/csq/ENST00000318249.2/synonymous-start-lost.txt int is_synonymous = shifted_del_synonymous(args, splice, ex_beg, ex_end); if ( is_synonymous ) { splice->csq |= CSQ_START_RETAINED; return SPLICE_OVERLAP; } } // coordinates that matter for consequences, eg AC>ACG trimmed to C>CG splice->ref_beg = splice->vcf.pos + splice->tbeg - 1; // 1b before the deleted base splice->ref_end = splice->vcf.pos + splice->vcf.rlen - splice->tend - 1; // the last deleted base #if XDBG fprintf(bcftools_stderr,"splice_csq_del: %s>%s .. ex=%d,%d beg,end=%d,%d tbeg,tend=%d,%d check_utr=%d start,stop,beg,end=%d,%d,%d,%d\n", splice->vcf.ref,splice->vcf.alt,ex_beg,ex_end,splice->ref_beg,splice->ref_end,splice->tbeg,splice->tend,splice->check_utr,splice->check_start,splice->check_stop,splice->check_region_beg,splice->check_region_end); #endif if ( splice->ref_beg + 1 < ex_beg ) // the part before the exon; ref_beg is off by -1 { if ( splice->check_region_beg ) { int csq = 0; if ( splice->check_utr ) { regitr_t *itr = regitr_init(NULL); const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,splice->vcf.rec)); if ( regidx_overlap(args->idx_utr,chr,splice->ref_beg,ex_beg-1, itr) ) // adjacent utr csq = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial); regitr_destroy(itr); } if ( !csq ) { char *ref = NULL, *alt = NULL; if ( splice->set_refalt ) // seq identity is checked only when tr->ref is available { // filling from the left does not work for ENST00000341065/frame3.vcf // CAG.GTGGCCAG CAG.GTGGCCAG // CA-.--GGCCAG vs CAG.---GCCAG // splice_build_hap(splice, ex_beg-1, -N_SPLICE_REGION_INTRON); // // filling from the right: splice_build_hap(splice, ex_beg - N_SPLICE_REGION_INTRON, N_SPLICE_REGION_INTRON); ref = splice->kref.s, alt = splice->kalt.s; } if ( splice->ref_end >= ex_beg - N_SPLICE_REGION_INTRON && splice->ref_beg < ex_beg - N_SPLICE_DONOR ) { splice->csq |= CSQ_SPLICE_REGION; if ( ref && alt && !strncmp(ref,alt,N_SPLICE_REGION_INTRON) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT; } if ( splice->ref_end >= ex_beg - N_SPLICE_DONOR ) { if ( splice->check_donor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_DONOR; if ( splice->check_acceptor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_ACCEPTOR; if ( ref && alt && !strncmp(ref+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,alt+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT; } } } if ( splice->ref_end >= ex_beg ) { splice->tbeg = splice->ref_beg - splice->vcf.pos + 1; splice->ref_beg = ex_beg - 1; if ( splice->tbeg + splice->tend == splice->vcf.alen ) { // the deletion overlaps ex_beg and cannot be easily realigned to the right if ( !splice->tend ) { splice->csq |= CSQ_CODING_SEQUENCE; return SPLICE_OVERLAP; } splice->tend--; } } } if ( ex_end < splice->ref_end ) // the part after the exon { if ( splice->check_region_end ) { int csq = 0; if ( splice->check_utr ) { regitr_t *itr = regitr_init(NULL); const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,splice->vcf.rec)); if ( regidx_overlap(args->idx_utr,chr,ex_end+1,splice->ref_end, itr) ) // adjacent utr csq = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial); regitr_destroy(itr); } if ( !csq ) { char *ref = NULL, *alt = NULL; if ( splice->set_refalt ) // seq identity is checked only when tr->ref is available { splice_build_hap(splice, ex_end+1, N_SPLICE_REGION_INTRON); // ref,alt positioned at the first intron base ref = splice->kref.s, alt = splice->kalt.s; } if ( splice->ref_beg < ex_end + N_SPLICE_REGION_INTRON && splice->ref_end > ex_end + N_SPLICE_DONOR ) { splice->csq |= CSQ_SPLICE_REGION; if ( ref && alt && !strncmp(ref,alt,N_SPLICE_REGION_INTRON) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT; } if ( splice->ref_beg < ex_end + N_SPLICE_DONOR ) { if ( splice->check_donor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_DONOR; if ( splice->check_acceptor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_ACCEPTOR; if ( ref && alt && !strncmp(ref+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,alt+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT; } } } if ( splice->ref_beg < ex_end ) { splice->tend = splice->vcf.rlen - (splice->ref_end - splice->vcf.pos + 1); splice->ref_end = ex_end; } } if ( splice->ref_end < ex_beg || splice->ref_beg >= ex_end ) { csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial); return SPLICE_OUTSIDE; } if ( splice->ref_beg < ex_beg + 2 ) // ref_beg is off by -1 { if ( splice->check_region_beg ) splice->csq |= CSQ_SPLICE_REGION; if ( splice->tr->strand==STRAND_FWD ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; } else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; } } if ( splice->ref_end > ex_end - 3 ) { if ( splice->check_region_end ) splice->csq |= CSQ_SPLICE_REGION; if ( splice->tr->strand==STRAND_REV ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; } else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; } } if ( splice->set_refalt ) { if ( splice->tbeg>0 ) splice->tbeg--; //why is this? if ( splice->vcf.rlen > splice->tbeg + splice->tend && splice->vcf.alen > splice->tbeg + splice->tend ) { splice->vcf.rlen -= splice->tbeg + splice->tend; splice->vcf.alen -= splice->tbeg + splice->tend; } splice->kref.l = 0; kputsn(splice->vcf.ref + splice->tbeg, splice->vcf.rlen, &splice->kref); splice->kalt.l = 0; kputsn(splice->vcf.alt + splice->tbeg, splice->vcf.alen, &splice->kalt); if ( (splice->ref_beg+1 < ex_beg && splice->ref_end >= ex_beg) || (splice->ref_beg+1 < ex_end && splice->ref_end >= ex_end) ) // ouch, ugly ENST00000409523/long-overlapping-del.vcf { int ref_beg = splice->ref_beg + splice->kalt.l - 1; // 0 for AAA>A, 1 for AAA>AC if ( ref_beg < splice->ref_end ) splice->csq |= (splice->ref_end - ref_beg)%3 ? CSQ_FRAMESHIFT_VARIANT : CSQ_INFRAME_DELETION; return SPLICE_OVERLAP; } } csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial); return SPLICE_INSIDE; } static inline int splice_csq_mnp(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end) { // not a real variant, can be ignored: eg ACGT>ACGT if ( splice->tbeg + splice->tend == splice->vcf.rlen ) return SPLICE_VAR_REF; splice->ref_beg = splice->vcf.pos + splice->tbeg; splice->ref_end = splice->vcf.pos + splice->vcf.rlen - splice->tend - 1; #if XDBG fprintf(bcftools_stderr,"mnp: %s>%s .. ex=%d,%d beg,end=%d,%d tbeg,tend=%d,%d check_utr=%d start,stop,beg,end=%d,%d,%d,%d\n", splice->vcf.ref,splice->vcf.alt,ex_beg,ex_end,splice->ref_beg,splice->ref_end,splice->tbeg,splice->tend,splice->check_utr,splice->check_start,splice->check_stop,splice->check_region_beg,splice->check_region_end); #endif if ( splice->ref_beg < ex_beg ) // the part before the exon { if ( splice->check_region_beg ) { int csq = 0; if ( splice->check_utr ) { regitr_t *itr = regitr_init(NULL); const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,splice->vcf.rec)); if ( regidx_overlap(args->idx_utr,chr,splice->ref_beg,ex_beg-1, itr) ) // adjacent utr csq = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial); regitr_destroy(itr); } if ( !csq ) { if ( splice->ref_end >= ex_beg - N_SPLICE_REGION_INTRON && splice->ref_beg < ex_beg - N_SPLICE_DONOR ) splice->csq |= CSQ_SPLICE_REGION; if ( splice->ref_end >= ex_beg - N_SPLICE_DONOR ) { if ( splice->check_donor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_DONOR; if ( splice->check_acceptor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_ACCEPTOR; } } } if ( splice->ref_end >= ex_beg ) { splice->tbeg = splice->ref_beg - splice->vcf.pos; splice->ref_beg = ex_beg; } } if ( ex_end < splice->ref_end ) // the part after the exon { if ( splice->check_region_end ) { int csq = 0; if ( splice->check_utr ) { regitr_t *itr = regitr_init(NULL); const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,splice->vcf.rec)); if ( regidx_overlap(args->idx_utr,chr,ex_end+1,splice->ref_end, itr) ) // adjacent utr csq = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial); regitr_destroy(itr); } if ( !csq ) { if ( splice->ref_beg <= ex_end + N_SPLICE_REGION_INTRON && splice->ref_end > ex_end + N_SPLICE_DONOR ) splice->csq |= CSQ_SPLICE_REGION; if ( splice->ref_beg <= ex_end + N_SPLICE_DONOR ) { if ( splice->check_donor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_DONOR; if ( splice->check_acceptor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_ACCEPTOR; } } } if ( splice->ref_beg <= ex_end ) { splice->tend = splice->vcf.rlen - (splice->ref_end - splice->vcf.pos + 1); splice->ref_end = ex_end; } } if ( splice->ref_end < ex_beg || splice->ref_beg > ex_end ) { csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial); return SPLICE_OUTSIDE; } if ( splice->ref_beg < ex_beg + 3 ) { if ( splice->check_region_beg ) splice->csq |= CSQ_SPLICE_REGION; if ( splice->tr->strand==STRAND_FWD ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; } else if ( splice->tr->strand==STRAND_REV ) { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; } } if ( splice->ref_end > ex_end - 3 ) { if ( splice->check_region_end ) splice->csq |= CSQ_SPLICE_REGION; if ( splice->tr->strand==STRAND_REV ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; } else if ( splice->tr->strand==STRAND_FWD ) { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; } } if ( splice->set_refalt ) { splice->vcf.rlen -= splice->tbeg + splice->tend; splice->kref.l = 0; kputsn(splice->vcf.ref + splice->tbeg, splice->vcf.rlen, &splice->kref); splice->kalt.l = 0; kputsn(splice->vcf.alt + splice->tbeg, splice->vcf.rlen, &splice->kalt); } csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial); return SPLICE_INSIDE; } static inline int splice_csq(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end) { splice->vcf.alen = strlen(splice->vcf.alt); int rlen1 = splice->vcf.rlen - 1, alen1 = splice->vcf.alen - 1, i = 0; splice->tbeg = 0, splice->tend = 0; // trim from the right, then from the left while ( i<=rlen1 && i<=alen1 ) { if ( splice->vcf.ref[rlen1-i] != splice->vcf.alt[alen1-i] ) break; i++; } splice->tend = i; rlen1 -= i, alen1 -= i, i = 0; while ( i<=rlen1 && i<=alen1 ) { if ( splice->vcf.ref[i] != splice->vcf.alt[i] ) break; i++; } splice->tbeg = i; // The mnp, ins and del code was split into near-identical functions for clarity and debugging; // possible todo: generalize once stable if ( splice->vcf.rlen==splice->vcf.alen ) return splice_csq_mnp(args, splice, ex_beg, ex_end); if ( splice->vcf.rlen < splice->vcf.alen ) return splice_csq_ins(args, splice, ex_beg, ex_end); if ( splice->vcf.rlen > splice->vcf.alen ) return splice_csq_del(args, splice, ex_beg, ex_end); return 0; } // return value: 0 added, 1 overlapping variant, 2 silent discard (intronic,alt=ref) int hap_init(args_t *args, hap_node_t *parent, hap_node_t *child, gf_cds_t *cds, bcf1_t *rec, int ial) { int i; kstring_t str = {0,0,0}; gf_tscript_t *tr = cds->tr; child->icds = cds->icds; // index of cds in the tscript's list of exons child->vcf_ial = ial; splice_t splice; splice_init(&splice, rec); splice.tr = tr; splice.vcf.ial = ial; splice.vcf.alt = rec->d.allele[ial]; splice.check_acceptor = splice.check_donor = splice.set_refalt = splice.check_utr = 1; if ( !(tr->trim & TRIM_5PRIME) ) { if ( tr->strand==STRAND_FWD ) { if ( child->icds==0 ) splice.check_start = 1; } else if ( tr->strand==STRAND_REV ) { if ( child->icds==tr->ncds-1 ) splice.check_start = 1; } } if ( !(tr->trim & TRIM_3PRIME) ) { if ( tr->strand==STRAND_FWD ) { if ( child->icds==tr->ncds-1 ) splice.check_stop = 1; } else if ( tr->strand==STRAND_REV ) { if ( child->icds==0 ) splice.check_stop = 1; } } if ( splice.check_start ) // do not check starts in incomplete CDS, defined as not starting with M { if ( tr->strand==STRAND_FWD ) { if ( dna2aa(TSCRIPT_AUX(tr)->ref+N_REF_PAD+cds->beg-tr->beg) != 'M' ) splice.check_start = 0; } else if ( tr->strand==STRAND_REV ) { if ( cdna2aa(TSCRIPT_AUX(tr)->ref+N_REF_PAD+cds->beg-tr->beg+cds->len-3) != 'M' ) splice.check_start = 0; } } if ( child->icds!=0 ) splice.check_region_beg = 1; if ( child->icds!=tr->ncds-1 ) splice.check_region_end = 1; #if XDBG fprintf(bcftools_stderr,"\nhap_init: %d [%s][%s] check start:%d,stop:%d\n",splice.vcf.pos+1,splice.vcf.ref,splice.vcf.alt,splice.check_start,splice.check_stop); #endif int ret = splice_csq(args, &splice, cds->beg, cds->beg + cds->len - 1); #if XDBG fprintf(bcftools_stderr,"cds splice_csq: %d [%s][%s] .. beg,end=%d %d, ret=%d, csq=%d\n\n",splice.vcf.pos+1,splice.kref.s,splice.kalt.s,splice.ref_beg+1,splice.ref_end+1,ret,splice.csq); #endif if ( ret==SPLICE_VAR_REF ) return 2; // not a variant, eg REF=CA ALT=CA if ( ret==SPLICE_OUTSIDE || ret==SPLICE_OVERLAP || splice.csq==CSQ_START_LOST ) // not a coding csq { free(splice.kref.s); free(splice.kalt.s); if ( !splice.csq ) return 2; // fully intronic, no csq // splice_region/acceptor/donor child->seq = NULL; child->sbeg = 0; child->rbeg = rec->pos; child->rlen = 0; child->dlen = 0; kputs(rec->d.allele[0],&str); kputc('>',&str); kputs(rec->d.allele[ial],&str); child->var = str.s; child->type = HAP_SSS; child->csq = splice.csq; child->rec = rec; return 0; } if ( splice.csq & CSQ_SYNONYMOUS_VARIANT ) splice.csq &= ~CSQ_SYNONYMOUS_VARIANT; // synonymous&splice,frame could become synonymous&frame,splice int dbeg = 0; if ( splice.ref_beg < cds->beg ) { // The vcf record overlaps the exon boundary, but the variant itself // should fit inside since we are here. This will need more work. // #1475227917 dbeg = cds->beg - splice.ref_beg; splice.kref.l -= dbeg; splice.ref_beg = cds->beg; assert( dbeg <= splice.kalt.l ); } assert( parent->type!=HAP_SSS ); if ( parent->type==HAP_CDS ) { i = parent->icds; if ( i!=cds->icds ) { // the variant is on a new exon, finish up the previous int len = tr->cds[i]->len - parent->rbeg - parent->rlen + tr->cds[i]->beg; if ( len > 0 ) kputsn_(TSCRIPT_AUX(tr)->ref + N_REF_PAD + parent->rbeg + parent->rlen - tr->beg, len, &str); } // append any skipped non-variant exons while ( ++i < cds->icds ) kputsn_(TSCRIPT_AUX(tr)->ref + N_REF_PAD + tr->cds[i]->beg - tr->beg, tr->cds[i]->len, &str); if ( parent->icds==child->icds ) { int len = splice.ref_beg - parent->rbeg - parent->rlen; if ( len < 0 ) // overlapping variants { free(str.s); free(splice.kref.s); free(splice.kalt.s); return 1; } kputsn_(TSCRIPT_AUX(tr)->ref + N_REF_PAD + parent->rbeg + parent->rlen - tr->beg, len, &str); } else kputsn_(TSCRIPT_AUX(tr)->ref + N_REF_PAD + cds->beg - tr->beg, splice.ref_beg - cds->beg, &str); } kputs(splice.kalt.s + dbeg, &str); child->seq = str.s; child->sbeg = cds->pos + (splice.ref_beg - cds->beg); child->rbeg = splice.ref_beg; child->rlen = splice.kref.l; child->type = HAP_CDS; child->prev = parent; child->rec = rec; child->csq = splice.csq; // set vlen and the "ref>alt" string { int rlen = strlen(rec->d.allele[0]); int alen = strlen(rec->d.allele[ial]); child->dlen = alen - rlen; child->var = (char*) malloc(rlen+alen+2); memcpy(child->var,rec->d.allele[0],rlen); child->var[rlen] = '>'; memcpy(child->var+rlen+1,rec->d.allele[ial],alen); child->var[rlen+alen+1] = 0; } // yuck, the whole CDS is modified/deleted, not ready for this, todo. if ( child->rbeg + child->rlen > cds->beg + cds->len ) { child->type = HAP_SSS; if ( !child->csq ) child->csq |= CSQ_CODING_SEQUENCE; // hack, specifically for ENST00000390520/deletion-overlap.vcf } free(splice.kref.s); free(splice.kalt.s); return 0; } void hap_destroy(hap_node_t *hap) { int i; for (i=0; inchild; i++) if ( hap->child[i] ) hap_destroy(hap->child[i]); for (i=0; imcsq_list; i++) free(hap->csq_list[i].type.vstr.s); free(hap->csq_list); free(hap->child); free(hap->cur_child); free(hap->seq); free(hap->var); free(hap); } /* ref: spliced reference and its length (ref.l) seq: part of the spliced query transcript on the reference strand to translate, its length (seq.l) and the total length of the complete transcript (seq.m) sbeg: seq offset within the spliced query transcript rbeg: seq offset within ref, 0-based rend: last base of seq within ref, plus one. If seq does not contain indels, it is rend=rbeg+seq->l strand: coding strand - 0:rev, 1:fwd tseq: translated sequence (aa) fill: frameshift, fill until the end (strand=fwd) or from the start (strand=rev) */ void cds_translate(kstring_t *_ref, kstring_t *_seq, uint32_t sbeg, uint32_t rbeg, uint32_t rend, int strand, kstring_t *tseq, int fill) { #if XDBG fprintf(bcftools_stderr,"\ntranslate: %d %d %d fill=%d seq.l=%d\n",sbeg,rbeg,rend,fill,(int)_seq->l); #endif char tmp[3], *codon, *end; int i, len, npad; kstring_t ref = *_ref; kstring_t seq = *_seq; tseq->l = 0; if ( !seq.l ) { kputc('?', tseq); return; } #define DBG 0 #if DBG fprintf(bcftools_stderr,"translate: sbeg,rbeg,rend=%d %d %d fill=%d seq.l=%d\n",sbeg,rbeg,rend,fill,(int)_seq->l); fprintf(bcftools_stderr," ref: l=%d %s\n", (int)ref.l,ref.s); fprintf(bcftools_stderr," seq: l=%d m=%d ", (int)seq.l,(int)seq.m); for (i=0; i1 fprintf(bcftools_stderr," npad: %d\n",npad); #endif assert( npad<=rbeg ); for (i=0; i1 fprintf(bcftools_stderr,"\t i=%d\n", i); #endif if ( i==3 ) { kputc_(dna2aa(tmp), tseq); #if DBG>1 fprintf(bcftools_stderr,"[1]%c%c%c\n",tmp[0],tmp[1],tmp[2]); #endif codon = seq.s + 3 - npad; // next codon end = codon + len - 1 - (len % 3); // last position of a valid codon while ( codon < end ) { kputc_(dna2aa(codon), tseq); #if DBG>1 fprintf(bcftools_stderr,"[2]%c%c%c\n",codon[0],codon[1],codon[2]); #endif codon += 3; } end = seq.s + seq.l - 1; for (i=0; codon+i<=end; i++) tmp[i] = codon[i]; } // right padding codon = ref.s + rend + N_REF_PAD; if ( i>0 ) { #if DBG>1 if(i==1)fprintf(bcftools_stderr,"[3]%c\n",tmp[0]); if(i==2)fprintf(bcftools_stderr,"[3]%c%c\n",tmp[0],tmp[1]); #endif for (; i<3; i++) { tmp[i] = *codon; codon++; } kputc_(dna2aa(tmp), tseq); #if DBG>1 fprintf(bcftools_stderr,"[4]%c%c%c\n",tmp[0],tmp[1],tmp[2]); #endif } if ( fill!=0 ) { end = ref.s + ref.l - N_REF_PAD; while ( codon+3 <= end ) { kputc_(dna2aa(codon), tseq); #if DBG>1 fprintf(bcftools_stderr,"[5]%c%c%c\t%c\n",codon[0],codon[1],codon[2],dna2aa(codon)); #endif codon += 3; } } } else if ( strand==STRAND_REV ) { // right padding - number of bases to take from ref npad = (seq.m - (sbeg + seq.l)) % 3; #if DBG>1 fprintf(bcftools_stderr," npad: %d\n",npad); #endif if ( !(npad>=0 && sbeg+seq.l+npad<=seq.m) ) fprintf(bcftools_stderr,"sbeg=%d seq.l=%d seq.m=%d npad=%d\n",sbeg,(int)seq.l,(int)seq.m,npad); assert( npad>=0 && sbeg+seq.l+npad<=seq.m ); // todo: first codon on the rev strand if ( npad==2 ) { tmp[1] = ref.s[rend+N_REF_PAD]; tmp[2] = ref.s[rend+N_REF_PAD+1]; i = 0; } else if ( npad==1 ) { tmp[2] = ref.s[rend+N_REF_PAD]; i = 1; } else i = 2; end = seq.s + seq.l; for (; i>=0 && end>seq.s; i--) tmp[i] = *(--end); #if DBG>1 fprintf(bcftools_stderr,"\t i=%d\n", i); if(i==1)fprintf(bcftools_stderr,"[0] %c\n",tmp[2]); if(i==0)fprintf(bcftools_stderr,"[0] %c%c\n",tmp[1],tmp[2]); #endif if ( i==-1 ) { #if DBG>1 fprintf(bcftools_stderr,"[1]%c%c%c\t%c\n",tmp[0],tmp[1],tmp[2], cdna2aa(tmp)); #endif kputc_(cdna2aa(tmp), tseq); codon = end - 3; while ( codon >= seq.s ) { kputc_(cdna2aa(codon), tseq); #if DBG>1 fprintf(bcftools_stderr,"[2]%c%c%c\t%c\n",codon[0],codon[1],codon[2], cdna2aa(codon)); #endif codon -= 3; } if ( seq.s-codon==2 ) { tmp[2] = seq.s[0]; i = 1; } else if ( seq.s-codon==1 ) { tmp[1] = seq.s[0]; tmp[2] = seq.s[1]; i = 0; } else i = -1; #if DBG>1 if(i==1)fprintf(bcftools_stderr,"[3] %c\n",tmp[2]); if(i==0)fprintf(bcftools_stderr,"[3] %c%c\n",tmp[1],tmp[2]); #endif } // left padding end = ref.s + N_REF_PAD + rbeg; if ( i>=0 ) { for (; i>=0 && end>=ref.s; i--) tmp[i] = *(--end); kputc_(cdna2aa(tmp), tseq); #if DBG>1 fprintf(bcftools_stderr,"[4]%c%c%c\t%c\n",tmp[0],tmp[1],tmp[2],cdna2aa(tmp)); #endif } if ( fill!=0 ) { codon = end - 3; while ( codon >= ref.s + N_REF_PAD ) { kputc_(cdna2aa(codon), tseq); #if DBG>1 fprintf(bcftools_stderr,"[5]%c%c%c\t%c\n",codon[0],codon[1],codon[2],cdna2aa(codon)); #endif codon -= 3; } } } else error("Should not happen: %d\n", strand); kputc_(0,tseq); tseq->l--; #if DBG fprintf(bcftools_stderr," tseq: %s\n", tseq->s); #endif } void tscript_splice_ref(gf_tscript_t *tr) { int i, len = 0; for (i=0; incds; i++) len += tr->cds[i]->len; TSCRIPT_AUX(tr)->nsref = len + 2*N_REF_PAD; TSCRIPT_AUX(tr)->sref = (char*) malloc(len + 1 + 2*N_REF_PAD); len = 0; memcpy(TSCRIPT_AUX(tr)->sref, TSCRIPT_AUX(tr)->ref + tr->cds[0]->beg - tr->beg, N_REF_PAD); len += N_REF_PAD; for (i=0; incds; i++) { memcpy(TSCRIPT_AUX(tr)->sref + len, TSCRIPT_AUX(tr)->ref + N_REF_PAD + tr->cds[i]->beg - tr->beg, tr->cds[i]->len); len += tr->cds[i]->len; } memcpy(TSCRIPT_AUX(tr)->sref + len, TSCRIPT_AUX(tr)->ref + N_REF_PAD + tr->cds[tr->ncds-1]->beg - tr->beg, N_REF_PAD); len += N_REF_PAD; TSCRIPT_AUX(tr)->sref[len] = 0; } // returns: 0 if consequence was added, 1 if it already exists or could not be added int csq_push(args_t *args, csq_t *csq, bcf1_t *rec) { #if XDBG fprintf(bcftools_stderr,"csq_push: %d .. %d\n",(int)rec->pos+1,csq->type.type); #endif khint_t k = kh_get(pos2vbuf, args->pos2vbuf, (int)csq->pos); vbuf_t *vbuf = (k == kh_end(args->pos2vbuf)) ? NULL : kh_val(args->pos2vbuf, k); if ( !vbuf ) error("This should not happen. %s:%d %s\n",bcf_seqname(args->hdr,rec),csq->pos+1,csq->type.vstr.s); int i; for (i=0; in; i++) if ( vbuf->vrec[i]->line==rec ) break; if ( i==vbuf->n ) error("This should not happen.. %s:%d %s\n", bcf_seqname(args->hdr,rec),csq->pos+1,csq->type.vstr.s); vrec_t *vrec = vbuf->vrec[i]; // if the variant overlaps donor/acceptor and also splice region, report only donor/acceptor if ( csq->type.type & CSQ_SPLICE_REGION && csq->type.type & (CSQ_SPLICE_DONOR|CSQ_SPLICE_ACCEPTOR) ) csq->type.type &= ~CSQ_SPLICE_REGION; if ( csq->type.type & CSQ_PRINTED_UPSTREAM ) { for (i=0; invcsq; i++) { // Same as below, to avoid records like // 3630 .. @3632,stop_lost|AL627309.1|ENST00000423372|protein_coding|- // 3632 .. stop_lost|AL627309.1|ENST00000423372|protein_coding|-|260*>260G|3630T>A+3632A>C if ( csq->type.type&CSQ_START_STOP && vrec->vcsq[i].type&CSQ_START_STOP ) { vrec->vcsq[i] = csq->type; goto exit_duplicate; } if ( !(vrec->vcsq[i].type & CSQ_PRINTED_UPSTREAM) ) continue; if ( csq->type.ref != vrec->vcsq[i].ref ) continue; goto exit_duplicate; } } else if ( csq->type.type & CSQ_COMPOUND ) { for (i=0; invcsq; i++) { if ( csq->type.trid != vrec->vcsq[i].trid && (csq->type.type|vrec->vcsq[i].type)&CSQ_PRN_TSCRIPT ) continue; if ( csq->type.biotype != vrec->vcsq[i].biotype ) continue; if ( csq->type.gene != vrec->vcsq[i].gene ) continue; if ( csq->type.vcf_ial != vrec->vcsq[i].vcf_ial ) continue; if ( (csq->type.type&CSQ_UPSTREAM_STOP)^(vrec->vcsq[i].type&CSQ_UPSTREAM_STOP) ) continue; // both must or mustn't have upstream_stop if ( csq->type.vstr.s || vrec->vcsq[i].vstr.s ) { // This is a bit hacky, but we want a simpler and more predictable output. The splice_csq() function // can trigger stop/start events based on indel overlap, then another stop/start event can be triggered // from add_csq() or test_cds_local() based on sequence comparison, and on output we could find two // consequences: // stop_lost|AL627309.1|ENST00000423372|protein_coding|- // stop_lost&inframe_insertion|AL627309.1|ENST00000423372|protein_coding|-|260*>260CL|3630T>TAAA if ( !csq->type.vstr.s || !vrec->vcsq[i].vstr.s ) { if ( csq->type.type&CSQ_START_STOP && vrec->vcsq[i].type&CSQ_START_STOP ) { vrec->vcsq[i].type |= csq->type.type; // remove stop_lost&synonymous if stop_retained set if ( vrec->vcsq[i].type&CSQ_STOP_RETAINED ) vrec->vcsq[i].type &= ~(CSQ_STOP_LOST|CSQ_SYNONYMOUS_VARIANT); if ( !vrec->vcsq[i].vstr.s ) vrec->vcsq[i].vstr = csq->type.vstr; goto exit_duplicate; } continue; } if ( strcmp(csq->type.vstr.s,vrec->vcsq[i].vstr.s) ) continue; } vrec->vcsq[i].type |= csq->type.type; goto exit_duplicate; } } else { for (i=0; invcsq; i++) { if ( csq->type.trid != vrec->vcsq[i].trid && (csq->type.type|vrec->vcsq[i].type)&CSQ_PRN_TSCRIPT) continue; if ( csq->type.biotype != vrec->vcsq[i].biotype ) continue; if ( !(vrec->vcsq[i].type & CSQ_COMPOUND) ) { vrec->vcsq[i].type |= csq->type.type; goto exit_duplicate; } if ( vrec->vcsq[i].type==(vrec->vcsq[i].type|csq->type.type) ) goto exit_duplicate; } } // no such csq yet in this vcf record csq->vrec = vrec; csq->idx = vrec->nvcsq++; hts_expand0(vcsq_t, vrec->nvcsq, vrec->mvcsq, vrec->vcsq); vrec->vcsq[i] = csq->type; return 0; exit_duplicate: csq->vrec = vrec; csq->idx = i; return 1; } // soff .. position of the variant within the trimmed query transcript // sbeg .. position of the variant within the query transcript // rbeg .. position on the reference transcript (if there are no indels, then rbeg=send) // rpos .. VCF position #define node2soff(i) (hap->stack[i].slen - (hap->stack[i].node->rlen + hap->stack[i].node->dlen)) #define node2sbeg(i) (hap->sbeg + node2soff(i)) #define node2send(i) (hap->sbeg + hap->stack[i].slen) #define node2rbeg(i) (hap->stack[i].node->sbeg) #define node2rend(i) (hap->stack[i].node->sbeg + hap->stack[i].node->rlen) #define node2rpos(i) (hap->stack[i].node->rec->pos) void kput_vcsq(args_t *args, vcsq_t *csq, kstring_t *str) { // Remove start/stop from incomplete CDS, but only if there is another // consequence as something must be reported if ( csq->type & CSQ_INCOMPLETE_CDS && (csq->type & ~(CSQ_START_STOP|CSQ_INCOMPLETE_CDS|CSQ_UPSTREAM_STOP)) ) csq->type &= ~(CSQ_START_STOP|CSQ_INCOMPLETE_CDS); // Remove missense from start/stops if ( csq->type & CSQ_START_STOP && csq->type & CSQ_MISSENSE_VARIANT ) csq->type &= ~CSQ_MISSENSE_VARIANT; if ( csq->type & CSQ_PRINTED_UPSTREAM && csq->ref ) { kputc_('@',str); kputw(csq->ref->pos+1, str); return; } if ( csq->type & CSQ_UPSTREAM_STOP ) kputc_('*',str); int has_csq = 0, i, n = sizeof(csq_strings)/sizeof(char*); for (i=1; itype&(1<type&(1<biotype==GF_NMD) && (csq->type & CSQ_PRN_NMD) ) { if ( has_csq ) kputc_('&',str); // just in case, this should always be true kputs("NMD_transcript",str); } kputc_('|', str); if ( csq->gene ) kputs(csq->gene , str); kputc_('|', str); // if ( csq->type & CSQ_PRN_TSCRIPT ) kputs(args->tscript_ids.str[csq->trid], str); if ( csq->type & CSQ_PRN_TSCRIPT ) kputs(gff_id2string(args->gff,transcript,csq->trid), str); kputc_('|', str); kputs(gf_type2gff_string(csq->biotype), str); if ( CSQ_PRN_STRAND(csq->type) || csq->vstr.l ) kputs(csq->strand==STRAND_FWD ? "|+" : (csq->strand==STRAND_REV ? "|-" : "|."), str); if ( csq->vstr.l ) kputs(csq->vstr.s, str); } void kprint_aa_prediction(args_t *args, int beg, kstring_t *aa, kstring_t *str) { if ( !args->brief_predictions || (int)aa->l - args->brief_predictions < 3 ) kputs(aa->s, str); else { int i, len = aa->l; if ( aa->s[len-1]=='*' ) len--; for (i=0; ibrief_predictions; i++) kputc(aa->s[i], str); kputs("..", str); kputw(beg+len, str); } } void hap_add_csq(args_t *args, hap_t *hap, hap_node_t *node, int tlen, int ibeg, int iend, int dlen, int indel) { int i; gf_tscript_t *tr = hap->tr; assert( tr->strand==STRAND_FWD || tr->strand==STRAND_REV ); int ref_node = tr->strand==STRAND_FWD ? ibeg : iend; int icsq = node->ncsq_list++; hts_expand0(csq_t,node->ncsq_list,node->mcsq_list,node->csq_list); csq_t *csq = &node->csq_list[icsq]; csq->pos = hap->stack[ref_node].node->rec->pos; csq->type.trid = tr->id; csq->type.vcf_ial = node->vcf_ial; csq->type.gene = tr->gene->name; csq->type.strand = tr->strand; csq->type.biotype = tr->type; // only now we see the translated sequence and can determine if the stop/start changes are real int rm_csq = 0; csq->type.type = 0; for (i=ibeg; i<=iend; i++) csq->type.type |= hap->stack[i].node->csq & CSQ_COMPOUND; if ( dlen==0 && indel ) csq->type.type |= CSQ_INFRAME_ALTERING; int has_upstream_stop = hap->upstream_stop; if ( hap->stack[ibeg].node->type != HAP_SSS ) { // check for truncating stops for (i=0; itref.l; i++) if ( hap->tref.s[i]=='*' ) break; if ( i!=hap->tref.l ) { hap->tref.l = i+1; hap->tref.s[i+1] = 0; } for (i=0; itseq.l; i++) if ( hap->tseq.s[i]=='*' ) break; if ( i!=hap->tseq.l ) { hap->tseq.l = i+1; hap->tseq.s[i+1] = 0; hap->upstream_stop = 1; } if ( csq->type.type & CSQ_STOP_LOST ) { if ( hap->tref.s[hap->tref.l-1]=='*' && hap->tref.s[hap->tref.l-1] == hap->tseq.s[hap->tseq.l-1] ) { rm_csq |= CSQ_STOP_LOST; csq->type.type |= CSQ_STOP_RETAINED; } else if ( hap->tref.s[hap->tref.l-1]!='*' ) { // This is CDS 3' incomplete ENSG00000173376/synon.vcf, can also be missense // We observe in real data a change to a stop, ENST00000528237/retained-stop-incomplete-cds.vcf if ( hap->tseq.s[hap->tseq.l-1] == '*' ) { rm_csq |= CSQ_STOP_GAINED; csq->type.type |= CSQ_STOP_RETAINED; } else csq->type.type |= CSQ_INCOMPLETE_CDS; } } if ( csq->type.type & CSQ_START_LOST && hap->tref.s[0]!='M' ) { rm_csq |= CSQ_START_LOST; csq->type.type &= ~CSQ_START_LOST; } if ( dlen!=0 ) { if ( dlen%3 ) csq->type.type |= CSQ_FRAMESHIFT_VARIANT; else if ( dlen<0 ) csq->type.type |= CSQ_INFRAME_DELETION; else csq->type.type |= CSQ_INFRAME_INSERTION; if ( hap->tref.s[hap->tref.l-1]!='*' && hap->tseq.s[hap->tseq.l-1]=='*' ) csq->type.type |= CSQ_STOP_GAINED; } else { int aa_change = 0; for (i=0; itref.l; i++) { if ( hap->tref.s[i] == hap->tseq.s[i] ) continue; aa_change = 1; if ( hap->tref.s[i] == '*' ) csq->type.type |= CSQ_STOP_LOST; else if ( hap->tseq.s[i] == '*' ) csq->type.type |= CSQ_STOP_GAINED; else csq->type.type |= CSQ_MISSENSE_VARIANT; } if ( !aa_change ) csq->type.type |= CSQ_SYNONYMOUS_VARIANT; } } // Check if compound inframe variants are real inframes, or if the stop codon occurs before the frameshift can be restored if ( ibeg!=iend && (csq->type.type & (CSQ_INFRAME_DELETION|CSQ_INFRAME_INSERTION|CSQ_INFRAME_ALTERING)) && hap->tseq.s[hap->tseq.l-1]=='*' ) { rm_csq |= CSQ_INFRAME_DELETION | CSQ_INFRAME_INSERTION | CSQ_INFRAME_ALTERING; csq->type.type |= CSQ_FRAMESHIFT_VARIANT | CSQ_STOP_GAINED; } if ( has_upstream_stop ) csq->type.type |= CSQ_UPSTREAM_STOP; csq->type.type &= ~rm_csq; if ( hap->stack[ibeg].node->type == HAP_SSS ) { node->csq_list[icsq].type.type |= hap->stack[ibeg].node->csq & ~rm_csq; node->csq_list[icsq].type.ref = hap->stack[ibeg].node->rec; node->csq_list[icsq].type.biotype = tr->type; csq_push(args, node->csq_list+icsq, hap->stack[ibeg].node->rec); return; } kstring_t str = node->csq_list[icsq].type.vstr; str.l = 0; // create the aa variant string int aa_rbeg = tr->strand==STRAND_FWD ? node2rbeg(ibeg)/3+1 : (TSCRIPT_AUX(hap->tr)->nsref - 2*N_REF_PAD - node2rend(iend))/3+1; int aa_sbeg = tr->strand==STRAND_FWD ? node2sbeg(ibeg)/3+1 : (tlen - node2send(iend))/3+1; kputc_('|', &str); kputw(aa_rbeg, &str); kprint_aa_prediction(args,aa_rbeg,&hap->tref,&str); if ( !(csq->type.type & CSQ_SYNONYMOUS_VARIANT) ) { kputc_('>', &str); kputw(aa_sbeg, &str); kprint_aa_prediction(args,aa_sbeg,&hap->tseq,&str); } kputc_('|', &str); // create the dna variant string and, in case of combined variants, // insert silent CSQ_PRINTED_UPSTREAM variants for (i=ibeg; i<=iend; i++) { if ( i>ibeg ) kputc_('+', &str); kputw(node2rpos(i)+1, &str); kputs(hap->stack[i].node->var, &str); } node->csq_list[icsq].type.vstr = str; csq_push(args, node->csq_list+icsq, hap->stack[ref_node].node->rec); for (i=ibeg; i<=iend; i++) { // csq are printed at one position only for combined variants, the rest is // silent and references the first if ( hap->stack[i].node->csq & ~CSQ_COMPOUND ) { node->ncsq_list++; hts_expand0(csq_t,node->ncsq_list,node->mcsq_list,node->csq_list); csq_t *tmp_csq = &node->csq_list[node->ncsq_list - 1]; tmp_csq->pos = hap->stack[i].node->rec->pos; tmp_csq->type.trid = tr->id; //??tmp_csq->type.vcf_ial = node->vcf_ial; .. this should not be needed for non-compound variants tmp_csq->type.gene = tr->gene->name; tmp_csq->type.strand = tr->strand; tmp_csq->type.type = hap->stack[i].node->csq & ~CSQ_COMPOUND & ~rm_csq; tmp_csq->type.biotype = tr->type; tmp_csq->type.vstr.l = 0; kputs(str.s,&tmp_csq->type.vstr); csq_push(args, tmp_csq, hap->stack[i].node->rec); } if ( i!=ref_node && (node->csq_list[icsq].type.type & CSQ_COMPOUND || !(hap->stack[i].node->csq & ~CSQ_COMPOUND)) ) { node->ncsq_list++; hts_expand0(csq_t,node->ncsq_list,node->mcsq_list,node->csq_list); csq_t *tmp_csq = &node->csq_list[node->ncsq_list - 1]; tmp_csq->pos = hap->stack[i].node->rec->pos; tmp_csq->type.trid = tr->id; //??tmp_csq->type.vcf_ial = node->vcf_ial; .. this should not be needed for non-compound variants tmp_csq->type.gene = tr->gene->name; tmp_csq->type.strand = tr->strand; tmp_csq->type.type = CSQ_PRINTED_UPSTREAM | hap->stack[i].node->csq; tmp_csq->type.biotype = tr->type; tmp_csq->type.ref = hap->stack[ref_node].node->rec; tmp_csq->type.vstr.l = 0; csq_push(args, tmp_csq, hap->stack[i].node->rec); } } } void hap_finalize(args_t *args, hap_t *hap) { gf_tscript_t *tr = hap->tr; if ( !TSCRIPT_AUX(tr)->sref ) tscript_splice_ref(tr); kstring_t sref; sref.s = TSCRIPT_AUX(tr)->sref; sref.l = TSCRIPT_AUX(tr)->nsref; sref.m = sref.l; int istack = 0; hts_expand(hstack_t,1,hap->mstack,hap->stack); hap->sseq.l = 0; hap->tseq.l = 0; hap->stack[0].node = TSCRIPT_AUX(tr)->root; hap->stack[0].ichild = -1; hap->stack[0].slen = 0; hap->stack[0].dlen = 0; while ( istack>=0 ) { hstack_t *stack = &hap->stack[istack]; hap_node_t *node = hap->stack[istack].node; while ( ++hap->stack[istack].ichild < node->nchild ) { if ( node->child[stack->ichild] ) break; } if ( stack->ichild == node->nchild ) { istack--; continue; } node = node->child[stack->ichild]; istack++; hts_expand(hstack_t,istack+1,hap->mstack,hap->stack); stack = &hap->stack[istack-1]; hap->stack[istack].node = node; hap->stack[istack].ichild = -1; hap->sseq.l = stack->slen; if ( node->type==HAP_CDS ) kputs(node->seq, &hap->sseq); hap->stack[istack].slen = hap->sseq.l; hap->stack[istack].dlen = hap->stack[istack-1].dlen + node->dlen; if ( !node->nend ) continue; // not a leaf node // The spliced sequence has been built for the current haplotype and stored // in hap->sseq. Now we break it and output as independent parts kstring_t sseq; sseq.m = sref.m - 2*N_REF_PAD + hap->stack[istack].dlen; // total length of the spliced query transcript hap->upstream_stop = 0; int i = 1, dlen = 0, ibeg, indel = 0; hap->sbeg = hap->stack[i].node->sbeg; assert( hap->stack[istack].node->type != HAP_SSS ); if ( tr->strand==STRAND_FWD ) { i = 0, ibeg = -1; while ( ++i <= istack ) { assert( hap->stack[i].node->type != HAP_SSS ); dlen += hap->stack[i].node->dlen; if ( hap->stack[i].node->dlen ) indel = 1; // This condition extends compound variants. if ( istack[i].node->dlen > 0 ) icur += hap->stack[i].node->dlen; else if ( hap->stack[i].node->dlen < 0 ) icur++; if ( icur/3 == inext/3 ) // in the same codon, can't be flushed yet { if ( ibeg==-1 ) ibeg = i; continue; } } if ( ibeg<0 ) ibeg = i; int ioff = node2soff(ibeg); int icur = node2sbeg(ibeg); int rbeg = node2rbeg(ibeg); int rend = node2rend(i); int fill = dlen%3; // alt if ( hap->sseq.l ) { sseq.l = hap->stack[i].slen - ioff; sseq.s = hap->sseq.s + ioff; } else // splice site overlap, see #1475227917 sseq.l = fill = 0; cds_translate(&sref, &sseq, icur,rbeg,rend, tr->strand, &hap->tseq, fill); // ref sseq.l = node2rend(i) - rbeg; sseq.s = sref.s + N_REF_PAD + rbeg; sseq.m = sref.m - 2*N_REF_PAD; cds_translate(&sref, &sseq, rbeg,rbeg,rend, tr->strand, &hap->tref, fill); sseq.m = sref.m - 2*N_REF_PAD + hap->stack[istack].dlen; hap_add_csq(args,hap,node,0, ibeg,i,dlen,indel); ibeg = -1; dlen = 0; indel = 0; } } else if ( tr->strand==STRAND_REV ) { i = istack + 1, ibeg = -1; while ( --i > 0 ) { assert ( hap->stack[i].node->type != HAP_SSS ); dlen += hap->stack[i].node->dlen; if ( hap->stack[i].node->dlen ) indel = 1; if ( i>1 ) { if ( dlen%3 ) { if ( ibeg==-1 ) ibeg = i; continue; } // the last base of the current variant vs the first base of the next // variant: are they in the same codon? (reverse strand) int icur = sseq.m - 1 - node2sbeg(i); int inext = sseq.m - 1 - node2sbeg(i-1); if ( hap->stack[i].node->dlen > 0 ) icur += hap->stack[i].node->dlen - 1; else if ( hap->stack[i].node->dlen < 0 ) icur -= hap->stack[i].node->dlen; if ( hap->stack[i-1].node->dlen > 0 ) inext -= hap->stack[i-1].node->dlen; if ( icur/3 == inext/3 ) { if ( ibeg==-1 ) ibeg = i; continue; } } if ( ibeg<0 ) ibeg = i; int ioff = node2soff(i); int icur = node2sbeg(i); int rbeg = node2rbeg(i); int rend = node2rend(ibeg); int fill = dlen%3; // alt if ( hap->sseq.l ) { sseq.l = hap->stack[ibeg].slen - ioff; sseq.s = hap->sseq.s + ioff; } else // splice site overlap, see #1475227917 sseq.l = fill = 0; cds_translate(&sref, &sseq, icur,rbeg,rend, tr->strand, &hap->tseq, fill); // ref sseq.l = node2rend(ibeg) - rbeg; sseq.s = sref.s + N_REF_PAD + rbeg; sseq.m = sref.m - 2*N_REF_PAD; cds_translate(&sref, &sseq, rbeg,rbeg,rend, tr->strand, &hap->tref, fill); sseq.m = sref.m - 2*N_REF_PAD + hap->stack[istack].dlen; hap_add_csq(args,hap,node,sseq.m, i,ibeg,dlen,indel); ibeg = -1; dlen = 0; indel = 0; } } } } static inline void csq_print_text(args_t *args, csq_t *csq, int ismpl, int ihap) { if ( csq->type.type & CSQ_PRINTED_UPSTREAM ) return; char *smpl = ismpl >= 0 ? args->hdr->samples[ismpl] : "-"; const char *chr = bcf_hdr_id2name(args->hdr,args->rid); fprintf(args->out,"CSQ\t%s\t", smpl); if ( ihap>0 ) fprintf(args->out,"%d", ihap); else fprintf(args->out,"-"); args->str.l = 0; kput_vcsq(args, &csq->type, &args->str); fprintf(args->out,"\t%s\t%d\t%s\n",chr,csq->pos+1,args->str.s); } static inline void hap_print_text(args_t *args, gf_tscript_t *tr, int ismpl, int ihap, hap_node_t *node) { if ( !node || !node->ncsq_list ) return; char *smpl = ismpl >= 0 ? args->hdr->samples[ismpl] : "-"; const char *chr = bcf_hdr_id2name(args->hdr,args->rid); int i; for (i=0; incsq_list; i++) { csq_t *csq = node->csq_list + i; if ( csq->type.type & CSQ_PRINTED_UPSTREAM ) continue; assert( csq->type.vstr.l ); fprintf(args->out,"CSQ\t%s\t", smpl); if ( ihap>0 ) fprintf(args->out,"%d", ihap); else fprintf(args->out,"-"); args->str.l = 0; kput_vcsq(args, &csq->type, &args->str); fprintf(args->out,"\t%s\t%d\t%s\n",chr,csq->pos+1,args->str.s); } } static inline void hap_stage_vcf(args_t *args, gf_tscript_t *tr, int ismpl, int ihap, hap_node_t *node) { if ( !node || !node->ncsq_list || ismpl<0 ) return; int i; for (i=0; incsq_list; i++) { csq_t *csq = node->csq_list + i; vrec_t *vrec = csq->vrec; int icsq2 = 2*csq->idx + ihap; if ( icsq2 >= args->ncsq2_max ) // more than ncsq2_max consequences, so can't fit it in FMT { if ( args->verbosity && (!args->ncsq2_small_warned || args->verbosity > 1) ) { fprintf(bcftools_stderr, "Warning: Too many consequences for sample %s at %s:%"PRId64", keeping the first %d and skipping the rest.\n", args->hdr->samples[ismpl],bcf_hdr_id2name(args->hdr,args->rid),(int64_t) vrec->line->pos+1,csq->idx); if ( !args->ncsq2_small_warned ) fprintf(bcftools_stderr," The limit can be increased by setting the --ncsq parameter. This warning is printed only once.\n"); } if ( args->ncsq2_small_warned < icsq2 ) args->ncsq2_small_warned = icsq2; break; } int ival, ibit; icsq2_to_bit(icsq2, &ival,&ibit); if ( vrec->nfmt < 1 + ival ) vrec->nfmt = 1 + ival; vrec->fmt_bm[ismpl*args->nfmt_bcsq + ival] |= 1 << ibit; } } void hap_flush(args_t *args, uint32_t pos) { int i,j; tr_heap_t *heap = args->active_tr; while ( heap->ndat && heap->dat[0]->end<=pos ) { gf_tscript_t *tr = heap->dat[0]; khp_delete(trhp, heap); args->hap->tr = tr; if ( TSCRIPT_AUX(tr)->root && TSCRIPT_AUX(tr)->root->nchild ) // normal, non-localized calling { hap_finalize(args, args->hap); if ( args->output_type==FT_TAB_TEXT ) // plain text output, not a vcf { if ( args->phase==PHASE_DROP_GT ) hap_print_text(args, tr, -1,0, TSCRIPT_AUX(tr)->hap[0]); else { for (i=0; ismpl->n; i++) { for (j=0; j<2; j++) hap_print_text(args, tr, args->smpl->idx[i],j+1, TSCRIPT_AUX(tr)->hap[i*2+j]); } } } else if ( args->phase!=PHASE_DROP_GT ) { for (i=0; ismpl->n; i++) { for (j=0; j<2; j++) hap_stage_vcf(args, tr, args->smpl->idx[i],j, TSCRIPT_AUX(tr)->hap[i*2+j]); } } } // mark the transcript for deletion. Cannot delete it immediately because // by-position VCF output will need them when flushed by vcf_buf_push args->nrm_tr++; hts_expand(gf_tscript_t*,args->nrm_tr,args->mrm_tr,args->rm_tr); args->rm_tr[args->nrm_tr-1] = tr; } } #define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; } vbuf_t *vbuf_push(args_t *args, bcf1_t **rec_ptr) { int i; assert(rec_ptr); bcf1_t *rec = *rec_ptr; // check for duplicate records i = args->vcf_rbuf.n ? rbuf_last(&args->vcf_rbuf) : -1; if ( i<0 || args->vcf_buf[i]->vrec[0]->line->pos!=rec->pos ) { // vcf record with a new pos rbuf_expand0(&args->vcf_rbuf, vbuf_t*, args->vcf_rbuf.n+1, args->vcf_buf); i = rbuf_append(&args->vcf_rbuf); if ( !args->vcf_buf[i] ) args->vcf_buf[i] = (vbuf_t*) calloc(1,sizeof(vbuf_t)); args->vcf_buf[i]->n = 0; args->vcf_buf[i]->keep_until = 0; } vbuf_t *vbuf = args->vcf_buf[i]; vbuf->n++; hts_expand0(vrec_t*, vbuf->n, vbuf->m, vbuf->vrec); if ( !vbuf->vrec[vbuf->n - 1] ) vbuf->vrec[vbuf->n - 1] = (vrec_t*) calloc(1,sizeof(vrec_t)); vrec_t *vrec = vbuf->vrec[vbuf->n - 1]; if ( args->phase!=PHASE_DROP_GT && args->smpl->n ) { if ( !vrec->fmt_bm ) vrec->fmt_bm = (uint32_t*) calloc(args->hdr_nsmpl,sizeof(*vrec->fmt_bm) * args->nfmt_bcsq); else memset(vrec->fmt_bm,0,args->hdr_nsmpl*sizeof(*vrec->fmt_bm) * args->nfmt_bcsq); } if ( !vrec->line ) vrec->line = bcf_init1(); SWAP(bcf1_t*, (*rec_ptr), vrec->line); int ret; khint_t k = kh_put(pos2vbuf, args->pos2vbuf, (int)rec->pos, &ret); kh_val(args->pos2vbuf,k) = vbuf; return vbuf; } void vbuf_flush(args_t *args, uint32_t pos) { int i,j; while ( args->vcf_rbuf.n ) { vbuf_t *vbuf; if ( !args->local_csq && args->active_tr->ndat ) { // check if the first active transcript starts beyond the first buffered VCF record, // cannot output buffered VCF lines (args.vbuf) until the active transcripts are gone vbuf = args->vcf_buf[ args->vcf_rbuf.f ]; if ( vbuf->keep_until > pos ) break; assert( vbuf->n ); } i = rbuf_shift(&args->vcf_rbuf); assert( i>=0 ); vbuf = args->vcf_buf[i]; int pos = vbuf->n ? vbuf->vrec[0]->line->pos : -1; for (i=0; in; i++) { vrec_t *vrec = vbuf->vrec[i]; if ( !args->out_fh ) // not a VCF output { vrec->nvcsq = 0; continue; } if ( !vrec->nvcsq ) { if ( bcf_write(args->out_fh, args->hdr, vrec->line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname?args->output_fname:"standard output"); int save_pos = vrec->line->pos; bcf_empty(vrec->line); vrec->line->pos = save_pos; // this is necessary for compound variants continue; } args->str.l = 0; kput_vcsq(args, &vrec->vcsq[0], &args->str); for (j=1; jnvcsq; j++) { kputc_(',', &args->str); kput_vcsq(args, &vrec->vcsq[j], &args->str); } bcf_update_info_string(args->hdr, vrec->line, args->bcsq_tag, args->str.s); if ( args->hdr_nsmpl ) { if ( vrec->nfmt < args->nfmt_bcsq ) for (j=1; jhdr_nsmpl; j++) memmove(&vrec->fmt_bm[j*vrec->nfmt], &vrec->fmt_bm[j*args->nfmt_bcsq], vrec->nfmt*sizeof(*vrec->fmt_bm)); bcf_update_format_int32(args->hdr, vrec->line, args->bcsq_tag, vrec->fmt_bm, args->hdr_nsmpl*vrec->nfmt); } vrec->nvcsq = 0; if ( bcf_write(args->out_fh, args->hdr, vrec->line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname?args->output_fname:"standard output"); int save_pos = vrec->line->pos; bcf_empty(vrec->line); vrec->line->pos = save_pos; } if ( pos!=-1 ) { khint_t k = kh_get(pos2vbuf, args->pos2vbuf, pos); if ( k != kh_end(args->pos2vbuf) ) kh_del(pos2vbuf, args->pos2vbuf, k); } vbuf->n = 0; } if ( args->active_tr->ndat ) return; for (i=0; inrm_tr; i++) { gf_tscript_t *tr = args->rm_tr[i]; tscript_t *aux = TSCRIPT_AUX(tr); if ( aux->root ) hap_destroy(aux->root); aux->root = NULL; free(aux->hap); free(aux->ref); free(aux->sref); free(aux); tr->aux = NULL; } args->nrm_tr = 0; args->ncsq_buf = 0; } void tscript_init_ref(args_t *args, gf_tscript_t *tr, const char *chr) { int i, len; int pad_beg = tr->beg >= N_REF_PAD ? N_REF_PAD : tr->beg; const char *tmp_chr = chr; if ( !faidx_has_seq(args->fai,tmp_chr) ) { tmp_chr = drop_chr_prefix(args,chr); if ( !faidx_has_seq(args->fai,tmp_chr) ) tmp_chr = add_chr_prefix(args,chr); } TSCRIPT_AUX(tr)->ref = faidx_fetch_seq(args->fai, tmp_chr, tr->beg - pad_beg, tr->end + N_REF_PAD, &len); if ( !TSCRIPT_AUX(tr)->ref ) error("faidx_fetch_seq failed %s:%d-%d\n", chr,tr->beg+1,tr->end+1); int pad_end = len - (tr->end - tr->beg + 1 + pad_beg); if ( pad_beg + pad_end != 2*N_REF_PAD ) { char *ref = (char*) malloc(tr->end - tr->beg + 1 + 2*N_REF_PAD + 1); for (i=0; i < N_REF_PAD - pad_beg; i++) ref[i] = 'N'; memcpy(ref+i, TSCRIPT_AUX(tr)->ref, len); len += i; for (i=0; i < N_REF_PAD - pad_end; i++) ref[i+len] = 'N'; ref[i+len] = 0; free(TSCRIPT_AUX(tr)->ref); TSCRIPT_AUX(tr)->ref = ref; } } static void sanity_check_ref(args_t *args, gf_tscript_t *tr, bcf1_t *rec) { int vbeg = 0; int rbeg = rec->pos - tr->beg + N_REF_PAD; if ( rbeg < 0 ) { vbeg += abs(rbeg); rbeg = 0; } char *ref = TSCRIPT_AUX(tr)->ref + rbeg; char *vcf = rec->d.allele[0] + vbeg; assert( vcf - rec->d.allele[0] < strlen(rec->d.allele[0]) && ref - TSCRIPT_AUX(tr)->ref < tr->end - tr->beg + 2*N_REF_PAD ); int i = 0; while ( ref[i] && vcf[i] ) { if ( ref[i]!=vcf[i] && toupper(ref[i])!=toupper(vcf[i]) ) error("Error: the fasta reference does not match the VCF REF allele at %s:%"PRId64" .. fasta=%c vcf=%c\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+vbeg+1,ref[i],vcf[i]); i++; } } int test_cds_local(args_t *args, bcf1_t *rec) { int i,j, ret = 0; const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,rec)); // note that the off-by-one extension of rlen is deliberate to account for insertions if ( !regidx_overlap(args->idx_cds,chr,rec->pos,rec->pos+rec->rlen, args->itr) ) return 0; // structures to fake the normal test_cds machinery hap_node_t root, node; root.type = HAP_ROOT; kstring_t *tref = &args->hap->tref, *tseq = &args->hap->tseq; while ( regitr_overlap(args->itr) ) { gf_cds_t *cds = regitr_payload(args->itr,gf_cds_t*); gf_tscript_t *tr = cds->tr; if ( !GF_is_coding(tr->type) ) continue; ret = 1; if ( !TSCRIPT_AUX(tr) ) { tr->aux = calloc(sizeof(tscript_t),1); tscript_init_ref(args, tr, chr); tscript_splice_ref(tr); khp_insert(trhp, args->active_tr, &tr); // only to clean the reference afterwards } sanity_check_ref(args, tr, rec); kstring_t sref; sref.s = TSCRIPT_AUX(tr)->sref; sref.l = TSCRIPT_AUX(tr)->nsref; sref.m = sref.l; for (i=1; in_allele; i++) { if ( rec->d.allele[i][0]=='<' || rec->d.allele[i][0]=='*' ) { continue; } if ( hap_init(args, &root, &node, cds, rec, i)!=0 ) continue; csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.vcf_ial = i; csq.type.gene = tr->gene->name; int csq_type = node.csq; // code repetition: it would be nice to reuse the code from hap_add_csq, needs refactoring though if ( node.type == HAP_SSS ) { csq.type.type = csq_type; csq_stage(args, &csq, rec); } else { kstring_t sseq; sseq.m = sref.m - 2*N_REF_PAD + node.dlen; sseq.s = node.seq; int alen = sseq.l = strlen(sseq.s); int fill = node.dlen%3 && alen ? 1 : 0; // see #1475227917 cds_translate(&sref, &sseq, node.sbeg,node.sbeg,node.sbeg+node.rlen, tr->strand, tseq, fill); sseq.m = sref.m - 2*N_REF_PAD; sseq.s = sref.s + N_REF_PAD + node.sbeg; sseq.l = node.rlen; cds_translate(&sref, &sseq, node.sbeg,node.sbeg,node.sbeg+node.rlen, tr->strand, tref, fill); // check for truncating stops for (j=0; jl; j++) if ( tref->s[j]=='*' ) break; if ( j!=tref->l ) { tref->l = j+1; tref->s[j+1] = 0; } for (j=0; jl; j++) if ( tseq->s[j]=='*' ) break; if ( j!=tseq->l ) { tseq->l = j+1; tseq->s[j+1] = 0; } if ( csq_type & CSQ_STOP_LOST ) { if ( tref->s[tref->l-1]=='*' && tref->s[tref->l-1] == tseq->s[tseq->l-1] ) { csq_type &= ~CSQ_STOP_LOST; csq_type |= CSQ_STOP_RETAINED; } else if (tref->s[tref->l-1]!='*' ) { // This is CDS 3' incomplete ENSG00000173376/synon.vcf, can also be missense // We observe in real data a change to a stop, ENST00000528237/retained-stop-incomplete-cds.vcf if ( tseq->s[tseq->l-1] == '*' ) { csq_type &= ~CSQ_STOP_GAINED; csq_type |= CSQ_STOP_RETAINED; } else csq_type |= CSQ_INCOMPLETE_CDS; } } if ( csq_type & CSQ_START_LOST && tref->s[0]!='M' ) csq_type &= ~CSQ_START_LOST; if ( node.dlen!=0 ) { if ( node.dlen%3 ) csq_type |= CSQ_FRAMESHIFT_VARIANT; else if ( node.dlen<0 ) csq_type |= CSQ_INFRAME_DELETION; else csq_type |= CSQ_INFRAME_INSERTION; if ( tref->s[tref->l-1]!='*' && tseq->s[tseq->l-1]=='*' ) csq_type |= CSQ_STOP_GAINED; } else { int aa_change = 0; for (j=0; jl; j++) { if ( tref->s[j] == tseq->s[j] ) continue; aa_change = 1; if ( tref->s[j] == '*' ) csq_type |= CSQ_STOP_LOST; else if ( tseq->s[j] == '*' ) csq_type |= CSQ_STOP_GAINED; else csq_type |= CSQ_MISSENSE_VARIANT; } if ( !aa_change ) csq_type |= CSQ_SYNONYMOUS_VARIANT; } if ( csq_type & CSQ_COMPOUND ) { // create the aa variant string kstring_t str = {0,0,0}; int aa_rbeg = tr->strand==STRAND_FWD ? node.sbeg/3+1 : (TSCRIPT_AUX(tr)->nsref - 2*N_REF_PAD - node.sbeg - node.rlen)/3+1; int aa_sbeg = tr->strand==STRAND_FWD ? node.sbeg/3+1 : (TSCRIPT_AUX(tr)->nsref - 2*N_REF_PAD + node.dlen - node.sbeg - alen)/3+1; kputc_('|', &str); kputw(aa_rbeg, &str); kprint_aa_prediction(args,aa_rbeg,tref,&str); if ( !(csq_type & CSQ_SYNONYMOUS_VARIANT) ) { kputc_('>', &str); kputw(aa_sbeg, &str); kprint_aa_prediction(args,aa_sbeg,tseq,&str); } kputc_('|', &str); kputw(rec->pos+1, &str); kputs(node.var, &str); csq.type.vstr = str; csq.type.type = csq_type & CSQ_COMPOUND; csq_stage(args, &csq, rec); // all this only to clean vstr when vrec is flushed if ( !TSCRIPT_AUX(tr)->root ) TSCRIPT_AUX(tr)->root = (hap_node_t*) calloc(1,sizeof(hap_node_t)); TSCRIPT_AUX(tr)->root->ncsq_list++; hts_expand0(csq_t,TSCRIPT_AUX(tr)->root->ncsq_list,TSCRIPT_AUX(tr)->root->mcsq_list,TSCRIPT_AUX(tr)->root->csq_list); csq_t *rm_csq = TSCRIPT_AUX(tr)->root->csq_list + TSCRIPT_AUX(tr)->root->ncsq_list - 1; rm_csq->type.vstr = str; } if ( csq_type & ~CSQ_COMPOUND ) { csq.type.type = csq_type & ~CSQ_COMPOUND; csq.type.vstr.l = 0; csq_stage(args, &csq, rec); } } free(node.seq); free(node.var); } } return ret; } int test_cds(args_t *args, bcf1_t *rec, vbuf_t *vbuf) { static int overlaps_warned = 0, multiploid_warned = 0; int i, ret = 0, hap_ret; const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,rec)); // note that the off-by-one extension of rlen is deliberate to account for insertions if ( !regidx_overlap(args->idx_cds,chr,rec->pos,rec->pos+rec->rlen, args->itr) ) return 0; while ( regitr_overlap(args->itr) ) { gf_cds_t *cds = regitr_payload(args->itr,gf_cds_t*); gf_tscript_t *tr = cds->tr; if ( !GF_is_coding(tr->type) ) continue; if ( vbuf->keep_until < tr->end ) vbuf->keep_until = tr->end; ret = 1; if ( !TSCRIPT_AUX(tr) ) { // initialize the transcript and its haplotype tree, fetch the reference sequence tr->aux = calloc(sizeof(tscript_t),1); tscript_init_ref(args, tr, chr); TSCRIPT_AUX(tr)->root = (hap_node_t*) calloc(1,sizeof(hap_node_t)); TSCRIPT_AUX(tr)->nhap = args->phase==PHASE_DROP_GT ? 1 : 2*args->smpl->n; // maximum ploidy = diploid TSCRIPT_AUX(tr)->hap = (hap_node_t**) malloc(TSCRIPT_AUX(tr)->nhap*sizeof(hap_node_t*)); for (i=0; inhap; i++) TSCRIPT_AUX(tr)->hap[i] = NULL; TSCRIPT_AUX(tr)->root->nend = TSCRIPT_AUX(tr)->nhap; TSCRIPT_AUX(tr)->root->type = HAP_ROOT; khp_insert(trhp, args->active_tr, &tr); } sanity_check_ref(args, tr, rec); if ( args->phase==PHASE_DROP_GT ) { if ( rec->d.allele[1][0]=='<' || rec->d.allele[1][0]=='*' ) { continue; } hap_node_t *parent = TSCRIPT_AUX(tr)->hap[0] ? TSCRIPT_AUX(tr)->hap[0] : TSCRIPT_AUX(tr)->root; hap_node_t *child = (hap_node_t*)calloc(1,sizeof(hap_node_t)); hap_ret = hap_init(args, parent, child, cds, rec, 1); if ( hap_ret!=0 ) { // overlapping or intron variant, cannot apply if ( hap_ret==1 ) { if ( args->verbosity && (!overlaps_warned || args->verbosity > 1) ) { fprintf(bcftools_stderr, "Warning: Skipping overlapping variants at %s:%"PRId64"\t%s>%s.\n", chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]); if ( !overlaps_warned ) fprintf(bcftools_stderr," This message is printed only once, the verbosity can be increased with `--verbose 2`\n"); overlaps_warned = 1; } if ( args->out ) fprintf(args->out,"LOG\tWarning: Skipping overlapping variants at %s:%"PRId64"\t%s>%s\n", chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]); } else ret = 1; // prevent reporting as intron in test_tscript hap_destroy(child); continue; } if ( child->type==HAP_SSS ) { csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.vcf_ial = 1; csq.type.gene = tr->gene->name; csq.type.type = child->csq; csq_stage(args, &csq, rec); hap_destroy(child); ret = 1; continue; } parent->nend--; parent->nchild = 1; parent->mchild = 1; parent->child = (hap_node_t**) malloc(sizeof(hap_node_t*)); parent->child[0] = child; TSCRIPT_AUX(tr)->hap[0] = child; TSCRIPT_AUX(tr)->hap[0]->nend = 1; continue; } // apply the VCF variants and extend the haplotype tree int j, ismpl, ihap, ngts = bcf_get_genotypes(args->hdr, rec, &args->gt_arr, &args->mgt_arr); ngts /= bcf_hdr_nsamples(args->hdr); if ( ngts!=1 && ngts!=2 ) { if ( args->verbosity && (!multiploid_warned || args->verbosity > 1) ) { fprintf(bcftools_stderr, "Warning: Skipping site with non-diploid/non-haploid genotypes at %s:%"PRId64"\t%s>%s.\n", chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]); if ( !multiploid_warned ) fprintf(bcftools_stderr," This message is printed only once, the verbosity can be increased with `--verbose 2`\n"); multiploid_warned = 1; } if ( args->out ) fprintf(args->out,"LOG\tWarning: Skipping site with non-diploid/non-haploid genotypes at %s:%"PRId64"\t%s>%s\n", chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]); continue; } for (ismpl=0; ismplsmpl->n; ismpl++) { int32_t *gt = args->gt_arr + args->smpl->idx[ismpl]*ngts; if ( gt[0]==bcf_gt_missing ) continue; if ( ngts>1 && gt[1]!=bcf_gt_missing && gt[1]!=bcf_int32_vector_end && bcf_gt_allele(gt[0])!=bcf_gt_allele(gt[1]) ) { if ( args->phase==PHASE_MERGE ) { if ( !bcf_gt_allele(gt[0]) ) gt[0] = gt[1]; } if ( !bcf_gt_is_phased(gt[0]) && !bcf_gt_is_phased(gt[1]) ) { if ( args->phase==PHASE_REQUIRE ) error("Unphased heterozygous genotype at %s:%"PRId64", sample %s. See the --phase option.\n", chr,(int64_t) rec->pos+1,args->hdr->samples[args->smpl->idx[ismpl]]); if ( args->phase==PHASE_SKIP ) continue; if ( args->phase==PHASE_NON_REF ) { if ( !bcf_gt_allele(gt[0]) ) gt[0] = gt[1]; else if ( !bcf_gt_allele(gt[1]) ) gt[1] = gt[0]; } } } for (ihap=0; ihapn_allele ); if ( rec->d.allele[ial][0]=='<' || rec->d.allele[ial][0]=='*' ) { continue; } hap_node_t *parent = TSCRIPT_AUX(tr)->hap[i] ? TSCRIPT_AUX(tr)->hap[i] : TSCRIPT_AUX(tr)->root; if ( parent->cur_rec==rec && parent->cur_child[ial]>=0 ) { // this haplotype has been seen in another sample TSCRIPT_AUX(tr)->hap[i] = parent->child[ parent->cur_child[ial] ]; TSCRIPT_AUX(tr)->hap[i]->nend++; parent->nend--; continue; } hap_node_t *child = (hap_node_t*)calloc(1,sizeof(hap_node_t)); hap_ret = hap_init(args, parent, child, cds, rec, ial); if ( hap_ret!=0 ) { // overlapping or intron variant, cannot apply if ( hap_ret==1 ) { if ( args->verbosity && (!overlaps_warned || args->verbosity > 1) ) { fprintf(bcftools_stderr, "Warning: Skipping overlapping variants at %s:%"PRId64", sample %s\t%s>%s.\n", chr,(int64_t) rec->pos+1,args->hdr->samples[args->smpl->idx[ismpl]],rec->d.allele[0],rec->d.allele[ial]); if ( !overlaps_warned ) fprintf(bcftools_stderr," This message is printed only once, the verbosity can be increased with `--verbose 2`\n"); overlaps_warned = 1; } if ( args->out ) fprintf(args->out,"LOG\tWarning: Skipping overlapping variants at %s:%"PRId64", sample %s\t%s>%s\n", chr,(int64_t) rec->pos+1,args->hdr->samples[args->smpl->idx[ismpl]],rec->d.allele[0],rec->d.allele[ial]); } hap_destroy(child); continue; } if ( child->type==HAP_SSS ) { csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.vcf_ial = ial; csq.type.gene = tr->gene->name; csq.type.type = child->csq; csq_stage(args, &csq, rec); hap_destroy(child); continue; } if ( parent->cur_rec!=rec ) { hts_expand(int,rec->n_allele,parent->mcur_child,parent->cur_child); for (j=0; jn_allele; j++) parent->cur_child[j] = -1; parent->cur_rec = rec; } j = parent->nchild++; hts_expand0(hap_node_t*,parent->nchild,parent->mchild,parent->child); parent->cur_child[ial] = j; parent->child[j] = child; TSCRIPT_AUX(tr)->hap[i] = child; TSCRIPT_AUX(tr)->hap[i]->nend++; parent->nend--; } } } return ret; } void csq_stage(args_t *args, csq_t *csq, bcf1_t *rec) { // known issues: tab output leads to unsorted output. This is because // coding haplotypes are printed in one go and buffering is not used // with tab output. VCF output is OK though. if ( csq_push(args, csq, rec)!=0 && args->phase==PHASE_DROP_GT ) return; // the consequence already exists int i,j,ngt = 0; if ( args->phase!=PHASE_DROP_GT ) { ngt = bcf_get_genotypes(args->hdr, rec, &args->gt_arr, &args->mgt_arr); if ( ngt>0 ) ngt /= bcf_hdr_nsamples(args->hdr); } if ( ngt<=0 ) { if ( args->output_type==FT_TAB_TEXT ) csq_print_text(args, csq, -1,0); return; } assert( ngt<=2 ); if ( args->output_type==FT_TAB_TEXT ) { for (i=0; ismpl->n; i++) { int32_t *gt = args->gt_arr + args->smpl->idx[i]*ngt; for (j=0; jtype.vcf_ial ) continue; csq_print_text(args, csq, args->smpl->idx[i],j+1); } } return; } vrec_t *vrec = csq->vrec; for (i=0; ismpl->n; i++) { int32_t *gt = args->gt_arr + args->smpl->idx[i]*ngt; for (j=0; jtype.vcf_ial ) continue; int icsq2 = 2*csq->idx + j; if ( icsq2 >= args->ncsq2_max ) // more than ncsq_max consequences, so can't fit it in FMT { int ismpl = args->smpl->idx[i]; if ( args->verbosity && (!args->ncsq2_small_warned || args->verbosity > 1) ) { fprintf(bcftools_stderr, "Warning: Too many consequences for sample %s at %s:%"PRId64", keeping the first %d and skipping the rest.\n", args->hdr->samples[ismpl],bcf_hdr_id2name(args->hdr,args->rid),(int64_t) vrec->line->pos+1,icsq2+1); if ( !args->ncsq2_small_warned ) fprintf(bcftools_stderr," The limit can be increased by setting the --ncsq parameter. This warning is printed only once.\n"); args->ncsq2_small_warned = 1; } if ( args->ncsq2_small_warned < icsq2 ) args->ncsq2_small_warned = icsq2; break; } int ival, ibit; icsq2_to_bit(icsq2, &ival,&ibit); if ( vrec->nfmt < 1 + ival ) vrec->nfmt = 1 + ival; vrec->fmt_bm[i*args->nfmt_bcsq + ival] |= 1 << ibit; } } } int test_utr(args_t *args, bcf1_t *rec) { const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,rec)); // note that the off-by-one extension of rlen is deliberate to account for insertions if ( !regidx_overlap(args->idx_utr,chr,rec->pos,rec->pos+rec->rlen, args->itr) ) return 0; splice_t splice; splice_init(&splice, rec); int i, ret = 0; while ( regitr_overlap(args->itr) ) { gf_utr_t *utr = regitr_payload(args->itr, gf_utr_t*); gf_tscript_t *tr = splice.tr = utr->tr; for (i=1; in_allele; i++) { if ( rec->d.allele[i][0]=='<' || rec->d.allele[i][0]=='*' ) { continue; } splice.vcf.alt = rec->d.allele[i]; splice.csq = 0; int splice_ret = splice_csq(args, &splice, utr->beg, utr->end); if ( splice_ret!=SPLICE_INSIDE && splice_ret!=SPLICE_OVERLAP ) continue; csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.type = utr->which==prime5 ? CSQ_UTR5 : CSQ_UTR3; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.vcf_ial = i; csq.type.gene = tr->gene->name; csq_stage(args, &csq, rec); ret = 1; } } assert(!splice.kref.s); assert(!splice.kalt.s); return ret; } int test_splice(args_t *args, bcf1_t *rec) { const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,rec)); if ( !regidx_overlap(args->idx_exon,chr,rec->pos,rec->pos + rec->rlen, args->itr) ) return 0; splice_t splice; splice_init(&splice, rec); splice.check_acceptor = splice.check_donor = 1; int i, ret = 0; while ( regitr_overlap(args->itr) ) { gf_exon_t *exon = regitr_payload(args->itr, gf_exon_t*); splice.tr = exon->tr; if ( !splice.tr->ncds ) continue; // not a coding transcript, no interest in splice sites splice.check_region_beg = splice.tr->beg==exon->beg ? 0 : 1; splice.check_region_end = splice.tr->end==exon->end ? 0 : 1; for (i=1; in_allele; i++) { if ( rec->d.allele[1][0]=='<' || rec->d.allele[1][0]=='*' ) { continue; } splice.vcf.alt = rec->d.allele[i]; splice.csq = 0; splice_csq(args, &splice, exon->beg, exon->end); if ( splice.csq ) ret = 1; } } free(splice.kref.s); free(splice.kalt.s); return ret; } int test_tscript(args_t *args, bcf1_t *rec) { const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,rec)); if ( !regidx_overlap(args->idx_tscript,chr,rec->pos,rec->pos+rec->rlen, args->itr) ) return 0; splice_t splice; splice_init(&splice, rec); int i, ret = 0; while ( regitr_overlap(args->itr) ) { gf_tscript_t *tr = splice.tr = regitr_payload(args->itr, gf_tscript_t*); for (i=1; in_allele; i++) { if ( rec->d.allele[i][0]=='<' || rec->d.allele[i][0]=='*' ) { continue; } splice.vcf.alt = rec->d.allele[i]; splice.csq = 0; int splice_ret = splice_csq(args, &splice, tr->beg, tr->end); if ( splice_ret!=SPLICE_INSIDE && splice_ret!=SPLICE_OVERLAP ) continue; // SPLICE_OUTSIDE or SPLICE_REF csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.type = GF_is_coding(tr->type) ? CSQ_INTRON : CSQ_NON_CODING; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.gene = tr->gene->name; csq_stage(args, &csq, rec); ret = 1; } } assert(!splice.kref.s); assert(!splice.kalt.s); return ret; } void test_symbolic_alt(args_t *args, bcf1_t *rec) { static int warned = 0; if ( args->verbosity && (!warned && args->verbosity > 0) ) { fprintf(bcftools_stderr,"Warning: The support for symbolic ALT insertions is experimental.\n"); warned = 1; } const char *chr = drop_chr_prefix(args, bcf_seqname(args->hdr,rec)); // only insertions atm int beg = rec->pos + 1; int end = beg; int csq_class = CSQ_ELONGATION; int hit = 0; if ( regidx_overlap(args->idx_cds,chr,beg,end, args->itr) ) { while ( regitr_overlap(args->itr) ) { csq_t csq; memset(&csq, 0, sizeof(csq_t)); gf_cds_t *cds = regitr_payload(args->itr,gf_cds_t*); gf_tscript_t *tr = cds->tr; csq.type.type = (GF_is_coding(tr->type) ? CSQ_CODING_SEQUENCE : CSQ_NON_CODING) | csq_class; csq.pos = rec->pos; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.gene = tr->gene->name; csq_stage(args, &csq, rec); hit = 1; } } if ( regidx_overlap(args->idx_utr,chr,beg,end, args->itr) ) { while ( regitr_overlap(args->itr) ) { csq_t csq; memset(&csq, 0, sizeof(csq_t)); gf_utr_t *utr = regitr_payload(args->itr, gf_utr_t*); gf_tscript_t *tr = utr->tr; csq.type.type = (utr->which==prime5 ? CSQ_UTR5 : CSQ_UTR3) | csq_class; csq.pos = rec->pos; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.gene = tr->gene->name; csq_stage(args, &csq, rec); hit = 1; } } if ( regidx_overlap(args->idx_exon,chr,beg,end, args->itr) ) { splice_t splice; splice_init(&splice, rec); splice.check_acceptor = splice.check_donor = 1; while ( regitr_overlap(args->itr) ) { gf_exon_t *exon = regitr_payload(args->itr, gf_exon_t*); splice.tr = exon->tr; if ( !splice.tr->ncds ) continue; // not a coding transcript, no interest in splice sites splice.check_region_beg = splice.tr->beg==exon->beg ? 0 : 1; splice.check_region_end = splice.tr->end==exon->end ? 0 : 1; splice.vcf.alt = rec->d.allele[1]; splice.csq = csq_class; splice_csq(args, &splice, exon->beg, exon->end); if ( splice.csq ) hit = 1; } } if ( !hit && regidx_overlap(args->idx_tscript,chr,beg,end, args->itr) ) { splice_t splice; splice_init(&splice, rec); while ( regitr_overlap(args->itr) ) { csq_t csq; memset(&csq, 0, sizeof(csq_t)); gf_tscript_t *tr = splice.tr = regitr_payload(args->itr, gf_tscript_t*); splice.vcf.alt = rec->d.allele[1]; splice.csq = csq_class; int splice_ret = splice_csq(args, &splice, tr->beg, tr->end); if ( splice_ret!=SPLICE_INSIDE && splice_ret!=SPLICE_OVERLAP ) continue; // SPLICE_OUTSIDE or SPLICE_REF csq.type.type = (GF_is_coding(tr->type) ? CSQ_INTRON : CSQ_NON_CODING) | csq_class; csq.pos = rec->pos; csq.type.biotype = tr->type; csq.type.strand = tr->strand; csq.type.trid = tr->id; csq.type.gene = tr->gene->name; csq_stage(args, &csq, rec); } } } void debug_print_buffers(args_t *args, int pos) { int i,j; fprintf(bcftools_stderr,"debug_print_buffers at %d\n", pos); fprintf(bcftools_stderr,"vbufs:\n"); for (i=0; ivcf_rbuf.n; i++) { int k = rbuf_kth(&args->vcf_rbuf, i); vbuf_t *vbuf = args->vcf_buf[k]; fprintf(bcftools_stderr,"\tvbuf %d:\n", i); for (j=0; jn; j++) { vrec_t *vrec = vbuf->vrec[j]; fprintf(bcftools_stderr,"\t\t%"PRId64" .. nvcsq=%d\n", (int64_t) vrec->line->pos+1, vrec->nvcsq); } } fprintf(bcftools_stderr,"pos2vbuf:"); khint_t k; for (k = 0; k < kh_end(args->pos2vbuf); ++k) if (kh_exist(args->pos2vbuf, k)) fprintf(bcftools_stderr," %d",1+(int)kh_key(args->pos2vbuf, k)); fprintf(bcftools_stderr,"\n"); fprintf(bcftools_stderr,"active_tr: %d\n", args->active_tr->ndat); } static void process(args_t *args, bcf1_t **rec_ptr) { if ( !rec_ptr ) { hap_flush(args, REGIDX_MAX); vbuf_flush(args, REGIDX_MAX); return; } bcf1_t *rec = *rec_ptr; static int32_t prev_rid = -1, prev_pos = -1; if ( prev_rid!=rec->rid ) { prev_rid = rec->rid; prev_pos = rec->pos; // Common error is to use different naming conventions in the fasta and the VCF (e.g. X vs chrX). // Perform a simple sanity check (that does not catch much), the chromosome must be present in the // reference file if ( !faidx_has_seq(args->fai,bcf_seqname(args->hdr,rec)) ) { if ( !faidx_has_seq(args->fai,drop_chr_prefix(args,bcf_seqname(args->hdr,rec))) && !faidx_has_seq(args->fai,add_chr_prefix(args,bcf_seqname(args->hdr,rec))) ) error("Error: the chromosome \"%s\" is not present in %s\n",bcf_seqname(args->hdr,rec),args->fa_fname); } } if ( prev_pos > rec->pos ) error("Error: The file is not sorted, %s:%d comes before %s:%"PRId64"\n",bcf_seqname(args->hdr,rec),prev_pos+1,bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); int call_csq = 1; if ( rec->n_allele < 2 ) call_csq = 0; // no alternate allele else if ( rec->n_allele==2 && (rec->d.allele[1][0]=='*' || rec->d.allele[1][1]=='*') ) call_csq = 0; // gVCF, not an alt allele else if ( rec->d.allele[1][0]=='<' ) { if ( strncmp("d.allele[1], 4) ) call_csq = 0; // only is supported at the moment } if ( call_csq && args->filter ) { call_csq = filter_test(args->filter, rec, NULL); if ( args->filter_logic==FLT_EXCLUDE ) call_csq = call_csq ? 0 : 1; } if ( !call_csq ) { if ( !args->out_fh ) return; // not a VCF output vbuf_push(args, rec_ptr); hap_flush(args, rec->pos-1); vbuf_flush(args, rec->pos-1); return; } if ( args->rid != rec->rid ) { hap_flush(args, REGIDX_MAX); vbuf_flush(args, REGIDX_MAX); } args->rid = rec->rid; vbuf_t *vbuf = vbuf_push(args, rec_ptr); if ( rec->d.allele[1][0]!='<' ) { int hit = args->local_csq ? test_cds_local(args, rec) : test_cds(args, rec, vbuf); hit += test_utr(args, rec); hit += test_splice(args, rec); if ( !hit ) test_tscript(args, rec); } else test_symbolic_alt(args, rec); if ( rec->pos > 0 ) { hap_flush(args, rec->pos-1); vbuf_flush(args, rec->pos-1); } return; } static const char *usage(void) { return "\n" "About: Haplotype-aware consequence caller.\n" "Usage: bcftools csq [OPTIONS] in.vcf\n" "\n" "Required options:\n" " -f, --fasta-ref FILE Reference file in fasta format\n" " -g, --gff-annot FILE GFF3 annotation file\n" "\n" "CSQ options:\n" " -B, --trim-protein-seq INT Abbreviate protein-changing predictions to max INT aminoacids\n" " -c, --custom-tag STRING Use this tag instead of the default BCSQ\n" " -l, --local-csq Localized predictions, consider only one VCF record at a time\n" " -n, --ncsq INT Maximum number of per-haplotype consequences to consider for each site [15]\n" " -p, --phase a|m|r|R|s How to handle unphased heterozygous genotypes: [r]\n" " a: take GTs as is, create haplotypes regardless of phase (0/1 -> 0|1)\n" " m: merge *all* GTs into a single haplotype (0/1 -> 1, 1/2 -> 1)\n" " r: require phased GTs, throw an error on unphased het GTs\n" " R: create non-reference haplotypes if possible (0/1 -> 1|1, 1/2 -> 1|2)\n" " s: skip unphased hets\n" "GFF options:\n" " --dump-gff FILE.gz Dump the parsed GFF file (for debugging purposes)\n" " --force Run even if some sanity checks fail\n" " --unify-chr-names 1|0 Automatically unify chromosome naming (e.g. chrX vs X) in GFF, fasta, and VCF [1]\n" "General options:\n" " -e, --exclude EXPR Exclude sites for which the expression is true\n" " -i, --include EXPR Select sites for which the expression is true\n" " --no-version Do not append version and command line to the header\n" " -o, --output FILE Write output to a file [standard output]\n" " -O, --output-type b|u|z|v|t[0-9] b: compressed BCF, u: uncompressed BCF, z: compressed VCF\n" " v: uncompressed VCF, t: plain tab-delimited text output, 0-9: compression level [v]\n" " -r, --regions REGION Restrict to comma-separated list of regions\n" " -R, --regions-file FILE Restrict to regions listed in a file\n" " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n" " -s, --samples -|LIST Samples to include or \"-\" to apply all variants and ignore samples\n" " -S, --samples-file FILE Samples to include\n" " -t, --targets REGION Similar to -r but streams rather than index-jumps\n" " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n" " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n" " --threads INT Use multithreading with worker threads [0]\n" " -v, --verbose INT Verbosity level 0-2 [1]\n" " -W, --write-index[=FMT] Automatically index the output files [off]\n" "\n" "Example:\n" " bcftools csq -f hs37d5.fa -g Homo_sapiens.GRCh37.87.gff3.gz in.vcf\n" "\n" " # GFF3 annotation files can be downloaded from Ensembl. e.g. for human:\n" " http://ftp.ensembl.org/pub/current_gff3/homo_sapiens/\n" " http://ftp.ensembl.org/pub/grch37/current/gff3/homo_sapiens/\n" "\n"; } int main_csq(int argc, char *argv[]) { args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->output_type = FT_VCF; args->bcsq_tag = "BCSQ"; args->ncsq2_max = 2*(16-1); // 1 bit is reserved for BCF missing values args->verbosity = 1; args->record_cmd_line = 1; args->clevel = -1; args->unify_chr_names = 1; static struct option loptions[] = { {"force",0,0,1}, {"threads",required_argument,NULL,2}, {"help",0,0,'h'}, {"ncsq",1,0,'n'}, {"brief-predictions",no_argument,0,'b'}, {"trim-protein-seq",required_argument,0,'B'}, {"custom-tag",1,0,'c'}, {"local-csq",0,0,'l'}, {"gff-annot",1,0,'g'}, {"fasta-ref",1,0,'f'}, {"include",1,0,'i'}, {"exclude",1,0,'e'}, {"output",1,0,'o'}, {"output-type",1,NULL,'O'}, {"phase",1,0,'p'}, {"quiet",0,0,'q'}, {"verbose",1,0,'v'}, {"regions",1,0,'r'}, {"regions-file",1,0,'R'}, {"regions-overlap",required_argument,NULL,4}, {"samples",1,0,'s'}, {"samples-file",1,0,'S'}, {"targets",1,0,'t'}, {"targets-file",1,0,'T'}, {"targets-overlap",required_argument,NULL,5}, {"no-version",no_argument,NULL,3}, {"write-index",optional_argument,NULL,'W'}, {"dump-gff",required_argument,NULL,7}, {"unify-chr-names",required_argument,NULL,8}, {0,0,0,0} }; int c, targets_is_file = 0, regions_is_file = 0; int regions_overlap = 1; int targets_overlap = 0; char *targets_list = NULL, *regions_list = NULL, *tmp; while ((c = getopt_long(argc, argv, "?hr:R:t:T:i:e:f:o:O:g:s:S:p:qc:ln:bB:v:W::",loptions,NULL)) >= 0) { switch (c) { case 1 : args->force = 1; break; case 2 : args->n_threads = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --threads %s\n", optarg); break; case 3 : args->record_cmd_line = 0; break; case 'b': args->brief_predictions = 1; fprintf(bcftools_stderr,"Warning: The -b option will be removed in future versions. Please use -B 1 instead.\n"); break; case 'B': args->brief_predictions = strtol(optarg,&tmp,10); if ( *tmp || args->brief_predictions<1 ) error("Could not parse argument: --trim-protein-seq %s\n", optarg); break; case 'l': args->local_csq = 1; break; case 'c': args->bcsq_tag = optarg; break; case 'q': error("Error: the -q option has been deprecated, use -v, --verbose instead.\n"); break; case 'v': args->verbosity = atoi(optarg); if ( args->verbosity<0 || args->verbosity>2 ) error("Error: expected integer 0-2 with -v, --verbose\n"); break; case 'p': switch (optarg[0]) { case 'a': args->phase = PHASE_AS_IS; break; case 'm': args->phase = PHASE_MERGE; break; case 'r': args->phase = PHASE_REQUIRE; break; case 'R': args->phase = PHASE_NON_REF; break; case 's': args->phase = PHASE_SKIP; break; default: error("The -p code \"%s\" not recognised\n", optarg); } break; case 'f': args->fa_fname = optarg; break; case 'g': args->gff_fname = optarg; break; case 'n': args->ncsq2_max = 2 * atoi(optarg); if ( args->ncsq2_max <= 0 ) error("Expected positive integer with -n, got %s\n", optarg); break; case 'o': args->output_fname = optarg; break; case 'O': switch (optarg[0]) { case 't': args->output_type = FT_TAB_TEXT; break; case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --output-type %s\n", optarg+1); } break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'r': regions_list = optarg; break; case 'R': regions_list = optarg; regions_is_file = 1; break; case 's': args->sample_list = optarg; break; case 'S': args->sample_list = optarg; args->sample_is_file = 1; break; case 't': targets_list = optarg; break; case 'T': targets_list = optarg; targets_is_file = 1; break; case 4 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 5 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 7 : args->dump_gff = optarg; break; case 8 : if ( !strcmp(optarg,"0") ) args->unify_chr_names = 0; else if ( !strcmp(optarg,"1") ) args->unify_chr_names = 1; else error("Could not parse: --unify-chr-names %s\n",optarg); break; case 'h': case '?': error("%s",usage()); default: error("The option not recognised: %s\n\n", optarg); break; } } char *fname = NULL; if ( optind==argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else error("%s", usage()); } else fname = argv[optind]; if ( argc - optind>1 ) error("%s", usage()); if ( !args->fa_fname ) error("Missing the --fasta-ref option\n"); if ( !args->gff_fname ) error("Missing the --gff option\n"); args->sr = bcf_sr_init(); if ( targets_list ) { bcf_sr_set_opt(args->sr,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->sr, targets_list, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", targets_list); } if ( regions_list ) { bcf_sr_set_opt(args->sr,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->sr, regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", regions_list); } if ( bcf_sr_set_threads(args->sr, args->n_threads)<0 ) error("Failed to create %d extra threads\n", args->n_threads); if ( !bcf_sr_add_reader(args->sr, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->sr->errnum)); args->hdr = bcf_sr_get_header(args->sr,0); init_data(args); while ( bcf_sr_next_line(args->sr) ) { process(args, &args->sr->readers[0].buffer[0]); } process(args,NULL); destroy_data(args); bcf_sr_destroy(args->sr); free(args); return 0; } pysam-0.23.0/bcftools/dbuf.h000066400000000000000000000034731475062545500156550ustar00rootroot00000000000000/* The MIT License Copyright (c) 2022 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Simple data buffer */ #ifndef __DBUF_H__ #define __DBUF_H__ #include typedef struct { size_t n,m; void **dat; } dbuf_t; static inline dbuf_t *dbuf_push(dbuf_t *buf, void *ptr) { if ( !buf ) buf = calloc(1,sizeof(dbuf_t)); buf->n++; hts_expand(void*,buf->n,buf->m,buf->dat); buf->dat[buf->n-1] = ptr; return buf; } static inline void *dbuf_ith(dbuf_t *buf, int i) { return buf->dat[i]; } static inline size_t dbuf_n(dbuf_t *buf) { return buf->n; } static inline void dbuf_destroy_free(dbuf_t *buf) { int i; for (i=0; in; i++) free(buf->dat[i]); free(buf->dat); free(buf); } #endif pysam-0.23.0/bcftools/dist.c000066400000000000000000000065161475062545500156740ustar00rootroot00000000000000/* The MIT License Copyright (c) 2016-2020 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include "dist.h" extern void error(const char *format, ...); struct _dist_t { uint64_t *bins, nvalues; int nbins; int npow; // the number of orders of magnitude to represent exactly int nexact; // pow(10,npow) int nlevel; }; dist_t *dist_init(int npow) { dist_t *dist = (dist_t*) calloc(1,sizeof(dist_t)); dist->npow = npow; dist->nexact = pow(10,npow); dist->nlevel = dist->nexact - pow(10,npow-1); return dist; } void dist_destroy(dist_t *dist) { if ( !dist ) return; free(dist->bins); free(dist); } int dist_nbins(dist_t *dist) { return dist->nbins; } int dist_nvalues(dist_t *dist) { return dist->nvalues; } uint32_t dist_insert(dist_t *dist, uint32_t value) { int ibin; if ( value <= dist->nexact ) ibin = value; else { int npow = (int) log10(value); int level = npow - dist->npow + 1; uint32_t step = pow(10, level); ibin = dist->nexact + dist->nlevel*(level-1) + (value - pow(10,npow)) / step; } if ( ibin >= dist->nbins ) { dist->bins = (uint64_t*) realloc(dist->bins, sizeof(*dist->bins)*(ibin+1)); memset(dist->bins + dist->nbins, 0, (ibin+1 - dist->nbins)*sizeof(*dist->bins)); dist->nbins = ibin+1; } dist->bins[ibin]++; dist->nvalues++; return ibin; } uint32_t dist_insert_n(dist_t *dist, uint32_t value, uint32_t cnt) { if ( !cnt ) return 0; int ibin = dist_insert(dist, value); dist->bins[ibin] += cnt - 1; dist->nvalues += cnt; return ibin; } uint64_t dist_get(dist_t *dist, uint32_t idx, uint32_t *beg, uint32_t *end) { if ( idx < dist->nexact ) { if ( beg ) *beg = idx; if ( end ) *end = idx + 1; } else { int level = (idx - dist->nexact) / dist->nlevel + 1; int bin = idx - dist->nexact - dist->nlevel*(level-1); uint32_t step = pow(10, level); uint32_t value = pow(10, level + dist->npow - 1) + step*bin; if ( beg ) *beg = value; if ( end ) *end = value + step; } return dist->bins[idx]; } pysam-0.23.0/bcftools/dist.c.pysam.c000066400000000000000000000065531475062545500172460ustar00rootroot00000000000000#include "bcftools.pysam.h" /* The MIT License Copyright (c) 2016-2020 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include "dist.h" extern void error(const char *format, ...); struct _dist_t { uint64_t *bins, nvalues; int nbins; int npow; // the number of orders of magnitude to represent exactly int nexact; // pow(10,npow) int nlevel; }; dist_t *dist_init(int npow) { dist_t *dist = (dist_t*) calloc(1,sizeof(dist_t)); dist->npow = npow; dist->nexact = pow(10,npow); dist->nlevel = dist->nexact - pow(10,npow-1); return dist; } void dist_destroy(dist_t *dist) { if ( !dist ) return; free(dist->bins); free(dist); } int dist_nbins(dist_t *dist) { return dist->nbins; } int dist_nvalues(dist_t *dist) { return dist->nvalues; } uint32_t dist_insert(dist_t *dist, uint32_t value) { int ibin; if ( value <= dist->nexact ) ibin = value; else { int npow = (int) log10(value); int level = npow - dist->npow + 1; uint32_t step = pow(10, level); ibin = dist->nexact + dist->nlevel*(level-1) + (value - pow(10,npow)) / step; } if ( ibin >= dist->nbins ) { dist->bins = (uint64_t*) realloc(dist->bins, sizeof(*dist->bins)*(ibin+1)); memset(dist->bins + dist->nbins, 0, (ibin+1 - dist->nbins)*sizeof(*dist->bins)); dist->nbins = ibin+1; } dist->bins[ibin]++; dist->nvalues++; return ibin; } uint32_t dist_insert_n(dist_t *dist, uint32_t value, uint32_t cnt) { if ( !cnt ) return 0; int ibin = dist_insert(dist, value); dist->bins[ibin] += cnt - 1; dist->nvalues += cnt; return ibin; } uint64_t dist_get(dist_t *dist, uint32_t idx, uint32_t *beg, uint32_t *end) { if ( idx < dist->nexact ) { if ( beg ) *beg = idx; if ( end ) *end = idx + 1; } else { int level = (idx - dist->nexact) / dist->nlevel + 1; int bin = idx - dist->nexact - dist->nlevel*(level-1); uint32_t step = pow(10, level); uint32_t value = pow(10, level + dist->npow - 1) + step*bin; if ( beg ) *beg = value; if ( end ) *end = value + step; } return dist->bins[idx]; } pysam-0.23.0/bcftools/dist.h000066400000000000000000000054421475062545500156760ustar00rootroot00000000000000/* The MIT License Copyright (c) 2016-2020 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Logarithmic binning Example of usage: // Initialize, make the binning exact up to 10^4, then add a log-step dist_t *dist = dist_init(4); // Insert values int i; for (i=0; i<1e6; i++) dist_insert(dist, i); // Number of bins used int n = dist_n(dist); // Now print the distribution uint32_t beg, end; for (i=0; i #include typedef struct _dist_t dist_t; /* * dist_init() - init bins */ dist_t *dist_init(int npow); void dist_destroy(dist_t *dist); /* dist_nbins() - get the number of bins */ int dist_nbins(dist_t *dist); /* dist_nvalues() - get the total number of values inserted */ int dist_nvalues(dist_t *dist); /* dist_insert() - insert new value dist_insert_n() - insert new value n times */ uint32_t dist_insert(dist_t *dist, uint32_t value); uint32_t dist_insert_n(dist_t *dist, uint32_t value, uint32_t cnt); /* dist_get() @idx: from the interval [0,dist_n-1] @beg,end: [beg,end) */ uint64_t dist_get(dist_t *dist, uint32_t idx, uint32_t *beg, uint32_t *end); #endif pysam-0.23.0/bcftools/edlib.c000066400000000000000000000640741475062545500160130ustar00rootroot00000000000000/* * A cut down C translated of the C++ edlib.cpp file. * Taken from edlib v0.1.0-166-g931be2b */ #include #include #include #include #include "edlib.h" typedef uint64_t Word; static const int WORD_SIZE = 64; // Size of Word in bits static const Word WORD_1 = (Word)1; static const Word HIGH_BIT_MASK = 1LL << 63; // 100..00 //#define MAX_UCHAR 255 #define MAX_UCHAR 7 // better cache usage for our data #ifndef MAX #define MAX(a,b) ((a)>(b)?(a):(b)) #endif typedef struct Block { Word P; // Pvin Word M; // Mvin int score; // score of last cell in block; } Block; /** * Defines equality relation on alphabet characters. * By default each character is always equal only to itself, but you can also provide additional equalities. */ typedef struct EqualityDefinition { bool matrix[MAX_UCHAR + 1][MAX_UCHAR + 1]; } EqualityDefinition; static EqualityDefinition * CreateEqualityDefinition(const char *alphabet, int alphabet_size, const EdlibEqualityPair* additionalEqualities, const int additionalEqualitiesLength) { EqualityDefinition *ed = malloc(sizeof(*ed)); for (size_t i = 0; i < alphabet_size; i++) { for (size_t j = 0; j < alphabet_size; j++) { ed->matrix[i][j] = (i == j); } } if (additionalEqualities != NULL) { for (int i = 0; i < additionalEqualitiesLength; i++) { const char *firstTransformed = strchr(alphabet, additionalEqualities[i].first); const char *secondTransformed = strchr(alphabet, additionalEqualities[i].second); if (firstTransformed && alphabet_size) { ed->matrix[firstTransformed - alphabet][secondTransformed - alphabet] = ed->matrix[secondTransformed - alphabet][firstTransformed - alphabet] = true; } } } return ed; } /** * @param a Element from transformed sequence. * @param b Element from transformed sequence. * @return True if a and b are defined as equal, false otherwise. */ static inline const /* attribute pure or const? */ bool equalityDefinition_areEqual(const EqualityDefinition *ed, unsigned char a, unsigned char b) { return ed->matrix[a][b]; } static int myersCalcEditDistanceSemiGlobal(const Word* Peq, int W, int maxNumBlocks, int queryLength, const unsigned char* target, int targetLength, int k, EdlibAlignMode mode, int* bestScore_, int** positions_, int* numPositions_); static char *transformSequences(const char* queryOriginal, int queryLength, const char* targetOriginal, int targetLength, unsigned char** queryTransformed, unsigned char** targetTransformed, int *alphabet_size); static inline int ceilDiv(int x, int y); static inline unsigned char* createReverseCopy(const unsigned char* seq, int length); static inline Word* buildPeq(const int alphabetLength, const unsigned char* query, const int queryLength, const EqualityDefinition* equalityDefinition); /** * Main edlib method. */ EdlibAlignResult edlibAlign(const char* const queryOriginal, const int queryLength, const char* const targetOriginal, const int targetLength, const EdlibAlignConfig config) { EdlibAlignResult result; result.status = EDLIB_STATUS_OK; result.editDistance = -1; result.endLocations = result.startLocations = NULL; result.numLocations = 0; result.alignment = NULL; result.alignmentLength = 0; result.alphabetLength = 0; /*------------ TRANSFORM SEQUENCES AND RECOGNIZE ALPHABET -----------*/ unsigned char* query, * target; int alphabet_size; char *alphabet = transformSequences(queryOriginal, queryLength, targetOriginal, targetLength, &query, &target, &alphabet_size); result.alphabetLength = alphabet_size; /*-------------------------------------------------------*/ // Handle special situation when at least one of the sequences has length 0. if (queryLength == 0 || targetLength == 0) { if (config.mode == EDLIB_MODE_NW) { result.editDistance = MAX(queryLength, targetLength); result.endLocations = malloc(sizeof(int) * 1); result.endLocations[0] = targetLength - 1; result.numLocations = 1; } else if (config.mode == EDLIB_MODE_SHW || config.mode == EDLIB_MODE_HW) { result.editDistance = queryLength; result.endLocations = malloc(sizeof(int) * 1); result.endLocations[0] = -1; result.numLocations = 1; } else { result.status = EDLIB_STATUS_ERROR; } free(query); free(target); free(alphabet); return result; } /*--------------------- INITIALIZATION ------------------*/ int maxNumBlocks = ceilDiv(queryLength, WORD_SIZE); // bmax in Myers int W = maxNumBlocks * WORD_SIZE - queryLength; // number of redundant cells in last level blocks EqualityDefinition *equalityDefinition = CreateEqualityDefinition(alphabet, alphabet_size, config.additionalEqualities, config.additionalEqualitiesLength); Word* Peq = buildPeq(alphabet_size, query, queryLength, equalityDefinition); /*-------------------------------------------------------*/ /*------------------ MAIN CALCULATION -------------------*/ // TODO: Store alignment data only after k is determined? That could make things faster. // int positionNW; // Used only when mode is NW. // AlignmentData* alignData = NULL; bool dynamicK = false; int k = config.k; if (k < 0) { // If valid k is not given, auto-adjust k until solution is found. dynamicK = true; k = WORD_SIZE; // Gives better results than smaller k. } do { if (config.mode == EDLIB_MODE_HW || config.mode == EDLIB_MODE_SHW) { myersCalcEditDistanceSemiGlobal(Peq, W, maxNumBlocks, queryLength, target, targetLength, k, config.mode, &(result.editDistance), &(result.endLocations), &(result.numLocations)); } else { // mode == EDLIB_MODE_NW // myersCalcEditDistanceNW(Peq, W, maxNumBlocks, // queryLength, target, targetLength, // k, &(result.editDistance), &positionNW, // false, &alignData, -1); } k *= 2; } while(dynamicK && result.editDistance == -1); if (result.editDistance >= 0) { // If there is solution. // If NW mode, set end location explicitly. if (config.mode == EDLIB_MODE_NW) { result.endLocations = malloc(sizeof(int) * 1); result.endLocations[0] = targetLength - 1; result.numLocations = 1; } // Find starting locations. if (config.task == EDLIB_TASK_LOC || config.task == EDLIB_TASK_PATH) { result.startLocations = malloc(result.numLocations * sizeof(int)); if (config.mode == EDLIB_MODE_HW) { // If HW, I need to calculate start locations. const unsigned char* rTarget = createReverseCopy(target, targetLength); const unsigned char* rQuery = createReverseCopy(query, queryLength); // Peq for reversed query. Word* rPeq = buildPeq(alphabet_size, rQuery, queryLength, equalityDefinition); for (int i = 0; i < result.numLocations; i++) { int endLocation = result.endLocations[i]; if (endLocation == -1) { // NOTE: Sometimes one of optimal solutions is that query starts before target, like this: // AAGG <- target // CCTT <- query // It will never be only optimal solution and it does not happen often, however it is // possible and in that case end location will be -1. What should we do with that? // Should we just skip reporting such end location, although it is a solution? // If we do report it, what is the start location? -4? -1? Nothing? // TODO: Figure this out. This has to do in general with how we think about start // and end locations. // Also, we have alignment later relying on this locations to limit the space of it's // search -> how can it do it right if these locations are negative or incorrect? result.startLocations[i] = 0; // I put 0 for now, but it does not make much sense. } else { int bestScoreSHW, numPositionsSHW; int* positionsSHW; myersCalcEditDistanceSemiGlobal( rPeq, W, maxNumBlocks, queryLength, rTarget + targetLength - endLocation - 1, endLocation + 1, result.editDistance, EDLIB_MODE_SHW, &bestScoreSHW, &positionsSHW, &numPositionsSHW); // Taking last location as start ensures that alignment will not start with insertions // if it can start with mismatches instead. result.startLocations[i] = endLocation - positionsSHW[numPositionsSHW - 1]; free(positionsSHW); } } free((void *)rTarget); free((void *)rQuery); free(rPeq); } else { // If mode is SHW or NW for (int i = 0; i < result.numLocations; i++) { result.startLocations[i] = 0; } } } } /*-------------------------------------------------------*/ //--- Free memory ---// free(Peq); free(query); free(target); free(alphabet); free(equalityDefinition); // DestroyAlignmentData(alignData); //-------------------// return result; } /** * Build Peq table for given query and alphabet. * Peq is table of dimensions alphabetLength+1 x maxNumBlocks. * Bit i of Peq[s * maxNumBlocks + b] is 1 if i-th symbol from block b of query equals symbol s, otherwise it is 0. * NOTICE: free returned array with free()! */ static inline Word* buildPeq(const int alphabetLength, const unsigned char* const query, const int queryLength, const EqualityDefinition* equalityDefinition) { int maxNumBlocks = ceilDiv(queryLength, WORD_SIZE); // table of dimensions alphabetLength+1 x maxNumBlocks. Last symbol is wildcard. Word* Peq = malloc((alphabetLength + 1) * maxNumBlocks * sizeof(*Peq)); // Build Peq (1 is match, 0 is mismatch). NOTE: last column is wildcard(symbol that matches anything) with just 1s // Optimised Peq building avoiding branching. for (int symbol = 0; symbol < alphabetLength; symbol++) { for (int b = 0; b < maxNumBlocks; b++) { Word PeqW = 0; for (int r = (b+1) * WORD_SIZE - 1; r >= b * WORD_SIZE; r--) { PeqW = (PeqW<<1) + (r >= queryLength || equalityDefinition_areEqual(equalityDefinition, query[r], symbol)); } Peq[symbol * maxNumBlocks + b] = PeqW; } } { int symbol = alphabetLength; for (int b = 0; b < maxNumBlocks; b++) { // Last symbol is wildcard, so it is all 1s Peq[symbol * maxNumBlocks + b] = (Word)-1; } } return Peq; } /** * Returns new sequence that is reverse of given sequence. * Free returned array with free() */ static inline unsigned char* createReverseCopy(const unsigned char* const seq, const int length) { unsigned char* rSeq = malloc(length); for (int i = 0; i < length; i++) { rSeq[i] = seq[length - i - 1]; } return rSeq; } /** * Corresponds to Advance_Block function from Myers. * Calculates one word(block), which is part of a column. * Highest bit of word (one most to the left) is most bottom cell of block from column. * Pv[i] and Mv[i] define vin of cell[i]: vin = cell[i] - cell[i-1]. * @param [in] Pv Bitset, Pv[i] == 1 if vin is +1, otherwise Pv[i] == 0. * @param [in] Mv Bitset, Mv[i] == 1 if vin is -1, otherwise Mv[i] == 0. * @param [in] Eq Bitset, Eq[i] == 1 if match, 0 if mismatch. * @param [in] hin Will be +1, 0 or -1. * @param [out] PvOut Bitset, PvOut[i] == 1 if vout is +1, otherwise PvOut[i] == 0. * @param [out] MvOut Bitset, MvOut[i] == 1 if vout is -1, otherwise MvOut[i] == 0. * @param [out] hout Will be +1, 0 or -1. */ static inline int calculateBlock(Word Pv, Word Mv, Word Eq, const int hin, Word *PvOut, Word *MvOut) { // hin can be 1, -1 or 0. // 1 -> 00...01 // 0 -> 00...00 // -1 -> 11...11 (2-complement) Word hinIsNeg = (Word)(hin >> 2) & WORD_1; // 00...001 if hin is -1, 00...000 if 0 or 1 Word Xv = Eq | Mv; // This is instruction below written using 'if': if (hin < 0) Eq |= (Word)1; Eq |= hinIsNeg; Word Xh = (((Eq & Pv) + Pv) ^ Pv) | Eq; Word Ph = Mv | ~(Xh | Pv); Word Mh = Pv & Xh; int hout = 0; // This is instruction below written using 'if': if (Ph & HIGH_BIT_MASK) hout = 1; hout = (Ph & HIGH_BIT_MASK) >> (WORD_SIZE - 1); // This is instruction below written using 'if': if (Mh & HIGH_BIT_MASK) hout = -1; hout -= (Mh & HIGH_BIT_MASK) >> (WORD_SIZE - 1); Ph <<= 1; Mh <<= 1; // This is instruction below written using 'if': if (hin < 0) Mh |= (Word)1; Mh |= hinIsNeg; // This is instruction below written using 'if': if (hin > 0) Ph |= (Word)1; Ph |= (Word)((hin + 1) >> 1); *PvOut = Mh | ~(Xv | Ph); *MvOut = Ph & Xv; return hout; } /** * Does ceiling division x / y. * Note: x and y must be non-negative and x + y must not overflow. */ static inline int ceilDiv(const int x, const int y) { return x % y ? x / y + 1 : x / y; } static inline int min(const int x, const int y) { return x < y ? x : y; } /** * @param [in] block * @return Values of cells in block, starting with bottom cell in block. */ static inline int *getBlockCellValues(const Block block) { int *scores = malloc(WORD_SIZE * sizeof(*scores)); int score = block.score; Word mask = HIGH_BIT_MASK; for (int i = 0; i < WORD_SIZE - 1; i++) { scores[i] = score; if (block.P & mask) score--; if (block.M & mask) score++; mask >>= 1; } scores[WORD_SIZE - 1] = score; return scores; } /** * @param [in] block * @param [in] k * @return True if all cells in block have value larger than k, otherwise false. */ static inline bool allBlockCellsLarger(const Block block, const int k) { int *scores = getBlockCellValues(block); for (int i = 0; i < WORD_SIZE; i++) { if (scores[i] <= k) { free(scores); return false; } } free(scores); return true; } /** * Uses Myers' bit-vector algorithm to find edit distance for one of semi-global alignment methods. * @param [in] Peq Query profile. * @param [in] W Size of padding in last block. * TODO: Calculate this directly from query, instead of passing it. * @param [in] maxNumBlocks Number of blocks needed to cover the whole query. * TODO: Calculate this directly from query, instead of passing it. * @param [in] queryLength * @param [in] target * @param [in] targetLength * @param [in] k * @param [in] mode EDLIB_MODE_HW or EDLIB_MODE_SHW * @param [out] bestScore_ Edit distance. * @param [out] positions_ Array of 0-indexed positions in target at which best score was found. Make sure to free this array with free(). * @param [out] numPositions_ Number of positions in the positions_ array. * @return Status. */ static int myersCalcEditDistanceSemiGlobal( const Word* const Peq, const int W, const int maxNumBlocks, const int queryLength, const unsigned char* const target, const int targetLength, int k, const EdlibAlignMode mode, int* const bestScore_, int** const positions_, int* const numPositions_) { *positions_ = NULL; *numPositions_ = 0; // firstBlock is 0-based index of first block in Ukkonen band. // lastBlock is 0-based index of last block in Ukkonen band. int firstBlock = 0; int lastBlock = min(ceilDiv(k + 1, WORD_SIZE), maxNumBlocks) - 1; // y in Myers Block *bl; // Current block Block* blocks = malloc(maxNumBlocks * sizeof(*blocks)); // For HW, solution will never be larger then queryLength. if (mode == EDLIB_MODE_HW) { k = min(queryLength, k); } // Each STRONG_REDUCE_NUM column is reduced in more expensive way. // This gives speed up of about 2 times for small k. const int STRONG_REDUCE_NUM = 2048; // Initialize P, M and score bl = blocks; for (int b = 0; b <= lastBlock; b++) { bl->score = (b + 1) * WORD_SIZE; bl->P = (Word)(-1); // All 1s bl->M = (Word)(0); bl++; } int bestScore = -1; #define MAX_POS 100 // maximum number of positions returned. int positions[MAX_POS]; int npositions = 0; const int startHout = mode == EDLIB_MODE_HW ? 0 : 1; // If 0 then gap before query is not penalized; const unsigned char* targetChar = target; for (int c = 0; c < targetLength; c++) { // for each column const Word* Peq_c = Peq + (*targetChar) * maxNumBlocks; //----------------------- Calculate column -------------------------// int hout = startHout; bl = blocks + firstBlock; Peq_c += firstBlock; for (int b = firstBlock; b <= lastBlock; b++) { hout = calculateBlock(bl->P, bl->M, *Peq_c, hout, &bl->P, &bl->M); bl->score += hout; bl++; Peq_c++; } bl--; Peq_c--; //------------------------------------------------------------------// //---------- Adjust number of blocks according to Ukkonen ----------// if ((lastBlock < maxNumBlocks - 1) && (bl->score - hout <= k) // bl is pointing to last block && ((*(Peq_c + 1) & WORD_1) || hout < 0)) { // Peq_c is pointing to last block // If score of left block is not too big, calculate one more block lastBlock++; bl++; Peq_c++; bl->P = (Word)(-1); // All 1s bl->M = (Word)(0); bl->score = (bl - 1)->score - hout + WORD_SIZE + calculateBlock(bl->P, bl->M, *Peq_c, hout, &bl->P, &bl->M); } else { while (lastBlock >= firstBlock && bl->score >= k + WORD_SIZE) { lastBlock--; bl--; Peq_c--; } } // Every some columns, do some expensive but also more efficient block reducing. // This is important! // // Reduce the band by decreasing last block if possible. if (c % STRONG_REDUCE_NUM == 0) { while (lastBlock >= 0 && lastBlock >= firstBlock && allBlockCellsLarger(*bl, k)) { lastBlock--; bl--; Peq_c--; } } // For HW, even if all cells are > k, there still may be solution in next // column because starting conditions at upper boundary are 0. // That means that first block is always candidate for solution, // and we can never end calculation before last column. if (mode == EDLIB_MODE_HW && lastBlock == -1) { lastBlock++; bl++; Peq_c++; } // Reduce band by increasing first block if possible. Not applicable to HW. if (mode != EDLIB_MODE_HW) { while (firstBlock <= lastBlock && blocks[firstBlock].score >= k + WORD_SIZE) { firstBlock++; } if (c % STRONG_REDUCE_NUM == 0) { // Do strong reduction every some blocks while (firstBlock <= lastBlock && allBlockCellsLarger(blocks[firstBlock], k)) { firstBlock++; } } } // If band stops to exist finish if (lastBlock < firstBlock) { *bestScore_ = bestScore; if (bestScore != -1) { *positions_ = malloc(npositions * sizeof(int)); *numPositions_ = npositions; memcpy(*positions_, positions, npositions * sizeof(int)); } free(blocks); return EDLIB_STATUS_OK; } //------------------------------------------------------------------// //------------------------- Update best score ----------------------// if (lastBlock == maxNumBlocks - 1) { int colScore = bl->score; if (colScore <= k) { // Scores > k dont have correct values (so we cannot use them), but are certainly > k. // NOTE: Score that I find in column c is actually score from column c-W if (bestScore == -1 || colScore <= bestScore) { if (colScore != bestScore) { npositions = 0; bestScore = colScore; // Change k so we will look only for equal or better // scores then the best found so far. k = bestScore; } if (npositions < MAX_POS) positions[npositions++] = c - W; } } } //------------------------------------------------------------------// targetChar++; } // Obtain results for last W columns from last column. if (lastBlock == maxNumBlocks - 1) { int *blockScores = getBlockCellValues(*bl); for (int i = 0; i < W; i++) { int colScore = blockScores[i + 1]; if (colScore <= k && (bestScore == -1 || colScore <= bestScore)) { if (colScore != bestScore) { npositions = 0; k = bestScore = colScore; } if (npositions < MAX_POS) positions[npositions++] = targetLength - W + i; } } free(blockScores); } *bestScore_ = bestScore; if (bestScore != -1) { *positions_ = malloc(npositions * sizeof(int)); *numPositions_ = npositions; memcpy(*positions_, positions, npositions * sizeof(int)); } free(blocks); return EDLIB_STATUS_OK; } /** * Takes char query and char target, recognizes alphabet and transforms them into unsigned char sequences * where elements in sequences are not any more letters of alphabet, but their index in alphabet. * Most of internal edlib functions expect such transformed sequences. * This function will allocate queryTransformed and targetTransformed, so make sure to free them when done. * Example: * Original sequences: "ACT" and "CGT". * Alphabet would be recognized as "ACTG". Alphabet length = 4. * Transformed sequences: [0, 1, 2] and [1, 3, 2]. * @param [in] queryOriginal * @param [in] queryLength * @param [in] targetOriginal * @param [in] targetLength * @param [out] queryTransformed It will contain values in range [0, alphabet length - 1]. * @param [out] targetTransformed It will contain values in range [0, alphabet length - 1]. * @return Alphabet as a string of unique characters, where index of each character is its value in transformed * sequences. */ static char *transformSequences(const char* const queryOriginal, const int queryLength, const char* const targetOriginal, const int targetLength, unsigned char** const queryTransformed, unsigned char** const targetTransformed, int *alphabet_size) { // Alphabet is constructed from letters that are present in sequences. // Each letter is assigned an ordinal number, starting from 0 up to alphabetLength - 1, // and new query and target are created in which letters are replaced with their ordinal numbers. // This query and target are used in all the calculations later. *queryTransformed = malloc(sizeof(unsigned char) * queryLength); *targetTransformed = malloc(sizeof(unsigned char) * targetLength); char *alphabet = malloc(MAX_UCHAR+1), *alphabet_cp = alphabet; // Alphabet information, it is constructed on fly while transforming sequences. // letterIdx[c] is index of letter c in alphabet. unsigned char letterIdx[MAX_UCHAR + 1]; bool inAlphabet[MAX_UCHAR + 1]; // inAlphabet[c] is true if c is in alphabet for (int i = 0; i < MAX_UCHAR + 1; i++) inAlphabet[i] = false; for (int i = 0; i < queryLength; i++) { unsigned char c = queryOriginal[i]; if (!inAlphabet[c]) { inAlphabet[c] = true; letterIdx[c] = alphabet_cp - alphabet; *alphabet_cp++ = queryOriginal[i]; } (*queryTransformed)[i] = letterIdx[c]; } for (int i = 0; i < targetLength; i++) { unsigned char c = targetOriginal[i]; if (!inAlphabet[c]) { inAlphabet[c] = true; letterIdx[c] = alphabet_cp - alphabet; *alphabet_cp++ = targetOriginal[i]; } (*targetTransformed)[i] = letterIdx[c]; } *alphabet_size = alphabet_cp - alphabet; return alphabet; } EdlibAlignConfig edlibNewAlignConfig(int k, EdlibAlignMode mode, EdlibAlignTask task, const EdlibEqualityPair* additionalEqualities, int additionalEqualitiesLength) { EdlibAlignConfig config; config.k = k; config.mode = mode; config.task = task; config.additionalEqualities = additionalEqualities; config.additionalEqualitiesLength = additionalEqualitiesLength; return config; } EdlibAlignConfig edlibDefaultAlignConfig(void) { return edlibNewAlignConfig(-1, EDLIB_MODE_NW, EDLIB_TASK_DISTANCE, NULL, 0); } void edlibFreeAlignResult(EdlibAlignResult result) { if (result.endLocations) free(result.endLocations); if (result.startLocations) free(result.startLocations); if (result.alignment) free(result.alignment); } pysam-0.23.0/bcftools/edlib.c.pysam.c000066400000000000000000000641311475062545500173560ustar00rootroot00000000000000#include "bcftools.pysam.h" /* * A cut down C translated of the C++ edlib.cpp file. * Taken from edlib v0.1.0-166-g931be2b */ #include #include #include #include #include "edlib.h" typedef uint64_t Word; static const int WORD_SIZE = 64; // Size of Word in bits static const Word WORD_1 = (Word)1; static const Word HIGH_BIT_MASK = 1LL << 63; // 100..00 //#define MAX_UCHAR 255 #define MAX_UCHAR 7 // better cache usage for our data #ifndef MAX #define MAX(a,b) ((a)>(b)?(a):(b)) #endif typedef struct Block { Word P; // Pvin Word M; // Mvin int score; // score of last cell in block; } Block; /** * Defines equality relation on alphabet characters. * By default each character is always equal only to itself, but you can also provide additional equalities. */ typedef struct EqualityDefinition { bool matrix[MAX_UCHAR + 1][MAX_UCHAR + 1]; } EqualityDefinition; static EqualityDefinition * CreateEqualityDefinition(const char *alphabet, int alphabet_size, const EdlibEqualityPair* additionalEqualities, const int additionalEqualitiesLength) { EqualityDefinition *ed = malloc(sizeof(*ed)); for (size_t i = 0; i < alphabet_size; i++) { for (size_t j = 0; j < alphabet_size; j++) { ed->matrix[i][j] = (i == j); } } if (additionalEqualities != NULL) { for (int i = 0; i < additionalEqualitiesLength; i++) { const char *firstTransformed = strchr(alphabet, additionalEqualities[i].first); const char *secondTransformed = strchr(alphabet, additionalEqualities[i].second); if (firstTransformed && alphabet_size) { ed->matrix[firstTransformed - alphabet][secondTransformed - alphabet] = ed->matrix[secondTransformed - alphabet][firstTransformed - alphabet] = true; } } } return ed; } /** * @param a Element from transformed sequence. * @param b Element from transformed sequence. * @return True if a and b are defined as equal, false otherwise. */ static inline const /* attribute pure or const? */ bool equalityDefinition_areEqual(const EqualityDefinition *ed, unsigned char a, unsigned char b) { return ed->matrix[a][b]; } static int myersCalcEditDistanceSemiGlobal(const Word* Peq, int W, int maxNumBlocks, int queryLength, const unsigned char* target, int targetLength, int k, EdlibAlignMode mode, int* bestScore_, int** positions_, int* numPositions_); static char *transformSequences(const char* queryOriginal, int queryLength, const char* targetOriginal, int targetLength, unsigned char** queryTransformed, unsigned char** targetTransformed, int *alphabet_size); static inline int ceilDiv(int x, int y); static inline unsigned char* createReverseCopy(const unsigned char* seq, int length); static inline Word* buildPeq(const int alphabetLength, const unsigned char* query, const int queryLength, const EqualityDefinition* equalityDefinition); /** * Main edlib method. */ EdlibAlignResult edlibAlign(const char* const queryOriginal, const int queryLength, const char* const targetOriginal, const int targetLength, const EdlibAlignConfig config) { EdlibAlignResult result; result.status = EDLIB_STATUS_OK; result.editDistance = -1; result.endLocations = result.startLocations = NULL; result.numLocations = 0; result.alignment = NULL; result.alignmentLength = 0; result.alphabetLength = 0; /*------------ TRANSFORM SEQUENCES AND RECOGNIZE ALPHABET -----------*/ unsigned char* query, * target; int alphabet_size; char *alphabet = transformSequences(queryOriginal, queryLength, targetOriginal, targetLength, &query, &target, &alphabet_size); result.alphabetLength = alphabet_size; /*-------------------------------------------------------*/ // Handle special situation when at least one of the sequences has length 0. if (queryLength == 0 || targetLength == 0) { if (config.mode == EDLIB_MODE_NW) { result.editDistance = MAX(queryLength, targetLength); result.endLocations = malloc(sizeof(int) * 1); result.endLocations[0] = targetLength - 1; result.numLocations = 1; } else if (config.mode == EDLIB_MODE_SHW || config.mode == EDLIB_MODE_HW) { result.editDistance = queryLength; result.endLocations = malloc(sizeof(int) * 1); result.endLocations[0] = -1; result.numLocations = 1; } else { result.status = EDLIB_STATUS_ERROR; } free(query); free(target); free(alphabet); return result; } /*--------------------- INITIALIZATION ------------------*/ int maxNumBlocks = ceilDiv(queryLength, WORD_SIZE); // bmax in Myers int W = maxNumBlocks * WORD_SIZE - queryLength; // number of redundant cells in last level blocks EqualityDefinition *equalityDefinition = CreateEqualityDefinition(alphabet, alphabet_size, config.additionalEqualities, config.additionalEqualitiesLength); Word* Peq = buildPeq(alphabet_size, query, queryLength, equalityDefinition); /*-------------------------------------------------------*/ /*------------------ MAIN CALCULATION -------------------*/ // TODO: Store alignment data only after k is determined? That could make things faster. // int positionNW; // Used only when mode is NW. // AlignmentData* alignData = NULL; bool dynamicK = false; int k = config.k; if (k < 0) { // If valid k is not given, auto-adjust k until solution is found. dynamicK = true; k = WORD_SIZE; // Gives better results than smaller k. } do { if (config.mode == EDLIB_MODE_HW || config.mode == EDLIB_MODE_SHW) { myersCalcEditDistanceSemiGlobal(Peq, W, maxNumBlocks, queryLength, target, targetLength, k, config.mode, &(result.editDistance), &(result.endLocations), &(result.numLocations)); } else { // mode == EDLIB_MODE_NW // myersCalcEditDistanceNW(Peq, W, maxNumBlocks, // queryLength, target, targetLength, // k, &(result.editDistance), &positionNW, // false, &alignData, -1); } k *= 2; } while(dynamicK && result.editDistance == -1); if (result.editDistance >= 0) { // If there is solution. // If NW mode, set end location explicitly. if (config.mode == EDLIB_MODE_NW) { result.endLocations = malloc(sizeof(int) * 1); result.endLocations[0] = targetLength - 1; result.numLocations = 1; } // Find starting locations. if (config.task == EDLIB_TASK_LOC || config.task == EDLIB_TASK_PATH) { result.startLocations = malloc(result.numLocations * sizeof(int)); if (config.mode == EDLIB_MODE_HW) { // If HW, I need to calculate start locations. const unsigned char* rTarget = createReverseCopy(target, targetLength); const unsigned char* rQuery = createReverseCopy(query, queryLength); // Peq for reversed query. Word* rPeq = buildPeq(alphabet_size, rQuery, queryLength, equalityDefinition); for (int i = 0; i < result.numLocations; i++) { int endLocation = result.endLocations[i]; if (endLocation == -1) { // NOTE: Sometimes one of optimal solutions is that query starts before target, like this: // AAGG <- target // CCTT <- query // It will never be only optimal solution and it does not happen often, however it is // possible and in that case end location will be -1. What should we do with that? // Should we just skip reporting such end location, although it is a solution? // If we do report it, what is the start location? -4? -1? Nothing? // TODO: Figure this out. This has to do in general with how we think about start // and end locations. // Also, we have alignment later relying on this locations to limit the space of it's // search -> how can it do it right if these locations are negative or incorrect? result.startLocations[i] = 0; // I put 0 for now, but it does not make much sense. } else { int bestScoreSHW, numPositionsSHW; int* positionsSHW; myersCalcEditDistanceSemiGlobal( rPeq, W, maxNumBlocks, queryLength, rTarget + targetLength - endLocation - 1, endLocation + 1, result.editDistance, EDLIB_MODE_SHW, &bestScoreSHW, &positionsSHW, &numPositionsSHW); // Taking last location as start ensures that alignment will not start with insertions // if it can start with mismatches instead. result.startLocations[i] = endLocation - positionsSHW[numPositionsSHW - 1]; free(positionsSHW); } } free((void *)rTarget); free((void *)rQuery); free(rPeq); } else { // If mode is SHW or NW for (int i = 0; i < result.numLocations; i++) { result.startLocations[i] = 0; } } } } /*-------------------------------------------------------*/ //--- Free memory ---// free(Peq); free(query); free(target); free(alphabet); free(equalityDefinition); // DestroyAlignmentData(alignData); //-------------------// return result; } /** * Build Peq table for given query and alphabet. * Peq is table of dimensions alphabetLength+1 x maxNumBlocks. * Bit i of Peq[s * maxNumBlocks + b] is 1 if i-th symbol from block b of query equals symbol s, otherwise it is 0. * NOTICE: free returned array with free()! */ static inline Word* buildPeq(const int alphabetLength, const unsigned char* const query, const int queryLength, const EqualityDefinition* equalityDefinition) { int maxNumBlocks = ceilDiv(queryLength, WORD_SIZE); // table of dimensions alphabetLength+1 x maxNumBlocks. Last symbol is wildcard. Word* Peq = malloc((alphabetLength + 1) * maxNumBlocks * sizeof(*Peq)); // Build Peq (1 is match, 0 is mismatch). NOTE: last column is wildcard(symbol that matches anything) with just 1s // Optimised Peq building avoiding branching. for (int symbol = 0; symbol < alphabetLength; symbol++) { for (int b = 0; b < maxNumBlocks; b++) { Word PeqW = 0; for (int r = (b+1) * WORD_SIZE - 1; r >= b * WORD_SIZE; r--) { PeqW = (PeqW<<1) + (r >= queryLength || equalityDefinition_areEqual(equalityDefinition, query[r], symbol)); } Peq[symbol * maxNumBlocks + b] = PeqW; } } { int symbol = alphabetLength; for (int b = 0; b < maxNumBlocks; b++) { // Last symbol is wildcard, so it is all 1s Peq[symbol * maxNumBlocks + b] = (Word)-1; } } return Peq; } /** * Returns new sequence that is reverse of given sequence. * Free returned array with free() */ static inline unsigned char* createReverseCopy(const unsigned char* const seq, const int length) { unsigned char* rSeq = malloc(length); for (int i = 0; i < length; i++) { rSeq[i] = seq[length - i - 1]; } return rSeq; } /** * Corresponds to Advance_Block function from Myers. * Calculates one word(block), which is part of a column. * Highest bit of word (one most to the left) is most bottom cell of block from column. * Pv[i] and Mv[i] define vin of cell[i]: vin = cell[i] - cell[i-1]. * @param [in] Pv Bitset, Pv[i] == 1 if vin is +1, otherwise Pv[i] == 0. * @param [in] Mv Bitset, Mv[i] == 1 if vin is -1, otherwise Mv[i] == 0. * @param [in] Eq Bitset, Eq[i] == 1 if match, 0 if mismatch. * @param [in] hin Will be +1, 0 or -1. * @param [out] PvOut Bitset, PvOut[i] == 1 if vout is +1, otherwise PvOut[i] == 0. * @param [out] MvOut Bitset, MvOut[i] == 1 if vout is -1, otherwise MvOut[i] == 0. * @param [out] hout Will be +1, 0 or -1. */ static inline int calculateBlock(Word Pv, Word Mv, Word Eq, const int hin, Word *PvOut, Word *MvOut) { // hin can be 1, -1 or 0. // 1 -> 00...01 // 0 -> 00...00 // -1 -> 11...11 (2-complement) Word hinIsNeg = (Word)(hin >> 2) & WORD_1; // 00...001 if hin is -1, 00...000 if 0 or 1 Word Xv = Eq | Mv; // This is instruction below written using 'if': if (hin < 0) Eq |= (Word)1; Eq |= hinIsNeg; Word Xh = (((Eq & Pv) + Pv) ^ Pv) | Eq; Word Ph = Mv | ~(Xh | Pv); Word Mh = Pv & Xh; int hout = 0; // This is instruction below written using 'if': if (Ph & HIGH_BIT_MASK) hout = 1; hout = (Ph & HIGH_BIT_MASK) >> (WORD_SIZE - 1); // This is instruction below written using 'if': if (Mh & HIGH_BIT_MASK) hout = -1; hout -= (Mh & HIGH_BIT_MASK) >> (WORD_SIZE - 1); Ph <<= 1; Mh <<= 1; // This is instruction below written using 'if': if (hin < 0) Mh |= (Word)1; Mh |= hinIsNeg; // This is instruction below written using 'if': if (hin > 0) Ph |= (Word)1; Ph |= (Word)((hin + 1) >> 1); *PvOut = Mh | ~(Xv | Ph); *MvOut = Ph & Xv; return hout; } /** * Does ceiling division x / y. * Note: x and y must be non-negative and x + y must not overflow. */ static inline int ceilDiv(const int x, const int y) { return x % y ? x / y + 1 : x / y; } static inline int min(const int x, const int y) { return x < y ? x : y; } /** * @param [in] block * @return Values of cells in block, starting with bottom cell in block. */ static inline int *getBlockCellValues(const Block block) { int *scores = malloc(WORD_SIZE * sizeof(*scores)); int score = block.score; Word mask = HIGH_BIT_MASK; for (int i = 0; i < WORD_SIZE - 1; i++) { scores[i] = score; if (block.P & mask) score--; if (block.M & mask) score++; mask >>= 1; } scores[WORD_SIZE - 1] = score; return scores; } /** * @param [in] block * @param [in] k * @return True if all cells in block have value larger than k, otherwise false. */ static inline bool allBlockCellsLarger(const Block block, const int k) { int *scores = getBlockCellValues(block); for (int i = 0; i < WORD_SIZE; i++) { if (scores[i] <= k) { free(scores); return false; } } free(scores); return true; } /** * Uses Myers' bit-vector algorithm to find edit distance for one of semi-global alignment methods. * @param [in] Peq Query profile. * @param [in] W Size of padding in last block. * TODO: Calculate this directly from query, instead of passing it. * @param [in] maxNumBlocks Number of blocks needed to cover the whole query. * TODO: Calculate this directly from query, instead of passing it. * @param [in] queryLength * @param [in] target * @param [in] targetLength * @param [in] k * @param [in] mode EDLIB_MODE_HW or EDLIB_MODE_SHW * @param [out] bestScore_ Edit distance. * @param [out] positions_ Array of 0-indexed positions in target at which best score was found. Make sure to free this array with free(). * @param [out] numPositions_ Number of positions in the positions_ array. * @return Status. */ static int myersCalcEditDistanceSemiGlobal( const Word* const Peq, const int W, const int maxNumBlocks, const int queryLength, const unsigned char* const target, const int targetLength, int k, const EdlibAlignMode mode, int* const bestScore_, int** const positions_, int* const numPositions_) { *positions_ = NULL; *numPositions_ = 0; // firstBlock is 0-based index of first block in Ukkonen band. // lastBlock is 0-based index of last block in Ukkonen band. int firstBlock = 0; int lastBlock = min(ceilDiv(k + 1, WORD_SIZE), maxNumBlocks) - 1; // y in Myers Block *bl; // Current block Block* blocks = malloc(maxNumBlocks * sizeof(*blocks)); // For HW, solution will never be larger then queryLength. if (mode == EDLIB_MODE_HW) { k = min(queryLength, k); } // Each STRONG_REDUCE_NUM column is reduced in more expensive way. // This gives speed up of about 2 times for small k. const int STRONG_REDUCE_NUM = 2048; // Initialize P, M and score bl = blocks; for (int b = 0; b <= lastBlock; b++) { bl->score = (b + 1) * WORD_SIZE; bl->P = (Word)(-1); // All 1s bl->M = (Word)(0); bl++; } int bestScore = -1; #define MAX_POS 100 // maximum number of positions returned. int positions[MAX_POS]; int npositions = 0; const int startHout = mode == EDLIB_MODE_HW ? 0 : 1; // If 0 then gap before query is not penalized; const unsigned char* targetChar = target; for (int c = 0; c < targetLength; c++) { // for each column const Word* Peq_c = Peq + (*targetChar) * maxNumBlocks; //----------------------- Calculate column -------------------------// int hout = startHout; bl = blocks + firstBlock; Peq_c += firstBlock; for (int b = firstBlock; b <= lastBlock; b++) { hout = calculateBlock(bl->P, bl->M, *Peq_c, hout, &bl->P, &bl->M); bl->score += hout; bl++; Peq_c++; } bl--; Peq_c--; //------------------------------------------------------------------// //---------- Adjust number of blocks according to Ukkonen ----------// if ((lastBlock < maxNumBlocks - 1) && (bl->score - hout <= k) // bl is pointing to last block && ((*(Peq_c + 1) & WORD_1) || hout < 0)) { // Peq_c is pointing to last block // If score of left block is not too big, calculate one more block lastBlock++; bl++; Peq_c++; bl->P = (Word)(-1); // All 1s bl->M = (Word)(0); bl->score = (bl - 1)->score - hout + WORD_SIZE + calculateBlock(bl->P, bl->M, *Peq_c, hout, &bl->P, &bl->M); } else { while (lastBlock >= firstBlock && bl->score >= k + WORD_SIZE) { lastBlock--; bl--; Peq_c--; } } // Every some columns, do some expensive but also more efficient block reducing. // This is important! // // Reduce the band by decreasing last block if possible. if (c % STRONG_REDUCE_NUM == 0) { while (lastBlock >= 0 && lastBlock >= firstBlock && allBlockCellsLarger(*bl, k)) { lastBlock--; bl--; Peq_c--; } } // For HW, even if all cells are > k, there still may be solution in next // column because starting conditions at upper boundary are 0. // That means that first block is always candidate for solution, // and we can never end calculation before last column. if (mode == EDLIB_MODE_HW && lastBlock == -1) { lastBlock++; bl++; Peq_c++; } // Reduce band by increasing first block if possible. Not applicable to HW. if (mode != EDLIB_MODE_HW) { while (firstBlock <= lastBlock && blocks[firstBlock].score >= k + WORD_SIZE) { firstBlock++; } if (c % STRONG_REDUCE_NUM == 0) { // Do strong reduction every some blocks while (firstBlock <= lastBlock && allBlockCellsLarger(blocks[firstBlock], k)) { firstBlock++; } } } // If band stops to exist finish if (lastBlock < firstBlock) { *bestScore_ = bestScore; if (bestScore != -1) { *positions_ = malloc(npositions * sizeof(int)); *numPositions_ = npositions; memcpy(*positions_, positions, npositions * sizeof(int)); } free(blocks); return EDLIB_STATUS_OK; } //------------------------------------------------------------------// //------------------------- Update best score ----------------------// if (lastBlock == maxNumBlocks - 1) { int colScore = bl->score; if (colScore <= k) { // Scores > k dont have correct values (so we cannot use them), but are certainly > k. // NOTE: Score that I find in column c is actually score from column c-W if (bestScore == -1 || colScore <= bestScore) { if (colScore != bestScore) { npositions = 0; bestScore = colScore; // Change k so we will look only for equal or better // scores then the best found so far. k = bestScore; } if (npositions < MAX_POS) positions[npositions++] = c - W; } } } //------------------------------------------------------------------// targetChar++; } // Obtain results for last W columns from last column. if (lastBlock == maxNumBlocks - 1) { int *blockScores = getBlockCellValues(*bl); for (int i = 0; i < W; i++) { int colScore = blockScores[i + 1]; if (colScore <= k && (bestScore == -1 || colScore <= bestScore)) { if (colScore != bestScore) { npositions = 0; k = bestScore = colScore; } if (npositions < MAX_POS) positions[npositions++] = targetLength - W + i; } } free(blockScores); } *bestScore_ = bestScore; if (bestScore != -1) { *positions_ = malloc(npositions * sizeof(int)); *numPositions_ = npositions; memcpy(*positions_, positions, npositions * sizeof(int)); } free(blocks); return EDLIB_STATUS_OK; } /** * Takes char query and char target, recognizes alphabet and transforms them into unsigned char sequences * where elements in sequences are not any more letters of alphabet, but their index in alphabet. * Most of internal edlib functions expect such transformed sequences. * This function will allocate queryTransformed and targetTransformed, so make sure to free them when done. * Example: * Original sequences: "ACT" and "CGT". * Alphabet would be recognized as "ACTG". Alphabet length = 4. * Transformed sequences: [0, 1, 2] and [1, 3, 2]. * @param [in] queryOriginal * @param [in] queryLength * @param [in] targetOriginal * @param [in] targetLength * @param [out] queryTransformed It will contain values in range [0, alphabet length - 1]. * @param [out] targetTransformed It will contain values in range [0, alphabet length - 1]. * @return Alphabet as a string of unique characters, where index of each character is its value in transformed * sequences. */ static char *transformSequences(const char* const queryOriginal, const int queryLength, const char* const targetOriginal, const int targetLength, unsigned char** const queryTransformed, unsigned char** const targetTransformed, int *alphabet_size) { // Alphabet is constructed from letters that are present in sequences. // Each letter is assigned an ordinal number, starting from 0 up to alphabetLength - 1, // and new query and target are created in which letters are replaced with their ordinal numbers. // This query and target are used in all the calculations later. *queryTransformed = malloc(sizeof(unsigned char) * queryLength); *targetTransformed = malloc(sizeof(unsigned char) * targetLength); char *alphabet = malloc(MAX_UCHAR+1), *alphabet_cp = alphabet; // Alphabet information, it is constructed on fly while transforming sequences. // letterIdx[c] is index of letter c in alphabet. unsigned char letterIdx[MAX_UCHAR + 1]; bool inAlphabet[MAX_UCHAR + 1]; // inAlphabet[c] is true if c is in alphabet for (int i = 0; i < MAX_UCHAR + 1; i++) inAlphabet[i] = false; for (int i = 0; i < queryLength; i++) { unsigned char c = queryOriginal[i]; if (!inAlphabet[c]) { inAlphabet[c] = true; letterIdx[c] = alphabet_cp - alphabet; *alphabet_cp++ = queryOriginal[i]; } (*queryTransformed)[i] = letterIdx[c]; } for (int i = 0; i < targetLength; i++) { unsigned char c = targetOriginal[i]; if (!inAlphabet[c]) { inAlphabet[c] = true; letterIdx[c] = alphabet_cp - alphabet; *alphabet_cp++ = targetOriginal[i]; } (*targetTransformed)[i] = letterIdx[c]; } *alphabet_size = alphabet_cp - alphabet; return alphabet; } EdlibAlignConfig edlibNewAlignConfig(int k, EdlibAlignMode mode, EdlibAlignTask task, const EdlibEqualityPair* additionalEqualities, int additionalEqualitiesLength) { EdlibAlignConfig config; config.k = k; config.mode = mode; config.task = task; config.additionalEqualities = additionalEqualities; config.additionalEqualitiesLength = additionalEqualitiesLength; return config; } EdlibAlignConfig edlibDefaultAlignConfig(void) { return edlibNewAlignConfig(-1, EDLIB_MODE_NW, EDLIB_TASK_DISTANCE, NULL, 0); } void edlibFreeAlignResult(EdlibAlignResult result) { if (result.endLocations) free(result.endLocations); if (result.startLocations) free(result.startLocations); if (result.alignment) free(result.alignment); } pysam-0.23.0/bcftools/edlib.h000066400000000000000000000254421475062545500160140ustar00rootroot00000000000000#ifndef EDLIB_H #define EDLIB_H /** * @file * @author Martin Sosic * @brief Main header file, containing all public functions and structures. */ // Define EDLIB_API macro to properly export symbols #ifdef EDLIB_SHARED # ifdef _WIN32 # ifdef EDLIB_BUILD # define EDLIB_API __declspec(dllexport) # else # define EDLIB_API __declspec(dllimport) # endif # else # define EDLIB_API __attribute__ ((visibility ("default"))) # endif #else # define EDLIB_API #endif #ifdef __cplusplus extern "C" { #endif // Status codes #define EDLIB_STATUS_OK 0 #define EDLIB_STATUS_ERROR 1 /** * Alignment methods - how should Edlib treat gaps before and after query? */ typedef enum { /** * Global method. This is the standard method. * Useful when you want to find out how similar is first sequence to second sequence. */ EDLIB_MODE_NW, /** * Prefix method. Similar to global method, but with a small twist - gap at query end is not penalized. * What that means is that deleting elements from the end of second sequence is "free"! * For example, if we had "AACT" and "AACTGGC", edit distance would be 0, because removing "GGC" from the end * of second sequence is "free" and does not count into total edit distance. This method is appropriate * when you want to find out how well first sequence fits at the beginning of second sequence. */ EDLIB_MODE_SHW, /** * Infix method. Similar as prefix method, but with one more twist - gaps at query end and start are * not penalized. What that means is that deleting elements from the start and end of second sequence is "free"! * For example, if we had ACT and CGACTGAC, edit distance would be 0, because removing CG from the start * and GAC from the end of second sequence is "free" and does not count into total edit distance. * This method is appropriate when you want to find out how well first sequence fits at any part of * second sequence. * For example, if your second sequence was a long text and your first sequence was a sentence from that text, * but slightly scrambled, you could use this method to discover how scrambled it is and where it fits in * that text. In bioinformatics, this method is appropriate for aligning read to a sequence. */ EDLIB_MODE_HW } EdlibAlignMode; /** * Alignment tasks - what do you want Edlib to do? */ typedef enum { EDLIB_TASK_DISTANCE, //!< Find edit distance and end locations. EDLIB_TASK_LOC, //!< Find edit distance, end locations and start locations. EDLIB_TASK_PATH //!< Find edit distance, end locations and start locations and alignment path. } EdlibAlignTask; /** * Describes cigar format. * @see http://samtools.github.io/hts-specs/SAMv1.pdf * @see http://drive5.com/usearch/manual/cigar.html */ typedef enum { EDLIB_CIGAR_STANDARD, //!< Match: 'M', Insertion: 'I', Deletion: 'D', Mismatch: 'M'. EDLIB_CIGAR_EXTENDED //!< Match: '=', Insertion: 'I', Deletion: 'D', Mismatch: 'X'. } EdlibCigarFormat; // Edit operations. #define EDLIB_EDOP_MATCH 0 //!< Match. #define EDLIB_EDOP_INSERT 1 //!< Insertion to target = deletion from query. #define EDLIB_EDOP_DELETE 2 //!< Deletion from target = insertion to query. #define EDLIB_EDOP_MISMATCH 3 //!< Mismatch. /** * @brief Defines two given characters as equal. */ typedef struct { char first; char second; } EdlibEqualityPair; /** * @brief Configuration object for edlibAlign() function. */ typedef struct { /** * Set k to non-negative value to tell edlib that edit distance is not larger than k. * Smaller k can significantly improve speed of computation. * If edit distance is larger than k, edlib will set edit distance to -1. * Set k to negative value and edlib will internally auto-adjust k until score is found. */ int k; /** * Alignment method. * EDLIB_MODE_NW: global (Needleman-Wunsch) * EDLIB_MODE_SHW: prefix. Gap after query is not penalized. * EDLIB_MODE_HW: infix. Gaps before and after query are not penalized. */ EdlibAlignMode mode; /** * Alignment task - tells Edlib what to calculate. Less to calculate, faster it is. * EDLIB_TASK_DISTANCE - find edit distance and end locations of optimal alignment paths in target. * EDLIB_TASK_LOC - find edit distance and start and end locations of optimal alignment paths in target. * EDLIB_TASK_PATH - find edit distance, alignment path (and start and end locations of it in target). */ EdlibAlignTask task; /** * List of pairs of characters, where each pair defines two characters as equal. * This way you can extend edlib's definition of equality (which is that each character is equal only * to itself). * This can be useful if you have some wildcard characters that should match multiple other characters, * or e.g. if you want edlib to be case insensitive. * Can be set to NULL if there are none. */ const EdlibEqualityPair* additionalEqualities; /** * Number of additional equalities, which is non-negative number. * 0 if there are none. */ int additionalEqualitiesLength; } EdlibAlignConfig; /** * Helper method for easy construction of configuration object. * @return Configuration object filled with given parameters. */ EDLIB_API EdlibAlignConfig edlibNewAlignConfig( int k, EdlibAlignMode mode, EdlibAlignTask task, const EdlibEqualityPair* additionalEqualities, int additionalEqualitiesLength ); /** * @return Default configuration object, with following defaults: * k = -1, mode = EDLIB_MODE_NW, task = EDLIB_TASK_DISTANCE, no additional equalities. */ EDLIB_API EdlibAlignConfig edlibDefaultAlignConfig(void); /** * Container for results of alignment done by edlibAlign() function. */ typedef struct { /** * EDLIB_STATUS_OK or EDLIB_STATUS_ERROR. If error, all other fields will have undefined values. */ int status; /** * -1 if k is non-negative and edit distance is larger than k. */ int editDistance; /** * Array of zero-based positions in target where optimal alignment paths end. * If gap after query is penalized, gap counts as part of query (NW), otherwise not. * Set to NULL if edit distance is larger than k. * If you do not free whole result object using edlibFreeAlignResult(), do not forget to use free(). */ int* endLocations; /** * Array of zero-based positions in target where optimal alignment paths start, * they correspond to endLocations. * If gap before query is penalized, gap counts as part of query (NW), otherwise not. * Set to NULL if not calculated or if edit distance is larger than k. * If you do not free whole result object using edlibFreeAlignResult(), do not forget to use free(). */ int* startLocations; /** * Number of end (and start) locations. */ int numLocations; /** * Alignment is found for first pair of start and end locations. * Set to NULL if not calculated. * Alignment is sequence of numbers: 0, 1, 2, 3. * 0 stands for match. * 1 stands for insertion to target. * 2 stands for insertion to query. * 3 stands for mismatch. * Alignment aligns query to target from beginning of query till end of query. * If gaps are not penalized, they are not in alignment. * If you do not free whole result object using edlibFreeAlignResult(), do not forget to use free(). */ unsigned char* alignment; /** * Length of alignment. */ int alignmentLength; /** * Number of different characters in query and target together. */ int alphabetLength; } EdlibAlignResult; /** * Frees memory in EdlibAlignResult that was allocated by edlib. * If you do not use it, make sure to free needed members manually using free(). */ EDLIB_API void edlibFreeAlignResult(EdlibAlignResult result); /** * Aligns two sequences (query and target) using edit distance (levenshtein distance). * Through config parameter, this function supports different alignment methods (global, prefix, infix), * as well as different modes of search (tasks). * It always returns edit distance and end locations of optimal alignment in target. * It optionally returns start locations of optimal alignment in target and alignment path, * if you choose appropriate tasks. * @param [in] query First sequence. * @param [in] queryLength Number of characters in first sequence. * @param [in] target Second sequence. * @param [in] targetLength Number of characters in second sequence. * @param [in] config Additional alignment parameters, like alignment method and wanted results. * @return Result of alignment, which can contain edit distance, start and end locations and alignment path. * Make sure to clean up the object using edlibFreeAlignResult() or by manually freeing needed members. */ EDLIB_API EdlibAlignResult edlibAlign( const char* query, int queryLength, const char* target, int targetLength, const EdlibAlignConfig config ); /** * Builds cigar string from given alignment sequence. * @param [in] alignment Alignment sequence. * 0 stands for match. * 1 stands for insertion to target. * 2 stands for insertion to query. * 3 stands for mismatch. * @param [in] alignmentLength * @param [in] cigarFormat Cigar will be returned in specified format. * @return Cigar string. * I stands for insertion. * D stands for deletion. * X stands for mismatch. (used only in extended format) * = stands for match. (used only in extended format) * M stands for (mis)match. (used only in standard format) * String is null terminated. * Needed memory is allocated and given pointer is set to it. * Do not forget to free it later using free()! */ EDLIB_API char* edlibAlignmentToCigar( const unsigned char* alignment, int alignmentLength, EdlibCigarFormat cigarFormat ); #ifdef __cplusplus } #endif #endif // EDLIB_H pysam-0.23.0/bcftools/em.c000066400000000000000000000212351475062545500153250ustar00rootroot00000000000000/* em.c -- mathematical functions. Copyright (C) 2010, 2011 Broad Institute. Portions copyright (C) 2013-2014 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include "kmin.h" #include "call.h" #define ITER_MAX 50 #define ITER_TRY 10 #define EPS 1e-5 extern double kf_gammaq(double, double); /* Generic routines */ // estimate site allele frequency in a very naive and inaccurate way static double est_freq(int n, const double *pdg) { int i, gcnt[3], tmp1; // get a rough estimate of the genotype frequency gcnt[0] = gcnt[1] = gcnt[2] = 0; for (i = 0; i < n; ++i) { const double *p = pdg + i * 3; if (p[0] != 1. || p[1] != 1. || p[2] != 1.) { int which = p[0] > p[1]? 0 : 1; which = p[which] > p[2]? which : 2; ++gcnt[which]; } } tmp1 = gcnt[0] + gcnt[1] + gcnt[2]; return (tmp1 == 0)? -1.0 : (.5 * gcnt[1] + gcnt[2]) / tmp1; } /* Single-locus EM */ typedef struct { int beg, end; const double *pdg; } minaux1_t; static double prob1(double f, void *data) { minaux1_t *a = (minaux1_t*)data; double p = 1., l = 0., f3[3]; int i; // printf("brent %lg\n", f); if (f < 0 || f > 1) return 1e300; f3[0] = (1.-f)*(1.-f); f3[1] = 2.*f*(1.-f); f3[2] = f*f; for (i = a->beg; i < a->end; ++i) { const double *pdg = a->pdg + i * 3; p *= pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2]; if (p < 1e-200) l -= log(p), p = 1.; } return l - log(p); } // one EM iteration for allele frequency estimate static double freq_iter(double *f, const double *_pdg, int beg, int end) { double f0 = *f, f3[3], err; int i; // printf("em %lg\n", *f); f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0; for (i = beg, f0 = 0.; i < end; ++i) { const double *pdg = _pdg + i * 3; f0 += (pdg[1] * f3[1] + 2. * pdg[2] * f3[2]) / (pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2]); } f0 /= (end - beg) * 2; err = fabs(f0 - *f); *f = f0; return err; } /* The following function combines EM and Brent's method. When the signal from * the data is strong, EM is faster but sometimes, EM may converge very slowly. * When this happens, we switch to Brent's method. The idea is learned from * Rasmus Nielsen. */ static double freqml(double f0, int beg, int end, const double *pdg) { int i; double f; for (i = 0, f = f0; i < ITER_TRY; ++i) if (freq_iter(&f, pdg, beg, end) < EPS) break; if (i == ITER_TRY) { // haven't converged yet; try Brent's method minaux1_t a; a.beg = beg; a.end = end; a.pdg = pdg; kmin_brent(prob1, f0 == f? .5*f0 : f0, f, (void*)&a, EPS, &f); } return f; } // one EM iteration for genotype frequency estimate static double g3_iter(double g[3], const double *_pdg, int beg, int end) { double err, gg[3]; int i; gg[0] = gg[1] = gg[2] = 0.; // printf("%lg,%lg,%lg\n", g[0], g[1], g[2]); for (i = beg; i < end; ++i) { double sum, tmp[3]; const double *pdg = _pdg + i * 3; tmp[0] = pdg[0] * g[0]; tmp[1] = pdg[1] * g[1]; tmp[2] = pdg[2] * g[2]; sum = (tmp[0] + tmp[1] + tmp[2]) * (end - beg); gg[0] += tmp[0] / sum; gg[1] += tmp[1] / sum; gg[2] += tmp[2] / sum; } err = fabs(gg[0] - g[0]) > fabs(gg[1] - g[1])? fabs(gg[0] - g[0]) : fabs(gg[1] - g[1]); err = err > fabs(gg[2] - g[2])? err : fabs(gg[2] - g[2]); g[0] = gg[0]; g[1] = gg[1]; g[2] = gg[2]; return err; } // perform likelihood ratio test static double lk_ratio_test(int n, int n1, const double *pdg, double f3[3][3]) { double r; int i; for (i = 0, r = 1.; i < n1; ++i) { const double *p = pdg + i * 3; r *= (p[0] * f3[1][0] + p[1] * f3[1][1] + p[2] * f3[1][2]) / (p[0] * f3[0][0] + p[1] * f3[0][1] + p[2] * f3[0][2]); } for (; i < n; ++i) { const double *p = pdg + i * 3; r *= (p[0] * f3[2][0] + p[1] * f3[2][1] + p[2] * f3[2][2]) / (p[0] * f3[0][0] + p[1] * f3[0][1] + p[2] * f3[0][2]); } return r; } // x[0]: ref frequency // x[1..3]: alt-alt, alt-ref, ref-ref frequenc // x[4]: HWE P-value // x[5..6]: group1 freq, group2 freq // x[7]: 1-degree P-value // x[8]: 2-degree P-value int bcf_em1(call_t *call, const bcf1_t *rec, int n1, int flag, double x[10]) { double *pdg; int i, n; //, n2; if (rec->n_allele < 2) return -1; // one allele only // initialization if (n1 < 0 || n1 > rec->n_sample) n1 = 0; if (flag & 1<<7) flag |= 7<<5; // compute group freq if LRT is required if (flag & 0xf<<1) flag |= 0xf<<1; n = rec->n_sample; //n2 = n - n1; pdg = call->pdg; if (pdg == 0) return -1; for (i = 0; i < 10; ++i) x[i] = -1.; // set to negative { if ((x[0] = est_freq(n, pdg)) < 0.) return -1; // no data x[0] = freqml(x[0], 0, n, pdg); } if (flag & (0xf<<1|3<<8)) { // estimate the genotype frequency and test HWE double *g = x + 1, f3[3], r; f3[0] = g[0] = (1 - x[0]) * (1 - x[0]); f3[1] = g[1] = 2 * x[0] * (1 - x[0]); f3[2] = g[2] = x[0] * x[0]; for (i = 0; i < ITER_MAX; ++i) if (g3_iter(g, pdg, 0, n) < EPS) break; // Hardy-Weinberg equilibrium (HWE) for (i = 0, r = 1.; i < n; ++i) { double *p = pdg + i * 3; r *= (p[0] * g[0] + p[1] * g[1] + p[2] * g[2]) / (p[0] * f3[0] + p[1] * f3[1] + p[2] * f3[2]); } x[4] = kf_gammaq(.5, log(r)); } if ((flag & 7<<5) && n1 > 0 && n1 < n) { // group frequency x[5] = freqml(x[0], 0, n1, pdg); x[6] = freqml(x[0], n1, n, pdg); } if ((flag & 1<<7) && n1 > 0 && n1 < n) { // 1-degree P-value double f[3], f3[3][3], tmp; f[0] = x[0]; f[1] = x[5]; f[2] = x[6]; for (i = 0; i < 3; ++i) f3[i][0] = (1-f[i])*(1-f[i]), f3[i][1] = 2*f[i]*(1-f[i]), f3[i][2] = f[i]*f[i]; tmp = log(lk_ratio_test(n, n1, pdg, f3)); if (tmp < 0) tmp = 0; x[7] = kf_gammaq(.5, tmp); } if ((flag & 3<<8) && n1 > 0 && n1 < n) { // 2-degree P-value double g[3][3], tmp; for (i = 0; i < 3; ++i) memcpy(g[i], x + 1, 3 * sizeof(double)); for (i = 0; i < ITER_MAX; ++i) if (g3_iter(g[1], pdg, 0, n1) < EPS) break; for (i = 0; i < ITER_MAX; ++i) if (g3_iter(g[2], pdg, n1, n) < EPS) break; tmp = log(lk_ratio_test(n, n1, pdg, g)); if (tmp < 0) tmp = 0; x[8] = kf_gammaq(1., tmp); } return 0; } /* Two-locus EM (LD) */ #define _G1(h, k) ((h>>1&1) + (k>>1&1)) #define _G2(h, k) ((h&1) + (k&1)) #if 0 // 0: the previous site; 1: the current site static int pair_freq_iter(int n, double *pdg[2], double f[4]) { double ff[4]; int i, k, h; // printf("%lf,%lf,%lf,%lf\n", f[0], f[1], f[2], f[3]); memset(ff, 0, 4 * sizeof(double)); for (i = 0; i < n; ++i) { double *p[2], sum, tmp; p[0] = pdg[0] + i * 3; p[1] = pdg[1] + i * 3; for (k = 0, sum = 0.; k < 4; ++k) for (h = 0; h < 4; ++h) sum += f[k] * f[h] * p[0][_G1(k,h)] * p[1][_G2(k,h)]; for (k = 0; k < 4; ++k) { tmp = f[0] * (p[0][_G1(0,k)] * p[1][_G2(0,k)] + p[0][_G1(k,0)] * p[1][_G2(k,0)]) + f[1] * (p[0][_G1(1,k)] * p[1][_G2(1,k)] + p[0][_G1(k,1)] * p[1][_G2(k,1)]) + f[2] * (p[0][_G1(2,k)] * p[1][_G2(2,k)] + p[0][_G1(k,2)] * p[1][_G2(k,2)]) + f[3] * (p[0][_G1(3,k)] * p[1][_G2(3,k)] + p[0][_G1(k,3)] * p[1][_G2(k,3)]); ff[k] += f[k] * tmp / sum; } } for (k = 0; k < 4; ++k) f[k] = ff[k] / (2 * n); return 0; } #endif pysam-0.23.0/bcftools/em.c.pysam.c000066400000000000000000000214021475062545500166720ustar00rootroot00000000000000#include "bcftools.pysam.h" /* em.c -- mathematical functions. Copyright (C) 2010, 2011 Broad Institute. Portions copyright (C) 2013-2014 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include "kmin.h" #include "call.h" #define ITER_MAX 50 #define ITER_TRY 10 #define EPS 1e-5 extern double kf_gammaq(double, double); /* Generic routines */ // estimate site allele frequency in a very naive and inaccurate way static double est_freq(int n, const double *pdg) { int i, gcnt[3], tmp1; // get a rough estimate of the genotype frequency gcnt[0] = gcnt[1] = gcnt[2] = 0; for (i = 0; i < n; ++i) { const double *p = pdg + i * 3; if (p[0] != 1. || p[1] != 1. || p[2] != 1.) { int which = p[0] > p[1]? 0 : 1; which = p[which] > p[2]? which : 2; ++gcnt[which]; } } tmp1 = gcnt[0] + gcnt[1] + gcnt[2]; return (tmp1 == 0)? -1.0 : (.5 * gcnt[1] + gcnt[2]) / tmp1; } /* Single-locus EM */ typedef struct { int beg, end; const double *pdg; } minaux1_t; static double prob1(double f, void *data) { minaux1_t *a = (minaux1_t*)data; double p = 1., l = 0., f3[3]; int i; // fprintf(bcftools_stdout, "brent %lg\n", f); if (f < 0 || f > 1) return 1e300; f3[0] = (1.-f)*(1.-f); f3[1] = 2.*f*(1.-f); f3[2] = f*f; for (i = a->beg; i < a->end; ++i) { const double *pdg = a->pdg + i * 3; p *= pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2]; if (p < 1e-200) l -= log(p), p = 1.; } return l - log(p); } // one EM iteration for allele frequency estimate static double freq_iter(double *f, const double *_pdg, int beg, int end) { double f0 = *f, f3[3], err; int i; // fprintf(bcftools_stdout, "em %lg\n", *f); f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0; for (i = beg, f0 = 0.; i < end; ++i) { const double *pdg = _pdg + i * 3; f0 += (pdg[1] * f3[1] + 2. * pdg[2] * f3[2]) / (pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2]); } f0 /= (end - beg) * 2; err = fabs(f0 - *f); *f = f0; return err; } /* The following function combines EM and Brent's method. When the signal from * the data is strong, EM is faster but sometimes, EM may converge very slowly. * When this happens, we switch to Brent's method. The idea is learned from * Rasmus Nielsen. */ static double freqml(double f0, int beg, int end, const double *pdg) { int i; double f; for (i = 0, f = f0; i < ITER_TRY; ++i) if (freq_iter(&f, pdg, beg, end) < EPS) break; if (i == ITER_TRY) { // haven't converged yet; try Brent's method minaux1_t a; a.beg = beg; a.end = end; a.pdg = pdg; kmin_brent(prob1, f0 == f? .5*f0 : f0, f, (void*)&a, EPS, &f); } return f; } // one EM iteration for genotype frequency estimate static double g3_iter(double g[3], const double *_pdg, int beg, int end) { double err, gg[3]; int i; gg[0] = gg[1] = gg[2] = 0.; // fprintf(bcftools_stdout, "%lg,%lg,%lg\n", g[0], g[1], g[2]); for (i = beg; i < end; ++i) { double sum, tmp[3]; const double *pdg = _pdg + i * 3; tmp[0] = pdg[0] * g[0]; tmp[1] = pdg[1] * g[1]; tmp[2] = pdg[2] * g[2]; sum = (tmp[0] + tmp[1] + tmp[2]) * (end - beg); gg[0] += tmp[0] / sum; gg[1] += tmp[1] / sum; gg[2] += tmp[2] / sum; } err = fabs(gg[0] - g[0]) > fabs(gg[1] - g[1])? fabs(gg[0] - g[0]) : fabs(gg[1] - g[1]); err = err > fabs(gg[2] - g[2])? err : fabs(gg[2] - g[2]); g[0] = gg[0]; g[1] = gg[1]; g[2] = gg[2]; return err; } // perform likelihood ratio test static double lk_ratio_test(int n, int n1, const double *pdg, double f3[3][3]) { double r; int i; for (i = 0, r = 1.; i < n1; ++i) { const double *p = pdg + i * 3; r *= (p[0] * f3[1][0] + p[1] * f3[1][1] + p[2] * f3[1][2]) / (p[0] * f3[0][0] + p[1] * f3[0][1] + p[2] * f3[0][2]); } for (; i < n; ++i) { const double *p = pdg + i * 3; r *= (p[0] * f3[2][0] + p[1] * f3[2][1] + p[2] * f3[2][2]) / (p[0] * f3[0][0] + p[1] * f3[0][1] + p[2] * f3[0][2]); } return r; } // x[0]: ref frequency // x[1..3]: alt-alt, alt-ref, ref-ref frequenc // x[4]: HWE P-value // x[5..6]: group1 freq, group2 freq // x[7]: 1-degree P-value // x[8]: 2-degree P-value int bcf_em1(call_t *call, const bcf1_t *rec, int n1, int flag, double x[10]) { double *pdg; int i, n; //, n2; if (rec->n_allele < 2) return -1; // one allele only // initialization if (n1 < 0 || n1 > rec->n_sample) n1 = 0; if (flag & 1<<7) flag |= 7<<5; // compute group freq if LRT is required if (flag & 0xf<<1) flag |= 0xf<<1; n = rec->n_sample; //n2 = n - n1; pdg = call->pdg; if (pdg == 0) return -1; for (i = 0; i < 10; ++i) x[i] = -1.; // set to negative { if ((x[0] = est_freq(n, pdg)) < 0.) return -1; // no data x[0] = freqml(x[0], 0, n, pdg); } if (flag & (0xf<<1|3<<8)) { // estimate the genotype frequency and test HWE double *g = x + 1, f3[3], r; f3[0] = g[0] = (1 - x[0]) * (1 - x[0]); f3[1] = g[1] = 2 * x[0] * (1 - x[0]); f3[2] = g[2] = x[0] * x[0]; for (i = 0; i < ITER_MAX; ++i) if (g3_iter(g, pdg, 0, n) < EPS) break; // Hardy-Weinberg equilibrium (HWE) for (i = 0, r = 1.; i < n; ++i) { double *p = pdg + i * 3; r *= (p[0] * g[0] + p[1] * g[1] + p[2] * g[2]) / (p[0] * f3[0] + p[1] * f3[1] + p[2] * f3[2]); } x[4] = kf_gammaq(.5, log(r)); } if ((flag & 7<<5) && n1 > 0 && n1 < n) { // group frequency x[5] = freqml(x[0], 0, n1, pdg); x[6] = freqml(x[0], n1, n, pdg); } if ((flag & 1<<7) && n1 > 0 && n1 < n) { // 1-degree P-value double f[3], f3[3][3], tmp; f[0] = x[0]; f[1] = x[5]; f[2] = x[6]; for (i = 0; i < 3; ++i) f3[i][0] = (1-f[i])*(1-f[i]), f3[i][1] = 2*f[i]*(1-f[i]), f3[i][2] = f[i]*f[i]; tmp = log(lk_ratio_test(n, n1, pdg, f3)); if (tmp < 0) tmp = 0; x[7] = kf_gammaq(.5, tmp); } if ((flag & 3<<8) && n1 > 0 && n1 < n) { // 2-degree P-value double g[3][3], tmp; for (i = 0; i < 3; ++i) memcpy(g[i], x + 1, 3 * sizeof(double)); for (i = 0; i < ITER_MAX; ++i) if (g3_iter(g[1], pdg, 0, n1) < EPS) break; for (i = 0; i < ITER_MAX; ++i) if (g3_iter(g[2], pdg, n1, n) < EPS) break; tmp = log(lk_ratio_test(n, n1, pdg, g)); if (tmp < 0) tmp = 0; x[8] = kf_gammaq(1., tmp); } return 0; } /* Two-locus EM (LD) */ #define _G1(h, k) ((h>>1&1) + (k>>1&1)) #define _G2(h, k) ((h&1) + (k&1)) #if 0 // 0: the previous site; 1: the current site static int pair_freq_iter(int n, double *pdg[2], double f[4]) { double ff[4]; int i, k, h; // fprintf(bcftools_stdout, "%lf,%lf,%lf,%lf\n", f[0], f[1], f[2], f[3]); memset(ff, 0, 4 * sizeof(double)); for (i = 0; i < n; ++i) { double *p[2], sum, tmp; p[0] = pdg[0] + i * 3; p[1] = pdg[1] + i * 3; for (k = 0, sum = 0.; k < 4; ++k) for (h = 0; h < 4; ++h) sum += f[k] * f[h] * p[0][_G1(k,h)] * p[1][_G2(k,h)]; for (k = 0; k < 4; ++k) { tmp = f[0] * (p[0][_G1(0,k)] * p[1][_G2(0,k)] + p[0][_G1(k,0)] * p[1][_G2(k,0)]) + f[1] * (p[0][_G1(1,k)] * p[1][_G2(1,k)] + p[0][_G1(k,1)] * p[1][_G2(k,1)]) + f[2] * (p[0][_G1(2,k)] * p[1][_G2(2,k)] + p[0][_G1(k,2)] * p[1][_G2(k,2)]) + f[3] * (p[0][_G1(3,k)] * p[1][_G2(3,k)] + p[0][_G1(k,3)] * p[1][_G2(k,3)]); ff[k] += f[k] * tmp / sum; } } for (k = 0; k < 4; ++k) f[k] = ff[k] / (2 * n); return 0; } #endif pysam-0.23.0/bcftools/extsort.c000066400000000000000000000174111475062545500164350ustar00rootroot00000000000000/* ext-sort.h -- sort on disk Copyright (C) 2020-2021 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include // for unlink() #include // for chmod() #include #include #ifdef _WIN32 #include #endif #include "bcftools.h" #include "extsort.h" #include "kheap.h" typedef struct { extsort_t *es; // this is to get access to extsort_cmp_f from kheap int fd; char *fname; void *dat; } blk_t; static inline int blk_is_smaller(blk_t **aptr, blk_t **bptr); KHEAP_INIT(blk, blk_t*, blk_is_smaller) /* defines khp_blk_t */ struct _extsort_t { size_t dat_size, mem, max_mem; char *tmp_prefix; extsort_cmp_f cmp; size_t nbuf, mbuf, nblk; blk_t **blk; void **buf, *tmp_dat; khp_blk_t *bhp; }; static inline int blk_is_smaller(blk_t **aptr, blk_t **bptr) { blk_t *a = *aptr; blk_t *b = *bptr; int ret = a->es->cmp(&a->dat,&b->dat); if ( ret < 0 ) return 1; return 0; } size_t parse_mem_string(const char *str); void extsort_set(extsort_t *es, extsort_opt_t key, void *value) { if ( key==DAT_SIZE ) { es->dat_size = *((size_t*)value); return; } if ( key==MAX_MEM ) { es->max_mem = parse_mem_string(*((const char**)value)); if ( es->max_mem <=0 ) error("Could not parse the memory string, expected positive number: %s\n",*((const char**)value)); return; } if ( key==TMP_PREFIX ) { es->tmp_prefix = init_tmp_prefix(*((const char**)value)); return; } if ( key==FUNC_CMP ) { es->cmp = *((extsort_cmp_f*)value); return; } } extsort_t *extsort_alloc(void) { extsort_t *es = (extsort_t*) calloc(1,sizeof(*es)); es->max_mem = 100e6; return es; } void extsort_init(extsort_t *es) { assert( es->cmp ); assert( es->dat_size ); if ( !es->tmp_prefix ) es->tmp_prefix = init_tmp_prefix(NULL); es->tmp_dat = malloc(es->dat_size); } void extsort_destroy(extsort_t *es) { int i; for (i=0; inblk; i++) { blk_t *blk = es->blk[i]; if ( blk->fd!=-1 ) #ifdef _WIN32 _close(blk->fd); #else close(blk->fd); #endif free(blk->fname); free(blk->dat); free(blk); } free(es->tmp_dat); free(es->tmp_prefix); free(es->blk); khp_destroy(blk, es->bhp); free(es); } static void _buf_flush(extsort_t *es) { int i; if ( !es->nbuf ) return; qsort(es->buf, es->nbuf, sizeof(void*), es->cmp); es->nblk++; es->blk = (blk_t**) realloc(es->blk, sizeof(blk_t*)*es->nblk); es->blk[es->nblk-1] = (blk_t*) calloc(1,sizeof(blk_t)); blk_t *blk = es->blk[es->nblk-1]; blk->es = es; blk->dat = malloc(es->dat_size); blk->fname = strdup(es->tmp_prefix); #ifdef _WIN32 for (i=0; i<100000; i++) { memcpy(blk->fname,es->tmp_prefix,strlen(es->tmp_prefix)); mktemp(blk->fname); blk->fd = _open(blk->fname, O_RDWR|O_CREAT|O_EXCL|O_BINARY|O_TEMPORARY, 0600); if ( blk->fd==-1 ) { if ( errno==EEXIST ) continue; error("Error: failed to open a temporary file %s\n",blk->fname); } break; } if ( !blk->fd ) error("Error: failed to create a unique temporary file name from %s\n",es->tmp_prefix); if ( _chmod(blk->fname, S_IRUSR|S_IWUSR)!=0 ) error("Error: failed to set permissions of the temporary file %s\n",blk->fname); #else if ( (blk->fd = mkstemp(blk->fname))==-1 ) error("Error: failed to open a temporary file %s\n",blk->fname); if ( fchmod(blk->fd,S_IRUSR|S_IWUSR)!=0 ) error("Error: failed to set permissions of the temporary file %s\n",blk->fname); unlink(blk->fname); // should auto delete when closed on linux, the descriptor remains open #endif for (i=0; inbuf; i++) { #ifdef _WIN32 if ( _write(blk->fd, es->buf[i], es->dat_size)!=es->dat_size ) error("Error: failed to write %zu bytes to the temporary file %s\n",es->dat_size,blk->fname); #else if ( write(blk->fd, es->buf[i], es->dat_size)!=es->dat_size ) error("Error: failed to write %zu bytes to the temporary file %s\n",es->dat_size,blk->fname); #endif free(es->buf[i]); } #ifdef _WIN32 if ( _lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname); #else if ( lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname); #endif es->nbuf = 0; es->mem = 0; } void extsort_push(extsort_t *es, void *dat) { int delta = sizeof(void*) + es->dat_size; if ( es->nbuf && es->mem + delta > es->max_mem ) _buf_flush(es); es->nbuf++; es->mem += delta; hts_expand(void*, es->nbuf, es->mbuf, es->buf); es->buf[es->nbuf-1] = dat; } // return number of elements read static ssize_t _blk_read(extsort_t *es, blk_t *blk) { ssize_t ret = 0; if ( blk->fd==-1 ) return ret; #ifdef _WIN32 ret = _read(blk->fd, blk->dat, es->dat_size); #else ret = read(blk->fd, blk->dat, es->dat_size); #endif if ( ret < 0 ) error("Error: failed to read from the temporary file %s\n", blk->fname); if ( ret == 0 ) { #ifdef _WIN32 if ( _close(blk->fd)!=0 ) error("Error: failed to close the temporary file %s\n", blk->fname); #else if ( close(blk->fd)!=0 ) error("Error: failed to close the temporary file %s\n", blk->fname); #endif blk->fd = -1; return ret; } if ( ret < es->dat_size ) error("Error: failed to read %zu bytes from the temporary file %s\n",es->dat_size,blk->fname); return ret; } void extsort_sort(extsort_t *es) { _buf_flush(es); free(es->buf); es->buf = NULL; es->bhp = khp_init(blk); // open all blocks, read one record from each, create a heap int i; for (i=0; inblk; i++) { blk_t *blk = es->blk[i]; #ifdef _WIN32 if ( _lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname); #else if ( lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname); #endif int ret = _blk_read(es, blk); if ( ret ) khp_insert(blk, es->bhp, &blk); } } void *extsort_shift(extsort_t *es) { if ( !es->bhp->ndat ) return NULL; blk_t *blk = es->bhp->dat[0]; // swap the pointer which keeps the location of user data so that it is not overwritten by the next read void *tmp = es->tmp_dat; es->tmp_dat = blk->dat; blk->dat = tmp; khp_delete(blk, es->bhp); int ret = _blk_read(es, blk); if ( ret ) khp_insert(blk, es->bhp, &blk); return es->tmp_dat; } pysam-0.23.0/bcftools/extsort.c.pysam.c000066400000000000000000000174461475062545500200160ustar00rootroot00000000000000#include "bcftools.pysam.h" /* ext-sort.h -- sort on disk Copyright (C) 2020-2021 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include // for unlink() #include // for chmod() #include #include #ifdef _WIN32 #include #endif #include "bcftools.h" #include "extsort.h" #include "kheap.h" typedef struct { extsort_t *es; // this is to get access to extsort_cmp_f from kheap int fd; char *fname; void *dat; } blk_t; static inline int blk_is_smaller(blk_t **aptr, blk_t **bptr); KHEAP_INIT(blk, blk_t*, blk_is_smaller) /* defines khp_blk_t */ struct _extsort_t { size_t dat_size, mem, max_mem; char *tmp_prefix; extsort_cmp_f cmp; size_t nbuf, mbuf, nblk; blk_t **blk; void **buf, *tmp_dat; khp_blk_t *bhp; }; static inline int blk_is_smaller(blk_t **aptr, blk_t **bptr) { blk_t *a = *aptr; blk_t *b = *bptr; int ret = a->es->cmp(&a->dat,&b->dat); if ( ret < 0 ) return 1; return 0; } size_t parse_mem_string(const char *str); void extsort_set(extsort_t *es, extsort_opt_t key, void *value) { if ( key==DAT_SIZE ) { es->dat_size = *((size_t*)value); return; } if ( key==MAX_MEM ) { es->max_mem = parse_mem_string(*((const char**)value)); if ( es->max_mem <=0 ) error("Could not parse the memory string, expected positive number: %s\n",*((const char**)value)); return; } if ( key==TMP_PREFIX ) { es->tmp_prefix = init_tmp_prefix(*((const char**)value)); return; } if ( key==FUNC_CMP ) { es->cmp = *((extsort_cmp_f*)value); return; } } extsort_t *extsort_alloc(void) { extsort_t *es = (extsort_t*) calloc(1,sizeof(*es)); es->max_mem = 100e6; return es; } void extsort_init(extsort_t *es) { assert( es->cmp ); assert( es->dat_size ); if ( !es->tmp_prefix ) es->tmp_prefix = init_tmp_prefix(NULL); es->tmp_dat = malloc(es->dat_size); } void extsort_destroy(extsort_t *es) { int i; for (i=0; inblk; i++) { blk_t *blk = es->blk[i]; if ( blk->fd!=-1 ) #ifdef _WIN32 _close(blk->fd); #else close(blk->fd); #endif free(blk->fname); free(blk->dat); free(blk); } free(es->tmp_dat); free(es->tmp_prefix); free(es->blk); khp_destroy(blk, es->bhp); free(es); } static void _buf_flush(extsort_t *es) { int i; if ( !es->nbuf ) return; qsort(es->buf, es->nbuf, sizeof(void*), es->cmp); es->nblk++; es->blk = (blk_t**) realloc(es->blk, sizeof(blk_t*)*es->nblk); es->blk[es->nblk-1] = (blk_t*) calloc(1,sizeof(blk_t)); blk_t *blk = es->blk[es->nblk-1]; blk->es = es; blk->dat = malloc(es->dat_size); blk->fname = strdup(es->tmp_prefix); #ifdef _WIN32 for (i=0; i<100000; i++) { memcpy(blk->fname,es->tmp_prefix,strlen(es->tmp_prefix)); mktemp(blk->fname); blk->fd = _open(blk->fname, O_RDWR|O_CREAT|O_EXCL|O_BINARY|O_TEMPORARY, 0600); if ( blk->fd==-1 ) { if ( errno==EEXIST ) continue; error("Error: failed to open a temporary file %s\n",blk->fname); } break; } if ( !blk->fd ) error("Error: failed to create a unique temporary file name from %s\n",es->tmp_prefix); if ( _chmod(blk->fname, S_IRUSR|S_IWUSR)!=0 ) error("Error: failed to set permissions of the temporary file %s\n",blk->fname); #else if ( (blk->fd = mkstemp(blk->fname))==-1 ) error("Error: failed to open a temporary file %s\n",blk->fname); if ( fchmod(blk->fd,S_IRUSR|S_IWUSR)!=0 ) error("Error: failed to set permissions of the temporary file %s\n",blk->fname); unlink(blk->fname); // should auto delete when closed on linux, the descriptor remains open #endif for (i=0; inbuf; i++) { #ifdef _WIN32 if ( _write(blk->fd, es->buf[i], es->dat_size)!=es->dat_size ) error("Error: failed to write %zu bytes to the temporary file %s\n",es->dat_size,blk->fname); #else if ( write(blk->fd, es->buf[i], es->dat_size)!=es->dat_size ) error("Error: failed to write %zu bytes to the temporary file %s\n",es->dat_size,blk->fname); #endif free(es->buf[i]); } #ifdef _WIN32 if ( _lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname); #else if ( lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname); #endif es->nbuf = 0; es->mem = 0; } void extsort_push(extsort_t *es, void *dat) { int delta = sizeof(void*) + es->dat_size; if ( es->nbuf && es->mem + delta > es->max_mem ) _buf_flush(es); es->nbuf++; es->mem += delta; hts_expand(void*, es->nbuf, es->mbuf, es->buf); es->buf[es->nbuf-1] = dat; } // return number of elements read static ssize_t _blk_read(extsort_t *es, blk_t *blk) { ssize_t ret = 0; if ( blk->fd==-1 ) return ret; #ifdef _WIN32 ret = _read(blk->fd, blk->dat, es->dat_size); #else ret = read(blk->fd, blk->dat, es->dat_size); #endif if ( ret < 0 ) error("Error: failed to read from the temporary file %s\n", blk->fname); if ( ret == 0 ) { #ifdef _WIN32 if ( _close(blk->fd)!=0 ) error("Error: failed to close the temporary file %s\n", blk->fname); #else if ( close(blk->fd)!=0 ) error("Error: failed to close the temporary file %s\n", blk->fname); #endif blk->fd = -1; return ret; } if ( ret < es->dat_size ) error("Error: failed to read %zu bytes from the temporary file %s\n",es->dat_size,blk->fname); return ret; } void extsort_sort(extsort_t *es) { _buf_flush(es); free(es->buf); es->buf = NULL; es->bhp = khp_init(blk); // open all blocks, read one record from each, create a heap int i; for (i=0; inblk; i++) { blk_t *blk = es->blk[i]; #ifdef _WIN32 if ( _lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname); #else if ( lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname); #endif int ret = _blk_read(es, blk); if ( ret ) khp_insert(blk, es->bhp, &blk); } } void *extsort_shift(extsort_t *es) { if ( !es->bhp->ndat ) return NULL; blk_t *blk = es->bhp->dat[0]; // swap the pointer which keeps the location of user data so that it is not overwritten by the next read void *tmp = es->tmp_dat; es->tmp_dat = blk->dat; blk->dat = tmp; khp_delete(blk, es->bhp); int ret = _blk_read(es, blk); if ( ret ) khp_insert(blk, es->bhp, &blk); return es->tmp_dat; } pysam-0.23.0/bcftools/extsort.h000066400000000000000000000042041475062545500164360ustar00rootroot00000000000000/* ext-sort.h -- sort on disk Copyright (C) 2020 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef __EXTSORT_H__ #define __EXTSORT_H__ //todo: return status to all functions typedef struct _extsort_t extsort_t; typedef int (*extsort_cmp_f) (const void *aptr, const void *bptr); // Modes of operation typedef enum { DAT_SIZE, // size_t .. assuming constant size records for now TMP_PREFIX, // const char* .. prefix of temporary files, XXXXXX will be appended MAX_MEM, // const char* .. maximum memory to use, e.g. 100MB FUNC_CMP, // extsort_cmp_f .. sort function } extsort_opt_t; #define extsort_set_opt(es,type,key,value) { type tmp = value; extsort_set(es, key, (void*)&tmp); } extsort_t *extsort_alloc(void); void extsort_set(extsort_t *es, extsort_opt_t key, void *value); void extsort_init(extsort_t *es); void extsort_push(extsort_t *es, void *dat); // dat will be freed by extsort later void extsort_sort(extsort_t *es); void *extsort_shift(extsort_t *es); void extsort_destroy(extsort_t *es); #endif pysam-0.23.0/bcftools/filter.c000066400000000000000000004624171475062545500162240ustar00rootroot00000000000000/* filter.c -- filter expressions. Copyright (C) 2013-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #ifndef _WIN32 #include #endif #include #include #include #include #include #include #include "config.h" #include "filter.h" #include "bcftools.h" #if ENABLE_PERL_FILTERS // Work around clang warning problems # if defined(__clang__) # define PERL_GCC_BRACE_GROUPS_FORBIDDEN # endif # define filter_t perl_filter_t # include # include # undef filter_t # define my_perl perl static int filter_ninit = 0; #endif #ifndef __FUNCTION__ # define __FUNCTION__ __func__ #endif typedef struct _token_t { // read-only values, same for all VCF lines int tok_type; // one of the TOK_* keys below int nargs; // with TOK_PERLSUB the first argument is the name of the subroutine char *key; // set only for string constants, otherwise NULL char *tag; // for debugging and printout only, VCF tag name double threshold; // filtering threshold int is_constant; // the threshold is set int hdr_id, hl_type, ht_type; // BCF header lookup ID and one of BCF_HL_* types and BCF_HT_* types int idx; // 0-based index to VCF vectors, // -2: list (e.g. [0,1,2] or [1..3] or [1..] or any field[*], which is equivalent to [0..]) // -3: select indices on the fly based on values in GT int *idxs; // set indexes to 0 to exclude, to 1 to include, and last element negative if unlimited; used by VCF retrievers only int nidxs, nuidxs; // size of idxs array and the number of elements set to 1 uint8_t *usmpl; // bitmask of used samples as set by idx, set for FORMAT fields, NULL otherwise int nsamples; // number of samples for format fields, 0 for info and other fields void (*setter)(filter_t *, bcf1_t *, struct _token_t *); int (*func)(filter_t *, bcf1_t *, struct _token_t *rtok, struct _token_t **stack, int nstack); void (*comparator)(struct _token_t *, struct _token_t *, struct _token_t *rtok, bcf1_t *); void *hash; // test presence of str value in the hash via comparator regex_t *regex; // precompiled regex for string comparison int iext; // for the use with filter_test_ext(), 1-based index to external values, 0=don't use // modified on filter evaluation at each VCF line double *values; kstring_t str_value; int is_str, is_missing; // is_missing is set only for constants, variables are controlled via nvalues int pass_site; // -1 not applicable, 0 fails, >0 pass uint8_t *pass_samples; // status of individual samples int nvalues, mvalues; // number of used values: n=0 for missing values, n=1 for scalars, for strings n=str_value.l int nval1; // number of per-sample fields or string length } token_t; struct _filter_t { bcf_hdr_t *hdr; char *str; int nfilters; token_t *filters, **flt_stack; // filtering input tokens (in RPN) and evaluation stack int32_t *tmpi; float *tmpf; kstring_t tmps; int max_unpack, mtmpi, mtmpf, nsamples; struct { bcf1_t *line; int32_t *buf, nbuf, mbuf; // GTs as obtained by bcf_get_genotypes() uint64_t *mask; // GTs as mask, e.g 0/0 is 1; 0/1 is 3, max 63 unique alleles } cached_GT; #if ENABLE_PERL_FILTERS PerlInterpreter *perl; #endif char **undef_tag, **used_tag; int nundef_tag, nused_tag; int status, exit_on_error; int n_ext; // number of external values to fill via filter_test_ext() int *ext; // types of external values to fill via filter_test_ext() }; #define TOK_VAL 0 #define TOK_LFT 1 // ( #define TOK_RGT 2 // ) #define TOK_LE 3 // less or equal #define TOK_LT 4 // less than #define TOK_EQ 5 // equal #define TOK_BT 6 // bigger than #define TOK_BE 7 // bigger or equal #define TOK_NE 8 // not equal #define TOK_OR 9 // | #define TOK_AND 10 // & #define TOK_ADD 11 // + #define TOK_SUB 12 // - #define TOK_MULT 13 // * #define TOK_DIV 14 // / #define TOK_MAX 15 #define TOK_MIN 16 #define TOK_AVG 17 #define TOK_AND_VEC 18 // && (operator applied in samples) #define TOK_OR_VEC 19 // || (operator applied in samples) #define TOK_LIKE 20 // ~ regular expression #define TOK_NLIKE 21 // !~ regular expression #define TOK_SUM 22 #define TOK_ABS 23 #define TOK_LEN 24 #define TOK_FUNC 25 #define TOK_CNT 26 #define TOK_PERLSUB 27 #define TOK_BINOM 28 #define TOK_PHRED 29 #define TOK_MEDIAN 30 #define TOK_STDEV 31 #define TOK_sMAX 32 #define TOK_sMIN 33 #define TOK_sAVG 34 #define TOK_sMEDIAN 35 #define TOK_sSTDEV 36 #define TOK_sSUM 37 #define TOK_IN 38 // contains, e.g. FILTER~"A" #define TOK_NOT_IN 39 // does not contain, e.g. FILTER!~"A" #define TOK_MODULO 40 // % #define TOK_EXT 41 // external values set before each filter_test_ext() call, can be one of {},{str},{int},{float} // 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 // ( ) [ < = > ] ! | & + - * / M m a A O ~ ^ S . l f c p b P i s % static int op_prec[] = {0,1,1,5,5,5,5,5,5,2,3, 6, 6, 7, 7, 8, 8, 8, 3, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 0}; #define TOKEN_STRING "x()[<=>]!|&+-*/MmaAO~^S.lfcpis" // this is only for debugging, not maintained diligently static void cmp_vector_strings(token_t *atok, token_t *btok, token_t *rtok); inline static void tok_init_samples(token_t *atok, token_t *btok, token_t *rtok); // Return negative values if it is a function with variable number of arguments static int filters_next_token(char **str, int *len) { char *tmp = *str; while ( *tmp && isspace(*tmp) ) tmp++; *str = tmp; *len = 0; // test for doubles: d.ddde[+-]dd if ( isdigit(*str[0]) || *str[0]=='.' ) // strtod would eat +/- { double HTS_UNUSED v = strtod(*str, &tmp); if ( *str!=tmp && (!tmp[0] || !isalnum(tmp[0])) ) { *len = tmp - (*str); return TOK_VAL; } tmp = *str; } if ( !strncasecmp(tmp,"SMPL_MAX(",9) ) { (*str) += 8; return TOK_sMAX; } if ( !strncasecmp(tmp,"SMPL_MIN(",9) ) { (*str) += 8; return TOK_sMIN; } if ( !strncasecmp(tmp,"SMPL_MEAN(",10) ) { (*str) += 9; return TOK_sAVG; } if ( !strncasecmp(tmp,"SMPL_MEDIAN(",12) ) { (*str) += 11; return TOK_sMEDIAN; } if ( !strncasecmp(tmp,"SMPL_AVG(",9) ) { (*str) += 8; return TOK_sAVG; } if ( !strncasecmp(tmp,"SMPL_STDEV(",11) ) { (*str) += 10; return TOK_sSTDEV; } if ( !strncasecmp(tmp,"SMPL_SUM(",9) ) { (*str) += 8; return TOK_sSUM; } if ( !strncasecmp(tmp,"sMAX(",5) ) { (*str) += 4; return TOK_sMAX; } if ( !strncasecmp(tmp,"sMIN(",5) ) { (*str) += 4; return TOK_sMIN; } if ( !strncasecmp(tmp,"sMEAN(",6) ) { (*str) += 5; return TOK_sAVG; } if ( !strncasecmp(tmp,"sMEDIAN(",8) ) { (*str) += 7; return TOK_sMEDIAN; } if ( !strncasecmp(tmp,"sAVG(",5) ) { (*str) += 4; return TOK_sAVG; } if ( !strncasecmp(tmp,"sSTDEV(",7) ) { (*str) += 6; return TOK_sSTDEV; } if ( !strncasecmp(tmp,"sSUM(",5) ) { (*str) += 4; return TOK_sSUM; } if ( !strncasecmp(tmp,"MAX(",4) ) { (*str) += 3; return TOK_MAX; } if ( !strncasecmp(tmp,"MIN(",4) ) { (*str) += 3; return TOK_MIN; } if ( !strncasecmp(tmp,"MEAN(",5) ) { (*str) += 4; return TOK_AVG; } if ( !strncasecmp(tmp,"MEDIAN(",7) ) { (*str) += 6; return TOK_MEDIAN; } if ( !strncasecmp(tmp,"AVG(",4) ) { (*str) += 3; return TOK_AVG; } if ( !strncasecmp(tmp,"STDEV(",6) ) { (*str) += 5; return TOK_STDEV; } if ( !strncasecmp(tmp,"SUM(",4) ) { (*str) += 3; return TOK_SUM; } if ( !strncasecmp(tmp,"ABS(",4) ) { (*str) += 3; return TOK_ABS; } if ( !strncasecmp(tmp,"COUNT(",4) ) { (*str) += 5; return TOK_CNT; } if ( !strncasecmp(tmp,"STRLEN(",7) ) { (*str) += 6; return TOK_LEN; } if ( !strncasecmp(tmp,"BINOM(",6) ) { (*str) += 5; return -TOK_BINOM; } if ( !strncasecmp(tmp,"PHRED(",6) ) { (*str) += 5; return TOK_PHRED; } if ( !strncasecmp(tmp,"%MAX(",5) ) { (*str) += 4; return TOK_MAX; } // for backward compatibility if ( !strncasecmp(tmp,"%MIN(",5) ) { (*str) += 4; return TOK_MIN; } // for backward compatibility if ( !strncasecmp(tmp,"%AVG(",5) ) { (*str) += 4; return TOK_AVG; } // for backward compatibility if ( !strncasecmp(tmp,"%SUM(",5) ) { (*str) += 4; return TOK_SUM; } // for backward compatibility if ( !strncasecmp(tmp,"INFO/",5) ) tmp += 5; if ( !strncasecmp(tmp,"FORMAT/",7) ) tmp += 7; if ( !strncasecmp(tmp,"FMT/",4) ) tmp += 4; if ( !strncasecmp(tmp,"PERL.",5) ) { (*str) += 5; return -TOK_PERLSUB; } if ( !strncasecmp(tmp,"N_PASS(",7) ) { *len = 6; (*str) += 6; return -TOK_FUNC; } if ( !strncasecmp(tmp,"F_PASS(",7) ) { *len = 6; (*str) += 6; return -TOK_FUNC; } if ( !strncasecmp(tmp,"%ILEN",5) ) { *len = 5; return TOK_VAL; } // to be able to distinguish between INFO/ILEN and on-the-fly ILEN if ( !strncasecmp(tmp,"{}",2) ) { *len = 2; return TOK_EXT; } if ( !strncasecmp(tmp,"{STR}",5) ) { *len = 5; return TOK_EXT; } if ( !strncasecmp(tmp,"{INT}",5) ) { *len = 5; return TOK_EXT; } if ( !strncasecmp(tmp,"{FLOAT}",7) ) { *len = 7; return TOK_EXT; } if ( tmp[0]=='@' ) // file name { while ( *tmp && !isspace(*tmp) && *tmp!='=' && *tmp!='!' ) tmp++; *len = tmp - (*str); return TOK_VAL; } int square_brackets = 0; while ( tmp[0] ) { if ( !square_brackets ) { if ( tmp[0]=='"' ) break; if ( tmp[0]=='\'' ) break; if ( isspace(tmp[0]) ) break; if ( tmp[0]=='<' ) break; if ( tmp[0]=='>' ) break; if ( tmp[0]=='=' ) break; if ( tmp[0]=='!' ) break; if ( tmp[0]=='&' ) break; if ( tmp[0]=='|' ) break; if ( tmp[0]=='(' ) break; if ( tmp[0]==')' ) break; if ( tmp[0]=='+' ) break; if ( tmp[0]=='*' ) break; if ( tmp[0]=='-' ) break; if ( tmp[0]=='/' ) break; if ( tmp[0]=='~' ) break; if ( tmp[0]=='%' ) break; } if ( tmp[0]==']' ) { if (square_brackets) tmp++; break; } if ( tmp[0]=='[' ) square_brackets++; tmp++; } if ( tmp > *str ) { *len = tmp - (*str); return TOK_VAL; } if ( tmp[0]=='"' || tmp[0]=='\'' ) { int quote = tmp[0]; tmp++; while ( *tmp && tmp[0]!=quote ) tmp++; if ( !*tmp ) return -1; // missing quotes *len = tmp - (*str) + 1; return TOK_VAL; } if ( tmp[0]=='!' ) { if ( tmp[1]=='=' ) { (*str) += 2; return TOK_NE; } if ( tmp[1]=='~' ) { (*str) += 2; return TOK_NLIKE; } } if ( tmp[0]=='<' ) { if ( tmp[1]=='=' ) { (*str) += 2; return TOK_LE; } (*str) += 1; return TOK_LT; } if ( tmp[0]=='>' ) { if ( tmp[1]=='=' ) { (*str) += 2; return TOK_BE; } (*str) += 1; return TOK_BT; } if ( tmp[0]=='=' ) { if ( tmp[1]=='=' ) { (*str) += 2; return TOK_EQ; } (*str) += 1; return TOK_EQ; } if ( tmp[0]=='(' ) { (*str) += 1; return TOK_LFT; } if ( tmp[0]==')' ) { (*str) += 1; return TOK_RGT; } if ( tmp[0]=='&' && tmp[1]=='&' ) { (*str) += 2; return TOK_AND_VEC; } if ( tmp[0]=='|' && tmp[1]=='|' ) { (*str) += 2; return TOK_OR_VEC; } if ( tmp[0]=='&' ) { (*str) += 1; return TOK_AND; } if ( tmp[0]=='|' ) { (*str) += 1; return TOK_OR; } if ( tmp[0]=='+' ) { (*str) += 1; return TOK_ADD; } if ( tmp[0]=='-' ) { (*str) += 1; return TOK_SUB; } if ( tmp[0]=='*' ) { (*str) += 1; return TOK_MULT; } if ( tmp[0]=='/' ) { (*str) += 1; return TOK_DIV; } if ( tmp[0]=='~' ) { (*str) += 1; return TOK_LIKE; } if ( tmp[0]=='%' ) { (*str) += 1; return TOK_MODULO; } *len = tmp - (*str); return TOK_VAL; } #define FILTER_OK 0 #define FILTER_ERR_UNKN_TAGS 1 #define FILTER_ERR_OTHER 2 static void filter_add_undef_tag(filter_t *filter, char *str) { int i; for (i=0; inundef_tag; i++) if ( !strcmp(str,filter->undef_tag[i]) ) break; if ( inundef_tag ) return; filter->nundef_tag++; filter->undef_tag = (char**)realloc(filter->undef_tag,sizeof(*filter->undef_tag)*filter->nundef_tag); if ( !filter->undef_tag ) error("Could not allocate memory\n"); filter->undef_tag[filter->nundef_tag-1] = strdup(str); if ( !filter->undef_tag[filter->nundef_tag-1] ) error("Could not allocate memory\n"); } const char **filter_list_undef_tags(filter_t *filter, int *ntags) { *ntags = filter->nundef_tag; return (const char**)filter->undef_tag; } static void filter_add_used_tag(filter_t *filter, const char *prefix, char *str) { int i; kstring_t tmp = {0,0,0}; if ( prefix ) kputs(prefix,&tmp); kputs(str,&tmp); for (i=0; inused_tag; i++) if ( !strcmp(tmp.s,filter->used_tag[i]) ) break; if ( inused_tag ) { free(tmp.s); return; } filter->nused_tag++; filter->used_tag = (char**)realloc(filter->used_tag,sizeof(*filter->used_tag)*filter->nused_tag); if ( !filter->used_tag ) error("Could not allocate memory\n"); filter->used_tag[filter->nused_tag-1] = tmp.s; if ( !filter->used_tag[filter->nused_tag-1] ) error("Could not allocate memory\n"); } const char **filter_list_used_tags(filter_t *filter, int *ntags) { *ntags = filter->nused_tag; return (const char**)filter->used_tag; } /* Simple path expansion, expands ~/, ~user, $var. The result must be freed by the caller. Based on jkb's staden code with some adjustments. https://sourceforge.net/p/staden/code/HEAD/tree/staden/trunk/src/Misc/getfile.c#l123 */ char *expand_path(char *path) { kstring_t str = {0,0,0}; if ( path[0] == '~' ) { if ( !path[1] || path[1] == '/' ) { #ifdef _WIN32 kputs(getenv("HOMEDRIVE"), &str); kputs(getenv("HOMEPATH"), &str); #else // ~ or ~/path kputs(getenv("HOME"), &str); if ( path[1] ) kputs(path+1, &str); #endif } #ifndef _WIN32 else { // user name: ~pd3/path char *end = path; while ( *end && *end!='/' ) end++; kputsn(path+1, end-path-1, &str); struct passwd *pwentry = getpwnam(str.s); str.l = 0; if ( !pwentry ) kputsn(path, end-path, &str); else kputs(pwentry->pw_dir, &str); kputs(end, &str); } #endif return ks_release(&str); } if ( path[0] == '$' ) { char *var = getenv(path+1); if ( var ) { kputs(var, &str); return ks_release(&str); } } return strdup(path); } static int filters_cache_genotypes(filter_t *flt, bcf1_t *line) { if ( flt->cached_GT.line==line ) return flt->cached_GT.nbuf > 0 ? 0 : -1; flt->cached_GT.line = line; flt->cached_GT.nbuf = bcf_get_genotypes(flt->hdr, line, &flt->cached_GT.buf, &flt->cached_GT.mbuf); if ( flt->cached_GT.nbuf<=0 ) return -1; if ( !flt->cached_GT.mask ) { flt->cached_GT.mask = (uint64_t*) malloc(sizeof(*flt->cached_GT.mask)*flt->nsamples); if ( !flt->cached_GT.mask ) error("Could not alloc %zu bytes\n",sizeof(*flt->cached_GT.mask)*flt->nsamples); } int i,j, ngt1 = flt->cached_GT.nbuf / line->n_sample; for (i=0; in_sample; i++) { int32_t *ptr = flt->cached_GT.buf + i*ngt1; flt->cached_GT.mask[i] = 0; for (j=0; j 63 ) { static int warned = 0; if ( !warned ) { fprintf(stderr,"Too many alleles, skipping GT filtering at this site %s:%"PRId64". " "(This warning is printed only once.)\n", bcf_seqname(flt->hdr,line),line->pos+1); warned = 1; } flt->cached_GT.nbuf = 0; return -1; } flt->cached_GT.mask[i] |= 1<qual; if ( bcf_float_is_missing(*ptr) ) bcf_double_set_missing(tok->values[0]); else tok->values[0] = (double)line->qual; tok->nvalues = 1; } static void filters_set_type(filter_t *flt, bcf1_t *line, token_t *tok) { tok->values[0] = bcf_get_variant_types(line); if ( !tok->values[0] ) tok->values[0] = 1; // mistake in htslib: VCF_* should start with 1 else tok->values[0] = ((int)tok->values[0]) << 1; tok->nvalues = 1; } static void filters_set_info(filter_t *flt, bcf1_t *line, token_t *tok) { assert( tok->hdr_id >=0 ); int i; for (i=0; in_info; i++) if ( line->d.info[i].key == tok->hdr_id ) break; if ( i==line->n_info ) tok->nvalues = tok->str_value.l = 0; else if ( line->d.info[i].type==BCF_BT_CHAR ) { int n = line->d.info[i].len; if ( n >= tok->str_value.m ) { tok->str_value.m = n + 1; tok->str_value.s = (char*) realloc(tok->str_value.s, tok->str_value.m); if ( !tok->str_value.s ) error("Failed to alloc %d bytes\n", (int)tok->str_value.m); } memcpy(tok->str_value.s, line->d.info[i].vptr, n); tok->str_value.s[n] = 0; tok->nvalues = tok->str_value.l = n; } else if ( line->d.info[i].type==BCF_BT_FLOAT ) { if ( bcf_float_is_missing(line->d.info[i].v1.f) ) tok->nvalues = 0; else { tok->values[0] = line->d.info[i].v1.f; tok->nvalues = 1; } tok->str_value.l = 0; } else { tok->str_value.l = 0; if ( line->d.info[i].type==BCF_BT_INT8 && line->d.info[i].v1.i==bcf_int8_missing ) tok->nvalues = 0; else if ( line->d.info[i].type==BCF_BT_INT16 && line->d.info[i].v1.i==bcf_int16_missing ) tok->nvalues = 0; else if ( line->d.info[i].type==BCF_BT_INT32 && line->d.info[i].v1.i==bcf_int32_missing ) tok->nvalues = 0; else { tok->values[0] = line->d.info[i].v1.i; tok->nvalues = 1; } } } static void filters_cmp_bit_and(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line) { int a = (int)(atok->nvalues?atok->values[0]:atok->threshold); int b = (int)(btok->nvalues?btok->values[0]:btok->threshold); if ( rtok->tok_type==TOK_LIKE ) rtok->pass_site = a&b ? 1 : 0; else rtok->pass_site = a&b ? 0 : 1; } static void filters_cmp_filter(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line) { // the btok values contain FILTER ids obtained by parsing the user expression int i,j; if ( rtok->tok_type==TOK_NOT_IN ) // fail if the query expression is a subset of the VCF FILTER { if ( !btok->nvalues ) // the query expression is ".", pass everything unless the VCF is also "." { if ( line->d.n_flt ) rtok->pass_site = 1; return; } if ( !line->d.n_flt ) // no filters at this VCF line and the query expression has a value { rtok->pass_site = 1; return; } for (j=0; jnvalues; j++) // some query expression value must be absent from VCF in order to pass { for (i=0; id.n_flt; i++) if ( btok->values[j]==line->d.flt[i] ) break; if ( i==line->d.n_flt ) break; // the query is not in the VCF } if ( j!=btok->nvalues ) rtok->pass_site = 1; return; } else if ( rtok->tok_type==TOK_IN ) { if ( !btok->nvalues ) // the query expression is ".", fail everything unless the VCF is also "." { if ( !line->d.n_flt ) rtok->pass_site = 1; return; } if ( !line->d.n_flt ) return; // no filters at this VCF line and the query expression has a value for (j=0; jnvalues; j++) // all of the query values must be present in the VCF in order to pass { for (i=0; id.n_flt; i++) if ( btok->values[j]==line->d.flt[i] ) break; if ( i==line->d.n_flt ) break; // the query is not in the VCF } if ( j==btok->nvalues ) rtok->pass_site = 1; return; } else if ( rtok->tok_type==TOK_NE ) // require anything but exact match { if ( btok->nvalues != line->d.n_flt ) { rtok->pass_site = 1; return; } if ( !btok->nvalues ) return; for (j=0; jnvalues; j++) // some of the query values must be absent from the VCF in order to pass { for (i=0; id.n_flt; i++) if ( btok->values[j]==line->d.flt[i] ) break; if ( i==line->d.n_flt ) break; // the query is not in the VCF } if ( j!=btok->nvalues ) rtok->pass_site = 1; return; } else if ( rtok->tok_type==TOK_EQ ) // require exact match { if ( btok->nvalues != line->d.n_flt ) return; if ( !btok->nvalues ) { rtok->pass_site = 1; return; } for (j=0; jnvalues; j++) // all of the query values must be present in the VCF in order to pass { for (i=0; id.n_flt; i++) if ( btok->values[j]==line->d.flt[i] ) break; if ( i==line->d.n_flt ) break; // the query is not in the VCF } if ( j==btok->nvalues ) rtok->pass_site = 1; return; } else error("Only ==, !=, ~, and !~ operators are supported for FILTER\n"); return; } static void filters_cmp_string_hash(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line) { if ( btok->hash ) { token_t *tmp = atok; atok = btok; btok = tmp; } if ( rtok->tok_type!=TOK_EQ && rtok->tok_type!=TOK_NE ) error("Only == and != operators are supported for strings read from a file\n"); // INFO if ( !btok->nsamples ) { // there is only one string value, e.g. STR[1]=@list.txt if ( btok->idx >= 0 ) { int ret = btok->str_value.s ? khash_str2int_has_key(atok->hash, btok->str_value.s) : 0; if ( rtok->tok_type==TOK_NE ) ret = ret ? 0 : 1; rtok->pass_site = ret; return; } // there can be multiple comma-separated string values, e.g. STR=@list.txt or STR[*]=@list.txt int ret = 0; char *ptr = btok->str_value.s; while ( *ptr ) { char *eptr = ptr + 1; while ( *eptr && *eptr!=',' ) eptr++; char keep = *eptr; *eptr = 0; ret |= khash_str2int_has_key(atok->hash, ptr); *eptr = keep; if ( !keep ) break; ptr = eptr + 1; } if ( rtok->tok_type==TOK_NE ) ret = ret ? 0 : 1; rtok->pass_site = ret; return; } // FORMAT tok_init_samples(atok, btok, rtok); rtok->pass_site = 0; int i; // there is only one string value, e.g. FMT/STR[*:1]=@list.txt if ( btok->idx >= 0 ) { for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; char *str = btok->str_value.s + i*btok->nval1; char keep = str[btok->nval1]; str[btok->nval1] = 0; int ret = khash_str2int_has_key(atok->hash, str); str[btok->nval1] = keep; if ( rtok->tok_type==TOK_NE ) ret = ret ? 0 : 1; rtok->pass_samples[i] = ret; rtok->pass_site |= ret; } return; } // there can be multiple comma-separated string values, e.g. FMT/STR=@list.txt for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; char *str = btok->str_value.s + i*btok->nval1; char keep = str[btok->nval1]; str[btok->nval1] = 0; // now str contains the block of per-sample comma-separated strings to loop over int ret = 0; char *ptr = str; while ( *ptr ) { char *eptr = ptr + 1; while ( *eptr && *eptr!=',' ) eptr++; char keep0 = *eptr; *eptr = 0; ret |= khash_str2int_has_key(atok->hash, ptr); *eptr = keep0; if ( !keep0 ) break; ptr = eptr + 1; } str[btok->nval1] = keep; if ( rtok->tok_type==TOK_NE ) ret = ret ? 0 : 1; rtok->pass_samples[i] = ret; rtok->pass_site |= ret; } } static void filters_cmp_id(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line) { if ( btok->hash ) { token_t *tmp = atok; atok = btok; btok = tmp; } char *id = line->d.id; int pass = 0; while ( id ) { char *ep = strchr(id,';'); if ( ep ) *ep = 0; if ( atok->hash ) { if ( rtok->tok_type!=TOK_EQ && rtok->tok_type!=TOK_NE ) error("Only == and != operators are supported for strings read from a file\n"); pass = khash_str2int_has_key(atok->hash, id); } else { if ( !btok->str_value.l ) error("Error occurred while evaluating the expression\n"); if ( rtok->tok_type==TOK_EQ || rtok->tok_type==TOK_NE ) pass = strcmp(btok->str_value.s,id) ? 0 : 1; else { if ( rtok->tok_type!=TOK_LIKE && rtok->tok_type!=TOK_NLIKE ) error("Only the following operators are supported for querying ID: ==, !=, ~, !~; the operator type %d is not supported (%p %p)\n", rtok->tok_type,atok->regex,btok->regex); regex_t *regex = atok->regex ? atok->regex : (btok->regex ? btok->regex : NULL); if ( !regex ) error("fixme: regex initialization failed\n"); pass = regexec(regex,id, 0,NULL,0) ? 0 : 1; } } if ( ep ) { *ep = ';'; id = ep + 1; } if ( pass || !ep ) break; } if ( rtok->tok_type==TOK_NE || rtok->tok_type==TOK_NE) pass = pass ? 0 : 1; rtok->pass_site = pass; } /** * bcf_get_info_value() - get single INFO value, int64_t or double * @line: BCF line * @info_id: tag ID, as returned by bcf_hdr_id2int * @ivec: 0-based index to retrieve, -1 when single value is expected * @vptr: pointer to memory location of sufficient size to accommodate * info_id's type * * The returned value is -1 if tag is not present, 0 if present but * values is missing or ivec is out of range, and 1 on success. */ static int bcf_get_info_value(bcf1_t *line, int info_id, int ivec, void *value) { int j; for (j=0; jn_info; j++) if ( line->d.info[j].key == info_id ) break; if ( j==line->n_info ) return -1; bcf_info_t *info = &line->d.info[j]; if ( info->len == 1 ) { if ( info->type==BCF_BT_FLOAT ) *((double*)value) = info->v1.f; else if ( info->type==BCF_BT_INT8 || info->type==BCF_BT_INT16 || info->type==BCF_BT_INT32 ) *((int64_t*)value) = info->v1.i; return 1; } if ( ivec<0 ) ivec = 0; if ( ivec>=info->len) return 0; #define BRANCH(type_t, convert, is_missing, is_vector_end, out_type_t) { \ uint8_t *p = info->vptr; \ for (j=0; jtype) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, int64_t); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, int64_t); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, val==bcf_int32_missing, val==bcf_int32_vector_end, int64_t); break; case BCF_BT_FLOAT: BRANCH(float, le_to_float, bcf_float_is_missing(val), bcf_float_is_vector_end(val), double); break; default: fprintf(stderr,"todo: type %d\n", info->type); exit(1); break; } #undef BRANCH return -1; // this shouldn't happen } static void filters_set_chrom(filter_t *flt, bcf1_t *line, token_t *tok) { tok->str_value.l = 0; kputs(bcf_seqname(flt->hdr,line), &tok->str_value); tok->nvalues = tok->str_value.l; tok->is_str = 1; } static void filters_set_pos(filter_t *flt, bcf1_t *line, token_t *tok) { tok->values[0] = line->pos+1; tok->nvalues = 1; } static void filters_set_info_int(filter_t *flt, bcf1_t *line, token_t *tok) { if ( tok->idx==-2 ) { tok->nvalues = bcf_get_info_int32(flt->hdr,line,tok->tag,&flt->tmpi,&flt->mtmpi); if ( tok->nvalues<=0 ) tok->nvalues = 0; else { hts_expand(double,tok->nvalues,tok->mvalues,tok->values); int i, j = 0, end = tok->idxs[tok->nidxs-1] < 0 ? tok->nvalues - 1 : tok->nidxs - 1; if ( end >= tok->nvalues ) end = tok->nvalues - 1; for (i=0; i<=end; i++) if ( i>=tok->nidxs || tok->idxs[i] ) tok->values[j++] = flt->tmpi[i]; tok->nvalues = j; } } else { int64_t value = 0; if ( bcf_get_info_value(line,tok->hdr_id,tok->idx,&value) <= 0 ) tok->nvalues = 0; else { tok->values[0] = value; tok->nvalues = 1; } } } static void filters_set_info_float(filter_t *flt, bcf1_t *line, token_t *tok) { if ( tok->idx==-2 ) { tok->nvalues = bcf_get_info_float(flt->hdr,line,tok->tag,&flt->tmpf,&flt->mtmpf); if ( tok->nvalues<=0 ) tok->nvalues = 0; else { hts_expand(double,tok->nvalues,tok->mvalues,tok->values); int i, j = 0, end = tok->idxs[tok->nidxs-1] < 0 ? tok->nvalues - 1 : tok->nidxs - 1; if ( end >= tok->nvalues ) end = tok->nvalues - 1; for (i=0; i<=end; i++) if ( i>=tok->nidxs || tok->idxs[i] ) { if ( bcf_float_is_missing(flt->tmpf[i]) ) bcf_double_set_missing(tok->values[j]); else tok->values[j] = flt->tmpf[i]; j++; } tok->nvalues = j; } } else { double value; if ( bcf_get_info_value(line,tok->hdr_id,tok->idx,&value) <= 0 ) tok->nvalues = 0; else { tok->values[0] = value; tok->nvalues = 1; } } } static void filters_set_info_string(filter_t *flt, bcf1_t *line, token_t *tok) { int32_t m = tok->str_value.m; int n = bcf_get_info_string(flt->hdr,line,tok->tag,&tok->str_value.s,&m); tok->str_value.m = m; if ( n<0 ) { tok->nvalues = tok->str_value.l = 0; return; } if ( tok->idx>=0 ) { // get ith field (i=tok->idx) int i = 0; char *ss = tok->str_value.s, *se = tok->str_value.s + n; while ( ssidx ) { if ( *ss==',' ) i++; ss++; } if ( ss==se || i!=tok->idx ) { tok->nvalues = tok->str_value.l = 0; return; } se = ss; while ( se - tok->str_value.s < n && *se!=',' ) se++; if ( ss==tok->str_value.s ) *se = 0; else { memmove(tok->str_value.s, ss, se-ss); tok->str_value.s[se-ss] = 0; } tok->str_value.l = se - ss; } else if ( tok->idx==-2 && tok->idxs[0]==-1 ) // keep all values, TAG[*] tok->str_value.l = n; else if ( tok->idx==-2 ) { flt->tmps.l = 0; ks_resize(&flt->tmps, n); int i, iend = tok->idxs[tok->nidxs-1] < 0 ? n - 1 : tok->nidxs - 1; if ( iend >= n ) iend = n - 1; char *beg = tok->str_value.s, *dst = flt->tmps.s; for (i=0; i<=iend; i++) { char *end = beg; while ( *end && *end!=',' ) end++; if ( i>=tok->nidxs || tok->idxs[i] ) { memcpy(dst, beg, end - beg); dst += end - beg; dst[0] = ','; dst++; } beg = end+1; } dst[0] = 0; tok->str_value.l = dst - flt->tmps.s; #define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; } SWAP(char *, flt->tmps.s, tok->str_value.s); SWAP(size_t, flt->tmps.m, tok->str_value.m); } tok->nvalues = tok->str_value.l; } static void filters_set_info_flag(filter_t *flt, bcf1_t *line, token_t *tok) { int j; for (j=0; jn_info; j++) if ( line->d.info[j].key == tok->hdr_id ) break; tok->values[0] = j==line->n_info ? 0 : 1; tok->nvalues = 1; } static void filters_set_format_int(filter_t *flt, bcf1_t *line, token_t *tok) { if ( line->n_sample != tok->nsamples ) error("Incorrect number of FORMAT fields at %s:%"PRId64" .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples); int nvals; if ( (nvals=bcf_get_format_int32(flt->hdr,line,tok->tag,&flt->tmpi,&flt->mtmpi))<0 ) { tok->nvalues = 0; return; } int i, nsrc1 = nvals / tok->nsamples; tok->nval1 = tok->idx >= 0 ? 1 : (tok->nuidxs ? tok->nuidxs : nsrc1); tok->nvalues = tok->nval1*tok->nsamples; hts_expand(double, tok->nvalues, tok->mvalues, tok->values); if ( tok->idx >= 0 ) // scalar or vector index { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; int32_t *ptr = flt->tmpi + i*nsrc1; if ( tok->idx>=nsrc1 || ptr[tok->idx]==bcf_int32_missing ) bcf_double_set_missing(tok->values[i]); else if ( ptr[tok->idx]==bcf_int32_vector_end ) bcf_double_set_vector_end(tok->values[i]); else tok->values[i] = ptr[tok->idx]; } } else if ( tok->idx==-3 ) { if ( filters_cache_genotypes(flt,line)!=0 ) { tok->nvalues = 0; return; } for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; int32_t *src = flt->tmpi + i*nsrc1; double *dst = tok->values + i*tok->nval1; int k, j = 0; for (k=0; kcached_GT.mask[i] & (1<nval1; j++) bcf_double_set_vector_end(dst[j]); } } else { int kend = tok->idxs[tok->nidxs-1] < 0 ? tok->nval1 : tok->nidxs; for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; int32_t *src = flt->tmpi + i*nsrc1; double *dst = tok->values + i*tok->nval1; int k, j = 0; for (k=0; knidxs && !tok->idxs[k] ) continue; if ( src[k]==bcf_int32_missing ) bcf_double_set_missing(dst[j]); else if ( src[k]==bcf_int32_vector_end ) bcf_double_set_vector_end(dst[j]); else dst[j] = src[k]; j++; } if ( j==0 ) { bcf_double_set_missing(dst[j]); j++; } while (j < tok->nval1) { bcf_double_set_vector_end(dst[j]); j++; } } } } static void filters_set_format_float(filter_t *flt, bcf1_t *line, token_t *tok) { if ( line->n_sample != tok->nsamples ) error("Incorrect number of FORMAT fields at %s:%"PRId64" .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples); int nvals; if ( (nvals=bcf_get_format_float(flt->hdr,line,tok->tag,&flt->tmpf,&flt->mtmpf))<0 ) { tok->nvalues = 0; return; } int i, nsrc1 = nvals / tok->nsamples; tok->nval1 = tok->idx >= 0 ? 1 : (tok->nuidxs ? tok->nuidxs : nsrc1); tok->nvalues = tok->nval1*tok->nsamples; hts_expand(double, tok->nvalues, tok->mvalues, tok->values); if ( tok->idx >= 0 ) // scalar or vector index { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; float *ptr = flt->tmpf + i*nsrc1; if ( tok->idx>=nsrc1 || bcf_float_is_missing(ptr[tok->idx]) ) bcf_double_set_missing(tok->values[i]); else if ( bcf_float_is_vector_end(ptr[tok->idx]) ) bcf_double_set_vector_end(tok->values[i]); else tok->values[i] = ptr[tok->idx]; } } else if ( tok->idx==-3 ) { if ( filters_cache_genotypes(flt,line)!=0 ) { tok->nvalues = 0; return; } for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; float *src = flt->tmpf + i*nsrc1; double *dst = tok->values + i*tok->nval1; int k, j = 0; for (k=0; kcached_GT.mask[i] & (1<nval1; j++) bcf_double_set_vector_end(dst[j]); } } else { int kend = tok->idxs[tok->nidxs-1] < 0 ? tok->nval1 : tok->nidxs; for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; float *src = flt->tmpf + i*nsrc1; double *dst = tok->values + i*tok->nval1; int k, j = 0; for (k=0; knidxs && !tok->idxs[k] ) continue; if ( bcf_float_is_missing(src[k]) ) bcf_double_set_missing(dst[j]); else if ( bcf_float_is_vector_end(src[k]) ) bcf_double_set_vector_end(dst[j]); else dst[j] = src[k]; j++; } if ( j==0 ) { bcf_double_set_missing(dst[j]); j++; } while (j < tok->nval1) { bcf_double_set_vector_end(dst[j]); j++; } } } } static void filters_set_format_string(filter_t *flt, bcf1_t *line, token_t *tok) { if ( line->n_sample != tok->nsamples ) error("Incorrect number of FORMAT fields at %s:%"PRId64" .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples); int i, ndim = tok->str_value.m; int nstr = bcf_get_format_char(flt->hdr, line, tok->tag, &tok->str_value.s, &ndim); tok->str_value.m = tok->str_value.l = ndim; kputc(0,&tok->str_value); // append the nul byte tok->str_value.l = tok->nvalues = 0; if ( nstr<0 ) return; if ( tok->idx==-3 && filters_cache_genotypes(flt,line)!=0 ) return; tok->nvalues = tok->str_value.l = nstr; tok->nval1 = nstr / tok->nsamples; for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; char *src = tok->str_value.s + i*tok->nval1, *dst = src; int ibeg = 0; int idx = 0; // idx-th field while ( ibeg < tok->nval1 ) { int iend = ibeg; while ( iend < tok->nval1 && src[iend] && src[iend]!=',' ) iend++; int keep = 0; if ( tok->idx >= 0 ) // single index, given explicitly, e.g. AD[:1] { if ( tok->idx==idx ) keep = 1; } else if ( tok->idx == -3 ) // given by GT index, e.g. AD[:GT] { if ( flt->cached_GT.mask[i] & (1<nidxs ) { if ( tok->idxs[idx] != 0 ) keep = 1; } else if ( tok->idxs[tok->nidxs-1] < 0 ) keep = 1; } if ( keep ) { if ( ibeg!=0 ) memmove(dst, src+ibeg, iend-ibeg+1); dst += iend - ibeg + 1; if ( tok->idx>=0 ) break; } if ( !src[iend] ) break; ibeg = iend + 1; idx++; } if ( dst==src ) { dst[0] = '.'; dst+=2; } if ( dst - src < tok->nval1 ) memset(dst-1, 0, tok->nval1 - (dst - src)); } } static void _filters_set_genotype(filter_t *flt, bcf1_t *line, token_t *tok, int type) { bcf_fmt_t *fmt = bcf_get_fmt(flt->hdr, line, "GT"); if ( !fmt ) { tok->nvalues = tok->str_value.l = 0; return; } int i,j, nsmpl = bcf_hdr_nsamples(flt->hdr), nvals1 = type==2 ? 3 : 4; if ( tok->str_value.m <= nvals1*nsmpl ) { tok->str_value.m = nvals1*nsmpl + 1; tok->str_value.s = (char*)realloc(tok->str_value.s, tok->str_value.m); } #define BRANCH_INT(type_t, convert, vector_end) \ { \ for (i=0; in_sample; i++) \ { \ uint8_t *ptr = fmt->p + i*fmt->size; \ int is_het = 0, has_ref = 0, missing = 0, jal = 0; \ for (j=0; jn; j++) \ { \ type_t ial = convert(&ptr[j * sizeof(type_t)]); \ if ( ial==vector_end ) break; /* smaller ploidy */ \ if ( bcf_gt_is_missing(ial) ) { missing=1; break; } /* missing allele */ \ if ( bcf_gt_allele(ial)==0 ) has_ref = 1; \ if ( j>0 ) \ { \ if ( bcf_gt_allele(ial)!=bcf_gt_allele(jal) ) is_het = 1; \ } \ jal = ial; \ } \ char *dst = &tok->str_value.s[nvals1*i]; \ if ( type==4 ) \ { \ if ( !j || missing ) dst[0]='m', dst[1]='i', dst[2]='s', dst[3] = 0; /* mis, missing genotype */ \ else if ( !has_ref ) dst[0]='a', dst[1]='l', dst[2]='t', dst[3] = 0; /* alt, no ref, must have alt allele */ \ else if ( !is_het ) dst[0]='r', dst[1]='e', dst[2]='f', dst[3] = 0; /* ref, must be ref-only, no alt alelle */ \ else dst[0]='a', dst[1]='l', dst[2]='t', dst[3] = 0; /* alt, is het, has alt allele */ \ } \ else if ( !j || missing ) dst[0]='.', dst[1]=0; /* ., missing genotype */ \ else if ( type==3 ) \ { \ if ( j==1 ) dst[0]='h', dst[1]='a', dst[2]='p', dst[3] = 0; /* hap, haploid */ \ else if ( !is_het ) dst[0]='h', dst[1]='o', dst[2]='m', dst[3] = 0; /* hom */ \ else dst[0]='h', dst[1]='e', dst[2]='t', dst[3] = 0; /* het */ \ } \ else \ { \ if ( j==1 ) \ { \ if ( has_ref ) dst[0]='r', dst[1]=0; /* r, haploid */ \ else dst[0]='a', dst[1]=0; /* a, haploid */ \ } \ else if ( !is_het ) \ { \ if ( has_ref ) dst[0]='r', dst[1]='r', dst[2] = 0; /* rr */ \ else dst[0]='a', dst[1]='a', dst[2] = 0; /* aa */ \ } \ else \ { \ if ( has_ref ) dst[0]='r', dst[1]='a', dst[2] = 0; /* ra */ \ else dst[0]='a', dst[1]='A', dst[2] = 0; /* aA */ \ } \ } \ } \ } switch (fmt->type) { case BCF_BT_INT8: BRANCH_INT(int8_t, le_to_i8, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH_INT(int16_t, le_to_i16, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH_INT(int32_t, le_to_i32, bcf_int32_vector_end); break; default: error("The GT type is not lineognised: %d at %s:%"PRId64"\n",fmt->type, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1); break; } #undef BRANCH_INT assert( tok->nsamples == nsmpl ); tok->nvalues = tok->str_value.l = nvals1*nsmpl; tok->str_value.s[tok->str_value.l] = 0; tok->nval1 = nvals1; } static void filters_set_genotype2(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 2); } // rr, ra, aa, aA etc static void filters_set_genotype3(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 3); } // hap, hom, het static void filters_set_genotype4(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 4); } // mis, alt, ref static void filters_set_genotype_string(filter_t *flt, bcf1_t *line, token_t *tok) { bcf_fmt_t *fmt = bcf_get_fmt(flt->hdr, line, "GT"); if ( !fmt ) { tok->nvalues = 0; return; } int i, blen = 4, nsmpl = line->n_sample; gt_length_too_big: tok->str_value.l = 0; for (i=0; istr_value.l; bcf_format_gt(fmt, i, &tok->str_value); kputc_(0, &tok->str_value); if ( tok->str_value.l - plen > blen ) { // too many alternate alleles or ploidy is too large, the genotype does not fit // three characters ("0/0" vs "10/10"). blen *= 2; goto gt_length_too_big; } plen = tok->str_value.l - plen; while ( plen < blen ) { kputc_(0, &tok->str_value); plen++; } } assert( tok->nsamples == nsmpl ); tok->nvalues = tok->str_value.l; tok->nval1 = blen; } static void filters_set_ilen(filter_t *flt, bcf1_t *line, token_t *tok) { tok->nvalues = line->n_allele - 1; hts_expand(double,tok->nvalues,tok->mvalues,tok->values); int i, rlen = strlen(line->d.allele[0]); for (i=1; in_allele; i++) { if ( line->d.allele[i][0]=='<' ) { bcf_double_set_missing(tok->values[i-1]); continue; } int alen = strlen(line->d.allele[i]); tok->values[i-1] = alen - rlen; } } static void filters_set_ref_string(filter_t *flt, bcf1_t *line, token_t *tok) { tok->str_value.l = 0; kputs(line->d.allele[0], &tok->str_value); tok->nvalues = tok->str_value.l; } static void filters_set_alt_string(filter_t *flt, bcf1_t *line, token_t *tok) { tok->str_value.l = 0; if ( tok->idx>=0 ) { if ( line->n_allele > tok->idx + 1 ) kputs(line->d.allele[tok->idx + 1], &tok->str_value); else kputc('.', &tok->str_value); } else if ( tok->idx==-2 ) { int i, end = tok->nuidxs ? tok->nuidxs : line->n_allele - 1; if ( end >= line->n_allele - 1 ) end = line->n_allele - 2; for (i=0; i<=end; i++) if ( i>=tok->nidxs || tok->idxs[i] ) { if ( tok->str_value.l ) kputc(',', &tok->str_value); kputs(line->d.allele[i+1], &tok->str_value); } } else if ( line->n_allele>1 ) { kputs(line->d.allele[1], &tok->str_value); int i; for (i=2; in_allele; i++) { kputc(',', &tok->str_value); kputs(line->d.allele[i], &tok->str_value); } } else if ( line->n_allele==1 ) kputc('.', &tok->str_value); tok->nvalues = tok->str_value.l; } static void filters_set_nmissing(filter_t *flt, bcf1_t *line, token_t *tok) { bcf_unpack(line, BCF_UN_FMT); if ( !line->n_sample ) { tok->nvalues = 1; tok->values[0] = 0; return; } int i,igt = bcf_hdr_id2int(flt->hdr, BCF_DT_ID, "GT"); bcf_fmt_t *fmt = NULL; for (i=0; in_fmt; i++) if ( line->d.fmt[i].id==igt ) { fmt = &line->d.fmt[i]; break; } if ( !fmt ) { tok->nvalues = 0; return; } int j,nmissing = 0; #define BRANCH(type_t, convert, is_vector_end) { \ for (i=0; in_sample; i++) \ { \ uint8_t *ptr = fmt->p + i*fmt->size; \ for (j=0; jn; j++) \ { \ type_t val = convert(&ptr[j * sizeof(type_t)]); \ if ( val==is_vector_end ) break; \ if ( val==bcf_gt_missing ) { nmissing++; break; } \ } \ } \ } switch (fmt->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, bcf_int32_vector_end); break; default: fprintf(stderr,"todo: type %d\n", fmt->type); exit(1); break; } #undef BRANCH tok->nvalues = 1; tok->values[0] = tok->tag[0]=='N' ? nmissing : (double)nmissing / line->n_sample; } static int func_npass(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { if ( nstack==0 ) error("Error parsing the expression\n"); token_t *tok = stack[nstack - 1]; if ( !tok->nsamples ) error("The function %s works with FORMAT fields\n", rtok->tag); assert(tok->usmpl); int i, npass = 0; for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; if ( tok->pass_samples[i] ) npass++; } hts_expand(double,1,rtok->mvalues,rtok->values); rtok->nsamples = 0; rtok->nvalues = 1; rtok->values[0] = rtok->tag[0]=='N' ? npass : (line->n_sample ? 1.0*npass/line->n_sample : 0); return 1; } static void filters_set_nalt(filter_t *flt, bcf1_t *line, token_t *tok) { tok->nvalues = 1; tok->values[0] = line->n_allele - 1; } static void filters_set_ac(filter_t *flt, bcf1_t *line, token_t *tok) { hts_expand(int32_t, line->n_allele, flt->mtmpi, flt->tmpi); if ( !bcf_calc_ac(flt->hdr, line, flt->tmpi, BCF_UN_INFO|BCF_UN_FMT) ) { tok->nvalues = 0; return; } int i, an = flt->tmpi[0]; for (i=1; in_allele; i++) an += flt->tmpi[i]; if ( !an ) { tok->nvalues = 0; return; } flt->tmpi[0] = an; // for filters_set_[mac|af|maf] if ( tok->idx>=0 ) { tok->nvalues = 1; tok->values[0] = tok->idx+1n_allele ? flt->tmpi[tok->idx+1] : 0; } else if ( line->n_allele==1 ) // no ALT { tok->nvalues = 1; tok->values[0] = 0; } else { hts_expand(double,line->n_allele,tok->mvalues,tok->values); for (i=1; in_allele; i++) tok->values[i-1] = flt->tmpi[i]; tok->nvalues = line->n_allele - 1; } } static void filters_set_an(filter_t *flt, bcf1_t *line, token_t *tok) { filters_set_ac(flt,line,tok); tok->values[0] = tok->nvalues ? flt->tmpi[0] : 0; tok->nvalues = 1; } static void filters_set_mac(filter_t *flt, bcf1_t *line, token_t *tok) { filters_set_ac(flt,line,tok); if ( !tok->nvalues ) return; int i, an = flt->tmpi[0]; for (i=0; invalues; i++) if ( tok->values[i] > an*0.5 ) tok->values[i] = an - tok->values[i]; } static void filters_set_af(filter_t *flt, bcf1_t *line, token_t *tok) { filters_set_ac(flt,line,tok); if ( !tok->nvalues ) return; int i, an = flt->tmpi[0]; for (i=0; invalues; i++) tok->values[i] /= (double)an; } static void filters_set_maf(filter_t *flt, bcf1_t *line, token_t *tok) { filters_set_ac(flt,line,tok); if ( !tok->nvalues ) return; int i, an = flt->tmpi[0]; for (i=0; invalues; i++) { tok->values[i] /= (double)an; if ( tok->values[i] > 0.5 ) tok->values[i] = 1 - tok->values[i]; } } static int func_max(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; rtok->nvalues = 0; if ( !tok->nvalues ) return 1; double *ptr, val = -HUGE_VAL; int i,j, has_value = 0; if ( tok->nsamples ) { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; has_value = 1; if ( val < ptr[j] ) val = ptr[j]; } } } else { for (i=0; invalues; i++) { if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) continue; has_value = 1; if ( val < tok->values[i] ) val = tok->values[i]; } } if ( has_value ) { rtok->values[0] = val; rtok->nvalues = has_value; } return 1; } static int func_smpl_max(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; if ( !tok->nsamples ) return func_max(flt,line,rtok,stack,nstack); rtok->nsamples = tok->nsamples; rtok->nvalues = tok->nsamples; rtok->nval1 = 1; hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values); assert(tok->usmpl); if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples); int i, j, has_value; double val, *ptr; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; val = -HUGE_VAL; has_value = 0; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; has_value = 1; if ( val < ptr[j] ) val = ptr[j]; } if ( has_value ) rtok->values[i] = val; else bcf_double_set_missing(rtok->values[i]); } return 1; } static int func_min(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; rtok->nvalues = 0; if ( !tok->nvalues ) return 1; double *ptr, val = HUGE_VAL; int i,j, has_value = 0; if ( tok->nsamples ) { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; has_value = 1; if ( val > ptr[j] ) val = ptr[j]; } } } else { for (i=0; invalues; i++) { if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) continue; has_value = 1; if ( val > tok->values[i] ) val = tok->values[i]; } } if ( has_value ) { rtok->values[0] = val; rtok->nvalues = has_value; } return 1; } static int func_smpl_min(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; if ( !tok->nsamples ) return func_min(flt,line,rtok,stack,nstack); rtok->nsamples = tok->nsamples; rtok->nvalues = tok->nsamples; rtok->nval1 = 1; hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values); assert(tok->usmpl); if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples); int i, j, has_value; double val, *ptr; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; val = HUGE_VAL; has_value = 0; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; has_value = 1; if ( val > ptr[j] ) val = ptr[j]; } if ( has_value ) rtok->values[i] = val; else bcf_double_set_missing(rtok->values[i]); } return 1; } static int func_avg(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; rtok->nvalues = 0; if ( !tok->nvalues ) return 1; double *ptr, val = 0; int i,j, n = 0; if ( tok->nsamples ) { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; val += ptr[j]; n++; } } } else { for (i=0; invalues; i++) if ( !bcf_double_is_missing_or_vector_end(tok->values[i]) ) { val += tok->values[i]; n++; } } if ( n ) { rtok->values[0] = val / n; rtok->nvalues = 1; } return 1; } static int func_smpl_avg(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack); rtok->nsamples = tok->nsamples; rtok->nvalues = tok->nsamples; rtok->nval1 = 1; hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values); assert(tok->usmpl); if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples); int i, j, n; double val, *ptr; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; val = 0; n = 0; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( !bcf_double_is_missing_or_vector_end(ptr[j]) ) { val += ptr[j]; n++; } } if ( n ) rtok->values[i] = val / n; else bcf_double_set_missing(rtok->values[i]); } return 1; } static int compare_doubles(const void *lhs, const void *rhs) { double arg1 = *(const double*) lhs; double arg2 = *(const double*) rhs; if (arg1 < arg2) return -1; if (arg1 > arg2) return 1; return 0; } static int func_median(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; rtok->nvalues = 0; if ( !tok->nvalues ) return 1; // sweep through all tok->values and while excluding all missing values reuse the very same array int i,j,k = 0, n = 0; if ( tok->nsamples ) { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) { k += tok->nval1; continue; } for (j=0; jnval1; k++,j++) { if ( bcf_double_is_missing_or_vector_end(tok->values[k]) ) continue; if ( n < k ) tok->values[n] = tok->values[k]; n++; } } } else { for (i=0; invalues; i++) { if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) continue; if ( n < i ) tok->values[n] = tok->values[i]; n++; } } if ( !n ) return 1; if ( n==1 ) rtok->values[0] = tok->values[0]; else { qsort(tok->values, n, sizeof(double), compare_doubles); rtok->values[0] = n % 2 ? tok->values[n/2] : (tok->values[n/2-1] + tok->values[n/2]) * 0.5; } rtok->nvalues = 1; return 1; } static int func_smpl_median(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack); rtok->nsamples = tok->nsamples; rtok->nvalues = tok->nsamples; rtok->nval1 = 1; hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values); assert(tok->usmpl); if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples); int i, j, n; double *ptr; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; n = 0; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; if ( n < j ) ptr[n] = ptr[j]; n++; } if ( n==0 ) bcf_double_set_missing(rtok->values[i]); else if ( n==1 ) rtok->values[i] = ptr[0]; else { qsort(ptr, n, sizeof(double), compare_doubles); rtok->values[i] = n % 2 ? ptr[n/2] : (ptr[n/2-1] + ptr[n/2]) * 0.5; } } return 1; } static int func_stddev(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; rtok->nvalues = 0; if ( !tok->nvalues ) return 1; // sweep through all tok->values and while excluding all missing values reuse the very same array int i,j,k = 0, n = 0; if ( tok->nsamples ) { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) { k += tok->nval1; continue; } for (j=0; jnval1; k++,j++) { if ( bcf_double_is_missing_or_vector_end(tok->values[k]) ) continue; if ( n < k ) tok->values[n] = tok->values[k]; n++; } } } else { for (i=0; invalues; i++) { if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) continue; if ( n < i ) tok->values[n] = tok->values[i]; n++; } } if ( !n ) return 1; if ( n==1 ) rtok->values[0] = 0; else { double sdev = 0, avg = 0; for (i=0; ivalues[i]; avg /= n; for (i=0; ivalues[i] - avg) * (tok->values[i] - avg); rtok->values[0] = sqrt(sdev/n); } rtok->nvalues = 1; return 1; } static int func_smpl_stddev(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack); rtok->nsamples = tok->nsamples; rtok->nvalues = tok->nsamples; rtok->nval1 = 1; hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values); assert(tok->usmpl); if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples); int i, j, n; double *ptr; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; n = 0; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; if ( n < j ) ptr[n] = ptr[j]; n++; } if ( n==0 ) bcf_double_set_missing(rtok->values[i]); else if ( n==1 ) rtok->values[i] = 0; else { double sdev = 0, avg = 0; for (j=0; jvalues[i] = sqrt(sdev/n); } } return 1; } static int func_sum(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { rtok->nvalues = 0; token_t *tok = stack[nstack - 1]; if ( !tok->nvalues ) return 1; double *ptr, val = 0; int i,j, n = 0; if ( tok->nsamples ) { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; val += ptr[j]; n++; } } } else { for (i=0; invalues; i++) if ( !bcf_double_is_missing_or_vector_end(tok->values[i]) ) { val += tok->values[i]; n++; } } if ( n ) { rtok->values[0] = val; rtok->nvalues = 1; } return 1; } static int func_smpl_sum(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack); rtok->nsamples = tok->nsamples; rtok->nvalues = tok->nsamples; rtok->nval1 = 1; hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values); assert(tok->usmpl); if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples); int i, j, has_value; double val, *ptr; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; val = 0; has_value = 0; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; has_value = 1; val += ptr[j]; } if ( has_value ) rtok->values[i] = val; else bcf_double_set_missing(rtok->values[i]); } return 1; } static int func_abs(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; if ( tok->is_str ) error("ABS() can be applied only on numeric values\n"); rtok->nsamples = tok->nsamples; rtok->nvalues = tok->nvalues; rtok->nval1 = tok->nval1; hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values); if ( tok->usmpl ) { if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples); } if ( !tok->nvalues ) return 1; hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values); int i,j,k = 0; if ( tok->usmpl ) { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) { k+= tok->nval1; continue; } for (j=0; jnval1; k++,j++) { if ( bcf_double_is_missing_or_vector_end(tok->values[k]) ) bcf_double_set_missing(rtok->values[k]); else rtok->values[k] = fabs(tok->values[k]); } } } else { for (i=0; invalues; i++) { if ( tok->usmpl && !tok->usmpl[i] ) continue; if ( bcf_double_is_missing(tok->values[i]) ) bcf_double_set_missing(rtok->values[i]); else if ( !bcf_double_is_vector_end(tok->values[i]) ) rtok->values[i] = fabs(tok->values[i]); } } return 1; } static int func_count(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; int i,j, cnt = 0; if ( tok->tag && tok->nsamples ) { // raw number of values in a FMT tag, e.g. COUNT(FMT/TAG) if ( tok->is_str ) error("todo: Type=String for COUNT on FORMAT fields?\n"); for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; double *ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) if ( !bcf_double_is_missing_or_vector_end(ptr[j]) ) cnt++; } } else if ( tok->nsamples ) { // number of samples that pass a processed FMT tag for (i=0; insamples; i++) if ( tok->pass_samples[i] ) cnt++; } else if ( tok->is_str ) { if ( tok->str_value.l ) cnt = 1; for (i=0; istr_value.l; i++) if ( tok->str_value.s[i]==',' ) cnt++; } else cnt = tok->nvalues; rtok->nvalues = 1; rtok->values[0] = cnt; return 1; } static int func_strlen(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; rtok->nvalues = rtok->str_value.l = 0; if ( !tok->str_value.l ) return 1; if ( tok->idx==-2 ) { int i = 0; char *ss = tok->str_value.s; while ( *ss ) { char *se = ss; while ( *se && *se!=',' ) se++; hts_expand(double, i+1, rtok->mvalues, rtok->values); if ( !*se ) rtok->values[i] = strlen(ss); else { *se = 0; rtok->values[i] = strlen(ss); *se = ','; } ss = *se ? se + 1 : se; i++; } rtok->nvalues = i; } else { if ( !tok->str_value.s[1] && tok->str_value.s[0]=='.' ) rtok->values[0] = 0; else rtok->values[0] = strlen(tok->str_value.s); rtok->nvalues = 1; } return 1; } static int func_binom(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { int i, istack = nstack - rtok->nargs; if ( rtok->nargs!=2 && rtok->nargs!=1 ) error("Error: binom() takes one or two arguments\n"); assert( istack>=0 ); // The expected mean is 0.5. Should we support also prob!=0.5? // // double prob = 0.5; // if ( nstack==3 ) // { // // three parameters, the first one must be a scalar: binom(0.25,AD[0],AD[1]) // if ( !stack[istack]->is_constant ) // error("The first argument of binom() must be a numeric constant if three parameters are given\n"); // prob = stack[istack]->threshold; // istack++; // } // else if ( nstack==2 && stack[istack]->is_constant ) // { // // two parameters, the first can be a scalar: binom(0.25,AD) or binom(AD[0],AD[1]) // prob = stack[istack]->threshold; // istack++; // } token_t *tok = stack[istack]; if ( tok->nsamples ) { // working with a FORMAT tag rtok->nval1 = 1; rtok->nvalues = tok->nsamples; rtok->nsamples = tok->nsamples; hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values); assert(tok->usmpl); if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples); if ( istack+1==nstack ) { // determine the index from the GT field: binom(AD) int ngt = bcf_get_genotypes(flt->hdr, line, &flt->tmpi, &flt->mtmpi); int max_ploidy = ngt/line->n_sample; if ( ngt <= 0 || max_ploidy < 2 ) // GT not present or not diploid, cannot set { for (i=0; insamples; i++) if ( rtok->usmpl[i] ) bcf_double_set_missing(rtok->values[i]); return rtok->nargs; } for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; int32_t *ptr = flt->tmpi + i*max_ploidy; if ( bcf_gt_is_missing(ptr[0]) || bcf_gt_is_missing(ptr[1]) || ptr[1]==bcf_int32_vector_end ) { bcf_double_set_missing(rtok->values[i]); continue; } int idx1 = bcf_gt_allele(ptr[0]); int idx2 = bcf_gt_allele(ptr[1]); if ( idx1>=line->n_allele ) error("Incorrect allele index at %s:%"PRId64", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]); if ( idx2>=line->n_allele ) error("Incorrect allele index at %s:%"PRId64", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]); double *vals = tok->values + tok->nval1*i; if ( bcf_double_is_missing_or_vector_end(vals[idx1]) || bcf_double_is_missing_or_vector_end(vals[idx2]) ) { bcf_double_set_missing(rtok->values[i]); continue; } rtok->values[i] = calc_binom_two_sided(vals[idx1],vals[idx2],0.5); if ( rtok->values[i] < 0 ) { bcf_double_set_missing(rtok->values[i]); continue; } } } else { // the fields given explicitly: binom(AD[:0],AD[:1]) token_t *tok2 = stack[istack+1]; if ( tok->nval1!=1 || tok2->nval1!=1 ) error("Expected one value per binom() argument, found %d and %d at %s:%"PRId64"\n",tok->nval1,tok2->nval1, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1); for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; double *ptr1 = tok->values + tok->nval1*i; double *ptr2 = tok2->values + tok2->nval1*i; if ( bcf_double_is_missing_or_vector_end(ptr1[0]) || bcf_double_is_missing_or_vector_end(ptr2[0]) ) { bcf_double_set_missing(rtok->values[i]); continue; } rtok->values[i] = calc_binom_two_sided(ptr1[0],ptr2[0],0.5); if ( rtok->values[i] < 0 ) { bcf_double_set_missing(rtok->values[i]); continue; } } } } else { // working with an INFO tag rtok->nvalues = 1; hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values); double *ptr1 = NULL, *ptr2 = NULL; if ( istack+1==nstack ) { // only one tag, expecting two values: binom(INFO/AD) if ( tok->nvalues==2 ) { ptr1 = &tok->values[0]; ptr2 = &tok->values[1]; } } else { // two tags, expecting one value in each: binom(INFO/AD[0],INFO/AD[1]) token_t *tok2 = stack[istack+1]; if ( tok->nvalues==1 && tok2->nvalues==1 ) { ptr1 = &tok->values[0]; ptr2 = &tok2->values[0]; } } if ( !ptr1 || !ptr2 || bcf_double_is_missing_or_vector_end(ptr1[0]) || bcf_double_is_missing_or_vector_end(ptr2[0]) ) bcf_double_set_missing(rtok->values[0]); else { rtok->values[0] = calc_binom_two_sided(ptr1[0],ptr2[0],0.5); if ( rtok->values[0] < 0 ) bcf_double_set_missing(rtok->values[0]); } } return rtok->nargs; } static int func_phred(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; if ( tok->is_str ) error("PHRED() can be applied only on numeric values\n"); rtok->nsamples = tok->nsamples; rtok->nval1 = tok->nval1; memcpy(rtok->pass_samples, tok->pass_samples, rtok->nsamples*sizeof(*rtok->pass_samples)); assert(tok->usmpl); if ( !rtok->usmpl ) { rtok->usmpl = (uint8_t*) malloc(tok->nsamples*sizeof(*rtok->usmpl)); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples*sizeof(*rtok->usmpl)); } rtok->nvalues = tok->nvalues; if ( !tok->nvalues ) return 1; hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values); int i,j,k = 0; if ( tok->usmpl ) { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) { k+= tok->nval1; continue; } for (j=0; jnval1; k++,j++) { if ( bcf_double_is_missing_or_vector_end(tok->values[k]) ) bcf_double_set_missing(rtok->values[k]); else rtok->values[k] = -4.34294481903*log(tok->values[k]); } } } else { for (i=0; invalues; i++) { if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) bcf_double_set_missing(rtok->values[i]); else rtok->values[i] = -4.34294481903*log(tok->values[i]); } } return 1; } inline static void tok_init_values(token_t *atok, token_t *btok, token_t *rtok) { token_t *tok; if ( (atok->nsamples || btok->nsamples) && (!atok->nsamples || !btok->nsamples) ) tok = atok->nsamples ? atok : btok; else tok = atok->nvalues > btok->nvalues ? atok : btok; rtok->nvalues = tok->nvalues; rtok->nval1 = tok->nval1; hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values); } inline static void tok_init_samples(token_t *atok, token_t *btok, token_t *rtok) { if ( (atok->nsamples || btok->nsamples) && !rtok->nsamples ) { rtok->nsamples = atok->nsamples ? atok->nsamples : btok->nsamples; rtok->usmpl = (uint8_t*) calloc(rtok->nsamples,1); int i; for (i=0; insamples; i++) rtok->usmpl[i] |= atok->usmpl[i]; for (i=0; insamples; i++) rtok->usmpl[i] |= btok->usmpl[i]; } if (rtok->nsamples) memset(rtok->pass_samples, 0, rtok->nsamples); } #define VECTOR_ARITHMETICS(atok,btok,_rtok,AOP,TYPE) \ { \ token_t *rtok = _rtok; \ int i, has_values = 0; \ if ( atok->nvalues && btok->nvalues ) \ { \ tok_init_values(atok, btok, rtok); \ tok_init_samples(atok, btok, rtok); \ if ( !atok->nsamples && !btok->nsamples ) \ { \ if ( atok->nvalues!=btok->nvalues && atok->nvalues!=1 && btok->nvalues!=1 ) \ error("Cannot run numeric operator in -i/-e filtering on vectors of different lengths: %d vs %d\n",atok->nvalues,btok->nvalues); \ int ir,ia = 0, ib = 0; \ for (ir=0; irnvalues; ir++) \ { \ if ( atok->nvalues > 1 ) ia = ir; \ if ( btok->nvalues > 1 ) ib = ir; \ if ( bcf_double_is_missing_or_vector_end(atok->values[ia]) || bcf_double_is_missing_or_vector_end(btok->values[ib]) ) \ { \ bcf_double_set_missing(rtok->values[ir]); \ continue; \ } \ has_values = 1; \ rtok->values[ir] = TYPE atok->values[ia] AOP TYPE btok->values[ib]; \ } \ } \ else if ( atok->nsamples && btok->nsamples ) \ { \ assert( atok->nsamples==btok->nsamples ); \ if ( atok->nval1!=btok->nval1 && atok->nval1!=1 && btok->nval1!=1 ) \ error("Cannot run numeric operator in -i/-e filtering on vectors of different lengths: %d vs %d\n",atok->nval1,btok->nval1); \ for (i=0; insamples; i++) \ { \ double *rval = rtok->values + i*rtok->nval1; \ double *aval = atok->values + i*atok->nval1; \ double *bval = btok->values + i*btok->nval1; \ int ir,ia = 0, ib = 0; \ for (ir=0; irnval1; ir++) \ { \ if ( atok->nval1 > 1 ) ia = ir; \ if ( btok->nval1 > 1 ) ib = ir; \ if ( bcf_double_is_missing_or_vector_end(aval[ia]) || bcf_double_is_missing_or_vector_end(bval[ib]) ) \ { \ bcf_double_set_missing(rval[ir]); \ continue; \ } \ has_values = 1; \ rval[ir] = TYPE aval[ia] AOP TYPE bval[ib]; \ } \ } \ } \ else if ( atok->nsamples ) \ { \ assert( btok->nvalues==1 ); \ if ( !bcf_double_is_missing_or_vector_end(btok->values[0]) ) \ { \ for (i=0; invalues; i++) \ { \ if ( bcf_double_is_missing_or_vector_end(atok->values[i]) ) \ { \ bcf_double_set_missing(rtok->values[i]); \ continue; \ } \ has_values = 1; \ rtok->values[i] = TYPE atok->values[i] AOP TYPE btok->values[0]; \ } \ } \ } \ else \ { \ assert( atok->nvalues==1 ); \ if ( !bcf_double_is_missing_or_vector_end(atok->values[0]) ) \ { \ for (i=0; invalues; i++) \ { \ if ( bcf_double_is_missing_or_vector_end(btok->values[i]) ) \ { \ bcf_double_set_missing(rtok->values[i]); \ continue; \ } \ has_values = 1; \ rtok->values[i] = TYPE atok->values[0] AOP TYPE btok->values[i]; \ } \ } \ } \ } \ if ( !has_values ) rtok->nvalues = 0; \ } static int vector_logic_or(filter_t *filter, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { if ( nstack < 2 ) error("Error occurred while processing the filter \"%s\"\n", filter->str); token_t *atok = stack[nstack-2]; token_t *btok = stack[nstack-1]; tok_init_samples(atok, btok, rtok); if ( !atok->pass_site && !btok->pass_site ) return 2; rtok->pass_site = 1; if ( !atok->nsamples && !btok->nsamples ) return 2; int i; if ( rtok->tok_type==TOK_OR_VEC ) // ||, select all samples if one is true { if ( (!atok->nsamples && !atok->pass_site) || (!btok->nsamples && !btok->pass_site) ) { // These two conditions are to ensure the following does not set all samples // at sites with QUAL<=30: // QUAL>30 || FMT/GQ>30 token_t *tok = atok->nsamples ? atok : btok; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; rtok->pass_samples[i] = tok->pass_samples[i]; } } else { for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; rtok->pass_samples[i] = 1; } } return 2; } // |, only select samples which are actually true if ( !atok->nsamples || !btok->nsamples ) { token_t *tok = atok->nsamples ? atok : btok; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; rtok->pass_samples[i] = tok->pass_samples[i]; } return 2; } assert( atok->nsamples==btok->nsamples ); for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; rtok->pass_samples[i] = atok->pass_samples[i] | btok->pass_samples[i]; } return 2; } static int vector_logic_and(filter_t *filter, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { if ( nstack < 2 ) error("Error occurred while processing the filter \"%s\". (nstack=%d)\n", filter->str,nstack); token_t *atok = stack[nstack-2]; token_t *btok = stack[nstack-1]; tok_init_samples(atok, btok, rtok); if ( !atok->pass_site || !btok->pass_site ) return 2; if ( !atok->nsamples && !btok->nsamples ) { rtok->pass_site = 1; return 2; } int i; if ( !atok->nsamples || !btok->nsamples ) { token_t *tok = atok->nsamples ? atok : btok; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; rtok->pass_samples[i] = tok->pass_samples[i]; } rtok->pass_site = 1; return 2; } assert( atok->nsamples==btok->nsamples ); if ( rtok->tok_type==TOK_AND_VEC ) // &&, can be true in different samples { for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; rtok->pass_samples[i] = atok->pass_samples[i] | btok->pass_samples[i]; } rtok->pass_site = 1; } else // &, must be true within one sample { for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; rtok->pass_samples[i] = atok->pass_samples[i] & btok->pass_samples[i]; if ( rtok->pass_samples[i] ) rtok->pass_site = 1; } } return 2; } // A note about comparisons: // When setting value by determining index from the genotype, we face the problem // of how to interpret truncating arrays. Say we have TAG defined as Number=. and // GT:TAG 1/1:0,1,2 0/0:0 // Then when querying we expect the following expression to evaluate for the second // sample as // -i 'TAG[1:1]="."' .. true // -i 'TAG[1:GT]="."' .. false // The problem is that the implementation truncates the number of fields, filling // usually fewer than the original number of per-sample values. This is fixed by // adding an exception that makes the code aware of this: the GT indexing can be // recognised by having tok->idx==-3 #define CMP_VECTORS(atok,btok,_rtok,CMP_OP,missing_logic) \ { \ token_t *rtok = _rtok; \ int i, j, k; \ tok_init_samples(atok, btok, rtok); \ if ( !atok->nsamples && !btok->nsamples ) \ { \ if ( !atok->nvalues && !btok->nvalues ) { rtok->pass_site = missing_logic[2]; } \ else if ( !atok->nvalues || !btok->nvalues ) \ { \ token_t *tok = atok->nvalues ? atok : btok; \ for (j=0; jnvalues; j++) \ { \ if ( bcf_double_is_missing_or_vector_end(tok->values[j]) ) \ { \ if ( missing_logic[2] ) { rtok->pass_site = 1; break; } \ } \ else if ( missing_logic[1] ) { rtok->pass_site = 1; break; } \ } \ } \ else \ { \ for (i=0; invalues; i++) \ { \ int amiss = bcf_double_is_missing_or_vector_end(atok->values[i]) ? 1 : 0; \ for (j=0; jnvalues; j++) \ { \ int nmiss = amiss + (bcf_double_is_missing_or_vector_end(btok->values[j]) ? 1 : 0); \ if ( nmiss ) \ { \ if ( missing_logic[nmiss] ) { rtok->pass_site = 1; i = atok->nvalues; break; } \ } \ else if ( atok->values[i] > 16777216 || btok->values[j] > 16777216 ) /* Ugly, see #871 */ \ { \ if ( atok->values[i] CMP_OP btok->values[j] ) { rtok->pass_site = 1; i = atok->nvalues; break; } \ } \ else if ( (float)atok->values[i] CMP_OP (float)btok->values[j] ) { rtok->pass_site = 1; i = atok->nvalues; break; } \ } \ } \ } \ } \ else \ { \ if ( !atok->nvalues && !btok->nvalues ) \ { \ if ( missing_logic[2] ) \ { \ for (i=0; insamples; i++) \ if ( rtok->usmpl[i] ) { rtok->pass_samples[i] = missing_logic[2]; rtok->pass_site = 1; } \ } \ } \ else if ( !atok->nvalues || !btok->nvalues ) \ { \ token_t *tok = atok->nvalues ? atok : btok; \ if ( !tok->nsamples ) \ { \ int miss = 0; \ for (j=0; jnvalues; j++) \ miss |= bcf_double_is_missing_or_vector_end(tok->values[j]) ? 1 : 0; \ if ( missing_logic[++miss] ) \ { \ for (i=0; insamples; i++) \ if ( rtok->usmpl[i] ) { rtok->pass_samples[i] = missing_logic[miss]; rtok->pass_site = 1; } \ } \ } \ else \ for (i=0; insamples; i++) \ { \ if ( !rtok->usmpl[i] ) continue; \ double *ptr = tok->values + i*tok->nval1; \ int miss = 0; \ for (j=0; jnval1; j++) \ miss |= bcf_double_is_missing_or_vector_end(ptr[j]) ? 1 : 0; \ if ( missing_logic[++miss] ) { rtok->pass_samples[i] = missing_logic[miss]; rtok->pass_site = 1; } \ } \ } \ else if ( atok->nsamples && btok->nsamples ) \ { \ if ( atok->nval1!=btok->nval1 ) error("Incompatible number of per-sample values in comparison: %d vs %d\n",atok->nval1,btok->nval1); \ if ( atok->nsamples!=btok->nsamples ) error("Incompatible number samples in comparison: %d vs %d\n",atok->nsamples,btok->nsamples); \ for (i=0; insamples; i++) \ { \ if ( !atok->usmpl[i] || !btok->usmpl[i] ) { rtok->usmpl[i] = 0; continue; } \ double *aptr = atok->values + i*atok->nval1; \ double *bptr = btok->values + i*btok->nval1; \ for (j=0; jnval1; j++) \ { \ if ( atok->idx==-3 && bcf_double_is_vector_end(aptr[j]) ) break; /* explained above */ \ if ( btok->idx==-3 && bcf_double_is_vector_end(bptr[j]) ) break; /* explained above */ \ int nmiss = bcf_double_is_missing_or_vector_end(aptr[j]) ? 1 : 0; \ if ( nmiss && !missing_logic[0] ) continue; /* any is missing => result is false */ \ nmiss += (bcf_double_is_missing_or_vector_end(bptr[j]) ? 1 : 0); \ if ( nmiss ) \ { \ if ( missing_logic[nmiss] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; break; } \ } \ else if ( aptr[j] > 16777216 || bptr[j] > 16777216 ) /* Ugly, see #871 */ \ { \ if ( aptr[j] CMP_OP bptr[j] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; break; } \ } \ else if ( (float)aptr[j] CMP_OP (float)bptr[j] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; break; } \ } \ } \ } \ else if ( atok->nsamples )\ { \ for (i=0; insamples; i++) \ { \ if ( !rtok->usmpl[i] ) continue; \ double *aptr = atok->values + i*atok->nval1; \ double *bptr = btok->values; \ for (j=0; jnval1; j++) \ { \ if ( atok->idx==-3 && bcf_double_is_vector_end(aptr[j]) ) break; /* explained above */ \ int miss = bcf_double_is_missing_or_vector_end(aptr[j]) ? 1 : 0; \ if ( miss && !missing_logic[0] ) continue; /* any is missing => result is false */ \ for (k=0; knvalues; k++) \ { \ int nmiss = miss + (bcf_double_is_missing_or_vector_end(bptr[k]) ? 1 : 0); \ if ( nmiss ) \ { \ if ( missing_logic[nmiss] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = atok->nval1; break; } \ } \ else if ( aptr[j] > 16777216 || bptr[k] > 16777216 ) /* Ugly, see #871 */ \ { \ if ( aptr[j] CMP_OP bptr[k] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = atok->nval1; break; } \ } \ else if ( (float)aptr[j] CMP_OP (float)bptr[k] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = atok->nval1; break; } \ } \ } \ } \ } \ else /* btok->nsamples */ \ { \ for (i=0; insamples; i++) \ { \ if ( !rtok->usmpl[i] ) continue; \ double *aptr = atok->values; \ double *bptr = btok->values + i*btok->nval1; \ for (j=0; jnval1; j++) \ { \ if ( atok->idx==-3 && bcf_double_is_vector_end(bptr[j]) ) break; /* explained above */ \ int miss = bcf_double_is_missing_or_vector_end(bptr[j]) ? 1 : 0; \ if ( miss && !missing_logic[0] ) continue; /* any is missing => result is false */ \ for (k=0; knvalues; k++) \ { \ int nmiss = miss + (bcf_double_is_missing_or_vector_end(aptr[k]) ? 1 : 0); \ if ( nmiss ) \ { \ if ( missing_logic[nmiss] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = btok->nval1; break; } \ } \ else if ( bptr[j] > 16777216 || aptr[k] > 16777216 ) /* Ugly, see #871 */ \ { \ if ( aptr[k] CMP_OP bptr[j] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = btok->nval1; break; } \ } \ else if ( (float)aptr[k] CMP_OP (float)bptr[j] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = btok->nval1; break; } \ } \ } \ } \ } \ } \ } static int _regex_vector_strings(regex_t *regex, char *str, size_t len, int logic, int *missing_logic) { char *end = str + len; while ( str < end && *str ) { char *mid = str; while ( mid < end && *mid && *mid!=',' ) mid++; int miss = mid - str == 1 && str[0]=='.' ? 1 : 0; if ( miss && missing_logic[miss] ) return 1; char tmp = *mid; *mid = 0; int match = regexec(regex, str, 0,NULL,0) ? 0 : 1; *mid = tmp; if ( logic==TOK_NLIKE ) match = match ? 0 : 1; if ( match ) return 1; if ( !*mid ) break; str = mid + 1; } return 0; } static inline int _has_missing_string(char *beg) { while ( *beg ) { char *end = beg; while ( *end && *end!=',' ) end++; if ( end-beg==1 && beg[0]=='.' ) return 1; if ( !*end ) break; beg = end + 1; } return 0; } // Compare two strings with multiple fields, for example "A,B,.,C"=="X,Y,A". // Returns 1 if any field matches, otherwise returns 0 static inline int _match_vector_strings(char *abeg, size_t alen, char *bstr, size_t blen, int logic, int *missing_logic) { char *aend = abeg + alen; char *bend = bstr + blen; while ( abeg < aend && *abeg ) { char *amid = abeg; while ( amid < aend && *amid && *amid!=',' ) amid++; int miss = amid - abeg == 1 && abeg[0]=='.' ? 1 : 0; char *bbeg = bstr; while ( bbeg < bend && *bbeg ) { char *bmid = bbeg; while ( bmid < bend && *bmid && *bmid!=',' ) bmid++; int nmiss = miss + (bmid - bbeg == 1 && bbeg[0]=='.' ? 1 : 0); if ( nmiss ) { if ( missing_logic[nmiss] ) return 1; } else { int match = amid-abeg==bmid-bbeg && !strncmp(abeg,bbeg,amid-abeg) ? 1 : 0; if ( logic==TOK_NE ) match = match==1 ? 0 : 1; if ( match ) return 1; } if ( !*bmid ) break; bbeg = bmid + 1; } if ( !*amid ) break; abeg = amid + 1; } return 0; } static void cmp_vector_strings(token_t *atok, token_t *btok, token_t *rtok) { tok_init_samples(atok, btok, rtok); int i, logic = rtok->tok_type; // TOK_EQ, TOK_NE, TOK_LIKE, TOK_NLIKE regex_t *regex = atok->regex ? atok->regex : (btok->regex ? btok->regex : NULL); assert( atok->nvalues==atok->str_value.l && btok->nvalues==btok->str_value.l ); assert( !atok->nsamples || !btok->nsamples ); assert( (!regex && (logic==TOK_EQ || logic==TOK_NE)) || (regex && (logic==TOK_LIKE || logic==TOK_NLIKE)) ); int missing_logic[] = {0,0,0}; if ( logic==TOK_EQ || logic==TOK_LIKE ) missing_logic[0] = missing_logic[2] = 1; else if ( logic==TOK_NE || logic==TOK_NLIKE ) missing_logic[0] = missing_logic[1] = 1; if ( !atok->nsamples && !btok->nsamples ) { if ( !atok->nvalues && !btok->nvalues ) { rtok->pass_site = missing_logic[2]; return; } if ( !atok->nvalues || !btok->nvalues ) { int miss = _has_missing_string(atok->nvalues ? atok->str_value.s : btok->str_value.s); if ( missing_logic[miss+1] ) rtok->pass_site = 1; return; } if ( !regex ) rtok->pass_site = _match_vector_strings(atok->str_value.s, atok->str_value.l, btok->str_value.s, btok->str_value.l, logic, missing_logic); else { token_t *tok = atok->regex ? btok : atok; rtok->pass_site = _regex_vector_strings(regex, tok->str_value.s, tok->str_value.l, logic, missing_logic); } return; } // The case of (!atok->nsamples || !btok->nsamples) if ( !atok->nvalues && !btok->nvalues ) { if ( missing_logic[2] ) { for (i=0; insamples; i++) if ( rtok->usmpl[i] ) { rtok->pass_samples[i] = missing_logic[2]; rtok->pass_site = 1; } } return; } if ( !atok->nvalues || !btok->nvalues ) { token_t *tok = atok->nvalues ? atok : btok; if ( !tok->nsamples ) { int miss = _has_missing_string(tok->str_value.s); if ( !missing_logic[miss+1] ) return; for (i=0; insamples; i++) if ( rtok->usmpl[i] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; } } else for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; int miss = _has_missing_string(tok->str_value.s + i*tok->nval1); if ( missing_logic[miss+1] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; } } return; } // The case of (!atok->nsamples || !btok->nsamples) && (atok->nvalues && btok->nvalues) token_t *xtok = atok->nsamples ? atok : btok; token_t *ytok = atok->nsamples ? btok : atok; assert( regex==ytok->regex ); for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; int match; if ( regex ) match = _regex_vector_strings(regex, xtok->str_value.s + i*xtok->nval1, xtok->nval1, logic, missing_logic); else match = _match_vector_strings(xtok->str_value.s + i*xtok->nval1, xtok->nval1, ytok->str_value.s, ytok->str_value.l, logic, missing_logic); if ( match ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; } } } static int parse_idxs(char *tag_idx, int **idxs, int *nidxs, int *idx) { // TAG[], TAG[*] .. any field; sets idx=-2, idxs[0]=-1 if ( *tag_idx==0 || !strcmp("*", tag_idx) ) { *idxs = (int*) malloc(sizeof(int)); (*idxs)[0] = -1; *nidxs = 1; *idx = -2; return 0; } if ( !strcmp("GT", tag_idx) ) { *idxs = (int*) malloc(sizeof(int)); (*idxs)[0] = -1; *nidxs = 1; *idx = -3; return 0; } // TAG[integer] .. one field; idx positive char *end, *beg = tag_idx; *idx = strtol(tag_idx, &end, 10); if ( *idx >= 0 && *end==0 ) return 0; // TAG[0,1] or TAG[0-2] or [1-] etc; idx=-2, idxs[...]=0,0,1,1,.. int i, ibeg = -1; while ( *beg ) { int num = strtol(beg, &end, 10); if ( end[0]==',' ) beg = end + 1; else if ( end[0]==0 ) beg = end; else if ( end[0]=='-' ) { beg = end + 1; ibeg = num; continue; } else return -1; if ( num >= *nidxs ) { *idxs = (int*) realloc(*idxs, sizeof(int)*(num+1)); memset(*idxs + *nidxs, 0, sizeof(int)*(num - *nidxs + 1)); *nidxs = num + 1; } if ( ibeg>=0 ) { for (i=ibeg; i<=num; i++) (*idxs)[i] = 1; ibeg = -1; } (*idxs)[num] = 1; } if ( ibeg >=0 ) { if ( ibeg >= *nidxs ) { *idxs = (int*) realloc(*idxs, sizeof(int)*(ibeg+1)); memset(*idxs + *nidxs, 0, sizeof(int)*(ibeg - *nidxs + 1)); *nidxs = ibeg + 1; } (*idxs)[ibeg] = -1; } *idx = -2; return 0; } static void parse_tag_idx(bcf_hdr_t *hdr, int is_fmt, char *tag, char *tag_idx, token_t *tok) // tag_idx points just after "TAG[" { int i, len = strlen(tag_idx); if ( tag_idx[len-1] == ']' ) tag_idx[len-1] = 0; char *ori = strdup(tag_idx); assert( !tok->idxs && !tok->usmpl ); int *idxs1 = NULL, nidxs1 = 0, idx1 = 0; int *idxs2 = NULL, nidxs2 = 0, idx2 = 0; int set_samples = 0; char *colon = strrchr(tag_idx, ':'); if ( tag_idx[0]=='@' ) // file list with sample names { if ( !is_fmt ) error("Could not parse \"%s\". (Not a FORMAT tag yet a sample list provided.)\n", ori); char *fname = expand_path(tag_idx+1); #ifdef _WIN32 if (fname && strlen(fname) > 2 && fname[1] == ':') // Deal with Windows paths, such as 'C:\..' colon = strrchr(fname+2, ':'); #endif int nsmpl; char **list = hts_readlist(fname, 1, &nsmpl); if ( !list && colon ) { if ( parse_idxs(colon+1, &idxs2, &nidxs2, &idx2) != 0 ) error("Could not parse the index: %s\n", ori); tok->idxs = idxs2; tok->nidxs = nidxs2; tok->idx = idx2; colon = strrchr(fname, ':'); *colon = 0; list = hts_readlist(fname, 1, &nsmpl); } if ( !list ) error("Could not read: %s\n", fname); free(fname); tok->nsamples = bcf_hdr_nsamples(hdr); tok->usmpl = (uint8_t*) calloc(tok->nsamples,1); for (i=0; iusmpl[ismpl] = 1; } free(list); if ( !colon ) { tok->idxs = (int*) malloc(sizeof(int)); tok->idxs[0] = -1; tok->nidxs = 1; tok->idx = -2; } } else if ( colon ) { if ( !is_fmt ) error("Could not parse the index \"%s\". (Not a FORMAT tag yet sample index implied.)\n", ori); *colon = 0; if ( parse_idxs(tag_idx, &idxs1, &nidxs1, &idx1) != 0 ) error("Could not parse the index: %s\n", ori); if ( parse_idxs(colon+1, &idxs2, &nidxs2, &idx2) != 0 ) error("Could not parse the index: %s\n", ori); tok->idxs = idxs2; tok->nidxs = nidxs2; tok->idx = idx2; set_samples = 1; } else { if ( parse_idxs(tag_idx, &idxs1, &nidxs1, &idx1) != 0 ) error("Could not parse the index: %s\n", ori); if ( is_fmt ) { if ( nidxs1==1 && idxs1[0]==-1 ) { tok->idxs = (int*) malloc(sizeof(int)); tok->idxs[0] = -1; tok->nidxs = 1; tok->idx = idx1; } else if ( bcf_hdr_id2number(hdr,BCF_HL_FMT,tok->hdr_id)!=1 ) error("The FORMAT tag %s can have multiple subfields, run as %s[sample:subfield]\n", tag,tag); else tok->idx = 0; set_samples = 1; } else { tok->idxs = idxs1; tok->nidxs = nidxs1; tok->idx = idx1; } } if ( set_samples ) { tok->nsamples = bcf_hdr_nsamples(hdr); tok->usmpl = (uint8_t*) calloc(tok->nsamples,1); if ( idx1>=0 ) { if ( idx1 >= bcf_hdr_nsamples(hdr) ) error("The sample index is too large: %s\n", ori); tok->usmpl[idx1] = 1; } else if ( idx1==-2 || idx1==-3 ) { for (i=0; i= bcf_hdr_nsamples(hdr) ) error("The sample index is too large: %s\n", ori); tok->usmpl[i] = 1; } if ( nidxs1 && idxs1[nidxs1-1]==-1 ) // open range, such as "7-" { for (; insamples; i++) tok->usmpl[i] = 1; } } else error("todo: %s:%d .. %d\n", __FILE__,__LINE__, idx2); free(idxs1); } free(ori); if ( tok->nidxs && tok->idxs[tok->nidxs-1]!=-1 ) { for (i=0; inidxs; i++) if ( tok->idxs[i] ) tok->nuidxs++; } } static int max_ac_an_unpack(bcf_hdr_t *hdr) { int hdr_id = bcf_hdr_id2int(hdr,BCF_DT_ID,"AC"); if ( hdr_id<0 ) return BCF_UN_FMT; if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,hdr_id) ) return BCF_UN_FMT; hdr_id = bcf_hdr_id2int(hdr,BCF_DT_ID,"AN"); if ( hdr_id<0 ) return BCF_UN_FMT; if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,hdr_id) ) return BCF_UN_FMT; return BCF_UN_INFO; } static int filters_init1_ext(filter_t *filter, char *str, int len, token_t *tok) { tok->hl_type = -1; tok->ht_type = -1; tok->tok_type = TOK_VAL; tok->hdr_id = -1; tok->pass_site = -1; tok->idx = 0; tok->iext = ++filter->n_ext; filter->ext = realloc(filter->ext,sizeof(*filter->ext)*filter->n_ext); if ( !strncasecmp(str,"{str}",len) ) { tok->ht_type = BCF_HT_STR; tok->is_str = 1; } else if ( !strncasecmp(str,"{int}",len) ) tok->ht_type = BCF_HT_INT; else if ( !strncasecmp(str,"{float}",len) ) tok->ht_type = BCF_HT_REAL; filter->ext[filter->n_ext-1] = tok->ht_type; return 0; } static int filters_init1(filter_t *filter, char *str, int len, token_t *tok) { tok->ht_type = -1; tok->hl_type = -1; tok->tok_type = TOK_VAL; tok->hdr_id = -1; tok->pass_site = -1; tok->idx = 0; // is this a string constant? if ( str[0]=='"' || str[0]=='\'' ) { int quote = str[0]; if ( str[len-1] != quote ) error("TODO: [%s]\n", filter->str); tok->key = (char*) calloc(len-1,sizeof(char)); hts_expand(double,1,tok->mvalues,tok->values); tok->values[0] = len-2; memcpy(tok->key,str+1,len-2); tok->key[len-2] = 0; tok->is_str = 1; tok->ht_type = BCF_HT_STR; tok->nvalues = len-2; if ( !strcmp(".",tok->key) ) tok->is_missing = 1; return 0; } // is it a file? if ( str[0]=='@' ) { tok->tag = (char*) calloc(len+1,sizeof(char)); memcpy(tok->tag,str,len); tok->tag[len] = 0; char *fname = expand_path(tok->tag+1); int i, n; char **list = hts_readlist(fname, 1, &n); if ( !list ) error("Could not read: %s\n", fname); free(fname); tok->hash = khash_str2int_init(); for (i=0; ihash,list[i]) ) khash_str2int_inc(tok->hash,list[i]); else free(list[i]); } free(list); return 0; } int is_fmt = -1; if ( !strncasecmp(str,"FMT/",4) ) { str += 4; len -= 4; is_fmt = 1; } else if ( !strncasecmp(str,"FORMAT/",7) ) { str += 7; len -= 7; is_fmt = 1; } else { if ( !strncasecmp(str,"INFO/",5) ) { is_fmt = 0; str += 5; len -= 5; } else if ( !strncasecmp(str,"QUAL",len) || !strncmp(str,"%QUAL",len) /* for backward compatibility */ ) { tok->setter = filters_set_qual; tok->tag = strdup("QUAL"); tok->ht_type = BCF_HT_REAL; filter_add_used_tag(filter,NULL,tok->tag); return 0; } else if ( !strncasecmp(str,"TYPE",len) || !strncmp(str,"%TYPE",len) /* for backward compatibility */ ) { tok->setter = filters_set_type; tok->tag = strdup("TYPE"); tok->ht_type = BCF_HT_STR; return 0; } else if ( !strncasecmp(str,"FILTER",len) || !strncmp(str,"%FILTER",len) /* for backward compatibility */ ) { tok->comparator = filters_cmp_filter; tok->tag = strdup("FILTER"); filter->max_unpack |= BCF_UN_FLT; tok->hl_type = BCF_HL_FLT; tok->ht_type = BCF_HT_STR; filter_add_used_tag(filter,NULL,tok->tag); return 0; } else if ( !strncasecmp(str,"ID",len) || !strncasecmp(str,"%ID",len) /* for backward compatibility */ ) { tok->comparator = filters_cmp_id; tok->tag = strdup("ID"); tok->ht_type = BCF_HT_STR; filter_add_used_tag(filter,NULL,tok->tag); return 0; } else if ( !strncasecmp(str,"CHROM",len) ) { tok->setter = &filters_set_chrom; tok->tag = strdup("CHROM"); tok->ht_type = BCF_HT_STR; filter_add_used_tag(filter,NULL,tok->tag); return 0; } else if ( !strncasecmp(str,"POS",len) ) { tok->setter = &filters_set_pos; tok->tag = strdup("POS"); tok->ht_type = BCF_HT_INT; filter_add_used_tag(filter,NULL,tok->tag); return 0; } else if ( !strncasecmp(str,"REF",len) ) { tok->setter = &filters_set_ref_string; tok->is_str = 1; tok->tag = strdup("REF"); tok->ht_type = BCF_HT_STR; filter_add_used_tag(filter,NULL,tok->tag); return 0; } else if ( !strncasecmp(str,"ALT",len) ) { tok->setter = &filters_set_alt_string; tok->is_str = 1; tok->tag = strdup("ALT"); tok->ht_type = BCF_HT_STR; tok->idxs = (int*) malloc(sizeof(int)); tok->idxs[0] = -1; tok->nidxs = 1; tok->idx = -2; filter_add_used_tag(filter,NULL,tok->tag); return 0; } else if ( !strncasecmp(str,"N_ALT",len) ) { tok->setter = &filters_set_nalt; tok->tag = strdup("N_ALT"); tok->ht_type = BCF_HT_INT; return 0; } else if ( !strncasecmp(str,"N_SAMPLES",len) ) { tok->tok_type = TOK_VAL; tok->threshold = bcf_hdr_nsamples(filter->hdr); tok->is_constant = 1; tok->ht_type = BCF_HT_INT; return 0; } else if ( !strncasecmp(str,"N_MISSING",len) ) { filter->max_unpack |= BCF_UN_FMT; tok->setter = &filters_set_nmissing; tok->tag = strdup("N_MISSING"); tok->ht_type = BCF_HT_INT; return 0; } else if ( !strncasecmp(str,"F_MISSING",len) ) { filter->max_unpack |= BCF_UN_FMT; tok->setter = &filters_set_nmissing; tok->tag = strdup("F_MISSING"); tok->ht_type = BCF_HT_REAL; return 0; } } // does it have array subscript? int is_array = 0; kstring_t tmp = {0,0,0}; kputsn(str, len, &tmp); if ( tmp.s[tmp.l-1] == ']' ) { int i; for (i=0; ihdr_id = bcf_hdr_id2int(filter->hdr,BCF_DT_ID,tmp.s); if ( is_fmt==-1 ) { if ( tok->hdr_id >=0 ) { int is_info = bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_INFO,tok->hdr_id) ? 1 : 0; is_fmt = bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_FMT,tok->hdr_id) ? 1 : 0; if ( is_info && is_fmt ) error("Error: ambiguous filtering expression, both INFO/%s and FORMAT/%s are defined in the VCF header.\n" , tmp.s,tmp.s); } if ( is_fmt==-1 ) is_fmt = 0; } if ( is_array ) { parse_tag_idx(filter->hdr, is_fmt, tmp.s, tmp.s+is_array, tok); if ( tok->idx==-3 && bcf_hdr_id2length(filter->hdr,BCF_HL_FMT,tok->hdr_id)!=BCF_VL_R ) error("Error: GT subscripts can be used only with Number=R tags\n"); } else if ( is_fmt && !tok->nsamples ) { int i; tok->nsamples = bcf_hdr_nsamples(filter->hdr); tok->usmpl = (uint8_t*) malloc(tok->nsamples); for (i=0; insamples; i++) tok->usmpl[i] = 1; } tok->hl_type = is_fmt ? BCF_HL_FMT : BCF_HL_INFO; if ( is_fmt ) filter->max_unpack |= BCF_UN_FMT; if ( tok->hdr_id>=0 ) { if ( is_fmt && !strcmp("GT",tmp.s) ) { tok->setter = &filters_set_genotype_string; tok->is_str = 1; tok->ht_type = BCF_HT_STR; } else if ( is_fmt ) { if ( !bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_FMT,tok->hdr_id) ) error("No such FORMAT field: %s\n", tmp.s); if ( bcf_hdr_id2number(filter->hdr,BCF_HL_FMT,tok->hdr_id)!=1 && !is_array ) { tok->idxs = (int*) malloc(sizeof(int)); tok->idxs[0] = -1; tok->nidxs = 1; tok->idx = -2; } switch ( bcf_hdr_id2type(filter->hdr,BCF_HL_FMT,tok->hdr_id) ) { case BCF_HT_INT: tok->setter = &filters_set_format_int; tok->ht_type = BCF_HT_INT; break; case BCF_HT_REAL: tok->setter = &filters_set_format_float; tok->ht_type = BCF_HT_REAL; break; case BCF_HT_STR: tok->setter = &filters_set_format_string; tok->ht_type = BCF_HT_STR; tok->is_str = 1; break; default: error("[%s:%d %s] FIXME\n", __FILE__,__LINE__,__FUNCTION__); } } else if ( !bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_INFO,tok->hdr_id) ) error("No such INFO field: %s\n", tmp.s); else { if ( bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id) == BCF_HT_FLAG ) { tok->setter = filters_set_info_flag; tok->ht_type = BCF_HT_INT; } else { tok->ht_type = bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id); if ( tok->ht_type == BCF_HT_STR ) tok->is_str = 1; if ( bcf_hdr_id2number(filter->hdr,BCF_HL_INFO,tok->hdr_id)==1 ) tok->setter = filters_set_info; else { switch ( bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id) ) { case BCF_HT_INT: tok->setter = &filters_set_info_int; break; case BCF_HT_REAL: tok->setter = &filters_set_info_float; break; case BCF_HT_STR: tok->setter = &filters_set_info_string; tok->is_str = 1; break; default: error("[%s:%d %s] FIXME\n", __FILE__,__LINE__,__FUNCTION__); } if (!is_array) { tok->idx = -2; tok->idxs = (int*) malloc(sizeof(int)); tok->idxs[0] = -1; tok->nidxs = 1; } } } filter->max_unpack |= BCF_UN_INFO; } tok->tag = strdup(tmp.s); if ( tmp.s ) free(tmp.s); filter_add_used_tag(filter,is_fmt ? "FORMAT/" : "INFO/",tok->tag); return 0; } else if ( !strcasecmp(tmp.s,"ALT") ) { tok->setter = &filters_set_alt_string; tok->is_str = 1; tok->ht_type = BCF_HT_STR; tok->tag = strdup(tmp.s); free(tmp.s); filter_add_used_tag(filter,NULL,tok->tag); return 0; } else if ( !strcasecmp(tmp.s,"AN") ) { filter->max_unpack |= BCF_UN_FMT; tok->setter = &filters_set_an; tok->tag = strdup("AN"); tok->ht_type = BCF_HT_INT; free(tmp.s); return 0; } else if ( !strcasecmp(tmp.s,"AC") ) { filter->max_unpack |= BCF_UN_FMT; tok->setter = &filters_set_ac; tok->tag = strdup("AC"); tok->ht_type = BCF_HT_INT; free(tmp.s); return 0; } else if ( !strcasecmp(tmp.s,"MAC") ) { filter->max_unpack |= max_ac_an_unpack(filter->hdr); tok->setter = &filters_set_mac; tok->tag = strdup("MAC"); tok->ht_type = BCF_HT_INT; free(tmp.s); return 0; } else if ( !strcasecmp(tmp.s,"AF") ) { filter->max_unpack |= max_ac_an_unpack(filter->hdr); tok->setter = &filters_set_af; tok->tag = strdup("AF"); tok->ht_type = BCF_HT_REAL; free(tmp.s); return 0; } else if ( !strcasecmp(tmp.s,"MAF") ) { filter->max_unpack |= max_ac_an_unpack(filter->hdr); tok->setter = &filters_set_maf; tok->tag = strdup("MAF"); tok->ht_type = BCF_HT_REAL; free(tmp.s); return 0; } else if ( !strcasecmp(tmp.s,"ILEN") || !strcasecmp(tmp.s,"%ILEN") ) { filter->max_unpack |= BCF_UN_STR; tok->setter = &filters_set_ilen; tok->tag = strdup("ILEN"); tok->ht_type = BCF_HT_INT; free(tmp.s); return 0; } // is it a value? Here we parse as integer/float separately and use strtof // rather than strtod, because the more accurate double representation // would invalidate floating point comparisons like QUAL=59.2, obtained via // htslib/vcf parser. // Update: use strtod() and force floats only in comparisons char *end; tok->threshold = strtol(tmp.s, &end, 10); // integer? if ( end - tmp.s != strlen(tmp.s) ) { errno = 0; tok->threshold = strtod(tmp.s, &end); // float? if ( errno!=0 || end!=tmp.s+len ) { if ( filter->exit_on_error ) error("[%s:%d %s] Error: the tag \"%s\" is not defined in the VCF header\n", __FILE__,__LINE__,__FUNCTION__,tmp.s); filter->status |= FILTER_ERR_UNKN_TAGS; filter_add_undef_tag(filter,tmp.s); } tok->ht_type = BCF_HT_REAL; } else tok->ht_type = BCF_HT_INT; tok->is_constant = 1; if ( tmp.s ) free(tmp.s); return 0; } static void filter_debug_print(token_t *toks, token_t **tok_ptrs, int ntoks) { int i; for (i=0; itok_type==TOK_VAL ) { if ( tok->key ) fprintf(stderr,"%s", tok->key); else if ( tok->tag ) fprintf(stderr,"%s", tok->tag); else fprintf(stderr,"%e", tok->threshold); } else fprintf(stderr,"%c", TOKEN_STRING[tok->tok_type]); if ( tok->setter ) fprintf(stderr,"\t[setter %p]", tok->setter); fprintf(stderr,"\n"); } } static void str_to_lower(char *str) { while ( *str ) { *str = tolower(*str); str++; } } static int perl_exec(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { #if ENABLE_PERL_FILTERS PerlInterpreter *perl = flt->perl; if ( !perl ) error("Error: perl expression without a perl script name\n"); dSP; ENTER; SAVETMPS; PUSHMARK(SP); int i,j, istack = nstack - rtok->nargs; for (i=istack+1; iis_str ) XPUSHs(sv_2mortal(newSVpvn(tok->str_value.s,tok->str_value.l))); else if ( tok->nvalues==1 ) XPUSHs(sv_2mortal(newSVnv(tok->values[0]))); else if ( tok->nvalues>1 ) { AV *av = newAV(); for (j=0; jnvalues; j++) av_push(av, newSVnv(tok->values[j])); SV *rv = newRV_inc((SV*)av); XPUSHs(rv); } else { bcf_double_set_missing(tok->values[0]); XPUSHs(sv_2mortal(newSVnv(tok->values[0]))); } } PUTBACK; // A possible future todo: provide a means to select samples and indexes, // expressions like this don't work yet // perl.filter(FMT/AD)[1:0] int nret = call_pv(stack[istack]->str_value.s, G_ARRAY); SPAGAIN; rtok->nvalues = nret; hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values); for (i=nret; i>0; i--) { rtok->values[i-1] = (double) POPn; if ( isnan(rtok->values[i-1]) ) bcf_double_set_missing(rtok->values[i-1]); } PUTBACK; FREETMPS; LEAVE; #else error("\nPerl filtering requires running `configure --enable-perl-filters` at compile time.\n\n"); #endif return rtok->nargs; } static void perl_init(filter_t *filter, char **str) { char *beg = *str; while ( *beg && isspace(*beg) ) beg++; if ( !*beg ) return; if ( strncasecmp("perl:", beg, 5) ) return; #if ENABLE_PERL_FILTERS beg += 5; char *end = beg; while ( *end && *end!=';' ) end++; // for now not escaping semicolons *str = end+1; if ( ++filter_ninit == 1 ) { // must be executed only once, even for multiple filters; first time here int argc = 0; char **argv = NULL; char **env = NULL; PERL_SYS_INIT3(&argc, &argv, &env); } filter->perl = perl_alloc(); PerlInterpreter *perl = filter->perl; if ( !perl ) error("perl_alloc failed\n"); perl_construct(perl); // name of the perl script to run char *rmme = (char*) calloc(end - beg + 1,1); memcpy(rmme, beg, end - beg); char *argv[] = { "", "" }; argv[1] = expand_path(rmme); free(rmme); PL_origalen = 1; // don't allow $0 change int ret = perl_parse(filter->perl, NULL, 2, argv, NULL); PL_exit_flags |= PERL_EXIT_DESTRUCT_END; if ( ret ) error("Failed to parse: %s\n", argv[1]); free(argv[1]); perl_run(perl); #else error("\nPerl filtering requires running `configure --enable-perl-filters` at compile time.\n\n"); #endif } static void perl_destroy(filter_t *filter) { #if ENABLE_PERL_FILTERS if ( !filter->perl ) return; PerlInterpreter *perl = filter->perl; perl_destruct(perl); perl_free(perl); if ( --filter_ninit <= 0 ) { // similarly to PERL_SYS_INIT3, can must be executed only once? todo: test PERL_SYS_TERM(); } #endif } // A very rudimentary heuristics to determine type, e.g. STR_TAG={} implies {str}. // Throws an error on anything more complex and asks for an explicit type. static void determine_ext_types(filter_t *filter, int ntok, token_t *tok) { int i; for (i=0; istr); for (i=0; iext[j]!=-1 && filter->ext[j]!=tok[i].ht_type ) error("[%s:%d %s] FIXME: this should not happen %d vs %d, iext=%d\n",__FILE__,__LINE__,__FUNCTION__,filter->ext[j],tok[i].ht_type,j); filter->ext[j] = tok[i].ht_type; if ( tok[i].ht_type==BCF_HT_STR ) tok[i].is_str = 1; } } // Parse filter expression and convert to reverse polish notation. Dijkstra's shunting-yard algorithm static filter_t *filter_init_(bcf_hdr_t *hdr, const char *str, int exit_on_error) { filter_t *filter = (filter_t *) calloc(1,sizeof(filter_t)); filter->str = strdup(str); filter->hdr = hdr; filter->max_unpack |= BCF_UN_STR; filter->exit_on_error = exit_on_error; int nops = 0, mops = 0; // operators stack int nout = 0, mout = 0; // filter tokens, RPN token_t *out = NULL; token_t *ops = NULL; char *tmp = filter->str; perl_init(filter, &tmp); int last_op = -1; while ( *tmp ) { int len, ret; ret = filters_next_token(&tmp, &len); if ( ret==-1 ) error("Missing quotes in: %s\n", str); // fprintf(stderr,"token=[%c] .. [%s] %d\n", TOKEN_STRING[ret], tmp, len); // int i; for (i=0; i0 && ops[nops-1].tok_type!=TOK_LFT ) { nout++; hts_expand0(token_t, nout, mout, out); out[nout-1] = ops[nops-1]; memset(&ops[nops-1],0,sizeof(token_t)); nops--; } if ( nops<=0 ) error("Could not parse: %s\n", str); memset(&ops[nops-1],0,sizeof(token_t)); nops--; } else if ( ret==TOK_EXT ) // external value { nout++; hts_expand0(token_t, nout, mout, out); filters_init1_ext(filter, tmp, len, &out[nout-1]); tmp += len; } else if ( ret!=TOK_VAL ) // one of the operators { // detect unary minus: replace -value with -1*(value) if ( ret==TOK_SUB && last_op!=TOK_VAL && last_op!=TOK_RGT ) { nout++; hts_expand0(token_t, nout, mout, out); token_t *tok = &out[nout-1]; tok->tok_type = TOK_VAL; tok->hdr_id = -1; tok->pass_site = -1; tok->threshold = -1.0; tok->is_constant = 1; ret = TOK_MULT; } else if ( ret == -TOK_FUNC ) { // this is different from TOK_PERLSUB,TOK_BINOM in that the expression inside the // brackets gets evaluated as normal expression nops++; hts_expand0(token_t, nops, mops, ops); token_t *tok = &ops[nops-1]; tok->tok_type = -ret; tok->hdr_id = -1; tok->pass_site = -1; tok->threshold = -1.0; if ( !strncasecmp(tmp-len,"N_PASS",6) ) { filter->max_unpack |= BCF_UN_FMT; tok->func = func_npass; tok->tag = strdup("N_PASS"); } else if ( !strncasecmp(tmp-len,"F_PASS",6) ) { filter->max_unpack |= BCF_UN_FMT; tok->func = func_npass; tok->tag = strdup("F_PASS"); } else error("The function \"%s\" is not supported\n", tmp-len); continue; } else if ( ret < 0 ) // variable number of arguments: TOK_PERLSUB,TOK_BINOM { ret = -ret; tmp += len; char *beg = tmp; kstring_t rmme = {0,0,0}; int i, margs, nargs = 0; if ( ret == TOK_PERLSUB ) { while ( *beg && ((isalnum(*beg) && !ispunct(*beg)) || *beg=='_') ) beg++; if ( *beg!='(' ) error("Could not parse the expression: %s\n", str); // the subroutine name kputc('"', &rmme); kputsn(tmp, beg-tmp, &rmme); kputc('"', &rmme); nout++; hts_expand0(token_t, nout, mout, out); filters_init1(filter, rmme.s, rmme.l, &out[nout-1]); nargs++; } char *end = beg; while ( *end && *end!=')' ) end++; if ( !*end ) error("Could not parse the expression: %s\n", str); // subroutine arguments rmme.l = 0; kputsn(beg+1, end-beg-1, &rmme); char **rmme_list = hts_readlist(rmme.s, 0, &margs); for (i=0; itok_type = ret; tok->nargs = nargs; tok->hdr_id = -1; tok->pass_site = -1; tok->threshold = -1.0; tmp = end + 1; continue; } else { while ( nops>0 && op_prec[ret] < op_prec[ops[nops-1].tok_type] ) { nout++; hts_expand0(token_t, nout, mout, out); out[nout-1] = ops[nops-1]; memset(&ops[nops-1],0,sizeof(token_t)); nops--; } } nops++; hts_expand0(token_t, nops, mops, ops); ops[nops-1].tok_type = ret; } else if ( !len ) // all tokes read or an error { if ( *tmp && !isspace(*tmp) ) error("Could not parse the expression: [%s]\n", str); break; // all tokens read } else // TOK_VAL: annotation name or value { nout++; hts_expand0(token_t, nout, mout, out); if ( tmp[len-1]==',' ) filters_init1(filter, tmp, len-1, &out[nout-1]); else filters_init1(filter, tmp, len, &out[nout-1]); tmp += len; } last_op = ret; } while ( nops>0 ) { if ( ops[nops-1].tok_type==TOK_LFT || ops[nops-1].tok_type==TOK_RGT ) error("Could not parse the expression: [%s]\n", filter->str); nout++; hts_expand0(token_t, nout, mout, out); out[nout-1] = ops[nops-1]; memset(&ops[nops-1],0,sizeof(token_t)); nops--; } if ( filter->status != FILTER_OK ) { if ( mops ) free(ops); filter->filters = out; filter->nfilters = nout; return filter; } // Determine types of external variables from the context determine_ext_types(filter,nout,out); // In the special cases of TYPE and FILTER the BCF header IDs are yet unknown. Walk through the // list of operators and convert the strings (e.g. "PASS") to BCF ids. The string value token must be // just before or after the FILTER token and they must be followed with a comparison operator. // At this point we also initialize regex expressions which, in RPN, must precede the LIKE/NLIKE operator. // Additionally, treat "." as missing value rather than a string in numeric equalities; that // @file is only used with ID; etc. // This code is fragile: improve me. static int comma_separator_warned = 0; int i; for (i=0; istr); if ( out[i].hash ) { int j = out[i+1].tok_type==TOK_VAL ? i+1 : i-1; if ( out[j].comparator!=filters_cmp_id ) { if ( out[j].comparator ) error("Error: could not parse the expression with \"@file_name\" syntax (possible todo)\n"); out[j].comparator = filters_cmp_string_hash; } } if ( out[i].tok_type==TOK_OR || out[i].tok_type==TOK_OR_VEC ) out[i].func = vector_logic_or; if ( out[i].tok_type==TOK_AND || out[i].tok_type==TOK_AND_VEC ) out[i].func = vector_logic_and; if ( out[i].tok_type==TOK_EQ || out[i].tok_type==TOK_NE ) { // Look for j="." and k numeric type int j = i-1, k = i-2; if ( !out[j].is_str ) { k = i-1, j = i-2; } if ( out[j].is_str && out[j].key && !strcmp(".",out[j].key) ) { int set_missing = 0; if ( out[k].hdr_id>0 ) { int type = bcf_hdr_id2type(filter->hdr,out[k].hl_type,out[k].hdr_id); if ( type==BCF_HT_INT ) set_missing = 1; else if ( type==BCF_HT_REAL ) set_missing = 1; } else if ( !strcmp("QUAL",out[k].tag) ) set_missing = 1; if ( set_missing ) { out[j].is_str = 0; out[j].is_missing = 1; bcf_double_set_missing(out[j].values[0]); } } } if ( out[i].tok_type==TOK_LIKE || out[i].tok_type==TOK_NLIKE ) { int j = i-1; if ( !out[j].key ) error("Could not parse the expression, wrong value for regex operator: %s\n", filter->str); out[j].regex = (regex_t *) malloc(sizeof(regex_t)); int cflags = REG_NOSUB; int len = strlen(out[j].key); if ( len>2 && out[j].key[len-1]=='i' && out[j].key[len-2]=='/' && out[j].key[len-3]!='\\' ) { out[j].key[len-2] = 0; cflags |= REG_ICASE; } if ( regcomp(out[j].regex, out[j].key, cflags) ) error("Could not compile the regex expression \"%s\": %s\n", out[j].key,filter->str); } if ( out[i].is_str && out[i].tok_type==TOK_VAL && out[i].key && strchr(out[i].key,',') ) { int print_note = 0; if ( out[i+1].tok_type==TOK_EQ || (out[i+1].is_str && out[i+2].tok_type==TOK_EQ) ) print_note = 1; else if ( out[i+1].tok_type==TOK_NE || (out[i+1].is_str && out[i+2].tok_type==TOK_NE) ) print_note = 1; if ( print_note && !comma_separator_warned ) { comma_separator_warned = 1; fprintf(stderr, "Warning: comma is interpreted as a separator and OR logic is used in string comparisons.\n" " (Search the manual for \"Comma in strings\" to learn more.)\n"); } } if ( out[i].tok_type!=TOK_VAL ) continue; if ( !out[i].tag ) continue; if ( out[i].setter==filters_set_type ) { if ( i+1==nout || !out[i+1].key ) error("Could not parse the expression: %s\n", filter->str); int itok, ival; if ( out[i+1].tok_type==TOK_EQ || out[i+1].tok_type==TOK_NE ) ival = i - 1, itok = i + 1; else if ( out[i+1].tok_type==TOK_LIKE || out[i+1].tok_type==TOK_NLIKE ) ival = i - 1, itok = i + 1; else if ( out[i+2].tok_type==TOK_EQ || out[i+2].tok_type==TOK_NE ) itok = i + 2, ival = i + 1; else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = i + 2, ival = i + 1; else error("[%s:%d %s] Could not parse the expression: %s\n", __FILE__,__LINE__,__FUNCTION__, filter->str); if ( !strcasecmp(out[ival].key,"snp") || !strcasecmp(out[ival].key,"snps") ) { out[ival].threshold = VCF_SNP<<1; out[ival].is_str = 0; } else if ( !strcasecmp(out[ival].key,"indel") || !strcasecmp(out[ival].key,"indels") ) { out[ival].threshold = VCF_INDEL<<1; out[ival].is_str = 0; } else if ( !strcasecmp(out[ival].key,"mnp") || !strcasecmp(out[ival].key,"mnps") ) { out[ival].threshold = VCF_MNP<<1; out[ival].is_str = 0; } else if ( !strcasecmp(out[ival].key,"other") ) { out[ival].threshold = VCF_OTHER<<1; out[ival].is_str = 0; } else if ( !strcasecmp(out[ival].key,"bnd") ) { out[ival].threshold = VCF_BND<<1; out[ival].is_str = 0; } else if ( !strcasecmp(out[ival].key,"overlap") ) { out[ival].threshold = VCF_OVERLAP<<1; out[ival].is_str = 0; } else if ( !strcasecmp(out[ival].key,"ref") ) { out[ival].threshold = 1; out[ival].is_str = 0; } else error("The type \"%s\" not recognised: %s\n", out[ival].key, filter->str); out[ival].is_constant = 1; if ( out[itok].tok_type==TOK_LIKE || out[itok].tok_type==TOK_NLIKE ) out[itok].comparator = filters_cmp_bit_and; out[ival].tag = out[ival].key; out[ival].key = NULL; i = itok; continue; } if ( !strcmp(out[i].tag,"GT") ) { if ( i+1==nout ) error("Could not parse the expression: %s\n", filter->str); int ival; if ( out[i+1].tok_type==TOK_EQ || out[i+1].tok_type==TOK_NE ) ival = i - 1; else if ( out[i+1].tok_type==TOK_LIKE || out[i+1].tok_type==TOK_NLIKE ) ival = i - 1; else if ( out[i+2].tok_type==TOK_EQ || out[i+2].tok_type==TOK_NE ) ival = i + 1; else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) ival = i + 1; else error("[%s:%d %s] Could not parse the expression: %s\n", __FILE__,__LINE__,__FUNCTION__, filter->str); if ( !out[ival].key ) error("Comparison between samples is not supported, sorry!\n"); // assign correct setters and unify expressions, eg ar->ra, HOM->hom, etc if ( !strcasecmp(out[ival].key,"hom") ) { out[i].setter = filters_set_genotype3; str_to_lower(out[ival].key); } else if ( !strcasecmp(out[ival].key,"het") ) { out[i].setter = filters_set_genotype3; str_to_lower(out[ival].key); } else if ( !strcasecmp(out[ival].key,"hap") ) { out[i].setter = filters_set_genotype3; str_to_lower(out[ival].key); } else if ( !strcasecmp(out[ival].key,"mis") ) { out[i].setter = filters_set_genotype4; str_to_lower(out[ival].key); } else if ( !strcasecmp(out[ival].key,"ref") ) { out[i].setter = filters_set_genotype4; str_to_lower(out[ival].key); } else if ( !strcasecmp(out[ival].key,"alt") ) { out[i].setter = filters_set_genotype4; str_to_lower(out[ival].key); } else if ( !strcasecmp(out[ival].key,"rr") ) { out[i].setter = filters_set_genotype2; str_to_lower(out[ival].key); } else if ( !strcasecmp(out[ival].key,"ra") || !strcasecmp(out[ival].key,"ar") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='r'; out[ival].key[1]='a'; } // ra else if ( !strcmp(out[ival].key,"aA") || !strcmp(out[ival].key,"Aa") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='a'; out[ival].key[1]='A'; } // aA else if ( !strcasecmp(out[ival].key,"aa") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='a'; out[ival].key[1]='a'; } // aa else if ( !strcasecmp(out[ival].key,"a") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='a'; out[ival].key[1]=0; } // a else if ( !strcasecmp(out[ival].key,"r") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='r'; out[ival].key[1]=0; } // r continue; } if ( out[i].hl_type==BCF_HL_FLT ) { if ( i+1==nout ) error("Could not parse the expression: %s\n", filter->str); int itok = i, ival; if ( out[i+1].tok_type==TOK_EQ || out[i+1].tok_type==TOK_NE ) ival = i - 1; else if ( out[i+1].tok_type==TOK_LIKE ) out[i+1].tok_type = TOK_IN, ival = i - 1; else if ( out[i+1].tok_type==TOK_NLIKE ) out[i+1].tok_type = TOK_NOT_IN, ival = i - 1; else if ( out[i+2].tok_type==TOK_EQ || out[i+2].tok_type==TOK_NE ) ival = ++i; else if ( out[i+2].tok_type==TOK_LIKE ) out[i+2].tok_type = TOK_IN, ival = ++i; else if ( out[i+2].tok_type==TOK_NLIKE ) out[i+2].tok_type = TOK_NOT_IN, ival = ++i; else error("[%s:%d %s] Could not parse the expression: %s\n", __FILE__,__LINE__,__FUNCTION__, filter->str); if ( out[ival].tok_type!=TOK_VAL || !out[ival].key ) error("[%s:%d %s] Could not parse the expression, an unquoted string value perhaps? %s\n", __FILE__,__LINE__,__FUNCTION__, filter->str); token_t *tok = &out[ival]; char *bp = tok->key; tok->nvalues = 0; int has_missing = 0; while ( *bp ) { char tmp, *ep = bp; while ( *ep && *ep!=';' ) ep++; tmp = *ep; *ep = 0; if ( !strcmp(".",bp) ) has_missing = 1; else { tok->nvalues++; hts_expand(double,tok->nvalues,tok->mvalues,tok->values); int id = bcf_hdr_id2int(filter->hdr, BCF_DT_ID, bp); if ( !bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_FLT,id) ) error("The filter \"%s\" not present in the VCF header\n", bp); tok->values[tok->nvalues-1] = id; } *ep = tmp; if ( !tmp ) break; bp = ep + 1; } if ( has_missing && tok->nvalues ) error("The FILTER expression cannot contain missing value AND filters: \"%s\" (%d)\n",tok->key,tok->nvalues); out[ival].tag = tok->key; tok->key = NULL; out[itok].hdr_id = tok->hdr_id; continue; } } filter->nsamples = filter->max_unpack&BCF_UN_FMT ? bcf_hdr_nsamples(filter->hdr) : 0; for (i=0; insamples ) { out[i].pass_samples = (uint8_t*)malloc(filter->nsamples); int j; for (j=0; jnsamples; j++) out[i].pass_samples[j] = 0; } } if (0) filter_debug_print(out, NULL, nout); if ( mops ) free(ops); filter->filters = out; filter->nfilters = nout; filter->flt_stack = (token_t **)malloc(sizeof(token_t*)*nout); return filter; } filter_t *filter_parse(bcf_hdr_t *hdr, const char *str) { return filter_init_(hdr, str, 0); } filter_t *filter_init(bcf_hdr_t *hdr, const char *str) { return filter_init_(hdr, str, 1); } void filter_destroy(filter_t *filter) { perl_destroy(filter); int i; for (i=0; infilters; i++) { if ( filter->filters[i].key ) free(filter->filters[i].key); free(filter->filters[i].str_value.s); free(filter->filters[i].tag); free(filter->filters[i].idxs); free(filter->filters[i].usmpl); free(filter->filters[i].values); free(filter->filters[i].pass_samples); if (filter->filters[i].hash) khash_str2int_destroy_free(filter->filters[i].hash); if (filter->filters[i].regex) { regfree(filter->filters[i].regex); free(filter->filters[i].regex); } } for (i=0; inundef_tag; i++) free(filter->undef_tag[i]); for (i=0; inused_tag; i++) free(filter->used_tag[i]); free(filter->ext); free(filter->undef_tag); free(filter->used_tag); free(filter->cached_GT.buf); free(filter->cached_GT.mask); free(filter->filters); free(filter->flt_stack); free(filter->str); free(filter->tmpi); free(filter->tmpf); free(filter->tmps.s); free(filter); } int filter_test_ext(filter_t *filter, bcf1_t *rec, const uint8_t **samples, const void **ext) { if ( !filter->n_ext ) return filter_test(filter,rec,samples); int i; for (i=0; infilters; i++) { token_t *tok = &filter->filters[i]; if ( !tok->iext ) continue; if ( !ext[tok->iext-1] ) { tok->is_missing = 1; tok->nvalues = 0; if ( filter->ext[tok->iext-1]==BCF_HT_STR ) tok->str_value.l = 0; continue; } tok->is_missing = 0; tok->nvalues = 1; if ( filter->ext[tok->iext-1]==BCF_HT_STR ) { tok->str_value.l = 0; kputs((const char*)ext[tok->iext-1],&tok->str_value); tok->nvalues = tok->str_value.l; } else if ( filter->ext[tok->iext-1]==BCF_HT_INT ) tok->values[0] = *((const int*)ext[tok->iext-1]); else if ( filter->ext[tok->iext-1]==BCF_HT_REAL ) tok->values[0] = *((const float*)ext[tok->iext-1]); } return filter_test(filter,rec,samples); } int filter_test(filter_t *filter, bcf1_t *line, const uint8_t **samples) { if ( filter->status != FILTER_OK ) error("Error: the caller did not check the filter status\n"); bcf_unpack(line, filter->max_unpack); int i, nstack = 0; for (i=0; infilters; i++) { filter->filters[i].pass_site = 0; if ( filter->filters[i].tok_type == TOK_VAL ) { if ( filter->filters[i].setter ) // variable, query the VCF line filter->filters[i].setter(filter, line, &filter->filters[i]); else if ( filter->filters[i].key ) // string constant { filter->filters[i].str_value.l = 0; kputs(filter->filters[i].key, &filter->filters[i].str_value); filter->filters[i].nvalues = filter->filters[i].str_value.l; } else if ( filter->filters[i].is_constant ) // numeric constant { filter->filters[i].values[0] = filter->filters[i].threshold; filter->filters[i].nvalues = 1; } filter->flt_stack[nstack++] = &filter->filters[i]; continue; } else if ( filter->filters[i].func ) { int nargs = filter->filters[i].func(filter, line, &filter->filters[i], filter->flt_stack, nstack); filter->flt_stack[nstack-nargs] = &filter->filters[i]; if ( --nargs > 0 ) nstack -= nargs; continue; } if ( nstack<2 ) error("Error occurred while processing the filter \"%s\" (1:%d)\n", filter->str,nstack); // too few values left on the stack int is_str = filter->flt_stack[nstack-1]->is_str + filter->flt_stack[nstack-2]->is_str; if ( filter->filters[i].tok_type == TOK_ADD ) { VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],+,(double)); filter->flt_stack[nstack-2] = &filter->filters[i]; nstack--; continue; } else if ( filter->filters[i].tok_type == TOK_SUB ) { VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],-,(double)); filter->flt_stack[nstack-2] = &filter->filters[i]; nstack--; continue; } else if ( filter->filters[i].tok_type == TOK_MULT ) { VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],*,(double)); filter->flt_stack[nstack-2] = &filter->filters[i]; nstack--; continue; } else if ( filter->filters[i].tok_type == TOK_DIV ) { VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],/,(double)); filter->flt_stack[nstack-2] = &filter->filters[i]; nstack--; continue; } else if ( filter->filters[i].tok_type == TOK_MODULO ) { VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],%,(int)); filter->flt_stack[nstack-2] = &filter->filters[i]; nstack--; continue; } // ideally, these comparators would become func, but this would require more work in init1() if ( filter->filters[i].comparator ) { filter->filters[i].comparator(filter->flt_stack[nstack-1],filter->flt_stack[nstack-2],&filter->filters[i],line); } else if ( filter->flt_stack[nstack-1]->comparator ) { filter->flt_stack[nstack-1]->comparator(filter->flt_stack[nstack-1],filter->flt_stack[nstack-2],&filter->filters[i],line); } else if ( filter->flt_stack[nstack-2]->comparator ) { filter->flt_stack[nstack-2]->comparator(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],line); } else if ( is_str==2 ) { cmp_vector_strings(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i]); } else { if ( is_str==1 ) error("Error: cannot use arithmetic operators to compare strings and numbers\n"); // Determine what to do with one [1] or both [2] sides missing. The first field [0] gives [1]|[2] int missing_logic[] = {0,0,0}; if ( filter->filters[i].tok_type == TOK_EQ ) { missing_logic[0] = missing_logic[2] = 1; } if ( filter->filters[i].tok_type == TOK_NE ) { missing_logic[0] = missing_logic[1] = 1; } if ( filter->filters[i].tok_type == TOK_EQ ) CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],==,missing_logic) else if ( filter->filters[i].tok_type == TOK_NE ) CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],!=,missing_logic) else if ( filter->filters[i].tok_type == TOK_LE ) CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],<=,missing_logic) else if ( filter->filters[i].tok_type == TOK_LT ) CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],<,missing_logic) else if ( filter->filters[i].tok_type == TOK_BT ) CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],>,missing_logic) else if ( filter->filters[i].tok_type == TOK_BE ) CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],>=,missing_logic) else error("todo: %s:%d .. type=%d\n", __FILE__,__LINE__,filter->filters[i].tok_type); } filter->flt_stack[nstack-2] = &filter->filters[i]; nstack--; } if ( nstack>1 ) error("Error occurred while processing the filter \"%s\" (2:%d)\n", filter->str,nstack); // too few values left on the stack if ( samples ) { *samples = filter->max_unpack&BCF_UN_FMT ? filter->flt_stack[0]->pass_samples : NULL; if ( *samples && !filter->flt_stack[0]->nsamples ) { for (i=0; insamples; i++) filter->flt_stack[0]->pass_samples[i] = filter->flt_stack[0]->pass_site; } } return filter->flt_stack[0]->pass_site; } int filter_max_unpack(filter_t *flt) { return flt->max_unpack; } const int *filter_ext_types(filter_t *filter, int *n_ext) { *n_ext = filter->n_ext; return filter->ext; } const double *filter_get_doubles(filter_t *filter, int *nval, int *nval1) { token_t *tok = filter->flt_stack[0]; if ( tok->nvalues ) { *nval = tok->nvalues; *nval1 = tok->nval1; } else { if ( !tok->values ) error("fixme in filter_get_doubles(): %s\n", filter->str); *nval = 1; *nval1 = 1; tok->values[0] = filter->flt_stack[0]->pass_site; } return tok->values; } void filter_set_samples(filter_t *filter, const uint8_t *samples) { int i,j; for (i=0; infilters; i++) { if ( !filter->filters[i].nsamples ) continue; for (j=0; jfilters[i].nsamples; j++) filter->filters[i].usmpl[j] = samples[j]; } } int filter_status(filter_t *filter) { return filter->status; } pysam-0.23.0/bcftools/filter.c.pysam.c000066400000000000000000004626631475062545500176000ustar00rootroot00000000000000#include "bcftools.pysam.h" /* filter.c -- filter expressions. Copyright (C) 2013-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #ifndef _WIN32 #include #endif #include #include #include #include #include #include #include "config.h" #include "filter.h" #include "bcftools.h" #if ENABLE_PERL_FILTERS // Work around clang warning problems # if defined(__clang__) # define PERL_GCC_BRACE_GROUPS_FORBIDDEN # endif # define filter_t perl_filter_t # include # include # undef filter_t # define my_perl perl static int filter_ninit = 0; #endif #ifndef __FUNCTION__ # define __FUNCTION__ __func__ #endif typedef struct _token_t { // read-only values, same for all VCF lines int tok_type; // one of the TOK_* keys below int nargs; // with TOK_PERLSUB the first argument is the name of the subroutine char *key; // set only for string constants, otherwise NULL char *tag; // for debugging and printout only, VCF tag name double threshold; // filtering threshold int is_constant; // the threshold is set int hdr_id, hl_type, ht_type; // BCF header lookup ID and one of BCF_HL_* types and BCF_HT_* types int idx; // 0-based index to VCF vectors, // -2: list (e.g. [0,1,2] or [1..3] or [1..] or any field[*], which is equivalent to [0..]) // -3: select indices on the fly based on values in GT int *idxs; // set indexes to 0 to exclude, to 1 to include, and last element negative if unlimited; used by VCF retrievers only int nidxs, nuidxs; // size of idxs array and the number of elements set to 1 uint8_t *usmpl; // bitmask of used samples as set by idx, set for FORMAT fields, NULL otherwise int nsamples; // number of samples for format fields, 0 for info and other fields void (*setter)(filter_t *, bcf1_t *, struct _token_t *); int (*func)(filter_t *, bcf1_t *, struct _token_t *rtok, struct _token_t **stack, int nstack); void (*comparator)(struct _token_t *, struct _token_t *, struct _token_t *rtok, bcf1_t *); void *hash; // test presence of str value in the hash via comparator regex_t *regex; // precompiled regex for string comparison int iext; // for the use with filter_test_ext(), 1-based index to external values, 0=don't use // modified on filter evaluation at each VCF line double *values; kstring_t str_value; int is_str, is_missing; // is_missing is set only for constants, variables are controlled via nvalues int pass_site; // -1 not applicable, 0 fails, >0 pass uint8_t *pass_samples; // status of individual samples int nvalues, mvalues; // number of used values: n=0 for missing values, n=1 for scalars, for strings n=str_value.l int nval1; // number of per-sample fields or string length } token_t; struct _filter_t { bcf_hdr_t *hdr; char *str; int nfilters; token_t *filters, **flt_stack; // filtering input tokens (in RPN) and evaluation stack int32_t *tmpi; float *tmpf; kstring_t tmps; int max_unpack, mtmpi, mtmpf, nsamples; struct { bcf1_t *line; int32_t *buf, nbuf, mbuf; // GTs as obtained by bcf_get_genotypes() uint64_t *mask; // GTs as mask, e.g 0/0 is 1; 0/1 is 3, max 63 unique alleles } cached_GT; #if ENABLE_PERL_FILTERS PerlInterpreter *perl; #endif char **undef_tag, **used_tag; int nundef_tag, nused_tag; int status, exit_on_error; int n_ext; // number of external values to fill via filter_test_ext() int *ext; // types of external values to fill via filter_test_ext() }; #define TOK_VAL 0 #define TOK_LFT 1 // ( #define TOK_RGT 2 // ) #define TOK_LE 3 // less or equal #define TOK_LT 4 // less than #define TOK_EQ 5 // equal #define TOK_BT 6 // bigger than #define TOK_BE 7 // bigger or equal #define TOK_NE 8 // not equal #define TOK_OR 9 // | #define TOK_AND 10 // & #define TOK_ADD 11 // + #define TOK_SUB 12 // - #define TOK_MULT 13 // * #define TOK_DIV 14 // / #define TOK_MAX 15 #define TOK_MIN 16 #define TOK_AVG 17 #define TOK_AND_VEC 18 // && (operator applied in samples) #define TOK_OR_VEC 19 // || (operator applied in samples) #define TOK_LIKE 20 // ~ regular expression #define TOK_NLIKE 21 // !~ regular expression #define TOK_SUM 22 #define TOK_ABS 23 #define TOK_LEN 24 #define TOK_FUNC 25 #define TOK_CNT 26 #define TOK_PERLSUB 27 #define TOK_BINOM 28 #define TOK_PHRED 29 #define TOK_MEDIAN 30 #define TOK_STDEV 31 #define TOK_sMAX 32 #define TOK_sMIN 33 #define TOK_sAVG 34 #define TOK_sMEDIAN 35 #define TOK_sSTDEV 36 #define TOK_sSUM 37 #define TOK_IN 38 // contains, e.g. FILTER~"A" #define TOK_NOT_IN 39 // does not contain, e.g. FILTER!~"A" #define TOK_MODULO 40 // % #define TOK_EXT 41 // external values set before each filter_test_ext() call, can be one of {},{str},{int},{float} // 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 // ( ) [ < = > ] ! | & + - * / M m a A O ~ ^ S . l f c p b P i s % static int op_prec[] = {0,1,1,5,5,5,5,5,5,2,3, 6, 6, 7, 7, 8, 8, 8, 3, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 0}; #define TOKEN_STRING "x()[<=>]!|&+-*/MmaAO~^S.lfcpis" // this is only for debugging, not maintained diligently static void cmp_vector_strings(token_t *atok, token_t *btok, token_t *rtok); inline static void tok_init_samples(token_t *atok, token_t *btok, token_t *rtok); // Return negative values if it is a function with variable number of arguments static int filters_next_token(char **str, int *len) { char *tmp = *str; while ( *tmp && isspace(*tmp) ) tmp++; *str = tmp; *len = 0; // test for doubles: d.ddde[+-]dd if ( isdigit(*str[0]) || *str[0]=='.' ) // strtod would eat +/- { double HTS_UNUSED v = strtod(*str, &tmp); if ( *str!=tmp && (!tmp[0] || !isalnum(tmp[0])) ) { *len = tmp - (*str); return TOK_VAL; } tmp = *str; } if ( !strncasecmp(tmp,"SMPL_MAX(",9) ) { (*str) += 8; return TOK_sMAX; } if ( !strncasecmp(tmp,"SMPL_MIN(",9) ) { (*str) += 8; return TOK_sMIN; } if ( !strncasecmp(tmp,"SMPL_MEAN(",10) ) { (*str) += 9; return TOK_sAVG; } if ( !strncasecmp(tmp,"SMPL_MEDIAN(",12) ) { (*str) += 11; return TOK_sMEDIAN; } if ( !strncasecmp(tmp,"SMPL_AVG(",9) ) { (*str) += 8; return TOK_sAVG; } if ( !strncasecmp(tmp,"SMPL_STDEV(",11) ) { (*str) += 10; return TOK_sSTDEV; } if ( !strncasecmp(tmp,"SMPL_SUM(",9) ) { (*str) += 8; return TOK_sSUM; } if ( !strncasecmp(tmp,"sMAX(",5) ) { (*str) += 4; return TOK_sMAX; } if ( !strncasecmp(tmp,"sMIN(",5) ) { (*str) += 4; return TOK_sMIN; } if ( !strncasecmp(tmp,"sMEAN(",6) ) { (*str) += 5; return TOK_sAVG; } if ( !strncasecmp(tmp,"sMEDIAN(",8) ) { (*str) += 7; return TOK_sMEDIAN; } if ( !strncasecmp(tmp,"sAVG(",5) ) { (*str) += 4; return TOK_sAVG; } if ( !strncasecmp(tmp,"sSTDEV(",7) ) { (*str) += 6; return TOK_sSTDEV; } if ( !strncasecmp(tmp,"sSUM(",5) ) { (*str) += 4; return TOK_sSUM; } if ( !strncasecmp(tmp,"MAX(",4) ) { (*str) += 3; return TOK_MAX; } if ( !strncasecmp(tmp,"MIN(",4) ) { (*str) += 3; return TOK_MIN; } if ( !strncasecmp(tmp,"MEAN(",5) ) { (*str) += 4; return TOK_AVG; } if ( !strncasecmp(tmp,"MEDIAN(",7) ) { (*str) += 6; return TOK_MEDIAN; } if ( !strncasecmp(tmp,"AVG(",4) ) { (*str) += 3; return TOK_AVG; } if ( !strncasecmp(tmp,"STDEV(",6) ) { (*str) += 5; return TOK_STDEV; } if ( !strncasecmp(tmp,"SUM(",4) ) { (*str) += 3; return TOK_SUM; } if ( !strncasecmp(tmp,"ABS(",4) ) { (*str) += 3; return TOK_ABS; } if ( !strncasecmp(tmp,"COUNT(",4) ) { (*str) += 5; return TOK_CNT; } if ( !strncasecmp(tmp,"STRLEN(",7) ) { (*str) += 6; return TOK_LEN; } if ( !strncasecmp(tmp,"BINOM(",6) ) { (*str) += 5; return -TOK_BINOM; } if ( !strncasecmp(tmp,"PHRED(",6) ) { (*str) += 5; return TOK_PHRED; } if ( !strncasecmp(tmp,"%MAX(",5) ) { (*str) += 4; return TOK_MAX; } // for backward compatibility if ( !strncasecmp(tmp,"%MIN(",5) ) { (*str) += 4; return TOK_MIN; } // for backward compatibility if ( !strncasecmp(tmp,"%AVG(",5) ) { (*str) += 4; return TOK_AVG; } // for backward compatibility if ( !strncasecmp(tmp,"%SUM(",5) ) { (*str) += 4; return TOK_SUM; } // for backward compatibility if ( !strncasecmp(tmp,"INFO/",5) ) tmp += 5; if ( !strncasecmp(tmp,"FORMAT/",7) ) tmp += 7; if ( !strncasecmp(tmp,"FMT/",4) ) tmp += 4; if ( !strncasecmp(tmp,"PERL.",5) ) { (*str) += 5; return -TOK_PERLSUB; } if ( !strncasecmp(tmp,"N_PASS(",7) ) { *len = 6; (*str) += 6; return -TOK_FUNC; } if ( !strncasecmp(tmp,"F_PASS(",7) ) { *len = 6; (*str) += 6; return -TOK_FUNC; } if ( !strncasecmp(tmp,"%ILEN",5) ) { *len = 5; return TOK_VAL; } // to be able to distinguish between INFO/ILEN and on-the-fly ILEN if ( !strncasecmp(tmp,"{}",2) ) { *len = 2; return TOK_EXT; } if ( !strncasecmp(tmp,"{STR}",5) ) { *len = 5; return TOK_EXT; } if ( !strncasecmp(tmp,"{INT}",5) ) { *len = 5; return TOK_EXT; } if ( !strncasecmp(tmp,"{FLOAT}",7) ) { *len = 7; return TOK_EXT; } if ( tmp[0]=='@' ) // file name { while ( *tmp && !isspace(*tmp) && *tmp!='=' && *tmp!='!' ) tmp++; *len = tmp - (*str); return TOK_VAL; } int square_brackets = 0; while ( tmp[0] ) { if ( !square_brackets ) { if ( tmp[0]=='"' ) break; if ( tmp[0]=='\'' ) break; if ( isspace(tmp[0]) ) break; if ( tmp[0]=='<' ) break; if ( tmp[0]=='>' ) break; if ( tmp[0]=='=' ) break; if ( tmp[0]=='!' ) break; if ( tmp[0]=='&' ) break; if ( tmp[0]=='|' ) break; if ( tmp[0]=='(' ) break; if ( tmp[0]==')' ) break; if ( tmp[0]=='+' ) break; if ( tmp[0]=='*' ) break; if ( tmp[0]=='-' ) break; if ( tmp[0]=='/' ) break; if ( tmp[0]=='~' ) break; if ( tmp[0]=='%' ) break; } if ( tmp[0]==']' ) { if (square_brackets) tmp++; break; } if ( tmp[0]=='[' ) square_brackets++; tmp++; } if ( tmp > *str ) { *len = tmp - (*str); return TOK_VAL; } if ( tmp[0]=='"' || tmp[0]=='\'' ) { int quote = tmp[0]; tmp++; while ( *tmp && tmp[0]!=quote ) tmp++; if ( !*tmp ) return -1; // missing quotes *len = tmp - (*str) + 1; return TOK_VAL; } if ( tmp[0]=='!' ) { if ( tmp[1]=='=' ) { (*str) += 2; return TOK_NE; } if ( tmp[1]=='~' ) { (*str) += 2; return TOK_NLIKE; } } if ( tmp[0]=='<' ) { if ( tmp[1]=='=' ) { (*str) += 2; return TOK_LE; } (*str) += 1; return TOK_LT; } if ( tmp[0]=='>' ) { if ( tmp[1]=='=' ) { (*str) += 2; return TOK_BE; } (*str) += 1; return TOK_BT; } if ( tmp[0]=='=' ) { if ( tmp[1]=='=' ) { (*str) += 2; return TOK_EQ; } (*str) += 1; return TOK_EQ; } if ( tmp[0]=='(' ) { (*str) += 1; return TOK_LFT; } if ( tmp[0]==')' ) { (*str) += 1; return TOK_RGT; } if ( tmp[0]=='&' && tmp[1]=='&' ) { (*str) += 2; return TOK_AND_VEC; } if ( tmp[0]=='|' && tmp[1]=='|' ) { (*str) += 2; return TOK_OR_VEC; } if ( tmp[0]=='&' ) { (*str) += 1; return TOK_AND; } if ( tmp[0]=='|' ) { (*str) += 1; return TOK_OR; } if ( tmp[0]=='+' ) { (*str) += 1; return TOK_ADD; } if ( tmp[0]=='-' ) { (*str) += 1; return TOK_SUB; } if ( tmp[0]=='*' ) { (*str) += 1; return TOK_MULT; } if ( tmp[0]=='/' ) { (*str) += 1; return TOK_DIV; } if ( tmp[0]=='~' ) { (*str) += 1; return TOK_LIKE; } if ( tmp[0]=='%' ) { (*str) += 1; return TOK_MODULO; } *len = tmp - (*str); return TOK_VAL; } #define FILTER_OK 0 #define FILTER_ERR_UNKN_TAGS 1 #define FILTER_ERR_OTHER 2 static void filter_add_undef_tag(filter_t *filter, char *str) { int i; for (i=0; inundef_tag; i++) if ( !strcmp(str,filter->undef_tag[i]) ) break; if ( inundef_tag ) return; filter->nundef_tag++; filter->undef_tag = (char**)realloc(filter->undef_tag,sizeof(*filter->undef_tag)*filter->nundef_tag); if ( !filter->undef_tag ) error("Could not allocate memory\n"); filter->undef_tag[filter->nundef_tag-1] = strdup(str); if ( !filter->undef_tag[filter->nundef_tag-1] ) error("Could not allocate memory\n"); } const char **filter_list_undef_tags(filter_t *filter, int *ntags) { *ntags = filter->nundef_tag; return (const char**)filter->undef_tag; } static void filter_add_used_tag(filter_t *filter, const char *prefix, char *str) { int i; kstring_t tmp = {0,0,0}; if ( prefix ) kputs(prefix,&tmp); kputs(str,&tmp); for (i=0; inused_tag; i++) if ( !strcmp(tmp.s,filter->used_tag[i]) ) break; if ( inused_tag ) { free(tmp.s); return; } filter->nused_tag++; filter->used_tag = (char**)realloc(filter->used_tag,sizeof(*filter->used_tag)*filter->nused_tag); if ( !filter->used_tag ) error("Could not allocate memory\n"); filter->used_tag[filter->nused_tag-1] = tmp.s; if ( !filter->used_tag[filter->nused_tag-1] ) error("Could not allocate memory\n"); } const char **filter_list_used_tags(filter_t *filter, int *ntags) { *ntags = filter->nused_tag; return (const char**)filter->used_tag; } /* Simple path expansion, expands ~/, ~user, $var. The result must be freed by the caller. Based on jkb's staden code with some adjustments. https://sourceforge.net/p/staden/code/HEAD/tree/staden/trunk/src/Misc/getfile.c#l123 */ char *expand_path(char *path) { kstring_t str = {0,0,0}; if ( path[0] == '~' ) { if ( !path[1] || path[1] == '/' ) { #ifdef _WIN32 kputs(getenv("HOMEDRIVE"), &str); kputs(getenv("HOMEPATH"), &str); #else // ~ or ~/path kputs(getenv("HOME"), &str); if ( path[1] ) kputs(path+1, &str); #endif } #ifndef _WIN32 else { // user name: ~pd3/path char *end = path; while ( *end && *end!='/' ) end++; kputsn(path+1, end-path-1, &str); struct passwd *pwentry = getpwnam(str.s); str.l = 0; if ( !pwentry ) kputsn(path, end-path, &str); else kputs(pwentry->pw_dir, &str); kputs(end, &str); } #endif return ks_release(&str); } if ( path[0] == '$' ) { char *var = getenv(path+1); if ( var ) { kputs(var, &str); return ks_release(&str); } } return strdup(path); } static int filters_cache_genotypes(filter_t *flt, bcf1_t *line) { if ( flt->cached_GT.line==line ) return flt->cached_GT.nbuf > 0 ? 0 : -1; flt->cached_GT.line = line; flt->cached_GT.nbuf = bcf_get_genotypes(flt->hdr, line, &flt->cached_GT.buf, &flt->cached_GT.mbuf); if ( flt->cached_GT.nbuf<=0 ) return -1; if ( !flt->cached_GT.mask ) { flt->cached_GT.mask = (uint64_t*) malloc(sizeof(*flt->cached_GT.mask)*flt->nsamples); if ( !flt->cached_GT.mask ) error("Could not alloc %zu bytes\n",sizeof(*flt->cached_GT.mask)*flt->nsamples); } int i,j, ngt1 = flt->cached_GT.nbuf / line->n_sample; for (i=0; in_sample; i++) { int32_t *ptr = flt->cached_GT.buf + i*ngt1; flt->cached_GT.mask[i] = 0; for (j=0; j 63 ) { static int warned = 0; if ( !warned ) { fprintf(bcftools_stderr,"Too many alleles, skipping GT filtering at this site %s:%"PRId64". " "(This warning is printed only once.)\n", bcf_seqname(flt->hdr,line),line->pos+1); warned = 1; } flt->cached_GT.nbuf = 0; return -1; } flt->cached_GT.mask[i] |= 1<qual; if ( bcf_float_is_missing(*ptr) ) bcf_double_set_missing(tok->values[0]); else tok->values[0] = (double)line->qual; tok->nvalues = 1; } static void filters_set_type(filter_t *flt, bcf1_t *line, token_t *tok) { tok->values[0] = bcf_get_variant_types(line); if ( !tok->values[0] ) tok->values[0] = 1; // mistake in htslib: VCF_* should start with 1 else tok->values[0] = ((int)tok->values[0]) << 1; tok->nvalues = 1; } static void filters_set_info(filter_t *flt, bcf1_t *line, token_t *tok) { assert( tok->hdr_id >=0 ); int i; for (i=0; in_info; i++) if ( line->d.info[i].key == tok->hdr_id ) break; if ( i==line->n_info ) tok->nvalues = tok->str_value.l = 0; else if ( line->d.info[i].type==BCF_BT_CHAR ) { int n = line->d.info[i].len; if ( n >= tok->str_value.m ) { tok->str_value.m = n + 1; tok->str_value.s = (char*) realloc(tok->str_value.s, tok->str_value.m); if ( !tok->str_value.s ) error("Failed to alloc %d bytes\n", (int)tok->str_value.m); } memcpy(tok->str_value.s, line->d.info[i].vptr, n); tok->str_value.s[n] = 0; tok->nvalues = tok->str_value.l = n; } else if ( line->d.info[i].type==BCF_BT_FLOAT ) { if ( bcf_float_is_missing(line->d.info[i].v1.f) ) tok->nvalues = 0; else { tok->values[0] = line->d.info[i].v1.f; tok->nvalues = 1; } tok->str_value.l = 0; } else { tok->str_value.l = 0; if ( line->d.info[i].type==BCF_BT_INT8 && line->d.info[i].v1.i==bcf_int8_missing ) tok->nvalues = 0; else if ( line->d.info[i].type==BCF_BT_INT16 && line->d.info[i].v1.i==bcf_int16_missing ) tok->nvalues = 0; else if ( line->d.info[i].type==BCF_BT_INT32 && line->d.info[i].v1.i==bcf_int32_missing ) tok->nvalues = 0; else { tok->values[0] = line->d.info[i].v1.i; tok->nvalues = 1; } } } static void filters_cmp_bit_and(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line) { int a = (int)(atok->nvalues?atok->values[0]:atok->threshold); int b = (int)(btok->nvalues?btok->values[0]:btok->threshold); if ( rtok->tok_type==TOK_LIKE ) rtok->pass_site = a&b ? 1 : 0; else rtok->pass_site = a&b ? 0 : 1; } static void filters_cmp_filter(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line) { // the btok values contain FILTER ids obtained by parsing the user expression int i,j; if ( rtok->tok_type==TOK_NOT_IN ) // fail if the query expression is a subset of the VCF FILTER { if ( !btok->nvalues ) // the query expression is ".", pass everything unless the VCF is also "." { if ( line->d.n_flt ) rtok->pass_site = 1; return; } if ( !line->d.n_flt ) // no filters at this VCF line and the query expression has a value { rtok->pass_site = 1; return; } for (j=0; jnvalues; j++) // some query expression value must be absent from VCF in order to pass { for (i=0; id.n_flt; i++) if ( btok->values[j]==line->d.flt[i] ) break; if ( i==line->d.n_flt ) break; // the query is not in the VCF } if ( j!=btok->nvalues ) rtok->pass_site = 1; return; } else if ( rtok->tok_type==TOK_IN ) { if ( !btok->nvalues ) // the query expression is ".", fail everything unless the VCF is also "." { if ( !line->d.n_flt ) rtok->pass_site = 1; return; } if ( !line->d.n_flt ) return; // no filters at this VCF line and the query expression has a value for (j=0; jnvalues; j++) // all of the query values must be present in the VCF in order to pass { for (i=0; id.n_flt; i++) if ( btok->values[j]==line->d.flt[i] ) break; if ( i==line->d.n_flt ) break; // the query is not in the VCF } if ( j==btok->nvalues ) rtok->pass_site = 1; return; } else if ( rtok->tok_type==TOK_NE ) // require anything but exact match { if ( btok->nvalues != line->d.n_flt ) { rtok->pass_site = 1; return; } if ( !btok->nvalues ) return; for (j=0; jnvalues; j++) // some of the query values must be absent from the VCF in order to pass { for (i=0; id.n_flt; i++) if ( btok->values[j]==line->d.flt[i] ) break; if ( i==line->d.n_flt ) break; // the query is not in the VCF } if ( j!=btok->nvalues ) rtok->pass_site = 1; return; } else if ( rtok->tok_type==TOK_EQ ) // require exact match { if ( btok->nvalues != line->d.n_flt ) return; if ( !btok->nvalues ) { rtok->pass_site = 1; return; } for (j=0; jnvalues; j++) // all of the query values must be present in the VCF in order to pass { for (i=0; id.n_flt; i++) if ( btok->values[j]==line->d.flt[i] ) break; if ( i==line->d.n_flt ) break; // the query is not in the VCF } if ( j==btok->nvalues ) rtok->pass_site = 1; return; } else error("Only ==, !=, ~, and !~ operators are supported for FILTER\n"); return; } static void filters_cmp_string_hash(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line) { if ( btok->hash ) { token_t *tmp = atok; atok = btok; btok = tmp; } if ( rtok->tok_type!=TOK_EQ && rtok->tok_type!=TOK_NE ) error("Only == and != operators are supported for strings read from a file\n"); // INFO if ( !btok->nsamples ) { // there is only one string value, e.g. STR[1]=@list.txt if ( btok->idx >= 0 ) { int ret = btok->str_value.s ? khash_str2int_has_key(atok->hash, btok->str_value.s) : 0; if ( rtok->tok_type==TOK_NE ) ret = ret ? 0 : 1; rtok->pass_site = ret; return; } // there can be multiple comma-separated string values, e.g. STR=@list.txt or STR[*]=@list.txt int ret = 0; char *ptr = btok->str_value.s; while ( *ptr ) { char *eptr = ptr + 1; while ( *eptr && *eptr!=',' ) eptr++; char keep = *eptr; *eptr = 0; ret |= khash_str2int_has_key(atok->hash, ptr); *eptr = keep; if ( !keep ) break; ptr = eptr + 1; } if ( rtok->tok_type==TOK_NE ) ret = ret ? 0 : 1; rtok->pass_site = ret; return; } // FORMAT tok_init_samples(atok, btok, rtok); rtok->pass_site = 0; int i; // there is only one string value, e.g. FMT/STR[*:1]=@list.txt if ( btok->idx >= 0 ) { for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; char *str = btok->str_value.s + i*btok->nval1; char keep = str[btok->nval1]; str[btok->nval1] = 0; int ret = khash_str2int_has_key(atok->hash, str); str[btok->nval1] = keep; if ( rtok->tok_type==TOK_NE ) ret = ret ? 0 : 1; rtok->pass_samples[i] = ret; rtok->pass_site |= ret; } return; } // there can be multiple comma-separated string values, e.g. FMT/STR=@list.txt for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; char *str = btok->str_value.s + i*btok->nval1; char keep = str[btok->nval1]; str[btok->nval1] = 0; // now str contains the block of per-sample comma-separated strings to loop over int ret = 0; char *ptr = str; while ( *ptr ) { char *eptr = ptr + 1; while ( *eptr && *eptr!=',' ) eptr++; char keep0 = *eptr; *eptr = 0; ret |= khash_str2int_has_key(atok->hash, ptr); *eptr = keep0; if ( !keep0 ) break; ptr = eptr + 1; } str[btok->nval1] = keep; if ( rtok->tok_type==TOK_NE ) ret = ret ? 0 : 1; rtok->pass_samples[i] = ret; rtok->pass_site |= ret; } } static void filters_cmp_id(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line) { if ( btok->hash ) { token_t *tmp = atok; atok = btok; btok = tmp; } char *id = line->d.id; int pass = 0; while ( id ) { char *ep = strchr(id,';'); if ( ep ) *ep = 0; if ( atok->hash ) { if ( rtok->tok_type!=TOK_EQ && rtok->tok_type!=TOK_NE ) error("Only == and != operators are supported for strings read from a file\n"); pass = khash_str2int_has_key(atok->hash, id); } else { if ( !btok->str_value.l ) error("Error occurred while evaluating the expression\n"); if ( rtok->tok_type==TOK_EQ || rtok->tok_type==TOK_NE ) pass = strcmp(btok->str_value.s,id) ? 0 : 1; else { if ( rtok->tok_type!=TOK_LIKE && rtok->tok_type!=TOK_NLIKE ) error("Only the following operators are supported for querying ID: ==, !=, ~, !~; the operator type %d is not supported (%p %p)\n", rtok->tok_type,atok->regex,btok->regex); regex_t *regex = atok->regex ? atok->regex : (btok->regex ? btok->regex : NULL); if ( !regex ) error("fixme: regex initialization failed\n"); pass = regexec(regex,id, 0,NULL,0) ? 0 : 1; } } if ( ep ) { *ep = ';'; id = ep + 1; } if ( pass || !ep ) break; } if ( rtok->tok_type==TOK_NE || rtok->tok_type==TOK_NE) pass = pass ? 0 : 1; rtok->pass_site = pass; } /** * bcf_get_info_value() - get single INFO value, int64_t or double * @line: BCF line * @info_id: tag ID, as returned by bcf_hdr_id2int * @ivec: 0-based index to retrieve, -1 when single value is expected * @vptr: pointer to memory location of sufficient size to accommodate * info_id's type * * The returned value is -1 if tag is not present, 0 if present but * values is missing or ivec is out of range, and 1 on success. */ static int bcf_get_info_value(bcf1_t *line, int info_id, int ivec, void *value) { int j; for (j=0; jn_info; j++) if ( line->d.info[j].key == info_id ) break; if ( j==line->n_info ) return -1; bcf_info_t *info = &line->d.info[j]; if ( info->len == 1 ) { if ( info->type==BCF_BT_FLOAT ) *((double*)value) = info->v1.f; else if ( info->type==BCF_BT_INT8 || info->type==BCF_BT_INT16 || info->type==BCF_BT_INT32 ) *((int64_t*)value) = info->v1.i; return 1; } if ( ivec<0 ) ivec = 0; if ( ivec>=info->len) return 0; #define BRANCH(type_t, convert, is_missing, is_vector_end, out_type_t) { \ uint8_t *p = info->vptr; \ for (j=0; jtype) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, int64_t); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, int64_t); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, val==bcf_int32_missing, val==bcf_int32_vector_end, int64_t); break; case BCF_BT_FLOAT: BRANCH(float, le_to_float, bcf_float_is_missing(val), bcf_float_is_vector_end(val), double); break; default: fprintf(bcftools_stderr,"todo: type %d\n", info->type); bcftools_exit(1); break; } #undef BRANCH return -1; // this shouldn't happen } static void filters_set_chrom(filter_t *flt, bcf1_t *line, token_t *tok) { tok->str_value.l = 0; kputs(bcf_seqname(flt->hdr,line), &tok->str_value); tok->nvalues = tok->str_value.l; tok->is_str = 1; } static void filters_set_pos(filter_t *flt, bcf1_t *line, token_t *tok) { tok->values[0] = line->pos+1; tok->nvalues = 1; } static void filters_set_info_int(filter_t *flt, bcf1_t *line, token_t *tok) { if ( tok->idx==-2 ) { tok->nvalues = bcf_get_info_int32(flt->hdr,line,tok->tag,&flt->tmpi,&flt->mtmpi); if ( tok->nvalues<=0 ) tok->nvalues = 0; else { hts_expand(double,tok->nvalues,tok->mvalues,tok->values); int i, j = 0, end = tok->idxs[tok->nidxs-1] < 0 ? tok->nvalues - 1 : tok->nidxs - 1; if ( end >= tok->nvalues ) end = tok->nvalues - 1; for (i=0; i<=end; i++) if ( i>=tok->nidxs || tok->idxs[i] ) tok->values[j++] = flt->tmpi[i]; tok->nvalues = j; } } else { int64_t value = 0; if ( bcf_get_info_value(line,tok->hdr_id,tok->idx,&value) <= 0 ) tok->nvalues = 0; else { tok->values[0] = value; tok->nvalues = 1; } } } static void filters_set_info_float(filter_t *flt, bcf1_t *line, token_t *tok) { if ( tok->idx==-2 ) { tok->nvalues = bcf_get_info_float(flt->hdr,line,tok->tag,&flt->tmpf,&flt->mtmpf); if ( tok->nvalues<=0 ) tok->nvalues = 0; else { hts_expand(double,tok->nvalues,tok->mvalues,tok->values); int i, j = 0, end = tok->idxs[tok->nidxs-1] < 0 ? tok->nvalues - 1 : tok->nidxs - 1; if ( end >= tok->nvalues ) end = tok->nvalues - 1; for (i=0; i<=end; i++) if ( i>=tok->nidxs || tok->idxs[i] ) { if ( bcf_float_is_missing(flt->tmpf[i]) ) bcf_double_set_missing(tok->values[j]); else tok->values[j] = flt->tmpf[i]; j++; } tok->nvalues = j; } } else { double value; if ( bcf_get_info_value(line,tok->hdr_id,tok->idx,&value) <= 0 ) tok->nvalues = 0; else { tok->values[0] = value; tok->nvalues = 1; } } } static void filters_set_info_string(filter_t *flt, bcf1_t *line, token_t *tok) { int32_t m = tok->str_value.m; int n = bcf_get_info_string(flt->hdr,line,tok->tag,&tok->str_value.s,&m); tok->str_value.m = m; if ( n<0 ) { tok->nvalues = tok->str_value.l = 0; return; } if ( tok->idx>=0 ) { // get ith field (i=tok->idx) int i = 0; char *ss = tok->str_value.s, *se = tok->str_value.s + n; while ( ssidx ) { if ( *ss==',' ) i++; ss++; } if ( ss==se || i!=tok->idx ) { tok->nvalues = tok->str_value.l = 0; return; } se = ss; while ( se - tok->str_value.s < n && *se!=',' ) se++; if ( ss==tok->str_value.s ) *se = 0; else { memmove(tok->str_value.s, ss, se-ss); tok->str_value.s[se-ss] = 0; } tok->str_value.l = se - ss; } else if ( tok->idx==-2 && tok->idxs[0]==-1 ) // keep all values, TAG[*] tok->str_value.l = n; else if ( tok->idx==-2 ) { flt->tmps.l = 0; ks_resize(&flt->tmps, n); int i, iend = tok->idxs[tok->nidxs-1] < 0 ? n - 1 : tok->nidxs - 1; if ( iend >= n ) iend = n - 1; char *beg = tok->str_value.s, *dst = flt->tmps.s; for (i=0; i<=iend; i++) { char *end = beg; while ( *end && *end!=',' ) end++; if ( i>=tok->nidxs || tok->idxs[i] ) { memcpy(dst, beg, end - beg); dst += end - beg; dst[0] = ','; dst++; } beg = end+1; } dst[0] = 0; tok->str_value.l = dst - flt->tmps.s; #define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; } SWAP(char *, flt->tmps.s, tok->str_value.s); SWAP(size_t, flt->tmps.m, tok->str_value.m); } tok->nvalues = tok->str_value.l; } static void filters_set_info_flag(filter_t *flt, bcf1_t *line, token_t *tok) { int j; for (j=0; jn_info; j++) if ( line->d.info[j].key == tok->hdr_id ) break; tok->values[0] = j==line->n_info ? 0 : 1; tok->nvalues = 1; } static void filters_set_format_int(filter_t *flt, bcf1_t *line, token_t *tok) { if ( line->n_sample != tok->nsamples ) error("Incorrect number of FORMAT fields at %s:%"PRId64" .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples); int nvals; if ( (nvals=bcf_get_format_int32(flt->hdr,line,tok->tag,&flt->tmpi,&flt->mtmpi))<0 ) { tok->nvalues = 0; return; } int i, nsrc1 = nvals / tok->nsamples; tok->nval1 = tok->idx >= 0 ? 1 : (tok->nuidxs ? tok->nuidxs : nsrc1); tok->nvalues = tok->nval1*tok->nsamples; hts_expand(double, tok->nvalues, tok->mvalues, tok->values); if ( tok->idx >= 0 ) // scalar or vector index { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; int32_t *ptr = flt->tmpi + i*nsrc1; if ( tok->idx>=nsrc1 || ptr[tok->idx]==bcf_int32_missing ) bcf_double_set_missing(tok->values[i]); else if ( ptr[tok->idx]==bcf_int32_vector_end ) bcf_double_set_vector_end(tok->values[i]); else tok->values[i] = ptr[tok->idx]; } } else if ( tok->idx==-3 ) { if ( filters_cache_genotypes(flt,line)!=0 ) { tok->nvalues = 0; return; } for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; int32_t *src = flt->tmpi + i*nsrc1; double *dst = tok->values + i*tok->nval1; int k, j = 0; for (k=0; kcached_GT.mask[i] & (1<nval1; j++) bcf_double_set_vector_end(dst[j]); } } else { int kend = tok->idxs[tok->nidxs-1] < 0 ? tok->nval1 : tok->nidxs; for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; int32_t *src = flt->tmpi + i*nsrc1; double *dst = tok->values + i*tok->nval1; int k, j = 0; for (k=0; knidxs && !tok->idxs[k] ) continue; if ( src[k]==bcf_int32_missing ) bcf_double_set_missing(dst[j]); else if ( src[k]==bcf_int32_vector_end ) bcf_double_set_vector_end(dst[j]); else dst[j] = src[k]; j++; } if ( j==0 ) { bcf_double_set_missing(dst[j]); j++; } while (j < tok->nval1) { bcf_double_set_vector_end(dst[j]); j++; } } } } static void filters_set_format_float(filter_t *flt, bcf1_t *line, token_t *tok) { if ( line->n_sample != tok->nsamples ) error("Incorrect number of FORMAT fields at %s:%"PRId64" .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples); int nvals; if ( (nvals=bcf_get_format_float(flt->hdr,line,tok->tag,&flt->tmpf,&flt->mtmpf))<0 ) { tok->nvalues = 0; return; } int i, nsrc1 = nvals / tok->nsamples; tok->nval1 = tok->idx >= 0 ? 1 : (tok->nuidxs ? tok->nuidxs : nsrc1); tok->nvalues = tok->nval1*tok->nsamples; hts_expand(double, tok->nvalues, tok->mvalues, tok->values); if ( tok->idx >= 0 ) // scalar or vector index { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; float *ptr = flt->tmpf + i*nsrc1; if ( tok->idx>=nsrc1 || bcf_float_is_missing(ptr[tok->idx]) ) bcf_double_set_missing(tok->values[i]); else if ( bcf_float_is_vector_end(ptr[tok->idx]) ) bcf_double_set_vector_end(tok->values[i]); else tok->values[i] = ptr[tok->idx]; } } else if ( tok->idx==-3 ) { if ( filters_cache_genotypes(flt,line)!=0 ) { tok->nvalues = 0; return; } for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; float *src = flt->tmpf + i*nsrc1; double *dst = tok->values + i*tok->nval1; int k, j = 0; for (k=0; kcached_GT.mask[i] & (1<nval1; j++) bcf_double_set_vector_end(dst[j]); } } else { int kend = tok->idxs[tok->nidxs-1] < 0 ? tok->nval1 : tok->nidxs; for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; float *src = flt->tmpf + i*nsrc1; double *dst = tok->values + i*tok->nval1; int k, j = 0; for (k=0; knidxs && !tok->idxs[k] ) continue; if ( bcf_float_is_missing(src[k]) ) bcf_double_set_missing(dst[j]); else if ( bcf_float_is_vector_end(src[k]) ) bcf_double_set_vector_end(dst[j]); else dst[j] = src[k]; j++; } if ( j==0 ) { bcf_double_set_missing(dst[j]); j++; } while (j < tok->nval1) { bcf_double_set_vector_end(dst[j]); j++; } } } } static void filters_set_format_string(filter_t *flt, bcf1_t *line, token_t *tok) { if ( line->n_sample != tok->nsamples ) error("Incorrect number of FORMAT fields at %s:%"PRId64" .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples); int i, ndim = tok->str_value.m; int nstr = bcf_get_format_char(flt->hdr, line, tok->tag, &tok->str_value.s, &ndim); tok->str_value.m = tok->str_value.l = ndim; kputc(0,&tok->str_value); // append the nul byte tok->str_value.l = tok->nvalues = 0; if ( nstr<0 ) return; if ( tok->idx==-3 && filters_cache_genotypes(flt,line)!=0 ) return; tok->nvalues = tok->str_value.l = nstr; tok->nval1 = nstr / tok->nsamples; for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; char *src = tok->str_value.s + i*tok->nval1, *dst = src; int ibeg = 0; int idx = 0; // idx-th field while ( ibeg < tok->nval1 ) { int iend = ibeg; while ( iend < tok->nval1 && src[iend] && src[iend]!=',' ) iend++; int keep = 0; if ( tok->idx >= 0 ) // single index, given explicitly, e.g. AD[:1] { if ( tok->idx==idx ) keep = 1; } else if ( tok->idx == -3 ) // given by GT index, e.g. AD[:GT] { if ( flt->cached_GT.mask[i] & (1<nidxs ) { if ( tok->idxs[idx] != 0 ) keep = 1; } else if ( tok->idxs[tok->nidxs-1] < 0 ) keep = 1; } if ( keep ) { if ( ibeg!=0 ) memmove(dst, src+ibeg, iend-ibeg+1); dst += iend - ibeg + 1; if ( tok->idx>=0 ) break; } if ( !src[iend] ) break; ibeg = iend + 1; idx++; } if ( dst==src ) { dst[0] = '.'; dst+=2; } if ( dst - src < tok->nval1 ) memset(dst-1, 0, tok->nval1 - (dst - src)); } } static void _filters_set_genotype(filter_t *flt, bcf1_t *line, token_t *tok, int type) { bcf_fmt_t *fmt = bcf_get_fmt(flt->hdr, line, "GT"); if ( !fmt ) { tok->nvalues = tok->str_value.l = 0; return; } int i,j, nsmpl = bcf_hdr_nsamples(flt->hdr), nvals1 = type==2 ? 3 : 4; if ( tok->str_value.m <= nvals1*nsmpl ) { tok->str_value.m = nvals1*nsmpl + 1; tok->str_value.s = (char*)realloc(tok->str_value.s, tok->str_value.m); } #define BRANCH_INT(type_t, convert, vector_end) \ { \ for (i=0; in_sample; i++) \ { \ uint8_t *ptr = fmt->p + i*fmt->size; \ int is_het = 0, has_ref = 0, missing = 0, jal = 0; \ for (j=0; jn; j++) \ { \ type_t ial = convert(&ptr[j * sizeof(type_t)]); \ if ( ial==vector_end ) break; /* smaller ploidy */ \ if ( bcf_gt_is_missing(ial) ) { missing=1; break; } /* missing allele */ \ if ( bcf_gt_allele(ial)==0 ) has_ref = 1; \ if ( j>0 ) \ { \ if ( bcf_gt_allele(ial)!=bcf_gt_allele(jal) ) is_het = 1; \ } \ jal = ial; \ } \ char *dst = &tok->str_value.s[nvals1*i]; \ if ( type==4 ) \ { \ if ( !j || missing ) dst[0]='m', dst[1]='i', dst[2]='s', dst[3] = 0; /* mis, missing genotype */ \ else if ( !has_ref ) dst[0]='a', dst[1]='l', dst[2]='t', dst[3] = 0; /* alt, no ref, must have alt allele */ \ else if ( !is_het ) dst[0]='r', dst[1]='e', dst[2]='f', dst[3] = 0; /* ref, must be ref-only, no alt alelle */ \ else dst[0]='a', dst[1]='l', dst[2]='t', dst[3] = 0; /* alt, is het, has alt allele */ \ } \ else if ( !j || missing ) dst[0]='.', dst[1]=0; /* ., missing genotype */ \ else if ( type==3 ) \ { \ if ( j==1 ) dst[0]='h', dst[1]='a', dst[2]='p', dst[3] = 0; /* hap, haploid */ \ else if ( !is_het ) dst[0]='h', dst[1]='o', dst[2]='m', dst[3] = 0; /* hom */ \ else dst[0]='h', dst[1]='e', dst[2]='t', dst[3] = 0; /* het */ \ } \ else \ { \ if ( j==1 ) \ { \ if ( has_ref ) dst[0]='r', dst[1]=0; /* r, haploid */ \ else dst[0]='a', dst[1]=0; /* a, haploid */ \ } \ else if ( !is_het ) \ { \ if ( has_ref ) dst[0]='r', dst[1]='r', dst[2] = 0; /* rr */ \ else dst[0]='a', dst[1]='a', dst[2] = 0; /* aa */ \ } \ else \ { \ if ( has_ref ) dst[0]='r', dst[1]='a', dst[2] = 0; /* ra */ \ else dst[0]='a', dst[1]='A', dst[2] = 0; /* aA */ \ } \ } \ } \ } switch (fmt->type) { case BCF_BT_INT8: BRANCH_INT(int8_t, le_to_i8, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH_INT(int16_t, le_to_i16, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH_INT(int32_t, le_to_i32, bcf_int32_vector_end); break; default: error("The GT type is not lineognised: %d at %s:%"PRId64"\n",fmt->type, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1); break; } #undef BRANCH_INT assert( tok->nsamples == nsmpl ); tok->nvalues = tok->str_value.l = nvals1*nsmpl; tok->str_value.s[tok->str_value.l] = 0; tok->nval1 = nvals1; } static void filters_set_genotype2(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 2); } // rr, ra, aa, aA etc static void filters_set_genotype3(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 3); } // hap, hom, het static void filters_set_genotype4(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 4); } // mis, alt, ref static void filters_set_genotype_string(filter_t *flt, bcf1_t *line, token_t *tok) { bcf_fmt_t *fmt = bcf_get_fmt(flt->hdr, line, "GT"); if ( !fmt ) { tok->nvalues = 0; return; } int i, blen = 4, nsmpl = line->n_sample; gt_length_too_big: tok->str_value.l = 0; for (i=0; istr_value.l; bcf_format_gt(fmt, i, &tok->str_value); kputc_(0, &tok->str_value); if ( tok->str_value.l - plen > blen ) { // too many alternate alleles or ploidy is too large, the genotype does not fit // three characters ("0/0" vs "10/10"). blen *= 2; goto gt_length_too_big; } plen = tok->str_value.l - plen; while ( plen < blen ) { kputc_(0, &tok->str_value); plen++; } } assert( tok->nsamples == nsmpl ); tok->nvalues = tok->str_value.l; tok->nval1 = blen; } static void filters_set_ilen(filter_t *flt, bcf1_t *line, token_t *tok) { tok->nvalues = line->n_allele - 1; hts_expand(double,tok->nvalues,tok->mvalues,tok->values); int i, rlen = strlen(line->d.allele[0]); for (i=1; in_allele; i++) { if ( line->d.allele[i][0]=='<' ) { bcf_double_set_missing(tok->values[i-1]); continue; } int alen = strlen(line->d.allele[i]); tok->values[i-1] = alen - rlen; } } static void filters_set_ref_string(filter_t *flt, bcf1_t *line, token_t *tok) { tok->str_value.l = 0; kputs(line->d.allele[0], &tok->str_value); tok->nvalues = tok->str_value.l; } static void filters_set_alt_string(filter_t *flt, bcf1_t *line, token_t *tok) { tok->str_value.l = 0; if ( tok->idx>=0 ) { if ( line->n_allele > tok->idx + 1 ) kputs(line->d.allele[tok->idx + 1], &tok->str_value); else kputc('.', &tok->str_value); } else if ( tok->idx==-2 ) { int i, end = tok->nuidxs ? tok->nuidxs : line->n_allele - 1; if ( end >= line->n_allele - 1 ) end = line->n_allele - 2; for (i=0; i<=end; i++) if ( i>=tok->nidxs || tok->idxs[i] ) { if ( tok->str_value.l ) kputc(',', &tok->str_value); kputs(line->d.allele[i+1], &tok->str_value); } } else if ( line->n_allele>1 ) { kputs(line->d.allele[1], &tok->str_value); int i; for (i=2; in_allele; i++) { kputc(',', &tok->str_value); kputs(line->d.allele[i], &tok->str_value); } } else if ( line->n_allele==1 ) kputc('.', &tok->str_value); tok->nvalues = tok->str_value.l; } static void filters_set_nmissing(filter_t *flt, bcf1_t *line, token_t *tok) { bcf_unpack(line, BCF_UN_FMT); if ( !line->n_sample ) { tok->nvalues = 1; tok->values[0] = 0; return; } int i,igt = bcf_hdr_id2int(flt->hdr, BCF_DT_ID, "GT"); bcf_fmt_t *fmt = NULL; for (i=0; in_fmt; i++) if ( line->d.fmt[i].id==igt ) { fmt = &line->d.fmt[i]; break; } if ( !fmt ) { tok->nvalues = 0; return; } int j,nmissing = 0; #define BRANCH(type_t, convert, is_vector_end) { \ for (i=0; in_sample; i++) \ { \ uint8_t *ptr = fmt->p + i*fmt->size; \ for (j=0; jn; j++) \ { \ type_t val = convert(&ptr[j * sizeof(type_t)]); \ if ( val==is_vector_end ) break; \ if ( val==bcf_gt_missing ) { nmissing++; break; } \ } \ } \ } switch (fmt->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, bcf_int32_vector_end); break; default: fprintf(bcftools_stderr,"todo: type %d\n", fmt->type); bcftools_exit(1); break; } #undef BRANCH tok->nvalues = 1; tok->values[0] = tok->tag[0]=='N' ? nmissing : (double)nmissing / line->n_sample; } static int func_npass(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { if ( nstack==0 ) error("Error parsing the expression\n"); token_t *tok = stack[nstack - 1]; if ( !tok->nsamples ) error("The function %s works with FORMAT fields\n", rtok->tag); assert(tok->usmpl); int i, npass = 0; for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; if ( tok->pass_samples[i] ) npass++; } hts_expand(double,1,rtok->mvalues,rtok->values); rtok->nsamples = 0; rtok->nvalues = 1; rtok->values[0] = rtok->tag[0]=='N' ? npass : (line->n_sample ? 1.0*npass/line->n_sample : 0); return 1; } static void filters_set_nalt(filter_t *flt, bcf1_t *line, token_t *tok) { tok->nvalues = 1; tok->values[0] = line->n_allele - 1; } static void filters_set_ac(filter_t *flt, bcf1_t *line, token_t *tok) { hts_expand(int32_t, line->n_allele, flt->mtmpi, flt->tmpi); if ( !bcf_calc_ac(flt->hdr, line, flt->tmpi, BCF_UN_INFO|BCF_UN_FMT) ) { tok->nvalues = 0; return; } int i, an = flt->tmpi[0]; for (i=1; in_allele; i++) an += flt->tmpi[i]; if ( !an ) { tok->nvalues = 0; return; } flt->tmpi[0] = an; // for filters_set_[mac|af|maf] if ( tok->idx>=0 ) { tok->nvalues = 1; tok->values[0] = tok->idx+1n_allele ? flt->tmpi[tok->idx+1] : 0; } else if ( line->n_allele==1 ) // no ALT { tok->nvalues = 1; tok->values[0] = 0; } else { hts_expand(double,line->n_allele,tok->mvalues,tok->values); for (i=1; in_allele; i++) tok->values[i-1] = flt->tmpi[i]; tok->nvalues = line->n_allele - 1; } } static void filters_set_an(filter_t *flt, bcf1_t *line, token_t *tok) { filters_set_ac(flt,line,tok); tok->values[0] = tok->nvalues ? flt->tmpi[0] : 0; tok->nvalues = 1; } static void filters_set_mac(filter_t *flt, bcf1_t *line, token_t *tok) { filters_set_ac(flt,line,tok); if ( !tok->nvalues ) return; int i, an = flt->tmpi[0]; for (i=0; invalues; i++) if ( tok->values[i] > an*0.5 ) tok->values[i] = an - tok->values[i]; } static void filters_set_af(filter_t *flt, bcf1_t *line, token_t *tok) { filters_set_ac(flt,line,tok); if ( !tok->nvalues ) return; int i, an = flt->tmpi[0]; for (i=0; invalues; i++) tok->values[i] /= (double)an; } static void filters_set_maf(filter_t *flt, bcf1_t *line, token_t *tok) { filters_set_ac(flt,line,tok); if ( !tok->nvalues ) return; int i, an = flt->tmpi[0]; for (i=0; invalues; i++) { tok->values[i] /= (double)an; if ( tok->values[i] > 0.5 ) tok->values[i] = 1 - tok->values[i]; } } static int func_max(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; rtok->nvalues = 0; if ( !tok->nvalues ) return 1; double *ptr, val = -HUGE_VAL; int i,j, has_value = 0; if ( tok->nsamples ) { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; has_value = 1; if ( val < ptr[j] ) val = ptr[j]; } } } else { for (i=0; invalues; i++) { if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) continue; has_value = 1; if ( val < tok->values[i] ) val = tok->values[i]; } } if ( has_value ) { rtok->values[0] = val; rtok->nvalues = has_value; } return 1; } static int func_smpl_max(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; if ( !tok->nsamples ) return func_max(flt,line,rtok,stack,nstack); rtok->nsamples = tok->nsamples; rtok->nvalues = tok->nsamples; rtok->nval1 = 1; hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values); assert(tok->usmpl); if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples); int i, j, has_value; double val, *ptr; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; val = -HUGE_VAL; has_value = 0; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; has_value = 1; if ( val < ptr[j] ) val = ptr[j]; } if ( has_value ) rtok->values[i] = val; else bcf_double_set_missing(rtok->values[i]); } return 1; } static int func_min(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; rtok->nvalues = 0; if ( !tok->nvalues ) return 1; double *ptr, val = HUGE_VAL; int i,j, has_value = 0; if ( tok->nsamples ) { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; has_value = 1; if ( val > ptr[j] ) val = ptr[j]; } } } else { for (i=0; invalues; i++) { if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) continue; has_value = 1; if ( val > tok->values[i] ) val = tok->values[i]; } } if ( has_value ) { rtok->values[0] = val; rtok->nvalues = has_value; } return 1; } static int func_smpl_min(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; if ( !tok->nsamples ) return func_min(flt,line,rtok,stack,nstack); rtok->nsamples = tok->nsamples; rtok->nvalues = tok->nsamples; rtok->nval1 = 1; hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values); assert(tok->usmpl); if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples); int i, j, has_value; double val, *ptr; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; val = HUGE_VAL; has_value = 0; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; has_value = 1; if ( val > ptr[j] ) val = ptr[j]; } if ( has_value ) rtok->values[i] = val; else bcf_double_set_missing(rtok->values[i]); } return 1; } static int func_avg(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; rtok->nvalues = 0; if ( !tok->nvalues ) return 1; double *ptr, val = 0; int i,j, n = 0; if ( tok->nsamples ) { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; val += ptr[j]; n++; } } } else { for (i=0; invalues; i++) if ( !bcf_double_is_missing_or_vector_end(tok->values[i]) ) { val += tok->values[i]; n++; } } if ( n ) { rtok->values[0] = val / n; rtok->nvalues = 1; } return 1; } static int func_smpl_avg(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack); rtok->nsamples = tok->nsamples; rtok->nvalues = tok->nsamples; rtok->nval1 = 1; hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values); assert(tok->usmpl); if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples); int i, j, n; double val, *ptr; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; val = 0; n = 0; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( !bcf_double_is_missing_or_vector_end(ptr[j]) ) { val += ptr[j]; n++; } } if ( n ) rtok->values[i] = val / n; else bcf_double_set_missing(rtok->values[i]); } return 1; } static int compare_doubles(const void *lhs, const void *rhs) { double arg1 = *(const double*) lhs; double arg2 = *(const double*) rhs; if (arg1 < arg2) return -1; if (arg1 > arg2) return 1; return 0; } static int func_median(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; rtok->nvalues = 0; if ( !tok->nvalues ) return 1; // sweep through all tok->values and while excluding all missing values reuse the very same array int i,j,k = 0, n = 0; if ( tok->nsamples ) { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) { k += tok->nval1; continue; } for (j=0; jnval1; k++,j++) { if ( bcf_double_is_missing_or_vector_end(tok->values[k]) ) continue; if ( n < k ) tok->values[n] = tok->values[k]; n++; } } } else { for (i=0; invalues; i++) { if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) continue; if ( n < i ) tok->values[n] = tok->values[i]; n++; } } if ( !n ) return 1; if ( n==1 ) rtok->values[0] = tok->values[0]; else { qsort(tok->values, n, sizeof(double), compare_doubles); rtok->values[0] = n % 2 ? tok->values[n/2] : (tok->values[n/2-1] + tok->values[n/2]) * 0.5; } rtok->nvalues = 1; return 1; } static int func_smpl_median(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack); rtok->nsamples = tok->nsamples; rtok->nvalues = tok->nsamples; rtok->nval1 = 1; hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values); assert(tok->usmpl); if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples); int i, j, n; double *ptr; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; n = 0; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; if ( n < j ) ptr[n] = ptr[j]; n++; } if ( n==0 ) bcf_double_set_missing(rtok->values[i]); else if ( n==1 ) rtok->values[i] = ptr[0]; else { qsort(ptr, n, sizeof(double), compare_doubles); rtok->values[i] = n % 2 ? ptr[n/2] : (ptr[n/2-1] + ptr[n/2]) * 0.5; } } return 1; } static int func_stddev(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; rtok->nvalues = 0; if ( !tok->nvalues ) return 1; // sweep through all tok->values and while excluding all missing values reuse the very same array int i,j,k = 0, n = 0; if ( tok->nsamples ) { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) { k += tok->nval1; continue; } for (j=0; jnval1; k++,j++) { if ( bcf_double_is_missing_or_vector_end(tok->values[k]) ) continue; if ( n < k ) tok->values[n] = tok->values[k]; n++; } } } else { for (i=0; invalues; i++) { if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) continue; if ( n < i ) tok->values[n] = tok->values[i]; n++; } } if ( !n ) return 1; if ( n==1 ) rtok->values[0] = 0; else { double sdev = 0, avg = 0; for (i=0; ivalues[i]; avg /= n; for (i=0; ivalues[i] - avg) * (tok->values[i] - avg); rtok->values[0] = sqrt(sdev/n); } rtok->nvalues = 1; return 1; } static int func_smpl_stddev(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack); rtok->nsamples = tok->nsamples; rtok->nvalues = tok->nsamples; rtok->nval1 = 1; hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values); assert(tok->usmpl); if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples); int i, j, n; double *ptr; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; n = 0; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; if ( n < j ) ptr[n] = ptr[j]; n++; } if ( n==0 ) bcf_double_set_missing(rtok->values[i]); else if ( n==1 ) rtok->values[i] = 0; else { double sdev = 0, avg = 0; for (j=0; jvalues[i] = sqrt(sdev/n); } } return 1; } static int func_sum(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { rtok->nvalues = 0; token_t *tok = stack[nstack - 1]; if ( !tok->nvalues ) return 1; double *ptr, val = 0; int i,j, n = 0; if ( tok->nsamples ) { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; val += ptr[j]; n++; } } } else { for (i=0; invalues; i++) if ( !bcf_double_is_missing_or_vector_end(tok->values[i]) ) { val += tok->values[i]; n++; } } if ( n ) { rtok->values[0] = val; rtok->nvalues = 1; } return 1; } static int func_smpl_sum(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack); rtok->nsamples = tok->nsamples; rtok->nvalues = tok->nsamples; rtok->nval1 = 1; hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values); assert(tok->usmpl); if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples); int i, j, has_value; double val, *ptr; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; val = 0; has_value = 0; ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) { if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue; has_value = 1; val += ptr[j]; } if ( has_value ) rtok->values[i] = val; else bcf_double_set_missing(rtok->values[i]); } return 1; } static int func_abs(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; if ( tok->is_str ) error("ABS() can be applied only on numeric values\n"); rtok->nsamples = tok->nsamples; rtok->nvalues = tok->nvalues; rtok->nval1 = tok->nval1; hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values); if ( tok->usmpl ) { if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples); } if ( !tok->nvalues ) return 1; hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values); int i,j,k = 0; if ( tok->usmpl ) { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) { k+= tok->nval1; continue; } for (j=0; jnval1; k++,j++) { if ( bcf_double_is_missing_or_vector_end(tok->values[k]) ) bcf_double_set_missing(rtok->values[k]); else rtok->values[k] = fabs(tok->values[k]); } } } else { for (i=0; invalues; i++) { if ( tok->usmpl && !tok->usmpl[i] ) continue; if ( bcf_double_is_missing(tok->values[i]) ) bcf_double_set_missing(rtok->values[i]); else if ( !bcf_double_is_vector_end(tok->values[i]) ) rtok->values[i] = fabs(tok->values[i]); } } return 1; } static int func_count(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; int i,j, cnt = 0; if ( tok->tag && tok->nsamples ) { // raw number of values in a FMT tag, e.g. COUNT(FMT/TAG) if ( tok->is_str ) error("todo: Type=String for COUNT on FORMAT fields?\n"); for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) continue; double *ptr = tok->values + i*tok->nval1; for (j=0; jnval1; j++) if ( !bcf_double_is_missing_or_vector_end(ptr[j]) ) cnt++; } } else if ( tok->nsamples ) { // number of samples that pass a processed FMT tag for (i=0; insamples; i++) if ( tok->pass_samples[i] ) cnt++; } else if ( tok->is_str ) { if ( tok->str_value.l ) cnt = 1; for (i=0; istr_value.l; i++) if ( tok->str_value.s[i]==',' ) cnt++; } else cnt = tok->nvalues; rtok->nvalues = 1; rtok->values[0] = cnt; return 1; } static int func_strlen(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; rtok->nvalues = rtok->str_value.l = 0; if ( !tok->str_value.l ) return 1; if ( tok->idx==-2 ) { int i = 0; char *ss = tok->str_value.s; while ( *ss ) { char *se = ss; while ( *se && *se!=',' ) se++; hts_expand(double, i+1, rtok->mvalues, rtok->values); if ( !*se ) rtok->values[i] = strlen(ss); else { *se = 0; rtok->values[i] = strlen(ss); *se = ','; } ss = *se ? se + 1 : se; i++; } rtok->nvalues = i; } else { if ( !tok->str_value.s[1] && tok->str_value.s[0]=='.' ) rtok->values[0] = 0; else rtok->values[0] = strlen(tok->str_value.s); rtok->nvalues = 1; } return 1; } static int func_binom(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { int i, istack = nstack - rtok->nargs; if ( rtok->nargs!=2 && rtok->nargs!=1 ) error("Error: binom() takes one or two arguments\n"); assert( istack>=0 ); // The expected mean is 0.5. Should we support also prob!=0.5? // // double prob = 0.5; // if ( nstack==3 ) // { // // three parameters, the first one must be a scalar: binom(0.25,AD[0],AD[1]) // if ( !stack[istack]->is_constant ) // error("The first argument of binom() must be a numeric constant if three parameters are given\n"); // prob = stack[istack]->threshold; // istack++; // } // else if ( nstack==2 && stack[istack]->is_constant ) // { // // two parameters, the first can be a scalar: binom(0.25,AD) or binom(AD[0],AD[1]) // prob = stack[istack]->threshold; // istack++; // } token_t *tok = stack[istack]; if ( tok->nsamples ) { // working with a FORMAT tag rtok->nval1 = 1; rtok->nvalues = tok->nsamples; rtok->nsamples = tok->nsamples; hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values); assert(tok->usmpl); if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples); if ( istack+1==nstack ) { // determine the index from the GT field: binom(AD) int ngt = bcf_get_genotypes(flt->hdr, line, &flt->tmpi, &flt->mtmpi); int max_ploidy = ngt/line->n_sample; if ( ngt <= 0 || max_ploidy < 2 ) // GT not present or not diploid, cannot set { for (i=0; insamples; i++) if ( rtok->usmpl[i] ) bcf_double_set_missing(rtok->values[i]); return rtok->nargs; } for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; int32_t *ptr = flt->tmpi + i*max_ploidy; if ( bcf_gt_is_missing(ptr[0]) || bcf_gt_is_missing(ptr[1]) || ptr[1]==bcf_int32_vector_end ) { bcf_double_set_missing(rtok->values[i]); continue; } int idx1 = bcf_gt_allele(ptr[0]); int idx2 = bcf_gt_allele(ptr[1]); if ( idx1>=line->n_allele ) error("Incorrect allele index at %s:%"PRId64", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]); if ( idx2>=line->n_allele ) error("Incorrect allele index at %s:%"PRId64", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]); double *vals = tok->values + tok->nval1*i; if ( bcf_double_is_missing_or_vector_end(vals[idx1]) || bcf_double_is_missing_or_vector_end(vals[idx2]) ) { bcf_double_set_missing(rtok->values[i]); continue; } rtok->values[i] = calc_binom_two_sided(vals[idx1],vals[idx2],0.5); if ( rtok->values[i] < 0 ) { bcf_double_set_missing(rtok->values[i]); continue; } } } else { // the fields given explicitly: binom(AD[:0],AD[:1]) token_t *tok2 = stack[istack+1]; if ( tok->nval1!=1 || tok2->nval1!=1 ) error("Expected one value per binom() argument, found %d and %d at %s:%"PRId64"\n",tok->nval1,tok2->nval1, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1); for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; double *ptr1 = tok->values + tok->nval1*i; double *ptr2 = tok2->values + tok2->nval1*i; if ( bcf_double_is_missing_or_vector_end(ptr1[0]) || bcf_double_is_missing_or_vector_end(ptr2[0]) ) { bcf_double_set_missing(rtok->values[i]); continue; } rtok->values[i] = calc_binom_two_sided(ptr1[0],ptr2[0],0.5); if ( rtok->values[i] < 0 ) { bcf_double_set_missing(rtok->values[i]); continue; } } } } else { // working with an INFO tag rtok->nvalues = 1; hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values); double *ptr1 = NULL, *ptr2 = NULL; if ( istack+1==nstack ) { // only one tag, expecting two values: binom(INFO/AD) if ( tok->nvalues==2 ) { ptr1 = &tok->values[0]; ptr2 = &tok->values[1]; } } else { // two tags, expecting one value in each: binom(INFO/AD[0],INFO/AD[1]) token_t *tok2 = stack[istack+1]; if ( tok->nvalues==1 && tok2->nvalues==1 ) { ptr1 = &tok->values[0]; ptr2 = &tok2->values[0]; } } if ( !ptr1 || !ptr2 || bcf_double_is_missing_or_vector_end(ptr1[0]) || bcf_double_is_missing_or_vector_end(ptr2[0]) ) bcf_double_set_missing(rtok->values[0]); else { rtok->values[0] = calc_binom_two_sided(ptr1[0],ptr2[0],0.5); if ( rtok->values[0] < 0 ) bcf_double_set_missing(rtok->values[0]); } } return rtok->nargs; } static int func_phred(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { token_t *tok = stack[nstack - 1]; if ( tok->is_str ) error("PHRED() can be applied only on numeric values\n"); rtok->nsamples = tok->nsamples; rtok->nval1 = tok->nval1; memcpy(rtok->pass_samples, tok->pass_samples, rtok->nsamples*sizeof(*rtok->pass_samples)); assert(tok->usmpl); if ( !rtok->usmpl ) { rtok->usmpl = (uint8_t*) malloc(tok->nsamples*sizeof(*rtok->usmpl)); memcpy(rtok->usmpl, tok->usmpl, tok->nsamples*sizeof(*rtok->usmpl)); } rtok->nvalues = tok->nvalues; if ( !tok->nvalues ) return 1; hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values); int i,j,k = 0; if ( tok->usmpl ) { for (i=0; insamples; i++) { if ( !tok->usmpl[i] ) { k+= tok->nval1; continue; } for (j=0; jnval1; k++,j++) { if ( bcf_double_is_missing_or_vector_end(tok->values[k]) ) bcf_double_set_missing(rtok->values[k]); else rtok->values[k] = -4.34294481903*log(tok->values[k]); } } } else { for (i=0; invalues; i++) { if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) bcf_double_set_missing(rtok->values[i]); else rtok->values[i] = -4.34294481903*log(tok->values[i]); } } return 1; } inline static void tok_init_values(token_t *atok, token_t *btok, token_t *rtok) { token_t *tok; if ( (atok->nsamples || btok->nsamples) && (!atok->nsamples || !btok->nsamples) ) tok = atok->nsamples ? atok : btok; else tok = atok->nvalues > btok->nvalues ? atok : btok; rtok->nvalues = tok->nvalues; rtok->nval1 = tok->nval1; hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values); } inline static void tok_init_samples(token_t *atok, token_t *btok, token_t *rtok) { if ( (atok->nsamples || btok->nsamples) && !rtok->nsamples ) { rtok->nsamples = atok->nsamples ? atok->nsamples : btok->nsamples; rtok->usmpl = (uint8_t*) calloc(rtok->nsamples,1); int i; for (i=0; insamples; i++) rtok->usmpl[i] |= atok->usmpl[i]; for (i=0; insamples; i++) rtok->usmpl[i] |= btok->usmpl[i]; } if (rtok->nsamples) memset(rtok->pass_samples, 0, rtok->nsamples); } #define VECTOR_ARITHMETICS(atok,btok,_rtok,AOP,TYPE) \ { \ token_t *rtok = _rtok; \ int i, has_values = 0; \ if ( atok->nvalues && btok->nvalues ) \ { \ tok_init_values(atok, btok, rtok); \ tok_init_samples(atok, btok, rtok); \ if ( !atok->nsamples && !btok->nsamples ) \ { \ if ( atok->nvalues!=btok->nvalues && atok->nvalues!=1 && btok->nvalues!=1 ) \ error("Cannot run numeric operator in -i/-e filtering on vectors of different lengths: %d vs %d\n",atok->nvalues,btok->nvalues); \ int ir,ia = 0, ib = 0; \ for (ir=0; irnvalues; ir++) \ { \ if ( atok->nvalues > 1 ) ia = ir; \ if ( btok->nvalues > 1 ) ib = ir; \ if ( bcf_double_is_missing_or_vector_end(atok->values[ia]) || bcf_double_is_missing_or_vector_end(btok->values[ib]) ) \ { \ bcf_double_set_missing(rtok->values[ir]); \ continue; \ } \ has_values = 1; \ rtok->values[ir] = TYPE atok->values[ia] AOP TYPE btok->values[ib]; \ } \ } \ else if ( atok->nsamples && btok->nsamples ) \ { \ assert( atok->nsamples==btok->nsamples ); \ if ( atok->nval1!=btok->nval1 && atok->nval1!=1 && btok->nval1!=1 ) \ error("Cannot run numeric operator in -i/-e filtering on vectors of different lengths: %d vs %d\n",atok->nval1,btok->nval1); \ for (i=0; insamples; i++) \ { \ double *rval = rtok->values + i*rtok->nval1; \ double *aval = atok->values + i*atok->nval1; \ double *bval = btok->values + i*btok->nval1; \ int ir,ia = 0, ib = 0; \ for (ir=0; irnval1; ir++) \ { \ if ( atok->nval1 > 1 ) ia = ir; \ if ( btok->nval1 > 1 ) ib = ir; \ if ( bcf_double_is_missing_or_vector_end(aval[ia]) || bcf_double_is_missing_or_vector_end(bval[ib]) ) \ { \ bcf_double_set_missing(rval[ir]); \ continue; \ } \ has_values = 1; \ rval[ir] = TYPE aval[ia] AOP TYPE bval[ib]; \ } \ } \ } \ else if ( atok->nsamples ) \ { \ assert( btok->nvalues==1 ); \ if ( !bcf_double_is_missing_or_vector_end(btok->values[0]) ) \ { \ for (i=0; invalues; i++) \ { \ if ( bcf_double_is_missing_or_vector_end(atok->values[i]) ) \ { \ bcf_double_set_missing(rtok->values[i]); \ continue; \ } \ has_values = 1; \ rtok->values[i] = TYPE atok->values[i] AOP TYPE btok->values[0]; \ } \ } \ } \ else \ { \ assert( atok->nvalues==1 ); \ if ( !bcf_double_is_missing_or_vector_end(atok->values[0]) ) \ { \ for (i=0; invalues; i++) \ { \ if ( bcf_double_is_missing_or_vector_end(btok->values[i]) ) \ { \ bcf_double_set_missing(rtok->values[i]); \ continue; \ } \ has_values = 1; \ rtok->values[i] = TYPE atok->values[0] AOP TYPE btok->values[i]; \ } \ } \ } \ } \ if ( !has_values ) rtok->nvalues = 0; \ } static int vector_logic_or(filter_t *filter, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { if ( nstack < 2 ) error("Error occurred while processing the filter \"%s\"\n", filter->str); token_t *atok = stack[nstack-2]; token_t *btok = stack[nstack-1]; tok_init_samples(atok, btok, rtok); if ( !atok->pass_site && !btok->pass_site ) return 2; rtok->pass_site = 1; if ( !atok->nsamples && !btok->nsamples ) return 2; int i; if ( rtok->tok_type==TOK_OR_VEC ) // ||, select all samples if one is true { if ( (!atok->nsamples && !atok->pass_site) || (!btok->nsamples && !btok->pass_site) ) { // These two conditions are to ensure the following does not set all samples // at sites with QUAL<=30: // QUAL>30 || FMT/GQ>30 token_t *tok = atok->nsamples ? atok : btok; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; rtok->pass_samples[i] = tok->pass_samples[i]; } } else { for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; rtok->pass_samples[i] = 1; } } return 2; } // |, only select samples which are actually true if ( !atok->nsamples || !btok->nsamples ) { token_t *tok = atok->nsamples ? atok : btok; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; rtok->pass_samples[i] = tok->pass_samples[i]; } return 2; } assert( atok->nsamples==btok->nsamples ); for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; rtok->pass_samples[i] = atok->pass_samples[i] | btok->pass_samples[i]; } return 2; } static int vector_logic_and(filter_t *filter, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { if ( nstack < 2 ) error("Error occurred while processing the filter \"%s\". (nstack=%d)\n", filter->str,nstack); token_t *atok = stack[nstack-2]; token_t *btok = stack[nstack-1]; tok_init_samples(atok, btok, rtok); if ( !atok->pass_site || !btok->pass_site ) return 2; if ( !atok->nsamples && !btok->nsamples ) { rtok->pass_site = 1; return 2; } int i; if ( !atok->nsamples || !btok->nsamples ) { token_t *tok = atok->nsamples ? atok : btok; for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; rtok->pass_samples[i] = tok->pass_samples[i]; } rtok->pass_site = 1; return 2; } assert( atok->nsamples==btok->nsamples ); if ( rtok->tok_type==TOK_AND_VEC ) // &&, can be true in different samples { for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; rtok->pass_samples[i] = atok->pass_samples[i] | btok->pass_samples[i]; } rtok->pass_site = 1; } else // &, must be true within one sample { for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; rtok->pass_samples[i] = atok->pass_samples[i] & btok->pass_samples[i]; if ( rtok->pass_samples[i] ) rtok->pass_site = 1; } } return 2; } // A note about comparisons: // When setting value by determining index from the genotype, we face the problem // of how to interpret truncating arrays. Say we have TAG defined as Number=. and // GT:TAG 1/1:0,1,2 0/0:0 // Then when querying we expect the following expression to evaluate for the second // sample as // -i 'TAG[1:1]="."' .. true // -i 'TAG[1:GT]="."' .. false // The problem is that the implementation truncates the number of fields, filling // usually fewer than the original number of per-sample values. This is fixed by // adding an exception that makes the code aware of this: the GT indexing can be // recognised by having tok->idx==-3 #define CMP_VECTORS(atok,btok,_rtok,CMP_OP,missing_logic) \ { \ token_t *rtok = _rtok; \ int i, j, k; \ tok_init_samples(atok, btok, rtok); \ if ( !atok->nsamples && !btok->nsamples ) \ { \ if ( !atok->nvalues && !btok->nvalues ) { rtok->pass_site = missing_logic[2]; } \ else if ( !atok->nvalues || !btok->nvalues ) \ { \ token_t *tok = atok->nvalues ? atok : btok; \ for (j=0; jnvalues; j++) \ { \ if ( bcf_double_is_missing_or_vector_end(tok->values[j]) ) \ { \ if ( missing_logic[2] ) { rtok->pass_site = 1; break; } \ } \ else if ( missing_logic[1] ) { rtok->pass_site = 1; break; } \ } \ } \ else \ { \ for (i=0; invalues; i++) \ { \ int amiss = bcf_double_is_missing_or_vector_end(atok->values[i]) ? 1 : 0; \ for (j=0; jnvalues; j++) \ { \ int nmiss = amiss + (bcf_double_is_missing_or_vector_end(btok->values[j]) ? 1 : 0); \ if ( nmiss ) \ { \ if ( missing_logic[nmiss] ) { rtok->pass_site = 1; i = atok->nvalues; break; } \ } \ else if ( atok->values[i] > 16777216 || btok->values[j] > 16777216 ) /* Ugly, see #871 */ \ { \ if ( atok->values[i] CMP_OP btok->values[j] ) { rtok->pass_site = 1; i = atok->nvalues; break; } \ } \ else if ( (float)atok->values[i] CMP_OP (float)btok->values[j] ) { rtok->pass_site = 1; i = atok->nvalues; break; } \ } \ } \ } \ } \ else \ { \ if ( !atok->nvalues && !btok->nvalues ) \ { \ if ( missing_logic[2] ) \ { \ for (i=0; insamples; i++) \ if ( rtok->usmpl[i] ) { rtok->pass_samples[i] = missing_logic[2]; rtok->pass_site = 1; } \ } \ } \ else if ( !atok->nvalues || !btok->nvalues ) \ { \ token_t *tok = atok->nvalues ? atok : btok; \ if ( !tok->nsamples ) \ { \ int miss = 0; \ for (j=0; jnvalues; j++) \ miss |= bcf_double_is_missing_or_vector_end(tok->values[j]) ? 1 : 0; \ if ( missing_logic[++miss] ) \ { \ for (i=0; insamples; i++) \ if ( rtok->usmpl[i] ) { rtok->pass_samples[i] = missing_logic[miss]; rtok->pass_site = 1; } \ } \ } \ else \ for (i=0; insamples; i++) \ { \ if ( !rtok->usmpl[i] ) continue; \ double *ptr = tok->values + i*tok->nval1; \ int miss = 0; \ for (j=0; jnval1; j++) \ miss |= bcf_double_is_missing_or_vector_end(ptr[j]) ? 1 : 0; \ if ( missing_logic[++miss] ) { rtok->pass_samples[i] = missing_logic[miss]; rtok->pass_site = 1; } \ } \ } \ else if ( atok->nsamples && btok->nsamples ) \ { \ if ( atok->nval1!=btok->nval1 ) error("Incompatible number of per-sample values in comparison: %d vs %d\n",atok->nval1,btok->nval1); \ if ( atok->nsamples!=btok->nsamples ) error("Incompatible number samples in comparison: %d vs %d\n",atok->nsamples,btok->nsamples); \ for (i=0; insamples; i++) \ { \ if ( !atok->usmpl[i] || !btok->usmpl[i] ) { rtok->usmpl[i] = 0; continue; } \ double *aptr = atok->values + i*atok->nval1; \ double *bptr = btok->values + i*btok->nval1; \ for (j=0; jnval1; j++) \ { \ if ( atok->idx==-3 && bcf_double_is_vector_end(aptr[j]) ) break; /* explained above */ \ if ( btok->idx==-3 && bcf_double_is_vector_end(bptr[j]) ) break; /* explained above */ \ int nmiss = bcf_double_is_missing_or_vector_end(aptr[j]) ? 1 : 0; \ if ( nmiss && !missing_logic[0] ) continue; /* any is missing => result is false */ \ nmiss += (bcf_double_is_missing_or_vector_end(bptr[j]) ? 1 : 0); \ if ( nmiss ) \ { \ if ( missing_logic[nmiss] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; break; } \ } \ else if ( aptr[j] > 16777216 || bptr[j] > 16777216 ) /* Ugly, see #871 */ \ { \ if ( aptr[j] CMP_OP bptr[j] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; break; } \ } \ else if ( (float)aptr[j] CMP_OP (float)bptr[j] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; break; } \ } \ } \ } \ else if ( atok->nsamples )\ { \ for (i=0; insamples; i++) \ { \ if ( !rtok->usmpl[i] ) continue; \ double *aptr = atok->values + i*atok->nval1; \ double *bptr = btok->values; \ for (j=0; jnval1; j++) \ { \ if ( atok->idx==-3 && bcf_double_is_vector_end(aptr[j]) ) break; /* explained above */ \ int miss = bcf_double_is_missing_or_vector_end(aptr[j]) ? 1 : 0; \ if ( miss && !missing_logic[0] ) continue; /* any is missing => result is false */ \ for (k=0; knvalues; k++) \ { \ int nmiss = miss + (bcf_double_is_missing_or_vector_end(bptr[k]) ? 1 : 0); \ if ( nmiss ) \ { \ if ( missing_logic[nmiss] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = atok->nval1; break; } \ } \ else if ( aptr[j] > 16777216 || bptr[k] > 16777216 ) /* Ugly, see #871 */ \ { \ if ( aptr[j] CMP_OP bptr[k] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = atok->nval1; break; } \ } \ else if ( (float)aptr[j] CMP_OP (float)bptr[k] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = atok->nval1; break; } \ } \ } \ } \ } \ else /* btok->nsamples */ \ { \ for (i=0; insamples; i++) \ { \ if ( !rtok->usmpl[i] ) continue; \ double *aptr = atok->values; \ double *bptr = btok->values + i*btok->nval1; \ for (j=0; jnval1; j++) \ { \ if ( atok->idx==-3 && bcf_double_is_vector_end(bptr[j]) ) break; /* explained above */ \ int miss = bcf_double_is_missing_or_vector_end(bptr[j]) ? 1 : 0; \ if ( miss && !missing_logic[0] ) continue; /* any is missing => result is false */ \ for (k=0; knvalues; k++) \ { \ int nmiss = miss + (bcf_double_is_missing_or_vector_end(aptr[k]) ? 1 : 0); \ if ( nmiss ) \ { \ if ( missing_logic[nmiss] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = btok->nval1; break; } \ } \ else if ( bptr[j] > 16777216 || aptr[k] > 16777216 ) /* Ugly, see #871 */ \ { \ if ( aptr[k] CMP_OP bptr[j] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = btok->nval1; break; } \ } \ else if ( (float)aptr[k] CMP_OP (float)bptr[j] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = btok->nval1; break; } \ } \ } \ } \ } \ } \ } static int _regex_vector_strings(regex_t *regex, char *str, size_t len, int logic, int *missing_logic) { char *end = str + len; while ( str < end && *str ) { char *mid = str; while ( mid < end && *mid && *mid!=',' ) mid++; int miss = mid - str == 1 && str[0]=='.' ? 1 : 0; if ( miss && missing_logic[miss] ) return 1; char tmp = *mid; *mid = 0; int match = regexec(regex, str, 0,NULL,0) ? 0 : 1; *mid = tmp; if ( logic==TOK_NLIKE ) match = match ? 0 : 1; if ( match ) return 1; if ( !*mid ) break; str = mid + 1; } return 0; } static inline int _has_missing_string(char *beg) { while ( *beg ) { char *end = beg; while ( *end && *end!=',' ) end++; if ( end-beg==1 && beg[0]=='.' ) return 1; if ( !*end ) break; beg = end + 1; } return 0; } // Compare two strings with multiple fields, for example "A,B,.,C"=="X,Y,A". // Returns 1 if any field matches, otherwise returns 0 static inline int _match_vector_strings(char *abeg, size_t alen, char *bstr, size_t blen, int logic, int *missing_logic) { char *aend = abeg + alen; char *bend = bstr + blen; while ( abeg < aend && *abeg ) { char *amid = abeg; while ( amid < aend && *amid && *amid!=',' ) amid++; int miss = amid - abeg == 1 && abeg[0]=='.' ? 1 : 0; char *bbeg = bstr; while ( bbeg < bend && *bbeg ) { char *bmid = bbeg; while ( bmid < bend && *bmid && *bmid!=',' ) bmid++; int nmiss = miss + (bmid - bbeg == 1 && bbeg[0]=='.' ? 1 : 0); if ( nmiss ) { if ( missing_logic[nmiss] ) return 1; } else { int match = amid-abeg==bmid-bbeg && !strncmp(abeg,bbeg,amid-abeg) ? 1 : 0; if ( logic==TOK_NE ) match = match==1 ? 0 : 1; if ( match ) return 1; } if ( !*bmid ) break; bbeg = bmid + 1; } if ( !*amid ) break; abeg = amid + 1; } return 0; } static void cmp_vector_strings(token_t *atok, token_t *btok, token_t *rtok) { tok_init_samples(atok, btok, rtok); int i, logic = rtok->tok_type; // TOK_EQ, TOK_NE, TOK_LIKE, TOK_NLIKE regex_t *regex = atok->regex ? atok->regex : (btok->regex ? btok->regex : NULL); assert( atok->nvalues==atok->str_value.l && btok->nvalues==btok->str_value.l ); assert( !atok->nsamples || !btok->nsamples ); assert( (!regex && (logic==TOK_EQ || logic==TOK_NE)) || (regex && (logic==TOK_LIKE || logic==TOK_NLIKE)) ); int missing_logic[] = {0,0,0}; if ( logic==TOK_EQ || logic==TOK_LIKE ) missing_logic[0] = missing_logic[2] = 1; else if ( logic==TOK_NE || logic==TOK_NLIKE ) missing_logic[0] = missing_logic[1] = 1; if ( !atok->nsamples && !btok->nsamples ) { if ( !atok->nvalues && !btok->nvalues ) { rtok->pass_site = missing_logic[2]; return; } if ( !atok->nvalues || !btok->nvalues ) { int miss = _has_missing_string(atok->nvalues ? atok->str_value.s : btok->str_value.s); if ( missing_logic[miss+1] ) rtok->pass_site = 1; return; } if ( !regex ) rtok->pass_site = _match_vector_strings(atok->str_value.s, atok->str_value.l, btok->str_value.s, btok->str_value.l, logic, missing_logic); else { token_t *tok = atok->regex ? btok : atok; rtok->pass_site = _regex_vector_strings(regex, tok->str_value.s, tok->str_value.l, logic, missing_logic); } return; } // The case of (!atok->nsamples || !btok->nsamples) if ( !atok->nvalues && !btok->nvalues ) { if ( missing_logic[2] ) { for (i=0; insamples; i++) if ( rtok->usmpl[i] ) { rtok->pass_samples[i] = missing_logic[2]; rtok->pass_site = 1; } } return; } if ( !atok->nvalues || !btok->nvalues ) { token_t *tok = atok->nvalues ? atok : btok; if ( !tok->nsamples ) { int miss = _has_missing_string(tok->str_value.s); if ( !missing_logic[miss+1] ) return; for (i=0; insamples; i++) if ( rtok->usmpl[i] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; } } else for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; int miss = _has_missing_string(tok->str_value.s + i*tok->nval1); if ( missing_logic[miss+1] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; } } return; } // The case of (!atok->nsamples || !btok->nsamples) && (atok->nvalues && btok->nvalues) token_t *xtok = atok->nsamples ? atok : btok; token_t *ytok = atok->nsamples ? btok : atok; assert( regex==ytok->regex ); for (i=0; insamples; i++) { if ( !rtok->usmpl[i] ) continue; int match; if ( regex ) match = _regex_vector_strings(regex, xtok->str_value.s + i*xtok->nval1, xtok->nval1, logic, missing_logic); else match = _match_vector_strings(xtok->str_value.s + i*xtok->nval1, xtok->nval1, ytok->str_value.s, ytok->str_value.l, logic, missing_logic); if ( match ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; } } } static int parse_idxs(char *tag_idx, int **idxs, int *nidxs, int *idx) { // TAG[], TAG[*] .. any field; sets idx=-2, idxs[0]=-1 if ( *tag_idx==0 || !strcmp("*", tag_idx) ) { *idxs = (int*) malloc(sizeof(int)); (*idxs)[0] = -1; *nidxs = 1; *idx = -2; return 0; } if ( !strcmp("GT", tag_idx) ) { *idxs = (int*) malloc(sizeof(int)); (*idxs)[0] = -1; *nidxs = 1; *idx = -3; return 0; } // TAG[integer] .. one field; idx positive char *end, *beg = tag_idx; *idx = strtol(tag_idx, &end, 10); if ( *idx >= 0 && *end==0 ) return 0; // TAG[0,1] or TAG[0-2] or [1-] etc; idx=-2, idxs[...]=0,0,1,1,.. int i, ibeg = -1; while ( *beg ) { int num = strtol(beg, &end, 10); if ( end[0]==',' ) beg = end + 1; else if ( end[0]==0 ) beg = end; else if ( end[0]=='-' ) { beg = end + 1; ibeg = num; continue; } else return -1; if ( num >= *nidxs ) { *idxs = (int*) realloc(*idxs, sizeof(int)*(num+1)); memset(*idxs + *nidxs, 0, sizeof(int)*(num - *nidxs + 1)); *nidxs = num + 1; } if ( ibeg>=0 ) { for (i=ibeg; i<=num; i++) (*idxs)[i] = 1; ibeg = -1; } (*idxs)[num] = 1; } if ( ibeg >=0 ) { if ( ibeg >= *nidxs ) { *idxs = (int*) realloc(*idxs, sizeof(int)*(ibeg+1)); memset(*idxs + *nidxs, 0, sizeof(int)*(ibeg - *nidxs + 1)); *nidxs = ibeg + 1; } (*idxs)[ibeg] = -1; } *idx = -2; return 0; } static void parse_tag_idx(bcf_hdr_t *hdr, int is_fmt, char *tag, char *tag_idx, token_t *tok) // tag_idx points just after "TAG[" { int i, len = strlen(tag_idx); if ( tag_idx[len-1] == ']' ) tag_idx[len-1] = 0; char *ori = strdup(tag_idx); assert( !tok->idxs && !tok->usmpl ); int *idxs1 = NULL, nidxs1 = 0, idx1 = 0; int *idxs2 = NULL, nidxs2 = 0, idx2 = 0; int set_samples = 0; char *colon = strrchr(tag_idx, ':'); if ( tag_idx[0]=='@' ) // file list with sample names { if ( !is_fmt ) error("Could not parse \"%s\". (Not a FORMAT tag yet a sample list provided.)\n", ori); char *fname = expand_path(tag_idx+1); #ifdef _WIN32 if (fname && strlen(fname) > 2 && fname[1] == ':') // Deal with Windows paths, such as 'C:\..' colon = strrchr(fname+2, ':'); #endif int nsmpl; char **list = hts_readlist(fname, 1, &nsmpl); if ( !list && colon ) { if ( parse_idxs(colon+1, &idxs2, &nidxs2, &idx2) != 0 ) error("Could not parse the index: %s\n", ori); tok->idxs = idxs2; tok->nidxs = nidxs2; tok->idx = idx2; colon = strrchr(fname, ':'); *colon = 0; list = hts_readlist(fname, 1, &nsmpl); } if ( !list ) error("Could not read: %s\n", fname); free(fname); tok->nsamples = bcf_hdr_nsamples(hdr); tok->usmpl = (uint8_t*) calloc(tok->nsamples,1); for (i=0; iusmpl[ismpl] = 1; } free(list); if ( !colon ) { tok->idxs = (int*) malloc(sizeof(int)); tok->idxs[0] = -1; tok->nidxs = 1; tok->idx = -2; } } else if ( colon ) { if ( !is_fmt ) error("Could not parse the index \"%s\". (Not a FORMAT tag yet sample index implied.)\n", ori); *colon = 0; if ( parse_idxs(tag_idx, &idxs1, &nidxs1, &idx1) != 0 ) error("Could not parse the index: %s\n", ori); if ( parse_idxs(colon+1, &idxs2, &nidxs2, &idx2) != 0 ) error("Could not parse the index: %s\n", ori); tok->idxs = idxs2; tok->nidxs = nidxs2; tok->idx = idx2; set_samples = 1; } else { if ( parse_idxs(tag_idx, &idxs1, &nidxs1, &idx1) != 0 ) error("Could not parse the index: %s\n", ori); if ( is_fmt ) { if ( nidxs1==1 && idxs1[0]==-1 ) { tok->idxs = (int*) malloc(sizeof(int)); tok->idxs[0] = -1; tok->nidxs = 1; tok->idx = idx1; } else if ( bcf_hdr_id2number(hdr,BCF_HL_FMT,tok->hdr_id)!=1 ) error("The FORMAT tag %s can have multiple subfields, run as %s[sample:subfield]\n", tag,tag); else tok->idx = 0; set_samples = 1; } else { tok->idxs = idxs1; tok->nidxs = nidxs1; tok->idx = idx1; } } if ( set_samples ) { tok->nsamples = bcf_hdr_nsamples(hdr); tok->usmpl = (uint8_t*) calloc(tok->nsamples,1); if ( idx1>=0 ) { if ( idx1 >= bcf_hdr_nsamples(hdr) ) error("The sample index is too large: %s\n", ori); tok->usmpl[idx1] = 1; } else if ( idx1==-2 || idx1==-3 ) { for (i=0; i= bcf_hdr_nsamples(hdr) ) error("The sample index is too large: %s\n", ori); tok->usmpl[i] = 1; } if ( nidxs1 && idxs1[nidxs1-1]==-1 ) // open range, such as "7-" { for (; insamples; i++) tok->usmpl[i] = 1; } } else error("todo: %s:%d .. %d\n", __FILE__,__LINE__, idx2); free(idxs1); } free(ori); if ( tok->nidxs && tok->idxs[tok->nidxs-1]!=-1 ) { for (i=0; inidxs; i++) if ( tok->idxs[i] ) tok->nuidxs++; } } static int max_ac_an_unpack(bcf_hdr_t *hdr) { int hdr_id = bcf_hdr_id2int(hdr,BCF_DT_ID,"AC"); if ( hdr_id<0 ) return BCF_UN_FMT; if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,hdr_id) ) return BCF_UN_FMT; hdr_id = bcf_hdr_id2int(hdr,BCF_DT_ID,"AN"); if ( hdr_id<0 ) return BCF_UN_FMT; if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,hdr_id) ) return BCF_UN_FMT; return BCF_UN_INFO; } static int filters_init1_ext(filter_t *filter, char *str, int len, token_t *tok) { tok->hl_type = -1; tok->ht_type = -1; tok->tok_type = TOK_VAL; tok->hdr_id = -1; tok->pass_site = -1; tok->idx = 0; tok->iext = ++filter->n_ext; filter->ext = realloc(filter->ext,sizeof(*filter->ext)*filter->n_ext); if ( !strncasecmp(str,"{str}",len) ) { tok->ht_type = BCF_HT_STR; tok->is_str = 1; } else if ( !strncasecmp(str,"{int}",len) ) tok->ht_type = BCF_HT_INT; else if ( !strncasecmp(str,"{float}",len) ) tok->ht_type = BCF_HT_REAL; filter->ext[filter->n_ext-1] = tok->ht_type; return 0; } static int filters_init1(filter_t *filter, char *str, int len, token_t *tok) { tok->ht_type = -1; tok->hl_type = -1; tok->tok_type = TOK_VAL; tok->hdr_id = -1; tok->pass_site = -1; tok->idx = 0; // is this a string constant? if ( str[0]=='"' || str[0]=='\'' ) { int quote = str[0]; if ( str[len-1] != quote ) error("TODO: [%s]\n", filter->str); tok->key = (char*) calloc(len-1,sizeof(char)); hts_expand(double,1,tok->mvalues,tok->values); tok->values[0] = len-2; memcpy(tok->key,str+1,len-2); tok->key[len-2] = 0; tok->is_str = 1; tok->ht_type = BCF_HT_STR; tok->nvalues = len-2; if ( !strcmp(".",tok->key) ) tok->is_missing = 1; return 0; } // is it a file? if ( str[0]=='@' ) { tok->tag = (char*) calloc(len+1,sizeof(char)); memcpy(tok->tag,str,len); tok->tag[len] = 0; char *fname = expand_path(tok->tag+1); int i, n; char **list = hts_readlist(fname, 1, &n); if ( !list ) error("Could not read: %s\n", fname); free(fname); tok->hash = khash_str2int_init(); for (i=0; ihash,list[i]) ) khash_str2int_inc(tok->hash,list[i]); else free(list[i]); } free(list); return 0; } int is_fmt = -1; if ( !strncasecmp(str,"FMT/",4) ) { str += 4; len -= 4; is_fmt = 1; } else if ( !strncasecmp(str,"FORMAT/",7) ) { str += 7; len -= 7; is_fmt = 1; } else { if ( !strncasecmp(str,"INFO/",5) ) { is_fmt = 0; str += 5; len -= 5; } else if ( !strncasecmp(str,"QUAL",len) || !strncmp(str,"%QUAL",len) /* for backward compatibility */ ) { tok->setter = filters_set_qual; tok->tag = strdup("QUAL"); tok->ht_type = BCF_HT_REAL; filter_add_used_tag(filter,NULL,tok->tag); return 0; } else if ( !strncasecmp(str,"TYPE",len) || !strncmp(str,"%TYPE",len) /* for backward compatibility */ ) { tok->setter = filters_set_type; tok->tag = strdup("TYPE"); tok->ht_type = BCF_HT_STR; return 0; } else if ( !strncasecmp(str,"FILTER",len) || !strncmp(str,"%FILTER",len) /* for backward compatibility */ ) { tok->comparator = filters_cmp_filter; tok->tag = strdup("FILTER"); filter->max_unpack |= BCF_UN_FLT; tok->hl_type = BCF_HL_FLT; tok->ht_type = BCF_HT_STR; filter_add_used_tag(filter,NULL,tok->tag); return 0; } else if ( !strncasecmp(str,"ID",len) || !strncasecmp(str,"%ID",len) /* for backward compatibility */ ) { tok->comparator = filters_cmp_id; tok->tag = strdup("ID"); tok->ht_type = BCF_HT_STR; filter_add_used_tag(filter,NULL,tok->tag); return 0; } else if ( !strncasecmp(str,"CHROM",len) ) { tok->setter = &filters_set_chrom; tok->tag = strdup("CHROM"); tok->ht_type = BCF_HT_STR; filter_add_used_tag(filter,NULL,tok->tag); return 0; } else if ( !strncasecmp(str,"POS",len) ) { tok->setter = &filters_set_pos; tok->tag = strdup("POS"); tok->ht_type = BCF_HT_INT; filter_add_used_tag(filter,NULL,tok->tag); return 0; } else if ( !strncasecmp(str,"REF",len) ) { tok->setter = &filters_set_ref_string; tok->is_str = 1; tok->tag = strdup("REF"); tok->ht_type = BCF_HT_STR; filter_add_used_tag(filter,NULL,tok->tag); return 0; } else if ( !strncasecmp(str,"ALT",len) ) { tok->setter = &filters_set_alt_string; tok->is_str = 1; tok->tag = strdup("ALT"); tok->ht_type = BCF_HT_STR; tok->idxs = (int*) malloc(sizeof(int)); tok->idxs[0] = -1; tok->nidxs = 1; tok->idx = -2; filter_add_used_tag(filter,NULL,tok->tag); return 0; } else if ( !strncasecmp(str,"N_ALT",len) ) { tok->setter = &filters_set_nalt; tok->tag = strdup("N_ALT"); tok->ht_type = BCF_HT_INT; return 0; } else if ( !strncasecmp(str,"N_SAMPLES",len) ) { tok->tok_type = TOK_VAL; tok->threshold = bcf_hdr_nsamples(filter->hdr); tok->is_constant = 1; tok->ht_type = BCF_HT_INT; return 0; } else if ( !strncasecmp(str,"N_MISSING",len) ) { filter->max_unpack |= BCF_UN_FMT; tok->setter = &filters_set_nmissing; tok->tag = strdup("N_MISSING"); tok->ht_type = BCF_HT_INT; return 0; } else if ( !strncasecmp(str,"F_MISSING",len) ) { filter->max_unpack |= BCF_UN_FMT; tok->setter = &filters_set_nmissing; tok->tag = strdup("F_MISSING"); tok->ht_type = BCF_HT_REAL; return 0; } } // does it have array subscript? int is_array = 0; kstring_t tmp = {0,0,0}; kputsn(str, len, &tmp); if ( tmp.s[tmp.l-1] == ']' ) { int i; for (i=0; ihdr_id = bcf_hdr_id2int(filter->hdr,BCF_DT_ID,tmp.s); if ( is_fmt==-1 ) { if ( tok->hdr_id >=0 ) { int is_info = bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_INFO,tok->hdr_id) ? 1 : 0; is_fmt = bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_FMT,tok->hdr_id) ? 1 : 0; if ( is_info && is_fmt ) error("Error: ambiguous filtering expression, both INFO/%s and FORMAT/%s are defined in the VCF header.\n" , tmp.s,tmp.s); } if ( is_fmt==-1 ) is_fmt = 0; } if ( is_array ) { parse_tag_idx(filter->hdr, is_fmt, tmp.s, tmp.s+is_array, tok); if ( tok->idx==-3 && bcf_hdr_id2length(filter->hdr,BCF_HL_FMT,tok->hdr_id)!=BCF_VL_R ) error("Error: GT subscripts can be used only with Number=R tags\n"); } else if ( is_fmt && !tok->nsamples ) { int i; tok->nsamples = bcf_hdr_nsamples(filter->hdr); tok->usmpl = (uint8_t*) malloc(tok->nsamples); for (i=0; insamples; i++) tok->usmpl[i] = 1; } tok->hl_type = is_fmt ? BCF_HL_FMT : BCF_HL_INFO; if ( is_fmt ) filter->max_unpack |= BCF_UN_FMT; if ( tok->hdr_id>=0 ) { if ( is_fmt && !strcmp("GT",tmp.s) ) { tok->setter = &filters_set_genotype_string; tok->is_str = 1; tok->ht_type = BCF_HT_STR; } else if ( is_fmt ) { if ( !bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_FMT,tok->hdr_id) ) error("No such FORMAT field: %s\n", tmp.s); if ( bcf_hdr_id2number(filter->hdr,BCF_HL_FMT,tok->hdr_id)!=1 && !is_array ) { tok->idxs = (int*) malloc(sizeof(int)); tok->idxs[0] = -1; tok->nidxs = 1; tok->idx = -2; } switch ( bcf_hdr_id2type(filter->hdr,BCF_HL_FMT,tok->hdr_id) ) { case BCF_HT_INT: tok->setter = &filters_set_format_int; tok->ht_type = BCF_HT_INT; break; case BCF_HT_REAL: tok->setter = &filters_set_format_float; tok->ht_type = BCF_HT_REAL; break; case BCF_HT_STR: tok->setter = &filters_set_format_string; tok->ht_type = BCF_HT_STR; tok->is_str = 1; break; default: error("[%s:%d %s] FIXME\n", __FILE__,__LINE__,__FUNCTION__); } } else if ( !bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_INFO,tok->hdr_id) ) error("No such INFO field: %s\n", tmp.s); else { if ( bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id) == BCF_HT_FLAG ) { tok->setter = filters_set_info_flag; tok->ht_type = BCF_HT_INT; } else { tok->ht_type = bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id); if ( tok->ht_type == BCF_HT_STR ) tok->is_str = 1; if ( bcf_hdr_id2number(filter->hdr,BCF_HL_INFO,tok->hdr_id)==1 ) tok->setter = filters_set_info; else { switch ( bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id) ) { case BCF_HT_INT: tok->setter = &filters_set_info_int; break; case BCF_HT_REAL: tok->setter = &filters_set_info_float; break; case BCF_HT_STR: tok->setter = &filters_set_info_string; tok->is_str = 1; break; default: error("[%s:%d %s] FIXME\n", __FILE__,__LINE__,__FUNCTION__); } if (!is_array) { tok->idx = -2; tok->idxs = (int*) malloc(sizeof(int)); tok->idxs[0] = -1; tok->nidxs = 1; } } } filter->max_unpack |= BCF_UN_INFO; } tok->tag = strdup(tmp.s); if ( tmp.s ) free(tmp.s); filter_add_used_tag(filter,is_fmt ? "FORMAT/" : "INFO/",tok->tag); return 0; } else if ( !strcasecmp(tmp.s,"ALT") ) { tok->setter = &filters_set_alt_string; tok->is_str = 1; tok->ht_type = BCF_HT_STR; tok->tag = strdup(tmp.s); free(tmp.s); filter_add_used_tag(filter,NULL,tok->tag); return 0; } else if ( !strcasecmp(tmp.s,"AN") ) { filter->max_unpack |= BCF_UN_FMT; tok->setter = &filters_set_an; tok->tag = strdup("AN"); tok->ht_type = BCF_HT_INT; free(tmp.s); return 0; } else if ( !strcasecmp(tmp.s,"AC") ) { filter->max_unpack |= BCF_UN_FMT; tok->setter = &filters_set_ac; tok->tag = strdup("AC"); tok->ht_type = BCF_HT_INT; free(tmp.s); return 0; } else if ( !strcasecmp(tmp.s,"MAC") ) { filter->max_unpack |= max_ac_an_unpack(filter->hdr); tok->setter = &filters_set_mac; tok->tag = strdup("MAC"); tok->ht_type = BCF_HT_INT; free(tmp.s); return 0; } else if ( !strcasecmp(tmp.s,"AF") ) { filter->max_unpack |= max_ac_an_unpack(filter->hdr); tok->setter = &filters_set_af; tok->tag = strdup("AF"); tok->ht_type = BCF_HT_REAL; free(tmp.s); return 0; } else if ( !strcasecmp(tmp.s,"MAF") ) { filter->max_unpack |= max_ac_an_unpack(filter->hdr); tok->setter = &filters_set_maf; tok->tag = strdup("MAF"); tok->ht_type = BCF_HT_REAL; free(tmp.s); return 0; } else if ( !strcasecmp(tmp.s,"ILEN") || !strcasecmp(tmp.s,"%ILEN") ) { filter->max_unpack |= BCF_UN_STR; tok->setter = &filters_set_ilen; tok->tag = strdup("ILEN"); tok->ht_type = BCF_HT_INT; free(tmp.s); return 0; } // is it a value? Here we parse as integer/float separately and use strtof // rather than strtod, because the more accurate double representation // would invalidate floating point comparisons like QUAL=59.2, obtained via // htslib/vcf parser. // Update: use strtod() and force floats only in comparisons char *end; tok->threshold = strtol(tmp.s, &end, 10); // integer? if ( end - tmp.s != strlen(tmp.s) ) { errno = 0; tok->threshold = strtod(tmp.s, &end); // float? if ( errno!=0 || end!=tmp.s+len ) { if ( filter->exit_on_error ) error("[%s:%d %s] Error: the tag \"%s\" is not defined in the VCF header\n", __FILE__,__LINE__,__FUNCTION__,tmp.s); filter->status |= FILTER_ERR_UNKN_TAGS; filter_add_undef_tag(filter,tmp.s); } tok->ht_type = BCF_HT_REAL; } else tok->ht_type = BCF_HT_INT; tok->is_constant = 1; if ( tmp.s ) free(tmp.s); return 0; } static void filter_debug_print(token_t *toks, token_t **tok_ptrs, int ntoks) { int i; for (i=0; itok_type==TOK_VAL ) { if ( tok->key ) fprintf(bcftools_stderr,"%s", tok->key); else if ( tok->tag ) fprintf(bcftools_stderr,"%s", tok->tag); else fprintf(bcftools_stderr,"%e", tok->threshold); } else fprintf(bcftools_stderr,"%c", TOKEN_STRING[tok->tok_type]); if ( tok->setter ) fprintf(bcftools_stderr,"\t[setter %p]", tok->setter); fprintf(bcftools_stderr,"\n"); } } static void str_to_lower(char *str) { while ( *str ) { *str = tolower(*str); str++; } } static int perl_exec(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { #if ENABLE_PERL_FILTERS PerlInterpreter *perl = flt->perl; if ( !perl ) error("Error: perl expression without a perl script name\n"); dSP; ENTER; SAVETMPS; PUSHMARK(SP); int i,j, istack = nstack - rtok->nargs; for (i=istack+1; iis_str ) XPUSHs(sv_2mortal(newSVpvn(tok->str_value.s,tok->str_value.l))); else if ( tok->nvalues==1 ) XPUSHs(sv_2mortal(newSVnv(tok->values[0]))); else if ( tok->nvalues>1 ) { AV *av = newAV(); for (j=0; jnvalues; j++) av_push(av, newSVnv(tok->values[j])); SV *rv = newRV_inc((SV*)av); XPUSHs(rv); } else { bcf_double_set_missing(tok->values[0]); XPUSHs(sv_2mortal(newSVnv(tok->values[0]))); } } PUTBACK; // A possible future todo: provide a means to select samples and indexes, // expressions like this don't work yet // perl.filter(FMT/AD)[1:0] int nret = call_pv(stack[istack]->str_value.s, G_ARRAY); SPAGAIN; rtok->nvalues = nret; hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values); for (i=nret; i>0; i--) { rtok->values[i-1] = (double) POPn; if ( isnan(rtok->values[i-1]) ) bcf_double_set_missing(rtok->values[i-1]); } PUTBACK; FREETMPS; LEAVE; #else error("\nPerl filtering requires running `configure --enable-perl-filters` at compile time.\n\n"); #endif return rtok->nargs; } static void perl_init(filter_t *filter, char **str) { char *beg = *str; while ( *beg && isspace(*beg) ) beg++; if ( !*beg ) return; if ( strncasecmp("perl:", beg, 5) ) return; #if ENABLE_PERL_FILTERS beg += 5; char *end = beg; while ( *end && *end!=';' ) end++; // for now not escaping semicolons *str = end+1; if ( ++filter_ninit == 1 ) { // must be executed only once, even for multiple filters; first time here int argc = 0; char **argv = NULL; char **env = NULL; PERL_SYS_INIT3(&argc, &argv, &env); } filter->perl = perl_alloc(); PerlInterpreter *perl = filter->perl; if ( !perl ) error("perl_alloc failed\n"); perl_construct(perl); // name of the perl script to run char *rmme = (char*) calloc(end - beg + 1,1); memcpy(rmme, beg, end - beg); char *argv[] = { "", "" }; argv[1] = expand_path(rmme); free(rmme); PL_origalen = 1; // don't allow $0 change int ret = perl_parse(filter->perl, NULL, 2, argv, NULL); PL_exit_flags |= PERL_EXIT_DESTRUCT_END; if ( ret ) error("Failed to parse: %s\n", argv[1]); free(argv[1]); perl_run(perl); #else error("\nPerl filtering requires running `configure --enable-perl-filters` at compile time.\n\n"); #endif } static void perl_destroy(filter_t *filter) { #if ENABLE_PERL_FILTERS if ( !filter->perl ) return; PerlInterpreter *perl = filter->perl; perl_destruct(perl); perl_free(perl); if ( --filter_ninit <= 0 ) { // similarly to PERL_SYS_INIT3, can must be executed only once? todo: test PERL_SYS_TERM(); } #endif } // A very rudimentary heuristics to determine type, e.g. STR_TAG={} implies {str}. // Throws an error on anything more complex and asks for an explicit type. static void determine_ext_types(filter_t *filter, int ntok, token_t *tok) { int i; for (i=0; istr); for (i=0; iext[j]!=-1 && filter->ext[j]!=tok[i].ht_type ) error("[%s:%d %s] FIXME: this should not happen %d vs %d, iext=%d\n",__FILE__,__LINE__,__FUNCTION__,filter->ext[j],tok[i].ht_type,j); filter->ext[j] = tok[i].ht_type; if ( tok[i].ht_type==BCF_HT_STR ) tok[i].is_str = 1; } } // Parse filter expression and convert to reverse polish notation. Dijkstra's shunting-yard algorithm static filter_t *filter_init_(bcf_hdr_t *hdr, const char *str, int exit_on_error) { filter_t *filter = (filter_t *) calloc(1,sizeof(filter_t)); filter->str = strdup(str); filter->hdr = hdr; filter->max_unpack |= BCF_UN_STR; filter->exit_on_error = exit_on_error; int nops = 0, mops = 0; // operators stack int nout = 0, mout = 0; // filter tokens, RPN token_t *out = NULL; token_t *ops = NULL; char *tmp = filter->str; perl_init(filter, &tmp); int last_op = -1; while ( *tmp ) { int len, ret; ret = filters_next_token(&tmp, &len); if ( ret==-1 ) error("Missing quotes in: %s\n", str); // fprintf(bcftools_stderr,"token=[%c] .. [%s] %d\n", TOKEN_STRING[ret], tmp, len); // int i; for (i=0; i0 && ops[nops-1].tok_type!=TOK_LFT ) { nout++; hts_expand0(token_t, nout, mout, out); out[nout-1] = ops[nops-1]; memset(&ops[nops-1],0,sizeof(token_t)); nops--; } if ( nops<=0 ) error("Could not parse: %s\n", str); memset(&ops[nops-1],0,sizeof(token_t)); nops--; } else if ( ret==TOK_EXT ) // external value { nout++; hts_expand0(token_t, nout, mout, out); filters_init1_ext(filter, tmp, len, &out[nout-1]); tmp += len; } else if ( ret!=TOK_VAL ) // one of the operators { // detect unary minus: replace -value with -1*(value) if ( ret==TOK_SUB && last_op!=TOK_VAL && last_op!=TOK_RGT ) { nout++; hts_expand0(token_t, nout, mout, out); token_t *tok = &out[nout-1]; tok->tok_type = TOK_VAL; tok->hdr_id = -1; tok->pass_site = -1; tok->threshold = -1.0; tok->is_constant = 1; ret = TOK_MULT; } else if ( ret == -TOK_FUNC ) { // this is different from TOK_PERLSUB,TOK_BINOM in that the expression inside the // brackets gets evaluated as normal expression nops++; hts_expand0(token_t, nops, mops, ops); token_t *tok = &ops[nops-1]; tok->tok_type = -ret; tok->hdr_id = -1; tok->pass_site = -1; tok->threshold = -1.0; if ( !strncasecmp(tmp-len,"N_PASS",6) ) { filter->max_unpack |= BCF_UN_FMT; tok->func = func_npass; tok->tag = strdup("N_PASS"); } else if ( !strncasecmp(tmp-len,"F_PASS",6) ) { filter->max_unpack |= BCF_UN_FMT; tok->func = func_npass; tok->tag = strdup("F_PASS"); } else error("The function \"%s\" is not supported\n", tmp-len); continue; } else if ( ret < 0 ) // variable number of arguments: TOK_PERLSUB,TOK_BINOM { ret = -ret; tmp += len; char *beg = tmp; kstring_t rmme = {0,0,0}; int i, margs, nargs = 0; if ( ret == TOK_PERLSUB ) { while ( *beg && ((isalnum(*beg) && !ispunct(*beg)) || *beg=='_') ) beg++; if ( *beg!='(' ) error("Could not parse the expression: %s\n", str); // the subroutine name kputc('"', &rmme); kputsn(tmp, beg-tmp, &rmme); kputc('"', &rmme); nout++; hts_expand0(token_t, nout, mout, out); filters_init1(filter, rmme.s, rmme.l, &out[nout-1]); nargs++; } char *end = beg; while ( *end && *end!=')' ) end++; if ( !*end ) error("Could not parse the expression: %s\n", str); // subroutine arguments rmme.l = 0; kputsn(beg+1, end-beg-1, &rmme); char **rmme_list = hts_readlist(rmme.s, 0, &margs); for (i=0; itok_type = ret; tok->nargs = nargs; tok->hdr_id = -1; tok->pass_site = -1; tok->threshold = -1.0; tmp = end + 1; continue; } else { while ( nops>0 && op_prec[ret] < op_prec[ops[nops-1].tok_type] ) { nout++; hts_expand0(token_t, nout, mout, out); out[nout-1] = ops[nops-1]; memset(&ops[nops-1],0,sizeof(token_t)); nops--; } } nops++; hts_expand0(token_t, nops, mops, ops); ops[nops-1].tok_type = ret; } else if ( !len ) // all tokes read or an error { if ( *tmp && !isspace(*tmp) ) error("Could not parse the expression: [%s]\n", str); break; // all tokens read } else // TOK_VAL: annotation name or value { nout++; hts_expand0(token_t, nout, mout, out); if ( tmp[len-1]==',' ) filters_init1(filter, tmp, len-1, &out[nout-1]); else filters_init1(filter, tmp, len, &out[nout-1]); tmp += len; } last_op = ret; } while ( nops>0 ) { if ( ops[nops-1].tok_type==TOK_LFT || ops[nops-1].tok_type==TOK_RGT ) error("Could not parse the expression: [%s]\n", filter->str); nout++; hts_expand0(token_t, nout, mout, out); out[nout-1] = ops[nops-1]; memset(&ops[nops-1],0,sizeof(token_t)); nops--; } if ( filter->status != FILTER_OK ) { if ( mops ) free(ops); filter->filters = out; filter->nfilters = nout; return filter; } // Determine types of external variables from the context determine_ext_types(filter,nout,out); // In the special cases of TYPE and FILTER the BCF header IDs are yet unknown. Walk through the // list of operators and convert the strings (e.g. "PASS") to BCF ids. The string value token must be // just before or after the FILTER token and they must be followed with a comparison operator. // At this point we also initialize regex expressions which, in RPN, must precede the LIKE/NLIKE operator. // Additionally, treat "." as missing value rather than a string in numeric equalities; that // @file is only used with ID; etc. // This code is fragile: improve me. static int comma_separator_warned = 0; int i; for (i=0; istr); if ( out[i].hash ) { int j = out[i+1].tok_type==TOK_VAL ? i+1 : i-1; if ( out[j].comparator!=filters_cmp_id ) { if ( out[j].comparator ) error("Error: could not parse the expression with \"@file_name\" syntax (possible todo)\n"); out[j].comparator = filters_cmp_string_hash; } } if ( out[i].tok_type==TOK_OR || out[i].tok_type==TOK_OR_VEC ) out[i].func = vector_logic_or; if ( out[i].tok_type==TOK_AND || out[i].tok_type==TOK_AND_VEC ) out[i].func = vector_logic_and; if ( out[i].tok_type==TOK_EQ || out[i].tok_type==TOK_NE ) { // Look for j="." and k numeric type int j = i-1, k = i-2; if ( !out[j].is_str ) { k = i-1, j = i-2; } if ( out[j].is_str && out[j].key && !strcmp(".",out[j].key) ) { int set_missing = 0; if ( out[k].hdr_id>0 ) { int type = bcf_hdr_id2type(filter->hdr,out[k].hl_type,out[k].hdr_id); if ( type==BCF_HT_INT ) set_missing = 1; else if ( type==BCF_HT_REAL ) set_missing = 1; } else if ( !strcmp("QUAL",out[k].tag) ) set_missing = 1; if ( set_missing ) { out[j].is_str = 0; out[j].is_missing = 1; bcf_double_set_missing(out[j].values[0]); } } } if ( out[i].tok_type==TOK_LIKE || out[i].tok_type==TOK_NLIKE ) { int j = i-1; if ( !out[j].key ) error("Could not parse the expression, wrong value for regex operator: %s\n", filter->str); out[j].regex = (regex_t *) malloc(sizeof(regex_t)); int cflags = REG_NOSUB; int len = strlen(out[j].key); if ( len>2 && out[j].key[len-1]=='i' && out[j].key[len-2]=='/' && out[j].key[len-3]!='\\' ) { out[j].key[len-2] = 0; cflags |= REG_ICASE; } if ( regcomp(out[j].regex, out[j].key, cflags) ) error("Could not compile the regex expression \"%s\": %s\n", out[j].key,filter->str); } if ( out[i].is_str && out[i].tok_type==TOK_VAL && out[i].key && strchr(out[i].key,',') ) { int print_note = 0; if ( out[i+1].tok_type==TOK_EQ || (out[i+1].is_str && out[i+2].tok_type==TOK_EQ) ) print_note = 1; else if ( out[i+1].tok_type==TOK_NE || (out[i+1].is_str && out[i+2].tok_type==TOK_NE) ) print_note = 1; if ( print_note && !comma_separator_warned ) { comma_separator_warned = 1; fprintf(bcftools_stderr, "Warning: comma is interpreted as a separator and OR logic is used in string comparisons.\n" " (Search the manual for \"Comma in strings\" to learn more.)\n"); } } if ( out[i].tok_type!=TOK_VAL ) continue; if ( !out[i].tag ) continue; if ( out[i].setter==filters_set_type ) { if ( i+1==nout || !out[i+1].key ) error("Could not parse the expression: %s\n", filter->str); int itok, ival; if ( out[i+1].tok_type==TOK_EQ || out[i+1].tok_type==TOK_NE ) ival = i - 1, itok = i + 1; else if ( out[i+1].tok_type==TOK_LIKE || out[i+1].tok_type==TOK_NLIKE ) ival = i - 1, itok = i + 1; else if ( out[i+2].tok_type==TOK_EQ || out[i+2].tok_type==TOK_NE ) itok = i + 2, ival = i + 1; else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = i + 2, ival = i + 1; else error("[%s:%d %s] Could not parse the expression: %s\n", __FILE__,__LINE__,__FUNCTION__, filter->str); if ( !strcasecmp(out[ival].key,"snp") || !strcasecmp(out[ival].key,"snps") ) { out[ival].threshold = VCF_SNP<<1; out[ival].is_str = 0; } else if ( !strcasecmp(out[ival].key,"indel") || !strcasecmp(out[ival].key,"indels") ) { out[ival].threshold = VCF_INDEL<<1; out[ival].is_str = 0; } else if ( !strcasecmp(out[ival].key,"mnp") || !strcasecmp(out[ival].key,"mnps") ) { out[ival].threshold = VCF_MNP<<1; out[ival].is_str = 0; } else if ( !strcasecmp(out[ival].key,"other") ) { out[ival].threshold = VCF_OTHER<<1; out[ival].is_str = 0; } else if ( !strcasecmp(out[ival].key,"bnd") ) { out[ival].threshold = VCF_BND<<1; out[ival].is_str = 0; } else if ( !strcasecmp(out[ival].key,"overlap") ) { out[ival].threshold = VCF_OVERLAP<<1; out[ival].is_str = 0; } else if ( !strcasecmp(out[ival].key,"ref") ) { out[ival].threshold = 1; out[ival].is_str = 0; } else error("The type \"%s\" not recognised: %s\n", out[ival].key, filter->str); out[ival].is_constant = 1; if ( out[itok].tok_type==TOK_LIKE || out[itok].tok_type==TOK_NLIKE ) out[itok].comparator = filters_cmp_bit_and; out[ival].tag = out[ival].key; out[ival].key = NULL; i = itok; continue; } if ( !strcmp(out[i].tag,"GT") ) { if ( i+1==nout ) error("Could not parse the expression: %s\n", filter->str); int ival; if ( out[i+1].tok_type==TOK_EQ || out[i+1].tok_type==TOK_NE ) ival = i - 1; else if ( out[i+1].tok_type==TOK_LIKE || out[i+1].tok_type==TOK_NLIKE ) ival = i - 1; else if ( out[i+2].tok_type==TOK_EQ || out[i+2].tok_type==TOK_NE ) ival = i + 1; else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) ival = i + 1; else error("[%s:%d %s] Could not parse the expression: %s\n", __FILE__,__LINE__,__FUNCTION__, filter->str); if ( !out[ival].key ) error("Comparison between samples is not supported, sorry!\n"); // assign correct setters and unify expressions, eg ar->ra, HOM->hom, etc if ( !strcasecmp(out[ival].key,"hom") ) { out[i].setter = filters_set_genotype3; str_to_lower(out[ival].key); } else if ( !strcasecmp(out[ival].key,"het") ) { out[i].setter = filters_set_genotype3; str_to_lower(out[ival].key); } else if ( !strcasecmp(out[ival].key,"hap") ) { out[i].setter = filters_set_genotype3; str_to_lower(out[ival].key); } else if ( !strcasecmp(out[ival].key,"mis") ) { out[i].setter = filters_set_genotype4; str_to_lower(out[ival].key); } else if ( !strcasecmp(out[ival].key,"ref") ) { out[i].setter = filters_set_genotype4; str_to_lower(out[ival].key); } else if ( !strcasecmp(out[ival].key,"alt") ) { out[i].setter = filters_set_genotype4; str_to_lower(out[ival].key); } else if ( !strcasecmp(out[ival].key,"rr") ) { out[i].setter = filters_set_genotype2; str_to_lower(out[ival].key); } else if ( !strcasecmp(out[ival].key,"ra") || !strcasecmp(out[ival].key,"ar") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='r'; out[ival].key[1]='a'; } // ra else if ( !strcmp(out[ival].key,"aA") || !strcmp(out[ival].key,"Aa") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='a'; out[ival].key[1]='A'; } // aA else if ( !strcasecmp(out[ival].key,"aa") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='a'; out[ival].key[1]='a'; } // aa else if ( !strcasecmp(out[ival].key,"a") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='a'; out[ival].key[1]=0; } // a else if ( !strcasecmp(out[ival].key,"r") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='r'; out[ival].key[1]=0; } // r continue; } if ( out[i].hl_type==BCF_HL_FLT ) { if ( i+1==nout ) error("Could not parse the expression: %s\n", filter->str); int itok = i, ival; if ( out[i+1].tok_type==TOK_EQ || out[i+1].tok_type==TOK_NE ) ival = i - 1; else if ( out[i+1].tok_type==TOK_LIKE ) out[i+1].tok_type = TOK_IN, ival = i - 1; else if ( out[i+1].tok_type==TOK_NLIKE ) out[i+1].tok_type = TOK_NOT_IN, ival = i - 1; else if ( out[i+2].tok_type==TOK_EQ || out[i+2].tok_type==TOK_NE ) ival = ++i; else if ( out[i+2].tok_type==TOK_LIKE ) out[i+2].tok_type = TOK_IN, ival = ++i; else if ( out[i+2].tok_type==TOK_NLIKE ) out[i+2].tok_type = TOK_NOT_IN, ival = ++i; else error("[%s:%d %s] Could not parse the expression: %s\n", __FILE__,__LINE__,__FUNCTION__, filter->str); if ( out[ival].tok_type!=TOK_VAL || !out[ival].key ) error("[%s:%d %s] Could not parse the expression, an unquoted string value perhaps? %s\n", __FILE__,__LINE__,__FUNCTION__, filter->str); token_t *tok = &out[ival]; char *bp = tok->key; tok->nvalues = 0; int has_missing = 0; while ( *bp ) { char tmp, *ep = bp; while ( *ep && *ep!=';' ) ep++; tmp = *ep; *ep = 0; if ( !strcmp(".",bp) ) has_missing = 1; else { tok->nvalues++; hts_expand(double,tok->nvalues,tok->mvalues,tok->values); int id = bcf_hdr_id2int(filter->hdr, BCF_DT_ID, bp); if ( !bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_FLT,id) ) error("The filter \"%s\" not present in the VCF header\n", bp); tok->values[tok->nvalues-1] = id; } *ep = tmp; if ( !tmp ) break; bp = ep + 1; } if ( has_missing && tok->nvalues ) error("The FILTER expression cannot contain missing value AND filters: \"%s\" (%d)\n",tok->key,tok->nvalues); out[ival].tag = tok->key; tok->key = NULL; out[itok].hdr_id = tok->hdr_id; continue; } } filter->nsamples = filter->max_unpack&BCF_UN_FMT ? bcf_hdr_nsamples(filter->hdr) : 0; for (i=0; insamples ) { out[i].pass_samples = (uint8_t*)malloc(filter->nsamples); int j; for (j=0; jnsamples; j++) out[i].pass_samples[j] = 0; } } if (0) filter_debug_print(out, NULL, nout); if ( mops ) free(ops); filter->filters = out; filter->nfilters = nout; filter->flt_stack = (token_t **)malloc(sizeof(token_t*)*nout); return filter; } filter_t *filter_parse(bcf_hdr_t *hdr, const char *str) { return filter_init_(hdr, str, 0); } filter_t *filter_init(bcf_hdr_t *hdr, const char *str) { return filter_init_(hdr, str, 1); } void filter_destroy(filter_t *filter) { perl_destroy(filter); int i; for (i=0; infilters; i++) { if ( filter->filters[i].key ) free(filter->filters[i].key); free(filter->filters[i].str_value.s); free(filter->filters[i].tag); free(filter->filters[i].idxs); free(filter->filters[i].usmpl); free(filter->filters[i].values); free(filter->filters[i].pass_samples); if (filter->filters[i].hash) khash_str2int_destroy_free(filter->filters[i].hash); if (filter->filters[i].regex) { regfree(filter->filters[i].regex); free(filter->filters[i].regex); } } for (i=0; inundef_tag; i++) free(filter->undef_tag[i]); for (i=0; inused_tag; i++) free(filter->used_tag[i]); free(filter->ext); free(filter->undef_tag); free(filter->used_tag); free(filter->cached_GT.buf); free(filter->cached_GT.mask); free(filter->filters); free(filter->flt_stack); free(filter->str); free(filter->tmpi); free(filter->tmpf); free(filter->tmps.s); free(filter); } int filter_test_ext(filter_t *filter, bcf1_t *rec, const uint8_t **samples, const void **ext) { if ( !filter->n_ext ) return filter_test(filter,rec,samples); int i; for (i=0; infilters; i++) { token_t *tok = &filter->filters[i]; if ( !tok->iext ) continue; if ( !ext[tok->iext-1] ) { tok->is_missing = 1; tok->nvalues = 0; if ( filter->ext[tok->iext-1]==BCF_HT_STR ) tok->str_value.l = 0; continue; } tok->is_missing = 0; tok->nvalues = 1; if ( filter->ext[tok->iext-1]==BCF_HT_STR ) { tok->str_value.l = 0; kputs((const char*)ext[tok->iext-1],&tok->str_value); tok->nvalues = tok->str_value.l; } else if ( filter->ext[tok->iext-1]==BCF_HT_INT ) tok->values[0] = *((const int*)ext[tok->iext-1]); else if ( filter->ext[tok->iext-1]==BCF_HT_REAL ) tok->values[0] = *((const float*)ext[tok->iext-1]); } return filter_test(filter,rec,samples); } int filter_test(filter_t *filter, bcf1_t *line, const uint8_t **samples) { if ( filter->status != FILTER_OK ) error("Error: the caller did not check the filter status\n"); bcf_unpack(line, filter->max_unpack); int i, nstack = 0; for (i=0; infilters; i++) { filter->filters[i].pass_site = 0; if ( filter->filters[i].tok_type == TOK_VAL ) { if ( filter->filters[i].setter ) // variable, query the VCF line filter->filters[i].setter(filter, line, &filter->filters[i]); else if ( filter->filters[i].key ) // string constant { filter->filters[i].str_value.l = 0; kputs(filter->filters[i].key, &filter->filters[i].str_value); filter->filters[i].nvalues = filter->filters[i].str_value.l; } else if ( filter->filters[i].is_constant ) // numeric constant { filter->filters[i].values[0] = filter->filters[i].threshold; filter->filters[i].nvalues = 1; } filter->flt_stack[nstack++] = &filter->filters[i]; continue; } else if ( filter->filters[i].func ) { int nargs = filter->filters[i].func(filter, line, &filter->filters[i], filter->flt_stack, nstack); filter->flt_stack[nstack-nargs] = &filter->filters[i]; if ( --nargs > 0 ) nstack -= nargs; continue; } if ( nstack<2 ) error("Error occurred while processing the filter \"%s\" (1:%d)\n", filter->str,nstack); // too few values left on the stack int is_str = filter->flt_stack[nstack-1]->is_str + filter->flt_stack[nstack-2]->is_str; if ( filter->filters[i].tok_type == TOK_ADD ) { VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],+,(double)); filter->flt_stack[nstack-2] = &filter->filters[i]; nstack--; continue; } else if ( filter->filters[i].tok_type == TOK_SUB ) { VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],-,(double)); filter->flt_stack[nstack-2] = &filter->filters[i]; nstack--; continue; } else if ( filter->filters[i].tok_type == TOK_MULT ) { VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],*,(double)); filter->flt_stack[nstack-2] = &filter->filters[i]; nstack--; continue; } else if ( filter->filters[i].tok_type == TOK_DIV ) { VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],/,(double)); filter->flt_stack[nstack-2] = &filter->filters[i]; nstack--; continue; } else if ( filter->filters[i].tok_type == TOK_MODULO ) { VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],%,(int)); filter->flt_stack[nstack-2] = &filter->filters[i]; nstack--; continue; } // ideally, these comparators would become func, but this would require more work in init1() if ( filter->filters[i].comparator ) { filter->filters[i].comparator(filter->flt_stack[nstack-1],filter->flt_stack[nstack-2],&filter->filters[i],line); } else if ( filter->flt_stack[nstack-1]->comparator ) { filter->flt_stack[nstack-1]->comparator(filter->flt_stack[nstack-1],filter->flt_stack[nstack-2],&filter->filters[i],line); } else if ( filter->flt_stack[nstack-2]->comparator ) { filter->flt_stack[nstack-2]->comparator(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],line); } else if ( is_str==2 ) { cmp_vector_strings(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i]); } else { if ( is_str==1 ) error("Error: cannot use arithmetic operators to compare strings and numbers\n"); // Determine what to do with one [1] or both [2] sides missing. The first field [0] gives [1]|[2] int missing_logic[] = {0,0,0}; if ( filter->filters[i].tok_type == TOK_EQ ) { missing_logic[0] = missing_logic[2] = 1; } if ( filter->filters[i].tok_type == TOK_NE ) { missing_logic[0] = missing_logic[1] = 1; } if ( filter->filters[i].tok_type == TOK_EQ ) CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],==,missing_logic) else if ( filter->filters[i].tok_type == TOK_NE ) CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],!=,missing_logic) else if ( filter->filters[i].tok_type == TOK_LE ) CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],<=,missing_logic) else if ( filter->filters[i].tok_type == TOK_LT ) CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],<,missing_logic) else if ( filter->filters[i].tok_type == TOK_BT ) CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],>,missing_logic) else if ( filter->filters[i].tok_type == TOK_BE ) CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],>=,missing_logic) else error("todo: %s:%d .. type=%d\n", __FILE__,__LINE__,filter->filters[i].tok_type); } filter->flt_stack[nstack-2] = &filter->filters[i]; nstack--; } if ( nstack>1 ) error("Error occurred while processing the filter \"%s\" (2:%d)\n", filter->str,nstack); // too few values left on the stack if ( samples ) { *samples = filter->max_unpack&BCF_UN_FMT ? filter->flt_stack[0]->pass_samples : NULL; if ( *samples && !filter->flt_stack[0]->nsamples ) { for (i=0; insamples; i++) filter->flt_stack[0]->pass_samples[i] = filter->flt_stack[0]->pass_site; } } return filter->flt_stack[0]->pass_site; } int filter_max_unpack(filter_t *flt) { return flt->max_unpack; } const int *filter_ext_types(filter_t *filter, int *n_ext) { *n_ext = filter->n_ext; return filter->ext; } const double *filter_get_doubles(filter_t *filter, int *nval, int *nval1) { token_t *tok = filter->flt_stack[0]; if ( tok->nvalues ) { *nval = tok->nvalues; *nval1 = tok->nval1; } else { if ( !tok->values ) error("fixme in filter_get_doubles(): %s\n", filter->str); *nval = 1; *nval1 = 1; tok->values[0] = filter->flt_stack[0]->pass_site; } return tok->values; } void filter_set_samples(filter_t *filter, const uint8_t *samples) { int i,j; for (i=0; infilters; i++) { if ( !filter->filters[i].nsamples ) continue; for (j=0; jfilters[i].nsamples; j++) filter->filters[i].usmpl[j] = samples[j]; } } int filter_status(filter_t *filter) { return filter->status; } pysam-0.23.0/bcftools/filter.h000066400000000000000000000101711475062545500162130ustar00rootroot00000000000000/* filter.h -- filter expressions. Copyright (C) 2013-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef __FILTER_H__ #define __FILTER_H__ #include typedef struct _filter_t filter_t; /** * @hdr: BCF header file * @str: see the bcftools filter command help for description. * See also the extended usage described in filter_test_ext(), * intended for programmatic access * Same as filter_parse() but exits on errors */ filter_t *filter_init(bcf_hdr_t *hdr, const char *str); void filter_destroy(filter_t *filter); /** * filter_test() - test whether the BCF record passes the test * @samples: if not NULL, a pointer to an array with samples statuses is * stored in the location referenced by @samples. The pointer * will be set to NULL if the FORMAT fields were not queried. * Returns 1 if the expression is true and 0 if false. */ int filter_test(filter_t *filter, bcf1_t *rec, const uint8_t **samples); /** * filter_test_ext() - same as filter_test(), but sets some of the terms * on the fly. An expression initialized with, say, * "STR_TAG={} | INT_TAG={} | FLT_TAG={}" takes three * additional pointer arguments which are expected to point to memory * area occupied by the appropriate type, see also filter_ext_types(). * The type determination is not fool-proof, in such case the type can * be given explicitly as eg "TAG={str}". * @ext: array of size 'n_ext' occupied with pointers to the data types * inferred from the expression given at the time of initialization. * The pointers set to NULL will be treated as if missing value "." * was given. * @n_ext: the size of 'ext' array */ int filter_test_ext(filter_t *filter, bcf1_t *rec, const uint8_t **samples, const void **ext); /** * filter_set_samples() - restrict filtering expression to samples. * Call after filter_init(). * @samples: use samples set to 1, ignore samples set 0 */ void filter_set_samples(filter_t *filter, const uint8_t *samples); /** * filter_get_doubles() - return a pointer to values from the last filter_test() evaluation */ const double *filter_get_doubles(filter_t *filter, int *nval, int *nval1); int filter_max_unpack(filter_t *filter); /** * filter_ext_types() - returns the number and BCF_HT_* types of external values * found in the filtering expression */ const int *filter_ext_types(filter_t *filter, int *n_ext); /** * Same as filter_init() but may not exit on some type of errors. The caller * must check if the returned value is not NULL and if the consequent call * of filter_status() returns FILTER_OK before the filter_pass() can be called. */ filter_t *filter_parse(bcf_hdr_t *hdr, const char *str); #define FILTER_OK 0 #define FILTER_ERR_UNKN_TAGS 1 #define FILTER_ERR_OTHER 2 /** * Check if filter_parse() was successful */ int filter_status(filter_t *filter); const char **filter_list_undef_tags(filter_t *filter, int *nundef); const char **filter_list_used_tags(filter_t *filter, int *nused); #endif pysam-0.23.0/bcftools/gff.c000066400000000000000000001257701475062545500154770ustar00rootroot00000000000000/* The MIT License Copyright (c) 2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "regidx.h" #include "gff.h" /* Helper structures, only for initialization ftr_t temporary list of all exons, CDS, UTRs */ KHASH_MAP_INIT_INT(int2tscript, gf_tscript_t*) KHASH_MAP_INIT_INT(int2gene, gf_gene_t*) typedef struct { int type; // GF_CDS, GF_EXON, GF_5UTR, GF_3UTR uint32_t beg; uint32_t end; uint32_t trid; uint32_t strand:2; // STRAND_{REV,FWD,UNK} uint32_t phase:2; // 0, 1, 2, or 3 for unknown uint32_t iseq:28; } ftr_t; /* Mapping from GFF ID string (such as ENST00000450305 or Zm00001d027230_P001) to integer id. To keep the memory requirements low, the original version relied on IDs in the form of a string prefix and a numerical id. However, it turns out that this assumption is not valid for some ensembl GFFs, see for example Zea_mays.AGPv4.36.gff3.gz */ typedef struct { void *str2id; // khash_str2int int nstr, mstr; char **str; // numeric id to string } id_tbl_t; typedef struct { // all exons, CDS, UTRs ftr_t *ftr; int nftr, mftr; // mapping from gene id to gf_gene_t kh_int2gene_t *gid2gene; // mapping from transcript id to tscript, for quick CDS anchoring kh_int2tscript_t *id2tr; // sequences void *seq2int; // str2int hash char **seq; int nseq, mseq; // ignored biotypes void *ignored_biotypes; id_tbl_t gene_ids; // temporary table for mapping between gene id (eg. Zm00001d027245) and a numeric idx // pointers to the current partially processed line char *id, *id_end, *parent, *parent_end, *biotype, *biotype_end, *chr, *chr_end, *name, *name_end, *type, *type_end; } aux_t; struct gff_t_ { const char *fname, *dump_fname; // the main regidx lookups, from chr:beg-end to overlapping features and // index iterator regidx_t *idx_cds, *idx_utr, *idx_exon, *idx_tscript; // temporary structures, deleted after initializtion aux_t init; // mapping between transcript id (eg. Zm00001d027245_T001) and a numeric idx id_tbl_t tscript_ids; int strip_chr_names, verbosity; int force; // force run under various conditions. Currently only to skip out-of-phase transcripts struct { int unknown_chr,unknown_tscript_biotype,unknown_strand,unknown_phase,duplicate_id; int unknown_cds_phase,incomplete_cds,wrong_phase,overlapping_cds; } warned; }; static const char *gf_strings_noncoding[] = { "MT_rRNA", "MT_tRNA", "lincRNA", "miRNA", "misc_RNA", "rRNA", "snRNA", "snoRNA", "processed_transcript", "antisense", "macro_lncRNA", "ribozyme", "sRNA", "scRNA", "scaRNA", "sense_intronic", "sense_overlapping", "pseudogene", "processed_pseudogene", "artifact", "IG_pseudogene", "IG_C_pseudogene", "IG_J_pseudogene", "IG_V_pseudogene", "TR_V_pseudogene", "TR_J_pseudogene", "MT_tRNA_pseudogene", "misc_RNA_pseudogene", "miRNA_pseudogene", "ribozyme", "retained_intron", "retrotransposed", "Trna_pseudogene", "transcribed_processed_pseudogene", "transcribed_unprocessed_pseudogene", "transcribed_unitary_pseudogene", "translated_unprocessed_pseudogene", "translated_processed_pseudogene", "known_ncRNA", "unitary_pseudogene", "unprocessed_pseudogene", "LRG_gene", "3_prime_overlapping_ncRNA", "disrupted_domain", "vaultRNA", "bidirectional_promoter_lncRNA", "ambiguous_orf", "lncRNA" }; static const char *gf_strings_coding[] = { "protein_coding", "polymorphic_pseudogene", "IG_C", "IG_D", "IG_J", "IG_LV", "IG_V", "TR_C", "TR_D", "TR_J", "TR_V", "NMD", "non_stop_decay"}; static const char *gf_strings_special[] = { "CDS", "exon", "3_prime_UTR", "5_prime_UTR" }; int gff_set(gff_t *gff, gff_opt_t key, ...) { va_list args; switch (key) { case dump_fname: va_start(args, key); gff->dump_fname = va_arg(args,char*); va_end(args); return 0; case force_out_of_phase: va_start(args, key); gff->force = va_arg(args,int); va_end(args); return 0; case strip_chr_names: va_start(args, key); gff->strip_chr_names = va_arg(args,int); va_end(args); return 0; case verbosity: va_start(args, key); gff->verbosity = va_arg(args,int); va_end(args); return 0; default: error("The key %d is not supported with gff_set\n",key); } return 0; } void *gff_get(gff_t *gff, gff_opt_t key) { switch (key) { case idx_cds: return gff->idx_cds; case idx_utr: return gff->idx_utr; case idx_exon: return gff->idx_exon; case idx_tscript: return gff->idx_tscript; default: error("The key %d is not supported with gff_get\n",key); } return NULL; } const char *gff_id2string(gff_t *gff, id_type_t type, int id) // currently only transcript ids { return gff->tscript_ids.str[id]; } const char *gf_type2gff_string(int type) { if ( !GF_is_coding(type) ) { if ( type < (1<init; char tmp = chr_end[1]; chr_end[1] = 0; int iseq; if ( khash_str2int_get(aux->seq2int, chr_beg, &iseq)!=0 ) { char *new_chr = strdup(chr_beg); hts_expand(char*, aux->nseq+1, aux->mseq, aux->seq); aux->seq[aux->nseq] = new_chr; iseq = khash_str2int_inc(aux->seq2int, aux->seq[aux->nseq]); aux->nseq++; assert( aux->nseq < 1<<29 ); // see gf_gene_t.iseq and ftr_t.iseq } chr_end[1] = tmp; return iseq; } static inline char *gff_skip(const char *line, char *ss) { while ( *ss && *ss!='\t' ) ss++; if ( !*ss ) error("[%s:%d %s] Could not parse the line: %s\n",__FILE__,__LINE__,__FUNCTION__,line); return ss+1; } static inline void gff_parse_chr(gff_t *gff, const char *line, char **chr_beg, char **chr_end) { char *se = (char*) line; while ( *se && *se!='\t' ) se++; if ( !*se ) error("[%s:%d %s] Could not parse the line: %s\n",__FILE__,__LINE__,__FUNCTION__,line); if ( gff->strip_chr_names && !strncasecmp("chr",line,3) ) line += 3; *chr_beg = (char*) line; *chr_end = se-1; } static inline char *gff_parse_beg_end(const char *line, char *ss, uint32_t *beg, uint32_t *end) { char *se = ss; *beg = strtol(ss, &se, 10) - 1; if ( ss==se ) error("[%s:%d %s] Could not parse the line:\n\t%s\n\t%s\n",__FILE__,__LINE__,__FUNCTION__,line,ss); ss = se+1; *end = strtol(ss, &se, 10) - 1; if ( ss==se ) error("[%s:%d %s] Could not parse the line: %s\n",__FILE__,__LINE__,__FUNCTION__,line); return se+1; } static void gff_id_init(id_tbl_t *tbl) { memset(tbl, 0, sizeof(*tbl)); tbl->str2id = khash_str2int_init(); } static void gff_id_destroy(id_tbl_t *tbl) { khash_str2int_destroy_free(tbl->str2id); free(tbl->str); } static inline int gff_id_register(id_tbl_t *tbl, char *beg, char *end, uint32_t *id_ptr) { char tmp = end[1]; end[1] = 0; int id; if ( khash_str2int_get(tbl->str2id, beg, &id) < 0 ) { id = tbl->nstr++; hts_expand(char*, tbl->nstr, tbl->mstr, tbl->str); tbl->str[id] = strdup(beg); khash_str2int_set(tbl->str2id, tbl->str[id], id); } end[1] = tmp; *id_ptr = id; return 0; } static inline int gff_parse_biotype(char *line) { if ( !line ) return -1; switch (*line) { case 'p': if ( !strncmp(line,"protein_coding",14) ) return GF_PROTEIN_CODING; else if ( !strncmp(line,"pseudogene",10) ) return GF_PSEUDOGENE; else if ( !strncmp(line,"processed_transcript",20) ) return GF_PROCESSED_TRANSCRIPT; else if ( !strncmp(line,"processed_pseudogene",20) ) return GF_PROCESSED_PSEUDOGENE; else if ( !strncmp(line,"polymorphic_pseudogene",22) ) return GF_POLYMORPHIC_PSEUDOGENE; break; case 'a': if ( !strncmp(line,"artifact",8) ) return GF_ARTIFACT; else if ( !strncmp(line,"antisense",9) ) return GF_ANTISENSE; else if ( !strncmp(line,"ambiguous_orf",13) ) return GF_AMBIGUOUS_ORF; break; case 'I': if ( !strncmp(line,"IG_pseudogene",13) ) return GF_IG_PSEUDOGENE; else if ( !strncmp(line,"IG_C_pseudogene",15) ) return GF_IG_C_PSEUDOGENE; else if ( !strncmp(line,"IG_J_pseudogene",15) ) return GF_IG_J_PSEUDOGENE; else if ( !strncmp(line,"IG_V_pseudogene",15) ) return GF_IG_V_PSEUDOGENE; else if ( !strncmp(line,"IG_C",4) ) return GF_IG_C; else if ( !strncmp(line,"IG_D",4) ) return GF_IG_D; else if ( !strncmp(line,"IG_J",4) ) return GF_IG_J; else if ( !strncmp(line,"IG_V",4) ) return GF_IG_V; else if ( !strncmp(line,"IG_LV",5) ) return GF_IG_LV; break; case 'T': if ( !strncmp(line,"TR_V_pseudogene",15) ) return GF_TR_V_PSEUDOGENE; else if ( !strncmp(line,"TR_J_pseudogene",15) ) return GF_TR_J_PSEUDOGENE; else if ( !strncmp(line,"TR_C",4) ) return GF_TR_C; else if ( !strncmp(line,"TR_D",4) ) return GF_TR_D; else if ( !strncmp(line,"TR_J",4) ) return GF_TR_J; else if ( !strncmp(line,"TR_V",4) ) return GF_TR_V; break; case 'M': if ( !strncmp(line,"Mt_tRNA_pseudogene",18) ) return GF_MT_tRNA_PSEUDOGENE; else if ( !strncasecmp(line,"Mt_tRNA",7) ) return GF_MT_tRNA; else if ( !strncasecmp(line,"Mt_rRNA",7) ) return GF_MT_tRNA; else if ( !strncasecmp(line,"MRNA",4) ) return GF_PROTEIN_CODING; break; case 'l': if ( !strncmp(line,"lincRNA",7) ) return GF_lincRNA; if ( !strncmp(line,"lncRNA",7) ) return GF_lncRNA; break; case 'm': if ( !strncmp(line,"macro_lncRNA",12) ) return GF_macro_lncRNA; else if ( !strncmp(line,"misc_RNA_pseudogene",19) ) return GF_misc_RNA_PSEUDOGENE; else if ( !strncmp(line,"miRNA_pseudogene",16) ) return GF_miRNA_PSEUDOGENE; else if ( !strncmp(line,"miRNA",5) ) return GF_miRNA; else if ( !strncmp(line,"misc_RNA",8) ) return GF_MISC_RNA; else if ( !strncasecmp(line,"mRNA",4) ) return GF_PROTEIN_CODING; break; case 'r': if ( !strncmp(line,"rRNA",4) ) return GF_rRNA; else if ( !strncmp(line,"ribozyme",8) ) return GF_RIBOZYME; else if ( !strncmp(line,"retained_intron",15) ) return GF_RETAINED_INTRON; else if ( !strncmp(line,"retrotransposed",15) ) return GF_RETROTRANSPOSED; break; case 's': if ( !strncmp(line,"snRNA",5) ) return GF_snRNA; else if ( !strncmp(line,"sRNA",4) ) return GF_sRNA; else if ( !strncmp(line,"scRNA",5) ) return GF_scRNA; else if ( !strncmp(line,"scaRNA",6) ) return GF_scaRNA; else if ( !strncmp(line,"snoRNA",6) ) return GF_snoRNA; else if ( !strncmp(line,"sense_intronic",14) ) return GF_SENSE_INTRONIC; else if ( !strncmp(line,"sense_overlapping",17) ) return GF_SENSE_OVERLAPPING; break; case 't': if ( !strncmp(line,"tRNA_pseudogene",15) ) return GF_tRNA_PSEUDOGENE; else if ( !strncmp(line,"transcribed_processed_pseudogene",32) ) return GF_TRANSCRIBED_PROCESSED_PSEUDOGENE; else if ( !strncmp(line,"transcribed_unprocessed_pseudogene",34) ) return GF_TRANSCRIBED_UNPROCESSED_PSEUDOGENE; else if ( !strncmp(line,"transcribed_unitary_pseudogene",30) ) return GF_TRANSCRIBED_UNITARY_PSEUDOGENE; else if ( !strncmp(line,"translated_unprocessed_pseudogene",33) ) return GF_TRANSLATED_UNPROCESSED_PSEUDOGENE; else if ( !strncmp(line,"translated_processed_pseudogene",31) ) return GF_TRANSLATED_PROCESSED_PSEUDOGENE; break; case 'n': if ( !strncmp(line,"nonsense_mediated_decay",23) ) return GF_NMD; else if ( !strncmp(line,"non_stop_decay",14) ) return GF_NON_STOP_DECAY; break; case 'N': if ( !strncmp(line,"NMD",3) ) return GF_NMD; break; case 'k': if ( !strncmp(line,"known_ncrna",11) ) return GF_KNOWN_NCRNA; break; case 'u': if ( !strncmp(line,"unitary_pseudogene",18) ) return GF_UNITARY_PSEUDOGENE; else if ( !strncmp(line,"unprocessed_pseudogene",22) ) return GF_UNPROCESSED_PSEUDOGENE; break; case 'L': if ( !strncmp(line,"LRG_gene",8) ) return GF_LRG_GENE; break; case '3': if ( !strncasecmp(line,"3prime_overlapping_ncRNA",24) ) return GF_3PRIME_OVERLAPPING_ncRNA; else if ( !strncasecmp(line,"3_prime_overlapping_ncRNA",25) ) return GF_3PRIME_OVERLAPPING_ncRNA; break; case 'd': if ( !strncmp(line,"disrupted_domain",16) ) return GF_DISRUPTED_DOMAIN; break; case 'v': if ( !strncmp(line,"vaultRNA",8) ) return GF_vaultRNA; break; case 'b': if ( !strncmp(line,"bidirectional_promoter_lncRNA",29) ) return GF_BIDIRECTIONAL_PROMOTER_lncRNA; break; } return 0; } static inline int gff_ignored_biotype(gff_t *gff, char *ss, char *se) { if ( !ss ) return 0; char tmp = se[1]; se[1] = 0; char *key = ss; int n = 0; if ( khash_str2int_get(gff->init.ignored_biotypes, ss, &n)!=0 ) key = strdup(ss); khash_str2int_set(gff->init.ignored_biotypes, key, n+1); se[1] = tmp; return 1; } static gf_gene_t *gene_init(aux_t *aux, uint32_t gene_id) { khint_t k = kh_get(int2gene, aux->gid2gene, (int)gene_id); gf_gene_t *gene = (k == kh_end(aux->gid2gene)) ? NULL : kh_val(aux->gid2gene, k); if ( !gene ) { gene = (gf_gene_t*) calloc(1,sizeof(gf_gene_t)); int ret; k = kh_put(int2gene, aux->gid2gene, (int)gene_id, &ret); kh_val(aux->gid2gene,k) = gene; } return gene; } static void gff_parse_transcript(gff_t *gff, const char *line, ftr_t *ftr) { aux_t *aux = &gff->init; ftr->type = gff_parse_biotype(aux->biotype); if ( ftr->type <= 0 ) { char tmp = aux->type_end[1]; aux->type_end[1] = 0; ftr->type = gff_parse_biotype(aux->type); aux->type_end[1] = tmp; } if ( ftr->type <= 0 ) { if ( !gff_ignored_biotype(gff,aux->biotype,aux->biotype_end) ) { if ( gff->verbosity > 0 ) { if ( !gff->warned.unknown_tscript_biotype || gff->verbosity > 1 ) fprintf(stderr,"Warning: Ignoring transcript with unknown biotype .. %s\n", line); gff->warned.unknown_tscript_biotype++; } } return; } if ( !aux->id ) error("[%s:%d %s] Could not parse the line, neither \"ID=transcript:\" nor \"ID=\" substring is present: %s\n",__FILE__,__LINE__,__FUNCTION__,line); if ( !aux->parent ) error("[%s:%d %s] Could not parse the line, neither \"Parent=gene:\" nor \"Parent=\" substring is present: %s\n",__FILE__,__LINE__,__FUNCTION__,line); uint32_t trid,gene_id; gff_id_register(&gff->tscript_ids, aux->id, aux->id_end, &trid); gff_id_register(&aux->gene_ids, aux->parent, aux->parent_end, &gene_id); gf_tscript_t *tr = (gf_tscript_t*) calloc(1,sizeof(gf_tscript_t)); tr->id = trid; tr->strand = ftr->strand; tr->gene = gene_init(aux, gene_id); tr->type = ftr->type; tr->beg = ftr->beg; tr->end = ftr->end; khint_t k; int ret; k = kh_put(int2tscript, aux->id2tr, (int)trid, &ret); kh_val(aux->id2tr,k) = tr; } // register exon, CDS, UTR static void gff_parse_exon(gff_t *gff, const char *line, ftr_t *ftr) { aux_t *aux = &gff->init; if ( !aux->parent ) error("[%s:%d %s] Could not parse the line, neither \"Parent=transcript:\" nor \"Parent=\" substring found: %s\n",__FILE__,__LINE__,__FUNCTION__,line); // associate with transcript id gff_id_register(&gff->tscript_ids, aux->parent, aux->parent_end, &ftr->trid); if ( ftr->strand==STRAND_UNK && gff->verbosity > 0 ) { if ( !gff->warned.unknown_strand || gff->verbosity > 1 ) fprintf(stderr,"Warning: Ignoring GFF feature with unknown strand .. %s\n",line); gff->warned.unknown_strand++; } if ( ftr->phase==CDS_PHASE_UNKN && gff->verbosity > 0 ) { if ( !gff->warned.unknown_phase|| gff->verbosity > 1 ) fprintf(stderr,"Warning: Ignoring GFF feature with unknown phase .. %s\n",line); gff->warned.unknown_phase++; } ftr->iseq = feature_set_seq(gff, aux->chr,aux->chr_end); } static void gff_parse_gene(gff_t *gff, const char *line, ftr_t *ftr) { aux_t *aux = &gff->init; if ( !aux->id ) return; uint32_t gene_id; gff_id_register(&aux->gene_ids, aux->id, aux->id_end, &gene_id); gf_gene_t *gene = gene_init(aux, gene_id); if ( gene->name ) { if ( !gff->warned.duplicate_id || gff->verbosity > 1 ) fprintf(stderr,"Warning: The GFF contains features with duplicate id .. %s\n",line); gff->warned.duplicate_id++; return; } gene->iseq = feature_set_seq(gff, aux->chr,aux->chr_end); gene->beg = ftr->beg; gene->end = ftr->end; gene->strand = ftr->strand; gene->id = gene_id; if ( aux->name ) { gene->name = (char*) malloc(aux->name_end - aux->name + 2); memcpy(gene->name,aux->name,aux->name_end - aux->name + 1); gene->name[aux->name_end - aux->name + 1] = 0; } else gene->name = strdup(aux->gene_ids.str[gene_id]); // Name= field is not present, use the gene ID instead } // Returns 0 for exons,CDS,UTRs to indicate these need to be pruned later and regidx built on them, // or -1 to indicate the structure needs not be saved (either because of an error or because saved // as transcript or gene.) static int gff_parse_line(gff_t *gff, char *line, ftr_t *ftr) { // - skip empty lines and commented lines // - columns // 1. chr // 2. // 3. CDS, transcript, gene, ... // 4-5. beg,end // 6. // 7. strand // 8. phase // 9. Parent=transcript:ENST(\d+);ID=...;biotype=... etc char *ss = line; if ( !*ss ) return -1; // skip blank lines if ( *ss=='#' ) return -1; // skip comments aux_t *aux = &gff->init; gff_parse_chr(gff, line, &aux->chr, &aux->chr_end); ss = gff_skip(line, aux->chr_end + 2); // 3rd column: is this a CDS, transcript, gene, etc.. The parsing order by frequency in Homo_sapiens.GRCh37.87.gff3 int is_gene_line = 0; ftr->type = 0; aux->type = ss; if ( !strncmp("exon\t",ss,5) ) { ftr->type = GF_EXON; ss += 5; } else if ( !strncmp("CDS\t",ss,4) ) { ftr->type = GF_CDS; ss += 4; } else if ( !strncmp("three_prime_UTR\t",ss,16) ) { ftr->type = GF_UTR3; ss += 16; } else if ( !strncmp("five_prime_UTR\t",ss,15) ) { ftr->type = GF_UTR5; ss += 15; } else if ( !strncmp("biological_region\t",ss,18) ) { return -1; } // skip else if ( !strncmp("gene\t",ss,5) ) { is_gene_line = 1; ss += 5; } else ss = gff_skip(line, ss); aux->type_end = ss - 1; // 4-5th columns: beg,end ss = gff_parse_beg_end(line, ss, &ftr->beg,&ftr->end); // 6th column: skip ss = gff_skip(line, ss); // 7th column: strand ftr->strand = -1; if ( *ss == '+' ) ftr->strand = STRAND_FWD; else if ( *ss == '-' ) ftr->strand = STRAND_REV; else ftr->strand = STRAND_UNK; ss += 2; // 8th column: phase (codon offset) ftr->phase = CDS_PHASE_UNKN; if ( *ss == '0' ) ftr->phase = 0; else if ( *ss == '1' ) ftr->phase = 1; else if ( *ss == '2' ) ftr->phase = 2; else if ( *ss == '.' ) ftr->phase = CDS_PHASE_UNKN; // exons and even CDS in some GFFs do not have phase ss += 2; // 9th column: id, parent, name, biotype aux->name = NULL, aux->id = NULL, aux->parent = NULL, aux->biotype = NULL; while ( *ss ) { char *es = ss; while ( *es && *es!=';' ) es++; if ( !strncmp(ss,"ID=",3) ) { ss += 3; aux->id_end = es - 1; aux->id = ss; if ( !strncmp(ss,"gene:",5) ) { aux->id += 5; is_gene_line = 1; } else if ( !strncmp(ss,"transcript:",11) ) aux->id += 11; } else if ( !strncmp(ss,"Name=",5) ) { aux->name = ss + 5; aux->name_end = es - 1; } else if ( !strncmp(ss,"Parent=",7) ) { ss += 7; aux->parent_end = es - 1; aux->parent = ss; if ( !strncmp(ss,"gene:",5) ) aux->parent += 5; else if ( !strncmp(ss,"transcript:",11) ) aux->parent += 11; } else if ( !strncmp(ss,"biotype=",8) ) { aux->biotype = ss + 8; aux->biotype_end = es - 1; } else if ( !strncmp(ss,"gene_biotype=",13) ) { aux->biotype = ss + 13; aux->biotype_end = es - 1; } if ( !*es ) break; ss = es + 1; } if ( is_gene_line || !aux->parent ) { gff_parse_gene(gff, line, ftr); return -1; } if ( ftr->type ) { gff_parse_exon(gff, line, ftr); return 0; } gff_parse_transcript(gff, line, ftr); return -1; } static int cmp_cds_ptr(const void *a, const void *b) { // comparison function for qsort of transcripts's CDS if ( (*((gf_cds_t**)a))->beg < (*((gf_cds_t**)b))->beg ) return -1; if ( (*((gf_cds_t**)a))->beg > (*((gf_cds_t**)b))->beg ) return 1; return 0; } static inline void chr_beg_end(aux_t *aux, int iseq, char **chr_beg, char **chr_end) { *chr_beg = *chr_end = aux->seq[iseq]; while ( (*chr_end)[1] ) (*chr_end)++; } static gf_tscript_t *tscript_init(aux_t *aux, uint32_t trid) { khint_t k = kh_get(int2tscript, aux->id2tr, (int)trid); gf_tscript_t *tr = (k == kh_end(aux->id2tr)) ? NULL : kh_val(aux->id2tr, k); assert( tr ); return tr; } static void register_cds(gff_t *gff, ftr_t *ftr) { // Make the CDS searchable via idx_cds. Note we do not malloc tr->cds just yet. // ftr is the result of parsing a gff CDS line aux_t *aux = &gff->init; gf_tscript_t *tr = tscript_init(aux, ftr->trid); if ( tr->strand != ftr->strand ) error("Conflicting strand in transcript %"PRIu32" .. %d vs %d\n",ftr->trid,tr->strand,ftr->strand); gf_cds_t *cds = (gf_cds_t*) malloc(sizeof(gf_cds_t)); cds->tr = tr; cds->beg = ftr->beg; cds->len = ftr->end - ftr->beg + 1; cds->icds = 0; // to keep valgrind on mac happy cds->phase = ftr->phase; hts_expand(gf_cds_t*,tr->ncds+1,tr->mcds,tr->cds); tr->cds[tr->ncds++] = cds; } static void register_utr(gff_t *gff, ftr_t *ftr) { aux_t *aux = &gff->init; gf_utr_t *utr = (gf_utr_t*) malloc(sizeof(gf_utr_t)); utr->which = ftr->type==GF_UTR3 ? prime3 : prime5; utr->beg = ftr->beg; utr->end = ftr->end; utr->tr = tscript_init(aux, ftr->trid); char *chr_beg, *chr_end; chr_beg_end(&gff->init, utr->tr->gene->iseq, &chr_beg, &chr_end); regidx_push(gff->idx_utr, chr_beg,chr_end, utr->beg,utr->end, &utr); } static void register_exon(gff_t *gff, ftr_t *ftr) { aux_t *aux = &gff->init; gf_exon_t *exon = (gf_exon_t*) malloc(sizeof(gf_exon_t)); exon->beg = ftr->beg; exon->end = ftr->end; exon->tr = tscript_init(aux, ftr->trid); char *chr_beg, *chr_end; chr_beg_end(&gff->init, exon->tr->gene->iseq, &chr_beg, &chr_end); regidx_push(gff->idx_exon, chr_beg,chr_end, exon->beg - N_SPLICE_REGION_INTRON, exon->end + N_SPLICE_REGION_INTRON, &exon); } static void tscript_init_cds(gff_t *gff) { aux_t *aux = &gff->init; // Sort CDS in all transcripts, set offsets, check their phase, length, create index (idx_cds) khint_t k; for (k=0; kid2tr); k++) { if ( !kh_exist(aux->id2tr, k) ) continue; gf_tscript_t *tr = (gf_tscript_t*) kh_val(aux->id2tr, k); // position-to-tscript lookup char *chr_beg, *chr_end; chr_beg_end(aux, tr->gene->iseq, &chr_beg, &chr_end); regidx_push(gff->idx_tscript, chr_beg, chr_end, tr->beg, tr->end, &tr); if ( !tr->ncds ) continue; // transcript with no CDS // sort CDs qsort(tr->cds, tr->ncds, sizeof(gf_cds_t*), cmp_cds_ptr); // trim non-coding start int i, len = 0; if ( tr->strand==STRAND_FWD ) { if ( tr->cds[0]->phase != CDS_PHASE_UNKN ) { if ( tr->cds[0]->phase ) tr->trim |= TRIM_5PRIME; tr->cds[0]->beg += tr->cds[0]->phase; tr->cds[0]->len -= tr->cds[0]->phase; tr->cds[0]->phase = 0; } // sanity check phase; the phase number in gff tells us how many bases to skip in this // feature to reach the first base of the next codon int tscript_ok = 1; for (i=0; incds; i++) { if ( tr->cds[i]->phase == CDS_PHASE_UNKN ) { if ( gff->verbosity > 0 ) { if ( !gff->warned.unknown_cds_phase || gff->verbosity > 1 ) fprintf(stderr,"Warning: CDS with unknown phase, could not verify reading frame in transcript %s\n",gff->tscript_ids.str[tr->id]); gff->warned.unknown_cds_phase++; } len += tr->cds[i]->len; continue; } int phase = tr->cds[i]->phase ? 3 - tr->cds[i]->phase : 0; if ( phase!=len%3 ) { if ( !gff->force ) error("Error: GFF3 assumption failed for transcript %s, CDS=%"PRIu32": phase!=len%%3 (phase=%d, len=%d). Use the --force option to proceed anyway (at your own risk).\n", gff->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len); if ( gff->verbosity > 0 ) { if ( !gff->warned.wrong_phase || gff->verbosity > 1 ) fprintf(stderr,"Warning: The GFF has inconsistent phase column in transcript %s, skipping. CDS pos=%"PRIu32": phase!=len%%3 (phase=%d, len=%d)\n", gff->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len); gff->warned.wrong_phase++; } tscript_ok = 0; break; } len += tr->cds[i]->len; } if ( !tscript_ok ) continue; // skip this transcript } else if ( tr->strand==STRAND_REV ) { if ( tr->cds[tr->ncds-1]->phase != CDS_PHASE_UNKN ) { // Check that the phase is not bigger than CDS length. Curiously, this can really happen, // see Mus_musculus.GRCm38.85.gff3.gz, transcript:ENSMUST00000163141. // This also fixes phase of 5' incomplete CDS, see test/csq/ENST00000520868/ENST00000520868.gff // todo: the same for the fwd strand i = tr->ncds - 1; int phase = tr->cds[i]->phase; if ( phase ) tr->trim |= TRIM_5PRIME; while ( i>=0 && phase > tr->cds[i]->len ) { phase -= tr->cds[i]->len; tr->cds[i]->phase = 0; tr->cds[i]->len = 0; i--; } if ( gff->verbosity > 0 && tr->cds[i]->phase ) { if ( !gff->warned.incomplete_cds || gff->verbosity > 1 ) fprintf(stderr,"Note: truncated transcript %s with incomplete CDS (this is very common)\n",gff->tscript_ids.str[tr->id]); gff->warned.incomplete_cds++; } tr->cds[i]->len -= tr->cds[i]->phase; tr->cds[i]->phase = 0; } // sanity check phase int tscript_ok = 1; for (i=tr->ncds-1; i>=0; i--) { if ( tr->cds[i]->phase == CDS_PHASE_UNKN ) { if ( gff->verbosity > 0 ) { if ( !gff->warned.unknown_cds_phase || gff->verbosity > 1 ) fprintf(stderr,"Warning: CDS with unknown phase, could not verify reading frame in transcript %s\n",gff->tscript_ids.str[tr->id]); gff->warned.unknown_cds_phase++; } len += tr->cds[i]->len; continue; } int phase = tr->cds[i]->phase ? 3 - tr->cds[i]->phase : 0; if ( phase!=len%3 ) { if ( !gff->force ) error("Error: GFF3 assumption failed for transcript %s, CDS=%"PRIu32": phase!=len%%3 (phase=%d, len=%d). Use the --force option to proceed anyway (at your own risk).\n", gff->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len); if ( gff->verbosity > 0 ) { if ( !gff->warned.wrong_phase || gff->verbosity > 1 ) fprintf(stderr,"Warning: The GFF has inconsistent phase column in transcript %s, skipping. CDS pos=%"PRIu32": phase!=len%%3 (phase=%d, len=%d)\n", gff->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len); gff->warned.wrong_phase++; } tscript_ok = 0; break; } len += tr->cds[i]->len; } if ( !tscript_ok ) continue; // skip this transcript } else continue; // unknown strand // set len. At the same check that CDS within a transcript do not overlap len = 0; for (i=0; incds; i++) { tr->cds[i]->icds = i; len += tr->cds[i]->len; if ( !i ) continue; gf_cds_t *a = tr->cds[i-1]; gf_cds_t *b = tr->cds[i]; if ( a->beg + a->len - 1 >= b->beg ) { if ( gff->verbosity > 0 ) { if ( !gff->warned.overlapping_cds || gff->verbosity > 1 ) fprintf(stderr,"Warning: GFF contains overlapping CDS %s, %"PRIu32"-%"PRIu32" and %"PRIu32"-%"PRIu32" (ribosomal slippage?)\n", gff->tscript_ids.str[tr->id], a->beg+1,a->beg+a->len, b->beg+1,b->beg+b->len); gff->warned.overlapping_cds++; } } } if ( len%3 != 0 ) { // There are 13k transcripts with incomplete 3' CDS. See for example ENST00000524289 // http://sep2015.archive.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000155868;r=5:157138846-157159019;t=ENST00000524289 // Also, the incomplete CDS can be too short (1 or 2bp), so it is not enough to trim the last one. if ( gff->verbosity > 0 ) { if ( !gff->warned.incomplete_cds || gff->verbosity > 1 ) fprintf(stderr,"Note: truncated transcript %s with incomplete CDS (this is very common)\n",gff->tscript_ids.str[tr->id]); gff->warned.incomplete_cds++; } tr->trim |= TRIM_3PRIME; if ( tr->strand==STRAND_FWD ) { i = tr->ncds - 1; while ( i>=0 && len%3 ) { int dlen = tr->cds[i]->len >= len%3 ? len%3 : tr->cds[i]->len; tr->cds[i]->len -= dlen; len -= dlen; i--; } } else if ( tr->strand==STRAND_REV ) { i = 0; while ( incds && len%3 ) { int dlen = tr->cds[i]->len >= len%3 ? len%3 : tr->cds[i]->len; tr->cds[i]->len -= dlen; tr->cds[i]->beg += dlen; len -= dlen; i++; } } } // set CDS offsets and insert into regidx len=0; for (i=0; incds; i++) { tr->cds[i]->pos = len; len += tr->cds[i]->len; regidx_push(gff->idx_cds, chr_beg,chr_end, tr->cds[i]->beg,tr->cds[i]->beg+tr->cds[i]->len-1, &tr->cds[i]); } } } static void regidx_free_gf(void *payload) { free(*((gf_cds_t**)payload)); } static void regidx_free_tscript(void *payload) { gf_tscript_t *tr = *((gf_tscript_t**)payload); free(tr->cds); free(tr); } static int gff_dump(gff_t *gff, const char *fname) { BGZF *out = bgzf_open(fname,"wg"); if ( !out ) error("Failed to open %s: %s\n", fname, strerror(errno)); kstring_t str = {0,0,0}; khint_t k; for (k=0; kinit.gid2gene); k++) { if ( !kh_exist(gff->init.gid2gene, k) ) continue; gf_gene_t *gene = (gf_gene_t*) kh_val(gff->init.gid2gene, k); char *gene_id = gff->init.gene_ids.str[gene->id]; str.l = 0; ksprintf(&str,"%s\t.\tgene\t%"PRIu32"\t%"PRIu32"\t.\t%c\t.\tID=%s;Name=%s;used=%d\n",gff->init.seq[gene->iseq],gene->beg+1,gene->end+1,gene->strand==STRAND_FWD?'+':(gene->strand==STRAND_REV?'-':'.'),gene_id,gene->name,gene->used); if ( bgzf_write(out, str.s, str.l) != str.l ) error("Error writing %s: %s\n", fname, strerror(errno)); } regitr_t *itr = regitr_init(gff->idx_tscript); while ( regitr_loop(itr) ) { gf_tscript_t *tr = regitr_payload(itr, gf_tscript_t*); char *gene_id = gff->init.gene_ids.str[tr->gene->id]; const char *type = tr->type==GF_PROTEIN_CODING ? "mRNA" : gf_type2gff_string(tr->type); str.l = 0; ksprintf(&str,"%s\t.\t%s\t%"PRIu32"\t%"PRIu32"\t.\t%c\t.\tID=%s;Parent=%s;biotype=%s;used=%d\n",itr->seq,type,itr->beg+1,itr->end+1,tr->strand==STRAND_FWD?'+':(tr->strand==STRAND_REV?'-':'.'),gff->tscript_ids.str[tr->id],gene_id,gf_type2gff_string(tr->type),tr->used); if ( bgzf_write(out, str.s, str.l) != str.l ) error("Error writing %s: %s\n", fname, strerror(errno)); } regitr_destroy(itr); itr = regitr_init(gff->idx_cds); while ( regitr_loop(itr) ) { gf_cds_t *cds = regitr_payload(itr,gf_cds_t*); gf_tscript_t *tr = cds->tr; str.l = 0; ksprintf(&str,"%s\t.\tCDS\t%"PRIu32"\t%"PRIu32"\t.\t%c\t%c\tParent=%s\n",itr->seq,cds->beg+1,cds->beg+cds->len,tr->strand==STRAND_FWD?'+':(tr->strand==STRAND_REV?'-':'.'),cds->phase==3?'.':cds->phase+(int)'0',gff->tscript_ids.str[tr->id]); if ( bgzf_write(out, str.s, str.l) != str.l ) error("Error writing %s: %s\n", fname, strerror(errno)); } regitr_destroy(itr); itr = regitr_init(gff->idx_utr); while ( regitr_loop(itr) ) { gf_utr_t *utr = regitr_payload(itr,gf_utr_t*); gf_tscript_t *tr = utr->tr; str.l = 0; ksprintf(&str,"%s\t.\t%s_prime_UTR\t%"PRIu32"\t%"PRIu32"\t.\t%c\t.\tParent=%s\n",itr->seq,utr->which==prime3?"three":"five",utr->beg+1,utr->end+1,tr->strand==STRAND_FWD?'+':(tr->strand==STRAND_REV?'-':'.'),gff->tscript_ids.str[tr->id]); if ( bgzf_write(out, str.s, str.l) != str.l ) error("Error writing %s: %s\n", fname, strerror(errno)); } regitr_destroy(itr); itr = regitr_init(gff->idx_exon); while ( regitr_loop(itr) ) { gf_exon_t *exon = regitr_payload(itr,gf_exon_t*); gf_tscript_t *tr = exon->tr; str.l = 0; ksprintf(&str,"%s\t.\texon\t%"PRIu32"\t%"PRIu32"\t.\t%c\t.\tParent=%s\n",itr->seq,exon->beg+1,exon->end+1,tr->strand==STRAND_FWD?'+':(tr->strand==STRAND_REV?'-':'.'),gff->tscript_ids.str[tr->id]); if ( bgzf_write(out, str.s, str.l) != str.l ) error("Error writing %s: %s\n", fname, strerror(errno)); } regitr_destroy(itr); if ( bgzf_close(out)!=0 ) error("Error: close failed .. %s\n", fname); free(str.s); return 0; } int gff_parse(gff_t *gff) { if ( gff->verbosity > 0 ) fprintf(stderr,"Parsing %s ...\n", gff->fname); aux_t *aux = &gff->init; aux->seq2int = khash_str2int_init(); // chrom's numeric id aux->gid2gene = kh_init(int2gene); // gene id to gf_gene_t, for idx_gene aux->id2tr = kh_init(int2tscript); // transcript id to tscript_t gff->idx_tscript = regidx_init(NULL, NULL, regidx_free_tscript, sizeof(gf_tscript_t*), NULL); aux->ignored_biotypes = khash_str2int_init(); gff_id_init(&aux->gene_ids); gff_id_init(&gff->tscript_ids); // parse gff kstring_t str = {0,0,0}; htsFile *fp = hts_open(gff->fname,"r"); if ( !fp ) error("Failed to read %s\n", gff->fname); while ( hts_getline(fp, KS_SEP_LINE, &str) > 0 ) { hts_expand(ftr_t, aux->nftr+1, aux->mftr, aux->ftr); int ret = gff_parse_line(gff, str.s, aux->ftr + aux->nftr); if ( !ret ) aux->nftr++; } free(str.s); if ( hts_close(fp)!=0 ) error("Close failed: %s\n", gff->fname); // process gff information: connect CDS and exons to transcripts gff->idx_cds = regidx_init(NULL, NULL, regidx_free_gf, sizeof(gf_cds_t*), NULL); gff->idx_utr = regidx_init(NULL, NULL, regidx_free_gf, sizeof(gf_utr_t*), NULL); gff->idx_exon = regidx_init(NULL, NULL, regidx_free_gf, sizeof(gf_exon_t*), NULL); int i; for (i=0; inftr; i++) { ftr_t *ftr = &aux->ftr[i]; // check whether to keep this feature: is there a mapping trid -> gene_id -> gene? khint_t k = kh_get(int2tscript, aux->id2tr, (int)ftr->trid); if ( k==kh_end(aux->id2tr) ) continue; // no corresponding transcript registered, must be an unsupported biotype gf_tscript_t *tr = kh_val(aux->id2tr,k); tr->used = 1; tr->gene->used = 1; // populate regidx by category: // ftr->type .. GF_CDS, GF_EXON, GF_UTR3, GF_UTR5 // gene->type .. GF_PROTEIN_CODING, GF_MT_rRNA, GF_IG_C, ... if ( ftr->type==GF_CDS ) register_cds(gff, ftr); else if ( ftr->type==GF_EXON ) register_exon(gff, ftr); else if ( ftr->type==GF_UTR5 ) register_utr(gff, ftr); else if ( ftr->type==GF_UTR3 ) register_utr(gff, ftr); else error("something: %s\t%"PRIu32"\t%"PRIu32"\t%s\t%s\n", aux->seq[ftr->iseq],ftr->beg+1,ftr->end+1,gff->tscript_ids.str[ftr->trid],gf_type2gff_string(ftr->type)); } tscript_init_cds(gff); if ( gff->verbosity > 0 ) { fprintf(stderr,"Indexed %d transcripts, %d exons, %d CDSs, %d UTRs\n", regidx_nregs(gff->idx_tscript), regidx_nregs(gff->idx_exon), regidx_nregs(gff->idx_cds), regidx_nregs(gff->idx_utr)); } if ( gff->verbosity > 0 && khash_str2int_size(aux->ignored_biotypes) ) { khash_t(str2int) *ign = (khash_t(str2int)*)aux->ignored_biotypes; fprintf(stderr,"Ignored the following biotypes:\n"); for (i = kh_begin(ign); i < kh_end(ign); i++) { if ( !kh_exist(ign,i)) continue; const char *biotype = kh_key(ign,i); if ( !strcmp(biotype,"TCE") ) biotype = "TCE (\"To be Experimentally Confirmed\")"; fprintf(stderr,"\t%dx\t.. %s\n", kh_value(ign,i), biotype); } } khash_str2int_destroy_free(aux->ignored_biotypes); // warned about unprinted warnings if ( gff->verbosity > 0 ) { int nwarn = 0; #define INC_NWARN(X) if (gff->warned.X) nwarn += gff->verbosity > 1 ? 0 : gff->warned.X - 1; INC_NWARN(unknown_chr); INC_NWARN(unknown_tscript_biotype); INC_NWARN(unknown_strand); INC_NWARN(unknown_phase); INC_NWARN(duplicate_id); INC_NWARN(unknown_cds_phase); INC_NWARN(incomplete_cds); INC_NWARN(wrong_phase); INC_NWARN(overlapping_cds); if ( nwarn > 0 ) fprintf(stderr,"Warning: %d warnings were suppressed, increase verbosity to see them all\n",nwarn); } if ( gff->dump_fname ) gff_dump(gff, gff->dump_fname); if ( !regidx_nregs(gff->idx_tscript) ) error("Error: No usable transcripts found, likely a failure to parse a non-standard GFF file. Please check if the misc/gff2gff\n" " or misc/gff2gff.py script can fix the problem (both do different things). See also the man page for the description\n" " of the expected format http://samtools.github.io/bcftools/bcftools-man.html#csq\n"); free(aux->seq); free(aux->ftr); khash_str2int_destroy_free(aux->seq2int); // keeping only to destroy the genes at the end: kh_destroy(int2gene,aux->gid2gene); kh_destroy(int2tscript,aux->id2tr); gff_id_destroy(&aux->gene_ids); return 0; } gff_t *gff_init(const char *fname) { gff_t *gff = calloc(sizeof(gff_t),1); gff->fname = fname; return gff; } void gff_destroy(gff_t *gff) { khint_t k; if ( gff->init.gid2gene ) { for (k=0; kinit.gid2gene); k++) { if ( !kh_exist(gff->init.gid2gene, k) ) continue; gf_gene_t *gene = (gf_gene_t*) kh_val(gff->init.gid2gene, k); free(gene->name); free(gene); } kh_destroy(int2gene,gff->init.gid2gene); } regidx_destroy(gff->idx_cds); regidx_destroy(gff->idx_utr); regidx_destroy(gff->idx_exon); regidx_destroy(gff->idx_tscript); gff_id_destroy(&gff->tscript_ids); free(gff); } pysam-0.23.0/bcftools/gff.c.pysam.c000066400000000000000000001262451475062545500170460ustar00rootroot00000000000000#include "bcftools.pysam.h" /* The MIT License Copyright (c) 2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "regidx.h" #include "gff.h" /* Helper structures, only for initialization ftr_t temporary list of all exons, CDS, UTRs */ KHASH_MAP_INIT_INT(int2tscript, gf_tscript_t*) KHASH_MAP_INIT_INT(int2gene, gf_gene_t*) typedef struct { int type; // GF_CDS, GF_EXON, GF_5UTR, GF_3UTR uint32_t beg; uint32_t end; uint32_t trid; uint32_t strand:2; // STRAND_{REV,FWD,UNK} uint32_t phase:2; // 0, 1, 2, or 3 for unknown uint32_t iseq:28; } ftr_t; /* Mapping from GFF ID string (such as ENST00000450305 or Zm00001d027230_P001) to integer id. To keep the memory requirements low, the original version relied on IDs in the form of a string prefix and a numerical id. However, it turns out that this assumption is not valid for some ensembl GFFs, see for example Zea_mays.AGPv4.36.gff3.gz */ typedef struct { void *str2id; // khash_str2int int nstr, mstr; char **str; // numeric id to string } id_tbl_t; typedef struct { // all exons, CDS, UTRs ftr_t *ftr; int nftr, mftr; // mapping from gene id to gf_gene_t kh_int2gene_t *gid2gene; // mapping from transcript id to tscript, for quick CDS anchoring kh_int2tscript_t *id2tr; // sequences void *seq2int; // str2int hash char **seq; int nseq, mseq; // ignored biotypes void *ignored_biotypes; id_tbl_t gene_ids; // temporary table for mapping between gene id (eg. Zm00001d027245) and a numeric idx // pointers to the current partially processed line char *id, *id_end, *parent, *parent_end, *biotype, *biotype_end, *chr, *chr_end, *name, *name_end, *type, *type_end; } aux_t; struct gff_t_ { const char *fname, *dump_fname; // the main regidx lookups, from chr:beg-end to overlapping features and // index iterator regidx_t *idx_cds, *idx_utr, *idx_exon, *idx_tscript; // temporary structures, deleted after initializtion aux_t init; // mapping between transcript id (eg. Zm00001d027245_T001) and a numeric idx id_tbl_t tscript_ids; int strip_chr_names, verbosity; int force; // force run under various conditions. Currently only to skip out-of-phase transcripts struct { int unknown_chr,unknown_tscript_biotype,unknown_strand,unknown_phase,duplicate_id; int unknown_cds_phase,incomplete_cds,wrong_phase,overlapping_cds; } warned; }; static const char *gf_strings_noncoding[] = { "MT_rRNA", "MT_tRNA", "lincRNA", "miRNA", "misc_RNA", "rRNA", "snRNA", "snoRNA", "processed_transcript", "antisense", "macro_lncRNA", "ribozyme", "sRNA", "scRNA", "scaRNA", "sense_intronic", "sense_overlapping", "pseudogene", "processed_pseudogene", "artifact", "IG_pseudogene", "IG_C_pseudogene", "IG_J_pseudogene", "IG_V_pseudogene", "TR_V_pseudogene", "TR_J_pseudogene", "MT_tRNA_pseudogene", "misc_RNA_pseudogene", "miRNA_pseudogene", "ribozyme", "retained_intron", "retrotransposed", "Trna_pseudogene", "transcribed_processed_pseudogene", "transcribed_unprocessed_pseudogene", "transcribed_unitary_pseudogene", "translated_unprocessed_pseudogene", "translated_processed_pseudogene", "known_ncRNA", "unitary_pseudogene", "unprocessed_pseudogene", "LRG_gene", "3_prime_overlapping_ncRNA", "disrupted_domain", "vaultRNA", "bidirectional_promoter_lncRNA", "ambiguous_orf", "lncRNA" }; static const char *gf_strings_coding[] = { "protein_coding", "polymorphic_pseudogene", "IG_C", "IG_D", "IG_J", "IG_LV", "IG_V", "TR_C", "TR_D", "TR_J", "TR_V", "NMD", "non_stop_decay"}; static const char *gf_strings_special[] = { "CDS", "exon", "3_prime_UTR", "5_prime_UTR" }; int gff_set(gff_t *gff, gff_opt_t key, ...) { va_list args; switch (key) { case dump_fname: va_start(args, key); gff->dump_fname = va_arg(args,char*); va_end(args); return 0; case force_out_of_phase: va_start(args, key); gff->force = va_arg(args,int); va_end(args); return 0; case strip_chr_names: va_start(args, key); gff->strip_chr_names = va_arg(args,int); va_end(args); return 0; case verbosity: va_start(args, key); gff->verbosity = va_arg(args,int); va_end(args); return 0; default: error("The key %d is not supported with gff_set\n",key); } return 0; } void *gff_get(gff_t *gff, gff_opt_t key) { switch (key) { case idx_cds: return gff->idx_cds; case idx_utr: return gff->idx_utr; case idx_exon: return gff->idx_exon; case idx_tscript: return gff->idx_tscript; default: error("The key %d is not supported with gff_get\n",key); } return NULL; } const char *gff_id2string(gff_t *gff, id_type_t type, int id) // currently only transcript ids { return gff->tscript_ids.str[id]; } const char *gf_type2gff_string(int type) { if ( !GF_is_coding(type) ) { if ( type < (1<init; char tmp = chr_end[1]; chr_end[1] = 0; int iseq; if ( khash_str2int_get(aux->seq2int, chr_beg, &iseq)!=0 ) { char *new_chr = strdup(chr_beg); hts_expand(char*, aux->nseq+1, aux->mseq, aux->seq); aux->seq[aux->nseq] = new_chr; iseq = khash_str2int_inc(aux->seq2int, aux->seq[aux->nseq]); aux->nseq++; assert( aux->nseq < 1<<29 ); // see gf_gene_t.iseq and ftr_t.iseq } chr_end[1] = tmp; return iseq; } static inline char *gff_skip(const char *line, char *ss) { while ( *ss && *ss!='\t' ) ss++; if ( !*ss ) error("[%s:%d %s] Could not parse the line: %s\n",__FILE__,__LINE__,__FUNCTION__,line); return ss+1; } static inline void gff_parse_chr(gff_t *gff, const char *line, char **chr_beg, char **chr_end) { char *se = (char*) line; while ( *se && *se!='\t' ) se++; if ( !*se ) error("[%s:%d %s] Could not parse the line: %s\n",__FILE__,__LINE__,__FUNCTION__,line); if ( gff->strip_chr_names && !strncasecmp("chr",line,3) ) line += 3; *chr_beg = (char*) line; *chr_end = se-1; } static inline char *gff_parse_beg_end(const char *line, char *ss, uint32_t *beg, uint32_t *end) { char *se = ss; *beg = strtol(ss, &se, 10) - 1; if ( ss==se ) error("[%s:%d %s] Could not parse the line:\n\t%s\n\t%s\n",__FILE__,__LINE__,__FUNCTION__,line,ss); ss = se+1; *end = strtol(ss, &se, 10) - 1; if ( ss==se ) error("[%s:%d %s] Could not parse the line: %s\n",__FILE__,__LINE__,__FUNCTION__,line); return se+1; } static void gff_id_init(id_tbl_t *tbl) { memset(tbl, 0, sizeof(*tbl)); tbl->str2id = khash_str2int_init(); } static void gff_id_destroy(id_tbl_t *tbl) { khash_str2int_destroy_free(tbl->str2id); free(tbl->str); } static inline int gff_id_register(id_tbl_t *tbl, char *beg, char *end, uint32_t *id_ptr) { char tmp = end[1]; end[1] = 0; int id; if ( khash_str2int_get(tbl->str2id, beg, &id) < 0 ) { id = tbl->nstr++; hts_expand(char*, tbl->nstr, tbl->mstr, tbl->str); tbl->str[id] = strdup(beg); khash_str2int_set(tbl->str2id, tbl->str[id], id); } end[1] = tmp; *id_ptr = id; return 0; } static inline int gff_parse_biotype(char *line) { if ( !line ) return -1; switch (*line) { case 'p': if ( !strncmp(line,"protein_coding",14) ) return GF_PROTEIN_CODING; else if ( !strncmp(line,"pseudogene",10) ) return GF_PSEUDOGENE; else if ( !strncmp(line,"processed_transcript",20) ) return GF_PROCESSED_TRANSCRIPT; else if ( !strncmp(line,"processed_pseudogene",20) ) return GF_PROCESSED_PSEUDOGENE; else if ( !strncmp(line,"polymorphic_pseudogene",22) ) return GF_POLYMORPHIC_PSEUDOGENE; break; case 'a': if ( !strncmp(line,"artifact",8) ) return GF_ARTIFACT; else if ( !strncmp(line,"antisense",9) ) return GF_ANTISENSE; else if ( !strncmp(line,"ambiguous_orf",13) ) return GF_AMBIGUOUS_ORF; break; case 'I': if ( !strncmp(line,"IG_pseudogene",13) ) return GF_IG_PSEUDOGENE; else if ( !strncmp(line,"IG_C_pseudogene",15) ) return GF_IG_C_PSEUDOGENE; else if ( !strncmp(line,"IG_J_pseudogene",15) ) return GF_IG_J_PSEUDOGENE; else if ( !strncmp(line,"IG_V_pseudogene",15) ) return GF_IG_V_PSEUDOGENE; else if ( !strncmp(line,"IG_C",4) ) return GF_IG_C; else if ( !strncmp(line,"IG_D",4) ) return GF_IG_D; else if ( !strncmp(line,"IG_J",4) ) return GF_IG_J; else if ( !strncmp(line,"IG_V",4) ) return GF_IG_V; else if ( !strncmp(line,"IG_LV",5) ) return GF_IG_LV; break; case 'T': if ( !strncmp(line,"TR_V_pseudogene",15) ) return GF_TR_V_PSEUDOGENE; else if ( !strncmp(line,"TR_J_pseudogene",15) ) return GF_TR_J_PSEUDOGENE; else if ( !strncmp(line,"TR_C",4) ) return GF_TR_C; else if ( !strncmp(line,"TR_D",4) ) return GF_TR_D; else if ( !strncmp(line,"TR_J",4) ) return GF_TR_J; else if ( !strncmp(line,"TR_V",4) ) return GF_TR_V; break; case 'M': if ( !strncmp(line,"Mt_tRNA_pseudogene",18) ) return GF_MT_tRNA_PSEUDOGENE; else if ( !strncasecmp(line,"Mt_tRNA",7) ) return GF_MT_tRNA; else if ( !strncasecmp(line,"Mt_rRNA",7) ) return GF_MT_tRNA; else if ( !strncasecmp(line,"MRNA",4) ) return GF_PROTEIN_CODING; break; case 'l': if ( !strncmp(line,"lincRNA",7) ) return GF_lincRNA; if ( !strncmp(line,"lncRNA",7) ) return GF_lncRNA; break; case 'm': if ( !strncmp(line,"macro_lncRNA",12) ) return GF_macro_lncRNA; else if ( !strncmp(line,"misc_RNA_pseudogene",19) ) return GF_misc_RNA_PSEUDOGENE; else if ( !strncmp(line,"miRNA_pseudogene",16) ) return GF_miRNA_PSEUDOGENE; else if ( !strncmp(line,"miRNA",5) ) return GF_miRNA; else if ( !strncmp(line,"misc_RNA",8) ) return GF_MISC_RNA; else if ( !strncasecmp(line,"mRNA",4) ) return GF_PROTEIN_CODING; break; case 'r': if ( !strncmp(line,"rRNA",4) ) return GF_rRNA; else if ( !strncmp(line,"ribozyme",8) ) return GF_RIBOZYME; else if ( !strncmp(line,"retained_intron",15) ) return GF_RETAINED_INTRON; else if ( !strncmp(line,"retrotransposed",15) ) return GF_RETROTRANSPOSED; break; case 's': if ( !strncmp(line,"snRNA",5) ) return GF_snRNA; else if ( !strncmp(line,"sRNA",4) ) return GF_sRNA; else if ( !strncmp(line,"scRNA",5) ) return GF_scRNA; else if ( !strncmp(line,"scaRNA",6) ) return GF_scaRNA; else if ( !strncmp(line,"snoRNA",6) ) return GF_snoRNA; else if ( !strncmp(line,"sense_intronic",14) ) return GF_SENSE_INTRONIC; else if ( !strncmp(line,"sense_overlapping",17) ) return GF_SENSE_OVERLAPPING; break; case 't': if ( !strncmp(line,"tRNA_pseudogene",15) ) return GF_tRNA_PSEUDOGENE; else if ( !strncmp(line,"transcribed_processed_pseudogene",32) ) return GF_TRANSCRIBED_PROCESSED_PSEUDOGENE; else if ( !strncmp(line,"transcribed_unprocessed_pseudogene",34) ) return GF_TRANSCRIBED_UNPROCESSED_PSEUDOGENE; else if ( !strncmp(line,"transcribed_unitary_pseudogene",30) ) return GF_TRANSCRIBED_UNITARY_PSEUDOGENE; else if ( !strncmp(line,"translated_unprocessed_pseudogene",33) ) return GF_TRANSLATED_UNPROCESSED_PSEUDOGENE; else if ( !strncmp(line,"translated_processed_pseudogene",31) ) return GF_TRANSLATED_PROCESSED_PSEUDOGENE; break; case 'n': if ( !strncmp(line,"nonsense_mediated_decay",23) ) return GF_NMD; else if ( !strncmp(line,"non_stop_decay",14) ) return GF_NON_STOP_DECAY; break; case 'N': if ( !strncmp(line,"NMD",3) ) return GF_NMD; break; case 'k': if ( !strncmp(line,"known_ncrna",11) ) return GF_KNOWN_NCRNA; break; case 'u': if ( !strncmp(line,"unitary_pseudogene",18) ) return GF_UNITARY_PSEUDOGENE; else if ( !strncmp(line,"unprocessed_pseudogene",22) ) return GF_UNPROCESSED_PSEUDOGENE; break; case 'L': if ( !strncmp(line,"LRG_gene",8) ) return GF_LRG_GENE; break; case '3': if ( !strncasecmp(line,"3prime_overlapping_ncRNA",24) ) return GF_3PRIME_OVERLAPPING_ncRNA; else if ( !strncasecmp(line,"3_prime_overlapping_ncRNA",25) ) return GF_3PRIME_OVERLAPPING_ncRNA; break; case 'd': if ( !strncmp(line,"disrupted_domain",16) ) return GF_DISRUPTED_DOMAIN; break; case 'v': if ( !strncmp(line,"vaultRNA",8) ) return GF_vaultRNA; break; case 'b': if ( !strncmp(line,"bidirectional_promoter_lncRNA",29) ) return GF_BIDIRECTIONAL_PROMOTER_lncRNA; break; } return 0; } static inline int gff_ignored_biotype(gff_t *gff, char *ss, char *se) { if ( !ss ) return 0; char tmp = se[1]; se[1] = 0; char *key = ss; int n = 0; if ( khash_str2int_get(gff->init.ignored_biotypes, ss, &n)!=0 ) key = strdup(ss); khash_str2int_set(gff->init.ignored_biotypes, key, n+1); se[1] = tmp; return 1; } static gf_gene_t *gene_init(aux_t *aux, uint32_t gene_id) { khint_t k = kh_get(int2gene, aux->gid2gene, (int)gene_id); gf_gene_t *gene = (k == kh_end(aux->gid2gene)) ? NULL : kh_val(aux->gid2gene, k); if ( !gene ) { gene = (gf_gene_t*) calloc(1,sizeof(gf_gene_t)); int ret; k = kh_put(int2gene, aux->gid2gene, (int)gene_id, &ret); kh_val(aux->gid2gene,k) = gene; } return gene; } static void gff_parse_transcript(gff_t *gff, const char *line, ftr_t *ftr) { aux_t *aux = &gff->init; ftr->type = gff_parse_biotype(aux->biotype); if ( ftr->type <= 0 ) { char tmp = aux->type_end[1]; aux->type_end[1] = 0; ftr->type = gff_parse_biotype(aux->type); aux->type_end[1] = tmp; } if ( ftr->type <= 0 ) { if ( !gff_ignored_biotype(gff,aux->biotype,aux->biotype_end) ) { if ( gff->verbosity > 0 ) { if ( !gff->warned.unknown_tscript_biotype || gff->verbosity > 1 ) fprintf(bcftools_stderr,"Warning: Ignoring transcript with unknown biotype .. %s\n", line); gff->warned.unknown_tscript_biotype++; } } return; } if ( !aux->id ) error("[%s:%d %s] Could not parse the line, neither \"ID=transcript:\" nor \"ID=\" substring is present: %s\n",__FILE__,__LINE__,__FUNCTION__,line); if ( !aux->parent ) error("[%s:%d %s] Could not parse the line, neither \"Parent=gene:\" nor \"Parent=\" substring is present: %s\n",__FILE__,__LINE__,__FUNCTION__,line); uint32_t trid,gene_id; gff_id_register(&gff->tscript_ids, aux->id, aux->id_end, &trid); gff_id_register(&aux->gene_ids, aux->parent, aux->parent_end, &gene_id); gf_tscript_t *tr = (gf_tscript_t*) calloc(1,sizeof(gf_tscript_t)); tr->id = trid; tr->strand = ftr->strand; tr->gene = gene_init(aux, gene_id); tr->type = ftr->type; tr->beg = ftr->beg; tr->end = ftr->end; khint_t k; int ret; k = kh_put(int2tscript, aux->id2tr, (int)trid, &ret); kh_val(aux->id2tr,k) = tr; } // register exon, CDS, UTR static void gff_parse_exon(gff_t *gff, const char *line, ftr_t *ftr) { aux_t *aux = &gff->init; if ( !aux->parent ) error("[%s:%d %s] Could not parse the line, neither \"Parent=transcript:\" nor \"Parent=\" substring found: %s\n",__FILE__,__LINE__,__FUNCTION__,line); // associate with transcript id gff_id_register(&gff->tscript_ids, aux->parent, aux->parent_end, &ftr->trid); if ( ftr->strand==STRAND_UNK && gff->verbosity > 0 ) { if ( !gff->warned.unknown_strand || gff->verbosity > 1 ) fprintf(bcftools_stderr,"Warning: Ignoring GFF feature with unknown strand .. %s\n",line); gff->warned.unknown_strand++; } if ( ftr->phase==CDS_PHASE_UNKN && gff->verbosity > 0 ) { if ( !gff->warned.unknown_phase|| gff->verbosity > 1 ) fprintf(bcftools_stderr,"Warning: Ignoring GFF feature with unknown phase .. %s\n",line); gff->warned.unknown_phase++; } ftr->iseq = feature_set_seq(gff, aux->chr,aux->chr_end); } static void gff_parse_gene(gff_t *gff, const char *line, ftr_t *ftr) { aux_t *aux = &gff->init; if ( !aux->id ) return; uint32_t gene_id; gff_id_register(&aux->gene_ids, aux->id, aux->id_end, &gene_id); gf_gene_t *gene = gene_init(aux, gene_id); if ( gene->name ) { if ( !gff->warned.duplicate_id || gff->verbosity > 1 ) fprintf(bcftools_stderr,"Warning: The GFF contains features with duplicate id .. %s\n",line); gff->warned.duplicate_id++; return; } gene->iseq = feature_set_seq(gff, aux->chr,aux->chr_end); gene->beg = ftr->beg; gene->end = ftr->end; gene->strand = ftr->strand; gene->id = gene_id; if ( aux->name ) { gene->name = (char*) malloc(aux->name_end - aux->name + 2); memcpy(gene->name,aux->name,aux->name_end - aux->name + 1); gene->name[aux->name_end - aux->name + 1] = 0; } else gene->name = strdup(aux->gene_ids.str[gene_id]); // Name= field is not present, use the gene ID instead } // Returns 0 for exons,CDS,UTRs to indicate these need to be pruned later and regidx built on them, // or -1 to indicate the structure needs not be saved (either because of an error or because saved // as transcript or gene.) static int gff_parse_line(gff_t *gff, char *line, ftr_t *ftr) { // - skip empty lines and commented lines // - columns // 1. chr // 2. // 3. CDS, transcript, gene, ... // 4-5. beg,end // 6. // 7. strand // 8. phase // 9. Parent=transcript:ENST(\d+);ID=...;biotype=... etc char *ss = line; if ( !*ss ) return -1; // skip blank lines if ( *ss=='#' ) return -1; // skip comments aux_t *aux = &gff->init; gff_parse_chr(gff, line, &aux->chr, &aux->chr_end); ss = gff_skip(line, aux->chr_end + 2); // 3rd column: is this a CDS, transcript, gene, etc.. The parsing order by frequency in Homo_sapiens.GRCh37.87.gff3 int is_gene_line = 0; ftr->type = 0; aux->type = ss; if ( !strncmp("exon\t",ss,5) ) { ftr->type = GF_EXON; ss += 5; } else if ( !strncmp("CDS\t",ss,4) ) { ftr->type = GF_CDS; ss += 4; } else if ( !strncmp("three_prime_UTR\t",ss,16) ) { ftr->type = GF_UTR3; ss += 16; } else if ( !strncmp("five_prime_UTR\t",ss,15) ) { ftr->type = GF_UTR5; ss += 15; } else if ( !strncmp("biological_region\t",ss,18) ) { return -1; } // skip else if ( !strncmp("gene\t",ss,5) ) { is_gene_line = 1; ss += 5; } else ss = gff_skip(line, ss); aux->type_end = ss - 1; // 4-5th columns: beg,end ss = gff_parse_beg_end(line, ss, &ftr->beg,&ftr->end); // 6th column: skip ss = gff_skip(line, ss); // 7th column: strand ftr->strand = -1; if ( *ss == '+' ) ftr->strand = STRAND_FWD; else if ( *ss == '-' ) ftr->strand = STRAND_REV; else ftr->strand = STRAND_UNK; ss += 2; // 8th column: phase (codon offset) ftr->phase = CDS_PHASE_UNKN; if ( *ss == '0' ) ftr->phase = 0; else if ( *ss == '1' ) ftr->phase = 1; else if ( *ss == '2' ) ftr->phase = 2; else if ( *ss == '.' ) ftr->phase = CDS_PHASE_UNKN; // exons and even CDS in some GFFs do not have phase ss += 2; // 9th column: id, parent, name, biotype aux->name = NULL, aux->id = NULL, aux->parent = NULL, aux->biotype = NULL; while ( *ss ) { char *es = ss; while ( *es && *es!=';' ) es++; if ( !strncmp(ss,"ID=",3) ) { ss += 3; aux->id_end = es - 1; aux->id = ss; if ( !strncmp(ss,"gene:",5) ) { aux->id += 5; is_gene_line = 1; } else if ( !strncmp(ss,"transcript:",11) ) aux->id += 11; } else if ( !strncmp(ss,"Name=",5) ) { aux->name = ss + 5; aux->name_end = es - 1; } else if ( !strncmp(ss,"Parent=",7) ) { ss += 7; aux->parent_end = es - 1; aux->parent = ss; if ( !strncmp(ss,"gene:",5) ) aux->parent += 5; else if ( !strncmp(ss,"transcript:",11) ) aux->parent += 11; } else if ( !strncmp(ss,"biotype=",8) ) { aux->biotype = ss + 8; aux->biotype_end = es - 1; } else if ( !strncmp(ss,"gene_biotype=",13) ) { aux->biotype = ss + 13; aux->biotype_end = es - 1; } if ( !*es ) break; ss = es + 1; } if ( is_gene_line || !aux->parent ) { gff_parse_gene(gff, line, ftr); return -1; } if ( ftr->type ) { gff_parse_exon(gff, line, ftr); return 0; } gff_parse_transcript(gff, line, ftr); return -1; } static int cmp_cds_ptr(const void *a, const void *b) { // comparison function for qsort of transcripts's CDS if ( (*((gf_cds_t**)a))->beg < (*((gf_cds_t**)b))->beg ) return -1; if ( (*((gf_cds_t**)a))->beg > (*((gf_cds_t**)b))->beg ) return 1; return 0; } static inline void chr_beg_end(aux_t *aux, int iseq, char **chr_beg, char **chr_end) { *chr_beg = *chr_end = aux->seq[iseq]; while ( (*chr_end)[1] ) (*chr_end)++; } static gf_tscript_t *tscript_init(aux_t *aux, uint32_t trid) { khint_t k = kh_get(int2tscript, aux->id2tr, (int)trid); gf_tscript_t *tr = (k == kh_end(aux->id2tr)) ? NULL : kh_val(aux->id2tr, k); assert( tr ); return tr; } static void register_cds(gff_t *gff, ftr_t *ftr) { // Make the CDS searchable via idx_cds. Note we do not malloc tr->cds just yet. // ftr is the result of parsing a gff CDS line aux_t *aux = &gff->init; gf_tscript_t *tr = tscript_init(aux, ftr->trid); if ( tr->strand != ftr->strand ) error("Conflicting strand in transcript %"PRIu32" .. %d vs %d\n",ftr->trid,tr->strand,ftr->strand); gf_cds_t *cds = (gf_cds_t*) malloc(sizeof(gf_cds_t)); cds->tr = tr; cds->beg = ftr->beg; cds->len = ftr->end - ftr->beg + 1; cds->icds = 0; // to keep valgrind on mac happy cds->phase = ftr->phase; hts_expand(gf_cds_t*,tr->ncds+1,tr->mcds,tr->cds); tr->cds[tr->ncds++] = cds; } static void register_utr(gff_t *gff, ftr_t *ftr) { aux_t *aux = &gff->init; gf_utr_t *utr = (gf_utr_t*) malloc(sizeof(gf_utr_t)); utr->which = ftr->type==GF_UTR3 ? prime3 : prime5; utr->beg = ftr->beg; utr->end = ftr->end; utr->tr = tscript_init(aux, ftr->trid); char *chr_beg, *chr_end; chr_beg_end(&gff->init, utr->tr->gene->iseq, &chr_beg, &chr_end); regidx_push(gff->idx_utr, chr_beg,chr_end, utr->beg,utr->end, &utr); } static void register_exon(gff_t *gff, ftr_t *ftr) { aux_t *aux = &gff->init; gf_exon_t *exon = (gf_exon_t*) malloc(sizeof(gf_exon_t)); exon->beg = ftr->beg; exon->end = ftr->end; exon->tr = tscript_init(aux, ftr->trid); char *chr_beg, *chr_end; chr_beg_end(&gff->init, exon->tr->gene->iseq, &chr_beg, &chr_end); regidx_push(gff->idx_exon, chr_beg,chr_end, exon->beg - N_SPLICE_REGION_INTRON, exon->end + N_SPLICE_REGION_INTRON, &exon); } static void tscript_init_cds(gff_t *gff) { aux_t *aux = &gff->init; // Sort CDS in all transcripts, set offsets, check their phase, length, create index (idx_cds) khint_t k; for (k=0; kid2tr); k++) { if ( !kh_exist(aux->id2tr, k) ) continue; gf_tscript_t *tr = (gf_tscript_t*) kh_val(aux->id2tr, k); // position-to-tscript lookup char *chr_beg, *chr_end; chr_beg_end(aux, tr->gene->iseq, &chr_beg, &chr_end); regidx_push(gff->idx_tscript, chr_beg, chr_end, tr->beg, tr->end, &tr); if ( !tr->ncds ) continue; // transcript with no CDS // sort CDs qsort(tr->cds, tr->ncds, sizeof(gf_cds_t*), cmp_cds_ptr); // trim non-coding start int i, len = 0; if ( tr->strand==STRAND_FWD ) { if ( tr->cds[0]->phase != CDS_PHASE_UNKN ) { if ( tr->cds[0]->phase ) tr->trim |= TRIM_5PRIME; tr->cds[0]->beg += tr->cds[0]->phase; tr->cds[0]->len -= tr->cds[0]->phase; tr->cds[0]->phase = 0; } // sanity check phase; the phase number in gff tells us how many bases to skip in this // feature to reach the first base of the next codon int tscript_ok = 1; for (i=0; incds; i++) { if ( tr->cds[i]->phase == CDS_PHASE_UNKN ) { if ( gff->verbosity > 0 ) { if ( !gff->warned.unknown_cds_phase || gff->verbosity > 1 ) fprintf(bcftools_stderr,"Warning: CDS with unknown phase, could not verify reading frame in transcript %s\n",gff->tscript_ids.str[tr->id]); gff->warned.unknown_cds_phase++; } len += tr->cds[i]->len; continue; } int phase = tr->cds[i]->phase ? 3 - tr->cds[i]->phase : 0; if ( phase!=len%3 ) { if ( !gff->force ) error("Error: GFF3 assumption failed for transcript %s, CDS=%"PRIu32": phase!=len%%3 (phase=%d, len=%d). Use the --force option to proceed anyway (at your own risk).\n", gff->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len); if ( gff->verbosity > 0 ) { if ( !gff->warned.wrong_phase || gff->verbosity > 1 ) fprintf(bcftools_stderr,"Warning: The GFF has inconsistent phase column in transcript %s, skipping. CDS pos=%"PRIu32": phase!=len%%3 (phase=%d, len=%d)\n", gff->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len); gff->warned.wrong_phase++; } tscript_ok = 0; break; } len += tr->cds[i]->len; } if ( !tscript_ok ) continue; // skip this transcript } else if ( tr->strand==STRAND_REV ) { if ( tr->cds[tr->ncds-1]->phase != CDS_PHASE_UNKN ) { // Check that the phase is not bigger than CDS length. Curiously, this can really happen, // see Mus_musculus.GRCm38.85.gff3.gz, transcript:ENSMUST00000163141. // This also fixes phase of 5' incomplete CDS, see test/csq/ENST00000520868/ENST00000520868.gff // todo: the same for the fwd strand i = tr->ncds - 1; int phase = tr->cds[i]->phase; if ( phase ) tr->trim |= TRIM_5PRIME; while ( i>=0 && phase > tr->cds[i]->len ) { phase -= tr->cds[i]->len; tr->cds[i]->phase = 0; tr->cds[i]->len = 0; i--; } if ( gff->verbosity > 0 && tr->cds[i]->phase ) { if ( !gff->warned.incomplete_cds || gff->verbosity > 1 ) fprintf(bcftools_stderr,"Note: truncated transcript %s with incomplete CDS (this is very common)\n",gff->tscript_ids.str[tr->id]); gff->warned.incomplete_cds++; } tr->cds[i]->len -= tr->cds[i]->phase; tr->cds[i]->phase = 0; } // sanity check phase int tscript_ok = 1; for (i=tr->ncds-1; i>=0; i--) { if ( tr->cds[i]->phase == CDS_PHASE_UNKN ) { if ( gff->verbosity > 0 ) { if ( !gff->warned.unknown_cds_phase || gff->verbosity > 1 ) fprintf(bcftools_stderr,"Warning: CDS with unknown phase, could not verify reading frame in transcript %s\n",gff->tscript_ids.str[tr->id]); gff->warned.unknown_cds_phase++; } len += tr->cds[i]->len; continue; } int phase = tr->cds[i]->phase ? 3 - tr->cds[i]->phase : 0; if ( phase!=len%3 ) { if ( !gff->force ) error("Error: GFF3 assumption failed for transcript %s, CDS=%"PRIu32": phase!=len%%3 (phase=%d, len=%d). Use the --force option to proceed anyway (at your own risk).\n", gff->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len); if ( gff->verbosity > 0 ) { if ( !gff->warned.wrong_phase || gff->verbosity > 1 ) fprintf(bcftools_stderr,"Warning: The GFF has inconsistent phase column in transcript %s, skipping. CDS pos=%"PRIu32": phase!=len%%3 (phase=%d, len=%d)\n", gff->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len); gff->warned.wrong_phase++; } tscript_ok = 0; break; } len += tr->cds[i]->len; } if ( !tscript_ok ) continue; // skip this transcript } else continue; // unknown strand // set len. At the same check that CDS within a transcript do not overlap len = 0; for (i=0; incds; i++) { tr->cds[i]->icds = i; len += tr->cds[i]->len; if ( !i ) continue; gf_cds_t *a = tr->cds[i-1]; gf_cds_t *b = tr->cds[i]; if ( a->beg + a->len - 1 >= b->beg ) { if ( gff->verbosity > 0 ) { if ( !gff->warned.overlapping_cds || gff->verbosity > 1 ) fprintf(bcftools_stderr,"Warning: GFF contains overlapping CDS %s, %"PRIu32"-%"PRIu32" and %"PRIu32"-%"PRIu32" (ribosomal slippage?)\n", gff->tscript_ids.str[tr->id], a->beg+1,a->beg+a->len, b->beg+1,b->beg+b->len); gff->warned.overlapping_cds++; } } } if ( len%3 != 0 ) { // There are 13k transcripts with incomplete 3' CDS. See for example ENST00000524289 // http://sep2015.archive.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000155868;r=5:157138846-157159019;t=ENST00000524289 // Also, the incomplete CDS can be too short (1 or 2bp), so it is not enough to trim the last one. if ( gff->verbosity > 0 ) { if ( !gff->warned.incomplete_cds || gff->verbosity > 1 ) fprintf(bcftools_stderr,"Note: truncated transcript %s with incomplete CDS (this is very common)\n",gff->tscript_ids.str[tr->id]); gff->warned.incomplete_cds++; } tr->trim |= TRIM_3PRIME; if ( tr->strand==STRAND_FWD ) { i = tr->ncds - 1; while ( i>=0 && len%3 ) { int dlen = tr->cds[i]->len >= len%3 ? len%3 : tr->cds[i]->len; tr->cds[i]->len -= dlen; len -= dlen; i--; } } else if ( tr->strand==STRAND_REV ) { i = 0; while ( incds && len%3 ) { int dlen = tr->cds[i]->len >= len%3 ? len%3 : tr->cds[i]->len; tr->cds[i]->len -= dlen; tr->cds[i]->beg += dlen; len -= dlen; i++; } } } // set CDS offsets and insert into regidx len=0; for (i=0; incds; i++) { tr->cds[i]->pos = len; len += tr->cds[i]->len; regidx_push(gff->idx_cds, chr_beg,chr_end, tr->cds[i]->beg,tr->cds[i]->beg+tr->cds[i]->len-1, &tr->cds[i]); } } } static void regidx_free_gf(void *payload) { free(*((gf_cds_t**)payload)); } static void regidx_free_tscript(void *payload) { gf_tscript_t *tr = *((gf_tscript_t**)payload); free(tr->cds); free(tr); } static int gff_dump(gff_t *gff, const char *fname) { BGZF *out = bgzf_open(fname,"wg"); if ( !out ) error("Failed to open %s: %s\n", fname, strerror(errno)); kstring_t str = {0,0,0}; khint_t k; for (k=0; kinit.gid2gene); k++) { if ( !kh_exist(gff->init.gid2gene, k) ) continue; gf_gene_t *gene = (gf_gene_t*) kh_val(gff->init.gid2gene, k); char *gene_id = gff->init.gene_ids.str[gene->id]; str.l = 0; ksprintf(&str,"%s\t.\tgene\t%"PRIu32"\t%"PRIu32"\t.\t%c\t.\tID=%s;Name=%s;used=%d\n",gff->init.seq[gene->iseq],gene->beg+1,gene->end+1,gene->strand==STRAND_FWD?'+':(gene->strand==STRAND_REV?'-':'.'),gene_id,gene->name,gene->used); if ( bgzf_write(out, str.s, str.l) != str.l ) error("Error writing %s: %s\n", fname, strerror(errno)); } regitr_t *itr = regitr_init(gff->idx_tscript); while ( regitr_loop(itr) ) { gf_tscript_t *tr = regitr_payload(itr, gf_tscript_t*); char *gene_id = gff->init.gene_ids.str[tr->gene->id]; const char *type = tr->type==GF_PROTEIN_CODING ? "mRNA" : gf_type2gff_string(tr->type); str.l = 0; ksprintf(&str,"%s\t.\t%s\t%"PRIu32"\t%"PRIu32"\t.\t%c\t.\tID=%s;Parent=%s;biotype=%s;used=%d\n",itr->seq,type,itr->beg+1,itr->end+1,tr->strand==STRAND_FWD?'+':(tr->strand==STRAND_REV?'-':'.'),gff->tscript_ids.str[tr->id],gene_id,gf_type2gff_string(tr->type),tr->used); if ( bgzf_write(out, str.s, str.l) != str.l ) error("Error writing %s: %s\n", fname, strerror(errno)); } regitr_destroy(itr); itr = regitr_init(gff->idx_cds); while ( regitr_loop(itr) ) { gf_cds_t *cds = regitr_payload(itr,gf_cds_t*); gf_tscript_t *tr = cds->tr; str.l = 0; ksprintf(&str,"%s\t.\tCDS\t%"PRIu32"\t%"PRIu32"\t.\t%c\t%c\tParent=%s\n",itr->seq,cds->beg+1,cds->beg+cds->len,tr->strand==STRAND_FWD?'+':(tr->strand==STRAND_REV?'-':'.'),cds->phase==3?'.':cds->phase+(int)'0',gff->tscript_ids.str[tr->id]); if ( bgzf_write(out, str.s, str.l) != str.l ) error("Error writing %s: %s\n", fname, strerror(errno)); } regitr_destroy(itr); itr = regitr_init(gff->idx_utr); while ( regitr_loop(itr) ) { gf_utr_t *utr = regitr_payload(itr,gf_utr_t*); gf_tscript_t *tr = utr->tr; str.l = 0; ksprintf(&str,"%s\t.\t%s_prime_UTR\t%"PRIu32"\t%"PRIu32"\t.\t%c\t.\tParent=%s\n",itr->seq,utr->which==prime3?"three":"five",utr->beg+1,utr->end+1,tr->strand==STRAND_FWD?'+':(tr->strand==STRAND_REV?'-':'.'),gff->tscript_ids.str[tr->id]); if ( bgzf_write(out, str.s, str.l) != str.l ) error("Error writing %s: %s\n", fname, strerror(errno)); } regitr_destroy(itr); itr = regitr_init(gff->idx_exon); while ( regitr_loop(itr) ) { gf_exon_t *exon = regitr_payload(itr,gf_exon_t*); gf_tscript_t *tr = exon->tr; str.l = 0; ksprintf(&str,"%s\t.\texon\t%"PRIu32"\t%"PRIu32"\t.\t%c\t.\tParent=%s\n",itr->seq,exon->beg+1,exon->end+1,tr->strand==STRAND_FWD?'+':(tr->strand==STRAND_REV?'-':'.'),gff->tscript_ids.str[tr->id]); if ( bgzf_write(out, str.s, str.l) != str.l ) error("Error writing %s: %s\n", fname, strerror(errno)); } regitr_destroy(itr); if ( bgzf_close(out)!=0 ) error("Error: close failed .. %s\n", fname); free(str.s); return 0; } int gff_parse(gff_t *gff) { if ( gff->verbosity > 0 ) fprintf(bcftools_stderr,"Parsing %s ...\n", gff->fname); aux_t *aux = &gff->init; aux->seq2int = khash_str2int_init(); // chrom's numeric id aux->gid2gene = kh_init(int2gene); // gene id to gf_gene_t, for idx_gene aux->id2tr = kh_init(int2tscript); // transcript id to tscript_t gff->idx_tscript = regidx_init(NULL, NULL, regidx_free_tscript, sizeof(gf_tscript_t*), NULL); aux->ignored_biotypes = khash_str2int_init(); gff_id_init(&aux->gene_ids); gff_id_init(&gff->tscript_ids); // parse gff kstring_t str = {0,0,0}; htsFile *fp = hts_open(gff->fname,"r"); if ( !fp ) error("Failed to read %s\n", gff->fname); while ( hts_getline(fp, KS_SEP_LINE, &str) > 0 ) { hts_expand(ftr_t, aux->nftr+1, aux->mftr, aux->ftr); int ret = gff_parse_line(gff, str.s, aux->ftr + aux->nftr); if ( !ret ) aux->nftr++; } free(str.s); if ( hts_close(fp)!=0 ) error("Close failed: %s\n", gff->fname); // process gff information: connect CDS and exons to transcripts gff->idx_cds = regidx_init(NULL, NULL, regidx_free_gf, sizeof(gf_cds_t*), NULL); gff->idx_utr = regidx_init(NULL, NULL, regidx_free_gf, sizeof(gf_utr_t*), NULL); gff->idx_exon = regidx_init(NULL, NULL, regidx_free_gf, sizeof(gf_exon_t*), NULL); int i; for (i=0; inftr; i++) { ftr_t *ftr = &aux->ftr[i]; // check whether to keep this feature: is there a mapping trid -> gene_id -> gene? khint_t k = kh_get(int2tscript, aux->id2tr, (int)ftr->trid); if ( k==kh_end(aux->id2tr) ) continue; // no corresponding transcript registered, must be an unsupported biotype gf_tscript_t *tr = kh_val(aux->id2tr,k); tr->used = 1; tr->gene->used = 1; // populate regidx by category: // ftr->type .. GF_CDS, GF_EXON, GF_UTR3, GF_UTR5 // gene->type .. GF_PROTEIN_CODING, GF_MT_rRNA, GF_IG_C, ... if ( ftr->type==GF_CDS ) register_cds(gff, ftr); else if ( ftr->type==GF_EXON ) register_exon(gff, ftr); else if ( ftr->type==GF_UTR5 ) register_utr(gff, ftr); else if ( ftr->type==GF_UTR3 ) register_utr(gff, ftr); else error("something: %s\t%"PRIu32"\t%"PRIu32"\t%s\t%s\n", aux->seq[ftr->iseq],ftr->beg+1,ftr->end+1,gff->tscript_ids.str[ftr->trid],gf_type2gff_string(ftr->type)); } tscript_init_cds(gff); if ( gff->verbosity > 0 ) { fprintf(bcftools_stderr,"Indexed %d transcripts, %d exons, %d CDSs, %d UTRs\n", regidx_nregs(gff->idx_tscript), regidx_nregs(gff->idx_exon), regidx_nregs(gff->idx_cds), regidx_nregs(gff->idx_utr)); } if ( gff->verbosity > 0 && khash_str2int_size(aux->ignored_biotypes) ) { khash_t(str2int) *ign = (khash_t(str2int)*)aux->ignored_biotypes; fprintf(bcftools_stderr,"Ignored the following biotypes:\n"); for (i = kh_begin(ign); i < kh_end(ign); i++) { if ( !kh_exist(ign,i)) continue; const char *biotype = kh_key(ign,i); if ( !strcmp(biotype,"TCE") ) biotype = "TCE (\"To be Experimentally Confirmed\")"; fprintf(bcftools_stderr,"\t%dx\t.. %s\n", kh_value(ign,i), biotype); } } khash_str2int_destroy_free(aux->ignored_biotypes); // warned about unprinted warnings if ( gff->verbosity > 0 ) { int nwarn = 0; #define INC_NWARN(X) if (gff->warned.X) nwarn += gff->verbosity > 1 ? 0 : gff->warned.X - 1; INC_NWARN(unknown_chr); INC_NWARN(unknown_tscript_biotype); INC_NWARN(unknown_strand); INC_NWARN(unknown_phase); INC_NWARN(duplicate_id); INC_NWARN(unknown_cds_phase); INC_NWARN(incomplete_cds); INC_NWARN(wrong_phase); INC_NWARN(overlapping_cds); if ( nwarn > 0 ) fprintf(bcftools_stderr,"Warning: %d warnings were suppressed, increase verbosity to see them all\n",nwarn); } if ( gff->dump_fname ) gff_dump(gff, gff->dump_fname); if ( !regidx_nregs(gff->idx_tscript) ) error("Error: No usable transcripts found, likely a failure to parse a non-standard GFF file. Please check if the misc/gff2gff\n" " or misc/gff2gff.py script can fix the problem (both do different things). See also the man page for the description\n" " of the expected format http://samtools.github.io/bcftools/bcftools-man.html#csq\n"); free(aux->seq); free(aux->ftr); khash_str2int_destroy_free(aux->seq2int); // keeping only to destroy the genes at the end: kh_destroy(int2gene,aux->gid2gene); kh_destroy(int2tscript,aux->id2tr); gff_id_destroy(&aux->gene_ids); return 0; } gff_t *gff_init(const char *fname) { gff_t *gff = calloc(sizeof(gff_t),1); gff->fname = fname; return gff; } void gff_destroy(gff_t *gff) { khint_t k; if ( gff->init.gid2gene ) { for (k=0; kinit.gid2gene); k++) { if ( !kh_exist(gff->init.gid2gene, k) ) continue; gf_gene_t *gene = (gf_gene_t*) kh_val(gff->init.gid2gene, k); free(gene->name); free(gene); } kh_destroy(int2gene,gff->init.gid2gene); } regidx_destroy(gff->idx_cds); regidx_destroy(gff->idx_utr); regidx_destroy(gff->idx_exon); regidx_destroy(gff->idx_tscript); gff_id_destroy(&gff->tscript_ids); free(gff); } pysam-0.23.0/bcftools/gff.h000066400000000000000000000311101475062545500154640ustar00rootroot00000000000000/* The MIT License Copyright (c) 2023-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* GFF parsing code refactored from csq.c Things that would be nice to have - dynamic N_REF_PAD - for stop-lost events (also in frameshifts) report the number of truncated aa's - memory could be greatly reduced by indexing gff (but it is quite compact already) - deletions that go beyond transcript boundaries are not checked at sequence level - alloc tscript->ref in hap_finalize, introduce fa_off_beg:16,fa_off_end:16 - see test/csq/ENST00000573314/insertion-overlap.vcf #1476288882 Read about transcript types here http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html https://www.gencodegenes.org/pages/biotypes.html List of supported biotypes antisense IG_C_gene IG_D_gene IG_J_gene IG_LV_gene IG_V_gene lincRNA lncRNA .. generic term for 3prime_overlapping_ncRNA, antisense, bidirectional_promoter_lncRNA, lincRNA, macro_lncRNA, non_coding, processed_transcript, sense_intronic, sense_overlapping macro_lncRNA miRNA misc_RNA Mt_rRNA Mt_tRNA polymorphic_pseudogene processed_transcript protein_coding, mRNA ribozyme rRNA sRNA scRNA scaRNA sense_intronic sense_overlapping snRNA snoRNA TR_C_gene TR_D_gene TR_J_gene TR_V_gene The gff parsing logic We collect features such by combining gff lines A,B,C as follows: A .. gene line with a supported biotype A.ID=~/^gene:/ B .. transcript line referencing A with supported biotype B.ID=~/^transcript:/ && B.Parent=~/^gene:A.ID/ C .. corresponding CDS, exon, and UTR lines: C[3] in {"CDS","exon","three_prime_UTR","five_prime_UTR"} && C.Parent=~/^transcript:B.ID/ For coding biotypes ("protein_coding" or "polymorphic_pseudogene") the complete chain link C -> B -> A is required. For the rest, link B -> A suffices. The supported consequence types, sorted by impact: splice_acceptor_variant .. end region of an intron changed (2bp at the 3' end of an intron) splice_donor_variant .. start region of an intron changed (2bp at the 5' end of an intron) stop_gained .. DNA sequence variant resulting in a stop codon frameshift_variant .. number of inserted/deleted bases not a multiple of three, disrupted translational frame stop_lost .. elongated transcript, stop codon changed start_lost .. the first codon changed inframe_altering .. combination of indels leading to unchanged reading frame and length inframe_insertion .. inserted coding sequence, unchanged reading frame inframe_deletion .. deleted coding sequence, unchanged reading frame missense_variant .. amino acid (aa) change, unchanged length splice_region_variant .. change within 1-3 bases of the exon or 3-8 bases of the intron synonymous_variant .. DNA sequence variant resulting in no amino acid change stop_retained_variant .. different stop codon start_retained_variant .. start codon retained by indel realignment non_coding_variant .. variant in non-coding sequence, such as RNA gene 5_prime_UTR_variant 3_prime_UTR_variant intron_variant .. reported only if none of the above intergenic_variant .. reported only if none of the above The annotation algorithm. The algorithm checks if the variant falls in a region of a supported type. The search is performed in the following order, until a match is found: 1. idx_cds(gf_cds_t) - lookup CDS by position, create haplotypes, call consequences 2. idx_utr(gf_utr_t) - check UTR hits 3. idx_exon(gf_exon_t) - check for splice variants 4. idx_tscript(tscript_t) - check for intronic variants, RNAs, etc. These regidx indexes are created by parsing a gff3 file as follows: 1. create the array "ftr" of all UTR, CDS, exons. This will be processed later and pruned based on transcript types we want to keep. In the same go, create the hash "id2tr" of transcripts to keep (based on biotype) which maps from transcript_id to a transcript. At the same time also build the hash "gid2gene" which maps from gene_id to gf_gene_t pointer. 2. build "idx_cds", "idx_tscript", "idx_utr" and "idx_exon" indexes. Use only features from "ftr" which are present in "id2tr". 3. clean data that won't be needed anymore: ftr, id2tr, gid2gene. Data structures. idx_cds, idx_utr, idx_exon, idx_tscript: as described above, regidx structures for fast lookup of exons/transcripts overlapping a region, the payload is a pointer to tscript.cds */ #ifndef GFF_H__ #define GFF_H__ #include #ifndef __FUNCTION__ # define __FUNCTION__ __func__ #endif // Definition of splice_region, splice_acceptor and splice_donor #define N_SPLICE_DONOR 2 #define N_SPLICE_REGION_EXON 3 #define N_SPLICE_REGION_INTRON 8 #define STRAND_REV 0 #define STRAND_FWD 1 #define STRAND_UNK 2 #define TRIM_NONE 0 #define TRIM_5PRIME 1 #define TRIM_3PRIME 2 // GFF line types #define GFF_UNKN_LINE 0 #define GFF_TSCRIPT_LINE 1 #define GFF_GENE_LINE 2 /* Genomic features, for fast lookup by position to overlapping features */ #define GF_coding_bit 6 #define GF_is_coding(x) ((x) & (1< Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include "gvcf.h" #include "bcftools.h" struct _gvcf_t { int *dp_range, ndp_range; // per-sample DP ranges int prev_range; // 0 if not in a block int32_t *dp, mdp, *pl, mpl, npl; int32_t *tmp, mtmp, *gts, ngts,mgts, nqsum,mqsum; float *qsum; int32_t rid, start, end, min_dp; kstring_t als; bcf1_t *line; }; void gvcf_update_header(gvcf_t *gvcf, bcf_hdr_t *hdr) { bcf_hdr_append(hdr,"##INFO="); bcf_hdr_append(hdr,"##INFO="); } gvcf_t *gvcf_init(const char *dp_ranges) { gvcf_t *gvcf = (gvcf_t*) calloc(1,sizeof(gvcf_t)); gvcf->line = bcf_init(); int n = 1; const char *ss = dp_ranges; while ( *ss ) { if ( *ss==',' ) n++; ss++; } gvcf->ndp_range = n; gvcf->dp_range = (int*) malloc(sizeof(int)*gvcf->ndp_range); n = 0; ss = dp_ranges; while ( *ss ) { char *se = (char*) ss; gvcf->dp_range[n++] = strtol(ss,&se,10); if ( se==ss ) return NULL; if ( *se==',' && se[1] ) { ss = se+1; continue; } else if ( !*se ) break; return NULL; } return gvcf; } void gvcf_destroy(gvcf_t *gvcf) { free(gvcf->dp_range); free(gvcf->dp); free(gvcf->pl); free(gvcf->tmp); free(gvcf->qsum); free(gvcf->gts); free(gvcf->als.s); if ( gvcf->line ) bcf_destroy(gvcf->line); free(gvcf); } bcf1_t *gvcf_write(gvcf_t *gvcf, htsFile *fh, bcf_hdr_t *hdr, bcf1_t *rec, int is_ref) { int i, ret, nsmpl = bcf_hdr_nsamples(hdr); int can_collapse = is_ref ? 1 : 0; int32_t dp_range = 0, min_dp = 0; // No record and nothing to flush? if ( !rec && !gvcf->prev_range ) return NULL; // Flush gVCF block if there are no more records, chr changed, a gap // encountered, or other conditions not met (block broken by a non-ref or DP too low). int needs_flush = can_collapse ? 0 : 1; // Can the record be included in a gVCF block? That is, is this a ref-only site? if ( rec && can_collapse ) { bcf_unpack(rec, BCF_UN_ALL); // per-sample depth ret = bcf_get_format_int32(hdr, rec, "DP", &gvcf->tmp, &gvcf->mtmp); if ( ret==nsmpl ) { min_dp = gvcf->tmp[0]; for (i=1; i gvcf->tmp[i] ) min_dp = gvcf->tmp[i]; for (i=0; indp_range; i++) if ( min_dp < gvcf->dp_range[i] ) break; dp_range = i; if ( !dp_range ) { // leave the record unchanged, DP is too small. Alternatively, return NULL here // to skip these sites needs_flush = 1; can_collapse = 0; } } else needs_flush = 1; // DP field not present } if ( gvcf->prev_range && gvcf->prev_range!=dp_range ) needs_flush = 1; if ( !rec || gvcf->rid!=rec->rid || rec->pos > gvcf->end+1 ) needs_flush = 1; // If prev_range is set, something can be flushed if ( gvcf->prev_range && needs_flush ) { // mpileup can output two records with the same position, SNP and // indel. Make sure the end position does not include the non-variant // SNP position just before the indel. if ( rec && rec->rid==gvcf->rid && rec->pos==gvcf->end ) gvcf->end--; gvcf->end++; // from 0-based to 1-based coordinate bcf_clear1(gvcf->line); gvcf->line->rid = gvcf->rid; gvcf->line->pos = gvcf->start; gvcf->line->rlen = gvcf->end - gvcf->start; bcf_update_alleles_str(hdr, gvcf->line, gvcf->als.s); if ( gvcf->start+1 < gvcf->end ) // create gVCF record only if it spans at least two sites bcf_update_info_int32(hdr, gvcf->line, "END", &gvcf->end, 1); bcf_update_info_int32(hdr, gvcf->line, "MIN_DP", &gvcf->min_dp, 1); if ( gvcf->nqsum>0 ) bcf_update_info_float(hdr, gvcf->line, "QS", gvcf->qsum, gvcf->nqsum); if ( gvcf->ngts ) bcf_update_genotypes(hdr,gvcf->line,gvcf->gts,gvcf->ngts); if ( gvcf->npl>0 ) bcf_update_format_int32(hdr, gvcf->line, "PL", gvcf->pl, gvcf->npl); bcf_update_format_int32(hdr, gvcf->line, "DP", gvcf->dp, nsmpl); if ( bcf_write1(fh, hdr, gvcf->line)!=0 ) error("[%s] Error: failed to write the record\n", __func__); gvcf->prev_range = 0; gvcf->rid = -1; gvcf->npl = 0; gvcf->nqsum = 0; gvcf->ngts = 0; if ( !rec ) return NULL; // just flushing the buffer, this was last record } if ( can_collapse ) { if ( !gvcf->prev_range ) { hts_expand(int32_t,nsmpl,gvcf->mdp,gvcf->dp); memcpy(gvcf->dp,gvcf->tmp,nsmpl*sizeof(int32_t)); // tmp still contains DP from rec gvcf->npl = bcf_get_format_int32(hdr, rec, "PL", &gvcf->pl, &gvcf->mpl); gvcf->nqsum = bcf_get_info_float(hdr,rec,"QS",&gvcf->qsum,&gvcf->mqsum); gvcf->ngts = bcf_get_genotypes(hdr,rec,&gvcf->gts,&gvcf->mgts); gvcf->rid = rec->rid; gvcf->start = rec->pos; gvcf->als.l = 0; kputs(rec->d.allele[0],&gvcf->als); for (i=1; in_allele; i++) { kputc(',',&gvcf->als); kputs(rec->d.allele[i],&gvcf->als); } gvcf->min_dp = min_dp; } else { if ( gvcf->min_dp > min_dp ) gvcf->min_dp = min_dp; for (i=0; idp[i] > gvcf->tmp[i] ) gvcf->dp[i] = gvcf->tmp[i]; ret = bcf_get_format_int32(hdr, rec, "PL", &gvcf->tmp, &gvcf->mtmp); if ( ret>=0 ) { if ( ret!=nsmpl*3 ) error("Unexpected number of PL fields\n"); for (i=0; ipl[3*i+1] > gvcf->tmp[3*i+1] ) { gvcf->pl[3*i+1] = gvcf->tmp[3*i+1]; gvcf->pl[3*i+2] = gvcf->tmp[3*i+2]; } else if ( gvcf->pl[3*i+1]==gvcf->tmp[3*i+1] && gvcf->pl[3*i+2] > gvcf->tmp[3*i+2] ) gvcf->pl[3*i+2] = gvcf->tmp[3*i+2]; } } else gvcf->npl = 0; } gvcf->prev_range = dp_range; if ( bcf_get_info_int32(hdr,rec,"END",&gvcf->tmp,&gvcf->mtmp)==1 ) gvcf->end = gvcf->tmp[0] - 1; // from 1-based to 0-based else gvcf->end = rec->pos; return NULL; } if ( is_ref && min_dp ) bcf_update_info_int32(hdr, rec, "MIN_DP", &min_dp, 1); return rec; } pysam-0.23.0/bcftools/gvcf.c.pysam.c000066400000000000000000000177251475062545500172330ustar00rootroot00000000000000#include "bcftools.pysam.h" /* gvcf.c -- support for gVCF files. Copyright (C) 2014-2015 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include "gvcf.h" #include "bcftools.h" struct _gvcf_t { int *dp_range, ndp_range; // per-sample DP ranges int prev_range; // 0 if not in a block int32_t *dp, mdp, *pl, mpl, npl; int32_t *tmp, mtmp, *gts, ngts,mgts, nqsum,mqsum; float *qsum; int32_t rid, start, end, min_dp; kstring_t als; bcf1_t *line; }; void gvcf_update_header(gvcf_t *gvcf, bcf_hdr_t *hdr) { bcf_hdr_append(hdr,"##INFO="); bcf_hdr_append(hdr,"##INFO="); } gvcf_t *gvcf_init(const char *dp_ranges) { gvcf_t *gvcf = (gvcf_t*) calloc(1,sizeof(gvcf_t)); gvcf->line = bcf_init(); int n = 1; const char *ss = dp_ranges; while ( *ss ) { if ( *ss==',' ) n++; ss++; } gvcf->ndp_range = n; gvcf->dp_range = (int*) malloc(sizeof(int)*gvcf->ndp_range); n = 0; ss = dp_ranges; while ( *ss ) { char *se = (char*) ss; gvcf->dp_range[n++] = strtol(ss,&se,10); if ( se==ss ) return NULL; if ( *se==',' && se[1] ) { ss = se+1; continue; } else if ( !*se ) break; return NULL; } return gvcf; } void gvcf_destroy(gvcf_t *gvcf) { free(gvcf->dp_range); free(gvcf->dp); free(gvcf->pl); free(gvcf->tmp); free(gvcf->qsum); free(gvcf->gts); free(gvcf->als.s); if ( gvcf->line ) bcf_destroy(gvcf->line); free(gvcf); } bcf1_t *gvcf_write(gvcf_t *gvcf, htsFile *fh, bcf_hdr_t *hdr, bcf1_t *rec, int is_ref) { int i, ret, nsmpl = bcf_hdr_nsamples(hdr); int can_collapse = is_ref ? 1 : 0; int32_t dp_range = 0, min_dp = 0; // No record and nothing to flush? if ( !rec && !gvcf->prev_range ) return NULL; // Flush gVCF block if there are no more records, chr changed, a gap // encountered, or other conditions not met (block broken by a non-ref or DP too low). int needs_flush = can_collapse ? 0 : 1; // Can the record be included in a gVCF block? That is, is this a ref-only site? if ( rec && can_collapse ) { bcf_unpack(rec, BCF_UN_ALL); // per-sample depth ret = bcf_get_format_int32(hdr, rec, "DP", &gvcf->tmp, &gvcf->mtmp); if ( ret==nsmpl ) { min_dp = gvcf->tmp[0]; for (i=1; i gvcf->tmp[i] ) min_dp = gvcf->tmp[i]; for (i=0; indp_range; i++) if ( min_dp < gvcf->dp_range[i] ) break; dp_range = i; if ( !dp_range ) { // leave the record unchanged, DP is too small. Alternatively, return NULL here // to skip these sites needs_flush = 1; can_collapse = 0; } } else needs_flush = 1; // DP field not present } if ( gvcf->prev_range && gvcf->prev_range!=dp_range ) needs_flush = 1; if ( !rec || gvcf->rid!=rec->rid || rec->pos > gvcf->end+1 ) needs_flush = 1; // If prev_range is set, something can be flushed if ( gvcf->prev_range && needs_flush ) { // mpileup can output two records with the same position, SNP and // indel. Make sure the end position does not include the non-variant // SNP position just before the indel. if ( rec && rec->rid==gvcf->rid && rec->pos==gvcf->end ) gvcf->end--; gvcf->end++; // from 0-based to 1-based coordinate bcf_clear1(gvcf->line); gvcf->line->rid = gvcf->rid; gvcf->line->pos = gvcf->start; gvcf->line->rlen = gvcf->end - gvcf->start; bcf_update_alleles_str(hdr, gvcf->line, gvcf->als.s); if ( gvcf->start+1 < gvcf->end ) // create gVCF record only if it spans at least two sites bcf_update_info_int32(hdr, gvcf->line, "END", &gvcf->end, 1); bcf_update_info_int32(hdr, gvcf->line, "MIN_DP", &gvcf->min_dp, 1); if ( gvcf->nqsum>0 ) bcf_update_info_float(hdr, gvcf->line, "QS", gvcf->qsum, gvcf->nqsum); if ( gvcf->ngts ) bcf_update_genotypes(hdr,gvcf->line,gvcf->gts,gvcf->ngts); if ( gvcf->npl>0 ) bcf_update_format_int32(hdr, gvcf->line, "PL", gvcf->pl, gvcf->npl); bcf_update_format_int32(hdr, gvcf->line, "DP", gvcf->dp, nsmpl); if ( bcf_write1(fh, hdr, gvcf->line)!=0 ) error("[%s] Error: failed to write the record\n", __func__); gvcf->prev_range = 0; gvcf->rid = -1; gvcf->npl = 0; gvcf->nqsum = 0; gvcf->ngts = 0; if ( !rec ) return NULL; // just flushing the buffer, this was last record } if ( can_collapse ) { if ( !gvcf->prev_range ) { hts_expand(int32_t,nsmpl,gvcf->mdp,gvcf->dp); memcpy(gvcf->dp,gvcf->tmp,nsmpl*sizeof(int32_t)); // tmp still contains DP from rec gvcf->npl = bcf_get_format_int32(hdr, rec, "PL", &gvcf->pl, &gvcf->mpl); gvcf->nqsum = bcf_get_info_float(hdr,rec,"QS",&gvcf->qsum,&gvcf->mqsum); gvcf->ngts = bcf_get_genotypes(hdr,rec,&gvcf->gts,&gvcf->mgts); gvcf->rid = rec->rid; gvcf->start = rec->pos; gvcf->als.l = 0; kputs(rec->d.allele[0],&gvcf->als); for (i=1; in_allele; i++) { kputc(',',&gvcf->als); kputs(rec->d.allele[i],&gvcf->als); } gvcf->min_dp = min_dp; } else { if ( gvcf->min_dp > min_dp ) gvcf->min_dp = min_dp; for (i=0; idp[i] > gvcf->tmp[i] ) gvcf->dp[i] = gvcf->tmp[i]; ret = bcf_get_format_int32(hdr, rec, "PL", &gvcf->tmp, &gvcf->mtmp); if ( ret>=0 ) { if ( ret!=nsmpl*3 ) error("Unexpected number of PL fields\n"); for (i=0; ipl[3*i+1] > gvcf->tmp[3*i+1] ) { gvcf->pl[3*i+1] = gvcf->tmp[3*i+1]; gvcf->pl[3*i+2] = gvcf->tmp[3*i+2]; } else if ( gvcf->pl[3*i+1]==gvcf->tmp[3*i+1] && gvcf->pl[3*i+2] > gvcf->tmp[3*i+2] ) gvcf->pl[3*i+2] = gvcf->tmp[3*i+2]; } } else gvcf->npl = 0; } gvcf->prev_range = dp_range; if ( bcf_get_info_int32(hdr,rec,"END",&gvcf->tmp,&gvcf->mtmp)==1 ) gvcf->end = gvcf->tmp[0] - 1; // from 1-based to 0-based else gvcf->end = rec->pos; return NULL; } if ( is_ref && min_dp ) bcf_update_info_int32(hdr, rec, "MIN_DP", &min_dp, 1); return rec; } pysam-0.23.0/bcftools/gvcf.h000066400000000000000000000030311475062545500156500ustar00rootroot00000000000000/* gvcf.[ch] - Helper functions for gVCF support The MIT License Copyright (c) 2015 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef __GVCF_H__ #define __GVCF_H__ #include "bcftools.h" typedef struct _gvcf_t gvcf_t; gvcf_t *gvcf_init(const char *dp_ranges); void gvcf_update_header(gvcf_t *gvcf, bcf_hdr_t *hdr); bcf1_t *gvcf_write(gvcf_t *gvcf, htsFile *fh, bcf_hdr_t *hdr, bcf1_t *rec, int is_ref); void gvcf_destroy(gvcf_t *gvcf); #endif pysam-0.23.0/bcftools/hclust.c000066400000000000000000000307271475062545500162340ustar00rootroot00000000000000/* The MIT License Copyright (c) 2016 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include "bcftools.h" #include "hclust.h" typedef struct _node_t { struct _node_t *akid, *bkid, *next, *prev, *parent; int id, idx; // id: unique node id; idx: current index to pdist float value; // max pairwise dist of elements within the node } node_t; struct _hclust_t { int ndat, nclust; // ndat: number of elements (pdist matrix size); nclust: current number of clusters float *pdist; // pairwise cluster distances, diagonal matrix accessed via the PDIST macro node_t *first, *last; // clusters are maintained in a double-linked list node_t **rmme; // convenience array to remove all allocated nodes at the end int nrmme; kstring_t str; // (for debugging) pointer to str.s is returned by create_dot() char **dbg; // (for debugging) created by create_list() via set_threshold() and returned by explain() int ndbg, mdbg; }; node_t *append_node(hclust_t *clust, int idx) { node_t *node = (node_t*) calloc(1,sizeof(node_t)); clust->nclust++; node->id = clust->nrmme; node->idx = idx; if ( !clust->first ) { clust->first = node; clust->last = node; } else { node->prev = clust->last; clust->last->next = node; clust->last = node; } if ( clust->nrmme >= clust->ndat*2 ) error("hclust fixme: %d vs %d\n",clust->nrmme,clust->ndat); clust->rmme[clust->nrmme++] = node; return node; } void remove_node(hclust_t *clust, node_t *node) { if ( node==clust->first ) clust->first = node->next; if ( node==clust->last ) clust->last = node->prev; if ( node->next ) node->next->prev = node->prev; if ( node->prev ) node->prev->next = node->next; clust->nclust--; } #if DEBUG void hclust_debug(hclust_t *clust) { int i; fprintf(stderr,"nrmme=%d nclust=%d\n", clust->nrmme,clust->nclust); for (i=0; inrmme; i++) { node_t *node = clust->rmme[i]; int akid = node->akid ? node->akid->id : -1; int bkid = node->bkid ? node->bkid->id : -1; int akidx = node->akid ? node->akid->idx : -1; int bkidx = node->bkid ? node->bkid->idx : -1; fprintf(stderr,"\t%d\t%d\t%f\t%d %d\t%d %d\n",node->id,node->idx,node->value,akid,bkid,akidx,bkidx); } int j; for (i=1; indat; i++) { int active = 0; node_t *node = clust->first; while (node) { if ( node->idx==i ) { active=1; break; } node = node->next; } fprintf(stderr,"%2d%c ",i,active?'*':' '); for (j=0; jpdist,i,j)==9 ) fprintf(stderr," ----- "); else fprintf(stderr," %f", PDIST(clust->pdist,i,j)); } fprintf(stderr,"\n"); } for (j=0; jndat-1; j++) fprintf(stderr," %6d ",j); fprintf(stderr,"\n"); } #endif hclust_t *hclust_init(int n, float *pdist) { hclust_t *clust = (hclust_t*) calloc(1,sizeof(hclust_t)); clust->ndat = n; clust->pdist = pdist; clust->rmme = (node_t**) calloc(n*2,sizeof(node_t*)); // init clusters int i; for (i=0; indat; i++) append_node(clust,i); // build the tree while ( clust->nclust>1 ) { // find two clusters with minimum distance float min_value = HUGE_VAL; node_t *iclust = clust->first->next; node_t *min_iclust = NULL, *min_jclust = NULL; while ( iclust ) { node_t *jclust = clust->first; while ( jclust!=iclust ) { float value = PDIST(clust->pdist,iclust->idx,jclust->idx); if ( value < min_value ) { min_value = value; min_iclust = iclust; min_jclust = jclust; } jclust = jclust->next; } iclust = iclust->next; } assert( min_iclust && min_jclust ); // pdist contains inf or nan, fix the caller remove_node(clust,min_iclust); remove_node(clust,min_jclust); // update the pairwise distances. We keep the matrix and as we are moving up the // tree, we use fewer columns/rows as the number of clusters decreases: we reuse // i-th and leave j-th unused. Inter-cluster distance is defined as maximum distance // between pairwise distances of elements within the cluster. iclust = clust->first; while ( iclust ) { if ( PDIST(clust->pdist,iclust->idx,min_iclust->idx) < PDIST(clust->pdist,iclust->idx,min_jclust->idx) ) PDIST(clust->pdist,iclust->idx,min_iclust->idx) = PDIST(clust->pdist,iclust->idx,min_jclust->idx); iclust = iclust->next; } node_t *node = append_node(clust,min_iclust->idx); node->akid = min_iclust; node->bkid = min_jclust; node->value = min_value; node->akid->parent = node; node->bkid->parent = node; } return clust; } void hclust_destroy(hclust_t *clust) { int i; for (i=0; inrmme; i++) free(clust->rmme[i]); free(clust->rmme); free(clust->dbg); free(clust->str.s); free(clust); } char *hclust_create_dot(hclust_t *clust, char **labels, float th) { clust->str.l = 0; ksprintf(&clust->str,"digraph myGraph {"); int i; for (i=0; inrmme; i++) { node_t *node = clust->rmme[i]; if ( node->value ) ksprintf(&clust->str,"\"%d\" [label=\"%f\"];", node->id,node->value); else ksprintf(&clust->str,"\"%d\" [label=\"%s\"];", node->id,labels[node->idx]); } for (i=0; inrmme; i++) { node_t *node = clust->rmme[i]; if ( node->akid ) { if ( node->value >= th && node->akid && node->akid->value < th ) ksprintf(&clust->str,"\"%d\" -> \"%d\" [color=\"#D43F3A\" penwidth=3];", node->id,node->akid->id); else ksprintf(&clust->str,"\"%d\" -> \"%d\";", node->id,node->akid->id); } if ( node->bkid ) { if ( node->value >= th && node->bkid && node->bkid->value < th ) ksprintf(&clust->str,"\"%d\" -> \"%d\" [color=\"#D43F3A\" penwidth=3];", node->id,node->bkid->id); else ksprintf(&clust->str,"\"%d\" -> \"%d\";", node->id,node->bkid->id); } } ksprintf(&clust->str,"};"); return clust->str.s; } char **hclust_explain(hclust_t *clust, int *nlines) { clust->ndbg = 0; char *beg = clust->str.s; while ( *beg ) { char *end = beg; while ( *end && *end!='\n' ) end++; clust->ndbg++; hts_expand(char*,clust->ndbg,clust->mdbg,clust->dbg); clust->dbg[clust->ndbg-1] = beg; if ( !*end ) break; *end = 0; beg = end + 1; } *nlines = clust->ndbg; return clust->dbg; } cluster_t *append_cluster(node_t *node, cluster_t *cluster, int *nclust, node_t **stack) { (*nclust)++; cluster = (cluster_t*) realloc(cluster,sizeof(cluster_t)*(*nclust)); cluster_t *clust = &cluster[*nclust-1]; clust->nmemb = 0; clust->memb = NULL; clust->dist = node->value; int nstack = 1; stack[0] = node; while ( nstack ) { node_t *node = stack[--nstack]; node_t *akid = node->akid; node_t *bkid = node->bkid; if ( node->akid ) { stack[nstack++] = akid; stack[nstack++] = bkid; } else { clust->nmemb++; clust->memb = (int*) realloc(clust->memb,sizeof(int)*clust->nmemb); clust->memb[clust->nmemb-1] = node->id; } } return cluster; } int cmp_nodes(const void *a, const void *b) { const node_t *an = *((const node_t**) a); const node_t *bn = *((const node_t**) b); if ( an->value < bn->value ) return -1; if ( an->value > bn->value ) return 1; return 0; } float calc_dev(node_t **dat, int n) { float avg = 0, dev = 0; int i; for (i=0; ivalue; avg /= n; for (i=0; ivalue - avg)*(dat[i]->value - avg); return sqrt(dev/n); } /* Heuristics to determine clustering cutoff: sort nodes by distance and split into two groups by minimizing the standard deviation. This works best when two elements from a single different sample are included in the mix. - min_inter_dist .. smaller values are always considered identical - max_intra_dist .. larger values are always considered different */ float hclust_set_threshold(hclust_t *clust, float min_inter_dist, float max_intra_dist) { node_t **dat = clust->rmme + clust->ndat; int i, ndat = clust->nrmme - clust->ndat; qsort(dat, ndat, sizeof(dat), cmp_nodes); clust->str.l = 0; float th, min_dev = HUGE_VAL; int imin = -1; for (i=0; i0 ) dev += calc_dev(dat,i); if ( i+1value; ksprintf(&clust->str,"DEV\t%f\t%f\n",th,dev); if ( min_dev > dev && th >= min_inter_dist ) { min_dev = dev; imin = i; } } if ( max_intra_dist > 0 ) th = max_intra_dist; // use fixed cutoff, the above was only for debugging output else { // dynamic cutoff max_intra_dist = fabs(max_intra_dist); th = imin==-1 ? max_intra_dist : dat[imin]->value; if ( th > max_intra_dist ) th = max_intra_dist; } ksprintf(&clust->str,"TH\t%f\n", th); ksprintf(&clust->str,"MAX_DIST\t%f\n", dat[ndat-1]->value); ksprintf(&clust->str,"MIN_INTER\t%f\n", min_inter_dist); ksprintf(&clust->str,"MAX_INTRA\t%f\n", max_intra_dist); return th; } cluster_t *hclust_create_list(hclust_t *clust, float min_inter_dist, float *max_intra_dist, int *nclust) { float cutoff = *max_intra_dist = hclust_set_threshold(clust, min_inter_dist, *max_intra_dist); node_t **stack = (node_t**) malloc(sizeof(node_t*)*clust->ndat); node_t **tmp = (node_t**) malloc(sizeof(node_t*)*clust->ndat); stack[0] = clust->first; int nstack = 1; cluster_t *cluster = NULL; int ncluster = 0; if ( stack[0]->value < cutoff ) { // all values are within the limits - create a single cluster cluster = append_cluster(stack[0], cluster, &ncluster, tmp); nstack = 0; } while ( nstack ) { node_t *node = stack[--nstack]; node_t *akid = node->akid; node_t *bkid = node->bkid; if ( !akid ) { cluster = append_cluster(node, cluster, &ncluster, tmp); continue; } if ( node->value >= cutoff && akid->value < cutoff ) cluster = append_cluster(akid, cluster, &ncluster, tmp); else stack[nstack++] = akid; if ( node->value >= cutoff && bkid->value < cutoff ) cluster = append_cluster(bkid, cluster, &ncluster, tmp); else stack[nstack++] = bkid; } free(tmp); free(stack); *nclust = ncluster; return cluster; } void hclust_destroy_list(cluster_t *clust, int nclust) { int i; for (i=0; i Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include "bcftools.h" #include "hclust.h" typedef struct _node_t { struct _node_t *akid, *bkid, *next, *prev, *parent; int id, idx; // id: unique node id; idx: current index to pdist float value; // max pairwise dist of elements within the node } node_t; struct _hclust_t { int ndat, nclust; // ndat: number of elements (pdist matrix size); nclust: current number of clusters float *pdist; // pairwise cluster distances, diagonal matrix accessed via the PDIST macro node_t *first, *last; // clusters are maintained in a double-linked list node_t **rmme; // convenience array to remove all allocated nodes at the end int nrmme; kstring_t str; // (for debugging) pointer to str.s is returned by create_dot() char **dbg; // (for debugging) created by create_list() via set_threshold() and returned by explain() int ndbg, mdbg; }; node_t *append_node(hclust_t *clust, int idx) { node_t *node = (node_t*) calloc(1,sizeof(node_t)); clust->nclust++; node->id = clust->nrmme; node->idx = idx; if ( !clust->first ) { clust->first = node; clust->last = node; } else { node->prev = clust->last; clust->last->next = node; clust->last = node; } if ( clust->nrmme >= clust->ndat*2 ) error("hclust fixme: %d vs %d\n",clust->nrmme,clust->ndat); clust->rmme[clust->nrmme++] = node; return node; } void remove_node(hclust_t *clust, node_t *node) { if ( node==clust->first ) clust->first = node->next; if ( node==clust->last ) clust->last = node->prev; if ( node->next ) node->next->prev = node->prev; if ( node->prev ) node->prev->next = node->next; clust->nclust--; } #if DEBUG void hclust_debug(hclust_t *clust) { int i; fprintf(bcftools_stderr,"nrmme=%d nclust=%d\n", clust->nrmme,clust->nclust); for (i=0; inrmme; i++) { node_t *node = clust->rmme[i]; int akid = node->akid ? node->akid->id : -1; int bkid = node->bkid ? node->bkid->id : -1; int akidx = node->akid ? node->akid->idx : -1; int bkidx = node->bkid ? node->bkid->idx : -1; fprintf(bcftools_stderr,"\t%d\t%d\t%f\t%d %d\t%d %d\n",node->id,node->idx,node->value,akid,bkid,akidx,bkidx); } int j; for (i=1; indat; i++) { int active = 0; node_t *node = clust->first; while (node) { if ( node->idx==i ) { active=1; break; } node = node->next; } fprintf(bcftools_stderr,"%2d%c ",i,active?'*':' '); for (j=0; jpdist,i,j)==9 ) fprintf(bcftools_stderr," ----- "); else fprintf(bcftools_stderr," %f", PDIST(clust->pdist,i,j)); } fprintf(bcftools_stderr,"\n"); } for (j=0; jndat-1; j++) fprintf(bcftools_stderr," %6d ",j); fprintf(bcftools_stderr,"\n"); } #endif hclust_t *hclust_init(int n, float *pdist) { hclust_t *clust = (hclust_t*) calloc(1,sizeof(hclust_t)); clust->ndat = n; clust->pdist = pdist; clust->rmme = (node_t**) calloc(n*2,sizeof(node_t*)); // init clusters int i; for (i=0; indat; i++) append_node(clust,i); // build the tree while ( clust->nclust>1 ) { // find two clusters with minimum distance float min_value = HUGE_VAL; node_t *iclust = clust->first->next; node_t *min_iclust = NULL, *min_jclust = NULL; while ( iclust ) { node_t *jclust = clust->first; while ( jclust!=iclust ) { float value = PDIST(clust->pdist,iclust->idx,jclust->idx); if ( value < min_value ) { min_value = value; min_iclust = iclust; min_jclust = jclust; } jclust = jclust->next; } iclust = iclust->next; } assert( min_iclust && min_jclust ); // pdist contains inf or nan, fix the caller remove_node(clust,min_iclust); remove_node(clust,min_jclust); // update the pairwise distances. We keep the matrix and as we are moving up the // tree, we use fewer columns/rows as the number of clusters decreases: we reuse // i-th and leave j-th unused. Inter-cluster distance is defined as maximum distance // between pairwise distances of elements within the cluster. iclust = clust->first; while ( iclust ) { if ( PDIST(clust->pdist,iclust->idx,min_iclust->idx) < PDIST(clust->pdist,iclust->idx,min_jclust->idx) ) PDIST(clust->pdist,iclust->idx,min_iclust->idx) = PDIST(clust->pdist,iclust->idx,min_jclust->idx); iclust = iclust->next; } node_t *node = append_node(clust,min_iclust->idx); node->akid = min_iclust; node->bkid = min_jclust; node->value = min_value; node->akid->parent = node; node->bkid->parent = node; } return clust; } void hclust_destroy(hclust_t *clust) { int i; for (i=0; inrmme; i++) free(clust->rmme[i]); free(clust->rmme); free(clust->dbg); free(clust->str.s); free(clust); } char *hclust_create_dot(hclust_t *clust, char **labels, float th) { clust->str.l = 0; ksprintf(&clust->str,"digraph myGraph {"); int i; for (i=0; inrmme; i++) { node_t *node = clust->rmme[i]; if ( node->value ) ksprintf(&clust->str,"\"%d\" [label=\"%f\"];", node->id,node->value); else ksprintf(&clust->str,"\"%d\" [label=\"%s\"];", node->id,labels[node->idx]); } for (i=0; inrmme; i++) { node_t *node = clust->rmme[i]; if ( node->akid ) { if ( node->value >= th && node->akid && node->akid->value < th ) ksprintf(&clust->str,"\"%d\" -> \"%d\" [color=\"#D43F3A\" penwidth=3];", node->id,node->akid->id); else ksprintf(&clust->str,"\"%d\" -> \"%d\";", node->id,node->akid->id); } if ( node->bkid ) { if ( node->value >= th && node->bkid && node->bkid->value < th ) ksprintf(&clust->str,"\"%d\" -> \"%d\" [color=\"#D43F3A\" penwidth=3];", node->id,node->bkid->id); else ksprintf(&clust->str,"\"%d\" -> \"%d\";", node->id,node->bkid->id); } } ksprintf(&clust->str,"};"); return clust->str.s; } char **hclust_explain(hclust_t *clust, int *nlines) { clust->ndbg = 0; char *beg = clust->str.s; while ( *beg ) { char *end = beg; while ( *end && *end!='\n' ) end++; clust->ndbg++; hts_expand(char*,clust->ndbg,clust->mdbg,clust->dbg); clust->dbg[clust->ndbg-1] = beg; if ( !*end ) break; *end = 0; beg = end + 1; } *nlines = clust->ndbg; return clust->dbg; } cluster_t *append_cluster(node_t *node, cluster_t *cluster, int *nclust, node_t **stack) { (*nclust)++; cluster = (cluster_t*) realloc(cluster,sizeof(cluster_t)*(*nclust)); cluster_t *clust = &cluster[*nclust-1]; clust->nmemb = 0; clust->memb = NULL; clust->dist = node->value; int nstack = 1; stack[0] = node; while ( nstack ) { node_t *node = stack[--nstack]; node_t *akid = node->akid; node_t *bkid = node->bkid; if ( node->akid ) { stack[nstack++] = akid; stack[nstack++] = bkid; } else { clust->nmemb++; clust->memb = (int*) realloc(clust->memb,sizeof(int)*clust->nmemb); clust->memb[clust->nmemb-1] = node->id; } } return cluster; } int cmp_nodes(const void *a, const void *b) { const node_t *an = *((const node_t**) a); const node_t *bn = *((const node_t**) b); if ( an->value < bn->value ) return -1; if ( an->value > bn->value ) return 1; return 0; } float calc_dev(node_t **dat, int n) { float avg = 0, dev = 0; int i; for (i=0; ivalue; avg /= n; for (i=0; ivalue - avg)*(dat[i]->value - avg); return sqrt(dev/n); } /* Heuristics to determine clustering cutoff: sort nodes by distance and split into two groups by minimizing the standard deviation. This works best when two elements from a single different sample are included in the mix. - min_inter_dist .. smaller values are always considered identical - max_intra_dist .. larger values are always considered different */ float hclust_set_threshold(hclust_t *clust, float min_inter_dist, float max_intra_dist) { node_t **dat = clust->rmme + clust->ndat; int i, ndat = clust->nrmme - clust->ndat; qsort(dat, ndat, sizeof(dat), cmp_nodes); clust->str.l = 0; float th, min_dev = HUGE_VAL; int imin = -1; for (i=0; i0 ) dev += calc_dev(dat,i); if ( i+1value; ksprintf(&clust->str,"DEV\t%f\t%f\n",th,dev); if ( min_dev > dev && th >= min_inter_dist ) { min_dev = dev; imin = i; } } if ( max_intra_dist > 0 ) th = max_intra_dist; // use fixed cutoff, the above was only for debugging output else { // dynamic cutoff max_intra_dist = fabs(max_intra_dist); th = imin==-1 ? max_intra_dist : dat[imin]->value; if ( th > max_intra_dist ) th = max_intra_dist; } ksprintf(&clust->str,"TH\t%f\n", th); ksprintf(&clust->str,"MAX_DIST\t%f\n", dat[ndat-1]->value); ksprintf(&clust->str,"MIN_INTER\t%f\n", min_inter_dist); ksprintf(&clust->str,"MAX_INTRA\t%f\n", max_intra_dist); return th; } cluster_t *hclust_create_list(hclust_t *clust, float min_inter_dist, float *max_intra_dist, int *nclust) { float cutoff = *max_intra_dist = hclust_set_threshold(clust, min_inter_dist, *max_intra_dist); node_t **stack = (node_t**) malloc(sizeof(node_t*)*clust->ndat); node_t **tmp = (node_t**) malloc(sizeof(node_t*)*clust->ndat); stack[0] = clust->first; int nstack = 1; cluster_t *cluster = NULL; int ncluster = 0; if ( stack[0]->value < cutoff ) { // all values are within the limits - create a single cluster cluster = append_cluster(stack[0], cluster, &ncluster, tmp); nstack = 0; } while ( nstack ) { node_t *node = stack[--nstack]; node_t *akid = node->akid; node_t *bkid = node->bkid; if ( !akid ) { cluster = append_cluster(node, cluster, &ncluster, tmp); continue; } if ( node->value >= cutoff && akid->value < cutoff ) cluster = append_cluster(akid, cluster, &ncluster, tmp); else stack[nstack++] = akid; if ( node->value >= cutoff && bkid->value < cutoff ) cluster = append_cluster(bkid, cluster, &ncluster, tmp); else stack[nstack++] = bkid; } free(tmp); free(stack); *nclust = ncluster; return cluster; } void hclust_destroy_list(cluster_t *clust, int nclust) { int i; for (i=0; i Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Simple hierarchical clustering */ #ifndef __HCLUST_H__ #define __HCLUST_H__ #include typedef struct _hclust_t hclust_t; typedef struct { float dist; int nmemb, *memb; } cluster_t; #define PDIST(mat,a,b) (mat)[((a)>(b)?((a)*((a)-1)/2+(b)):((b)*((b)-1)/2+(a)))] /* * hclust_init() - init and run clustering * @n: number of elements * @pdist: pairwise distances. The array will be modified by hclust and * must exist until hclust_destroy() is called */ hclust_t *hclust_init(int n, float *pdist); void hclust_destroy(hclust_t *clust); /* * hclust_create_list() - returns a list of clusters * @min_inter_dist: minimum inter-cluster distance. If smaller, elements are considered * homogenous, belonging to the same cluster. * @max_intra_dist: maximum intra-cluster distance allowed. If smaller than 0, * the threshold can be heuristically lowered, otherwise considered * a fixed cutoff. The pointer will be filled to the cutoff actually used. */ cluster_t *hclust_create_list(hclust_t *clust, float min_inter_dist, float *max_intra_dist, int *nclust); void hclust_destroy_list(cluster_t *clust, int nclust); /* * Access debugging data used in the decision making process. Note that this * must be called immediately after hclust_create_list because other calls, * such as hclust_create_dot(), invalidate the temporary data structures. */ char **hclust_explain(hclust_t *clust, int *nlines); char *hclust_create_dot(hclust_t *clust, char **labels, float th); #endif pysam-0.23.0/bcftools/hex.h000066400000000000000000000057151475062545500155220ustar00rootroot00000000000000// VariantKey // // hex.h // // @category Libraries // @author Nicola Asuni // @link https://github.com/tecnickcom/variantkey // @license MIT [LICENSE](https://raw.githubusercontent.com/tecnickcom/variantkey/main/LICENSE) // @copyright 2017-2018 GENOMICS plc // // LICENSE // // Copyright (c) 2017-2018 GENOMICS plc // // Permission is hereby granted, free of charge, to any person obtaining a copy // of this software and associated documentation files (the "Software"), to deal // in the Software without restriction, including without limitation the rights // to use, copy, modify, merge, publish, distribute, sublicense, and/or sell // copies of the Software, and to permit persons to whom the Software is // furnished to do so, subject to the following conditions: // // The above copyright notice and this permission notice shall be included in // all copies or substantial portions of the Software. // // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR // IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, // FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE // AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER // LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN // THE SOFTWARE. /** * @file hex.h * @brief Utility functions to manipulate strings. * * Collection of utility functions to manipulate strings. */ #ifndef ASTRING_H #define ASTRING_H #include #include /** @brief Returns uint64_t hexadecimal string (16 characters). * * @param n Number to parse * @param str String buffer to be returned (it must be sized 17 bytes at least). * * @return Upon successful return, these function returns the number of characters processed * (excluding the null byte used to end output to strings). * If the buffer size is not sufficient, then the return value is the number of characters required for * buffer string, including the terminating null byte. */ static inline size_t hex_uint64_t(uint64_t n, char *str) { return sprintf(str, "%016" PRIx64, n); } /** @brief Parses a 16 chars hexadecimal string and returns the code. * * @param s Hexadecimal string to parse (it must contain 16 hexadecimal characters). * * @return uint64_t unsigned integer number. */ static inline uint64_t parse_hex_uint64_t(const char *s) { uint64_t v = 0; uint8_t b; size_t i; for (i = 0; i < 16; i++) { b = s[i]; if (b >= 'a') { b -= ('a' - 10); // a-f } else { if (b >= 'A') { b -= ('A' - 10); // A-F } else { b -= '0'; // 0-9 } } v = ((v << 4) | b); } return v; } #endif // ASTRING_H pysam-0.23.0/bcftools/khash_str2str.h000066400000000000000000000061331475062545500175320ustar00rootroot00000000000000/* khash_str2str.h -- C-string to C-string hash table. Copyright (C) 2014,2016 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef KHASH_STR2STR_H #define KHASH_STR2STR_H #include KHASH_MAP_INIT_STR(str2str, const char*) /* * Wrappers for khash dictionaries used by mpileup. */ static inline void *khash_str2str_init(void) { return kh_init(str2str); } /* * Destroy the hash structure, but not the keys */ static inline void khash_str2str_destroy(void *_hash) { khash_t(str2str) *hash = (khash_t(str2str)*)_hash; if (hash) kh_destroy(str2str, hash); // Note that strings are not freed. } /* * Destroys both the hash structure and the keys */ static inline void khash_str2str_destroy_free(void *_hash) { khash_t(str2str) *hash = (khash_t(str2str)*)_hash; khint_t k; if (hash == 0) return; for (k = 0; k < kh_end(hash); ++k) if (kh_exist(hash, k)) free((char*)kh_key(hash, k)); kh_destroy(str2str, hash); } /* * Destroys the hash structure, the keys and the values */ static inline void khash_str2str_destroy_free_all(void *_hash) { khash_t(str2str) *hash = (khash_t(str2str)*)_hash; khint_t k; if (hash == 0) return; for (k = 0; k < kh_end(hash); ++k) if (kh_exist(hash, k)) { free((char*)kh_key(hash, k)); free((char*)kh_val(hash, k)); } kh_destroy(str2str, hash); } /* * Returns value if key exists or NULL if not */ static inline char *khash_str2str_get(void *_hash, const char *str) { khash_t(str2str) *hash = (khash_t(str2str)*)_hash; khint_t k = kh_get(str2str, hash, str); if ( k == kh_end(hash) ) return NULL; return (char*)kh_val(hash, k); } /* * Set a new key,value pair. On success returns the bin index, on * error -1 is returned. */ static inline int khash_str2str_set(void *_hash, const char *str, const char *value) { khint_t k; int ret; khash_t(str2str) *hash = (khash_t(str2str)*)_hash; if ( !hash ) return -1; k = kh_put(str2str, hash, str, &ret); kh_val(hash,k) = value; return k; } #endif pysam-0.23.0/bcftools/kheap.h000066400000000000000000000170561475062545500160270ustar00rootroot00000000000000/* The MIT License Copyright (C) 2016 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Usage example: #include "kheap.h" // First we prepare the user data to store, in this example it is a // struct with a single element "key", and a comparator function // "is_smaller". In this example the comparator defines a min heap (as // opposed to a max heap). typedef struct { uint32_t key; } data_t; static inline int is_smaller(data_t *a, data_t *b) { return a->key < b->key ? 1 : 0; } data_t data[3] = { {3}, {2}, {1} }; // Heap declaration, "mh" is an arbitrary string. The typedef is not // required, it is just a convenience shortcut so that we can use // "heap_t" instead of the generic "khp_mh_t" automatically created by // the KHEAP_INIT macro. KHEAP_INIT(mh, data_t, is_smaller) typedef khp_mh_t heap_t; // Initialize the heap, insert the test data, then retrieve them back, // sorted. Multiple heaps with the same name "mh" can be created and // used simultaneously, as long as they all use the same data type // "data_t". heap_t *heap = khp_init(mh); // When inserting a new element, the heap stores a copy of the memory // area pointed to by the third argument. for (int i=0; i<3; i++) khp_insert(mh, heap, &data[i]); while (heap->ndat) { printf("%d\n", heap->dat[0].pos); khp_delete(mh, heap); } // Clean up khp_destroy(mh, heap); */ #ifndef __KHEAP_H__ #define __KHEAP_H__ #include #ifndef kroundup32 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif #ifndef kh_inline #ifdef _MSC_VER #define kh_inline __inline #else #define kh_inline inline #endif #endif /* kh_inline */ #ifndef klib_unused #if (defined __clang__ && __clang_major__ >= 3) || (defined __GNUC__ && __GNUC__ >= 3) #define klib_unused __attribute__ ((__unused__)) #else #define klib_unused #endif #endif /* klib_unused */ #define __KHEAP_TYPE(name, kheap_t) \ typedef struct { \ int ndat, mdat; \ kheap_t *dat; \ kheap_t tmp; \ } khp_##name##_t; #define khp_parent(i) (((i)-1)/2) #define khp_lchild(i) (2*(i)+1) #define khp_rchild(i) (2*(i)+2) #define khp_swap(hp,i,j) { \ ((hp)->tmp) = ((hp)->dat[i]); \ ((hp)->dat[i]) = ((hp)->dat[j]); \ ((hp)->dat[j]) = ((hp)->tmp); \ } #define __KHEAP_IMPL(name, SCOPE, kheap_t, __cmp) \ SCOPE khp_##name##_t *khp_init_##name(void) \ { \ return (khp_##name##_t*)calloc(1, sizeof(khp_##name##_t)); \ } \ SCOPE void khp_destroy_##name(khp_##name##_t *heap) \ { \ if (heap) free(heap->dat); \ free(heap); \ } \ SCOPE int khp_insert_##name(khp_##name##_t *heap, kheap_t *dat) \ { \ heap->ndat++; \ if ( heap->ndat > heap->mdat ) \ { \ heap->mdat = heap->ndat; \ kroundup32(heap->mdat); \ heap->dat = (kheap_t*)realloc(heap->dat, heap->mdat*sizeof(kheap_t)); \ memset(heap->dat + heap->ndat, 0, (heap->mdat - heap->ndat)*sizeof(kheap_t)); \ } \ int i = heap->ndat - 1; \ while ( i && __cmp(dat,&heap->dat[khp_parent(i)]) ) \ { \ heap->dat[i] = heap->dat[khp_parent(i)]; \ i = khp_parent(i); \ } \ heap->dat[i] = *dat; \ return i; \ } \ SCOPE void khp_heapify_##name(khp_##name##_t *heap, int i) \ { \ /*todo: loop instead of a recursive function? */ \ int extreme = khp_lchild(i) < heap->ndat && __cmp(&heap->dat[khp_lchild(i)],&heap->dat[i]) ? khp_lchild(i) : i; \ if ( khp_rchild(i) < heap->ndat && __cmp(&heap->dat[khp_rchild(i)],&heap->dat[extreme]) ) extreme = khp_rchild(i); \ if ( extreme != i ) \ { \ khp_swap(heap,i,extreme); \ khp_heapify_##name(heap,extreme); \ } \ } \ SCOPE void khp_delete_##name(khp_##name##_t *heap) \ { \ if ( !heap || !heap->ndat ) return; \ heap->dat[0] = heap->dat[--heap->ndat]; \ khp_heapify_##name(heap, 0); \ } \ #define KHEAP_INIT(name, kheap_t, __cmp) \ __KHEAP_TYPE(name, kheap_t) \ __KHEAP_IMPL(name, static kh_inline klib_unused, kheap_t, __cmp) #define khp_init(name) khp_init_##name() #define khp_destroy(name, heap) khp_destroy_##name(heap) #define khp_insert(name, heap, dat) khp_insert_##name(heap, dat) #define khp_delete(name, heap) khp_delete_##name(heap) #endif pysam-0.23.0/bcftools/kmin.c000066400000000000000000000161451475062545500156660ustar00rootroot00000000000000/* The MIT License Copyright (c) 2008, 2010 by Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Hooke-Jeeves algorithm for nonlinear minimization Based on the pseudocodes by Bell and Pike (CACM 9(9):684-685), and the revision by Tomlin and Smith (CACM 12(11):637-638). Both of the papers are comments on Kaupe's Algorithm 178 "Direct Search" (ACM 6(6):313-314). The original algorithm was designed by Hooke and Jeeves (ACM 8:212-229). This program is further revised according to Johnson's implementation at Netlib (opt/hooke.c). Hooke-Jeeves algorithm is very simple and it works quite well on a few examples. However, it might fail to converge due to its heuristic nature. A possible improvement, as is suggested by Johnson, may be to choose a small r at the beginning to quickly approach to the minimum and a large r at later step to hit the minimum. */ #include #include #include #include "kmin.h" static double __kmin_hj_aux(kmin_f func, int n, double *x1, void *data, double fx1, double *dx, int *n_calls) { int k, j = *n_calls; double ftmp; for (k = 0; k != n; ++k) { x1[k] += dx[k]; ftmp = func(n, x1, data); ++j; if (ftmp < fx1) fx1 = ftmp; else { /* search the opposite direction */ dx[k] = 0.0 - dx[k]; x1[k] += dx[k] + dx[k]; ftmp = func(n, x1, data); ++j; if (ftmp < fx1) fx1 = ftmp; else x1[k] -= dx[k]; /* back to the original x[k] */ } } *n_calls = j; return fx1; /* here: fx1=f(n,x1) */ } double kmin_hj(kmin_f func, int n, double *x, void *data, double r, double eps, int max_calls) { double fx, fx1, *x1, *dx, radius; int k, n_calls = 0; x1 = (double*)calloc(n, sizeof(double)); dx = (double*)calloc(n, sizeof(double)); for (k = 0; k != n; ++k) { /* initial directions, based on MGJ */ dx[k] = fabs(x[k]) * r; if (dx[k] == 0) dx[k] = r; } radius = r; fx1 = fx = func(n, x, data); ++n_calls; for (;;) { memcpy(x1, x, n * sizeof(double)); /* x1 = x */ fx1 = __kmin_hj_aux(func, n, x1, data, fx, dx, &n_calls); while (fx1 < fx) { for (k = 0; k != n; ++k) { double t = x[k]; dx[k] = x1[k] > x[k]? fabs(dx[k]) : 0.0 - fabs(dx[k]); x[k] = x1[k]; x1[k] = x1[k] + x1[k] - t; } fx = fx1; if (n_calls >= max_calls) break; fx1 = func(n, x1, data); ++n_calls; fx1 = __kmin_hj_aux(func, n, x1, data, fx1, dx, &n_calls); if (fx1 >= fx) break; for (k = 0; k != n; ++k) if (fabs(x1[k] - x[k]) > .5 * fabs(dx[k])) break; if (k == n) break; } if (radius >= eps) { if (n_calls >= max_calls) break; radius *= r; for (k = 0; k != n; ++k) dx[k] *= r; } else break; /* converge */ } free(x1); free(dx); return fx1; } // I copied this function somewhere several years ago with some of my modifications, but I forgot the source. double kmin_brent(kmin1_f func, double a, double b, void *data, double tol, double *xmin) { double bound, u, r, q, fu, tmp, fa, fb, fc, c; const double gold1 = 1.6180339887; const double gold2 = 0.3819660113; const double tiny = 1e-20; const int max_iter = 100; double e, d, w, v, mid, tol1, tol2, p, eold, fv, fw; int iter; fa = func(a, data); fb = func(b, data); if (fb > fa) { // swap, such that f(a) > f(b) tmp = a; a = b; b = tmp; tmp = fa; fa = fb; fb = tmp; } c = b + gold1 * (b - a), fc = func(c, data); // golden section extrapolation while (fb > fc) { bound = b + 100.0 * (c - b); // the farthest point where we want to go r = (b - a) * (fb - fc); q = (b - c) * (fb - fa); if (fabs(q - r) < tiny) { // avoid 0 denominator tmp = q > r? tiny : 0.0 - tiny; } else tmp = q - r; u = b - ((b - c) * q - (b - a) * r) / (2.0 * tmp); // u is the parabolic extrapolation point if ((b > u && u > c) || (b < u && u < c)) { // u lies between b and c fu = func(u, data); if (fu < fc) { // (b,u,c) bracket the minimum a = b; b = u; fa = fb; fb = fu; break; } else if (fu > fb) { // (a,b,u) bracket the minimum c = u; fc = fu; break; } u = c + gold1 * (c - b); fu = func(u, data); // golden section extrapolation } else if ((c > u && u > bound) || (c < u && u < bound)) { // u lies between c and bound fu = func(u, data); if (fu < fc) { // fb > fc > fu b = c; c = u; u = c + gold1 * (c - b); fb = fc; fc = fu; fu = func(u, data); } else { // (b,c,u) bracket the minimum a = b; b = c; c = u; fa = fb; fb = fc; fc = fu; break; } } else if ((u > bound && bound > c) || (u < bound && bound < c)) { // u goes beyond the bound u = bound; fu = func(u, data); } else { // u goes the other way around, use golden section extrapolation u = c + gold1 * (c - b); fu = func(u, data); } a = b; b = c; c = u; fa = fb; fb = fc; fc = fu; } if (a > c) u = a, a = c, c = u; // swap // now, afb and fb tol1) { // related to parabolic interpolation r = (b - w) * (fb - fv); q = (b - v) * (fb - fw); p = (b - v) * q - (b - w) * r; q = 2.0 * (q - r); if (q > 0.0) p = 0.0 - p; else q = 0.0 - q; eold = e; e = d; if (fabs(p) >= fabs(0.5 * q * eold) || p <= q * (a - b) || p >= q * (c - b)) { d = gold2 * (e = (b >= mid ? a - b : c - b)); } else { d = p / q; u = b + d; // actual parabolic interpolation happens here if (u - a < tol2 || c - u < tol2) d = (mid > b)? tol1 : 0.0 - tol1; } } else d = gold2 * (e = (b >= mid ? a - b : c - b)); // golden section interpolation u = fabs(d) >= tol1 ? b + d : b + (d > 0.0? tol1 : -tol1); fu = func(u, data); if (fu <= fb) { // u is the minimum point so far if (u >= b) a = b; else c = b; v = w; w = b; b = u; fv = fw; fw = fb; fb = fu; } else { // adjust (a,c) and (u,v,w) if (u < b) a = u; else c = u; if (fu <= fw || w == b) { v = w; w = u; fv = fw; fw = fu; } else if (fu <= fv || v == b || v == w) { v = u; fv = fu; } } } *xmin = b; return fb; } pysam-0.23.0/bcftools/kmin.c.pysam.c000066400000000000000000000162021475062545500172310ustar00rootroot00000000000000#include "bcftools.pysam.h" /* The MIT License Copyright (c) 2008, 2010 by Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Hooke-Jeeves algorithm for nonlinear minimization Based on the pseudocodes by Bell and Pike (CACM 9(9):684-685), and the revision by Tomlin and Smith (CACM 12(11):637-638). Both of the papers are comments on Kaupe's Algorithm 178 "Direct Search" (ACM 6(6):313-314). The original algorithm was designed by Hooke and Jeeves (ACM 8:212-229). This program is further revised according to Johnson's implementation at Netlib (opt/hooke.c). Hooke-Jeeves algorithm is very simple and it works quite well on a few examples. However, it might fail to converge due to its heuristic nature. A possible improvement, as is suggested by Johnson, may be to choose a small r at the beginning to quickly approach to the minimum and a large r at later step to hit the minimum. */ #include #include #include #include "kmin.h" static double __kmin_hj_aux(kmin_f func, int n, double *x1, void *data, double fx1, double *dx, int *n_calls) { int k, j = *n_calls; double ftmp; for (k = 0; k != n; ++k) { x1[k] += dx[k]; ftmp = func(n, x1, data); ++j; if (ftmp < fx1) fx1 = ftmp; else { /* search the opposite direction */ dx[k] = 0.0 - dx[k]; x1[k] += dx[k] + dx[k]; ftmp = func(n, x1, data); ++j; if (ftmp < fx1) fx1 = ftmp; else x1[k] -= dx[k]; /* back to the original x[k] */ } } *n_calls = j; return fx1; /* here: fx1=f(n,x1) */ } double kmin_hj(kmin_f func, int n, double *x, void *data, double r, double eps, int max_calls) { double fx, fx1, *x1, *dx, radius; int k, n_calls = 0; x1 = (double*)calloc(n, sizeof(double)); dx = (double*)calloc(n, sizeof(double)); for (k = 0; k != n; ++k) { /* initial directions, based on MGJ */ dx[k] = fabs(x[k]) * r; if (dx[k] == 0) dx[k] = r; } radius = r; fx1 = fx = func(n, x, data); ++n_calls; for (;;) { memcpy(x1, x, n * sizeof(double)); /* x1 = x */ fx1 = __kmin_hj_aux(func, n, x1, data, fx, dx, &n_calls); while (fx1 < fx) { for (k = 0; k != n; ++k) { double t = x[k]; dx[k] = x1[k] > x[k]? fabs(dx[k]) : 0.0 - fabs(dx[k]); x[k] = x1[k]; x1[k] = x1[k] + x1[k] - t; } fx = fx1; if (n_calls >= max_calls) break; fx1 = func(n, x1, data); ++n_calls; fx1 = __kmin_hj_aux(func, n, x1, data, fx1, dx, &n_calls); if (fx1 >= fx) break; for (k = 0; k != n; ++k) if (fabs(x1[k] - x[k]) > .5 * fabs(dx[k])) break; if (k == n) break; } if (radius >= eps) { if (n_calls >= max_calls) break; radius *= r; for (k = 0; k != n; ++k) dx[k] *= r; } else break; /* converge */ } free(x1); free(dx); return fx1; } // I copied this function somewhere several years ago with some of my modifications, but I forgot the source. double kmin_brent(kmin1_f func, double a, double b, void *data, double tol, double *xmin) { double bound, u, r, q, fu, tmp, fa, fb, fc, c; const double gold1 = 1.6180339887; const double gold2 = 0.3819660113; const double tiny = 1e-20; const int max_iter = 100; double e, d, w, v, mid, tol1, tol2, p, eold, fv, fw; int iter; fa = func(a, data); fb = func(b, data); if (fb > fa) { // swap, such that f(a) > f(b) tmp = a; a = b; b = tmp; tmp = fa; fa = fb; fb = tmp; } c = b + gold1 * (b - a), fc = func(c, data); // golden section extrapolation while (fb > fc) { bound = b + 100.0 * (c - b); // the farthest point where we want to go r = (b - a) * (fb - fc); q = (b - c) * (fb - fa); if (fabs(q - r) < tiny) { // avoid 0 denominator tmp = q > r? tiny : 0.0 - tiny; } else tmp = q - r; u = b - ((b - c) * q - (b - a) * r) / (2.0 * tmp); // u is the parabolic extrapolation point if ((b > u && u > c) || (b < u && u < c)) { // u lies between b and c fu = func(u, data); if (fu < fc) { // (b,u,c) bracket the minimum a = b; b = u; fa = fb; fb = fu; break; } else if (fu > fb) { // (a,b,u) bracket the minimum c = u; fc = fu; break; } u = c + gold1 * (c - b); fu = func(u, data); // golden section extrapolation } else if ((c > u && u > bound) || (c < u && u < bound)) { // u lies between c and bound fu = func(u, data); if (fu < fc) { // fb > fc > fu b = c; c = u; u = c + gold1 * (c - b); fb = fc; fc = fu; fu = func(u, data); } else { // (b,c,u) bracket the minimum a = b; b = c; c = u; fa = fb; fb = fc; fc = fu; break; } } else if ((u > bound && bound > c) || (u < bound && bound < c)) { // u goes beyond the bound u = bound; fu = func(u, data); } else { // u goes the other way around, use golden section extrapolation u = c + gold1 * (c - b); fu = func(u, data); } a = b; b = c; c = u; fa = fb; fb = fc; fc = fu; } if (a > c) u = a, a = c, c = u; // swap // now, afb and fb tol1) { // related to parabolic interpolation r = (b - w) * (fb - fv); q = (b - v) * (fb - fw); p = (b - v) * q - (b - w) * r; q = 2.0 * (q - r); if (q > 0.0) p = 0.0 - p; else q = 0.0 - q; eold = e; e = d; if (fabs(p) >= fabs(0.5 * q * eold) || p <= q * (a - b) || p >= q * (c - b)) { d = gold2 * (e = (b >= mid ? a - b : c - b)); } else { d = p / q; u = b + d; // actual parabolic interpolation happens here if (u - a < tol2 || c - u < tol2) d = (mid > b)? tol1 : 0.0 - tol1; } } else d = gold2 * (e = (b >= mid ? a - b : c - b)); // golden section interpolation u = fabs(d) >= tol1 ? b + d : b + (d > 0.0? tol1 : -tol1); fu = func(u, data); if (fu <= fb) { // u is the minimum point so far if (u >= b) a = b; else c = b; v = w; w = b; b = u; fv = fw; fw = fb; fb = fu; } else { // adjust (a,c) and (u,v,w) if (u < b) a = u; else c = u; if (fu <= fw || w == b) { v = w; w = u; fv = fw; fw = fu; } else if (fu <= fv || v == b || v == w) { v = u; fv = fu; } } } *xmin = b; return fb; } pysam-0.23.0/bcftools/kmin.h000066400000000000000000000031231475062545500156630ustar00rootroot00000000000000/* Copyright (c) 2008, 2010 by Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef KMIN_H #define KMIN_H #define KMIN_RADIUS 0.5 #define KMIN_EPS 1e-7 #define KMIN_MAXCALL 50000 typedef double (*kmin_f)(int, double*, void*); typedef double (*kmin1_f)(double, void*); #ifdef __cplusplus extern "C" { #endif double kmin_hj(kmin_f func, int n, double *x, void *data, double r, double eps, int max_calls); double kmin_brent(kmin1_f func, double a, double b, void *data, double tol, double *xmin); #ifdef __cplusplus } #endif #endif pysam-0.23.0/bcftools/main.c000066400000000000000000000233641475062545500156550ustar00rootroot00000000000000/* main.c -- main bcftools command front-end. Copyright (C) 2012-2021 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include "config.h" #include #include #include #include #include #include #include "version.h" #include "bcftools.h" int main_tabix(int argc, char *argv[]); int main_vcfindex(int argc, char *argv[]); int main_vcfstats(int argc, char *argv[]); int main_vcfisec(int argc, char *argv[]); int main_vcfmerge(int argc, char *argv[]); int main_vcfquery(int argc, char *argv[]); int main_vcffilter(int argc, char *argv[]); int main_vcfsom(int argc, char *argv[]); int main_vcfnorm(int argc, char *argv[]); int main_vcfgtcheck(int argc, char *argv[]); int main_vcfview(int argc, char *argv[]); int main_vcfhead(int argc, char *argv[]); int main_vcfcall(int argc, char *argv[]); int main_vcfannotate(int argc, char *argv[]); int main_vcfroh(int argc, char *argv[]); int main_vcfconcat(int argc, char *argv[]); int main_reheader(int argc, char *argv[]); int main_vcfconvert(int argc, char *argv[]); int main_vcfcnv(int argc, char *argv[]); #if USE_GPL int main_polysomy(int argc, char *argv[]); #endif #ifdef ENABLE_BCF_PLUGINS int main_plugin(int argc, char *argv[]); int count_plugins(void); #endif int main_consensus(int argc, char *argv[]); int main_csq(int argc, char *argv[]); int main_mpileup(int argc, char *argv[]); int main_sort(int argc, char *argv[]); typedef struct { int (*func)(int, char*[]); const char *alias, *help; } cmd_t; static cmd_t cmds[] = { { .func = NULL, .alias = "Indexing", .help = NULL }, { .func = main_vcfindex, .alias = "index", .help = "index VCF/BCF files" }, { .func = main_tabix, .alias = "tabix", .help = "-tabix for BGZF'd BED, GFF, SAM, VCF and more" // do not advertise; only keep here for testing }, { .func = NULL, .alias = "VCF/BCF manipulation", .help = NULL }, { .func = main_vcfannotate, .alias = "annotate", .help = "annotate and edit VCF/BCF files", }, { .func = main_vcfconcat, .alias = "concat", .help = "concatenate VCF/BCF files from the same set of samples" }, { .func = main_vcfconvert, .alias = "convert", .help = "convert VCF/BCF files to different formats and back" }, { .func = main_vcfhead, .alias = "head", .help = "view VCF/BCF file headers" }, { .func = main_vcfisec, .alias = "isec", .help = "intersections of VCF/BCF files" }, { .func = main_vcfmerge, .alias = "merge", .help = "merge VCF/BCF files files from non-overlapping sample sets" }, { .func = main_vcfnorm, .alias = "norm", .help = "left-align and normalize indels" }, #ifdef ENABLE_BCF_PLUGINS { .func = main_plugin, .alias = "plugin", .help = "user-defined plugins" }, #endif { .func = main_vcfquery, .alias = "query", .help = "transform VCF/BCF into user-defined formats" }, { .func = main_reheader, .alias = "reheader", .help = "modify VCF/BCF header, change sample names" }, { .func = main_sort, .alias = "sort", .help = "sort VCF/BCF file" }, { .func = main_vcfview, .alias = "view", .help = "VCF/BCF conversion, view, subset and filter VCF/BCF files" }, { .func = NULL, .alias = "VCF/BCF analysis", .help = NULL }, { .func = main_vcfcall, .alias = "call", .help = "SNP/indel calling" }, { .func = main_consensus, .alias = "consensus", .help = "create consensus sequence by applying VCF variants" }, { .func = main_vcfcnv, .alias = "cnv", .help = "HMM CNV calling" }, { .func = main_csq, .alias = "csq", .help = "call variation consequences" }, { .func = main_vcffilter, .alias = "filter", .help = "filter VCF/BCF files using fixed thresholds" }, { .func = main_vcfgtcheck, .alias = "gtcheck", .help = "check sample concordance, detect sample swaps and contamination" }, { .func = main_mpileup, .alias = "mpileup", .help = "multi-way pileup producing genotype likelihoods" }, #if USE_GPL { .func = main_polysomy, .alias = "polysomy", .help = "detect number of chromosomal copies", }, #endif { .func = main_vcfroh, .alias = "roh", .help = "identify runs of autozygosity (HMM)", }, { .func = main_vcfstats, .alias = "stats", .help = "produce VCF/BCF stats" }, { .func = main_vcfsom, .alias = "som", .help = "-filter using Self-Organized Maps (experimental)" // do not advertise }, { .func = NULL, .alias = NULL, .help = NULL } }; char *bcftools_version(void) { return BCFTOOLS_VERSION; } static void usage(FILE *fp) { fprintf(fp, "\n"); fprintf(fp, "Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)\n"); #if USE_GPL fprintf(fp, "License: GNU GPLv3+, due to use of the GNU Scientific Library\n"); #endif fprintf(fp, "Version: %s (using htslib %s)\n", bcftools_version(), hts_version()); fprintf(fp, "\n"); fprintf(fp, "Usage: bcftools [--version|--version-only] [--help] \n"); fprintf(fp, "\n"); fprintf(fp, "Commands:\n"); int i = 0; const char *sep = NULL; while (cmds[i].alias) { if ( !cmds[i].func ) sep = cmds[i].alias; if ( sep ) { fprintf(fp, "\n -- %s\n", sep); sep = NULL; } if ( cmds[i].func && cmds[i].help[0]!='-' ) fprintf(fp, " %-12s %s\n", cmds[i].alias, cmds[i].help); i++; } #if ENABLE_BCF_PLUGINS fprintf(fp,"\n -- Plugins (collection of programs for calling, file manipulation & analysis)\n"); int nplugins = count_plugins(); if ( nplugins ) fprintf(fp," %d plugins available, run \"bcftools plugin -lv\" to see a complete list\n", nplugins); else fprintf(fp," 0 plugins available, run \"bcftools plugin -l\" for help\n"); #endif fprintf(fp,"\n"); fprintf(fp, " Most commands accept VCF, bgzipped VCF, and BCF with the file type detected\n" " automatically even when streaming from a pipe. Indexed VCF and BCF will work\n" " in all situations. Un-indexed VCF and BCF and streams will work in most but\n" " not all situations.\n"); fprintf(fp,"\n"); } // This is a tricky one, but on Windows the filename wildcard expansion is done by // the application and not by the shell, as traditionally it never had a "shell". // Even now, DOS and Powershell do not do this expansion (but bash does). // // This means that Mingw/Msys implements code before main() that takes e.g. "*" and // expands it up to a list of matching filenames. This in turn breaks things like // specifying "*" as a region (all the unmapped reads). We take a hard line here - // filename expansion is the task of the shell, not our application! #ifdef _WIN32 int _CRT_glob = 0; #endif int main(int argc, char *argv[]) { if (argc < 2) { usage(stderr); return 1; } if (strcmp(argv[1], "version") == 0 || strcmp(argv[1], "--version") == 0 || strcmp(argv[1], "-v") == 0) { printf("bcftools %s\nUsing htslib %s\nCopyright (C) 2024 Genome Research Ltd.\n", bcftools_version(), hts_version()); #if USE_GPL printf("License GPLv3+: GNU GPL version 3 or later \n"); #else printf("License Expat: The MIT/Expat license\n"); #endif printf("This is free software: you are free to change and redistribute it.\nThere is NO WARRANTY, to the extent permitted by law.\n"); return 0; } else if (strcmp(argv[1], "--version-only") == 0) { printf("%s+htslib-%s\n", bcftools_version(), hts_version()); return 0; } else if (strcmp(argv[1], "help") == 0 || strcmp(argv[1], "--help") == 0 || strcmp(argv[1], "-h") == 0) { if (argc == 2) { usage(stdout); return 0; } // Otherwise change "bcftools help COMMAND [...]" to "bcftools COMMAND"; // main_xyz() functions by convention display the subcommand's usage // when invoked without any arguments. argv++; argc = 2; } else if ( argv[1][0]=='+' ) { // "bcftools plugin name" can be run as "bcftools +name" argv[1]++; argv[0] = "plugin"; argv--; argc++; } int i = 0; while (cmds[i].alias) { if (cmds[i].func && strcmp(argv[1],cmds[i].alias)==0) { return cmds[i].func(argc-1,argv+1); } i++; } fprintf(stderr, "[E::%s] unrecognized command '%s'\n", __func__, argv[1]); return 1; } pysam-0.23.0/bcftools/main.c.pysam.c000066400000000000000000000236171475062545500172270ustar00rootroot00000000000000#include "bcftools.pysam.h" /* main.c -- main bcftools command front-end. Copyright (C) 2012-2021 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include "config.h" #include #include #include #include #include #include #include "version.h" #include "bcftools.h" int main_tabix(int argc, char *argv[]); int main_vcfindex(int argc, char *argv[]); int main_vcfstats(int argc, char *argv[]); int main_vcfisec(int argc, char *argv[]); int main_vcfmerge(int argc, char *argv[]); int main_vcfquery(int argc, char *argv[]); int main_vcffilter(int argc, char *argv[]); int main_vcfsom(int argc, char *argv[]); int main_vcfnorm(int argc, char *argv[]); int main_vcfgtcheck(int argc, char *argv[]); int main_vcfview(int argc, char *argv[]); int main_vcfhead(int argc, char *argv[]); int main_vcfcall(int argc, char *argv[]); int main_vcfannotate(int argc, char *argv[]); int main_vcfroh(int argc, char *argv[]); int main_vcfconcat(int argc, char *argv[]); int main_reheader(int argc, char *argv[]); int main_vcfconvert(int argc, char *argv[]); int main_vcfcnv(int argc, char *argv[]); #if USE_GPL int main_polysomy(int argc, char *argv[]); #endif #ifdef ENABLE_BCF_PLUGINS int main_plugin(int argc, char *argv[]); int count_plugins(void); #endif int main_consensus(int argc, char *argv[]); int main_csq(int argc, char *argv[]); int main_mpileup(int argc, char *argv[]); int main_sort(int argc, char *argv[]); typedef struct { int (*func)(int, char*[]); const char *alias, *help; } cmd_t; static cmd_t cmds[] = { { .func = NULL, .alias = "Indexing", .help = NULL }, { .func = main_vcfindex, .alias = "index", .help = "index VCF/BCF files" }, { .func = main_tabix, .alias = "tabix", .help = "-tabix for BGZF'd BED, GFF, SAM, VCF and more" // do not advertise; only keep here for testing }, { .func = NULL, .alias = "VCF/BCF manipulation", .help = NULL }, { .func = main_vcfannotate, .alias = "annotate", .help = "annotate and edit VCF/BCF files", }, { .func = main_vcfconcat, .alias = "concat", .help = "concatenate VCF/BCF files from the same set of samples" }, { .func = main_vcfconvert, .alias = "convert", .help = "convert VCF/BCF files to different formats and back" }, { .func = main_vcfhead, .alias = "head", .help = "view VCF/BCF file headers" }, { .func = main_vcfisec, .alias = "isec", .help = "intersections of VCF/BCF files" }, { .func = main_vcfmerge, .alias = "merge", .help = "merge VCF/BCF files files from non-overlapping sample sets" }, { .func = main_vcfnorm, .alias = "norm", .help = "left-align and normalize indels" }, #ifdef ENABLE_BCF_PLUGINS { .func = main_plugin, .alias = "plugin", .help = "user-defined plugins" }, #endif { .func = main_vcfquery, .alias = "query", .help = "transform VCF/BCF into user-defined formats" }, { .func = main_reheader, .alias = "reheader", .help = "modify VCF/BCF header, change sample names" }, { .func = main_sort, .alias = "sort", .help = "sort VCF/BCF file" }, { .func = main_vcfview, .alias = "view", .help = "VCF/BCF conversion, view, subset and filter VCF/BCF files" }, { .func = NULL, .alias = "VCF/BCF analysis", .help = NULL }, { .func = main_vcfcall, .alias = "call", .help = "SNP/indel calling" }, { .func = main_consensus, .alias = "consensus", .help = "create consensus sequence by applying VCF variants" }, { .func = main_vcfcnv, .alias = "cnv", .help = "HMM CNV calling" }, { .func = main_csq, .alias = "csq", .help = "call variation consequences" }, { .func = main_vcffilter, .alias = "filter", .help = "filter VCF/BCF files using fixed thresholds" }, { .func = main_vcfgtcheck, .alias = "gtcheck", .help = "check sample concordance, detect sample swaps and contamination" }, { .func = main_mpileup, .alias = "mpileup", .help = "multi-way pileup producing genotype likelihoods" }, #if USE_GPL { .func = main_polysomy, .alias = "polysomy", .help = "detect number of chromosomal copies", }, #endif { .func = main_vcfroh, .alias = "roh", .help = "identify runs of autozygosity (HMM)", }, { .func = main_vcfstats, .alias = "stats", .help = "produce VCF/BCF stats" }, { .func = main_vcfsom, .alias = "som", .help = "-filter using Self-Organized Maps (experimental)" // do not advertise }, { .func = NULL, .alias = NULL, .help = NULL } }; char *bcftools_version(void) { return BCFTOOLS_VERSION; } static void usage(FILE *fp) { fprintf(fp, "\n"); fprintf(fp, "Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)\n"); #if USE_GPL fprintf(fp, "License: GNU GPLv3+, due to use of the GNU Scientific Library\n"); #endif fprintf(fp, "Version: %s (using htslib %s)\n", bcftools_version(), hts_version()); fprintf(fp, "\n"); fprintf(fp, "Usage: bcftools [--version|--version-only] [--help] \n"); fprintf(fp, "\n"); fprintf(fp, "Commands:\n"); int i = 0; const char *sep = NULL; while (cmds[i].alias) { if ( !cmds[i].func ) sep = cmds[i].alias; if ( sep ) { fprintf(fp, "\n -- %s\n", sep); sep = NULL; } if ( cmds[i].func && cmds[i].help[0]!='-' ) fprintf(fp, " %-12s %s\n", cmds[i].alias, cmds[i].help); i++; } #if ENABLE_BCF_PLUGINS fprintf(fp,"\n -- Plugins (collection of programs for calling, file manipulation & analysis)\n"); int nplugins = count_plugins(); if ( nplugins ) fprintf(fp," %d plugins available, run \"bcftools plugin -lv\" to see a complete list\n", nplugins); else fprintf(fp," 0 plugins available, run \"bcftools plugin -l\" for help\n"); #endif fprintf(fp,"\n"); fprintf(fp, " Most commands accept VCF, bgzipped VCF, and BCF with the file type detected\n" " automatically even when streaming from a pipe. Indexed VCF and BCF will work\n" " in all situations. Un-indexed VCF and BCF and streams will work in most but\n" " not all situations.\n"); fprintf(fp,"\n"); } // This is a tricky one, but on Windows the filename wildcard expansion is done by // the application and not by the shell, as traditionally it never had a "shell". // Even now, DOS and Powershell do not do this expansion (but bash does). // // This means that Mingw/Msys implements code before main() that takes e.g. "*" and // expands it up to a list of matching filenames. This in turn breaks things like // specifying "*" as a region (all the unmapped reads). We take a hard line here - // filename expansion is the task of the shell, not our application! #ifdef _WIN32 int _CRT_glob = 0; #endif int bcftools_main(int argc, char *argv[]) { if (argc < 2) { usage(bcftools_stderr); return 1; } if (strcmp(argv[1], "version") == 0 || strcmp(argv[1], "--version") == 0 || strcmp(argv[1], "-v") == 0) { fprintf(bcftools_stdout, "bcftools %s\nUsing htslib %s\nCopyright (C) 2024 Genome Research Ltd.\n", bcftools_version(), hts_version()); #if USE_GPL fprintf(bcftools_stdout, "License GPLv3+: GNU GPL version 3 or later \n"); #else fprintf(bcftools_stdout, "License Expat: The MIT/Expat license\n"); #endif fprintf(bcftools_stdout, "This is free software: you are free to change and redistribute it.\nThere is NO WARRANTY, to the extent permitted by law.\n"); return 0; } else if (strcmp(argv[1], "--version-only") == 0) { fprintf(bcftools_stdout, "%s+htslib-%s\n", bcftools_version(), hts_version()); return 0; } else if (strcmp(argv[1], "help") == 0 || strcmp(argv[1], "--help") == 0 || strcmp(argv[1], "-h") == 0) { if (argc == 2) { usage(bcftools_stdout); return 0; } // Otherwise change "bcftools help COMMAND [...]" to "bcftools COMMAND"; // main_xyz() functions by convention display the subcommand's usage // when invoked without any arguments. argv++; argc = 2; } else if ( argv[1][0]=='+' ) { // "bcftools plugin name" can be run as "bcftools +name" argv[1]++; argv[0] = "plugin"; argv--; argc++; } int i = 0; while (cmds[i].alias) { if (cmds[i].func && strcmp(argv[1],cmds[i].alias)==0) { return cmds[i].func(argc-1,argv+1); } i++; } fprintf(bcftools_stderr, "[E::%s] unrecognized command '%s'\n", __func__, argv[1]); return 1; } pysam-0.23.0/bcftools/mcall.c000066400000000000000000001771221475062545500160230ustar00rootroot00000000000000/* mcall.c -- multiallelic and rare variant calling. Copyright (C) 2012-2022 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "call.h" #include "prob1.h" // Using priors for GTs does not seem to be mathematically justified. Although // it seems effective in removing false calls, it also flips a significant // proportion of HET genotypes. Better is to filter by FORMAT/GQ using // `bcftools filter`. #define USE_PRIOR_FOR_GTS 0 // Go with uniform PLs for samples with no coverage. If unset, missing // genotypes is reported instead. #define FLAT_PDG_FOR_MISSING 0 int test16(float *anno16, anno16_t *a); void qcall_init(call_t *call) { return; } void qcall_destroy(call_t *call) { return; } int qcall(call_t *call, bcf1_t *rec) { // QCall format: // chromosome, position, reference allele, depth, mapping quality, 0, .. error("TODO: qcall output\n"); return 0; } void call_init_pl2p(call_t *call) { int i; for (i=0; i<256; i++) call->pl2p[i] = pow(10., -i/10.); } // Macros for accessing call->trio and call->ntrio #define FTYPE_222 0 // family type: all diploid #define FTYPE_121 1 // chrX, the child is a boy #define FTYPE_122 2 // chrX, a girl #define FTYPE_101 3 // chrY, boy #define FTYPE_100 4 // chrY, girl #define GT_SKIP 0xf // empty genotype (chrY in females) #define IS_POW2(x) (!((x) & ((x) - 1))) // zero is permitted #define IS_HOM(x) IS_POW2(x) // Pkij = P(k|i,j) tells how likely it is to be a het if the parents // are homs etc. The consistency of i,j,k has been already checked. // Parameters are alleles and ploidy of father, mother, kid // Returns 2/Pkij. int calc_Pkij(int fals, int mals, int kals, int fpl, int mpl, int kpl) { int als = fals|mals|kals; if ( IS_HOM(als) ) return 2; // all are the same: child must be a HOM, P=1 if ( fpl==1 ) { if ( kpl==1 ) // chr X, the child is a boy, the copy is inherited from the mother { if ( IS_HOM(mals) ) return 2; // 0 11 -> P(1) = 1 return 4; // 0 01 -> P(0) = P(1) = 1/2 } // chr X, the child is a girl if ( IS_HOM(mals) ) return 2; // 0 11 -> P(01) = 1 return 4; // 0 01 -> P(00) = P(01) = 1/2 } if ( IS_HOM(fals) && IS_HOM(mals) ) return 2; // 00 11 01, the child must be a HET, P=1 if ( !IS_HOM(fals) && !IS_HOM(mals) ) { if ( IS_HOM(kals) ) return 8; // 01 01 00 or 01 01 11, P(k=HOM) = 1/4 return 4; // 01 01 01, P(k=HET) = 1/2 } return 4; // 00 01, P(k=HET) = P(k=HOM) = 1/2 } // Initialize ntrio and trio: ntrio lists the number of possible // genotypes given combination of haploid/diploid genomes and the // number of alleles. trio lists allowed genotype combinations: // 4bit: 2/Pkij, 4: father, 4: mother, 4: child // See also mcall_call_trio_genotypes() // static void mcall_init_trios(call_t *call) { if ( call->prior_AN ) { int id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,call->prior_AN); if ( id==-1 ) error("No such tag \"%s\"\n", call->prior_AN); if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) ) error("No such FORMAT tag \"%s\"\n", call->prior_AN); id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,call->prior_AC); if ( id==-1 ) error("No such tag \"%s\"\n", call->prior_AC); if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) ) error("No such FORMAT tag \"%s\"\n", call->prior_AC); } // 23, 138, 478 possible diploid trio genotypes with 2, 3, 4 alleles call->ntrio[FTYPE_222][2] = 15; call->ntrio[FTYPE_222][3] = 78; call->ntrio[FTYPE_222][4] = 250; call->ntrio[FTYPE_121][2] = 8; call->ntrio[FTYPE_121][3] = 27; call->ntrio[FTYPE_121][4] = 64; call->ntrio[FTYPE_122][2] = 8; call->ntrio[FTYPE_122][3] = 27; call->ntrio[FTYPE_122][4] = 64; call->ntrio[FTYPE_101][2] = 2; call->ntrio[FTYPE_101][3] = 3; call->ntrio[FTYPE_101][4] = 4; call->ntrio[FTYPE_100][2] = 2; call->ntrio[FTYPE_100][3] = 3; call->ntrio[FTYPE_100][4] = 4; int nals, itype; for (itype=0; itype<=4; itype++) { for (nals=2; nals<=4; nals++) call->trio[itype][nals] = (uint16_t*) malloc(sizeof(uint16_t)*call->ntrio[itype][nals]); } // max 10 possible diploid genotypes int gts[10]; for (nals=2; nals<=4; nals++) { int i,j,k, n = 0, ngts = 0; for (i=0; itrio[FTYPE_222][nals][n++] = Pkij<<12 | i<<8 | j<<4 | k; // father, mother, child } assert( n==call->ntrio[FTYPE_222][nals] ); // 121: chrX, boy n = 0; for (i=0; itrio[FTYPE_121][nals][n++] = Pkij<<12 | i<<8 | j<<4 | k; } assert( n==call->ntrio[FTYPE_121][nals] ); // 122: chrX, girl n = 0; for (i=0; itrio[FTYPE_122][nals][n++] = Pkij<<12 | i<<8 | j<<4 | k; } assert( n==call->ntrio[FTYPE_122][nals] ); // 101: chrY, boy n = 0; for (i=0; itrio[FTYPE_101][nals][n++] = 1<<12 | i<<8 | GT_SKIP<<4 | k; } assert( n==call->ntrio[FTYPE_101][nals] ); // 100: chrY, girl n = 0; for (i=0; itrio[FTYPE_100][nals][n++] = 1<<12 | i<<8 | GT_SKIP<<4 | GT_SKIP; } assert( n==call->ntrio[FTYPE_100][nals] ); } call->GLs = (double*) calloc(bcf_hdr_nsamples(call->hdr)*10,sizeof(double)); int i, j; for (i=0; infams; i++) { family_t *fam = &call->fams[i]; int ploidy[3]; for (j=0; j<3; j++) ploidy[j] = call->ploidy[fam->sample[j]]; if ( ploidy[FATHER]==2 ) // not X, not Y { if ( ploidy[MOTHER]!=2 || ploidy[CHILD]!=2 ) error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]); fam->type = FTYPE_222; continue; } if ( ploidy[FATHER]!=1 || ploidy[MOTHER]==1 ) error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]); if ( ploidy[MOTHER]==2 ) // X { if ( ploidy[CHILD]==0 ) error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]); fam->type = ploidy[CHILD]==2 ? FTYPE_122 : FTYPE_121; // a girl or a boy } else // Y { if ( ploidy[CHILD]==2 ) error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]); fam->type = ploidy[CHILD]==0 ? FTYPE_100 : FTYPE_101; // a girl or a boy } } } static void mcall_destroy_trios(call_t *call) { int i, j; for (i=2; i<=4; i++) for (j=0; j<=4; j++) free(call->trio[j][i]); } static void init_sample_groups(call_t *call) { int i, nsmpl = bcf_hdr_nsamples(call->hdr); if ( !call->sample_groups ) { // standard pooled calling, all samples in the same group call->nsmpl_grp = 1; call->smpl_grp = (smpl_grp_t*)calloc(1,sizeof(*call->smpl_grp)); call->smpl_grp[0].nsmpl = nsmpl; call->smpl_grp[0].smpl = (uint32_t*)calloc(call->smpl_grp[0].nsmpl,sizeof(uint32_t)); for (i=0; ismpl_grp[0].smpl[i] = i; return; } if ( call->sample_groups_tag ) { // Is the tag defined in the header? int tag_id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,call->sample_groups_tag); if ( tag_id==-1 ) error("No such tag \"%s\"\n",call->sample_groups_tag); if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) error("No such FORMAT tag \"%s\"\n", call->sample_groups_tag); } else { int tag_id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,"QS"); if ( tag_id >= 0 && bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) call->sample_groups_tag = "QS"; else { tag_id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,"AD"); if ( tag_id >= 0 && bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) call->sample_groups_tag = "AD"; else error("Error: neither \"AD\" nor \"QS\" FORMAT tag exists and no alternative given with -G\n"); } } // Read samples/groups if ( !strcmp("-",call->sample_groups) ) { // single-sample calling, each sample creates its own group call->nsmpl_grp = nsmpl; call->smpl_grp = (smpl_grp_t*)calloc(nsmpl,sizeof(*call->smpl_grp)); for (i=0; ismpl_grp[i].nsmpl = 1; call->smpl_grp[i].smpl = (uint32_t*)calloc(call->smpl_grp[i].nsmpl,sizeof(uint32_t)); call->smpl_grp[i].smpl[0] = i; } } else { int nlines; char **lines = hts_readlist(call->sample_groups, 1, &nlines); if ( !lines ) error("Could not read the file: %s\n", call->sample_groups); uint32_t *smpl2grp = (uint32_t*)calloc(nsmpl,sizeof(uint32_t)); uint32_t *grp2n = (uint32_t*)calloc(nsmpl,sizeof(uint32_t)); void *grp2idx = khash_str2int_init(); call->nsmpl_grp = 0; for (i=0; isample_groups,lines[i]); char *tmp = ptr; while ( *ptr && isspace(*ptr) ) ptr++; if ( !*ptr ) error("Could not parse the line in %s, expected a sample name followed by tab and a population name: %s\n",call->sample_groups,lines[i]); *tmp = 0; int ismpl = bcf_hdr_id2int(call->hdr, BCF_DT_SAMPLE, lines[i]); if ( ismpl<0 ) continue; if ( smpl2grp[ismpl] ) error("Error: the sample \"%s\" is listed twice in %s\n", lines[i],call->sample_groups); if ( !khash_str2int_has_key(grp2idx,ptr+1) ) { khash_str2int_set(grp2idx, ptr+1, call->nsmpl_grp); call->nsmpl_grp++; } int igrp = -1; if ( khash_str2int_get(grp2idx, ptr+1, &igrp)!=0 ) error("This should not happen, fixme: %s\n",ptr+1); grp2n[igrp]++; smpl2grp[ismpl] = igrp+1; // +1 to distinguish unlisted samples } khash_str2int_destroy(grp2idx); if ( !call->nsmpl_grp ) error("Could not parse the file, no matching samples found: %s\n", call->sample_groups); call->smpl_grp = (smpl_grp_t*)calloc(call->nsmpl_grp,sizeof(*call->smpl_grp)); for (i=0; ihdr->samples[i],call->sample_groups); int igrp = smpl2grp[i] - 1; if ( !call->smpl_grp[igrp].nsmpl ) call->smpl_grp[igrp].smpl = (uint32_t*)calloc(grp2n[igrp],sizeof(uint32_t)); call->smpl_grp[igrp].smpl[call->smpl_grp[igrp].nsmpl] = i; call->smpl_grp[igrp].nsmpl++; } free(smpl2grp); free(grp2n); for (i=0; insmpl_grp; i++) { free(call->smpl_grp[i].qsum); free(call->smpl_grp[i].smpl); } free(call->smpl_grp); } void mcall_init(call_t *call) { init_sample_groups(call); call_init_pl2p(call); call->nals_map = 5; call->als_map = (int*) malloc(sizeof(int)*call->nals_map); call->npl_map = 5*(5+1)/2; // will be expanded later if necessary call->pl_map = (int*) malloc(sizeof(int)*call->npl_map); call->gts = (int32_t*) calloc(bcf_hdr_nsamples(call->hdr)*2,sizeof(int32_t)); // assuming at most diploid everywhere if ( call->flag & CALL_CONSTR_TRIO ) { call->cgts = (int32_t*) calloc(bcf_hdr_nsamples(call->hdr),sizeof(int32_t)); call->ugts = (int32_t*) calloc(bcf_hdr_nsamples(call->hdr),sizeof(int32_t)); mcall_init_trios(call); bcf_hdr_append(call->hdr,"##FORMAT="); bcf_hdr_append(call->hdr,"##FORMAT="); } if ( call->flag & CALL_CONSTR_ALLELES ) call->vcmp = vcmp_init(); bcf_hdr_append(call->hdr,"##FORMAT="); if ( call->output_tags & CALL_FMT_GQ ) bcf_hdr_append(call->hdr,"##FORMAT="); if ( call->output_tags & CALL_FMT_GP ) bcf_hdr_append(call->hdr,"##FORMAT="); if ( call->output_tags & (CALL_FMT_GQ|CALL_FMT_GP) ) call->GQs = (int32_t*) malloc(sizeof(int32_t)*bcf_hdr_nsamples(call->hdr)); bcf_hdr_append(call->hdr,"##INFO="); bcf_hdr_append(call->hdr,"##INFO="); bcf_hdr_append(call->hdr,"##INFO="); bcf_hdr_append(call->hdr,"##INFO="); if ( call->output_tags & CALL_FMT_PV4 ) bcf_hdr_append(call->hdr,"##INFO=\n"); // init the prior if ( call->theta>0 ) { int i, n = 0; if ( !call->ploidy ) n = 2*bcf_hdr_nsamples(call->hdr); // all are diploid else { for (i=0; ihdr); i++) n += call->ploidy[i]; } // Watterson factor, here aM_1 = aM_2 = 1 double aM = 1; for (i=2; itheta *= aM; if ( call->theta >= 1 ) { fprintf(stderr,"The prior is too big (theta*aM=%.2f), going with 0.99\n", call->theta); call->theta = 0.99; } call->theta = log(call->theta); } } void mcall_destroy(call_t *call) { destroy_sample_groups(call); if (call->vcmp) vcmp_destroy(call->vcmp); free(call->itmp); mcall_destroy_trios(call); free(call->GPs); free(call->ADs); free(call->GLs); free(call->GQs); free(call->anno16); free(call->PLs); free(call->als_map); free(call->pl_map); free(call->gts); free(call->cgts); free(call->ugts); free(call->pdg); free(call->als); free(call->ac); return; } // Inits P(D|G): convert PLs from log space and normalize. In case of zero // depth, missing PLs are all zero. In this case, pdg's are set to 0 // so that the corresponding genotypes can be set as missing and the // qual calculation is not affected. // Missing values are replaced by generic likelihoods when X (unseen allele) is // present. // NB: While the -m calling model uses the pdgs in canonical order, // the original samtools -c calling code uses pdgs in reverse order (AA comes // first, RR last). // NB: Ploidy is not taken into account here, which is incorrect. void set_pdg(double *pl2p, int *PLs, double *pdg, int n_smpl, int n_gt, int unseen) { int i, j, nals; // find out the number of alleles, expecting diploid genotype likelihoods bcf_gt2alleles(n_gt-1, &i, &nals); assert( i==nals ); nals++; for (i=0; i new(j) for (i=0; ials_map[i] = nout++; else call->als_map[i] = -1; } if ( !call->pl_map ) return; // pl_map: new(k) -> old(l) int k = 0, l = 0; for (i=0; ipl_map[k++] = l; l++; } } } /** log(exp(a)+exp(b)) */ static inline double logsumexp2(double a, double b) { if ( a>b ) return log(1 + exp(b-a)) + a; else return log(1 + exp(a-b)) + b; } // Macro to set the most likely alleles #define UPDATE_MAX_LKs(als,sum) { \ if ( max_lknsmpl; int ngts = nals*(nals+1)/2; // Single allele for (ia=0; iapdg + grp->smpl[ismpl]*ngts + iaa; if ( *pdg ) { lk_tot += log(*pdg); lk_tot_set = 1; } } if ( ia==0 ) ref_lk = lk_tot; // likelihood of 0/0 for all samples else lk_tot += call->theta; // the prior UPDATE_MAX_LKs(1<0 && lk_tot_set); } // Two alleles if ( nals>1 ) { for (ia=0; iaqsum[ia]==0 ) continue; int iaa = (ia+1)*(ia+2)/2-1; for (ib=0; ibqsum[ib]==0 ) continue; double lk_tot = 0; int lk_tot_set = 0; double fa = grp->qsum[ia]/(grp->qsum[ia] + grp->qsum[ib]); double fb = grp->qsum[ib]/(grp->qsum[ia] + grp->qsum[ib]); double fa2 = fa*fa; double fb2 = fb*fb; double fab = 2*fa*fb; int is, ibb = (ib+1)*(ib+2)/2-1, iab = iaa - ia + ib; for (is=0; issmpl[is]; double *pdg = call->pdg + ismpl*ngts; double val = 0; if ( !call->ploidy || call->ploidy[ismpl]==2 ) val = fa2*pdg[iaa] + fb2*pdg[ibb] + fab*pdg[iab]; else if ( call->ploidy && call->ploidy[ismpl]==1 ) val = fa*pdg[iaa] + fb*pdg[ibb]; if ( val ) { lk_tot += log(val); lk_tot_set = 1; } } if ( ia!=0 ) lk_tot += call->theta; // the prior if ( ib!=0 ) lk_tot += call->theta; UPDATE_MAX_LKs(1<2 ) { for (ia=0; iaqsum[ia]==0 ) continue; int iaa = (ia+1)*(ia+2)/2-1; for (ib=0; ibqsum[ib]==0 ) continue; int ibb = (ib+1)*(ib+2)/2-1; int iab = iaa - ia + ib; for (ic=0; icqsum[ic]==0 ) continue; double lk_tot = 0; int lk_tot_set = 0; double fa = grp->qsum[ia]/(grp->qsum[ia] + grp->qsum[ib] + grp->qsum[ic]); double fb = grp->qsum[ib]/(grp->qsum[ia] + grp->qsum[ib] + grp->qsum[ic]); double fc = grp->qsum[ic]/(grp->qsum[ia] + grp->qsum[ib] + grp->qsum[ic]); double fa2 = fa*fa; double fb2 = fb*fb; double fc2 = fc*fc; double fab = 2*fa*fb, fac = 2*fa*fc, fbc = 2*fb*fc; int is, icc = (ic+1)*(ic+2)/2-1; int iac = iaa - ia + ic, ibc = ibb - ib + ic; for (is=0; issmpl[is]; double *pdg = call->pdg + ismpl*ngts; double val = 0; if ( !call->ploidy || call->ploidy[ismpl]==2 ) val = fa2*pdg[iaa] + fb2*pdg[ibb] + fc2*pdg[icc] + fab*pdg[iab] + fac*pdg[iac] + fbc*pdg[ibc]; else if ( call->ploidy && call->ploidy[ismpl]==1 ) val = fa*pdg[iaa] + fb*pdg[ibb] + fc*pdg[icc]; if ( val ) { lk_tot += log(val); lk_tot_set = 1; } } if ( ia!=0 ) lk_tot += call->theta; // the prior if ( ib!=0 ) lk_tot += call->theta; // the prior if ( ic!=0 ) lk_tot += call->theta; // the prior UPDATE_MAX_LKs(1<max_lk = max_lk; grp->ref_lk = ref_lk; grp->lk_sum = lk_sum; grp->als = max_als; grp->nals = n; return n; } // Sets GT=0/0 or GT=. if PL=0,0,0 static void mcall_set_ref_genotypes(call_t *call, int nals_ori) { int i; int ngts = nals_ori*(nals_ori+1)/2; // need this to distinguish between GT=0/0 vs GT=. int nsmpl = bcf_hdr_nsamples(call->hdr); for (i=0; iac[i] = 0; // nals_new<=nals_ori, never mind setting extra 0's // Set all genotypes to 0/0 or 0 int *gts = call->gts; double *pdg = call->pdg; int isample; for (isample = 0; isample < nsmpl; isample++) { int ploidy = call->ploidy ? call->ploidy[isample] : 2; for (i=0; iac[0] += ploidy; } gts += 2; pdg += ngts; } } static void mcall_call_genotypes(call_t *call, int nals_ori, smpl_grp_t *grp) { int ia, ib, i; int ngts_ori = nals_ori*(nals_ori+1)/2; int ngts_new = call->nals_new*(call->nals_new+1)/2; int nsmpl = grp->nsmpl; #if USE_PRIOR_FOR_GTS float prior = exp(call->theta); #endif int is; for (is = 0; is < nsmpl; is++) { int ismpl = grp->smpl[is]; double *pdg = call->pdg + ismpl*ngts_ori; float *gps = call->GPs + ismpl*ngts_new; int *gts = call->gts + ismpl*2; int ploidy = call->ploidy ? call->ploidy[ismpl] : 2; assert( ploidy>=0 && ploidy<=2 ); if ( !ploidy ) { gts[0] = bcf_gt_missing; gts[1] = bcf_int32_vector_end; gps[0] = -1; continue; } #if !FLAT_PDG_FOR_MISSING // Skip samples with zero depth, they have all pdg's equal to 0 for (i=0; ials & 1<qsum[ia]*grp->qsum[ia] : pdg[iaa]*grp->qsum[ia]; #if USE_PRIOR_FOR_GTS if ( ia!=0 ) lk *= prior; #endif int igt = ploidy==2 ? bcf_alleles2gt(call->als_map[ia],call->als_map[ia]) : call->als_map[ia]; gps[igt] = lk; if ( best_lk < lk ) { best_lk = lk; gts[0] = bcf_gt_unphased(call->als_map[ia]); } } if ( ploidy==2 ) { gts[1] = gts[0]; for (ia=0; iaals & 1<als & 1<qsum[ia]*grp->qsum[ib]; #if USE_PRIOR_FOR_GTS if ( ia!=0 ) lk *= prior; if ( ib!=0 ) lk *= prior; #endif int igt = bcf_alleles2gt(call->als_map[ia],call->als_map[ib]); gps[igt] = lk; if ( best_lk < lk ) { best_lk = lk; gts[0] = bcf_gt_unphased(call->als_map[ib]); gts[1] = bcf_gt_unphased(call->als_map[ia]); } } } } else gts[1] = bcf_int32_vector_end; call->ac[ bcf_gt_allele(gts[0]) ]++; if ( gts[1]!=bcf_int32_vector_end ) call->ac[ bcf_gt_allele(gts[1]) ]++; } if ( !(call->output_tags & (CALL_FMT_GQ|CALL_FMT_GP)) ) return; double max, sum; for (is=0; issmpl[is]; float *gps = call->GPs + ismpl*ngts_new; int nmax; if ( call->ploidy ) { if ( call->ploidy[ismpl]==2 ) nmax = ngts_new; else if ( call->ploidy[ismpl]==1 ) nmax = grp->nals; else nmax = 0; } else nmax = ngts_new; max = gps[0]; if ( max<0 || nmax==0 ) { // no call if ( call->output_tags & CALL_FMT_GP ) { for (i=0; iGQs[ismpl] = 0; continue; } sum = gps[0]; for (i=1; iGQs[ismpl] = max<=INT8_MAX ? max : INT8_MAX; if ( call->output_tags & CALL_FMT_GP ) { assert( max ); for (i=0; ihdr); int ngts = nals*(nals+1)/2; int nout_gts = nals_new*(nals_new+1)/2; double *gls = call->GLs - nout_gts; double *pdg = call->pdg - ngts; // Calculate individuals' genotype likelihoods P(X=i) int isample; for (isample = 0; isample < nsmpl; isample++) { int ploidy = call->ploidy ? call->ploidy[isample] : 2; int32_t *gts = call->ugts + isample; gls += nout_gts; pdg += ngts; // Skip samples with all pdg's equal to 1. These have zero depth. for (i=0; ismpl_grp.grp[call->smpl_grp.smpl2grp[isample]]; double sum_lk = 0; double best_lk = 0; for (ia=0; iaals_map[ia],call->als_map[ia]); double lk = ploidy==2 ? pdg[iaa]*grp->qsum[ia]*grp->qsum[ia] : pdg[iaa]*grp->qsum[ia]; sum_lk += lk; gls[idx] = lk; if ( best_lk < lk ) { best_lk = lk; gts[0] = bcf_alleles2gt(call->als_map[ia],call->als_map[ia]); } } if ( ploidy==2 ) { for (ia=0; iaals_map[ia],call->als_map[ib]); double lk = 2*pdg[iab]*grp->qsum[ia]*grp->qsum[ib]; sum_lk += lk; gls[idx] = lk; if ( best_lk < lk ) { best_lk = lk; gts[0] = bcf_alleles2gt(call->als_map[ib],call->als_map[ia]); } } } } for (i=0; itrio_Pm_ins<0 && call->trio_Pm_del<0 ) trio_Pm = call->trio_Pm_SNPs; // the same Pm for indels and SNPs requested else { int ret = bcf_get_variant_types(rec); if ( !(ret & VCF_INDEL) ) trio_Pm = call->trio_Pm_SNPs; else { if ( call->trio_Pm_ins<0 ) // dynamic calculation, trio_Pm_del holds the scaling factor { trio_Pm = rec->d.var[1].n<0 ? -21.9313 - 0.2856*rec->d.var[1].n : -22.8689 + 0.2994*rec->d.var[1].n; trio_Pm = 1 - call->trio_Pm_del * exp(trio_Pm); } else // snps and indels set explicitly { trio_Pm = rec->d.var[1].n<0 ? call->trio_Pm_del : call->trio_Pm_ins; } } } // Calculate constrained likelihoods and determine genotypes int ifm; for (ifm=0; ifmnfams; ifm++) { family_t *fam = &call->fams[ifm]; int ntrio = call->ntrio[fam->type][nals_new]; uint16_t *trio = call->trio[fam->type][nals_new]; // Unconstrained likelihood int uc_itr = 0; double uc_lk = 0; for (i=0; i<3; i++) // for father, mother, child { int ismpl = fam->sample[i]; double *gl = call->GLs + nout_gts*ismpl; if ( gl[0]==1 ) continue; int j, jmax = 0; double max = gl[0]; for (j=1; jsample[i]; double *gl = call->GLs + nout_gts*ismpl; if ( gl[0]==1 ) continue; int igt = trio[itr]>>((2-i)*4) & 0xf; assert( !call->ploidy || call->ploidy[ismpl]>0 ); if ( igt==GT_SKIP ) continue; lk += gl[igt]; npresent++; // fprintf(stderr," %e", gl[igt]); } // fprintf(stderr,"\t\t"); double Pkij = npresent==3 ? (double)2/(trio[itr]>>12) : 1; // with missing genotypes Pkij's are different lk += log(1 - trio_Pm * (1 - Pkij)); // fprintf(stderr,"%d%d%d\t%e\t%.2f\n", trio[itr]>>8&0xf,trio[itr]>>4&0xf,trio[itr]&0xf, lk, Pkij); if ( c_lk < lk ) { c_lk = lk; c_itr = trio[itr]; } if ( uc_itr==trio[itr] ) uc_is_mendelian = 1; } if ( !uc_is_mendelian ) { uc_lk += log(1 - trio_Pm); // fprintf(stderr,"c_lk=%e uc_lk=%e c_itr=%d%d%d uc_itr=%d%d%d\n", c_lk,uc_lk,c_itr>>8&0xf,c_itr>>4&0xf,c_itr&0xf,uc_itr>>8&0xf,uc_itr>>4&0xf,uc_itr&0xf); if ( c_lk < uc_lk ) { c_lk = uc_lk; c_itr = uc_itr; } } // fprintf(stderr,"best_lk=%e best_itr=%d%d%d uc_itr=%d%d%d\n", c_lk,c_itr>>8&0xf,c_itr>>4&0xf,c_itr&0xf,uc_itr>>8&0xf,uc_itr>>4&0xf,uc_itr&0xf); // Set genotypes for father, mother, child and calculate genotype qualities for (i=0; i<3; i++) { // GT int ismpl = fam->sample[i]; int igt = c_itr>>((2-i)*4) & 0xf; double *gl = call->GLs + nout_gts*ismpl; int32_t *gts = call->cgts + ismpl; if ( gl[0]==1 || igt==GT_SKIP ) // zero depth, set missing genotypes { gts[0] = -1; // bcf_float_set_missing(call->GQs[ismpl]); continue; } gts[0] = igt; #if 0 // todo: Genotype Qualities // // GQ: for each family member i sum over all genotypes j,k keeping igt fixed double lk_sum = 0; for (itr=0; itr>((2-i)*4) & 0xf) ) continue; double lk = 0; int j; for (j=0; j<3; j++) { int jsmpl = fam->sample[j]; double *gl = call->GLs + ngts*jsmpl; if ( gl[0]==1 ) continue; int jgt = trio[itr]>>((2-j)*4) & 0xf; if ( jgt==GT_SKIP ) continue; lk += gl[jgt]; } double Pkij = (double)2/(trio[itr]>>12); lk += log(1 - trio_Pm * (1 - Pkij)); lk_sum = logsumexp2(lk_sum, lk); } if ( !uc_is_mendelian && (best_itr>>((2-i)*4)&0xf)==(uc_itr>>((2-i)*4)&0xf) ) lk_sum = logsumexp2(lk_sum,uc_lk); call->GQs[ismpl] = -4.3429*(best_lk - lk_sum); #endif } } for (i=0; i<4; i++) call->ac[i] = 0; call->nhets = 0; call->ndiploid = 0; // Test if CGT,UGT are needed int ucgts_needed = 0; int32_t *cgts = call->cgts - 1; int32_t *ugts = call->ugts - 1; int32_t *gts = call->gts - 2; for (isample = 0; isample < nsmpl; isample++) { int ploidy = call->ploidy ? call->ploidy[isample] : 2; cgts++; ugts++; gts += 2; if ( ugts[0]==-1 ) { gts[0] = bcf_gt_missing; gts[1] = ploidy==2 ? bcf_gt_missing : bcf_int32_vector_end; continue; } int a,b; if ( cgts[0]!=ugts[0] ) { bcf_gt2alleles(cgts[0], &a, &b); gts[0] = bcf_gt_unphased(a); gts[1] = ploidy==1 ? bcf_int32_vector_end : bcf_gt_unphased(b); } else { bcf_gt2alleles(ugts[0], &a, &b); gts[0] = bcf_gt_unphased(a); gts[1] = ploidy==1 ? bcf_int32_vector_end : bcf_gt_unphased(b); } if ( cgts[0]!=ugts[0] ) ucgts_needed = 1; call->ac[a]++; if ( ploidy==2 ) { call->ac[b]++; call->ndiploid++; if ( a!=b ) call->nhets++; } } if ( ucgts_needed ) { // Some GTs are different bcf_update_format_int32(call->hdr,rec,"UGT",call->ugts,nsmpl); bcf_update_format_int32(call->hdr,rec,"CGT",call->cgts,nsmpl); } } #endif static void mcall_trim_and_update_PLs(call_t *call, bcf1_t *rec, int nals_ori, int nals_new) { int npls_src = nals_ori*(nals_ori+1)/2; int npls_dst = nals_new*(nals_new+1)/2; // number of PL values in diploid samples, ori and new if ( call->all_diploid && npls_src == npls_dst ) return; int *pls_src = call->PLs, *pls_dst = call->PLs; int nsmpl = bcf_hdr_nsamples(call->hdr); int isample, ia; for (isample = 0; isample < nsmpl; isample++) { int ploidy = call->ploidy ? call->ploidy[isample] : 2; if ( ploidy==2 ) { for (ia=0; iapl_map[ia] ]; } else if ( ploidy==1 ) { for (ia=0; iapl_map[isrc] ]; } if ( ia1 in mcall() } pls_src += npls_src; pls_dst += npls_dst; } bcf_update_format_int32(call->hdr, rec, "PL", call->PLs, npls_dst*nsmpl); } void mcall_trim_and_update_numberR(call_t *call, bcf1_t *rec, int nals_ori, int nals_new) { if ( nals_ori==nals_new ) return; int i,j, nret, size = sizeof(float); void *tmp_ori = call->itmp, *tmp_new = call->PLs; // reusing PLs storage which is not used at this point int ntmp_ori = call->n_itmp, ntmp_new = call->mPLs; // INFO fields for (i=0; in_info; i++) { bcf_info_t *info = &rec->d.info[i]; int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_INFO,info->key); if ( vlen!=BCF_VL_R ) continue; // not a Number=R tag int type = bcf_hdr_id2type(call->hdr,BCF_HL_INFO,info->key); const char *key = bcf_hdr_int2id(call->hdr,BCF_DT_ID,info->key); nret = bcf_get_info_values(call->hdr, rec, key, &tmp_ori, &ntmp_ori, type); if ( nret<=0 ) continue; if ( nals_new==1 ) bcf_update_info_int32(call->hdr, rec, key, tmp_ori, 1); // has to be the REF, the order could not change else { for (j=0; jals_map[j]; if ( k==-1 ) continue; // to be dropped memcpy((char *)tmp_new+size*k, (char *)tmp_ori+size*j, size); } bcf_update_info_int32(call->hdr, rec, key, tmp_new, nals_new); } } // FORMAT fields for (i=0; in_fmt; i++) { bcf_fmt_t *fmt = &rec->d.fmt[i]; int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id); if ( vlen!=BCF_VL_R ) continue; // not a Number=R tag int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id); const char *key = bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id); nret = bcf_get_format_values(call->hdr, rec, key, &tmp_ori, &ntmp_ori, type); if (nret<=0) continue; int nsmpl = bcf_hdr_nsamples(call->hdr); assert( nret==nals_ori*nsmpl ); for (j=0; jals_map[k]; if ( l==-1 ) continue; // to be dropped memcpy(ptr_dst+size*l, ptr_src+size*k, size); } } bcf_update_format_int32(call->hdr, rec, key, tmp_new, nals_new*nsmpl); } call->PLs = (int32_t*) tmp_new; call->mPLs = ntmp_new; call->itmp = (int32_t*) tmp_ori; call->n_itmp = ntmp_ori; } // NB: in this function we temporarily use calls->als_map for a different // purpose to store mapping from new (target) alleles to original alleles. // static int mcall_constrain_alleles(call_t *call, bcf1_t *rec, int *unseen) { assert( call->tgt_als->n ); hts_expand(char*,call->tgt_als->n+1,call->nals,call->als); hts_expand(int,call->tgt_als->n+1,call->nals_map,call->als_map); hts_expand(int,(call->tgt_als->n+1)*(call->tgt_als->n+2)/2,call->npl_map,call->pl_map); int has_new = 0; int i, j, nals = 1; for (i=1; inals_map; i++) call->als_map[i] = -1; if ( vcmp_set_ref(call->vcmp, rec->d.allele[0], call->tgt_als->allele[0]) < 0 ) error("The reference alleles are not compatible at %s:%d .. %s vs %s\n", call->hdr->id[BCF_DT_CTG][rec->rid].key,rec->pos+1,call->tgt_als->allele[0],rec->d.allele[0]); // create mapping from new to old alleles call->als[0] = call->tgt_als->allele[0]; call->als_map[0] = 0; for (i=1; itgt_als->n; i++) { call->als[nals] = call->tgt_als->allele[i]; j = vcmp_find_allele(call->vcmp, rec->d.allele+1, rec->n_allele - 1, call->tgt_als->allele[i]); if ( j>=0 ) { // existing allele call->als_map[nals] = j+1; } else { // There is a new allele in targets which is not present in VCF. // We use the X allele to estimate PLs. Note that X may not be // present at multiallelic indels sites. In that case we use the // last allele anyway, because the least likely allele comes last // in mpileup's ALT output. call->als_map[nals] = (*unseen)>=0 ? *unseen : rec->n_allele - 1; has_new = 1; } nals++; } if ( *unseen ) { call->als_map[nals] = *unseen; call->als[nals] = rec->d.allele[*unseen]; nals++; } if ( !has_new && nals==rec->n_allele ) return 0; bcf_update_alleles(call->hdr, rec, (const char**)call->als, nals); // create mapping from new PL to old PL int k = 0; for (i=0; ials_map[i], b = call->als_map[j]; call->pl_map[k++] = a>b ? a*(a+1)/2 + b : b*(b+1)/2 + a; } } // update PL call->nPLs = bcf_get_format_int32(call->hdr, rec, "PL", &call->PLs, &call->mPLs); int nsmpl = bcf_hdr_nsamples(call->hdr); int npls_ori = call->nPLs / nsmpl; int npls_new = k; hts_expand(int32_t,npls_new*nsmpl,call->n_itmp,call->itmp); int *ori_pl = call->PLs, *new_pl = call->itmp; for (i=0; ipl_map[k]]; if ( new_pl[k]==bcf_int32_missing && *unseen>=0 ) { // missing value, and there is an unseen allele: identify the // alleles and use the lk of either AX or XX int k_ori = call->pl_map[k], ia, ib; bcf_gt2alleles(k_ori, &ia, &ib); k_ori = bcf_alleles2gt(ia,*unseen); if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(ib,*unseen); if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(*unseen,*unseen); new_pl[k] = ori_pl[k_ori]; } if ( !k && new_pl[k]==bcf_int32_vector_end ) new_pl[k]=bcf_int32_missing; } ori_pl += npls_ori; new_pl += npls_new; } bcf_update_format_int32(call->hdr, rec, "PL", call->itmp, npls_new*nsmpl); // update QS, use temporarily call->GPs to store the values int nqs = bcf_get_info_float(call->hdr, rec, "QS", &call->smpl_grp[0].qsum, &call->smpl_grp[0].nqsum); hts_expand(float,nals,call->nGPs,call->GPs); for (i=0; iGPs[i] = call->als_map[i]smpl_grp[0].qsum[call->als_map[i]] : 0; bcf_update_info_float(call->hdr, rec, "QS", call->GPs, nals); // update any Number=R tags void *tmp_ori = call->itmp, *tmp_new = call->PLs; // reusing PLs storage which is not used at this point int ntmp_ori = call->n_itmp, ntmp_new = call->mPLs; for (i=0; in_fmt; i++) { bcf_fmt_t *fmt = &rec->d.fmt[i]; int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id); if ( vlen!=BCF_VL_R ) continue; // not a Number=R tag // NB:works only for BCF_HT_INT and BCF_HT_REAL int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id); assert( type==BCF_HT_INT || type==BCF_HT_REAL ); assert( sizeof(float)==sizeof(int32_t) ); const char *key = bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id); int nret = bcf_get_format_values(call->hdr, rec, key, &tmp_ori, &ntmp_ori, type); if (nret<=0) continue; int nsmpl = bcf_hdr_nsamples(call->hdr); int size1 = sizeof(float); hts_expand(float, nsmpl * nals, ntmp_new, tmp_new); for (j=0; jn; uint8_t *ptr_new = (uint8_t *) tmp_new + j*nals*size1; for (k=0; kals_map[k]; memcpy(dst,src,size1); } } nret = bcf_update_format(call->hdr, rec, key, tmp_new, nsmpl*nals, type); assert( nret==0 ); } call->PLs = (int32_t*) tmp_new; call->mPLs = ntmp_new; call->itmp = (int32_t*) tmp_ori; call->n_itmp = ntmp_ori; if ( *unseen ) *unseen = nals-1; return 0; } /** * This function implements the multiallelic calling model. It has two major parts: * 1) determine the most likely set of alleles and calculate the quality of ref/non-ref site * 2) determine and set the genotypes * In various places in between, the BCF record gets updated. */ int mcall(call_t *call, bcf1_t *rec) { int i,j, unseen = call->unseen; // Force alleles when calling genotypes given alleles was requested if ( call->flag & CALL_CONSTR_ALLELES && mcall_constrain_alleles(call, rec, &unseen)!=0 ) return -2; int nsmpl = bcf_hdr_nsamples(call->hdr); int nals_ori = rec->n_allele; hts_expand(int,nals_ori,call->nac,call->ac); hts_expand(int,nals_ori,call->nals_map,call->als_map); hts_expand(int,nals_ori*(nals_ori+1)/2,call->npl_map,call->pl_map); // Get the genotype likelihoods call->nPLs = bcf_get_format_int32(call->hdr, rec, "PL", &call->PLs, &call->mPLs); if ( call->nPLs!=nsmpl*nals_ori*(nals_ori+1)/2 && call->nPLs!=nsmpl*nals_ori ) // a mixture of diploid and haploid or haploid only error("Wrong number of PL fields? nals=%d npl=%d\n", nals_ori,call->nPLs); // Convert PLs to probabilities int ngts_ori = nals_ori*(nals_ori+1)/2; hts_expand(double, call->nPLs, call->npdg, call->pdg); set_pdg(call->pl2p, call->PLs, call->pdg, nsmpl, ngts_ori, unseen); // Get sum of qualities, serves as an AF estimate, f_x = QS/N in Eq. 1 in call-m math notes. if ( call->nsmpl_grp == 1 ) { int nqs = bcf_get_info_float(call->hdr, rec, "QS", &call->smpl_grp[0].qsum, &call->smpl_grp[0].nqsum); if ( nqs<=0 ) error("The QS annotation not present at %s:%d\n", bcf_seqname(call->hdr,rec),rec->pos+1); if ( nqs < nals_ori ) { // Some of the listed alleles do not have the corresponding QS field. This is // typically ref-only site with <*> in ALT. hts_expand(float,nals_ori,call->smpl_grp[0].nqsum,call->smpl_grp[0].qsum); for (i=nqs; ismpl_grp[0].qsum[i] = 0; } } else { for (j=0; jnsmpl_grp; j++) { hts_expand(float,nals_ori,call->smpl_grp[j].nqsum,call->smpl_grp[j].qsum); memset(call->smpl_grp[j].qsum, 0, sizeof(float)*nals_ori); } // Use FORMAT/AD or FORMAT/QS int nad = bcf_get_format_int32(call->hdr, rec, call->sample_groups_tag, &call->ADs, &call->nADs); if ( nad<1 ) error("Error: FORMAT/%s is required with the -G option, mpileup must be run with \"-a AD\" or \"-a QS\"\n",call->sample_groups_tag); nad /= bcf_hdr_nsamples(call->hdr); for (i=0; insmpl_grp; i++) { int is; smpl_grp_t *grp = &call->smpl_grp[i]; hts_expand(float,nals_ori,grp->nqsum,grp->qsum); for (j=0; jqsum[j] = 0; for (is=0; isnsmpl; is++) { int ismpl = grp->smpl[is]; int32_t *ptr = call->ADs + ismpl*nad; float sum = 0; for (j=0; jqsum[j] += ptr[j]/sum; } } } } } // If available, take into account reference panel AFs if ( call->prior_AN && bcf_get_info_int32(call->hdr, rec, call->prior_AN ,&call->ac, &call->nac)==1 ) { int an = call->ac[0]; // number of alleles total, proceed only if not zero; reuse call->ac if ( an > 0 && bcf_get_info_int32(call->hdr, rec, call->prior_AC ,&call->ac, &call->nac)==nals_ori-1 ) // number of ALT alleles { int ac0 = an; // this will become the number of REFs for (i=0; iac[i]==bcf_int32_vector_end ) break; if ( call->ac[i]==bcf_int32_missing ) continue; ac0 -= call->ac[i]; // here an*0.5 is the number of samples in the populatio and ac*0.5 is the AF weighted by the number of samples for (j=0; jnsmpl_grp; j++) call->smpl_grp[j].qsum[i+1] = (call->smpl_grp[j].qsum[i+1] + 0.5*call->ac[i]) / (call->smpl_grp[j].nsmpl + 0.5*an); } if ( ac0<0 ) error("Incorrect %s,%s values at %s:%d\n", call->prior_AN,call->prior_AC,bcf_seqname(call->hdr,rec),rec->pos+1); for (j=0; jnsmpl_grp; j++) call->smpl_grp[j].qsum[0] = (call->smpl_grp[j].qsum[0] + 0.5*ac0) / (call->smpl_grp[j].nsmpl + 0.5*an); } } // normalize so that QS sums to 1 for each group for (j=0; jnsmpl_grp; j++) { float sum = 0; for (i=0; ismpl_grp[j].qsum[i]; if ( sum ) for (i=0; ismpl_grp[j].qsum[i] /= sum; } bcf_update_info_int32(call->hdr, rec, "QS", NULL, 0); // remove QS tag if ( nals_ori > 8*sizeof(call->als_new) ) { fprintf(stderr,"Too many alleles at %s:%"PRId64", skipping.\n", bcf_seqname(call->hdr,rec),(int64_t) rec->pos+1); return 0; } // For each group find the best combination of alleles call->als_new = 0; double ref_lk = -HUGE_VAL, lk_sum = -HUGE_VAL, max_qual = -HUGE_VAL; for (j=0; jnsmpl_grp; j++) { smpl_grp_t *grp = &call->smpl_grp[j]; mcall_find_best_alleles(call, nals_ori, grp); call->als_new |= grp->als; if ( grp->max_lk==-HUGE_VAL ) continue; double qual = -4.343*(grp->ref_lk - logsumexp2(grp->lk_sum,grp->ref_lk)); if ( max_qual < qual ) { max_qual = qual; lk_sum = grp->lk_sum; ref_lk = grp->ref_lk; } } // Make sure the REF allele is always present if ( !(call->als_new&1) ) call->als_new |= 1; int is_variant = call->als_new==1 ? 0 : 1; if ( call->flag & CALL_VARONLY && !is_variant ) return 0; call->nals_new = 0; for (i=0; iflag&CALL_KEEP_UNSEEN) && i==unseen && call->nals_new==1 ) { call->nals_new++; call->als_new |= 1<0 && i==unseen ) continue; if ( call->flag & CALL_KEEPALT ) call->als_new |= 1<als_new & (1<nals_new++; } init_allele_trimming_maps(call,nals_ori,call->als_new); int nAC = 0; if ( call->als_new==1 ) // only REF allele on output { mcall_set_ref_genotypes(call,nals_ori); bcf_update_format_int32(call->hdr, rec, "PL", NULL, 0); // remove PL, useless now } else if ( !is_variant ) { mcall_set_ref_genotypes(call,nals_ori); // running with -A, prevent mcall_call_genotypes from putting some ALT back mcall_trim_and_update_PLs(call, rec, nals_ori, call->nals_new); } else { // The most likely set of alleles includes non-reference allele (or was enforced), call genotypes. // Note that it is a valid outcome if the called genotypes exclude some of the ALTs. int ngts_new = call->nals_new*(call->nals_new+1)/2; hts_expand(float,ngts_new*nsmpl,call->nGPs,call->GPs); for (i=0; inals_new; i++) call->ac[i] = 0; if ( call->flag & CALL_CONSTR_TRIO && call->nals_new>4 ) { fprintf(stderr,"Too many alleles at %s:%"PRId64", skipping.\n", bcf_seqname(call->hdr,rec),(int64_t) rec->pos+1); return 0; } if ( call->output_tags & (CALL_FMT_GQ|CALL_FMT_GP) ) { memset(call->GPs,0,nsmpl*ngts_new*sizeof(*call->GPs)); memset(call->GQs,0,nsmpl*sizeof(*call->GQs)); } for (i=0; insmpl_grp; i++) { if ( call->flag & CALL_CONSTR_TRIO ) error("todo: constrained trio calling temporarily disabled\n"); //mcall_call_trio_genotypes(call,rec,nals,&call->smpl_grp[i]); else mcall_call_genotypes(call,nals_ori,&call->smpl_grp[i]); } // Skip the site if all samples are 0/0. This can happen occasionally. for (i=1; inals_new; i++) nAC += call->ac[i]; if ( !nAC && call->flag & CALL_VARONLY ) return 0; if ( call->output_tags & CALL_FMT_GP ) bcf_update_format_float(call->hdr, rec, "GP", call->GPs, nsmpl*ngts_new); if ( call->output_tags & CALL_FMT_GQ ) bcf_update_format_int32(call->hdr, rec, "GQ", call->GQs, nsmpl); mcall_trim_and_update_PLs(call,rec,nals_ori,call->nals_new); } if ( nals_ori!=call->nals_new ) mcall_trim_and_update_numberR(call,rec,nals_ori,call->nals_new); // Set QUAL if ( nAC ) { // Quality of a variant site. fabs() to avoid negative zeros in VCF output when CALL_KEEPALT is set rec->qual = max_qual; } else { // Set the quality of a REF site if ( lk_sum!=-HUGE_VAL ) // no support from (high quality) reads, so QUAL=1-prior rec->qual = -4.343*(lk_sum - logsumexp2(lk_sum,ref_lk)); else if ( call->ac[0] ) rec->qual = call->theta ? -4.343*call->theta : 0; else bcf_float_set_missing(rec->qual); } // AC, AN if ( call->nals_new>1 ) bcf_update_info_int32(call->hdr, rec, "AC", call->ac+1, call->nals_new-1); nAC += call->ac[0]; bcf_update_info_int32(call->hdr, rec, "AN", &nAC, 1); // Remove unused alleles hts_expand(char*,call->nals_new,call->nals,call->als); for (i=0; ials_map[i]>=0 ) call->als[call->als_map[i]] = rec->d.allele[i]; bcf_update_alleles(call->hdr, rec, (const char**)call->als, call->nals_new); bcf_update_genotypes(call->hdr, rec, call->gts, nsmpl*2); // DP4 and PV4 tags if ( bcf_get_info_float(call->hdr, rec, "I16", &call->anno16, &call->n16)==16 ) { int32_t dp[4]; dp[0] = call->anno16[0]; dp[1] = call->anno16[1]; dp[2] = call->anno16[2]; dp[3] = call->anno16[3]; bcf_update_info_int32(call->hdr, rec, "DP4", dp, 4); int32_t mq = (call->anno16[8]+call->anno16[10])/(call->anno16[0]+call->anno16[1]+call->anno16[2]+call->anno16[3]); bcf_update_info_int32(call->hdr, rec, "MQ", &mq, 1); if ( call->output_tags & CALL_FMT_PV4 ) { anno16_t a; float tmpf[4]; int is_tested = test16(call->anno16, &a) >= 0 && a.is_tested ? 1 : 0; if ( is_tested ) { for (i=0; i<4; i++) tmpf[i] = a.p[i]; bcf_update_info_float(call->hdr, rec, "PV4", tmpf, 4); } } } bcf_update_info_int32(call->hdr, rec, "I16", NULL, 0); // remove I16 tag return is_variant ? call->nals_new : 1; } pysam-0.23.0/bcftools/mcall.c.pysam.c000066400000000000000000001772671475062545500174060ustar00rootroot00000000000000#include "bcftools.pysam.h" /* mcall.c -- multiallelic and rare variant calling. Copyright (C) 2012-2022 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "call.h" #include "prob1.h" // Using priors for GTs does not seem to be mathematically justified. Although // it seems effective in removing false calls, it also flips a significant // proportion of HET genotypes. Better is to filter by FORMAT/GQ using // `bcftools filter`. #define USE_PRIOR_FOR_GTS 0 // Go with uniform PLs for samples with no coverage. If unset, missing // genotypes is reported instead. #define FLAT_PDG_FOR_MISSING 0 int test16(float *anno16, anno16_t *a); void qcall_init(call_t *call) { return; } void qcall_destroy(call_t *call) { return; } int qcall(call_t *call, bcf1_t *rec) { // QCall format: // chromosome, position, reference allele, depth, mapping quality, 0, .. error("TODO: qcall output\n"); return 0; } void call_init_pl2p(call_t *call) { int i; for (i=0; i<256; i++) call->pl2p[i] = pow(10., -i/10.); } // Macros for accessing call->trio and call->ntrio #define FTYPE_222 0 // family type: all diploid #define FTYPE_121 1 // chrX, the child is a boy #define FTYPE_122 2 // chrX, a girl #define FTYPE_101 3 // chrY, boy #define FTYPE_100 4 // chrY, girl #define GT_SKIP 0xf // empty genotype (chrY in females) #define IS_POW2(x) (!((x) & ((x) - 1))) // zero is permitted #define IS_HOM(x) IS_POW2(x) // Pkij = P(k|i,j) tells how likely it is to be a het if the parents // are homs etc. The consistency of i,j,k has been already checked. // Parameters are alleles and ploidy of father, mother, kid // Returns 2/Pkij. int calc_Pkij(int fals, int mals, int kals, int fpl, int mpl, int kpl) { int als = fals|mals|kals; if ( IS_HOM(als) ) return 2; // all are the same: child must be a HOM, P=1 if ( fpl==1 ) { if ( kpl==1 ) // chr X, the child is a boy, the copy is inherited from the mother { if ( IS_HOM(mals) ) return 2; // 0 11 -> P(1) = 1 return 4; // 0 01 -> P(0) = P(1) = 1/2 } // chr X, the child is a girl if ( IS_HOM(mals) ) return 2; // 0 11 -> P(01) = 1 return 4; // 0 01 -> P(00) = P(01) = 1/2 } if ( IS_HOM(fals) && IS_HOM(mals) ) return 2; // 00 11 01, the child must be a HET, P=1 if ( !IS_HOM(fals) && !IS_HOM(mals) ) { if ( IS_HOM(kals) ) return 8; // 01 01 00 or 01 01 11, P(k=HOM) = 1/4 return 4; // 01 01 01, P(k=HET) = 1/2 } return 4; // 00 01, P(k=HET) = P(k=HOM) = 1/2 } // Initialize ntrio and trio: ntrio lists the number of possible // genotypes given combination of haploid/diploid genomes and the // number of alleles. trio lists allowed genotype combinations: // 4bit: 2/Pkij, 4: father, 4: mother, 4: child // See also mcall_call_trio_genotypes() // static void mcall_init_trios(call_t *call) { if ( call->prior_AN ) { int id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,call->prior_AN); if ( id==-1 ) error("No such tag \"%s\"\n", call->prior_AN); if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) ) error("No such FORMAT tag \"%s\"\n", call->prior_AN); id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,call->prior_AC); if ( id==-1 ) error("No such tag \"%s\"\n", call->prior_AC); if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) ) error("No such FORMAT tag \"%s\"\n", call->prior_AC); } // 23, 138, 478 possible diploid trio genotypes with 2, 3, 4 alleles call->ntrio[FTYPE_222][2] = 15; call->ntrio[FTYPE_222][3] = 78; call->ntrio[FTYPE_222][4] = 250; call->ntrio[FTYPE_121][2] = 8; call->ntrio[FTYPE_121][3] = 27; call->ntrio[FTYPE_121][4] = 64; call->ntrio[FTYPE_122][2] = 8; call->ntrio[FTYPE_122][3] = 27; call->ntrio[FTYPE_122][4] = 64; call->ntrio[FTYPE_101][2] = 2; call->ntrio[FTYPE_101][3] = 3; call->ntrio[FTYPE_101][4] = 4; call->ntrio[FTYPE_100][2] = 2; call->ntrio[FTYPE_100][3] = 3; call->ntrio[FTYPE_100][4] = 4; int nals, itype; for (itype=0; itype<=4; itype++) { for (nals=2; nals<=4; nals++) call->trio[itype][nals] = (uint16_t*) malloc(sizeof(uint16_t)*call->ntrio[itype][nals]); } // max 10 possible diploid genotypes int gts[10]; for (nals=2; nals<=4; nals++) { int i,j,k, n = 0, ngts = 0; for (i=0; itrio[FTYPE_222][nals][n++] = Pkij<<12 | i<<8 | j<<4 | k; // father, mother, child } assert( n==call->ntrio[FTYPE_222][nals] ); // 121: chrX, boy n = 0; for (i=0; itrio[FTYPE_121][nals][n++] = Pkij<<12 | i<<8 | j<<4 | k; } assert( n==call->ntrio[FTYPE_121][nals] ); // 122: chrX, girl n = 0; for (i=0; itrio[FTYPE_122][nals][n++] = Pkij<<12 | i<<8 | j<<4 | k; } assert( n==call->ntrio[FTYPE_122][nals] ); // 101: chrY, boy n = 0; for (i=0; itrio[FTYPE_101][nals][n++] = 1<<12 | i<<8 | GT_SKIP<<4 | k; } assert( n==call->ntrio[FTYPE_101][nals] ); // 100: chrY, girl n = 0; for (i=0; itrio[FTYPE_100][nals][n++] = 1<<12 | i<<8 | GT_SKIP<<4 | GT_SKIP; } assert( n==call->ntrio[FTYPE_100][nals] ); } call->GLs = (double*) calloc(bcf_hdr_nsamples(call->hdr)*10,sizeof(double)); int i, j; for (i=0; infams; i++) { family_t *fam = &call->fams[i]; int ploidy[3]; for (j=0; j<3; j++) ploidy[j] = call->ploidy[fam->sample[j]]; if ( ploidy[FATHER]==2 ) // not X, not Y { if ( ploidy[MOTHER]!=2 || ploidy[CHILD]!=2 ) error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]); fam->type = FTYPE_222; continue; } if ( ploidy[FATHER]!=1 || ploidy[MOTHER]==1 ) error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]); if ( ploidy[MOTHER]==2 ) // X { if ( ploidy[CHILD]==0 ) error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]); fam->type = ploidy[CHILD]==2 ? FTYPE_122 : FTYPE_121; // a girl or a boy } else // Y { if ( ploidy[CHILD]==2 ) error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]); fam->type = ploidy[CHILD]==0 ? FTYPE_100 : FTYPE_101; // a girl or a boy } } } static void mcall_destroy_trios(call_t *call) { int i, j; for (i=2; i<=4; i++) for (j=0; j<=4; j++) free(call->trio[j][i]); } static void init_sample_groups(call_t *call) { int i, nsmpl = bcf_hdr_nsamples(call->hdr); if ( !call->sample_groups ) { // standard pooled calling, all samples in the same group call->nsmpl_grp = 1; call->smpl_grp = (smpl_grp_t*)calloc(1,sizeof(*call->smpl_grp)); call->smpl_grp[0].nsmpl = nsmpl; call->smpl_grp[0].smpl = (uint32_t*)calloc(call->smpl_grp[0].nsmpl,sizeof(uint32_t)); for (i=0; ismpl_grp[0].smpl[i] = i; return; } if ( call->sample_groups_tag ) { // Is the tag defined in the header? int tag_id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,call->sample_groups_tag); if ( tag_id==-1 ) error("No such tag \"%s\"\n",call->sample_groups_tag); if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) error("No such FORMAT tag \"%s\"\n", call->sample_groups_tag); } else { int tag_id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,"QS"); if ( tag_id >= 0 && bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) call->sample_groups_tag = "QS"; else { tag_id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,"AD"); if ( tag_id >= 0 && bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) call->sample_groups_tag = "AD"; else error("Error: neither \"AD\" nor \"QS\" FORMAT tag exists and no alternative given with -G\n"); } } // Read samples/groups if ( !strcmp("-",call->sample_groups) ) { // single-sample calling, each sample creates its own group call->nsmpl_grp = nsmpl; call->smpl_grp = (smpl_grp_t*)calloc(nsmpl,sizeof(*call->smpl_grp)); for (i=0; ismpl_grp[i].nsmpl = 1; call->smpl_grp[i].smpl = (uint32_t*)calloc(call->smpl_grp[i].nsmpl,sizeof(uint32_t)); call->smpl_grp[i].smpl[0] = i; } } else { int nlines; char **lines = hts_readlist(call->sample_groups, 1, &nlines); if ( !lines ) error("Could not read the file: %s\n", call->sample_groups); uint32_t *smpl2grp = (uint32_t*)calloc(nsmpl,sizeof(uint32_t)); uint32_t *grp2n = (uint32_t*)calloc(nsmpl,sizeof(uint32_t)); void *grp2idx = khash_str2int_init(); call->nsmpl_grp = 0; for (i=0; isample_groups,lines[i]); char *tmp = ptr; while ( *ptr && isspace(*ptr) ) ptr++; if ( !*ptr ) error("Could not parse the line in %s, expected a sample name followed by tab and a population name: %s\n",call->sample_groups,lines[i]); *tmp = 0; int ismpl = bcf_hdr_id2int(call->hdr, BCF_DT_SAMPLE, lines[i]); if ( ismpl<0 ) continue; if ( smpl2grp[ismpl] ) error("Error: the sample \"%s\" is listed twice in %s\n", lines[i],call->sample_groups); if ( !khash_str2int_has_key(grp2idx,ptr+1) ) { khash_str2int_set(grp2idx, ptr+1, call->nsmpl_grp); call->nsmpl_grp++; } int igrp = -1; if ( khash_str2int_get(grp2idx, ptr+1, &igrp)!=0 ) error("This should not happen, fixme: %s\n",ptr+1); grp2n[igrp]++; smpl2grp[ismpl] = igrp+1; // +1 to distinguish unlisted samples } khash_str2int_destroy(grp2idx); if ( !call->nsmpl_grp ) error("Could not parse the file, no matching samples found: %s\n", call->sample_groups); call->smpl_grp = (smpl_grp_t*)calloc(call->nsmpl_grp,sizeof(*call->smpl_grp)); for (i=0; ihdr->samples[i],call->sample_groups); int igrp = smpl2grp[i] - 1; if ( !call->smpl_grp[igrp].nsmpl ) call->smpl_grp[igrp].smpl = (uint32_t*)calloc(grp2n[igrp],sizeof(uint32_t)); call->smpl_grp[igrp].smpl[call->smpl_grp[igrp].nsmpl] = i; call->smpl_grp[igrp].nsmpl++; } free(smpl2grp); free(grp2n); for (i=0; insmpl_grp; i++) { free(call->smpl_grp[i].qsum); free(call->smpl_grp[i].smpl); } free(call->smpl_grp); } void mcall_init(call_t *call) { init_sample_groups(call); call_init_pl2p(call); call->nals_map = 5; call->als_map = (int*) malloc(sizeof(int)*call->nals_map); call->npl_map = 5*(5+1)/2; // will be expanded later if necessary call->pl_map = (int*) malloc(sizeof(int)*call->npl_map); call->gts = (int32_t*) calloc(bcf_hdr_nsamples(call->hdr)*2,sizeof(int32_t)); // assuming at most diploid everywhere if ( call->flag & CALL_CONSTR_TRIO ) { call->cgts = (int32_t*) calloc(bcf_hdr_nsamples(call->hdr),sizeof(int32_t)); call->ugts = (int32_t*) calloc(bcf_hdr_nsamples(call->hdr),sizeof(int32_t)); mcall_init_trios(call); bcf_hdr_append(call->hdr,"##FORMAT="); bcf_hdr_append(call->hdr,"##FORMAT="); } if ( call->flag & CALL_CONSTR_ALLELES ) call->vcmp = vcmp_init(); bcf_hdr_append(call->hdr,"##FORMAT="); if ( call->output_tags & CALL_FMT_GQ ) bcf_hdr_append(call->hdr,"##FORMAT="); if ( call->output_tags & CALL_FMT_GP ) bcf_hdr_append(call->hdr,"##FORMAT="); if ( call->output_tags & (CALL_FMT_GQ|CALL_FMT_GP) ) call->GQs = (int32_t*) malloc(sizeof(int32_t)*bcf_hdr_nsamples(call->hdr)); bcf_hdr_append(call->hdr,"##INFO="); bcf_hdr_append(call->hdr,"##INFO="); bcf_hdr_append(call->hdr,"##INFO="); bcf_hdr_append(call->hdr,"##INFO="); if ( call->output_tags & CALL_FMT_PV4 ) bcf_hdr_append(call->hdr,"##INFO=\n"); // init the prior if ( call->theta>0 ) { int i, n = 0; if ( !call->ploidy ) n = 2*bcf_hdr_nsamples(call->hdr); // all are diploid else { for (i=0; ihdr); i++) n += call->ploidy[i]; } // Watterson factor, here aM_1 = aM_2 = 1 double aM = 1; for (i=2; itheta *= aM; if ( call->theta >= 1 ) { fprintf(bcftools_stderr,"The prior is too big (theta*aM=%.2f), going with 0.99\n", call->theta); call->theta = 0.99; } call->theta = log(call->theta); } } void mcall_destroy(call_t *call) { destroy_sample_groups(call); if (call->vcmp) vcmp_destroy(call->vcmp); free(call->itmp); mcall_destroy_trios(call); free(call->GPs); free(call->ADs); free(call->GLs); free(call->GQs); free(call->anno16); free(call->PLs); free(call->als_map); free(call->pl_map); free(call->gts); free(call->cgts); free(call->ugts); free(call->pdg); free(call->als); free(call->ac); return; } // Inits P(D|G): convert PLs from log space and normalize. In case of zero // depth, missing PLs are all zero. In this case, pdg's are set to 0 // so that the corresponding genotypes can be set as missing and the // qual calculation is not affected. // Missing values are replaced by generic likelihoods when X (unseen allele) is // present. // NB: While the -m calling model uses the pdgs in canonical order, // the original samtools -c calling code uses pdgs in reverse order (AA comes // first, RR last). // NB: Ploidy is not taken into account here, which is incorrect. void set_pdg(double *pl2p, int *PLs, double *pdg, int n_smpl, int n_gt, int unseen) { int i, j, nals; // find out the number of alleles, expecting diploid genotype likelihoods bcf_gt2alleles(n_gt-1, &i, &nals); assert( i==nals ); nals++; for (i=0; i new(j) for (i=0; ials_map[i] = nout++; else call->als_map[i] = -1; } if ( !call->pl_map ) return; // pl_map: new(k) -> old(l) int k = 0, l = 0; for (i=0; ipl_map[k++] = l; l++; } } } /** log(exp(a)+exp(b)) */ static inline double logsumexp2(double a, double b) { if ( a>b ) return log(1 + exp(b-a)) + a; else return log(1 + exp(a-b)) + b; } // Macro to set the most likely alleles #define UPDATE_MAX_LKs(als,sum) { \ if ( max_lknsmpl; int ngts = nals*(nals+1)/2; // Single allele for (ia=0; iapdg + grp->smpl[ismpl]*ngts + iaa; if ( *pdg ) { lk_tot += log(*pdg); lk_tot_set = 1; } } if ( ia==0 ) ref_lk = lk_tot; // likelihood of 0/0 for all samples else lk_tot += call->theta; // the prior UPDATE_MAX_LKs(1<0 && lk_tot_set); } // Two alleles if ( nals>1 ) { for (ia=0; iaqsum[ia]==0 ) continue; int iaa = (ia+1)*(ia+2)/2-1; for (ib=0; ibqsum[ib]==0 ) continue; double lk_tot = 0; int lk_tot_set = 0; double fa = grp->qsum[ia]/(grp->qsum[ia] + grp->qsum[ib]); double fb = grp->qsum[ib]/(grp->qsum[ia] + grp->qsum[ib]); double fa2 = fa*fa; double fb2 = fb*fb; double fab = 2*fa*fb; int is, ibb = (ib+1)*(ib+2)/2-1, iab = iaa - ia + ib; for (is=0; issmpl[is]; double *pdg = call->pdg + ismpl*ngts; double val = 0; if ( !call->ploidy || call->ploidy[ismpl]==2 ) val = fa2*pdg[iaa] + fb2*pdg[ibb] + fab*pdg[iab]; else if ( call->ploidy && call->ploidy[ismpl]==1 ) val = fa*pdg[iaa] + fb*pdg[ibb]; if ( val ) { lk_tot += log(val); lk_tot_set = 1; } } if ( ia!=0 ) lk_tot += call->theta; // the prior if ( ib!=0 ) lk_tot += call->theta; UPDATE_MAX_LKs(1<2 ) { for (ia=0; iaqsum[ia]==0 ) continue; int iaa = (ia+1)*(ia+2)/2-1; for (ib=0; ibqsum[ib]==0 ) continue; int ibb = (ib+1)*(ib+2)/2-1; int iab = iaa - ia + ib; for (ic=0; icqsum[ic]==0 ) continue; double lk_tot = 0; int lk_tot_set = 0; double fa = grp->qsum[ia]/(grp->qsum[ia] + grp->qsum[ib] + grp->qsum[ic]); double fb = grp->qsum[ib]/(grp->qsum[ia] + grp->qsum[ib] + grp->qsum[ic]); double fc = grp->qsum[ic]/(grp->qsum[ia] + grp->qsum[ib] + grp->qsum[ic]); double fa2 = fa*fa; double fb2 = fb*fb; double fc2 = fc*fc; double fab = 2*fa*fb, fac = 2*fa*fc, fbc = 2*fb*fc; int is, icc = (ic+1)*(ic+2)/2-1; int iac = iaa - ia + ic, ibc = ibb - ib + ic; for (is=0; issmpl[is]; double *pdg = call->pdg + ismpl*ngts; double val = 0; if ( !call->ploidy || call->ploidy[ismpl]==2 ) val = fa2*pdg[iaa] + fb2*pdg[ibb] + fc2*pdg[icc] + fab*pdg[iab] + fac*pdg[iac] + fbc*pdg[ibc]; else if ( call->ploidy && call->ploidy[ismpl]==1 ) val = fa*pdg[iaa] + fb*pdg[ibb] + fc*pdg[icc]; if ( val ) { lk_tot += log(val); lk_tot_set = 1; } } if ( ia!=0 ) lk_tot += call->theta; // the prior if ( ib!=0 ) lk_tot += call->theta; // the prior if ( ic!=0 ) lk_tot += call->theta; // the prior UPDATE_MAX_LKs(1<max_lk = max_lk; grp->ref_lk = ref_lk; grp->lk_sum = lk_sum; grp->als = max_als; grp->nals = n; return n; } // Sets GT=0/0 or GT=. if PL=0,0,0 static void mcall_set_ref_genotypes(call_t *call, int nals_ori) { int i; int ngts = nals_ori*(nals_ori+1)/2; // need this to distinguish between GT=0/0 vs GT=. int nsmpl = bcf_hdr_nsamples(call->hdr); for (i=0; iac[i] = 0; // nals_new<=nals_ori, never mind setting extra 0's // Set all genotypes to 0/0 or 0 int *gts = call->gts; double *pdg = call->pdg; int isample; for (isample = 0; isample < nsmpl; isample++) { int ploidy = call->ploidy ? call->ploidy[isample] : 2; for (i=0; iac[0] += ploidy; } gts += 2; pdg += ngts; } } static void mcall_call_genotypes(call_t *call, int nals_ori, smpl_grp_t *grp) { int ia, ib, i; int ngts_ori = nals_ori*(nals_ori+1)/2; int ngts_new = call->nals_new*(call->nals_new+1)/2; int nsmpl = grp->nsmpl; #if USE_PRIOR_FOR_GTS float prior = exp(call->theta); #endif int is; for (is = 0; is < nsmpl; is++) { int ismpl = grp->smpl[is]; double *pdg = call->pdg + ismpl*ngts_ori; float *gps = call->GPs + ismpl*ngts_new; int *gts = call->gts + ismpl*2; int ploidy = call->ploidy ? call->ploidy[ismpl] : 2; assert( ploidy>=0 && ploidy<=2 ); if ( !ploidy ) { gts[0] = bcf_gt_missing; gts[1] = bcf_int32_vector_end; gps[0] = -1; continue; } #if !FLAT_PDG_FOR_MISSING // Skip samples with zero depth, they have all pdg's equal to 0 for (i=0; ials & 1<qsum[ia]*grp->qsum[ia] : pdg[iaa]*grp->qsum[ia]; #if USE_PRIOR_FOR_GTS if ( ia!=0 ) lk *= prior; #endif int igt = ploidy==2 ? bcf_alleles2gt(call->als_map[ia],call->als_map[ia]) : call->als_map[ia]; gps[igt] = lk; if ( best_lk < lk ) { best_lk = lk; gts[0] = bcf_gt_unphased(call->als_map[ia]); } } if ( ploidy==2 ) { gts[1] = gts[0]; for (ia=0; iaals & 1<als & 1<qsum[ia]*grp->qsum[ib]; #if USE_PRIOR_FOR_GTS if ( ia!=0 ) lk *= prior; if ( ib!=0 ) lk *= prior; #endif int igt = bcf_alleles2gt(call->als_map[ia],call->als_map[ib]); gps[igt] = lk; if ( best_lk < lk ) { best_lk = lk; gts[0] = bcf_gt_unphased(call->als_map[ib]); gts[1] = bcf_gt_unphased(call->als_map[ia]); } } } } else gts[1] = bcf_int32_vector_end; call->ac[ bcf_gt_allele(gts[0]) ]++; if ( gts[1]!=bcf_int32_vector_end ) call->ac[ bcf_gt_allele(gts[1]) ]++; } if ( !(call->output_tags & (CALL_FMT_GQ|CALL_FMT_GP)) ) return; double max, sum; for (is=0; issmpl[is]; float *gps = call->GPs + ismpl*ngts_new; int nmax; if ( call->ploidy ) { if ( call->ploidy[ismpl]==2 ) nmax = ngts_new; else if ( call->ploidy[ismpl]==1 ) nmax = grp->nals; else nmax = 0; } else nmax = ngts_new; max = gps[0]; if ( max<0 || nmax==0 ) { // no call if ( call->output_tags & CALL_FMT_GP ) { for (i=0; iGQs[ismpl] = 0; continue; } sum = gps[0]; for (i=1; iGQs[ismpl] = max<=INT8_MAX ? max : INT8_MAX; if ( call->output_tags & CALL_FMT_GP ) { assert( max ); for (i=0; ihdr); int ngts = nals*(nals+1)/2; int nout_gts = nals_new*(nals_new+1)/2; double *gls = call->GLs - nout_gts; double *pdg = call->pdg - ngts; // Calculate individuals' genotype likelihoods P(X=i) int isample; for (isample = 0; isample < nsmpl; isample++) { int ploidy = call->ploidy ? call->ploidy[isample] : 2; int32_t *gts = call->ugts + isample; gls += nout_gts; pdg += ngts; // Skip samples with all pdg's equal to 1. These have zero depth. for (i=0; ismpl_grp.grp[call->smpl_grp.smpl2grp[isample]]; double sum_lk = 0; double best_lk = 0; for (ia=0; iaals_map[ia],call->als_map[ia]); double lk = ploidy==2 ? pdg[iaa]*grp->qsum[ia]*grp->qsum[ia] : pdg[iaa]*grp->qsum[ia]; sum_lk += lk; gls[idx] = lk; if ( best_lk < lk ) { best_lk = lk; gts[0] = bcf_alleles2gt(call->als_map[ia],call->als_map[ia]); } } if ( ploidy==2 ) { for (ia=0; iaals_map[ia],call->als_map[ib]); double lk = 2*pdg[iab]*grp->qsum[ia]*grp->qsum[ib]; sum_lk += lk; gls[idx] = lk; if ( best_lk < lk ) { best_lk = lk; gts[0] = bcf_alleles2gt(call->als_map[ib],call->als_map[ia]); } } } } for (i=0; itrio_Pm_ins<0 && call->trio_Pm_del<0 ) trio_Pm = call->trio_Pm_SNPs; // the same Pm for indels and SNPs requested else { int ret = bcf_get_variant_types(rec); if ( !(ret & VCF_INDEL) ) trio_Pm = call->trio_Pm_SNPs; else { if ( call->trio_Pm_ins<0 ) // dynamic calculation, trio_Pm_del holds the scaling factor { trio_Pm = rec->d.var[1].n<0 ? -21.9313 - 0.2856*rec->d.var[1].n : -22.8689 + 0.2994*rec->d.var[1].n; trio_Pm = 1 - call->trio_Pm_del * exp(trio_Pm); } else // snps and indels set explicitly { trio_Pm = rec->d.var[1].n<0 ? call->trio_Pm_del : call->trio_Pm_ins; } } } // Calculate constrained likelihoods and determine genotypes int ifm; for (ifm=0; ifmnfams; ifm++) { family_t *fam = &call->fams[ifm]; int ntrio = call->ntrio[fam->type][nals_new]; uint16_t *trio = call->trio[fam->type][nals_new]; // Unconstrained likelihood int uc_itr = 0; double uc_lk = 0; for (i=0; i<3; i++) // for father, mother, child { int ismpl = fam->sample[i]; double *gl = call->GLs + nout_gts*ismpl; if ( gl[0]==1 ) continue; int j, jmax = 0; double max = gl[0]; for (j=1; jsample[i]; double *gl = call->GLs + nout_gts*ismpl; if ( gl[0]==1 ) continue; int igt = trio[itr]>>((2-i)*4) & 0xf; assert( !call->ploidy || call->ploidy[ismpl]>0 ); if ( igt==GT_SKIP ) continue; lk += gl[igt]; npresent++; // fprintf(bcftools_stderr," %e", gl[igt]); } // fprintf(bcftools_stderr,"\t\t"); double Pkij = npresent==3 ? (double)2/(trio[itr]>>12) : 1; // with missing genotypes Pkij's are different lk += log(1 - trio_Pm * (1 - Pkij)); // fprintf(bcftools_stderr,"%d%d%d\t%e\t%.2f\n", trio[itr]>>8&0xf,trio[itr]>>4&0xf,trio[itr]&0xf, lk, Pkij); if ( c_lk < lk ) { c_lk = lk; c_itr = trio[itr]; } if ( uc_itr==trio[itr] ) uc_is_mendelian = 1; } if ( !uc_is_mendelian ) { uc_lk += log(1 - trio_Pm); // fprintf(bcftools_stderr,"c_lk=%e uc_lk=%e c_itr=%d%d%d uc_itr=%d%d%d\n", c_lk,uc_lk,c_itr>>8&0xf,c_itr>>4&0xf,c_itr&0xf,uc_itr>>8&0xf,uc_itr>>4&0xf,uc_itr&0xf); if ( c_lk < uc_lk ) { c_lk = uc_lk; c_itr = uc_itr; } } // fprintf(bcftools_stderr,"best_lk=%e best_itr=%d%d%d uc_itr=%d%d%d\n", c_lk,c_itr>>8&0xf,c_itr>>4&0xf,c_itr&0xf,uc_itr>>8&0xf,uc_itr>>4&0xf,uc_itr&0xf); // Set genotypes for father, mother, child and calculate genotype qualities for (i=0; i<3; i++) { // GT int ismpl = fam->sample[i]; int igt = c_itr>>((2-i)*4) & 0xf; double *gl = call->GLs + nout_gts*ismpl; int32_t *gts = call->cgts + ismpl; if ( gl[0]==1 || igt==GT_SKIP ) // zero depth, set missing genotypes { gts[0] = -1; // bcf_float_set_missing(call->GQs[ismpl]); continue; } gts[0] = igt; #if 0 // todo: Genotype Qualities // // GQ: for each family member i sum over all genotypes j,k keeping igt fixed double lk_sum = 0; for (itr=0; itr>((2-i)*4) & 0xf) ) continue; double lk = 0; int j; for (j=0; j<3; j++) { int jsmpl = fam->sample[j]; double *gl = call->GLs + ngts*jsmpl; if ( gl[0]==1 ) continue; int jgt = trio[itr]>>((2-j)*4) & 0xf; if ( jgt==GT_SKIP ) continue; lk += gl[jgt]; } double Pkij = (double)2/(trio[itr]>>12); lk += log(1 - trio_Pm * (1 - Pkij)); lk_sum = logsumexp2(lk_sum, lk); } if ( !uc_is_mendelian && (best_itr>>((2-i)*4)&0xf)==(uc_itr>>((2-i)*4)&0xf) ) lk_sum = logsumexp2(lk_sum,uc_lk); call->GQs[ismpl] = -4.3429*(best_lk - lk_sum); #endif } } for (i=0; i<4; i++) call->ac[i] = 0; call->nhets = 0; call->ndiploid = 0; // Test if CGT,UGT are needed int ucgts_needed = 0; int32_t *cgts = call->cgts - 1; int32_t *ugts = call->ugts - 1; int32_t *gts = call->gts - 2; for (isample = 0; isample < nsmpl; isample++) { int ploidy = call->ploidy ? call->ploidy[isample] : 2; cgts++; ugts++; gts += 2; if ( ugts[0]==-1 ) { gts[0] = bcf_gt_missing; gts[1] = ploidy==2 ? bcf_gt_missing : bcf_int32_vector_end; continue; } int a,b; if ( cgts[0]!=ugts[0] ) { bcf_gt2alleles(cgts[0], &a, &b); gts[0] = bcf_gt_unphased(a); gts[1] = ploidy==1 ? bcf_int32_vector_end : bcf_gt_unphased(b); } else { bcf_gt2alleles(ugts[0], &a, &b); gts[0] = bcf_gt_unphased(a); gts[1] = ploidy==1 ? bcf_int32_vector_end : bcf_gt_unphased(b); } if ( cgts[0]!=ugts[0] ) ucgts_needed = 1; call->ac[a]++; if ( ploidy==2 ) { call->ac[b]++; call->ndiploid++; if ( a!=b ) call->nhets++; } } if ( ucgts_needed ) { // Some GTs are different bcf_update_format_int32(call->hdr,rec,"UGT",call->ugts,nsmpl); bcf_update_format_int32(call->hdr,rec,"CGT",call->cgts,nsmpl); } } #endif static void mcall_trim_and_update_PLs(call_t *call, bcf1_t *rec, int nals_ori, int nals_new) { int npls_src = nals_ori*(nals_ori+1)/2; int npls_dst = nals_new*(nals_new+1)/2; // number of PL values in diploid samples, ori and new if ( call->all_diploid && npls_src == npls_dst ) return; int *pls_src = call->PLs, *pls_dst = call->PLs; int nsmpl = bcf_hdr_nsamples(call->hdr); int isample, ia; for (isample = 0; isample < nsmpl; isample++) { int ploidy = call->ploidy ? call->ploidy[isample] : 2; if ( ploidy==2 ) { for (ia=0; iapl_map[ia] ]; } else if ( ploidy==1 ) { for (ia=0; iapl_map[isrc] ]; } if ( ia1 in mcall() } pls_src += npls_src; pls_dst += npls_dst; } bcf_update_format_int32(call->hdr, rec, "PL", call->PLs, npls_dst*nsmpl); } void mcall_trim_and_update_numberR(call_t *call, bcf1_t *rec, int nals_ori, int nals_new) { if ( nals_ori==nals_new ) return; int i,j, nret, size = sizeof(float); void *tmp_ori = call->itmp, *tmp_new = call->PLs; // reusing PLs storage which is not used at this point int ntmp_ori = call->n_itmp, ntmp_new = call->mPLs; // INFO fields for (i=0; in_info; i++) { bcf_info_t *info = &rec->d.info[i]; int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_INFO,info->key); if ( vlen!=BCF_VL_R ) continue; // not a Number=R tag int type = bcf_hdr_id2type(call->hdr,BCF_HL_INFO,info->key); const char *key = bcf_hdr_int2id(call->hdr,BCF_DT_ID,info->key); nret = bcf_get_info_values(call->hdr, rec, key, &tmp_ori, &ntmp_ori, type); if ( nret<=0 ) continue; if ( nals_new==1 ) bcf_update_info_int32(call->hdr, rec, key, tmp_ori, 1); // has to be the REF, the order could not change else { for (j=0; jals_map[j]; if ( k==-1 ) continue; // to be dropped memcpy((char *)tmp_new+size*k, (char *)tmp_ori+size*j, size); } bcf_update_info_int32(call->hdr, rec, key, tmp_new, nals_new); } } // FORMAT fields for (i=0; in_fmt; i++) { bcf_fmt_t *fmt = &rec->d.fmt[i]; int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id); if ( vlen!=BCF_VL_R ) continue; // not a Number=R tag int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id); const char *key = bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id); nret = bcf_get_format_values(call->hdr, rec, key, &tmp_ori, &ntmp_ori, type); if (nret<=0) continue; int nsmpl = bcf_hdr_nsamples(call->hdr); assert( nret==nals_ori*nsmpl ); for (j=0; jals_map[k]; if ( l==-1 ) continue; // to be dropped memcpy(ptr_dst+size*l, ptr_src+size*k, size); } } bcf_update_format_int32(call->hdr, rec, key, tmp_new, nals_new*nsmpl); } call->PLs = (int32_t*) tmp_new; call->mPLs = ntmp_new; call->itmp = (int32_t*) tmp_ori; call->n_itmp = ntmp_ori; } // NB: in this function we temporarily use calls->als_map for a different // purpose to store mapping from new (target) alleles to original alleles. // static int mcall_constrain_alleles(call_t *call, bcf1_t *rec, int *unseen) { assert( call->tgt_als->n ); hts_expand(char*,call->tgt_als->n+1,call->nals,call->als); hts_expand(int,call->tgt_als->n+1,call->nals_map,call->als_map); hts_expand(int,(call->tgt_als->n+1)*(call->tgt_als->n+2)/2,call->npl_map,call->pl_map); int has_new = 0; int i, j, nals = 1; for (i=1; inals_map; i++) call->als_map[i] = -1; if ( vcmp_set_ref(call->vcmp, rec->d.allele[0], call->tgt_als->allele[0]) < 0 ) error("The reference alleles are not compatible at %s:%d .. %s vs %s\n", call->hdr->id[BCF_DT_CTG][rec->rid].key,rec->pos+1,call->tgt_als->allele[0],rec->d.allele[0]); // create mapping from new to old alleles call->als[0] = call->tgt_als->allele[0]; call->als_map[0] = 0; for (i=1; itgt_als->n; i++) { call->als[nals] = call->tgt_als->allele[i]; j = vcmp_find_allele(call->vcmp, rec->d.allele+1, rec->n_allele - 1, call->tgt_als->allele[i]); if ( j>=0 ) { // existing allele call->als_map[nals] = j+1; } else { // There is a new allele in targets which is not present in VCF. // We use the X allele to estimate PLs. Note that X may not be // present at multiallelic indels sites. In that case we use the // last allele anyway, because the least likely allele comes last // in mpileup's ALT output. call->als_map[nals] = (*unseen)>=0 ? *unseen : rec->n_allele - 1; has_new = 1; } nals++; } if ( *unseen ) { call->als_map[nals] = *unseen; call->als[nals] = rec->d.allele[*unseen]; nals++; } if ( !has_new && nals==rec->n_allele ) return 0; bcf_update_alleles(call->hdr, rec, (const char**)call->als, nals); // create mapping from new PL to old PL int k = 0; for (i=0; ials_map[i], b = call->als_map[j]; call->pl_map[k++] = a>b ? a*(a+1)/2 + b : b*(b+1)/2 + a; } } // update PL call->nPLs = bcf_get_format_int32(call->hdr, rec, "PL", &call->PLs, &call->mPLs); int nsmpl = bcf_hdr_nsamples(call->hdr); int npls_ori = call->nPLs / nsmpl; int npls_new = k; hts_expand(int32_t,npls_new*nsmpl,call->n_itmp,call->itmp); int *ori_pl = call->PLs, *new_pl = call->itmp; for (i=0; ipl_map[k]]; if ( new_pl[k]==bcf_int32_missing && *unseen>=0 ) { // missing value, and there is an unseen allele: identify the // alleles and use the lk of either AX or XX int k_ori = call->pl_map[k], ia, ib; bcf_gt2alleles(k_ori, &ia, &ib); k_ori = bcf_alleles2gt(ia,*unseen); if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(ib,*unseen); if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(*unseen,*unseen); new_pl[k] = ori_pl[k_ori]; } if ( !k && new_pl[k]==bcf_int32_vector_end ) new_pl[k]=bcf_int32_missing; } ori_pl += npls_ori; new_pl += npls_new; } bcf_update_format_int32(call->hdr, rec, "PL", call->itmp, npls_new*nsmpl); // update QS, use temporarily call->GPs to store the values int nqs = bcf_get_info_float(call->hdr, rec, "QS", &call->smpl_grp[0].qsum, &call->smpl_grp[0].nqsum); hts_expand(float,nals,call->nGPs,call->GPs); for (i=0; iGPs[i] = call->als_map[i]smpl_grp[0].qsum[call->als_map[i]] : 0; bcf_update_info_float(call->hdr, rec, "QS", call->GPs, nals); // update any Number=R tags void *tmp_ori = call->itmp, *tmp_new = call->PLs; // reusing PLs storage which is not used at this point int ntmp_ori = call->n_itmp, ntmp_new = call->mPLs; for (i=0; in_fmt; i++) { bcf_fmt_t *fmt = &rec->d.fmt[i]; int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id); if ( vlen!=BCF_VL_R ) continue; // not a Number=R tag // NB:works only for BCF_HT_INT and BCF_HT_REAL int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id); assert( type==BCF_HT_INT || type==BCF_HT_REAL ); assert( sizeof(float)==sizeof(int32_t) ); const char *key = bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id); int nret = bcf_get_format_values(call->hdr, rec, key, &tmp_ori, &ntmp_ori, type); if (nret<=0) continue; int nsmpl = bcf_hdr_nsamples(call->hdr); int size1 = sizeof(float); hts_expand(float, nsmpl * nals, ntmp_new, tmp_new); for (j=0; jn; uint8_t *ptr_new = (uint8_t *) tmp_new + j*nals*size1; for (k=0; kals_map[k]; memcpy(dst,src,size1); } } nret = bcf_update_format(call->hdr, rec, key, tmp_new, nsmpl*nals, type); assert( nret==0 ); } call->PLs = (int32_t*) tmp_new; call->mPLs = ntmp_new; call->itmp = (int32_t*) tmp_ori; call->n_itmp = ntmp_ori; if ( *unseen ) *unseen = nals-1; return 0; } /** * This function implements the multiallelic calling model. It has two major parts: * 1) determine the most likely set of alleles and calculate the quality of ref/non-ref site * 2) determine and set the genotypes * In various places in between, the BCF record gets updated. */ int mcall(call_t *call, bcf1_t *rec) { int i,j, unseen = call->unseen; // Force alleles when calling genotypes given alleles was requested if ( call->flag & CALL_CONSTR_ALLELES && mcall_constrain_alleles(call, rec, &unseen)!=0 ) return -2; int nsmpl = bcf_hdr_nsamples(call->hdr); int nals_ori = rec->n_allele; hts_expand(int,nals_ori,call->nac,call->ac); hts_expand(int,nals_ori,call->nals_map,call->als_map); hts_expand(int,nals_ori*(nals_ori+1)/2,call->npl_map,call->pl_map); // Get the genotype likelihoods call->nPLs = bcf_get_format_int32(call->hdr, rec, "PL", &call->PLs, &call->mPLs); if ( call->nPLs!=nsmpl*nals_ori*(nals_ori+1)/2 && call->nPLs!=nsmpl*nals_ori ) // a mixture of diploid and haploid or haploid only error("Wrong number of PL fields? nals=%d npl=%d\n", nals_ori,call->nPLs); // Convert PLs to probabilities int ngts_ori = nals_ori*(nals_ori+1)/2; hts_expand(double, call->nPLs, call->npdg, call->pdg); set_pdg(call->pl2p, call->PLs, call->pdg, nsmpl, ngts_ori, unseen); // Get sum of qualities, serves as an AF estimate, f_x = QS/N in Eq. 1 in call-m math notes. if ( call->nsmpl_grp == 1 ) { int nqs = bcf_get_info_float(call->hdr, rec, "QS", &call->smpl_grp[0].qsum, &call->smpl_grp[0].nqsum); if ( nqs<=0 ) error("The QS annotation not present at %s:%d\n", bcf_seqname(call->hdr,rec),rec->pos+1); if ( nqs < nals_ori ) { // Some of the listed alleles do not have the corresponding QS field. This is // typically ref-only site with <*> in ALT. hts_expand(float,nals_ori,call->smpl_grp[0].nqsum,call->smpl_grp[0].qsum); for (i=nqs; ismpl_grp[0].qsum[i] = 0; } } else { for (j=0; jnsmpl_grp; j++) { hts_expand(float,nals_ori,call->smpl_grp[j].nqsum,call->smpl_grp[j].qsum); memset(call->smpl_grp[j].qsum, 0, sizeof(float)*nals_ori); } // Use FORMAT/AD or FORMAT/QS int nad = bcf_get_format_int32(call->hdr, rec, call->sample_groups_tag, &call->ADs, &call->nADs); if ( nad<1 ) error("Error: FORMAT/%s is required with the -G option, mpileup must be run with \"-a AD\" or \"-a QS\"\n",call->sample_groups_tag); nad /= bcf_hdr_nsamples(call->hdr); for (i=0; insmpl_grp; i++) { int is; smpl_grp_t *grp = &call->smpl_grp[i]; hts_expand(float,nals_ori,grp->nqsum,grp->qsum); for (j=0; jqsum[j] = 0; for (is=0; isnsmpl; is++) { int ismpl = grp->smpl[is]; int32_t *ptr = call->ADs + ismpl*nad; float sum = 0; for (j=0; jqsum[j] += ptr[j]/sum; } } } } } // If available, take into account reference panel AFs if ( call->prior_AN && bcf_get_info_int32(call->hdr, rec, call->prior_AN ,&call->ac, &call->nac)==1 ) { int an = call->ac[0]; // number of alleles total, proceed only if not zero; reuse call->ac if ( an > 0 && bcf_get_info_int32(call->hdr, rec, call->prior_AC ,&call->ac, &call->nac)==nals_ori-1 ) // number of ALT alleles { int ac0 = an; // this will become the number of REFs for (i=0; iac[i]==bcf_int32_vector_end ) break; if ( call->ac[i]==bcf_int32_missing ) continue; ac0 -= call->ac[i]; // here an*0.5 is the number of samples in the populatio and ac*0.5 is the AF weighted by the number of samples for (j=0; jnsmpl_grp; j++) call->smpl_grp[j].qsum[i+1] = (call->smpl_grp[j].qsum[i+1] + 0.5*call->ac[i]) / (call->smpl_grp[j].nsmpl + 0.5*an); } if ( ac0<0 ) error("Incorrect %s,%s values at %s:%d\n", call->prior_AN,call->prior_AC,bcf_seqname(call->hdr,rec),rec->pos+1); for (j=0; jnsmpl_grp; j++) call->smpl_grp[j].qsum[0] = (call->smpl_grp[j].qsum[0] + 0.5*ac0) / (call->smpl_grp[j].nsmpl + 0.5*an); } } // normalize so that QS sums to 1 for each group for (j=0; jnsmpl_grp; j++) { float sum = 0; for (i=0; ismpl_grp[j].qsum[i]; if ( sum ) for (i=0; ismpl_grp[j].qsum[i] /= sum; } bcf_update_info_int32(call->hdr, rec, "QS", NULL, 0); // remove QS tag if ( nals_ori > 8*sizeof(call->als_new) ) { fprintf(bcftools_stderr,"Too many alleles at %s:%"PRId64", skipping.\n", bcf_seqname(call->hdr,rec),(int64_t) rec->pos+1); return 0; } // For each group find the best combination of alleles call->als_new = 0; double ref_lk = -HUGE_VAL, lk_sum = -HUGE_VAL, max_qual = -HUGE_VAL; for (j=0; jnsmpl_grp; j++) { smpl_grp_t *grp = &call->smpl_grp[j]; mcall_find_best_alleles(call, nals_ori, grp); call->als_new |= grp->als; if ( grp->max_lk==-HUGE_VAL ) continue; double qual = -4.343*(grp->ref_lk - logsumexp2(grp->lk_sum,grp->ref_lk)); if ( max_qual < qual ) { max_qual = qual; lk_sum = grp->lk_sum; ref_lk = grp->ref_lk; } } // Make sure the REF allele is always present if ( !(call->als_new&1) ) call->als_new |= 1; int is_variant = call->als_new==1 ? 0 : 1; if ( call->flag & CALL_VARONLY && !is_variant ) return 0; call->nals_new = 0; for (i=0; iflag&CALL_KEEP_UNSEEN) && i==unseen && call->nals_new==1 ) { call->nals_new++; call->als_new |= 1<0 && i==unseen ) continue; if ( call->flag & CALL_KEEPALT ) call->als_new |= 1<als_new & (1<nals_new++; } init_allele_trimming_maps(call,nals_ori,call->als_new); int nAC = 0; if ( call->als_new==1 ) // only REF allele on output { mcall_set_ref_genotypes(call,nals_ori); bcf_update_format_int32(call->hdr, rec, "PL", NULL, 0); // remove PL, useless now } else if ( !is_variant ) { mcall_set_ref_genotypes(call,nals_ori); // running with -A, prevent mcall_call_genotypes from putting some ALT back mcall_trim_and_update_PLs(call, rec, nals_ori, call->nals_new); } else { // The most likely set of alleles includes non-reference allele (or was enforced), call genotypes. // Note that it is a valid outcome if the called genotypes exclude some of the ALTs. int ngts_new = call->nals_new*(call->nals_new+1)/2; hts_expand(float,ngts_new*nsmpl,call->nGPs,call->GPs); for (i=0; inals_new; i++) call->ac[i] = 0; if ( call->flag & CALL_CONSTR_TRIO && call->nals_new>4 ) { fprintf(bcftools_stderr,"Too many alleles at %s:%"PRId64", skipping.\n", bcf_seqname(call->hdr,rec),(int64_t) rec->pos+1); return 0; } if ( call->output_tags & (CALL_FMT_GQ|CALL_FMT_GP) ) { memset(call->GPs,0,nsmpl*ngts_new*sizeof(*call->GPs)); memset(call->GQs,0,nsmpl*sizeof(*call->GQs)); } for (i=0; insmpl_grp; i++) { if ( call->flag & CALL_CONSTR_TRIO ) error("todo: constrained trio calling temporarily disabled\n"); //mcall_call_trio_genotypes(call,rec,nals,&call->smpl_grp[i]); else mcall_call_genotypes(call,nals_ori,&call->smpl_grp[i]); } // Skip the site if all samples are 0/0. This can happen occasionally. for (i=1; inals_new; i++) nAC += call->ac[i]; if ( !nAC && call->flag & CALL_VARONLY ) return 0; if ( call->output_tags & CALL_FMT_GP ) bcf_update_format_float(call->hdr, rec, "GP", call->GPs, nsmpl*ngts_new); if ( call->output_tags & CALL_FMT_GQ ) bcf_update_format_int32(call->hdr, rec, "GQ", call->GQs, nsmpl); mcall_trim_and_update_PLs(call,rec,nals_ori,call->nals_new); } if ( nals_ori!=call->nals_new ) mcall_trim_and_update_numberR(call,rec,nals_ori,call->nals_new); // Set QUAL if ( nAC ) { // Quality of a variant site. fabs() to avoid negative zeros in VCF output when CALL_KEEPALT is set rec->qual = max_qual; } else { // Set the quality of a REF site if ( lk_sum!=-HUGE_VAL ) // no support from (high quality) reads, so QUAL=1-prior rec->qual = -4.343*(lk_sum - logsumexp2(lk_sum,ref_lk)); else if ( call->ac[0] ) rec->qual = call->theta ? -4.343*call->theta : 0; else bcf_float_set_missing(rec->qual); } // AC, AN if ( call->nals_new>1 ) bcf_update_info_int32(call->hdr, rec, "AC", call->ac+1, call->nals_new-1); nAC += call->ac[0]; bcf_update_info_int32(call->hdr, rec, "AN", &nAC, 1); // Remove unused alleles hts_expand(char*,call->nals_new,call->nals,call->als); for (i=0; ials_map[i]>=0 ) call->als[call->als_map[i]] = rec->d.allele[i]; bcf_update_alleles(call->hdr, rec, (const char**)call->als, call->nals_new); bcf_update_genotypes(call->hdr, rec, call->gts, nsmpl*2); // DP4 and PV4 tags if ( bcf_get_info_float(call->hdr, rec, "I16", &call->anno16, &call->n16)==16 ) { int32_t dp[4]; dp[0] = call->anno16[0]; dp[1] = call->anno16[1]; dp[2] = call->anno16[2]; dp[3] = call->anno16[3]; bcf_update_info_int32(call->hdr, rec, "DP4", dp, 4); int32_t mq = (call->anno16[8]+call->anno16[10])/(call->anno16[0]+call->anno16[1]+call->anno16[2]+call->anno16[3]); bcf_update_info_int32(call->hdr, rec, "MQ", &mq, 1); if ( call->output_tags & CALL_FMT_PV4 ) { anno16_t a; float tmpf[4]; int is_tested = test16(call->anno16, &a) >= 0 && a.is_tested ? 1 : 0; if ( is_tested ) { for (i=0; i<4; i++) tmpf[i] = a.p[i]; bcf_update_info_float(call->hdr, rec, "PV4", tmpf, 4); } } } bcf_update_info_int32(call->hdr, rec, "I16", NULL, 0); // remove I16 tag return is_variant ? call->nals_new : 1; } pysam-0.23.0/bcftools/mpileup.c000066400000000000000000002410461475062545500164030ustar00rootroot00000000000000/* mpileup.c -- mpileup subcommand. Previously bam_plcmd.c from samtools Copyright (C) 2008-2024 Genome Research Ltd. Portions copyright (C) 2009-2012 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "regidx.h" #include "bcftools.h" #include "bam2bcf.h" #include "bam_sample.h" #include "gvcf.h" #define MPLP_BCF 1 #define MPLP_VCF (1<<1) #define MPLP_NO_COMP (1<<2) #define MPLP_NO_ORPHAN (1<<3) #define MPLP_REALN (1<<4) #define MPLP_NO_INDEL (1<<5) #define MPLP_REDO_BAQ (1<<6) #define MPLP_ILLUMINA13 (1<<7) #define MPLP_IGNORE_RG (1<<8) #define MPLP_PRINT_POS (1<<9) #define MPLP_PRINT_MAPQ (1<<10) #define MPLP_PER_SAMPLE (1<<11) #define MPLP_SMART_OVERLAPS (1<<12) #define MPLP_REALN_PARTIAL (1<<13) typedef struct _mplp_aux_t mplp_aux_t; typedef struct _mplp_pileup_t mplp_pileup_t; // Data shared by all bam files typedef struct { int min_mq, flag, min_baseQ, max_baseQ, delta_baseQ, capQ_thres, max_depth, max_indel_depth, max_read_len, ambig_reads; uint32_t fmt_flag; int rflag_skip_any_unset, rflag_skip_all_unset, rflag_skip_any_set, rflag_skip_all_set, output_type; int openQ, extQ, tandemQ, min_support, indel_win_size; // for indels int seqQ_offset; double min_frac; // for indels double indel_bias, poly_mqual; double del_bias; // compensate for diff deletion vs insertion error rates double vs_ref; char *reg_fname, *pl_list, *fai_fname, *output_fname; int reg_is_file, record_cmd_line, n_threads, clevel; faidx_t *fai; regidx_t *bed, *reg; // bed: skipping regions, reg: index-jump to regions regitr_t *bed_itr, *reg_itr; int bed_logic; // 1: include region, 0: exclude region gvcf_t *gvcf; // auxiliary structures for calling bcf_callaux_t *bca; bcf_callret1_t *bcr; bcf_call_t bc; bam_mplp_t iter; mplp_aux_t **mplp_data; int nfiles; char **files; mplp_pileup_t *gplp; int *n_plp; const bam_pileup1_t **plp; bam_smpl_t *bsmpl; kstring_t buf; bcf1_t *bcf_rec; htsFile *bcf_fp; bcf_hdr_t *bcf_hdr; int indels_v20; int edlib; int argc; char **argv; int write_index; char *index_fn; } mplp_conf_t; typedef struct { char *ref[2]; int ref_id[2]; int ref_len[2]; } mplp_ref_t; #define MPLP_REF_INIT {{NULL,NULL},{-1,-1},{0,0}} // Data specific to each bam file struct _mplp_aux_t { samFile *fp; hts_itr_t *iter; bam_hdr_t *h; mplp_ref_t *ref; const mplp_conf_t *conf; int bam_id; hts_idx_t *idx; // maintained only with more than one -r regions }; // Data passed to htslib/mpileup struct _mplp_pileup_t { int n; int *n_plp, *m_plp; bam_pileup1_t **plp; }; static int mplp_get_ref(mplp_aux_t *ma, int tid, char **ref, int *ref_len) { mplp_ref_t *r = ma->ref; //printf("get ref %d {%d/%p, %d/%p}\n", tid, r->ref_id[0], r->ref[0], r->ref_id[1], r->ref[1]); if (!r || !ma->conf->fai) { *ref = NULL; return 0; } // Do we need to reference count this so multiple mplp_aux_t can // track which references are in use? // For now we just cache the last two. Sufficient? if (tid == r->ref_id[0]) { *ref = r->ref[0]; *ref_len = r->ref_len[0]; return 1; } if (tid == r->ref_id[1]) { // Last, swap over int tmp; tmp = r->ref_id[0]; r->ref_id[0] = r->ref_id[1]; r->ref_id[1] = tmp; tmp = r->ref_len[0]; r->ref_len[0] = r->ref_len[1]; r->ref_len[1] = tmp; char *tc; tc = r->ref[0]; r->ref[0] = r->ref[1]; r->ref[1] = tc; *ref = r->ref[0]; *ref_len = r->ref_len[0]; return 1; } // New, so migrate to old and load new free(r->ref[1]); r->ref[1] = r->ref[0]; r->ref_id[1] = r->ref_id[0]; r->ref_len[1] = r->ref_len[0]; r->ref_id[0] = tid; r->ref[0] = faidx_fetch_seq(ma->conf->fai, ma->h->target_name[r->ref_id[0]], 0, INT_MAX, &r->ref_len[0]); if (!r->ref[0]) { r->ref[0] = NULL; r->ref_id[0] = -1; r->ref_len[0] = 0; *ref = NULL; return 0; } *ref = r->ref[0]; *ref_len = r->ref_len[0]; return 1; } static int mplp_func(void *data, bam1_t *b) { char *ref; mplp_aux_t *ma = (mplp_aux_t*)data; int ret, ref_len; while (1) { int has_ref; ret = ma->iter? sam_itr_next(ma->fp, ma->iter, b) : sam_read1(ma->fp, ma->h, b); if (ret < 0) break; // The 'B' cigar operation is not part of the specification, considering as obsolete. // bam_remove_B(b); if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) continue; // exclude unmapped reads if (ma->conf->rflag_skip_any_unset && (ma->conf->rflag_skip_any_unset&b->core.flag)!=ma->conf->rflag_skip_any_unset) continue; if (ma->conf->rflag_skip_all_set && (ma->conf->rflag_skip_all_set&b->core.flag)==ma->conf->rflag_skip_all_set) continue; if (ma->conf->rflag_skip_all_unset && !(ma->conf->rflag_skip_all_unset&b->core.flag)) continue; if (ma->conf->rflag_skip_any_set && ma->conf->rflag_skip_any_set&b->core.flag) continue; if (ma->conf->bed) { // test overlap regitr_t *itr = ma->conf->bed_itr; int beg = b->core.pos, end = bam_endpos(b)-1; int overlap = regidx_overlap(ma->conf->bed, ma->h->target_name[b->core.tid],beg,end, itr); if ( !ma->conf->bed_logic && !overlap ) { // exclude only reads which are fully contained in the region while ( regitr_overlap(itr) ) { if ( beg < itr->beg ) { overlap = 1; break; } if ( end > itr->end ) { overlap = 1; break; } } } if ( !overlap ) continue; } if ( bam_smpl_get_sample_id(ma->conf->bsmpl,ma->bam_id,b)<0 ) continue; if (ma->conf->flag & MPLP_ILLUMINA13) { int i; uint8_t *qual = bam_get_qual(b); for (i = 0; i < b->core.l_qseq; ++i) qual[i] = qual[i] > 31? qual[i] - 31 : 0; } if (ma->conf->fai && b->core.tid >= 0) { has_ref = mplp_get_ref(ma, b->core.tid, &ref, &ref_len); if (has_ref && ref_len <= b->core.pos) { // exclude reads outside of the reference sequence fprintf(stderr,"[%s] Skipping because %"PRId64" is outside of %d [ref:%d]\n", __func__, (int64_t) b->core.pos, ref_len, b->core.tid); continue; } } else { has_ref = 0; } // Allow sufficient room for bam_aux_append of ZQ tag without // a realloc and consequent breakage of pileup's cached pointers. if (has_ref && (ma->conf->flag &MPLP_REALN) && !bam_aux_get(b, "ZQ")) { // Doing sam_prob_realn later is problematic as it adds to // the tag list (ZQ or BQ), which causes a realloc of b->data. // This happens after pileup has built a hash table on the // read name. It's a deficiency in pileup IMO. // We could implement a new sam_prob_realn that returns ZQ // somewhere else and cache it ourselves (pileup clientdata), // but for now we simply use a workaround. // // We create a fake tag of the correct length, which we remove // just prior calling sam_prob_realn so we can guarantee there is // room. (We can't just make room now as bam_copy1 removes it // again). if (b->core.l_qseq > 500) { uint8_t *ZQ = malloc((uint32_t)b->core.l_qseq+1); memset(ZQ, '@', b->core.l_qseq); ZQ[b->core.l_qseq] = 0; bam_aux_append(b, "_Q", 'Z', b->core.l_qseq+1, ZQ); free(ZQ); } else { static uint8_t ZQ[501] = "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"; ZQ[b->core.l_qseq] = 0; bam_aux_append(b, "_Q", 'Z', b->core.l_qseq+1, ZQ); ZQ[b->core.l_qseq] = '@'; } } if (has_ref && ma->conf->capQ_thres > 10) { int q = sam_cap_mapq(b, ref, ref_len, ma->conf->capQ_thres); if (q < 0) continue; // skip else if (b->core.qual > q) b->core.qual = q; } if (b->core.qual < ma->conf->min_mq) continue; else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) continue; return ret; }; return ret; } // Called once per new bam added to the pileup. // We cache sample information here so we don't have to keep recomputing this // on each and every pileup column. If FMT/SCR annotation is requested, a flag // is set to indicate the presence of a soft clip. static int pileup_constructor(void *data, const bam1_t *b, bam_pileup_cd *cd) { cd->p = calloc(1,sizeof(plp_cd_t)); PLP_NM(cd) = PLP_NM_UNSET; mplp_aux_t *ma = (mplp_aux_t *)data; int n = bam_smpl_get_sample_id(ma->conf->bsmpl, ma->bam_id, (bam1_t *)b); PLP_SET_SAMPLE_ID(cd, n); // Whether read has a soft-clip is used in mplp_realn's heuristics. // TODO: consider whether clip length is beneficial to use? int i; for (i=0; icore.n_cigar; i++) { int cig = bam_get_cigar(b)[i] & BAM_CIGAR_MASK; if (cig == BAM_CSOFT_CLIP) { PLP_SET_SOFT_CLIP(cd); break; } } if (ma->conf->flag & MPLP_REALN) { int i; // int tot_ins = 0; // int p = 0; uint32_t *cigar = bam_get_cigar(b); for (i=0; icore.n_cigar; i++) { int cig = cigar[i] & BAM_CIGAR_MASK; // if (bam_cigar_type(cig) & 2) // p += cigar[i] >> BAM_CIGAR_SHIFT; if (cig == BAM_CINS || cig == BAM_CDEL || cig == BAM_CREF_SKIP) { // tot_ins += cigar[i] >> BAM_CIGAR_SHIFT; // Possible further optimsation, check tot_ins==1 later // (and remove break) so we can detect single bp indels. // We may want to focus BAQ on more complex regions only. PLP_SET_INDEL(cd); break; } // TODO: proper p->cd struct and have cd->i as a size rather // than a flag. // Then aggregate together the sizes and if just 1 size for all // reads or 2 sizes for approx 50/50 split in all reads, then // treat this as a well-aligned variant and don't run BAQ. } } return 0; } static int pileup_destructor(void *data, const bam1_t *b, bam_pileup_cd *cd) { free(cd->p); return 0; } static void group_smpl(mplp_pileup_t *m, bam_smpl_t *bsmpl, int n, int *n_plp, const bam_pileup1_t **plp) { int i, j; memset(m->n_plp, 0, m->n * sizeof(int)); for (i = 0; i < n; ++i) // iterate over all bams { for (j = 0; j < n_plp[i]; ++j) // iterate over all reads available at this position { const bam_pileup1_t *p = plp[i] + j; int id = PLP_SAMPLE_ID(&(p->cd)); if (m->n_plp[id] == m->m_plp[id]) { m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8; m->plp[id] = (bam_pileup1_t*) realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]); } m->plp[id][m->n_plp[id]++] = *p; } } } static void flush_bcf_records(mplp_conf_t *conf, htsFile *fp, bcf_hdr_t *hdr, bcf1_t *rec) { if ( !conf->gvcf ) { if ( rec && bcf_write1(fp, hdr, rec)!=0 ) error("[%s] Error: failed to write the record to %s\n", __func__,conf->output_fname?conf->output_fname:"standard output"); return; } if ( !rec ) { gvcf_write(conf->gvcf, fp, hdr, NULL, 0); return; } int is_ref = 0; if ( rec->n_allele==1 ) is_ref = 1; else if ( rec->n_allele==2 ) { // second allele is mpileup's X, not a variant if ( rec->d.allele[1][0]=='<' && rec->d.allele[1][1]=='*' && rec->d.allele[1][2]=='>' ) is_ref = 1; } rec = gvcf_write(conf->gvcf, fp, hdr, rec, is_ref); if ( rec && bcf_write1(fp,hdr,rec)!=0 ) error("[%s] Error: failed to write the record to %s\n", __func__,conf->output_fname?conf->output_fname:"standard output"); } /* * Loops for an indel at this position. * * Only reads that overlap an indel loci get realigned. This considerably * reduces the cost of running BAQ while keeping the main benefits. * * TODO: also consider only realigning reads that don't span the indel * by more than a certain amount either-side. Ie focus BAQ only on reads * ending adjacent to the indel, where the alignment is most likely to * be wrong. (2nd TODO: do this based on sequence context; STRs bad, unique * data good.) * * NB: this may sadly realign after we've already used the data. Hmm... */ static void mplp_realn(int n, int *n_plp, const bam_pileup1_t **plp, int flag, int max_read_len, char *ref, int ref_len, int pos) { int i, j, has_indel = 0, has_clip = 0, nt = 0; int min_indel = INT_MAX, max_indel = INT_MIN; // Is an indel present. // NB: don't bother even checking if very long as almost guaranteed // to have indel (and likely soft-clips too). for (i = 0; i < n; i++) { // iterate over bams nt += n_plp[i]; for (j = 0; j < n_plp[i]; j++) { // iterate over reads bam_pileup1_t *p = (bam_pileup1_t *)plp[i] + j; has_indel += (PLP_HAS_INDEL(&p->cd) || p->indel) ? 1 : 0; // Has_clip is almost always true for very long reads // (eg PacBio CCS), but these rarely matter as the clip // is likely a long way from this indel. has_clip += (PLP_HAS_SOFT_CLIP(&p->cd)) ? 1 : 0; if (max_indel < p->indel) max_indel = p->indel; if (min_indel > p->indel) min_indel = p->indel; } } if (flag & MPLP_REALN_PARTIAL) { if (has_indel == 0 || (has_clip < 0.2*nt && max_indel == min_indel && (has_indel < 0.1*nt /*|| has_indel > 0.9*nt*/ || has_indel == 1))) return; } // Realign for (i = 0; i < n; i++) { // iterate over bams for (j = 0; j < n_plp[i]; j++) { // iterate over reads const bam_pileup1_t *p = plp[i] + j; bam1_t *b = p->b; // Avoid doing multiple times. // // Note we cannot modify p->cd.i here with a PLP_SET macro // because the cd item is held by mpileup in an lbnode_t // struct and copied over to the pileup struct for each // iteration, essentially making p->cd.i read only. // // We could use our own structure (p->cd.p), allocated during // the constructor, but for simplicity we play dirty and // abuse an unused flag bit instead. if ( PLP_IS_REALN(&(p->cd)) ) continue; PLP_SET_REALN(&(p->cd)); if (b->core.l_qseq > max_read_len) continue; // Check p->cigar_ind and see what cigar elements are before // and after. How close is this location to the end of the // read? Only realign if we don't span by more than X bases. // // Again, best only done on deeper data as BAQ helps // disproportionately more on shallow data sets. // // This rescues some of the false negatives that are caused by // systematic reduction in quality due to sample vs ref alignment. // At deep coverage we skip realigning more reads as we have sufficient depth. // This rescues for false negatives. At shallow depth we pay for this with // more FP so are more stringent on spanning size. #define REALN_DIST (40+10*(nt<40)+10*(nt<20)) uint32_t *cig = bam_get_cigar(b); int ncig = b->core.n_cigar; // Don't realign reads where indel is in middle? // On long read data we don't care about soft-clips at the ends. // For short read data, we always calc BAQ on these as they're // a common source of false positives. if ((flag & MPLP_REALN_PARTIAL) && nt > 15 && ncig > 1) { // Left & right cigar op match. int lr = b->core.l_qseq > 500; int lm = 0, rm = 0, k, nm = 0; for (k = 0; k < ncig; k++) { int cop = bam_cigar_op(cig[k]); if (lr && (cop == BAM_CHARD_CLIP || cop == BAM_CSOFT_CLIP)) continue; if (cop == BAM_CMATCH || cop == BAM_CDIFF || cop == BAM_CEQUAL) { lm += bam_cigar_oplen(cig[k]); nm++; } else { break; } } // if everything is a match (or sequence (mis)match) then move on // because we don't have an indel in the middle if (nm != ncig) { for (k = ncig-1; k >= 0; k--) { int cop = bam_cigar_op(cig[k]); if (lr && (cop == BAM_CHARD_CLIP || cop == BAM_CSOFT_CLIP)) continue; if (cop == BAM_CMATCH || cop == BAM_CDIFF || cop == BAM_CEQUAL) rm += bam_cigar_oplen(cig[k]); else break; } if (lm >= REALN_DIST*4 && rm >= REALN_DIST*4) continue; if (lm >= REALN_DIST && rm >= REALN_DIST && has_clip < (0.15+0.05*(nt>20))*nt) continue; } } if (b->core.l_qseq > 500) { // don't do BAQ on long-read data if it's going to // cause us to have a large band-with and costly in CPU int rl = bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(b)); if (abs(rl - b->core.l_qseq) * b->core.l_qseq >= 500000) continue; } // Fudge: make room for ZQ tag. uint8_t *_Q = bam_aux_get(b, "_Q"); if (_Q) bam_aux_del(b, _Q); sam_prob_realn(b, ref, ref_len, (flag & MPLP_REDO_BAQ) ? 7 : 3); } } return; } static int mpileup_reg(mplp_conf_t *conf, uint32_t beg, uint32_t end) { bam_hdr_t *hdr = conf->mplp_data[0]->h; // header of first file in input list int ret, i, tid, pos, ref_len; char *ref; while ( (ret=bam_mplp_auto(conf->iter, &tid, &pos, conf->n_plp, conf->plp)) > 0) { if ( posend ) continue; if ( conf->bed && tid >= 0 ) { int overlap = regidx_overlap(conf->bed, hdr->target_name[tid], pos, pos, NULL); if ( !conf->bed_logic ) overlap = overlap ? 0 : 1; if ( !overlap ) continue; } int has_ref = mplp_get_ref(conf->mplp_data[0], tid, &ref, &ref_len); if (has_ref && (conf->flag & MPLP_REALN)) mplp_realn(conf->nfiles, conf->n_plp, conf->plp, conf->flag, conf->max_read_len, ref, ref_len, pos); int total_depth, _ref0, ref16; for (i = total_depth = 0; i < conf->nfiles; ++i) total_depth += conf->n_plp[i]; group_smpl(conf->gplp, conf->bsmpl, conf->nfiles, conf->n_plp, conf->plp); _ref0 = (ref && pos < ref_len)? ref[pos] : 'N'; ref16 = seq_nt16_table[_ref0]; bcf_callaux_clean(conf->bca, &conf->bc); for (i = 0; i < conf->gplp->n; ++i) bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], ref16, conf->bca, conf->bcr + i); conf->bc.tid = tid; conf->bc.pos = pos; bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, ref16, &conf->bc); bcf_clear1(conf->bcf_rec); bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, conf->bca, 0); flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec); // call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring? // check me: rghash in bcf_call_gap_prep() should have no effect, reads mplp_func already excludes them if (!(conf->flag&MPLP_NO_INDEL) && total_depth < conf->max_indel_depth) { bcf_callaux_clean(conf->bca, &conf->bc); conf->bca->chr = tid>=0 ? hdr->target_name[tid] : NULL; int iret; if (conf->edlib) iret = bcf_edlib_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref, ref_len); else if ( conf->indels_v20 ) iret = bcf_iaux_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref); else iret = bcf_call_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref); if ( iret>=0 ) { for (i = 0; i < conf->gplp->n; ++i) bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], -1, conf->bca, conf->bcr + i); if (bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, -1, &conf->bc) >= 0) { bcf_clear1(conf->bcf_rec); bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, conf->bca, ref); flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec); } } } } return ret; } static int mpileup(mplp_conf_t *conf) { if (conf->nfiles == 0) { fprintf(stderr,"[%s] no input file/data given\n", __func__); exit(EXIT_FAILURE); } mplp_ref_t mp_ref = MPLP_REF_INIT; conf->gplp = (mplp_pileup_t *) calloc(1,sizeof(mplp_pileup_t)); conf->mplp_data = (mplp_aux_t**) calloc(conf->nfiles, sizeof(mplp_aux_t*)); conf->plp = (const bam_pileup1_t**) calloc(conf->nfiles, sizeof(bam_pileup1_t*)); conf->n_plp = (int*) calloc(conf->nfiles, sizeof(int)); // Allow to run mpileup on multiple regions in one go. This comes at cost: the bai index // must be kept in the memory for the whole time which can be a problem with many bams. // Therefore if none or only one region is requested, we initialize the bam iterator as // before and free the index. Only when multiple regions are queried, we keep the index. int nregs = 0; if ( conf->reg_fname ) { if ( conf->reg_is_file ) { conf->reg = regidx_init(conf->reg_fname,NULL,NULL,0,NULL); if ( !conf->reg ) { fprintf(stderr,"Could not parse the regions: %s\n", conf->reg_fname); exit(EXIT_FAILURE); } } else { conf->reg = regidx_init(NULL,regidx_parse_reg,NULL,sizeof(char*),NULL); if ( regidx_insert_list(conf->reg,conf->reg_fname,',') !=0 ) { fprintf(stderr,"Could not parse the regions: %s\n", conf->reg_fname); exit(EXIT_FAILURE); } } nregs = regidx_nregs(conf->reg); if ( nregs ) { // the regions list can be empty, see #2250 conf->reg_itr = regitr_init(conf->reg); regitr_loop(conf->reg_itr); // region iterator now positioned at the first region } } // read the header of each file in the list and initialize data // beware: mpileup has always assumed that tid's are consistent in the headers, add sanity check at least! bam_hdr_t *hdr = NULL; // header of first file in input list int i; for (i = 0; i < conf->nfiles; ++i) { bam_hdr_t *h_tmp; conf->mplp_data[i] = (mplp_aux_t*) calloc(1, sizeof(mplp_aux_t)); conf->mplp_data[i]->fp = sam_open(conf->files[i], "rb"); if ( !conf->mplp_data[i]->fp ) { fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, conf->files[i], strerror(errno)); exit(EXIT_FAILURE); } if (hts_set_opt(conf->mplp_data[i]->fp, CRAM_OPT_DECODE_MD, 1)) { fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n"); exit(EXIT_FAILURE); } if (conf->fai_fname && hts_set_fai_filename(conf->mplp_data[i]->fp, conf->fai_fname) != 0) { fprintf(stderr, "[%s] failed to process %s: %s\n", __func__, conf->fai_fname, strerror(errno)); exit(EXIT_FAILURE); } conf->mplp_data[i]->conf = conf; conf->mplp_data[i]->ref = &mp_ref; h_tmp = sam_hdr_read(conf->mplp_data[i]->fp); if ( !h_tmp ) { fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, conf->files[i]); exit(EXIT_FAILURE); } conf->mplp_data[i]->h = i ? hdr : h_tmp; // for j==0, "h" has not been set yet conf->mplp_data[i]->bam_id = bam_smpl_add_bam(conf->bsmpl,h_tmp->text,conf->files[i]); if ( conf->mplp_data[i]->bam_id<0 ) { // no usable readgroups in this bam, it can be skipped sam_close(conf->mplp_data[i]->fp); free(conf->mplp_data[i]); bam_hdr_destroy(h_tmp); free(conf->files[i]); if ( i+1nfiles ) memmove(&conf->files[i],&conf->files[i+1],sizeof(*conf->files)*(conf->nfiles-i-1)); conf->nfiles--; i--; continue; } if (conf->reg && nregs) { hts_idx_t *idx = sam_index_load(conf->mplp_data[i]->fp, conf->files[i]); if (idx == NULL) { fprintf(stderr, "[%s] fail to load index for %s\n", __func__, conf->files[i]); exit(EXIT_FAILURE); } conf->buf.l = 0; ksprintf(&conf->buf,"%s:%u-%u",conf->reg_itr->seq,conf->reg_itr->beg+1,conf->reg_itr->end+1); conf->mplp_data[i]->iter = sam_itr_querys(idx, conf->mplp_data[i]->h, conf->buf.s); if ( !conf->mplp_data[i]->iter ) { conf->mplp_data[i]->iter = sam_itr_querys(idx, conf->mplp_data[i]->h, conf->reg_itr->seq); if ( conf->mplp_data[i]->iter ) { fprintf(stderr,"[E::%s] fail to parse region '%s'\n", __func__, conf->buf.s); exit(EXIT_FAILURE); } fprintf(stderr,"[E::%s] the sequence \"%s\" not found: %s\n",__func__,conf->reg_itr->seq,conf->files[i]); exit(EXIT_FAILURE); } if ( nregs==1 ) // no need to keep the index in memory hts_idx_destroy(idx); else conf->mplp_data[i]->idx = idx; } if ( !hdr ) hdr = h_tmp; /* save the header of first file in list */ else { // FIXME: check consistency between h and h_tmp bam_hdr_destroy(h_tmp); // we store only the first file's header; it's (alleged to be) // compatible with the i-th file's target_name lookup needs conf->mplp_data[i]->h = hdr; } } if ( !hdr ) { fprintf(stderr, "[%s] failed to find a file header with usable read groups\n", __func__); exit(EXIT_FAILURE); } // allocate data storage proportionate to number of samples being studied sm->n bam_smpl_get_samples(conf->bsmpl, &conf->gplp->n); conf->gplp->n_plp = (int*) calloc(conf->gplp->n, sizeof(int)); conf->gplp->m_plp = (int*) calloc(conf->gplp->n, sizeof(int)); conf->gplp->plp = (bam_pileup1_t**) calloc(conf->gplp->n, sizeof(bam_pileup1_t*)); fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, conf->gplp->n, conf->nfiles); // write the VCF header char wmode[8]; set_wmode(wmode,conf->output_type,conf->output_fname,conf->clevel); conf->bcf_fp = hts_open(conf->output_fname ? conf->output_fname : "-", wmode); if (conf->bcf_fp == NULL) { fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname? conf->output_fname : "standard output", strerror(errno)); exit(EXIT_FAILURE); } if ( conf->n_threads ) hts_set_threads(conf->bcf_fp, conf->n_threads); // BCF header creation conf->bcf_hdr = bcf_hdr_init("w"); conf->buf.l = 0; if (conf->record_cmd_line) { ksprintf(&conf->buf, "##bcftoolsVersion=%s+htslib-%s\n",bcftools_version(),hts_version()); bcf_hdr_append(conf->bcf_hdr, conf->buf.s); conf->buf.l = 0; ksprintf(&conf->buf, "##bcftoolsCommand=mpileup"); for (i=1; iargc; i++) ksprintf(&conf->buf, " %s", conf->argv[i]); kputc('\n', &conf->buf); bcf_hdr_append(conf->bcf_hdr, conf->buf.s); } if (conf->fai_fname) { conf->buf.l = 0; ksprintf(&conf->buf, "##reference=file://%s\n", conf->fai_fname); bcf_hdr_append(conf->bcf_hdr, conf->buf.s); } // Translate BAM @SQ tags to BCF ##contig tags // todo: use/write new BAM header manipulation routines, fill also UR, M5 for (i=0; in_targets; i++) { conf->buf.l = 0; ksprintf(&conf->buf, "##contig=", hdr->target_name[i], hdr->target_len[i]); bcf_hdr_append(conf->bcf_hdr, conf->buf.s); } conf->buf.l = 0; bcf_hdr_append(conf->bcf_hdr,"##ALT="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_IDV ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_IMF ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_VDB ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_RPBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_MQBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_BQBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_MQSBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_MIN_PL_SUM ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_NM ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_NMBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_FMT_NMBZ ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_INFO_SCBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_FS ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_SGB ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_MQ0F ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_FMT_DP ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_FMT_DV ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_FMT_DPR ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_INFO_DPR ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_FMT_DP4 ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_FMT_SP ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_FMT_AD ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_FMT_ADF ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_FMT_ADR ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_FMT_QS ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_INFO_AD ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_ADF ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_SCR ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_FMT_SCR ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_INFO_ADR ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->gvcf ) gvcf_update_header(conf->gvcf, conf->bcf_hdr); int nsmpl; const char **smpl = bam_smpl_get_samples(conf->bsmpl, &nsmpl); for (i=0; ibcf_hdr, smpl[i]); if ( bcf_hdr_write(conf->bcf_fp, conf->bcf_hdr)!=0 ) error("[%s] Error: failed to write the header to %s\n",__func__,conf->output_fname?conf->output_fname:"standard output"); if ( init_index2(conf->bcf_fp,conf->bcf_hdr,conf->output_fname, &conf->index_fn, conf->write_index) < 0 ) error("Error: failed to initialise index for %s\n",conf->output_fname); conf->bca = bcf_call_init(-1., conf->min_baseQ, conf->max_baseQ, conf->delta_baseQ); conf->bcr = (bcf_callret1_t*) calloc(nsmpl, sizeof(bcf_callret1_t)); conf->bca->openQ = conf->openQ, conf->bca->extQ = conf->extQ, conf->bca->tandemQ = conf->tandemQ; conf->bca->indel_bias = conf->indel_bias; conf->bca->del_bias = conf->del_bias; conf->bca->min_frac = conf->min_frac; conf->bca->min_support = conf->min_support; conf->bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE; conf->bca->fmt_flag = conf->fmt_flag; conf->bca->ambig_reads = conf->ambig_reads; conf->bca->indel_win_size = conf->indel_win_size; conf->bca->indels_v20 = conf->indels_v20; conf->bca->edlib = conf->edlib; conf->bca->seqQ_offset = conf->seqQ_offset; conf->bca->poly_mqual = conf->poly_mqual; conf->bca->vs_ref = conf->vs_ref; conf->bc.bcf_hdr = conf->bcf_hdr; conf->bc.n = nsmpl; conf->bc.PL = (int32_t*) malloc(15 * nsmpl * sizeof(*conf->bc.PL)); conf->bc.QS = (int32_t*) malloc(nsmpl*sizeof(*conf->bc.QS)*B2B_MAX_ALLELES); for (i=0; ibcr[i].QS = conf->bc.QS + i*B2B_MAX_ALLELES; if (conf->fmt_flag) { assert( sizeof(float)==sizeof(int32_t) ); conf->bc.DP4 = (int32_t*) malloc(nsmpl * sizeof(int32_t) * 4); conf->bc.fmt_arr = (uint8_t*) malloc(nsmpl * sizeof(float)); // all fmt_flag fields, float and int32 if ( conf->fmt_flag&(B2B_INFO_DPR|B2B_FMT_DPR|B2B_INFO_AD|B2B_INFO_ADF|B2B_INFO_ADR|B2B_FMT_AD|B2B_FMT_ADF|B2B_FMT_ADR) ) { // first B2B_MAX_ALLELES fields for total numbers, the rest per-sample conf->bc.ADR = (int32_t*) malloc((nsmpl+1)*B2B_MAX_ALLELES*sizeof(int32_t)); conf->bc.ADF = (int32_t*) malloc((nsmpl+1)*B2B_MAX_ALLELES*sizeof(int32_t)); for (i=0; ibcr[i].ADR = conf->bc.ADR + (i+1)*B2B_MAX_ALLELES; conf->bcr[i].ADF = conf->bc.ADF + (i+1)*B2B_MAX_ALLELES; } } if ( conf->fmt_flag&(B2B_INFO_SCR|B2B_FMT_SCR) ) conf->bc.SCR = (int32_t*) malloc((nsmpl+1)*sizeof(*conf->bc.SCR)); } int nnmbz = (conf->fmt_flag&B2B_FMT_NMBZ) ? nsmpl + 1 : 1; conf->bc.ref_nm = (int32_t*) malloc(sizeof(*conf->bc.ref_nm) * nnmbz * B2B_N_NM); conf->bc.alt_nm = (int32_t*) malloc(sizeof(*conf->bc.alt_nm) * nnmbz * B2B_N_NM); conf->bc.mwu_nm = (float*) malloc((nsmpl+1)*sizeof(*conf->bc.mwu_nm)); conf->bca->ref_nm = conf->bc.ref_nm; // this is just to make the arrays available in bcf_call_glfgen() conf->bca->alt_nm = conf->bc.alt_nm; if ( conf->fmt_flag&B2B_FMT_NMBZ ) { for (i=0; ibcr[i].ref_nm = conf->bc.ref_nm + (i+1)*B2B_N_NM; for (i=0; ibcr[i].alt_nm = conf->bc.alt_nm + (i+1)*B2B_N_NM; } // init mpileup conf->iter = bam_mplp_init(conf->nfiles, mplp_func, (void**)conf->mplp_data); if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(conf->iter); fprintf(stderr, "[%s] maximum number of reads per input file set to -d %d\n", __func__, conf->max_depth); if ( (double)conf->max_depth * conf->nfiles > 1<<20) fprintf(stderr, "Warning: Potential memory hog, up to %.0fM reads in the pileup!\n", (double)conf->max_depth*conf->nfiles); if ( (double)conf->max_depth * conf->nfiles / nsmpl < 250 ) fprintf(stderr, "Note: The maximum per-sample depth with -d %d is %.1fx\n", conf->max_depth,(double)conf->max_depth * conf->nfiles / nsmpl); bam_mplp_set_maxcnt(conf->iter, conf->max_depth); conf->max_indel_depth = conf->max_indel_depth * nsmpl; conf->bcf_rec = bcf_init1(); bam_mplp_constructor(conf->iter, pileup_constructor); bam_mplp_destructor(conf->iter, pileup_destructor); // Run mpileup for multiple regions int ret = 0; if ( nregs ) { int ireg = 0; do { // first region is already positioned if ( ireg++ > 0 ) { conf->buf.l = 0; ksprintf(&conf->buf,"%s:%u-%u",conf->reg_itr->seq,conf->reg_itr->beg+1,conf->reg_itr->end+1); for (i=0; infiles; i++) { hts_itr_destroy(conf->mplp_data[i]->iter); conf->mplp_data[i]->iter = sam_itr_querys(conf->mplp_data[i]->idx, conf->mplp_data[i]->h, conf->buf.s); if ( !conf->mplp_data[i]->iter ) { conf->mplp_data[i]->iter = sam_itr_querys(conf->mplp_data[i]->idx, conf->mplp_data[i]->h, conf->reg_itr->seq); if ( conf->mplp_data[i]->iter ) { fprintf(stderr,"[E::%s] fail to parse region '%s'\n", __func__, conf->buf.s); exit(EXIT_FAILURE); } fprintf(stderr,"[E::%s] the sequence \"%s\" not found: %s\n",__func__,conf->reg_itr->seq,conf->files[i]); exit(EXIT_FAILURE); } bam_mplp_reset(conf->iter); } } ret = mpileup_reg(conf,conf->reg_itr->beg,conf->reg_itr->end); if ( ret<0 ) break; } while ( regitr_loop(conf->reg_itr) ); } else if ( !conf->reg ) ret = mpileup_reg(conf,0,UINT32_MAX); if ( ret<0 ) { fprintf(stderr, "[%s] failed to read from input file\n", __func__); exit(EXIT_FAILURE); } flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, NULL); // clean up free(conf->bc.tmp.s); bcf_destroy1(conf->bcf_rec); if (conf->bcf_fp) { if ( conf->write_index ) { if ( bcf_idx_save(conf->bcf_fp)<0 ) { if ( hts_close(conf->bcf_fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,conf->output_fname); error("Error: cannot write to index %s\n",conf->index_fn); } free(conf->index_fn); } if ( hts_close(conf->bcf_fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,conf->output_fname); bcf_hdr_destroy(conf->bcf_hdr); bcf_call_destroy(conf->bca); free(conf->bc.PL); free(conf->bc.DP4); free(conf->bc.ADR); free(conf->bc.ADF); free(conf->bc.SCR); free(conf->bc.QS); free(conf->bc.ref_nm); free(conf->bc.alt_nm); free(conf->bc.fmt_arr); free(conf->bc.mwu_nm); free(conf->bcr); } if ( conf->gvcf ) gvcf_destroy(conf->gvcf); free(conf->buf.s); for (i = 0; i < conf->gplp->n; ++i) free(conf->gplp->plp[i]); free(conf->gplp->plp); free(conf->gplp->n_plp); free(conf->gplp->m_plp); free(conf->gplp); bam_mplp_destroy(conf->iter); bam_hdr_destroy(hdr); for (i = 0; i < conf->nfiles; ++i) { if ( nregs>1 ) hts_idx_destroy(conf->mplp_data[i]->idx); sam_close(conf->mplp_data[i]->fp); if ( conf->mplp_data[i]->iter) hts_itr_destroy(conf->mplp_data[i]->iter); free(conf->mplp_data[i]); } if ( conf->reg_itr ) regitr_destroy(conf->reg_itr); free(conf->mplp_data); free(conf->plp); free(conf->n_plp); free(mp_ref.ref[0]); free(mp_ref.ref[1]); return 0; } static int is_url(const char *s) { static const char uri_scheme_chars[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+.-"; return s[strspn(s, uri_scheme_chars)] == ':'; } #define MAX_PATH_LEN 1024 int read_file_list(const char *file_list,int *n,char **argv[]) { char buf[MAX_PATH_LEN]; int len, nfiles = 0; char **files = NULL; struct stat sb; *n = 0; *argv = NULL; FILE *fh = fopen(file_list,"r"); if ( !fh ) { fprintf(stderr,"%s: %s\n", file_list,strerror(errno)); return 1; } files = (char**) calloc(nfiles,sizeof(char*)); nfiles = 0; while ( fgets(buf,MAX_PATH_LEN,fh) ) { // allow empty lines and trailing spaces len = strlen(buf); while ( len>0 && isspace(buf[len-1]) ) len--; if ( !len ) continue; // check sanity of the file list buf[len] = 0; if (! (is_url(buf) || stat(buf, &sb) == 0)) { // no such file, check if it is safe to print its name int i, safe_to_print = 1; for (i=0; irflag_skip_all_set); char *tmp_skip_any_unset = bam_flag2str(mplp->rflag_skip_any_unset); char *tmp_skip_all_unset = bam_flag2str(mplp->rflag_skip_all_unset); char *tmp_skip_any_set = bam_flag2str(mplp->rflag_skip_any_set); // Display usage information, formatted for the standard 80 columns. // (The unusual string formatting here aids the readability of this // source code in 80 columns, to the extent that's possible.) fprintf(fp, "\n" "Usage: bcftools mpileup [options] in1.bam [in2.bam [...]]\n" "\n" "Input options:\n" " -6, --illumina1.3+ Quality is in the Illumina-1.3+ encoding\n" " -A, --count-orphans Include anomalous read pairs, with flag PAIRED but not PROPER_PAIR set\n" " -b, --bam-list FILE List of input BAM filenames, one per line\n" " -B, --no-BAQ Disable BAQ (per-Base Alignment Quality)\n" " -C, --adjust-MQ INT Adjust mapping quality [0]\n" " -D, --full-BAQ Apply BAQ everywhere, not just in problematic regions\n" " -d, --max-depth INT Max raw per-file depth; avoids excessive memory usage [%d]\n", mplp->max_depth); fprintf(fp, " -E, --redo-BAQ Recalculate BAQ on the fly, ignore existing BQs\n" " -f, --fasta-ref FILE Faidx indexed reference sequence file\n" " --no-reference Do not require fasta reference file\n" " -G, --read-groups FILE Select or exclude read groups listed in the file\n" " -q, --min-MQ INT Skip alignments with mapQ smaller than INT [%d]\n", mplp->min_mq); fprintf(fp, " -Q, --min-BQ INT Skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ); fprintf(fp, " --max-BQ INT Limit baseQ/BAQ to no more than INT [%d]\n", mplp->max_baseQ); fprintf(fp, " --delta-BQ INT Use neighbour_qual + INT if less than qual [%d]\n", mplp->delta_baseQ); fprintf(fp, " -r, --regions REG[,...] Comma separated list of regions in which pileup is generated\n" " -R, --regions-file FILE Restrict to regions listed in a file\n" " --ignore-RG Ignore RG tags (one BAM = one sample)\n" " --ls, --skip-all-set STR|INT Skip reads with all of the bits set []\n"); fprintf(fp, " --ns, --skip-any-set STR|INT Skip reads with any of the bits set [%s]\n", tmp_skip_any_set); fprintf(fp, " --lu, --skip-all-unset STR|INT Skip reads with all of the bits unset []\n" " --nu, --skip-any-unset STR|INT Skip reads with any of the bits unset []\n"); fprintf(fp, " -s, --samples LIST Comma separated list of samples to include\n" " -S, --samples-file FILE File of samples to include\n" " -t, --targets REG[,...] Similar to -r but streams rather than index-jumps\n" " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n" " -x, --ignore-overlaps Disable read-pair overlap detection\n" " --seed INT Random number seed used for sampling deep regions [0]\n" "\n" "Output options:\n" " -a, --annotate LIST Optional tags to output; '\\?' to list available tags []\n" " -g, --gvcf INT[,...] Group non-variant sites into gVCF blocks according\n" " To minimum per-sample DP\n" " --no-version Do not append version and command line to the header\n" " -o, --output FILE Write output to FILE [standard output]\n" " -O, --output-type TYPE 'b' compressed BCF; 'u' uncompressed BCF;\n" " 'z' compressed VCF; 'v' uncompressed VCF; 0-9 compression level [v]\n" " --threads INT Use multithreading with INT worker threads [0]\n" " -W, --write-index[=FMT] Automatically index the output files [off]\n" "\n" "SNP/INDEL genotype likelihoods options:\n" " -X, --config STR Specify platform profile (use \"-X list\" for details)\n" " -e, --ext-prob INT Phred-scaled gap extension seq error probability [%d]\n", mplp->extQ); fprintf(fp, " -F, --gap-frac FLOAT Minimum fraction of gapped reads [%g]\n", mplp->min_frac); fprintf(fp, " -h, --tandem-qual INT Coefficient for homopolymer errors [%d]\n", mplp->tandemQ); fprintf(fp, " -I, --skip-indels Do not perform indel calling\n" " -L, --max-idepth INT Maximum per-file depth for INDEL calling [%d]\n", mplp->max_indel_depth); fprintf(fp, " -m, --min-ireads INT Minimum number gapped reads for indel candidates [%d]\n", mplp->min_support); fprintf(fp, " -M, --max-read-len INT Maximum length of read to pass to BAQ algorithm [%d]\n", mplp->max_read_len); fprintf(fp, " -o, --open-prob INT Phred-scaled gap open seq error probability [%d]\n", mplp->openQ); fprintf(fp, " -p, --per-sample-mF Apply -m and -F per-sample for increased sensitivity\n" " -P, --platforms STR Comma separated list of platforms for indels [all]\n" " --ar, --ambig-reads STR What to do with ambiguous indel reads: drop,incAD,incAD0 [drop]\n"); fprintf(fp, " --indel-bias FLOAT Raise to favour recall over precision [%.2f]\n", mplp->indel_bias); fprintf(fp, " --del-bias FLOAT Relative likelihood of insertion to deletion [%.2f]\n", mplp->del_bias); fprintf(fp, " --score-vs-ref FLOAT\n" " Ratio of score vs ref (1) or 2nd-best allele (0) [%.2f]\n", mplp->vs_ref); fprintf(fp, " --indel-size INT Approximate maximum indel size considered [%d]\n", mplp->indel_win_size); fprintf(fp, " --indels-2.0 New EXPERIMENTAL indel calling model (diploid reference consensus)\n" " --indels-cns New EXPERIMENTAL indel calling model with edlib\n" " --seqq-offset Indel-cns tuning for indel seq-qual scores [120]\n" " --no-indels-cns Disable CNS mode, to use after a -X profile\n" " --poly-mqual (Edlib mode) Use minimum quality within homopolymers\n"); fprintf(fp,"\n"); fprintf(fp, "Notes: Assuming diploid individuals.\n\n" "Example:\n" " # See also http://samtools.github.io/bcftools/howtos/variant-calling.html\n" " bcftools mpileup -Ou -f reference.fa alignments.bam | bcftools call -mv -Ob -o calls.bcf\n" "\n"); free(tmp_skip_all_set); free(tmp_skip_any_unset); free(tmp_skip_all_unset); free(tmp_skip_any_set); } static void print_profiles(void) { printf( "Configuration profiles activated with -X, --config:\n\n" "1.12\n" " -Q13 -h100 -m1 -F0.002\n\n" "bgi, bgi-1.20\n" " --indels-cns -B --indel-size 80 -F0.1 --indel-bias 0.9 --seqq-offset 120\n\n" "illumina-1.18\n" " --indel-size 110\n\n" "illumina\n" "illumina-1.20\n" " --indels-cns --indel-size 110\n\n" "ont\n" " -B -Q5 --max-BQ 30 -I\n\n" "ont-sup, ont-sup-1.20\n" " --indels-cns -B -Q1 --max-BQ 35 -F0.2 -o15 -e1 -h110 --delta-BQ 99\\\n" " --del-bias 0.4 --indel-bias 0.7 --poly-mqual --seqq-offset 130\\\n" " --indel-size 80\n\n" "pacbio-ccs-1.18\n" " -D -Q5 --max-BQ 50 -F0.1 -o25 -e1 --delta-BQ 10 \\\n" " -M99999 --indel-size 110\n\n" "pacbio-ccs, pacbio-ccs-1.20\n" " --indels-cns -B -Q5 --max-BQ 50 -F0.1 -o25 -e1 -h300 --delta-BQ 10 \\\n" " --del-bias 0.4 --poly-mqual --indel-bias 0.9 --seqq-offset 118\\\n" " --indel-size 80 --score-vs-ref 0.7\n\n" "ultima, ultima-1.20\n" " --indels-cns -B -Q1 --max-BQ 30 -F0.15 -o20 -e10 -h250 --delta-BQ 10 \\\n" " --del-bias 0.3 --indel-bias 0.7 --poly-mqual --seqq-offset 140 \\\n" " --indel-size 80 --score-vs-ref 0.3\n\n" "\n"); } int main_mpileup(int argc, char *argv[]) { int c, i, ret = 1; const char *file_list = NULL; char **fn = NULL; int nfiles = 0, use_orphan = 0, noref = 0; mplp_conf_t mplp; memset(&mplp, 0, sizeof(mplp_conf_t)); mplp.min_baseQ = 1; mplp.max_baseQ = 60; mplp.delta_baseQ = 30; mplp.capQ_thres = 0; mplp.max_depth = 250; mplp.max_indel_depth = 250; mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 500; mplp.min_frac = 0.05; mplp.indel_bias = 1.0; mplp.min_support = 2; mplp.vs_ref = 0; mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN | MPLP_REALN_PARTIAL | MPLP_SMART_OVERLAPS; mplp.argc = argc; mplp.argv = argv; mplp.rflag_skip_any_set = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP; mplp.output_fname = NULL; mplp.output_type = FT_VCF; mplp.record_cmd_line = 1; mplp.n_threads = 0; mplp.bsmpl = bam_smpl_init(); // the default to be changed in future, see also parse_format_flag() mplp.fmt_flag = B2B_INFO_BQBZ|B2B_INFO_IDV|B2B_INFO_IMF|B2B_INFO_MQ0F|B2B_INFO_MQBZ|B2B_INFO_MQSBZ|B2B_INFO_RPBZ|B2B_INFO_SCBZ|B2B_INFO_SGB|B2B_INFO_VDB|B2B_FMT_AD; mplp.max_read_len = 500; mplp.ambig_reads = B2B_DROP; mplp.indel_win_size = 110; mplp.poly_mqual = 0; mplp.seqQ_offset = 120; mplp.clevel = -1; mplp.del_bias = 0; // even insertion and deletion likelhoods. hts_srand48(0); static const struct option lopts[] = { {"nu", required_argument, NULL, 16}, {"lu", required_argument, NULL, 17}, {"rf", required_argument, NULL, 17}, // old --rf, --incl-flags = --lu, --skip-all-unset {"ns", required_argument, NULL, 18}, {"ff", required_argument, NULL, 18}, // old --ff, --excl-flags = --ns, --skip-any-set {"ls", required_argument, NULL, 19}, {"skip-any-unset", required_argument, NULL, 16}, {"skip-all-unset", required_argument, NULL, 17}, {"skip-any-set", required_argument, NULL, 18}, {"skip-all-set", required_argument, NULL, 19}, {"output", required_argument, NULL, 3}, {"open-prob", required_argument, NULL, 4}, {"ignore-RG", no_argument, NULL, 5}, {"ignore-rg", no_argument, NULL, 5}, {"gvcf", required_argument, NULL, 'g'}, {"no-reference", no_argument, NULL, 7}, {"no-version", no_argument, NULL, 8}, {"threads",required_argument,NULL,9}, {"illumina1.3+", no_argument, NULL, '6'}, {"count-orphans", no_argument, NULL, 'A'}, {"bam-list", required_argument, NULL, 'b'}, {"no-BAQ", no_argument, NULL, 'B'}, {"no-baq", no_argument, NULL, 'B'}, {"full-BAQ", no_argument, NULL, 'D'}, {"full-baq", no_argument, NULL, 'D'}, {"adjust-MQ", required_argument, NULL, 'C'}, {"adjust-mq", required_argument, NULL, 'C'}, {"max-depth", required_argument, NULL, 'd'}, {"redo-BAQ", no_argument, NULL, 'E'}, {"redo-baq", no_argument, NULL, 'E'}, {"fasta-ref", required_argument, NULL, 'f'}, {"read-groups", required_argument, NULL, 'G'}, {"region", required_argument, NULL, 'r'}, {"regions", required_argument, NULL, 'r'}, {"regions-file", required_argument, NULL, 'R'}, {"targets", required_argument, NULL, 't'}, {"targets-file", required_argument, NULL, 'T'}, {"min-MQ", required_argument, NULL, 'q'}, {"min-mq", required_argument, NULL, 'q'}, {"min-BQ", required_argument, NULL, 'Q'}, {"min-bq", required_argument, NULL, 'Q'}, {"max-bq", required_argument, NULL, 11}, {"max-BQ", required_argument, NULL, 11}, {"delta-BQ", required_argument, NULL, 12}, {"ignore-overlaps", no_argument, NULL, 'x'}, {"output-type", required_argument, NULL, 'O'}, {"samples", required_argument, NULL, 's'}, {"samples-file", required_argument, NULL, 'S'}, {"annotate", required_argument, NULL, 'a'}, {"ext-prob", required_argument, NULL, 'e'}, {"gap-frac", required_argument, NULL, 'F'}, {"indel-bias", required_argument, NULL, 10}, {"indel-size", required_argument, NULL, 15}, {"indels-2.0", no_argument, NULL, 20}, {"indels-cns", no_argument, NULL, 22}, {"no-indels-cns", no_argument, NULL, 25}, {"tandem-qual", required_argument, NULL, 'h'}, {"skip-indels", no_argument, NULL, 'I'}, {"max-idepth", required_argument, NULL, 'L'}, {"min-ireads", required_argument, NULL, 'm'}, {"per-sample-mF", no_argument, NULL, 'p'}, {"per-sample-mf", no_argument, NULL, 'p'}, {"platforms", required_argument, NULL, 'P'}, {"max-read-len", required_argument, NULL, 'M'}, {"config", required_argument, NULL, 'X'}, {"seed", required_argument, NULL, 13}, {"ambig-reads", required_argument, NULL, 14}, {"ar", required_argument, NULL, 14}, {"write-index",optional_argument,NULL,'W'}, {"del-bias", required_argument, NULL, 23}, {"poly-mqual", no_argument, NULL, 24}, {"no-poly-mqual", no_argument, NULL, 26}, {"score-vs-ref",required_argument, NULL, 27}, {"seqq-offset", required_argument, NULL, 28}, {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "Ag:f:r:R:q:Q:C:BDd:L:b:P:po:e:h:Im:F:EG:6O:xa:s:S:t:T:M:X:UW::",lopts,NULL)) >= 0) { switch (c) { case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break; case 16 : mplp.rflag_skip_any_unset = bam_str2flag(optarg); if ( mplp.rflag_skip_any_unset <0 ) { fprintf(stderr,"Could not parse --nf %s\n", optarg); goto err; } break; case 17 : mplp.rflag_skip_all_unset = bam_str2flag(optarg); if ( mplp.rflag_skip_all_unset<0 ) { fprintf(stderr,"Could not parse --if %s\n", optarg); goto err; } break; case 18 : mplp.rflag_skip_any_set = bam_str2flag(optarg); if ( mplp.rflag_skip_any_set <0 ) { fprintf(stderr,"Could not parse --ef %s\n", optarg); goto err; } break; case 19 : mplp.rflag_skip_all_set = bam_str2flag(optarg); if ( mplp.rflag_skip_all_set <0 ) { fprintf(stderr,"Could not parse --df %s\n", optarg); goto err; } break; case 3 : mplp.output_fname = optarg; break; case 4 : mplp.openQ = atoi(optarg); break; case 5 : bam_smpl_ignore_readgroups(mplp.bsmpl); break; case 'g': mplp.gvcf = gvcf_init(optarg); if ( !mplp.gvcf ) error("Could not parse: --gvcf %s\n", optarg); break; case 'f': mplp.fai = fai_load(optarg); if (mplp.fai == NULL) goto err; mplp.fai_fname = optarg; break; case 7 : noref = 1; break; case 8 : mplp.record_cmd_line = 0; break; case 9 : mplp.n_threads = strtol(optarg, 0, 0); break; case 'd': mplp.max_depth = atoi(optarg); break; case 'r': mplp.reg_fname = strdup(optarg); break; case 'R': mplp.reg_fname = strdup(optarg); mplp.reg_is_file = 1; break; case 't': // In the original version the whole BAM was streamed which is inefficient // with few BED intervals and big BAMs. Todo: devise a heuristic to determine // best strategy, that is streaming or jumping. if ( optarg[0]=='^' ) optarg++; else mplp.bed_logic = 1; mplp.bed = regidx_init(NULL,regidx_parse_reg,NULL,0,NULL); mplp.bed_itr = regitr_init(mplp.bed); if ( regidx_insert_list(mplp.bed,optarg,',') !=0 ) { fprintf(stderr,"Could not parse the targets: %s\n", optarg); exit(EXIT_FAILURE); } break; case 'T': if ( optarg[0]=='^' ) optarg++; else mplp.bed_logic = 1; mplp.bed = regidx_init(optarg,NULL,NULL,0,NULL); if (!mplp.bed) { fprintf(stderr, "bcftools mpileup: Could not read file \"%s\"", optarg); goto err; } break; case 'P': mplp.pl_list = strdup(optarg); break; case 'p': mplp.flag |= MPLP_PER_SAMPLE; break; case 'B': mplp.flag &= ~MPLP_REALN; break; case 'D': mplp.flag &= ~MPLP_REALN_PARTIAL; break; case 'I': mplp.flag |= MPLP_NO_INDEL; break; case 'E': mplp.flag |= MPLP_REDO_BAQ; break; case '6': mplp.flag |= MPLP_ILLUMINA13; break; case 's': if ( bam_smpl_add_samples(mplp.bsmpl,optarg,0)<0 ) error("Could not read samples: %s\n",optarg); break; case 'S': if ( bam_smpl_add_samples(mplp.bsmpl,optarg,1)<0 ) error("Could not read samples: %s\n",optarg); break; case 'O': switch (optarg[0]) { case 'b': mplp.output_type = FT_BCF_GZ; break; case 'u': mplp.output_type = FT_BCF; break; case 'z': mplp.output_type = FT_VCF_GZ; break; case 'v': mplp.output_type = FT_VCF; break; default: { char *tmp; mplp.clevel = strtol(optarg,&tmp,10); if ( *tmp || mplp.clevel<0 || mplp.clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { char *tmp; mplp.clevel = strtol(optarg+1,&tmp,10); if ( *tmp || mplp.clevel<0 || mplp.clevel>9 ) error("Could not parse argument: --output-type %s\n", optarg+1); } break; case 'C': mplp.capQ_thres = atoi(optarg); break; case 'q': mplp.min_mq = atoi(optarg); break; case 'Q': mplp.min_baseQ = atoi(optarg); break; case 11: mplp.max_baseQ = atoi(optarg); break; case 12: mplp.delta_baseQ = atoi(optarg); break; case 'b': file_list = optarg; break; case 'o': { char *end; long value = strtol(optarg, &end, 10); // Distinguish between -o INT and -o FILE (a bit of a hack!) if (*end == '\0') mplp.openQ = value; else mplp.output_fname = optarg; } break; case 'e': mplp.extQ = atoi(optarg); break; case 'h': mplp.tandemQ = atoi(optarg); break; case 10: // --indel-bias (inverted so higher => more indels called) if (atof(optarg) < 1e-2) mplp.indel_bias = 1/1e2; else mplp.indel_bias = 1/atof(optarg); break; case 27: mplp.vs_ref = atof(optarg); //if (mplp.vs_ref < 0) mplp.vs_ref = 0; if (mplp.vs_ref > 1) mplp.vs_ref = 1; break; case 15: { char *tmp; mplp.indel_win_size = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --indel-size %s\n", optarg); if ( mplp.indel_win_size < 20 ) { mplp.indel_win_size = 20; fprintf(stderr,"Warning: running with --indel-size %d, the requested value is too small\n",mplp.indel_win_size); } } break; case 20: mplp.indels_v20 = 1; mplp.edlib = 0; break; case 'W': if (!(mplp.write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 22: mplp.edlib = 1; mplp.indels_v20 = 0; break; case 25: mplp.edlib = 0; break; case 28: mplp.seqQ_offset = atoi(optarg); if (mplp.seqQ_offset < 100) mplp.seqQ_offset = 100; if (mplp.seqQ_offset > 200) mplp.seqQ_offset = 200; break; case 23: mplp.del_bias = atof(optarg); break; case 24: mplp.poly_mqual = 1; break; case 26: mplp.poly_mqual = 0; break; case 'A': use_orphan = 1; break; case 'F': mplp.min_frac = atof(optarg); break; case 'm': mplp.min_support = atoi(optarg); break; case 'L': mplp.max_indel_depth = atoi(optarg); break; case 'G': bam_smpl_add_readgroups(mplp.bsmpl, optarg, 1); break; case 'a': if (optarg[0]=='?') { list_annotations(stderr); goto err; } parse_format_flag(&mplp.fmt_flag,optarg); break; case 'M': mplp.max_read_len = atoi(optarg); break; case 'X': if (strcasecmp(optarg, "pacbio-ccs-1.18") == 0) { mplp.min_frac = 0.1; mplp.min_baseQ = 5; mplp.max_baseQ = 50; mplp.delta_baseQ = 10; mplp.openQ = 25; mplp.extQ = 1; mplp.flag |= MPLP_REALN_PARTIAL; mplp.max_read_len = 99999; } else if (strcasecmp(optarg, "pacbio-ccs") == 0 || strcasecmp(optarg, "pacbio-ccs-1.20") == 0) { mplp.min_frac = 0.1; mplp.min_baseQ = 5; mplp.max_baseQ = 50; mplp.delta_baseQ = 10; mplp.tandemQ = 300; mplp.openQ = 25; mplp.extQ = 1; mplp.flag &= ~MPLP_REALN; mplp.del_bias = 0.4; mplp.indel_bias = 1/.9; mplp.seqQ_offset = 118; mplp.poly_mqual = 1; mplp.edlib = 1; mplp.vs_ref = 0.7; mplp.indel_win_size = 80; } else if (strcasecmp(optarg, "ont") == 0) { fprintf(stderr, "With old ONT data may be beneficial to also run bcftools call with " "a higher -P, eg -P0.01 or -P 0.1\n"); mplp.min_baseQ = 5; mplp.max_baseQ = 30; mplp.flag &= ~MPLP_REALN; mplp.flag |= MPLP_NO_INDEL; } else if (strcasecmp(optarg, "ont-sup") == 0 || strcasecmp(optarg, "ont-sup-1.20") == 0) { mplp.min_frac = 0.2; mplp.min_baseQ = 1; mplp.max_baseQ = 35; mplp.delta_baseQ = 99; mplp.openQ = 15; mplp.extQ = 1; mplp.flag &= ~MPLP_REALN; mplp.max_read_len = 9999999; mplp.del_bias = 0.4; mplp.poly_mqual = 1; mplp.edlib = 1; // If we increase -h then we can increase bias denominator too mplp.tandemQ = 110; mplp.indel_bias = 1/0.7; mplp.seqQ_offset = 130; mplp.indel_win_size = 80; } else if (strcasecmp(optarg, "ultima") == 0 || strcasecmp(optarg, "ultima-1.20") == 0) { mplp.min_frac = 0.15; mplp.min_baseQ = 1; mplp.max_baseQ = 30; mplp.delta_baseQ = 10; mplp.openQ = 20; mplp.extQ = 10; mplp.tandemQ = 250; mplp.flag &= ~MPLP_REALN; mplp.del_bias = 0.3; mplp.poly_mqual = 1; mplp.edlib = 1; mplp.indel_bias = 1/0.7; mplp.seqQ_offset = 140; mplp.vs_ref = 0.3; mplp.indel_win_size = 80; } else if (strcasecmp(optarg, "1.12") == 0) { // 1.12 and earlier mplp.min_frac = 0.002; mplp.min_support = 1; mplp.min_baseQ = 13; mplp.tandemQ = 100; mplp.flag &= ~MPLP_REALN_PARTIAL; mplp.flag |= MPLP_REALN; } else if (strcasecmp(optarg, "illumina-1.18") == 0) { mplp.indel_win_size = 110; mplp.flag |= MPLP_REALN_PARTIAL; } else if (strcasecmp(optarg, "illumina") == 0 || strcasecmp(optarg, "illumina-1.20") == 0) { mplp.edlib = 1; mplp.indel_win_size = 110; mplp.flag |= MPLP_REALN_PARTIAL; mplp.indel_bias = 1; mplp.seqQ_offset = 125; //mplp.indel_win_size = 80; TEST? } else if (strcasecmp(optarg, "bgi") == 0 || strcasecmp(optarg, "bgi-1.20") == 0) { mplp.min_frac = 0.1; mplp.edlib = 1; mplp.indel_bias = 1; mplp.seqQ_offset = 120; mplp.flag |= MPLP_REALN_PARTIAL; mplp.indel_win_size = 80; } else if (strcasecmp(optarg, "list") == 0 || strcasecmp(optarg, "help") == 0) { print_profiles(); goto err; } else { fprintf(stderr, "Unknown configuration name '%s'\n" "Please use '-X list' to show available choices.\n", optarg); goto err; } break; case 13: hts_srand48(atoi(optarg)); break; case 14: if ( !strcasecmp(optarg,"drop") ) mplp.ambig_reads = B2B_DROP; else if ( !strcasecmp(optarg,"incAD") ) mplp.ambig_reads = B2B_INC_AD; else if ( !strcasecmp(optarg,"incAD0") ) mplp.ambig_reads = B2B_INC_AD0; else error("The option to --ambig-reads not recognised: %s\n",optarg); break; default: fprintf(stderr,"Invalid option: '%c'\n", c); goto err; } } if ( mplp.gvcf && !(mplp.fmt_flag&B2B_FMT_DP) ) { fprintf(stderr,"[warning] The -a DP option is required with --gvcf, switching on.\n"); mplp.fmt_flag |= B2B_FMT_DP; } if ( mplp.flag&(MPLP_BCF|MPLP_VCF|MPLP_NO_COMP) ) { if ( mplp.flag&MPLP_VCF ) { if ( mplp.flag&MPLP_NO_COMP ) mplp.output_type = FT_VCF; else mplp.output_type = FT_VCF_GZ; } else if ( mplp.flag&MPLP_BCF ) { if ( mplp.flag&MPLP_NO_COMP ) mplp.output_type = FT_BCF; else mplp.output_type = FT_BCF_GZ; } } if ( !(mplp.flag&MPLP_REALN) && mplp.flag&MPLP_REDO_BAQ ) { fprintf(stderr,"Error: The -B option cannot be combined with -E\n"); goto err; } if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN; if (argc == 1) { print_usage(stderr, &mplp); goto err; } if (!mplp.fai && !noref) { fprintf(stderr,"Error: mpileup requires the --fasta-ref option by default; use --no-reference to run without a fasta reference\n"); goto err; } if (file_list) { if ( read_file_list(file_list,&nfiles,&fn) ) goto err; mplp.files = fn; mplp.nfiles = nfiles; } else { mplp.nfiles = argc - optind; mplp.files = (char**) malloc(mplp.nfiles*sizeof(char*)); for (i=0; i Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "regidx.h" #include "bcftools.h" #include "bam2bcf.h" #include "bam_sample.h" #include "gvcf.h" #define MPLP_BCF 1 #define MPLP_VCF (1<<1) #define MPLP_NO_COMP (1<<2) #define MPLP_NO_ORPHAN (1<<3) #define MPLP_REALN (1<<4) #define MPLP_NO_INDEL (1<<5) #define MPLP_REDO_BAQ (1<<6) #define MPLP_ILLUMINA13 (1<<7) #define MPLP_IGNORE_RG (1<<8) #define MPLP_PRINT_POS (1<<9) #define MPLP_PRINT_MAPQ (1<<10) #define MPLP_PER_SAMPLE (1<<11) #define MPLP_SMART_OVERLAPS (1<<12) #define MPLP_REALN_PARTIAL (1<<13) typedef struct _mplp_aux_t mplp_aux_t; typedef struct _mplp_pileup_t mplp_pileup_t; // Data shared by all bam files typedef struct { int min_mq, flag, min_baseQ, max_baseQ, delta_baseQ, capQ_thres, max_depth, max_indel_depth, max_read_len, ambig_reads; uint32_t fmt_flag; int rflag_skip_any_unset, rflag_skip_all_unset, rflag_skip_any_set, rflag_skip_all_set, output_type; int openQ, extQ, tandemQ, min_support, indel_win_size; // for indels int seqQ_offset; double min_frac; // for indels double indel_bias, poly_mqual; double del_bias; // compensate for diff deletion vs insertion error rates double vs_ref; char *reg_fname, *pl_list, *fai_fname, *output_fname; int reg_is_file, record_cmd_line, n_threads, clevel; faidx_t *fai; regidx_t *bed, *reg; // bed: skipping regions, reg: index-jump to regions regitr_t *bed_itr, *reg_itr; int bed_logic; // 1: include region, 0: exclude region gvcf_t *gvcf; // auxiliary structures for calling bcf_callaux_t *bca; bcf_callret1_t *bcr; bcf_call_t bc; bam_mplp_t iter; mplp_aux_t **mplp_data; int nfiles; char **files; mplp_pileup_t *gplp; int *n_plp; const bam_pileup1_t **plp; bam_smpl_t *bsmpl; kstring_t buf; bcf1_t *bcf_rec; htsFile *bcf_fp; bcf_hdr_t *bcf_hdr; int indels_v20; int edlib; int argc; char **argv; int write_index; char *index_fn; } mplp_conf_t; typedef struct { char *ref[2]; int ref_id[2]; int ref_len[2]; } mplp_ref_t; #define MPLP_REF_INIT {{NULL,NULL},{-1,-1},{0,0}} // Data specific to each bam file struct _mplp_aux_t { samFile *fp; hts_itr_t *iter; bam_hdr_t *h; mplp_ref_t *ref; const mplp_conf_t *conf; int bam_id; hts_idx_t *idx; // maintained only with more than one -r regions }; // Data passed to htslib/mpileup struct _mplp_pileup_t { int n; int *n_plp, *m_plp; bam_pileup1_t **plp; }; static int mplp_get_ref(mplp_aux_t *ma, int tid, char **ref, int *ref_len) { mplp_ref_t *r = ma->ref; //printf("get ref %d {%d/%p, %d/%p}\n", tid, r->ref_id[0], r->ref[0], r->ref_id[1], r->ref[1]); if (!r || !ma->conf->fai) { *ref = NULL; return 0; } // Do we need to reference count this so multiple mplp_aux_t can // track which references are in use? // For now we just cache the last two. Sufficient? if (tid == r->ref_id[0]) { *ref = r->ref[0]; *ref_len = r->ref_len[0]; return 1; } if (tid == r->ref_id[1]) { // Last, swap over int tmp; tmp = r->ref_id[0]; r->ref_id[0] = r->ref_id[1]; r->ref_id[1] = tmp; tmp = r->ref_len[0]; r->ref_len[0] = r->ref_len[1]; r->ref_len[1] = tmp; char *tc; tc = r->ref[0]; r->ref[0] = r->ref[1]; r->ref[1] = tc; *ref = r->ref[0]; *ref_len = r->ref_len[0]; return 1; } // New, so migrate to old and load new free(r->ref[1]); r->ref[1] = r->ref[0]; r->ref_id[1] = r->ref_id[0]; r->ref_len[1] = r->ref_len[0]; r->ref_id[0] = tid; r->ref[0] = faidx_fetch_seq(ma->conf->fai, ma->h->target_name[r->ref_id[0]], 0, INT_MAX, &r->ref_len[0]); if (!r->ref[0]) { r->ref[0] = NULL; r->ref_id[0] = -1; r->ref_len[0] = 0; *ref = NULL; return 0; } *ref = r->ref[0]; *ref_len = r->ref_len[0]; return 1; } static int mplp_func(void *data, bam1_t *b) { char *ref; mplp_aux_t *ma = (mplp_aux_t*)data; int ret, ref_len; while (1) { int has_ref; ret = ma->iter? sam_itr_next(ma->fp, ma->iter, b) : sam_read1(ma->fp, ma->h, b); if (ret < 0) break; // The 'B' cigar operation is not part of the specification, considering as obsolete. // bam_remove_B(b); if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) continue; // exclude unmapped reads if (ma->conf->rflag_skip_any_unset && (ma->conf->rflag_skip_any_unset&b->core.flag)!=ma->conf->rflag_skip_any_unset) continue; if (ma->conf->rflag_skip_all_set && (ma->conf->rflag_skip_all_set&b->core.flag)==ma->conf->rflag_skip_all_set) continue; if (ma->conf->rflag_skip_all_unset && !(ma->conf->rflag_skip_all_unset&b->core.flag)) continue; if (ma->conf->rflag_skip_any_set && ma->conf->rflag_skip_any_set&b->core.flag) continue; if (ma->conf->bed) { // test overlap regitr_t *itr = ma->conf->bed_itr; int beg = b->core.pos, end = bam_endpos(b)-1; int overlap = regidx_overlap(ma->conf->bed, ma->h->target_name[b->core.tid],beg,end, itr); if ( !ma->conf->bed_logic && !overlap ) { // exclude only reads which are fully contained in the region while ( regitr_overlap(itr) ) { if ( beg < itr->beg ) { overlap = 1; break; } if ( end > itr->end ) { overlap = 1; break; } } } if ( !overlap ) continue; } if ( bam_smpl_get_sample_id(ma->conf->bsmpl,ma->bam_id,b)<0 ) continue; if (ma->conf->flag & MPLP_ILLUMINA13) { int i; uint8_t *qual = bam_get_qual(b); for (i = 0; i < b->core.l_qseq; ++i) qual[i] = qual[i] > 31? qual[i] - 31 : 0; } if (ma->conf->fai && b->core.tid >= 0) { has_ref = mplp_get_ref(ma, b->core.tid, &ref, &ref_len); if (has_ref && ref_len <= b->core.pos) { // exclude reads outside of the reference sequence fprintf(bcftools_stderr,"[%s] Skipping because %"PRId64" is outside of %d [ref:%d]\n", __func__, (int64_t) b->core.pos, ref_len, b->core.tid); continue; } } else { has_ref = 0; } // Allow sufficient room for bam_aux_append of ZQ tag without // a realloc and consequent breakage of pileup's cached pointers. if (has_ref && (ma->conf->flag &MPLP_REALN) && !bam_aux_get(b, "ZQ")) { // Doing sam_prob_realn later is problematic as it adds to // the tag list (ZQ or BQ), which causes a realloc of b->data. // This happens after pileup has built a hash table on the // read name. It's a deficiency in pileup IMO. // We could implement a new sam_prob_realn that returns ZQ // somewhere else and cache it ourselves (pileup clientdata), // but for now we simply use a workaround. // // We create a fake tag of the correct length, which we remove // just prior calling sam_prob_realn so we can guarantee there is // room. (We can't just make room now as bam_copy1 removes it // again). if (b->core.l_qseq > 500) { uint8_t *ZQ = malloc((uint32_t)b->core.l_qseq+1); memset(ZQ, '@', b->core.l_qseq); ZQ[b->core.l_qseq] = 0; bam_aux_append(b, "_Q", 'Z', b->core.l_qseq+1, ZQ); free(ZQ); } else { static uint8_t ZQ[501] = "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"; ZQ[b->core.l_qseq] = 0; bam_aux_append(b, "_Q", 'Z', b->core.l_qseq+1, ZQ); ZQ[b->core.l_qseq] = '@'; } } if (has_ref && ma->conf->capQ_thres > 10) { int q = sam_cap_mapq(b, ref, ref_len, ma->conf->capQ_thres); if (q < 0) continue; // skip else if (b->core.qual > q) b->core.qual = q; } if (b->core.qual < ma->conf->min_mq) continue; else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) continue; return ret; }; return ret; } // Called once per new bam added to the pileup. // We cache sample information here so we don't have to keep recomputing this // on each and every pileup column. If FMT/SCR annotation is requested, a flag // is set to indicate the presence of a soft clip. static int pileup_constructor(void *data, const bam1_t *b, bam_pileup_cd *cd) { cd->p = calloc(1,sizeof(plp_cd_t)); PLP_NM(cd) = PLP_NM_UNSET; mplp_aux_t *ma = (mplp_aux_t *)data; int n = bam_smpl_get_sample_id(ma->conf->bsmpl, ma->bam_id, (bam1_t *)b); PLP_SET_SAMPLE_ID(cd, n); // Whether read has a soft-clip is used in mplp_realn's heuristics. // TODO: consider whether clip length is beneficial to use? int i; for (i=0; icore.n_cigar; i++) { int cig = bam_get_cigar(b)[i] & BAM_CIGAR_MASK; if (cig == BAM_CSOFT_CLIP) { PLP_SET_SOFT_CLIP(cd); break; } } if (ma->conf->flag & MPLP_REALN) { int i; // int tot_ins = 0; // int p = 0; uint32_t *cigar = bam_get_cigar(b); for (i=0; icore.n_cigar; i++) { int cig = cigar[i] & BAM_CIGAR_MASK; // if (bam_cigar_type(cig) & 2) // p += cigar[i] >> BAM_CIGAR_SHIFT; if (cig == BAM_CINS || cig == BAM_CDEL || cig == BAM_CREF_SKIP) { // tot_ins += cigar[i] >> BAM_CIGAR_SHIFT; // Possible further optimsation, check tot_ins==1 later // (and remove break) so we can detect single bp indels. // We may want to focus BAQ on more complex regions only. PLP_SET_INDEL(cd); break; } // TODO: proper p->cd struct and have cd->i as a size rather // than a flag. // Then aggregate together the sizes and if just 1 size for all // reads or 2 sizes for approx 50/50 split in all reads, then // treat this as a well-aligned variant and don't run BAQ. } } return 0; } static int pileup_destructor(void *data, const bam1_t *b, bam_pileup_cd *cd) { free(cd->p); return 0; } static void group_smpl(mplp_pileup_t *m, bam_smpl_t *bsmpl, int n, int *n_plp, const bam_pileup1_t **plp) { int i, j; memset(m->n_plp, 0, m->n * sizeof(int)); for (i = 0; i < n; ++i) // iterate over all bams { for (j = 0; j < n_plp[i]; ++j) // iterate over all reads available at this position { const bam_pileup1_t *p = plp[i] + j; int id = PLP_SAMPLE_ID(&(p->cd)); if (m->n_plp[id] == m->m_plp[id]) { m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8; m->plp[id] = (bam_pileup1_t*) realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]); } m->plp[id][m->n_plp[id]++] = *p; } } } static void flush_bcf_records(mplp_conf_t *conf, htsFile *fp, bcf_hdr_t *hdr, bcf1_t *rec) { if ( !conf->gvcf ) { if ( rec && bcf_write1(fp, hdr, rec)!=0 ) error("[%s] Error: failed to write the record to %s\n", __func__,conf->output_fname?conf->output_fname:"standard output"); return; } if ( !rec ) { gvcf_write(conf->gvcf, fp, hdr, NULL, 0); return; } int is_ref = 0; if ( rec->n_allele==1 ) is_ref = 1; else if ( rec->n_allele==2 ) { // second allele is mpileup's X, not a variant if ( rec->d.allele[1][0]=='<' && rec->d.allele[1][1]=='*' && rec->d.allele[1][2]=='>' ) is_ref = 1; } rec = gvcf_write(conf->gvcf, fp, hdr, rec, is_ref); if ( rec && bcf_write1(fp,hdr,rec)!=0 ) error("[%s] Error: failed to write the record to %s\n", __func__,conf->output_fname?conf->output_fname:"standard output"); } /* * Loops for an indel at this position. * * Only reads that overlap an indel loci get realigned. This considerably * reduces the cost of running BAQ while keeping the main benefits. * * TODO: also consider only realigning reads that don't span the indel * by more than a certain amount either-side. Ie focus BAQ only on reads * ending adjacent to the indel, where the alignment is most likely to * be wrong. (2nd TODO: do this based on sequence context; STRs bad, unique * data good.) * * NB: this may sadly realign after we've already used the data. Hmm... */ static void mplp_realn(int n, int *n_plp, const bam_pileup1_t **plp, int flag, int max_read_len, char *ref, int ref_len, int pos) { int i, j, has_indel = 0, has_clip = 0, nt = 0; int min_indel = INT_MAX, max_indel = INT_MIN; // Is an indel present. // NB: don't bother even checking if very long as almost guaranteed // to have indel (and likely soft-clips too). for (i = 0; i < n; i++) { // iterate over bams nt += n_plp[i]; for (j = 0; j < n_plp[i]; j++) { // iterate over reads bam_pileup1_t *p = (bam_pileup1_t *)plp[i] + j; has_indel += (PLP_HAS_INDEL(&p->cd) || p->indel) ? 1 : 0; // Has_clip is almost always true for very long reads // (eg PacBio CCS), but these rarely matter as the clip // is likely a long way from this indel. has_clip += (PLP_HAS_SOFT_CLIP(&p->cd)) ? 1 : 0; if (max_indel < p->indel) max_indel = p->indel; if (min_indel > p->indel) min_indel = p->indel; } } if (flag & MPLP_REALN_PARTIAL) { if (has_indel == 0 || (has_clip < 0.2*nt && max_indel == min_indel && (has_indel < 0.1*nt /*|| has_indel > 0.9*nt*/ || has_indel == 1))) return; } // Realign for (i = 0; i < n; i++) { // iterate over bams for (j = 0; j < n_plp[i]; j++) { // iterate over reads const bam_pileup1_t *p = plp[i] + j; bam1_t *b = p->b; // Avoid doing multiple times. // // Note we cannot modify p->cd.i here with a PLP_SET macro // because the cd item is held by mpileup in an lbnode_t // struct and copied over to the pileup struct for each // iteration, essentially making p->cd.i read only. // // We could use our own structure (p->cd.p), allocated during // the constructor, but for simplicity we play dirty and // abuse an unused flag bit instead. if ( PLP_IS_REALN(&(p->cd)) ) continue; PLP_SET_REALN(&(p->cd)); if (b->core.l_qseq > max_read_len) continue; // Check p->cigar_ind and see what cigar elements are before // and after. How close is this location to the end of the // read? Only realign if we don't span by more than X bases. // // Again, best only done on deeper data as BAQ helps // disproportionately more on shallow data sets. // // This rescues some of the false negatives that are caused by // systematic reduction in quality due to sample vs ref alignment. // At deep coverage we skip realigning more reads as we have sufficient depth. // This rescues for false negatives. At shallow depth we pay for this with // more FP so are more stringent on spanning size. #define REALN_DIST (40+10*(nt<40)+10*(nt<20)) uint32_t *cig = bam_get_cigar(b); int ncig = b->core.n_cigar; // Don't realign reads where indel is in middle? // On long read data we don't care about soft-clips at the ends. // For short read data, we always calc BAQ on these as they're // a common source of false positives. if ((flag & MPLP_REALN_PARTIAL) && nt > 15 && ncig > 1) { // Left & right cigar op match. int lr = b->core.l_qseq > 500; int lm = 0, rm = 0, k, nm = 0; for (k = 0; k < ncig; k++) { int cop = bam_cigar_op(cig[k]); if (lr && (cop == BAM_CHARD_CLIP || cop == BAM_CSOFT_CLIP)) continue; if (cop == BAM_CMATCH || cop == BAM_CDIFF || cop == BAM_CEQUAL) { lm += bam_cigar_oplen(cig[k]); nm++; } else { break; } } // if everything is a match (or sequence (mis)match) then move on // because we don't have an indel in the middle if (nm != ncig) { for (k = ncig-1; k >= 0; k--) { int cop = bam_cigar_op(cig[k]); if (lr && (cop == BAM_CHARD_CLIP || cop == BAM_CSOFT_CLIP)) continue; if (cop == BAM_CMATCH || cop == BAM_CDIFF || cop == BAM_CEQUAL) rm += bam_cigar_oplen(cig[k]); else break; } if (lm >= REALN_DIST*4 && rm >= REALN_DIST*4) continue; if (lm >= REALN_DIST && rm >= REALN_DIST && has_clip < (0.15+0.05*(nt>20))*nt) continue; } } if (b->core.l_qseq > 500) { // don't do BAQ on long-read data if it's going to // cause us to have a large band-with and costly in CPU int rl = bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(b)); if (abs(rl - b->core.l_qseq) * b->core.l_qseq >= 500000) continue; } // Fudge: make room for ZQ tag. uint8_t *_Q = bam_aux_get(b, "_Q"); if (_Q) bam_aux_del(b, _Q); sam_prob_realn(b, ref, ref_len, (flag & MPLP_REDO_BAQ) ? 7 : 3); } } return; } static int mpileup_reg(mplp_conf_t *conf, uint32_t beg, uint32_t end) { bam_hdr_t *hdr = conf->mplp_data[0]->h; // header of first file in input list int ret, i, tid, pos, ref_len; char *ref; while ( (ret=bam_mplp_auto(conf->iter, &tid, &pos, conf->n_plp, conf->plp)) > 0) { if ( posend ) continue; if ( conf->bed && tid >= 0 ) { int overlap = regidx_overlap(conf->bed, hdr->target_name[tid], pos, pos, NULL); if ( !conf->bed_logic ) overlap = overlap ? 0 : 1; if ( !overlap ) continue; } int has_ref = mplp_get_ref(conf->mplp_data[0], tid, &ref, &ref_len); if (has_ref && (conf->flag & MPLP_REALN)) mplp_realn(conf->nfiles, conf->n_plp, conf->plp, conf->flag, conf->max_read_len, ref, ref_len, pos); int total_depth, _ref0, ref16; for (i = total_depth = 0; i < conf->nfiles; ++i) total_depth += conf->n_plp[i]; group_smpl(conf->gplp, conf->bsmpl, conf->nfiles, conf->n_plp, conf->plp); _ref0 = (ref && pos < ref_len)? ref[pos] : 'N'; ref16 = seq_nt16_table[_ref0]; bcf_callaux_clean(conf->bca, &conf->bc); for (i = 0; i < conf->gplp->n; ++i) bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], ref16, conf->bca, conf->bcr + i); conf->bc.tid = tid; conf->bc.pos = pos; bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, ref16, &conf->bc); bcf_clear1(conf->bcf_rec); bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, conf->bca, 0); flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec); // call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring? // check me: rghash in bcf_call_gap_prep() should have no effect, reads mplp_func already excludes them if (!(conf->flag&MPLP_NO_INDEL) && total_depth < conf->max_indel_depth) { bcf_callaux_clean(conf->bca, &conf->bc); conf->bca->chr = tid>=0 ? hdr->target_name[tid] : NULL; int iret; if (conf->edlib) iret = bcf_edlib_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref, ref_len); else if ( conf->indels_v20 ) iret = bcf_iaux_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref); else iret = bcf_call_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref); if ( iret>=0 ) { for (i = 0; i < conf->gplp->n; ++i) bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], -1, conf->bca, conf->bcr + i); if (bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, -1, &conf->bc) >= 0) { bcf_clear1(conf->bcf_rec); bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, conf->bca, ref); flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec); } } } } return ret; } static int mpileup(mplp_conf_t *conf) { if (conf->nfiles == 0) { fprintf(bcftools_stderr,"[%s] no input file/data given\n", __func__); bcftools_exit(EXIT_FAILURE); } mplp_ref_t mp_ref = MPLP_REF_INIT; conf->gplp = (mplp_pileup_t *) calloc(1,sizeof(mplp_pileup_t)); conf->mplp_data = (mplp_aux_t**) calloc(conf->nfiles, sizeof(mplp_aux_t*)); conf->plp = (const bam_pileup1_t**) calloc(conf->nfiles, sizeof(bam_pileup1_t*)); conf->n_plp = (int*) calloc(conf->nfiles, sizeof(int)); // Allow to run mpileup on multiple regions in one go. This comes at cost: the bai index // must be kept in the memory for the whole time which can be a problem with many bams. // Therefore if none or only one region is requested, we initialize the bam iterator as // before and free the index. Only when multiple regions are queried, we keep the index. int nregs = 0; if ( conf->reg_fname ) { if ( conf->reg_is_file ) { conf->reg = regidx_init(conf->reg_fname,NULL,NULL,0,NULL); if ( !conf->reg ) { fprintf(bcftools_stderr,"Could not parse the regions: %s\n", conf->reg_fname); bcftools_exit(EXIT_FAILURE); } } else { conf->reg = regidx_init(NULL,regidx_parse_reg,NULL,sizeof(char*),NULL); if ( regidx_insert_list(conf->reg,conf->reg_fname,',') !=0 ) { fprintf(bcftools_stderr,"Could not parse the regions: %s\n", conf->reg_fname); bcftools_exit(EXIT_FAILURE); } } nregs = regidx_nregs(conf->reg); if ( nregs ) { // the regions list can be empty, see #2250 conf->reg_itr = regitr_init(conf->reg); regitr_loop(conf->reg_itr); // region iterator now positioned at the first region } } // read the header of each file in the list and initialize data // beware: mpileup has always assumed that tid's are consistent in the headers, add sanity check at least! bam_hdr_t *hdr = NULL; // header of first file in input list int i; for (i = 0; i < conf->nfiles; ++i) { bam_hdr_t *h_tmp; conf->mplp_data[i] = (mplp_aux_t*) calloc(1, sizeof(mplp_aux_t)); conf->mplp_data[i]->fp = sam_open(conf->files[i], "rb"); if ( !conf->mplp_data[i]->fp ) { fprintf(bcftools_stderr, "[%s] failed to open %s: %s\n", __func__, conf->files[i], strerror(errno)); bcftools_exit(EXIT_FAILURE); } if (hts_set_opt(conf->mplp_data[i]->fp, CRAM_OPT_DECODE_MD, 1)) { fprintf(bcftools_stderr, "Failed to set CRAM_OPT_DECODE_MD value\n"); bcftools_exit(EXIT_FAILURE); } if (conf->fai_fname && hts_set_fai_filename(conf->mplp_data[i]->fp, conf->fai_fname) != 0) { fprintf(bcftools_stderr, "[%s] failed to process %s: %s\n", __func__, conf->fai_fname, strerror(errno)); bcftools_exit(EXIT_FAILURE); } conf->mplp_data[i]->conf = conf; conf->mplp_data[i]->ref = &mp_ref; h_tmp = sam_hdr_read(conf->mplp_data[i]->fp); if ( !h_tmp ) { fprintf(bcftools_stderr,"[%s] fail to read the header of %s\n", __func__, conf->files[i]); bcftools_exit(EXIT_FAILURE); } conf->mplp_data[i]->h = i ? hdr : h_tmp; // for j==0, "h" has not been set yet conf->mplp_data[i]->bam_id = bam_smpl_add_bam(conf->bsmpl,h_tmp->text,conf->files[i]); if ( conf->mplp_data[i]->bam_id<0 ) { // no usable readgroups in this bam, it can be skipped sam_close(conf->mplp_data[i]->fp); free(conf->mplp_data[i]); bam_hdr_destroy(h_tmp); free(conf->files[i]); if ( i+1nfiles ) memmove(&conf->files[i],&conf->files[i+1],sizeof(*conf->files)*(conf->nfiles-i-1)); conf->nfiles--; i--; continue; } if (conf->reg && nregs) { hts_idx_t *idx = sam_index_load(conf->mplp_data[i]->fp, conf->files[i]); if (idx == NULL) { fprintf(bcftools_stderr, "[%s] fail to load index for %s\n", __func__, conf->files[i]); bcftools_exit(EXIT_FAILURE); } conf->buf.l = 0; ksprintf(&conf->buf,"%s:%u-%u",conf->reg_itr->seq,conf->reg_itr->beg+1,conf->reg_itr->end+1); conf->mplp_data[i]->iter = sam_itr_querys(idx, conf->mplp_data[i]->h, conf->buf.s); if ( !conf->mplp_data[i]->iter ) { conf->mplp_data[i]->iter = sam_itr_querys(idx, conf->mplp_data[i]->h, conf->reg_itr->seq); if ( conf->mplp_data[i]->iter ) { fprintf(bcftools_stderr,"[E::%s] fail to parse region '%s'\n", __func__, conf->buf.s); bcftools_exit(EXIT_FAILURE); } fprintf(bcftools_stderr,"[E::%s] the sequence \"%s\" not found: %s\n",__func__,conf->reg_itr->seq,conf->files[i]); bcftools_exit(EXIT_FAILURE); } if ( nregs==1 ) // no need to keep the index in memory hts_idx_destroy(idx); else conf->mplp_data[i]->idx = idx; } if ( !hdr ) hdr = h_tmp; /* save the header of first file in list */ else { // FIXME: check consistency between h and h_tmp bam_hdr_destroy(h_tmp); // we store only the first file's header; it's (alleged to be) // compatible with the i-th file's target_name lookup needs conf->mplp_data[i]->h = hdr; } } if ( !hdr ) { fprintf(bcftools_stderr, "[%s] failed to find a file header with usable read groups\n", __func__); bcftools_exit(EXIT_FAILURE); } // allocate data storage proportionate to number of samples being studied sm->n bam_smpl_get_samples(conf->bsmpl, &conf->gplp->n); conf->gplp->n_plp = (int*) calloc(conf->gplp->n, sizeof(int)); conf->gplp->m_plp = (int*) calloc(conf->gplp->n, sizeof(int)); conf->gplp->plp = (bam_pileup1_t**) calloc(conf->gplp->n, sizeof(bam_pileup1_t*)); fprintf(bcftools_stderr, "[%s] %d samples in %d input files\n", __func__, conf->gplp->n, conf->nfiles); // write the VCF header char wmode[8]; set_wmode(wmode,conf->output_type,conf->output_fname,conf->clevel); conf->bcf_fp = hts_open(conf->output_fname ? conf->output_fname : "-", wmode); if (conf->bcf_fp == NULL) { fprintf(bcftools_stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname? conf->output_fname : "standard output", strerror(errno)); bcftools_exit(EXIT_FAILURE); } if ( conf->n_threads ) hts_set_threads(conf->bcf_fp, conf->n_threads); // BCF header creation conf->bcf_hdr = bcf_hdr_init("w"); conf->buf.l = 0; if (conf->record_cmd_line) { ksprintf(&conf->buf, "##bcftoolsVersion=%s+htslib-%s\n",bcftools_version(),hts_version()); bcf_hdr_append(conf->bcf_hdr, conf->buf.s); conf->buf.l = 0; ksprintf(&conf->buf, "##bcftoolsCommand=mpileup"); for (i=1; iargc; i++) ksprintf(&conf->buf, " %s", conf->argv[i]); kputc('\n', &conf->buf); bcf_hdr_append(conf->bcf_hdr, conf->buf.s); } if (conf->fai_fname) { conf->buf.l = 0; ksprintf(&conf->buf, "##reference=file://%s\n", conf->fai_fname); bcf_hdr_append(conf->bcf_hdr, conf->buf.s); } // Translate BAM @SQ tags to BCF ##contig tags // todo: use/write new BAM header manipulation routines, fill also UR, M5 for (i=0; in_targets; i++) { conf->buf.l = 0; ksprintf(&conf->buf, "##contig=", hdr->target_name[i], hdr->target_len[i]); bcf_hdr_append(conf->bcf_hdr, conf->buf.s); } conf->buf.l = 0; bcf_hdr_append(conf->bcf_hdr,"##ALT="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_IDV ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_IMF ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_VDB ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_RPBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_MQBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_BQBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_MQSBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_MIN_PL_SUM ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_NM ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_NMBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_FMT_NMBZ ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_INFO_SCBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_FS ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_SGB ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_MQ0F ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_FMT_DP ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_FMT_DV ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_FMT_DPR ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_INFO_DPR ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_FMT_DP4 ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_FMT_SP ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_FMT_AD ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_FMT_ADF ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_FMT_ADR ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_FMT_QS ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_INFO_AD ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_ADF ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_SCR ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_FMT_SCR ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_INFO_ADR ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->gvcf ) gvcf_update_header(conf->gvcf, conf->bcf_hdr); int nsmpl; const char **smpl = bam_smpl_get_samples(conf->bsmpl, &nsmpl); for (i=0; ibcf_hdr, smpl[i]); if ( bcf_hdr_write(conf->bcf_fp, conf->bcf_hdr)!=0 ) error("[%s] Error: failed to write the header to %s\n",__func__,conf->output_fname?conf->output_fname:"standard output"); if ( init_index2(conf->bcf_fp,conf->bcf_hdr,conf->output_fname, &conf->index_fn, conf->write_index) < 0 ) error("Error: failed to initialise index for %s\n",conf->output_fname); conf->bca = bcf_call_init(-1., conf->min_baseQ, conf->max_baseQ, conf->delta_baseQ); conf->bcr = (bcf_callret1_t*) calloc(nsmpl, sizeof(bcf_callret1_t)); conf->bca->openQ = conf->openQ, conf->bca->extQ = conf->extQ, conf->bca->tandemQ = conf->tandemQ; conf->bca->indel_bias = conf->indel_bias; conf->bca->del_bias = conf->del_bias; conf->bca->min_frac = conf->min_frac; conf->bca->min_support = conf->min_support; conf->bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE; conf->bca->fmt_flag = conf->fmt_flag; conf->bca->ambig_reads = conf->ambig_reads; conf->bca->indel_win_size = conf->indel_win_size; conf->bca->indels_v20 = conf->indels_v20; conf->bca->edlib = conf->edlib; conf->bca->seqQ_offset = conf->seqQ_offset; conf->bca->poly_mqual = conf->poly_mqual; conf->bca->vs_ref = conf->vs_ref; conf->bc.bcf_hdr = conf->bcf_hdr; conf->bc.n = nsmpl; conf->bc.PL = (int32_t*) malloc(15 * nsmpl * sizeof(*conf->bc.PL)); conf->bc.QS = (int32_t*) malloc(nsmpl*sizeof(*conf->bc.QS)*B2B_MAX_ALLELES); for (i=0; ibcr[i].QS = conf->bc.QS + i*B2B_MAX_ALLELES; if (conf->fmt_flag) { assert( sizeof(float)==sizeof(int32_t) ); conf->bc.DP4 = (int32_t*) malloc(nsmpl * sizeof(int32_t) * 4); conf->bc.fmt_arr = (uint8_t*) malloc(nsmpl * sizeof(float)); // all fmt_flag fields, float and int32 if ( conf->fmt_flag&(B2B_INFO_DPR|B2B_FMT_DPR|B2B_INFO_AD|B2B_INFO_ADF|B2B_INFO_ADR|B2B_FMT_AD|B2B_FMT_ADF|B2B_FMT_ADR) ) { // first B2B_MAX_ALLELES fields for total numbers, the rest per-sample conf->bc.ADR = (int32_t*) malloc((nsmpl+1)*B2B_MAX_ALLELES*sizeof(int32_t)); conf->bc.ADF = (int32_t*) malloc((nsmpl+1)*B2B_MAX_ALLELES*sizeof(int32_t)); for (i=0; ibcr[i].ADR = conf->bc.ADR + (i+1)*B2B_MAX_ALLELES; conf->bcr[i].ADF = conf->bc.ADF + (i+1)*B2B_MAX_ALLELES; } } if ( conf->fmt_flag&(B2B_INFO_SCR|B2B_FMT_SCR) ) conf->bc.SCR = (int32_t*) malloc((nsmpl+1)*sizeof(*conf->bc.SCR)); } int nnmbz = (conf->fmt_flag&B2B_FMT_NMBZ) ? nsmpl + 1 : 1; conf->bc.ref_nm = (int32_t*) malloc(sizeof(*conf->bc.ref_nm) * nnmbz * B2B_N_NM); conf->bc.alt_nm = (int32_t*) malloc(sizeof(*conf->bc.alt_nm) * nnmbz * B2B_N_NM); conf->bc.mwu_nm = (float*) malloc((nsmpl+1)*sizeof(*conf->bc.mwu_nm)); conf->bca->ref_nm = conf->bc.ref_nm; // this is just to make the arrays available in bcf_call_glfgen() conf->bca->alt_nm = conf->bc.alt_nm; if ( conf->fmt_flag&B2B_FMT_NMBZ ) { for (i=0; ibcr[i].ref_nm = conf->bc.ref_nm + (i+1)*B2B_N_NM; for (i=0; ibcr[i].alt_nm = conf->bc.alt_nm + (i+1)*B2B_N_NM; } // init mpileup conf->iter = bam_mplp_init(conf->nfiles, mplp_func, (void**)conf->mplp_data); if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(conf->iter); fprintf(bcftools_stderr, "[%s] maximum number of reads per input file set to -d %d\n", __func__, conf->max_depth); if ( (double)conf->max_depth * conf->nfiles > 1<<20) fprintf(bcftools_stderr, "Warning: Potential memory hog, up to %.0fM reads in the pileup!\n", (double)conf->max_depth*conf->nfiles); if ( (double)conf->max_depth * conf->nfiles / nsmpl < 250 ) fprintf(bcftools_stderr, "Note: The maximum per-sample depth with -d %d is %.1fx\n", conf->max_depth,(double)conf->max_depth * conf->nfiles / nsmpl); bam_mplp_set_maxcnt(conf->iter, conf->max_depth); conf->max_indel_depth = conf->max_indel_depth * nsmpl; conf->bcf_rec = bcf_init1(); bam_mplp_constructor(conf->iter, pileup_constructor); bam_mplp_destructor(conf->iter, pileup_destructor); // Run mpileup for multiple regions int ret = 0; if ( nregs ) { int ireg = 0; do { // first region is already positioned if ( ireg++ > 0 ) { conf->buf.l = 0; ksprintf(&conf->buf,"%s:%u-%u",conf->reg_itr->seq,conf->reg_itr->beg+1,conf->reg_itr->end+1); for (i=0; infiles; i++) { hts_itr_destroy(conf->mplp_data[i]->iter); conf->mplp_data[i]->iter = sam_itr_querys(conf->mplp_data[i]->idx, conf->mplp_data[i]->h, conf->buf.s); if ( !conf->mplp_data[i]->iter ) { conf->mplp_data[i]->iter = sam_itr_querys(conf->mplp_data[i]->idx, conf->mplp_data[i]->h, conf->reg_itr->seq); if ( conf->mplp_data[i]->iter ) { fprintf(bcftools_stderr,"[E::%s] fail to parse region '%s'\n", __func__, conf->buf.s); bcftools_exit(EXIT_FAILURE); } fprintf(bcftools_stderr,"[E::%s] the sequence \"%s\" not found: %s\n",__func__,conf->reg_itr->seq,conf->files[i]); bcftools_exit(EXIT_FAILURE); } bam_mplp_reset(conf->iter); } } ret = mpileup_reg(conf,conf->reg_itr->beg,conf->reg_itr->end); if ( ret<0 ) break; } while ( regitr_loop(conf->reg_itr) ); } else if ( !conf->reg ) ret = mpileup_reg(conf,0,UINT32_MAX); if ( ret<0 ) { fprintf(bcftools_stderr, "[%s] failed to read from input file\n", __func__); bcftools_exit(EXIT_FAILURE); } flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, NULL); // clean up free(conf->bc.tmp.s); bcf_destroy1(conf->bcf_rec); if (conf->bcf_fp) { if ( conf->write_index ) { if ( bcf_idx_save(conf->bcf_fp)<0 ) { if ( hts_close(conf->bcf_fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,conf->output_fname); error("Error: cannot write to index %s\n",conf->index_fn); } free(conf->index_fn); } if ( hts_close(conf->bcf_fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,conf->output_fname); bcf_hdr_destroy(conf->bcf_hdr); bcf_call_destroy(conf->bca); free(conf->bc.PL); free(conf->bc.DP4); free(conf->bc.ADR); free(conf->bc.ADF); free(conf->bc.SCR); free(conf->bc.QS); free(conf->bc.ref_nm); free(conf->bc.alt_nm); free(conf->bc.fmt_arr); free(conf->bc.mwu_nm); free(conf->bcr); } if ( conf->gvcf ) gvcf_destroy(conf->gvcf); free(conf->buf.s); for (i = 0; i < conf->gplp->n; ++i) free(conf->gplp->plp[i]); free(conf->gplp->plp); free(conf->gplp->n_plp); free(conf->gplp->m_plp); free(conf->gplp); bam_mplp_destroy(conf->iter); bam_hdr_destroy(hdr); for (i = 0; i < conf->nfiles; ++i) { if ( nregs>1 ) hts_idx_destroy(conf->mplp_data[i]->idx); sam_close(conf->mplp_data[i]->fp); if ( conf->mplp_data[i]->iter) hts_itr_destroy(conf->mplp_data[i]->iter); free(conf->mplp_data[i]); } if ( conf->reg_itr ) regitr_destroy(conf->reg_itr); free(conf->mplp_data); free(conf->plp); free(conf->n_plp); free(mp_ref.ref[0]); free(mp_ref.ref[1]); return 0; } static int is_url(const char *s) { static const char uri_scheme_chars[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+.-"; return s[strspn(s, uri_scheme_chars)] == ':'; } #define MAX_PATH_LEN 1024 int read_file_list(const char *file_list,int *n,char **argv[]) { char buf[MAX_PATH_LEN]; int len, nfiles = 0; char **files = NULL; struct stat sb; *n = 0; *argv = NULL; FILE *fh = fopen(file_list,"r"); if ( !fh ) { fprintf(bcftools_stderr,"%s: %s\n", file_list,strerror(errno)); return 1; } files = (char**) calloc(nfiles,sizeof(char*)); nfiles = 0; while ( fgets(buf,MAX_PATH_LEN,fh) ) { // allow empty lines and trailing spaces len = strlen(buf); while ( len>0 && isspace(buf[len-1]) ) len--; if ( !len ) continue; // check sanity of the file list buf[len] = 0; if (! (is_url(buf) || stat(buf, &sb) == 0)) { // no such file, check if it is safe to print its name int i, safe_to_print = 1; for (i=0; irflag_skip_all_set); char *tmp_skip_any_unset = bam_flag2str(mplp->rflag_skip_any_unset); char *tmp_skip_all_unset = bam_flag2str(mplp->rflag_skip_all_unset); char *tmp_skip_any_set = bam_flag2str(mplp->rflag_skip_any_set); // Display usage information, formatted for the standard 80 columns. // (The unusual string formatting here aids the readability of this // source code in 80 columns, to the extent that's possible.) fprintf(fp, "\n" "Usage: bcftools mpileup [options] in1.bam [in2.bam [...]]\n" "\n" "Input options:\n" " -6, --illumina1.3+ Quality is in the Illumina-1.3+ encoding\n" " -A, --count-orphans Include anomalous read pairs, with flag PAIRED but not PROPER_PAIR set\n" " -b, --bam-list FILE List of input BAM filenames, one per line\n" " -B, --no-BAQ Disable BAQ (per-Base Alignment Quality)\n" " -C, --adjust-MQ INT Adjust mapping quality [0]\n" " -D, --full-BAQ Apply BAQ everywhere, not just in problematic regions\n" " -d, --max-depth INT Max raw per-file depth; avoids excessive memory usage [%d]\n", mplp->max_depth); fprintf(fp, " -E, --redo-BAQ Recalculate BAQ on the fly, ignore existing BQs\n" " -f, --fasta-ref FILE Faidx indexed reference sequence file\n" " --no-reference Do not require fasta reference file\n" " -G, --read-groups FILE Select or exclude read groups listed in the file\n" " -q, --min-MQ INT Skip alignments with mapQ smaller than INT [%d]\n", mplp->min_mq); fprintf(fp, " -Q, --min-BQ INT Skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ); fprintf(fp, " --max-BQ INT Limit baseQ/BAQ to no more than INT [%d]\n", mplp->max_baseQ); fprintf(fp, " --delta-BQ INT Use neighbour_qual + INT if less than qual [%d]\n", mplp->delta_baseQ); fprintf(fp, " -r, --regions REG[,...] Comma separated list of regions in which pileup is generated\n" " -R, --regions-file FILE Restrict to regions listed in a file\n" " --ignore-RG Ignore RG tags (one BAM = one sample)\n" " --ls, --skip-all-set STR|INT Skip reads with all of the bits set []\n"); fprintf(fp, " --ns, --skip-any-set STR|INT Skip reads with any of the bits set [%s]\n", tmp_skip_any_set); fprintf(fp, " --lu, --skip-all-unset STR|INT Skip reads with all of the bits unset []\n" " --nu, --skip-any-unset STR|INT Skip reads with any of the bits unset []\n"); fprintf(fp, " -s, --samples LIST Comma separated list of samples to include\n" " -S, --samples-file FILE File of samples to include\n" " -t, --targets REG[,...] Similar to -r but streams rather than index-jumps\n" " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n" " -x, --ignore-overlaps Disable read-pair overlap detection\n" " --seed INT Random number seed used for sampling deep regions [0]\n" "\n" "Output options:\n" " -a, --annotate LIST Optional tags to output; '\\?' to list available tags []\n" " -g, --gvcf INT[,...] Group non-variant sites into gVCF blocks according\n" " To minimum per-sample DP\n" " --no-version Do not append version and command line to the header\n" " -o, --output FILE Write output to FILE [standard output]\n" " -O, --output-type TYPE 'b' compressed BCF; 'u' uncompressed BCF;\n" " 'z' compressed VCF; 'v' uncompressed VCF; 0-9 compression level [v]\n" " --threads INT Use multithreading with INT worker threads [0]\n" " -W, --write-index[=FMT] Automatically index the output files [off]\n" "\n" "SNP/INDEL genotype likelihoods options:\n" " -X, --config STR Specify platform profile (use \"-X list\" for details)\n" " -e, --ext-prob INT Phred-scaled gap extension seq error probability [%d]\n", mplp->extQ); fprintf(fp, " -F, --gap-frac FLOAT Minimum fraction of gapped reads [%g]\n", mplp->min_frac); fprintf(fp, " -h, --tandem-qual INT Coefficient for homopolymer errors [%d]\n", mplp->tandemQ); fprintf(fp, " -I, --skip-indels Do not perform indel calling\n" " -L, --max-idepth INT Maximum per-file depth for INDEL calling [%d]\n", mplp->max_indel_depth); fprintf(fp, " -m, --min-ireads INT Minimum number gapped reads for indel candidates [%d]\n", mplp->min_support); fprintf(fp, " -M, --max-read-len INT Maximum length of read to pass to BAQ algorithm [%d]\n", mplp->max_read_len); fprintf(fp, " -o, --open-prob INT Phred-scaled gap open seq error probability [%d]\n", mplp->openQ); fprintf(fp, " -p, --per-sample-mF Apply -m and -F per-sample for increased sensitivity\n" " -P, --platforms STR Comma separated list of platforms for indels [all]\n" " --ar, --ambig-reads STR What to do with ambiguous indel reads: drop,incAD,incAD0 [drop]\n"); fprintf(fp, " --indel-bias FLOAT Raise to favour recall over precision [%.2f]\n", mplp->indel_bias); fprintf(fp, " --del-bias FLOAT Relative likelihood of insertion to deletion [%.2f]\n", mplp->del_bias); fprintf(fp, " --score-vs-ref FLOAT\n" " Ratio of score vs ref (1) or 2nd-best allele (0) [%.2f]\n", mplp->vs_ref); fprintf(fp, " --indel-size INT Approximate maximum indel size considered [%d]\n", mplp->indel_win_size); fprintf(fp, " --indels-2.0 New EXPERIMENTAL indel calling model (diploid reference consensus)\n" " --indels-cns New EXPERIMENTAL indel calling model with edlib\n" " --seqq-offset Indel-cns tuning for indel seq-qual scores [120]\n" " --no-indels-cns Disable CNS mode, to use after a -X profile\n" " --poly-mqual (Edlib mode) Use minimum quality within homopolymers\n"); fprintf(fp,"\n"); fprintf(fp, "Notes: Assuming diploid individuals.\n\n" "Example:\n" " # See also http://samtools.github.io/bcftools/howtos/variant-calling.html\n" " bcftools mpileup -Ou -f reference.fa alignments.bam | bcftools call -mv -Ob -o calls.bcf\n" "\n"); free(tmp_skip_all_set); free(tmp_skip_any_unset); free(tmp_skip_all_unset); free(tmp_skip_any_set); } static void print_profiles(void) { fprintf(bcftools_stdout, "Configuration profiles activated with -X, --config:\n\n" "1.12\n" " -Q13 -h100 -m1 -F0.002\n\n" "bgi, bgi-1.20\n" " --indels-cns -B --indel-size 80 -F0.1 --indel-bias 0.9 --seqq-offset 120\n\n" "illumina-1.18\n" " --indel-size 110\n\n" "illumina\n" "illumina-1.20\n" " --indels-cns --indel-size 110\n\n" "ont\n" " -B -Q5 --max-BQ 30 -I\n\n" "ont-sup, ont-sup-1.20\n" " --indels-cns -B -Q1 --max-BQ 35 -F0.2 -o15 -e1 -h110 --delta-BQ 99\\\n" " --del-bias 0.4 --indel-bias 0.7 --poly-mqual --seqq-offset 130\\\n" " --indel-size 80\n\n" "pacbio-ccs-1.18\n" " -D -Q5 --max-BQ 50 -F0.1 -o25 -e1 --delta-BQ 10 \\\n" " -M99999 --indel-size 110\n\n" "pacbio-ccs, pacbio-ccs-1.20\n" " --indels-cns -B -Q5 --max-BQ 50 -F0.1 -o25 -e1 -h300 --delta-BQ 10 \\\n" " --del-bias 0.4 --poly-mqual --indel-bias 0.9 --seqq-offset 118\\\n" " --indel-size 80 --score-vs-ref 0.7\n\n" "ultima, ultima-1.20\n" " --indels-cns -B -Q1 --max-BQ 30 -F0.15 -o20 -e10 -h250 --delta-BQ 10 \\\n" " --del-bias 0.3 --indel-bias 0.7 --poly-mqual --seqq-offset 140 \\\n" " --indel-size 80 --score-vs-ref 0.3\n\n" "\n"); } int main_mpileup(int argc, char *argv[]) { int c, i, ret = 1; const char *file_list = NULL; char **fn = NULL; int nfiles = 0, use_orphan = 0, noref = 0; mplp_conf_t mplp; memset(&mplp, 0, sizeof(mplp_conf_t)); mplp.min_baseQ = 1; mplp.max_baseQ = 60; mplp.delta_baseQ = 30; mplp.capQ_thres = 0; mplp.max_depth = 250; mplp.max_indel_depth = 250; mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 500; mplp.min_frac = 0.05; mplp.indel_bias = 1.0; mplp.min_support = 2; mplp.vs_ref = 0; mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN | MPLP_REALN_PARTIAL | MPLP_SMART_OVERLAPS; mplp.argc = argc; mplp.argv = argv; mplp.rflag_skip_any_set = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP; mplp.output_fname = NULL; mplp.output_type = FT_VCF; mplp.record_cmd_line = 1; mplp.n_threads = 0; mplp.bsmpl = bam_smpl_init(); // the default to be changed in future, see also parse_format_flag() mplp.fmt_flag = B2B_INFO_BQBZ|B2B_INFO_IDV|B2B_INFO_IMF|B2B_INFO_MQ0F|B2B_INFO_MQBZ|B2B_INFO_MQSBZ|B2B_INFO_RPBZ|B2B_INFO_SCBZ|B2B_INFO_SGB|B2B_INFO_VDB|B2B_FMT_AD; mplp.max_read_len = 500; mplp.ambig_reads = B2B_DROP; mplp.indel_win_size = 110; mplp.poly_mqual = 0; mplp.seqQ_offset = 120; mplp.clevel = -1; mplp.del_bias = 0; // even insertion and deletion likelhoods. hts_srand48(0); static const struct option lopts[] = { {"nu", required_argument, NULL, 16}, {"lu", required_argument, NULL, 17}, {"rf", required_argument, NULL, 17}, // old --rf, --incl-flags = --lu, --skip-all-unset {"ns", required_argument, NULL, 18}, {"ff", required_argument, NULL, 18}, // old --ff, --excl-flags = --ns, --skip-any-set {"ls", required_argument, NULL, 19}, {"skip-any-unset", required_argument, NULL, 16}, {"skip-all-unset", required_argument, NULL, 17}, {"skip-any-set", required_argument, NULL, 18}, {"skip-all-set", required_argument, NULL, 19}, {"output", required_argument, NULL, 3}, {"open-prob", required_argument, NULL, 4}, {"ignore-RG", no_argument, NULL, 5}, {"ignore-rg", no_argument, NULL, 5}, {"gvcf", required_argument, NULL, 'g'}, {"no-reference", no_argument, NULL, 7}, {"no-version", no_argument, NULL, 8}, {"threads",required_argument,NULL,9}, {"illumina1.3+", no_argument, NULL, '6'}, {"count-orphans", no_argument, NULL, 'A'}, {"bam-list", required_argument, NULL, 'b'}, {"no-BAQ", no_argument, NULL, 'B'}, {"no-baq", no_argument, NULL, 'B'}, {"full-BAQ", no_argument, NULL, 'D'}, {"full-baq", no_argument, NULL, 'D'}, {"adjust-MQ", required_argument, NULL, 'C'}, {"adjust-mq", required_argument, NULL, 'C'}, {"max-depth", required_argument, NULL, 'd'}, {"redo-BAQ", no_argument, NULL, 'E'}, {"redo-baq", no_argument, NULL, 'E'}, {"fasta-ref", required_argument, NULL, 'f'}, {"read-groups", required_argument, NULL, 'G'}, {"region", required_argument, NULL, 'r'}, {"regions", required_argument, NULL, 'r'}, {"regions-file", required_argument, NULL, 'R'}, {"targets", required_argument, NULL, 't'}, {"targets-file", required_argument, NULL, 'T'}, {"min-MQ", required_argument, NULL, 'q'}, {"min-mq", required_argument, NULL, 'q'}, {"min-BQ", required_argument, NULL, 'Q'}, {"min-bq", required_argument, NULL, 'Q'}, {"max-bq", required_argument, NULL, 11}, {"max-BQ", required_argument, NULL, 11}, {"delta-BQ", required_argument, NULL, 12}, {"ignore-overlaps", no_argument, NULL, 'x'}, {"output-type", required_argument, NULL, 'O'}, {"samples", required_argument, NULL, 's'}, {"samples-file", required_argument, NULL, 'S'}, {"annotate", required_argument, NULL, 'a'}, {"ext-prob", required_argument, NULL, 'e'}, {"gap-frac", required_argument, NULL, 'F'}, {"indel-bias", required_argument, NULL, 10}, {"indel-size", required_argument, NULL, 15}, {"indels-2.0", no_argument, NULL, 20}, {"indels-cns", no_argument, NULL, 22}, {"no-indels-cns", no_argument, NULL, 25}, {"tandem-qual", required_argument, NULL, 'h'}, {"skip-indels", no_argument, NULL, 'I'}, {"max-idepth", required_argument, NULL, 'L'}, {"min-ireads", required_argument, NULL, 'm'}, {"per-sample-mF", no_argument, NULL, 'p'}, {"per-sample-mf", no_argument, NULL, 'p'}, {"platforms", required_argument, NULL, 'P'}, {"max-read-len", required_argument, NULL, 'M'}, {"config", required_argument, NULL, 'X'}, {"seed", required_argument, NULL, 13}, {"ambig-reads", required_argument, NULL, 14}, {"ar", required_argument, NULL, 14}, {"write-index",optional_argument,NULL,'W'}, {"del-bias", required_argument, NULL, 23}, {"poly-mqual", no_argument, NULL, 24}, {"no-poly-mqual", no_argument, NULL, 26}, {"score-vs-ref",required_argument, NULL, 27}, {"seqq-offset", required_argument, NULL, 28}, {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "Ag:f:r:R:q:Q:C:BDd:L:b:P:po:e:h:Im:F:EG:6O:xa:s:S:t:T:M:X:UW::",lopts,NULL)) >= 0) { switch (c) { case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break; case 16 : mplp.rflag_skip_any_unset = bam_str2flag(optarg); if ( mplp.rflag_skip_any_unset <0 ) { fprintf(bcftools_stderr,"Could not parse --nf %s\n", optarg); goto err; } break; case 17 : mplp.rflag_skip_all_unset = bam_str2flag(optarg); if ( mplp.rflag_skip_all_unset<0 ) { fprintf(bcftools_stderr,"Could not parse --if %s\n", optarg); goto err; } break; case 18 : mplp.rflag_skip_any_set = bam_str2flag(optarg); if ( mplp.rflag_skip_any_set <0 ) { fprintf(bcftools_stderr,"Could not parse --ef %s\n", optarg); goto err; } break; case 19 : mplp.rflag_skip_all_set = bam_str2flag(optarg); if ( mplp.rflag_skip_all_set <0 ) { fprintf(bcftools_stderr,"Could not parse --df %s\n", optarg); goto err; } break; case 3 : mplp.output_fname = optarg; break; case 4 : mplp.openQ = atoi(optarg); break; case 5 : bam_smpl_ignore_readgroups(mplp.bsmpl); break; case 'g': mplp.gvcf = gvcf_init(optarg); if ( !mplp.gvcf ) error("Could not parse: --gvcf %s\n", optarg); break; case 'f': mplp.fai = fai_load(optarg); if (mplp.fai == NULL) goto err; mplp.fai_fname = optarg; break; case 7 : noref = 1; break; case 8 : mplp.record_cmd_line = 0; break; case 9 : mplp.n_threads = strtol(optarg, 0, 0); break; case 'd': mplp.max_depth = atoi(optarg); break; case 'r': mplp.reg_fname = strdup(optarg); break; case 'R': mplp.reg_fname = strdup(optarg); mplp.reg_is_file = 1; break; case 't': // In the original version the whole BAM was streamed which is inefficient // with few BED intervals and big BAMs. Todo: devise a heuristic to determine // best strategy, that is streaming or jumping. if ( optarg[0]=='^' ) optarg++; else mplp.bed_logic = 1; mplp.bed = regidx_init(NULL,regidx_parse_reg,NULL,0,NULL); mplp.bed_itr = regitr_init(mplp.bed); if ( regidx_insert_list(mplp.bed,optarg,',') !=0 ) { fprintf(bcftools_stderr,"Could not parse the targets: %s\n", optarg); bcftools_exit(EXIT_FAILURE); } break; case 'T': if ( optarg[0]=='^' ) optarg++; else mplp.bed_logic = 1; mplp.bed = regidx_init(optarg,NULL,NULL,0,NULL); if (!mplp.bed) { fprintf(bcftools_stderr, "bcftools mpileup: Could not read file \"%s\"", optarg); goto err; } break; case 'P': mplp.pl_list = strdup(optarg); break; case 'p': mplp.flag |= MPLP_PER_SAMPLE; break; case 'B': mplp.flag &= ~MPLP_REALN; break; case 'D': mplp.flag &= ~MPLP_REALN_PARTIAL; break; case 'I': mplp.flag |= MPLP_NO_INDEL; break; case 'E': mplp.flag |= MPLP_REDO_BAQ; break; case '6': mplp.flag |= MPLP_ILLUMINA13; break; case 's': if ( bam_smpl_add_samples(mplp.bsmpl,optarg,0)<0 ) error("Could not read samples: %s\n",optarg); break; case 'S': if ( bam_smpl_add_samples(mplp.bsmpl,optarg,1)<0 ) error("Could not read samples: %s\n",optarg); break; case 'O': switch (optarg[0]) { case 'b': mplp.output_type = FT_BCF_GZ; break; case 'u': mplp.output_type = FT_BCF; break; case 'z': mplp.output_type = FT_VCF_GZ; break; case 'v': mplp.output_type = FT_VCF; break; default: { char *tmp; mplp.clevel = strtol(optarg,&tmp,10); if ( *tmp || mplp.clevel<0 || mplp.clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { char *tmp; mplp.clevel = strtol(optarg+1,&tmp,10); if ( *tmp || mplp.clevel<0 || mplp.clevel>9 ) error("Could not parse argument: --output-type %s\n", optarg+1); } break; case 'C': mplp.capQ_thres = atoi(optarg); break; case 'q': mplp.min_mq = atoi(optarg); break; case 'Q': mplp.min_baseQ = atoi(optarg); break; case 11: mplp.max_baseQ = atoi(optarg); break; case 12: mplp.delta_baseQ = atoi(optarg); break; case 'b': file_list = optarg; break; case 'o': { char *end; long value = strtol(optarg, &end, 10); // Distinguish between -o INT and -o FILE (a bit of a hack!) if (*end == '\0') mplp.openQ = value; else mplp.output_fname = optarg; } break; case 'e': mplp.extQ = atoi(optarg); break; case 'h': mplp.tandemQ = atoi(optarg); break; case 10: // --indel-bias (inverted so higher => more indels called) if (atof(optarg) < 1e-2) mplp.indel_bias = 1/1e2; else mplp.indel_bias = 1/atof(optarg); break; case 27: mplp.vs_ref = atof(optarg); //if (mplp.vs_ref < 0) mplp.vs_ref = 0; if (mplp.vs_ref > 1) mplp.vs_ref = 1; break; case 15: { char *tmp; mplp.indel_win_size = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --indel-size %s\n", optarg); if ( mplp.indel_win_size < 20 ) { mplp.indel_win_size = 20; fprintf(bcftools_stderr,"Warning: running with --indel-size %d, the requested value is too small\n",mplp.indel_win_size); } } break; case 20: mplp.indels_v20 = 1; mplp.edlib = 0; break; case 'W': if (!(mplp.write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 22: mplp.edlib = 1; mplp.indels_v20 = 0; break; case 25: mplp.edlib = 0; break; case 28: mplp.seqQ_offset = atoi(optarg); if (mplp.seqQ_offset < 100) mplp.seqQ_offset = 100; if (mplp.seqQ_offset > 200) mplp.seqQ_offset = 200; break; case 23: mplp.del_bias = atof(optarg); break; case 24: mplp.poly_mqual = 1; break; case 26: mplp.poly_mqual = 0; break; case 'A': use_orphan = 1; break; case 'F': mplp.min_frac = atof(optarg); break; case 'm': mplp.min_support = atoi(optarg); break; case 'L': mplp.max_indel_depth = atoi(optarg); break; case 'G': bam_smpl_add_readgroups(mplp.bsmpl, optarg, 1); break; case 'a': if (optarg[0]=='?') { list_annotations(bcftools_stderr); goto err; } parse_format_flag(&mplp.fmt_flag,optarg); break; case 'M': mplp.max_read_len = atoi(optarg); break; case 'X': if (strcasecmp(optarg, "pacbio-ccs-1.18") == 0) { mplp.min_frac = 0.1; mplp.min_baseQ = 5; mplp.max_baseQ = 50; mplp.delta_baseQ = 10; mplp.openQ = 25; mplp.extQ = 1; mplp.flag |= MPLP_REALN_PARTIAL; mplp.max_read_len = 99999; } else if (strcasecmp(optarg, "pacbio-ccs") == 0 || strcasecmp(optarg, "pacbio-ccs-1.20") == 0) { mplp.min_frac = 0.1; mplp.min_baseQ = 5; mplp.max_baseQ = 50; mplp.delta_baseQ = 10; mplp.tandemQ = 300; mplp.openQ = 25; mplp.extQ = 1; mplp.flag &= ~MPLP_REALN; mplp.del_bias = 0.4; mplp.indel_bias = 1/.9; mplp.seqQ_offset = 118; mplp.poly_mqual = 1; mplp.edlib = 1; mplp.vs_ref = 0.7; mplp.indel_win_size = 80; } else if (strcasecmp(optarg, "ont") == 0) { fprintf(bcftools_stderr, "With old ONT data may be beneficial to also run bcftools call with " "a higher -P, eg -P0.01 or -P 0.1\n"); mplp.min_baseQ = 5; mplp.max_baseQ = 30; mplp.flag &= ~MPLP_REALN; mplp.flag |= MPLP_NO_INDEL; } else if (strcasecmp(optarg, "ont-sup") == 0 || strcasecmp(optarg, "ont-sup-1.20") == 0) { mplp.min_frac = 0.2; mplp.min_baseQ = 1; mplp.max_baseQ = 35; mplp.delta_baseQ = 99; mplp.openQ = 15; mplp.extQ = 1; mplp.flag &= ~MPLP_REALN; mplp.max_read_len = 9999999; mplp.del_bias = 0.4; mplp.poly_mqual = 1; mplp.edlib = 1; // If we increase -h then we can increase bias denominator too mplp.tandemQ = 110; mplp.indel_bias = 1/0.7; mplp.seqQ_offset = 130; mplp.indel_win_size = 80; } else if (strcasecmp(optarg, "ultima") == 0 || strcasecmp(optarg, "ultima-1.20") == 0) { mplp.min_frac = 0.15; mplp.min_baseQ = 1; mplp.max_baseQ = 30; mplp.delta_baseQ = 10; mplp.openQ = 20; mplp.extQ = 10; mplp.tandemQ = 250; mplp.flag &= ~MPLP_REALN; mplp.del_bias = 0.3; mplp.poly_mqual = 1; mplp.edlib = 1; mplp.indel_bias = 1/0.7; mplp.seqQ_offset = 140; mplp.vs_ref = 0.3; mplp.indel_win_size = 80; } else if (strcasecmp(optarg, "1.12") == 0) { // 1.12 and earlier mplp.min_frac = 0.002; mplp.min_support = 1; mplp.min_baseQ = 13; mplp.tandemQ = 100; mplp.flag &= ~MPLP_REALN_PARTIAL; mplp.flag |= MPLP_REALN; } else if (strcasecmp(optarg, "illumina-1.18") == 0) { mplp.indel_win_size = 110; mplp.flag |= MPLP_REALN_PARTIAL; } else if (strcasecmp(optarg, "illumina") == 0 || strcasecmp(optarg, "illumina-1.20") == 0) { mplp.edlib = 1; mplp.indel_win_size = 110; mplp.flag |= MPLP_REALN_PARTIAL; mplp.indel_bias = 1; mplp.seqQ_offset = 125; //mplp.indel_win_size = 80; TEST? } else if (strcasecmp(optarg, "bgi") == 0 || strcasecmp(optarg, "bgi-1.20") == 0) { mplp.min_frac = 0.1; mplp.edlib = 1; mplp.indel_bias = 1; mplp.seqQ_offset = 120; mplp.flag |= MPLP_REALN_PARTIAL; mplp.indel_win_size = 80; } else if (strcasecmp(optarg, "list") == 0 || strcasecmp(optarg, "help") == 0) { print_profiles(); goto err; } else { fprintf(bcftools_stderr, "Unknown configuration name '%s'\n" "Please use '-X list' to show available choices.\n", optarg); goto err; } break; case 13: hts_srand48(atoi(optarg)); break; case 14: if ( !strcasecmp(optarg,"drop") ) mplp.ambig_reads = B2B_DROP; else if ( !strcasecmp(optarg,"incAD") ) mplp.ambig_reads = B2B_INC_AD; else if ( !strcasecmp(optarg,"incAD0") ) mplp.ambig_reads = B2B_INC_AD0; else error("The option to --ambig-reads not recognised: %s\n",optarg); break; default: fprintf(bcftools_stderr,"Invalid option: '%c'\n", c); goto err; } } if ( mplp.gvcf && !(mplp.fmt_flag&B2B_FMT_DP) ) { fprintf(bcftools_stderr,"[warning] The -a DP option is required with --gvcf, switching on.\n"); mplp.fmt_flag |= B2B_FMT_DP; } if ( mplp.flag&(MPLP_BCF|MPLP_VCF|MPLP_NO_COMP) ) { if ( mplp.flag&MPLP_VCF ) { if ( mplp.flag&MPLP_NO_COMP ) mplp.output_type = FT_VCF; else mplp.output_type = FT_VCF_GZ; } else if ( mplp.flag&MPLP_BCF ) { if ( mplp.flag&MPLP_NO_COMP ) mplp.output_type = FT_BCF; else mplp.output_type = FT_BCF_GZ; } } if ( !(mplp.flag&MPLP_REALN) && mplp.flag&MPLP_REDO_BAQ ) { fprintf(bcftools_stderr,"Error: The -B option cannot be combined with -E\n"); goto err; } if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN; if (argc == 1) { print_usage(bcftools_stderr, &mplp); goto err; } if (!mplp.fai && !noref) { fprintf(bcftools_stderr,"Error: mpileup requires the --fasta-ref option by default; use --no-reference to run without a fasta reference\n"); goto err; } if (file_list) { if ( read_file_list(file_list,&nfiles,&fn) ) goto err; mplp.files = fn; mplp.nfiles = nfiles; } else { mplp.nfiles = argc - optind; mplp.files = (char**) malloc(mplp.nfiles*sizeof(char*)); for (i=0; i Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ // Code to build this table is below #ifdef BUILD_MW #include double mann_whitney_1947(int n, int m, int U) { if (U<0) return 0; if (n==0||m==0) return U==0 ? 1 : 0; return (double)n/(n+m)*mann_whitney_1947(n-1,m,U-m) + (double)m/(n+m)*mann_whitney_1947(n,m-1,U); } int main(void) { int i, j, k; printf("static double mw[6][6][50] = // [2-7][2-7][0-49]\n{\n"); for (i = 2; i < 8; i++) { printf(" {\n"); for (j = 2; j < 8; j++) { printf(" {\n"); for (k = 0; k < 50; k++) { printf(" %.17f,\n", mann_whitney_1947(i,j,k)); } printf(" },\n"); } printf(" },\n"); } printf("};\n"); return 0; } #endif static double mw[6][6][50] = // [2-7][2-7][0-49] { { { 0.16666666666666666, 0.16666666666666666, 0.33333333333333331, 0.16666666666666666, 0.16666666666666666, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, }, { 0.09999999999999999, 0.09999999999999999, 0.19999999999999998, 0.20000000000000001, 0.20000000000000001, 0.10000000000000001, 0.10000000000000001, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, }, { 0.06666666666666665, 0.06666666666666665, 0.13333333333333330, 0.13333333333333333, 0.20000000000000001, 0.13333333333333333, 0.13333333333333333, 0.06666666666666667, 0.06666666666666667, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 0.00000000000000000, 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Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include "bcftools.h" #include "ploidy.h" struct _ploidy_t { int nsex, msex; // number of genders, m:number of allocated elements in id2sex array int dflt, min, max; // ploidy: default, min and max (only explicitly listed) int *sex2dflt; regidx_t *idx; regitr_t *itr; void *sex2id; char **id2sex; kstring_t tmp_str; }; typedef struct { int sex, ploidy; } sex_ploidy_t; regidx_t *ploidy_regions(ploidy_t *ploidy) { return ploidy->idx; } int ploidy_parse(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr) { int i, ret; ploidy_t *ploidy = (ploidy_t*) usr; void *sex2id = ploidy->sex2id; // Check for special case of default ploidy "* * * " int default_ploidy_def = 0; char *ss = (char*) line; while ( *ss && isspace(*ss) ) ss++; if ( ss[0]=='*' && (!ss[1] || isspace(ss[1])) ) default_ploidy_def = 1; // definition of default ploidy, chr="*" else { // Fill CHR,FROM,TO ret = regidx_parse_tab(line,chr_beg,chr_end,beg,end,NULL,NULL); if ( ret!=0 ) return ret; } // Skip the fields already parsed by regidx_parse_tab ss = (char*) line; while ( *ss && isspace(*ss) ) ss++; for (i=0; i<3; i++) { while ( *ss && !isspace(*ss) ) ss++; if ( !*ss ) return -2; // wrong number of fields while ( *ss && isspace(*ss) ) ss++; } if ( !*ss ) return -2; // Parse the payload char *se = ss; while ( *se && !isspace(*se) ) se++; if ( !*se || se==ss ) error("Could not parse: %s\n", line); ploidy->tmp_str.l = 0; kputsn(ss,se-ss,&ploidy->tmp_str); sex_ploidy_t *sp = (sex_ploidy_t*) payload; if ( khash_str2int_get(sex2id, ploidy->tmp_str.s, &sp->sex) != 0 ) { ploidy->nsex++; hts_expand0(char*,ploidy->nsex,ploidy->msex,ploidy->id2sex); ploidy->id2sex[ploidy->nsex-1] = strdup(ploidy->tmp_str.s); sp->sex = khash_str2int_inc(ploidy->sex2id, ploidy->id2sex[ploidy->nsex-1]); ploidy->sex2dflt = (int*) realloc(ploidy->sex2dflt,sizeof(int)*ploidy->nsex); ploidy->sex2dflt[ploidy->nsex-1] = -1; } ss = se; while ( *se && isspace(*se) ) se++; if ( !*se ) error("Could not parse: %s\n", line); sp->ploidy = strtol(ss,&se,10); if ( ss==se ) error("Could not parse: %s\n", line); if ( ploidy->min<0 || sp->ploidy < ploidy->min ) ploidy->min = sp->ploidy; if ( ploidy->max<0 || sp->ploidy > ploidy->max ) ploidy->max = sp->ploidy; // Special case, chr="*" stands for a default value if ( default_ploidy_def ) { ploidy->sex2dflt[ploidy->nsex-1] = sp->ploidy; return -1; } return 0; } static void _set_defaults(ploidy_t *ploidy, int dflt) { int i; if ( khash_str2int_get(ploidy->sex2id, "*", &i) == 0 ) dflt = ploidy->sex2dflt[i]; for (i=0; insex; i++) if ( ploidy->sex2dflt[i]==-1 ) ploidy->sex2dflt[i] = dflt; ploidy->dflt = dflt; if ( ploidy->min<0 || dflt < ploidy->min ) ploidy->min = dflt; if ( ploidy->max<0 || dflt > ploidy->max ) ploidy->max = dflt; } ploidy_t *ploidy_init(const char *fname, int dflt) { ploidy_t *pld = (ploidy_t*) calloc(1,sizeof(ploidy_t)); if ( !pld ) return NULL; pld->min = pld->max = -1; pld->sex2id = khash_str2int_init(); pld->idx = regidx_init(fname,ploidy_parse,NULL,sizeof(sex_ploidy_t),pld); if ( !pld->idx ) { ploidy_destroy(pld); return NULL; } pld->itr = regitr_init(pld->idx); _set_defaults(pld,dflt); return pld; } ploidy_t *ploidy_init_string(const char *str, int dflt) { ploidy_t *pld = (ploidy_t*) calloc(1,sizeof(ploidy_t)); if ( !pld ) return NULL; pld->min = pld->max = -1; pld->sex2id = khash_str2int_init(); pld->idx = regidx_init(NULL,ploidy_parse,NULL,sizeof(sex_ploidy_t),pld); pld->itr = regitr_init(pld->idx); kstring_t tmp = {0,0,0}; const char *ss = str; while ( *ss ) { while ( *ss && isspace(*ss) ) ss++; const char *se = ss; while ( *se && *se!='\r' && *se!='\n' ) se++; tmp.l = 0; kputsn(ss, se-ss, &tmp); regidx_insert(pld->idx,tmp.s); while ( *se && isspace(*se) ) se++; ss = se; } free(tmp.s); _set_defaults(pld,dflt); return pld; } void ploidy_destroy(ploidy_t *ploidy) { if ( ploidy->sex2id ) khash_str2int_destroy_free(ploidy->sex2id); if ( ploidy->itr ) regitr_destroy(ploidy->itr); if ( ploidy->idx ) regidx_destroy(ploidy->idx); free(ploidy->id2sex); free(ploidy->tmp_str.s); free(ploidy->sex2dflt); free(ploidy); } int ploidy_query(ploidy_t *ploidy, char *seq, int pos, int *sex2ploidy, int *min, int *max) { int i, ret = regidx_overlap(ploidy->idx, seq,pos,pos, ploidy->itr); if ( !sex2ploidy && !min && !max ) return ret; if ( !ret ) { // no overlap if ( min ) *min = ploidy->dflt; if ( max ) *max = ploidy->dflt; if ( sex2ploidy ) for (i=0; insex; i++) sex2ploidy[i] = ploidy->sex2dflt[i]; return 0; } int _min = INT_MAX, _max = -1; if ( sex2ploidy ) for (i=0; insex; i++) sex2ploidy[i] = ploidy->dflt; while ( regitr_overlap(ploidy->itr) ) { int sex = regitr_payload(ploidy->itr,sex_ploidy_t).sex; int pld = regitr_payload(ploidy->itr,sex_ploidy_t).ploidy; if ( pld!=ploidy->dflt ) { if ( sex2ploidy ) sex2ploidy[ sex ] = pld; if ( _min > pld ) _min = pld; if ( _max < pld ) _max = pld; } } if ( _max==-1 ) _max = _min = ploidy->dflt; if ( max ) *max = _max; if ( min ) *min = _min; return 1; } int ploidy_nsex(ploidy_t *ploidy) { return ploidy->nsex; } char *ploidy_id2sex(ploidy_t *ploidy, int id) { if ( id<0 || id>=ploidy->nsex ) return NULL; return ploidy->id2sex[id]; } int ploidy_sex2id(ploidy_t *ploidy, char *sex) { int id; if ( khash_str2int_get(ploidy->sex2id,sex,&id)!=0 ) return -1; return id; } int ploidy_add_sex(ploidy_t *ploidy, const char *sex) { int id; if ( khash_str2int_get(ploidy->sex2id, sex, &id)==0 ) return id; ploidy->nsex++; hts_expand0(char*,ploidy->nsex,ploidy->msex,ploidy->id2sex); ploidy->id2sex[ploidy->nsex-1] = strdup(sex); ploidy->sex2dflt = (int*) realloc(ploidy->sex2dflt,sizeof(int)*ploidy->nsex); ploidy->sex2dflt[ploidy->nsex-1] = ploidy->dflt; return khash_str2int_inc(ploidy->sex2id, ploidy->id2sex[ploidy->nsex-1]); } int ploidy_max(ploidy_t *ploidy) { return ploidy->dflt > ploidy->max ? ploidy->dflt : ploidy->max; } int ploidy_min(ploidy_t *ploidy) { return ploidy->dflt < ploidy->min ? ploidy->dflt : ploidy->min; } pysam-0.23.0/bcftools/ploidy.c.pysam.c000066400000000000000000000177441475062545500176070ustar00rootroot00000000000000#include "bcftools.pysam.h" /* Copyright (C) 2014-2016 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include "bcftools.h" #include "ploidy.h" struct _ploidy_t { int nsex, msex; // number of genders, m:number of allocated elements in id2sex array int dflt, min, max; // ploidy: default, min and max (only explicitly listed) int *sex2dflt; regidx_t *idx; regitr_t *itr; void *sex2id; char **id2sex; kstring_t tmp_str; }; typedef struct { int sex, ploidy; } sex_ploidy_t; regidx_t *ploidy_regions(ploidy_t *ploidy) { return ploidy->idx; } int ploidy_parse(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr) { int i, ret; ploidy_t *ploidy = (ploidy_t*) usr; void *sex2id = ploidy->sex2id; // Check for special case of default ploidy "* * * " int default_ploidy_def = 0; char *ss = (char*) line; while ( *ss && isspace(*ss) ) ss++; if ( ss[0]=='*' && (!ss[1] || isspace(ss[1])) ) default_ploidy_def = 1; // definition of default ploidy, chr="*" else { // Fill CHR,FROM,TO ret = regidx_parse_tab(line,chr_beg,chr_end,beg,end,NULL,NULL); if ( ret!=0 ) return ret; } // Skip the fields already parsed by regidx_parse_tab ss = (char*) line; while ( *ss && isspace(*ss) ) ss++; for (i=0; i<3; i++) { while ( *ss && !isspace(*ss) ) ss++; if ( !*ss ) return -2; // wrong number of fields while ( *ss && isspace(*ss) ) ss++; } if ( !*ss ) return -2; // Parse the payload char *se = ss; while ( *se && !isspace(*se) ) se++; if ( !*se || se==ss ) error("Could not parse: %s\n", line); ploidy->tmp_str.l = 0; kputsn(ss,se-ss,&ploidy->tmp_str); sex_ploidy_t *sp = (sex_ploidy_t*) payload; if ( khash_str2int_get(sex2id, ploidy->tmp_str.s, &sp->sex) != 0 ) { ploidy->nsex++; hts_expand0(char*,ploidy->nsex,ploidy->msex,ploidy->id2sex); ploidy->id2sex[ploidy->nsex-1] = strdup(ploidy->tmp_str.s); sp->sex = khash_str2int_inc(ploidy->sex2id, ploidy->id2sex[ploidy->nsex-1]); ploidy->sex2dflt = (int*) realloc(ploidy->sex2dflt,sizeof(int)*ploidy->nsex); ploidy->sex2dflt[ploidy->nsex-1] = -1; } ss = se; while ( *se && isspace(*se) ) se++; if ( !*se ) error("Could not parse: %s\n", line); sp->ploidy = strtol(ss,&se,10); if ( ss==se ) error("Could not parse: %s\n", line); if ( ploidy->min<0 || sp->ploidy < ploidy->min ) ploidy->min = sp->ploidy; if ( ploidy->max<0 || sp->ploidy > ploidy->max ) ploidy->max = sp->ploidy; // Special case, chr="*" stands for a default value if ( default_ploidy_def ) { ploidy->sex2dflt[ploidy->nsex-1] = sp->ploidy; return -1; } return 0; } static void _set_defaults(ploidy_t *ploidy, int dflt) { int i; if ( khash_str2int_get(ploidy->sex2id, "*", &i) == 0 ) dflt = ploidy->sex2dflt[i]; for (i=0; insex; i++) if ( ploidy->sex2dflt[i]==-1 ) ploidy->sex2dflt[i] = dflt; ploidy->dflt = dflt; if ( ploidy->min<0 || dflt < ploidy->min ) ploidy->min = dflt; if ( ploidy->max<0 || dflt > ploidy->max ) ploidy->max = dflt; } ploidy_t *ploidy_init(const char *fname, int dflt) { ploidy_t *pld = (ploidy_t*) calloc(1,sizeof(ploidy_t)); if ( !pld ) return NULL; pld->min = pld->max = -1; pld->sex2id = khash_str2int_init(); pld->idx = regidx_init(fname,ploidy_parse,NULL,sizeof(sex_ploidy_t),pld); if ( !pld->idx ) { ploidy_destroy(pld); return NULL; } pld->itr = regitr_init(pld->idx); _set_defaults(pld,dflt); return pld; } ploidy_t *ploidy_init_string(const char *str, int dflt) { ploidy_t *pld = (ploidy_t*) calloc(1,sizeof(ploidy_t)); if ( !pld ) return NULL; pld->min = pld->max = -1; pld->sex2id = khash_str2int_init(); pld->idx = regidx_init(NULL,ploidy_parse,NULL,sizeof(sex_ploidy_t),pld); pld->itr = regitr_init(pld->idx); kstring_t tmp = {0,0,0}; const char *ss = str; while ( *ss ) { while ( *ss && isspace(*ss) ) ss++; const char *se = ss; while ( *se && *se!='\r' && *se!='\n' ) se++; tmp.l = 0; kputsn(ss, se-ss, &tmp); regidx_insert(pld->idx,tmp.s); while ( *se && isspace(*se) ) se++; ss = se; } free(tmp.s); _set_defaults(pld,dflt); return pld; } void ploidy_destroy(ploidy_t *ploidy) { if ( ploidy->sex2id ) khash_str2int_destroy_free(ploidy->sex2id); if ( ploidy->itr ) regitr_destroy(ploidy->itr); if ( ploidy->idx ) regidx_destroy(ploidy->idx); free(ploidy->id2sex); free(ploidy->tmp_str.s); free(ploidy->sex2dflt); free(ploidy); } int ploidy_query(ploidy_t *ploidy, char *seq, int pos, int *sex2ploidy, int *min, int *max) { int i, ret = regidx_overlap(ploidy->idx, seq,pos,pos, ploidy->itr); if ( !sex2ploidy && !min && !max ) return ret; if ( !ret ) { // no overlap if ( min ) *min = ploidy->dflt; if ( max ) *max = ploidy->dflt; if ( sex2ploidy ) for (i=0; insex; i++) sex2ploidy[i] = ploidy->sex2dflt[i]; return 0; } int _min = INT_MAX, _max = -1; if ( sex2ploidy ) for (i=0; insex; i++) sex2ploidy[i] = ploidy->dflt; while ( regitr_overlap(ploidy->itr) ) { int sex = regitr_payload(ploidy->itr,sex_ploidy_t).sex; int pld = regitr_payload(ploidy->itr,sex_ploidy_t).ploidy; if ( pld!=ploidy->dflt ) { if ( sex2ploidy ) sex2ploidy[ sex ] = pld; if ( _min > pld ) _min = pld; if ( _max < pld ) _max = pld; } } if ( _max==-1 ) _max = _min = ploidy->dflt; if ( max ) *max = _max; if ( min ) *min = _min; return 1; } int ploidy_nsex(ploidy_t *ploidy) { return ploidy->nsex; } char *ploidy_id2sex(ploidy_t *ploidy, int id) { if ( id<0 || id>=ploidy->nsex ) return NULL; return ploidy->id2sex[id]; } int ploidy_sex2id(ploidy_t *ploidy, char *sex) { int id; if ( khash_str2int_get(ploidy->sex2id,sex,&id)!=0 ) return -1; return id; } int ploidy_add_sex(ploidy_t *ploidy, const char *sex) { int id; if ( khash_str2int_get(ploidy->sex2id, sex, &id)==0 ) return id; ploidy->nsex++; hts_expand0(char*,ploidy->nsex,ploidy->msex,ploidy->id2sex); ploidy->id2sex[ploidy->nsex-1] = strdup(sex); ploidy->sex2dflt = (int*) realloc(ploidy->sex2dflt,sizeof(int)*ploidy->nsex); ploidy->sex2dflt[ploidy->nsex-1] = ploidy->dflt; return khash_str2int_inc(ploidy->sex2id, ploidy->id2sex[ploidy->nsex-1]); } int ploidy_max(ploidy_t *ploidy) { return ploidy->dflt > ploidy->max ? ploidy->dflt : ploidy->max; } int ploidy_min(ploidy_t *ploidy) { return ploidy->dflt < ploidy->min ? ploidy->dflt : ploidy->min; } pysam-0.23.0/bcftools/ploidy.h000066400000000000000000000104761475062545500162360ustar00rootroot00000000000000/* Copyright (C) 2014-2015 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Lookup from region and sex to ploidy. Example of usage: int default_ploidy = 2; ploidy_t *pld = ploidy_init(fname, default_ploidy); int nsex = ploidy_nsex(pld); int *sex2ploidy = malloc(sizeof(int)*nsex); ploidy_query(pld, "X",60000, sex2ploidy, NULL, NULL); for (i=0; i Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "prob1.h" #define MC_MAX_EM_ITER 16 #define MC_EM_EPS 1e-5 #define MC_DEF_INDEL 0.15 void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x) { int i; for (i = 0; i < ma->M; ++i) ma->phi_indel[i] = ma->phi[i] * x; ma->phi_indel[ma->M] = 1. - ma->phi[ma->M] * x; } static void init_prior(int type, double theta, int M, double *phi) { int i; if (type == MC_PTYPE_COND2) { for (i = 0; i <= M; ++i) phi[i] = 2. * (i + 1) / (M + 1) / (M + 2); } else if (type == MC_PTYPE_FLAT) { for (i = 0; i <= M; ++i) phi[i] = 1. / (M + 1); } else { double sum; for (i = 0, sum = 0.; i < M; ++i) sum += (phi[i] = theta / (M - i)); phi[M] = 1. - sum; } } void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta) { init_prior(type, theta, ma->M, ma->phi); bcf_p1_indel_prior(ma, MC_DEF_INDEL); } void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta) { if (ma->n1 <= 0 || ma->n1 >= ma->M) return; init_prior(type, theta, 2*ma->n1, ma->phi1); init_prior(type, theta, 2*(ma->n - ma->n1), ma->phi2); } /* Initialise a bcf_p1aux_t */ bcf_p1aux_t *bcf_p1_init(int n_smpl, uint8_t *ploidy) { bcf_p1aux_t *ma; int i; ma = (bcf_p1aux_t*) calloc(1, sizeof(bcf_p1aux_t)); ma->n1 = -1; ma->n = n_smpl; ma->M = 2 * n_smpl; if (ploidy) { ma->ploidy = (uint8_t*) malloc(n_smpl); memcpy(ma->ploidy, ploidy, n_smpl); for (i = 0, ma->M = 0; i < n_smpl; ++i) ma->M += ploidy[i]; if (ma->M == 2 * n_smpl) { free(ma->ploidy); ma->ploidy = 0; } } ma->q2p = (double*) calloc(256, sizeof(double)); ma->pdg = (double*) calloc(3 * ma->n, sizeof(double)); ma->phi = (double*) calloc(ma->M + 1, sizeof(double)); ma->phi_indel = (double*) calloc(ma->M + 1, sizeof(double)); ma->phi1 = (double*) calloc(ma->M + 1, sizeof(double)); ma->phi2 = (double*) calloc(ma->M + 1, sizeof(double)); ma->z = (double*) calloc(ma->M + 1, sizeof(double)); ma->zswap = (double*) calloc(ma->M + 1, sizeof(double)); ma->z1 = (double*) calloc(ma->M + 1, sizeof(double)); // actually we do not need this large ma->z2 = (double*) calloc(ma->M + 1, sizeof(double)); ma->afs = (double*) calloc(ma->M + 1, sizeof(double)); ma->afs1 = (double*) calloc(ma->M + 1, sizeof(double)); ma->lf = (double*) calloc(ma->M + 1, sizeof(double)); for (i = 0; i < 256; ++i) ma->q2p[i] = pow(10., -i / 10.); for (i = 0; i <= ma->M; ++i) ma->lf[i] = lgamma(i + 1); bcf_p1_init_prior(ma, MC_PTYPE_FULL, 1e-3); // the simplest prior return ma; } int bcf_p1_get_M(bcf_p1aux_t *b) { return b->M; } int bcf_p1_set_n1(bcf_p1aux_t *b, int n1) { if (n1 == 0 || n1 >= b->n) return -1; if (b->M != b->n * 2) { fprintf(stderr, "[%s] unable to set `n1' when there are haploid samples.\n", __func__); return -1; } b->n1 = n1; return 0; } void bcf_p1_destroy(bcf_p1aux_t *ma) { if (ma) { int k; free(ma->lf); if (ma->hg && ma->n1 > 0) { for (k = 0; k <= 2*ma->n1; ++k) free(ma->hg[k]); free(ma->hg); } free(ma->ploidy); free(ma->q2p); free(ma->pdg); free(ma->phi); free(ma->phi_indel); free(ma->phi1); free(ma->phi2); free(ma->z); free(ma->zswap); free(ma->z1); free(ma->z2); free(ma->afs); free(ma->afs1); free(ma); } } extern double kf_gammap(double s, double z); int test16(bcf1_t *b, anno16_t *a); /* Calculate P(D|g) */ static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma) { int i, j; long p_a[16], *p=p_a, tmp; if (b->n_allele > 16) p = (long*) malloc(b->n_allele * sizeof(long)); memset(p, 0, sizeof(long) * b->n_allele); // Set P(D|g) for each sample and sum phread likelihoods across all samples to create lk for (j = 0; j < ma->n; ++j) { // Fetch the PL array for the sample const int *pi = ma->PL + j * ma->PL_len; // Fetch the P(D|g) array for the sample double *pdg = ma->pdg + j * 3; pdg[0] = ma->q2p[pi[2]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]]; for (i = 0; i < b->n_allele; ++i) p[i] += (int)pi[(i+1)*(i+2)/2-1]; } for (i = 0; i < b->n_allele; ++i) p[i] = p[i]<<4 | i; for (i = 1; i < b->n_allele; ++i) // insertion sort for (j = i; j > 0 && p[j] < p[j-1]; --j) tmp = p[j], p[j] = p[j-1], p[j-1] = tmp; for (i = b->n_allele - 1; i >= 0; --i) if ((p[i]&0xf) == 0) break; if (p != p_a) free(p); return i; } /* f0 is freq of the ref allele */ int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k, int is_var) { double sum, g[3]; double max, f3[3], *pdg = ma->pdg + k * 3; int q, i, max_i, ploidy; /* determine ploidy */ ploidy = ma->ploidy? ma->ploidy[k] : 2; if (ploidy == 2) { /* given allele frequency we can determine how many of each * genotype we have by HWE p=1-q PP=p^2 PQ&QP=2*p*q QQ=q^2 */ f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0; } else { f3[0] = 1. - f0; f3[1] = 0; f3[2] = f0; } for (i = 0, sum = 0.; i < 3; ++i) sum += (g[i] = pdg[i] * f3[i]); /* normalise g and then determine max */ for (i = 0, max = -1., max_i = 0; i < 3; ++i) { g[i] /= sum; if (g[i] > max) max = g[i], max_i = i; } if ( !is_var ) { max_i = 2; max = g[2]; } // force 0/0 genotype if the site is non-variant max = 1. - max; if (max < 1e-308) max = 1e-308; q = (int)(-4.343 * log(max) + .499); if (q > 99) q = 99; return q<<2|max_i; } // If likelihoods fall below this they get squashed to 0 #define TINY 1e-20 static void mc_cal_y_core(bcf_p1aux_t *ma, int beg) { double *z[2], *tmp, *pdg; int _j, last_min, last_max; assert(beg == 0 || ma->M == ma->n*2); z[0] = ma->z; z[1] = ma->zswap; pdg = ma->pdg; memset(z[0], 0, sizeof(double) * (ma->M + 1)); memset(z[1], 0, sizeof(double) * (ma->M + 1)); z[0][0] = 1.; last_min = last_max = 0; ma->t = 0.; if (ma->M == ma->n * 2) { int M = 0; for (_j = beg; _j < ma->n; ++_j) { int k, j = _j - beg, _min = last_min, _max = last_max, M0; double p[3], sum; M0 = M; M += 2; // Fetch P(D|g) for this sample pdg = ma->pdg + _j * 3; p[0] = pdg[0]; p[1] = 2. * pdg[1]; p[2] = pdg[2]; for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.; for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.; _max += 2; if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k]; if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1]; for (k = _min < 2? 2 : _min; k <= _max; ++k) z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1] + k*(k-1)* p[2] * z[0][k-2]; for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k]; ma->t += log(sum / (M * (M - 1.))); for (k = _min; k <= _max; ++k) z[1][k] /= sum; if (_min >= 1) z[1][_min-1] = 0.; if (_min >= 2) z[1][_min-2] = 0.; // If we are not on the last sample if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.; if (_j == ma->n1 - 1) { // set pop1; ma->n1==-1 when unset ma->t1 = ma->t; memcpy(ma->z1, z[1], sizeof(double) * (ma->n1 * 2 + 1)); } tmp = z[0]; z[0] = z[1]; z[1] = tmp; last_min = _min; last_max = _max; } //for (_j = 0; _j < last_min; ++_j) z[0][_j] = 0.; // TODO: are these necessary? //for (_j = last_max + 1; _j < ma->M; ++_j) z[0][_j] = 0.; } else { // this block is very similar to the block above; these two might be merged in future int j, M = 0; for (j = 0; j < ma->n; ++j) { int k, M0, _min = last_min, _max = last_max; double p[3], sum; // Fetch P(D|g) for this sample pdg = ma->pdg + j * 3; for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.; for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.; M0 = M; M += ma->ploidy[j]; if (ma->ploidy[j] == 1) { p[0] = pdg[0]; p[1] = pdg[2]; _max++; if (_min == 0) k = 0, z[1][k] = (M0+1-k) * p[0] * z[0][k]; for (k = _min < 1? 1 : _min; k <= _max; ++k) z[1][k] = (M0+1-k) * p[0] * z[0][k] + k * p[1] * z[0][k-1]; for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k]; ma->t += log(sum / M); for (k = _min; k <= _max; ++k) z[1][k] /= sum; if (_min >= 1) z[1][_min-1] = 0.; // If we are not on the last sample if (j < ma->n - 1) z[1][_max+1] = 0.; } else if (ma->ploidy[j] == 2) { p[0] = pdg[0]; p[1] = 2 * pdg[1]; p[2] = pdg[2]; _max += 2; if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k]; if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1]; for (k = _min < 2? 2 : _min; k <= _max; ++k) z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1] + k*(k-1)* p[2] * z[0][k-2]; for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k]; ma->t += log(sum / (M * (M - 1.))); for (k = _min; k <= _max; ++k) z[1][k] /= sum; if (_min >= 1) z[1][_min-1] = 0.; if (_min >= 2) z[1][_min-2] = 0.; // If we are not on the last sample if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.; } tmp = z[0]; z[0] = z[1]; z[1] = tmp; last_min = _min; last_max = _max; } } if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1)); } static void mc_cal_y(bcf_p1aux_t *ma) { if (ma->n1 > 0 && ma->n1 < ma->n && ma->M == ma->n * 2) { // NB: ma->n1 is ineffective when there are haploid samples int k; long double x; memset(ma->z1, 0, sizeof(double) * (2 * ma->n1 + 1)); memset(ma->z2, 0, sizeof(double) * (2 * (ma->n - ma->n1) + 1)); ma->t1 = ma->t2 = 0.; mc_cal_y_core(ma, ma->n1); ma->t2 = ma->t; memcpy(ma->z2, ma->z, sizeof(double) * (2 * (ma->n - ma->n1) + 1)); mc_cal_y_core(ma, 0); // rescale z x = expl(ma->t - (ma->t1 + ma->t2)); for (k = 0; k <= ma->M; ++k) ma->z[k] *= x; } else mc_cal_y_core(ma, 0); } #define CONTRAST_TINY 1e-30 extern double kf_gammaq(double s, double z); // incomplete gamma function for chi^2 test static inline double chi2_test(int a, int b, int c, int d) { double x, z; x = (double)(a+b) * (c+d) * (b+d) * (a+c); if (x == 0.) return 1; z = a * d - b * c; return kf_gammaq(.5, .5 * z * z * (a+b+c+d) / x); } // chi2=(a+b+c+d)(ad-bc)^2/[(a+b)(c+d)(a+c)(b+d)] static inline double contrast2_aux(const bcf_p1aux_t *p1, double sum, int k1, int k2, double x[3]) { double p = p1->phi[k1+k2] * p1->z1[k1] * p1->z2[k2] / sum * p1->hg[k1][k2]; int n1 = p1->n1, n2 = p1->n - p1->n1; if (p < CONTRAST_TINY) return -1; if (.5*k1/n1 < .5*k2/n2) x[1] += p; else if (.5*k1/n1 > .5*k2/n2) x[2] += p; else x[0] += p; return p * chi2_test(k1, k2, (n1<<1) - k1, (n2<<1) - k2); } static double contrast2(bcf_p1aux_t *p1, double ret[3]) { int k, k1, k2, k10, k20, n1, n2; double sum; // get n1 and n2 n1 = p1->n1; n2 = p1->n - p1->n1; if (n1 <= 0 || n2 <= 0) return 0.; if (p1->hg == 0) { // initialize the hypergeometric distribution /* NB: the hg matrix may take a lot of memory when there are many samples. There is a way to avoid precomputing this matrix, but it is slower and quite intricate. The following computation in this block can be accelerated with a similar strategy, but perhaps this is not a serious concern for now. */ double tmp = lgamma(2*(n1+n2)+1) - (lgamma(2*n1+1) + lgamma(2*n2+1)); p1->hg = (double**) calloc(2*n1+1, sizeof(double*)); for (k1 = 0; k1 <= 2*n1; ++k1) { p1->hg[k1] = (double*)calloc(2*n2+1, sizeof(double)); for (k2 = 0; k2 <= 2*n2; ++k2) p1->hg[k1][k2] = exp(lgamma(k1+k2+1) + lgamma(p1->M-k1-k2+1) - (lgamma(k1+1) + lgamma(k2+1) + lgamma(2*n1-k1+1) + lgamma(2*n2-k2+1) + tmp)); } } { // compute long double suml = 0; for (k = 0; k <= p1->M; ++k) suml += p1->phi[k] * p1->z[k]; sum = suml; } { // get the max k1 and k2 double max; int max_k; for (k = 0, max = 0, max_k = -1; k <= 2*n1; ++k) { double x = p1->phi1[k] * p1->z1[k]; if (x > max) max = x, max_k = k; } k10 = max_k; for (k = 0, max = 0, max_k = -1; k <= 2*n2; ++k) { double x = p1->phi2[k] * p1->z2[k]; if (x > max) max = x, max_k = k; } k20 = max_k; } { // We can do the following with one nested loop, but that is an O(N^2) thing. The following code block is much faster for large N. double x[3], y; long double z = 0., L[2]; x[0] = x[1] = x[2] = 0; L[0] = L[1] = 0; for (k1 = k10; k1 >= 0; --k1) { for (k2 = k20; k2 >= 0; --k2) { if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break; else z += y; } for (k2 = k20 + 1; k2 <= 2*n2; ++k2) { if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break; else z += y; } } ret[0] = x[0]; ret[1] = x[1]; ret[2] = x[2]; x[0] = x[1] = x[2] = 0; for (k1 = k10 + 1; k1 <= 2*n1; ++k1) { for (k2 = k20; k2 >= 0; --k2) { if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break; else z += y; } for (k2 = k20 + 1; k2 <= 2*n2; ++k2) { if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break; else z += y; } } ret[0] += x[0]; ret[1] += x[1]; ret[2] += x[2]; if (ret[0] + ret[1] + ret[2] < 0.95) { // in case of bad things happened ret[0] = ret[1] = ret[2] = 0; L[0] = L[1] = 0; for (k1 = 0, z = 0.; k1 <= 2*n1; ++k1) for (k2 = 0; k2 <= 2*n2; ++k2) if ((y = contrast2_aux(p1, sum, k1, k2, ret)) >= 0) z += y; if (ret[0] + ret[1] + ret[2] < 0.95) // It seems that this may be caused by floating point errors. I do not really understand why... z = 1.0, ret[0] = ret[1] = ret[2] = 1./3; } return (double)z; } } static double mc_cal_afs(bcf_p1aux_t *ma, double *p_ref_folded, double *p_var_folded) { int k; long double sum = 0., sum2; double *phi = ma->is_indel? ma->phi_indel : ma->phi; memset(ma->afs1, 0, sizeof(double) * (ma->M + 1)); mc_cal_y(ma); // compute AFS // MP15: is this using equation 20 from doi:10.1093/bioinformatics/btr509? for (k = 0, sum = 0.; k <= ma->M; ++k) sum += (long double)phi[k] * ma->z[k]; for (k = 0; k <= ma->M; ++k) { ma->afs1[k] = phi[k] * ma->z[k] / sum; if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return -1.; } // compute folded variant probability for (k = 0, sum = 0.; k <= ma->M; ++k) sum += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k]; for (k = 1, sum2 = 0.; k < ma->M; ++k) sum2 += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k]; *p_var_folded = sum2 / sum; *p_ref_folded = (phi[k] + phi[ma->M - k]) / 2. * (ma->z[ma->M] + ma->z[0]) / sum; // the expected frequency for (k = 0, sum = 0.; k <= ma->M; ++k) { ma->afs[k] += ma->afs1[k]; sum += k * ma->afs1[k]; } return sum / ma->M; } int bcf_p1_cal(call_t *call, bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst) { int i, k; long double sum = 0.; ma->is_indel = bcf_is_snp(b) ? 0 : 1; rst->perm_rank = -1; ma->PL = call->PLs; ma->PL_len = call->nPLs / b->n_sample; if (b->n_allele < 2) return -1; // FIXME: find a better solution rst->rank0 = cal_pdg(b, ma); rst->f_exp = mc_cal_afs(ma, &rst->p_ref_folded, &rst->p_var_folded); rst->p_ref = ma->afs1[ma->M]; for (k = 0, sum = 0.; k < ma->M; ++k) sum += ma->afs1[k]; rst->p_var = (double)sum; { // compute the allele count double max = -1; rst->ac = -1; for (k = 0; k <= ma->M; ++k) if (max < ma->z[k]) max = ma->z[k], rst->ac = k; rst->ac = ma->M - rst->ac; } // calculate f_flat and f_em for (k = 0, sum = 0.; k <= ma->M; ++k) sum += (long double)ma->z[k]; rst->f_flat = 0.; for (k = 0; k <= ma->M; ++k) { double p = ma->z[k] / sum; rst->f_flat += k * p; } rst->f_flat /= ma->M; { // estimate equal-tail credible interval (95% level) int l, h; double p; for (i = 0, p = 0.; i <= ma->M; ++i) if (p + ma->afs1[i] > 0.025) break; else p += ma->afs1[i]; l = i; for (i = ma->M, p = 0.; i >= 0; --i) if (p + ma->afs1[i] > 0.025) break; else p += ma->afs1[i]; h = i; rst->cil = (double)(ma->M - h) / ma->M; rst->cih = (double)(ma->M - l) / ma->M; } if (ma->n1 > 0) { // compute LRT double max0, max1, max2; for (k = 0, max0 = -1; k <= ma->M; ++k) if (max0 < ma->z[k]) max0 = ma->z[k]; for (k = 0, max1 = -1; k <= ma->n1 * 2; ++k) if (max1 < ma->z1[k]) max1 = ma->z1[k]; for (k = 0, max2 = -1; k <= ma->M - ma->n1 * 2; ++k) if (max2 < ma->z2[k]) max2 = ma->z2[k]; rst->lrt = log(max1 * max2 / max0); rst->lrt = rst->lrt < 0? 1 : kf_gammaq(.5, rst->lrt); } else rst->lrt = -1.0; rst->cmp[0] = rst->cmp[1] = rst->cmp[2] = rst->p_chi2 = -1.0; if (do_contrast && rst->p_var > 0.5) // skip contrast2() if the locus is a strong non-variant rst->p_chi2 = contrast2(ma, rst->cmp); return 0; } void bcf_p1_dump_afs(bcf_p1aux_t *ma) { int k; fprintf(stderr, "[afs]"); for (k = 0; k <= ma->M; ++k) fprintf(stderr, " %d:%.3lf", k, ma->afs[ma->M - k]); fprintf(stderr, "\n"); memset(ma->afs, 0, sizeof(double) * (ma->M + 1)); } pysam-0.23.0/bcftools/prob1.c.pysam.c000066400000000000000000000475641475062545500173350ustar00rootroot00000000000000#include "bcftools.pysam.h" /* prob1.c -- mathematical utility functions. Copyright (C) 2010, 2011 Broad Institute. Copyright (C) 2012, 2013-2014, 2017 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "prob1.h" #define MC_MAX_EM_ITER 16 #define MC_EM_EPS 1e-5 #define MC_DEF_INDEL 0.15 void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x) { int i; for (i = 0; i < ma->M; ++i) ma->phi_indel[i] = ma->phi[i] * x; ma->phi_indel[ma->M] = 1. - ma->phi[ma->M] * x; } static void init_prior(int type, double theta, int M, double *phi) { int i; if (type == MC_PTYPE_COND2) { for (i = 0; i <= M; ++i) phi[i] = 2. * (i + 1) / (M + 1) / (M + 2); } else if (type == MC_PTYPE_FLAT) { for (i = 0; i <= M; ++i) phi[i] = 1. / (M + 1); } else { double sum; for (i = 0, sum = 0.; i < M; ++i) sum += (phi[i] = theta / (M - i)); phi[M] = 1. - sum; } } void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta) { init_prior(type, theta, ma->M, ma->phi); bcf_p1_indel_prior(ma, MC_DEF_INDEL); } void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta) { if (ma->n1 <= 0 || ma->n1 >= ma->M) return; init_prior(type, theta, 2*ma->n1, ma->phi1); init_prior(type, theta, 2*(ma->n - ma->n1), ma->phi2); } /* Initialise a bcf_p1aux_t */ bcf_p1aux_t *bcf_p1_init(int n_smpl, uint8_t *ploidy) { bcf_p1aux_t *ma; int i; ma = (bcf_p1aux_t*) calloc(1, sizeof(bcf_p1aux_t)); ma->n1 = -1; ma->n = n_smpl; ma->M = 2 * n_smpl; if (ploidy) { ma->ploidy = (uint8_t*) malloc(n_smpl); memcpy(ma->ploidy, ploidy, n_smpl); for (i = 0, ma->M = 0; i < n_smpl; ++i) ma->M += ploidy[i]; if (ma->M == 2 * n_smpl) { free(ma->ploidy); ma->ploidy = 0; } } ma->q2p = (double*) calloc(256, sizeof(double)); ma->pdg = (double*) calloc(3 * ma->n, sizeof(double)); ma->phi = (double*) calloc(ma->M + 1, sizeof(double)); ma->phi_indel = (double*) calloc(ma->M + 1, sizeof(double)); ma->phi1 = (double*) calloc(ma->M + 1, sizeof(double)); ma->phi2 = (double*) calloc(ma->M + 1, sizeof(double)); ma->z = (double*) calloc(ma->M + 1, sizeof(double)); ma->zswap = (double*) calloc(ma->M + 1, sizeof(double)); ma->z1 = (double*) calloc(ma->M + 1, sizeof(double)); // actually we do not need this large ma->z2 = (double*) calloc(ma->M + 1, sizeof(double)); ma->afs = (double*) calloc(ma->M + 1, sizeof(double)); ma->afs1 = (double*) calloc(ma->M + 1, sizeof(double)); ma->lf = (double*) calloc(ma->M + 1, sizeof(double)); for (i = 0; i < 256; ++i) ma->q2p[i] = pow(10., -i / 10.); for (i = 0; i <= ma->M; ++i) ma->lf[i] = lgamma(i + 1); bcf_p1_init_prior(ma, MC_PTYPE_FULL, 1e-3); // the simplest prior return ma; } int bcf_p1_get_M(bcf_p1aux_t *b) { return b->M; } int bcf_p1_set_n1(bcf_p1aux_t *b, int n1) { if (n1 == 0 || n1 >= b->n) return -1; if (b->M != b->n * 2) { fprintf(bcftools_stderr, "[%s] unable to set `n1' when there are haploid samples.\n", __func__); return -1; } b->n1 = n1; return 0; } void bcf_p1_destroy(bcf_p1aux_t *ma) { if (ma) { int k; free(ma->lf); if (ma->hg && ma->n1 > 0) { for (k = 0; k <= 2*ma->n1; ++k) free(ma->hg[k]); free(ma->hg); } free(ma->ploidy); free(ma->q2p); free(ma->pdg); free(ma->phi); free(ma->phi_indel); free(ma->phi1); free(ma->phi2); free(ma->z); free(ma->zswap); free(ma->z1); free(ma->z2); free(ma->afs); free(ma->afs1); free(ma); } } extern double kf_gammap(double s, double z); int test16(bcf1_t *b, anno16_t *a); /* Calculate P(D|g) */ static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma) { int i, j; long p_a[16], *p=p_a, tmp; if (b->n_allele > 16) p = (long*) malloc(b->n_allele * sizeof(long)); memset(p, 0, sizeof(long) * b->n_allele); // Set P(D|g) for each sample and sum phread likelihoods across all samples to create lk for (j = 0; j < ma->n; ++j) { // Fetch the PL array for the sample const int *pi = ma->PL + j * ma->PL_len; // Fetch the P(D|g) array for the sample double *pdg = ma->pdg + j * 3; pdg[0] = ma->q2p[pi[2]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]]; for (i = 0; i < b->n_allele; ++i) p[i] += (int)pi[(i+1)*(i+2)/2-1]; } for (i = 0; i < b->n_allele; ++i) p[i] = p[i]<<4 | i; for (i = 1; i < b->n_allele; ++i) // insertion sort for (j = i; j > 0 && p[j] < p[j-1]; --j) tmp = p[j], p[j] = p[j-1], p[j-1] = tmp; for (i = b->n_allele - 1; i >= 0; --i) if ((p[i]&0xf) == 0) break; if (p != p_a) free(p); return i; } /* f0 is freq of the ref allele */ int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k, int is_var) { double sum, g[3]; double max, f3[3], *pdg = ma->pdg + k * 3; int q, i, max_i, ploidy; /* determine ploidy */ ploidy = ma->ploidy? ma->ploidy[k] : 2; if (ploidy == 2) { /* given allele frequency we can determine how many of each * genotype we have by HWE p=1-q PP=p^2 PQ&QP=2*p*q QQ=q^2 */ f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0; } else { f3[0] = 1. - f0; f3[1] = 0; f3[2] = f0; } for (i = 0, sum = 0.; i < 3; ++i) sum += (g[i] = pdg[i] * f3[i]); /* normalise g and then determine max */ for (i = 0, max = -1., max_i = 0; i < 3; ++i) { g[i] /= sum; if (g[i] > max) max = g[i], max_i = i; } if ( !is_var ) { max_i = 2; max = g[2]; } // force 0/0 genotype if the site is non-variant max = 1. - max; if (max < 1e-308) max = 1e-308; q = (int)(-4.343 * log(max) + .499); if (q > 99) q = 99; return q<<2|max_i; } // If likelihoods fall below this they get squashed to 0 #define TINY 1e-20 static void mc_cal_y_core(bcf_p1aux_t *ma, int beg) { double *z[2], *tmp, *pdg; int _j, last_min, last_max; assert(beg == 0 || ma->M == ma->n*2); z[0] = ma->z; z[1] = ma->zswap; pdg = ma->pdg; memset(z[0], 0, sizeof(double) * (ma->M + 1)); memset(z[1], 0, sizeof(double) * (ma->M + 1)); z[0][0] = 1.; last_min = last_max = 0; ma->t = 0.; if (ma->M == ma->n * 2) { int M = 0; for (_j = beg; _j < ma->n; ++_j) { int k, j = _j - beg, _min = last_min, _max = last_max, M0; double p[3], sum; M0 = M; M += 2; // Fetch P(D|g) for this sample pdg = ma->pdg + _j * 3; p[0] = pdg[0]; p[1] = 2. * pdg[1]; p[2] = pdg[2]; for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.; for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.; _max += 2; if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k]; if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1]; for (k = _min < 2? 2 : _min; k <= _max; ++k) z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1] + k*(k-1)* p[2] * z[0][k-2]; for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k]; ma->t += log(sum / (M * (M - 1.))); for (k = _min; k <= _max; ++k) z[1][k] /= sum; if (_min >= 1) z[1][_min-1] = 0.; if (_min >= 2) z[1][_min-2] = 0.; // If we are not on the last sample if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.; if (_j == ma->n1 - 1) { // set pop1; ma->n1==-1 when unset ma->t1 = ma->t; memcpy(ma->z1, z[1], sizeof(double) * (ma->n1 * 2 + 1)); } tmp = z[0]; z[0] = z[1]; z[1] = tmp; last_min = _min; last_max = _max; } //for (_j = 0; _j < last_min; ++_j) z[0][_j] = 0.; // TODO: are these necessary? //for (_j = last_max + 1; _j < ma->M; ++_j) z[0][_j] = 0.; } else { // this block is very similar to the block above; these two might be merged in future int j, M = 0; for (j = 0; j < ma->n; ++j) { int k, M0, _min = last_min, _max = last_max; double p[3], sum; // Fetch P(D|g) for this sample pdg = ma->pdg + j * 3; for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.; for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.; M0 = M; M += ma->ploidy[j]; if (ma->ploidy[j] == 1) { p[0] = pdg[0]; p[1] = pdg[2]; _max++; if (_min == 0) k = 0, z[1][k] = (M0+1-k) * p[0] * z[0][k]; for (k = _min < 1? 1 : _min; k <= _max; ++k) z[1][k] = (M0+1-k) * p[0] * z[0][k] + k * p[1] * z[0][k-1]; for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k]; ma->t += log(sum / M); for (k = _min; k <= _max; ++k) z[1][k] /= sum; if (_min >= 1) z[1][_min-1] = 0.; // If we are not on the last sample if (j < ma->n - 1) z[1][_max+1] = 0.; } else if (ma->ploidy[j] == 2) { p[0] = pdg[0]; p[1] = 2 * pdg[1]; p[2] = pdg[2]; _max += 2; if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k]; if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1]; for (k = _min < 2? 2 : _min; k <= _max; ++k) z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1] + k*(k-1)* p[2] * z[0][k-2]; for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k]; ma->t += log(sum / (M * (M - 1.))); for (k = _min; k <= _max; ++k) z[1][k] /= sum; if (_min >= 1) z[1][_min-1] = 0.; if (_min >= 2) z[1][_min-2] = 0.; // If we are not on the last sample if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.; } tmp = z[0]; z[0] = z[1]; z[1] = tmp; last_min = _min; last_max = _max; } } if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1)); } static void mc_cal_y(bcf_p1aux_t *ma) { if (ma->n1 > 0 && ma->n1 < ma->n && ma->M == ma->n * 2) { // NB: ma->n1 is ineffective when there are haploid samples int k; long double x; memset(ma->z1, 0, sizeof(double) * (2 * ma->n1 + 1)); memset(ma->z2, 0, sizeof(double) * (2 * (ma->n - ma->n1) + 1)); ma->t1 = ma->t2 = 0.; mc_cal_y_core(ma, ma->n1); ma->t2 = ma->t; memcpy(ma->z2, ma->z, sizeof(double) * (2 * (ma->n - ma->n1) + 1)); mc_cal_y_core(ma, 0); // rescale z x = expl(ma->t - (ma->t1 + ma->t2)); for (k = 0; k <= ma->M; ++k) ma->z[k] *= x; } else mc_cal_y_core(ma, 0); } #define CONTRAST_TINY 1e-30 extern double kf_gammaq(double s, double z); // incomplete gamma function for chi^2 test static inline double chi2_test(int a, int b, int c, int d) { double x, z; x = (double)(a+b) * (c+d) * (b+d) * (a+c); if (x == 0.) return 1; z = a * d - b * c; return kf_gammaq(.5, .5 * z * z * (a+b+c+d) / x); } // chi2=(a+b+c+d)(ad-bc)^2/[(a+b)(c+d)(a+c)(b+d)] static inline double contrast2_aux(const bcf_p1aux_t *p1, double sum, int k1, int k2, double x[3]) { double p = p1->phi[k1+k2] * p1->z1[k1] * p1->z2[k2] / sum * p1->hg[k1][k2]; int n1 = p1->n1, n2 = p1->n - p1->n1; if (p < CONTRAST_TINY) return -1; if (.5*k1/n1 < .5*k2/n2) x[1] += p; else if (.5*k1/n1 > .5*k2/n2) x[2] += p; else x[0] += p; return p * chi2_test(k1, k2, (n1<<1) - k1, (n2<<1) - k2); } static double contrast2(bcf_p1aux_t *p1, double ret[3]) { int k, k1, k2, k10, k20, n1, n2; double sum; // get n1 and n2 n1 = p1->n1; n2 = p1->n - p1->n1; if (n1 <= 0 || n2 <= 0) return 0.; if (p1->hg == 0) { // initialize the hypergeometric distribution /* NB: the hg matrix may take a lot of memory when there are many samples. There is a way to avoid precomputing this matrix, but it is slower and quite intricate. The following computation in this block can be accelerated with a similar strategy, but perhaps this is not a serious concern for now. */ double tmp = lgamma(2*(n1+n2)+1) - (lgamma(2*n1+1) + lgamma(2*n2+1)); p1->hg = (double**) calloc(2*n1+1, sizeof(double*)); for (k1 = 0; k1 <= 2*n1; ++k1) { p1->hg[k1] = (double*)calloc(2*n2+1, sizeof(double)); for (k2 = 0; k2 <= 2*n2; ++k2) p1->hg[k1][k2] = exp(lgamma(k1+k2+1) + lgamma(p1->M-k1-k2+1) - (lgamma(k1+1) + lgamma(k2+1) + lgamma(2*n1-k1+1) + lgamma(2*n2-k2+1) + tmp)); } } { // compute long double suml = 0; for (k = 0; k <= p1->M; ++k) suml += p1->phi[k] * p1->z[k]; sum = suml; } { // get the max k1 and k2 double max; int max_k; for (k = 0, max = 0, max_k = -1; k <= 2*n1; ++k) { double x = p1->phi1[k] * p1->z1[k]; if (x > max) max = x, max_k = k; } k10 = max_k; for (k = 0, max = 0, max_k = -1; k <= 2*n2; ++k) { double x = p1->phi2[k] * p1->z2[k]; if (x > max) max = x, max_k = k; } k20 = max_k; } { // We can do the following with one nested loop, but that is an O(N^2) thing. The following code block is much faster for large N. double x[3], y; long double z = 0., L[2]; x[0] = x[1] = x[2] = 0; L[0] = L[1] = 0; for (k1 = k10; k1 >= 0; --k1) { for (k2 = k20; k2 >= 0; --k2) { if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break; else z += y; } for (k2 = k20 + 1; k2 <= 2*n2; ++k2) { if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break; else z += y; } } ret[0] = x[0]; ret[1] = x[1]; ret[2] = x[2]; x[0] = x[1] = x[2] = 0; for (k1 = k10 + 1; k1 <= 2*n1; ++k1) { for (k2 = k20; k2 >= 0; --k2) { if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break; else z += y; } for (k2 = k20 + 1; k2 <= 2*n2; ++k2) { if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break; else z += y; } } ret[0] += x[0]; ret[1] += x[1]; ret[2] += x[2]; if (ret[0] + ret[1] + ret[2] < 0.95) { // in case of bad things happened ret[0] = ret[1] = ret[2] = 0; L[0] = L[1] = 0; for (k1 = 0, z = 0.; k1 <= 2*n1; ++k1) for (k2 = 0; k2 <= 2*n2; ++k2) if ((y = contrast2_aux(p1, sum, k1, k2, ret)) >= 0) z += y; if (ret[0] + ret[1] + ret[2] < 0.95) // It seems that this may be caused by floating point errors. I do not really understand why... z = 1.0, ret[0] = ret[1] = ret[2] = 1./3; } return (double)z; } } static double mc_cal_afs(bcf_p1aux_t *ma, double *p_ref_folded, double *p_var_folded) { int k; long double sum = 0., sum2; double *phi = ma->is_indel? ma->phi_indel : ma->phi; memset(ma->afs1, 0, sizeof(double) * (ma->M + 1)); mc_cal_y(ma); // compute AFS // MP15: is this using equation 20 from doi:10.1093/bioinformatics/btr509? for (k = 0, sum = 0.; k <= ma->M; ++k) sum += (long double)phi[k] * ma->z[k]; for (k = 0; k <= ma->M; ++k) { ma->afs1[k] = phi[k] * ma->z[k] / sum; if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return -1.; } // compute folded variant probability for (k = 0, sum = 0.; k <= ma->M; ++k) sum += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k]; for (k = 1, sum2 = 0.; k < ma->M; ++k) sum2 += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k]; *p_var_folded = sum2 / sum; *p_ref_folded = (phi[k] + phi[ma->M - k]) / 2. * (ma->z[ma->M] + ma->z[0]) / sum; // the expected frequency for (k = 0, sum = 0.; k <= ma->M; ++k) { ma->afs[k] += ma->afs1[k]; sum += k * ma->afs1[k]; } return sum / ma->M; } int bcf_p1_cal(call_t *call, bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst) { int i, k; long double sum = 0.; ma->is_indel = bcf_is_snp(b) ? 0 : 1; rst->perm_rank = -1; ma->PL = call->PLs; ma->PL_len = call->nPLs / b->n_sample; if (b->n_allele < 2) return -1; // FIXME: find a better solution rst->rank0 = cal_pdg(b, ma); rst->f_exp = mc_cal_afs(ma, &rst->p_ref_folded, &rst->p_var_folded); rst->p_ref = ma->afs1[ma->M]; for (k = 0, sum = 0.; k < ma->M; ++k) sum += ma->afs1[k]; rst->p_var = (double)sum; { // compute the allele count double max = -1; rst->ac = -1; for (k = 0; k <= ma->M; ++k) if (max < ma->z[k]) max = ma->z[k], rst->ac = k; rst->ac = ma->M - rst->ac; } // calculate f_flat and f_em for (k = 0, sum = 0.; k <= ma->M; ++k) sum += (long double)ma->z[k]; rst->f_flat = 0.; for (k = 0; k <= ma->M; ++k) { double p = ma->z[k] / sum; rst->f_flat += k * p; } rst->f_flat /= ma->M; { // estimate equal-tail credible interval (95% level) int l, h; double p; for (i = 0, p = 0.; i <= ma->M; ++i) if (p + ma->afs1[i] > 0.025) break; else p += ma->afs1[i]; l = i; for (i = ma->M, p = 0.; i >= 0; --i) if (p + ma->afs1[i] > 0.025) break; else p += ma->afs1[i]; h = i; rst->cil = (double)(ma->M - h) / ma->M; rst->cih = (double)(ma->M - l) / ma->M; } if (ma->n1 > 0) { // compute LRT double max0, max1, max2; for (k = 0, max0 = -1; k <= ma->M; ++k) if (max0 < ma->z[k]) max0 = ma->z[k]; for (k = 0, max1 = -1; k <= ma->n1 * 2; ++k) if (max1 < ma->z1[k]) max1 = ma->z1[k]; for (k = 0, max2 = -1; k <= ma->M - ma->n1 * 2; ++k) if (max2 < ma->z2[k]) max2 = ma->z2[k]; rst->lrt = log(max1 * max2 / max0); rst->lrt = rst->lrt < 0? 1 : kf_gammaq(.5, rst->lrt); } else rst->lrt = -1.0; rst->cmp[0] = rst->cmp[1] = rst->cmp[2] = rst->p_chi2 = -1.0; if (do_contrast && rst->p_var > 0.5) // skip contrast2() if the locus is a strong non-variant rst->p_chi2 = contrast2(ma, rst->cmp); return 0; } void bcf_p1_dump_afs(bcf_p1aux_t *ma) { int k; fprintf(bcftools_stderr, "[afs]"); for (k = 0; k <= ma->M; ++k) fprintf(bcftools_stderr, " %d:%.3lf", k, ma->afs[ma->M - k]); fprintf(bcftools_stderr, "\n"); memset(ma->afs, 0, sizeof(double) * (ma->M + 1)); } pysam-0.23.0/bcftools/prob1.h000066400000000000000000000067441475062545500157640ustar00rootroot00000000000000/* prob1.h -- mathematical utility functions. Copyright (C) 2010, 2011 Broad Institute. Copyright (C) 2012, 2013-2014 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef BCF_PROB1_H #define BCF_PROB1_H #include #include "call.h" typedef struct { int n; // Number of samples int M; // Total number of chromosomes across all samples (n*2 if all samples are diploid) int n1; int is_indel; uint8_t *ploidy; // haploid or diploid ONLY double *q2p, *pdg; // q2p maps from phread scaled to real likelihood, pdg -> P(D|g) double *phi; // Probability of seeing k reference alleles double *phi_indel; double *z, *zswap; // aux for afs double *z1, *z2, *phi1, *phi2; // only calculated when n1 is set double **hg; // hypergeometric distribution double *lf; // log factorial double t, t1, t2; double *afs, *afs1; // afs: accumulative allele frequency spectrum (AFS); afs1: site posterior distribution const int *PL; // point to PL int PL_len; int cons_llr; // pair and trio calling int64_t cons_gt; } bcf_p1aux_t; typedef struct { int rank0, perm_rank; // NB: perm_rank is always set to -1 by bcf_p1_cal() int ac; // ML alternative allele count double f_exp, f_flat, p_ref_folded, p_ref, p_var_folded, p_var; double cil, cih; double cmp[3], p_chi2, lrt; // used by contrast2() } bcf_p1rst_t; typedef struct { double p[4]; double edb, mqb, bqb; // end distance bias, mapQ bias, baseQ bias int mq, depth, is_tested, d[4]; } anno16_t; #define MC_PTYPE_FULL 1 #define MC_PTYPE_COND2 2 #define MC_PTYPE_FLAT 3 #ifdef __cplusplus extern "C" { #endif bcf_p1aux_t *bcf_p1_init(int n_smpl, uint8_t *ploidy); void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta); void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta); void bcf_p1_destroy(bcf_p1aux_t *ma); void bcf_p1_set_ploidy(bcf1_t *b, bcf_p1aux_t *ma); int bcf_p1_cal(call_t *call, bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst); int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k, int is_var); void bcf_p1_dump_afs(bcf_p1aux_t *ma); int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn); int bcf_p1_set_n1(bcf_p1aux_t *b, int n1); void bcf_p1_set_folded(bcf_p1aux_t *p1a); // only effective when set_n1() is not called int bcf_em1(call_t *call, const bcf1_t *b, int n1, int flag, double x[10]); #ifdef __cplusplus } #endif #endif pysam-0.23.0/bcftools/rbuf.h000066400000000000000000000165701475062545500156750ustar00rootroot00000000000000/* rbuf.h -- round buffers. Copyright (C) 2013-2014, 2017 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef __RBUF_H__ #define __RBUF_H__ #include typedef struct { int m,n,f; // m: allocated size, n: number of elements in the buffer, f: first element } rbuf_t; /** * rbuf_init() - initialize round buffer * @rbuf: the rbuf_t holder * @size: the maximum number of elements * */ static inline void rbuf_init(rbuf_t *rbuf, int size) { rbuf->m = size; rbuf->n = rbuf->f = 0; } /** * rbuf_kth() - get index of the k-th element of the round buffer * @rbuf: the rbuf_t holder * @k: 0-based index. If negative, return k-th element from the end, 1-based */ static inline int rbuf_kth(rbuf_t *rbuf, int k) { if ( k >= rbuf->n ) return -1; if ( k < 0 ) { k = rbuf->n + k; if ( k < 0 ) return -1; } int i = k + rbuf->f; if ( i >= rbuf->m ) i -= rbuf->m; return i; } /** * rbuf_last() - get index of the last element of the round buffer * @rbuf: the rbuf_t holder */ #define rbuf_last(rbuf) rbuf_kth(rbuf, -1) /** * rbuf_l2ridx() - get 0-based rbuf index which corresponds to i-th linear index * @rbuf: the rbuf_t holder * @idx: 0-based linear index * * Returns 0-based circular index or -1 if out of bounds */ static inline int rbuf_l2ridx(rbuf_t *rbuf, int idx) { if ( idx < 0 || idx >= rbuf->n ) return -1; if ( idx >= rbuf->f ) { int i = idx - rbuf->f; if ( i >= rbuf->n ) return -1; return i; } int i = rbuf->m - rbuf->f + idx; if ( i >= rbuf->n ) return -1; return i; } /** * rbuf_next() - get index of the next element in the round buffer * @rbuf: the rbuf_t holder * @i: pointer to the last rbuf index. Set to -1 before the first call. * * Sets i to the next position in the buffer. The return value indicates if * the position points to a valid element (1) or if there are no more elements * after *i (0). When the end is reached, *i is set to the first element in the * buffer. */ static inline int rbuf_next(rbuf_t *rbuf, int *i) { if ( !rbuf->n ) return 0; if ( *i==-1 ) { *i = rbuf->f; return 1; } int n = (rbuf->f <= *i) ? *i - rbuf->f + 1 : *i + rbuf->m - rbuf->f + 1; if ( ++(*i) >= rbuf->m ) *i = 0; if ( n < rbuf->n ) return 1; *i = rbuf->f; return 0; } /** * rbuf_prev() - get index of the previous element in the round buffer * @rbuf: the rbuf_t holder * @i: pointer to the last rbuf index. Set to -1 before the first call. * * Sets i to the previous position in the buffer. The return value indicates if * the position points to a valid element (1) or if there are no more elements * before *i (0). */ static inline int rbuf_prev(rbuf_t *rbuf, int *i) { if ( !rbuf->n || *i==rbuf->f ) return 0; if ( *i==-1 ) { *i = rbuf_last(rbuf); return 1; } if ( --(*i) < 0 ) *i = rbuf->m - 1; return 1; } /** * rbuf_prepend() - register new element at the start of the round buffer * @rbuf: the rbuf_t holder * * Returns index of the newly inserted element. */ static inline int rbuf_prepend(rbuf_t *rbuf) { if ( rbuf->n < rbuf->m ) rbuf->n++; rbuf->f = rbuf->f > 0 ? rbuf->f - 1 : rbuf->m - 1; return rbuf->f; } /** * rbuf_append() - register new element at the end of the round buffer * @rbuf: the rbuf_t holder * * Returns index of the newly inserted element. */ static inline int rbuf_append(rbuf_t *rbuf) { if ( rbuf->n < rbuf->m ) { rbuf->n++; int i = rbuf->f + rbuf->n; return i <= rbuf->m ? i - 1 : i - rbuf->m - 1; } rbuf->f++; if ( rbuf->f >= rbuf->m ) { rbuf->f = 0; return rbuf->m - 1; } return rbuf->f - 1; } /** * rbuf_shift() - removes first element from the buffer * @rbuf: the rbuf_t holder * * Returns index of the removed element. */ static inline int rbuf_shift(rbuf_t *rbuf) { if ( !rbuf->n ) return -1; int ret = rbuf->f; rbuf->f++; if ( rbuf->f >= rbuf->m ) rbuf->f = 0; rbuf->n--; return ret; } /** * rbuf_shift_n() - removes first n elements from the buffer * @rbuf: the rbuf_t holder * @n: number of elements to remove */ static inline void rbuf_shift_n(rbuf_t *rbuf, int n) { if ( n >= rbuf->n ) { rbuf->n = rbuf->f = 0; return; } rbuf->n -= n; rbuf->f += n; if ( rbuf->f >= rbuf->m ) rbuf->f -= rbuf->m; } /** * rbuf_expand0() - expand round buffer and set the newly allocated elements to 0 * @rbuf: the rbuf holder * @type_t: data type * @n: requested number of elements * @data: data array to be realloced * * Note: The new array is linearized and leaves the rbuf.f offset untouched, * thus the size of the new buffer is determined by the current position. */ #define rbuf_expand0(rbuf,type_t,n,data) \ { \ if ( n > (rbuf)->m ) \ { \ int m = n + (rbuf)->f; \ m--, m|=m>>1, m|=m>>2, m|=m>>4, m|=m>>8, m|=m>>16, m++; /* kroundup32 */ \ data = (type_t*) realloc(data, sizeof(type_t)*m); \ type_t *ptr = data; \ memset(ptr+(rbuf)->m,0,sizeof(type_t)*(m-(rbuf)->m)); \ if ( (rbuf)->f ) \ { \ memcpy(ptr+(rbuf)->m,ptr,sizeof(type_t)*(rbuf)->f); \ memset(ptr,0,sizeof(type_t)*(rbuf)->f); \ } \ (rbuf)->m = m; \ } \ } /** * rbuf_remove_kth() - remove k-th rbuf element (0-based) and memmove the data block * @rbuf: the rbuf holder * @type_t: data type * @k: k-th element to remove * @data: data array to be modified */ #define rbuf_remove_kth(rbuf, type_t, kth, data) \ { \ int k = rbuf_kth(rbuf, kth); \ if ( k < (rbuf)->f ) /* shrink from back */ \ { \ int l = rbuf_kth(rbuf, -1); \ if ( k < l ) \ { \ type_t tmp = (data)[k]; \ memmove(data+k, data+k+1, (l - k)*sizeof(type_t)); \ (data)[l] = tmp; \ } \ (rbuf)->n--; \ } \ else /* shrink from front */ \ { \ if ( k > (rbuf)->f ) \ { \ type_t tmp = (data)[k]; \ memmove(&data[(rbuf)->f+1], &data[(rbuf)->f], (k - (rbuf)->f)*sizeof(type_t)); \ (data)[(rbuf)->f] = tmp; \ } \ (rbuf)->f++; \ (rbuf)->n--; \ if ( (rbuf)->f == (rbuf)->m ) (rbuf)->f = 0; \ } \ } #endif pysam-0.23.0/bcftools/read_consensus.c000066400000000000000000000713271475062545500177460ustar00rootroot00000000000000/* read_consensus.c -- create and maintain consensus of reads Copyright (C) 2022 Genome Research Ltd. Author: pd3@sanger Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include "bcftools.h" #include "read_consensus.h" #include "cigar_state.h" #include "kheap.h" // Frequency arrays for each variant type #define NI 10 // number of alternative insertion sequences at one position in a single sample typedef struct { char *nt16_seq[NI]; int len[NI]; int freq[NI]; } ins_freq_t; typedef struct { int len[NI]; int freq[NI]; } del_freq_t; #define BF_DEL 5 typedef struct { int base[6]; // frequencies of A,C,G,T,N,deletion } base_freq_t; // Candidate variants for each interesting position to build consensus haplotypes enum variant_type { snv, ins, del, done }; typedef struct { enum variant_type vtype; hts_pos_t pos; // variant position (reference sequence coordinates), indels follow VCF convention int idx; // temporary 0-based index to rcns.cvar int which, // base/ins/del in rcns.[base|ins|del]_freq array depth; // coverage at the position float af, af_dev; // variant allele frequency (just for debugging printout) and absolute af deviation from 0.5 } candidate_var_t; static inline int cvar_not_preferred(candidate_var_t *a, candidate_var_t *b) { if ( a->af_dev == b->af_dev ) return a->depth < b->depth ? 1 : 0; return a->af_dev > b->af_dev ? 1 : 0; } KHEAP_INIT(cvh, candidate_var_t, cvar_not_preferred); typedef khp_cvh_t cvar_heap_t; #define MAX_NCVAR 8 // This results in alloc() of 2^MAX_NCVAR possible haplotypes #define NHAP (1<mfreq; i++) { ins_freq_t *ifrq = &rcns->ins_freq[i]; for (j=0; jnt16_seq[j]; j++) free(ifrq->nt16_seq[j]); } for (i=0; i<2; i++) free(rcns->cns[i].seq); free(rcns->ins_freq); free(rcns->del_freq); free(rcns->base_freq); free(rcns->stmp); khp_destroy(cvh,rcns->cv_heap); free(rcns); } static int init_arrays(read_cns_t *rcns) { int i,j,n = rcns->end - rcns->beg + 1; if ( n > rcns->mfreq ) { ins_freq_t *ifrq = (ins_freq_t*) realloc(rcns->ins_freq,sizeof(*rcns->ins_freq)*n); if ( !ifrq ) return -1; rcns->ins_freq = ifrq; memset(ifrq+rcns->mfreq,0,sizeof(*rcns->ins_freq)*(n-rcns->mfreq)); del_freq_t *dfrq = (del_freq_t*) realloc(rcns->del_freq,sizeof(*rcns->del_freq)*n); if ( !dfrq ) return -1; rcns->del_freq = dfrq; memset(dfrq+rcns->mfreq,0,sizeof(*rcns->del_freq)*(n-rcns->mfreq)); base_freq_t *bfrq = (base_freq_t*) realloc(rcns->base_freq,sizeof(*rcns->base_freq)*n); if ( !bfrq ) return -1; rcns->base_freq = bfrq; memset(bfrq+rcns->mfreq,0,sizeof(*rcns->base_freq)*(n-rcns->mfreq)); rcns->mfreq = n; } memset(rcns->base_freq,0,sizeof(*rcns->base_freq)*n); memset(rcns->del_freq,0,sizeof(*rcns->del_freq)*n); for (i=0; iins_freq[i]; for (j=0; jnt16_seq[j]; j++) free(ifrq->nt16_seq[j]); } memset(rcns->ins_freq,0,sizeof(*rcns->ins_freq)*n); return 0; } int rcns_reset(read_cns_t *rcns, hts_pos_t pos, hts_pos_t beg, hts_pos_t end) { rcns->band = 0; rcns->pos = pos; rcns->beg = beg; rcns->end = end; int i; for (i=0; i<2; i++) rcns->cns[i].nseq = rcns->cns[i].ipos = 0; // this should not be necessary if the caller did run all steps while (rcns->cv_heap->ndat) khp_delete(cvh, rcns->cv_heap); return init_arrays(rcns); } static inline void add_base(read_cns_t *rcns, int ref_pos, int nt16) { int i = ref_pos - rcns->beg; rcns->base_freq[i].base[seq_nt16_int[nt16]]++; } static void add_ins(read_cns_t *rcns, int ref_pos, int seq_pos, uint8_t *raw_seq, int len) { int i = ref_pos - rcns->beg; ins_freq_t *ifrq = &rcns->ins_freq[i]; char *str; if ( rcns->mstmp < len ) { str = realloc(rcns->stmp,len*sizeof(*str)); if ( !str ) return; rcns->mstmp = len; rcns->stmp = str; } else str = rcns->stmp; for (i=0; int16_seq[i]; i++) if ( ifrq->len[i]==len && !memcmp(ifrq->nt16_seq[i],str,len) ) break; if ( i>=NI ) return; // too many choices, typically homopolymers in long reads; discard if ( !ifrq->nt16_seq[i] ) // new insertion { if ( !(ifrq->nt16_seq[i]=malloc(len)) ) return; memcpy(ifrq->nt16_seq[i], str, len); ifrq->len[i] = len; } ifrq->freq[i]++; } static void add_del(read_cns_t *rcns, int ref_pos, int len) { int i = ref_pos - rcns->beg; int j,n = rcns->end - rcns->beg + 1; if ( i + len + 1 < n ) n = i + len + 1; for (j=i+1; jbase_freq[j].base[BF_DEL]++; del_freq_t *dfrq = &rcns->del_freq[i]; for (i=0; ilen[i]; i++) if ( dfrq->len[i]==len ) break; if ( i>=NI ) return; // too many choices, typically homopolymers in long reads; discard if ( !dfrq->len[i] ) dfrq->len[i] = len; // new deletion dfrq->freq[i]++; } read_cns_t *rcns_init(hts_pos_t pos, hts_pos_t beg, hts_pos_t end) { read_cns_t *rcns = (read_cns_t*) calloc(1,sizeof(read_cns_t)); rcns->pos = pos; rcns->beg = beg; rcns->end = end; rcns->cv_heap = khp_init(cvh); if ( init_arrays(rcns)!=0 ) { rcns_destroy(rcns); return NULL; } return rcns; } int rcns_set_reads(read_cns_t *rcns, bam_pileup1_t *plp, int nplp) { // save the reads for phasing, this can be called multiple times rcns->plp = plp; rcns->nplp = nplp; // fill consensus arrays int i,j,k, local_band_max = 0; // maximum absolute deviation from diagonal for (i=0; ib; int x = b->core.pos; // ref coordinate int y = 0; // seq coordinate uint32_t *cigar = bam_get_cigar(b); uint8_t *seq = bam_get_seq(b); int local_band = 0; // current deviation from diagonal for (k = 0; k < b->core.n_cigar; ++k) { int op = cigar[k] & BAM_CIGAR_MASK; int len = cigar[k] >> BAM_CIGAR_SHIFT; if ( op==BAM_CSOFT_CLIP ) y += len; else if ( op==BAM_CMATCH || op==BAM_CEQUAL || op==BAM_CDIFF ) { if ( xend && x+len>rcns->beg ) { int j_beg = rcns->beg > x ? rcns->beg - x : 0; // how many bases to skip in the ref and qry int j_end = rcns->end < x + len - 1 ? rcns->end - x : len - 1; x += j_beg; y += j_beg; for (j=j_beg; j<=j_end; j++, x++, y++) add_base(rcns,x,bam_seqi(seq,y)); } else { x += len; y += len; } } else if ( op==BAM_CINS ) { if ( x>rcns->beg && xend ) { local_band += p->indel; add_ins(rcns,x-1,y,seq,len); // x-1: one base before as in VCF } y += len; } else if ( op==BAM_CDEL || op==BAM_CREF_SKIP ) /* note: unsure about BAM_CREF_SKIP, don't have data to test */ { if ( x>rcns->beg && x+len-1<=rcns->end ) { local_band += -p->indel; add_del(rcns,x-1,len); // x-1: one base before as in VCF } x += len; } else if ( op==BAM_CHARD_CLIP ) continue; else error("rcns_set_reads todo: unknown cigar operator %d\n",op); if ( local_band_max < local_band ) local_band_max = local_band; } // Track the biggest deviation +/- from diagonal, used in BAQ alignment step. if ( rcns->band < local_band_max ) rcns->band = local_band_max; } return 0; } #if DEBUG_RCNS static void debug_print_base_freqs(read_cns_t *rcns, const char *ref) { int i,j,k,n = rcns->end - rcns->beg + 1; fprintf(stderr,"beg,end,pos=%d %d %d\n",(int)rcns->beg,(int)rcns->end,(int)rcns->pos); base_freq_t *bfreq = rcns->base_freq; ins_freq_t *ifreq = rcns->ins_freq; del_freq_t *dfreq = rcns->del_freq; for (i=0; ibeg+i+1,ref[i]); for (j=0; j<6; j++) fprintf(stderr,"\t%d%s",bfreq[i].base[j],ref[i]=="ACGTNi"[j]?"*":""); fprintf(stderr,"\t"); for (j=0; jncvar; i++) { candidate_var_t *var = &rcns->cvar[i]; fprintf(stderr,"\tvar%d pos=%"PRIhts_pos" idx=%d vtype=%s which=%d depth=%d af=%f af_dev=%f\n", i,var->pos+1,var->idx,vtype2string(var->vtype),var->which,var->depth,var->af,var->af_dev); } } static void debug_print_haplotype_frequency_spectrum(read_cns_t *rcns) { int i,j; fprintf(stderr,"Haplotype frequencies (bits from left correspond to var0,1,..):\n"); for (i=0; ihap_freq[i] ) continue; fprintf(stderr,"\t%d: ",i); for (j=0; jncvar; j++) fprintf(stderr,"%d", i&(1<hap_freq[i]); } } static void debug_print_consensus(read_cns_t *rcns, const char *ref) { int i,j,n = rcns->end - rcns->beg + 1; fprintf(stderr,"ref: "); for (i=0; icns[i].nseq ) break; fprintf(stderr,"Consensus%d: ",i); for (j=0; j<=rcns->cns[i].ipos; j++) fprintf(stderr,"%c","ACGTN"[(int)rcns->cns[i].seq[j]]); fprintf(stderr,"#"); for (; jcns[i].nseq; j++) fprintf(stderr,"%c","ACGTN"[(int)rcns->cns[i].seq[j]]); fprintf(stderr,"\n"); } } #else #define debug_print_base_freqs(rcns,ref) #define debug_print_candidate_variants(rcns) #define debug_print_haplotype_frequency_spectrum(rcns) #define debug_print_consensus(rcns,ref) #endif static int cvar_pos_cmp(const void *aptr, const void *bptr) { candidate_var_t *a = (candidate_var_t*)aptr; candidate_var_t *b = (candidate_var_t*)bptr; if ( a->pos < b->pos ) return -1; if ( a->pos > b->pos ) return 1; if ( a->vtype < b->vtype ) return -1; if ( a->vtype > b->vtype ) return 1; if ( a->which < b->which ) return -1; if ( a->which > b->which ) return 1; return 0; } static void register_variant(read_cns_t *rcns, enum variant_type vtype, int cns_pos, int which, int depth, float freq) { cvar_heap_t *cv_heap = rcns->cv_heap; if ( vtype==done ) { rcns->ncvar = 0; while (cv_heap->ndat) { rcns->cvar[rcns->ncvar++] = cv_heap->dat[0]; khp_delete(cvh,cv_heap); } // sort the variants by pos,type,which to make determination of haplotypes from reads faster if ( rcns->ncvar ) qsort(rcns->cvar, rcns->ncvar, sizeof(*rcns->cvar), cvar_pos_cmp); return; } candidate_var_t var; var.pos = cns_pos + rcns->beg; var.which = which; var.vtype = vtype; var.depth = depth; var.af_dev = fabs(0.5-freq); var.af = freq; int free_slot; // keep the number of variants small, maximum MAX_NCVAR if ( rcns->ncvar==MAX_NCVAR ) { if ( cvar_not_preferred(&var,&cv_heap->dat[0]) ) return; // no need to add, the new variant is worse than the heap's worst one free_slot = cv_heap->dat[0].idx; khp_delete(cvh,cv_heap); } else free_slot = rcns->ncvar++; var.idx = free_slot; rcns->cvar[free_slot] = var; khp_insert(cvh,cv_heap,&var); } // Identify candidate variant positions. (Note that homozygous variants are not considered // as those will be added trivially by taking the consensus base.) The detection limit is // for now hard-wired. This has only indirect effect on sensitivity, will just not contribute // to the consensus template when realigning. static int select_candidate_variants(read_cns_t *rcns, const char *ref) { const float af_th = 0.1; int i,j, n = rcns->end - rcns->beg + 1; int max_ins_len = 0; // maximum total length of all insertions applied to allocate big enough buffers base_freq_t *bfreq = rcns->base_freq; ins_freq_t *ifreq = rcns->ins_freq; del_freq_t *dfreq = rcns->del_freq; for (i=0; ipos - rcns->beg ) continue; // creating consensus from everything but the variants at the current position int dp = 0; for (j=0; j<4; j++) dp += bfreq[i].base[j]; for (j=0; jaf_th && af<(1-af_th) ) register_variant(rcns,snv,i,j,dp,af); } for (j=0; jaf_th && af<(1-af_th) ) register_variant(rcns,del,i,j,dp,af); } for (j=0; jaf_th && af<(1-af_th) ) register_variant(rcns,ins,i,j,dp,af); } } register_variant(rcns,done,0,0,0,0); // finalize // Reallocate buffers if ( rcns->mcns < n + max_ins_len ) { n += max_ins_len; for (i=0; i<2; i++) { char *seq = (char*) realloc(rcns->cns[i].seq,sizeof(char)*n); if ( !seq ) return -1; rcns->cns[i].seq = seq; } rcns->mcns = n; } // Find the longest deletion at the query position i = rcns->pos - rcns->beg; rcns->max_del = 0; for (j=0; jmax_del < dfreq[i].len[j] ) rcns->max_del = dfreq[i].len[j]; } return 0; } static int create_haplotype_frequency_spectrum(read_cns_t *rcns) { memset(rcns->hap_freq,0,sizeof(rcns->hap_freq)); int i; for (i=0; inplp; i++) // for each read... { const bam_pileup1_t *p = rcns->plp + i; cigar_state_t cigar; cstate_init(&cigar,p->b); int j,k,hap = 0; for (j=0; jncvar; j++) { candidate_var_t *cvar = &rcns->cvar[j]; if ( cvar->vtype==snv ) { int iseq = cstate_seek_op_fwd(&cigar, cvar->pos, BAM_CMATCH, NULL); if ( iseq==-2 ) break; if ( iseq==-1 ) continue; int nt16 = bam_seqi(cigar.seq, iseq); if ( seq_nt16_int[nt16]==cvar->which ) hap |= 1<vtype==ins ) { int len; ins_freq_t *ifrq = &rcns->ins_freq[cvar->pos - rcns->beg]; int iseq = cstate_seek_op_fwd(&cigar, cvar->pos+1, BAM_CINS, &len); if ( iseq==-2 ) break; if ( iseq==-1 ) continue; if ( len!=ifrq->len[cvar->which] ) continue; for (k=0; klen[cvar->which]; k++) if ( bam_seqi(cigar.seq,iseq+k)!=ifrq->nt16_seq[cvar->which][k] ) break; if ( k==ifrq->len[cvar->which] ) hap |= 1<vtype==del ) { int len; del_freq_t *dfrq = &rcns->del_freq[cvar->pos - rcns->beg]; int ret = cstate_seek_op_fwd(&cigar, cvar->pos+1, BAM_CDEL, &len); if ( ret==-2 ) break; if ( ret==-1 ) continue; if ( len!=dfrq->len[cvar->which] ) continue; hap |= 1<hap_freq[hap]++; } return 0; } typedef struct { int haplotype, count; } ii_t; static int ii_cmp(const void *a, const void *b) { if ( ((ii_t*)a)->count > ((ii_t*)b)->count ) return -1; if ( ((ii_t*)a)->count < ((ii_t*)b)->count ) return 1; return 0; } // Select two most common haplotypes trying to account for 1bp errors. Haplotypes // are represented as 8-bit numbers, each bit corresponds to one candidate variant. static int correct_haplotype_errors(read_cns_t *rcns) { int i,j, tot = 0; ii_t freq[NHAP]; for (i=0; ihap_freq[i]; tot += rcns->hap_freq[i]; } qsort(freq, NHAP, sizeof(ii_t), ii_cmp); // sort haplotypes in descending order for (i=NHAP-1; i>1; i--) { if ( !freq[i].count ) continue; if ( freq[1].count > tot - freq[0].count - freq[1].count ) break; // the top2 hapotypes cannot change anymore // Find a similar haplotype with the highest frequency. Assuming errors go in 0->1 // direction only and considering one error only. int count = freq[i].count, max_hap = 0; for (j=0; j=0 && haphap_freq[hap] ) count = rcns->hap_freq[hap], max_hap = hap; } if ( count == freq[i].count ) continue; // Update frequency and sort the two modified elements count = freq[i].count; freq[i].count = 0; rcns->hap_freq[freq[i].haplotype] = 0; rcns->hap_freq[max_hap] += count; for (j=i+1; j=0; j--) { if ( freq[j].haplotype==max_hap ) freq[j].count += count; // update the best matching haplotype if ( freq[j].count < freq[j+1].count ) { ii_t tmp = freq[j]; freq[j] = freq[j+1]; freq[j+1] = tmp; } } } // Use only one consensus if the next best haplotype is populated by less than 10% of reads rcns->ncns = ((float)freq[1].count / (freq[0].count + freq[1].count) < 0.1) ? 1 : 2; // Remove unused candidate variants from the top two haplotypes int hap0 = freq[0].haplotype; int hap1 = rcns->ncns==2 ? freq[1].haplotype : 0; rcns->cns_hap[0] = 0; rcns->cns_hap[1] = 0; for (i=0,j=0; icvar[j] = rcns->cvar[i]; if ( hap0 & (1U<cns_hap[0] |= 1U<cns_hap[1] |= 1U<ncvar = j; #if DEBUG_RCNS // This only matters for debugging print memset(rcns->hap_freq,0,NHAP*sizeof(*rcns->hap_freq)); rcns->hap_freq[rcns->cns_hap[1]] = freq[1].count; // NB: the order matters when ncns==1 rcns->hap_freq[rcns->cns_hap[0]] = freq[0].count; #endif return 0; } // Check how frequent are insertions adjacent to the j-th position. Note that reads with an // insertion usually increment also bfreq counts at this position, but not necessarily so, // therefore the counts are approximate static inline void apply_consensus_insertion(read_cns_t *rcns, cns_seq_t *cns, int j, int ivar) { // Only apply consensus insertions that are not being tested by bam2bcf_iaux, i.e. not at the current pos hts_pos_t ref_pos = rcns->beg + j; if ( rcns->pos == ref_pos ) return; // Only apply when there is no insertion at this position registered as a variant while ( ivar < rcns->ncvar && rcns->cvar[ivar].pos == ref_pos ) { if ( rcns->cvar[ivar].vtype == ins ) return; ivar++; } base_freq_t *bfreq = rcns->base_freq; ins_freq_t *ifreq = rcns->ins_freq; int k, nreads = 0; for (k=0; k max_freq*2 ) return; int len = ifreq[j].len[kmax]; char *seq = ifreq[j].nt16_seq[kmax]; for (k=0; kseq[cns->nseq++] = seq_nt16_int[(int)seq[k]]; } // For each position of the realignment window apply either the candidate variants // from ith haplotype or decide on the base/ins/del by majority vote static void create_consensus(read_cns_t *rcns, const char *ref, int ith) { int n = rcns->end - rcns->beg + 1; cns_seq_t *cns = &rcns->cns[ith]; base_freq_t *bfreq = rcns->base_freq; ins_freq_t *ifreq = rcns->ins_freq; del_freq_t *dfreq = rcns->del_freq; hts_pos_t prev_pos = 0; int j,k, ivar = 0; for (j=0; jbeg + j; if ( rcns->pos == ref_pos ) cns->ipos = cns->nseq; while ( ivar < rcns->ncvar && rcns->cvar[ivar].pos < ref_pos ) ivar++; if ( ivar >= rcns->ncvar || rcns->cvar[ivar].pos != ref_pos ) { // This position is not recognised as a het variant so take the most frequent base, including // a deletion if that is most frequent. However, for deleted bases make sure they are not part // of the deletion that is being tested at this positions int max_freq = 0, kmax = seq_nt16_int[seq_nt16_table[(int)ref[j]]]; int nk = ( ref_pos < rcns->pos || ref_pos > rcns->pos + rcns->max_del ) ? BF_DEL+1 : BF_DEL; for (k=0; kseq[cns->nseq++] = kmax; } // Only apply consensus insertions that are not being tested by bam2bcf_iaux, i.e. not at the current pos apply_consensus_insertion(rcns, cns, j, ivar); continue; } int which = rcns->cvar[ivar].which; if ( !(rcns->cns_hap[ith] & (1U<cvar[ivar].vtype==snv && rcns->cvar[ivar].which==k ) continue; if ( max_freq < bfreq[j].base[k] ) max_freq = bfreq[j].base[k], kmax = k; } if ( kmax!=BF_DEL && (!cns->nseq || prev_pos != ref_pos) ) { prev_pos = ref_pos; cns->seq[cns->nseq++] = kmax; } apply_consensus_insertion(rcns, cns, j, ivar); continue; } if ( rcns->cvar[ivar].vtype == snv ) { prev_pos = ref_pos; cns->seq[cns->nseq++] = which; apply_consensus_insertion(rcns, cns, j, ivar); continue; } // There can be multiple variants at this position, for example snv+ins. SNVs come first // thanks to cvar_pos_cmp(), make sure the base has not been added already. if ( !cns->nseq || prev_pos != ref_pos ) { int max_freq = 0, kmax = seq_nt16_int[seq_nt16_table[(int)ref[j]]]; for (k=0; k<6; k++) { if ( rcns->cvar[ivar].vtype==snv && rcns->cvar[ivar].which==k ) continue; if ( max_freq < bfreq[j].base[k] ) max_freq = bfreq[j].base[k], kmax = k; } if ( kmax!=BF_DEL ) { prev_pos = ref_pos; cns->seq[cns->nseq++] = kmax; } } if ( rcns->cvar[ivar].vtype == ins ) { int len = ifreq[j].len[which]; char *seq = ifreq[j].nt16_seq[which]; for (k=0; kseq[cns->nseq++] = seq_nt16_int[(int)seq[k]]; } } else if ( rcns->cvar[ivar].vtype == del ) j += dfreq[j].len[which]; } } // The algorithm: // 1. Identify heterozygous variant positions // 2. Sort variants by abs(variant_allele_freq-0.5) in descending order // 3. Take the top sorted variants (up to 8 to fit in uint8_t) and count the number of // corresponding reads to create frequency spectrum // 4. Correct errors, collapse to the requested number of haplotypes (consensus sequences) // using majority vote for the distribution tail cns_seq_t *rcns_get_consensus(read_cns_t *rcns, const char *ref) { debug_print_base_freqs(rcns, ref); select_candidate_variants(rcns, ref); debug_print_candidate_variants(rcns); if ( rcns->ncvar ) { create_haplotype_frequency_spectrum(rcns); debug_print_haplotype_frequency_spectrum(rcns); correct_haplotype_errors(rcns); debug_print_candidate_variants(rcns); debug_print_haplotype_frequency_spectrum(rcns); } else { rcns->cns_hap[0] = 0; rcns->ncns = 1; } // create consensus int i; for (i=0; incns; i++) create_consensus(rcns,ref,i); debug_print_consensus(rcns,ref); return rcns->cns; } pysam-0.23.0/bcftools/read_consensus.c.pysam.c000066400000000000000000000717141475062545500213170ustar00rootroot00000000000000#include "bcftools.pysam.h" /* read_consensus.c -- create and maintain consensus of reads Copyright (C) 2022 Genome Research Ltd. Author: pd3@sanger Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include "bcftools.h" #include "read_consensus.h" #include "cigar_state.h" #include "kheap.h" // Frequency arrays for each variant type #define NI 10 // number of alternative insertion sequences at one position in a single sample typedef struct { char *nt16_seq[NI]; int len[NI]; int freq[NI]; } ins_freq_t; typedef struct { int len[NI]; int freq[NI]; } del_freq_t; #define BF_DEL 5 typedef struct { int base[6]; // frequencies of A,C,G,T,N,deletion } base_freq_t; // Candidate variants for each interesting position to build consensus haplotypes enum variant_type { snv, ins, del, done }; typedef struct { enum variant_type vtype; hts_pos_t pos; // variant position (reference sequence coordinates), indels follow VCF convention int idx; // temporary 0-based index to rcns.cvar int which, // base/ins/del in rcns.[base|ins|del]_freq array depth; // coverage at the position float af, af_dev; // variant allele frequency (just for debugging printout) and absolute af deviation from 0.5 } candidate_var_t; static inline int cvar_not_preferred(candidate_var_t *a, candidate_var_t *b) { if ( a->af_dev == b->af_dev ) return a->depth < b->depth ? 1 : 0; return a->af_dev > b->af_dev ? 1 : 0; } KHEAP_INIT(cvh, candidate_var_t, cvar_not_preferred); typedef khp_cvh_t cvar_heap_t; #define MAX_NCVAR 8 // This results in alloc() of 2^MAX_NCVAR possible haplotypes #define NHAP (1<mfreq; i++) { ins_freq_t *ifrq = &rcns->ins_freq[i]; for (j=0; jnt16_seq[j]; j++) free(ifrq->nt16_seq[j]); } for (i=0; i<2; i++) free(rcns->cns[i].seq); free(rcns->ins_freq); free(rcns->del_freq); free(rcns->base_freq); free(rcns->stmp); khp_destroy(cvh,rcns->cv_heap); free(rcns); } static int init_arrays(read_cns_t *rcns) { int i,j,n = rcns->end - rcns->beg + 1; if ( n > rcns->mfreq ) { ins_freq_t *ifrq = (ins_freq_t*) realloc(rcns->ins_freq,sizeof(*rcns->ins_freq)*n); if ( !ifrq ) return -1; rcns->ins_freq = ifrq; memset(ifrq+rcns->mfreq,0,sizeof(*rcns->ins_freq)*(n-rcns->mfreq)); del_freq_t *dfrq = (del_freq_t*) realloc(rcns->del_freq,sizeof(*rcns->del_freq)*n); if ( !dfrq ) return -1; rcns->del_freq = dfrq; memset(dfrq+rcns->mfreq,0,sizeof(*rcns->del_freq)*(n-rcns->mfreq)); base_freq_t *bfrq = (base_freq_t*) realloc(rcns->base_freq,sizeof(*rcns->base_freq)*n); if ( !bfrq ) return -1; rcns->base_freq = bfrq; memset(bfrq+rcns->mfreq,0,sizeof(*rcns->base_freq)*(n-rcns->mfreq)); rcns->mfreq = n; } memset(rcns->base_freq,0,sizeof(*rcns->base_freq)*n); memset(rcns->del_freq,0,sizeof(*rcns->del_freq)*n); for (i=0; iins_freq[i]; for (j=0; jnt16_seq[j]; j++) free(ifrq->nt16_seq[j]); } memset(rcns->ins_freq,0,sizeof(*rcns->ins_freq)*n); return 0; } int rcns_reset(read_cns_t *rcns, hts_pos_t pos, hts_pos_t beg, hts_pos_t end) { rcns->band = 0; rcns->pos = pos; rcns->beg = beg; rcns->end = end; int i; for (i=0; i<2; i++) rcns->cns[i].nseq = rcns->cns[i].ipos = 0; // this should not be necessary if the caller did run all steps while (rcns->cv_heap->ndat) khp_delete(cvh, rcns->cv_heap); return init_arrays(rcns); } static inline void add_base(read_cns_t *rcns, int ref_pos, int nt16) { int i = ref_pos - rcns->beg; rcns->base_freq[i].base[seq_nt16_int[nt16]]++; } static void add_ins(read_cns_t *rcns, int ref_pos, int seq_pos, uint8_t *raw_seq, int len) { int i = ref_pos - rcns->beg; ins_freq_t *ifrq = &rcns->ins_freq[i]; char *str; if ( rcns->mstmp < len ) { str = realloc(rcns->stmp,len*sizeof(*str)); if ( !str ) return; rcns->mstmp = len; rcns->stmp = str; } else str = rcns->stmp; for (i=0; int16_seq[i]; i++) if ( ifrq->len[i]==len && !memcmp(ifrq->nt16_seq[i],str,len) ) break; if ( i>=NI ) return; // too many choices, typically homopolymers in long reads; discard if ( !ifrq->nt16_seq[i] ) // new insertion { if ( !(ifrq->nt16_seq[i]=malloc(len)) ) return; memcpy(ifrq->nt16_seq[i], str, len); ifrq->len[i] = len; } ifrq->freq[i]++; } static void add_del(read_cns_t *rcns, int ref_pos, int len) { int i = ref_pos - rcns->beg; int j,n = rcns->end - rcns->beg + 1; if ( i + len + 1 < n ) n = i + len + 1; for (j=i+1; jbase_freq[j].base[BF_DEL]++; del_freq_t *dfrq = &rcns->del_freq[i]; for (i=0; ilen[i]; i++) if ( dfrq->len[i]==len ) break; if ( i>=NI ) return; // too many choices, typically homopolymers in long reads; discard if ( !dfrq->len[i] ) dfrq->len[i] = len; // new deletion dfrq->freq[i]++; } read_cns_t *rcns_init(hts_pos_t pos, hts_pos_t beg, hts_pos_t end) { read_cns_t *rcns = (read_cns_t*) calloc(1,sizeof(read_cns_t)); rcns->pos = pos; rcns->beg = beg; rcns->end = end; rcns->cv_heap = khp_init(cvh); if ( init_arrays(rcns)!=0 ) { rcns_destroy(rcns); return NULL; } return rcns; } int rcns_set_reads(read_cns_t *rcns, bam_pileup1_t *plp, int nplp) { // save the reads for phasing, this can be called multiple times rcns->plp = plp; rcns->nplp = nplp; // fill consensus arrays int i,j,k, local_band_max = 0; // maximum absolute deviation from diagonal for (i=0; ib; int x = b->core.pos; // ref coordinate int y = 0; // seq coordinate uint32_t *cigar = bam_get_cigar(b); uint8_t *seq = bam_get_seq(b); int local_band = 0; // current deviation from diagonal for (k = 0; k < b->core.n_cigar; ++k) { int op = cigar[k] & BAM_CIGAR_MASK; int len = cigar[k] >> BAM_CIGAR_SHIFT; if ( op==BAM_CSOFT_CLIP ) y += len; else if ( op==BAM_CMATCH || op==BAM_CEQUAL || op==BAM_CDIFF ) { if ( xend && x+len>rcns->beg ) { int j_beg = rcns->beg > x ? rcns->beg - x : 0; // how many bases to skip in the ref and qry int j_end = rcns->end < x + len - 1 ? rcns->end - x : len - 1; x += j_beg; y += j_beg; for (j=j_beg; j<=j_end; j++, x++, y++) add_base(rcns,x,bam_seqi(seq,y)); } else { x += len; y += len; } } else if ( op==BAM_CINS ) { if ( x>rcns->beg && xend ) { local_band += p->indel; add_ins(rcns,x-1,y,seq,len); // x-1: one base before as in VCF } y += len; } else if ( op==BAM_CDEL || op==BAM_CREF_SKIP ) /* note: unsure about BAM_CREF_SKIP, don't have data to test */ { if ( x>rcns->beg && x+len-1<=rcns->end ) { local_band += -p->indel; add_del(rcns,x-1,len); // x-1: one base before as in VCF } x += len; } else if ( op==BAM_CHARD_CLIP ) continue; else error("rcns_set_reads todo: unknown cigar operator %d\n",op); if ( local_band_max < local_band ) local_band_max = local_band; } // Track the biggest deviation +/- from diagonal, used in BAQ alignment step. if ( rcns->band < local_band_max ) rcns->band = local_band_max; } return 0; } #if DEBUG_RCNS static void debug_print_base_freqs(read_cns_t *rcns, const char *ref) { int i,j,k,n = rcns->end - rcns->beg + 1; fprintf(bcftools_stderr,"beg,end,pos=%d %d %d\n",(int)rcns->beg,(int)rcns->end,(int)rcns->pos); base_freq_t *bfreq = rcns->base_freq; ins_freq_t *ifreq = rcns->ins_freq; del_freq_t *dfreq = rcns->del_freq; for (i=0; ibeg+i+1,ref[i]); for (j=0; j<6; j++) fprintf(bcftools_stderr,"\t%d%s",bfreq[i].base[j],ref[i]=="ACGTNi"[j]?"*":""); fprintf(bcftools_stderr,"\t"); for (j=0; jncvar; i++) { candidate_var_t *var = &rcns->cvar[i]; fprintf(bcftools_stderr,"\tvar%d pos=%"PRIhts_pos" idx=%d vtype=%s which=%d depth=%d af=%f af_dev=%f\n", i,var->pos+1,var->idx,vtype2string(var->vtype),var->which,var->depth,var->af,var->af_dev); } } static void debug_print_haplotype_frequency_spectrum(read_cns_t *rcns) { int i,j; fprintf(bcftools_stderr,"Haplotype frequencies (bits from left correspond to var0,1,..):\n"); for (i=0; ihap_freq[i] ) continue; fprintf(bcftools_stderr,"\t%d: ",i); for (j=0; jncvar; j++) fprintf(bcftools_stderr,"%d", i&(1<hap_freq[i]); } } static void debug_print_consensus(read_cns_t *rcns, const char *ref) { int i,j,n = rcns->end - rcns->beg + 1; fprintf(bcftools_stderr,"ref: "); for (i=0; icns[i].nseq ) break; fprintf(bcftools_stderr,"Consensus%d: ",i); for (j=0; j<=rcns->cns[i].ipos; j++) fprintf(bcftools_stderr,"%c","ACGTN"[(int)rcns->cns[i].seq[j]]); fprintf(bcftools_stderr,"#"); for (; jcns[i].nseq; j++) fprintf(bcftools_stderr,"%c","ACGTN"[(int)rcns->cns[i].seq[j]]); fprintf(bcftools_stderr,"\n"); } } #else #define debug_print_base_freqs(rcns,ref) #define debug_print_candidate_variants(rcns) #define debug_print_haplotype_frequency_spectrum(rcns) #define debug_print_consensus(rcns,ref) #endif static int cvar_pos_cmp(const void *aptr, const void *bptr) { candidate_var_t *a = (candidate_var_t*)aptr; candidate_var_t *b = (candidate_var_t*)bptr; if ( a->pos < b->pos ) return -1; if ( a->pos > b->pos ) return 1; if ( a->vtype < b->vtype ) return -1; if ( a->vtype > b->vtype ) return 1; if ( a->which < b->which ) return -1; if ( a->which > b->which ) return 1; return 0; } static void register_variant(read_cns_t *rcns, enum variant_type vtype, int cns_pos, int which, int depth, float freq) { cvar_heap_t *cv_heap = rcns->cv_heap; if ( vtype==done ) { rcns->ncvar = 0; while (cv_heap->ndat) { rcns->cvar[rcns->ncvar++] = cv_heap->dat[0]; khp_delete(cvh,cv_heap); } // sort the variants by pos,type,which to make determination of haplotypes from reads faster if ( rcns->ncvar ) qsort(rcns->cvar, rcns->ncvar, sizeof(*rcns->cvar), cvar_pos_cmp); return; } candidate_var_t var; var.pos = cns_pos + rcns->beg; var.which = which; var.vtype = vtype; var.depth = depth; var.af_dev = fabs(0.5-freq); var.af = freq; int free_slot; // keep the number of variants small, maximum MAX_NCVAR if ( rcns->ncvar==MAX_NCVAR ) { if ( cvar_not_preferred(&var,&cv_heap->dat[0]) ) return; // no need to add, the new variant is worse than the heap's worst one free_slot = cv_heap->dat[0].idx; khp_delete(cvh,cv_heap); } else free_slot = rcns->ncvar++; var.idx = free_slot; rcns->cvar[free_slot] = var; khp_insert(cvh,cv_heap,&var); } // Identify candidate variant positions. (Note that homozygous variants are not considered // as those will be added trivially by taking the consensus base.) The detection limit is // for now hard-wired. This has only indirect effect on sensitivity, will just not contribute // to the consensus template when realigning. static int select_candidate_variants(read_cns_t *rcns, const char *ref) { const float af_th = 0.1; int i,j, n = rcns->end - rcns->beg + 1; int max_ins_len = 0; // maximum total length of all insertions applied to allocate big enough buffers base_freq_t *bfreq = rcns->base_freq; ins_freq_t *ifreq = rcns->ins_freq; del_freq_t *dfreq = rcns->del_freq; for (i=0; ipos - rcns->beg ) continue; // creating consensus from everything but the variants at the current position int dp = 0; for (j=0; j<4; j++) dp += bfreq[i].base[j]; for (j=0; jaf_th && af<(1-af_th) ) register_variant(rcns,snv,i,j,dp,af); } for (j=0; jaf_th && af<(1-af_th) ) register_variant(rcns,del,i,j,dp,af); } for (j=0; jaf_th && af<(1-af_th) ) register_variant(rcns,ins,i,j,dp,af); } } register_variant(rcns,done,0,0,0,0); // finalize // Reallocate buffers if ( rcns->mcns < n + max_ins_len ) { n += max_ins_len; for (i=0; i<2; i++) { char *seq = (char*) realloc(rcns->cns[i].seq,sizeof(char)*n); if ( !seq ) return -1; rcns->cns[i].seq = seq; } rcns->mcns = n; } // Find the longest deletion at the query position i = rcns->pos - rcns->beg; rcns->max_del = 0; for (j=0; jmax_del < dfreq[i].len[j] ) rcns->max_del = dfreq[i].len[j]; } return 0; } static int create_haplotype_frequency_spectrum(read_cns_t *rcns) { memset(rcns->hap_freq,0,sizeof(rcns->hap_freq)); int i; for (i=0; inplp; i++) // for each read... { const bam_pileup1_t *p = rcns->plp + i; cigar_state_t cigar; cstate_init(&cigar,p->b); int j,k,hap = 0; for (j=0; jncvar; j++) { candidate_var_t *cvar = &rcns->cvar[j]; if ( cvar->vtype==snv ) { int iseq = cstate_seek_op_fwd(&cigar, cvar->pos, BAM_CMATCH, NULL); if ( iseq==-2 ) break; if ( iseq==-1 ) continue; int nt16 = bam_seqi(cigar.seq, iseq); if ( seq_nt16_int[nt16]==cvar->which ) hap |= 1<vtype==ins ) { int len; ins_freq_t *ifrq = &rcns->ins_freq[cvar->pos - rcns->beg]; int iseq = cstate_seek_op_fwd(&cigar, cvar->pos+1, BAM_CINS, &len); if ( iseq==-2 ) break; if ( iseq==-1 ) continue; if ( len!=ifrq->len[cvar->which] ) continue; for (k=0; klen[cvar->which]; k++) if ( bam_seqi(cigar.seq,iseq+k)!=ifrq->nt16_seq[cvar->which][k] ) break; if ( k==ifrq->len[cvar->which] ) hap |= 1<vtype==del ) { int len; del_freq_t *dfrq = &rcns->del_freq[cvar->pos - rcns->beg]; int ret = cstate_seek_op_fwd(&cigar, cvar->pos+1, BAM_CDEL, &len); if ( ret==-2 ) break; if ( ret==-1 ) continue; if ( len!=dfrq->len[cvar->which] ) continue; hap |= 1<hap_freq[hap]++; } return 0; } typedef struct { int haplotype, count; } ii_t; static int ii_cmp(const void *a, const void *b) { if ( ((ii_t*)a)->count > ((ii_t*)b)->count ) return -1; if ( ((ii_t*)a)->count < ((ii_t*)b)->count ) return 1; return 0; } // Select two most common haplotypes trying to account for 1bp errors. Haplotypes // are represented as 8-bit numbers, each bit corresponds to one candidate variant. static int correct_haplotype_errors(read_cns_t *rcns) { int i,j, tot = 0; ii_t freq[NHAP]; for (i=0; ihap_freq[i]; tot += rcns->hap_freq[i]; } qsort(freq, NHAP, sizeof(ii_t), ii_cmp); // sort haplotypes in descending order for (i=NHAP-1; i>1; i--) { if ( !freq[i].count ) continue; if ( freq[1].count > tot - freq[0].count - freq[1].count ) break; // the top2 hapotypes cannot change anymore // Find a similar haplotype with the highest frequency. Assuming errors go in 0->1 // direction only and considering one error only. int count = freq[i].count, max_hap = 0; for (j=0; j=0 && haphap_freq[hap] ) count = rcns->hap_freq[hap], max_hap = hap; } if ( count == freq[i].count ) continue; // Update frequency and sort the two modified elements count = freq[i].count; freq[i].count = 0; rcns->hap_freq[freq[i].haplotype] = 0; rcns->hap_freq[max_hap] += count; for (j=i+1; j=0; j--) { if ( freq[j].haplotype==max_hap ) freq[j].count += count; // update the best matching haplotype if ( freq[j].count < freq[j+1].count ) { ii_t tmp = freq[j]; freq[j] = freq[j+1]; freq[j+1] = tmp; } } } // Use only one consensus if the next best haplotype is populated by less than 10% of reads rcns->ncns = ((float)freq[1].count / (freq[0].count + freq[1].count) < 0.1) ? 1 : 2; // Remove unused candidate variants from the top two haplotypes int hap0 = freq[0].haplotype; int hap1 = rcns->ncns==2 ? freq[1].haplotype : 0; rcns->cns_hap[0] = 0; rcns->cns_hap[1] = 0; for (i=0,j=0; icvar[j] = rcns->cvar[i]; if ( hap0 & (1U<cns_hap[0] |= 1U<cns_hap[1] |= 1U<ncvar = j; #if DEBUG_RCNS // This only matters for debugging print memset(rcns->hap_freq,0,NHAP*sizeof(*rcns->hap_freq)); rcns->hap_freq[rcns->cns_hap[1]] = freq[1].count; // NB: the order matters when ncns==1 rcns->hap_freq[rcns->cns_hap[0]] = freq[0].count; #endif return 0; } // Check how frequent are insertions adjacent to the j-th position. Note that reads with an // insertion usually increment also bfreq counts at this position, but not necessarily so, // therefore the counts are approximate static inline void apply_consensus_insertion(read_cns_t *rcns, cns_seq_t *cns, int j, int ivar) { // Only apply consensus insertions that are not being tested by bam2bcf_iaux, i.e. not at the current pos hts_pos_t ref_pos = rcns->beg + j; if ( rcns->pos == ref_pos ) return; // Only apply when there is no insertion at this position registered as a variant while ( ivar < rcns->ncvar && rcns->cvar[ivar].pos == ref_pos ) { if ( rcns->cvar[ivar].vtype == ins ) return; ivar++; } base_freq_t *bfreq = rcns->base_freq; ins_freq_t *ifreq = rcns->ins_freq; int k, nreads = 0; for (k=0; k max_freq*2 ) return; int len = ifreq[j].len[kmax]; char *seq = ifreq[j].nt16_seq[kmax]; for (k=0; kseq[cns->nseq++] = seq_nt16_int[(int)seq[k]]; } // For each position of the realignment window apply either the candidate variants // from ith haplotype or decide on the base/ins/del by majority vote static void create_consensus(read_cns_t *rcns, const char *ref, int ith) { int n = rcns->end - rcns->beg + 1; cns_seq_t *cns = &rcns->cns[ith]; base_freq_t *bfreq = rcns->base_freq; ins_freq_t *ifreq = rcns->ins_freq; del_freq_t *dfreq = rcns->del_freq; hts_pos_t prev_pos = 0; int j,k, ivar = 0; for (j=0; jbeg + j; if ( rcns->pos == ref_pos ) cns->ipos = cns->nseq; while ( ivar < rcns->ncvar && rcns->cvar[ivar].pos < ref_pos ) ivar++; if ( ivar >= rcns->ncvar || rcns->cvar[ivar].pos != ref_pos ) { // This position is not recognised as a het variant so take the most frequent base, including // a deletion if that is most frequent. However, for deleted bases make sure they are not part // of the deletion that is being tested at this positions int max_freq = 0, kmax = seq_nt16_int[seq_nt16_table[(int)ref[j]]]; int nk = ( ref_pos < rcns->pos || ref_pos > rcns->pos + rcns->max_del ) ? BF_DEL+1 : BF_DEL; for (k=0; kseq[cns->nseq++] = kmax; } // Only apply consensus insertions that are not being tested by bam2bcf_iaux, i.e. not at the current pos apply_consensus_insertion(rcns, cns, j, ivar); continue; } int which = rcns->cvar[ivar].which; if ( !(rcns->cns_hap[ith] & (1U<cvar[ivar].vtype==snv && rcns->cvar[ivar].which==k ) continue; if ( max_freq < bfreq[j].base[k] ) max_freq = bfreq[j].base[k], kmax = k; } if ( kmax!=BF_DEL && (!cns->nseq || prev_pos != ref_pos) ) { prev_pos = ref_pos; cns->seq[cns->nseq++] = kmax; } apply_consensus_insertion(rcns, cns, j, ivar); continue; } if ( rcns->cvar[ivar].vtype == snv ) { prev_pos = ref_pos; cns->seq[cns->nseq++] = which; apply_consensus_insertion(rcns, cns, j, ivar); continue; } // There can be multiple variants at this position, for example snv+ins. SNVs come first // thanks to cvar_pos_cmp(), make sure the base has not been added already. if ( !cns->nseq || prev_pos != ref_pos ) { int max_freq = 0, kmax = seq_nt16_int[seq_nt16_table[(int)ref[j]]]; for (k=0; k<6; k++) { if ( rcns->cvar[ivar].vtype==snv && rcns->cvar[ivar].which==k ) continue; if ( max_freq < bfreq[j].base[k] ) max_freq = bfreq[j].base[k], kmax = k; } if ( kmax!=BF_DEL ) { prev_pos = ref_pos; cns->seq[cns->nseq++] = kmax; } } if ( rcns->cvar[ivar].vtype == ins ) { int len = ifreq[j].len[which]; char *seq = ifreq[j].nt16_seq[which]; for (k=0; kseq[cns->nseq++] = seq_nt16_int[(int)seq[k]]; } } else if ( rcns->cvar[ivar].vtype == del ) j += dfreq[j].len[which]; } } // The algorithm: // 1. Identify heterozygous variant positions // 2. Sort variants by abs(variant_allele_freq-0.5) in descending order // 3. Take the top sorted variants (up to 8 to fit in uint8_t) and count the number of // corresponding reads to create frequency spectrum // 4. Correct errors, collapse to the requested number of haplotypes (consensus sequences) // using majority vote for the distribution tail cns_seq_t *rcns_get_consensus(read_cns_t *rcns, const char *ref) { debug_print_base_freqs(rcns, ref); select_candidate_variants(rcns, ref); debug_print_candidate_variants(rcns); if ( rcns->ncvar ) { create_haplotype_frequency_spectrum(rcns); debug_print_haplotype_frequency_spectrum(rcns); correct_haplotype_errors(rcns); debug_print_candidate_variants(rcns); debug_print_haplotype_frequency_spectrum(rcns); } else { rcns->cns_hap[0] = 0; rcns->ncns = 1; } // create consensus int i; for (i=0; incns; i++) create_consensus(rcns,ref,i); debug_print_consensus(rcns,ref); return rcns->cns; } pysam-0.23.0/bcftools/read_consensus.h000066400000000000000000000044651475062545500177520ustar00rootroot00000000000000/* read_consensus.h -- create and maintain consensus of reads Copyright (C) 2022 Genome Research Ltd. Author: pd3@sanger Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef READ_CONSENSUS_H #define READ_CONSENSUS_H #include #include #include #ifndef DEBUG_RCNS #define DEBUG_RCNS 0 #endif typedef struct { char *seq; // nt5 sequence: "ACGTN"[(int)seq[i]] int nseq, ipos; // the sequence length and the `pos` index relative to seq } cns_seq_t; typedef struct _read_cns_t read_cns_t; // Init and destroy read consensus read_cns_t *rcns_init(hts_pos_t pos, hts_pos_t beg, hts_pos_t end); void rcns_destroy(read_cns_t *rcns); // Reset the structures for new sample and/or position int rcns_reset(read_cns_t *rcns, hts_pos_t pos, hts_pos_t beg, hts_pos_t end); // Add reads to consensus. The provided structures must continue to exist // until rcns_get_consensus() is called. // // Todo (easy): allow it to be called once or multiple times, eg for // creating a shared consensus for multiple samples int rcns_set_reads(read_cns_t *rcns, bam_pileup1_t *plp, int nplp); // Generate up to two consensus sequences, cns_seq[1].nseq is 0 when only // the first is set cns_seq_t *rcns_get_consensus(read_cns_t *rcns, const char *ref); #endif pysam-0.23.0/bcftools/regidx.c000066400000000000000000000440461475062545500162130ustar00rootroot00000000000000/* Copyright (C) 2014-2018 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include "regidx.h" #define MAX_COOR_0 REGIDX_MAX // CSI and hts_itr_query limit, 0-based #define iBIN(x) ((x)>>13) typedef struct { uint32_t beg, end; } reg_t; typedef struct { uint32_t pos, ireg; // y-coordinate and a pointer to reglist.reg and reglist.dat } pos_t; typedef struct _reglist_t reglist_t; typedef struct { uint32_t beg, end, ireg; // query coordinates and the active region regidx_t *ridx; reglist_t *list; int active; } _itr_t; // List of regions for one chromosome. struct _reglist_t { uint32_t *idx, nidx; // index to list.reg+1 uint32_t nreg, mreg; // n:used, m:allocated reg_t *reg; // regions void *dat; // payload data char *seq; // sequence name int unsorted; }; // Container of all sequences struct _regidx_t { int nseq, mseq; // n:used, m:alloced reglist_t *seq; // regions for each sequence void *seq2regs; // hash for fast lookup from chr name to regions char **seq_names; regidx_free_f free; // function to free any data allocated by regidx_parse_f regidx_parse_f parse; // parse one input line void *usr; // user data to pass to regidx_parse_f int payload_size; void *payload; // temporary payload data set by regidx_parse_f (sequence is not known beforehand) kstring_t str; }; int regidx_seq_nregs(regidx_t *idx, const char *seq) { int iseq; if ( khash_str2int_get(idx->seq2regs, seq, &iseq)!=0 ) return 0; // no such sequence return idx->seq[iseq].nreg; } int regidx_nregs(regidx_t *idx) { int i, nreg = 0; for (i=0; inseq; i++) nreg += idx->seq[i].nreg; return nreg; } char **regidx_seq_names(regidx_t *idx, int *n) { *n = idx->nseq; return idx->seq_names; } int regidx_insert_list(regidx_t *idx, char *line, char delim) { kstring_t tmp = {0,0,0}; char *ss = line; while ( *ss ) { char *se = ss; while ( *se && *se!=delim ) se++; tmp.l = 0; kputsn(ss, se-ss, &tmp); if ( regidx_insert(idx,tmp.s) < 0 ) { free(tmp.s); return -1; } if ( !*se ) break; ss = se+1; } free(tmp.s); return 0; } static inline int cmp_regs(reg_t *a, reg_t *b) { if ( a->beg < b->beg ) return -1; if ( a->beg > b->beg ) return 1; if ( a->end < b->end ) return 1; // longer intervals come first if ( a->end > b->end ) return -1; return 0; } static int cmp_reg_ptrs(const void *a, const void *b) { return cmp_regs((reg_t*)a,(reg_t*)b); } static int cmp_reg_ptrs2(const void *a, const void *b) { return cmp_regs(*((reg_t**)a),*((reg_t**)b)); } inline int regidx_push(regidx_t *idx, char *chr_beg, char *chr_end, uint32_t beg, uint32_t end, void *payload) { if ( beg > MAX_COOR_0 ) beg = MAX_COOR_0; if ( end > MAX_COOR_0 ) end = MAX_COOR_0; int rid; idx->str.l = 0; kputsn(chr_beg, chr_end-chr_beg+1, &idx->str); if ( khash_str2int_get(idx->seq2regs, idx->str.s, &rid)!=0 ) { // new chromosome idx->nseq++; int m_prev = idx->mseq; hts_expand0(reglist_t,idx->nseq,idx->mseq,idx->seq); hts_expand0(char*,idx->nseq,m_prev,idx->seq_names); idx->seq_names[idx->nseq-1] = strdup(idx->str.s); rid = khash_str2int_inc(idx->seq2regs, idx->seq_names[idx->nseq-1]); } reglist_t *list = &idx->seq[rid]; list->seq = idx->seq_names[rid]; list->nreg++; int mreg = list->mreg; hts_expand(reg_t,list->nreg,list->mreg,list->reg); list->reg[list->nreg-1].beg = beg; list->reg[list->nreg-1].end = end; if ( idx->payload_size ) { if ( mreg != list->mreg ) list->dat = realloc(list->dat,idx->payload_size*list->mreg); memcpy((char *)list->dat + idx->payload_size*(list->nreg-1), payload, idx->payload_size); } if ( !list->unsorted && list->nreg>1 && cmp_regs(&list->reg[list->nreg-2],&list->reg[list->nreg-1])>0 ) list->unsorted = 1; return 0; } int regidx_insert(regidx_t *idx, char *line) { if ( !line ) return 0; char *chr_from, *chr_to; uint32_t beg,end; int ret = idx->parse(line,&chr_from,&chr_to,&beg,&end,idx->payload,idx->usr); if ( ret==-2 ) return -1; // error if ( ret==-1 ) return 0; // skip the line regidx_push(idx, chr_from,chr_to,beg,end,idx->payload); return 0; } regidx_t *regidx_init_string(const char *str, regidx_parse_f parser, regidx_free_f free_f, size_t payload_size, void *usr_dat) { regidx_t *idx = (regidx_t*) calloc(1,sizeof(regidx_t)); if ( !idx ) return NULL; idx->free = free_f; idx->parse = parser ? parser : regidx_parse_tab; idx->usr = usr_dat; idx->seq2regs = khash_str2int_init(); idx->payload_size = payload_size; if ( payload_size ) idx->payload = malloc(payload_size); kstring_t tmp = {0,0,0}; const char *ss = str; while ( *ss ) { while ( *ss && isspace(*ss) ) ss++; const char *se = ss; while ( *se && *se!='\r' && *se!='\n' ) se++; tmp.l = 0; kputsn(ss, se-ss, &tmp); regidx_insert(idx,tmp.s); while ( *se && isspace(*se) ) se++; ss = se; } free(tmp.s); return idx; } regidx_t *regidx_init(const char *fname, regidx_parse_f parser, regidx_free_f free_f, size_t payload_size, void *usr_dat) { if ( !parser ) { if ( !fname ) parser = regidx_parse_tab; else { int len = strlen(fname); if ( len>=7 && !strcasecmp(".bed.gz",fname+len-7) ) parser = regidx_parse_bed; else if ( len>=8 && !strcasecmp(".bed.bgz",fname+len-8) ) parser = regidx_parse_bed; else if ( len>=4 && !strcasecmp(".bed",fname+len-4) ) parser = regidx_parse_bed; else if ( len>=4 && !strcasecmp(".vcf",fname+len-4) ) parser = regidx_parse_vcf; else if ( len>=7 && !strcasecmp(".vcf.gz",fname+len-7) ) parser = regidx_parse_vcf; else parser = regidx_parse_tab; } } regidx_t *idx = (regidx_t*) calloc(1,sizeof(regidx_t)); idx->free = free_f; idx->parse = parser; idx->usr = usr_dat; idx->seq2regs = khash_str2int_init(); idx->payload_size = payload_size; if ( payload_size ) idx->payload = malloc(payload_size); if ( !fname ) return idx; kstring_t str = {0,0,0}; htsFile *fp = hts_open(fname,"r"); if ( !fp ) goto error; while ( hts_getline(fp, KS_SEP_LINE, &str) > 0 ) { if ( regidx_insert(idx, str.s) ) goto error; } free(str.s); if ( hts_close(fp)!=0 ) { fprintf(stderr,"[%s] Error: close failed .. %s\n", __func__,fname); goto error; } return idx; error: free(str.s); if ( fp ) hts_close(fp); regidx_destroy(idx); return NULL; } void regidx_destroy(regidx_t *idx) { int i, j; for (i=0; inseq; i++) { reglist_t *list = &idx->seq[i]; if ( idx->free ) { for (j=0; jnreg; j++) idx->free((char *)list->dat + idx->payload_size*j); } free(list->dat); free(list->reg); free(list->idx); } free(idx->seq_names); free(idx->seq); free(idx->str.s); free(idx->payload); khash_str2int_destroy_free(idx->seq2regs); free(idx); } int _reglist_build_index(regidx_t *regidx, reglist_t *list) { int i; if ( list->unsorted ) { if ( !regidx->payload_size ) qsort(list->reg,list->nreg,sizeof(reg_t),cmp_reg_ptrs); else { reg_t **ptr = (reg_t**) malloc(sizeof(reg_t*)*list->nreg); for (i=0; inreg; i++) ptr[i] = list->reg + i; qsort(ptr,list->nreg,sizeof(*ptr),cmp_reg_ptrs2); void *tmp_dat = malloc(regidx->payload_size*list->nreg); for (i=0; inreg; i++) { size_t iori = ptr[i] - list->reg; memcpy((char *)tmp_dat+i*regidx->payload_size, (char *)list->dat+iori*regidx->payload_size, regidx->payload_size); } free(list->dat); list->dat = tmp_dat; reg_t *tmp_reg = (reg_t*) malloc(sizeof(reg_t)*list->nreg); for (i=0; inreg; i++) { size_t iori = ptr[i] - list->reg; tmp_reg[i] = list->reg[iori]; } free(ptr); free(list->reg); list->reg = tmp_reg; list->mreg = list->nreg; } list->unsorted = 0; } list->nidx = 0; int j,k, midx = 0; for (j=0; jnreg; j++) { int ibeg = iBIN(list->reg[j].beg); int iend = iBIN(list->reg[j].end); if ( midx <= iend ) { int old_midx = midx; midx = iend + 1; kroundup32(midx); list->idx = (uint32_t*) realloc(list->idx, midx*sizeof(uint32_t)); memset(list->idx+old_midx, 0, sizeof(uint32_t)*(midx-old_midx)); } if ( ibeg==iend ) { if ( !list->idx[ibeg] ) list->idx[ibeg] = j + 1; } else { for (k=ibeg; k<=iend; k++) if ( !list->idx[k] ) list->idx[k] = j + 1; } if ( list->nidx < iend+1 ) list->nidx = iend+1; } return 0; } int regidx_overlap(regidx_t *regidx, const char *chr, uint32_t beg, uint32_t end, regitr_t *regitr) { if ( regitr ) regitr->seq = NULL; int iseq, ireg; if ( khash_str2int_get(regidx->seq2regs, chr, &iseq)!=0 ) return 0; // no such sequence reglist_t *list = ®idx->seq[iseq]; if ( !list->nreg ) return 0; if ( list->nreg==1 ) { if ( beg > list->reg[0].end ) return 0; if ( end < list->reg[0].beg ) return 0; ireg = 0; } else { if ( !list->idx ) _reglist_build_index(regidx,list); int ibeg = iBIN(beg); if ( ibeg >= list->nidx ) return 0; // beg is too big // find a matching region uint32_t i = list->idx[ibeg]; if ( !i ) { int iend = iBIN(end); if ( iend > list->nidx ) iend = list->nidx; for (i=ibeg; i<=iend; i++) if ( list->idx[i] ) break; if ( i>iend ) return 0; i = list->idx[i]; } for (ireg=i-1; iregnreg; ireg++) { if ( list->reg[ireg].beg > end ) return 0; // no match, past the query region if ( list->reg[ireg].end >= beg && list->reg[ireg].beg <= end ) break; // found } if ( ireg >= list->nreg ) return 0; // no match } if ( !regitr ) return 1; // match, but no more info to save // may need to iterate over the matching regions later _itr_t *itr = (_itr_t*)regitr->itr; itr->ridx = regidx; itr->list = list; itr->beg = beg; itr->end = end; itr->ireg = ireg; itr->active = 0; regitr->seq = list->seq; regitr->beg = list->reg[ireg].beg; regitr->end = list->reg[ireg].end; if ( regidx->payload_size ) regitr->payload = (char *)list->dat + regidx->payload_size*ireg; return 1; } int regidx_parse_bed(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr) { char *ss = (char*) line; while ( *ss && isspace(*ss) ) ss++; if ( !*ss ) return -1; // skip blank lines if ( *ss=='#' ) return -1; // skip comments char *se = ss; while ( *se && !isspace(*se) ) se++; *chr_beg = ss; *chr_end = se-1; if ( !*se ) { // just the chromosome name *beg = 0; *end = MAX_COOR_0; return 0; } ss = se+1; *beg = strtod(ss, &se); if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; } ss = se+1; *end = strtod(ss, &se) - 1; if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; } return 0; } int regidx_parse_tab(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr) { char *ss = (char*) line; while ( *ss && isspace(*ss) ) ss++; if ( !*ss ) return -1; // skip blank lines if ( *ss=='#' ) return -1; // skip comments char *se = ss; while ( *se && !isspace(*se) ) se++; *chr_beg = ss; *chr_end = se-1; if ( !*se ) { // just the chromosome name *beg = 0; *end = MAX_COOR_0; return 0; } ss = se+1; *beg = strtod(ss, &se); if ( ss==se ) { fprintf(stderr,"Could not parse tab line: %s\n", line); return -2; } if ( *beg==0 ) { fprintf(stderr,"Could not parse tab line, expected 1-based coordinate: %s\n", line); return -2; } (*beg)--; if ( !se[0] || !se[1] ) *end = *beg; else { ss = se+1; *end = strtod(ss, &se); if ( ss==se || (*se && !isspace(*se)) ) *end = *beg; else if ( *end==0 ) { fprintf(stderr,"Could not parse tab line, expected 1-based coordinate: %s\n", line); return -2; } else (*end)--; } return 0; } int regidx_parse_vcf(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr) { int ret = regidx_parse_tab(line, chr_beg, chr_end, beg, end, payload, usr); if ( !ret ) *end = *beg; return ret; } int regidx_parse_reg(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr) { char *ss = (char*) line; while ( *ss && isspace(*ss) ) ss++; if ( !*ss ) return -1; // skip blank lines if ( *ss=='#' ) return -1; // skip comments char *se = ss; while ( *se && *se!=':' ) se++; *chr_beg = ss; *chr_end = se-1; if ( !*se ) { *beg = 0; *end = MAX_COOR_0; return 0; } ss = se+1; *beg = strtod(ss, &se); if ( ss==se ) { fprintf(stderr,"Could not parse reg line: %s\n", line); return -2; } if ( *beg==0 ) { fprintf(stderr,"Could not parse reg line, expected 1-based coordinate: %s\n", line); return -2; } (*beg)--; if ( !se[0] || !se[1] ) *end = se[0]=='-' ? MAX_COOR_0 : *beg; else { ss = se+1; *end = strtod(ss, &se); if ( ss==se ) *end = *beg; else if ( *end==0 ) { fprintf(stderr,"Could not parse reg line, expected 1-based coordinate: %s\n", line); return -2; } else (*end)--; } return 0; } regitr_t *regitr_init(regidx_t *regidx) { regitr_t *regitr = (regitr_t*) calloc(1,sizeof(regitr_t)); regitr->itr = (_itr_t*) calloc(1,sizeof(_itr_t)); _itr_t *itr = (_itr_t*) regitr->itr; itr->ridx = regidx; itr->list = NULL; return regitr; } void regitr_reset(regidx_t *regidx, regitr_t *regitr) { _itr_t *itr = (_itr_t*) regitr->itr; memset(itr,0,sizeof(_itr_t)); itr->ridx = regidx; } void regitr_destroy(regitr_t *regitr) { free(regitr->itr); free(regitr); } int regitr_overlap(regitr_t *regitr) { if ( !regitr->seq ) return 0; _itr_t *itr = (_itr_t*) regitr->itr; if ( !itr->active ) { // is this the first call after regidx_overlap? itr->active = 1; itr->ireg++; return 1; } reglist_t *list = itr->list; int i; for (i=itr->ireg; inreg; i++) { if ( list->reg[i].beg > itr->end ) return 0; // no match, past the query region if ( list->reg[i].end >= itr->beg && list->reg[i].beg <= itr->end ) break; // found } if ( i >= list->nreg ) return 0; // no match itr->ireg = i + 1; regitr->seq = list->seq; regitr->beg = list->reg[i].beg; regitr->end = list->reg[i].end; if ( itr->ridx->payload_size ) regitr->payload = (char *)list->dat + itr->ridx->payload_size*i; return 1; } int regitr_loop(regitr_t *regitr) { _itr_t *itr = (_itr_t*) regitr->itr; regidx_t *regidx = itr->ridx; if ( !itr->list ) // first time here { itr->list = regidx->seq; itr->ireg = 0; } size_t iseq = itr->list - regidx->seq; if ( iseq >= regidx->nseq ) return 0; if ( itr->ireg >= itr->list->nreg ) { iseq++; if ( iseq >= regidx->nseq ) return 0; // no more sequences, done itr->ireg = 0; itr->list = ®idx->seq[iseq]; } regitr->seq = itr->list->seq; regitr->beg = itr->list->reg[itr->ireg].beg; regitr->end = itr->list->reg[itr->ireg].end; if ( regidx->payload_size ) regitr->payload = (char *)itr->list->dat + regidx->payload_size*itr->ireg; itr->ireg++; return 1; } void regitr_copy(regitr_t *dst, regitr_t *src) { _itr_t *dst_itr = (_itr_t*) dst->itr; _itr_t *src_itr = (_itr_t*) src->itr; *dst_itr = *src_itr; *dst = *src; dst->itr = dst_itr; } pysam-0.23.0/bcftools/regidx.c.pysam.c000066400000000000000000000442241475062545500175620ustar00rootroot00000000000000#include "bcftools.pysam.h" /* Copyright (C) 2014-2018 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include "regidx.h" #define MAX_COOR_0 REGIDX_MAX // CSI and hts_itr_query limit, 0-based #define iBIN(x) ((x)>>13) typedef struct { uint32_t beg, end; } reg_t; typedef struct { uint32_t pos, ireg; // y-coordinate and a pointer to reglist.reg and reglist.dat } pos_t; typedef struct _reglist_t reglist_t; typedef struct { uint32_t beg, end, ireg; // query coordinates and the active region regidx_t *ridx; reglist_t *list; int active; } _itr_t; // List of regions for one chromosome. struct _reglist_t { uint32_t *idx, nidx; // index to list.reg+1 uint32_t nreg, mreg; // n:used, m:allocated reg_t *reg; // regions void *dat; // payload data char *seq; // sequence name int unsorted; }; // Container of all sequences struct _regidx_t { int nseq, mseq; // n:used, m:alloced reglist_t *seq; // regions for each sequence void *seq2regs; // hash for fast lookup from chr name to regions char **seq_names; regidx_free_f free; // function to free any data allocated by regidx_parse_f regidx_parse_f parse; // parse one input line void *usr; // user data to pass to regidx_parse_f int payload_size; void *payload; // temporary payload data set by regidx_parse_f (sequence is not known beforehand) kstring_t str; }; int regidx_seq_nregs(regidx_t *idx, const char *seq) { int iseq; if ( khash_str2int_get(idx->seq2regs, seq, &iseq)!=0 ) return 0; // no such sequence return idx->seq[iseq].nreg; } int regidx_nregs(regidx_t *idx) { int i, nreg = 0; for (i=0; inseq; i++) nreg += idx->seq[i].nreg; return nreg; } char **regidx_seq_names(regidx_t *idx, int *n) { *n = idx->nseq; return idx->seq_names; } int regidx_insert_list(regidx_t *idx, char *line, char delim) { kstring_t tmp = {0,0,0}; char *ss = line; while ( *ss ) { char *se = ss; while ( *se && *se!=delim ) se++; tmp.l = 0; kputsn(ss, se-ss, &tmp); if ( regidx_insert(idx,tmp.s) < 0 ) { free(tmp.s); return -1; } if ( !*se ) break; ss = se+1; } free(tmp.s); return 0; } static inline int cmp_regs(reg_t *a, reg_t *b) { if ( a->beg < b->beg ) return -1; if ( a->beg > b->beg ) return 1; if ( a->end < b->end ) return 1; // longer intervals come first if ( a->end > b->end ) return -1; return 0; } static int cmp_reg_ptrs(const void *a, const void *b) { return cmp_regs((reg_t*)a,(reg_t*)b); } static int cmp_reg_ptrs2(const void *a, const void *b) { return cmp_regs(*((reg_t**)a),*((reg_t**)b)); } inline int regidx_push(regidx_t *idx, char *chr_beg, char *chr_end, uint32_t beg, uint32_t end, void *payload) { if ( beg > MAX_COOR_0 ) beg = MAX_COOR_0; if ( end > MAX_COOR_0 ) end = MAX_COOR_0; int rid; idx->str.l = 0; kputsn(chr_beg, chr_end-chr_beg+1, &idx->str); if ( khash_str2int_get(idx->seq2regs, idx->str.s, &rid)!=0 ) { // new chromosome idx->nseq++; int m_prev = idx->mseq; hts_expand0(reglist_t,idx->nseq,idx->mseq,idx->seq); hts_expand0(char*,idx->nseq,m_prev,idx->seq_names); idx->seq_names[idx->nseq-1] = strdup(idx->str.s); rid = khash_str2int_inc(idx->seq2regs, idx->seq_names[idx->nseq-1]); } reglist_t *list = &idx->seq[rid]; list->seq = idx->seq_names[rid]; list->nreg++; int mreg = list->mreg; hts_expand(reg_t,list->nreg,list->mreg,list->reg); list->reg[list->nreg-1].beg = beg; list->reg[list->nreg-1].end = end; if ( idx->payload_size ) { if ( mreg != list->mreg ) list->dat = realloc(list->dat,idx->payload_size*list->mreg); memcpy((char *)list->dat + idx->payload_size*(list->nreg-1), payload, idx->payload_size); } if ( !list->unsorted && list->nreg>1 && cmp_regs(&list->reg[list->nreg-2],&list->reg[list->nreg-1])>0 ) list->unsorted = 1; return 0; } int regidx_insert(regidx_t *idx, char *line) { if ( !line ) return 0; char *chr_from, *chr_to; uint32_t beg,end; int ret = idx->parse(line,&chr_from,&chr_to,&beg,&end,idx->payload,idx->usr); if ( ret==-2 ) return -1; // error if ( ret==-1 ) return 0; // skip the line regidx_push(idx, chr_from,chr_to,beg,end,idx->payload); return 0; } regidx_t *regidx_init_string(const char *str, regidx_parse_f parser, regidx_free_f free_f, size_t payload_size, void *usr_dat) { regidx_t *idx = (regidx_t*) calloc(1,sizeof(regidx_t)); if ( !idx ) return NULL; idx->free = free_f; idx->parse = parser ? parser : regidx_parse_tab; idx->usr = usr_dat; idx->seq2regs = khash_str2int_init(); idx->payload_size = payload_size; if ( payload_size ) idx->payload = malloc(payload_size); kstring_t tmp = {0,0,0}; const char *ss = str; while ( *ss ) { while ( *ss && isspace(*ss) ) ss++; const char *se = ss; while ( *se && *se!='\r' && *se!='\n' ) se++; tmp.l = 0; kputsn(ss, se-ss, &tmp); regidx_insert(idx,tmp.s); while ( *se && isspace(*se) ) se++; ss = se; } free(tmp.s); return idx; } regidx_t *regidx_init(const char *fname, regidx_parse_f parser, regidx_free_f free_f, size_t payload_size, void *usr_dat) { if ( !parser ) { if ( !fname ) parser = regidx_parse_tab; else { int len = strlen(fname); if ( len>=7 && !strcasecmp(".bed.gz",fname+len-7) ) parser = regidx_parse_bed; else if ( len>=8 && !strcasecmp(".bed.bgz",fname+len-8) ) parser = regidx_parse_bed; else if ( len>=4 && !strcasecmp(".bed",fname+len-4) ) parser = regidx_parse_bed; else if ( len>=4 && !strcasecmp(".vcf",fname+len-4) ) parser = regidx_parse_vcf; else if ( len>=7 && !strcasecmp(".vcf.gz",fname+len-7) ) parser = regidx_parse_vcf; else parser = regidx_parse_tab; } } regidx_t *idx = (regidx_t*) calloc(1,sizeof(regidx_t)); idx->free = free_f; idx->parse = parser; idx->usr = usr_dat; idx->seq2regs = khash_str2int_init(); idx->payload_size = payload_size; if ( payload_size ) idx->payload = malloc(payload_size); if ( !fname ) return idx; kstring_t str = {0,0,0}; htsFile *fp = hts_open(fname,"r"); if ( !fp ) goto error; while ( hts_getline(fp, KS_SEP_LINE, &str) > 0 ) { if ( regidx_insert(idx, str.s) ) goto error; } free(str.s); if ( hts_close(fp)!=0 ) { fprintf(bcftools_stderr,"[%s] Error: close failed .. %s\n", __func__,fname); goto error; } return idx; error: free(str.s); if ( fp ) hts_close(fp); regidx_destroy(idx); return NULL; } void regidx_destroy(regidx_t *idx) { int i, j; for (i=0; inseq; i++) { reglist_t *list = &idx->seq[i]; if ( idx->free ) { for (j=0; jnreg; j++) idx->free((char *)list->dat + idx->payload_size*j); } free(list->dat); free(list->reg); free(list->idx); } free(idx->seq_names); free(idx->seq); free(idx->str.s); free(idx->payload); khash_str2int_destroy_free(idx->seq2regs); free(idx); } int _reglist_build_index(regidx_t *regidx, reglist_t *list) { int i; if ( list->unsorted ) { if ( !regidx->payload_size ) qsort(list->reg,list->nreg,sizeof(reg_t),cmp_reg_ptrs); else { reg_t **ptr = (reg_t**) malloc(sizeof(reg_t*)*list->nreg); for (i=0; inreg; i++) ptr[i] = list->reg + i; qsort(ptr,list->nreg,sizeof(*ptr),cmp_reg_ptrs2); void *tmp_dat = malloc(regidx->payload_size*list->nreg); for (i=0; inreg; i++) { size_t iori = ptr[i] - list->reg; memcpy((char *)tmp_dat+i*regidx->payload_size, (char *)list->dat+iori*regidx->payload_size, regidx->payload_size); } free(list->dat); list->dat = tmp_dat; reg_t *tmp_reg = (reg_t*) malloc(sizeof(reg_t)*list->nreg); for (i=0; inreg; i++) { size_t iori = ptr[i] - list->reg; tmp_reg[i] = list->reg[iori]; } free(ptr); free(list->reg); list->reg = tmp_reg; list->mreg = list->nreg; } list->unsorted = 0; } list->nidx = 0; int j,k, midx = 0; for (j=0; jnreg; j++) { int ibeg = iBIN(list->reg[j].beg); int iend = iBIN(list->reg[j].end); if ( midx <= iend ) { int old_midx = midx; midx = iend + 1; kroundup32(midx); list->idx = (uint32_t*) realloc(list->idx, midx*sizeof(uint32_t)); memset(list->idx+old_midx, 0, sizeof(uint32_t)*(midx-old_midx)); } if ( ibeg==iend ) { if ( !list->idx[ibeg] ) list->idx[ibeg] = j + 1; } else { for (k=ibeg; k<=iend; k++) if ( !list->idx[k] ) list->idx[k] = j + 1; } if ( list->nidx < iend+1 ) list->nidx = iend+1; } return 0; } int regidx_overlap(regidx_t *regidx, const char *chr, uint32_t beg, uint32_t end, regitr_t *regitr) { if ( regitr ) regitr->seq = NULL; int iseq, ireg; if ( khash_str2int_get(regidx->seq2regs, chr, &iseq)!=0 ) return 0; // no such sequence reglist_t *list = ®idx->seq[iseq]; if ( !list->nreg ) return 0; if ( list->nreg==1 ) { if ( beg > list->reg[0].end ) return 0; if ( end < list->reg[0].beg ) return 0; ireg = 0; } else { if ( !list->idx ) _reglist_build_index(regidx,list); int ibeg = iBIN(beg); if ( ibeg >= list->nidx ) return 0; // beg is too big // find a matching region uint32_t i = list->idx[ibeg]; if ( !i ) { int iend = iBIN(end); if ( iend > list->nidx ) iend = list->nidx; for (i=ibeg; i<=iend; i++) if ( list->idx[i] ) break; if ( i>iend ) return 0; i = list->idx[i]; } for (ireg=i-1; iregnreg; ireg++) { if ( list->reg[ireg].beg > end ) return 0; // no match, past the query region if ( list->reg[ireg].end >= beg && list->reg[ireg].beg <= end ) break; // found } if ( ireg >= list->nreg ) return 0; // no match } if ( !regitr ) return 1; // match, but no more info to save // may need to iterate over the matching regions later _itr_t *itr = (_itr_t*)regitr->itr; itr->ridx = regidx; itr->list = list; itr->beg = beg; itr->end = end; itr->ireg = ireg; itr->active = 0; regitr->seq = list->seq; regitr->beg = list->reg[ireg].beg; regitr->end = list->reg[ireg].end; if ( regidx->payload_size ) regitr->payload = (char *)list->dat + regidx->payload_size*ireg; return 1; } int regidx_parse_bed(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr) { char *ss = (char*) line; while ( *ss && isspace(*ss) ) ss++; if ( !*ss ) return -1; // skip blank lines if ( *ss=='#' ) return -1; // skip comments char *se = ss; while ( *se && !isspace(*se) ) se++; *chr_beg = ss; *chr_end = se-1; if ( !*se ) { // just the chromosome name *beg = 0; *end = MAX_COOR_0; return 0; } ss = se+1; *beg = strtod(ss, &se); if ( ss==se ) { fprintf(bcftools_stderr,"Could not parse bed line: %s\n", line); return -2; } ss = se+1; *end = strtod(ss, &se) - 1; if ( ss==se ) { fprintf(bcftools_stderr,"Could not parse bed line: %s\n", line); return -2; } return 0; } int regidx_parse_tab(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr) { char *ss = (char*) line; while ( *ss && isspace(*ss) ) ss++; if ( !*ss ) return -1; // skip blank lines if ( *ss=='#' ) return -1; // skip comments char *se = ss; while ( *se && !isspace(*se) ) se++; *chr_beg = ss; *chr_end = se-1; if ( !*se ) { // just the chromosome name *beg = 0; *end = MAX_COOR_0; return 0; } ss = se+1; *beg = strtod(ss, &se); if ( ss==se ) { fprintf(bcftools_stderr,"Could not parse tab line: %s\n", line); return -2; } if ( *beg==0 ) { fprintf(bcftools_stderr,"Could not parse tab line, expected 1-based coordinate: %s\n", line); return -2; } (*beg)--; if ( !se[0] || !se[1] ) *end = *beg; else { ss = se+1; *end = strtod(ss, &se); if ( ss==se || (*se && !isspace(*se)) ) *end = *beg; else if ( *end==0 ) { fprintf(bcftools_stderr,"Could not parse tab line, expected 1-based coordinate: %s\n", line); return -2; } else (*end)--; } return 0; } int regidx_parse_vcf(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr) { int ret = regidx_parse_tab(line, chr_beg, chr_end, beg, end, payload, usr); if ( !ret ) *end = *beg; return ret; } int regidx_parse_reg(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr) { char *ss = (char*) line; while ( *ss && isspace(*ss) ) ss++; if ( !*ss ) return -1; // skip blank lines if ( *ss=='#' ) return -1; // skip comments char *se = ss; while ( *se && *se!=':' ) se++; *chr_beg = ss; *chr_end = se-1; if ( !*se ) { *beg = 0; *end = MAX_COOR_0; return 0; } ss = se+1; *beg = strtod(ss, &se); if ( ss==se ) { fprintf(bcftools_stderr,"Could not parse reg line: %s\n", line); return -2; } if ( *beg==0 ) { fprintf(bcftools_stderr,"Could not parse reg line, expected 1-based coordinate: %s\n", line); return -2; } (*beg)--; if ( !se[0] || !se[1] ) *end = se[0]=='-' ? MAX_COOR_0 : *beg; else { ss = se+1; *end = strtod(ss, &se); if ( ss==se ) *end = *beg; else if ( *end==0 ) { fprintf(bcftools_stderr,"Could not parse reg line, expected 1-based coordinate: %s\n", line); return -2; } else (*end)--; } return 0; } regitr_t *regitr_init(regidx_t *regidx) { regitr_t *regitr = (regitr_t*) calloc(1,sizeof(regitr_t)); regitr->itr = (_itr_t*) calloc(1,sizeof(_itr_t)); _itr_t *itr = (_itr_t*) regitr->itr; itr->ridx = regidx; itr->list = NULL; return regitr; } void regitr_reset(regidx_t *regidx, regitr_t *regitr) { _itr_t *itr = (_itr_t*) regitr->itr; memset(itr,0,sizeof(_itr_t)); itr->ridx = regidx; } void regitr_destroy(regitr_t *regitr) { free(regitr->itr); free(regitr); } int regitr_overlap(regitr_t *regitr) { if ( !regitr->seq ) return 0; _itr_t *itr = (_itr_t*) regitr->itr; if ( !itr->active ) { // is this the first call after regidx_overlap? itr->active = 1; itr->ireg++; return 1; } reglist_t *list = itr->list; int i; for (i=itr->ireg; inreg; i++) { if ( list->reg[i].beg > itr->end ) return 0; // no match, past the query region if ( list->reg[i].end >= itr->beg && list->reg[i].beg <= itr->end ) break; // found } if ( i >= list->nreg ) return 0; // no match itr->ireg = i + 1; regitr->seq = list->seq; regitr->beg = list->reg[i].beg; regitr->end = list->reg[i].end; if ( itr->ridx->payload_size ) regitr->payload = (char *)list->dat + itr->ridx->payload_size*i; return 1; } int regitr_loop(regitr_t *regitr) { _itr_t *itr = (_itr_t*) regitr->itr; regidx_t *regidx = itr->ridx; if ( !itr->list ) // first time here { itr->list = regidx->seq; itr->ireg = 0; } size_t iseq = itr->list - regidx->seq; if ( iseq >= regidx->nseq ) return 0; if ( itr->ireg >= itr->list->nreg ) { iseq++; if ( iseq >= regidx->nseq ) return 0; // no more sequences, done itr->ireg = 0; itr->list = ®idx->seq[iseq]; } regitr->seq = itr->list->seq; regitr->beg = itr->list->reg[itr->ireg].beg; regitr->end = itr->list->reg[itr->ireg].end; if ( regidx->payload_size ) regitr->payload = (char *)itr->list->dat + regidx->payload_size*itr->ireg; itr->ireg++; return 1; } void regitr_copy(regitr_t *dst, regitr_t *src) { _itr_t *dst_itr = (_itr_t*) dst->itr; _itr_t *src_itr = (_itr_t*) src->itr; *dst_itr = *src_itr; *dst = *src; dst->itr = dst_itr; } pysam-0.23.0/bcftools/regidx.h000066400000000000000000000207521475062545500162160ustar00rootroot00000000000000/* Copyright (C) 2014-2016, 2018 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Region indexing with an optional payload. Example of usage: // Init the parser and print regions. In this example the payload is a // pointer to a string. For the description of parse_custom and // free_custom functions, see regidx_parse_f and regidx_free_f below, // and for working example see test/test-regidx.c. regidx_t *idx = regidx_init(in_fname,parse_custom,free_custom,sizeof(char*),NULL); // Query overlap with chr:beg-end (beg,end are 1-based coordinates) regitr_t *itr = regitr_init(idx); if ( regidx_overlap(idx, chr,beg-1,end-1, itr) ) printf("There is an overlap!\n"); while ( regitr_overlap(itr) ) { printf("[%d,%d] overlaps with [%d,%d], payload=%s\n", beg,end, itr->beg+1, itr->end+1, regitr_payload(itr,char*)); } regidx_destroy(idx); regitr_destroy(itr); Another example, loop over all regions: regidx_t *idx = regidx_init(in_fname,NULL,NULL,0,NULL); regitr_t *itr = regitr_init(idx); while ( regitr_loop(itr) ) printf("chr=%s beg=%d end=%d\n", itr->seq, itr->beg+1, itr->end+1); regidx_destroy(idx); regitr_destroy(itr); */ #ifndef __REGIDX_H__ #define __REGIDX_H__ #include #include /* Avoid conflicts with HTSlib's regidx_* functions. */ #define regidx_destroy bcftools_regidx_destroy #define regidx_init bcftools_regidx_init #define regidx_init_string bcftools_regidx_init_string #define regidx_insert bcftools_regidx_insert #define regidx_insert_list bcftools_regidx_insert_list #define regidx_nregs bcftools_regidx_nregs #define regidx_overlap bcftools_regidx_overlap #define regidx_parse_bed bcftools_regidx_parse_bed #define regidx_parse_reg bcftools_regidx_parse_reg #define regidx_parse_tab bcftools_regidx_parse_tab #define regidx_parse_vcf bcftools_regidx_parse_vcf #define regidx_push bcftools_regidx_push #define regidx_seq_names bcftools_regidx_seq_names #define regidx_seq_nregs bcftools_regidx_seq_nregs #define regitr_copy bcftools_regitr_copy #define regitr_destroy bcftools_regitr_destroy #define regitr_init bcftools_regitr_init #define regitr_loop bcftools_regitr_loop #define regitr_overlap bcftools_regitr_overlap #define regitr_reset bcftools_regitr_reset #ifdef __cplusplus extern "C" { #endif #define REGIDX_MAX 2147483646 // maximum regidx coordinate (0-based) typedef struct _regidx_t regidx_t; typedef struct { uint32_t beg,end; void *payload; char *seq; void *itr; } regitr_t; #define regitr_payload(itr,type_t) (*((type_t*)(itr)->payload)) /* * regidx_parse_f - Function to parse one input line, such as regidx_parse_bed * or regidx_parse_tab below. The function is expected to set `chr_from` and * `chr_to` to point to first and last character of chromosome name and set * coordinates `beg` and `end` (0-based, inclusive). If regidx_init() was * called with non-zero payload_size, the `payload` points to a memory * location of the payload_size and `usr` is the data passed to regidx_init(). * Any memory allocated by the function will be freed by regidx_free_f called * by regidx_destroy(). * * Return value: 0 on success, -1 to skip a record, -2 on fatal error. */ typedef int (*regidx_parse_f)(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr); typedef void (*regidx_free_f)(void *payload); /* * A note about the parsers: * - leading spaces are ignored * - lines starting with "#" are ignored */ int regidx_parse_bed(const char*,char**,char**,uint32_t*,uint32_t*,void*,void*); // CHROM or whitespace-sepatated CHROM,FROM,TO (0-based,right-open) int regidx_parse_tab(const char*,char**,char**,uint32_t*,uint32_t*,void*,void*); // CHROM or whitespace-separated CHROM,POS (1-based, inclusive) int regidx_parse_reg(const char*,char**,char**,uint32_t*,uint32_t*,void*,void*); // CHROM, CHROM:POS, CHROM:FROM-TO, CHROM:FROM- (1-based, inclusive) int regidx_parse_vcf(const char*,char**,char**,uint32_t*,uint32_t*,void*,void*); /* * regidx_init() - creates new index * regidx_init_string() - creates new index, from a string rather than from a file * * @param fname: input file name or NULL if regions will be added one-by-one via regidx_insert() * @param parsef: regidx_parse_bed, regidx_parse_tab or see description of regidx_parse_f. If NULL, * the format will be autodetected, currently either regidx_parse_tab (the default) or * regidx_parse_bed (file must be named 'bed' or 'bed.gz') will be used. Note that * the exact autodetection algorithm will change. * @param freef: NULL or see description of regidx_parse_f * @param payload_size: 0 with regidx_parse_bed, regidx_parse_tab or see regidx_parse_f * @param usr: optional user data passed to regidx_parse_f * * Returns index on success or NULL on error. */ regidx_t *regidx_init(const char *fname, regidx_parse_f parsef, regidx_free_f freef, size_t payload_size, void *usr); regidx_t *regidx_init_string(const char *string, regidx_parse_f parsef, regidx_free_f freef, size_t payload_size, void *usr); /* * regidx_destroy() - free memory allocated by regidx_init */ void regidx_destroy(regidx_t *idx); /* * regidx_overlap() - check overlap of the location chr:from-to with regions * @param beg,end: 0-based start, end coordinate (inclusive) * @param itr: pointer to iterator, can be NULL if regidx_loop not needed * * Returns 0 if there is no overlap or 1 if overlap is found. The overlapping * regions can be iterated as shown in the example above. */ int regidx_overlap(regidx_t *idx, const char *chr, uint32_t beg, uint32_t end, regitr_t *itr); /* * regidx_insert() - add a new region. * regidx_insert_list() - add new regions from a list * regidx_push() - low level insertion of a new region * * Returns 0 on success or -1 on error. */ int regidx_insert(regidx_t *idx, char *line); int regidx_insert_list(regidx_t *idx, char *line, char delim); int regidx_push(regidx_t *idx, char *chr_beg, char *chr_end, uint32_t beg, uint32_t end, void *payload); /* * regidx_seq_names() - return list of all sequence names */ char **regidx_seq_names(regidx_t *idx, int *n); /* * regidx_seq_nregs() - number of regions * regidx_nregs() - total number of regions */ int regidx_seq_nregs(regidx_t *idx, const char *seq); int regidx_nregs(regidx_t *idx); /* * regitr_init() - initialize an iterator. The idx parameter is required only * with regitr_loop. If only regitr_overlap is called, NULL * can be given. * * regitr_reset() - initialize an iterator for a repeated regitr_loop cycle. * Not required with regitr_overlap. */ regitr_t *regitr_init(regidx_t *idx); void regitr_destroy(regitr_t *itr); void regitr_reset(regidx_t *idx, regitr_t *itr); /* * regitr_overlap() - next overlapping region * Returns 0 when done or 1 when itr is set to next region */ int regitr_overlap(regitr_t *itr); /* * regitr_loop() - loop over all regions * Returns 0 when done or 1 when itr is set to next region */ int regitr_loop(regitr_t *itr); /* * regitr_copy() - create a copy of an iterator for a repeated iteration with regitr_loop */ void regitr_copy(regitr_t *dst, regitr_t *src); #ifdef __cplusplus } #endif #endif pysam-0.23.0/bcftools/reheader.c000066400000000000000000000634571475062545500165170ustar00rootroot00000000000000/* reheader.c -- reheader subcommand. Copyright (C) 2014-2022,2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #ifdef _WIN32 #include #endif #include #include #include // for hts_get_bgzfp() #include #include #include #include #include "bcftools.h" #include "khash_str2str.h" typedef struct _args_t { char **argv, *fname, *samples_fname, *header_fname, *output_fname; char *fai_fname; htsFile *fp; faidx_t *fai; htsFormat type; htsThreadPool *threads; int argc, n_threads; } args_t; static inline int is_escaped(const char *min, const char *str) { int n = 0; while ( --str>=min && *str=='\\' ) n++; return n%2; } static char *copy_and_update_contig_line(faidx_t *fai, char *line, void *chr_seen, kstring_t *dst) { kstring_t key = {0,0,0}, val = {0,0,0}, tmp = {0,0,0}; char *chr_name = NULL, *p, *q = line + 9; // skip ##contig= char *end = q; int nopen = 1; hts_pos_t chr_len = 0; while ( *end && *end!='\n' ) end++; while ( *q && *q!='\n' && nopen>0 ) { p = ++q; while ( *q && (*q==' ' || *q=='\t') ) { p++; q++; } // ^[A-Za-z_][0-9A-Za-z_.]*$ if (p==q && *q && (isalpha(*q) || *q=='_')) { q++; while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++; } int n = q-p; int m = 0; while ( *q && (*q==' ' || *q=='\t') ) { q++; m++; } if ( *q!='=' || !n ) { char *x = q; while ( *x && *x!='\n' ) x++; *x = '\0'; error("Could not parse the line: %s [%s][%s]\n", line,p,q); } key.l = 0; kputsn(p,q-p-m,&key); p = ++q; while ( *q && (*q==' ' || *q=='\t') ) { p++; q++; } int quoted = *p=='"' ? 1 : 0; if ( quoted ) p++, q++; while ( *q && *q != '\n' ) { if ( quoted ) { if ( *q=='"' && !is_escaped(p,q) ) break; } else { if ( *q=='<' ) nopen++; if ( *q=='>' ) nopen--; if ( !nopen ) break; if ( *q==',' && nopen==1 ) break; } q++; } char *r = q; while ( r > p && r[-1] == ' ' ) r--; val.l = 0; kputsn(p,r-p,&val); if ( quoted && *q=='"' ) q++; if ( *q=='>' ) { nopen--; q++; } if ( !strcmp("length",key.s) ) continue; if ( !strcmp("ID",key.s) ) { if ( khash_str2int_has_key(chr_seen,val.s) ) continue; chr_len = faidx_seq_len64(fai, val.s); if ( chr_len==-1 ) { free(val.s); free(key.s); free(tmp.s); return end; // the sequence is not in fai, remove } chr_name = strdup(val.s); khash_str2int_inc(chr_seen, chr_name); continue; } kputc(',',&tmp); kputs(key.s,&tmp); kputc('=',&tmp); if ( quoted ) kputc('"',&tmp); kputs(val.s,&tmp); if ( quoted ) kputc('"',&tmp); } if ( !chr_name ) return end; ksprintf(dst,"##contig=",chr_name,chr_len,tmp.l ? tmp.s : ""); free(key.s); free(val.s); free(tmp.s); return q; } char *init_tmp_prefix(const char *tmp_prefix) { kstring_t prefix = {0,0,0}; if ( tmp_prefix ) { ksprintf(&prefix,"%sXXXXXX",tmp_prefix); return prefix.s; } char *tmpdir = getenv("TMPDIR"); if ( tmpdir ) kputs(tmpdir, &prefix); else { #ifdef _WIN32 char tmp_path[MAX_PATH]; int ret = GetTempPath(MAX_PATH, tmp_path); if (!ret || ret > MAX_PATH) error("Could not get the path to the temporary folder\n"); kputs(tmp_path, &prefix); #else kputs("/tmp", &prefix); #endif } kputs("/bcftools.XXXXXX", &prefix); return prefix.s; } static void update_from_fai(faidx_t *fai, kstring_t *hdr_txt) { kstring_t hdr_txt_new = {0,0,0}; // update the existing contig lines and remove lines not present in the fai file void *chr_seen = khash_str2int_init(); char *tmp, *beg = hdr_txt->s; while ( beg && *beg ) { tmp = strstr(beg, "\n##contig=<"); if ( !tmp ) break; kputsn(beg, tmp-beg+1, &hdr_txt_new); size_t l_prev = hdr_txt_new.l; beg = copy_and_update_contig_line(fai,tmp+1,chr_seen, &hdr_txt_new); if ( l_prev==hdr_txt_new.l ) hdr_txt_new.l--; // nothing was added, remove the newline } if ( !beg || !(tmp=strstr(beg,"\n#CHROM")) ) error("Failed to parse the header, #CHROM not found\n"); kputsn(beg, tmp-beg+1, &hdr_txt_new); // add any new contig lines int i, n = faidx_nseq(fai); for (i=0; i\n",faidx_iseq(fai,i),faidx_seq_len64(fai,faidx_iseq(fai,i))); } kputs(tmp+1,&hdr_txt_new); // Switch the new header content for the old free(hdr_txt->s); memcpy(hdr_txt, &hdr_txt_new, sizeof(*hdr_txt)); khash_str2int_destroy_free(chr_seen); } static void read_header_file(char *fname, kstring_t *hdr) { kstring_t tmp = {0,0,0}; hdr->l = 0; htsFile *fp = hts_open(fname, "r"); if ( !fp ) error("Could not read: %s\n", fname); while ( hts_getline(fp, KS_SEP_LINE, &tmp) > 0 ) { kputsn(tmp.s,tmp.l,hdr); kputc('\n',hdr); } if ( hts_close(fp) ) error("Close failed: %s\n", fname); free(tmp.s); while ( hdr->l>0 && isspace(hdr->s[hdr->l-1]) ) hdr->l--; // remove trailing newlines kputc('\n',hdr); } static int set_sample_pairs(char **samples, int nsamples, kstring_t *hdr, int idx) { int i, j, n; kstring_t key = {0,0,0}; kstring_t val = {0,0,0}; // Are these samples "old-name new-name" pairs? void *hash = khash_str2str_init(); for (i=0; il>0 && isspace(hdr->s[hdr->l-1]) ) hdr->l--; // remove trailing newlines hdr->s[hdr->l] = 0; kstring_t tmp = {0,0,0}; i = j = n = 0; // i:traverse the #CHROM line 1 by 1; j:points to the last column while ( hdr->s[idx+i] ) { if ( hdr->s[idx+i]=='\t' ) { hdr->s[idx+i] = 0; if ( ++n>9 ) { char *new_name = khash_str2str_get(hash,hdr->s+idx+j); kputs(new_name ? new_name : hdr->s+idx+j, &tmp); } else kputs(hdr->s+idx+j, &tmp); kputc('\t',&tmp); j = ++i; continue; } i++; } char *new_name = khash_str2str_get(hash,hdr->s+idx+j); kputs(new_name ? new_name : hdr->s+idx+j, &tmp); khash_str2str_destroy_free_all(hash); hdr->l = idx; kputs(tmp.s, hdr); kputc('\n', hdr); free(tmp.s); return 1; } static void set_samples(char **samples, int nsamples, kstring_t *hdr) { // Find the beginning of the #CHROM line int i = hdr->l - 2, ncols = 0; while ( i>=0 && hdr->s[i]!='\n' ) { if ( hdr->s[i]=='\t' ) ncols++; i--; } if ( i<0 || strncmp(hdr->s+i+1,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT",45) ) { if ( i>0 && !strncmp(hdr->s+i+1,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",38) ) error("Error: missing FORMAT fields, cowardly refusing to add samples\n"); error("Could not parse the header: %s\n", hdr->s); } // Are the samples "old-sample new-sample" pairs? if ( set_sample_pairs(samples,nsamples,hdr, i+1) ) return; // Replace all samples if ( ncols!=nsamples+8 ) fprintf(stderr, "Warning: different number of samples: %d vs %d\n", nsamples,ncols-8); ncols = 0; while ( ncols!=9 ) { i++; if ( hdr->s[i]=='\t' ) ncols++; } hdr->l = i; for (i=0; ifp); if ( !fp || bgzf_read_block(fp) != 0 || !fp->block_length ) error("Failed to read %s: %s\n", args->fname, strerror(errno)); kstring_t hdr = {0,0,0}; char *buffer = (char*) fp->uncompressed_block; // Read the header and find the position of the data block if ( buffer[0]!='#' ) error("Could not parse the header, expected '#', found '%c'\n", buffer[0]); int skip_until = 1; // end of the header in the current uncompressed block while (1) { if ( buffer[skip_until]=='\n' ) { skip_until++; if ( skip_until>=fp->block_length ) { kputsn(buffer,skip_until,&hdr); if ( bgzf_read_block(fp) != 0 ) error("Error reading %s\n", args->fname); if ( !fp->block_length ) break; skip_until = 0; } // The header has finished if ( buffer[skip_until]!='#' ) { kputsn(buffer,skip_until,&hdr); break; } } skip_until++; if ( skip_until>=fp->block_length ) { kputsn(buffer,fp->block_length,&hdr); if ( bgzf_read_block(fp) != 0 ) error("Error reading %s\n", args->fname); if ( !fp->block_length ) break; skip_until = 0; } } int nsamples = 0; char **samples = NULL; if ( args->samples_fname ) { samples = hts_readlines(args->samples_fname, &nsamples); if ( !samples || !nsamples ) error("Error reading the --samples file \"%s\"\n", args->samples_fname); } if ( args->header_fname ) { free(hdr.s); hdr.s = NULL; hdr.l = hdr.m = 0; read_header_file(args->header_fname, &hdr); } if ( args->fai ) update_from_fai(args->fai, &hdr); if ( samples ) { set_samples(samples, nsamples, &hdr); int i; for (i=0; ioutput_fname ? args->output_fname : "-","w");; if ( bgzf_write(bgzf_out, hdr.s, hdr.l) < 0 ) error("Can't write BGZF header (code %d)\n", bgzf_out->errcode); free(hdr.s); // Output all remaining data read with the header block if ( fp->block_length - skip_until > 0 ) { if ( bgzf_write(bgzf_out, buffer+skip_until, fp->block_length-skip_until)<0 ) error("Error: %d\n",fp->errcode); } if ( bgzf_flush(bgzf_out)<0 ) error("Error: %d\n",bgzf_out->errcode); // Stream the rest of the file without as it is, without decompressing ssize_t nread; const size_t page_size = 32768; char *buf = (char*) malloc(page_size); while (1) { nread = bgzf_raw_read(fp, buf, page_size); if ( nread<=0 ) break; int count = bgzf_raw_write(bgzf_out, buf, nread); if (count != nread) error("Write failed, wrote %d instead of %d bytes.\n", count,(int)nread); } if (bgzf_close(bgzf_out) < 0) error("Error closing %s: %d\n",args->output_fname ? args->output_fname : "-",bgzf_out->errcode); if (hts_close(args->fp)) error("Error closing %s: %d\n",args->fname,fp->errcode); free(buf); } static void reheader_vcf(args_t *args) { kstring_t hdr = {0,0,0}; htsFile *fp = args->fp; while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 ) { kputc('\n',&fp->line); // hts_getline eats the newline character if ( fp->line.s[0]!='#' ) break; kputsn(fp->line.s,fp->line.l,&hdr); } int nsamples = 0; char **samples = NULL; if ( args->samples_fname ) { samples = hts_readlines(args->samples_fname, &nsamples); if ( !samples || !nsamples ) error("Error reading the --samples file \"%s\"\n", args->samples_fname); } if ( args->header_fname ) { free(hdr.s); hdr.s = NULL; hdr.l = hdr.m = 0; read_header_file(args->header_fname, &hdr); } if ( args->fai ) update_from_fai(args->fai, &hdr); if ( samples ) { set_samples(samples, nsamples, &hdr); int i; for (i=0; ioutput_fname ? open(args->output_fname, O_WRONLY|O_CREAT|O_TRUNC, 0666) : STDOUT_FILENO; if ( out==-1 ) error("%s: %s\n", args->output_fname,strerror(errno)); if ( write(out, hdr.s, hdr.l)!=hdr.l ) error("Failed to write %"PRIu64" bytes\n", (uint64_t)hdr.l); free(hdr.s); if ( fp->line.l ) { if ( write(out, fp->line.s, fp->line.l)!=fp->line.l ) error("Failed to write %"PRIu64" bytes\n", (uint64_t)fp->line.l); } while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 ) // uncompressed file implies small size, we don't worry about speed { kputc('\n',&fp->line); if ( write(out, fp->line.s, fp->line.l)!=fp->line.l ) error("Failed to write %"PRIu64" bytes\n", (uint64_t)fp->line.l); } if ( hts_close(fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fname); if ( close(out)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname); } static bcf_hdr_t *strip_header(bcf_hdr_t *src, bcf_hdr_t *dst) { bcf_hrec_t *src_hrec, *dst_hrec, *tmp; bcf_hdr_t *out = bcf_hdr_init("r"); int i; for (i=0; inhrec; i++) { // first insert lines which do not code BCF ids, their order does not matter dst_hrec = dst->hrec[i]; if ( dst_hrec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->type== BCF_HL_CTG ) continue; bcf_hdr_add_hrec(out, bcf_hrec_dup(dst_hrec)); } for (i=0; inhrec; i++) { // now transfer header lines which define BCF ids src_hrec = src->hrec[i]; if ( src_hrec->type==BCF_HL_FLT || src_hrec->type==BCF_HL_INFO || src_hrec->type==BCF_HL_FMT || src_hrec->type== BCF_HL_CTG ) { int j = bcf_hrec_find_key(src_hrec, "ID"); dst_hrec = bcf_hdr_get_hrec(dst, src_hrec->type, "ID", src_hrec->vals[j], NULL); if ( !dst_hrec ) continue; tmp = bcf_hrec_dup(dst_hrec); j = bcf_hrec_find_key(src_hrec, "IDX"); if ( j>=0 ) { j = atoi(src_hrec->vals[j]); if (hrec_add_idx(tmp, j) < 0) error_errno("[%s] Failed to add IDX header", __func__); } bcf_hdr_add_hrec(out, tmp); } } if (bcf_hdr_sync(out) < 0) error_errno("[%s] Failed to update header", __func__); for (i=0; inhrec; i++) { // finally add new structured fields dst_hrec = dst->hrec[i]; if ( dst_hrec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->type== BCF_HL_CTG ) { int j = bcf_hrec_find_key(dst_hrec, "ID"); tmp = bcf_hdr_get_hrec(out, dst_hrec->type, "ID", dst_hrec->vals[j], NULL); if ( !tmp ) bcf_hdr_add_hrec(out, bcf_hrec_dup(dst_hrec)); } } for (i=0; in[BCF_DT_SAMPLE]; i++) bcf_hdr_add_sample(out, dst->samples[i]); bcf_hdr_destroy(dst); return out; } static void reheader_bcf(args_t *args, int is_compressed) { htsFile *fp = args->fp; if ( args->n_threads > 0 ) { args->threads = (htsThreadPool *) calloc(1, sizeof(htsThreadPool)); if ( !args->threads ) error("Could not allocate memory\n"); if ( !(args->threads->pool = hts_tpool_init(args->n_threads)) ) error("Could not initialize threading\n"); hts_set_thread_pool(fp, args->threads); } bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to read the header: %s\n", args->fname); kstring_t htxt = {0,0,0}; bcf_hdr_format(hdr, 1, &htxt); int i, nsamples = 0; char **samples = NULL; if ( args->samples_fname ) { samples = hts_readlines(args->samples_fname, &nsamples); if ( !samples || !nsamples ) error("Error reading the --samples file \"%s\"\n", args->samples_fname); } if ( args->header_fname ) { free(htxt.s); htxt.s = NULL; htxt.l = htxt.m = 0; read_header_file(args->header_fname, &htxt); } if ( args->fai ) update_from_fai(args->fai, &htxt); if ( samples ) { set_samples(samples, nsamples, &htxt); for (i=0; iheader_fname ) hdr_out = strip_header(hdr, hdr_out); // write the header and the body htsFile *fp_out = hts_open(args->output_fname ? args->output_fname : "-",is_compressed ? "wb" : "wbu"); if ( !fp_out ) error("%s: %s\n", args->output_fname ? args->output_fname : "-", strerror(errno)); if ( args->threads ) hts_set_thread_pool(fp_out, args->threads); if ( bcf_hdr_write(fp_out, hdr_out)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname ? args->output_fname : "standard output"); bcf1_t *rec = bcf_init(); while ( bcf_read(fp, hdr, rec)==0 ) { // sanity checking, this slows things down. Make it optional? bcf_unpack(rec, BCF_UN_ALL); if ( rec->rid >= hdr_out->n[BCF_DT_CTG] || strcmp(bcf_hdr_int2id(hdr,BCF_DT_CTG,rec->rid),bcf_hdr_int2id(hdr_out,BCF_DT_CTG,rec->rid)) ) error("The CHROM is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_CTG,rec->rid)); for (i=0; id.n_flt; i++) { int id = rec->d.flt[i]; if ( id >= hdr_out->n[BCF_DT_ID] ) break; if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FLT,id) ) break; if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) ) error("FIXME: Broken FILTER ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key); } if ( i!=rec->d.n_flt ) error("The FILTER is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.flt[i])); for (i=0; in_info; i++) { int id = rec->d.info[i].key; if ( id >= hdr_out->n[BCF_DT_ID] ) break; if ( !hdr_out->id[BCF_DT_ID][id].key ) break; if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_INFO,id) ) break; if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) ) error("FIXME: Broken INFO ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key); } if ( i!=rec->n_info ) error("The INFO tag is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.info[i].key)); for (i=0; in_fmt; i++) { int id = rec->d.fmt[i].id; if ( id >= hdr_out->n[BCF_DT_ID] ) break; if ( !hdr_out->id[BCF_DT_ID][id].key ) break; if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FMT,id) ) break; if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) ) error("FIXME: Broken FORMAT ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key); } if ( i!=rec->n_fmt ) error("The FORMAT tag is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.fmt[i].id)); if ( bcf_write(fp_out,hdr_out,rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname ? args->output_fname : "standard output"); } bcf_destroy(rec); free(htxt.s); if ( hts_close(fp_out)!=0 ) error("[%s] Error: failed to close the file %s\n",__func__,args->output_fname ? args->output_fname : "standard output"); if ( hts_close(fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fname); bcf_hdr_destroy(hdr_out); bcf_hdr_destroy(hdr); if ( args->threads ) { hts_tpool_destroy(args->threads->pool); free(args->threads); } } static void usage(args_t *args) { fprintf(stderr, "\n"); fprintf(stderr, "About: Modify header of VCF/BCF files, change sample names.\n"); fprintf(stderr, "Usage: bcftools reheader [OPTIONS] \n"); fprintf(stderr, "\n"); fprintf(stderr, "Options:\n"); fprintf(stderr, " -f, --fai FILE update sequences and their lengths from the .fai file\n"); fprintf(stderr, " -h, --header FILE new header\n"); fprintf(stderr, " -o, --output FILE write output to a file [standard output]\n"); fprintf(stderr, " -s, --samples FILE new sample names\n"); fprintf(stderr, " -T, --temp-prefix PATH ignored; was template for temporary file name\n"); fprintf(stderr, " --threads INT use multithreading with worker threads (BCF only) [0]\n"); fprintf(stderr, "\n"); fprintf(stderr, "Example:\n"); fprintf(stderr, " # Write out the header to be modified\n"); fprintf(stderr, " bcftools view -h old.bcf > header.txt\n"); fprintf(stderr, "\n"); fprintf(stderr, " # Edit the header using your favorite text editor\n"); fprintf(stderr, " vi header.txt\n"); fprintf(stderr, "\n"); fprintf(stderr, " # Reheader the file\n"); fprintf(stderr, " bcftools reheader -h header.txt -o new.bcf old.bcf\n"); fprintf(stderr, "\n"); exit(1); } int main_reheader(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; static struct option loptions[] = { {"temp-prefix",1,0,'T'}, {"fai",1,0,'f'}, {"output",1,0,'o'}, {"header",1,0,'h'}, {"samples",1,0,'s'}, {"threads",1,NULL,1}, {0,0,0,0} }; while ((c = getopt_long(argc, argv, "s:h:o:f:T:",loptions,NULL)) >= 0) { switch (c) { case 1 : args->n_threads = strtol(optarg, 0, 0); break; case 'T': break; // unused - was temp file prefix case 'f': args->fai_fname = optarg; break; case 'o': args->output_fname = optarg; break; case 's': args->samples_fname = optarg; break; case 'h': args->header_fname = optarg; break; case '?': usage(args); break; default: error("Unknown argument: %s\n", optarg); } } if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) args->fname = "-"; // reading from stdin else usage(args); } else args->fname = argv[optind]; if ( args->fai_fname ) { args->fai = fai_load3(args->fai_fname,args->fai_fname,NULL,FAI_FASTA); if ( !args->fai ) error("Could not parse %s\n", args->fai_fname); } if ( !args->samples_fname && !args->header_fname && !args->fai) usage(args); if ( !args->fname ) usage(args); args->fp = hts_open(args->fname,"r"); if ( !args->fp ) error("Failed to read from %s\n", !strcmp("-",args->fname)?"standard input":args->fname); args->type = *hts_get_format(args->fp); if ( args->type.format==vcf ) { if ( args->type.compression==bgzf ) reheader_vcf_gz(args); else if ( args->type.compression==no_compression ) reheader_vcf(args); else if ( args->type.compression==gzip ) error("Error: cannot reheader gzip-compressed files, first convert with `bcftools view --output-type` to a supported format\n"); else error("Error: the compression type of \"%s\" is not recognised/supported\n", args->fname); } else reheader_bcf(args, args->type.compression==bgzf || args->type.compression==gzip); if (args->fai) fai_destroy(args->fai); free(args); return 0; } pysam-0.23.0/bcftools/reheader.c.pysam.c000066400000000000000000000640441475062545500200610ustar00rootroot00000000000000#include "bcftools.pysam.h" /* reheader.c -- reheader subcommand. Copyright (C) 2014-2022,2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #ifdef _WIN32 #include #endif #include #include #include // for hts_get_bgzfp() #include #include #include #include #include "bcftools.h" #include "khash_str2str.h" typedef struct _args_t { char **argv, *fname, *samples_fname, *header_fname, *output_fname; char *fai_fname; htsFile *fp; faidx_t *fai; htsFormat type; htsThreadPool *threads; int argc, n_threads; } args_t; static inline int is_escaped(const char *min, const char *str) { int n = 0; while ( --str>=min && *str=='\\' ) n++; return n%2; } static char *copy_and_update_contig_line(faidx_t *fai, char *line, void *chr_seen, kstring_t *dst) { kstring_t key = {0,0,0}, val = {0,0,0}, tmp = {0,0,0}; char *chr_name = NULL, *p, *q = line + 9; // skip ##contig= char *end = q; int nopen = 1; hts_pos_t chr_len = 0; while ( *end && *end!='\n' ) end++; while ( *q && *q!='\n' && nopen>0 ) { p = ++q; while ( *q && (*q==' ' || *q=='\t') ) { p++; q++; } // ^[A-Za-z_][0-9A-Za-z_.]*$ if (p==q && *q && (isalpha(*q) || *q=='_')) { q++; while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++; } int n = q-p; int m = 0; while ( *q && (*q==' ' || *q=='\t') ) { q++; m++; } if ( *q!='=' || !n ) { char *x = q; while ( *x && *x!='\n' ) x++; *x = '\0'; error("Could not parse the line: %s [%s][%s]\n", line,p,q); } key.l = 0; kputsn(p,q-p-m,&key); p = ++q; while ( *q && (*q==' ' || *q=='\t') ) { p++; q++; } int quoted = *p=='"' ? 1 : 0; if ( quoted ) p++, q++; while ( *q && *q != '\n' ) { if ( quoted ) { if ( *q=='"' && !is_escaped(p,q) ) break; } else { if ( *q=='<' ) nopen++; if ( *q=='>' ) nopen--; if ( !nopen ) break; if ( *q==',' && nopen==1 ) break; } q++; } char *r = q; while ( r > p && r[-1] == ' ' ) r--; val.l = 0; kputsn(p,r-p,&val); if ( quoted && *q=='"' ) q++; if ( *q=='>' ) { nopen--; q++; } if ( !strcmp("length",key.s) ) continue; if ( !strcmp("ID",key.s) ) { if ( khash_str2int_has_key(chr_seen,val.s) ) continue; chr_len = faidx_seq_len64(fai, val.s); if ( chr_len==-1 ) { free(val.s); free(key.s); free(tmp.s); return end; // the sequence is not in fai, remove } chr_name = strdup(val.s); khash_str2int_inc(chr_seen, chr_name); continue; } kputc(',',&tmp); kputs(key.s,&tmp); kputc('=',&tmp); if ( quoted ) kputc('"',&tmp); kputs(val.s,&tmp); if ( quoted ) kputc('"',&tmp); } if ( !chr_name ) return end; ksprintf(dst,"##contig=",chr_name,chr_len,tmp.l ? tmp.s : ""); free(key.s); free(val.s); free(tmp.s); return q; } char *init_tmp_prefix(const char *tmp_prefix) { kstring_t prefix = {0,0,0}; if ( tmp_prefix ) { ksprintf(&prefix,"%sXXXXXX",tmp_prefix); return prefix.s; } char *tmpdir = getenv("TMPDIR"); if ( tmpdir ) kputs(tmpdir, &prefix); else { #ifdef _WIN32 char tmp_path[MAX_PATH]; int ret = GetTempPath(MAX_PATH, tmp_path); if (!ret || ret > MAX_PATH) error("Could not get the path to the temporary folder\n"); kputs(tmp_path, &prefix); #else kputs("/tmp", &prefix); #endif } kputs("/bcftools.XXXXXX", &prefix); return prefix.s; } static void update_from_fai(faidx_t *fai, kstring_t *hdr_txt) { kstring_t hdr_txt_new = {0,0,0}; // update the existing contig lines and remove lines not present in the fai file void *chr_seen = khash_str2int_init(); char *tmp, *beg = hdr_txt->s; while ( beg && *beg ) { tmp = strstr(beg, "\n##contig=<"); if ( !tmp ) break; kputsn(beg, tmp-beg+1, &hdr_txt_new); size_t l_prev = hdr_txt_new.l; beg = copy_and_update_contig_line(fai,tmp+1,chr_seen, &hdr_txt_new); if ( l_prev==hdr_txt_new.l ) hdr_txt_new.l--; // nothing was added, remove the newline } if ( !beg || !(tmp=strstr(beg,"\n#CHROM")) ) error("Failed to parse the header, #CHROM not found\n"); kputsn(beg, tmp-beg+1, &hdr_txt_new); // add any new contig lines int i, n = faidx_nseq(fai); for (i=0; i\n",faidx_iseq(fai,i),faidx_seq_len64(fai,faidx_iseq(fai,i))); } kputs(tmp+1,&hdr_txt_new); // Switch the new header content for the old free(hdr_txt->s); memcpy(hdr_txt, &hdr_txt_new, sizeof(*hdr_txt)); khash_str2int_destroy_free(chr_seen); } static void read_header_file(char *fname, kstring_t *hdr) { kstring_t tmp = {0,0,0}; hdr->l = 0; htsFile *fp = hts_open(fname, "r"); if ( !fp ) error("Could not read: %s\n", fname); while ( hts_getline(fp, KS_SEP_LINE, &tmp) > 0 ) { kputsn(tmp.s,tmp.l,hdr); kputc('\n',hdr); } if ( hts_close(fp) ) error("Close failed: %s\n", fname); free(tmp.s); while ( hdr->l>0 && isspace(hdr->s[hdr->l-1]) ) hdr->l--; // remove trailing newlines kputc('\n',hdr); } static int set_sample_pairs(char **samples, int nsamples, kstring_t *hdr, int idx) { int i, j, n; kstring_t key = {0,0,0}; kstring_t val = {0,0,0}; // Are these samples "old-name new-name" pairs? void *hash = khash_str2str_init(); for (i=0; il>0 && isspace(hdr->s[hdr->l-1]) ) hdr->l--; // remove trailing newlines hdr->s[hdr->l] = 0; kstring_t tmp = {0,0,0}; i = j = n = 0; // i:traverse the #CHROM line 1 by 1; j:points to the last column while ( hdr->s[idx+i] ) { if ( hdr->s[idx+i]=='\t' ) { hdr->s[idx+i] = 0; if ( ++n>9 ) { char *new_name = khash_str2str_get(hash,hdr->s+idx+j); kputs(new_name ? new_name : hdr->s+idx+j, &tmp); } else kputs(hdr->s+idx+j, &tmp); kputc('\t',&tmp); j = ++i; continue; } i++; } char *new_name = khash_str2str_get(hash,hdr->s+idx+j); kputs(new_name ? new_name : hdr->s+idx+j, &tmp); khash_str2str_destroy_free_all(hash); hdr->l = idx; kputs(tmp.s, hdr); kputc('\n', hdr); free(tmp.s); return 1; } static void set_samples(char **samples, int nsamples, kstring_t *hdr) { // Find the beginning of the #CHROM line int i = hdr->l - 2, ncols = 0; while ( i>=0 && hdr->s[i]!='\n' ) { if ( hdr->s[i]=='\t' ) ncols++; i--; } if ( i<0 || strncmp(hdr->s+i+1,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT",45) ) { if ( i>0 && !strncmp(hdr->s+i+1,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",38) ) error("Error: missing FORMAT fields, cowardly refusing to add samples\n"); error("Could not parse the header: %s\n", hdr->s); } // Are the samples "old-sample new-sample" pairs? if ( set_sample_pairs(samples,nsamples,hdr, i+1) ) return; // Replace all samples if ( ncols!=nsamples+8 ) fprintf(bcftools_stderr, "Warning: different number of samples: %d vs %d\n", nsamples,ncols-8); ncols = 0; while ( ncols!=9 ) { i++; if ( hdr->s[i]=='\t' ) ncols++; } hdr->l = i; for (i=0; ifp); if ( !fp || bgzf_read_block(fp) != 0 || !fp->block_length ) error("Failed to read %s: %s\n", args->fname, strerror(errno)); kstring_t hdr = {0,0,0}; char *buffer = (char*) fp->uncompressed_block; // Read the header and find the position of the data block if ( buffer[0]!='#' ) error("Could not parse the header, expected '#', found '%c'\n", buffer[0]); int skip_until = 1; // end of the header in the current uncompressed block while (1) { if ( buffer[skip_until]=='\n' ) { skip_until++; if ( skip_until>=fp->block_length ) { kputsn(buffer,skip_until,&hdr); if ( bgzf_read_block(fp) != 0 ) error("Error reading %s\n", args->fname); if ( !fp->block_length ) break; skip_until = 0; } // The header has finished if ( buffer[skip_until]!='#' ) { kputsn(buffer,skip_until,&hdr); break; } } skip_until++; if ( skip_until>=fp->block_length ) { kputsn(buffer,fp->block_length,&hdr); if ( bgzf_read_block(fp) != 0 ) error("Error reading %s\n", args->fname); if ( !fp->block_length ) break; skip_until = 0; } } int nsamples = 0; char **samples = NULL; if ( args->samples_fname ) { samples = hts_readlines(args->samples_fname, &nsamples); if ( !samples || !nsamples ) error("Error reading the --samples file \"%s\"\n", args->samples_fname); } if ( args->header_fname ) { free(hdr.s); hdr.s = NULL; hdr.l = hdr.m = 0; read_header_file(args->header_fname, &hdr); } if ( args->fai ) update_from_fai(args->fai, &hdr); if ( samples ) { set_samples(samples, nsamples, &hdr); int i; for (i=0; ioutput_fname ? args->output_fname : "-","w");; if ( bgzf_write(bgzf_out, hdr.s, hdr.l) < 0 ) error("Can't write BGZF header (code %d)\n", bgzf_out->errcode); free(hdr.s); // Output all remaining data read with the header block if ( fp->block_length - skip_until > 0 ) { if ( bgzf_write(bgzf_out, buffer+skip_until, fp->block_length-skip_until)<0 ) error("Error: %d\n",fp->errcode); } if ( bgzf_flush(bgzf_out)<0 ) error("Error: %d\n",bgzf_out->errcode); // Stream the rest of the file without as it is, without decompressing ssize_t nread; const size_t page_size = 32768; char *buf = (char*) malloc(page_size); while (1) { nread = bgzf_raw_read(fp, buf, page_size); if ( nread<=0 ) break; int count = bgzf_raw_write(bgzf_out, buf, nread); if (count != nread) error("Write failed, wrote %d instead of %d bytes.\n", count,(int)nread); } if (bgzf_close(bgzf_out) < 0) error("Error closing %s: %d\n",args->output_fname ? args->output_fname : "-",bgzf_out->errcode); if (hts_close(args->fp)) error("Error closing %s: %d\n",args->fname,fp->errcode); free(buf); } static void reheader_vcf(args_t *args) { kstring_t hdr = {0,0,0}; htsFile *fp = args->fp; while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 ) { kputc('\n',&fp->line); // hts_getline eats the newline character if ( fp->line.s[0]!='#' ) break; kputsn(fp->line.s,fp->line.l,&hdr); } int nsamples = 0; char **samples = NULL; if ( args->samples_fname ) { samples = hts_readlines(args->samples_fname, &nsamples); if ( !samples || !nsamples ) error("Error reading the --samples file \"%s\"\n", args->samples_fname); } if ( args->header_fname ) { free(hdr.s); hdr.s = NULL; hdr.l = hdr.m = 0; read_header_file(args->header_fname, &hdr); } if ( args->fai ) update_from_fai(args->fai, &hdr); if ( samples ) { set_samples(samples, nsamples, &hdr); int i; for (i=0; ioutput_fname ? open(args->output_fname, O_WRONLY|O_CREAT|O_TRUNC, 0666) : STDOUT_FILENO; if ( out==-1 ) error("%s: %s\n", args->output_fname,strerror(errno)); if ( write(out, hdr.s, hdr.l)!=hdr.l ) error("Failed to write %"PRIu64" bytes\n", (uint64_t)hdr.l); free(hdr.s); if ( fp->line.l ) { if ( write(out, fp->line.s, fp->line.l)!=fp->line.l ) error("Failed to write %"PRIu64" bytes\n", (uint64_t)fp->line.l); } while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 ) // uncompressed file implies small size, we don't worry about speed { kputc('\n',&fp->line); if ( write(out, fp->line.s, fp->line.l)!=fp->line.l ) error("Failed to write %"PRIu64" bytes\n", (uint64_t)fp->line.l); } if ( hts_close(fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fname); if ( close(out)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname); } static bcf_hdr_t *strip_header(bcf_hdr_t *src, bcf_hdr_t *dst) { bcf_hrec_t *src_hrec, *dst_hrec, *tmp; bcf_hdr_t *out = bcf_hdr_init("r"); int i; for (i=0; inhrec; i++) { // first insert lines which do not code BCF ids, their order does not matter dst_hrec = dst->hrec[i]; if ( dst_hrec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->type== BCF_HL_CTG ) continue; bcf_hdr_add_hrec(out, bcf_hrec_dup(dst_hrec)); } for (i=0; inhrec; i++) { // now transfer header lines which define BCF ids src_hrec = src->hrec[i]; if ( src_hrec->type==BCF_HL_FLT || src_hrec->type==BCF_HL_INFO || src_hrec->type==BCF_HL_FMT || src_hrec->type== BCF_HL_CTG ) { int j = bcf_hrec_find_key(src_hrec, "ID"); dst_hrec = bcf_hdr_get_hrec(dst, src_hrec->type, "ID", src_hrec->vals[j], NULL); if ( !dst_hrec ) continue; tmp = bcf_hrec_dup(dst_hrec); j = bcf_hrec_find_key(src_hrec, "IDX"); if ( j>=0 ) { j = atoi(src_hrec->vals[j]); if (hrec_add_idx(tmp, j) < 0) error_errno("[%s] Failed to add IDX header", __func__); } bcf_hdr_add_hrec(out, tmp); } } if (bcf_hdr_sync(out) < 0) error_errno("[%s] Failed to update header", __func__); for (i=0; inhrec; i++) { // finally add new structured fields dst_hrec = dst->hrec[i]; if ( dst_hrec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->type== BCF_HL_CTG ) { int j = bcf_hrec_find_key(dst_hrec, "ID"); tmp = bcf_hdr_get_hrec(out, dst_hrec->type, "ID", dst_hrec->vals[j], NULL); if ( !tmp ) bcf_hdr_add_hrec(out, bcf_hrec_dup(dst_hrec)); } } for (i=0; in[BCF_DT_SAMPLE]; i++) bcf_hdr_add_sample(out, dst->samples[i]); bcf_hdr_destroy(dst); return out; } static void reheader_bcf(args_t *args, int is_compressed) { htsFile *fp = args->fp; if ( args->n_threads > 0 ) { args->threads = (htsThreadPool *) calloc(1, sizeof(htsThreadPool)); if ( !args->threads ) error("Could not allocate memory\n"); if ( !(args->threads->pool = hts_tpool_init(args->n_threads)) ) error("Could not initialize threading\n"); hts_set_thread_pool(fp, args->threads); } bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to read the header: %s\n", args->fname); kstring_t htxt = {0,0,0}; bcf_hdr_format(hdr, 1, &htxt); int i, nsamples = 0; char **samples = NULL; if ( args->samples_fname ) { samples = hts_readlines(args->samples_fname, &nsamples); if ( !samples || !nsamples ) error("Error reading the --samples file \"%s\"\n", args->samples_fname); } if ( args->header_fname ) { free(htxt.s); htxt.s = NULL; htxt.l = htxt.m = 0; read_header_file(args->header_fname, &htxt); } if ( args->fai ) update_from_fai(args->fai, &htxt); if ( samples ) { set_samples(samples, nsamples, &htxt); for (i=0; iheader_fname ) hdr_out = strip_header(hdr, hdr_out); // write the header and the body htsFile *fp_out = hts_open(args->output_fname ? args->output_fname : "-",is_compressed ? "wb" : "wbu"); if ( !fp_out ) error("%s: %s\n", args->output_fname ? args->output_fname : "-", strerror(errno)); if ( args->threads ) hts_set_thread_pool(fp_out, args->threads); if ( bcf_hdr_write(fp_out, hdr_out)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname ? args->output_fname : "standard output"); bcf1_t *rec = bcf_init(); while ( bcf_read(fp, hdr, rec)==0 ) { // sanity checking, this slows things down. Make it optional? bcf_unpack(rec, BCF_UN_ALL); if ( rec->rid >= hdr_out->n[BCF_DT_CTG] || strcmp(bcf_hdr_int2id(hdr,BCF_DT_CTG,rec->rid),bcf_hdr_int2id(hdr_out,BCF_DT_CTG,rec->rid)) ) error("The CHROM is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_CTG,rec->rid)); for (i=0; id.n_flt; i++) { int id = rec->d.flt[i]; if ( id >= hdr_out->n[BCF_DT_ID] ) break; if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FLT,id) ) break; if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) ) error("FIXME: Broken FILTER ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key); } if ( i!=rec->d.n_flt ) error("The FILTER is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.flt[i])); for (i=0; in_info; i++) { int id = rec->d.info[i].key; if ( id >= hdr_out->n[BCF_DT_ID] ) break; if ( !hdr_out->id[BCF_DT_ID][id].key ) break; if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_INFO,id) ) break; if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) ) error("FIXME: Broken INFO ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key); } if ( i!=rec->n_info ) error("The INFO tag is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.info[i].key)); for (i=0; in_fmt; i++) { int id = rec->d.fmt[i].id; if ( id >= hdr_out->n[BCF_DT_ID] ) break; if ( !hdr_out->id[BCF_DT_ID][id].key ) break; if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FMT,id) ) break; if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) ) error("FIXME: Broken FORMAT ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key); } if ( i!=rec->n_fmt ) error("The FORMAT tag is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.fmt[i].id)); if ( bcf_write(fp_out,hdr_out,rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname ? args->output_fname : "standard output"); } bcf_destroy(rec); free(htxt.s); if ( hts_close(fp_out)!=0 ) error("[%s] Error: failed to close the file %s\n",__func__,args->output_fname ? args->output_fname : "standard output"); if ( hts_close(fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fname); bcf_hdr_destroy(hdr_out); bcf_hdr_destroy(hdr); if ( args->threads ) { hts_tpool_destroy(args->threads->pool); free(args->threads); } } static void usage(args_t *args) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: Modify header of VCF/BCF files, change sample names.\n"); fprintf(bcftools_stderr, "Usage: bcftools reheader [OPTIONS] \n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Options:\n"); fprintf(bcftools_stderr, " -f, --fai FILE update sequences and their lengths from the .fai file\n"); fprintf(bcftools_stderr, " -h, --header FILE new header\n"); fprintf(bcftools_stderr, " -o, --output FILE write output to a file [standard output]\n"); fprintf(bcftools_stderr, " -s, --samples FILE new sample names\n"); fprintf(bcftools_stderr, " -T, --temp-prefix PATH ignored; was template for temporary file name\n"); fprintf(bcftools_stderr, " --threads INT use multithreading with worker threads (BCF only) [0]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Example:\n"); fprintf(bcftools_stderr, " # Write out the header to be modified\n"); fprintf(bcftools_stderr, " bcftools view -h old.bcf > header.txt\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, " # Edit the header using your favorite text editor\n"); fprintf(bcftools_stderr, " vi header.txt\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, " # Reheader the file\n"); fprintf(bcftools_stderr, " bcftools reheader -h header.txt -o new.bcf old.bcf\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int main_reheader(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; static struct option loptions[] = { {"temp-prefix",1,0,'T'}, {"fai",1,0,'f'}, {"output",1,0,'o'}, {"header",1,0,'h'}, {"samples",1,0,'s'}, {"threads",1,NULL,1}, {0,0,0,0} }; while ((c = getopt_long(argc, argv, "s:h:o:f:T:",loptions,NULL)) >= 0) { switch (c) { case 1 : args->n_threads = strtol(optarg, 0, 0); break; case 'T': break; // unused - was temp file prefix case 'f': args->fai_fname = optarg; break; case 'o': args->output_fname = optarg; break; case 's': args->samples_fname = optarg; break; case 'h': args->header_fname = optarg; break; case '?': usage(args); break; default: error("Unknown argument: %s\n", optarg); } } if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) args->fname = "-"; // reading from stdin else usage(args); } else args->fname = argv[optind]; if ( args->fai_fname ) { args->fai = fai_load3(args->fai_fname,args->fai_fname,NULL,FAI_FASTA); if ( !args->fai ) error("Could not parse %s\n", args->fai_fname); } if ( !args->samples_fname && !args->header_fname && !args->fai) usage(args); if ( !args->fname ) usage(args); args->fp = hts_open(args->fname,"r"); if ( !args->fp ) error("Failed to read from %s\n", !strcmp("-",args->fname)?"standard input":args->fname); args->type = *hts_get_format(args->fp); if ( args->type.format==vcf ) { if ( args->type.compression==bgzf ) reheader_vcf_gz(args); else if ( args->type.compression==no_compression ) reheader_vcf(args); else if ( args->type.compression==gzip ) error("Error: cannot reheader gzip-compressed files, first convert with `bcftools view --output-type` to a supported format\n"); else error("Error: the compression type of \"%s\" is not recognised/supported\n", args->fname); } else reheader_bcf(args, args->type.compression==bgzf || args->type.compression==gzip); if (args->fai) fai_destroy(args->fai); free(args); return 0; } pysam-0.23.0/bcftools/smpl_ilist.c000066400000000000000000000121711475062545500171020ustar00rootroot00000000000000/* Copyright (C) 2016-2021 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include "bcftools.h" #include "smpl_ilist.h" void smpl_ilist_destroy(smpl_ilist_t *smpl) { int i; if ( smpl->pair ) { for (i=0; in; i++) free(smpl->pair[i]); free(smpl->pair); } free(smpl->idx); free(smpl); } static inline int is_space_or_escaped(const char *min, const char *str) { if ( !isspace(*str) ) return 0; int n = 0; while ( --str>=min && *str=='\\' ) n++; return n%2 ? 0 : 1; } smpl_ilist_t *smpl_ilist_init(bcf_hdr_t *hdr, char *sample_list, int is_file, int flags) { smpl_ilist_t *smpl = (smpl_ilist_t*) calloc(1,sizeof(smpl_ilist_t)); int i; if ( !sample_list ) { smpl->n = bcf_hdr_nsamples(hdr); smpl->idx = (int*) malloc(sizeof(int)*smpl->n); for (i=0; in; i++) smpl->idx[i] = i; return smpl; } int negate = sample_list[0]=='^' ? 1 : 0; int nlist; char **list = hts_readlist(negate?sample_list+1:sample_list, is_file, &nlist); if ( !list ) error("Could not parse %s\n", sample_list); if ( negate && (flags&SMPL_REORDER) ) flags &= ~SMPL_REORDER; // preserve the VCF order unless flags&SMPL_REORDER is set int j = 0; int *tmp = (int*)calloc(bcf_hdr_nsamples(hdr),sizeof(int)); char **pair = NULL; for (i=0; in++; } if ( flags & SMPL_REORDER ) { smpl->idx = tmp; for (i=0; in = bcf_hdr_nsamples(hdr) - smpl->n; smpl->idx = (int*) malloc(sizeof(int)*smpl->n); j = 0; if ( !negate ) { if ( pair ) smpl->pair = (char**) calloc(smpl->n,sizeof(char*)); for (i=0; iidx[j] = i; if ( pair && pair[i] ) smpl->pair[j] = pair[i]; j++; } } else { for (i=0; iidx[j++] = i; } free(tmp); free(pair); for (i=0; in = bcf_hdr_nsamples(hdr_a); smpl->idx = (int*) malloc(sizeof(int)*smpl->n); for (i=0; in; i++) { const char *name = bcf_hdr_int2id(hdr_a, BCF_DT_SAMPLE, i); smpl->idx[i] = bcf_hdr_id2int(hdr_b, BCF_DT_SAMPLE, name); if ( flags&SMPL_STRICT && smpl->idx[i]<0 ) error("The sample %s is not present in the second file\n", name); } return smpl; } pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c000066400000000000000000000122371475062545500204560ustar00rootroot00000000000000#include "bcftools.pysam.h" /* Copyright (C) 2016-2021 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include "bcftools.h" #include "smpl_ilist.h" void smpl_ilist_destroy(smpl_ilist_t *smpl) { int i; if ( smpl->pair ) { for (i=0; in; i++) free(smpl->pair[i]); free(smpl->pair); } free(smpl->idx); free(smpl); } static inline int is_space_or_escaped(const char *min, const char *str) { if ( !isspace(*str) ) return 0; int n = 0; while ( --str>=min && *str=='\\' ) n++; return n%2 ? 0 : 1; } smpl_ilist_t *smpl_ilist_init(bcf_hdr_t *hdr, char *sample_list, int is_file, int flags) { smpl_ilist_t *smpl = (smpl_ilist_t*) calloc(1,sizeof(smpl_ilist_t)); int i; if ( !sample_list ) { smpl->n = bcf_hdr_nsamples(hdr); smpl->idx = (int*) malloc(sizeof(int)*smpl->n); for (i=0; in; i++) smpl->idx[i] = i; return smpl; } int negate = sample_list[0]=='^' ? 1 : 0; int nlist; char **list = hts_readlist(negate?sample_list+1:sample_list, is_file, &nlist); if ( !list ) error("Could not parse %s\n", sample_list); if ( negate && (flags&SMPL_REORDER) ) flags &= ~SMPL_REORDER; // preserve the VCF order unless flags&SMPL_REORDER is set int j = 0; int *tmp = (int*)calloc(bcf_hdr_nsamples(hdr),sizeof(int)); char **pair = NULL; for (i=0; in++; } if ( flags & SMPL_REORDER ) { smpl->idx = tmp; for (i=0; in = bcf_hdr_nsamples(hdr) - smpl->n; smpl->idx = (int*) malloc(sizeof(int)*smpl->n); j = 0; if ( !negate ) { if ( pair ) smpl->pair = (char**) calloc(smpl->n,sizeof(char*)); for (i=0; iidx[j] = i; if ( pair && pair[i] ) smpl->pair[j] = pair[i]; j++; } } else { for (i=0; iidx[j++] = i; } free(tmp); free(pair); for (i=0; in = bcf_hdr_nsamples(hdr_a); smpl->idx = (int*) malloc(sizeof(int)*smpl->n); for (i=0; in; i++) { const char *name = bcf_hdr_int2id(hdr_a, BCF_DT_SAMPLE, i); smpl->idx[i] = bcf_hdr_id2int(hdr_b, BCF_DT_SAMPLE, name); if ( flags&SMPL_STRICT && smpl->idx[i]<0 ) error("The sample %s is not present in the second file\n", name); } return smpl; } pysam-0.23.0/bcftools/smpl_ilist.h000066400000000000000000000043111475062545500171040ustar00rootroot00000000000000/* Copyright (C) 2016-2021 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Parse --samples and --samples-file */ #ifndef __SMPL_ILIST_H__ #define __SMPL_ILIST_H__ #include #define SMPL_NONE 0 // flexible error recovery #define SMPL_STRICT 1 // samples must exist #define SMPL_SINGLE 2 // single sample expected #define SMPL_PAIR1 4 // two samples expected, the first is from the bcf hdr #define SMPL_PAIR2 8 // two samples expected, the second is from the bcf hdr #define SMPL_VERBOSE 16 // print warnings #define SMPL_REORDER 32 // reorder samples as asked, sample_list[i] points to the VCF header index typedef struct { char **pair; // the other sample in the pair int *idx; // index to bcf_hdr_t.samples; the first (SMPL_SINGLE|SMPL_PAIR1) or second sample (SMPL_PAIR2) int n; } smpl_ilist_t; // Pass NULL for sample_list to get all samples smpl_ilist_t *smpl_ilist_init(bcf_hdr_t *hdr, char *sample_list, int is_file, int flags); smpl_ilist_t *smpl_ilist_map(bcf_hdr_t *hdr_a, bcf_hdr_t *hdr_b, int flags); void smpl_ilist_destroy(smpl_ilist_t *smpl); #endif pysam-0.23.0/bcftools/str_finder.c000066400000000000000000000247251475062545500170720ustar00rootroot00000000000000/* str_finder.c -- Short Tandem Repeat finder. Originally from Crumble (https://github.com/jkbonfield/crumble) Copyright (C) 2015-2016, 2021-2022 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include "str_finder.h" #include "utlist.h" #define MAX(a,b) ((a)>(b)?(a):(b)) #define MIN(a,b) ((a)<(b)?(a):(b)) typedef unsigned char uc; static void add_rep(rep_ele **list, char *cons, int clen, int pos, int rlen, int lower_only, unsigned int w) { rep_ele *el, *tmp, *prev; char *cp1, *cp2, *cp_end; int i; // Already handled this in previous overlap? if (*list) { tmp = DL_TAIL(*list); if (tmp->start <= pos-rlen*2+1 && tmp->end >= pos) return; } // Find current and last occurrence of repeated word. cp2 = &cons[pos+1]; // If unpadded, this is quicker: cp1 = &cons[pos+1-rlen]; for (cp1 = &cons[pos], i = 1; i < rlen; cp1--) // compensate for pads if (*cp1 == '*') continue; else i++; while (*cp1 == '*') cp1--; // Scan ahead to see how much further it goes. cp_end = &cons[clen]; while (cp2 < cp_end) { if (*cp1 != *cp2) break; w<<=2; w|=*cp2; cp1++; cp2++; } if (!(el = malloc(sizeof(*el)))) return; el->end = pos + cp2-&cons[pos+1]; el->rep_len = rlen; pos++; while (rlen--) { while (cons[--pos] == '*'); while (cons[--pos] == '*'); } //pos++; while (pos > 1 && cons[pos-1] == '*') pos--; el->start = pos; // Check it meets the lower-case only criteria if (lower_only) { int lc = 0; for (i = el->start; i <= el->end; i++) { if (islower(cons[i])) { lc = 1; break; } } if (!lc) { free(el); return; } } // Remove any older items on the list that are entirely contained within el if (*list) { tmp = DL_TAIL(*list); do { prev = tmp->prev; if (tmp->end < el->start) break; if (tmp->start >= el->start) { DL_DELETE(*list, tmp); free(tmp); } if (tmp == DL_HEAD(*list)) break; tmp = prev; } while (*list); } DL_APPEND(*list, el); return; } /* * Finds repeated homopolymers up to 8-mers. * Note this assumes cons is 0-3, so N of 4 may rarely give false hits. * * Returns a list of rep_ele structs holding the start,end tuples of repeats; * NULL on failure. */ rep_ele *find_STR64(char *cons, int len, int lower_only) { int i, j; uint64_t w = 0; rep_ele *reps = NULL; for (i = j = 0; i < len && j < 26; i++) { if (cons[i] == '*') continue; w <<= 2; w |= cons[i]; //printf("%3d %c w=%08x\n", i, cons[i], w); if (j>= 1 && (w&0x0003) == ((w>> 2)&0x0003)) add_rep(&reps, cons, len, i, 1, lower_only, w); if (j>= 3 && (w&0x000f) == ((w>> 4)&0x000f)) add_rep(&reps, cons, len, i, 2, lower_only, w); if (j>= 5 && (w&0x003f) == ((w>> 6)&0x003f)) add_rep(&reps, cons, len, i, 3, lower_only, w); if (j>= 7 && (w&0x00ff) == ((w>> 8)&0x00ff)) add_rep(&reps, cons, len, i, 4, lower_only, w); if (j>= 9 && (w&0x03ff) == ((w>>10)&0x03ff)) add_rep(&reps, cons, len, i, 5, lower_only, w); if (j>=11 && (w&0x0fff) == ((w>>12)&0x0fff)) add_rep(&reps, cons, len, i, 6, lower_only, w); if (j>=13 && (w&0x3fff) == ((w>>14)&0x3fff)) add_rep(&reps, cons, len, i, 7, lower_only, w); if (j>=15 && (w&0xffff) == ((w>>16)&0xffff)) add_rep(&reps, cons, len, i, 8, lower_only, w); if (j>=17 && (w&0x003ffff) == ((w>>18)&0x003ffff)) add_rep(&reps, cons, len, i, 9, lower_only, w); if (j>=19 && (w&0x00fffff) == ((w>>20)&0x00fffff)) add_rep(&reps, cons, len, i,10, lower_only, w); if (j>=21 && (w&0x03fffff) == ((w>>22)&0x03fffff)) add_rep(&reps, cons, len, i,11, lower_only, w); if (j>=23 && (w&0x0ffffff) == ((w>>24)&0x0ffffff)) add_rep(&reps, cons, len, i,12, lower_only, w); if (j>=24 && (w&0x3ffffff) == ((w>>26)&0x3ffffff)) add_rep(&reps, cons, len, i,13, lower_only, w); j++; } for (; i < len; i++) { if (cons[i] == '*') continue; w <<= 2; w |= cons[i]; //printf("%3d %c w=%08x\n", i, cons[i], w); if ((w&0xfffffff) == ((w>>28)&0xfffffff)) add_rep(&reps, cons, len, i, 14, lower_only, w); else if ((w&0x3ffffff) == ((w>>26)&0x3ffffff)) add_rep(&reps, cons, len, i, 13, lower_only, w); else if ((w&0x0ffffff) == ((w>>24)&0x0ffffff)) add_rep(&reps, cons, len, i, 12, lower_only, w); else if ((w&0x03fffff) == ((w>>22)&0x03fffff)) add_rep(&reps, cons, len, i, 11, lower_only, w); else if ((w&0x00fffff) == ((w>>20)&0x00fffff)) add_rep(&reps, cons, len, i, 10, lower_only, w); else if ((w&0x003ffff) == ((w>>18)&0x003ffff)) add_rep(&reps, cons, len, i, 9, lower_only, w); else if ((w&0xffff) == ((w>>16)&0xffff)) add_rep(&reps, cons, len, i, 8, lower_only, w); else if ((w&0x3fff) == ((w>>14)&0x3fff)) add_rep(&reps, cons, len, i, 7, lower_only, w); else if ((w&0x0fff) == ((w>>12)&0x0fff)) add_rep(&reps, cons, len, i, 6, lower_only, w); else if ((w&0x03ff) == ((w>>10)&0x03ff)) add_rep(&reps, cons, len, i, 5, lower_only, w); else if ((w&0x00ff) == ((w>> 8)&0x00ff)) add_rep(&reps, cons, len, i, 4, lower_only, w); else if ((w&0x003f) == ((w>> 6)&0x003f)) add_rep(&reps, cons, len, i, 3, lower_only, w); else if ((w&0x000f) == ((w>> 4)&0x000f)) add_rep(&reps, cons, len, i, 2, lower_only, w); else if ((w&0x0003) == ((w>> 2)&0x0003)) add_rep(&reps, cons, len, i, 1, lower_only, w); } return reps; } rep_ele *find_STR(char *cons, int len, int lower_only) { int i, j; uint32_t w = 0; rep_ele *reps = NULL; for (i = j = 0; i < len && j < 15; i++) { if (cons[i] == '*') continue; w <<= 2; w |= cons[i]; //printf("%3d %c w=%08x\n", i, cons[i], w); if (j>= 1 && (w&0x0003) == ((w>> 2)&0x0003)) add_rep(&reps, cons, len, i, 1, lower_only, w); if (j>= 3 && (w&0x000f) == ((w>> 4)&0x000f)) add_rep(&reps, cons, len, i, 2, lower_only, w); if (j>= 5 && (w&0x003f) == ((w>> 6)&0x003f)) add_rep(&reps, cons, len, i, 3, lower_only, w); if (j>= 7 && (w&0x00ff) == ((w>> 8)&0x00ff)) add_rep(&reps, cons, len, i, 4, lower_only, w); if (j>= 9 && (w&0x03ff) == ((w>>10)&0x03ff)) add_rep(&reps, cons, len, i, 5, lower_only, w); if (j>=11 && (w&0x0fff) == ((w>>12)&0x0fff)) add_rep(&reps, cons, len, i, 6, lower_only, w); if (j>=13 && (w&0x3fff) == ((w>>14)&0x3fff)) add_rep(&reps, cons, len, i, 7, lower_only, w); j++; } for (; i < len; i++) { if (cons[i] == '*') continue; w <<= 2; w |= cons[i]; //printf("%3d %c w=%08x\n", i, cons[i], w); if ((w&0xffff) == ((w>>16)&0xffff)) add_rep(&reps, cons, len, i, 8, lower_only, w); else if ((w&0x3fff) == ((w>>14)&0x3fff)) add_rep(&reps, cons, len, i, 7, lower_only, w); else if ((w&0x0fff) == ((w>>12)&0x0fff)) add_rep(&reps, cons, len, i, 6, lower_only, w); else if ((w&0x03ff) == ((w>>10)&0x03ff)) add_rep(&reps, cons, len, i, 5, lower_only, w); else if ((w&0x00ff) == ((w>> 8)&0x00ff)) add_rep(&reps, cons, len, i, 4, lower_only, w); else if ((w&0x003f) == ((w>> 6)&0x003f)) add_rep(&reps, cons, len, i, 3, lower_only, w); else if ((w&0x000f) == ((w>> 4)&0x000f)) add_rep(&reps, cons, len, i, 2, lower_only, w); else if ((w&0x0003) == ((w>> 2)&0x0003)) add_rep(&reps, cons, len, i, 1, lower_only, w); } return reps; } /* ----------------------------------------------------------------------------- * Computes repeat regions in the consensus and then provides a bit mask * indicating the extend of the STRs. * * The purpose of this is to identify where a read needs to span the entire * region in order to validate how many copies of a repeat word are present. * This only really has a major impact when indels are involved. * * For example, given this multiple alignment: * * S1 GATCGGACGAGAG * S2 GATCGGACGAGAGAGAGAGAGT * S3 GATCGGACGAGAGAGAGAG**TCGGAC * S4 GGACGAGAGAGAGAGAGTCGGAC * S5 CGAGAGAGAGAG**TCGGAC * S6 AGAGAGAGTCGGAC * * We have subseq of GAGAGAGAGAG** vs GAGAGAGAGAGAG. The first and last * (S1 and S6) sequences do not span and so we do not know which allele they * match. Specifically as the pad is at the right hand end, the alignment of * S6 gives incorrect weight to the consensus as it is stating AG when it * may actually be ** at that point. * * By identifying the repeats we can soft clip as follows: * * S1 GATCGGACgagag * S2 GATCGGACGAGAGAGAGAGAGT * S3 GATCGGACGAGAGAGAGAG**TCGGAC * S4 GGACGAGAGAGAGAGAGTCGGAC * S5 CGAGAGAGAGAG**TCGGAC * S6 agagagagTCGGAC * * Returns an array of STR vs no-STR values. * 0 => non repetitive. * 1+ => repeat with consecutive bit-number for repeat size. * * Eg: AGGGGAGGAGAAGAC * 1111 1111 * 2222222 * 444444 * => 011331137754440 */ char *cons_mark_STR(char *cons, int len, int lower_only) { rep_ele *reps, *elt, *tmp; char *str; str = calloc(1, len); reps = find_STR(cons, len, lower_only); DL_FOREACH_SAFE(reps, elt, tmp) { int i, v = 0; //printf("%2d .. %2d %.*s\n", elt->start, elt->end, // elt->end - elt->start+1, &cons[elt->start]); // What is there? for (i = MAX(elt->start-1,0); i <= MIN(elt->end+1,len-1); i++) v |= str[i]; for (i = 0; i < 8; i++) { if (!(v&(1<start; i <= elt->end; i++) str[i] |= v; DL_DELETE(reps, elt); free(elt); } return str; } pysam-0.23.0/bcftools/str_finder.c.pysam.c000066400000000000000000000247621475062545500204440ustar00rootroot00000000000000#include "bcftools.pysam.h" /* str_finder.c -- Short Tandem Repeat finder. Originally from Crumble (https://github.com/jkbonfield/crumble) Copyright (C) 2015-2016, 2021-2022 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include "str_finder.h" #include "utlist.h" #define MAX(a,b) ((a)>(b)?(a):(b)) #define MIN(a,b) ((a)<(b)?(a):(b)) typedef unsigned char uc; static void add_rep(rep_ele **list, char *cons, int clen, int pos, int rlen, int lower_only, unsigned int w) { rep_ele *el, *tmp, *prev; char *cp1, *cp2, *cp_end; int i; // Already handled this in previous overlap? if (*list) { tmp = DL_TAIL(*list); if (tmp->start <= pos-rlen*2+1 && tmp->end >= pos) return; } // Find current and last occurrence of repeated word. cp2 = &cons[pos+1]; // If unpadded, this is quicker: cp1 = &cons[pos+1-rlen]; for (cp1 = &cons[pos], i = 1; i < rlen; cp1--) // compensate for pads if (*cp1 == '*') continue; else i++; while (*cp1 == '*') cp1--; // Scan ahead to see how much further it goes. cp_end = &cons[clen]; while (cp2 < cp_end) { if (*cp1 != *cp2) break; w<<=2; w|=*cp2; cp1++; cp2++; } if (!(el = malloc(sizeof(*el)))) return; el->end = pos + cp2-&cons[pos+1]; el->rep_len = rlen; pos++; while (rlen--) { while (cons[--pos] == '*'); while (cons[--pos] == '*'); } //pos++; while (pos > 1 && cons[pos-1] == '*') pos--; el->start = pos; // Check it meets the lower-case only criteria if (lower_only) { int lc = 0; for (i = el->start; i <= el->end; i++) { if (islower(cons[i])) { lc = 1; break; } } if (!lc) { free(el); return; } } // Remove any older items on the list that are entirely contained within el if (*list) { tmp = DL_TAIL(*list); do { prev = tmp->prev; if (tmp->end < el->start) break; if (tmp->start >= el->start) { DL_DELETE(*list, tmp); free(tmp); } if (tmp == DL_HEAD(*list)) break; tmp = prev; } while (*list); } DL_APPEND(*list, el); return; } /* * Finds repeated homopolymers up to 8-mers. * Note this assumes cons is 0-3, so N of 4 may rarely give false hits. * * Returns a list of rep_ele structs holding the start,end tuples of repeats; * NULL on failure. */ rep_ele *find_STR64(char *cons, int len, int lower_only) { int i, j; uint64_t w = 0; rep_ele *reps = NULL; for (i = j = 0; i < len && j < 26; i++) { if (cons[i] == '*') continue; w <<= 2; w |= cons[i]; //printf("%3d %c w=%08x\n", i, cons[i], w); if (j>= 1 && (w&0x0003) == ((w>> 2)&0x0003)) add_rep(&reps, cons, len, i, 1, lower_only, w); if (j>= 3 && (w&0x000f) == ((w>> 4)&0x000f)) add_rep(&reps, cons, len, i, 2, lower_only, w); if (j>= 5 && (w&0x003f) == ((w>> 6)&0x003f)) add_rep(&reps, cons, len, i, 3, lower_only, w); if (j>= 7 && (w&0x00ff) == ((w>> 8)&0x00ff)) add_rep(&reps, cons, len, i, 4, lower_only, w); if (j>= 9 && (w&0x03ff) == ((w>>10)&0x03ff)) add_rep(&reps, cons, len, i, 5, lower_only, w); if (j>=11 && (w&0x0fff) == ((w>>12)&0x0fff)) add_rep(&reps, cons, len, i, 6, lower_only, w); if (j>=13 && (w&0x3fff) == ((w>>14)&0x3fff)) add_rep(&reps, cons, len, i, 7, lower_only, w); if (j>=15 && (w&0xffff) == ((w>>16)&0xffff)) add_rep(&reps, cons, len, i, 8, lower_only, w); if (j>=17 && (w&0x003ffff) == ((w>>18)&0x003ffff)) add_rep(&reps, cons, len, i, 9, lower_only, w); if (j>=19 && (w&0x00fffff) == ((w>>20)&0x00fffff)) add_rep(&reps, cons, len, i,10, lower_only, w); if (j>=21 && (w&0x03fffff) == ((w>>22)&0x03fffff)) add_rep(&reps, cons, len, i,11, lower_only, w); if (j>=23 && (w&0x0ffffff) == ((w>>24)&0x0ffffff)) add_rep(&reps, cons, len, i,12, lower_only, w); if (j>=24 && (w&0x3ffffff) == ((w>>26)&0x3ffffff)) add_rep(&reps, cons, len, i,13, lower_only, w); j++; } for (; i < len; i++) { if (cons[i] == '*') continue; w <<= 2; w |= cons[i]; //printf("%3d %c w=%08x\n", i, cons[i], w); if ((w&0xfffffff) == ((w>>28)&0xfffffff)) add_rep(&reps, cons, len, i, 14, lower_only, w); else if ((w&0x3ffffff) == ((w>>26)&0x3ffffff)) add_rep(&reps, cons, len, i, 13, lower_only, w); else if ((w&0x0ffffff) == ((w>>24)&0x0ffffff)) add_rep(&reps, cons, len, i, 12, lower_only, w); else if ((w&0x03fffff) == ((w>>22)&0x03fffff)) add_rep(&reps, cons, len, i, 11, lower_only, w); else if ((w&0x00fffff) == ((w>>20)&0x00fffff)) add_rep(&reps, cons, len, i, 10, lower_only, w); else if ((w&0x003ffff) == ((w>>18)&0x003ffff)) add_rep(&reps, cons, len, i, 9, lower_only, w); else if ((w&0xffff) == ((w>>16)&0xffff)) add_rep(&reps, cons, len, i, 8, lower_only, w); else if ((w&0x3fff) == ((w>>14)&0x3fff)) add_rep(&reps, cons, len, i, 7, lower_only, w); else if ((w&0x0fff) == ((w>>12)&0x0fff)) add_rep(&reps, cons, len, i, 6, lower_only, w); else if ((w&0x03ff) == ((w>>10)&0x03ff)) add_rep(&reps, cons, len, i, 5, lower_only, w); else if ((w&0x00ff) == ((w>> 8)&0x00ff)) add_rep(&reps, cons, len, i, 4, lower_only, w); else if ((w&0x003f) == ((w>> 6)&0x003f)) add_rep(&reps, cons, len, i, 3, lower_only, w); else if ((w&0x000f) == ((w>> 4)&0x000f)) add_rep(&reps, cons, len, i, 2, lower_only, w); else if ((w&0x0003) == ((w>> 2)&0x0003)) add_rep(&reps, cons, len, i, 1, lower_only, w); } return reps; } rep_ele *find_STR(char *cons, int len, int lower_only) { int i, j; uint32_t w = 0; rep_ele *reps = NULL; for (i = j = 0; i < len && j < 15; i++) { if (cons[i] == '*') continue; w <<= 2; w |= cons[i]; //printf("%3d %c w=%08x\n", i, cons[i], w); if (j>= 1 && (w&0x0003) == ((w>> 2)&0x0003)) add_rep(&reps, cons, len, i, 1, lower_only, w); if (j>= 3 && (w&0x000f) == ((w>> 4)&0x000f)) add_rep(&reps, cons, len, i, 2, lower_only, w); if (j>= 5 && (w&0x003f) == ((w>> 6)&0x003f)) add_rep(&reps, cons, len, i, 3, lower_only, w); if (j>= 7 && (w&0x00ff) == ((w>> 8)&0x00ff)) add_rep(&reps, cons, len, i, 4, lower_only, w); if (j>= 9 && (w&0x03ff) == ((w>>10)&0x03ff)) add_rep(&reps, cons, len, i, 5, lower_only, w); if (j>=11 && (w&0x0fff) == ((w>>12)&0x0fff)) add_rep(&reps, cons, len, i, 6, lower_only, w); if (j>=13 && (w&0x3fff) == ((w>>14)&0x3fff)) add_rep(&reps, cons, len, i, 7, lower_only, w); j++; } for (; i < len; i++) { if (cons[i] == '*') continue; w <<= 2; w |= cons[i]; //printf("%3d %c w=%08x\n", i, cons[i], w); if ((w&0xffff) == ((w>>16)&0xffff)) add_rep(&reps, cons, len, i, 8, lower_only, w); else if ((w&0x3fff) == ((w>>14)&0x3fff)) add_rep(&reps, cons, len, i, 7, lower_only, w); else if ((w&0x0fff) == ((w>>12)&0x0fff)) add_rep(&reps, cons, len, i, 6, lower_only, w); else if ((w&0x03ff) == ((w>>10)&0x03ff)) add_rep(&reps, cons, len, i, 5, lower_only, w); else if ((w&0x00ff) == ((w>> 8)&0x00ff)) add_rep(&reps, cons, len, i, 4, lower_only, w); else if ((w&0x003f) == ((w>> 6)&0x003f)) add_rep(&reps, cons, len, i, 3, lower_only, w); else if ((w&0x000f) == ((w>> 4)&0x000f)) add_rep(&reps, cons, len, i, 2, lower_only, w); else if ((w&0x0003) == ((w>> 2)&0x0003)) add_rep(&reps, cons, len, i, 1, lower_only, w); } return reps; } /* ----------------------------------------------------------------------------- * Computes repeat regions in the consensus and then provides a bit mask * indicating the extend of the STRs. * * The purpose of this is to identify where a read needs to span the entire * region in order to validate how many copies of a repeat word are present. * This only really has a major impact when indels are involved. * * For example, given this multiple alignment: * * S1 GATCGGACGAGAG * S2 GATCGGACGAGAGAGAGAGAGT * S3 GATCGGACGAGAGAGAGAG**TCGGAC * S4 GGACGAGAGAGAGAGAGTCGGAC * S5 CGAGAGAGAGAG**TCGGAC * S6 AGAGAGAGTCGGAC * * We have subseq of GAGAGAGAGAG** vs GAGAGAGAGAGAG. The first and last * (S1 and S6) sequences do not span and so we do not know which allele they * match. Specifically as the pad is at the right hand end, the alignment of * S6 gives incorrect weight to the consensus as it is stating AG when it * may actually be ** at that point. * * By identifying the repeats we can soft clip as follows: * * S1 GATCGGACgagag * S2 GATCGGACGAGAGAGAGAGAGT * S3 GATCGGACGAGAGAGAGAG**TCGGAC * S4 GGACGAGAGAGAGAGAGTCGGAC * S5 CGAGAGAGAGAG**TCGGAC * S6 agagagagTCGGAC * * Returns an array of STR vs no-STR values. * 0 => non repetitive. * 1+ => repeat with consecutive bit-number for repeat size. * * Eg: AGGGGAGGAGAAGAC * 1111 1111 * 2222222 * 444444 * => 011331137754440 */ char *cons_mark_STR(char *cons, int len, int lower_only) { rep_ele *reps, *elt, *tmp; char *str; str = calloc(1, len); reps = find_STR(cons, len, lower_only); DL_FOREACH_SAFE(reps, elt, tmp) { int i, v = 0; //printf("%2d .. %2d %.*s\n", elt->start, elt->end, // elt->end - elt->start+1, &cons[elt->start]); // What is there? for (i = MAX(elt->start-1,0); i <= MIN(elt->end+1,len-1); i++) v |= str[i]; for (i = 0; i < 8; i++) { if (!(v&(1<start; i <= elt->end; i++) str[i] |= v; DL_DELETE(reps, elt); free(elt); } return str; } pysam-0.23.0/bcftools/str_finder.h000066400000000000000000000045541475062545500170750ustar00rootroot00000000000000/* str_finder.c -- Short Tandem Repeat finder. Originally from Crumble (https://github.com/jkbonfield/crumble) Copyright (C) 2015-2016, 2021, 2023 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef _STR_FINDER_H_ #define _STR_FINDER_H_ #include "utlist.h" typedef struct rep_ele { int start, end, rep_len; struct rep_ele *prev; struct rep_ele *next; } rep_ele; /* * Finds repeated homopolymers up to 8-mers. * * If lower_only is true then it only adds STRs for regions that * contain at least one lower-case base. This can be used as a marker * for looking for specific types of repeats. * (One use for this is to only mark STRs that overlap a heterozygous * indel region.) * * Returns a list of rep_ele structs holding the start,end tuples of repeats; * NULL on failure. */ rep_ele *find_STR(char *cons, int len, int lower_only); /* As above, but use a longer hash with longer STR elements found */ rep_ele *find_STR64(char *cons, int len, int lower_only); /* * Returns an array of STR vs no-STR values. * 0 => non repetitive. * 1+ => repeat with consecutive bit-number for repeat size. * * Eg: AGGGGAGGAGAAGAC * 1111 1111 * 2222222 * 444444 * => 011331137754440 */ char *cons_mark_STR(char *cons, int len, int lower_only); #endif /* _STR_FINDER_H_ */ pysam-0.23.0/bcftools/tabix.c000066400000000000000000000131001475062545500160230ustar00rootroot00000000000000/* tabix.c -- tabix subcommand. Copyright (C) 2012 Broad Institute. Copyright (C) 2013, 2016 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include int main_tabix(int argc, char *argv[]) { int c, min_shift = -1, is_force = 0, is_all = 0, detect = 1; tbx_conf_t conf = tbx_conf_gff; while ((c = getopt(argc, argv, "0fap:s:b:e:S:c:m:")) >= 0) if (c == '0') conf.preset |= TBX_UCSC; else if (c == 'f') is_force = 1; else if (c == 'a') is_all = 1; else if (c == 'm') min_shift = atoi(optarg); else if (c == 's') conf.sc = atoi(optarg); else if (c == 'b') conf.bc = atoi(optarg); else if (c == 'e') conf.ec = atoi(optarg); else if (c == 'c') conf.meta_char = *optarg; else if (c == 'S') conf.line_skip = atoi(optarg); else if (c == 'p') { if (strcmp(optarg, "gff") == 0) conf = tbx_conf_gff; else if (strcmp(optarg, "bed") == 0) conf = tbx_conf_bed; else if (strcmp(optarg, "sam") == 0) conf = tbx_conf_sam; else if (strcmp(optarg, "vcf") == 0) conf = tbx_conf_vcf; else { fprintf(stderr, "The type '%s' not recognised\n", optarg); return 1; detect = 0; } } if (optind == argc) { fprintf(stderr, "\nUsage: bcftools tabix [options] [reg1 [...]]\n\n"); fprintf(stderr, "Options: -p STR preset: gff, bed, sam or vcf [gff]\n"); fprintf(stderr, " -s INT column number for sequence names (suppressed by -p) [1]\n"); fprintf(stderr, " -b INT column number for region start [4]\n"); fprintf(stderr, " -e INT column number for region end (if no end, set INT to -b) [5]\n"); fprintf(stderr, " -0 specify coordinates are zero-based\n"); fprintf(stderr, " -S INT skip first INT lines [0]\n"); fprintf(stderr, " -c CHAR skip lines starting with CHAR [null]\n"); fprintf(stderr, " -a print all records\n"); fprintf(stderr, " -f force to overwrite existing index\n"); fprintf(stderr, " -m INT set the minimal interval size to 1<= 0) puts(s.s); bgzf_close(fp); free(s.s); } else if (optind + 2 > argc) { // create index if ( detect ) { // auto-detect file type by file name int l = strlen(argv[optind]); if (l>=7 && strcasecmp(argv[optind]+l-7, ".gff.gz") == 0) conf = tbx_conf_gff; else if (l>=7 && strcasecmp(argv[optind]+l-7, ".bed.gz") == 0) conf = tbx_conf_bed; else if (l>=7 && strcasecmp(argv[optind]+l-7, ".sam.gz") == 0) conf = tbx_conf_sam; else if (l>=7 && strcasecmp(argv[optind]+l-7, ".vcf.gz") == 0) conf = tbx_conf_vcf; } if (!is_force) { char *fn; FILE *fp; fn = (char*)malloc(strlen(argv[optind]) + 5); strcat(strcpy(fn, argv[optind]), min_shift <= 0? ".tbi" : ".csi"); if ((fp = fopen(fn, "rb")) != 0) { fclose(fp); free(fn); fprintf(stderr, "[E::%s] the index file exists; use option '-f' to overwrite\n", __func__); return 1; } free(fn); } if ( tbx_index_build(argv[optind], min_shift, &conf) ) { fprintf(stderr,"tbx_index_build failed: Is the file bgzip-compressed? Was wrong -p [type] option used?\n"); return 1; } } else { // read with random access tbx_t *tbx; BGZF *fp; kstring_t s; int i; if ((tbx = tbx_index_load(argv[optind])) == 0) return 1; if ((fp = bgzf_open(argv[optind], "r")) == 0) return 1; s.s = 0; s.l = s.m = 0; for (i = optind + 1; i < argc; ++i) { hts_itr_t *itr; if ((itr = tbx_itr_querys(tbx, argv[i])) == 0) continue; while (tbx_bgzf_itr_next(fp, tbx, itr, &s) >= 0) puts(s.s); tbx_itr_destroy(itr); } free(s.s); bgzf_close(fp); tbx_destroy(tbx); } return 0; } pysam-0.23.0/bcftools/tabix.c.pysam.c000066400000000000000000000133661475062545500174120ustar00rootroot00000000000000#include "bcftools.pysam.h" /* tabix.c -- tabix subcommand. Copyright (C) 2012 Broad Institute. Copyright (C) 2013, 2016 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include int main_tabix(int argc, char *argv[]) { int c, min_shift = -1, is_force = 0, is_all = 0, detect = 1; tbx_conf_t conf = tbx_conf_gff; while ((c = getopt(argc, argv, "0fap:s:b:e:S:c:m:")) >= 0) if (c == '0') conf.preset |= TBX_UCSC; else if (c == 'f') is_force = 1; else if (c == 'a') is_all = 1; else if (c == 'm') min_shift = atoi(optarg); else if (c == 's') conf.sc = atoi(optarg); else if (c == 'b') conf.bc = atoi(optarg); else if (c == 'e') conf.ec = atoi(optarg); else if (c == 'c') conf.meta_char = *optarg; else if (c == 'S') conf.line_skip = atoi(optarg); else if (c == 'p') { if (strcmp(optarg, "gff") == 0) conf = tbx_conf_gff; else if (strcmp(optarg, "bed") == 0) conf = tbx_conf_bed; else if (strcmp(optarg, "sam") == 0) conf = tbx_conf_sam; else if (strcmp(optarg, "vcf") == 0) conf = tbx_conf_vcf; else { fprintf(bcftools_stderr, "The type '%s' not recognised\n", optarg); return 1; detect = 0; } } if (optind == argc) { fprintf(bcftools_stderr, "\nUsage: bcftools tabix [options] [reg1 [...]]\n\n"); fprintf(bcftools_stderr, "Options: -p STR preset: gff, bed, sam or vcf [gff]\n"); fprintf(bcftools_stderr, " -s INT column number for sequence names (suppressed by -p) [1]\n"); fprintf(bcftools_stderr, " -b INT column number for region start [4]\n"); fprintf(bcftools_stderr, " -e INT column number for region end (if no end, set INT to -b) [5]\n"); fprintf(bcftools_stderr, " -0 specify coordinates are zero-based\n"); fprintf(bcftools_stderr, " -S INT skip first INT lines [0]\n"); fprintf(bcftools_stderr, " -c CHAR skip lines starting with CHAR [null]\n"); fprintf(bcftools_stderr, " -a print all records\n"); fprintf(bcftools_stderr, " -f force to overwrite existing index\n"); fprintf(bcftools_stderr, " -m INT set the minimal interval size to 1<= 0) bcftools_puts(s.s); bgzf_close(fp); free(s.s); } else if (optind + 2 > argc) { // create index if ( detect ) { // auto-detect file type by file name int l = strlen(argv[optind]); if (l>=7 && strcasecmp(argv[optind]+l-7, ".gff.gz") == 0) conf = tbx_conf_gff; else if (l>=7 && strcasecmp(argv[optind]+l-7, ".bed.gz") == 0) conf = tbx_conf_bed; else if (l>=7 && strcasecmp(argv[optind]+l-7, ".sam.gz") == 0) conf = tbx_conf_sam; else if (l>=7 && strcasecmp(argv[optind]+l-7, ".vcf.gz") == 0) conf = tbx_conf_vcf; } if (!is_force) { char *fn; FILE *fp; fn = (char*)malloc(strlen(argv[optind]) + 5); strcat(strcpy(fn, argv[optind]), min_shift <= 0? ".tbi" : ".csi"); if ((fp = fopen(fn, "rb")) != 0) { fclose(fp); free(fn); fprintf(bcftools_stderr, "[E::%s] the index file exists; use option '-f' to overwrite\n", __func__); return 1; } free(fn); } if ( tbx_index_build(argv[optind], min_shift, &conf) ) { fprintf(bcftools_stderr,"tbx_index_build failed: Is the file bgzip-compressed? Was wrong -p [type] option used?\n"); return 1; } } else { // read with random access tbx_t *tbx; BGZF *fp; kstring_t s; int i; if ((tbx = tbx_index_load(argv[optind])) == 0) return 1; if ((fp = bgzf_open(argv[optind], "r")) == 0) return 1; s.s = 0; s.l = s.m = 0; for (i = optind + 1; i < argc; ++i) { hts_itr_t *itr; if ((itr = tbx_itr_querys(tbx, argv[i])) == 0) continue; while (tbx_bgzf_itr_next(fp, tbx, itr, &s) >= 0) bcftools_puts(s.s); tbx_itr_destroy(itr); } free(s.s); bgzf_close(fp); tbx_destroy(tbx); } return 0; } pysam-0.23.0/bcftools/tsv2vcf.c000066400000000000000000000075261475062545500163300ustar00rootroot00000000000000/* tsv2vcf.c -- convert from whitespace-separated fields to VCF Copyright (C) 2014-2021 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include "tsv2vcf.h" tsv_t *tsv_init(const char *str) { tsv_t *tsv = (tsv_t *) calloc(1,sizeof(tsv_t)); kstring_t tmp = {0,0,0}; const char *ss = str, *se = ss; tsv->ncols = 0; while ( *ss ) { if ( *se && *se!=',' ) { se++; continue; } tsv->ncols++; tsv->cols = (tsv_col_t*) realloc(tsv->cols,sizeof(tsv_col_t)*tsv->ncols); tsv->cols[tsv->ncols-1].name = NULL; tsv->cols[tsv->ncols-1].setter = NULL; tmp.l = 0; kputsn(ss, se-ss, &tmp); if ( strcasecmp("-",tmp.s) ) tsv->cols[tsv->ncols-1].name = strdup(tmp.s); if ( !*se ) break; ss = ++se; } free(tmp.s); return tsv; } void tsv_destroy(tsv_t *tsv) { int i; for (i=0; incols; i++) free(tsv->cols[i].name); free(tsv->cols); free(tsv); } int tsv_register(tsv_t *tsv, const char *id, tsv_setter_t setter, void *usr) { int i; for (i=0; incols; i++) { if ( !tsv->cols[i].name || strcasecmp(tsv->cols[i].name,id) ) continue; tsv->cols[i].setter = setter; tsv->cols[i].usr = usr; return 0; } return -1; } int tsv_parse(tsv_t *tsv, bcf1_t *rec, char *str) { int status = 0; tsv->icol = 0; tsv->ss = tsv->se = str; while ( *tsv->ss && tsv->icol < tsv->ncols ) { while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++; if ( tsv->cols[tsv->icol].setter ) { int ret = tsv->cols[tsv->icol].setter(tsv,rec,tsv->cols[tsv->icol].usr); if ( ret<0 ) return -1; status++; } while ( *tsv->se && isspace(*tsv->se) ) tsv->se++; tsv->ss = tsv->se; tsv->icol++; } return status ? 0 : -1; } int tsv_setter_chrom(tsv_t *tsv, bcf1_t *rec, void *usr) { char tmp = *tsv->se; *tsv->se = 0; rec->rid = bcf_hdr_name2id((bcf_hdr_t*)usr, tsv->ss); *tsv->se = tmp; return rec->rid==-1 ? -1 : 0; } int tsv_setter_pos(tsv_t *tsv, bcf1_t *rec, void *usr) { char *endptr; rec->pos = strtol(tsv->ss, &endptr, 10) - 1; if ( tsv->ss==endptr ) return -1; return 0; } int tsv_setter_id(tsv_t *tsv, bcf1_t *rec, void *usr) { char tmp = *tsv->se; *tsv->se = 0; bcf_update_id((bcf_hdr_t*)usr, rec, tsv->ss); *tsv->se = tmp; return 0; } int tsv_setter_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr) { bcf_hdr_t *hdr = (bcf_hdr_t*)usr; char *sb = tsv->ss; while ( *sb && !isspace(*sb) ) sb++; if ( !*sb ) return -1; char tmp = *sb; *sb = ','; bcf_update_alleles_str(hdr, rec, tsv->ss); *sb = tmp; return 0; } pysam-0.23.0/bcftools/tsv2vcf.c.pysam.c000066400000000000000000000075631475062545500177020ustar00rootroot00000000000000#include "bcftools.pysam.h" /* tsv2vcf.c -- convert from whitespace-separated fields to VCF Copyright (C) 2014-2021 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include "tsv2vcf.h" tsv_t *tsv_init(const char *str) { tsv_t *tsv = (tsv_t *) calloc(1,sizeof(tsv_t)); kstring_t tmp = {0,0,0}; const char *ss = str, *se = ss; tsv->ncols = 0; while ( *ss ) { if ( *se && *se!=',' ) { se++; continue; } tsv->ncols++; tsv->cols = (tsv_col_t*) realloc(tsv->cols,sizeof(tsv_col_t)*tsv->ncols); tsv->cols[tsv->ncols-1].name = NULL; tsv->cols[tsv->ncols-1].setter = NULL; tmp.l = 0; kputsn(ss, se-ss, &tmp); if ( strcasecmp("-",tmp.s) ) tsv->cols[tsv->ncols-1].name = strdup(tmp.s); if ( !*se ) break; ss = ++se; } free(tmp.s); return tsv; } void tsv_destroy(tsv_t *tsv) { int i; for (i=0; incols; i++) free(tsv->cols[i].name); free(tsv->cols); free(tsv); } int tsv_register(tsv_t *tsv, const char *id, tsv_setter_t setter, void *usr) { int i; for (i=0; incols; i++) { if ( !tsv->cols[i].name || strcasecmp(tsv->cols[i].name,id) ) continue; tsv->cols[i].setter = setter; tsv->cols[i].usr = usr; return 0; } return -1; } int tsv_parse(tsv_t *tsv, bcf1_t *rec, char *str) { int status = 0; tsv->icol = 0; tsv->ss = tsv->se = str; while ( *tsv->ss && tsv->icol < tsv->ncols ) { while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++; if ( tsv->cols[tsv->icol].setter ) { int ret = tsv->cols[tsv->icol].setter(tsv,rec,tsv->cols[tsv->icol].usr); if ( ret<0 ) return -1; status++; } while ( *tsv->se && isspace(*tsv->se) ) tsv->se++; tsv->ss = tsv->se; tsv->icol++; } return status ? 0 : -1; } int tsv_setter_chrom(tsv_t *tsv, bcf1_t *rec, void *usr) { char tmp = *tsv->se; *tsv->se = 0; rec->rid = bcf_hdr_name2id((bcf_hdr_t*)usr, tsv->ss); *tsv->se = tmp; return rec->rid==-1 ? -1 : 0; } int tsv_setter_pos(tsv_t *tsv, bcf1_t *rec, void *usr) { char *endptr; rec->pos = strtol(tsv->ss, &endptr, 10) - 1; if ( tsv->ss==endptr ) return -1; return 0; } int tsv_setter_id(tsv_t *tsv, bcf1_t *rec, void *usr) { char tmp = *tsv->se; *tsv->se = 0; bcf_update_id((bcf_hdr_t*)usr, rec, tsv->ss); *tsv->se = tmp; return 0; } int tsv_setter_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr) { bcf_hdr_t *hdr = (bcf_hdr_t*)usr; char *sb = tsv->ss; while ( *sb && !isspace(*sb) ) sb++; if ( !*sb ) return -1; char tmp = *sb; *sb = ','; bcf_update_alleles_str(hdr, rec, tsv->ss); *sb = tmp; return 0; } pysam-0.23.0/bcftools/tsv2vcf.h000066400000000000000000000052421475062545500163260ustar00rootroot00000000000000/* tsv2vcf.h -- convert from whitespace-separated fields to VCF Copyright (C) 2014-2021 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef __TSV2VCF_H__ #define __TSV2VCF_H__ #include typedef struct _tsv_t tsv_t; typedef int (*tsv_setter_t)(tsv_t *, bcf1_t *, void *); typedef struct { char *name; tsv_setter_t setter; void *usr; } tsv_col_t; struct _tsv_t { int ncols, icol; tsv_col_t *cols; char *se, *ss; }; tsv_t *tsv_init(const char *str); void tsv_destroy(tsv_t *tsv); int tsv_register(tsv_t *tsv, const char *id, tsv_setter_t setter, void *usr); /** * tsv_parse() - parse tsv line and fill VCF record * Returns 0 on success or -1 on parse error */ int tsv_parse(tsv_t *tsv, bcf1_t *rec, char *str); /** * tstv_next() - position ss,se to next field; first pass with ss=se=str * Returns 0 on success, or -1 if no more fields */ static inline int tsv_next(tsv_t *tsv) { if ( !*tsv->se ) return -1; if ( tsv->ss==tsv->se ) { while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++; return 0; } while ( *tsv->se && isspace(*tsv->se) ) tsv->se++; tsv->ss = tsv->se; while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++; return 0; } /** * The setters return 0 on success or negative value if the line is to be skipped. */ int tsv_setter_chrom(tsv_t *tsv, bcf1_t *rec, void *usr); int tsv_setter_pos(tsv_t *tsv, bcf1_t *rec, void *usr); int tsv_setter_id(tsv_t *tsv, bcf1_t *rec, void *usr); int tsv_setter_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr); // usr must point to bcf_hdr_t #endif pysam-0.23.0/bcftools/utlist.h000066400000000000000000001552521475062545500162640ustar00rootroot00000000000000/* Copyright (c) 2007-2014, Troy D. Hanson http://troydhanson.github.com/uthash/ All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef UTLIST_H #define UTLIST_H #define UTLIST_VERSION 1.9.9 #include /* * This file contains macros to manipulate singly and doubly-linked lists. * * 1. LL_ macros: singly-linked lists. * 2. DL_ macros: doubly-linked lists. * 3. CDL_ macros: circular doubly-linked lists. * * To use singly-linked lists, your structure must have a "next" pointer. * To use doubly-linked lists, your structure must "prev" and "next" pointers. * Either way, the pointer to the head of the list must be initialized to NULL. * * ----------------.EXAMPLE ------------------------- * struct item { * int id; * struct item *prev, *next; * } * * struct item *list = NULL: * * int main() { * struct item *item; * ... allocate and populate item ... * DL_APPEND(list, item); * } * -------------------------------------------------- * * For doubly-linked lists, the append and delete macros are O(1) * For singly-linked lists, append and delete are O(n) but prepend is O(1) * The sort macro is O(n log(n)) for all types of single/double/circular lists. */ /* These macros use decltype or the earlier __typeof GNU extension. As decltype is only available in newer compilers (VS2010 or gcc 4.3+ when compiling c++ code), this code uses whatever method is needed or, for VS2008 where neither is available, uses casting workarounds. */ #ifdef _MSC_VER /* MS compiler */ #if _MSC_VER >= 1600 && defined(__cplusplus) /* VS2010 or newer in C++ mode */ #define LDECLTYPE(x) decltype(x) #else /* VS2008 or older (or VS2010 in C mode) */ #define NO_DECLTYPE #define LDECLTYPE(x) char* #endif #elif defined(__ICCARM__) #define NO_DECLTYPE #define LDECLTYPE(x) char* #else /* GNU, Sun and other compilers */ #define LDECLTYPE(x) __typeof(x) #endif /* for VS2008 we use some workarounds to get around the lack of decltype, * namely, we always reassign our tmp variable to the list head if we need * to dereference its prev/next pointers, and save/restore the real head.*/ #ifdef NO_DECLTYPE #define _SV(elt,list) _tmp = (char*)(list); {char **_alias = (char**)&(list); *_alias = (elt); } #define _NEXT(elt,list,next) ((char*)((list)->next)) #define _NEXTASGN(elt,list,to,next) { char **_alias = (char**)&((list)->next); *_alias=(char*)(to); } /* #define _PREV(elt,list,prev) ((char*)((list)->prev)) */ #define _PREVASGN(elt,list,to,prev) { char **_alias = (char**)&((list)->prev); *_alias=(char*)(to); } #define _RS(list) { char **_alias = (char**)&(list); *_alias=_tmp; } #define _CASTASGN(a,b) { char **_alias = (char**)&(a); *_alias=(char*)(b); } #else #define _SV(elt,list) #define _NEXT(elt,list,next) ((elt)->next) #define _NEXTASGN(elt,list,to,next) ((elt)->next)=(to) /* #define _PREV(elt,list,prev) ((elt)->prev) */ #define _PREVASGN(elt,list,to,prev) ((elt)->prev)=(to) #define _RS(list) #define _CASTASGN(a,b) (a)=(b) #endif /****************************************************************************** * The sort macro is an adaptation of Simon Tatham's O(n log(n)) mergesort * * Unwieldy variable names used here to avoid shadowing passed-in variables. * *****************************************************************************/ #define LL_SORT(list, cmp) \ LL_SORT2(list, cmp, next) #define LL_SORT2(list, cmp, next) \ do { \ LDECLTYPE(list) _ls_p; \ LDECLTYPE(list) _ls_q; \ LDECLTYPE(list) _ls_e; \ LDECLTYPE(list) _ls_tail; \ int _ls_insize, _ls_nmerges, _ls_psize, _ls_qsize, _ls_i, _ls_looping; \ if (list) { \ _ls_insize = 1; \ _ls_looping = 1; \ while (_ls_looping) { \ _CASTASGN(_ls_p,list); \ list = NULL; \ _ls_tail = NULL; \ _ls_nmerges = 0; \ while (_ls_p) { \ _ls_nmerges++; \ _ls_q = _ls_p; \ _ls_psize = 0; \ for (_ls_i = 0; _ls_i < _ls_insize; _ls_i++) { \ _ls_psize++; \ _SV(_ls_q,list); _ls_q = _NEXT(_ls_q,list,next); _RS(list); \ if (!_ls_q) break; \ } \ _ls_qsize = _ls_insize; \ while (_ls_psize > 0 || (_ls_qsize > 0 && _ls_q)) { \ if (_ls_psize == 0) { \ _ls_e = _ls_q; _SV(_ls_q,list); _ls_q = \ _NEXT(_ls_q,list,next); _RS(list); _ls_qsize--; \ } else if (_ls_qsize == 0 || !_ls_q) { \ _ls_e = _ls_p; _SV(_ls_p,list); _ls_p = \ _NEXT(_ls_p,list,next); _RS(list); _ls_psize--; \ } else if (cmp(_ls_p,_ls_q) <= 0) { \ _ls_e = _ls_p; _SV(_ls_p,list); _ls_p = \ _NEXT(_ls_p,list,next); _RS(list); _ls_psize--; \ } else { \ _ls_e = _ls_q; _SV(_ls_q,list); _ls_q = \ _NEXT(_ls_q,list,next); _RS(list); _ls_qsize--; \ } \ if (_ls_tail) { \ _SV(_ls_tail,list); _NEXTASGN(_ls_tail,list,_ls_e,next); _RS(list); \ } else { \ _CASTASGN(list,_ls_e); \ } \ _ls_tail = _ls_e; \ } \ _ls_p = _ls_q; \ } \ if (_ls_tail) { \ _SV(_ls_tail,list); _NEXTASGN(_ls_tail,list,NULL,next); _RS(list); \ } \ if (_ls_nmerges <= 1) { \ _ls_looping=0; \ } \ _ls_insize *= 2; \ } \ } \ } while (0) #define DL_SORT(list, cmp) \ DL_SORT2(list, cmp, prev, next) #define DL_SORT2(list, cmp, prev, next) \ do { \ LDECLTYPE(list) _ls_p; \ LDECLTYPE(list) _ls_q; \ LDECLTYPE(list) _ls_e; \ LDECLTYPE(list) _ls_tail; \ int _ls_insize, _ls_nmerges, _ls_psize, _ls_qsize, _ls_i, _ls_looping; \ if (list) { \ _ls_insize = 1; \ _ls_looping = 1; \ while (_ls_looping) { \ _CASTASGN(_ls_p,list); \ list = NULL; \ _ls_tail = NULL; \ _ls_nmerges = 0; \ while (_ls_p) { \ _ls_nmerges++; \ _ls_q = _ls_p; \ _ls_psize = 0; \ for (_ls_i = 0; _ls_i < _ls_insize; _ls_i++) { \ _ls_psize++; \ _SV(_ls_q,list); _ls_q = _NEXT(_ls_q,list,next); _RS(list); \ if (!_ls_q) break; \ } \ _ls_qsize = _ls_insize; \ while (_ls_psize > 0 || (_ls_qsize > 0 && _ls_q)) { \ if (_ls_psize == 0) { \ _ls_e = _ls_q; _SV(_ls_q,list); _ls_q = \ _NEXT(_ls_q,list,next); _RS(list); _ls_qsize--; \ } else if (_ls_qsize == 0 || !_ls_q) { \ _ls_e = _ls_p; _SV(_ls_p,list); _ls_p = \ _NEXT(_ls_p,list,next); _RS(list); _ls_psize--; \ } else if (cmp(_ls_p,_ls_q) <= 0) { \ _ls_e = _ls_p; _SV(_ls_p,list); _ls_p = \ _NEXT(_ls_p,list,next); _RS(list); _ls_psize--; \ } else { \ _ls_e = _ls_q; _SV(_ls_q,list); _ls_q = \ _NEXT(_ls_q,list,next); _RS(list); _ls_qsize--; \ } \ if (_ls_tail) { \ _SV(_ls_tail,list); _NEXTASGN(_ls_tail,list,_ls_e,next); _RS(list); \ } else { \ _CASTASGN(list,_ls_e); \ } \ _SV(_ls_e,list); _PREVASGN(_ls_e,list,_ls_tail,prev); _RS(list); \ _ls_tail = _ls_e; \ } \ _ls_p = _ls_q; \ } \ _CASTASGN(list->prev, _ls_tail); \ _SV(_ls_tail,list); _NEXTASGN(_ls_tail,list,NULL,next); _RS(list); \ if (_ls_nmerges <= 1) { \ _ls_looping=0; \ } \ _ls_insize *= 2; \ } \ } \ } while (0) #define DL_HEAD(list) (list) #define DL_TAIL(list) ((list) ? (list)->prev : NULL) #define CDL_SORT(list, cmp) \ CDL_SORT2(list, cmp, prev, next) #define CDL_SORT2(list, cmp, prev, next) \ do { \ LDECLTYPE(list) _ls_p; \ LDECLTYPE(list) _ls_q; \ LDECLTYPE(list) _ls_e; \ LDECLTYPE(list) _ls_tail; \ LDECLTYPE(list) _ls_oldhead; \ LDECLTYPE(list) _tmp; \ int _ls_insize, _ls_nmerges, _ls_psize, _ls_qsize, _ls_i, _ls_looping; \ if (list) { \ _ls_insize = 1; \ _ls_looping = 1; \ while (_ls_looping) { \ _CASTASGN(_ls_p,list); \ _CASTASGN(_ls_oldhead,list); \ list = NULL; \ _ls_tail = NULL; \ _ls_nmerges = 0; \ while (_ls_p) { \ _ls_nmerges++; \ _ls_q = _ls_p; \ _ls_psize = 0; \ for (_ls_i = 0; _ls_i < _ls_insize; _ls_i++) { \ _ls_psize++; \ _SV(_ls_q,list); \ if (_NEXT(_ls_q,list,next) == _ls_oldhead) { \ _ls_q = NULL; \ } else { \ _ls_q = _NEXT(_ls_q,list,next); \ } \ _RS(list); \ if (!_ls_q) break; \ } \ _ls_qsize = _ls_insize; \ while (_ls_psize > 0 || (_ls_qsize > 0 && _ls_q)) { \ if (_ls_psize == 0) { \ _ls_e = _ls_q; _SV(_ls_q,list); _ls_q = \ _NEXT(_ls_q,list,next); _RS(list); _ls_qsize--; \ if (_ls_q == _ls_oldhead) { _ls_q = NULL; } \ } else if (_ls_qsize == 0 || !_ls_q) { \ _ls_e = _ls_p; _SV(_ls_p,list); _ls_p = \ _NEXT(_ls_p,list,next); _RS(list); _ls_psize--; \ if (_ls_p == _ls_oldhead) { _ls_p = NULL; } \ } else if (cmp(_ls_p,_ls_q) <= 0) { \ _ls_e = _ls_p; _SV(_ls_p,list); _ls_p = \ _NEXT(_ls_p,list,next); _RS(list); _ls_psize--; \ if (_ls_p == _ls_oldhead) { _ls_p = NULL; } \ } else { \ _ls_e = _ls_q; _SV(_ls_q,list); _ls_q = \ _NEXT(_ls_q,list,next); _RS(list); _ls_qsize--; \ if (_ls_q == _ls_oldhead) { _ls_q = NULL; } \ } \ if (_ls_tail) { \ _SV(_ls_tail,list); _NEXTASGN(_ls_tail,list,_ls_e,next); _RS(list); \ } else { \ _CASTASGN(list,_ls_e); \ } \ _SV(_ls_e,list); _PREVASGN(_ls_e,list,_ls_tail,prev); _RS(list); \ _ls_tail = _ls_e; \ } \ _ls_p = _ls_q; \ } \ _CASTASGN(list->prev,_ls_tail); \ _CASTASGN(_tmp,list); \ _SV(_ls_tail,list); _NEXTASGN(_ls_tail,list,_tmp,next); _RS(list); \ if (_ls_nmerges <= 1) { \ _ls_looping=0; \ } \ _ls_insize *= 2; \ } \ } \ } while (0) /****************************************************************************** * singly linked list macros (non-circular) * *****************************************************************************/ #define LL_PREPEND(head,add) \ LL_PREPEND2(head,add,next) #define LL_PREPEND2(head,add,next) \ do { \ (add)->next = head; \ head = add; \ } while (0) #define LL_CONCAT(head1,head2) \ LL_CONCAT2(head1,head2,next) #define LL_CONCAT2(head1,head2,next) \ do { \ LDECLTYPE(head1) _tmp; \ if (head1) { \ _tmp = head1; \ while (_tmp->next) { _tmp = _tmp->next; } \ _tmp->next=(head2); \ } else { \ (head1)=(head2); \ } \ } while (0) #define LL_APPEND(head,add) \ LL_APPEND2(head,add,next) #define LL_APPEND2(head,add,next) \ do { \ LDECLTYPE(head) _tmp; \ (add)->next=NULL; \ if (head) { \ _tmp = head; \ while (_tmp->next) { _tmp = _tmp->next; } \ _tmp->next=(add); \ } else { \ (head)=(add); \ } \ } while (0) #define LL_DELETE(head,del) \ LL_DELETE2(head,del,next) #define LL_DELETE2(head,del,next) \ do { \ LDECLTYPE(head) _tmp; \ if ((head) == (del)) { \ (head)=(head)->next; \ } else { \ _tmp = head; \ while (_tmp->next && (_tmp->next != (del))) { \ _tmp = _tmp->next; \ } \ if (_tmp->next) { \ _tmp->next = ((del)->next); \ } \ } \ } while (0) /* Here are VS2008 replacements for LL_APPEND and LL_DELETE */ #define LL_APPEND_VS2008(head,add) \ LL_APPEND2_VS2008(head,add,next) #define LL_APPEND2_VS2008(head,add,next) \ do { \ if (head) { \ (add)->next = head; /* use add->next as a temp variable */ \ while ((add)->next->next) { (add)->next = (add)->next->next; } \ (add)->next->next=(add); \ } else { \ (head)=(add); \ } \ (add)->next=NULL; \ } while (0) #define LL_DELETE_VS2008(head,del) \ LL_DELETE2_VS2008(head,del,next) #define LL_DELETE2_VS2008(head,del,next) \ do { \ if ((head) == (del)) { \ (head)=(head)->next; \ } else { \ char *_tmp = (char*)(head); \ while ((head)->next && ((head)->next != (del))) { \ head = (head)->next; \ } \ if ((head)->next) { \ (head)->next = ((del)->next); \ } \ { \ char **_head_alias = (char**)&(head); \ *_head_alias = _tmp; \ } \ } \ } while (0) #ifdef NO_DECLTYPE #undef LL_APPEND #define LL_APPEND LL_APPEND_VS2008 #undef LL_DELETE #define LL_DELETE LL_DELETE_VS2008 #undef LL_DELETE2 #define LL_DELETE2 LL_DELETE2_VS2008 #undef LL_APPEND2 #define LL_APPEND2 LL_APPEND2_VS2008 #undef LL_CONCAT /* no LL_CONCAT_VS2008 */ #undef DL_CONCAT /* no DL_CONCAT_VS2008 */ #endif /* end VS2008 replacements */ #define LL_COUNT(head,el,counter) \ LL_COUNT2(head,el,counter,next) \ #define LL_COUNT2(head,el,counter,next) \ { \ counter = 0; \ LL_FOREACH2(head,el,next){ ++counter; } \ } #define LL_FOREACH(head,el) \ LL_FOREACH2(head,el,next) #define LL_FOREACH2(head,el,next) \ for(el=head;el;el=(el)->next) #define LL_FOREACH_SAFE(head,el,tmp) \ LL_FOREACH_SAFE2(head,el,tmp,next) #define LL_FOREACH_SAFE2(head,el,tmp,next) \ for((el)=(head);(el) && (tmp = (el)->next, 1); (el) = tmp) #define LL_SEARCH_SCALAR(head,out,field,val) \ LL_SEARCH_SCALAR2(head,out,field,val,next) #define LL_SEARCH_SCALAR2(head,out,field,val,next) \ do { \ LL_FOREACH2(head,out,next) { \ if ((out)->field == (val)) break; \ } \ } while(0) #define LL_SEARCH(head,out,elt,cmp) \ LL_SEARCH2(head,out,elt,cmp,next) #define LL_SEARCH2(head,out,elt,cmp,next) \ do { \ LL_FOREACH2(head,out,next) { \ if ((cmp(out,elt))==0) break; \ } \ } while(0) #define LL_REPLACE_ELEM(head, el, add) \ do { \ LDECLTYPE(head) _tmp; \ assert(head != NULL); \ assert(el != NULL); \ assert(add != NULL); \ (add)->next = (el)->next; \ if ((head) == (el)) { \ (head) = (add); \ } else { \ _tmp = head; \ while (_tmp->next && (_tmp->next != (el))) { \ _tmp = _tmp->next; \ } \ if (_tmp->next) { \ _tmp->next = (add); \ } \ } \ } while (0) #define LL_PREPEND_ELEM(head, el, add) \ do { \ LDECLTYPE(head) _tmp; \ assert(head != NULL); \ assert(el != NULL); \ assert(add != NULL); \ (add)->next = (el); \ if ((head) == (el)) { \ (head) = (add); \ } else { \ _tmp = head; \ while (_tmp->next && (_tmp->next != (el))) { \ _tmp = _tmp->next; \ } \ if (_tmp->next) { \ _tmp->next = (add); \ } \ } \ } while (0) \ /****************************************************************************** * doubly linked list macros (non-circular) * *****************************************************************************/ #define DL_PREPEND(head,add) \ DL_PREPEND2(head,add,prev,next) #define DL_PREPEND2(head,add,prev,next) \ do { \ (add)->next = head; \ if (head) { \ (add)->prev = (head)->prev; \ (head)->prev = (add); \ } else { \ (add)->prev = (add); \ } \ (head) = (add); \ } while (0) #define DL_APPEND(head,add) \ DL_APPEND2(head,add,prev,next) #define DL_APPEND2(head,add,prev,next) \ do { \ if (head) { \ (add)->prev = (head)->prev; \ (head)->prev->next = (add); \ (head)->prev = (add); \ (add)->next = NULL; \ } else { \ (head)=(add); \ (head)->prev = (head); \ (head)->next = NULL; \ } \ } while (0) #define DL_CONCAT(head1,head2) \ DL_CONCAT2(head1,head2,prev,next) #define DL_CONCAT2(head1,head2,prev,next) \ do { \ LDECLTYPE(head1) _tmp; \ if (head2) { \ if (head1) { \ _tmp = (head2)->prev; \ (head2)->prev = (head1)->prev; \ (head1)->prev->next = (head2); \ (head1)->prev = _tmp; \ } else { \ (head1)=(head2); \ } \ } \ } while (0) #define DL_DELETE(head,del) \ DL_DELETE2(head,del,prev,next) #define DL_DELETE2(head,del,prev,next) \ do { \ assert((del)->prev != NULL); \ if ((del)->prev == (del)) { \ (head)=NULL; \ } else if ((del)==(head)) { \ (del)->next->prev = (del)->prev; \ (head) = (del)->next; \ } else { \ (del)->prev->next = (del)->next; \ if ((del)->next) { \ (del)->next->prev = (del)->prev; \ } else { \ (head)->prev = (del)->prev; \ } \ } \ } while (0) #define DL_COUNT(head,el,counter) \ DL_COUNT2(head,el,counter,next) \ #define DL_COUNT2(head,el,counter,next) \ { \ counter = 0; \ DL_FOREACH2(head,el,next){ ++counter; } \ } #define DL_FOREACH(head,el) \ DL_FOREACH2(head,el,next) #define DL_FOREACH2(head,el,next) \ for(el=head;el;el=(el)->next) /* this version is safe for deleting the elements during iteration */ #define DL_FOREACH_SAFE(head,el,tmp) \ DL_FOREACH_SAFE2(head,el,tmp,next) #define DL_FOREACH_SAFE2(head,el,tmp,next) \ for((el)=(head);(el) && (tmp = (el)->next, 1); (el) = tmp) /* these are identical to their singly-linked list counterparts */ #define DL_SEARCH_SCALAR LL_SEARCH_SCALAR #define DL_SEARCH LL_SEARCH #define DL_SEARCH_SCALAR2 LL_SEARCH_SCALAR2 #define DL_SEARCH2 LL_SEARCH2 #define DL_REPLACE_ELEM(head, el, add) \ do { \ assert(head != NULL); \ assert(el != NULL); \ assert(add != NULL); \ if ((head) == (el)) { \ (head) = (add); \ (add)->next = (el)->next; \ if ((el)->next == NULL) { \ (add)->prev = (add); \ } else { \ (add)->prev = (el)->prev; \ (add)->next->prev = (add); \ } \ } else { \ (add)->next = (el)->next; \ (add)->prev = (el)->prev; \ (add)->prev->next = (add); \ if ((el)->next == NULL) { \ (head)->prev = (add); \ } else { \ (add)->next->prev = (add); \ } \ } \ } while (0) #define DL_PREPEND_ELEM(head, el, add) \ do { \ assert(head != NULL); \ assert(el != NULL); \ assert(add != NULL); \ (add)->next = (el); \ (add)->prev = (el)->prev; \ (el)->prev = (add); \ if ((head) == (el)) { \ (head) = (add); \ } else { \ (add)->prev->next = (add); \ } \ } while (0) \ /****************************************************************************** * circular doubly linked list macros * *****************************************************************************/ #define CDL_PREPEND(head,add) \ CDL_PREPEND2(head,add,prev,next) #define CDL_PREPEND2(head,add,prev,next) \ do { \ if (head) { \ (add)->prev = (head)->prev; \ (add)->next = (head); \ (head)->prev = (add); \ (add)->prev->next = (add); \ } else { \ (add)->prev = (add); \ (add)->next = (add); \ } \ (head)=(add); \ } while (0) #define CDL_DELETE(head,del) \ CDL_DELETE2(head,del,prev,next) #define CDL_DELETE2(head,del,prev,next) \ do { \ if ( ((head)==(del)) && ((head)->next == (head))) { \ (head) = 0L; \ } else { \ (del)->next->prev = (del)->prev; \ (del)->prev->next = (del)->next; \ if ((del) == (head)) (head)=(del)->next; \ } \ } while (0) #define CDL_COUNT(head,el,counter) \ CDL_COUNT2(head,el,counter,next) \ #define CDL_COUNT2(head, el, counter,next) \ { \ counter = 0; \ CDL_FOREACH2(head,el,next){ ++counter; } \ } #define CDL_FOREACH(head,el) \ CDL_FOREACH2(head,el,next) #define CDL_FOREACH2(head,el,next) \ for(el=head;el;el=((el)->next==head ? 0L : (el)->next)) #define CDL_FOREACH_SAFE(head,el,tmp1,tmp2) \ CDL_FOREACH_SAFE2(head,el,tmp1,tmp2,prev,next) #define CDL_FOREACH_SAFE2(head,el,tmp1,tmp2,prev,next) \ for((el)=(head), ((tmp1)=(head)?((head)->prev):NULL); \ (el) && ((tmp2)=(el)->next, 1); \ ((el) = (((el)==(tmp1)) ? 0L : (tmp2)))) #define CDL_SEARCH_SCALAR(head,out,field,val) \ CDL_SEARCH_SCALAR2(head,out,field,val,next) #define CDL_SEARCH_SCALAR2(head,out,field,val,next) \ do { \ CDL_FOREACH2(head,out,next) { \ if ((out)->field == (val)) break; \ } \ } while(0) #define CDL_SEARCH(head,out,elt,cmp) \ CDL_SEARCH2(head,out,elt,cmp,next) #define CDL_SEARCH2(head,out,elt,cmp,next) \ do { \ CDL_FOREACH2(head,out,next) { \ if ((cmp(out,elt))==0) break; \ } \ } while(0) #define CDL_REPLACE_ELEM(head, el, add) \ do { \ assert(head != NULL); \ assert(el != NULL); \ assert(add != NULL); \ if ((el)->next == (el)) { \ (add)->next = (add); \ (add)->prev = (add); \ (head) = (add); \ } else { \ (add)->next = (el)->next; \ (add)->prev = (el)->prev; \ (add)->next->prev = (add); \ (add)->prev->next = (add); \ if ((head) == (el)) { \ (head) = (add); \ } \ } \ } while (0) #define CDL_PREPEND_ELEM(head, el, add) \ do { \ assert(head != NULL); \ assert(el != NULL); \ assert(add != NULL); \ (add)->next = (el); \ (add)->prev = (el)->prev; \ (el)->prev = (add); \ (add)->prev->next = (add); \ if ((head) == (el)) { \ (head) = (add); \ } \ } while (0) \ #endif /* UTLIST_H */ pysam-0.23.0/bcftools/variantkey.h000066400000000000000000000530101475062545500171020ustar00rootroot00000000000000// VariantKey // // variantkey.h // // @category Libraries // @author Nicola Asuni // @link https://github.com/tecnickcom/variantkey // @license MIT [LICENSE](https://raw.githubusercontent.com/tecnickcom/variantkey/main/LICENSE) // @copyright 2017-2018 GENOMICS plc, 2018-2023 Nicola Asuni - Tecnick.com // // LICENSE // // Copyright (c) 2017-2018 GENOMICS plc // Copyright (c) 2018-2023 Nicola Asuni - Tecnick.com // // Permission is hereby granted, free of charge, to any person obtaining a copy // of this software and associated documentation files (the "Software"), to deal // in the Software without restriction, including without limitation the rights // to use, copy, modify, merge, publish, distribute, sublicense, and/or sell // copies of the Software, and to permit persons to whom the Software is // furnished to do so, subject to the following conditions: // // The above copyright notice and this permission notice shall be included in // all copies or substantial portions of the Software. // // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR // IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, // FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE // AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER // LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN // THE SOFTWARE. /** * @file variantkey.h * @brief VariantKey main functions. * * The functions provided here allow the generation and processing of a 64 bit Unsigned Integer Keys for Human Genetic Variants. * The VariantKey is sortable for chromosome and position, * and it is also fully reversible for variants with up to 11 bases between Reference and Alternate alleles. * It can be used to sort, search and match variant-based data easily and very quickly. */ #ifndef VARIANTKEY_H #define VARIANTKEY_H #include #include #include #include "hex.h" #define VKMASK_CHROM 0xF800000000000000 //!< VariantKey binary mask for CHROM [ 11111000 00000000 00000000 00000000 00000000 00000000 00000000 00000000 ] #define VKMASK_POS 0x07FFFFFF80000000 //!< VariantKey binary mask for POS [ 00000111 11111111 11111111 11111111 10000000 00000000 00000000 00000000 ] #define VKMASK_CHROMPOS 0xFFFFFFFF80000000 //!< VariantKey binary mask for CHROM+POS [ 11111111 11111111 11111111 11111111 10000000 00000000 00000000 00000000 ] #define VKMASK_REFALT 0x000000007FFFFFFF //!< VariantKey binary mask for REF+ALT [ 00000000 00000000 00000000 00000000 01111111 11111111 11111111 11111111 ] #define VKSHIFT_CHROM 59 //!< CHROM LSB position from the VariantKey LSB #define VKSHIFT_POS 31 //!< POS LSB position from the VariantKey LSB #define MAXUINT32 0xFFFFFFFF //!< Maximum value for uint32_t /** * VariantKey struct. * Contains the numerically encoded VariantKey components (CHROM, POS, REF+ALT). */ typedef struct variantkey_t { uint8_t chrom; //!< Chromosome encoded number (only the LSB 5 bit are used) uint32_t pos; //!< Reference position, with the first base having position 0 (only the LSB 28 bit are used) uint32_t refalt; //!< Code for Reference and Alternate allele (only the LSB 31 bits are used) } variantkey_t; /** * Struct containing the minimum and maximum VariantKey values for range searches. */ typedef struct vkrange_t { uint64_t min; //!< Minimum VariantKey value for any given REF+ALT encoding uint64_t max; //!< Maximum VariantKey value for any given REF+ALT encoding } vkrange_t; /** @brief Returns the encoding for a numerical chromosome input. * * @param chrom Chromosome. An identifier from the reference genome, no white-space permitted. * @param size Length of the chrom string, excluding the terminating null byte. * * @return CHROM code */ static inline uint8_t encode_numeric_chrom(const char *chrom, size_t size) { size_t i; uint8_t v = (chrom[0] - '0'); for (i = 1; i < size; i++) { if ((chrom[i] > '9') || (chrom[i] < '0')) { return 0; // NA: a character that is not a number was found. } v = ((v * 10) + (chrom[i] - '0')); } return v; } /** @brief Returns a true value (1) if the input chrom has 'chr' prefix (case insensitive). * * @param chrom Chromosome. An identifier from the reference genome, no white-space permitted. * @param size Length of the chrom string, excluding the terminating null byte. * * @return True (1) if the chr prefix is present. */ static inline int has_chrom_chr_prefix(const char *chrom, size_t size) { return ((size > 3) && ((chrom[0] == 'c') || (chrom[0] == 'C')) && ((chrom[1] == 'h') || (chrom[1] == 'H')) && ((chrom[2] == 'r') || (chrom[2] == 'R'))); } /** @brief Returns chromosome numerical encoding. * * @param chrom Chromosome. An identifier from the reference genome, no white-space permitted. * @param size Length of the chrom string, excluding the terminating null byte. * * @return CHROM code or 0 in case of invalid input. */ static inline uint8_t encode_chrom(const char *chrom, size_t size) { // X = 23; Y = 24; M = 25; any other letter is mapped to 0: static const uint8_t onecharmap[] = { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* M X Y */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,25, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,23,24, 0, 0, 0, 0, 0, 0, /* m x y */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,25, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,23,24, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, }; if (has_chrom_chr_prefix(chrom, size)) { // remove "chr" prefix chrom += 3; size -= 3; } if (size == 0) { return 0; } if ((chrom[0] <= '9') && (chrom[0] >= '0')) { return encode_numeric_chrom(chrom, size); } if ((size == 1) || ((size == 2) && ((chrom[1] == 'T') || (chrom[1] == 't')))) { return onecharmap[((uint8_t)chrom[0])]; } return 0; // NA } /** @brief Decode the chromosome numerical code. * * @param code CHROM code. * @param chrom CHROM string buffer to be returned. Its size should be enough to contain the results (max 4 bytes). * * @return If successful, the total number of characters written is returned, * excluding the null-character appended at the end of the string, * otherwise a negative number is returned in case of failure. */ static inline size_t decode_chrom(uint8_t code, char *chrom) { if ((code < 1) || (code > 25)) { return sprintf(chrom, "NA"); } if (code < 23) { return sprintf(chrom, "%" PRIu8, code); } static const char *map[] = {"X", "Y", "MT"}; return sprintf(chrom, "%s", map[(code - 23)]); } static inline uint32_t encode_base(const uint8_t c) { /* Encode base: A = 0 C = 1 G = 2 T = 3 */ static const uint32_t map[] = { 4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, /*A C G T*/ 4,0,4,1,4,4,4,2,4,4,4,4,4,4,4,4,4,4,4,4,3,4,4,4,4,4,4,4,4,4,4,4, /*a c g t*/ 4,0,4,1,4,4,4,2,4,4,4,4,4,4,4,4,4,4,4,4,3,4,4,4,4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, }; return map[c]; } static inline int encode_allele(uint32_t *h, uint8_t *bitpos, const char *str, size_t size) { uint32_t v; while (size--) { v = encode_base(*str++); if (v > 3) { return -1; } *bitpos -= 2; *h |= (v << *bitpos); } return 0; } static inline uint32_t encode_refalt_rev(const char *ref, size_t sizeref, const char *alt, size_t sizealt) { //[******** ******** ******** ******** *RRRRAAA A1122334 45566778 8990011*] uint32_t h = 0; h |= ((uint32_t)(sizeref) << 27); // RRRR: length of (REF - 1) h |= ((uint32_t)(sizealt) << 23); // AAAA: length of (ALT - 1) uint8_t bitpos = 23; if ((encode_allele(&h, &bitpos, ref, sizeref) < 0) || (encode_allele(&h, &bitpos, alt, sizealt) < 0)) { return MAXUINT32; // error code } return h; } // Mix two 32 bit hash numbers using a MurmurHash3-like algorithm static inline uint32_t muxhash(uint32_t k, uint32_t h) { k *= 0xcc9e2d51; k = (k >> 17) | (k << 15); k *= 0x1b873593; h ^= k; h = (h >> 19) | (h << 13); return ((h * 5) + 0xe6546b64); } static inline uint32_t encode_packchar(int c) { if (c < 'A') { return 27; } if (c >= 'a') { return (uint32_t)(c - 'a' + 1); } return (uint32_t)(c - 'A' + 1); } // pack blocks of 6 characters in 32 bit (6 x 5 bit + 2 spare bit) [ 01111122 22233333 44444555 55666660 ] static inline uint32_t pack_chars_tail(const char *str, size_t size) { uint32_t h = 0; const char *pos = (str + size - 1); switch (size) { case 5: h ^= encode_packchar(*pos--) << (1 + (5 * 1)); // fall through case 4: h ^= encode_packchar(*pos--) << (1 + (5 * 2)); // fall through case 3: h ^= encode_packchar(*pos--) << (1 + (5 * 3)); // fall through case 2: h ^= encode_packchar(*pos--) << (1 + (5 * 4)); // fall through case 1: h ^= encode_packchar(*pos) << (1 + (5 * 5)); } return h; } static inline uint32_t pack_chars(const char *str) { const char *pos = (str + 5); return ((encode_packchar(*pos) << 1) ^ (encode_packchar(*(pos-1)) << (1 + (5 * 1))) ^ (encode_packchar(*(pos-2)) << (1 + (5 * 2))) ^ (encode_packchar(*(pos-3)) << (1 + (5 * 3))) ^ (encode_packchar(*(pos-4)) << (1 + (5 * 4))) ^ (encode_packchar(*(pos-5)) << (1 + (5 * 5)))); } // Return a 32 bit hash of a nucleotide string static inline uint32_t hash32(const char *str, size_t size) { uint32_t h = 0; size_t len = 6; while (size >= len) { h = muxhash(pack_chars(str), h); str += len; size -= len; } if (size > 0) { h = muxhash(pack_chars_tail(str, size), h); } return h; } static inline uint32_t encode_refalt_hash(const char *ref, size_t sizeref, const char *alt, size_t sizealt) { // 0x3 is the separator character between REF and ALT [00000000 00000000 00000000 00000011] uint32_t h = muxhash(hash32(alt, sizealt), muxhash(0x3, hash32(ref, sizeref))); // MurmurHash3 finalization mix - force all bits of a hash block to avalanche h ^= h >> 16; h *= 0x85ebca6b; h ^= h >> 13; h *= 0xc2b2ae35; h ^= h >> 16; return ((h >> 1) | 0x1); // 0x1 is the set bit to indicate HASH mode [00000000 00000000 00000000 00000001] } /** @brief Returns reference+alternate numerical encoding. * * @param ref Reference allele. String containing a sequence of nucleotide letters. * The value in the pos field refers to the position of the first nucleotide in the String. * Characters must be A-Z, a-z or * * @param sizeref Length of the ref string, excluding the terminating null byte. * @param alt Alternate non-reference allele string. * Characters must be A-Z, a-z or * * @param sizealt Length of the alt string, excluding the terminating null byte. * * @return REF+ALT code */ static inline uint32_t encode_refalt(const char *ref, size_t sizeref, const char *alt, size_t sizealt) { if ((sizeref + sizealt) <= 11) { uint32_t h = encode_refalt_rev(ref, sizeref, alt, sizealt); if (h != MAXUINT32) { return h; } } return encode_refalt_hash(ref, sizeref, alt, sizealt); } static inline char decode_base(uint32_t code, int bitpos) { static const char base[4] = {'A', 'C', 'G', 'T'}; return base[((code >> bitpos) & 0x3)]; // 0x3 is the 2 bit mask [00000011] } static inline size_t decode_refalt_rev(uint32_t code, char *ref, size_t *sizeref, char *alt, size_t *sizealt) { *sizeref = (size_t)((code & 0x78000000) >> 27); // [01111000 00000000 00000000 00000000] *sizealt = (size_t)((code & 0x07800000) >> 23); // [00000111 10000000 00000000 00000000] switch (*sizeref) { case 10: ref[9] = decode_base(code, (3 + (2 * 0))); // fall through case 9: ref[8] = decode_base(code, (3 + (2 * 1))); // fall through case 8: ref[7] = decode_base(code, (3 + (2 * 2))); // fall through case 7: ref[6] = decode_base(code, (3 + (2 * 3))); // fall through case 6: ref[5] = decode_base(code, (3 + (2 * 4))); // fall through case 5: ref[4] = decode_base(code, (3 + (2 * 5))); // fall through case 4: ref[3] = decode_base(code, (3 + (2 * 6))); // fall through case 3: ref[2] = decode_base(code, (3 + (2 * 7))); // fall through case 2: ref[1] = decode_base(code, (3 + (2 * 8))); // fall through case 1: ref[0] = decode_base(code, (3 + (2 * 9))); } ref[*sizeref] = 0; uint8_t bitpos = (23 - ((*sizeref) << 1)); switch (*sizealt) { case 10: alt[9] = decode_base(code, bitpos - (2 * 10)); // fall through case 9: alt[8] = decode_base(code, bitpos - (2 * 9)); // fall through case 8: alt[7] = decode_base(code, bitpos - (2 * 8)); // fall through case 7: alt[6] = decode_base(code, bitpos - (2 * 7)); // fall through case 6: alt[5] = decode_base(code, bitpos - (2 * 6)); // fall through case 5: alt[4] = decode_base(code, bitpos - (2 * 5)); // fall through case 4: alt[3] = decode_base(code, bitpos - (2 * 4)); // fall through case 3: alt[2] = decode_base(code, bitpos - (2 * 3)); // fall through case 2: alt[1] = decode_base(code, bitpos - (2 * 2)); // fall through case 1: alt[0] = decode_base(code, bitpos - (2 * 1)); } alt[*sizealt] = 0; return (*sizeref + *sizealt); } /** @brief Decode the 32 bit REF+ALT code if reversible (if it has 11 or less bases in total and only contains ACGT letters). * * @param code REF+ALT code * @param ref REF string buffer to be returned. * @param sizeref Pointer to the size of the ref buffer, excluding the terminating null byte. * This will contain the final ref size. * @param alt ALT string buffer to be returned. * @param sizealt Pointer to the size of the alt buffer, excluding the terminating null byte. * This will contain the final alt size. * * @return If the code is reversible, then the total number of characters of REF+ALT is returned. * Otherwise 0 is returned. */ static inline size_t decode_refalt(uint32_t code, char *ref, size_t *sizeref, char *alt, size_t *sizealt) { if (code & 0x1) // check last bit { return 0; // non-reversible encoding } return decode_refalt_rev(code, ref, sizeref, alt, sizealt); } /** @brief Returns a 64 bit variant key based on the pre-encoded CHROM, POS (0-based) and REF+ALT. * * @param chrom Encoded Chromosome (see encode_chrom). * @param pos Position. The reference position, with the first base having position 0. * @param refalt Encoded Reference + Alternate (see encode_refalt). * * @return VariantKey 64 bit code. */ static inline uint64_t encode_variantkey(uint8_t chrom, uint32_t pos, uint32_t refalt) { return (((uint64_t)chrom << VKSHIFT_CHROM) | ((uint64_t)pos << VKSHIFT_POS) | (uint64_t)refalt); } /** @brief Extract the CHROM code from VariantKey. * * @param vk VariantKey code. * * @return CHROM code. */ static inline uint8_t extract_variantkey_chrom(uint64_t vk) { return (uint8_t)((vk & VKMASK_CHROM) >> VKSHIFT_CHROM); } /** @brief Extract the POS code from VariantKey. * * @param vk VariantKey code. * * @return POS. */ static inline uint32_t extract_variantkey_pos(uint64_t vk) { return (uint32_t)((vk & VKMASK_POS) >> VKSHIFT_POS); } /** @brief Extract the REF+ALT code from VariantKey. * * @param vk VariantKey code. * * @return REF+ALT code. */ static inline uint32_t extract_variantkey_refalt(uint64_t vk) { return (uint32_t)(vk & VKMASK_REFALT); } /** @brief Decode a VariantKey code and returns the components as variantkey_t structure. * * @param code VariantKey code. * @param vk Decoded variantkey structure. */ static inline void decode_variantkey(uint64_t code, variantkey_t *vk) { vk->chrom = extract_variantkey_chrom(code); vk->pos = extract_variantkey_pos(code); vk->refalt = extract_variantkey_refalt(code); } /** * Returns a 64 bit variant key based on CHROM, POS (0-based), REF, ALT. * The variant should be already normalized (see normalize_variant or use normalized_variantkey). * * @param chrom Chromosome. An identifier from the reference genome, no white-space or leading zeros permitted. * @param sizechrom Length of the chrom string, excluding the terminating null byte. * @param pos Position. The reference position, with the first base having position 0. * @param ref Reference allele. String containing a sequence of nucleotide letters. * The value in the pos field refers to the position of the first nucleotide in the String. * Characters must be A-Z, a-z or * * @param sizeref Length of the ref string, excluding the terminating null byte. * @param alt Alternate non-reference allele string. * Characters must be A-Z, a-z or * * @param sizealt Length of the alt string, excluding the terminating null byte. * * @return VariantKey 64 bit code. */ static inline uint64_t variantkey(const char *chrom, size_t sizechrom, uint32_t pos, const char *ref, size_t sizeref, const char *alt, size_t sizealt) { return encode_variantkey(encode_chrom(chrom, sizechrom), pos, encode_refalt(ref, sizeref, alt, sizealt)); } /** @brief Returns minimum and maximum VariantKeys for range searches. * * @param chrom Chromosome encoded number. * @param pos_min Start reference position, with the first base having position 0. * @param pos_max End reference position, with the first base having position 0. * @param range VariantKey range values. */ static inline void variantkey_range(uint8_t chrom, uint32_t pos_min, uint32_t pos_max, vkrange_t *range) { uint64_t c = ((uint64_t)chrom << VKSHIFT_CHROM); range->min = (c | ((uint64_t)pos_min << VKSHIFT_POS)); range->max = (c | ((uint64_t)pos_max << VKSHIFT_POS) | VKMASK_REFALT); } static inline int8_t compare_uint64_t(uint64_t a, uint64_t b) { return (a < b) ? -1 : (a > b); } /** @brief Compares two VariantKeys by chromosome only. * * @param vka The first VariantKey to be compared. * @param vkb The second VariantKey to be compared. * * @return -1 if the first chromosome is smaller than the second, 0 if they are equal and 1 if the first is greater than the second. */ static inline int8_t compare_variantkey_chrom(uint64_t vka, uint64_t vkb) { return compare_uint64_t((vka >> VKSHIFT_CHROM), (vkb >> VKSHIFT_CHROM)); } /** @brief Compares two VariantKeys by chromosome and position. * * @param vka The first VariantKey to be compared. * @param vkb The second VariantKey to be compared. * * @return -1 if the first CHROM+POS is smaller than the second, 0 if they are equal and 1 if the first is greater than the second. */ static inline int8_t compare_variantkey_chrom_pos(uint64_t vka, uint64_t vkb) { return compare_uint64_t((vka >> VKSHIFT_POS), (vkb >> VKSHIFT_POS)); } /** @brief Returns VariantKey hexadecimal string (16 characters). * * The string represent a 64 bit number or: * - 5 bit for CHROM * - 28 bit for POS * - 31 bit for REF+ALT * * @param vk VariantKey code. * @param str String buffer to be returned (it must be sized 17 bytes at least). * * @return Upon successful return, these function returns the number of characters processed * (excluding the null byte used to end output to strings). * If the buffer size is not sufficient, then the return value is the number of characters required for * buffer string, including the terminating null byte. */ static inline size_t variantkey_hex(uint64_t vk, char *str) { return hex_uint64_t(vk, str); } /** @brief Parses a VariantKey hexadecimal string and returns the code. * * @param vs VariantKey hexadecimal string (it must contain 16 hexadecimal characters). * * @return A VariantKey code. */ static inline uint64_t parse_variantkey_hex(const char *vs) { return parse_hex_uint64_t(vs); } #endif // VARIANTKEY_H pysam-0.23.0/bcftools/vcfannotate.c000066400000000000000000005115321475062545500172400ustar00rootroot00000000000000/* vcfannotate.c -- Annotate and edit VCF/BCF files. Copyright (C) 2013-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "vcmp.h" #include "filter.h" #include "convert.h" #include "smpl_ilist.h" #include "regidx.h" #include "dbuf.h" struct _args_t; typedef struct _rm_tag_t { char *key; int hdr_id; void (*handler)(struct _args_t *, bcf1_t *, struct _rm_tag_t *); } rm_tag_t; typedef struct { char **cols; int ncols, mcols; char **als; int nals, mals; kstring_t line; int rid, start, end; } annot_line_t; #define REPLACE_MISSING (1<<0) // -c +TAG .. replace only missing values #define REPLACE_ALL (1<<1) // -c TAG .. replace both missing and existing values #define REPLACE_NON_MISSING (1<<2) // -c -TAG .. replace only if tgt is not missing #define SET_OR_APPEND (1<<3) // -c =TAG .. set new value if missing or non-existent, append otherwise #define MATCH_VALUE (1<<4) // -c ~ID .. do not set, just match the value #define CARRY_OVER_MISSING (1<<5) // -c .TAG .. carry over source missing values as well #define MM_FIRST 0 // if multiple annotation lines overlap a VCF record, use the first, discarding the rest #define MM_APPEND 1 // append, possibly multiple times #define MM_UNIQUE 2 // append, only unique values #define MM_SUM 3 #define MM_AVG 4 #define MM_MIN 5 #define MM_MAX 6 #define MM_APPEND_MISSING 7 // missing values will be transferred as well typedef struct _annot_col_t { int icol, replace, number; // number: one of BCF_VL_* types char *hdr_key_src, *hdr_key_dst; // The setters return 0 on successful update of the bcf record, negative value (bcf_update_* return status) on errors, // or 1 on (repeated partial updates) concluded with a src=NULL call int (*setter)(struct _args_t *, bcf1_t *dst, struct _annot_col_t *, void *src); // the last is the annotation line, either src bcf1_t or annot_line_t int (*getter)(struct _args_t *, bcf1_t *src, struct _annot_col_t *, void **ptr, int *mptr); int merge_method; // one of the MM_* defines khash_t(str2int) *mm_str_hash; // lookup table to ensure uniqueness of added string values kstring_t mm_kstr; size_t mm_dbl_nalloc, // the allocated size --merge-logic values array mm_dbl_nused, // the number of used elements in the mm_dbl array mm_dbl_ndat; // the number of merged rows (for calculating the average) double *mm_dbl; void *ptr; int mptr, done; } annot_col_t; typedef struct { char *name; // column name int ht_type; // type, one of BCF_HT_STR,BCF_HT_INT,BCF_HT_REAL int icol; // index of the annotation column to use union { // memory area with the current annotation value to pass to filter_test_ext int i; float f; char *s; }; } ext_t; // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 #define MARK_LISTED 1 #define MARK_UNLISTED 2 typedef struct _args_t { bcf_srs_t *files; bcf_hdr_t *hdr, *hdr_out, *tgts_hdr; htsFile *out_fh; int output_type, n_threads, clevel; bcf_sr_regions_t *tgts; char *index_fn; int write_index; regidx_t *tgt_idx; // keep everything in memory only with .tab annotation file and -c BEG,END columns regitr_t *tgt_itr; int tgt_is_bed; filter_t *filter, *filter_ext; // only one is initialized, the latter contains external values to set dynamically on the fly char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE int keep_sites; rm_tag_t *rm; // tags scheduled for removal int nrm; int flt_keep_pass; // when all filters removed, reset to PASS vcmp_t *vcmp; // for matching annotation and VCF lines by allele annot_line_t *alines; // buffered annotation lines annot_line_t *aline_missing; uint32_t *srt_alines; // sorted indexes (iALT<<16 || iAline) int nalines, malines, nsrt_alines, msrt_alines; int ref_idx, alt_idx, chr_idx, beg_idx, end_idx; // -1 if not present annot_col_t *cols; // column indexes and setters int ncols; int match_id; // set iff `-c ~ID` given, -1 otherwise int match_end; // set iff `-c ~INFO/END` is given, -1 otherwise char *set_ids_fmt; convert_t *set_ids; int set_ids_replace; // external values for dynamic -i/-e expressions int n_ext; ext_t *ext; void **ext_ptr; int nsmpl_annot; int *sample_map, nsample_map, sample_is_file; // map[idst] -> isrc uint8_t *src_smpl_pld, *dst_smpl_pld; // for Number=G format fields int mtmpi, mtmpf, mtmps; int mtmpi2, mtmpf2, mtmps2; int mtmpi3, mtmpf3, mtmps3; int32_t *tmpi, *tmpi2, *tmpi3; float *tmpf, *tmpf2, *tmpf3; char *tmps, *tmps2, **tmpp, **tmpp2; kstring_t tmpks; char **argv, *output_fname, *targets_fname, *regions_list, *header_fname; char *remove_annots, *columns, *rename_chrs, *rename_annots, *sample_names, *mark_sites; char **rename_annots_map; char *min_overlap_str; float min_overlap_ann, min_overlap_vcf; int rename_annots_nmap; kstring_t merge_method_str; int argc, drop_header, record_cmd_line, tgts_is_vcf, mark_sites_logic, force, single_overlaps; int columns_is_file, has_append_mode, pair_logic; dbuf_t *header_lines; bcf1_t *current_rec; // current record for local setters } args_t; char *msprintf(const char *fmt, ...); int parse_with_payload(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr) { args_t *args = (args_t*) usr; int ret = args->tgt_is_bed ? regidx_parse_bed(line, chr_beg, chr_end, beg, end, NULL, NULL) : regidx_parse_tab(line, chr_beg, chr_end, beg, end, NULL, NULL); if ( ret<0 ) return ret; *((char **)payload) = strdup(line); return 0; } void free_payload(void *payload) { char *str = *((char**)payload); free(str); } void remove_id(args_t *args, bcf1_t *line, rm_tag_t *tag) { bcf_update_id(args->hdr,line,NULL); } void remove_filter(args_t *args, bcf1_t *line, rm_tag_t *tag) { if ( tag->key && tag->hdr_id<0 ) { error("Error: Cannot proceed, not even with the --force option, bad things could happen.\n" " Note that \"bcftools annotate -x FILTER\" can be used to remove ALL filters.\n" " Even better, use \"bcftools view -h\" and \"bcftools reheader\" to fix the header!\n" ); } if ( !tag->key ) bcf_update_filter(args->hdr, line, NULL, args->flt_keep_pass); else bcf_remove_filter(args->hdr, line, tag->hdr_id, args->flt_keep_pass); } void remove_qual(args_t *args, bcf1_t *line, rm_tag_t *tag) { bcf_float_set_missing(line->qual); } void remove_info(args_t *args, bcf1_t *line, rm_tag_t *tag) { // remove all INFO fields if ( !(line->unpacked & BCF_UN_INFO) ) bcf_unpack(line, BCF_UN_INFO); int i; for (i=0; in_info; i++) { bcf_info_t *inf = &line->d.info[i]; if ( !strcmp("END",bcf_hdr_int2id(args->hdr,BCF_DT_ID,inf->key)) ) line->rlen = line->n_allele ? strlen(line->d.allele[0]) : 0; if ( inf->vptr_free ) { free(inf->vptr - inf->vptr_off); inf->vptr_free = 0; } line->d.shared_dirty |= BCF1_DIRTY_INF; inf->vptr = NULL; inf->vptr_off = inf->vptr_len = 0; } } void remove_info_tag(args_t *args, bcf1_t *line, rm_tag_t *tag) { bcf_update_info(args->hdr, line, tag->key, NULL, 0, BCF_HT_INT); // the type does not matter with n=0 } void remove_format_tag(args_t *args, bcf1_t *line, rm_tag_t *tag) { bcf_update_format(args->hdr, line, tag->key, NULL, 0, BCF_HT_INT); // the type does not matter with n=0 } void remove_format(args_t *args, bcf1_t *line, rm_tag_t *tag) { // remove all FORMAT fields except GT if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT); int i; for (i=0; in_fmt; i++) { bcf_fmt_t *fmt = &line->d.fmt[i]; const char *key = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id); if ( key[0]=='G' && key[1]=='T' && !key[2] ) continue; if ( fmt->p_free ) { free(fmt->p - fmt->p_off); fmt->p_free = 0; } line->d.indiv_dirty = 1; fmt->p = NULL; } } #include "htslib/khash.h" KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t) typedef khash_t(vdict) vdict_t; static void remove_hdr_lines(bcf_hdr_t *hdr, int type) { int i = 0, nrm = 0; while ( inhrec ) { if ( hdr->hrec[i]->type!=type ) { i++; continue; } bcf_hrec_t *hrec = hdr->hrec[i]; if ( type==BCF_HL_FMT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG ) { // everything except FORMAT/GT int id = bcf_hrec_find_key(hrec, "ID"); if ( id>=0 ) { if ( type==BCF_HL_FMT && !strcmp(hrec->vals[id],"GT") ) { i++; continue; } vdict_t *d = type==BCF_HL_CTG ? (vdict_t*)hdr->dict[BCF_DT_CTG] : (vdict_t*)hdr->dict[BCF_DT_ID]; khint_t k = kh_get(vdict, d, hdr->hrec[i]->vals[id]); kh_val(d, k).hrec[type==BCF_HL_CTG?0:type] = NULL; kh_val(d, k).info[type] |= 0xf; } } nrm++; hdr->nhrec--; if ( i < hdr->nhrec ) memmove(&hdr->hrec[i],&hdr->hrec[i+1],(hdr->nhrec-i)*sizeof(bcf_hrec_t*)); bcf_hrec_destroy(hrec); } if ( nrm ) { if (bcf_hdr_sync(hdr) < 0) error_errno("[%s] Failed to update header", __func__); } } static void init_remove_annots(args_t *args) { int keep_info = 0, keep_fmt = 0, keep_flt = 0; void *keep = khash_str2int_init(); kstring_t str = {0,0,0}; char *ss = args->remove_annots; int i, ntags, needs_info = 0; if ( args->set_ids ) { const char **tags = convert_list_used_tags(args->set_ids,&ntags); for (i=0; inrm++; args->rm = (rm_tag_t*) realloc(args->rm,sizeof(rm_tag_t)*args->nrm); rm_tag_t *tag = &args->rm[args->nrm-1]; tag->key = NULL; int type = BCF_HL_GEN; if ( !strncasecmp("INFO/",ss,5) ) { type = BCF_HL_INFO; ss += 5; } else if ( !strncasecmp("INF/",ss,4) ) { type = BCF_HL_INFO; ss += 4; } else if ( !strncasecmp("FORMAT/",ss,7) ) { type = BCF_HL_FMT; ss += 7; } else if ( !strncasecmp("FMT/",ss,4) ) { type = BCF_HL_FMT; ss += 4; } else if ( !strncasecmp("FILTER/",ss,7) ) { type = BCF_HL_FLT; ss += 7; } else if ( !strncasecmp("^INFO/",ss,6) ) { type = BCF_HL_INFO; ss += 6; keep_info = 1; } else if ( !strncasecmp("^INF/",ss,5) ) { type = BCF_HL_INFO; ss += 5; keep_info = 1; } else if ( !strncasecmp("^FORMAT/",ss,8) ) { type = BCF_HL_FMT; ss += 8; keep_fmt = 1; } else if ( !strncasecmp("^FMT/",ss,5) ) { type = BCF_HL_FMT; ss += 5; keep_fmt = 1; } else if ( !strncasecmp("^FILTER/",ss,8) ) { type = BCF_HL_FLT; ss += 8; keep_flt = 1; } char *se = ss; while ( *se && *se!=',' ) se++; str.l = 0; kputsn(ss, se-ss, &str); if ( type==BCF_HL_FLT ) { if ( !keep_flt ) { args->flt_keep_pass = 1; tag->handler = remove_filter; tag->key = strdup(str.s); tag->hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, tag->key); if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FLT,tag->hdr_id) ) { if ( args->keep_sites ) error("Error: The filter \"%s\" is not defined in the header, cannot use the -k option\n", str.s); else fprintf(stderr,"Warning: The filter \"%s\" is not defined in the header\n", str.s); } else if ( !args->keep_sites ) bcf_hdr_remove(args->hdr_out,BCF_HL_FLT,tag->key); } else { int value, ret = khash_str2int_get(keep, str.s, &value); if ( ret==-1 ) khash_str2int_set(keep, strdup(str.s),1<nrm--; } } else if ( type!=BCF_HL_GEN ) { int id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,str.s); if ( !bcf_hdr_idinfo_exists(args->hdr,type,id) ) { if ( args->keep_sites ) error("Error: The tag \"%s\" is not defined in the header, cannot use the -k option\n", str.s); else fprintf(stderr,"Warning: The tag \"%s\" not defined in the header\n", str.s); tag->key = strdup(str.s); if ( type==BCF_HL_INFO ) { tag->handler = remove_info_tag; if ( needs_info ) error("Error: `--remove INFO/%s` is executed first, cannot combine with `--set-id %s`\n",tag->key,args->set_ids_fmt); } else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag; } else if ( (type==BCF_HL_FMT && keep_fmt) || (type==BCF_HL_INFO && keep_info) ) { int value, ret = khash_str2int_get(keep, str.s, &value); if ( ret==-1 ) khash_str2int_set(keep, strdup(str.s),1<nrm--; } else { tag->key = strdup(str.s); if ( type==BCF_HL_INFO ) { tag->handler = remove_info_tag; if ( needs_info ) error("Error: `--remove INFO/%s` is executed first, cannot combine with `--set-id %s`\n",tag->key,args->set_ids_fmt); } else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag; if ( !args->keep_sites ) bcf_hdr_remove(args->hdr_out,type,tag->key); } } else if ( !strcasecmp("ID",str.s) ) tag->handler = remove_id; else if ( !strcasecmp("FILTER",str.s) ) { tag->handler = remove_filter; if ( !args->keep_sites ) remove_hdr_lines(args->hdr_out,BCF_HL_FLT); } else if ( !strcasecmp("QUAL",str.s) ) tag->handler = remove_qual; else if ( !strcasecmp("INFO",str.s) ) { if ( needs_info ) error("Error: `--remove INFO` is executed first, cannot combine with `--set-id %s`\n",args->set_ids_fmt); tag->handler = remove_info; if ( !args->keep_sites ) remove_hdr_lines(args->hdr_out,BCF_HL_INFO); } else if ( !strcasecmp("FMT",str.s) || !strcasecmp("FORMAT",str.s) ) { tag->handler = remove_format; if ( !args->keep_sites ) remove_hdr_lines(args->hdr_out,BCF_HL_FMT); } else if ( str.l ) { int id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, str.s); if ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_INFO,id) ) error("Error: did you mean INFO/%s?\n",str.s); if ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,id) ) error("Error: did you mean FORMAT/%s?\n",str.s); if ( !args->keep_sites ) { if ( str.s[0]=='#' && str.s[1]=='#' ) bcf_hdr_remove(args->hdr_out,BCF_HL_GEN,str.s+2); else bcf_hdr_remove(args->hdr_out,BCF_HL_STR,str.s); } args->nrm--; } ss = *se ? se+1 : se; } free(str.s); if ( keep_flt || keep_info || keep_fmt ) { int j; for (j=0; jhdr->nhrec; j++) { bcf_hrec_t *hrec = args->hdr->hrec[j]; if ( hrec->type!=BCF_HL_FLT && hrec->type!=BCF_HL_INFO && hrec->type!=BCF_HL_FMT ) continue; if ( !keep_flt && hrec->type==BCF_HL_FLT ) continue; if ( !keep_info && hrec->type==BCF_HL_INFO ) continue; if ( !keep_fmt && hrec->type==BCF_HL_FMT ) continue; int k = bcf_hrec_find_key(hrec,"ID"); assert( k>=0 ); // this should always be true for valid VCFs int value, ret = khash_str2int_get(keep,hrec->vals[k],&value); if ( ret==0 && value>>hrec->type ) // keep { if ( hrec->type==BCF_HL_FLT && !strcmp("PASS",hrec->vals[k]) ) args->flt_keep_pass = 1; continue; } args->nrm++; args->rm = (rm_tag_t*) realloc(args->rm,sizeof(rm_tag_t)*args->nrm); rm_tag_t *tag = &args->rm[args->nrm-1]; if ( hrec->type==BCF_HL_INFO ) tag->handler = remove_info_tag; else if ( hrec->type==BCF_HL_FMT ) tag->handler = remove_format_tag; else { tag->handler = remove_filter; tag->hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, hrec->vals[k]); } tag->key = strdup(hrec->vals[k]); if ( !args->keep_sites ) bcf_hdr_remove(args->hdr_out,hrec->type,tag->key); } } khash_str2int_destroy_free(keep); if ( !args->nrm ) error("No matching tag in -x %s\n", args->remove_annots); if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update header", __func__); } static void init_header_lines(args_t *args) { if ( args->header_fname ) { htsFile *file = hts_open(args->header_fname, "rb"); if ( !file ) error("Error reading %s\n", args->header_fname); kstring_t str = {0,0,0}; while ( hts_getline(file, KS_SEP_LINE, &str) > 0 ) { if ( bcf_hdr_append(args->hdr_out,str.s) ) error("Could not parse %s: %s\n", args->header_fname, str.s); bcf_hdr_append(args->hdr,str.s); // the input file may not have the header line if run with -h (and nothing else) } if ( hts_close(file)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->header_fname); free(str.s); } if ( args->header_lines ) { int i, n = dbuf_n(args->header_lines); for (i=0; iheader_lines,i); if ( bcf_hdr_append(args->hdr_out,line) ) error("Could not parse the header line: %s\n", line); bcf_hdr_append(args->hdr,line); // the input file may not have the header line if run with -H (and nothing else) } dbuf_destroy_free(args->header_lines); args->header_lines = NULL; } if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update output header", __func__); if (bcf_hdr_sync(args->hdr) < 0) error_errno("[%s] Failed to update input header", __func__); } static int vcf_getter_info_str2str(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr) { return bcf_get_info_string(args->tgts_hdr,rec,col->hdr_key_src,ptr,mptr); } static int vcf_getter_id2str(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr) { char *str = *((char**)ptr); int i, len = strlen(rec->d.id); if ( len >= *mptr ) str = realloc(str, len+1); for (i=0; id.id[i]==';' ? ',' : rec->d.id[i]; str[len] = 0; *((char**)ptr) = str; *mptr = len+1; return len; } inline static int vcf_getter_filter2str_core(bcf_hdr_t *hdr, bcf1_t *rec, char **ptr, int *mptr) { if ( !(rec->unpacked & BCF_UN_FLT) ) bcf_unpack(rec, BCF_UN_FLT); kstring_t str; str.s = *ptr; str.m = *mptr; str.l = 0; int i; if ( rec->d.n_flt ) { for (i=0; id.n_flt; i++) { if (i) kputc(',', &str); kputs(bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.flt[i]), &str); } } else kputc('.', &str); *ptr = str.s; *mptr = str.m; return str.l; } static int vcf_getter_filter2str_local(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr) { return vcf_getter_filter2str_core(args->hdr_out, args->current_rec, (char**)ptr, mptr); } static int vcf_getter_filter2str(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr) { return vcf_getter_filter2str_core(args->tgts_hdr, rec, (char**)ptr, mptr); } static int setter_filter(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( !data ) error("Error: the --merge-logic option cannot be used with FILTER (yet?)\n"); // note: so far this works only with one filter, not a list of filters annot_line_t *tab = (annot_line_t*) data; if ( tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) // don't overwrite with a missing value unless asked { if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_update_filter(args->hdr_out,line,NULL,0); return 0; } hts_expand(int,1,args->mtmpi,args->tmpi); args->tmpi[0] = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, tab->cols[col->icol]); if ( args->tmpi[0]<0 ) error("The FILTER \"%s\" is not defined in the header, was the -h option provided?\n", tab->cols[col->icol]); if ( col->replace & SET_OR_APPEND ) return bcf_add_filter(args->hdr_out,line,args->tmpi[0]); if ( !(col->replace & REPLACE_MISSING) ) { bcf_update_filter(args->hdr_out,line,NULL,0); return bcf_update_filter(args->hdr_out,line,args->tmpi,1); } // only update missing FILTER if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT); if ( !line->d.n_flt ) return bcf_update_filter(args->hdr_out,line,args->tmpi,1); return 0; } static int vcf_setter_filter(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { int i, ret = 0; bcf1_t *rec = (bcf1_t*) data; if ( !(rec->unpacked & BCF_UN_FLT) ) bcf_unpack(rec, BCF_UN_FLT); if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT); if ( !rec->d.n_flt ) // don't overwrite with a missing value unless asked { if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_update_filter(args->hdr_out,line,NULL,0); return 0; } if ( col->replace & (SET_OR_APPEND|REPLACE_MISSING) ) { if ( (col->replace & REPLACE_MISSING) && line->d.n_flt ) return 0; // only update missing FILTER for (i=0; id.n_flt; i++) { const char *flt = bcf_hdr_int2id(args->files->readers[1].header, BCF_DT_ID, rec->d.flt[i]); if ( bcf_add_filter(args->hdr_out,line,bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt)) < 0 ) ret = -1; } return ret; } hts_expand(int,rec->d.n_flt,args->mtmpi,args->tmpi); for (i=0; id.n_flt; i++) { const char *flt = bcf_hdr_int2id(args->files->readers[1].header, BCF_DT_ID, rec->d.flt[i]); args->tmpi[i] = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt); } bcf_update_filter(args->hdr_out,line,NULL,0); return bcf_update_filter(args->hdr_out,line,args->tmpi,rec->d.n_flt); } static int setter_pos(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { annot_line_t *tab = (annot_line_t*) data; if ( tab->cols[col->icol] && tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) return 0; // don't replace with "." char *tmp; int pos = strtol(tab->cols[col->icol], &tmp, 10); if ( tmp==tab->cols[col->icol] ) error("Could not parse -POS at %s:%"PRId64" .. [%s]\n",bcf_seqname(args->hdr,line),(int64_t)line->pos+1,tab->cols[col->icol]); line->pos = pos - 1; return 0; } static int setter_id(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( !data ) error("Error: the --merge-logic option cannot be used with ID (yet?)\n"); if ( col->replace & MATCH_VALUE ) return 0; // possible cases: // IN ANNOT OUT ACHIEVED_BY // x y x -c +ID // x y y -c ID // x y x,y -c =ID // x . x -c +ID, ID // x . . -x ID // . y y -c +ID, -c ID // annot_line_t *tab = (annot_line_t*) data; if ( tab->cols[col->icol] && tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) return 0; // don't replace with "." if ( col->replace & SET_OR_APPEND ) return bcf_add_id(args->hdr_out,line,tab->cols[col->icol]); if ( !(col->replace & REPLACE_MISSING) ) return bcf_update_id(args->hdr_out,line,tab->cols[col->icol]); // running with +ID, only update missing ids if ( !line->d.id || (line->d.id[0]=='.' && !line->d.id[1]) ) return bcf_update_id(args->hdr_out,line,tab->cols[col->icol]); return 0; } static int vcf_setter_id(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( col->replace & MATCH_VALUE ) return 0; bcf1_t *rec = (bcf1_t*) data; char *id; if ( col->getter ) { int nret = col->getter(args,rec,col,&col->ptr,&col->mptr); id = (char*) col->ptr; if ( nret<=0 || (nret==1 && *id=='.') ) return 0; // don't replace with "." } else { if ( rec->d.id && rec->d.id[0]=='.' && !rec->d.id[1] ) return 0; // don't replace with "." id = rec->d.id; } if ( col->replace & SET_OR_APPEND ) return bcf_add_id(args->hdr_out,line,id); if ( !(col->replace & REPLACE_MISSING) ) return bcf_update_id(args->hdr_out,line,id); // running with +ID, only update missing ids if ( !line->d.id || (line->d.id[0]=='.' && !line->d.id[1]) ) return bcf_update_id(args->hdr_out,line,id); return 0; } static int vcf_setter_ref(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; if ( !strcmp(rec->d.allele[0],line->d.allele[0]) ) return 0; // no update necessary const char **als = (const char**) malloc(sizeof(char*)*line->n_allele); als[0] = rec->d.allele[0]; int i; for (i=1; in_allele; i++) als[i] = line->d.allele[i]; int ret = bcf_update_alleles(args->hdr_out, line, als, line->n_allele); free(als); return ret; } static int vcf_setter_alt(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; int i; if ( line->n_allele>1 && (col->replace & REPLACE_MISSING) ) return 0; if ( rec->n_allele==line->n_allele ) { for (i=1; in_allele; i++) if ( strcmp(rec->d.allele[i],line->d.allele[i]) ) break; if ( i==rec->n_allele ) return 0; // no update necessary } const char **als = (const char**) malloc(sizeof(char*)*rec->n_allele); als[0] = line->d.allele[0]; for (i=1; in_allele; i++) als[i] = rec->d.allele[i]; int ret = bcf_update_alleles(args->hdr_out, line, als, rec->n_allele); free(als); return ret; } static int setter_qual(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( !data ) error("Error: the --merge-logic option cannot be used with QUAL (yet?)\n"); annot_line_t *tab = (annot_line_t*) data; char *str = tab->cols[col->icol]; if ( str[0]=='.' && str[1]==0 ) // don't overwrite with a missing value unless asked { if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_float_set_missing(line->qual); return 0; } if ( (col->replace & REPLACE_MISSING) && !bcf_float_is_missing(line->qual) ) return 0; line->qual = strtod(str, &str); if ( str == tab->cols[col->icol] ) error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]); return 0; } static int vcf_setter_qual(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; if ( bcf_float_is_missing(rec->qual) ) // don't overwrite with a missing value unless asked { if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_float_set_missing(line->qual); return 0; } if ( (col->replace & REPLACE_MISSING) && !bcf_float_is_missing(line->qual) ) return 0; line->qual = rec->qual; return 0; } static int setter_info_flag(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( !data ) error("Error: the --merge-logic option cannot be used with INFO type=Flag (yet?)\n"); annot_line_t *tab = (annot_line_t*) data; char *str = tab->cols[col->icol]; if ( str[0]=='.' && str[1]==0 ) // don't overwrite with a missing value unless asked { if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,0); return 0; } if ( str[0]=='1' && str[1]==0 ) return bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,1); if ( str[0]=='0' && str[1]==0 ) return bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,0); error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]); return -1; } static int vcf_setter_info_flag(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; int flag = bcf_get_info_flag(args->files->readers[1].header,rec,col->hdr_key_src,NULL,NULL); bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,flag); return 0; } static int setter_ARinfo_int32(args_t *args, bcf1_t *line, annot_col_t *col, int nals, char **als, int ntmpi) { if ( col->number==BCF_VL_A && ntmpi!=nals-1 && (ntmpi!=1 || args->tmpi[0]!=bcf_int32_missing || args->tmpi[1]!=bcf_int32_vector_end) ) error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", ntmpi,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); else if ( col->number==BCF_VL_R && ntmpi!=nals && (ntmpi!=1 || args->tmpi[0]!=bcf_int32_missing || args->tmpi[1]!=bcf_int32_vector_end) ) error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", ntmpi,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int ndst = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele; int *map = vcmp_map_ARvalues(args->vcmp,ndst,nals,als,line->n_allele,line->d.allele); if ( !map ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); // fill in any missing values in the target VCF (or all, if not present) int ntmpi2 = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpi2, &args->mtmpi2); if ( ntmpi2 < ndst ) hts_expand(int32_t,ndst,args->mtmpi2,args->tmpi2); int i; for (i=0; itmpi2[i] = bcf_int32_missing; continue; } if ( ntmpi2==ndst && (col->replace & REPLACE_MISSING) && args->tmpi2[i]!=bcf_int32_missing && args->tmpi2[i]!=bcf_int32_vector_end ) continue; args->tmpi2[i] = args->tmpi[ map[i] ]; } return bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi2,ndst); } static int setter_info_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { annot_line_t *tab = (annot_line_t*) data; // This is a bit hacky, only to reuse existing code with minimal changes: // -c =TAG will now behave as -l TAG:APPEND for integers if ( col->replace & SET_OR_APPEND ) col->merge_method=MM_APPEND; if ( !tab ) { if ( col->merge_method!=MM_SUM && col->merge_method!=MM_AVG && col->merge_method!=MM_MIN && col->merge_method!=MM_MAX && col->merge_method!=MM_APPEND && col->merge_method!=MM_APPEND_MISSING ) error("Error: at the moment only the sum,avg,min,max,append,append-missing options are supported with --merge-logic for INFO type=Integer\n"); } int i,ntmpi = 0; if ( (col->replace & SET_OR_APPEND) && !col->mm_dbl_nused ) { ntmpi = bcf_get_info_int32(args->hdr, line, col->hdr_key_dst, &args->tmpi, &args->mtmpi); if ( ntmpi>0 && (args->tmpi[0]!=bcf_int32_missing || (col->replace & CARRY_OVER_MISSING)) ) { col->mm_dbl_nused = col->mm_dbl_ndat = ntmpi; hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl); for (i=0; imm_dbl[i] = args->tmpi[i]; col->mm_dbl_ndat = 1; } ntmpi = 0; } if ( tab ) // has data, not flushing yet { char *str = tab->cols[col->icol], *end = str; if ( str[0]=='.' && str[1]==0 && col->merge_method!=MM_APPEND_MISSING && !(col->replace & CARRY_OVER_MISSING) ) return 1; while ( *end ) { ntmpi++; hts_expand(int32_t,ntmpi,args->mtmpi,args->tmpi); if ( str[0]=='.' && (str[1]==0 || str[1]==',') ) { if ( col->merge_method==MM_APPEND_MISSING || (col->replace & CARRY_OVER_MISSING) ) args->tmpi[ntmpi-1] = bcf_int32_missing; else ntmpi--; if ( str[1]==0 ) end = str+1; str += 2; } else { args->tmpi[ntmpi-1] = strtol(str, &end, 10); if ( end==str ) error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]); str = end+1; } } if ( col->merge_method!=MM_FIRST ) { if ( !col->mm_dbl_nused ) { col->mm_dbl_nused = ntmpi; hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl); for (i=0; imm_dbl[i] = args->tmpi[i]; } else { if ( col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING ) { int nori = col->mm_dbl_nused; col->mm_dbl_nused += ntmpi; hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl); for (i=0; imm_dbl[i+nori] = args->tmpi[i]; } else { if ( ntmpi!=col->mm_dbl_nused ) error("Error: cannot merge fields of unequal length\n"); if ( col->merge_method==MM_SUM || col->merge_method==MM_AVG ) for (i=0; imm_dbl[i] += args->tmpi[i]; else if ( col->merge_method==MM_MIN ) for (i=0; imm_dbl[i] > args->tmpi[i] ) col->mm_dbl[i] = args->tmpi[i]; } else if ( col->merge_method==MM_MAX ) for (i=0; imm_dbl[i] < args->tmpi[i] ) col->mm_dbl[i] = args->tmpi[i]; } } } col->mm_dbl_ndat++; return 1; } } else if ( col->merge_method==MM_SUM || col->merge_method==MM_MIN || col->merge_method==MM_MAX || col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING ) { ntmpi = col->mm_dbl_nused; hts_expand(int32_t,ntmpi,args->mtmpi,args->tmpi); for (i=0; itmpi[i] = col->mm_dbl[i]; col->mm_dbl_nused = col->mm_dbl_ndat = 0; } else if ( col->merge_method==MM_AVG ) { ntmpi = col->mm_dbl_nused; hts_expand(int32_t,ntmpi,args->mtmpi,args->tmpi); for (i=0; itmpi[i] = col->mm_dbl[i]/col->mm_dbl_ndat; col->mm_dbl_nused = col->mm_dbl_ndat = 0; } if ( col->number==BCF_VL_A || col->number==BCF_VL_R ) return setter_ARinfo_int32(args,line,col,tab->nals,tab->als,ntmpi); if ( col->replace & REPLACE_MISSING ) { int ret = bcf_get_info_int32(args->hdr, line, col->hdr_key_dst, &args->tmpi2, &args->mtmpi2); if ( ret>0 && args->tmpi2[0]!=bcf_int32_missing ) return 0; } return bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi,ntmpi); } static int vcf_setter_info_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; int ntmpi = bcf_get_info_int32(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpi,&args->mtmpi); if ( ntmpi < 0 ) return 0; // nothing to add if ( col->number==BCF_VL_A || col->number==BCF_VL_R ) return setter_ARinfo_int32(args,line,col,rec->n_allele,rec->d.allele,ntmpi); if ( col->replace & REPLACE_MISSING ) { int ret = bcf_get_info_int32(args->hdr, line, col->hdr_key_dst, &args->tmpi2, &args->mtmpi2); if ( ret>0 && args->tmpi2[0]!=bcf_int32_missing ) return 0; } return bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi,ntmpi); } static int setter_ARinfo_real(args_t *args, bcf1_t *line, annot_col_t *col, int nals, char **als, int ntmpf) { if ( col->number==BCF_VL_A && ntmpf!=nals-1 && (ntmpf!=1 || !bcf_float_is_missing(args->tmpf[0]) || !bcf_float_is_vector_end(args->tmpf[0])) ) error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", ntmpf,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); else if ( col->number==BCF_VL_R && ntmpf!=nals && (ntmpf!=1 || !bcf_float_is_missing(args->tmpf[0]) || !bcf_float_is_vector_end(args->tmpf[0])) ) error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", ntmpf,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int ndst = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele; int *map = vcmp_map_ARvalues(args->vcmp,ndst,nals,als,line->n_allele,line->d.allele); if ( !map ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); // fill in any missing values in the target VCF (or all, if not present) int ntmpf2 = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf2, &args->mtmpf2); if ( ntmpf2 < ndst ) hts_expand(float,ndst,args->mtmpf2,args->tmpf2); int i; for (i=0; itmpf2[i]); continue; } if ( ntmpf2==ndst && (col->replace & REPLACE_MISSING) && !bcf_float_is_missing(args->tmpf2[i]) && !bcf_float_is_vector_end(args->tmpf2[i]) ) continue; args->tmpf2[i] = args->tmpf[ map[i] ]; } return bcf_update_info_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf2,ndst); } static int setter_info_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { annot_line_t *tab = (annot_line_t*) data; // This is a bit hacky, only to reuse existing code with minimal changes: // -c =TAG will now behave as -l TAG:APPEND for floats if ( col->replace & SET_OR_APPEND ) col->merge_method=MM_APPEND; if ( !tab ) { if ( col->merge_method!=MM_SUM && col->merge_method!=MM_AVG && col->merge_method!=MM_MIN && col->merge_method!=MM_MAX && col->merge_method!=MM_APPEND && col->merge_method!=MM_APPEND_MISSING ) error("Error: at the moment only the sum,avg,min,max,append,append-missing options are supported with --merge-logic for INFO type=Float\n"); } int i,ntmpf = 0; if ( (col->replace & SET_OR_APPEND) && !col->mm_dbl_nused ) { ntmpf = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf, &args->mtmpf); if ( ntmpf>0 && (!bcf_float_is_missing(args->tmpf[0]) || (col->replace & CARRY_OVER_MISSING)) ) { col->mm_dbl_nused = ntmpf; hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl); for (i=0; itmpf[i]) ) bcf_double_set_missing(col->mm_dbl[i]); else col->mm_dbl[i] = args->tmpf[i]; col->mm_dbl_ndat = 1; } ntmpf = 0; } if ( tab ) // data row, not just flushing { char *str = tab->cols[col->icol], *end = str; if ( str[0]=='.' && str[1]==0 && col->merge_method!=MM_APPEND_MISSING && !(col->replace & CARRY_OVER_MISSING) ) return 1; while ( *end ) { ntmpf++; hts_expand(float,ntmpf,args->mtmpf,args->tmpf); if ( str[0]=='.' && (str[1]==0 || str[1]==',') ) { if ( col->merge_method==MM_APPEND_MISSING || (col->replace & CARRY_OVER_MISSING) ) bcf_float_set_missing(args->tmpf[ntmpf-1]); else ntmpf--; if ( str[1]==0 ) end = str+1; str += 2; } else { args->tmpf[ntmpf-1] = strtod(str, &end); if ( end==str ) error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]); str = end+1; } } if ( col->merge_method!=MM_FIRST ) { if ( !col->mm_dbl_nused ) { col->mm_dbl_nused = ntmpf; hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl); for (i=0; itmpf[i]) ) bcf_double_set_missing(col->mm_dbl[i]); else col->mm_dbl[i] = args->tmpf[i]; } } else { if ( col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING ) { int nori = col->mm_dbl_nused; col->mm_dbl_nused += ntmpf; hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl); for (i=0; itmpf[i]) ) bcf_double_set_missing(col->mm_dbl[i+nori]); else col->mm_dbl[i+nori] = args->tmpf[i]; } } else { if ( ntmpf!=col->mm_dbl_nused ) error("Error: cannot merge fields of unequal length\n"); if ( col->merge_method==MM_SUM || col->merge_method==MM_AVG ) for (i=0; imm_dbl[i] += args->tmpf[i]; else if ( col->merge_method==MM_MIN ) for (i=0; imm_dbl[i] > args->tmpf[i] ) col->mm_dbl[i] = args->tmpf[i]; } else if ( col->merge_method==MM_MAX ) for (i=0; imm_dbl[i] < args->tmpf[i] ) col->mm_dbl[i] = args->tmpf[i]; } } } col->mm_dbl_ndat++; return 1; } } else if ( col->merge_method==MM_SUM || col->merge_method==MM_MIN || col->merge_method==MM_MAX || col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING ) { ntmpf = col->mm_dbl_nused; hts_expand(int32_t,ntmpf,args->mtmpf,args->tmpf); for (i=0; imm_dbl[i]) ) bcf_float_set_missing(args->tmpf[i]); else args->tmpf[i] = col->mm_dbl[i]; } col->mm_dbl_nused = col->mm_dbl_ndat = 0; } else if ( col->merge_method==MM_AVG ) { ntmpf = col->mm_dbl_nused; hts_expand(int32_t,ntmpf,args->mtmpf,args->tmpf); for (i=0; itmpf[i] = col->mm_dbl[i]/col->mm_dbl_ndat; col->mm_dbl_nused = col->mm_dbl_ndat = 0; } if ( col->number==BCF_VL_A || col->number==BCF_VL_R ) return setter_ARinfo_real(args,line,col,tab->nals,tab->als,ntmpf); if ( col->replace & REPLACE_MISSING ) { int ret = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf2, &args->mtmpf2); if ( ret>0 && !bcf_float_is_missing(args->tmpf2[0]) ) return 0; } return bcf_update_info_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf,ntmpf); } static int vcf_setter_info_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; int ntmpf = bcf_get_info_float(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpf,&args->mtmpf); if ( ntmpf < 0 ) return 0; // nothing to add if ( col->number==BCF_VL_A || col->number==BCF_VL_R ) return setter_ARinfo_real(args,line,col,rec->n_allele,rec->d.allele,ntmpf); if ( col->replace & REPLACE_MISSING ) { int ret = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf2, &args->mtmpf2); if ( ret>0 && !bcf_float_is_missing(args->tmpf2[0]) ) return 0; } return bcf_update_info_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf,ntmpf); } int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst); // see vcfmerge.c static int setter_ARinfo_string(args_t *args, bcf1_t *line, annot_col_t *col, int nals, char **als) { assert( col->merge_method==MM_FIRST ); int nsrc = 1, lsrc = 0; while ( args->tmps[lsrc] ) { if ( args->tmps[lsrc]==',' ) nsrc++; lsrc++; } if ( col->number==BCF_VL_A && nsrc!=nals-1 && (nsrc!=1 || args->tmps[0]!='.' || args->tmps[1]!=0 ) ) error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", nsrc,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); else if ( col->number==BCF_VL_R && nsrc!=nals && (nsrc!=1 || args->tmps[0]!='.' || args->tmps[1]!=0 ) ) error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", nsrc,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int ndst = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele; int *map = vcmp_map_ARvalues(args->vcmp,ndst,nals,als,line->n_allele,line->d.allele); if ( !map ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); // fill in any missing values in the target VCF (or all, if not present) int i, empty = 0, nstr, mstr = args->tmpks.m; nstr = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &args->tmpks.s, &mstr); args->tmpks.m = mstr; if ( nstr<0 || (nstr==1 && args->tmpks.s[0]=='.' && args->tmpks.s[1]==0) ) { empty = 0; args->tmpks.l = 0; kputc('.',&args->tmpks); for (i=1; itmpks); } else args->tmpks.l = nstr; for (i=0; itmpks,i); continue; } if ( col->replace & REPLACE_MISSING ) { // Do not replace filled values. The field must be looked up again because // of realloc in copy_string_field int n = 0; char *str = args->tmpks.s; while ( *str && ntmps,map[i],lsrc,&args->tmpks,i); if ( ret!=0 ) error("[%s:%d %s] Failed to copy a string field\n", __FILE__,__LINE__,__func__); } return bcf_update_info_string(args->hdr_out,line,col->hdr_key_dst,args->tmpks.s); } void khash_str2int_clear_free(void *_hash) { khash_t(str2int) *hash = (khash_t(str2int)*)_hash; khint_t k; if (hash == 0) return; for (k = 0; k < kh_end(hash); ++k) if (kh_exist(hash, k)) free((char*)kh_key(hash, k)); kh_clear(str2int, hash); } static const char *escape_string(const char *str, char needle[], char **rmme, size_t *len) { kstring_t tmp = {0,0,0}; const char *bp = str, *ep = str; while ( *ep ) { int i = 0; while ( needle[i] && needle[i]!=*ep ) i++; if ( !needle[i] ) { ep++; continue; } kputsn(bp,ep-bp,&tmp); ksprintf(&tmp,"%%%X",*ep); bp = ++ep; } if ( !tmp.l ) { *len = strlen(str); return str; } kputs(bp,&tmp); *len = tmp.l; *rmme = tmp.s; return tmp.s; } static int setter_info_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( (col->replace & REPLACE_MISSING) && col->number!=BCF_VL_A && col->number!=BCF_VL_R ) { int ret = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &args->tmps2, &args->mtmps2); if ( ret>0 && (args->tmps2[0]!='.' || args->tmps2[1]!=0) ) return 0; } // This is a bit hacky, only to reuse existing code with minimal changes: // -c =TAG will now behave as -l TAG:unique for strings if ( col->replace & SET_OR_APPEND ) col->merge_method=MM_UNIQUE; annot_line_t *tab = (annot_line_t*) data; const char *escaped = NULL; char *rmme = NULL; size_t len = 0; if ( tab ) { char *str = tab->cols[col->icol]; if ( !str || !*str ) return 0; if ( !str[1] && str[0]=='.' && col->merge_method!=MM_APPEND_MISSING && !(col->replace & CARRY_OVER_MISSING) ) return 1; char needle[] = {';','=',0}; escaped = escape_string(tab->cols[col->icol],needle,&rmme,&len); } if ( col->merge_method!=MM_FIRST ) { if ( col->number==BCF_VL_A || col->number==BCF_VL_R ) error("Error: the --merge-logic option cannot be used with INFO tags Type=String,Number={A,R,G}\n"); if ( data ) { assert( col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING || col->merge_method==MM_UNIQUE ); if ( col->merge_method==MM_UNIQUE ) { if ( !col->mm_str_hash ) col->mm_str_hash = (khash_t(str2int)*)khash_str2int_init(); if ( khash_str2int_has_key(col->mm_str_hash, escaped) ) { free(rmme); return 1; } khash_str2int_inc(col->mm_str_hash, strdup(escaped)); } if ( (col->replace & SET_OR_APPEND) && !col->mm_kstr.l ) { int m = col->mm_kstr.m; int n = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &col->mm_kstr.s, &m); col->mm_kstr.m = m; if ( n>0 && ((col->replace & CARRY_OVER_MISSING) || col->mm_kstr.s[0]!='.' || col->mm_kstr.s[1]) ) col->mm_kstr.l = n; } if ( col->mm_kstr.l ) kputc(',',&col->mm_kstr); kputs(escaped, &col->mm_kstr); free(rmme); return 1; } if ( col->mm_kstr.l ) { hts_expand(char,col->mm_kstr.l+1,args->mtmps,args->tmps); memcpy(args->tmps,col->mm_kstr.s,col->mm_kstr.l+1); } else { free(rmme); return 0; } // flush the line if ( col->merge_method==MM_UNIQUE ) khash_str2int_clear_free(col->mm_str_hash); col->mm_kstr.l = 0; } else { assert(tab); hts_expand(char,len+1,args->mtmps,args->tmps); memcpy(args->tmps,escaped,len+1); if ( col->number==BCF_VL_A || col->number==BCF_VL_R ) return setter_ARinfo_string(args,line,col,tab->nals,tab->als); } int ret = bcf_update_info_string(args->hdr_out,line,col->hdr_key_dst,args->tmps); free(rmme); return ret; } static int vcf_setter_info_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; if ( col->getter ) col->getter(args,rec,col,(void**)&args->tmps, &args->mtmps); else { int ntmps = bcf_get_info_string(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmps,&args->mtmps); if ( ntmps < 0 ) return 0; // nothing to add } if ( col->number==BCF_VL_A || col->number==BCF_VL_R ) return setter_ARinfo_string(args,line,col,rec->n_allele,rec->d.allele); if ( col->replace & REPLACE_MISSING ) { int ret = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &args->tmps2, &args->mtmps2); if ( ret>0 && (args->tmps2[0]!='.' || args->tmps2[1]!=0) ) return 0; } return bcf_update_info_string(args->hdr_out,line,col->hdr_key_dst,args->tmps); } static int genotypes_to_string(args_t *args, int nsrc1, int32_t *src, int nsmpl_dst, kstring_t *str) { int i, isrc, idst; int blen = nsrc1 > 1 ? nsrc1 + 1 : 1; // typically the genotypes take three bytes 0/1, no 0-termination is needed gt_length_too_big: str->l = 0; for (idst=0; idstsample_map ? args->sample_map[idst] : idst; if ( isrc==-1 ) { kputc_('.', str); for (i=1; i < blen; i++) kputc_(0, str); continue; } size_t plen = str->l; int32_t *ptr = src + isrc*nsrc1; for (i=0; il - plen > blen ) { // too many alternate alleles or ploidy is too large, the genotype does not fit // three characters ("0/0" vs "10/10"). blen *= 2; goto gt_length_too_big; } plen = str->l - plen; while ( plen < blen ) { kputc_(0, str); plen++; } } return 0; } static int vcf_setter_format_gt(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; int nsrc = bcf_get_genotypes(args->files->readers[1].header,rec,&args->tmpi,&args->mtmpi); if ( nsrc==-3 ) return 0; // the tag is not present if ( nsrc<=0 ) return 1; // error // Genotypes are internally represented as integers. This is a complication when // adding as a different Type=String field, such as FMT/newGT:=GT if ( strcmp(col->hdr_key_src,col->hdr_key_dst) ) { int nsmpl_dst = bcf_hdr_nsamples(args->hdr_out); int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header); genotypes_to_string(args,nsrc/nsmpl_src,args->tmpi,nsmpl_dst,&args->tmpks); return bcf_update_format_char(args->hdr_out,line,col->hdr_key_dst,args->tmpks.s,args->tmpks.l); } if ( !args->sample_map ) return bcf_update_genotypes(args->hdr_out,line,args->tmpi,nsrc); int i, j, ndst = bcf_get_genotypes(args->hdr,line,&args->tmpi2,&args->mtmpi2); if ( ndst > 0 ) ndst /= bcf_hdr_nsamples(args->hdr_out); nsrc /= bcf_hdr_nsamples(args->files->readers[1].header); if ( ndst<=0 ) // field not present in dst file { if ( col->replace & REPLACE_NON_MISSING ) return 0; hts_expand(int32_t, nsrc*bcf_hdr_nsamples(args->hdr_out), args->mtmpi2, args->tmpi2); for (i=0; ihdr_out); i++) { int32_t *dst = args->tmpi2 + nsrc*i; if ( args->sample_map[i]==-1 ) { dst[0] = bcf_gt_missing; for (j=1; jtmpi + nsrc*args->sample_map[i]; for (j=0; jhdr_out,line,args->tmpi2,nsrc*bcf_hdr_nsamples(args->hdr_out)); } else if ( ndst >= nsrc ) { for (i=0; ihdr_out); i++) { if ( args->sample_map[i]==-1 ) continue; int32_t *src = args->tmpi + nsrc*args->sample_map[i]; int32_t *dst = args->tmpi2 + ndst*i; if ( (col->replace & REPLACE_NON_MISSING) && bcf_gt_is_missing(dst[0]) ) continue; if ( (col->replace & REPLACE_MISSING) && !bcf_gt_is_missing(dst[0]) ) continue; for (j=0; jhdr_out,line,args->tmpi2,ndst*bcf_hdr_nsamples(args->hdr_out)); } else // ndst < nsrc { hts_expand(int32_t, nsrc*bcf_hdr_nsamples(args->hdr_out), args->mtmpi3, args->tmpi3); for (i=0; ihdr_out); i++) { int32_t *ori = args->tmpi2 + ndst*i; int32_t *dst = args->tmpi3 + nsrc*i; int keep_ori = 0; if ( args->sample_map[i]==-1 ) keep_ori = 1; else if ( (col->replace & REPLACE_NON_MISSING) && bcf_gt_is_missing(ori[0]) ) keep_ori = 1; else if ( (col->replace & REPLACE_MISSING) && !bcf_gt_is_missing(ori[0]) ) keep_ori = 1; if ( keep_ori ) { for (j=0; jtmpi + nsrc*args->sample_map[i]; for (j=0; jhdr_out,line,args->tmpi3,nsrc*bcf_hdr_nsamples(args->hdr_out)); } } static int count_vals(annot_line_t *tab, int icol_beg, int icol_end) { int i, nmax = 1; for (i=icol_beg; icols[i], *end = str; if ( str[0]=='.' && !str[1] ) { // missing value if ( !nmax ) nmax = 1; continue; } int n = 1; while ( *end ) { if ( *end==',' ) n++; end++; } if ( nmaxsample_map ) return bcf_update_format_int32(args->hdr_out,line,col->hdr_key_dst,vals,nvals*args->nsmpl_annot); int i, j, ndst = bcf_get_format_int32(args->hdr,line,col->hdr_key_dst,&args->tmpi2,&args->mtmpi2); if ( ndst > 0 ) ndst /= bcf_hdr_nsamples(args->hdr_out); if ( ndst<=0 ) { if ( col->replace & REPLACE_NON_MISSING ) return 0; // overwrite only if present hts_expand(int32_t, nvals*bcf_hdr_nsamples(args->hdr_out), args->mtmpi2, args->tmpi2); for (i=0; ihdr_out); i++) { int32_t *dst = args->tmpi2 + nvals*i; if ( args->sample_map[i]==-1 ) { dst[0] = bcf_int32_missing; for (j=1; jsample_map[i]; for (j=0; jhdr_out,line,col->hdr_key_dst,args->tmpi2,nvals*bcf_hdr_nsamples(args->hdr_out)); } else if ( ndst >= nvals ) { for (i=0; ihdr_out); i++) { if ( args->sample_map[i]==-1 ) continue; int32_t *src = vals + nvals*args->sample_map[i]; int32_t *dst = args->tmpi2 + ndst*i; // possible cases: // in annot out // x y x TAG,-TAG,=TAG .. REPLACE_ALL, REPLACE_NON_MISSING, SET_OR_APPEND // x y y +TAG .. REPLACE_MISSING // . y . =TAG .. SET_OR_APPEND // . y y TAG,+TAG,-TAG .. REPLACE_ALL, REPLACE_MISSING, REPLACE_NON_MISSING // x . x TAG,+TAG .. REPLACE_ALL, REPLACE_MISSING // x . . -TAG .. REPLACE_NON_MISSING if ( col->replace & REPLACE_NON_MISSING ) { if ( dst[0]==bcf_int32_missing ) continue; } else if ( col->replace & REPLACE_MISSING ) { if ( dst[0]!=bcf_int32_missing ) continue; } else if ( col->replace & REPLACE_ALL ) { if ( src[0]==bcf_int32_missing ) continue; } for (j=0; jhdr_out,line,col->hdr_key_dst,args->tmpi2,ndst*bcf_hdr_nsamples(args->hdr_out)); } else // ndst < nvals { hts_expand(int32_t, nvals*bcf_hdr_nsamples(args->hdr_out), args->mtmpi3, args->tmpi3); for (i=0; ihdr_out); i++) { int32_t *ann = vals + nvals*args->sample_map[i]; int32_t *ori = args->tmpi2 + ndst*i; // ori vcf line int32_t *dst = args->tmpi3 + nvals*i; // expanded buffer int use_new_ann = 1; if ( args->sample_map[i]==-1 ) use_new_ann = 0; else if ( col->replace & REPLACE_NON_MISSING ) { if ( ori[0]==bcf_int32_missing ) use_new_ann = 0; } else if ( col->replace & REPLACE_MISSING ) { if ( ori[0]!=bcf_int32_missing ) use_new_ann = 0; } else if ( col->replace & REPLACE_ALL ) { if ( ann[0]==bcf_int32_missing ) use_new_ann = 0; } if ( !use_new_ann ) { for (j=0; jhdr_out,line,col->hdr_key_dst,args->tmpi3,nvals*bcf_hdr_nsamples(args->hdr_out)); } } static int core_setter_format_real(args_t *args, bcf1_t *line, annot_col_t *col, float *vals, int nvals) { if ( !args->sample_map ) return bcf_update_format_float(args->hdr_out,line,col->hdr_key_dst,vals,nvals*args->nsmpl_annot); int i, j, ndst = bcf_get_format_float(args->hdr,line,col->hdr_key_dst,&args->tmpf2,&args->mtmpf2); if ( ndst > 0 ) ndst /= bcf_hdr_nsamples(args->hdr_out); if ( ndst<=0 ) { if ( col->replace & REPLACE_NON_MISSING ) return 0; // overwrite only if present hts_expand(float, nvals*bcf_hdr_nsamples(args->hdr_out), args->mtmpf2, args->tmpf2); for (i=0; ihdr_out); i++) { float *dst = args->tmpf2 + nvals*i; if ( args->sample_map[i]==-1 ) { bcf_float_set_missing(dst[0]); for (j=1; jsample_map[i]; for (j=0; jhdr_out,line,col->hdr_key_dst,args->tmpf2,nvals*bcf_hdr_nsamples(args->hdr_out)); } else if ( ndst >= nvals ) { for (i=0; ihdr_out); i++) { if ( args->sample_map[i]==-1 ) continue; float *src = vals + nvals*args->sample_map[i]; float *dst = args->tmpf2 + ndst*i; if ( col->replace & REPLACE_NON_MISSING ) { if ( bcf_float_is_missing(dst[0]) ) continue; } else if ( col->replace & REPLACE_MISSING ) { if ( !bcf_float_is_missing(dst[0]) ) continue; } else if ( col->replace & REPLACE_ALL ) { if ( bcf_float_is_missing(src[0]) ) continue; } for (j=0; jhdr_out,line,col->hdr_key_dst,args->tmpf2,ndst*bcf_hdr_nsamples(args->hdr_out)); } else // ndst < nvals { hts_expand(float, nvals*bcf_hdr_nsamples(args->hdr_out), args->mtmpf3, args->tmpf3); for (i=0; ihdr_out); i++) { float *ann = vals + nvals*args->sample_map[i]; float *ori = args->tmpf2 + ndst*i; // ori vcf line float *dst = args->tmpf3 + nvals*i; // expanded buffer int use_new_ann = 1; if ( args->sample_map[i]==-1 ) use_new_ann = 0; else if ( col->replace & REPLACE_NON_MISSING ) { if ( bcf_float_is_missing(ori[0]) ) use_new_ann = 0; } else if ( col->replace & REPLACE_MISSING ) { if ( !bcf_float_is_missing(ori[0]) ) use_new_ann = 0; } else if ( col->replace & REPLACE_ALL ) { if ( bcf_float_is_missing(ann[0]) ) use_new_ann = 0; } if ( !use_new_ann ) { for (j=0; jhdr_out,line,col->hdr_key_dst,args->tmpf3,nvals*bcf_hdr_nsamples(args->hdr_out)); } } static int core_setter_format_str(args_t *args, bcf1_t *line, annot_col_t *col, char **vals) { if ( !args->sample_map ) return bcf_update_format_string(args->hdr_out,line,col->hdr_key_dst,(const char**)vals,args->nsmpl_annot); int i; args->tmpp2[0] = args->tmps2; int ret = bcf_get_format_string(args->hdr,line,col->hdr_key_dst,&args->tmpp2,&args->mtmps2); args->tmps2 = args->tmpp2[0]; // tmps2 might be realloced int nsmpl = bcf_hdr_nsamples(args->hdr_out); if ( ret<=0 ) // not present in dst { hts_expand(char,bcf_hdr_nsamples(args->hdr_out)*2,args->mtmps2,args->tmps2); char *tmp = args->tmps2; for (i=0; itmpp2[i] = tmp; tmp += 2; } } for (i=0; isample_map[i]==-1 ) continue; char **src = vals + args->sample_map[i]; char **dst = args->tmpp2 + i; if ( col->replace & REPLACE_NON_MISSING ) { if ( (*dst)[0]=='.' && (*dst)[1]==0 ) continue; } else if ( col->replace & REPLACE_MISSING ) { if ( (*dst)[0]!='.' || (*dst)[1]!=0 ) continue; } else if ( col->replace & REPLACE_ALL ) { if ( (*src)[0]=='.' && (*src)[1]==0 ) continue; } *dst = *src; } return bcf_update_format_string(args->hdr_out,line,col->hdr_key_dst,(const char**)args->tmpp2,nsmpl); } static int setter_format_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( !data ) error("Error: the --merge-logic option cannot be used with FORMAT tags (yet?)\n"); annot_line_t *tab = (annot_line_t*) data; if ( col->icol+args->nsmpl_annot > tab->ncols ) error("Incorrect number of values for %s at %s:%"PRId64"\n",col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int nvals = count_vals(tab,col->icol,col->icol+args->nsmpl_annot); hts_expand(int32_t,nvals*args->nsmpl_annot,args->mtmpi,args->tmpi); int icol = col->icol, ismpl; for (ismpl=0; ismplnsmpl_annot; ismpl++) { int32_t *ptr = args->tmpi + ismpl*nvals; int ival = 0; char *str = tab->cols[icol]; while ( *str ) { if ( str[0]=='.' && (!str[1] || str[1]==',') ) // missing value { ptr[ival++] = bcf_int32_missing; str += str[1] ? 2 : 1; continue; } char *end = str; ptr[ival] = strtol(str, &end, 10); if ( end==str ) error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]); ival++; str = *end ? end+1 : end; } while ( ivaltmpi,nvals); } static int setter_format_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( !data ) error("Error: the --merge-logic option cannot be used with FORMAT tags (yet?)\n"); annot_line_t *tab = (annot_line_t*) data; if ( col->icol+args->nsmpl_annot > tab->ncols ) error("Incorrect number of values for %s at %s:%"PRId64"\n",col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int nvals = count_vals(tab,col->icol,col->icol+args->nsmpl_annot); hts_expand(float,nvals*args->nsmpl_annot,args->mtmpf,args->tmpf); int icol = col->icol, ismpl; for (ismpl=0; ismplnsmpl_annot; ismpl++) { float *ptr = args->tmpf + ismpl*nvals; int ival = 0; char *str = tab->cols[icol]; while ( *str ) { if ( str[0]=='.' && (!str[1] || str[1]==',') ) // missing value { bcf_float_set_missing(ptr[ival]); ival++; str += str[1] ? 2 : 1; continue; } char *end = str; ptr[ival] = strtod(str, &end); if ( end==str ) error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]); ival++; str = *end ? end+1 : end; } while ( ivaltmpf,nvals); } static int setter_format_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( !data ) error("Error: the --merge-logic option cannot be used with FORMAT tags (yet?)\n"); annot_line_t *tab = (annot_line_t*) data; if ( col->icol+args->nsmpl_annot > tab->ncols ) error("Incorrect number of values for %s at %s:%"PRId64"\n",col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); char needle[] = {':',0}; int ismpl; for (ismpl=0; ismplnsmpl_annot; ismpl++) { size_t len; char *rmme = NULL; const char *str = escape_string(tab->cols[col->icol + ismpl],needle,&rmme,&len); args->tmpp[ismpl] = rmme ? rmme : strdup(str); } int ret = core_setter_format_str(args,line,col,args->tmpp); for (ismpl=0; ismplnsmpl_annot; ismpl++) free(args->tmpp[ismpl]); return ret; } static int determine_ploidy(int nals, int *vals, int nvals1, uint8_t *smpl, int nsmpl) { int i, j, ndip = nals*(nals+1)/2, max_ploidy = 0; for (i=0; ifiles->readers[1].header,rec,col->hdr_key_src,&args->tmpi,&args->mtmpi); if ( nsrc==-3 ) return 0; // the tag is not present if ( nsrc<=0 ) return 1; // error int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header); int nsrc1 = nsrc / nsmpl_src; if ( col->number!=BCF_VL_G && col->number!=BCF_VL_R && col->number!=BCF_VL_A ) return core_setter_format_int(args,line,col,args->tmpi,nsrc1); // create mapping from src to dst genotypes, haploid and diploid version int nmap_hap = col->number==BCF_VL_G || col->number==BCF_VL_R ? rec->n_allele : rec->n_allele - 1; int *map_hap = vcmp_map_ARvalues(args->vcmp,nmap_hap,line->n_allele,line->d.allele,rec->n_allele,rec->d.allele); if ( !map_hap ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int i, j; if ( rec->n_allele==line->n_allele ) { // alleles unchanged? for (i=0; in_allele; i++) if ( map_hap[i]!=i ) break; if ( i==rec->n_allele ) return core_setter_format_int(args,line,col,args->tmpi,nsrc1); } int nsmpl_dst = rec->n_sample; int ndst = bcf_get_format_int32(args->hdr,line,col->hdr_key_dst,&args->tmpi2,&args->mtmpi2); int ndst1 = ndst / nsmpl_dst; if ( ndst <= 0 ) { if ( col->replace & REPLACE_NON_MISSING ) return 0; // overwrite only if present if ( col->number==BCF_VL_G ) ndst1 = line->n_allele*(line->n_allele+1)/2; else ndst1 = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele; hts_expand(int, ndst1*nsmpl_dst, args->mtmpi2, args->tmpi2); for (i=0; itmpi2 + i*ndst1; for (j=0; jnumber==BCF_VL_G ) { map_dip = vcmp_map_dipGvalues(args->vcmp, &nmap_dip); if ( !args->src_smpl_pld ) { args->src_smpl_pld = (uint8_t*) malloc(nsmpl_src); args->dst_smpl_pld = (uint8_t*) malloc(nsmpl_dst); } int pld_src = determine_ploidy(rec->n_allele, args->tmpi, nsrc1, args->src_smpl_pld, nsmpl_src); if ( pld_src<0 ) error("Unexpected number of %s values (%d) for %d alleles at %s:%"PRId64"\n", col->hdr_key_src,-pld_src, rec->n_allele, bcf_seqname(bcf_sr_get_header(args->files,1),rec),(int64_t) rec->pos+1); int pld_dst = determine_ploidy(line->n_allele, args->tmpi2, ndst1, args->dst_smpl_pld, nsmpl_dst); if ( pld_dst<0 ) error("Unexpected number of %s values (%d) for %d alleles at %s:%"PRId64"\n", col->hdr_key_src,-pld_dst, line->n_allele, bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int ndst1_new = pld_dst==1 ? line->n_allele : line->n_allele*(line->n_allele+1)/2; if ( ndst1_new != ndst1 ) { if ( ndst1 ) error("todo: %s ndst1!=ndst .. %d %d at %s:%"PRId64"\n",col->hdr_key_src,ndst1_new,ndst1,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); ndst1 = ndst1_new; hts_expand(int32_t, ndst1*nsmpl_dst, args->mtmpi2, args->tmpi2); } } else if ( !ndst1 ) { ndst1 = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele; hts_expand(int32_t, ndst1*nsmpl_dst, args->mtmpi2, args->tmpi2); } for (i=0; isample_map ? args->sample_map[i] : i; int32_t *ptr_src = args->tmpi + i*nsrc1; int32_t *ptr_dst = args->tmpi2 + ii*ndst1; if ( col->number==BCF_VL_G ) { if ( args->src_smpl_pld[ii] > 0 && args->dst_smpl_pld[i] > 0 && args->src_smpl_pld[ii]!=args->dst_smpl_pld[i] ) error("Sample ploidy differs at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); if ( !args->dst_smpl_pld[i] ) for (j=0; jnumber!=BCF_VL_G || args->src_smpl_pld[i]==1 ) { for (j=0; j=0 ) ptr_dst[k] = ptr_src[j]; } if ( col->number==BCF_VL_G ) for (j=line->n_allele; j=0 ) ptr_dst[k] = ptr_src[j]; } } } return bcf_update_format_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi2,nsmpl_dst*ndst1); } static int vcf_setter_format_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; int nsrc = bcf_get_format_float(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpf,&args->mtmpf); if ( nsrc==-3 ) return 0; // the tag is not present if ( nsrc<=0 ) return 1; // error int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header); int nsrc1 = nsrc / nsmpl_src; if ( col->number!=BCF_VL_G && col->number!=BCF_VL_R && col->number!=BCF_VL_A ) return core_setter_format_real(args,line,col,args->tmpf,nsrc1); // create mapping from src to dst genotypes, haploid and diploid version int nmap_hap = col->number==BCF_VL_G || col->number==BCF_VL_R ? rec->n_allele : rec->n_allele - 1; int *map_hap = vcmp_map_ARvalues(args->vcmp,nmap_hap,line->n_allele,line->d.allele,rec->n_allele,rec->d.allele); if ( !map_hap ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int i, j; if ( rec->n_allele==line->n_allele ) { // alleles unchanged? for (i=0; in_allele; i++) if ( map_hap[i]!=i ) break; if ( i==rec->n_allele ) return core_setter_format_real(args,line,col,args->tmpf,nsrc1); } int nsmpl_dst = rec->n_sample; int ndst = bcf_get_format_float(args->hdr,line,col->hdr_key_dst,&args->tmpf2,&args->mtmpf2); int ndst1 = ndst / nsmpl_dst; if ( ndst <= 0 ) { if ( col->replace & REPLACE_NON_MISSING ) return 0; // overwrite only if present if ( col->number==BCF_VL_G ) ndst1 = line->n_allele*(line->n_allele+1)/2; else ndst1 = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele; hts_expand(float, ndst1*nsmpl_dst, args->mtmpf2, args->tmpf2); for (i=0; itmpf2 + i*ndst1; for (j=0; jnumber==BCF_VL_G ) { map_dip = vcmp_map_dipGvalues(args->vcmp, &nmap_dip); if ( !args->src_smpl_pld ) { args->src_smpl_pld = (uint8_t*) malloc(nsmpl_src); args->dst_smpl_pld = (uint8_t*) malloc(nsmpl_dst); } int pld_src = determine_ploidy(rec->n_allele, args->tmpi, nsrc1, args->src_smpl_pld, nsmpl_src); if ( pld_src<0 ) error("Unexpected number of %s values (%d) for %d alleles at %s:%"PRId64"\n", col->hdr_key_src,-pld_src, rec->n_allele, bcf_seqname(bcf_sr_get_header(args->files,1),rec),(int64_t) rec->pos+1); int pld_dst = determine_ploidy(line->n_allele, args->tmpi2, ndst1, args->dst_smpl_pld, nsmpl_dst); if ( pld_dst<0 ) error("Unexpected number of %s values (%d) for %d alleles at %s:%"PRId64"\n", col->hdr_key_src,-pld_dst, line->n_allele, bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int ndst1_new = pld_dst==1 ? line->n_allele : line->n_allele*(line->n_allele+1)/2; if ( ndst1_new != ndst1 ) { if ( ndst1 ) error("todo: %s ndst1!=ndst .. %d %d at %s:%"PRId64"\n",col->hdr_key_src,ndst1_new,ndst1,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); ndst1 = ndst1_new; hts_expand(float, ndst1*nsmpl_dst, args->mtmpf2, args->tmpf2); } } else if ( !ndst1 ) { ndst1 = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele; hts_expand(float, ndst1*nsmpl_dst, args->mtmpf2, args->tmpf2); } for (i=0; isample_map ? args->sample_map[i] : i; float *ptr_src = args->tmpf + i*nsrc1; float *ptr_dst = args->tmpf2 + ii*ndst1; if ( col->number==BCF_VL_G ) { if ( args->src_smpl_pld[ii] > 0 && args->dst_smpl_pld[i] > 0 && args->src_smpl_pld[ii]!=args->dst_smpl_pld[i] ) error("Sample ploidy differs at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); if ( !args->dst_smpl_pld[i] ) for (j=0; jnumber!=BCF_VL_G || args->src_smpl_pld[i]==1 ) { for (j=0; j=0 ) { if ( bcf_float_is_missing(ptr_src[j]) ) bcf_float_set_missing(ptr_dst[k]); else if ( bcf_float_is_vector_end(ptr_src[j]) ) bcf_float_set_vector_end(ptr_dst[k]); else ptr_dst[k] = ptr_src[j]; } } if ( col->number==BCF_VL_G ) for (j=line->n_allele; j=0 ) { if ( bcf_float_is_missing(ptr_src[j]) ) bcf_float_set_missing(ptr_dst[k]); else if ( bcf_float_is_vector_end(ptr_src[j]) ) bcf_float_set_vector_end(ptr_dst[k]); else ptr_dst[k] = ptr_src[j]; } } } } return bcf_update_format_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf2,nsmpl_dst*ndst1); } static int vcf_setter_format_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; args->tmpp[0] = args->tmps; int ret = bcf_get_format_string(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpp,&args->mtmps); args->tmps = args->tmpp[0]; // tmps might be realloced if ( ret==-3 ) return 0; // the tag is not present if ( ret<=0 ) return 1; // error if ( strcmp("GT",col->hdr_key_dst) ) return core_setter_format_str(args,line,col,args->tmpp); // Genotypes are internally represented as integers. This is a complication for FMT/GT:=oldGT // First determine the maximum number of alleles per-sample ndst1 int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header); int nsmpl_dst = bcf_hdr_nsamples(args->hdr_out); int isrc,idst, ndst1 = 0, nsrc1 = ret / nsmpl_src; char *ptr = args->tmps, *ptr_end = ptr + ret; while ( ptr < ptr_end ) { char *smpl_end = ptr + nsrc1; int n = 1; while ( ptr < smpl_end ) { if ( *ptr=='/' || *ptr=='|' ) n++; ptr++; } if ( ndst1 < n ) ndst1 = n; } assert( ndst1 ); int ndst = ndst1*nsmpl_dst; hts_expand(int32_t,ndst,args->mtmpi,args->tmpi); hts_expand(char,ret+1,args->mtmps,args->tmps); args->tmps[ret] = 0; // the FORMAT string may not be 0-terminated for (idst=0; idsttmpi + idst*ndst1; isrc = args->sample_map ? args->sample_map[idst] : idst; if ( isrc==-1 ) { dst[0] = bcf_gt_missing; for (i=1; itmps + isrc*nsrc1, *tmp; char *keep_ptr = beg+nsrc1, keep = *keep_ptr; *keep_ptr = 0; while ( *beg ) { char *end = beg; while ( *end && *end!='/' && *end!='|' ) end++; if ( *beg=='.' && end-beg==1 ) dst[i] = bcf_gt_missing; else { if ( *end=='|' ) is_phased = 1; dst[i] = strtol(beg, &tmp, 10); if ( tmp!=end ) error("Could not parse the %s field at %s:%"PRId64" in %s\n", col->hdr_key_src,bcf_seqname(args->files->readers[1].header,rec),(int64_t) rec->pos+1,args->targets_fname); if ( dst[i] >= line->n_allele ) error("The source allele index is bigger than the number of destination alleles at %s:%"PRId64"\n", bcf_seqname(args->files->readers[1].header,rec),(int64_t) rec->pos+1); dst[i] = is_phased ? bcf_gt_phased(dst[i]) : bcf_gt_unphased(dst[i]); } beg = *end ? end+1 : end; i++; } *keep_ptr = keep; for (; ihdr_out,line,args->tmpi,ndst); } static int init_sample_map(args_t *args, bcf_hdr_t *src, bcf_hdr_t *dst) { int i; if ( !args->sample_names ) { args->nsmpl_annot = bcf_hdr_nsamples(dst); // tab annotation file, expecting that all samples are present: sample map not needed if ( !src ) return 0; int nmatch = 0; for (i=0; isamples[i]); if ( id!=-1 ) nmatch++; } if ( !nmatch ) return -1; // No matching samples found in the source and the destination file args->nsample_map = bcf_hdr_nsamples(dst); args->sample_map = (int*) malloc(sizeof(int)*args->nsample_map); for (i=0; insample_map; i++) { int id = bcf_hdr_id2int(src, BCF_DT_SAMPLE, dst->samples[i]); args->sample_map[i] = id; // idst -> isrc, -1 if not present } return 1; } args->nsample_map = bcf_hdr_nsamples(dst); args->sample_map = (int*) malloc(sizeof(int)*args->nsample_map); for (i=0; insample_map; i++) args->sample_map[i] = -1; int flags = !src ? SMPL_STRICT|SMPL_SINGLE|SMPL_REORDER : SMPL_STRICT|SMPL_SINGLE|SMPL_PAIR2; // is tab vs vcf annotation file smpl_ilist_t *ilist = smpl_ilist_init(dst, args->sample_names, args->sample_is_file, flags); // gives mapping dst->src if ( !ilist || !ilist->n ) error("Could not parse the samples: %s\n", args->sample_names); args->nsmpl_annot = ilist->n; int need_sample_map = args->nsmpl_annot==bcf_hdr_nsamples(dst) ? 0 : 1; for (i=0; insmpl_annot; i++) { int idst = ilist->idx[i]; const char *src_name = ilist->pair && ilist->pair[i] ? ilist->pair[i] : bcf_hdr_int2id(dst, BCF_DT_SAMPLE, idst); int isrc = i; if ( src ) // the annotation file is a VCF, not a tab-delimited file { isrc = bcf_hdr_id2int(src, BCF_DT_SAMPLE, src_name); if ( isrc==-1 ) error("Sample \"%s\" not found in the annotation file\n", src_name); } if ( isrc!=idst ) need_sample_map = 1; args->sample_map[idst] = isrc; } smpl_ilist_destroy(ilist); return need_sample_map; } static char *columns_complement(char *columns, void **skip_info, void **skip_fmt) { kstring_t str = {0,0,0}; char *ss = columns, *se = ss; while ( *ss ) { if ( *se && *se!=',' ) { se++; continue; } if ( *ss!='^' ) { if ( str.l ) kputc(',',&str); kputsn(ss, se-ss, &str); if ( !*se ) break; ss = ++se; continue; } if ( !strncasecmp("^INFO/",ss,6) ) { if ( !*skip_info ) { *skip_info = khash_str2int_init(); if ( str.l ) kputc(',',&str); kputs("INFO",&str); } char tmp = *se; *se = 0; khash_str2int_inc(*skip_info, strdup(ss+6)); *se = tmp; } else if ( !strncasecmp("^FORMAT/",ss,8) || !strncasecmp("^FMT/",ss,5) ) { int n = !strncasecmp("^FMT/",ss,5) ? 5 : 8; if ( !*skip_fmt ) { *skip_fmt = khash_str2int_init(); if ( str.l ) kputc(',',&str); kputs("FORMAT",&str); } char tmp = *se; *se = 0; khash_str2int_inc(*skip_fmt, strdup(ss+n)); *se = tmp; } else { if ( !*skip_info ) { *skip_info = khash_str2int_init(); if ( str.l ) kputc(',',&str); kputs("INFO",&str); } char tmp = *se; *se = 0; khash_str2int_inc(*skip_info, strdup(ss+1)); *se = tmp; } if ( !*se ) break; ss = ++se; } free(columns); return str.s; } static void bcf_hrec_format_rename(bcf_hrec_t *hrec, char *tag, kstring_t *str) { int j, nout = 0; ksprintf(str, "##%s=<", hrec->key); for (j=0; jnkeys; j++) { if ( !strcmp("IDX",hrec->keys[j]) ) continue; if ( nout ) kputc(',',str); if ( !strcmp("ID", hrec->keys[j]) ) ksprintf(str,"%s=%s", hrec->keys[j], tag); else ksprintf(str,"%s=%s", hrec->keys[j], hrec->vals[j]); nout++; } ksprintf(str,">\n"); } static char *set_replace_mode(char *ss, int *replace) { int mode = 0; while (*ss) { if ( *ss=='+' ) mode |= REPLACE_MISSING; else if ( *ss=='-' ) mode |= REPLACE_NON_MISSING; else if ( *ss=='=' ) mode |= SET_OR_APPEND; else if ( *ss=='.' ) mode |= CARRY_OVER_MISSING; else break; ss++; } if ( !mode ) mode = REPLACE_ALL; // is exactly one bit set? // if ( mode && !(mode && ((mode & mode-1) == 0)) ) *replace = mode; return ss; } static void rename_annots_push(args_t *args, char *src, char *dst); static void init_columns(args_t *args) { int need_sample_map = 0; int sample_map_ok = init_sample_map(args, args->tgts_is_vcf?args->files->readers[1].header:NULL, args->hdr); kstring_t tmp = {0,0,0}; if ( args->columns_is_file ) { int i,n; char **str = hts_readlist(args->columns, args->columns_is_file, &n); if ( !str ) error("Could not parse %s\n", args->columns); for (i=0; imerge_method_str.l ) kputc(',',&args->merge_method_str); kputs(str[i],&args->merge_method_str); kputc(':',&args->merge_method_str); kputs(ptr,&args->merge_method_str); } } if ( tmp.l ) kputc(',',&tmp); kputs(str[i],&tmp); free(str[i]); } free(str); free(args->columns); args->columns = tmp.s; tmp.l = tmp.m = 0; tmp.s = NULL; } void *skip_fmt = NULL, *skip_info = NULL; if ( args->tgts_is_vcf ) args->columns = columns_complement(args->columns, &skip_info, &skip_fmt); kstring_t str = {0,0,0}; char *ss = args->columns, *se = ss; args->ncols = 0; int icol = -1, has_fmt_str = 0; while ( *ss ) { char *ptr; if ( *se && *se!=',' ) { se++; continue; } int replace; ss = set_replace_mode(ss, &replace); icol++; str.l = 0; kputsn(ss, se-ss, &str); if ( !str.s[0] || !strcasecmp("-",str.s) ) ; else if ( !strcasecmp("CHROM",str.s) ) args->chr_idx = icol; else if ( !strcasecmp("POS",str.s) ) { if ( replace==REPLACE_NON_MISSING && !args->tgts_is_vcf ) { args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; col->setter = setter_pos; col->hdr_key_src = strdup(str.s); col->hdr_key_dst = strdup(str.s); args->match_end = icol; } else args->beg_idx = icol; } else if ( !strcasecmp("FROM",str.s) || !strcasecmp("BEG",str.s) ) args->beg_idx = icol; else if ( !strcasecmp("TO",str.s) || !strcasecmp("END",str.s) ) args->end_idx = icol; else if ( !strcasecmp("REF",str.s) ) { if ( args->tgts_is_vcf ) { args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->setter = vcf_setter_ref; col->hdr_key_src = strdup(str.s); col->hdr_key_dst = strdup(str.s); } else args->ref_idx = icol; } else if ( !strcasecmp("ALT",str.s) ) { if ( args->tgts_is_vcf ) { args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->setter = vcf_setter_alt; col->hdr_key_src = strdup(str.s); col->hdr_key_dst = strdup(str.s); col->replace = replace; if ( args->pair_logic==-1 ) bcf_sr_set_opt(args->files,BCF_SR_PAIR_LOGIC,BCF_SR_PAIR_BOTH_REF); } else args->alt_idx = icol; } else if ( !strcasecmp("ID",str.s) || !strcasecmp("~ID",str.s) ) { if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -ID feature has not been implemented yet.\n"); if ( str.s[0]=='~' ) replace = MATCH_VALUE; if ( args->tgts_is_vcf && (replace & MATCH_VALUE) ) error("todo: -c ~ID with -a VCF?\n"); args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; col->setter = args->tgts_is_vcf ? vcf_setter_id : setter_id; col->hdr_key_src = strdup(str.s); col->hdr_key_dst = strdup(str.s); if ( replace & MATCH_VALUE ) args->match_id = icol; } else if ( !strcasecmp("~INFO/END",str.s) && !args->tgts_is_vcf ) { replace = MATCH_VALUE; args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; col->setter = NULL; col->hdr_key_src = strdup(str.s); col->hdr_key_dst = strdup(str.s); args->match_end = icol; } else if ( !strcasecmp("~POS",str.s) ) { error("Error: the use of ~POS has been deprecated, use -POS to transfer the column POS.\n"); } else if ( str.s[0]=='~' ) { args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = MATCH_VALUE; col->setter = NULL; col->hdr_key_src = strdup(str.s+1); } else if ( !strcasecmp("-POS",str.s) && !args->tgts_is_vcf ) { if ( args->tgts_is_vcf ) error("Error: cannot use -POS, position can be replaced only from a tab-delimited file\n"); args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; col->setter = setter_pos; col->hdr_key_src = strdup(str.s); col->hdr_key_dst = strdup(str.s); args->match_end = icol; } else if ( !strncasecmp("ID:=",str.s,4) ) // transfer a tag from INFO to ID column { if ( !args->tgts_is_vcf ) error("The annotation source must be a VCF for \"%s\"\n",str.s); if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -ID feature has not been implemented yet.\n"); args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; col->setter = vcf_setter_id; col->getter = vcf_getter_info_str2str; str.s[2] = 0; col->hdr_key_dst = strdup(str.s); col->hdr_key_src = strncasecmp("INFO/",str.s+4,5) ? strdup(str.s+4) : strdup(str.s+4+5); int hdr_id = bcf_hdr_id2int(args->tgts_hdr, BCF_DT_ID,col->hdr_key_src); if ( !bcf_hdr_idinfo_exists(args->tgts_hdr,BCF_HL_INFO,hdr_id) ) error("The INFO tag \"%s\" is not defined in %s\n", col->hdr_key_src, args->targets_fname); if ( bcf_hdr_id2type(args->tgts_hdr,BCF_HL_INFO,hdr_id)!=BCF_HT_STR ) error("Only Type=String tags can be used to annotate the ID column\n"); } else if ( (ptr=strstr(str.s,":=")) && (!args->targets_fname || !strncasecmp(ptr+2,"./",2)) ) { *ptr = 0; if ( !strncasecmp(str.s,"INFO/",5) && (!strcasecmp(ptr+2,"FILTER") || !strcasecmp(ptr+2,"./FILTER")) ) { // -a not present and transferring filter, needs to be a local transfer args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; col->setter = vcf_setter_info_str; col->getter = vcf_getter_filter2str_local; col->hdr_key_src = strdup(ptr+2); col->hdr_key_dst = strdup(str.s+5); tmp.l = 0; ksprintf(&tmp,"##INFO=",col->hdr_key_dst); bcf_hdr_append(args->hdr_out, tmp.s); if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update header", __func__); int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, col->hdr_key_dst); col->number = bcf_hdr_id2length(args->hdr_out,BCF_HL_INFO,hdr_id); } else rename_annots_push(args,ptr+2,str.s); *ptr = ':'; } else if ( !strcasecmp("FILTER",str.s) ) { if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -FILTER feature has not been implemented yet.\n"); args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; col->setter = args->tgts_is_vcf ? vcf_setter_filter : setter_filter; col->hdr_key_src = strdup(str.s); col->hdr_key_dst = strdup(str.s); if ( args->tgts_is_vcf ) { bcf_hdr_t *tgts_hdr = args->files->readers[1].header; int j; for (j=0; jnhrec; j++) { bcf_hrec_t *hrec = tgts_hdr->hrec[j]; if ( hrec->type!=BCF_HL_FLT ) continue; int k = bcf_hrec_find_key(hrec,"ID"); if ( k<0 ) error("[%s] Failed to parse the header, the ID attribute not found", __func__); tmp.l = 0; bcf_hrec_format(hrec, &tmp); bcf_hdr_append(args->hdr_out, tmp.s); } if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update header", __func__); } } else if ( !strcasecmp("QUAL",str.s) ) { if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -QUAL feature has not been implemented yet.\n"); if ( replace & SET_OR_APPEND ) error("Apologies, the =QUAL feature has not been implemented yet.\n"); args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; col->setter = args->tgts_is_vcf ? vcf_setter_qual : setter_qual; col->hdr_key_src = strdup(str.s); col->hdr_key_dst = strdup(str.s); } else if ( args->tgts_is_vcf && !strcasecmp("INFO",str.s) ) // All INFO fields { if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -INFO/TAG feature has not been implemented yet.\n"); if ( replace & SET_OR_APPEND ) error("Apologies, the =INFO feature has not been implemented yet.\n"); bcf_hdr_t *tgts_hdr = args->files->readers[1].header; int j; for (j=0; jnhrec; j++) { bcf_hrec_t *hrec = tgts_hdr->hrec[j]; if ( hrec->type!=BCF_HL_INFO ) continue; int k = bcf_hrec_find_key(hrec,"ID"); assert( k>=0 ); // this should always be true for valid VCFs if ( skip_info && khash_str2int_has_key(skip_info,hrec->vals[k]) ) continue; tmp.l = 0; bcf_hrec_format(hrec, &tmp); bcf_hdr_append(args->hdr_out, tmp.s); if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update header", __func__); int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, hrec->vals[k]); args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = -1; col->replace = replace; col->hdr_key_src = strdup(hrec->vals[k]); col->hdr_key_dst = strdup(hrec->vals[k]); col->number = bcf_hdr_id2length(args->hdr_out,BCF_HL_INFO,hdr_id); switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_INFO,hdr_id) ) { case BCF_HT_FLAG: col->setter = vcf_setter_info_flag; break; case BCF_HT_INT: col->setter = vcf_setter_info_int; break; case BCF_HT_REAL: col->setter = vcf_setter_info_real; break; case BCF_HT_STR: col->setter = vcf_setter_info_str; break; default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_INFO,hdr_id)); } } } else if ( args->tgts_is_vcf && (!strcasecmp("FORMAT",str.s) || !strcasecmp("FMT",str.s)) ) // All FORMAT fields { bcf_hdr_t *tgts_hdr = args->files->readers[1].header; need_sample_map = 1; int j; for (j=0; jnhrec; j++) { bcf_hrec_t *hrec = tgts_hdr->hrec[j]; if ( hrec->type!=BCF_HL_FMT) continue; int k = bcf_hrec_find_key(hrec,"ID"); assert( k>=0 ); // this should always be true for valid VCFs if ( skip_fmt && khash_str2int_has_key(skip_fmt,hrec->vals[k]) ) continue; tmp.l = 0; bcf_hrec_format(hrec, &tmp); bcf_hdr_append(args->hdr_out, tmp.s); if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update header", __func__); int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, hrec->vals[k]); args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = -1; col->replace = replace; col->hdr_key_src = strdup(hrec->vals[k]); col->hdr_key_dst = strdup(hrec->vals[k]); if ( !strcasecmp("GT",col->hdr_key_src) ) { if ( !args->tgts_is_vcf ) error("The FORMAT/GT field can be currently populated only from a VCF\n"); col->setter = vcf_setter_format_gt; } else switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id) ) { case BCF_HT_INT: col->setter = vcf_setter_format_int; break; case BCF_HT_REAL: col->setter = vcf_setter_format_real; break; case BCF_HT_STR: col->setter = vcf_setter_format_str; has_fmt_str = 1; break; default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id)); } hdr_id = bcf_hdr_id2int(tgts_hdr, BCF_DT_ID, hrec->vals[k]); col->number = bcf_hdr_id2length(tgts_hdr,BCF_HL_FMT,hdr_id); } } else if ( !strncasecmp("FORMAT/",str.s, 7) || !strncasecmp("FMT/",str.s,4) ) { char *key_dst = str.s + (!strncasecmp("FMT/",str.s,4) ? 4 : 7); char *key_src = strstr(key_dst,":="); if ( key_src ) { *key_src = 0; key_src += 2; if ( !strncasecmp("FORMAT/",key_src,7) ) key_src += 7; else if ( !strncasecmp("FMT/",key_src,4) ) key_src += 4; } else key_src = key_dst; need_sample_map = 1; if ( args->tgts_is_vcf ) { bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->files->readers[1].header, BCF_HL_FMT, "ID", key_src, NULL); if ( !hrec ) error("No such annotation \"%s\" in %s\n", key_src,args->targets_fname); tmp.l = 0; bcf_hrec_format_rename(hrec, key_dst, &tmp); bcf_hdr_append(args->hdr_out, tmp.s); if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update header", __func__); } int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, key_dst); if ( !bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_FMT,hdr_id) ) error("The FORMAT tag \"%s\" is not defined in %s, was the -h option provided?\n", str.s, args->targets_fname); args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); if ( !args->tgts_is_vcf ) { col->icol = icol; icol += args->nsmpl_annot - 1; } else col->icol = -1; col->replace = replace; col->hdr_key_src = strdup(key_src); col->hdr_key_dst = strdup(key_dst); if ( !strcasecmp("GT",key_src) ) { if ( !args->tgts_is_vcf ) error("The FORMAT/GT field can be currently populated only from a VCF\n"); col->setter = vcf_setter_format_gt; } else switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id) ) { case BCF_HT_INT: col->setter = args->tgts_is_vcf ? vcf_setter_format_int : setter_format_int; break; case BCF_HT_REAL: col->setter = args->tgts_is_vcf ? vcf_setter_format_real : setter_format_real; break; case BCF_HT_STR: col->setter = args->tgts_is_vcf ? vcf_setter_format_str : setter_format_str; has_fmt_str = 1; break; default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id)); } if ( args->tgts_is_vcf ) { bcf_hdr_t *tgts_hdr = args->files->readers[1].header; hdr_id = bcf_hdr_id2int(tgts_hdr, BCF_DT_ID, col->hdr_key_src); col->number = bcf_hdr_id2length(tgts_hdr,BCF_HL_FMT,hdr_id); } } else { if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -INFO/TAG feature has not been implemented yet.\n"); if ( replace & SET_OR_APPEND ) { if ( args->tgts_is_vcf ) error("Error: the =INFO/TAG feature is currently supported only with TAB annotation files and has limitations\n" " (the annotation type is modified to \"Number=.\" and allele ordering is disregarded)\n"); fprintf(stderr,"Warning: the =INFO/TAG feature modifies the annotation to \"Number=.\" and disregards allele ordering\n"); } args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; int explicit_src_info = 0; int explicit_dst_info = 0; char *key_dst; if ( !strncasecmp("INFO/",str.s,5) ) { key_dst = str.s + 5; explicit_dst_info = 1; } else if ( !strcasecmp("~INFO/END",str.s) ) { key_dst = str.s + 6; explicit_dst_info = 1; } else key_dst = str.s; char *key_src = strstr(key_dst,":="); if ( key_src ) { *key_src = 0; key_src += 2; if ( !strncasecmp("INFO/",key_src,5) ) { key_src += 5; explicit_src_info = 1; } else if ( !strncasecmp("FMT/",key_src,4) || !strncasecmp("FORMAT/",key_src,5) ) { key_src[-2] = ':'; error("Did you mean \"FMT/%s\" rather than \"%s\"?\n",str.s,str.s); } else if ( !strcasecmp("FILTER",key_src) && args->tgts_is_vcf ) { col->getter = vcf_getter_filter2str; } } else key_src = key_dst; col->hdr_key_src = strdup(key_src); col->hdr_key_dst = strdup(key_dst); int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, key_dst); if ( !bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_INFO,hdr_id) ) { if ( args->tgts_is_vcf ) // reading annotations from a VCF, add a new header line { if ( !strcasecmp("ID",key_src) && !explicit_src_info ) { // transferring ID column into a new INFO tag tmp.l = 0; ksprintf(&tmp,"##INFO=",key_dst); } else if ( !strcasecmp("FILTER",key_src) && !explicit_src_info ) { // transferring FILTER column into a new INFO tag tmp.l = 0; ksprintf(&tmp,"##INFO=",key_dst); } else { bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->files->readers[1].header, BCF_HL_INFO, "ID", key_src, NULL); if ( !hrec ) { if ( explicit_dst_info+explicit_src_info==0 && bcf_hdr_get_hrec(args->files->readers[1].header, BCF_HL_FMT, "ID", key_src, NULL) ) error("Did you mean \"FMT/%s\" rather than \"%s\"?\n",str.s,str.s); char *ptr = strchr(key_src,'='); if ( ptr ) { *ptr = 0; tmp.l = 0; ksprintf(&tmp,"%s:=%s",key_src,ptr+1); *ptr = '='; error("The INFO tag \"%s\" is not defined, is this what you want \"%s\" ?\n",key_src,tmp.s); } error("The INFO tag \"%s\" is not defined in %s, was the -h option provided?\n", key_src,args->files->readers[1].fname); } tmp.l = 0; bcf_hrec_format_rename(hrec, key_dst, &tmp); } bcf_hdr_append(args->hdr_out, tmp.s); if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update header", __func__); hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, key_dst); } else error("The INFO tag \"%s\" is not defined in %s, was the -h option provided?\n", key_dst, args->targets_fname); assert( bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_INFO,hdr_id) ); } if ( args->tgts_is_vcf ) { if ( !strcasecmp("ID",key_src) && !explicit_src_info ) col->getter = vcf_getter_id2str; else if ( !strcasecmp("FILTER",key_src) && !explicit_src_info ) col->getter = vcf_getter_filter2str; } col->number = bcf_hdr_id2length(args->hdr_out,BCF_HL_INFO,hdr_id); switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_INFO,hdr_id) ) { case BCF_HT_FLAG: col->setter = args->tgts_is_vcf ? vcf_setter_info_flag : setter_info_flag; break; case BCF_HT_INT: col->setter = args->tgts_is_vcf ? vcf_setter_info_int : setter_info_int; break; case BCF_HT_REAL: col->setter = args->tgts_is_vcf ? vcf_setter_info_real : setter_info_real; break; case BCF_HT_STR: col->setter = args->tgts_is_vcf ? vcf_setter_info_str : setter_info_str; break; default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_INFO,hdr_id)); } if ( replace & SET_OR_APPEND ) // change to Number=. { bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->hdr_out, BCF_HL_INFO, "ID", key_dst, NULL); if ( !hrec ) error("Uh, could not find the new tag \"%s\" in the header\n", key_dst); hrec = bcf_hrec_dup(hrec); int j = bcf_hrec_find_key(hrec, "Number"); if ( j<0 ) error("Uh, could not find the entry Number in the header record of %s\n",key_dst); free(hrec->vals[j]); hrec->vals[j] = strdup("."); bcf_hdr_remove(args->hdr_out,BCF_HL_INFO, key_dst); bcf_hdr_add_hrec(args->hdr_out, hrec); } } if ( !*se ) break; ss = ++se; } free(str.s); free(tmp.s); free(args->columns); if ( skip_info ) khash_str2int_destroy_free(skip_info); if ( skip_fmt ) khash_str2int_destroy_free(skip_fmt); if ( has_fmt_str ) { int n = bcf_hdr_nsamples(args->hdr_out); if ( args->tgts_is_vcf && nfiles->readers[1].header) ) n = bcf_hdr_nsamples(args->files->readers[1].header); args->tmpp = (char**)malloc(sizeof(char*)*n); args->tmpp2 = (char**)malloc(sizeof(char*)*n); } if ( !need_sample_map ) { free(args->sample_map); args->sample_map = NULL; } else if ( sample_map_ok<0 ) error("No matching samples in source and destination file?\n"); } static void init_merge_method(args_t *args) { int i; for (i=0; incols; i++) { args->cols[i].merge_method = MM_FIRST; args->cols[i].mm_str_hash = NULL; args->cols[i].mm_dbl = NULL; args->cols[i].mm_dbl_nalloc = args->cols[i].mm_dbl_nused = args->cols[i].mm_dbl_ndat = 0; memset(&args->cols[i].mm_kstr, 0, sizeof(args->cols[i].mm_kstr)); } if ( !args->merge_method_str.l ) return; if ( args->tgts_is_vcf ) error("Error: the --merge-logic is intended for use with BED or TAB-delimited files only.\n"); if ( !args->tgt_idx && !args->tgts ) error("Error: BEG,END (or FROM,TO) columns or REF,ALT columns are expected with the --merge-logic option.\n"); char *sb = args->merge_method_str.s; while ( *sb ) { char *se = sb; while ( *se && *se!=',' ) se++; args->tmpks.l = 0; kputsn(sb, se-sb, &args->tmpks); kputc(0, &args->tmpks); char *mm_type_str = args->tmpks.s + args->tmpks.l; while ( *mm_type_str!=':' && mm_type_str > args->tmpks.s ) mm_type_str--; if ( *mm_type_str!=':' ) error("Error: could not parse the argument to --merge-logic: %s\n", args->merge_method_str.s); *mm_type_str = 0; mm_type_str++; int mm_type = MM_FIRST; if ( !strcasecmp("unique",mm_type_str) ) mm_type = MM_UNIQUE; else if ( !strcasecmp("first",mm_type_str) ) mm_type = MM_FIRST; else if ( !strcasecmp("append",mm_type_str) ) mm_type = MM_APPEND; else if ( !strcasecmp("append-missing",mm_type_str) ) { mm_type = MM_APPEND_MISSING; if ( args->ref_idx!=-1 ) args->has_append_mode = 1; } else if ( !strcasecmp("sum",mm_type_str) ) mm_type = MM_SUM; else if ( !strcasecmp("avg",mm_type_str) ) mm_type = MM_AVG; else if ( !strcasecmp("min",mm_type_str) ) mm_type = MM_MIN; else if ( !strcasecmp("max",mm_type_str) ) mm_type = MM_MAX; else error("Error: could not parse --merge-logic %s, the logic \"%s\" is not recognised\n", args->merge_method_str.s,mm_type_str); for (i=0; incols; i++) { if ( strcmp(args->cols[i].hdr_key_dst,args->tmpks.s) ) continue; if ( (mm_type==MM_APPEND || mm_type==MM_APPEND_MISSING) && args->cols[i].number!=BCF_VL_VAR ) error("Error: --merge-logic append can be requested only for tags of variable length (Number=.)\n"); args->cols[i].merge_method = mm_type; break; } if ( i==args->ncols ) error("No such tag in the destination file: %s\n", args->tmpks.s); sb = *se ? se + 1 : se; } if ( args->has_append_mode ) { // create a missing line to insert missing values when VCF ALT finds no match in the annotation file args->aline_missing = (annot_line_t*)calloc(1,sizeof(*args->aline_missing)); int ncol = 0; for (i=0; incols; i++) if ( ncol < args->cols[i].icol + 1 ) ncol = args->cols[i].icol + 1; if ( ncol < args->ref_idx + 1 ) ncol = args->ref_idx + 1; args->aline_missing->mcols = ncol; args->aline_missing->ncols = ncol; args->aline_missing->cols = (char**) malloc(ncol*sizeof(char*)); for (i=0; ialine_missing->cols[i] = strdup("."); } } static void rename_chrs(args_t *args, char *fname) { int n, i; char **map = hts_readlist(fname, 1, &n); if ( !map ) error("Could not read: %s\n", fname); for (i=0; ihdr_out, map[i]); bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->hdr_out, BCF_HL_CTG, "ID", map[i], NULL); if ( !hrec ) continue; // the sequence not present int j = bcf_hrec_find_key(hrec, "ID"); assert( j>=0 ); free(hrec->vals[j]); ss++; while ( *ss && isspace(*ss) ) ss++; char *se = ss; while ( *se && !isspace(*se) ) se++; *se = 0; hrec->vals[j] = strdup(ss); args->hdr_out->id[BCF_DT_CTG][rid].key = hrec->vals[j]; } for (i=0; ihdr_out, BCF_DT_ID, ori_tag); if ( id<0 ) return 1; bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->hdr_out, type, "ID", ori_tag, NULL); if ( !hrec ) return 1; // the ID attribute not present int j = bcf_hrec_find_key(hrec, "ID"); assert( j>=0 ); free(hrec->vals[j]); char *ptr = new_tag; while ( *ptr && !isspace(*ptr) ) ptr++; *ptr = 0; hrec->vals[j] = strdup(new_tag); args->hdr_out->id[BCF_DT_ID][id].key = hrec->vals[j]; return 0; } static void rename_annots(args_t *args) { int i; if ( args->rename_annots ) { args->rename_annots_map = hts_readlist(args->rename_annots, 1, &args->rename_annots_nmap); if ( !args->rename_annots_map ) error("Could not read: %s\n", args->rename_annots); } for (i=0; irename_annots_nmap; i++) { char *ptr = args->rename_annots_map[i]; while ( *ptr && !isspace(*ptr) ) ptr++; if ( !*ptr ) error("Could not parse: %s\n", args->rename_annots_map[i]); char *rmme = ptr; *ptr = 0; ptr++; while ( *ptr && isspace(*ptr) ) ptr++; if ( !*ptr ) { *rmme = ' '; error("Could not parse: %s\n", args->rename_annots_map[i]); } if ( rename_annots_core(args, args->rename_annots_map[i], ptr) < 0 ) error("Cannot rename \"%s\" to \"%s\"\n",args->rename_annots_map[i],ptr); } } static void rename_annots_push(args_t *args, char *src, char *dst) { args->rename_annots_nmap++; args->rename_annots_map = (char**)realloc(args->rename_annots_map,sizeof(*args->rename_annots_map)*args->rename_annots_nmap); kstring_t str = {0,0,0}; ksprintf(&str,"%s %s",src,dst); args->rename_annots_map[ args->rename_annots_nmap - 1 ] = str.s; } static void init_filters(args_t *args) { // Check if the -i/-e expressions contain external values that should be determined // on the fly from the annotation file. The expressions can be given as // TAG={NAME} // TAG={str:NAME} // TAG={int:NAME} // TAG={float:NAME} kstring_t str = {0,0,0}; char *src = strdup(args->filter_str); int len = 0; while (1) { char *beg = strchr(src+len,'{'); if ( !beg ) break; // check if "{" appears inside quotes, in such case do not modify char skip = 0; char *tmp = src; while ( tmpfilter_str); // unbalanced quotation; todo: check for escape char len = tmp - src + 1; skip = 1; } if ( skip ) continue; char *end = ++beg; while ( *end && *end!='}' ) end++; if ( !*end ) error("Could not parse the expression: %s\n",args->filter_str); *end = 0; // explicit typing? int type = -1; tmp = beg; while ( *tmp && *tmp!=':' ) tmp++; if ( *tmp ) { *tmp = 0; if ( !strcasecmp(beg,"str") ) type = BCF_HT_STR; else if ( !strcasecmp(beg,"int") ) type = BCF_HT_INT; else if ( !strcasecmp(beg,"float") ) type = BCF_HT_REAL; } args->n_ext++; args->ext = (ext_t*)realloc(args->ext,sizeof(*args->ext)*args->n_ext); ext_t *ext = &args->ext[args->n_ext-1]; ext->ht_type = type; ext->name = strdup(beg); if ( beg-1 > src ) kputsn(src,beg-1-src,&str); if ( type==-1 ) kputs("{}",&str); else if ( type==BCF_HT_STR ) kputs("{str}",&str); else if ( type==BCF_HT_INT ) kputs("{int}",&str); else if ( type==BCF_HT_REAL ) kputs("{float}",&str); len = str.l; kputs(end+1,&str); free(src); src = strdup(str.s); str.l = 0; } args->filter = filter_init(args->hdr, src); free(src); free(str.s); int i,j,n_ext; const int *ext_type = filter_ext_types(args->filter, &n_ext); if ( n_ext != args->n_ext ) error("Failed to parse the expression, unexpected number of dynamic variables (%d vs %d): %s\n",n_ext,args->n_ext,args->filter_str); if ( !args->n_ext ) return; if ( !args->tgts ) error("Error: dynamic variables in -i/-e expressions can be currently used only with tab-delimited file, not with VCF (todo)\n"); // contains external values args->ext_ptr = malloc(sizeof(*args->ext_ptr)*args->n_ext); for (i=0; in_ext; i++) args->ext[i].ht_type = ext_type[i]; args->filter_ext = args->filter; args->filter = NULL; // set the column idx if ( args->ncols ) { for (i=0; in_ext; i++) { for (j=0; jncols; j++) { if ( strcmp(args->ext[i].name,args->cols[j].hdr_key_src) ) continue; args->ext[i].icol = args->cols[j].icol; break; } if ( j==args->ncols ) error("No such column: %s\n",args->ext[i].name); } } } static void init_data(args_t *args) { args->hdr = args->files->readers[0].header; args->hdr_out = bcf_hdr_dup(args->hdr); if ( args->set_ids_fmt ) { if ( args->set_ids_fmt[0]=='+' ) { args->set_ids_replace = 0; args->set_ids_fmt++; } args->set_ids = convert_init(args->hdr_out, NULL, 0, args->set_ids_fmt); } if ( args->remove_annots ) init_remove_annots(args); if ( args->header_fname || args->header_lines ) init_header_lines(args); if ( args->targets_fname && args->tgts_is_vcf ) { // reading annots from a VCF if ( !bcf_sr_add_reader(args->files, args->targets_fname) ) error("Failed to open %s: %s\n", args->targets_fname,bcf_sr_strerror(args->files->errnum)); args->tgts_hdr = args->files->readers[1].header; } if ( args->columns ) init_columns(args); if ( args->targets_fname && !args->tgts_is_vcf ) { if ( !args->columns ) error("The -c option not given\n"); if ( args->chr_idx==-1 ) error("The -c CHROM option not given\n"); if ( args->beg_idx==-1 ) error("The -c POS option not given\n"); if ( args->single_overlaps && args->merge_method_str.l ) error("The options --merge-logic and --single-overlaps cannot be combined\n"); if ( args->end_idx==-1 || (args->single_overlaps && !args->merge_method_str.l) ) { args->end_idx = -args->beg_idx - 1; args->tgts = bcf_sr_regions_init(args->targets_fname,1,args->chr_idx,args->beg_idx,args->end_idx); if ( !args->tgts ) error("Could not initialize the annotation file: %s\n", args->targets_fname); if ( !args->tgts->tbx ) error("Expected tabix-indexed annotation file: %s\n", args->targets_fname); } else { if ( args->ref_idx!=-1 ) error("Error: the REF columns will be ignored when BEG,END (or FROM,TO) is present. Replace END (or TO) with \"-\".\n"); int len = strlen(args->targets_fname); if ( len>=7 && !strcasecmp(".bed.gz",args->targets_fname+len-7) ) args->tgt_is_bed = 1; else if ( len>=8 && !strcasecmp(".bed.bgz",args->targets_fname+len-8) ) args->tgt_is_bed = 1; else if ( len>=4 && !strcasecmp(".bed",args->targets_fname+len-4) ) args->tgt_is_bed = 1; args->tgt_idx = regidx_init(args->targets_fname,parse_with_payload,free_payload,sizeof(char*),args); if ( !args->tgt_idx ) error("Failed to parse: %s\n", args->targets_fname); args->tgt_itr = regitr_init(args->tgt_idx); args->nalines++; hts_expand0(annot_line_t,args->nalines,args->malines,args->alines); } if ( args->min_overlap_str ) { char *tmp = args->min_overlap_str; if ( args->min_overlap_str[0] != ':' ) { args->min_overlap_ann = strtod(args->min_overlap_str,&tmp); if ( args->min_overlap_ann < 0 || args->min_overlap_ann > 1 || (*tmp && *tmp!=':') ) error("Could not parse \"--min-overlap %s\", expected value(s) between 0-1\n", args->min_overlap_str); } if ( *tmp && *tmp==':' ) { args->min_overlap_vcf = strtod(tmp+1,&tmp); if ( args->min_overlap_vcf < 0 || args->min_overlap_vcf > 1 || *tmp ) error("Could not parse \"--min-overlap %s\", expected value(s) between 0-1\n", args->min_overlap_str); } } } init_merge_method(args); args->vcmp = vcmp_init(); if ( args->filter_str ) init_filters(args); if ( args->mark_sites ) { if ( !args->targets_fname ) { if ( args->mark_sites_logic!=MARK_LISTED ) error("The -a option not given but -%s logic was requested\n",args->mark_sites); fprintf(stderr,"Note: The -a option not given, all sites will be annotated with INFO/%s\n",args->mark_sites); bcf_hdr_printf(args->hdr_out,"##INFO=", args->mark_sites,args->mark_sites); } else bcf_hdr_printf(args->hdr_out,"##INFO=", args->mark_sites,args->mark_sites_logic==MARK_LISTED?"":"not ",args->mark_sites); } if (args->record_cmd_line) bcf_hdr_append_version(args->hdr_out, args->argc, args->argv, "bcftools_annotate"); if ( !args->drop_header ) { if ( args->rename_chrs ) rename_chrs(args, args->rename_chrs); if ( args->rename_annots || args->rename_annots_map ) rename_annots(args); char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( args->out_fh == NULL ) error("[%s] Error: cannot write to \"%s\": %s\n", __func__,args->output_fname, strerror(errno)); if ( args->n_threads ) hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->files->p); if ( bcf_hdr_write(args->out_fh, args->hdr_out)!=0 ) error("[%s] Error: failed to write the header to %s\n", __func__,args->output_fname); if ( init_index2(args->out_fh,args->hdr,args->output_fname, &args->index_fn, args->write_index) < 0 ) error("Error: failed to initialise index for %s\n",args->output_fname); } } static void destroy_data(args_t *args) { int i; for (i=0; in_ext; i++) { free(args->ext[i].name); if ( args->ext[i].ht_type!=BCF_HT_STR ) continue; } free(args->ext_ptr); free(args->ext); for (i=0; inrm; i++) free(args->rm[i].key); free(args->rm); if ( args->hdr_out ) bcf_hdr_destroy(args->hdr_out); if (args->vcmp) vcmp_destroy(args->vcmp); for (i=0; incols; i++) { free(args->cols[i].hdr_key_src); free(args->cols[i].hdr_key_dst); free(args->cols[i].mm_kstr.s); if ( args->cols[i].mm_str_hash ) khash_str2int_destroy_free(args->cols[i].mm_str_hash); free(args->cols[i].mm_dbl); free(args->cols[i].ptr); } free(args->cols); if ( args->aline_missing ) { for (i=0; ialine_missing->ncols; i++) free(args->aline_missing->cols[i]); free(args->aline_missing->cols); free(args->aline_missing); } for (i=0; imalines; i++) { free(args->alines[i].cols); free(args->alines[i].als); free(args->alines[i].line.s); } free(args->alines); free(args->srt_alines); if ( args->tgt_idx ) { regidx_destroy(args->tgt_idx); regitr_destroy(args->tgt_itr); } if ( args->rename_annots_map ) { for (i=0; irename_annots_nmap; i++) free(args->rename_annots_map[i]); free(args->rename_annots_map); } if ( args->tgts ) bcf_sr_regions_destroy(args->tgts); free(args->tmpks.s); free(args->tmpi); free(args->tmpf); free(args->tmps); free(args->tmpp); free(args->tmpi2); free(args->tmpf2); free(args->tmps2); free(args->tmpp2); free(args->tmpi3); free(args->tmpf3); free(args->src_smpl_pld); free(args->dst_smpl_pld); if ( args->set_ids ) convert_destroy(args->set_ids); if ( args->filter ) filter_destroy(args->filter); if ( args->filter_ext ) filter_destroy(args->filter_ext); if (args->out_fh) { if ( args->write_index ) { if ( bcf_idx_save(args->out_fh)<0 ) { if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"stdout"); } free(args->sample_map); free(args->merge_method_str.s); } static void parse_annot_line(args_t *args, char *str, annot_line_t *tmp) { tmp->line.l = 0; kputs(str, &tmp->line); char *s = tmp->line.s; tmp->ncols = 1; hts_expand(char*,tmp->ncols,tmp->mcols,tmp->cols); tmp->cols[0] = s; while ( *s ) { if ( *s=='\t' ) { tmp->ncols++; hts_expand(char*,tmp->ncols,tmp->mcols,tmp->cols); tmp->cols[tmp->ncols-1] = s+1; *s = 0; } s++; } if ( args->ref_idx != -1 ) { if ( args->ref_idx >= tmp->ncols ) error("Could not parse the line, expected %d+ columns, found %d:\n\t%s\n",args->ref_idx+1,tmp->ncols,str); if ( args->alt_idx >= tmp->ncols ) error("Could not parse the line, expected %d+ columns, found %d:\n\t%s\n",args->alt_idx+1,tmp->ncols,str); tmp->nals = 2; hts_expand(char*,tmp->nals,tmp->mals,tmp->als); tmp->als[0] = tmp->cols[args->ref_idx]; tmp->als[1] = s = tmp->cols[args->alt_idx]; while ( *s ) { if ( *s==',' ) { tmp->nals++; hts_expand(char*,tmp->nals,tmp->mals,tmp->als); tmp->als[tmp->nals-1] = s+1; *s = 0; } s++; } } } static void buffer_annot_lines(args_t *args, bcf1_t *line, int start_pos, int end_pos) { if ( args->nalines && args->alines[0].rid != line->rid ) args->nalines = 0; int i = 0; while ( inalines ) { if ( line->pos > args->alines[i].end ) { args->nalines--; if ( args->nalines && inalines ) { annot_line_t tmp = args->alines[i]; memmove(&args->alines[i],&args->alines[i+1],(args->nalines-i)*sizeof(annot_line_t)); args->alines[args->nalines] = tmp; } } else i++; } if ( !args->filter_ext && args->ref_idx==-1 && args->nalines ) return; while ( !bcf_sr_regions_overlap(args->tgts, bcf_seqname(args->hdr,line), start_pos,end_pos) ) { if ( args->nalines + 1 == 0xffff ) break; // likely a symbolic allele, don't let the buffer overflow args->nalines++; hts_expand0(annot_line_t,args->nalines,args->malines,args->alines); annot_line_t *tmp = &args->alines[args->nalines-1]; tmp->rid = line->rid; tmp->start = args->tgts->start; tmp->end = args->tgts->end; parse_annot_line(args, args->tgts->line.s, tmp); if ( args->filter_ext || args->ref_idx != -1 ) { int iseq = args->tgts->iseq; if ( bcf_sr_regions_next(args->tgts)<0 || args->tgts->iseq!=iseq ) break; } else break; } } // search string in semicolon separated strings (xx vs aa;bb) static int str_match(char *needle, char *haystack) { int len = strlen(needle); char *ptr = haystack; while ( *ptr && (ptr=strstr(ptr,needle)) ) { if ( ptr[len]!=0 && ptr[len]!=';' ) ptr++; // a prefix, not a match else if ( ptr==haystack || ptr[-1]==';' ) return 1; // a match ptr++; // a suffix, not a match } return 0; } // search common string in semicolon separated strings (xx;yy;zz vs aa;bb) static int strstr_match(char *a, char *b) { char *beg = a; while ( *beg ) { char *end = beg; while ( *end && *end!=';' ) end++; char tmp = *end; if ( *end==';' ) *end = 0; int ret = str_match(beg,b); *end = tmp; if ( ret || !*end ) return ret; beg = end + 1; } return 0; } static int annotate_from_regidx(args_t *args, bcf1_t *line) { int j; int has_overlap = 0; for (j=0; jncols; j++) args->cols[j].done = 0; if ( regidx_overlap(args->tgt_idx, bcf_seqname(args->hdr,line),line->pos,line->pos+line->rlen-1, args->tgt_itr) ) { hts_pos_t vcf_end = line->pos + line->rlen - 1; while ( regitr_overlap(args->tgt_itr) ) { annot_line_t *tmp = &args->alines[0]; tmp->rid = line->rid; tmp->start = args->tgt_itr->beg; tmp->end = args->tgt_itr->end; // Check min overlap int len_ann = tmp->end - tmp->start + 1; int len_vcf = line->rlen; int isec = (tmp->end < vcf_end ? tmp->end : vcf_end) - (tmp->start > line->pos ? tmp->start : line->pos) + 1; assert( isec > 0 ); if ( args->min_overlap_ann && args->min_overlap_ann > (float)isec/len_ann ) continue; if ( args->min_overlap_vcf && args->min_overlap_vcf > (float)isec/len_vcf ) continue; parse_annot_line(args, regitr_payload(args->tgt_itr,char*), tmp); // If a plain BED file is provided and we are asked to just mark overlapping sites, there are // no additional columns. Not sure if there can be any side effects for ill-formatted BED files // with variable number of columns if ( !args->ncols && args->mark_sites ) has_overlap = 1; for (j=0; jncols; j++) { if ( args->cols[j].done==1 ) continue; int ret = args->cols[j].setter(args,line,&args->cols[j],tmp); if ( ret < 0 ) error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); if ( ret==0 ) args->cols[j].done = 1; has_overlap = 1; } } } for (j=0; jncols; j++) { if ( args->cols[j].done==1 || args->cols[j].merge_method == MM_FIRST ) continue; if ( !args->cols[j].setter ) continue; if ( args->cols[j].setter(args,line,&args->cols[j],NULL) < 0 ) error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); } return has_overlap; } static int pass_filter_test_ext(args_t *args, bcf1_t *line, annot_line_t *ann) { char *tmp; int i; for (i=0; in_ext; i++) { int j = args->ext[i].icol; if ( args->ext[i].ht_type==BCF_HT_STR ) args->ext_ptr[i] = args->ext[i].s = ann->cols[j]; else if ( args->ext[i].ht_type==BCF_HT_INT ) { args->ext[i].i = strtol(ann->cols[j],&tmp,10); if ( *tmp ) { if ( strcmp(".",ann->cols[j]) ) error("Error: could not parse the annotation file, expected an integer, found \"%s\"\n",ann->cols[j]); args->ext_ptr[i] = NULL; } else args->ext_ptr[i] = &args->ext[i].i; } else if ( args->ext[i].ht_type==BCF_HT_REAL ) { args->ext[i].f = strtod(ann->cols[j],&tmp); if ( *tmp ) { if ( strcmp(".",ann->cols[j]) ) error("Error: could not parse the annotation file, expected a float, found \"%s\"\n",ann->cols[j]); args->ext_ptr[i] = NULL; } else args->ext_ptr[i] = &args->ext[i].f; } } int pass = filter_test_ext(args->filter_ext,line,NULL,(const void**)args->ext_ptr); if ( args->filter_logic==FLT_EXCLUDE ) pass = pass ? 0 : 1; return pass; } static int annotate_from_tab(args_t *args, bcf1_t *line) { int i,j; int has_overlap = 0; // Buffer annotation lines. When multiple ALT alleles are present in the annotation file, at least one // must match some of the VCF alleles. If the append-missing mode is set (and REF+ALT is requested), the // buffered lines will annotate the VCF respecting the order in ALT and when no matching line is found // for an ALT, missing value is appended instead. int end_pos = line->pos + line->rlen - 1; buffer_annot_lines(args, line, line->pos, end_pos); args->nsrt_alines = 0; hts_expand(uint32_t,args->nalines,args->msrt_alines,args->srt_alines); if ( args->nalines >= 0xffff || line->n_allele >= 0xffff ) error("Error: too many alleles or annotation lines in the buffer at %s:%"PRId64" (todo:skip?)\n",bcf_seqname(args->hdr,line),(int64_t) line->pos+1); kstring_t match_end = {0,0,0}; if ( args->match_end>=0 && bcf_get_info_int32(args->hdr,line,"END",&args->tmpi,&args->mtmpi)==1 ) kputw(args->tmpi[0],&match_end); // Find matching lines for (i=0; inalines; i++) { if ( line->pos > args->alines[i].end || end_pos < args->alines[i].start ) continue; if ( args->ref_idx != -1 ) // REF+ALT matching requested { if ( line->pos!=args->alines[i].start || vcmp_set_ref(args->vcmp, line->d.allele[0], args->alines[i].als[0]) < 0 ) continue; // refs are not compatible for (j=1; jalines[i].nals; j++) { int ialt; if ( line->n_allele==1 && args->alines[i].als[j][0]=='.' && args->alines[i].als[j][1]==0 ) // match: no ALT allele in VCF and annot file has "." ialt = 0; else { ialt = vcmp_find_allele(args->vcmp, line->d.allele+1, line->n_allele - 1, args->alines[i].als[j]); if ( ialt < 0 ) continue; ialt++; } if ( args->match_id>=0 && !strstr_match(line->d.id,args->alines[i].cols[args->match_id]) ) continue; if ( args->match_end>=0 && match_end.l && strcmp(match_end.s,args->alines[i].cols[args->match_end]) ) continue; if ( args->filter_ext && !pass_filter_test_ext(args,line,&args->alines[i]) ) continue; args->srt_alines[args->nsrt_alines++] = (ialt<<16) | i; has_overlap = 1; break; } } else if ( args->filter_ext ) { if ( pass_filter_test_ext(args,line,&args->alines[i]) ) { args->srt_alines[args->nsrt_alines++] = (0xffff<<16) | i; has_overlap = 1; } } else // overlap, REF+ALT matching not requested { args->srt_alines[args->nsrt_alines++] = (0xffff<<16) | i; has_overlap = 1; } } free(match_end.s); if ( !has_overlap && args->filter_ext && !args->keep_sites ) return has_overlap; // Sort lines if needed if ( args->has_append_mode ) { // insertion sort by VCF ALT index (top bits) and alines index (low bits) uint32_t tmp; for (i=1; insrt_alines; i++) for (j=i; j>0 && args->srt_alines[j] < args->srt_alines[j-1]; j--) tmp = args->srt_alines[j], args->srt_alines[j] = args->srt_alines[j-1], args->srt_alines[j-1] = tmp; } // Annotate for (j=0; jncols; j++) args->cols[j].done = 0; int ialt_exp = 1; for (i=0; insrt_alines; i++) { int ialt = args->srt_alines[i] >> 16; int ilin = args->srt_alines[i] & 0xffff; if ( args->has_append_mode ) { if ( ialt_exp > ialt ) continue; // multiple annotation lines for the same position if ( ialt_exp < ialt ) { // REF+ALT matching requested, append-missing mode: insert "." if no annotation line was found for the ALT while ( ialt_exp++ < ialt ) { for (j=0; jncols; j++) { if ( args->cols[j].merge_method != MM_APPEND_MISSING ) continue; if ( args->cols[j].done==1 ) continue; if ( !args->cols[j].setter ) continue; int ret = args->cols[j].setter(args,line,&args->cols[j],args->aline_missing); if ( ret < 0 ) error("fixme: Could not set missing %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); if ( ret==0 ) args->cols[j].done = 1; } } } } for (j=0; jncols; j++) { if ( args->cols[j].done==1 ) continue; if ( !args->cols[j].setter ) continue; int ret = args->cols[j].setter(args,line,&args->cols[j],&args->alines[ilin]); if ( ret < 0 ) error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); if ( ret==0 ) args->cols[j].done = 1; } ialt_exp = ialt + 1; } if ( args->nsrt_alines ) { // In the append-missing mode fill missing values to all trailing ALTs, but only if at least one // record was found. Otherwise leave the row will be left without annotation. if ( args->has_append_mode && ialt_exp < line->n_allele ) { while ( ialt_exp++ < line->n_allele ) { for (j=0; jncols; j++) { if ( args->cols[j].merge_method != MM_APPEND_MISSING ) continue; if ( args->cols[j].done==1 ) continue; if ( !args->cols[j].setter ) continue; int ret = args->cols[j].setter(args,line,&args->cols[j],args->aline_missing); if ( ret < 0 ) error("fixme: Could not set missing %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); if ( ret==0 ) args->cols[j].done = 1; } } } // Flush for (j=0; jncols; j++) { if ( args->cols[j].done==1 || args->cols[j].merge_method == MM_FIRST ) continue; if ( !args->cols[j].setter ) continue; int ret = args->cols[j].setter(args,line,&args->cols[j],NULL); if ( ret < 0 ) error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); } } return has_overlap; } static int annotate_from_vcf(args_t *args, bcf1_t *line) { if ( !bcf_sr_has_line(args->files,1) ) return 0; int j; bcf1_t *aline = bcf_sr_get_line(args->files,1); for (j=0; jncols; j++) { if ( !args->cols[j].setter ) continue; if ( args->cols[j].setter(args,line,&args->cols[j],aline) ) error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); } return 1; } static int annotate_from_self(args_t *args, bcf1_t *line) { int j; for (j=0; jncols; j++) { if ( !args->cols[j].setter ) continue; if ( args->cols[j].setter(args,line,&args->cols[j],NULL) ) error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); } return 0; } static int annotate_line(args_t *args, bcf1_t *line) { args->current_rec = line; int i; for (i=0; inrm; i++) args->rm[i].handler(args, line, &args->rm[i]); int has_overlap = 0; if ( args->tgt_idx ) has_overlap = annotate_from_regidx(args,line); else if ( args->tgts ) has_overlap = annotate_from_tab(args,line); else if ( args->files->nreaders == 2 ) has_overlap = annotate_from_vcf(args,line); else if ( args->ncols ) has_overlap = annotate_from_self(args,line); if ( args->set_ids ) { args->tmpks.l = 0; convert_line(args->set_ids, line, &args->tmpks); if ( args->tmpks.l ) { int replace = 0; if ( args->set_ids_replace ) replace = 1; else if ( !line->d.id || (line->d.id[0]=='.' && !line->d.id[1]) ) replace = 1; if ( replace ) bcf_update_id(args->hdr_out,line,args->tmpks.s); } } if ( args->mark_sites ) { if ( !args->targets_fname ) has_overlap = 1; // ideally, we'd like to be far more general than this in future, see https://github.com/samtools/bcftools/issues/87 if ( args->mark_sites_logic==MARK_LISTED ) bcf_update_info_flag(args->hdr_out,line,args->mark_sites,NULL,has_overlap?1:0); else bcf_update_info_flag(args->hdr_out,line,args->mark_sites,NULL,has_overlap?0:1); } return has_overlap; } static void usage(args_t *args) { fprintf(stderr, "\n"); fprintf(stderr, "About: Annotate and edit VCF/BCF files.\n"); fprintf(stderr, "Usage: bcftools annotate [options] VCF\n"); fprintf(stderr, "\n"); fprintf(stderr, "Options:\n"); fprintf(stderr, " -a, --annotations FILE VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+\n"); fprintf(stderr, " -c, --columns LIST List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details\n"); fprintf(stderr, " -C, --columns-file FILE Read -c columns from FILE, one name per row, with optional --merge-logic TYPE: NAME[ TYPE]\n"); fprintf(stderr, " -e, --exclude EXPR Exclude sites for which the expression is true (see man page for details)\n"); fprintf(stderr, " --force Continue despite parsing error (at your own risk!)\n"); fprintf(stderr, " -H, --header-line STR Header line which should be appended to the VCF header, can be given multiple times\n"); fprintf(stderr, " -h, --header-lines FILE Lines which should be appended to the VCF header\n"); fprintf(stderr, " -I, --set-id [+]FORMAT Set ID column using a `bcftools query`-like expression, see man page for details\n"); fprintf(stderr, " -i, --include EXPR Select sites for which the expression is true (see man page for details)\n"); fprintf(stderr, " -k, --keep-sites Leave -i/-e sites unchanged instead of discarding them\n"); fprintf(stderr, " -l, --merge-logic TAG:TYPE Merge logic for multiple overlapping regions (see man page for details), EXPERIMENTAL\n"); fprintf(stderr, " -m, --mark-sites [+-]TAG Add INFO/TAG flag to sites which are (\"+\") or are not (\"-\") listed in the -a file\n"); fprintf(stderr, " --min-overlap ANN:VCF Required overlap as a fraction of variant in the -a file (ANN), the VCF (:VCF), or reciprocal (ANN:VCF)\n"); fprintf(stderr, " --no-version Do not append version and command line to the header\n"); fprintf(stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(stderr, " --pair-logic STR Matching records by , see man page for details [some]\n"); fprintf(stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(stderr, " -R, --regions-file FILE Restrict to regions listed in FILE\n"); fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " --rename-annots FILE Rename annotations: TYPE/old\\tnew, where TYPE is one of FILTER,INFO,FORMAT\n"); fprintf(stderr, " --rename-chrs FILE Rename sequences according to the mapping: old\\tnew\n"); fprintf(stderr, " -s, --samples [^]LIST Comma separated list of samples to annotate (or exclude with \"^\" prefix)\n"); fprintf(stderr, " -S, --samples-file [^]FILE File of samples to annotate (or exclude with \"^\" prefix)\n"); fprintf(stderr, " --single-overlaps Keep memory low by avoiding complexities arising from handling multiple overlapping intervals\n"); fprintf(stderr, " -x, --remove LIST List of annotations (e.g. ID,INFO/DP,FORMAT/DP,FILTER) to remove (or keep with \"^\" prefix). See man page for details\n"); fprintf(stderr, " --threads INT Number of extra output compression threads [0]\n"); fprintf(stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(stderr, "\n"); fprintf(stderr, "Examples:\n"); fprintf(stderr, " http://samtools.github.io/bcftools/howtos/annotate.html\n"); fprintf(stderr, "\n"); exit(1); } int main_vcfannotate(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->files = bcf_sr_init(); args->output_fname = "-"; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->ref_idx = args->alt_idx = args->chr_idx = args->beg_idx = args->end_idx = -1; args->set_ids_replace = 1; args->match_id = -1; args->match_end = -1; args->clevel = -1; args->pair_logic = -1; int regions_is_file = 0; int regions_overlap = 1; static struct option loptions[] = { {"keep-sites",no_argument,NULL,'k'}, {"mark-sites",required_argument,NULL,'m'}, {"set-id",required_argument,NULL,'I'}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"threads",required_argument,NULL,9}, {"annotations",required_argument,NULL,'a'}, {"merge-logic",required_argument,NULL,'l'}, {"collapse",required_argument,NULL,2}, {"pair-logic",required_argument,NULL,2}, {"include",required_argument,NULL,'i'}, {"exclude",required_argument,NULL,'e'}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,3}, {"remove",required_argument,NULL,'x'}, {"columns-file",required_argument,NULL,'C'}, {"columns",required_argument,NULL,'c'}, {"rename-annots",required_argument,NULL,11}, {"rename-chrs",required_argument,NULL,1}, {"header-lines",required_argument,NULL,'h'}, {"header-line",required_argument,NULL,'H'}, {"samples",required_argument,NULL,'s'}, {"samples-file",required_argument,NULL,'S'}, {"single-overlaps",no_argument,NULL,10}, {"min-overlap",required_argument,NULL,12}, {"no-version",no_argument,NULL,8}, {"force",no_argument,NULL,'f'}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "h:H:?o:O:r:R:a:x:c:C:i:e:S:s:I:m:kl:fW::",loptions,NULL)) >= 0) { switch (c) { case 'f': args->force = 1; break; case 'k': args->keep_sites = 1; break; case 'm': args->mark_sites_logic = MARK_LISTED; if ( optarg[0]=='+' ) args->mark_sites = optarg+1; else if ( optarg[0]=='-' ) { args->mark_sites = optarg+1; args->mark_sites_logic = MARK_UNLISTED; } else args->mark_sites = optarg; break; case 'l': if ( args->merge_method_str.l ) kputc(',',&args->merge_method_str); kputs(optarg,&args->merge_method_str); break; case 'I': args->set_ids_fmt = optarg; break; case 's': args->sample_names = optarg; break; case 'S': args->sample_names = optarg; args->sample_is_file = 1; break; case 'c': args->columns = strdup(optarg); break; case 'C': args->columns = strdup(optarg); args->columns_is_file = 1; break; case 'o': args->output_fname = optarg; break; case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } }; if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'x': args->remove_annots = optarg; break; case 'a': args->targets_fname = optarg; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 'h': args->header_fname = optarg; break; case 'H': args->header_lines = dbuf_push(args->header_lines,strdup(optarg)); break; case 1 : args->rename_chrs = optarg; break; case 2 : if ( args->pair_logic==-1 ) args->pair_logic = 0; if ( !strcmp(optarg,"snps") ) args->pair_logic |= BCF_SR_PAIR_SNP_REF; else if ( !strcmp(optarg,"indels") ) args->pair_logic |= BCF_SR_PAIR_INDEL_REF; else if ( !strcmp(optarg,"both") ) args->pair_logic |= BCF_SR_PAIR_BOTH_REF; else if ( !strcmp(optarg,"any") ) args->pair_logic |= BCF_SR_PAIR_ANY; else if ( !strcmp(optarg,"all") ) args->pair_logic |= BCF_SR_PAIR_ANY; else if ( !strcmp(optarg,"some") ) args->pair_logic |= BCF_SR_PAIR_SOME; else if ( !strcmp(optarg,"none") ) args->pair_logic = BCF_SR_PAIR_EXACT; else if ( !strcmp(optarg,"exact") ) args->pair_logic = BCF_SR_PAIR_EXACT; else error("The --pair-logic string \"%s\" not recognised.\n", optarg); break; case 3 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 8 : args->record_cmd_line = 0; break; case 10 : args->single_overlaps = 1; break; case 11 : args->rename_annots = optarg; break; case 12 : args->min_overlap_str = optarg; break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case '?': usage(args); break; default: error("Unknown argument: %s\n", optarg); } } char *fname = NULL; if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else usage(args); } else fname = argv[optind]; if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( args->targets_fname ) { htsFile *fp = hts_open(args->targets_fname,"r"); if ( !fp ) error("Failed to open %s\n", args->targets_fname); htsFormat type = *hts_get_format(fp); hts_close(fp); if ( type.format==vcf || type.format==bcf ) { args->tgts_is_vcf = 1; args->files->require_index = 1; bcf_sr_set_opt(args->files,BCF_SR_PAIR_LOGIC,args->pair_logic>=0 ? args->pair_logic : BCF_SR_PAIR_SOME); if ( args->min_overlap_str ) error("The --min-overlap option cannot be used when annotating from a VCF\n"); } } if ( args->min_overlap_str && args->single_overlaps ) error("The options --single-overlaps and --min-overlap cannot be combined\n"); if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n"); if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); static int line_errcode_warned = 0; init_data(args); while ( bcf_sr_next_line(args->files) ) { if ( !bcf_sr_has_line(args->files,0) ) continue; bcf1_t *line = bcf_sr_get_line(args->files,0); if ( line->errcode ) { if ( !args->force ) error("Encountered an error, cannot proceed. Please check the error output above.\n" "If feeling adventurous, use the --force option. (At your own risk!)\n"); else if ( !line_errcode_warned ) { fprintf(stderr, "Warning: Encountered an error, proceeding only because --force was given.\n" " Note that this can result in a segfault or a silent corruption of the output file!\n"); line_errcode_warned = 1; line->errcode = 0; } } if ( args->filter ) { int pass = filter_test(args->filter, line, NULL); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { if ( args->keep_sites && bcf_write1(args->out_fh, args->hdr_out, line)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args->output_fname); continue; } } int keep = annotate_line(args, line); if ( args->filter_ext && !args->keep_sites && !keep ) continue; if ( bcf_write1(args->out_fh, args->hdr_out, line)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args->output_fname); } destroy_data(args); bcf_sr_destroy(args->files); free(args); return 0; } pysam-0.23.0/bcftools/vcfannotate.c.pysam.c000066400000000000000000005124141475062545500206110ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfannotate.c -- Annotate and edit VCF/BCF files. Copyright (C) 2013-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "vcmp.h" #include "filter.h" #include "convert.h" #include "smpl_ilist.h" #include "regidx.h" #include "dbuf.h" struct _args_t; typedef struct _rm_tag_t { char *key; int hdr_id; void (*handler)(struct _args_t *, bcf1_t *, struct _rm_tag_t *); } rm_tag_t; typedef struct { char **cols; int ncols, mcols; char **als; int nals, mals; kstring_t line; int rid, start, end; } annot_line_t; #define REPLACE_MISSING (1<<0) // -c +TAG .. replace only missing values #define REPLACE_ALL (1<<1) // -c TAG .. replace both missing and existing values #define REPLACE_NON_MISSING (1<<2) // -c -TAG .. replace only if tgt is not missing #define SET_OR_APPEND (1<<3) // -c =TAG .. set new value if missing or non-existent, append otherwise #define MATCH_VALUE (1<<4) // -c ~ID .. do not set, just match the value #define CARRY_OVER_MISSING (1<<5) // -c .TAG .. carry over source missing values as well #define MM_FIRST 0 // if multiple annotation lines overlap a VCF record, use the first, discarding the rest #define MM_APPEND 1 // append, possibly multiple times #define MM_UNIQUE 2 // append, only unique values #define MM_SUM 3 #define MM_AVG 4 #define MM_MIN 5 #define MM_MAX 6 #define MM_APPEND_MISSING 7 // missing values will be transferred as well typedef struct _annot_col_t { int icol, replace, number; // number: one of BCF_VL_* types char *hdr_key_src, *hdr_key_dst; // The setters return 0 on successful update of the bcf record, negative value (bcf_update_* return status) on errors, // or 1 on (repeated partial updates) concluded with a src=NULL call int (*setter)(struct _args_t *, bcf1_t *dst, struct _annot_col_t *, void *src); // the last is the annotation line, either src bcf1_t or annot_line_t int (*getter)(struct _args_t *, bcf1_t *src, struct _annot_col_t *, void **ptr, int *mptr); int merge_method; // one of the MM_* defines khash_t(str2int) *mm_str_hash; // lookup table to ensure uniqueness of added string values kstring_t mm_kstr; size_t mm_dbl_nalloc, // the allocated size --merge-logic values array mm_dbl_nused, // the number of used elements in the mm_dbl array mm_dbl_ndat; // the number of merged rows (for calculating the average) double *mm_dbl; void *ptr; int mptr, done; } annot_col_t; typedef struct { char *name; // column name int ht_type; // type, one of BCF_HT_STR,BCF_HT_INT,BCF_HT_REAL int icol; // index of the annotation column to use union { // memory area with the current annotation value to pass to filter_test_ext int i; float f; char *s; }; } ext_t; // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 #define MARK_LISTED 1 #define MARK_UNLISTED 2 typedef struct _args_t { bcf_srs_t *files; bcf_hdr_t *hdr, *hdr_out, *tgts_hdr; htsFile *out_fh; int output_type, n_threads, clevel; bcf_sr_regions_t *tgts; char *index_fn; int write_index; regidx_t *tgt_idx; // keep everything in memory only with .tab annotation file and -c BEG,END columns regitr_t *tgt_itr; int tgt_is_bed; filter_t *filter, *filter_ext; // only one is initialized, the latter contains external values to set dynamically on the fly char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE int keep_sites; rm_tag_t *rm; // tags scheduled for removal int nrm; int flt_keep_pass; // when all filters removed, reset to PASS vcmp_t *vcmp; // for matching annotation and VCF lines by allele annot_line_t *alines; // buffered annotation lines annot_line_t *aline_missing; uint32_t *srt_alines; // sorted indexes (iALT<<16 || iAline) int nalines, malines, nsrt_alines, msrt_alines; int ref_idx, alt_idx, chr_idx, beg_idx, end_idx; // -1 if not present annot_col_t *cols; // column indexes and setters int ncols; int match_id; // set iff `-c ~ID` given, -1 otherwise int match_end; // set iff `-c ~INFO/END` is given, -1 otherwise char *set_ids_fmt; convert_t *set_ids; int set_ids_replace; // external values for dynamic -i/-e expressions int n_ext; ext_t *ext; void **ext_ptr; int nsmpl_annot; int *sample_map, nsample_map, sample_is_file; // map[idst] -> isrc uint8_t *src_smpl_pld, *dst_smpl_pld; // for Number=G format fields int mtmpi, mtmpf, mtmps; int mtmpi2, mtmpf2, mtmps2; int mtmpi3, mtmpf3, mtmps3; int32_t *tmpi, *tmpi2, *tmpi3; float *tmpf, *tmpf2, *tmpf3; char *tmps, *tmps2, **tmpp, **tmpp2; kstring_t tmpks; char **argv, *output_fname, *targets_fname, *regions_list, *header_fname; char *remove_annots, *columns, *rename_chrs, *rename_annots, *sample_names, *mark_sites; char **rename_annots_map; char *min_overlap_str; float min_overlap_ann, min_overlap_vcf; int rename_annots_nmap; kstring_t merge_method_str; int argc, drop_header, record_cmd_line, tgts_is_vcf, mark_sites_logic, force, single_overlaps; int columns_is_file, has_append_mode, pair_logic; dbuf_t *header_lines; bcf1_t *current_rec; // current record for local setters } args_t; char *msprintf(const char *fmt, ...); int parse_with_payload(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr) { args_t *args = (args_t*) usr; int ret = args->tgt_is_bed ? regidx_parse_bed(line, chr_beg, chr_end, beg, end, NULL, NULL) : regidx_parse_tab(line, chr_beg, chr_end, beg, end, NULL, NULL); if ( ret<0 ) return ret; *((char **)payload) = strdup(line); return 0; } void free_payload(void *payload) { char *str = *((char**)payload); free(str); } void remove_id(args_t *args, bcf1_t *line, rm_tag_t *tag) { bcf_update_id(args->hdr,line,NULL); } void remove_filter(args_t *args, bcf1_t *line, rm_tag_t *tag) { if ( tag->key && tag->hdr_id<0 ) { error("Error: Cannot proceed, not even with the --force option, bad things could happen.\n" " Note that \"bcftools annotate -x FILTER\" can be used to remove ALL filters.\n" " Even better, use \"bcftools view -h\" and \"bcftools reheader\" to fix the header!\n" ); } if ( !tag->key ) bcf_update_filter(args->hdr, line, NULL, args->flt_keep_pass); else bcf_remove_filter(args->hdr, line, tag->hdr_id, args->flt_keep_pass); } void remove_qual(args_t *args, bcf1_t *line, rm_tag_t *tag) { bcf_float_set_missing(line->qual); } void remove_info(args_t *args, bcf1_t *line, rm_tag_t *tag) { // remove all INFO fields if ( !(line->unpacked & BCF_UN_INFO) ) bcf_unpack(line, BCF_UN_INFO); int i; for (i=0; in_info; i++) { bcf_info_t *inf = &line->d.info[i]; if ( !strcmp("END",bcf_hdr_int2id(args->hdr,BCF_DT_ID,inf->key)) ) line->rlen = line->n_allele ? strlen(line->d.allele[0]) : 0; if ( inf->vptr_free ) { free(inf->vptr - inf->vptr_off); inf->vptr_free = 0; } line->d.shared_dirty |= BCF1_DIRTY_INF; inf->vptr = NULL; inf->vptr_off = inf->vptr_len = 0; } } void remove_info_tag(args_t *args, bcf1_t *line, rm_tag_t *tag) { bcf_update_info(args->hdr, line, tag->key, NULL, 0, BCF_HT_INT); // the type does not matter with n=0 } void remove_format_tag(args_t *args, bcf1_t *line, rm_tag_t *tag) { bcf_update_format(args->hdr, line, tag->key, NULL, 0, BCF_HT_INT); // the type does not matter with n=0 } void remove_format(args_t *args, bcf1_t *line, rm_tag_t *tag) { // remove all FORMAT fields except GT if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT); int i; for (i=0; in_fmt; i++) { bcf_fmt_t *fmt = &line->d.fmt[i]; const char *key = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id); if ( key[0]=='G' && key[1]=='T' && !key[2] ) continue; if ( fmt->p_free ) { free(fmt->p - fmt->p_off); fmt->p_free = 0; } line->d.indiv_dirty = 1; fmt->p = NULL; } } #include "htslib/khash.h" KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t) typedef khash_t(vdict) vdict_t; static void remove_hdr_lines(bcf_hdr_t *hdr, int type) { int i = 0, nrm = 0; while ( inhrec ) { if ( hdr->hrec[i]->type!=type ) { i++; continue; } bcf_hrec_t *hrec = hdr->hrec[i]; if ( type==BCF_HL_FMT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG ) { // everything except FORMAT/GT int id = bcf_hrec_find_key(hrec, "ID"); if ( id>=0 ) { if ( type==BCF_HL_FMT && !strcmp(hrec->vals[id],"GT") ) { i++; continue; } vdict_t *d = type==BCF_HL_CTG ? (vdict_t*)hdr->dict[BCF_DT_CTG] : (vdict_t*)hdr->dict[BCF_DT_ID]; khint_t k = kh_get(vdict, d, hdr->hrec[i]->vals[id]); kh_val(d, k).hrec[type==BCF_HL_CTG?0:type] = NULL; kh_val(d, k).info[type] |= 0xf; } } nrm++; hdr->nhrec--; if ( i < hdr->nhrec ) memmove(&hdr->hrec[i],&hdr->hrec[i+1],(hdr->nhrec-i)*sizeof(bcf_hrec_t*)); bcf_hrec_destroy(hrec); } if ( nrm ) { if (bcf_hdr_sync(hdr) < 0) error_errno("[%s] Failed to update header", __func__); } } static void init_remove_annots(args_t *args) { int keep_info = 0, keep_fmt = 0, keep_flt = 0; void *keep = khash_str2int_init(); kstring_t str = {0,0,0}; char *ss = args->remove_annots; int i, ntags, needs_info = 0; if ( args->set_ids ) { const char **tags = convert_list_used_tags(args->set_ids,&ntags); for (i=0; inrm++; args->rm = (rm_tag_t*) realloc(args->rm,sizeof(rm_tag_t)*args->nrm); rm_tag_t *tag = &args->rm[args->nrm-1]; tag->key = NULL; int type = BCF_HL_GEN; if ( !strncasecmp("INFO/",ss,5) ) { type = BCF_HL_INFO; ss += 5; } else if ( !strncasecmp("INF/",ss,4) ) { type = BCF_HL_INFO; ss += 4; } else if ( !strncasecmp("FORMAT/",ss,7) ) { type = BCF_HL_FMT; ss += 7; } else if ( !strncasecmp("FMT/",ss,4) ) { type = BCF_HL_FMT; ss += 4; } else if ( !strncasecmp("FILTER/",ss,7) ) { type = BCF_HL_FLT; ss += 7; } else if ( !strncasecmp("^INFO/",ss,6) ) { type = BCF_HL_INFO; ss += 6; keep_info = 1; } else if ( !strncasecmp("^INF/",ss,5) ) { type = BCF_HL_INFO; ss += 5; keep_info = 1; } else if ( !strncasecmp("^FORMAT/",ss,8) ) { type = BCF_HL_FMT; ss += 8; keep_fmt = 1; } else if ( !strncasecmp("^FMT/",ss,5) ) { type = BCF_HL_FMT; ss += 5; keep_fmt = 1; } else if ( !strncasecmp("^FILTER/",ss,8) ) { type = BCF_HL_FLT; ss += 8; keep_flt = 1; } char *se = ss; while ( *se && *se!=',' ) se++; str.l = 0; kputsn(ss, se-ss, &str); if ( type==BCF_HL_FLT ) { if ( !keep_flt ) { args->flt_keep_pass = 1; tag->handler = remove_filter; tag->key = strdup(str.s); tag->hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, tag->key); if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FLT,tag->hdr_id) ) { if ( args->keep_sites ) error("Error: The filter \"%s\" is not defined in the header, cannot use the -k option\n", str.s); else fprintf(bcftools_stderr,"Warning: The filter \"%s\" is not defined in the header\n", str.s); } else if ( !args->keep_sites ) bcf_hdr_remove(args->hdr_out,BCF_HL_FLT,tag->key); } else { int value, ret = khash_str2int_get(keep, str.s, &value); if ( ret==-1 ) khash_str2int_set(keep, strdup(str.s),1<nrm--; } } else if ( type!=BCF_HL_GEN ) { int id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,str.s); if ( !bcf_hdr_idinfo_exists(args->hdr,type,id) ) { if ( args->keep_sites ) error("Error: The tag \"%s\" is not defined in the header, cannot use the -k option\n", str.s); else fprintf(bcftools_stderr,"Warning: The tag \"%s\" not defined in the header\n", str.s); tag->key = strdup(str.s); if ( type==BCF_HL_INFO ) { tag->handler = remove_info_tag; if ( needs_info ) error("Error: `--remove INFO/%s` is executed first, cannot combine with `--set-id %s`\n",tag->key,args->set_ids_fmt); } else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag; } else if ( (type==BCF_HL_FMT && keep_fmt) || (type==BCF_HL_INFO && keep_info) ) { int value, ret = khash_str2int_get(keep, str.s, &value); if ( ret==-1 ) khash_str2int_set(keep, strdup(str.s),1<nrm--; } else { tag->key = strdup(str.s); if ( type==BCF_HL_INFO ) { tag->handler = remove_info_tag; if ( needs_info ) error("Error: `--remove INFO/%s` is executed first, cannot combine with `--set-id %s`\n",tag->key,args->set_ids_fmt); } else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag; if ( !args->keep_sites ) bcf_hdr_remove(args->hdr_out,type,tag->key); } } else if ( !strcasecmp("ID",str.s) ) tag->handler = remove_id; else if ( !strcasecmp("FILTER",str.s) ) { tag->handler = remove_filter; if ( !args->keep_sites ) remove_hdr_lines(args->hdr_out,BCF_HL_FLT); } else if ( !strcasecmp("QUAL",str.s) ) tag->handler = remove_qual; else if ( !strcasecmp("INFO",str.s) ) { if ( needs_info ) error("Error: `--remove INFO` is executed first, cannot combine with `--set-id %s`\n",args->set_ids_fmt); tag->handler = remove_info; if ( !args->keep_sites ) remove_hdr_lines(args->hdr_out,BCF_HL_INFO); } else if ( !strcasecmp("FMT",str.s) || !strcasecmp("FORMAT",str.s) ) { tag->handler = remove_format; if ( !args->keep_sites ) remove_hdr_lines(args->hdr_out,BCF_HL_FMT); } else if ( str.l ) { int id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, str.s); if ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_INFO,id) ) error("Error: did you mean INFO/%s?\n",str.s); if ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,id) ) error("Error: did you mean FORMAT/%s?\n",str.s); if ( !args->keep_sites ) { if ( str.s[0]=='#' && str.s[1]=='#' ) bcf_hdr_remove(args->hdr_out,BCF_HL_GEN,str.s+2); else bcf_hdr_remove(args->hdr_out,BCF_HL_STR,str.s); } args->nrm--; } ss = *se ? se+1 : se; } free(str.s); if ( keep_flt || keep_info || keep_fmt ) { int j; for (j=0; jhdr->nhrec; j++) { bcf_hrec_t *hrec = args->hdr->hrec[j]; if ( hrec->type!=BCF_HL_FLT && hrec->type!=BCF_HL_INFO && hrec->type!=BCF_HL_FMT ) continue; if ( !keep_flt && hrec->type==BCF_HL_FLT ) continue; if ( !keep_info && hrec->type==BCF_HL_INFO ) continue; if ( !keep_fmt && hrec->type==BCF_HL_FMT ) continue; int k = bcf_hrec_find_key(hrec,"ID"); assert( k>=0 ); // this should always be true for valid VCFs int value, ret = khash_str2int_get(keep,hrec->vals[k],&value); if ( ret==0 && value>>hrec->type ) // keep { if ( hrec->type==BCF_HL_FLT && !strcmp("PASS",hrec->vals[k]) ) args->flt_keep_pass = 1; continue; } args->nrm++; args->rm = (rm_tag_t*) realloc(args->rm,sizeof(rm_tag_t)*args->nrm); rm_tag_t *tag = &args->rm[args->nrm-1]; if ( hrec->type==BCF_HL_INFO ) tag->handler = remove_info_tag; else if ( hrec->type==BCF_HL_FMT ) tag->handler = remove_format_tag; else { tag->handler = remove_filter; tag->hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, hrec->vals[k]); } tag->key = strdup(hrec->vals[k]); if ( !args->keep_sites ) bcf_hdr_remove(args->hdr_out,hrec->type,tag->key); } } khash_str2int_destroy_free(keep); if ( !args->nrm ) error("No matching tag in -x %s\n", args->remove_annots); if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update header", __func__); } static void init_header_lines(args_t *args) { if ( args->header_fname ) { htsFile *file = hts_open(args->header_fname, "rb"); if ( !file ) error("Error reading %s\n", args->header_fname); kstring_t str = {0,0,0}; while ( hts_getline(file, KS_SEP_LINE, &str) > 0 ) { if ( bcf_hdr_append(args->hdr_out,str.s) ) error("Could not parse %s: %s\n", args->header_fname, str.s); bcf_hdr_append(args->hdr,str.s); // the input file may not have the header line if run with -h (and nothing else) } if ( hts_close(file)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->header_fname); free(str.s); } if ( args->header_lines ) { int i, n = dbuf_n(args->header_lines); for (i=0; iheader_lines,i); if ( bcf_hdr_append(args->hdr_out,line) ) error("Could not parse the header line: %s\n", line); bcf_hdr_append(args->hdr,line); // the input file may not have the header line if run with -H (and nothing else) } dbuf_destroy_free(args->header_lines); args->header_lines = NULL; } if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update output header", __func__); if (bcf_hdr_sync(args->hdr) < 0) error_errno("[%s] Failed to update input header", __func__); } static int vcf_getter_info_str2str(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr) { return bcf_get_info_string(args->tgts_hdr,rec,col->hdr_key_src,ptr,mptr); } static int vcf_getter_id2str(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr) { char *str = *((char**)ptr); int i, len = strlen(rec->d.id); if ( len >= *mptr ) str = realloc(str, len+1); for (i=0; id.id[i]==';' ? ',' : rec->d.id[i]; str[len] = 0; *((char**)ptr) = str; *mptr = len+1; return len; } inline static int vcf_getter_filter2str_core(bcf_hdr_t *hdr, bcf1_t *rec, char **ptr, int *mptr) { if ( !(rec->unpacked & BCF_UN_FLT) ) bcf_unpack(rec, BCF_UN_FLT); kstring_t str; str.s = *ptr; str.m = *mptr; str.l = 0; int i; if ( rec->d.n_flt ) { for (i=0; id.n_flt; i++) { if (i) kputc(',', &str); kputs(bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.flt[i]), &str); } } else kputc('.', &str); *ptr = str.s; *mptr = str.m; return str.l; } static int vcf_getter_filter2str_local(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr) { return vcf_getter_filter2str_core(args->hdr_out, args->current_rec, (char**)ptr, mptr); } static int vcf_getter_filter2str(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr) { return vcf_getter_filter2str_core(args->tgts_hdr, rec, (char**)ptr, mptr); } static int setter_filter(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( !data ) error("Error: the --merge-logic option cannot be used with FILTER (yet?)\n"); // note: so far this works only with one filter, not a list of filters annot_line_t *tab = (annot_line_t*) data; if ( tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) // don't overwrite with a missing value unless asked { if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_update_filter(args->hdr_out,line,NULL,0); return 0; } hts_expand(int,1,args->mtmpi,args->tmpi); args->tmpi[0] = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, tab->cols[col->icol]); if ( args->tmpi[0]<0 ) error("The FILTER \"%s\" is not defined in the header, was the -h option provided?\n", tab->cols[col->icol]); if ( col->replace & SET_OR_APPEND ) return bcf_add_filter(args->hdr_out,line,args->tmpi[0]); if ( !(col->replace & REPLACE_MISSING) ) { bcf_update_filter(args->hdr_out,line,NULL,0); return bcf_update_filter(args->hdr_out,line,args->tmpi,1); } // only update missing FILTER if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT); if ( !line->d.n_flt ) return bcf_update_filter(args->hdr_out,line,args->tmpi,1); return 0; } static int vcf_setter_filter(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { int i, ret = 0; bcf1_t *rec = (bcf1_t*) data; if ( !(rec->unpacked & BCF_UN_FLT) ) bcf_unpack(rec, BCF_UN_FLT); if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT); if ( !rec->d.n_flt ) // don't overwrite with a missing value unless asked { if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_update_filter(args->hdr_out,line,NULL,0); return 0; } if ( col->replace & (SET_OR_APPEND|REPLACE_MISSING) ) { if ( (col->replace & REPLACE_MISSING) && line->d.n_flt ) return 0; // only update missing FILTER for (i=0; id.n_flt; i++) { const char *flt = bcf_hdr_int2id(args->files->readers[1].header, BCF_DT_ID, rec->d.flt[i]); if ( bcf_add_filter(args->hdr_out,line,bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt)) < 0 ) ret = -1; } return ret; } hts_expand(int,rec->d.n_flt,args->mtmpi,args->tmpi); for (i=0; id.n_flt; i++) { const char *flt = bcf_hdr_int2id(args->files->readers[1].header, BCF_DT_ID, rec->d.flt[i]); args->tmpi[i] = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt); } bcf_update_filter(args->hdr_out,line,NULL,0); return bcf_update_filter(args->hdr_out,line,args->tmpi,rec->d.n_flt); } static int setter_pos(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { annot_line_t *tab = (annot_line_t*) data; if ( tab->cols[col->icol] && tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) return 0; // don't replace with "." char *tmp; int pos = strtol(tab->cols[col->icol], &tmp, 10); if ( tmp==tab->cols[col->icol] ) error("Could not parse -POS at %s:%"PRId64" .. [%s]\n",bcf_seqname(args->hdr,line),(int64_t)line->pos+1,tab->cols[col->icol]); line->pos = pos - 1; return 0; } static int setter_id(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( !data ) error("Error: the --merge-logic option cannot be used with ID (yet?)\n"); if ( col->replace & MATCH_VALUE ) return 0; // possible cases: // IN ANNOT OUT ACHIEVED_BY // x y x -c +ID // x y y -c ID // x y x,y -c =ID // x . x -c +ID, ID // x . . -x ID // . y y -c +ID, -c ID // annot_line_t *tab = (annot_line_t*) data; if ( tab->cols[col->icol] && tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) return 0; // don't replace with "." if ( col->replace & SET_OR_APPEND ) return bcf_add_id(args->hdr_out,line,tab->cols[col->icol]); if ( !(col->replace & REPLACE_MISSING) ) return bcf_update_id(args->hdr_out,line,tab->cols[col->icol]); // running with +ID, only update missing ids if ( !line->d.id || (line->d.id[0]=='.' && !line->d.id[1]) ) return bcf_update_id(args->hdr_out,line,tab->cols[col->icol]); return 0; } static int vcf_setter_id(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( col->replace & MATCH_VALUE ) return 0; bcf1_t *rec = (bcf1_t*) data; char *id; if ( col->getter ) { int nret = col->getter(args,rec,col,&col->ptr,&col->mptr); id = (char*) col->ptr; if ( nret<=0 || (nret==1 && *id=='.') ) return 0; // don't replace with "." } else { if ( rec->d.id && rec->d.id[0]=='.' && !rec->d.id[1] ) return 0; // don't replace with "." id = rec->d.id; } if ( col->replace & SET_OR_APPEND ) return bcf_add_id(args->hdr_out,line,id); if ( !(col->replace & REPLACE_MISSING) ) return bcf_update_id(args->hdr_out,line,id); // running with +ID, only update missing ids if ( !line->d.id || (line->d.id[0]=='.' && !line->d.id[1]) ) return bcf_update_id(args->hdr_out,line,id); return 0; } static int vcf_setter_ref(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; if ( !strcmp(rec->d.allele[0],line->d.allele[0]) ) return 0; // no update necessary const char **als = (const char**) malloc(sizeof(char*)*line->n_allele); als[0] = rec->d.allele[0]; int i; for (i=1; in_allele; i++) als[i] = line->d.allele[i]; int ret = bcf_update_alleles(args->hdr_out, line, als, line->n_allele); free(als); return ret; } static int vcf_setter_alt(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; int i; if ( line->n_allele>1 && (col->replace & REPLACE_MISSING) ) return 0; if ( rec->n_allele==line->n_allele ) { for (i=1; in_allele; i++) if ( strcmp(rec->d.allele[i],line->d.allele[i]) ) break; if ( i==rec->n_allele ) return 0; // no update necessary } const char **als = (const char**) malloc(sizeof(char*)*rec->n_allele); als[0] = line->d.allele[0]; for (i=1; in_allele; i++) als[i] = rec->d.allele[i]; int ret = bcf_update_alleles(args->hdr_out, line, als, rec->n_allele); free(als); return ret; } static int setter_qual(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( !data ) error("Error: the --merge-logic option cannot be used with QUAL (yet?)\n"); annot_line_t *tab = (annot_line_t*) data; char *str = tab->cols[col->icol]; if ( str[0]=='.' && str[1]==0 ) // don't overwrite with a missing value unless asked { if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_float_set_missing(line->qual); return 0; } if ( (col->replace & REPLACE_MISSING) && !bcf_float_is_missing(line->qual) ) return 0; line->qual = strtod(str, &str); if ( str == tab->cols[col->icol] ) error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]); return 0; } static int vcf_setter_qual(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; if ( bcf_float_is_missing(rec->qual) ) // don't overwrite with a missing value unless asked { if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_float_set_missing(line->qual); return 0; } if ( (col->replace & REPLACE_MISSING) && !bcf_float_is_missing(line->qual) ) return 0; line->qual = rec->qual; return 0; } static int setter_info_flag(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( !data ) error("Error: the --merge-logic option cannot be used with INFO type=Flag (yet?)\n"); annot_line_t *tab = (annot_line_t*) data; char *str = tab->cols[col->icol]; if ( str[0]=='.' && str[1]==0 ) // don't overwrite with a missing value unless asked { if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,0); return 0; } if ( str[0]=='1' && str[1]==0 ) return bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,1); if ( str[0]=='0' && str[1]==0 ) return bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,0); error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]); return -1; } static int vcf_setter_info_flag(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; int flag = bcf_get_info_flag(args->files->readers[1].header,rec,col->hdr_key_src,NULL,NULL); bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,flag); return 0; } static int setter_ARinfo_int32(args_t *args, bcf1_t *line, annot_col_t *col, int nals, char **als, int ntmpi) { if ( col->number==BCF_VL_A && ntmpi!=nals-1 && (ntmpi!=1 || args->tmpi[0]!=bcf_int32_missing || args->tmpi[1]!=bcf_int32_vector_end) ) error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", ntmpi,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); else if ( col->number==BCF_VL_R && ntmpi!=nals && (ntmpi!=1 || args->tmpi[0]!=bcf_int32_missing || args->tmpi[1]!=bcf_int32_vector_end) ) error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", ntmpi,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int ndst = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele; int *map = vcmp_map_ARvalues(args->vcmp,ndst,nals,als,line->n_allele,line->d.allele); if ( !map ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); // fill in any missing values in the target VCF (or all, if not present) int ntmpi2 = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpi2, &args->mtmpi2); if ( ntmpi2 < ndst ) hts_expand(int32_t,ndst,args->mtmpi2,args->tmpi2); int i; for (i=0; itmpi2[i] = bcf_int32_missing; continue; } if ( ntmpi2==ndst && (col->replace & REPLACE_MISSING) && args->tmpi2[i]!=bcf_int32_missing && args->tmpi2[i]!=bcf_int32_vector_end ) continue; args->tmpi2[i] = args->tmpi[ map[i] ]; } return bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi2,ndst); } static int setter_info_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { annot_line_t *tab = (annot_line_t*) data; // This is a bit hacky, only to reuse existing code with minimal changes: // -c =TAG will now behave as -l TAG:APPEND for integers if ( col->replace & SET_OR_APPEND ) col->merge_method=MM_APPEND; if ( !tab ) { if ( col->merge_method!=MM_SUM && col->merge_method!=MM_AVG && col->merge_method!=MM_MIN && col->merge_method!=MM_MAX && col->merge_method!=MM_APPEND && col->merge_method!=MM_APPEND_MISSING ) error("Error: at the moment only the sum,avg,min,max,append,append-missing options are supported with --merge-logic for INFO type=Integer\n"); } int i,ntmpi = 0; if ( (col->replace & SET_OR_APPEND) && !col->mm_dbl_nused ) { ntmpi = bcf_get_info_int32(args->hdr, line, col->hdr_key_dst, &args->tmpi, &args->mtmpi); if ( ntmpi>0 && (args->tmpi[0]!=bcf_int32_missing || (col->replace & CARRY_OVER_MISSING)) ) { col->mm_dbl_nused = col->mm_dbl_ndat = ntmpi; hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl); for (i=0; imm_dbl[i] = args->tmpi[i]; col->mm_dbl_ndat = 1; } ntmpi = 0; } if ( tab ) // has data, not flushing yet { char *str = tab->cols[col->icol], *end = str; if ( str[0]=='.' && str[1]==0 && col->merge_method!=MM_APPEND_MISSING && !(col->replace & CARRY_OVER_MISSING) ) return 1; while ( *end ) { ntmpi++; hts_expand(int32_t,ntmpi,args->mtmpi,args->tmpi); if ( str[0]=='.' && (str[1]==0 || str[1]==',') ) { if ( col->merge_method==MM_APPEND_MISSING || (col->replace & CARRY_OVER_MISSING) ) args->tmpi[ntmpi-1] = bcf_int32_missing; else ntmpi--; if ( str[1]==0 ) end = str+1; str += 2; } else { args->tmpi[ntmpi-1] = strtol(str, &end, 10); if ( end==str ) error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]); str = end+1; } } if ( col->merge_method!=MM_FIRST ) { if ( !col->mm_dbl_nused ) { col->mm_dbl_nused = ntmpi; hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl); for (i=0; imm_dbl[i] = args->tmpi[i]; } else { if ( col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING ) { int nori = col->mm_dbl_nused; col->mm_dbl_nused += ntmpi; hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl); for (i=0; imm_dbl[i+nori] = args->tmpi[i]; } else { if ( ntmpi!=col->mm_dbl_nused ) error("Error: cannot merge fields of unequal length\n"); if ( col->merge_method==MM_SUM || col->merge_method==MM_AVG ) for (i=0; imm_dbl[i] += args->tmpi[i]; else if ( col->merge_method==MM_MIN ) for (i=0; imm_dbl[i] > args->tmpi[i] ) col->mm_dbl[i] = args->tmpi[i]; } else if ( col->merge_method==MM_MAX ) for (i=0; imm_dbl[i] < args->tmpi[i] ) col->mm_dbl[i] = args->tmpi[i]; } } } col->mm_dbl_ndat++; return 1; } } else if ( col->merge_method==MM_SUM || col->merge_method==MM_MIN || col->merge_method==MM_MAX || col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING ) { ntmpi = col->mm_dbl_nused; hts_expand(int32_t,ntmpi,args->mtmpi,args->tmpi); for (i=0; itmpi[i] = col->mm_dbl[i]; col->mm_dbl_nused = col->mm_dbl_ndat = 0; } else if ( col->merge_method==MM_AVG ) { ntmpi = col->mm_dbl_nused; hts_expand(int32_t,ntmpi,args->mtmpi,args->tmpi); for (i=0; itmpi[i] = col->mm_dbl[i]/col->mm_dbl_ndat; col->mm_dbl_nused = col->mm_dbl_ndat = 0; } if ( col->number==BCF_VL_A || col->number==BCF_VL_R ) return setter_ARinfo_int32(args,line,col,tab->nals,tab->als,ntmpi); if ( col->replace & REPLACE_MISSING ) { int ret = bcf_get_info_int32(args->hdr, line, col->hdr_key_dst, &args->tmpi2, &args->mtmpi2); if ( ret>0 && args->tmpi2[0]!=bcf_int32_missing ) return 0; } return bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi,ntmpi); } static int vcf_setter_info_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; int ntmpi = bcf_get_info_int32(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpi,&args->mtmpi); if ( ntmpi < 0 ) return 0; // nothing to add if ( col->number==BCF_VL_A || col->number==BCF_VL_R ) return setter_ARinfo_int32(args,line,col,rec->n_allele,rec->d.allele,ntmpi); if ( col->replace & REPLACE_MISSING ) { int ret = bcf_get_info_int32(args->hdr, line, col->hdr_key_dst, &args->tmpi2, &args->mtmpi2); if ( ret>0 && args->tmpi2[0]!=bcf_int32_missing ) return 0; } return bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi,ntmpi); } static int setter_ARinfo_real(args_t *args, bcf1_t *line, annot_col_t *col, int nals, char **als, int ntmpf) { if ( col->number==BCF_VL_A && ntmpf!=nals-1 && (ntmpf!=1 || !bcf_float_is_missing(args->tmpf[0]) || !bcf_float_is_vector_end(args->tmpf[0])) ) error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", ntmpf,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); else if ( col->number==BCF_VL_R && ntmpf!=nals && (ntmpf!=1 || !bcf_float_is_missing(args->tmpf[0]) || !bcf_float_is_vector_end(args->tmpf[0])) ) error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", ntmpf,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int ndst = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele; int *map = vcmp_map_ARvalues(args->vcmp,ndst,nals,als,line->n_allele,line->d.allele); if ( !map ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); // fill in any missing values in the target VCF (or all, if not present) int ntmpf2 = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf2, &args->mtmpf2); if ( ntmpf2 < ndst ) hts_expand(float,ndst,args->mtmpf2,args->tmpf2); int i; for (i=0; itmpf2[i]); continue; } if ( ntmpf2==ndst && (col->replace & REPLACE_MISSING) && !bcf_float_is_missing(args->tmpf2[i]) && !bcf_float_is_vector_end(args->tmpf2[i]) ) continue; args->tmpf2[i] = args->tmpf[ map[i] ]; } return bcf_update_info_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf2,ndst); } static int setter_info_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { annot_line_t *tab = (annot_line_t*) data; // This is a bit hacky, only to reuse existing code with minimal changes: // -c =TAG will now behave as -l TAG:APPEND for floats if ( col->replace & SET_OR_APPEND ) col->merge_method=MM_APPEND; if ( !tab ) { if ( col->merge_method!=MM_SUM && col->merge_method!=MM_AVG && col->merge_method!=MM_MIN && col->merge_method!=MM_MAX && col->merge_method!=MM_APPEND && col->merge_method!=MM_APPEND_MISSING ) error("Error: at the moment only the sum,avg,min,max,append,append-missing options are supported with --merge-logic for INFO type=Float\n"); } int i,ntmpf = 0; if ( (col->replace & SET_OR_APPEND) && !col->mm_dbl_nused ) { ntmpf = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf, &args->mtmpf); if ( ntmpf>0 && (!bcf_float_is_missing(args->tmpf[0]) || (col->replace & CARRY_OVER_MISSING)) ) { col->mm_dbl_nused = ntmpf; hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl); for (i=0; itmpf[i]) ) bcf_double_set_missing(col->mm_dbl[i]); else col->mm_dbl[i] = args->tmpf[i]; col->mm_dbl_ndat = 1; } ntmpf = 0; } if ( tab ) // data row, not just flushing { char *str = tab->cols[col->icol], *end = str; if ( str[0]=='.' && str[1]==0 && col->merge_method!=MM_APPEND_MISSING && !(col->replace & CARRY_OVER_MISSING) ) return 1; while ( *end ) { ntmpf++; hts_expand(float,ntmpf,args->mtmpf,args->tmpf); if ( str[0]=='.' && (str[1]==0 || str[1]==',') ) { if ( col->merge_method==MM_APPEND_MISSING || (col->replace & CARRY_OVER_MISSING) ) bcf_float_set_missing(args->tmpf[ntmpf-1]); else ntmpf--; if ( str[1]==0 ) end = str+1; str += 2; } else { args->tmpf[ntmpf-1] = strtod(str, &end); if ( end==str ) error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]); str = end+1; } } if ( col->merge_method!=MM_FIRST ) { if ( !col->mm_dbl_nused ) { col->mm_dbl_nused = ntmpf; hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl); for (i=0; itmpf[i]) ) bcf_double_set_missing(col->mm_dbl[i]); else col->mm_dbl[i] = args->tmpf[i]; } } else { if ( col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING ) { int nori = col->mm_dbl_nused; col->mm_dbl_nused += ntmpf; hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl); for (i=0; itmpf[i]) ) bcf_double_set_missing(col->mm_dbl[i+nori]); else col->mm_dbl[i+nori] = args->tmpf[i]; } } else { if ( ntmpf!=col->mm_dbl_nused ) error("Error: cannot merge fields of unequal length\n"); if ( col->merge_method==MM_SUM || col->merge_method==MM_AVG ) for (i=0; imm_dbl[i] += args->tmpf[i]; else if ( col->merge_method==MM_MIN ) for (i=0; imm_dbl[i] > args->tmpf[i] ) col->mm_dbl[i] = args->tmpf[i]; } else if ( col->merge_method==MM_MAX ) for (i=0; imm_dbl[i] < args->tmpf[i] ) col->mm_dbl[i] = args->tmpf[i]; } } } col->mm_dbl_ndat++; return 1; } } else if ( col->merge_method==MM_SUM || col->merge_method==MM_MIN || col->merge_method==MM_MAX || col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING ) { ntmpf = col->mm_dbl_nused; hts_expand(int32_t,ntmpf,args->mtmpf,args->tmpf); for (i=0; imm_dbl[i]) ) bcf_float_set_missing(args->tmpf[i]); else args->tmpf[i] = col->mm_dbl[i]; } col->mm_dbl_nused = col->mm_dbl_ndat = 0; } else if ( col->merge_method==MM_AVG ) { ntmpf = col->mm_dbl_nused; hts_expand(int32_t,ntmpf,args->mtmpf,args->tmpf); for (i=0; itmpf[i] = col->mm_dbl[i]/col->mm_dbl_ndat; col->mm_dbl_nused = col->mm_dbl_ndat = 0; } if ( col->number==BCF_VL_A || col->number==BCF_VL_R ) return setter_ARinfo_real(args,line,col,tab->nals,tab->als,ntmpf); if ( col->replace & REPLACE_MISSING ) { int ret = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf2, &args->mtmpf2); if ( ret>0 && !bcf_float_is_missing(args->tmpf2[0]) ) return 0; } return bcf_update_info_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf,ntmpf); } static int vcf_setter_info_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; int ntmpf = bcf_get_info_float(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpf,&args->mtmpf); if ( ntmpf < 0 ) return 0; // nothing to add if ( col->number==BCF_VL_A || col->number==BCF_VL_R ) return setter_ARinfo_real(args,line,col,rec->n_allele,rec->d.allele,ntmpf); if ( col->replace & REPLACE_MISSING ) { int ret = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf2, &args->mtmpf2); if ( ret>0 && !bcf_float_is_missing(args->tmpf2[0]) ) return 0; } return bcf_update_info_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf,ntmpf); } int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst); // see vcfmerge.c static int setter_ARinfo_string(args_t *args, bcf1_t *line, annot_col_t *col, int nals, char **als) { assert( col->merge_method==MM_FIRST ); int nsrc = 1, lsrc = 0; while ( args->tmps[lsrc] ) { if ( args->tmps[lsrc]==',' ) nsrc++; lsrc++; } if ( col->number==BCF_VL_A && nsrc!=nals-1 && (nsrc!=1 || args->tmps[0]!='.' || args->tmps[1]!=0 ) ) error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", nsrc,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); else if ( col->number==BCF_VL_R && nsrc!=nals && (nsrc!=1 || args->tmps[0]!='.' || args->tmps[1]!=0 ) ) error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", nsrc,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int ndst = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele; int *map = vcmp_map_ARvalues(args->vcmp,ndst,nals,als,line->n_allele,line->d.allele); if ( !map ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); // fill in any missing values in the target VCF (or all, if not present) int i, empty = 0, nstr, mstr = args->tmpks.m; nstr = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &args->tmpks.s, &mstr); args->tmpks.m = mstr; if ( nstr<0 || (nstr==1 && args->tmpks.s[0]=='.' && args->tmpks.s[1]==0) ) { empty = 0; args->tmpks.l = 0; kputc('.',&args->tmpks); for (i=1; itmpks); } else args->tmpks.l = nstr; for (i=0; itmpks,i); continue; } if ( col->replace & REPLACE_MISSING ) { // Do not replace filled values. The field must be looked up again because // of realloc in copy_string_field int n = 0; char *str = args->tmpks.s; while ( *str && ntmps,map[i],lsrc,&args->tmpks,i); if ( ret!=0 ) error("[%s:%d %s] Failed to copy a string field\n", __FILE__,__LINE__,__func__); } return bcf_update_info_string(args->hdr_out,line,col->hdr_key_dst,args->tmpks.s); } void khash_str2int_clear_free(void *_hash) { khash_t(str2int) *hash = (khash_t(str2int)*)_hash; khint_t k; if (hash == 0) return; for (k = 0; k < kh_end(hash); ++k) if (kh_exist(hash, k)) free((char*)kh_key(hash, k)); kh_clear(str2int, hash); } static const char *escape_string(const char *str, char needle[], char **rmme, size_t *len) { kstring_t tmp = {0,0,0}; const char *bp = str, *ep = str; while ( *ep ) { int i = 0; while ( needle[i] && needle[i]!=*ep ) i++; if ( !needle[i] ) { ep++; continue; } kputsn(bp,ep-bp,&tmp); ksprintf(&tmp,"%%%X",*ep); bp = ++ep; } if ( !tmp.l ) { *len = strlen(str); return str; } kputs(bp,&tmp); *len = tmp.l; *rmme = tmp.s; return tmp.s; } static int setter_info_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( (col->replace & REPLACE_MISSING) && col->number!=BCF_VL_A && col->number!=BCF_VL_R ) { int ret = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &args->tmps2, &args->mtmps2); if ( ret>0 && (args->tmps2[0]!='.' || args->tmps2[1]!=0) ) return 0; } // This is a bit hacky, only to reuse existing code with minimal changes: // -c =TAG will now behave as -l TAG:unique for strings if ( col->replace & SET_OR_APPEND ) col->merge_method=MM_UNIQUE; annot_line_t *tab = (annot_line_t*) data; const char *escaped = NULL; char *rmme = NULL; size_t len = 0; if ( tab ) { char *str = tab->cols[col->icol]; if ( !str || !*str ) return 0; if ( !str[1] && str[0]=='.' && col->merge_method!=MM_APPEND_MISSING && !(col->replace & CARRY_OVER_MISSING) ) return 1; char needle[] = {';','=',0}; escaped = escape_string(tab->cols[col->icol],needle,&rmme,&len); } if ( col->merge_method!=MM_FIRST ) { if ( col->number==BCF_VL_A || col->number==BCF_VL_R ) error("Error: the --merge-logic option cannot be used with INFO tags Type=String,Number={A,R,G}\n"); if ( data ) { assert( col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING || col->merge_method==MM_UNIQUE ); if ( col->merge_method==MM_UNIQUE ) { if ( !col->mm_str_hash ) col->mm_str_hash = (khash_t(str2int)*)khash_str2int_init(); if ( khash_str2int_has_key(col->mm_str_hash, escaped) ) { free(rmme); return 1; } khash_str2int_inc(col->mm_str_hash, strdup(escaped)); } if ( (col->replace & SET_OR_APPEND) && !col->mm_kstr.l ) { int m = col->mm_kstr.m; int n = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &col->mm_kstr.s, &m); col->mm_kstr.m = m; if ( n>0 && ((col->replace & CARRY_OVER_MISSING) || col->mm_kstr.s[0]!='.' || col->mm_kstr.s[1]) ) col->mm_kstr.l = n; } if ( col->mm_kstr.l ) kputc(',',&col->mm_kstr); kputs(escaped, &col->mm_kstr); free(rmme); return 1; } if ( col->mm_kstr.l ) { hts_expand(char,col->mm_kstr.l+1,args->mtmps,args->tmps); memcpy(args->tmps,col->mm_kstr.s,col->mm_kstr.l+1); } else { free(rmme); return 0; } // flush the line if ( col->merge_method==MM_UNIQUE ) khash_str2int_clear_free(col->mm_str_hash); col->mm_kstr.l = 0; } else { assert(tab); hts_expand(char,len+1,args->mtmps,args->tmps); memcpy(args->tmps,escaped,len+1); if ( col->number==BCF_VL_A || col->number==BCF_VL_R ) return setter_ARinfo_string(args,line,col,tab->nals,tab->als); } int ret = bcf_update_info_string(args->hdr_out,line,col->hdr_key_dst,args->tmps); free(rmme); return ret; } static int vcf_setter_info_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; if ( col->getter ) col->getter(args,rec,col,(void**)&args->tmps, &args->mtmps); else { int ntmps = bcf_get_info_string(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmps,&args->mtmps); if ( ntmps < 0 ) return 0; // nothing to add } if ( col->number==BCF_VL_A || col->number==BCF_VL_R ) return setter_ARinfo_string(args,line,col,rec->n_allele,rec->d.allele); if ( col->replace & REPLACE_MISSING ) { int ret = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &args->tmps2, &args->mtmps2); if ( ret>0 && (args->tmps2[0]!='.' || args->tmps2[1]!=0) ) return 0; } return bcf_update_info_string(args->hdr_out,line,col->hdr_key_dst,args->tmps); } static int genotypes_to_string(args_t *args, int nsrc1, int32_t *src, int nsmpl_dst, kstring_t *str) { int i, isrc, idst; int blen = nsrc1 > 1 ? nsrc1 + 1 : 1; // typically the genotypes take three bytes 0/1, no 0-termination is needed gt_length_too_big: str->l = 0; for (idst=0; idstsample_map ? args->sample_map[idst] : idst; if ( isrc==-1 ) { kputc_('.', str); for (i=1; i < blen; i++) kputc_(0, str); continue; } size_t plen = str->l; int32_t *ptr = src + isrc*nsrc1; for (i=0; il - plen > blen ) { // too many alternate alleles or ploidy is too large, the genotype does not fit // three characters ("0/0" vs "10/10"). blen *= 2; goto gt_length_too_big; } plen = str->l - plen; while ( plen < blen ) { kputc_(0, str); plen++; } } return 0; } static int vcf_setter_format_gt(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; int nsrc = bcf_get_genotypes(args->files->readers[1].header,rec,&args->tmpi,&args->mtmpi); if ( nsrc==-3 ) return 0; // the tag is not present if ( nsrc<=0 ) return 1; // error // Genotypes are internally represented as integers. This is a complication when // adding as a different Type=String field, such as FMT/newGT:=GT if ( strcmp(col->hdr_key_src,col->hdr_key_dst) ) { int nsmpl_dst = bcf_hdr_nsamples(args->hdr_out); int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header); genotypes_to_string(args,nsrc/nsmpl_src,args->tmpi,nsmpl_dst,&args->tmpks); return bcf_update_format_char(args->hdr_out,line,col->hdr_key_dst,args->tmpks.s,args->tmpks.l); } if ( !args->sample_map ) return bcf_update_genotypes(args->hdr_out,line,args->tmpi,nsrc); int i, j, ndst = bcf_get_genotypes(args->hdr,line,&args->tmpi2,&args->mtmpi2); if ( ndst > 0 ) ndst /= bcf_hdr_nsamples(args->hdr_out); nsrc /= bcf_hdr_nsamples(args->files->readers[1].header); if ( ndst<=0 ) // field not present in dst file { if ( col->replace & REPLACE_NON_MISSING ) return 0; hts_expand(int32_t, nsrc*bcf_hdr_nsamples(args->hdr_out), args->mtmpi2, args->tmpi2); for (i=0; ihdr_out); i++) { int32_t *dst = args->tmpi2 + nsrc*i; if ( args->sample_map[i]==-1 ) { dst[0] = bcf_gt_missing; for (j=1; jtmpi + nsrc*args->sample_map[i]; for (j=0; jhdr_out,line,args->tmpi2,nsrc*bcf_hdr_nsamples(args->hdr_out)); } else if ( ndst >= nsrc ) { for (i=0; ihdr_out); i++) { if ( args->sample_map[i]==-1 ) continue; int32_t *src = args->tmpi + nsrc*args->sample_map[i]; int32_t *dst = args->tmpi2 + ndst*i; if ( (col->replace & REPLACE_NON_MISSING) && bcf_gt_is_missing(dst[0]) ) continue; if ( (col->replace & REPLACE_MISSING) && !bcf_gt_is_missing(dst[0]) ) continue; for (j=0; jhdr_out,line,args->tmpi2,ndst*bcf_hdr_nsamples(args->hdr_out)); } else // ndst < nsrc { hts_expand(int32_t, nsrc*bcf_hdr_nsamples(args->hdr_out), args->mtmpi3, args->tmpi3); for (i=0; ihdr_out); i++) { int32_t *ori = args->tmpi2 + ndst*i; int32_t *dst = args->tmpi3 + nsrc*i; int keep_ori = 0; if ( args->sample_map[i]==-1 ) keep_ori = 1; else if ( (col->replace & REPLACE_NON_MISSING) && bcf_gt_is_missing(ori[0]) ) keep_ori = 1; else if ( (col->replace & REPLACE_MISSING) && !bcf_gt_is_missing(ori[0]) ) keep_ori = 1; if ( keep_ori ) { for (j=0; jtmpi + nsrc*args->sample_map[i]; for (j=0; jhdr_out,line,args->tmpi3,nsrc*bcf_hdr_nsamples(args->hdr_out)); } } static int count_vals(annot_line_t *tab, int icol_beg, int icol_end) { int i, nmax = 1; for (i=icol_beg; icols[i], *end = str; if ( str[0]=='.' && !str[1] ) { // missing value if ( !nmax ) nmax = 1; continue; } int n = 1; while ( *end ) { if ( *end==',' ) n++; end++; } if ( nmaxsample_map ) return bcf_update_format_int32(args->hdr_out,line,col->hdr_key_dst,vals,nvals*args->nsmpl_annot); int i, j, ndst = bcf_get_format_int32(args->hdr,line,col->hdr_key_dst,&args->tmpi2,&args->mtmpi2); if ( ndst > 0 ) ndst /= bcf_hdr_nsamples(args->hdr_out); if ( ndst<=0 ) { if ( col->replace & REPLACE_NON_MISSING ) return 0; // overwrite only if present hts_expand(int32_t, nvals*bcf_hdr_nsamples(args->hdr_out), args->mtmpi2, args->tmpi2); for (i=0; ihdr_out); i++) { int32_t *dst = args->tmpi2 + nvals*i; if ( args->sample_map[i]==-1 ) { dst[0] = bcf_int32_missing; for (j=1; jsample_map[i]; for (j=0; jhdr_out,line,col->hdr_key_dst,args->tmpi2,nvals*bcf_hdr_nsamples(args->hdr_out)); } else if ( ndst >= nvals ) { for (i=0; ihdr_out); i++) { if ( args->sample_map[i]==-1 ) continue; int32_t *src = vals + nvals*args->sample_map[i]; int32_t *dst = args->tmpi2 + ndst*i; // possible cases: // in annot out // x y x TAG,-TAG,=TAG .. REPLACE_ALL, REPLACE_NON_MISSING, SET_OR_APPEND // x y y +TAG .. REPLACE_MISSING // . y . =TAG .. SET_OR_APPEND // . y y TAG,+TAG,-TAG .. REPLACE_ALL, REPLACE_MISSING, REPLACE_NON_MISSING // x . x TAG,+TAG .. REPLACE_ALL, REPLACE_MISSING // x . . -TAG .. REPLACE_NON_MISSING if ( col->replace & REPLACE_NON_MISSING ) { if ( dst[0]==bcf_int32_missing ) continue; } else if ( col->replace & REPLACE_MISSING ) { if ( dst[0]!=bcf_int32_missing ) continue; } else if ( col->replace & REPLACE_ALL ) { if ( src[0]==bcf_int32_missing ) continue; } for (j=0; jhdr_out,line,col->hdr_key_dst,args->tmpi2,ndst*bcf_hdr_nsamples(args->hdr_out)); } else // ndst < nvals { hts_expand(int32_t, nvals*bcf_hdr_nsamples(args->hdr_out), args->mtmpi3, args->tmpi3); for (i=0; ihdr_out); i++) { int32_t *ann = vals + nvals*args->sample_map[i]; int32_t *ori = args->tmpi2 + ndst*i; // ori vcf line int32_t *dst = args->tmpi3 + nvals*i; // expanded buffer int use_new_ann = 1; if ( args->sample_map[i]==-1 ) use_new_ann = 0; else if ( col->replace & REPLACE_NON_MISSING ) { if ( ori[0]==bcf_int32_missing ) use_new_ann = 0; } else if ( col->replace & REPLACE_MISSING ) { if ( ori[0]!=bcf_int32_missing ) use_new_ann = 0; } else if ( col->replace & REPLACE_ALL ) { if ( ann[0]==bcf_int32_missing ) use_new_ann = 0; } if ( !use_new_ann ) { for (j=0; jhdr_out,line,col->hdr_key_dst,args->tmpi3,nvals*bcf_hdr_nsamples(args->hdr_out)); } } static int core_setter_format_real(args_t *args, bcf1_t *line, annot_col_t *col, float *vals, int nvals) { if ( !args->sample_map ) return bcf_update_format_float(args->hdr_out,line,col->hdr_key_dst,vals,nvals*args->nsmpl_annot); int i, j, ndst = bcf_get_format_float(args->hdr,line,col->hdr_key_dst,&args->tmpf2,&args->mtmpf2); if ( ndst > 0 ) ndst /= bcf_hdr_nsamples(args->hdr_out); if ( ndst<=0 ) { if ( col->replace & REPLACE_NON_MISSING ) return 0; // overwrite only if present hts_expand(float, nvals*bcf_hdr_nsamples(args->hdr_out), args->mtmpf2, args->tmpf2); for (i=0; ihdr_out); i++) { float *dst = args->tmpf2 + nvals*i; if ( args->sample_map[i]==-1 ) { bcf_float_set_missing(dst[0]); for (j=1; jsample_map[i]; for (j=0; jhdr_out,line,col->hdr_key_dst,args->tmpf2,nvals*bcf_hdr_nsamples(args->hdr_out)); } else if ( ndst >= nvals ) { for (i=0; ihdr_out); i++) { if ( args->sample_map[i]==-1 ) continue; float *src = vals + nvals*args->sample_map[i]; float *dst = args->tmpf2 + ndst*i; if ( col->replace & REPLACE_NON_MISSING ) { if ( bcf_float_is_missing(dst[0]) ) continue; } else if ( col->replace & REPLACE_MISSING ) { if ( !bcf_float_is_missing(dst[0]) ) continue; } else if ( col->replace & REPLACE_ALL ) { if ( bcf_float_is_missing(src[0]) ) continue; } for (j=0; jhdr_out,line,col->hdr_key_dst,args->tmpf2,ndst*bcf_hdr_nsamples(args->hdr_out)); } else // ndst < nvals { hts_expand(float, nvals*bcf_hdr_nsamples(args->hdr_out), args->mtmpf3, args->tmpf3); for (i=0; ihdr_out); i++) { float *ann = vals + nvals*args->sample_map[i]; float *ori = args->tmpf2 + ndst*i; // ori vcf line float *dst = args->tmpf3 + nvals*i; // expanded buffer int use_new_ann = 1; if ( args->sample_map[i]==-1 ) use_new_ann = 0; else if ( col->replace & REPLACE_NON_MISSING ) { if ( bcf_float_is_missing(ori[0]) ) use_new_ann = 0; } else if ( col->replace & REPLACE_MISSING ) { if ( !bcf_float_is_missing(ori[0]) ) use_new_ann = 0; } else if ( col->replace & REPLACE_ALL ) { if ( bcf_float_is_missing(ann[0]) ) use_new_ann = 0; } if ( !use_new_ann ) { for (j=0; jhdr_out,line,col->hdr_key_dst,args->tmpf3,nvals*bcf_hdr_nsamples(args->hdr_out)); } } static int core_setter_format_str(args_t *args, bcf1_t *line, annot_col_t *col, char **vals) { if ( !args->sample_map ) return bcf_update_format_string(args->hdr_out,line,col->hdr_key_dst,(const char**)vals,args->nsmpl_annot); int i; args->tmpp2[0] = args->tmps2; int ret = bcf_get_format_string(args->hdr,line,col->hdr_key_dst,&args->tmpp2,&args->mtmps2); args->tmps2 = args->tmpp2[0]; // tmps2 might be realloced int nsmpl = bcf_hdr_nsamples(args->hdr_out); if ( ret<=0 ) // not present in dst { hts_expand(char,bcf_hdr_nsamples(args->hdr_out)*2,args->mtmps2,args->tmps2); char *tmp = args->tmps2; for (i=0; itmpp2[i] = tmp; tmp += 2; } } for (i=0; isample_map[i]==-1 ) continue; char **src = vals + args->sample_map[i]; char **dst = args->tmpp2 + i; if ( col->replace & REPLACE_NON_MISSING ) { if ( (*dst)[0]=='.' && (*dst)[1]==0 ) continue; } else if ( col->replace & REPLACE_MISSING ) { if ( (*dst)[0]!='.' || (*dst)[1]!=0 ) continue; } else if ( col->replace & REPLACE_ALL ) { if ( (*src)[0]=='.' && (*src)[1]==0 ) continue; } *dst = *src; } return bcf_update_format_string(args->hdr_out,line,col->hdr_key_dst,(const char**)args->tmpp2,nsmpl); } static int setter_format_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( !data ) error("Error: the --merge-logic option cannot be used with FORMAT tags (yet?)\n"); annot_line_t *tab = (annot_line_t*) data; if ( col->icol+args->nsmpl_annot > tab->ncols ) error("Incorrect number of values for %s at %s:%"PRId64"\n",col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int nvals = count_vals(tab,col->icol,col->icol+args->nsmpl_annot); hts_expand(int32_t,nvals*args->nsmpl_annot,args->mtmpi,args->tmpi); int icol = col->icol, ismpl; for (ismpl=0; ismplnsmpl_annot; ismpl++) { int32_t *ptr = args->tmpi + ismpl*nvals; int ival = 0; char *str = tab->cols[icol]; while ( *str ) { if ( str[0]=='.' && (!str[1] || str[1]==',') ) // missing value { ptr[ival++] = bcf_int32_missing; str += str[1] ? 2 : 1; continue; } char *end = str; ptr[ival] = strtol(str, &end, 10); if ( end==str ) error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]); ival++; str = *end ? end+1 : end; } while ( ivaltmpi,nvals); } static int setter_format_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( !data ) error("Error: the --merge-logic option cannot be used with FORMAT tags (yet?)\n"); annot_line_t *tab = (annot_line_t*) data; if ( col->icol+args->nsmpl_annot > tab->ncols ) error("Incorrect number of values for %s at %s:%"PRId64"\n",col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int nvals = count_vals(tab,col->icol,col->icol+args->nsmpl_annot); hts_expand(float,nvals*args->nsmpl_annot,args->mtmpf,args->tmpf); int icol = col->icol, ismpl; for (ismpl=0; ismplnsmpl_annot; ismpl++) { float *ptr = args->tmpf + ismpl*nvals; int ival = 0; char *str = tab->cols[icol]; while ( *str ) { if ( str[0]=='.' && (!str[1] || str[1]==',') ) // missing value { bcf_float_set_missing(ptr[ival]); ival++; str += str[1] ? 2 : 1; continue; } char *end = str; ptr[ival] = strtod(str, &end); if ( end==str ) error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]); ival++; str = *end ? end+1 : end; } while ( ivaltmpf,nvals); } static int setter_format_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { if ( !data ) error("Error: the --merge-logic option cannot be used with FORMAT tags (yet?)\n"); annot_line_t *tab = (annot_line_t*) data; if ( col->icol+args->nsmpl_annot > tab->ncols ) error("Incorrect number of values for %s at %s:%"PRId64"\n",col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); char needle[] = {':',0}; int ismpl; for (ismpl=0; ismplnsmpl_annot; ismpl++) { size_t len; char *rmme = NULL; const char *str = escape_string(tab->cols[col->icol + ismpl],needle,&rmme,&len); args->tmpp[ismpl] = rmme ? rmme : strdup(str); } int ret = core_setter_format_str(args,line,col,args->tmpp); for (ismpl=0; ismplnsmpl_annot; ismpl++) free(args->tmpp[ismpl]); return ret; } static int determine_ploidy(int nals, int *vals, int nvals1, uint8_t *smpl, int nsmpl) { int i, j, ndip = nals*(nals+1)/2, max_ploidy = 0; for (i=0; ifiles->readers[1].header,rec,col->hdr_key_src,&args->tmpi,&args->mtmpi); if ( nsrc==-3 ) return 0; // the tag is not present if ( nsrc<=0 ) return 1; // error int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header); int nsrc1 = nsrc / nsmpl_src; if ( col->number!=BCF_VL_G && col->number!=BCF_VL_R && col->number!=BCF_VL_A ) return core_setter_format_int(args,line,col,args->tmpi,nsrc1); // create mapping from src to dst genotypes, haploid and diploid version int nmap_hap = col->number==BCF_VL_G || col->number==BCF_VL_R ? rec->n_allele : rec->n_allele - 1; int *map_hap = vcmp_map_ARvalues(args->vcmp,nmap_hap,line->n_allele,line->d.allele,rec->n_allele,rec->d.allele); if ( !map_hap ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int i, j; if ( rec->n_allele==line->n_allele ) { // alleles unchanged? for (i=0; in_allele; i++) if ( map_hap[i]!=i ) break; if ( i==rec->n_allele ) return core_setter_format_int(args,line,col,args->tmpi,nsrc1); } int nsmpl_dst = rec->n_sample; int ndst = bcf_get_format_int32(args->hdr,line,col->hdr_key_dst,&args->tmpi2,&args->mtmpi2); int ndst1 = ndst / nsmpl_dst; if ( ndst <= 0 ) { if ( col->replace & REPLACE_NON_MISSING ) return 0; // overwrite only if present if ( col->number==BCF_VL_G ) ndst1 = line->n_allele*(line->n_allele+1)/2; else ndst1 = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele; hts_expand(int, ndst1*nsmpl_dst, args->mtmpi2, args->tmpi2); for (i=0; itmpi2 + i*ndst1; for (j=0; jnumber==BCF_VL_G ) { map_dip = vcmp_map_dipGvalues(args->vcmp, &nmap_dip); if ( !args->src_smpl_pld ) { args->src_smpl_pld = (uint8_t*) malloc(nsmpl_src); args->dst_smpl_pld = (uint8_t*) malloc(nsmpl_dst); } int pld_src = determine_ploidy(rec->n_allele, args->tmpi, nsrc1, args->src_smpl_pld, nsmpl_src); if ( pld_src<0 ) error("Unexpected number of %s values (%d) for %d alleles at %s:%"PRId64"\n", col->hdr_key_src,-pld_src, rec->n_allele, bcf_seqname(bcf_sr_get_header(args->files,1),rec),(int64_t) rec->pos+1); int pld_dst = determine_ploidy(line->n_allele, args->tmpi2, ndst1, args->dst_smpl_pld, nsmpl_dst); if ( pld_dst<0 ) error("Unexpected number of %s values (%d) for %d alleles at %s:%"PRId64"\n", col->hdr_key_src,-pld_dst, line->n_allele, bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int ndst1_new = pld_dst==1 ? line->n_allele : line->n_allele*(line->n_allele+1)/2; if ( ndst1_new != ndst1 ) { if ( ndst1 ) error("todo: %s ndst1!=ndst .. %d %d at %s:%"PRId64"\n",col->hdr_key_src,ndst1_new,ndst1,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); ndst1 = ndst1_new; hts_expand(int32_t, ndst1*nsmpl_dst, args->mtmpi2, args->tmpi2); } } else if ( !ndst1 ) { ndst1 = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele; hts_expand(int32_t, ndst1*nsmpl_dst, args->mtmpi2, args->tmpi2); } for (i=0; isample_map ? args->sample_map[i] : i; int32_t *ptr_src = args->tmpi + i*nsrc1; int32_t *ptr_dst = args->tmpi2 + ii*ndst1; if ( col->number==BCF_VL_G ) { if ( args->src_smpl_pld[ii] > 0 && args->dst_smpl_pld[i] > 0 && args->src_smpl_pld[ii]!=args->dst_smpl_pld[i] ) error("Sample ploidy differs at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); if ( !args->dst_smpl_pld[i] ) for (j=0; jnumber!=BCF_VL_G || args->src_smpl_pld[i]==1 ) { for (j=0; j=0 ) ptr_dst[k] = ptr_src[j]; } if ( col->number==BCF_VL_G ) for (j=line->n_allele; j=0 ) ptr_dst[k] = ptr_src[j]; } } } return bcf_update_format_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi2,nsmpl_dst*ndst1); } static int vcf_setter_format_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; int nsrc = bcf_get_format_float(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpf,&args->mtmpf); if ( nsrc==-3 ) return 0; // the tag is not present if ( nsrc<=0 ) return 1; // error int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header); int nsrc1 = nsrc / nsmpl_src; if ( col->number!=BCF_VL_G && col->number!=BCF_VL_R && col->number!=BCF_VL_A ) return core_setter_format_real(args,line,col,args->tmpf,nsrc1); // create mapping from src to dst genotypes, haploid and diploid version int nmap_hap = col->number==BCF_VL_G || col->number==BCF_VL_R ? rec->n_allele : rec->n_allele - 1; int *map_hap = vcmp_map_ARvalues(args->vcmp,nmap_hap,line->n_allele,line->d.allele,rec->n_allele,rec->d.allele); if ( !map_hap ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int i, j; if ( rec->n_allele==line->n_allele ) { // alleles unchanged? for (i=0; in_allele; i++) if ( map_hap[i]!=i ) break; if ( i==rec->n_allele ) return core_setter_format_real(args,line,col,args->tmpf,nsrc1); } int nsmpl_dst = rec->n_sample; int ndst = bcf_get_format_float(args->hdr,line,col->hdr_key_dst,&args->tmpf2,&args->mtmpf2); int ndst1 = ndst / nsmpl_dst; if ( ndst <= 0 ) { if ( col->replace & REPLACE_NON_MISSING ) return 0; // overwrite only if present if ( col->number==BCF_VL_G ) ndst1 = line->n_allele*(line->n_allele+1)/2; else ndst1 = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele; hts_expand(float, ndst1*nsmpl_dst, args->mtmpf2, args->tmpf2); for (i=0; itmpf2 + i*ndst1; for (j=0; jnumber==BCF_VL_G ) { map_dip = vcmp_map_dipGvalues(args->vcmp, &nmap_dip); if ( !args->src_smpl_pld ) { args->src_smpl_pld = (uint8_t*) malloc(nsmpl_src); args->dst_smpl_pld = (uint8_t*) malloc(nsmpl_dst); } int pld_src = determine_ploidy(rec->n_allele, args->tmpi, nsrc1, args->src_smpl_pld, nsmpl_src); if ( pld_src<0 ) error("Unexpected number of %s values (%d) for %d alleles at %s:%"PRId64"\n", col->hdr_key_src,-pld_src, rec->n_allele, bcf_seqname(bcf_sr_get_header(args->files,1),rec),(int64_t) rec->pos+1); int pld_dst = determine_ploidy(line->n_allele, args->tmpi2, ndst1, args->dst_smpl_pld, nsmpl_dst); if ( pld_dst<0 ) error("Unexpected number of %s values (%d) for %d alleles at %s:%"PRId64"\n", col->hdr_key_src,-pld_dst, line->n_allele, bcf_seqname(args->hdr,line),(int64_t) line->pos+1); int ndst1_new = pld_dst==1 ? line->n_allele : line->n_allele*(line->n_allele+1)/2; if ( ndst1_new != ndst1 ) { if ( ndst1 ) error("todo: %s ndst1!=ndst .. %d %d at %s:%"PRId64"\n",col->hdr_key_src,ndst1_new,ndst1,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); ndst1 = ndst1_new; hts_expand(float, ndst1*nsmpl_dst, args->mtmpf2, args->tmpf2); } } else if ( !ndst1 ) { ndst1 = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele; hts_expand(float, ndst1*nsmpl_dst, args->mtmpf2, args->tmpf2); } for (i=0; isample_map ? args->sample_map[i] : i; float *ptr_src = args->tmpf + i*nsrc1; float *ptr_dst = args->tmpf2 + ii*ndst1; if ( col->number==BCF_VL_G ) { if ( args->src_smpl_pld[ii] > 0 && args->dst_smpl_pld[i] > 0 && args->src_smpl_pld[ii]!=args->dst_smpl_pld[i] ) error("Sample ploidy differs at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); if ( !args->dst_smpl_pld[i] ) for (j=0; jnumber!=BCF_VL_G || args->src_smpl_pld[i]==1 ) { for (j=0; j=0 ) { if ( bcf_float_is_missing(ptr_src[j]) ) bcf_float_set_missing(ptr_dst[k]); else if ( bcf_float_is_vector_end(ptr_src[j]) ) bcf_float_set_vector_end(ptr_dst[k]); else ptr_dst[k] = ptr_src[j]; } } if ( col->number==BCF_VL_G ) for (j=line->n_allele; j=0 ) { if ( bcf_float_is_missing(ptr_src[j]) ) bcf_float_set_missing(ptr_dst[k]); else if ( bcf_float_is_vector_end(ptr_src[j]) ) bcf_float_set_vector_end(ptr_dst[k]); else ptr_dst[k] = ptr_src[j]; } } } } return bcf_update_format_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf2,nsmpl_dst*ndst1); } static int vcf_setter_format_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data) { bcf1_t *rec = (bcf1_t*) data; args->tmpp[0] = args->tmps; int ret = bcf_get_format_string(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpp,&args->mtmps); args->tmps = args->tmpp[0]; // tmps might be realloced if ( ret==-3 ) return 0; // the tag is not present if ( ret<=0 ) return 1; // error if ( strcmp("GT",col->hdr_key_dst) ) return core_setter_format_str(args,line,col,args->tmpp); // Genotypes are internally represented as integers. This is a complication for FMT/GT:=oldGT // First determine the maximum number of alleles per-sample ndst1 int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header); int nsmpl_dst = bcf_hdr_nsamples(args->hdr_out); int isrc,idst, ndst1 = 0, nsrc1 = ret / nsmpl_src; char *ptr = args->tmps, *ptr_end = ptr + ret; while ( ptr < ptr_end ) { char *smpl_end = ptr + nsrc1; int n = 1; while ( ptr < smpl_end ) { if ( *ptr=='/' || *ptr=='|' ) n++; ptr++; } if ( ndst1 < n ) ndst1 = n; } assert( ndst1 ); int ndst = ndst1*nsmpl_dst; hts_expand(int32_t,ndst,args->mtmpi,args->tmpi); hts_expand(char,ret+1,args->mtmps,args->tmps); args->tmps[ret] = 0; // the FORMAT string may not be 0-terminated for (idst=0; idsttmpi + idst*ndst1; isrc = args->sample_map ? args->sample_map[idst] : idst; if ( isrc==-1 ) { dst[0] = bcf_gt_missing; for (i=1; itmps + isrc*nsrc1, *tmp; char *keep_ptr = beg+nsrc1, keep = *keep_ptr; *keep_ptr = 0; while ( *beg ) { char *end = beg; while ( *end && *end!='/' && *end!='|' ) end++; if ( *beg=='.' && end-beg==1 ) dst[i] = bcf_gt_missing; else { if ( *end=='|' ) is_phased = 1; dst[i] = strtol(beg, &tmp, 10); if ( tmp!=end ) error("Could not parse the %s field at %s:%"PRId64" in %s\n", col->hdr_key_src,bcf_seqname(args->files->readers[1].header,rec),(int64_t) rec->pos+1,args->targets_fname); if ( dst[i] >= line->n_allele ) error("The source allele index is bigger than the number of destination alleles at %s:%"PRId64"\n", bcf_seqname(args->files->readers[1].header,rec),(int64_t) rec->pos+1); dst[i] = is_phased ? bcf_gt_phased(dst[i]) : bcf_gt_unphased(dst[i]); } beg = *end ? end+1 : end; i++; } *keep_ptr = keep; for (; ihdr_out,line,args->tmpi,ndst); } static int init_sample_map(args_t *args, bcf_hdr_t *src, bcf_hdr_t *dst) { int i; if ( !args->sample_names ) { args->nsmpl_annot = bcf_hdr_nsamples(dst); // tab annotation file, expecting that all samples are present: sample map not needed if ( !src ) return 0; int nmatch = 0; for (i=0; isamples[i]); if ( id!=-1 ) nmatch++; } if ( !nmatch ) return -1; // No matching samples found in the source and the destination file args->nsample_map = bcf_hdr_nsamples(dst); args->sample_map = (int*) malloc(sizeof(int)*args->nsample_map); for (i=0; insample_map; i++) { int id = bcf_hdr_id2int(src, BCF_DT_SAMPLE, dst->samples[i]); args->sample_map[i] = id; // idst -> isrc, -1 if not present } return 1; } args->nsample_map = bcf_hdr_nsamples(dst); args->sample_map = (int*) malloc(sizeof(int)*args->nsample_map); for (i=0; insample_map; i++) args->sample_map[i] = -1; int flags = !src ? SMPL_STRICT|SMPL_SINGLE|SMPL_REORDER : SMPL_STRICT|SMPL_SINGLE|SMPL_PAIR2; // is tab vs vcf annotation file smpl_ilist_t *ilist = smpl_ilist_init(dst, args->sample_names, args->sample_is_file, flags); // gives mapping dst->src if ( !ilist || !ilist->n ) error("Could not parse the samples: %s\n", args->sample_names); args->nsmpl_annot = ilist->n; int need_sample_map = args->nsmpl_annot==bcf_hdr_nsamples(dst) ? 0 : 1; for (i=0; insmpl_annot; i++) { int idst = ilist->idx[i]; const char *src_name = ilist->pair && ilist->pair[i] ? ilist->pair[i] : bcf_hdr_int2id(dst, BCF_DT_SAMPLE, idst); int isrc = i; if ( src ) // the annotation file is a VCF, not a tab-delimited file { isrc = bcf_hdr_id2int(src, BCF_DT_SAMPLE, src_name); if ( isrc==-1 ) error("Sample \"%s\" not found in the annotation file\n", src_name); } if ( isrc!=idst ) need_sample_map = 1; args->sample_map[idst] = isrc; } smpl_ilist_destroy(ilist); return need_sample_map; } static char *columns_complement(char *columns, void **skip_info, void **skip_fmt) { kstring_t str = {0,0,0}; char *ss = columns, *se = ss; while ( *ss ) { if ( *se && *se!=',' ) { se++; continue; } if ( *ss!='^' ) { if ( str.l ) kputc(',',&str); kputsn(ss, se-ss, &str); if ( !*se ) break; ss = ++se; continue; } if ( !strncasecmp("^INFO/",ss,6) ) { if ( !*skip_info ) { *skip_info = khash_str2int_init(); if ( str.l ) kputc(',',&str); kputs("INFO",&str); } char tmp = *se; *se = 0; khash_str2int_inc(*skip_info, strdup(ss+6)); *se = tmp; } else if ( !strncasecmp("^FORMAT/",ss,8) || !strncasecmp("^FMT/",ss,5) ) { int n = !strncasecmp("^FMT/",ss,5) ? 5 : 8; if ( !*skip_fmt ) { *skip_fmt = khash_str2int_init(); if ( str.l ) kputc(',',&str); kputs("FORMAT",&str); } char tmp = *se; *se = 0; khash_str2int_inc(*skip_fmt, strdup(ss+n)); *se = tmp; } else { if ( !*skip_info ) { *skip_info = khash_str2int_init(); if ( str.l ) kputc(',',&str); kputs("INFO",&str); } char tmp = *se; *se = 0; khash_str2int_inc(*skip_info, strdup(ss+1)); *se = tmp; } if ( !*se ) break; ss = ++se; } free(columns); return str.s; } static void bcf_hrec_format_rename(bcf_hrec_t *hrec, char *tag, kstring_t *str) { int j, nout = 0; ksprintf(str, "##%s=<", hrec->key); for (j=0; jnkeys; j++) { if ( !strcmp("IDX",hrec->keys[j]) ) continue; if ( nout ) kputc(',',str); if ( !strcmp("ID", hrec->keys[j]) ) ksprintf(str,"%s=%s", hrec->keys[j], tag); else ksprintf(str,"%s=%s", hrec->keys[j], hrec->vals[j]); nout++; } ksprintf(str,">\n"); } static char *set_replace_mode(char *ss, int *replace) { int mode = 0; while (*ss) { if ( *ss=='+' ) mode |= REPLACE_MISSING; else if ( *ss=='-' ) mode |= REPLACE_NON_MISSING; else if ( *ss=='=' ) mode |= SET_OR_APPEND; else if ( *ss=='.' ) mode |= CARRY_OVER_MISSING; else break; ss++; } if ( !mode ) mode = REPLACE_ALL; // is exactly one bit set? // if ( mode && !(mode && ((mode & mode-1) == 0)) ) *replace = mode; return ss; } static void rename_annots_push(args_t *args, char *src, char *dst); static void init_columns(args_t *args) { int need_sample_map = 0; int sample_map_ok = init_sample_map(args, args->tgts_is_vcf?args->files->readers[1].header:NULL, args->hdr); kstring_t tmp = {0,0,0}; if ( args->columns_is_file ) { int i,n; char **str = hts_readlist(args->columns, args->columns_is_file, &n); if ( !str ) error("Could not parse %s\n", args->columns); for (i=0; imerge_method_str.l ) kputc(',',&args->merge_method_str); kputs(str[i],&args->merge_method_str); kputc(':',&args->merge_method_str); kputs(ptr,&args->merge_method_str); } } if ( tmp.l ) kputc(',',&tmp); kputs(str[i],&tmp); free(str[i]); } free(str); free(args->columns); args->columns = tmp.s; tmp.l = tmp.m = 0; tmp.s = NULL; } void *skip_fmt = NULL, *skip_info = NULL; if ( args->tgts_is_vcf ) args->columns = columns_complement(args->columns, &skip_info, &skip_fmt); kstring_t str = {0,0,0}; char *ss = args->columns, *se = ss; args->ncols = 0; int icol = -1, has_fmt_str = 0; while ( *ss ) { char *ptr; if ( *se && *se!=',' ) { se++; continue; } int replace; ss = set_replace_mode(ss, &replace); icol++; str.l = 0; kputsn(ss, se-ss, &str); if ( !str.s[0] || !strcasecmp("-",str.s) ) ; else if ( !strcasecmp("CHROM",str.s) ) args->chr_idx = icol; else if ( !strcasecmp("POS",str.s) ) { if ( replace==REPLACE_NON_MISSING && !args->tgts_is_vcf ) { args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; col->setter = setter_pos; col->hdr_key_src = strdup(str.s); col->hdr_key_dst = strdup(str.s); args->match_end = icol; } else args->beg_idx = icol; } else if ( !strcasecmp("FROM",str.s) || !strcasecmp("BEG",str.s) ) args->beg_idx = icol; else if ( !strcasecmp("TO",str.s) || !strcasecmp("END",str.s) ) args->end_idx = icol; else if ( !strcasecmp("REF",str.s) ) { if ( args->tgts_is_vcf ) { args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->setter = vcf_setter_ref; col->hdr_key_src = strdup(str.s); col->hdr_key_dst = strdup(str.s); } else args->ref_idx = icol; } else if ( !strcasecmp("ALT",str.s) ) { if ( args->tgts_is_vcf ) { args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->setter = vcf_setter_alt; col->hdr_key_src = strdup(str.s); col->hdr_key_dst = strdup(str.s); col->replace = replace; if ( args->pair_logic==-1 ) bcf_sr_set_opt(args->files,BCF_SR_PAIR_LOGIC,BCF_SR_PAIR_BOTH_REF); } else args->alt_idx = icol; } else if ( !strcasecmp("ID",str.s) || !strcasecmp("~ID",str.s) ) { if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -ID feature has not been implemented yet.\n"); if ( str.s[0]=='~' ) replace = MATCH_VALUE; if ( args->tgts_is_vcf && (replace & MATCH_VALUE) ) error("todo: -c ~ID with -a VCF?\n"); args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; col->setter = args->tgts_is_vcf ? vcf_setter_id : setter_id; col->hdr_key_src = strdup(str.s); col->hdr_key_dst = strdup(str.s); if ( replace & MATCH_VALUE ) args->match_id = icol; } else if ( !strcasecmp("~INFO/END",str.s) && !args->tgts_is_vcf ) { replace = MATCH_VALUE; args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; col->setter = NULL; col->hdr_key_src = strdup(str.s); col->hdr_key_dst = strdup(str.s); args->match_end = icol; } else if ( !strcasecmp("~POS",str.s) ) { error("Error: the use of ~POS has been deprecated, use -POS to transfer the column POS.\n"); } else if ( str.s[0]=='~' ) { args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = MATCH_VALUE; col->setter = NULL; col->hdr_key_src = strdup(str.s+1); } else if ( !strcasecmp("-POS",str.s) && !args->tgts_is_vcf ) { if ( args->tgts_is_vcf ) error("Error: cannot use -POS, position can be replaced only from a tab-delimited file\n"); args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; col->setter = setter_pos; col->hdr_key_src = strdup(str.s); col->hdr_key_dst = strdup(str.s); args->match_end = icol; } else if ( !strncasecmp("ID:=",str.s,4) ) // transfer a tag from INFO to ID column { if ( !args->tgts_is_vcf ) error("The annotation source must be a VCF for \"%s\"\n",str.s); if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -ID feature has not been implemented yet.\n"); args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; col->setter = vcf_setter_id; col->getter = vcf_getter_info_str2str; str.s[2] = 0; col->hdr_key_dst = strdup(str.s); col->hdr_key_src = strncasecmp("INFO/",str.s+4,5) ? strdup(str.s+4) : strdup(str.s+4+5); int hdr_id = bcf_hdr_id2int(args->tgts_hdr, BCF_DT_ID,col->hdr_key_src); if ( !bcf_hdr_idinfo_exists(args->tgts_hdr,BCF_HL_INFO,hdr_id) ) error("The INFO tag \"%s\" is not defined in %s\n", col->hdr_key_src, args->targets_fname); if ( bcf_hdr_id2type(args->tgts_hdr,BCF_HL_INFO,hdr_id)!=BCF_HT_STR ) error("Only Type=String tags can be used to annotate the ID column\n"); } else if ( (ptr=strstr(str.s,":=")) && (!args->targets_fname || !strncasecmp(ptr+2,"./",2)) ) { *ptr = 0; if ( !strncasecmp(str.s,"INFO/",5) && (!strcasecmp(ptr+2,"FILTER") || !strcasecmp(ptr+2,"./FILTER")) ) { // -a not present and transferring filter, needs to be a local transfer args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; col->setter = vcf_setter_info_str; col->getter = vcf_getter_filter2str_local; col->hdr_key_src = strdup(ptr+2); col->hdr_key_dst = strdup(str.s+5); tmp.l = 0; ksprintf(&tmp,"##INFO=",col->hdr_key_dst); bcf_hdr_append(args->hdr_out, tmp.s); if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update header", __func__); int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, col->hdr_key_dst); col->number = bcf_hdr_id2length(args->hdr_out,BCF_HL_INFO,hdr_id); } else rename_annots_push(args,ptr+2,str.s); *ptr = ':'; } else if ( !strcasecmp("FILTER",str.s) ) { if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -FILTER feature has not been implemented yet.\n"); args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; col->setter = args->tgts_is_vcf ? vcf_setter_filter : setter_filter; col->hdr_key_src = strdup(str.s); col->hdr_key_dst = strdup(str.s); if ( args->tgts_is_vcf ) { bcf_hdr_t *tgts_hdr = args->files->readers[1].header; int j; for (j=0; jnhrec; j++) { bcf_hrec_t *hrec = tgts_hdr->hrec[j]; if ( hrec->type!=BCF_HL_FLT ) continue; int k = bcf_hrec_find_key(hrec,"ID"); if ( k<0 ) error("[%s] Failed to parse the header, the ID attribute not found", __func__); tmp.l = 0; bcf_hrec_format(hrec, &tmp); bcf_hdr_append(args->hdr_out, tmp.s); } if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update header", __func__); } } else if ( !strcasecmp("QUAL",str.s) ) { if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -QUAL feature has not been implemented yet.\n"); if ( replace & SET_OR_APPEND ) error("Apologies, the =QUAL feature has not been implemented yet.\n"); args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; col->setter = args->tgts_is_vcf ? vcf_setter_qual : setter_qual; col->hdr_key_src = strdup(str.s); col->hdr_key_dst = strdup(str.s); } else if ( args->tgts_is_vcf && !strcasecmp("INFO",str.s) ) // All INFO fields { if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -INFO/TAG feature has not been implemented yet.\n"); if ( replace & SET_OR_APPEND ) error("Apologies, the =INFO feature has not been implemented yet.\n"); bcf_hdr_t *tgts_hdr = args->files->readers[1].header; int j; for (j=0; jnhrec; j++) { bcf_hrec_t *hrec = tgts_hdr->hrec[j]; if ( hrec->type!=BCF_HL_INFO ) continue; int k = bcf_hrec_find_key(hrec,"ID"); assert( k>=0 ); // this should always be true for valid VCFs if ( skip_info && khash_str2int_has_key(skip_info,hrec->vals[k]) ) continue; tmp.l = 0; bcf_hrec_format(hrec, &tmp); bcf_hdr_append(args->hdr_out, tmp.s); if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update header", __func__); int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, hrec->vals[k]); args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = -1; col->replace = replace; col->hdr_key_src = strdup(hrec->vals[k]); col->hdr_key_dst = strdup(hrec->vals[k]); col->number = bcf_hdr_id2length(args->hdr_out,BCF_HL_INFO,hdr_id); switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_INFO,hdr_id) ) { case BCF_HT_FLAG: col->setter = vcf_setter_info_flag; break; case BCF_HT_INT: col->setter = vcf_setter_info_int; break; case BCF_HT_REAL: col->setter = vcf_setter_info_real; break; case BCF_HT_STR: col->setter = vcf_setter_info_str; break; default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_INFO,hdr_id)); } } } else if ( args->tgts_is_vcf && (!strcasecmp("FORMAT",str.s) || !strcasecmp("FMT",str.s)) ) // All FORMAT fields { bcf_hdr_t *tgts_hdr = args->files->readers[1].header; need_sample_map = 1; int j; for (j=0; jnhrec; j++) { bcf_hrec_t *hrec = tgts_hdr->hrec[j]; if ( hrec->type!=BCF_HL_FMT) continue; int k = bcf_hrec_find_key(hrec,"ID"); assert( k>=0 ); // this should always be true for valid VCFs if ( skip_fmt && khash_str2int_has_key(skip_fmt,hrec->vals[k]) ) continue; tmp.l = 0; bcf_hrec_format(hrec, &tmp); bcf_hdr_append(args->hdr_out, tmp.s); if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update header", __func__); int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, hrec->vals[k]); args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = -1; col->replace = replace; col->hdr_key_src = strdup(hrec->vals[k]); col->hdr_key_dst = strdup(hrec->vals[k]); if ( !strcasecmp("GT",col->hdr_key_src) ) { if ( !args->tgts_is_vcf ) error("The FORMAT/GT field can be currently populated only from a VCF\n"); col->setter = vcf_setter_format_gt; } else switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id) ) { case BCF_HT_INT: col->setter = vcf_setter_format_int; break; case BCF_HT_REAL: col->setter = vcf_setter_format_real; break; case BCF_HT_STR: col->setter = vcf_setter_format_str; has_fmt_str = 1; break; default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id)); } hdr_id = bcf_hdr_id2int(tgts_hdr, BCF_DT_ID, hrec->vals[k]); col->number = bcf_hdr_id2length(tgts_hdr,BCF_HL_FMT,hdr_id); } } else if ( !strncasecmp("FORMAT/",str.s, 7) || !strncasecmp("FMT/",str.s,4) ) { char *key_dst = str.s + (!strncasecmp("FMT/",str.s,4) ? 4 : 7); char *key_src = strstr(key_dst,":="); if ( key_src ) { *key_src = 0; key_src += 2; if ( !strncasecmp("FORMAT/",key_src,7) ) key_src += 7; else if ( !strncasecmp("FMT/",key_src,4) ) key_src += 4; } else key_src = key_dst; need_sample_map = 1; if ( args->tgts_is_vcf ) { bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->files->readers[1].header, BCF_HL_FMT, "ID", key_src, NULL); if ( !hrec ) error("No such annotation \"%s\" in %s\n", key_src,args->targets_fname); tmp.l = 0; bcf_hrec_format_rename(hrec, key_dst, &tmp); bcf_hdr_append(args->hdr_out, tmp.s); if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update header", __func__); } int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, key_dst); if ( !bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_FMT,hdr_id) ) error("The FORMAT tag \"%s\" is not defined in %s, was the -h option provided?\n", str.s, args->targets_fname); args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); if ( !args->tgts_is_vcf ) { col->icol = icol; icol += args->nsmpl_annot - 1; } else col->icol = -1; col->replace = replace; col->hdr_key_src = strdup(key_src); col->hdr_key_dst = strdup(key_dst); if ( !strcasecmp("GT",key_src) ) { if ( !args->tgts_is_vcf ) error("The FORMAT/GT field can be currently populated only from a VCF\n"); col->setter = vcf_setter_format_gt; } else switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id) ) { case BCF_HT_INT: col->setter = args->tgts_is_vcf ? vcf_setter_format_int : setter_format_int; break; case BCF_HT_REAL: col->setter = args->tgts_is_vcf ? vcf_setter_format_real : setter_format_real; break; case BCF_HT_STR: col->setter = args->tgts_is_vcf ? vcf_setter_format_str : setter_format_str; has_fmt_str = 1; break; default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id)); } if ( args->tgts_is_vcf ) { bcf_hdr_t *tgts_hdr = args->files->readers[1].header; hdr_id = bcf_hdr_id2int(tgts_hdr, BCF_DT_ID, col->hdr_key_src); col->number = bcf_hdr_id2length(tgts_hdr,BCF_HL_FMT,hdr_id); } } else { if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -INFO/TAG feature has not been implemented yet.\n"); if ( replace & SET_OR_APPEND ) { if ( args->tgts_is_vcf ) error("Error: the =INFO/TAG feature is currently supported only with TAB annotation files and has limitations\n" " (the annotation type is modified to \"Number=.\" and allele ordering is disregarded)\n"); fprintf(bcftools_stderr,"Warning: the =INFO/TAG feature modifies the annotation to \"Number=.\" and disregards allele ordering\n"); } args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols); annot_col_t *col = &args->cols[args->ncols-1]; memset(col,0,sizeof(*col)); col->icol = icol; col->replace = replace; int explicit_src_info = 0; int explicit_dst_info = 0; char *key_dst; if ( !strncasecmp("INFO/",str.s,5) ) { key_dst = str.s + 5; explicit_dst_info = 1; } else if ( !strcasecmp("~INFO/END",str.s) ) { key_dst = str.s + 6; explicit_dst_info = 1; } else key_dst = str.s; char *key_src = strstr(key_dst,":="); if ( key_src ) { *key_src = 0; key_src += 2; if ( !strncasecmp("INFO/",key_src,5) ) { key_src += 5; explicit_src_info = 1; } else if ( !strncasecmp("FMT/",key_src,4) || !strncasecmp("FORMAT/",key_src,5) ) { key_src[-2] = ':'; error("Did you mean \"FMT/%s\" rather than \"%s\"?\n",str.s,str.s); } else if ( !strcasecmp("FILTER",key_src) && args->tgts_is_vcf ) { col->getter = vcf_getter_filter2str; } } else key_src = key_dst; col->hdr_key_src = strdup(key_src); col->hdr_key_dst = strdup(key_dst); int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, key_dst); if ( !bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_INFO,hdr_id) ) { if ( args->tgts_is_vcf ) // reading annotations from a VCF, add a new header line { if ( !strcasecmp("ID",key_src) && !explicit_src_info ) { // transferring ID column into a new INFO tag tmp.l = 0; ksprintf(&tmp,"##INFO=",key_dst); } else if ( !strcasecmp("FILTER",key_src) && !explicit_src_info ) { // transferring FILTER column into a new INFO tag tmp.l = 0; ksprintf(&tmp,"##INFO=",key_dst); } else { bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->files->readers[1].header, BCF_HL_INFO, "ID", key_src, NULL); if ( !hrec ) { if ( explicit_dst_info+explicit_src_info==0 && bcf_hdr_get_hrec(args->files->readers[1].header, BCF_HL_FMT, "ID", key_src, NULL) ) error("Did you mean \"FMT/%s\" rather than \"%s\"?\n",str.s,str.s); char *ptr = strchr(key_src,'='); if ( ptr ) { *ptr = 0; tmp.l = 0; ksprintf(&tmp,"%s:=%s",key_src,ptr+1); *ptr = '='; error("The INFO tag \"%s\" is not defined, is this what you want \"%s\" ?\n",key_src,tmp.s); } error("The INFO tag \"%s\" is not defined in %s, was the -h option provided?\n", key_src,args->files->readers[1].fname); } tmp.l = 0; bcf_hrec_format_rename(hrec, key_dst, &tmp); } bcf_hdr_append(args->hdr_out, tmp.s); if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update header", __func__); hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, key_dst); } else error("The INFO tag \"%s\" is not defined in %s, was the -h option provided?\n", key_dst, args->targets_fname); assert( bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_INFO,hdr_id) ); } if ( args->tgts_is_vcf ) { if ( !strcasecmp("ID",key_src) && !explicit_src_info ) col->getter = vcf_getter_id2str; else if ( !strcasecmp("FILTER",key_src) && !explicit_src_info ) col->getter = vcf_getter_filter2str; } col->number = bcf_hdr_id2length(args->hdr_out,BCF_HL_INFO,hdr_id); switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_INFO,hdr_id) ) { case BCF_HT_FLAG: col->setter = args->tgts_is_vcf ? vcf_setter_info_flag : setter_info_flag; break; case BCF_HT_INT: col->setter = args->tgts_is_vcf ? vcf_setter_info_int : setter_info_int; break; case BCF_HT_REAL: col->setter = args->tgts_is_vcf ? vcf_setter_info_real : setter_info_real; break; case BCF_HT_STR: col->setter = args->tgts_is_vcf ? vcf_setter_info_str : setter_info_str; break; default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_INFO,hdr_id)); } if ( replace & SET_OR_APPEND ) // change to Number=. { bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->hdr_out, BCF_HL_INFO, "ID", key_dst, NULL); if ( !hrec ) error("Uh, could not find the new tag \"%s\" in the header\n", key_dst); hrec = bcf_hrec_dup(hrec); int j = bcf_hrec_find_key(hrec, "Number"); if ( j<0 ) error("Uh, could not find the entry Number in the header record of %s\n",key_dst); free(hrec->vals[j]); hrec->vals[j] = strdup("."); bcf_hdr_remove(args->hdr_out,BCF_HL_INFO, key_dst); bcf_hdr_add_hrec(args->hdr_out, hrec); } } if ( !*se ) break; ss = ++se; } free(str.s); free(tmp.s); free(args->columns); if ( skip_info ) khash_str2int_destroy_free(skip_info); if ( skip_fmt ) khash_str2int_destroy_free(skip_fmt); if ( has_fmt_str ) { int n = bcf_hdr_nsamples(args->hdr_out); if ( args->tgts_is_vcf && nfiles->readers[1].header) ) n = bcf_hdr_nsamples(args->files->readers[1].header); args->tmpp = (char**)malloc(sizeof(char*)*n); args->tmpp2 = (char**)malloc(sizeof(char*)*n); } if ( !need_sample_map ) { free(args->sample_map); args->sample_map = NULL; } else if ( sample_map_ok<0 ) error("No matching samples in source and destination file?\n"); } static void init_merge_method(args_t *args) { int i; for (i=0; incols; i++) { args->cols[i].merge_method = MM_FIRST; args->cols[i].mm_str_hash = NULL; args->cols[i].mm_dbl = NULL; args->cols[i].mm_dbl_nalloc = args->cols[i].mm_dbl_nused = args->cols[i].mm_dbl_ndat = 0; memset(&args->cols[i].mm_kstr, 0, sizeof(args->cols[i].mm_kstr)); } if ( !args->merge_method_str.l ) return; if ( args->tgts_is_vcf ) error("Error: the --merge-logic is intended for use with BED or TAB-delimited files only.\n"); if ( !args->tgt_idx && !args->tgts ) error("Error: BEG,END (or FROM,TO) columns or REF,ALT columns are expected with the --merge-logic option.\n"); char *sb = args->merge_method_str.s; while ( *sb ) { char *se = sb; while ( *se && *se!=',' ) se++; args->tmpks.l = 0; kputsn(sb, se-sb, &args->tmpks); kputc(0, &args->tmpks); char *mm_type_str = args->tmpks.s + args->tmpks.l; while ( *mm_type_str!=':' && mm_type_str > args->tmpks.s ) mm_type_str--; if ( *mm_type_str!=':' ) error("Error: could not parse the argument to --merge-logic: %s\n", args->merge_method_str.s); *mm_type_str = 0; mm_type_str++; int mm_type = MM_FIRST; if ( !strcasecmp("unique",mm_type_str) ) mm_type = MM_UNIQUE; else if ( !strcasecmp("first",mm_type_str) ) mm_type = MM_FIRST; else if ( !strcasecmp("append",mm_type_str) ) mm_type = MM_APPEND; else if ( !strcasecmp("append-missing",mm_type_str) ) { mm_type = MM_APPEND_MISSING; if ( args->ref_idx!=-1 ) args->has_append_mode = 1; } else if ( !strcasecmp("sum",mm_type_str) ) mm_type = MM_SUM; else if ( !strcasecmp("avg",mm_type_str) ) mm_type = MM_AVG; else if ( !strcasecmp("min",mm_type_str) ) mm_type = MM_MIN; else if ( !strcasecmp("max",mm_type_str) ) mm_type = MM_MAX; else error("Error: could not parse --merge-logic %s, the logic \"%s\" is not recognised\n", args->merge_method_str.s,mm_type_str); for (i=0; incols; i++) { if ( strcmp(args->cols[i].hdr_key_dst,args->tmpks.s) ) continue; if ( (mm_type==MM_APPEND || mm_type==MM_APPEND_MISSING) && args->cols[i].number!=BCF_VL_VAR ) error("Error: --merge-logic append can be requested only for tags of variable length (Number=.)\n"); args->cols[i].merge_method = mm_type; break; } if ( i==args->ncols ) error("No such tag in the destination file: %s\n", args->tmpks.s); sb = *se ? se + 1 : se; } if ( args->has_append_mode ) { // create a missing line to insert missing values when VCF ALT finds no match in the annotation file args->aline_missing = (annot_line_t*)calloc(1,sizeof(*args->aline_missing)); int ncol = 0; for (i=0; incols; i++) if ( ncol < args->cols[i].icol + 1 ) ncol = args->cols[i].icol + 1; if ( ncol < args->ref_idx + 1 ) ncol = args->ref_idx + 1; args->aline_missing->mcols = ncol; args->aline_missing->ncols = ncol; args->aline_missing->cols = (char**) malloc(ncol*sizeof(char*)); for (i=0; ialine_missing->cols[i] = strdup("."); } } static void rename_chrs(args_t *args, char *fname) { int n, i; char **map = hts_readlist(fname, 1, &n); if ( !map ) error("Could not read: %s\n", fname); for (i=0; ihdr_out, map[i]); bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->hdr_out, BCF_HL_CTG, "ID", map[i], NULL); if ( !hrec ) continue; // the sequence not present int j = bcf_hrec_find_key(hrec, "ID"); assert( j>=0 ); free(hrec->vals[j]); ss++; while ( *ss && isspace(*ss) ) ss++; char *se = ss; while ( *se && !isspace(*se) ) se++; *se = 0; hrec->vals[j] = strdup(ss); args->hdr_out->id[BCF_DT_CTG][rid].key = hrec->vals[j]; } for (i=0; ihdr_out, BCF_DT_ID, ori_tag); if ( id<0 ) return 1; bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->hdr_out, type, "ID", ori_tag, NULL); if ( !hrec ) return 1; // the ID attribute not present int j = bcf_hrec_find_key(hrec, "ID"); assert( j>=0 ); free(hrec->vals[j]); char *ptr = new_tag; while ( *ptr && !isspace(*ptr) ) ptr++; *ptr = 0; hrec->vals[j] = strdup(new_tag); args->hdr_out->id[BCF_DT_ID][id].key = hrec->vals[j]; return 0; } static void rename_annots(args_t *args) { int i; if ( args->rename_annots ) { args->rename_annots_map = hts_readlist(args->rename_annots, 1, &args->rename_annots_nmap); if ( !args->rename_annots_map ) error("Could not read: %s\n", args->rename_annots); } for (i=0; irename_annots_nmap; i++) { char *ptr = args->rename_annots_map[i]; while ( *ptr && !isspace(*ptr) ) ptr++; if ( !*ptr ) error("Could not parse: %s\n", args->rename_annots_map[i]); char *rmme = ptr; *ptr = 0; ptr++; while ( *ptr && isspace(*ptr) ) ptr++; if ( !*ptr ) { *rmme = ' '; error("Could not parse: %s\n", args->rename_annots_map[i]); } if ( rename_annots_core(args, args->rename_annots_map[i], ptr) < 0 ) error("Cannot rename \"%s\" to \"%s\"\n",args->rename_annots_map[i],ptr); } } static void rename_annots_push(args_t *args, char *src, char *dst) { args->rename_annots_nmap++; args->rename_annots_map = (char**)realloc(args->rename_annots_map,sizeof(*args->rename_annots_map)*args->rename_annots_nmap); kstring_t str = {0,0,0}; ksprintf(&str,"%s %s",src,dst); args->rename_annots_map[ args->rename_annots_nmap - 1 ] = str.s; } static void init_filters(args_t *args) { // Check if the -i/-e expressions contain external values that should be determined // on the fly from the annotation file. The expressions can be given as // TAG={NAME} // TAG={str:NAME} // TAG={int:NAME} // TAG={float:NAME} kstring_t str = {0,0,0}; char *src = strdup(args->filter_str); int len = 0; while (1) { char *beg = strchr(src+len,'{'); if ( !beg ) break; // check if "{" appears inside quotes, in such case do not modify char skip = 0; char *tmp = src; while ( tmpfilter_str); // unbalanced quotation; todo: check for escape char len = tmp - src + 1; skip = 1; } if ( skip ) continue; char *end = ++beg; while ( *end && *end!='}' ) end++; if ( !*end ) error("Could not parse the expression: %s\n",args->filter_str); *end = 0; // explicit typing? int type = -1; tmp = beg; while ( *tmp && *tmp!=':' ) tmp++; if ( *tmp ) { *tmp = 0; if ( !strcasecmp(beg,"str") ) type = BCF_HT_STR; else if ( !strcasecmp(beg,"int") ) type = BCF_HT_INT; else if ( !strcasecmp(beg,"float") ) type = BCF_HT_REAL; } args->n_ext++; args->ext = (ext_t*)realloc(args->ext,sizeof(*args->ext)*args->n_ext); ext_t *ext = &args->ext[args->n_ext-1]; ext->ht_type = type; ext->name = strdup(beg); if ( beg-1 > src ) kputsn(src,beg-1-src,&str); if ( type==-1 ) kputs("{}",&str); else if ( type==BCF_HT_STR ) kputs("{str}",&str); else if ( type==BCF_HT_INT ) kputs("{int}",&str); else if ( type==BCF_HT_REAL ) kputs("{float}",&str); len = str.l; kputs(end+1,&str); free(src); src = strdup(str.s); str.l = 0; } args->filter = filter_init(args->hdr, src); free(src); free(str.s); int i,j,n_ext; const int *ext_type = filter_ext_types(args->filter, &n_ext); if ( n_ext != args->n_ext ) error("Failed to parse the expression, unexpected number of dynamic variables (%d vs %d): %s\n",n_ext,args->n_ext,args->filter_str); if ( !args->n_ext ) return; if ( !args->tgts ) error("Error: dynamic variables in -i/-e expressions can be currently used only with tab-delimited file, not with VCF (todo)\n"); // contains external values args->ext_ptr = malloc(sizeof(*args->ext_ptr)*args->n_ext); for (i=0; in_ext; i++) args->ext[i].ht_type = ext_type[i]; args->filter_ext = args->filter; args->filter = NULL; // set the column idx if ( args->ncols ) { for (i=0; in_ext; i++) { for (j=0; jncols; j++) { if ( strcmp(args->ext[i].name,args->cols[j].hdr_key_src) ) continue; args->ext[i].icol = args->cols[j].icol; break; } if ( j==args->ncols ) error("No such column: %s\n",args->ext[i].name); } } } static void init_data(args_t *args) { args->hdr = args->files->readers[0].header; args->hdr_out = bcf_hdr_dup(args->hdr); if ( args->set_ids_fmt ) { if ( args->set_ids_fmt[0]=='+' ) { args->set_ids_replace = 0; args->set_ids_fmt++; } args->set_ids = convert_init(args->hdr_out, NULL, 0, args->set_ids_fmt); } if ( args->remove_annots ) init_remove_annots(args); if ( args->header_fname || args->header_lines ) init_header_lines(args); if ( args->targets_fname && args->tgts_is_vcf ) { // reading annots from a VCF if ( !bcf_sr_add_reader(args->files, args->targets_fname) ) error("Failed to open %s: %s\n", args->targets_fname,bcf_sr_strerror(args->files->errnum)); args->tgts_hdr = args->files->readers[1].header; } if ( args->columns ) init_columns(args); if ( args->targets_fname && !args->tgts_is_vcf ) { if ( !args->columns ) error("The -c option not given\n"); if ( args->chr_idx==-1 ) error("The -c CHROM option not given\n"); if ( args->beg_idx==-1 ) error("The -c POS option not given\n"); if ( args->single_overlaps && args->merge_method_str.l ) error("The options --merge-logic and --single-overlaps cannot be combined\n"); if ( args->end_idx==-1 || (args->single_overlaps && !args->merge_method_str.l) ) { args->end_idx = -args->beg_idx - 1; args->tgts = bcf_sr_regions_init(args->targets_fname,1,args->chr_idx,args->beg_idx,args->end_idx); if ( !args->tgts ) error("Could not initialize the annotation file: %s\n", args->targets_fname); if ( !args->tgts->tbx ) error("Expected tabix-indexed annotation file: %s\n", args->targets_fname); } else { if ( args->ref_idx!=-1 ) error("Error: the REF columns will be ignored when BEG,END (or FROM,TO) is present. Replace END (or TO) with \"-\".\n"); int len = strlen(args->targets_fname); if ( len>=7 && !strcasecmp(".bed.gz",args->targets_fname+len-7) ) args->tgt_is_bed = 1; else if ( len>=8 && !strcasecmp(".bed.bgz",args->targets_fname+len-8) ) args->tgt_is_bed = 1; else if ( len>=4 && !strcasecmp(".bed",args->targets_fname+len-4) ) args->tgt_is_bed = 1; args->tgt_idx = regidx_init(args->targets_fname,parse_with_payload,free_payload,sizeof(char*),args); if ( !args->tgt_idx ) error("Failed to parse: %s\n", args->targets_fname); args->tgt_itr = regitr_init(args->tgt_idx); args->nalines++; hts_expand0(annot_line_t,args->nalines,args->malines,args->alines); } if ( args->min_overlap_str ) { char *tmp = args->min_overlap_str; if ( args->min_overlap_str[0] != ':' ) { args->min_overlap_ann = strtod(args->min_overlap_str,&tmp); if ( args->min_overlap_ann < 0 || args->min_overlap_ann > 1 || (*tmp && *tmp!=':') ) error("Could not parse \"--min-overlap %s\", expected value(s) between 0-1\n", args->min_overlap_str); } if ( *tmp && *tmp==':' ) { args->min_overlap_vcf = strtod(tmp+1,&tmp); if ( args->min_overlap_vcf < 0 || args->min_overlap_vcf > 1 || *tmp ) error("Could not parse \"--min-overlap %s\", expected value(s) between 0-1\n", args->min_overlap_str); } } } init_merge_method(args); args->vcmp = vcmp_init(); if ( args->filter_str ) init_filters(args); if ( args->mark_sites ) { if ( !args->targets_fname ) { if ( args->mark_sites_logic!=MARK_LISTED ) error("The -a option not given but -%s logic was requested\n",args->mark_sites); fprintf(bcftools_stderr,"Note: The -a option not given, all sites will be annotated with INFO/%s\n",args->mark_sites); bcf_hdr_printf(args->hdr_out,"##INFO=", args->mark_sites,args->mark_sites); } else bcf_hdr_printf(args->hdr_out,"##INFO=", args->mark_sites,args->mark_sites_logic==MARK_LISTED?"":"not ",args->mark_sites); } if (args->record_cmd_line) bcf_hdr_append_version(args->hdr_out, args->argc, args->argv, "bcftools_annotate"); if ( !args->drop_header ) { if ( args->rename_chrs ) rename_chrs(args, args->rename_chrs); if ( args->rename_annots || args->rename_annots_map ) rename_annots(args); char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( args->out_fh == NULL ) error("[%s] Error: cannot write to \"%s\": %s\n", __func__,args->output_fname, strerror(errno)); if ( args->n_threads ) hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->files->p); if ( bcf_hdr_write(args->out_fh, args->hdr_out)!=0 ) error("[%s] Error: failed to write the header to %s\n", __func__,args->output_fname); if ( init_index2(args->out_fh,args->hdr,args->output_fname, &args->index_fn, args->write_index) < 0 ) error("Error: failed to initialise index for %s\n",args->output_fname); } } static void destroy_data(args_t *args) { int i; for (i=0; in_ext; i++) { free(args->ext[i].name); if ( args->ext[i].ht_type!=BCF_HT_STR ) continue; } free(args->ext_ptr); free(args->ext); for (i=0; inrm; i++) free(args->rm[i].key); free(args->rm); if ( args->hdr_out ) bcf_hdr_destroy(args->hdr_out); if (args->vcmp) vcmp_destroy(args->vcmp); for (i=0; incols; i++) { free(args->cols[i].hdr_key_src); free(args->cols[i].hdr_key_dst); free(args->cols[i].mm_kstr.s); if ( args->cols[i].mm_str_hash ) khash_str2int_destroy_free(args->cols[i].mm_str_hash); free(args->cols[i].mm_dbl); free(args->cols[i].ptr); } free(args->cols); if ( args->aline_missing ) { for (i=0; ialine_missing->ncols; i++) free(args->aline_missing->cols[i]); free(args->aline_missing->cols); free(args->aline_missing); } for (i=0; imalines; i++) { free(args->alines[i].cols); free(args->alines[i].als); free(args->alines[i].line.s); } free(args->alines); free(args->srt_alines); if ( args->tgt_idx ) { regidx_destroy(args->tgt_idx); regitr_destroy(args->tgt_itr); } if ( args->rename_annots_map ) { for (i=0; irename_annots_nmap; i++) free(args->rename_annots_map[i]); free(args->rename_annots_map); } if ( args->tgts ) bcf_sr_regions_destroy(args->tgts); free(args->tmpks.s); free(args->tmpi); free(args->tmpf); free(args->tmps); free(args->tmpp); free(args->tmpi2); free(args->tmpf2); free(args->tmps2); free(args->tmpp2); free(args->tmpi3); free(args->tmpf3); free(args->src_smpl_pld); free(args->dst_smpl_pld); if ( args->set_ids ) convert_destroy(args->set_ids); if ( args->filter ) filter_destroy(args->filter); if ( args->filter_ext ) filter_destroy(args->filter_ext); if (args->out_fh) { if ( args->write_index ) { if ( bcf_idx_save(args->out_fh)<0 ) { if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"bcftools_stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"bcftools_stdout"); } free(args->sample_map); free(args->merge_method_str.s); } static void parse_annot_line(args_t *args, char *str, annot_line_t *tmp) { tmp->line.l = 0; kputs(str, &tmp->line); char *s = tmp->line.s; tmp->ncols = 1; hts_expand(char*,tmp->ncols,tmp->mcols,tmp->cols); tmp->cols[0] = s; while ( *s ) { if ( *s=='\t' ) { tmp->ncols++; hts_expand(char*,tmp->ncols,tmp->mcols,tmp->cols); tmp->cols[tmp->ncols-1] = s+1; *s = 0; } s++; } if ( args->ref_idx != -1 ) { if ( args->ref_idx >= tmp->ncols ) error("Could not parse the line, expected %d+ columns, found %d:\n\t%s\n",args->ref_idx+1,tmp->ncols,str); if ( args->alt_idx >= tmp->ncols ) error("Could not parse the line, expected %d+ columns, found %d:\n\t%s\n",args->alt_idx+1,tmp->ncols,str); tmp->nals = 2; hts_expand(char*,tmp->nals,tmp->mals,tmp->als); tmp->als[0] = tmp->cols[args->ref_idx]; tmp->als[1] = s = tmp->cols[args->alt_idx]; while ( *s ) { if ( *s==',' ) { tmp->nals++; hts_expand(char*,tmp->nals,tmp->mals,tmp->als); tmp->als[tmp->nals-1] = s+1; *s = 0; } s++; } } } static void buffer_annot_lines(args_t *args, bcf1_t *line, int start_pos, int end_pos) { if ( args->nalines && args->alines[0].rid != line->rid ) args->nalines = 0; int i = 0; while ( inalines ) { if ( line->pos > args->alines[i].end ) { args->nalines--; if ( args->nalines && inalines ) { annot_line_t tmp = args->alines[i]; memmove(&args->alines[i],&args->alines[i+1],(args->nalines-i)*sizeof(annot_line_t)); args->alines[args->nalines] = tmp; } } else i++; } if ( !args->filter_ext && args->ref_idx==-1 && args->nalines ) return; while ( !bcf_sr_regions_overlap(args->tgts, bcf_seqname(args->hdr,line), start_pos,end_pos) ) { if ( args->nalines + 1 == 0xffff ) break; // likely a symbolic allele, don't let the buffer overflow args->nalines++; hts_expand0(annot_line_t,args->nalines,args->malines,args->alines); annot_line_t *tmp = &args->alines[args->nalines-1]; tmp->rid = line->rid; tmp->start = args->tgts->start; tmp->end = args->tgts->end; parse_annot_line(args, args->tgts->line.s, tmp); if ( args->filter_ext || args->ref_idx != -1 ) { int iseq = args->tgts->iseq; if ( bcf_sr_regions_next(args->tgts)<0 || args->tgts->iseq!=iseq ) break; } else break; } } // search string in semicolon separated strings (xx vs aa;bb) static int str_match(char *needle, char *haystack) { int len = strlen(needle); char *ptr = haystack; while ( *ptr && (ptr=strstr(ptr,needle)) ) { if ( ptr[len]!=0 && ptr[len]!=';' ) ptr++; // a prefix, not a match else if ( ptr==haystack || ptr[-1]==';' ) return 1; // a match ptr++; // a suffix, not a match } return 0; } // search common string in semicolon separated strings (xx;yy;zz vs aa;bb) static int strstr_match(char *a, char *b) { char *beg = a; while ( *beg ) { char *end = beg; while ( *end && *end!=';' ) end++; char tmp = *end; if ( *end==';' ) *end = 0; int ret = str_match(beg,b); *end = tmp; if ( ret || !*end ) return ret; beg = end + 1; } return 0; } static int annotate_from_regidx(args_t *args, bcf1_t *line) { int j; int has_overlap = 0; for (j=0; jncols; j++) args->cols[j].done = 0; if ( regidx_overlap(args->tgt_idx, bcf_seqname(args->hdr,line),line->pos,line->pos+line->rlen-1, args->tgt_itr) ) { hts_pos_t vcf_end = line->pos + line->rlen - 1; while ( regitr_overlap(args->tgt_itr) ) { annot_line_t *tmp = &args->alines[0]; tmp->rid = line->rid; tmp->start = args->tgt_itr->beg; tmp->end = args->tgt_itr->end; // Check min overlap int len_ann = tmp->end - tmp->start + 1; int len_vcf = line->rlen; int isec = (tmp->end < vcf_end ? tmp->end : vcf_end) - (tmp->start > line->pos ? tmp->start : line->pos) + 1; assert( isec > 0 ); if ( args->min_overlap_ann && args->min_overlap_ann > (float)isec/len_ann ) continue; if ( args->min_overlap_vcf && args->min_overlap_vcf > (float)isec/len_vcf ) continue; parse_annot_line(args, regitr_payload(args->tgt_itr,char*), tmp); // If a plain BED file is provided and we are asked to just mark overlapping sites, there are // no additional columns. Not sure if there can be any side effects for ill-formatted BED files // with variable number of columns if ( !args->ncols && args->mark_sites ) has_overlap = 1; for (j=0; jncols; j++) { if ( args->cols[j].done==1 ) continue; int ret = args->cols[j].setter(args,line,&args->cols[j],tmp); if ( ret < 0 ) error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); if ( ret==0 ) args->cols[j].done = 1; has_overlap = 1; } } } for (j=0; jncols; j++) { if ( args->cols[j].done==1 || args->cols[j].merge_method == MM_FIRST ) continue; if ( !args->cols[j].setter ) continue; if ( args->cols[j].setter(args,line,&args->cols[j],NULL) < 0 ) error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); } return has_overlap; } static int pass_filter_test_ext(args_t *args, bcf1_t *line, annot_line_t *ann) { char *tmp; int i; for (i=0; in_ext; i++) { int j = args->ext[i].icol; if ( args->ext[i].ht_type==BCF_HT_STR ) args->ext_ptr[i] = args->ext[i].s = ann->cols[j]; else if ( args->ext[i].ht_type==BCF_HT_INT ) { args->ext[i].i = strtol(ann->cols[j],&tmp,10); if ( *tmp ) { if ( strcmp(".",ann->cols[j]) ) error("Error: could not parse the annotation file, expected an integer, found \"%s\"\n",ann->cols[j]); args->ext_ptr[i] = NULL; } else args->ext_ptr[i] = &args->ext[i].i; } else if ( args->ext[i].ht_type==BCF_HT_REAL ) { args->ext[i].f = strtod(ann->cols[j],&tmp); if ( *tmp ) { if ( strcmp(".",ann->cols[j]) ) error("Error: could not parse the annotation file, expected a float, found \"%s\"\n",ann->cols[j]); args->ext_ptr[i] = NULL; } else args->ext_ptr[i] = &args->ext[i].f; } } int pass = filter_test_ext(args->filter_ext,line,NULL,(const void**)args->ext_ptr); if ( args->filter_logic==FLT_EXCLUDE ) pass = pass ? 0 : 1; return pass; } static int annotate_from_tab(args_t *args, bcf1_t *line) { int i,j; int has_overlap = 0; // Buffer annotation lines. When multiple ALT alleles are present in the annotation file, at least one // must match some of the VCF alleles. If the append-missing mode is set (and REF+ALT is requested), the // buffered lines will annotate the VCF respecting the order in ALT and when no matching line is found // for an ALT, missing value is appended instead. int end_pos = line->pos + line->rlen - 1; buffer_annot_lines(args, line, line->pos, end_pos); args->nsrt_alines = 0; hts_expand(uint32_t,args->nalines,args->msrt_alines,args->srt_alines); if ( args->nalines >= 0xffff || line->n_allele >= 0xffff ) error("Error: too many alleles or annotation lines in the buffer at %s:%"PRId64" (todo:skip?)\n",bcf_seqname(args->hdr,line),(int64_t) line->pos+1); kstring_t match_end = {0,0,0}; if ( args->match_end>=0 && bcf_get_info_int32(args->hdr,line,"END",&args->tmpi,&args->mtmpi)==1 ) kputw(args->tmpi[0],&match_end); // Find matching lines for (i=0; inalines; i++) { if ( line->pos > args->alines[i].end || end_pos < args->alines[i].start ) continue; if ( args->ref_idx != -1 ) // REF+ALT matching requested { if ( line->pos!=args->alines[i].start || vcmp_set_ref(args->vcmp, line->d.allele[0], args->alines[i].als[0]) < 0 ) continue; // refs are not compatible for (j=1; jalines[i].nals; j++) { int ialt; if ( line->n_allele==1 && args->alines[i].als[j][0]=='.' && args->alines[i].als[j][1]==0 ) // match: no ALT allele in VCF and annot file has "." ialt = 0; else { ialt = vcmp_find_allele(args->vcmp, line->d.allele+1, line->n_allele - 1, args->alines[i].als[j]); if ( ialt < 0 ) continue; ialt++; } if ( args->match_id>=0 && !strstr_match(line->d.id,args->alines[i].cols[args->match_id]) ) continue; if ( args->match_end>=0 && match_end.l && strcmp(match_end.s,args->alines[i].cols[args->match_end]) ) continue; if ( args->filter_ext && !pass_filter_test_ext(args,line,&args->alines[i]) ) continue; args->srt_alines[args->nsrt_alines++] = (ialt<<16) | i; has_overlap = 1; break; } } else if ( args->filter_ext ) { if ( pass_filter_test_ext(args,line,&args->alines[i]) ) { args->srt_alines[args->nsrt_alines++] = (0xffff<<16) | i; has_overlap = 1; } } else // overlap, REF+ALT matching not requested { args->srt_alines[args->nsrt_alines++] = (0xffff<<16) | i; has_overlap = 1; } } free(match_end.s); if ( !has_overlap && args->filter_ext && !args->keep_sites ) return has_overlap; // Sort lines if needed if ( args->has_append_mode ) { // insertion sort by VCF ALT index (top bits) and alines index (low bits) uint32_t tmp; for (i=1; insrt_alines; i++) for (j=i; j>0 && args->srt_alines[j] < args->srt_alines[j-1]; j--) tmp = args->srt_alines[j], args->srt_alines[j] = args->srt_alines[j-1], args->srt_alines[j-1] = tmp; } // Annotate for (j=0; jncols; j++) args->cols[j].done = 0; int ialt_exp = 1; for (i=0; insrt_alines; i++) { int ialt = args->srt_alines[i] >> 16; int ilin = args->srt_alines[i] & 0xffff; if ( args->has_append_mode ) { if ( ialt_exp > ialt ) continue; // multiple annotation lines for the same position if ( ialt_exp < ialt ) { // REF+ALT matching requested, append-missing mode: insert "." if no annotation line was found for the ALT while ( ialt_exp++ < ialt ) { for (j=0; jncols; j++) { if ( args->cols[j].merge_method != MM_APPEND_MISSING ) continue; if ( args->cols[j].done==1 ) continue; if ( !args->cols[j].setter ) continue; int ret = args->cols[j].setter(args,line,&args->cols[j],args->aline_missing); if ( ret < 0 ) error("fixme: Could not set missing %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); if ( ret==0 ) args->cols[j].done = 1; } } } } for (j=0; jncols; j++) { if ( args->cols[j].done==1 ) continue; if ( !args->cols[j].setter ) continue; int ret = args->cols[j].setter(args,line,&args->cols[j],&args->alines[ilin]); if ( ret < 0 ) error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); if ( ret==0 ) args->cols[j].done = 1; } ialt_exp = ialt + 1; } if ( args->nsrt_alines ) { // In the append-missing mode fill missing values to all trailing ALTs, but only if at least one // record was found. Otherwise leave the row will be left without annotation. if ( args->has_append_mode && ialt_exp < line->n_allele ) { while ( ialt_exp++ < line->n_allele ) { for (j=0; jncols; j++) { if ( args->cols[j].merge_method != MM_APPEND_MISSING ) continue; if ( args->cols[j].done==1 ) continue; if ( !args->cols[j].setter ) continue; int ret = args->cols[j].setter(args,line,&args->cols[j],args->aline_missing); if ( ret < 0 ) error("fixme: Could not set missing %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); if ( ret==0 ) args->cols[j].done = 1; } } } // Flush for (j=0; jncols; j++) { if ( args->cols[j].done==1 || args->cols[j].merge_method == MM_FIRST ) continue; if ( !args->cols[j].setter ) continue; int ret = args->cols[j].setter(args,line,&args->cols[j],NULL); if ( ret < 0 ) error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); } } return has_overlap; } static int annotate_from_vcf(args_t *args, bcf1_t *line) { if ( !bcf_sr_has_line(args->files,1) ) return 0; int j; bcf1_t *aline = bcf_sr_get_line(args->files,1); for (j=0; jncols; j++) { if ( !args->cols[j].setter ) continue; if ( args->cols[j].setter(args,line,&args->cols[j],aline) ) error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); } return 1; } static int annotate_from_self(args_t *args, bcf1_t *line) { int j; for (j=0; jncols; j++) { if ( !args->cols[j].setter ) continue; if ( args->cols[j].setter(args,line,&args->cols[j],NULL) ) error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1); } return 0; } static int annotate_line(args_t *args, bcf1_t *line) { args->current_rec = line; int i; for (i=0; inrm; i++) args->rm[i].handler(args, line, &args->rm[i]); int has_overlap = 0; if ( args->tgt_idx ) has_overlap = annotate_from_regidx(args,line); else if ( args->tgts ) has_overlap = annotate_from_tab(args,line); else if ( args->files->nreaders == 2 ) has_overlap = annotate_from_vcf(args,line); else if ( args->ncols ) has_overlap = annotate_from_self(args,line); if ( args->set_ids ) { args->tmpks.l = 0; convert_line(args->set_ids, line, &args->tmpks); if ( args->tmpks.l ) { int replace = 0; if ( args->set_ids_replace ) replace = 1; else if ( !line->d.id || (line->d.id[0]=='.' && !line->d.id[1]) ) replace = 1; if ( replace ) bcf_update_id(args->hdr_out,line,args->tmpks.s); } } if ( args->mark_sites ) { if ( !args->targets_fname ) has_overlap = 1; // ideally, we'd like to be far more general than this in future, see https://github.com/samtools/bcftools/issues/87 if ( args->mark_sites_logic==MARK_LISTED ) bcf_update_info_flag(args->hdr_out,line,args->mark_sites,NULL,has_overlap?1:0); else bcf_update_info_flag(args->hdr_out,line,args->mark_sites,NULL,has_overlap?0:1); } return has_overlap; } static void usage(args_t *args) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: Annotate and edit VCF/BCF files.\n"); fprintf(bcftools_stderr, "Usage: bcftools annotate [options] VCF\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Options:\n"); fprintf(bcftools_stderr, " -a, --annotations FILE VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+\n"); fprintf(bcftools_stderr, " -c, --columns LIST List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details\n"); fprintf(bcftools_stderr, " -C, --columns-file FILE Read -c columns from FILE, one name per row, with optional --merge-logic TYPE: NAME[ TYPE]\n"); fprintf(bcftools_stderr, " -e, --exclude EXPR Exclude sites for which the expression is true (see man page for details)\n"); fprintf(bcftools_stderr, " --force Continue despite parsing error (at your own risk!)\n"); fprintf(bcftools_stderr, " -H, --header-line STR Header line which should be appended to the VCF header, can be given multiple times\n"); fprintf(bcftools_stderr, " -h, --header-lines FILE Lines which should be appended to the VCF header\n"); fprintf(bcftools_stderr, " -I, --set-id [+]FORMAT Set ID column using a `bcftools query`-like expression, see man page for details\n"); fprintf(bcftools_stderr, " -i, --include EXPR Select sites for which the expression is true (see man page for details)\n"); fprintf(bcftools_stderr, " -k, --keep-sites Leave -i/-e sites unchanged instead of discarding them\n"); fprintf(bcftools_stderr, " -l, --merge-logic TAG:TYPE Merge logic for multiple overlapping regions (see man page for details), EXPERIMENTAL\n"); fprintf(bcftools_stderr, " -m, --mark-sites [+-]TAG Add INFO/TAG flag to sites which are (\"+\") or are not (\"-\") listed in the -a file\n"); fprintf(bcftools_stderr, " --min-overlap ANN:VCF Required overlap as a fraction of variant in the -a file (ANN), the VCF (:VCF), or reciprocal (ANN:VCF)\n"); fprintf(bcftools_stderr, " --no-version Do not append version and command line to the header\n"); fprintf(bcftools_stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(bcftools_stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(bcftools_stderr, " --pair-logic STR Matching records by , see man page for details [some]\n"); fprintf(bcftools_stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(bcftools_stderr, " -R, --regions-file FILE Restrict to regions listed in FILE\n"); fprintf(bcftools_stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " --rename-annots FILE Rename annotations: TYPE/old\\tnew, where TYPE is one of FILTER,INFO,FORMAT\n"); fprintf(bcftools_stderr, " --rename-chrs FILE Rename sequences according to the mapping: old\\tnew\n"); fprintf(bcftools_stderr, " -s, --samples [^]LIST Comma separated list of samples to annotate (or exclude with \"^\" prefix)\n"); fprintf(bcftools_stderr, " -S, --samples-file [^]FILE File of samples to annotate (or exclude with \"^\" prefix)\n"); fprintf(bcftools_stderr, " --single-overlaps Keep memory low by avoiding complexities arising from handling multiple overlapping intervals\n"); fprintf(bcftools_stderr, " -x, --remove LIST List of annotations (e.g. ID,INFO/DP,FORMAT/DP,FILTER) to remove (or keep with \"^\" prefix). See man page for details\n"); fprintf(bcftools_stderr, " --threads INT Number of extra output compression threads [0]\n"); fprintf(bcftools_stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Examples:\n"); fprintf(bcftools_stderr, " http://samtools.github.io/bcftools/howtos/annotate.html\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int main_vcfannotate(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->files = bcf_sr_init(); args->output_fname = "-"; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->ref_idx = args->alt_idx = args->chr_idx = args->beg_idx = args->end_idx = -1; args->set_ids_replace = 1; args->match_id = -1; args->match_end = -1; args->clevel = -1; args->pair_logic = -1; int regions_is_file = 0; int regions_overlap = 1; static struct option loptions[] = { {"keep-sites",no_argument,NULL,'k'}, {"mark-sites",required_argument,NULL,'m'}, {"set-id",required_argument,NULL,'I'}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"threads",required_argument,NULL,9}, {"annotations",required_argument,NULL,'a'}, {"merge-logic",required_argument,NULL,'l'}, {"collapse",required_argument,NULL,2}, {"pair-logic",required_argument,NULL,2}, {"include",required_argument,NULL,'i'}, {"exclude",required_argument,NULL,'e'}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,3}, {"remove",required_argument,NULL,'x'}, {"columns-file",required_argument,NULL,'C'}, {"columns",required_argument,NULL,'c'}, {"rename-annots",required_argument,NULL,11}, {"rename-chrs",required_argument,NULL,1}, {"header-lines",required_argument,NULL,'h'}, {"header-line",required_argument,NULL,'H'}, {"samples",required_argument,NULL,'s'}, {"samples-file",required_argument,NULL,'S'}, {"single-overlaps",no_argument,NULL,10}, {"min-overlap",required_argument,NULL,12}, {"no-version",no_argument,NULL,8}, {"force",no_argument,NULL,'f'}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "h:H:?o:O:r:R:a:x:c:C:i:e:S:s:I:m:kl:fW::",loptions,NULL)) >= 0) { switch (c) { case 'f': args->force = 1; break; case 'k': args->keep_sites = 1; break; case 'm': args->mark_sites_logic = MARK_LISTED; if ( optarg[0]=='+' ) args->mark_sites = optarg+1; else if ( optarg[0]=='-' ) { args->mark_sites = optarg+1; args->mark_sites_logic = MARK_UNLISTED; } else args->mark_sites = optarg; break; case 'l': if ( args->merge_method_str.l ) kputc(',',&args->merge_method_str); kputs(optarg,&args->merge_method_str); break; case 'I': args->set_ids_fmt = optarg; break; case 's': args->sample_names = optarg; break; case 'S': args->sample_names = optarg; args->sample_is_file = 1; break; case 'c': args->columns = strdup(optarg); break; case 'C': args->columns = strdup(optarg); args->columns_is_file = 1; break; case 'o': args->output_fname = optarg; break; case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } }; if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'x': args->remove_annots = optarg; break; case 'a': args->targets_fname = optarg; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 'h': args->header_fname = optarg; break; case 'H': args->header_lines = dbuf_push(args->header_lines,strdup(optarg)); break; case 1 : args->rename_chrs = optarg; break; case 2 : if ( args->pair_logic==-1 ) args->pair_logic = 0; if ( !strcmp(optarg,"snps") ) args->pair_logic |= BCF_SR_PAIR_SNP_REF; else if ( !strcmp(optarg,"indels") ) args->pair_logic |= BCF_SR_PAIR_INDEL_REF; else if ( !strcmp(optarg,"both") ) args->pair_logic |= BCF_SR_PAIR_BOTH_REF; else if ( !strcmp(optarg,"any") ) args->pair_logic |= BCF_SR_PAIR_ANY; else if ( !strcmp(optarg,"all") ) args->pair_logic |= BCF_SR_PAIR_ANY; else if ( !strcmp(optarg,"some") ) args->pair_logic |= BCF_SR_PAIR_SOME; else if ( !strcmp(optarg,"none") ) args->pair_logic = BCF_SR_PAIR_EXACT; else if ( !strcmp(optarg,"exact") ) args->pair_logic = BCF_SR_PAIR_EXACT; else error("The --pair-logic string \"%s\" not recognised.\n", optarg); break; case 3 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 8 : args->record_cmd_line = 0; break; case 10 : args->single_overlaps = 1; break; case 11 : args->rename_annots = optarg; break; case 12 : args->min_overlap_str = optarg; break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case '?': usage(args); break; default: error("Unknown argument: %s\n", optarg); } } char *fname = NULL; if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else usage(args); } else fname = argv[optind]; if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( args->targets_fname ) { htsFile *fp = hts_open(args->targets_fname,"r"); if ( !fp ) error("Failed to open %s\n", args->targets_fname); htsFormat type = *hts_get_format(fp); hts_close(fp); if ( type.format==vcf || type.format==bcf ) { args->tgts_is_vcf = 1; args->files->require_index = 1; bcf_sr_set_opt(args->files,BCF_SR_PAIR_LOGIC,args->pair_logic>=0 ? args->pair_logic : BCF_SR_PAIR_SOME); if ( args->min_overlap_str ) error("The --min-overlap option cannot be used when annotating from a VCF\n"); } } if ( args->min_overlap_str && args->single_overlaps ) error("The options --single-overlaps and --min-overlap cannot be combined\n"); if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n"); if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); static int line_errcode_warned = 0; init_data(args); while ( bcf_sr_next_line(args->files) ) { if ( !bcf_sr_has_line(args->files,0) ) continue; bcf1_t *line = bcf_sr_get_line(args->files,0); if ( line->errcode ) { if ( !args->force ) error("Encountered an error, cannot proceed. Please check the error output above.\n" "If feeling adventurous, use the --force option. (At your own risk!)\n"); else if ( !line_errcode_warned ) { fprintf(bcftools_stderr, "Warning: Encountered an error, proceeding only because --force was given.\n" " Note that this can result in a segfault or a silent corruption of the output file!\n"); line_errcode_warned = 1; line->errcode = 0; } } if ( args->filter ) { int pass = filter_test(args->filter, line, NULL); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { if ( args->keep_sites && bcf_write1(args->out_fh, args->hdr_out, line)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args->output_fname); continue; } } int keep = annotate_line(args, line); if ( args->filter_ext && !args->keep_sites && !keep ) continue; if ( bcf_write1(args->out_fh, args->hdr_out, line)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args->output_fname); } destroy_data(args); bcf_sr_destroy(args->files); free(args); return 0; } pysam-0.23.0/bcftools/vcfbuf.c000066400000000000000000000665101475062545500162040ustar00rootroot00000000000000/* The MIT License Copyright (c) 2016-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "bcftools.h" #include "vcfbuf.h" #include "rbuf.h" typedef struct { double max[VCFBUF_LD_N]; int rand_missing, filter1; } ld_t; typedef struct { bcf1_t *rec; double af; unsigned int af_set:1, filter:1, idx:30; } vcfrec_t; #define PRUNE_MODE_MAX_AF 1 #define PRUNE_MODE_1ST 2 #define PRUNE_MODE_RAND 3 typedef struct { int max_sites, mvrec, mac, mfarr, mode; int *ac, *idx; float *farr; char *af_tag; vcfrec_t **vrec; } prune_t; #define MARK_OVERLAP 1 #define MARK_DUP 2 #define MARK_EXPR 3 #define MARK_MISSING_SCALAR 0 // actual value to use #define MARK_MISSING_MAX_DP 1 // max overlap_t.value scaled by INFO/DP // temporary internal structure for iterative overlap removal by mark_t.expr typedef struct { double value; // the sort value int rmme, idx; // mark for removal, index in vcfbuf_t.rbuf int dp; // with MARK_MISSING_MAX_DP, INFO/DP is used extrapolate missing QUAL kbitset_t *bset; // mark which records it overlaps with, given as 0-based indexes to vcfbuf_t.rbuf bcf1_t *rec; } overlap_t; typedef struct { // modes int mode; char *expr; // sites marked according to expr, returned to the caller via vcfbuf_get() rbuf_t rbuf; uint8_t *mark; int last; // MARK_OVERLAP int overlap_rid, overlap_end; // MARK_EXPR int nbuf; overlap_t *buf, **buf_ptr; int missing_expr; // the value to use when min(QUAL) encounters a missing value float missing_value; // the default missing value float max_qual; // with MARK_MISSING_MAX_DP int max_qual_dp; // int ntmpi; // temporary int array and the allocated memory int32_t *tmpi; } mark_t; struct _vcfbuf_t { int win, // maximum number of sites in the buffer, either number of sites (<0) or bp (<0) dummy; // the caller maintains the buffer via push/peek/flush bcf_hdr_t *hdr; vcfrec_t *vcf; rbuf_t rbuf; ld_t ld; prune_t prune; mark_t mark; enum { clean, dirty } status; }; vcfbuf_t *vcfbuf_init(bcf_hdr_t *hdr, int win) { vcfbuf_t *buf = (vcfbuf_t*) calloc(1,sizeof(vcfbuf_t)); buf->hdr = hdr; buf->win = win; buf->status = clean; buf->mark.overlap_rid = -1; int i; for (i=0; ild.max[i] = HUGE_VAL; rbuf_init(&buf->rbuf, 0); return buf; } void vcfbuf_destroy(vcfbuf_t *buf) { int i; for (i=0; irbuf.m; i++) if ( buf->vcf[i].rec ) bcf_destroy(buf->vcf[i].rec); free(buf->vcf); free(buf->prune.farr); free(buf->prune.vrec); free(buf->prune.ac); free(buf->prune.af_tag); free(buf->prune.idx); free(buf->mark.mark); free(buf->mark.expr); for (i=0; imark.nbuf; i++) kbs_destroy(buf->mark.buf[i].bset); free(buf->mark.buf); free(buf->mark.buf_ptr); free(buf->mark.tmpi); free(buf); } int vcfbuf_set(vcfbuf_t *buf, vcfbuf_opt_t key, ...) { va_list args; switch (key) { case LD_FILTER1: va_start(args, key); buf->ld.filter1 = va_arg(args,int); va_end(args); return 0; case LD_RAND_MISSING: va_start(args, key); buf->ld.rand_missing = va_arg(args,int); va_end(args); return 0; case LD_MAX_R2: va_start(args, key); buf->ld.max[VCFBUF_LD_IDX_R2] = va_arg(args,double); va_end(args); return 0; case LD_MAX_LD: va_start(args, key); buf->ld.max[VCFBUF_LD_IDX_LD] = va_arg(args,double); va_end(args); return 0; case LD_MAX_HD: va_start(args, key); buf->ld.max[VCFBUF_LD_IDX_HD] = va_arg(args,double); va_end(args); return 0; case VCFBUF_DUMMY: va_start(args, key); buf->dummy = va_arg(args,int); va_end(args); return 0; case PRUNE_NSITES: va_start(args, key); buf->prune.max_sites = va_arg(args,int); if ( !buf->prune.mode ) buf->prune.mode = PRUNE_MODE_MAX_AF; va_end(args); return 0; case PRUNE_NSITES_MODE: va_start(args, key); char *mode = va_arg(args,char*); va_end(args); if ( !strcasecmp(mode,"maxAF") ) buf->prune.mode = PRUNE_MODE_MAX_AF; else if ( !strcasecmp(mode,"1st") ) buf->prune.mode = PRUNE_MODE_1ST; else if ( !strcasecmp(mode,"rand") ) buf->prune.mode = PRUNE_MODE_RAND; else error("The mode \"%s\" is not recognised\n",mode); return 0; case PRUNE_AF_TAG: va_start(args, key); buf->prune.af_tag = strdup(va_arg(args,char*)); va_end(args); return 0; case MARK: va_start(args, key); buf->mark.expr = strdup(va_arg(args,char*)); if ( !strcasecmp(buf->mark.expr,"overlap") ) buf->mark.mode = MARK_OVERLAP; else if ( !strcasecmp(buf->mark.expr,"dup") ) buf->mark.mode = MARK_DUP; else buf->mark.mode = MARK_EXPR; va_end(args); return 0; case MARK_MISSING_EXPR: va_start(args, key); char *expr = va_arg(args,char*); if ( !strcasecmp(expr,"0") ) { buf->mark.missing_expr = MARK_MISSING_SCALAR; buf->mark.missing_value = 0; } else if ( !strcasecmp(expr,"DP") ) { if ( buf->mark.mode!=MARK_EXPR ) error("Only the combination of --mark 'min(QUAL)' with --missing DP is currently supported\n"); buf->mark.missing_expr = MARK_MISSING_MAX_DP; } else error("todo: MARK_MISSING_EXPR=%s\n",expr); va_end(args); return 0; } return 0; } void *vcfbuf_get(vcfbuf_t *buf, vcfbuf_opt_t key, ...) { va_list args; va_start(args, key); if ( key==MARK ) return &buf->mark.last; va_end(args); return NULL; } int vcfbuf_nsites(vcfbuf_t *buf) { return buf->rbuf.n; } bcf1_t *vcfbuf_push(vcfbuf_t *buf, bcf1_t *rec) { // make sure the caller is using the buffer correctly and calls vcfbuf_flush() // before placing next vcfbuf_push() call assert(buf->status!=dirty); if ( !buf->dummy ) buf->status = dirty; rbuf_expand0(&buf->rbuf, vcfrec_t, buf->rbuf.n+1, buf->vcf); int i = rbuf_append(&buf->rbuf); if ( !buf->vcf[i].rec ) buf->vcf[i].rec = bcf_init1(); bcf1_t *ret = buf->vcf[i].rec; buf->vcf[i].rec = rec; buf->vcf[i].af_set = 0; buf->vcf[i].filter = buf->ld.filter1; buf->ld.filter1 = 0; return ret; } bcf1_t *vcfbuf_peek(vcfbuf_t *buf, int idx) { buf->status = clean; int i = rbuf_kth(&buf->rbuf, idx); return i<0 ? NULL : buf->vcf[i].rec; } bcf1_t *vcfbuf_remove(vcfbuf_t *buf, int idx) { int i = rbuf_kth(&buf->rbuf, idx); if ( i<0 ) return NULL; bcf1_t *rec = buf->vcf[i].rec; rbuf_remove_kth(&buf->rbuf, vcfrec_t, idx, buf->vcf); return rec; } static int cmpvrec(const void *_a, const void *_b) { vcfrec_t *a = *((vcfrec_t**) _a); vcfrec_t *b = *((vcfrec_t**) _b); if ( a->af < b->af ) return -1; if ( a->af == b->af ) return 0; return 1; } static int cmpint_desc(const void *_a, const void *_b) { int a = *((int*)_a); int b = *((int*)_b); if ( a < b ) return 1; if ( a == b ) return 0; return -1; } static void _prune_sites(vcfbuf_t *buf, int flush_all) { int nbuf = flush_all ? buf->rbuf.n : buf->rbuf.n - 1; int nprune = nbuf - buf->prune.max_sites; int i,k,irec = 0; if ( buf->prune.mode==PRUNE_MODE_1ST ) { int eoff = flush_all ? 1 : 2; for (i=0; irbuf, vcfrec_t, buf->rbuf.n - eoff, buf->vcf); return; } if ( buf->prune.mode==PRUNE_MODE_RAND ) { int eoff = flush_all ? 0 : 1; for (i=0; irbuf.n - eoff) * hts_drand48(); rbuf_remove_kth(&buf->rbuf, vcfrec_t, j, buf->vcf); } return; } if ( nbuf > buf->prune.mvrec ) { buf->prune.idx = (int*) realloc(buf->prune.idx, nbuf*sizeof(int)); buf->prune.vrec = (vcfrec_t**) realloc(buf->prune.vrec, nbuf*sizeof(vcfrec_t*)); buf->prune.mvrec = nbuf; } // set allele frequency and prepare buffer for sorting for (i=-1; rbuf_next(&buf->rbuf,&i) && irecvcf[i].rec; if ( line->n_allele > buf->prune.mac ) { buf->prune.ac = (int*) realloc(buf->prune.ac, line->n_allele*sizeof(*buf->prune.ac)); buf->prune.mac = line->n_allele; } if ( !buf->vcf[i].af_set ) { buf->vcf[i].af = 0; if ( buf->prune.af_tag ) { if ( bcf_get_info_float(buf->hdr,line,buf->prune.af_tag,&buf->prune.farr, &buf->prune.mfarr) > 0 ) buf->vcf[i].af = buf->prune.farr[0]; } else if ( bcf_calc_ac(buf->hdr, line, buf->prune.ac, BCF_UN_INFO|BCF_UN_FMT) ) { int ntot = buf->prune.ac[0], nalt = 0; for (k=1; kn_allele; k++) nalt += buf->prune.ac[k]; buf->vcf[i].af = ntot ? (float)nalt/ntot : 0; } buf->vcf[i].af_set = 1; } buf->vcf[i].idx = irec; buf->prune.vrec[irec++] = &buf->vcf[i]; } // sort by allele frequency, low AF will be removed preferentially qsort(buf->prune.vrec, nbuf, sizeof(*buf->prune.vrec), cmpvrec); // sort the rbuf indexes to be pruned descendently so that j-th rbuf index // is removed before i-th index if iprune.idx[i] = buf->prune.vrec[i]->idx; qsort(buf->prune.idx, nprune, sizeof(int), cmpint_desc); for (i=0; irbuf, vcfrec_t, buf->prune.idx[i], buf->vcf); } static int mark_dup_can_flush_(vcfbuf_t *buf, int flush_all) { int flush = flush_all; mark_t *mark = &buf->mark; if ( buf->status==dirty ) { // a new site was just added by vcfbuf_push() rbuf_expand0(&mark->rbuf, uint8_t, buf->rbuf.n, mark->mark); int i = rbuf_append(&mark->rbuf); mark->mark[i] = 0; if ( buf->rbuf.n==1 ) goto flush; // there is at least one previous site, check if it's a duplicate int k1 = rbuf_kth(&buf->rbuf, -1); int k2 = rbuf_kth(&buf->rbuf, -2); vcfrec_t *rec1 = &buf->vcf[k1]; vcfrec_t *rec2 = &buf->vcf[k2]; int is_dup = 1; if ( rec1->rec->rid!=rec2->rec->rid ) is_dup = 0; else if ( rec1->rec->pos!=rec2->rec->pos ) is_dup = 0; if ( is_dup ) { // it is, mark the last two sites as duplicates int k1 = rbuf_kth(&mark->rbuf, -1); int k2 = rbuf_kth(&mark->rbuf, -2); mark->mark[k1] = 1; mark->mark[k2] = 1; goto flush; } // the last site is not a duplicate with the previous, all sites but the last one can be flushed flush = 1; } else if ( buf->rbuf.n > 1 ) flush = 1; flush: if ( !flush ) return 0; int i = rbuf_shift(&mark->rbuf); mark->last = mark->mark[i]; return 1; } static int mark_overlap_helper_(vcfbuf_t *buf, int flush_all) { if ( buf->status!=dirty ) return flush_all; int flush = flush_all; mark_t *mark = &buf->mark; // a new site was just added by vcfbuf_push() buf->status = clean; rbuf_expand0(&mark->rbuf, uint8_t, buf->rbuf.n, mark->mark); int i = rbuf_append(&mark->rbuf); mark->mark[i] = 0; // determine beg and end of the last record that was just added i = rbuf_last(&buf->rbuf); vcfrec_t *last = &buf->vcf[i]; if ( mark->overlap_rid != last->rec->rid ) mark->overlap_end = 0; int beg_pos = last->rec->pos; int end_pos = last->rec->pos + last->rec->rlen - 1; // Assuming left-aligned indels. In case it is a deletion, the real variant // starts one base after. If an insertion, the overlap with previous is zero int imin = last->rec->rlen; for (i=0; irec->n_allele; i++) { char *ref = last->rec->d.allele[0]; char *alt = last->rec->d.allele[i]; if ( *alt == '<' ) continue; // ignore symbolic alleles while ( *ref && *alt && nt_to_upper(*ref)==nt_to_upper(*alt) ) { ref++; alt++; } if ( imin > ref - last->rec->d.allele[0] ) imin = ref - last->rec->d.allele[0]; } if ( beg_pos <= mark->overlap_end ) { // the new site overlaps with the previous beg_pos += imin; if ( beg_pos > end_pos ) end_pos = beg_pos; } if ( buf->rbuf.n==1 ) { mark->overlap_rid = last->rec->rid; mark->overlap_end = end_pos; return flush; } if ( beg_pos <= mark->overlap_end ) { if ( mark->overlap_end < end_pos ) mark->overlap_end = end_pos; int k1 = rbuf_kth(&mark->rbuf, -1); int k2 = rbuf_kth(&mark->rbuf, -2); mark->mark[k1] = 1; mark->mark[k2] = 1; } else { if ( mark->overlap_end < end_pos ) mark->overlap_end = end_pos; flush = 1; } return flush; } static int mark_overlap_can_flush_(vcfbuf_t *buf, int flush_all) { int flush = flush_all; if ( buf->status==dirty ) flush = mark_overlap_helper_(buf,flush_all); else if ( buf->rbuf.n > 1 ) flush = 1; if ( !flush ) return 0; mark_t *mark = &buf->mark; int i = rbuf_shift(&mark->rbuf); mark->last = mark->mark[i]; return 1; } static int records_overlap(bcf1_t *a, bcf1_t *b) { if ( a->rid != b->rid ) return 0; if ( a->pos + a->rlen - 1 < b->pos ) return 0; return 1; } static int cmp_overlap_ptr_asc(const void *aptr, const void *bptr) { overlap_t *a = *((overlap_t**)aptr); overlap_t *b = *((overlap_t**)bptr); if ( a->value < b->value ) return -1; if ( a->value > b->value ) return 1; return 0; } static void mark_expr_missing_reset_(vcfbuf_t *buf) { buf->mark.max_qual = 0; buf->mark.max_qual_dp = 0; } static void mark_expr_missing_prep_(vcfbuf_t *buf, overlap_t *olap) { int nval = bcf_get_info_int32(buf->hdr,olap->rec,"DP",&buf->mark.tmpi,&buf->mark.ntmpi); if ( nval!=1 ) return; olap->dp = buf->mark.tmpi[0]; if ( bcf_float_is_missing(olap->rec->qual) ) return; if ( buf->mark.max_qual < olap->rec->qual ) { buf->mark.max_qual = olap->rec->qual; buf->mark.max_qual_dp = olap->dp; } } static void mark_expr_missing_set_(vcfbuf_t *buf, overlap_t *olap) { if ( !bcf_float_is_missing(olap->rec->qual) ) return; if ( !buf->mark.max_qual_dp ) return; // scale QUAL of the most confident variant in the overlap proportionally to the coverage // and use that to prioritize the records olap->value = buf->mark.max_qual * olap->dp / buf->mark.max_qual_dp; } static int mark_expr_can_flush_(vcfbuf_t *buf, int flush_all) { mark_t *mark = &buf->mark; if ( strcasecmp("min(QUAL)",mark->expr) ) error("Todo; at this time only min(QUAL) is supported\n"); int flush = flush_all; if ( buf->status==dirty ) { flush = mark_overlap_helper_(buf,flush_all); if ( !flush ) return 0; if ( mark->missing_expr==MARK_MISSING_MAX_DP ) mark_expr_missing_reset_(buf); // init overlaps, each overlap_t structure keeps a list of overlapping records, symmetrical size_t nori = mark->nbuf; hts_resize(overlap_t, buf->rbuf.n, &mark->nbuf, &mark->buf, HTS_RESIZE_CLEAR); hts_resize(overlap_t*, buf->rbuf.n, &nori, &mark->buf_ptr, HTS_RESIZE_CLEAR); int i; for (i=0; irbuf.n; i++) { overlap_t *oi = &mark->buf[i]; int j = rbuf_kth(&buf->rbuf, i); assert(j>=0); bcf1_t *rec = buf->vcf[j].rec; assert(rec); oi->rec = rec; // todo: other than QUAL values oi->value = bcf_float_is_missing(rec->qual) ? mark->missing_value : rec->qual; if ( mark->missing_expr==MARK_MISSING_MAX_DP ) mark_expr_missing_prep_(buf,oi); if ( oi->bset ) { kbs_resize(&oi->bset,buf->rbuf.n); kbs_clear(oi->bset); } else oi->bset = kbs_init(buf->rbuf.n); oi->idx = i; mark->buf_ptr[i] = oi; mark->mark[oi->idx] = 0; } int nolap = 0; for (i=0; irbuf.n; i++) { overlap_t *oi = &mark->buf[i]; if ( mark->missing_expr==MARK_MISSING_MAX_DP ) mark_expr_missing_set_(buf,oi); int j; for (j=i+1; jrbuf.n; j++) { overlap_t *oj = &mark->buf[j]; if ( !records_overlap(oi->rec,oj->rec) ) continue; kbs_insert(oi->bset,j); kbs_insert(oj->bset,i); nolap++; } } // sort according to the requested criteria, currently only min(QUAL) qsort(mark->buf_ptr,buf->rbuf.n,sizeof(*mark->buf_ptr),cmp_overlap_ptr_asc); // todo: other than min() // go through the list sorted by overlap_t.value, eg QUAL for (i=0; nolap && irbuf.n; i++) { kbitset_iter_t itr; overlap_t *oi = mark->buf_ptr[i]; kbs_start(&itr); int j; while ((j=kbs_next(oi->bset, &itr)) >= 0) { kbs_delete(oi->bset,j); assert(nolap); assert(kbs_exists(mark->buf[j].bset,oi->idx)); kbs_delete(mark->buf[j].bset,oi->idx); nolap--; } j = rbuf_kth(&mark->rbuf,oi->idx); mark->mark[j] = 1; } } else if ( buf->rbuf.n > 1 ) flush = 1; if ( !flush ) return 0; int i = rbuf_shift(&mark->rbuf); mark->last = mark->mark[i]; return 1; } bcf1_t *vcfbuf_flush(vcfbuf_t *buf, int flush_all) { int i,j; // nothing to do, no lines in the buffer if ( buf->rbuf.n==0 ) return NULL; // dummy mode, always flushing if ( buf->dummy ) goto ret; // pruning mode if ( buf->win ) { int can_flush = flush_all; i = rbuf_kth(&buf->rbuf, 0); // first j = rbuf_last(&buf->rbuf); // last if ( buf->vcf[i].rec->rid != buf->vcf[j].rec->rid ) can_flush = 1; else if ( buf->win > 0 ) { if ( buf->rbuf.n > buf->win ) can_flush = 1; } else if ( buf->win < 0 ) { if ( !(buf->vcf[i].rec->pos - buf->vcf[j].rec->pos > buf->win) ) can_flush = 1; } buf->status = clean; if ( !can_flush ) return NULL; if ( buf->prune.max_sites && buf->prune.max_sites < buf->rbuf.n ) _prune_sites(buf, flush_all); goto ret; } // overlaps and duplicates if ( buf->mark.mode ) { int can_flush = 0; if ( buf->mark.mode==MARK_OVERLAP ) { if ( mark_overlap_can_flush_(buf,flush_all) ) can_flush = 1; } else if ( buf->mark.mode==MARK_DUP ) { if ( mark_dup_can_flush_(buf,flush_all) ) can_flush = 1; } if ( buf->mark.mode==MARK_EXPR ) { if ( mark_expr_can_flush_(buf,flush_all) ) can_flush = 1; } buf->status = clean; if ( !can_flush ) return NULL; goto ret; } ret: buf->status = clean; i = rbuf_shift(&buf->rbuf); return buf->vcf[i].rec; } static double _estimate_af(int8_t *ptr, int size, int nvals, int nsamples) { int i,j, nref = 0, nalt = 0; for (i=0; in_sample!=brec->n_sample ) error("Different number of samples: %d vs %d\n",arec->n_sample,brec->n_sample); assert( arec->n_sample ); int i,j,igt = bcf_hdr_id2int(buf->hdr, BCF_DT_ID, "GT"); bcf_unpack(arec, BCF_UN_FMT); bcf_unpack(brec, BCF_UN_FMT); bcf_fmt_t *afmt = NULL, *bfmt = NULL; for (i=0; in_fmt; i++) if ( arec->d.fmt[i].id==igt ) { afmt = &arec->d.fmt[i]; break; } if ( !afmt ) return -1; // no GT tag for (i=0; in_fmt; i++) if ( brec->d.fmt[i].id==igt ) { bfmt = &brec->d.fmt[i]; break; } if ( !bfmt ) return -1; // no GT tag if ( afmt->n==0 ) return -1; // empty?! if ( bfmt->n==0 ) return -1; // empty?! if ( afmt->type!=BCF_BT_INT8 ) error("TODO: the GT fmt_type is not int8!\n"); if ( bfmt->type!=BCF_BT_INT8 ) error("TODO: the GT fmt_type is not int8!\n"); // Determine allele frequencies, this is to sample randomly missing genotypes double aaf = 0, baf = 0; if ( buf->ld.rand_missing ) { aaf = _estimate_af((int8_t*)afmt->p, afmt->size, afmt->n, arec->n_sample); baf = _estimate_af((int8_t*)bfmt->p, bfmt->size, bfmt->n, brec->n_sample); } // Calculate r2, lf, hd double nhd[] = {0,0,0,0,0,0,0,0,0}; double ab = 0, aa = 0, bb = 0, a = 0, b = 0; int nab = 0, ndiff = 0; int an_tot = 0, bn_tot = 0; for (i=0; in_sample; i++) { int8_t *aptr = (int8_t*) (afmt->p + i*afmt->size); int8_t *bptr = (int8_t*) (bfmt->p + i*bfmt->size); int adsg = 0, bdsg = 0; // dosages (0,1,2) at sites (a,b) int an = 0, bn = 0; // number of alleles at sites (a,b) for (j=0; jn; j++) { if ( aptr[j]==bcf_int8_vector_end ) break; if ( aptr[j]==bcf_gt_missing ) { if ( !buf->ld.rand_missing ) break; if ( hts_drand48() >= aaf ) adsg += 1; } else if ( bcf_gt_allele(aptr[j]) ) adsg += 1; an++; } for (j=0; jn; j++) { if ( bptr[j]==bcf_int8_vector_end ) break; if ( bptr[j]==bcf_gt_missing ) { if ( !buf->ld.rand_missing ) break; if ( hts_drand48() >= baf ) bdsg += 1; } else if ( bcf_gt_allele(bptr[j]) ) bdsg += 1; bn++; } if ( an && bn ) { an_tot += an; aa += adsg*adsg; a += adsg; bn_tot += bn; bb += bdsg*bdsg; b += bdsg; if ( adsg!=bdsg ) ndiff++; ab += adsg*bdsg; nab++; } if ( an==2 && bn==2 ) // for now only diploid genotypes { assert( adsg<=2 && bdsg<=2 ); nhd[ bdsg*3 + adsg ]++; } } if ( !nab ) return -1; // no data in common for the two sites double pa = a/an_tot; double pb = b/bn_tot; double cor; if ( !ndiff ) cor = 1; else { if ( aa == a*a/nab || bb == b*b/nab ) // zero variance, add small noise { aa += 1e-4; bb += 1e-4; ab += 1e-4; a += 1e-2; b += 1e-2; nab++; } cor = (ab - a*b/nab) / sqrt(aa - a*a/nab) / sqrt(bb - b*b/nab); } ld->val[VCFBUF_LD_IDX_R2] = cor * cor; // Lewontin's normalization of D. Also we cap at 1 as the calculation // can result in values bigger than 1 for high AFs. ld->val[VCFBUF_LD_IDX_LD] = cor * sqrt(pa*(1-pa)*pb*(1-pb)); double norm; if ( ld->val[VCFBUF_LD_IDX_LD] < 0 ) norm = -pa*pb > -(1-pa)*(1-pb) ? -pa*pb : -(1-pa)*(1-pb); else norm = pa*(1-pb) > (1-pa)*pb ? pa*(1-pb) : (1-pa)*pb; if ( norm ) ld->val[VCFBUF_LD_IDX_LD] = fabs(norm) > fabs(ld->val[VCFBUF_LD_IDX_LD]) ? ld->val[VCFBUF_LD_IDX_LD]/norm : 1; if ( !ld->val[VCFBUF_LD_IDX_LD] ) ld->val[VCFBUF_LD_IDX_LD] = fabs(ld->val[VCFBUF_LD_IDX_LD]); // avoid "-0" on output ld->val[VCFBUF_LD_IDX_HD] = (nhd[0] + nhd[1]/2. + nhd[3]/2. + nhd[4]/4.)*(nhd[4]/4. + nhd[5]/2. + nhd[7]/2. + nhd[8]) - (nhd[1]/2. + nhd[2] + nhd[4]/4. + nhd[5]/2.)*(nhd[3]/2. + nhd[4]/4. + nhd[6] + nhd[7]/2.); ld->val[VCFBUF_LD_IDX_HD] /= nab; ld->val[VCFBUF_LD_IDX_HD] /= nab+1; return 0; } int vcfbuf_ld(vcfbuf_t *buf, bcf1_t *rec, vcfbuf_ld_t *ld) { int ret = -1; if ( !buf->rbuf.n ) return ret; int j, i = buf->rbuf.f; // Relying on vcfbuf being properly flushed - all sites in the buffer // must come from the same chromosome if ( buf->vcf[i].rec->rid != rec->rid ) return ret; vcfbuf_ld_t tmp; for (j=0; jval[j] = -HUGE_VAL; ld->rec[j] = NULL; } for (i=-1; rbuf_next(&buf->rbuf,&i); ) { if ( buf->vcf[i].filter ) continue; if ( _calc_r2_ld(buf, buf->vcf[i].rec, rec, &tmp) < 0 ) continue; // missing genotypes int done = 0; for (j=0; jval[j] < tmp.val[j] ) { ld->val[j] = tmp.val[j]; ld->rec[j] = buf->vcf[i].rec; } if ( buf->ld.max[j] < tmp.val[j] ) done = 1; ret = 0; } if ( done ) return ret; } return ret; } pysam-0.23.0/bcftools/vcfbuf.c.pysam.c000066400000000000000000000665451475062545500175650ustar00rootroot00000000000000#include "bcftools.pysam.h" /* The MIT License Copyright (c) 2016-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "bcftools.h" #include "vcfbuf.h" #include "rbuf.h" typedef struct { double max[VCFBUF_LD_N]; int rand_missing, filter1; } ld_t; typedef struct { bcf1_t *rec; double af; unsigned int af_set:1, filter:1, idx:30; } vcfrec_t; #define PRUNE_MODE_MAX_AF 1 #define PRUNE_MODE_1ST 2 #define PRUNE_MODE_RAND 3 typedef struct { int max_sites, mvrec, mac, mfarr, mode; int *ac, *idx; float *farr; char *af_tag; vcfrec_t **vrec; } prune_t; #define MARK_OVERLAP 1 #define MARK_DUP 2 #define MARK_EXPR 3 #define MARK_MISSING_SCALAR 0 // actual value to use #define MARK_MISSING_MAX_DP 1 // max overlap_t.value scaled by INFO/DP // temporary internal structure for iterative overlap removal by mark_t.expr typedef struct { double value; // the sort value int rmme, idx; // mark for removal, index in vcfbuf_t.rbuf int dp; // with MARK_MISSING_MAX_DP, INFO/DP is used extrapolate missing QUAL kbitset_t *bset; // mark which records it overlaps with, given as 0-based indexes to vcfbuf_t.rbuf bcf1_t *rec; } overlap_t; typedef struct { // modes int mode; char *expr; // sites marked according to expr, returned to the caller via vcfbuf_get() rbuf_t rbuf; uint8_t *mark; int last; // MARK_OVERLAP int overlap_rid, overlap_end; // MARK_EXPR int nbuf; overlap_t *buf, **buf_ptr; int missing_expr; // the value to use when min(QUAL) encounters a missing value float missing_value; // the default missing value float max_qual; // with MARK_MISSING_MAX_DP int max_qual_dp; // int ntmpi; // temporary int array and the allocated memory int32_t *tmpi; } mark_t; struct _vcfbuf_t { int win, // maximum number of sites in the buffer, either number of sites (<0) or bp (<0) dummy; // the caller maintains the buffer via push/peek/flush bcf_hdr_t *hdr; vcfrec_t *vcf; rbuf_t rbuf; ld_t ld; prune_t prune; mark_t mark; enum { clean, dirty } status; }; vcfbuf_t *vcfbuf_init(bcf_hdr_t *hdr, int win) { vcfbuf_t *buf = (vcfbuf_t*) calloc(1,sizeof(vcfbuf_t)); buf->hdr = hdr; buf->win = win; buf->status = clean; buf->mark.overlap_rid = -1; int i; for (i=0; ild.max[i] = HUGE_VAL; rbuf_init(&buf->rbuf, 0); return buf; } void vcfbuf_destroy(vcfbuf_t *buf) { int i; for (i=0; irbuf.m; i++) if ( buf->vcf[i].rec ) bcf_destroy(buf->vcf[i].rec); free(buf->vcf); free(buf->prune.farr); free(buf->prune.vrec); free(buf->prune.ac); free(buf->prune.af_tag); free(buf->prune.idx); free(buf->mark.mark); free(buf->mark.expr); for (i=0; imark.nbuf; i++) kbs_destroy(buf->mark.buf[i].bset); free(buf->mark.buf); free(buf->mark.buf_ptr); free(buf->mark.tmpi); free(buf); } int vcfbuf_set(vcfbuf_t *buf, vcfbuf_opt_t key, ...) { va_list args; switch (key) { case LD_FILTER1: va_start(args, key); buf->ld.filter1 = va_arg(args,int); va_end(args); return 0; case LD_RAND_MISSING: va_start(args, key); buf->ld.rand_missing = va_arg(args,int); va_end(args); return 0; case LD_MAX_R2: va_start(args, key); buf->ld.max[VCFBUF_LD_IDX_R2] = va_arg(args,double); va_end(args); return 0; case LD_MAX_LD: va_start(args, key); buf->ld.max[VCFBUF_LD_IDX_LD] = va_arg(args,double); va_end(args); return 0; case LD_MAX_HD: va_start(args, key); buf->ld.max[VCFBUF_LD_IDX_HD] = va_arg(args,double); va_end(args); return 0; case VCFBUF_DUMMY: va_start(args, key); buf->dummy = va_arg(args,int); va_end(args); return 0; case PRUNE_NSITES: va_start(args, key); buf->prune.max_sites = va_arg(args,int); if ( !buf->prune.mode ) buf->prune.mode = PRUNE_MODE_MAX_AF; va_end(args); return 0; case PRUNE_NSITES_MODE: va_start(args, key); char *mode = va_arg(args,char*); va_end(args); if ( !strcasecmp(mode,"maxAF") ) buf->prune.mode = PRUNE_MODE_MAX_AF; else if ( !strcasecmp(mode,"1st") ) buf->prune.mode = PRUNE_MODE_1ST; else if ( !strcasecmp(mode,"rand") ) buf->prune.mode = PRUNE_MODE_RAND; else error("The mode \"%s\" is not recognised\n",mode); return 0; case PRUNE_AF_TAG: va_start(args, key); buf->prune.af_tag = strdup(va_arg(args,char*)); va_end(args); return 0; case MARK: va_start(args, key); buf->mark.expr = strdup(va_arg(args,char*)); if ( !strcasecmp(buf->mark.expr,"overlap") ) buf->mark.mode = MARK_OVERLAP; else if ( !strcasecmp(buf->mark.expr,"dup") ) buf->mark.mode = MARK_DUP; else buf->mark.mode = MARK_EXPR; va_end(args); return 0; case MARK_MISSING_EXPR: va_start(args, key); char *expr = va_arg(args,char*); if ( !strcasecmp(expr,"0") ) { buf->mark.missing_expr = MARK_MISSING_SCALAR; buf->mark.missing_value = 0; } else if ( !strcasecmp(expr,"DP") ) { if ( buf->mark.mode!=MARK_EXPR ) error("Only the combination of --mark 'min(QUAL)' with --missing DP is currently supported\n"); buf->mark.missing_expr = MARK_MISSING_MAX_DP; } else error("todo: MARK_MISSING_EXPR=%s\n",expr); va_end(args); return 0; } return 0; } void *vcfbuf_get(vcfbuf_t *buf, vcfbuf_opt_t key, ...) { va_list args; va_start(args, key); if ( key==MARK ) return &buf->mark.last; va_end(args); return NULL; } int vcfbuf_nsites(vcfbuf_t *buf) { return buf->rbuf.n; } bcf1_t *vcfbuf_push(vcfbuf_t *buf, bcf1_t *rec) { // make sure the caller is using the buffer correctly and calls vcfbuf_flush() // before placing next vcfbuf_push() call assert(buf->status!=dirty); if ( !buf->dummy ) buf->status = dirty; rbuf_expand0(&buf->rbuf, vcfrec_t, buf->rbuf.n+1, buf->vcf); int i = rbuf_append(&buf->rbuf); if ( !buf->vcf[i].rec ) buf->vcf[i].rec = bcf_init1(); bcf1_t *ret = buf->vcf[i].rec; buf->vcf[i].rec = rec; buf->vcf[i].af_set = 0; buf->vcf[i].filter = buf->ld.filter1; buf->ld.filter1 = 0; return ret; } bcf1_t *vcfbuf_peek(vcfbuf_t *buf, int idx) { buf->status = clean; int i = rbuf_kth(&buf->rbuf, idx); return i<0 ? NULL : buf->vcf[i].rec; } bcf1_t *vcfbuf_remove(vcfbuf_t *buf, int idx) { int i = rbuf_kth(&buf->rbuf, idx); if ( i<0 ) return NULL; bcf1_t *rec = buf->vcf[i].rec; rbuf_remove_kth(&buf->rbuf, vcfrec_t, idx, buf->vcf); return rec; } static int cmpvrec(const void *_a, const void *_b) { vcfrec_t *a = *((vcfrec_t**) _a); vcfrec_t *b = *((vcfrec_t**) _b); if ( a->af < b->af ) return -1; if ( a->af == b->af ) return 0; return 1; } static int cmpint_desc(const void *_a, const void *_b) { int a = *((int*)_a); int b = *((int*)_b); if ( a < b ) return 1; if ( a == b ) return 0; return -1; } static void _prune_sites(vcfbuf_t *buf, int flush_all) { int nbuf = flush_all ? buf->rbuf.n : buf->rbuf.n - 1; int nprune = nbuf - buf->prune.max_sites; int i,k,irec = 0; if ( buf->prune.mode==PRUNE_MODE_1ST ) { int eoff = flush_all ? 1 : 2; for (i=0; irbuf, vcfrec_t, buf->rbuf.n - eoff, buf->vcf); return; } if ( buf->prune.mode==PRUNE_MODE_RAND ) { int eoff = flush_all ? 0 : 1; for (i=0; irbuf.n - eoff) * hts_drand48(); rbuf_remove_kth(&buf->rbuf, vcfrec_t, j, buf->vcf); } return; } if ( nbuf > buf->prune.mvrec ) { buf->prune.idx = (int*) realloc(buf->prune.idx, nbuf*sizeof(int)); buf->prune.vrec = (vcfrec_t**) realloc(buf->prune.vrec, nbuf*sizeof(vcfrec_t*)); buf->prune.mvrec = nbuf; } // set allele frequency and prepare buffer for sorting for (i=-1; rbuf_next(&buf->rbuf,&i) && irecvcf[i].rec; if ( line->n_allele > buf->prune.mac ) { buf->prune.ac = (int*) realloc(buf->prune.ac, line->n_allele*sizeof(*buf->prune.ac)); buf->prune.mac = line->n_allele; } if ( !buf->vcf[i].af_set ) { buf->vcf[i].af = 0; if ( buf->prune.af_tag ) { if ( bcf_get_info_float(buf->hdr,line,buf->prune.af_tag,&buf->prune.farr, &buf->prune.mfarr) > 0 ) buf->vcf[i].af = buf->prune.farr[0]; } else if ( bcf_calc_ac(buf->hdr, line, buf->prune.ac, BCF_UN_INFO|BCF_UN_FMT) ) { int ntot = buf->prune.ac[0], nalt = 0; for (k=1; kn_allele; k++) nalt += buf->prune.ac[k]; buf->vcf[i].af = ntot ? (float)nalt/ntot : 0; } buf->vcf[i].af_set = 1; } buf->vcf[i].idx = irec; buf->prune.vrec[irec++] = &buf->vcf[i]; } // sort by allele frequency, low AF will be removed preferentially qsort(buf->prune.vrec, nbuf, sizeof(*buf->prune.vrec), cmpvrec); // sort the rbuf indexes to be pruned descendently so that j-th rbuf index // is removed before i-th index if iprune.idx[i] = buf->prune.vrec[i]->idx; qsort(buf->prune.idx, nprune, sizeof(int), cmpint_desc); for (i=0; irbuf, vcfrec_t, buf->prune.idx[i], buf->vcf); } static int mark_dup_can_flush_(vcfbuf_t *buf, int flush_all) { int flush = flush_all; mark_t *mark = &buf->mark; if ( buf->status==dirty ) { // a new site was just added by vcfbuf_push() rbuf_expand0(&mark->rbuf, uint8_t, buf->rbuf.n, mark->mark); int i = rbuf_append(&mark->rbuf); mark->mark[i] = 0; if ( buf->rbuf.n==1 ) goto flush; // there is at least one previous site, check if it's a duplicate int k1 = rbuf_kth(&buf->rbuf, -1); int k2 = rbuf_kth(&buf->rbuf, -2); vcfrec_t *rec1 = &buf->vcf[k1]; vcfrec_t *rec2 = &buf->vcf[k2]; int is_dup = 1; if ( rec1->rec->rid!=rec2->rec->rid ) is_dup = 0; else if ( rec1->rec->pos!=rec2->rec->pos ) is_dup = 0; if ( is_dup ) { // it is, mark the last two sites as duplicates int k1 = rbuf_kth(&mark->rbuf, -1); int k2 = rbuf_kth(&mark->rbuf, -2); mark->mark[k1] = 1; mark->mark[k2] = 1; goto flush; } // the last site is not a duplicate with the previous, all sites but the last one can be flushed flush = 1; } else if ( buf->rbuf.n > 1 ) flush = 1; flush: if ( !flush ) return 0; int i = rbuf_shift(&mark->rbuf); mark->last = mark->mark[i]; return 1; } static int mark_overlap_helper_(vcfbuf_t *buf, int flush_all) { if ( buf->status!=dirty ) return flush_all; int flush = flush_all; mark_t *mark = &buf->mark; // a new site was just added by vcfbuf_push() buf->status = clean; rbuf_expand0(&mark->rbuf, uint8_t, buf->rbuf.n, mark->mark); int i = rbuf_append(&mark->rbuf); mark->mark[i] = 0; // determine beg and end of the last record that was just added i = rbuf_last(&buf->rbuf); vcfrec_t *last = &buf->vcf[i]; if ( mark->overlap_rid != last->rec->rid ) mark->overlap_end = 0; int beg_pos = last->rec->pos; int end_pos = last->rec->pos + last->rec->rlen - 1; // Assuming left-aligned indels. In case it is a deletion, the real variant // starts one base after. If an insertion, the overlap with previous is zero int imin = last->rec->rlen; for (i=0; irec->n_allele; i++) { char *ref = last->rec->d.allele[0]; char *alt = last->rec->d.allele[i]; if ( *alt == '<' ) continue; // ignore symbolic alleles while ( *ref && *alt && nt_to_upper(*ref)==nt_to_upper(*alt) ) { ref++; alt++; } if ( imin > ref - last->rec->d.allele[0] ) imin = ref - last->rec->d.allele[0]; } if ( beg_pos <= mark->overlap_end ) { // the new site overlaps with the previous beg_pos += imin; if ( beg_pos > end_pos ) end_pos = beg_pos; } if ( buf->rbuf.n==1 ) { mark->overlap_rid = last->rec->rid; mark->overlap_end = end_pos; return flush; } if ( beg_pos <= mark->overlap_end ) { if ( mark->overlap_end < end_pos ) mark->overlap_end = end_pos; int k1 = rbuf_kth(&mark->rbuf, -1); int k2 = rbuf_kth(&mark->rbuf, -2); mark->mark[k1] = 1; mark->mark[k2] = 1; } else { if ( mark->overlap_end < end_pos ) mark->overlap_end = end_pos; flush = 1; } return flush; } static int mark_overlap_can_flush_(vcfbuf_t *buf, int flush_all) { int flush = flush_all; if ( buf->status==dirty ) flush = mark_overlap_helper_(buf,flush_all); else if ( buf->rbuf.n > 1 ) flush = 1; if ( !flush ) return 0; mark_t *mark = &buf->mark; int i = rbuf_shift(&mark->rbuf); mark->last = mark->mark[i]; return 1; } static int records_overlap(bcf1_t *a, bcf1_t *b) { if ( a->rid != b->rid ) return 0; if ( a->pos + a->rlen - 1 < b->pos ) return 0; return 1; } static int cmp_overlap_ptr_asc(const void *aptr, const void *bptr) { overlap_t *a = *((overlap_t**)aptr); overlap_t *b = *((overlap_t**)bptr); if ( a->value < b->value ) return -1; if ( a->value > b->value ) return 1; return 0; } static void mark_expr_missing_reset_(vcfbuf_t *buf) { buf->mark.max_qual = 0; buf->mark.max_qual_dp = 0; } static void mark_expr_missing_prep_(vcfbuf_t *buf, overlap_t *olap) { int nval = bcf_get_info_int32(buf->hdr,olap->rec,"DP",&buf->mark.tmpi,&buf->mark.ntmpi); if ( nval!=1 ) return; olap->dp = buf->mark.tmpi[0]; if ( bcf_float_is_missing(olap->rec->qual) ) return; if ( buf->mark.max_qual < olap->rec->qual ) { buf->mark.max_qual = olap->rec->qual; buf->mark.max_qual_dp = olap->dp; } } static void mark_expr_missing_set_(vcfbuf_t *buf, overlap_t *olap) { if ( !bcf_float_is_missing(olap->rec->qual) ) return; if ( !buf->mark.max_qual_dp ) return; // scale QUAL of the most confident variant in the overlap proportionally to the coverage // and use that to prioritize the records olap->value = buf->mark.max_qual * olap->dp / buf->mark.max_qual_dp; } static int mark_expr_can_flush_(vcfbuf_t *buf, int flush_all) { mark_t *mark = &buf->mark; if ( strcasecmp("min(QUAL)",mark->expr) ) error("Todo; at this time only min(QUAL) is supported\n"); int flush = flush_all; if ( buf->status==dirty ) { flush = mark_overlap_helper_(buf,flush_all); if ( !flush ) return 0; if ( mark->missing_expr==MARK_MISSING_MAX_DP ) mark_expr_missing_reset_(buf); // init overlaps, each overlap_t structure keeps a list of overlapping records, symmetrical size_t nori = mark->nbuf; hts_resize(overlap_t, buf->rbuf.n, &mark->nbuf, &mark->buf, HTS_RESIZE_CLEAR); hts_resize(overlap_t*, buf->rbuf.n, &nori, &mark->buf_ptr, HTS_RESIZE_CLEAR); int i; for (i=0; irbuf.n; i++) { overlap_t *oi = &mark->buf[i]; int j = rbuf_kth(&buf->rbuf, i); assert(j>=0); bcf1_t *rec = buf->vcf[j].rec; assert(rec); oi->rec = rec; // todo: other than QUAL values oi->value = bcf_float_is_missing(rec->qual) ? mark->missing_value : rec->qual; if ( mark->missing_expr==MARK_MISSING_MAX_DP ) mark_expr_missing_prep_(buf,oi); if ( oi->bset ) { kbs_resize(&oi->bset,buf->rbuf.n); kbs_clear(oi->bset); } else oi->bset = kbs_init(buf->rbuf.n); oi->idx = i; mark->buf_ptr[i] = oi; mark->mark[oi->idx] = 0; } int nolap = 0; for (i=0; irbuf.n; i++) { overlap_t *oi = &mark->buf[i]; if ( mark->missing_expr==MARK_MISSING_MAX_DP ) mark_expr_missing_set_(buf,oi); int j; for (j=i+1; jrbuf.n; j++) { overlap_t *oj = &mark->buf[j]; if ( !records_overlap(oi->rec,oj->rec) ) continue; kbs_insert(oi->bset,j); kbs_insert(oj->bset,i); nolap++; } } // sort according to the requested criteria, currently only min(QUAL) qsort(mark->buf_ptr,buf->rbuf.n,sizeof(*mark->buf_ptr),cmp_overlap_ptr_asc); // todo: other than min() // go through the list sorted by overlap_t.value, eg QUAL for (i=0; nolap && irbuf.n; i++) { kbitset_iter_t itr; overlap_t *oi = mark->buf_ptr[i]; kbs_start(&itr); int j; while ((j=kbs_next(oi->bset, &itr)) >= 0) { kbs_delete(oi->bset,j); assert(nolap); assert(kbs_exists(mark->buf[j].bset,oi->idx)); kbs_delete(mark->buf[j].bset,oi->idx); nolap--; } j = rbuf_kth(&mark->rbuf,oi->idx); mark->mark[j] = 1; } } else if ( buf->rbuf.n > 1 ) flush = 1; if ( !flush ) return 0; int i = rbuf_shift(&mark->rbuf); mark->last = mark->mark[i]; return 1; } bcf1_t *vcfbuf_flush(vcfbuf_t *buf, int flush_all) { int i,j; // nothing to do, no lines in the buffer if ( buf->rbuf.n==0 ) return NULL; // dummy mode, always flushing if ( buf->dummy ) goto ret; // pruning mode if ( buf->win ) { int can_flush = flush_all; i = rbuf_kth(&buf->rbuf, 0); // first j = rbuf_last(&buf->rbuf); // last if ( buf->vcf[i].rec->rid != buf->vcf[j].rec->rid ) can_flush = 1; else if ( buf->win > 0 ) { if ( buf->rbuf.n > buf->win ) can_flush = 1; } else if ( buf->win < 0 ) { if ( !(buf->vcf[i].rec->pos - buf->vcf[j].rec->pos > buf->win) ) can_flush = 1; } buf->status = clean; if ( !can_flush ) return NULL; if ( buf->prune.max_sites && buf->prune.max_sites < buf->rbuf.n ) _prune_sites(buf, flush_all); goto ret; } // overlaps and duplicates if ( buf->mark.mode ) { int can_flush = 0; if ( buf->mark.mode==MARK_OVERLAP ) { if ( mark_overlap_can_flush_(buf,flush_all) ) can_flush = 1; } else if ( buf->mark.mode==MARK_DUP ) { if ( mark_dup_can_flush_(buf,flush_all) ) can_flush = 1; } if ( buf->mark.mode==MARK_EXPR ) { if ( mark_expr_can_flush_(buf,flush_all) ) can_flush = 1; } buf->status = clean; if ( !can_flush ) return NULL; goto ret; } ret: buf->status = clean; i = rbuf_shift(&buf->rbuf); return buf->vcf[i].rec; } static double _estimate_af(int8_t *ptr, int size, int nvals, int nsamples) { int i,j, nref = 0, nalt = 0; for (i=0; in_sample!=brec->n_sample ) error("Different number of samples: %d vs %d\n",arec->n_sample,brec->n_sample); assert( arec->n_sample ); int i,j,igt = bcf_hdr_id2int(buf->hdr, BCF_DT_ID, "GT"); bcf_unpack(arec, BCF_UN_FMT); bcf_unpack(brec, BCF_UN_FMT); bcf_fmt_t *afmt = NULL, *bfmt = NULL; for (i=0; in_fmt; i++) if ( arec->d.fmt[i].id==igt ) { afmt = &arec->d.fmt[i]; break; } if ( !afmt ) return -1; // no GT tag for (i=0; in_fmt; i++) if ( brec->d.fmt[i].id==igt ) { bfmt = &brec->d.fmt[i]; break; } if ( !bfmt ) return -1; // no GT tag if ( afmt->n==0 ) return -1; // empty?! if ( bfmt->n==0 ) return -1; // empty?! if ( afmt->type!=BCF_BT_INT8 ) error("TODO: the GT fmt_type is not int8!\n"); if ( bfmt->type!=BCF_BT_INT8 ) error("TODO: the GT fmt_type is not int8!\n"); // Determine allele frequencies, this is to sample randomly missing genotypes double aaf = 0, baf = 0; if ( buf->ld.rand_missing ) { aaf = _estimate_af((int8_t*)afmt->p, afmt->size, afmt->n, arec->n_sample); baf = _estimate_af((int8_t*)bfmt->p, bfmt->size, bfmt->n, brec->n_sample); } // Calculate r2, lf, hd double nhd[] = {0,0,0,0,0,0,0,0,0}; double ab = 0, aa = 0, bb = 0, a = 0, b = 0; int nab = 0, ndiff = 0; int an_tot = 0, bn_tot = 0; for (i=0; in_sample; i++) { int8_t *aptr = (int8_t*) (afmt->p + i*afmt->size); int8_t *bptr = (int8_t*) (bfmt->p + i*bfmt->size); int adsg = 0, bdsg = 0; // dosages (0,1,2) at sites (a,b) int an = 0, bn = 0; // number of alleles at sites (a,b) for (j=0; jn; j++) { if ( aptr[j]==bcf_int8_vector_end ) break; if ( aptr[j]==bcf_gt_missing ) { if ( !buf->ld.rand_missing ) break; if ( hts_drand48() >= aaf ) adsg += 1; } else if ( bcf_gt_allele(aptr[j]) ) adsg += 1; an++; } for (j=0; jn; j++) { if ( bptr[j]==bcf_int8_vector_end ) break; if ( bptr[j]==bcf_gt_missing ) { if ( !buf->ld.rand_missing ) break; if ( hts_drand48() >= baf ) bdsg += 1; } else if ( bcf_gt_allele(bptr[j]) ) bdsg += 1; bn++; } if ( an && bn ) { an_tot += an; aa += adsg*adsg; a += adsg; bn_tot += bn; bb += bdsg*bdsg; b += bdsg; if ( adsg!=bdsg ) ndiff++; ab += adsg*bdsg; nab++; } if ( an==2 && bn==2 ) // for now only diploid genotypes { assert( adsg<=2 && bdsg<=2 ); nhd[ bdsg*3 + adsg ]++; } } if ( !nab ) return -1; // no data in common for the two sites double pa = a/an_tot; double pb = b/bn_tot; double cor; if ( !ndiff ) cor = 1; else { if ( aa == a*a/nab || bb == b*b/nab ) // zero variance, add small noise { aa += 1e-4; bb += 1e-4; ab += 1e-4; a += 1e-2; b += 1e-2; nab++; } cor = (ab - a*b/nab) / sqrt(aa - a*a/nab) / sqrt(bb - b*b/nab); } ld->val[VCFBUF_LD_IDX_R2] = cor * cor; // Lewontin's normalization of D. Also we cap at 1 as the calculation // can result in values bigger than 1 for high AFs. ld->val[VCFBUF_LD_IDX_LD] = cor * sqrt(pa*(1-pa)*pb*(1-pb)); double norm; if ( ld->val[VCFBUF_LD_IDX_LD] < 0 ) norm = -pa*pb > -(1-pa)*(1-pb) ? -pa*pb : -(1-pa)*(1-pb); else norm = pa*(1-pb) > (1-pa)*pb ? pa*(1-pb) : (1-pa)*pb; if ( norm ) ld->val[VCFBUF_LD_IDX_LD] = fabs(norm) > fabs(ld->val[VCFBUF_LD_IDX_LD]) ? ld->val[VCFBUF_LD_IDX_LD]/norm : 1; if ( !ld->val[VCFBUF_LD_IDX_LD] ) ld->val[VCFBUF_LD_IDX_LD] = fabs(ld->val[VCFBUF_LD_IDX_LD]); // avoid "-0" on output ld->val[VCFBUF_LD_IDX_HD] = (nhd[0] + nhd[1]/2. + nhd[3]/2. + nhd[4]/4.)*(nhd[4]/4. + nhd[5]/2. + nhd[7]/2. + nhd[8]) - (nhd[1]/2. + nhd[2] + nhd[4]/4. + nhd[5]/2.)*(nhd[3]/2. + nhd[4]/4. + nhd[6] + nhd[7]/2.); ld->val[VCFBUF_LD_IDX_HD] /= nab; ld->val[VCFBUF_LD_IDX_HD] /= nab+1; return 0; } int vcfbuf_ld(vcfbuf_t *buf, bcf1_t *rec, vcfbuf_ld_t *ld) { int ret = -1; if ( !buf->rbuf.n ) return ret; int j, i = buf->rbuf.f; // Relying on vcfbuf being properly flushed - all sites in the buffer // must come from the same chromosome if ( buf->vcf[i].rec->rid != rec->rid ) return ret; vcfbuf_ld_t tmp; for (j=0; jval[j] = -HUGE_VAL; ld->rec[j] = NULL; } for (i=-1; rbuf_next(&buf->rbuf,&i); ) { if ( buf->vcf[i].filter ) continue; if ( _calc_r2_ld(buf, buf->vcf[i].rec, rec, &tmp) < 0 ) continue; // missing genotypes int done = 0; for (j=0; jval[j] < tmp.val[j] ) { ld->val[j] = tmp.val[j]; ld->rec[j] = buf->vcf[i].rec; } if ( buf->ld.max[j] < tmp.val[j] ) done = 1; ret = 0; } if ( done ) return ret; } return ret; } pysam-0.23.0/bcftools/vcfbuf.h000066400000000000000000000134341475062545500162060ustar00rootroot00000000000000/* The MIT License Copyright (c) 2017-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Buffer VCF records and perform operations on the buffer */ #ifndef __VCFBUF_H__ #define __VCFBUF_H__ #include typedef struct _vcfbuf_t vcfbuf_t; // Modes of operation typedef enum { VCFBUF_DUMMY, // int {0,1}, the caller maintains the buffer via push/peek/flush, nothing is removed by vcfbuf // pruning PRUNE_NSITES, // int, leave max this many sites in the window PRUNE_NSITES_MODE, // char *, maxAF (keep sites with max AF), 1st (sites that come first), rand (pick randomly) PRUNE_AF_TAG, // char *, use this INFO/AF tag with VCFBUF_NSITES // duplicates and overlaps MARK, // w: char *, resolve overlaps by preferentially removing sites according to EXPR: // min(QUAL) .. remove sites with lowest QUAL until overlaps are resolved // overlap .. select all overlapping sites // dup .. select duplicate sites // r: use as // while ( (rec=vcfbuf_flush(buf,flush_all)) ) // { // int is_marked = vcfbuf_get_val(buf,int,MARK); // if ( is_marked ) do_something(rec); // } MARK_MISSING_EXPR, // char *, what to do when missing value are encountered with min(QUAL) // 0 .. set to 0 (the default) // DP .. scale max quality in the window proportionally to INFO/DP // LD related options LD_RAND_MISSING, // randomize rather than ignore missing genotypes LD_FILTER1, // exclude the next record inserted by vcfbuf_push() from LD analysis LD_MAX_R2, // If set, vcfbuf_ld() will stop at the first record that exceeds the R2, LD_MAX_LD, // LD, or HD threshold. When multiple are set, the OR logic is applied LD_MAX_HD, // } vcfbuf_opt_t; /** * vcfbuf_set() - set various options, see the vcfbuf_opt_t keys for the complete list * * Returns 0 if the call succeeded, or negative number on error. */ int vcfbuf_set(vcfbuf_t *buf, vcfbuf_opt_t key, ...); // returns 0 on success /** * vcfbuf_get() - get various options, see the vcfbuf_opt_t keys * vcfbuf_get_val() - wrapper for `vcfbuf_get()` to return typed value * * The former returns pointer to the memory area populated by the requested setting, * its type can be inferred from the vcfbuf_opt_t documentation. */ void *vcfbuf_get(vcfbuf_t *buf, vcfbuf_opt_t key, ...); #define vcfbuf_get_val(buf,type,key) (*(type*)vcfbuf_get(buf, key)) /* * vcfbuf_init() - init buffer * @win: number of sites (>0), bp (<0) */ vcfbuf_t *vcfbuf_init(bcf_hdr_t *hdr, int win); void vcfbuf_destroy(vcfbuf_t *buf); /* * vcfbuf_push() - push a new site for analysis. * * Note that vcfbuf_flush() or vcfbuf_peek() must be called before next site is pushed. */ bcf1_t *vcfbuf_push(vcfbuf_t *buf, bcf1_t *rec); /* * vcfbuf_peek() - return pointer to i-th record in the buffer but do not remove it from the buffer * @idx: 0-based index to buffered lines */ bcf1_t *vcfbuf_peek(vcfbuf_t *buf, int idx); /* * vcfbuf_remove() - return pointer to i-th record in the buffer and remove it from the buffer * @idx: 0-based index to buffered lines */ bcf1_t *vcfbuf_remove(vcfbuf_t *buf, int idx); /* * vcfbuf_flush() - returns the next record or NULL, depending on the mode of operation and * the content of the buffer * * @flush_all: 1 if no more vcfbuf_push() calls will follow, 0 otherwise */ bcf1_t *vcfbuf_flush(vcfbuf_t *buf, int flush_all); /* * vcfbuf_nsites() - return the number of sites in the buffer */ int vcfbuf_nsites(vcfbuf_t *buf); /* * vcfbuf_ld() - find records with maximum LD values or the values in first record that exceeds thresholds * set by vcfbuf_set_opt(..,LD_MAX*,..) * * Returns 0 on success or -1 if no values were filled. * * @val: will be filled with the values * .. correlation coefficient r-squared * .. Lewontin's D' (PMID: 19433632) * .. Ragsdale's \hat{D} (doi:10.1093/molbev/msz265) * @rec: corresponding positions or NULL if the value(s) has not been set */ #define VCFBUF_LD_N 3 #define VCFBUF_LD_IDX_R2 0 #define VCFBUF_LD_IDX_LD 1 #define VCFBUF_LD_IDX_HD 2 typedef struct { double val[VCFBUF_LD_N]; // r2, ld, hd bcf1_t *rec[VCFBUF_LD_N]; // record with max r2, ld, hd } vcfbuf_ld_t; int vcfbuf_ld(vcfbuf_t *buf, bcf1_t *rec, vcfbuf_ld_t *ld); #endif pysam-0.23.0/bcftools/vcfcall.c000066400000000000000000001406501475062545500163410ustar00rootroot00000000000000/* vcfcall.c -- SNP/indel variant calling from VCF/BCF. Copyright (C) 2013-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "call.h" #include "prob1.h" #include "ploidy.h" #include "gvcf.h" #include "regidx.h" #include "vcfbuf.h" void error(const char *format, ...); #define CF_NO_GENO 1 #define CF_INS_MISSED (1<<1) #define CF_CCALL (1<<2) // (1<<3) // (1<<4) // (1<<5) #define CF_ACGT_ONLY (1<<6) #define CF_QCALL (1<<7) #define CF_ADJLD (1<<8) #define CF_NO_INDEL (1<<9) #define CF_ANNO_MAX (1<<10) #define CF_MCALL (1<<11) #define CF_PAIRCALL (1<<12) #define CF_QCNT (1<<13) #define CF_INDEL_ONLY (1<<14) typedef struct { tgt_als_t *als; int nmatch_als, ibuf; } rec_tgt_t; typedef struct { int flag; // combination of CF_* flags above int output_type, n_threads, record_cmd_line, clevel; htsFile *bcf_in, *out_fh; char *bcf_fname, *output_fname; char **samples; // for subsampling and ploidy int nsamples, *samples_map; // mapping from output sample names to original VCF char *regions, *targets; // regions to process int regions_is_file, targets_is_file, regions_overlap; regidx_t *tgt_idx; regitr_t *tgt_itr, *tgt_itr_prev, *tgt_itr_tmp; vcfbuf_t *vcfbuf; char *samples_fname; int samples_is_file; int *sample2sex; // mapping for ploidy. If negative, interpreted as -1*ploidy int *sex2ploidy, *sex2ploidy_prev, nsex; ploidy_t *ploidy; gvcf_t *gvcf; bcf1_t *missed_line; call_t aux; // parameters and temporary data kstring_t str; int argc; char **argv; char *index_fn; int write_index; // int flag, prior_type, n1, n_sub, *sublist, n_perm; // uint32_t *trio_aux; // char *prior_file, **subsam; // uint8_t *ploidy; // double theta, pref, indel_frac, min_smpl_frac, min_lrt; // Permutation tests // int n_perm, *seeds; // double min_perm_p; // void *bed; } args_t; static char **add_sample(void *name2idx, char **lines, int *nlines, int *mlines, char *name, char sex, int *ith) { int ret = khash_str2int_get(name2idx, name, ith); if ( ret==0 ) return lines; hts_expand(char*,(*nlines+1),*mlines,lines); int len = strlen(name); lines[*nlines] = (char*) malloc(len+3); memcpy(lines[*nlines],name,len); lines[*nlines][len] = ' '; lines[*nlines][len+1] = sex; lines[*nlines][len+2] = 0; *ith = *nlines; (*nlines)++; khash_str2int_set(name2idx, strdup(name), *ith); return lines; } typedef struct { const char *alias, *about, *ploidy; } ploidy_predef_t; static ploidy_predef_t ploidy_predefs[] = { { .alias = "GRCh37", .about = "Human Genome reference assembly GRCh37 / hg19", .ploidy = "X 1 60000 M 1\n" "X 2699521 154931043 M 1\n" "Y 1 59373566 M 1\n" "Y 1 59373566 F 0\n" "MT 1 16569 M 1\n" "MT 1 16569 F 1\n" "chrX 1 60000 M 1\n" "chrX 2699521 154931043 M 1\n" "chrY 1 59373566 M 1\n" "chrY 1 59373566 F 0\n" "chrM 1 16569 M 1\n" "chrM 1 16569 F 1\n" "* * * M 2\n" "* * * F 2\n" }, { .alias = "GRCh38", .about = "Human Genome reference assembly GRCh38 / hg38", .ploidy = "X 1 9999 M 1\n" "X 2781480 155701381 M 1\n" "Y 1 57227415 M 1\n" "Y 1 57227415 F 0\n" "MT 1 16569 M 1\n" "MT 1 16569 F 1\n" "chrX 1 9999 M 1\n" "chrX 2781480 155701381 M 1\n" "chrY 1 57227415 M 1\n" "chrY 1 57227415 F 0\n" "chrM 1 16569 M 1\n" "chrM 1 16569 F 1\n" "* * * M 2\n" "* * * F 2\n" }, { .alias = "X", .about = "Treat male samples as haploid and female as diploid regardless of the chromosome name", .ploidy = "* * * M 1\n" "* * * F 2\n" }, { .alias = "Y", .about = "Treat male samples as haploid and female as no-copy, regardless of the chromosome name", .ploidy = "* * * M 1\n" "* * * F 0\n" }, { .alias = "1", .about = "Treat all samples as haploid", .ploidy = "* * * * 1\n" }, { .alias = "2", .about = "Treat all samples as diploid", .ploidy = "* * * * 2\n" }, { .alias = NULL, .about = NULL, .ploidy = NULL, } }; // only 5 columns are required and the first is ignored: // ignored,sample,father(or 0),mother(or 0),sex(1=M,2=F) static char **parse_ped_samples(call_t *call, char **vals, int nvals, int *nsmpl) { int i, j, mlines = 0, nlines = 0; kstring_t str = {0,0,0}, fam_str = {0,0,0}; void *name2idx = khash_str2int_init(); char **lines = NULL; for (i=0; infams++; hts_expand(family_t, call->nfams, call->mfams, call->fams); family_t *fam = &call->fams[call->nfams-1]; fam_str.l = 0; ksprintf(&fam_str,"father=%s, mother=%s, child=%s", col_ends[1]+1,col_ends[2]+1,col_ends[0]+1); fam->name = strdup(fam_str.s); if ( !khash_str2int_has_key(name2idx, col_ends[1]+1) ) lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[1]+1, 'M', &fam->sample[FATHER]); if ( !khash_str2int_has_key(name2idx, col_ends[2]+1) ) lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[2]+1, 'F', &fam->sample[MOTHER]); khash_str2int_get(name2idx, col_ends[0]+1, &fam->sample[CHILD]); khash_str2int_get(name2idx, col_ends[1]+1, &fam->sample[FATHER]); khash_str2int_get(name2idx, col_ends[2]+1, &fam->sample[MOTHER]); } } free(str.s); free(fam_str.s); khash_str2int_destroy_free(name2idx); if ( i!=nvals ) return NULL; // not a ped file *nsmpl = nlines; return lines; } /* * Reads sample names and their ploidy (optional) from a file. * Alternatively, if no such file exists, the file name is interpreted * as a comma-separated list of samples. When ploidy is not present, * the default ploidy 2 is assumed. */ static void set_samples(args_t *args, const char *fn, int is_file) { int i, nlines; char **lines = hts_readlist(fn, is_file, &nlines); if ( !lines ) error("Could not read the file: %s\n", fn); int nsmpls; char **smpls = parse_ped_samples(&args->aux, lines, nlines, &nsmpls); if ( smpls ) { for (i=0; isamples_map = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr)); // for subsetting args->sample2sex = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr)); int dflt_sex_id = ploidy_nsex(args->ploidy) - 1; for (i=0; iaux.hdr); i++) args->sample2sex[i] = dflt_sex_id; int *old2new = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr)); for (i=0; iaux.hdr); i++) old2new[i] = -1; int nsmpl = 0, map_needed = 0; for (i=0; iaux.hdr, BCF_DT_SAMPLE, ss); if ( ismpl < 0 ) { fprintf(stderr,"Warning: No such sample in the VCF: %s\n",ss); continue; } if ( old2new[ismpl] != -1 ) { fprintf(stderr,"Warning: The sample is listed multiple times: %s\n",ss); continue; } ss = se+(x != '\0'); while ( *ss && isspace(*ss) ) ss++; if ( !*ss ) ss = "2"; // default ploidy se = ss; while ( *se && !isspace(*se) ) se++; if ( se==ss ) { *xptr = x; error("Could not parse: \"%s\"\n", lines[i]); } if ( ss[1]==0 && (ss[0]=='0' || ss[0]=='1' || ss[0]=='2') ) args->sample2sex[nsmpl] = -1*(ss[0]-'0'); else args->sample2sex[nsmpl] = ploidy_add_sex(args->ploidy, ss); if ( ismpl!=nsmpl ) map_needed = 1; args->samples_map[nsmpl] = ismpl; old2new[ismpl] = nsmpl; nsmpl++; } for (i=0; iaux.nfams; i++) { int j, nmiss = 0; family_t *fam = &args->aux.fams[i]; for (j=0; j<3; j++) { fam->sample[i] = old2new[fam->sample[i]]; if ( fam->sample[i]<0 ) nmiss++; } assert( nmiss==0 || nmiss==3 ); } free(old2new); if ( !map_needed ) { free(args->samples_map); args->samples_map = NULL; } args->nsamples = nsmpl; args->samples = lines; } static void init_missed_line(args_t *args) { int i; for (i=0; iaux.hdr); i++) { args->aux.gts[i*2] = bcf_gt_missing; args->aux.gts[i*2+1] = bcf_int32_vector_end; } args->missed_line = bcf_init1(); bcf_update_genotypes(args->aux.hdr, args->missed_line, args->aux.gts, 2*bcf_hdr_nsamples(args->aux.hdr)); bcf_float_set_missing(args->missed_line->qual); } static int tgt_parse(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr) { char *ss = (char*) line; while ( *ss && isspace(*ss) ) ss++; if ( !*ss ) { fprintf(stderr,"Could not parse the line: %s\n", line); return -2; } if ( *ss=='#' ) return -1; // skip comments char *se = ss; while ( *se && !isspace(*se) ) se++; *chr_beg = ss; *chr_end = se-1; if ( !*se ) { fprintf(stderr,"Could not parse the line: %s\n", line); return -2; } ss = se+1; *beg = strtod(ss, &se); if ( ss==se ) { fprintf(stderr,"Could not parse tab line: %s\n", line); return -2; } if ( *beg==0 ) { fprintf(stderr,"Could not parse tab line, expected 1-based coordinate: %s\n", line); return -2; } (*beg)--; *end = *beg; if ( !usr ) return 0; // allele information not required ss = se+1; tgt_als_t *als = (tgt_als_t*)payload; als->used = 0; als->n = 0; als->allele = NULL; while ( *ss ) { se = ss; while ( *se && *se!=',' && !isspace(*se) ) se++; als->n++; als->allele = (char**)realloc(als->allele,als->n*sizeof(*als->allele)); als->allele[als->n-1] = (char*)malloc(se-ss+1); memcpy(als->allele[als->n-1],ss,se-ss); als->allele[als->n-1][se-ss] = 0; ss = se+1; if ( !*se || isspace(*se) ) break; } if ( als->n<2 ) error("Unable to parse the -T file; expected CHROM\\tPOS\\tREF,ALT with -C alleles but found instead:\n\t%s\n",line); return 0; } static void tgt_free(void *payload) { tgt_als_t *als = (tgt_als_t*)payload; int i; for (i=0; in; i++) free(als->allele[i]); free(als->allele); } static void tgt_flush_region(args_t *args, char *chr, uint32_t beg, uint32_t end) { if ( !regidx_overlap(args->tgt_idx, chr,beg,end,args->tgt_itr_tmp) ) return; while ( regitr_overlap(args->tgt_itr_tmp) ) { if ( args->tgt_itr_tmp->beg < beg ) continue; tgt_als_t *tgt_als = ®itr_payload(args->tgt_itr_tmp,tgt_als_t); if ( tgt_als->used ) continue; args->missed_line->rid = bcf_hdr_name2id(args->aux.hdr,chr); args->missed_line->pos = args->tgt_itr_tmp->beg; bcf_unpack(args->missed_line,BCF_UN_ALL); bcf_update_alleles(args->aux.hdr, args->missed_line, (const char**)tgt_als->allele, tgt_als->n); tgt_als->used = 1; if ( bcf_write1(args->out_fh, args->aux.hdr, args->missed_line)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args->output_fname); } } static void tgt_flush(args_t *args, bcf1_t *rec) { if ( rec ) { char *chr = (char*)bcf_seqname(args->aux.hdr,rec); if ( !args->tgt_itr_prev ) // first record tgt_flush_region(args,chr,0,rec->pos-1); else if ( strcmp(chr,args->tgt_itr_prev->seq) ) // first record on a new chromosome { tgt_flush_region(args,args->tgt_itr_prev->seq,args->tgt_itr_prev->beg+1,REGIDX_MAX); tgt_flush_region(args,chr,0,rec->pos-1); } else // another record on the same chromosome tgt_flush_region(args,args->tgt_itr_prev->seq,args->tgt_itr_prev->beg,rec->pos-1); } else { // flush everything if ( args->tgt_itr_prev ) tgt_flush_region(args,args->tgt_itr_prev->seq,args->tgt_itr_prev->beg,REGIDX_MAX); int i, nchr = 0; char **chr = regidx_seq_names(args->tgt_idx, &nchr); for (i=0; i" is not present at indels sites and there are no other symbolic alleles than <*> if ( als[1][0]=='<' ) return 0; int i; for (i=0; ivcfbuf ) { while ( bcf_sr_next_line(args->aux.srs) ) { rec = args->aux.srs->readers[0].buffer[0]; if ( args->aux.srs->errnum || rec->errcode ) error("Error: could not parse the input VCF\n"); if ( args->tgt_idx ) { if ( !regidx_overlap(args->tgt_idx, bcf_seqname(args->aux.hdr,rec),rec->pos,rec->pos,args->tgt_itr) ) continue; // For backward compatibility: require the exact position, not an interval overlap int pos_match = 0; while ( regitr_overlap(args->tgt_itr) ) { if ( args->tgt_itr->beg != rec->pos ) continue; pos_match = 1; break; } if ( !pos_match ) continue; } if ( args->samples_map ) bcf_subset(args->aux.hdr, rec, args->nsamples, args->samples_map); bcf_unpack(rec, BCF_UN_STR); return rec; } return NULL; } // If we are here,-C alleles was given and vcfbuf and tgt_idx are set // Fill the buffer with duplicate lines int vcfbuf_full = 1; int nbuf = vcfbuf_nsites(args->vcfbuf); bcf1_t *rec0 = NULL, *recN = NULL; if ( nbuf==0 ) vcfbuf_full = 0; else if ( nbuf==1 ) { vcfbuf_full = 0; rec0 = vcfbuf_peek(args->vcfbuf, 0); } else { rec0 = vcfbuf_peek(args->vcfbuf, 0); recN = vcfbuf_peek(args->vcfbuf, nbuf-1); if ( rec0->rid == recN->rid && rec0->pos == recN->pos ) vcfbuf_full = 0; } if ( !vcfbuf_full ) { while ( bcf_sr_next_line(args->aux.srs) ) { rec = args->aux.srs->readers[0].buffer[0]; if ( args->aux.srs->errnum || rec->errcode ) error("Error: could not parse the input VCF\n"); if ( !regidx_overlap(args->tgt_idx, bcf_seqname(args->aux.hdr,rec),rec->pos,rec->pos,args->tgt_itr) ) continue; // as above: require the exact position, not an interval overlap int exact_match = 0; while ( regitr_overlap(args->tgt_itr) ) { if ( args->tgt_itr->beg != rec->pos ) continue; exact_match = 1; break; } if ( !exact_match ) continue; if ( args->samples_map ) bcf_subset(args->aux.hdr, rec, args->nsamples, args->samples_map); bcf_unpack(rec, BCF_UN_STR); if ( !rec0 ) rec0 = rec; recN = rec; args->aux.srs->readers[0].buffer[0] = vcfbuf_push(args->vcfbuf, rec); if ( rec0->rid!=recN->rid || rec0->pos!=recN->pos ) break; } } nbuf = vcfbuf_nsites(args->vcfbuf); int n, i,j; for (n=nbuf; n>1; n--) { recN = vcfbuf_peek(args->vcfbuf, n-1); if ( rec0->rid==recN->rid && rec0->pos==recN->pos ) break; } if ( n==0 ) { assert( !nbuf ); return NULL; } // Find the VCF and tab record with the best matching combination of alleles, prioritize // records of the same type (snp vs indel) rec_tgt_t rec_tgt; memset(&rec_tgt,0,sizeof(rec_tgt)); regidx_overlap(args->tgt_idx, bcf_seqname(args->aux.hdr,rec0),rec0->pos,rec0->pos,args->tgt_itr); regitr_t *tmp_itr = regitr_init(args->tgt_idx); for (i=0; itgt_itr); rec = vcfbuf_peek(args->vcfbuf, i); int rec_indel = is_indel(rec->n_allele, rec->d.allele) ? 1 : -1; while ( regitr_overlap(tmp_itr) ) { if ( tmp_itr->beg != rec->pos ) continue; tgt_als_t *als = ®itr_payload(tmp_itr,tgt_als_t); if ( als->used ) continue; int nmatch_als = 0; vcmp_t *vcmp = vcmp_init(); int ret = vcmp_set_ref(vcmp, rec->d.allele[0], als->allele[0]); if ( ret==0 ) { nmatch_als++; if ( rec->n_allele > 1 && als->n > 1 ) { for (j=1; jn; j++) { if ( vcmp_find_allele(vcmp, rec->d.allele+1, rec->n_allele-1, als->allele[j])>=0 ) nmatch_als++; } } } int als_indel = is_indel(als->n, als->allele) ? 1 : -1; nmatch_als *= rec_indel*als_indel; if ( nmatch_als > rec_tgt.nmatch_als || !rec_tgt.als ) { rec_tgt.nmatch_als = nmatch_als; rec_tgt.als = als; rec_tgt.ibuf = i; } vcmp_destroy(vcmp); } } regitr_destroy(tmp_itr); args->aux.tgt_als = rec_tgt.als; if ( rec_tgt.als ) rec_tgt.als->used = 1; rec = vcfbuf_remove(args->vcfbuf, rec_tgt.ibuf); return rec; } static void init_data(args_t *args) { args->aux.srs = bcf_sr_init(); // Open files for input and output, initialize structures if ( args->targets ) { args->tgt_idx = regidx_init(args->targets, tgt_parse, args->aux.flag&CALL_CONSTR_ALLELES ? tgt_free : (regidx_free_f) NULL, sizeof(tgt_als_t), args->aux.flag&CALL_CONSTR_ALLELES ? args : NULL); args->tgt_itr = regitr_init(args->tgt_idx); args->tgt_itr_tmp = regitr_init(args->tgt_idx); } if ( args->regions ) { bcf_sr_set_opt(args->aux.srs,BCF_SR_REGIONS_OVERLAP,args->regions_overlap); if ( bcf_sr_set_regions(args->aux.srs, args->regions, args->regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions); } if ( !bcf_sr_add_reader(args->aux.srs, args->bcf_fname) ) error("Failed to read from %s: %s\n", !strcmp("-",args->bcf_fname)?"standard input":args->bcf_fname,bcf_sr_strerror(args->aux.srs->errnum)); args->aux.hdr = bcf_sr_get_header(args->aux.srs,0); int i; if ( args->samples_fname ) { set_samples(args, args->samples_fname, args->samples_is_file); if ( args->aux.flag&CALL_CONSTR_TRIO ) { if ( 3*args->aux.nfams!=args->nsamples ) error("Expected only trios in %s, sorry!\n", args->samples_fname); fprintf(stderr,"Detected %d samples in %d trio families\n", args->nsamples,args->aux.nfams); } } if ( args->ploidy ) { args->nsex = ploidy_nsex(args->ploidy); args->sex2ploidy = (int*) calloc(args->nsex,sizeof(int)); args->sex2ploidy_prev = (int*) calloc(args->nsex,sizeof(int)); if ( !args->nsamples ) { args->nsamples = bcf_hdr_nsamples(args->aux.hdr); args->sample2sex = (int*) malloc(sizeof(int)*args->nsamples); for (i=0; insamples; i++) args->sample2sex[i] = args->nsex - 1; } } if ( args->nsamples ) { args->aux.ploidy = (uint8_t*) malloc(args->nsamples); for (i=0; insamples; i++) args->aux.ploidy[i] = ploidy_max(args->ploidy); for (i=0; insex; i++) args->sex2ploidy_prev[i] = ploidy_max(args->ploidy); for (i=0; insamples; i++) if ( args->sample2sex[i] >= args->nsex ) args->sample2sex[i] = args->nsex - 1; } if ( args->gvcf ) { int id = bcf_hdr_id2int(args->aux.hdr,BCF_DT_ID,"DP"); if ( id<0 || !bcf_hdr_idinfo_exists(args->aux.hdr,BCF_HL_FMT,id) ) error("--gvcf output mode requires FORMAT/DP tag, which is not present in the input header\n"); gvcf_update_header(args->gvcf, args->aux.hdr); } if ( args->samples_map ) { args->aux.hdr = bcf_hdr_subset(bcf_sr_get_header(args->aux.srs,0), args->nsamples, args->samples, args->samples_map); if ( !args->aux.hdr ) error("Error occurred while subsetting samples\n"); for (i=0; insamples; i++) if ( args->samples_map[i]<0 ) error("No such sample: %s\n", args->samples[i]); if ( !bcf_hdr_nsamples(args->aux.hdr) ) error("No matching sample found\n"); } else { args->aux.hdr = bcf_hdr_dup(bcf_sr_get_header(args->aux.srs,0)); if ( args->samples ) { for (i=0; insamples; i++) if ( bcf_hdr_id2int(args->aux.hdr,BCF_DT_SAMPLE,args->samples[i])<0 ) error("No such sample: %s\n", args->samples[i]); } } if ( args->aux.flag & CALL_CONSTR_ALLELES ) { args->vcfbuf = vcfbuf_init(args->aux.hdr, 0); vcfbuf_set(args->vcfbuf,VCFBUF_DUMMY,1); } char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( args->out_fh == NULL ) error("Error: cannot write to \"%s\": %s\n", args->output_fname, strerror(errno)); if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads); if ( args->flag & CF_QCALL ) return; if ( args->flag & CF_MCALL ) mcall_init(&args->aux); if ( args->flag & CF_CCALL ) ccall_init(&args->aux); bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "QS"); bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "I16"); if (args->record_cmd_line) bcf_hdr_append_version(args->aux.hdr, args->argc, args->argv, "bcftools_call"); if ( bcf_hdr_write(args->out_fh, args->aux.hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname); if ( init_index2(args->out_fh,args->aux.hdr,args->output_fname, &args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->output_fname); if ( args->flag&CF_INS_MISSED ) init_missed_line(args); } static void destroy_data(args_t *args) { if ( args->vcfbuf ) vcfbuf_destroy(args->vcfbuf); if ( args->tgt_idx ) { regidx_destroy(args->tgt_idx); regitr_destroy(args->tgt_itr); regitr_destroy(args->tgt_itr_tmp); if ( args->tgt_itr_prev ) regitr_destroy(args->tgt_itr_prev); } if ( args->flag & CF_CCALL ) ccall_destroy(&args->aux); else if ( args->flag & CF_MCALL ) mcall_destroy(&args->aux); else if ( args->flag & CF_QCALL ) qcall_destroy(&args->aux); int i; if ( args->samples ) { for (i=0; insamples; i++) free(args->samples[i]); } if ( args->aux.fams ) { for (i=0; iaux.nfams; i++) free(args->aux.fams[i].name); free(args->aux.fams); } if ( args->missed_line ) bcf_destroy(args->missed_line); ploidy_destroy(args->ploidy); free(args->sex2ploidy); free(args->sex2ploidy_prev); free(args->samples); free(args->samples_map); free(args->sample2sex); free(args->aux.ploidy); free(args->str.s); if ( args->gvcf ) gvcf_destroy(args->gvcf); bcf_hdr_destroy(args->aux.hdr); if ( args->write_index ) { if ( bcf_idx_save(args->out_fh)<0 ) { if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname); bcf_sr_destroy(args->aux.srs); } void parse_novel_rate(args_t *args, const char *str) { if ( sscanf(str,"%le,%le,%le",&args->aux.trio_Pm_SNPs,&args->aux.trio_Pm_del,&args->aux.trio_Pm_ins)==3 ) // explicit for all { args->aux.trio_Pm_SNPs = 1 - args->aux.trio_Pm_SNPs; args->aux.trio_Pm_del = 1 - args->aux.trio_Pm_del; args->aux.trio_Pm_ins = 1 - args->aux.trio_Pm_ins; } else if ( sscanf(str,"%le,%le",&args->aux.trio_Pm_SNPs,&args->aux.trio_Pm_del)==2 ) // dynamic for indels { args->aux.trio_Pm_SNPs = 1 - args->aux.trio_Pm_SNPs; args->aux.trio_Pm_ins = -1; // negative value for dynamic calculation } else if ( sscanf(str,"%le",&args->aux.trio_Pm_SNPs)==1 ) // same for all { args->aux.trio_Pm_SNPs = 1 - args->aux.trio_Pm_SNPs; args->aux.trio_Pm_del = -1; args->aux.trio_Pm_ins = -1; } else error("Could not parse --novel-rate %s\n", str); } static void list_annotations(FILE *fp) { fprintf(fp, "\n" "Optional INFO annotations available with -m (\"INFO/\" prefix is optional):\n" " INFO/PV4 .. P-values for strand bias, baseQ bias, mapQ bias and tail distance bias (Number=4,Type=Float)\n" "\n" "Optional FORMAT annotations available with -m (\"FORMAT/\" prefix is optional):\n" " FORMAT/GQ .. Phred-scaled genotype quality (Number=1,Type=Integer)\n" " FORMAT/GP .. Phred-scaled genotype posterior probabilities (Number=G,Type=Float)\n" "\n"); } static int parse_output_tags(const char *str) { int flag = 0; const char *ss = str; while ( *ss ) { const char *se = ss; while ( *se && *se!=',' ) se++; if ( !strncasecmp(ss,"GQ",se-ss) || !strncasecmp(ss,"FORMAT/GQ",se-ss) || !strncasecmp(ss,"FMT/GQ",se-ss) ) flag |= CALL_FMT_GQ; else if ( !strncasecmp(ss,"GP",se-ss) || !strncasecmp(ss,"FORMAT/GP",se-ss) || !strncasecmp(ss,"FMT/GP",se-ss) ) flag |= CALL_FMT_GP; else if ( !strncasecmp(ss,"PV4",se-ss) || !strncasecmp(ss,"INFO/PV4",se-ss) ) flag |= CALL_FMT_PV4; else { fprintf(stderr,"Could not parse \"%s\"\n", str); exit(1); } if ( !*se ) break; ss = se + 1; } return flag; } static void set_ploidy(args_t *args, bcf1_t *rec) { ploidy_query(args->ploidy,(char*)bcf_seqname(args->aux.hdr,rec),rec->pos,args->sex2ploidy,NULL,NULL); int i; for (i=0; insex; i++) if ( args->sex2ploidy[i]!=args->sex2ploidy_prev[i] ) break; if ( i==args->nsex ) return; // ploidy same as previously for (i=0; insamples; i++) { if ( args->sample2sex[i]<0 ) args->aux.ploidy[i] = -1*args->sample2sex[i]; else args->aux.ploidy[i] = args->sex2ploidy[args->sample2sex[i]]; } int *tmp = args->sex2ploidy; args->sex2ploidy = args->sex2ploidy_prev; args->sex2ploidy_prev = tmp; } ploidy_t *init_ploidy(char *alias) { const ploidy_predef_t *pld = ploidy_predefs; int detailed = 0, len = strlen(alias); if ( alias[len-1]=='?' ) { detailed = 1; alias[len-1] = 0; } while ( pld->alias && strcasecmp(alias,pld->alias) ) pld++; if ( !pld->alias ) { fprintf(stderr,"\nPRE-DEFINED PLOIDY FILES\n\n"); fprintf(stderr," * Columns are: CHROM,FROM,TO,SEX,PLOIDY\n"); fprintf(stderr," * Coordinates are 1-based inclusive.\n"); fprintf(stderr," * A '*' means any value not otherwise defined.\n\n"); pld = ploidy_predefs; while ( pld->alias ) { fprintf(stderr,"%s\n .. %s\n\n", pld->alias,pld->about); if ( detailed ) fprintf(stderr,"%s\n", pld->ploidy); pld++; } fprintf(stderr,"Run as --ploidy (e.g. --ploidy GRCh37).\n"); fprintf(stderr,"To see the detailed ploidy definition, append a question mark (e.g. --ploidy GRCh37?).\n"); fprintf(stderr,"\n"); exit(-1); } else if ( detailed ) { fprintf(stderr,"%s", pld->ploidy); exit(-1); } return ploidy_init_string(pld->ploidy,2); } static void usage(args_t *args) { fprintf(stderr, "\n"); fprintf(stderr, "About: SNP/indel variant calling from VCF/BCF. To be used in conjunction with bcftools mpileup.\n"); fprintf(stderr, " This command replaces the former \"bcftools view\" caller. Some of the original\n"); fprintf(stderr, " functionality has been temporarily lost in the process of transition to htslib,\n"); fprintf(stderr, " but will be added back on popular demand. The original calling model can be\n"); fprintf(stderr, " invoked with the -c option.\n"); fprintf(stderr, "Usage: bcftools call [options] \n"); fprintf(stderr, "\n"); fprintf(stderr, "File format options:\n"); fprintf(stderr, " --no-version Do not append version and command line to the header\n"); fprintf(stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(stderr, " -O, --output-type b|u|z|v Output type: 'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n"); fprintf(stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(stderr, " --ploidy ASSEMBLY[?] Predefined ploidy, 'list' to print available settings, append '?' for details [2]\n"); fprintf(stderr, " --ploidy-file FILE Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY\n"); fprintf(stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " -s, --samples LIST List of samples to include [all samples]\n"); fprintf(stderr, " -S, --samples-file FILE PED file or a file with an optional column with sex (see man page for details) [all samples]\n"); fprintf(stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(stderr, " --threads INT Use multithreading with INT worker threads [0]\n"); fprintf(stderr, "\n"); fprintf(stderr, "Input/output options:\n"); fprintf(stderr, " -A, --keep-alts Keep all possible alternate alleles at variant sites\n"); fprintf(stderr, " -*, --keep-unseen-allele Keep the unobserved allele <*> or \n"); fprintf(stderr, " -a, --annotate LIST Optional tags to output (lowercase allowed); '?' to list available tags\n"); fprintf(stderr, " -F, --prior-freqs AN,AC Use prior allele frequencies, determined from these pre-filled tags\n"); fprintf(stderr, " -G, --group-samples FILE|- Group samples by population (file with \"sample\\tgroup\") or \"-\" for single-sample calling.\n"); fprintf(stderr, " This requires FORMAT/QS or other Number=R,Type=Integer tag such as FORMAT/AD\n"); fprintf(stderr, " --group-samples-tag TAG The tag to use with -G, by default FORMAT/QS and FORMAT/AD are checked automatically\n"); fprintf(stderr, " -g, --gvcf INT,[...] Group non-variant sites into gVCF blocks by minimum per-sample DP\n"); fprintf(stderr, " -i, --insert-missed Output also sites missed by mpileup but present in -T\n"); fprintf(stderr, " -M, --keep-masked-ref Keep sites with masked reference allele (REF=N)\n"); fprintf(stderr, " -V, --skip-variants TYPE Skip indels/snps\n"); fprintf(stderr, " -v, --variants-only Output variant sites only\n"); fprintf(stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(stderr, "\n"); fprintf(stderr, "Consensus/variant calling options:\n"); fprintf(stderr, " -c, --consensus-caller The original calling method (conflicts with -m)\n"); fprintf(stderr, " -C, --constrain STR One of: alleles, trio (see manual)\n"); fprintf(stderr, " -m, --multiallelic-caller Alternative model for multiallelic and rare-variant calling (conflicts with -c)\n"); fprintf(stderr, " -n, --novel-rate FLOAT,[...] Likelihood of novel mutation for constrained trio calling, see man page for details [1e-8,1e-9,1e-9]\n"); fprintf(stderr, " -p, --pval-threshold FLOAT Variant if P(ref|D)aux.min_lrt); // fprintf(stderr, " -U INT number of permutations for association testing (effective with -1) [0]\n"); // fprintf(stderr, " -X FLOAT only perform permutations for P(chi^2)aux.min_perm_p); fprintf(stderr, "\n"); exit(-1); } int main_vcfcall(int argc, char *argv[]) { char *ploidy_fname = NULL, *ploidy = NULL; args_t args; memset(&args, 0, sizeof(args_t)); args.argc = argc; args.argv = argv; args.aux.prior_type = -1; args.aux.indel_frac = -1; args.aux.theta = 1.1e-3; args.aux.pref = 0.5; args.aux.min_perm_p = 0.01; args.aux.min_lrt = 1; args.flag = CF_ACGT_ONLY; args.output_fname = "-"; args.output_type = FT_VCF; args.n_threads = 0; args.record_cmd_line = 1; args.aux.trio_Pm_SNPs = 1 - 1e-8; args.aux.trio_Pm_ins = args.aux.trio_Pm_del = 1 - 1e-9; args.regions_overlap = 1; args.clevel = -1; int c; static struct option loptions[] = { {"help",no_argument,NULL,'h'}, {"format-fields",required_argument,NULL,'f'}, {"annotate",required_argument,NULL,'a'}, {"prior-freqs",required_argument,NULL,'F'}, {"gvcf",required_argument,NULL,'g'}, {"group-samples",required_argument,NULL,'G'}, {"group-samples-tag",required_argument,NULL,3}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,4}, {"samples",required_argument,NULL,'s'}, {"samples-file",required_argument,NULL,'S'}, {"targets",required_argument,NULL,'t'}, {"targets-file",required_argument,NULL,'T'}, {"threads",required_argument,NULL,9}, {"keep-alts",no_argument,NULL,'A'}, {"keep-unseen-allele",no_argument,NULL,'*'}, {"insert-missed",no_argument,NULL,'i'}, {"skip-Ns",no_argument,NULL,'N'}, // now the new default {"keep-masked-refs",no_argument,NULL,'M'}, {"skip-variants",required_argument,NULL,'V'}, {"variants-only",no_argument,NULL,'v'}, {"consensus-caller",no_argument,NULL,'c'}, {"constrain",required_argument,NULL,'C'}, {"multiallelic-caller",no_argument,NULL,'m'}, {"pval-threshold",required_argument,NULL,'p'}, {"prior",required_argument,NULL,'P'}, {"novel-rate",required_argument,NULL,'n'}, {"ploidy",required_argument,NULL,1}, {"ploidy-file",required_argument,NULL,2}, {"chromosome-X",no_argument,NULL,'X'}, {"chromosome-Y",no_argument,NULL,'Y'}, {"no-version",no_argument,NULL,8}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp = NULL; while ((c = getopt_long(argc, argv, "h?o:O:r:R:s:S:t:T:A*NMV:vcmp:C:n:P:f:a:ig:XYF:G:W::", loptions, NULL)) >= 0) { switch (c) { case 2 : ploidy_fname = optarg; break; case 1 : ploidy = optarg; break; case 'X': ploidy = "X"; fprintf(stderr,"Warning: -X will be deprecated, please use --ploidy instead.\n"); break; case 'Y': ploidy = "Y"; fprintf(stderr,"Warning: -Y will be deprecated, please use --ploidy instead.\n"); break; case 'G': args.aux.sample_groups = optarg; break; case 3 : args.aux.sample_groups_tag = optarg; break; case 'f': fprintf(stderr,"Warning: -f, --format-fields will be deprecated, please use -a, --annotate instead.\n"); case 'a': if (optarg[0]=='?') { list_annotations(stderr); return 1; } args.aux.output_tags |= parse_output_tags(optarg); break; case 'M': args.flag &= ~CF_ACGT_ONLY; break; // keep sites where REF is N case 'N': args.flag |= CF_ACGT_ONLY; break; // omit sites where first base in REF is N (the new default) case 'A': args.aux.flag |= CALL_KEEPALT; break; case '*': args.aux.flag |= CALL_KEEP_UNSEEN; break; case 'c': args.flag |= CF_CCALL; break; // the original EM based calling method case 'i': args.flag |= CF_INS_MISSED; break; case 'v': args.aux.flag |= CALL_VARONLY; break; case 'F': args.aux.prior_AN = optarg; args.aux.prior_AC = strchr(optarg,','); if ( !args.aux.prior_AC ) error("Expected two tags with -F (e.g. AN,AC), got \"%s\"\n",optarg); *args.aux.prior_AC = 0; args.aux.prior_AC++; break; case 'g': args.gvcf = gvcf_init(optarg); if ( !args.gvcf ) error("Could not parse: --gvcf %s\n", optarg); break; case 'o': args.output_fname = optarg; break; case 'O': switch (optarg[0]) { case 'b': args.output_type = FT_BCF_GZ; break; case 'u': args.output_type = FT_BCF; break; case 'z': args.output_type = FT_VCF_GZ; break; case 'v': args.output_type = FT_VCF; break; default: { args.clevel = strtol(optarg,&tmp,10); if ( *tmp || args.clevel<0 || args.clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { args.clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args.clevel<0 || args.clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'C': if ( !strcasecmp(optarg,"alleles") ) args.aux.flag |= CALL_CONSTR_ALLELES; else if ( !strcasecmp(optarg,"trio") ) args.aux.flag |= CALL_CONSTR_TRIO; else error("Unknown argument to -C: \"%s\"\n", optarg); break; case 'V': if ( !strcasecmp(optarg,"snps") ) args.flag |= CF_INDEL_ONLY; else if ( !strcasecmp(optarg,"indels") ) args.flag |= CF_NO_INDEL; else error("Unknown skip category \"%s\" (-S argument must be \"snps\" or \"indels\")\n", optarg); break; case 'm': args.flag |= CF_MCALL; break; // multiallelic calling method case 'p': args.aux.pref = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: --pval-threshold %s\n", optarg); break; case 'P': args.aux.theta = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse, expected float argument: -P %s\n", optarg); break; case 'n': parse_novel_rate(&args,optarg); break; case 'r': args.regions = optarg; break; case 'R': args.regions = optarg; args.regions_is_file = 1; break; case 't': args.targets = optarg; break; case 'T': args.targets = optarg; args.targets_is_file = 1; break; case 's': args.samples_fname = optarg; break; case 'S': args.samples_fname = optarg; args.samples_is_file = 1; break; case 9 : args.n_threads = strtol(optarg, 0, 0); break; case 8 : args.record_cmd_line = 0; break; case 4 : args.regions_overlap = parse_overlap_option(optarg); if ( args.regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 'W': if (!(args.write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; default: usage(&args); } } // Sanity check options and initialize if ( ploidy_fname ) args.ploidy = ploidy_init(ploidy_fname, 2); else if ( ploidy ) args.ploidy = init_ploidy(ploidy); if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) args.bcf_fname = "-"; // reading from stdin else usage(&args); } else args.bcf_fname = argv[optind++]; if ( !ploidy_fname && !ploidy ) { if ( !args.samples_is_file ) fprintf(stderr,"Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n"); args.ploidy = ploidy_init_string("* * * 0 0\n* * * 1 1\n* * * 2 2\n",2); } if ( !args.ploidy ) error("Could not initialize ploidy\n"); if ( (args.flag & CF_CCALL ? 1 : 0) + (args.flag & CF_MCALL ? 1 : 0) + (args.flag & CF_QCALL ? 1 : 0) > 1 ) error("Only one of -c or -m options can be given\n"); if ( !(args.flag & CF_CCALL) && !(args.flag & CF_MCALL) && !(args.flag & CF_QCALL) ) error("Expected -c or -m option\n"); if ( (args.flag & CF_CCALL ? 1: 0) && args.gvcf ) error("gvcf -g option not functional with -c calling mode yet\n"); if ( args.aux.n_perm && args.aux.ngrp1_samples<=0 ) error("Expected -1 with -U\n"); // not sure about this, please fix if ( args.aux.flag & CALL_CONSTR_ALLELES ) { if ( !args.targets ) error("Expected -t or -T with \"-C alleles\"\n"); if ( !(args.flag & CF_MCALL) ) error("The \"-C alleles\" mode requires -m\n"); } if ( args.flag & CF_INS_MISSED && !(args.aux.flag&CALL_CONSTR_ALLELES) ) error("The -i option requires -C alleles\n"); if ( args.aux.flag&CALL_VARONLY && args.gvcf ) error("The two options cannot be combined: --variants-only and --gvcf\n"); if ( args.aux.sample_groups && !(args.flag & CF_MCALL) ) error("The -G feature is supported only with the -m calling mode\n"); init_data(&args); bcf1_t *bcf_rec; while ( (bcf_rec = next_line(&args)) ) { // Skip duplicate positions with all matching `-C alleles -T` used up if ( args.aux.flag&CALL_CONSTR_ALLELES && !args.aux.tgt_als ) continue; // Skip unwanted sites int i, is_indel = bcf_is_snp(bcf_rec) ? 0 : 1; if ( (args.flag & CF_INDEL_ONLY) && !is_indel ) continue; if ( (args.flag & CF_NO_INDEL) && is_indel ) continue; if ( (args.flag & CF_ACGT_ONLY) && (bcf_rec->d.allele[0][0]=='N' || bcf_rec->d.allele[0][0]=='n') ) continue; // REF[0] is 'N' // Which allele is symbolic? All SNPs should have it, but not indels args.aux.unseen = 0; for (i=1; in_allele; i++) { if ( bcf_rec->d.allele[i][0]=='X' ) { args.aux.unseen = i; break; } // old X if ( bcf_rec->d.allele[i][0]=='<' ) { if ( bcf_rec->d.allele[i][1]=='X' && bcf_rec->d.allele[i][2]=='>' ) { args.aux.unseen = i; break; } // old if ( bcf_rec->d.allele[i][1]=='*' && bcf_rec->d.allele[i][2]=='>' ) { args.aux.unseen = i; break; } // new <*> } } int is_ref = (bcf_rec->n_allele==1 || (bcf_rec->n_allele==2 && args.aux.unseen>0)) ? 1 : 0; if ( is_ref && args.aux.flag&CALL_VARONLY ) continue; bcf_unpack(bcf_rec, BCF_UN_ALL); if ( args.nsex ) set_ploidy(&args, bcf_rec); // Various output modes: QCall output (todo) if ( args.flag & CF_QCALL ) { qcall(&args.aux, bcf_rec); continue; } if ( args.flag & CF_INS_MISSED ) { tgt_flush(&args,bcf_rec); if ( !args.tgt_itr_prev ) args.tgt_itr_prev = regitr_init(args.tgt_idx); regitr_copy(args.tgt_itr_prev, args.tgt_itr); } // Calling modes which output VCFs int ret; if ( args.flag & CF_MCALL ) ret = mcall(&args.aux, bcf_rec); else ret = ccall(&args.aux, bcf_rec); if ( ret==-1 ) error("Something is wrong\n"); else if ( ret==-2 ) continue; // skip the site // Normal output if ( (args.aux.flag & CALL_VARONLY) && ret==0 && !args.gvcf ) continue; // not a variant if ( args.gvcf ) bcf_rec = gvcf_write(args.gvcf, args.out_fh, args.aux.hdr, bcf_rec, ret==1?1:0); if ( bcf_rec && bcf_write1(args.out_fh, args.aux.hdr, bcf_rec)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args.output_fname); } if ( args.gvcf ) gvcf_write(args.gvcf, args.out_fh, args.aux.hdr, NULL, 0); if ( args.flag & CF_INS_MISSED ) tgt_flush(&args,NULL); destroy_data(&args); return 0; } pysam-0.23.0/bcftools/vcfcall.c.pysam.c000066400000000000000000001423021475062545500177060ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfcall.c -- SNP/indel variant calling from VCF/BCF. Copyright (C) 2013-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "call.h" #include "prob1.h" #include "ploidy.h" #include "gvcf.h" #include "regidx.h" #include "vcfbuf.h" void error(const char *format, ...); #define CF_NO_GENO 1 #define CF_INS_MISSED (1<<1) #define CF_CCALL (1<<2) // (1<<3) // (1<<4) // (1<<5) #define CF_ACGT_ONLY (1<<6) #define CF_QCALL (1<<7) #define CF_ADJLD (1<<8) #define CF_NO_INDEL (1<<9) #define CF_ANNO_MAX (1<<10) #define CF_MCALL (1<<11) #define CF_PAIRCALL (1<<12) #define CF_QCNT (1<<13) #define CF_INDEL_ONLY (1<<14) typedef struct { tgt_als_t *als; int nmatch_als, ibuf; } rec_tgt_t; typedef struct { int flag; // combination of CF_* flags above int output_type, n_threads, record_cmd_line, clevel; htsFile *bcf_in, *out_fh; char *bcf_fname, *output_fname; char **samples; // for subsampling and ploidy int nsamples, *samples_map; // mapping from output sample names to original VCF char *regions, *targets; // regions to process int regions_is_file, targets_is_file, regions_overlap; regidx_t *tgt_idx; regitr_t *tgt_itr, *tgt_itr_prev, *tgt_itr_tmp; vcfbuf_t *vcfbuf; char *samples_fname; int samples_is_file; int *sample2sex; // mapping for ploidy. If negative, interpreted as -1*ploidy int *sex2ploidy, *sex2ploidy_prev, nsex; ploidy_t *ploidy; gvcf_t *gvcf; bcf1_t *missed_line; call_t aux; // parameters and temporary data kstring_t str; int argc; char **argv; char *index_fn; int write_index; // int flag, prior_type, n1, n_sub, *sublist, n_perm; // uint32_t *trio_aux; // char *prior_file, **subsam; // uint8_t *ploidy; // double theta, pref, indel_frac, min_smpl_frac, min_lrt; // Permutation tests // int n_perm, *seeds; // double min_perm_p; // void *bed; } args_t; static char **add_sample(void *name2idx, char **lines, int *nlines, int *mlines, char *name, char sex, int *ith) { int ret = khash_str2int_get(name2idx, name, ith); if ( ret==0 ) return lines; hts_expand(char*,(*nlines+1),*mlines,lines); int len = strlen(name); lines[*nlines] = (char*) malloc(len+3); memcpy(lines[*nlines],name,len); lines[*nlines][len] = ' '; lines[*nlines][len+1] = sex; lines[*nlines][len+2] = 0; *ith = *nlines; (*nlines)++; khash_str2int_set(name2idx, strdup(name), *ith); return lines; } typedef struct { const char *alias, *about, *ploidy; } ploidy_predef_t; static ploidy_predef_t ploidy_predefs[] = { { .alias = "GRCh37", .about = "Human Genome reference assembly GRCh37 / hg19", .ploidy = "X 1 60000 M 1\n" "X 2699521 154931043 M 1\n" "Y 1 59373566 M 1\n" "Y 1 59373566 F 0\n" "MT 1 16569 M 1\n" "MT 1 16569 F 1\n" "chrX 1 60000 M 1\n" "chrX 2699521 154931043 M 1\n" "chrY 1 59373566 M 1\n" "chrY 1 59373566 F 0\n" "chrM 1 16569 M 1\n" "chrM 1 16569 F 1\n" "* * * M 2\n" "* * * F 2\n" }, { .alias = "GRCh38", .about = "Human Genome reference assembly GRCh38 / hg38", .ploidy = "X 1 9999 M 1\n" "X 2781480 155701381 M 1\n" "Y 1 57227415 M 1\n" "Y 1 57227415 F 0\n" "MT 1 16569 M 1\n" "MT 1 16569 F 1\n" "chrX 1 9999 M 1\n" "chrX 2781480 155701381 M 1\n" "chrY 1 57227415 M 1\n" "chrY 1 57227415 F 0\n" "chrM 1 16569 M 1\n" "chrM 1 16569 F 1\n" "* * * M 2\n" "* * * F 2\n" }, { .alias = "X", .about = "Treat male samples as haploid and female as diploid regardless of the chromosome name", .ploidy = "* * * M 1\n" "* * * F 2\n" }, { .alias = "Y", .about = "Treat male samples as haploid and female as no-copy, regardless of the chromosome name", .ploidy = "* * * M 1\n" "* * * F 0\n" }, { .alias = "1", .about = "Treat all samples as haploid", .ploidy = "* * * * 1\n" }, { .alias = "2", .about = "Treat all samples as diploid", .ploidy = "* * * * 2\n" }, { .alias = NULL, .about = NULL, .ploidy = NULL, } }; // only 5 columns are required and the first is ignored: // ignored,sample,father(or 0),mother(or 0),sex(1=M,2=F) static char **parse_ped_samples(call_t *call, char **vals, int nvals, int *nsmpl) { int i, j, mlines = 0, nlines = 0; kstring_t str = {0,0,0}, fam_str = {0,0,0}; void *name2idx = khash_str2int_init(); char **lines = NULL; for (i=0; infams++; hts_expand(family_t, call->nfams, call->mfams, call->fams); family_t *fam = &call->fams[call->nfams-1]; fam_str.l = 0; ksprintf(&fam_str,"father=%s, mother=%s, child=%s", col_ends[1]+1,col_ends[2]+1,col_ends[0]+1); fam->name = strdup(fam_str.s); if ( !khash_str2int_has_key(name2idx, col_ends[1]+1) ) lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[1]+1, 'M', &fam->sample[FATHER]); if ( !khash_str2int_has_key(name2idx, col_ends[2]+1) ) lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[2]+1, 'F', &fam->sample[MOTHER]); khash_str2int_get(name2idx, col_ends[0]+1, &fam->sample[CHILD]); khash_str2int_get(name2idx, col_ends[1]+1, &fam->sample[FATHER]); khash_str2int_get(name2idx, col_ends[2]+1, &fam->sample[MOTHER]); } } free(str.s); free(fam_str.s); khash_str2int_destroy_free(name2idx); if ( i!=nvals ) return NULL; // not a ped file *nsmpl = nlines; return lines; } /* * Reads sample names and their ploidy (optional) from a file. * Alternatively, if no such file exists, the file name is interpreted * as a comma-separated list of samples. When ploidy is not present, * the default ploidy 2 is assumed. */ static void set_samples(args_t *args, const char *fn, int is_file) { int i, nlines; char **lines = hts_readlist(fn, is_file, &nlines); if ( !lines ) error("Could not read the file: %s\n", fn); int nsmpls; char **smpls = parse_ped_samples(&args->aux, lines, nlines, &nsmpls); if ( smpls ) { for (i=0; isamples_map = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr)); // for subsetting args->sample2sex = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr)); int dflt_sex_id = ploidy_nsex(args->ploidy) - 1; for (i=0; iaux.hdr); i++) args->sample2sex[i] = dflt_sex_id; int *old2new = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr)); for (i=0; iaux.hdr); i++) old2new[i] = -1; int nsmpl = 0, map_needed = 0; for (i=0; iaux.hdr, BCF_DT_SAMPLE, ss); if ( ismpl < 0 ) { fprintf(bcftools_stderr,"Warning: No such sample in the VCF: %s\n",ss); continue; } if ( old2new[ismpl] != -1 ) { fprintf(bcftools_stderr,"Warning: The sample is listed multiple times: %s\n",ss); continue; } ss = se+(x != '\0'); while ( *ss && isspace(*ss) ) ss++; if ( !*ss ) ss = "2"; // default ploidy se = ss; while ( *se && !isspace(*se) ) se++; if ( se==ss ) { *xptr = x; error("Could not parse: \"%s\"\n", lines[i]); } if ( ss[1]==0 && (ss[0]=='0' || ss[0]=='1' || ss[0]=='2') ) args->sample2sex[nsmpl] = -1*(ss[0]-'0'); else args->sample2sex[nsmpl] = ploidy_add_sex(args->ploidy, ss); if ( ismpl!=nsmpl ) map_needed = 1; args->samples_map[nsmpl] = ismpl; old2new[ismpl] = nsmpl; nsmpl++; } for (i=0; iaux.nfams; i++) { int j, nmiss = 0; family_t *fam = &args->aux.fams[i]; for (j=0; j<3; j++) { fam->sample[i] = old2new[fam->sample[i]]; if ( fam->sample[i]<0 ) nmiss++; } assert( nmiss==0 || nmiss==3 ); } free(old2new); if ( !map_needed ) { free(args->samples_map); args->samples_map = NULL; } args->nsamples = nsmpl; args->samples = lines; } static void init_missed_line(args_t *args) { int i; for (i=0; iaux.hdr); i++) { args->aux.gts[i*2] = bcf_gt_missing; args->aux.gts[i*2+1] = bcf_int32_vector_end; } args->missed_line = bcf_init1(); bcf_update_genotypes(args->aux.hdr, args->missed_line, args->aux.gts, 2*bcf_hdr_nsamples(args->aux.hdr)); bcf_float_set_missing(args->missed_line->qual); } static int tgt_parse(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr) { char *ss = (char*) line; while ( *ss && isspace(*ss) ) ss++; if ( !*ss ) { fprintf(bcftools_stderr,"Could not parse the line: %s\n", line); return -2; } if ( *ss=='#' ) return -1; // skip comments char *se = ss; while ( *se && !isspace(*se) ) se++; *chr_beg = ss; *chr_end = se-1; if ( !*se ) { fprintf(bcftools_stderr,"Could not parse the line: %s\n", line); return -2; } ss = se+1; *beg = strtod(ss, &se); if ( ss==se ) { fprintf(bcftools_stderr,"Could not parse tab line: %s\n", line); return -2; } if ( *beg==0 ) { fprintf(bcftools_stderr,"Could not parse tab line, expected 1-based coordinate: %s\n", line); return -2; } (*beg)--; *end = *beg; if ( !usr ) return 0; // allele information not required ss = se+1; tgt_als_t *als = (tgt_als_t*)payload; als->used = 0; als->n = 0; als->allele = NULL; while ( *ss ) { se = ss; while ( *se && *se!=',' && !isspace(*se) ) se++; als->n++; als->allele = (char**)realloc(als->allele,als->n*sizeof(*als->allele)); als->allele[als->n-1] = (char*)malloc(se-ss+1); memcpy(als->allele[als->n-1],ss,se-ss); als->allele[als->n-1][se-ss] = 0; ss = se+1; if ( !*se || isspace(*se) ) break; } if ( als->n<2 ) error("Unable to parse the -T file; expected CHROM\\tPOS\\tREF,ALT with -C alleles but found instead:\n\t%s\n",line); return 0; } static void tgt_free(void *payload) { tgt_als_t *als = (tgt_als_t*)payload; int i; for (i=0; in; i++) free(als->allele[i]); free(als->allele); } static void tgt_flush_region(args_t *args, char *chr, uint32_t beg, uint32_t end) { if ( !regidx_overlap(args->tgt_idx, chr,beg,end,args->tgt_itr_tmp) ) return; while ( regitr_overlap(args->tgt_itr_tmp) ) { if ( args->tgt_itr_tmp->beg < beg ) continue; tgt_als_t *tgt_als = ®itr_payload(args->tgt_itr_tmp,tgt_als_t); if ( tgt_als->used ) continue; args->missed_line->rid = bcf_hdr_name2id(args->aux.hdr,chr); args->missed_line->pos = args->tgt_itr_tmp->beg; bcf_unpack(args->missed_line,BCF_UN_ALL); bcf_update_alleles(args->aux.hdr, args->missed_line, (const char**)tgt_als->allele, tgt_als->n); tgt_als->used = 1; if ( bcf_write1(args->out_fh, args->aux.hdr, args->missed_line)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args->output_fname); } } static void tgt_flush(args_t *args, bcf1_t *rec) { if ( rec ) { char *chr = (char*)bcf_seqname(args->aux.hdr,rec); if ( !args->tgt_itr_prev ) // first record tgt_flush_region(args,chr,0,rec->pos-1); else if ( strcmp(chr,args->tgt_itr_prev->seq) ) // first record on a new chromosome { tgt_flush_region(args,args->tgt_itr_prev->seq,args->tgt_itr_prev->beg+1,REGIDX_MAX); tgt_flush_region(args,chr,0,rec->pos-1); } else // another record on the same chromosome tgt_flush_region(args,args->tgt_itr_prev->seq,args->tgt_itr_prev->beg,rec->pos-1); } else { // flush everything if ( args->tgt_itr_prev ) tgt_flush_region(args,args->tgt_itr_prev->seq,args->tgt_itr_prev->beg,REGIDX_MAX); int i, nchr = 0; char **chr = regidx_seq_names(args->tgt_idx, &nchr); for (i=0; i" is not present at indels sites and there are no other symbolic alleles than <*> if ( als[1][0]=='<' ) return 0; int i; for (i=0; ivcfbuf ) { while ( bcf_sr_next_line(args->aux.srs) ) { rec = args->aux.srs->readers[0].buffer[0]; if ( args->aux.srs->errnum || rec->errcode ) error("Error: could not parse the input VCF\n"); if ( args->tgt_idx ) { if ( !regidx_overlap(args->tgt_idx, bcf_seqname(args->aux.hdr,rec),rec->pos,rec->pos,args->tgt_itr) ) continue; // For backward compatibility: require the exact position, not an interval overlap int pos_match = 0; while ( regitr_overlap(args->tgt_itr) ) { if ( args->tgt_itr->beg != rec->pos ) continue; pos_match = 1; break; } if ( !pos_match ) continue; } if ( args->samples_map ) bcf_subset(args->aux.hdr, rec, args->nsamples, args->samples_map); bcf_unpack(rec, BCF_UN_STR); return rec; } return NULL; } // If we are here,-C alleles was given and vcfbuf and tgt_idx are set // Fill the buffer with duplicate lines int vcfbuf_full = 1; int nbuf = vcfbuf_nsites(args->vcfbuf); bcf1_t *rec0 = NULL, *recN = NULL; if ( nbuf==0 ) vcfbuf_full = 0; else if ( nbuf==1 ) { vcfbuf_full = 0; rec0 = vcfbuf_peek(args->vcfbuf, 0); } else { rec0 = vcfbuf_peek(args->vcfbuf, 0); recN = vcfbuf_peek(args->vcfbuf, nbuf-1); if ( rec0->rid == recN->rid && rec0->pos == recN->pos ) vcfbuf_full = 0; } if ( !vcfbuf_full ) { while ( bcf_sr_next_line(args->aux.srs) ) { rec = args->aux.srs->readers[0].buffer[0]; if ( args->aux.srs->errnum || rec->errcode ) error("Error: could not parse the input VCF\n"); if ( !regidx_overlap(args->tgt_idx, bcf_seqname(args->aux.hdr,rec),rec->pos,rec->pos,args->tgt_itr) ) continue; // as above: require the exact position, not an interval overlap int exact_match = 0; while ( regitr_overlap(args->tgt_itr) ) { if ( args->tgt_itr->beg != rec->pos ) continue; exact_match = 1; break; } if ( !exact_match ) continue; if ( args->samples_map ) bcf_subset(args->aux.hdr, rec, args->nsamples, args->samples_map); bcf_unpack(rec, BCF_UN_STR); if ( !rec0 ) rec0 = rec; recN = rec; args->aux.srs->readers[0].buffer[0] = vcfbuf_push(args->vcfbuf, rec); if ( rec0->rid!=recN->rid || rec0->pos!=recN->pos ) break; } } nbuf = vcfbuf_nsites(args->vcfbuf); int n, i,j; for (n=nbuf; n>1; n--) { recN = vcfbuf_peek(args->vcfbuf, n-1); if ( rec0->rid==recN->rid && rec0->pos==recN->pos ) break; } if ( n==0 ) { assert( !nbuf ); return NULL; } // Find the VCF and tab record with the best matching combination of alleles, prioritize // records of the same type (snp vs indel) rec_tgt_t rec_tgt; memset(&rec_tgt,0,sizeof(rec_tgt)); regidx_overlap(args->tgt_idx, bcf_seqname(args->aux.hdr,rec0),rec0->pos,rec0->pos,args->tgt_itr); regitr_t *tmp_itr = regitr_init(args->tgt_idx); for (i=0; itgt_itr); rec = vcfbuf_peek(args->vcfbuf, i); int rec_indel = is_indel(rec->n_allele, rec->d.allele) ? 1 : -1; while ( regitr_overlap(tmp_itr) ) { if ( tmp_itr->beg != rec->pos ) continue; tgt_als_t *als = ®itr_payload(tmp_itr,tgt_als_t); if ( als->used ) continue; int nmatch_als = 0; vcmp_t *vcmp = vcmp_init(); int ret = vcmp_set_ref(vcmp, rec->d.allele[0], als->allele[0]); if ( ret==0 ) { nmatch_als++; if ( rec->n_allele > 1 && als->n > 1 ) { for (j=1; jn; j++) { if ( vcmp_find_allele(vcmp, rec->d.allele+1, rec->n_allele-1, als->allele[j])>=0 ) nmatch_als++; } } } int als_indel = is_indel(als->n, als->allele) ? 1 : -1; nmatch_als *= rec_indel*als_indel; if ( nmatch_als > rec_tgt.nmatch_als || !rec_tgt.als ) { rec_tgt.nmatch_als = nmatch_als; rec_tgt.als = als; rec_tgt.ibuf = i; } vcmp_destroy(vcmp); } } regitr_destroy(tmp_itr); args->aux.tgt_als = rec_tgt.als; if ( rec_tgt.als ) rec_tgt.als->used = 1; rec = vcfbuf_remove(args->vcfbuf, rec_tgt.ibuf); return rec; } static void init_data(args_t *args) { args->aux.srs = bcf_sr_init(); // Open files for input and output, initialize structures if ( args->targets ) { args->tgt_idx = regidx_init(args->targets, tgt_parse, args->aux.flag&CALL_CONSTR_ALLELES ? tgt_free : (regidx_free_f) NULL, sizeof(tgt_als_t), args->aux.flag&CALL_CONSTR_ALLELES ? args : NULL); args->tgt_itr = regitr_init(args->tgt_idx); args->tgt_itr_tmp = regitr_init(args->tgt_idx); } if ( args->regions ) { bcf_sr_set_opt(args->aux.srs,BCF_SR_REGIONS_OVERLAP,args->regions_overlap); if ( bcf_sr_set_regions(args->aux.srs, args->regions, args->regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions); } if ( !bcf_sr_add_reader(args->aux.srs, args->bcf_fname) ) error("Failed to read from %s: %s\n", !strcmp("-",args->bcf_fname)?"standard input":args->bcf_fname,bcf_sr_strerror(args->aux.srs->errnum)); args->aux.hdr = bcf_sr_get_header(args->aux.srs,0); int i; if ( args->samples_fname ) { set_samples(args, args->samples_fname, args->samples_is_file); if ( args->aux.flag&CALL_CONSTR_TRIO ) { if ( 3*args->aux.nfams!=args->nsamples ) error("Expected only trios in %s, sorry!\n", args->samples_fname); fprintf(bcftools_stderr,"Detected %d samples in %d trio families\n", args->nsamples,args->aux.nfams); } } if ( args->ploidy ) { args->nsex = ploidy_nsex(args->ploidy); args->sex2ploidy = (int*) calloc(args->nsex,sizeof(int)); args->sex2ploidy_prev = (int*) calloc(args->nsex,sizeof(int)); if ( !args->nsamples ) { args->nsamples = bcf_hdr_nsamples(args->aux.hdr); args->sample2sex = (int*) malloc(sizeof(int)*args->nsamples); for (i=0; insamples; i++) args->sample2sex[i] = args->nsex - 1; } } if ( args->nsamples ) { args->aux.ploidy = (uint8_t*) malloc(args->nsamples); for (i=0; insamples; i++) args->aux.ploidy[i] = ploidy_max(args->ploidy); for (i=0; insex; i++) args->sex2ploidy_prev[i] = ploidy_max(args->ploidy); for (i=0; insamples; i++) if ( args->sample2sex[i] >= args->nsex ) args->sample2sex[i] = args->nsex - 1; } if ( args->gvcf ) { int id = bcf_hdr_id2int(args->aux.hdr,BCF_DT_ID,"DP"); if ( id<0 || !bcf_hdr_idinfo_exists(args->aux.hdr,BCF_HL_FMT,id) ) error("--gvcf output mode requires FORMAT/DP tag, which is not present in the input header\n"); gvcf_update_header(args->gvcf, args->aux.hdr); } if ( args->samples_map ) { args->aux.hdr = bcf_hdr_subset(bcf_sr_get_header(args->aux.srs,0), args->nsamples, args->samples, args->samples_map); if ( !args->aux.hdr ) error("Error occurred while subsetting samples\n"); for (i=0; insamples; i++) if ( args->samples_map[i]<0 ) error("No such sample: %s\n", args->samples[i]); if ( !bcf_hdr_nsamples(args->aux.hdr) ) error("No matching sample found\n"); } else { args->aux.hdr = bcf_hdr_dup(bcf_sr_get_header(args->aux.srs,0)); if ( args->samples ) { for (i=0; insamples; i++) if ( bcf_hdr_id2int(args->aux.hdr,BCF_DT_SAMPLE,args->samples[i])<0 ) error("No such sample: %s\n", args->samples[i]); } } if ( args->aux.flag & CALL_CONSTR_ALLELES ) { args->vcfbuf = vcfbuf_init(args->aux.hdr, 0); vcfbuf_set(args->vcfbuf,VCFBUF_DUMMY,1); } char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( args->out_fh == NULL ) error("Error: cannot write to \"%s\": %s\n", args->output_fname, strerror(errno)); if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads); if ( args->flag & CF_QCALL ) return; if ( args->flag & CF_MCALL ) mcall_init(&args->aux); if ( args->flag & CF_CCALL ) ccall_init(&args->aux); bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "QS"); bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "I16"); if (args->record_cmd_line) bcf_hdr_append_version(args->aux.hdr, args->argc, args->argv, "bcftools_call"); if ( bcf_hdr_write(args->out_fh, args->aux.hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname); if ( init_index2(args->out_fh,args->aux.hdr,args->output_fname, &args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->output_fname); if ( args->flag&CF_INS_MISSED ) init_missed_line(args); } static void destroy_data(args_t *args) { if ( args->vcfbuf ) vcfbuf_destroy(args->vcfbuf); if ( args->tgt_idx ) { regidx_destroy(args->tgt_idx); regitr_destroy(args->tgt_itr); regitr_destroy(args->tgt_itr_tmp); if ( args->tgt_itr_prev ) regitr_destroy(args->tgt_itr_prev); } if ( args->flag & CF_CCALL ) ccall_destroy(&args->aux); else if ( args->flag & CF_MCALL ) mcall_destroy(&args->aux); else if ( args->flag & CF_QCALL ) qcall_destroy(&args->aux); int i; if ( args->samples ) { for (i=0; insamples; i++) free(args->samples[i]); } if ( args->aux.fams ) { for (i=0; iaux.nfams; i++) free(args->aux.fams[i].name); free(args->aux.fams); } if ( args->missed_line ) bcf_destroy(args->missed_line); ploidy_destroy(args->ploidy); free(args->sex2ploidy); free(args->sex2ploidy_prev); free(args->samples); free(args->samples_map); free(args->sample2sex); free(args->aux.ploidy); free(args->str.s); if ( args->gvcf ) gvcf_destroy(args->gvcf); bcf_hdr_destroy(args->aux.hdr); if ( args->write_index ) { if ( bcf_idx_save(args->out_fh)<0 ) { if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"bcftools_stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname); bcf_sr_destroy(args->aux.srs); } void parse_novel_rate(args_t *args, const char *str) { if ( sscanf(str,"%le,%le,%le",&args->aux.trio_Pm_SNPs,&args->aux.trio_Pm_del,&args->aux.trio_Pm_ins)==3 ) // explicit for all { args->aux.trio_Pm_SNPs = 1 - args->aux.trio_Pm_SNPs; args->aux.trio_Pm_del = 1 - args->aux.trio_Pm_del; args->aux.trio_Pm_ins = 1 - args->aux.trio_Pm_ins; } else if ( sscanf(str,"%le,%le",&args->aux.trio_Pm_SNPs,&args->aux.trio_Pm_del)==2 ) // dynamic for indels { args->aux.trio_Pm_SNPs = 1 - args->aux.trio_Pm_SNPs; args->aux.trio_Pm_ins = -1; // negative value for dynamic calculation } else if ( sscanf(str,"%le",&args->aux.trio_Pm_SNPs)==1 ) // same for all { args->aux.trio_Pm_SNPs = 1 - args->aux.trio_Pm_SNPs; args->aux.trio_Pm_del = -1; args->aux.trio_Pm_ins = -1; } else error("Could not parse --novel-rate %s\n", str); } static void list_annotations(FILE *fp) { fprintf(fp, "\n" "Optional INFO annotations available with -m (\"INFO/\" prefix is optional):\n" " INFO/PV4 .. P-values for strand bias, baseQ bias, mapQ bias and tail distance bias (Number=4,Type=Float)\n" "\n" "Optional FORMAT annotations available with -m (\"FORMAT/\" prefix is optional):\n" " FORMAT/GQ .. Phred-scaled genotype quality (Number=1,Type=Integer)\n" " FORMAT/GP .. Phred-scaled genotype posterior probabilities (Number=G,Type=Float)\n" "\n"); } static int parse_output_tags(const char *str) { int flag = 0; const char *ss = str; while ( *ss ) { const char *se = ss; while ( *se && *se!=',' ) se++; if ( !strncasecmp(ss,"GQ",se-ss) || !strncasecmp(ss,"FORMAT/GQ",se-ss) || !strncasecmp(ss,"FMT/GQ",se-ss) ) flag |= CALL_FMT_GQ; else if ( !strncasecmp(ss,"GP",se-ss) || !strncasecmp(ss,"FORMAT/GP",se-ss) || !strncasecmp(ss,"FMT/GP",se-ss) ) flag |= CALL_FMT_GP; else if ( !strncasecmp(ss,"PV4",se-ss) || !strncasecmp(ss,"INFO/PV4",se-ss) ) flag |= CALL_FMT_PV4; else { fprintf(bcftools_stderr,"Could not parse \"%s\"\n", str); bcftools_exit(1); } if ( !*se ) break; ss = se + 1; } return flag; } static void set_ploidy(args_t *args, bcf1_t *rec) { ploidy_query(args->ploidy,(char*)bcf_seqname(args->aux.hdr,rec),rec->pos,args->sex2ploidy,NULL,NULL); int i; for (i=0; insex; i++) if ( args->sex2ploidy[i]!=args->sex2ploidy_prev[i] ) break; if ( i==args->nsex ) return; // ploidy same as previously for (i=0; insamples; i++) { if ( args->sample2sex[i]<0 ) args->aux.ploidy[i] = -1*args->sample2sex[i]; else args->aux.ploidy[i] = args->sex2ploidy[args->sample2sex[i]]; } int *tmp = args->sex2ploidy; args->sex2ploidy = args->sex2ploidy_prev; args->sex2ploidy_prev = tmp; } ploidy_t *init_ploidy(char *alias) { const ploidy_predef_t *pld = ploidy_predefs; int detailed = 0, len = strlen(alias); if ( alias[len-1]=='?' ) { detailed = 1; alias[len-1] = 0; } while ( pld->alias && strcasecmp(alias,pld->alias) ) pld++; if ( !pld->alias ) { fprintf(bcftools_stderr,"\nPRE-DEFINED PLOIDY FILES\n\n"); fprintf(bcftools_stderr," * Columns are: CHROM,FROM,TO,SEX,PLOIDY\n"); fprintf(bcftools_stderr," * Coordinates are 1-based inclusive.\n"); fprintf(bcftools_stderr," * A '*' means any value not otherwise defined.\n\n"); pld = ploidy_predefs; while ( pld->alias ) { fprintf(bcftools_stderr,"%s\n .. %s\n\n", pld->alias,pld->about); if ( detailed ) fprintf(bcftools_stderr,"%s\n", pld->ploidy); pld++; } fprintf(bcftools_stderr,"Run as --ploidy (e.g. --ploidy GRCh37).\n"); fprintf(bcftools_stderr,"To see the detailed ploidy definition, append a question mark (e.g. --ploidy GRCh37?).\n"); fprintf(bcftools_stderr,"\n"); bcftools_exit(-1); } else if ( detailed ) { fprintf(bcftools_stderr,"%s", pld->ploidy); bcftools_exit(-1); } return ploidy_init_string(pld->ploidy,2); } static void usage(args_t *args) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: SNP/indel variant calling from VCF/BCF. To be used in conjunction with bcftools mpileup.\n"); fprintf(bcftools_stderr, " This command replaces the former \"bcftools view\" caller. Some of the original\n"); fprintf(bcftools_stderr, " functionality has been temporarily lost in the process of transition to htslib,\n"); fprintf(bcftools_stderr, " but will be added back on popular demand. The original calling model can be\n"); fprintf(bcftools_stderr, " invoked with the -c option.\n"); fprintf(bcftools_stderr, "Usage: bcftools call [options] \n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "File format options:\n"); fprintf(bcftools_stderr, " --no-version Do not append version and command line to the header\n"); fprintf(bcftools_stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(bcftools_stderr, " -O, --output-type b|u|z|v Output type: 'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n"); fprintf(bcftools_stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(bcftools_stderr, " --ploidy ASSEMBLY[?] Predefined ploidy, 'list' to print available settings, append '?' for details [2]\n"); fprintf(bcftools_stderr, " --ploidy-file FILE Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY\n"); fprintf(bcftools_stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(bcftools_stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(bcftools_stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " -s, --samples LIST List of samples to include [all samples]\n"); fprintf(bcftools_stderr, " -S, --samples-file FILE PED file or a file with an optional column with sex (see man page for details) [all samples]\n"); fprintf(bcftools_stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " --threads INT Use multithreading with INT worker threads [0]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Input/output options:\n"); fprintf(bcftools_stderr, " -A, --keep-alts Keep all possible alternate alleles at variant sites\n"); fprintf(bcftools_stderr, " -*, --keep-unseen-allele Keep the unobserved allele <*> or \n"); fprintf(bcftools_stderr, " -a, --annotate LIST Optional tags to output (lowercase allowed); '?' to list available tags\n"); fprintf(bcftools_stderr, " -F, --prior-freqs AN,AC Use prior allele frequencies, determined from these pre-filled tags\n"); fprintf(bcftools_stderr, " -G, --group-samples FILE|- Group samples by population (file with \"sample\\tgroup\") or \"-\" for single-sample calling.\n"); fprintf(bcftools_stderr, " This requires FORMAT/QS or other Number=R,Type=Integer tag such as FORMAT/AD\n"); fprintf(bcftools_stderr, " --group-samples-tag TAG The tag to use with -G, by default FORMAT/QS and FORMAT/AD are checked automatically\n"); fprintf(bcftools_stderr, " -g, --gvcf INT,[...] Group non-variant sites into gVCF blocks by minimum per-sample DP\n"); fprintf(bcftools_stderr, " -i, --insert-missed Output also sites missed by mpileup but present in -T\n"); fprintf(bcftools_stderr, " -M, --keep-masked-ref Keep sites with masked reference allele (REF=N)\n"); fprintf(bcftools_stderr, " -V, --skip-variants TYPE Skip indels/snps\n"); fprintf(bcftools_stderr, " -v, --variants-only Output variant sites only\n"); fprintf(bcftools_stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Consensus/variant calling options:\n"); fprintf(bcftools_stderr, " -c, --consensus-caller The original calling method (conflicts with -m)\n"); fprintf(bcftools_stderr, " -C, --constrain STR One of: alleles, trio (see manual)\n"); fprintf(bcftools_stderr, " -m, --multiallelic-caller Alternative model for multiallelic and rare-variant calling (conflicts with -c)\n"); fprintf(bcftools_stderr, " -n, --novel-rate FLOAT,[...] Likelihood of novel mutation for constrained trio calling, see man page for details [1e-8,1e-9,1e-9]\n"); fprintf(bcftools_stderr, " -p, --pval-threshold FLOAT Variant if P(ref|D)aux.min_lrt); // fprintf(bcftools_stderr, " -U INT number of permutations for association testing (effective with -1) [0]\n"); // fprintf(bcftools_stderr, " -X FLOAT only perform permutations for P(chi^2)aux.min_perm_p); fprintf(bcftools_stderr, "\n"); bcftools_exit(-1); } int main_vcfcall(int argc, char *argv[]) { char *ploidy_fname = NULL, *ploidy = NULL; args_t args; memset(&args, 0, sizeof(args_t)); args.argc = argc; args.argv = argv; args.aux.prior_type = -1; args.aux.indel_frac = -1; args.aux.theta = 1.1e-3; args.aux.pref = 0.5; args.aux.min_perm_p = 0.01; args.aux.min_lrt = 1; args.flag = CF_ACGT_ONLY; args.output_fname = "-"; args.output_type = FT_VCF; args.n_threads = 0; args.record_cmd_line = 1; args.aux.trio_Pm_SNPs = 1 - 1e-8; args.aux.trio_Pm_ins = args.aux.trio_Pm_del = 1 - 1e-9; args.regions_overlap = 1; args.clevel = -1; int c; static struct option loptions[] = { {"help",no_argument,NULL,'h'}, {"format-fields",required_argument,NULL,'f'}, {"annotate",required_argument,NULL,'a'}, {"prior-freqs",required_argument,NULL,'F'}, {"gvcf",required_argument,NULL,'g'}, {"group-samples",required_argument,NULL,'G'}, {"group-samples-tag",required_argument,NULL,3}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,4}, {"samples",required_argument,NULL,'s'}, {"samples-file",required_argument,NULL,'S'}, {"targets",required_argument,NULL,'t'}, {"targets-file",required_argument,NULL,'T'}, {"threads",required_argument,NULL,9}, {"keep-alts",no_argument,NULL,'A'}, {"keep-unseen-allele",no_argument,NULL,'*'}, {"insert-missed",no_argument,NULL,'i'}, {"skip-Ns",no_argument,NULL,'N'}, // now the new default {"keep-masked-refs",no_argument,NULL,'M'}, {"skip-variants",required_argument,NULL,'V'}, {"variants-only",no_argument,NULL,'v'}, {"consensus-caller",no_argument,NULL,'c'}, {"constrain",required_argument,NULL,'C'}, {"multiallelic-caller",no_argument,NULL,'m'}, {"pval-threshold",required_argument,NULL,'p'}, {"prior",required_argument,NULL,'P'}, {"novel-rate",required_argument,NULL,'n'}, {"ploidy",required_argument,NULL,1}, {"ploidy-file",required_argument,NULL,2}, {"chromosome-X",no_argument,NULL,'X'}, {"chromosome-Y",no_argument,NULL,'Y'}, {"no-version",no_argument,NULL,8}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp = NULL; while ((c = getopt_long(argc, argv, "h?o:O:r:R:s:S:t:T:A*NMV:vcmp:C:n:P:f:a:ig:XYF:G:W::", loptions, NULL)) >= 0) { switch (c) { case 2 : ploidy_fname = optarg; break; case 1 : ploidy = optarg; break; case 'X': ploidy = "X"; fprintf(bcftools_stderr,"Warning: -X will be deprecated, please use --ploidy instead.\n"); break; case 'Y': ploidy = "Y"; fprintf(bcftools_stderr,"Warning: -Y will be deprecated, please use --ploidy instead.\n"); break; case 'G': args.aux.sample_groups = optarg; break; case 3 : args.aux.sample_groups_tag = optarg; break; case 'f': fprintf(bcftools_stderr,"Warning: -f, --format-fields will be deprecated, please use -a, --annotate instead.\n"); case 'a': if (optarg[0]=='?') { list_annotations(bcftools_stderr); return 1; } args.aux.output_tags |= parse_output_tags(optarg); break; case 'M': args.flag &= ~CF_ACGT_ONLY; break; // keep sites where REF is N case 'N': args.flag |= CF_ACGT_ONLY; break; // omit sites where first base in REF is N (the new default) case 'A': args.aux.flag |= CALL_KEEPALT; break; case '*': args.aux.flag |= CALL_KEEP_UNSEEN; break; case 'c': args.flag |= CF_CCALL; break; // the original EM based calling method case 'i': args.flag |= CF_INS_MISSED; break; case 'v': args.aux.flag |= CALL_VARONLY; break; case 'F': args.aux.prior_AN = optarg; args.aux.prior_AC = strchr(optarg,','); if ( !args.aux.prior_AC ) error("Expected two tags with -F (e.g. AN,AC), got \"%s\"\n",optarg); *args.aux.prior_AC = 0; args.aux.prior_AC++; break; case 'g': args.gvcf = gvcf_init(optarg); if ( !args.gvcf ) error("Could not parse: --gvcf %s\n", optarg); break; case 'o': args.output_fname = optarg; break; case 'O': switch (optarg[0]) { case 'b': args.output_type = FT_BCF_GZ; break; case 'u': args.output_type = FT_BCF; break; case 'z': args.output_type = FT_VCF_GZ; break; case 'v': args.output_type = FT_VCF; break; default: { args.clevel = strtol(optarg,&tmp,10); if ( *tmp || args.clevel<0 || args.clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { args.clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args.clevel<0 || args.clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'C': if ( !strcasecmp(optarg,"alleles") ) args.aux.flag |= CALL_CONSTR_ALLELES; else if ( !strcasecmp(optarg,"trio") ) args.aux.flag |= CALL_CONSTR_TRIO; else error("Unknown argument to -C: \"%s\"\n", optarg); break; case 'V': if ( !strcasecmp(optarg,"snps") ) args.flag |= CF_INDEL_ONLY; else if ( !strcasecmp(optarg,"indels") ) args.flag |= CF_NO_INDEL; else error("Unknown skip category \"%s\" (-S argument must be \"snps\" or \"indels\")\n", optarg); break; case 'm': args.flag |= CF_MCALL; break; // multiallelic calling method case 'p': args.aux.pref = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: --pval-threshold %s\n", optarg); break; case 'P': args.aux.theta = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse, expected float argument: -P %s\n", optarg); break; case 'n': parse_novel_rate(&args,optarg); break; case 'r': args.regions = optarg; break; case 'R': args.regions = optarg; args.regions_is_file = 1; break; case 't': args.targets = optarg; break; case 'T': args.targets = optarg; args.targets_is_file = 1; break; case 's': args.samples_fname = optarg; break; case 'S': args.samples_fname = optarg; args.samples_is_file = 1; break; case 9 : args.n_threads = strtol(optarg, 0, 0); break; case 8 : args.record_cmd_line = 0; break; case 4 : args.regions_overlap = parse_overlap_option(optarg); if ( args.regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 'W': if (!(args.write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; default: usage(&args); } } // Sanity check options and initialize if ( ploidy_fname ) args.ploidy = ploidy_init(ploidy_fname, 2); else if ( ploidy ) args.ploidy = init_ploidy(ploidy); if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) args.bcf_fname = "-"; // reading from stdin else usage(&args); } else args.bcf_fname = argv[optind++]; if ( !ploidy_fname && !ploidy ) { if ( !args.samples_is_file ) fprintf(bcftools_stderr,"Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n"); args.ploidy = ploidy_init_string("* * * 0 0\n* * * 1 1\n* * * 2 2\n",2); } if ( !args.ploidy ) error("Could not initialize ploidy\n"); if ( (args.flag & CF_CCALL ? 1 : 0) + (args.flag & CF_MCALL ? 1 : 0) + (args.flag & CF_QCALL ? 1 : 0) > 1 ) error("Only one of -c or -m options can be given\n"); if ( !(args.flag & CF_CCALL) && !(args.flag & CF_MCALL) && !(args.flag & CF_QCALL) ) error("Expected -c or -m option\n"); if ( (args.flag & CF_CCALL ? 1: 0) && args.gvcf ) error("gvcf -g option not functional with -c calling mode yet\n"); if ( args.aux.n_perm && args.aux.ngrp1_samples<=0 ) error("Expected -1 with -U\n"); // not sure about this, please fix if ( args.aux.flag & CALL_CONSTR_ALLELES ) { if ( !args.targets ) error("Expected -t or -T with \"-C alleles\"\n"); if ( !(args.flag & CF_MCALL) ) error("The \"-C alleles\" mode requires -m\n"); } if ( args.flag & CF_INS_MISSED && !(args.aux.flag&CALL_CONSTR_ALLELES) ) error("The -i option requires -C alleles\n"); if ( args.aux.flag&CALL_VARONLY && args.gvcf ) error("The two options cannot be combined: --variants-only and --gvcf\n"); if ( args.aux.sample_groups && !(args.flag & CF_MCALL) ) error("The -G feature is supported only with the -m calling mode\n"); init_data(&args); bcf1_t *bcf_rec; while ( (bcf_rec = next_line(&args)) ) { // Skip duplicate positions with all matching `-C alleles -T` used up if ( args.aux.flag&CALL_CONSTR_ALLELES && !args.aux.tgt_als ) continue; // Skip unwanted sites int i, is_indel = bcf_is_snp(bcf_rec) ? 0 : 1; if ( (args.flag & CF_INDEL_ONLY) && !is_indel ) continue; if ( (args.flag & CF_NO_INDEL) && is_indel ) continue; if ( (args.flag & CF_ACGT_ONLY) && (bcf_rec->d.allele[0][0]=='N' || bcf_rec->d.allele[0][0]=='n') ) continue; // REF[0] is 'N' // Which allele is symbolic? All SNPs should have it, but not indels args.aux.unseen = 0; for (i=1; in_allele; i++) { if ( bcf_rec->d.allele[i][0]=='X' ) { args.aux.unseen = i; break; } // old X if ( bcf_rec->d.allele[i][0]=='<' ) { if ( bcf_rec->d.allele[i][1]=='X' && bcf_rec->d.allele[i][2]=='>' ) { args.aux.unseen = i; break; } // old if ( bcf_rec->d.allele[i][1]=='*' && bcf_rec->d.allele[i][2]=='>' ) { args.aux.unseen = i; break; } // new <*> } } int is_ref = (bcf_rec->n_allele==1 || (bcf_rec->n_allele==2 && args.aux.unseen>0)) ? 1 : 0; if ( is_ref && args.aux.flag&CALL_VARONLY ) continue; bcf_unpack(bcf_rec, BCF_UN_ALL); if ( args.nsex ) set_ploidy(&args, bcf_rec); // Various output modes: QCall output (todo) if ( args.flag & CF_QCALL ) { qcall(&args.aux, bcf_rec); continue; } if ( args.flag & CF_INS_MISSED ) { tgt_flush(&args,bcf_rec); if ( !args.tgt_itr_prev ) args.tgt_itr_prev = regitr_init(args.tgt_idx); regitr_copy(args.tgt_itr_prev, args.tgt_itr); } // Calling modes which output VCFs int ret; if ( args.flag & CF_MCALL ) ret = mcall(&args.aux, bcf_rec); else ret = ccall(&args.aux, bcf_rec); if ( ret==-1 ) error("Something is wrong\n"); else if ( ret==-2 ) continue; // skip the site // Normal output if ( (args.aux.flag & CALL_VARONLY) && ret==0 && !args.gvcf ) continue; // not a variant if ( args.gvcf ) bcf_rec = gvcf_write(args.gvcf, args.out_fh, args.aux.hdr, bcf_rec, ret==1?1:0); if ( bcf_rec && bcf_write1(args.out_fh, args.aux.hdr, bcf_rec)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args.output_fname); } if ( args.gvcf ) gvcf_write(args.gvcf, args.out_fh, args.aux.hdr, NULL, 0); if ( args.flag & CF_INS_MISSED ) tgt_flush(&args,NULL); destroy_data(&args); return 0; } pysam-0.23.0/bcftools/vcfcnv.c000066400000000000000000001640321475062545500162140ustar00rootroot00000000000000/* The MIT License Copyright (c) 2014-2022 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Known issues: - The --AF-file option behaves like --targets-file, sites not listed in the AFs are skipped. */ #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "HMM.h" #include "rbuf.h" #define DBG0 0 #define N_STATES 4 #define CN0 0 #define CN1 1 #define CN2 2 #define CN3 3 typedef struct { float mean, dev2, norm; } gauss_param_t; typedef struct { char *name; int idx; // VCF sample index float *lrr,*baf, baf_dev2, baf_dev2_dflt, lrr_dev2; float cell_frac, cell_frac_dflt; gauss_param_t gauss_param[18]; double pobs[N_STATES]; FILE *dat_fh, *cn_fh, *summary_fh; char *dat_fname, *cn_fname, *summary_fname; } sample_t; typedef struct _args_t { bcf_srs_t *files; bcf_hdr_t *hdr; int prev_rid, ntot, nused; sample_t query_sample, control_sample; int nstates; // number of states: N_STATES for one sample, N_STATES^2 for two samples double lrr_bias, baf_bias; // LRR/BAF weights double same_prob, ij_prob; // prior of both samples being the same and the transition probability P(i|j) double err_prob; // constant probability of erroneous measurement float *nonref_afs, nonref_af, nonref_af_dflt, fRR, fRA, fAA, *tmpf; unsigned long int nRR, nRA, nAA; int mtmpf; double *tprob, *tprob_arr; // array of transition matrices, precalculated up to ntprob_arr positions double *iprobs; // states' initial probabilities int ntprob_arr; hmm_t *hmm; double *eprob; // emission probs [nstates*nsites,msites] uint32_t *sites; // positions [nsites,msites] int nsites, msites; double baum_welch_th, optimize_frac; float plot_th; FILE *summary_fh; char **argv, *regions_list, *summary_fname, *output_dir; char *targets_list, *af_fname; int argc, verbose, lrr_smooth_win; } args_t; FILE *open_file(char **fname, const char *mode, const char *fmt, ...) HTS_FORMAT(HTS_PRINTF_FMT, 3, 4); static inline void hmm2cn_state(int nstates, int i, int *a, int *b) { *a = i / N_STATES; *b = i - (*a)*N_STATES; } static double *init_tprob_matrix(int ndim, double ij_prob, double same_prob) { int i,j; double *mat = (double*) malloc(sizeof(double)*ndim*ndim); assert( ndim==N_STATES || ndim==N_STATES*N_STATES); if ( ndim==N_STATES ) // one sample { double pii = 1 - ij_prob*(N_STATES-1); if ( pii < ij_prob ) error("Error: -x set a bit too high, P(x|x) < P(x|y): %e vs %e\n", pii,ij_prob); for (j=0; jdat_fh = open_file(&smpl->dat_fname,"w","%s/dat.%s.tab",dir,smpl->name); if ( !smpl->dat_fh ) error("Error opening file: %s/dat.%s.tab\n",dir,smpl->name); smpl->cn_fh = open_file(&smpl->cn_fname,"w","%s/cn.%s.tab",dir,smpl->name); if ( !smpl->cn_fh ) error("Error opening file: %s/cn.%s.tab\n",dir,smpl->name); smpl->summary_fh = open_file(&smpl->summary_fname,"w","%s/summary.%s.tab",dir,smpl->name); if ( !smpl->summary_fh ) error("Error opening file: %s/summary.%s.tab\n",dir,smpl->name); fprintf(smpl->dat_fh,"# [1]Chromosome\t[2]Position\t[3]BAF\t[4]LRR\n"); fprintf(smpl->cn_fh,"# [1]Chromosome\t[2]Position\t[3]CN\t[4]P(CN0)\t[5]P(CN1)\t[6]P(CN2)\t[7]P(CN3)\n"); fprintf(smpl->summary_fh,"# RG, Regions [2]Chromosome\t[3]Start\t[4]End\t[5]Copy Number state\t[6]Quality\t[7]nSites\t[8]nHETs\n"); } static void close_sample_files(sample_t *smpl) { if ( fclose(smpl->dat_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,smpl->dat_fname); if ( fclose(smpl->cn_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,smpl->cn_fname); if ( fclose(smpl->summary_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,smpl->summary_fname); } static double norm_cdf(double mean, double dev); static void init_data(args_t *args) { args->prev_rid = -1; args->hdr = args->files->readers[0].header; if ( !args->query_sample.name ) { if ( bcf_hdr_nsamples(args->hdr)>1 ) error("Multi-sample VCF, missing the -s option\n"); args->query_sample.name = strdup(args->hdr->samples[0]); } else if ( bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->query_sample.name)<0 ) error("The sample \"%s\" not found\n", args->query_sample.name); if ( !args->files->readers[0].file->is_bin ) { int ret; kstring_t tmp = {0,0,0}; if ( args->control_sample.name ) { ksprintf(&tmp, "%s,%s", args->query_sample.name,args->control_sample.name); ret = bcf_hdr_set_samples(args->hdr, tmp.s, 0); } else { ret = bcf_hdr_set_samples(args->hdr, args->query_sample.name, 0); tmp.s = args->query_sample.name; } if ( ret<0 ) error("Error parsing the list of samples: %s\n", tmp.s); else if ( ret>0 ) error("The sample not found in the VCF: %s\n", ret==1 ? args->query_sample.name : args->control_sample.name); if ( args->control_sample.name ) free(tmp.s); } args->query_sample.idx = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->query_sample.name); args->control_sample.idx = args->control_sample.name ? bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->control_sample.name) : -1; args->nstates = args->control_sample.name ? N_STATES*N_STATES : N_STATES; args->tprob = init_tprob_matrix(args->nstates, args->ij_prob, args->same_prob); args->iprobs = init_iprobs(args->nstates, args->same_prob); args->hmm = hmm_init(args->nstates, args->tprob, 10000); hmm_init_states(args->hmm, args->iprobs); args->summary_fh = stdout; init_sample_files(&args->query_sample, args->output_dir); if ( args->control_sample.name ) { init_sample_files(&args->control_sample, args->output_dir); args->summary_fh = open_file(&args->summary_fname,"w","%s/summary.tab",args->output_dir); } else args->summary_fh = NULL; // one sample only, no two-file summary int i; FILE *fh = args->summary_fh ? args->summary_fh : args->query_sample.summary_fh; fprintf(fh, "# This file was produced by: bcftools cnv(%s+htslib-%s)\n", bcftools_version(),hts_version()); fprintf(fh, "# The command line was:\tbcftools %s", args->argv[0]); for (i=1; iargc; i++) fprintf(fh, " %s",args->argv[i]); if ( args->control_sample.name ) fprintf(fh, "\n#\n" "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Copy number:%s\t[7]Quality" "\t[8]nSites in (5)\t[9]nHETs in (5)\t[10]nSites in (6)\t[11]nHETs in(6)\n", args->query_sample.name,args->control_sample.name ); else fprintf(fh, "\n#\n" "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Quality\t[7]nSites\t[8]nHETs\n", args->query_sample.name ); if ( args->optimize_frac ) { fprintf(args->query_sample.summary_fh, "# CF, cell fraction estimate\t[2]Chromosome\t[3]Start\t[4]End\t[5]Cell fraction\t[6]BAF deviation\n"); if ( args->control_sample.name ) { fprintf(args->control_sample.summary_fh, "# CF, cell fraction estimate\t[2]Chromosome\t[3]Start\t[4]End\t[5]Cell fraction\t[6]BAF deviation\n"); fprintf(args->summary_fh, "# CF, cell fraction estimate\t[2]Chromosome\t[3]Start\t[4]End\t" "[5]Cell fraction:%s\t[6]Cell fraction:%s\t[7]BAF deviation:%s\t[8]BAF deviation:%s\n", args->query_sample.name,args->control_sample.name, args->query_sample.name,args->control_sample.name ); } } } char *msprintf(const char *fmt, ...); static void py_plot_cnv(char *script, float th) { if ( th>100 ) return; // create no plots char *cmd = msprintf("python %s -p %f", script, th); int ret = system(cmd); if ( ret) fprintf(stderr, "The command returned non-zero status %d: %s\n", ret, cmd); free(cmd); } static void plot_sample(args_t *args, sample_t *smpl) { char *fname; FILE *fp = open_file(&fname,"w","%s/plot.%s.py",args->output_dir,smpl->name); fprintf(fp, "import matplotlib as mpl\n" "mpl.use('Agg')\n" "import matplotlib.pyplot as plt\n" "import csv\n" "import numpy as np\n" "csv.register_dialect('tab', delimiter='\\t', quoting=csv.QUOTE_NONE)\n" "\n" "dat = {}\n" "with open('%s', 'r') as f:\n" " reader = csv.reader(f, 'tab')\n" " for row in reader:\n" " chr = row[0]\n" " if chr[0]=='#': continue\n" " if chr not in dat: dat[chr] = []\n" " dat[chr].append([int(row[1]), float(row[2]), float(row[3])])\n" "\n" "cnv = {}\n" "with open('%s', 'r') as f:\n" " reader = csv.reader(f, 'tab')\n" " for row in reader:\n" " chr = row[0]\n" " if chr[0]=='#': continue\n" " if chr not in cnv: cnv[chr] = []\n" " row[2] = int(row[2]) + 0.5\n" " row[1] = int(row[1])\n" " cnv[chr].append(row[1:])\n" "\n" "for chr in dat:\n" " fig,(ax1, ax2, ax3) = plt.subplots(3,1,figsize=(10,8),sharex=True)\n" " ax1.plot([x[0] for x in dat[chr]],[x[2] for x in dat[chr]], '.', ms=3)\n" " ax2.plot([x[0] for x in dat[chr]],[x[1] for x in dat[chr]], '.', ms=3)\n" " cn_dat = cnv[chr]\n" " xgrid = [float(x[0]) for x in cn_dat]\n" " ygrid = np.linspace(0,5,6)\n" " xgrid, ygrid = np.meshgrid(xgrid, ygrid)\n" " heat = np.zeros_like(xgrid)\n" " for x in range(len(heat[0])-1):\n" " heat[0][x] = cn_dat[x][2]\n" " heat[1][x] = cn_dat[x][3]\n" " heat[2][x] = cn_dat[x][4]\n" " heat[3][x] = cn_dat[x][5]\n" " mesh = ax3.pcolormesh(xgrid, ygrid, heat, cmap='bwr_r', shading='auto', alpha=0)\n" " mesh.set_clim(vmin=-1,vmax=1)\n" " ax3.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'.-',ms=3,color='black')\n" " fig.suptitle('%s (chr '+chr+')')\n" " ax1.set_title('Log-R intensities Ratio',fontsize=10)\n" " ax2.set_title('B-Allele Frequency',fontsize=10)\n" " ax3.set_title('Copy Number Variation',fontsize=10)\n" " ax1.set_ylabel('LRR')\n" " ax2.set_ylabel('BAF')\n" " ax3.set_ylabel('CN')\n" " ax3.set_xlabel('Coordinate (chrom '+chr+')',fontsize=10)\n" " ax3.set_ylim(-0.1,4.1)\n" " ax3.set_yticks([0.5,1.5,2.5,3.5])\n" " ax3.set_yticklabels(['CN0','CN1','CN2','CN3'])\n" " plt.subplots_adjust(left=0.08,right=0.95,bottom=0.08,top=0.92)\n" " plt.savefig('%s/plot.%s.chr'+chr+'.png')\n" " plt.close()\n" "\n", smpl->dat_fname,smpl->cn_fname,smpl->name,args->output_dir,smpl->name ); fclose(fp); py_plot_cnv(fname, args->plot_th); free(fname); } static void create_plots(args_t *args) { close_sample_files(&args->query_sample); if ( args->control_sample.name ) close_sample_files(&args->control_sample); if ( args->summary_fh ) fclose(args->summary_fh); if ( !args->control_sample.name ) { plot_sample(args, &args->query_sample); return; } char *fname; FILE *fp = open_file(&fname,"w","%s/plot.%s.%s.py",args->output_dir,args->control_sample.name,args->query_sample.name); fprintf(fp, "import matplotlib as mpl\n" "mpl.use('Agg')\n" "import matplotlib.pyplot as plt\n" "import csv,argparse\n" "import numpy as np\n" "csv.register_dialect('tab', delimiter='\\t', quoting=csv.QUOTE_NONE)\n" "\n" "control_sample = '%s'\n" "query_sample = '%s'\n" "\n" "parser = argparse.ArgumentParser()\n" "parser.add_argument('-p', '--plot-threshold', type=float)\n" "parser.add_argument('-c', '--chromosome')\n" "args = parser.parse_args()\n" "if args.plot_threshold==None: args.plot_threshold = 0\n" "\n" "def chroms_to_plot(th):\n" " dat = {}\n" " with open('%s/summary.tab', 'r') as f:\n" " reader = csv.reader(f, 'tab')\n" " for row in reader:\n" " if row[0]!='RG': continue\n" " chr = row[1]\n" " start = row[2]\n" " end = row[3]\n" " qual = float(row[6])\n" " if row[4]==row[5] and args.plot_threshold!=0: continue\n" " if chr not in dat: dat[chr] = 0.0\n" " if qual > dat[chr]: dat[chr] = qual\n" " out = {}\n" " for chr in dat:\n" " if (chr not in dat) or dat[chr]0: diff.append([b[i-1][0],b[i-1][1],a[i-1][1]])\n" " diff.append([b[i][0],b[i][1],a[i][1]])\n" " elif len(diff):\n" " diff.append([b[i][0],b[i][1],a[i][1]])\n" " out.append(diff)\n" " diff = []\n" " if len(diff): out.append(diff)\n" " return out\n" "\n" "for chr in sorted(plot_chroms.keys()):\n" " control_dat = []\n" " control_cnv = []\n" " query_dat = []\n" " query_cnv = []\n" " read_dat('%s',control_dat,chr)\n" " read_dat('%s',query_dat,chr)\n" " read_cnv('%s',control_cnv,chr)\n" " read_cnv('%s',query_cnv,chr)\n" "\n" " fig,(ax1,ax2,ax3,ax4,ax5,ax6) = plt.subplots(6,1,figsize=(10,8),sharex=True)\n" " ax1.plot([x[0] for x in control_dat],[x[2] for x in control_dat], '.', ms=3,color='red')\n" " ax2.plot([x[0] for x in control_dat],[x[1] for x in control_dat], '.', ms=3,color='red')\n" " cn_dat = control_cnv\n" " xgrid = [float(x[0]) for x in cn_dat]\n" " ygrid = np.linspace(0,5,6)\n" " xgrid, ygrid = np.meshgrid(xgrid, ygrid)\n" " heat = np.zeros_like(xgrid)\n" " for x in range(len(heat[0])-1):\n" " heat[0][x] = cn_dat[x][2]\n" " heat[1][x] = cn_dat[x][3]\n" " heat[2][x] = cn_dat[x][4]\n" " heat[3][x] = cn_dat[x][5]\n" " mesh = ax3.pcolormesh(xgrid, ygrid, heat, cmap='bwr', shading='auto', alpha=0)\n" " mesh.set_clim(vmin=-1,vmax=1)\n" " ax3.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'-',ms=3,color='black',lw=1.7)\n" "\n" " ax6.plot([x[0] for x in query_dat],[x[2] for x in query_dat], '.', ms=3)\n" " ax5.plot([x[0] for x in query_dat],[x[1] for x in query_dat], '.', ms=3)\n" " cn_dat = query_cnv\n" " xgrid = [float(x[0]) for x in cn_dat]\n" " ygrid = np.linspace(0,5,6)\n" " xgrid, ygrid = np.meshgrid(xgrid, ygrid)\n" " heat = np.zeros_like(xgrid)\n" " for x in range(len(heat[0])-1):\n" " heat[0][x] = cn_dat[x][2]\n" " heat[1][x] = cn_dat[x][3]\n" " heat[2][x] = cn_dat[x][4]\n" " heat[3][x] = cn_dat[x][5]\n" " mesh = ax4.pcolormesh(xgrid, ygrid, heat, cmap='bwr_r')\n" " mesh.set_clim(vmin=-1,vmax=1)\n" " ax4.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'-',ms=3,color='black',lw=1.7)\n" " ax3.annotate(control_sample, xy=(0.02,0.1), xycoords='axes fraction', color='red',fontsize=12, va='bottom',ha='left')\n" " ax4.annotate(query_sample, xy=(0.02,0.9), xycoords='axes fraction', color='blue',fontsize=12, va='top',ha='left')\n" "\n" " diffs = find_diffs(control_cnv,query_cnv)\n" " for diff in diffs:\n" " ax3.plot([x[0] for x in diff],[x[1] for x in diff],'-',ms=3,color='blue',lw=1.7)\n" " ax4.plot([x[0] for x in diff],[x[2] for x in diff],'-',ms=3,color='red',lw=1.7)\n" "\n" " fig.suptitle('chr '+chr+', '+control_sample+' vs '+query_sample)\n" " ax1.tick_params(axis='both', labelsize=8)\n" " ax2.tick_params(axis='both', labelsize=8)\n" " ax3.tick_params(axis='both', labelsize=8)\n" " ax4.tick_params(axis='both', labelsize=8)\n" " ax5.tick_params(axis='both', labelsize=8)\n" " ax6.tick_params(axis='both', labelsize=8)\n" " ax6.set_xlabel('Coordinate (chrom '+chr+')',fontsize=8)\n" " ax1.set_ylabel('LRR')\n" " ax2.set_ylabel('BAF')\n" " ax3.set_ylabel('CN')\n" " ax6.set_ylabel('LRR')\n" " ax5.set_ylabel('BAF')\n" " ax4.set_ylabel('CN')\n" " ax3.set_ylim(-0.1,4.1)\n" " ax3.set_yticks([0.5,1.5,2.5,3.5])\n" " ax3.set_yticklabels(['CN0','CN1','CN2','CN3'])\n" " ax4.set_ylim(-0.1,4.1)\n" " ax4.set_yticks([0.5,1.5,2.5,3.5])\n" " ax4.set_yticklabels(['CN0','CN1','CN2','CN3'])\n" " plt.subplots_adjust(left=0.08,right=0.95,bottom=0.08,top=0.92,hspace=0)\n" " plt.savefig('%s/plot.%s.%s.chr'+chr+'.png')\n" " plt.close()\n" "\n", args->control_sample.name,args->query_sample.name, args->output_dir, args->control_sample.dat_fname,args->query_sample.dat_fname, args->control_sample.cn_fname,args->query_sample.cn_fname, args->output_dir,args->control_sample.name,args->query_sample.name ); fclose(fp); py_plot_cnv(fname,args->plot_th); free(fname); } static void destroy_data(args_t *args) { bcf_sr_destroy(args->files); hmm_destroy(args->hmm); free(args->tmpf); free(args->sites); free(args->eprob); free(args->tprob); free(args->iprobs); free(args->summary_fname); free(args->nonref_afs); free(args->query_sample.baf); free(args->query_sample.lrr); free(args->control_sample.baf); free(args->control_sample.lrr); free(args->query_sample.name); free(args->query_sample.dat_fname); free(args->query_sample.cn_fname); free(args->query_sample.summary_fname); free(args->control_sample.dat_fname); free(args->control_sample.cn_fname); free(args->control_sample.summary_fname); } static inline char copy_number_state(args_t *args, int istate, int ismpl) { char code[] = "01234"; if ( !args->control_sample.name ) return code[istate]; int idx = ismpl ? istate - (istate/N_STATES)*N_STATES : istate/N_STATES; return code[idx]; } static double avg_ii_prob(int n, double *mat) { int i; double avg = 0; for (i=0; igauss_param[0])) #define GAUSS_CN1_PK_A(smpl) (&((smpl)->gauss_param[1])) #define GAUSS_CN2_PK_RR(smpl) (&((smpl)->gauss_param[2])) #define GAUSS_CN2_PK_RA(smpl) (&((smpl)->gauss_param[3])) #define GAUSS_CN2_PK_AA(smpl) (&((smpl)->gauss_param[4])) #define GAUSS_CN3_PK_RRR(smpl) (&((smpl)->gauss_param[5])) #define GAUSS_CN3_PK_RRA(smpl) (&((smpl)->gauss_param[6])) #define GAUSS_CN3_PK_RAA(smpl) (&((smpl)->gauss_param[7])) #define GAUSS_CN3_PK_AAA(smpl) (&((smpl)->gauss_param[8])) static inline double norm_prob(double baf, gauss_param_t *param) { return exp(-(baf-param->mean)*(baf-param->mean)*0.5/param->dev2) / param->norm / sqrt(2*M_PI*param->dev2); } static int set_observed_prob(args_t *args, sample_t *smpl, int isite) { float baf = smpl->baf[isite]; float lrr = args->lrr_bias>0 ? smpl->lrr[isite] : 0; float fRR = args->fRR; float fRA = args->fRA; float fAA = args->fAA; if ( baf<0 ) { // no call: either some technical issue or the call could not be made because it is CN0 int i; smpl->pobs[CN0] = 0.5; for (i=1; ipobs[i] = (1.0-smpl->pobs[CN0])/(N_STATES-1); return 0; } double cn1_baf = norm_prob(baf,GAUSS_CN1_PK_R(smpl)) * (fRR + fRA*0.5) + norm_prob(baf,GAUSS_CN1_PK_A(smpl)) * (fAA + fRA*0.5) ; double cn2_baf = norm_prob(baf,GAUSS_CN2_PK_RR(smpl)) * fRR + norm_prob(baf,GAUSS_CN2_PK_RA(smpl)) * fRA + norm_prob(baf,GAUSS_CN2_PK_AA(smpl)) * fAA; double cn3_baf = norm_prob(baf,GAUSS_CN3_PK_RRR(smpl)) * fRR + norm_prob(baf,GAUSS_CN3_PK_RRA(smpl)) * fRA*0.5 + norm_prob(baf,GAUSS_CN3_PK_RAA(smpl)) * fRA*0.5 + norm_prob(baf,GAUSS_CN3_PK_AAA(smpl)) * fAA; double norm = cn1_baf + cn2_baf + cn3_baf; cn1_baf /= norm; cn2_baf /= norm; cn3_baf /= norm; #if DBG0 if ( args->verbose ) fprintf(stderr,"%f\t%f %f %f\n", baf,cn1_baf,cn2_baf,cn3_baf); #endif double cn1_lrr = exp(-(lrr + 0.45)*(lrr + 0.45)/smpl->lrr_dev2); double cn2_lrr = exp(-(lrr - 0.00)*(lrr - 0.00)/smpl->lrr_dev2); double cn3_lrr = exp(-(lrr - 0.30)*(lrr - 0.30)/smpl->lrr_dev2); smpl->pobs[CN0] = 0; smpl->pobs[CN1] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn1_baf)*(1 - args->lrr_bias + args->lrr_bias*cn1_lrr); smpl->pobs[CN2] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn2_baf)*(1 - args->lrr_bias + args->lrr_bias*cn2_lrr); smpl->pobs[CN3] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn3_baf)*(1 - args->lrr_bias + args->lrr_bias*cn3_lrr); return 0; } static void set_emission_prob(args_t *args, int isite) { double *eprob = &args->eprob[args->nstates*isite]; int i; for (i=0; iquery_sample.pobs[i]; } static void set_emission_prob2(args_t *args, int isite) { double *eprob = &args->eprob[args->nstates*isite]; int i, j; for (i=0; iquery_sample.pobs[i]*args->control_sample.pobs[j]; } } } static void set_gauss_params(args_t *args, sample_t *smpl); static double norm_cdf(double mean, double dev) { double bot = 0, top = 1; top = 1 - 0.5*erfc((top-mean)/(dev*sqrt(2))); bot = 1 - 0.5*erfc((bot-mean)/(dev*sqrt(2))); return top-bot; } static void set_emission_probs(args_t *args) { if ( !args->af_fname ) { args->fRR = 0.76; args->fRA = 0.14; args->fAA = 0.098; } set_gauss_params(args, &args->query_sample); if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample); #if DBG0 args->verbose = 1; args->query_sample.baf[0] = 0; set_observed_prob(args,&args->query_sample,0); args->query_sample.baf[0] = 1/3.; set_observed_prob(args,&args->query_sample,0); args->query_sample.baf[0] = 1/2.; set_observed_prob(args,&args->query_sample,0); args->query_sample.baf[0] = 2/3.; set_observed_prob(args,&args->query_sample,0); args->query_sample.baf[0] = 1; set_observed_prob(args,&args->query_sample,0); args->verbose = 0; #endif int i; for (i=0; insites; i++) { if ( args->af_fname ) { args->fRR = (1-args->nonref_afs[i])*(1-args->nonref_afs[i]); args->fRA = 2*args->nonref_afs[i]*(1-args->nonref_afs[i]); args->fAA = args->nonref_afs[i]*args->nonref_afs[i]; } set_observed_prob(args,&args->query_sample,i); if ( args->control_sample.name ) { set_observed_prob(args,&args->control_sample,i); set_emission_prob2(args,i); } else set_emission_prob(args,i); } } static void smooth_data(float *dat, int ndat, int win) { if ( win<=1 ) return; int i,j, k1 = win/2, k2 = win-k1; rbuf_t rbuf; rbuf_init(&rbuf,win); float sum = 0, *buf = (float*)malloc(sizeof(float)*win); for (i=0; i=k1 ) { j = rbuf_shift(&rbuf); sum -= buf[j]; } if ( i+k2gauss_param[i].dev2 = smpl->baf_dev2; double dev = sqrt(smpl->baf_dev2); GAUSS_CN1_PK_R(smpl)->mean = 0; GAUSS_CN1_PK_A(smpl)->mean = 1; GAUSS_CN1_PK_R(smpl)->norm = norm_cdf(GAUSS_CN1_PK_R(smpl)->mean,dev); GAUSS_CN1_PK_A(smpl)->norm = norm_cdf(GAUSS_CN1_PK_A(smpl)->mean,dev); GAUSS_CN2_PK_RR(smpl)->mean = 0; GAUSS_CN2_PK_RA(smpl)->mean = 0.5; GAUSS_CN2_PK_AA(smpl)->mean = 1; GAUSS_CN2_PK_RR(smpl)->norm = norm_cdf(GAUSS_CN2_PK_RR(smpl)->mean,dev); GAUSS_CN2_PK_RA(smpl)->norm = norm_cdf(GAUSS_CN2_PK_RA(smpl)->mean,dev); GAUSS_CN2_PK_AA(smpl)->norm = norm_cdf(GAUSS_CN2_PK_AA(smpl)->mean,dev); GAUSS_CN3_PK_RRR(smpl)->mean = 0; GAUSS_CN3_PK_RRA(smpl)->mean = 1.0/(2+smpl->cell_frac); GAUSS_CN3_PK_RAA(smpl)->mean = (1.0+smpl->cell_frac)/(2+smpl->cell_frac); GAUSS_CN3_PK_AAA(smpl)->mean = 1; GAUSS_CN3_PK_RRR(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RRR(smpl)->mean,dev); GAUSS_CN3_PK_RRA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RRA(smpl)->mean,dev); GAUSS_CN3_PK_RAA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RAA(smpl)->mean,dev); GAUSS_CN3_PK_AAA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_AAA(smpl)->mean,dev); } static int update_sample_args(args_t *args, sample_t *smpl, int ismpl) { hmm_t *hmm = args->hmm; double *fwd = hmm_get_fwd_bwd_prob(hmm); int nstates = hmm_get_nstates(hmm); // estimate the BAF mean and deviation for CN3 double mean_cn3 = 0, norm_cn3 = 0; double baf_dev2 = 0, baf_AA_dev2 = 0, norm_baf_AA_dev2 = 0; // experimental: smooth CN3 probs to bias toward bigger events, this lowers // the FP rate when the data is noisy hts_expand(float,args->nsites,args->mtmpf,args->tmpf); int i, j, k = 0; for (i=0; insites; i++) { float baf = smpl->baf[i]; if ( baf>4/5.) continue; // skip AA genotypes if ( baf>0.5 ) baf = 1 - baf; // the bands should be symmetric if ( baf<1/5.) continue; // skip RR genotypes double prob_cn3 = 0, *probs = fwd + i*nstates; if ( !args->control_sample.name ) { prob_cn3 = probs[CN3]; } else if ( ismpl==0 ) { // query sample: CN3 probability must be recovered from all states of the control sample for (j=0; jtmpf[k++] = prob_cn3; } smooth_data(args->tmpf, k, 50); k = 0; for (i=0; insites; i++) { float baf = smpl->baf[i]; if ( baf>4/5.) { baf_AA_dev2 += (1.0-baf)*(1.0-baf); norm_baf_AA_dev2++; continue; } // skip AA genotypes if ( baf>0.5 ) baf = 1 - baf; // the bands should be symmetric if ( baf<1/5.) continue; // skip RR genotypes double prob_cn3 = args->tmpf[k++]; mean_cn3 += prob_cn3 * baf; norm_cn3 += prob_cn3; } if ( !norm_cn3 ) { smpl->cell_frac = 1.0; return 1; } mean_cn3 /= norm_cn3; k = 0; for (i=0; insites; i++) { float baf = smpl->baf[i]; if ( baf>0.5 ) baf = 1 - baf; // the bands should be symmetric if ( baf<1/5.) continue; // skip RR,AA genotypes double prob_cn3 = args->tmpf[k++]; baf_dev2 += prob_cn3 * (baf - mean_cn3)*(baf - mean_cn3); } /* A noisy CN2 band is hard to distinguish from two CN3 bands which are close to each other. Set a threshold on the minimum separation based on the BAF deviation at p=0.95 */ baf_dev2 /= norm_cn3; baf_AA_dev2 /= norm_baf_AA_dev2; if ( baf_dev2 < baf_AA_dev2 ) baf_dev2 = baf_AA_dev2; double max_mean_cn3 = 0.5 - sqrt(baf_dev2)*1.644854; // R: qnorm(0.95)=1.644854 //fprintf(stderr,"dev=%f AA_dev=%f max_mean_cn3=%f mean_cn3=%f\n", baf_dev2,baf_AA_dev2,max_mean_cn3,mean_cn3); assert( max_mean_cn3>0 ); double new_frac = 1./mean_cn3 - 2; if ( mean_cn3 > max_mean_cn3 || new_frac < args->optimize_frac ) { // out of bounds, beyond our detection limits. Give up and say it converged smpl->cell_frac = 1.0; return 1; } if ( new_frac>1 ) new_frac = 1; int converged = fabs(new_frac - smpl->cell_frac) < 1e-1 ? 1 : 0; // Update dev2, but stay within safe limits if ( baf_dev2 > 3*smpl->baf_dev2_dflt ) baf_dev2 = 3*smpl->baf_dev2_dflt; else if ( baf_dev2 < 0.5*smpl->baf_dev2_dflt ) baf_dev2 = 0.5*smpl->baf_dev2_dflt; smpl->cell_frac = new_frac; smpl->baf_dev2 = baf_dev2; return converged; } // Update parameters which depend on the estimated fraction of aberrant cells // in CN3. Returns 0 if the current estimate did not need to be updated or 1 // if there was a change. static int update_args(args_t *args) { int converged = update_sample_args(args, &args->query_sample, 0); if ( args->control_sample.name ) { converged += update_sample_args(args, &args->control_sample, 1); return converged==2 ? 0 : 1; } return converged ? 0 : 1; } // for an approximate estimate of the number of het genotypes in a region #define BAF_LIKELY_HET(val) (val)>0.25 && (val)<0.75 static void cnv_flush_viterbi(args_t *args) { if ( !args->nsites ) return; // Set HMM transition matrix for the new chromsome again. This is for case // Baum-Welch was used, which is experimental, largerly unsupported and not // done by default. hmm_t *hmm = args->hmm; hmm_set_tprob(args->hmm, args->tprob, 10000); // Smooth LRR values to reduce noise if ( args->lrr_bias > 0 ) { smooth_data(args->query_sample.lrr,args->nsites, args->lrr_smooth_win); if ( args->control_sample.name ) smooth_data(args->control_sample.lrr,args->nsites, args->lrr_smooth_win); } // Set the BAF peak likelihoods, such as P(RRR|CN3), taking account the // estimated fraction of aberrant cells in the mixture. With the new chromosome, // reset the fraction to the default value. args->query_sample.cell_frac = args->query_sample.cell_frac_dflt; args->control_sample.cell_frac = args->control_sample.cell_frac_dflt; args->query_sample.baf_dev2 = args->query_sample.baf_dev2_dflt; args->control_sample.baf_dev2 = args->control_sample.baf_dev2_dflt; set_gauss_params(args, &args->query_sample); if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample); if ( args->optimize_frac ) { int niter = 0; fprintf(stderr,"Attempting to estimate the fraction of aberrant cells (chr %s):\n", bcf_hdr_id2name(args->hdr,args->prev_rid)); do { fprintf(stderr,"\t.. %f %f", args->query_sample.cell_frac,args->query_sample.baf_dev2); if ( args->control_sample.name ) fprintf(stderr,"\t.. %f %f", args->control_sample.cell_frac,args->control_sample.baf_dev2); fprintf(stderr,"\n"); set_emission_probs(args); hmm_run_fwd_bwd(hmm, args->nsites, args->eprob, args->sites); } while ( update_args(args) && ++niter<20 ); if ( niter>=20 ) { // no convergence args->query_sample.cell_frac = args->query_sample.cell_frac_dflt; args->control_sample.cell_frac = args->control_sample.cell_frac_dflt; args->query_sample.baf_dev2 = args->query_sample.baf_dev2_dflt; args->control_sample.baf_dev2 = args->control_sample.baf_dev2_dflt; set_gauss_params(args, &args->query_sample); if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample); } fprintf(stderr,"\t.. %f %f", args->query_sample.cell_frac,args->query_sample.baf_dev2); if ( args->control_sample.name ) fprintf(stderr,"\t.. %f %f", args->control_sample.cell_frac,args->control_sample.baf_dev2); fprintf(stderr,"\n"); fprintf(args->query_sample.summary_fh,"CF\t%s\t%d\t%d\t%.2f\t%f\n", bcf_hdr_id2name(args->hdr,args->prev_rid),args->sites[0]+1,args->sites[args->nsites-1]+1, args->query_sample.cell_frac,sqrt(args->query_sample.baf_dev2)); if ( args->control_sample.name ) { fprintf(args->control_sample.summary_fh,"CF\t%s\t%d\t%d\t%.2f\t%f\n", bcf_hdr_id2name(args->hdr,args->prev_rid),args->sites[0]+1,args->sites[args->nsites-1]+1, args->control_sample.cell_frac,sqrt(args->control_sample.baf_dev2)); fprintf(args->summary_fh,"CF\t%s\t%d\t%d\t%.2f\t%.2f\t%f\t%f\n", bcf_hdr_id2name(args->hdr,args->prev_rid),args->sites[0]+1,args->sites[args->nsites-1]+1, args->query_sample.cell_frac, args->control_sample.cell_frac, sqrt(args->query_sample.baf_dev2), sqrt(args->control_sample.baf_dev2)); } } set_emission_probs(args); while ( args->baum_welch_th!=0 ) { int nstates = hmm_get_nstates(hmm); double ori_ii = avg_ii_prob(nstates,hmm_get_tprob(hmm)); hmm_run_baum_welch(hmm, args->nsites, args->eprob, args->sites); double new_ii = avg_ii_prob(nstates,hmm_get_tprob(hmm)); fprintf(stderr,"%e\t%e\t%e\n", ori_ii,new_ii,new_ii-ori_ii); double *tprob = init_tprob_matrix(nstates, 1-new_ii, args->same_prob); hmm_set_tprob(args->hmm, tprob, 10000); double *tprob_arr = hmm_get_tprob(hmm); free(tprob); if ( fabs(new_ii - ori_ii) < args->baum_welch_th ) { int i,j; for (i=0; insites, args->eprob, args->sites); hmm_run_fwd_bwd(hmm, args->nsites, args->eprob, args->sites); // Output the results uint8_t *vpath = hmm_get_viterbi_path(hmm); double qual = 0, *fwd = hmm_get_fwd_bwd_prob(hmm); int i,j, isite, start_cn = vpath[0], start_pos = args->sites[0], istart_pos = 0; int ctrl_ntot = 0, smpl_ntot = 0, ctrl_nhet = 0, smpl_nhet = 0; for (isite=0; isitensites; isite++) { int state = vpath[args->nstates*isite]; double *pval = fwd + isite*args->nstates; qual += pval[start_cn]; // output CN and fwd-bwd likelihood for each site if ( args->query_sample.cn_fh ) { fprintf(args->query_sample.cn_fh, "%s\t%d\t%c", bcf_hdr_id2name(args->hdr,args->prev_rid), args->sites[isite]+1, copy_number_state(args,state,0)); if ( !args->control_sample.cn_fh ) for (i=0; instates; i++) fprintf(args->query_sample.cn_fh, "\t%f", pval[i]); else for (i=0; iquery_sample.cn_fh, "\t%f", sum); } fprintf(args->query_sample.cn_fh, "\n"); if ( args->query_sample.baf[isite]>=0 ) // if non-missing { if ( BAF_LIKELY_HET(args->query_sample.baf[isite]) ) smpl_nhet++; smpl_ntot++; } } if ( args->control_sample.cn_fh ) { fprintf(args->control_sample.cn_fh, "%s\t%d\t%c", bcf_hdr_id2name(args->hdr,args->prev_rid), args->sites[isite]+1, copy_number_state(args,state,1)); for (i=0; icontrol_sample.cn_fh, "\t%f", sum); } fprintf(args->control_sample.cn_fh, "\n"); if ( args->control_sample.baf[isite]>=0 ) // if non-missing { if ( BAF_LIKELY_HET(args->control_sample.baf[isite]) ) ctrl_nhet++; ctrl_ntot++; } } if ( start_cn != state ) { char start_cn_query = copy_number_state(args,start_cn,0); qual = phred_score(1 - qual/(isite - istart_pos)); fprintf(args->query_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n", bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_query,qual,smpl_ntot,smpl_nhet); if ( args->control_sample.name ) { // regions 0-based, half-open char start_cn_ctrl = copy_number_state(args,start_cn,1); fprintf(args->control_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n", bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_ctrl,qual,ctrl_ntot,ctrl_nhet); fprintf(args->summary_fh,"RG\t%s\t%d\t%d\t%c\t%c\t%.1f\t%d\t%d\t%d\t%d\n", bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_query,start_cn_ctrl,qual,smpl_ntot,smpl_nhet,ctrl_ntot,ctrl_nhet); } istart_pos = isite; start_pos = args->sites[isite]; start_cn = state; qual = 0; smpl_ntot = smpl_nhet = ctrl_ntot = ctrl_nhet = 0; } } qual = phred_score(1 - qual/(isite - istart_pos)); char start_cn_query = copy_number_state(args,start_cn,0); fprintf(args->query_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n", bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_query,qual,smpl_ntot,smpl_nhet); if ( args->control_sample.name ) { char start_cn_ctrl = copy_number_state(args,start_cn,1); fprintf(args->control_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n", bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_ctrl,qual,ctrl_ntot,ctrl_nhet); fprintf(args->summary_fh,"RG\t%s\t%d\t%d\t%c\t%c\t%.1f\t%d\t%d\t%d\t%d\n", bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_query,start_cn_ctrl,qual,smpl_ntot,smpl_nhet,ctrl_ntot,ctrl_nhet); } } static int parse_lrr_baf(sample_t *smpl, bcf_fmt_t *baf_fmt, bcf_fmt_t *lrr_fmt, float *baf, float *lrr) { *baf = ((float*)(baf_fmt->p + baf_fmt->size*smpl->idx))[0]; if ( bcf_float_is_missing(*baf) || isnan(*baf) ) *baf = -0.1; // arbitrary negative value == missing value if ( lrr_fmt ) { *lrr = ((float*)(lrr_fmt->p + lrr_fmt->size*smpl->idx))[0]; if ( bcf_float_is_missing(*lrr) || isnan(*lrr) ) { *lrr = 0; *baf = -0.1; } } else *lrr = 0; return *baf<0 ? 0 : 1; } static void cnv_next_line(args_t *args, bcf1_t *line) { if ( !line ) { // Done, flush viterbi cnv_flush_viterbi(args); return; } if ( line->rid!=args->prev_rid ) { // New chromosome cnv_flush_viterbi(args); args->prev_rid = line->rid; args->nsites = 0; args->nRR = args->nAA = args->nRA = 0; } // Process line args->ntot++; bcf_fmt_t *baf_fmt, *lrr_fmt = NULL; if ( !(baf_fmt = bcf_get_fmt(args->hdr, line, "BAF")) ) return; if ( args->lrr_bias>0 && !(lrr_fmt = bcf_get_fmt(args->hdr, line, "LRR")) ) return; float baf1,lrr1,baf2,lrr2; int ret = 0; ret += parse_lrr_baf(&args->query_sample, baf_fmt,lrr_fmt,&baf1,&lrr1); ret += parse_lrr_baf(&args->control_sample,baf_fmt,lrr_fmt,&baf2,&lrr2); if ( !ret ) return; // Realloc buffers needed to store observed data and used by viterbi and fwd-bwd args->nsites++; int m = args->msites; hts_expand(uint32_t,args->nsites,args->msites,args->sites); if ( args->msites!=m ) { args->eprob = (double*) realloc(args->eprob,sizeof(double)*args->msites*args->nstates); if ( args->control_sample.name ) { args->control_sample.lrr = (float*) realloc(args->control_sample.lrr,sizeof(float)*args->msites); args->control_sample.baf = (float*) realloc(args->control_sample.baf,sizeof(float)*args->msites); } args->query_sample.lrr = (float*) realloc(args->query_sample.lrr,sizeof(float)*args->msites); args->query_sample.baf = (float*) realloc(args->query_sample.baf,sizeof(float)*args->msites); if ( args->af_fname ) args->nonref_afs = (float*) realloc(args->nonref_afs,sizeof(float)*args->msites); } args->sites[args->nsites-1] = line->pos; args->query_sample.lrr[args->nsites-1] = lrr1; args->query_sample.baf[args->nsites-1] = baf1; if ( args->af_fname ) { double alt_freq; args->nonref_afs[args->nsites-1] = read_AF(args->files->targets,line,&alt_freq)<0 ? args->nonref_af_dflt : alt_freq; } if ( args->control_sample.name ) { args->control_sample.lrr[args->nsites-1] = lrr2; args->control_sample.baf[args->nsites-1] = baf2; if ( baf2>=0 ) // skip missing values fprintf(args->control_sample.dat_fh,"%s\t%"PRId64"\t%.3f\t%.3f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), (int64_t) line->pos+1,baf2,lrr2); } if ( baf1>=0 ) // skip missing values fprintf(args->query_sample.dat_fh,"%s\t%"PRId64"\t%.3f\t%.3f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), (int64_t) line->pos+1,baf1,lrr1); if ( baf1>=0 ) { if ( baf1<1/5. ) args->nRR++; else if ( baf1>4/5. ) args->nAA++; else args->nRA++; } args->nused++; } static void usage(args_t *args) { fprintf(stderr, "\n"); fprintf(stderr, "About: Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R\n"); fprintf(stderr, " Ratio intensity (LRR). The HMM considers the following copy number states: CN 2\n"); fprintf(stderr, " (normal), 1 (single-copy loss), 0 (complete loss), 3 (single-copy gain)\n"); fprintf(stderr, "Usage: bcftools cnv [OPTIONS] FILE.vcf\n"); fprintf(stderr, "General Options:\n"); fprintf(stderr, " -c, --control-sample STRING Optional control sample name to highlight differences\n"); fprintf(stderr, " -f, --AF-file FILE Read allele frequencies from file (CHR\\tPOS\\tREF,ALT\\tAF)\n"); fprintf(stderr, " -o, --output-dir PATH \n"); fprintf(stderr, " -p, --plot-threshold FLOAT Plot aberrant chromosomes with quality at least FLOAT\n"); fprintf(stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " -s, --query-sample STRING Query samply name\n"); fprintf(stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(stderr, "HMM Options:\n"); fprintf(stderr, " -a, --aberrant FLOAT[,FLOAT] Fraction of aberrant cells in query and control [1.0,1.0]\n"); fprintf(stderr, " -b, --BAF-weight FLOAT Relative contribution from BAF [1]\n"); fprintf(stderr, " -d, --BAF-dev FLOAT[,FLOAT] Expected BAF deviation in query and control [0.04,0.04]\n"); // experimental fprintf(stderr, " -e, --err-prob FLOAT Uniform error probability [1e-4]\n"); fprintf(stderr, " -k, --LRR-dev FLOAT[,FLOAT] Expected LRR deviation [0.2,0.2]\n"); // experimental fprintf(stderr, " -l, --LRR-weight FLOAT Relative contribution from LRR [0.2]\n"); fprintf(stderr, " -L, --LRR-smooth-win INT Window of LRR moving average smoothing [10]\n"); fprintf(stderr, " -O, --optimize FLOAT Estimate fraction of aberrant cells down to FLOAT [1.0]\n"); fprintf(stderr, " -P, --same-prob FLOA> Prior probability of -s/-c being the same [0.5]\n"); fprintf(stderr, " -x, --xy-prob FLOAT P(x|y) transition probability [1e-9]\n"); fprintf(stderr, "\n"); exit(1); } int main_vcfcnv(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->files = bcf_sr_init(); args->plot_th = 1e9; // by default plot none args->nonref_af_dflt = 0.1; args->lrr_smooth_win = 10; args->query_sample.cell_frac_dflt = 1; args->control_sample.cell_frac_dflt = 1; // How much FORMAT/LRR and FORMAT/BAF matter args->lrr_bias = 0.2; args->baf_bias = 1.0; args->err_prob = 1e-4; // Transition probability to a different state and the prior of both samples being the same args->ij_prob = 1e-9; args->same_prob = 0.5; // Squared std dev of BAF and LRR values (gaussian noise), estimated from real data (hets, one sample, one chr) args->query_sample.baf_dev2_dflt = args->control_sample.baf_dev2_dflt = 0.04*0.04; // illumina: 0.03 args->query_sample.lrr_dev2 = args->control_sample.lrr_dev2 = 0.2*0.2; //0.20*0.20; // illumina: 0.18 int regions_is_file = 0, targets_is_file = 0; int regions_overlap = 1; int targets_overlap = 0; static struct option loptions[] = { {"BAF-dev",1,0,'d'}, {"LRR-dev",1,0,'k'}, {"LRR-smooth-win",1,0,'L'}, {"AF-file",1,0,'f'}, {"baum-welch",1,0,'W'}, // hidden {"optimize",1,0,'O'}, {"aberrant",1,0,'a'}, {"err-prob",1,0,'e'}, {"BAF-weight",1,0,'b'}, {"LRR-weight",1,0,'l'}, {"same-prob",1,0,'P'}, {"xy-prob",1,0,'x'}, {"query-sample",1,0,'s'}, {"control-sample",1,0,'c'}, {"targets",1,0,'t'}, {"targets-file",1,0,'T'}, {"targets-overlap",required_argument,NULL,4}, {"regions",1,0,'r'}, {"regions-file",1,0,'R'}, {"regions-overlap",required_argument,NULL,3}, {"plot-threshold",1,0,'p'}, {"output-dir",1,0,'o'}, {0,0,0,0} }; char *tmp = NULL; while ((c = getopt_long(argc, argv, "h?r:R:t:T:s:o:p:l:T:c:b:P:x:e:O:W::f:a:L:d:k:",loptions,NULL)) >= 0) { switch (c) { case 'L': args->lrr_smooth_win = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse: --LRR-smooth-win %s\n", optarg); break; case 'f': args->af_fname = optarg; break; case 'O': args->optimize_frac = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -O %s\n", optarg); break; case 'd': args->query_sample.baf_dev2_dflt = strtod(optarg,&tmp); if ( *tmp ) { if ( *tmp!=',') error("Could not parse: -d %s\n", optarg); args->control_sample.baf_dev2_dflt = strtod(tmp+1,&tmp); if ( *tmp ) error("Could not parse: -d %s\n", optarg); } else args->control_sample.baf_dev2_dflt = args->query_sample.baf_dev2_dflt; args->query_sample.baf_dev2_dflt *= args->query_sample.baf_dev2_dflt; args->control_sample.baf_dev2_dflt *= args->control_sample.baf_dev2_dflt; break; case 'k': args->query_sample.lrr_dev2 = strtod(optarg,&tmp); if ( *tmp ) { if ( *tmp!=',') error("Could not parse: -k %s\n", optarg); args->control_sample.lrr_dev2 = strtod(tmp+1,&tmp); if ( *tmp ) error("Could not parse: -d %s\n", optarg); } else args->control_sample.lrr_dev2 = args->query_sample.lrr_dev2; args->query_sample.lrr_dev2 *= args->query_sample.lrr_dev2; args->control_sample.lrr_dev2 *= args->control_sample.lrr_dev2; break; case 'a': args->query_sample.cell_frac_dflt = strtod(optarg,&tmp); if ( *tmp ) { if ( *tmp!=',') error("Could not parse: -a %s\n", optarg); args->control_sample.cell_frac_dflt = strtod(tmp+1,&tmp); if ( *tmp ) error("Could not parse: -a %s\n", optarg); } break; case 'W': args->baum_welch_th = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -W %s\n", optarg); break; case 'e': args->err_prob = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -e %s\n", optarg); break; case 'b': args->baf_bias = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -b %s\n", optarg); break; case 'x': args->ij_prob = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -x %s\n", optarg); break; case 'P': args->same_prob = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -P %s\n", optarg); break; case 'l': args->lrr_bias = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -l %s\n", optarg); break; case 'p': args->plot_th = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -p %s\n", optarg); break; case 'o': args->output_dir = optarg; break; case 's': args->query_sample.name = strdup(optarg); break; case 'c': args->control_sample.name = optarg; break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; targets_is_file = 1; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 3 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 4 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 'h': case '?': usage(args); break; default: error("Unknown argument: %s\n", optarg); } } char *fname = NULL; if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; } else fname = argv[optind]; if ( !fname ) usage(args); if ( !args->output_dir ) error("Expected -o option\n"); if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } if ( args->af_fname ) { if ( bcf_sr_set_targets(args->files, args->af_fname, 1, 3)<0 ) error("Failed to read the targets: %s\n", args->af_fname); } if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); init_data(args); while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = bcf_sr_get_line(args->files,0); cnv_next_line(args, line); } cnv_next_line(args, NULL); create_plots(args); fprintf(stderr,"Number of lines: total/processed: %d/%d\n", args->ntot,args->nused); destroy_data(args); free(args); return 0; } pysam-0.23.0/bcftools/vcfcnv.c.pysam.c000066400000000000000000001647361475062545500176000ustar00rootroot00000000000000#include "bcftools.pysam.h" /* The MIT License Copyright (c) 2014-2022 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Known issues: - The --AF-file option behaves like --targets-file, sites not listed in the AFs are skipped. */ #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "HMM.h" #include "rbuf.h" #define DBG0 0 #define N_STATES 4 #define CN0 0 #define CN1 1 #define CN2 2 #define CN3 3 typedef struct { float mean, dev2, norm; } gauss_param_t; typedef struct { char *name; int idx; // VCF sample index float *lrr,*baf, baf_dev2, baf_dev2_dflt, lrr_dev2; float cell_frac, cell_frac_dflt; gauss_param_t gauss_param[18]; double pobs[N_STATES]; FILE *dat_fh, *cn_fh, *summary_fh; char *dat_fname, *cn_fname, *summary_fname; } sample_t; typedef struct _args_t { bcf_srs_t *files; bcf_hdr_t *hdr; int prev_rid, ntot, nused; sample_t query_sample, control_sample; int nstates; // number of states: N_STATES for one sample, N_STATES^2 for two samples double lrr_bias, baf_bias; // LRR/BAF weights double same_prob, ij_prob; // prior of both samples being the same and the transition probability P(i|j) double err_prob; // constant probability of erroneous measurement float *nonref_afs, nonref_af, nonref_af_dflt, fRR, fRA, fAA, *tmpf; unsigned long int nRR, nRA, nAA; int mtmpf; double *tprob, *tprob_arr; // array of transition matrices, precalculated up to ntprob_arr positions double *iprobs; // states' initial probabilities int ntprob_arr; hmm_t *hmm; double *eprob; // emission probs [nstates*nsites,msites] uint32_t *sites; // positions [nsites,msites] int nsites, msites; double baum_welch_th, optimize_frac; float plot_th; FILE *summary_fh; char **argv, *regions_list, *summary_fname, *output_dir; char *targets_list, *af_fname; int argc, verbose, lrr_smooth_win; } args_t; FILE *open_file(char **fname, const char *mode, const char *fmt, ...) HTS_FORMAT(HTS_PRINTF_FMT, 3, 4); static inline void hmm2cn_state(int nstates, int i, int *a, int *b) { *a = i / N_STATES; *b = i - (*a)*N_STATES; } static double *init_tprob_matrix(int ndim, double ij_prob, double same_prob) { int i,j; double *mat = (double*) malloc(sizeof(double)*ndim*ndim); assert( ndim==N_STATES || ndim==N_STATES*N_STATES); if ( ndim==N_STATES ) // one sample { double pii = 1 - ij_prob*(N_STATES-1); if ( pii < ij_prob ) error("Error: -x set a bit too high, P(x|x) < P(x|y): %e vs %e\n", pii,ij_prob); for (j=0; jdat_fh = open_file(&smpl->dat_fname,"w","%s/dat.%s.tab",dir,smpl->name); if ( !smpl->dat_fh ) error("Error opening file: %s/dat.%s.tab\n",dir,smpl->name); smpl->cn_fh = open_file(&smpl->cn_fname,"w","%s/cn.%s.tab",dir,smpl->name); if ( !smpl->cn_fh ) error("Error opening file: %s/cn.%s.tab\n",dir,smpl->name); smpl->summary_fh = open_file(&smpl->summary_fname,"w","%s/summary.%s.tab",dir,smpl->name); if ( !smpl->summary_fh ) error("Error opening file: %s/summary.%s.tab\n",dir,smpl->name); fprintf(smpl->dat_fh,"# [1]Chromosome\t[2]Position\t[3]BAF\t[4]LRR\n"); fprintf(smpl->cn_fh,"# [1]Chromosome\t[2]Position\t[3]CN\t[4]P(CN0)\t[5]P(CN1)\t[6]P(CN2)\t[7]P(CN3)\n"); fprintf(smpl->summary_fh,"# RG, Regions [2]Chromosome\t[3]Start\t[4]End\t[5]Copy Number state\t[6]Quality\t[7]nSites\t[8]nHETs\n"); } static void close_sample_files(sample_t *smpl) { if ( fclose(smpl->dat_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,smpl->dat_fname); if ( fclose(smpl->cn_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,smpl->cn_fname); if ( fclose(smpl->summary_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,smpl->summary_fname); } static double norm_cdf(double mean, double dev); static void init_data(args_t *args) { args->prev_rid = -1; args->hdr = args->files->readers[0].header; if ( !args->query_sample.name ) { if ( bcf_hdr_nsamples(args->hdr)>1 ) error("Multi-sample VCF, missing the -s option\n"); args->query_sample.name = strdup(args->hdr->samples[0]); } else if ( bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->query_sample.name)<0 ) error("The sample \"%s\" not found\n", args->query_sample.name); if ( !args->files->readers[0].file->is_bin ) { int ret; kstring_t tmp = {0,0,0}; if ( args->control_sample.name ) { ksprintf(&tmp, "%s,%s", args->query_sample.name,args->control_sample.name); ret = bcf_hdr_set_samples(args->hdr, tmp.s, 0); } else { ret = bcf_hdr_set_samples(args->hdr, args->query_sample.name, 0); tmp.s = args->query_sample.name; } if ( ret<0 ) error("Error parsing the list of samples: %s\n", tmp.s); else if ( ret>0 ) error("The sample not found in the VCF: %s\n", ret==1 ? args->query_sample.name : args->control_sample.name); if ( args->control_sample.name ) free(tmp.s); } args->query_sample.idx = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->query_sample.name); args->control_sample.idx = args->control_sample.name ? bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->control_sample.name) : -1; args->nstates = args->control_sample.name ? N_STATES*N_STATES : N_STATES; args->tprob = init_tprob_matrix(args->nstates, args->ij_prob, args->same_prob); args->iprobs = init_iprobs(args->nstates, args->same_prob); args->hmm = hmm_init(args->nstates, args->tprob, 10000); hmm_init_states(args->hmm, args->iprobs); args->summary_fh = bcftools_stdout; init_sample_files(&args->query_sample, args->output_dir); if ( args->control_sample.name ) { init_sample_files(&args->control_sample, args->output_dir); args->summary_fh = open_file(&args->summary_fname,"w","%s/summary.tab",args->output_dir); } else args->summary_fh = NULL; // one sample only, no two-file summary int i; FILE *fh = args->summary_fh ? args->summary_fh : args->query_sample.summary_fh; fprintf(fh, "# This file was produced by: bcftools cnv(%s+htslib-%s)\n", bcftools_version(),hts_version()); fprintf(fh, "# The command line was:\tbcftools %s", args->argv[0]); for (i=1; iargc; i++) fprintf(fh, " %s",args->argv[i]); if ( args->control_sample.name ) fprintf(fh, "\n#\n" "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Copy number:%s\t[7]Quality" "\t[8]nSites in (5)\t[9]nHETs in (5)\t[10]nSites in (6)\t[11]nHETs in(6)\n", args->query_sample.name,args->control_sample.name ); else fprintf(fh, "\n#\n" "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Quality\t[7]nSites\t[8]nHETs\n", args->query_sample.name ); if ( args->optimize_frac ) { fprintf(args->query_sample.summary_fh, "# CF, cell fraction estimate\t[2]Chromosome\t[3]Start\t[4]End\t[5]Cell fraction\t[6]BAF deviation\n"); if ( args->control_sample.name ) { fprintf(args->control_sample.summary_fh, "# CF, cell fraction estimate\t[2]Chromosome\t[3]Start\t[4]End\t[5]Cell fraction\t[6]BAF deviation\n"); fprintf(args->summary_fh, "# CF, cell fraction estimate\t[2]Chromosome\t[3]Start\t[4]End\t" "[5]Cell fraction:%s\t[6]Cell fraction:%s\t[7]BAF deviation:%s\t[8]BAF deviation:%s\n", args->query_sample.name,args->control_sample.name, args->query_sample.name,args->control_sample.name ); } } } char *msprintf(const char *fmt, ...); static void py_plot_cnv(char *script, float th) { if ( th>100 ) return; // create no plots char *cmd = msprintf("python %s -p %f", script, th); int ret = system(cmd); if ( ret) fprintf(bcftools_stderr, "The command returned non-zero status %d: %s\n", ret, cmd); free(cmd); } static void plot_sample(args_t *args, sample_t *smpl) { char *fname; FILE *fp = open_file(&fname,"w","%s/plot.%s.py",args->output_dir,smpl->name); fprintf(fp, "import matplotlib as mpl\n" "mpl.use('Agg')\n" "import matplotlib.pyplot as plt\n" "import csv\n" "import numpy as np\n" "csv.register_dialect('tab', delimiter='\\t', quoting=csv.QUOTE_NONE)\n" "\n" "dat = {}\n" "with open('%s', 'r') as f:\n" " reader = csv.reader(f, 'tab')\n" " for row in reader:\n" " chr = row[0]\n" " if chr[0]=='#': continue\n" " if chr not in dat: dat[chr] = []\n" " dat[chr].append([int(row[1]), float(row[2]), float(row[3])])\n" "\n" "cnv = {}\n" "with open('%s', 'r') as f:\n" " reader = csv.reader(f, 'tab')\n" " for row in reader:\n" " chr = row[0]\n" " if chr[0]=='#': continue\n" " if chr not in cnv: cnv[chr] = []\n" " row[2] = int(row[2]) + 0.5\n" " row[1] = int(row[1])\n" " cnv[chr].append(row[1:])\n" "\n" "for chr in dat:\n" " fig,(ax1, ax2, ax3) = plt.subplots(3,1,figsize=(10,8),sharex=True)\n" " ax1.plot([x[0] for x in dat[chr]],[x[2] for x in dat[chr]], '.', ms=3)\n" " ax2.plot([x[0] for x in dat[chr]],[x[1] for x in dat[chr]], '.', ms=3)\n" " cn_dat = cnv[chr]\n" " xgrid = [float(x[0]) for x in cn_dat]\n" " ygrid = np.linspace(0,5,6)\n" " xgrid, ygrid = np.meshgrid(xgrid, ygrid)\n" " heat = np.zeros_like(xgrid)\n" " for x in range(len(heat[0])-1):\n" " heat[0][x] = cn_dat[x][2]\n" " heat[1][x] = cn_dat[x][3]\n" " heat[2][x] = cn_dat[x][4]\n" " heat[3][x] = cn_dat[x][5]\n" " mesh = ax3.pcolormesh(xgrid, ygrid, heat, cmap='bwr_r', shading='auto', alpha=0)\n" " mesh.set_clim(vmin=-1,vmax=1)\n" " ax3.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'.-',ms=3,color='black')\n" " fig.suptitle('%s (chr '+chr+')')\n" " ax1.set_title('Log-R intensities Ratio',fontsize=10)\n" " ax2.set_title('B-Allele Frequency',fontsize=10)\n" " ax3.set_title('Copy Number Variation',fontsize=10)\n" " ax1.set_ylabel('LRR')\n" " ax2.set_ylabel('BAF')\n" " ax3.set_ylabel('CN')\n" " ax3.set_xlabel('Coordinate (chrom '+chr+')',fontsize=10)\n" " ax3.set_ylim(-0.1,4.1)\n" " ax3.set_yticks([0.5,1.5,2.5,3.5])\n" " ax3.set_yticklabels(['CN0','CN1','CN2','CN3'])\n" " plt.subplots_adjust(left=0.08,right=0.95,bottom=0.08,top=0.92)\n" " plt.savefig('%s/plot.%s.chr'+chr+'.png')\n" " plt.close()\n" "\n", smpl->dat_fname,smpl->cn_fname,smpl->name,args->output_dir,smpl->name ); fclose(fp); py_plot_cnv(fname, args->plot_th); free(fname); } static void create_plots(args_t *args) { close_sample_files(&args->query_sample); if ( args->control_sample.name ) close_sample_files(&args->control_sample); if ( args->summary_fh ) fclose(args->summary_fh); if ( !args->control_sample.name ) { plot_sample(args, &args->query_sample); return; } char *fname; FILE *fp = open_file(&fname,"w","%s/plot.%s.%s.py",args->output_dir,args->control_sample.name,args->query_sample.name); fprintf(fp, "import matplotlib as mpl\n" "mpl.use('Agg')\n" "import matplotlib.pyplot as plt\n" "import csv,argparse\n" "import numpy as np\n" "csv.register_dialect('tab', delimiter='\\t', quoting=csv.QUOTE_NONE)\n" "\n" "control_sample = '%s'\n" "query_sample = '%s'\n" "\n" "parser = argparse.ArgumentParser()\n" "parser.add_argument('-p', '--plot-threshold', type=float)\n" "parser.add_argument('-c', '--chromosome')\n" "args = parser.parse_args()\n" "if args.plot_threshold==None: args.plot_threshold = 0\n" "\n" "def chroms_to_plot(th):\n" " dat = {}\n" " with open('%s/summary.tab', 'r') as f:\n" " reader = csv.reader(f, 'tab')\n" " for row in reader:\n" " if row[0]!='RG': continue\n" " chr = row[1]\n" " start = row[2]\n" " end = row[3]\n" " qual = float(row[6])\n" " if row[4]==row[5] and args.plot_threshold!=0: continue\n" " if chr not in dat: dat[chr] = 0.0\n" " if qual > dat[chr]: dat[chr] = qual\n" " out = {}\n" " for chr in dat:\n" " if (chr not in dat) or dat[chr]0: diff.append([b[i-1][0],b[i-1][1],a[i-1][1]])\n" " diff.append([b[i][0],b[i][1],a[i][1]])\n" " elif len(diff):\n" " diff.append([b[i][0],b[i][1],a[i][1]])\n" " out.append(diff)\n" " diff = []\n" " if len(diff): out.append(diff)\n" " return out\n" "\n" "for chr in sorted(plot_chroms.keys()):\n" " control_dat = []\n" " control_cnv = []\n" " query_dat = []\n" " query_cnv = []\n" " read_dat('%s',control_dat,chr)\n" " read_dat('%s',query_dat,chr)\n" " read_cnv('%s',control_cnv,chr)\n" " read_cnv('%s',query_cnv,chr)\n" "\n" " fig,(ax1,ax2,ax3,ax4,ax5,ax6) = plt.subplots(6,1,figsize=(10,8),sharex=True)\n" " ax1.plot([x[0] for x in control_dat],[x[2] for x in control_dat], '.', ms=3,color='red')\n" " ax2.plot([x[0] for x in control_dat],[x[1] for x in control_dat], '.', ms=3,color='red')\n" " cn_dat = control_cnv\n" " xgrid = [float(x[0]) for x in cn_dat]\n" " ygrid = np.linspace(0,5,6)\n" " xgrid, ygrid = np.meshgrid(xgrid, ygrid)\n" " heat = np.zeros_like(xgrid)\n" " for x in range(len(heat[0])-1):\n" " heat[0][x] = cn_dat[x][2]\n" " heat[1][x] = cn_dat[x][3]\n" " heat[2][x] = cn_dat[x][4]\n" " heat[3][x] = cn_dat[x][5]\n" " mesh = ax3.pcolormesh(xgrid, ygrid, heat, cmap='bwr', shading='auto', alpha=0)\n" " mesh.set_clim(vmin=-1,vmax=1)\n" " ax3.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'-',ms=3,color='black',lw=1.7)\n" "\n" " ax6.plot([x[0] for x in query_dat],[x[2] for x in query_dat], '.', ms=3)\n" " ax5.plot([x[0] for x in query_dat],[x[1] for x in query_dat], '.', ms=3)\n" " cn_dat = query_cnv\n" " xgrid = [float(x[0]) for x in cn_dat]\n" " ygrid = np.linspace(0,5,6)\n" " xgrid, ygrid = np.meshgrid(xgrid, ygrid)\n" " heat = np.zeros_like(xgrid)\n" " for x in range(len(heat[0])-1):\n" " heat[0][x] = cn_dat[x][2]\n" " heat[1][x] = cn_dat[x][3]\n" " heat[2][x] = cn_dat[x][4]\n" " heat[3][x] = cn_dat[x][5]\n" " mesh = ax4.pcolormesh(xgrid, ygrid, heat, cmap='bwr_r')\n" " mesh.set_clim(vmin=-1,vmax=1)\n" " ax4.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'-',ms=3,color='black',lw=1.7)\n" " ax3.annotate(control_sample, xy=(0.02,0.1), xycoords='axes fraction', color='red',fontsize=12, va='bottom',ha='left')\n" " ax4.annotate(query_sample, xy=(0.02,0.9), xycoords='axes fraction', color='blue',fontsize=12, va='top',ha='left')\n" "\n" " diffs = find_diffs(control_cnv,query_cnv)\n" " for diff in diffs:\n" " ax3.plot([x[0] for x in diff],[x[1] for x in diff],'-',ms=3,color='blue',lw=1.7)\n" " ax4.plot([x[0] for x in diff],[x[2] for x in diff],'-',ms=3,color='red',lw=1.7)\n" "\n" " fig.suptitle('chr '+chr+', '+control_sample+' vs '+query_sample)\n" " ax1.tick_params(axis='both', labelsize=8)\n" " ax2.tick_params(axis='both', labelsize=8)\n" " ax3.tick_params(axis='both', labelsize=8)\n" " ax4.tick_params(axis='both', labelsize=8)\n" " ax5.tick_params(axis='both', labelsize=8)\n" " ax6.tick_params(axis='both', labelsize=8)\n" " ax6.set_xlabel('Coordinate (chrom '+chr+')',fontsize=8)\n" " ax1.set_ylabel('LRR')\n" " ax2.set_ylabel('BAF')\n" " ax3.set_ylabel('CN')\n" " ax6.set_ylabel('LRR')\n" " ax5.set_ylabel('BAF')\n" " ax4.set_ylabel('CN')\n" " ax3.set_ylim(-0.1,4.1)\n" " ax3.set_yticks([0.5,1.5,2.5,3.5])\n" " ax3.set_yticklabels(['CN0','CN1','CN2','CN3'])\n" " ax4.set_ylim(-0.1,4.1)\n" " ax4.set_yticks([0.5,1.5,2.5,3.5])\n" " ax4.set_yticklabels(['CN0','CN1','CN2','CN3'])\n" " plt.subplots_adjust(left=0.08,right=0.95,bottom=0.08,top=0.92,hspace=0)\n" " plt.savefig('%s/plot.%s.%s.chr'+chr+'.png')\n" " plt.close()\n" "\n", args->control_sample.name,args->query_sample.name, args->output_dir, args->control_sample.dat_fname,args->query_sample.dat_fname, args->control_sample.cn_fname,args->query_sample.cn_fname, args->output_dir,args->control_sample.name,args->query_sample.name ); fclose(fp); py_plot_cnv(fname,args->plot_th); free(fname); } static void destroy_data(args_t *args) { bcf_sr_destroy(args->files); hmm_destroy(args->hmm); free(args->tmpf); free(args->sites); free(args->eprob); free(args->tprob); free(args->iprobs); free(args->summary_fname); free(args->nonref_afs); free(args->query_sample.baf); free(args->query_sample.lrr); free(args->control_sample.baf); free(args->control_sample.lrr); free(args->query_sample.name); free(args->query_sample.dat_fname); free(args->query_sample.cn_fname); free(args->query_sample.summary_fname); free(args->control_sample.dat_fname); free(args->control_sample.cn_fname); free(args->control_sample.summary_fname); } static inline char copy_number_state(args_t *args, int istate, int ismpl) { char code[] = "01234"; if ( !args->control_sample.name ) return code[istate]; int idx = ismpl ? istate - (istate/N_STATES)*N_STATES : istate/N_STATES; return code[idx]; } static double avg_ii_prob(int n, double *mat) { int i; double avg = 0; for (i=0; igauss_param[0])) #define GAUSS_CN1_PK_A(smpl) (&((smpl)->gauss_param[1])) #define GAUSS_CN2_PK_RR(smpl) (&((smpl)->gauss_param[2])) #define GAUSS_CN2_PK_RA(smpl) (&((smpl)->gauss_param[3])) #define GAUSS_CN2_PK_AA(smpl) (&((smpl)->gauss_param[4])) #define GAUSS_CN3_PK_RRR(smpl) (&((smpl)->gauss_param[5])) #define GAUSS_CN3_PK_RRA(smpl) (&((smpl)->gauss_param[6])) #define GAUSS_CN3_PK_RAA(smpl) (&((smpl)->gauss_param[7])) #define GAUSS_CN3_PK_AAA(smpl) (&((smpl)->gauss_param[8])) static inline double norm_prob(double baf, gauss_param_t *param) { return exp(-(baf-param->mean)*(baf-param->mean)*0.5/param->dev2) / param->norm / sqrt(2*M_PI*param->dev2); } static int set_observed_prob(args_t *args, sample_t *smpl, int isite) { float baf = smpl->baf[isite]; float lrr = args->lrr_bias>0 ? smpl->lrr[isite] : 0; float fRR = args->fRR; float fRA = args->fRA; float fAA = args->fAA; if ( baf<0 ) { // no call: either some technical issue or the call could not be made because it is CN0 int i; smpl->pobs[CN0] = 0.5; for (i=1; ipobs[i] = (1.0-smpl->pobs[CN0])/(N_STATES-1); return 0; } double cn1_baf = norm_prob(baf,GAUSS_CN1_PK_R(smpl)) * (fRR + fRA*0.5) + norm_prob(baf,GAUSS_CN1_PK_A(smpl)) * (fAA + fRA*0.5) ; double cn2_baf = norm_prob(baf,GAUSS_CN2_PK_RR(smpl)) * fRR + norm_prob(baf,GAUSS_CN2_PK_RA(smpl)) * fRA + norm_prob(baf,GAUSS_CN2_PK_AA(smpl)) * fAA; double cn3_baf = norm_prob(baf,GAUSS_CN3_PK_RRR(smpl)) * fRR + norm_prob(baf,GAUSS_CN3_PK_RRA(smpl)) * fRA*0.5 + norm_prob(baf,GAUSS_CN3_PK_RAA(smpl)) * fRA*0.5 + norm_prob(baf,GAUSS_CN3_PK_AAA(smpl)) * fAA; double norm = cn1_baf + cn2_baf + cn3_baf; cn1_baf /= norm; cn2_baf /= norm; cn3_baf /= norm; #if DBG0 if ( args->verbose ) fprintf(bcftools_stderr,"%f\t%f %f %f\n", baf,cn1_baf,cn2_baf,cn3_baf); #endif double cn1_lrr = exp(-(lrr + 0.45)*(lrr + 0.45)/smpl->lrr_dev2); double cn2_lrr = exp(-(lrr - 0.00)*(lrr - 0.00)/smpl->lrr_dev2); double cn3_lrr = exp(-(lrr - 0.30)*(lrr - 0.30)/smpl->lrr_dev2); smpl->pobs[CN0] = 0; smpl->pobs[CN1] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn1_baf)*(1 - args->lrr_bias + args->lrr_bias*cn1_lrr); smpl->pobs[CN2] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn2_baf)*(1 - args->lrr_bias + args->lrr_bias*cn2_lrr); smpl->pobs[CN3] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn3_baf)*(1 - args->lrr_bias + args->lrr_bias*cn3_lrr); return 0; } static void set_emission_prob(args_t *args, int isite) { double *eprob = &args->eprob[args->nstates*isite]; int i; for (i=0; iquery_sample.pobs[i]; } static void set_emission_prob2(args_t *args, int isite) { double *eprob = &args->eprob[args->nstates*isite]; int i, j; for (i=0; iquery_sample.pobs[i]*args->control_sample.pobs[j]; } } } static void set_gauss_params(args_t *args, sample_t *smpl); static double norm_cdf(double mean, double dev) { double bot = 0, top = 1; top = 1 - 0.5*erfc((top-mean)/(dev*sqrt(2))); bot = 1 - 0.5*erfc((bot-mean)/(dev*sqrt(2))); return top-bot; } static void set_emission_probs(args_t *args) { if ( !args->af_fname ) { args->fRR = 0.76; args->fRA = 0.14; args->fAA = 0.098; } set_gauss_params(args, &args->query_sample); if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample); #if DBG0 args->verbose = 1; args->query_sample.baf[0] = 0; set_observed_prob(args,&args->query_sample,0); args->query_sample.baf[0] = 1/3.; set_observed_prob(args,&args->query_sample,0); args->query_sample.baf[0] = 1/2.; set_observed_prob(args,&args->query_sample,0); args->query_sample.baf[0] = 2/3.; set_observed_prob(args,&args->query_sample,0); args->query_sample.baf[0] = 1; set_observed_prob(args,&args->query_sample,0); args->verbose = 0; #endif int i; for (i=0; insites; i++) { if ( args->af_fname ) { args->fRR = (1-args->nonref_afs[i])*(1-args->nonref_afs[i]); args->fRA = 2*args->nonref_afs[i]*(1-args->nonref_afs[i]); args->fAA = args->nonref_afs[i]*args->nonref_afs[i]; } set_observed_prob(args,&args->query_sample,i); if ( args->control_sample.name ) { set_observed_prob(args,&args->control_sample,i); set_emission_prob2(args,i); } else set_emission_prob(args,i); } } static void smooth_data(float *dat, int ndat, int win) { if ( win<=1 ) return; int i,j, k1 = win/2, k2 = win-k1; rbuf_t rbuf; rbuf_init(&rbuf,win); float sum = 0, *buf = (float*)malloc(sizeof(float)*win); for (i=0; i=k1 ) { j = rbuf_shift(&rbuf); sum -= buf[j]; } if ( i+k2gauss_param[i].dev2 = smpl->baf_dev2; double dev = sqrt(smpl->baf_dev2); GAUSS_CN1_PK_R(smpl)->mean = 0; GAUSS_CN1_PK_A(smpl)->mean = 1; GAUSS_CN1_PK_R(smpl)->norm = norm_cdf(GAUSS_CN1_PK_R(smpl)->mean,dev); GAUSS_CN1_PK_A(smpl)->norm = norm_cdf(GAUSS_CN1_PK_A(smpl)->mean,dev); GAUSS_CN2_PK_RR(smpl)->mean = 0; GAUSS_CN2_PK_RA(smpl)->mean = 0.5; GAUSS_CN2_PK_AA(smpl)->mean = 1; GAUSS_CN2_PK_RR(smpl)->norm = norm_cdf(GAUSS_CN2_PK_RR(smpl)->mean,dev); GAUSS_CN2_PK_RA(smpl)->norm = norm_cdf(GAUSS_CN2_PK_RA(smpl)->mean,dev); GAUSS_CN2_PK_AA(smpl)->norm = norm_cdf(GAUSS_CN2_PK_AA(smpl)->mean,dev); GAUSS_CN3_PK_RRR(smpl)->mean = 0; GAUSS_CN3_PK_RRA(smpl)->mean = 1.0/(2+smpl->cell_frac); GAUSS_CN3_PK_RAA(smpl)->mean = (1.0+smpl->cell_frac)/(2+smpl->cell_frac); GAUSS_CN3_PK_AAA(smpl)->mean = 1; GAUSS_CN3_PK_RRR(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RRR(smpl)->mean,dev); GAUSS_CN3_PK_RRA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RRA(smpl)->mean,dev); GAUSS_CN3_PK_RAA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RAA(smpl)->mean,dev); GAUSS_CN3_PK_AAA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_AAA(smpl)->mean,dev); } static int update_sample_args(args_t *args, sample_t *smpl, int ismpl) { hmm_t *hmm = args->hmm; double *fwd = hmm_get_fwd_bwd_prob(hmm); int nstates = hmm_get_nstates(hmm); // estimate the BAF mean and deviation for CN3 double mean_cn3 = 0, norm_cn3 = 0; double baf_dev2 = 0, baf_AA_dev2 = 0, norm_baf_AA_dev2 = 0; // experimental: smooth CN3 probs to bias toward bigger events, this lowers // the FP rate when the data is noisy hts_expand(float,args->nsites,args->mtmpf,args->tmpf); int i, j, k = 0; for (i=0; insites; i++) { float baf = smpl->baf[i]; if ( baf>4/5.) continue; // skip AA genotypes if ( baf>0.5 ) baf = 1 - baf; // the bands should be symmetric if ( baf<1/5.) continue; // skip RR genotypes double prob_cn3 = 0, *probs = fwd + i*nstates; if ( !args->control_sample.name ) { prob_cn3 = probs[CN3]; } else if ( ismpl==0 ) { // query sample: CN3 probability must be recovered from all states of the control sample for (j=0; jtmpf[k++] = prob_cn3; } smooth_data(args->tmpf, k, 50); k = 0; for (i=0; insites; i++) { float baf = smpl->baf[i]; if ( baf>4/5.) { baf_AA_dev2 += (1.0-baf)*(1.0-baf); norm_baf_AA_dev2++; continue; } // skip AA genotypes if ( baf>0.5 ) baf = 1 - baf; // the bands should be symmetric if ( baf<1/5.) continue; // skip RR genotypes double prob_cn3 = args->tmpf[k++]; mean_cn3 += prob_cn3 * baf; norm_cn3 += prob_cn3; } if ( !norm_cn3 ) { smpl->cell_frac = 1.0; return 1; } mean_cn3 /= norm_cn3; k = 0; for (i=0; insites; i++) { float baf = smpl->baf[i]; if ( baf>0.5 ) baf = 1 - baf; // the bands should be symmetric if ( baf<1/5.) continue; // skip RR,AA genotypes double prob_cn3 = args->tmpf[k++]; baf_dev2 += prob_cn3 * (baf - mean_cn3)*(baf - mean_cn3); } /* A noisy CN2 band is hard to distinguish from two CN3 bands which are close to each other. Set a threshold on the minimum separation based on the BAF deviation at p=0.95 */ baf_dev2 /= norm_cn3; baf_AA_dev2 /= norm_baf_AA_dev2; if ( baf_dev2 < baf_AA_dev2 ) baf_dev2 = baf_AA_dev2; double max_mean_cn3 = 0.5 - sqrt(baf_dev2)*1.644854; // R: qnorm(0.95)=1.644854 //fprintf(bcftools_stderr,"dev=%f AA_dev=%f max_mean_cn3=%f mean_cn3=%f\n", baf_dev2,baf_AA_dev2,max_mean_cn3,mean_cn3); assert( max_mean_cn3>0 ); double new_frac = 1./mean_cn3 - 2; if ( mean_cn3 > max_mean_cn3 || new_frac < args->optimize_frac ) { // out of bounds, beyond our detection limits. Give up and say it converged smpl->cell_frac = 1.0; return 1; } if ( new_frac>1 ) new_frac = 1; int converged = fabs(new_frac - smpl->cell_frac) < 1e-1 ? 1 : 0; // Update dev2, but stay within safe limits if ( baf_dev2 > 3*smpl->baf_dev2_dflt ) baf_dev2 = 3*smpl->baf_dev2_dflt; else if ( baf_dev2 < 0.5*smpl->baf_dev2_dflt ) baf_dev2 = 0.5*smpl->baf_dev2_dflt; smpl->cell_frac = new_frac; smpl->baf_dev2 = baf_dev2; return converged; } // Update parameters which depend on the estimated fraction of aberrant cells // in CN3. Returns 0 if the current estimate did not need to be updated or 1 // if there was a change. static int update_args(args_t *args) { int converged = update_sample_args(args, &args->query_sample, 0); if ( args->control_sample.name ) { converged += update_sample_args(args, &args->control_sample, 1); return converged==2 ? 0 : 1; } return converged ? 0 : 1; } // for an approximate estimate of the number of het genotypes in a region #define BAF_LIKELY_HET(val) (val)>0.25 && (val)<0.75 static void cnv_flush_viterbi(args_t *args) { if ( !args->nsites ) return; // Set HMM transition matrix for the new chromsome again. This is for case // Baum-Welch was used, which is experimental, largerly unsupported and not // done by default. hmm_t *hmm = args->hmm; hmm_set_tprob(args->hmm, args->tprob, 10000); // Smooth LRR values to reduce noise if ( args->lrr_bias > 0 ) { smooth_data(args->query_sample.lrr,args->nsites, args->lrr_smooth_win); if ( args->control_sample.name ) smooth_data(args->control_sample.lrr,args->nsites, args->lrr_smooth_win); } // Set the BAF peak likelihoods, such as P(RRR|CN3), taking account the // estimated fraction of aberrant cells in the mixture. With the new chromosome, // reset the fraction to the default value. args->query_sample.cell_frac = args->query_sample.cell_frac_dflt; args->control_sample.cell_frac = args->control_sample.cell_frac_dflt; args->query_sample.baf_dev2 = args->query_sample.baf_dev2_dflt; args->control_sample.baf_dev2 = args->control_sample.baf_dev2_dflt; set_gauss_params(args, &args->query_sample); if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample); if ( args->optimize_frac ) { int niter = 0; fprintf(bcftools_stderr,"Attempting to estimate the fraction of aberrant cells (chr %s):\n", bcf_hdr_id2name(args->hdr,args->prev_rid)); do { fprintf(bcftools_stderr,"\t.. %f %f", args->query_sample.cell_frac,args->query_sample.baf_dev2); if ( args->control_sample.name ) fprintf(bcftools_stderr,"\t.. %f %f", args->control_sample.cell_frac,args->control_sample.baf_dev2); fprintf(bcftools_stderr,"\n"); set_emission_probs(args); hmm_run_fwd_bwd(hmm, args->nsites, args->eprob, args->sites); } while ( update_args(args) && ++niter<20 ); if ( niter>=20 ) { // no convergence args->query_sample.cell_frac = args->query_sample.cell_frac_dflt; args->control_sample.cell_frac = args->control_sample.cell_frac_dflt; args->query_sample.baf_dev2 = args->query_sample.baf_dev2_dflt; args->control_sample.baf_dev2 = args->control_sample.baf_dev2_dflt; set_gauss_params(args, &args->query_sample); if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample); } fprintf(bcftools_stderr,"\t.. %f %f", args->query_sample.cell_frac,args->query_sample.baf_dev2); if ( args->control_sample.name ) fprintf(bcftools_stderr,"\t.. %f %f", args->control_sample.cell_frac,args->control_sample.baf_dev2); fprintf(bcftools_stderr,"\n"); fprintf(args->query_sample.summary_fh,"CF\t%s\t%d\t%d\t%.2f\t%f\n", bcf_hdr_id2name(args->hdr,args->prev_rid),args->sites[0]+1,args->sites[args->nsites-1]+1, args->query_sample.cell_frac,sqrt(args->query_sample.baf_dev2)); if ( args->control_sample.name ) { fprintf(args->control_sample.summary_fh,"CF\t%s\t%d\t%d\t%.2f\t%f\n", bcf_hdr_id2name(args->hdr,args->prev_rid),args->sites[0]+1,args->sites[args->nsites-1]+1, args->control_sample.cell_frac,sqrt(args->control_sample.baf_dev2)); fprintf(args->summary_fh,"CF\t%s\t%d\t%d\t%.2f\t%.2f\t%f\t%f\n", bcf_hdr_id2name(args->hdr,args->prev_rid),args->sites[0]+1,args->sites[args->nsites-1]+1, args->query_sample.cell_frac, args->control_sample.cell_frac, sqrt(args->query_sample.baf_dev2), sqrt(args->control_sample.baf_dev2)); } } set_emission_probs(args); while ( args->baum_welch_th!=0 ) { int nstates = hmm_get_nstates(hmm); double ori_ii = avg_ii_prob(nstates,hmm_get_tprob(hmm)); hmm_run_baum_welch(hmm, args->nsites, args->eprob, args->sites); double new_ii = avg_ii_prob(nstates,hmm_get_tprob(hmm)); fprintf(bcftools_stderr,"%e\t%e\t%e\n", ori_ii,new_ii,new_ii-ori_ii); double *tprob = init_tprob_matrix(nstates, 1-new_ii, args->same_prob); hmm_set_tprob(args->hmm, tprob, 10000); double *tprob_arr = hmm_get_tprob(hmm); free(tprob); if ( fabs(new_ii - ori_ii) < args->baum_welch_th ) { int i,j; for (i=0; insites, args->eprob, args->sites); hmm_run_fwd_bwd(hmm, args->nsites, args->eprob, args->sites); // Output the results uint8_t *vpath = hmm_get_viterbi_path(hmm); double qual = 0, *fwd = hmm_get_fwd_bwd_prob(hmm); int i,j, isite, start_cn = vpath[0], start_pos = args->sites[0], istart_pos = 0; int ctrl_ntot = 0, smpl_ntot = 0, ctrl_nhet = 0, smpl_nhet = 0; for (isite=0; isitensites; isite++) { int state = vpath[args->nstates*isite]; double *pval = fwd + isite*args->nstates; qual += pval[start_cn]; // output CN and fwd-bwd likelihood for each site if ( args->query_sample.cn_fh ) { fprintf(args->query_sample.cn_fh, "%s\t%d\t%c", bcf_hdr_id2name(args->hdr,args->prev_rid), args->sites[isite]+1, copy_number_state(args,state,0)); if ( !args->control_sample.cn_fh ) for (i=0; instates; i++) fprintf(args->query_sample.cn_fh, "\t%f", pval[i]); else for (i=0; iquery_sample.cn_fh, "\t%f", sum); } fprintf(args->query_sample.cn_fh, "\n"); if ( args->query_sample.baf[isite]>=0 ) // if non-missing { if ( BAF_LIKELY_HET(args->query_sample.baf[isite]) ) smpl_nhet++; smpl_ntot++; } } if ( args->control_sample.cn_fh ) { fprintf(args->control_sample.cn_fh, "%s\t%d\t%c", bcf_hdr_id2name(args->hdr,args->prev_rid), args->sites[isite]+1, copy_number_state(args,state,1)); for (i=0; icontrol_sample.cn_fh, "\t%f", sum); } fprintf(args->control_sample.cn_fh, "\n"); if ( args->control_sample.baf[isite]>=0 ) // if non-missing { if ( BAF_LIKELY_HET(args->control_sample.baf[isite]) ) ctrl_nhet++; ctrl_ntot++; } } if ( start_cn != state ) { char start_cn_query = copy_number_state(args,start_cn,0); qual = phred_score(1 - qual/(isite - istart_pos)); fprintf(args->query_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n", bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_query,qual,smpl_ntot,smpl_nhet); if ( args->control_sample.name ) { // regions 0-based, half-open char start_cn_ctrl = copy_number_state(args,start_cn,1); fprintf(args->control_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n", bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_ctrl,qual,ctrl_ntot,ctrl_nhet); fprintf(args->summary_fh,"RG\t%s\t%d\t%d\t%c\t%c\t%.1f\t%d\t%d\t%d\t%d\n", bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_query,start_cn_ctrl,qual,smpl_ntot,smpl_nhet,ctrl_ntot,ctrl_nhet); } istart_pos = isite; start_pos = args->sites[isite]; start_cn = state; qual = 0; smpl_ntot = smpl_nhet = ctrl_ntot = ctrl_nhet = 0; } } qual = phred_score(1 - qual/(isite - istart_pos)); char start_cn_query = copy_number_state(args,start_cn,0); fprintf(args->query_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n", bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_query,qual,smpl_ntot,smpl_nhet); if ( args->control_sample.name ) { char start_cn_ctrl = copy_number_state(args,start_cn,1); fprintf(args->control_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n", bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_ctrl,qual,ctrl_ntot,ctrl_nhet); fprintf(args->summary_fh,"RG\t%s\t%d\t%d\t%c\t%c\t%.1f\t%d\t%d\t%d\t%d\n", bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_query,start_cn_ctrl,qual,smpl_ntot,smpl_nhet,ctrl_ntot,ctrl_nhet); } } static int parse_lrr_baf(sample_t *smpl, bcf_fmt_t *baf_fmt, bcf_fmt_t *lrr_fmt, float *baf, float *lrr) { *baf = ((float*)(baf_fmt->p + baf_fmt->size*smpl->idx))[0]; if ( bcf_float_is_missing(*baf) || isnan(*baf) ) *baf = -0.1; // arbitrary negative value == missing value if ( lrr_fmt ) { *lrr = ((float*)(lrr_fmt->p + lrr_fmt->size*smpl->idx))[0]; if ( bcf_float_is_missing(*lrr) || isnan(*lrr) ) { *lrr = 0; *baf = -0.1; } } else *lrr = 0; return *baf<0 ? 0 : 1; } static void cnv_next_line(args_t *args, bcf1_t *line) { if ( !line ) { // Done, flush viterbi cnv_flush_viterbi(args); return; } if ( line->rid!=args->prev_rid ) { // New chromosome cnv_flush_viterbi(args); args->prev_rid = line->rid; args->nsites = 0; args->nRR = args->nAA = args->nRA = 0; } // Process line args->ntot++; bcf_fmt_t *baf_fmt, *lrr_fmt = NULL; if ( !(baf_fmt = bcf_get_fmt(args->hdr, line, "BAF")) ) return; if ( args->lrr_bias>0 && !(lrr_fmt = bcf_get_fmt(args->hdr, line, "LRR")) ) return; float baf1,lrr1,baf2,lrr2; int ret = 0; ret += parse_lrr_baf(&args->query_sample, baf_fmt,lrr_fmt,&baf1,&lrr1); ret += parse_lrr_baf(&args->control_sample,baf_fmt,lrr_fmt,&baf2,&lrr2); if ( !ret ) return; // Realloc buffers needed to store observed data and used by viterbi and fwd-bwd args->nsites++; int m = args->msites; hts_expand(uint32_t,args->nsites,args->msites,args->sites); if ( args->msites!=m ) { args->eprob = (double*) realloc(args->eprob,sizeof(double)*args->msites*args->nstates); if ( args->control_sample.name ) { args->control_sample.lrr = (float*) realloc(args->control_sample.lrr,sizeof(float)*args->msites); args->control_sample.baf = (float*) realloc(args->control_sample.baf,sizeof(float)*args->msites); } args->query_sample.lrr = (float*) realloc(args->query_sample.lrr,sizeof(float)*args->msites); args->query_sample.baf = (float*) realloc(args->query_sample.baf,sizeof(float)*args->msites); if ( args->af_fname ) args->nonref_afs = (float*) realloc(args->nonref_afs,sizeof(float)*args->msites); } args->sites[args->nsites-1] = line->pos; args->query_sample.lrr[args->nsites-1] = lrr1; args->query_sample.baf[args->nsites-1] = baf1; if ( args->af_fname ) { double alt_freq; args->nonref_afs[args->nsites-1] = read_AF(args->files->targets,line,&alt_freq)<0 ? args->nonref_af_dflt : alt_freq; } if ( args->control_sample.name ) { args->control_sample.lrr[args->nsites-1] = lrr2; args->control_sample.baf[args->nsites-1] = baf2; if ( baf2>=0 ) // skip missing values fprintf(args->control_sample.dat_fh,"%s\t%"PRId64"\t%.3f\t%.3f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), (int64_t) line->pos+1,baf2,lrr2); } if ( baf1>=0 ) // skip missing values fprintf(args->query_sample.dat_fh,"%s\t%"PRId64"\t%.3f\t%.3f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), (int64_t) line->pos+1,baf1,lrr1); if ( baf1>=0 ) { if ( baf1<1/5. ) args->nRR++; else if ( baf1>4/5. ) args->nAA++; else args->nRA++; } args->nused++; } static void usage(args_t *args) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R\n"); fprintf(bcftools_stderr, " Ratio intensity (LRR). The HMM considers the following copy number states: CN 2\n"); fprintf(bcftools_stderr, " (normal), 1 (single-copy loss), 0 (complete loss), 3 (single-copy gain)\n"); fprintf(bcftools_stderr, "Usage: bcftools cnv [OPTIONS] FILE.vcf\n"); fprintf(bcftools_stderr, "General Options:\n"); fprintf(bcftools_stderr, " -c, --control-sample STRING Optional control sample name to highlight differences\n"); fprintf(bcftools_stderr, " -f, --AF-file FILE Read allele frequencies from file (CHR\\tPOS\\tREF,ALT\\tAF)\n"); fprintf(bcftools_stderr, " -o, --output-dir PATH \n"); fprintf(bcftools_stderr, " -p, --plot-threshold FLOAT Plot aberrant chromosomes with quality at least FLOAT\n"); fprintf(bcftools_stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(bcftools_stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(bcftools_stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " -s, --query-sample STRING Query samply name\n"); fprintf(bcftools_stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(bcftools_stderr, "HMM Options:\n"); fprintf(bcftools_stderr, " -a, --aberrant FLOAT[,FLOAT] Fraction of aberrant cells in query and control [1.0,1.0]\n"); fprintf(bcftools_stderr, " -b, --BAF-weight FLOAT Relative contribution from BAF [1]\n"); fprintf(bcftools_stderr, " -d, --BAF-dev FLOAT[,FLOAT] Expected BAF deviation in query and control [0.04,0.04]\n"); // experimental fprintf(bcftools_stderr, " -e, --err-prob FLOAT Uniform error probability [1e-4]\n"); fprintf(bcftools_stderr, " -k, --LRR-dev FLOAT[,FLOAT] Expected LRR deviation [0.2,0.2]\n"); // experimental fprintf(bcftools_stderr, " -l, --LRR-weight FLOAT Relative contribution from LRR [0.2]\n"); fprintf(bcftools_stderr, " -L, --LRR-smooth-win INT Window of LRR moving average smoothing [10]\n"); fprintf(bcftools_stderr, " -O, --optimize FLOAT Estimate fraction of aberrant cells down to FLOAT [1.0]\n"); fprintf(bcftools_stderr, " -P, --same-prob FLOA> Prior probability of -s/-c being the same [0.5]\n"); fprintf(bcftools_stderr, " -x, --xy-prob FLOAT P(x|y) transition probability [1e-9]\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int main_vcfcnv(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->files = bcf_sr_init(); args->plot_th = 1e9; // by default plot none args->nonref_af_dflt = 0.1; args->lrr_smooth_win = 10; args->query_sample.cell_frac_dflt = 1; args->control_sample.cell_frac_dflt = 1; // How much FORMAT/LRR and FORMAT/BAF matter args->lrr_bias = 0.2; args->baf_bias = 1.0; args->err_prob = 1e-4; // Transition probability to a different state and the prior of both samples being the same args->ij_prob = 1e-9; args->same_prob = 0.5; // Squared std dev of BAF and LRR values (gaussian noise), estimated from real data (hets, one sample, one chr) args->query_sample.baf_dev2_dflt = args->control_sample.baf_dev2_dflt = 0.04*0.04; // illumina: 0.03 args->query_sample.lrr_dev2 = args->control_sample.lrr_dev2 = 0.2*0.2; //0.20*0.20; // illumina: 0.18 int regions_is_file = 0, targets_is_file = 0; int regions_overlap = 1; int targets_overlap = 0; static struct option loptions[] = { {"BAF-dev",1,0,'d'}, {"LRR-dev",1,0,'k'}, {"LRR-smooth-win",1,0,'L'}, {"AF-file",1,0,'f'}, {"baum-welch",1,0,'W'}, // hidden {"optimize",1,0,'O'}, {"aberrant",1,0,'a'}, {"err-prob",1,0,'e'}, {"BAF-weight",1,0,'b'}, {"LRR-weight",1,0,'l'}, {"same-prob",1,0,'P'}, {"xy-prob",1,0,'x'}, {"query-sample",1,0,'s'}, {"control-sample",1,0,'c'}, {"targets",1,0,'t'}, {"targets-file",1,0,'T'}, {"targets-overlap",required_argument,NULL,4}, {"regions",1,0,'r'}, {"regions-file",1,0,'R'}, {"regions-overlap",required_argument,NULL,3}, {"plot-threshold",1,0,'p'}, {"output-dir",1,0,'o'}, {0,0,0,0} }; char *tmp = NULL; while ((c = getopt_long(argc, argv, "h?r:R:t:T:s:o:p:l:T:c:b:P:x:e:O:W::f:a:L:d:k:",loptions,NULL)) >= 0) { switch (c) { case 'L': args->lrr_smooth_win = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse: --LRR-smooth-win %s\n", optarg); break; case 'f': args->af_fname = optarg; break; case 'O': args->optimize_frac = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -O %s\n", optarg); break; case 'd': args->query_sample.baf_dev2_dflt = strtod(optarg,&tmp); if ( *tmp ) { if ( *tmp!=',') error("Could not parse: -d %s\n", optarg); args->control_sample.baf_dev2_dflt = strtod(tmp+1,&tmp); if ( *tmp ) error("Could not parse: -d %s\n", optarg); } else args->control_sample.baf_dev2_dflt = args->query_sample.baf_dev2_dflt; args->query_sample.baf_dev2_dflt *= args->query_sample.baf_dev2_dflt; args->control_sample.baf_dev2_dflt *= args->control_sample.baf_dev2_dflt; break; case 'k': args->query_sample.lrr_dev2 = strtod(optarg,&tmp); if ( *tmp ) { if ( *tmp!=',') error("Could not parse: -k %s\n", optarg); args->control_sample.lrr_dev2 = strtod(tmp+1,&tmp); if ( *tmp ) error("Could not parse: -d %s\n", optarg); } else args->control_sample.lrr_dev2 = args->query_sample.lrr_dev2; args->query_sample.lrr_dev2 *= args->query_sample.lrr_dev2; args->control_sample.lrr_dev2 *= args->control_sample.lrr_dev2; break; case 'a': args->query_sample.cell_frac_dflt = strtod(optarg,&tmp); if ( *tmp ) { if ( *tmp!=',') error("Could not parse: -a %s\n", optarg); args->control_sample.cell_frac_dflt = strtod(tmp+1,&tmp); if ( *tmp ) error("Could not parse: -a %s\n", optarg); } break; case 'W': args->baum_welch_th = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -W %s\n", optarg); break; case 'e': args->err_prob = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -e %s\n", optarg); break; case 'b': args->baf_bias = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -b %s\n", optarg); break; case 'x': args->ij_prob = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -x %s\n", optarg); break; case 'P': args->same_prob = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -P %s\n", optarg); break; case 'l': args->lrr_bias = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -l %s\n", optarg); break; case 'p': args->plot_th = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -p %s\n", optarg); break; case 'o': args->output_dir = optarg; break; case 's': args->query_sample.name = strdup(optarg); break; case 'c': args->control_sample.name = optarg; break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; targets_is_file = 1; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 3 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 4 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 'h': case '?': usage(args); break; default: error("Unknown argument: %s\n", optarg); } } char *fname = NULL; if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; } else fname = argv[optind]; if ( !fname ) usage(args); if ( !args->output_dir ) error("Expected -o option\n"); if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } if ( args->af_fname ) { if ( bcf_sr_set_targets(args->files, args->af_fname, 1, 3)<0 ) error("Failed to read the targets: %s\n", args->af_fname); } if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); init_data(args); while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = bcf_sr_get_line(args->files,0); cnv_next_line(args, line); } cnv_next_line(args, NULL); create_plots(args); fprintf(bcftools_stderr,"Number of lines: total/processed: %d/%d\n", args->ntot,args->nused); destroy_data(args); free(args); return 0; } pysam-0.23.0/bcftools/vcfconcat.c000066400000000000000000001451041475062545500166740ustar00rootroot00000000000000/* vcfconcat.c -- Concatenate or combine VCF/BCF files. Copyright (C) 2013-2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include // for hts_get_bgzfp() #include #include #include #include "bcftools.h" typedef struct _args_t { bcf_srs_t *files; htsFile *out_fh; int output_type, n_threads, record_cmd_line, clevel; bcf_hdr_t *out_hdr; int *seen_seq; char *index_fn; int write_index; // phasing int *start_pos, start_tid, ifname; int *swap_phase, nswap, *nmatch, *nmism; bcf1_t **buf; uint8_t *buf_mask; int nbuf, mbuf, prev_chr, min_PQ, prev_pos_check; int32_t *GTa, *GTb, mGTa, mGTb, *phase_qual, *phase_set; char **argv, *output_fname, *file_list, **fnames, *remove_dups, *regions_list; int argc, nfnames, allow_overlaps, phased_concat, regions_is_file, regions_overlap; int compact_PS, phase_set_changed, naive_concat, naive_concat_trust_headers; int verbose, explicit_output_type, ligate_force, ligate_warn; int sites_only; htsThreadPool *tpool; } args_t; static bcf_hdr_t *drop_hdr_genotypes(args_t *args, bcf_hdr_t *hdr) { if ( !args->sites_only ) return hdr; bcf_hdr_t *rmme = hdr; hdr = bcf_hdr_subset(rmme, 0, 0, 0); bcf_hdr_remove(hdr, BCF_HL_FMT, NULL); bcf_hdr_destroy(rmme); return hdr; } static void init_data(args_t *args) { bcf1_t *line = NULL; // With phased concat, the chunks overlap and come in the right order. To // avoid opening all files at once, store start positions to recognise need // for the next one. This way we can keep only two open chunks at once. if ( args->phased_concat ) { args->start_pos = (int*) malloc(sizeof(int)*args->nfnames); line = bcf_init(); } if ( args->verbose ) fprintf(stderr,"Checking the headers and starting positions of %d files\n", args->nfnames); kstring_t str = {0,0,0}; int i, prev_chrid = -1; for (i=0; infnames; i++) { htsFile *fp = hts_open(args->fnames[i], "r"); if ( !fp ) error("Failed to open: %s\n", args->fnames[i]); bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to parse header: %s\n", args->fnames[i]); hdr = drop_hdr_genotypes(args, hdr); args->out_hdr = bcf_hdr_merge(args->out_hdr,hdr); if ( bcf_hdr_nsamples(hdr) != bcf_hdr_nsamples(args->out_hdr) ) error("Different number of samples in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]); int j; for (j=0; jout_hdr->samples[j],hdr->samples[j]) ) error("Different sample names in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]); if ( args->phased_concat ) { int ret = bcf_read(fp, hdr, line); if ( ret!=0 ) args->start_pos[i] = -2; // empty file else { int chrid = bcf_hdr_id2int(args->out_hdr,BCF_DT_CTG,bcf_seqname(hdr,line)); args->start_pos[i] = chrid==prev_chrid ? line->pos : -1; prev_chrid = chrid; } } bcf_hdr_destroy(hdr); if ( hts_close(fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fnames[i]); } free(str.s); if ( line ) bcf_destroy(line); args->seen_seq = (int*) calloc(args->out_hdr->n[BCF_DT_CTG],sizeof(int)); if ( args->phased_concat ) { bcf_hdr_append(args->out_hdr,"##FORMAT="); bcf_hdr_append(args->out_hdr,"##FORMAT="); } if (args->record_cmd_line) bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_concat"); char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno)); if ( args->allow_overlaps || args->phased_concat ) { args->files = bcf_sr_init(); args->files->require_index = 1; } if ( args->n_threads ) { if ( args->files ) { if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n"); args->tpool = args->files->p; } else { args->tpool = (htsThreadPool*) calloc(1, sizeof(htsThreadPool)); if ( !args->tpool ) error("Failed to allocate memory\n"); if ( !(args->tpool->pool = hts_tpool_init(args->n_threads)) ) error("Failed to initialize %d threads\n",args->n_threads); } hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->tpool); } if ( bcf_hdr_write(args->out_fh, args->out_hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname); if ( init_index2(args->out_fh,args->out_hdr,args->output_fname, &args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->output_fname); if ( args->allow_overlaps ) { if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, args->regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( args->remove_dups ) { if ( !strcmp(args->remove_dups,"snps") ) args->files->collapse |= COLLAPSE_SNPS; else if ( !strcmp(args->remove_dups,"indels") ) args->files->collapse |= COLLAPSE_INDELS; else if ( !strcmp(args->remove_dups,"both") ) args->files->collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS; else if ( !strcmp(args->remove_dups,"any") ) args->files->collapse |= COLLAPSE_ANY; else if ( !strcmp(args->remove_dups,"all") ) args->files->collapse |= COLLAPSE_ANY; else if ( !strcmp(args->remove_dups,"none") ) args->files->collapse = COLLAPSE_NONE; else if ( !strcmp(args->remove_dups,"exact") ) args->files->collapse = COLLAPSE_NONE; else error("The -D string \"%s\" not recognised.\n", args->remove_dups); } for (i=0; infnames; i++) if ( !bcf_sr_add_reader(args->files,args->fnames[i]) ) error("Failed to open %s: %s\n", args->fnames[i],bcf_sr_strerror(args->files->errnum)); } else if ( args->phased_concat ) { // Remove empty files from the list int nok = 0; while (1) { while ( noknfnames && args->start_pos[nok]!=-2 ) nok++; if ( nok==args->nfnames ) break; i = nok; while ( infnames && args->start_pos[i]==-2 ) i++; if ( i==args->nfnames ) break; int tmp = args->start_pos[nok]; args->start_pos[nok] = args->start_pos[i]; args->start_pos[i] = tmp; char *str = args->fnames[nok]; args->fnames[nok] = args->fnames[i]; args->fnames[i] = str; } for (i=nok; infnames; i++) free(args->fnames[i]); args->nfnames = nok; for (i=1; infnames; i++) if ( args->start_pos[i-1]!=-1 && args->start_pos[i]!=-1 && args->start_pos[i]start_pos[i-1] ) error("The files not in ascending order: %d in %s, %d in %s\n", args->start_pos[i-1]+1,args->fnames[i-1],args->start_pos[i]+1,args->fnames[i]); args->prev_chr = -1; args->swap_phase = (int*) calloc(bcf_hdr_nsamples(args->out_hdr),sizeof(int)); args->nmatch = (int*) calloc(bcf_hdr_nsamples(args->out_hdr),sizeof(int)); args->nmism = (int*) calloc(bcf_hdr_nsamples(args->out_hdr),sizeof(int)); args->phase_qual = (int32_t*) malloc(bcf_hdr_nsamples(args->out_hdr)*sizeof(int32_t)); args->phase_set = (int32_t*) malloc(bcf_hdr_nsamples(args->out_hdr)*sizeof(int32_t)); args->ifname = 0; } } static void destroy_data(args_t *args) { int i; if ( args->out_fh ) { if ( args->write_index ) { if ( bcf_idx_save(args->out_fh)<0 ) { if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n",args->output_fname?args->output_fname:"stdout"); } if ( args->tpool && !args->files ) { hts_tpool_destroy(args->tpool->pool); free(args->tpool); } if ( args->files ) bcf_sr_destroy(args->files); if ( args->out_hdr ) bcf_hdr_destroy(args->out_hdr); free(args->seen_seq); free(args->start_pos); free(args->swap_phase); for (i=0; imbuf; i++) bcf_destroy(args->buf[i]); free(args->buf); free(args->buf_mask); free(args->GTa); free(args->GTb); free(args->nmatch); free(args->nmism); free(args->phase_qual); free(args->phase_set); for (i=0; infnames; i++) free(args->fnames[i]); free(args->fnames); } int vcf_write_line(htsFile *fp, kstring_t *line); #define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; } static void phase_update(args_t *args, bcf_hdr_t *hdr, bcf1_t *rec) { int i, nGTs = bcf_get_genotypes(hdr, rec, &args->GTa, &args->mGTa); if ( nGTs <= 0 ) return; // GT field is not present for (i=0; iswap_phase[i] ) continue; int *gt = &args->GTa[i*2]; if ( bcf_gt_is_missing(gt[0]) || gt[1]==bcf_int32_vector_end ) continue; if ( !bcf_gt_is_phased(gt[1]) ) continue; SWAP(int, gt[0], gt[1]); gt[1] |= 1; } bcf_update_genotypes(hdr,rec,args->GTa,nGTs); } static void phased_flush(args_t *args) { if ( !args->nbuf ) return; bcf_hdr_t *ahdr = args->files->readers[0].header; bcf_hdr_t *bhdr = args->files->readers[1].header; int i, j, nsmpl = bcf_hdr_nsamples(args->out_hdr); static int gt_absent_warned = 0; for (i=0; inbuf; i+=2) { if ( args->buf_mask[i/2]!=3 ) continue; bcf1_t *arec = args->buf[i]; bcf1_t *brec = args->buf[i+1]; int nGTs = bcf_get_genotypes(ahdr, arec, &args->GTa, &args->mGTa); if ( nGTs < 0 ) { if ( !gt_absent_warned ) { fprintf(stderr,"GT is not present at %s:%"PRId64". (This warning is printed only once.)\n", bcf_seqname(ahdr,arec), (int64_t) arec->pos+1); gt_absent_warned = 1; } continue; } if ( nGTs != 2*nsmpl ) continue; // not diploid nGTs = bcf_get_genotypes(bhdr, brec, &args->GTb, &args->mGTb); if ( nGTs < 0 ) { if ( !gt_absent_warned ) { fprintf(stderr,"GT is not present at %s:%"PRId64". (This warning is printed only once.)\n", bcf_seqname(bhdr,brec), (int64_t) brec->pos+1); gt_absent_warned = 1; } continue; } if ( nGTs != 2*nsmpl ) continue; // not diploid for (j=0; jGTa[j*2]; int *gtb = &args->GTb[j*2]; if ( gta[1]==bcf_int32_vector_end || gtb[1]==bcf_int32_vector_end ) continue; if ( bcf_gt_is_missing(gta[0]) || bcf_gt_is_missing(gta[1]) || bcf_gt_is_missing(gtb[0]) || bcf_gt_is_missing(gtb[1]) ) continue; if ( !bcf_gt_is_phased(gta[1]) || !bcf_gt_is_phased(gtb[1]) ) continue; if ( bcf_gt_allele(gta[0])==bcf_gt_allele(gta[1]) || bcf_gt_allele(gtb[0])==bcf_gt_allele(gtb[1]) ) continue; if ( bcf_gt_allele(gta[0])==bcf_gt_allele(gtb[0]) && bcf_gt_allele(gta[1])==bcf_gt_allele(gtb[1]) ) { if ( args->swap_phase[j] ) args->nmism[j]++; else args->nmatch[j]++; } if ( bcf_gt_allele(gta[0])==bcf_gt_allele(gtb[1]) && bcf_gt_allele(gta[1])==bcf_gt_allele(gtb[0]) ) { if ( args->swap_phase[j] ) args->nmatch[j]++; else args->nmism[j]++; } } } for (i=0; inbuf/2; i+=2) { bcf1_t *rec; bcf_hdr_t *hdr; int mask = args->buf_mask[i/2]; if ( mask & 1 ) { rec = args->buf[i]; hdr = args->files->readers[0].header; } else { rec = args->buf[i+1]; hdr = args->files->readers[1].header; } bcf_translate(args->out_hdr, hdr, rec); if ( args->nswap && (mask&1) ) phase_update(args, args->out_hdr, rec); if ( !args->compact_PS || args->phase_set_changed ) { bcf_update_format_int32(args->out_hdr,rec,"PS",args->phase_set,nsmpl); args->phase_set_changed = 0; } if ( bcf_write(args->out_fh, args->out_hdr, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); if ( rec->pos < args->prev_pos_check ) error("FIXME, disorder: %s:%"PRId64" vs %d [1]\n", bcf_seqname(hdr,rec),(int64_t)rec->pos+1,args->prev_pos_check+1); args->prev_pos_check = rec->pos; } args->nswap = 0; for (j=0; jnmatch[j] >= args->nmism[j] ) args->swap_phase[j] = 0; else { args->swap_phase[j] = 1; args->nswap++; } if ( args->nmatch[j] && args->nmism[j] ) { // Entropy-inspired quality. The factor 0.7 shifts and scales to (0,1) double f = (double)args->nmatch[j]/(args->nmatch[j]+args->nmism[j]); args->phase_qual[j] = 99*(0.7 + f*log(f) + (1-f)*log(1-f))/0.7; } else args->phase_qual[j] = 99; args->nmatch[j] = 0; args->nmism[j] = 0; } int PQ_printed = 0; for (; inbuf; i+=2) { bcf1_t *rec; bcf_hdr_t *hdr; int mask = args->buf_mask[i/2]; if ( mask & 2 ) { rec = args->buf[i+1]; hdr = args->files->readers[1].header; } else { rec = args->buf[i]; hdr = args->files->readers[0].header; } bcf_translate(args->out_hdr, hdr, rec); if ( !PQ_printed && mask==3 ) { bcf_update_format_int32(args->out_hdr,rec,"PQ",args->phase_qual,nsmpl); PQ_printed = 1; for (j=0; jphase_qual[j] < args->min_PQ ) { args->phase_set[j] = rec->pos+1; args->phase_set_changed = 1; } else if ( args->compact_PS ) args->phase_set[j] = bcf_int32_missing; } if ( args->nswap ) phase_update(args, args->out_hdr, rec); if ( !args->compact_PS || args->phase_set_changed ) { bcf_update_format_int32(args->out_hdr,rec,"PS",args->phase_set,nsmpl); args->phase_set_changed = 0; } if ( bcf_write(args->out_fh, args->out_hdr, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); if ( rec->pos < args->prev_pos_check ) error("FIXME, disorder: %s:%"PRId64" vs %d [2]\n", bcf_seqname(hdr,rec),(int64_t)rec->pos+1,args->prev_pos_check+1); args->prev_pos_check = rec->pos; } args->nbuf = 0; } static void phased_push(args_t *args, bcf1_t *arec, bcf1_t *brec, int is_overlap) { bcf_hdr_t *ahdr = arec ? bcf_sr_get_header(args->files,0) : NULL; bcf_hdr_t *bhdr = brec ? bcf_sr_get_header(args->files,1) : NULL; if ( arec && arec->errcode ) error("Parse error at %s:%"PRId64", cannot proceed: %s\n", bcf_seqname(ahdr,arec),(int64_t) arec->pos+1, args->files->readers[0].fname); if ( brec && brec->errcode ) error("Parse error at %s:%"PRId64", cannot proceed: %s\n", bcf_seqname(bhdr,brec),(int64_t) brec->pos+1, args->files->readers[1].fname); int i, nsmpl = bcf_hdr_nsamples(args->out_hdr); int chr_id = arec ? bcf_hdr_name2id(args->out_hdr,bcf_seqname(ahdr,arec)) : bcf_hdr_name2id(args->out_hdr,bcf_seqname(bhdr,brec)); if ( args->prev_chr<0 || args->prev_chr!=chr_id ) { if ( args->prev_chr>=0 ) phased_flush(args); for (i=0; iphase_set[i] = arec ? arec->pos+1 : brec->pos+1; args->phase_set_changed = 1; if ( args->seen_seq[chr_id] ) error("The chromosome block %s is not contiguous\n", arec ? bcf_seqname(ahdr,arec) : bcf_seqname(bhdr,brec)); args->seen_seq[chr_id] = 1; args->prev_chr = chr_id; args->prev_pos_check = -1; } if ( !is_overlap ) { assert(arec); bcf_translate(args->out_hdr, ahdr, arec); if ( args->nswap ) phase_update(args, args->out_hdr, arec); if ( !args->compact_PS || args->phase_set_changed ) { bcf_update_format_int32(args->out_hdr,arec,"PS",args->phase_set,nsmpl); args->phase_set_changed = 0; } if ( bcf_write(args->out_fh, args->out_hdr, arec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); if ( arec->pos < args->prev_pos_check ) error("FIXME, disorder: %s:%"PRId64" in %s vs %d written [3]\n", bcf_seqname(ahdr,arec), (int64_t) arec->pos+1,args->files->readers[0].fname, args->prev_pos_check+1); args->prev_pos_check = arec->pos; return; } int m = args->mbuf; args->nbuf += 2; hts_expand(bcf1_t*,args->nbuf,args->mbuf,args->buf); if ( m < args->mbuf ) args->buf_mask = (uint8_t*)realloc(args->buf_mask,sizeof(*args->buf_mask)*args->mbuf); for (i=m; imbuf; i++) args->buf[i] = bcf_init1(); if ( arec ) SWAP(bcf1_t*, args->files->readers[0].buffer[0], args->buf[args->nbuf-2]); if ( brec ) SWAP(bcf1_t*, args->files->readers[1].buffer[0], args->buf[args->nbuf-1]); args->buf_mask[args->nbuf/2-1] = (arec?1:0) | (brec?2:0); } static int _get_active_index(bcf_srs_t *sr) { int i; for (i=0; inreaders; i++) if ( bcf_sr_has_line(sr,i) ) return i; return -1; } static void concat(args_t *args) { static int site_drop_warned = 0; int i; if ( args->phased_concat ) // phased concat { // keep only two open files at a time while ( args->ifname < args->nfnames ) { int new_file = 0; while ( args->files->nreaders < 2 && args->ifname < args->nfnames ) { if ( !bcf_sr_add_reader(args->files,args->fnames[args->ifname]) ) error("Failed to open %s: %s\n", args->fnames[args->ifname],bcf_sr_strerror(args->files->errnum)); new_file = 1; args->ifname++; if ( args->start_pos[args->ifname-1]==-1 ) break; // new chromosome, start with only one file open if ( args->ifname < args->nfnames && args->start_pos[args->ifname]==-1 ) break; // next file starts on a different chromosome } // is there a line from the previous run? Seek the newly opened reader to that position int seek_pos = -1; int seek_chr = -1; if ( bcf_sr_has_line(args->files,0) ) { bcf1_t *line = bcf_sr_get_line(args->files,0); bcf_sr_seek(args->files, bcf_seqname(args->files->readers[0].header,line), line->pos); seek_pos = line->pos; seek_chr = bcf_hdr_name2id(args->out_hdr, bcf_seqname(args->files->readers[0].header,line)); } else if ( new_file ) bcf_sr_seek(args->files,NULL,0); // set to start int nret, ir; while ( (nret = bcf_sr_next_line(args->files)) ) { int is_overlap = args->files->nreaders==1 ? 0 : 1; if ( !bcf_sr_has_line(args->files,0) ) // no input from the first reader { // We are assuming that there is a perfect overlap, sites which are not present in both files are dropped if ( bcf_sr_region_done(args->files,0) ) { phased_flush(args); bcf_sr_remove_reader(args->files, 0); is_overlap = 0; } else if ( args->ligate_warn ) { if ( !site_drop_warned ) { ir = _get_active_index(args->files); fprintf(stderr, "Warning: Dropping the site %s:%"PRId64". The --ligate option is intended for VCFs with perfect\n" " overlap, sites in overlapping regions present in one but missing in other are dropped.\n" " This warning is printed only once.\n", bcf_seqname(bcf_sr_get_header(args->files,ir),bcf_sr_get_line(args->files,ir)), (int64_t) bcf_sr_get_line(args->files,ir)->pos+1); site_drop_warned = 1; } continue; } else if ( !args->ligate_force ) { ir = _get_active_index(args->files); error("Error: The --ligate option is intended for VCFs with perfect overlap, the site %s:%"PRId64" breaks the assumption\n", bcf_seqname(bcf_sr_get_header(args->files,ir),bcf_sr_get_line(args->files,ir)), (int64_t) bcf_sr_get_line(args->files,ir)->pos+1); } } // Get a line to learn about current position ir = _get_active_index(args->files); bcf1_t *line = bcf_sr_get_line(args->files,ir); // This can happen after bcf_sr_seek: indel may start before the coordinate which we seek to. if ( seek_chr>=0 && seek_pos>line->pos && seek_chr==bcf_hdr_name2id(args->out_hdr, bcf_seqname(args->files->readers[ir].header,line)) ) continue; seek_pos = seek_chr = -1; // Check if the position overlaps with the next, yet unopened, reader int must_seek = 0; while ( args->ifname < args->nfnames && args->start_pos[args->ifname]!=-1 && line->pos >= args->start_pos[args->ifname] ) { must_seek = 1; if ( !bcf_sr_add_reader(args->files,args->fnames[args->ifname]) ) error("Failed to open %s: %s\n", args->fnames[args->ifname],bcf_sr_strerror(args->files->errnum)); args->ifname++; } if ( must_seek ) { bcf_sr_seek(args->files, bcf_seqname(args->files->readers[ir].header,line), line->pos); seek_pos = line->pos; seek_chr = bcf_hdr_name2id(args->out_hdr, bcf_seqname(args->files->readers[ir].header,line)); continue; } // We are assuming that there is a perfect overlap, sites which are not present in both files are dropped if ( args->files->nreaders>1 && !bcf_sr_has_line(args->files,1) && !bcf_sr_region_done(args->files,1) && !args->ligate_force ) { if ( args->ligate_warn && !site_drop_warned ) { ir = _get_active_index(args->files); fprintf(stderr, "Warning: Dropping the site %s:%"PRId64". The --ligate option is intended for VCFs with perfect\n" " overlap, sites in overlapping regions present in one but missing in other are dropped.\n" " This warning is printed only once.\n", bcf_seqname(bcf_sr_get_header(args->files,ir),line), (int64_t) line->pos+1); site_drop_warned = 1; } else if ( !args->ligate_warn ) { ir = _get_active_index(args->files); error("Error: The --ligate option is intended for VCFs with perfect overlap, the site %s:%"PRId64" breaks the assumption\n", bcf_seqname(bcf_sr_get_header(args->files,ir),bcf_sr_get_line(args->files,ir)), (int64_t) bcf_sr_get_line(args->files,ir)->pos+1); } continue; } bcf1_t *line0 = bcf_sr_get_line(args->files,0); bcf1_t *line1 = args->files->nreaders > 1 ? bcf_sr_get_line(args->files,1) : NULL; phased_push(args, line0, line1, is_overlap); } if ( args->files->nreaders ) { phased_flush(args); while ( args->files->nreaders ) bcf_sr_remove_reader(args->files, 0); } } } else if ( args->files ) // combining overlapping files, using synced reader { while ( bcf_sr_next_line(args->files) ) { for (i=0; ifiles->nreaders; i++) { bcf1_t *line = bcf_sr_get_line(args->files,i); if ( !line ) continue; if ( args->sites_only ) bcf_subset(args->out_hdr, line, 0, 0); bcf_translate(args->out_hdr, args->files->readers[i].header, line); if ( bcf_write1(args->out_fh, args->out_hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); if ( args->remove_dups ) break; } } } else // concatenate as is { struct timeval t0, t1; kstring_t tmp = {0,0,0}; int prev_chr_id = -1, prev_pos; bcf1_t *line = bcf_init(); for (i=0; infnames; i++) { if ( args->verbose ) { fprintf(stderr,"Concatenating %s", args->fnames[i]); gettimeofday(&t0, NULL); } htsFile *fp = hts_open(args->fnames[i], "r"); if ( !fp ) error("\nFailed to open: %s\n", args->fnames[i]); if ( args->n_threads ) hts_set_opt(fp, HTS_OPT_THREAD_POOL, args->tpool); bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("\nFailed to parse header: %s\n", args->fnames[i]); if ( args->sites_only ) { bcf_hdr_t *hdr_ori = hdr; hdr = bcf_hdr_subset(hdr_ori, 0, 0, 0); bcf_hdr_remove(hdr, BCF_HL_FMT, NULL); bcf_hdr_destroy(hdr_ori); } if ( !fp->is_bin && args->output_type&FT_VCF ) { line->max_unpack = BCF_UN_STR; // if VCF is on both input and output, avoid VCF to BCF conversion while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 ) { char *str = fp->line.s; // remove genotypes if ( args->sites_only ) { int ntab = 0; while ( *str ) { if ( *str == '\t' && ++ntab==8 ) { *str = 0; break; } str++; } str = fp->line.s; } while ( *str && *str!='\t' ) str++; tmp.l = 0; kputsn(fp->line.s,str-fp->line.s,&tmp); int chr_id = bcf_hdr_name2id(args->out_hdr, tmp.s); if ( chr_id<0 ) error("\nThe sequence \"%s\" not defined in the header: %s\n(Quick workaround: index the file.)\n", tmp.s, args->fnames[i]); if ( prev_chr_id!=chr_id ) { prev_pos = -1; if ( args->seen_seq[chr_id] ) error("\nThe chromosome block %s is not contiguous, consider running with -a.\n", tmp.s); } char *end; int pos = strtol(str+1,&end,10) - 1; if ( end==str+1 ) error("Could not parse line: %s\n", fp->line.s); if ( prev_pos > pos ) error("\nThe chromosome block %s is not sorted, consider running with -a.\n", tmp.s); args->seen_seq[chr_id] = 1; prev_chr_id = chr_id; if ( vcf_write_line(args->out_fh, &fp->line)!=0 ) error("\nFailed to write %"PRIu64" bytes\n", (uint64_t)fp->line.l); } } else { // BCF conversion is required line->max_unpack = 0; while ( bcf_read(fp, hdr, line)==0 ) { if ( args->sites_only ) bcf_subset(args->out_hdr, line, 0, 0); bcf_translate(args->out_hdr, hdr, line); if ( prev_chr_id!=line->rid ) { prev_pos = -1; if ( args->seen_seq[line->rid] ) error("\nThe chromosome block %s is not contiguous, consider running with -a.\n", bcf_seqname(args->out_hdr, line)); } if ( prev_pos > line->pos ) error("\nThe chromosome block %s is not sorted, consider running with -a.\n", bcf_seqname(args->out_hdr, line)); args->seen_seq[line->rid] = 1; prev_chr_id = line->rid; if ( bcf_write(args->out_fh, args->out_hdr, line)!=0 ) error("\nFailed to write\n"); } } bcf_hdr_destroy(hdr); hts_close(fp); if ( args->verbose ) { gettimeofday(&t1, NULL); double delta = (t1.tv_sec - t0.tv_sec) * 1e6 + (t1.tv_usec - t0.tv_usec); fprintf(stderr,"\t%f seconds\n",delta/1e6); } } bcf_destroy(line); free(tmp.s); } } int print_vcf_gz_header(BGZF *fp, BGZF *bgzf_out, int print_header, kstring_t *tmp) { char *buffer = (char*) fp->uncompressed_block; // Read the header and find the position of the data block if ( buffer[0]!='#' ) error("Could not parse the header, expected '#', found '%c'\n", buffer[0]); int nskip = 1; // end of the header in the current uncompressed block while (1) { if ( buffer[nskip]=='\n' ) { nskip++; if ( nskip>=fp->block_length ) { kputsn(buffer,nskip,tmp); if ( bgzf_read_block(fp) != 0 ) return -1; if ( !fp->block_length ) break; nskip = 0; } // The header has finished if ( buffer[nskip]!='#' ) { kputsn(buffer,nskip,tmp); break; } } nskip++; if ( nskip>=fp->block_length ) { kputsn(buffer,fp->block_length,tmp); if ( bgzf_read_block(fp) != 0 ) return -1; if ( !fp->block_length ) break; nskip = 0; } } if ( print_header ) { if ( bgzf_write(bgzf_out,tmp->s,tmp->l) != tmp->l ) error("Failed to write %"PRIu64" bytes\n", (uint64_t)tmp->l); tmp->l = 0; } return nskip; } static inline int unpackInt16(const uint8_t *buffer) { return buffer[0] | buffer[1] << 8; } static int check_header(const uint8_t *header) { if ( header[0] != 31 || header[1] != 139 || header[2] != 8 ) return -2; return ((header[3] & 4) != 0 && unpackInt16((uint8_t*)&header[10]) == 6 && header[12] == 'B' && header[13] == 'C' && unpackInt16((uint8_t*)&header[14]) == 2) ? 0 : -1; } static void _check_hrecs(const bcf_hdr_t *hdr0, const bcf_hdr_t *hdr, char *fname0, char *fname) { int j; for (j=0; jnhrec; j++) { bcf_hrec_t *hrec0 = hdr0->hrec[j]; if ( hrec0->type!=BCF_HL_FLT && hrec0->type!=BCF_HL_INFO && hrec0->type!=BCF_HL_FMT && hrec0->type!=BCF_HL_CTG ) continue; // skip fields w/o IDX int itag = bcf_hrec_find_key(hrec0, "ID"); bcf_hrec_t *hrec = bcf_hdr_get_hrec(hdr, hrec0->type, "ID", hrec0->vals[itag], NULL); char *type = NULL; if ( hrec0->type==BCF_HL_FLT ) type = "FILTER"; if ( hrec0->type==BCF_HL_INFO ) type = "INFO"; if ( hrec0->type==BCF_HL_FMT ) type = "FORMAT"; if ( hrec0->type==BCF_HL_CTG ) type = "contig"; if ( !hrec ) error("Cannot use --naive, incompatible headers, the tag %s/%s not present in %s\n",type,hrec0->vals[itag],fname); int idx0 = bcf_hrec_find_key(hrec0, "IDX"); int idx = bcf_hrec_find_key(hrec, "IDX"); if ( idx0<0 || idx<0 ) error("fixme: unexpected IDX<0 for %s/%s in %s or %s\n",type,hrec0->vals[itag],fname0,fname); if ( strcmp(hrec0->vals[idx0],hrec->vals[idx]) ) error("Cannot use --naive, use --naive-force instead: different order the tag %s/%s in %s vs %s\n",type,hrec0->vals[itag],fname0,fname); } } static void naive_concat_check_headers(args_t *args) { fprintf(stderr,"Checking the headers of %d files.\n",args->nfnames); bcf_hdr_t *hdr0 = NULL; int i,j; for (i=0; infnames; i++) { htsFile *fp = hts_open(args->fnames[i], "r"); if ( !fp ) error("Failed to open: %s\n", args->fnames[i]); bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to parse header: %s\n", args->fnames[i]); htsFormat type = *hts_get_format(fp); hts_close(fp); if ( i==0 ) { hdr0 = hdr; continue; } // check the samples if ( bcf_hdr_nsamples(hdr0)!=bcf_hdr_nsamples(hdr) ) error("Cannot concatenate, different number of samples: %d vs %d in %s vs %s\n",bcf_hdr_nsamples(hdr0),bcf_hdr_nsamples(hdr),args->fnames[0],args->fnames[i]); for (j=0; jsamples[j],hdr->samples[j]) ) error("Cannot concatenate, different samples in %s vs %s\n",args->fnames[0],args->fnames[i]); // if BCF, check if tag IDs are consistent in the dictionary of strings if ( type.compression!=bgzf ) error("The --naive option works only for compressed BCFs or VCFs, sorry :-/\n"); _check_hrecs(hdr0,hdr,args->fnames[0],args->fnames[i]); _check_hrecs(hdr,hdr0,args->fnames[i],args->fnames[0]); bcf_hdr_destroy(hdr); } if ( hdr0 ) bcf_hdr_destroy(hdr0); fprintf(stderr,"Done, the headers are compatible.\n"); } static void naive_concat(args_t *args) { if ( !args->naive_concat_trust_headers ) naive_concat_check_headers(args); // only compressed BCF atm BGZF *bgzf_out = bgzf_open(args->output_fname,"w");; htsFormat output_type; output_type.format = (args->output_type & FT_VCF) ? vcf : bcf; output_type.compression = (args->output_type & FT_GZ) ? bgzf : no_compression; struct timeval t0, t1; const size_t page_size = BGZF_MAX_BLOCK_SIZE; uint8_t *buf = (uint8_t*) malloc(page_size); kstring_t tmp = {0,0,0}; int i, file_types = 0; for (i=0; infnames; i++) { if ( args->verbose ) { fprintf(stderr,"Concatenating %s", args->fnames[i]); gettimeofday(&t0, NULL); } htsFile *hts_fp = hts_open(args->fnames[i],"r"); if ( !hts_fp ) error("\nFailed to open: %s\n", args->fnames[i]); htsFormat type = *hts_get_format(hts_fp); if ( type.compression!=bgzf ) error("\nThe --naive option works only for compressed BCFs or VCFs\n"); file_types |= type.format==vcf ? 1 : 2; if ( file_types==3 ) error("\nThe --naive option works only for compressed files of the same type, all BCFs or all VCFs\n"); if ( args->explicit_output_type ) { if ( output_type.format!=type.format ) error("\nThe --naive option works only for the output of the same type, all BCFs or all VCFs\n"); if ( output_type.compression!=type.compression ) error("\nThe --naive option works only for the output of the same compression type\n"); } BGZF *fp = hts_get_bgzfp(hts_fp); if ( !fp || bgzf_read_block(fp) != 0 || !fp->block_length ) error("\nFailed to read %s: %s\n", args->fnames[i], strerror(errno)); int nskip; if ( type.format==bcf ) { const size_t magic_len = 5 + 4; // "Magic" string + header length uint8_t magic[magic_len]; if ( bgzf_read(fp, magic, magic_len) != magic_len ) error("\nFailed to read the BCF header in %s\n", args->fnames[i]); // First five bytes are the "Magic" string if (strncmp((char*)magic, "BCF\2\2", 5) != 0) error("\nInvalid BCF magic string in %s\n", args->fnames[i]); // Next four are the header length (little-endian) tmp.l = le_to_u32(magic + 5); hts_expand(char,tmp.l,tmp.m,tmp.s); if ( bgzf_read(fp, tmp.s, tmp.l) != tmp.l ) error("\nFailed to read the BCF header in %s\n", args->fnames[i]); // write only the first header if ( i==0 ) { if ( bgzf_write(bgzf_out, magic, magic_len) != magic_len ) error("\nFailed to write %zu bytes to %s\n", magic_len,args->output_fname); if ( bgzf_write(bgzf_out, tmp.s, tmp.l) != tmp.l) error("\nFailed to write %"PRId64" bytes to %s\n", (uint64_t)tmp.l,args->output_fname); } nskip = fp->block_offset; } else { nskip = print_vcf_gz_header(fp, bgzf_out, i==0?1:0, &tmp); if ( nskip==-1 ) error("\nError reading %s\n", args->fnames[i]); } // Output all non-header data that were read together with the header block if ( fp->block_length - nskip > 0 ) { if ( bgzf_write(bgzf_out, (char *)fp->uncompressed_block+nskip, fp->block_length-nskip)<0 ) error("\nError: %d\n",fp->errcode); } if ( bgzf_flush(bgzf_out)<0 ) error("\nError: %d\n",bgzf_out->errcode); // Stream the rest of the file as it is, without recompressing, but remove BGZF EOF blocks // The final bgzf eof block will be added by bgzf_close. ssize_t nread, nblock, nwr; const int nheader = 18, neof = 28; const uint8_t *eof = (uint8_t*) "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0"; while (1) { nread = bgzf_raw_read(fp, buf, nheader); if ( !nread ) break; if ( nread != nheader || check_header(buf)!=0 ) error("\nCould not parse the header of a bgzf block: %s\n",args->fnames[i]); nblock = unpackInt16(buf+16) + 1; assert( nblock <= page_size && nblock >= nheader ); nread += bgzf_raw_read(fp, buf+nheader, nblock - nheader); if ( nread!=nblock ) error("\nCould not read %"PRId64" bytes: %s\n",(uint64_t)nblock,args->fnames[i]); if ( nread==neof && !memcmp(buf,eof,neof) ) continue; nwr = bgzf_raw_write(bgzf_out, buf, nread); if ( nwr != nread ) error("\nWrite failed, wrote %"PRId64" instead of %d bytes.\n", (uint64_t)nwr,(int)nread); } if (hts_close(hts_fp)) error("\nClose failed: %s\n",args->fnames[i]); if ( args->verbose ) { gettimeofday(&t1, NULL); double delta = (t1.tv_sec - t0.tv_sec) * 1e6 + (t1.tv_usec - t0.tv_usec); fprintf(stderr,"\t%f seconds\n",delta/1e6); } } free(buf); free(tmp.s); if (bgzf_close(bgzf_out) < 0) error("Error: %d\n",bgzf_out->errcode); } static void usage(args_t *args) { fprintf(stderr, "\n"); fprintf(stderr, "About: Concatenate or combine VCF/BCF files. All source files must have the same sample\n"); fprintf(stderr, " columns appearing in the same order. The program can be used, for example, to\n"); fprintf(stderr, " concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel\n"); fprintf(stderr, " VCF into one. The input files must be sorted by chr and position. The files\n"); fprintf(stderr, " must be given in the correct order to produce sorted VCF on output unless\n"); fprintf(stderr, " the -a, --allow-overlaps option is specified. With the --naive option, the files\n"); fprintf(stderr, " are concatenated without being recompressed, which is very fast.\n"); fprintf(stderr, "Usage: bcftools concat [options] [ [...]]\n"); fprintf(stderr, "\n"); fprintf(stderr, "Options:\n"); fprintf(stderr, " -a, --allow-overlaps First coordinate of the next file can precede last record of the current file.\n"); fprintf(stderr, " -c, --compact-PS Do not output PS tag at each site, only at the start of a new phase set block.\n"); fprintf(stderr, " -d, --rm-dups STRING Output duplicate records present in multiple files only once: \n"); fprintf(stderr, " -D, --remove-duplicates Alias for -d exact\n"); fprintf(stderr, " -f, --file-list FILE Read the list of files from a file.\n"); fprintf(stderr, " -G, --drop-genotypes Drop individual genotype information.\n"); fprintf(stderr, " -l, --ligate Ligate phased VCFs by matching phase at overlapping haplotypes\n"); fprintf(stderr, " --ligate-force Ligate even non-overlapping chunks, keep all sites\n"); fprintf(stderr, " --ligate-warn Drop sites in imperfect overlaps\n"); fprintf(stderr, " --no-version Do not append version and command line to the header\n"); fprintf(stderr, " -n, --naive Concatenate files without recompression, a header check compatibility is performed\n"); fprintf(stderr, " --naive-force Same as --naive, but header compatibility is not checked. Dangerous, use with caution.\n"); fprintf(stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(stderr, " -q, --min-PQ INT Break phase set if phasing quality is lower than [30]\n"); fprintf(stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " --threads INT Use multithreading with worker threads [0]\n"); fprintf(stderr, " -v, --verbose 0|1 Set verbosity level [1]\n"); fprintf(stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(stderr, "\n"); exit(1); } int main_vcfconcat(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->output_fname = "-"; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->min_PQ = 30; args->verbose = 1; args->clevel = -1; static struct option loptions[] = { {"verbose",required_argument,NULL,'v'}, {"naive",no_argument,NULL,'n'}, {"naive-force",no_argument,NULL,7}, {"compact-PS",no_argument,NULL,'c'}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,12}, {"remove-duplicates",no_argument,NULL,'D'}, {"rm-dups",required_argument,NULL,'d'}, {"allow-overlaps",no_argument,NULL,'a'}, {"ligate",no_argument,NULL,'l'}, {"ligate-force",no_argument,NULL,10}, {"ligate-warn",no_argument,NULL,11}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"threads",required_argument,NULL,9}, {"file-list",required_argument,NULL,'f'}, {"min-PQ",required_argument,NULL,'q'}, {"no-version",no_argument,NULL,8}, {"write-index",optional_argument,NULL,'W'}, {"drop-genotypes",no_argument,NULL,'G'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "h:?o:O:f:alq:Dd:Gr:R:cnv:W::",loptions,NULL)) >= 0) { switch (c) { case 'c': args->compact_PS = 1; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; args->regions_is_file = 1; break; case 'd': args->remove_dups = optarg; break; case 'D': args->remove_dups = "exact"; break; case 'q': args->min_PQ = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --min-PQ %s\n", optarg); break; case 'n': args->naive_concat = 1; break; case 'a': args->allow_overlaps = 1; break; case 'l': args->phased_concat = 1; break; case 'f': args->file_list = optarg; break; case 'G': args->sites_only = 1; break; case 'o': args->output_fname = optarg; break; case 'O': args->explicit_output_type = 1; switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } }; if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 10 : args->ligate_force = 1; break; case 11 : args->ligate_warn = 1; break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 8 : args->record_cmd_line = 0; break; case 7 : args->naive_concat = 1; args->naive_concat_trust_headers = 1; break; case 12 : args->regions_overlap = parse_overlap_option(optarg); if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 'v': args->verbose = strtol(optarg, &tmp, 0); if ( *tmp || args->verbose<0 || args->verbose>1 ) error("Error: currently only --verbose 0 or --verbose 1 is supported\n"); break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 'h': case '?': usage(args); break; default: error("Unknown argument: %s\n", optarg); } } while ( optindnfnames++; args->fnames = (char **)realloc(args->fnames,sizeof(char*)*args->nfnames); args->fnames[args->nfnames-1] = strdup(argv[optind]); optind++; } if ( args->ligate_force && args->ligate_warn ) error("The options cannot be combined: --ligate-force and --ligate-warn\n"); if ( args->allow_overlaps && args->phased_concat ) error("The options -a and -l should not be combined. Please run with -l only.\n"); if ( args->sites_only && args->phased_concat ) error("The options --drop-genotypes and --ligate cannot be combined\n"); if ( args->compact_PS && !args->phased_concat ) error("The -c option is intended only with -l\n"); if ( args->file_list ) { if ( args->nfnames ) error("Cannot combine -l with file names on command line.\n"); args->fnames = hts_readlines(args->file_list, &args->nfnames); if ( !args->fnames ) error("Could not read the file: %s\n", args->file_list); } if ( !args->nfnames ) usage(args); if ( args->remove_dups && !args->allow_overlaps ) error("The -D option is supported only with -a\n"); if ( args->regions_list && !args->allow_overlaps ) error("The -r/-R option is supported only with -a\n"); if ( args->naive_concat ) { if ( args->write_index ) error("Error: cannot --write-index in the %s mode\n",args->naive_concat_trust_headers?"--naive-force":"--naive"); if ( args->allow_overlaps ) error("The option --naive cannot be combined with --allow-overlaps\n"); if ( args->phased_concat ) error("The option --naive cannot be combined with --ligate\n"); if ( args->sites_only ) error("The option --naive cannot be combined with --drop-genotypes\n"); naive_concat(args); destroy_data(args); free(args); return 0; } init_data(args); concat(args); destroy_data(args); free(args); return 0; } pysam-0.23.0/bcftools/vcfconcat.c.pysam.c000066400000000000000000001460101475062545500202420ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfconcat.c -- Concatenate or combine VCF/BCF files. Copyright (C) 2013-2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include // for hts_get_bgzfp() #include #include #include #include "bcftools.h" typedef struct _args_t { bcf_srs_t *files; htsFile *out_fh; int output_type, n_threads, record_cmd_line, clevel; bcf_hdr_t *out_hdr; int *seen_seq; char *index_fn; int write_index; // phasing int *start_pos, start_tid, ifname; int *swap_phase, nswap, *nmatch, *nmism; bcf1_t **buf; uint8_t *buf_mask; int nbuf, mbuf, prev_chr, min_PQ, prev_pos_check; int32_t *GTa, *GTb, mGTa, mGTb, *phase_qual, *phase_set; char **argv, *output_fname, *file_list, **fnames, *remove_dups, *regions_list; int argc, nfnames, allow_overlaps, phased_concat, regions_is_file, regions_overlap; int compact_PS, phase_set_changed, naive_concat, naive_concat_trust_headers; int verbose, explicit_output_type, ligate_force, ligate_warn; int sites_only; htsThreadPool *tpool; } args_t; static bcf_hdr_t *drop_hdr_genotypes(args_t *args, bcf_hdr_t *hdr) { if ( !args->sites_only ) return hdr; bcf_hdr_t *rmme = hdr; hdr = bcf_hdr_subset(rmme, 0, 0, 0); bcf_hdr_remove(hdr, BCF_HL_FMT, NULL); bcf_hdr_destroy(rmme); return hdr; } static void init_data(args_t *args) { bcf1_t *line = NULL; // With phased concat, the chunks overlap and come in the right order. To // avoid opening all files at once, store start positions to recognise need // for the next one. This way we can keep only two open chunks at once. if ( args->phased_concat ) { args->start_pos = (int*) malloc(sizeof(int)*args->nfnames); line = bcf_init(); } if ( args->verbose ) fprintf(bcftools_stderr,"Checking the headers and starting positions of %d files\n", args->nfnames); kstring_t str = {0,0,0}; int i, prev_chrid = -1; for (i=0; infnames; i++) { htsFile *fp = hts_open(args->fnames[i], "r"); if ( !fp ) error("Failed to open: %s\n", args->fnames[i]); bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to parse header: %s\n", args->fnames[i]); hdr = drop_hdr_genotypes(args, hdr); args->out_hdr = bcf_hdr_merge(args->out_hdr,hdr); if ( bcf_hdr_nsamples(hdr) != bcf_hdr_nsamples(args->out_hdr) ) error("Different number of samples in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]); int j; for (j=0; jout_hdr->samples[j],hdr->samples[j]) ) error("Different sample names in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]); if ( args->phased_concat ) { int ret = bcf_read(fp, hdr, line); if ( ret!=0 ) args->start_pos[i] = -2; // empty file else { int chrid = bcf_hdr_id2int(args->out_hdr,BCF_DT_CTG,bcf_seqname(hdr,line)); args->start_pos[i] = chrid==prev_chrid ? line->pos : -1; prev_chrid = chrid; } } bcf_hdr_destroy(hdr); if ( hts_close(fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fnames[i]); } free(str.s); if ( line ) bcf_destroy(line); args->seen_seq = (int*) calloc(args->out_hdr->n[BCF_DT_CTG],sizeof(int)); if ( args->phased_concat ) { bcf_hdr_append(args->out_hdr,"##FORMAT="); bcf_hdr_append(args->out_hdr,"##FORMAT="); } if (args->record_cmd_line) bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_concat"); char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno)); if ( args->allow_overlaps || args->phased_concat ) { args->files = bcf_sr_init(); args->files->require_index = 1; } if ( args->n_threads ) { if ( args->files ) { if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n"); args->tpool = args->files->p; } else { args->tpool = (htsThreadPool*) calloc(1, sizeof(htsThreadPool)); if ( !args->tpool ) error("Failed to allocate memory\n"); if ( !(args->tpool->pool = hts_tpool_init(args->n_threads)) ) error("Failed to initialize %d threads\n",args->n_threads); } hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->tpool); } if ( bcf_hdr_write(args->out_fh, args->out_hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname); if ( init_index2(args->out_fh,args->out_hdr,args->output_fname, &args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->output_fname); if ( args->allow_overlaps ) { if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, args->regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( args->remove_dups ) { if ( !strcmp(args->remove_dups,"snps") ) args->files->collapse |= COLLAPSE_SNPS; else if ( !strcmp(args->remove_dups,"indels") ) args->files->collapse |= COLLAPSE_INDELS; else if ( !strcmp(args->remove_dups,"both") ) args->files->collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS; else if ( !strcmp(args->remove_dups,"any") ) args->files->collapse |= COLLAPSE_ANY; else if ( !strcmp(args->remove_dups,"all") ) args->files->collapse |= COLLAPSE_ANY; else if ( !strcmp(args->remove_dups,"none") ) args->files->collapse = COLLAPSE_NONE; else if ( !strcmp(args->remove_dups,"exact") ) args->files->collapse = COLLAPSE_NONE; else error("The -D string \"%s\" not recognised.\n", args->remove_dups); } for (i=0; infnames; i++) if ( !bcf_sr_add_reader(args->files,args->fnames[i]) ) error("Failed to open %s: %s\n", args->fnames[i],bcf_sr_strerror(args->files->errnum)); } else if ( args->phased_concat ) { // Remove empty files from the list int nok = 0; while (1) { while ( noknfnames && args->start_pos[nok]!=-2 ) nok++; if ( nok==args->nfnames ) break; i = nok; while ( infnames && args->start_pos[i]==-2 ) i++; if ( i==args->nfnames ) break; int tmp = args->start_pos[nok]; args->start_pos[nok] = args->start_pos[i]; args->start_pos[i] = tmp; char *str = args->fnames[nok]; args->fnames[nok] = args->fnames[i]; args->fnames[i] = str; } for (i=nok; infnames; i++) free(args->fnames[i]); args->nfnames = nok; for (i=1; infnames; i++) if ( args->start_pos[i-1]!=-1 && args->start_pos[i]!=-1 && args->start_pos[i]start_pos[i-1] ) error("The files not in ascending order: %d in %s, %d in %s\n", args->start_pos[i-1]+1,args->fnames[i-1],args->start_pos[i]+1,args->fnames[i]); args->prev_chr = -1; args->swap_phase = (int*) calloc(bcf_hdr_nsamples(args->out_hdr),sizeof(int)); args->nmatch = (int*) calloc(bcf_hdr_nsamples(args->out_hdr),sizeof(int)); args->nmism = (int*) calloc(bcf_hdr_nsamples(args->out_hdr),sizeof(int)); args->phase_qual = (int32_t*) malloc(bcf_hdr_nsamples(args->out_hdr)*sizeof(int32_t)); args->phase_set = (int32_t*) malloc(bcf_hdr_nsamples(args->out_hdr)*sizeof(int32_t)); args->ifname = 0; } } static void destroy_data(args_t *args) { int i; if ( args->out_fh ) { if ( args->write_index ) { if ( bcf_idx_save(args->out_fh)<0 ) { if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"bcftools_stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n",args->output_fname?args->output_fname:"bcftools_stdout"); } if ( args->tpool && !args->files ) { hts_tpool_destroy(args->tpool->pool); free(args->tpool); } if ( args->files ) bcf_sr_destroy(args->files); if ( args->out_hdr ) bcf_hdr_destroy(args->out_hdr); free(args->seen_seq); free(args->start_pos); free(args->swap_phase); for (i=0; imbuf; i++) bcf_destroy(args->buf[i]); free(args->buf); free(args->buf_mask); free(args->GTa); free(args->GTb); free(args->nmatch); free(args->nmism); free(args->phase_qual); free(args->phase_set); for (i=0; infnames; i++) free(args->fnames[i]); free(args->fnames); } int vcf_write_line(htsFile *fp, kstring_t *line); #define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; } static void phase_update(args_t *args, bcf_hdr_t *hdr, bcf1_t *rec) { int i, nGTs = bcf_get_genotypes(hdr, rec, &args->GTa, &args->mGTa); if ( nGTs <= 0 ) return; // GT field is not present for (i=0; iswap_phase[i] ) continue; int *gt = &args->GTa[i*2]; if ( bcf_gt_is_missing(gt[0]) || gt[1]==bcf_int32_vector_end ) continue; if ( !bcf_gt_is_phased(gt[1]) ) continue; SWAP(int, gt[0], gt[1]); gt[1] |= 1; } bcf_update_genotypes(hdr,rec,args->GTa,nGTs); } static void phased_flush(args_t *args) { if ( !args->nbuf ) return; bcf_hdr_t *ahdr = args->files->readers[0].header; bcf_hdr_t *bhdr = args->files->readers[1].header; int i, j, nsmpl = bcf_hdr_nsamples(args->out_hdr); static int gt_absent_warned = 0; for (i=0; inbuf; i+=2) { if ( args->buf_mask[i/2]!=3 ) continue; bcf1_t *arec = args->buf[i]; bcf1_t *brec = args->buf[i+1]; int nGTs = bcf_get_genotypes(ahdr, arec, &args->GTa, &args->mGTa); if ( nGTs < 0 ) { if ( !gt_absent_warned ) { fprintf(bcftools_stderr,"GT is not present at %s:%"PRId64". (This warning is printed only once.)\n", bcf_seqname(ahdr,arec), (int64_t) arec->pos+1); gt_absent_warned = 1; } continue; } if ( nGTs != 2*nsmpl ) continue; // not diploid nGTs = bcf_get_genotypes(bhdr, brec, &args->GTb, &args->mGTb); if ( nGTs < 0 ) { if ( !gt_absent_warned ) { fprintf(bcftools_stderr,"GT is not present at %s:%"PRId64". (This warning is printed only once.)\n", bcf_seqname(bhdr,brec), (int64_t) brec->pos+1); gt_absent_warned = 1; } continue; } if ( nGTs != 2*nsmpl ) continue; // not diploid for (j=0; jGTa[j*2]; int *gtb = &args->GTb[j*2]; if ( gta[1]==bcf_int32_vector_end || gtb[1]==bcf_int32_vector_end ) continue; if ( bcf_gt_is_missing(gta[0]) || bcf_gt_is_missing(gta[1]) || bcf_gt_is_missing(gtb[0]) || bcf_gt_is_missing(gtb[1]) ) continue; if ( !bcf_gt_is_phased(gta[1]) || !bcf_gt_is_phased(gtb[1]) ) continue; if ( bcf_gt_allele(gta[0])==bcf_gt_allele(gta[1]) || bcf_gt_allele(gtb[0])==bcf_gt_allele(gtb[1]) ) continue; if ( bcf_gt_allele(gta[0])==bcf_gt_allele(gtb[0]) && bcf_gt_allele(gta[1])==bcf_gt_allele(gtb[1]) ) { if ( args->swap_phase[j] ) args->nmism[j]++; else args->nmatch[j]++; } if ( bcf_gt_allele(gta[0])==bcf_gt_allele(gtb[1]) && bcf_gt_allele(gta[1])==bcf_gt_allele(gtb[0]) ) { if ( args->swap_phase[j] ) args->nmatch[j]++; else args->nmism[j]++; } } } for (i=0; inbuf/2; i+=2) { bcf1_t *rec; bcf_hdr_t *hdr; int mask = args->buf_mask[i/2]; if ( mask & 1 ) { rec = args->buf[i]; hdr = args->files->readers[0].header; } else { rec = args->buf[i+1]; hdr = args->files->readers[1].header; } bcf_translate(args->out_hdr, hdr, rec); if ( args->nswap && (mask&1) ) phase_update(args, args->out_hdr, rec); if ( !args->compact_PS || args->phase_set_changed ) { bcf_update_format_int32(args->out_hdr,rec,"PS",args->phase_set,nsmpl); args->phase_set_changed = 0; } if ( bcf_write(args->out_fh, args->out_hdr, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); if ( rec->pos < args->prev_pos_check ) error("FIXME, disorder: %s:%"PRId64" vs %d [1]\n", bcf_seqname(hdr,rec),(int64_t)rec->pos+1,args->prev_pos_check+1); args->prev_pos_check = rec->pos; } args->nswap = 0; for (j=0; jnmatch[j] >= args->nmism[j] ) args->swap_phase[j] = 0; else { args->swap_phase[j] = 1; args->nswap++; } if ( args->nmatch[j] && args->nmism[j] ) { // Entropy-inspired quality. The factor 0.7 shifts and scales to (0,1) double f = (double)args->nmatch[j]/(args->nmatch[j]+args->nmism[j]); args->phase_qual[j] = 99*(0.7 + f*log(f) + (1-f)*log(1-f))/0.7; } else args->phase_qual[j] = 99; args->nmatch[j] = 0; args->nmism[j] = 0; } int PQ_printed = 0; for (; inbuf; i+=2) { bcf1_t *rec; bcf_hdr_t *hdr; int mask = args->buf_mask[i/2]; if ( mask & 2 ) { rec = args->buf[i+1]; hdr = args->files->readers[1].header; } else { rec = args->buf[i]; hdr = args->files->readers[0].header; } bcf_translate(args->out_hdr, hdr, rec); if ( !PQ_printed && mask==3 ) { bcf_update_format_int32(args->out_hdr,rec,"PQ",args->phase_qual,nsmpl); PQ_printed = 1; for (j=0; jphase_qual[j] < args->min_PQ ) { args->phase_set[j] = rec->pos+1; args->phase_set_changed = 1; } else if ( args->compact_PS ) args->phase_set[j] = bcf_int32_missing; } if ( args->nswap ) phase_update(args, args->out_hdr, rec); if ( !args->compact_PS || args->phase_set_changed ) { bcf_update_format_int32(args->out_hdr,rec,"PS",args->phase_set,nsmpl); args->phase_set_changed = 0; } if ( bcf_write(args->out_fh, args->out_hdr, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); if ( rec->pos < args->prev_pos_check ) error("FIXME, disorder: %s:%"PRId64" vs %d [2]\n", bcf_seqname(hdr,rec),(int64_t)rec->pos+1,args->prev_pos_check+1); args->prev_pos_check = rec->pos; } args->nbuf = 0; } static void phased_push(args_t *args, bcf1_t *arec, bcf1_t *brec, int is_overlap) { bcf_hdr_t *ahdr = arec ? bcf_sr_get_header(args->files,0) : NULL; bcf_hdr_t *bhdr = brec ? bcf_sr_get_header(args->files,1) : NULL; if ( arec && arec->errcode ) error("Parse error at %s:%"PRId64", cannot proceed: %s\n", bcf_seqname(ahdr,arec),(int64_t) arec->pos+1, args->files->readers[0].fname); if ( brec && brec->errcode ) error("Parse error at %s:%"PRId64", cannot proceed: %s\n", bcf_seqname(bhdr,brec),(int64_t) brec->pos+1, args->files->readers[1].fname); int i, nsmpl = bcf_hdr_nsamples(args->out_hdr); int chr_id = arec ? bcf_hdr_name2id(args->out_hdr,bcf_seqname(ahdr,arec)) : bcf_hdr_name2id(args->out_hdr,bcf_seqname(bhdr,brec)); if ( args->prev_chr<0 || args->prev_chr!=chr_id ) { if ( args->prev_chr>=0 ) phased_flush(args); for (i=0; iphase_set[i] = arec ? arec->pos+1 : brec->pos+1; args->phase_set_changed = 1; if ( args->seen_seq[chr_id] ) error("The chromosome block %s is not contiguous\n", arec ? bcf_seqname(ahdr,arec) : bcf_seqname(bhdr,brec)); args->seen_seq[chr_id] = 1; args->prev_chr = chr_id; args->prev_pos_check = -1; } if ( !is_overlap ) { assert(arec); bcf_translate(args->out_hdr, ahdr, arec); if ( args->nswap ) phase_update(args, args->out_hdr, arec); if ( !args->compact_PS || args->phase_set_changed ) { bcf_update_format_int32(args->out_hdr,arec,"PS",args->phase_set,nsmpl); args->phase_set_changed = 0; } if ( bcf_write(args->out_fh, args->out_hdr, arec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); if ( arec->pos < args->prev_pos_check ) error("FIXME, disorder: %s:%"PRId64" in %s vs %d written [3]\n", bcf_seqname(ahdr,arec), (int64_t) arec->pos+1,args->files->readers[0].fname, args->prev_pos_check+1); args->prev_pos_check = arec->pos; return; } int m = args->mbuf; args->nbuf += 2; hts_expand(bcf1_t*,args->nbuf,args->mbuf,args->buf); if ( m < args->mbuf ) args->buf_mask = (uint8_t*)realloc(args->buf_mask,sizeof(*args->buf_mask)*args->mbuf); for (i=m; imbuf; i++) args->buf[i] = bcf_init1(); if ( arec ) SWAP(bcf1_t*, args->files->readers[0].buffer[0], args->buf[args->nbuf-2]); if ( brec ) SWAP(bcf1_t*, args->files->readers[1].buffer[0], args->buf[args->nbuf-1]); args->buf_mask[args->nbuf/2-1] = (arec?1:0) | (brec?2:0); } static int _get_active_index(bcf_srs_t *sr) { int i; for (i=0; inreaders; i++) if ( bcf_sr_has_line(sr,i) ) return i; return -1; } static void concat(args_t *args) { static int site_drop_warned = 0; int i; if ( args->phased_concat ) // phased concat { // keep only two open files at a time while ( args->ifname < args->nfnames ) { int new_file = 0; while ( args->files->nreaders < 2 && args->ifname < args->nfnames ) { if ( !bcf_sr_add_reader(args->files,args->fnames[args->ifname]) ) error("Failed to open %s: %s\n", args->fnames[args->ifname],bcf_sr_strerror(args->files->errnum)); new_file = 1; args->ifname++; if ( args->start_pos[args->ifname-1]==-1 ) break; // new chromosome, start with only one file open if ( args->ifname < args->nfnames && args->start_pos[args->ifname]==-1 ) break; // next file starts on a different chromosome } // is there a line from the previous run? Seek the newly opened reader to that position int seek_pos = -1; int seek_chr = -1; if ( bcf_sr_has_line(args->files,0) ) { bcf1_t *line = bcf_sr_get_line(args->files,0); bcf_sr_seek(args->files, bcf_seqname(args->files->readers[0].header,line), line->pos); seek_pos = line->pos; seek_chr = bcf_hdr_name2id(args->out_hdr, bcf_seqname(args->files->readers[0].header,line)); } else if ( new_file ) bcf_sr_seek(args->files,NULL,0); // set to start int nret, ir; while ( (nret = bcf_sr_next_line(args->files)) ) { int is_overlap = args->files->nreaders==1 ? 0 : 1; if ( !bcf_sr_has_line(args->files,0) ) // no input from the first reader { // We are assuming that there is a perfect overlap, sites which are not present in both files are dropped if ( bcf_sr_region_done(args->files,0) ) { phased_flush(args); bcf_sr_remove_reader(args->files, 0); is_overlap = 0; } else if ( args->ligate_warn ) { if ( !site_drop_warned ) { ir = _get_active_index(args->files); fprintf(bcftools_stderr, "Warning: Dropping the site %s:%"PRId64". The --ligate option is intended for VCFs with perfect\n" " overlap, sites in overlapping regions present in one but missing in other are dropped.\n" " This warning is printed only once.\n", bcf_seqname(bcf_sr_get_header(args->files,ir),bcf_sr_get_line(args->files,ir)), (int64_t) bcf_sr_get_line(args->files,ir)->pos+1); site_drop_warned = 1; } continue; } else if ( !args->ligate_force ) { ir = _get_active_index(args->files); error("Error: The --ligate option is intended for VCFs with perfect overlap, the site %s:%"PRId64" breaks the assumption\n", bcf_seqname(bcf_sr_get_header(args->files,ir),bcf_sr_get_line(args->files,ir)), (int64_t) bcf_sr_get_line(args->files,ir)->pos+1); } } // Get a line to learn about current position ir = _get_active_index(args->files); bcf1_t *line = bcf_sr_get_line(args->files,ir); // This can happen after bcf_sr_seek: indel may start before the coordinate which we seek to. if ( seek_chr>=0 && seek_pos>line->pos && seek_chr==bcf_hdr_name2id(args->out_hdr, bcf_seqname(args->files->readers[ir].header,line)) ) continue; seek_pos = seek_chr = -1; // Check if the position overlaps with the next, yet unopened, reader int must_seek = 0; while ( args->ifname < args->nfnames && args->start_pos[args->ifname]!=-1 && line->pos >= args->start_pos[args->ifname] ) { must_seek = 1; if ( !bcf_sr_add_reader(args->files,args->fnames[args->ifname]) ) error("Failed to open %s: %s\n", args->fnames[args->ifname],bcf_sr_strerror(args->files->errnum)); args->ifname++; } if ( must_seek ) { bcf_sr_seek(args->files, bcf_seqname(args->files->readers[ir].header,line), line->pos); seek_pos = line->pos; seek_chr = bcf_hdr_name2id(args->out_hdr, bcf_seqname(args->files->readers[ir].header,line)); continue; } // We are assuming that there is a perfect overlap, sites which are not present in both files are dropped if ( args->files->nreaders>1 && !bcf_sr_has_line(args->files,1) && !bcf_sr_region_done(args->files,1) && !args->ligate_force ) { if ( args->ligate_warn && !site_drop_warned ) { ir = _get_active_index(args->files); fprintf(bcftools_stderr, "Warning: Dropping the site %s:%"PRId64". The --ligate option is intended for VCFs with perfect\n" " overlap, sites in overlapping regions present in one but missing in other are dropped.\n" " This warning is printed only once.\n", bcf_seqname(bcf_sr_get_header(args->files,ir),line), (int64_t) line->pos+1); site_drop_warned = 1; } else if ( !args->ligate_warn ) { ir = _get_active_index(args->files); error("Error: The --ligate option is intended for VCFs with perfect overlap, the site %s:%"PRId64" breaks the assumption\n", bcf_seqname(bcf_sr_get_header(args->files,ir),bcf_sr_get_line(args->files,ir)), (int64_t) bcf_sr_get_line(args->files,ir)->pos+1); } continue; } bcf1_t *line0 = bcf_sr_get_line(args->files,0); bcf1_t *line1 = args->files->nreaders > 1 ? bcf_sr_get_line(args->files,1) : NULL; phased_push(args, line0, line1, is_overlap); } if ( args->files->nreaders ) { phased_flush(args); while ( args->files->nreaders ) bcf_sr_remove_reader(args->files, 0); } } } else if ( args->files ) // combining overlapping files, using synced reader { while ( bcf_sr_next_line(args->files) ) { for (i=0; ifiles->nreaders; i++) { bcf1_t *line = bcf_sr_get_line(args->files,i); if ( !line ) continue; if ( args->sites_only ) bcf_subset(args->out_hdr, line, 0, 0); bcf_translate(args->out_hdr, args->files->readers[i].header, line); if ( bcf_write1(args->out_fh, args->out_hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); if ( args->remove_dups ) break; } } } else // concatenate as is { struct timeval t0, t1; kstring_t tmp = {0,0,0}; int prev_chr_id = -1, prev_pos; bcf1_t *line = bcf_init(); for (i=0; infnames; i++) { if ( args->verbose ) { fprintf(bcftools_stderr,"Concatenating %s", args->fnames[i]); gettimeofday(&t0, NULL); } htsFile *fp = hts_open(args->fnames[i], "r"); if ( !fp ) error("\nFailed to open: %s\n", args->fnames[i]); if ( args->n_threads ) hts_set_opt(fp, HTS_OPT_THREAD_POOL, args->tpool); bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("\nFailed to parse header: %s\n", args->fnames[i]); if ( args->sites_only ) { bcf_hdr_t *hdr_ori = hdr; hdr = bcf_hdr_subset(hdr_ori, 0, 0, 0); bcf_hdr_remove(hdr, BCF_HL_FMT, NULL); bcf_hdr_destroy(hdr_ori); } if ( !fp->is_bin && args->output_type&FT_VCF ) { line->max_unpack = BCF_UN_STR; // if VCF is on both input and output, avoid VCF to BCF conversion while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 ) { char *str = fp->line.s; // remove genotypes if ( args->sites_only ) { int ntab = 0; while ( *str ) { if ( *str == '\t' && ++ntab==8 ) { *str = 0; break; } str++; } str = fp->line.s; } while ( *str && *str!='\t' ) str++; tmp.l = 0; kputsn(fp->line.s,str-fp->line.s,&tmp); int chr_id = bcf_hdr_name2id(args->out_hdr, tmp.s); if ( chr_id<0 ) error("\nThe sequence \"%s\" not defined in the header: %s\n(Quick workaround: index the file.)\n", tmp.s, args->fnames[i]); if ( prev_chr_id!=chr_id ) { prev_pos = -1; if ( args->seen_seq[chr_id] ) error("\nThe chromosome block %s is not contiguous, consider running with -a.\n", tmp.s); } char *end; int pos = strtol(str+1,&end,10) - 1; if ( end==str+1 ) error("Could not parse line: %s\n", fp->line.s); if ( prev_pos > pos ) error("\nThe chromosome block %s is not sorted, consider running with -a.\n", tmp.s); args->seen_seq[chr_id] = 1; prev_chr_id = chr_id; if ( vcf_write_line(args->out_fh, &fp->line)!=0 ) error("\nFailed to write %"PRIu64" bytes\n", (uint64_t)fp->line.l); } } else { // BCF conversion is required line->max_unpack = 0; while ( bcf_read(fp, hdr, line)==0 ) { if ( args->sites_only ) bcf_subset(args->out_hdr, line, 0, 0); bcf_translate(args->out_hdr, hdr, line); if ( prev_chr_id!=line->rid ) { prev_pos = -1; if ( args->seen_seq[line->rid] ) error("\nThe chromosome block %s is not contiguous, consider running with -a.\n", bcf_seqname(args->out_hdr, line)); } if ( prev_pos > line->pos ) error("\nThe chromosome block %s is not sorted, consider running with -a.\n", bcf_seqname(args->out_hdr, line)); args->seen_seq[line->rid] = 1; prev_chr_id = line->rid; if ( bcf_write(args->out_fh, args->out_hdr, line)!=0 ) error("\nFailed to write\n"); } } bcf_hdr_destroy(hdr); hts_close(fp); if ( args->verbose ) { gettimeofday(&t1, NULL); double delta = (t1.tv_sec - t0.tv_sec) * 1e6 + (t1.tv_usec - t0.tv_usec); fprintf(bcftools_stderr,"\t%f seconds\n",delta/1e6); } } bcf_destroy(line); free(tmp.s); } } int print_vcf_gz_header(BGZF *fp, BGZF *bgzf_out, int print_header, kstring_t *tmp) { char *buffer = (char*) fp->uncompressed_block; // Read the header and find the position of the data block if ( buffer[0]!='#' ) error("Could not parse the header, expected '#', found '%c'\n", buffer[0]); int nskip = 1; // end of the header in the current uncompressed block while (1) { if ( buffer[nskip]=='\n' ) { nskip++; if ( nskip>=fp->block_length ) { kputsn(buffer,nskip,tmp); if ( bgzf_read_block(fp) != 0 ) return -1; if ( !fp->block_length ) break; nskip = 0; } // The header has finished if ( buffer[nskip]!='#' ) { kputsn(buffer,nskip,tmp); break; } } nskip++; if ( nskip>=fp->block_length ) { kputsn(buffer,fp->block_length,tmp); if ( bgzf_read_block(fp) != 0 ) return -1; if ( !fp->block_length ) break; nskip = 0; } } if ( print_header ) { if ( bgzf_write(bgzf_out,tmp->s,tmp->l) != tmp->l ) error("Failed to write %"PRIu64" bytes\n", (uint64_t)tmp->l); tmp->l = 0; } return nskip; } static inline int unpackInt16(const uint8_t *buffer) { return buffer[0] | buffer[1] << 8; } static int check_header(const uint8_t *header) { if ( header[0] != 31 || header[1] != 139 || header[2] != 8 ) return -2; return ((header[3] & 4) != 0 && unpackInt16((uint8_t*)&header[10]) == 6 && header[12] == 'B' && header[13] == 'C' && unpackInt16((uint8_t*)&header[14]) == 2) ? 0 : -1; } static void _check_hrecs(const bcf_hdr_t *hdr0, const bcf_hdr_t *hdr, char *fname0, char *fname) { int j; for (j=0; jnhrec; j++) { bcf_hrec_t *hrec0 = hdr0->hrec[j]; if ( hrec0->type!=BCF_HL_FLT && hrec0->type!=BCF_HL_INFO && hrec0->type!=BCF_HL_FMT && hrec0->type!=BCF_HL_CTG ) continue; // skip fields w/o IDX int itag = bcf_hrec_find_key(hrec0, "ID"); bcf_hrec_t *hrec = bcf_hdr_get_hrec(hdr, hrec0->type, "ID", hrec0->vals[itag], NULL); char *type = NULL; if ( hrec0->type==BCF_HL_FLT ) type = "FILTER"; if ( hrec0->type==BCF_HL_INFO ) type = "INFO"; if ( hrec0->type==BCF_HL_FMT ) type = "FORMAT"; if ( hrec0->type==BCF_HL_CTG ) type = "contig"; if ( !hrec ) error("Cannot use --naive, incompatible headers, the tag %s/%s not present in %s\n",type,hrec0->vals[itag],fname); int idx0 = bcf_hrec_find_key(hrec0, "IDX"); int idx = bcf_hrec_find_key(hrec, "IDX"); if ( idx0<0 || idx<0 ) error("fixme: unexpected IDX<0 for %s/%s in %s or %s\n",type,hrec0->vals[itag],fname0,fname); if ( strcmp(hrec0->vals[idx0],hrec->vals[idx]) ) error("Cannot use --naive, use --naive-force instead: different order the tag %s/%s in %s vs %s\n",type,hrec0->vals[itag],fname0,fname); } } static void naive_concat_check_headers(args_t *args) { fprintf(bcftools_stderr,"Checking the headers of %d files.\n",args->nfnames); bcf_hdr_t *hdr0 = NULL; int i,j; for (i=0; infnames; i++) { htsFile *fp = hts_open(args->fnames[i], "r"); if ( !fp ) error("Failed to open: %s\n", args->fnames[i]); bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to parse header: %s\n", args->fnames[i]); htsFormat type = *hts_get_format(fp); hts_close(fp); if ( i==0 ) { hdr0 = hdr; continue; } // check the samples if ( bcf_hdr_nsamples(hdr0)!=bcf_hdr_nsamples(hdr) ) error("Cannot concatenate, different number of samples: %d vs %d in %s vs %s\n",bcf_hdr_nsamples(hdr0),bcf_hdr_nsamples(hdr),args->fnames[0],args->fnames[i]); for (j=0; jsamples[j],hdr->samples[j]) ) error("Cannot concatenate, different samples in %s vs %s\n",args->fnames[0],args->fnames[i]); // if BCF, check if tag IDs are consistent in the dictionary of strings if ( type.compression!=bgzf ) error("The --naive option works only for compressed BCFs or VCFs, sorry :-/\n"); _check_hrecs(hdr0,hdr,args->fnames[0],args->fnames[i]); _check_hrecs(hdr,hdr0,args->fnames[i],args->fnames[0]); bcf_hdr_destroy(hdr); } if ( hdr0 ) bcf_hdr_destroy(hdr0); fprintf(bcftools_stderr,"Done, the headers are compatible.\n"); } static void naive_concat(args_t *args) { if ( !args->naive_concat_trust_headers ) naive_concat_check_headers(args); // only compressed BCF atm BGZF *bgzf_out = bgzf_open(args->output_fname,"w");; htsFormat output_type; output_type.format = (args->output_type & FT_VCF) ? vcf : bcf; output_type.compression = (args->output_type & FT_GZ) ? bgzf : no_compression; struct timeval t0, t1; const size_t page_size = BGZF_MAX_BLOCK_SIZE; uint8_t *buf = (uint8_t*) malloc(page_size); kstring_t tmp = {0,0,0}; int i, file_types = 0; for (i=0; infnames; i++) { if ( args->verbose ) { fprintf(bcftools_stderr,"Concatenating %s", args->fnames[i]); gettimeofday(&t0, NULL); } htsFile *hts_fp = hts_open(args->fnames[i],"r"); if ( !hts_fp ) error("\nFailed to open: %s\n", args->fnames[i]); htsFormat type = *hts_get_format(hts_fp); if ( type.compression!=bgzf ) error("\nThe --naive option works only for compressed BCFs or VCFs\n"); file_types |= type.format==vcf ? 1 : 2; if ( file_types==3 ) error("\nThe --naive option works only for compressed files of the same type, all BCFs or all VCFs\n"); if ( args->explicit_output_type ) { if ( output_type.format!=type.format ) error("\nThe --naive option works only for the output of the same type, all BCFs or all VCFs\n"); if ( output_type.compression!=type.compression ) error("\nThe --naive option works only for the output of the same compression type\n"); } BGZF *fp = hts_get_bgzfp(hts_fp); if ( !fp || bgzf_read_block(fp) != 0 || !fp->block_length ) error("\nFailed to read %s: %s\n", args->fnames[i], strerror(errno)); int nskip; if ( type.format==bcf ) { const size_t magic_len = 5 + 4; // "Magic" string + header length uint8_t magic[magic_len]; if ( bgzf_read(fp, magic, magic_len) != magic_len ) error("\nFailed to read the BCF header in %s\n", args->fnames[i]); // First five bytes are the "Magic" string if (strncmp((char*)magic, "BCF\2\2", 5) != 0) error("\nInvalid BCF magic string in %s\n", args->fnames[i]); // Next four are the header length (little-endian) tmp.l = le_to_u32(magic + 5); hts_expand(char,tmp.l,tmp.m,tmp.s); if ( bgzf_read(fp, tmp.s, tmp.l) != tmp.l ) error("\nFailed to read the BCF header in %s\n", args->fnames[i]); // write only the first header if ( i==0 ) { if ( bgzf_write(bgzf_out, magic, magic_len) != magic_len ) error("\nFailed to write %zu bytes to %s\n", magic_len,args->output_fname); if ( bgzf_write(bgzf_out, tmp.s, tmp.l) != tmp.l) error("\nFailed to write %"PRId64" bytes to %s\n", (uint64_t)tmp.l,args->output_fname); } nskip = fp->block_offset; } else { nskip = print_vcf_gz_header(fp, bgzf_out, i==0?1:0, &tmp); if ( nskip==-1 ) error("\nError reading %s\n", args->fnames[i]); } // Output all non-header data that were read together with the header block if ( fp->block_length - nskip > 0 ) { if ( bgzf_write(bgzf_out, (char *)fp->uncompressed_block+nskip, fp->block_length-nskip)<0 ) error("\nError: %d\n",fp->errcode); } if ( bgzf_flush(bgzf_out)<0 ) error("\nError: %d\n",bgzf_out->errcode); // Stream the rest of the file as it is, without recompressing, but remove BGZF EOF blocks // The final bgzf eof block will be added by bgzf_close. ssize_t nread, nblock, nwr; const int nheader = 18, neof = 28; const uint8_t *eof = (uint8_t*) "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0"; while (1) { nread = bgzf_raw_read(fp, buf, nheader); if ( !nread ) break; if ( nread != nheader || check_header(buf)!=0 ) error("\nCould not parse the header of a bgzf block: %s\n",args->fnames[i]); nblock = unpackInt16(buf+16) + 1; assert( nblock <= page_size && nblock >= nheader ); nread += bgzf_raw_read(fp, buf+nheader, nblock - nheader); if ( nread!=nblock ) error("\nCould not read %"PRId64" bytes: %s\n",(uint64_t)nblock,args->fnames[i]); if ( nread==neof && !memcmp(buf,eof,neof) ) continue; nwr = bgzf_raw_write(bgzf_out, buf, nread); if ( nwr != nread ) error("\nWrite failed, wrote %"PRId64" instead of %d bytes.\n", (uint64_t)nwr,(int)nread); } if (hts_close(hts_fp)) error("\nClose failed: %s\n",args->fnames[i]); if ( args->verbose ) { gettimeofday(&t1, NULL); double delta = (t1.tv_sec - t0.tv_sec) * 1e6 + (t1.tv_usec - t0.tv_usec); fprintf(bcftools_stderr,"\t%f seconds\n",delta/1e6); } } free(buf); free(tmp.s); if (bgzf_close(bgzf_out) < 0) error("Error: %d\n",bgzf_out->errcode); } static void usage(args_t *args) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: Concatenate or combine VCF/BCF files. All source files must have the same sample\n"); fprintf(bcftools_stderr, " columns appearing in the same order. The program can be used, for example, to\n"); fprintf(bcftools_stderr, " concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel\n"); fprintf(bcftools_stderr, " VCF into one. The input files must be sorted by chr and position. The files\n"); fprintf(bcftools_stderr, " must be given in the correct order to produce sorted VCF on output unless\n"); fprintf(bcftools_stderr, " the -a, --allow-overlaps option is specified. With the --naive option, the files\n"); fprintf(bcftools_stderr, " are concatenated without being recompressed, which is very fast.\n"); fprintf(bcftools_stderr, "Usage: bcftools concat [options] [ [...]]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Options:\n"); fprintf(bcftools_stderr, " -a, --allow-overlaps First coordinate of the next file can precede last record of the current file.\n"); fprintf(bcftools_stderr, " -c, --compact-PS Do not output PS tag at each site, only at the start of a new phase set block.\n"); fprintf(bcftools_stderr, " -d, --rm-dups STRING Output duplicate records present in multiple files only once: \n"); fprintf(bcftools_stderr, " -D, --remove-duplicates Alias for -d exact\n"); fprintf(bcftools_stderr, " -f, --file-list FILE Read the list of files from a file.\n"); fprintf(bcftools_stderr, " -G, --drop-genotypes Drop individual genotype information.\n"); fprintf(bcftools_stderr, " -l, --ligate Ligate phased VCFs by matching phase at overlapping haplotypes\n"); fprintf(bcftools_stderr, " --ligate-force Ligate even non-overlapping chunks, keep all sites\n"); fprintf(bcftools_stderr, " --ligate-warn Drop sites in imperfect overlaps\n"); fprintf(bcftools_stderr, " --no-version Do not append version and command line to the header\n"); fprintf(bcftools_stderr, " -n, --naive Concatenate files without recompression, a header check compatibility is performed\n"); fprintf(bcftools_stderr, " --naive-force Same as --naive, but header compatibility is not checked. Dangerous, use with caution.\n"); fprintf(bcftools_stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(bcftools_stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(bcftools_stderr, " -q, --min-PQ INT Break phase set if phasing quality is lower than [30]\n"); fprintf(bcftools_stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(bcftools_stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(bcftools_stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " --threads INT Use multithreading with worker threads [0]\n"); fprintf(bcftools_stderr, " -v, --verbose 0|1 Set verbosity level [1]\n"); fprintf(bcftools_stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int main_vcfconcat(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->output_fname = "-"; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->min_PQ = 30; args->verbose = 1; args->clevel = -1; static struct option loptions[] = { {"verbose",required_argument,NULL,'v'}, {"naive",no_argument,NULL,'n'}, {"naive-force",no_argument,NULL,7}, {"compact-PS",no_argument,NULL,'c'}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,12}, {"remove-duplicates",no_argument,NULL,'D'}, {"rm-dups",required_argument,NULL,'d'}, {"allow-overlaps",no_argument,NULL,'a'}, {"ligate",no_argument,NULL,'l'}, {"ligate-force",no_argument,NULL,10}, {"ligate-warn",no_argument,NULL,11}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"threads",required_argument,NULL,9}, {"file-list",required_argument,NULL,'f'}, {"min-PQ",required_argument,NULL,'q'}, {"no-version",no_argument,NULL,8}, {"write-index",optional_argument,NULL,'W'}, {"drop-genotypes",no_argument,NULL,'G'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "h:?o:O:f:alq:Dd:Gr:R:cnv:W::",loptions,NULL)) >= 0) { switch (c) { case 'c': args->compact_PS = 1; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; args->regions_is_file = 1; break; case 'd': args->remove_dups = optarg; break; case 'D': args->remove_dups = "exact"; break; case 'q': args->min_PQ = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --min-PQ %s\n", optarg); break; case 'n': args->naive_concat = 1; break; case 'a': args->allow_overlaps = 1; break; case 'l': args->phased_concat = 1; break; case 'f': args->file_list = optarg; break; case 'G': args->sites_only = 1; break; case 'o': args->output_fname = optarg; break; case 'O': args->explicit_output_type = 1; switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } }; if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 10 : args->ligate_force = 1; break; case 11 : args->ligate_warn = 1; break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 8 : args->record_cmd_line = 0; break; case 7 : args->naive_concat = 1; args->naive_concat_trust_headers = 1; break; case 12 : args->regions_overlap = parse_overlap_option(optarg); if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 'v': args->verbose = strtol(optarg, &tmp, 0); if ( *tmp || args->verbose<0 || args->verbose>1 ) error("Error: currently only --verbose 0 or --verbose 1 is supported\n"); break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 'h': case '?': usage(args); break; default: error("Unknown argument: %s\n", optarg); } } while ( optindnfnames++; args->fnames = (char **)realloc(args->fnames,sizeof(char*)*args->nfnames); args->fnames[args->nfnames-1] = strdup(argv[optind]); optind++; } if ( args->ligate_force && args->ligate_warn ) error("The options cannot be combined: --ligate-force and --ligate-warn\n"); if ( args->allow_overlaps && args->phased_concat ) error("The options -a and -l should not be combined. Please run with -l only.\n"); if ( args->sites_only && args->phased_concat ) error("The options --drop-genotypes and --ligate cannot be combined\n"); if ( args->compact_PS && !args->phased_concat ) error("The -c option is intended only with -l\n"); if ( args->file_list ) { if ( args->nfnames ) error("Cannot combine -l with file names on command line.\n"); args->fnames = hts_readlines(args->file_list, &args->nfnames); if ( !args->fnames ) error("Could not read the file: %s\n", args->file_list); } if ( !args->nfnames ) usage(args); if ( args->remove_dups && !args->allow_overlaps ) error("The -D option is supported only with -a\n"); if ( args->regions_list && !args->allow_overlaps ) error("The -r/-R option is supported only with -a\n"); if ( args->naive_concat ) { if ( args->write_index ) error("Error: cannot --write-index in the %s mode\n",args->naive_concat_trust_headers?"--naive-force":"--naive"); if ( args->allow_overlaps ) error("The option --naive cannot be combined with --allow-overlaps\n"); if ( args->phased_concat ) error("The option --naive cannot be combined with --ligate\n"); if ( args->sites_only ) error("The option --naive cannot be combined with --drop-genotypes\n"); naive_concat(args); destroy_data(args); free(args); return 0; } init_data(args); concat(args); destroy_data(args); free(args); return 0; } pysam-0.23.0/bcftools/vcfconvert.c000066400000000000000000002207631475062545500171120ustar00rootroot00000000000000/* vcfconvert.c -- convert between VCF/BCF and related formats. Copyright (C) 2013-2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "filter.h" #include "convert.h" #include "tsv2vcf.h" // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 typedef struct _args_t args_t; struct _args_t { faidx_t *ref; filter_t *filter; char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE convert_t *convert; bcf_srs_t *files; bcf_hdr_t *header; void (*convert_func)(struct _args_t *); struct { int total, skipped, hom_rr, het_ra, hom_aa, het_aa, missing, written; } n; kstring_t str; int32_t *gts; float *flt; int rev_als, output_vcf_ids, hap2dip, gen_3N6; int nsamples, *samples, sample_is_file, targets_is_file, regions_is_file, output_type; int regions_overlap, targets_overlap; char **argv, *sample_list, *targets_list, *regions_list, *tag, *columns; char *outfname, *infname, *ref_fname, *sex_fname; int argc, n_threads, record_cmd_line, keep_duplicates, clevel; char *index_fn; int write_index; struct { kstring_t ref,alt,refalt; } tsv; }; static void destroy_data(args_t *args) { if ( args->ref ) fai_destroy(args->ref); if ( args->convert) convert_destroy(args->convert); if ( args->filter ) filter_destroy(args->filter); free(args->samples); if ( args->files ) bcf_sr_destroy(args->files); } static void open_vcf(args_t *args, const char *format_str) { args->files = bcf_sr_init(); if ( args->n_threads && bcf_sr_set_threads(args->files, args->n_threads)!=0 ) error("Could not initialize --threads %d\n", args->n_threads); if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, args->regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,args->targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list, args->targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } if ( !bcf_sr_add_reader(args->files, args->infname) ) error("Failed to open %s: %s\n", args->infname,bcf_sr_strerror(args->files->errnum)); args->header = args->files->readers[0].header; if ( args->filter_str ) args->filter = filter_init(args->header, args->filter_str); int i, nsamples = 0, *samples = NULL; if ( args->sample_list && strcmp("-",args->sample_list) ) { for (i=0; ifiles->nreaders; i++) { int ret = bcf_hdr_set_samples(args->files->readers[i].header,args->sample_list,args->sample_is_file); if ( ret<0 ) error("Error parsing the sample list\n"); else if ( ret>0 ) error("Sample name mismatch: sample #%d not found in the header\n", ret); } if ( args->sample_list[0]!='^' ) { // the sample ordering may be different if not negated int n; char **smpls = hts_readlist(args->sample_list, args->sample_is_file, &n); if ( !smpls ) error("Could not parse %s\n", args->sample_list); if ( n!=bcf_hdr_nsamples(args->files->readers[0].header) ) error("The number of samples does not match, perhaps some are present multiple times?\n"); nsamples = bcf_hdr_nsamples(args->files->readers[0].header); samples = (int*) malloc(sizeof(int)*nsamples); for (i=0; ifiles->readers[0].header, BCF_DT_SAMPLE,smpls[i]); free(smpls[i]); } free(smpls); } } if ( format_str ) args->convert = convert_init(args->header, samples, nsamples, format_str); free(samples); } static int _set_ref_alt(args_t *args, bcf1_t *rec) { args->tsv.refalt.l = 0; kputs(args->tsv.ref.s, &args->tsv.refalt); if ( strcmp(".",args->tsv.alt.s) && strcmp(args->tsv.ref.s,args->tsv.alt.s) ) { kputc(',', &args->tsv.refalt); kputs(args->tsv.alt.s, &args->tsv.refalt); } bcf_update_alleles_str(args->header, rec, args->tsv.refalt.s); args->tsv.ref.l = 0; args->tsv.alt.l = 0; args->tsv.refalt.l = 0; return 0; } static int tsv_setter_ref(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*) usr; kputsn(tsv->ss,tsv->se - tsv->ss,&args->tsv.ref); if ( args->tsv.alt.l ) return _set_ref_alt(args,rec); return 0; } static int tsv_setter_alt(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*) usr; kputsn(tsv->ss,tsv->se - tsv->ss,&args->tsv.alt); if ( args->tsv.ref.l ) return _set_ref_alt(args,rec); return 0; } // Try to set CHROM:POS_REF_ALT[_END]. Return 0 on success, -1 on error static int _set_chrom_pos_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*) usr; char tmp, *se = tsv->ss, *ss = tsv->ss; while ( se < tsv->se && *se!=':' ) se++; if ( *se!=':' ) return -1; tmp = *se; *se = 0; int rid = bcf_hdr_name2id(args->header,ss); *se = tmp; if ( rid<0 ) return -1; // POS hts_pos_t pos = strtol(se+1,&ss,10); if ( ss==se+1 ) return -1; pos--; // REF,ALT args->str.l = 0; se = ++ss; while ( se < tsv->se && *se!='_' ) se++; if ( *se!='_' ) return -1; kputsn(ss,se-ss,&args->str); ss = ++se; while ( se < tsv->se && *se!='_' && isspace(*tsv->se) ) se++; if ( se < tsv->se && *se!='_' && isspace(*tsv->se) ) return -1; kputc(',',&args->str); kputsn(ss,se-ss,&args->str); // END - optional if (*se && *se=='_') { long end = strtol(se+1,&ss,10); if ( ss==se+1 ) return -1; if (end < 1 || end > INT32_MAX) return -1; int32_t e = end; // bcf_update_info_int32 needs an int32_t pointer bcf_update_info_int32(args->header, rec, "END", &e, 1); } rec->rid = rid; rec->pos = pos; bcf_update_alleles_str(args->header, rec, args->str.s); return 0; } static int tsv_setter_chrom_pos_ref_alt_or_chrom(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*)usr; int ret = _set_chrom_pos_ref_alt(tsv,rec,usr); if ( !ret ) return ret; return tsv_setter_chrom(tsv,rec,args->header); } static int tsv_setter_chrom_pos_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr) { int ret = _set_chrom_pos_ref_alt(tsv,rec,usr); if ( ret!=0 ) error("Could not parse the CHROM:POS_REF_ALT[_END] string: %s\n", tsv->ss); return ret; } // This function must be called first, then tsv_setter_chrom_pos_ref_alt_id_or_die. // One of them is expected to find the CHROM:POS_REF_ALT[_END] string, if not, die. static int tsv_setter_chrom_pos_ref_alt_or_id(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*)usr; if ( _set_chrom_pos_ref_alt(tsv,rec,usr)==0 ) return 0; rec->pos = -1; // mark the record as unset if ( !args->output_vcf_ids) return 0; return tsv_setter_id(tsv,rec,usr); } static int tsv_setter_chrom_pos_ref_alt_id_or_die(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*)usr; if ( rec->pos!=-1 ) { if ( !args->output_vcf_ids ) return 0; return tsv_setter_id(tsv,rec,usr); } return tsv_setter_chrom_pos_ref_alt(tsv,rec,usr); } static int tsv_setter_verify_pos(tsv_t *tsv, bcf1_t *rec, void *usr) { char *se; int pos = strtol(tsv->ss,&se,10); if ( tsv->ss==se ) error("Could not parse POS: %s\n", tsv->ss); if ( rec->pos != pos-1 ) error("POS mismatch: %s\n", tsv->ss); return 0; } static int tsv_setter_verify_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*) usr; args->rev_als = 0; char tmp = *tsv->se; *tsv->se = 0; if ( strcmp(tsv->ss,rec->d.allele[0]) ) { if ( strcmp(tsv->ss,rec->d.allele[1]) ) { *tsv->se = tmp; error("REF/ALT mismatch: [%s][%s]\n", tsv->ss,rec->d.allele[1]); } args->rev_als = 1; } *tsv->se = tmp; while ( *tsv->se && isspace(*tsv->se) ) tsv->se++; tsv->ss = tsv->se; while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++; tmp = *tsv->se; *tsv->se = 0; if ( !args->rev_als && strcmp(tsv->ss,rec->d.allele[1]) ) { *tsv->se = tmp; error("REF/ALT mismatch: [%s][%s]\n", tsv->ss,rec->d.allele[1]); } else if ( args->rev_als && strcmp(tsv->ss,rec->d.allele[0]) ) { *tsv->se = tmp; error("REF/ALT mismatch: [%s][%s]\n", tsv->ss,rec->d.allele[0]); } *tsv->se = tmp; return 0; } static int tsv_setter_gt_gp(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*) usr; int i, nsamples = bcf_hdr_nsamples(args->header); for (i=0; iss, &tsv->se); if ( tsv->ss==tsv->se ) { fprintf(stderr,"Could not parse first value of %d-th sample\n", i+1); return -1; } tsv->ss = tsv->se+1; ab = strtod(tsv->ss, &tsv->se); if ( tsv->ss==tsv->se ) { fprintf(stderr,"Could not parse second value of %d-th sample\n", i+1); return -1; } tsv->ss = tsv->se+1; bb = strtod(tsv->ss, &tsv->se); if ( tsv->ss==tsv->se ) { fprintf(stderr,"Could not parse third value of %d-th sample\n", i+1); return -1; } tsv->ss = tsv->se+1; if ( args->rev_als ) { float tmp = bb; bb = aa; aa = tmp; } args->flt[3*i+0] = aa; args->flt[3*i+1] = ab; args->flt[3*i+2] = bb; if ( aa >= ab ) { if ( aa >= bb ) args->gts[2*i+0] = args->gts[2*i+1] = bcf_gt_unphased(0); else args->gts[2*i+0] = args->gts[2*i+1] = bcf_gt_unphased(1); } else if ( ab >= bb ) { args->gts[2*i+0] = bcf_gt_unphased(0); args->gts[2*i+1] = bcf_gt_unphased(1); } else args->gts[2*i+0] = args->gts[2*i+1] = bcf_gt_unphased(1); } if ( *tsv->se ) error("Could not parse: %s\n", tsv->ss); if ( bcf_update_genotypes(args->header,rec,args->gts,nsamples*2) ) error("Could not update GT field\n"); if ( bcf_update_format_float(args->header,rec,"GP",args->flt,nsamples*3) ) error("Could not update GP field\n"); return 0; } static int tsv_setter_haps(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*) usr; int i, nsamples = bcf_hdr_nsamples(args->header); int32_t a0, a1; if ( args->rev_als ) { a0 = bcf_gt_phased(1); a1 = bcf_gt_phased(0); } else { a0 = bcf_gt_phased(0); a1 = bcf_gt_phased(1); } // up is short for "unphased" int nup = 0; for (i=0; iss + 4*i + nup; int up = 0, all; for (all=0; all < 2; all++){ // checking for premature ending if ( !ss[0] || !ss[1] || !ss[2] || (up && (!ss[3] || !ss[4]) ) ) { fprintf(stderr,"Wrong number of fields at %d-th sample ([%c][%c][%c]). ",i+1,ss[0],ss[1],ss[2]); return -1; } switch(ss[all*2+up]){ case '0': args->gts[2*i+all] = a0; break; case '1' : args->gts[2*i+all] = a1; break; case '?' : // there is no macro to express phased missing allele args->gts[2*i+all] = bcf_gt_phased(-1); break; case '-' : args->gts[2*i+all] = bcf_int32_vector_end; break; default : fprintf(stderr,"Could not parse: [%c][%s]\n", ss[all*2+up],tsv->ss); return -1; } if( ss[all*2+up+1]=='*' ) up = up + 1; } if(up && up != 2) { fprintf(stderr,"Missing unphased marker '*': [%c][%s]", ss[2+up], tsv->ss); return -1; } // change alleles to unphased if the alleles are unphased if ( up ) { args->gts[2*i] = bcf_gt_unphased(bcf_gt_allele(args->gts[2*i])); args->gts[2*i+1] = bcf_gt_unphased(bcf_gt_allele(args->gts[2*i+1])); } nup = nup + up; } if ( tsv->ss[(nsamples-1)*4+3+nup] ) { fprintf(stderr,"nup: %d", nup); fprintf(stderr,"Wrong number of fields (%d-th column = [%c]). ", nsamples*2,tsv->ss[(nsamples-1)*4+nup]); return -1; } if ( bcf_update_genotypes(args->header,rec,args->gts,nsamples*2) ) error("Could not update GT field\n"); return 0; } static void gensample_to_vcf(args_t *args) { /* * Inpute: IMPUTE2 output (indentation changed here for clarity): * * 20:62116619_C_T 20:62116619 62116619 C T 0.969 0.031 0 ... * --- 20:62116698_C_A 62116698 C A 1 0 0 ... * * Second column is expected in the form of CHROM:POS_REF_ALT. We use second * column because the first can be empty ("--") when filling sites from reference * panel. When the option --vcf-ids is given, the first column is used to set the * VCF ID. * * Output: VCF with filled GT,GP * */ kstring_t line = {0,0,0}; char *gen_fname = NULL, *sample_fname = NULL; sample_fname = strchr(args->infname,','); if ( !sample_fname ) { args->str.l = 0; ksprintf(&args->str,"%s.gen.gz", args->infname); gen_fname = strdup(args->str.s); args->str.l = 0; ksprintf(&args->str,"%s.samples", args->infname); sample_fname = strdup(args->str.s); } else { *sample_fname = 0; gen_fname = strdup(args->infname); sample_fname = strdup(sample_fname+1); } htsFile *gen_fh = hts_open(gen_fname, "r"); if ( !gen_fh ) error("Could not read: %s\n", gen_fname); if ( hts_getline(gen_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", gen_fname); // Find out the chromosome name, depending on the format variant (--3N6 or plain) and the ordering // of the columns (CHROM:POS_REF_ALT comes first or second) args->str.l = 0; char *sb = line.s, *se = line.s; while ( *se && !isspace(*se) ) se++; if ( !*se ) error("Could not determine CHROM in %s: %s\n", gen_fname,line.s); if ( args->gen_3N6 ) // first column, just CHROM kputsn(sb, se-sb, &args->str); else // first or second column, part of CHROM:POS_REF_ALT { char *sc = strchr(sb,':'); if ( !sc || sc > se ) { while ( *se && !isspace(*se) ) se++; if ( !*se ) error("Could not determine CHROM in %s: %s\n", gen_fname,line.s); sb = ++se; sc = strchr(sb,':'); if ( !sc ) error("Could not determine CHROM in %s: %s\n", gen_fname,line.s); } kputsn(sb, sc-sb, &args->str); } // Initialize and print the VCF header, args->str.s contains the chr name args->header = bcf_hdr_init("w"); bcf_hdr_append(args->header, "##INFO="); bcf_hdr_append(args->header, "##FORMAT="); bcf_hdr_append(args->header, "##FORMAT="); bcf_hdr_printf(args->header, "##contig=", args->str.s,0x7fffffff); // MAX_CSI_COOR if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert"); tsv_t *tsv; if ( args->gen_3N6 ) { tsv = tsv_init("CHROM,CHROM_POS_REF_ALT,ID,POS,REF_ALT,GT_GP"); tsv_register(tsv, "CHROM", tsv_setter_chrom, args->header); } else tsv = tsv_init("CHROM_POS_REF_ALT,ID,POS,REF_ALT,GT_GP"); tsv_register(tsv, "CHROM_POS_REF_ALT", tsv_setter_chrom_pos_ref_alt_or_id, args); tsv_register(tsv, "ID", tsv_setter_chrom_pos_ref_alt_id_or_die, args); tsv_register(tsv, "POS", tsv_setter_verify_pos, NULL); tsv_register(tsv, "REF_ALT", tsv_setter_verify_ref_alt, args); tsv_register(tsv, "GT_GP", tsv_setter_gt_gp, args); // Find out sample names int i, nsamples; char **samples = hts_readlist(sample_fname, 1, &nsamples); if ( !samples ) error("Could not read %s\n", sample_fname); for (i=2; iheader,samples[i]); } for (i=0; ioutput_type,args->outfname,args->clevel); htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode); if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno)); if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads); if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->outfname); if ( init_index2(out_fh,args->header,args->outfname,&args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->outfname); bcf1_t *rec = bcf_init(); nsamples -= 2; args->gts = (int32_t *) malloc(sizeof(int32_t)*nsamples*2); args->flt = (float *) malloc(sizeof(float)*nsamples*3); do { bcf_clear(rec); args->n.total++; if ( !tsv_parse(tsv, rec, line.s) ) { if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); } else error("Error occurred while parsing: %s\n", line.s); } while ( hts_getline(gen_fh, KS_SEP_LINE, &line)>0 ); if ( args->write_index ) { if ( bcf_idx_save(out_fh)<0 ) { if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); if ( hts_close(gen_fh) ) error("Close failed: %s\n", gen_fname); bcf_hdr_destroy(args->header); bcf_destroy(rec); free(sample_fname); free(gen_fname); free(args->str.s); free(line.s); free(args->gts); free(args->flt); tsv_destroy(tsv); fprintf(stderr,"Number of processed rows: \t%d\n", args->n.total); } static void haplegendsample_to_vcf(args_t *args) { /* * Convert from IMPUTE2 hap/legend/sample output files to VCF * * hap: * 0 1 0 1 * legend: * id position a0 a1 * 1:186946386_G_T 186946386 G T * sample: * sample population group sex * sample1 sample1 sample1 2 * sample2 sample2 sample2 2 * * Output: VCF with filled GT */ kstring_t line = {0,0,0}; if ( args->output_vcf_ids ) error( "The option --haplegendsample2vcf cannot be combined with --vcf-ids. This is because the\n" "ID column must be formatted as \"CHROM:POS_REF_ALT\" to check sanity of the operation\n"); char *hap_fname = NULL, *leg_fname = NULL, *sample_fname = NULL; sample_fname = strchr(args->infname,','); if ( !sample_fname ) { args->str.l = 0; ksprintf(&args->str,"%s.hap.gz", args->infname); hap_fname = strdup(args->str.s); args->str.l = 0; ksprintf(&args->str,"%s.samples", args->infname); sample_fname = strdup(args->str.s); args->str.l = 0; ksprintf(&args->str,"%s.legend.gz", args->infname); leg_fname = strdup(args->str.s); } else { char *ss = sample_fname, *se = strchr(ss+1,','); if ( !se ) error("Could not parse hap/legend/sample file names: %s\n", args->infname); *ss = 0; *se = 0; hap_fname = strdup(args->infname); leg_fname = strdup(ss+1); sample_fname = strdup(se+1); } htsFile *hap_fh = hts_open(hap_fname, "r"); if ( !hap_fh ) error("Could not read: %s\n", hap_fname); htsFile *leg_fh = hts_open(leg_fname,"r"); if ( !leg_fh ) error("Could not read: %s\n", leg_fname); // Eat up first legend line, then determine chromosome name if ( hts_getline(leg_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", leg_fname); if ( hts_getline(leg_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", leg_fname); // Find out the chromosome name, sample names, init and print the VCF header args->str.l = 0; char *se = strchr(line.s,':'); if ( !se ) error("Expected CHROM:POS_REF_ALT in first column of %s\n", leg_fname); kputsn(line.s, se-line.s, &args->str); tsv_t *leg_tsv = tsv_init("CHROM_POS_REF_ALT,POS,REF_ALT"); tsv_register(leg_tsv, "CHROM_POS_REF_ALT", tsv_setter_chrom_pos_ref_alt, args); tsv_register(leg_tsv, "POS", tsv_setter_verify_pos, NULL); tsv_register(leg_tsv, "REF_ALT", tsv_setter_verify_ref_alt, args); tsv_t *hap_tsv = tsv_init("HAPS"); tsv_register(hap_tsv, "HAPS", tsv_setter_haps, args); args->header = bcf_hdr_init("w"); bcf_hdr_append(args->header, "##INFO="); bcf_hdr_append(args->header, "##FORMAT="); bcf_hdr_printf(args->header, "##contig=", args->str.s,0x7fffffff); // MAX_CSI_COOR if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert"); int i, nrows, nsamples; char **samples = hts_readlist(sample_fname, 1, &nrows); if ( !samples ) error("Could not read %s\n", sample_fname); nsamples = nrows - 1; // sample_fname should contain a header line, so need to ignore first row // returned from hts_readlist (i=1, and not i=0) for (i=1; iheader,samples[i]); } bcf_hdr_add_sample(args->header,NULL); for (i=0; ioutput_type,args->outfname,args->clevel); htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode); if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno)); if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads); if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->outfname); if ( init_index2(out_fh,args->header,args->outfname,&args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->outfname); bcf1_t *rec = bcf_init(); args->gts = (int32_t *) malloc(sizeof(int32_t)*nsamples*2); while (1) { bcf_clear(rec); args->n.total++; if ( tsv_parse(leg_tsv, rec, line.s) ) error("Error occurred while parsing %s: %s\n", leg_fname,line.s); if ( hts_getline(hap_fh, KS_SEP_LINE, &line)<=0 ) error("Different number of records in %s and %s?\n", leg_fname,hap_fname); if ( tsv_parse(hap_tsv, rec, line.s) ) error("Error occurred while parsing %s: %s\n", hap_fname,line.s); if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); if ( hts_getline(leg_fh, KS_SEP_LINE, &line)<=0 ) { if ( hts_getline(hap_fh, KS_SEP_LINE, &line)>0 ) error("Different number of records in %s and %s?\n", leg_fname,hap_fname); break; } } if ( args->write_index ) { if ( bcf_idx_save(out_fh)<0 ) { if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); if ( hts_close(hap_fh) ) error("Close failed: %s\n", hap_fname); if ( hts_close(leg_fh) ) error("Close failed: %s\n", leg_fname); bcf_hdr_destroy(args->header); bcf_destroy(rec); free(sample_fname); free(hap_fname); free(leg_fname); free(args->str.s); free(line.s); free(args->gts); tsv_destroy(hap_tsv); tsv_destroy(leg_tsv); fprintf(stderr,"Number of processed rows: \t%d\n", args->n.total); } static void hapsample_to_vcf(args_t *args) { /* * Input: SHAPEIT output * * 20:19995888_A_G rsid1 19995888 A G 0 0 0 0 ... * 20 20:19995888_A_G 19995888 A G 0 0 0 0 ... * * First column is expected in the form of CHROM:POS_REF_ALT * * Output: VCF with filled GT * */ kstring_t line = {0,0,0}; char *hap_fname = NULL, *sample_fname = NULL; sample_fname = strchr(args->infname,','); if ( !sample_fname ) { args->str.l = 0; ksprintf(&args->str,"%s.hap.gz", args->infname); hap_fname = strdup(args->str.s); args->str.l = 0; ksprintf(&args->str,"%s.samples", args->infname); sample_fname = strdup(args->str.s); } else { *sample_fname = 0; hap_fname = strdup(args->infname); sample_fname = strdup(sample_fname+1); } htsFile *hap_fh = hts_open(hap_fname, "r"); if ( !hap_fh ) error("Could not read: %s\n", hap_fname); if ( hts_getline(hap_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", hap_fname); // Find out the chromosome name, it can be either in the first or second column args->str.l = 0; char *sb = line.s, *se = line.s; while ( *se && !isspace(*se) ) se++; if ( !*se ) error("Could not determine CHROM in %s: %s\n", hap_fname,line.s); if ( !args->output_vcf_ids ) { // first column should be just CHROM, but the second must be CHROM:POS_REF_ALT, use that sb = ++se; while ( *se && !isspace(*se) ) se++; if ( !*se ) error("Could not determine CHROM in %s: %s\n", hap_fname,line.s); if ( !strchr(sb,':') ) error("Could not determine CHROM in the second column of %s: %s\n", hap_fname,line.s); } // Parse CHROM:POS_REF_ALT char *sc = strchr(sb,':'); if ( !sc || sc > se ) error("Could not determine CHROM in %s: %s\n", hap_fname,line.s); kputsn(sb, sc-sb, &args->str); // Initialize and print the VCF header, args->str.s contains the chr name args->header = bcf_hdr_init("w"); bcf_hdr_append(args->header, "##INFO="); bcf_hdr_append(args->header, "##FORMAT="); bcf_hdr_printf(args->header, "##contig=", args->str.s,0x7fffffff); // MAX_CSI_COOR if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert"); tsv_t *tsv; if ( args->output_vcf_ids ) { tsv = tsv_init("CHROM_POS_REF_ALT,ID,POS,REF_ALT,HAPS"); tsv_register(tsv, "ID", tsv_setter_id, args); } else { tsv = tsv_init("CHROM,CHROM_POS_REF_ALT,POS,REF_ALT,HAPS"); tsv_register(tsv, "CHROM", tsv_setter_chrom_pos_ref_alt_or_chrom, args); } tsv_register(tsv, "CHROM_POS_REF_ALT", tsv_setter_chrom_pos_ref_alt, args); tsv_register(tsv, "POS", tsv_setter_verify_pos, NULL); tsv_register(tsv, "REF_ALT", tsv_setter_verify_ref_alt, args); tsv_register(tsv, "HAPS", tsv_setter_haps, args); int i, nsamples; char **samples = hts_readlist(sample_fname, 1, &nsamples); if ( !samples ) error("Could not read %s\n", sample_fname); for (i=2; iheader,samples[i]); } bcf_hdr_add_sample(args->header,NULL); for (i=0; ioutput_type,args->outfname,args->clevel); htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode); if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno)); if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads); if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); if ( init_index2(out_fh,args->header,args->outfname,&args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->outfname); bcf1_t *rec = bcf_init(); nsamples -= 2; args->gts = (int32_t *) malloc(sizeof(int32_t)*nsamples*2); do { bcf_clear(rec); args->n.total++; if ( !tsv_parse(tsv, rec, line.s) ) { if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); } else error("Error occurred while parsing: %s\n", line.s); } while ( hts_getline(hap_fh, KS_SEP_LINE, &line)>0 ); if ( args->write_index ) { if ( bcf_idx_save(out_fh)<0 ) { if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); if ( hts_close(hap_fh) ) error("Close failed: %s\n", hap_fname); bcf_hdr_destroy(args->header); bcf_destroy(rec); free(sample_fname); free(hap_fname); free(args->str.s); free(line.s); free(args->gts); tsv_destroy(tsv); fprintf(stderr,"Number of processed rows: \t%d\n", args->n.total); } char *init_sample2sex(bcf_hdr_t *hdr, char *sex_fname) { int i, nlines; char *sample2sex = (char*) calloc(bcf_hdr_nsamples(hdr),1); char **lines = hts_readlist(sex_fname, 1, &nlines); if ( !lines ) error("Could not read %s\n", sex_fname); for (i=0; igen_3N6 ) kputs("%CHROM ", &str); kputs("%CHROM:%POS\\_%REF\\_%FIRST_ALT ", &str); // insert rsid as second column if needed if ( args->output_vcf_ids ) kputs("%ID ", &str); else kputs("%CHROM:%POS\\_%REF\\_%FIRST_ALT ", &str); kputs("%POS %REF %FIRST_ALT", &str); if ( !args->tag || !strcmp(args->tag,"GT") ) kputs("%_GT_TO_PROB3",&str); else if ( !strcmp(args->tag,"PL") ) kputs("%_PL_TO_PROB3",&str); else if ( !strcmp(args->tag,"GP") ) kputs("%_GP_TO_PROB3",&str); else error("todo: --tag %s\n", args->tag); kputs("\n", &str); open_vcf(args,str.s); int ret, gen_compressed = 1, sample_compressed = 0; char *gen_fname = NULL, *sample_fname = NULL; str.l = 0; kputs(args->outfname,&str); int n_files = 0, i; char **files = hts_readlist(str.s, 0, &n_files); if ( n_files==1 ) { int l = str.l; kputs(".samples",&str); sample_fname = strdup(str.s); str.l = l; kputs(".gen.gz",&str); gen_fname = strdup(str.s); } else if ( n_files==2 ) { if (strlen(files[0]) && strcmp(files[0],".")!=0) gen_fname = strdup(files[0]); if (strlen(files[1]) && strcmp(files[1],".")!=0) sample_fname = strdup(files[1]); } else { error("Error parsing --gensample filenames: %s\n", args->outfname); } for (i=0; i3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0; if (gen_fname) fprintf(stderr, "Gen file: %s\n", gen_fname); if (sample_fname) fprintf(stderr, "Sample file: %s\n", sample_fname); // write samples file if (sample_fname) { char *sample2sex = NULL; if ( args->sex_fname ) sample2sex = init_sample2sex(args->header,args->sex_fname); int i; BGZF *sout = bgzf_open(sample_fname, sample_compressed ? "wg" : "wu"); str.l = 0; kputs(sample2sex ? "ID_1 ID_2 missing sex\n0 0 0 0\n" : "ID_1 ID_2 missing\n0 0 0\n", &str); ret = bgzf_write(sout, str.s, str.l); if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno)); for (i=0; iheader); i++) { str.l = 0; if ( sample2sex ) ksprintf(&str, "%s %s 0 %c\n", args->header->samples[i],args->header->samples[i],sample2sex[i]); else ksprintf(&str, "%s %s 0\n", args->header->samples[i],args->header->samples[i]); ret = bgzf_write(sout, str.s, str.l); if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno)); } if ( bgzf_close(sout)!=0 ) error("Error closing %s: %s\n", sample_fname, strerror(errno)); free(sample_fname); free(sample2sex); } if (!gen_fname) { if ( str.m ) free(str.s); return; } int prev_rid = -1, prev_pos = -1; int no_alt = 0, non_biallelic = 0, filtered = 0, ndup = 0, nok = 0; BGZF *gout = bgzf_open(gen_fname, gen_compressed ? "wg" : "wu"); while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = bcf_sr_get_line(args->files,0); if ( args->filter ) { int pass = filter_test(args->filter, line, NULL); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { filtered++; continue; } } // ALT allele is required if ( line->n_allele<2 ) { no_alt++; continue; } // biallelic required if ( line->n_allele>2 ) { if (!non_biallelic) fprintf(stderr, "Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n"); non_biallelic++; continue; } // skip duplicate lines, or otherwise shapeit complains if ( !args->keep_duplicates && prev_rid==line->rid && prev_pos==line->pos ) { ndup++; continue; } prev_rid = line->rid; prev_pos = line->pos; str.l = 0; convert_line(args->convert, line, &str); if ( str.l ) { int ret = bgzf_write(gout, str.s, str.l); if ( ret!= str.l ) error("Error writing %s: %s\n", gen_fname,strerror(errno)); nok++; } } fprintf(stderr, "%d records written, %d skipped: %d/%d/%d/%d no-ALT/non-biallelic/filtered/duplicated\n", nok, no_alt+non_biallelic+filtered+ndup, no_alt, non_biallelic, filtered, ndup); if ( str.m ) free(str.s); if ( bgzf_close(gout)!=0 ) error("Error closing %s: %s\n", gen_fname,strerror(errno)); free(gen_fname); } static void vcf_to_haplegendsample(args_t *args) { kstring_t str = {0,0,0}; if ( args->hap2dip ) kputs("%_GT_TO_HAP2\n", &str); else kputs("%_GT_TO_HAP\n", &str); open_vcf(args,str.s); int ret, hap_compressed = 1, legend_compressed = 1, sample_compressed = 0; char *hap_fname = NULL, *legend_fname = NULL, *sample_fname = NULL; str.l = 0; kputs(args->outfname,&str); int n_files = 0, i; char **files = hts_readlist(str.s, 0, &n_files); if ( n_files==1 ) { int l = str.l; kputs(".samples",&str); sample_fname = strdup(str.s); str.l = l; kputs(".legend.gz",&str); legend_fname = strdup(str.s); str.l = l; kputs(".hap.gz",&str); hap_fname = strdup(str.s); } else if ( n_files==3 ) { if (strlen(files[0]) && strcmp(files[0],".")!=0) hap_fname = strdup(files[0]); if (strlen(files[1]) && strcmp(files[1],".")!=0) legend_fname = strdup(files[1]); if (strlen(files[2]) && strcmp(files[2],".")!=0) sample_fname = strdup(files[2]); } else { error("Error parsing --hapslegendsample filenames: %s\n", args->outfname); } for (i=0; i3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0; if (hap_fname) fprintf(stderr, "Hap file: %s\n", hap_fname); if (legend_fname) fprintf(stderr, "Legend file: %s\n", legend_fname); if (sample_fname) fprintf(stderr, "Sample file: %s\n", sample_fname); // write samples file if (sample_fname) { char *sample2sex = NULL; if ( args->sex_fname ) sample2sex = init_sample2sex(args->header,args->sex_fname); int i; BGZF *sout = bgzf_open(sample_fname, sample_compressed ? "wg" : "wu"); str.l = 0; kputs("sample population group sex\n", &str); ret = bgzf_write(sout, str.s, str.l); if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno)); for (i=0; iheader); i++) { str.l = 0; ksprintf(&str, "%s %s %s %c\n", args->header->samples[i], args->header->samples[i], args->header->samples[i], sample2sex ? sample2sex[i] : '2'); ret = bgzf_write(sout, str.s, str.l); if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno)); } if ( bgzf_close(sout)!=0 ) error("Error closing %s: %s\n", sample_fname, strerror(errno)); free(sample_fname); free(sample2sex); } if (!hap_fname && !legend_fname) { if ( str.m ) free(str.s); return; } // open haps and legend outputs BGZF *hout = hap_fname ? bgzf_open(hap_fname, hap_compressed ? "wg" : "wu") : NULL; if ( hap_compressed && args->n_threads ) bgzf_thread_pool(hout, args->files->p->pool, args->files->p->qsize); BGZF *lout = legend_fname ? bgzf_open(legend_fname, legend_compressed ? "wg" : "wu") : NULL; if (legend_fname) { str.l = 0; kputs("id position a0 a1\n", &str); ret = bgzf_write(lout, str.s, str.l); if ( ret != str.l ) error("Error writing %s: %s\n", legend_fname, strerror(errno)); } int no_alt = 0, non_biallelic = 0, filtered = 0, nok = 0; while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = bcf_sr_get_line(args->files,0); if ( args->filter ) { int pass = filter_test(args->filter, line, NULL); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { filtered++; continue; } } // ALT allele is required if ( line->n_allele<2 ) { no_alt++; continue; } // biallelic required if ( line->n_allele>2 ) { if (!non_biallelic) fprintf(stderr, "Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n"); non_biallelic++; continue; } str.l = 0; convert_line(args->convert, line, &str); if ( !str.l ) continue; // write haps file if (hap_fname) { ret = bgzf_write(hout, str.s, str.l); // write hap file if ( ret != str.l ) error("Error writing %s: %s\n", hap_fname, strerror(errno)); } if (legend_fname) { str.l = 0; if ( args->output_vcf_ids && (line->d.id[0]!='.' || line->d.id[1]!=0) ) ksprintf(&str, "%s %"PRId64" %s %s\n", line->d.id, (int64_t) line->pos+1, line->d.allele[0], line->d.allele[1]); else ksprintf(&str, "%s:%"PRId64"_%s_%s %"PRId64" %s %s\n", bcf_seqname(args->header, line), (int64_t) line->pos+1, line->d.allele[0], line->d.allele[1], (int64_t) line->pos+1, line->d.allele[0], line->d.allele[1]); // write legend file ret = bgzf_write(lout, str.s, str.l); if ( ret != str.l ) error("Error writing %s: %s\n", legend_fname, strerror(errno)); } nok++; } fprintf(stderr, "%d records written, %d skipped: %d/%d/%d no-ALT/non-biallelic/filtered\n", nok,no_alt+non_biallelic+filtered, no_alt, non_biallelic, filtered); if ( str.m ) free(str.s); if ( hout && bgzf_close(hout)!=0 ) error("Error closing %s: %s\n", hap_fname, strerror(errno)); if ( lout && bgzf_close(lout)!=0 ) error("Error closing %s: %s\n", legend_fname, strerror(errno)); if (hap_fname) free(hap_fname); if (legend_fname) free(legend_fname); } static void vcf_to_hapsample(args_t *args) { /* * WTCCC style haplotypes file * see https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#hapsample * * These are essentially the haplotypes from the impute2 format with some * legend info tacked on to the first 5 columns * */ kstring_t str = {0,0,0}; // print ID instead of CHROM:POS_REF_ALT1 if ( args->output_vcf_ids ) kputs("%CHROM:%POS\\_%REF\\_%FIRST_ALT %ID %POS %REF %FIRST_ALT ", &str); else kputs("%CHROM %CHROM:%POS\\_%REF\\_%FIRST_ALT %POS %REF %FIRST_ALT ", &str); if ( args->hap2dip ) kputs("%_GT_TO_HAP2\n", &str); else kputs("%_GT_TO_HAP\n", &str); open_vcf(args,str.s); int ret, hap_compressed = 1, sample_compressed = 0; char *hap_fname = NULL, *sample_fname = NULL; str.l = 0; kputs(args->outfname,&str); int n_files = 0, i; char **files = hts_readlist(str.s, 0, &n_files); if ( n_files==1 ) { int l = str.l; kputs(".samples",&str); sample_fname = strdup(str.s); str.l = l; kputs(".hap.gz",&str); hap_fname = strdup(str.s); } else if ( n_files==2 ) { if (strlen(files[0]) && strcmp(files[0],".")!=0) hap_fname = strdup(files[0]); if (strlen(files[1]) && strcmp(files[1],".")!=0) sample_fname = strdup(files[1]); } else { error("Error parsing --hapsample filenames: %s\n", args->outfname); } for (i=0; i3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0; if (hap_fname) fprintf(stderr, "Hap file: %s\n", hap_fname); if (sample_fname) fprintf(stderr, "Sample file: %s\n", sample_fname); // write samples file if (sample_fname) { char *sample2sex = NULL; if ( args->sex_fname ) sample2sex = init_sample2sex(args->header,args->sex_fname); int i; BGZF *sout = bgzf_open(sample_fname, sample_compressed ? "wg" : "wu"); str.l = 0; kputs(sample2sex ? "ID_1 ID_2 missing sex\n0 0 0 0\n" : "ID_1 ID_2 missing\n0 0 0\n", &str); ret = bgzf_write(sout, str.s, str.l); if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno)); for (i=0; iheader); i++) { str.l = 0; if ( sample2sex ) ksprintf(&str, "%s %s 0 %c\n", args->header->samples[i],args->header->samples[i],sample2sex[i]); else ksprintf(&str, "%s %s 0\n", args->header->samples[i],args->header->samples[i]); ret = bgzf_write(sout, str.s, str.l); if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno)); } if ( bgzf_close(sout)!=0 ) error("Error closing %s: %s\n", sample_fname, strerror(errno)); free(sample_fname); free(sample2sex); } if (!hap_fname) { if ( str.m ) free(str.s); return; } // open haps output BGZF *hout = hap_fname ? bgzf_open(hap_fname, hap_compressed ? "wg" : "wu") : NULL; if ( hap_compressed && args->n_threads ) bgzf_thread_pool(hout, args->files->p->pool, args->files->p->qsize); int no_alt = 0, non_biallelic = 0, filtered = 0, nok = 0; while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = bcf_sr_get_line(args->files,0); if ( args->filter ) { int pass = filter_test(args->filter, line, NULL); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { filtered++; continue; } } // ALT allele is required if ( line->n_allele<2 ) { no_alt++; continue; } // biallelic required if ( line->n_allele>2 ) { if (!non_biallelic) fprintf(stderr, "Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n"); non_biallelic++; continue; } str.l = 0; convert_line(args->convert, line, &str); if ( !str.l ) continue; // write haps file if (hap_fname) { ret = bgzf_write(hout, str.s, str.l); // write hap file if ( ret != str.l ) error("Error writing %s: %s\n", hap_fname, strerror(errno)); } nok++; } fprintf(stderr, "%d records written, %d skipped: %d/%d/%d no-ALT/non-biallelic/filtered\n", nok, no_alt+non_biallelic+filtered, no_alt, non_biallelic, filtered); if ( str.m ) free(str.s); if ( hout && bgzf_close(hout)!=0 ) error("Error closing %s: %s\n", hap_fname, strerror(errno)); if (hap_fname) free(hap_fname); } static void bcf_hdr_set_chrs(bcf_hdr_t *hdr, faidx_t *fai) { int i, n = faidx_nseq(fai); for (i=0; i", seq,len); } } static inline int acgt_to_5(char base) { if ( base=='A' ) return 0; if ( base=='C' ) return 1; if ( base=='G' ) return 2; if ( base=='T' ) return 3; return 4; } static inline int tsv_setter_aa1(args_t *args, char *ss, char *se, int alleles[], int *nals, int ref, int32_t *gts) { if ( se - ss > 2 ) return -1; // currently only SNPs if ( ss[0]=='-' || ss[0]=='.' ) { // missing GT gts[0] = bcf_gt_missing; gts[1] = bcf_gt_missing; args->n.missing++; return 0; } if ( ss[0]=='I' ) return -2; // skip insertions/deletions for now if ( ss[0]=='D' ) return -2; int a0 = acgt_to_5(toupper(ss[0])); int a1 = ss[1] ? acgt_to_5(toupper(ss[1])) : a0; if ( alleles[a0]<0 ) alleles[a0] = (*nals)++; if ( alleles[a1]<0 ) alleles[a1] = (*nals)++; gts[0] = bcf_gt_unphased(alleles[a0]); gts[1] = ss[1] ? bcf_gt_unphased(alleles[a1]) : bcf_int32_vector_end; if ( ref==a0 && ref==a1 ) args->n.hom_rr++; // hom ref: RR else if ( ref==a0 ) args->n.het_ra++; // het: RA else if ( ref==a1 ) args->n.het_ra++; // het: AR else if ( a0==a1 ) args->n.hom_aa++; // hom-alt: AA else args->n.het_aa++; // non-ref het: AA return 0; } static int tsv_setter_aa(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*) usr; int len; char *ref = faidx_fetch_seq(args->ref, (char*)bcf_hdr_id2name(args->header,rec->rid), rec->pos, rec->pos, &len); if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_hdr_id2name(args->header,rec->rid),(int64_t) rec->pos+1); int nals = 1, alleles[5] = { -1, -1, -1, -1, -1 }; // a,c,g,t,n ref[0] = toupper(ref[0]); int iref = acgt_to_5(ref[0]); alleles[iref] = 0; rec->n_sample = bcf_hdr_nsamples(args->header); int i, ret; for (i=0; in_sample; i++) { if ( i>0 ) { ret = tsv_next(tsv); if ( ret==-1 ) error("Too few columns for %d samples at %s:%"PRId64"\n", rec->n_sample,bcf_hdr_id2name(args->header,rec->rid),(int64_t) rec->pos+1); } ret = tsv_setter_aa1(args, tsv->ss, tsv->se, alleles, &nals, iref, args->gts+i*2); if ( ret==-1 ) error("Error parsing the site %s:%"PRId64", expected two characters\n", bcf_hdr_id2name(args->header,rec->rid),(int64_t) rec->pos+1); if ( ret==-2 ) { // something else than a SNP free(ref); return -1; } } args->str.l = 0; kputc(ref[0], &args->str); for (i=0; i<5; i++) { if ( alleles[i]>0 ) { kputc(',', &args->str); kputc("ACGTN"[i], &args->str); } } bcf_update_alleles_str(args->header, rec, args->str.s); if ( bcf_update_genotypes(args->header,rec,args->gts,rec->n_sample*2) ) error("Could not update the GT field\n"); free(ref); return 0; } static void tsv_to_vcf(args_t *args) { if ( !args->ref_fname ) error("--tsv2vcf requires the --fasta-ref option\n"); args->ref = fai_load(args->ref_fname); if ( !args->ref ) error("Could not load the reference %s\n", args->ref_fname); args->header = bcf_hdr_init("w"); bcf_hdr_set_chrs(args->header, args->ref); bcf_hdr_append(args->header, "##FORMAT="); if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert"); int i, nsmpl; char **smpl; if ( args->sample_list ) { smpl = hts_readlist(args->sample_list, args->sample_is_file, &nsmpl); if ( !smpl ) error("Could not parse %s\n", args->sample_list); for (i=0; iheader, smpl[i]); free(smpl[i]); } free(smpl); bcf_hdr_add_sample(args->header, NULL); args->gts = (int32_t *) malloc(sizeof(int32_t)*nsmpl*2); } char wmode[8]; set_wmode(wmode,args->output_type,args->outfname,args->clevel); htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode); if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno)); if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads); if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); if ( init_index2(out_fh,args->header,args->outfname,&args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->outfname); tsv_t *tsv = tsv_init(args->columns ? args->columns : "ID,CHROM,POS,AA"); if ( tsv_register(tsv, "CHROM", tsv_setter_chrom, args->header) < 0 ) error("Expected CHROM column\n"); if ( tsv_register(tsv, "POS", tsv_setter_pos, NULL) < 0 ) error("Expected POS column\n"); if ( tsv_register(tsv, "ID", tsv_setter_id, args->header) < 0 && !args->columns ) error("Expected ID column\n"); if ( tsv_register(tsv, "AA", tsv_setter_aa, args) < 0 ) { if ( args->sample_list ) error("Expected AA column with -s/-S\n"); if ( tsv_register(tsv, "REF", tsv_setter_ref, args) < 0 || tsv_register(tsv, "ALT", tsv_setter_alt, args) < 0 ) error("Expected REF and ALT columns when AA was not given\n"); } bcf1_t *rec = bcf_init(); bcf_float_set_missing(rec->qual); kstring_t line = {0,0,0}; htsFile *in_fh = hts_open(args->infname, "r"); if ( !in_fh ) error("Could not read: %s\n", args->infname); while ( hts_getline(in_fh, KS_SEP_LINE, &line) > 0 ) { if ( line.s[0]=='#' ) continue; // skip comments bcf_clear(rec); args->n.total++; if ( !tsv_parse(tsv, rec, line.s) ) { if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); args->n.written++; } else args->n.skipped++; } if ( hts_close(in_fh) ) error("Close failed: %s\n", args->infname); free(line.s); if ( args->write_index ) { if ( bcf_idx_save(out_fh)<0 ) { if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } bcf_hdr_destroy(args->header); if ( hts_close(out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->outfname); tsv_destroy(tsv); bcf_destroy(rec); free(args->str.s); free(args->gts); free(args->tsv.ref.s); free(args->tsv.alt.s); free(args->tsv.refalt.s); fprintf(stderr,"Rows total: \t%d\n", args->n.total); fprintf(stderr,"Rows skipped: \t%d\n", args->n.skipped); fprintf(stderr,"Sites written: \t%d\n", args->n.written); if ( args->sample_list ) { fprintf(stderr,"Missing GTs: \t%d\n", args->n.missing); fprintf(stderr,"Hom RR: \t%d\n", args->n.hom_rr); fprintf(stderr,"Het RA: \t%d\n", args->n.het_ra); fprintf(stderr,"Hom AA: \t%d\n", args->n.hom_aa); fprintf(stderr,"Het AA: \t%d\n", args->n.het_aa); } } static void vcf_to_vcf(args_t *args) { open_vcf(args,NULL); char wmode[8]; set_wmode(wmode,args->output_type,args->outfname,args->clevel); htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode); if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno)); if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads); bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0); if ( bcf_hdr_write(out_fh,hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); if ( init_index2(out_fh,args->header,args->outfname,&args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->outfname); while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = bcf_sr_get_line(args->files,0); if ( args->filter ) { int pass = filter_test(args->filter, line, NULL); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) continue; } if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); } if ( args->write_index ) { if ( bcf_idx_save(out_fh)<0 ) { if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->outfname); } static void gvcf_to_vcf(args_t *args) { if ( !args->ref_fname ) error("--gvcf2vcf requires the --fasta-ref option\n"); args->ref = fai_load(args->ref_fname); if ( !args->ref ) error("Could not load the fai index for reference %s\n", args->ref_fname); open_vcf(args,NULL); char wmode[8]; set_wmode(wmode,args->output_type,args->outfname,args->clevel); htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode); if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno)); if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads); bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0); if (args->record_cmd_line) bcf_hdr_append_version(hdr, args->argc, args->argv, "bcftools_convert"); if ( bcf_hdr_write(out_fh,hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); if ( init_index2(out_fh,hdr,args->outfname,&args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->outfname); int32_t *itmp = NULL, nitmp = 0; while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = bcf_sr_get_line(args->files,0); if ( args->filter ) { int pass = filter_test(args->filter, line, NULL); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); continue; } } // check if alleles compatible with being a gVCF record // ALT must be one of ., <*>, , // check for INFO/END is below int i, gallele = -1; if (line->n_allele==1) gallele = 0; // illumina/bcftools-call gvcf (if INFO/END present) else if ( line->d.allele[1][0]=='<' ) { for (i=1; in_allele; i++) { if ( line->d.allele[i][1]=='*' && line->d.allele[i][2]=='>' && line->d.allele[i][3]=='\0' ) { gallele = i; break; } // mpileup/spec compliant gVCF if ( line->d.allele[i][1]=='X' && line->d.allele[i][2]=='>' && line->d.allele[i][3]=='\0' ) { gallele = i; break; } // old mpileup gVCF if ( strcmp(line->d.allele[i],"")==0 ) { gallele = i; break; } // GATK gVCF } } // no gVCF compatible alleles if (gallele<0) { if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); continue; } int nend = bcf_get_info_int32(hdr,line,"END",&itmp,&nitmp); if ( nend!=1 ) { // No INFO/END => not gVCF record if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); continue; } bcf_update_info_int32(hdr,line,"END",NULL,0); int pos, len; for (pos=line->pos; pospos = pos; char *ref = faidx_fetch_seq(args->ref, (char*)bcf_hdr_id2name(hdr,line->rid), line->pos, line->pos, &len); if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_hdr_id2name(hdr,line->rid),(int64_t) line->pos+1); strncpy(line->d.allele[0],ref,len); if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); free(ref); } } free(itmp); if ( args->write_index ) { if ( bcf_idx_save(out_fh)<0 ) { if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->outfname); } static void usage(void) { fprintf(stderr, "\n"); fprintf(stderr, "About: Converts VCF/BCF to other formats and back. See man page for file\n"); fprintf(stderr, " formats details. When specifying output files explicitly instead\n"); fprintf(stderr, " of with PREFIX, one can use '-' for stdout and '.' to suppress.\n"); fprintf(stderr, "Usage: bcftools convert [OPTIONS] INPUT_FILE\n"); fprintf(stderr, "\n"); fprintf(stderr, "VCF input options:\n"); fprintf(stderr, " -e, --exclude EXPR Exclude sites for which the expression is true\n"); fprintf(stderr, " -i, --include EXPR Select sites for which the expression is true\n"); fprintf(stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " -s, --samples LIST List of samples to include\n"); fprintf(stderr, " -S, --samples-file FILE File of samples to include\n"); fprintf(stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(stderr, "\n"); fprintf(stderr, "VCF output options:\n"); fprintf(stderr, " --no-version Do not append version and command line to the header\n"); fprintf(stderr, " -o, --output FILE Output file name [stdout]\n"); fprintf(stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(stderr, " --threads INT Use multithreading with INT worker threads [0]\n"); fprintf(stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(stderr, "\n"); fprintf(stderr, "GEN/SAMPLE conversion (input/output from IMPUTE2):\n"); fprintf(stderr, " -G, --gensample2vcf ... |,\n"); fprintf(stderr, " -g, --gensample ... |,\n"); fprintf(stderr, " --3N6 Use 3*N+6 column format instead of the old 3*N+5 column format\n"); fprintf(stderr, " --tag STRING Tag to take values for .gen file: GT,PL,GL,GP [GT]\n"); fprintf(stderr, " --chrom Output chromosome in first column instead of CHROM:POS_REF_ALT\n"); fprintf(stderr, " --keep-duplicates Keep duplicate positions\n"); fprintf(stderr, " --sex FILE Output sex column in the sample-file, input format is: Sample\\t[MF]\n"); fprintf(stderr, " --vcf-ids Output VCF IDs in second column instead of CHROM:POS_REF_ALT\n"); fprintf(stderr, "\n"); fprintf(stderr, "gVCF conversion:\n"); fprintf(stderr, " --gvcf2vcf Expand gVCF reference blocks\n"); fprintf(stderr, " -f, --fasta-ref FILE Reference sequence in fasta format\n"); fprintf(stderr, "\n"); fprintf(stderr, "HAP/SAMPLE conversion (output from SHAPEIT):\n"); fprintf(stderr, " --hapsample2vcf ... |,\n"); fprintf(stderr, " --hapsample ... |,\n"); fprintf(stderr, " --haploid2diploid Convert haploid genotypes to diploid homozygotes\n"); fprintf(stderr, " --sex FILE Output sex column in the sample-file, input format is: Sample\\t[MF]\n"); fprintf(stderr, " --vcf-ids Output VCF IDs instead of CHROM:POS_REF_ALT\n"); fprintf(stderr, "\n"); fprintf(stderr, "HAP/LEGEND/SAMPLE conversion:\n"); fprintf(stderr, " -H, --haplegendsample2vcf ... |,,\n"); fprintf(stderr, " -h, --haplegendsample ... |,,\n"); fprintf(stderr, " --haploid2diploid Convert haploid genotypes to diploid homozygotes\n"); fprintf(stderr, " --sex FILE Output sex column in the sample-file, input format is: Sample\\t[MF]\n"); fprintf(stderr, " --vcf-ids Output VCF IDs instead of CHROM:POS_REF_ALT\n"); fprintf(stderr, "\n"); fprintf(stderr, "TSV conversion:\n"); fprintf(stderr, " --tsv2vcf FILE\n"); fprintf(stderr, " -c, --columns STRING Columns of the input tsv file, see man page for details [ID,CHROM,POS,AA]\n"); fprintf(stderr, " -f, --fasta-ref FILE Reference sequence in fasta format\n"); fprintf(stderr, " -s, --samples LIST List of sample names\n"); fprintf(stderr, " -S, --samples-file FILE File of sample names\n"); fprintf(stderr, "\n"); // fprintf(stderr, "PLINK options:\n"); // fprintf(stderr, " -p, --plink |,,|,,|,\n"); // fprintf(stderr, " --tped make tped file instead\n"); // fprintf(stderr, " --bin make binary bed/fam/bim files\n"); // fprintf(stderr, "\n"); // fprintf(stderr, "PBWT options:\n"); // fprintf(stderr, " -b, --pbwt or ,,,\n"); // fprintf(stderr, "\n"); exit(1); } int main_vcfconvert(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->outfname = "-"; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->regions_overlap = 1; args->targets_overlap = 0; args->clevel = -1; static struct option loptions[] = { {"include",required_argument,NULL,'i'}, {"exclude",required_argument,NULL,'e'}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"threads",required_argument,NULL,9}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,13}, {"targets",required_argument,NULL,'t'}, {"targets-file",required_argument,NULL,'T'}, {"targets-overlap",required_argument,NULL,14}, {"samples",required_argument,NULL,'s'}, {"samples-file",required_argument,NULL,'S'}, {"sex",required_argument,NULL,11}, {"gensample",required_argument,NULL,'g'}, {"gensample2vcf",required_argument,NULL,'G'}, {"tag",required_argument,NULL,1}, {"chrom",no_argument,NULL,8}, {"3N6",no_argument,NULL,15}, {"tsv2vcf",required_argument,NULL,2}, {"hapsample",required_argument,NULL,7}, {"hapsample2vcf",required_argument,NULL,3}, {"vcf-ids",no_argument,NULL,4}, {"haploid2diploid",no_argument,NULL,5}, {"gvcf2vcf",no_argument,NULL,6}, {"haplegendsample",required_argument,NULL,'h'}, {"haplegendsample2vcf",required_argument,NULL,'H'}, {"columns",required_argument,NULL,'c'}, {"fasta-ref",required_argument,NULL,'f'}, {"no-version",no_argument,NULL,10}, {"keep-duplicates",no_argument,NULL,12}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "?h:r:R:s:S:t:T:i:e:g:G:o:O:c:f:H:W::",loptions,NULL)) >= 0) { switch (c) { case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; args->regions_is_file = 1; break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; args->targets_is_file = 1; break; case 's': args->sample_list = optarg; break; case 'S': args->sample_list = optarg; args->sample_is_file = 1; break; case 'g': args->convert_func = vcf_to_gensample; args->outfname = optarg; break; case 'G': args->convert_func = gensample_to_vcf; args->infname = optarg; break; case 1 : args->tag = optarg; break; case 2 : args->convert_func = tsv_to_vcf; args->infname = optarg; break; case 3 : args->convert_func = hapsample_to_vcf; args->infname = optarg; break; case 4 : args->output_vcf_ids = 1; break; case 5 : args->hap2dip = 1; break; case 6 : args->convert_func = gvcf_to_vcf; break; case 7 : args->convert_func = vcf_to_hapsample; args->outfname = optarg; break; case 8 : error("The --chrom option has been deprecated, please use --3N6 instead\n"); break; case 15 : args->gen_3N6 = 1; break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 'H': args->convert_func = haplegendsample_to_vcf; args->infname = optarg; break; case 'f': args->ref_fname = optarg; break; case 'c': args->columns = optarg; break; case 'o': args->outfname = optarg; break; case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'h': args->convert_func = vcf_to_haplegendsample; args->outfname = optarg; break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 10 : args->record_cmd_line = 0; break; case 11 : args->sex_fname = optarg; break; case 12 : args->keep_duplicates = 1; break; case 13 : args->regions_overlap = parse_overlap_option(optarg); if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 14 : args->targets_overlap = parse_overlap_option(optarg); if ( args->targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case '?': usage(); break; default: error("Unknown argument: %s\n", optarg); } } if ( !args->infname ) { if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) args->infname = "-"; } else args->infname = argv[optind]; } if ( !args->infname ) usage(); if ( args->convert_func ) args->convert_func(args); else vcf_to_vcf(args); destroy_data(args); free(args); return 0; } pysam-0.23.0/bcftools/vcfconvert.c.pysam.c000066400000000000000000002226571475062545500204670ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfconvert.c -- convert between VCF/BCF and related formats. Copyright (C) 2013-2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "filter.h" #include "convert.h" #include "tsv2vcf.h" // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 typedef struct _args_t args_t; struct _args_t { faidx_t *ref; filter_t *filter; char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE convert_t *convert; bcf_srs_t *files; bcf_hdr_t *header; void (*convert_func)(struct _args_t *); struct { int total, skipped, hom_rr, het_ra, hom_aa, het_aa, missing, written; } n; kstring_t str; int32_t *gts; float *flt; int rev_als, output_vcf_ids, hap2dip, gen_3N6; int nsamples, *samples, sample_is_file, targets_is_file, regions_is_file, output_type; int regions_overlap, targets_overlap; char **argv, *sample_list, *targets_list, *regions_list, *tag, *columns; char *outfname, *infname, *ref_fname, *sex_fname; int argc, n_threads, record_cmd_line, keep_duplicates, clevel; char *index_fn; int write_index; struct { kstring_t ref,alt,refalt; } tsv; }; static void destroy_data(args_t *args) { if ( args->ref ) fai_destroy(args->ref); if ( args->convert) convert_destroy(args->convert); if ( args->filter ) filter_destroy(args->filter); free(args->samples); if ( args->files ) bcf_sr_destroy(args->files); } static void open_vcf(args_t *args, const char *format_str) { args->files = bcf_sr_init(); if ( args->n_threads && bcf_sr_set_threads(args->files, args->n_threads)!=0 ) error("Could not initialize --threads %d\n", args->n_threads); if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, args->regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,args->targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list, args->targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } if ( !bcf_sr_add_reader(args->files, args->infname) ) error("Failed to open %s: %s\n", args->infname,bcf_sr_strerror(args->files->errnum)); args->header = args->files->readers[0].header; if ( args->filter_str ) args->filter = filter_init(args->header, args->filter_str); int i, nsamples = 0, *samples = NULL; if ( args->sample_list && strcmp("-",args->sample_list) ) { for (i=0; ifiles->nreaders; i++) { int ret = bcf_hdr_set_samples(args->files->readers[i].header,args->sample_list,args->sample_is_file); if ( ret<0 ) error("Error parsing the sample list\n"); else if ( ret>0 ) error("Sample name mismatch: sample #%d not found in the header\n", ret); } if ( args->sample_list[0]!='^' ) { // the sample ordering may be different if not negated int n; char **smpls = hts_readlist(args->sample_list, args->sample_is_file, &n); if ( !smpls ) error("Could not parse %s\n", args->sample_list); if ( n!=bcf_hdr_nsamples(args->files->readers[0].header) ) error("The number of samples does not match, perhaps some are present multiple times?\n"); nsamples = bcf_hdr_nsamples(args->files->readers[0].header); samples = (int*) malloc(sizeof(int)*nsamples); for (i=0; ifiles->readers[0].header, BCF_DT_SAMPLE,smpls[i]); free(smpls[i]); } free(smpls); } } if ( format_str ) args->convert = convert_init(args->header, samples, nsamples, format_str); free(samples); } static int _set_ref_alt(args_t *args, bcf1_t *rec) { args->tsv.refalt.l = 0; kputs(args->tsv.ref.s, &args->tsv.refalt); if ( strcmp(".",args->tsv.alt.s) && strcmp(args->tsv.ref.s,args->tsv.alt.s) ) { kputc(',', &args->tsv.refalt); kputs(args->tsv.alt.s, &args->tsv.refalt); } bcf_update_alleles_str(args->header, rec, args->tsv.refalt.s); args->tsv.ref.l = 0; args->tsv.alt.l = 0; args->tsv.refalt.l = 0; return 0; } static int tsv_setter_ref(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*) usr; kputsn(tsv->ss,tsv->se - tsv->ss,&args->tsv.ref); if ( args->tsv.alt.l ) return _set_ref_alt(args,rec); return 0; } static int tsv_setter_alt(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*) usr; kputsn(tsv->ss,tsv->se - tsv->ss,&args->tsv.alt); if ( args->tsv.ref.l ) return _set_ref_alt(args,rec); return 0; } // Try to set CHROM:POS_REF_ALT[_END]. Return 0 on success, -1 on error static int _set_chrom_pos_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*) usr; char tmp, *se = tsv->ss, *ss = tsv->ss; while ( se < tsv->se && *se!=':' ) se++; if ( *se!=':' ) return -1; tmp = *se; *se = 0; int rid = bcf_hdr_name2id(args->header,ss); *se = tmp; if ( rid<0 ) return -1; // POS hts_pos_t pos = strtol(se+1,&ss,10); if ( ss==se+1 ) return -1; pos--; // REF,ALT args->str.l = 0; se = ++ss; while ( se < tsv->se && *se!='_' ) se++; if ( *se!='_' ) return -1; kputsn(ss,se-ss,&args->str); ss = ++se; while ( se < tsv->se && *se!='_' && isspace(*tsv->se) ) se++; if ( se < tsv->se && *se!='_' && isspace(*tsv->se) ) return -1; kputc(',',&args->str); kputsn(ss,se-ss,&args->str); // END - optional if (*se && *se=='_') { long end = strtol(se+1,&ss,10); if ( ss==se+1 ) return -1; if (end < 1 || end > INT32_MAX) return -1; int32_t e = end; // bcf_update_info_int32 needs an int32_t pointer bcf_update_info_int32(args->header, rec, "END", &e, 1); } rec->rid = rid; rec->pos = pos; bcf_update_alleles_str(args->header, rec, args->str.s); return 0; } static int tsv_setter_chrom_pos_ref_alt_or_chrom(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*)usr; int ret = _set_chrom_pos_ref_alt(tsv,rec,usr); if ( !ret ) return ret; return tsv_setter_chrom(tsv,rec,args->header); } static int tsv_setter_chrom_pos_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr) { int ret = _set_chrom_pos_ref_alt(tsv,rec,usr); if ( ret!=0 ) error("Could not parse the CHROM:POS_REF_ALT[_END] string: %s\n", tsv->ss); return ret; } // This function must be called first, then tsv_setter_chrom_pos_ref_alt_id_or_die. // One of them is expected to find the CHROM:POS_REF_ALT[_END] string, if not, die. static int tsv_setter_chrom_pos_ref_alt_or_id(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*)usr; if ( _set_chrom_pos_ref_alt(tsv,rec,usr)==0 ) return 0; rec->pos = -1; // mark the record as unset if ( !args->output_vcf_ids) return 0; return tsv_setter_id(tsv,rec,usr); } static int tsv_setter_chrom_pos_ref_alt_id_or_die(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*)usr; if ( rec->pos!=-1 ) { if ( !args->output_vcf_ids ) return 0; return tsv_setter_id(tsv,rec,usr); } return tsv_setter_chrom_pos_ref_alt(tsv,rec,usr); } static int tsv_setter_verify_pos(tsv_t *tsv, bcf1_t *rec, void *usr) { char *se; int pos = strtol(tsv->ss,&se,10); if ( tsv->ss==se ) error("Could not parse POS: %s\n", tsv->ss); if ( rec->pos != pos-1 ) error("POS mismatch: %s\n", tsv->ss); return 0; } static int tsv_setter_verify_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*) usr; args->rev_als = 0; char tmp = *tsv->se; *tsv->se = 0; if ( strcmp(tsv->ss,rec->d.allele[0]) ) { if ( strcmp(tsv->ss,rec->d.allele[1]) ) { *tsv->se = tmp; error("REF/ALT mismatch: [%s][%s]\n", tsv->ss,rec->d.allele[1]); } args->rev_als = 1; } *tsv->se = tmp; while ( *tsv->se && isspace(*tsv->se) ) tsv->se++; tsv->ss = tsv->se; while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++; tmp = *tsv->se; *tsv->se = 0; if ( !args->rev_als && strcmp(tsv->ss,rec->d.allele[1]) ) { *tsv->se = tmp; error("REF/ALT mismatch: [%s][%s]\n", tsv->ss,rec->d.allele[1]); } else if ( args->rev_als && strcmp(tsv->ss,rec->d.allele[0]) ) { *tsv->se = tmp; error("REF/ALT mismatch: [%s][%s]\n", tsv->ss,rec->d.allele[0]); } *tsv->se = tmp; return 0; } static int tsv_setter_gt_gp(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*) usr; int i, nsamples = bcf_hdr_nsamples(args->header); for (i=0; iss, &tsv->se); if ( tsv->ss==tsv->se ) { fprintf(bcftools_stderr,"Could not parse first value of %d-th sample\n", i+1); return -1; } tsv->ss = tsv->se+1; ab = strtod(tsv->ss, &tsv->se); if ( tsv->ss==tsv->se ) { fprintf(bcftools_stderr,"Could not parse second value of %d-th sample\n", i+1); return -1; } tsv->ss = tsv->se+1; bb = strtod(tsv->ss, &tsv->se); if ( tsv->ss==tsv->se ) { fprintf(bcftools_stderr,"Could not parse third value of %d-th sample\n", i+1); return -1; } tsv->ss = tsv->se+1; if ( args->rev_als ) { float tmp = bb; bb = aa; aa = tmp; } args->flt[3*i+0] = aa; args->flt[3*i+1] = ab; args->flt[3*i+2] = bb; if ( aa >= ab ) { if ( aa >= bb ) args->gts[2*i+0] = args->gts[2*i+1] = bcf_gt_unphased(0); else args->gts[2*i+0] = args->gts[2*i+1] = bcf_gt_unphased(1); } else if ( ab >= bb ) { args->gts[2*i+0] = bcf_gt_unphased(0); args->gts[2*i+1] = bcf_gt_unphased(1); } else args->gts[2*i+0] = args->gts[2*i+1] = bcf_gt_unphased(1); } if ( *tsv->se ) error("Could not parse: %s\n", tsv->ss); if ( bcf_update_genotypes(args->header,rec,args->gts,nsamples*2) ) error("Could not update GT field\n"); if ( bcf_update_format_float(args->header,rec,"GP",args->flt,nsamples*3) ) error("Could not update GP field\n"); return 0; } static int tsv_setter_haps(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*) usr; int i, nsamples = bcf_hdr_nsamples(args->header); int32_t a0, a1; if ( args->rev_als ) { a0 = bcf_gt_phased(1); a1 = bcf_gt_phased(0); } else { a0 = bcf_gt_phased(0); a1 = bcf_gt_phased(1); } // up is short for "unphased" int nup = 0; for (i=0; iss + 4*i + nup; int up = 0, all; for (all=0; all < 2; all++){ // checking for premature ending if ( !ss[0] || !ss[1] || !ss[2] || (up && (!ss[3] || !ss[4]) ) ) { fprintf(bcftools_stderr,"Wrong number of fields at %d-th sample ([%c][%c][%c]). ",i+1,ss[0],ss[1],ss[2]); return -1; } switch(ss[all*2+up]){ case '0': args->gts[2*i+all] = a0; break; case '1' : args->gts[2*i+all] = a1; break; case '?' : // there is no macro to express phased missing allele args->gts[2*i+all] = bcf_gt_phased(-1); break; case '-' : args->gts[2*i+all] = bcf_int32_vector_end; break; default : fprintf(bcftools_stderr,"Could not parse: [%c][%s]\n", ss[all*2+up],tsv->ss); return -1; } if( ss[all*2+up+1]=='*' ) up = up + 1; } if(up && up != 2) { fprintf(bcftools_stderr,"Missing unphased marker '*': [%c][%s]", ss[2+up], tsv->ss); return -1; } // change alleles to unphased if the alleles are unphased if ( up ) { args->gts[2*i] = bcf_gt_unphased(bcf_gt_allele(args->gts[2*i])); args->gts[2*i+1] = bcf_gt_unphased(bcf_gt_allele(args->gts[2*i+1])); } nup = nup + up; } if ( tsv->ss[(nsamples-1)*4+3+nup] ) { fprintf(bcftools_stderr,"nup: %d", nup); fprintf(bcftools_stderr,"Wrong number of fields (%d-th column = [%c]). ", nsamples*2,tsv->ss[(nsamples-1)*4+nup]); return -1; } if ( bcf_update_genotypes(args->header,rec,args->gts,nsamples*2) ) error("Could not update GT field\n"); return 0; } static void gensample_to_vcf(args_t *args) { /* * Inpute: IMPUTE2 output (indentation changed here for clarity): * * 20:62116619_C_T 20:62116619 62116619 C T 0.969 0.031 0 ... * --- 20:62116698_C_A 62116698 C A 1 0 0 ... * * Second column is expected in the form of CHROM:POS_REF_ALT. We use second * column because the first can be empty ("--") when filling sites from reference * panel. When the option --vcf-ids is given, the first column is used to set the * VCF ID. * * Output: VCF with filled GT,GP * */ kstring_t line = {0,0,0}; char *gen_fname = NULL, *sample_fname = NULL; sample_fname = strchr(args->infname,','); if ( !sample_fname ) { args->str.l = 0; ksprintf(&args->str,"%s.gen.gz", args->infname); gen_fname = strdup(args->str.s); args->str.l = 0; ksprintf(&args->str,"%s.samples", args->infname); sample_fname = strdup(args->str.s); } else { *sample_fname = 0; gen_fname = strdup(args->infname); sample_fname = strdup(sample_fname+1); } htsFile *gen_fh = hts_open(gen_fname, "r"); if ( !gen_fh ) error("Could not read: %s\n", gen_fname); if ( hts_getline(gen_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", gen_fname); // Find out the chromosome name, depending on the format variant (--3N6 or plain) and the ordering // of the columns (CHROM:POS_REF_ALT comes first or second) args->str.l = 0; char *sb = line.s, *se = line.s; while ( *se && !isspace(*se) ) se++; if ( !*se ) error("Could not determine CHROM in %s: %s\n", gen_fname,line.s); if ( args->gen_3N6 ) // first column, just CHROM kputsn(sb, se-sb, &args->str); else // first or second column, part of CHROM:POS_REF_ALT { char *sc = strchr(sb,':'); if ( !sc || sc > se ) { while ( *se && !isspace(*se) ) se++; if ( !*se ) error("Could not determine CHROM in %s: %s\n", gen_fname,line.s); sb = ++se; sc = strchr(sb,':'); if ( !sc ) error("Could not determine CHROM in %s: %s\n", gen_fname,line.s); } kputsn(sb, sc-sb, &args->str); } // Initialize and print the VCF header, args->str.s contains the chr name args->header = bcf_hdr_init("w"); bcf_hdr_append(args->header, "##INFO="); bcf_hdr_append(args->header, "##FORMAT="); bcf_hdr_append(args->header, "##FORMAT="); bcf_hdr_printf(args->header, "##contig=", args->str.s,0x7fffffff); // MAX_CSI_COOR if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert"); tsv_t *tsv; if ( args->gen_3N6 ) { tsv = tsv_init("CHROM,CHROM_POS_REF_ALT,ID,POS,REF_ALT,GT_GP"); tsv_register(tsv, "CHROM", tsv_setter_chrom, args->header); } else tsv = tsv_init("CHROM_POS_REF_ALT,ID,POS,REF_ALT,GT_GP"); tsv_register(tsv, "CHROM_POS_REF_ALT", tsv_setter_chrom_pos_ref_alt_or_id, args); tsv_register(tsv, "ID", tsv_setter_chrom_pos_ref_alt_id_or_die, args); tsv_register(tsv, "POS", tsv_setter_verify_pos, NULL); tsv_register(tsv, "REF_ALT", tsv_setter_verify_ref_alt, args); tsv_register(tsv, "GT_GP", tsv_setter_gt_gp, args); // Find out sample names int i, nsamples; char **samples = hts_readlist(sample_fname, 1, &nsamples); if ( !samples ) error("Could not read %s\n", sample_fname); for (i=2; iheader,samples[i]); } for (i=0; ioutput_type,args->outfname,args->clevel); htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode); if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno)); if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads); if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->outfname); if ( init_index2(out_fh,args->header,args->outfname,&args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->outfname); bcf1_t *rec = bcf_init(); nsamples -= 2; args->gts = (int32_t *) malloc(sizeof(int32_t)*nsamples*2); args->flt = (float *) malloc(sizeof(float)*nsamples*3); do { bcf_clear(rec); args->n.total++; if ( !tsv_parse(tsv, rec, line.s) ) { if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); } else error("Error occurred while parsing: %s\n", line.s); } while ( hts_getline(gen_fh, KS_SEP_LINE, &line)>0 ); if ( args->write_index ) { if ( bcf_idx_save(out_fh)<0 ) { if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); if ( hts_close(gen_fh) ) error("Close failed: %s\n", gen_fname); bcf_hdr_destroy(args->header); bcf_destroy(rec); free(sample_fname); free(gen_fname); free(args->str.s); free(line.s); free(args->gts); free(args->flt); tsv_destroy(tsv); fprintf(bcftools_stderr,"Number of processed rows: \t%d\n", args->n.total); } static void haplegendsample_to_vcf(args_t *args) { /* * Convert from IMPUTE2 hap/legend/sample output files to VCF * * hap: * 0 1 0 1 * legend: * id position a0 a1 * 1:186946386_G_T 186946386 G T * sample: * sample population group sex * sample1 sample1 sample1 2 * sample2 sample2 sample2 2 * * Output: VCF with filled GT */ kstring_t line = {0,0,0}; if ( args->output_vcf_ids ) error( "The option --haplegendsample2vcf cannot be combined with --vcf-ids. This is because the\n" "ID column must be formatted as \"CHROM:POS_REF_ALT\" to check sanity of the operation\n"); char *hap_fname = NULL, *leg_fname = NULL, *sample_fname = NULL; sample_fname = strchr(args->infname,','); if ( !sample_fname ) { args->str.l = 0; ksprintf(&args->str,"%s.hap.gz", args->infname); hap_fname = strdup(args->str.s); args->str.l = 0; ksprintf(&args->str,"%s.samples", args->infname); sample_fname = strdup(args->str.s); args->str.l = 0; ksprintf(&args->str,"%s.legend.gz", args->infname); leg_fname = strdup(args->str.s); } else { char *ss = sample_fname, *se = strchr(ss+1,','); if ( !se ) error("Could not parse hap/legend/sample file names: %s\n", args->infname); *ss = 0; *se = 0; hap_fname = strdup(args->infname); leg_fname = strdup(ss+1); sample_fname = strdup(se+1); } htsFile *hap_fh = hts_open(hap_fname, "r"); if ( !hap_fh ) error("Could not read: %s\n", hap_fname); htsFile *leg_fh = hts_open(leg_fname,"r"); if ( !leg_fh ) error("Could not read: %s\n", leg_fname); // Eat up first legend line, then determine chromosome name if ( hts_getline(leg_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", leg_fname); if ( hts_getline(leg_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", leg_fname); // Find out the chromosome name, sample names, init and print the VCF header args->str.l = 0; char *se = strchr(line.s,':'); if ( !se ) error("Expected CHROM:POS_REF_ALT in first column of %s\n", leg_fname); kputsn(line.s, se-line.s, &args->str); tsv_t *leg_tsv = tsv_init("CHROM_POS_REF_ALT,POS,REF_ALT"); tsv_register(leg_tsv, "CHROM_POS_REF_ALT", tsv_setter_chrom_pos_ref_alt, args); tsv_register(leg_tsv, "POS", tsv_setter_verify_pos, NULL); tsv_register(leg_tsv, "REF_ALT", tsv_setter_verify_ref_alt, args); tsv_t *hap_tsv = tsv_init("HAPS"); tsv_register(hap_tsv, "HAPS", tsv_setter_haps, args); args->header = bcf_hdr_init("w"); bcf_hdr_append(args->header, "##INFO="); bcf_hdr_append(args->header, "##FORMAT="); bcf_hdr_printf(args->header, "##contig=", args->str.s,0x7fffffff); // MAX_CSI_COOR if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert"); int i, nrows, nsamples; char **samples = hts_readlist(sample_fname, 1, &nrows); if ( !samples ) error("Could not read %s\n", sample_fname); nsamples = nrows - 1; // sample_fname should contain a header line, so need to ignore first row // returned from hts_readlist (i=1, and not i=0) for (i=1; iheader,samples[i]); } bcf_hdr_add_sample(args->header,NULL); for (i=0; ioutput_type,args->outfname,args->clevel); htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode); if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno)); if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads); if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->outfname); if ( init_index2(out_fh,args->header,args->outfname,&args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->outfname); bcf1_t *rec = bcf_init(); args->gts = (int32_t *) malloc(sizeof(int32_t)*nsamples*2); while (1) { bcf_clear(rec); args->n.total++; if ( tsv_parse(leg_tsv, rec, line.s) ) error("Error occurred while parsing %s: %s\n", leg_fname,line.s); if ( hts_getline(hap_fh, KS_SEP_LINE, &line)<=0 ) error("Different number of records in %s and %s?\n", leg_fname,hap_fname); if ( tsv_parse(hap_tsv, rec, line.s) ) error("Error occurred while parsing %s: %s\n", hap_fname,line.s); if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); if ( hts_getline(leg_fh, KS_SEP_LINE, &line)<=0 ) { if ( hts_getline(hap_fh, KS_SEP_LINE, &line)>0 ) error("Different number of records in %s and %s?\n", leg_fname,hap_fname); break; } } if ( args->write_index ) { if ( bcf_idx_save(out_fh)<0 ) { if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); if ( hts_close(hap_fh) ) error("Close failed: %s\n", hap_fname); if ( hts_close(leg_fh) ) error("Close failed: %s\n", leg_fname); bcf_hdr_destroy(args->header); bcf_destroy(rec); free(sample_fname); free(hap_fname); free(leg_fname); free(args->str.s); free(line.s); free(args->gts); tsv_destroy(hap_tsv); tsv_destroy(leg_tsv); fprintf(bcftools_stderr,"Number of processed rows: \t%d\n", args->n.total); } static void hapsample_to_vcf(args_t *args) { /* * Input: SHAPEIT output * * 20:19995888_A_G rsid1 19995888 A G 0 0 0 0 ... * 20 20:19995888_A_G 19995888 A G 0 0 0 0 ... * * First column is expected in the form of CHROM:POS_REF_ALT * * Output: VCF with filled GT * */ kstring_t line = {0,0,0}; char *hap_fname = NULL, *sample_fname = NULL; sample_fname = strchr(args->infname,','); if ( !sample_fname ) { args->str.l = 0; ksprintf(&args->str,"%s.hap.gz", args->infname); hap_fname = strdup(args->str.s); args->str.l = 0; ksprintf(&args->str,"%s.samples", args->infname); sample_fname = strdup(args->str.s); } else { *sample_fname = 0; hap_fname = strdup(args->infname); sample_fname = strdup(sample_fname+1); } htsFile *hap_fh = hts_open(hap_fname, "r"); if ( !hap_fh ) error("Could not read: %s\n", hap_fname); if ( hts_getline(hap_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", hap_fname); // Find out the chromosome name, it can be either in the first or second column args->str.l = 0; char *sb = line.s, *se = line.s; while ( *se && !isspace(*se) ) se++; if ( !*se ) error("Could not determine CHROM in %s: %s\n", hap_fname,line.s); if ( !args->output_vcf_ids ) { // first column should be just CHROM, but the second must be CHROM:POS_REF_ALT, use that sb = ++se; while ( *se && !isspace(*se) ) se++; if ( !*se ) error("Could not determine CHROM in %s: %s\n", hap_fname,line.s); if ( !strchr(sb,':') ) error("Could not determine CHROM in the second column of %s: %s\n", hap_fname,line.s); } // Parse CHROM:POS_REF_ALT char *sc = strchr(sb,':'); if ( !sc || sc > se ) error("Could not determine CHROM in %s: %s\n", hap_fname,line.s); kputsn(sb, sc-sb, &args->str); // Initialize and print the VCF header, args->str.s contains the chr name args->header = bcf_hdr_init("w"); bcf_hdr_append(args->header, "##INFO="); bcf_hdr_append(args->header, "##FORMAT="); bcf_hdr_printf(args->header, "##contig=", args->str.s,0x7fffffff); // MAX_CSI_COOR if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert"); tsv_t *tsv; if ( args->output_vcf_ids ) { tsv = tsv_init("CHROM_POS_REF_ALT,ID,POS,REF_ALT,HAPS"); tsv_register(tsv, "ID", tsv_setter_id, args); } else { tsv = tsv_init("CHROM,CHROM_POS_REF_ALT,POS,REF_ALT,HAPS"); tsv_register(tsv, "CHROM", tsv_setter_chrom_pos_ref_alt_or_chrom, args); } tsv_register(tsv, "CHROM_POS_REF_ALT", tsv_setter_chrom_pos_ref_alt, args); tsv_register(tsv, "POS", tsv_setter_verify_pos, NULL); tsv_register(tsv, "REF_ALT", tsv_setter_verify_ref_alt, args); tsv_register(tsv, "HAPS", tsv_setter_haps, args); int i, nsamples; char **samples = hts_readlist(sample_fname, 1, &nsamples); if ( !samples ) error("Could not read %s\n", sample_fname); for (i=2; iheader,samples[i]); } bcf_hdr_add_sample(args->header,NULL); for (i=0; ioutput_type,args->outfname,args->clevel); htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode); if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno)); if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads); if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); if ( init_index2(out_fh,args->header,args->outfname,&args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->outfname); bcf1_t *rec = bcf_init(); nsamples -= 2; args->gts = (int32_t *) malloc(sizeof(int32_t)*nsamples*2); do { bcf_clear(rec); args->n.total++; if ( !tsv_parse(tsv, rec, line.s) ) { if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); } else error("Error occurred while parsing: %s\n", line.s); } while ( hts_getline(hap_fh, KS_SEP_LINE, &line)>0 ); if ( args->write_index ) { if ( bcf_idx_save(out_fh)<0 ) { if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); if ( hts_close(hap_fh) ) error("Close failed: %s\n", hap_fname); bcf_hdr_destroy(args->header); bcf_destroy(rec); free(sample_fname); free(hap_fname); free(args->str.s); free(line.s); free(args->gts); tsv_destroy(tsv); fprintf(bcftools_stderr,"Number of processed rows: \t%d\n", args->n.total); } char *init_sample2sex(bcf_hdr_t *hdr, char *sex_fname) { int i, nlines; char *sample2sex = (char*) calloc(bcf_hdr_nsamples(hdr),1); char **lines = hts_readlist(sex_fname, 1, &nlines); if ( !lines ) error("Could not read %s\n", sex_fname); for (i=0; igen_3N6 ) kputs("%CHROM ", &str); kputs("%CHROM:%POS\\_%REF\\_%FIRST_ALT ", &str); // insert rsid as second column if needed if ( args->output_vcf_ids ) kputs("%ID ", &str); else kputs("%CHROM:%POS\\_%REF\\_%FIRST_ALT ", &str); kputs("%POS %REF %FIRST_ALT", &str); if ( !args->tag || !strcmp(args->tag,"GT") ) kputs("%_GT_TO_PROB3",&str); else if ( !strcmp(args->tag,"PL") ) kputs("%_PL_TO_PROB3",&str); else if ( !strcmp(args->tag,"GP") ) kputs("%_GP_TO_PROB3",&str); else error("todo: --tag %s\n", args->tag); kputs("\n", &str); open_vcf(args,str.s); int ret, gen_compressed = 1, sample_compressed = 0; char *gen_fname = NULL, *sample_fname = NULL; str.l = 0; kputs(args->outfname,&str); int n_files = 0, i; char **files = hts_readlist(str.s, 0, &n_files); if ( n_files==1 ) { int l = str.l; kputs(".samples",&str); sample_fname = strdup(str.s); str.l = l; kputs(".gen.gz",&str); gen_fname = strdup(str.s); } else if ( n_files==2 ) { if (strlen(files[0]) && strcmp(files[0],".")!=0) gen_fname = strdup(files[0]); if (strlen(files[1]) && strcmp(files[1],".")!=0) sample_fname = strdup(files[1]); } else { error("Error parsing --gensample filenames: %s\n", args->outfname); } for (i=0; i3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0; if (gen_fname) fprintf(bcftools_stderr, "Gen file: %s\n", gen_fname); if (sample_fname) fprintf(bcftools_stderr, "Sample file: %s\n", sample_fname); // write samples file if (sample_fname) { char *sample2sex = NULL; if ( args->sex_fname ) sample2sex = init_sample2sex(args->header,args->sex_fname); int i; BGZF *sout = bgzf_open(sample_fname, sample_compressed ? "wg" : "wu"); str.l = 0; kputs(sample2sex ? "ID_1 ID_2 missing sex\n0 0 0 0\n" : "ID_1 ID_2 missing\n0 0 0\n", &str); ret = bgzf_write(sout, str.s, str.l); if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno)); for (i=0; iheader); i++) { str.l = 0; if ( sample2sex ) ksprintf(&str, "%s %s 0 %c\n", args->header->samples[i],args->header->samples[i],sample2sex[i]); else ksprintf(&str, "%s %s 0\n", args->header->samples[i],args->header->samples[i]); ret = bgzf_write(sout, str.s, str.l); if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno)); } if ( bgzf_close(sout)!=0 ) error("Error closing %s: %s\n", sample_fname, strerror(errno)); free(sample_fname); free(sample2sex); } if (!gen_fname) { if ( str.m ) free(str.s); return; } int prev_rid = -1, prev_pos = -1; int no_alt = 0, non_biallelic = 0, filtered = 0, ndup = 0, nok = 0; BGZF *gout = bgzf_open(gen_fname, gen_compressed ? "wg" : "wu"); while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = bcf_sr_get_line(args->files,0); if ( args->filter ) { int pass = filter_test(args->filter, line, NULL); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { filtered++; continue; } } // ALT allele is required if ( line->n_allele<2 ) { no_alt++; continue; } // biallelic required if ( line->n_allele>2 ) { if (!non_biallelic) fprintf(bcftools_stderr, "Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n"); non_biallelic++; continue; } // skip duplicate lines, or otherwise shapeit complains if ( !args->keep_duplicates && prev_rid==line->rid && prev_pos==line->pos ) { ndup++; continue; } prev_rid = line->rid; prev_pos = line->pos; str.l = 0; convert_line(args->convert, line, &str); if ( str.l ) { int ret = bgzf_write(gout, str.s, str.l); if ( ret!= str.l ) error("Error writing %s: %s\n", gen_fname,strerror(errno)); nok++; } } fprintf(bcftools_stderr, "%d records written, %d skipped: %d/%d/%d/%d no-ALT/non-biallelic/filtered/duplicated\n", nok, no_alt+non_biallelic+filtered+ndup, no_alt, non_biallelic, filtered, ndup); if ( str.m ) free(str.s); if ( bgzf_close(gout)!=0 ) error("Error closing %s: %s\n", gen_fname,strerror(errno)); free(gen_fname); } static void vcf_to_haplegendsample(args_t *args) { kstring_t str = {0,0,0}; if ( args->hap2dip ) kputs("%_GT_TO_HAP2\n", &str); else kputs("%_GT_TO_HAP\n", &str); open_vcf(args,str.s); int ret, hap_compressed = 1, legend_compressed = 1, sample_compressed = 0; char *hap_fname = NULL, *legend_fname = NULL, *sample_fname = NULL; str.l = 0; kputs(args->outfname,&str); int n_files = 0, i; char **files = hts_readlist(str.s, 0, &n_files); if ( n_files==1 ) { int l = str.l; kputs(".samples",&str); sample_fname = strdup(str.s); str.l = l; kputs(".legend.gz",&str); legend_fname = strdup(str.s); str.l = l; kputs(".hap.gz",&str); hap_fname = strdup(str.s); } else if ( n_files==3 ) { if (strlen(files[0]) && strcmp(files[0],".")!=0) hap_fname = strdup(files[0]); if (strlen(files[1]) && strcmp(files[1],".")!=0) legend_fname = strdup(files[1]); if (strlen(files[2]) && strcmp(files[2],".")!=0) sample_fname = strdup(files[2]); } else { error("Error parsing --hapslegendsample filenames: %s\n", args->outfname); } for (i=0; i3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0; if (hap_fname) fprintf(bcftools_stderr, "Hap file: %s\n", hap_fname); if (legend_fname) fprintf(bcftools_stderr, "Legend file: %s\n", legend_fname); if (sample_fname) fprintf(bcftools_stderr, "Sample file: %s\n", sample_fname); // write samples file if (sample_fname) { char *sample2sex = NULL; if ( args->sex_fname ) sample2sex = init_sample2sex(args->header,args->sex_fname); int i; BGZF *sout = bgzf_open(sample_fname, sample_compressed ? "wg" : "wu"); str.l = 0; kputs("sample population group sex\n", &str); ret = bgzf_write(sout, str.s, str.l); if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno)); for (i=0; iheader); i++) { str.l = 0; ksprintf(&str, "%s %s %s %c\n", args->header->samples[i], args->header->samples[i], args->header->samples[i], sample2sex ? sample2sex[i] : '2'); ret = bgzf_write(sout, str.s, str.l); if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno)); } if ( bgzf_close(sout)!=0 ) error("Error closing %s: %s\n", sample_fname, strerror(errno)); free(sample_fname); free(sample2sex); } if (!hap_fname && !legend_fname) { if ( str.m ) free(str.s); return; } // open haps and legend outputs BGZF *hout = hap_fname ? bgzf_open(hap_fname, hap_compressed ? "wg" : "wu") : NULL; if ( hap_compressed && args->n_threads ) bgzf_thread_pool(hout, args->files->p->pool, args->files->p->qsize); BGZF *lout = legend_fname ? bgzf_open(legend_fname, legend_compressed ? "wg" : "wu") : NULL; if (legend_fname) { str.l = 0; kputs("id position a0 a1\n", &str); ret = bgzf_write(lout, str.s, str.l); if ( ret != str.l ) error("Error writing %s: %s\n", legend_fname, strerror(errno)); } int no_alt = 0, non_biallelic = 0, filtered = 0, nok = 0; while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = bcf_sr_get_line(args->files,0); if ( args->filter ) { int pass = filter_test(args->filter, line, NULL); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { filtered++; continue; } } // ALT allele is required if ( line->n_allele<2 ) { no_alt++; continue; } // biallelic required if ( line->n_allele>2 ) { if (!non_biallelic) fprintf(bcftools_stderr, "Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n"); non_biallelic++; continue; } str.l = 0; convert_line(args->convert, line, &str); if ( !str.l ) continue; // write haps file if (hap_fname) { ret = bgzf_write(hout, str.s, str.l); // write hap file if ( ret != str.l ) error("Error writing %s: %s\n", hap_fname, strerror(errno)); } if (legend_fname) { str.l = 0; if ( args->output_vcf_ids && (line->d.id[0]!='.' || line->d.id[1]!=0) ) ksprintf(&str, "%s %"PRId64" %s %s\n", line->d.id, (int64_t) line->pos+1, line->d.allele[0], line->d.allele[1]); else ksprintf(&str, "%s:%"PRId64"_%s_%s %"PRId64" %s %s\n", bcf_seqname(args->header, line), (int64_t) line->pos+1, line->d.allele[0], line->d.allele[1], (int64_t) line->pos+1, line->d.allele[0], line->d.allele[1]); // write legend file ret = bgzf_write(lout, str.s, str.l); if ( ret != str.l ) error("Error writing %s: %s\n", legend_fname, strerror(errno)); } nok++; } fprintf(bcftools_stderr, "%d records written, %d skipped: %d/%d/%d no-ALT/non-biallelic/filtered\n", nok,no_alt+non_biallelic+filtered, no_alt, non_biallelic, filtered); if ( str.m ) free(str.s); if ( hout && bgzf_close(hout)!=0 ) error("Error closing %s: %s\n", hap_fname, strerror(errno)); if ( lout && bgzf_close(lout)!=0 ) error("Error closing %s: %s\n", legend_fname, strerror(errno)); if (hap_fname) free(hap_fname); if (legend_fname) free(legend_fname); } static void vcf_to_hapsample(args_t *args) { /* * WTCCC style haplotypes file * see https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#hapsample * * These are essentially the haplotypes from the impute2 format with some * legend info tacked on to the first 5 columns * */ kstring_t str = {0,0,0}; // print ID instead of CHROM:POS_REF_ALT1 if ( args->output_vcf_ids ) kputs("%CHROM:%POS\\_%REF\\_%FIRST_ALT %ID %POS %REF %FIRST_ALT ", &str); else kputs("%CHROM %CHROM:%POS\\_%REF\\_%FIRST_ALT %POS %REF %FIRST_ALT ", &str); if ( args->hap2dip ) kputs("%_GT_TO_HAP2\n", &str); else kputs("%_GT_TO_HAP\n", &str); open_vcf(args,str.s); int ret, hap_compressed = 1, sample_compressed = 0; char *hap_fname = NULL, *sample_fname = NULL; str.l = 0; kputs(args->outfname,&str); int n_files = 0, i; char **files = hts_readlist(str.s, 0, &n_files); if ( n_files==1 ) { int l = str.l; kputs(".samples",&str); sample_fname = strdup(str.s); str.l = l; kputs(".hap.gz",&str); hap_fname = strdup(str.s); } else if ( n_files==2 ) { if (strlen(files[0]) && strcmp(files[0],".")!=0) hap_fname = strdup(files[0]); if (strlen(files[1]) && strcmp(files[1],".")!=0) sample_fname = strdup(files[1]); } else { error("Error parsing --hapsample filenames: %s\n", args->outfname); } for (i=0; i3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0; if (hap_fname) fprintf(bcftools_stderr, "Hap file: %s\n", hap_fname); if (sample_fname) fprintf(bcftools_stderr, "Sample file: %s\n", sample_fname); // write samples file if (sample_fname) { char *sample2sex = NULL; if ( args->sex_fname ) sample2sex = init_sample2sex(args->header,args->sex_fname); int i; BGZF *sout = bgzf_open(sample_fname, sample_compressed ? "wg" : "wu"); str.l = 0; kputs(sample2sex ? "ID_1 ID_2 missing sex\n0 0 0 0\n" : "ID_1 ID_2 missing\n0 0 0\n", &str); ret = bgzf_write(sout, str.s, str.l); if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno)); for (i=0; iheader); i++) { str.l = 0; if ( sample2sex ) ksprintf(&str, "%s %s 0 %c\n", args->header->samples[i],args->header->samples[i],sample2sex[i]); else ksprintf(&str, "%s %s 0\n", args->header->samples[i],args->header->samples[i]); ret = bgzf_write(sout, str.s, str.l); if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno)); } if ( bgzf_close(sout)!=0 ) error("Error closing %s: %s\n", sample_fname, strerror(errno)); free(sample_fname); free(sample2sex); } if (!hap_fname) { if ( str.m ) free(str.s); return; } // open haps output BGZF *hout = hap_fname ? bgzf_open(hap_fname, hap_compressed ? "wg" : "wu") : NULL; if ( hap_compressed && args->n_threads ) bgzf_thread_pool(hout, args->files->p->pool, args->files->p->qsize); int no_alt = 0, non_biallelic = 0, filtered = 0, nok = 0; while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = bcf_sr_get_line(args->files,0); if ( args->filter ) { int pass = filter_test(args->filter, line, NULL); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { filtered++; continue; } } // ALT allele is required if ( line->n_allele<2 ) { no_alt++; continue; } // biallelic required if ( line->n_allele>2 ) { if (!non_biallelic) fprintf(bcftools_stderr, "Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n"); non_biallelic++; continue; } str.l = 0; convert_line(args->convert, line, &str); if ( !str.l ) continue; // write haps file if (hap_fname) { ret = bgzf_write(hout, str.s, str.l); // write hap file if ( ret != str.l ) error("Error writing %s: %s\n", hap_fname, strerror(errno)); } nok++; } fprintf(bcftools_stderr, "%d records written, %d skipped: %d/%d/%d no-ALT/non-biallelic/filtered\n", nok, no_alt+non_biallelic+filtered, no_alt, non_biallelic, filtered); if ( str.m ) free(str.s); if ( hout && bgzf_close(hout)!=0 ) error("Error closing %s: %s\n", hap_fname, strerror(errno)); if (hap_fname) free(hap_fname); } static void bcf_hdr_set_chrs(bcf_hdr_t *hdr, faidx_t *fai) { int i, n = faidx_nseq(fai); for (i=0; i", seq,len); } } static inline int acgt_to_5(char base) { if ( base=='A' ) return 0; if ( base=='C' ) return 1; if ( base=='G' ) return 2; if ( base=='T' ) return 3; return 4; } static inline int tsv_setter_aa1(args_t *args, char *ss, char *se, int alleles[], int *nals, int ref, int32_t *gts) { if ( se - ss > 2 ) return -1; // currently only SNPs if ( ss[0]=='-' || ss[0]=='.' ) { // missing GT gts[0] = bcf_gt_missing; gts[1] = bcf_gt_missing; args->n.missing++; return 0; } if ( ss[0]=='I' ) return -2; // skip insertions/deletions for now if ( ss[0]=='D' ) return -2; int a0 = acgt_to_5(toupper(ss[0])); int a1 = ss[1] ? acgt_to_5(toupper(ss[1])) : a0; if ( alleles[a0]<0 ) alleles[a0] = (*nals)++; if ( alleles[a1]<0 ) alleles[a1] = (*nals)++; gts[0] = bcf_gt_unphased(alleles[a0]); gts[1] = ss[1] ? bcf_gt_unphased(alleles[a1]) : bcf_int32_vector_end; if ( ref==a0 && ref==a1 ) args->n.hom_rr++; // hom ref: RR else if ( ref==a0 ) args->n.het_ra++; // het: RA else if ( ref==a1 ) args->n.het_ra++; // het: AR else if ( a0==a1 ) args->n.hom_aa++; // hom-alt: AA else args->n.het_aa++; // non-ref het: AA return 0; } static int tsv_setter_aa(tsv_t *tsv, bcf1_t *rec, void *usr) { args_t *args = (args_t*) usr; int len; char *ref = faidx_fetch_seq(args->ref, (char*)bcf_hdr_id2name(args->header,rec->rid), rec->pos, rec->pos, &len); if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_hdr_id2name(args->header,rec->rid),(int64_t) rec->pos+1); int nals = 1, alleles[5] = { -1, -1, -1, -1, -1 }; // a,c,g,t,n ref[0] = toupper(ref[0]); int iref = acgt_to_5(ref[0]); alleles[iref] = 0; rec->n_sample = bcf_hdr_nsamples(args->header); int i, ret; for (i=0; in_sample; i++) { if ( i>0 ) { ret = tsv_next(tsv); if ( ret==-1 ) error("Too few columns for %d samples at %s:%"PRId64"\n", rec->n_sample,bcf_hdr_id2name(args->header,rec->rid),(int64_t) rec->pos+1); } ret = tsv_setter_aa1(args, tsv->ss, tsv->se, alleles, &nals, iref, args->gts+i*2); if ( ret==-1 ) error("Error parsing the site %s:%"PRId64", expected two characters\n", bcf_hdr_id2name(args->header,rec->rid),(int64_t) rec->pos+1); if ( ret==-2 ) { // something else than a SNP free(ref); return -1; } } args->str.l = 0; kputc(ref[0], &args->str); for (i=0; i<5; i++) { if ( alleles[i]>0 ) { kputc(',', &args->str); kputc("ACGTN"[i], &args->str); } } bcf_update_alleles_str(args->header, rec, args->str.s); if ( bcf_update_genotypes(args->header,rec,args->gts,rec->n_sample*2) ) error("Could not update the GT field\n"); free(ref); return 0; } static void tsv_to_vcf(args_t *args) { if ( !args->ref_fname ) error("--tsv2vcf requires the --fasta-ref option\n"); args->ref = fai_load(args->ref_fname); if ( !args->ref ) error("Could not load the reference %s\n", args->ref_fname); args->header = bcf_hdr_init("w"); bcf_hdr_set_chrs(args->header, args->ref); bcf_hdr_append(args->header, "##FORMAT="); if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert"); int i, nsmpl; char **smpl; if ( args->sample_list ) { smpl = hts_readlist(args->sample_list, args->sample_is_file, &nsmpl); if ( !smpl ) error("Could not parse %s\n", args->sample_list); for (i=0; iheader, smpl[i]); free(smpl[i]); } free(smpl); bcf_hdr_add_sample(args->header, NULL); args->gts = (int32_t *) malloc(sizeof(int32_t)*nsmpl*2); } char wmode[8]; set_wmode(wmode,args->output_type,args->outfname,args->clevel); htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode); if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno)); if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads); if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); if ( init_index2(out_fh,args->header,args->outfname,&args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->outfname); tsv_t *tsv = tsv_init(args->columns ? args->columns : "ID,CHROM,POS,AA"); if ( tsv_register(tsv, "CHROM", tsv_setter_chrom, args->header) < 0 ) error("Expected CHROM column\n"); if ( tsv_register(tsv, "POS", tsv_setter_pos, NULL) < 0 ) error("Expected POS column\n"); if ( tsv_register(tsv, "ID", tsv_setter_id, args->header) < 0 && !args->columns ) error("Expected ID column\n"); if ( tsv_register(tsv, "AA", tsv_setter_aa, args) < 0 ) { if ( args->sample_list ) error("Expected AA column with -s/-S\n"); if ( tsv_register(tsv, "REF", tsv_setter_ref, args) < 0 || tsv_register(tsv, "ALT", tsv_setter_alt, args) < 0 ) error("Expected REF and ALT columns when AA was not given\n"); } bcf1_t *rec = bcf_init(); bcf_float_set_missing(rec->qual); kstring_t line = {0,0,0}; htsFile *in_fh = hts_open(args->infname, "r"); if ( !in_fh ) error("Could not read: %s\n", args->infname); while ( hts_getline(in_fh, KS_SEP_LINE, &line) > 0 ) { if ( line.s[0]=='#' ) continue; // skip comments bcf_clear(rec); args->n.total++; if ( !tsv_parse(tsv, rec, line.s) ) { if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); args->n.written++; } else args->n.skipped++; } if ( hts_close(in_fh) ) error("Close failed: %s\n", args->infname); free(line.s); if ( args->write_index ) { if ( bcf_idx_save(out_fh)<0 ) { if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } bcf_hdr_destroy(args->header); if ( hts_close(out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->outfname); tsv_destroy(tsv); bcf_destroy(rec); free(args->str.s); free(args->gts); free(args->tsv.ref.s); free(args->tsv.alt.s); free(args->tsv.refalt.s); fprintf(bcftools_stderr,"Rows total: \t%d\n", args->n.total); fprintf(bcftools_stderr,"Rows skipped: \t%d\n", args->n.skipped); fprintf(bcftools_stderr,"Sites written: \t%d\n", args->n.written); if ( args->sample_list ) { fprintf(bcftools_stderr,"Missing GTs: \t%d\n", args->n.missing); fprintf(bcftools_stderr,"Hom RR: \t%d\n", args->n.hom_rr); fprintf(bcftools_stderr,"Het RA: \t%d\n", args->n.het_ra); fprintf(bcftools_stderr,"Hom AA: \t%d\n", args->n.hom_aa); fprintf(bcftools_stderr,"Het AA: \t%d\n", args->n.het_aa); } } static void vcf_to_vcf(args_t *args) { open_vcf(args,NULL); char wmode[8]; set_wmode(wmode,args->output_type,args->outfname,args->clevel); htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode); if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno)); if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads); bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0); if ( bcf_hdr_write(out_fh,hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); if ( init_index2(out_fh,args->header,args->outfname,&args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->outfname); while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = bcf_sr_get_line(args->files,0); if ( args->filter ) { int pass = filter_test(args->filter, line, NULL); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) continue; } if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); } if ( args->write_index ) { if ( bcf_idx_save(out_fh)<0 ) { if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->outfname); } static void gvcf_to_vcf(args_t *args) { if ( !args->ref_fname ) error("--gvcf2vcf requires the --fasta-ref option\n"); args->ref = fai_load(args->ref_fname); if ( !args->ref ) error("Could not load the fai index for reference %s\n", args->ref_fname); open_vcf(args,NULL); char wmode[8]; set_wmode(wmode,args->output_type,args->outfname,args->clevel); htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode); if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno)); if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads); bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0); if (args->record_cmd_line) bcf_hdr_append_version(hdr, args->argc, args->argv, "bcftools_convert"); if ( bcf_hdr_write(out_fh,hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); if ( init_index2(out_fh,hdr,args->outfname,&args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->outfname); int32_t *itmp = NULL, nitmp = 0; while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = bcf_sr_get_line(args->files,0); if ( args->filter ) { int pass = filter_test(args->filter, line, NULL); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); continue; } } // check if alleles compatible with being a gVCF record // ALT must be one of ., <*>, , // check for INFO/END is below int i, gallele = -1; if (line->n_allele==1) gallele = 0; // illumina/bcftools-call gvcf (if INFO/END present) else if ( line->d.allele[1][0]=='<' ) { for (i=1; in_allele; i++) { if ( line->d.allele[i][1]=='*' && line->d.allele[i][2]=='>' && line->d.allele[i][3]=='\0' ) { gallele = i; break; } // mpileup/spec compliant gVCF if ( line->d.allele[i][1]=='X' && line->d.allele[i][2]=='>' && line->d.allele[i][3]=='\0' ) { gallele = i; break; } // old mpileup gVCF if ( strcmp(line->d.allele[i],"")==0 ) { gallele = i; break; } // GATK gVCF } } // no gVCF compatible alleles if (gallele<0) { if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); continue; } int nend = bcf_get_info_int32(hdr,line,"END",&itmp,&nitmp); if ( nend!=1 ) { // No INFO/END => not gVCF record if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); continue; } bcf_update_info_int32(hdr,line,"END",NULL,0); int pos, len; for (pos=line->pos; pospos = pos; char *ref = faidx_fetch_seq(args->ref, (char*)bcf_hdr_id2name(hdr,line->rid), line->pos, line->pos, &len); if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_hdr_id2name(hdr,line->rid),(int64_t) line->pos+1); strncpy(line->d.allele[0],ref,len); if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname); free(ref); } } free(itmp); if ( args->write_index ) { if ( bcf_idx_save(out_fh)<0 ) { if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->outfname); } static void usage(void) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: Converts VCF/BCF to other formats and back. See man page for file\n"); fprintf(bcftools_stderr, " formats details. When specifying output files explicitly instead\n"); fprintf(bcftools_stderr, " of with PREFIX, one can use '-' for bcftools_stdout and '.' to suppress.\n"); fprintf(bcftools_stderr, "Usage: bcftools convert [OPTIONS] INPUT_FILE\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "VCF input options:\n"); fprintf(bcftools_stderr, " -e, --exclude EXPR Exclude sites for which the expression is true\n"); fprintf(bcftools_stderr, " -i, --include EXPR Select sites for which the expression is true\n"); fprintf(bcftools_stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(bcftools_stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(bcftools_stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " -s, --samples LIST List of samples to include\n"); fprintf(bcftools_stderr, " -S, --samples-file FILE File of samples to include\n"); fprintf(bcftools_stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "VCF output options:\n"); fprintf(bcftools_stderr, " --no-version Do not append version and command line to the header\n"); fprintf(bcftools_stderr, " -o, --output FILE Output file name [bcftools_stdout]\n"); fprintf(bcftools_stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(bcftools_stderr, " --threads INT Use multithreading with INT worker threads [0]\n"); fprintf(bcftools_stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "GEN/SAMPLE conversion (input/output from IMPUTE2):\n"); fprintf(bcftools_stderr, " -G, --gensample2vcf ... |,\n"); fprintf(bcftools_stderr, " -g, --gensample ... |,\n"); fprintf(bcftools_stderr, " --3N6 Use 3*N+6 column format instead of the old 3*N+5 column format\n"); fprintf(bcftools_stderr, " --tag STRING Tag to take values for .gen file: GT,PL,GL,GP [GT]\n"); fprintf(bcftools_stderr, " --chrom Output chromosome in first column instead of CHROM:POS_REF_ALT\n"); fprintf(bcftools_stderr, " --keep-duplicates Keep duplicate positions\n"); fprintf(bcftools_stderr, " --sex FILE Output sex column in the sample-file, input format is: Sample\\t[MF]\n"); fprintf(bcftools_stderr, " --vcf-ids Output VCF IDs in second column instead of CHROM:POS_REF_ALT\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "gVCF conversion:\n"); fprintf(bcftools_stderr, " --gvcf2vcf Expand gVCF reference blocks\n"); fprintf(bcftools_stderr, " -f, --fasta-ref FILE Reference sequence in fasta format\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "HAP/SAMPLE conversion (output from SHAPEIT):\n"); fprintf(bcftools_stderr, " --hapsample2vcf ... |,\n"); fprintf(bcftools_stderr, " --hapsample ... |,\n"); fprintf(bcftools_stderr, " --haploid2diploid Convert haploid genotypes to diploid homozygotes\n"); fprintf(bcftools_stderr, " --sex FILE Output sex column in the sample-file, input format is: Sample\\t[MF]\n"); fprintf(bcftools_stderr, " --vcf-ids Output VCF IDs instead of CHROM:POS_REF_ALT\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "HAP/LEGEND/SAMPLE conversion:\n"); fprintf(bcftools_stderr, " -H, --haplegendsample2vcf ... |,,\n"); fprintf(bcftools_stderr, " -h, --haplegendsample ... |,,\n"); fprintf(bcftools_stderr, " --haploid2diploid Convert haploid genotypes to diploid homozygotes\n"); fprintf(bcftools_stderr, " --sex FILE Output sex column in the sample-file, input format is: Sample\\t[MF]\n"); fprintf(bcftools_stderr, " --vcf-ids Output VCF IDs instead of CHROM:POS_REF_ALT\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "TSV conversion:\n"); fprintf(bcftools_stderr, " --tsv2vcf FILE\n"); fprintf(bcftools_stderr, " -c, --columns STRING Columns of the input tsv file, see man page for details [ID,CHROM,POS,AA]\n"); fprintf(bcftools_stderr, " -f, --fasta-ref FILE Reference sequence in fasta format\n"); fprintf(bcftools_stderr, " -s, --samples LIST List of sample names\n"); fprintf(bcftools_stderr, " -S, --samples-file FILE File of sample names\n"); fprintf(bcftools_stderr, "\n"); // fprintf(bcftools_stderr, "PLINK options:\n"); // fprintf(bcftools_stderr, " -p, --plink |,,|,,|,\n"); // fprintf(bcftools_stderr, " --tped make tped file instead\n"); // fprintf(bcftools_stderr, " --bin make binary bed/fam/bim files\n"); // fprintf(bcftools_stderr, "\n"); // fprintf(bcftools_stderr, "PBWT options:\n"); // fprintf(bcftools_stderr, " -b, --pbwt or ,,,\n"); // fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int main_vcfconvert(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->outfname = "-"; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->regions_overlap = 1; args->targets_overlap = 0; args->clevel = -1; static struct option loptions[] = { {"include",required_argument,NULL,'i'}, {"exclude",required_argument,NULL,'e'}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"threads",required_argument,NULL,9}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,13}, {"targets",required_argument,NULL,'t'}, {"targets-file",required_argument,NULL,'T'}, {"targets-overlap",required_argument,NULL,14}, {"samples",required_argument,NULL,'s'}, {"samples-file",required_argument,NULL,'S'}, {"sex",required_argument,NULL,11}, {"gensample",required_argument,NULL,'g'}, {"gensample2vcf",required_argument,NULL,'G'}, {"tag",required_argument,NULL,1}, {"chrom",no_argument,NULL,8}, {"3N6",no_argument,NULL,15}, {"tsv2vcf",required_argument,NULL,2}, {"hapsample",required_argument,NULL,7}, {"hapsample2vcf",required_argument,NULL,3}, {"vcf-ids",no_argument,NULL,4}, {"haploid2diploid",no_argument,NULL,5}, {"gvcf2vcf",no_argument,NULL,6}, {"haplegendsample",required_argument,NULL,'h'}, {"haplegendsample2vcf",required_argument,NULL,'H'}, {"columns",required_argument,NULL,'c'}, {"fasta-ref",required_argument,NULL,'f'}, {"no-version",no_argument,NULL,10}, {"keep-duplicates",no_argument,NULL,12}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "?h:r:R:s:S:t:T:i:e:g:G:o:O:c:f:H:W::",loptions,NULL)) >= 0) { switch (c) { case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; args->regions_is_file = 1; break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; args->targets_is_file = 1; break; case 's': args->sample_list = optarg; break; case 'S': args->sample_list = optarg; args->sample_is_file = 1; break; case 'g': args->convert_func = vcf_to_gensample; args->outfname = optarg; break; case 'G': args->convert_func = gensample_to_vcf; args->infname = optarg; break; case 1 : args->tag = optarg; break; case 2 : args->convert_func = tsv_to_vcf; args->infname = optarg; break; case 3 : args->convert_func = hapsample_to_vcf; args->infname = optarg; break; case 4 : args->output_vcf_ids = 1; break; case 5 : args->hap2dip = 1; break; case 6 : args->convert_func = gvcf_to_vcf; break; case 7 : args->convert_func = vcf_to_hapsample; args->outfname = optarg; break; case 8 : error("The --chrom option has been deprecated, please use --3N6 instead\n"); break; case 15 : args->gen_3N6 = 1; break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 'H': args->convert_func = haplegendsample_to_vcf; args->infname = optarg; break; case 'f': args->ref_fname = optarg; break; case 'c': args->columns = optarg; break; case 'o': args->outfname = optarg; break; case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'h': args->convert_func = vcf_to_haplegendsample; args->outfname = optarg; break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 10 : args->record_cmd_line = 0; break; case 11 : args->sex_fname = optarg; break; case 12 : args->keep_duplicates = 1; break; case 13 : args->regions_overlap = parse_overlap_option(optarg); if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 14 : args->targets_overlap = parse_overlap_option(optarg); if ( args->targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case '?': usage(); break; default: error("Unknown argument: %s\n", optarg); } } if ( !args->infname ) { if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) args->infname = "-"; } else args->infname = argv[optind]; } if ( !args->infname ) usage(); if ( args->convert_func ) args->convert_func(args); else vcf_to_vcf(args); destroy_data(args); free(args); return 0; } pysam-0.23.0/bcftools/vcffilter.c000066400000000000000000000754651475062545500167260ustar00rootroot00000000000000/* vcffilter.c -- Apply fixed-threshold filters. Copyright (C) 2013-2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "filter.h" #include "rbuf.h" #include "regidx.h" // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 // FILTER columns annotation: replace or add to existing FILTERs; set FILTER to PASS at good sites? #define ANNOT_ADD 1 #define ANNOT_RESET 2 // Set genotypes of filtered samples #define SET_GTS_MISSING 1 #define SET_GTS_REF 2 typedef struct _args_t { filter_t *filter; char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE const uint8_t *smpl_pass; int set_gts; char *soft_filter; // drop failed sites or annotate FILTER column? int annot_mode; // add to existing FILTER annotation or replace? Otherwise reset FILTER to PASS or leave as it is? int flt_fail, flt_pass; // BCF ids of fail and pass filters int snp_gap, snp_gap_type, indel_gap, IndelGap_id, SnpGap_id; char *snp_gap_str; int32_t ntmpi, *tmpi, ntmp_ac, *tmp_ac; rbuf_t rbuf; bcf1_t **rbuf_lines; bcf_srs_t *files; bcf_hdr_t *hdr; htsFile *out_fh; int output_type, n_threads, clevel; char **argv, *output_fname, *targets_list, *regions_list, *mask_list; int argc, record_cmd_line, mask_is_file, mask_overlap, mask_negate; regidx_t *mask; char *index_fn; int write_index; } args_t; static void init_data(args_t *args) { char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno)); if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads); if ( args->mask_list ) { if ( args->mask_list[0]=='^' ) args->mask_negate = 1; if ( args->mask_is_file ) args->mask = regidx_init(args->mask_negate?args->mask_list+1:args->mask_list,NULL,NULL,0,NULL); else { char *rmme = strdup(args->mask_negate?args->mask_list+1:args->mask_list), *tmp = rmme; while ( *tmp ) { if ( *tmp==',' ) *tmp = '\n'; tmp++; } args->mask = regidx_init_string(rmme, regidx_parse_reg, NULL, 0, NULL); free(rmme); } if ( !args->mask ) error("Could not initialize the mask: %s\n",args->mask_list); } args->hdr = args->files->readers[0].header; args->flt_pass = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"PASS"); assert( !args->flt_pass ); // sanity check: required by BCF spec if ( args->soft_filter && (args->filter_logic || args->mask_list) ) { kstring_t flt_name = {0,0,0}; if ( strcmp(args->soft_filter,"+") ) kputs(args->soft_filter, &flt_name); else { // Make up a filter name int i = 0, id = -1; do { ksprintf(&flt_name,"Filter%d", ++i); id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,flt_name.s); } while ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FLT,id) ); } kstring_t tmp = {0,0,0}; if ( args->filter_logic ) { // -i or -e: append FILTER line ksprintf(&tmp,"Set if %s: ",args->filter_logic & FLT_INCLUDE ? "not true" : "true"); // escape quotes char *t = args->filter_str; while ( *t ) { if ( *t=='"' ) kputc('\\',&tmp); kputc(*t,&tmp); t++; } } else if ( args->mask_list ) ksprintf(&tmp,"Record masked by region"); int ret = bcf_hdr_printf(args->hdr, "##FILTER=", flt_name.s,tmp.s); if ( ret!=0 ) error("Failed to append header line: ##FILTER=\n", flt_name.s,tmp.s); args->flt_fail = bcf_hdr_id2int(args->hdr,BCF_DT_ID,flt_name.s); assert( args->flt_fail>=0 ); free(flt_name.s); free(tmp.s); } if ( args->snp_gap || args->indel_gap ) { if ( !args->filter_logic && args->soft_filter && strcmp(args->soft_filter,"+") ) { kstring_t tmp = {0,0,0}; if ( args->snp_gap ) kputs("\"SnpGap\"", &tmp); if ( args->indel_gap ) { if ( tmp.s ) kputs(" and ", &tmp); kputs("\"IndelGap\"", &tmp); } if ( strncmp(tmp.s+1,args->soft_filter,tmp.l-2) ) fprintf(stderr,"Warning: using %s filter name instead of \"%s\"\n", tmp.s,args->soft_filter); free(tmp.s); } rbuf_init(&args->rbuf, 64); args->rbuf_lines = (bcf1_t**) calloc(args->rbuf.m, sizeof(bcf1_t*)); if ( args->snp_gap ) { bcf_hdr_printf(args->hdr, "##FILTER=", args->snp_gap,args->snp_gap_str); args->SnpGap_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "SnpGap"); assert( args->SnpGap_id>=0 ); } if ( args->indel_gap ) { bcf_hdr_printf(args->hdr, "##FILTER=", args->indel_gap); args->IndelGap_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "IndelGap"); assert( args->IndelGap_id>=0 ); } } if (args->record_cmd_line) bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_filter"); if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); } static void destroy_data(args_t *args) { if ( args->rbuf_lines ) { int i; for (i=0; irbuf.m; i++) if ( args->rbuf_lines[i] ) bcf_destroy1(args->rbuf_lines[i]); free(args->rbuf_lines); } if ( args->filter ) filter_destroy(args->filter); free(args->tmpi); free(args->tmp_ac); if ( args->mask ) regidx_destroy(args->mask); } static void flush_buffer(args_t *args, int n) { int i, j; for (i=0; irbuf); bcf1_t *rec = args->rbuf_lines[k]; int pass = 1; if ( !args->soft_filter ) { for (j=0; jd.n_flt; j++) { if ( args->indel_gap && rec->d.flt[j]==args->IndelGap_id ) { pass = 0; break; } if ( args->snp_gap && rec->d.flt[j]==args->SnpGap_id ) { pass = 0; break; } } } if ( pass && bcf_write1(args->out_fh, args->hdr, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); } } #define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; } static void buffered_filters(args_t *args, bcf1_t *line) { /** * The logic of SnpGap=3. The SNPs at positions 1 and 7 are filtered, * positions 0 and 8 are not: * 0123456789 * ref .G.GT..G.. * del .A.G-..A.. * Here the positions 1 and 6 are filtered, 0 and 7 are not: * 0123-456789 * ref .G.G-..G.. * ins .A.GT..A.. * * The logic of IndelGap=2. The second indel is filtered: * 012345678901 * ref .GT.GT..GT.. * del .G-.G-..G-.. * And similarly here, the second is filtered: * 01 23 456 78 * ref .A-.A-..A-.. * ins .AT.AT..AT.. */ // To avoid additional data structure, we abuse bcf1_t's var and var_type records. const int SnpGap_set = 1 << (8*sizeof(int)/2); const int IndelGap_set = 1 << (8*sizeof(int)/2-1); const int IndelGap_flush = 1 << (8*sizeof(int)/2-2); int var_type = 0, i; if ( line ) { // Still on the same chromosome? int ilast = rbuf_last(&args->rbuf); if ( ilast>=0 && line->rid != args->rbuf_lines[ilast]->rid ) flush_buffer(args, args->rbuf.n); // new chromosome, flush everything rbuf_expand0(&args->rbuf,bcf1_t*,args->rbuf.n,args->rbuf_lines); // Insert the new record in the buffer. The line would be overwritten in // the next bcf_sr_next_line call, therefore we need to swap it with an // unused one ilast = rbuf_append(&args->rbuf); if ( !args->rbuf_lines[ilast] ) args->rbuf_lines[ilast] = bcf_init1(); SWAP(bcf1_t*, args->files->readers[0].buffer[0], args->rbuf_lines[ilast]); var_type = bcf_get_variant_types(line); // Find out the size of an indel. The indel boundaries are based on REF // (POS+1,POS+rlen-1). This is not entirely correct: mpileup likes to // output REF=CAGAGAGAGA, ALT=CAGAGAGAGAGA where REF=C,ALT=CGA could be // used. This filter is therefore more strict and may remove some valid // SNPs. // Set the REF allele's length to max deletion length or to 1 if a SNP or an insertion. line->d.var[0].n = line->rlen; } int k_flush = 1; if ( args->indel_gap ) { k_flush = 0; // Find indels which are too close to each other int last_to = -1; for (i=-1; rbuf_next(&args->rbuf,&i); ) { bcf1_t *rec = args->rbuf_lines[i]; int rec_from = rec->pos; if ( last_to!=-1 && last_to < rec_from ) break; k_flush++; if ( !(rec->d.var_type & VCF_INDEL) ) continue; rec->d.var_type |= IndelGap_set; last_to = args->indel_gap + rec->pos + rec->d.var[0].n - 1; } if ( i==args->rbuf.f && line && last_to!=-1 ) k_flush = 0; if ( k_flush || !line ) { // Select the best indel from the cluster of k_flush indels int k = 0, max_ac = -1, imax_ac = -1, max_qual = -1, imax_qual = -1; for (i=-1; rbuf_next(&args->rbuf,&i) && krbuf_lines[i]; if ( !(rec->d.var_type & IndelGap_set) ) continue; hts_expand(int, rec->n_allele, args->ntmpi, args->tmpi); int ret = bcf_calc_ac(args->hdr, rec, args->tmpi, BCF_UN_ALL); if ( imax_ac==-1 || (ret && max_ac < args->tmpi[1]) ) { max_ac = args->tmpi[1]; imax_ac = i; } if ( imax_qual==-1 || max_qual < rec->qual ) { max_qual = rec->qual; imax_qual = i; } } // Filter all but the best indel (with the best QUAL, bigger AC, or take the first if neither QUAL nor AC are available) k = 0; for (i=-1; rbuf_next(&args->rbuf,&i) && krbuf_lines[i]; if ( !(rec->d.var_type & IndelGap_set) ) continue; rec->d.var_type |= IndelGap_flush; int do_filter = 0; if ( max_qual>0 ) { if ( i!=imax_qual ) do_filter = 1; } else if ( i!=imax_ac ) do_filter = 1; if ( do_filter ) bcf_add_filter(args->hdr, args->rbuf_lines[i], args->IndelGap_id); } } } if ( !line ) { // Finished: flush everything flush_buffer(args, args->rbuf.n); return; } int j_flush = 1; if ( args->snp_gap ) { j_flush = 0; int last_from = line->pos; for (i=-1; rbuf_next(&args->rbuf,&i); ) { bcf1_t *rec = args->rbuf_lines[i]; int rec_to = rec->pos + rec->d.var[0].n - 1; // last position affected by the variant if ( rec_to + args->snp_gap < last_from ) j_flush++; else if ( (var_type & args->snp_gap_type) && (rec->d.var_type & VCF_SNP) && !(rec->d.var_type & SnpGap_set) ) { // this SNP has not been SnpGap-filtered yet rec->d.var_type |= SnpGap_set; bcf_add_filter(args->hdr, rec, args->SnpGap_id); } else if ( (var_type & VCF_SNP) && (rec->d.var_type & args->snp_gap_type) ) { // the line which we are adding is a SNP and needs to be filtered line->d.var_type |= SnpGap_set; bcf_add_filter(args->hdr, line, args->SnpGap_id); break; } } } flush_buffer(args, j_flush < k_flush ? j_flush : k_flush); } static void set_genotypes(args_t *args, bcf1_t *line, int pass_site) { int i,j; if ( !bcf_hdr_nsamples(args->hdr) ) return; if ( args->smpl_pass ) { int npass = 0; for (i=0; ihdr); i++) npass += args->smpl_pass[i]; // return if all samples pass if ( npass==bcf_hdr_nsamples(args->hdr) && (args->filter_logic & FLT_INCLUDE) ) return; if ( npass==0 && (args->filter_logic & FLT_EXCLUDE) ) return; } else if ( pass_site ) return; int an = 0, has_an = bcf_get_info_int32(args->hdr, line, "AN", &args->tmp_ac, &args->ntmp_ac); if ( has_an==1 ) an = args->tmp_ac[0]; else has_an = 0; int has_ac = bcf_get_info_int32(args->hdr, line, "AC", &args->tmp_ac, &args->ntmp_ac); has_ac = has_ac==line->n_allele-1 ? 1 : 0; int new_gt = 0, ngts = bcf_get_format_int32(args->hdr, line, "GT", &args->tmpi, &args->ntmpi); ngts /= bcf_hdr_nsamples(args->hdr); if ( args->set_gts==SET_GTS_MISSING ) new_gt = bcf_gt_missing; else if ( args->set_gts==SET_GTS_REF ) new_gt = bcf_gt_unphased(0); else error("todo: set_gts=%d\n", args->set_gts); for (i=0; ihdr); i++) { if ( args->smpl_pass ) { int pass = args->smpl_pass[i]; if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( pass ) continue; } int32_t *gts = args->tmpi + ngts*i; for (j=0; jset_gts==SET_GTS_MISSING && !bcf_gt_is_missing(gts[j]) ) { int ial = bcf_gt_allele(gts[j]); if ( has_ac && ial>0 && ial<=line->n_allele ) args->tmp_ac[ ial-1 ]--; an--; } else if ( args->set_gts==SET_GTS_REF ) { int ial = bcf_gt_allele(gts[j]); if ( bcf_gt_is_missing(gts[j]) ) an++; else if ( has_ac && ial>0 && ial<=line->n_allele ) args->tmp_ac[ ial-1 ]--; } gts[j] = new_gt; } } bcf_update_genotypes(args->hdr,line,args->tmpi,ngts*bcf_hdr_nsamples(args->hdr)); if ( has_an ) bcf_update_info_int32(args->hdr,line,"AN",&an,1); if ( has_ac ) bcf_update_info_int32(args->hdr,line,"AC",args->tmp_ac,line->n_allele-1); } static void _set_variant_boundaries(bcf1_t *rec, hts_pos_t *beg, hts_pos_t *end) { hts_pos_t off; if ( rec->n_allele ) { off = rec->rlen; bcf_unpack(rec, BCF_UN_STR); int i; for (i=1; in_allele; i++) { // Make symbolic alleles start at POS, although this is not strictly true for // , where POS should be the position BEFORE the deletion/insertion. // However, since arbitrary symbolic alleles can be defined by the user, we // will simplify the interpretation of --targets-overlap and --region-overlap. int j = 0; char *ref = rec->d.allele[0]; char *alt = rec->d.allele[i]; while ( ref[j] && alt[j] && ref[j]==alt[j] ) j++; if ( off > j ) off = j; if ( !off ) break; } } else off = 0; *beg = rec->pos + off; *end = rec->pos + rec->rlen - 1; } static void usage(args_t *args) { fprintf(stderr, "\n"); fprintf(stderr, "About: Apply fixed-threshold filters.\n"); fprintf(stderr, "Usage: bcftools filter [options] \n"); fprintf(stderr, "\n"); fprintf(stderr, "Options:\n"); fprintf(stderr, " -e, --exclude EXPR Exclude sites for which the expression is true (see man page for details)\n"); fprintf(stderr, " -g, --SnpGap INT[:TYPE] Filter SNPs within base pairs of an indel (the default) or any combination of indel,mnp,bnd,other,overlap\n"); fprintf(stderr, " -G, --IndelGap INT Filter clusters of indels separated by or fewer base pairs allowing only one to pass\n"); fprintf(stderr, " -i, --include EXPR Include only sites for which the expression is true (see man page for details\n"); fprintf(stderr, " --mask [^]REGION Soft filter regions, \"^\" to negate\n"); fprintf(stderr, " -M, --mask-file [^]FILE Soft filter regions listed in a file, \"^\" to negate\n"); fprintf(stderr, " --mask-overlap 0|1|2 Mask if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " -m, --mode [+x] \"+\": do not replace but add to existing FILTER; \"x\": reset filters at sites which pass\n"); fprintf(stderr, " --no-version Do not append version and command line to the header\n"); fprintf(stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " -s, --soft-filter STRING Annotate FILTER column with or unique filter name (\"Filter%%d\") made up by the program (\"+\")\n"); fprintf(stderr, " -S, --set-GTs .|0 Set genotypes of failed samples to missing (.) or ref (0)\n"); fprintf(stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(stderr, " --threads INT Use multithreading with worker threads [0]\n"); fprintf(stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(stderr, "\n"); exit(1); } int main_vcffilter(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->files = bcf_sr_init(); args->output_fname = "-"; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->clevel = -1; int regions_is_file = 0, targets_is_file = 0; int regions_overlap = 1; int targets_overlap = 0; args->mask_overlap = 1; static struct option loptions[] = { {"set-GTs",required_argument,NULL,'S'}, {"mode",required_argument,NULL,'m'}, {"mask",required_argument,NULL,10}, {"mask-file",required_argument,NULL,'M'}, {"mask-overlap",required_argument,NULL,11}, {"soft-filter",required_argument,NULL,'s'}, {"exclude",required_argument,NULL,'e'}, {"include",required_argument,NULL,'i'}, {"targets",required_argument,NULL,'t'}, {"targets-file",required_argument,NULL,'T'}, {"targets-overlap",required_argument,NULL,4}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,3}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"threads",required_argument,NULL,9}, {"SnpGap",required_argument,NULL,'g'}, {"IndelGap",required_argument,NULL,'G'}, {"no-version",no_argument,NULL,8}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "e:i:t:T:r:R:h?s:m:M:o:O:g:G:S:W::",loptions,NULL)) >= 0) { switch (c) { case 'g': args->snp_gap = strtol(optarg,&tmp,10); if ( *tmp && *tmp!=':' ) error("Could not parse argument: --SnpGap %s\n", optarg); if ( *tmp==':' ) { args->snp_gap_str = tmp+1; int i,n; char **keys = hts_readlist(tmp+1,0,&n); for(i=0; isnp_gap_type |= VCF_INDEL; else if ( !strcasecmp(keys[i],"mnp") ) args->snp_gap_type |= VCF_MNP; else if ( !strcasecmp(keys[i],"bnd") ) args->snp_gap_type |= VCF_BND; else if ( !strcasecmp(keys[i],"other") ) args->snp_gap_type |= VCF_OTHER; else if ( !strcasecmp(keys[i],"overlap") ) args->snp_gap_type |= VCF_OVERLAP; else error("Could not parse \"%s\" in \"--SnpGap %s\"\n", keys[i], optarg); free(keys[i]); } if ( n ) free(keys); } else { args->snp_gap_type = VCF_INDEL; args->snp_gap_str = "indel"; } break; case 'G': args->indel_gap = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --IndelGap %s\n", optarg); break; case 'o': args->output_fname = optarg; break; case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 's': args->soft_filter = optarg; break; case 'm': if ( strchr(optarg,'x') ) args->annot_mode |= ANNOT_RESET; if ( strchr(optarg,'+') ) args->annot_mode |= ANNOT_ADD; break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; targets_is_file = 1; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'S': if ( !strcmp(".",optarg) ) args->set_gts = SET_GTS_MISSING; else if ( !strcmp("0",optarg) ) args->set_gts = SET_GTS_REF; else error("The argument to -S not recognised: %s\n", optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 8 : args->record_cmd_line = 0; break; case 3 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 4 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 10 : args->mask_list = optarg; break; case 'M' : args->mask_list = optarg; args->mask_is_file = 1; break; case 11 : if ( !strcasecmp(optarg,"0") ) args->mask_overlap = 0; else if ( !strcasecmp(optarg,"1") ) args->mask_overlap = 1; else if ( !strcasecmp(optarg,"2") ) args->mask_overlap = 2; else error("Could not parse: --mask-overlap %s\n",optarg); break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 'h': case '?': usage(args); break; default: error("Unknown argument: %s\n", optarg); } } if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n"); char *fname = NULL; if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else usage(args); } else fname = argv[optind]; if ( args->mask_list && !args->soft_filter ) error("The option --soft-filter is required with --mask and --mask-file options\n"); // read in the regions from the command line if ( args->regions_list ) { args->files->require_index = 1; bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } else if ( optind+1 < argc ) { int i; kstring_t tmp = {0,0,0}; kputs(argv[optind+1],&tmp); for (i=optind+2; ifiles->require_index = 1; bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, tmp.s, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); free(tmp.s); } if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list,targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); init_data(args); if ( bcf_hdr_write(args->out_fh, args->hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname); if ( init_index2(args->out_fh,args->hdr,args->output_fname,&args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->output_fname); while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = bcf_sr_get_line(args->files, 0); int pass = 1; if ( args->filter ) { pass = filter_test(args->filter, line, &args->smpl_pass); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; } if ( args->mask ) { hts_pos_t beg, end; if ( args->mask_overlap==0 ) beg = end = line->pos; else if ( args->mask_overlap==1 ) beg = line->pos, end = line->pos + line->rlen - 1; else _set_variant_boundaries(line,&beg,&end); int mpass = regidx_overlap(args->mask,bcf_seqname(args->hdr,line),beg,end,NULL) ? 0 : 1; if ( args->mask_negate ) mpass = mpass ? 0 : 1; pass &= mpass; } if ( args->soft_filter || args->set_gts || pass ) { if ( pass ) { bcf_unpack(line,BCF_UN_FLT); if ( args->annot_mode & ANNOT_RESET || !line->d.n_flt ) bcf_add_filter(args->hdr, line, args->flt_pass); } else if ( args->soft_filter ) { if ( (args->annot_mode & ANNOT_ADD) ) bcf_add_filter(args->hdr, line, args->flt_fail); else bcf_update_filter(args->hdr, line, &args->flt_fail, 1); } if ( args->set_gts ) set_genotypes(args, line, pass); if ( !args->rbuf_lines ) { if ( bcf_write1(args->out_fh, args->hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); } else buffered_filters(args, line); } } buffered_filters(args, NULL); if ( args->write_index ) { if ( bcf_idx_save(args->out_fh)<0 ) { if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname); destroy_data(args); bcf_sr_destroy(args->files); free(args); return 0; } pysam-0.23.0/bcftools/vcffilter.c.pysam.c000066400000000000000000000761401475062545500202660ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcffilter.c -- Apply fixed-threshold filters. Copyright (C) 2013-2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "filter.h" #include "rbuf.h" #include "regidx.h" // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 // FILTER columns annotation: replace or add to existing FILTERs; set FILTER to PASS at good sites? #define ANNOT_ADD 1 #define ANNOT_RESET 2 // Set genotypes of filtered samples #define SET_GTS_MISSING 1 #define SET_GTS_REF 2 typedef struct _args_t { filter_t *filter; char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE const uint8_t *smpl_pass; int set_gts; char *soft_filter; // drop failed sites or annotate FILTER column? int annot_mode; // add to existing FILTER annotation or replace? Otherwise reset FILTER to PASS or leave as it is? int flt_fail, flt_pass; // BCF ids of fail and pass filters int snp_gap, snp_gap_type, indel_gap, IndelGap_id, SnpGap_id; char *snp_gap_str; int32_t ntmpi, *tmpi, ntmp_ac, *tmp_ac; rbuf_t rbuf; bcf1_t **rbuf_lines; bcf_srs_t *files; bcf_hdr_t *hdr; htsFile *out_fh; int output_type, n_threads, clevel; char **argv, *output_fname, *targets_list, *regions_list, *mask_list; int argc, record_cmd_line, mask_is_file, mask_overlap, mask_negate; regidx_t *mask; char *index_fn; int write_index; } args_t; static void init_data(args_t *args) { char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno)); if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads); if ( args->mask_list ) { if ( args->mask_list[0]=='^' ) args->mask_negate = 1; if ( args->mask_is_file ) args->mask = regidx_init(args->mask_negate?args->mask_list+1:args->mask_list,NULL,NULL,0,NULL); else { char *rmme = strdup(args->mask_negate?args->mask_list+1:args->mask_list), *tmp = rmme; while ( *tmp ) { if ( *tmp==',' ) *tmp = '\n'; tmp++; } args->mask = regidx_init_string(rmme, regidx_parse_reg, NULL, 0, NULL); free(rmme); } if ( !args->mask ) error("Could not initialize the mask: %s\n",args->mask_list); } args->hdr = args->files->readers[0].header; args->flt_pass = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"PASS"); assert( !args->flt_pass ); // sanity check: required by BCF spec if ( args->soft_filter && (args->filter_logic || args->mask_list) ) { kstring_t flt_name = {0,0,0}; if ( strcmp(args->soft_filter,"+") ) kputs(args->soft_filter, &flt_name); else { // Make up a filter name int i = 0, id = -1; do { ksprintf(&flt_name,"Filter%d", ++i); id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,flt_name.s); } while ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FLT,id) ); } kstring_t tmp = {0,0,0}; if ( args->filter_logic ) { // -i or -e: append FILTER line ksprintf(&tmp,"Set if %s: ",args->filter_logic & FLT_INCLUDE ? "not true" : "true"); // escape quotes char *t = args->filter_str; while ( *t ) { if ( *t=='"' ) kputc('\\',&tmp); kputc(*t,&tmp); t++; } } else if ( args->mask_list ) ksprintf(&tmp,"Record masked by region"); int ret = bcf_hdr_printf(args->hdr, "##FILTER=", flt_name.s,tmp.s); if ( ret!=0 ) error("Failed to append header line: ##FILTER=\n", flt_name.s,tmp.s); args->flt_fail = bcf_hdr_id2int(args->hdr,BCF_DT_ID,flt_name.s); assert( args->flt_fail>=0 ); free(flt_name.s); free(tmp.s); } if ( args->snp_gap || args->indel_gap ) { if ( !args->filter_logic && args->soft_filter && strcmp(args->soft_filter,"+") ) { kstring_t tmp = {0,0,0}; if ( args->snp_gap ) kputs("\"SnpGap\"", &tmp); if ( args->indel_gap ) { if ( tmp.s ) kputs(" and ", &tmp); kputs("\"IndelGap\"", &tmp); } if ( strncmp(tmp.s+1,args->soft_filter,tmp.l-2) ) fprintf(bcftools_stderr,"Warning: using %s filter name instead of \"%s\"\n", tmp.s,args->soft_filter); free(tmp.s); } rbuf_init(&args->rbuf, 64); args->rbuf_lines = (bcf1_t**) calloc(args->rbuf.m, sizeof(bcf1_t*)); if ( args->snp_gap ) { bcf_hdr_printf(args->hdr, "##FILTER=", args->snp_gap,args->snp_gap_str); args->SnpGap_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "SnpGap"); assert( args->SnpGap_id>=0 ); } if ( args->indel_gap ) { bcf_hdr_printf(args->hdr, "##FILTER=", args->indel_gap); args->IndelGap_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "IndelGap"); assert( args->IndelGap_id>=0 ); } } if (args->record_cmd_line) bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_filter"); if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); } static void destroy_data(args_t *args) { if ( args->rbuf_lines ) { int i; for (i=0; irbuf.m; i++) if ( args->rbuf_lines[i] ) bcf_destroy1(args->rbuf_lines[i]); free(args->rbuf_lines); } if ( args->filter ) filter_destroy(args->filter); free(args->tmpi); free(args->tmp_ac); if ( args->mask ) regidx_destroy(args->mask); } static void flush_buffer(args_t *args, int n) { int i, j; for (i=0; irbuf); bcf1_t *rec = args->rbuf_lines[k]; int pass = 1; if ( !args->soft_filter ) { for (j=0; jd.n_flt; j++) { if ( args->indel_gap && rec->d.flt[j]==args->IndelGap_id ) { pass = 0; break; } if ( args->snp_gap && rec->d.flt[j]==args->SnpGap_id ) { pass = 0; break; } } } if ( pass && bcf_write1(args->out_fh, args->hdr, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); } } #define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; } static void buffered_filters(args_t *args, bcf1_t *line) { /** * The logic of SnpGap=3. The SNPs at positions 1 and 7 are filtered, * positions 0 and 8 are not: * 0123456789 * ref .G.GT..G.. * del .A.G-..A.. * Here the positions 1 and 6 are filtered, 0 and 7 are not: * 0123-456789 * ref .G.G-..G.. * ins .A.GT..A.. * * The logic of IndelGap=2. The second indel is filtered: * 012345678901 * ref .GT.GT..GT.. * del .G-.G-..G-.. * And similarly here, the second is filtered: * 01 23 456 78 * ref .A-.A-..A-.. * ins .AT.AT..AT.. */ // To avoid additional data structure, we abuse bcf1_t's var and var_type records. const int SnpGap_set = 1 << (8*sizeof(int)/2); const int IndelGap_set = 1 << (8*sizeof(int)/2-1); const int IndelGap_flush = 1 << (8*sizeof(int)/2-2); int var_type = 0, i; if ( line ) { // Still on the same chromosome? int ilast = rbuf_last(&args->rbuf); if ( ilast>=0 && line->rid != args->rbuf_lines[ilast]->rid ) flush_buffer(args, args->rbuf.n); // new chromosome, flush everything rbuf_expand0(&args->rbuf,bcf1_t*,args->rbuf.n,args->rbuf_lines); // Insert the new record in the buffer. The line would be overwritten in // the next bcf_sr_next_line call, therefore we need to swap it with an // unused one ilast = rbuf_append(&args->rbuf); if ( !args->rbuf_lines[ilast] ) args->rbuf_lines[ilast] = bcf_init1(); SWAP(bcf1_t*, args->files->readers[0].buffer[0], args->rbuf_lines[ilast]); var_type = bcf_get_variant_types(line); // Find out the size of an indel. The indel boundaries are based on REF // (POS+1,POS+rlen-1). This is not entirely correct: mpileup likes to // output REF=CAGAGAGAGA, ALT=CAGAGAGAGAGA where REF=C,ALT=CGA could be // used. This filter is therefore more strict and may remove some valid // SNPs. // Set the REF allele's length to max deletion length or to 1 if a SNP or an insertion. line->d.var[0].n = line->rlen; } int k_flush = 1; if ( args->indel_gap ) { k_flush = 0; // Find indels which are too close to each other int last_to = -1; for (i=-1; rbuf_next(&args->rbuf,&i); ) { bcf1_t *rec = args->rbuf_lines[i]; int rec_from = rec->pos; if ( last_to!=-1 && last_to < rec_from ) break; k_flush++; if ( !(rec->d.var_type & VCF_INDEL) ) continue; rec->d.var_type |= IndelGap_set; last_to = args->indel_gap + rec->pos + rec->d.var[0].n - 1; } if ( i==args->rbuf.f && line && last_to!=-1 ) k_flush = 0; if ( k_flush || !line ) { // Select the best indel from the cluster of k_flush indels int k = 0, max_ac = -1, imax_ac = -1, max_qual = -1, imax_qual = -1; for (i=-1; rbuf_next(&args->rbuf,&i) && krbuf_lines[i]; if ( !(rec->d.var_type & IndelGap_set) ) continue; hts_expand(int, rec->n_allele, args->ntmpi, args->tmpi); int ret = bcf_calc_ac(args->hdr, rec, args->tmpi, BCF_UN_ALL); if ( imax_ac==-1 || (ret && max_ac < args->tmpi[1]) ) { max_ac = args->tmpi[1]; imax_ac = i; } if ( imax_qual==-1 || max_qual < rec->qual ) { max_qual = rec->qual; imax_qual = i; } } // Filter all but the best indel (with the best QUAL, bigger AC, or take the first if neither QUAL nor AC are available) k = 0; for (i=-1; rbuf_next(&args->rbuf,&i) && krbuf_lines[i]; if ( !(rec->d.var_type & IndelGap_set) ) continue; rec->d.var_type |= IndelGap_flush; int do_filter = 0; if ( max_qual>0 ) { if ( i!=imax_qual ) do_filter = 1; } else if ( i!=imax_ac ) do_filter = 1; if ( do_filter ) bcf_add_filter(args->hdr, args->rbuf_lines[i], args->IndelGap_id); } } } if ( !line ) { // Finished: flush everything flush_buffer(args, args->rbuf.n); return; } int j_flush = 1; if ( args->snp_gap ) { j_flush = 0; int last_from = line->pos; for (i=-1; rbuf_next(&args->rbuf,&i); ) { bcf1_t *rec = args->rbuf_lines[i]; int rec_to = rec->pos + rec->d.var[0].n - 1; // last position affected by the variant if ( rec_to + args->snp_gap < last_from ) j_flush++; else if ( (var_type & args->snp_gap_type) && (rec->d.var_type & VCF_SNP) && !(rec->d.var_type & SnpGap_set) ) { // this SNP has not been SnpGap-filtered yet rec->d.var_type |= SnpGap_set; bcf_add_filter(args->hdr, rec, args->SnpGap_id); } else if ( (var_type & VCF_SNP) && (rec->d.var_type & args->snp_gap_type) ) { // the line which we are adding is a SNP and needs to be filtered line->d.var_type |= SnpGap_set; bcf_add_filter(args->hdr, line, args->SnpGap_id); break; } } } flush_buffer(args, j_flush < k_flush ? j_flush : k_flush); } static void set_genotypes(args_t *args, bcf1_t *line, int pass_site) { int i,j; if ( !bcf_hdr_nsamples(args->hdr) ) return; if ( args->smpl_pass ) { int npass = 0; for (i=0; ihdr); i++) npass += args->smpl_pass[i]; // return if all samples pass if ( npass==bcf_hdr_nsamples(args->hdr) && (args->filter_logic & FLT_INCLUDE) ) return; if ( npass==0 && (args->filter_logic & FLT_EXCLUDE) ) return; } else if ( pass_site ) return; int an = 0, has_an = bcf_get_info_int32(args->hdr, line, "AN", &args->tmp_ac, &args->ntmp_ac); if ( has_an==1 ) an = args->tmp_ac[0]; else has_an = 0; int has_ac = bcf_get_info_int32(args->hdr, line, "AC", &args->tmp_ac, &args->ntmp_ac); has_ac = has_ac==line->n_allele-1 ? 1 : 0; int new_gt = 0, ngts = bcf_get_format_int32(args->hdr, line, "GT", &args->tmpi, &args->ntmpi); ngts /= bcf_hdr_nsamples(args->hdr); if ( args->set_gts==SET_GTS_MISSING ) new_gt = bcf_gt_missing; else if ( args->set_gts==SET_GTS_REF ) new_gt = bcf_gt_unphased(0); else error("todo: set_gts=%d\n", args->set_gts); for (i=0; ihdr); i++) { if ( args->smpl_pass ) { int pass = args->smpl_pass[i]; if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( pass ) continue; } int32_t *gts = args->tmpi + ngts*i; for (j=0; jset_gts==SET_GTS_MISSING && !bcf_gt_is_missing(gts[j]) ) { int ial = bcf_gt_allele(gts[j]); if ( has_ac && ial>0 && ial<=line->n_allele ) args->tmp_ac[ ial-1 ]--; an--; } else if ( args->set_gts==SET_GTS_REF ) { int ial = bcf_gt_allele(gts[j]); if ( bcf_gt_is_missing(gts[j]) ) an++; else if ( has_ac && ial>0 && ial<=line->n_allele ) args->tmp_ac[ ial-1 ]--; } gts[j] = new_gt; } } bcf_update_genotypes(args->hdr,line,args->tmpi,ngts*bcf_hdr_nsamples(args->hdr)); if ( has_an ) bcf_update_info_int32(args->hdr,line,"AN",&an,1); if ( has_ac ) bcf_update_info_int32(args->hdr,line,"AC",args->tmp_ac,line->n_allele-1); } static void _set_variant_boundaries(bcf1_t *rec, hts_pos_t *beg, hts_pos_t *end) { hts_pos_t off; if ( rec->n_allele ) { off = rec->rlen; bcf_unpack(rec, BCF_UN_STR); int i; for (i=1; in_allele; i++) { // Make symbolic alleles start at POS, although this is not strictly true for // , where POS should be the position BEFORE the deletion/insertion. // However, since arbitrary symbolic alleles can be defined by the user, we // will simplify the interpretation of --targets-overlap and --region-overlap. int j = 0; char *ref = rec->d.allele[0]; char *alt = rec->d.allele[i]; while ( ref[j] && alt[j] && ref[j]==alt[j] ) j++; if ( off > j ) off = j; if ( !off ) break; } } else off = 0; *beg = rec->pos + off; *end = rec->pos + rec->rlen - 1; } static void usage(args_t *args) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: Apply fixed-threshold filters.\n"); fprintf(bcftools_stderr, "Usage: bcftools filter [options] \n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Options:\n"); fprintf(bcftools_stderr, " -e, --exclude EXPR Exclude sites for which the expression is true (see man page for details)\n"); fprintf(bcftools_stderr, " -g, --SnpGap INT[:TYPE] Filter SNPs within base pairs of an indel (the default) or any combination of indel,mnp,bnd,other,overlap\n"); fprintf(bcftools_stderr, " -G, --IndelGap INT Filter clusters of indels separated by or fewer base pairs allowing only one to pass\n"); fprintf(bcftools_stderr, " -i, --include EXPR Include only sites for which the expression is true (see man page for details\n"); fprintf(bcftools_stderr, " --mask [^]REGION Soft filter regions, \"^\" to negate\n"); fprintf(bcftools_stderr, " -M, --mask-file [^]FILE Soft filter regions listed in a file, \"^\" to negate\n"); fprintf(bcftools_stderr, " --mask-overlap 0|1|2 Mask if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " -m, --mode [+x] \"+\": do not replace but add to existing FILTER; \"x\": reset filters at sites which pass\n"); fprintf(bcftools_stderr, " --no-version Do not append version and command line to the header\n"); fprintf(bcftools_stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(bcftools_stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(bcftools_stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(bcftools_stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(bcftools_stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " -s, --soft-filter STRING Annotate FILTER column with or unique filter name (\"Filter%%d\") made up by the program (\"+\")\n"); fprintf(bcftools_stderr, " -S, --set-GTs .|0 Set genotypes of failed samples to missing (.) or ref (0)\n"); fprintf(bcftools_stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(bcftools_stderr, " --threads INT Use multithreading with worker threads [0]\n"); fprintf(bcftools_stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int main_vcffilter(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->files = bcf_sr_init(); args->output_fname = "-"; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->clevel = -1; int regions_is_file = 0, targets_is_file = 0; int regions_overlap = 1; int targets_overlap = 0; args->mask_overlap = 1; static struct option loptions[] = { {"set-GTs",required_argument,NULL,'S'}, {"mode",required_argument,NULL,'m'}, {"mask",required_argument,NULL,10}, {"mask-file",required_argument,NULL,'M'}, {"mask-overlap",required_argument,NULL,11}, {"soft-filter",required_argument,NULL,'s'}, {"exclude",required_argument,NULL,'e'}, {"include",required_argument,NULL,'i'}, {"targets",required_argument,NULL,'t'}, {"targets-file",required_argument,NULL,'T'}, {"targets-overlap",required_argument,NULL,4}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,3}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"threads",required_argument,NULL,9}, {"SnpGap",required_argument,NULL,'g'}, {"IndelGap",required_argument,NULL,'G'}, {"no-version",no_argument,NULL,8}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "e:i:t:T:r:R:h?s:m:M:o:O:g:G:S:W::",loptions,NULL)) >= 0) { switch (c) { case 'g': args->snp_gap = strtol(optarg,&tmp,10); if ( *tmp && *tmp!=':' ) error("Could not parse argument: --SnpGap %s\n", optarg); if ( *tmp==':' ) { args->snp_gap_str = tmp+1; int i,n; char **keys = hts_readlist(tmp+1,0,&n); for(i=0; isnp_gap_type |= VCF_INDEL; else if ( !strcasecmp(keys[i],"mnp") ) args->snp_gap_type |= VCF_MNP; else if ( !strcasecmp(keys[i],"bnd") ) args->snp_gap_type |= VCF_BND; else if ( !strcasecmp(keys[i],"other") ) args->snp_gap_type |= VCF_OTHER; else if ( !strcasecmp(keys[i],"overlap") ) args->snp_gap_type |= VCF_OVERLAP; else error("Could not parse \"%s\" in \"--SnpGap %s\"\n", keys[i], optarg); free(keys[i]); } if ( n ) free(keys); } else { args->snp_gap_type = VCF_INDEL; args->snp_gap_str = "indel"; } break; case 'G': args->indel_gap = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --IndelGap %s\n", optarg); break; case 'o': args->output_fname = optarg; break; case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 's': args->soft_filter = optarg; break; case 'm': if ( strchr(optarg,'x') ) args->annot_mode |= ANNOT_RESET; if ( strchr(optarg,'+') ) args->annot_mode |= ANNOT_ADD; break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; targets_is_file = 1; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'S': if ( !strcmp(".",optarg) ) args->set_gts = SET_GTS_MISSING; else if ( !strcmp("0",optarg) ) args->set_gts = SET_GTS_REF; else error("The argument to -S not recognised: %s\n", optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 8 : args->record_cmd_line = 0; break; case 3 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 4 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 10 : args->mask_list = optarg; break; case 'M' : args->mask_list = optarg; args->mask_is_file = 1; break; case 11 : if ( !strcasecmp(optarg,"0") ) args->mask_overlap = 0; else if ( !strcasecmp(optarg,"1") ) args->mask_overlap = 1; else if ( !strcasecmp(optarg,"2") ) args->mask_overlap = 2; else error("Could not parse: --mask-overlap %s\n",optarg); break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 'h': case '?': usage(args); break; default: error("Unknown argument: %s\n", optarg); } } if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n"); char *fname = NULL; if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else usage(args); } else fname = argv[optind]; if ( args->mask_list && !args->soft_filter ) error("The option --soft-filter is required with --mask and --mask-file options\n"); // read in the regions from the command line if ( args->regions_list ) { args->files->require_index = 1; bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } else if ( optind+1 < argc ) { int i; kstring_t tmp = {0,0,0}; kputs(argv[optind+1],&tmp); for (i=optind+2; ifiles->require_index = 1; bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, tmp.s, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); free(tmp.s); } if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list,targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); init_data(args); if ( bcf_hdr_write(args->out_fh, args->hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname); if ( init_index2(args->out_fh,args->hdr,args->output_fname,&args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->output_fname); while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = bcf_sr_get_line(args->files, 0); int pass = 1; if ( args->filter ) { pass = filter_test(args->filter, line, &args->smpl_pass); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; } if ( args->mask ) { hts_pos_t beg, end; if ( args->mask_overlap==0 ) beg = end = line->pos; else if ( args->mask_overlap==1 ) beg = line->pos, end = line->pos + line->rlen - 1; else _set_variant_boundaries(line,&beg,&end); int mpass = regidx_overlap(args->mask,bcf_seqname(args->hdr,line),beg,end,NULL) ? 0 : 1; if ( args->mask_negate ) mpass = mpass ? 0 : 1; pass &= mpass; } if ( args->soft_filter || args->set_gts || pass ) { if ( pass ) { bcf_unpack(line,BCF_UN_FLT); if ( args->annot_mode & ANNOT_RESET || !line->d.n_flt ) bcf_add_filter(args->hdr, line, args->flt_pass); } else if ( args->soft_filter ) { if ( (args->annot_mode & ANNOT_ADD) ) bcf_add_filter(args->hdr, line, args->flt_fail); else bcf_update_filter(args->hdr, line, &args->flt_fail, 1); } if ( args->set_gts ) set_genotypes(args, line, pass); if ( !args->rbuf_lines ) { if ( bcf_write1(args->out_fh, args->hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); } else buffered_filters(args, line); } } buffered_filters(args, NULL); if ( args->write_index ) { if ( bcf_idx_save(args->out_fh)<0 ) { if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"bcftools_stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname); destroy_data(args); bcf_sr_destroy(args->files); free(args); return 0; } pysam-0.23.0/bcftools/vcfgtcheck.c000066400000000000000000001774621475062545500170510ustar00rootroot00000000000000/* vcfgtcheck.c -- Check sample identity. Copyright (C) 2013-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "extsort.h" //#include "hclust.h" #include "filter.h" // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 typedef struct { int iqry, igt; } pair_t; typedef struct { bcf_srs_t *files; // first reader is the query VCF - single sample normally or multi-sample for cross-check bcf_hdr_t *gt_hdr, *qry_hdr; // VCF with genotypes to compare against and the query VCF char *cwd, **argv, *gt_samples, *qry_samples, *regions, *targets, *qry_fname, *gt_fname, *pair_samples; char *output_fname; int argc, gt_samples_is_file, qry_samples_is_file, regions_is_file, targets_is_file, pair_samples_is_file, output_type;; int regions_overlap, targets_overlap, clevel; int qry_use_GT,gt_use_GT, nqry_smpl,ngt_smpl, *qry_smpl,*gt_smpl; int nused[2][2]; double *pdiff, *qry_prob, *gt_prob; uint32_t *ndiff,*ncnt,*nmatch,ncmp, npairs; int32_t *qry_arr,*gt_arr, nqry_arr,ngt_arr; uint8_t *qry_dsg, *gt_dsg; pair_t *pairs; double *hwe_prob, dsg2prob[8][3], pl2prob[256]; double min_inter_err, max_intra_err; int all_sites, hom_only, ntop, cross_check, calc_hwe_prob, sort_by_hwe, dry_run, gt_err; BGZF *out_fh; unsigned int nskip_no_match, nskip_not_ba, nskip_mono, nskip_no_data, nskip_dip_GT, nskip_dip_PL, nskip_filter; kstring_t kstr; // for --distinctive-sites double distinctive_sites; kbitset_t *kbs_diff; size_t diff_sites_size; extsort_t *es; char *es_tmp_prefix, *es_max_mem; // include or exclude sites which match the filters filter_t *qry_filter, *gt_filter; char *qry_filter_str, *gt_filter_str; int qry_filter_logic, gt_filter_logic; // FLT_INCLUDE or FLT_EXCLUDE } args_t; static void set_cwd(args_t *args) { int i; char *buf; size_t nbuf = 500; args->cwd = (char*) malloc(sizeof(char)*nbuf); for (i=0; i<5; i++) { if ( (buf = getcwd(args->cwd, nbuf)) ) break; nbuf *= 2; args->cwd = (char*) realloc(args->cwd, sizeof(char)*nbuf); } assert(buf); } static void print_header(args_t *args) { args->kstr.l = 0; ksprintf(&args->kstr, "# This file was produced by bcftools (%s+htslib-%s), the command line was:\n", bcftools_version(), hts_version()); ksprintf(&args->kstr, "# \t bcftools %s ", args->argv[0]); int i; for (i=1; iargc; i++) ksprintf(&args->kstr, " %s",args->argv[i]); ksprintf(&args->kstr, "\n# and the working directory was:\n"); ksprintf(&args->kstr, "# \t %s\n#\n", args->cwd); if ( bgzf_write(args->out_fh, args->kstr.s, args->kstr.l)!=args->kstr.l ) error("Failed to write to %s\n", args->output_fname); } static int cmp_int(const void *_a, const void *_b) { int a = *((int*)_a); int b = *((int*)_b); if ( a < b ) return -1; if ( a > b ) return 1; return 0; } static int cmp_pair(const void *_a, const void *_b) { pair_t *a = (pair_t*)_a; pair_t *b = (pair_t*)_b; if ( a->iqry < b->iqry ) return -1; if ( a->iqry > b->iqry ) return 1; if ( a->igt < b->igt ) return -1; if ( a->igt > b->igt ) return 1; return 0; } typedef struct { uint32_t ndiff,rid,pos,rand; // rand is to shuffle sites with the same ndiff from across all chromosomes unsigned long kbs_dat[1]; } diff_sites_t; #if DBG static void diff_sites_debug_print(args_t *args, diff_sites_t *ds) { int i; memcpy(args->kbs_diff->b,ds->kbs_dat,args->kbs_diff->n*sizeof(unsigned long)); fprintf(stderr,"%s:%d\t%d\t",bcf_hdr_id2name(args->qry_hdr,ds->rid),ds->pos+1,ds->ndiff); for (i=0; inpairs; i++) fprintf(stderr,"%d",kbs_exists(args->kbs_diff,i)?1:0); fprintf(stderr,"\n"); } #endif static int diff_sites_cmp(const void *aptr, const void *bptr) { diff_sites_t *a = *((diff_sites_t**)aptr); diff_sites_t *b = *((diff_sites_t**)bptr); if ( a->ndiff < b->ndiff ) return 1; // descending order if ( a->ndiff > b->ndiff ) return -1; if ( a->rand < b->rand ) return -1; if ( a->rand > b->rand ) return 1; return 0; } static void diff_sites_init(args_t *args) { int nsites = args->distinctive_sites<=1 ? args->npairs*args->distinctive_sites : args->distinctive_sites; if ( nsites<=0 ) error("The value for --distinctive-sites was set too low: %d\n",nsites); if ( nsites > args->npairs ) { fprintf(stderr,"Warning: The value for --distinctive-sites is bigger than is the number of pairs, all discordant sites be printed.\n"); nsites = args->npairs; args->distinctive_sites = args->npairs + 1; } else args->distinctive_sites = nsites; args->kbs_diff = kbs_init(args->npairs); size_t n = (args->npairs + KBS_ELTBITS-1) / KBS_ELTBITS; assert( n==args->kbs_diff->n ); args->diff_sites_size = sizeof(diff_sites_t) + (n-1)*sizeof(unsigned long); args->es = extsort_alloc(); extsort_set_opt(args->es,size_t,DAT_SIZE,args->diff_sites_size); extsort_set_opt(args->es,const char*,TMP_PREFIX,args->es_tmp_prefix); extsort_set_opt(args->es,const char*,MAX_MEM,args->es_max_mem); extsort_set_opt(args->es,extsort_cmp_f,FUNC_CMP,diff_sites_cmp); extsort_init(args->es); } static void diff_sites_destroy(args_t *args) { kbs_destroy(args->kbs_diff); extsort_destroy(args->es); } static inline void diff_sites_reset(args_t *args) { kbs_clear(args->kbs_diff); } static inline void diff_sites_push(args_t *args, int ndiff, int rid, int pos) { diff_sites_t *dat = (diff_sites_t*) malloc(args->diff_sites_size); memset(dat,0,sizeof(*dat)); // for debugging: prevent warnings about uninitialized memory coming from struct padding (not needed after rand added) dat->ndiff = ndiff; dat->rid = rid; dat->pos = pos; dat->rand = hts_lrand48(); memcpy(dat->kbs_dat,args->kbs_diff->b,args->kbs_diff->n*sizeof(unsigned long)); extsort_push(args->es,dat); } static inline int diff_sites_shift(args_t *args, int *ndiff, int *rid, int *pos) { diff_sites_t *dat = (diff_sites_t*) extsort_shift(args->es); if ( !dat ) return 0; *ndiff = dat->ndiff; *rid = dat->rid; *pos = dat->pos; memcpy(args->kbs_diff->b,dat->kbs_dat,args->kbs_diff->n*sizeof(unsigned long)); return 1; } static void init_samples(char *list, int list_is_file, int **smpl, int *nsmpl, bcf_hdr_t *hdr, char *vcf_fname) { int i; if ( !strcmp(list,"-") ) { *nsmpl = bcf_hdr_nsamples(hdr); *smpl = (int*) malloc(sizeof(**smpl)*(*nsmpl)); for (i=0; i<*nsmpl; i++) (*smpl)[i] = i; return; } char **tmp = hts_readlist(list, list_is_file, nsmpl); if ( !tmp || !*nsmpl ) error("Failed to parse %s\n", list); *smpl = (int*) malloc(sizeof(**smpl)*(*nsmpl)); for (i=0; i<*nsmpl; i++) { int idx = bcf_hdr_id2int(hdr, BCF_DT_SAMPLE, tmp[i]); if ( idx<0 ) error("No such sample in %s: [%s]\n",vcf_fname,tmp[i]); (*smpl)[i] = idx; free(tmp[i]); } free(tmp); qsort(*smpl,*nsmpl,sizeof(**smpl),cmp_int); // check for duplicates for (i=1; i<*nsmpl; i++) if ( (*smpl)[i-1]==(*smpl)[i] ) error("Error: the sample \"%s\" is listed twice in %s\n", hdr->samples[(*smpl)[i]],list); } static void init_data(args_t *args) { hts_srand48(0); args->files = bcf_sr_init(); if ( args->regions ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions, args->regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions); } if ( args->targets ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,args->targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets, args->targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets); } if ( args->gt_fname ) bcf_sr_set_opt(args->files, BCF_SR_REQUIRE_IDX); if ( !bcf_sr_add_reader(args->files,args->qry_fname) ) error("Failed to open %s: %s\n", args->qry_fname,bcf_sr_strerror(args->files->errnum)); if ( args->gt_fname && !bcf_sr_add_reader(args->files, args->gt_fname) ) error("Failed to read from %s: %s\n", !strcmp("-",args->gt_fname)?"standard input":args->gt_fname,bcf_sr_strerror(args->files->errnum)); args->qry_hdr = bcf_sr_get_header(args->files,0); if ( !bcf_hdr_nsamples(args->qry_hdr) ) error("No samples in %s?\n", args->qry_fname); if ( args->gt_fname ) { args->gt_hdr = bcf_sr_get_header(args->files,1); if ( !bcf_hdr_nsamples(args->gt_hdr) ) error("No samples in %s?\n", args->gt_fname); } if ( args->gt_hdr && args->gt_filter_str ) args->gt_filter = filter_init(args->gt_hdr, args->gt_filter_str); if ( args->qry_hdr && args->qry_filter_str ) args->qry_filter = filter_init(args->qry_hdr, args->qry_filter_str); // Determine whether GT or PL will be used if ( args->qry_use_GT==-1 ) // not set by -u, qry uses PL by default { if ( bcf_hdr_id2int(args->qry_hdr,BCF_DT_ID,"PL")>=0 ) args->qry_use_GT = 0; else if ( bcf_hdr_id2int(args->qry_hdr,BCF_DT_ID,"GT")>=0 ) args->qry_use_GT = 1; else error("[E::%s] Neither PL nor GT tag is present in the header of %s\n", __func__, args->qry_fname); } else if ( args->qry_use_GT==1 ) { if ( bcf_hdr_id2int(args->qry_hdr,BCF_DT_ID,"GT")<0 ) error("[E::%s] The GT tag is not present in the header of %s\n", __func__, args->qry_fname); } else if ( bcf_hdr_id2int(args->qry_hdr,BCF_DT_ID,"PL")<0 ) error("[E::%s] The PL tag is not present in the header of %s\n", __func__, args->qry_fname); if ( args->gt_hdr ) { if ( args->gt_use_GT==-1 ) // not set by -u, gt uses GT by default { if ( bcf_hdr_id2int(args->gt_hdr,BCF_DT_ID,"GT")>=0 ) args->gt_use_GT = 1; else if ( bcf_hdr_id2int(args->gt_hdr,BCF_DT_ID,"PL")>=0 ) args->gt_use_GT = 0; else error("[E::%s] Neither PL nor GT tag is present in the header of %s\n", __func__, args->gt_fname); } else if ( args->gt_use_GT==1 ) { if ( bcf_hdr_id2int(args->gt_hdr,BCF_DT_ID,"GT")<0 ) error("[E::%s] The GT tag is not present in the header of %s\n", __func__, args->gt_fname); } else if ( bcf_hdr_id2int(args->gt_hdr,BCF_DT_ID,"PL")<0 ) error("[E::%s] The PL tag is not present in the header of %s\n", __func__, args->gt_fname); } else args->gt_use_GT = args->qry_use_GT; // Prepare samples int i,j; args->nqry_smpl = bcf_hdr_nsamples(args->qry_hdr); if ( args->qry_samples ) { init_samples(args->qry_samples, args->qry_samples_is_file, &args->qry_smpl, &args->nqry_smpl, args->qry_hdr, args->qry_fname); } if ( args->gt_samples ) { init_samples(args->gt_samples, args->gt_samples_is_file, &args->gt_smpl, &args->ngt_smpl, args->gt_hdr ? args->gt_hdr : args->qry_hdr, args->gt_fname ? args->gt_fname : args->qry_fname); } else if ( args->pair_samples ) { int npairs; char **tmp = hts_readlist(args->pair_samples, args->pair_samples_is_file, &npairs); if ( !tmp || !npairs ) error("Failed to parse %s\n", args->pair_samples); if ( !args->pair_samples_is_file && npairs%2 ) error("Expected even number of comma-delimited samples with -p\n"); args->npairs = args->pair_samples_is_file ? npairs : npairs/2; args->pairs = (pair_t*) calloc(args->npairs,sizeof(*args->pairs)); if ( !args->pair_samples_is_file ) { for (i=0; inpairs; i++) { args->pairs[i].iqry = bcf_hdr_id2int(args->qry_hdr, BCF_DT_SAMPLE, tmp[2*i]); args->pairs[i].igt = bcf_hdr_id2int(args->gt_hdr?args->gt_hdr:args->qry_hdr, BCF_DT_SAMPLE, tmp[2*i+1]); if ( args->pairs[i].iqry < 0 ) error("No such sample in %s: [%s]\n",args->qry_fname,tmp[2*i]); if ( args->pairs[i].igt < 0 ) error("No such sample in %s: [%s]\n",args->gt_fname?args->gt_fname:args->qry_fname,tmp[2*i+1]); free(tmp[2*i]); free(tmp[2*i+1]); } } else { for (i=0; inpairs; i++) { char *ptr = tmp[i]; while ( *ptr && !isspace(*ptr) ) ptr++; if ( !*ptr ) error("Could not parse %s: %s\n",args->pair_samples,tmp[i]); *ptr = 0; args->pairs[i].iqry = bcf_hdr_id2int(args->qry_hdr, BCF_DT_SAMPLE, tmp[i]); if ( args->pairs[i].iqry < 0 ) error("No such sample in %s: [%s]\n",args->qry_fname,tmp[i]); ptr++; while ( *ptr && isspace(*ptr) ) ptr++; args->pairs[i].igt = bcf_hdr_id2int(args->gt_hdr?args->gt_hdr:args->qry_hdr, BCF_DT_SAMPLE, ptr); if ( args->pairs[i].igt < 0 ) error("No such sample in %s: [%s]\n",args->gt_fname?args->gt_fname:args->qry_fname,ptr); free(tmp[i]); } } free(tmp); qsort(args->pairs,args->npairs,sizeof(*args->pairs),cmp_pair); } else if ( args->gt_hdr ) args->ngt_smpl = bcf_hdr_nsamples(args->gt_hdr); if ( !args->ngt_smpl ) { args->ngt_smpl = args->nqry_smpl; args->gt_smpl = args->qry_smpl; args->cross_check = 1; } // The data arrays if ( !args->npairs ) args->npairs = args->cross_check ? args->nqry_smpl*(args->nqry_smpl+1)/2 : args->ngt_smpl*args->nqry_smpl; if ( !args->pair_samples ) { args->qry_dsg = (uint8_t*) malloc(args->nqry_smpl); args->gt_dsg = args->cross_check ? args->qry_dsg : (uint8_t*) malloc(args->ngt_smpl); } if ( args->gt_err ) { args->pdiff = (double*) calloc(args->npairs,sizeof(*args->pdiff)); // log probability of pair samples being the same args->qry_prob = (double*) malloc(3*args->nqry_smpl*sizeof(*args->qry_prob)); args->gt_prob = args->cross_check ? args->qry_prob : (double*) malloc(3*args->ngt_smpl*sizeof(*args->gt_prob)); // Convert genotypes to genotype likelihoods given by -E, the probability of reading one allele incorrectly. In this // simple model we have: // - probability of reading an allele incorrectly, eg. 0 as 1 or 1 as 0 // P(0|1) = P(1|0) = e // - probability of genotype G={00,01,11} being correct given observed dosage {0,1,2} and the // genotyping error probability e: // P(00|0) = 1 P(00|1) = e P(00|2) = e^2 // P(01|0) = e P(01|1) = 1 P(01|2) = e // P(11|0) = e^2 P(11|1) = e P(11|2) = 1 // // dsg2prob: the first index is bitmask of 8 possible dsg combinations (only 1<<0,1<<2,1<<3 are set, accessing // anything else indicated an error, this is just to reuse gt_to_dsg(); the second index are the corresponding // probabilities of 0/0, 0/1, and 1/1 genotypes // for (i=0; i<8; i++) for (j=0; j<3; j++) args->dsg2prob[i][j] = HUGE_VAL; double eprob = pow(10,-0.1*args->gt_err); // convert from phred score to probability args->dsg2prob[1][0] = 0; // P(00|0) = 1 args->dsg2prob[1][1] = -log(eprob); // P(01|0) = e args->dsg2prob[1][2] = -2*log(eprob); // P(11|0) = e^2 args->dsg2prob[2][0] = -log(eprob); // P(00|1) = e args->dsg2prob[2][1] = 0; // P(01|1) = 1 args->dsg2prob[2][2] = -log(eprob); // P(11|1) = e args->dsg2prob[4][0] = -2*log(eprob); // P(00|2) = e^2 args->dsg2prob[4][1] = -log(eprob); // P(01|2) = e args->dsg2prob[4][2] = 0; // P(11|2) = 1 // lookup table to avoid exponentiation for (i=0; i<256; i++) args->pl2prob[i] = pow(10,-0.1*i); } else args->ndiff = (uint32_t*) calloc(args->npairs,sizeof(*args->ndiff)); // number of differing genotypes for each pair of samples args->ncnt = (uint32_t*) calloc(args->npairs,sizeof(*args->ncnt)); // number of comparisons performed (non-missing data) if ( !args->ncnt ) error("Error: failed to allocate %.1f Mb\n", args->npairs*sizeof(*args->ncnt)/1e6); if ( args->calc_hwe_prob ) { // prob of the observed sequence of matches given site AFs and HWE args->hwe_prob = (double*) calloc(args->npairs,sizeof(*args->hwe_prob)); if ( !args->hwe_prob ) error("Error: failed to allocate %.1f Mb. Run with --no-HWE-prob to save some memory.\n", args->npairs*sizeof(*args->hwe_prob)/1e6); args->nmatch = (uint32_t*) calloc(args->npairs,sizeof(*args->ncnt)); // number of matches, used only with calc_hwe_prob if ( !args->nmatch ) error("Error: failed to allocate %.1f Mb.\n", args->npairs*sizeof(*args->ncnt)/1e6); } if ( args->distinctive_sites ) diff_sites_init(args); args->out_fh = bgzf_open(args->output_fname, args->output_type&FT_GZ ? "wg" : "wu"); if ( args->out_fh == NULL ) error("[%s] Error: cannot write to %s: %s\n", __func__,args->output_fname ? args->output_fname : "standard output", strerror(errno)); print_header(args); } static void destroy_data(args_t *args) { free(args->kstr.s); if ( args->gt_filter ) filter_destroy(args->gt_filter); if ( args->qry_filter ) filter_destroy(args->qry_filter); if ( args->gt_dsg!=args->qry_dsg ) free(args->gt_dsg); free(args->qry_dsg); if ( args->gt_prob!=args->qry_prob ) free(args->gt_prob); free(args->qry_prob); free(args->es_max_mem); if ( bgzf_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"stdout"); if ( args->distinctive_sites ) diff_sites_destroy(args); free(args->hwe_prob); free(args->cwd); free(args->qry_arr); if ( args->gt_hdr ) free(args->gt_arr); free(args->pdiff); free(args->ndiff); free(args->ncnt); free(args->nmatch); free(args->qry_smpl); if ( args->gt_smpl!=args->qry_smpl ) free(args->gt_smpl); free(args->pairs); bcf_sr_destroy(args->files); } static inline uint8_t gt_to_dsg(int32_t *ptr) { if ( bcf_gt_is_missing(ptr[0]) || bcf_gt_is_missing(ptr[1]) || ptr[1]==bcf_int32_vector_end ) return 0; uint8_t dsg = (bcf_gt_allele(ptr[0])?1:0) + (bcf_gt_allele(ptr[1])?1:0); return 1<dsg2prob[dsg][0]; prob[1] = args->dsg2prob[dsg][1]; prob[2] = args->dsg2prob[dsg][2]; } return dsg; } static inline uint8_t pl_to_prob(args_t *args, int32_t *ptr, double *prob) { uint8_t dsg = pl_to_dsg(ptr); if ( dsg ) { prob[0] = (ptr[0]>=0 && ptr[0]<255) ? args->pl2prob[ptr[0]] : args->pl2prob[255]; prob[1] = (ptr[1]>=0 && ptr[1]<255) ? args->pl2prob[ptr[1]] : args->pl2prob[255]; prob[2] = (ptr[2]>=0 && ptr[2]<255) ? args->pl2prob[ptr[2]] : args->pl2prob[255]; double sum = prob[0] + prob[1] + prob[2]; prob[0] /= sum; prob[1] /= sum; prob[2] /= sum; prob[0] = -log(prob[0]); prob[1] = -log(prob[1]); prob[2] = -log(prob[2]); } return dsg; } static int set_data(args_t *args, bcf_hdr_t *hdr, bcf1_t *rec, int32_t **arr, int32_t *narr, int *narr1, int *use_GT) { static int warn_dip_GT = 1; static int warn_dip_PL = 1; int i; for (i=0; i<2; i++) { if ( *use_GT ) { int ret = bcf_get_genotypes(hdr,rec,arr,narr); if ( ret < 0 ) { if ( !i ) { *use_GT = 0; continue; } args->nskip_no_data++; return -1; } if ( ret != 2*bcf_hdr_nsamples(hdr) ) { if ( warn_dip_GT ) { fprintf(stderr,"INFO: skipping %s:%"PRIhts_pos", only diploid FORMAT/GT fields supported. (This is printed only once.)\n", bcf_seqname(hdr,rec),rec->pos+1); warn_dip_GT = 0; } args->nskip_dip_GT++; return -1; } *narr1 = 2; return 0; } int ret = bcf_get_format_int32(hdr,rec,"PL",arr,narr); if ( ret < 0 ) { if ( !i ) { *use_GT = 1; continue; } args->nskip_no_data++; return -1; } if ( ret != 3*bcf_hdr_nsamples(hdr) ) { if ( warn_dip_PL ) { fprintf(stderr,"INFO: skipping %s:%"PRIhts_pos", only diploid FORMAT/PL fields supported. (This is printed only once.)\n", bcf_seqname(hdr,rec),rec->pos+1); warn_dip_PL = 0; } args->nskip_dip_PL++; return -1; } *narr1 = 3; return 0; } return -1; // should never reach } static void process_line(args_t *args) { int i,j,k, nqry1, ngt1, ret; bcf1_t *gt_rec = NULL, *qry_rec = bcf_sr_get_line(args->files,0); // the query file if ( args->qry_filter ) { int pass = filter_test(args->qry_filter, qry_rec, NULL); if ( args->qry_filter_logic==FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { args->nskip_filter++; return; } } int qry_use_GT = args->qry_use_GT; int gt_use_GT = args->gt_use_GT; ret = set_data(args, args->qry_hdr, qry_rec, &args->qry_arr, &args->nqry_arr, &nqry1, &qry_use_GT); if ( ret<0 ) return; if ( args->gt_hdr ) { gt_rec = bcf_sr_get_line(args->files,1); if ( args->gt_filter ) { int pass = filter_test(args->gt_filter, gt_rec, NULL); if ( args->gt_filter_logic==FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { args->nskip_filter++; return; } } ret = set_data(args, args->gt_hdr, gt_rec, &args->gt_arr, &args->ngt_arr, &ngt1, >_use_GT); if ( ret<0 ) return; } else { ngt1 = nqry1; args->gt_arr = args->qry_arr; } // stats: number of compared sites, and used tags args->ncmp++; args->nused[qry_use_GT][gt_use_GT]++; double hwe_dsg[8]; if ( args->calc_hwe_prob ) { int ac[2]; if ( args->gt_hdr ) { if ( bcf_calc_ac(args->gt_hdr, gt_rec, ac, BCF_UN_INFO|BCF_UN_FMT)!=1 ) error("todo: bcf_calc_ac() failed\n"); } else if ( bcf_calc_ac(args->qry_hdr, qry_rec, ac, BCF_UN_INFO|BCF_UN_FMT)!=1 ) error("todo: bcf_calc_ac() failed\n"); // Calculate HWE probability for each possible qry+gt dosage combination. The alternate allele dosage // values returned by gt_to_prob() below are 0,1,2,4 (0=missing, 1<<0, 1<<1, 1<<2). We consider only // biallelic sites, therefore we work with eight genotype combinations. // // The array hwe_dsg is accessed with hwe_dsg[qry_dsg & gt_dsg] and is constructed to account for PL uncertainty // when we encounter less informative PL, such as PL=0,0,10, where multiple dosage values are equally // likely. If we allowed complete uncertainty (PL=0,0,0), we'd have up to eight possible genotype // mask combinations: from e.g. 0=(gt_dsg=1<<0 & qry_dsg=1<<1) to 7=(gt_dsg=1<<0|1<<1|1<<2 & qry_dsg=1<<0|1<<1|1<<2). // Note the extreme case of 1|2|4 is skipped, see pl_to_dsg(). // // When the dosage is uncertain, we take the minimum of their corresponding HWE value, for example // hwe[0] = 0 // hwe[1] = (1-AF)**2 // hwe[2] = 2*AF*(1-AF) // hwe[4] = AF**2 // hwe[3] = min{hwe[1],hwe[2]} double hwe[3]; // while hwe_dsg iterates over dsg bitmasks (0..7), hwe iterates over dsg (0,1,2) double af = ac[0]+ac[1] ? (double)ac[1]/(ac[0]+ac[1]) : 1e-6; hwe[0] = -log((1-af)*(1-af)); hwe[1] = -log(2*af*(1-af)); hwe[2] = -log(af*af); hwe_dsg[0] = 0; for (i=1; i<8; i++) { hwe_dsg[i] = HUGE_VAL; for (k=0; k<3; k++) { if ( ((1< hwe[k] ) hwe_dsg[i] = hwe[k]; } } } // The sample pairs were given explicitly via -p/-P options if ( args->pairs ) { if ( !args->gt_err ) { int ndiff = 0; if ( args->kbs_diff ) diff_sites_reset(args); for (i=0; inpairs; i++) { int32_t *ptr; uint8_t qry_dsg, gt_dsg; ptr = args->gt_arr + args->pairs[i].igt*ngt1; gt_dsg = gt_use_GT ? gt_to_dsg(ptr) : pl_to_dsg(ptr); if ( !gt_dsg ) continue; // missing value if ( args->hom_only && !(gt_dsg&5) ) continue; // not a hom ptr = args->qry_arr + args->pairs[i].iqry*nqry1; qry_dsg = qry_use_GT ? gt_to_dsg(ptr) : pl_to_dsg(ptr); if ( !qry_dsg ) continue; // missing value int match = qry_dsg & gt_dsg; if ( !match ) { args->ndiff[i]++; if ( args->kbs_diff ) { ndiff++; kbs_insert(args->kbs_diff, i); } } else if ( args->calc_hwe_prob ) { args->hwe_prob[i] += hwe_dsg[match]; args->nmatch[i]++; } args->ncnt[i]++; } if ( ndiff ) diff_sites_push(args, ndiff, qry_rec->rid, qry_rec->pos); } else // gt_err set { for (i=0; inpairs; i++) { int32_t *ptr; double qry_prob[3], gt_prob[3]; uint8_t qry_dsg, gt_dsg; ptr = args->gt_arr + args->pairs[i].igt*ngt1; gt_dsg = gt_use_GT ? gt_to_prob(args,ptr,gt_prob) : pl_to_prob(args,ptr,gt_prob); if ( !gt_dsg ) continue; // missing value if ( args->hom_only && !(gt_dsg&5) ) continue; // not a hom ptr = args->qry_arr + args->pairs[i].iqry*nqry1; qry_dsg = qry_use_GT ? gt_to_prob(args,ptr,qry_prob) : pl_to_prob(args,ptr,qry_prob); if ( !qry_dsg ) continue; // missing value double min = qry_prob[0] + gt_prob[0]; qry_prob[1] += gt_prob[1]; if ( min > qry_prob[1] ) min = qry_prob[1]; qry_prob[2] += gt_prob[2]; if ( min > qry_prob[2] ) min = qry_prob[2]; args->pdiff[i] += min; if ( args->calc_hwe_prob ) { int match = qry_dsg & gt_dsg; args->hwe_prob[i] += hwe_dsg[match]; if ( match ) args->nmatch[i]++; } args->ncnt[i]++; } } return; } int idx=0; if ( !args->gt_err ) { for (i=0; inqry_smpl; i++) { int iqry = args->qry_smpl ? args->qry_smpl[i] : i; int32_t *ptr = args->qry_arr + nqry1*iqry; args->qry_dsg[i] = qry_use_GT ? gt_to_dsg(ptr) : pl_to_dsg(ptr); } if ( !args->cross_check ) // in this case gt_dsg points to qry_dsg { for (i=0; ingt_smpl; i++) { int igt = args->gt_smpl ? args->gt_smpl[i] : i; int32_t *ptr = args->gt_arr + ngt1*igt; args->gt_dsg[i] = gt_use_GT ? gt_to_dsg(ptr) : pl_to_dsg(ptr); if ( args->hom_only && !(args->gt_dsg[i]&5) ) args->gt_dsg[i] = 0; // not a hom, set to a missing value } } for (i=0; inqry_smpl; i++) { int ngt = args->cross_check ? i : args->ngt_smpl; // two files or a sub-diagonal cross-check mode? if ( !args->qry_dsg[i] ) { idx += ngt; continue; } // missing value for (j=0; jgt_dsg[j] ) { idx++; continue; } // missing value int match = args->qry_dsg[i] & args->gt_dsg[j]; if ( !match ) args->ndiff[idx]++; else if ( args->calc_hwe_prob ) { args->hwe_prob[idx] += hwe_dsg[match]; args->nmatch[idx]++; } args->ncnt[idx]++; idx++; } } } else // gt_err set { for (i=0; inqry_smpl; i++) { int iqry = args->qry_smpl ? args->qry_smpl[i] : i; int32_t *ptr = args->qry_arr + nqry1*iqry; args->qry_dsg[i] = qry_use_GT ? gt_to_prob(args,ptr,args->qry_prob+i*3) : pl_to_prob(args,ptr,args->qry_prob+i*3); } if ( !args->cross_check ) // in this case gt_dsg points to qry_dsg { for (i=0; ingt_smpl; i++) { int igt = args->gt_smpl ? args->gt_smpl[i] : i; int32_t *ptr = args->gt_arr + ngt1*igt; args->gt_dsg[i] = gt_use_GT ? gt_to_prob(args,ptr,args->gt_prob+i*3) : pl_to_prob(args,ptr,args->gt_prob+i*3); if ( args->hom_only && !(args->gt_dsg[i]&5) ) args->gt_dsg[i] = 0; // not a hom, set to a missing value } } for (i=0; inqry_smpl; i++) { int ngt = args->cross_check ? i : args->ngt_smpl; // two files or a sub-diagonal cross-check mode? if ( !args->qry_dsg[i] ) { idx += ngt; continue; } // missing value for (j=0; jgt_dsg[j] ) { idx++; continue; } // missing value double min = args->qry_prob[i*3] + args->gt_prob[j*3]; if ( min > args->qry_prob[i*3+1] + args->gt_prob[j*3+1] ) min = args->qry_prob[i*3+1] + args->gt_prob[j*3+1]; if ( min > args->qry_prob[i*3+2] + args->gt_prob[j*3+2] ) min = args->qry_prob[i*3+2] + args->gt_prob[j*3+2]; args->pdiff[idx] += min; if ( args->calc_hwe_prob ) { int match = args->qry_dsg[i] & args->gt_dsg[j]; args->hwe_prob[idx] += hwe_dsg[match]; if ( match ) args->nmatch[idx]++; } args->ncnt[idx]++; idx++; } } } } typedef struct { int ism, idx; double val; } idbl_t; static int cmp_idbl(const void *_a, const void *_b) { idbl_t *a = (idbl_t*)_a; idbl_t *b = (idbl_t*)_b; if ( a->val < b->val ) return -1; if ( a->val > b->val ) return 1; return 0; } static void report_distinctive_sites(args_t *args) { extsort_sort(args->es); args->kstr.l = 0; ksprintf(&args->kstr,"# DS, distinctive sites:\n"); ksprintf(&args->kstr,"# - chromosome\n"); ksprintf(&args->kstr,"# - position\n"); ksprintf(&args->kstr,"# - cumulative number of pairs distinguished by this block\n"); ksprintf(&args->kstr,"# - block id\n"); ksprintf(&args->kstr,"#DS\t[2]Chromosome\t[3]Position\t[4]Cumulative number of distinct pairs\t[5]Block id\n"); kbitset_t *kbs_blk = kbs_init(args->npairs); kbitset_iter_t itr; int i,ndiff,rid,pos,ndiff_tot = 0, iblock = 0; int ndiff_min = args->distinctive_sites <= args->npairs ? args->distinctive_sites : args->npairs; while ( diff_sites_shift(args,&ndiff,&rid,&pos) ) { int ndiff_new = 0, ndiff_dbg = 0; kbs_start(&itr); while ( (i=kbs_next(args->kbs_diff, &itr))>=0 ) { ndiff_dbg++; if ( kbs_exists(kbs_blk,i) ) continue; // already set kbs_insert(kbs_blk,i); ndiff_new++; } if ( ndiff_dbg!=ndiff ) error("Corrupted data, fixme: %d vs %d\n",ndiff_dbg,ndiff); if ( !ndiff_new ) continue; // no new pair distinguished by this site ndiff_tot += ndiff_new; args->kstr.l = 0; ksprintf(&args->kstr,"DS\t%s\t%d\t%d\t%d\n",bcf_hdr_id2name(args->qry_hdr,rid),pos+1,ndiff_tot,iblock); if ( bgzf_write(args->out_fh, args->kstr.s, args->kstr.l)!=args->kstr.l ) error("Failed to write to %s\n", args->output_fname); if ( ndiff_tot < ndiff_min ) continue; // fewer than the requested number of pairs can be distinguished at this point iblock++; ndiff_tot = 0; kbs_clear(kbs_blk); } kbs_destroy(kbs_blk); } static void report(args_t *args) { args->kstr.l = 0; ksprintf(&args->kstr,"INFO\tsites-compared\t%u\n",args->ncmp); ksprintf(&args->kstr,"INFO\tsites-skipped-no-match\t%u\n",args->nskip_no_match); ksprintf(&args->kstr,"INFO\tsites-skipped-multiallelic\t%u\n",args->nskip_not_ba); ksprintf(&args->kstr,"INFO\tsites-skipped-monoallelic\t%u\n",args->nskip_mono); ksprintf(&args->kstr,"INFO\tsites-skipped-no-data\t%u\n",args->nskip_no_data); ksprintf(&args->kstr,"INFO\tsites-skipped-GT-not-diploid\t%u\n",args->nskip_dip_GT); ksprintf(&args->kstr,"INFO\tsites-skipped-PL-not-diploid\t%u\n",args->nskip_dip_PL); ksprintf(&args->kstr,"INFO\tsites-skipped-filtering-expression\t%u\n",args->nskip_filter); ksprintf(&args->kstr,"INFO\tsites-used-PL-vs-PL\t%u\n",args->nused[0][0]); ksprintf(&args->kstr,"INFO\tsites-used-PL-vs-GT\t%u\n",args->nused[0][1]); ksprintf(&args->kstr,"INFO\tsites-used-GT-vs-PL\t%u\n",args->nused[1][0]); ksprintf(&args->kstr,"INFO\tsites-used-GT-vs-GT\t%u\n",args->nused[1][1]); ksprintf(&args->kstr,"# DCv2, discordance version 2:\n"); ksprintf(&args->kstr,"# - Query sample\n"); ksprintf(&args->kstr,"# - Genotyped sample\n"); ksprintf(&args->kstr,"# - Discordance, given either as an abstract score or number of mismatches, see the options -E/-u\n" "# in man page for details. Note that samples with high missingness have fewer sites compared,\n" "# which results in lower overall discordance. Therefore it is advisable to use the average score\n" "# per site rather than the absolute value, i.e. divide the value by the number of sites compared\n" "# (smaller value = better match)\n"); ksprintf(&args->kstr,"# - Average negative log of HWE probability at matching sites, attempts to quantify the following\n" "# intuition: rare genotype matches are more informative than common genotype matches, hence two\n" "# samples with similar discordance can be further stratified by the HWE score (bigger value = better\n" "# match, the observed concordance was less likely to occur by chance)\n"); ksprintf(&args->kstr,"# - Number of sites compared for this pair of samples (bigger = more informative)\n"); ksprintf(&args->kstr,"# - Number of matching genotypes\n"); ksprintf(&args->kstr,"#DCv2\t[2]Query Sample\t[3]Genotyped Sample\t[4]Discordance\t[5]Average -log P(HWE)\t[6]Number of sites compared\t[7]Number of matching genotypes\n"); if ( bgzf_write(args->out_fh, args->kstr.s, args->kstr.l)!=args->kstr.l ) error("Failed to write to %s\n", args->output_fname); int trim = args->ntop; if ( !args->pairs ) { if ( !args->ngt_smpl && args->nqry_smpl <= args->ntop ) trim = 0; if ( args->ngt_smpl && args->ngt_smpl <= args->ntop ) trim = 0; } if ( args->pairs ) { int i; for (i=0; inpairs; i++) { args->kstr.l = 0; int iqry = args->pairs[i].iqry; int igt = args->pairs[i].igt; if ( args->ndiff ) { ksprintf(&args->kstr,"DCv2\t%s\t%s\t%u\t%e\t%u\t%u\n", args->qry_hdr->samples[iqry], args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt], args->ndiff[i], (args->calc_hwe_prob && args->nmatch[i]) ? args->hwe_prob[i]/args->nmatch[i] : 0, args->ncnt[i], args->nmatch[i]); } else { ksprintf(&args->kstr,"DCv2\t%s\t%s\t%e\t%e\t%u\t%u\n", args->qry_hdr->samples[iqry], args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt], args->pdiff[i], (args->calc_hwe_prob && args->nmatch[i]) ? args->hwe_prob[i]/args->nmatch[i] : 0, args->ncnt[i], args->nmatch[i]); } if ( bgzf_write(args->out_fh, args->kstr.s, args->kstr.l)!=args->kstr.l ) error("Failed to write to %s\n", args->output_fname); } } else if ( !trim ) { int i,j,idx=0; for (i=0; inqry_smpl; i++) { int iqry = args->qry_smpl ? args->qry_smpl[i] : i; int ngt = args->cross_check ? i : args->ngt_smpl; for (j=0; jkstr.l = 0; int igt = args->gt_smpl ? args->gt_smpl[j] : j; if ( args->ndiff ) { ksprintf(&args->kstr,"DCv2\t%s\t%s\t%u\t%e\t%u\t%u\n", args->qry_hdr->samples[iqry], args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt], args->ndiff[idx], (args->calc_hwe_prob && args->nmatch[idx]) ? args->hwe_prob[idx]/args->nmatch[idx] : 0, args->ncnt[idx], args->calc_hwe_prob ? args->nmatch[idx] : 0); } else { ksprintf(&args->kstr,"DCv2\t%s\t%s\t%e\t%e\t%u\t%u\n", args->qry_hdr->samples[iqry], args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt], args->pdiff[idx], (args->calc_hwe_prob && args->nmatch[idx]) ? args->hwe_prob[idx]/args->nmatch[idx] : 0, args->ncnt[idx], args->calc_hwe_prob ? args->nmatch[idx] : 0); } if ( bgzf_write(args->out_fh, args->kstr.s, args->kstr.l)!=args->kstr.l ) error("Failed to write to %s\n", args->output_fname); idx++; } } } else if ( !args->cross_check ) { idbl_t *arr = (idbl_t*)malloc(sizeof(*arr)*args->ngt_smpl); int i,j; for (i=0; inqry_smpl; i++) { int idx = i*args->ngt_smpl; for (j=0; jngt_smpl; j++) { if ( args->sort_by_hwe ) arr[j].val = args->nmatch[idx] ? -args->hwe_prob[idx]/args->nmatch[idx] : 0; // -args->hwe_prob[idx]; else if ( args->ndiff ) arr[j].val = args->ncnt[idx] ? (double)args->ndiff[idx]/args->ncnt[idx] : 0; else arr[j].val = args->ncnt[idx] ? args->pdiff[idx]/args->ncnt[idx] : 0; arr[j].ism = j; arr[j].idx = idx; idx++; } qsort(arr, args->ngt_smpl, sizeof(*arr), cmp_idbl); int iqry = args->qry_smpl ? args->qry_smpl[i] : i; for (j=0; jntop; j++) { args->kstr.l = 0; int idx = arr[j].idx; int igt = args->gt_smpl ? args->gt_smpl[arr[j].ism] : arr[j].ism; if ( args->ndiff ) { ksprintf(&args->kstr,"DCv2\t%s\t%s\t%u\t%e\t%u\t%u\n", args->qry_hdr->samples[iqry], args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt], args->ndiff[idx], (args->calc_hwe_prob && args->nmatch[idx]) ? args->hwe_prob[idx]/args->nmatch[idx] : 0, args->ncnt[idx], args->calc_hwe_prob ? args->nmatch[idx] : 0); } else { ksprintf(&args->kstr,"DCv2\t%s\t%s\t%e\t%e\t%u\t%u\n", args->qry_hdr->samples[iqry], args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt], args->pdiff[idx], (args->calc_hwe_prob && args->nmatch[idx]) ? args->hwe_prob[idx]/args->nmatch[idx] : 0, args->ncnt[idx], args->calc_hwe_prob ? args->nmatch[idx] : 0); } if ( bgzf_write(args->out_fh, args->kstr.s, args->kstr.l)!=args->kstr.l ) error("Failed to write to %s\n", args->output_fname); } } free(arr); } else { int narr = args->nqry_smpl-1; idbl_t *arr = (idbl_t*)malloc(sizeof(*arr)*narr); int i,j,k,idx; for (i=0; inqry_smpl; i++) { k = 0, idx = i*(i-1)/2; for (j=0; jsort_by_hwe ) arr[k].val = args->nmatch[idx] ? -args->hwe_prob[idx]/args->nmatch[idx] : 0; else if ( args->ndiff ) arr[k].val = args->ncnt[idx] ? (double)args->ndiff[idx]/args->ncnt[idx] : 0; else arr[k].val = args->ncnt[idx] ? args->pdiff[idx]/args->ncnt[idx] : 0; arr[k].ism = j; arr[k].idx = idx; idx++; k++; } for (; jsort_by_hwe ) arr[k].val = args->nmatch[idx] ? -args->hwe_prob[idx]/args->nmatch[idx] : 0; else if ( args->ndiff ) arr[k].val = args->ncnt[idx] ? (double)args->ndiff[idx]/args->ncnt[idx] : 0; else arr[k].val = args->ncnt[idx] ? args->pdiff[idx]/args->ncnt[idx] : 0; arr[k].ism = j + 1; arr[k].idx = idx; k++; } qsort(arr, narr, sizeof(*arr), cmp_idbl); int iqry = args->qry_smpl ? args->qry_smpl[i] : i; for (j=0; jntop; j++) { args->kstr.l = 0; if ( i <= arr[j].ism ) continue; int idx = arr[j].idx; int igt = args->qry_smpl ? args->qry_smpl[arr[j].ism] : arr[j].ism; if ( args->ndiff ) { ksprintf(&args->kstr,"DCv2\t%s\t%s\t%u\t%e\t%u\t%u\n", args->qry_hdr->samples[iqry], args->qry_hdr->samples[igt], args->ndiff[idx], (args->calc_hwe_prob && args->nmatch[idx]) ? args->hwe_prob[idx]/args->nmatch[idx] : 0, args->ncnt[idx], args->calc_hwe_prob ? args->nmatch[idx] : 0); } else { ksprintf(&args->kstr,"DCv2\t%s\t%s\t%e\t%e\t%u\t%u\n", args->qry_hdr->samples[iqry], args->qry_hdr->samples[igt], args->pdiff[idx], (args->calc_hwe_prob && args->nmatch[idx]) ? args->hwe_prob[idx]/args->nmatch[idx] : 0, args->ncnt[idx], args->calc_hwe_prob ? args->nmatch[idx] : 0); } if ( bgzf_write(args->out_fh, args->kstr.s, args->kstr.l)!=args->kstr.l ) error("Failed to write to %s\n", args->output_fname); } } free(arr); } } static int is_input_okay(args_t *args, int nmatch) { int i; const char *msg; bcf_hdr_t *hdr; bcf1_t *rec; if ( args->gt_hdr && nmatch!=2 ) { if ( args->nskip_no_match++ ) return 0; for (i=0; i<2; i++) { rec = bcf_sr_get_line(args->files,i); if ( rec ) break; } hdr = bcf_sr_get_header(args->files,i); fprintf(stderr,"INFO: skipping %s:%"PRIhts_pos", no record with matching POS+ALT. (This is printed only once.)\n", bcf_seqname(hdr,rec),rec->pos+1); return 0; } for (i=0; i<2; i++) { hdr = bcf_sr_get_header(args->files,i); rec = bcf_sr_get_line(args->files,i); if ( rec->n_allele>2 ) { if ( args->nskip_not_ba++ ) return 0; msg = "not a biallelic site, run `bcftools norm -m -` first"; goto not_okay; } if ( bcf_get_variant_types(rec)==VCF_REF ) { if ( args->nskip_mono++ ) return 0; msg = "monoallelic site"; goto not_okay; } if ( !args->gt_hdr ) break; } return 1; not_okay: fprintf(stderr,"INFO: skipping %s:%"PRIhts_pos", %s. (This is printed only once.)\n", bcf_seqname(hdr,rec),rec->pos+1,msg); return 0; } static void usage(void) { fprintf(stderr, "\n"); fprintf(stderr, "About: Check sample identity. With no -g BCF given, multi-sample cross-check is performed.\n"); fprintf(stderr, "Usage: bcftools gtcheck [options] [-g ] \n"); fprintf(stderr, "\n"); fprintf(stderr, "Options:\n"); //fprintf(stderr, " -a, --all-sites Output comparison for all sites\n"); //fprintf(stderr, " -c, --cluster MIN,MAX Min inter- and max intra-sample error [0.23,-0.3]\n"); fprintf(stderr, " --distinctive-sites Find sites that can distinguish between at least NUM sample pairs.\n"); fprintf(stderr, " NUM[,MEM[,TMP]] If the number is smaller or equal to 1, it is interpreted as the fraction of pairs.\n"); fprintf(stderr, " The optional MEM string sets the maximum memory used for in-memory sorting [500M]\n"); #ifdef _WIN32 fprintf(stderr, " and TMP is a prefix of temporary files used by external sorting [/bcftools.XXXXXX]\n"); #else fprintf(stderr, " and TMP is a prefix of temporary files used by external sorting [/tmp/bcftools.XXXXXX]\n"); #endif fprintf(stderr, " --dry-run Stop after first record to estimate required time\n"); fprintf(stderr, " -E, --error-probability INT Phred-scaled probability of genotyping error, 0 for faster but less accurate results [40]\n"); fprintf(stderr, " -e, --exclude [qry|gt]:EXPR Exclude sites for which the expression is true\n"); fprintf(stderr, " -g, --genotypes FILE Genotypes to compare against\n"); fprintf(stderr, " -H, --homs-only Homozygous genotypes only, useful with low coverage data (requires -g)\n"); fprintf(stderr, " -i, --include [qry|gt]:EXPR Include sites for which the expression is true\n"); fprintf(stderr, " --n-matches INT Print only top INT matches for each sample (sorted by average score), 0 for unlimited.\n"); fprintf(stderr, " Use negative value to sort by HWE probability rather than by discordance [0]\n"); fprintf(stderr, " --no-HWE-prob Disable calculation of HWE probability\n"); fprintf(stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(stderr, " -O, --output-type t|z t: plain tab-delimited text output, z: compressed [t]\n"); fprintf(stderr, " -p, --pairs LIST Comma-separated sample pairs to compare (qry,gt[,qry,gt..] with -g or qry,qry[,qry,qry..] w/o)\n"); fprintf(stderr, " -P, --pairs-file FILE File with tab-delimited sample pairs to compare (qry,gt with -g or qry,qry w/o)\n"); fprintf(stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " -s, --samples [qry|gt]:LIST List of query or -g samples, \"-\" to select all samples (by default all samples are compared)\n"); fprintf(stderr, " -S, --samples-file [qry|gt]:FILE File with the query or -g samples to compare\n"); fprintf(stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(stderr, " -u, --use TAG1[,TAG2] Which tag to use in the query file (TAG1) and the -g file (TAG2) [PL,GT]\n"); fprintf(stderr, "Examples:\n"); fprintf(stderr, " # Check discordance of all samples from B against all samples in A\n"); fprintf(stderr, " bcftools gtcheck -g A.bcf B.bcf\n"); fprintf(stderr, "\n"); fprintf(stderr, " # Limit comparisons to the given list of samples\n"); fprintf(stderr, " bcftools gtcheck -s gt:a1,a2,a3 -s qry:b1,b2 -g A.bcf B.bcf\n"); fprintf(stderr, "\n"); fprintf(stderr, " # Compare only two pairs a1,b1 and a1,b2\n"); fprintf(stderr, " bcftools gtcheck -p a1,b1,a1,b2 -g A.bcf B.bcf\n"); fprintf(stderr, "\n"); exit(1); } int main_vcfgtcheck(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; set_cwd(args); args->qry_use_GT = -1; args->gt_use_GT = -1; args->calc_hwe_prob = 1; args->gt_err = 40; args->regions_overlap = 1; args->targets_overlap = 0; args->output_fname = "-"; // external sort for --distinctive-sites #ifdef _WIN32 args->es_tmp_prefix = NULL; #else args->es_tmp_prefix = "/tmp/bcftools-gtcheck"; #endif args->es_max_mem = strdup("500M"); // In simulated sample swaps the minimum error was 0.3 and maximum intra-sample error was 0.23 // - min_inter: pairs with smaller err value will be considered identical // - max_intra: pairs with err value bigger than abs(max_intra_err) will be considered // different. If negative, the cutoff may be heuristically lowered args->min_inter_err = 0.23; args->max_intra_err = -0.3; static struct option loptions[] = { {"error-probability",1,0,'E'}, // note this used to be 'e', but can easily auto-detect to assure backward compatibility {"exclude",required_argument,0,'e'}, {"include",required_argument,0,'i'}, {"output",required_argument,0,'o'}, {"output-type",required_argument,NULL,'O'}, {"use",1,0,'u'}, {"cluster",1,0,'c'}, {"GTs-only",1,0,'G'}, {"all-sites",0,0,'a'}, {"homs-only",0,0,'H'}, {"help",0,0,'h'}, {"genotypes",1,0,'g'}, {"plot",1,0,'p'}, {"samples",1,0,'s'}, {"samples-file",1,0,'S'}, {"n-matches",1,0,2}, {"no-HWE-prob",0,0,3}, {"target-sample",1,0,4}, {"dry-run",0,0,5}, {"distinctive-sites",1,0,6}, {"regions",1,0,'r'}, {"regions-file",1,0,'R'}, {"regions-overlap",required_argument,NULL,7}, {"targets",1,0,'t'}, {"targets-file",1,0,'T'}, {"targets-overlap",required_argument,NULL,8}, {"pairs",1,0,'p'}, {"pairs-file",1,0,'P'}, {0,0,0,0} }; char *tmp; while ((c = getopt_long(argc, argv, "hg:p:s:S:p:P:Hr:R:at:T:G:c:u:e:E:i:o:O:",loptions,NULL)) >= 0) { switch (c) { case 'o': args->output_fname = optarg; break; case 'O': switch (optarg[0]) { case 't': args->output_type = FT_TAB_TEXT; break; case 'z': args->output_type = FT_VCF_GZ; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --output-type %s\n", optarg+1); } break; case 'e': if ( !strncasecmp("gt:",optarg,3) ) { if ( args->gt_filter_str ) error("Error: only one -i or -e expression can be given for gt:, and they cannot be combined\n"); args->gt_filter_str = optarg; args->gt_filter_logic |= FLT_EXCLUDE; } else if ( !strncasecmp("qry:",optarg,4) ) { if ( args->qry_filter_str ) error("Error: only one -i or -e expression can be given for qry:, and they cannot be combined\n"); args->qry_filter_str = optarg; args->qry_filter_logic |= FLT_EXCLUDE; } else { // this could be the old -e, --error-probability option args->gt_err = strtol(optarg,&tmp,10); if ( !tmp || *tmp ) { // it is not args->gt_filter_str = optarg; args->qry_filter_str = optarg; args->gt_filter_logic |= FLT_EXCLUDE; args->qry_filter_logic |= FLT_EXCLUDE; } else { fprintf(stderr,"[warning] auto-detected the old format --error-probability option, please switch from -e to -E.\n"); } } break; case 'i': if ( !strncasecmp("gt:",optarg,3) ) { if ( args->gt_filter_str ) error("Error: only one -i or -e expression can be given for gt:, and they cannot be combined\n"); args->gt_filter_str = optarg; args->gt_filter_logic |= FLT_INCLUDE; } else if ( !strncasecmp("qry:",optarg,4) ) { if ( args->qry_filter_str ) error("Error: only one -i or -e expression can be given for qry:, and they cannot be combined\n"); args->qry_filter_str = optarg; args->qry_filter_logic |= FLT_INCLUDE; } else { args->gt_filter_str = optarg; args->qry_filter_str = optarg; args->gt_filter_logic |= FLT_INCLUDE; args->qry_filter_logic |= FLT_INCLUDE; } break; case 'E': args->gt_err = strtol(optarg,&tmp,10); if ( !tmp || *tmp ) error("Could not parse: --error-probability %s\n", optarg); break; case 'u': { int i,nlist; char **list = hts_readlist(optarg, 0, &nlist); if ( !list || nlist<=0 || nlist>2 ) error("Failed to parse --use %s\n", optarg); if ( !strcasecmp("GT",list[0]) ) args->qry_use_GT = 1; else if ( !strcasecmp("PL",list[0]) ) args->qry_use_GT = 0; else error("Failed to parse --use %s; only GT and PL are supported\n", optarg); if ( nlist==2 ) { if ( !strcasecmp("GT",list[1]) ) args->gt_use_GT = 1; else if ( !strcasecmp("PL",list[1]) ) args->gt_use_GT = 0; else error("Failed to parse --use %s; only GT and PL are supported\n", optarg); } else args->gt_use_GT = args->qry_use_GT; for (i=0; intop = strtol(optarg,&tmp,10); if ( !tmp || *tmp ) error("Could not parse: --n-matches %s\n", optarg); if ( args->ntop < 0 ) { args->sort_by_hwe = 1; args->ntop *= -1; } break; case 3 : args->calc_hwe_prob = 0; break; case 4 : error("The option -S, --target-sample has been deprecated\n"); break; case 5 : args->dry_run = 1; break; case 6 : args->distinctive_sites = strtod(optarg,&tmp); if ( *tmp ) { if ( *tmp!=',' ) error("Could not parse: --distinctive-sites %s\n", optarg); tmp++; free(args->es_max_mem); args->es_max_mem = strdup(tmp); while ( *tmp && *tmp!=',' ) tmp++; if ( *tmp ) { *tmp = 0; args->es_tmp_prefix = tmp+1; } } args->gt_err = 0; break; case 'c': error("The -c option is to be implemented, please open an issue on github\n"); args->min_inter_err = strtod(optarg,&tmp); if ( *tmp ) { if ( *tmp!=',') error("Could not parse: -c %s\n", optarg); args->max_intra_err = strtod(tmp+1,&tmp); if ( *tmp ) error("Could not parse: -c %s\n", optarg); } break; case 'G': error("The option -G, --GTs-only has been deprecated\n"); break; case 'a': args->all_sites = 1; error("The -a option is to be implemented, please open an issue on github\n"); break; case 'H': args->hom_only = 1; break; case 'g': args->gt_fname = optarg; break; // case 'p': args->plot = optarg; break; case 's': if ( !strncasecmp("gt:",optarg,3) ) args->gt_samples = optarg+3; else if ( !strncasecmp("qry:",optarg,4) ) args->qry_samples = optarg+4; else error("Which one? Query samples (qry:%s) or genotype samples (gt:%s)?\n",optarg,optarg); break; case 'S': if ( !strncasecmp("gt:",optarg,3) ) args->gt_samples = optarg+3, args->gt_samples_is_file = 1; else if ( !strncasecmp("qry:",optarg,4) ) args->qry_samples = optarg+4, args->qry_samples_is_file = 1; else error("Which one? Query samples (qry:%s) or genotype samples (gt:%s)?\n",optarg,optarg); break; case 'p': args->pair_samples = optarg; break; case 'P': args->pair_samples = optarg; args->pair_samples_is_file = 1; break; case 'r': args->regions = optarg; break; case 'R': args->regions = optarg; args->regions_is_file = 1; break; case 't': args->targets = optarg; break; case 'T': args->targets = optarg; args->targets_is_file = 1; break; case 7 : args->regions_overlap = parse_overlap_option(optarg); if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 8 : args->targets_overlap = parse_overlap_option(optarg); if ( args->targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 'h': case '?': usage(); break; default: error("Unknown argument: %s\n", optarg); } } if ( optind==argc ) { if ( !isatty(fileno((FILE *)stdin)) ) args->qry_fname = "-"; // reading from stdin else usage(); // no files given } else args->qry_fname = argv[optind]; if ( argc>optind+1 ) error("Error: too many files given, run with -h for help\n"); // too many files given if ( args->pair_samples ) { if ( args->gt_samples || args->qry_samples ) error("The -p/-P option cannot be combined with -s/-S\n"); if ( args->ntop ) error("The --n-matches option cannot be combined with -p/-P\n"); } if ( args->distinctive_sites && !args->pair_samples ) error("The experimental option --distinctive-sites requires -p/-P\n"); if ( args->hom_only && !args->gt_fname ) error("The option --homs-only requires --genotypes\n"); if ( args->distinctive_sites && args->gt_err ) error("The option --distinctive-sites cannot be combined with --error-probability\n"); init_data(args); int ret; while ( (ret=bcf_sr_next_line(args->files)) ) { if ( !is_input_okay(args,ret) ) continue; // time one record to give the user an estimate with very big files struct timeval t0, t1; if ( !args->ncmp ) gettimeofday(&t0, NULL); process_line(args); if ( args->ncmp==1 ) { gettimeofday(&t1, NULL); double delta = (t1.tv_sec - t0.tv_sec) * 1e6 + (t1.tv_usec - t0.tv_usec); fprintf(stderr,"INFO:\tTime required to process one record .. %f seconds\n",delta/1e6); args->kstr.l = 0; ksprintf(&args->kstr,"INFO\tTime required to process one record .. %f seconds\n",delta/1e6); if ( bgzf_write(args->out_fh, args->kstr.s, args->kstr.l)!=args->kstr.l ) error("Failed to write to %s\n", args->output_fname); if ( args->dry_run ) break; } } if ( !args->dry_run ) { report(args); if ( args->distinctive_sites ) report_distinctive_sites(args); } destroy_data(args); free(args); return 0; } pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c000066400000000000000000002005071475062545500204050ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfgtcheck.c -- Check sample identity. Copyright (C) 2013-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "extsort.h" //#include "hclust.h" #include "filter.h" // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 typedef struct { int iqry, igt; } pair_t; typedef struct { bcf_srs_t *files; // first reader is the query VCF - single sample normally or multi-sample for cross-check bcf_hdr_t *gt_hdr, *qry_hdr; // VCF with genotypes to compare against and the query VCF char *cwd, **argv, *gt_samples, *qry_samples, *regions, *targets, *qry_fname, *gt_fname, *pair_samples; char *output_fname; int argc, gt_samples_is_file, qry_samples_is_file, regions_is_file, targets_is_file, pair_samples_is_file, output_type;; int regions_overlap, targets_overlap, clevel; int qry_use_GT,gt_use_GT, nqry_smpl,ngt_smpl, *qry_smpl,*gt_smpl; int nused[2][2]; double *pdiff, *qry_prob, *gt_prob; uint32_t *ndiff,*ncnt,*nmatch,ncmp, npairs; int32_t *qry_arr,*gt_arr, nqry_arr,ngt_arr; uint8_t *qry_dsg, *gt_dsg; pair_t *pairs; double *hwe_prob, dsg2prob[8][3], pl2prob[256]; double min_inter_err, max_intra_err; int all_sites, hom_only, ntop, cross_check, calc_hwe_prob, sort_by_hwe, dry_run, gt_err; BGZF *out_fh; unsigned int nskip_no_match, nskip_not_ba, nskip_mono, nskip_no_data, nskip_dip_GT, nskip_dip_PL, nskip_filter; kstring_t kstr; // for --distinctive-sites double distinctive_sites; kbitset_t *kbs_diff; size_t diff_sites_size; extsort_t *es; char *es_tmp_prefix, *es_max_mem; // include or exclude sites which match the filters filter_t *qry_filter, *gt_filter; char *qry_filter_str, *gt_filter_str; int qry_filter_logic, gt_filter_logic; // FLT_INCLUDE or FLT_EXCLUDE } args_t; static void set_cwd(args_t *args) { int i; char *buf; size_t nbuf = 500; args->cwd = (char*) malloc(sizeof(char)*nbuf); for (i=0; i<5; i++) { if ( (buf = getcwd(args->cwd, nbuf)) ) break; nbuf *= 2; args->cwd = (char*) realloc(args->cwd, sizeof(char)*nbuf); } assert(buf); } static void print_header(args_t *args) { args->kstr.l = 0; ksprintf(&args->kstr, "# This file was produced by bcftools (%s+htslib-%s), the command line was:\n", bcftools_version(), hts_version()); ksprintf(&args->kstr, "# \t bcftools %s ", args->argv[0]); int i; for (i=1; iargc; i++) ksprintf(&args->kstr, " %s",args->argv[i]); ksprintf(&args->kstr, "\n# and the working directory was:\n"); ksprintf(&args->kstr, "# \t %s\n#\n", args->cwd); if ( bgzf_write(args->out_fh, args->kstr.s, args->kstr.l)!=args->kstr.l ) error("Failed to write to %s\n", args->output_fname); } static int cmp_int(const void *_a, const void *_b) { int a = *((int*)_a); int b = *((int*)_b); if ( a < b ) return -1; if ( a > b ) return 1; return 0; } static int cmp_pair(const void *_a, const void *_b) { pair_t *a = (pair_t*)_a; pair_t *b = (pair_t*)_b; if ( a->iqry < b->iqry ) return -1; if ( a->iqry > b->iqry ) return 1; if ( a->igt < b->igt ) return -1; if ( a->igt > b->igt ) return 1; return 0; } typedef struct { uint32_t ndiff,rid,pos,rand; // rand is to shuffle sites with the same ndiff from across all chromosomes unsigned long kbs_dat[1]; } diff_sites_t; #if DBG static void diff_sites_debug_print(args_t *args, diff_sites_t *ds) { int i; memcpy(args->kbs_diff->b,ds->kbs_dat,args->kbs_diff->n*sizeof(unsigned long)); fprintf(bcftools_stderr,"%s:%d\t%d\t",bcf_hdr_id2name(args->qry_hdr,ds->rid),ds->pos+1,ds->ndiff); for (i=0; inpairs; i++) fprintf(bcftools_stderr,"%d",kbs_exists(args->kbs_diff,i)?1:0); fprintf(bcftools_stderr,"\n"); } #endif static int diff_sites_cmp(const void *aptr, const void *bptr) { diff_sites_t *a = *((diff_sites_t**)aptr); diff_sites_t *b = *((diff_sites_t**)bptr); if ( a->ndiff < b->ndiff ) return 1; // descending order if ( a->ndiff > b->ndiff ) return -1; if ( a->rand < b->rand ) return -1; if ( a->rand > b->rand ) return 1; return 0; } static void diff_sites_init(args_t *args) { int nsites = args->distinctive_sites<=1 ? args->npairs*args->distinctive_sites : args->distinctive_sites; if ( nsites<=0 ) error("The value for --distinctive-sites was set too low: %d\n",nsites); if ( nsites > args->npairs ) { fprintf(bcftools_stderr,"Warning: The value for --distinctive-sites is bigger than is the number of pairs, all discordant sites be printed.\n"); nsites = args->npairs; args->distinctive_sites = args->npairs + 1; } else args->distinctive_sites = nsites; args->kbs_diff = kbs_init(args->npairs); size_t n = (args->npairs + KBS_ELTBITS-1) / KBS_ELTBITS; assert( n==args->kbs_diff->n ); args->diff_sites_size = sizeof(diff_sites_t) + (n-1)*sizeof(unsigned long); args->es = extsort_alloc(); extsort_set_opt(args->es,size_t,DAT_SIZE,args->diff_sites_size); extsort_set_opt(args->es,const char*,TMP_PREFIX,args->es_tmp_prefix); extsort_set_opt(args->es,const char*,MAX_MEM,args->es_max_mem); extsort_set_opt(args->es,extsort_cmp_f,FUNC_CMP,diff_sites_cmp); extsort_init(args->es); } static void diff_sites_destroy(args_t *args) { kbs_destroy(args->kbs_diff); extsort_destroy(args->es); } static inline void diff_sites_reset(args_t *args) { kbs_clear(args->kbs_diff); } static inline void diff_sites_push(args_t *args, int ndiff, int rid, int pos) { diff_sites_t *dat = (diff_sites_t*) malloc(args->diff_sites_size); memset(dat,0,sizeof(*dat)); // for debugging: prevent warnings about uninitialized memory coming from struct padding (not needed after rand added) dat->ndiff = ndiff; dat->rid = rid; dat->pos = pos; dat->rand = hts_lrand48(); memcpy(dat->kbs_dat,args->kbs_diff->b,args->kbs_diff->n*sizeof(unsigned long)); extsort_push(args->es,dat); } static inline int diff_sites_shift(args_t *args, int *ndiff, int *rid, int *pos) { diff_sites_t *dat = (diff_sites_t*) extsort_shift(args->es); if ( !dat ) return 0; *ndiff = dat->ndiff; *rid = dat->rid; *pos = dat->pos; memcpy(args->kbs_diff->b,dat->kbs_dat,args->kbs_diff->n*sizeof(unsigned long)); return 1; } static void init_samples(char *list, int list_is_file, int **smpl, int *nsmpl, bcf_hdr_t *hdr, char *vcf_fname) { int i; if ( !strcmp(list,"-") ) { *nsmpl = bcf_hdr_nsamples(hdr); *smpl = (int*) malloc(sizeof(**smpl)*(*nsmpl)); for (i=0; i<*nsmpl; i++) (*smpl)[i] = i; return; } char **tmp = hts_readlist(list, list_is_file, nsmpl); if ( !tmp || !*nsmpl ) error("Failed to parse %s\n", list); *smpl = (int*) malloc(sizeof(**smpl)*(*nsmpl)); for (i=0; i<*nsmpl; i++) { int idx = bcf_hdr_id2int(hdr, BCF_DT_SAMPLE, tmp[i]); if ( idx<0 ) error("No such sample in %s: [%s]\n",vcf_fname,tmp[i]); (*smpl)[i] = idx; free(tmp[i]); } free(tmp); qsort(*smpl,*nsmpl,sizeof(**smpl),cmp_int); // check for duplicates for (i=1; i<*nsmpl; i++) if ( (*smpl)[i-1]==(*smpl)[i] ) error("Error: the sample \"%s\" is listed twice in %s\n", hdr->samples[(*smpl)[i]],list); } static void init_data(args_t *args) { hts_srand48(0); args->files = bcf_sr_init(); if ( args->regions ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions, args->regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions); } if ( args->targets ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,args->targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets, args->targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets); } if ( args->gt_fname ) bcf_sr_set_opt(args->files, BCF_SR_REQUIRE_IDX); if ( !bcf_sr_add_reader(args->files,args->qry_fname) ) error("Failed to open %s: %s\n", args->qry_fname,bcf_sr_strerror(args->files->errnum)); if ( args->gt_fname && !bcf_sr_add_reader(args->files, args->gt_fname) ) error("Failed to read from %s: %s\n", !strcmp("-",args->gt_fname)?"standard input":args->gt_fname,bcf_sr_strerror(args->files->errnum)); args->qry_hdr = bcf_sr_get_header(args->files,0); if ( !bcf_hdr_nsamples(args->qry_hdr) ) error("No samples in %s?\n", args->qry_fname); if ( args->gt_fname ) { args->gt_hdr = bcf_sr_get_header(args->files,1); if ( !bcf_hdr_nsamples(args->gt_hdr) ) error("No samples in %s?\n", args->gt_fname); } if ( args->gt_hdr && args->gt_filter_str ) args->gt_filter = filter_init(args->gt_hdr, args->gt_filter_str); if ( args->qry_hdr && args->qry_filter_str ) args->qry_filter = filter_init(args->qry_hdr, args->qry_filter_str); // Determine whether GT or PL will be used if ( args->qry_use_GT==-1 ) // not set by -u, qry uses PL by default { if ( bcf_hdr_id2int(args->qry_hdr,BCF_DT_ID,"PL")>=0 ) args->qry_use_GT = 0; else if ( bcf_hdr_id2int(args->qry_hdr,BCF_DT_ID,"GT")>=0 ) args->qry_use_GT = 1; else error("[E::%s] Neither PL nor GT tag is present in the header of %s\n", __func__, args->qry_fname); } else if ( args->qry_use_GT==1 ) { if ( bcf_hdr_id2int(args->qry_hdr,BCF_DT_ID,"GT")<0 ) error("[E::%s] The GT tag is not present in the header of %s\n", __func__, args->qry_fname); } else if ( bcf_hdr_id2int(args->qry_hdr,BCF_DT_ID,"PL")<0 ) error("[E::%s] The PL tag is not present in the header of %s\n", __func__, args->qry_fname); if ( args->gt_hdr ) { if ( args->gt_use_GT==-1 ) // not set by -u, gt uses GT by default { if ( bcf_hdr_id2int(args->gt_hdr,BCF_DT_ID,"GT")>=0 ) args->gt_use_GT = 1; else if ( bcf_hdr_id2int(args->gt_hdr,BCF_DT_ID,"PL")>=0 ) args->gt_use_GT = 0; else error("[E::%s] Neither PL nor GT tag is present in the header of %s\n", __func__, args->gt_fname); } else if ( args->gt_use_GT==1 ) { if ( bcf_hdr_id2int(args->gt_hdr,BCF_DT_ID,"GT")<0 ) error("[E::%s] The GT tag is not present in the header of %s\n", __func__, args->gt_fname); } else if ( bcf_hdr_id2int(args->gt_hdr,BCF_DT_ID,"PL")<0 ) error("[E::%s] The PL tag is not present in the header of %s\n", __func__, args->gt_fname); } else args->gt_use_GT = args->qry_use_GT; // Prepare samples int i,j; args->nqry_smpl = bcf_hdr_nsamples(args->qry_hdr); if ( args->qry_samples ) { init_samples(args->qry_samples, args->qry_samples_is_file, &args->qry_smpl, &args->nqry_smpl, args->qry_hdr, args->qry_fname); } if ( args->gt_samples ) { init_samples(args->gt_samples, args->gt_samples_is_file, &args->gt_smpl, &args->ngt_smpl, args->gt_hdr ? args->gt_hdr : args->qry_hdr, args->gt_fname ? args->gt_fname : args->qry_fname); } else if ( args->pair_samples ) { int npairs; char **tmp = hts_readlist(args->pair_samples, args->pair_samples_is_file, &npairs); if ( !tmp || !npairs ) error("Failed to parse %s\n", args->pair_samples); if ( !args->pair_samples_is_file && npairs%2 ) error("Expected even number of comma-delimited samples with -p\n"); args->npairs = args->pair_samples_is_file ? npairs : npairs/2; args->pairs = (pair_t*) calloc(args->npairs,sizeof(*args->pairs)); if ( !args->pair_samples_is_file ) { for (i=0; inpairs; i++) { args->pairs[i].iqry = bcf_hdr_id2int(args->qry_hdr, BCF_DT_SAMPLE, tmp[2*i]); args->pairs[i].igt = bcf_hdr_id2int(args->gt_hdr?args->gt_hdr:args->qry_hdr, BCF_DT_SAMPLE, tmp[2*i+1]); if ( args->pairs[i].iqry < 0 ) error("No such sample in %s: [%s]\n",args->qry_fname,tmp[2*i]); if ( args->pairs[i].igt < 0 ) error("No such sample in %s: [%s]\n",args->gt_fname?args->gt_fname:args->qry_fname,tmp[2*i+1]); free(tmp[2*i]); free(tmp[2*i+1]); } } else { for (i=0; inpairs; i++) { char *ptr = tmp[i]; while ( *ptr && !isspace(*ptr) ) ptr++; if ( !*ptr ) error("Could not parse %s: %s\n",args->pair_samples,tmp[i]); *ptr = 0; args->pairs[i].iqry = bcf_hdr_id2int(args->qry_hdr, BCF_DT_SAMPLE, tmp[i]); if ( args->pairs[i].iqry < 0 ) error("No such sample in %s: [%s]\n",args->qry_fname,tmp[i]); ptr++; while ( *ptr && isspace(*ptr) ) ptr++; args->pairs[i].igt = bcf_hdr_id2int(args->gt_hdr?args->gt_hdr:args->qry_hdr, BCF_DT_SAMPLE, ptr); if ( args->pairs[i].igt < 0 ) error("No such sample in %s: [%s]\n",args->gt_fname?args->gt_fname:args->qry_fname,ptr); free(tmp[i]); } } free(tmp); qsort(args->pairs,args->npairs,sizeof(*args->pairs),cmp_pair); } else if ( args->gt_hdr ) args->ngt_smpl = bcf_hdr_nsamples(args->gt_hdr); if ( !args->ngt_smpl ) { args->ngt_smpl = args->nqry_smpl; args->gt_smpl = args->qry_smpl; args->cross_check = 1; } // The data arrays if ( !args->npairs ) args->npairs = args->cross_check ? args->nqry_smpl*(args->nqry_smpl+1)/2 : args->ngt_smpl*args->nqry_smpl; if ( !args->pair_samples ) { args->qry_dsg = (uint8_t*) malloc(args->nqry_smpl); args->gt_dsg = args->cross_check ? args->qry_dsg : (uint8_t*) malloc(args->ngt_smpl); } if ( args->gt_err ) { args->pdiff = (double*) calloc(args->npairs,sizeof(*args->pdiff)); // log probability of pair samples being the same args->qry_prob = (double*) malloc(3*args->nqry_smpl*sizeof(*args->qry_prob)); args->gt_prob = args->cross_check ? args->qry_prob : (double*) malloc(3*args->ngt_smpl*sizeof(*args->gt_prob)); // Convert genotypes to genotype likelihoods given by -E, the probability of reading one allele incorrectly. In this // simple model we have: // - probability of reading an allele incorrectly, eg. 0 as 1 or 1 as 0 // P(0|1) = P(1|0) = e // - probability of genotype G={00,01,11} being correct given observed dosage {0,1,2} and the // genotyping error probability e: // P(00|0) = 1 P(00|1) = e P(00|2) = e^2 // P(01|0) = e P(01|1) = 1 P(01|2) = e // P(11|0) = e^2 P(11|1) = e P(11|2) = 1 // // dsg2prob: the first index is bitmask of 8 possible dsg combinations (only 1<<0,1<<2,1<<3 are set, accessing // anything else indicated an error, this is just to reuse gt_to_dsg(); the second index are the corresponding // probabilities of 0/0, 0/1, and 1/1 genotypes // for (i=0; i<8; i++) for (j=0; j<3; j++) args->dsg2prob[i][j] = HUGE_VAL; double eprob = pow(10,-0.1*args->gt_err); // convert from phred score to probability args->dsg2prob[1][0] = 0; // P(00|0) = 1 args->dsg2prob[1][1] = -log(eprob); // P(01|0) = e args->dsg2prob[1][2] = -2*log(eprob); // P(11|0) = e^2 args->dsg2prob[2][0] = -log(eprob); // P(00|1) = e args->dsg2prob[2][1] = 0; // P(01|1) = 1 args->dsg2prob[2][2] = -log(eprob); // P(11|1) = e args->dsg2prob[4][0] = -2*log(eprob); // P(00|2) = e^2 args->dsg2prob[4][1] = -log(eprob); // P(01|2) = e args->dsg2prob[4][2] = 0; // P(11|2) = 1 // lookup table to avoid exponentiation for (i=0; i<256; i++) args->pl2prob[i] = pow(10,-0.1*i); } else args->ndiff = (uint32_t*) calloc(args->npairs,sizeof(*args->ndiff)); // number of differing genotypes for each pair of samples args->ncnt = (uint32_t*) calloc(args->npairs,sizeof(*args->ncnt)); // number of comparisons performed (non-missing data) if ( !args->ncnt ) error("Error: failed to allocate %.1f Mb\n", args->npairs*sizeof(*args->ncnt)/1e6); if ( args->calc_hwe_prob ) { // prob of the observed sequence of matches given site AFs and HWE args->hwe_prob = (double*) calloc(args->npairs,sizeof(*args->hwe_prob)); if ( !args->hwe_prob ) error("Error: failed to allocate %.1f Mb. Run with --no-HWE-prob to save some memory.\n", args->npairs*sizeof(*args->hwe_prob)/1e6); args->nmatch = (uint32_t*) calloc(args->npairs,sizeof(*args->ncnt)); // number of matches, used only with calc_hwe_prob if ( !args->nmatch ) error("Error: failed to allocate %.1f Mb.\n", args->npairs*sizeof(*args->ncnt)/1e6); } if ( args->distinctive_sites ) diff_sites_init(args); args->out_fh = bgzf_open(args->output_fname, args->output_type&FT_GZ ? "wg" : "wu"); if ( args->out_fh == NULL ) error("[%s] Error: cannot write to %s: %s\n", __func__,args->output_fname ? args->output_fname : "standard output", strerror(errno)); print_header(args); } static void destroy_data(args_t *args) { free(args->kstr.s); if ( args->gt_filter ) filter_destroy(args->gt_filter); if ( args->qry_filter ) filter_destroy(args->qry_filter); if ( args->gt_dsg!=args->qry_dsg ) free(args->gt_dsg); free(args->qry_dsg); if ( args->gt_prob!=args->qry_prob ) free(args->gt_prob); free(args->qry_prob); free(args->es_max_mem); if ( bgzf_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"bcftools_stdout"); if ( args->distinctive_sites ) diff_sites_destroy(args); free(args->hwe_prob); free(args->cwd); free(args->qry_arr); if ( args->gt_hdr ) free(args->gt_arr); free(args->pdiff); free(args->ndiff); free(args->ncnt); free(args->nmatch); free(args->qry_smpl); if ( args->gt_smpl!=args->qry_smpl ) free(args->gt_smpl); free(args->pairs); bcf_sr_destroy(args->files); } static inline uint8_t gt_to_dsg(int32_t *ptr) { if ( bcf_gt_is_missing(ptr[0]) || bcf_gt_is_missing(ptr[1]) || ptr[1]==bcf_int32_vector_end ) return 0; uint8_t dsg = (bcf_gt_allele(ptr[0])?1:0) + (bcf_gt_allele(ptr[1])?1:0); return 1<dsg2prob[dsg][0]; prob[1] = args->dsg2prob[dsg][1]; prob[2] = args->dsg2prob[dsg][2]; } return dsg; } static inline uint8_t pl_to_prob(args_t *args, int32_t *ptr, double *prob) { uint8_t dsg = pl_to_dsg(ptr); if ( dsg ) { prob[0] = (ptr[0]>=0 && ptr[0]<255) ? args->pl2prob[ptr[0]] : args->pl2prob[255]; prob[1] = (ptr[1]>=0 && ptr[1]<255) ? args->pl2prob[ptr[1]] : args->pl2prob[255]; prob[2] = (ptr[2]>=0 && ptr[2]<255) ? args->pl2prob[ptr[2]] : args->pl2prob[255]; double sum = prob[0] + prob[1] + prob[2]; prob[0] /= sum; prob[1] /= sum; prob[2] /= sum; prob[0] = -log(prob[0]); prob[1] = -log(prob[1]); prob[2] = -log(prob[2]); } return dsg; } static int set_data(args_t *args, bcf_hdr_t *hdr, bcf1_t *rec, int32_t **arr, int32_t *narr, int *narr1, int *use_GT) { static int warn_dip_GT = 1; static int warn_dip_PL = 1; int i; for (i=0; i<2; i++) { if ( *use_GT ) { int ret = bcf_get_genotypes(hdr,rec,arr,narr); if ( ret < 0 ) { if ( !i ) { *use_GT = 0; continue; } args->nskip_no_data++; return -1; } if ( ret != 2*bcf_hdr_nsamples(hdr) ) { if ( warn_dip_GT ) { fprintf(bcftools_stderr,"INFO: skipping %s:%"PRIhts_pos", only diploid FORMAT/GT fields supported. (This is printed only once.)\n", bcf_seqname(hdr,rec),rec->pos+1); warn_dip_GT = 0; } args->nskip_dip_GT++; return -1; } *narr1 = 2; return 0; } int ret = bcf_get_format_int32(hdr,rec,"PL",arr,narr); if ( ret < 0 ) { if ( !i ) { *use_GT = 1; continue; } args->nskip_no_data++; return -1; } if ( ret != 3*bcf_hdr_nsamples(hdr) ) { if ( warn_dip_PL ) { fprintf(bcftools_stderr,"INFO: skipping %s:%"PRIhts_pos", only diploid FORMAT/PL fields supported. (This is printed only once.)\n", bcf_seqname(hdr,rec),rec->pos+1); warn_dip_PL = 0; } args->nskip_dip_PL++; return -1; } *narr1 = 3; return 0; } return -1; // should never reach } static void process_line(args_t *args) { int i,j,k, nqry1, ngt1, ret; bcf1_t *gt_rec = NULL, *qry_rec = bcf_sr_get_line(args->files,0); // the query file if ( args->qry_filter ) { int pass = filter_test(args->qry_filter, qry_rec, NULL); if ( args->qry_filter_logic==FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { args->nskip_filter++; return; } } int qry_use_GT = args->qry_use_GT; int gt_use_GT = args->gt_use_GT; ret = set_data(args, args->qry_hdr, qry_rec, &args->qry_arr, &args->nqry_arr, &nqry1, &qry_use_GT); if ( ret<0 ) return; if ( args->gt_hdr ) { gt_rec = bcf_sr_get_line(args->files,1); if ( args->gt_filter ) { int pass = filter_test(args->gt_filter, gt_rec, NULL); if ( args->gt_filter_logic==FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { args->nskip_filter++; return; } } ret = set_data(args, args->gt_hdr, gt_rec, &args->gt_arr, &args->ngt_arr, &ngt1, >_use_GT); if ( ret<0 ) return; } else { ngt1 = nqry1; args->gt_arr = args->qry_arr; } // stats: number of compared sites, and used tags args->ncmp++; args->nused[qry_use_GT][gt_use_GT]++; double hwe_dsg[8]; if ( args->calc_hwe_prob ) { int ac[2]; if ( args->gt_hdr ) { if ( bcf_calc_ac(args->gt_hdr, gt_rec, ac, BCF_UN_INFO|BCF_UN_FMT)!=1 ) error("todo: bcf_calc_ac() failed\n"); } else if ( bcf_calc_ac(args->qry_hdr, qry_rec, ac, BCF_UN_INFO|BCF_UN_FMT)!=1 ) error("todo: bcf_calc_ac() failed\n"); // Calculate HWE probability for each possible qry+gt dosage combination. The alternate allele dosage // values returned by gt_to_prob() below are 0,1,2,4 (0=missing, 1<<0, 1<<1, 1<<2). We consider only // biallelic sites, therefore we work with eight genotype combinations. // // The array hwe_dsg is accessed with hwe_dsg[qry_dsg & gt_dsg] and is constructed to account for PL uncertainty // when we encounter less informative PL, such as PL=0,0,10, where multiple dosage values are equally // likely. If we allowed complete uncertainty (PL=0,0,0), we'd have up to eight possible genotype // mask combinations: from e.g. 0=(gt_dsg=1<<0 & qry_dsg=1<<1) to 7=(gt_dsg=1<<0|1<<1|1<<2 & qry_dsg=1<<0|1<<1|1<<2). // Note the extreme case of 1|2|4 is skipped, see pl_to_dsg(). // // When the dosage is uncertain, we take the minimum of their corresponding HWE value, for example // hwe[0] = 0 // hwe[1] = (1-AF)**2 // hwe[2] = 2*AF*(1-AF) // hwe[4] = AF**2 // hwe[3] = min{hwe[1],hwe[2]} double hwe[3]; // while hwe_dsg iterates over dsg bitmasks (0..7), hwe iterates over dsg (0,1,2) double af = ac[0]+ac[1] ? (double)ac[1]/(ac[0]+ac[1]) : 1e-6; hwe[0] = -log((1-af)*(1-af)); hwe[1] = -log(2*af*(1-af)); hwe[2] = -log(af*af); hwe_dsg[0] = 0; for (i=1; i<8; i++) { hwe_dsg[i] = HUGE_VAL; for (k=0; k<3; k++) { if ( ((1< hwe[k] ) hwe_dsg[i] = hwe[k]; } } } // The sample pairs were given explicitly via -p/-P options if ( args->pairs ) { if ( !args->gt_err ) { int ndiff = 0; if ( args->kbs_diff ) diff_sites_reset(args); for (i=0; inpairs; i++) { int32_t *ptr; uint8_t qry_dsg, gt_dsg; ptr = args->gt_arr + args->pairs[i].igt*ngt1; gt_dsg = gt_use_GT ? gt_to_dsg(ptr) : pl_to_dsg(ptr); if ( !gt_dsg ) continue; // missing value if ( args->hom_only && !(gt_dsg&5) ) continue; // not a hom ptr = args->qry_arr + args->pairs[i].iqry*nqry1; qry_dsg = qry_use_GT ? gt_to_dsg(ptr) : pl_to_dsg(ptr); if ( !qry_dsg ) continue; // missing value int match = qry_dsg & gt_dsg; if ( !match ) { args->ndiff[i]++; if ( args->kbs_diff ) { ndiff++; kbs_insert(args->kbs_diff, i); } } else if ( args->calc_hwe_prob ) { args->hwe_prob[i] += hwe_dsg[match]; args->nmatch[i]++; } args->ncnt[i]++; } if ( ndiff ) diff_sites_push(args, ndiff, qry_rec->rid, qry_rec->pos); } else // gt_err set { for (i=0; inpairs; i++) { int32_t *ptr; double qry_prob[3], gt_prob[3]; uint8_t qry_dsg, gt_dsg; ptr = args->gt_arr + args->pairs[i].igt*ngt1; gt_dsg = gt_use_GT ? gt_to_prob(args,ptr,gt_prob) : pl_to_prob(args,ptr,gt_prob); if ( !gt_dsg ) continue; // missing value if ( args->hom_only && !(gt_dsg&5) ) continue; // not a hom ptr = args->qry_arr + args->pairs[i].iqry*nqry1; qry_dsg = qry_use_GT ? gt_to_prob(args,ptr,qry_prob) : pl_to_prob(args,ptr,qry_prob); if ( !qry_dsg ) continue; // missing value double min = qry_prob[0] + gt_prob[0]; qry_prob[1] += gt_prob[1]; if ( min > qry_prob[1] ) min = qry_prob[1]; qry_prob[2] += gt_prob[2]; if ( min > qry_prob[2] ) min = qry_prob[2]; args->pdiff[i] += min; if ( args->calc_hwe_prob ) { int match = qry_dsg & gt_dsg; args->hwe_prob[i] += hwe_dsg[match]; if ( match ) args->nmatch[i]++; } args->ncnt[i]++; } } return; } int idx=0; if ( !args->gt_err ) { for (i=0; inqry_smpl; i++) { int iqry = args->qry_smpl ? args->qry_smpl[i] : i; int32_t *ptr = args->qry_arr + nqry1*iqry; args->qry_dsg[i] = qry_use_GT ? gt_to_dsg(ptr) : pl_to_dsg(ptr); } if ( !args->cross_check ) // in this case gt_dsg points to qry_dsg { for (i=0; ingt_smpl; i++) { int igt = args->gt_smpl ? args->gt_smpl[i] : i; int32_t *ptr = args->gt_arr + ngt1*igt; args->gt_dsg[i] = gt_use_GT ? gt_to_dsg(ptr) : pl_to_dsg(ptr); if ( args->hom_only && !(args->gt_dsg[i]&5) ) args->gt_dsg[i] = 0; // not a hom, set to a missing value } } for (i=0; inqry_smpl; i++) { int ngt = args->cross_check ? i : args->ngt_smpl; // two files or a sub-diagonal cross-check mode? if ( !args->qry_dsg[i] ) { idx += ngt; continue; } // missing value for (j=0; jgt_dsg[j] ) { idx++; continue; } // missing value int match = args->qry_dsg[i] & args->gt_dsg[j]; if ( !match ) args->ndiff[idx]++; else if ( args->calc_hwe_prob ) { args->hwe_prob[idx] += hwe_dsg[match]; args->nmatch[idx]++; } args->ncnt[idx]++; idx++; } } } else // gt_err set { for (i=0; inqry_smpl; i++) { int iqry = args->qry_smpl ? args->qry_smpl[i] : i; int32_t *ptr = args->qry_arr + nqry1*iqry; args->qry_dsg[i] = qry_use_GT ? gt_to_prob(args,ptr,args->qry_prob+i*3) : pl_to_prob(args,ptr,args->qry_prob+i*3); } if ( !args->cross_check ) // in this case gt_dsg points to qry_dsg { for (i=0; ingt_smpl; i++) { int igt = args->gt_smpl ? args->gt_smpl[i] : i; int32_t *ptr = args->gt_arr + ngt1*igt; args->gt_dsg[i] = gt_use_GT ? gt_to_prob(args,ptr,args->gt_prob+i*3) : pl_to_prob(args,ptr,args->gt_prob+i*3); if ( args->hom_only && !(args->gt_dsg[i]&5) ) args->gt_dsg[i] = 0; // not a hom, set to a missing value } } for (i=0; inqry_smpl; i++) { int ngt = args->cross_check ? i : args->ngt_smpl; // two files or a sub-diagonal cross-check mode? if ( !args->qry_dsg[i] ) { idx += ngt; continue; } // missing value for (j=0; jgt_dsg[j] ) { idx++; continue; } // missing value double min = args->qry_prob[i*3] + args->gt_prob[j*3]; if ( min > args->qry_prob[i*3+1] + args->gt_prob[j*3+1] ) min = args->qry_prob[i*3+1] + args->gt_prob[j*3+1]; if ( min > args->qry_prob[i*3+2] + args->gt_prob[j*3+2] ) min = args->qry_prob[i*3+2] + args->gt_prob[j*3+2]; args->pdiff[idx] += min; if ( args->calc_hwe_prob ) { int match = args->qry_dsg[i] & args->gt_dsg[j]; args->hwe_prob[idx] += hwe_dsg[match]; if ( match ) args->nmatch[idx]++; } args->ncnt[idx]++; idx++; } } } } typedef struct { int ism, idx; double val; } idbl_t; static int cmp_idbl(const void *_a, const void *_b) { idbl_t *a = (idbl_t*)_a; idbl_t *b = (idbl_t*)_b; if ( a->val < b->val ) return -1; if ( a->val > b->val ) return 1; return 0; } static void report_distinctive_sites(args_t *args) { extsort_sort(args->es); args->kstr.l = 0; ksprintf(&args->kstr,"# DS, distinctive sites:\n"); ksprintf(&args->kstr,"# - chromosome\n"); ksprintf(&args->kstr,"# - position\n"); ksprintf(&args->kstr,"# - cumulative number of pairs distinguished by this block\n"); ksprintf(&args->kstr,"# - block id\n"); ksprintf(&args->kstr,"#DS\t[2]Chromosome\t[3]Position\t[4]Cumulative number of distinct pairs\t[5]Block id\n"); kbitset_t *kbs_blk = kbs_init(args->npairs); kbitset_iter_t itr; int i,ndiff,rid,pos,ndiff_tot = 0, iblock = 0; int ndiff_min = args->distinctive_sites <= args->npairs ? args->distinctive_sites : args->npairs; while ( diff_sites_shift(args,&ndiff,&rid,&pos) ) { int ndiff_new = 0, ndiff_dbg = 0; kbs_start(&itr); while ( (i=kbs_next(args->kbs_diff, &itr))>=0 ) { ndiff_dbg++; if ( kbs_exists(kbs_blk,i) ) continue; // already set kbs_insert(kbs_blk,i); ndiff_new++; } if ( ndiff_dbg!=ndiff ) error("Corrupted data, fixme: %d vs %d\n",ndiff_dbg,ndiff); if ( !ndiff_new ) continue; // no new pair distinguished by this site ndiff_tot += ndiff_new; args->kstr.l = 0; ksprintf(&args->kstr,"DS\t%s\t%d\t%d\t%d\n",bcf_hdr_id2name(args->qry_hdr,rid),pos+1,ndiff_tot,iblock); if ( bgzf_write(args->out_fh, args->kstr.s, args->kstr.l)!=args->kstr.l ) error("Failed to write to %s\n", args->output_fname); if ( ndiff_tot < ndiff_min ) continue; // fewer than the requested number of pairs can be distinguished at this point iblock++; ndiff_tot = 0; kbs_clear(kbs_blk); } kbs_destroy(kbs_blk); } static void report(args_t *args) { args->kstr.l = 0; ksprintf(&args->kstr,"INFO\tsites-compared\t%u\n",args->ncmp); ksprintf(&args->kstr,"INFO\tsites-skipped-no-match\t%u\n",args->nskip_no_match); ksprintf(&args->kstr,"INFO\tsites-skipped-multiallelic\t%u\n",args->nskip_not_ba); ksprintf(&args->kstr,"INFO\tsites-skipped-monoallelic\t%u\n",args->nskip_mono); ksprintf(&args->kstr,"INFO\tsites-skipped-no-data\t%u\n",args->nskip_no_data); ksprintf(&args->kstr,"INFO\tsites-skipped-GT-not-diploid\t%u\n",args->nskip_dip_GT); ksprintf(&args->kstr,"INFO\tsites-skipped-PL-not-diploid\t%u\n",args->nskip_dip_PL); ksprintf(&args->kstr,"INFO\tsites-skipped-filtering-expression\t%u\n",args->nskip_filter); ksprintf(&args->kstr,"INFO\tsites-used-PL-vs-PL\t%u\n",args->nused[0][0]); ksprintf(&args->kstr,"INFO\tsites-used-PL-vs-GT\t%u\n",args->nused[0][1]); ksprintf(&args->kstr,"INFO\tsites-used-GT-vs-PL\t%u\n",args->nused[1][0]); ksprintf(&args->kstr,"INFO\tsites-used-GT-vs-GT\t%u\n",args->nused[1][1]); ksprintf(&args->kstr,"# DCv2, discordance version 2:\n"); ksprintf(&args->kstr,"# - Query sample\n"); ksprintf(&args->kstr,"# - Genotyped sample\n"); ksprintf(&args->kstr,"# - Discordance, given either as an abstract score or number of mismatches, see the options -E/-u\n" "# in man page for details. Note that samples with high missingness have fewer sites compared,\n" "# which results in lower overall discordance. Therefore it is advisable to use the average score\n" "# per site rather than the absolute value, i.e. divide the value by the number of sites compared\n" "# (smaller value = better match)\n"); ksprintf(&args->kstr,"# - Average negative log of HWE probability at matching sites, attempts to quantify the following\n" "# intuition: rare genotype matches are more informative than common genotype matches, hence two\n" "# samples with similar discordance can be further stratified by the HWE score (bigger value = better\n" "# match, the observed concordance was less likely to occur by chance)\n"); ksprintf(&args->kstr,"# - Number of sites compared for this pair of samples (bigger = more informative)\n"); ksprintf(&args->kstr,"# - Number of matching genotypes\n"); ksprintf(&args->kstr,"#DCv2\t[2]Query Sample\t[3]Genotyped Sample\t[4]Discordance\t[5]Average -log P(HWE)\t[6]Number of sites compared\t[7]Number of matching genotypes\n"); if ( bgzf_write(args->out_fh, args->kstr.s, args->kstr.l)!=args->kstr.l ) error("Failed to write to %s\n", args->output_fname); int trim = args->ntop; if ( !args->pairs ) { if ( !args->ngt_smpl && args->nqry_smpl <= args->ntop ) trim = 0; if ( args->ngt_smpl && args->ngt_smpl <= args->ntop ) trim = 0; } if ( args->pairs ) { int i; for (i=0; inpairs; i++) { args->kstr.l = 0; int iqry = args->pairs[i].iqry; int igt = args->pairs[i].igt; if ( args->ndiff ) { ksprintf(&args->kstr,"DCv2\t%s\t%s\t%u\t%e\t%u\t%u\n", args->qry_hdr->samples[iqry], args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt], args->ndiff[i], (args->calc_hwe_prob && args->nmatch[i]) ? args->hwe_prob[i]/args->nmatch[i] : 0, args->ncnt[i], args->nmatch[i]); } else { ksprintf(&args->kstr,"DCv2\t%s\t%s\t%e\t%e\t%u\t%u\n", args->qry_hdr->samples[iqry], args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt], args->pdiff[i], (args->calc_hwe_prob && args->nmatch[i]) ? args->hwe_prob[i]/args->nmatch[i] : 0, args->ncnt[i], args->nmatch[i]); } if ( bgzf_write(args->out_fh, args->kstr.s, args->kstr.l)!=args->kstr.l ) error("Failed to write to %s\n", args->output_fname); } } else if ( !trim ) { int i,j,idx=0; for (i=0; inqry_smpl; i++) { int iqry = args->qry_smpl ? args->qry_smpl[i] : i; int ngt = args->cross_check ? i : args->ngt_smpl; for (j=0; jkstr.l = 0; int igt = args->gt_smpl ? args->gt_smpl[j] : j; if ( args->ndiff ) { ksprintf(&args->kstr,"DCv2\t%s\t%s\t%u\t%e\t%u\t%u\n", args->qry_hdr->samples[iqry], args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt], args->ndiff[idx], (args->calc_hwe_prob && args->nmatch[idx]) ? args->hwe_prob[idx]/args->nmatch[idx] : 0, args->ncnt[idx], args->calc_hwe_prob ? args->nmatch[idx] : 0); } else { ksprintf(&args->kstr,"DCv2\t%s\t%s\t%e\t%e\t%u\t%u\n", args->qry_hdr->samples[iqry], args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt], args->pdiff[idx], (args->calc_hwe_prob && args->nmatch[idx]) ? args->hwe_prob[idx]/args->nmatch[idx] : 0, args->ncnt[idx], args->calc_hwe_prob ? args->nmatch[idx] : 0); } if ( bgzf_write(args->out_fh, args->kstr.s, args->kstr.l)!=args->kstr.l ) error("Failed to write to %s\n", args->output_fname); idx++; } } } else if ( !args->cross_check ) { idbl_t *arr = (idbl_t*)malloc(sizeof(*arr)*args->ngt_smpl); int i,j; for (i=0; inqry_smpl; i++) { int idx = i*args->ngt_smpl; for (j=0; jngt_smpl; j++) { if ( args->sort_by_hwe ) arr[j].val = args->nmatch[idx] ? -args->hwe_prob[idx]/args->nmatch[idx] : 0; // -args->hwe_prob[idx]; else if ( args->ndiff ) arr[j].val = args->ncnt[idx] ? (double)args->ndiff[idx]/args->ncnt[idx] : 0; else arr[j].val = args->ncnt[idx] ? args->pdiff[idx]/args->ncnt[idx] : 0; arr[j].ism = j; arr[j].idx = idx; idx++; } qsort(arr, args->ngt_smpl, sizeof(*arr), cmp_idbl); int iqry = args->qry_smpl ? args->qry_smpl[i] : i; for (j=0; jntop; j++) { args->kstr.l = 0; int idx = arr[j].idx; int igt = args->gt_smpl ? args->gt_smpl[arr[j].ism] : arr[j].ism; if ( args->ndiff ) { ksprintf(&args->kstr,"DCv2\t%s\t%s\t%u\t%e\t%u\t%u\n", args->qry_hdr->samples[iqry], args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt], args->ndiff[idx], (args->calc_hwe_prob && args->nmatch[idx]) ? args->hwe_prob[idx]/args->nmatch[idx] : 0, args->ncnt[idx], args->calc_hwe_prob ? args->nmatch[idx] : 0); } else { ksprintf(&args->kstr,"DCv2\t%s\t%s\t%e\t%e\t%u\t%u\n", args->qry_hdr->samples[iqry], args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt], args->pdiff[idx], (args->calc_hwe_prob && args->nmatch[idx]) ? args->hwe_prob[idx]/args->nmatch[idx] : 0, args->ncnt[idx], args->calc_hwe_prob ? args->nmatch[idx] : 0); } if ( bgzf_write(args->out_fh, args->kstr.s, args->kstr.l)!=args->kstr.l ) error("Failed to write to %s\n", args->output_fname); } } free(arr); } else { int narr = args->nqry_smpl-1; idbl_t *arr = (idbl_t*)malloc(sizeof(*arr)*narr); int i,j,k,idx; for (i=0; inqry_smpl; i++) { k = 0, idx = i*(i-1)/2; for (j=0; jsort_by_hwe ) arr[k].val = args->nmatch[idx] ? -args->hwe_prob[idx]/args->nmatch[idx] : 0; else if ( args->ndiff ) arr[k].val = args->ncnt[idx] ? (double)args->ndiff[idx]/args->ncnt[idx] : 0; else arr[k].val = args->ncnt[idx] ? args->pdiff[idx]/args->ncnt[idx] : 0; arr[k].ism = j; arr[k].idx = idx; idx++; k++; } for (; jsort_by_hwe ) arr[k].val = args->nmatch[idx] ? -args->hwe_prob[idx]/args->nmatch[idx] : 0; else if ( args->ndiff ) arr[k].val = args->ncnt[idx] ? (double)args->ndiff[idx]/args->ncnt[idx] : 0; else arr[k].val = args->ncnt[idx] ? args->pdiff[idx]/args->ncnt[idx] : 0; arr[k].ism = j + 1; arr[k].idx = idx; k++; } qsort(arr, narr, sizeof(*arr), cmp_idbl); int iqry = args->qry_smpl ? args->qry_smpl[i] : i; for (j=0; jntop; j++) { args->kstr.l = 0; if ( i <= arr[j].ism ) continue; int idx = arr[j].idx; int igt = args->qry_smpl ? args->qry_smpl[arr[j].ism] : arr[j].ism; if ( args->ndiff ) { ksprintf(&args->kstr,"DCv2\t%s\t%s\t%u\t%e\t%u\t%u\n", args->qry_hdr->samples[iqry], args->qry_hdr->samples[igt], args->ndiff[idx], (args->calc_hwe_prob && args->nmatch[idx]) ? args->hwe_prob[idx]/args->nmatch[idx] : 0, args->ncnt[idx], args->calc_hwe_prob ? args->nmatch[idx] : 0); } else { ksprintf(&args->kstr,"DCv2\t%s\t%s\t%e\t%e\t%u\t%u\n", args->qry_hdr->samples[iqry], args->qry_hdr->samples[igt], args->pdiff[idx], (args->calc_hwe_prob && args->nmatch[idx]) ? args->hwe_prob[idx]/args->nmatch[idx] : 0, args->ncnt[idx], args->calc_hwe_prob ? args->nmatch[idx] : 0); } if ( bgzf_write(args->out_fh, args->kstr.s, args->kstr.l)!=args->kstr.l ) error("Failed to write to %s\n", args->output_fname); } } free(arr); } } static int is_input_okay(args_t *args, int nmatch) { int i; const char *msg; bcf_hdr_t *hdr; bcf1_t *rec; if ( args->gt_hdr && nmatch!=2 ) { if ( args->nskip_no_match++ ) return 0; for (i=0; i<2; i++) { rec = bcf_sr_get_line(args->files,i); if ( rec ) break; } hdr = bcf_sr_get_header(args->files,i); fprintf(bcftools_stderr,"INFO: skipping %s:%"PRIhts_pos", no record with matching POS+ALT. (This is printed only once.)\n", bcf_seqname(hdr,rec),rec->pos+1); return 0; } for (i=0; i<2; i++) { hdr = bcf_sr_get_header(args->files,i); rec = bcf_sr_get_line(args->files,i); if ( rec->n_allele>2 ) { if ( args->nskip_not_ba++ ) return 0; msg = "not a biallelic site, run `bcftools norm -m -` first"; goto not_okay; } if ( bcf_get_variant_types(rec)==VCF_REF ) { if ( args->nskip_mono++ ) return 0; msg = "monoallelic site"; goto not_okay; } if ( !args->gt_hdr ) break; } return 1; not_okay: fprintf(bcftools_stderr,"INFO: skipping %s:%"PRIhts_pos", %s. (This is printed only once.)\n", bcf_seqname(hdr,rec),rec->pos+1,msg); return 0; } static void usage(void) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: Check sample identity. With no -g BCF given, multi-sample cross-check is performed.\n"); fprintf(bcftools_stderr, "Usage: bcftools gtcheck [options] [-g ] \n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Options:\n"); //fprintf(bcftools_stderr, " -a, --all-sites Output comparison for all sites\n"); //fprintf(bcftools_stderr, " -c, --cluster MIN,MAX Min inter- and max intra-sample error [0.23,-0.3]\n"); fprintf(bcftools_stderr, " --distinctive-sites Find sites that can distinguish between at least NUM sample pairs.\n"); fprintf(bcftools_stderr, " NUM[,MEM[,TMP]] If the number is smaller or equal to 1, it is interpreted as the fraction of pairs.\n"); fprintf(bcftools_stderr, " The optional MEM string sets the maximum memory used for in-memory sorting [500M]\n"); #ifdef _WIN32 fprintf(bcftools_stderr, " and TMP is a prefix of temporary files used by external sorting [/bcftools.XXXXXX]\n"); #else fprintf(bcftools_stderr, " and TMP is a prefix of temporary files used by external sorting [/tmp/bcftools.XXXXXX]\n"); #endif fprintf(bcftools_stderr, " --dry-run Stop after first record to estimate required time\n"); fprintf(bcftools_stderr, " -E, --error-probability INT Phred-scaled probability of genotyping error, 0 for faster but less accurate results [40]\n"); fprintf(bcftools_stderr, " -e, --exclude [qry|gt]:EXPR Exclude sites for which the expression is true\n"); fprintf(bcftools_stderr, " -g, --genotypes FILE Genotypes to compare against\n"); fprintf(bcftools_stderr, " -H, --homs-only Homozygous genotypes only, useful with low coverage data (requires -g)\n"); fprintf(bcftools_stderr, " -i, --include [qry|gt]:EXPR Include sites for which the expression is true\n"); fprintf(bcftools_stderr, " --n-matches INT Print only top INT matches for each sample (sorted by average score), 0 for unlimited.\n"); fprintf(bcftools_stderr, " Use negative value to sort by HWE probability rather than by discordance [0]\n"); fprintf(bcftools_stderr, " --no-HWE-prob Disable calculation of HWE probability\n"); fprintf(bcftools_stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(bcftools_stderr, " -O, --output-type t|z t: plain tab-delimited text output, z: compressed [t]\n"); fprintf(bcftools_stderr, " -p, --pairs LIST Comma-separated sample pairs to compare (qry,gt[,qry,gt..] with -g or qry,qry[,qry,qry..] w/o)\n"); fprintf(bcftools_stderr, " -P, --pairs-file FILE File with tab-delimited sample pairs to compare (qry,gt with -g or qry,qry w/o)\n"); fprintf(bcftools_stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(bcftools_stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(bcftools_stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " -s, --samples [qry|gt]:LIST List of query or -g samples, \"-\" to select all samples (by default all samples are compared)\n"); fprintf(bcftools_stderr, " -S, --samples-file [qry|gt]:FILE File with the query or -g samples to compare\n"); fprintf(bcftools_stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(bcftools_stderr, " -u, --use TAG1[,TAG2] Which tag to use in the query file (TAG1) and the -g file (TAG2) [PL,GT]\n"); fprintf(bcftools_stderr, "Examples:\n"); fprintf(bcftools_stderr, " # Check discordance of all samples from B against all samples in A\n"); fprintf(bcftools_stderr, " bcftools gtcheck -g A.bcf B.bcf\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, " # Limit comparisons to the given list of samples\n"); fprintf(bcftools_stderr, " bcftools gtcheck -s gt:a1,a2,a3 -s qry:b1,b2 -g A.bcf B.bcf\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, " # Compare only two pairs a1,b1 and a1,b2\n"); fprintf(bcftools_stderr, " bcftools gtcheck -p a1,b1,a1,b2 -g A.bcf B.bcf\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int main_vcfgtcheck(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; set_cwd(args); args->qry_use_GT = -1; args->gt_use_GT = -1; args->calc_hwe_prob = 1; args->gt_err = 40; args->regions_overlap = 1; args->targets_overlap = 0; args->output_fname = "-"; // external sort for --distinctive-sites #ifdef _WIN32 args->es_tmp_prefix = NULL; #else args->es_tmp_prefix = "/tmp/bcftools-gtcheck"; #endif args->es_max_mem = strdup("500M"); // In simulated sample swaps the minimum error was 0.3 and maximum intra-sample error was 0.23 // - min_inter: pairs with smaller err value will be considered identical // - max_intra: pairs with err value bigger than abs(max_intra_err) will be considered // different. If negative, the cutoff may be heuristically lowered args->min_inter_err = 0.23; args->max_intra_err = -0.3; static struct option loptions[] = { {"error-probability",1,0,'E'}, // note this used to be 'e', but can easily auto-detect to assure backward compatibility {"exclude",required_argument,0,'e'}, {"include",required_argument,0,'i'}, {"output",required_argument,0,'o'}, {"output-type",required_argument,NULL,'O'}, {"use",1,0,'u'}, {"cluster",1,0,'c'}, {"GTs-only",1,0,'G'}, {"all-sites",0,0,'a'}, {"homs-only",0,0,'H'}, {"help",0,0,'h'}, {"genotypes",1,0,'g'}, {"plot",1,0,'p'}, {"samples",1,0,'s'}, {"samples-file",1,0,'S'}, {"n-matches",1,0,2}, {"no-HWE-prob",0,0,3}, {"target-sample",1,0,4}, {"dry-run",0,0,5}, {"distinctive-sites",1,0,6}, {"regions",1,0,'r'}, {"regions-file",1,0,'R'}, {"regions-overlap",required_argument,NULL,7}, {"targets",1,0,'t'}, {"targets-file",1,0,'T'}, {"targets-overlap",required_argument,NULL,8}, {"pairs",1,0,'p'}, {"pairs-file",1,0,'P'}, {0,0,0,0} }; char *tmp; while ((c = getopt_long(argc, argv, "hg:p:s:S:p:P:Hr:R:at:T:G:c:u:e:E:i:o:O:",loptions,NULL)) >= 0) { switch (c) { case 'o': args->output_fname = optarg; break; case 'O': switch (optarg[0]) { case 't': args->output_type = FT_TAB_TEXT; break; case 'z': args->output_type = FT_VCF_GZ; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --output-type %s\n", optarg+1); } break; case 'e': if ( !strncasecmp("gt:",optarg,3) ) { if ( args->gt_filter_str ) error("Error: only one -i or -e expression can be given for gt:, and they cannot be combined\n"); args->gt_filter_str = optarg; args->gt_filter_logic |= FLT_EXCLUDE; } else if ( !strncasecmp("qry:",optarg,4) ) { if ( args->qry_filter_str ) error("Error: only one -i or -e expression can be given for qry:, and they cannot be combined\n"); args->qry_filter_str = optarg; args->qry_filter_logic |= FLT_EXCLUDE; } else { // this could be the old -e, --error-probability option args->gt_err = strtol(optarg,&tmp,10); if ( !tmp || *tmp ) { // it is not args->gt_filter_str = optarg; args->qry_filter_str = optarg; args->gt_filter_logic |= FLT_EXCLUDE; args->qry_filter_logic |= FLT_EXCLUDE; } else { fprintf(bcftools_stderr,"[warning] auto-detected the old format --error-probability option, please switch from -e to -E.\n"); } } break; case 'i': if ( !strncasecmp("gt:",optarg,3) ) { if ( args->gt_filter_str ) error("Error: only one -i or -e expression can be given for gt:, and they cannot be combined\n"); args->gt_filter_str = optarg; args->gt_filter_logic |= FLT_INCLUDE; } else if ( !strncasecmp("qry:",optarg,4) ) { if ( args->qry_filter_str ) error("Error: only one -i or -e expression can be given for qry:, and they cannot be combined\n"); args->qry_filter_str = optarg; args->qry_filter_logic |= FLT_INCLUDE; } else { args->gt_filter_str = optarg; args->qry_filter_str = optarg; args->gt_filter_logic |= FLT_INCLUDE; args->qry_filter_logic |= FLT_INCLUDE; } break; case 'E': args->gt_err = strtol(optarg,&tmp,10); if ( !tmp || *tmp ) error("Could not parse: --error-probability %s\n", optarg); break; case 'u': { int i,nlist; char **list = hts_readlist(optarg, 0, &nlist); if ( !list || nlist<=0 || nlist>2 ) error("Failed to parse --use %s\n", optarg); if ( !strcasecmp("GT",list[0]) ) args->qry_use_GT = 1; else if ( !strcasecmp("PL",list[0]) ) args->qry_use_GT = 0; else error("Failed to parse --use %s; only GT and PL are supported\n", optarg); if ( nlist==2 ) { if ( !strcasecmp("GT",list[1]) ) args->gt_use_GT = 1; else if ( !strcasecmp("PL",list[1]) ) args->gt_use_GT = 0; else error("Failed to parse --use %s; only GT and PL are supported\n", optarg); } else args->gt_use_GT = args->qry_use_GT; for (i=0; intop = strtol(optarg,&tmp,10); if ( !tmp || *tmp ) error("Could not parse: --n-matches %s\n", optarg); if ( args->ntop < 0 ) { args->sort_by_hwe = 1; args->ntop *= -1; } break; case 3 : args->calc_hwe_prob = 0; break; case 4 : error("The option -S, --target-sample has been deprecated\n"); break; case 5 : args->dry_run = 1; break; case 6 : args->distinctive_sites = strtod(optarg,&tmp); if ( *tmp ) { if ( *tmp!=',' ) error("Could not parse: --distinctive-sites %s\n", optarg); tmp++; free(args->es_max_mem); args->es_max_mem = strdup(tmp); while ( *tmp && *tmp!=',' ) tmp++; if ( *tmp ) { *tmp = 0; args->es_tmp_prefix = tmp+1; } } args->gt_err = 0; break; case 'c': error("The -c option is to be implemented, please open an issue on github\n"); args->min_inter_err = strtod(optarg,&tmp); if ( *tmp ) { if ( *tmp!=',') error("Could not parse: -c %s\n", optarg); args->max_intra_err = strtod(tmp+1,&tmp); if ( *tmp ) error("Could not parse: -c %s\n", optarg); } break; case 'G': error("The option -G, --GTs-only has been deprecated\n"); break; case 'a': args->all_sites = 1; error("The -a option is to be implemented, please open an issue on github\n"); break; case 'H': args->hom_only = 1; break; case 'g': args->gt_fname = optarg; break; // case 'p': args->plot = optarg; break; case 's': if ( !strncasecmp("gt:",optarg,3) ) args->gt_samples = optarg+3; else if ( !strncasecmp("qry:",optarg,4) ) args->qry_samples = optarg+4; else error("Which one? Query samples (qry:%s) or genotype samples (gt:%s)?\n",optarg,optarg); break; case 'S': if ( !strncasecmp("gt:",optarg,3) ) args->gt_samples = optarg+3, args->gt_samples_is_file = 1; else if ( !strncasecmp("qry:",optarg,4) ) args->qry_samples = optarg+4, args->qry_samples_is_file = 1; else error("Which one? Query samples (qry:%s) or genotype samples (gt:%s)?\n",optarg,optarg); break; case 'p': args->pair_samples = optarg; break; case 'P': args->pair_samples = optarg; args->pair_samples_is_file = 1; break; case 'r': args->regions = optarg; break; case 'R': args->regions = optarg; args->regions_is_file = 1; break; case 't': args->targets = optarg; break; case 'T': args->targets = optarg; args->targets_is_file = 1; break; case 7 : args->regions_overlap = parse_overlap_option(optarg); if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 8 : args->targets_overlap = parse_overlap_option(optarg); if ( args->targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 'h': case '?': usage(); break; default: error("Unknown argument: %s\n", optarg); } } if ( optind==argc ) { if ( !isatty(fileno((FILE *)stdin)) ) args->qry_fname = "-"; // reading from stdin else usage(); // no files given } else args->qry_fname = argv[optind]; if ( argc>optind+1 ) error("Error: too many files given, run with -h for help\n"); // too many files given if ( args->pair_samples ) { if ( args->gt_samples || args->qry_samples ) error("The -p/-P option cannot be combined with -s/-S\n"); if ( args->ntop ) error("The --n-matches option cannot be combined with -p/-P\n"); } if ( args->distinctive_sites && !args->pair_samples ) error("The experimental option --distinctive-sites requires -p/-P\n"); if ( args->hom_only && !args->gt_fname ) error("The option --homs-only requires --genotypes\n"); if ( args->distinctive_sites && args->gt_err ) error("The option --distinctive-sites cannot be combined with --error-probability\n"); init_data(args); int ret; while ( (ret=bcf_sr_next_line(args->files)) ) { if ( !is_input_okay(args,ret) ) continue; // time one record to give the user an estimate with very big files struct timeval t0, t1; if ( !args->ncmp ) gettimeofday(&t0, NULL); process_line(args); if ( args->ncmp==1 ) { gettimeofday(&t1, NULL); double delta = (t1.tv_sec - t0.tv_sec) * 1e6 + (t1.tv_usec - t0.tv_usec); fprintf(bcftools_stderr,"INFO:\tTime required to process one record .. %f seconds\n",delta/1e6); args->kstr.l = 0; ksprintf(&args->kstr,"INFO\tTime required to process one record .. %f seconds\n",delta/1e6); if ( bgzf_write(args->out_fh, args->kstr.s, args->kstr.l)!=args->kstr.l ) error("Failed to write to %s\n", args->output_fname); if ( args->dry_run ) break; } } if ( !args->dry_run ) { report(args); if ( args->distinctive_sites ) report_distinctive_sites(args); } destroy_data(args); free(args); return 0; } pysam-0.23.0/bcftools/vcfhead.c000066400000000000000000000116311475062545500163230ustar00rootroot00000000000000/* vcfhead.c -- view VCF/BCF file headers. Copyright (C) 2021 University of Glasgow. Copyright (C) 2023 Genome Research Ltd. Author: John Marshall Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "bcftools.h" int main_vcfhead(int argc, char *argv[]) { static const char usage[] = "\n" "About: Displays VCF/BCF headers and optionally the first few variant records\n" "Usage: bcftools head [OPTION]... [FILE]\n" "\n" "Options:\n" " -h, --headers INT Display INT header lines [all]\n" " -n, --records INT Display INT variant record lines [none]\n" " -s, --samples INT Display INT records starting with the #CHROM header line [none]\n" "\n"; static const struct option loptions[] = { { "headers", required_argument, NULL, 'h' }, { "records", required_argument, NULL, 'n' }, { "samples", required_argument, NULL, 's' }, { NULL, 0, NULL, 0 } }; int all_headers = 1; int samples = 0; uint64_t nheaders = 0; uint64_t nrecords = 0; int c, nargs; while ((c = getopt_long(argc, argv, "h:n:s:", loptions, NULL)) >= 0) switch (c) { case 'h': all_headers = 0; nheaders = strtoull(optarg, NULL, 0); break; case 'n': nrecords = strtoull(optarg, NULL, 0); break; case 's': nrecords = strtoull(optarg, NULL, 0); samples = 1; break; default: fputs(usage, stderr); return EXIT_FAILURE; } if ( samples && all_headers ) all_headers = 0; nargs = argc - optind; if (nargs == 0 && isatty(STDIN_FILENO)) { fputs(usage, stdout); return EXIT_SUCCESS; } else if (nargs > 1) { fputs(usage, stderr); return EXIT_FAILURE; } const char *fname = (nargs == 1)? argv[optind] : "-"; vcfFile *fp = bcf_open(fname, "r"); if (fp == NULL) { if (strcmp(fname, "-") != 0) error_errno("[%s] Can't open \"%s\"", __func__, fname); else error_errno("[%s] Can't open standard input", __func__); } bcf_hdr_t *hdr = bcf_hdr_read(fp); if (hdr == NULL) { bcf_close(fp); if (strcmp(fname, "-") != 0) error("[%s] Can't read headers from \"%s\"\n", __func__, fname); else error("[%s] Can't read headers\n", __func__); } kstring_t str = KS_INITIALIZE; if (all_headers) { bcf_hdr_format(hdr, 0, &str); fputs(ks_str(&str), stdout); } else if (nheaders > 0 || samples ) { bcf_hdr_format(hdr, 0, &str); char *lim = str.s; uint64_t n; int samples_printed = 0; for (n = 0; n < nheaders; n++) { if ( samples && !strncmp(lim,"#CHROM\t",7) ) samples_printed = 1; lim = strchr(lim, '\n'); if (lim) lim++; else break; } if ( nheaders ) { char tmp; if (lim) { tmp = *lim; *lim = '\0'; } fputs(ks_str(&str), stdout); if (lim) *lim = tmp; } if ( lim && samples && !samples_printed ) { while ( lim && *lim ) { if ( !strncmp(lim,"#CHROM\t",7) ) { fputs(lim, stdout); break; } lim = strchr(lim, '\n'); if (lim) lim++; else break; } } } if (nrecords > 0) { bcf1_t *rec = bcf_init(); uint64_t n; for (n = 0; n < nrecords && bcf_read(fp, hdr, rec) >= 0; n++) { ks_clear(&str); if (vcf_format(hdr, rec, &str) >= 0) fputs(ks_str(&str), stdout); else fprintf(stderr, "[%s] Record #%"PRIu64 " is invalid\n", __func__, n+1); } bcf_destroy(rec); } ks_free(&str); bcf_hdr_destroy(hdr); bcf_close(fp); return EXIT_SUCCESS; } pysam-0.23.0/bcftools/vcfhead.c.pysam.c000066400000000000000000000117761475062545500177060ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfhead.c -- view VCF/BCF file headers. Copyright (C) 2021 University of Glasgow. Copyright (C) 2023 Genome Research Ltd. Author: John Marshall Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "bcftools.h" int main_vcfhead(int argc, char *argv[]) { static const char usage[] = "\n" "About: Displays VCF/BCF headers and optionally the first few variant records\n" "Usage: bcftools head [OPTION]... [FILE]\n" "\n" "Options:\n" " -h, --headers INT Display INT header lines [all]\n" " -n, --records INT Display INT variant record lines [none]\n" " -s, --samples INT Display INT records starting with the #CHROM header line [none]\n" "\n"; static const struct option loptions[] = { { "headers", required_argument, NULL, 'h' }, { "records", required_argument, NULL, 'n' }, { "samples", required_argument, NULL, 's' }, { NULL, 0, NULL, 0 } }; int all_headers = 1; int samples = 0; uint64_t nheaders = 0; uint64_t nrecords = 0; int c, nargs; while ((c = getopt_long(argc, argv, "h:n:s:", loptions, NULL)) >= 0) switch (c) { case 'h': all_headers = 0; nheaders = strtoull(optarg, NULL, 0); break; case 'n': nrecords = strtoull(optarg, NULL, 0); break; case 's': nrecords = strtoull(optarg, NULL, 0); samples = 1; break; default: fputs(usage, bcftools_stderr); return EXIT_FAILURE; } if ( samples && all_headers ) all_headers = 0; nargs = argc - optind; if (nargs == 0 && isatty(STDIN_FILENO)) { fputs(usage, bcftools_stdout); return EXIT_SUCCESS; } else if (nargs > 1) { fputs(usage, bcftools_stderr); return EXIT_FAILURE; } const char *fname = (nargs == 1)? argv[optind] : "-"; vcfFile *fp = bcf_open(fname, "r"); if (fp == NULL) { if (strcmp(fname, "-") != 0) error_errno("[%s] Can't open \"%s\"", __func__, fname); else error_errno("[%s] Can't open standard input", __func__); } bcf_hdr_t *hdr = bcf_hdr_read(fp); if (hdr == NULL) { bcf_close(fp); if (strcmp(fname, "-") != 0) error("[%s] Can't read headers from \"%s\"\n", __func__, fname); else error("[%s] Can't read headers\n", __func__); } kstring_t str = KS_INITIALIZE; if (all_headers) { bcf_hdr_format(hdr, 0, &str); fputs(ks_str(&str), bcftools_stdout); } else if (nheaders > 0 || samples ) { bcf_hdr_format(hdr, 0, &str); char *lim = str.s; uint64_t n; int samples_printed = 0; for (n = 0; n < nheaders; n++) { if ( samples && !strncmp(lim,"#CHROM\t",7) ) samples_printed = 1; lim = strchr(lim, '\n'); if (lim) lim++; else break; } if ( nheaders ) { char tmp; if (lim) { tmp = *lim; *lim = '\0'; } fputs(ks_str(&str), bcftools_stdout); if (lim) *lim = tmp; } if ( lim && samples && !samples_printed ) { while ( lim && *lim ) { if ( !strncmp(lim,"#CHROM\t",7) ) { fputs(lim, bcftools_stdout); break; } lim = strchr(lim, '\n'); if (lim) lim++; else break; } } } if (nrecords > 0) { bcf1_t *rec = bcf_init(); uint64_t n; for (n = 0; n < nrecords && bcf_read(fp, hdr, rec) >= 0; n++) { ks_clear(&str); if (vcf_format(hdr, rec, &str) >= 0) fputs(ks_str(&str), bcftools_stdout); else fprintf(bcftools_stderr, "[%s] Record #%"PRIu64 " is invalid\n", __func__, n+1); } bcf_destroy(rec); } ks_free(&str); bcf_hdr_destroy(hdr); bcf_close(fp); return EXIT_SUCCESS; } pysam-0.23.0/bcftools/vcfindex.c000066400000000000000000000273361475062545500165420ustar00rootroot00000000000000/* vcfindex.c -- Index bgzip compressed VCF/BCF files for random access. Copyright (C) 2014-2024 Genome Research Ltd. Author: Shane McCarthy Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #define __STDC_FORMAT_MACROS #include #include #include #include "bcftools.h" #define BCF_LIDX_SHIFT 14 enum { per_contig = 1, all_contigs = 2, total = 4 }; static void usage(void) { fprintf(stderr, "\n"); fprintf(stderr, "About: Index bgzip compressed VCF/BCF files for random access.\n"); fprintf(stderr, "Usage: bcftools index [options] |\n"); fprintf(stderr, "\n"); fprintf(stderr, "Indexing options:\n"); fprintf(stderr, " -c, --csi generate CSI-format index for VCF/BCF files [default]\n"); fprintf(stderr, " -f, --force overwrite index if it already exists\n"); fprintf(stderr, " -m, --min-shift INT set minimal interval size for CSI indices to 2^INT [14]\n"); fprintf(stderr, " -o, --output FILE optional output index file name\n"); fprintf(stderr, " -t, --tbi generate TBI-format index for VCF files\n"); fprintf(stderr, " --threads INT use multithreading with INT worker threads [0]\n"); fprintf(stderr, "\n"); fprintf(stderr, "Stats options:\n"); fprintf(stderr, " -a, --all with --stats, print stats for all contigs even when zero\n"); fprintf(stderr, " -n, --nrecords print number of records based on existing index file\n"); fprintf(stderr, " -s, --stats print per contig stats based on existing index file\n"); fprintf(stderr, "\n"); exit(1); } int vcf_index_stats(char *fname, int stats) { const char **seq = NULL; int tid, nseq = 0, ret = 0; tbx_t *tbx = NULL; bcf_hdr_t *hdr = NULL; hts_idx_t *idx = NULL; htsFile *fp = NULL; uint64_t sum = 0; char *fntemp = NULL, *fnidx = NULL; /* * First, has the user provided an index file? If per contig stats * are requested, open the variant file (together with the index file, * if provided), since the contig names can only be retrieved from its * header. Otherwise, use just the corresponding index file to count * the total number of records. */ int len = strlen(fname); int idx_only = 0; if ( (fnidx = strstr(fname, HTS_IDX_DELIM)) != NULL ) { fntemp = strdup(fname); if ( !fntemp ) return 1; fntemp[fnidx-fname] = 0; fname = fntemp; fnidx += strlen(HTS_IDX_DELIM); } else if ( len>4 && (!strcasecmp(".csi",fname+len-4) || !strcasecmp(".tbi",fname+len-4)) ) { fnidx = fname; fntemp = strdup(fname); fname = fntemp; fname[len-4] = 0; idx_only = 1; } if ( stats&per_contig ) { if ( idx_only ) { struct stat buf; if ( stat(fname, &buf)==0 ) idx_only = 0; } enum htsExactFormat fmt; if ( !idx_only ) { fp = hts_open(fname,"r"); if ( !fp ) { fprintf(stderr,"Could not read %s\n", fname); ret = 1; goto cleanup; } hdr = bcf_hdr_read(fp); if ( !hdr ) { fprintf(stderr,"Could not read the header: %s\n", fname); ret = 1; goto cleanup; } fmt = hts_get_format(fp)->format; } else { int len = strlen(fnidx); if ( !strcasecmp(".tbi",fnidx+len-4) ) fmt = vcf; else fmt = bcf; } if ( fmt==vcf ) { tbx = tbx_index_load2(fname, fnidx); if ( !tbx ) { fprintf(stderr,"Could not load index for VCF: %s\n", fname); return 1; } } else if ( fmt==bcf ) { idx = bcf_index_load2(fname, fnidx); if ( !idx ) { fprintf(stderr,"Could not load index for BCF file: %s\n", fname); return 1; } } else { fprintf(stderr,"Could not detect the file type as VCF or BCF: %s\n", fname); return 1; } } else if ( fnidx ) { char *ext = strrchr(fnidx, '.'); if ( ext && strcmp(ext, ".tbi") == 0 ) { tbx = tbx_index_load2(fname, fnidx); } else if ( ext && strcmp(ext, ".csi") == 0 ) { idx = bcf_index_load2(fname, fnidx); } if ( !tbx && !idx ) { fprintf(stderr,"Could not load index file '%s'\n", fnidx); ret = 1; goto cleanup; } } else { char *ext = strrchr(fname, '.'); if ( ext && strcmp(ext, ".bcf") == 0 ) { idx = bcf_index_load(fname); } else if ( ext && (ext-fname) > 4 && strcmp(ext-4, ".vcf.gz") == 0 ) { tbx = tbx_index_load(fname); } } if ( !tbx && !idx ) { fprintf(stderr,"No index file could be found for '%s'. Use 'bcftools index' to create one\n", fname); ret = 1; goto cleanup; } if ( tbx ) { seq = tbx_seqnames(tbx, &nseq); } else { nseq = hts_idx_nseq(idx); } if ( !tbx && !hdr ) fprintf(stderr,"Warning: cannot determine contig names given the .csi index alone\n"); for (tid=0; tididx : idx, tid, &records, &v); sum += records; if ( (stats&total) || (records == 0 && !(stats&all_contigs)) ) continue; const char *ctg_name = tbx ? seq[tid] : hdr ? bcf_hdr_id2name(hdr, tid) : "n/a"; bcf_hrec_t *hrec = hdr ? bcf_hdr_get_hrec(hdr, BCF_HL_CTG, "ID", ctg_name, NULL) : NULL; int hkey = hrec ? bcf_hrec_find_key(hrec, "length") : -1; printf("%s\t%s\t", ctg_name, hkey<0?".":hrec->vals[hkey]); if (ret >= 0) printf("%" PRIu64 "\n", records); else printf(".\n"); } if ( !sum ) { // No counts found. // Is this because index version has no stored count data, or no records? bcf1_t *rec = bcf_init1(); if (fp && hdr && rec && bcf_read1(fp, hdr, rec) >= 0) { fprintf(stderr,"index of %s does not contain any count metadata. Please re-index with a newer version of bcftools or tabix.\n", fname); ret = 1; } bcf_destroy1(rec); } if ( (stats&total) && !ret ) { printf("%" PRIu64 "\n", sum); } cleanup: free(seq); free(fntemp); if ( fp && hts_close(fp)!=0 ) error("[%s] Error: close failed\n", __func__); bcf_hdr_destroy(hdr); if (tbx) tbx_destroy(tbx); if (idx) hts_idx_destroy(idx); return ret; } int main_vcfindex(int argc, char *argv[]) { int c, force = 0, tbi = 0, stats = 0, n_threads = 0; int min_shift = BCF_LIDX_SHIFT; char *outfn = NULL; static struct option loptions[] = { {"all",no_argument,NULL,'a'}, {"csi",no_argument,NULL,'c'}, {"tbi",no_argument,NULL,'t'}, {"force",no_argument,NULL,'f'}, {"min-shift",required_argument,NULL,'m'}, {"stats",no_argument,NULL,'s'}, {"nrecords",no_argument,NULL,'n'}, {"threads",required_argument,NULL,9}, {"output-file",required_argument,NULL,'o'}, {"output",required_argument,NULL,'o'}, {NULL, 0, NULL, 0} }; char *tmp; while ((c = getopt_long(argc, argv, "ctfm:snao:", loptions, NULL)) >= 0) { switch (c) { case 'c': tbi = 0; break; case 't': tbi = 1; min_shift = 0; break; case 'f': force = 1; break; case 'm': min_shift = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --min-shift %s\n", optarg); break; case 's': stats |= per_contig; break; case 'n': stats |= total; break; case 'a': stats |= all_contigs; break; case 9: n_threads = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --threads %s\n", optarg); break; case 'o': outfn = optarg; break; default: usage(); } } if (!min_shift) tbi = 1; if (stats > total) { fprintf(stderr, "[E::%s] expected only one of --stats or --nrecords options\n", __func__); return 1; } if (tbi && min_shift>0) { fprintf(stderr, "[E::%s] min-shift option only expected for CSI indices \n", __func__); return 1; } if (min_shift < 0 || min_shift > 30) { fprintf(stderr, "[E::%s] expected min_shift in range [0,30] (%d)\n", __func__, min_shift); return 1; } char *fname = NULL; if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else usage(); } else fname = argv[optind]; if (stats) return vcf_index_stats(fname, stats); kstring_t idx_fname = {0,0,0}; if (outfn) kputs(outfn,&idx_fname); else { if (!strcmp(fname, "-")) { fprintf(stderr, "[E::%s] must specify an output path for index file when reading VCF/BCF from stdin\n", __func__); return 1; } ksprintf(&idx_fname, "%s.%s", fname, tbi ? "tbi" : "csi"); } if (!force) { // Before complaining about existing index, check if the VCF file isn't newer. struct stat stat_tbi, stat_file; if ( stat(idx_fname.s, &stat_tbi)==0 ) { stat(fname, &stat_file); if ( stat_file.st_mtime <= stat_tbi.st_mtime ) { fprintf(stderr,"[E::%s] the index file exists. Please use '-f' to overwrite %s\n", __func__, idx_fname.s); free(idx_fname.s); return 1; } } // check for truncated files, allow only with -f BGZF *fp = bgzf_open(fname, "r"); if ( !fp ) error("index: failed to open %s\n", fname); if ( bgzf_compression(fp)!=2 ) error("index: the file is not BGZF compressed, cannot index: %s\n", fname); if ( bgzf_check_EOF(fp)!=1 ) error("index: the input is probably truncated, use -f to index anyway: %s\n", fname); if ( bgzf_close(fp)!=0 ) error("index: close failed: %s\n", fname); } int ret = bcf_index_build3(fname, idx_fname.s, min_shift, n_threads); free(idx_fname.s); if (ret != 0) { if (ret == -2) error("index: failed to open \"%s\"\n", fname); else if (ret == -3) error("index: \"%s\" is in a format that cannot be usefully indexed\n", fname); else error("index: failed to create index for \"%s\"\n", fname); } return 0; } pysam-0.23.0/bcftools/vcfindex.c.pysam.c000066400000000000000000000301431475062545500201010ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfindex.c -- Index bgzip compressed VCF/BCF files for random access. Copyright (C) 2014-2024 Genome Research Ltd. Author: Shane McCarthy Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #define __STDC_FORMAT_MACROS #include #include #include #include "bcftools.h" #define BCF_LIDX_SHIFT 14 enum { per_contig = 1, all_contigs = 2, total = 4 }; static void usage(void) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: Index bgzip compressed VCF/BCF files for random access.\n"); fprintf(bcftools_stderr, "Usage: bcftools index [options] |\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Indexing options:\n"); fprintf(bcftools_stderr, " -c, --csi generate CSI-format index for VCF/BCF files [default]\n"); fprintf(bcftools_stderr, " -f, --force overwrite index if it already exists\n"); fprintf(bcftools_stderr, " -m, --min-shift INT set minimal interval size for CSI indices to 2^INT [14]\n"); fprintf(bcftools_stderr, " -o, --output FILE optional output index file name\n"); fprintf(bcftools_stderr, " -t, --tbi generate TBI-format index for VCF files\n"); fprintf(bcftools_stderr, " --threads INT use multithreading with INT worker threads [0]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Stats options:\n"); fprintf(bcftools_stderr, " -a, --all with --stats, print stats for all contigs even when zero\n"); fprintf(bcftools_stderr, " -n, --nrecords print number of records based on existing index file\n"); fprintf(bcftools_stderr, " -s, --stats print per contig stats based on existing index file\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int vcf_index_stats(char *fname, int stats) { const char **seq = NULL; int tid, nseq = 0, ret = 0; tbx_t *tbx = NULL; bcf_hdr_t *hdr = NULL; hts_idx_t *idx = NULL; htsFile *fp = NULL; uint64_t sum = 0; char *fntemp = NULL, *fnidx = NULL; /* * First, has the user provided an index file? If per contig stats * are requested, open the variant file (together with the index file, * if provided), since the contig names can only be retrieved from its * header. Otherwise, use just the corresponding index file to count * the total number of records. */ int len = strlen(fname); int idx_only = 0; if ( (fnidx = strstr(fname, HTS_IDX_DELIM)) != NULL ) { fntemp = strdup(fname); if ( !fntemp ) return 1; fntemp[fnidx-fname] = 0; fname = fntemp; fnidx += strlen(HTS_IDX_DELIM); } else if ( len>4 && (!strcasecmp(".csi",fname+len-4) || !strcasecmp(".tbi",fname+len-4)) ) { fnidx = fname; fntemp = strdup(fname); fname = fntemp; fname[len-4] = 0; idx_only = 1; } if ( stats&per_contig ) { if ( idx_only ) { struct stat buf; if ( stat(fname, &buf)==0 ) idx_only = 0; } enum htsExactFormat fmt; if ( !idx_only ) { fp = hts_open(fname,"r"); if ( !fp ) { fprintf(bcftools_stderr,"Could not read %s\n", fname); ret = 1; goto cleanup; } hdr = bcf_hdr_read(fp); if ( !hdr ) { fprintf(bcftools_stderr,"Could not read the header: %s\n", fname); ret = 1; goto cleanup; } fmt = hts_get_format(fp)->format; } else { int len = strlen(fnidx); if ( !strcasecmp(".tbi",fnidx+len-4) ) fmt = vcf; else fmt = bcf; } if ( fmt==vcf ) { tbx = tbx_index_load2(fname, fnidx); if ( !tbx ) { fprintf(bcftools_stderr,"Could not load index for VCF: %s\n", fname); return 1; } } else if ( fmt==bcf ) { idx = bcf_index_load2(fname, fnidx); if ( !idx ) { fprintf(bcftools_stderr,"Could not load index for BCF file: %s\n", fname); return 1; } } else { fprintf(bcftools_stderr,"Could not detect the file type as VCF or BCF: %s\n", fname); return 1; } } else if ( fnidx ) { char *ext = strrchr(fnidx, '.'); if ( ext && strcmp(ext, ".tbi") == 0 ) { tbx = tbx_index_load2(fname, fnidx); } else if ( ext && strcmp(ext, ".csi") == 0 ) { idx = bcf_index_load2(fname, fnidx); } if ( !tbx && !idx ) { fprintf(bcftools_stderr,"Could not load index file '%s'\n", fnidx); ret = 1; goto cleanup; } } else { char *ext = strrchr(fname, '.'); if ( ext && strcmp(ext, ".bcf") == 0 ) { idx = bcf_index_load(fname); } else if ( ext && (ext-fname) > 4 && strcmp(ext-4, ".vcf.gz") == 0 ) { tbx = tbx_index_load(fname); } } if ( !tbx && !idx ) { fprintf(bcftools_stderr,"No index file could be found for '%s'. Use 'bcftools index' to create one\n", fname); ret = 1; goto cleanup; } if ( tbx ) { seq = tbx_seqnames(tbx, &nseq); } else { nseq = hts_idx_nseq(idx); } if ( !tbx && !hdr ) fprintf(bcftools_stderr,"Warning: cannot determine contig names given the .csi index alone\n"); for (tid=0; tididx : idx, tid, &records, &v); sum += records; if ( (stats&total) || (records == 0 && !(stats&all_contigs)) ) continue; const char *ctg_name = tbx ? seq[tid] : hdr ? bcf_hdr_id2name(hdr, tid) : "n/a"; bcf_hrec_t *hrec = hdr ? bcf_hdr_get_hrec(hdr, BCF_HL_CTG, "ID", ctg_name, NULL) : NULL; int hkey = hrec ? bcf_hrec_find_key(hrec, "length") : -1; fprintf(bcftools_stdout, "%s\t%s\t", ctg_name, hkey<0?".":hrec->vals[hkey]); if (ret >= 0) fprintf(bcftools_stdout, "%" PRIu64 "\n", records); else fprintf(bcftools_stdout, ".\n"); } if ( !sum ) { // No counts found. // Is this because index version has no stored count data, or no records? bcf1_t *rec = bcf_init1(); if (fp && hdr && rec && bcf_read1(fp, hdr, rec) >= 0) { fprintf(bcftools_stderr,"index of %s does not contain any count metadata. Please re-index with a newer version of bcftools or tabix.\n", fname); ret = 1; } bcf_destroy1(rec); } if ( (stats&total) && !ret ) { fprintf(bcftools_stdout, "%" PRIu64 "\n", sum); } cleanup: free(seq); free(fntemp); if ( fp && hts_close(fp)!=0 ) error("[%s] Error: close failed\n", __func__); bcf_hdr_destroy(hdr); if (tbx) tbx_destroy(tbx); if (idx) hts_idx_destroy(idx); return ret; } int main_vcfindex(int argc, char *argv[]) { int c, force = 0, tbi = 0, stats = 0, n_threads = 0; int min_shift = BCF_LIDX_SHIFT; char *outfn = NULL; static struct option loptions[] = { {"all",no_argument,NULL,'a'}, {"csi",no_argument,NULL,'c'}, {"tbi",no_argument,NULL,'t'}, {"force",no_argument,NULL,'f'}, {"min-shift",required_argument,NULL,'m'}, {"stats",no_argument,NULL,'s'}, {"nrecords",no_argument,NULL,'n'}, {"threads",required_argument,NULL,9}, {"output-file",required_argument,NULL,'o'}, {"output",required_argument,NULL,'o'}, {NULL, 0, NULL, 0} }; char *tmp; while ((c = getopt_long(argc, argv, "ctfm:snao:", loptions, NULL)) >= 0) { switch (c) { case 'c': tbi = 0; break; case 't': tbi = 1; min_shift = 0; break; case 'f': force = 1; break; case 'm': min_shift = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --min-shift %s\n", optarg); break; case 's': stats |= per_contig; break; case 'n': stats |= total; break; case 'a': stats |= all_contigs; break; case 9: n_threads = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --threads %s\n", optarg); break; case 'o': outfn = optarg; break; default: usage(); } } if (!min_shift) tbi = 1; if (stats > total) { fprintf(bcftools_stderr, "[E::%s] expected only one of --stats or --nrecords options\n", __func__); return 1; } if (tbi && min_shift>0) { fprintf(bcftools_stderr, "[E::%s] min-shift option only expected for CSI indices \n", __func__); return 1; } if (min_shift < 0 || min_shift > 30) { fprintf(bcftools_stderr, "[E::%s] expected min_shift in range [0,30] (%d)\n", __func__, min_shift); return 1; } char *fname = NULL; if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else usage(); } else fname = argv[optind]; if (stats) return vcf_index_stats(fname, stats); kstring_t idx_fname = {0,0,0}; if (outfn) kputs(outfn,&idx_fname); else { if (!strcmp(fname, "-")) { fprintf(bcftools_stderr, "[E::%s] must specify an output path for index file when reading VCF/BCF from stdin\n", __func__); return 1; } ksprintf(&idx_fname, "%s.%s", fname, tbi ? "tbi" : "csi"); } if (!force) { // Before complaining about existing index, check if the VCF file isn't newer. struct stat stat_tbi, stat_file; if ( stat(idx_fname.s, &stat_tbi)==0 ) { stat(fname, &stat_file); if ( stat_file.st_mtime <= stat_tbi.st_mtime ) { fprintf(bcftools_stderr,"[E::%s] the index file exists. Please use '-f' to overwrite %s\n", __func__, idx_fname.s); free(idx_fname.s); return 1; } } // check for truncated files, allow only with -f BGZF *fp = bgzf_open(fname, "r"); if ( !fp ) error("index: failed to open %s\n", fname); if ( bgzf_compression(fp)!=2 ) error("index: the file is not BGZF compressed, cannot index: %s\n", fname); if ( bgzf_check_EOF(fp)!=1 ) error("index: the input is probably truncated, use -f to index anyway: %s\n", fname); if ( bgzf_close(fp)!=0 ) error("index: close failed: %s\n", fname); } int ret = bcf_index_build3(fname, idx_fname.s, min_shift, n_threads); free(idx_fname.s); if (ret != 0) { if (ret == -2) error("index: failed to open \"%s\"\n", fname); else if (ret == -3) error("index: \"%s\" is in a format that cannot be usefully indexed\n", fname); else error("index: failed to create index for \"%s\"\n", fname); } return 0; } pysam-0.23.0/bcftools/vcfisec.c000066400000000000000000000741341475062545500163540ustar00rootroot00000000000000/* vcfisec.c -- Create intersections, unions and complements of VCF files. Copyright (C) 2012-2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "filter.h" #define OP_PLUS 1 #define OP_MINUS 2 #define OP_EQUAL 3 #define OP_VENN 4 #define OP_COMPLEMENT 5 #define OP_EXACT 6 // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 typedef struct { int isec_op, isec_n, *write, iwrite, nwrite, output_type, n_threads, clevel; int nflt, *flt_logic; filter_t **flt; char **flt_expr; bcf_srs_t *files; FILE *fh_log, *fh_sites; htsFile **fh_out; char **argv, *prefix, *output_fname, **fnames, *write_files, *targets_list, *regions_list; char *isec_exact, *file_list; int argc, record_cmd_line; char *index_fn; int write_index; } args_t; /** * mkdir_p() - create new directory for a file $fname * @fname: the file name to create the directory for, the part after last "/" is ignored */ void HTS_FORMAT(HTS_PRINTF_FMT, 1, 2) mkdir_p(const char *fmt, ...) { va_list ap; va_start(ap, fmt); int n = vsnprintf(NULL, 0, fmt, ap) + 2; va_end(ap); char *tmp = (char*)malloc(n); if (!tmp) error("Couldn't allocate space for path: %s\n", strerror(errno)); va_start(ap, fmt); vsnprintf(tmp, n, fmt, ap); va_end(ap); char *p = tmp+1; while (*p) { while (*p && *p!='/') p++; if ( !*p ) break; char ctmp = *p; *p = 0; int ret = mkdir(tmp,S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH); if ( ret!=0 && errno!=EEXIST ) error("Error creating directory %s: %s\n", tmp,strerror(errno)); *p = ctmp; while ( *p && *p=='/' ) p++; } free(tmp); } /** * open_file() - open new file creating the file name using vsnprintf * @fname: if not NULL, on output will point to newly allocated fname string * @mode: if NULL, only the file name string will be created * @fmt: vsnprintf format and args * * Returns open file descriptor or NULL if mode is NULL. */ FILE * HTS_FORMAT(HTS_PRINTF_FMT, 3, 4) open_file(char **fname, const char *mode, const char *fmt, ...) { va_list ap; va_start(ap, fmt); int n = vsnprintf(NULL, 0, fmt, ap) + 2; va_end(ap); char *str = (char*)malloc(n); va_start(ap, fmt); vsnprintf(str, n, fmt, ap); va_end(ap); mkdir_p("%s", str); if ( !mode ) { if ( !fname ) error("Uh: expected fname or mode\n"); *fname = str; return NULL; } FILE *fp = fopen(str,mode); if ( fname ) *fname = str; else free(str); return fp; } void isec_vcf(args_t *args) { bcf_srs_t *files = args->files; kstring_t str = {0,0,0}; htsFile *out_fh = NULL; // When only one VCF is output, print VCF to stdout or -o file int out_std = 0; if ( args->nwrite==1 && !args->prefix ) out_std = 1; if ( args->targets_list && files->nreaders==1 ) out_std = 1; if ( out_std ) { char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( out_fh == NULL ) error("Can't write to %s: %s\n", args->output_fname? args->output_fname : "standard output", strerror(errno)); if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads); if (args->record_cmd_line) bcf_hdr_append_version(files->readers[args->iwrite].header,args->argc,args->argv,"bcftools_isec"); if ( bcf_hdr_write(out_fh, files->readers[args->iwrite].header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname?args->output_fname:"standard output"); if ( init_index2(out_fh,files->readers[args->iwrite].header, args->output_fname,&args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n", args->output_fname?args->output_fname:"standard output"); } if ( !args->nwrite && !out_std && !args->prefix ) fprintf(stderr,"Note: -w option not given, printing list of sites...\n"); int n; while ( (n=bcf_sr_next_line(files)) ) { bcf_sr_t *reader = NULL; bcf1_t *line = NULL; int i, ret = 0; for (i=0; inreaders; i++) { if ( !bcf_sr_has_line(files,i) ) continue; if ( args->nflt && args->flt[i] ) { bcf1_t *rec = bcf_sr_get_line(files, i); int pass = filter_test(args->flt[i], rec, NULL); if ( args->flt_logic[i] & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { files->has_line[i] = 0; n--; continue; } } if ( !line ) { line = files->readers[i].buffer[0]; reader = &files->readers[i]; } ret |= 1<isec_op) { case OP_COMPLEMENT: if ( n!=1 || !bcf_sr_has_line(files,0) ) continue; break; case OP_EQUAL: if ( n != args->isec_n ) continue; break; case OP_PLUS: if ( n < args->isec_n ) continue; break; case OP_MINUS: if ( n > args->isec_n ) continue; break; case OP_EXACT: for (i=0; inreaders; i++) if ( files->has_line[i] != args->isec_exact[i] ) break; if ( inreaders ) continue; break; } if ( out_std ) { if ( bcf_sr_has_line(files,args->iwrite) && bcf_write1(out_fh, files->readers[args->iwrite].header, files->readers[args->iwrite].buffer[0])!=0 ) error("[%s] Error: cannot write to %s\n", __func__, args->output_fname ? args->output_fname : "standard output"); continue; } else if ( args->fh_sites ) { str.l = 0; kputs(reader->header->id[BCF_DT_CTG][line->rid].key, &str); kputc('\t', &str); kputw(line->pos+1, &str); kputc('\t', &str); if (line->n_allele > 0) kputs(line->d.allele[0], &str); else kputc('.', &str); kputc('\t', &str); if (line->n_allele > 1) kputs(line->d.allele[1], &str); else kputc('.', &str); for (i=2; in_allele; i++) { kputc(',', &str); kputs(line->d.allele[i], &str); } kputc('\t', &str); for (i=0; inreaders; i++) kputc(bcf_sr_has_line(files,i)?'1':'0', &str); kputc('\n', &str); if ( fwrite(str.s,sizeof(char),str.l,args->fh_sites)!=str.l ) error("[%s] Error: failed to write %d bytes to %s\n", __func__,(int)str.l,args->output_fname ? args->output_fname : "standard output"); } if ( args->prefix ) { if ( args->isec_op==OP_VENN && ret==3 ) { if ( !args->nwrite || args->write[0] ) { if ( bcf_write1(args->fh_out[2], bcf_sr_get_header(files,0), bcf_sr_get_line(files,0))!=0 ) error("[%s] Error: cannot write\n", __func__); } if ( !args->nwrite || args->write[1] ) { if ( bcf_write1(args->fh_out[3], bcf_sr_get_header(files,1), bcf_sr_get_line(files,1))!=0 ) error("[%s] Error: cannot write\n", __func__); } } else { for (i=0; inreaders; i++) { if ( !bcf_sr_has_line(files,i) ) continue; if ( args->write && !args->write[i] ) continue; if ( bcf_write1(args->fh_out[i], files->readers[i].header, files->readers[i].buffer[0])!=0 ) error("[%s] Error: cannot write\n", __func__); } } } } if ( str.s ) free(str.s); if ( out_fh ) { if ( args->write_index ) { if ( bcf_idx_save(out_fh)<0 ) { if ( hts_close(out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname? args->output_fname : "-"); } } static void add_filter(args_t *args, char *expr, int logic) { args->nflt++; args->flt_expr = (char**) realloc(args->flt_expr,sizeof(char*)*args->nflt); args->flt_logic = (int*) realloc(args->flt_logic,sizeof(int)*args->nflt); args->flt = (filter_t**) realloc(args->flt,sizeof(filter_t*)*args->nflt); if ( expr[0]=='-' && expr[1]==0 ) { args->flt_expr[args->nflt-1] = NULL; args->flt[args->nflt-1] = NULL; } else args->flt_expr[args->nflt-1] = expr; args->flt_logic[args->nflt-1] = logic; } static void destroy_data(args_t *args); static void init_data(args_t *args) { int i; if ( args->nflt ) { if ( args->nflt > 1 && args->nflt!=args->files->nreaders ) error("Error: expected either one -i/-e option or as many as there are input files\n"); if ( args->nflt < args->files->nreaders ) { if ( !args->flt_expr[0] ) error("Error: useless use of -i/-e\n"); args->nflt = args->files->nreaders; args->flt_expr = (char**) realloc(args->flt_expr,sizeof(char*)*args->nflt); args->flt_logic = (int*) realloc(args->flt_logic,sizeof(int)*args->nflt); args->flt = (filter_t**) realloc(args->flt,sizeof(filter_t*)*args->nflt); for (i=1; inflt; i++) { args->flt_expr[i] = args->flt_expr[0]; args->flt_logic[i] = args->flt_logic[0]; args->flt[i] = filter_init(args->files->readers[i].header,args->flt_expr[i]); } args->flt[0] = filter_init(args->files->readers[0].header,args->flt_expr[0]); } else { for (i=0; ifiles->nreaders; i++) { if ( !args->flt_expr[i] ) continue; args->flt[i] = filter_init(args->files->readers[i].header,args->flt_expr[i]); } } } if ( args->isec_op==OP_EXACT ) { if ( strlen(args->isec_exact)!=args->files->nreaders ) error("The number of files does not match the bitmask: %d vs %s\n", args->files->nreaders,args->isec_exact); for (i=0; ifiles->nreaders; i++) if ( args->isec_exact[i]!='0' && args->isec_exact[i]!='1' ) error("Unexpected bitmask: %s\n",args->isec_exact); for (i=0; ifiles->nreaders; i++) args->isec_exact[i] -= '0'; } // Which files to write: parse the string passed with -w char *p = args->write_files; while (p && *p) { if ( !args->write ) args->write = (int*) calloc(args->files->nreaders,sizeof(int)); if ( sscanf(p,"%d",&i)!=1 ) error("Could not parse --write %s\n", args->write_files); if ( i<=0 || i>args->files->nreaders ) error("The index is out of range: %d (-w %s)\n", i, args->write_files); args->write[i-1] = 1; args->iwrite = i-1; args->nwrite++; while (*p && *p!=',') p++; if ( *p==',' ) p++; } if ( args->nwrite>1 && !args->prefix ) error("Expected -p when multiple output files given: --write %s\n", args->write_files); if ( args->isec_op==OP_COMPLEMENT && args->nwrite ) { if ( args->nwrite>1 ) error("Multiple files to -w make no sense with -C\n"); if ( !args->write[0] ) error("Only -w1 makes sense with -C\n"); } if ( args->prefix ) { // Init output directory and create the readme file args->fh_log = open_file(NULL,"w","%s/README.txt", args->prefix); if ( !args->fh_log ) error("%s/README.txt: %s\n", args->prefix, strerror(errno)); fprintf(args->fh_log,"This file was produced by vcfisec.\n"); fprintf(args->fh_log,"The command line was:\tbcftools %s ", args->argv[0]); int i; for (i=1; iargc; i++) fprintf(args->fh_log," %s",args->argv[i]); fprintf(args->fh_log,"\n\nUsing the following file names:\n"); const char *suffix = "vcf"; if ( args->output_type & FT_BCF ) suffix = "bcf"; else if ( args->output_type & FT_GZ ) suffix = "vcf.gz"; // Open output files and write the legend if ( args->isec_op==OP_VENN ) { args->fh_out = (htsFile**) malloc(sizeof(htsFile*)*4); args->fnames = (char**) calloc(4,sizeof(char*)); #define OPEN_FILE(i,j) { \ open_file(&args->fnames[i], NULL, "%s/%04d.%s", args->prefix, i, suffix); \ char wmode[8]; \ set_wmode(wmode,args->output_type,args->fnames[i],args->clevel); \ args->fh_out[i] = hts_open(args->fnames[i], wmode); \ if ( !args->fh_out[i] ) error("Could not open %s\n", args->fnames[i]); \ if ( args->n_threads ) hts_set_threads(args->fh_out[i], args->n_threads); \ if (args->record_cmd_line) bcf_hdr_append_version(args->files->readers[j].header,args->argc,args->argv,"bcftools_isec"); \ if ( bcf_hdr_write(args->fh_out[i], args->files->readers[j].header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->fnames[i]); \ } if ( !args->nwrite || args->write[0] ) { OPEN_FILE(0,0); fprintf(args->fh_log,"%s\tfor records private to\t%s\n", args->fnames[0], args->files->readers[0].fname); } if ( !args->nwrite || args->write[1] ) { OPEN_FILE(1,1); fprintf(args->fh_log,"%s\tfor records private to\t%s\n", args->fnames[1], args->files->readers[1].fname); } if ( !args->nwrite || args->write[0] ) { OPEN_FILE(2,0); fprintf(args->fh_log,"%s\tfor records from %s shared by both\t%s %s\n", args->fnames[2], args->files->readers[0].fname, args->files->readers[0].fname, args->files->readers[1].fname); } if ( !args->nwrite || args->write[1] ) { OPEN_FILE(3,1); fprintf(args->fh_log,"%s\tfor records from %s shared by both\t%s %s\n", args->fnames[3], args->files->readers[1].fname, args->files->readers[0].fname, args->files->readers[1].fname); } } else { // Init one output file for each reader args->fh_out = (htsFile**) calloc(args->files->nreaders, sizeof(htsFile*)); args->fnames = (char**) calloc(args->files->nreaders, sizeof(char*)); for (i=0; ifiles->nreaders; i++) { if ( args->write && !args->write[i] ) continue; if ( args->isec_op==OP_COMPLEMENT && i>0 ) break; OPEN_FILE(i,i); fprintf(args->fh_log,"%s\tfor stripped\t%s\n", args->fnames[i], args->files->readers[i].fname); } #undef OPEN_FILE } args->fh_sites = open_file(NULL, "w", "%s/sites.txt", args->prefix); if ( !args->fh_sites ) error("%s/sites.txt: %s\n", args->prefix, strerror(errno)); } else { if (args->output_fname) { args->fh_sites = fopen(args->output_fname, "w"); if ( args->fh_sites == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno)); } else args->fh_sites = stdout; } } static void destroy_data(args_t *args) { int i; if ( args->nflt ) { for (i=0; inflt; i++) { if ( !args->flt[i] ) continue; filter_destroy(args->flt[i]); } free(args->flt_expr); free(args->flt); free(args->flt_logic); } if ( args->prefix ) { fclose(args->fh_log); int n = args->isec_op==OP_VENN ? 4 : args->files->nreaders; for (i=0; ifnames[i] ) continue; if ( hts_close(args->fh_out[i])!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fnames[i]); int is_tbi = !args->write_index || (args->write_index&127) == HTS_FMT_TBI; if ( args->output_type==FT_VCF_GZ && is_tbi ) { tbx_conf_t conf = tbx_conf_vcf; tbx_index_build(args->fnames[i], -1, &conf); } else if ( args->output_type==FT_BCF_GZ || !is_tbi ) { if ( bcf_index_build(args->fnames[i],14) ) error("Could not index %s\n", args->fnames[i]); } free(args->fnames[i]); } free(args->fh_out); free(args->fnames); if ( args->fh_sites ) fclose(args->fh_sites); if ( args->write ) free(args->write); } } static void usage(void) { fprintf(stderr, "\n"); fprintf(stderr, "About: Create intersections, unions and complements of VCF files.\n"); fprintf(stderr, "Usage: bcftools isec [options] [...]\n"); fprintf(stderr, "\n"); fprintf(stderr, "Options:\n"); fprintf(stderr, " -c, --collapse STRING Treat as identical records with , see man page for details [none]\n"); fprintf(stderr, " -C, --complement Output positions present only in the first file but missing in the others\n"); fprintf(stderr, " -e, --exclude EXPR Exclude sites for which the expression is true\n"); fprintf(stderr, " -f, --apply-filters LIST Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n"); fprintf(stderr, " -i, --include EXPR Include only sites for which the expression is true\n"); fprintf(stderr, " -l, --file-list FILE Read the input file names from the file\n"); fprintf(stderr, " --no-version Do not append version and command line to the header\n"); fprintf(stderr, " -n, --nfiles [+-=~]INT Output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files\n"); fprintf(stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(stderr, " -p, --prefix DIR If given, subset each of the input files accordingly, see also -w\n"); fprintf(stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(stderr, " --threads INT Use multithreading with worker threads [0]\n"); fprintf(stderr, " -w, --write LIST List of files to write with -p given as 1-based indexes. By default, all files are written\n"); fprintf(stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(stderr, "\n"); fprintf(stderr, "Examples:\n"); fprintf(stderr, " # Create intersection and complements of two sets saving the output in dir/*\n"); fprintf(stderr, " bcftools isec A.vcf.gz B.vcf.gz -p dir\n"); fprintf(stderr, "\n"); fprintf(stderr, " # Filter sites in A and B (but not in C) and create intersection\n"); fprintf(stderr, " bcftools isec -e'MAF<0.01' -i'dbSNP=1' -e - A.vcf.gz B.vcf.gz C.vcf.gz -p dir\n"); fprintf(stderr, "\n"); fprintf(stderr, " # Extract and write records from A shared by both A and B using exact allele match\n"); fprintf(stderr, " bcftools isec A.vcf.gz B.vcf.gz -p dir -n =2 -w 1\n"); fprintf(stderr, "\n"); fprintf(stderr, " # Extract and write records from C found in A and C but not in B\n"); fprintf(stderr, " bcftools isec A.vcf.gz B.vcf.gz C.vcf.gz -p dir -n~101 -w 3\n"); fprintf(stderr, "\n"); fprintf(stderr, " # Extract records private to A or B comparing by position only\n"); fprintf(stderr, " bcftools isec A.vcf.gz B.vcf.gz -p dir -n -1 -c all\n"); fprintf(stderr, "\n"); exit(1); } int main_vcfisec(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->files = bcf_sr_init(); args->argc = argc; args->argv = argv; args->output_fname = NULL; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->clevel = -1; int targets_is_file = 0, regions_is_file = 0; int regions_overlap = 1; int targets_overlap = 0; static struct option loptions[] = { {"help",no_argument,NULL,'h'}, {"exclude",required_argument,NULL,'e'}, {"include",required_argument,NULL,'i'}, {"collapse",required_argument,NULL,'c'}, {"complement",no_argument,NULL,'C'}, {"apply-filters",required_argument,NULL,'f'}, {"file-list",required_argument,NULL,'l'}, {"nfiles",required_argument,NULL,'n'}, {"prefix",required_argument,NULL,'p'}, {"write",required_argument,NULL,'w'}, {"targets",required_argument,NULL,'t'}, {"targets-file",required_argument,NULL,'T'}, {"targets-overlap",required_argument,NULL,4}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,3}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"threads",required_argument,NULL,9}, {"no-version",no_argument,NULL,8}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "hc:r:R:p:n:w:t:T:Cf:o:O:i:e:l:W::",loptions,NULL)) >= 0) { switch (c) { case 'o': args->output_fname = optarg; break; case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'c': if ( !strcmp(optarg,"snps") ) args->files->collapse |= COLLAPSE_SNPS; else if ( !strcmp(optarg,"indels") ) args->files->collapse |= COLLAPSE_INDELS; else if ( !strcmp(optarg,"both") ) args->files->collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS; else if ( !strcmp(optarg,"any") ) args->files->collapse |= COLLAPSE_ANY; else if ( !strcmp(optarg,"all") ) args->files->collapse |= COLLAPSE_ANY; else if ( !strcmp(optarg,"some") ) args->files->collapse |= COLLAPSE_SOME; else if ( !strcmp(optarg,"none") ) args->files->collapse = COLLAPSE_NONE; else error("The --collapse string \"%s\" not recognised.\n", optarg); break; case 'f': args->files->apply_filters = optarg; break; case 'C': if ( args->isec_op!=0 && args->isec_op!=OP_COMPLEMENT ) error("Error: either -C or -n should be given, not both.\n"); args->isec_op = OP_COMPLEMENT; break; case 'l': args->file_list = optarg; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; targets_is_file = 1; break; case 'p': args->prefix = optarg; break; case 'w': if ( args->write_files ) error("The option -w accepts a list of indices and can be given only once\n"); args->write_files = optarg; break; case 'i': add_filter(args, optarg, FLT_INCLUDE); break; case 'e': add_filter(args, optarg, FLT_EXCLUDE); break; case 'n': { if ( args->isec_op!=0 && args->isec_op==OP_COMPLEMENT ) error("Error: either -C or -n should be given, not both.\n"); if ( args->isec_op!=0 ) error("Error: -n should be given only once.\n"); char *p = optarg; if ( *p=='-' ) { args->isec_op = OP_MINUS; p++; } else if ( *p=='+' ) { args->isec_op = OP_PLUS; p++; } else if ( *p=='=' ) { args->isec_op = OP_EQUAL; p++; } else if ( *p=='~' ) { args->isec_op = OP_EXACT; p++; } else if ( isdigit(*p) ) args->isec_op = OP_EQUAL; else error("Could not parse --nfiles %s\n", optarg); if ( args->isec_op == OP_EXACT ) args->isec_exact = p; else if ( sscanf(p,"%d",&args->isec_n)!=1 ) error("Could not parse --nfiles %s\n", optarg); } break; case 3 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 4 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 8 : args->record_cmd_line = 0; break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 'h': case '?': usage(); break; default: error("Unknown argument: %s\n", optarg); } } if ( argc-optind<1 && !args->file_list ) usage(); // no file given int nfiles = 0,i; char **files = NULL; if ( args->file_list ) { files = hts_readlines(args->file_list, &nfiles); if ( !files ) error("Failed to read from %s\n", args->file_list); } if ( optind0; i--) files[n+i-1] = files[n+i-2]; for (i=0; itargets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file,0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( nfiles==2 && !args->isec_op ) { args->isec_op = OP_VENN; if ( !args->prefix ) error("Expected the -p option\n"); } if ( !args->isec_op ) { args->isec_op = OP_PLUS; args->isec_n = 1; } args->files->require_index = 1; for (i=0; ifiles, files[i]) ) error("Failed to open %s: %s\n", files[i],bcf_sr_strerror(args->files->errnum)); free(files[i]); } free(files); init_data(args); isec_vcf(args); destroy_data(args); bcf_sr_destroy(args->files); free(args); return 0; } pysam-0.23.0/bcftools/vcfisec.c.pysam.c000066400000000000000000000750401475062545500177220ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfisec.c -- Create intersections, unions and complements of VCF files. Copyright (C) 2012-2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "filter.h" #define OP_PLUS 1 #define OP_MINUS 2 #define OP_EQUAL 3 #define OP_VENN 4 #define OP_COMPLEMENT 5 #define OP_EXACT 6 // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 typedef struct { int isec_op, isec_n, *write, iwrite, nwrite, output_type, n_threads, clevel; int nflt, *flt_logic; filter_t **flt; char **flt_expr; bcf_srs_t *files; FILE *fh_log, *fh_sites; htsFile **fh_out; char **argv, *prefix, *output_fname, **fnames, *write_files, *targets_list, *regions_list; char *isec_exact, *file_list; int argc, record_cmd_line; char *index_fn; int write_index; } args_t; /** * mkdir_p() - create new directory for a file $fname * @fname: the file name to create the directory for, the part after last "/" is ignored */ void HTS_FORMAT(HTS_PRINTF_FMT, 1, 2) mkdir_p(const char *fmt, ...) { va_list ap; va_start(ap, fmt); int n = vsnprintf(NULL, 0, fmt, ap) + 2; va_end(ap); char *tmp = (char*)malloc(n); if (!tmp) error("Couldn't allocate space for path: %s\n", strerror(errno)); va_start(ap, fmt); vsnprintf(tmp, n, fmt, ap); va_end(ap); char *p = tmp+1; while (*p) { while (*p && *p!='/') p++; if ( !*p ) break; char ctmp = *p; *p = 0; int ret = mkdir(tmp,S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH); if ( ret!=0 && errno!=EEXIST ) error("Error creating directory %s: %s\n", tmp,strerror(errno)); *p = ctmp; while ( *p && *p=='/' ) p++; } free(tmp); } /** * open_file() - open new file creating the file name using vsnprintf * @fname: if not NULL, on output will point to newly allocated fname string * @mode: if NULL, only the file name string will be created * @fmt: vsnprintf format and args * * Returns open file descriptor or NULL if mode is NULL. */ FILE * HTS_FORMAT(HTS_PRINTF_FMT, 3, 4) open_file(char **fname, const char *mode, const char *fmt, ...) { va_list ap; va_start(ap, fmt); int n = vsnprintf(NULL, 0, fmt, ap) + 2; va_end(ap); char *str = (char*)malloc(n); va_start(ap, fmt); vsnprintf(str, n, fmt, ap); va_end(ap); mkdir_p("%s", str); if ( !mode ) { if ( !fname ) error("Uh: expected fname or mode\n"); *fname = str; return NULL; } FILE *fp = fopen(str,mode); if ( fname ) *fname = str; else free(str); return fp; } void isec_vcf(args_t *args) { bcf_srs_t *files = args->files; kstring_t str = {0,0,0}; htsFile *out_fh = NULL; // When only one VCF is output, print VCF to bcftools_stdout or -o file int out_std = 0; if ( args->nwrite==1 && !args->prefix ) out_std = 1; if ( args->targets_list && files->nreaders==1 ) out_std = 1; if ( out_std ) { char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( out_fh == NULL ) error("Can't write to %s: %s\n", args->output_fname? args->output_fname : "standard output", strerror(errno)); if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads); if (args->record_cmd_line) bcf_hdr_append_version(files->readers[args->iwrite].header,args->argc,args->argv,"bcftools_isec"); if ( bcf_hdr_write(out_fh, files->readers[args->iwrite].header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname?args->output_fname:"standard output"); if ( init_index2(out_fh,files->readers[args->iwrite].header, args->output_fname,&args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n", args->output_fname?args->output_fname:"standard output"); } if ( !args->nwrite && !out_std && !args->prefix ) fprintf(bcftools_stderr,"Note: -w option not given, printing list of sites...\n"); int n; while ( (n=bcf_sr_next_line(files)) ) { bcf_sr_t *reader = NULL; bcf1_t *line = NULL; int i, ret = 0; for (i=0; inreaders; i++) { if ( !bcf_sr_has_line(files,i) ) continue; if ( args->nflt && args->flt[i] ) { bcf1_t *rec = bcf_sr_get_line(files, i); int pass = filter_test(args->flt[i], rec, NULL); if ( args->flt_logic[i] & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { files->has_line[i] = 0; n--; continue; } } if ( !line ) { line = files->readers[i].buffer[0]; reader = &files->readers[i]; } ret |= 1<isec_op) { case OP_COMPLEMENT: if ( n!=1 || !bcf_sr_has_line(files,0) ) continue; break; case OP_EQUAL: if ( n != args->isec_n ) continue; break; case OP_PLUS: if ( n < args->isec_n ) continue; break; case OP_MINUS: if ( n > args->isec_n ) continue; break; case OP_EXACT: for (i=0; inreaders; i++) if ( files->has_line[i] != args->isec_exact[i] ) break; if ( inreaders ) continue; break; } if ( out_std ) { if ( bcf_sr_has_line(files,args->iwrite) && bcf_write1(out_fh, files->readers[args->iwrite].header, files->readers[args->iwrite].buffer[0])!=0 ) error("[%s] Error: cannot write to %s\n", __func__, args->output_fname ? args->output_fname : "standard output"); continue; } else if ( args->fh_sites ) { str.l = 0; kputs(reader->header->id[BCF_DT_CTG][line->rid].key, &str); kputc('\t', &str); kputw(line->pos+1, &str); kputc('\t', &str); if (line->n_allele > 0) kputs(line->d.allele[0], &str); else kputc('.', &str); kputc('\t', &str); if (line->n_allele > 1) kputs(line->d.allele[1], &str); else kputc('.', &str); for (i=2; in_allele; i++) { kputc(',', &str); kputs(line->d.allele[i], &str); } kputc('\t', &str); for (i=0; inreaders; i++) kputc(bcf_sr_has_line(files,i)?'1':'0', &str); kputc('\n', &str); if ( fwrite(str.s,sizeof(char),str.l,args->fh_sites)!=str.l ) error("[%s] Error: failed to write %d bytes to %s\n", __func__,(int)str.l,args->output_fname ? args->output_fname : "standard output"); } if ( args->prefix ) { if ( args->isec_op==OP_VENN && ret==3 ) { if ( !args->nwrite || args->write[0] ) { if ( bcf_write1(args->fh_out[2], bcf_sr_get_header(files,0), bcf_sr_get_line(files,0))!=0 ) error("[%s] Error: cannot write\n", __func__); } if ( !args->nwrite || args->write[1] ) { if ( bcf_write1(args->fh_out[3], bcf_sr_get_header(files,1), bcf_sr_get_line(files,1))!=0 ) error("[%s] Error: cannot write\n", __func__); } } else { for (i=0; inreaders; i++) { if ( !bcf_sr_has_line(files,i) ) continue; if ( args->write && !args->write[i] ) continue; if ( bcf_write1(args->fh_out[i], files->readers[i].header, files->readers[i].buffer[0])!=0 ) error("[%s] Error: cannot write\n", __func__); } } } } if ( str.s ) free(str.s); if ( out_fh ) { if ( args->write_index ) { if ( bcf_idx_save(out_fh)<0 ) { if ( hts_close(out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"bcftools_stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname? args->output_fname : "-"); } } static void add_filter(args_t *args, char *expr, int logic) { args->nflt++; args->flt_expr = (char**) realloc(args->flt_expr,sizeof(char*)*args->nflt); args->flt_logic = (int*) realloc(args->flt_logic,sizeof(int)*args->nflt); args->flt = (filter_t**) realloc(args->flt,sizeof(filter_t*)*args->nflt); if ( expr[0]=='-' && expr[1]==0 ) { args->flt_expr[args->nflt-1] = NULL; args->flt[args->nflt-1] = NULL; } else args->flt_expr[args->nflt-1] = expr; args->flt_logic[args->nflt-1] = logic; } static void destroy_data(args_t *args); static void init_data(args_t *args) { int i; if ( args->nflt ) { if ( args->nflt > 1 && args->nflt!=args->files->nreaders ) error("Error: expected either one -i/-e option or as many as there are input files\n"); if ( args->nflt < args->files->nreaders ) { if ( !args->flt_expr[0] ) error("Error: useless use of -i/-e\n"); args->nflt = args->files->nreaders; args->flt_expr = (char**) realloc(args->flt_expr,sizeof(char*)*args->nflt); args->flt_logic = (int*) realloc(args->flt_logic,sizeof(int)*args->nflt); args->flt = (filter_t**) realloc(args->flt,sizeof(filter_t*)*args->nflt); for (i=1; inflt; i++) { args->flt_expr[i] = args->flt_expr[0]; args->flt_logic[i] = args->flt_logic[0]; args->flt[i] = filter_init(args->files->readers[i].header,args->flt_expr[i]); } args->flt[0] = filter_init(args->files->readers[0].header,args->flt_expr[0]); } else { for (i=0; ifiles->nreaders; i++) { if ( !args->flt_expr[i] ) continue; args->flt[i] = filter_init(args->files->readers[i].header,args->flt_expr[i]); } } } if ( args->isec_op==OP_EXACT ) { if ( strlen(args->isec_exact)!=args->files->nreaders ) error("The number of files does not match the bitmask: %d vs %s\n", args->files->nreaders,args->isec_exact); for (i=0; ifiles->nreaders; i++) if ( args->isec_exact[i]!='0' && args->isec_exact[i]!='1' ) error("Unexpected bitmask: %s\n",args->isec_exact); for (i=0; ifiles->nreaders; i++) args->isec_exact[i] -= '0'; } // Which files to write: parse the string passed with -w char *p = args->write_files; while (p && *p) { if ( !args->write ) args->write = (int*) calloc(args->files->nreaders,sizeof(int)); if ( sscanf(p,"%d",&i)!=1 ) error("Could not parse --write %s\n", args->write_files); if ( i<=0 || i>args->files->nreaders ) error("The index is out of range: %d (-w %s)\n", i, args->write_files); args->write[i-1] = 1; args->iwrite = i-1; args->nwrite++; while (*p && *p!=',') p++; if ( *p==',' ) p++; } if ( args->nwrite>1 && !args->prefix ) error("Expected -p when multiple output files given: --write %s\n", args->write_files); if ( args->isec_op==OP_COMPLEMENT && args->nwrite ) { if ( args->nwrite>1 ) error("Multiple files to -w make no sense with -C\n"); if ( !args->write[0] ) error("Only -w1 makes sense with -C\n"); } if ( args->prefix ) { // Init output directory and create the readme file args->fh_log = open_file(NULL,"w","%s/README.txt", args->prefix); if ( !args->fh_log ) error("%s/README.txt: %s\n", args->prefix, strerror(errno)); fprintf(args->fh_log,"This file was produced by vcfisec.\n"); fprintf(args->fh_log,"The command line was:\tbcftools %s ", args->argv[0]); int i; for (i=1; iargc; i++) fprintf(args->fh_log," %s",args->argv[i]); fprintf(args->fh_log,"\n\nUsing the following file names:\n"); const char *suffix = "vcf"; if ( args->output_type & FT_BCF ) suffix = "bcf"; else if ( args->output_type & FT_GZ ) suffix = "vcf.gz"; // Open output files and write the legend if ( args->isec_op==OP_VENN ) { args->fh_out = (htsFile**) malloc(sizeof(htsFile*)*4); args->fnames = (char**) calloc(4,sizeof(char*)); #define OPEN_FILE(i,j) { \ open_file(&args->fnames[i], NULL, "%s/%04d.%s", args->prefix, i, suffix); \ char wmode[8]; \ set_wmode(wmode,args->output_type,args->fnames[i],args->clevel); \ args->fh_out[i] = hts_open(args->fnames[i], wmode); \ if ( !args->fh_out[i] ) error("Could not open %s\n", args->fnames[i]); \ if ( args->n_threads ) hts_set_threads(args->fh_out[i], args->n_threads); \ if (args->record_cmd_line) bcf_hdr_append_version(args->files->readers[j].header,args->argc,args->argv,"bcftools_isec"); \ if ( bcf_hdr_write(args->fh_out[i], args->files->readers[j].header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->fnames[i]); \ } if ( !args->nwrite || args->write[0] ) { OPEN_FILE(0,0); fprintf(args->fh_log,"%s\tfor records private to\t%s\n", args->fnames[0], args->files->readers[0].fname); } if ( !args->nwrite || args->write[1] ) { OPEN_FILE(1,1); fprintf(args->fh_log,"%s\tfor records private to\t%s\n", args->fnames[1], args->files->readers[1].fname); } if ( !args->nwrite || args->write[0] ) { OPEN_FILE(2,0); fprintf(args->fh_log,"%s\tfor records from %s shared by both\t%s %s\n", args->fnames[2], args->files->readers[0].fname, args->files->readers[0].fname, args->files->readers[1].fname); } if ( !args->nwrite || args->write[1] ) { OPEN_FILE(3,1); fprintf(args->fh_log,"%s\tfor records from %s shared by both\t%s %s\n", args->fnames[3], args->files->readers[1].fname, args->files->readers[0].fname, args->files->readers[1].fname); } } else { // Init one output file for each reader args->fh_out = (htsFile**) calloc(args->files->nreaders, sizeof(htsFile*)); args->fnames = (char**) calloc(args->files->nreaders, sizeof(char*)); for (i=0; ifiles->nreaders; i++) { if ( args->write && !args->write[i] ) continue; if ( args->isec_op==OP_COMPLEMENT && i>0 ) break; OPEN_FILE(i,i); fprintf(args->fh_log,"%s\tfor stripped\t%s\n", args->fnames[i], args->files->readers[i].fname); } #undef OPEN_FILE } args->fh_sites = open_file(NULL, "w", "%s/sites.txt", args->prefix); if ( !args->fh_sites ) error("%s/sites.txt: %s\n", args->prefix, strerror(errno)); } else { if (args->output_fname) { args->fh_sites = fopen(args->output_fname, "w"); if ( args->fh_sites == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno)); } else args->fh_sites = bcftools_stdout; } } static void destroy_data(args_t *args) { int i; if ( args->nflt ) { for (i=0; inflt; i++) { if ( !args->flt[i] ) continue; filter_destroy(args->flt[i]); } free(args->flt_expr); free(args->flt); free(args->flt_logic); } if ( args->prefix ) { fclose(args->fh_log); int n = args->isec_op==OP_VENN ? 4 : args->files->nreaders; for (i=0; ifnames[i] ) continue; if ( hts_close(args->fh_out[i])!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fnames[i]); int is_tbi = !args->write_index || (args->write_index&127) == HTS_FMT_TBI; if ( args->output_type==FT_VCF_GZ && is_tbi ) { tbx_conf_t conf = tbx_conf_vcf; tbx_index_build(args->fnames[i], -1, &conf); } else if ( args->output_type==FT_BCF_GZ || !is_tbi ) { if ( bcf_index_build(args->fnames[i],14) ) error("Could not index %s\n", args->fnames[i]); } free(args->fnames[i]); } free(args->fh_out); free(args->fnames); if ( args->fh_sites ) fclose(args->fh_sites); if ( args->write ) free(args->write); } } static void usage(void) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: Create intersections, unions and complements of VCF files.\n"); fprintf(bcftools_stderr, "Usage: bcftools isec [options] [...]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Options:\n"); fprintf(bcftools_stderr, " -c, --collapse STRING Treat as identical records with , see man page for details [none]\n"); fprintf(bcftools_stderr, " -C, --complement Output positions present only in the first file but missing in the others\n"); fprintf(bcftools_stderr, " -e, --exclude EXPR Exclude sites for which the expression is true\n"); fprintf(bcftools_stderr, " -f, --apply-filters LIST Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n"); fprintf(bcftools_stderr, " -i, --include EXPR Include only sites for which the expression is true\n"); fprintf(bcftools_stderr, " -l, --file-list FILE Read the input file names from the file\n"); fprintf(bcftools_stderr, " --no-version Do not append version and command line to the header\n"); fprintf(bcftools_stderr, " -n, --nfiles [+-=~]INT Output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files\n"); fprintf(bcftools_stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(bcftools_stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(bcftools_stderr, " -p, --prefix DIR If given, subset each of the input files accordingly, see also -w\n"); fprintf(bcftools_stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(bcftools_stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(bcftools_stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(bcftools_stderr, " --threads INT Use multithreading with worker threads [0]\n"); fprintf(bcftools_stderr, " -w, --write LIST List of files to write with -p given as 1-based indexes. By default, all files are written\n"); fprintf(bcftools_stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Examples:\n"); fprintf(bcftools_stderr, " # Create intersection and complements of two sets saving the output in dir/*\n"); fprintf(bcftools_stderr, " bcftools isec A.vcf.gz B.vcf.gz -p dir\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, " # Filter sites in A and B (but not in C) and create intersection\n"); fprintf(bcftools_stderr, " bcftools isec -e'MAF<0.01' -i'dbSNP=1' -e - A.vcf.gz B.vcf.gz C.vcf.gz -p dir\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, " # Extract and write records from A shared by both A and B using exact allele match\n"); fprintf(bcftools_stderr, " bcftools isec A.vcf.gz B.vcf.gz -p dir -n =2 -w 1\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, " # Extract and write records from C found in A and C but not in B\n"); fprintf(bcftools_stderr, " bcftools isec A.vcf.gz B.vcf.gz C.vcf.gz -p dir -n~101 -w 3\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, " # Extract records private to A or B comparing by position only\n"); fprintf(bcftools_stderr, " bcftools isec A.vcf.gz B.vcf.gz -p dir -n -1 -c all\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int main_vcfisec(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->files = bcf_sr_init(); args->argc = argc; args->argv = argv; args->output_fname = NULL; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->clevel = -1; int targets_is_file = 0, regions_is_file = 0; int regions_overlap = 1; int targets_overlap = 0; static struct option loptions[] = { {"help",no_argument,NULL,'h'}, {"exclude",required_argument,NULL,'e'}, {"include",required_argument,NULL,'i'}, {"collapse",required_argument,NULL,'c'}, {"complement",no_argument,NULL,'C'}, {"apply-filters",required_argument,NULL,'f'}, {"file-list",required_argument,NULL,'l'}, {"nfiles",required_argument,NULL,'n'}, {"prefix",required_argument,NULL,'p'}, {"write",required_argument,NULL,'w'}, {"targets",required_argument,NULL,'t'}, {"targets-file",required_argument,NULL,'T'}, {"targets-overlap",required_argument,NULL,4}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,3}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"threads",required_argument,NULL,9}, {"no-version",no_argument,NULL,8}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "hc:r:R:p:n:w:t:T:Cf:o:O:i:e:l:W::",loptions,NULL)) >= 0) { switch (c) { case 'o': args->output_fname = optarg; break; case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'c': if ( !strcmp(optarg,"snps") ) args->files->collapse |= COLLAPSE_SNPS; else if ( !strcmp(optarg,"indels") ) args->files->collapse |= COLLAPSE_INDELS; else if ( !strcmp(optarg,"both") ) args->files->collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS; else if ( !strcmp(optarg,"any") ) args->files->collapse |= COLLAPSE_ANY; else if ( !strcmp(optarg,"all") ) args->files->collapse |= COLLAPSE_ANY; else if ( !strcmp(optarg,"some") ) args->files->collapse |= COLLAPSE_SOME; else if ( !strcmp(optarg,"none") ) args->files->collapse = COLLAPSE_NONE; else error("The --collapse string \"%s\" not recognised.\n", optarg); break; case 'f': args->files->apply_filters = optarg; break; case 'C': if ( args->isec_op!=0 && args->isec_op!=OP_COMPLEMENT ) error("Error: either -C or -n should be given, not both.\n"); args->isec_op = OP_COMPLEMENT; break; case 'l': args->file_list = optarg; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; targets_is_file = 1; break; case 'p': args->prefix = optarg; break; case 'w': if ( args->write_files ) error("The option -w accepts a list of indices and can be given only once\n"); args->write_files = optarg; break; case 'i': add_filter(args, optarg, FLT_INCLUDE); break; case 'e': add_filter(args, optarg, FLT_EXCLUDE); break; case 'n': { if ( args->isec_op!=0 && args->isec_op==OP_COMPLEMENT ) error("Error: either -C or -n should be given, not both.\n"); if ( args->isec_op!=0 ) error("Error: -n should be given only once.\n"); char *p = optarg; if ( *p=='-' ) { args->isec_op = OP_MINUS; p++; } else if ( *p=='+' ) { args->isec_op = OP_PLUS; p++; } else if ( *p=='=' ) { args->isec_op = OP_EQUAL; p++; } else if ( *p=='~' ) { args->isec_op = OP_EXACT; p++; } else if ( isdigit(*p) ) args->isec_op = OP_EQUAL; else error("Could not parse --nfiles %s\n", optarg); if ( args->isec_op == OP_EXACT ) args->isec_exact = p; else if ( sscanf(p,"%d",&args->isec_n)!=1 ) error("Could not parse --nfiles %s\n", optarg); } break; case 3 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 4 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 8 : args->record_cmd_line = 0; break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 'h': case '?': usage(); break; default: error("Unknown argument: %s\n", optarg); } } if ( argc-optind<1 && !args->file_list ) usage(); // no file given int nfiles = 0,i; char **files = NULL; if ( args->file_list ) { files = hts_readlines(args->file_list, &nfiles); if ( !files ) error("Failed to read from %s\n", args->file_list); } if ( optind0; i--) files[n+i-1] = files[n+i-2]; for (i=0; itargets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file,0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( nfiles==2 && !args->isec_op ) { args->isec_op = OP_VENN; if ( !args->prefix ) error("Expected the -p option\n"); } if ( !args->isec_op ) { args->isec_op = OP_PLUS; args->isec_n = 1; } args->files->require_index = 1; for (i=0; ifiles, files[i]) ) error("Failed to open %s: %s\n", files[i],bcf_sr_strerror(args->files->errnum)); free(files[i]); } free(files); init_data(args); isec_vcf(args); destroy_data(args); bcf_sr_destroy(args->files); free(args); return 0; } pysam-0.23.0/bcftools/vcfmerge.c000066400000000000000000004503411475062545500165260ustar00rootroot00000000000000/* vcfmerge.c -- Merge multiple VCF/BCF files to create one multi-sample file. Copyright (C) 2012-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "regidx.h" #include "vcmp.h" #define DBG 0 #define COLLAPSE_SNP_INS_DEL (1<<10) #include KHASH_MAP_INIT_STR(strdict, int) typedef khash_t(strdict) strdict_t; #define FLT_LOGIC_ADD 0 #define FLT_LOGIC_REMOVE 1 #define SKIP_DONE 1 // the record was processed #define SKIP_DIFF 2 // not compatible, merge later #define IS_VL_G(hdr,id) (bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_G) #define IS_VL_A(hdr,id) (bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_A) #define IS_VL_R(hdr,id) (bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_R) #define SWAP(type_t,a,b) { type_t tmp = (a); (a) = (b); (b) = tmp; } #define PL2PROB_MAX 1024 // Rules for merging FORMAT Number=A,G,R vectors with missing values #define MERGE_MISSING_DOT 0 // leave as is, i.e. use a missing value "." #define MERGE_MISSING_CONST 1 // use a constant value #define MERGE_MISSING_MAX 2 // use the existing maximum value typedef struct _missing_rule_t { char *hdr_tag; int type; float value; } missing_rule_t; // For merging INFO Number=A,G,R tags typedef struct { const char *hdr_tag; int type, nvals; int nbuf, mbuf; uint8_t *buf; } AGR_info_t; // Rules for merging arbitrary INFO tags typedef struct _info_rule_t { char *hdr_tag; void (*merger)(bcf_hdr_t *hdr, bcf1_t *line, struct _info_rule_t *rule); int type; // one of BCF_HT_* int block_size; // number of values in a block int type_size; // size of the corresponding BCF_HT_* type int nblocks; // number of blocks in nvals (the number of merged files) int nvals, mvals; // used and total size of vals array void *vals; // the info tag values } info_rule_t; typedef struct { bcf1_t *line; int end, active; // end: 0-based INFO/END } gvcf_aux_t; // Auxiliary merge data for selecting the right combination // of buffered records across multiple readers. maux1_t // corresponds to one buffered line. typedef struct { int skip; int *map; // mapping from input alleles to the array of output alleles (set by merge_alleles) int mmap; // size of map array (only buffer[i].n_allele is actually used) int als_differ; int var_types; // variant types in this record, shifted by <<1 to account for VCF_REF } maux1_t; // Buffered lines for a single reader typedef struct { int rid; // current rid int beg,end; // valid ranges in reader's buffer [beg,end). Maintained by maux_reset and gvcf_flush. int unkn_allele;// the index of the unknown allele (<*>, ) int cur; // current line or -1 if none int mrec; // allocated size of buf maux1_t *rec; // buffer to keep reader's lines bcf1_t **lines; // source buffer: either gvcf or readers' buffer int var_types; // reader's variant types in the active [beg,end] window } buffer_t; typedef struct { int n, pos, var_types; // number of readers; current position; variant types at this position across all available records int *als_types, // allele type of each output allele mals_types; char *chr; // current chromosome char **als, **out_als; // merged alleles (temp, may contain empty records) and merged alleles ready for output int nals, mals, nout_als, mout_als; // size of the output array int *cnt, ncnt; // number of records that refer to the alleles int *smpl_ploidy, *smpl_nGsize; // ploidy and derived number of values in Number=G tags, updated for each line (todo: cache for missing cases) const char **fmt_key;// temporary short-lived array to store output tag names bcf_fmt_t **fmt_map; // i-th output FORMAT field corresponds in j-th reader to i*nreader+j, first row is reserved for GT int nfmt_map; // number of rows in the fmt_map array int *agr_map, nagr_map, magr_map; // mapping between Number=AGR element indexes, from src idxs to dst file idxs void *tmp_arr; size_t ntmp_arr; buffer_t *buf; AGR_info_t *AGR_info; int nAGR_info, mAGR_info; bcf_srs_t *files; int gvcf_min, // min buffered gvcf END position (NB: gvcf_min is 1-based) or 0 if no active lines are present gvcf_break; // 0-based position of a next record which breaks a gVCF block gvcf_aux_t *gvcf; // buffer of gVCF lines, for each reader one line int nout_smpl; kstring_t *str; int32_t *laa; // localized alternate alleles given as input-based indexes in per-sample blocks of (args->local_alleles+1) values, 0 is always first int nlaa, laa_dirty; // number of LAA alleles actually used at this site, and was any L* added? int32_t *tmpi, *k2k; double *tmpd, *pl2prob; // mapping from phred-score likelihoods (PL) to probability int ntmpi, ntmpd, nk2k; } maux_t; typedef struct { vcmp_t *vcmp; maux_t *maux; regidx_t *regs; // apply regions only after the blocks are expanded regitr_t *regs_itr; int header_only, collapse, output_type, force_samples, force_single, merge_by_id, do_gvcf, filter_logic, missing_to_ref, no_index; char *header_fname, *output_fname, *regions_list, *info_rules, *file_list; faidx_t *gvcf_fai; info_rule_t *rules; int nrules; char *missing_rules_str; missing_rule_t *missing_rules; // lookup for -M, --missing-rules int nmissing_rules; strdict_t *tmph; kstring_t tmps; bcf_srs_t *files; bcf1_t *out_line; htsFile *out_fh; bcf_hdr_t *out_hdr; char **argv; int argc, n_threads, record_cmd_line, clevel; int local_alleles; // the value of -L option int keep_AC_AN; char *index_fn; int write_index; int trim_star_allele; // 0=don't trim; 1=trim at variant sites; 2=trim at all sites } args_t; static bcf1_t *maux_get_line(args_t *args, int i) { maux_t *ma = args->maux; int ibuf = ma->buf[i].cur; if ( ibuf >= 0 ) return ma->buf[i].lines[ibuf]; return NULL; } static void info_rules_merge_sum(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule) { if ( !rule->nvals ) return; int i, j, ndim = rule->block_size; #define BRANCH(type_t,is_missing) { \ type_t *ptr = (type_t*) rule->vals; \ for (i=0; invals; i++) if ( is_missing ) ptr[i] = 0; \ for (i=1; inblocks; i++) \ { \ for (j=0; jtype) { case BCF_HT_INT: BRANCH(int32_t, ptr[i]==bcf_int32_missing); break; case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i])); break; default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type); } #undef BRANCH bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type); } static void info_rules_merge_avg(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule) { if ( !rule->nvals ) return; int i, j, ndim = rule->block_size; #define BRANCH(type_t,is_missing) { \ type_t *ptr = (type_t*) rule->vals; \ for (i=0; invals; i++) if ( is_missing ) ptr[i] = 0; \ for (j=0; jnblocks; i++) sum += ptr[j+i*ndim]; \ ptr[j] = sum / rule->nblocks; \ } \ } switch (rule->type) { case BCF_HT_INT: BRANCH(int32_t, ptr[i]==bcf_int32_missing); break; case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i])); break; default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type); } #undef BRANCH bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type); } static void info_rules_merge_min(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule) { if ( !rule->nvals ) return; int i, j, ndim = rule->block_size; #define BRANCH(type_t,is_missing,set_missing,huge_val) { \ type_t *ptr = (type_t*) rule->vals; \ for (i=0; invals; i++) if ( is_missing ) ptr[i] = huge_val; \ for (i=1; inblocks; i++) \ { \ for (j=0; j ptr[j+i*ndim] ) ptr[j] = ptr[j+i*ndim]; \ } \ for (i=0; invals; i++) if ( ptr[i]==huge_val ) set_missing; \ } switch (rule->type) { case BCF_HT_INT: BRANCH(int32_t, ptr[i]==bcf_int32_missing, ptr[i]=bcf_int32_missing, INT32_MAX); break; case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i]), bcf_float_set_missing(ptr[i]), HUGE_VAL); break; default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type); } #undef BRANCH bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type); } static void info_rules_merge_max(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule) { if ( !rule->nvals ) return; int i, j, ndim = rule->block_size; #define BRANCH(type_t,is_missing,set_missing,huge_val) { \ type_t *ptr = (type_t*) rule->vals; \ for (i=0; invals; i++) if ( is_missing ) ptr[i] = huge_val; \ for (i=1; inblocks; i++) \ { \ for (j=0; jnvals; i++) if ( ptr[i]==huge_val ) set_missing; \ } switch (rule->type) { case BCF_HT_INT: BRANCH(int32_t, ptr[i]==bcf_int32_missing, ptr[i]=bcf_int32_missing, INT32_MIN); break; case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i]), bcf_float_set_missing(ptr[i]), -HUGE_VAL); break; default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type); } #undef BRANCH bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type); } static void info_rules_merge_join(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule) { if ( !rule->nvals ) return; if ( rule->type==BCF_HT_STR ) { ((char*)rule->vals)[rule->nvals] = 0; bcf_update_info_string(hdr,line,rule->hdr_tag,rule->vals); } else { int isrc, idst = 0; #define BRANCH(type_t,is_missing,is_vector_end) { \ type_t *ptr = (type_t*) rule->vals; \ for (isrc=0; isrcnvals; isrc++) \ { \ if ( is_vector_end ) break; \ if ( is_missing ) continue; \ if ( idst!=isrc ) ptr[idst] = ptr[isrc]; \ idst++; \ } \ } switch (rule->type) { case BCF_HT_INT: BRANCH(int32_t, ptr[isrc]==bcf_int32_missing, ptr[isrc]==bcf_int32_vector_end); break; case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[isrc]), bcf_float_is_vector_end(ptr[isrc])); break; default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type); } #undef BRANCH rule->nvals = idst; bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,rule->nvals,rule->type); } } static int missing_rules_comp_key2(const void *a, const void *b) { missing_rule_t *rule1 = (missing_rule_t*) a; missing_rule_t *rule2 = (missing_rule_t*) b; return strcmp(rule1->hdr_tag, rule2->hdr_tag); } static int missing_rules_comp_key(const void *a, const void *b) { char *key = (char*) a; missing_rule_t *rule = (missing_rule_t*) b; return strcmp(key, rule->hdr_tag); } static void missing_rules_init(args_t *args) { kstring_t str = {0,0,0}; if ( args->missing_rules_str ) { if ( !strcmp("-",args->missing_rules_str) ) kputs("PL:.,AD:.",&str); else kputs(args->missing_rules_str,&str); } else if ( args->do_gvcf ) kputs("PL:max,AD:0",&str); else return; args->nmissing_rules = 1; char *ss = str.s, *tmp = ss; int n = 0; while ( *ss ) { if ( *ss==':' ) { *ss = 0; n++; if ( n%2==0 ) error("Could not parse --missing-rules: \"%s\"\n", args->missing_rules_str); } else if ( *ss==',' ) { *ss = 0; args->nmissing_rules++; n++; if ( n%2==1 ) error("Could not parse --missing-rules: \"%s\"\n", args->missing_rules_str); } ss++; } if ( n%2==0 ) error("Could not parse --missing-rules: \"%s\"\n", args->missing_rules_str); args->missing_rules = (missing_rule_t*) calloc(args->nmissing_rules,sizeof(missing_rule_t)); n = args->nmissing_rules; args->nmissing_rules = 0; ss = tmp; while ( args->nmissing_rules < n ) { missing_rule_t *rule = &args->missing_rules[args->nmissing_rules]; rule->hdr_tag = strdup(ss); int id = bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, rule->hdr_tag); if ( !bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_FMT,id) ) { if ( args->missing_rules_str ) error("The FORMAT tag is not defined in the header: \"%s\"\n", rule->hdr_tag); free(rule->hdr_tag); n--; ss = strchr(ss, '\0'); ss++; if ( !*ss ) error("Could not parse --missing-rules, missing logic of \"%s\"\n", rule->hdr_tag); ss = strchr(ss, '\0'); ss++; continue; } ss = strchr(ss, '\0'); ss++; if ( !*ss ) error("Could not parse --missing-rules, missing logic of \"%s\"\n", rule->hdr_tag); if ( !strcasecmp(ss,".") ) rule->type = MERGE_MISSING_DOT; else if ( !strcasecmp(ss,"max") ) rule->type = MERGE_MISSING_MAX; else { char *tmp = ss; rule->value = strtod(ss, &tmp); if ( *tmp ) error("Could not parse --missing-rules: \"%s\"\n", args->missing_rules_str); rule->type = MERGE_MISSING_CONST; } ss = strchr(ss, '\0'); ss++; args->nmissing_rules++; } qsort(args->missing_rules, args->nmissing_rules, sizeof(*args->missing_rules), missing_rules_comp_key2); free(str.s); } static void missing_rules_destroy(args_t *args) { int i; for (i=0; inmissing_rules; i++) { missing_rule_t *rule = &args->missing_rules[i]; free(rule->hdr_tag); } free(args->missing_rules); } static int info_rules_comp_key2(const void *a, const void *b) { info_rule_t *rule1 = (info_rule_t*) a; info_rule_t *rule2 = (info_rule_t*) b; return strcmp(rule1->hdr_tag, rule2->hdr_tag); } static int info_rules_comp_key(const void *a, const void *b) { char *key = (char*) a; info_rule_t *rule = (info_rule_t*) b; return strcmp(key, rule->hdr_tag); } static void info_rules_init(args_t *args) { if ( args->info_rules && !strcmp("-",args->info_rules) ) return; kstring_t str = {0,0,0}; if ( !args->info_rules ) { if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "DP")) ) kputs("DP:sum",&str); if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "DP4")) ) { if ( str.l ) kputc(',',&str); kputs("DP4:sum",&str); } if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "QS")) ) { if ( str.l ) kputc(',',&str); kputs("QS:sum",&str); } if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "MIN_DP")) ) { if ( str.l ) kputc(',',&str); kputs("MIN_DP:min",&str); } if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "MinDP")) ) { if ( str.l ) kputc(',',&str); kputs("MinDP:min",&str); } if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "I16")) ) { if ( str.l ) kputc(',',&str); kputs("I16:sum",&str); } if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "IDV")) ) { if ( str.l ) kputc(',',&str); kputs("IDV:max",&str); } if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "IMF")) ) { if ( str.l ) kputc(',',&str); kputs("IMF:max",&str); } if ( !bcf_hdr_nsamples(args->out_hdr) ) { if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "AN")) ) { if ( str.l ) kputc(',',&str); kputs("AN:sum",&str); } if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "AC")) ) { if ( str.l ) kputc(',',&str); kputs("AC:sum",&str); } } if ( !str.l ) return; args->info_rules = str.s; } args->nrules = 1; char *ss = strdup(args->info_rules), *tmp = ss; int n = 0; while ( *ss ) { if ( *ss==':' ) { *ss = 0; n++; if ( n%2==0 ) error("Could not parse INFO rules: \"%s\"\n", args->info_rules); } else if ( *ss==',' ) { *ss = 0; args->nrules++; n++; if ( n%2==1 ) error("Could not parse INFO rules: \"%s\"\n", args->info_rules); } ss++; } if ( n%2==0 ) error("Could not parse INFO rules: \"%s\"\n", args->info_rules); args->rules = (info_rule_t*) calloc(args->nrules,sizeof(info_rule_t)); n = 0; ss = tmp; while ( n < args->nrules ) { info_rule_t *rule = &args->rules[n]; rule->hdr_tag = strdup(ss); int id = bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, rule->hdr_tag); if ( !bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,id) ) error("The INFO tag is not defined in the header: \"%s\"\n", rule->hdr_tag); rule->type = bcf_hdr_id2type(args->out_hdr,BCF_HL_INFO,id); if ( rule->type==BCF_HT_INT ) rule->type_size = sizeof(int32_t); else if ( rule->type==BCF_HT_REAL ) rule->type_size = sizeof(float); else if ( rule->type==BCF_HT_STR ) rule->type_size = sizeof(char); else error("The INFO rule \"%s\" is not supported; the tag \"%s\" type is %d\n", ss,rule->hdr_tag,rule->type); if ( !strcmp(rule->hdr_tag,"AC") || !strcmp(rule->hdr_tag,"AN") ) args->keep_AC_AN = 1; ss = strchr(ss, '\0'); ss++; if ( !*ss ) error("Could not parse INFO rules, missing logic of \"%s\"\n", rule->hdr_tag); int is_join = 0; if ( !strcasecmp(ss,"sum") ) rule->merger = info_rules_merge_sum; else if ( !strcasecmp(ss,"avg") ) rule->merger = info_rules_merge_avg; else if ( !strcasecmp(ss,"min") ) rule->merger = info_rules_merge_min; else if ( !strcasecmp(ss,"max") ) rule->merger = info_rules_merge_max; else if ( !strcasecmp(ss,"join") ) { rule->merger = info_rules_merge_join; is_join = 1; } else error("The rule logic \"%s\" not recognised\n", ss); if ( !is_join && rule->type==BCF_HT_STR ) error("Numeric operation \"%s\" requested on non-numeric field: %s\n", ss, rule->hdr_tag); if ( bcf_hdr_id2number(args->out_hdr,BCF_HL_INFO,id)==0xfffff ) { int is_agr = ( bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)==BCF_VL_A || bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)==BCF_VL_G || bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)==BCF_VL_R ) ? 1 : 0; if ( is_join && bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)!=BCF_VL_VAR ) { bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->out_hdr, BCF_HL_INFO, "ID", rule->hdr_tag, NULL); hrec = bcf_hrec_dup(hrec); int i = bcf_hrec_find_key(hrec, "Number"); if ( i<0 ) error("Uh, could not find the entry Number in the header record of %s\n",rule->hdr_tag); free(hrec->vals[i]); hrec->vals[i] = strdup("."); bcf_hdr_remove(args->out_hdr,BCF_HL_INFO, rule->hdr_tag); bcf_hdr_add_hrec(args->out_hdr, hrec); } if ( !is_join && !is_agr ) error("Only fixed-length vectors are supported with -i %s:%s\n", ss, rule->hdr_tag); } ss = strchr(ss, '\0'); ss++; n++; } free(str.s); free(tmp); qsort(args->rules, args->nrules, sizeof(*args->rules), info_rules_comp_key2); } static void info_rules_destroy(args_t *args) { int i; for (i=0; inrules; i++) { info_rule_t *rule = &args->rules[i]; free(rule->hdr_tag); free(rule->vals); } free(args->rules); } static void info_rules_reset(args_t *args) { int i; for (i=0; inrules; i++) args->rules[i].nblocks = args->rules[i].nvals = args->rules[i].block_size = 0; } static int info_rules_add_values(args_t *args, bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule, maux1_t *als, int var_len) { int msize = args->maux->ntmp_arr / rule->type_size; int ret = bcf_get_info_values(hdr, line, rule->hdr_tag, &args->maux->tmp_arr, &msize, rule->type); if ( ret<=0 ) error("FIXME: error parsing %s at %s:%"PRId64" .. %d\n", rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1,ret); args->maux->ntmp_arr = msize * rule->type_size; rule->nblocks++; if ( rule->type==BCF_HT_STR ) { int need_comma = rule->nblocks==1 ? 0 : 1; hts_expand(char,rule->nvals+ret+need_comma+1,rule->mvals,rule->vals); // 1 for null-termination char *tmp = (char*) rule->vals + rule->nvals; if ( rule->nvals>0 ) { *tmp = ','; tmp++; } strncpy(tmp,(char*)args->maux->tmp_arr,ret); rule->nvals += ret + need_comma; return 1; } int i, j; if ( var_len==BCF_VL_A ) { if ( ret!=line->n_allele-1 ) error("Wrong number of %s fields at %s:%"PRId64"\n",rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1); args->maux->nagr_map = ret; hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map); // create mapping from source file ALT indexes to dst file indexes for (i=0; imaux->agr_map[i] = als->map[i+1] - 1; rule->block_size = args->maux->nout_als - 1; } else if ( var_len==BCF_VL_R ) { if ( ret!=line->n_allele ) error("Wrong number of %s fields at %s:%"PRId64"\n",rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1); args->maux->nagr_map = ret; hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map); for (i=0; imaux->agr_map[i] = als->map[i]; rule->block_size = args->maux->nout_als; } else if ( var_len==BCF_VL_G ) { args->maux->nagr_map = bcf_alleles2gt(line->n_allele-1,line->n_allele-1)+1; if ( ret!=line->n_allele && ret!=args->maux->nagr_map ) error("Wrong number of %s fields at %s:%"PRId64"\n",rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1); if ( ret==line->n_allele ) // haploid { args->maux->nagr_map = line->n_allele; hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map); for (i=0; imaux->agr_map[i] = als->map[i]; rule->block_size = args->maux->nout_als; } else { hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map); int k_src = 0; for (i=0; in_allele; i++) { for (j=0; j<=i; j++) { args->maux->agr_map[k_src] = bcf_alleles2gt(als->map[i],als->map[j]); k_src++; } } rule->block_size = bcf_alleles2gt(args->maux->nout_als-1,args->maux->nout_als-1)+1; } } else { if ( rule->nblocks>1 && ret!=rule->block_size ) error("Mismatch in number of values for INFO/%s at %s:%"PRId64"\n", rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1); rule->block_size = ret; args->maux->nagr_map = 0; } #define BRANCH(src_type_t,dst_type_t,set_missing) { \ src_type_t *src = (src_type_t *) args->maux->tmp_arr; \ hts_expand0(dst_type_t,(rule->nvals+rule->block_size),rule->mvals,rule->vals); \ dst_type_t *dst = (dst_type_t *) rule->vals + rule->nvals; \ rule->nvals += rule->block_size; \ if ( !args->maux->nagr_map ) \ { \ for (i=0; iblock_size; i++) set_missing; \ for (i=0; imaux->agr_map[i]] = src[i]; \ } \ } switch (rule->type) { case BCF_HT_INT: BRANCH(int, int32_t, dst[i] = bcf_int32_missing); break; case BCF_HT_REAL: BRANCH(float, float, bcf_float_set_missing(dst[i])); break; default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type); } #undef BRANCH return 1; } int bcf_hdr_sync(bcf_hdr_t *h); void merge_headers(bcf_hdr_t *hw, const bcf_hdr_t *hr, const char *clash_prefix, int force_samples) { // header lines hw = bcf_hdr_merge(hw, hr); // samples int i; for (i=0; isamples[i]; while ( bcf_hdr_id2int(hw, BCF_DT_SAMPLE, name)!=-1 ) { // there is a sample with the same name if ( !force_samples ) error("Error: Duplicate sample names (%s), use --force-samples to proceed anyway.\n", name); // Resolve conflicting samples names. For example, replace: // A + A with A,2:A // A,2:A + A with A,2:A,2:2:A int len = strlen(name) + strlen(clash_prefix) + 1; char *tmp = (char*) malloc(sizeof(char)*(len+1)); sprintf(tmp,"%s:%s",clash_prefix,name); free(rmme); rmme = name = tmp; } bcf_hdr_add_sample(hw,name); free(rmme); } } void debug_als(char **als, int nals) { int k; for (k=0; k=lens[j] ) done = 1; if ( als[j][lens[j]-i] != als[0][lens[0]-i] ) { done = 1; break; } } if ( done ) break; i++; } if ( i>1 ) { i--; als[0][lens[0]-i] = 0; for (j=1; j0, * 1->2, and 2->3. */ char **merge_alleles(char **a, int na, int *map, char **b, int *nb, int *mb) { // reference allele never changes map[0] = 0; int i,j; int rla = !a[0][1] ? 1 : strlen(a[0]); int rlb = !b[0][1] ? 1 : strlen(b[0]); // the most common case: same SNPs if ( na==2 && *nb==2 && rla==1 && rlb==1 && a[1][0]==b[1][0] && !a[1][1] && !b[1][1] ) { map[1] = 1; return b; } // Sanity check: reference prefixes must be identical if ( strncmp(a[0],b[0],rlarlb ) { for (i=0; i<*nb; i++) { if ( b[i][0]=='<' ) continue; // symbolic allele, do not modify if ( b[i][0]=='*' ) continue; // overlapping deletion (*), do not modify int l = strlen(b[i]); b[i] = (char*) realloc(b[i],l+rla-rlb+1); memcpy(b[i]+l,a[0]+rlb,rla-rlb+1); } } // now check if the $a alleles are present and if not add them for (i=1; irla && a[i][0]!='<' && a[i][0]!='*' ) // $a alleles need expanding and not a symbolic allele or * { int l = strlen(a[i]); ai = (char*) malloc(l+rlb-rla+1); memcpy(ai,a[i],l); memcpy(ai+l,b[0]+rla,rlb-rla+1); const_ai = 0; } else ai = a[i]; for (j=1; j<*nb; j++) if ( !strcasecmp(ai,b[j]) ) break; if ( j<*nb ) // $b already has the same allele { map[i] = j; if ( !const_ai ) free(ai); continue; } // new allele map[i] = *nb; b[*nb] = const_ai ? strdup(ai) : ai; (*nb)++; } return b; } maux_t *maux_init(args_t *args) { bcf_srs_t *files = args->files; maux_t *ma = (maux_t*) calloc(1,sizeof(maux_t)); ma->n = files->nreaders; ma->files = files; int i, n_smpl = 0; for (i=0; in; i++) n_smpl += bcf_hdr_nsamples(files->readers[i].header); ma->nout_smpl = n_smpl; assert( n_smpl==bcf_hdr_nsamples(args->out_hdr) ); if ( args->do_gvcf ) { ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n for (i=0; in; i++) ma->gvcf[i].line = bcf_init1(); } ma->smpl_ploidy = (int*) calloc(n_smpl,sizeof(int)); ma->smpl_nGsize = (int*) malloc(n_smpl*sizeof(int)); ma->buf = (buffer_t*) calloc(ma->n,sizeof(buffer_t)); for (i=0; in; i++) ma->buf[i].rid = -1; ma->str = (kstring_t*) calloc(n_smpl,sizeof(kstring_t)); if ( args->local_alleles ) { ma->laa = (int32_t*)malloc(sizeof(*ma->laa)*ma->nout_smpl*(1+args->local_alleles)); ma->pl2prob = (double*)malloc(PL2PROB_MAX*sizeof(*ma->pl2prob)); for (i=0; ipl2prob[i] = pow(10,-0.1*i); } return ma; } void maux_destroy(maux_t *ma) { int i,j; for (i=0; inout_smpl; i++) free(ma->str[i].s); free(ma->str); free(ma->als_types); for (i=0; imals; i++) { free(ma->als[i]); ma->als[i] = NULL; } for (i=0; in; i++) // for each reader { for (j=0; jbuf[i].mrec; j++) // for each buffered line free(ma->buf[i].rec[j].map); free(ma->buf[i].rec); } free(ma->buf); if ( ma->gvcf ) { for (i=0; in; i++) bcf_destroy(ma->gvcf[i].line); free(ma->gvcf); } for (i=0; imAGR_info; i++) free(ma->AGR_info[i].buf); free(ma->agr_map); free(ma->AGR_info); if (ma->ntmp_arr) free(ma->tmp_arr); if (ma->nfmt_map) free(ma->fmt_map); free(ma->fmt_key); // ma->inf freed in bcf_destroy1 for (i=0; imals; i++) free(ma->als[i]); if (ma->mout_als) free(ma->out_als); free(ma->als); free(ma->cnt); free(ma->smpl_ploidy); free(ma->smpl_nGsize); free(ma->chr); free(ma->laa); free(ma->tmpi); free(ma->k2k); free(ma->tmpd); free(ma->pl2prob); free(ma); } void maux_expand1(buffer_t *buf, int size) { if ( buf->mrec < size ) { hts_expand0(maux1_t,size,buf->mrec,buf->rec); buf->mrec = size; } } void maux_reset(maux_t *ma, int *rid_tab) { int i,j; for (i=0; in; i++) maux_expand1(&ma->buf[i],ma->files->readers[i].nbuffer+1); for (i=0; imals; i++) { free(ma->als[i]); ma->als[i] = NULL; } const char *chr = NULL; ma->nals = 0; ma->pos = -1; for (i=0; in; i++) { if ( !bcf_sr_has_line(ma->files,i) ) continue; bcf1_t *line = bcf_sr_get_line(ma->files,i); bcf_hdr_t *hdr = bcf_sr_get_header(ma->files,i); chr = bcf_seqname(hdr,line); ma->pos = line->pos; break; } int new_chr = 0; if ( chr && (!ma->chr || strcmp(ma->chr,chr)) ) { free(ma->chr); ma->chr = strdup(chr); new_chr = 1; } for (i=0; in; i++) { bcf_hdr_t *hdr = bcf_sr_get_header(ma->files,i); if (new_chr) rid_tab[i] = bcf_hdr_name2id(hdr,chr); ma->buf[i].rid = rid_tab[i]; ma->buf[i].beg = bcf_sr_has_line(ma->files,i) ? 0 : 1; for (j=ma->buf[i].beg; j<=ma->files->readers[i].nbuffer; j++) { ma->buf[i].rec[j].skip = 0; ma->buf[i].rec[j].var_types = 0; bcf1_t *line = ma->files->readers[i].buffer[j]; if ( line->rid!=ma->buf[i].rid || line->pos!=ma->pos ) break; } ma->buf[i].end = j; ma->buf[i].cur = -1; if ( ma->buf[i].beg < ma->buf[i].end ) { ma->buf[i].lines = ma->files->readers[i].buffer; if ( ma->gvcf ) ma->gvcf[i].active = 0; // gvcf block cannot overlap with the next record } if ( new_chr && ma->gvcf ) ma->gvcf[i].active = 0; // make sure to close active gvcf block on new chr } } void maux_debug(maux_t *ma, int ir, int ib) { printf("[%d,%d]\t", ir,ib); int i; for (i=0; inals; i++) { printf(" %s [%d]", ma->als[i], ma->cnt[i]); } printf("\n"); } void merge_chrom2qual(args_t *args, bcf1_t *out) { bcf_srs_t *files = args->files; bcf_hdr_t *out_hdr = args->out_hdr; int i, ret; khiter_t kitr; strdict_t *tmph = args->tmph; kh_clear(strdict, tmph); kstring_t *tmps = &args->tmps; tmps->l = 0; maux_t *ma = args->maux; int *al_idxs = (int*) calloc(ma->nals,sizeof(int)); bcf_float_set_missing(out->qual); // CHROM, POS, ID, QUAL out->pos = -1; for (i=0; inreaders; i++) { bcf1_t *line = maux_get_line(args, i); if ( !line ) continue; bcf_unpack(line, BCF_UN_ALL); bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; // not all maux alleles are always used, mark the ones we'll need int j; for (j=1; jn_allele; j++) { int irec = ma->buf[i].cur; al_idxs[ ma->buf[i].rec[irec].map[j] ] = 1; } // position if ( out->pos==-1 ) { const char *chr = hdr->id[BCF_DT_CTG][line->rid].key; out->rid = bcf_hdr_name2id(out_hdr, chr); if ( strcmp(chr,out_hdr->id[BCF_DT_CTG][out->rid].key) ) error("Uh\n"); out->pos = line->pos; } // ID if ( line->d.id[0]!='.' || line->d.id[1] ) { kitr = kh_get(strdict, tmph, line->d.id); if ( kitr == kh_end(tmph) ) { if ( tmps->l ) kputc(';', tmps); kputs(line->d.id, tmps); kh_put(strdict, tmph, line->d.id, &ret); } } // set QUAL to the max qual value. Not exactly correct, but good enough for now if ( !bcf_float_is_missing(line->qual) ) { if ( bcf_float_is_missing(out->qual) || out->qual < line->qual ) out->qual = line->qual; } } // set ID if ( !tmps->l ) kputs(".", tmps); bcf_update_id(out_hdr, out, tmps->s); // set alleles ma->nout_als = 0; for (i=1; inals; i++) { if ( !al_idxs[i] ) continue; ma->nout_als++; // Adjust the indexes, the allele map could be created for multiple collapsed records, // some of which might be unused for this output line int ir, j; for (ir=0; irnreaders; ir++) { ma->buf[ir].unkn_allele = 0; bcf1_t *line = maux_get_line(args,ir); if ( !line ) continue; for (j=1; jn_allele; j++) { int irec = ma->buf[ir].cur; if ( ma->buf[ir].rec[irec].map[j]==i ) ma->buf[ir].rec[irec].map[j] = ma->nout_als; if ( bcf_has_variant_type(line,j,VCF_REF) && line->d.allele[j][0]=='<' ) ma->buf[ir].unkn_allele = j; } } } // Expand the arrays and realloc the alleles string. Note that all alleles are in a single allocated block. ma->nout_als++; hts_expand0(char*, ma->nout_als, ma->mout_als, ma->out_als); int k = 0; for (i=0; inals; i++) if ( i==0 || al_idxs[i] ) ma->out_als[k++] = strdup(ma->als[i]); if ( k!=ma->nout_als ) error("Error: could not merge alleles at %s:%"PRId64", sanity check failed: %d!=%d\n",bcf_seqname(out_hdr,out),out->pos+1,k,ma->nout_als); normalize_alleles(ma->out_als, ma->nout_als); bcf_update_alleles(out_hdr, out, (const char**) ma->out_als, ma->nout_als); free(al_idxs); for (i=0; inout_als; i++) free(ma->out_als[i]); } void merge_filter(args_t *args, bcf1_t *out) { bcf_srs_t *files = args->files; bcf_hdr_t *out_hdr = args->out_hdr; int i, ret; if ( args->filter_logic == FLT_LOGIC_REMOVE ) { for (i=0; inreaders; i++) { bcf1_t *line = maux_get_line(args, i); if ( !line ) continue; bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; if ( bcf_has_filter(hdr, line, "PASS") ) break; } if ( inreaders ) { int flt_id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, "PASS"); bcf_add_filter(out_hdr, out, flt_id); return; } } khiter_t kitr; strdict_t *tmph = args->tmph; kh_clear(strdict, tmph); out->d.n_flt = 0; for (i=0; inreaders; i++) { bcf1_t *line = maux_get_line(args, i); if ( !line ) continue; bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; int k; for (k=0; kd.n_flt; k++) { const char *flt = hdr->id[BCF_DT_ID][line->d.flt[k]].key; kitr = kh_get(strdict, tmph, flt); if ( kitr == kh_end(tmph) ) { int id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, flt); if ( id==-1 ) error("Error: The filter is not defined in the header: %s\n", flt); hts_expand(int,out->d.n_flt+1,out->d.m_flt,out->d.flt); out->d.flt[out->d.n_flt] = id; out->d.n_flt++; kh_put(strdict, tmph, flt, &ret); } } } // Check if PASS is not mixed with other filters if ( out->d.n_flt>1 ) { int id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, "PASS"); for (i=0; id.n_flt; i++) if ( out->d.flt[i]==id ) break; if ( id.n_flt ) { out->d.n_flt--; for (; id.n_flt; i++) out->d.flt[i] = out->d.flt[i+1]; } } } static void bcf_info_set_id(bcf1_t *line, bcf_info_t *info, int id, kstring_t *tmp_str) { uint8_t *ptr = info->vptr - info->vptr_off; bcf_dec_typed_int1(ptr, &ptr); tmp_str->l = 0; bcf_enc_int1(tmp_str, id); if ( tmp_str->l == ptr - info->vptr + info->vptr_off ) { // the new id is represented with the same number of bytes memcpy(info->vptr - info->vptr_off, tmp_str->s, tmp_str->l); return; } kputsn_(ptr, info->vptr - ptr, tmp_str); info->vptr_off = tmp_str->l; kputsn_(info->vptr, info->len << bcf_type_shift[info->type], tmp_str); info->vptr = (uint8_t*) tmp_str->s + info->vptr_off; tmp_str->s = NULL; tmp_str->m = 0; tmp_str->l = 0; } /* * copy_string_field() - copy a comma-separated field * @param src: source string * @param isrc: index of the field to copy * @param src_len: length of source string (excluding the terminating \0) * @param dst: destination kstring (must be initialized with missing values, e.g. as ".") * @param idst: index of the destination field */ int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst) { int ith_src = 0, start_src = 0; // i-th field in src string while ( ith_srcl ) { if ( dst->s[start_dst]==',' ) { ith_dst++; } start_dst++; } if ( ith_dst!=idst ) return -2; int end_dst = start_dst; while ( end_dstl && dst->s[end_dst]!=',' ) end_dst++; if ( end_dst - start_dst>1 || dst->s[start_dst]!='.' ) return 0; // do not overwrite non-empty values // Now start_dst and end_dst are indexes to the destination memory area // which needs to be replaced with nsrc_cpy // source bytes, end_dst points just after. int ndst_shift = nsrc_cpy - (end_dst - start_dst); int ndst_move = dst->l - end_dst + 1; // how many bytes must be moved (including \0) if ( ndst_shift ) { ks_resize(dst, dst->l + ndst_shift + 1); // plus \0 memmove(dst->s+end_dst+ndst_shift, dst->s+end_dst, ndst_move); } memcpy(dst->s+start_dst, src+start_src, nsrc_cpy); dst->l += ndst_shift; return 0; } static void merge_AGR_info_tag(bcf_hdr_t *hdr, bcf1_t *line, bcf_info_t *info, int len, maux1_t *als, AGR_info_t *agr) { int i; if ( !agr->nbuf ) { if ( info->type==BCF_BT_INT8 || info->type==BCF_BT_INT16 || info->type==BCF_BT_INT32 || info->type==BCF_BT_FLOAT ) { agr->nbuf = 4 * agr->nvals; hts_expand(uint8_t,agr->nbuf,agr->mbuf,agr->buf); if ( info->type!=BCF_BT_FLOAT ) { int32_t *tmp = (int32_t*) agr->buf; for (i=0; invals; i++) tmp[i] = bcf_int32_missing; } else { float *tmp = (float*) agr->buf; for (i=0; invals; i++) bcf_float_set_missing(tmp[i]); } } else if ( info->type==BCF_BT_CHAR ) { kstring_t tmp; tmp.l = 0; tmp.m = agr->mbuf; tmp.s = (char*)agr->buf; kputc('.',&tmp); for (i=1; invals; i++) kputs(",.",&tmp); agr->mbuf = tmp.m; agr->nbuf = tmp.l; agr->buf = (uint8_t*)tmp.s; } else error("Not ready for type [%d]: %s at %"PRId64"\n", info->type,agr->hdr_tag,(int64_t) line->pos+1); } if ( info->type==BCF_BT_INT8 || info->type==BCF_BT_INT16 || info->type==BCF_BT_INT32 || info->type==BCF_BT_FLOAT ) { if ( len==BCF_VL_A || len==BCF_VL_R ) { int ifrom = len==BCF_VL_A ? 1 : 0; #define BRANCH(type_t, convert, is_missing, is_vector_end, out_type_t) { \ uint8_t *src = info->vptr; \ out_type_t *tgt = (out_type_t *) agr->buf; \ int iori, inew; \ for (iori=ifrom; iorin_allele; iori++, src += sizeof(type_t)) \ { \ type_t val = convert(src); \ if ( is_vector_end ) break; \ if ( is_missing ) continue; \ inew = als->map[iori] - ifrom; \ tgt[inew] = val; \ } \ } switch (info->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, int); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, int); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, val==bcf_int32_missing, val==bcf_int32_vector_end, int); break; case BCF_BT_FLOAT: BRANCH(float, le_to_float, bcf_float_is_missing(val), bcf_float_is_vector_end(val), float); break; default: fprintf(stderr,"TODO: %s:%d .. info->type=%d\n", __FILE__,__LINE__, info->type); exit(1); } #undef BRANCH } else { #define BRANCH(type_t, convert, is_missing, is_vector_end, out_type_t) { \ uint8_t *src = info->vptr; \ out_type_t *tgt = (out_type_t *) agr->buf; \ int iori,jori, inew,jnew; \ for (iori=0; iorin_allele; iori++) \ { \ inew = als->map[iori]; \ for (jori=0; jori<=iori; jori++) \ { \ jnew = als->map[jori]; \ int kori = iori*(iori+1)/2 + jori; \ type_t val = convert(&src[kori * sizeof(type_t)]); \ if ( is_vector_end ) break; \ if ( is_missing ) continue; \ int knew = inew>jnew ? inew*(inew+1)/2 + jnew : jnew*(jnew+1)/2 + inew; \ tgt[knew] = val; \ } \ if ( jori<=iori ) break; \ } \ } switch (info->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, int); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, int); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, val==bcf_int32_missing, val==bcf_int32_vector_end, int); break; case BCF_BT_FLOAT: BRANCH(float, le_to_float, bcf_float_is_missing(val), bcf_float_is_vector_end(val), float); break; default: fprintf(stderr,"TODO: %s:%d .. info->type=%d\n", __FILE__,__LINE__, info->type); exit(1); } #undef BRANCH } } else { kstring_t tmp; tmp.l = agr->nbuf; tmp.m = agr->mbuf; tmp.s = (char*)agr->buf; if ( len==BCF_VL_A || len==BCF_VL_R ) { int iori, ifrom = len==BCF_VL_A ? 1 : 0; for (iori=ifrom; iorin_allele; iori++) { int ret = copy_string_field((char*)info->vptr, iori-ifrom, info->len, &tmp, als->map[iori]-ifrom); if ( ret ) error("Error at %s:%"PRId64": wrong number of fields in %s?\n", bcf_seqname(hdr,line),(int64_t) line->pos+1,agr->hdr_tag); } } else { int iori,jori, inew,jnew; for (iori=0; iorin_allele; iori++) { inew = als->map[iori]; for (jori=0; jori<=iori; jori++) { jnew = als->map[jori]; int kori = iori*(iori+1)/2 + jori; int knew = bcf_alleles2gt(inew,jnew); int ret = copy_string_field((char*)info->vptr, kori, info->len, &tmp, knew); if ( ret ) error("Error at %s:%"PRId64": wrong number of fields in %s?\n", bcf_seqname(hdr,line),(int64_t) line->pos+1,agr->hdr_tag); } } } agr->mbuf = tmp.m; agr->nbuf = tmp.l; agr->buf = (uint8_t*)tmp.s; } } void merge_info(args_t *args, bcf1_t *out) { bcf_srs_t *files = args->files; bcf_hdr_t *out_hdr = args->out_hdr; int i, j, ret; khiter_t kitr; strdict_t *tmph = args->tmph; kh_clear(strdict, tmph); maux_t *ma = args->maux; ma->nAGR_info = 0; out->n_info = 0; info_rules_reset(args); for (i=0; inreaders; i++) { bcf1_t *line = maux_get_line(args,i); if ( !line ) continue; int irec = ma->buf[i].cur; bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; for (j=0; jn_info; j++) { bcf_info_t *inf = &line->d.info[j]; const char *key = hdr->id[BCF_DT_ID][inf->key].key; // AC and AN are done in merge_format() after genotypes are done if (!args->keep_AC_AN && (key[0] == 'A' && (key[1] == 'C' || key[1] == 'N') && key[2] == 0)) continue; int id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, key); if ( id==-1 ) error("Error: The INFO field is not defined in the header: %s\n", key); kitr = kh_get(strdict, tmph, key); // have we seen the tag in one of the readers? int len = bcf_hdr_id2length(hdr,BCF_HL_INFO,inf->key); if ( args->nrules ) { info_rule_t *rule = (info_rule_t*) bsearch(key, args->rules, args->nrules, sizeof(*args->rules), info_rules_comp_key); if ( rule ) { maux1_t *als = ( len==BCF_VL_A || len==BCF_VL_G || len==BCF_VL_R ) ? &ma->buf[i].rec[irec] : NULL; if ( info_rules_add_values(args, hdr, line, rule, als, len) ) continue; } } // Todo: Number=AGR tags should use the newer info_rules_* functions (info_rules_merge_first to be added) // and merge_AGR_info_tag to be made obsolete. if ( len==BCF_VL_A || len==BCF_VL_G || len==BCF_VL_R ) // Number=R,G,A requires special treatment { if ( kitr == kh_end(tmph) ) { // seeing this key for the first time ma->nAGR_info++; hts_expand0(AGR_info_t,ma->nAGR_info,ma->mAGR_info,ma->AGR_info); kitr = kh_put(strdict, tmph, key, &ret); kh_val(tmph,kitr) = ma->nAGR_info - 1; ma->AGR_info[ma->nAGR_info-1].hdr_tag = key; ma->AGR_info[ma->nAGR_info-1].type = bcf_hdr_id2type(hdr,BCF_HL_INFO,inf->key); ma->AGR_info[ma->nAGR_info-1].nbuf = 0; // size of the buffer switch (len) { case BCF_VL_A: ma->AGR_info[ma->nAGR_info-1].nvals = ma->nout_als - 1; break; case BCF_VL_G: ma->AGR_info[ma->nAGR_info-1].nvals = bcf_alleles2gt(ma->nout_als-1,ma->nout_als-1)+1; break; case BCF_VL_R: ma->AGR_info[ma->nAGR_info-1].nvals = ma->nout_als; break; } } kitr = kh_get(strdict, tmph, key); int idx = kh_val(tmph, kitr); if ( idx<0 ) error("Error occurred while processing INFO tag \"%s\" at %s:%"PRId64"\n", key,bcf_seqname(hdr,line),(int64_t) line->pos+1); merge_AGR_info_tag(hdr, line,inf,len,&ma->buf[i].rec[irec],&ma->AGR_info[idx]); continue; } if ( kitr == kh_end(tmph) ) { // Seeing this key for the first time. Although quite hacky, // this is faster than anything else given the data structures.. hts_expand0(bcf_info_t,out->n_info+1,out->d.m_info,out->d.info); out->d.info[out->n_info].key = id; out->d.info[out->n_info].type = inf->type; out->d.info[out->n_info].len = inf->len; out->d.info[out->n_info].v1.i = inf->v1.i; out->d.info[out->n_info].v1.f = inf->v1.f; out->d.info[out->n_info].vptr_off = inf->vptr_off; out->d.info[out->n_info].vptr_len = inf->vptr_len; out->d.info[out->n_info].vptr_free = 1; out->d.info[out->n_info].vptr = (uint8_t*) malloc(inf->vptr_len+inf->vptr_off); memcpy(out->d.info[out->n_info].vptr,inf->vptr-inf->vptr_off, inf->vptr_len+inf->vptr_off); out->d.info[out->n_info].vptr += inf->vptr_off; if ( (args->output_type & FT_BCF) && id!=bcf_hdr_id2int(hdr, BCF_DT_ID, key) ) bcf_info_set_id(out, &out->d.info[out->n_info], id, &args->tmps); out->d.shared_dirty |= BCF1_DIRTY_INF; out->n_info++; kitr = kh_put(strdict, tmph, key, &ret); kh_val(tmph,kitr) = -(out->n_info-1); // arbitrary negative value } } } for (i=0; inrules; i++) args->rules[i].merger(args->out_hdr, out, &args->rules[i]); for (i=0; inAGR_info; i++) { AGR_info_t *agr = &ma->AGR_info[i]; bcf_update_info(out_hdr,out,agr->hdr_tag,agr->buf,agr->nvals,agr->type); } } void update_AN_AC(bcf_hdr_t *hdr, bcf1_t *line) { int32_t an = 0, *tmp = (int32_t*) malloc(sizeof(int)*line->n_allele); int ret = bcf_calc_ac(hdr, line, tmp, BCF_UN_FMT); if ( ret>0 ) { int i; for (i=0; in_allele; i++) an += tmp[i]; bcf_update_info_int32(hdr, line, "AN", &an, 1); bcf_update_info_int32(hdr, line, "AC", tmp+1, line->n_allele-1); } free(tmp); } static inline int max_used_gt_ploidy(bcf_fmt_t *fmt, int nsmpl) { int i,j, max_ploidy = 0; #define BRANCH(type_t, convert, vector_end) { \ uint8_t *ptr = fmt->p; \ for (i=0; in; j++) \ if ( convert(&ptr[j * sizeof(type_t)])==vector_end ) break; \ if ( j==fmt->n ) \ { \ /* all fields were used */ \ if ( max_ploidy < j ) max_ploidy = j; \ break; \ } \ if ( max_ploidy < j ) max_ploidy = j; \ ptr += fmt->n * sizeof(type_t); \ } \ } switch (fmt->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, bcf_int32_vector_end); break; default: error("Unexpected case: %d\n", fmt->type); } #undef BRANCH return max_ploidy; } // Sets ma->laa to local indexes relevant for each sample or missing/vector_end. // The indexes are with respect to the source indexes and must be translated as // the very last step. void init_local_alleles(args_t *args, bcf1_t *out, int ifmt_PL) { bcf_srs_t *files = args->files; maux_t *ma = args->maux; int i,j,k,l, ismpl = 0, nlaa = 0; static int warned = 0; hts_expand(double,out->n_allele,ma->ntmpd,ma->tmpd); // allele probabilities hts_expand(int,out->n_allele,ma->ntmpi,ma->tmpi); // indexes of the sorted probabilities // Let map[] be the mapping from src to output idx. Then k2k[] is mapping from src allele idxs to src allele idxs // reordered so that if in_allele,ma->nk2k,ma->k2k); // Determine local alleles: either take all that are present in the reader or use PL to determine the best // subset for each sample. The alleles must be listed in the order of the alleles in the output file. for (i=0; inreaders; i++) { bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; bcf_fmt_t *fmt_ori = ma->fmt_map[files->nreaders*ifmt_PL+i]; bcf1_t *line = maux_get_line(args, i); int nsmpl = bcf_hdr_nsamples(hdr); if ( line ) { if ( nlaa < line->n_allele - 1 ) nlaa = line->n_allele - 1 <= args->local_alleles ? line->n_allele - 1 : args->local_alleles; for (j=0; jn_allele; j++) ma->k2k[j] = j; if ( line->n_allele <= args->local_alleles + 1 ) { // sort to the output order, insertion sort, ascending int *map = ma->buf[i].rec[ma->buf[i].cur].map; int *k2k = ma->k2k; int tmp; for (k=1; kn_allele; k++) for (l=k; l>0 && map[k2k[l]] < map[k2k[l-1]]; l--) tmp = k2k[l], k2k[l] = k2k[l-1], k2k[l-1] = tmp; // fewer than the allowed number of alleles, use all alleles from this file for (j=0; jlaa + (1+args->local_alleles)*ismpl; for (k=0; kn_allele; k++) ptr[k] = k2k[k]; for (; k<=args->local_alleles; k++) ptr[k] = bcf_int32_vector_end; ismpl++; } continue; } } if ( !line || !fmt_ori ) { // no values, fill in missing values for (j=0; jlaa + (1+args->local_alleles)*ismpl; ptr[0] = bcf_int32_missing; for (k=1; k<=args->local_alleles; k++) ptr[k] = bcf_int32_vector_end; ismpl++; } continue; } // there are more alternate alleles in the input files than is allowed on output, need to subset if ( ifmt_PL==-1 ) { if ( !warned ) fprintf(stderr,"Warning: local alleles are determined from FORMAT/PL but the tag is missing, cannot apply --local-alleles\n"); warned = 1; ma->nlaa = 0; return; } if ( !IS_VL_G(hdr, fmt_ori->id) ) error("FORMAT/PL must be defined as Number=G\n"); if ( 2*fmt_ori->n != line->n_allele*(line->n_allele+1) ) error("Todo: haploid PL to LPL\n"); int *map = ma->buf[i].rec[ma->buf[i].cur].map; double *allele_prob = ma->tmpd; int *idx = ma->tmpi; #define BRANCH(src_type_t, convert, src_is_missing, src_is_vector_end, pl2prob_idx) { \ uint8_t *src = fmt_ori->p; \ for (j=0; jn_allele; k++) allele_prob[k] = 0; \ for (k=0; kn_allele; k++) \ for (l=0; l<=k; l++) \ { \ src_type_t val = convert(src); \ if ( !(src_is_missing) && !(src_is_vector_end) ) \ { \ double prob = ma->pl2prob[pl2prob_idx]; \ allele_prob[k] += prob; \ allele_prob[l] += prob; \ } \ src += sizeof(src_type_t); \ } \ /* insertion sort by allele probability, descending order, with the twist that REF (idx=0) always comes first */ \ allele_prob++; idx[0] = -1; idx++; /* keep REF first */ \ int si,sj,tmp; \ for (si=0; sin_allele-1; si++) idx[si] = si; \ for (si=1; sin_allele-1; si++) \ for (sj=si; sj>0 && allele_prob[idx[sj]] > allele_prob[idx[sj-1]]; sj--) \ tmp = idx[sj], idx[sj] = idx[sj-1], idx[sj-1] = tmp; \ /*for debugging only: test order*/ \ for (si=1; sin_allele-1; si++) \ assert( allele_prob[idx[si-1]] >= allele_prob[idx[si]] ); \ allele_prob--; idx--; /* this was to keep REF first */ \ int32_t *ptr = ma->laa + (1+args->local_alleles)*ismpl; \ ptr[0] = 0; \ for (k=1; k<=args->local_alleles && kn_allele; k++) ptr[k] = idx[k]+1; \ int kmax = k; \ for (; k<=args->local_alleles; k++) ptr[k] = bcf_int32_vector_end; \ /* insertion sort by indexes to the output order, ascending */ \ for (k=1; k0 && map[ptr[l]] < map[ptr[l-1]]; l--) \ tmp = ptr[l], ptr[l] = ptr[l-1], ptr[l-1] = tmp; \ ismpl++; \ } \ } switch (fmt_ori->type) { case BCF_BT_INT8: BRANCH( int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, val); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, val>=0 && val=0 && valtype); } #undef BRANCH } ma->nlaa = nlaa; } void update_local_alleles(args_t *args, bcf1_t *out) { bcf_srs_t *files = args->files; maux_t *ma = args->maux; int i,j,k,ismpl=0,nsamples = bcf_hdr_nsamples(args->out_hdr); for (i=0; inreaders; i++) { int irec = ma->buf[i].cur; bcf_sr_t *reader = &files->readers[i]; int nsmpl = bcf_hdr_nsamples(reader->header); for (k=0; klaa + ismpl*(1+args->local_alleles); int32_t *dst = ma->laa + ismpl*ma->nlaa; j = 0; if ( irec>=0 ) { for (; jnlaa; j++) { if ( src[j+1]==bcf_int32_missing ) dst[j] = bcf_int32_missing; else if ( src[j+1]==bcf_int32_vector_end ) break; else dst[j] = ma->buf[i].rec[irec].map[src[j+1]]; } } if ( j==0 ) dst[j++] = bcf_int32_missing; for (; jnlaa; j++) src[j] = bcf_int32_vector_end; ismpl++; } } bcf_update_format_int32(args->out_hdr, out, "LAA", ma->laa, nsamples*ma->nlaa); } void merge_GT(args_t *args, bcf_fmt_t **fmt_map, bcf1_t *out) { bcf_srs_t *files = args->files; bcf_hdr_t *out_hdr = args->out_hdr; maux_t *ma = args->maux; int i, ismpl = 0, nsamples = bcf_hdr_nsamples(out_hdr); static int warned = 0; int nsize = 0; for (i=0; inreaders; i++) { bcf_fmt_t *fmt = fmt_map[i]; if ( !fmt ) continue; int pld = max_used_gt_ploidy(fmt_map[i], bcf_hdr_nsamples(bcf_sr_get_header(args->files,i))); if ( nsize < pld ) nsize = pld; } if ( nsize==0 ) nsize = 1; size_t msize = sizeof(int32_t)*nsize*nsamples; if ( msize > 2147483647 ) { if ( !warned ) fprintf(stderr,"Warning: Too many genotypes at %s:%"PRId64", requires %zu bytes, skipping.\n", bcf_seqname(out_hdr,out),(int64_t) out->pos+1,msize); warned = 1; return; } if ( ma->ntmp_arr < msize ) { ma->tmp_arr = realloc(ma->tmp_arr, msize); if ( !ma->tmp_arr ) error("Could not allocate %zu bytes\n",msize); ma->ntmp_arr = msize; } memset(ma->smpl_ploidy,0,nsamples*sizeof(int)); int default_gt = args->missing_to_ref ? bcf_gt_unphased(0) : bcf_gt_missing; for (i=0; inreaders; i++) { bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; bcf_fmt_t *fmt_ori = fmt_map[i]; int32_t *tmp = (int32_t *) ma->tmp_arr + ismpl*nsize; int irec = ma->buf[i].cur; int j,k; if ( !fmt_ori ) { // missing values: assume maximum ploidy for (j=0; jsmpl_ploidy[ismpl+j]++; } tmp += nsize; } ismpl += bcf_hdr_nsamples(hdr); continue; } #define BRANCH(type_t, convert, vector_end) { \ uint8_t *p_ori = fmt_ori->p; \ if ( !ma->buf[i].rec[irec].als_differ ) \ { \ /* the allele numbering is unchanged */ \ for (j=0; jn; k++) \ { \ type_t val = convert(&p_ori[k * sizeof(type_t)]); \ if ( val==vector_end ) break; /* smaller ploidy */ \ ma->smpl_ploidy[ismpl+j]++; \ if ( bcf_gt_is_missing(val) ) tmp[k] = 0; /* missing allele */ \ else tmp[k] = val; \ } \ for (; kn * sizeof(type_t); \ } \ ismpl += bcf_hdr_nsamples(hdr); \ continue; \ } \ /* allele numbering needs to be changed */ \ for (j=0; jn; k++) \ { \ type_t val = convert(&p_ori[k * sizeof(type_t)]); \ if ( val==vector_end ) break; /* smaller ploidy */ \ ma->smpl_ploidy[ismpl+j]++; \ if ( bcf_gt_is_missing(val) ) tmp[k] = 0; /* missing allele */ \ else \ { \ int al = (val>>1) - 1; \ al = al<=0 ? al + 1 : ma->buf[i].rec[irec].map[al] + 1; \ tmp[k] = (al << 1) | ((val)&1); \ } \ } \ for (; kn * sizeof(type_t); \ } \ ismpl += bcf_hdr_nsamples(hdr); \ } switch (fmt_ori->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, bcf_int32_vector_end); break; default: error("Unexpected case: %d\n", fmt_ori->type); } #undef BRANCH } bcf_update_format_int32(out_hdr, out, "GT", (int32_t*)ma->tmp_arr, nsamples*nsize); } void merge_format_string(args_t *args, const char *key, bcf_fmt_t **fmt_map, bcf1_t *out, int length, int nsize) { bcf_srs_t *files = args->files; bcf_hdr_t *out_hdr = args->out_hdr; maux_t *ma = args->maux; int i,j, nsamples = bcf_hdr_nsamples(out_hdr); static int warned = 0; // initialize empty strings, a dot for each value, e.g. ".,.,." int nmax = 0; for (i=0; istr[i]; if ( length==BCF_VL_FIXED || length==BCF_VL_VAR ) { str->l = 1; ks_resize(str, str->l+1); str->s[0] = '.'; } else { str->l = nsize*2 - 1; ks_resize(str, str->l+1); str->s[0] = '.'; for (j=1; js[j*2-1] = ',', str->s[j*2] = '.'; } str->s[str->l] = 0; if ( nmax < str->l ) nmax = str->l; } // fill in values for each sample int ismpl = 0; for (i=0; inreaders; i++) { bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; bcf_fmt_t *fmt_ori = fmt_map[i]; if ( !fmt_ori ) { // the field is not present in this file ismpl += bcf_hdr_nsamples(hdr); continue; } bcf1_t *line = maux_get_line(args, i); int irec = ma->buf[i].cur; char *src = (char*) fmt_ori->p; if ( length==BCF_VL_FIXED || length==BCF_VL_VAR || (line->n_allele==out->n_allele && !ma->buf[i].rec[irec].als_differ) ) { // alleles unchanged, copy over for (j=0; jstr[ismpl++]; str->l = 0; kputsn(src, fmt_ori->n, str); if ( nmax < str->l ) nmax = str->l; src += fmt_ori->n; } continue; } // NB, what is below is not the fastest way, copy_string_field() keeps // finding the indexes repeatedly at multiallelic sites if ( length==BCF_VL_A || length==BCF_VL_R ) { int ifrom = length==BCF_VL_A ? 1 : 0; for (j=0; jstr[ismpl++]; int iori,inew; for (iori=ifrom; iorin_allele; iori++) { inew = ma->buf[i].rec[irec].map[iori] - ifrom; int ret = copy_string_field(src, iori - ifrom, fmt_ori->size, str, inew); if ( ret<-1 ) error("[E::%s] fixme: internal error at %s:%"PRId64" .. %d\n",__func__,bcf_seqname(hdr,line),(int64_t) line->pos+1,ret); } if ( nmax < str->l ) nmax = str->l; src += fmt_ori->size; } continue; } assert( length==BCF_VL_G ); error("[E::%s] Merging of Number=G FORMAT strings (in your case FORMAT/%s) is not supported yet, sorry!\n" "Please open an issue on github if this feature is essential for you. However, note that using FORMAT strings is not\n" "a good idea in general - it is slow to parse and does not compress well, it is better to use integer codes instead.\n" "If you don't really need it, use `bcftools annotate -x` to remove the annotation before merging.\n", __func__,key); } // update the record size_t msize = nsamples*nmax; if ( msize > 2147483647 ) { if ( !warned ) fprintf(stderr,"Warning: The row size is too big for FORMAT/%s at %s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(out_hdr,out),(int64_t) out->pos+1,msize); warned = 1; return; } if ( ma->ntmp_arr < msize ) { ma->tmp_arr = realloc(ma->tmp_arr, msize); if ( !ma->tmp_arr ) error("Could not allocate %zu bytes\n",msize); ma->ntmp_arr = msize; } char *tgt = (char*) ma->tmp_arr; for (i=0; istr[i].s, ma->str[i].l); if ( ma->str[i].l < nmax ) memset(tgt + ma->str[i].l, 0, nmax - ma->str[i].l); tgt += nmax; } bcf_update_format_char(out_hdr, out, key, (float*)ma->tmp_arr, nsamples*nmax); } // Note: only diploid Number=G tags only for now void merge_localized_numberG_format_field(args_t *args, bcf_fmt_t **fmt_map, bcf1_t *out, int irdr) { int i,j,k, nsamples = bcf_hdr_nsamples(args->out_hdr); bcf_srs_t *files = args->files; maux_t *ma = args->maux; bcf_fmt_t *fmt = fmt_map[irdr]; const char *key = files->readers[irdr].header->id[BCF_DT_ID][fmt_map[irdr]->id].key; size_t nsize = (ma->nlaa+1)*(ma->nlaa+2)/2; // max number of Number=G localized fields size_t msize = sizeof(float)>sizeof(int32_t) ? sizeof(float) : sizeof(int32_t); msize *= nsamples*nsize; if ( msize > 2147483647 ) { static int warned = 0; if ( !warned ) fprintf(stderr,"Warning: The row size is too big for FORMAT/%s at %s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,msize); warned = 1; return; } if ( ma->ntmp_arr < msize ) { ma->tmp_arr = realloc(ma->tmp_arr, msize); if ( !ma->tmp_arr ) error("Failed to allocate %zu bytes at %s:%"PRId64" for FORMAT/%s\n", msize,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,key); ma->ntmp_arr = msize; } int ismpl = 0; for (i=0; inreaders; i++) { bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; bcf_fmt_t *fmt_ori = fmt_map[i]; bcf1_t *line = maux_get_line(args, i); int nsmpl = bcf_hdr_nsamples(hdr); if ( !fmt_ori ) { // fill missing values #define BRANCH(tgt_type_t, tgt_set_missing, tgt_set_vector_end) { \ for (j=0; jtmp_arr + ismpl*nsize; \ tgt_set_missing; \ for (k=1; ktype) { case BCF_BT_INT8: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_INT16: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_FLOAT: BRANCH(float, bcf_float_set_missing(*tgt), bcf_float_set_vector_end(*tgt)); break; default: error("Unexpected case: %d, %s\n", fmt->type, key); } #undef BRANCH continue; } if ( 2*fmt_ori->n!=line->n_allele*(line->n_allele+1) ) error("Todo: localization of missing or haploid Number=G tags\n"); // localize #define BRANCH(tgt_type_t, src_type_t, convert, src_is_missing, src_is_vector_end, tgt_set_missing, tgt_set_vector_end) { \ for (j=0; jp + sizeof(src_type_t)*j*fmt_ori->n; \ tgt_type_t *tgt = (tgt_type_t *) ma->tmp_arr + ismpl*nsize; \ int *laa = ma->laa + (1+args->local_alleles)*ismpl; \ int ii,ij,tgt_idx = 0; \ for (ii=0; ii<=ma->nlaa; ii++) \ { \ if ( laa[ii]==bcf_int32_missing || laa[ii]==bcf_int32_vector_end ) break; \ for (ij=0; ij<=ii; ij++) \ { \ int src_idx = bcf_alleles2gt(laa[ii],laa[ij]); \ src_type_t val = convert(&src[src_idx * sizeof(src_type_t)]); \ if ( src_is_missing ) tgt_set_missing; \ else if ( src_is_vector_end ) break; \ else tgt[tgt_idx] = val; \ tgt_idx++; \ } \ } \ if ( !tgt_idx ) { tgt_set_missing; tgt_idx++; } \ for (; tgt_idxtype) { case BCF_BT_INT8: BRANCH(int32_t, int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break; case BCF_BT_INT16: BRANCH(int32_t, int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, int32_t, le_to_i16, val==bcf_int32_missing, val==bcf_int32_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break; case BCF_BT_FLOAT: BRANCH(float, float, le_to_float, bcf_float_is_missing(val), bcf_float_is_vector_end(val), bcf_float_set_missing(tgt[tgt_idx]), bcf_float_set_vector_end(tgt[tgt_idx])); break; default: error("Unexpected case: %d, %s\n", fmt_ori->type, key); } #undef BRANCH } args->tmps.l = 0; kputc('L',&args->tmps); kputs(key,&args->tmps); if ( fmt_map[irdr]->type==BCF_BT_FLOAT ) bcf_update_format_float(args->out_hdr, out, args->tmps.s, (float*)ma->tmp_arr, nsamples*nsize); else bcf_update_format_int32(args->out_hdr, out, args->tmps.s, (int32_t*)ma->tmp_arr, nsamples*nsize); ma->laa_dirty = 1; } void merge_localized_numberAR_format_field(args_t *args, bcf_fmt_t **fmt_map, bcf1_t *out, int irdr) { int i,j,k, nsamples = bcf_hdr_nsamples(args->out_hdr); bcf_srs_t *files = args->files; maux_t *ma = args->maux; bcf_fmt_t *fmt = fmt_map[irdr]; const char *key = files->readers[irdr].header->id[BCF_DT_ID][fmt->id].key; size_t nsize = IS_VL_R(files->readers[irdr].header, fmt->id) ? ma->nlaa + 1 : ma->nlaa; size_t msize = sizeof(float)>sizeof(int32_t) ? sizeof(float) : sizeof(int32_t); msize *= nsamples*nsize; if ( msize > 2147483647 ) { static int warned = 0; if ( !warned ) fprintf(stderr,"Warning: The row size is too big for FORMAT/%s at %s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,msize); warned = 1; return; } if ( ma->ntmp_arr < msize ) { ma->tmp_arr = realloc(ma->tmp_arr, msize); if ( !ma->tmp_arr ) error("Failed to allocate %zu bytes at %s:%"PRId64" for FORMAT/%s\n", msize,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,key); ma->ntmp_arr = msize; } int ismpl = 0, ibeg = IS_VL_R(files->readers[irdr].header, fmt->id) ? 0 : 1;; for (i=0; inreaders; i++) { bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; bcf_fmt_t *fmt_ori = fmt_map[i]; int nsmpl = bcf_hdr_nsamples(hdr); if ( !fmt_ori ) { // fill missing values #define BRANCH(tgt_type_t, tgt_set_missing, tgt_set_vector_end) { \ for (j=0; jtmp_arr + ismpl*nsize; \ tgt_set_missing; \ for (k=1; ktype) { case BCF_BT_INT8: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_INT16: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_FLOAT: BRANCH(float, bcf_float_set_missing(*tgt), bcf_float_set_vector_end(*tgt)); break; default: error("Unexpected case: %d, %s\n", fmt->type, key); } #undef BRANCH continue; } // localize #define BRANCH(tgt_type_t, src_type_t, convert, src_is_missing, src_is_vector_end, tgt_set_missing, tgt_set_vector_end) { \ for (j=0; jp + sizeof(src_type_t)*j*fmt_ori->n; \ tgt_type_t *tgt = (tgt_type_t *) ma->tmp_arr + ismpl*nsize; \ int *laa = ma->laa + (1+args->local_alleles)*ismpl; \ int ii,tgt_idx = 0; \ for (ii=ibeg; ii<=ma->nlaa; ii++) \ { \ if ( laa[ii]==bcf_int32_missing || laa[ii]==bcf_int32_vector_end ) break; \ int src_idx = laa[ii] - ibeg; \ src_type_t val = convert(&src[src_idx * sizeof(src_type_t)]); \ if ( src_is_missing ) tgt_set_missing; \ else if ( src_is_vector_end ) break; \ else tgt[tgt_idx] = val; \ tgt_idx++; \ } \ if ( !tgt_idx ) { tgt_set_missing; tgt_idx++; } \ for (; tgt_idxtype) { case BCF_BT_INT8: BRANCH(int32_t, int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break; case BCF_BT_INT16: BRANCH(int32_t, int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, int32_t, le_to_i32, val==bcf_int32_missing, val==bcf_int32_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break; case BCF_BT_FLOAT: BRANCH(float, float, le_to_float, bcf_float_is_missing(val), bcf_float_is_vector_end(val), bcf_float_set_missing(tgt[tgt_idx]), bcf_float_set_vector_end(tgt[tgt_idx])); break; default: error("Unexpected case: %d, %s\n", fmt_ori->type, key); } #undef BRANCH } args->tmps.l = 0; kputc('L',&args->tmps); kputs(key,&args->tmps); if ( fmt_map[irdr]->type==BCF_BT_FLOAT ) bcf_update_format_float(args->out_hdr, out, args->tmps.s, (float*)ma->tmp_arr, nsamples*nsize); else bcf_update_format_int32(args->out_hdr, out, args->tmps.s, (int32_t*)ma->tmp_arr, nsamples*nsize); ma->laa_dirty = 1; } void merge_format_field(args_t *args, bcf_fmt_t **fmt_map, missing_rule_t *mrule, bcf1_t *out) { bcf_srs_t *files = args->files; bcf_hdr_t *out_hdr = args->out_hdr; maux_t *ma = args->maux; int i, ismpl = 0, nsamples = bcf_hdr_nsamples(out_hdr); static int warned = 0; const char *key = NULL; size_t nsize = 0, length = BCF_VL_FIXED; int type = -1; for (i=0; inreaders; i++) { if ( !maux_get_line(args,i) ) continue; if ( !fmt_map[i] ) continue; if ( !key ) key = files->readers[i].header->id[BCF_DT_ID][fmt_map[i]->id].key; type = fmt_map[i]->type; if ( IS_VL_G(files->readers[i].header, fmt_map[i]->id) ) { length = BCF_VL_G; nsize = out->n_allele*(out->n_allele + 1)/2; break; } if ( IS_VL_A(files->readers[i].header, fmt_map[i]->id) ) { length = BCF_VL_A; nsize = out->n_allele - 1; break; } if ( IS_VL_R(files->readers[i].header, fmt_map[i]->id) ) { length = BCF_VL_R; nsize = out->n_allele; break; } if ( fmt_map[i]->n > nsize ) nsize = fmt_map[i]->n; } if ( ma->nlaa && length!=BCF_VL_FIXED ) { if ( length==BCF_VL_G ) merge_localized_numberG_format_field(args,fmt_map,out,i); else if ( length==BCF_VL_A || length==BCF_VL_R ) merge_localized_numberAR_format_field(args,fmt_map,out,i); return; } if ( type==BCF_BT_CHAR ) { merge_format_string(args, key, fmt_map, out, length, nsize); return; } size_t msize = sizeof(float)>sizeof(int32_t) ? sizeof(float) : sizeof(int32_t); msize *= nsamples*nsize; if ( msize > 2147483647 ) { if ( !warned ) fprintf(stderr,"Warning: The row size is too big for FORMAT/%s at %s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(out_hdr,out),(int64_t) out->pos+1,msize); warned = 1; return; } if ( ma->ntmp_arr < msize ) { ma->tmp_arr = realloc(ma->tmp_arr, msize); if ( !ma->tmp_arr ) error("Failed to allocate %zu bytes at %s:%"PRId64" for FORMAT/%s\n", msize,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,key); ma->ntmp_arr = msize; } // Fill the temp array for all samples by collecting values from all files for (i=0; inreaders; i++) { bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; bcf_fmt_t *fmt_ori = fmt_map[i]; bcf1_t *line = maux_get_line(args, i); int irec = ma->buf[i].cur; if ( fmt_ori ) { type = fmt_ori->type; int nals_ori = line->n_allele; if ( length==BCF_VL_G ) { // if all fields are missing then n==1 is valid if ( fmt_ori->n!=1 && fmt_ori->n != nals_ori*(nals_ori+1)/2 && fmt_map[i]->n != nals_ori ) error("Incorrect number of FORMAT/%s values at %s:%"PRId64", cannot merge. The tag is defined as Number=G, but found\n" "%d values and %d alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields\n", key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,fmt_ori->n,nals_ori); } else if ( length==BCF_VL_A ) { if ( fmt_ori->n!=1 && fmt_ori->n != nals_ori-1 ) error("Incorrect number of FORMAT/%s values at %s:%"PRId64", cannot merge. The tag is defined as Number=A, but found\n" "%d values and %d alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields\n", key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,fmt_ori->n,nals_ori); } else if ( length==BCF_VL_R ) { if ( fmt_ori->n!=1 && fmt_ori->n != nals_ori ) error("Incorrect number of FORMAT/%s values at %s:%"PRId64", cannot merge. The tag is defined as Number=R, but found\n" "%d values and %d alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields\n", key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,fmt_ori->n,nals_ori); } } // set the values #define BRANCH(tgt_type_t, src_type_t, convert, src_is_missing, src_is_vector_end, tgt_set_missing, tgt_set_vector_end) { \ int j, l, k; \ tgt_type_t *tgt = (tgt_type_t *) ma->tmp_arr + ismpl*nsize; \ if ( !fmt_ori ) \ { \ /* the field is not present in this file, set missing values */ \ for (j=0; jp; \ if ( (length!=BCF_VL_G && length!=BCF_VL_A && length!=BCF_VL_R) || (line->n_allele==out->n_allele && !ma->buf[i].rec[irec].als_differ) ) \ { \ /* alleles unchanged, copy over */ \ for (j=0; jn; l++) \ { \ if ( src_is_vector_end ) break; \ else if ( src_is_missing ) tgt_set_missing; \ else *tgt = convert(src); \ tgt++; src += sizeof(src_type_t); \ } \ for (k=l; kn - l); \ } \ ismpl += bcf_hdr_nsamples(hdr); \ continue; \ } \ /* allele numbering needs to be changed */ \ if ( length==BCF_VL_G ) \ { \ /* Number=G tags */ \ for (j=0; jtmp_arr + (ismpl+j)*nsize; \ src = fmt_ori->p + sizeof(src_type_t) * j * fmt_ori->n; \ int tag_missing = src_is_missing && fmt_ori->n==1; \ if ( src_is_missing && fmt_ori->n>1 ) { \ src += sizeof(src_type_t); \ tag_missing = src_is_vector_end ; \ } \ if ( tag_missing ) \ { \ /* tag with missing value "." */ \ tgt_set_missing; \ for (l=1; lsmpl_ploidy[ismpl+j]==1 ? 1 : 0; \ int ngsize = haploid ? out->n_allele : out->n_allele*(out->n_allele + 1)/2; \ if ( ma->buf[i].unkn_allele ) /* Use value from the unknown allele when available */ \ { \ src = fmt_ori->p + sizeof(src_type_t)*j*fmt_ori->n; \ int iunkn = haploid ? ma->buf[i].unkn_allele : (ma->buf[i].unkn_allele+1)*(ma->buf[i].unkn_allele + 2)/2 - 1; \ src_type_t val = convert(&src[iunkn * sizeof(src_type_t)]); \ for (l=0; ltype==MERGE_MISSING_CONST ) \ { \ for (l=0; lvalue; tgt++; } \ } \ else if ( mrule && mrule->type==MERGE_MISSING_MAX ) \ { \ src = fmt_ori->p + sizeof(src_type_t)*j*fmt_ori->n; \ src_type_t max = convert(src); \ for (l=1; ln; l++) \ { \ src_type_t val = convert(&src[l * sizeof(src_type_t)]); \ if ( max < val ) max = val; \ } \ for (l=0; ln_allele; iori++) \ { \ inew = ma->buf[i].rec[irec].map[iori]; \ src = fmt_ori->p + (j*fmt_ori->n + iori) * sizeof(src_type_t); \ tgt = (tgt_type_t *) ma->tmp_arr + (ismpl+j)*nsize + inew; \ if ( src_is_vector_end ) break; \ if ( src_is_missing ) tgt_set_missing; \ else *tgt = convert(src); \ } \ } \ else \ { \ /* Diploid */ \ int iori,jori, inew,jnew; \ for (iori=0; iorin_allele; iori++) \ { \ inew = ma->buf[i].rec[irec].map[iori]; \ for (jori=0; jori<=iori; jori++) \ { \ jnew = ma->buf[i].rec[irec].map[jori]; \ int kori = iori*(iori+1)/2 + jori; \ int knew = inew>jnew ? inew*(inew+1)/2 + jnew : jnew*(jnew+1)/2 + inew; \ src = fmt_ori->p + (j*fmt_ori->n + kori) * sizeof(src_type_t); \ tgt = (tgt_type_t *) ma->tmp_arr + (ismpl+j)*nsize + knew; \ if ( src_is_vector_end ) \ { \ iori = line->n_allele; \ break; \ } \ if ( src_is_missing ) tgt_set_missing; \ else *tgt = convert(src); \ } \ } \ } \ } \ } \ else \ { \ /* Number=A or Number=R tags */ \ int ifrom = length==BCF_VL_A ? 1 : 0; \ for (j=0; jtmp_arr + (ismpl+j)*nsize; \ src = fmt_ori->p + j*fmt_ori->size; \ int tag_missing = src_is_missing && fmt_ori->n==1; \ if ( src_is_missing && fmt_ori->n>1 ) { \ src += sizeof(src_type_t); \ tag_missing = src_is_vector_end ; \ } \ if ( tag_missing ) \ { \ /* tag with missing value "." */ \ tgt_set_missing; \ for (l=1; lp + j*fmt_ori->size; \ if ( ma->buf[i].unkn_allele ) /* Use value from the unknown allele when available */ \ { \ int iunkn = ma->buf[i].unkn_allele; \ src_type_t val = convert(&src[iunkn * sizeof(src_type_t)]); \ for (l=0; ltype==MERGE_MISSING_CONST ) \ { \ for (l=0; lvalue; tgt++; } \ } \ else if ( mrule && mrule->type==MERGE_MISSING_MAX ) \ { \ src = fmt_ori->p + sizeof(src_type_t)*j*fmt_ori->n; \ src_type_t max = convert(src); \ for (l=1; ln; l++) \ { \ src_type_t val = convert(&src[l * sizeof(src_type_t)]); \ if ( max < val ) max = val; \ } \ for (l=0; ln_allele; iori++) \ { \ inew = ma->buf[i].rec[irec].map[iori] - ifrom; \ tgt = (tgt_type_t *) ma->tmp_arr + (ismpl+j)*nsize + inew; \ if ( src_is_vector_end ) break; \ if ( src_is_missing ) tgt_set_missing; \ else *tgt = convert(src); \ src += sizeof(src_type_t); \ } \ } \ } \ ismpl += bcf_hdr_nsamples(hdr); \ } switch (type) { case BCF_BT_INT8: BRANCH(int32_t, int8_t, le_to_i8, le_to_i8(src)==bcf_int8_missing, le_to_i8(src)==bcf_int8_vector_end, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_INT16: BRANCH(int32_t, int16_t, le_to_i16, le_to_i16(src)==bcf_int16_missing, le_to_i16(src)==bcf_int16_vector_end, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, int32_t, le_to_i32, le_to_i32(src)==bcf_int32_missing, le_to_i32(src)==bcf_int32_vector_end, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_FLOAT: BRANCH(float, float, le_to_float, bcf_float_is_missing(le_to_float(src)), bcf_float_is_vector_end(le_to_float(src)), bcf_float_set_missing(*tgt), bcf_float_set_vector_end(*tgt)); break; default: error("Unexpected case: %d, %s\n", type, key); } #undef BRANCH } if ( type==BCF_BT_FLOAT ) bcf_update_format_float(out_hdr, out, key, (float*)ma->tmp_arr, nsamples*nsize); else bcf_update_format_int32(out_hdr, out, key, (int32_t*)ma->tmp_arr, nsamples*nsize); } void merge_format(args_t *args, bcf1_t *out) { bcf_srs_t *files = args->files; bcf_hdr_t *out_hdr = args->out_hdr; maux_t *ma = args->maux; if ( !ma->nfmt_map ) { ma->nfmt_map = 2; ma->fmt_map = (bcf_fmt_t**) calloc(ma->nfmt_map*files->nreaders, sizeof(bcf_fmt_t*)); ma->fmt_key = (const char**) malloc(ma->nfmt_map*sizeof(*ma->fmt_key)); } else memset(ma->fmt_map, 0, ma->nfmt_map*files->nreaders*sizeof(bcf_fmt_t**)); khiter_t kitr; strdict_t *tmph = args->tmph; kh_clear(strdict, tmph); int i, j, ret, has_GT = 0, has_PL = -1, max_ifmt = 0; // max fmt index for (i=0; inreaders; i++) { bcf1_t *line = maux_get_line(args,i); if ( !line ) continue; bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; for (j=0; jn_fmt; j++) { // Was this tag already seen? bcf_fmt_t *fmt = &line->d.fmt[j]; const char *key = hdr->id[BCF_DT_ID][fmt->id].key; kitr = kh_get(strdict, tmph, key); int ifmt; if ( kitr != kh_end(tmph) ) ifmt = kh_value(tmph, kitr); // seen else { // new FORMAT tag if ( key[0]=='G' && key[1]=='T' && key[2]==0 ) { has_GT = 1; ifmt = 0; } else { ifmt = ++max_ifmt; if ( max_ifmt >= ma->nfmt_map ) { ma->fmt_map = (bcf_fmt_t**) realloc(ma->fmt_map, sizeof(bcf_fmt_t*)*(max_ifmt+1)*files->nreaders); memset(ma->fmt_map+ma->nfmt_map*files->nreaders, 0, (max_ifmt-ma->nfmt_map+1)*files->nreaders*sizeof(bcf_fmt_t*)); ma->fmt_key = (const char**) realloc(ma->fmt_key, sizeof(*ma->fmt_key)*(max_ifmt+1)); ma->nfmt_map = max_ifmt+1; } if ( key[0]=='P' && key[1]=='L' && key[2]==0 ) { has_PL = ifmt; } ma->fmt_key[max_ifmt] = key; } kitr = kh_put(strdict, tmph, key, &ret); kh_value(tmph, kitr) = ifmt; } ma->fmt_map[ifmt*files->nreaders+i] = fmt; } // Check if the allele numbering must be changed int irec = ma->buf[i].cur; for (j=1; jn_allele; j++) if ( ma->buf[i].rec[irec].map[j]!=j ) break; ma->buf[i].rec[irec].als_differ = j==line->n_allele ? 0 : 1; } if ( args->local_alleles ) { ma->laa_dirty = ma->nlaa = 0; if ( out->n_allele > args->local_alleles + 1 ) init_local_alleles(args, out, has_PL); } out->n_sample = bcf_hdr_nsamples(out_hdr); if ( has_GT ) merge_GT(args, ma->fmt_map, out); if ( !args->keep_AC_AN ) update_AN_AC(out_hdr, out); for (i=1; i<=max_ifmt; i++) { missing_rule_t *rule = (missing_rule_t*) bsearch(ma->fmt_key[i], args->missing_rules, args->nmissing_rules, sizeof(*args->missing_rules), missing_rules_comp_key); merge_format_field(args, &ma->fmt_map[i*files->nreaders], rule, out); } if ( ma->laa_dirty ) update_local_alleles(args, out); out->d.indiv_dirty = 1; } void gvcf_set_alleles(args_t *args) { int i,k; bcf_srs_t *files = args->files; maux_t *maux = args->maux; gvcf_aux_t *gaux = maux->gvcf; for (i=0; inals; i++) { free(maux->als[i]); maux->als[i] = NULL; } maux->nals = 0; for (i=0; inreaders; i++) { if ( !gaux[i].active ) continue; bcf1_t *line = maux_get_line(args, i); if ( !line ) continue; int irec = maux->buf[i].cur; hts_expand(int, line->n_allele, maux->buf[i].rec[irec].mmap, maux->buf[i].rec[irec].map); if ( !maux->nals ) // first record, copy the alleles to the output { maux->nals = line->n_allele; hts_expand0(char*, maux->nals, maux->mals, maux->als); hts_expand0(int, maux->nals, maux->ncnt, maux->cnt); for (k=0; knals; k++) { if ( maux->als[k] ) free(maux->als[k]); maux->als[k] = strdup(line->d.allele[k]); maux->buf[i].rec[irec].map[k] = k; } } else { maux->als = merge_alleles(line->d.allele, line->n_allele, maux->buf[i].rec[irec].map, maux->als, &maux->nals, &maux->mals); if ( !maux->als ) { bcf_hdr_t *hdr = bcf_sr_get_header(args->files,i); error("Failed to merge alleles at %s:%"PRId64"\n",bcf_seqname(hdr,line),(int64_t) line->pos+1); } } } } /* Output staged gVCF blocks, end is the last position of the block. Assuming gaux[i].active flags are set and maux_get_line returns correct lines. Both start,end coordinates are 0-based. */ void gvcf_write_block(args_t *args, int start, int end) { int i; maux_t *maux = args->maux; gvcf_aux_t *gaux = maux->gvcf; assert(gaux); // Update POS int min = INT_MAX; // the minimum active gVCF INFO/END (0-based) char ref = 'N'; for (i=0; ifiles->nreaders; i++) { if ( !gaux[i].active ) continue; if ( ref=='N' && gaux[i].line->pos==start ) ref = gaux[i].line->d.allele[0][0]; gaux[i].line->pos = start; } for (i=0; ifiles->nreaders; i++) { if ( !gaux[i].active ) continue; if ( gaux[i].end < start ) { gaux[i].active = 0; maux->buf[i].cur = -1; continue; } gaux[i].line->d.allele[0][0] = ref; if ( min > gaux[i].end ) min = gaux[i].end; } // Check for valid gVCF blocks in this region if ( min==INT_MAX ) // this probably should not happen { assert(0); maux->gvcf_min = 0; return; } bcf1_t *out = args->out_line; gvcf_set_alleles(args); // Merge the staged lines merge_chrom2qual(args, out); merge_filter(args, out); merge_info(args, out); merge_format(args, out); if ( args->gvcf_fai && out->d.allele[0][0]=='N' ) { int slen = 0; char *seq = faidx_fetch_seq(args->gvcf_fai,maux->chr,out->pos,out->pos,&slen); if (!seq) exit(1); // faidx_fetch_seq has already reported the error. if (slen) { out->d.allele[0][0] = seq[0]; free(seq); } } // Update END boundary if ( end > start ) { end++; bcf_update_info_int32(args->out_hdr, out, "END", &end, 1); } else bcf_update_info_int32(args->out_hdr, out, "END", NULL, 0); int iunseen; if ( args->trim_star_allele && (out->n_allele > 2 || args->trim_star_allele > 1) && (iunseen=get_unseen_allele(out)) && iunseen>0 ) { // the unobserved star allele should be trimmed, either it is variant site or trimming of all sites was requested kbitset_t *rm_set = kbs_init(out->n_allele); kbs_insert(rm_set, iunseen); if ( bcf_remove_allele_set(args->out_hdr,out,rm_set) ) error("[%s] Error: failed to trim the unobserved allele at %s:%"PRIhts_pos"\n",__func__,bcf_seqname(args->out_hdr,out),out->pos+1); kbs_destroy(rm_set); } if ( bcf_write1(args->out_fh, args->out_hdr, out)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); bcf_clear1(out); // Inactivate blocks which do not extend beyond END and find new gvcf_min min = INT_MAX; for (i=0; ifiles->nreaders; i++) { if ( !gaux[i].active ) continue; if ( gaux[i].end < end ) { gaux[i].active = 0; maux->buf[i].cur = -1; continue; } // next min END position bigger than the current one if ( maux->gvcf_min < gaux[i].end+1 && min > gaux[i].end+1 ) min = gaux[i].end + 1; } maux->gvcf_min = min==INT_MAX ? 0 : min; } /* Flush staged gVCF blocks. Flush everything if there are no more lines (done=1) or if there is a new chromosome. If still on the same chromosome, all hanging blocks must be ended by creating new records: A 1 END=10 B 3 END=7 C 3 END=5 out 1 END=2 A . . 3 END=5 A B C 6 END=7 A B . 8 END=10 A . . */ void gvcf_flush(args_t *args, int done) { int i; maux_t *maux = args->maux; if ( !maux->chr ) return; // first time here, nothing to flush int flush_until = INT_MAX; if ( !done ) { // Get current position and chromosome for (i=0; in; i++) if ( bcf_sr_has_line(maux->files,i) ) break; bcf1_t *line = bcf_sr_get_line(maux->files,i); bcf_hdr_t *hdr = bcf_sr_get_header(maux->files,i); if ( !strcmp(maux->chr,bcf_seqname(hdr,line)) ) flush_until = line->pos; // still on the same chr } // When called on a region, trim the blocks accordingly int start = maux->gvcf_break>=0 ? maux->gvcf_break + 1 : maux->pos; // the start of a new gvcf block to output if ( args->regs ) { int rstart = -1, rend = -1; if ( regidx_overlap(args->regs,maux->chr,start,flush_until,args->regs_itr) ) { // In case there are multiple regions, we treat them as one rstart = args->regs_itr->beg; while ( regitr_overlap(args->regs_itr) ) rend = args->regs_itr->end; } if ( rstart > start ) start = rstart; if ( rend < flush_until ) flush_until = rend+1; } // output all finished blocks while ( maux->gvcf_min && start < flush_until ) { // does the block end before the new line or is it interrupted? int tmp = maux->gvcf_min < flush_until ? maux->gvcf_min : flush_until; if ( start > tmp-1 ) break; gvcf_write_block(args,start,tmp-1); // gvcf_min is 1-based, passing 0-based coordinates start = tmp; } } static inline int is_gvcf_block(bcf1_t *line) { if ( line->rlen<=1 ) return 0; if ( strlen(line->d.allele[0])==line->rlen ) return 0; if ( line->n_allele==1 ) return 1; int i; for (i=1; in_allele; i++) { if ( !strcmp(line->d.allele[i],"<*>") ) return 1; if ( !strcmp(line->d.allele[i],"") ) return 1; if ( !strcmp(line->d.allele[i],"") ) return 1; } return 0; } /* Check incoming lines for new gVCF blocks, set pointer to the current source buffer (gvcf or readers). In contrast to gvcf_flush, this function can be called only after maux_reset as it relies on updated maux buffers. The coordinate is 0-based */ void gvcf_stage(args_t *args, int pos) { maux_t *maux = args->maux; gvcf_aux_t *gaux = maux->gvcf; bcf_srs_t *files = args->files; int32_t *end = (int32_t*) maux->tmp_arr; int i, nend = maux->ntmp_arr / sizeof(int32_t); maux->gvcf_break = -1; maux->gvcf_min = INT_MAX; for (i=0; inreaders; i++) { if ( gaux[i].active && gaux[i].end < pos ) gaux[i].active = 0; if ( gaux[i].active ) { // gvcf block should not overlap with another record if ( maux->gvcf_min > gaux[i].end+1 ) maux->gvcf_min = gaux[i].end + 1; maux->buf[i].beg = 0; maux->buf[i].end = 1; maux->buf[i].cur = 0; continue; } // Does any of the lines have END set? It is enough to check only the // first line, there should be no duplicate records with END in gVCF if ( maux->buf[i].beg==maux->buf[i].end ) continue; // no new record int irec = maux->buf[i].beg; bcf_hdr_t *hdr = bcf_sr_get_header(files, i); bcf1_t *line = args->files->readers[i].buffer[irec]; int ret = is_gvcf_block(line) ? bcf_get_info_int32(hdr,line,"END",&end,&nend) : 0; if ( ret==1 ) { if ( end[0] == line->pos + 1 ) // POS and INFO/END are identical, treat as if a normal w/o INFO/END { maux->gvcf_break = line->pos; continue; } if ( end[0] <= line->pos ) error("Error: Incorrect END at %s:%"PRId64" .. END=%d\n", bcf_seqname(hdr,line),(int64_t) line->pos+1,end[0]); // END is set, this is a new gVCF block. Cache this line in gaux[i] and swap with // an empty record: the gaux line must be kept until we reach its END. gaux[i].active = 1; gaux[i].end = end[0] - 1; SWAP(bcf1_t*,args->files->readers[i].buffer[irec],gaux[i].line); gaux[i].line->pos = pos; maux->buf[i].lines = &gaux[i].line; maux->buf[i].beg = 0; maux->buf[i].end = 1; maux->buf[i].cur = 0; // Set the rid,pos of the swapped line in the buffer or else the // synced reader will have a problem with the next line // args->files->readers[i].buffer[irec]->rid = maux->buf[i].rid; args->files->readers[i].buffer[irec]->pos = maux->pos; // Update block offsets if ( maux->gvcf_min > gaux[i].end+1 ) maux->gvcf_min = gaux[i].end + 1; } else maux->gvcf_break = line->pos; // must break the gvcf block } maux->ntmp_arr = nend * sizeof(int32_t); maux->tmp_arr = end; if ( maux->gvcf_min==INT_MAX ) maux->gvcf_min = 0; } void debug_buffers(FILE *fp, bcf_srs_t *files); void debug_buffer(FILE *fp, bcf_srs_t *files, int reader); /* Flush all buffered and processed records with the same coordinate. Note that synced reader discards buffer[0], so that needs to stay untouched. */ void clean_buffer(args_t *args) { maux_t *ma = args->maux; int ir; for (ir=0; irn; ir++) { // Invalidate pointer to reader's buffer or else gvcf_flush will attempt // to use the old lines via maux_get_line() if ( ma->gvcf ) { if ( ma->gvcf[ir].active ) { if ( ma->pos > ma->gvcf[ir].end ) ma->gvcf[ir].active = 0; else if ( ma->buf[ir].cur==-1 ) ma->buf[ir].cur = ma->buf[ir].beg; // re-activate interrupted gVCF block } if ( !ma->gvcf[ir].active ) ma->buf[ir].cur = -1; } bcf_sr_t *reader = bcf_sr_get_reader(args->files,ir); if ( !reader->nbuffer ) continue; // nothing to clean bcf1_t **buf = reader->buffer; if ( buf[1]->rid!=ma->buf[ir].rid || buf[1]->pos!=ma->pos ) continue; // nothing to flush int a = 1, b = 2; while ( b<=reader->nbuffer && buf[b]->rid==ma->buf[ir].rid && buf[b]->pos==ma->pos ) b++; // b now points to the first line we want to preserve while ( b<=reader->nbuffer ) { SWAP(bcf1_t*, buf[a], buf[b]); a++; b++; } reader->nbuffer -= b-a; } } void debug_maux(args_t *args) { bcf_srs_t *files = args->files; maux_t *maux = args->maux; int j,k,l; fprintf(stderr,"Alleles to merge at %d, nals=%d\n", maux->pos+1,maux->nals); for (j=0; jnreaders; j++) { bcf_sr_t *reader = &files->readers[j]; buffer_t *buf = &maux->buf[j]; fprintf(stderr," reader %d (k=%d-%d): ", j,buf->beg,buf->end); for (k=buf->beg; kend; k++) { if ( buf->rec[k].skip & SKIP_DONE ) { fprintf(stderr," DONE"); continue; } bcf1_t *line = reader->buffer[k]; // selected for merging by can_merge fprintf(stderr,"\t"); if ( buf->cur==k ) fprintf(stderr,"!"); // selected for merging by stage_line if ( buf->rec[k].skip ) fprintf(stderr,"["); // this record cannot be merged in this round if ( !line->n_allele && maux->gvcf[j].active ) fprintf(stderr,"<*>"); for (l=0; ln_allele; l++) fprintf(stderr,"%s%s", l==0?"":",", line->d.allele[l]); if ( buf->rec[k].skip ) fprintf(stderr,"]"); } fprintf(stderr,"\n"); } fprintf(stderr," counts: "); for (j=0; jnals; j++) fprintf(stderr,"%s %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(stderr,"\n\n"); } void debug_state(args_t *args) { maux_t *maux = args->maux; int i,j; fprintf(stderr,"State after position=%d done:\n",maux->pos+1); for (i=0; ifiles->nreaders; i++) { fprintf(stderr,"\treader %d:\tcur,beg,end=% d,%d,%d", i,maux->buf[i].cur,maux->buf[i].beg,maux->buf[i].end); if ( maux->buf[i].cur >=0 ) { bcf_hdr_t *hdr = bcf_sr_get_header(args->files,i); const char *chr = bcf_hdr_id2name(hdr, maux->buf[i].rid); fprintf(stderr,"\t"); for (j=maux->buf[i].beg; jbuf[i].end; j++) fprintf(stderr," %s:%"PRId64,chr,(int64_t) maux->buf[i].lines[j]->pos+1); } fprintf(stderr,"\n"); } fprintf(stderr,"\tgvcf_min=%d\n", args->maux->gvcf_min); for (i=0; ifiles->nreaders; i++) { fprintf(stderr,"\t\treader %d:\tgvcf_active=%d", i,maux->gvcf[i].active); if ( maux->gvcf[i].active ) fprintf(stderr,"\tpos,end=%"PRId64",%"PRId64, (int64_t) maux->gvcf[i].line->pos+1,(int64_t) maux->gvcf[i].end+1); fprintf(stderr,"\n"); } fprintf(stderr,"\n"); } // Lines can come with any combination of variant types. We use a subset of types defined in vcf.h // but shift by two bits to account for VCF_REF defined as 0 (design flaw in vcf.h, my fault) static const int snp_mask = (VCF_SNP<<1)|(VCF_MNP<<1), indel_mask = (VCF_INDEL<<1), ins_mask = VCF_INS<<1, del_mask = VCF_DEL<<1, ref_mask = 1; // Can these types be merged given the -m settings? Despite the function's name, its focus is on // excluding incompatible records, there will be a finer matching later in stage_line() static inline int types_compatible(args_t *args, int selected_types, buffer_t *buf, int irec) { int k; maux_t *maux = args->maux; bcf1_t *rec = buf->lines[irec]; int rec_types = buf->rec[irec].var_types; assert( selected_types ); // this is trivially true, set in can_merge() if ( args->collapse & COLLAPSE_ANY ) return 1; // can merge anything with anything // REF and gVCF_REF with no other alleles present can be merged with anything if ( (selected_types&ref_mask) && !(selected_types&(~ref_mask)) ) return 1; if ( (rec_types&ref_mask) && !(rec_types&(~ref_mask)) ) return 1; if ( args->collapse!=COLLAPSE_NONE ) { // If we are here, one the following modes must have been set: both,snps,indels,snp-ins-del // Include the new record if // - rec has SNV, we already have SNV, and -m is both,snps,snp-ins-del // - rec has indel, we already have an indel, and -m both,indels,snp-ins-del if ( args->collapse&(COLLAPSE_SNPS|COLLAPSE_SNP_INS_DEL) ) { if ( (rec_types&snp_mask) && (selected_types&snp_mask) ) return 1; } if ( args->collapse&COLLAPSE_INDELS ) { if ( (rec_types&indel_mask) && (selected_types&indel_mask) ) return 1; } if ( args->collapse&COLLAPSE_SNP_INS_DEL ) { if ( (rec_types&ins_mask) && (selected_types&ins_mask) ) return 1; if ( (rec_types&del_mask) && (selected_types&del_mask) ) return 1; } // Whatever is left, allow to match if the alleles match exactly } // The -m none mode or exact matching requested // Simple test first: are the variants of the same type? int x = selected_types >> 1; // remove REF int y = rec_types >> 1; // remove REF while ( x && y ) { x>>=1; y>>=1; } if ( x || y ) return 0; // the types differ if ( vcmp_set_ref(args->vcmp,maux->als[0],rec->d.allele[0]) < 0 ) return 0; // refs are not compatible for (k=1; kn_allele; k++) { if ( bcf_has_variant_type(rec,k,VCF_REF) ) continue; // this must be gVCF_REF (<*> or ) if ( vcmp_find_allele(args->vcmp,maux->als+1,maux->nals-1,rec->d.allele[k])>=0 ) break; } if ( k==rec->n_allele ) return 0; // this record has a new allele rec->d.allele[k] return 1; // all alleles in rec are also in the records selected thus far, perhaps save for gVCF_REF } static void maux_update_alleles(args_t *args, int ireader, int irec) { int k; bcf_sr_t *reader = &args->files->readers[ireader]; maux_t *maux = args->maux; buffer_t *buf = &maux->buf[ireader]; maux1_t *ma1 = &buf->rec[irec]; bcf1_t *line = buf->lines[irec]; hts_expand(int, line->n_allele, ma1->mmap, ma1->map); if ( !maux->nals ) // first record to be merged, copy the alleles to the output { maux->nals = line->n_allele; hts_expand0(char*, maux->nals, maux->mals, maux->als); hts_expand0(int, maux->nals, maux->ncnt, maux->cnt); hts_expand0(int, maux->nals, maux->mals_types, maux->als_types); for (k=0; knals; k++) { free(maux->als[k]); maux->als[k] = strdup(line->d.allele[k]); ma1->map[k] = k; maux->cnt[k] = 1; int var_type = bcf_has_variant_type(line, k, VCF_ANY); if ( args->collapse==COLLAPSE_SNP_INS_DEL ) var_type &= ~VCF_INDEL; maux->als_types[k] = var_type ? var_type<<1 : ref_mask; } return; } // normalize alleles maux->als = merge_alleles(line->d.allele, line->n_allele, ma1->map, maux->als, &maux->nals, &maux->mals); if ( !maux->als ) error("Failed to merge alleles at %s:%"PRId64" in %s\n",maux->chr,(int64_t) line->pos+1,reader->fname); hts_expand0(int, maux->nals, maux->ncnt, maux->cnt); hts_expand0(int, maux->nals, maux->mals_types, maux->als_types); for (k=1; kn_allele; k++) { int ik = ma1->map[k]; int var_type = bcf_has_variant_type(line, k, VCF_ANY); if ( args->collapse==COLLAPSE_SNP_INS_DEL ) var_type &= ~VCF_INDEL; maux->als_types[ik] = var_type ? var_type<<1 : ref_mask; maux->cnt[ik]++; // how many times an allele appears in the files } maux->cnt[0]++; } /* Determine which lines remain to be merged across readers at the current position and are compatible given the -m criteria. This is indicated by maux1_t.skip: 0=compatible, SKIP_DONE=the record is done, SKIP_DIFF=not compatible and will be included next time. At the same time count how many times is each allele present across the readers and records so that we can prioritize the records with the same alleles to come first. In the end maximum one record at a time can be selected from each reader and that witll be done in stage_line(). The function maux_reset already initialized structures for this position, so here each reader comes with the beg,end indexes that point to records with the same maux_t.pos position. */ int can_merge(args_t *args) { bcf_srs_t *files = args->files; maux_t *maux = args->maux; gvcf_aux_t *gaux = maux->gvcf; char *id = NULL, ref = 'N'; int i,j, ntodo = 0; for (i=0; inals; i++) { free(maux->als[i]); maux->als[i] = NULL; maux->cnt[i] = 0; } maux->var_types = maux->nals = 0; // In this loop we do the following: // - remember the first encountered ID if matching by ID // - count the number of unprocessed records at this position // - collect all variant types at this position. This is to be able to perform -m matching and // print SNVs first, then indels, then gVCF blocks // - init the 'skip' variable to SKIP_DIFF for each record that has not been used yet for (i=0; inreaders; i++) { buffer_t *buf = &maux->buf[i]; buf->var_types = 0; if ( gaux && gaux[i].active ) // active gvcf block { buf->rec[buf->beg].skip = SKIP_DIFF; maux->var_types |= ref_mask; buf->var_types |= ref_mask; buf->rec[buf->beg].var_types = ref_mask; continue; } // for gvcf: find out REF at this position if ( buf->beg < buf->end && ref=='N' ) ref = buf->lines[buf->beg]->d.allele[0][0]; for (j=buf->beg; jend; j++) { if ( buf->rec[j].skip & SKIP_DONE ) continue; buf->rec[j].skip = SKIP_DIFF; ntodo++; bcf1_t *line = buf->lines[j]; if ( args->merge_by_id && !id ) { id = line->d.id; continue; } // set ID when merging by id if ( !buf->rec[j].var_types ) { int var_type = bcf_has_variant_types(line, VCF_ANY, bcf_match_overlap); if ( var_type < 0 ) error("bcf_has_variant_types() failed."); if ( args->collapse==COLLAPSE_SNP_INS_DEL ) { // need to distinguish between ins and del so strip the VCF_INDEL flag var_type &= ~VCF_INDEL; } var_type = var_type ? var_type<<1 : ref_mask; if ( args->do_gvcf && is_gvcf_block(line) ) var_type |= ref_mask; buf->rec[j].var_types = var_type; } maux->var_types |= buf->rec[j].var_types; buf->var_types |= buf->rec[j].var_types; } } if ( !ntodo ) return 0; int selected_types = 0; // In this loop we select from each reader compatible candidate lines. // (i.e. SNPs or indels). Go through all files and all lines at this // position and normalize relevant alleles. // REF-only sites may be associated with both SNPs and indels. for (i=0; inreaders; i++) { buffer_t *buf = &maux->buf[i]; if ( gaux && gaux[i].active ) { // gVCF records inherited from an upstream gVCF block have incorrect or missing allele and position gaux[i].line->d.allele[0][0] = ref; gaux[i].line->pos = maux->pos; maux_update_alleles(args, i, buf->beg); selected_types |= ref_mask; continue; } for (j=buf->beg; jend; j++) { if ( buf->rec[j].skip & SKIP_DONE ) continue; bcf1_t *line = buf->lines[j]; // ptr to reader's buffer or gvcf buffer int line_types = buf->rec[j].var_types; // select relevant lines if ( args->merge_by_id ) { if ( strcmp(id,line->d.id) ) continue; // matching by ID and it does not match the selected record } else if ( selected_types && !types_compatible(args,selected_types,buf,j) ) continue; else { // First time here, choosing the first line: prioritize SNPs when available in the -m snps,both modes if ( (args->collapse&COLLAPSE_SNPS || args->collapse==COLLAPSE_NONE) // asked to merge SNVs into multiallelics && (maux->var_types&snp_mask) // there are SNVs at the current position && !(buf->rec[j].var_types&(snp_mask|ref_mask)) // and this record is not a SNV nor ref ) continue; } selected_types |= line_types; buf->rec[j].skip = 0; // the j-th record from i-th reader can be included. Final decision will be made in stage_line maux_update_alleles(args, i, j); } } return 1; } /* Select records that have the same alleles; the input ordering of indels must not matter. Multiple VCF lines can be emitted from this loop. We expect only very few alleles and not many records with the same position in the buffers, therefore the nested loops should not slow us much. */ void stage_line(args_t *args) { bcf_srs_t *files = args->files; maux_t *maux = args->maux; // Take the most frequent allele present in multiple files, REF and gVCF_REF is skipped. int i,j,k,icnt = -1; for (i=1; inals; i++) { if ( maux->als_types[i] & ref_mask ) continue; if ( icnt==-1 || maux->cnt[icnt] < maux->cnt[i] ) icnt = i; } int selected_type = icnt>0 ? maux->als_types[icnt] : ref_mask; int nout = 0; for (i=0; inreaders; i++) { buffer_t *buf = &maux->buf[i]; buf->cur = -1; if ( buf->beg >= buf->end ) continue; // No lines in the buffer at this site // find lines with the same allele for (j=buf->beg; jend; j++) { if ( buf->rec[j].skip ) { int is_gvcf = maux->gvcf && maux->gvcf[i].active ? 1 : 0; if ( !is_gvcf && is_gvcf_block(buf->lines[j]) ) is_gvcf = 1; if ( !is_gvcf ) continue; // done or not compatible } if ( args->merge_by_id ) break; // if merging by ID and the line is compatible, the this is THE line // skip if the reader has a record that matches the most frequent allele and this record is not it if ( (selected_type & buf->var_types) && !(selected_type & buf->rec[j].var_types) ) continue; // if the reader does not have the most frequent allele type but is a ref, accept if ( !(selected_type & buf->var_types) && (buf->rec[j].var_types & ref_mask) ) break; if ( selected_type==ref_mask ) break; // accept if the record has the most frequent allele for (k=0; klines[j]->n_allele; k++) if ( icnt==buf->rec[j].map[k] ) break; if ( klines[j]->n_allele ) break; } if ( j>=buf->end ) { // no matching allele found in this file if ( args->collapse==COLLAPSE_NONE ) continue; // exact matching requested, skip // choose something compatible to create a multiallelic site given the -m criteria for (j=buf->beg; jend; j++) { if ( buf->rec[j].skip ) continue; // done or not compatible if ( args->collapse&COLLAPSE_ANY ) break; // anything can be merged int line_type = buf->rec[j].var_types; if ( maux->var_types&snp_mask && line_type&snp_mask && (args->collapse&COLLAPSE_SNPS) ) break; if ( maux->var_types&indel_mask && line_type&indel_mask && (args->collapse&COLLAPSE_INDELS) ) break; if ( maux->var_types&ins_mask && line_type&ins_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break; if ( maux->var_types&del_mask && line_type&del_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break; if ( line_type&ref_mask ) { if ( maux->var_types&snp_mask && (args->collapse&COLLAPSE_SNPS) ) break; if ( maux->var_types&indel_mask && (args->collapse&COLLAPSE_INDELS) ) break; if ( maux->var_types&ins_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break; if ( maux->var_types&del_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break; if ( maux->var_types&ref_mask ) break; } else if ( maux->var_types&ref_mask ) { if ( line_type&snp_mask && (args->collapse&COLLAPSE_SNPS) ) break; if ( line_type&indel_mask && (args->collapse&COLLAPSE_INDELS) ) break; if ( line_type&ins_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break; if ( line_type&del_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break; } } } if ( jend ) { // found a suitable line for merging buf->cur = j; } } // debug_maux(args); // Mark lines staged for merging as finished so that they are ignored next time for (i=0; inreaders; i++) { buffer_t *buf = &maux->buf[i]; if ( buf->cur == -1 ) continue; buf->rec[buf->cur].skip = SKIP_DONE; nout++; } assert( nout ); } void merge_line(args_t *args) { bcf1_t *out = args->out_line; merge_chrom2qual(args, out); if ( args->regs && !regidx_overlap(args->regs,args->maux->chr,out->pos,out->pos+out->rlen-1,NULL) ) return; merge_filter(args, out); merge_info(args, out); if ( args->do_gvcf ) bcf_update_info_int32(args->out_hdr, out, "END", NULL, 0); merge_format(args, out); int iunseen; if ( args->trim_star_allele && (out->n_allele > 2 || args->trim_star_allele > 1) && (iunseen=get_unseen_allele(out)) && iunseen>0 ) { // the unobserved star allele should be trimmed, either it is variant site or trimming of all sites was requested kbitset_t *rm_set = kbs_init(out->n_allele); kbs_insert(rm_set, iunseen); if ( bcf_remove_allele_set(args->out_hdr,out,rm_set) ) error("[%s] Error: failed to trim the unobserved allele at %s:%"PRIhts_pos"\n",__func__,bcf_seqname(args->out_hdr,out),out->pos+1); kbs_destroy(rm_set); } if ( bcf_write1(args->out_fh, args->out_hdr, out)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); bcf_clear1(out); } void bcf_hdr_append_version(bcf_hdr_t *hdr, int argc, char **argv, const char *cmd) { kstring_t str = {0,0,0}; int e = 0; if (ksprintf(&str,"##%sVersion=%s+htslib-%s\n", cmd, bcftools_version(), hts_version()) < 0) goto fail; if (bcf_hdr_append(hdr,str.s) < 0) goto fail; str.l = 0; e |= ksprintf(&str,"##%sCommand=%s", cmd, argv[0]) < 0; int i; for (i=1; inhrec; i++) { if ( hdr->hrec[i]->type!=BCF_HL_FMT ) continue; j = bcf_hrec_find_key(hdr->hrec[i],"ID"); if ( j<0 ) continue; char *key = hdr->hrec[i]->vals[j]; int id = bcf_hdr_id2int(hdr, BCF_DT_ID, key); assert( id>=0 ); int localize = 0; if ( bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_G ) localize = 1; if ( bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_A ) localize = 1; if ( bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_R ) localize = 1; if ( !localize ) continue; args->tmps.l = 0; uint32_t e = 0, nout = 0; e |= ksprintf(&args->tmps, "##%s=<", hdr->hrec[i]->key) < 0; for (j=0; jhrec[i]->nkeys; j++) { if ( !strcmp("IDX",hdr->hrec[i]->keys[j]) ) continue; if ( nout ) e |= kputc(',',&args->tmps) < 0; if ( !strcmp("ID",hdr->hrec[i]->keys[j]) ) e |= ksprintf(&args->tmps,"%s=L%s", hdr->hrec[i]->keys[j], hdr->hrec[i]->vals[j]) < 0; else if ( !strcmp("Number",hdr->hrec[i]->keys[j]) ) e |= ksprintf(&args->tmps,"Number=.") < 0; else if ( !strcmp("Description",hdr->hrec[i]->keys[j]) && hdr->hrec[i]->vals[j][0]=='"' ) e |= ksprintf(&args->tmps,"Description=\"Localized field: %s", hdr->hrec[i]->vals[j]+1) < 0; else e |= ksprintf(&args->tmps,"%s=%s", hdr->hrec[i]->keys[j], hdr->hrec[i]->vals[j]) < 0; nout++; } e |= ksprintf(&args->tmps,">\n") < 0; if ( e ) error("Failed to format the header line for %s\n", key); nstr++; hts_expand(char*,nstr,mstr,str); str[nstr-1] = strdup(args->tmps.s); } if ( !nstr ) return; bcf_hdr_append(hdr,"##FORMAT="); for (i=0; ioutput_type,args->output_fname,args->clevel); args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno)); if ( args->n_threads ) hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->files->p); //hts_set_threads(args->out_fh, args->n_threads); args->out_hdr = bcf_hdr_init("w"); if ( args->header_fname ) { if ( bcf_hdr_set(args->out_hdr,args->header_fname) ) error("Could not read/parse the header: %s\n", args->header_fname); } else { int i; for (i=0; ifiles->nreaders; i++) { char buf[24]; snprintf(buf,sizeof buf,"%d",i+1); merge_headers(args->out_hdr, args->files->readers[i].header,buf,args->force_samples); } if ( args->local_alleles ) hdr_add_localized_tags(args, args->out_hdr); if (args->record_cmd_line) bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_merge"); if (bcf_hdr_sync(args->out_hdr) < 0) error_errno("[%s] Failed to update header", __func__); } info_rules_init(args); missing_rules_init(args); bcf_hdr_set_version(args->out_hdr, bcf_hdr_get_version(args->files->readers[0].header)); if ( bcf_hdr_write(args->out_fh, args->out_hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); if ( args->header_only ) { bcf_hdr_destroy(args->out_hdr); if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname); return; } else if ( init_index2(args->out_fh,args->out_hdr,args->output_fname, &args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->output_fname); args->vcmp = vcmp_init(); args->maux = maux_init(args); args->out_line = bcf_init1(); args->tmph = kh_init(strdict); int *rid_tab = calloc(args->maux->n, sizeof(*rid_tab)); if (!rid_tab) error("[%s:%d] Could not allocate %zu bytes\n", __FILE__, __LINE__, args->maux->n*sizeof(*rid_tab)); while ( bcf_sr_next_line(args->files) ) { // output cached gVCF blocks which end before the new record if ( args->do_gvcf ) gvcf_flush(args,0); maux_reset(args->maux, rid_tab); // determine which of the new records are gvcf blocks if ( args->do_gvcf ) gvcf_stage(args, args->maux->pos); while ( can_merge(args) ) { stage_line(args); merge_line(args); } clean_buffer(args); // debug_state(args); } free(rid_tab); if ( args->do_gvcf ) gvcf_flush(args,1); info_rules_destroy(args); missing_rules_destroy(args); maux_destroy(args->maux); bcf_hdr_destroy(args->out_hdr); if ( args->write_index ) { if ( bcf_idx_save(args->out_fh)<0 ) { if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname?args->output_fname:"stdout"); bcf_destroy1(args->out_line); kh_destroy(strdict, args->tmph); if ( args->tmps.m ) free(args->tmps.s); if ( args->vcmp ) vcmp_destroy(args->vcmp); } static void usage(void) { fprintf(stderr, "\n"); fprintf(stderr, "About: Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file.\n"); fprintf(stderr, " Note that only records from different files can be merged, never from the same file. For\n"); fprintf(stderr, " \"vertical\" merge take a look at \"bcftools norm\" instead.\n"); fprintf(stderr, "Usage: bcftools merge [options] [...]\n"); fprintf(stderr, "\n"); fprintf(stderr, "Options:\n"); fprintf(stderr, " --force-no-index Merge unindexed files, synonymous to --no-index\n"); fprintf(stderr, " --force-samples Resolve duplicate sample names\n"); fprintf(stderr, " --force-single Run even if there is only one file on input\n"); fprintf(stderr, " --print-header Print only the merged header and exit\n"); fprintf(stderr, " --use-header FILE Use the provided header\n"); fprintf(stderr, " -0 --missing-to-ref Assume genotypes at missing sites are 0/0\n"); fprintf(stderr, " -f, --apply-filters LIST Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n"); fprintf(stderr, " -F, --filter-logic x|+ Remove filters if some input is PASS (\"x\"), or apply all filters (\"+\") [+]\n"); fprintf(stderr, " -g, --gvcf -|REF.FA Merge gVCF blocks, INFO/END tag is expected. Implies -i QS:sum,MinDP:min,MIN_DP:min,I16:sum,IDV:max,IMF:max -M PL:max,AD:0\n"); fprintf(stderr, " -i, --info-rules TAG:METHOD,.. Rules for merging INFO fields (method is one of sum,avg,min,max,join) or \"-\" to turn off the default [DP:sum,DP4:sum]\n"); fprintf(stderr, " -l, --file-list FILE Read file names from the file\n"); fprintf(stderr, " -L, --local-alleles INT If more than INT alt alleles are encountered, drop FMT/PL and output LAA+LPL instead; 0=unlimited [0]\n"); fprintf(stderr, " -m, --merge STRING[*|**] Allow multiallelic records for snps,indels,both,snp-ins-del,all,none,id,*,**; see man page for details [both]\n"); fprintf(stderr, " -M, --missing-rules TAG:METHOD Rules for replacing missing values in numeric vectors (.,0,max) when unknown allele <*> is not present [.]\n"); fprintf(stderr, " --no-index Merge unindexed files, the same chromosomal order is required and -r/-R are not allowed\n"); fprintf(stderr, " --no-version Do not append version and command line to the header\n"); fprintf(stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " --threads INT Use multithreading with INT worker threads [0]\n"); fprintf(stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(stderr, "\n"); exit(1); } int main_vcfmerge(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->files = bcf_sr_init(); args->argc = argc; args->argv = argv; args->output_fname = "-"; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->collapse = COLLAPSE_BOTH; args->clevel = -1; int regions_is_file = 0; int regions_overlap = 1; static struct option loptions[] = { {"help",no_argument,NULL,'h'}, {"merge",required_argument,NULL,'m'}, {"local-alleles",required_argument,NULL,'L'}, {"gvcf",required_argument,NULL,'g'}, {"file-list",required_argument,NULL,'l'}, {"missing-to-ref",no_argument,NULL,'0'}, {"apply-filters",required_argument,NULL,'f'}, {"use-header",required_argument,NULL,1}, {"print-header",no_argument,NULL,2}, {"force-samples",no_argument,NULL,3}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"threads",required_argument,NULL,9}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,4}, {"info-rules",required_argument,NULL,'i'}, {"missing-rules",required_argument,NULL,'M'}, {"no-version",no_argument,NULL,8}, {"no-index",no_argument,NULL,10}, {"force-no-index",no_argument,NULL,10}, {"force-single",no_argument,NULL,12}, {"filter-logic",required_argument,NULL,'F'}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "hm:f:r:R:o:O:i:M:l:g:F:0L:W::",loptions,NULL)) >= 0) { switch (c) { case 'L': args->local_alleles = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --local-alleles %s\n", optarg); if ( args->local_alleles < 1 ) error("Error: \"--local-alleles %s\" makes no sense, expected value bigger or equal than 1\n", optarg); break; case 'F': if ( !strcmp(optarg,"+") ) args->filter_logic = FLT_LOGIC_ADD; else if ( !strcmp(optarg,"x") ) args->filter_logic = FLT_LOGIC_REMOVE; else error("Filter logic not recognised: %s\n", optarg); break; case '0': args->missing_to_ref = 1; break; case 'g': args->do_gvcf = 1; if ( strcmp("-",optarg) ) { args->gvcf_fai = fai_load(optarg); if ( !args->gvcf_fai ) error("Failed to load the fai index: %s\n", optarg); } break; case 'l': args->file_list = optarg; break; case 'i': args->info_rules = optarg; break; case 'M': args->missing_rules_str = optarg; break; case 'o': args->output_fname = optarg; break; case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'm': { int len = strlen(optarg); if ( optarg[len-1]=='*' ) { args->trim_star_allele++; len--; } if ( optarg[len-1]=='*' ) { args->trim_star_allele++; len--; } if ( optarg[len-1]==',' ) len--; args->collapse = COLLAPSE_NONE; if ( !strncmp(optarg,"snp-ins-del",len) ) args->collapse = COLLAPSE_SNP_INS_DEL|COLLAPSE_SNPS; else if ( !strncmp(optarg,"snps",len) ) args->collapse |= COLLAPSE_SNPS; else if ( !strncmp(optarg,"indels",len) ) args->collapse |= COLLAPSE_INDELS; else if ( !strncmp(optarg,"id",len) ) { args->collapse = COLLAPSE_NONE; args->merge_by_id = 1; } else if ( !strncmp(optarg,"any",len) ) args->collapse |= COLLAPSE_ANY; else if ( !strncmp(optarg,"all",len) ) args->collapse |= COLLAPSE_ANY; else if ( !strncmp(optarg,"both",len) ) args->collapse |= COLLAPSE_BOTH; else if ( !strncmp(optarg,"none",len) ) args->collapse = COLLAPSE_NONE; else error("The -m type \"%s\" is not recognised.\n", optarg); break; } case 'f': args->files->apply_filters = optarg; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 1 : args->header_fname = optarg; break; case 2 : args->header_only = 1; break; case 3 : args->force_samples = 1; break; case 4 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 8 : args->record_cmd_line = 0; break; case 10 : args->no_index = 1; break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 12 : args->force_single = 1; break; case 'h': case '?': usage(); break; default: error("Unknown argument: %s\n", optarg); } } if ( argc==optind && !args->file_list ) usage(); if ( args->no_index ) { if ( args->regions_list ) error("Error: cannot combine --no-index with -r/-R\n"); bcf_sr_set_opt(args->files,BCF_SR_ALLOW_NO_IDX); } else bcf_sr_set_opt(args->files,BCF_SR_REQUIRE_IDX); if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); if ( regions_is_file ) args->regs = regidx_init(args->regions_list,NULL,NULL,sizeof(char*),NULL); else { args->regs = regidx_init(NULL,regidx_parse_reg,NULL,sizeof(char*),NULL); if ( regidx_insert_list(args->regs,args->regions_list,',') !=0 ) error("Could not parse the regions: %s\n", args->regions_list); regidx_insert(args->regs,NULL); } if ( !args->regs ) error("Could not parse the regions: %s\n", args->regions_list); args->regs_itr = regitr_init(args->regs); } if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n"); while (optindfiles, argv[optind]) ) error("Failed to open %s: %s\n", argv[optind],bcf_sr_strerror(args->files->errnum)); optind++; } if ( args->file_list ) { int nfiles, i; char **files = hts_readlines(args->file_list, &nfiles); if ( !files ) error("Failed to read from %s\n", args->file_list); for (i=0;ifiles, files[i]) ) error("Failed to open %s: %s\n", files[i],bcf_sr_strerror(args->files->errnum)); for (i=0; ifiles->nreaders ) usage(); if ( args->files->nreaders==1 && !args->force_single ) error("Expected two or more files to merge, got only one. Use --force-single to proceed anyway\n"); merge_vcf(args); bcf_sr_destroy(args->files); if ( args->regs ) regidx_destroy(args->regs); if ( args->regs_itr ) regitr_destroy(args->regs_itr); if ( args->gvcf_fai ) fai_destroy(args->gvcf_fai); free(args); return 0; } pysam-0.23.0/bcftools/vcfmerge.c.pysam.c000066400000000000000000004516631475062545500201070ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfmerge.c -- Merge multiple VCF/BCF files to create one multi-sample file. Copyright (C) 2012-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "regidx.h" #include "vcmp.h" #define DBG 0 #define COLLAPSE_SNP_INS_DEL (1<<10) #include KHASH_MAP_INIT_STR(strdict, int) typedef khash_t(strdict) strdict_t; #define FLT_LOGIC_ADD 0 #define FLT_LOGIC_REMOVE 1 #define SKIP_DONE 1 // the record was processed #define SKIP_DIFF 2 // not compatible, merge later #define IS_VL_G(hdr,id) (bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_G) #define IS_VL_A(hdr,id) (bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_A) #define IS_VL_R(hdr,id) (bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_R) #define SWAP(type_t,a,b) { type_t tmp = (a); (a) = (b); (b) = tmp; } #define PL2PROB_MAX 1024 // Rules for merging FORMAT Number=A,G,R vectors with missing values #define MERGE_MISSING_DOT 0 // leave as is, i.e. use a missing value "." #define MERGE_MISSING_CONST 1 // use a constant value #define MERGE_MISSING_MAX 2 // use the existing maximum value typedef struct _missing_rule_t { char *hdr_tag; int type; float value; } missing_rule_t; // For merging INFO Number=A,G,R tags typedef struct { const char *hdr_tag; int type, nvals; int nbuf, mbuf; uint8_t *buf; } AGR_info_t; // Rules for merging arbitrary INFO tags typedef struct _info_rule_t { char *hdr_tag; void (*merger)(bcf_hdr_t *hdr, bcf1_t *line, struct _info_rule_t *rule); int type; // one of BCF_HT_* int block_size; // number of values in a block int type_size; // size of the corresponding BCF_HT_* type int nblocks; // number of blocks in nvals (the number of merged files) int nvals, mvals; // used and total size of vals array void *vals; // the info tag values } info_rule_t; typedef struct { bcf1_t *line; int end, active; // end: 0-based INFO/END } gvcf_aux_t; // Auxiliary merge data for selecting the right combination // of buffered records across multiple readers. maux1_t // corresponds to one buffered line. typedef struct { int skip; int *map; // mapping from input alleles to the array of output alleles (set by merge_alleles) int mmap; // size of map array (only buffer[i].n_allele is actually used) int als_differ; int var_types; // variant types in this record, shifted by <<1 to account for VCF_REF } maux1_t; // Buffered lines for a single reader typedef struct { int rid; // current rid int beg,end; // valid ranges in reader's buffer [beg,end). Maintained by maux_reset and gvcf_flush. int unkn_allele;// the index of the unknown allele (<*>, ) int cur; // current line or -1 if none int mrec; // allocated size of buf maux1_t *rec; // buffer to keep reader's lines bcf1_t **lines; // source buffer: either gvcf or readers' buffer int var_types; // reader's variant types in the active [beg,end] window } buffer_t; typedef struct { int n, pos, var_types; // number of readers; current position; variant types at this position across all available records int *als_types, // allele type of each output allele mals_types; char *chr; // current chromosome char **als, **out_als; // merged alleles (temp, may contain empty records) and merged alleles ready for output int nals, mals, nout_als, mout_als; // size of the output array int *cnt, ncnt; // number of records that refer to the alleles int *smpl_ploidy, *smpl_nGsize; // ploidy and derived number of values in Number=G tags, updated for each line (todo: cache for missing cases) const char **fmt_key;// temporary short-lived array to store output tag names bcf_fmt_t **fmt_map; // i-th output FORMAT field corresponds in j-th reader to i*nreader+j, first row is reserved for GT int nfmt_map; // number of rows in the fmt_map array int *agr_map, nagr_map, magr_map; // mapping between Number=AGR element indexes, from src idxs to dst file idxs void *tmp_arr; size_t ntmp_arr; buffer_t *buf; AGR_info_t *AGR_info; int nAGR_info, mAGR_info; bcf_srs_t *files; int gvcf_min, // min buffered gvcf END position (NB: gvcf_min is 1-based) or 0 if no active lines are present gvcf_break; // 0-based position of a next record which breaks a gVCF block gvcf_aux_t *gvcf; // buffer of gVCF lines, for each reader one line int nout_smpl; kstring_t *str; int32_t *laa; // localized alternate alleles given as input-based indexes in per-sample blocks of (args->local_alleles+1) values, 0 is always first int nlaa, laa_dirty; // number of LAA alleles actually used at this site, and was any L* added? int32_t *tmpi, *k2k; double *tmpd, *pl2prob; // mapping from phred-score likelihoods (PL) to probability int ntmpi, ntmpd, nk2k; } maux_t; typedef struct { vcmp_t *vcmp; maux_t *maux; regidx_t *regs; // apply regions only after the blocks are expanded regitr_t *regs_itr; int header_only, collapse, output_type, force_samples, force_single, merge_by_id, do_gvcf, filter_logic, missing_to_ref, no_index; char *header_fname, *output_fname, *regions_list, *info_rules, *file_list; faidx_t *gvcf_fai; info_rule_t *rules; int nrules; char *missing_rules_str; missing_rule_t *missing_rules; // lookup for -M, --missing-rules int nmissing_rules; strdict_t *tmph; kstring_t tmps; bcf_srs_t *files; bcf1_t *out_line; htsFile *out_fh; bcf_hdr_t *out_hdr; char **argv; int argc, n_threads, record_cmd_line, clevel; int local_alleles; // the value of -L option int keep_AC_AN; char *index_fn; int write_index; int trim_star_allele; // 0=don't trim; 1=trim at variant sites; 2=trim at all sites } args_t; static bcf1_t *maux_get_line(args_t *args, int i) { maux_t *ma = args->maux; int ibuf = ma->buf[i].cur; if ( ibuf >= 0 ) return ma->buf[i].lines[ibuf]; return NULL; } static void info_rules_merge_sum(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule) { if ( !rule->nvals ) return; int i, j, ndim = rule->block_size; #define BRANCH(type_t,is_missing) { \ type_t *ptr = (type_t*) rule->vals; \ for (i=0; invals; i++) if ( is_missing ) ptr[i] = 0; \ for (i=1; inblocks; i++) \ { \ for (j=0; jtype) { case BCF_HT_INT: BRANCH(int32_t, ptr[i]==bcf_int32_missing); break; case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i])); break; default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type); } #undef BRANCH bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type); } static void info_rules_merge_avg(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule) { if ( !rule->nvals ) return; int i, j, ndim = rule->block_size; #define BRANCH(type_t,is_missing) { \ type_t *ptr = (type_t*) rule->vals; \ for (i=0; invals; i++) if ( is_missing ) ptr[i] = 0; \ for (j=0; jnblocks; i++) sum += ptr[j+i*ndim]; \ ptr[j] = sum / rule->nblocks; \ } \ } switch (rule->type) { case BCF_HT_INT: BRANCH(int32_t, ptr[i]==bcf_int32_missing); break; case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i])); break; default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type); } #undef BRANCH bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type); } static void info_rules_merge_min(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule) { if ( !rule->nvals ) return; int i, j, ndim = rule->block_size; #define BRANCH(type_t,is_missing,set_missing,huge_val) { \ type_t *ptr = (type_t*) rule->vals; \ for (i=0; invals; i++) if ( is_missing ) ptr[i] = huge_val; \ for (i=1; inblocks; i++) \ { \ for (j=0; j ptr[j+i*ndim] ) ptr[j] = ptr[j+i*ndim]; \ } \ for (i=0; invals; i++) if ( ptr[i]==huge_val ) set_missing; \ } switch (rule->type) { case BCF_HT_INT: BRANCH(int32_t, ptr[i]==bcf_int32_missing, ptr[i]=bcf_int32_missing, INT32_MAX); break; case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i]), bcf_float_set_missing(ptr[i]), HUGE_VAL); break; default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type); } #undef BRANCH bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type); } static void info_rules_merge_max(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule) { if ( !rule->nvals ) return; int i, j, ndim = rule->block_size; #define BRANCH(type_t,is_missing,set_missing,huge_val) { \ type_t *ptr = (type_t*) rule->vals; \ for (i=0; invals; i++) if ( is_missing ) ptr[i] = huge_val; \ for (i=1; inblocks; i++) \ { \ for (j=0; jnvals; i++) if ( ptr[i]==huge_val ) set_missing; \ } switch (rule->type) { case BCF_HT_INT: BRANCH(int32_t, ptr[i]==bcf_int32_missing, ptr[i]=bcf_int32_missing, INT32_MIN); break; case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i]), bcf_float_set_missing(ptr[i]), -HUGE_VAL); break; default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type); } #undef BRANCH bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type); } static void info_rules_merge_join(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule) { if ( !rule->nvals ) return; if ( rule->type==BCF_HT_STR ) { ((char*)rule->vals)[rule->nvals] = 0; bcf_update_info_string(hdr,line,rule->hdr_tag,rule->vals); } else { int isrc, idst = 0; #define BRANCH(type_t,is_missing,is_vector_end) { \ type_t *ptr = (type_t*) rule->vals; \ for (isrc=0; isrcnvals; isrc++) \ { \ if ( is_vector_end ) break; \ if ( is_missing ) continue; \ if ( idst!=isrc ) ptr[idst] = ptr[isrc]; \ idst++; \ } \ } switch (rule->type) { case BCF_HT_INT: BRANCH(int32_t, ptr[isrc]==bcf_int32_missing, ptr[isrc]==bcf_int32_vector_end); break; case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[isrc]), bcf_float_is_vector_end(ptr[isrc])); break; default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type); } #undef BRANCH rule->nvals = idst; bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,rule->nvals,rule->type); } } static int missing_rules_comp_key2(const void *a, const void *b) { missing_rule_t *rule1 = (missing_rule_t*) a; missing_rule_t *rule2 = (missing_rule_t*) b; return strcmp(rule1->hdr_tag, rule2->hdr_tag); } static int missing_rules_comp_key(const void *a, const void *b) { char *key = (char*) a; missing_rule_t *rule = (missing_rule_t*) b; return strcmp(key, rule->hdr_tag); } static void missing_rules_init(args_t *args) { kstring_t str = {0,0,0}; if ( args->missing_rules_str ) { if ( !strcmp("-",args->missing_rules_str) ) kputs("PL:.,AD:.",&str); else kputs(args->missing_rules_str,&str); } else if ( args->do_gvcf ) kputs("PL:max,AD:0",&str); else return; args->nmissing_rules = 1; char *ss = str.s, *tmp = ss; int n = 0; while ( *ss ) { if ( *ss==':' ) { *ss = 0; n++; if ( n%2==0 ) error("Could not parse --missing-rules: \"%s\"\n", args->missing_rules_str); } else if ( *ss==',' ) { *ss = 0; args->nmissing_rules++; n++; if ( n%2==1 ) error("Could not parse --missing-rules: \"%s\"\n", args->missing_rules_str); } ss++; } if ( n%2==0 ) error("Could not parse --missing-rules: \"%s\"\n", args->missing_rules_str); args->missing_rules = (missing_rule_t*) calloc(args->nmissing_rules,sizeof(missing_rule_t)); n = args->nmissing_rules; args->nmissing_rules = 0; ss = tmp; while ( args->nmissing_rules < n ) { missing_rule_t *rule = &args->missing_rules[args->nmissing_rules]; rule->hdr_tag = strdup(ss); int id = bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, rule->hdr_tag); if ( !bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_FMT,id) ) { if ( args->missing_rules_str ) error("The FORMAT tag is not defined in the header: \"%s\"\n", rule->hdr_tag); free(rule->hdr_tag); n--; ss = strchr(ss, '\0'); ss++; if ( !*ss ) error("Could not parse --missing-rules, missing logic of \"%s\"\n", rule->hdr_tag); ss = strchr(ss, '\0'); ss++; continue; } ss = strchr(ss, '\0'); ss++; if ( !*ss ) error("Could not parse --missing-rules, missing logic of \"%s\"\n", rule->hdr_tag); if ( !strcasecmp(ss,".") ) rule->type = MERGE_MISSING_DOT; else if ( !strcasecmp(ss,"max") ) rule->type = MERGE_MISSING_MAX; else { char *tmp = ss; rule->value = strtod(ss, &tmp); if ( *tmp ) error("Could not parse --missing-rules: \"%s\"\n", args->missing_rules_str); rule->type = MERGE_MISSING_CONST; } ss = strchr(ss, '\0'); ss++; args->nmissing_rules++; } qsort(args->missing_rules, args->nmissing_rules, sizeof(*args->missing_rules), missing_rules_comp_key2); free(str.s); } static void missing_rules_destroy(args_t *args) { int i; for (i=0; inmissing_rules; i++) { missing_rule_t *rule = &args->missing_rules[i]; free(rule->hdr_tag); } free(args->missing_rules); } static int info_rules_comp_key2(const void *a, const void *b) { info_rule_t *rule1 = (info_rule_t*) a; info_rule_t *rule2 = (info_rule_t*) b; return strcmp(rule1->hdr_tag, rule2->hdr_tag); } static int info_rules_comp_key(const void *a, const void *b) { char *key = (char*) a; info_rule_t *rule = (info_rule_t*) b; return strcmp(key, rule->hdr_tag); } static void info_rules_init(args_t *args) { if ( args->info_rules && !strcmp("-",args->info_rules) ) return; kstring_t str = {0,0,0}; if ( !args->info_rules ) { if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "DP")) ) kputs("DP:sum",&str); if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "DP4")) ) { if ( str.l ) kputc(',',&str); kputs("DP4:sum",&str); } if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "QS")) ) { if ( str.l ) kputc(',',&str); kputs("QS:sum",&str); } if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "MIN_DP")) ) { if ( str.l ) kputc(',',&str); kputs("MIN_DP:min",&str); } if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "MinDP")) ) { if ( str.l ) kputc(',',&str); kputs("MinDP:min",&str); } if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "I16")) ) { if ( str.l ) kputc(',',&str); kputs("I16:sum",&str); } if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "IDV")) ) { if ( str.l ) kputc(',',&str); kputs("IDV:max",&str); } if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "IMF")) ) { if ( str.l ) kputc(',',&str); kputs("IMF:max",&str); } if ( !bcf_hdr_nsamples(args->out_hdr) ) { if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "AN")) ) { if ( str.l ) kputc(',',&str); kputs("AN:sum",&str); } if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "AC")) ) { if ( str.l ) kputc(',',&str); kputs("AC:sum",&str); } } if ( !str.l ) return; args->info_rules = str.s; } args->nrules = 1; char *ss = strdup(args->info_rules), *tmp = ss; int n = 0; while ( *ss ) { if ( *ss==':' ) { *ss = 0; n++; if ( n%2==0 ) error("Could not parse INFO rules: \"%s\"\n", args->info_rules); } else if ( *ss==',' ) { *ss = 0; args->nrules++; n++; if ( n%2==1 ) error("Could not parse INFO rules: \"%s\"\n", args->info_rules); } ss++; } if ( n%2==0 ) error("Could not parse INFO rules: \"%s\"\n", args->info_rules); args->rules = (info_rule_t*) calloc(args->nrules,sizeof(info_rule_t)); n = 0; ss = tmp; while ( n < args->nrules ) { info_rule_t *rule = &args->rules[n]; rule->hdr_tag = strdup(ss); int id = bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, rule->hdr_tag); if ( !bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,id) ) error("The INFO tag is not defined in the header: \"%s\"\n", rule->hdr_tag); rule->type = bcf_hdr_id2type(args->out_hdr,BCF_HL_INFO,id); if ( rule->type==BCF_HT_INT ) rule->type_size = sizeof(int32_t); else if ( rule->type==BCF_HT_REAL ) rule->type_size = sizeof(float); else if ( rule->type==BCF_HT_STR ) rule->type_size = sizeof(char); else error("The INFO rule \"%s\" is not supported; the tag \"%s\" type is %d\n", ss,rule->hdr_tag,rule->type); if ( !strcmp(rule->hdr_tag,"AC") || !strcmp(rule->hdr_tag,"AN") ) args->keep_AC_AN = 1; ss = strchr(ss, '\0'); ss++; if ( !*ss ) error("Could not parse INFO rules, missing logic of \"%s\"\n", rule->hdr_tag); int is_join = 0; if ( !strcasecmp(ss,"sum") ) rule->merger = info_rules_merge_sum; else if ( !strcasecmp(ss,"avg") ) rule->merger = info_rules_merge_avg; else if ( !strcasecmp(ss,"min") ) rule->merger = info_rules_merge_min; else if ( !strcasecmp(ss,"max") ) rule->merger = info_rules_merge_max; else if ( !strcasecmp(ss,"join") ) { rule->merger = info_rules_merge_join; is_join = 1; } else error("The rule logic \"%s\" not recognised\n", ss); if ( !is_join && rule->type==BCF_HT_STR ) error("Numeric operation \"%s\" requested on non-numeric field: %s\n", ss, rule->hdr_tag); if ( bcf_hdr_id2number(args->out_hdr,BCF_HL_INFO,id)==0xfffff ) { int is_agr = ( bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)==BCF_VL_A || bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)==BCF_VL_G || bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)==BCF_VL_R ) ? 1 : 0; if ( is_join && bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)!=BCF_VL_VAR ) { bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->out_hdr, BCF_HL_INFO, "ID", rule->hdr_tag, NULL); hrec = bcf_hrec_dup(hrec); int i = bcf_hrec_find_key(hrec, "Number"); if ( i<0 ) error("Uh, could not find the entry Number in the header record of %s\n",rule->hdr_tag); free(hrec->vals[i]); hrec->vals[i] = strdup("."); bcf_hdr_remove(args->out_hdr,BCF_HL_INFO, rule->hdr_tag); bcf_hdr_add_hrec(args->out_hdr, hrec); } if ( !is_join && !is_agr ) error("Only fixed-length vectors are supported with -i %s:%s\n", ss, rule->hdr_tag); } ss = strchr(ss, '\0'); ss++; n++; } free(str.s); free(tmp); qsort(args->rules, args->nrules, sizeof(*args->rules), info_rules_comp_key2); } static void info_rules_destroy(args_t *args) { int i; for (i=0; inrules; i++) { info_rule_t *rule = &args->rules[i]; free(rule->hdr_tag); free(rule->vals); } free(args->rules); } static void info_rules_reset(args_t *args) { int i; for (i=0; inrules; i++) args->rules[i].nblocks = args->rules[i].nvals = args->rules[i].block_size = 0; } static int info_rules_add_values(args_t *args, bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule, maux1_t *als, int var_len) { int msize = args->maux->ntmp_arr / rule->type_size; int ret = bcf_get_info_values(hdr, line, rule->hdr_tag, &args->maux->tmp_arr, &msize, rule->type); if ( ret<=0 ) error("FIXME: error parsing %s at %s:%"PRId64" .. %d\n", rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1,ret); args->maux->ntmp_arr = msize * rule->type_size; rule->nblocks++; if ( rule->type==BCF_HT_STR ) { int need_comma = rule->nblocks==1 ? 0 : 1; hts_expand(char,rule->nvals+ret+need_comma+1,rule->mvals,rule->vals); // 1 for null-termination char *tmp = (char*) rule->vals + rule->nvals; if ( rule->nvals>0 ) { *tmp = ','; tmp++; } strncpy(tmp,(char*)args->maux->tmp_arr,ret); rule->nvals += ret + need_comma; return 1; } int i, j; if ( var_len==BCF_VL_A ) { if ( ret!=line->n_allele-1 ) error("Wrong number of %s fields at %s:%"PRId64"\n",rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1); args->maux->nagr_map = ret; hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map); // create mapping from source file ALT indexes to dst file indexes for (i=0; imaux->agr_map[i] = als->map[i+1] - 1; rule->block_size = args->maux->nout_als - 1; } else if ( var_len==BCF_VL_R ) { if ( ret!=line->n_allele ) error("Wrong number of %s fields at %s:%"PRId64"\n",rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1); args->maux->nagr_map = ret; hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map); for (i=0; imaux->agr_map[i] = als->map[i]; rule->block_size = args->maux->nout_als; } else if ( var_len==BCF_VL_G ) { args->maux->nagr_map = bcf_alleles2gt(line->n_allele-1,line->n_allele-1)+1; if ( ret!=line->n_allele && ret!=args->maux->nagr_map ) error("Wrong number of %s fields at %s:%"PRId64"\n",rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1); if ( ret==line->n_allele ) // haploid { args->maux->nagr_map = line->n_allele; hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map); for (i=0; imaux->agr_map[i] = als->map[i]; rule->block_size = args->maux->nout_als; } else { hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map); int k_src = 0; for (i=0; in_allele; i++) { for (j=0; j<=i; j++) { args->maux->agr_map[k_src] = bcf_alleles2gt(als->map[i],als->map[j]); k_src++; } } rule->block_size = bcf_alleles2gt(args->maux->nout_als-1,args->maux->nout_als-1)+1; } } else { if ( rule->nblocks>1 && ret!=rule->block_size ) error("Mismatch in number of values for INFO/%s at %s:%"PRId64"\n", rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1); rule->block_size = ret; args->maux->nagr_map = 0; } #define BRANCH(src_type_t,dst_type_t,set_missing) { \ src_type_t *src = (src_type_t *) args->maux->tmp_arr; \ hts_expand0(dst_type_t,(rule->nvals+rule->block_size),rule->mvals,rule->vals); \ dst_type_t *dst = (dst_type_t *) rule->vals + rule->nvals; \ rule->nvals += rule->block_size; \ if ( !args->maux->nagr_map ) \ { \ for (i=0; iblock_size; i++) set_missing; \ for (i=0; imaux->agr_map[i]] = src[i]; \ } \ } switch (rule->type) { case BCF_HT_INT: BRANCH(int, int32_t, dst[i] = bcf_int32_missing); break; case BCF_HT_REAL: BRANCH(float, float, bcf_float_set_missing(dst[i])); break; default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type); } #undef BRANCH return 1; } int bcf_hdr_sync(bcf_hdr_t *h); void merge_headers(bcf_hdr_t *hw, const bcf_hdr_t *hr, const char *clash_prefix, int force_samples) { // header lines hw = bcf_hdr_merge(hw, hr); // samples int i; for (i=0; isamples[i]; while ( bcf_hdr_id2int(hw, BCF_DT_SAMPLE, name)!=-1 ) { // there is a sample with the same name if ( !force_samples ) error("Error: Duplicate sample names (%s), use --force-samples to proceed anyway.\n", name); // Resolve conflicting samples names. For example, replace: // A + A with A,2:A // A,2:A + A with A,2:A,2:2:A int len = strlen(name) + strlen(clash_prefix) + 1; char *tmp = (char*) malloc(sizeof(char)*(len+1)); sprintf(tmp,"%s:%s",clash_prefix,name); free(rmme); rmme = name = tmp; } bcf_hdr_add_sample(hw,name); free(rmme); } } void debug_als(char **als, int nals) { int k; for (k=0; k=lens[j] ) done = 1; if ( als[j][lens[j]-i] != als[0][lens[0]-i] ) { done = 1; break; } } if ( done ) break; i++; } if ( i>1 ) { i--; als[0][lens[0]-i] = 0; for (j=1; j0, * 1->2, and 2->3. */ char **merge_alleles(char **a, int na, int *map, char **b, int *nb, int *mb) { // reference allele never changes map[0] = 0; int i,j; int rla = !a[0][1] ? 1 : strlen(a[0]); int rlb = !b[0][1] ? 1 : strlen(b[0]); // the most common case: same SNPs if ( na==2 && *nb==2 && rla==1 && rlb==1 && a[1][0]==b[1][0] && !a[1][1] && !b[1][1] ) { map[1] = 1; return b; } // Sanity check: reference prefixes must be identical if ( strncmp(a[0],b[0],rlarlb ) { for (i=0; i<*nb; i++) { if ( b[i][0]=='<' ) continue; // symbolic allele, do not modify if ( b[i][0]=='*' ) continue; // overlapping deletion (*), do not modify int l = strlen(b[i]); b[i] = (char*) realloc(b[i],l+rla-rlb+1); memcpy(b[i]+l,a[0]+rlb,rla-rlb+1); } } // now check if the $a alleles are present and if not add them for (i=1; irla && a[i][0]!='<' && a[i][0]!='*' ) // $a alleles need expanding and not a symbolic allele or * { int l = strlen(a[i]); ai = (char*) malloc(l+rlb-rla+1); memcpy(ai,a[i],l); memcpy(ai+l,b[0]+rla,rlb-rla+1); const_ai = 0; } else ai = a[i]; for (j=1; j<*nb; j++) if ( !strcasecmp(ai,b[j]) ) break; if ( j<*nb ) // $b already has the same allele { map[i] = j; if ( !const_ai ) free(ai); continue; } // new allele map[i] = *nb; b[*nb] = const_ai ? strdup(ai) : ai; (*nb)++; } return b; } maux_t *maux_init(args_t *args) { bcf_srs_t *files = args->files; maux_t *ma = (maux_t*) calloc(1,sizeof(maux_t)); ma->n = files->nreaders; ma->files = files; int i, n_smpl = 0; for (i=0; in; i++) n_smpl += bcf_hdr_nsamples(files->readers[i].header); ma->nout_smpl = n_smpl; assert( n_smpl==bcf_hdr_nsamples(args->out_hdr) ); if ( args->do_gvcf ) { ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n for (i=0; in; i++) ma->gvcf[i].line = bcf_init1(); } ma->smpl_ploidy = (int*) calloc(n_smpl,sizeof(int)); ma->smpl_nGsize = (int*) malloc(n_smpl*sizeof(int)); ma->buf = (buffer_t*) calloc(ma->n,sizeof(buffer_t)); for (i=0; in; i++) ma->buf[i].rid = -1; ma->str = (kstring_t*) calloc(n_smpl,sizeof(kstring_t)); if ( args->local_alleles ) { ma->laa = (int32_t*)malloc(sizeof(*ma->laa)*ma->nout_smpl*(1+args->local_alleles)); ma->pl2prob = (double*)malloc(PL2PROB_MAX*sizeof(*ma->pl2prob)); for (i=0; ipl2prob[i] = pow(10,-0.1*i); } return ma; } void maux_destroy(maux_t *ma) { int i,j; for (i=0; inout_smpl; i++) free(ma->str[i].s); free(ma->str); free(ma->als_types); for (i=0; imals; i++) { free(ma->als[i]); ma->als[i] = NULL; } for (i=0; in; i++) // for each reader { for (j=0; jbuf[i].mrec; j++) // for each buffered line free(ma->buf[i].rec[j].map); free(ma->buf[i].rec); } free(ma->buf); if ( ma->gvcf ) { for (i=0; in; i++) bcf_destroy(ma->gvcf[i].line); free(ma->gvcf); } for (i=0; imAGR_info; i++) free(ma->AGR_info[i].buf); free(ma->agr_map); free(ma->AGR_info); if (ma->ntmp_arr) free(ma->tmp_arr); if (ma->nfmt_map) free(ma->fmt_map); free(ma->fmt_key); // ma->inf freed in bcf_destroy1 for (i=0; imals; i++) free(ma->als[i]); if (ma->mout_als) free(ma->out_als); free(ma->als); free(ma->cnt); free(ma->smpl_ploidy); free(ma->smpl_nGsize); free(ma->chr); free(ma->laa); free(ma->tmpi); free(ma->k2k); free(ma->tmpd); free(ma->pl2prob); free(ma); } void maux_expand1(buffer_t *buf, int size) { if ( buf->mrec < size ) { hts_expand0(maux1_t,size,buf->mrec,buf->rec); buf->mrec = size; } } void maux_reset(maux_t *ma, int *rid_tab) { int i,j; for (i=0; in; i++) maux_expand1(&ma->buf[i],ma->files->readers[i].nbuffer+1); for (i=0; imals; i++) { free(ma->als[i]); ma->als[i] = NULL; } const char *chr = NULL; ma->nals = 0; ma->pos = -1; for (i=0; in; i++) { if ( !bcf_sr_has_line(ma->files,i) ) continue; bcf1_t *line = bcf_sr_get_line(ma->files,i); bcf_hdr_t *hdr = bcf_sr_get_header(ma->files,i); chr = bcf_seqname(hdr,line); ma->pos = line->pos; break; } int new_chr = 0; if ( chr && (!ma->chr || strcmp(ma->chr,chr)) ) { free(ma->chr); ma->chr = strdup(chr); new_chr = 1; } for (i=0; in; i++) { bcf_hdr_t *hdr = bcf_sr_get_header(ma->files,i); if (new_chr) rid_tab[i] = bcf_hdr_name2id(hdr,chr); ma->buf[i].rid = rid_tab[i]; ma->buf[i].beg = bcf_sr_has_line(ma->files,i) ? 0 : 1; for (j=ma->buf[i].beg; j<=ma->files->readers[i].nbuffer; j++) { ma->buf[i].rec[j].skip = 0; ma->buf[i].rec[j].var_types = 0; bcf1_t *line = ma->files->readers[i].buffer[j]; if ( line->rid!=ma->buf[i].rid || line->pos!=ma->pos ) break; } ma->buf[i].end = j; ma->buf[i].cur = -1; if ( ma->buf[i].beg < ma->buf[i].end ) { ma->buf[i].lines = ma->files->readers[i].buffer; if ( ma->gvcf ) ma->gvcf[i].active = 0; // gvcf block cannot overlap with the next record } if ( new_chr && ma->gvcf ) ma->gvcf[i].active = 0; // make sure to close active gvcf block on new chr } } void maux_debug(maux_t *ma, int ir, int ib) { fprintf(bcftools_stdout, "[%d,%d]\t", ir,ib); int i; for (i=0; inals; i++) { fprintf(bcftools_stdout, " %s [%d]", ma->als[i], ma->cnt[i]); } fprintf(bcftools_stdout, "\n"); } void merge_chrom2qual(args_t *args, bcf1_t *out) { bcf_srs_t *files = args->files; bcf_hdr_t *out_hdr = args->out_hdr; int i, ret; khiter_t kitr; strdict_t *tmph = args->tmph; kh_clear(strdict, tmph); kstring_t *tmps = &args->tmps; tmps->l = 0; maux_t *ma = args->maux; int *al_idxs = (int*) calloc(ma->nals,sizeof(int)); bcf_float_set_missing(out->qual); // CHROM, POS, ID, QUAL out->pos = -1; for (i=0; inreaders; i++) { bcf1_t *line = maux_get_line(args, i); if ( !line ) continue; bcf_unpack(line, BCF_UN_ALL); bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; // not all maux alleles are always used, mark the ones we'll need int j; for (j=1; jn_allele; j++) { int irec = ma->buf[i].cur; al_idxs[ ma->buf[i].rec[irec].map[j] ] = 1; } // position if ( out->pos==-1 ) { const char *chr = hdr->id[BCF_DT_CTG][line->rid].key; out->rid = bcf_hdr_name2id(out_hdr, chr); if ( strcmp(chr,out_hdr->id[BCF_DT_CTG][out->rid].key) ) error("Uh\n"); out->pos = line->pos; } // ID if ( line->d.id[0]!='.' || line->d.id[1] ) { kitr = kh_get(strdict, tmph, line->d.id); if ( kitr == kh_end(tmph) ) { if ( tmps->l ) kputc(';', tmps); kputs(line->d.id, tmps); kh_put(strdict, tmph, line->d.id, &ret); } } // set QUAL to the max qual value. Not exactly correct, but good enough for now if ( !bcf_float_is_missing(line->qual) ) { if ( bcf_float_is_missing(out->qual) || out->qual < line->qual ) out->qual = line->qual; } } // set ID if ( !tmps->l ) kputs(".", tmps); bcf_update_id(out_hdr, out, tmps->s); // set alleles ma->nout_als = 0; for (i=1; inals; i++) { if ( !al_idxs[i] ) continue; ma->nout_als++; // Adjust the indexes, the allele map could be created for multiple collapsed records, // some of which might be unused for this output line int ir, j; for (ir=0; irnreaders; ir++) { ma->buf[ir].unkn_allele = 0; bcf1_t *line = maux_get_line(args,ir); if ( !line ) continue; for (j=1; jn_allele; j++) { int irec = ma->buf[ir].cur; if ( ma->buf[ir].rec[irec].map[j]==i ) ma->buf[ir].rec[irec].map[j] = ma->nout_als; if ( bcf_has_variant_type(line,j,VCF_REF) && line->d.allele[j][0]=='<' ) ma->buf[ir].unkn_allele = j; } } } // Expand the arrays and realloc the alleles string. Note that all alleles are in a single allocated block. ma->nout_als++; hts_expand0(char*, ma->nout_als, ma->mout_als, ma->out_als); int k = 0; for (i=0; inals; i++) if ( i==0 || al_idxs[i] ) ma->out_als[k++] = strdup(ma->als[i]); if ( k!=ma->nout_als ) error("Error: could not merge alleles at %s:%"PRId64", sanity check failed: %d!=%d\n",bcf_seqname(out_hdr,out),out->pos+1,k,ma->nout_als); normalize_alleles(ma->out_als, ma->nout_als); bcf_update_alleles(out_hdr, out, (const char**) ma->out_als, ma->nout_als); free(al_idxs); for (i=0; inout_als; i++) free(ma->out_als[i]); } void merge_filter(args_t *args, bcf1_t *out) { bcf_srs_t *files = args->files; bcf_hdr_t *out_hdr = args->out_hdr; int i, ret; if ( args->filter_logic == FLT_LOGIC_REMOVE ) { for (i=0; inreaders; i++) { bcf1_t *line = maux_get_line(args, i); if ( !line ) continue; bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; if ( bcf_has_filter(hdr, line, "PASS") ) break; } if ( inreaders ) { int flt_id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, "PASS"); bcf_add_filter(out_hdr, out, flt_id); return; } } khiter_t kitr; strdict_t *tmph = args->tmph; kh_clear(strdict, tmph); out->d.n_flt = 0; for (i=0; inreaders; i++) { bcf1_t *line = maux_get_line(args, i); if ( !line ) continue; bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; int k; for (k=0; kd.n_flt; k++) { const char *flt = hdr->id[BCF_DT_ID][line->d.flt[k]].key; kitr = kh_get(strdict, tmph, flt); if ( kitr == kh_end(tmph) ) { int id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, flt); if ( id==-1 ) error("Error: The filter is not defined in the header: %s\n", flt); hts_expand(int,out->d.n_flt+1,out->d.m_flt,out->d.flt); out->d.flt[out->d.n_flt] = id; out->d.n_flt++; kh_put(strdict, tmph, flt, &ret); } } } // Check if PASS is not mixed with other filters if ( out->d.n_flt>1 ) { int id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, "PASS"); for (i=0; id.n_flt; i++) if ( out->d.flt[i]==id ) break; if ( id.n_flt ) { out->d.n_flt--; for (; id.n_flt; i++) out->d.flt[i] = out->d.flt[i+1]; } } } static void bcf_info_set_id(bcf1_t *line, bcf_info_t *info, int id, kstring_t *tmp_str) { uint8_t *ptr = info->vptr - info->vptr_off; bcf_dec_typed_int1(ptr, &ptr); tmp_str->l = 0; bcf_enc_int1(tmp_str, id); if ( tmp_str->l == ptr - info->vptr + info->vptr_off ) { // the new id is represented with the same number of bytes memcpy(info->vptr - info->vptr_off, tmp_str->s, tmp_str->l); return; } kputsn_(ptr, info->vptr - ptr, tmp_str); info->vptr_off = tmp_str->l; kputsn_(info->vptr, info->len << bcf_type_shift[info->type], tmp_str); info->vptr = (uint8_t*) tmp_str->s + info->vptr_off; tmp_str->s = NULL; tmp_str->m = 0; tmp_str->l = 0; } /* * copy_string_field() - copy a comma-separated field * @param src: source string * @param isrc: index of the field to copy * @param src_len: length of source string (excluding the terminating \0) * @param dst: destination kstring (must be initialized with missing values, e.g. as ".") * @param idst: index of the destination field */ int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst) { int ith_src = 0, start_src = 0; // i-th field in src string while ( ith_srcl ) { if ( dst->s[start_dst]==',' ) { ith_dst++; } start_dst++; } if ( ith_dst!=idst ) return -2; int end_dst = start_dst; while ( end_dstl && dst->s[end_dst]!=',' ) end_dst++; if ( end_dst - start_dst>1 || dst->s[start_dst]!='.' ) return 0; // do not overwrite non-empty values // Now start_dst and end_dst are indexes to the destination memory area // which needs to be replaced with nsrc_cpy // source bytes, end_dst points just after. int ndst_shift = nsrc_cpy - (end_dst - start_dst); int ndst_move = dst->l - end_dst + 1; // how many bytes must be moved (including \0) if ( ndst_shift ) { ks_resize(dst, dst->l + ndst_shift + 1); // plus \0 memmove(dst->s+end_dst+ndst_shift, dst->s+end_dst, ndst_move); } memcpy(dst->s+start_dst, src+start_src, nsrc_cpy); dst->l += ndst_shift; return 0; } static void merge_AGR_info_tag(bcf_hdr_t *hdr, bcf1_t *line, bcf_info_t *info, int len, maux1_t *als, AGR_info_t *agr) { int i; if ( !agr->nbuf ) { if ( info->type==BCF_BT_INT8 || info->type==BCF_BT_INT16 || info->type==BCF_BT_INT32 || info->type==BCF_BT_FLOAT ) { agr->nbuf = 4 * agr->nvals; hts_expand(uint8_t,agr->nbuf,agr->mbuf,agr->buf); if ( info->type!=BCF_BT_FLOAT ) { int32_t *tmp = (int32_t*) agr->buf; for (i=0; invals; i++) tmp[i] = bcf_int32_missing; } else { float *tmp = (float*) agr->buf; for (i=0; invals; i++) bcf_float_set_missing(tmp[i]); } } else if ( info->type==BCF_BT_CHAR ) { kstring_t tmp; tmp.l = 0; tmp.m = agr->mbuf; tmp.s = (char*)agr->buf; kputc('.',&tmp); for (i=1; invals; i++) kputs(",.",&tmp); agr->mbuf = tmp.m; agr->nbuf = tmp.l; agr->buf = (uint8_t*)tmp.s; } else error("Not ready for type [%d]: %s at %"PRId64"\n", info->type,agr->hdr_tag,(int64_t) line->pos+1); } if ( info->type==BCF_BT_INT8 || info->type==BCF_BT_INT16 || info->type==BCF_BT_INT32 || info->type==BCF_BT_FLOAT ) { if ( len==BCF_VL_A || len==BCF_VL_R ) { int ifrom = len==BCF_VL_A ? 1 : 0; #define BRANCH(type_t, convert, is_missing, is_vector_end, out_type_t) { \ uint8_t *src = info->vptr; \ out_type_t *tgt = (out_type_t *) agr->buf; \ int iori, inew; \ for (iori=ifrom; iorin_allele; iori++, src += sizeof(type_t)) \ { \ type_t val = convert(src); \ if ( is_vector_end ) break; \ if ( is_missing ) continue; \ inew = als->map[iori] - ifrom; \ tgt[inew] = val; \ } \ } switch (info->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, int); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, int); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, val==bcf_int32_missing, val==bcf_int32_vector_end, int); break; case BCF_BT_FLOAT: BRANCH(float, le_to_float, bcf_float_is_missing(val), bcf_float_is_vector_end(val), float); break; default: fprintf(bcftools_stderr,"TODO: %s:%d .. info->type=%d\n", __FILE__,__LINE__, info->type); bcftools_exit(1); } #undef BRANCH } else { #define BRANCH(type_t, convert, is_missing, is_vector_end, out_type_t) { \ uint8_t *src = info->vptr; \ out_type_t *tgt = (out_type_t *) agr->buf; \ int iori,jori, inew,jnew; \ for (iori=0; iorin_allele; iori++) \ { \ inew = als->map[iori]; \ for (jori=0; jori<=iori; jori++) \ { \ jnew = als->map[jori]; \ int kori = iori*(iori+1)/2 + jori; \ type_t val = convert(&src[kori * sizeof(type_t)]); \ if ( is_vector_end ) break; \ if ( is_missing ) continue; \ int knew = inew>jnew ? inew*(inew+1)/2 + jnew : jnew*(jnew+1)/2 + inew; \ tgt[knew] = val; \ } \ if ( jori<=iori ) break; \ } \ } switch (info->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, int); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, int); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, val==bcf_int32_missing, val==bcf_int32_vector_end, int); break; case BCF_BT_FLOAT: BRANCH(float, le_to_float, bcf_float_is_missing(val), bcf_float_is_vector_end(val), float); break; default: fprintf(bcftools_stderr,"TODO: %s:%d .. info->type=%d\n", __FILE__,__LINE__, info->type); bcftools_exit(1); } #undef BRANCH } } else { kstring_t tmp; tmp.l = agr->nbuf; tmp.m = agr->mbuf; tmp.s = (char*)agr->buf; if ( len==BCF_VL_A || len==BCF_VL_R ) { int iori, ifrom = len==BCF_VL_A ? 1 : 0; for (iori=ifrom; iorin_allele; iori++) { int ret = copy_string_field((char*)info->vptr, iori-ifrom, info->len, &tmp, als->map[iori]-ifrom); if ( ret ) error("Error at %s:%"PRId64": wrong number of fields in %s?\n", bcf_seqname(hdr,line),(int64_t) line->pos+1,agr->hdr_tag); } } else { int iori,jori, inew,jnew; for (iori=0; iorin_allele; iori++) { inew = als->map[iori]; for (jori=0; jori<=iori; jori++) { jnew = als->map[jori]; int kori = iori*(iori+1)/2 + jori; int knew = bcf_alleles2gt(inew,jnew); int ret = copy_string_field((char*)info->vptr, kori, info->len, &tmp, knew); if ( ret ) error("Error at %s:%"PRId64": wrong number of fields in %s?\n", bcf_seqname(hdr,line),(int64_t) line->pos+1,agr->hdr_tag); } } } agr->mbuf = tmp.m; agr->nbuf = tmp.l; agr->buf = (uint8_t*)tmp.s; } } void merge_info(args_t *args, bcf1_t *out) { bcf_srs_t *files = args->files; bcf_hdr_t *out_hdr = args->out_hdr; int i, j, ret; khiter_t kitr; strdict_t *tmph = args->tmph; kh_clear(strdict, tmph); maux_t *ma = args->maux; ma->nAGR_info = 0; out->n_info = 0; info_rules_reset(args); for (i=0; inreaders; i++) { bcf1_t *line = maux_get_line(args,i); if ( !line ) continue; int irec = ma->buf[i].cur; bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; for (j=0; jn_info; j++) { bcf_info_t *inf = &line->d.info[j]; const char *key = hdr->id[BCF_DT_ID][inf->key].key; // AC and AN are done in merge_format() after genotypes are done if (!args->keep_AC_AN && (key[0] == 'A' && (key[1] == 'C' || key[1] == 'N') && key[2] == 0)) continue; int id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, key); if ( id==-1 ) error("Error: The INFO field is not defined in the header: %s\n", key); kitr = kh_get(strdict, tmph, key); // have we seen the tag in one of the readers? int len = bcf_hdr_id2length(hdr,BCF_HL_INFO,inf->key); if ( args->nrules ) { info_rule_t *rule = (info_rule_t*) bsearch(key, args->rules, args->nrules, sizeof(*args->rules), info_rules_comp_key); if ( rule ) { maux1_t *als = ( len==BCF_VL_A || len==BCF_VL_G || len==BCF_VL_R ) ? &ma->buf[i].rec[irec] : NULL; if ( info_rules_add_values(args, hdr, line, rule, als, len) ) continue; } } // Todo: Number=AGR tags should use the newer info_rules_* functions (info_rules_merge_first to be added) // and merge_AGR_info_tag to be made obsolete. if ( len==BCF_VL_A || len==BCF_VL_G || len==BCF_VL_R ) // Number=R,G,A requires special treatment { if ( kitr == kh_end(tmph) ) { // seeing this key for the first time ma->nAGR_info++; hts_expand0(AGR_info_t,ma->nAGR_info,ma->mAGR_info,ma->AGR_info); kitr = kh_put(strdict, tmph, key, &ret); kh_val(tmph,kitr) = ma->nAGR_info - 1; ma->AGR_info[ma->nAGR_info-1].hdr_tag = key; ma->AGR_info[ma->nAGR_info-1].type = bcf_hdr_id2type(hdr,BCF_HL_INFO,inf->key); ma->AGR_info[ma->nAGR_info-1].nbuf = 0; // size of the buffer switch (len) { case BCF_VL_A: ma->AGR_info[ma->nAGR_info-1].nvals = ma->nout_als - 1; break; case BCF_VL_G: ma->AGR_info[ma->nAGR_info-1].nvals = bcf_alleles2gt(ma->nout_als-1,ma->nout_als-1)+1; break; case BCF_VL_R: ma->AGR_info[ma->nAGR_info-1].nvals = ma->nout_als; break; } } kitr = kh_get(strdict, tmph, key); int idx = kh_val(tmph, kitr); if ( idx<0 ) error("Error occurred while processing INFO tag \"%s\" at %s:%"PRId64"\n", key,bcf_seqname(hdr,line),(int64_t) line->pos+1); merge_AGR_info_tag(hdr, line,inf,len,&ma->buf[i].rec[irec],&ma->AGR_info[idx]); continue; } if ( kitr == kh_end(tmph) ) { // Seeing this key for the first time. Although quite hacky, // this is faster than anything else given the data structures.. hts_expand0(bcf_info_t,out->n_info+1,out->d.m_info,out->d.info); out->d.info[out->n_info].key = id; out->d.info[out->n_info].type = inf->type; out->d.info[out->n_info].len = inf->len; out->d.info[out->n_info].v1.i = inf->v1.i; out->d.info[out->n_info].v1.f = inf->v1.f; out->d.info[out->n_info].vptr_off = inf->vptr_off; out->d.info[out->n_info].vptr_len = inf->vptr_len; out->d.info[out->n_info].vptr_free = 1; out->d.info[out->n_info].vptr = (uint8_t*) malloc(inf->vptr_len+inf->vptr_off); memcpy(out->d.info[out->n_info].vptr,inf->vptr-inf->vptr_off, inf->vptr_len+inf->vptr_off); out->d.info[out->n_info].vptr += inf->vptr_off; if ( (args->output_type & FT_BCF) && id!=bcf_hdr_id2int(hdr, BCF_DT_ID, key) ) bcf_info_set_id(out, &out->d.info[out->n_info], id, &args->tmps); out->d.shared_dirty |= BCF1_DIRTY_INF; out->n_info++; kitr = kh_put(strdict, tmph, key, &ret); kh_val(tmph,kitr) = -(out->n_info-1); // arbitrary negative value } } } for (i=0; inrules; i++) args->rules[i].merger(args->out_hdr, out, &args->rules[i]); for (i=0; inAGR_info; i++) { AGR_info_t *agr = &ma->AGR_info[i]; bcf_update_info(out_hdr,out,agr->hdr_tag,agr->buf,agr->nvals,agr->type); } } void update_AN_AC(bcf_hdr_t *hdr, bcf1_t *line) { int32_t an = 0, *tmp = (int32_t*) malloc(sizeof(int)*line->n_allele); int ret = bcf_calc_ac(hdr, line, tmp, BCF_UN_FMT); if ( ret>0 ) { int i; for (i=0; in_allele; i++) an += tmp[i]; bcf_update_info_int32(hdr, line, "AN", &an, 1); bcf_update_info_int32(hdr, line, "AC", tmp+1, line->n_allele-1); } free(tmp); } static inline int max_used_gt_ploidy(bcf_fmt_t *fmt, int nsmpl) { int i,j, max_ploidy = 0; #define BRANCH(type_t, convert, vector_end) { \ uint8_t *ptr = fmt->p; \ for (i=0; in; j++) \ if ( convert(&ptr[j * sizeof(type_t)])==vector_end ) break; \ if ( j==fmt->n ) \ { \ /* all fields were used */ \ if ( max_ploidy < j ) max_ploidy = j; \ break; \ } \ if ( max_ploidy < j ) max_ploidy = j; \ ptr += fmt->n * sizeof(type_t); \ } \ } switch (fmt->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, bcf_int32_vector_end); break; default: error("Unexpected case: %d\n", fmt->type); } #undef BRANCH return max_ploidy; } // Sets ma->laa to local indexes relevant for each sample or missing/vector_end. // The indexes are with respect to the source indexes and must be translated as // the very last step. void init_local_alleles(args_t *args, bcf1_t *out, int ifmt_PL) { bcf_srs_t *files = args->files; maux_t *ma = args->maux; int i,j,k,l, ismpl = 0, nlaa = 0; static int warned = 0; hts_expand(double,out->n_allele,ma->ntmpd,ma->tmpd); // allele probabilities hts_expand(int,out->n_allele,ma->ntmpi,ma->tmpi); // indexes of the sorted probabilities // Let map[] be the mapping from src to output idx. Then k2k[] is mapping from src allele idxs to src allele idxs // reordered so that if in_allele,ma->nk2k,ma->k2k); // Determine local alleles: either take all that are present in the reader or use PL to determine the best // subset for each sample. The alleles must be listed in the order of the alleles in the output file. for (i=0; inreaders; i++) { bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; bcf_fmt_t *fmt_ori = ma->fmt_map[files->nreaders*ifmt_PL+i]; bcf1_t *line = maux_get_line(args, i); int nsmpl = bcf_hdr_nsamples(hdr); if ( line ) { if ( nlaa < line->n_allele - 1 ) nlaa = line->n_allele - 1 <= args->local_alleles ? line->n_allele - 1 : args->local_alleles; for (j=0; jn_allele; j++) ma->k2k[j] = j; if ( line->n_allele <= args->local_alleles + 1 ) { // sort to the output order, insertion sort, ascending int *map = ma->buf[i].rec[ma->buf[i].cur].map; int *k2k = ma->k2k; int tmp; for (k=1; kn_allele; k++) for (l=k; l>0 && map[k2k[l]] < map[k2k[l-1]]; l--) tmp = k2k[l], k2k[l] = k2k[l-1], k2k[l-1] = tmp; // fewer than the allowed number of alleles, use all alleles from this file for (j=0; jlaa + (1+args->local_alleles)*ismpl; for (k=0; kn_allele; k++) ptr[k] = k2k[k]; for (; k<=args->local_alleles; k++) ptr[k] = bcf_int32_vector_end; ismpl++; } continue; } } if ( !line || !fmt_ori ) { // no values, fill in missing values for (j=0; jlaa + (1+args->local_alleles)*ismpl; ptr[0] = bcf_int32_missing; for (k=1; k<=args->local_alleles; k++) ptr[k] = bcf_int32_vector_end; ismpl++; } continue; } // there are more alternate alleles in the input files than is allowed on output, need to subset if ( ifmt_PL==-1 ) { if ( !warned ) fprintf(bcftools_stderr,"Warning: local alleles are determined from FORMAT/PL but the tag is missing, cannot apply --local-alleles\n"); warned = 1; ma->nlaa = 0; return; } if ( !IS_VL_G(hdr, fmt_ori->id) ) error("FORMAT/PL must be defined as Number=G\n"); if ( 2*fmt_ori->n != line->n_allele*(line->n_allele+1) ) error("Todo: haploid PL to LPL\n"); int *map = ma->buf[i].rec[ma->buf[i].cur].map; double *allele_prob = ma->tmpd; int *idx = ma->tmpi; #define BRANCH(src_type_t, convert, src_is_missing, src_is_vector_end, pl2prob_idx) { \ uint8_t *src = fmt_ori->p; \ for (j=0; jn_allele; k++) allele_prob[k] = 0; \ for (k=0; kn_allele; k++) \ for (l=0; l<=k; l++) \ { \ src_type_t val = convert(src); \ if ( !(src_is_missing) && !(src_is_vector_end) ) \ { \ double prob = ma->pl2prob[pl2prob_idx]; \ allele_prob[k] += prob; \ allele_prob[l] += prob; \ } \ src += sizeof(src_type_t); \ } \ /* insertion sort by allele probability, descending order, with the twist that REF (idx=0) always comes first */ \ allele_prob++; idx[0] = -1; idx++; /* keep REF first */ \ int si,sj,tmp; \ for (si=0; sin_allele-1; si++) idx[si] = si; \ for (si=1; sin_allele-1; si++) \ for (sj=si; sj>0 && allele_prob[idx[sj]] > allele_prob[idx[sj-1]]; sj--) \ tmp = idx[sj], idx[sj] = idx[sj-1], idx[sj-1] = tmp; \ /*for debugging only: test order*/ \ for (si=1; sin_allele-1; si++) \ assert( allele_prob[idx[si-1]] >= allele_prob[idx[si]] ); \ allele_prob--; idx--; /* this was to keep REF first */ \ int32_t *ptr = ma->laa + (1+args->local_alleles)*ismpl; \ ptr[0] = 0; \ for (k=1; k<=args->local_alleles && kn_allele; k++) ptr[k] = idx[k]+1; \ int kmax = k; \ for (; k<=args->local_alleles; k++) ptr[k] = bcf_int32_vector_end; \ /* insertion sort by indexes to the output order, ascending */ \ for (k=1; k0 && map[ptr[l]] < map[ptr[l-1]]; l--) \ tmp = ptr[l], ptr[l] = ptr[l-1], ptr[l-1] = tmp; \ ismpl++; \ } \ } switch (fmt_ori->type) { case BCF_BT_INT8: BRANCH( int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, val); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, val>=0 && val=0 && valtype); } #undef BRANCH } ma->nlaa = nlaa; } void update_local_alleles(args_t *args, bcf1_t *out) { bcf_srs_t *files = args->files; maux_t *ma = args->maux; int i,j,k,ismpl=0,nsamples = bcf_hdr_nsamples(args->out_hdr); for (i=0; inreaders; i++) { int irec = ma->buf[i].cur; bcf_sr_t *reader = &files->readers[i]; int nsmpl = bcf_hdr_nsamples(reader->header); for (k=0; klaa + ismpl*(1+args->local_alleles); int32_t *dst = ma->laa + ismpl*ma->nlaa; j = 0; if ( irec>=0 ) { for (; jnlaa; j++) { if ( src[j+1]==bcf_int32_missing ) dst[j] = bcf_int32_missing; else if ( src[j+1]==bcf_int32_vector_end ) break; else dst[j] = ma->buf[i].rec[irec].map[src[j+1]]; } } if ( j==0 ) dst[j++] = bcf_int32_missing; for (; jnlaa; j++) src[j] = bcf_int32_vector_end; ismpl++; } } bcf_update_format_int32(args->out_hdr, out, "LAA", ma->laa, nsamples*ma->nlaa); } void merge_GT(args_t *args, bcf_fmt_t **fmt_map, bcf1_t *out) { bcf_srs_t *files = args->files; bcf_hdr_t *out_hdr = args->out_hdr; maux_t *ma = args->maux; int i, ismpl = 0, nsamples = bcf_hdr_nsamples(out_hdr); static int warned = 0; int nsize = 0; for (i=0; inreaders; i++) { bcf_fmt_t *fmt = fmt_map[i]; if ( !fmt ) continue; int pld = max_used_gt_ploidy(fmt_map[i], bcf_hdr_nsamples(bcf_sr_get_header(args->files,i))); if ( nsize < pld ) nsize = pld; } if ( nsize==0 ) nsize = 1; size_t msize = sizeof(int32_t)*nsize*nsamples; if ( msize > 2147483647 ) { if ( !warned ) fprintf(bcftools_stderr,"Warning: Too many genotypes at %s:%"PRId64", requires %zu bytes, skipping.\n", bcf_seqname(out_hdr,out),(int64_t) out->pos+1,msize); warned = 1; return; } if ( ma->ntmp_arr < msize ) { ma->tmp_arr = realloc(ma->tmp_arr, msize); if ( !ma->tmp_arr ) error("Could not allocate %zu bytes\n",msize); ma->ntmp_arr = msize; } memset(ma->smpl_ploidy,0,nsamples*sizeof(int)); int default_gt = args->missing_to_ref ? bcf_gt_unphased(0) : bcf_gt_missing; for (i=0; inreaders; i++) { bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; bcf_fmt_t *fmt_ori = fmt_map[i]; int32_t *tmp = (int32_t *) ma->tmp_arr + ismpl*nsize; int irec = ma->buf[i].cur; int j,k; if ( !fmt_ori ) { // missing values: assume maximum ploidy for (j=0; jsmpl_ploidy[ismpl+j]++; } tmp += nsize; } ismpl += bcf_hdr_nsamples(hdr); continue; } #define BRANCH(type_t, convert, vector_end) { \ uint8_t *p_ori = fmt_ori->p; \ if ( !ma->buf[i].rec[irec].als_differ ) \ { \ /* the allele numbering is unchanged */ \ for (j=0; jn; k++) \ { \ type_t val = convert(&p_ori[k * sizeof(type_t)]); \ if ( val==vector_end ) break; /* smaller ploidy */ \ ma->smpl_ploidy[ismpl+j]++; \ if ( bcf_gt_is_missing(val) ) tmp[k] = 0; /* missing allele */ \ else tmp[k] = val; \ } \ for (; kn * sizeof(type_t); \ } \ ismpl += bcf_hdr_nsamples(hdr); \ continue; \ } \ /* allele numbering needs to be changed */ \ for (j=0; jn; k++) \ { \ type_t val = convert(&p_ori[k * sizeof(type_t)]); \ if ( val==vector_end ) break; /* smaller ploidy */ \ ma->smpl_ploidy[ismpl+j]++; \ if ( bcf_gt_is_missing(val) ) tmp[k] = 0; /* missing allele */ \ else \ { \ int al = (val>>1) - 1; \ al = al<=0 ? al + 1 : ma->buf[i].rec[irec].map[al] + 1; \ tmp[k] = (al << 1) | ((val)&1); \ } \ } \ for (; kn * sizeof(type_t); \ } \ ismpl += bcf_hdr_nsamples(hdr); \ } switch (fmt_ori->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, bcf_int32_vector_end); break; default: error("Unexpected case: %d\n", fmt_ori->type); } #undef BRANCH } bcf_update_format_int32(out_hdr, out, "GT", (int32_t*)ma->tmp_arr, nsamples*nsize); } void merge_format_string(args_t *args, const char *key, bcf_fmt_t **fmt_map, bcf1_t *out, int length, int nsize) { bcf_srs_t *files = args->files; bcf_hdr_t *out_hdr = args->out_hdr; maux_t *ma = args->maux; int i,j, nsamples = bcf_hdr_nsamples(out_hdr); static int warned = 0; // initialize empty strings, a dot for each value, e.g. ".,.,." int nmax = 0; for (i=0; istr[i]; if ( length==BCF_VL_FIXED || length==BCF_VL_VAR ) { str->l = 1; ks_resize(str, str->l+1); str->s[0] = '.'; } else { str->l = nsize*2 - 1; ks_resize(str, str->l+1); str->s[0] = '.'; for (j=1; js[j*2-1] = ',', str->s[j*2] = '.'; } str->s[str->l] = 0; if ( nmax < str->l ) nmax = str->l; } // fill in values for each sample int ismpl = 0; for (i=0; inreaders; i++) { bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; bcf_fmt_t *fmt_ori = fmt_map[i]; if ( !fmt_ori ) { // the field is not present in this file ismpl += bcf_hdr_nsamples(hdr); continue; } bcf1_t *line = maux_get_line(args, i); int irec = ma->buf[i].cur; char *src = (char*) fmt_ori->p; if ( length==BCF_VL_FIXED || length==BCF_VL_VAR || (line->n_allele==out->n_allele && !ma->buf[i].rec[irec].als_differ) ) { // alleles unchanged, copy over for (j=0; jstr[ismpl++]; str->l = 0; kputsn(src, fmt_ori->n, str); if ( nmax < str->l ) nmax = str->l; src += fmt_ori->n; } continue; } // NB, what is below is not the fastest way, copy_string_field() keeps // finding the indexes repeatedly at multiallelic sites if ( length==BCF_VL_A || length==BCF_VL_R ) { int ifrom = length==BCF_VL_A ? 1 : 0; for (j=0; jstr[ismpl++]; int iori,inew; for (iori=ifrom; iorin_allele; iori++) { inew = ma->buf[i].rec[irec].map[iori] - ifrom; int ret = copy_string_field(src, iori - ifrom, fmt_ori->size, str, inew); if ( ret<-1 ) error("[E::%s] fixme: internal error at %s:%"PRId64" .. %d\n",__func__,bcf_seqname(hdr,line),(int64_t) line->pos+1,ret); } if ( nmax < str->l ) nmax = str->l; src += fmt_ori->size; } continue; } assert( length==BCF_VL_G ); error("[E::%s] Merging of Number=G FORMAT strings (in your case FORMAT/%s) is not supported yet, sorry!\n" "Please open an issue on github if this feature is essential for you. However, note that using FORMAT strings is not\n" "a good idea in general - it is slow to parse and does not compress well, it is better to use integer codes instead.\n" "If you don't really need it, use `bcftools annotate -x` to remove the annotation before merging.\n", __func__,key); } // update the record size_t msize = nsamples*nmax; if ( msize > 2147483647 ) { if ( !warned ) fprintf(bcftools_stderr,"Warning: The row size is too big for FORMAT/%s at %s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(out_hdr,out),(int64_t) out->pos+1,msize); warned = 1; return; } if ( ma->ntmp_arr < msize ) { ma->tmp_arr = realloc(ma->tmp_arr, msize); if ( !ma->tmp_arr ) error("Could not allocate %zu bytes\n",msize); ma->ntmp_arr = msize; } char *tgt = (char*) ma->tmp_arr; for (i=0; istr[i].s, ma->str[i].l); if ( ma->str[i].l < nmax ) memset(tgt + ma->str[i].l, 0, nmax - ma->str[i].l); tgt += nmax; } bcf_update_format_char(out_hdr, out, key, (float*)ma->tmp_arr, nsamples*nmax); } // Note: only diploid Number=G tags only for now void merge_localized_numberG_format_field(args_t *args, bcf_fmt_t **fmt_map, bcf1_t *out, int irdr) { int i,j,k, nsamples = bcf_hdr_nsamples(args->out_hdr); bcf_srs_t *files = args->files; maux_t *ma = args->maux; bcf_fmt_t *fmt = fmt_map[irdr]; const char *key = files->readers[irdr].header->id[BCF_DT_ID][fmt_map[irdr]->id].key; size_t nsize = (ma->nlaa+1)*(ma->nlaa+2)/2; // max number of Number=G localized fields size_t msize = sizeof(float)>sizeof(int32_t) ? sizeof(float) : sizeof(int32_t); msize *= nsamples*nsize; if ( msize > 2147483647 ) { static int warned = 0; if ( !warned ) fprintf(bcftools_stderr,"Warning: The row size is too big for FORMAT/%s at %s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,msize); warned = 1; return; } if ( ma->ntmp_arr < msize ) { ma->tmp_arr = realloc(ma->tmp_arr, msize); if ( !ma->tmp_arr ) error("Failed to allocate %zu bytes at %s:%"PRId64" for FORMAT/%s\n", msize,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,key); ma->ntmp_arr = msize; } int ismpl = 0; for (i=0; inreaders; i++) { bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; bcf_fmt_t *fmt_ori = fmt_map[i]; bcf1_t *line = maux_get_line(args, i); int nsmpl = bcf_hdr_nsamples(hdr); if ( !fmt_ori ) { // fill missing values #define BRANCH(tgt_type_t, tgt_set_missing, tgt_set_vector_end) { \ for (j=0; jtmp_arr + ismpl*nsize; \ tgt_set_missing; \ for (k=1; ktype) { case BCF_BT_INT8: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_INT16: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_FLOAT: BRANCH(float, bcf_float_set_missing(*tgt), bcf_float_set_vector_end(*tgt)); break; default: error("Unexpected case: %d, %s\n", fmt->type, key); } #undef BRANCH continue; } if ( 2*fmt_ori->n!=line->n_allele*(line->n_allele+1) ) error("Todo: localization of missing or haploid Number=G tags\n"); // localize #define BRANCH(tgt_type_t, src_type_t, convert, src_is_missing, src_is_vector_end, tgt_set_missing, tgt_set_vector_end) { \ for (j=0; jp + sizeof(src_type_t)*j*fmt_ori->n; \ tgt_type_t *tgt = (tgt_type_t *) ma->tmp_arr + ismpl*nsize; \ int *laa = ma->laa + (1+args->local_alleles)*ismpl; \ int ii,ij,tgt_idx = 0; \ for (ii=0; ii<=ma->nlaa; ii++) \ { \ if ( laa[ii]==bcf_int32_missing || laa[ii]==bcf_int32_vector_end ) break; \ for (ij=0; ij<=ii; ij++) \ { \ int src_idx = bcf_alleles2gt(laa[ii],laa[ij]); \ src_type_t val = convert(&src[src_idx * sizeof(src_type_t)]); \ if ( src_is_missing ) tgt_set_missing; \ else if ( src_is_vector_end ) break; \ else tgt[tgt_idx] = val; \ tgt_idx++; \ } \ } \ if ( !tgt_idx ) { tgt_set_missing; tgt_idx++; } \ for (; tgt_idxtype) { case BCF_BT_INT8: BRANCH(int32_t, int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break; case BCF_BT_INT16: BRANCH(int32_t, int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, int32_t, le_to_i16, val==bcf_int32_missing, val==bcf_int32_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break; case BCF_BT_FLOAT: BRANCH(float, float, le_to_float, bcf_float_is_missing(val), bcf_float_is_vector_end(val), bcf_float_set_missing(tgt[tgt_idx]), bcf_float_set_vector_end(tgt[tgt_idx])); break; default: error("Unexpected case: %d, %s\n", fmt_ori->type, key); } #undef BRANCH } args->tmps.l = 0; kputc('L',&args->tmps); kputs(key,&args->tmps); if ( fmt_map[irdr]->type==BCF_BT_FLOAT ) bcf_update_format_float(args->out_hdr, out, args->tmps.s, (float*)ma->tmp_arr, nsamples*nsize); else bcf_update_format_int32(args->out_hdr, out, args->tmps.s, (int32_t*)ma->tmp_arr, nsamples*nsize); ma->laa_dirty = 1; } void merge_localized_numberAR_format_field(args_t *args, bcf_fmt_t **fmt_map, bcf1_t *out, int irdr) { int i,j,k, nsamples = bcf_hdr_nsamples(args->out_hdr); bcf_srs_t *files = args->files; maux_t *ma = args->maux; bcf_fmt_t *fmt = fmt_map[irdr]; const char *key = files->readers[irdr].header->id[BCF_DT_ID][fmt->id].key; size_t nsize = IS_VL_R(files->readers[irdr].header, fmt->id) ? ma->nlaa + 1 : ma->nlaa; size_t msize = sizeof(float)>sizeof(int32_t) ? sizeof(float) : sizeof(int32_t); msize *= nsamples*nsize; if ( msize > 2147483647 ) { static int warned = 0; if ( !warned ) fprintf(bcftools_stderr,"Warning: The row size is too big for FORMAT/%s at %s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,msize); warned = 1; return; } if ( ma->ntmp_arr < msize ) { ma->tmp_arr = realloc(ma->tmp_arr, msize); if ( !ma->tmp_arr ) error("Failed to allocate %zu bytes at %s:%"PRId64" for FORMAT/%s\n", msize,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,key); ma->ntmp_arr = msize; } int ismpl = 0, ibeg = IS_VL_R(files->readers[irdr].header, fmt->id) ? 0 : 1;; for (i=0; inreaders; i++) { bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; bcf_fmt_t *fmt_ori = fmt_map[i]; int nsmpl = bcf_hdr_nsamples(hdr); if ( !fmt_ori ) { // fill missing values #define BRANCH(tgt_type_t, tgt_set_missing, tgt_set_vector_end) { \ for (j=0; jtmp_arr + ismpl*nsize; \ tgt_set_missing; \ for (k=1; ktype) { case BCF_BT_INT8: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_INT16: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_FLOAT: BRANCH(float, bcf_float_set_missing(*tgt), bcf_float_set_vector_end(*tgt)); break; default: error("Unexpected case: %d, %s\n", fmt->type, key); } #undef BRANCH continue; } // localize #define BRANCH(tgt_type_t, src_type_t, convert, src_is_missing, src_is_vector_end, tgt_set_missing, tgt_set_vector_end) { \ for (j=0; jp + sizeof(src_type_t)*j*fmt_ori->n; \ tgt_type_t *tgt = (tgt_type_t *) ma->tmp_arr + ismpl*nsize; \ int *laa = ma->laa + (1+args->local_alleles)*ismpl; \ int ii,tgt_idx = 0; \ for (ii=ibeg; ii<=ma->nlaa; ii++) \ { \ if ( laa[ii]==bcf_int32_missing || laa[ii]==bcf_int32_vector_end ) break; \ int src_idx = laa[ii] - ibeg; \ src_type_t val = convert(&src[src_idx * sizeof(src_type_t)]); \ if ( src_is_missing ) tgt_set_missing; \ else if ( src_is_vector_end ) break; \ else tgt[tgt_idx] = val; \ tgt_idx++; \ } \ if ( !tgt_idx ) { tgt_set_missing; tgt_idx++; } \ for (; tgt_idxtype) { case BCF_BT_INT8: BRANCH(int32_t, int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break; case BCF_BT_INT16: BRANCH(int32_t, int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, int32_t, le_to_i32, val==bcf_int32_missing, val==bcf_int32_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break; case BCF_BT_FLOAT: BRANCH(float, float, le_to_float, bcf_float_is_missing(val), bcf_float_is_vector_end(val), bcf_float_set_missing(tgt[tgt_idx]), bcf_float_set_vector_end(tgt[tgt_idx])); break; default: error("Unexpected case: %d, %s\n", fmt_ori->type, key); } #undef BRANCH } args->tmps.l = 0; kputc('L',&args->tmps); kputs(key,&args->tmps); if ( fmt_map[irdr]->type==BCF_BT_FLOAT ) bcf_update_format_float(args->out_hdr, out, args->tmps.s, (float*)ma->tmp_arr, nsamples*nsize); else bcf_update_format_int32(args->out_hdr, out, args->tmps.s, (int32_t*)ma->tmp_arr, nsamples*nsize); ma->laa_dirty = 1; } void merge_format_field(args_t *args, bcf_fmt_t **fmt_map, missing_rule_t *mrule, bcf1_t *out) { bcf_srs_t *files = args->files; bcf_hdr_t *out_hdr = args->out_hdr; maux_t *ma = args->maux; int i, ismpl = 0, nsamples = bcf_hdr_nsamples(out_hdr); static int warned = 0; const char *key = NULL; size_t nsize = 0, length = BCF_VL_FIXED; int type = -1; for (i=0; inreaders; i++) { if ( !maux_get_line(args,i) ) continue; if ( !fmt_map[i] ) continue; if ( !key ) key = files->readers[i].header->id[BCF_DT_ID][fmt_map[i]->id].key; type = fmt_map[i]->type; if ( IS_VL_G(files->readers[i].header, fmt_map[i]->id) ) { length = BCF_VL_G; nsize = out->n_allele*(out->n_allele + 1)/2; break; } if ( IS_VL_A(files->readers[i].header, fmt_map[i]->id) ) { length = BCF_VL_A; nsize = out->n_allele - 1; break; } if ( IS_VL_R(files->readers[i].header, fmt_map[i]->id) ) { length = BCF_VL_R; nsize = out->n_allele; break; } if ( fmt_map[i]->n > nsize ) nsize = fmt_map[i]->n; } if ( ma->nlaa && length!=BCF_VL_FIXED ) { if ( length==BCF_VL_G ) merge_localized_numberG_format_field(args,fmt_map,out,i); else if ( length==BCF_VL_A || length==BCF_VL_R ) merge_localized_numberAR_format_field(args,fmt_map,out,i); return; } if ( type==BCF_BT_CHAR ) { merge_format_string(args, key, fmt_map, out, length, nsize); return; } size_t msize = sizeof(float)>sizeof(int32_t) ? sizeof(float) : sizeof(int32_t); msize *= nsamples*nsize; if ( msize > 2147483647 ) { if ( !warned ) fprintf(bcftools_stderr,"Warning: The row size is too big for FORMAT/%s at %s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(out_hdr,out),(int64_t) out->pos+1,msize); warned = 1; return; } if ( ma->ntmp_arr < msize ) { ma->tmp_arr = realloc(ma->tmp_arr, msize); if ( !ma->tmp_arr ) error("Failed to allocate %zu bytes at %s:%"PRId64" for FORMAT/%s\n", msize,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,key); ma->ntmp_arr = msize; } // Fill the temp array for all samples by collecting values from all files for (i=0; inreaders; i++) { bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; bcf_fmt_t *fmt_ori = fmt_map[i]; bcf1_t *line = maux_get_line(args, i); int irec = ma->buf[i].cur; if ( fmt_ori ) { type = fmt_ori->type; int nals_ori = line->n_allele; if ( length==BCF_VL_G ) { // if all fields are missing then n==1 is valid if ( fmt_ori->n!=1 && fmt_ori->n != nals_ori*(nals_ori+1)/2 && fmt_map[i]->n != nals_ori ) error("Incorrect number of FORMAT/%s values at %s:%"PRId64", cannot merge. The tag is defined as Number=G, but found\n" "%d values and %d alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields\n", key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,fmt_ori->n,nals_ori); } else if ( length==BCF_VL_A ) { if ( fmt_ori->n!=1 && fmt_ori->n != nals_ori-1 ) error("Incorrect number of FORMAT/%s values at %s:%"PRId64", cannot merge. The tag is defined as Number=A, but found\n" "%d values and %d alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields\n", key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,fmt_ori->n,nals_ori); } else if ( length==BCF_VL_R ) { if ( fmt_ori->n!=1 && fmt_ori->n != nals_ori ) error("Incorrect number of FORMAT/%s values at %s:%"PRId64", cannot merge. The tag is defined as Number=R, but found\n" "%d values and %d alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields\n", key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,fmt_ori->n,nals_ori); } } // set the values #define BRANCH(tgt_type_t, src_type_t, convert, src_is_missing, src_is_vector_end, tgt_set_missing, tgt_set_vector_end) { \ int j, l, k; \ tgt_type_t *tgt = (tgt_type_t *) ma->tmp_arr + ismpl*nsize; \ if ( !fmt_ori ) \ { \ /* the field is not present in this file, set missing values */ \ for (j=0; jp; \ if ( (length!=BCF_VL_G && length!=BCF_VL_A && length!=BCF_VL_R) || (line->n_allele==out->n_allele && !ma->buf[i].rec[irec].als_differ) ) \ { \ /* alleles unchanged, copy over */ \ for (j=0; jn; l++) \ { \ if ( src_is_vector_end ) break; \ else if ( src_is_missing ) tgt_set_missing; \ else *tgt = convert(src); \ tgt++; src += sizeof(src_type_t); \ } \ for (k=l; kn - l); \ } \ ismpl += bcf_hdr_nsamples(hdr); \ continue; \ } \ /* allele numbering needs to be changed */ \ if ( length==BCF_VL_G ) \ { \ /* Number=G tags */ \ for (j=0; jtmp_arr + (ismpl+j)*nsize; \ src = fmt_ori->p + sizeof(src_type_t) * j * fmt_ori->n; \ int tag_missing = src_is_missing && fmt_ori->n==1; \ if ( src_is_missing && fmt_ori->n>1 ) { \ src += sizeof(src_type_t); \ tag_missing = src_is_vector_end ; \ } \ if ( tag_missing ) \ { \ /* tag with missing value "." */ \ tgt_set_missing; \ for (l=1; lsmpl_ploidy[ismpl+j]==1 ? 1 : 0; \ int ngsize = haploid ? out->n_allele : out->n_allele*(out->n_allele + 1)/2; \ if ( ma->buf[i].unkn_allele ) /* Use value from the unknown allele when available */ \ { \ src = fmt_ori->p + sizeof(src_type_t)*j*fmt_ori->n; \ int iunkn = haploid ? ma->buf[i].unkn_allele : (ma->buf[i].unkn_allele+1)*(ma->buf[i].unkn_allele + 2)/2 - 1; \ src_type_t val = convert(&src[iunkn * sizeof(src_type_t)]); \ for (l=0; ltype==MERGE_MISSING_CONST ) \ { \ for (l=0; lvalue; tgt++; } \ } \ else if ( mrule && mrule->type==MERGE_MISSING_MAX ) \ { \ src = fmt_ori->p + sizeof(src_type_t)*j*fmt_ori->n; \ src_type_t max = convert(src); \ for (l=1; ln; l++) \ { \ src_type_t val = convert(&src[l * sizeof(src_type_t)]); \ if ( max < val ) max = val; \ } \ for (l=0; ln_allele; iori++) \ { \ inew = ma->buf[i].rec[irec].map[iori]; \ src = fmt_ori->p + (j*fmt_ori->n + iori) * sizeof(src_type_t); \ tgt = (tgt_type_t *) ma->tmp_arr + (ismpl+j)*nsize + inew; \ if ( src_is_vector_end ) break; \ if ( src_is_missing ) tgt_set_missing; \ else *tgt = convert(src); \ } \ } \ else \ { \ /* Diploid */ \ int iori,jori, inew,jnew; \ for (iori=0; iorin_allele; iori++) \ { \ inew = ma->buf[i].rec[irec].map[iori]; \ for (jori=0; jori<=iori; jori++) \ { \ jnew = ma->buf[i].rec[irec].map[jori]; \ int kori = iori*(iori+1)/2 + jori; \ int knew = inew>jnew ? inew*(inew+1)/2 + jnew : jnew*(jnew+1)/2 + inew; \ src = fmt_ori->p + (j*fmt_ori->n + kori) * sizeof(src_type_t); \ tgt = (tgt_type_t *) ma->tmp_arr + (ismpl+j)*nsize + knew; \ if ( src_is_vector_end ) \ { \ iori = line->n_allele; \ break; \ } \ if ( src_is_missing ) tgt_set_missing; \ else *tgt = convert(src); \ } \ } \ } \ } \ } \ else \ { \ /* Number=A or Number=R tags */ \ int ifrom = length==BCF_VL_A ? 1 : 0; \ for (j=0; jtmp_arr + (ismpl+j)*nsize; \ src = fmt_ori->p + j*fmt_ori->size; \ int tag_missing = src_is_missing && fmt_ori->n==1; \ if ( src_is_missing && fmt_ori->n>1 ) { \ src += sizeof(src_type_t); \ tag_missing = src_is_vector_end ; \ } \ if ( tag_missing ) \ { \ /* tag with missing value "." */ \ tgt_set_missing; \ for (l=1; lp + j*fmt_ori->size; \ if ( ma->buf[i].unkn_allele ) /* Use value from the unknown allele when available */ \ { \ int iunkn = ma->buf[i].unkn_allele; \ src_type_t val = convert(&src[iunkn * sizeof(src_type_t)]); \ for (l=0; ltype==MERGE_MISSING_CONST ) \ { \ for (l=0; lvalue; tgt++; } \ } \ else if ( mrule && mrule->type==MERGE_MISSING_MAX ) \ { \ src = fmt_ori->p + sizeof(src_type_t)*j*fmt_ori->n; \ src_type_t max = convert(src); \ for (l=1; ln; l++) \ { \ src_type_t val = convert(&src[l * sizeof(src_type_t)]); \ if ( max < val ) max = val; \ } \ for (l=0; ln_allele; iori++) \ { \ inew = ma->buf[i].rec[irec].map[iori] - ifrom; \ tgt = (tgt_type_t *) ma->tmp_arr + (ismpl+j)*nsize + inew; \ if ( src_is_vector_end ) break; \ if ( src_is_missing ) tgt_set_missing; \ else *tgt = convert(src); \ src += sizeof(src_type_t); \ } \ } \ } \ ismpl += bcf_hdr_nsamples(hdr); \ } switch (type) { case BCF_BT_INT8: BRANCH(int32_t, int8_t, le_to_i8, le_to_i8(src)==bcf_int8_missing, le_to_i8(src)==bcf_int8_vector_end, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_INT16: BRANCH(int32_t, int16_t, le_to_i16, le_to_i16(src)==bcf_int16_missing, le_to_i16(src)==bcf_int16_vector_end, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, int32_t, le_to_i32, le_to_i32(src)==bcf_int32_missing, le_to_i32(src)==bcf_int32_vector_end, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break; case BCF_BT_FLOAT: BRANCH(float, float, le_to_float, bcf_float_is_missing(le_to_float(src)), bcf_float_is_vector_end(le_to_float(src)), bcf_float_set_missing(*tgt), bcf_float_set_vector_end(*tgt)); break; default: error("Unexpected case: %d, %s\n", type, key); } #undef BRANCH } if ( type==BCF_BT_FLOAT ) bcf_update_format_float(out_hdr, out, key, (float*)ma->tmp_arr, nsamples*nsize); else bcf_update_format_int32(out_hdr, out, key, (int32_t*)ma->tmp_arr, nsamples*nsize); } void merge_format(args_t *args, bcf1_t *out) { bcf_srs_t *files = args->files; bcf_hdr_t *out_hdr = args->out_hdr; maux_t *ma = args->maux; if ( !ma->nfmt_map ) { ma->nfmt_map = 2; ma->fmt_map = (bcf_fmt_t**) calloc(ma->nfmt_map*files->nreaders, sizeof(bcf_fmt_t*)); ma->fmt_key = (const char**) malloc(ma->nfmt_map*sizeof(*ma->fmt_key)); } else memset(ma->fmt_map, 0, ma->nfmt_map*files->nreaders*sizeof(bcf_fmt_t**)); khiter_t kitr; strdict_t *tmph = args->tmph; kh_clear(strdict, tmph); int i, j, ret, has_GT = 0, has_PL = -1, max_ifmt = 0; // max fmt index for (i=0; inreaders; i++) { bcf1_t *line = maux_get_line(args,i); if ( !line ) continue; bcf_sr_t *reader = &files->readers[i]; bcf_hdr_t *hdr = reader->header; for (j=0; jn_fmt; j++) { // Was this tag already seen? bcf_fmt_t *fmt = &line->d.fmt[j]; const char *key = hdr->id[BCF_DT_ID][fmt->id].key; kitr = kh_get(strdict, tmph, key); int ifmt; if ( kitr != kh_end(tmph) ) ifmt = kh_value(tmph, kitr); // seen else { // new FORMAT tag if ( key[0]=='G' && key[1]=='T' && key[2]==0 ) { has_GT = 1; ifmt = 0; } else { ifmt = ++max_ifmt; if ( max_ifmt >= ma->nfmt_map ) { ma->fmt_map = (bcf_fmt_t**) realloc(ma->fmt_map, sizeof(bcf_fmt_t*)*(max_ifmt+1)*files->nreaders); memset(ma->fmt_map+ma->nfmt_map*files->nreaders, 0, (max_ifmt-ma->nfmt_map+1)*files->nreaders*sizeof(bcf_fmt_t*)); ma->fmt_key = (const char**) realloc(ma->fmt_key, sizeof(*ma->fmt_key)*(max_ifmt+1)); ma->nfmt_map = max_ifmt+1; } if ( key[0]=='P' && key[1]=='L' && key[2]==0 ) { has_PL = ifmt; } ma->fmt_key[max_ifmt] = key; } kitr = kh_put(strdict, tmph, key, &ret); kh_value(tmph, kitr) = ifmt; } ma->fmt_map[ifmt*files->nreaders+i] = fmt; } // Check if the allele numbering must be changed int irec = ma->buf[i].cur; for (j=1; jn_allele; j++) if ( ma->buf[i].rec[irec].map[j]!=j ) break; ma->buf[i].rec[irec].als_differ = j==line->n_allele ? 0 : 1; } if ( args->local_alleles ) { ma->laa_dirty = ma->nlaa = 0; if ( out->n_allele > args->local_alleles + 1 ) init_local_alleles(args, out, has_PL); } out->n_sample = bcf_hdr_nsamples(out_hdr); if ( has_GT ) merge_GT(args, ma->fmt_map, out); if ( !args->keep_AC_AN ) update_AN_AC(out_hdr, out); for (i=1; i<=max_ifmt; i++) { missing_rule_t *rule = (missing_rule_t*) bsearch(ma->fmt_key[i], args->missing_rules, args->nmissing_rules, sizeof(*args->missing_rules), missing_rules_comp_key); merge_format_field(args, &ma->fmt_map[i*files->nreaders], rule, out); } if ( ma->laa_dirty ) update_local_alleles(args, out); out->d.indiv_dirty = 1; } void gvcf_set_alleles(args_t *args) { int i,k; bcf_srs_t *files = args->files; maux_t *maux = args->maux; gvcf_aux_t *gaux = maux->gvcf; for (i=0; inals; i++) { free(maux->als[i]); maux->als[i] = NULL; } maux->nals = 0; for (i=0; inreaders; i++) { if ( !gaux[i].active ) continue; bcf1_t *line = maux_get_line(args, i); if ( !line ) continue; int irec = maux->buf[i].cur; hts_expand(int, line->n_allele, maux->buf[i].rec[irec].mmap, maux->buf[i].rec[irec].map); if ( !maux->nals ) // first record, copy the alleles to the output { maux->nals = line->n_allele; hts_expand0(char*, maux->nals, maux->mals, maux->als); hts_expand0(int, maux->nals, maux->ncnt, maux->cnt); for (k=0; knals; k++) { if ( maux->als[k] ) free(maux->als[k]); maux->als[k] = strdup(line->d.allele[k]); maux->buf[i].rec[irec].map[k] = k; } } else { maux->als = merge_alleles(line->d.allele, line->n_allele, maux->buf[i].rec[irec].map, maux->als, &maux->nals, &maux->mals); if ( !maux->als ) { bcf_hdr_t *hdr = bcf_sr_get_header(args->files,i); error("Failed to merge alleles at %s:%"PRId64"\n",bcf_seqname(hdr,line),(int64_t) line->pos+1); } } } } /* Output staged gVCF blocks, end is the last position of the block. Assuming gaux[i].active flags are set and maux_get_line returns correct lines. Both start,end coordinates are 0-based. */ void gvcf_write_block(args_t *args, int start, int end) { int i; maux_t *maux = args->maux; gvcf_aux_t *gaux = maux->gvcf; assert(gaux); // Update POS int min = INT_MAX; // the minimum active gVCF INFO/END (0-based) char ref = 'N'; for (i=0; ifiles->nreaders; i++) { if ( !gaux[i].active ) continue; if ( ref=='N' && gaux[i].line->pos==start ) ref = gaux[i].line->d.allele[0][0]; gaux[i].line->pos = start; } for (i=0; ifiles->nreaders; i++) { if ( !gaux[i].active ) continue; if ( gaux[i].end < start ) { gaux[i].active = 0; maux->buf[i].cur = -1; continue; } gaux[i].line->d.allele[0][0] = ref; if ( min > gaux[i].end ) min = gaux[i].end; } // Check for valid gVCF blocks in this region if ( min==INT_MAX ) // this probably should not happen { assert(0); maux->gvcf_min = 0; return; } bcf1_t *out = args->out_line; gvcf_set_alleles(args); // Merge the staged lines merge_chrom2qual(args, out); merge_filter(args, out); merge_info(args, out); merge_format(args, out); if ( args->gvcf_fai && out->d.allele[0][0]=='N' ) { int slen = 0; char *seq = faidx_fetch_seq(args->gvcf_fai,maux->chr,out->pos,out->pos,&slen); if (!seq) bcftools_exit(1); // faidx_fetch_seq has already reported the error. if (slen) { out->d.allele[0][0] = seq[0]; free(seq); } } // Update END boundary if ( end > start ) { end++; bcf_update_info_int32(args->out_hdr, out, "END", &end, 1); } else bcf_update_info_int32(args->out_hdr, out, "END", NULL, 0); int iunseen; if ( args->trim_star_allele && (out->n_allele > 2 || args->trim_star_allele > 1) && (iunseen=get_unseen_allele(out)) && iunseen>0 ) { // the unobserved star allele should be trimmed, either it is variant site or trimming of all sites was requested kbitset_t *rm_set = kbs_init(out->n_allele); kbs_insert(rm_set, iunseen); if ( bcf_remove_allele_set(args->out_hdr,out,rm_set) ) error("[%s] Error: failed to trim the unobserved allele at %s:%"PRIhts_pos"\n",__func__,bcf_seqname(args->out_hdr,out),out->pos+1); kbs_destroy(rm_set); } if ( bcf_write1(args->out_fh, args->out_hdr, out)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); bcf_clear1(out); // Inactivate blocks which do not extend beyond END and find new gvcf_min min = INT_MAX; for (i=0; ifiles->nreaders; i++) { if ( !gaux[i].active ) continue; if ( gaux[i].end < end ) { gaux[i].active = 0; maux->buf[i].cur = -1; continue; } // next min END position bigger than the current one if ( maux->gvcf_min < gaux[i].end+1 && min > gaux[i].end+1 ) min = gaux[i].end + 1; } maux->gvcf_min = min==INT_MAX ? 0 : min; } /* Flush staged gVCF blocks. Flush everything if there are no more lines (done=1) or if there is a new chromosome. If still on the same chromosome, all hanging blocks must be ended by creating new records: A 1 END=10 B 3 END=7 C 3 END=5 out 1 END=2 A . . 3 END=5 A B C 6 END=7 A B . 8 END=10 A . . */ void gvcf_flush(args_t *args, int done) { int i; maux_t *maux = args->maux; if ( !maux->chr ) return; // first time here, nothing to flush int flush_until = INT_MAX; if ( !done ) { // Get current position and chromosome for (i=0; in; i++) if ( bcf_sr_has_line(maux->files,i) ) break; bcf1_t *line = bcf_sr_get_line(maux->files,i); bcf_hdr_t *hdr = bcf_sr_get_header(maux->files,i); if ( !strcmp(maux->chr,bcf_seqname(hdr,line)) ) flush_until = line->pos; // still on the same chr } // When called on a region, trim the blocks accordingly int start = maux->gvcf_break>=0 ? maux->gvcf_break + 1 : maux->pos; // the start of a new gvcf block to output if ( args->regs ) { int rstart = -1, rend = -1; if ( regidx_overlap(args->regs,maux->chr,start,flush_until,args->regs_itr) ) { // In case there are multiple regions, we treat them as one rstart = args->regs_itr->beg; while ( regitr_overlap(args->regs_itr) ) rend = args->regs_itr->end; } if ( rstart > start ) start = rstart; if ( rend < flush_until ) flush_until = rend+1; } // output all finished blocks while ( maux->gvcf_min && start < flush_until ) { // does the block end before the new line or is it interrupted? int tmp = maux->gvcf_min < flush_until ? maux->gvcf_min : flush_until; if ( start > tmp-1 ) break; gvcf_write_block(args,start,tmp-1); // gvcf_min is 1-based, passing 0-based coordinates start = tmp; } } static inline int is_gvcf_block(bcf1_t *line) { if ( line->rlen<=1 ) return 0; if ( strlen(line->d.allele[0])==line->rlen ) return 0; if ( line->n_allele==1 ) return 1; int i; for (i=1; in_allele; i++) { if ( !strcmp(line->d.allele[i],"<*>") ) return 1; if ( !strcmp(line->d.allele[i],"") ) return 1; if ( !strcmp(line->d.allele[i],"") ) return 1; } return 0; } /* Check incoming lines for new gVCF blocks, set pointer to the current source buffer (gvcf or readers). In contrast to gvcf_flush, this function can be called only after maux_reset as it relies on updated maux buffers. The coordinate is 0-based */ void gvcf_stage(args_t *args, int pos) { maux_t *maux = args->maux; gvcf_aux_t *gaux = maux->gvcf; bcf_srs_t *files = args->files; int32_t *end = (int32_t*) maux->tmp_arr; int i, nend = maux->ntmp_arr / sizeof(int32_t); maux->gvcf_break = -1; maux->gvcf_min = INT_MAX; for (i=0; inreaders; i++) { if ( gaux[i].active && gaux[i].end < pos ) gaux[i].active = 0; if ( gaux[i].active ) { // gvcf block should not overlap with another record if ( maux->gvcf_min > gaux[i].end+1 ) maux->gvcf_min = gaux[i].end + 1; maux->buf[i].beg = 0; maux->buf[i].end = 1; maux->buf[i].cur = 0; continue; } // Does any of the lines have END set? It is enough to check only the // first line, there should be no duplicate records with END in gVCF if ( maux->buf[i].beg==maux->buf[i].end ) continue; // no new record int irec = maux->buf[i].beg; bcf_hdr_t *hdr = bcf_sr_get_header(files, i); bcf1_t *line = args->files->readers[i].buffer[irec]; int ret = is_gvcf_block(line) ? bcf_get_info_int32(hdr,line,"END",&end,&nend) : 0; if ( ret==1 ) { if ( end[0] == line->pos + 1 ) // POS and INFO/END are identical, treat as if a normal w/o INFO/END { maux->gvcf_break = line->pos; continue; } if ( end[0] <= line->pos ) error("Error: Incorrect END at %s:%"PRId64" .. END=%d\n", bcf_seqname(hdr,line),(int64_t) line->pos+1,end[0]); // END is set, this is a new gVCF block. Cache this line in gaux[i] and swap with // an empty record: the gaux line must be kept until we reach its END. gaux[i].active = 1; gaux[i].end = end[0] - 1; SWAP(bcf1_t*,args->files->readers[i].buffer[irec],gaux[i].line); gaux[i].line->pos = pos; maux->buf[i].lines = &gaux[i].line; maux->buf[i].beg = 0; maux->buf[i].end = 1; maux->buf[i].cur = 0; // Set the rid,pos of the swapped line in the buffer or else the // synced reader will have a problem with the next line // args->files->readers[i].buffer[irec]->rid = maux->buf[i].rid; args->files->readers[i].buffer[irec]->pos = maux->pos; // Update block offsets if ( maux->gvcf_min > gaux[i].end+1 ) maux->gvcf_min = gaux[i].end + 1; } else maux->gvcf_break = line->pos; // must break the gvcf block } maux->ntmp_arr = nend * sizeof(int32_t); maux->tmp_arr = end; if ( maux->gvcf_min==INT_MAX ) maux->gvcf_min = 0; } void debug_buffers(FILE *fp, bcf_srs_t *files); void debug_buffer(FILE *fp, bcf_srs_t *files, int reader); /* Flush all buffered and processed records with the same coordinate. Note that synced reader discards buffer[0], so that needs to stay untouched. */ void clean_buffer(args_t *args) { maux_t *ma = args->maux; int ir; for (ir=0; irn; ir++) { // Invalidate pointer to reader's buffer or else gvcf_flush will attempt // to use the old lines via maux_get_line() if ( ma->gvcf ) { if ( ma->gvcf[ir].active ) { if ( ma->pos > ma->gvcf[ir].end ) ma->gvcf[ir].active = 0; else if ( ma->buf[ir].cur==-1 ) ma->buf[ir].cur = ma->buf[ir].beg; // re-activate interrupted gVCF block } if ( !ma->gvcf[ir].active ) ma->buf[ir].cur = -1; } bcf_sr_t *reader = bcf_sr_get_reader(args->files,ir); if ( !reader->nbuffer ) continue; // nothing to clean bcf1_t **buf = reader->buffer; if ( buf[1]->rid!=ma->buf[ir].rid || buf[1]->pos!=ma->pos ) continue; // nothing to flush int a = 1, b = 2; while ( b<=reader->nbuffer && buf[b]->rid==ma->buf[ir].rid && buf[b]->pos==ma->pos ) b++; // b now points to the first line we want to preserve while ( b<=reader->nbuffer ) { SWAP(bcf1_t*, buf[a], buf[b]); a++; b++; } reader->nbuffer -= b-a; } } void debug_maux(args_t *args) { bcf_srs_t *files = args->files; maux_t *maux = args->maux; int j,k,l; fprintf(bcftools_stderr,"Alleles to merge at %d, nals=%d\n", maux->pos+1,maux->nals); for (j=0; jnreaders; j++) { bcf_sr_t *reader = &files->readers[j]; buffer_t *buf = &maux->buf[j]; fprintf(bcftools_stderr," reader %d (k=%d-%d): ", j,buf->beg,buf->end); for (k=buf->beg; kend; k++) { if ( buf->rec[k].skip & SKIP_DONE ) { fprintf(bcftools_stderr," DONE"); continue; } bcf1_t *line = reader->buffer[k]; // selected for merging by can_merge fprintf(bcftools_stderr,"\t"); if ( buf->cur==k ) fprintf(bcftools_stderr,"!"); // selected for merging by stage_line if ( buf->rec[k].skip ) fprintf(bcftools_stderr,"["); // this record cannot be merged in this round if ( !line->n_allele && maux->gvcf[j].active ) fprintf(bcftools_stderr,"<*>"); for (l=0; ln_allele; l++) fprintf(bcftools_stderr,"%s%s", l==0?"":",", line->d.allele[l]); if ( buf->rec[k].skip ) fprintf(bcftools_stderr,"]"); } fprintf(bcftools_stderr,"\n"); } fprintf(bcftools_stderr," counts: "); for (j=0; jnals; j++) fprintf(bcftools_stderr,"%s %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(bcftools_stderr,"\n\n"); } void debug_state(args_t *args) { maux_t *maux = args->maux; int i,j; fprintf(bcftools_stderr,"State after position=%d done:\n",maux->pos+1); for (i=0; ifiles->nreaders; i++) { fprintf(bcftools_stderr,"\treader %d:\tcur,beg,end=% d,%d,%d", i,maux->buf[i].cur,maux->buf[i].beg,maux->buf[i].end); if ( maux->buf[i].cur >=0 ) { bcf_hdr_t *hdr = bcf_sr_get_header(args->files,i); const char *chr = bcf_hdr_id2name(hdr, maux->buf[i].rid); fprintf(bcftools_stderr,"\t"); for (j=maux->buf[i].beg; jbuf[i].end; j++) fprintf(bcftools_stderr," %s:%"PRId64,chr,(int64_t) maux->buf[i].lines[j]->pos+1); } fprintf(bcftools_stderr,"\n"); } fprintf(bcftools_stderr,"\tgvcf_min=%d\n", args->maux->gvcf_min); for (i=0; ifiles->nreaders; i++) { fprintf(bcftools_stderr,"\t\treader %d:\tgvcf_active=%d", i,maux->gvcf[i].active); if ( maux->gvcf[i].active ) fprintf(bcftools_stderr,"\tpos,end=%"PRId64",%"PRId64, (int64_t) maux->gvcf[i].line->pos+1,(int64_t) maux->gvcf[i].end+1); fprintf(bcftools_stderr,"\n"); } fprintf(bcftools_stderr,"\n"); } // Lines can come with any combination of variant types. We use a subset of types defined in vcf.h // but shift by two bits to account for VCF_REF defined as 0 (design flaw in vcf.h, my fault) static const int snp_mask = (VCF_SNP<<1)|(VCF_MNP<<1), indel_mask = (VCF_INDEL<<1), ins_mask = VCF_INS<<1, del_mask = VCF_DEL<<1, ref_mask = 1; // Can these types be merged given the -m settings? Despite the function's name, its focus is on // excluding incompatible records, there will be a finer matching later in stage_line() static inline int types_compatible(args_t *args, int selected_types, buffer_t *buf, int irec) { int k; maux_t *maux = args->maux; bcf1_t *rec = buf->lines[irec]; int rec_types = buf->rec[irec].var_types; assert( selected_types ); // this is trivially true, set in can_merge() if ( args->collapse & COLLAPSE_ANY ) return 1; // can merge anything with anything // REF and gVCF_REF with no other alleles present can be merged with anything if ( (selected_types&ref_mask) && !(selected_types&(~ref_mask)) ) return 1; if ( (rec_types&ref_mask) && !(rec_types&(~ref_mask)) ) return 1; if ( args->collapse!=COLLAPSE_NONE ) { // If we are here, one the following modes must have been set: both,snps,indels,snp-ins-del // Include the new record if // - rec has SNV, we already have SNV, and -m is both,snps,snp-ins-del // - rec has indel, we already have an indel, and -m both,indels,snp-ins-del if ( args->collapse&(COLLAPSE_SNPS|COLLAPSE_SNP_INS_DEL) ) { if ( (rec_types&snp_mask) && (selected_types&snp_mask) ) return 1; } if ( args->collapse&COLLAPSE_INDELS ) { if ( (rec_types&indel_mask) && (selected_types&indel_mask) ) return 1; } if ( args->collapse&COLLAPSE_SNP_INS_DEL ) { if ( (rec_types&ins_mask) && (selected_types&ins_mask) ) return 1; if ( (rec_types&del_mask) && (selected_types&del_mask) ) return 1; } // Whatever is left, allow to match if the alleles match exactly } // The -m none mode or exact matching requested // Simple test first: are the variants of the same type? int x = selected_types >> 1; // remove REF int y = rec_types >> 1; // remove REF while ( x && y ) { x>>=1; y>>=1; } if ( x || y ) return 0; // the types differ if ( vcmp_set_ref(args->vcmp,maux->als[0],rec->d.allele[0]) < 0 ) return 0; // refs are not compatible for (k=1; kn_allele; k++) { if ( bcf_has_variant_type(rec,k,VCF_REF) ) continue; // this must be gVCF_REF (<*> or ) if ( vcmp_find_allele(args->vcmp,maux->als+1,maux->nals-1,rec->d.allele[k])>=0 ) break; } if ( k==rec->n_allele ) return 0; // this record has a new allele rec->d.allele[k] return 1; // all alleles in rec are also in the records selected thus far, perhaps save for gVCF_REF } static void maux_update_alleles(args_t *args, int ireader, int irec) { int k; bcf_sr_t *reader = &args->files->readers[ireader]; maux_t *maux = args->maux; buffer_t *buf = &maux->buf[ireader]; maux1_t *ma1 = &buf->rec[irec]; bcf1_t *line = buf->lines[irec]; hts_expand(int, line->n_allele, ma1->mmap, ma1->map); if ( !maux->nals ) // first record to be merged, copy the alleles to the output { maux->nals = line->n_allele; hts_expand0(char*, maux->nals, maux->mals, maux->als); hts_expand0(int, maux->nals, maux->ncnt, maux->cnt); hts_expand0(int, maux->nals, maux->mals_types, maux->als_types); for (k=0; knals; k++) { free(maux->als[k]); maux->als[k] = strdup(line->d.allele[k]); ma1->map[k] = k; maux->cnt[k] = 1; int var_type = bcf_has_variant_type(line, k, VCF_ANY); if ( args->collapse==COLLAPSE_SNP_INS_DEL ) var_type &= ~VCF_INDEL; maux->als_types[k] = var_type ? var_type<<1 : ref_mask; } return; } // normalize alleles maux->als = merge_alleles(line->d.allele, line->n_allele, ma1->map, maux->als, &maux->nals, &maux->mals); if ( !maux->als ) error("Failed to merge alleles at %s:%"PRId64" in %s\n",maux->chr,(int64_t) line->pos+1,reader->fname); hts_expand0(int, maux->nals, maux->ncnt, maux->cnt); hts_expand0(int, maux->nals, maux->mals_types, maux->als_types); for (k=1; kn_allele; k++) { int ik = ma1->map[k]; int var_type = bcf_has_variant_type(line, k, VCF_ANY); if ( args->collapse==COLLAPSE_SNP_INS_DEL ) var_type &= ~VCF_INDEL; maux->als_types[ik] = var_type ? var_type<<1 : ref_mask; maux->cnt[ik]++; // how many times an allele appears in the files } maux->cnt[0]++; } /* Determine which lines remain to be merged across readers at the current position and are compatible given the -m criteria. This is indicated by maux1_t.skip: 0=compatible, SKIP_DONE=the record is done, SKIP_DIFF=not compatible and will be included next time. At the same time count how many times is each allele present across the readers and records so that we can prioritize the records with the same alleles to come first. In the end maximum one record at a time can be selected from each reader and that witll be done in stage_line(). The function maux_reset already initialized structures for this position, so here each reader comes with the beg,end indexes that point to records with the same maux_t.pos position. */ int can_merge(args_t *args) { bcf_srs_t *files = args->files; maux_t *maux = args->maux; gvcf_aux_t *gaux = maux->gvcf; char *id = NULL, ref = 'N'; int i,j, ntodo = 0; for (i=0; inals; i++) { free(maux->als[i]); maux->als[i] = NULL; maux->cnt[i] = 0; } maux->var_types = maux->nals = 0; // In this loop we do the following: // - remember the first encountered ID if matching by ID // - count the number of unprocessed records at this position // - collect all variant types at this position. This is to be able to perform -m matching and // print SNVs first, then indels, then gVCF blocks // - init the 'skip' variable to SKIP_DIFF for each record that has not been used yet for (i=0; inreaders; i++) { buffer_t *buf = &maux->buf[i]; buf->var_types = 0; if ( gaux && gaux[i].active ) // active gvcf block { buf->rec[buf->beg].skip = SKIP_DIFF; maux->var_types |= ref_mask; buf->var_types |= ref_mask; buf->rec[buf->beg].var_types = ref_mask; continue; } // for gvcf: find out REF at this position if ( buf->beg < buf->end && ref=='N' ) ref = buf->lines[buf->beg]->d.allele[0][0]; for (j=buf->beg; jend; j++) { if ( buf->rec[j].skip & SKIP_DONE ) continue; buf->rec[j].skip = SKIP_DIFF; ntodo++; bcf1_t *line = buf->lines[j]; if ( args->merge_by_id && !id ) { id = line->d.id; continue; } // set ID when merging by id if ( !buf->rec[j].var_types ) { int var_type = bcf_has_variant_types(line, VCF_ANY, bcf_match_overlap); if ( var_type < 0 ) error("bcf_has_variant_types() failed."); if ( args->collapse==COLLAPSE_SNP_INS_DEL ) { // need to distinguish between ins and del so strip the VCF_INDEL flag var_type &= ~VCF_INDEL; } var_type = var_type ? var_type<<1 : ref_mask; if ( args->do_gvcf && is_gvcf_block(line) ) var_type |= ref_mask; buf->rec[j].var_types = var_type; } maux->var_types |= buf->rec[j].var_types; buf->var_types |= buf->rec[j].var_types; } } if ( !ntodo ) return 0; int selected_types = 0; // In this loop we select from each reader compatible candidate lines. // (i.e. SNPs or indels). Go through all files and all lines at this // position and normalize relevant alleles. // REF-only sites may be associated with both SNPs and indels. for (i=0; inreaders; i++) { buffer_t *buf = &maux->buf[i]; if ( gaux && gaux[i].active ) { // gVCF records inherited from an upstream gVCF block have incorrect or missing allele and position gaux[i].line->d.allele[0][0] = ref; gaux[i].line->pos = maux->pos; maux_update_alleles(args, i, buf->beg); selected_types |= ref_mask; continue; } for (j=buf->beg; jend; j++) { if ( buf->rec[j].skip & SKIP_DONE ) continue; bcf1_t *line = buf->lines[j]; // ptr to reader's buffer or gvcf buffer int line_types = buf->rec[j].var_types; // select relevant lines if ( args->merge_by_id ) { if ( strcmp(id,line->d.id) ) continue; // matching by ID and it does not match the selected record } else if ( selected_types && !types_compatible(args,selected_types,buf,j) ) continue; else { // First time here, choosing the first line: prioritize SNPs when available in the -m snps,both modes if ( (args->collapse&COLLAPSE_SNPS || args->collapse==COLLAPSE_NONE) // asked to merge SNVs into multiallelics && (maux->var_types&snp_mask) // there are SNVs at the current position && !(buf->rec[j].var_types&(snp_mask|ref_mask)) // and this record is not a SNV nor ref ) continue; } selected_types |= line_types; buf->rec[j].skip = 0; // the j-th record from i-th reader can be included. Final decision will be made in stage_line maux_update_alleles(args, i, j); } } return 1; } /* Select records that have the same alleles; the input ordering of indels must not matter. Multiple VCF lines can be emitted from this loop. We expect only very few alleles and not many records with the same position in the buffers, therefore the nested loops should not slow us much. */ void stage_line(args_t *args) { bcf_srs_t *files = args->files; maux_t *maux = args->maux; // Take the most frequent allele present in multiple files, REF and gVCF_REF is skipped. int i,j,k,icnt = -1; for (i=1; inals; i++) { if ( maux->als_types[i] & ref_mask ) continue; if ( icnt==-1 || maux->cnt[icnt] < maux->cnt[i] ) icnt = i; } int selected_type = icnt>0 ? maux->als_types[icnt] : ref_mask; int nout = 0; for (i=0; inreaders; i++) { buffer_t *buf = &maux->buf[i]; buf->cur = -1; if ( buf->beg >= buf->end ) continue; // No lines in the buffer at this site // find lines with the same allele for (j=buf->beg; jend; j++) { if ( buf->rec[j].skip ) { int is_gvcf = maux->gvcf && maux->gvcf[i].active ? 1 : 0; if ( !is_gvcf && is_gvcf_block(buf->lines[j]) ) is_gvcf = 1; if ( !is_gvcf ) continue; // done or not compatible } if ( args->merge_by_id ) break; // if merging by ID and the line is compatible, the this is THE line // skip if the reader has a record that matches the most frequent allele and this record is not it if ( (selected_type & buf->var_types) && !(selected_type & buf->rec[j].var_types) ) continue; // if the reader does not have the most frequent allele type but is a ref, accept if ( !(selected_type & buf->var_types) && (buf->rec[j].var_types & ref_mask) ) break; if ( selected_type==ref_mask ) break; // accept if the record has the most frequent allele for (k=0; klines[j]->n_allele; k++) if ( icnt==buf->rec[j].map[k] ) break; if ( klines[j]->n_allele ) break; } if ( j>=buf->end ) { // no matching allele found in this file if ( args->collapse==COLLAPSE_NONE ) continue; // exact matching requested, skip // choose something compatible to create a multiallelic site given the -m criteria for (j=buf->beg; jend; j++) { if ( buf->rec[j].skip ) continue; // done or not compatible if ( args->collapse&COLLAPSE_ANY ) break; // anything can be merged int line_type = buf->rec[j].var_types; if ( maux->var_types&snp_mask && line_type&snp_mask && (args->collapse&COLLAPSE_SNPS) ) break; if ( maux->var_types&indel_mask && line_type&indel_mask && (args->collapse&COLLAPSE_INDELS) ) break; if ( maux->var_types&ins_mask && line_type&ins_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break; if ( maux->var_types&del_mask && line_type&del_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break; if ( line_type&ref_mask ) { if ( maux->var_types&snp_mask && (args->collapse&COLLAPSE_SNPS) ) break; if ( maux->var_types&indel_mask && (args->collapse&COLLAPSE_INDELS) ) break; if ( maux->var_types&ins_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break; if ( maux->var_types&del_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break; if ( maux->var_types&ref_mask ) break; } else if ( maux->var_types&ref_mask ) { if ( line_type&snp_mask && (args->collapse&COLLAPSE_SNPS) ) break; if ( line_type&indel_mask && (args->collapse&COLLAPSE_INDELS) ) break; if ( line_type&ins_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break; if ( line_type&del_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break; } } } if ( jend ) { // found a suitable line for merging buf->cur = j; } } // debug_maux(args); // Mark lines staged for merging as finished so that they are ignored next time for (i=0; inreaders; i++) { buffer_t *buf = &maux->buf[i]; if ( buf->cur == -1 ) continue; buf->rec[buf->cur].skip = SKIP_DONE; nout++; } assert( nout ); } void merge_line(args_t *args) { bcf1_t *out = args->out_line; merge_chrom2qual(args, out); if ( args->regs && !regidx_overlap(args->regs,args->maux->chr,out->pos,out->pos+out->rlen-1,NULL) ) return; merge_filter(args, out); merge_info(args, out); if ( args->do_gvcf ) bcf_update_info_int32(args->out_hdr, out, "END", NULL, 0); merge_format(args, out); int iunseen; if ( args->trim_star_allele && (out->n_allele > 2 || args->trim_star_allele > 1) && (iunseen=get_unseen_allele(out)) && iunseen>0 ) { // the unobserved star allele should be trimmed, either it is variant site or trimming of all sites was requested kbitset_t *rm_set = kbs_init(out->n_allele); kbs_insert(rm_set, iunseen); if ( bcf_remove_allele_set(args->out_hdr,out,rm_set) ) error("[%s] Error: failed to trim the unobserved allele at %s:%"PRIhts_pos"\n",__func__,bcf_seqname(args->out_hdr,out),out->pos+1); kbs_destroy(rm_set); } if ( bcf_write1(args->out_fh, args->out_hdr, out)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); bcf_clear1(out); } void bcf_hdr_append_version(bcf_hdr_t *hdr, int argc, char **argv, const char *cmd) { kstring_t str = {0,0,0}; int e = 0; if (ksprintf(&str,"##%sVersion=%s+htslib-%s\n", cmd, bcftools_version(), hts_version()) < 0) goto fail; if (bcf_hdr_append(hdr,str.s) < 0) goto fail; str.l = 0; e |= ksprintf(&str,"##%sCommand=%s", cmd, argv[0]) < 0; int i; for (i=1; inhrec; i++) { if ( hdr->hrec[i]->type!=BCF_HL_FMT ) continue; j = bcf_hrec_find_key(hdr->hrec[i],"ID"); if ( j<0 ) continue; char *key = hdr->hrec[i]->vals[j]; int id = bcf_hdr_id2int(hdr, BCF_DT_ID, key); assert( id>=0 ); int localize = 0; if ( bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_G ) localize = 1; if ( bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_A ) localize = 1; if ( bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_R ) localize = 1; if ( !localize ) continue; args->tmps.l = 0; uint32_t e = 0, nout = 0; e |= ksprintf(&args->tmps, "##%s=<", hdr->hrec[i]->key) < 0; for (j=0; jhrec[i]->nkeys; j++) { if ( !strcmp("IDX",hdr->hrec[i]->keys[j]) ) continue; if ( nout ) e |= kputc(',',&args->tmps) < 0; if ( !strcmp("ID",hdr->hrec[i]->keys[j]) ) e |= ksprintf(&args->tmps,"%s=L%s", hdr->hrec[i]->keys[j], hdr->hrec[i]->vals[j]) < 0; else if ( !strcmp("Number",hdr->hrec[i]->keys[j]) ) e |= ksprintf(&args->tmps,"Number=.") < 0; else if ( !strcmp("Description",hdr->hrec[i]->keys[j]) && hdr->hrec[i]->vals[j][0]=='"' ) e |= ksprintf(&args->tmps,"Description=\"Localized field: %s", hdr->hrec[i]->vals[j]+1) < 0; else e |= ksprintf(&args->tmps,"%s=%s", hdr->hrec[i]->keys[j], hdr->hrec[i]->vals[j]) < 0; nout++; } e |= ksprintf(&args->tmps,">\n") < 0; if ( e ) error("Failed to format the header line for %s\n", key); nstr++; hts_expand(char*,nstr,mstr,str); str[nstr-1] = strdup(args->tmps.s); } if ( !nstr ) return; bcf_hdr_append(hdr,"##FORMAT="); for (i=0; ioutput_type,args->output_fname,args->clevel); args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno)); if ( args->n_threads ) hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->files->p); //hts_set_threads(args->out_fh, args->n_threads); args->out_hdr = bcf_hdr_init("w"); if ( args->header_fname ) { if ( bcf_hdr_set(args->out_hdr,args->header_fname) ) error("Could not read/parse the header: %s\n", args->header_fname); } else { int i; for (i=0; ifiles->nreaders; i++) { char buf[24]; snprintf(buf,sizeof buf,"%d",i+1); merge_headers(args->out_hdr, args->files->readers[i].header,buf,args->force_samples); } if ( args->local_alleles ) hdr_add_localized_tags(args, args->out_hdr); if (args->record_cmd_line) bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_merge"); if (bcf_hdr_sync(args->out_hdr) < 0) error_errno("[%s] Failed to update header", __func__); } info_rules_init(args); missing_rules_init(args); bcf_hdr_set_version(args->out_hdr, bcf_hdr_get_version(args->files->readers[0].header)); if ( bcf_hdr_write(args->out_fh, args->out_hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); if ( args->header_only ) { bcf_hdr_destroy(args->out_hdr); if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname); return; } else if ( init_index2(args->out_fh,args->out_hdr,args->output_fname, &args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->output_fname); args->vcmp = vcmp_init(); args->maux = maux_init(args); args->out_line = bcf_init1(); args->tmph = kh_init(strdict); int *rid_tab = calloc(args->maux->n, sizeof(*rid_tab)); if (!rid_tab) error("[%s:%d] Could not allocate %zu bytes\n", __FILE__, __LINE__, args->maux->n*sizeof(*rid_tab)); while ( bcf_sr_next_line(args->files) ) { // output cached gVCF blocks which end before the new record if ( args->do_gvcf ) gvcf_flush(args,0); maux_reset(args->maux, rid_tab); // determine which of the new records are gvcf blocks if ( args->do_gvcf ) gvcf_stage(args, args->maux->pos); while ( can_merge(args) ) { stage_line(args); merge_line(args); } clean_buffer(args); // debug_state(args); } free(rid_tab); if ( args->do_gvcf ) gvcf_flush(args,1); info_rules_destroy(args); missing_rules_destroy(args); maux_destroy(args->maux); bcf_hdr_destroy(args->out_hdr); if ( args->write_index ) { if ( bcf_idx_save(args->out_fh)<0 ) { if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"bcftools_stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname?args->output_fname:"bcftools_stdout"); bcf_destroy1(args->out_line); kh_destroy(strdict, args->tmph); if ( args->tmps.m ) free(args->tmps.s); if ( args->vcmp ) vcmp_destroy(args->vcmp); } static void usage(void) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file.\n"); fprintf(bcftools_stderr, " Note that only records from different files can be merged, never from the same file. For\n"); fprintf(bcftools_stderr, " \"vertical\" merge take a look at \"bcftools norm\" instead.\n"); fprintf(bcftools_stderr, "Usage: bcftools merge [options] [...]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Options:\n"); fprintf(bcftools_stderr, " --force-no-index Merge unindexed files, synonymous to --no-index\n"); fprintf(bcftools_stderr, " --force-samples Resolve duplicate sample names\n"); fprintf(bcftools_stderr, " --force-single Run even if there is only one file on input\n"); fprintf(bcftools_stderr, " --print-header Print only the merged header and exit\n"); fprintf(bcftools_stderr, " --use-header FILE Use the provided header\n"); fprintf(bcftools_stderr, " -0 --missing-to-ref Assume genotypes at missing sites are 0/0\n"); fprintf(bcftools_stderr, " -f, --apply-filters LIST Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n"); fprintf(bcftools_stderr, " -F, --filter-logic x|+ Remove filters if some input is PASS (\"x\"), or apply all filters (\"+\") [+]\n"); fprintf(bcftools_stderr, " -g, --gvcf -|REF.FA Merge gVCF blocks, INFO/END tag is expected. Implies -i QS:sum,MinDP:min,MIN_DP:min,I16:sum,IDV:max,IMF:max -M PL:max,AD:0\n"); fprintf(bcftools_stderr, " -i, --info-rules TAG:METHOD,.. Rules for merging INFO fields (method is one of sum,avg,min,max,join) or \"-\" to turn off the default [DP:sum,DP4:sum]\n"); fprintf(bcftools_stderr, " -l, --file-list FILE Read file names from the file\n"); fprintf(bcftools_stderr, " -L, --local-alleles INT If more than INT alt alleles are encountered, drop FMT/PL and output LAA+LPL instead; 0=unlimited [0]\n"); fprintf(bcftools_stderr, " -m, --merge STRING[*|**] Allow multiallelic records for snps,indels,both,snp-ins-del,all,none,id,*,**; see man page for details [both]\n"); fprintf(bcftools_stderr, " -M, --missing-rules TAG:METHOD Rules for replacing missing values in numeric vectors (.,0,max) when unknown allele <*> is not present [.]\n"); fprintf(bcftools_stderr, " --no-index Merge unindexed files, the same chromosomal order is required and -r/-R are not allowed\n"); fprintf(bcftools_stderr, " --no-version Do not append version and command line to the header\n"); fprintf(bcftools_stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(bcftools_stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(bcftools_stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(bcftools_stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(bcftools_stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " --threads INT Use multithreading with INT worker threads [0]\n"); fprintf(bcftools_stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int main_vcfmerge(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->files = bcf_sr_init(); args->argc = argc; args->argv = argv; args->output_fname = "-"; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->collapse = COLLAPSE_BOTH; args->clevel = -1; int regions_is_file = 0; int regions_overlap = 1; static struct option loptions[] = { {"help",no_argument,NULL,'h'}, {"merge",required_argument,NULL,'m'}, {"local-alleles",required_argument,NULL,'L'}, {"gvcf",required_argument,NULL,'g'}, {"file-list",required_argument,NULL,'l'}, {"missing-to-ref",no_argument,NULL,'0'}, {"apply-filters",required_argument,NULL,'f'}, {"use-header",required_argument,NULL,1}, {"print-header",no_argument,NULL,2}, {"force-samples",no_argument,NULL,3}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"threads",required_argument,NULL,9}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,4}, {"info-rules",required_argument,NULL,'i'}, {"missing-rules",required_argument,NULL,'M'}, {"no-version",no_argument,NULL,8}, {"no-index",no_argument,NULL,10}, {"force-no-index",no_argument,NULL,10}, {"force-single",no_argument,NULL,12}, {"filter-logic",required_argument,NULL,'F'}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "hm:f:r:R:o:O:i:M:l:g:F:0L:W::",loptions,NULL)) >= 0) { switch (c) { case 'L': args->local_alleles = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --local-alleles %s\n", optarg); if ( args->local_alleles < 1 ) error("Error: \"--local-alleles %s\" makes no sense, expected value bigger or equal than 1\n", optarg); break; case 'F': if ( !strcmp(optarg,"+") ) args->filter_logic = FLT_LOGIC_ADD; else if ( !strcmp(optarg,"x") ) args->filter_logic = FLT_LOGIC_REMOVE; else error("Filter logic not recognised: %s\n", optarg); break; case '0': args->missing_to_ref = 1; break; case 'g': args->do_gvcf = 1; if ( strcmp("-",optarg) ) { args->gvcf_fai = fai_load(optarg); if ( !args->gvcf_fai ) error("Failed to load the fai index: %s\n", optarg); } break; case 'l': args->file_list = optarg; break; case 'i': args->info_rules = optarg; break; case 'M': args->missing_rules_str = optarg; break; case 'o': args->output_fname = optarg; break; case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'm': { int len = strlen(optarg); if ( optarg[len-1]=='*' ) { args->trim_star_allele++; len--; } if ( optarg[len-1]=='*' ) { args->trim_star_allele++; len--; } if ( optarg[len-1]==',' ) len--; args->collapse = COLLAPSE_NONE; if ( !strncmp(optarg,"snp-ins-del",len) ) args->collapse = COLLAPSE_SNP_INS_DEL|COLLAPSE_SNPS; else if ( !strncmp(optarg,"snps",len) ) args->collapse |= COLLAPSE_SNPS; else if ( !strncmp(optarg,"indels",len) ) args->collapse |= COLLAPSE_INDELS; else if ( !strncmp(optarg,"id",len) ) { args->collapse = COLLAPSE_NONE; args->merge_by_id = 1; } else if ( !strncmp(optarg,"any",len) ) args->collapse |= COLLAPSE_ANY; else if ( !strncmp(optarg,"all",len) ) args->collapse |= COLLAPSE_ANY; else if ( !strncmp(optarg,"both",len) ) args->collapse |= COLLAPSE_BOTH; else if ( !strncmp(optarg,"none",len) ) args->collapse = COLLAPSE_NONE; else error("The -m type \"%s\" is not recognised.\n", optarg); break; } case 'f': args->files->apply_filters = optarg; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 1 : args->header_fname = optarg; break; case 2 : args->header_only = 1; break; case 3 : args->force_samples = 1; break; case 4 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 8 : args->record_cmd_line = 0; break; case 10 : args->no_index = 1; break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 12 : args->force_single = 1; break; case 'h': case '?': usage(); break; default: error("Unknown argument: %s\n", optarg); } } if ( argc==optind && !args->file_list ) usage(); if ( args->no_index ) { if ( args->regions_list ) error("Error: cannot combine --no-index with -r/-R\n"); bcf_sr_set_opt(args->files,BCF_SR_ALLOW_NO_IDX); } else bcf_sr_set_opt(args->files,BCF_SR_REQUIRE_IDX); if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); if ( regions_is_file ) args->regs = regidx_init(args->regions_list,NULL,NULL,sizeof(char*),NULL); else { args->regs = regidx_init(NULL,regidx_parse_reg,NULL,sizeof(char*),NULL); if ( regidx_insert_list(args->regs,args->regions_list,',') !=0 ) error("Could not parse the regions: %s\n", args->regions_list); regidx_insert(args->regs,NULL); } if ( !args->regs ) error("Could not parse the regions: %s\n", args->regions_list); args->regs_itr = regitr_init(args->regs); } if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n"); while (optindfiles, argv[optind]) ) error("Failed to open %s: %s\n", argv[optind],bcf_sr_strerror(args->files->errnum)); optind++; } if ( args->file_list ) { int nfiles, i; char **files = hts_readlines(args->file_list, &nfiles); if ( !files ) error("Failed to read from %s\n", args->file_list); for (i=0;ifiles, files[i]) ) error("Failed to open %s: %s\n", files[i],bcf_sr_strerror(args->files->errnum)); for (i=0; ifiles->nreaders ) usage(); if ( args->files->nreaders==1 && !args->force_single ) error("Expected two or more files to merge, got only one. Use --force-single to proceed anyway\n"); merge_vcf(args); bcf_sr_destroy(args->files); if ( args->regs ) regidx_destroy(args->regs); if ( args->regs_itr ) regitr_destroy(args->regs_itr); if ( args->gvcf_fai ) fai_destroy(args->gvcf_fai); free(args); return 0; } pysam-0.23.0/bcftools/vcfnorm.c000066400000000000000000003331221475062545500163770ustar00rootroot00000000000000/* vcfnorm.c -- Left-align and normalize indels. Copyright (C) 2013-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "rbuf.h" #include "abuf.h" #include "gff.h" #include "regidx.h" #include "filter.h" #define CHECK_REF_EXIT 1 #define CHECK_REF_WARN 2 #define CHECK_REF_SKIP 4 #define CHECK_REF_FIX 8 #define MROWS_SPLIT 1 #define MROWS_MERGE 2 // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 // for -m+, mapping from allele indexes of a single input record // to allele indexes of output record typedef struct { int nals, mals, *map; } map_t; // primitive comparison of two records' alleles via hashes; normalized alleles assumed typedef struct { int n; // number of alleles char *ref, *alt; void *hash; // str2int hash } cmpals1_t; typedef struct { cmpals1_t *cmpals; int ncmpals, mcmpals; } cmpals_t; typedef struct { char *tseq, *seq; int mseq; bcf1_t **lines, **tmp_lines, **mrows, *mrow_out; int ntmp_lines, mtmp_lines, nmrows, mmrows, mrows_first; map_t *maps; // mrow map for each buffered record char **als; int mmaps, nals, mals; uint8_t *tmp_arr1, *tmp_arr2, *diploid; int32_t *int32_arr; int ntmp_arr1, ntmp_arr2, nint32_arr; kstring_t *tmp_str; kstring_t *tmp_als, *tmp_sym, tmp_kstr; int ntmp_als, ntmp_sym; rbuf_t rbuf; int buf_win; // maximum distance between two records to consider int aln_win; // the realignment window size (maximum repeat size) bcf_srs_t *files; // using the synced reader only for -r option bcf_hdr_t *hdr, *out_hdr; cmpals_t cmpals_in, cmpals_out; faidx_t *fai; struct { int tot, set, swap; } nref; char **argv, *output_fname, *ref_fname, *vcf_fname, *region, *targets; int argc, rmdup, output_type, n_threads, check_ref, strict_filter, do_indels, clevel; int nchanged, nskipped, nsplit, njoined, ntotal, nfilter, mrows_op, mrows_collapse, parsimonious; int record_cmd_line, force, force_warned, keep_sum_ad; abuf_t *abuf; abuf_opt_t atomize; int use_star_allele, ma_use_ref_allele; char *old_rec_tag; htsFile *out; char *index_fn; int write_index, gff_verbosity; int right_align; char *gff_fname; gff_t *gff; regidx_t *idx_tscript; regitr_t *itr_tscript; int (*cmp_func)(const void *aptr, const void *bptr); char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE int filter_pass; filter_t *filter; } args_t; static inline int replace_iupac_codes(char *seq, int nseq) { // Replace ambiguity codes with N for now, it awaits to be seen what the VCF spec codifies in the end int i, n = 0; for (i=0; id.allele[0]); int i,j, maxlen = reflen, len; for (i=1; in_allele; i++) { int len = strlen(line->d.allele[i]); if ( maxlen < len ) maxlen = len; } char *ref = faidx_fetch_seq(args->fai, (char*)bcf_seqname(args->hdr,line), line->pos, line->pos+maxlen-1, &len); if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); replace_iupac_codes(ref,len); args->nref.tot++; // is the REF different? If not, we are done if ( !strncasecmp(line->d.allele[0],ref,reflen) ) { free(ref); return; } // is the REF allele missing? if ( reflen==1 && line->d.allele[0][0]=='.' ) { line->d.allele[0][0] = ref[0]; args->nref.set++; free(ref); bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele); return; } // does REF or ALT contain non-standard bases? int has_non_acgtn = 0; for (i=0; in_allele; i++) { if ( line->d.allele[i][0]=='<' ) continue; has_non_acgtn += replace_iupac_codes(line->d.allele[i],strlen(line->d.allele[i])); } if ( has_non_acgtn ) { args->nref.set++; bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele); if ( !strncasecmp(line->d.allele[0],ref,reflen) ) { free(ref); return; } } // does the REF allele contain N's ? int fix = 0; for (i=0; id.allele[0][i]!='N' ) continue; if ( ref[i]=='N' ) continue; line->d.allele[0][i] = ref[i]; fix++; for (j=1; jn_allele; j++) { int len = strlen(line->d.allele[j]); if ( len <= i || line->d.allele[j][i]!='N' ) continue; line->d.allele[j][i] = ref[i]; fix++; } } if ( fix ) { args->nref.set++; bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele); if ( !strncasecmp(line->d.allele[0],ref,reflen) ) { free(ref); return; } } // is it swapped? for (i=1; in_allele; i++) { int len = strlen(line->d.allele[i]); if ( !strncasecmp(line->d.allele[i],ref,len) ) break; } kstring_t str = {0,0,0}; if ( i==line->n_allele ) // none of the alternate alleles matches the reference { args->nref.set++; kputsn(ref,reflen,&str); for (i=1; in_allele; i++) { kputc(',',&str); kputs(line->d.allele[i],&str); } bcf_update_alleles_str(args->out_hdr,line,str.s); free(ref); free(str.s); return; } // one of the alternate alleles matches the reference, assume it's a simple swap kputs(line->d.allele[i],&str); for (j=1; jn_allele; j++) { kputc(',',&str); if ( j==i ) kputs(line->d.allele[0],&str); else kputs(line->d.allele[j],&str); } bcf_update_alleles_str(args->out_hdr,line,str.s); args->nref.swap++; free(ref); free(str.s); // swap genotypes int ntmp = args->ntmp_arr1 / sizeof(int32_t); // reuse tmp_arr declared as uint8_t int ngts = bcf_get_genotypes(args->hdr, line, &args->tmp_arr1, &ntmp); args->ntmp_arr1 = ntmp * sizeof(int32_t); int32_t *gts = (int32_t*) args->tmp_arr1; int ni = 0; for (j=0; jout_hdr,line,gts,ngts); // update AC int nac = bcf_get_info_int32(args->hdr, line, "AC", &args->tmp_arr1, &ntmp); args->ntmp_arr1 = ntmp * sizeof(int32_t); if ( i <= nac ) { int32_t *ac = (int32_t*)args->tmp_arr1; ac[i-1] = ni; bcf_update_info_int32(args->out_hdr, line, "AC", ac, nac); } } static void fix_dup_alt(args_t *args, bcf1_t *line) { // update alleles, create a mapping between old and new indexes hts_expand(uint8_t,line->n_allele,args->ntmp_arr1,args->tmp_arr1); args->tmp_arr1[0] = 0; // ref always unchanged int i, j, nals = line->n_allele, nals_ori = line->n_allele; for (i=1, j=1; in_allele; i++) { if ( strcasecmp(line->d.allele[0],line->d.allele[i]) ) { args->tmp_arr1[i] = j++; continue; } args->tmp_arr1[i] = 0; nals--; } for (i=1, j=1; in_allele; i++) { if ( !args->tmp_arr1[i] ) continue; line->d.allele[j++] = line->d.allele[i]; } bcf_update_alleles(args->out_hdr, line, (const char**)line->d.allele, nals); // update genotypes int ntmp = args->ntmp_arr2 / sizeof(int32_t); // reuse tmp_arr declared as uint8_t int ngts = bcf_get_genotypes(args->hdr, line, &args->tmp_arr2, &ntmp); args->ntmp_arr2 = ntmp * sizeof(int32_t); int32_t *gts = (int32_t*) args->tmp_arr2; int changed = 0; for (i=0; itmp_arr1[ial] ) continue; int ial_new = ialtmp_arr1[ial] : 0; gts[i] = bcf_gt_is_phased(gts[i]) ? bcf_gt_phased(ial_new) : bcf_gt_unphased(ial_new); changed = 1; } if ( changed ) bcf_update_genotypes(args->out_hdr,line,gts,ngts); } static void set_old_rec_tag(args_t *args, bcf1_t *dst, bcf1_t *src, int ialt) { if ( !args->old_rec_tag ) return; // only update if the tag is not present already, there can be multiple normalization steps int i, id = bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, args->old_rec_tag); bcf_unpack(dst, BCF_UN_INFO); for (i=0; in_info; i++) { bcf_info_t *inf = &dst->d.info[i]; if ( inf && inf->key == id ) return; } args->tmp_kstr.l = 0; ksprintf(&args->tmp_kstr,"%s|%"PRIhts_pos"|%s|",bcf_seqname(args->hdr,src),src->pos+1,src->d.allele[0]); for (i=1; in_allele; i++) { kputs(src->d.allele[i],&args->tmp_kstr); if ( i+1n_allele ) kputc(',',&args->tmp_kstr); } if ( ialt>0 ) { kputc('|',&args->tmp_kstr); kputw(ialt,&args->tmp_kstr); } if ( (bcf_update_info_string(args->out_hdr, dst, args->old_rec_tag, args->tmp_kstr.s))!=0 ) error("An error occurred while updating INFO/%s\n",args->old_rec_tag); } static int is_left_align(args_t *args, bcf1_t *line) { if ( args->right_align ) return 0; if ( !args->gff ) return 1; const char *chr = bcf_seqname(args->hdr,line); if ( !strncasecmp("chr",chr,3) ) chr += 3; // strip 'chr' prefix, that's what we requested the GFF reader to do if ( !regidx_overlap(args->idx_tscript,chr,line->pos,line->pos+line->rlen, args->itr_tscript) ) return 1; // if there are two conflicting overlapping transcripts, go with the default left-alignment int has_fwd = 0; while ( regitr_overlap(args->itr_tscript) ) { gf_tscript_t *tr = regitr_payload(args->itr_tscript, gf_tscript_t*); if ( tr->strand==STRAND_FWD ) has_fwd = 1; if ( tr->strand==STRAND_REV ) return 1; } // either no hit at all (then left-align) or everything was on fwd strand (then right-align) return has_fwd ? 0 : 1; } static hts_pos_t realign_left(args_t *args, bcf1_t *line) { // trim from right char *ref = NULL; int i; hts_pos_t nref=0, new_pos = line->pos; kstring_t *als = args->tmp_als; while (1) { // is the rightmost base identical in all alleles? int min_len = als[0].l; for (i=1; in_allele; i++) { if ( toupper(als[0].s[ als[0].l-1 ]) != toupper(als[i].s[ als[i].l-1 ]) ) break; if ( als[i].l < min_len ) min_len = als[i].l; } if ( i!=line->n_allele ) break; // there are differences, cannot be trimmed if ( min_len<=1 && new_pos==0 ) break; int pad_from_left = 0; for (i=0; in_allele; i++) // trim all alleles { als[i].l--; if ( !als[i].l ) pad_from_left = 1; } if ( pad_from_left ) { // extend all alleles to the left by aln_win bases (unless close to the chr start). // Extra bases will be trimmed from the left after this loop is done int npad = new_pos >= args->aln_win ? args->aln_win : new_pos; free(ref); ref = faidx_fetch_seq64(args->fai, bcf_seqname(args->hdr,line), new_pos-npad, new_pos-1, &nref); if ( !ref ) error("faidx_fetch_seq64 failed at %s:%"PRId64"\n", bcf_seqname(args->hdr,line), (int64_t) new_pos-npad+1); replace_iupac_codes(ref,nref); for (i=0; in_allele; i++) { ks_resize(&als[i], als[i].l + npad); if ( als[i].l ) memmove(als[i].s+npad,als[i].s,als[i].l); memcpy(als[i].s,ref,npad); als[i].l += npad; } new_pos -= npad; } } free(ref); // trim from left int ntrim_left = 0; while (1) { // is the first base identical in all alleles? int min_len = als[0].l - ntrim_left; for (i=1; in_allele; i++) { if ( toupper(als[0].s[ntrim_left]) != toupper(als[i].s[ntrim_left]) ) break; if ( min_len > als[i].l - ntrim_left ) min_len = als[i].l - ntrim_left; } if ( i!=line->n_allele || min_len<=1 ) break; // there are differences, cannot be trimmed ntrim_left++; } if ( ntrim_left ) { for (i=0; in_allele; i++) { memmove(als[i].s,als[i].s+ntrim_left,als[i].l-ntrim_left); als[i].l -= ntrim_left; } new_pos += ntrim_left; } return new_pos; } static hts_pos_t realign_right(args_t *args, bcf1_t *line) { char *ref = NULL; int i; hts_pos_t new_pos = line->pos, nref = 0; kstring_t *als = args->tmp_als; // trim from left int ntrim_left = 0, npad_right = line->rlen, has_indel = 0; while (1) { // is the leftmost base identical in all alleles? int min_len = als[0].l - ntrim_left; for (i=1; in_allele; i++) { if ( als[0].l!=als[i].l ) has_indel = 1; if ( toupper(als[0].s[ntrim_left]) != toupper(als[i].s[ntrim_left]) ) break; if ( min_len > als[i].l - ntrim_left ) min_len = als[i].l - ntrim_left; } if ( i!=line->n_allele ) break; // there are differences, cannot be trimmed further ntrim_left++; if ( min_len<=1 ) // pad from the right { free(ref); ref = faidx_fetch_seq64(args->fai, bcf_seqname(args->hdr,line), line->pos + npad_right, line->pos + npad_right + args->aln_win, &nref); if ( !ref ) error("faidx_fetch_seq64 failed at %s:%"PRIhts_pos"\n",bcf_seqname(args->hdr,line), new_pos + ntrim_left); npad_right += args->aln_win; replace_iupac_codes(ref,nref); for (i=0; in_allele; i++) kputs(ref, &als[i]); } } ntrim_left -= has_indel; if ( ntrim_left > 0 ) { for (i=0; in_allele; i++) { memmove(als[i].s, als[i].s + ntrim_left, als[i].l - ntrim_left); als[i].l -= ntrim_left; } new_pos += ntrim_left; } free(ref); // trim from right while (1) { // is the last base identical in all alleles? int min_len = als[0].l; for (i=1; in_allele; i++) { if ( toupper(als[0].s[ als[0].l-1 ]) != toupper(als[i].s[ als[i].l-1 ]) ) break; if ( min_len > als[i].l ) min_len = als[i].l; } if ( i!=line->n_allele || min_len<=1 ) break; // there are differences, cannot be trimmed more for (i=0; in_allele; i++) { als[i].l--; als[i].s[als[i].l]=0; } } return new_pos; } #define ERR_DUP_ALLELE -2 #define ERR_REF_MISMATCH -1 #define ERR_OK 0 #define ERR_SYMBOLIC 1 #define ERR_SPANNING_DELETION 2 static int realign(args_t *args, bcf1_t *line) { bcf_unpack(line, BCF_UN_STR); // Sanity check REF int i, nref, reflen = strlen(line->d.allele[0]); char *ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos, line->pos+reflen-1, &nref); if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", args->hdr->id[BCF_DT_CTG][line->rid].key, (int64_t) line->pos+1); seq_to_upper(ref,0); replace_iupac_codes(ref,nref); // any non-ACGT character in fasta ref is replaced with N // does VCF REF contain non-standard bases? if ( has_non_acgtn(line->d.allele[0],reflen) ) { if ( args->check_ref==CHECK_REF_EXIT ) error("Non-ACGTN reference allele at %s:%"PRId64" .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,ref,line->d.allele[0]); if ( args->check_ref & CHECK_REF_WARN ) fprintf(stderr,"NON_ACGTN_REF\t%s\t%"PRId64"\t%s\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,line->d.allele[0]); free(ref); return ERR_REF_MISMATCH; } if ( strcasecmp(ref,line->d.allele[0]) ) { if ( args->check_ref==CHECK_REF_EXIT ) error("Reference allele mismatch at %s:%"PRId64" .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,ref,line->d.allele[0]); if ( args->check_ref & CHECK_REF_WARN ) fprintf(stderr,"REF_MISMATCH\t%s\t%"PRId64"\t%s\t%s\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,line->d.allele[0],ref); free(ref); return ERR_REF_MISMATCH; } free(ref); ref = NULL; if ( line->n_allele == 1 ) // a REF { if ( line->rlen > 1 ) { line->d.allele[0][1] = 0; bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele); } return ERR_OK; } if ( bcf_get_variant_types(line)==VCF_BND ) return ERR_SYMBOLIC; // breakend, not an error // make a copy of each allele for trimming hts_expand0(kstring_t,line->n_allele,args->ntmp_als,args->tmp_als); // the actual sequence to realign hts_expand0(kstring_t,line->n_allele,args->ntmp_sym,args->tmp_sym); // the original symbolic allele strings to output kstring_t *als = args->tmp_als; kstring_t *sym = args->tmp_sym; int symbolic_alts = 1; for (i=0; in_allele; i++) { sym[i].l = 0; if ( line->d.allele[i][0]=='<' ) { // symbolic allele, only and will be realigned // TODO: there should be check for symbolic allele length. If too big, perhaps should not attempt realignment int32_t sv_len = 0; if ( !strncmp("d.allele[i],4) ) sv_len = -line->rlen; else if ( !strncmp("d.allele[i],4) ) { if ( bcf_get_info_int32(args->hdr,line,"SVLEN",&args->int32_arr,&args->nint32_arr)==1 ) sv_len = args->int32_arr[0]; } if ( !sv_len ) return ERR_SYMBOLIC; als[i].l = 0; if ( sv_len<0 ) { // del, expand REF and replace ALT, for example, replace "REF=C ALT=" with "REF=CAT ALT=C" if ( nref < line->rlen ) { free(ref); reflen = line->rlen; ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos, line->pos+reflen-1, &nref); if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", args->hdr->id[BCF_DT_CTG][line->rid].key, (int64_t) line->pos+1); seq_to_upper(ref,0); replace_iupac_codes(ref,nref); // any non-ACGT character in fasta ref is replaced with N als[0].l = 0; kputs(ref, &als[0]); } kputsn(als[0].s,1,&als[i]); } else // sv_len>0 { // dup, replace "REF=C ALT=" with "REF=C ALT=CAT" free(ref); ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos, line->pos+sv_len, &nref); if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", args->hdr->id[BCF_DT_CTG][line->rid].key, (int64_t) line->pos+1); seq_to_upper(ref,0); replace_iupac_codes(ref,nref); // any non-ACGT character in fasta ref is replaced with N kputs(ref,&als[i]); } kputs(line->d.allele[i],&sym[i]); // preserve the symbolic allele string continue; } if ( i>0 ) symbolic_alts = 0; if ( line->d.allele[i][0]=='*' ) return ERR_SPANNING_DELETION; // spanning deletion if ( has_non_acgtn(line->d.allele[i],line->shared.l) ) { if ( args->check_ref==CHECK_REF_EXIT ) error("Non-ACGTN alternate allele at %s:%"PRId64" .. VCF:'%s'\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,line->d.allele[i]); if ( args->check_ref & CHECK_REF_WARN ) fprintf(stderr,"NON_ACGTN_ALT\t%s\t%"PRId64"\t%s\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,line->d.allele[i]); return ERR_REF_MISMATCH; } als[i].l = 0; kputs(line->d.allele[i], &als[i]); seq_to_upper(als[i].s,0); if ( i>0 && als[i].l==als[0].l && !strcasecmp(als[0].s,als[i].s) ) return ERR_DUP_ALLELE; } free(ref); ref = NULL; // which direction are we aligning? int left_align = is_left_align(args, line); hts_pos_t new_pos; if ( left_align ) new_pos = realign_left(args, line); else new_pos = realign_right(args, line); // Have the alleles changed? Consider could have expanded the REF allele. In that // case it must be trimmed, however the new REF length must reflect the entire length. als[0].s[ als[0].l ] = 0; // for strcmp to work int new_reflen = strlen(als[0].s); if ( symbolic_alts ) { als[0].l = 1; als[0].s[ als[0].l ] = 0; } if ( new_pos==line->pos && !strcasecmp(line->d.allele[0],als[0].s) ) return ERR_OK; set_old_rec_tag(args, line, line, 0); // Create new block of alleles and update args->tmp_kstr.l = 0; for (i=0; in_allele; i++) { if (i>0) kputc(',',&args->tmp_kstr); if ( sym[i].l ) kputs(sym[i].s,&args->tmp_kstr); else kputsn(als[i].s,als[i].l,&args->tmp_kstr); } args->tmp_kstr.s[ args->tmp_kstr.l ] = 0; bcf_update_alleles_str(args->out_hdr,line,args->tmp_kstr.s); args->nchanged++; // Update INFO/END if necessary if ( (new_pos!=line->pos || reflen!=new_reflen) && bcf_get_info_int32(args->hdr, line, "END", &args->int32_arr, &args->nint32_arr)==1 ) { // bcf_update_alleles_str() messed up rlen because line->pos changed. This will be fixed by bcf_update_info_int32() line->pos = new_pos; args->int32_arr[0] = line->pos + new_reflen; bcf_update_info_int32(args->out_hdr, line, "END", args->int32_arr, 1); } line->pos = new_pos; return ERR_OK; } static void split_info_numeric(args_t *args, bcf1_t *src, bcf_info_t *info, int ialt, bcf1_t *dst) { #define BRANCH_NUMERIC(type,type_t,is_vector_end,is_missing) \ { \ const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key); \ int ntmp = args->ntmp_arr1 / sizeof(type_t); \ int ret = bcf_get_info_##type(args->hdr,src,tag,&args->tmp_arr1,&ntmp); \ args->ntmp_arr1 = ntmp * sizeof(type_t); \ assert( ret>0 ); \ type_t *vals = (type_t*) args->tmp_arr1; \ int len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key); \ if ( len==BCF_VL_A ) \ { \ if ( ret!=src->n_allele-1 ) \ { \ if ( args->force && !args->force_warned ) \ { \ fprintf(stderr, \ "Warning: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n" \ " (This warning is printed only once.)\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele-1,ret); \ args->force_warned = 1; \ } \ if ( args->force ) \ { \ bcf_update_info_##type(args->out_hdr,dst,tag,NULL,0); \ return; \ } \ error("Error: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d. Use --force to proceed anyway.\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele-1,ret); \ } \ bcf_update_info_##type(args->out_hdr,dst,tag,vals+ialt,1); \ } \ else if ( len==BCF_VL_R ) \ { \ if ( ret!=src->n_allele ) \ { \ if ( args->force && !args->force_warned ) \ { \ fprintf(stderr, \ "Warning: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n" \ " (This warning is printed only once.)\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele,ret); \ args->force_warned = 1; \ } \ if ( args->force ) \ { \ bcf_update_info_##type(args->out_hdr,dst,tag,NULL,0); \ return; \ } \ error("Error: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d. Use --force to proceed anyway.\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele,ret); \ } \ if ( args->keep_sum_ad >= 0 && args->keep_sum_ad==info->key ) \ { \ int j; \ for (j=1; jlen; j++) \ if ( j!=ialt+1 && !(is_missing) && !(is_vector_end) ) vals[0] += vals[j]; \ vals[1] = vals[ialt+1]; \ } \ else \ { \ if ( ialt!=0 ) vals[1] = vals[ialt+1]; \ } \ bcf_update_info_##type(args->out_hdr,dst,tag,vals,2); \ } \ else if ( len==BCF_VL_G ) \ { \ if ( ret!=src->n_allele*(src->n_allele+1)/2 ) \ { \ if ( args->force && !args->force_warned ) \ { \ fprintf(stderr, \ "Warning: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n" \ " (This warning is printed only once.)\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*(src->n_allele+1)/2,ret); \ args->force_warned = 1; \ } \ if ( args->force ) \ { \ bcf_update_info_##type(args->out_hdr,dst,tag,NULL,0); \ return; \ } \ error("Error: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d. Use --force to proceed anyway.\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*(src->n_allele+1)/2,ret); \ } \ if ( ialt!=0 ) \ { \ vals[1] = vals[bcf_alleles2gt(0,ialt+1)]; \ vals[2] = vals[bcf_alleles2gt(ialt+1,ialt+1)]; \ } \ bcf_update_info_##type(args->out_hdr,dst,tag,vals,3); \ } \ else \ bcf_update_info_##type(args->out_hdr,dst,tag,vals,ret); \ } switch (bcf_hdr_id2type(args->hdr,BCF_HL_INFO,info->key)) { case BCF_HT_INT: BRANCH_NUMERIC(int32, int32_t, vals[j]==bcf_int32_vector_end, vals[j]==bcf_int32_missing); break; case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_is_vector_end(vals[j]), bcf_float_is_missing(vals[j])); break; } #undef BRANCH_NUMERIC } // Find nth field in a comma-separated list in src and move it to dst. // The dst and src memory areas may overlap, end points just after the last valid src // character. // On success returns pointer to the end of the parsed field and increments ndst by the // number of memmoved characters. Returns NULL if the field was not found. static inline char *string_move_nth(char *dst, char *src, char *end, int nth, size_t *ndst) { if ( src>=end ) return NULL; char *ss = src, *se = src; int j = 0; while ( *se && se<(end) ) { if ( *se==',' ) { if ( j==nth ) break; j++; ss = se+1; } se++; } if ( j!=nth ) return NULL; if ( ss>=end ) return NULL; if ( !*ss ) return NULL; int n = se - ss; memmove((dst),ss,n); *ndst += n; return se; } static void split_info_string(args_t *args, bcf1_t *src, bcf_info_t *info, int ialt, bcf1_t *dst) { const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key); int ret = bcf_get_info_string(args->hdr,src,tag,&args->tmp_arr1,&args->ntmp_arr1); assert( ret>0 ); kstring_t str; str.m = args->ntmp_arr1; str.l = ret; str.s = (char*) args->tmp_arr1; int len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key); if ( len==BCF_VL_A ) { char *end = str.s + str.l; char *tmp = str.s; str.l = 0; tmp = string_move_nth(str.s,tmp,end,ialt,&str.l); if ( !tmp ) str.l = 1, str.s[0] = '.'; kputc_(0,&str); bcf_update_info_string(args->out_hdr,dst,tag,str.s); } else if ( len==BCF_VL_R ) { char *end = str.s + str.l; char *tmp = str.s; str.l = 0; tmp = string_move_nth(str.s,tmp,end,0,&str.l); if ( tmp ) { kputc_(',',&str); tmp = string_move_nth(str.s+str.l,tmp+1,end,ialt,&str.l); // ialt is 0-based index to ALT } if ( !tmp ) str.l = 1, str.s[0] = '.'; kputc_(0,&str); bcf_update_info_string(args->out_hdr,dst,tag,str.s); } else if ( len==BCF_VL_G ) { int i0a = bcf_alleles2gt(0,ialt+1), iaa = bcf_alleles2gt(ialt+1,ialt+1); char *end = str.s + str.l; char *tmp = str.s; str.l = 0; tmp = string_move_nth(str.s,tmp,end,0,&str.l); if ( tmp ) { kputc_(',',&str); tmp = string_move_nth(str.s+str.l,tmp+1,end,i0a-1,&str.l); } if ( tmp ) { kputc_(',',&str); tmp = string_move_nth(str.s+str.l,tmp+1,end,iaa-i0a-1,&str.l); } if ( !tmp ) str.l = 1, str.s[0] = '.'; kputc_(0,&str); bcf_update_info_string(args->out_hdr,dst,tag,str.s); } else bcf_update_info_string(args->out_hdr,dst,tag,str.s); if ( args->ntmp_arr1 < str.m ) { args->ntmp_arr1 = str.m; args->tmp_arr1 = (uint8_t*)str.s; } } static void split_info_flag(args_t *args, bcf1_t *src, bcf_info_t *info, int ialt, bcf1_t *dst) { const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key); int ret = bcf_get_info_flag(args->hdr,src,tag,&args->tmp_arr1,&args->ntmp_arr1); bcf_update_info_flag(args->out_hdr,dst,tag,NULL,ret); } static void split_format_genotype(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int ialt, bcf1_t *dst) { int ntmp = args->ntmp_arr1 / 4; int ngts = bcf_get_genotypes(args->hdr,src,&args->tmp_arr1,&ntmp); args->ntmp_arr1 = ntmp * 4; assert( ngts >0 ); int32_t *gt = (int32_t*) args->tmp_arr1; int i, j, nsmpl = bcf_hdr_nsamples(args->hdr); ngts /= nsmpl; for (i=0; ima_use_ref_allele ) gt[j] = bcf_gt_unphased(0) | bcf_gt_is_phased(gt[j]); // set to REF else gt[j] = bcf_gt_missing | bcf_gt_is_phased(gt[j]); // set to missing } gt += ngts; } bcf_update_genotypes(args->out_hdr,dst,args->tmp_arr1,ngts*nsmpl); } static void split_format_numeric(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int ialt, bcf1_t *dst) { #define BRANCH_NUMERIC(type,type_t,is_vector_end,is_missing,set_vector_end,set_missing) \ { \ const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id); \ int ntmp = args->ntmp_arr1 / sizeof(type_t); \ int nvals = bcf_get_format_##type(args->hdr,src,tag,&args->tmp_arr1,&ntmp); \ args->ntmp_arr1 = ntmp * sizeof(type_t); \ assert( nvals>0 ); \ type_t *vals = (type_t *) args->tmp_arr1; \ int len = bcf_hdr_id2length(args->hdr,BCF_HL_FMT,fmt->id); \ int i,j, nsmpl = bcf_hdr_nsamples(args->hdr); \ if ( nvals==nsmpl ) /* all values are missing */ \ { \ bcf_update_format_##type(args->out_hdr,dst,tag,vals,nsmpl); \ return; \ } \ if ( len==BCF_VL_A ) \ { \ if ( nvals!=(src->n_allele-1)*nsmpl ) \ { \ if ( args->force && !args->force_warned ) \ { \ fprintf(stderr, \ "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Removing the field.\n" \ " (This warning is printed only once.)\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \ args->force_warned = 1; \ } \ if ( args->force ) \ { \ bcf_update_format_##type(args->out_hdr,dst,tag,NULL,0); \ return; \ } \ error("Error: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Use --force to proceed anyway.\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \ } \ nvals /= nsmpl; \ type_t *src_vals = vals, *dst_vals = vals; \ for (i=0; iout_hdr,dst,tag,vals,nsmpl); \ } \ else if ( len==BCF_VL_R ) \ { \ if ( nvals!=src->n_allele*nsmpl ) \ { \ if ( args->force && !args->force_warned ) \ { \ fprintf(stderr, \ "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Removing the field.\n" \ " (This warning is printed only once.)\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \ args->force_warned = 1; \ } \ if ( args->force ) \ { \ bcf_update_format_##type(args->out_hdr,dst,tag,NULL,0); \ return; \ } \ error("Error: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Use --force to proceed anyway.\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*nsmpl,nvals); \ } \ nvals /= nsmpl; \ type_t *src_vals = vals, *dst_vals = vals; \ if ( args->keep_sum_ad >= 0 && args->keep_sum_ad==fmt->id ) \ { \ for (i=0; iout_hdr,dst,tag,vals,nsmpl*2); \ } \ else if ( len==BCF_VL_G ) \ { \ if ( nvals!=src->n_allele*(src->n_allele+1)/2*nsmpl && nvals!=src->n_allele*nsmpl ) \ { \ if ( args->force && !args->force_warned ) \ { \ fprintf(stderr, \ "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Removing the field.\n" \ " (This warning is printed only once.)\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \ args->force_warned = 1; \ } \ if ( args->force ) \ { \ bcf_update_format_##type(args->out_hdr,dst,tag,NULL,0); \ return; \ } \ error("Error at %s:%"PRId64", the tag %s has wrong number of fields. Use --force to proceed anyway.\n", \ bcf_seqname(args->hdr,src),(int64_t) src->pos+1,bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id)); \ } \ nvals /= nsmpl; \ int all_haploid = nvals==src->n_allele ? 1 : 0; \ type_t *src_vals = vals, *dst_vals = vals; \ for (i=0; iout_hdr,dst,tag,vals,all_haploid ? nsmpl*2 : nsmpl*3); \ } \ else \ bcf_update_format_##type(args->out_hdr,dst,tag,vals,nvals); \ } switch (bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id)) { case BCF_HT_INT: BRANCH_NUMERIC(int32, int32_t, src_vals[isrc]==bcf_int32_vector_end, src_vals[isrc]==bcf_int32_missing, dst_vals[idst]=bcf_int32_vector_end, dst_vals[idst]=bcf_int32_missing); break; case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_is_vector_end(src_vals[isrc]), bcf_float_is_missing(src_vals[isrc]), bcf_float_set_vector_end(dst_vals[idst]), bcf_float_set_missing(src_vals[idst])); break; } #undef BRANCH_NUMERIC } static void squeeze_format_char(char *str, int src_blen, int dst_blen, int n) { int i, isrc = 0, idst = 0; for (i=0; ihdr,BCF_DT_ID,fmt->id); int ret = bcf_get_format_char(args->hdr,src,tag,&args->tmp_arr1,&args->ntmp_arr1); if ( !ret ) return; // all values can be empty, leave out the tag, no need to panic assert( ret>0 ); int nsmpl = bcf_hdr_nsamples(args->hdr); int blen = ret/nsmpl; // per-sample field length assert( blen>0 ); kstring_t str; str.m = args->ntmp_arr1; str.s = (char*) args->tmp_arr1; str.l = ret; int tag_len = bcf_hdr_id2length(args->hdr,BCF_HL_FMT,fmt->id); if ( tag_len==BCF_VL_A ) { int i, maxlen = 0; char *ptr = str.s; for (i=0; iout_hdr,dst,tag,str.s,nsmpl*maxlen); } else if ( tag_len==BCF_VL_R ) { int i, maxlen = 0; char *ptr = str.s; for (i=0; iout_hdr,dst,tag,str.s,nsmpl*maxlen); } else if ( tag_len==BCF_VL_G ) { int i, maxlen = 0, i0a = bcf_alleles2gt(0,ialt+1), iaa = bcf_alleles2gt(ialt+1,ialt+1); char *ptr = str.s; for (i=0; in_allele*(src->n_allele+1)/2 && nfields!=src->n_allele ) { if ( args->force && !args->force_warned ) { fprintf(stderr, "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d or %d, found %d. Removing the field.\n" " (This warning is printed only once.)\n", tag,bcf_seqname(args->hdr,src),(int64_t)src->pos+1,src->n_allele*(src->n_allele+1)/2,src->n_allele,nfields); args->force_warned = 1; } if ( args->force ) { bcf_update_format_char(args->out_hdr,dst,tag,NULL,0); return; } error("Error: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d or %d, found %d. Use --force to proceed anyway.\n", tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*(src->n_allele+1)/2,src->n_allele,nfields); } char *tmp = ptr; char *end = ptr + blen; size_t len = 0; tmp = string_move_nth(ptr,tmp,end,0,&len); if ( nfields==src->n_allele ) // haploid { if ( tmp ) { ptr[len++] = ','; tmp = string_move_nth(ptr+len,tmp+1,end,ialt,&len); } } else // diploid { if ( tmp ) { ptr[len++] = ','; tmp = string_move_nth(ptr+len,tmp+1,end,i0a-1,&len); } if ( tmp ) { ptr[len++] = ','; tmp = string_move_nth(ptr+len,tmp+1,end,iaa-i0a-1,&len); } } if ( !tmp ) ptr[0] = '.', len = 1; if ( maxlen < len ) maxlen = len; while (lenout_hdr,dst,tag,str.s,nsmpl*maxlen); } else bcf_update_format_char(args->out_hdr,dst,tag,str.s,str.l); } static void split_multiallelic_to_biallelics(args_t *args, bcf1_t *line) { int i; bcf_unpack(line, BCF_UN_ALL); // Init the target biallelic lines args->ntmp_lines = line->n_allele-1; if ( args->mtmp_lines < args->ntmp_lines ) { args->tmp_lines = (bcf1_t **)realloc(args->tmp_lines,sizeof(bcf1_t*)*args->ntmp_lines); for (i=args->mtmp_lines; intmp_lines; i++) args->tmp_lines[i] = NULL; args->mtmp_lines = args->ntmp_lines; } kstring_t tmp = {0,0,0}; kputs(line->d.allele[0], &tmp); kputc(',', &tmp); int rlen = tmp.l; int gt_id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"GT"); for (i=0; intmp_lines; i++) // for each ALT allele { if ( !args->tmp_lines[i] ) args->tmp_lines[i] = bcf_init1(); bcf1_t *dst = args->tmp_lines[i]; bcf_clear(dst); dst->rid = line->rid; dst->pos = line->pos; dst->qual = line->qual; // Not quite sure how to handle IDs, they can be assigned to a specific // ALT. For now we leave the ID unchanged for all. bcf_update_id(args->out_hdr, dst, line->d.id ? line->d.id : "."); tmp.l = rlen; kputs(line->d.allele[i+1],&tmp); bcf_update_alleles_str(args->out_hdr,dst,tmp.s); if ( line->d.n_flt ) bcf_update_filter(args->hdr, dst, line->d.flt, line->d.n_flt); int j; for (j=0; jn_info; j++) { bcf_info_t *info = &line->d.info[j]; int type = bcf_hdr_id2type(args->hdr,BCF_HL_INFO,info->key); if ( type==BCF_HT_INT || type==BCF_HT_REAL ) split_info_numeric(args, line, info, i, dst); else if ( type==BCF_HT_FLAG ) split_info_flag(args, line, info, i, dst); else split_info_string(args, line, info, i, dst); } set_old_rec_tag(args, dst, line, i + 1); // 1-based indexes dst->n_sample = line->n_sample; for (j=0; jn_fmt; j++) { bcf_fmt_t *fmt = &line->d.fmt[j]; int type = bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id); if ( fmt->id==gt_id ) split_format_genotype(args, line, fmt, i, dst); else if ( type==BCF_HT_INT || type==BCF_HT_REAL ) split_format_numeric(args, line, fmt, i, dst); else split_format_string(args, line, fmt, i, dst); } } free(tmp.s); } // Enlarge FORMAT array containing nsmpl samples each with nals_ori values // to accommodate nvals values for each sample, filling the gaps with missing // values. Works also for INFO arrays, with nsmpl set to 1. #define ENLARGE_ARRAY(type_t,set_missing,arr,narr_bytes,nsmpl,nvals_ori,nvals) \ { \ int nbytes_new = (nsmpl)*(nvals)*sizeof(type_t); \ hts_expand(uint8_t,nbytes_new,narr_bytes,arr); \ int ismpl, k; \ for (ismpl=nsmpl-1; ismpl>=0; ismpl--) \ { \ type_t *dst_ptr = ((type_t*)arr) + ismpl*(nvals); \ type_t *src_ptr = ((type_t*)arr) + ismpl*nvals_ori; \ memmove(dst_ptr,src_ptr,sizeof(type_t)*nvals_ori); \ for (k=nvals_ori; khdr,BCF_DT_ID,info->key); \ int ntmp = args->ntmp_arr1 / sizeof(type_t); \ int nvals_ori = bcf_get_info_##type(args->hdr,lines[0],tag,&args->tmp_arr1,&ntmp); \ args->ntmp_arr1 = ntmp * sizeof(type_t); \ assert( nvals_ori>0 ); \ type_t *vals = (type_t*) args->tmp_arr1, *vals2; \ int i,k,len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key); \ if ( len==BCF_VL_A ) \ { \ if (nvals_ori!=lines[0]->n_allele - 1) \ error("vcfnorm: number of fields in first record at position %s:%"PRId64" for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),(int64_t) lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele-1); \ int nvals = dst->n_allele - 1; \ ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \ vals = (type_t*) args->tmp_arr1; \ for (i=1; intmp_arr2 / sizeof(type_t); \ int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \ if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \ args->ntmp_arr2 = ntmp2 * sizeof(type_t); \ if (nvals2!=lines[i]->n_allele-1) \ error("vcfnorm: could not merge INFO tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \ vals2 = (type_t*) args->tmp_arr2; \ for (k=0; kmaps[i].map[k+1] - 1 ] = vals2[k]; \ } \ } \ bcf_update_info_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals); \ } \ else if ( len==BCF_VL_R ) \ { \ if (nvals_ori!=lines[0]->n_allele) \ error("vcfnorm: number of fields in first record at position %s:%"PRId64" for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),(int64_t) lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele); \ int nvals = dst->n_allele; \ ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \ vals = (type_t*) args->tmp_arr1; \ for (i=1; intmp_arr2 / sizeof(type_t); \ int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \ if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \ args->ntmp_arr2 = ntmp2 * sizeof(type_t); \ if (nvals2!=lines[i]->n_allele) \ error("vcfnorm: could not merge INFO tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \ vals2 = (type_t*) args->tmp_arr2; \ for (k=0; kmaps[i].map[k] ] = vals2[k]; \ } \ } \ bcf_update_info_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals); \ } \ else if ( len==BCF_VL_G ) \ { \ /* expecting diploid gt in INFO */ \ if (nvals_ori!=lines[0]->n_allele*(lines[0]->n_allele+1)/2) { \ fprintf(stderr, "todo: merge Number=G INFO fields for haploid sites\n"); \ error("vcfnorm: number of fields in first record at position %s:%"PRId64" for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),(int64_t) lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele*(lines[0]->n_allele+1)/2); \ } \ int nvals = dst->n_allele*(dst->n_allele+1)/2; \ ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \ vals = (type_t*) args->tmp_arr1; \ for (i=1; intmp_arr2 / sizeof(type_t); \ int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \ if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \ args->ntmp_arr2 = ntmp2 * sizeof(type_t); \ if (nvals2!=lines[i]->n_allele*(lines[i]->n_allele+1)/2) \ error("vcfnorm: could not merge INFO tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \ vals2 = (type_t*) args->tmp_arr2; \ int ia,ib; \ k = 0; \ for (ia=0; ian_allele; ia++) \ { \ for (ib=0; ib<=ia; ib++) \ { \ if ( is_vector_end ) break; \ int l = bcf_alleles2gt(args->maps[i].map[ia],args->maps[i].map[ib]); \ vals[l] = vals2[k]; \ k++; \ } \ } \ } \ bcf_update_info_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals); \ } \ else \ bcf_update_info_##type(args->out_hdr,dst,tag,vals,nvals_ori); \ } switch (bcf_hdr_id2type(args->hdr,BCF_HL_INFO,info->key)) { case BCF_HT_INT: BRANCH_NUMERIC(int32, int32_t, dst_ptr[k]=bcf_int32_missing, vals2[k]==bcf_int32_vector_end); break; case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_set_missing(dst_ptr[k]), bcf_float_is_vector_end(vals2[k])); break; } #undef BRANCH_NUMERIC } static void merge_info_flag(args_t *args, bcf1_t **lines, int nlines, bcf_info_t *info, bcf1_t *dst) { const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key); int ret = bcf_get_info_flag(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1); bcf_update_info_flag(args->out_hdr,dst,tag,NULL,ret); } int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst); // see vcfmerge.c static void merge_info_string(args_t *args, bcf1_t **lines, int nlines, bcf_info_t *info, bcf1_t *dst) { const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key); kstring_t str; str.m = args->ntmp_arr1; str.l = 0; str.s = (char*) args->tmp_arr1; int i, j, len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key); if ( len==BCF_VL_A || len==BCF_VL_R ) { int jfrom = len==BCF_VL_A ? 1 : 0; kputc('.',&str); for (i=jfrom+1; in_allele; i++) kputs(",.",&str); for (i=0; ihdr,lines[i],tag); if (!src) continue; for (j=jfrom; jn_allele; j++) copy_string_field((char*)src->vptr, j-jfrom, src->len, &str, args->maps[i].map[j]-jfrom); } str.s[str.l] = 0; args->tmp_arr1 = (uint8_t*) str.s; args->ntmp_arr1 = str.m; bcf_update_info_string(args->out_hdr,dst,tag,str.s); } else if ( len==BCF_VL_G ) { int ngts = dst->n_allele*(dst->n_allele+1)/2; kputc('.',&str); for (i=1; ihdr,lines[i],tag); if (!src) continue; int iori, jori, kori = 0; for (iori=0; iorin_allele; iori++) { int inew = args->maps[i].map[iori]; for (jori=0; jori<=iori; jori++) { int jnew = args->maps[i].map[jori]; int knew = bcf_alleles2gt(inew,jnew); copy_string_field((char*)src->vptr,kori,src->len,&str,knew); kori++; } } } str.s[str.l] = 0; args->tmp_arr1 = (uint8_t*) str.s; args->ntmp_arr1 = str.m; bcf_update_info_string(args->out_hdr,dst,tag,str.s); } else { bcf_get_info_string(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1); bcf_update_info_string(args->out_hdr,dst,tag,args->tmp_arr1); } } static int gt_array_grow_ploidy(args_t *args, uint8_t **tmp_arr, int *ntmp_arr, int ngt_ori, int ngt_new, int nsmpl) { *ntmp_arr = 4*ngt_new*nsmpl; int32_t *ptr = (int32_t*)realloc(*tmp_arr,*ntmp_arr); if ( !ptr ) error("Error: failed to allocate %d bytes\n",*ntmp_arr); *tmp_arr = (uint8_t*) ptr; int i,j; for (i=nsmpl-1; i>=0; i--) { int32_t *src = ptr + i*ngt_ori; int32_t *dst = ptr + i*ngt_new; for (j=ngt_new; j>ngt_ori; j--) dst[j-1] = bcf_int32_vector_end; for (j=ngt_ori; j>0; j--) dst[j-1] = src[j-1]; } return ngt_new; } static void merge_format_genotype(args_t *args, bcf1_t **lines, int nlines, bcf_fmt_t *fmt, bcf1_t *dst) { // reusing int8_t arrays as int32_t arrays int ntmp = args->ntmp_arr1 / 4; int ngts = bcf_get_genotypes(args->hdr,lines[0],&args->tmp_arr1,&ntmp); args->ntmp_arr1 = ntmp * 4; assert( ngts >0 ); int nsmpl = bcf_hdr_nsamples(args->hdr); ngts /= nsmpl; int i, j, k,k2; for (i=1; intmp_arr2 / 4; int ngts2 = bcf_get_genotypes(args->hdr,lines[i],&args->tmp_arr2,&ntmp2); args->ntmp_arr2 = ntmp2 * 4; ngts2 /= nsmpl; int ploidy_changed = ngts - ngts2; if ( ngts < ngts2 ) ngts = gt_array_grow_ploidy(args,&args->tmp_arr1,&args->ntmp_arr1,ngts,ngts2,nsmpl); if ( ngts > ngts2 ) ngts2 = gt_array_grow_ploidy(args,&args->tmp_arr2,&args->ntmp_arr2,ngts2,ngts,nsmpl); int32_t *gt = (int32_t*) args->tmp_arr1; // the first, destination line int32_t *gt2 = (int32_t*) args->tmp_arr2; // one of the subsequent lines, i.e. the source line for (j=0; j=args->maps[i].nals ) error("Error at %s:%"PRId64": incorrect allele index %d\n",bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1,ial2); // The destination allele int ial = args->maps[i].map[ial2]; if ( gt[k2]==bcf_int32_vector_end || bcf_gt_is_missing(gt[k2]) || !bcf_gt_allele(gt[k2]) ) gt[k2] = (gt[k2]!=bcf_int32_vector_end && bcf_gt_is_phased(gt[k2])) ? bcf_gt_phased(ial) : bcf_gt_unphased(ial); else { // conflict, the first line has non-zero allele, use the old way, possibly disrupt the phasing for (k=0; kout_hdr,dst,args->tmp_arr1,ngts*nsmpl); } static int diploid_to_haploid(int size, int nsmpl, int nals, uint8_t *vals) { int i, dsrc = size*nals*(nals+1)/2, ddst = size*nals; uint8_t *src_ptr = vals + dsrc, *dst_ptr = vals + ddst; for (i=1; ihdr,BCF_DT_ID,fmt->id); \ int ntmp = args->ntmp_arr1 / sizeof(type_t); \ int nvals_ori = bcf_get_format_##type(args->hdr,lines[0],tag,&args->tmp_arr1,&ntmp); \ args->ntmp_arr1 = ntmp * sizeof(type_t); \ assert( nvals_ori>0 ); \ type_t *vals2, *vals = (type_t *) args->tmp_arr1; \ int len = bcf_hdr_id2length(args->hdr,BCF_HL_FMT,fmt->id); \ int i, j, k, nsmpl = bcf_hdr_nsamples(args->hdr); \ nvals_ori /= nsmpl; \ if ( len==BCF_VL_A ) \ { \ int nvals = dst->n_allele - 1; \ ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,nsmpl,nvals_ori,nvals); \ for (i=1; intmp_arr2 / sizeof(type_t); \ int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \ if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \ args->ntmp_arr2 = ntmp2 * sizeof(type_t); \ nvals2 /= nsmpl; \ if (nvals2!=lines[i]->n_allele-1) \ error("vcfnorm: could not merge FORMAT tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \ vals = (type_t*) args->tmp_arr1; \ vals2 = (type_t*) args->tmp_arr2; \ for (j=0; jmaps[i].map[k+1] - 1 ] = vals2[k]; \ } \ vals += nvals; \ vals2 += nvals2; \ } \ } \ bcf_update_format_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals*nsmpl); \ } \ else if ( len==BCF_VL_R ) \ { \ int nvals = dst->n_allele; \ ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,nsmpl,nvals_ori,nvals); \ for (i=1; intmp_arr2 / sizeof(type_t); \ int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \ if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \ args->ntmp_arr2 = ntmp2 * sizeof(type_t); \ nvals2 /= nsmpl; \ if (nvals2!=lines[i]->n_allele) \ error("vcfnorm: could not merge FORMAT tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \ vals = (type_t*) args->tmp_arr1; \ vals2 = (type_t*) args->tmp_arr2; \ for (j=0; jmaps[i].map[k] ] = vals2[k]; \ } \ vals += nvals; \ vals2 += nvals2; \ } \ } \ bcf_update_format_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals*nsmpl); \ } \ else if ( len==BCF_VL_G ) \ { \ /* which samples are diploid */ \ memset(args->diploid,0,nsmpl); \ int all_haploid = 1; \ if ( nvals_ori > lines[0]->n_allele ) /* line possibly diploid */ \ { \ vals2 = (type_t*) args->tmp_arr1; \ int ndiploid = lines[0]->n_allele*(lines[0]->n_allele+1)/2; \ for (i=0; idiploid[i] ) \ { \ for (k=0; kdiploid[i] = 1; all_haploid = 0; }\ } \ vals2 += nvals_ori; \ } \ } \ int nvals = dst->n_allele*(dst->n_allele+1)/2; \ ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,nsmpl,nvals_ori,nvals); \ for (i=1; intmp_arr2 / sizeof(type_t); \ int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \ if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \ args->ntmp_arr2 = ntmp2 * sizeof(type_t); \ nvals2 /= nsmpl; \ int ndiploid = lines[i]->n_allele*(lines[i]->n_allele+1)/2; \ int line_diploid = nvals2==ndiploid ? 1 : 0; \ if (!(nvals2==1 || nvals2==lines[i]->n_allele || nvals2==lines[i]->n_allele*(lines[i]->n_allele+1)/2)) \ error("vcfnorm: could not merge FORMAT tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \ vals = (type_t*) args->tmp_arr1; \ vals2 = (type_t*) args->tmp_arr2; \ for (j=0; jdiploid[j] ) { args->diploid[j] = 1; all_haploid = 0; } \ if ( !smpl_diploid ) \ { \ for (k=0; kn_allele; k++) vals[args->maps[i].map[k]] = vals2[k]; \ } \ else \ { \ k = 0; \ int ia,ib; \ for (ia=0; ian_allele; ia++) \ { \ for (ib=0; ib<=ia; ib++) \ { \ int l = bcf_alleles2gt(args->maps[i].map[ia],args->maps[i].map[ib]); \ vals[l] = vals2[k]; \ k++; \ } \ } \ } \ vals += nvals; \ vals2 += nvals2; \ } \ } \ if ( all_haploid ) \ nvals = diploid_to_haploid(sizeof(type_t),nsmpl,dst->n_allele,args->tmp_arr1); \ else \ {\ k = dst->n_allele;\ vals2 = (type_t*) args->tmp_arr1;\ for (i=0; idiploid[i] ) set_vector_end;\ vals2 += nvals;\ }\ }\ bcf_update_format_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals*nsmpl); \ } \ else \ bcf_update_format_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals_ori*nsmpl); \ } switch (bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id)) { case BCF_HT_INT: BRANCH_NUMERIC(int32, int32_t, dst_ptr[k]=bcf_int32_missing, vals2[k]==bcf_int32_vector_end, vals2[k]=bcf_int32_vector_end); break; case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_set_missing(dst_ptr[k]), bcf_float_is_vector_end(vals2[k]), bcf_float_set_vector_end(vals2[k])); break; } #undef BRANCH_NUMERIC } static void merge_format_string(args_t *args, bcf1_t **lines, int nlines, bcf_fmt_t *fmt, bcf1_t *dst) { const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id); int i, j, k, len = bcf_hdr_id2length(args->hdr,BCF_HL_FMT,fmt->id); if ( len!=BCF_VL_A && len!=BCF_VL_R && len!=BCF_VL_G ) { int nret = bcf_get_format_char(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1); bcf_update_format_char(args->out_hdr,dst,tag,args->tmp_arr1,nret); return; } int nsmpl = bcf_hdr_nsamples(args->hdr); for (i=0; itmp_str[i].l = 0; if ( len==BCF_VL_A || len==BCF_VL_R ) { int jfrom = len==BCF_VL_A ? 1 : 0; for (i=0; itmp_str[i]; kputc('.',tmp); for (k=jfrom+1; kn_allele; k++) kputs(",.",tmp); } for (i=0; ihdr,lines[i],tag,&args->tmp_arr1,&args->ntmp_arr1); if (nret<0) continue; /* format tag does not exist in this record, skip */ nret /= nsmpl; for (k=0; ktmp_str[k]; char *src = (char*)args->tmp_arr1 + k*nret; for (j=jfrom; jn_allele; j++) copy_string_field(src, j-jfrom, nret, tmp, args->maps[i].map[j]-jfrom); } } } else if ( len==BCF_VL_G ) { hts_expand(uint8_t,nsmpl,args->ntmp_arr2,args->tmp_arr2); uint8_t *haploid = args->tmp_arr2; int nret = bcf_get_format_char(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1); nret /= nsmpl; for (i=0; itmp_arr1 + i*nret, *se = ss+nret; int nfields = 1; while ( *ss && ssn_allele ) { haploid[i] = 1; nfields = dst->n_allele; } else if ( nfields==lines[0]->n_allele*(lines[0]->n_allele+1)/2 ) { haploid[i] = 0; nfields = dst->n_allele*(dst->n_allele+1)/2; } else error("The field %s at %s:%"PRId64" neither diploid nor haploid?\n", tag,bcf_seqname(args->hdr,dst),(int64_t) dst->pos+1); kstring_t *tmp = &args->tmp_str[i]; kputc('.',tmp); for (j=1; jhdr,lines[i],tag,&args->tmp_arr1,&args->ntmp_arr1); if (nret<0) continue; /* format tag does not exist in this record, skip */ nret /= nsmpl; } for (k=0; ktmp_str[k]; char *src = (char*)args->tmp_arr1 + k*nret; if ( haploid[k] ) { for (j=0; jn_allele; j++) copy_string_field(src,j,nret, tmp, args->maps[i].map[j]); } else { int iori, jori, kori = 0; for (iori=0; iorin_allele; iori++) { int inew = args->maps[i].map[iori]; for (jori=0; jori<=iori; jori++) { int jnew = args->maps[i].map[jori]; int knew = bcf_alleles2gt(inew,jnew); copy_string_field(src,kori,nret,tmp,knew); kori++; } } } } } } kstring_t str; str.m = args->ntmp_arr2; str.l = 0; str.s = (char*) args->tmp_arr2; int max_len = 0; for (i=0; itmp_str[i].l ) max_len = args->tmp_str[i].l; for (i=0; itmp_str[i]; kputsn(tmp->s,tmp->l,&str); for (j=tmp->l; jntmp_arr2 = str.m; args->tmp_arr2 = (uint8_t*)str.s; bcf_update_format_char(args->out_hdr,dst,tag,str.s,str.l); } char **merge_alleles(char **a, int na, int *map, char **b, int *nb, int *mb); // see vcfmerge.c static void merge_biallelics_to_multiallelic(args_t *args, bcf1_t *dst, bcf1_t **lines, int nlines) { int i; for (i=0; irid = lines[0]->rid; dst->pos = lines[0]->pos; // take max for QUAL bcf_float_set_missing(dst->qual); for (i=0; iqual)) continue; if (bcf_float_is_missing(dst->qual) || dst->qualqual) dst->qual = lines[i]->qual; } bcf_update_id(args->out_hdr, dst, lines[0]->d.id); // Merge and set the alleles, create a mapping from source allele indexes to dst idxs hts_expand0(map_t,nlines,args->mmaps,args->maps); // a mapping for each line args->nals = args->maps[0].nals = lines[0]->n_allele; hts_expand(int,args->maps[0].nals,args->maps[0].mals,args->maps[0].map); hts_expand(char*,args->nals,args->mals,args->als); for (i=0; imaps[0].nals; i++) { args->maps[0].map[i] = i; args->als[i] = strdup(lines[0]->d.allele[i]); } for (i=1; id.id[0]!='.' || lines[i]->d.id[1]) bcf_add_id(args->out_hdr, dst, lines[i]->d.id); args->maps[i].nals = lines[i]->n_allele; hts_expand(int,args->maps[i].nals,args->maps[i].mals,args->maps[i].map); args->als = merge_alleles(lines[i]->d.allele, lines[i]->n_allele, args->maps[i].map, args->als, &args->nals, &args->mals); if ( !args->als ) error("Failed to merge alleles at %s:%"PRId64"\n", bcf_seqname(args->hdr,dst),(int64_t) dst->pos+1); } bcf_update_alleles(args->out_hdr, dst, (const char**)args->als, args->nals); for (i=0; inals; i++) { free(args->als[i]); args->als[i] = NULL; } if ( lines[0]->d.n_flt ) bcf_update_filter(args->out_hdr, dst, lines[0]->d.flt, lines[0]->d.n_flt); for (i=1; id.n_flt; j++) { // if strict_filter, set FILTER to PASS if any site PASS // otherwise accumulate FILTERs if (lines[i]->d.flt[j] == bcf_hdr_id2int(args->hdr, BCF_DT_ID, "PASS")) { if (args->strict_filter) { bcf_update_filter(args->out_hdr, dst, lines[i]->d.flt, lines[i]->d.n_flt); break; } else continue; } bcf_add_filter(args->out_hdr, dst, lines[i]->d.flt[j]); } } // merge info for (i=0; in_info; i++) { bcf_info_t *info = &lines[0]->d.info[i]; int type = bcf_hdr_id2type(args->hdr,BCF_HL_INFO,info->key); if ( type==BCF_HT_INT || type==BCF_HT_REAL ) merge_info_numeric(args, lines, nlines, info, dst); else if ( type==BCF_HT_FLAG ) merge_info_flag(args, lines, nlines, info, dst); else merge_info_string(args, lines, nlines, info, dst); } // merge format int gt_id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"GT"); dst->n_sample = lines[0]->n_sample; for (i=0; in_fmt; i++) { bcf_fmt_t *fmt = &lines[0]->d.fmt[i]; int type = bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id); if ( fmt->id==gt_id ) merge_format_genotype(args, lines, nlines, fmt, dst); else if ( type==BCF_HT_INT || type==BCF_HT_REAL ) merge_format_numeric(args, lines, nlines, fmt, dst); else merge_format_string(args, lines, nlines, fmt, dst); } args->njoined++; } #define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; } static void mrows_push(args_t *args, bcf1_t **line) { int i,m; if ( !args->nmrows ) args->mrows_first = 0; args->nmrows++; m = args->mmrows; hts_expand(bcf1_t*,args->nmrows,args->mmrows,args->mrows); for (i=m; immrows; i++) args->mrows[i] = bcf_init1(); SWAP(bcf1_t*, args->mrows[args->nmrows-1], *line); if ( args->mrows_collapse==COLLAPSE_ANY ) return; // move the line up the sorted list so that the same variant types end up together int cur_type = bcf_get_variant_types(args->mrows[args->nmrows-1]); i = args->mrows_first + args->nmrows - 1; while (i>0) { int prev_type = bcf_get_variant_types(args->mrows[i-1]); if ( prev_type <= cur_type ) break; bcf1_t *tmp = args->mrows[i-1]; args->mrows[i-1] = args->mrows[i]; args->mrows[i] = tmp; i--; } } static int mrows_can_flush(args_t *args, bcf1_t *line) { if ( !args->nmrows ) return 0; int ibeg = args->mrows_first; if ( args->mrows[ibeg]->rid != line->rid ) return 1; if ( args->mrows[ibeg]->pos != line->pos ) return 1; return 0; } static bcf1_t *mrows_flush(args_t *args) { if ( !args->nmrows ) return NULL; int ibeg = args->mrows_first; //fprintf(stderr,"flush: ibeg=%d n=%d\n",ibeg,args->nmrows); //int i; //for (i=ibeg; inmrows; i++) // fprintf(stderr,"\ti=%d type=%d %s %s\n",i,bcf_get_variant_types(args->mrows[i]),args->mrows[i]->d.allele[0],args->mrows[i]->d.allele[1]); if ( args->nmrows==1 ) { args->nmrows = 0; return args->mrows[ibeg]; } if ( args->mrows_collapse==COLLAPSE_ANY ) { // merge everything with anything bcf_clear(args->mrow_out); merge_biallelics_to_multiallelic(args, args->mrow_out, &args->mrows[ibeg], args->nmrows - ibeg); args->nmrows = 0; return args->mrow_out; } int j; int types[] = { VCF_SNP, VCF_MNP, VCF_INDEL, VCF_OTHER, -1 }; // merge everything within the same category if ( args->mrows_collapse==COLLAPSE_SNPS ) types[1] = -1; // merge SNPs only else if ( args->mrows_collapse==COLLAPSE_INDELS ) types[0] = VCF_INDEL, types[1] = -1; // merge indels only for (j=0; types[j]!=-1; j++) { int i, type = types[j]; // to keep the compiler happy for (i=ibeg; inmrows; i++) { type = bcf_get_variant_types(args->mrows[i]); if ( type!=types[j] && type!=VCF_REF ) break; } if ( i==ibeg+1 && type!=VCF_REF ) { // just one line of this type, no merging, but multiple lines of different type follow args->nmrows--; args->mrows_first++; return args->mrows[ibeg]; } if ( i>ibeg ) { // more than one line, merging is needed int nflush = i - ibeg; bcf_clear(args->mrow_out); merge_biallelics_to_multiallelic(args, args->mrow_out, &args->mrows[ibeg], nflush); args->nmrows -= nflush; args->mrows_first += nflush; return args->mrow_out; } } args->nmrows--; args->mrows_first++; return args->mrows[ibeg]; } static char *strdup_alt_svlen(args_t *args, bcf1_t *rec, int ial) { if ( rec->d.allele[ial][0]!='<' ) return strdup(rec->d.allele[ial]); int ntmp = args->ntmp_arr1 / sizeof(int32_t); int n = bcf_get_info_int32(args->hdr, rec, "SVLEN", &args->tmp_arr1, &ntmp); args->ntmp_arr1 = ntmp * sizeof(int32_t); int32_t *svlen = (int32_t *) args->tmp_arr1; if ( n<=0 ) return strdup(rec->d.allele[ial]); if ( n+1 != rec->n_allele ) { // there should be as many SVLEN numbers as there are ALT alleles static int warned = 0; if ( !warned ) { fprintf(stderr,"TODO: different number of ALT alleles and SVLEN fields %s:%"PRIhts_pos"\n",bcf_seqname(args->hdr,rec),rec->pos+1); warned = 1; } } kstring_t str = {0,0,0}; ksprintf(&str,"%s.%d",rec->d.allele[ial],svlen[ial-1]); return str.s; } static void cmpals_add(args_t *args, cmpals_t *ca, bcf1_t *rec) { ca->ncmpals++; hts_expand0(cmpals1_t, ca->ncmpals, ca->mcmpals, ca->cmpals); cmpals1_t *cmpals = ca->cmpals + ca->ncmpals - 1; free(cmpals->ref); cmpals->ref = strdup(rec->d.allele[0]); cmpals->n = rec->n_allele; if ( rec->n_allele==2 ) { free(cmpals->alt); cmpals->alt = strdup_alt_svlen(args,rec,1); } else { if ( cmpals->hash ) khash_str2int_destroy_free(cmpals->hash); cmpals->hash = khash_str2int_init(); int i; for (i=1; in_allele; i++) khash_str2int_inc(cmpals->hash, strdup(rec->d.allele[i])); } } static int cmpals_match(args_t *args, cmpals_t *ca, bcf1_t *rec) { int i, j; char *alt_svlen = rec->n_allele==2 ? strdup_alt_svlen(args,rec,1) : NULL; for (i=0; incmpals; i++) { cmpals1_t *cmpals = ca->cmpals + i; if ( rec->n_allele != cmpals->n ) continue; // NB. assuming both are normalized if ( strcasecmp(rec->d.allele[0], cmpals->ref) ) continue; // the most frequent case if ( rec->n_allele==2 ) { if ( strcasecmp(alt_svlen, cmpals->alt) ) continue; free(alt_svlen); return 1; } khash_t(str2int) *hash = (khash_t(str2int)*) cmpals->hash; for (j=1; jn_allele; j++) if ( !khash_str2int_has_key(hash, rec->d.allele[j]) ) break; if ( jn_allele ) continue; return 1; } free(alt_svlen); return 0; } static void cmpals_reset(cmpals_t *ca) { ca->ncmpals = 0; } static void cmpals_destroy(cmpals_t *ca) { int i; for (i=0; imcmpals; i++) { cmpals1_t *cmpals = ca->cmpals + i; free(cmpals->ref); free(cmpals->alt); if ( cmpals->hash ) khash_str2int_destroy_free(cmpals->hash); } free(ca->cmpals); } static void flush_buffer(args_t *args, htsFile *file, int n) { bcf1_t *line; int i, k; int prev_rid = -1, prev_pos = -1, prev_type = 0; for (i=0; irbuf); if ( args->mrows_op==MROWS_MERGE ) { if ( mrows_can_flush(args, args->lines[k]) ) { while ( (line=mrows_flush(args)) ) if ( bcf_write1(file, args->out_hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); } mrows_push(args, &args->lines[k]); continue; } else if ( args->rmdup ) { int line_type = bcf_get_variant_types(args->lines[k]); if ( prev_rid>=0 && prev_rid==args->lines[k]->rid && prev_pos==args->lines[k]->pos ) { if ( args->rmdup & BCF_SR_PAIR_ANY ) continue; // rmdup by position only if ( args->rmdup & BCF_SR_PAIR_SNPS && line_type&(VCF_SNP|VCF_MNP) && prev_type&(VCF_SNP|VCF_MNP) ) continue; if ( args->rmdup & BCF_SR_PAIR_INDELS && line_type&(VCF_INDEL) && prev_type&(VCF_INDEL) ) continue; if ( args->rmdup & BCF_SR_PAIR_EXACT && cmpals_match(args, &args->cmpals_out, args->lines[k]) ) continue; } else { prev_rid = args->lines[k]->rid; prev_pos = args->lines[k]->pos; prev_type = 0; if ( args->rmdup & BCF_SR_PAIR_EXACT ) cmpals_reset(&args->cmpals_out); } prev_type |= line_type; if ( args->rmdup & BCF_SR_PAIR_EXACT ) cmpals_add(args,&args->cmpals_out, args->lines[k]); } if ( bcf_write1(file, args->out_hdr, args->lines[k])!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); } if ( args->mrows_op==MROWS_MERGE && !args->rbuf.n ) { while ( (line=mrows_flush(args)) ) if ( bcf_write1(file, args->out_hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); } } static void init_data(args_t *args) { args->hdr = args->files->readers[0].header; if ( args->keep_sum_ad ) { args->keep_sum_ad = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"AD"); if ( args->keep_sum_ad < 0 ) error("Error: --keep-sum-ad requested but the tag AD is not present\n"); } else args->keep_sum_ad = -1; args->out_hdr = args->hdr; if ( args->old_rec_tag ) bcf_hdr_printf(args->out_hdr,"##INFO=",args->old_rec_tag); rbuf_init(&args->rbuf, 100); args->lines = (bcf1_t**) calloc(args->rbuf.m, sizeof(bcf1_t*)); if ( args->ref_fname ) { args->fai = fai_load(args->ref_fname); if ( !args->fai ) error("Failed to load the fai index: %s\n", args->ref_fname); } if ( args->mrows_op==MROWS_MERGE ) { args->mrow_out = bcf_init1(); args->tmp_str = (kstring_t*) calloc(bcf_hdr_nsamples(args->hdr),sizeof(kstring_t)); args->diploid = (uint8_t*) malloc(bcf_hdr_nsamples(args->hdr)); } if ( args->atomize==SPLIT ) { args->abuf = abuf_init(args->hdr, SPLIT); abuf_set_opt(args->abuf, bcf_hdr_t*, BCF_HDR, args->out_hdr); if ( args->old_rec_tag ) { abuf_set_opt(args->abuf, const char*, INFO_TAG, args->old_rec_tag); if ( bcf_hdr_sync(args->out_hdr)!=0 ) error("bcf_hdr_sync failed\n"); } abuf_set_opt(args->abuf, int, STAR_ALLELE, args->use_star_allele); } if ( args->gff_fname ) { args->gff = gff_init(args->gff_fname); gff_set(args->gff,verbosity,args->gff_verbosity); gff_set(args->gff,strip_chr_names,1); gff_parse(args->gff); args->idx_tscript = gff_get(args->gff,idx_tscript); args->itr_tscript = regitr_init(NULL); } if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); args->filter_pass = 1; args->out_hdr = bcf_hdr_dup(args->out_hdr); } static void destroy_data(args_t *args) { if ( args->filter ) filter_destroy(args->filter); if ( args->gff ) { gff_destroy(args->gff); regitr_destroy(args->itr_tscript); } cmpals_destroy(&args->cmpals_in); cmpals_destroy(&args->cmpals_out); int i; for (i=0; irbuf.m; i++) if ( args->lines[i] ) bcf_destroy1(args->lines[i]); free(args->lines); for (i=0; imtmp_lines; i++) if ( args->tmp_lines[i] ) bcf_destroy1(args->tmp_lines[i]); free(args->tmp_lines); for (i=0; immrows; i++) bcf_destroy1(args->mrows[i]); free(args->mrows); for (i=0; immaps; i++) free(args->maps[i].map); for (i=0; intmp_als; i++) free(args->tmp_als[i].s); for (i=0; intmp_sym; i++) free(args->tmp_sym[i].s); free(args->tmp_als); free(args->tmp_sym); free(args->tmp_kstr.s); if ( args->tmp_str ) { for (i=0; ihdr); i++) free(args->tmp_str[i].s); free(args->tmp_str); } free(args->maps); free(args->als); free(args->int32_arr); free(args->tmp_arr1); free(args->tmp_arr2); free(args->diploid); if ( args->abuf ) abuf_destroy(args->abuf); bcf_hdr_destroy(args->out_hdr); if ( args->mrow_out ) bcf_destroy1(args->mrow_out); if ( args->fai ) fai_destroy(args->fai); if ( args->mseq ) free(args->seq); } static void normalize_line(args_t *args, bcf1_t *line) { if ( args->fai ) { if ( args->filter_pass && (args->check_ref & CHECK_REF_FIX) ) fix_ref(args, line); if ( args->do_indels ) { int ret = args->filter_pass ? realign(args, line) : ERR_OK; // exclude broken VCF lines if ( ret==ERR_REF_MISMATCH && args->check_ref & CHECK_REF_SKIP ) { args->nskipped++; return; } if ( ret==ERR_DUP_ALLELE ) { if ( args->check_ref & CHECK_REF_FIX ) fix_dup_alt(args, line); else if ( args->check_ref==CHECK_REF_EXIT ) error("Duplicate alleles at %s:%"PRId64"; run with -cw to turn the error into warning or with -cs to fix.\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); else if ( args->check_ref & CHECK_REF_WARN ) fprintf(stderr,"ALT_DUP\t%s\t%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); } } } if ( args->filter_pass && args->atomize==SPLIT ) abuf_push(args->abuf,line); while (1) { if ( args->filter_pass && args->atomize==SPLIT ) { line = abuf_flush(args->abuf, 0); if ( !line ) break; } // insert into sorted buffer rbuf_expand0(&args->rbuf,bcf1_t*,args->rbuf.n+1,args->lines); int i,j; i = j = rbuf_append(&args->rbuf); if ( args->lines[i] ) bcf_destroy(args->lines[i]); args->lines[i] = bcf_dup(line); while ( rbuf_prev(&args->rbuf,&i) ) { if ( args->lines[i]->rid==args->lines[j]->rid ) { bcf_unpack(args->lines[i], BCF_UN_STR); bcf_unpack(args->lines[j], BCF_UN_STR); if ( args->cmp_func(&args->lines[i], &args->lines[j]) > 0) SWAP(bcf1_t*, args->lines[i], args->lines[j]); } j = i; } if ( !args->filter_pass || args->atomize!=SPLIT ) break; } } // return 0 on success, 1 when done static int split_and_normalize(args_t *args) { if ( !bcf_sr_next_line(args->files) ) return 1; bcf1_t *line = bcf_sr_get_line(args->files,0); args->ntotal++; if ( args->filter ) { args->filter_pass = filter_test(args->filter,line,NULL); if ( args->filter_logic==FLT_EXCLUDE ) args->filter_pass = args->filter_pass ? 0 : 1; if ( !args->filter_pass ) args->nfilter++; } if ( args->mrows_op!=MROWS_SPLIT || line->n_allele<=2 || !args->filter_pass ) { // normal operation, no splitting normalize_line(args, line); return 0; } // any restrictions on variant types to split? if ( args->mrows_collapse!=COLLAPSE_BOTH && args->mrows_collapse!=COLLAPSE_ANY ) { int type = args->mrows_collapse==COLLAPSE_SNPS ? VCF_SNP : VCF_INDEL; if ( !(bcf_get_variant_types(line) & type) ) { normalize_line(args, line); return 0; } } args->nsplit++; split_multiallelic_to_biallelics(args, line); int j; for (j=0; jntmp_lines; j++) normalize_line(args, args->tmp_lines[j]); return 0; } static void normalize_vcf(args_t *args) { char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); args->out = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( args->out == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno)); if ( args->n_threads ) hts_set_opt(args->out, HTS_OPT_THREAD_POOL, args->files->p); if (args->record_cmd_line) bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_norm"); if ( bcf_hdr_write(args->out, args->out_hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); if ( init_index2(args->out,args->out_hdr,args->output_fname, &args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->output_fname); while (1) { // buffer lines until a different position is reached int done = 0; while (1) { done = split_and_normalize(args); if ( done ) break; // no more lines available int i = args->rbuf.f; int j = rbuf_last(&args->rbuf); if ( args->lines[i]->rid != args->lines[j]->rid ) break; if ( args->lines[i]->pos != args->lines[j]->pos ) break; } if ( done ) break; // find out how many sites to flush int ifst = args->rbuf.f; int ilast = rbuf_last(&args->rbuf); int i, j = 0; for (i=-1; rbuf_next(&args->rbuf,&i); ) { if ( args->lines[ifst]->rid != args->lines[ilast]->rid ) { // there are two chromosomes in the buffer, count how many are on the first chromosome if ( args->lines[ifst]->rid != args->lines[i]->rid ) break; j++; continue; } // there is just one chromosome, flush only lines that are unlikely to change order on // realigning (the buf_win constant) if ( args->lines[ilast]->pos - args->lines[i]->pos < args->buf_win ) break; j++; } if ( j>0 ) flush_buffer(args, args->out, j); } flush_buffer(args, args->out, args->rbuf.n); if ( args->write_index ) { if ( bcf_idx_save(args->out)<0 ) { if ( hts_close(args->out)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(args->out)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname); fprintf(stderr,"Lines total/split/joined/realigned/removed/skipped:\t%d/%d/%d/%d/%d/%d\n", args->ntotal,args->nsplit,args->njoined,args->nchanged,args->nskipped,args->nfilter); if ( args->check_ref & CHECK_REF_FIX ) fprintf(stderr,"REF/ALT total/modified/added: \t%d/%d/%d\n", args->nref.tot,args->nref.swap,args->nref.set); } static void usage(void) { fprintf(stderr, "\n"); fprintf(stderr, "About: Left-align and normalize indels; check if REF alleles match the reference;\n"); fprintf(stderr, " split multiallelic sites into multiple rows; recover multiallelics from\n"); fprintf(stderr, " multiple rows.\n"); fprintf(stderr, "Usage: bcftools norm [options] \n"); fprintf(stderr, "\n"); fprintf(stderr, "Options:\n"); fprintf(stderr, " -a, --atomize Decompose complex variants (e.g. MNVs become consecutive SNVs)\n"); fprintf(stderr, " --atom-overlaps '*'|. Use the star allele (*) for overlapping alleles or set to missing (.) [*]\n"); fprintf(stderr, " -c, --check-ref e|w|x|s Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites [e]\n"); fprintf(stderr, " -D, --remove-duplicates Remove duplicate lines of the same type.\n"); fprintf(stderr, " -d, --rm-dup TYPE Remove duplicate snps|indels|both|all|exact\n"); fprintf(stderr, " -e, --exclude EXPR Do not normalize records for which the expression is true (see man page for details)\n"); fprintf(stderr, " -f, --fasta-ref FILE Reference sequence\n"); fprintf(stderr, " --force Try to proceed even if malformed tags are encountered. Experimental, use at your own risk\n"); fprintf(stderr, " -g, --gff-annot FILE Follow HGVS 3'rule and right-align variants in transcripts on the forward strand\n"); fprintf(stderr, " -i, --include EXPR Normalize only records for which the expression is true (see man page for details)\n"); fprintf(stderr, " --keep-sum TAG,.. Keep vector sum constant when splitting multiallelics (see github issue #360)\n"); fprintf(stderr, " -m, --multiallelics -|+TYPE Split multiallelics (-) or join biallelics (+), type: snps|indels|both|any [both]\n"); fprintf(stderr, " --multi-overlaps 0|. Fill in the reference (0) or missing (.) allele when splitting multiallelics [0]\n"); fprintf(stderr, " --no-version Do not append version and command line to the header\n"); fprintf(stderr, " -N, --do-not-normalize Do not normalize indels (with -m or -c s)\n"); fprintf(stderr, " --old-rec-tag STR Annotate modified records with INFO/STR indicating the original variant\n"); fprintf(stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " -s, --strict-filter When merging (-m+), merged site is PASS only if all sites being merged PASS\n"); fprintf(stderr, " -S, --sort METHOD Sort order: chr_pos,lex [chr_pos]\n"); fprintf(stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(stderr, " --threads INT Use multithreading with INT worker threads [0]\n"); fprintf(stderr, " -v, --verbose INT Verbosity level (0-2) of GFF parsing [1]\n"); fprintf(stderr, " -w, --site-win INT Buffer for sorting lines which changed position during realignment [1000]\n"); fprintf(stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(stderr, "\n"); fprintf(stderr, "Examples:\n"); fprintf(stderr, " # normalize and left-align indels\n"); fprintf(stderr, " bcftools norm -f ref.fa in.vcf\n"); fprintf(stderr, "\n"); fprintf(stderr, " # split multi-allelic sites\n"); fprintf(stderr, " bcftools norm -m- in.vcf\n"); fprintf(stderr, "\n"); exit(1); } int main_vcfnorm(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->files = bcf_sr_init(); args->output_fname = "-"; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->aln_win = 100; args->buf_win = 1000; args->mrows_collapse = COLLAPSE_BOTH; args->do_indels = 1; args->ma_use_ref_allele = 1; args->clevel = -1; int region_is_file = 0; int targets_is_file = 0; args->use_star_allele = 1; args->gff_verbosity = 1; int regions_overlap = 1; int targets_overlap = 0; args->cmp_func = cmp_bcf_pos; static struct option loptions[] = { {"help",no_argument,NULL,'h'}, {"force",no_argument,NULL,7}, {"atomize",no_argument,NULL,'a'}, {"atom-overlaps",required_argument,NULL,11}, {"include",required_argument,NULL,'i'}, {"exclude",required_argument,NULL,'e'}, {"old-rec-tag",required_argument,NULL,12}, {"keep-sum",required_argument,NULL,10}, {"fasta-ref",required_argument,NULL,'f'}, {"sort",required_argument,NULL,'S'}, {"gff-annot",required_argument,NULL,'g'}, {"right-align",no_argument,NULL,15}, // undocumented, only for debugging {"do-not-normalize",no_argument,NULL,'N'}, {"multiallelics",required_argument,NULL,'m'}, {"multi-overlaps",required_argument,NULL,13}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,1}, {"targets",required_argument,NULL,'t'}, {"targets-file",required_argument,NULL,'T'}, {"targets-overlap",required_argument,NULL,2}, {"site-win",required_argument,NULL,'w'}, {"remove-duplicates",no_argument,NULL,'D'}, {"rm-dup",required_argument,NULL,'d'}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"threads",required_argument,NULL,9}, {"check-ref",required_argument,NULL,'c'}, {"strict-filter",no_argument,NULL,'s'}, {"no-version",no_argument,NULL,8}, {"write-index",optional_argument,NULL,'W'}, {"verbose",required_argument,NULL,'v'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "hr:R:f:w:Dd:o:O:c:m:t:T:sNag:W::v:S:i:e:",loptions,NULL)) >= 0) { switch (c) { case 10: // possibly generalize this also to INFO/AD and other tags if ( strcasecmp("ad",optarg) ) error("Error: only --keep-sum AD is currently supported. See https://github.com/samtools/bcftools/issues/360 for more.\n"); args->keep_sum_ad = 1; // this will be set to the header id or -1 in init_data break; case 'g': args->gff_fname = optarg; break; case 'v': args->gff_verbosity = atoi(optarg); if ( args->gff_verbosity<0 || args->gff_verbosity>2 ) error("Error: expected integer 0-2 with -v, --verbose\n"); break; case 'a': args->atomize = SPLIT; break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'S': if ( !strcasecmp(optarg,"pos") ) args->cmp_func = cmp_bcf_pos; else if ( !strcasecmp(optarg,"lex") ) args->cmp_func = cmp_bcf_pos_ref_alt; else error("Error: the sort order --sort %s is not recognised\n",optarg); break; case 11 : if ( optarg[0]=='*' ) args->use_star_allele = 1; else if ( optarg[0]=='.' ) args->use_star_allele = 0; else error("Invalid argument to --atom-overlaps. Perhaps you wanted: \"--atom-overlaps '*'\"?\n"); break; case 12 : args->old_rec_tag = optarg; break; case 13 : if ( optarg[0]=='0' ) args->ma_use_ref_allele = 1; else if ( optarg[0]=='.' ) args->ma_use_ref_allele = 0; else error("Invalid argument to --multi-overlaps\n"); break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 15 : args->right_align = 1; break; case 'N': args->do_indels = 0; break; case 'd': if ( !strcmp("snps",optarg) ) args->rmdup = BCF_SR_PAIR_SNPS; else if ( !strcmp("indels",optarg) ) args->rmdup = BCF_SR_PAIR_INDELS; else if ( !strcmp("both",optarg) ) args->rmdup = BCF_SR_PAIR_BOTH; else if ( !strcmp("all",optarg) ) args->rmdup = BCF_SR_PAIR_ANY; else if ( !strcmp("any",optarg) ) args->rmdup = BCF_SR_PAIR_ANY; else if ( !strcmp("none",optarg) ) args->rmdup = BCF_SR_PAIR_EXACT; else if ( !strcmp("exact",optarg) ) args->rmdup = BCF_SR_PAIR_EXACT; else error("The argument to -d not recognised: %s\n", optarg); break; case 'm': if ( optarg[0]=='-' ) args->mrows_op = MROWS_SPLIT; else if ( optarg[0]=='+' ) args->mrows_op = MROWS_MERGE; else error("Expected '+' or '-' with -m\n"); if ( optarg[1]!=0 ) { if ( !strcmp("snps",optarg+1) ) args->mrows_collapse = COLLAPSE_SNPS; else if ( !strcmp("indels",optarg+1) ) args->mrows_collapse = COLLAPSE_INDELS; else if ( !strcmp("both",optarg+1) ) args->mrows_collapse = COLLAPSE_BOTH; else if ( !strcmp("any",optarg+1) ) args->mrows_collapse = COLLAPSE_ANY; else error("The argument to -m not recognised: %s\n", optarg); } break; case 'c': if ( strchr(optarg,'w') ) args->check_ref |= CHECK_REF_WARN; if ( strchr(optarg,'x') ) args->check_ref |= CHECK_REF_SKIP; if ( strchr(optarg,'s') ) args->check_ref |= CHECK_REF_FIX; if ( strchr(optarg,'e') ) args->check_ref = CHECK_REF_EXIT; // overrides the above break; case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'o': args->output_fname = optarg; break; case 'D': fprintf(stderr,"Warning: `-D` is functional but deprecated, replaced by and alias of `-d none`.\n"); args->rmdup = BCF_SR_PAIR_EXACT; break; case 's': args->strict_filter = 1; break; case 'f': args->ref_fname = optarg; break; case 'r': args->region = optarg; break; case 'R': args->region = optarg; region_is_file = 1; break; case 't': args->targets = optarg; break; case 'T': args->targets = optarg; targets_is_file = 1; break; case 'w': args->buf_win = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --site-win %s\n", optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 8 : args->record_cmd_line = 0; break; case 7 : args->force = 1; break; case 1 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 2 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 'h': case '?': usage(); break; default: error("Unknown argument: %s\n", optarg); } } char *fname = NULL; if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else usage(); } else fname = argv[optind]; if ( !args->ref_fname && !args->mrows_op && !args->rmdup && args->atomize==NONE ) error("Expected -a, -f, -m, -D or -d option\n"); if ( !args->check_ref && args->ref_fname ) args->check_ref = CHECK_REF_EXIT; if ( args->check_ref && !args->ref_fname ) error("Expected --fasta-ref with --check-ref\n"); if ( args->region ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->region,region_is_file)<0 ) error("Failed to read the regions: %s\n", args->region); } if ( args->targets ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets,targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets); } if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n"); if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); init_data(args); normalize_vcf(args); destroy_data(args); bcf_sr_destroy(args->files); free(args); return 0; } pysam-0.23.0/bcftools/vcfnorm.c.pysam.c000066400000000000000000003342701475062545500177550ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfnorm.c -- Left-align and normalize indels. Copyright (C) 2013-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "rbuf.h" #include "abuf.h" #include "gff.h" #include "regidx.h" #include "filter.h" #define CHECK_REF_EXIT 1 #define CHECK_REF_WARN 2 #define CHECK_REF_SKIP 4 #define CHECK_REF_FIX 8 #define MROWS_SPLIT 1 #define MROWS_MERGE 2 // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 // for -m+, mapping from allele indexes of a single input record // to allele indexes of output record typedef struct { int nals, mals, *map; } map_t; // primitive comparison of two records' alleles via hashes; normalized alleles assumed typedef struct { int n; // number of alleles char *ref, *alt; void *hash; // str2int hash } cmpals1_t; typedef struct { cmpals1_t *cmpals; int ncmpals, mcmpals; } cmpals_t; typedef struct { char *tseq, *seq; int mseq; bcf1_t **lines, **tmp_lines, **mrows, *mrow_out; int ntmp_lines, mtmp_lines, nmrows, mmrows, mrows_first; map_t *maps; // mrow map for each buffered record char **als; int mmaps, nals, mals; uint8_t *tmp_arr1, *tmp_arr2, *diploid; int32_t *int32_arr; int ntmp_arr1, ntmp_arr2, nint32_arr; kstring_t *tmp_str; kstring_t *tmp_als, *tmp_sym, tmp_kstr; int ntmp_als, ntmp_sym; rbuf_t rbuf; int buf_win; // maximum distance between two records to consider int aln_win; // the realignment window size (maximum repeat size) bcf_srs_t *files; // using the synced reader only for -r option bcf_hdr_t *hdr, *out_hdr; cmpals_t cmpals_in, cmpals_out; faidx_t *fai; struct { int tot, set, swap; } nref; char **argv, *output_fname, *ref_fname, *vcf_fname, *region, *targets; int argc, rmdup, output_type, n_threads, check_ref, strict_filter, do_indels, clevel; int nchanged, nskipped, nsplit, njoined, ntotal, nfilter, mrows_op, mrows_collapse, parsimonious; int record_cmd_line, force, force_warned, keep_sum_ad; abuf_t *abuf; abuf_opt_t atomize; int use_star_allele, ma_use_ref_allele; char *old_rec_tag; htsFile *out; char *index_fn; int write_index, gff_verbosity; int right_align; char *gff_fname; gff_t *gff; regidx_t *idx_tscript; regitr_t *itr_tscript; int (*cmp_func)(const void *aptr, const void *bptr); char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE int filter_pass; filter_t *filter; } args_t; static inline int replace_iupac_codes(char *seq, int nseq) { // Replace ambiguity codes with N for now, it awaits to be seen what the VCF spec codifies in the end int i, n = 0; for (i=0; id.allele[0]); int i,j, maxlen = reflen, len; for (i=1; in_allele; i++) { int len = strlen(line->d.allele[i]); if ( maxlen < len ) maxlen = len; } char *ref = faidx_fetch_seq(args->fai, (char*)bcf_seqname(args->hdr,line), line->pos, line->pos+maxlen-1, &len); if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); replace_iupac_codes(ref,len); args->nref.tot++; // is the REF different? If not, we are done if ( !strncasecmp(line->d.allele[0],ref,reflen) ) { free(ref); return; } // is the REF allele missing? if ( reflen==1 && line->d.allele[0][0]=='.' ) { line->d.allele[0][0] = ref[0]; args->nref.set++; free(ref); bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele); return; } // does REF or ALT contain non-standard bases? int has_non_acgtn = 0; for (i=0; in_allele; i++) { if ( line->d.allele[i][0]=='<' ) continue; has_non_acgtn += replace_iupac_codes(line->d.allele[i],strlen(line->d.allele[i])); } if ( has_non_acgtn ) { args->nref.set++; bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele); if ( !strncasecmp(line->d.allele[0],ref,reflen) ) { free(ref); return; } } // does the REF allele contain N's ? int fix = 0; for (i=0; id.allele[0][i]!='N' ) continue; if ( ref[i]=='N' ) continue; line->d.allele[0][i] = ref[i]; fix++; for (j=1; jn_allele; j++) { int len = strlen(line->d.allele[j]); if ( len <= i || line->d.allele[j][i]!='N' ) continue; line->d.allele[j][i] = ref[i]; fix++; } } if ( fix ) { args->nref.set++; bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele); if ( !strncasecmp(line->d.allele[0],ref,reflen) ) { free(ref); return; } } // is it swapped? for (i=1; in_allele; i++) { int len = strlen(line->d.allele[i]); if ( !strncasecmp(line->d.allele[i],ref,len) ) break; } kstring_t str = {0,0,0}; if ( i==line->n_allele ) // none of the alternate alleles matches the reference { args->nref.set++; kputsn(ref,reflen,&str); for (i=1; in_allele; i++) { kputc(',',&str); kputs(line->d.allele[i],&str); } bcf_update_alleles_str(args->out_hdr,line,str.s); free(ref); free(str.s); return; } // one of the alternate alleles matches the reference, assume it's a simple swap kputs(line->d.allele[i],&str); for (j=1; jn_allele; j++) { kputc(',',&str); if ( j==i ) kputs(line->d.allele[0],&str); else kputs(line->d.allele[j],&str); } bcf_update_alleles_str(args->out_hdr,line,str.s); args->nref.swap++; free(ref); free(str.s); // swap genotypes int ntmp = args->ntmp_arr1 / sizeof(int32_t); // reuse tmp_arr declared as uint8_t int ngts = bcf_get_genotypes(args->hdr, line, &args->tmp_arr1, &ntmp); args->ntmp_arr1 = ntmp * sizeof(int32_t); int32_t *gts = (int32_t*) args->tmp_arr1; int ni = 0; for (j=0; jout_hdr,line,gts,ngts); // update AC int nac = bcf_get_info_int32(args->hdr, line, "AC", &args->tmp_arr1, &ntmp); args->ntmp_arr1 = ntmp * sizeof(int32_t); if ( i <= nac ) { int32_t *ac = (int32_t*)args->tmp_arr1; ac[i-1] = ni; bcf_update_info_int32(args->out_hdr, line, "AC", ac, nac); } } static void fix_dup_alt(args_t *args, bcf1_t *line) { // update alleles, create a mapping between old and new indexes hts_expand(uint8_t,line->n_allele,args->ntmp_arr1,args->tmp_arr1); args->tmp_arr1[0] = 0; // ref always unchanged int i, j, nals = line->n_allele, nals_ori = line->n_allele; for (i=1, j=1; in_allele; i++) { if ( strcasecmp(line->d.allele[0],line->d.allele[i]) ) { args->tmp_arr1[i] = j++; continue; } args->tmp_arr1[i] = 0; nals--; } for (i=1, j=1; in_allele; i++) { if ( !args->tmp_arr1[i] ) continue; line->d.allele[j++] = line->d.allele[i]; } bcf_update_alleles(args->out_hdr, line, (const char**)line->d.allele, nals); // update genotypes int ntmp = args->ntmp_arr2 / sizeof(int32_t); // reuse tmp_arr declared as uint8_t int ngts = bcf_get_genotypes(args->hdr, line, &args->tmp_arr2, &ntmp); args->ntmp_arr2 = ntmp * sizeof(int32_t); int32_t *gts = (int32_t*) args->tmp_arr2; int changed = 0; for (i=0; itmp_arr1[ial] ) continue; int ial_new = ialtmp_arr1[ial] : 0; gts[i] = bcf_gt_is_phased(gts[i]) ? bcf_gt_phased(ial_new) : bcf_gt_unphased(ial_new); changed = 1; } if ( changed ) bcf_update_genotypes(args->out_hdr,line,gts,ngts); } static void set_old_rec_tag(args_t *args, bcf1_t *dst, bcf1_t *src, int ialt) { if ( !args->old_rec_tag ) return; // only update if the tag is not present already, there can be multiple normalization steps int i, id = bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, args->old_rec_tag); bcf_unpack(dst, BCF_UN_INFO); for (i=0; in_info; i++) { bcf_info_t *inf = &dst->d.info[i]; if ( inf && inf->key == id ) return; } args->tmp_kstr.l = 0; ksprintf(&args->tmp_kstr,"%s|%"PRIhts_pos"|%s|",bcf_seqname(args->hdr,src),src->pos+1,src->d.allele[0]); for (i=1; in_allele; i++) { kputs(src->d.allele[i],&args->tmp_kstr); if ( i+1n_allele ) kputc(',',&args->tmp_kstr); } if ( ialt>0 ) { kputc('|',&args->tmp_kstr); kputw(ialt,&args->tmp_kstr); } if ( (bcf_update_info_string(args->out_hdr, dst, args->old_rec_tag, args->tmp_kstr.s))!=0 ) error("An error occurred while updating INFO/%s\n",args->old_rec_tag); } static int is_left_align(args_t *args, bcf1_t *line) { if ( args->right_align ) return 0; if ( !args->gff ) return 1; const char *chr = bcf_seqname(args->hdr,line); if ( !strncasecmp("chr",chr,3) ) chr += 3; // strip 'chr' prefix, that's what we requested the GFF reader to do if ( !regidx_overlap(args->idx_tscript,chr,line->pos,line->pos+line->rlen, args->itr_tscript) ) return 1; // if there are two conflicting overlapping transcripts, go with the default left-alignment int has_fwd = 0; while ( regitr_overlap(args->itr_tscript) ) { gf_tscript_t *tr = regitr_payload(args->itr_tscript, gf_tscript_t*); if ( tr->strand==STRAND_FWD ) has_fwd = 1; if ( tr->strand==STRAND_REV ) return 1; } // either no hit at all (then left-align) or everything was on fwd strand (then right-align) return has_fwd ? 0 : 1; } static hts_pos_t realign_left(args_t *args, bcf1_t *line) { // trim from right char *ref = NULL; int i; hts_pos_t nref=0, new_pos = line->pos; kstring_t *als = args->tmp_als; while (1) { // is the rightmost base identical in all alleles? int min_len = als[0].l; for (i=1; in_allele; i++) { if ( toupper(als[0].s[ als[0].l-1 ]) != toupper(als[i].s[ als[i].l-1 ]) ) break; if ( als[i].l < min_len ) min_len = als[i].l; } if ( i!=line->n_allele ) break; // there are differences, cannot be trimmed if ( min_len<=1 && new_pos==0 ) break; int pad_from_left = 0; for (i=0; in_allele; i++) // trim all alleles { als[i].l--; if ( !als[i].l ) pad_from_left = 1; } if ( pad_from_left ) { // extend all alleles to the left by aln_win bases (unless close to the chr start). // Extra bases will be trimmed from the left after this loop is done int npad = new_pos >= args->aln_win ? args->aln_win : new_pos; free(ref); ref = faidx_fetch_seq64(args->fai, bcf_seqname(args->hdr,line), new_pos-npad, new_pos-1, &nref); if ( !ref ) error("faidx_fetch_seq64 failed at %s:%"PRId64"\n", bcf_seqname(args->hdr,line), (int64_t) new_pos-npad+1); replace_iupac_codes(ref,nref); for (i=0; in_allele; i++) { ks_resize(&als[i], als[i].l + npad); if ( als[i].l ) memmove(als[i].s+npad,als[i].s,als[i].l); memcpy(als[i].s,ref,npad); als[i].l += npad; } new_pos -= npad; } } free(ref); // trim from left int ntrim_left = 0; while (1) { // is the first base identical in all alleles? int min_len = als[0].l - ntrim_left; for (i=1; in_allele; i++) { if ( toupper(als[0].s[ntrim_left]) != toupper(als[i].s[ntrim_left]) ) break; if ( min_len > als[i].l - ntrim_left ) min_len = als[i].l - ntrim_left; } if ( i!=line->n_allele || min_len<=1 ) break; // there are differences, cannot be trimmed ntrim_left++; } if ( ntrim_left ) { for (i=0; in_allele; i++) { memmove(als[i].s,als[i].s+ntrim_left,als[i].l-ntrim_left); als[i].l -= ntrim_left; } new_pos += ntrim_left; } return new_pos; } static hts_pos_t realign_right(args_t *args, bcf1_t *line) { char *ref = NULL; int i; hts_pos_t new_pos = line->pos, nref = 0; kstring_t *als = args->tmp_als; // trim from left int ntrim_left = 0, npad_right = line->rlen, has_indel = 0; while (1) { // is the leftmost base identical in all alleles? int min_len = als[0].l - ntrim_left; for (i=1; in_allele; i++) { if ( als[0].l!=als[i].l ) has_indel = 1; if ( toupper(als[0].s[ntrim_left]) != toupper(als[i].s[ntrim_left]) ) break; if ( min_len > als[i].l - ntrim_left ) min_len = als[i].l - ntrim_left; } if ( i!=line->n_allele ) break; // there are differences, cannot be trimmed further ntrim_left++; if ( min_len<=1 ) // pad from the right { free(ref); ref = faidx_fetch_seq64(args->fai, bcf_seqname(args->hdr,line), line->pos + npad_right, line->pos + npad_right + args->aln_win, &nref); if ( !ref ) error("faidx_fetch_seq64 failed at %s:%"PRIhts_pos"\n",bcf_seqname(args->hdr,line), new_pos + ntrim_left); npad_right += args->aln_win; replace_iupac_codes(ref,nref); for (i=0; in_allele; i++) kputs(ref, &als[i]); } } ntrim_left -= has_indel; if ( ntrim_left > 0 ) { for (i=0; in_allele; i++) { memmove(als[i].s, als[i].s + ntrim_left, als[i].l - ntrim_left); als[i].l -= ntrim_left; } new_pos += ntrim_left; } free(ref); // trim from right while (1) { // is the last base identical in all alleles? int min_len = als[0].l; for (i=1; in_allele; i++) { if ( toupper(als[0].s[ als[0].l-1 ]) != toupper(als[i].s[ als[i].l-1 ]) ) break; if ( min_len > als[i].l ) min_len = als[i].l; } if ( i!=line->n_allele || min_len<=1 ) break; // there are differences, cannot be trimmed more for (i=0; in_allele; i++) { als[i].l--; als[i].s[als[i].l]=0; } } return new_pos; } #define ERR_DUP_ALLELE -2 #define ERR_REF_MISMATCH -1 #define ERR_OK 0 #define ERR_SYMBOLIC 1 #define ERR_SPANNING_DELETION 2 static int realign(args_t *args, bcf1_t *line) { bcf_unpack(line, BCF_UN_STR); // Sanity check REF int i, nref, reflen = strlen(line->d.allele[0]); char *ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos, line->pos+reflen-1, &nref); if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", args->hdr->id[BCF_DT_CTG][line->rid].key, (int64_t) line->pos+1); seq_to_upper(ref,0); replace_iupac_codes(ref,nref); // any non-ACGT character in fasta ref is replaced with N // does VCF REF contain non-standard bases? if ( has_non_acgtn(line->d.allele[0],reflen) ) { if ( args->check_ref==CHECK_REF_EXIT ) error("Non-ACGTN reference allele at %s:%"PRId64" .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,ref,line->d.allele[0]); if ( args->check_ref & CHECK_REF_WARN ) fprintf(bcftools_stderr,"NON_ACGTN_REF\t%s\t%"PRId64"\t%s\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,line->d.allele[0]); free(ref); return ERR_REF_MISMATCH; } if ( strcasecmp(ref,line->d.allele[0]) ) { if ( args->check_ref==CHECK_REF_EXIT ) error("Reference allele mismatch at %s:%"PRId64" .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,ref,line->d.allele[0]); if ( args->check_ref & CHECK_REF_WARN ) fprintf(bcftools_stderr,"REF_MISMATCH\t%s\t%"PRId64"\t%s\t%s\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,line->d.allele[0],ref); free(ref); return ERR_REF_MISMATCH; } free(ref); ref = NULL; if ( line->n_allele == 1 ) // a REF { if ( line->rlen > 1 ) { line->d.allele[0][1] = 0; bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele); } return ERR_OK; } if ( bcf_get_variant_types(line)==VCF_BND ) return ERR_SYMBOLIC; // breakend, not an error // make a copy of each allele for trimming hts_expand0(kstring_t,line->n_allele,args->ntmp_als,args->tmp_als); // the actual sequence to realign hts_expand0(kstring_t,line->n_allele,args->ntmp_sym,args->tmp_sym); // the original symbolic allele strings to output kstring_t *als = args->tmp_als; kstring_t *sym = args->tmp_sym; int symbolic_alts = 1; for (i=0; in_allele; i++) { sym[i].l = 0; if ( line->d.allele[i][0]=='<' ) { // symbolic allele, only and will be realigned // TODO: there should be check for symbolic allele length. If too big, perhaps should not attempt realignment int32_t sv_len = 0; if ( !strncmp("d.allele[i],4) ) sv_len = -line->rlen; else if ( !strncmp("d.allele[i],4) ) { if ( bcf_get_info_int32(args->hdr,line,"SVLEN",&args->int32_arr,&args->nint32_arr)==1 ) sv_len = args->int32_arr[0]; } if ( !sv_len ) return ERR_SYMBOLIC; als[i].l = 0; if ( sv_len<0 ) { // del, expand REF and replace ALT, for example, replace "REF=C ALT=" with "REF=CAT ALT=C" if ( nref < line->rlen ) { free(ref); reflen = line->rlen; ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos, line->pos+reflen-1, &nref); if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", args->hdr->id[BCF_DT_CTG][line->rid].key, (int64_t) line->pos+1); seq_to_upper(ref,0); replace_iupac_codes(ref,nref); // any non-ACGT character in fasta ref is replaced with N als[0].l = 0; kputs(ref, &als[0]); } kputsn(als[0].s,1,&als[i]); } else // sv_len>0 { // dup, replace "REF=C ALT=" with "REF=C ALT=CAT" free(ref); ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos, line->pos+sv_len, &nref); if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", args->hdr->id[BCF_DT_CTG][line->rid].key, (int64_t) line->pos+1); seq_to_upper(ref,0); replace_iupac_codes(ref,nref); // any non-ACGT character in fasta ref is replaced with N kputs(ref,&als[i]); } kputs(line->d.allele[i],&sym[i]); // preserve the symbolic allele string continue; } if ( i>0 ) symbolic_alts = 0; if ( line->d.allele[i][0]=='*' ) return ERR_SPANNING_DELETION; // spanning deletion if ( has_non_acgtn(line->d.allele[i],line->shared.l) ) { if ( args->check_ref==CHECK_REF_EXIT ) error("Non-ACGTN alternate allele at %s:%"PRId64" .. VCF:'%s'\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,line->d.allele[i]); if ( args->check_ref & CHECK_REF_WARN ) fprintf(bcftools_stderr,"NON_ACGTN_ALT\t%s\t%"PRId64"\t%s\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,line->d.allele[i]); return ERR_REF_MISMATCH; } als[i].l = 0; kputs(line->d.allele[i], &als[i]); seq_to_upper(als[i].s,0); if ( i>0 && als[i].l==als[0].l && !strcasecmp(als[0].s,als[i].s) ) return ERR_DUP_ALLELE; } free(ref); ref = NULL; // which direction are we aligning? int left_align = is_left_align(args, line); hts_pos_t new_pos; if ( left_align ) new_pos = realign_left(args, line); else new_pos = realign_right(args, line); // Have the alleles changed? Consider could have expanded the REF allele. In that // case it must be trimmed, however the new REF length must reflect the entire length. als[0].s[ als[0].l ] = 0; // for strcmp to work int new_reflen = strlen(als[0].s); if ( symbolic_alts ) { als[0].l = 1; als[0].s[ als[0].l ] = 0; } if ( new_pos==line->pos && !strcasecmp(line->d.allele[0],als[0].s) ) return ERR_OK; set_old_rec_tag(args, line, line, 0); // Create new block of alleles and update args->tmp_kstr.l = 0; for (i=0; in_allele; i++) { if (i>0) kputc(',',&args->tmp_kstr); if ( sym[i].l ) kputs(sym[i].s,&args->tmp_kstr); else kputsn(als[i].s,als[i].l,&args->tmp_kstr); } args->tmp_kstr.s[ args->tmp_kstr.l ] = 0; bcf_update_alleles_str(args->out_hdr,line,args->tmp_kstr.s); args->nchanged++; // Update INFO/END if necessary if ( (new_pos!=line->pos || reflen!=new_reflen) && bcf_get_info_int32(args->hdr, line, "END", &args->int32_arr, &args->nint32_arr)==1 ) { // bcf_update_alleles_str() messed up rlen because line->pos changed. This will be fixed by bcf_update_info_int32() line->pos = new_pos; args->int32_arr[0] = line->pos + new_reflen; bcf_update_info_int32(args->out_hdr, line, "END", args->int32_arr, 1); } line->pos = new_pos; return ERR_OK; } static void split_info_numeric(args_t *args, bcf1_t *src, bcf_info_t *info, int ialt, bcf1_t *dst) { #define BRANCH_NUMERIC(type,type_t,is_vector_end,is_missing) \ { \ const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key); \ int ntmp = args->ntmp_arr1 / sizeof(type_t); \ int ret = bcf_get_info_##type(args->hdr,src,tag,&args->tmp_arr1,&ntmp); \ args->ntmp_arr1 = ntmp * sizeof(type_t); \ assert( ret>0 ); \ type_t *vals = (type_t*) args->tmp_arr1; \ int len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key); \ if ( len==BCF_VL_A ) \ { \ if ( ret!=src->n_allele-1 ) \ { \ if ( args->force && !args->force_warned ) \ { \ fprintf(bcftools_stderr, \ "Warning: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n" \ " (This warning is printed only once.)\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele-1,ret); \ args->force_warned = 1; \ } \ if ( args->force ) \ { \ bcf_update_info_##type(args->out_hdr,dst,tag,NULL,0); \ return; \ } \ error("Error: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d. Use --force to proceed anyway.\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele-1,ret); \ } \ bcf_update_info_##type(args->out_hdr,dst,tag,vals+ialt,1); \ } \ else if ( len==BCF_VL_R ) \ { \ if ( ret!=src->n_allele ) \ { \ if ( args->force && !args->force_warned ) \ { \ fprintf(bcftools_stderr, \ "Warning: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n" \ " (This warning is printed only once.)\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele,ret); \ args->force_warned = 1; \ } \ if ( args->force ) \ { \ bcf_update_info_##type(args->out_hdr,dst,tag,NULL,0); \ return; \ } \ error("Error: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d. Use --force to proceed anyway.\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele,ret); \ } \ if ( args->keep_sum_ad >= 0 && args->keep_sum_ad==info->key ) \ { \ int j; \ for (j=1; jlen; j++) \ if ( j!=ialt+1 && !(is_missing) && !(is_vector_end) ) vals[0] += vals[j]; \ vals[1] = vals[ialt+1]; \ } \ else \ { \ if ( ialt!=0 ) vals[1] = vals[ialt+1]; \ } \ bcf_update_info_##type(args->out_hdr,dst,tag,vals,2); \ } \ else if ( len==BCF_VL_G ) \ { \ if ( ret!=src->n_allele*(src->n_allele+1)/2 ) \ { \ if ( args->force && !args->force_warned ) \ { \ fprintf(bcftools_stderr, \ "Warning: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n" \ " (This warning is printed only once.)\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*(src->n_allele+1)/2,ret); \ args->force_warned = 1; \ } \ if ( args->force ) \ { \ bcf_update_info_##type(args->out_hdr,dst,tag,NULL,0); \ return; \ } \ error("Error: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d. Use --force to proceed anyway.\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*(src->n_allele+1)/2,ret); \ } \ if ( ialt!=0 ) \ { \ vals[1] = vals[bcf_alleles2gt(0,ialt+1)]; \ vals[2] = vals[bcf_alleles2gt(ialt+1,ialt+1)]; \ } \ bcf_update_info_##type(args->out_hdr,dst,tag,vals,3); \ } \ else \ bcf_update_info_##type(args->out_hdr,dst,tag,vals,ret); \ } switch (bcf_hdr_id2type(args->hdr,BCF_HL_INFO,info->key)) { case BCF_HT_INT: BRANCH_NUMERIC(int32, int32_t, vals[j]==bcf_int32_vector_end, vals[j]==bcf_int32_missing); break; case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_is_vector_end(vals[j]), bcf_float_is_missing(vals[j])); break; } #undef BRANCH_NUMERIC } // Find nth field in a comma-separated list in src and move it to dst. // The dst and src memory areas may overlap, end points just after the last valid src // character. // On success returns pointer to the end of the parsed field and increments ndst by the // number of memmoved characters. Returns NULL if the field was not found. static inline char *string_move_nth(char *dst, char *src, char *end, int nth, size_t *ndst) { if ( src>=end ) return NULL; char *ss = src, *se = src; int j = 0; while ( *se && se<(end) ) { if ( *se==',' ) { if ( j==nth ) break; j++; ss = se+1; } se++; } if ( j!=nth ) return NULL; if ( ss>=end ) return NULL; if ( !*ss ) return NULL; int n = se - ss; memmove((dst),ss,n); *ndst += n; return se; } static void split_info_string(args_t *args, bcf1_t *src, bcf_info_t *info, int ialt, bcf1_t *dst) { const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key); int ret = bcf_get_info_string(args->hdr,src,tag,&args->tmp_arr1,&args->ntmp_arr1); assert( ret>0 ); kstring_t str; str.m = args->ntmp_arr1; str.l = ret; str.s = (char*) args->tmp_arr1; int len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key); if ( len==BCF_VL_A ) { char *end = str.s + str.l; char *tmp = str.s; str.l = 0; tmp = string_move_nth(str.s,tmp,end,ialt,&str.l); if ( !tmp ) str.l = 1, str.s[0] = '.'; kputc_(0,&str); bcf_update_info_string(args->out_hdr,dst,tag,str.s); } else if ( len==BCF_VL_R ) { char *end = str.s + str.l; char *tmp = str.s; str.l = 0; tmp = string_move_nth(str.s,tmp,end,0,&str.l); if ( tmp ) { kputc_(',',&str); tmp = string_move_nth(str.s+str.l,tmp+1,end,ialt,&str.l); // ialt is 0-based index to ALT } if ( !tmp ) str.l = 1, str.s[0] = '.'; kputc_(0,&str); bcf_update_info_string(args->out_hdr,dst,tag,str.s); } else if ( len==BCF_VL_G ) { int i0a = bcf_alleles2gt(0,ialt+1), iaa = bcf_alleles2gt(ialt+1,ialt+1); char *end = str.s + str.l; char *tmp = str.s; str.l = 0; tmp = string_move_nth(str.s,tmp,end,0,&str.l); if ( tmp ) { kputc_(',',&str); tmp = string_move_nth(str.s+str.l,tmp+1,end,i0a-1,&str.l); } if ( tmp ) { kputc_(',',&str); tmp = string_move_nth(str.s+str.l,tmp+1,end,iaa-i0a-1,&str.l); } if ( !tmp ) str.l = 1, str.s[0] = '.'; kputc_(0,&str); bcf_update_info_string(args->out_hdr,dst,tag,str.s); } else bcf_update_info_string(args->out_hdr,dst,tag,str.s); if ( args->ntmp_arr1 < str.m ) { args->ntmp_arr1 = str.m; args->tmp_arr1 = (uint8_t*)str.s; } } static void split_info_flag(args_t *args, bcf1_t *src, bcf_info_t *info, int ialt, bcf1_t *dst) { const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key); int ret = bcf_get_info_flag(args->hdr,src,tag,&args->tmp_arr1,&args->ntmp_arr1); bcf_update_info_flag(args->out_hdr,dst,tag,NULL,ret); } static void split_format_genotype(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int ialt, bcf1_t *dst) { int ntmp = args->ntmp_arr1 / 4; int ngts = bcf_get_genotypes(args->hdr,src,&args->tmp_arr1,&ntmp); args->ntmp_arr1 = ntmp * 4; assert( ngts >0 ); int32_t *gt = (int32_t*) args->tmp_arr1; int i, j, nsmpl = bcf_hdr_nsamples(args->hdr); ngts /= nsmpl; for (i=0; ima_use_ref_allele ) gt[j] = bcf_gt_unphased(0) | bcf_gt_is_phased(gt[j]); // set to REF else gt[j] = bcf_gt_missing | bcf_gt_is_phased(gt[j]); // set to missing } gt += ngts; } bcf_update_genotypes(args->out_hdr,dst,args->tmp_arr1,ngts*nsmpl); } static void split_format_numeric(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int ialt, bcf1_t *dst) { #define BRANCH_NUMERIC(type,type_t,is_vector_end,is_missing,set_vector_end,set_missing) \ { \ const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id); \ int ntmp = args->ntmp_arr1 / sizeof(type_t); \ int nvals = bcf_get_format_##type(args->hdr,src,tag,&args->tmp_arr1,&ntmp); \ args->ntmp_arr1 = ntmp * sizeof(type_t); \ assert( nvals>0 ); \ type_t *vals = (type_t *) args->tmp_arr1; \ int len = bcf_hdr_id2length(args->hdr,BCF_HL_FMT,fmt->id); \ int i,j, nsmpl = bcf_hdr_nsamples(args->hdr); \ if ( nvals==nsmpl ) /* all values are missing */ \ { \ bcf_update_format_##type(args->out_hdr,dst,tag,vals,nsmpl); \ return; \ } \ if ( len==BCF_VL_A ) \ { \ if ( nvals!=(src->n_allele-1)*nsmpl ) \ { \ if ( args->force && !args->force_warned ) \ { \ fprintf(bcftools_stderr, \ "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Removing the field.\n" \ " (This warning is printed only once.)\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \ args->force_warned = 1; \ } \ if ( args->force ) \ { \ bcf_update_format_##type(args->out_hdr,dst,tag,NULL,0); \ return; \ } \ error("Error: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Use --force to proceed anyway.\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \ } \ nvals /= nsmpl; \ type_t *src_vals = vals, *dst_vals = vals; \ for (i=0; iout_hdr,dst,tag,vals,nsmpl); \ } \ else if ( len==BCF_VL_R ) \ { \ if ( nvals!=src->n_allele*nsmpl ) \ { \ if ( args->force && !args->force_warned ) \ { \ fprintf(bcftools_stderr, \ "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Removing the field.\n" \ " (This warning is printed only once.)\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \ args->force_warned = 1; \ } \ if ( args->force ) \ { \ bcf_update_format_##type(args->out_hdr,dst,tag,NULL,0); \ return; \ } \ error("Error: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Use --force to proceed anyway.\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*nsmpl,nvals); \ } \ nvals /= nsmpl; \ type_t *src_vals = vals, *dst_vals = vals; \ if ( args->keep_sum_ad >= 0 && args->keep_sum_ad==fmt->id ) \ { \ for (i=0; iout_hdr,dst,tag,vals,nsmpl*2); \ } \ else if ( len==BCF_VL_G ) \ { \ if ( nvals!=src->n_allele*(src->n_allele+1)/2*nsmpl && nvals!=src->n_allele*nsmpl ) \ { \ if ( args->force && !args->force_warned ) \ { \ fprintf(bcftools_stderr, \ "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Removing the field.\n" \ " (This warning is printed only once.)\n", \ tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \ args->force_warned = 1; \ } \ if ( args->force ) \ { \ bcf_update_format_##type(args->out_hdr,dst,tag,NULL,0); \ return; \ } \ error("Error at %s:%"PRId64", the tag %s has wrong number of fields. Use --force to proceed anyway.\n", \ bcf_seqname(args->hdr,src),(int64_t) src->pos+1,bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id)); \ } \ nvals /= nsmpl; \ int all_haploid = nvals==src->n_allele ? 1 : 0; \ type_t *src_vals = vals, *dst_vals = vals; \ for (i=0; iout_hdr,dst,tag,vals,all_haploid ? nsmpl*2 : nsmpl*3); \ } \ else \ bcf_update_format_##type(args->out_hdr,dst,tag,vals,nvals); \ } switch (bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id)) { case BCF_HT_INT: BRANCH_NUMERIC(int32, int32_t, src_vals[isrc]==bcf_int32_vector_end, src_vals[isrc]==bcf_int32_missing, dst_vals[idst]=bcf_int32_vector_end, dst_vals[idst]=bcf_int32_missing); break; case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_is_vector_end(src_vals[isrc]), bcf_float_is_missing(src_vals[isrc]), bcf_float_set_vector_end(dst_vals[idst]), bcf_float_set_missing(src_vals[idst])); break; } #undef BRANCH_NUMERIC } static void squeeze_format_char(char *str, int src_blen, int dst_blen, int n) { int i, isrc = 0, idst = 0; for (i=0; ihdr,BCF_DT_ID,fmt->id); int ret = bcf_get_format_char(args->hdr,src,tag,&args->tmp_arr1,&args->ntmp_arr1); if ( !ret ) return; // all values can be empty, leave out the tag, no need to panic assert( ret>0 ); int nsmpl = bcf_hdr_nsamples(args->hdr); int blen = ret/nsmpl; // per-sample field length assert( blen>0 ); kstring_t str; str.m = args->ntmp_arr1; str.s = (char*) args->tmp_arr1; str.l = ret; int tag_len = bcf_hdr_id2length(args->hdr,BCF_HL_FMT,fmt->id); if ( tag_len==BCF_VL_A ) { int i, maxlen = 0; char *ptr = str.s; for (i=0; iout_hdr,dst,tag,str.s,nsmpl*maxlen); } else if ( tag_len==BCF_VL_R ) { int i, maxlen = 0; char *ptr = str.s; for (i=0; iout_hdr,dst,tag,str.s,nsmpl*maxlen); } else if ( tag_len==BCF_VL_G ) { int i, maxlen = 0, i0a = bcf_alleles2gt(0,ialt+1), iaa = bcf_alleles2gt(ialt+1,ialt+1); char *ptr = str.s; for (i=0; in_allele*(src->n_allele+1)/2 && nfields!=src->n_allele ) { if ( args->force && !args->force_warned ) { fprintf(bcftools_stderr, "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d or %d, found %d. Removing the field.\n" " (This warning is printed only once.)\n", tag,bcf_seqname(args->hdr,src),(int64_t)src->pos+1,src->n_allele*(src->n_allele+1)/2,src->n_allele,nfields); args->force_warned = 1; } if ( args->force ) { bcf_update_format_char(args->out_hdr,dst,tag,NULL,0); return; } error("Error: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d or %d, found %d. Use --force to proceed anyway.\n", tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*(src->n_allele+1)/2,src->n_allele,nfields); } char *tmp = ptr; char *end = ptr + blen; size_t len = 0; tmp = string_move_nth(ptr,tmp,end,0,&len); if ( nfields==src->n_allele ) // haploid { if ( tmp ) { ptr[len++] = ','; tmp = string_move_nth(ptr+len,tmp+1,end,ialt,&len); } } else // diploid { if ( tmp ) { ptr[len++] = ','; tmp = string_move_nth(ptr+len,tmp+1,end,i0a-1,&len); } if ( tmp ) { ptr[len++] = ','; tmp = string_move_nth(ptr+len,tmp+1,end,iaa-i0a-1,&len); } } if ( !tmp ) ptr[0] = '.', len = 1; if ( maxlen < len ) maxlen = len; while (lenout_hdr,dst,tag,str.s,nsmpl*maxlen); } else bcf_update_format_char(args->out_hdr,dst,tag,str.s,str.l); } static void split_multiallelic_to_biallelics(args_t *args, bcf1_t *line) { int i; bcf_unpack(line, BCF_UN_ALL); // Init the target biallelic lines args->ntmp_lines = line->n_allele-1; if ( args->mtmp_lines < args->ntmp_lines ) { args->tmp_lines = (bcf1_t **)realloc(args->tmp_lines,sizeof(bcf1_t*)*args->ntmp_lines); for (i=args->mtmp_lines; intmp_lines; i++) args->tmp_lines[i] = NULL; args->mtmp_lines = args->ntmp_lines; } kstring_t tmp = {0,0,0}; kputs(line->d.allele[0], &tmp); kputc(',', &tmp); int rlen = tmp.l; int gt_id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"GT"); for (i=0; intmp_lines; i++) // for each ALT allele { if ( !args->tmp_lines[i] ) args->tmp_lines[i] = bcf_init1(); bcf1_t *dst = args->tmp_lines[i]; bcf_clear(dst); dst->rid = line->rid; dst->pos = line->pos; dst->qual = line->qual; // Not quite sure how to handle IDs, they can be assigned to a specific // ALT. For now we leave the ID unchanged for all. bcf_update_id(args->out_hdr, dst, line->d.id ? line->d.id : "."); tmp.l = rlen; kputs(line->d.allele[i+1],&tmp); bcf_update_alleles_str(args->out_hdr,dst,tmp.s); if ( line->d.n_flt ) bcf_update_filter(args->hdr, dst, line->d.flt, line->d.n_flt); int j; for (j=0; jn_info; j++) { bcf_info_t *info = &line->d.info[j]; int type = bcf_hdr_id2type(args->hdr,BCF_HL_INFO,info->key); if ( type==BCF_HT_INT || type==BCF_HT_REAL ) split_info_numeric(args, line, info, i, dst); else if ( type==BCF_HT_FLAG ) split_info_flag(args, line, info, i, dst); else split_info_string(args, line, info, i, dst); } set_old_rec_tag(args, dst, line, i + 1); // 1-based indexes dst->n_sample = line->n_sample; for (j=0; jn_fmt; j++) { bcf_fmt_t *fmt = &line->d.fmt[j]; int type = bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id); if ( fmt->id==gt_id ) split_format_genotype(args, line, fmt, i, dst); else if ( type==BCF_HT_INT || type==BCF_HT_REAL ) split_format_numeric(args, line, fmt, i, dst); else split_format_string(args, line, fmt, i, dst); } } free(tmp.s); } // Enlarge FORMAT array containing nsmpl samples each with nals_ori values // to accommodate nvals values for each sample, filling the gaps with missing // values. Works also for INFO arrays, with nsmpl set to 1. #define ENLARGE_ARRAY(type_t,set_missing,arr,narr_bytes,nsmpl,nvals_ori,nvals) \ { \ int nbytes_new = (nsmpl)*(nvals)*sizeof(type_t); \ hts_expand(uint8_t,nbytes_new,narr_bytes,arr); \ int ismpl, k; \ for (ismpl=nsmpl-1; ismpl>=0; ismpl--) \ { \ type_t *dst_ptr = ((type_t*)arr) + ismpl*(nvals); \ type_t *src_ptr = ((type_t*)arr) + ismpl*nvals_ori; \ memmove(dst_ptr,src_ptr,sizeof(type_t)*nvals_ori); \ for (k=nvals_ori; khdr,BCF_DT_ID,info->key); \ int ntmp = args->ntmp_arr1 / sizeof(type_t); \ int nvals_ori = bcf_get_info_##type(args->hdr,lines[0],tag,&args->tmp_arr1,&ntmp); \ args->ntmp_arr1 = ntmp * sizeof(type_t); \ assert( nvals_ori>0 ); \ type_t *vals = (type_t*) args->tmp_arr1, *vals2; \ int i,k,len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key); \ if ( len==BCF_VL_A ) \ { \ if (nvals_ori!=lines[0]->n_allele - 1) \ error("vcfnorm: number of fields in first record at position %s:%"PRId64" for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),(int64_t) lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele-1); \ int nvals = dst->n_allele - 1; \ ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \ vals = (type_t*) args->tmp_arr1; \ for (i=1; intmp_arr2 / sizeof(type_t); \ int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \ if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \ args->ntmp_arr2 = ntmp2 * sizeof(type_t); \ if (nvals2!=lines[i]->n_allele-1) \ error("vcfnorm: could not merge INFO tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \ vals2 = (type_t*) args->tmp_arr2; \ for (k=0; kmaps[i].map[k+1] - 1 ] = vals2[k]; \ } \ } \ bcf_update_info_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals); \ } \ else if ( len==BCF_VL_R ) \ { \ if (nvals_ori!=lines[0]->n_allele) \ error("vcfnorm: number of fields in first record at position %s:%"PRId64" for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),(int64_t) lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele); \ int nvals = dst->n_allele; \ ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \ vals = (type_t*) args->tmp_arr1; \ for (i=1; intmp_arr2 / sizeof(type_t); \ int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \ if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \ args->ntmp_arr2 = ntmp2 * sizeof(type_t); \ if (nvals2!=lines[i]->n_allele) \ error("vcfnorm: could not merge INFO tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \ vals2 = (type_t*) args->tmp_arr2; \ for (k=0; kmaps[i].map[k] ] = vals2[k]; \ } \ } \ bcf_update_info_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals); \ } \ else if ( len==BCF_VL_G ) \ { \ /* expecting diploid gt in INFO */ \ if (nvals_ori!=lines[0]->n_allele*(lines[0]->n_allele+1)/2) { \ fprintf(bcftools_stderr, "todo: merge Number=G INFO fields for haploid sites\n"); \ error("vcfnorm: number of fields in first record at position %s:%"PRId64" for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),(int64_t) lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele*(lines[0]->n_allele+1)/2); \ } \ int nvals = dst->n_allele*(dst->n_allele+1)/2; \ ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \ vals = (type_t*) args->tmp_arr1; \ for (i=1; intmp_arr2 / sizeof(type_t); \ int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \ if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \ args->ntmp_arr2 = ntmp2 * sizeof(type_t); \ if (nvals2!=lines[i]->n_allele*(lines[i]->n_allele+1)/2) \ error("vcfnorm: could not merge INFO tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \ vals2 = (type_t*) args->tmp_arr2; \ int ia,ib; \ k = 0; \ for (ia=0; ian_allele; ia++) \ { \ for (ib=0; ib<=ia; ib++) \ { \ if ( is_vector_end ) break; \ int l = bcf_alleles2gt(args->maps[i].map[ia],args->maps[i].map[ib]); \ vals[l] = vals2[k]; \ k++; \ } \ } \ } \ bcf_update_info_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals); \ } \ else \ bcf_update_info_##type(args->out_hdr,dst,tag,vals,nvals_ori); \ } switch (bcf_hdr_id2type(args->hdr,BCF_HL_INFO,info->key)) { case BCF_HT_INT: BRANCH_NUMERIC(int32, int32_t, dst_ptr[k]=bcf_int32_missing, vals2[k]==bcf_int32_vector_end); break; case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_set_missing(dst_ptr[k]), bcf_float_is_vector_end(vals2[k])); break; } #undef BRANCH_NUMERIC } static void merge_info_flag(args_t *args, bcf1_t **lines, int nlines, bcf_info_t *info, bcf1_t *dst) { const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key); int ret = bcf_get_info_flag(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1); bcf_update_info_flag(args->out_hdr,dst,tag,NULL,ret); } int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst); // see vcfmerge.c static void merge_info_string(args_t *args, bcf1_t **lines, int nlines, bcf_info_t *info, bcf1_t *dst) { const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key); kstring_t str; str.m = args->ntmp_arr1; str.l = 0; str.s = (char*) args->tmp_arr1; int i, j, len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key); if ( len==BCF_VL_A || len==BCF_VL_R ) { int jfrom = len==BCF_VL_A ? 1 : 0; kputc('.',&str); for (i=jfrom+1; in_allele; i++) kputs(",.",&str); for (i=0; ihdr,lines[i],tag); if (!src) continue; for (j=jfrom; jn_allele; j++) copy_string_field((char*)src->vptr, j-jfrom, src->len, &str, args->maps[i].map[j]-jfrom); } str.s[str.l] = 0; args->tmp_arr1 = (uint8_t*) str.s; args->ntmp_arr1 = str.m; bcf_update_info_string(args->out_hdr,dst,tag,str.s); } else if ( len==BCF_VL_G ) { int ngts = dst->n_allele*(dst->n_allele+1)/2; kputc('.',&str); for (i=1; ihdr,lines[i],tag); if (!src) continue; int iori, jori, kori = 0; for (iori=0; iorin_allele; iori++) { int inew = args->maps[i].map[iori]; for (jori=0; jori<=iori; jori++) { int jnew = args->maps[i].map[jori]; int knew = bcf_alleles2gt(inew,jnew); copy_string_field((char*)src->vptr,kori,src->len,&str,knew); kori++; } } } str.s[str.l] = 0; args->tmp_arr1 = (uint8_t*) str.s; args->ntmp_arr1 = str.m; bcf_update_info_string(args->out_hdr,dst,tag,str.s); } else { bcf_get_info_string(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1); bcf_update_info_string(args->out_hdr,dst,tag,args->tmp_arr1); } } static int gt_array_grow_ploidy(args_t *args, uint8_t **tmp_arr, int *ntmp_arr, int ngt_ori, int ngt_new, int nsmpl) { *ntmp_arr = 4*ngt_new*nsmpl; int32_t *ptr = (int32_t*)realloc(*tmp_arr,*ntmp_arr); if ( !ptr ) error("Error: failed to allocate %d bytes\n",*ntmp_arr); *tmp_arr = (uint8_t*) ptr; int i,j; for (i=nsmpl-1; i>=0; i--) { int32_t *src = ptr + i*ngt_ori; int32_t *dst = ptr + i*ngt_new; for (j=ngt_new; j>ngt_ori; j--) dst[j-1] = bcf_int32_vector_end; for (j=ngt_ori; j>0; j--) dst[j-1] = src[j-1]; } return ngt_new; } static void merge_format_genotype(args_t *args, bcf1_t **lines, int nlines, bcf_fmt_t *fmt, bcf1_t *dst) { // reusing int8_t arrays as int32_t arrays int ntmp = args->ntmp_arr1 / 4; int ngts = bcf_get_genotypes(args->hdr,lines[0],&args->tmp_arr1,&ntmp); args->ntmp_arr1 = ntmp * 4; assert( ngts >0 ); int nsmpl = bcf_hdr_nsamples(args->hdr); ngts /= nsmpl; int i, j, k,k2; for (i=1; intmp_arr2 / 4; int ngts2 = bcf_get_genotypes(args->hdr,lines[i],&args->tmp_arr2,&ntmp2); args->ntmp_arr2 = ntmp2 * 4; ngts2 /= nsmpl; int ploidy_changed = ngts - ngts2; if ( ngts < ngts2 ) ngts = gt_array_grow_ploidy(args,&args->tmp_arr1,&args->ntmp_arr1,ngts,ngts2,nsmpl); if ( ngts > ngts2 ) ngts2 = gt_array_grow_ploidy(args,&args->tmp_arr2,&args->ntmp_arr2,ngts2,ngts,nsmpl); int32_t *gt = (int32_t*) args->tmp_arr1; // the first, destination line int32_t *gt2 = (int32_t*) args->tmp_arr2; // one of the subsequent lines, i.e. the source line for (j=0; j=args->maps[i].nals ) error("Error at %s:%"PRId64": incorrect allele index %d\n",bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1,ial2); // The destination allele int ial = args->maps[i].map[ial2]; if ( gt[k2]==bcf_int32_vector_end || bcf_gt_is_missing(gt[k2]) || !bcf_gt_allele(gt[k2]) ) gt[k2] = (gt[k2]!=bcf_int32_vector_end && bcf_gt_is_phased(gt[k2])) ? bcf_gt_phased(ial) : bcf_gt_unphased(ial); else { // conflict, the first line has non-zero allele, use the old way, possibly disrupt the phasing for (k=0; kout_hdr,dst,args->tmp_arr1,ngts*nsmpl); } static int diploid_to_haploid(int size, int nsmpl, int nals, uint8_t *vals) { int i, dsrc = size*nals*(nals+1)/2, ddst = size*nals; uint8_t *src_ptr = vals + dsrc, *dst_ptr = vals + ddst; for (i=1; ihdr,BCF_DT_ID,fmt->id); \ int ntmp = args->ntmp_arr1 / sizeof(type_t); \ int nvals_ori = bcf_get_format_##type(args->hdr,lines[0],tag,&args->tmp_arr1,&ntmp); \ args->ntmp_arr1 = ntmp * sizeof(type_t); \ assert( nvals_ori>0 ); \ type_t *vals2, *vals = (type_t *) args->tmp_arr1; \ int len = bcf_hdr_id2length(args->hdr,BCF_HL_FMT,fmt->id); \ int i, j, k, nsmpl = bcf_hdr_nsamples(args->hdr); \ nvals_ori /= nsmpl; \ if ( len==BCF_VL_A ) \ { \ int nvals = dst->n_allele - 1; \ ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,nsmpl,nvals_ori,nvals); \ for (i=1; intmp_arr2 / sizeof(type_t); \ int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \ if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \ args->ntmp_arr2 = ntmp2 * sizeof(type_t); \ nvals2 /= nsmpl; \ if (nvals2!=lines[i]->n_allele-1) \ error("vcfnorm: could not merge FORMAT tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \ vals = (type_t*) args->tmp_arr1; \ vals2 = (type_t*) args->tmp_arr2; \ for (j=0; jmaps[i].map[k+1] - 1 ] = vals2[k]; \ } \ vals += nvals; \ vals2 += nvals2; \ } \ } \ bcf_update_format_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals*nsmpl); \ } \ else if ( len==BCF_VL_R ) \ { \ int nvals = dst->n_allele; \ ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,nsmpl,nvals_ori,nvals); \ for (i=1; intmp_arr2 / sizeof(type_t); \ int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \ if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \ args->ntmp_arr2 = ntmp2 * sizeof(type_t); \ nvals2 /= nsmpl; \ if (nvals2!=lines[i]->n_allele) \ error("vcfnorm: could not merge FORMAT tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \ vals = (type_t*) args->tmp_arr1; \ vals2 = (type_t*) args->tmp_arr2; \ for (j=0; jmaps[i].map[k] ] = vals2[k]; \ } \ vals += nvals; \ vals2 += nvals2; \ } \ } \ bcf_update_format_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals*nsmpl); \ } \ else if ( len==BCF_VL_G ) \ { \ /* which samples are diploid */ \ memset(args->diploid,0,nsmpl); \ int all_haploid = 1; \ if ( nvals_ori > lines[0]->n_allele ) /* line possibly diploid */ \ { \ vals2 = (type_t*) args->tmp_arr1; \ int ndiploid = lines[0]->n_allele*(lines[0]->n_allele+1)/2; \ for (i=0; idiploid[i] ) \ { \ for (k=0; kdiploid[i] = 1; all_haploid = 0; }\ } \ vals2 += nvals_ori; \ } \ } \ int nvals = dst->n_allele*(dst->n_allele+1)/2; \ ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,nsmpl,nvals_ori,nvals); \ for (i=1; intmp_arr2 / sizeof(type_t); \ int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \ if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \ args->ntmp_arr2 = ntmp2 * sizeof(type_t); \ nvals2 /= nsmpl; \ int ndiploid = lines[i]->n_allele*(lines[i]->n_allele+1)/2; \ int line_diploid = nvals2==ndiploid ? 1 : 0; \ if (!(nvals2==1 || nvals2==lines[i]->n_allele || nvals2==lines[i]->n_allele*(lines[i]->n_allele+1)/2)) \ error("vcfnorm: could not merge FORMAT tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \ vals = (type_t*) args->tmp_arr1; \ vals2 = (type_t*) args->tmp_arr2; \ for (j=0; jdiploid[j] ) { args->diploid[j] = 1; all_haploid = 0; } \ if ( !smpl_diploid ) \ { \ for (k=0; kn_allele; k++) vals[args->maps[i].map[k]] = vals2[k]; \ } \ else \ { \ k = 0; \ int ia,ib; \ for (ia=0; ian_allele; ia++) \ { \ for (ib=0; ib<=ia; ib++) \ { \ int l = bcf_alleles2gt(args->maps[i].map[ia],args->maps[i].map[ib]); \ vals[l] = vals2[k]; \ k++; \ } \ } \ } \ vals += nvals; \ vals2 += nvals2; \ } \ } \ if ( all_haploid ) \ nvals = diploid_to_haploid(sizeof(type_t),nsmpl,dst->n_allele,args->tmp_arr1); \ else \ {\ k = dst->n_allele;\ vals2 = (type_t*) args->tmp_arr1;\ for (i=0; idiploid[i] ) set_vector_end;\ vals2 += nvals;\ }\ }\ bcf_update_format_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals*nsmpl); \ } \ else \ bcf_update_format_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals_ori*nsmpl); \ } switch (bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id)) { case BCF_HT_INT: BRANCH_NUMERIC(int32, int32_t, dst_ptr[k]=bcf_int32_missing, vals2[k]==bcf_int32_vector_end, vals2[k]=bcf_int32_vector_end); break; case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_set_missing(dst_ptr[k]), bcf_float_is_vector_end(vals2[k]), bcf_float_set_vector_end(vals2[k])); break; } #undef BRANCH_NUMERIC } static void merge_format_string(args_t *args, bcf1_t **lines, int nlines, bcf_fmt_t *fmt, bcf1_t *dst) { const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id); int i, j, k, len = bcf_hdr_id2length(args->hdr,BCF_HL_FMT,fmt->id); if ( len!=BCF_VL_A && len!=BCF_VL_R && len!=BCF_VL_G ) { int nret = bcf_get_format_char(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1); bcf_update_format_char(args->out_hdr,dst,tag,args->tmp_arr1,nret); return; } int nsmpl = bcf_hdr_nsamples(args->hdr); for (i=0; itmp_str[i].l = 0; if ( len==BCF_VL_A || len==BCF_VL_R ) { int jfrom = len==BCF_VL_A ? 1 : 0; for (i=0; itmp_str[i]; kputc('.',tmp); for (k=jfrom+1; kn_allele; k++) kputs(",.",tmp); } for (i=0; ihdr,lines[i],tag,&args->tmp_arr1,&args->ntmp_arr1); if (nret<0) continue; /* format tag does not exist in this record, skip */ nret /= nsmpl; for (k=0; ktmp_str[k]; char *src = (char*)args->tmp_arr1 + k*nret; for (j=jfrom; jn_allele; j++) copy_string_field(src, j-jfrom, nret, tmp, args->maps[i].map[j]-jfrom); } } } else if ( len==BCF_VL_G ) { hts_expand(uint8_t,nsmpl,args->ntmp_arr2,args->tmp_arr2); uint8_t *haploid = args->tmp_arr2; int nret = bcf_get_format_char(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1); nret /= nsmpl; for (i=0; itmp_arr1 + i*nret, *se = ss+nret; int nfields = 1; while ( *ss && ssn_allele ) { haploid[i] = 1; nfields = dst->n_allele; } else if ( nfields==lines[0]->n_allele*(lines[0]->n_allele+1)/2 ) { haploid[i] = 0; nfields = dst->n_allele*(dst->n_allele+1)/2; } else error("The field %s at %s:%"PRId64" neither diploid nor haploid?\n", tag,bcf_seqname(args->hdr,dst),(int64_t) dst->pos+1); kstring_t *tmp = &args->tmp_str[i]; kputc('.',tmp); for (j=1; jhdr,lines[i],tag,&args->tmp_arr1,&args->ntmp_arr1); if (nret<0) continue; /* format tag does not exist in this record, skip */ nret /= nsmpl; } for (k=0; ktmp_str[k]; char *src = (char*)args->tmp_arr1 + k*nret; if ( haploid[k] ) { for (j=0; jn_allele; j++) copy_string_field(src,j,nret, tmp, args->maps[i].map[j]); } else { int iori, jori, kori = 0; for (iori=0; iorin_allele; iori++) { int inew = args->maps[i].map[iori]; for (jori=0; jori<=iori; jori++) { int jnew = args->maps[i].map[jori]; int knew = bcf_alleles2gt(inew,jnew); copy_string_field(src,kori,nret,tmp,knew); kori++; } } } } } } kstring_t str; str.m = args->ntmp_arr2; str.l = 0; str.s = (char*) args->tmp_arr2; int max_len = 0; for (i=0; itmp_str[i].l ) max_len = args->tmp_str[i].l; for (i=0; itmp_str[i]; kputsn(tmp->s,tmp->l,&str); for (j=tmp->l; jntmp_arr2 = str.m; args->tmp_arr2 = (uint8_t*)str.s; bcf_update_format_char(args->out_hdr,dst,tag,str.s,str.l); } char **merge_alleles(char **a, int na, int *map, char **b, int *nb, int *mb); // see vcfmerge.c static void merge_biallelics_to_multiallelic(args_t *args, bcf1_t *dst, bcf1_t **lines, int nlines) { int i; for (i=0; irid = lines[0]->rid; dst->pos = lines[0]->pos; // take max for QUAL bcf_float_set_missing(dst->qual); for (i=0; iqual)) continue; if (bcf_float_is_missing(dst->qual) || dst->qualqual) dst->qual = lines[i]->qual; } bcf_update_id(args->out_hdr, dst, lines[0]->d.id); // Merge and set the alleles, create a mapping from source allele indexes to dst idxs hts_expand0(map_t,nlines,args->mmaps,args->maps); // a mapping for each line args->nals = args->maps[0].nals = lines[0]->n_allele; hts_expand(int,args->maps[0].nals,args->maps[0].mals,args->maps[0].map); hts_expand(char*,args->nals,args->mals,args->als); for (i=0; imaps[0].nals; i++) { args->maps[0].map[i] = i; args->als[i] = strdup(lines[0]->d.allele[i]); } for (i=1; id.id[0]!='.' || lines[i]->d.id[1]) bcf_add_id(args->out_hdr, dst, lines[i]->d.id); args->maps[i].nals = lines[i]->n_allele; hts_expand(int,args->maps[i].nals,args->maps[i].mals,args->maps[i].map); args->als = merge_alleles(lines[i]->d.allele, lines[i]->n_allele, args->maps[i].map, args->als, &args->nals, &args->mals); if ( !args->als ) error("Failed to merge alleles at %s:%"PRId64"\n", bcf_seqname(args->hdr,dst),(int64_t) dst->pos+1); } bcf_update_alleles(args->out_hdr, dst, (const char**)args->als, args->nals); for (i=0; inals; i++) { free(args->als[i]); args->als[i] = NULL; } if ( lines[0]->d.n_flt ) bcf_update_filter(args->out_hdr, dst, lines[0]->d.flt, lines[0]->d.n_flt); for (i=1; id.n_flt; j++) { // if strict_filter, set FILTER to PASS if any site PASS // otherwise accumulate FILTERs if (lines[i]->d.flt[j] == bcf_hdr_id2int(args->hdr, BCF_DT_ID, "PASS")) { if (args->strict_filter) { bcf_update_filter(args->out_hdr, dst, lines[i]->d.flt, lines[i]->d.n_flt); break; } else continue; } bcf_add_filter(args->out_hdr, dst, lines[i]->d.flt[j]); } } // merge info for (i=0; in_info; i++) { bcf_info_t *info = &lines[0]->d.info[i]; int type = bcf_hdr_id2type(args->hdr,BCF_HL_INFO,info->key); if ( type==BCF_HT_INT || type==BCF_HT_REAL ) merge_info_numeric(args, lines, nlines, info, dst); else if ( type==BCF_HT_FLAG ) merge_info_flag(args, lines, nlines, info, dst); else merge_info_string(args, lines, nlines, info, dst); } // merge format int gt_id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"GT"); dst->n_sample = lines[0]->n_sample; for (i=0; in_fmt; i++) { bcf_fmt_t *fmt = &lines[0]->d.fmt[i]; int type = bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id); if ( fmt->id==gt_id ) merge_format_genotype(args, lines, nlines, fmt, dst); else if ( type==BCF_HT_INT || type==BCF_HT_REAL ) merge_format_numeric(args, lines, nlines, fmt, dst); else merge_format_string(args, lines, nlines, fmt, dst); } args->njoined++; } #define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; } static void mrows_push(args_t *args, bcf1_t **line) { int i,m; if ( !args->nmrows ) args->mrows_first = 0; args->nmrows++; m = args->mmrows; hts_expand(bcf1_t*,args->nmrows,args->mmrows,args->mrows); for (i=m; immrows; i++) args->mrows[i] = bcf_init1(); SWAP(bcf1_t*, args->mrows[args->nmrows-1], *line); if ( args->mrows_collapse==COLLAPSE_ANY ) return; // move the line up the sorted list so that the same variant types end up together int cur_type = bcf_get_variant_types(args->mrows[args->nmrows-1]); i = args->mrows_first + args->nmrows - 1; while (i>0) { int prev_type = bcf_get_variant_types(args->mrows[i-1]); if ( prev_type <= cur_type ) break; bcf1_t *tmp = args->mrows[i-1]; args->mrows[i-1] = args->mrows[i]; args->mrows[i] = tmp; i--; } } static int mrows_can_flush(args_t *args, bcf1_t *line) { if ( !args->nmrows ) return 0; int ibeg = args->mrows_first; if ( args->mrows[ibeg]->rid != line->rid ) return 1; if ( args->mrows[ibeg]->pos != line->pos ) return 1; return 0; } static bcf1_t *mrows_flush(args_t *args) { if ( !args->nmrows ) return NULL; int ibeg = args->mrows_first; //fprintf(bcftools_stderr,"flush: ibeg=%d n=%d\n",ibeg,args->nmrows); //int i; //for (i=ibeg; inmrows; i++) // fprintf(bcftools_stderr,"\ti=%d type=%d %s %s\n",i,bcf_get_variant_types(args->mrows[i]),args->mrows[i]->d.allele[0],args->mrows[i]->d.allele[1]); if ( args->nmrows==1 ) { args->nmrows = 0; return args->mrows[ibeg]; } if ( args->mrows_collapse==COLLAPSE_ANY ) { // merge everything with anything bcf_clear(args->mrow_out); merge_biallelics_to_multiallelic(args, args->mrow_out, &args->mrows[ibeg], args->nmrows - ibeg); args->nmrows = 0; return args->mrow_out; } int j; int types[] = { VCF_SNP, VCF_MNP, VCF_INDEL, VCF_OTHER, -1 }; // merge everything within the same category if ( args->mrows_collapse==COLLAPSE_SNPS ) types[1] = -1; // merge SNPs only else if ( args->mrows_collapse==COLLAPSE_INDELS ) types[0] = VCF_INDEL, types[1] = -1; // merge indels only for (j=0; types[j]!=-1; j++) { int i, type = types[j]; // to keep the compiler happy for (i=ibeg; inmrows; i++) { type = bcf_get_variant_types(args->mrows[i]); if ( type!=types[j] && type!=VCF_REF ) break; } if ( i==ibeg+1 && type!=VCF_REF ) { // just one line of this type, no merging, but multiple lines of different type follow args->nmrows--; args->mrows_first++; return args->mrows[ibeg]; } if ( i>ibeg ) { // more than one line, merging is needed int nflush = i - ibeg; bcf_clear(args->mrow_out); merge_biallelics_to_multiallelic(args, args->mrow_out, &args->mrows[ibeg], nflush); args->nmrows -= nflush; args->mrows_first += nflush; return args->mrow_out; } } args->nmrows--; args->mrows_first++; return args->mrows[ibeg]; } static char *strdup_alt_svlen(args_t *args, bcf1_t *rec, int ial) { if ( rec->d.allele[ial][0]!='<' ) return strdup(rec->d.allele[ial]); int ntmp = args->ntmp_arr1 / sizeof(int32_t); int n = bcf_get_info_int32(args->hdr, rec, "SVLEN", &args->tmp_arr1, &ntmp); args->ntmp_arr1 = ntmp * sizeof(int32_t); int32_t *svlen = (int32_t *) args->tmp_arr1; if ( n<=0 ) return strdup(rec->d.allele[ial]); if ( n+1 != rec->n_allele ) { // there should be as many SVLEN numbers as there are ALT alleles static int warned = 0; if ( !warned ) { fprintf(bcftools_stderr,"TODO: different number of ALT alleles and SVLEN fields %s:%"PRIhts_pos"\n",bcf_seqname(args->hdr,rec),rec->pos+1); warned = 1; } } kstring_t str = {0,0,0}; ksprintf(&str,"%s.%d",rec->d.allele[ial],svlen[ial-1]); return str.s; } static void cmpals_add(args_t *args, cmpals_t *ca, bcf1_t *rec) { ca->ncmpals++; hts_expand0(cmpals1_t, ca->ncmpals, ca->mcmpals, ca->cmpals); cmpals1_t *cmpals = ca->cmpals + ca->ncmpals - 1; free(cmpals->ref); cmpals->ref = strdup(rec->d.allele[0]); cmpals->n = rec->n_allele; if ( rec->n_allele==2 ) { free(cmpals->alt); cmpals->alt = strdup_alt_svlen(args,rec,1); } else { if ( cmpals->hash ) khash_str2int_destroy_free(cmpals->hash); cmpals->hash = khash_str2int_init(); int i; for (i=1; in_allele; i++) khash_str2int_inc(cmpals->hash, strdup(rec->d.allele[i])); } } static int cmpals_match(args_t *args, cmpals_t *ca, bcf1_t *rec) { int i, j; char *alt_svlen = rec->n_allele==2 ? strdup_alt_svlen(args,rec,1) : NULL; for (i=0; incmpals; i++) { cmpals1_t *cmpals = ca->cmpals + i; if ( rec->n_allele != cmpals->n ) continue; // NB. assuming both are normalized if ( strcasecmp(rec->d.allele[0], cmpals->ref) ) continue; // the most frequent case if ( rec->n_allele==2 ) { if ( strcasecmp(alt_svlen, cmpals->alt) ) continue; free(alt_svlen); return 1; } khash_t(str2int) *hash = (khash_t(str2int)*) cmpals->hash; for (j=1; jn_allele; j++) if ( !khash_str2int_has_key(hash, rec->d.allele[j]) ) break; if ( jn_allele ) continue; return 1; } free(alt_svlen); return 0; } static void cmpals_reset(cmpals_t *ca) { ca->ncmpals = 0; } static void cmpals_destroy(cmpals_t *ca) { int i; for (i=0; imcmpals; i++) { cmpals1_t *cmpals = ca->cmpals + i; free(cmpals->ref); free(cmpals->alt); if ( cmpals->hash ) khash_str2int_destroy_free(cmpals->hash); } free(ca->cmpals); } static void flush_buffer(args_t *args, htsFile *file, int n) { bcf1_t *line; int i, k; int prev_rid = -1, prev_pos = -1, prev_type = 0; for (i=0; irbuf); if ( args->mrows_op==MROWS_MERGE ) { if ( mrows_can_flush(args, args->lines[k]) ) { while ( (line=mrows_flush(args)) ) if ( bcf_write1(file, args->out_hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); } mrows_push(args, &args->lines[k]); continue; } else if ( args->rmdup ) { int line_type = bcf_get_variant_types(args->lines[k]); if ( prev_rid>=0 && prev_rid==args->lines[k]->rid && prev_pos==args->lines[k]->pos ) { if ( args->rmdup & BCF_SR_PAIR_ANY ) continue; // rmdup by position only if ( args->rmdup & BCF_SR_PAIR_SNPS && line_type&(VCF_SNP|VCF_MNP) && prev_type&(VCF_SNP|VCF_MNP) ) continue; if ( args->rmdup & BCF_SR_PAIR_INDELS && line_type&(VCF_INDEL) && prev_type&(VCF_INDEL) ) continue; if ( args->rmdup & BCF_SR_PAIR_EXACT && cmpals_match(args, &args->cmpals_out, args->lines[k]) ) continue; } else { prev_rid = args->lines[k]->rid; prev_pos = args->lines[k]->pos; prev_type = 0; if ( args->rmdup & BCF_SR_PAIR_EXACT ) cmpals_reset(&args->cmpals_out); } prev_type |= line_type; if ( args->rmdup & BCF_SR_PAIR_EXACT ) cmpals_add(args,&args->cmpals_out, args->lines[k]); } if ( bcf_write1(file, args->out_hdr, args->lines[k])!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); } if ( args->mrows_op==MROWS_MERGE && !args->rbuf.n ) { while ( (line=mrows_flush(args)) ) if ( bcf_write1(file, args->out_hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); } } static void init_data(args_t *args) { args->hdr = args->files->readers[0].header; if ( args->keep_sum_ad ) { args->keep_sum_ad = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"AD"); if ( args->keep_sum_ad < 0 ) error("Error: --keep-sum-ad requested but the tag AD is not present\n"); } else args->keep_sum_ad = -1; args->out_hdr = args->hdr; if ( args->old_rec_tag ) bcf_hdr_printf(args->out_hdr,"##INFO=",args->old_rec_tag); rbuf_init(&args->rbuf, 100); args->lines = (bcf1_t**) calloc(args->rbuf.m, sizeof(bcf1_t*)); if ( args->ref_fname ) { args->fai = fai_load(args->ref_fname); if ( !args->fai ) error("Failed to load the fai index: %s\n", args->ref_fname); } if ( args->mrows_op==MROWS_MERGE ) { args->mrow_out = bcf_init1(); args->tmp_str = (kstring_t*) calloc(bcf_hdr_nsamples(args->hdr),sizeof(kstring_t)); args->diploid = (uint8_t*) malloc(bcf_hdr_nsamples(args->hdr)); } if ( args->atomize==SPLIT ) { args->abuf = abuf_init(args->hdr, SPLIT); abuf_set_opt(args->abuf, bcf_hdr_t*, BCF_HDR, args->out_hdr); if ( args->old_rec_tag ) { abuf_set_opt(args->abuf, const char*, INFO_TAG, args->old_rec_tag); if ( bcf_hdr_sync(args->out_hdr)!=0 ) error("bcf_hdr_sync failed\n"); } abuf_set_opt(args->abuf, int, STAR_ALLELE, args->use_star_allele); } if ( args->gff_fname ) { args->gff = gff_init(args->gff_fname); gff_set(args->gff,verbosity,args->gff_verbosity); gff_set(args->gff,strip_chr_names,1); gff_parse(args->gff); args->idx_tscript = gff_get(args->gff,idx_tscript); args->itr_tscript = regitr_init(NULL); } if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); args->filter_pass = 1; args->out_hdr = bcf_hdr_dup(args->out_hdr); } static void destroy_data(args_t *args) { if ( args->filter ) filter_destroy(args->filter); if ( args->gff ) { gff_destroy(args->gff); regitr_destroy(args->itr_tscript); } cmpals_destroy(&args->cmpals_in); cmpals_destroy(&args->cmpals_out); int i; for (i=0; irbuf.m; i++) if ( args->lines[i] ) bcf_destroy1(args->lines[i]); free(args->lines); for (i=0; imtmp_lines; i++) if ( args->tmp_lines[i] ) bcf_destroy1(args->tmp_lines[i]); free(args->tmp_lines); for (i=0; immrows; i++) bcf_destroy1(args->mrows[i]); free(args->mrows); for (i=0; immaps; i++) free(args->maps[i].map); for (i=0; intmp_als; i++) free(args->tmp_als[i].s); for (i=0; intmp_sym; i++) free(args->tmp_sym[i].s); free(args->tmp_als); free(args->tmp_sym); free(args->tmp_kstr.s); if ( args->tmp_str ) { for (i=0; ihdr); i++) free(args->tmp_str[i].s); free(args->tmp_str); } free(args->maps); free(args->als); free(args->int32_arr); free(args->tmp_arr1); free(args->tmp_arr2); free(args->diploid); if ( args->abuf ) abuf_destroy(args->abuf); bcf_hdr_destroy(args->out_hdr); if ( args->mrow_out ) bcf_destroy1(args->mrow_out); if ( args->fai ) fai_destroy(args->fai); if ( args->mseq ) free(args->seq); } static void normalize_line(args_t *args, bcf1_t *line) { if ( args->fai ) { if ( args->filter_pass && (args->check_ref & CHECK_REF_FIX) ) fix_ref(args, line); if ( args->do_indels ) { int ret = args->filter_pass ? realign(args, line) : ERR_OK; // exclude broken VCF lines if ( ret==ERR_REF_MISMATCH && args->check_ref & CHECK_REF_SKIP ) { args->nskipped++; return; } if ( ret==ERR_DUP_ALLELE ) { if ( args->check_ref & CHECK_REF_FIX ) fix_dup_alt(args, line); else if ( args->check_ref==CHECK_REF_EXIT ) error("Duplicate alleles at %s:%"PRId64"; run with -cw to turn the error into warning or with -cs to fix.\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); else if ( args->check_ref & CHECK_REF_WARN ) fprintf(bcftools_stderr,"ALT_DUP\t%s\t%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1); } } } if ( args->filter_pass && args->atomize==SPLIT ) abuf_push(args->abuf,line); while (1) { if ( args->filter_pass && args->atomize==SPLIT ) { line = abuf_flush(args->abuf, 0); if ( !line ) break; } // insert into sorted buffer rbuf_expand0(&args->rbuf,bcf1_t*,args->rbuf.n+1,args->lines); int i,j; i = j = rbuf_append(&args->rbuf); if ( args->lines[i] ) bcf_destroy(args->lines[i]); args->lines[i] = bcf_dup(line); while ( rbuf_prev(&args->rbuf,&i) ) { if ( args->lines[i]->rid==args->lines[j]->rid ) { bcf_unpack(args->lines[i], BCF_UN_STR); bcf_unpack(args->lines[j], BCF_UN_STR); if ( args->cmp_func(&args->lines[i], &args->lines[j]) > 0) SWAP(bcf1_t*, args->lines[i], args->lines[j]); } j = i; } if ( !args->filter_pass || args->atomize!=SPLIT ) break; } } // return 0 on success, 1 when done static int split_and_normalize(args_t *args) { if ( !bcf_sr_next_line(args->files) ) return 1; bcf1_t *line = bcf_sr_get_line(args->files,0); args->ntotal++; if ( args->filter ) { args->filter_pass = filter_test(args->filter,line,NULL); if ( args->filter_logic==FLT_EXCLUDE ) args->filter_pass = args->filter_pass ? 0 : 1; if ( !args->filter_pass ) args->nfilter++; } if ( args->mrows_op!=MROWS_SPLIT || line->n_allele<=2 || !args->filter_pass ) { // normal operation, no splitting normalize_line(args, line); return 0; } // any restrictions on variant types to split? if ( args->mrows_collapse!=COLLAPSE_BOTH && args->mrows_collapse!=COLLAPSE_ANY ) { int type = args->mrows_collapse==COLLAPSE_SNPS ? VCF_SNP : VCF_INDEL; if ( !(bcf_get_variant_types(line) & type) ) { normalize_line(args, line); return 0; } } args->nsplit++; split_multiallelic_to_biallelics(args, line); int j; for (j=0; jntmp_lines; j++) normalize_line(args, args->tmp_lines[j]); return 0; } static void normalize_vcf(args_t *args) { char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); args->out = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( args->out == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno)); if ( args->n_threads ) hts_set_opt(args->out, HTS_OPT_THREAD_POOL, args->files->p); if (args->record_cmd_line) bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_norm"); if ( bcf_hdr_write(args->out, args->out_hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); if ( init_index2(args->out,args->out_hdr,args->output_fname, &args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->output_fname); while (1) { // buffer lines until a different position is reached int done = 0; while (1) { done = split_and_normalize(args); if ( done ) break; // no more lines available int i = args->rbuf.f; int j = rbuf_last(&args->rbuf); if ( args->lines[i]->rid != args->lines[j]->rid ) break; if ( args->lines[i]->pos != args->lines[j]->pos ) break; } if ( done ) break; // find out how many sites to flush int ifst = args->rbuf.f; int ilast = rbuf_last(&args->rbuf); int i, j = 0; for (i=-1; rbuf_next(&args->rbuf,&i); ) { if ( args->lines[ifst]->rid != args->lines[ilast]->rid ) { // there are two chromosomes in the buffer, count how many are on the first chromosome if ( args->lines[ifst]->rid != args->lines[i]->rid ) break; j++; continue; } // there is just one chromosome, flush only lines that are unlikely to change order on // realigning (the buf_win constant) if ( args->lines[ilast]->pos - args->lines[i]->pos < args->buf_win ) break; j++; } if ( j>0 ) flush_buffer(args, args->out, j); } flush_buffer(args, args->out, args->rbuf.n); if ( args->write_index ) { if ( bcf_idx_save(args->out)<0 ) { if ( hts_close(args->out)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"bcftools_stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(args->out)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname); fprintf(bcftools_stderr,"Lines total/split/joined/realigned/removed/skipped:\t%d/%d/%d/%d/%d/%d\n", args->ntotal,args->nsplit,args->njoined,args->nchanged,args->nskipped,args->nfilter); if ( args->check_ref & CHECK_REF_FIX ) fprintf(bcftools_stderr,"REF/ALT total/modified/added: \t%d/%d/%d\n", args->nref.tot,args->nref.swap,args->nref.set); } static void usage(void) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: Left-align and normalize indels; check if REF alleles match the reference;\n"); fprintf(bcftools_stderr, " split multiallelic sites into multiple rows; recover multiallelics from\n"); fprintf(bcftools_stderr, " multiple rows.\n"); fprintf(bcftools_stderr, "Usage: bcftools norm [options] \n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Options:\n"); fprintf(bcftools_stderr, " -a, --atomize Decompose complex variants (e.g. MNVs become consecutive SNVs)\n"); fprintf(bcftools_stderr, " --atom-overlaps '*'|. Use the star allele (*) for overlapping alleles or set to missing (.) [*]\n"); fprintf(bcftools_stderr, " -c, --check-ref e|w|x|s Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites [e]\n"); fprintf(bcftools_stderr, " -D, --remove-duplicates Remove duplicate lines of the same type.\n"); fprintf(bcftools_stderr, " -d, --rm-dup TYPE Remove duplicate snps|indels|both|all|exact\n"); fprintf(bcftools_stderr, " -e, --exclude EXPR Do not normalize records for which the expression is true (see man page for details)\n"); fprintf(bcftools_stderr, " -f, --fasta-ref FILE Reference sequence\n"); fprintf(bcftools_stderr, " --force Try to proceed even if malformed tags are encountered. Experimental, use at your own risk\n"); fprintf(bcftools_stderr, " -g, --gff-annot FILE Follow HGVS 3'rule and right-align variants in transcripts on the forward strand\n"); fprintf(bcftools_stderr, " -i, --include EXPR Normalize only records for which the expression is true (see man page for details)\n"); fprintf(bcftools_stderr, " --keep-sum TAG,.. Keep vector sum constant when splitting multiallelics (see github issue #360)\n"); fprintf(bcftools_stderr, " -m, --multiallelics -|+TYPE Split multiallelics (-) or join biallelics (+), type: snps|indels|both|any [both]\n"); fprintf(bcftools_stderr, " --multi-overlaps 0|. Fill in the reference (0) or missing (.) allele when splitting multiallelics [0]\n"); fprintf(bcftools_stderr, " --no-version Do not append version and command line to the header\n"); fprintf(bcftools_stderr, " -N, --do-not-normalize Do not normalize indels (with -m or -c s)\n"); fprintf(bcftools_stderr, " --old-rec-tag STR Annotate modified records with INFO/STR indicating the original variant\n"); fprintf(bcftools_stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(bcftools_stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(bcftools_stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(bcftools_stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(bcftools_stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " -s, --strict-filter When merging (-m+), merged site is PASS only if all sites being merged PASS\n"); fprintf(bcftools_stderr, " -S, --sort METHOD Sort order: chr_pos,lex [chr_pos]\n"); fprintf(bcftools_stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(bcftools_stderr, " --threads INT Use multithreading with INT worker threads [0]\n"); fprintf(bcftools_stderr, " -v, --verbose INT Verbosity level (0-2) of GFF parsing [1]\n"); fprintf(bcftools_stderr, " -w, --site-win INT Buffer for sorting lines which changed position during realignment [1000]\n"); fprintf(bcftools_stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Examples:\n"); fprintf(bcftools_stderr, " # normalize and left-align indels\n"); fprintf(bcftools_stderr, " bcftools norm -f ref.fa in.vcf\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, " # split multi-allelic sites\n"); fprintf(bcftools_stderr, " bcftools norm -m- in.vcf\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int main_vcfnorm(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->files = bcf_sr_init(); args->output_fname = "-"; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->aln_win = 100; args->buf_win = 1000; args->mrows_collapse = COLLAPSE_BOTH; args->do_indels = 1; args->ma_use_ref_allele = 1; args->clevel = -1; int region_is_file = 0; int targets_is_file = 0; args->use_star_allele = 1; args->gff_verbosity = 1; int regions_overlap = 1; int targets_overlap = 0; args->cmp_func = cmp_bcf_pos; static struct option loptions[] = { {"help",no_argument,NULL,'h'}, {"force",no_argument,NULL,7}, {"atomize",no_argument,NULL,'a'}, {"atom-overlaps",required_argument,NULL,11}, {"include",required_argument,NULL,'i'}, {"exclude",required_argument,NULL,'e'}, {"old-rec-tag",required_argument,NULL,12}, {"keep-sum",required_argument,NULL,10}, {"fasta-ref",required_argument,NULL,'f'}, {"sort",required_argument,NULL,'S'}, {"gff-annot",required_argument,NULL,'g'}, {"right-align",no_argument,NULL,15}, // undocumented, only for debugging {"do-not-normalize",no_argument,NULL,'N'}, {"multiallelics",required_argument,NULL,'m'}, {"multi-overlaps",required_argument,NULL,13}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,1}, {"targets",required_argument,NULL,'t'}, {"targets-file",required_argument,NULL,'T'}, {"targets-overlap",required_argument,NULL,2}, {"site-win",required_argument,NULL,'w'}, {"remove-duplicates",no_argument,NULL,'D'}, {"rm-dup",required_argument,NULL,'d'}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"threads",required_argument,NULL,9}, {"check-ref",required_argument,NULL,'c'}, {"strict-filter",no_argument,NULL,'s'}, {"no-version",no_argument,NULL,8}, {"write-index",optional_argument,NULL,'W'}, {"verbose",required_argument,NULL,'v'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "hr:R:f:w:Dd:o:O:c:m:t:T:sNag:W::v:S:i:e:",loptions,NULL)) >= 0) { switch (c) { case 10: // possibly generalize this also to INFO/AD and other tags if ( strcasecmp("ad",optarg) ) error("Error: only --keep-sum AD is currently supported. See https://github.com/samtools/bcftools/issues/360 for more.\n"); args->keep_sum_ad = 1; // this will be set to the header id or -1 in init_data break; case 'g': args->gff_fname = optarg; break; case 'v': args->gff_verbosity = atoi(optarg); if ( args->gff_verbosity<0 || args->gff_verbosity>2 ) error("Error: expected integer 0-2 with -v, --verbose\n"); break; case 'a': args->atomize = SPLIT; break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'S': if ( !strcasecmp(optarg,"pos") ) args->cmp_func = cmp_bcf_pos; else if ( !strcasecmp(optarg,"lex") ) args->cmp_func = cmp_bcf_pos_ref_alt; else error("Error: the sort order --sort %s is not recognised\n",optarg); break; case 11 : if ( optarg[0]=='*' ) args->use_star_allele = 1; else if ( optarg[0]=='.' ) args->use_star_allele = 0; else error("Invalid argument to --atom-overlaps. Perhaps you wanted: \"--atom-overlaps '*'\"?\n"); break; case 12 : args->old_rec_tag = optarg; break; case 13 : if ( optarg[0]=='0' ) args->ma_use_ref_allele = 1; else if ( optarg[0]=='.' ) args->ma_use_ref_allele = 0; else error("Invalid argument to --multi-overlaps\n"); break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 15 : args->right_align = 1; break; case 'N': args->do_indels = 0; break; case 'd': if ( !strcmp("snps",optarg) ) args->rmdup = BCF_SR_PAIR_SNPS; else if ( !strcmp("indels",optarg) ) args->rmdup = BCF_SR_PAIR_INDELS; else if ( !strcmp("both",optarg) ) args->rmdup = BCF_SR_PAIR_BOTH; else if ( !strcmp("all",optarg) ) args->rmdup = BCF_SR_PAIR_ANY; else if ( !strcmp("any",optarg) ) args->rmdup = BCF_SR_PAIR_ANY; else if ( !strcmp("none",optarg) ) args->rmdup = BCF_SR_PAIR_EXACT; else if ( !strcmp("exact",optarg) ) args->rmdup = BCF_SR_PAIR_EXACT; else error("The argument to -d not recognised: %s\n", optarg); break; case 'm': if ( optarg[0]=='-' ) args->mrows_op = MROWS_SPLIT; else if ( optarg[0]=='+' ) args->mrows_op = MROWS_MERGE; else error("Expected '+' or '-' with -m\n"); if ( optarg[1]!=0 ) { if ( !strcmp("snps",optarg+1) ) args->mrows_collapse = COLLAPSE_SNPS; else if ( !strcmp("indels",optarg+1) ) args->mrows_collapse = COLLAPSE_INDELS; else if ( !strcmp("both",optarg+1) ) args->mrows_collapse = COLLAPSE_BOTH; else if ( !strcmp("any",optarg+1) ) args->mrows_collapse = COLLAPSE_ANY; else error("The argument to -m not recognised: %s\n", optarg); } break; case 'c': if ( strchr(optarg,'w') ) args->check_ref |= CHECK_REF_WARN; if ( strchr(optarg,'x') ) args->check_ref |= CHECK_REF_SKIP; if ( strchr(optarg,'s') ) args->check_ref |= CHECK_REF_FIX; if ( strchr(optarg,'e') ) args->check_ref = CHECK_REF_EXIT; // overrides the above break; case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } } if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'o': args->output_fname = optarg; break; case 'D': fprintf(bcftools_stderr,"Warning: `-D` is functional but deprecated, replaced by and alias of `-d none`.\n"); args->rmdup = BCF_SR_PAIR_EXACT; break; case 's': args->strict_filter = 1; break; case 'f': args->ref_fname = optarg; break; case 'r': args->region = optarg; break; case 'R': args->region = optarg; region_is_file = 1; break; case 't': args->targets = optarg; break; case 'T': args->targets = optarg; targets_is_file = 1; break; case 'w': args->buf_win = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --site-win %s\n", optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 8 : args->record_cmd_line = 0; break; case 7 : args->force = 1; break; case 1 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 2 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 'h': case '?': usage(); break; default: error("Unknown argument: %s\n", optarg); } } char *fname = NULL; if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else usage(); } else fname = argv[optind]; if ( !args->ref_fname && !args->mrows_op && !args->rmdup && args->atomize==NONE ) error("Expected -a, -f, -m, -D or -d option\n"); if ( !args->check_ref && args->ref_fname ) args->check_ref = CHECK_REF_EXIT; if ( args->check_ref && !args->ref_fname ) error("Expected --fasta-ref with --check-ref\n"); if ( args->region ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->region,region_is_file)<0 ) error("Failed to read the regions: %s\n", args->region); } if ( args->targets ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets,targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets); } if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n"); if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); init_data(args); normalize_vcf(args); destroy_data(args); bcf_sr_destroy(args->files); free(args); return 0; } pysam-0.23.0/bcftools/vcfplugin.c000066400000000000000000000676601475062545500167350ustar00rootroot00000000000000/* vcfplugin.c -- plugin modules for operating on VCF/BCF files. Copyright (C) 2013-2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include "config.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #ifdef _WIN32 #include #else #include #endif #include "bcftools.h" #include "vcmp.h" #include "filter.h" #ifdef ENABLE_BCF_PLUGINS typedef struct _plugin_t plugin_t; /** * Plugin API: * ---------- * const char *about(void) * - short description used by 'bcftools plugin -lv' * * const char *usage(void) * - longer description used by 'bcftools +name -h' * * int run(int argc, char **argv) * - if implemented, the control is immediately handed over to the plugin, * none of the init/process/destroy functions is called. Return 0 on * success or non-zero value on error. * * int init(int argc, char **argv, bcf_hdr_t *in_hdr, bcf_hdr_t *out_hdr) * - called once at startup, it initializes local variables. * Return 1 to suppress normal VCF/BCF header output, -1 on critical * errors, 0 otherwise. * * bcf1_t *process(bcf1_t *rec) * - called for each VCF record, return NULL for no output * * void destroy(void) * - called after all lines have been processed to clean up */ typedef void (*dl_version_f) (const char **, const char **); typedef int (*dl_run_f) (int, char **); typedef int (*dl_init_f) (int, char **, bcf_hdr_t *, bcf_hdr_t *); typedef char* (*dl_about_f) (void); typedef char* (*dl_usage_f) (void); typedef bcf1_t* (*dl_process_f) (bcf1_t *); typedef void (*dl_destroy_f) (void); struct _plugin_t { int argc; char *name, **argv; dl_version_f version; dl_run_f run; dl_init_f init; dl_about_f about; dl_usage_f usage; dl_process_f process; dl_destroy_f destroy; void *handle; }; struct _args_t; typedef struct _rm_tag_t { char *key; int hdr_id; void (*handler)(struct _args_t *, bcf1_t *, struct _rm_tag_t *); } rm_tag_t; typedef struct { char **cols; int ncols, mcols; char **als; int nals, mals; kstring_t line; int rid, start, end; } annot_line_t; typedef struct _annot_col_t { int icol, replace; char *hdr_key; int (*setter)(struct _args_t *, bcf1_t *, struct _annot_col_t *, void*); } annot_col_t; // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 typedef struct _args_t { bcf_srs_t *files; bcf_hdr_t *hdr, *hdr_out; htsFile *out_fh; int output_type, n_threads, clevel; filter_t *filter; char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE plugin_t plugin; int nplugin_paths; char **plugin_paths; char **argv, *output_fname, *regions_list, *targets_list; int argc, drop_header, verbose, record_cmd_line, plist_only; char *index_fn; int write_index; } args_t; char *msprintf(const char *fmt, ...); static void add_plugin_paths(args_t *args, const char *path) { while (1) { size_t len = strcspn(path, HTS_PATH_SEPARATOR_STR); if ( len == 0 ) { #ifdef PLUGINPATH add_plugin_paths(args, PLUGINPATH); #endif } else { char *dir = (char *) malloc(len + 1); strncpy(dir, path, len); dir[len] = '\0'; struct stat st; if ( stat(dir, &st) == 0 ) { args->plugin_paths = (char**) realloc(args->plugin_paths,sizeof(char*)*(args->nplugin_paths+1)); args->plugin_paths[args->nplugin_paths] = dir; args->nplugin_paths++; if ( args->verbose > 1 && strcmp(".",dir) ) fprintf(stderr, "plugin directory %s .. ok\n", dir); } else { if ( args->verbose > 1 ) fprintf(stderr, "plugin directory %s .. %s\n", dir, strerror(errno)); free(dir); } } path += len; if ( *path == HTS_PATH_SEPARATOR_CHAR ) path++; else break; } } static void init_plugin_paths(args_t *args) { if ( args->nplugin_paths!=-1 ) return; args->nplugin_paths = 0; args->plugin_paths = NULL; char *path = getenv("BCFTOOLS_PLUGINS"); add_plugin_paths(args, path ? path : ""); } static void *dlopen_plugin(args_t *args, const char *fname) { init_plugin_paths(args); void *handle; char *tmp; int is_absolute_path = 0; #ifdef _WIN32 // Windows accepts both forward slash (/) and backslash (\) as folder separator // and can have any path prefixed by the drive letter and a colon (:). if ( fname[0]=='/' || fname[0]=='\\') is_absolute_path = 1; else if ( fname[0] && fname[1]==':' && (fname[2]=='/' || fname[2]=='\\') ) is_absolute_path = 1; #else if ( fname[0]=='/' ) is_absolute_path = 1; #endif kstring_t err = {0,0,0}; if ( !is_absolute_path ) { int i; for (i=0; inplugin_paths; i++) { tmp = msprintf("%s/%s%s", args->plugin_paths[i], fname, PLUGIN_EXT); #ifdef _WIN32 handle = LoadLibraryA(tmp); #else handle = dlopen(tmp, RTLD_NOW); // valgrind complains about unfreed memory, not our problem though #endif if ( !handle ) #ifdef _WIN32 ksprintf(&err,"LoadLibraryA .. %lu\n", GetLastError()); #else ksprintf(&err,"%s:\n\tdlopen .. %s\n", tmp,dlerror()); #endif else if ( args->verbose > 1 ) fprintf(stderr,"%s:\n\tplugin open .. ok\n", tmp); free(tmp); if ( handle ) return handle; } } #ifdef _WIN32 handle = LoadLibraryA(fname); #else handle = dlopen(fname, RTLD_NOW); #endif if ( !handle ) #ifdef _WIN32 ksprintf(&err,"LoadLibraryA .. %lu\n", GetLastError()); #else ksprintf(&err,"%s:\n\tdlopen .. %s\n", fname,dlerror()); #endif else if ( args->verbose > 1 ) fprintf(stderr,"%s:\n\tplugin open .. ok\n", fname); if ( !handle && (!args->plist_only || args->verbose>1) ) fprintf(stderr,"%s",err.s); free(err.s); return handle; } static void print_plugin_usage_hint(const char *name) { if ( name ) fprintf(stderr, "\nThe bcftools plugin \"%s\" was not found or is not functional", name); else fprintf(stderr, "\nNo functional bcftools plugins were found"); if ( !getenv("BCFTOOLS_PLUGINS") ) { fprintf(stderr,". The environment variable BCFTOOLS_PLUGINS is not set"); #ifdef PLUGINPATH fprintf(stderr,"\nand no usable plugins were found in %s", PLUGINPATH); #endif fprintf(stderr,".\n\n"); } else { fprintf(stderr, " in\n\tBCFTOOLS_PLUGINS=\"%s\".\n\n" "- Is the plugin path correct?\n\n" "- Run \"bcftools plugin -l\" or \"bcftools plugin -lvv\" for a list of available plugins.\n" "\n", getenv("BCFTOOLS_PLUGINS") ); } } static int load_plugin(args_t *args, const char *fname, int exit_on_error, plugin_t *plugin) { plugin->name = strdup(fname); plugin->handle = dlopen_plugin(args, fname); if ( !plugin->handle ) { if ( exit_on_error ) { print_plugin_usage_hint(fname); error("Could not load \"%s\".\n\n", fname); } return -1; } #ifdef _WIN32 plugin->init = (dl_init_f) GetProcAddress(plugin->handle, "init"); if ( plugin->init && args->verbose > 1 ) fprintf(stderr,"\tinit .. ok\n"); plugin->run = (dl_run_f) GetProcAddress(plugin->handle, "run"); if ( plugin->run && args->verbose > 1 ) fprintf(stderr,"\trun .. ok\n"); if ( !plugin->init && !plugin->run ) { if ( exit_on_error ) error("Could not initialize %s, neither run or init found \n", plugin->name); else if ( args->verbose > 1 ) fprintf(stderr,"\tinit/run .. not found\n"); return -1; } plugin->version = (dl_version_f) GetProcAddress(plugin->handle, "version"); if ( !plugin->version ) { if ( exit_on_error ) error("Could not initialize %s: version string not found\n", plugin->name); else if ( args->verbose > 1 ) fprintf(stderr,"\tversion .. not found\n"); return -1; } plugin->about = (dl_about_f) GetProcAddress(plugin->handle, "about"); if ( !plugin->about ) { if ( exit_on_error ) error("Could not initialize %s: about string not found\n", plugin->name); return -1; } plugin->usage = (dl_about_f) GetProcAddress(plugin->handle, "usage"); if ( !plugin->usage ) plugin->usage = plugin->about; if ( plugin->run ) return 0; plugin->process = (dl_process_f) GetProcAddress(plugin->handle, "process"); if ( !plugin->process ) { if ( exit_on_error ) error("Could not initialize %s: process method not found\n", plugin->name); return -1; } plugin->destroy = (dl_destroy_f) GetProcAddress(plugin->handle, "destroy"); if ( !plugin->destroy ) { if ( exit_on_error ) error("Could not initialize %s: destroy method not found\n", plugin->name); return -1; } #else dlerror(); plugin->init = (dl_init_f) dlsym(plugin->handle, "init"); char *ret = dlerror(); if ( ret ) plugin->init = NULL; else if ( args->verbose > 1 ) fprintf(stderr,"\tinit .. ok\n"); plugin->run = (dl_run_f) dlsym(plugin->handle, "run"); ret = dlerror(); if ( ret ) plugin->run = NULL; else if ( args->verbose > 1 ) fprintf(stderr,"\trun .. ok\n"); if ( !plugin->init && !plugin->run ) { if ( exit_on_error ) error("Could not initialize %s, neither run or init found \n", plugin->name); else if ( args->verbose > 1 ) fprintf(stderr,"\tinit/run .. not found\n"); return -1; } plugin->version = (dl_version_f) dlsym(plugin->handle, "version"); ret = dlerror(); if ( ret ) { if ( exit_on_error ) error("Could not initialize %s, version string not found\n", plugin->name); else if ( args->verbose > 1 ) fprintf(stderr,"\tversion .. not found\n"); return -1; } plugin->about = (dl_about_f) dlsym(plugin->handle, "about"); ret = dlerror(); if ( ret ) { if ( exit_on_error ) error("Could not initialize %s: %s\n", plugin->name, ret); return -1; } plugin->usage = (dl_about_f) dlsym(plugin->handle, "usage"); ret = dlerror(); if ( ret ) plugin->usage = plugin->about; if ( plugin->run ) return 0; plugin->process = (dl_process_f) dlsym(plugin->handle, "process"); ret = dlerror(); if ( ret ) { if ( exit_on_error ) error("Could not initialize %s: %s\n", plugin->name, ret); return -1; } plugin->destroy = (dl_destroy_f) dlsym(plugin->handle, "destroy"); ret = dlerror(); if ( ret ) { if ( exit_on_error ) error("Could not initialize %s: %s\n", plugin->name, ret); return -1; } #endif return 0; } static void check_version(args_t *args) { static int warned_bcftools = 0, warned_htslib = 0; const char *bver, *hver; args->plugin.version(&bver, &hver); if ( strcmp(bver,bcftools_version()) && !warned_bcftools ) { fprintf(stderr,"WARNING: bcftools version mismatch .. bcftools at %s, the plugin \"%s\" at %s\n", bcftools_version(),args->plugin.name,bver); warned_bcftools = 1; } if ( strcmp(hver,hts_version()) && !warned_htslib ) { fprintf(stderr,"WARNING: htslib version mismatch .. bcftools at %s, the plugin \"%s\" at %s\n", hts_version(),args->plugin.name,hver); warned_htslib = 1; } } static void init_plugin(args_t *args) { int ret = args->plugin.init(args->plugin.argc,args->plugin.argv,args->hdr,args->hdr_out); if ( ret<0 ) error("The plugin exited with an error.\n"); check_version(args); args->drop_header += ret; } static int cmp_plugin_name(const void *p1, const void *p2) { plugin_t *a = (plugin_t*) p1; plugin_t *b = (plugin_t*) p2; return strcmp(a->name,b->name); } // If args=NULL then returns the number of plugins available. Otherwise prints the // plugins on stdout and returns 0 on success. static int list_plugins(args_t *args) { plugin_t *plugins = NULL; int nplugins = 0, mplugins = 0; int count_only = 0; args_t _args; if ( !args ) { memset(&_args,0,sizeof(_args)); args = &_args; args->nplugin_paths = -1; count_only = 1; } init_plugin_paths(args); kstring_t str = {0,0,0}; int plugin_ext_len = strlen(PLUGIN_EXT); int i; for (i=0; inplugin_paths; i++) { DIR *dp = opendir(args->plugin_paths[i]); if ( dp==NULL ) continue; struct dirent *ep; while ( (ep=readdir(dp)) ) { int len = strlen(ep->d_name); if ( strcasecmp(PLUGIN_EXT,ep->d_name+len-plugin_ext_len) ) continue; str.l = 0; ksprintf(&str,"%s/%s", args->plugin_paths[i],ep->d_name); hts_expand(plugin_t, nplugins+1, mplugins, plugins); if ( load_plugin(args, str.s, 0, &plugins[nplugins]) < 0 ) continue; nplugins++; str.l = 0; kputs(ep->d_name, &str); int l = str.l - 1; while ( l>=0 && str.s[l]!='.' ) l--; if ( l>=0 ) str.s[l] = 0; free(plugins[nplugins-1].name); plugins[nplugins-1].name = strdup(str.s); // use a short name } closedir(dp); } if ( count_only ) { free(str.s); return nplugins; } if ( nplugins ) { qsort(plugins, nplugins, sizeof(plugins[0]), cmp_plugin_name); for (i=0; iverbose ) printf("\n-- %s --\n%s", plugins[i].name, plugins[i].about()); else printf("%s\n", plugins[i].name); } if ( args->verbose ) printf("\n"); } else print_plugin_usage_hint(NULL); free(str.s); return nplugins ? 0 : 1; } int count_plugins(void) { return list_plugins(NULL); } static void init_data(args_t *args) { args->hdr = args->files->readers[0].header; args->hdr_out = bcf_hdr_dup(args->hdr); init_plugin(args); if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); if (args->record_cmd_line) bcf_hdr_append_version(args->hdr_out, args->argc, args->argv, "bcftools_plugin"); if ( !args->drop_header ) { char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno)); if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads); if ( bcf_hdr_write(args->out_fh, args->hdr_out)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); if ( init_index2(args->out_fh,args->hdr_out,args->output_fname, &args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->output_fname); } } static void destroy_data(args_t *args) { free(args->plugin.name); if ( args->plugin.destroy ) args->plugin.destroy(); #ifdef _WIN32 FreeLibrary(args->plugin.handle); #else dlclose(args->plugin.handle); #endif if ( args->hdr_out ) bcf_hdr_destroy(args->hdr_out); if ( args->nplugin_paths>0 ) { int i; for (i=0; inplugin_paths; i++) free(args->plugin_paths[i]); free(args->plugin_paths); } if ( args->filter ) filter_destroy(args->filter); if (args->out_fh ) { if ( args->write_index ) { if ( bcf_idx_save(args->out_fh)<0 ) { if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname); } } static void usage(args_t *args) { fprintf(stderr, "\n"); fprintf(stderr, "About: Run user defined plugin\n"); fprintf(stderr, "Usage: bcftools plugin [OPTIONS] [-- PLUGIN_OPTIONS]\n"); fprintf(stderr, " bcftools +name [OPTIONS] [-- PLUGIN_OPTIONS]\n"); fprintf(stderr, "\n"); fprintf(stderr, "VCF input options:\n"); fprintf(stderr, " -e, --exclude EXPR Exclude sites for which the expression is true\n"); fprintf(stderr, " -i, --include EXPR Select sites for which the expression is true\n"); fprintf(stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(stderr, "VCF output options:\n"); fprintf(stderr, " --no-version Do not append version and command line to the header\n"); fprintf(stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(stderr, " --threads INTT Use multithreading with worker threads [0]\n"); fprintf(stderr, "Plugin options:\n"); fprintf(stderr, " -h, --help List plugin's options\n"); fprintf(stderr, " -l, --list-plugins List available plugins. See BCFTOOLS_PLUGINS environment variable and man page for details\n"); fprintf(stderr, " -v, --verbose Print verbose information, -vv increases verbosity\n"); fprintf(stderr, " -V, --version Print version string and exit\n"); fprintf(stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(stderr, "\n"); exit(1); } static int is_verbose(int argc, char *argv[]) { int c, verbose = 0, opterr_ori = opterr; static struct option loptions[] = { {"verbose",no_argument,NULL,'v'}, {NULL,0,NULL,0} }; opterr = 0; while ((c = getopt_long(argc, argv, "-v",loptions,NULL)) >= 0) { switch (c) { case 'v': verbose++; break; case 1: default: break; } } opterr = opterr_ori; optind = 0; return verbose; } int main_plugin(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->output_fname = "-"; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->nplugin_paths = -1; args->clevel = -1; int regions_is_file = 0, targets_is_file = 0, usage_only = 0, version_only = 0; int regions_overlap = 1; int targets_overlap = 0; if ( argc==1 ) usage(args); char *plugin_name = NULL; if ( argv[1][0]!='-' ) { args->verbose = is_verbose(argc, argv); plugin_name = argv[1]; argc--; argv++; load_plugin(args, plugin_name, 1, &args->plugin); if ( args->plugin.run ) { check_version(args); int ret = args->plugin.run(argc, argv); destroy_data(args); free(args); return ret; } } static struct option loptions[] = { {"version",no_argument,NULL,'V'}, {"verbose",no_argument,NULL,'v'}, {"help",no_argument,NULL,'h'}, {"list-plugins",no_argument,NULL,'l'}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"threads",required_argument,NULL,9}, {"include",required_argument,NULL,'i'}, {"exclude",required_argument,NULL,'e'}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,1}, {"targets",required_argument,NULL,'t'}, {"targets-file",required_argument,NULL,'T'}, {"targets-overlap",required_argument,NULL,2}, {"no-version",no_argument,NULL,8}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "h?o:O:r:R:t:T:li:e:vVW::",loptions,NULL)) >= 0) { switch (c) { case 'V': version_only = 1; break; case 'v': args->verbose++; break; case 'o': args->output_fname = optarg; break; case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } }; if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; targets_is_file = 1; break; case 'l': args->plist_only = 1; break; case 1 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 2 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 8 : args->record_cmd_line = 0; break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case '?': case 'h': usage_only = 1; break; default: error("Unknown argument: %s\n", optarg); } } if ( args->plist_only ) return list_plugins(args); if ( !plugin_name ) usage(args); if ( version_only ) { const char *bver, *hver; args->plugin.version(&bver, &hver); printf("bcftools %s using htslib %s\n", bcftools_version(), hts_version()); printf("plugin at %s using htslib %s\n\n", bver, hver); return 0; } if ( usage_only ) { if ( args->plugin.usage ) fprintf(stderr,"%s",args->plugin.usage()); else fprintf(stderr,"Usage: bcftools +%s [General Options] -- [Plugin Options]\n",plugin_name); return 0; } char *fname = NULL; if ( optind>=argc || (argv[optind][0]=='-' && argv[optind][1]) ) { args->plugin.argc = argc - optind + 1; args->plugin.argv = argv + optind - 1; if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else if ( optind>=argc ) usage(args); else { optind = 1; init_plugin(args); } } else { fname = argv[optind]; args->plugin.argc = argc - optind; args->plugin.argv = argv + optind; } optind = 0; args->files = bcf_sr_init(); if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); args->files->collapse |= COLLAPSE_SOME; } if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); init_data(args); while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = bcf_sr_get_line(args->files,0); if ( args->filter ) { int pass = filter_test(args->filter, line, NULL); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) continue; } line = args->plugin.process(line); if ( line ) { if ( line->errcode ) error("[E::main_plugin] Unchecked error (%d), exiting\n",line->errcode); if ( bcf_write1(args->out_fh, args->hdr_out, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); } } destroy_data(args); bcf_sr_destroy(args->files); free(args); return 0; } #else /* ENABLE_BCF_PLUGINS */ int main_plugin(int argc, char *argv[]) { fprintf(stderr, "bcftools plugins are disabled. To use them, you will need to rebuild\n" "bcftools from the source distribution with plugins enabled.\n"); return 1; } #endif /* ENABLE_BCF_PLUGINS */ pysam-0.23.0/bcftools/vcfplugin.c.pysam.c000066400000000000000000000710041475062545500202710ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfplugin.c -- plugin modules for operating on VCF/BCF files. Copyright (C) 2013-2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include "config.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #ifdef _WIN32 #include #else #include #endif #include "bcftools.h" #include "vcmp.h" #include "filter.h" #ifdef ENABLE_BCF_PLUGINS typedef struct _plugin_t plugin_t; /** * Plugin API: * ---------- * const char *about(void) * - short description used by 'bcftools plugin -lv' * * const char *usage(void) * - longer description used by 'bcftools +name -h' * * int run(int argc, char **argv) * - if implemented, the control is immediately handed over to the plugin, * none of the init/process/destroy functions is called. Return 0 on * success or non-zero value on error. * * int init(int argc, char **argv, bcf_hdr_t *in_hdr, bcf_hdr_t *out_hdr) * - called once at startup, it initializes local variables. * Return 1 to suppress normal VCF/BCF header output, -1 on critical * errors, 0 otherwise. * * bcf1_t *process(bcf1_t *rec) * - called for each VCF record, return NULL for no output * * void destroy(void) * - called after all lines have been processed to clean up */ typedef void (*dl_version_f) (const char **, const char **); typedef int (*dl_run_f) (int, char **); typedef int (*dl_init_f) (int, char **, bcf_hdr_t *, bcf_hdr_t *); typedef char* (*dl_about_f) (void); typedef char* (*dl_usage_f) (void); typedef bcf1_t* (*dl_process_f) (bcf1_t *); typedef void (*dl_destroy_f) (void); struct _plugin_t { int argc; char *name, **argv; dl_version_f version; dl_run_f run; dl_init_f init; dl_about_f about; dl_usage_f usage; dl_process_f process; dl_destroy_f destroy; void *handle; }; struct _args_t; typedef struct _rm_tag_t { char *key; int hdr_id; void (*handler)(struct _args_t *, bcf1_t *, struct _rm_tag_t *); } rm_tag_t; typedef struct { char **cols; int ncols, mcols; char **als; int nals, mals; kstring_t line; int rid, start, end; } annot_line_t; typedef struct _annot_col_t { int icol, replace; char *hdr_key; int (*setter)(struct _args_t *, bcf1_t *, struct _annot_col_t *, void*); } annot_col_t; // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 typedef struct _args_t { bcf_srs_t *files; bcf_hdr_t *hdr, *hdr_out; htsFile *out_fh; int output_type, n_threads, clevel; filter_t *filter; char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE plugin_t plugin; int nplugin_paths; char **plugin_paths; char **argv, *output_fname, *regions_list, *targets_list; int argc, drop_header, verbose, record_cmd_line, plist_only; char *index_fn; int write_index; } args_t; char *msprintf(const char *fmt, ...); static void add_plugin_paths(args_t *args, const char *path) { while (1) { size_t len = strcspn(path, HTS_PATH_SEPARATOR_STR); if ( len == 0 ) { #ifdef PLUGINPATH add_plugin_paths(args, PLUGINPATH); #endif } else { char *dir = (char *) malloc(len + 1); strncpy(dir, path, len); dir[len] = '\0'; struct stat st; if ( stat(dir, &st) == 0 ) { args->plugin_paths = (char**) realloc(args->plugin_paths,sizeof(char*)*(args->nplugin_paths+1)); args->plugin_paths[args->nplugin_paths] = dir; args->nplugin_paths++; if ( args->verbose > 1 && strcmp(".",dir) ) fprintf(bcftools_stderr, "plugin directory %s .. ok\n", dir); } else { if ( args->verbose > 1 ) fprintf(bcftools_stderr, "plugin directory %s .. %s\n", dir, strerror(errno)); free(dir); } } path += len; if ( *path == HTS_PATH_SEPARATOR_CHAR ) path++; else break; } } static void init_plugin_paths(args_t *args) { if ( args->nplugin_paths!=-1 ) return; args->nplugin_paths = 0; args->plugin_paths = NULL; char *path = getenv("BCFTOOLS_PLUGINS"); add_plugin_paths(args, path ? path : ""); } static void *dlopen_plugin(args_t *args, const char *fname) { init_plugin_paths(args); void *handle; char *tmp; int is_absolute_path = 0; #ifdef _WIN32 // Windows accepts both forward slash (/) and backslash (\) as folder separator // and can have any path prefixed by the drive letter and a colon (:). if ( fname[0]=='/' || fname[0]=='\\') is_absolute_path = 1; else if ( fname[0] && fname[1]==':' && (fname[2]=='/' || fname[2]=='\\') ) is_absolute_path = 1; #else if ( fname[0]=='/' ) is_absolute_path = 1; #endif kstring_t err = {0,0,0}; if ( !is_absolute_path ) { int i; for (i=0; inplugin_paths; i++) { tmp = msprintf("%s/%s%s", args->plugin_paths[i], fname, PLUGIN_EXT); #ifdef _WIN32 handle = LoadLibraryA(tmp); #else handle = dlopen(tmp, RTLD_NOW); // valgrind complains about unfreed memory, not our problem though #endif if ( !handle ) #ifdef _WIN32 ksprintf(&err,"LoadLibraryA .. %lu\n", GetLastError()); #else ksprintf(&err,"%s:\n\tdlopen .. %s\n", tmp,dlerror()); #endif else if ( args->verbose > 1 ) fprintf(bcftools_stderr,"%s:\n\tplugin open .. ok\n", tmp); free(tmp); if ( handle ) return handle; } } #ifdef _WIN32 handle = LoadLibraryA(fname); #else handle = dlopen(fname, RTLD_NOW); #endif if ( !handle ) #ifdef _WIN32 ksprintf(&err,"LoadLibraryA .. %lu\n", GetLastError()); #else ksprintf(&err,"%s:\n\tdlopen .. %s\n", fname,dlerror()); #endif else if ( args->verbose > 1 ) fprintf(bcftools_stderr,"%s:\n\tplugin open .. ok\n", fname); if ( !handle && (!args->plist_only || args->verbose>1) ) fprintf(bcftools_stderr,"%s",err.s); free(err.s); return handle; } static void print_plugin_usage_hint(const char *name) { if ( name ) fprintf(bcftools_stderr, "\nThe bcftools plugin \"%s\" was not found or is not functional", name); else fprintf(bcftools_stderr, "\nNo functional bcftools plugins were found"); if ( !getenv("BCFTOOLS_PLUGINS") ) { fprintf(bcftools_stderr,". The environment variable BCFTOOLS_PLUGINS is not set"); #ifdef PLUGINPATH fprintf(bcftools_stderr,"\nand no usable plugins were found in %s", PLUGINPATH); #endif fprintf(bcftools_stderr,".\n\n"); } else { fprintf(bcftools_stderr, " in\n\tBCFTOOLS_PLUGINS=\"%s\".\n\n" "- Is the plugin path correct?\n\n" "- Run \"bcftools plugin -l\" or \"bcftools plugin -lvv\" for a list of available plugins.\n" "\n", getenv("BCFTOOLS_PLUGINS") ); } } static int load_plugin(args_t *args, const char *fname, int exit_on_error, plugin_t *plugin) { plugin->name = strdup(fname); plugin->handle = dlopen_plugin(args, fname); if ( !plugin->handle ) { if ( exit_on_error ) { print_plugin_usage_hint(fname); error("Could not load \"%s\".\n\n", fname); } return -1; } #ifdef _WIN32 plugin->init = (dl_init_f) GetProcAddress(plugin->handle, "init"); if ( plugin->init && args->verbose > 1 ) fprintf(bcftools_stderr,"\tinit .. ok\n"); plugin->run = (dl_run_f) GetProcAddress(plugin->handle, "run"); if ( plugin->run && args->verbose > 1 ) fprintf(bcftools_stderr,"\trun .. ok\n"); if ( !plugin->init && !plugin->run ) { if ( exit_on_error ) error("Could not initialize %s, neither run or init found \n", plugin->name); else if ( args->verbose > 1 ) fprintf(bcftools_stderr,"\tinit/run .. not found\n"); return -1; } plugin->version = (dl_version_f) GetProcAddress(plugin->handle, "version"); if ( !plugin->version ) { if ( exit_on_error ) error("Could not initialize %s: version string not found\n", plugin->name); else if ( args->verbose > 1 ) fprintf(bcftools_stderr,"\tversion .. not found\n"); return -1; } plugin->about = (dl_about_f) GetProcAddress(plugin->handle, "about"); if ( !plugin->about ) { if ( exit_on_error ) error("Could not initialize %s: about string not found\n", plugin->name); return -1; } plugin->usage = (dl_about_f) GetProcAddress(plugin->handle, "usage"); if ( !plugin->usage ) plugin->usage = plugin->about; if ( plugin->run ) return 0; plugin->process = (dl_process_f) GetProcAddress(plugin->handle, "process"); if ( !plugin->process ) { if ( exit_on_error ) error("Could not initialize %s: process method not found\n", plugin->name); return -1; } plugin->destroy = (dl_destroy_f) GetProcAddress(plugin->handle, "destroy"); if ( !plugin->destroy ) { if ( exit_on_error ) error("Could not initialize %s: destroy method not found\n", plugin->name); return -1; } #else dlerror(); plugin->init = (dl_init_f) dlsym(plugin->handle, "init"); char *ret = dlerror(); if ( ret ) plugin->init = NULL; else if ( args->verbose > 1 ) fprintf(bcftools_stderr,"\tinit .. ok\n"); plugin->run = (dl_run_f) dlsym(plugin->handle, "run"); ret = dlerror(); if ( ret ) plugin->run = NULL; else if ( args->verbose > 1 ) fprintf(bcftools_stderr,"\trun .. ok\n"); if ( !plugin->init && !plugin->run ) { if ( exit_on_error ) error("Could not initialize %s, neither run or init found \n", plugin->name); else if ( args->verbose > 1 ) fprintf(bcftools_stderr,"\tinit/run .. not found\n"); return -1; } plugin->version = (dl_version_f) dlsym(plugin->handle, "version"); ret = dlerror(); if ( ret ) { if ( exit_on_error ) error("Could not initialize %s, version string not found\n", plugin->name); else if ( args->verbose > 1 ) fprintf(bcftools_stderr,"\tversion .. not found\n"); return -1; } plugin->about = (dl_about_f) dlsym(plugin->handle, "about"); ret = dlerror(); if ( ret ) { if ( exit_on_error ) error("Could not initialize %s: %s\n", plugin->name, ret); return -1; } plugin->usage = (dl_about_f) dlsym(plugin->handle, "usage"); ret = dlerror(); if ( ret ) plugin->usage = plugin->about; if ( plugin->run ) return 0; plugin->process = (dl_process_f) dlsym(plugin->handle, "process"); ret = dlerror(); if ( ret ) { if ( exit_on_error ) error("Could not initialize %s: %s\n", plugin->name, ret); return -1; } plugin->destroy = (dl_destroy_f) dlsym(plugin->handle, "destroy"); ret = dlerror(); if ( ret ) { if ( exit_on_error ) error("Could not initialize %s: %s\n", plugin->name, ret); return -1; } #endif return 0; } static void check_version(args_t *args) { static int warned_bcftools = 0, warned_htslib = 0; const char *bver, *hver; args->plugin.version(&bver, &hver); if ( strcmp(bver,bcftools_version()) && !warned_bcftools ) { fprintf(bcftools_stderr,"WARNING: bcftools version mismatch .. bcftools at %s, the plugin \"%s\" at %s\n", bcftools_version(),args->plugin.name,bver); warned_bcftools = 1; } if ( strcmp(hver,hts_version()) && !warned_htslib ) { fprintf(bcftools_stderr,"WARNING: htslib version mismatch .. bcftools at %s, the plugin \"%s\" at %s\n", hts_version(),args->plugin.name,hver); warned_htslib = 1; } } static void init_plugin(args_t *args) { int ret = args->plugin.init(args->plugin.argc,args->plugin.argv,args->hdr,args->hdr_out); if ( ret<0 ) error("The plugin exited with an error.\n"); check_version(args); args->drop_header += ret; } static int cmp_plugin_name(const void *p1, const void *p2) { plugin_t *a = (plugin_t*) p1; plugin_t *b = (plugin_t*) p2; return strcmp(a->name,b->name); } // If args=NULL then returns the number of plugins available. Otherwise prints the // plugins on bcftools_stdout and returns 0 on success. static int list_plugins(args_t *args) { plugin_t *plugins = NULL; int nplugins = 0, mplugins = 0; int count_only = 0; args_t _args; if ( !args ) { memset(&_args,0,sizeof(_args)); args = &_args; args->nplugin_paths = -1; count_only = 1; } init_plugin_paths(args); kstring_t str = {0,0,0}; int plugin_ext_len = strlen(PLUGIN_EXT); int i; for (i=0; inplugin_paths; i++) { DIR *dp = opendir(args->plugin_paths[i]); if ( dp==NULL ) continue; struct dirent *ep; while ( (ep=readdir(dp)) ) { int len = strlen(ep->d_name); if ( strcasecmp(PLUGIN_EXT,ep->d_name+len-plugin_ext_len) ) continue; str.l = 0; ksprintf(&str,"%s/%s", args->plugin_paths[i],ep->d_name); hts_expand(plugin_t, nplugins+1, mplugins, plugins); if ( load_plugin(args, str.s, 0, &plugins[nplugins]) < 0 ) continue; nplugins++; str.l = 0; kputs(ep->d_name, &str); int l = str.l - 1; while ( l>=0 && str.s[l]!='.' ) l--; if ( l>=0 ) str.s[l] = 0; free(plugins[nplugins-1].name); plugins[nplugins-1].name = strdup(str.s); // use a short name } closedir(dp); } if ( count_only ) { free(str.s); return nplugins; } if ( nplugins ) { qsort(plugins, nplugins, sizeof(plugins[0]), cmp_plugin_name); for (i=0; iverbose ) fprintf(bcftools_stdout, "\n-- %s --\n%s", plugins[i].name, plugins[i].about()); else fprintf(bcftools_stdout, "%s\n", plugins[i].name); } if ( args->verbose ) fprintf(bcftools_stdout, "\n"); } else print_plugin_usage_hint(NULL); free(str.s); return nplugins ? 0 : 1; } int count_plugins(void) { return list_plugins(NULL); } static void init_data(args_t *args) { args->hdr = args->files->readers[0].header; args->hdr_out = bcf_hdr_dup(args->hdr); init_plugin(args); if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); if (args->record_cmd_line) bcf_hdr_append_version(args->hdr_out, args->argc, args->argv, "bcftools_plugin"); if ( !args->drop_header ) { char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno)); if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads); if ( bcf_hdr_write(args->out_fh, args->hdr_out)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); if ( init_index2(args->out_fh,args->hdr_out,args->output_fname, &args->index_fn, args->write_index)<0 ) error("Error: failed to initialise index for %s\n",args->output_fname); } } static void destroy_data(args_t *args) { free(args->plugin.name); if ( args->plugin.destroy ) args->plugin.destroy(); #ifdef _WIN32 FreeLibrary(args->plugin.handle); #else dlclose(args->plugin.handle); #endif if ( args->hdr_out ) bcf_hdr_destroy(args->hdr_out); if ( args->nplugin_paths>0 ) { int i; for (i=0; inplugin_paths; i++) free(args->plugin_paths[i]); free(args->plugin_paths); } if ( args->filter ) filter_destroy(args->filter); if (args->out_fh ) { if ( args->write_index ) { if ( bcf_idx_save(args->out_fh)<0 ) { if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"bcftools_stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname); } } static void usage(args_t *args) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: Run user defined plugin\n"); fprintf(bcftools_stderr, "Usage: bcftools plugin [OPTIONS] [-- PLUGIN_OPTIONS]\n"); fprintf(bcftools_stderr, " bcftools +name [OPTIONS] [-- PLUGIN_OPTIONS]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "VCF input options:\n"); fprintf(bcftools_stderr, " -e, --exclude EXPR Exclude sites for which the expression is true\n"); fprintf(bcftools_stderr, " -i, --include EXPR Select sites for which the expression is true\n"); fprintf(bcftools_stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(bcftools_stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(bcftools_stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(bcftools_stderr, "VCF output options:\n"); fprintf(bcftools_stderr, " --no-version Do not append version and command line to the header\n"); fprintf(bcftools_stderr, " -o, --output FILE Write output to a file [standard output]\n"); fprintf(bcftools_stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(bcftools_stderr, " --threads INTT Use multithreading with worker threads [0]\n"); fprintf(bcftools_stderr, "Plugin options:\n"); fprintf(bcftools_stderr, " -h, --help List plugin's options\n"); fprintf(bcftools_stderr, " -l, --list-plugins List available plugins. See BCFTOOLS_PLUGINS environment variable and man page for details\n"); fprintf(bcftools_stderr, " -v, --verbose Print verbose information, -vv increases verbosity\n"); fprintf(bcftools_stderr, " -V, --version Print version string and exit\n"); fprintf(bcftools_stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } static int is_verbose(int argc, char *argv[]) { int c, verbose = 0, opterr_ori = opterr; static struct option loptions[] = { {"verbose",no_argument,NULL,'v'}, {NULL,0,NULL,0} }; opterr = 0; while ((c = getopt_long(argc, argv, "-v",loptions,NULL)) >= 0) { switch (c) { case 'v': verbose++; break; case 1: default: break; } } opterr = opterr_ori; optind = 0; return verbose; } int main_plugin(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->output_fname = "-"; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->nplugin_paths = -1; args->clevel = -1; int regions_is_file = 0, targets_is_file = 0, usage_only = 0, version_only = 0; int regions_overlap = 1; int targets_overlap = 0; if ( argc==1 ) usage(args); char *plugin_name = NULL; if ( argv[1][0]!='-' ) { args->verbose = is_verbose(argc, argv); plugin_name = argv[1]; argc--; argv++; load_plugin(args, plugin_name, 1, &args->plugin); if ( args->plugin.run ) { check_version(args); int ret = args->plugin.run(argc, argv); destroy_data(args); free(args); return ret; } } static struct option loptions[] = { {"version",no_argument,NULL,'V'}, {"verbose",no_argument,NULL,'v'}, {"help",no_argument,NULL,'h'}, {"list-plugins",no_argument,NULL,'l'}, {"output",required_argument,NULL,'o'}, {"output-type",required_argument,NULL,'O'}, {"threads",required_argument,NULL,9}, {"include",required_argument,NULL,'i'}, {"exclude",required_argument,NULL,'e'}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,1}, {"targets",required_argument,NULL,'t'}, {"targets-file",required_argument,NULL,'T'}, {"targets-overlap",required_argument,NULL,2}, {"no-version",no_argument,NULL,8}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "h?o:O:r:R:t:T:li:e:vVW::",loptions,NULL)) >= 0) { switch (c) { case 'V': version_only = 1; break; case 'v': args->verbose++; break; case 'o': args->output_fname = optarg; break; case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } }; if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; targets_is_file = 1; break; case 'l': args->plist_only = 1; break; case 1 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 2 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 8 : args->record_cmd_line = 0; break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case '?': case 'h': usage_only = 1; break; default: error("Unknown argument: %s\n", optarg); } } if ( args->plist_only ) return list_plugins(args); if ( !plugin_name ) usage(args); if ( version_only ) { const char *bver, *hver; args->plugin.version(&bver, &hver); fprintf(bcftools_stdout, "bcftools %s using htslib %s\n", bcftools_version(), hts_version()); fprintf(bcftools_stdout, "plugin at %s using htslib %s\n\n", bver, hver); return 0; } if ( usage_only ) { if ( args->plugin.usage ) fprintf(bcftools_stderr,"%s",args->plugin.usage()); else fprintf(bcftools_stderr,"Usage: bcftools +%s [General Options] -- [Plugin Options]\n",plugin_name); return 0; } char *fname = NULL; if ( optind>=argc || (argv[optind][0]=='-' && argv[optind][1]) ) { args->plugin.argc = argc - optind + 1; args->plugin.argv = argv + optind - 1; if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else if ( optind>=argc ) usage(args); else { optind = 1; init_plugin(args); } } else { fname = argv[optind]; args->plugin.argc = argc - optind; args->plugin.argv = argv + optind; } optind = 0; args->files = bcf_sr_init(); if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); args->files->collapse |= COLLAPSE_SOME; } if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); init_data(args); while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = bcf_sr_get_line(args->files,0); if ( args->filter ) { int pass = filter_test(args->filter, line, NULL); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) continue; } line = args->plugin.process(line); if ( line ) { if ( line->errcode ) error("[E::main_plugin] Unchecked error (%d), exiting\n",line->errcode); if ( bcf_write1(args->out_fh, args->hdr_out, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); } } destroy_data(args); bcf_sr_destroy(args->files); free(args); return 0; } #else /* ENABLE_BCF_PLUGINS */ int main_plugin(int argc, char *argv[]) { fprintf(bcftools_stderr, "bcftools plugins are disabled. To use them, you will need to rebuild\n" "bcftools from the source distribution with plugins enabled.\n"); return 1; } #endif /* ENABLE_BCF_PLUGINS */ pysam-0.23.0/bcftools/vcfquery.c000066400000000000000000000457471475062545500166060ustar00rootroot00000000000000/* vcfquery.c -- Extracts fields from VCF/BCF file. Copyright (C) 2013-2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "filter.h" #include "convert.h" #include "smpl_ilist.h" // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 typedef struct { filter_t *filter; char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE uint8_t *smpl_pass; convert_t *convert; bcf_srs_t *files; bcf_hdr_t *header; int sample_is_file; char **argv, *format_str, *sample_list, *targets_list, *regions_list, *vcf_list, *fn_out; char *print_filtered; int argc, list_columns, print_header, allow_undef_tags, force_samples, force_newline; FILE *out; } args_t; static void destroy_list(char **list, int n) { int i; for (i=0; iheader = args->files->readers[0].header; int i, nsamples = 0, *samples = NULL; if ( args->sample_list && strcmp("-",args->sample_list) ) { for (i=0; ifiles->nreaders; i++) { // This tells htslib to subset samples directly when reading. Also the header is modified to // include only the requested samples int ret = bcf_hdr_set_samples(args->files->readers[i].header,args->sample_list,args->sample_is_file); if ( ret<0 ) error("Error parsing the sample list\n"); else if ( ret>0 && !args->force_samples ) error("Error: sample #%d not found in the header, user --force-samples to proceed anyway\n", ret); } int flags = SMPL_REORDER; smpl_ilist_t *ilist = smpl_ilist_init(args->files->readers[0].header, args->sample_list, args->sample_is_file, flags); nsamples = ilist->n; samples = (int*) malloc(sizeof(int)*nsamples); for (i=0; in; i++) samples[i] = ilist->idx[i]; smpl_ilist_destroy(ilist); } args->convert = convert_init(args->header, samples, nsamples, args->format_str); if ( args->force_newline ) convert_set_option(args->convert, force_newline, 1); convert_set_option(args->convert, subset_samples, &args->smpl_pass); if ( args->allow_undef_tags ) convert_set_option(args->convert, allow_undef_tags, 1); if ( args->print_header>1 ) convert_set_option(args->convert, no_hdr_indices, 1); free(samples); int max_unpack = convert_max_unpack(args->convert); if ( args->filter_str ) { args->filter = filter_init(args->header, args->filter_str); max_unpack |= filter_max_unpack(args->filter); } args->files->max_unpack = max_unpack; if ( !args->filter || args->print_filtered || !(filter_max_unpack(args->filter) & BCF_UN_FMT) ) convert_set_option(args->convert, header_samples, 1); if ( args->print_filtered ) convert_set_option(args->convert, print_filtered, args->print_filtered); } static void destroy_data(args_t *args) { convert_destroy(args->convert); if ( args->filter ) filter_destroy(args->filter); } static void query_vcf(args_t *args) { kstring_t str = {0,0,0}; if ( args->print_header ) { convert_header(args->convert,&str); if ( fwrite(str.s, str.l, 1, args->out)!=1 ) error("[%s] Error: cannot write to %s\n", __func__,args->fn_out?args->fn_out:"standard output"); } int i,max_convert_unpack = convert_max_unpack(args->convert); int max_filter_unpack = args->filter ? filter_max_unpack(args->filter) : 0; while ( bcf_sr_next_line(args->files) ) { if ( !bcf_sr_has_line(args->files,0) ) continue; bcf1_t *line = args->files->readers[0].buffer[0]; bcf_unpack(line, args->files->max_unpack); if ( args->filter ) { int pass = filter_test(args->filter, line, (const uint8_t**) &args->smpl_pass); if ( args->filter_logic & FLT_EXCLUDE ) { // This code addresses this problem: // -i can include a site but exclude a sample // -e exclude a site but include a sample if ( pass ) { if ( !args->smpl_pass ) continue; if ( !(max_convert_unpack & BCF_UN_FMT) && !(max_filter_unpack & BCF_UN_FMT) ) continue; pass = 0; for (i=0; in_sample; i++) { if ( args->smpl_pass[i] ) args->smpl_pass[i] = 0; else { args->smpl_pass[i] = 1; pass = 1; } } if ( !pass ) continue; } else if ( args->smpl_pass ) for (i=0; in_sample; i++) args->smpl_pass[i] = 1; } else if ( !pass ) continue; } str.l = 0; convert_line(args->convert, line, &str); if ( str.l && fwrite(str.s, str.l, 1, args->out)!=1 ) error("[%s] Error: cannot write to %s\n", __func__,args->fn_out?args->fn_out:"standard output"); } if ( str.m ) free(str.s); } static void list_columns(args_t *args) { int negate = 0; int i; bcf_sr_t *reader = &args->files->readers[0]; void *has_sample = NULL; if ( args->sample_list ) { if ( args->sample_list[0]=='^' ) negate = 1; has_sample = khash_str2int_init(); int i, nsmpl; char **smpl = hts_readlist(negate ? args->sample_list+1 : args->sample_list, args->sample_is_file, &nsmpl); if ( !smpl ) error("Error: failed to read %s\n", negate ? args->sample_list+1 : args->sample_list); for (i=0; iheader,BCF_DT_SAMPLE,smpl[i])<0 && !args->force_samples ) error("Error: sample #%d not found in the header, user --force-samples to proceed anyway\n", i+1); khash_str2int_inc(has_sample, smpl[i]); } free(smpl); } for (i=0; iheader); i++) { int skip = 0; if ( negate ) { if ( khash_str2int_has_key(has_sample, reader->header->samples[i]) ) skip = 1; } else if ( has_sample && !khash_str2int_has_key(has_sample, reader->header->samples[i]) ) skip = 1; if ( skip ) continue; printf("%s\n", reader->header->samples[i]); } if ( has_sample ) khash_str2int_destroy_free(has_sample); } static char **copy_header(bcf_hdr_t *hdr, char **src, int nsrc) { char **dst = (char**) malloc(sizeof(char*)*nsrc); int i; for (i=0; i [ [...]]\n"); fprintf(stderr, "\n"); fprintf(stderr, "Options:\n"); fprintf(stderr, " -e, --exclude EXPR Exclude sites for which the expression is true (see man page for details)\n"); fprintf(stderr, " --force-samples Only warn about unknown subset samples\n"); fprintf(stderr, " -F, --print-filtered STR Output STR for samples failing the -i/-e filtering expression\n"); fprintf(stderr, " -f, --format STRING See man page for details\n"); fprintf(stderr, " -H, --print-header Print header, -HH to omit column indices\n"); fprintf(stderr, " -i, --include EXPR Select sites for which the expression is true (see man page for details)\n"); fprintf(stderr, " -l, --list-samples Print the list of samples and exit\n"); fprintf(stderr, " -N, --disable-automatic-newline Disable automatic addition of newline character when not present\n"); fprintf(stderr, " -o, --output FILE Output file name [stdout]\n"); fprintf(stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " -s, --samples LIST List of samples to include\n"); fprintf(stderr, " -S, --samples-file FILE File of samples to include\n"); fprintf(stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(stderr, " -u, --allow-undef-tags Print \".\" for undefined tags\n"); fprintf(stderr, " -v, --vcf-list FILE Process multiple VCFs listed in the file\n"); fprintf(stderr, "\n"); fprintf(stderr, "Examples:\n"); fprintf(stderr, "\tbcftools query -f '%%CHROM\\t%%POS\\t%%REF\\t%%ALT[\\t%%SAMPLE=%%GT]\\n' file.vcf.gz\n"); fprintf(stderr, "\t# For more examples see http://samtools.github.io/bcftools/bcftools.html#query\n"); fprintf(stderr, "\n"); exit(1); } int main_vcfquery(int argc, char *argv[]) { int c, collapse = 0; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->force_newline = 1; int regions_is_file = 0, targets_is_file = 0; int regions_overlap = 1; int targets_overlap = 0; static struct option loptions[] = { {"help",0,0,'h'}, {"list-samples",0,0,'l'}, {"disable-automatic-newline",required_argument,NULL,'N'}, {"include",1,0,'i'}, {"exclude",1,0,'e'}, {"print-filtered",1,0,'F'}, {"format",1,0,'f'}, {"force-samples",0,0,3}, {"output-file",1,0,'o'}, {"output",1,0,'o'}, {"regions",1,0,'r'}, {"regions-file",1,0,'R'}, {"regions-overlap",required_argument,NULL,1}, {"targets",1,0,'t'}, {"targets-file",1,0,'T'}, {"targets-overlap",required_argument,NULL,2}, {"annots",1,0,'a'}, {"samples",1,0,'s'}, {"samples-file",1,0,'S'}, {"print-header",0,0,'H'}, {"collapse",1,0,'c'}, {"vcf-list",1,0,'v'}, {"allow-undef-tags",0,0,'u'}, {0,0,0,0} }; while ((c = getopt_long(argc, argv, "hlr:R:F:f:a:s:S:Ht:T:c:v:i:e:o:uN",loptions,NULL)) >= 0) { switch (c) { case 'o': args->fn_out = optarg; break; case 'F': args->print_filtered = optarg; break; case 'f': args->format_str = strdup(optarg); break; case 'N': args->force_newline = 0; break; case 'H': args->print_header++; break; case 'v': args->vcf_list = optarg; break; case 'c': error("The --collapse option is obsolete, pipe through `bcftools norm -c` instead.\n"); break; case 'a': { kstring_t str = {0,0,0}; kputs("%CHROM\t%POS\t%MASK\t%REF\t%ALT\t%", &str); char *p = optarg; while ( *p ) { if ( *p==',' ) kputs("\t%", &str); else kputc(*p, &str); p++; } kputc('\n', &str); args->format_str = str.s; break; } case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; targets_is_file = 1; break; case 'l': args->list_columns = 1; break; case 'u': args->allow_undef_tags = 1; break; case 's': args->sample_list = optarg; break; case 'S': args->sample_list = optarg; args->sample_is_file = 1; break; case 1 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 2 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 3 : args->force_samples = 1; break; case 'h': case '?': usage(); break; default: error("Unknown argument: %s\n", optarg); } } char *fname = NULL; if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; } else fname = argv[optind]; if ( args->list_columns ) { if ( !fname ) error("Missing the VCF file name\n"); args->files = bcf_sr_init(); if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); list_columns(args); bcf_sr_destroy(args->files); free(args); return 0; } if ( !args->format_str ) { if ( argc==1 && !fname ) usage(); error("Error: Missing the --format option\n"); } args->out = args->fn_out ? fopen(args->fn_out, "w") : stdout; if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno)); if ( !args->vcf_list ) { if ( !fname ) usage(); args->files = bcf_sr_init(); if ( optind+1 < argc ) args->files->require_index = 1; if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } while ( fname ) { if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); fname = ++optind < argc ? argv[optind] : NULL; } init_data(args); query_vcf(args); free(args->format_str); destroy_data(args); bcf_sr_destroy(args->files); if ( fclose(args->out)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fn_out); free(args); return 0; } // multiple VCFs int i, k, nfiles, prev_nsamples = 0; char **fnames, **prev_samples = NULL; fnames = hts_readlist(args->vcf_list, 1, &nfiles); if ( !fnames ) error("Error: failed to read %s\n", args->vcf_list); if ( !nfiles ) error("No files in %s?\n", args->vcf_list); for (i=0; ifiles = bcf_sr_init(); args->files->collapse = collapse; if ( args->regions_list && bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); if ( optind < argc ) args->files->require_index = 1; if ( args->targets_list ) { if ( bcf_sr_set_targets(args->files, args->targets_list,targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } if ( !bcf_sr_add_reader(args->files, fnames[i]) ) error("Failed to open %s: %s\n", fnames[i],bcf_sr_strerror(args->files->errnum)); for (k=optind; kfiles, argv[k]) ) error("Failed to open %s: %s\n", argv[k],bcf_sr_strerror(args->files->errnum)); init_data(args); if ( i==0 ) { prev_samples = copy_header(args->header, args->files->readers[0].header->samples, bcf_hdr_nsamples(args->files->readers[0].header)); prev_nsamples = bcf_hdr_nsamples(args->files->readers[0].header); } else { args->print_header = 0; if ( compare_header(args->header, args->files->readers[0].header->samples, bcf_hdr_nsamples(args->files->readers[0].header), prev_samples, prev_nsamples) ) error("Different samples in %s and %s\n", fnames[i-1],fnames[i]); } query_vcf(args); destroy_data(args); bcf_sr_destroy(args->files); } if ( fclose(args->out)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fn_out);; destroy_list(fnames, nfiles); destroy_list(prev_samples, prev_nsamples); free(args->format_str); free(args); return 0; } pysam-0.23.0/bcftools/vcfquery.c.pysam.c000066400000000000000000000464661475062545500201560ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfquery.c -- Extracts fields from VCF/BCF file. Copyright (C) 2013-2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "filter.h" #include "convert.h" #include "smpl_ilist.h" // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 typedef struct { filter_t *filter; char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE uint8_t *smpl_pass; convert_t *convert; bcf_srs_t *files; bcf_hdr_t *header; int sample_is_file; char **argv, *format_str, *sample_list, *targets_list, *regions_list, *vcf_list, *fn_out; char *print_filtered; int argc, list_columns, print_header, allow_undef_tags, force_samples, force_newline; FILE *out; } args_t; static void destroy_list(char **list, int n) { int i; for (i=0; iheader = args->files->readers[0].header; int i, nsamples = 0, *samples = NULL; if ( args->sample_list && strcmp("-",args->sample_list) ) { for (i=0; ifiles->nreaders; i++) { // This tells htslib to subset samples directly when reading. Also the header is modified to // include only the requested samples int ret = bcf_hdr_set_samples(args->files->readers[i].header,args->sample_list,args->sample_is_file); if ( ret<0 ) error("Error parsing the sample list\n"); else if ( ret>0 && !args->force_samples ) error("Error: sample #%d not found in the header, user --force-samples to proceed anyway\n", ret); } int flags = SMPL_REORDER; smpl_ilist_t *ilist = smpl_ilist_init(args->files->readers[0].header, args->sample_list, args->sample_is_file, flags); nsamples = ilist->n; samples = (int*) malloc(sizeof(int)*nsamples); for (i=0; in; i++) samples[i] = ilist->idx[i]; smpl_ilist_destroy(ilist); } args->convert = convert_init(args->header, samples, nsamples, args->format_str); if ( args->force_newline ) convert_set_option(args->convert, force_newline, 1); convert_set_option(args->convert, subset_samples, &args->smpl_pass); if ( args->allow_undef_tags ) convert_set_option(args->convert, allow_undef_tags, 1); if ( args->print_header>1 ) convert_set_option(args->convert, no_hdr_indices, 1); free(samples); int max_unpack = convert_max_unpack(args->convert); if ( args->filter_str ) { args->filter = filter_init(args->header, args->filter_str); max_unpack |= filter_max_unpack(args->filter); } args->files->max_unpack = max_unpack; if ( !args->filter || args->print_filtered || !(filter_max_unpack(args->filter) & BCF_UN_FMT) ) convert_set_option(args->convert, header_samples, 1); if ( args->print_filtered ) convert_set_option(args->convert, print_filtered, args->print_filtered); } static void destroy_data(args_t *args) { convert_destroy(args->convert); if ( args->filter ) filter_destroy(args->filter); } static void query_vcf(args_t *args) { kstring_t str = {0,0,0}; if ( args->print_header ) { convert_header(args->convert,&str); if ( fwrite(str.s, str.l, 1, args->out)!=1 ) error("[%s] Error: cannot write to %s\n", __func__,args->fn_out?args->fn_out:"standard output"); } int i,max_convert_unpack = convert_max_unpack(args->convert); int max_filter_unpack = args->filter ? filter_max_unpack(args->filter) : 0; while ( bcf_sr_next_line(args->files) ) { if ( !bcf_sr_has_line(args->files,0) ) continue; bcf1_t *line = args->files->readers[0].buffer[0]; bcf_unpack(line, args->files->max_unpack); if ( args->filter ) { int pass = filter_test(args->filter, line, (const uint8_t**) &args->smpl_pass); if ( args->filter_logic & FLT_EXCLUDE ) { // This code addresses this problem: // -i can include a site but exclude a sample // -e exclude a site but include a sample if ( pass ) { if ( !args->smpl_pass ) continue; if ( !(max_convert_unpack & BCF_UN_FMT) && !(max_filter_unpack & BCF_UN_FMT) ) continue; pass = 0; for (i=0; in_sample; i++) { if ( args->smpl_pass[i] ) args->smpl_pass[i] = 0; else { args->smpl_pass[i] = 1; pass = 1; } } if ( !pass ) continue; } else if ( args->smpl_pass ) for (i=0; in_sample; i++) args->smpl_pass[i] = 1; } else if ( !pass ) continue; } str.l = 0; convert_line(args->convert, line, &str); if ( str.l && fwrite(str.s, str.l, 1, args->out)!=1 ) error("[%s] Error: cannot write to %s\n", __func__,args->fn_out?args->fn_out:"standard output"); } if ( str.m ) free(str.s); } static void list_columns(args_t *args) { int negate = 0; int i; bcf_sr_t *reader = &args->files->readers[0]; void *has_sample = NULL; if ( args->sample_list ) { if ( args->sample_list[0]=='^' ) negate = 1; has_sample = khash_str2int_init(); int i, nsmpl; char **smpl = hts_readlist(negate ? args->sample_list+1 : args->sample_list, args->sample_is_file, &nsmpl); if ( !smpl ) error("Error: failed to read %s\n", negate ? args->sample_list+1 : args->sample_list); for (i=0; iheader,BCF_DT_SAMPLE,smpl[i])<0 && !args->force_samples ) error("Error: sample #%d not found in the header, user --force-samples to proceed anyway\n", i+1); khash_str2int_inc(has_sample, smpl[i]); } free(smpl); } for (i=0; iheader); i++) { int skip = 0; if ( negate ) { if ( khash_str2int_has_key(has_sample, reader->header->samples[i]) ) skip = 1; } else if ( has_sample && !khash_str2int_has_key(has_sample, reader->header->samples[i]) ) skip = 1; if ( skip ) continue; fprintf(bcftools_stdout, "%s\n", reader->header->samples[i]); } if ( has_sample ) khash_str2int_destroy_free(has_sample); } static char **copy_header(bcf_hdr_t *hdr, char **src, int nsrc) { char **dst = (char**) malloc(sizeof(char*)*nsrc); int i; for (i=0; i [ [...]]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Options:\n"); fprintf(bcftools_stderr, " -e, --exclude EXPR Exclude sites for which the expression is true (see man page for details)\n"); fprintf(bcftools_stderr, " --force-samples Only warn about unknown subset samples\n"); fprintf(bcftools_stderr, " -F, --print-filtered STR Output STR for samples failing the -i/-e filtering expression\n"); fprintf(bcftools_stderr, " -f, --format STRING See man page for details\n"); fprintf(bcftools_stderr, " -H, --print-header Print header, -HH to omit column indices\n"); fprintf(bcftools_stderr, " -i, --include EXPR Select sites for which the expression is true (see man page for details)\n"); fprintf(bcftools_stderr, " -l, --list-samples Print the list of samples and exit\n"); fprintf(bcftools_stderr, " -N, --disable-automatic-newline Disable automatic addition of newline character when not present\n"); fprintf(bcftools_stderr, " -o, --output FILE Output file name [bcftools_stdout]\n"); fprintf(bcftools_stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(bcftools_stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(bcftools_stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " -s, --samples LIST List of samples to include\n"); fprintf(bcftools_stderr, " -S, --samples-file FILE File of samples to include\n"); fprintf(bcftools_stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(bcftools_stderr, " -u, --allow-undef-tags Print \".\" for undefined tags\n"); fprintf(bcftools_stderr, " -v, --vcf-list FILE Process multiple VCFs listed in the file\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Examples:\n"); fprintf(bcftools_stderr, "\tbcftools query -f '%%CHROM\\t%%POS\\t%%REF\\t%%ALT[\\t%%SAMPLE=%%GT]\\n' file.vcf.gz\n"); fprintf(bcftools_stderr, "\t# For more examples see http://samtools.github.io/bcftools/bcftools.html#query\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int main_vcfquery(int argc, char *argv[]) { int c, collapse = 0; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->force_newline = 1; int regions_is_file = 0, targets_is_file = 0; int regions_overlap = 1; int targets_overlap = 0; static struct option loptions[] = { {"help",0,0,'h'}, {"list-samples",0,0,'l'}, {"disable-automatic-newline",required_argument,NULL,'N'}, {"include",1,0,'i'}, {"exclude",1,0,'e'}, {"print-filtered",1,0,'F'}, {"format",1,0,'f'}, {"force-samples",0,0,3}, {"output-file",1,0,'o'}, {"output",1,0,'o'}, {"regions",1,0,'r'}, {"regions-file",1,0,'R'}, {"regions-overlap",required_argument,NULL,1}, {"targets",1,0,'t'}, {"targets-file",1,0,'T'}, {"targets-overlap",required_argument,NULL,2}, {"annots",1,0,'a'}, {"samples",1,0,'s'}, {"samples-file",1,0,'S'}, {"print-header",0,0,'H'}, {"collapse",1,0,'c'}, {"vcf-list",1,0,'v'}, {"allow-undef-tags",0,0,'u'}, {0,0,0,0} }; while ((c = getopt_long(argc, argv, "hlr:R:F:f:a:s:S:Ht:T:c:v:i:e:o:uN",loptions,NULL)) >= 0) { switch (c) { case 'o': args->fn_out = optarg; break; case 'F': args->print_filtered = optarg; break; case 'f': args->format_str = strdup(optarg); break; case 'N': args->force_newline = 0; break; case 'H': args->print_header++; break; case 'v': args->vcf_list = optarg; break; case 'c': error("The --collapse option is obsolete, pipe through `bcftools norm -c` instead.\n"); break; case 'a': { kstring_t str = {0,0,0}; kputs("%CHROM\t%POS\t%MASK\t%REF\t%ALT\t%", &str); char *p = optarg; while ( *p ) { if ( *p==',' ) kputs("\t%", &str); else kputc(*p, &str); p++; } kputc('\n', &str); args->format_str = str.s; break; } case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; targets_is_file = 1; break; case 'l': args->list_columns = 1; break; case 'u': args->allow_undef_tags = 1; break; case 's': args->sample_list = optarg; break; case 'S': args->sample_list = optarg; args->sample_is_file = 1; break; case 1 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 2 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 3 : args->force_samples = 1; break; case 'h': case '?': usage(); break; default: error("Unknown argument: %s\n", optarg); } } char *fname = NULL; if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; } else fname = argv[optind]; if ( args->list_columns ) { if ( !fname ) error("Missing the VCF file name\n"); args->files = bcf_sr_init(); if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); list_columns(args); bcf_sr_destroy(args->files); free(args); return 0; } if ( !args->format_str ) { if ( argc==1 && !fname ) usage(); error("Error: Missing the --format option\n"); } args->out = args->fn_out ? fopen(args->fn_out, "w") : bcftools_stdout; if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno)); if ( !args->vcf_list ) { if ( !fname ) usage(); args->files = bcf_sr_init(); if ( optind+1 < argc ) args->files->require_index = 1; if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } while ( fname ) { if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); fname = ++optind < argc ? argv[optind] : NULL; } init_data(args); query_vcf(args); free(args->format_str); destroy_data(args); bcf_sr_destroy(args->files); if ( fclose(args->out)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fn_out); free(args); return 0; } // multiple VCFs int i, k, nfiles, prev_nsamples = 0; char **fnames, **prev_samples = NULL; fnames = hts_readlist(args->vcf_list, 1, &nfiles); if ( !fnames ) error("Error: failed to read %s\n", args->vcf_list); if ( !nfiles ) error("No files in %s?\n", args->vcf_list); for (i=0; ifiles = bcf_sr_init(); args->files->collapse = collapse; if ( args->regions_list && bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); if ( optind < argc ) args->files->require_index = 1; if ( args->targets_list ) { if ( bcf_sr_set_targets(args->files, args->targets_list,targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } if ( !bcf_sr_add_reader(args->files, fnames[i]) ) error("Failed to open %s: %s\n", fnames[i],bcf_sr_strerror(args->files->errnum)); for (k=optind; kfiles, argv[k]) ) error("Failed to open %s: %s\n", argv[k],bcf_sr_strerror(args->files->errnum)); init_data(args); if ( i==0 ) { prev_samples = copy_header(args->header, args->files->readers[0].header->samples, bcf_hdr_nsamples(args->files->readers[0].header)); prev_nsamples = bcf_hdr_nsamples(args->files->readers[0].header); } else { args->print_header = 0; if ( compare_header(args->header, args->files->readers[0].header->samples, bcf_hdr_nsamples(args->files->readers[0].header), prev_samples, prev_nsamples) ) error("Different samples in %s and %s\n", fnames[i-1],fnames[i]); } query_vcf(args); destroy_data(args); bcf_sr_destroy(args->files); } if ( fclose(args->out)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fn_out);; destroy_list(fnames, nfiles); destroy_list(prev_samples, prev_nsamples); free(args->format_str); free(args); return 0; } pysam-0.23.0/bcftools/vcfroh.c000066400000000000000000001436721475062545500162250ustar00rootroot00000000000000/* vcfroh.c -- HMM model for detecting runs of autozygosity. Copyright (C) 2013-2022 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "HMM.h" #include "smpl_ilist.h" #include "filter.h" #define STATE_HW 0 // normal state, follows Hardy-Weinberg allele frequencies #define STATE_AZ 1 // autozygous state #define OUTPUT_ST (1<<1) #define OUTPUT_RG (1<<2) #define OUTPUT_GZ (1<<3) // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 /** Genetic map */ typedef struct { int pos; double rate; } genmap_t; /** HMM data for each sample */ typedef struct { double *eprob; // emission probs [2*nsites,msites] uint32_t *sites; // positions [nsites,msites] int nsites, msites; int igenmap; // current position in genmap int nused; // some stats to detect if things didn't go wrong int nrid, *rid, *rid_off; // for viterbi training, keep all chromosomes void *snapshot; // hmm snapshot struct { uint32_t beg,end,nqual; double qual; int rid, state; } rg; } smpl_t; typedef struct _args_t { bcf_srs_t *files; bcf_hdr_t *hdr; double t2AZ, t2HW; // P(AZ|HW) and P(HW|AZ) parameters double unseen_PL, dflt_AF; char *genmap_fname; genmap_t *genmap; int ngenmap, mgenmap, igenmap; double rec_rate; // constant recombination rate if > 0 hmm_t *hmm; double baum_welch_th; int nrids, *rids, *rid_offs; // multiple chroms with vi_training int nbuf_max, nbuf_olap; float *AFs; int32_t *itmp; int mAFs, nitmp, mitmp, pl_hdr_id, gt_hdr_id; double pl2p[256], *pdg; int32_t skip_rid, prev_rid, prev_pos; int ntot; // some stats to detect if things didn't go wrong int nno_af; // number of sites rejected because AF could not be determined int nfiltered; // .. because of filters int nno_alt, nmultiallelic, ndup; smpl_t *smpl; // HMM data for each sample smpl_ilist_t *af_smpl; // list of samples to estimate AF from (--estimate-AF) smpl_ilist_t *roh_smpl; // list of samples to analyze (--samples, --samples-file) char *estimate_AF; // list of samples for AF estimate and query sample int af_from_PL; // estimate AF from FMT/PL rather than FMT/GT char **argv, *targets_list, *regions_list, *af_fname, *af_tag, *samples, *buffer_size, *output_fname; int argc, fake_PLs, snps_only, vi_training, samples_is_file, output_type, skip_homref, n_threads; int include_noalt_sites; BGZF *out; kstring_t str; int filter_logic; filter_t *filter; char *filter_str; } args_t; void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob); void set_tprob_rrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob); void *smalloc(size_t size) { void *mem = malloc(size); if ( !mem ) error("malloc: Could not allocate %d bytes\n", (int)size); return mem; } static inline int max255(int i) { return i < 256 ? i : 255; } static void init_data(args_t *args) { int i; args->prev_rid = args->skip_rid = -1; args->hdr = args->files->readers[0].header; if ( !bcf_hdr_nsamples(args->hdr) ) error("No samples in the VCF?\n"); if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); if ( !args->fake_PLs ) { args->pl_hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "PL"); if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,args->pl_hdr_id) ) error("Error: The FORMAT/PL tag not found in the header, consider running with -G\n"); if ( bcf_hdr_id2type(args->hdr,BCF_HL_FMT,args->pl_hdr_id)!=BCF_HT_INT ) error("Error: The FORMAT/PL tag not defined as Integer in the header\n"); } if ( args->estimate_AF ) { if ( !strncmp("GT,",args->estimate_AF,3) ) args->estimate_AF += 3; else if ( !strncmp("PL,",args->estimate_AF,3) ) { args->estimate_AF += 3; args->af_from_PL = 1; } if ( strcmp("-",args->estimate_AF) ) args->af_smpl = smpl_ilist_init(args->hdr, args->estimate_AF, 1, SMPL_NONE|SMPL_VERBOSE); } if ( args->estimate_AF || args->fake_PLs ) { if ( args->af_from_PL ) { args->pl_hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "PL"); if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,args->pl_hdr_id) ) error("Error: The FORMAT/PL tag not found in the header\n"); } else { args->gt_hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "GT"); if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,args->gt_hdr_id) ) error("Error: The FORMAT/GT tag not found in the header\n"); } } if ( args->fake_PLs ) { args->gt_hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "GT"); if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,args->gt_hdr_id) ) error("Error: The FORMAT/GT tag not found in the header\n"); } args->roh_smpl = smpl_ilist_init(args->hdr, args->samples, args->samples_is_file, SMPL_NONE|SMPL_VERBOSE); if ( args->samples ) { // we may be able to subset to a few samples, for a text VCF this can be a major speedup if ( (bcf_sr_get_reader(args->files,0))->file->format.format==vcf ) { kstring_t str = {0,0,0}; smpl_ilist_t *tmp = args->roh_smpl, *rmme = NULL; if ( args->af_smpl ) { for (i=0; iroh_smpl->n; i++) { if ( str.l ) kputc(',', &str); kputs(args->hdr->samples[args->roh_smpl->idx[i]], &str); } for (i=0; iaf_smpl->n; i++) { kputc(',', &str); kputs(args->hdr->samples[args->af_smpl->idx[i]], &str); } rmme = tmp = smpl_ilist_init(args->hdr, str.s, 0, SMPL_NONE); } if ( tmp->n < bcf_hdr_nsamples(args->hdr) ) { str.l = 0; for (i=0; in; i++) { if ( str.l ) kputc(',', &str); kputs(args->hdr->samples[tmp->idx[i]], &str); } int ret = bcf_hdr_set_samples(args->hdr, str.s, 0); if ( ret<0 ) error("Error parsing the list of samples: %s\n", str.s); else if ( ret>0 ) error("The %d-th sample not found in the VCF: %s\n", ret,str.s); // update sample ids smpl_ilist_destroy(args->roh_smpl); args->roh_smpl = smpl_ilist_init(args->hdr, args->samples, args->samples_is_file, SMPL_NONE); if ( args->af_smpl ) { smpl_ilist_destroy(args->af_smpl); args->af_smpl = smpl_ilist_init(args->hdr, args->estimate_AF, 1, SMPL_NONE); } } free(str.s); if ( rmme ) smpl_ilist_destroy(rmme); } } // check whether all samples are in this list. If so, the lookup will not be needed if ( args->af_smpl && args->af_smpl->n == bcf_hdr_nsamples(args->hdr) ) { // all samples are in this list smpl_ilist_destroy(args->af_smpl); args->af_smpl = NULL; } if ( args->buffer_size ) { args->nbuf_olap = -1; char *end; double tmp = strtod(args->buffer_size,&end); if ( *end ) { if ( *end!=',') error("Could not parse: --buffer-size %s\n", args->buffer_size); args->nbuf_olap = strtol(end+1,&end,10); if ( *end || args->nbuf_olap<0 ) error("Could not parse: --buffer-size %s\n", args->buffer_size); } if ( tmp<0 ) args->nbuf_max = fabs(tmp)*1e6/(4+8*2)/args->roh_smpl->n; else args->nbuf_max = tmp; if ( args->nbuf_olap<0 ) args->nbuf_olap = args->nbuf_max*0.01; } fprintf(stderr,"Number of target samples: %d\n", args->roh_smpl->n); fprintf(stderr,"Number of --estimate-AF samples: %d\n", args->af_smpl ? args->af_smpl->n : (args->estimate_AF ? bcf_hdr_nsamples(args->hdr) : 0)); fprintf(stderr,"Number of sites in the buffer/overlap: "); if ( args->nbuf_max ) fprintf(stderr,"%d/%d\n", args->nbuf_max,args->nbuf_olap); else fprintf(stderr,"unlimited\n"); args->smpl = (smpl_t*) calloc(args->roh_smpl->n,sizeof(smpl_t)); for (i=0; i<256; i++) args->pl2p[i] = pow(10., -i/10.); // Init transition matrix and HMM double tprob[4]; MAT(tprob,2,STATE_HW,STATE_HW) = 1 - args->t2AZ; MAT(tprob,2,STATE_HW,STATE_AZ) = args->t2HW; MAT(tprob,2,STATE_AZ,STATE_HW) = args->t2AZ; MAT(tprob,2,STATE_AZ,STATE_AZ) = 1 - args->t2HW; args->hmm = hmm_init(2, tprob, 10000); if ( args->genmap_fname ) hmm_set_tprob_func(args->hmm, set_tprob_genmap, args); else if ( args->rec_rate > 0 ) hmm_set_tprob_func(args->hmm, set_tprob_rrate, args); args->out = bgzf_open(strcmp("stdout",args->output_fname)?args->output_fname:"-", args->output_type&OUTPUT_GZ ? "wg" : "wu"); if ( !args->out ) error("Failed to open %s: %s\n", args->output_fname, strerror(errno)); // print header args->str.l = 0; ksprintf(&args->str, "# This file was produced by: bcftools roh(%s+htslib-%s)\n", bcftools_version(),hts_version()); ksprintf(&args->str, "# The command line was:\tbcftools %s", args->argv[0]); for (i=1; iargc; i++) ksprintf(&args->str, " %s",args->argv[i]); ksprintf(&args->str, "\n#\n"); if ( args->output_type & OUTPUT_RG ) { i = 2; ksprintf(&args->str, "# RG"); ksprintf(&args->str, "\t[%d]Sample", i++); ksprintf(&args->str, "\t[%d]Chromosome", i++); ksprintf(&args->str, "\t[%d]Start", i++); ksprintf(&args->str, "\t[%d]End", i++); ksprintf(&args->str, "\t[%d]Length (bp)", i++); ksprintf(&args->str, "\t[%d]Number of markers", i++); ksprintf(&args->str, "\t[%d]Quality (average fwd-bwd phred score)", i++); ksprintf(&args->str, "\n"); } if ( args->output_type & OUTPUT_ST ) { i = 2; ksprintf(&args->str, "# ST"); ksprintf(&args->str, "\t[%d]Sample", i++); ksprintf(&args->str, "\t[%d]Chromosome", i++); ksprintf(&args->str, "\t[%d]Position", i++); ksprintf(&args->str, "\t[%d]State (0:HW, 1:AZ)", i++); ksprintf(&args->str, "\t[%d]Quality (fwd-bwd phred score)", i++); ksprintf(&args->str, "\n"); } if ( args->vi_training) { i = 2; ksprintf(&args->str, "# VT, Viterbi Training"); ksprintf(&args->str, "\t[%d]Sample", i++); ksprintf(&args->str, "\t[%d]Iteration", i++); ksprintf(&args->str, "\t[%d]dAZ", i++); ksprintf(&args->str, "\t[%d]dHW", i++); ksprintf(&args->str, "\t[%d]1 - P(HW|HW)", i++); ksprintf(&args->str, "\t[%d]P(AZ|HW)", i++); ksprintf(&args->str, "\t[%d]1 - P(AZ|AZ)", i++); ksprintf(&args->str, "\t[%d]P(HW|AZ)", i++); ksprintf(&args->str, "\n"); } if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno)); } static void destroy_data(args_t *args) { if ( args->filter ) filter_destroy(args->filter); if ( bgzf_close(args->out)!=0 ) error("Error: close failed .. %s\n", args->output_fname); int i; for (i=0; iroh_smpl->n; i++) { free(args->smpl[i].eprob); free(args->smpl[i].sites); free(args->smpl[i].rid); free(args->smpl[i].rid_off); free(args->smpl[i].snapshot); } free(args->str.s); free(args->smpl); if ( args->af_smpl ) smpl_ilist_destroy(args->af_smpl); smpl_ilist_destroy(args->roh_smpl); free(args->rids); free(args->rid_offs); hmm_destroy(args->hmm); bcf_sr_destroy(args->files); free(args->AFs); free(args->pdg); free(args->genmap); free(args->itmp); free(args->samples); } static int load_genmap(args_t *args, const char *chr) { if ( !args->genmap_fname ) { args->ngenmap = 0; return 0; } kstring_t str = {0,0,0}; char *fname = strstr(args->genmap_fname,"{CHROM}"); if ( fname ) { kputsn(args->genmap_fname, fname - args->genmap_fname, &str); kputs(chr, &str); kputs(fname+7,&str); fname = str.s; } else fname = args->genmap_fname; htsFile *fp = hts_open(fname, "rb"); if ( !fp ) { args->ngenmap = 0; return -1; } hts_getline(fp, KS_SEP_LINE, &str); if ( strcmp(str.s,"position COMBINED_rate(cM/Mb) Genetic_Map(cM)") ) error("Unexpected header in %s, found:\n\t[%s], but expected:\n\t[position COMBINED_rate(cM/Mb) Genetic_Map(cM)]\n", fname, str.s); args->ngenmap = args->igenmap = 0; while ( hts_getline(fp, KS_SEP_LINE, &str) > 0 ) { args->ngenmap++; hts_expand(genmap_t,args->ngenmap,args->mgenmap,args->genmap); genmap_t *gm = &args->genmap[args->ngenmap-1]; // position, convert to 0-based char *tmp, *end; gm->pos = strtol(str.s, &tmp, 10); if ( str.s==tmp ) error("Could not parse %s: %s\n", fname, str.s); gm->pos -= 1; // skip second column tmp++; while ( *tmp && !isspace(*tmp) ) tmp++; // read the genetic map in cM, scale from % to likelihood gm->rate = strtod(tmp+1, &end); if ( tmp+1==end ) error("Could not parse %s: %s\n", fname, str.s); gm->rate *= 0.01; } if ( !args->ngenmap ) error("Genetic map empty?\n"); if ( hts_close(fp) ) error("Close failed\n"); free(str.s); return 0; } static double get_genmap_rate(args_t *args, int start, int end) { // position i to be equal to or smaller than start int i = args->igenmap; if ( args->genmap[i].pos > start ) { while ( i>0 && args->genmap[i].pos > start ) i--; } else { while ( i+1ngenmap && args->genmap[i+1].pos < start ) i++; } // position j to be equal or larger than end int j = i; while ( j+1ngenmap && args->genmap[j].pos < end ) j++; if ( i==j ) { args->igenmap = i; return 0; } if ( start < args->genmap[i].pos ) start = args->genmap[i].pos; if ( end > args->genmap[j].pos ) end = args->genmap[j].pos; double rate = (args->genmap[j].rate - args->genmap[i].rate)/(args->genmap[j].pos - args->genmap[i].pos) * (end-start); args->igenmap = j; return rate; } void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob) { args_t *args = (args_t*) data; double ci = get_genmap_rate(args, prev_pos, pos); if ( args->rec_rate ) ci *= args->rec_rate; if ( ci > 1 ) ci = 1; MAT(tprob,2,STATE_HW,STATE_AZ) *= ci; MAT(tprob,2,STATE_AZ,STATE_HW) *= ci; MAT(tprob,2,STATE_AZ,STATE_AZ) = 1 - MAT(tprob,2,STATE_HW,STATE_AZ); MAT(tprob,2,STATE_HW,STATE_HW) = 1 - MAT(tprob,2,STATE_AZ,STATE_HW); } void set_tprob_rrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob) { args_t *args = (args_t*) data; double ci = (pos - prev_pos) * args->rec_rate; if ( ci > 1 ) ci = 1; MAT(tprob,2,STATE_HW,STATE_AZ) *= ci; MAT(tprob,2,STATE_AZ,STATE_HW) *= ci; MAT(tprob,2,STATE_AZ,STATE_AZ) = 1 - MAT(tprob,2,STATE_HW,STATE_AZ); MAT(tprob,2,STATE_HW,STATE_HW) = 1 - MAT(tprob,2,STATE_AZ,STATE_HW); } /** * This function implements the HMM model: * D = Data, AZ = autozygosity, HW = Hardy-Weinberg (non-autozygosity), * f = non-ref allele frequency * * Emission probabilities: * oAZ = P_i(D|AZ) = (1-f)*P(D|RR) + f*P(D|AA) * oHW = P_i(D|HW) = (1-f)^2 * P(D|RR) + f^2 * P(D|AA) + 2*f*(1-f)*P(D|RA) * * Transition probabilities: * tAZ = P(AZ|HW) .. parameter * tHW = P(HW|AZ) .. parameter * * ci = P_i(C) .. probability of cross-over at site i, from genetic map * * AZi = P_i(AZ) .. probability of site i being AZ/non-AZ, scaled so that AZi+HWi = 1 * HWi = P_i(HW) * * P_i(AZ|HW) = P(AZ|HW) * ci * HW{i-1} = tAZ * ci * (1 - AZ{i-1}) * P_i(HW|AZ) = P(HW|AZ) * ci * AZ{i-1} = tHW * ci * AZ{i-1} * P_i(AZ|AZ) = 1 - P_i(HW|AZ) * P_i(HW|HW) = 1 - P_i(AZ|HW) * */ static void flush_viterbi(args_t *args, int ismpl) { smpl_t *smpl = &args->smpl[ismpl]; if ( !smpl->nsites ) return; const char *name = args->hdr->samples[ args->roh_smpl->idx[ismpl] ]; int i,j,k; if ( !args->vi_training ) // single viterbi pass { hmm_restore(args->hmm, smpl->snapshot); int end = (args->nbuf_max && smpl->nsites >= args->nbuf_max && smpl->nsites > args->nbuf_olap) ? smpl->nsites - args->nbuf_olap : smpl->nsites; if ( end < smpl->nsites ) smpl->snapshot = hmm_snapshot(args->hmm, smpl->snapshot, smpl->sites[smpl->nsites - args->nbuf_olap - 1]); args->igenmap = smpl->igenmap; hmm_run_viterbi(args->hmm, smpl->nsites, smpl->eprob, smpl->sites); hmm_run_fwd_bwd(args->hmm, smpl->nsites, smpl->eprob, smpl->sites); double *fwd = hmm_get_fwd_bwd_prob(args->hmm); const char *chr = bcf_hdr_id2name(args->hdr,args->prev_rid); uint8_t *vpath = hmm_get_viterbi_path(args->hmm); for (i=0; ioutput_type & OUTPUT_ST ) { args->str.l = 0; ksprintf(&args->str, "ST\t%s\t%s\t%d\t%d\t%.1f\n", name,chr,smpl->sites[i]+1, state, qual); if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno)); } if ( args->output_type & OUTPUT_RG ) { if ( state!=smpl->rg.state ) { if ( !state ) // the region ends, flush { args->str.l = 0; ksprintf(&args->str, "RG\t%s\t%s\t%d\t%d\t%d\t%d\t%.1f\n",name,bcf_hdr_id2name(args->hdr,smpl->rg.rid), smpl->rg.beg+1,smpl->rg.end+1,smpl->rg.end-smpl->rg.beg+1,smpl->rg.nqual,smpl->rg.qual/smpl->rg.nqual); if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno)); smpl->rg.state = 0; } else { smpl->rg.state = 1; smpl->rg.beg = smpl->sites[i]; smpl->rg.end = smpl->sites[i]; smpl->rg.rid = args->prev_rid; smpl->rg.qual = qual; smpl->rg.nqual = 1; } } else if ( state ) { smpl->rg.nqual++; smpl->rg.qual += qual; smpl->rg.end = smpl->sites[i]; } } } if ( end < smpl->nsites ) { end = smpl->nsites - args->nbuf_olap; memmove(smpl->sites, smpl->sites + end, sizeof(*smpl->sites)*args->nbuf_olap); memmove(smpl->eprob, smpl->eprob + end*2, sizeof(*smpl->eprob)*args->nbuf_olap*2); smpl->nsites = args->nbuf_olap; smpl->igenmap = args->igenmap; } else { smpl->nsites = 0; smpl->igenmap = 0; if ( smpl->rg.state ) { args->str.l = 0; ksprintf(&args->str, "RG\t%s\t%s\t%d\t%d\t%d\t%d\t%.1f\n",name,bcf_hdr_id2name(args->hdr,smpl->rg.rid), smpl->rg.beg+1,smpl->rg.end+1,smpl->rg.end-smpl->rg.beg+1,smpl->rg.nqual,smpl->rg.qual/smpl->rg.nqual); if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno)); smpl->rg.state = 0; } } return; } // viterbi training, multiple chromosomes double t2az_prev, t2hw_prev; double deltaz, delthw; double *tprob_arr = hmm_get_tprob(args->hmm); MAT(tprob_arr,2,STATE_HW,STATE_HW) = 1 - args->t2AZ; MAT(tprob_arr,2,STATE_HW,STATE_AZ) = args->t2HW; MAT(tprob_arr,2,STATE_AZ,STATE_HW) = args->t2AZ; MAT(tprob_arr,2,STATE_AZ,STATE_AZ) = 1 - args->t2HW; hmm_set_tprob(args->hmm, tprob_arr, 10000); int niter = 0; do { tprob_arr = hmm_get_tprob(args->hmm); t2az_prev = MAT(tprob_arr,2,STATE_AZ,STATE_HW); //args->t2AZ; t2hw_prev = MAT(tprob_arr,2,STATE_HW,STATE_AZ); //args->t2HW; double tprob_new[] = { 0,0,0,0 }; for (i=0; inrid; i++) { int ioff = smpl->rid_off[i]; int nsites = (i+1==smpl->nrid ? smpl->nsites : smpl->rid_off[i+1]) - ioff; args->igenmap = 0; tprob_arr = hmm_run_baum_welch(args->hmm, nsites, smpl->eprob+ioff*2, smpl->sites+ioff); for (j=0; j<2; j++) for (k=0; k<2; k++) MAT(tprob_new,2,j,k) += MAT(tprob_arr,2,j,k); } for (j=0; j<2; j++) for (k=0; k<2; k++) MAT(tprob_new,2,j,k) /= smpl->nrid; hmm_set_tprob(args->hmm, tprob_new, 10000); deltaz = fabs(MAT(tprob_new,2,STATE_AZ,STATE_HW)-t2az_prev); delthw = fabs(MAT(tprob_new,2,STATE_HW,STATE_AZ)-t2hw_prev); niter++; args->str.l = 0; ksprintf(&args->str, "VT\t%s\t%d\t%e\t%e\t%e\t%e\t%e\t%e\n", name,niter,deltaz,delthw, 1-MAT(tprob_new,2,STATE_HW,STATE_HW),MAT(tprob_new,2,STATE_AZ,STATE_HW), 1-MAT(tprob_new,2,STATE_AZ,STATE_AZ),MAT(tprob_new,2,STATE_HW,STATE_AZ)); if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno)); } while ( deltaz > args->baum_welch_th || delthw > args->baum_welch_th ); // output the results for (i=0; inrid; i++) { int ioff = smpl->rid_off[i]; int nsites = (i+1==smpl->nrid ? smpl->nsites : smpl->rid_off[i+1]) - ioff; args->igenmap = 0; hmm_run_viterbi(args->hmm, nsites, smpl->eprob+ioff*2, smpl->sites+ioff); hmm_run_fwd_bwd(args->hmm, nsites, smpl->eprob+ioff*2, smpl->sites+ioff); uint8_t *vpath = hmm_get_viterbi_path(args->hmm); double *fwd = hmm_get_fwd_bwd_prob(args->hmm); const char *chr = bcf_hdr_id2name(args->hdr,smpl->rid[i]); for (j=0; jstr.l = 0; ksprintf(&args->str, "ROH\t%s\t%s\t%d\t%d\t%.1f\n", name,chr,smpl->sites[ioff+j]+1, state, phred_score(1.0-pval[state])); if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno)); } } } int read_AF(bcf_sr_regions_t *tgt, bcf1_t *line, double *alt_freq) { if ( tgt->nals < 2 ) error("Expected two comma-separated alleles (REF,ALT) in the third column of %s, found:\n\t%s\n", tgt->fname,tgt->line.s); if ( tgt->nals != line->n_allele ) return -1; // number of alleles does not match int i; for (i=0; inals; i++) if ( strcmp(line->d.allele[i],tgt->als[i]) ) break; // we could be smarter, see vcmp if ( inals ) return -1; char *tmp, *str = tgt->line.s; i = 0; while ( *str && i<3 ) { if ( *str=='\t' ) i++; str++; } *alt_freq = strtod(str, &tmp); if ( *tmp && !isspace(*tmp) ) { if ( str[0]=='.' && (!str[1] || isspace(str[1])) ) return -1; // missing value error("Could not parse: [%s]\n", tgt->line.s); } if ( *alt_freq<0 || *alt_freq>1 ) error("Could not parse AF: [%s]\n", tgt->line.s); return 0; } int8_t *get_GT(args_t *args, bcf1_t *line) { int i; for (i=0; in_fmt; i++) if ( line->d.fmt[i].id==args->gt_hdr_id ) break; if ( i==line->n_fmt ) return NULL; // the tag is not present in this record bcf_fmt_t *fmt = &line->d.fmt[i]; if ( fmt->n!=2 ) return NULL; // not diploid if ( fmt->type!=BCF_BT_INT8 ) error("This is unexpected, GT type is %d\n", fmt->type); return (int8_t*) fmt->p; } int estimate_AF_from_GT(args_t *args, int8_t *gt, double *alt_freq) { int i, nalt = 0, nref = 0; if ( args->af_smpl ) // subset samples for AF estimate { for (i=0; iaf_smpl->n; i++) { int ismpl = args->af_smpl->idx[i]; if ( bcf_gt_is_missing(gt[2*ismpl]) || bcf_gt_is_missing(gt[2*ismpl+1]) ) continue; if ( bcf_gt_allele(gt[2*ismpl]) ) nalt++; else nref++; if ( bcf_gt_allele(gt[2*ismpl+1]) ) nalt++; else nref++; } } else // all samples used in AF estimate { int8_t *end = gt + 2*bcf_hdr_nsamples(args->hdr); while ( gt < end ) { if ( bcf_gt_is_missing(gt[0]) || bcf_gt_is_missing(gt[1]) ) { gt += 2; continue; } if ( bcf_gt_allele(gt[0]) ) nalt++; else nref++; if ( bcf_gt_allele(gt[1]) ) nalt++; else nref++; gt += 2; } } if ( !nalt && !nref ) return -1; *alt_freq = (double)nalt / (nalt + nref); return 0; } int estimate_AF_from_PL(args_t *args, bcf_fmt_t *fmt_pl, int ial, double *alt_freq) { double af = 0; int i, j, naf = 0; int irr = bcf_alleles2gt(0,0), ira = bcf_alleles2gt(0,ial), iaa = bcf_alleles2gt(ial,ial); if ( iaa >= fmt_pl->n ) return -1; // not diploid or wrong number of fields if ( args->af_smpl ) // subset samples for AF estimate { #define BRANCH(type_t) \ { \ for (i=0; iaf_smpl->n; i++) \ { \ int ismpl = args->af_smpl->idx[i]; \ type_t *p = (type_t*)fmt_pl->p + fmt_pl->n*ismpl; \ if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue; /* missing value */ \ if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue; /* all values are the same */ \ double prob[3], norm = 0; \ prob[0] = args->pl2p[ max255(p[irr]) ]; \ prob[1] = args->pl2p[ max255(p[ira]) ]; \ prob[2] = args->pl2p[ max255(p[iaa]) ]; \ for (j=0; j<3; j++) norm += prob[j]; \ for (j=0; j<3; j++) prob[j] /= norm; \ af += 0.5*prob[1] + prob[2]; \ naf++; \ } \ } switch (fmt_pl->type) { case BCF_BT_INT8: BRANCH(int8_t); break; case BCF_BT_INT16: BRANCH(int16_t); break; case BCF_BT_INT32: BRANCH(int32_t); break; default: fprintf(stderr,"Unknown format type for PL: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt_pl->type); exit(1); } #undef BRANCH } else // all samples used in AF estimate { int nsmpl = bcf_hdr_nsamples(args->hdr); #define BRANCH(type_t) \ { \ type_t *p = (type_t*)fmt_pl->p; \ p -= fmt_pl->n; \ for (i=0; in; \ if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue; /* missing value */ \ if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue; /* all values are the same */ \ double prob[3], norm = 0; \ prob[0] = args->pl2p[ max255(p[irr]) ]; \ prob[1] = args->pl2p[ max255(p[ira]) ]; \ prob[2] = args->pl2p[ max255(p[iaa]) ]; \ for (j=0; j<3; j++) norm += prob[j]; \ for (j=0; j<3; j++) prob[j] /= norm; \ af += 0.5*prob[1] + prob[2]; \ naf++; \ } \ } switch (fmt_pl->type) { case BCF_BT_INT8: BRANCH(int8_t); break; case BCF_BT_INT16: BRANCH(int16_t); break; case BCF_BT_INT32: BRANCH(int32_t); break; default: fprintf(stderr,"Unknown format type for PL: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt_pl->type); exit(1); } #undef BRANCH } if ( !naf ) return -1; *alt_freq = af / naf; return 0; } bcf_fmt_t *get_PL(args_t *args, bcf1_t *line) { int i; for (i=0; in_fmt; i++) if ( line->d.fmt[i].id==args->pl_hdr_id ) return &line->d.fmt[i]; return NULL; } int process_line(args_t *args, bcf1_t *line, int ial) { if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT); double alt_freq; int8_t *GTs = NULL; bcf_fmt_t *fmt_pl = NULL; // Set allele frequency int ret = 0, i,j; if ( args->af_tag ) { // Use an INFO tag provided by the user ret = bcf_get_info_float(args->hdr, line, args->af_tag, &args->AFs, &args->mAFs); if ( ret>0 ) alt_freq = args->AFs[ial-1]; if ( ret==-2 ) error("Type mismatch for INFO/%s tag at %s:%"PRId64"\n", args->af_tag, bcf_seqname(args->hdr,line), (int64_t) line->pos+1); } else if ( args->af_fname ) { // Read AF from a file ret = read_AF(args->files->targets, line, &alt_freq); } else if ( args->dflt_AF > 0 ) { alt_freq = args->dflt_AF; } else if ( args->estimate_AF ) { // Estimate AF from GTs or PLs of all samples or samples listed in a file if ( args->af_from_PL ) { fmt_pl = get_PL(args, line); if ( !fmt_pl ) return -1; ret = estimate_AF_from_PL(args, fmt_pl, ial, &alt_freq); } else { GTs = get_GT(args, line); if ( !GTs ) return -1; ret = estimate_AF_from_GT(args, GTs, &alt_freq); } } else { // Use AC/AN int AC = -1, AN = 0; ret = bcf_get_info_int32(args->hdr, line, "AN", &args->itmp, &args->mitmp); if ( ret==1 ) { AN = args->itmp[0]; ret = bcf_get_info_int32(args->hdr, line, "AC", &args->itmp, &args->mitmp); if ( ret>0 ) AC = args->itmp[0]; } if ( AN<=0 || AC<0 ) ret = -1; else alt_freq = (double) AC/AN; } if ( args->dflt_AF>0 && (ret<0 || alt_freq==0.0) ) alt_freq = args->dflt_AF; else if ( ret<0 ) { args->nno_af++; return ret; } else if ( alt_freq==0.0 ) { args->nno_af++; return -1; } int irr = bcf_alleles2gt(0,0), ira = bcf_alleles2gt(0,ial), iaa = bcf_alleles2gt(ial,ial); if ( args->fake_PLs ) { if ( !GTs ) GTs = get_GT(args, line); } else { fmt_pl = get_PL(args, line); if ( !fmt_pl ) return -1; if ( iaa >= fmt_pl->n ) return -1; // not diploid or wrong number of fields } for (i=0; iroh_smpl->n; i++) { int ismpl = args->roh_smpl->idx[i]; // set P(D|G) double pdg[3]; if ( args->fake_PLs ) { int8_t *gt = GTs + 2*ismpl; if ( bcf_gt_is_missing(gt[0]) || bcf_gt_is_missing(gt[1]) ) continue; int a = bcf_gt_allele(gt[0]); int b = bcf_gt_allele(gt[1]); if ( a!=b ) { pdg[0] = pdg[2] = args->unseen_PL; pdg[1] = 1 - 2*args->unseen_PL; } else if ( a==0 ) { pdg[0] = 1 - args->unseen_PL - args->unseen_PL*args->unseen_PL; pdg[1] = args->unseen_PL; pdg[2] = args->unseen_PL*args->unseen_PL; } else { pdg[0] = args->unseen_PL*args->unseen_PL; pdg[1] = args->unseen_PL; pdg[2] = 1 - args->unseen_PL - args->unseen_PL*args->unseen_PL; } } else { #define BRANCH(type_t) \ { \ type_t *p = (type_t*)fmt_pl->p + fmt_pl->n*ismpl; \ if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue; /* missing value */ \ if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue; /* all values are the same */ \ pdg[0] = args->pl2p[ max255(p[irr]) ]; \ pdg[1] = args->pl2p[ max255(p[ira]) ]; \ pdg[2] = args->pl2p[ max255(p[iaa]) ]; \ } switch (fmt_pl->type) { case BCF_BT_INT8: BRANCH(int8_t); break; case BCF_BT_INT16: BRANCH(int16_t); break; case BCF_BT_INT32: BRANCH(int32_t); break; default: fprintf(stderr,"Unknown format type for PL: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt_pl->type); exit(1); } #undef BRANCH } double sum = pdg[0] + pdg[1] + pdg[2]; if ( !sum ) continue; for (j=0; j<3; j++) pdg[j] /= sum; if ( args->skip_homref && pdg[0]>0.99 ) continue; smpl_t *smpl = &args->smpl[i]; smpl->nused++; if ( smpl->nsites >= smpl->msites ) { hts_expand(uint32_t,smpl->nsites+1,smpl->msites,smpl->sites); smpl->eprob = (double*) realloc(smpl->eprob,sizeof(*smpl->eprob)*smpl->msites*2); if ( !smpl->eprob ) error("Error: failed to alloc %"PRIu64" bytes\n", (uint64_t)(sizeof(*smpl->eprob)*smpl->msites*2)); } // Calculate emission probabilities P(D|AZ) and P(D|HW) double *eprob = &smpl->eprob[2*smpl->nsites]; eprob[STATE_AZ] = pdg[0]*(1-alt_freq) + pdg[2]*alt_freq; eprob[STATE_HW] = pdg[0]*(1-alt_freq)*(1-alt_freq) + 2*pdg[1]*(1-alt_freq)*alt_freq + pdg[2]*alt_freq*alt_freq; smpl->sites[smpl->nsites] = line->pos; smpl->nsites++; if ( args->vi_training ) { if ( !smpl->nrid || line->rid!=smpl->rid[smpl->nrid-1] ) { smpl->nrid++; smpl->rid = (int*) realloc(smpl->rid,sizeof(*smpl->rid)*smpl->nrid); smpl->rid[smpl->nrid-1] = line->rid; smpl->rid_off = (int*) realloc(smpl->rid_off,sizeof(*smpl->rid_off)*smpl->nrid); smpl->rid_off[smpl->nrid-1] = smpl->nsites - 1; } } else if ( args->nbuf_max && smpl->nsites >= args->nbuf_max ) flush_viterbi(args, i); } return 0; } static void vcfroh(args_t *args, bcf1_t *line) { int i; // Are we done? if ( !line ) { for (i=0; iroh_smpl->n; i++) flush_viterbi(args, i); return; } // Skip unwanted lines, for simplicity we consider only biallelic sites if ( line->rid == args->skip_rid ) return; // This can be raw callable VCF with the symbolic unseen allele <*> int ial = 0, nalt = line->n_allele - 1; for (i=1; in_allele; i++) { if ( !strcmp("<*>",line->d.allele[i]) || !strcmp("",line->d.allele[i]) ) nalt--; else if ( !ial ) ial = i; } if ( !nalt ) // no ALT allele { args->nno_alt++; if ( !args->include_noalt_sites ) return; } else if ( nalt>1 ) { args->nmultiallelic++; return; } if ( args->snps_only && !bcf_is_snp(line) ) return; // Initialize genetic map int skip_rid = 0; if ( args->prev_rid<0 ) skip_rid = load_genmap(args, bcf_seqname(args->hdr,line)); // New chromosome? if ( args->prev_rid!=line->rid ) { if ( !args->vi_training ) { for (i=0; iroh_smpl->n; i++) { flush_viterbi(args, i); hmm_reset(args->hmm, args->smpl[i].snapshot); } } args->prev_rid = line->rid; args->prev_pos = line->pos; skip_rid = load_genmap(args, bcf_seqname(args->hdr,line)); } else if ( args->prev_pos == line->pos ) { args->ndup++; return; // skip duplicate positions } if ( skip_rid ) { fprintf(stderr,"Skipping the sequence, no genmap for %s\n", bcf_seqname(args->hdr,line)); args->skip_rid = line->rid; return; } if ( args->prev_pos > line->pos ) error("The file is not sorted?!\n"); args->prev_rid = line->rid; args->prev_pos = line->pos; // parse the new line process_line(args, line, ial); } static void usage(args_t *args) { fprintf(stderr, "\n"); fprintf(stderr, "About: HMM model for detecting runs of autozygosity.\n"); fprintf(stderr, "Usage: bcftools roh [options] \n"); fprintf(stderr, "\n"); fprintf(stderr, "General Options:\n"); fprintf(stderr, " --AF-dflt if AF is not known, use this allele frequency [skip]\n"); fprintf(stderr, " --AF-tag use TAG for allele frequency\n"); fprintf(stderr, " --AF-file read allele frequencies from file (CHR\\tPOS\\tREF,ALT\\tAF)\n"); fprintf(stderr, " -b --buffer-size buffer size and the number of overlapping sites, 0 for unlimited [0]\n"); fprintf(stderr, " If the first number is negative, it is interpreted as the maximum memory to\n"); fprintf(stderr, " use, in MB. The default overlap is set to roughly 1%% of the buffer size.\n"); fprintf(stderr, " -e, --estimate-AF [TAG], estimate AF from FORMAT/TAG (GT or PL) of all samples (\"-\") or samples listed\n"); fprintf(stderr, " in . If TAG is not given, the frequency is estimated from GT by default\n"); fprintf(stderr, " --exclude exclude sites for which the expression is true\n"); fprintf(stderr, " -G, --GTs-only use GTs and ignore PLs, instead using for PL of the two least likely genotypes.\n"); fprintf(stderr, " Safe value to use is 30 to account for GT errors.\n"); fprintf(stderr, " --include select sites for which the expression is true\n"); fprintf(stderr, " -i, --ignore-homref skip hom-ref genotypes (0/0)\n"); fprintf(stderr, " --include-noalt include sites with no ALT allele (ignored by default)\n"); fprintf(stderr, " -I, --skip-indels skip indels as their genotypes are enriched for errors\n"); fprintf(stderr, " -m, --genetic-map genetic map in IMPUTE2 format, single file or mask, where string \"{CHROM}\"\n"); fprintf(stderr, " is replaced with chromosome name\n"); fprintf(stderr, " -M, --rec-rate constant recombination rate per bp\n"); fprintf(stderr, " -o, --output write output to a file [standard output]\n"); fprintf(stderr, " -O, --output-type [srz] output s:per-site, r:regions, z:compressed [sr]\n"); fprintf(stderr, " -r, --regions restrict to comma-separated list of regions\n"); fprintf(stderr, " -R, --regions-file restrict to regions listed in a file\n"); fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " -s, --samples list of samples to analyze [all samples]\n"); fprintf(stderr, " -S, --samples-file file of samples to analyze [all samples]\n"); fprintf(stderr, " -t, --targets similar to -r but streams rather than index-jumps\n"); fprintf(stderr, " -T, --targets-file similar to -R but streams rather than index-jumps\n"); fprintf(stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(stderr, " --threads use multithreading with worker threads [0]\n"); fprintf(stderr, "\n"); fprintf(stderr, "HMM Options:\n"); fprintf(stderr, " -a, --hw-to-az P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state [6.7e-8]\n"); fprintf(stderr, " -H, --az-to-hw P(HW|AZ) transition probability from AZ to HW state [5e-9]\n"); fprintf(stderr, " -V, --viterbi-training estimate HMM parameters, is the convergence threshold, e.g. 1e-10 (experimental)\n"); fprintf(stderr, "\n"); exit(1); } int main_vcfroh(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->files = bcf_sr_init(); args->t2AZ = 6.7e-8; args->t2HW = 5e-9; args->rec_rate = 0; int regions_is_file = 0, targets_is_file = 0; int regions_overlap = 1; int targets_overlap = 0; static struct option loptions[] = { {"AF-tag",1,0,0}, {"AF-file",1,0,1}, {"AF-dflt",1,0,2}, {"include",1,0,3}, {"exclude",1,0,4}, {"include-noalt",0,0,5}, {"buffer-size",1,0,'b'}, {"ignore-homref",0,0,'i'}, {"estimate-AF",1,0,'e'}, {"output",1,0,'o'}, {"output-type",1,0,'O'}, {"GTs-only",1,0,'G'}, {"samples",1,0,'s'}, {"samples-file",1,0,'S'}, {"hw-to-az",1,0,'a'}, {"az-to-hw",1,0,'H'}, {"viterbi-training",1,0,'V'}, {"targets",1,0,'t'}, {"targets-file",1,0,'T'}, {"targets-overlap",required_argument,NULL,6}, {"regions",1,0,'r'}, {"regions-file",1,0,'R'}, {"regions-overlap",required_argument,NULL,7}, {"genetic-map",1,0,'m'}, {"rec-rate",1,0,'M'}, {"skip-indels",0,0,'I'}, {"threads",1,0,9}, {0,0,0,0} }; int naf_opts = 0; char *tmp; while ((c = getopt_long(argc, argv, "h?r:R:t:T:H:a:s:S:m:M:G:Ia:e:V:b:O:o:i",loptions,NULL)) >= 0) { switch (c) { case 0: args->af_tag = optarg; naf_opts++; break; case 1: args->af_fname = optarg; naf_opts++; break; case 2: args->dflt_AF = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: --AF-dflt %s\n", optarg); break; case 3 : if ( args->filter_str ) error("Error: only one --include or --exclude expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 4 : if ( args->filter_str ) error("Error: only one --include or --exclude expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 5: args->include_noalt_sites = 1; break; case 'o': args->output_fname = optarg; break; case 'O': if ( strchr(optarg,'s') || strchr(optarg,'S') ) args->output_type |= OUTPUT_ST; if ( strchr(optarg,'r') || strchr(optarg,'R') ) args->output_type |= OUTPUT_RG; if ( strchr(optarg,'z') || strchr(optarg,'z') ) args->output_type |= OUTPUT_GZ; break; case 'e': args->estimate_AF = optarg; naf_opts++; break; case 'b': args->buffer_size = optarg; break; case 'i': args->skip_homref = 1; break; case 'I': args->snps_only = 1; break; case 'G': args->fake_PLs = 1; args->unseen_PL = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -G %s\n", optarg); args->unseen_PL = pow(10,-args->unseen_PL/10.); break; case 'm': args->genmap_fname = optarg; break; case 'M': args->rec_rate = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -M %s\n", optarg); break; case 's': args->samples = strdup(optarg); break; case 'S': args->samples = strdup(optarg); args->samples_is_file = 1; break; case 'a': args->t2AZ = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -a %s\n", optarg); break; case 'H': args->t2HW = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -H %s\n", optarg); break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; targets_is_file = 1; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 6 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 7 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 'V': args->vi_training = 1; args->baum_welch_th = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: --viterbi-training %s\n", optarg); break; case 'h': case '?': usage(args); break; default: error("Unknown argument: %s\n", optarg); } } if ( !args->output_fname ) args->output_fname = "stdout"; if ( !args->output_type || args->output_type==OUTPUT_GZ ) args->output_type |= OUTPUT_ST|OUTPUT_RG; char *fname = NULL; if ( optind==argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else usage(args); } else fname = argv[optind]; if ( args->vi_training && args->buffer_size ) error("Error: cannot use -b with -V\n"); if ( args->t2AZ<0 || args->t2AZ>1 ) error("Error: The parameter --hw-to-az is not in [0,1] .. %e\n", args->t2AZ); if ( args->t2HW<0 || args->t2HW>1 ) error("Error: The parameter --az-to-hw is not in [0,1] .. %e\n", args->t2HW); if ( naf_opts>1 ) error("Error: The options --AF-tag, --AF-file and -e are mutually exclusive\n"); if ( args->af_fname && args->targets_list ) error("Error: The options --AF-file and -t are mutually exclusive\n"); if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } if ( args->af_fname ) { if ( bcf_sr_set_targets(args->files, args->af_fname, 1, 3)<0 ) error("Failed to read the targets: %s\n", args->af_fname); } if ( args->n_threads && bcf_sr_set_threads(args->files, args->n_threads)<0) error("Failed to create threads\n"); if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); init_data(args); while ( bcf_sr_next_line(args->files) ) { args->ntot++; bcf1_t *line = bcf_sr_get_line(args->files,0); if ( args->filter ) { int pass = filter_test(args->filter, line, NULL); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { args->nfiltered++; continue; } } vcfroh(args, line); } vcfroh(args, NULL); int i, nmin = 0; for (i=0; iroh_smpl->n; i++) if ( !i || args->smpl[i].nused < nmin ) nmin = args->smpl[i].nused; if ( args->af_fname ) fprintf(stderr,"Number of lines overlapping with --AF-file/processed: %d/%d\n", args->ntot,nmin); else fprintf(stderr,"Number of lines total/processed: %d/%d\n", args->ntot,nmin); fprintf(stderr,"Number of lines filtered/no AF/no alt/multiallelic/dup: %d/%d/%d/%d/%d\n", args->nfiltered,args->nno_af,args->nno_alt,args->nmultiallelic,args->ndup); if ( nmin==0 ) { fprintf(stderr,"No usable sites were found.\n"); if ( !naf_opts && !args->dflt_AF ) fprintf(stderr, " Consider using one of the AF options.\n"); } destroy_data(args); free(args); return 0; } pysam-0.23.0/bcftools/vcfroh.c.pysam.c000066400000000000000000001447631475062545500176000ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfroh.c -- HMM model for detecting runs of autozygosity. Copyright (C) 2013-2022 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "HMM.h" #include "smpl_ilist.h" #include "filter.h" #define STATE_HW 0 // normal state, follows Hardy-Weinberg allele frequencies #define STATE_AZ 1 // autozygous state #define OUTPUT_ST (1<<1) #define OUTPUT_RG (1<<2) #define OUTPUT_GZ (1<<3) // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 /** Genetic map */ typedef struct { int pos; double rate; } genmap_t; /** HMM data for each sample */ typedef struct { double *eprob; // emission probs [2*nsites,msites] uint32_t *sites; // positions [nsites,msites] int nsites, msites; int igenmap; // current position in genmap int nused; // some stats to detect if things didn't go wrong int nrid, *rid, *rid_off; // for viterbi training, keep all chromosomes void *snapshot; // hmm snapshot struct { uint32_t beg,end,nqual; double qual; int rid, state; } rg; } smpl_t; typedef struct _args_t { bcf_srs_t *files; bcf_hdr_t *hdr; double t2AZ, t2HW; // P(AZ|HW) and P(HW|AZ) parameters double unseen_PL, dflt_AF; char *genmap_fname; genmap_t *genmap; int ngenmap, mgenmap, igenmap; double rec_rate; // constant recombination rate if > 0 hmm_t *hmm; double baum_welch_th; int nrids, *rids, *rid_offs; // multiple chroms with vi_training int nbuf_max, nbuf_olap; float *AFs; int32_t *itmp; int mAFs, nitmp, mitmp, pl_hdr_id, gt_hdr_id; double pl2p[256], *pdg; int32_t skip_rid, prev_rid, prev_pos; int ntot; // some stats to detect if things didn't go wrong int nno_af; // number of sites rejected because AF could not be determined int nfiltered; // .. because of filters int nno_alt, nmultiallelic, ndup; smpl_t *smpl; // HMM data for each sample smpl_ilist_t *af_smpl; // list of samples to estimate AF from (--estimate-AF) smpl_ilist_t *roh_smpl; // list of samples to analyze (--samples, --samples-file) char *estimate_AF; // list of samples for AF estimate and query sample int af_from_PL; // estimate AF from FMT/PL rather than FMT/GT char **argv, *targets_list, *regions_list, *af_fname, *af_tag, *samples, *buffer_size, *output_fname; int argc, fake_PLs, snps_only, vi_training, samples_is_file, output_type, skip_homref, n_threads; int include_noalt_sites; BGZF *out; kstring_t str; int filter_logic; filter_t *filter; char *filter_str; } args_t; void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob); void set_tprob_rrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob); void *smalloc(size_t size) { void *mem = malloc(size); if ( !mem ) error("malloc: Could not allocate %d bytes\n", (int)size); return mem; } static inline int max255(int i) { return i < 256 ? i : 255; } static void init_data(args_t *args) { int i; args->prev_rid = args->skip_rid = -1; args->hdr = args->files->readers[0].header; if ( !bcf_hdr_nsamples(args->hdr) ) error("No samples in the VCF?\n"); if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); if ( !args->fake_PLs ) { args->pl_hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "PL"); if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,args->pl_hdr_id) ) error("Error: The FORMAT/PL tag not found in the header, consider running with -G\n"); if ( bcf_hdr_id2type(args->hdr,BCF_HL_FMT,args->pl_hdr_id)!=BCF_HT_INT ) error("Error: The FORMAT/PL tag not defined as Integer in the header\n"); } if ( args->estimate_AF ) { if ( !strncmp("GT,",args->estimate_AF,3) ) args->estimate_AF += 3; else if ( !strncmp("PL,",args->estimate_AF,3) ) { args->estimate_AF += 3; args->af_from_PL = 1; } if ( strcmp("-",args->estimate_AF) ) args->af_smpl = smpl_ilist_init(args->hdr, args->estimate_AF, 1, SMPL_NONE|SMPL_VERBOSE); } if ( args->estimate_AF || args->fake_PLs ) { if ( args->af_from_PL ) { args->pl_hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "PL"); if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,args->pl_hdr_id) ) error("Error: The FORMAT/PL tag not found in the header\n"); } else { args->gt_hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "GT"); if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,args->gt_hdr_id) ) error("Error: The FORMAT/GT tag not found in the header\n"); } } if ( args->fake_PLs ) { args->gt_hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "GT"); if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,args->gt_hdr_id) ) error("Error: The FORMAT/GT tag not found in the header\n"); } args->roh_smpl = smpl_ilist_init(args->hdr, args->samples, args->samples_is_file, SMPL_NONE|SMPL_VERBOSE); if ( args->samples ) { // we may be able to subset to a few samples, for a text VCF this can be a major speedup if ( (bcf_sr_get_reader(args->files,0))->file->format.format==vcf ) { kstring_t str = {0,0,0}; smpl_ilist_t *tmp = args->roh_smpl, *rmme = NULL; if ( args->af_smpl ) { for (i=0; iroh_smpl->n; i++) { if ( str.l ) kputc(',', &str); kputs(args->hdr->samples[args->roh_smpl->idx[i]], &str); } for (i=0; iaf_smpl->n; i++) { kputc(',', &str); kputs(args->hdr->samples[args->af_smpl->idx[i]], &str); } rmme = tmp = smpl_ilist_init(args->hdr, str.s, 0, SMPL_NONE); } if ( tmp->n < bcf_hdr_nsamples(args->hdr) ) { str.l = 0; for (i=0; in; i++) { if ( str.l ) kputc(',', &str); kputs(args->hdr->samples[tmp->idx[i]], &str); } int ret = bcf_hdr_set_samples(args->hdr, str.s, 0); if ( ret<0 ) error("Error parsing the list of samples: %s\n", str.s); else if ( ret>0 ) error("The %d-th sample not found in the VCF: %s\n", ret,str.s); // update sample ids smpl_ilist_destroy(args->roh_smpl); args->roh_smpl = smpl_ilist_init(args->hdr, args->samples, args->samples_is_file, SMPL_NONE); if ( args->af_smpl ) { smpl_ilist_destroy(args->af_smpl); args->af_smpl = smpl_ilist_init(args->hdr, args->estimate_AF, 1, SMPL_NONE); } } free(str.s); if ( rmme ) smpl_ilist_destroy(rmme); } } // check whether all samples are in this list. If so, the lookup will not be needed if ( args->af_smpl && args->af_smpl->n == bcf_hdr_nsamples(args->hdr) ) { // all samples are in this list smpl_ilist_destroy(args->af_smpl); args->af_smpl = NULL; } if ( args->buffer_size ) { args->nbuf_olap = -1; char *end; double tmp = strtod(args->buffer_size,&end); if ( *end ) { if ( *end!=',') error("Could not parse: --buffer-size %s\n", args->buffer_size); args->nbuf_olap = strtol(end+1,&end,10); if ( *end || args->nbuf_olap<0 ) error("Could not parse: --buffer-size %s\n", args->buffer_size); } if ( tmp<0 ) args->nbuf_max = fabs(tmp)*1e6/(4+8*2)/args->roh_smpl->n; else args->nbuf_max = tmp; if ( args->nbuf_olap<0 ) args->nbuf_olap = args->nbuf_max*0.01; } fprintf(bcftools_stderr,"Number of target samples: %d\n", args->roh_smpl->n); fprintf(bcftools_stderr,"Number of --estimate-AF samples: %d\n", args->af_smpl ? args->af_smpl->n : (args->estimate_AF ? bcf_hdr_nsamples(args->hdr) : 0)); fprintf(bcftools_stderr,"Number of sites in the buffer/overlap: "); if ( args->nbuf_max ) fprintf(bcftools_stderr,"%d/%d\n", args->nbuf_max,args->nbuf_olap); else fprintf(bcftools_stderr,"unlimited\n"); args->smpl = (smpl_t*) calloc(args->roh_smpl->n,sizeof(smpl_t)); for (i=0; i<256; i++) args->pl2p[i] = pow(10., -i/10.); // Init transition matrix and HMM double tprob[4]; MAT(tprob,2,STATE_HW,STATE_HW) = 1 - args->t2AZ; MAT(tprob,2,STATE_HW,STATE_AZ) = args->t2HW; MAT(tprob,2,STATE_AZ,STATE_HW) = args->t2AZ; MAT(tprob,2,STATE_AZ,STATE_AZ) = 1 - args->t2HW; args->hmm = hmm_init(2, tprob, 10000); if ( args->genmap_fname ) hmm_set_tprob_func(args->hmm, set_tprob_genmap, args); else if ( args->rec_rate > 0 ) hmm_set_tprob_func(args->hmm, set_tprob_rrate, args); args->out = bgzf_open(strcmp("bcftools_stdout",args->output_fname)?args->output_fname:"-", args->output_type&OUTPUT_GZ ? "wg" : "wu"); if ( !args->out ) error("Failed to open %s: %s\n", args->output_fname, strerror(errno)); // print header args->str.l = 0; ksprintf(&args->str, "# This file was produced by: bcftools roh(%s+htslib-%s)\n", bcftools_version(),hts_version()); ksprintf(&args->str, "# The command line was:\tbcftools %s", args->argv[0]); for (i=1; iargc; i++) ksprintf(&args->str, " %s",args->argv[i]); ksprintf(&args->str, "\n#\n"); if ( args->output_type & OUTPUT_RG ) { i = 2; ksprintf(&args->str, "# RG"); ksprintf(&args->str, "\t[%d]Sample", i++); ksprintf(&args->str, "\t[%d]Chromosome", i++); ksprintf(&args->str, "\t[%d]Start", i++); ksprintf(&args->str, "\t[%d]End", i++); ksprintf(&args->str, "\t[%d]Length (bp)", i++); ksprintf(&args->str, "\t[%d]Number of markers", i++); ksprintf(&args->str, "\t[%d]Quality (average fwd-bwd phred score)", i++); ksprintf(&args->str, "\n"); } if ( args->output_type & OUTPUT_ST ) { i = 2; ksprintf(&args->str, "# ST"); ksprintf(&args->str, "\t[%d]Sample", i++); ksprintf(&args->str, "\t[%d]Chromosome", i++); ksprintf(&args->str, "\t[%d]Position", i++); ksprintf(&args->str, "\t[%d]State (0:HW, 1:AZ)", i++); ksprintf(&args->str, "\t[%d]Quality (fwd-bwd phred score)", i++); ksprintf(&args->str, "\n"); } if ( args->vi_training) { i = 2; ksprintf(&args->str, "# VT, Viterbi Training"); ksprintf(&args->str, "\t[%d]Sample", i++); ksprintf(&args->str, "\t[%d]Iteration", i++); ksprintf(&args->str, "\t[%d]dAZ", i++); ksprintf(&args->str, "\t[%d]dHW", i++); ksprintf(&args->str, "\t[%d]1 - P(HW|HW)", i++); ksprintf(&args->str, "\t[%d]P(AZ|HW)", i++); ksprintf(&args->str, "\t[%d]1 - P(AZ|AZ)", i++); ksprintf(&args->str, "\t[%d]P(HW|AZ)", i++); ksprintf(&args->str, "\n"); } if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno)); } static void destroy_data(args_t *args) { if ( args->filter ) filter_destroy(args->filter); if ( bgzf_close(args->out)!=0 ) error("Error: close failed .. %s\n", args->output_fname); int i; for (i=0; iroh_smpl->n; i++) { free(args->smpl[i].eprob); free(args->smpl[i].sites); free(args->smpl[i].rid); free(args->smpl[i].rid_off); free(args->smpl[i].snapshot); } free(args->str.s); free(args->smpl); if ( args->af_smpl ) smpl_ilist_destroy(args->af_smpl); smpl_ilist_destroy(args->roh_smpl); free(args->rids); free(args->rid_offs); hmm_destroy(args->hmm); bcf_sr_destroy(args->files); free(args->AFs); free(args->pdg); free(args->genmap); free(args->itmp); free(args->samples); } static int load_genmap(args_t *args, const char *chr) { if ( !args->genmap_fname ) { args->ngenmap = 0; return 0; } kstring_t str = {0,0,0}; char *fname = strstr(args->genmap_fname,"{CHROM}"); if ( fname ) { kputsn(args->genmap_fname, fname - args->genmap_fname, &str); kputs(chr, &str); kputs(fname+7,&str); fname = str.s; } else fname = args->genmap_fname; htsFile *fp = hts_open(fname, "rb"); if ( !fp ) { args->ngenmap = 0; return -1; } hts_getline(fp, KS_SEP_LINE, &str); if ( strcmp(str.s,"position COMBINED_rate(cM/Mb) Genetic_Map(cM)") ) error("Unexpected header in %s, found:\n\t[%s], but expected:\n\t[position COMBINED_rate(cM/Mb) Genetic_Map(cM)]\n", fname, str.s); args->ngenmap = args->igenmap = 0; while ( hts_getline(fp, KS_SEP_LINE, &str) > 0 ) { args->ngenmap++; hts_expand(genmap_t,args->ngenmap,args->mgenmap,args->genmap); genmap_t *gm = &args->genmap[args->ngenmap-1]; // position, convert to 0-based char *tmp, *end; gm->pos = strtol(str.s, &tmp, 10); if ( str.s==tmp ) error("Could not parse %s: %s\n", fname, str.s); gm->pos -= 1; // skip second column tmp++; while ( *tmp && !isspace(*tmp) ) tmp++; // read the genetic map in cM, scale from % to likelihood gm->rate = strtod(tmp+1, &end); if ( tmp+1==end ) error("Could not parse %s: %s\n", fname, str.s); gm->rate *= 0.01; } if ( !args->ngenmap ) error("Genetic map empty?\n"); if ( hts_close(fp) ) error("Close failed\n"); free(str.s); return 0; } static double get_genmap_rate(args_t *args, int start, int end) { // position i to be equal to or smaller than start int i = args->igenmap; if ( args->genmap[i].pos > start ) { while ( i>0 && args->genmap[i].pos > start ) i--; } else { while ( i+1ngenmap && args->genmap[i+1].pos < start ) i++; } // position j to be equal or larger than end int j = i; while ( j+1ngenmap && args->genmap[j].pos < end ) j++; if ( i==j ) { args->igenmap = i; return 0; } if ( start < args->genmap[i].pos ) start = args->genmap[i].pos; if ( end > args->genmap[j].pos ) end = args->genmap[j].pos; double rate = (args->genmap[j].rate - args->genmap[i].rate)/(args->genmap[j].pos - args->genmap[i].pos) * (end-start); args->igenmap = j; return rate; } void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob) { args_t *args = (args_t*) data; double ci = get_genmap_rate(args, prev_pos, pos); if ( args->rec_rate ) ci *= args->rec_rate; if ( ci > 1 ) ci = 1; MAT(tprob,2,STATE_HW,STATE_AZ) *= ci; MAT(tprob,2,STATE_AZ,STATE_HW) *= ci; MAT(tprob,2,STATE_AZ,STATE_AZ) = 1 - MAT(tprob,2,STATE_HW,STATE_AZ); MAT(tprob,2,STATE_HW,STATE_HW) = 1 - MAT(tprob,2,STATE_AZ,STATE_HW); } void set_tprob_rrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob) { args_t *args = (args_t*) data; double ci = (pos - prev_pos) * args->rec_rate; if ( ci > 1 ) ci = 1; MAT(tprob,2,STATE_HW,STATE_AZ) *= ci; MAT(tprob,2,STATE_AZ,STATE_HW) *= ci; MAT(tprob,2,STATE_AZ,STATE_AZ) = 1 - MAT(tprob,2,STATE_HW,STATE_AZ); MAT(tprob,2,STATE_HW,STATE_HW) = 1 - MAT(tprob,2,STATE_AZ,STATE_HW); } /** * This function implements the HMM model: * D = Data, AZ = autozygosity, HW = Hardy-Weinberg (non-autozygosity), * f = non-ref allele frequency * * Emission probabilities: * oAZ = P_i(D|AZ) = (1-f)*P(D|RR) + f*P(D|AA) * oHW = P_i(D|HW) = (1-f)^2 * P(D|RR) + f^2 * P(D|AA) + 2*f*(1-f)*P(D|RA) * * Transition probabilities: * tAZ = P(AZ|HW) .. parameter * tHW = P(HW|AZ) .. parameter * * ci = P_i(C) .. probability of cross-over at site i, from genetic map * * AZi = P_i(AZ) .. probability of site i being AZ/non-AZ, scaled so that AZi+HWi = 1 * HWi = P_i(HW) * * P_i(AZ|HW) = P(AZ|HW) * ci * HW{i-1} = tAZ * ci * (1 - AZ{i-1}) * P_i(HW|AZ) = P(HW|AZ) * ci * AZ{i-1} = tHW * ci * AZ{i-1} * P_i(AZ|AZ) = 1 - P_i(HW|AZ) * P_i(HW|HW) = 1 - P_i(AZ|HW) * */ static void flush_viterbi(args_t *args, int ismpl) { smpl_t *smpl = &args->smpl[ismpl]; if ( !smpl->nsites ) return; const char *name = args->hdr->samples[ args->roh_smpl->idx[ismpl] ]; int i,j,k; if ( !args->vi_training ) // single viterbi pass { hmm_restore(args->hmm, smpl->snapshot); int end = (args->nbuf_max && smpl->nsites >= args->nbuf_max && smpl->nsites > args->nbuf_olap) ? smpl->nsites - args->nbuf_olap : smpl->nsites; if ( end < smpl->nsites ) smpl->snapshot = hmm_snapshot(args->hmm, smpl->snapshot, smpl->sites[smpl->nsites - args->nbuf_olap - 1]); args->igenmap = smpl->igenmap; hmm_run_viterbi(args->hmm, smpl->nsites, smpl->eprob, smpl->sites); hmm_run_fwd_bwd(args->hmm, smpl->nsites, smpl->eprob, smpl->sites); double *fwd = hmm_get_fwd_bwd_prob(args->hmm); const char *chr = bcf_hdr_id2name(args->hdr,args->prev_rid); uint8_t *vpath = hmm_get_viterbi_path(args->hmm); for (i=0; ioutput_type & OUTPUT_ST ) { args->str.l = 0; ksprintf(&args->str, "ST\t%s\t%s\t%d\t%d\t%.1f\n", name,chr,smpl->sites[i]+1, state, qual); if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno)); } if ( args->output_type & OUTPUT_RG ) { if ( state!=smpl->rg.state ) { if ( !state ) // the region ends, flush { args->str.l = 0; ksprintf(&args->str, "RG\t%s\t%s\t%d\t%d\t%d\t%d\t%.1f\n",name,bcf_hdr_id2name(args->hdr,smpl->rg.rid), smpl->rg.beg+1,smpl->rg.end+1,smpl->rg.end-smpl->rg.beg+1,smpl->rg.nqual,smpl->rg.qual/smpl->rg.nqual); if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno)); smpl->rg.state = 0; } else { smpl->rg.state = 1; smpl->rg.beg = smpl->sites[i]; smpl->rg.end = smpl->sites[i]; smpl->rg.rid = args->prev_rid; smpl->rg.qual = qual; smpl->rg.nqual = 1; } } else if ( state ) { smpl->rg.nqual++; smpl->rg.qual += qual; smpl->rg.end = smpl->sites[i]; } } } if ( end < smpl->nsites ) { end = smpl->nsites - args->nbuf_olap; memmove(smpl->sites, smpl->sites + end, sizeof(*smpl->sites)*args->nbuf_olap); memmove(smpl->eprob, smpl->eprob + end*2, sizeof(*smpl->eprob)*args->nbuf_olap*2); smpl->nsites = args->nbuf_olap; smpl->igenmap = args->igenmap; } else { smpl->nsites = 0; smpl->igenmap = 0; if ( smpl->rg.state ) { args->str.l = 0; ksprintf(&args->str, "RG\t%s\t%s\t%d\t%d\t%d\t%d\t%.1f\n",name,bcf_hdr_id2name(args->hdr,smpl->rg.rid), smpl->rg.beg+1,smpl->rg.end+1,smpl->rg.end-smpl->rg.beg+1,smpl->rg.nqual,smpl->rg.qual/smpl->rg.nqual); if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno)); smpl->rg.state = 0; } } return; } // viterbi training, multiple chromosomes double t2az_prev, t2hw_prev; double deltaz, delthw; double *tprob_arr = hmm_get_tprob(args->hmm); MAT(tprob_arr,2,STATE_HW,STATE_HW) = 1 - args->t2AZ; MAT(tprob_arr,2,STATE_HW,STATE_AZ) = args->t2HW; MAT(tprob_arr,2,STATE_AZ,STATE_HW) = args->t2AZ; MAT(tprob_arr,2,STATE_AZ,STATE_AZ) = 1 - args->t2HW; hmm_set_tprob(args->hmm, tprob_arr, 10000); int niter = 0; do { tprob_arr = hmm_get_tprob(args->hmm); t2az_prev = MAT(tprob_arr,2,STATE_AZ,STATE_HW); //args->t2AZ; t2hw_prev = MAT(tprob_arr,2,STATE_HW,STATE_AZ); //args->t2HW; double tprob_new[] = { 0,0,0,0 }; for (i=0; inrid; i++) { int ioff = smpl->rid_off[i]; int nsites = (i+1==smpl->nrid ? smpl->nsites : smpl->rid_off[i+1]) - ioff; args->igenmap = 0; tprob_arr = hmm_run_baum_welch(args->hmm, nsites, smpl->eprob+ioff*2, smpl->sites+ioff); for (j=0; j<2; j++) for (k=0; k<2; k++) MAT(tprob_new,2,j,k) += MAT(tprob_arr,2,j,k); } for (j=0; j<2; j++) for (k=0; k<2; k++) MAT(tprob_new,2,j,k) /= smpl->nrid; hmm_set_tprob(args->hmm, tprob_new, 10000); deltaz = fabs(MAT(tprob_new,2,STATE_AZ,STATE_HW)-t2az_prev); delthw = fabs(MAT(tprob_new,2,STATE_HW,STATE_AZ)-t2hw_prev); niter++; args->str.l = 0; ksprintf(&args->str, "VT\t%s\t%d\t%e\t%e\t%e\t%e\t%e\t%e\n", name,niter,deltaz,delthw, 1-MAT(tprob_new,2,STATE_HW,STATE_HW),MAT(tprob_new,2,STATE_AZ,STATE_HW), 1-MAT(tprob_new,2,STATE_AZ,STATE_AZ),MAT(tprob_new,2,STATE_HW,STATE_AZ)); if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno)); } while ( deltaz > args->baum_welch_th || delthw > args->baum_welch_th ); // output the results for (i=0; inrid; i++) { int ioff = smpl->rid_off[i]; int nsites = (i+1==smpl->nrid ? smpl->nsites : smpl->rid_off[i+1]) - ioff; args->igenmap = 0; hmm_run_viterbi(args->hmm, nsites, smpl->eprob+ioff*2, smpl->sites+ioff); hmm_run_fwd_bwd(args->hmm, nsites, smpl->eprob+ioff*2, smpl->sites+ioff); uint8_t *vpath = hmm_get_viterbi_path(args->hmm); double *fwd = hmm_get_fwd_bwd_prob(args->hmm); const char *chr = bcf_hdr_id2name(args->hdr,smpl->rid[i]); for (j=0; jstr.l = 0; ksprintf(&args->str, "ROH\t%s\t%s\t%d\t%d\t%.1f\n", name,chr,smpl->sites[ioff+j]+1, state, phred_score(1.0-pval[state])); if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno)); } } } int read_AF(bcf_sr_regions_t *tgt, bcf1_t *line, double *alt_freq) { if ( tgt->nals < 2 ) error("Expected two comma-separated alleles (REF,ALT) in the third column of %s, found:\n\t%s\n", tgt->fname,tgt->line.s); if ( tgt->nals != line->n_allele ) return -1; // number of alleles does not match int i; for (i=0; inals; i++) if ( strcmp(line->d.allele[i],tgt->als[i]) ) break; // we could be smarter, see vcmp if ( inals ) return -1; char *tmp, *str = tgt->line.s; i = 0; while ( *str && i<3 ) { if ( *str=='\t' ) i++; str++; } *alt_freq = strtod(str, &tmp); if ( *tmp && !isspace(*tmp) ) { if ( str[0]=='.' && (!str[1] || isspace(str[1])) ) return -1; // missing value error("Could not parse: [%s]\n", tgt->line.s); } if ( *alt_freq<0 || *alt_freq>1 ) error("Could not parse AF: [%s]\n", tgt->line.s); return 0; } int8_t *get_GT(args_t *args, bcf1_t *line) { int i; for (i=0; in_fmt; i++) if ( line->d.fmt[i].id==args->gt_hdr_id ) break; if ( i==line->n_fmt ) return NULL; // the tag is not present in this record bcf_fmt_t *fmt = &line->d.fmt[i]; if ( fmt->n!=2 ) return NULL; // not diploid if ( fmt->type!=BCF_BT_INT8 ) error("This is unexpected, GT type is %d\n", fmt->type); return (int8_t*) fmt->p; } int estimate_AF_from_GT(args_t *args, int8_t *gt, double *alt_freq) { int i, nalt = 0, nref = 0; if ( args->af_smpl ) // subset samples for AF estimate { for (i=0; iaf_smpl->n; i++) { int ismpl = args->af_smpl->idx[i]; if ( bcf_gt_is_missing(gt[2*ismpl]) || bcf_gt_is_missing(gt[2*ismpl+1]) ) continue; if ( bcf_gt_allele(gt[2*ismpl]) ) nalt++; else nref++; if ( bcf_gt_allele(gt[2*ismpl+1]) ) nalt++; else nref++; } } else // all samples used in AF estimate { int8_t *end = gt + 2*bcf_hdr_nsamples(args->hdr); while ( gt < end ) { if ( bcf_gt_is_missing(gt[0]) || bcf_gt_is_missing(gt[1]) ) { gt += 2; continue; } if ( bcf_gt_allele(gt[0]) ) nalt++; else nref++; if ( bcf_gt_allele(gt[1]) ) nalt++; else nref++; gt += 2; } } if ( !nalt && !nref ) return -1; *alt_freq = (double)nalt / (nalt + nref); return 0; } int estimate_AF_from_PL(args_t *args, bcf_fmt_t *fmt_pl, int ial, double *alt_freq) { double af = 0; int i, j, naf = 0; int irr = bcf_alleles2gt(0,0), ira = bcf_alleles2gt(0,ial), iaa = bcf_alleles2gt(ial,ial); if ( iaa >= fmt_pl->n ) return -1; // not diploid or wrong number of fields if ( args->af_smpl ) // subset samples for AF estimate { #define BRANCH(type_t) \ { \ for (i=0; iaf_smpl->n; i++) \ { \ int ismpl = args->af_smpl->idx[i]; \ type_t *p = (type_t*)fmt_pl->p + fmt_pl->n*ismpl; \ if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue; /* missing value */ \ if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue; /* all values are the same */ \ double prob[3], norm = 0; \ prob[0] = args->pl2p[ max255(p[irr]) ]; \ prob[1] = args->pl2p[ max255(p[ira]) ]; \ prob[2] = args->pl2p[ max255(p[iaa]) ]; \ for (j=0; j<3; j++) norm += prob[j]; \ for (j=0; j<3; j++) prob[j] /= norm; \ af += 0.5*prob[1] + prob[2]; \ naf++; \ } \ } switch (fmt_pl->type) { case BCF_BT_INT8: BRANCH(int8_t); break; case BCF_BT_INT16: BRANCH(int16_t); break; case BCF_BT_INT32: BRANCH(int32_t); break; default: fprintf(bcftools_stderr,"Unknown format type for PL: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt_pl->type); bcftools_exit(1); } #undef BRANCH } else // all samples used in AF estimate { int nsmpl = bcf_hdr_nsamples(args->hdr); #define BRANCH(type_t) \ { \ type_t *p = (type_t*)fmt_pl->p; \ p -= fmt_pl->n; \ for (i=0; in; \ if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue; /* missing value */ \ if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue; /* all values are the same */ \ double prob[3], norm = 0; \ prob[0] = args->pl2p[ max255(p[irr]) ]; \ prob[1] = args->pl2p[ max255(p[ira]) ]; \ prob[2] = args->pl2p[ max255(p[iaa]) ]; \ for (j=0; j<3; j++) norm += prob[j]; \ for (j=0; j<3; j++) prob[j] /= norm; \ af += 0.5*prob[1] + prob[2]; \ naf++; \ } \ } switch (fmt_pl->type) { case BCF_BT_INT8: BRANCH(int8_t); break; case BCF_BT_INT16: BRANCH(int16_t); break; case BCF_BT_INT32: BRANCH(int32_t); break; default: fprintf(bcftools_stderr,"Unknown format type for PL: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt_pl->type); bcftools_exit(1); } #undef BRANCH } if ( !naf ) return -1; *alt_freq = af / naf; return 0; } bcf_fmt_t *get_PL(args_t *args, bcf1_t *line) { int i; for (i=0; in_fmt; i++) if ( line->d.fmt[i].id==args->pl_hdr_id ) return &line->d.fmt[i]; return NULL; } int process_line(args_t *args, bcf1_t *line, int ial) { if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT); double alt_freq; int8_t *GTs = NULL; bcf_fmt_t *fmt_pl = NULL; // Set allele frequency int ret = 0, i,j; if ( args->af_tag ) { // Use an INFO tag provided by the user ret = bcf_get_info_float(args->hdr, line, args->af_tag, &args->AFs, &args->mAFs); if ( ret>0 ) alt_freq = args->AFs[ial-1]; if ( ret==-2 ) error("Type mismatch for INFO/%s tag at %s:%"PRId64"\n", args->af_tag, bcf_seqname(args->hdr,line), (int64_t) line->pos+1); } else if ( args->af_fname ) { // Read AF from a file ret = read_AF(args->files->targets, line, &alt_freq); } else if ( args->dflt_AF > 0 ) { alt_freq = args->dflt_AF; } else if ( args->estimate_AF ) { // Estimate AF from GTs or PLs of all samples or samples listed in a file if ( args->af_from_PL ) { fmt_pl = get_PL(args, line); if ( !fmt_pl ) return -1; ret = estimate_AF_from_PL(args, fmt_pl, ial, &alt_freq); } else { GTs = get_GT(args, line); if ( !GTs ) return -1; ret = estimate_AF_from_GT(args, GTs, &alt_freq); } } else { // Use AC/AN int AC = -1, AN = 0; ret = bcf_get_info_int32(args->hdr, line, "AN", &args->itmp, &args->mitmp); if ( ret==1 ) { AN = args->itmp[0]; ret = bcf_get_info_int32(args->hdr, line, "AC", &args->itmp, &args->mitmp); if ( ret>0 ) AC = args->itmp[0]; } if ( AN<=0 || AC<0 ) ret = -1; else alt_freq = (double) AC/AN; } if ( args->dflt_AF>0 && (ret<0 || alt_freq==0.0) ) alt_freq = args->dflt_AF; else if ( ret<0 ) { args->nno_af++; return ret; } else if ( alt_freq==0.0 ) { args->nno_af++; return -1; } int irr = bcf_alleles2gt(0,0), ira = bcf_alleles2gt(0,ial), iaa = bcf_alleles2gt(ial,ial); if ( args->fake_PLs ) { if ( !GTs ) GTs = get_GT(args, line); } else { fmt_pl = get_PL(args, line); if ( !fmt_pl ) return -1; if ( iaa >= fmt_pl->n ) return -1; // not diploid or wrong number of fields } for (i=0; iroh_smpl->n; i++) { int ismpl = args->roh_smpl->idx[i]; // set P(D|G) double pdg[3]; if ( args->fake_PLs ) { int8_t *gt = GTs + 2*ismpl; if ( bcf_gt_is_missing(gt[0]) || bcf_gt_is_missing(gt[1]) ) continue; int a = bcf_gt_allele(gt[0]); int b = bcf_gt_allele(gt[1]); if ( a!=b ) { pdg[0] = pdg[2] = args->unseen_PL; pdg[1] = 1 - 2*args->unseen_PL; } else if ( a==0 ) { pdg[0] = 1 - args->unseen_PL - args->unseen_PL*args->unseen_PL; pdg[1] = args->unseen_PL; pdg[2] = args->unseen_PL*args->unseen_PL; } else { pdg[0] = args->unseen_PL*args->unseen_PL; pdg[1] = args->unseen_PL; pdg[2] = 1 - args->unseen_PL - args->unseen_PL*args->unseen_PL; } } else { #define BRANCH(type_t) \ { \ type_t *p = (type_t*)fmt_pl->p + fmt_pl->n*ismpl; \ if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue; /* missing value */ \ if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue; /* all values are the same */ \ pdg[0] = args->pl2p[ max255(p[irr]) ]; \ pdg[1] = args->pl2p[ max255(p[ira]) ]; \ pdg[2] = args->pl2p[ max255(p[iaa]) ]; \ } switch (fmt_pl->type) { case BCF_BT_INT8: BRANCH(int8_t); break; case BCF_BT_INT16: BRANCH(int16_t); break; case BCF_BT_INT32: BRANCH(int32_t); break; default: fprintf(bcftools_stderr,"Unknown format type for PL: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt_pl->type); bcftools_exit(1); } #undef BRANCH } double sum = pdg[0] + pdg[1] + pdg[2]; if ( !sum ) continue; for (j=0; j<3; j++) pdg[j] /= sum; if ( args->skip_homref && pdg[0]>0.99 ) continue; smpl_t *smpl = &args->smpl[i]; smpl->nused++; if ( smpl->nsites >= smpl->msites ) { hts_expand(uint32_t,smpl->nsites+1,smpl->msites,smpl->sites); smpl->eprob = (double*) realloc(smpl->eprob,sizeof(*smpl->eprob)*smpl->msites*2); if ( !smpl->eprob ) error("Error: failed to alloc %"PRIu64" bytes\n", (uint64_t)(sizeof(*smpl->eprob)*smpl->msites*2)); } // Calculate emission probabilities P(D|AZ) and P(D|HW) double *eprob = &smpl->eprob[2*smpl->nsites]; eprob[STATE_AZ] = pdg[0]*(1-alt_freq) + pdg[2]*alt_freq; eprob[STATE_HW] = pdg[0]*(1-alt_freq)*(1-alt_freq) + 2*pdg[1]*(1-alt_freq)*alt_freq + pdg[2]*alt_freq*alt_freq; smpl->sites[smpl->nsites] = line->pos; smpl->nsites++; if ( args->vi_training ) { if ( !smpl->nrid || line->rid!=smpl->rid[smpl->nrid-1] ) { smpl->nrid++; smpl->rid = (int*) realloc(smpl->rid,sizeof(*smpl->rid)*smpl->nrid); smpl->rid[smpl->nrid-1] = line->rid; smpl->rid_off = (int*) realloc(smpl->rid_off,sizeof(*smpl->rid_off)*smpl->nrid); smpl->rid_off[smpl->nrid-1] = smpl->nsites - 1; } } else if ( args->nbuf_max && smpl->nsites >= args->nbuf_max ) flush_viterbi(args, i); } return 0; } static void vcfroh(args_t *args, bcf1_t *line) { int i; // Are we done? if ( !line ) { for (i=0; iroh_smpl->n; i++) flush_viterbi(args, i); return; } // Skip unwanted lines, for simplicity we consider only biallelic sites if ( line->rid == args->skip_rid ) return; // This can be raw callable VCF with the symbolic unseen allele <*> int ial = 0, nalt = line->n_allele - 1; for (i=1; in_allele; i++) { if ( !strcmp("<*>",line->d.allele[i]) || !strcmp("",line->d.allele[i]) ) nalt--; else if ( !ial ) ial = i; } if ( !nalt ) // no ALT allele { args->nno_alt++; if ( !args->include_noalt_sites ) return; } else if ( nalt>1 ) { args->nmultiallelic++; return; } if ( args->snps_only && !bcf_is_snp(line) ) return; // Initialize genetic map int skip_rid = 0; if ( args->prev_rid<0 ) skip_rid = load_genmap(args, bcf_seqname(args->hdr,line)); // New chromosome? if ( args->prev_rid!=line->rid ) { if ( !args->vi_training ) { for (i=0; iroh_smpl->n; i++) { flush_viterbi(args, i); hmm_reset(args->hmm, args->smpl[i].snapshot); } } args->prev_rid = line->rid; args->prev_pos = line->pos; skip_rid = load_genmap(args, bcf_seqname(args->hdr,line)); } else if ( args->prev_pos == line->pos ) { args->ndup++; return; // skip duplicate positions } if ( skip_rid ) { fprintf(bcftools_stderr,"Skipping the sequence, no genmap for %s\n", bcf_seqname(args->hdr,line)); args->skip_rid = line->rid; return; } if ( args->prev_pos > line->pos ) error("The file is not sorted?!\n"); args->prev_rid = line->rid; args->prev_pos = line->pos; // parse the new line process_line(args, line, ial); } static void usage(args_t *args) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: HMM model for detecting runs of autozygosity.\n"); fprintf(bcftools_stderr, "Usage: bcftools roh [options] \n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "General Options:\n"); fprintf(bcftools_stderr, " --AF-dflt if AF is not known, use this allele frequency [skip]\n"); fprintf(bcftools_stderr, " --AF-tag use TAG for allele frequency\n"); fprintf(bcftools_stderr, " --AF-file read allele frequencies from file (CHR\\tPOS\\tREF,ALT\\tAF)\n"); fprintf(bcftools_stderr, " -b --buffer-size buffer size and the number of overlapping sites, 0 for unlimited [0]\n"); fprintf(bcftools_stderr, " If the first number is negative, it is interpreted as the maximum memory to\n"); fprintf(bcftools_stderr, " use, in MB. The default overlap is set to roughly 1%% of the buffer size.\n"); fprintf(bcftools_stderr, " -e, --estimate-AF [TAG], estimate AF from FORMAT/TAG (GT or PL) of all samples (\"-\") or samples listed\n"); fprintf(bcftools_stderr, " in . If TAG is not given, the frequency is estimated from GT by default\n"); fprintf(bcftools_stderr, " --exclude exclude sites for which the expression is true\n"); fprintf(bcftools_stderr, " -G, --GTs-only use GTs and ignore PLs, instead using for PL of the two least likely genotypes.\n"); fprintf(bcftools_stderr, " Safe value to use is 30 to account for GT errors.\n"); fprintf(bcftools_stderr, " --include select sites for which the expression is true\n"); fprintf(bcftools_stderr, " -i, --ignore-homref skip hom-ref genotypes (0/0)\n"); fprintf(bcftools_stderr, " --include-noalt include sites with no ALT allele (ignored by default)\n"); fprintf(bcftools_stderr, " -I, --skip-indels skip indels as their genotypes are enriched for errors\n"); fprintf(bcftools_stderr, " -m, --genetic-map genetic map in IMPUTE2 format, single file or mask, where string \"{CHROM}\"\n"); fprintf(bcftools_stderr, " is replaced with chromosome name\n"); fprintf(bcftools_stderr, " -M, --rec-rate constant recombination rate per bp\n"); fprintf(bcftools_stderr, " -o, --output write output to a file [standard output]\n"); fprintf(bcftools_stderr, " -O, --output-type [srz] output s:per-site, r:regions, z:compressed [sr]\n"); fprintf(bcftools_stderr, " -r, --regions restrict to comma-separated list of regions\n"); fprintf(bcftools_stderr, " -R, --regions-file restrict to regions listed in a file\n"); fprintf(bcftools_stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " -s, --samples list of samples to analyze [all samples]\n"); fprintf(bcftools_stderr, " -S, --samples-file file of samples to analyze [all samples]\n"); fprintf(bcftools_stderr, " -t, --targets similar to -r but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " -T, --targets-file similar to -R but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(bcftools_stderr, " --threads use multithreading with worker threads [0]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "HMM Options:\n"); fprintf(bcftools_stderr, " -a, --hw-to-az P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state [6.7e-8]\n"); fprintf(bcftools_stderr, " -H, --az-to-hw P(HW|AZ) transition probability from AZ to HW state [5e-9]\n"); fprintf(bcftools_stderr, " -V, --viterbi-training estimate HMM parameters, is the convergence threshold, e.g. 1e-10 (experimental)\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int main_vcfroh(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->files = bcf_sr_init(); args->t2AZ = 6.7e-8; args->t2HW = 5e-9; args->rec_rate = 0; int regions_is_file = 0, targets_is_file = 0; int regions_overlap = 1; int targets_overlap = 0; static struct option loptions[] = { {"AF-tag",1,0,0}, {"AF-file",1,0,1}, {"AF-dflt",1,0,2}, {"include",1,0,3}, {"exclude",1,0,4}, {"include-noalt",0,0,5}, {"buffer-size",1,0,'b'}, {"ignore-homref",0,0,'i'}, {"estimate-AF",1,0,'e'}, {"output",1,0,'o'}, {"output-type",1,0,'O'}, {"GTs-only",1,0,'G'}, {"samples",1,0,'s'}, {"samples-file",1,0,'S'}, {"hw-to-az",1,0,'a'}, {"az-to-hw",1,0,'H'}, {"viterbi-training",1,0,'V'}, {"targets",1,0,'t'}, {"targets-file",1,0,'T'}, {"targets-overlap",required_argument,NULL,6}, {"regions",1,0,'r'}, {"regions-file",1,0,'R'}, {"regions-overlap",required_argument,NULL,7}, {"genetic-map",1,0,'m'}, {"rec-rate",1,0,'M'}, {"skip-indels",0,0,'I'}, {"threads",1,0,9}, {0,0,0,0} }; int naf_opts = 0; char *tmp; while ((c = getopt_long(argc, argv, "h?r:R:t:T:H:a:s:S:m:M:G:Ia:e:V:b:O:o:i",loptions,NULL)) >= 0) { switch (c) { case 0: args->af_tag = optarg; naf_opts++; break; case 1: args->af_fname = optarg; naf_opts++; break; case 2: args->dflt_AF = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: --AF-dflt %s\n", optarg); break; case 3 : if ( args->filter_str ) error("Error: only one --include or --exclude expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 4 : if ( args->filter_str ) error("Error: only one --include or --exclude expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 5: args->include_noalt_sites = 1; break; case 'o': args->output_fname = optarg; break; case 'O': if ( strchr(optarg,'s') || strchr(optarg,'S') ) args->output_type |= OUTPUT_ST; if ( strchr(optarg,'r') || strchr(optarg,'R') ) args->output_type |= OUTPUT_RG; if ( strchr(optarg,'z') || strchr(optarg,'z') ) args->output_type |= OUTPUT_GZ; break; case 'e': args->estimate_AF = optarg; naf_opts++; break; case 'b': args->buffer_size = optarg; break; case 'i': args->skip_homref = 1; break; case 'I': args->snps_only = 1; break; case 'G': args->fake_PLs = 1; args->unseen_PL = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -G %s\n", optarg); args->unseen_PL = pow(10,-args->unseen_PL/10.); break; case 'm': args->genmap_fname = optarg; break; case 'M': args->rec_rate = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -M %s\n", optarg); break; case 's': args->samples = strdup(optarg); break; case 'S': args->samples = strdup(optarg); args->samples_is_file = 1; break; case 'a': args->t2AZ = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -a %s\n", optarg); break; case 'H': args->t2HW = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -H %s\n", optarg); break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; targets_is_file = 1; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 6 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 7 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 'V': args->vi_training = 1; args->baum_welch_th = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: --viterbi-training %s\n", optarg); break; case 'h': case '?': usage(args); break; default: error("Unknown argument: %s\n", optarg); } } if ( !args->output_fname ) args->output_fname = "bcftools_stdout"; if ( !args->output_type || args->output_type==OUTPUT_GZ ) args->output_type |= OUTPUT_ST|OUTPUT_RG; char *fname = NULL; if ( optind==argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else usage(args); } else fname = argv[optind]; if ( args->vi_training && args->buffer_size ) error("Error: cannot use -b with -V\n"); if ( args->t2AZ<0 || args->t2AZ>1 ) error("Error: The parameter --hw-to-az is not in [0,1] .. %e\n", args->t2AZ); if ( args->t2HW<0 || args->t2HW>1 ) error("Error: The parameter --az-to-hw is not in [0,1] .. %e\n", args->t2HW); if ( naf_opts>1 ) error("Error: The options --AF-tag, --AF-file and -e are mutually exclusive\n"); if ( args->af_fname && args->targets_list ) error("Error: The options --AF-file and -t are mutually exclusive\n"); if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } if ( args->af_fname ) { if ( bcf_sr_set_targets(args->files, args->af_fname, 1, 3)<0 ) error("Failed to read the targets: %s\n", args->af_fname); } if ( args->n_threads && bcf_sr_set_threads(args->files, args->n_threads)<0) error("Failed to create threads\n"); if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); init_data(args); while ( bcf_sr_next_line(args->files) ) { args->ntot++; bcf1_t *line = bcf_sr_get_line(args->files,0); if ( args->filter ) { int pass = filter_test(args->filter, line, NULL); if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; if ( !pass ) { args->nfiltered++; continue; } } vcfroh(args, line); } vcfroh(args, NULL); int i, nmin = 0; for (i=0; iroh_smpl->n; i++) if ( !i || args->smpl[i].nused < nmin ) nmin = args->smpl[i].nused; if ( args->af_fname ) fprintf(bcftools_stderr,"Number of lines overlapping with --AF-file/processed: %d/%d\n", args->ntot,nmin); else fprintf(bcftools_stderr,"Number of lines total/processed: %d/%d\n", args->ntot,nmin); fprintf(bcftools_stderr,"Number of lines filtered/no AF/no alt/multiallelic/dup: %d/%d/%d/%d/%d\n", args->nfiltered,args->nno_af,args->nno_alt,args->nmultiallelic,args->ndup); if ( nmin==0 ) { fprintf(bcftools_stderr,"No usable sites were found.\n"); if ( !naf_opts && !args->dflt_AF ) fprintf(bcftools_stderr, " Consider using one of the AF options.\n"); } destroy_data(args); free(args); return 0; } pysam-0.23.0/bcftools/vcfsom.c000066400000000000000000000577131475062545500162330ustar00rootroot00000000000000/* vcfsom.c -- SOM (Self-Organizing Map) filtering. Copyright (C) 2013-2014, 2020 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #define SOM_TRAIN 1 #define SOM_CLASSIFY 2 typedef struct { int ndim; // dimension of the map (2D, 3D, ...) int nbin; // number of bins in th map int size; // pow(nbin,ndim) int kdim; // dimension of the input vectors int nt, t; // total number of learning cycles and the current cycle double *w, *c; // weights and counts (sum of learning influence) double learn; // learning rate double bmu_th; // best-matching unit threshold int *a_idx, *b_idx; // temp arrays for traversing variable number of nested loops double *div; // dtto } som_t; typedef struct { // SOM parameters double bmu_th, learn; int ndim, nbin, ntrain, t; int nfold; // n-fold cross validation = the number of SOMs som_t **som; // annots reader's data htsFile *file; // reader kstring_t str; // temporary string for the reader int dclass, mvals; double *vals; // training data double *train_dat; int *train_class, mtrain_class, mtrain_dat; int rand_seed, good_class, bad_class; char **argv, *fname, *prefix; int argc, action, train_bad, merge; } args_t; static void usage(void); FILE *open_file(char **fname, const char *mode, const char *fmt, ...) HTS_FORMAT(HTS_PRINTF_FMT, 3, 4); char * HTS_FORMAT(HTS_PRINTF_FMT, 1, 2) msprintf(const char *fmt, ...) { va_list ap; va_start(ap, fmt); int n = vsnprintf(NULL, 0, fmt, ap) + 2; va_end(ap); char *str = (char*)malloc(n); va_start(ap, fmt); vsnprintf(str, n, fmt, ap); va_end(ap); return str; } /* * char *t, *p = str; * t = column_next(p, '\t'); * if ( strlen("")==t-p && !strncmp(p,"",t-p) ) printf("found!\n"); * * char *t; * t = column_next(str, '\t'); if ( !*t ) error("expected field\n", str); * t = column_next(t+1, '\t'); if ( !*t ) error("expected field\n", str); */ static inline char *column_next(char *start, char delim) { char *end = start; while (*end && *end!=delim) end++; return end; } /** * annots_reader_next() - reads next line from annots.tab.gz and sets: class, vals * Returns 1 on successful read or 0 if no further record could be read. */ int annots_reader_next(args_t *args) { args->str.l = 0; if ( hts_getline(args->file,'\n',&args->str)<=0 ) return 0; char *t, *line = args->str.s; if ( !args->mvals ) { t = line; while ( *t ) { if ( *t=='\t' ) args->mvals++; t++; } args->vals = (double*) malloc(args->mvals*sizeof(double)); } // class args->dclass = atoi(line); t = column_next(line, '\t'); // values int i; for (i=0; imvals; i++) { if ( !*t ) error("Could not parse %d-th data field: is the line truncated?\nThe line was: [%s]\n",i+2,line); args->vals[i] = atof(++t); t = column_next(t,'\t'); } return 1; } void annots_reader_reset(args_t *args) { if ( args->file ) hts_close(args->file); if ( !args->fname ) error("annots_reader_reset: no fname\n"); args->file = hts_open(args->fname, "r"); } void annots_reader_close(args_t *args) { hts_close(args->file); } static void som_write_map(char *prefix, som_t **som, int nsom) { FILE *fp = open_file(NULL,"w","%s.som",prefix); size_t nw; if ( (nw=fwrite("SOMv1",5,1,fp))!=5 ) error("Failed to write 5 bytes\n"); if ( (nw=fwrite(&nsom,sizeof(int),1,fp))!=sizeof(int) ) error("Failed to write %zu bytes\n",sizeof(int)); int i; for (i=0; isize,sizeof(int),1,fp))!=sizeof(int) ) error("Failed to write %zu bytes\n",sizeof(int)); if ( (nw=fwrite(&som[i]->kdim,sizeof(int),1,fp))!=sizeof(int) ) error("Failed to write %zu bytes\n",sizeof(int)); if ( (nw=fwrite(som[i]->w,sizeof(double),som[i]->size*som[i]->kdim,fp))!=sizeof(double)*som[i]->size*som[i]->kdim ) error("Failed to write %zu bytes\n",sizeof(double)*som[i]->size*som[i]->kdim); if ( (nw=fwrite(som[i]->c,sizeof(double),som[i]->size,fp))!=sizeof(double)*som[i]->size ) error("Failed to write %zu bytes\n",sizeof(double)*som[i]->size); } if ( fclose(fp) ) error("%s.som: fclose failed\n",prefix); } static som_t** som_load_map(char *prefix, int *nsom) { FILE *fp = open_file(NULL,"r","%s.som",prefix); char buf[5]; if ( fread(buf,5,1,fp)!=1 || strncmp(buf,"SOMv1",5) ) error("Could not parse %s.som\n", prefix); if ( fread(nsom,sizeof(int),1,fp)!=1 ) error("Could not read %s.som\n", prefix); som_t **som = (som_t**)malloc(*nsom*sizeof(som_t*)); int i; for (i=0; i<*nsom; i++) { som[i] = (som_t*) calloc(1,sizeof(som_t)); if ( fread(&som[i]->size,sizeof(int),1,fp) != 1 ) error("Could not read %s.som\n", prefix); if ( fread(&som[i]->kdim,sizeof(int),1,fp) != 1 ) error("Could not read %s.som\n", prefix); som[i]->w = (double*) malloc(sizeof(double)*som[i]->size*som[i]->kdim); som[i]->c = (double*) malloc(sizeof(double)*som[i]->size); if ( fread(som[i]->w,sizeof(double),som[i]->size*som[i]->kdim,fp) != som[i]->size*som[i]->kdim ) error("Could not read from %s.som\n", prefix); if ( fread(som[i]->c,sizeof(double),som[i]->size,fp) != som[i]->size ) error("Could not read from %s.som\n", prefix); } if ( fclose(fp) ) error("%s.som: fclose failed\n",prefix); return som; } static void som_create_plot(som_t *som, char *prefix) { if ( som->ndim!=2 ) return; char *fname; FILE *fp = open_file(&fname,"w","%s.py",prefix); fprintf(fp, "import matplotlib as mpl\n" "mpl.use('Agg')\n" "import matplotlib.pyplot as plt\n" "\n" "dat = [\n" ); int i,j; double *val = som->c; for (i=0; inbin; i++) { fprintf(fp,"["); for (j=0; jnbin; j++) { if ( j>0 ) fprintf(fp,","); fprintf(fp,"%e", *val); val++; } fprintf(fp,"],\n"); } fprintf(fp, "]\n" "fig = plt.figure()\n" "ax1 = plt.subplot(111)\n" "im1 = ax1.imshow(dat)\n" "fig.colorbar(im1)\n" "plt.savefig('%s.png')\n" "plt.close()\n" "\n", prefix ); fclose(fp); free(fname); } // Find the best matching unit: the node with minimum distance from the input vector static inline int som_find_bmu(som_t *som, double *vec, double *dist) { double *ptr = som->w; double min_dist = HUGE_VAL; int min_idx = 0; int i, k; for (i=0; isize; i++) { double dist = 0; for (k=0; kkdim; k++) dist += (vec[k] - ptr[k]) * (vec[k] - ptr[k]); if ( dist < min_dist ) { min_dist = dist; min_idx = i; } ptr += som->kdim; } if ( dist ) *dist = min_dist; return min_idx; } static inline double som_get_score(som_t *som, double *vec, double bmu_th) { double *ptr = som->w; double min_dist = HUGE_VAL; int i, k; for (i=0; isize; i++) { if ( som->c[i] >= bmu_th ) { double dist = 0; for (k=0; kkdim; k++) dist += (vec[k] - ptr[k]) * (vec[k] - ptr[k]); if ( dist < min_dist ) min_dist = dist; } ptr += som->kdim; } return sqrt(min_dist); } // Convert flat index to that of a k-dimensional cube static inline void som_idx_to_ndim(som_t *som, int idx, int *ndim) { int i; double sub = 0; ndim[0] = idx/som->div[0]; for (i=1; indim; i++) { sub += ndim[i-1] * som->div[i-1]; ndim[i] = (idx - sub)/som->div[i]; } } static void som_train_site(som_t *som, double *vec, int update_counts) { // update learning rate and learning radius som->t++; double dt = exp(-som->t/som->nt); double learning_rate = som->learn * dt; double radius = som->nbin * dt; radius *= radius; // find the best matching unit and its indexes int min_idx = som_find_bmu(som, vec, NULL); som_idx_to_ndim(som, min_idx, som->a_idx); // update the weights: traverse the map and make all nodes within the // radius more similar to the input vector double *ptr = som->w; double *cnt = som->c; int i, j, k; for (i=0; isize; i++) { som_idx_to_ndim(som, i, som->b_idx); double dist = 0; for (j=0; jndim; j++) dist += (som->a_idx[j] - som->b_idx[j]) * (som->a_idx[j] - som->b_idx[j]); if ( dist <= radius ) { double influence = exp(-dist*dist*0.5/radius) * learning_rate; for (k=0; kkdim; k++) ptr[k] += influence * (vec[k] - ptr[k]); // Bad sites may help to shape the map, but only nodes with big enough // influence will be used for classification. if ( update_counts ) *cnt += influence; } ptr += som->kdim; cnt++; } } static void som_norm_counts(som_t *som) { int i; double max = 0; for (i=0; isize; i++) if ( max < som->c[i] ) max = som->c[i]; for (i=0; isize; i++) som->c[i] /= max; } static som_t *som_init(args_t *args) { som_t *som = (som_t*) calloc(1,sizeof(som_t)); som->ndim = args->ndim; som->nbin = args->nbin; som->kdim = args->mvals; som->nt = args->ntrain; som->learn = args->learn; som->bmu_th = args->bmu_th; som->size = pow(som->nbin,som->ndim); som->w = (double*) malloc(sizeof(double)*som->size*som->kdim); if ( !som->w ) error("Could not alloc %"PRIu64" bytes [nbin=%d ndim=%d kdim=%d]\n", (uint64_t)(sizeof(double)*som->size*som->kdim),som->nbin,som->ndim,som->kdim); som->c = (double*) calloc(som->size,sizeof(double)); if ( !som->w ) error("Could not alloc %"PRIu64" bytes [nbin=%d ndim=%d]\n", (uint64_t)(sizeof(double)*som->size),som->nbin,som->ndim); int i; for (i=0; isize*som->kdim; i++) som->w[i] = random(); som->a_idx = (int*) malloc(sizeof(int)*som->ndim); som->b_idx = (int*) malloc(sizeof(int)*som->ndim); som->div = (double*) malloc(sizeof(double)*som->ndim); for (i=0; indim; i++) som->div[i] = pow(som->nbin,som->ndim-i-1); return som; } static void som_destroy(som_t *som) { free(som->a_idx); free(som->b_idx); free(som->div); free(som->w); free(som->c); free(som); } static void init_data(args_t *args) { // Get first line to learn the vector size annots_reader_reset(args); annots_reader_next(args); if ( args->action==SOM_CLASSIFY ) args->som = som_load_map(args->prefix,&args->nfold); } static void destroy_data(args_t *args) { int i; if ( args->som ) { for (i=0; infold; i++) som_destroy(args->som[i]); } free(args->train_dat); free(args->train_class); free(args->som); free(args->vals); free(args->str.s); } #define MERGE_MIN 0 #define MERGE_MAX 1 #define MERGE_AVG 2 static double get_min_score(args_t *args, int iskip) { int i; double score, min_score = HUGE_VAL; for (i=0; infold; i++) { if ( i==iskip ) continue; score = som_get_score(args->som[i], args->vals, args->bmu_th); if ( i==0 || score < min_score ) min_score = score; } return min_score; } static double get_max_score(args_t *args, int iskip) { int i; double score, max_score = -HUGE_VAL; for (i=0; infold; i++) { if ( i==iskip ) continue; score = som_get_score(args->som[i], args->vals, args->bmu_th); if ( i==0 || max_score < score ) max_score = score; } return max_score; } static double get_avg_score(args_t *args, int iskip) { int i, n = 0; double score = 0; for (i=0; infold; i++) { if ( i==iskip ) continue; score += som_get_score(args->som[i], args->vals, args->bmu_th); n++; } return score/n; } static int cmpfloat_desc(const void *a, const void *b) { float fa = *((float*)a); float fb = *((float*)b); if ( fafb ) return -1; return 0; } static void create_eval_plot(args_t *args) { FILE *fp = open_file(NULL,"w","%s.eval.py", args->prefix); fprintf(fp, "import matplotlib as mpl\n" "mpl.use('Agg')\n" "import matplotlib.pyplot as plt\n" "\n" "import csv\n" "csv.register_dialect('tab', delimiter='\\t', quoting=csv.QUOTE_NONE)\n" "dat = []\n" "with open('%s.eval', 'r') as f:\n" "\treader = csv.reader(f, 'tab')\n" "\tfor row in reader:\n" "\t\tif row[0][0]!='#': dat.append(row)\n" "\n" "fig = plt.figure()\n" "ax1 = plt.subplot(111)\n" "ax1.plot([x[0] for x in dat],[x[1] for x in dat],'g',label='Good')\n" "ax1.plot([x[0] for x in dat],[x[2] for x in dat],'r',label='Bad')\n" "ax1.set_xlabel('SOM score')\n" "ax1.set_ylabel('Number of training sites')\n" "ax1.legend(loc='best',prop={'size':8},frameon=False)\n" "plt.savefig('%s.eval.png')\n" "plt.close()\n" "\n", args->prefix,args->prefix ); fclose(fp); } static void do_train(args_t *args) { // read training sites int i, igood = 0, ibad = 0, ngood = 0, nbad = 0, ntrain = 0; annots_reader_reset(args); while ( annots_reader_next(args) ) { // determine which of the nfold's SOMs to train int isom = 0; if ( args->dclass == args->good_class ) { if ( ++igood >= args->nfold ) igood = 0; isom = igood; ngood++; } else if ( args->dclass == args->bad_class ) { if ( ++ibad >= args->nfold ) ibad = 0; isom = ibad; nbad++; } else error("Could not determine the class: %d (vs %d and %d)\n", args->dclass,args->good_class,args->bad_class); // save the values for evaluation ntrain++; hts_expand(double, ntrain*args->mvals, args->mtrain_dat, args->train_dat); hts_expand(int, ntrain, args->mtrain_class, args->train_class); memcpy(args->train_dat+(ntrain-1)*args->mvals, args->vals, args->mvals*sizeof(double)); args->train_class[ntrain-1] = (args->dclass==args->good_class ? 1 : 0) | isom<<1; // store class + chunk used for training } annots_reader_close(args); // init maps if ( !args->ntrain ) args->ntrain = ngood/args->nfold; srandom(args->rand_seed); args->som = (som_t**) malloc(sizeof(som_t*)*args->nfold); for (i=0; infold; i++) args->som[i] = som_init(args); // train for (i=0; itrain_class[i] & 1; int isom = args->train_class[i] >> 1; if ( is_good || args->train_bad ) som_train_site(args->som[isom], args->train_dat+i*args->mvals, is_good); } // norm and create plots for (i=0; infold; i++) { som_norm_counts(args->som[i]); if ( args->prefix ) { char *bname = msprintf("%s.som.%d", args->prefix,i); som_create_plot(args->som[i], bname); free(bname); } } // evaluate float *good = (float*) malloc(sizeof(float)*ngood); assert(good); float *bad = (float*) malloc(sizeof(float)*nbad); assert(bad); igood = ibad = 0; double max_score = sqrt(args->som[0]->kdim); for (i=0; itrain_class[i] & 1; int isom = args->train_class[i] >> 1; // this vector was used for training isom-th SOM, skip if ( args->nfold==1 ) isom = -1; memcpy(args->vals, args->train_dat+i*args->mvals, args->mvals*sizeof(double)); switch (args->merge) { case MERGE_MIN: score = get_min_score(args, isom); break; case MERGE_MAX: score = get_max_score(args, isom); break; case MERGE_AVG: score = get_avg_score(args, isom); break; } score = 1.0 - score/max_score; if ( is_good ) good[igood++] = score; else bad[ibad++] = score; } qsort(good, ngood, sizeof(float), cmpfloat_desc); qsort(bad, nbad, sizeof(float), cmpfloat_desc); FILE *fp = NULL; if ( args->prefix ) fp = open_file(NULL,"w","%s.eval", args->prefix); igood = 0; ibad = 0; float prev_score = good[0]>bad[0] ? good[0] : bad[0]; int printed = 0; while ( igood 0.9 ) { printf("%.2f\t%.2f\t%e\t# %% of bad [1] and good [2] sites at a cutoff [3]\n", 100.*ibad/nbad,100.*igood/ngood,prev_score); printed = 1; } if ( igoodbad[ibad] ? good[igood] : bad[ibad]; else if ( igoodprefix,strerror(errno)); create_eval_plot(args); som_write_map(args->prefix, args->som, args->nfold); } free(good); free(bad); } static void do_classify(args_t *args) { annots_reader_reset(args); double max_score = sqrt(args->som[0]->kdim); while ( annots_reader_next(args) ) { double score = 0; switch (args->merge) { case MERGE_MIN: score = get_min_score(args, -1); break; case MERGE_MAX: score = get_max_score(args, -1); break; case MERGE_AVG: score = get_avg_score(args, -1); break; } printf("%e\n", 1.0 - score/max_score); } annots_reader_close(args); } static void usage(void) { fprintf(stderr, "\n"); fprintf(stderr, "About: SOM (Self-Organizing Map) filtering.\n"); fprintf(stderr, "Usage: bcftools som --train [options] \n"); fprintf(stderr, " bcftools som --classify [options]\n"); fprintf(stderr, "\n"); fprintf(stderr, "Model training options:\n"); fprintf(stderr, " -f, --nfold n-fold cross-validation (number of maps) [5]\n"); fprintf(stderr, " -p, --prefix prefix of output files\n"); fprintf(stderr, " -s, --size map size [20]\n"); fprintf(stderr, " -t, --train \n"); fprintf(stderr, "\n"); fprintf(stderr, "Classifying options:\n"); fprintf(stderr, " -c, --classify \n"); fprintf(stderr, "\n"); fprintf(stderr, "Experimental training options (no reason to change):\n"); fprintf(stderr, " -b, --bmu-threshold threshold for selection of best-matching unit [0.9]\n"); fprintf(stderr, " -d, --som-dimension SOM dimension [2]\n"); fprintf(stderr, " -e, --exclude-bad exclude bad sites from training, use for evaluation only\n"); fprintf(stderr, " -l, --learning-rate learning rate [1.0]\n"); fprintf(stderr, " -m, --merge -f merge algorithm [avg]\n"); fprintf(stderr, " -n, --ntrain-sites effective number of training sites [number of good sites]\n"); fprintf(stderr, " -r, --random-seed random seed, 0 for time() [1]\n"); fprintf(stderr, "\n"); exit(1); } int main_vcfsom(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->nbin = 20; args->learn = 1.0; args->bmu_th = 0.9; args->nfold = 5; args->rand_seed = 1; args->ndim = 2; args->bad_class = 1; args->good_class = 2; args->merge = MERGE_AVG; args->train_bad = 1; static struct option loptions[] = { {"help",0,0,'h'}, {"prefix",1,0,'p'}, {"ntrain-sites",1,0,'n'}, {"random-seed",1,0,'r'}, {"bmu-threshold",1,0,'b'}, {"exclude-bad",0,0,'e'}, {"learning-rate",1,0,'l'}, {"size",1,0,'s'}, {"som-dimension",1,0,'d'}, {"nfold",1,0,'f'}, {"merge",1,0,'m'}, {"train",0,0,'t'}, {"classify",0,0,'c'}, {0,0,0,0} }; while ((c = getopt_long(argc, argv, "htcp:n:r:b:l:s:f:d:m:e",loptions,NULL)) >= 0) { switch (c) { case 'e': args->train_bad = 0; break; case 'm': if ( !strcmp(optarg,"min") ) args->merge = MERGE_MIN; else if ( !strcmp(optarg,"max") ) args->merge = MERGE_MAX; else if ( !strcmp(optarg,"avg") ) args->merge = MERGE_AVG; else error("The -m method not recognised: %s\n", optarg); break; case 'p': args->prefix = optarg; break; case 'n': args->ntrain = atoi(optarg); break; case 'r': args->rand_seed = atoi(optarg); break; case 'b': args->bmu_th = atof(optarg); break; case 'l': args->learn = atof(optarg); break; case 's': args->nbin = atoi(optarg); break; case 'f': args->nfold = atoi(optarg); break; case 'd': args->ndim = atoi(optarg); if ( args->ndim<2 ) error("Expected -d >=2, got %d\n", args->ndim); if ( args->ndim>3 ) fprintf(stderr,"Warning: This will take a long time and is not going to make the results better: -d %d\n", args->ndim); break; case 't': args->action = SOM_TRAIN; break; case 'c': args->action = SOM_CLASSIFY; break; case 'h': case '?': usage(); break; default: error("Unknown argument: %s\n", optarg); } } if ( !args->rand_seed ) args->rand_seed = time(NULL); if ( argc!=optind+1 ) usage(); args->fname = argv[optind]; init_data(args); if ( args->action == SOM_TRAIN ) do_train(args); else if ( args->action == SOM_CLASSIFY ) do_classify(args); destroy_data(args); free(args); return 0; } pysam-0.23.0/bcftools/vcfsom.c.pysam.c000066400000000000000000000604211475062545500175720ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfsom.c -- SOM (Self-Organizing Map) filtering. Copyright (C) 2013-2014, 2020 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #define SOM_TRAIN 1 #define SOM_CLASSIFY 2 typedef struct { int ndim; // dimension of the map (2D, 3D, ...) int nbin; // number of bins in th map int size; // pow(nbin,ndim) int kdim; // dimension of the input vectors int nt, t; // total number of learning cycles and the current cycle double *w, *c; // weights and counts (sum of learning influence) double learn; // learning rate double bmu_th; // best-matching unit threshold int *a_idx, *b_idx; // temp arrays for traversing variable number of nested loops double *div; // dtto } som_t; typedef struct { // SOM parameters double bmu_th, learn; int ndim, nbin, ntrain, t; int nfold; // n-fold cross validation = the number of SOMs som_t **som; // annots reader's data htsFile *file; // reader kstring_t str; // temporary string for the reader int dclass, mvals; double *vals; // training data double *train_dat; int *train_class, mtrain_class, mtrain_dat; int rand_seed, good_class, bad_class; char **argv, *fname, *prefix; int argc, action, train_bad, merge; } args_t; static void usage(void); FILE *open_file(char **fname, const char *mode, const char *fmt, ...) HTS_FORMAT(HTS_PRINTF_FMT, 3, 4); char * HTS_FORMAT(HTS_PRINTF_FMT, 1, 2) msprintf(const char *fmt, ...) { va_list ap; va_start(ap, fmt); int n = vsnprintf(NULL, 0, fmt, ap) + 2; va_end(ap); char *str = (char*)malloc(n); va_start(ap, fmt); vsnprintf(str, n, fmt, ap); va_end(ap); return str; } /* * char *t, *p = str; * t = column_next(p, '\t'); * if ( strlen("")==t-p && !strncmp(p,"",t-p) ) fprintf(bcftools_stdout, "found!\n"); * * char *t; * t = column_next(str, '\t'); if ( !*t ) error("expected field\n", str); * t = column_next(t+1, '\t'); if ( !*t ) error("expected field\n", str); */ static inline char *column_next(char *start, char delim) { char *end = start; while (*end && *end!=delim) end++; return end; } /** * annots_reader_next() - reads next line from annots.tab.gz and sets: class, vals * Returns 1 on successful read or 0 if no further record could be read. */ int annots_reader_next(args_t *args) { args->str.l = 0; if ( hts_getline(args->file,'\n',&args->str)<=0 ) return 0; char *t, *line = args->str.s; if ( !args->mvals ) { t = line; while ( *t ) { if ( *t=='\t' ) args->mvals++; t++; } args->vals = (double*) malloc(args->mvals*sizeof(double)); } // class args->dclass = atoi(line); t = column_next(line, '\t'); // values int i; for (i=0; imvals; i++) { if ( !*t ) error("Could not parse %d-th data field: is the line truncated?\nThe line was: [%s]\n",i+2,line); args->vals[i] = atof(++t); t = column_next(t,'\t'); } return 1; } void annots_reader_reset(args_t *args) { if ( args->file ) hts_close(args->file); if ( !args->fname ) error("annots_reader_reset: no fname\n"); args->file = hts_open(args->fname, "r"); } void annots_reader_close(args_t *args) { hts_close(args->file); } static void som_write_map(char *prefix, som_t **som, int nsom) { FILE *fp = open_file(NULL,"w","%s.som",prefix); size_t nw; if ( (nw=fwrite("SOMv1",5,1,fp))!=5 ) error("Failed to write 5 bytes\n"); if ( (nw=fwrite(&nsom,sizeof(int),1,fp))!=sizeof(int) ) error("Failed to write %zu bytes\n",sizeof(int)); int i; for (i=0; isize,sizeof(int),1,fp))!=sizeof(int) ) error("Failed to write %zu bytes\n",sizeof(int)); if ( (nw=fwrite(&som[i]->kdim,sizeof(int),1,fp))!=sizeof(int) ) error("Failed to write %zu bytes\n",sizeof(int)); if ( (nw=fwrite(som[i]->w,sizeof(double),som[i]->size*som[i]->kdim,fp))!=sizeof(double)*som[i]->size*som[i]->kdim ) error("Failed to write %zu bytes\n",sizeof(double)*som[i]->size*som[i]->kdim); if ( (nw=fwrite(som[i]->c,sizeof(double),som[i]->size,fp))!=sizeof(double)*som[i]->size ) error("Failed to write %zu bytes\n",sizeof(double)*som[i]->size); } if ( fclose(fp) ) error("%s.som: fclose failed\n",prefix); } static som_t** som_load_map(char *prefix, int *nsom) { FILE *fp = open_file(NULL,"r","%s.som",prefix); char buf[5]; if ( fread(buf,5,1,fp)!=1 || strncmp(buf,"SOMv1",5) ) error("Could not parse %s.som\n", prefix); if ( fread(nsom,sizeof(int),1,fp)!=1 ) error("Could not read %s.som\n", prefix); som_t **som = (som_t**)malloc(*nsom*sizeof(som_t*)); int i; for (i=0; i<*nsom; i++) { som[i] = (som_t*) calloc(1,sizeof(som_t)); if ( fread(&som[i]->size,sizeof(int),1,fp) != 1 ) error("Could not read %s.som\n", prefix); if ( fread(&som[i]->kdim,sizeof(int),1,fp) != 1 ) error("Could not read %s.som\n", prefix); som[i]->w = (double*) malloc(sizeof(double)*som[i]->size*som[i]->kdim); som[i]->c = (double*) malloc(sizeof(double)*som[i]->size); if ( fread(som[i]->w,sizeof(double),som[i]->size*som[i]->kdim,fp) != som[i]->size*som[i]->kdim ) error("Could not read from %s.som\n", prefix); if ( fread(som[i]->c,sizeof(double),som[i]->size,fp) != som[i]->size ) error("Could not read from %s.som\n", prefix); } if ( fclose(fp) ) error("%s.som: fclose failed\n",prefix); return som; } static void som_create_plot(som_t *som, char *prefix) { if ( som->ndim!=2 ) return; char *fname; FILE *fp = open_file(&fname,"w","%s.py",prefix); fprintf(fp, "import matplotlib as mpl\n" "mpl.use('Agg')\n" "import matplotlib.pyplot as plt\n" "\n" "dat = [\n" ); int i,j; double *val = som->c; for (i=0; inbin; i++) { fprintf(fp,"["); for (j=0; jnbin; j++) { if ( j>0 ) fprintf(fp,","); fprintf(fp,"%e", *val); val++; } fprintf(fp,"],\n"); } fprintf(fp, "]\n" "fig = plt.figure()\n" "ax1 = plt.subplot(111)\n" "im1 = ax1.imshow(dat)\n" "fig.colorbar(im1)\n" "plt.savefig('%s.png')\n" "plt.close()\n" "\n", prefix ); fclose(fp); free(fname); } // Find the best matching unit: the node with minimum distance from the input vector static inline int som_find_bmu(som_t *som, double *vec, double *dist) { double *ptr = som->w; double min_dist = HUGE_VAL; int min_idx = 0; int i, k; for (i=0; isize; i++) { double dist = 0; for (k=0; kkdim; k++) dist += (vec[k] - ptr[k]) * (vec[k] - ptr[k]); if ( dist < min_dist ) { min_dist = dist; min_idx = i; } ptr += som->kdim; } if ( dist ) *dist = min_dist; return min_idx; } static inline double som_get_score(som_t *som, double *vec, double bmu_th) { double *ptr = som->w; double min_dist = HUGE_VAL; int i, k; for (i=0; isize; i++) { if ( som->c[i] >= bmu_th ) { double dist = 0; for (k=0; kkdim; k++) dist += (vec[k] - ptr[k]) * (vec[k] - ptr[k]); if ( dist < min_dist ) min_dist = dist; } ptr += som->kdim; } return sqrt(min_dist); } // Convert flat index to that of a k-dimensional cube static inline void som_idx_to_ndim(som_t *som, int idx, int *ndim) { int i; double sub = 0; ndim[0] = idx/som->div[0]; for (i=1; indim; i++) { sub += ndim[i-1] * som->div[i-1]; ndim[i] = (idx - sub)/som->div[i]; } } static void som_train_site(som_t *som, double *vec, int update_counts) { // update learning rate and learning radius som->t++; double dt = exp(-som->t/som->nt); double learning_rate = som->learn * dt; double radius = som->nbin * dt; radius *= radius; // find the best matching unit and its indexes int min_idx = som_find_bmu(som, vec, NULL); som_idx_to_ndim(som, min_idx, som->a_idx); // update the weights: traverse the map and make all nodes within the // radius more similar to the input vector double *ptr = som->w; double *cnt = som->c; int i, j, k; for (i=0; isize; i++) { som_idx_to_ndim(som, i, som->b_idx); double dist = 0; for (j=0; jndim; j++) dist += (som->a_idx[j] - som->b_idx[j]) * (som->a_idx[j] - som->b_idx[j]); if ( dist <= radius ) { double influence = exp(-dist*dist*0.5/radius) * learning_rate; for (k=0; kkdim; k++) ptr[k] += influence * (vec[k] - ptr[k]); // Bad sites may help to shape the map, but only nodes with big enough // influence will be used for classification. if ( update_counts ) *cnt += influence; } ptr += som->kdim; cnt++; } } static void som_norm_counts(som_t *som) { int i; double max = 0; for (i=0; isize; i++) if ( max < som->c[i] ) max = som->c[i]; for (i=0; isize; i++) som->c[i] /= max; } static som_t *som_init(args_t *args) { som_t *som = (som_t*) calloc(1,sizeof(som_t)); som->ndim = args->ndim; som->nbin = args->nbin; som->kdim = args->mvals; som->nt = args->ntrain; som->learn = args->learn; som->bmu_th = args->bmu_th; som->size = pow(som->nbin,som->ndim); som->w = (double*) malloc(sizeof(double)*som->size*som->kdim); if ( !som->w ) error("Could not alloc %"PRIu64" bytes [nbin=%d ndim=%d kdim=%d]\n", (uint64_t)(sizeof(double)*som->size*som->kdim),som->nbin,som->ndim,som->kdim); som->c = (double*) calloc(som->size,sizeof(double)); if ( !som->w ) error("Could not alloc %"PRIu64" bytes [nbin=%d ndim=%d]\n", (uint64_t)(sizeof(double)*som->size),som->nbin,som->ndim); int i; for (i=0; isize*som->kdim; i++) som->w[i] = random(); som->a_idx = (int*) malloc(sizeof(int)*som->ndim); som->b_idx = (int*) malloc(sizeof(int)*som->ndim); som->div = (double*) malloc(sizeof(double)*som->ndim); for (i=0; indim; i++) som->div[i] = pow(som->nbin,som->ndim-i-1); return som; } static void som_destroy(som_t *som) { free(som->a_idx); free(som->b_idx); free(som->div); free(som->w); free(som->c); free(som); } static void init_data(args_t *args) { // Get first line to learn the vector size annots_reader_reset(args); annots_reader_next(args); if ( args->action==SOM_CLASSIFY ) args->som = som_load_map(args->prefix,&args->nfold); } static void destroy_data(args_t *args) { int i; if ( args->som ) { for (i=0; infold; i++) som_destroy(args->som[i]); } free(args->train_dat); free(args->train_class); free(args->som); free(args->vals); free(args->str.s); } #define MERGE_MIN 0 #define MERGE_MAX 1 #define MERGE_AVG 2 static double get_min_score(args_t *args, int iskip) { int i; double score, min_score = HUGE_VAL; for (i=0; infold; i++) { if ( i==iskip ) continue; score = som_get_score(args->som[i], args->vals, args->bmu_th); if ( i==0 || score < min_score ) min_score = score; } return min_score; } static double get_max_score(args_t *args, int iskip) { int i; double score, max_score = -HUGE_VAL; for (i=0; infold; i++) { if ( i==iskip ) continue; score = som_get_score(args->som[i], args->vals, args->bmu_th); if ( i==0 || max_score < score ) max_score = score; } return max_score; } static double get_avg_score(args_t *args, int iskip) { int i, n = 0; double score = 0; for (i=0; infold; i++) { if ( i==iskip ) continue; score += som_get_score(args->som[i], args->vals, args->bmu_th); n++; } return score/n; } static int cmpfloat_desc(const void *a, const void *b) { float fa = *((float*)a); float fb = *((float*)b); if ( fafb ) return -1; return 0; } static void create_eval_plot(args_t *args) { FILE *fp = open_file(NULL,"w","%s.eval.py", args->prefix); fprintf(fp, "import matplotlib as mpl\n" "mpl.use('Agg')\n" "import matplotlib.pyplot as plt\n" "\n" "import csv\n" "csv.register_dialect('tab', delimiter='\\t', quoting=csv.QUOTE_NONE)\n" "dat = []\n" "with open('%s.eval', 'r') as f:\n" "\treader = csv.reader(f, 'tab')\n" "\tfor row in reader:\n" "\t\tif row[0][0]!='#': dat.append(row)\n" "\n" "fig = plt.figure()\n" "ax1 = plt.subplot(111)\n" "ax1.plot([x[0] for x in dat],[x[1] for x in dat],'g',label='Good')\n" "ax1.plot([x[0] for x in dat],[x[2] for x in dat],'r',label='Bad')\n" "ax1.set_xlabel('SOM score')\n" "ax1.set_ylabel('Number of training sites')\n" "ax1.legend(loc='best',prop={'size':8},frameon=False)\n" "plt.savefig('%s.eval.png')\n" "plt.close()\n" "\n", args->prefix,args->prefix ); fclose(fp); } static void do_train(args_t *args) { // read training sites int i, igood = 0, ibad = 0, ngood = 0, nbad = 0, ntrain = 0; annots_reader_reset(args); while ( annots_reader_next(args) ) { // determine which of the nfold's SOMs to train int isom = 0; if ( args->dclass == args->good_class ) { if ( ++igood >= args->nfold ) igood = 0; isom = igood; ngood++; } else if ( args->dclass == args->bad_class ) { if ( ++ibad >= args->nfold ) ibad = 0; isom = ibad; nbad++; } else error("Could not determine the class: %d (vs %d and %d)\n", args->dclass,args->good_class,args->bad_class); // save the values for evaluation ntrain++; hts_expand(double, ntrain*args->mvals, args->mtrain_dat, args->train_dat); hts_expand(int, ntrain, args->mtrain_class, args->train_class); memcpy(args->train_dat+(ntrain-1)*args->mvals, args->vals, args->mvals*sizeof(double)); args->train_class[ntrain-1] = (args->dclass==args->good_class ? 1 : 0) | isom<<1; // store class + chunk used for training } annots_reader_close(args); // init maps if ( !args->ntrain ) args->ntrain = ngood/args->nfold; srandom(args->rand_seed); args->som = (som_t**) malloc(sizeof(som_t*)*args->nfold); for (i=0; infold; i++) args->som[i] = som_init(args); // train for (i=0; itrain_class[i] & 1; int isom = args->train_class[i] >> 1; if ( is_good || args->train_bad ) som_train_site(args->som[isom], args->train_dat+i*args->mvals, is_good); } // norm and create plots for (i=0; infold; i++) { som_norm_counts(args->som[i]); if ( args->prefix ) { char *bname = msprintf("%s.som.%d", args->prefix,i); som_create_plot(args->som[i], bname); free(bname); } } // evaluate float *good = (float*) malloc(sizeof(float)*ngood); assert(good); float *bad = (float*) malloc(sizeof(float)*nbad); assert(bad); igood = ibad = 0; double max_score = sqrt(args->som[0]->kdim); for (i=0; itrain_class[i] & 1; int isom = args->train_class[i] >> 1; // this vector was used for training isom-th SOM, skip if ( args->nfold==1 ) isom = -1; memcpy(args->vals, args->train_dat+i*args->mvals, args->mvals*sizeof(double)); switch (args->merge) { case MERGE_MIN: score = get_min_score(args, isom); break; case MERGE_MAX: score = get_max_score(args, isom); break; case MERGE_AVG: score = get_avg_score(args, isom); break; } score = 1.0 - score/max_score; if ( is_good ) good[igood++] = score; else bad[ibad++] = score; } qsort(good, ngood, sizeof(float), cmpfloat_desc); qsort(bad, nbad, sizeof(float), cmpfloat_desc); FILE *fp = NULL; if ( args->prefix ) fp = open_file(NULL,"w","%s.eval", args->prefix); igood = 0; ibad = 0; float prev_score = good[0]>bad[0] ? good[0] : bad[0]; int printed = 0; while ( igood 0.9 ) { fprintf(bcftools_stdout, "%.2f\t%.2f\t%e\t# %% of bad [1] and good [2] sites at a cutoff [3]\n", 100.*ibad/nbad,100.*igood/ngood,prev_score); printed = 1; } if ( igoodbad[ibad] ? good[igood] : bad[ibad]; else if ( igoodprefix,strerror(errno)); create_eval_plot(args); som_write_map(args->prefix, args->som, args->nfold); } free(good); free(bad); } static void do_classify(args_t *args) { annots_reader_reset(args); double max_score = sqrt(args->som[0]->kdim); while ( annots_reader_next(args) ) { double score = 0; switch (args->merge) { case MERGE_MIN: score = get_min_score(args, -1); break; case MERGE_MAX: score = get_max_score(args, -1); break; case MERGE_AVG: score = get_avg_score(args, -1); break; } fprintf(bcftools_stdout, "%e\n", 1.0 - score/max_score); } annots_reader_close(args); } static void usage(void) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: SOM (Self-Organizing Map) filtering.\n"); fprintf(bcftools_stderr, "Usage: bcftools som --train [options] \n"); fprintf(bcftools_stderr, " bcftools som --classify [options]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Model training options:\n"); fprintf(bcftools_stderr, " -f, --nfold n-fold cross-validation (number of maps) [5]\n"); fprintf(bcftools_stderr, " -p, --prefix prefix of output files\n"); fprintf(bcftools_stderr, " -s, --size map size [20]\n"); fprintf(bcftools_stderr, " -t, --train \n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Classifying options:\n"); fprintf(bcftools_stderr, " -c, --classify \n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Experimental training options (no reason to change):\n"); fprintf(bcftools_stderr, " -b, --bmu-threshold threshold for selection of best-matching unit [0.9]\n"); fprintf(bcftools_stderr, " -d, --som-dimension SOM dimension [2]\n"); fprintf(bcftools_stderr, " -e, --exclude-bad exclude bad sites from training, use for evaluation only\n"); fprintf(bcftools_stderr, " -l, --learning-rate learning rate [1.0]\n"); fprintf(bcftools_stderr, " -m, --merge -f merge algorithm [avg]\n"); fprintf(bcftools_stderr, " -n, --ntrain-sites effective number of training sites [number of good sites]\n"); fprintf(bcftools_stderr, " -r, --random-seed random seed, 0 for time() [1]\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int main_vcfsom(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->nbin = 20; args->learn = 1.0; args->bmu_th = 0.9; args->nfold = 5; args->rand_seed = 1; args->ndim = 2; args->bad_class = 1; args->good_class = 2; args->merge = MERGE_AVG; args->train_bad = 1; static struct option loptions[] = { {"help",0,0,'h'}, {"prefix",1,0,'p'}, {"ntrain-sites",1,0,'n'}, {"random-seed",1,0,'r'}, {"bmu-threshold",1,0,'b'}, {"exclude-bad",0,0,'e'}, {"learning-rate",1,0,'l'}, {"size",1,0,'s'}, {"som-dimension",1,0,'d'}, {"nfold",1,0,'f'}, {"merge",1,0,'m'}, {"train",0,0,'t'}, {"classify",0,0,'c'}, {0,0,0,0} }; while ((c = getopt_long(argc, argv, "htcp:n:r:b:l:s:f:d:m:e",loptions,NULL)) >= 0) { switch (c) { case 'e': args->train_bad = 0; break; case 'm': if ( !strcmp(optarg,"min") ) args->merge = MERGE_MIN; else if ( !strcmp(optarg,"max") ) args->merge = MERGE_MAX; else if ( !strcmp(optarg,"avg") ) args->merge = MERGE_AVG; else error("The -m method not recognised: %s\n", optarg); break; case 'p': args->prefix = optarg; break; case 'n': args->ntrain = atoi(optarg); break; case 'r': args->rand_seed = atoi(optarg); break; case 'b': args->bmu_th = atof(optarg); break; case 'l': args->learn = atof(optarg); break; case 's': args->nbin = atoi(optarg); break; case 'f': args->nfold = atoi(optarg); break; case 'd': args->ndim = atoi(optarg); if ( args->ndim<2 ) error("Expected -d >=2, got %d\n", args->ndim); if ( args->ndim>3 ) fprintf(bcftools_stderr,"Warning: This will take a long time and is not going to make the results better: -d %d\n", args->ndim); break; case 't': args->action = SOM_TRAIN; break; case 'c': args->action = SOM_CLASSIFY; break; case 'h': case '?': usage(); break; default: error("Unknown argument: %s\n", optarg); } } if ( !args->rand_seed ) args->rand_seed = time(NULL); if ( argc!=optind+1 ) usage(); args->fname = argv[optind]; init_data(args); if ( args->action == SOM_TRAIN ) do_train(args); else if ( args->action == SOM_CLASSIFY ) do_classify(args); destroy_data(args); free(args); return 0; } pysam-0.23.0/bcftools/vcfsort.c000066400000000000000000000624611475062545500164200ustar00rootroot00000000000000/* vcfsort.c -- sort subcommand Copyright (C) 2017-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #ifdef _WIN32 #include #endif #include #include #include #include #include #include "kheap.h" #include "bcftools.h" #define MAX_TMP_FILES_PER_LAYER 32 #define MERGE_LAYERS 12 #define MAX_TMP_FILES (MAX_TMP_FILES_PER_LAYER * MERGE_LAYERS) typedef struct { char *fname; htsFile *fh; BGZF *bgz; size_t idx; bcf1_t *rec; int is_merged; } blk_t; typedef struct { size_t len; hts_pos_t pos; int rid; float qual; uint8_t data[]; } packed_bcf_t; typedef struct _args_t { bcf_hdr_t *hdr; char **argv, *fname, *output_fname, *tmp_dir; int argc, output_type, clevel; size_t max_mem, mem; packed_bcf_t **buf; uint8_t *mem_block; size_t nbuf, mbuf, nblk, tmp_count; blk_t blk[MAX_TMP_FILES]; uint32_t tmp_layers[MERGE_LAYERS]; int write_index; } args_t; void clean_files(args_t *args) { int i; fprintf(stderr,"Cleaning\n"); for (i=0; iblk[i]; if ( blk->fname ) { unlink(blk->fname); free(blk->fname); } if ( blk->rec ) bcf_destroy(blk->rec); } rmdir(args->tmp_dir); } void HTS_FORMAT(HTS_PRINTF_FMT, 2, 3) HTS_NORETURN clean_files_and_throw(args_t *args, const char *format, ...) { va_list ap; va_start(ap, format); vfprintf(stderr, format, ap); va_end(ap); clean_files(args); exit(-1); } int cmp_bcf_pos(const void *aptr, const void *bptr) { bcf1_t *a = *((bcf1_t**)aptr); bcf1_t *b = *((bcf1_t**)bptr); if ( a->rid < b->rid ) return -1; if ( a->rid > b->rid ) return 1; if ( a->pos < b->pos ) return -1; if ( a->pos > b->pos ) return 1; return 0; } int cmp_bcf_pos_ref_alt(const void *aptr, const void *bptr) { bcf1_t *a = *((bcf1_t**)aptr); bcf1_t *b = *((bcf1_t**)bptr); if ( a->rid < b->rid ) return -1; if ( a->rid > b->rid ) return 1; if ( a->pos < b->pos ) return -1; if ( a->pos > b->pos ) return 1; // Sort the same chr:pos records lexicographically by ref,alt. // This will be called rarely so should not slow the sorting down // noticeably. int i; for (i=0; in_allele; i++) { if ( i >= b->n_allele ) return 1; int ret = strcasecmp(a->d.allele[i],b->d.allele[i]); if ( ret ) return ret; } if ( a->n_allele < b->n_allele ) return -1; return 0; } static int cmp_packed_bcf_pos_ref_alt(const void *aptr, const void *bptr) { packed_bcf_t *a = *(packed_bcf_t **) aptr; packed_bcf_t *b = *(packed_bcf_t **) bptr; if ( a->rid < b->rid ) return -1; if ( a->rid > b->rid ) return 1; if ( a->pos < b->pos ) return -1; if ( a->pos > b->pos ) return 1; // Sort lexicographically by ref,alt. These are stored tab-separated // as the first item in packed_bcf_t::data return strcmp((char *) a->data, (char *) b->data); } static int cmp_packed_bcf_pos_ref_alt_stable(const void *aptr, const void *bptr) { // cmp_bcf_pos_ref_alt() with tie-breaker to make qsort stable int res = cmp_packed_bcf_pos_ref_alt(aptr, bptr); if (res != 0) return res; // Got a tie - use the position in the original input to break it. // As everything is read into a big memory buffer, for most records // we can just compare the pointers directly. The exception is // any record that didn't quite fit in the memory buffer, causing it to be // flushed. Those are flagged by setting packed_bcf_t::len = SIZE_MAX, and // as they were the last record in the segment, they should always sort // after unflagged records. packed_bcf_t *a = *(packed_bcf_t **) aptr; packed_bcf_t *b = *(packed_bcf_t **) bptr; if (a->len == SIZE_MAX) return 1; if (b->len == SIZE_MAX) return -1; return a < b ? -1 : 1; } static uint8_t *pack_unsigned(uint8_t *data, uint64_t val) { do { *data++ = (val & 0x7f) | ((val > 0x7f) ? 0x80 : 0); val >>= 7; } while (val > 0); return data; } static uint8_t *pack_hts_pos(uint8_t *data, hts_pos_t val) { uint64_t sign = val < 0; uint64_t v = val < 0 ? -(val + 1) : val; v = v << 1 | sign; return pack_unsigned(data, v); } static uint8_t *pack_bcf_data(packed_bcf_t *dest, const bcf1_t *src, int outside_buffer) { uint32_t i; uint8_t *data = dest->data; uint8_t *start = dest->data; dest->pos = src->pos; dest->rid = src->rid; dest->qual = src->qual; // Copy in alleles, for the comparison function for (i = 0; i < src->n_allele; i++) { size_t l = strlen(src->d.allele[i]); if (i > 0) *data++ = '\t'; memcpy(data, src->d.allele[i], l); data += l; } *data++ = '\0'; if (outside_buffer) { dest->len = SIZE_MAX; memcpy(data, &src, sizeof(src)); data += sizeof(src); return data; } data = pack_hts_pos(data, src->rlen); data = pack_unsigned(data, src->n_info); data = pack_unsigned(data, src->n_allele); data = pack_unsigned(data, src->n_fmt); data = pack_unsigned(data, src->n_sample); data = pack_unsigned(data, src->shared.l); data = pack_unsigned(data, src->indiv.l); if (src->shared.l) memcpy(data, src->shared.s, src->shared.l); data += src->shared.l; if (src->indiv.l) memcpy(data, src->indiv.s, src->indiv.l); data += src->indiv.l; dest->len = data - start; return data; } static int write_packed_bcf(BGZF *fp, packed_bcf_t *src) { // Write pos, rid, qual size_t len = src->data - (uint8_t *) &src->pos; if (bgzf_write_small(fp, &src->pos, len) < len) return -1; // Skip the copy of the alleles size_t skip = strlen((char *) src->data) + 1; // Write everything else if (src->len < SIZE_MAX) { // In main memory block len = src->len - skip; if (bgzf_write_small(fp, src->data + skip, len) < len) return -1; } else { // Record didn't fit in the main block. To minimize the // overflow, its packed_bcf_t data will be imcomplete. A pointer to // its bcf1_t struct will have been placed after the allele data // so we can finish the packing job and write it in the same format // the rest of the data bcf1_t *rec; uint8_t tmp[100], *data = tmp; memcpy(&rec, src->data + skip, sizeof(rec)); data = pack_hts_pos(data, rec->rlen); data = pack_unsigned(data, rec->n_info); data = pack_unsigned(data, rec->n_allele); data = pack_unsigned(data, rec->n_fmt); data = pack_unsigned(data, rec->n_sample); data = pack_unsigned(data, rec->shared.l); data = pack_unsigned(data, rec->indiv.l); if (bgzf_write_small(fp, tmp, data - tmp) < data - tmp) return -1; if (rec->shared.l > 0 && bgzf_write_small(fp, rec->shared.s, rec->shared.l) < rec->shared.l) return -1; if (rec->indiv.l > 0 && bgzf_write_small(fp, rec->indiv.s, rec->indiv.l) < rec->indiv.l) return -1; } return 0; } static uint64_t unpack_unsigned(BGZF *fp, int *err) { uint8_t data; uint64_t val = 0; uint32_t i = 0; if (bgzf_read_small(fp, &data, sizeof(data)) <= 0) goto short_read; while (data & 0x80) { val |= (uint64_t)(data & 0x7f) << i; i += 7; if (bgzf_read_small(fp, &data, sizeof(data)) <= 0) goto short_read; } val |= (uint64_t)data << i; return val; short_read: *err = 1; return 0; } static hts_pos_t unpack_hts_pos(BGZF *fp, int *err) { uint64_t v = unpack_unsigned(fp, err); if ((v & 1) == 0) return (hts_pos_t)(v >> 1); else return -(hts_pos_t)(v >> 1) - 1; } static int read_packed_bcf(BGZF *fp, bcf1_t *dest) { int err = 0; packed_bcf_t tmp; size_t len = tmp.data - (uint8_t *) &tmp.pos; bcf_clear(dest); ssize_t got = bgzf_read_small(fp, &tmp.pos, len); if (got == 0) return -1; // EOF if (got < len) return -2; // Error or short read dest->pos = tmp.pos; dest->rid = tmp.rid; dest->qual = tmp.qual; dest->rlen = unpack_hts_pos(fp, &err); dest->n_info = unpack_unsigned(fp, &err); dest->n_allele = unpack_unsigned(fp, &err); dest->n_fmt = unpack_unsigned(fp, &err); dest->n_sample = unpack_unsigned(fp, &err); len = unpack_unsigned(fp, &err); if (ks_resize(&dest->shared, len) != 0) return -2; dest->shared.l = len; len = unpack_unsigned(fp, &err); if (ks_resize(&dest->indiv, len) != 0) return -2; dest->indiv.l = len; err |= bgzf_read_small(fp, dest->shared.s, dest->shared.l) < dest->shared.l; err |= bgzf_read_small(fp, dest->indiv.s, dest->indiv.l) < dest->indiv.l; return err == 0 ? 0 : -2; } void open_tmp_file(args_t *args, blk_t *blk, int is_merged) { kstring_t str = {0,0,0}; int tries = 1000; blk->fh = NULL; blk->bgz = NULL; do { if (ksprintf(ks_clear(&str), "%s/%05zd%s", args->tmp_dir, args->tmp_count++, is_merged ? ".bcf" : "") < 0) { clean_files_and_throw(args, "%s", strerror(errno)); } if (is_merged) blk->fh = hts_open(str.s, "wbx1"); else blk->bgz = bgzf_open(str.s, "wx1"); if ( blk->fh == NULL && blk->bgz == NULL && (errno != EEXIST || --tries <= 0)) { clean_files_and_throw(args, "Cannot write %s: %s\n", str.s, strerror(errno)); } } while (blk->fh == NULL && blk->bgz == NULL); blk->fname = ks_release(&str); blk->idx = args->tmp_count - 1; } void do_partial_merge(args_t *args); void buf_flush(args_t *args, bcf1_t *last_rec) { if ( !args->nbuf ) return; qsort(args->buf, args->nbuf, sizeof(*args->buf), cmp_packed_bcf_pos_ref_alt_stable); if (args->tmp_layers[0] >= MAX_TMP_FILES_PER_LAYER) do_partial_merge(args); assert(args->nblk < MAX_TMP_FILES); blk_t *blk = &args->blk[args->nblk]; blk->is_merged = 0; args->nblk++; args->tmp_layers[0]++; assert(blk->fname == NULL && blk->fh == NULL && blk->bgz == NULL); open_tmp_file(args, blk, 0); int i; for (i=0; inbuf; i++) { if ( write_packed_bcf(blk->bgz, args->buf[i])!=0 ) clean_files_and_throw(args, "[%s] Error: cannot write to %s\n", __func__,blk->fname); } if ( bgzf_close(blk->bgz)!=0 ) clean_files_and_throw(args, "[%s] Error: close failed .. %s\n", __func__,blk->fname); blk->bgz = NULL; args->nbuf = 0; args->mem = 0; } static inline uint8_t *_align_up(uint8_t *ptr) { return (uint8_t*)(((size_t)ptr + 8 - 1) & ~((size_t)(8 - 1))); } #define varint_size(X) ((sizeof(X) * 8 + 7) / 7) // worst case void buf_push(args_t *args, bcf1_t *rec) { size_t delta = sizeof(rec->pos) + sizeof(rec->rid) + sizeof(rec->qual) + varint_size(rec->rlen) + varint_size(2) // n_info + varint_size(2) // n_allele + varint_size(1) // n_fmt + varint_size(3) // n_sample + varint_size(rec->shared.l) + varint_size(rec->indiv.l) + rec->shared.l + rec->indiv.l + rec->unpack_size[1] // Alleles + 8; // the number of _align_up() calls if ( delta > args->max_mem - args->mem ) { packed_bcf_t *tmp = malloc(sizeof(*tmp) + rec->unpack_size[1] * sizeof(bcf1_t *)); if (!tmp) clean_files_and_throw(args, "[%s] Out of memory\n", __func__); pack_bcf_data(tmp, rec, 1); args->nbuf++; hts_expand(bcf1_t*, args->nbuf, args->mbuf, args->buf); args->buf[args->nbuf-1] = tmp; buf_flush(args, rec); free(tmp); bcf_destroy(rec); return; } // make sure nothing has changed in htslib assert( rec->unpacked==BCF_UN_STR && !rec->d.flt && !rec->d.info && !rec->d.fmt && !rec->d.var ); uint8_t *ptr_beg = args->mem_block + args->mem; uint8_t *ptr = _align_up(ptr_beg); packed_bcf_t *packed_rec = (packed_bcf_t *) ptr; ptr = pack_bcf_data(packed_rec, rec, 0); args->nbuf++; hts_expand(bcf1_t*, args->nbuf, args->mbuf, args->buf); args->buf[args->nbuf-1] = packed_rec; delta = ptr - ptr_beg; args->mem += delta; assert( args->mem <= args->max_mem ); bcf_destroy(rec); } void sort_blocks(args_t *args) { htsFile *in = hts_open(args->fname, "r"); if ( !in ) clean_files_and_throw(args, "Could not read %s\n", args->fname); args->hdr = bcf_hdr_read(in); if ( !args->hdr) clean_files_and_throw(args, "Could not read VCF/BCF headers from %s\n", args->fname); while ( 1 ) { bcf1_t *rec = bcf_init(); int ret = bcf_read1(in, args->hdr, rec); if ( ret < -1 ) clean_files_and_throw(args,"Error encountered while parsing the input\n"); if ( ret == -1 ) { bcf_destroy(rec); break; } if ( rec->errcode ) clean_files_and_throw(args,"Error encountered while parsing the input at %s:%"PRIhts_pos"\n",bcf_seqname(args->hdr,rec),rec->pos+1); bcf_unpack(rec, BCF_UN_STR); buf_push(args, rec); } buf_flush(args, NULL); free(args->buf); if ( hts_close(in)!=0 ) clean_files_and_throw(args,"Close failed: %s\n", args->fname); } static inline int blk_is_smaller(blk_t **aptr, blk_t **bptr) { blk_t *a = *aptr; blk_t *b = *bptr; int ret = cmp_bcf_pos_ref_alt(&a->rec, &b->rec); if ( ret < 0 ) return 1; if (ret == 0 && a->idx < b->idx) return 1; return 0; } KHEAP_INIT(blk, blk_t*, blk_is_smaller) void blk_read(args_t *args, khp_blk_t *bhp, bcf_hdr_t *hdr, blk_t *blk) { int ret; if (blk->is_merged) { if ( !blk->fh ) return; ret = bcf_read(blk->fh, hdr, blk->rec); } else { if ( !blk->bgz ) return; ret = read_packed_bcf(blk->bgz, blk->rec); } if ( ret < -1 ) clean_files_and_throw(args, "Error reading %s\n", blk->fname); if ( ret == -1 ) { if (blk->is_merged) { if ( hts_close(blk->fh)!=0 ) clean_files_and_throw(args, "Close failed: %s\n", blk->fname); blk->fh = NULL; return; } else { if ( bgzf_close(blk->bgz) != 0) clean_files_and_throw(args, "Close failed: %s\n", blk->fname); blk->bgz = NULL; return; } } bcf_unpack(blk->rec, BCF_UN_STR); khp_insert(blk, bhp, &blk); } void merge_blocks(args_t *args, htsFile *out, const char *output_fname, int idx_fmt, size_t from) { khp_blk_t *bhp = khp_init(blk); char *index_fn = NULL; size_t i; for (i=from; inblk; i++) { blk_t *blk = &args->blk[i]; if (blk->is_merged) { blk->fh = hts_open(blk->fname, "r"); if ( !blk->fh ) clean_files_and_throw(args, "Could not read %s: %s\n", blk->fname, strerror(errno)); bcf_hdr_t *hdr = bcf_hdr_read(blk->fh); bcf_hdr_destroy(hdr); } else { blk->bgz = bgzf_open(blk->fname, "r"); if (!blk->bgz) clean_files_and_throw(args, "Could not read %s: %s\n", blk->fname, strerror(errno)); } blk_read(args, bhp, args->hdr, blk); } if ( bcf_hdr_write(out, args->hdr)!=0 ) clean_files_and_throw(args, "[%s] Error: cannot write to %s\n", __func__, output_fname); if (idx_fmt) { if ( init_index2(out,args->hdr,output_fname,&index_fn,idx_fmt)<0 ) error("Error: failed to initialise index for %s\n",output_fname); } while ( bhp->ndat ) { blk_t *blk = bhp->dat[0]; if ( bcf_write(out, args->hdr, blk->rec)!=0 ) clean_files_and_throw(args, "[%s] Error: cannot write to %s\n", __func__,args->output_fname); khp_delete(blk, bhp); blk_read(args, bhp, args->hdr, blk); } if ( idx_fmt ) { if ( bcf_idx_save(out)<0 ) { if ( hts_close(out)!=0 ) error("Error: close failed .. %s\n", output_fname); error("Error: cannot write to index %s\n", index_fn); } free(index_fn); } for (i = from; i < args->nblk; i++) { blk_t *blk = &args->blk[i]; if (unlink(blk->fname) != 0) clean_files_and_throw(args, "Couldn't remove temporary file %s\n", blk->fname); free(blk->fname); blk->fname = NULL; } khp_destroy(blk, bhp); } void do_partial_merge(args_t *args) { uint32_t to_layer = 0; size_t to_merge = 0; // Temp. files are arranged in layers of at most MAX_TMP_FILES_PER_LAYER. // When a layer is full, it is merged into the next layer up. Each // layer will therefore contain files with exponentially more records // then the previous one, but will be merged exponentially less frequently. // The result is that the overall complexity will remain O(n*log(n)) // even if we need to do lots of partial merges. while (to_layer < MERGE_LAYERS && args->tmp_layers[to_layer] >= MAX_TMP_FILES_PER_LAYER) { to_merge += args->tmp_layers[to_layer]; args->tmp_layers[to_layer] = 0; to_layer++; } assert(to_merge > 0 && to_merge <= args->nblk); if (to_layer == MERGE_LAYERS) { // Edge case - if we've got here, we've completely used the // temp file allocation, so merge absolutely everything and // leave one file at the highest level. Strictly this breaks // the O(n*log(n)) complexity, but unless MERGE_LAYERS and // MAX_TMP_FILES_PER_LAYER are too small it would take so long // to get here it should never actually happen... assert(to_merge == MAX_TMP_FILES_PER_LAYER * MERGE_LAYERS); to_layer = MERGE_LAYERS - 1; } blk_t tmp = { NULL }; open_tmp_file(args, &tmp, 1); merge_blocks(args, tmp.fh, tmp.fname, 0, args->nblk - to_merge); if (hts_close(tmp.fh) != 0) clean_files_and_throw(args, "Close failed: %s\n", tmp.fname); args->nblk -= to_merge; assert(args->blk[args->nblk].fh == NULL); assert(args->blk[args->nblk].fname == NULL); args->blk[args->nblk].is_merged = 1; args->blk[args->nblk].idx = tmp.idx; args->blk[args->nblk++].fname = tmp.fname; args->tmp_layers[to_layer]++; } void merge_to_output(args_t *args) { char wmode[8] = { 0 }; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); const char *output_fname = args->output_fname ? args->output_fname : "-"; htsFile *out = hts_open(output_fname, wmode); if (!out) clean_files_and_throw(args, "[%s] Error: cannot open %s\n", __func__, output_fname); fprintf(stderr,"Merging %zd temporary files\n", args->nblk); merge_blocks(args, out, output_fname, args->write_index, 0); fprintf(stderr,"Done\n"); if ( hts_close(out)!=0 ) clean_files_and_throw(args, "Close failed: %s\n", output_fname); clean_files(args); } static void usage(args_t *args) { fprintf(stderr, "\n"); fprintf(stderr, "About: Sort VCF/BCF file.\n"); fprintf(stderr, "Usage: bcftools sort [OPTIONS] \n"); fprintf(stderr, "\n"); fprintf(stderr, "Options:\n"); fprintf(stderr, " -m, --max-mem FLOAT[kMG] maximum memory to use [768M]\n"); // using metric units, 1M=1e6 fprintf(stderr, " -o, --output FILE output file name [stdout]\n"); fprintf(stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); #ifdef _WIN32 fprintf(stderr, " -T, --temp-dir DIR temporary files [/bcftools.XXXXXX]\n"); #else fprintf(stderr, " -T, --temp-dir DIR temporary files [/tmp/bcftools.XXXXXX]\n"); #endif fprintf(stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(stderr, "\n"); exit(1); } size_t parse_mem_string(const char *str) { char *tmp; double mem = strtod(str, &tmp); if ( tmp==str ) error("Could not parse the memory string: \"%s\"\n", str); if ( !strcasecmp("k",tmp) ) mem *= 1000; else if ( !strcasecmp("m",tmp) ) mem *= 1000*1000; else if ( !strcasecmp("g",tmp) ) mem *= 1000*1000*1000; return mem; } static void init(args_t *args) { size_t i; args->max_mem *= 0.9; args->mem_block = malloc(args->max_mem); if ( !args->mem_block ) error("Error: could not allocate %zu bytes of memory, try reducing --max-mem\n",args->max_mem); args->mem = 0; for (i = 0; i < MAX_TMP_FILES; i++) { args->blk[i].fname = NULL; args->blk[i].rec = bcf_init(); if (!args->blk[i].rec) clean_files_and_throw(args,"Couldn't allocate bcf record\n"); } args->tmp_dir = init_tmp_prefix(args->tmp_dir); #ifdef _WIN32 int ret = mkdir(mktemp(args->tmp_dir), 0700); if ( ret ) error("mkdir(%s) failed: %s\n", args->tmp_dir,strerror(errno)); #else char *tmp = mkdtemp(args->tmp_dir); if ( !tmp ) error("mkdtemp(%s) failed: %s\n", args->tmp_dir,strerror(errno)); int ret = chmod(tmp, S_IRUSR|S_IWUSR|S_IXUSR); if ( ret ) error("chmod(%s,S_IRUSR|S_IWUSR|S_IXUSR) failed: %s\n", args->tmp_dir,strerror(errno)); #endif fprintf(stderr,"Writing to %s\n", args->tmp_dir); } static void destroy(args_t *args) { bcf_hdr_destroy(args->hdr); free(args->mem_block); free(args->tmp_dir); free(args); } int main_sort(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->max_mem = 768*1000*1000; args->output_fname = "-"; args->clevel = -1; static struct option loptions[] = { {"max-mem",required_argument,NULL,'m'}, {"temp-dir",required_argument,NULL,'T'}, {"output-type",required_argument,NULL,'O'}, {"output-file",required_argument,NULL,'o'}, {"output",required_argument,NULL,'o'}, {"help",no_argument,NULL,'h'}, {"write-index",optional_argument,NULL,'W'}, {0,0,0,0} }; char *tmp; while ((c = getopt_long(argc, argv, "m:T:O:o:W::h?",loptions,NULL)) >= 0) { switch (c) { case 'm': args->max_mem = parse_mem_string(optarg); break; case 'T': args->tmp_dir = optarg; break; case 'o': args->output_fname = optarg; break; case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } }; if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 'h': case '?': usage(args); break; default: error("Unknown argument: %s\n", optarg); } } if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) args->fname = "-"; // reading from stdin else usage(args); } else args->fname = argv[optind]; init(args); sort_blocks(args); merge_to_output(args); destroy(args); return 0; } pysam-0.23.0/bcftools/vcfsort.c.pysam.c000066400000000000000000000630021475062545500177610ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfsort.c -- sort subcommand Copyright (C) 2017-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #ifdef _WIN32 #include #endif #include #include #include #include #include #include "kheap.h" #include "bcftools.h" #define MAX_TMP_FILES_PER_LAYER 32 #define MERGE_LAYERS 12 #define MAX_TMP_FILES (MAX_TMP_FILES_PER_LAYER * MERGE_LAYERS) typedef struct { char *fname; htsFile *fh; BGZF *bgz; size_t idx; bcf1_t *rec; int is_merged; } blk_t; typedef struct { size_t len; hts_pos_t pos; int rid; float qual; uint8_t data[]; } packed_bcf_t; typedef struct _args_t { bcf_hdr_t *hdr; char **argv, *fname, *output_fname, *tmp_dir; int argc, output_type, clevel; size_t max_mem, mem; packed_bcf_t **buf; uint8_t *mem_block; size_t nbuf, mbuf, nblk, tmp_count; blk_t blk[MAX_TMP_FILES]; uint32_t tmp_layers[MERGE_LAYERS]; int write_index; } args_t; void clean_files(args_t *args) { int i; fprintf(bcftools_stderr,"Cleaning\n"); for (i=0; iblk[i]; if ( blk->fname ) { unlink(blk->fname); free(blk->fname); } if ( blk->rec ) bcf_destroy(blk->rec); } rmdir(args->tmp_dir); } void HTS_FORMAT(HTS_PRINTF_FMT, 2, 3) HTS_NORETURN clean_files_and_throw(args_t *args, const char *format, ...) { va_list ap; va_start(ap, format); vfprintf(bcftools_stderr, format, ap); va_end(ap); clean_files(args); bcftools_exit(-1); } int cmp_bcf_pos(const void *aptr, const void *bptr) { bcf1_t *a = *((bcf1_t**)aptr); bcf1_t *b = *((bcf1_t**)bptr); if ( a->rid < b->rid ) return -1; if ( a->rid > b->rid ) return 1; if ( a->pos < b->pos ) return -1; if ( a->pos > b->pos ) return 1; return 0; } int cmp_bcf_pos_ref_alt(const void *aptr, const void *bptr) { bcf1_t *a = *((bcf1_t**)aptr); bcf1_t *b = *((bcf1_t**)bptr); if ( a->rid < b->rid ) return -1; if ( a->rid > b->rid ) return 1; if ( a->pos < b->pos ) return -1; if ( a->pos > b->pos ) return 1; // Sort the same chr:pos records lexicographically by ref,alt. // This will be called rarely so should not slow the sorting down // noticeably. int i; for (i=0; in_allele; i++) { if ( i >= b->n_allele ) return 1; int ret = strcasecmp(a->d.allele[i],b->d.allele[i]); if ( ret ) return ret; } if ( a->n_allele < b->n_allele ) return -1; return 0; } static int cmp_packed_bcf_pos_ref_alt(const void *aptr, const void *bptr) { packed_bcf_t *a = *(packed_bcf_t **) aptr; packed_bcf_t *b = *(packed_bcf_t **) bptr; if ( a->rid < b->rid ) return -1; if ( a->rid > b->rid ) return 1; if ( a->pos < b->pos ) return -1; if ( a->pos > b->pos ) return 1; // Sort lexicographically by ref,alt. These are stored tab-separated // as the first item in packed_bcf_t::data return strcmp((char *) a->data, (char *) b->data); } static int cmp_packed_bcf_pos_ref_alt_stable(const void *aptr, const void *bptr) { // cmp_bcf_pos_ref_alt() with tie-breaker to make qsort stable int res = cmp_packed_bcf_pos_ref_alt(aptr, bptr); if (res != 0) return res; // Got a tie - use the position in the original input to break it. // As everything is read into a big memory buffer, for most records // we can just compare the pointers directly. The exception is // any record that didn't quite fit in the memory buffer, causing it to be // flushed. Those are flagged by setting packed_bcf_t::len = SIZE_MAX, and // as they were the last record in the segment, they should always sort // after unflagged records. packed_bcf_t *a = *(packed_bcf_t **) aptr; packed_bcf_t *b = *(packed_bcf_t **) bptr; if (a->len == SIZE_MAX) return 1; if (b->len == SIZE_MAX) return -1; return a < b ? -1 : 1; } static uint8_t *pack_unsigned(uint8_t *data, uint64_t val) { do { *data++ = (val & 0x7f) | ((val > 0x7f) ? 0x80 : 0); val >>= 7; } while (val > 0); return data; } static uint8_t *pack_hts_pos(uint8_t *data, hts_pos_t val) { uint64_t sign = val < 0; uint64_t v = val < 0 ? -(val + 1) : val; v = v << 1 | sign; return pack_unsigned(data, v); } static uint8_t *pack_bcf_data(packed_bcf_t *dest, const bcf1_t *src, int outside_buffer) { uint32_t i; uint8_t *data = dest->data; uint8_t *start = dest->data; dest->pos = src->pos; dest->rid = src->rid; dest->qual = src->qual; // Copy in alleles, for the comparison function for (i = 0; i < src->n_allele; i++) { size_t l = strlen(src->d.allele[i]); if (i > 0) *data++ = '\t'; memcpy(data, src->d.allele[i], l); data += l; } *data++ = '\0'; if (outside_buffer) { dest->len = SIZE_MAX; memcpy(data, &src, sizeof(src)); data += sizeof(src); return data; } data = pack_hts_pos(data, src->rlen); data = pack_unsigned(data, src->n_info); data = pack_unsigned(data, src->n_allele); data = pack_unsigned(data, src->n_fmt); data = pack_unsigned(data, src->n_sample); data = pack_unsigned(data, src->shared.l); data = pack_unsigned(data, src->indiv.l); if (src->shared.l) memcpy(data, src->shared.s, src->shared.l); data += src->shared.l; if (src->indiv.l) memcpy(data, src->indiv.s, src->indiv.l); data += src->indiv.l; dest->len = data - start; return data; } static int write_packed_bcf(BGZF *fp, packed_bcf_t *src) { // Write pos, rid, qual size_t len = src->data - (uint8_t *) &src->pos; if (bgzf_write_small(fp, &src->pos, len) < len) return -1; // Skip the copy of the alleles size_t skip = strlen((char *) src->data) + 1; // Write everything else if (src->len < SIZE_MAX) { // In main memory block len = src->len - skip; if (bgzf_write_small(fp, src->data + skip, len) < len) return -1; } else { // Record didn't fit in the main block. To minimize the // overflow, its packed_bcf_t data will be imcomplete. A pointer to // its bcf1_t struct will have been placed after the allele data // so we can finish the packing job and write it in the same format // the rest of the data bcf1_t *rec; uint8_t tmp[100], *data = tmp; memcpy(&rec, src->data + skip, sizeof(rec)); data = pack_hts_pos(data, rec->rlen); data = pack_unsigned(data, rec->n_info); data = pack_unsigned(data, rec->n_allele); data = pack_unsigned(data, rec->n_fmt); data = pack_unsigned(data, rec->n_sample); data = pack_unsigned(data, rec->shared.l); data = pack_unsigned(data, rec->indiv.l); if (bgzf_write_small(fp, tmp, data - tmp) < data - tmp) return -1; if (rec->shared.l > 0 && bgzf_write_small(fp, rec->shared.s, rec->shared.l) < rec->shared.l) return -1; if (rec->indiv.l > 0 && bgzf_write_small(fp, rec->indiv.s, rec->indiv.l) < rec->indiv.l) return -1; } return 0; } static uint64_t unpack_unsigned(BGZF *fp, int *err) { uint8_t data; uint64_t val = 0; uint32_t i = 0; if (bgzf_read_small(fp, &data, sizeof(data)) <= 0) goto short_read; while (data & 0x80) { val |= (uint64_t)(data & 0x7f) << i; i += 7; if (bgzf_read_small(fp, &data, sizeof(data)) <= 0) goto short_read; } val |= (uint64_t)data << i; return val; short_read: *err = 1; return 0; } static hts_pos_t unpack_hts_pos(BGZF *fp, int *err) { uint64_t v = unpack_unsigned(fp, err); if ((v & 1) == 0) return (hts_pos_t)(v >> 1); else return -(hts_pos_t)(v >> 1) - 1; } static int read_packed_bcf(BGZF *fp, bcf1_t *dest) { int err = 0; packed_bcf_t tmp; size_t len = tmp.data - (uint8_t *) &tmp.pos; bcf_clear(dest); ssize_t got = bgzf_read_small(fp, &tmp.pos, len); if (got == 0) return -1; // EOF if (got < len) return -2; // Error or short read dest->pos = tmp.pos; dest->rid = tmp.rid; dest->qual = tmp.qual; dest->rlen = unpack_hts_pos(fp, &err); dest->n_info = unpack_unsigned(fp, &err); dest->n_allele = unpack_unsigned(fp, &err); dest->n_fmt = unpack_unsigned(fp, &err); dest->n_sample = unpack_unsigned(fp, &err); len = unpack_unsigned(fp, &err); if (ks_resize(&dest->shared, len) != 0) return -2; dest->shared.l = len; len = unpack_unsigned(fp, &err); if (ks_resize(&dest->indiv, len) != 0) return -2; dest->indiv.l = len; err |= bgzf_read_small(fp, dest->shared.s, dest->shared.l) < dest->shared.l; err |= bgzf_read_small(fp, dest->indiv.s, dest->indiv.l) < dest->indiv.l; return err == 0 ? 0 : -2; } void open_tmp_file(args_t *args, blk_t *blk, int is_merged) { kstring_t str = {0,0,0}; int tries = 1000; blk->fh = NULL; blk->bgz = NULL; do { if (ksprintf(ks_clear(&str), "%s/%05zd%s", args->tmp_dir, args->tmp_count++, is_merged ? ".bcf" : "") < 0) { clean_files_and_throw(args, "%s", strerror(errno)); } if (is_merged) blk->fh = hts_open(str.s, "wbx1"); else blk->bgz = bgzf_open(str.s, "wx1"); if ( blk->fh == NULL && blk->bgz == NULL && (errno != EEXIST || --tries <= 0)) { clean_files_and_throw(args, "Cannot write %s: %s\n", str.s, strerror(errno)); } } while (blk->fh == NULL && blk->bgz == NULL); blk->fname = ks_release(&str); blk->idx = args->tmp_count - 1; } void do_partial_merge(args_t *args); void buf_flush(args_t *args, bcf1_t *last_rec) { if ( !args->nbuf ) return; qsort(args->buf, args->nbuf, sizeof(*args->buf), cmp_packed_bcf_pos_ref_alt_stable); if (args->tmp_layers[0] >= MAX_TMP_FILES_PER_LAYER) do_partial_merge(args); assert(args->nblk < MAX_TMP_FILES); blk_t *blk = &args->blk[args->nblk]; blk->is_merged = 0; args->nblk++; args->tmp_layers[0]++; assert(blk->fname == NULL && blk->fh == NULL && blk->bgz == NULL); open_tmp_file(args, blk, 0); int i; for (i=0; inbuf; i++) { if ( write_packed_bcf(blk->bgz, args->buf[i])!=0 ) clean_files_and_throw(args, "[%s] Error: cannot write to %s\n", __func__,blk->fname); } if ( bgzf_close(blk->bgz)!=0 ) clean_files_and_throw(args, "[%s] Error: close failed .. %s\n", __func__,blk->fname); blk->bgz = NULL; args->nbuf = 0; args->mem = 0; } static inline uint8_t *_align_up(uint8_t *ptr) { return (uint8_t*)(((size_t)ptr + 8 - 1) & ~((size_t)(8 - 1))); } #define varint_size(X) ((sizeof(X) * 8 + 7) / 7) // worst case void buf_push(args_t *args, bcf1_t *rec) { size_t delta = sizeof(rec->pos) + sizeof(rec->rid) + sizeof(rec->qual) + varint_size(rec->rlen) + varint_size(2) // n_info + varint_size(2) // n_allele + varint_size(1) // n_fmt + varint_size(3) // n_sample + varint_size(rec->shared.l) + varint_size(rec->indiv.l) + rec->shared.l + rec->indiv.l + rec->unpack_size[1] // Alleles + 8; // the number of _align_up() calls if ( delta > args->max_mem - args->mem ) { packed_bcf_t *tmp = malloc(sizeof(*tmp) + rec->unpack_size[1] * sizeof(bcf1_t *)); if (!tmp) clean_files_and_throw(args, "[%s] Out of memory\n", __func__); pack_bcf_data(tmp, rec, 1); args->nbuf++; hts_expand(bcf1_t*, args->nbuf, args->mbuf, args->buf); args->buf[args->nbuf-1] = tmp; buf_flush(args, rec); free(tmp); bcf_destroy(rec); return; } // make sure nothing has changed in htslib assert( rec->unpacked==BCF_UN_STR && !rec->d.flt && !rec->d.info && !rec->d.fmt && !rec->d.var ); uint8_t *ptr_beg = args->mem_block + args->mem; uint8_t *ptr = _align_up(ptr_beg); packed_bcf_t *packed_rec = (packed_bcf_t *) ptr; ptr = pack_bcf_data(packed_rec, rec, 0); args->nbuf++; hts_expand(bcf1_t*, args->nbuf, args->mbuf, args->buf); args->buf[args->nbuf-1] = packed_rec; delta = ptr - ptr_beg; args->mem += delta; assert( args->mem <= args->max_mem ); bcf_destroy(rec); } void sort_blocks(args_t *args) { htsFile *in = hts_open(args->fname, "r"); if ( !in ) clean_files_and_throw(args, "Could not read %s\n", args->fname); args->hdr = bcf_hdr_read(in); if ( !args->hdr) clean_files_and_throw(args, "Could not read VCF/BCF headers from %s\n", args->fname); while ( 1 ) { bcf1_t *rec = bcf_init(); int ret = bcf_read1(in, args->hdr, rec); if ( ret < -1 ) clean_files_and_throw(args,"Error encountered while parsing the input\n"); if ( ret == -1 ) { bcf_destroy(rec); break; } if ( rec->errcode ) clean_files_and_throw(args,"Error encountered while parsing the input at %s:%"PRIhts_pos"\n",bcf_seqname(args->hdr,rec),rec->pos+1); bcf_unpack(rec, BCF_UN_STR); buf_push(args, rec); } buf_flush(args, NULL); free(args->buf); if ( hts_close(in)!=0 ) clean_files_and_throw(args,"Close failed: %s\n", args->fname); } static inline int blk_is_smaller(blk_t **aptr, blk_t **bptr) { blk_t *a = *aptr; blk_t *b = *bptr; int ret = cmp_bcf_pos_ref_alt(&a->rec, &b->rec); if ( ret < 0 ) return 1; if (ret == 0 && a->idx < b->idx) return 1; return 0; } KHEAP_INIT(blk, blk_t*, blk_is_smaller) void blk_read(args_t *args, khp_blk_t *bhp, bcf_hdr_t *hdr, blk_t *blk) { int ret; if (blk->is_merged) { if ( !blk->fh ) return; ret = bcf_read(blk->fh, hdr, blk->rec); } else { if ( !blk->bgz ) return; ret = read_packed_bcf(blk->bgz, blk->rec); } if ( ret < -1 ) clean_files_and_throw(args, "Error reading %s\n", blk->fname); if ( ret == -1 ) { if (blk->is_merged) { if ( hts_close(blk->fh)!=0 ) clean_files_and_throw(args, "Close failed: %s\n", blk->fname); blk->fh = NULL; return; } else { if ( bgzf_close(blk->bgz) != 0) clean_files_and_throw(args, "Close failed: %s\n", blk->fname); blk->bgz = NULL; return; } } bcf_unpack(blk->rec, BCF_UN_STR); khp_insert(blk, bhp, &blk); } void merge_blocks(args_t *args, htsFile *out, const char *output_fname, int idx_fmt, size_t from) { khp_blk_t *bhp = khp_init(blk); char *index_fn = NULL; size_t i; for (i=from; inblk; i++) { blk_t *blk = &args->blk[i]; if (blk->is_merged) { blk->fh = hts_open(blk->fname, "r"); if ( !blk->fh ) clean_files_and_throw(args, "Could not read %s: %s\n", blk->fname, strerror(errno)); bcf_hdr_t *hdr = bcf_hdr_read(blk->fh); bcf_hdr_destroy(hdr); } else { blk->bgz = bgzf_open(blk->fname, "r"); if (!blk->bgz) clean_files_and_throw(args, "Could not read %s: %s\n", blk->fname, strerror(errno)); } blk_read(args, bhp, args->hdr, blk); } if ( bcf_hdr_write(out, args->hdr)!=0 ) clean_files_and_throw(args, "[%s] Error: cannot write to %s\n", __func__, output_fname); if (idx_fmt) { if ( init_index2(out,args->hdr,output_fname,&index_fn,idx_fmt)<0 ) error("Error: failed to initialise index for %s\n",output_fname); } while ( bhp->ndat ) { blk_t *blk = bhp->dat[0]; if ( bcf_write(out, args->hdr, blk->rec)!=0 ) clean_files_and_throw(args, "[%s] Error: cannot write to %s\n", __func__,args->output_fname); khp_delete(blk, bhp); blk_read(args, bhp, args->hdr, blk); } if ( idx_fmt ) { if ( bcf_idx_save(out)<0 ) { if ( hts_close(out)!=0 ) error("Error: close failed .. %s\n", output_fname); error("Error: cannot write to index %s\n", index_fn); } free(index_fn); } for (i = from; i < args->nblk; i++) { blk_t *blk = &args->blk[i]; if (unlink(blk->fname) != 0) clean_files_and_throw(args, "Couldn't remove temporary file %s\n", blk->fname); free(blk->fname); blk->fname = NULL; } khp_destroy(blk, bhp); } void do_partial_merge(args_t *args) { uint32_t to_layer = 0; size_t to_merge = 0; // Temp. files are arranged in layers of at most MAX_TMP_FILES_PER_LAYER. // When a layer is full, it is merged into the next layer up. Each // layer will therefore contain files with exponentially more records // then the previous one, but will be merged exponentially less frequently. // The result is that the overall complexity will remain O(n*log(n)) // even if we need to do lots of partial merges. while (to_layer < MERGE_LAYERS && args->tmp_layers[to_layer] >= MAX_TMP_FILES_PER_LAYER) { to_merge += args->tmp_layers[to_layer]; args->tmp_layers[to_layer] = 0; to_layer++; } assert(to_merge > 0 && to_merge <= args->nblk); if (to_layer == MERGE_LAYERS) { // Edge case - if we've got here, we've completely used the // temp file allocation, so merge absolutely everything and // leave one file at the highest level. Strictly this breaks // the O(n*log(n)) complexity, but unless MERGE_LAYERS and // MAX_TMP_FILES_PER_LAYER are too small it would take so long // to get here it should never actually happen... assert(to_merge == MAX_TMP_FILES_PER_LAYER * MERGE_LAYERS); to_layer = MERGE_LAYERS - 1; } blk_t tmp = { NULL }; open_tmp_file(args, &tmp, 1); merge_blocks(args, tmp.fh, tmp.fname, 0, args->nblk - to_merge); if (hts_close(tmp.fh) != 0) clean_files_and_throw(args, "Close failed: %s\n", tmp.fname); args->nblk -= to_merge; assert(args->blk[args->nblk].fh == NULL); assert(args->blk[args->nblk].fname == NULL); args->blk[args->nblk].is_merged = 1; args->blk[args->nblk].idx = tmp.idx; args->blk[args->nblk++].fname = tmp.fname; args->tmp_layers[to_layer]++; } void merge_to_output(args_t *args) { char wmode[8] = { 0 }; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); const char *output_fname = args->output_fname ? args->output_fname : "-"; htsFile *out = hts_open(output_fname, wmode); if (!out) clean_files_and_throw(args, "[%s] Error: cannot open %s\n", __func__, output_fname); fprintf(bcftools_stderr,"Merging %zd temporary files\n", args->nblk); merge_blocks(args, out, output_fname, args->write_index, 0); fprintf(bcftools_stderr,"Done\n"); if ( hts_close(out)!=0 ) clean_files_and_throw(args, "Close failed: %s\n", output_fname); clean_files(args); } static void usage(args_t *args) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: Sort VCF/BCF file.\n"); fprintf(bcftools_stderr, "Usage: bcftools sort [OPTIONS] \n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Options:\n"); fprintf(bcftools_stderr, " -m, --max-mem FLOAT[kMG] maximum memory to use [768M]\n"); // using metric units, 1M=1e6 fprintf(bcftools_stderr, " -o, --output FILE output file name [bcftools_stdout]\n"); fprintf(bcftools_stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); #ifdef _WIN32 fprintf(bcftools_stderr, " -T, --temp-dir DIR temporary files [/bcftools.XXXXXX]\n"); #else fprintf(bcftools_stderr, " -T, --temp-dir DIR temporary files [/tmp/bcftools.XXXXXX]\n"); #endif fprintf(bcftools_stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } size_t parse_mem_string(const char *str) { char *tmp; double mem = strtod(str, &tmp); if ( tmp==str ) error("Could not parse the memory string: \"%s\"\n", str); if ( !strcasecmp("k",tmp) ) mem *= 1000; else if ( !strcasecmp("m",tmp) ) mem *= 1000*1000; else if ( !strcasecmp("g",tmp) ) mem *= 1000*1000*1000; return mem; } static void init(args_t *args) { size_t i; args->max_mem *= 0.9; args->mem_block = malloc(args->max_mem); if ( !args->mem_block ) error("Error: could not allocate %zu bytes of memory, try reducing --max-mem\n",args->max_mem); args->mem = 0; for (i = 0; i < MAX_TMP_FILES; i++) { args->blk[i].fname = NULL; args->blk[i].rec = bcf_init(); if (!args->blk[i].rec) clean_files_and_throw(args,"Couldn't allocate bcf record\n"); } args->tmp_dir = init_tmp_prefix(args->tmp_dir); #ifdef _WIN32 int ret = mkdir(mktemp(args->tmp_dir), 0700); if ( ret ) error("mkdir(%s) failed: %s\n", args->tmp_dir,strerror(errno)); #else char *tmp = mkdtemp(args->tmp_dir); if ( !tmp ) error("mkdtemp(%s) failed: %s\n", args->tmp_dir,strerror(errno)); int ret = chmod(tmp, S_IRUSR|S_IWUSR|S_IXUSR); if ( ret ) error("chmod(%s,S_IRUSR|S_IWUSR|S_IXUSR) failed: %s\n", args->tmp_dir,strerror(errno)); #endif fprintf(bcftools_stderr,"Writing to %s\n", args->tmp_dir); } static void destroy(args_t *args) { bcf_hdr_destroy(args->hdr); free(args->mem_block); free(args->tmp_dir); free(args); } int main_sort(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->max_mem = 768*1000*1000; args->output_fname = "-"; args->clevel = -1; static struct option loptions[] = { {"max-mem",required_argument,NULL,'m'}, {"temp-dir",required_argument,NULL,'T'}, {"output-type",required_argument,NULL,'O'}, {"output-file",required_argument,NULL,'o'}, {"output",required_argument,NULL,'o'}, {"help",no_argument,NULL,'h'}, {"write-index",optional_argument,NULL,'W'}, {0,0,0,0} }; char *tmp; while ((c = getopt_long(argc, argv, "m:T:O:o:W::h?",loptions,NULL)) >= 0) { switch (c) { case 'm': args->max_mem = parse_mem_string(optarg); break; case 'T': args->tmp_dir = optarg; break; case 'o': args->output_fname = optarg; break; case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } }; if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case 'h': case '?': usage(args); break; default: error("Unknown argument: %s\n", optarg); } } if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) args->fname = "-"; // reading from stdin else usage(args); } else args->fname = argv[optind]; init(args); sort_blocks(args); merge_to_output(args); destroy(args); return 0; } pysam-0.23.0/bcftools/vcfstats.c000066400000000000000000002505411475062545500165650ustar00rootroot00000000000000/* vcfstats.c -- Produces stats which can be plotted using plot-vcfstats. Copyright (C) 2012-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Notes and known issues: - SN ts/tv calculation includes all non-ref alleles listed in ALT while per-sample ts/tv takes the first non-ref allele only, something to consider with many non-ref HETs. */ #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "filter.h" #include "bin.h" #include "dist.h" // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 #define HWE_STATS 1 #define QUAL_STATS 1 #define IRC_STATS 1 #define IRC_RLEN 10 #define NA_STRING "0" typedef struct { char *tag; float min, max; uint64_t *vals_ts, *vals_tv; void *val; int nbins, type, m_val, idx; } user_stats_t; typedef struct { int min, max, step, m_vals; uint64_t *vals; } idist_t; // variant allele frequency (fraction of alt allele in pileup as determined from AD) collected into 0.05 bins typedef struct { int snv[21], indel[21]; } vaf_t; typedef struct { uint64_t n_snps, n_indels, n_mnps, n_others, n_mals, n_snp_mals, n_records, n_noalts; int *af_ts, *af_tv, *af_snps; // first bin of af_* stats are singletons #if HWE_STATS int *af_hwe; #endif #if IRC_STATS int n_repeat[IRC_RLEN][4], n_repeat_na; // number of indels which are repeat-consistent, repeat-inconsistent (dels and ins), and not applicable int *af_repeats[3]; #endif int ts_alt1, tv_alt1; #if QUAL_STATS // Values are rounded to one significant digit and 1 is added (Q*10+1); missing and negative values go in the first bin // Only SNPs that are the 1st alternate allele are counted dist_t *qual_ts, *qual_tv, *qual_indels; #endif int *insertions, *deletions, m_indel; // maximum indel length int in_frame, out_frame, na_frame, in_frame_alt1, out_frame_alt1, na_frame_alt1; int subst[15]; int *smpl_hets, *smpl_homRR, *smpl_homAA, *smpl_ts, *smpl_tv, *smpl_indels, *smpl_ndp, *smpl_sngl; int *smpl_hapRef, *smpl_hapAlt, *smpl_missing; int *smpl_ins_hets, *smpl_del_hets, *smpl_ins_homs, *smpl_del_homs; int *smpl_frm_shifts; // not-applicable, in-frame, out-frame vaf_t vaf, *smpl_vaf; // total (INFO/AD) and per-sample (FMT/VAF) VAF distributions unsigned long int *smpl_dp; idist_t dp, dp_sites; int nusr; user_stats_t *usr; double *dvaf; // distribution of the mean indel-allele frequency by length: -m_indel,-(m_indel-1),...-1,0,1,..,m_indel uint32_t *nvaf; } stats_t; typedef struct { uint64_t gt2gt[5][5]; // number of RR->RR, RR->RA, etc. matches/mismatches; see type2stats /* Pearson's R^2 is used for aggregate R^2 y, yy .. sum of dosage and squared dosage in the query VCF (second file) x, xx .. sum of squared dosage in the truth VCF (first file) n .. number of genotypes */ double y, yy, x, xx, yx, n; } gtcmp_t; typedef struct { char *seq; int pos, cnt, len; } _idc1_t; typedef struct { faidx_t *ref; _idc1_t *dat; int ndat, mdat; } indel_ctx_t; typedef struct { // stats stats_t stats[3]; int *tmp_iaf, ntmp_iaf, m_af, m_qual, naf_hwe, mtmp_frm; uint8_t *tmp_frm; int dp_min, dp_max, dp_step; gtcmp_t *smpl_gts_snps, *smpl_gts_indels; gtcmp_t *af_gts_snps, *af_gts_indels; // first bin of af_* stats are singletons bin_t *af_bins; float *farr; int32_t *iarr; int mfarr, miarr; int nref_tot, nhet_tot, nalt_tot, n_nref, i_nref; // indel context indel_ctx_t *indel_ctx; char *ref_fname; // user stats int nusr; user_stats_t *usr; // other bcf_srs_t *files; bcf_sr_regions_t *exons; char **argv, *exons_fname, *regions_list, *samples_list, *targets_list, *af_bins_list, *af_tag; int argc, verbose_sites, first_allele_only, samples_is_file; int split_by_id, nstats; filter_t *filter[2]; char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE int n_threads; } args_t; static int type2dosage[6], type2ploidy[6], type2stats[7]; static void idist_init(idist_t *d, int min, int max, int step) { d->min = min; d->max = max; d->step = step; d->m_vals = 4 + (d->max - d->min)/d->step; d->vals = (uint64_t*) calloc(d->m_vals,sizeof(uint64_t)); } static void idist_destroy(idist_t *d) { if ( d->vals ) free(d->vals); } static inline uint64_t *idist(idist_t *d, int val) { if ( val < d->min ) return &d->vals[0]; if ( val > d->max ) return &d->vals[d->m_vals-1]; return &d->vals[1 + (val - d->min) / d->step]; } static inline int idist_i2bin(idist_t *d, int i) { if ( i<=0 ) return d->min; if ( i>= d->m_vals ) return d->max; return i-1+d->min; } #define IC_DBG 0 #if IC_DBG static void _indel_ctx_print1(_idc1_t *idc) { int i; fprintf(stdout, "%d\t", idc->cnt); for (i=0; ilen; i++) fputc(idc->seq[i], stdout); fputc('\n', stdout); } static void _indel_ctx_print(indel_ctx_t *ctx) { int i; for (i=0; indat; i++) _indel_ctx_print1(&ctx->dat[i]); fputc('\n',stdout); } #endif static int _indel_ctx_lookup(indel_ctx_t *ctx, char *seq, int seq_len, int *hit) { // binary search int min = 0, max = ctx->ndat - 1; while ( min<=max ) { int i = (min+max)/2; int cmp = strncmp(seq, ctx->dat[i].seq, seq_len); if ( cmp<0 ) max = i - 1; else if ( cmp>0 ) min = i + 1; else { if ( seq_len==ctx->dat[i].len ) { *hit = 1; return i; } else if ( seq_lendat[i].len ) max = i - 1; else min = i + 1; } } *hit = 0; return max; } static void _indel_ctx_insert(indel_ctx_t *ctx, char *seq, int seq_len, int pos) { int idat, hit, i; idat = _indel_ctx_lookup(ctx, seq, seq_len, &hit); if ( !hit ) { if ( pos>0 ) return; idat++; ctx->ndat++; hts_expand(_idc1_t, ctx->ndat+1, ctx->mdat, ctx->dat); if ( idatndat && ctx->ndat>1 ) memmove(&ctx->dat[idat+1], &ctx->dat[idat], (ctx->ndat - idat - 1)*sizeof(_idc1_t)); ctx->dat[idat].len = seq_len; ctx->dat[idat].cnt = 1; ctx->dat[idat].pos = pos; ctx->dat[idat].seq = (char*) malloc(sizeof(char)*(seq_len+1)); for (i=0; idat[idat].seq[i] = seq[i]; ctx->dat[idat].seq[i] = 0; return; } if ( ctx->dat[idat].pos + seq_len == pos ) { ctx->dat[idat].cnt++; ctx->dat[idat].pos = pos; } } indel_ctx_t *indel_ctx_init(char *fa_ref_fname) { indel_ctx_t *ctx = (indel_ctx_t *) calloc(1,sizeof(indel_ctx_t)); ctx->ref = fai_load(fa_ref_fname); if ( !ctx->ref ) { free(ctx); return NULL; } return ctx; } void indel_ctx_destroy(indel_ctx_t *ctx) { fai_destroy(ctx->ref); if ( ctx->mdat ) free(ctx->dat); free(ctx); } /** * indel_ctx_type() - determine indel context type * @ctx: * @chr: chromosome name * @pos: position of the first @ref base, 1-based * @ref: reference allele * @alt: alternate allele. Only first of multiple comma-separated alleles is * considered * @nrep: number of repeated elements (w) * @nlen: length of a single repeat element (w) * * Returns the INDEL length, negative for deletions, positive for insertions */ int indel_ctx_type(indel_ctx_t *ctx, char *chr, int pos, char *ref, char *alt, int *nrep, int *nlen) { const int win_size = 50; // hard-wired for now const int rep_len = IRC_RLEN; // hard-wired for now int ref_len = strlen(ref); int alt_len = 0; while ( alt[alt_len] && alt[alt_len]!=',' ) alt_len++; int i, fai_ref_len; char *fai_ref = faidx_fetch_seq(ctx->ref, chr, pos-1, pos+win_size, &fai_ref_len); for (i=0; i96 ) fai_ref[i] -= 32; // Sanity check: the reference sequence must match the REF allele for (i=0; indat = 0; for (i=0; indat; i++) { if ( max_cnt < ctx->dat[i].cnt || (max_cnt==ctx->dat[i].cnt && max_len < ctx->dat[i].len) ) { max_cnt = ctx->dat[i].cnt; max_len = ctx->dat[i].len; } free(ctx->dat[i].seq); } free(fai_ref); *nrep = max_cnt; *nlen = max_len; return alt_len - ref_len; } static void add_user_stats(args_t *args, char *str) { args->nusr++; args->usr = (user_stats_t*) realloc(args->usr,sizeof(user_stats_t)*args->nusr); user_stats_t *usr = &args->usr[args->nusr-1]; memset(usr,0,sizeof(*usr)); usr->min = 0; usr->max = 1; usr->nbins = 100; usr->idx = 0; char *tmp = str; while ( *tmp && *tmp!=':' ) tmp++; // Tag with an index or just tag? (e.g. PV4[1] vs DP) if ( tmp > str && tmp[-1]==']' ) { char *ptr = tmp; while ( ptr>str && *ptr!='[' ) ptr--; if ( *ptr=='[' ) { char *ptr2; usr->idx = strtol(ptr+1, &ptr2, 10); if ( ptr+1==ptr2 || ptr2 != tmp-1 ) error("Could not parse the index in \"%s\" (ptr=%s;ptr2=%s(%p),tmp=%s(%p),idx=%d)\n", str,ptr,ptr2,ptr2,tmp,tmp,usr->idx); if ( usr->idx<0 ) error("Error: negative index is not allowed: \"%s\"\n", str); *ptr = 0; } } usr->tag = (char*)calloc(tmp-str+2,sizeof(char)); memcpy(usr->tag,str,tmp-str); if ( *tmp ) { char *ptr = ++tmp; usr->min = strtod(tmp, &ptr); if ( tmp==ptr ) error("Could not parse %s\n", str); tmp = ptr+1; } if ( *tmp ) { char *ptr = tmp; usr->max = strtod(tmp, &ptr); if ( tmp==ptr ) error("Could not parse %s\n", str); tmp = ptr+1; } if ( *tmp ) { char *ptr = tmp; usr->nbins = strtol(tmp, &ptr, 10); if ( tmp==ptr ) error("Could not parse %s\n", str); if ( usr->nbins<=0 ) error("Number of bins does not make sense (%d): %s.\n", usr->nbins, str); } } static void init_user_stats(args_t *args, bcf_hdr_t *hdr, stats_t *stats) { stats->nusr = args->nusr; stats->usr = (user_stats_t*)malloc(sizeof(user_stats_t)*args->nusr); if (args->nusr) memcpy(stats->usr,args->usr,args->nusr*sizeof(user_stats_t)); int i; for (i=0; inusr; i++) { user_stats_t *usr = &stats->usr[i]; usr->vals_ts = (uint64_t*)calloc(usr->nbins,sizeof(uint64_t)); usr->vals_tv = (uint64_t*)calloc(usr->nbins,sizeof(uint64_t)); int id = bcf_hdr_id2int(hdr,BCF_DT_ID,usr->tag); if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,id) ) error("The INFO tag \"%s\" is not defined in the header\n", usr->tag); usr->type = bcf_hdr_id2type(hdr,BCF_HL_INFO,id); if ( usr->type!=BCF_HT_REAL && usr->type!=BCF_HT_INT ) error("The INFO tag \"%s\" is not of Float or Integer type (%d)\n", usr->tag, usr->type); } } static void init_stats(args_t *args) { int i; args->nstats = args->files->nreaders==1 ? 1 : 3; if ( args->split_by_id ) args->nstats = 2; if ( args->filter_str ) { args->filter[0] = filter_init(bcf_sr_get_header(args->files,0), args->filter_str); if ( args->files->nreaders==2 ) args->filter[1] = filter_init(bcf_sr_get_header(args->files,1), args->filter_str); args->files->max_unpack |= filter_max_unpack(args->filter[0]); } // AF corresponds to AC but is more robust to mixtures of haploid and diploid GTs if ( !args->af_bins_list ) { args->m_af = 101; for (i=0; ifiles->nreaders; i++) if ( bcf_hdr_nsamples(args->files->readers[i].header) + 1> args->m_af ) args->m_af = bcf_hdr_nsamples(args->files->readers[i].header) + 1; } else { args->af_bins = bin_init(args->af_bins_list,0,1); // m_af is used also for other af arrays, where the first bin is for // singletons. However, since the last element is unused in af_bins // (n boundaries form n-1 intervals), the m_af count is good for both. args->m_af = bin_get_size(args->af_bins); } bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0); if ( args->af_tag && !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,bcf_hdr_id2int(hdr,BCF_DT_ID,args->af_tag)) ) error("No such INFO tag: %s\n", args->af_tag); int id, has_fmt_ad = ((id=bcf_hdr_id2int(hdr,BCF_DT_ID,"AD"))>=0 && bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id)) ? 1 : 0; #if QUAL_STATS args->m_qual = 999; #endif #if HWE_STATS args->naf_hwe = 100; #endif if ( args->samples_list ) { if ( !bcf_sr_set_samples(args->files,args->samples_list,args->samples_is_file) ) { if ( !bcf_hdr_nsamples(args->files->readers[0].header) ) error("No sample columns in %s\n", args->files->readers[0].fname); error("Unable to parse the samples: \"%s\"\n", args->samples_list); } args->af_gts_snps = (gtcmp_t *) calloc(args->m_af,sizeof(gtcmp_t)); args->af_gts_indels = (gtcmp_t *) calloc(args->m_af,sizeof(gtcmp_t)); args->smpl_gts_snps = (gtcmp_t *) calloc(args->files->n_smpl,sizeof(gtcmp_t)); args->smpl_gts_indels = (gtcmp_t *) calloc(args->files->n_smpl,sizeof(gtcmp_t)); } for (i=0; instats; i++) { stats_t *stats = &args->stats[i]; stats->m_indel = 60; stats->insertions = (int*) calloc(stats->m_indel,sizeof(int)); stats->deletions = (int*) calloc(stats->m_indel,sizeof(int)); stats->af_ts = (int*) calloc(args->m_af,sizeof(int)); stats->af_tv = (int*) calloc(args->m_af,sizeof(int)); stats->af_snps = (int*) calloc(args->m_af,sizeof(int)); int j; for (j=0; j<3; j++) stats->af_repeats[j] = (int*) calloc(args->m_af,sizeof(int)); #if QUAL_STATS stats->qual_ts = dist_init(5); stats->qual_tv = dist_init(5); stats->qual_indels = dist_init(5); #endif if ( args->files->n_smpl ) { stats->smpl_missing = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_hets = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_homAA = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_homRR = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_hapRef = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_hapAlt = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_ins_hets = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_del_hets = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_ins_homs = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_del_homs = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_ts = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_tv = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_indels = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_dp = (unsigned long int *) calloc(args->files->n_smpl,sizeof(unsigned long int)); stats->smpl_ndp = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_sngl = (int *) calloc(args->files->n_smpl,sizeof(int)); if ( has_fmt_ad ) stats->smpl_vaf = (vaf_t*) calloc(args->files->n_smpl,sizeof(vaf_t)); #if HWE_STATS stats->af_hwe = (int*) calloc(args->m_af*args->naf_hwe,sizeof(int)); #endif if ( args->exons_fname ) stats->smpl_frm_shifts = (int*) calloc(args->files->n_smpl*3,sizeof(int)); stats->nvaf = (uint32_t*) calloc(stats->m_indel*2+1,sizeof(*stats->nvaf)); stats->dvaf = (double*) calloc(stats->m_indel*2+1,sizeof(*stats->dvaf)); } idist_init(&stats->dp, args->dp_min,args->dp_max,args->dp_step); idist_init(&stats->dp_sites, args->dp_min,args->dp_max,args->dp_step); init_user_stats(args, i!=1 ? args->files->readers[0].header : args->files->readers[1].header, stats); } if ( args->exons_fname ) { args->exons = bcf_sr_regions_init(args->exons_fname,1,0,1,2); if ( !args->exons ) error("Error occurred while reading, was the file compressed with bgzip: %s?\n", args->exons_fname); } #if IRC_STATS if ( args->ref_fname ) args->indel_ctx = indel_ctx_init(args->ref_fname); #endif type2dosage[GT_HOM_RR] = 0; type2dosage[GT_HET_RA] = 1; type2dosage[GT_HOM_AA] = 2; type2dosage[GT_HET_AA] = 2; type2dosage[GT_HAPL_R] = 0; type2dosage[GT_HAPL_A] = 1; type2ploidy[GT_HOM_RR] = 1; type2ploidy[GT_HET_RA] = 1; type2ploidy[GT_HOM_AA] = 1; type2ploidy[GT_HET_AA] = 1; type2ploidy[GT_HAPL_R] = -1; type2ploidy[GT_HAPL_A] = -1; type2stats[GT_HOM_RR] = 0; type2stats[GT_HET_RA] = 1; type2stats[GT_HOM_AA] = 2; type2stats[GT_HET_AA] = 3; type2stats[GT_HAPL_R] = 0; type2stats[GT_HAPL_A] = 2; type2stats[GT_UNKN] = 4; } static void destroy_stats(args_t *args) { int id, j; for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; if (stats->af_ts) free(stats->af_ts); if (stats->af_tv) free(stats->af_tv); if (stats->af_snps) free(stats->af_snps); for (j=0; j<3; j++) if (stats->af_repeats[j]) free(stats->af_repeats[j]); #if QUAL_STATS if (stats->qual_ts) dist_destroy(stats->qual_ts); if (stats->qual_tv) dist_destroy(stats->qual_tv); if (stats->qual_indels) dist_destroy(stats->qual_indels); #endif #if HWE_STATS free(stats->af_hwe); #endif free(stats->insertions); free(stats->deletions); free(stats->smpl_missing); free(stats->smpl_hets); free(stats->smpl_homAA); free(stats->smpl_homRR); free(stats->smpl_hapRef); free(stats->smpl_hapAlt); free(stats->smpl_ins_homs); free(stats->smpl_del_homs); free(stats->smpl_ins_hets); free(stats->smpl_del_hets); free(stats->smpl_ts); free(stats->smpl_tv); free(stats->smpl_indels); free(stats->smpl_dp); free(stats->smpl_ndp); free(stats->smpl_sngl); free(stats->smpl_vaf); idist_destroy(&stats->dp); idist_destroy(&stats->dp_sites); for (j=0; jnusr; j++) { free(stats->usr[j].vals_ts); free(stats->usr[j].vals_tv); free(stats->usr[j].val); } free(stats->usr); if ( args->exons ) free(stats->smpl_frm_shifts); free(stats->nvaf); free(stats->dvaf); } for (j=0; jnusr; j++) free(args->usr[j].tag); if ( args->af_bins ) bin_destroy(args->af_bins); free(args->farr); free(args->iarr); free(args->usr); free(args->tmp_frm); free(args->tmp_iaf); if (args->exons) bcf_sr_regions_destroy(args->exons); free(args->af_gts_snps); free(args->af_gts_indels); free(args->smpl_gts_snps); free(args->smpl_gts_indels); if (args->indel_ctx) indel_ctx_destroy(args->indel_ctx); if (args->filter[0]) filter_destroy(args->filter[0]); if (args->filter[1]) filter_destroy(args->filter[1]); } // The arary tmp_iaf keeps the index of AF bin for each allele, the first bin is for singletons. // The number of bins, either m_af (101) or as given by the user in --af-bins static void init_iaf(args_t *args, bcf_sr_t *reader) { bcf1_t *line = reader->buffer[0]; hts_expand(int32_t,line->n_allele,args->ntmp_iaf,args->tmp_iaf); int i, ret; if ( args->af_tag ) { ret = bcf_get_info_float(reader->header, line, args->af_tag, &args->farr, &args->mfarr); if ( ret<=0 || ret!=line->n_allele-1 ) { // the AF tag is not present or wrong number of values, put in the singletons/unknown bin for (i=0; in_allele; i++) args->tmp_iaf[i] = 0; return; } args->tmp_iaf[0] = 0; for (i=1; in_allele; i++) { float af = args->farr[i-1]; if ( af<0 ) af = 0; else if ( af>1 ) af = 1; int iaf = args->af_bins ? bin_get_idx(args->af_bins,af) : af*(args->m_af-2); args->tmp_iaf[i] = iaf + 1; // the first tmp_iaf bin is reserved for singletons } return; } // tmp_iaf is first filled with AC counts in calc_ac and then transformed to // an index to af_gts_snps ret = bcf_calc_ac(reader->header, line, args->tmp_iaf, args->samples_list ? BCF_UN_INFO|BCF_UN_FMT : BCF_UN_INFO); if ( !ret ) { for (i=0; in_allele; i++) args->tmp_iaf[i] = 0; // singletons/unknown bin return; } int an = 0; for (i=0; in_allele; i++) an += args->tmp_iaf[i]; args->tmp_iaf[0] = 0; for (i=1; in_allele; i++) { if ( args->tmp_iaf[i]==1 ) args->tmp_iaf[i] = 0; // singletons into the first bin else if ( !an ) args->tmp_iaf[i] = 1; // no genotype at all, put to the AF=0 bin else { float af = (float) args->tmp_iaf[i] / an; if ( af<0 ) af = 0; else if ( af>1 ) af = 1; int iaf = args->af_bins ? bin_get_idx(args->af_bins,af) : af*(args->m_af-2); args->tmp_iaf[i] = iaf + 1; } } } static inline void do_mnp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) { stats->n_mnps++; } static inline void do_other_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) { stats->n_others++; } static void do_indel_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) { stats->n_indels++; bcf1_t *line = reader->buffer[0]; #if QUAL_STATS int iqual = (isnan(line->qual) || line->qual<0) ? 0 : 1 + (int)(line->qual*10); dist_insert(stats->qual_indels, iqual); #endif // Check if the indel is near an exon for the frameshift statistics int i, exon_overlap = 0; if ( args->exons ) { if ( !bcf_sr_regions_overlap(args->exons, bcf_seqname(reader->header,line),line->pos,line->pos) ) exon_overlap = 1; hts_expand(uint8_t,line->n_allele,args->mtmp_frm,args->tmp_frm); for (i=0; in_allele; i++) args->tmp_frm[i] = 0; } for (i=1; in_allele; i++) { if ( args->first_allele_only && i>1 ) break; int is_indel = bcf_has_variant_type(line,i,VCF_INDEL); if (is_indel < 0) error("bcf_has_variant_type() failed."); if ( !is_indel ) continue; int len = bcf_variant_length(line, i); #if IRC_STATS // Indel repeat consistency if ( args->indel_ctx ) { int nrep, nlen, ndel; ndel = indel_ctx_type(args->indel_ctx, (char*)reader->header->id[BCF_DT_CTG][line->rid].key, line->pos+1, line->d.allele[0], line->d.allele[i], &nrep, &nlen); if ( nlen<=1 || nrep<=1 ) { // not a repeat or a single base repeat stats->n_repeat_na++; stats->af_repeats[2][ args->tmp_iaf[i] ]++; } else { if ( abs(ndel) % nlen ) { // the length of the inserted/deleted sequence is not consistent with the repeat element stats->n_repeat[nlen-1][ndel<0 ? 1 : 3]++; stats->af_repeats[1][ args->tmp_iaf[i] ]++; } else { // the length consistent with the repeat stats->n_repeat[nlen-1][ndel<0 ? 0 : 2]++; stats->af_repeats[0][ args->tmp_iaf[i] ]++; } } } else stats->af_repeats[2][ args->tmp_iaf[i] ]++; #endif // Check the frameshifts int tlen = 0; if ( args->exons && exon_overlap ) // there is an exon { if ( len>0 ) { // insertion if ( args->exons->start <= line->pos && args->exons->end > line->pos ) tlen = abs(len); } else if ( args->exons->start <= line->pos + abs(len) ) { // deletion tlen = abs(len); if ( line->pos < args->exons->start ) // trim the beginning tlen -= args->exons->start - line->pos + 1; if ( args->exons->end < line->pos + abs(len) ) // trim the end tlen -= line->pos + abs(len) - args->exons->end; } } if ( tlen ) // there are some deleted/inserted bases in the exon { if ( tlen%3 ) { stats->out_frame++; args->tmp_frm[i] = 2; } else { stats->in_frame++; args->tmp_frm[i] = 1; } if ( i==1 ) { if ( tlen%3 ) stats->out_frame_alt1++; else stats->in_frame_alt1++; } } else // no exon affected { if ( i==1 ) stats->na_frame_alt1++; stats->na_frame++; } // Indel length distribution int *ptr = stats->insertions; if ( len<0 ) { len *= -1; ptr = stats->deletions; } if ( --len >= stats->m_indel ) len = stats->m_indel-1; ptr[len]++; } } static void do_user_stats(stats_t *stats, bcf_sr_t *reader, int is_ts) { int i, nval; for (i=0; inusr; i++) { user_stats_t *usr = &stats->usr[i]; uint64_t *vals = is_ts ? usr->vals_ts : usr->vals_tv; float val; if ( usr->type==BCF_HT_REAL ) { if ( (nval=bcf_get_info_float(reader->header,reader->buffer[0],usr->tag,&usr->val,&usr->m_val))<=0 ) continue; if ( usr->idx >= nval ) continue; val = ((float*)usr->val)[usr->idx]; } else { if ( (nval=bcf_get_info_int32(reader->header,reader->buffer[0],usr->tag,&usr->val,&usr->m_val))<=0 ) continue; if ( usr->idx >= nval ) continue; val = ((int32_t*)usr->val)[usr->idx]; } int idx; if ( val<=usr->min ) idx = 0; else if ( val>=usr->max ) idx = usr->nbins - 1; else idx = (val - usr->min)/(usr->max - usr->min) * (usr->nbins-1); vals[idx]++; } } static void do_snp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) { stats->n_snps++; bcf1_t *line = reader->buffer[0]; int ref = bcf_acgt2int(*line->d.allele[0]); if ( ref<0 ) return; #if QUAL_STATS int iqual = (isnan(line->qual) || line->qual<0) ? 0 : 1 + (int)(line->qual*10); #endif int i; for (i=1; in_allele; i++) { if ( args->first_allele_only && i>1 ) break; if ( !(bcf_get_variant_type(line,i)&VCF_SNP) ) continue; int alt = bcf_acgt2int(*line->d.allele[i]); if ( alt<0 || ref==alt ) continue; stats->subst[ref<<2|alt]++; int iaf = args->tmp_iaf[i]; stats->af_snps[iaf]++; if ( abs(ref-alt)==2 ) { if (i==1) { stats->ts_alt1++; #if QUAL_STATS dist_insert(stats->qual_ts,iqual); #endif do_user_stats(stats, reader, 1); } stats->af_ts[iaf]++; } else { if (i==1) { stats->tv_alt1++; #if QUAL_STATS dist_insert(stats->qual_tv,iqual); #endif do_user_stats(stats, reader, 0); } stats->af_tv[iaf]++; } } } // Returns the max non-ref AD value static inline int get_ad(bcf1_t *line, bcf_fmt_t *ad_fmt_ptr, int ismpl, int *ial) { int iv, ad = 0; *ial = 0; #define BRANCH_INT(type_t,missing,vector_end) { \ type_t *ptr = (type_t *) (ad_fmt_ptr->p + ad_fmt_ptr->size*ismpl); \ for (iv=1; ivn && ivn_allele; iv++) \ { \ if ( ptr[iv]==vector_end ) break; \ if ( ptr[iv]==missing ) continue; \ if ( ad < ptr[iv] ) { ad = ptr[iv]; *ial = iv; }\ } \ } switch (ad_fmt_ptr->type) { case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_missing, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break; default: fprintf(stderr, "[E::%s] todo: %d\n", __func__, ad_fmt_ptr->type); exit(1); break; } #undef BRANCH_INT return ad; } static inline int get_iad(bcf1_t *line, bcf_fmt_t *ad_fmt_ptr, int ismpl, int ial) { #define BRANCH_INT(type_t,missing,vector_end) { \ type_t *ptr = (type_t *) (ad_fmt_ptr->p + ad_fmt_ptr->size*ismpl); \ if ( ptr[ial]==vector_end ) return 0; \ if ( ptr[ial]==missing ) return 0; \ return ptr[ial]; \ } switch (ad_fmt_ptr->type) { case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_missing, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break; default: fprintf(stderr, "[E::%s] todo: %d\n", __func__, ad_fmt_ptr->type); exit(1); break; } #undef BRANCH_INT } static inline void update_dvaf(stats_t *stats, bcf1_t *line, int ial, float vaf) { int len = line->d.var[ial].n; if ( len < -stats->m_indel ) len = -stats->m_indel; else if ( len > stats->m_indel ) len = stats->m_indel; int bin = stats->m_indel + len; stats->nvaf[bin]++; stats->dvaf[bin] += vaf; } #define vaf2bin(vaf) ((int)nearbyintf((vaf)/0.05)) static inline void update_vaf(vaf_t *smpl_vaf, bcf1_t *line, int ial, float vaf) { if ( vaf>=0 && vaf<=1 ) { int idx = vaf2bin(vaf); if ( bcf_get_variant_type(line,ial)==VCF_SNP ) smpl_vaf->snv[idx]++; else smpl_vaf->indel[idx]++; } } static inline int calc_sample_depth(args_t *args, int ismpl, bcf_fmt_t *ad_fmt_ptr, bcf_fmt_t *dp_fmt_ptr) { if ( dp_fmt_ptr ) { #define BRANCH_INT(type_t,missing,vector_end) { \ type_t *ptr = (type_t *) (dp_fmt_ptr->p + dp_fmt_ptr->size*ismpl); \ if ( *ptr==missing || *ptr==vector_end ) return -1; \ return *ptr; \ } switch (dp_fmt_ptr->type) { case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_missing, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break; default: fprintf(stderr, "[E::%s] todo: %d\n", __func__, dp_fmt_ptr->type); exit(1); break; } #undef BRANCH_INT } if ( ad_fmt_ptr ) { int iv, dp = 0, has_value = 0; #define BRANCH_INT(type_t,missing,vector_end) { \ type_t *ptr = (type_t *) (ad_fmt_ptr->p + ad_fmt_ptr->size*ismpl); \ for (iv=0; ivn; iv++) \ { \ if ( ptr[iv]==vector_end ) break; \ if ( ptr[iv]==missing ) continue; \ has_value = 1; \ dp += ptr[iv]; \ } \ } switch (ad_fmt_ptr->type) { case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_missing, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break; default: fprintf(stderr, "[E::%s] todo: %d\n", __func__, ad_fmt_ptr->type); exit(1); break; } #undef BRANCH_INT if ( !has_value ) return -1; return dp; } return -1; } static inline void sample_gt_stats(args_t *args, stats_t *stats, bcf1_t *line, int ismpl, int gt, int ial, int jal) { if ( gt==GT_UNKN ) { stats->smpl_missing[ismpl]++; return; } int var_type = 0; if ( ial>0 ) var_type |= bcf_get_variant_type(line,ial); if ( jal>0 ) var_type |= bcf_get_variant_type(line,jal); if ( gt==GT_HAPL_R || gt==GT_HAPL_A ) { if ( var_type&VCF_INDEL && stats->smpl_frm_shifts ) { assert( ialn_allele ); stats->smpl_frm_shifts[ismpl*3 + args->tmp_frm[ial]]++; } if ( gt == GT_HAPL_R ) stats->smpl_hapRef[ismpl]++; if ( gt == GT_HAPL_A ) stats->smpl_hapAlt[ismpl]++; return; } if ( gt != GT_HOM_RR ) { args->n_nref++; args->i_nref = ismpl; } #if HWE_STATS switch (gt) { case GT_HOM_RR: args->nref_tot++; break; case GT_HET_RA: args->nhet_tot++; break; case GT_HET_AA: case GT_HOM_AA: args->nalt_tot++; break; } #endif if ( var_type&VCF_SNP || var_type==VCF_REF ) // count ALT=. as SNP { if ( gt == GT_HET_RA ) stats->smpl_hets[ismpl]++; else if ( gt == GT_HET_AA ) stats->smpl_hets[ismpl]++; else if ( gt == GT_HOM_RR ) stats->smpl_homRR[ismpl]++; else if ( gt == GT_HOM_AA ) stats->smpl_homAA[ismpl]++; if ( gt != GT_HOM_RR && line->d.var[ial].type&VCF_SNP ) // this is safe, bcf_get_variant_types has been already called { int ref = bcf_acgt2int(*line->d.allele[0]); int alt = bcf_acgt2int(*line->d.allele[ial]); if ( alt<0 ) return; if ( abs(ref-alt)==2 ) stats->smpl_ts[ismpl]++; else stats->smpl_tv[ismpl]++; } if ( gt != GT_HOM_RR && line->d.var[jal].type&VCF_SNP && ial!=jal ) { int ref = bcf_acgt2int(*line->d.allele[0]); int alt = bcf_acgt2int(*line->d.allele[jal]); if ( alt<0 ) return; if ( abs(ref-alt)==2 ) stats->smpl_ts[ismpl]++; else stats->smpl_tv[ismpl]++; } } if ( var_type&VCF_INDEL ) { if ( gt != GT_HOM_RR ) { stats->smpl_indels[ismpl]++; if ( gt==GT_HET_RA || gt==GT_HET_AA ) { int is_ins = 0, is_del = 0; if ( bcf_get_variant_type(line,ial)&VCF_INDEL ) { if ( line->d.var[ial].n < 0 ) is_del = 1; else is_ins = 1; } if ( bcf_get_variant_type(line,jal)&VCF_INDEL ) { if ( line->d.var[jal].n < 0 ) is_del = 1; else is_ins = 1; } // Note that alt-het genotypes with both ins and del allele are counted twice!! if ( is_del ) stats->smpl_del_hets[ismpl]++; if ( is_ins ) stats->smpl_ins_hets[ismpl]++; } else if ( gt==GT_HOM_AA ) { if ( line->d.var[ial].n < 0 ) stats->smpl_del_homs[ismpl]++; else stats->smpl_ins_homs[ismpl]++; } } if ( stats->smpl_frm_shifts ) { assert( ialn_allele && jaln_allele ); stats->smpl_frm_shifts[ismpl*3 + args->tmp_frm[ial]]++; stats->smpl_frm_shifts[ismpl*3 + args->tmp_frm[jal]]++; } } } static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int matched) { bcf_srs_t *files = args->files; bcf1_t *line = reader->buffer[0]; args->nref_tot = 0; args->nhet_tot = 0; args->nalt_tot = 0; args->n_nref = 0; args->i_nref = 0; bcf_fmt_t *gt_fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"GT"); bcf_fmt_t *ad_fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"AD"); bcf_fmt_t *dp_fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"DP"); int is; for (is=0; isfiles->n_smpl; is++) { // Determine depth int dp = calc_sample_depth(args,is,ad_fmt_ptr,dp_fmt_ptr); if ( dp>0 ) { (*idist(&stats->dp, dp))++; stats->smpl_ndp[is]++; stats->smpl_dp[is] += dp; } // Determine genotype int ial, jal, gt=GT_UNKN; if ( gt_fmt_ptr ) { gt = bcf_gt_type(gt_fmt_ptr, reader->samples[is], &ial, &jal); sample_gt_stats(args,stats,line,is,gt,ial,jal); } // Determine variant allele frequency if ( dp>0 && ad_fmt_ptr ) { float iad = 0, jad = 0; if ( gt==GT_UNKN ) // GT not available { iad = get_ad(line,ad_fmt_ptr,is,&ial); } else if ( gt!=GT_UNKN ) { iad = ial==0 ? 0 : get_iad(line,ad_fmt_ptr,is,ial); jad = jal==0 ? 0 : get_iad(line,ad_fmt_ptr,is,jal); } if ( iad ) { update_dvaf(stats,line,ial,(float)iad/dp); update_vaf(&stats->smpl_vaf[is],line,ial,(float)iad/dp); } if ( jad && iad!=jad ) { update_dvaf(stats,line,jal,(float)jad/dp); update_vaf(&stats->smpl_vaf[is],line,jal,(float)jad/dp); } } } if ( args->n_nref==1 ) stats->smpl_sngl[args->i_nref]++; #if HWE_STATS if ( gt_fmt_ptr && line->n_allele > 1 && (args->nref_tot || args->nhet_tot || args->nalt_tot) ) { // Number of heterozygous genotypes observed for any given allele frequency. This is used // by plot-vcfstats to show the observed vs expected number of hets. There the expected number // of hets is calculated from the probability P(het) = 2*AF*(1-AF). // The array af_hwe is organized as follows // m_af .. number of allele frequency bins // naf_hwe .. the number of het genotype frequency bins // iallele_freq*naf_hwe + ihet_freq // float het_frac = (float)args->nhet_tot / (args->nref_tot + args->nhet_tot + args->nalt_tot); int ihet_freq = het_frac * (args->naf_hwe - 1); int idx = ihet_freq + args->tmp_iaf[1] * args->naf_hwe; stats->af_hwe[idx]++; } #endif if ( matched==3 ) { int is; bcf_fmt_t *fmt0, *fmt1; fmt0 = bcf_get_fmt(files->readers[0].header,files->readers[0].buffer[0],"GT"); if ( !fmt0 ) return; fmt1 = bcf_get_fmt(files->readers[1].header,files->readers[1].buffer[0],"GT"); if ( !fmt1 ) return; // only the first ALT allele is considered if (args->ntmp_iaf <= 1) return; // Do not consider invariate sites int iaf = args->tmp_iaf[1]; int line_type = bcf_get_variant_types(files->readers[0].buffer[0]); gtcmp_t *af_stats = line_type&VCF_SNP ? args->af_gts_snps : args->af_gts_indels; gtcmp_t *smpl_stats = line_type&VCF_SNP ? args->smpl_gts_snps : args->smpl_gts_indels; for (is=0; isn_smpl; is++) { // Simplified comparison: only 0/0, 0/1, 1/1 is looked at as the identity of // actual alleles can be enforced by running without the -c option. int gt0 = bcf_gt_type(fmt0, files->readers[0].samples[is], NULL, NULL); int gt1 = bcf_gt_type(fmt1, files->readers[1].samples[is], NULL, NULL); int idx0 = type2stats[gt0]; int idx1 = type2stats[gt1]; af_stats[iaf].gt2gt[idx0][idx1]++; smpl_stats[is].gt2gt[idx0][idx1]++; if ( gt0 == GT_UNKN || gt1 == GT_UNKN ) continue; if ( type2ploidy[gt0]*type2ploidy[gt1] == -1 ) continue; // cannot compare diploid and haploid genotypes float y = type2dosage[gt0]; float x = type2dosage[gt1]; smpl_stats[is].yx += y*x; smpl_stats[is].x += x; smpl_stats[is].xx += x*x; smpl_stats[is].y += y; smpl_stats[is].yy += y*y; smpl_stats[is].n += 1; af_stats[iaf].yx += y*x; af_stats[iaf].x += x; af_stats[iaf].xx += x*x; af_stats[iaf].y += y; af_stats[iaf].yy += y*y; af_stats[iaf].n += 1; } if ( args->verbose_sites ) { int nm = 0, nmm = 0, nrefm = 0; for (is=0; isn_smpl; is++) { int gt = bcf_gt_type(fmt0, files->readers[0].samples[is], NULL, NULL); if ( gt == GT_UNKN ) continue; int gt2 = bcf_gt_type(fmt1, files->readers[1].samples[is], NULL, NULL); if ( gt2 == GT_UNKN ) continue; if ( gt != gt2 ) { nmm++; bcf_sr_t *reader = &files->readers[0]; printf("DBG\t%s\t%"PRId64"\t%s\t%d\t%d\n",reader->header->id[BCF_DT_CTG][reader->buffer[0]->rid].key,(int64_t) reader->buffer[0]->pos+1,files->samples[is],gt,gt2); } else { if ( gt!=GT_HOM_RR ) nrefm++; nm++; } } float nrd = nrefm+nmm ? 100.*nmm/(nrefm+nmm) : 0; printf("PSD\t%s\t%"PRId64"\t%d\t%d\t%f\n", reader->header->id[BCF_DT_CTG][reader->buffer[0]->rid].key,(int64_t) reader->buffer[0]->pos+1,nm,nmm,nrd); } } } static void do_vcf_stats(args_t *args) { bcf_srs_t *files = args->files; assert( sizeof(int)>files->nreaders ); while ( bcf_sr_next_line(files) ) { bcf_sr_t *reader = NULL; bcf1_t *line = NULL; int ret = 0, i, pass = 1; for (i=0; inreaders; i++) { if ( !bcf_sr_has_line(files,i) ) continue; if ( args->filter[i] ) { int is_ok = filter_test(args->filter[i], bcf_sr_get_line(files,i), NULL); if ( args->filter_logic & FLT_EXCLUDE ) is_ok = is_ok ? 0 : 1; if ( !is_ok ) { pass = 0; break; } } ret |= 1<readers[i]; line = bcf_sr_get_line(files,i); } } if ( !pass ) continue; int line_type = bcf_get_variant_types(line); init_iaf(args, reader); stats_t *stats = &args->stats[ret-1]; if ( args->split_by_id && line->d.id[0]=='.' && !line->d.id[1] ) stats = &args->stats[1]; stats->n_records++; if ( line_type==VCF_REF ) stats->n_noalts++; if ( line_type&VCF_SNP ) do_snp_stats(args, stats, reader); if ( line_type&VCF_INDEL ) do_indel_stats(args, stats, reader); if ( line_type&VCF_MNP ) do_mnp_stats(args, stats, reader); if ( line_type&VCF_OTHER ) do_other_stats(args, stats, reader); if ( line->n_allele>2 ) { stats->n_mals++; if ( line_type == VCF_SNP ) stats->n_snp_mals++; // note: this will be fooled by C>C,T } if ( files->n_smpl ) do_sample_stats(args, stats, reader, ret); if ( bcf_get_info_int32(reader->header,line,"DP",&args->iarr,&args->miarr)==1 ) (*idist(&stats->dp_sites, args->iarr[0]))++; } } static void print_header(args_t *args) { int i; printf("# This file was produced by bcftools stats (%s+htslib-%s) and can be plotted using plot-vcfstats.\n", bcftools_version(),hts_version()); printf("# The command line was:\tbcftools %s ", args->argv[0]); for (i=1; iargc; i++) printf(" %s",args->argv[i]); printf("\n#\n"); printf("# Definition of sets:\n# ID\t[2]id\t[3]tab-separated file names\n"); if ( args->files->nreaders==1 ) { const char *fname = strcmp("-",args->files->readers[0].fname) ? args->files->readers[0].fname : ""; if ( args->split_by_id ) { printf("ID\t0\t%s:known (sites with ID different from \".\")\n", fname); printf("ID\t1\t%s:novel (sites where ID column is \".\")\n", fname); } else printf("ID\t0\t%s\n", fname); } else { const char *fname0 = strcmp("-",args->files->readers[0].fname) ? args->files->readers[0].fname : ""; const char *fname1 = strcmp("-",args->files->readers[1].fname) ? args->files->readers[1].fname : ""; printf("ID\t0\t%s\n", fname0); printf("ID\t1\t%s\n", fname1); printf("ID\t2\t%s\t%s\n", fname0,fname1); if ( args->verbose_sites ) { printf( "# Verbose per-site discordance output.\n" "# PSD\t[2]CHROM\t[3]POS\t[4]Number of matches\t[5]Number of mismatches\t[6]NRD\n"); printf( "# Verbose per-site and per-sample output. Genotype codes: %d:HomRefRef, %d:HomAltAlt, %d:HetAltRef, %d:HetAltAlt, %d:haploidRef, %d:haploidAlt\n" "# DBG\t[2]CHROM\t[3]POS\t[4]Sample\t[5]GT in %s\t[6]GT in %s\n", GT_HOM_RR, GT_HOM_AA, GT_HET_RA, GT_HET_AA, GT_HAPL_R, GT_HAPL_A, fname0,fname1); } } } #define T2S(x) type2stats[x] static void print_stats(args_t *args) { int i, j,k, id; printf("# SN, Summary numbers:\n"); printf("# number of records .. number of data rows in the VCF\n"); printf("# number of no-ALTs .. reference-only sites, ALT is either \".\" or identical to REF\n"); printf("# number of SNPs .. number of rows with a SNP\n"); printf("# number of MNPs .. number of rows with a MNP, such as CC>TT\n"); printf("# number of indels .. number of rows with an indel\n"); printf("# number of others .. number of rows with other type, for example a symbolic allele or\n"); printf("# a complex substitution, such as ACT>TCGA\n"); printf("# number of multiallelic sites .. number of rows with multiple alternate alleles\n"); printf("# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs\n"); printf("# \n"); printf("# Note that rows containing multiple types will be counted multiple times, in each\n"); printf("# counter. For example, a row with a SNP and an indel increments both the SNP and\n"); printf("# the indel counter.\n"); printf("# \n"); printf("# SN\t[2]id\t[3]key\t[4]value\n"); for (id=0; idfiles->nreaders; id++) printf("SN\t%d\tnumber of samples:\t%d\n", id, bcf_hdr_nsamples(args->files->readers[id].header)); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; printf("SN\t%d\tnumber of records:\t%"PRIu64"\n", id, stats->n_records); printf("SN\t%d\tnumber of no-ALTs:\t%"PRIu64"\n", id, stats->n_noalts); printf("SN\t%d\tnumber of SNPs:\t%"PRIu64"\n", id, stats->n_snps); printf("SN\t%d\tnumber of MNPs:\t%"PRIu64"\n", id, stats->n_mnps); printf("SN\t%d\tnumber of indels:\t%"PRIu64"\n", id, stats->n_indels); printf("SN\t%d\tnumber of others:\t%"PRIu64"\n", id, stats->n_others); printf("SN\t%d\tnumber of multiallelic sites:\t%"PRIu64"\n", id, stats->n_mals); printf("SN\t%d\tnumber of multiallelic SNP sites:\t%"PRIu64"\n", id, stats->n_snp_mals); } printf("# TSTV, transitions/transversions\n" "# - transitions, see https://en.wikipedia.org/wiki/Transition_(genetics)\n" "# - transversions, see https://en.wikipedia.org/wiki/Transversion\n"); printf("# TSTV\t[2]id\t[3]ts\t[4]tv\t[5]ts/tv\t[6]ts (1st ALT)\t[7]tv (1st ALT)\t[8]ts/tv (1st ALT)\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; int ts=0,tv=0; for (i=0; im_af; i++) { ts += stats->af_ts[i]; tv += stats->af_tv[i]; } printf("TSTV\t%d\t%d\t%d\t%.2f\t%d\t%d\t%.2f\n", id,ts,tv,tv?(float)ts/tv:0, stats->ts_alt1,stats->tv_alt1,stats->tv_alt1?(float)stats->ts_alt1/stats->tv_alt1:0); } if ( args->exons_fname ) { printf("# FS, Indel frameshifts:\n# FS\t[2]id\t[3]in-frame\t[4]out-frame\t[5]not applicable\t[6]out/(in+out) ratio\t[7]in-frame (1st ALT)\t[8]out-frame (1st ALT)\t[9]not applicable (1st ALT)\t[10]out/(in+out) ratio (1st ALT)\n"); for (id=0; idnstats; id++) { int in=args->stats[id].in_frame, out=args->stats[id].out_frame, na=args->stats[id].na_frame; int in1=args->stats[id].in_frame_alt1, out1=args->stats[id].out_frame_alt1, na1=args->stats[id].na_frame_alt1; printf("FS\t%d\t%d\t%d\t%d\t%.2f\t%d\t%d\t%d\t%.2f\n", id, in,out,na,out?(float)out/(in+out):0,in1,out1,na1,out1?(float)out1/(in1+out1):0); } } if ( args->indel_ctx ) { printf("# ICS, Indel context:\n" "# - repeat-consistent, inconsistent and n/a: experimental and useless stats [DEPRECATED]\n"); printf("# ICS\t[2]id\t[3]repeat-consistent\t[4]repeat-inconsistent\t[5]not applicable\t[6]c/(c+i) ratio\n"); for (id=0; idnstats; id++) { int nc = 0, ni = 0, na = args->stats[id].n_repeat_na; for (i=0; istats[id].n_repeat[i][0] + args->stats[id].n_repeat[i][2]; ni += args->stats[id].n_repeat[i][1] + args->stats[id].n_repeat[i][3]; } printf("ICS\t%d\t%d\t%d\t%d\t%.4f\n", id, nc,ni,na,nc+ni ? (float)nc/(nc+ni) : 0.0); } printf("# ICL, Indel context by length:\n" "# - repeat-consistent, inconsistent and n/a: experimental and useless stats [DEPRECATED]\n"); printf("# ICL\t[2]id\t[3]length of repeat element\t[4]repeat-consistent deletions)\t[5]repeat-inconsistent deletions\t[6]consistent insertions\t[7]inconsistent insertions\t[8]c/(c+i) ratio\n"); for (id=0; idnstats; id++) { for (i=1; istats[id].n_repeat[i][0]+args->stats[id].n_repeat[i][2], ni = args->stats[id].n_repeat[i][1]+args->stats[id].n_repeat[i][3]; printf("ICL\t%d\t%d\t%d\t%d\t%d\t%d\t%.4f\n", id, i+1, args->stats[id].n_repeat[i][0],args->stats[id].n_repeat[i][1],args->stats[id].n_repeat[i][2],args->stats[id].n_repeat[i][3], nc+ni ? (float)nc/(nc+ni) : 0.0); } } } printf("# SiS, Singleton stats:\n" "# - allele count, i.e. the number of singleton genotypes (AC=1)\n" "# - number of transitions, see above\n" "# - number of transversions, see above\n" "# - repeat-consistent, inconsistent and n/a: experimental and useless stats [DEPRECATED]\n"); printf("# SiS\t[2]id\t[3]allele count\t[4]number of SNPs\t[5]number of transitions\t[6]number of transversions\t[7]number of indels\t[8]repeat-consistent\t[9]repeat-inconsistent\t[10]not applicable\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; printf("SiS\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", id,1,stats->af_snps[0],stats->af_ts[0],stats->af_tv[0], stats->af_repeats[0][0]+stats->af_repeats[1][0]+stats->af_repeats[2][0],stats->af_repeats[0][0],stats->af_repeats[1][0],stats->af_repeats[2][0]); // put the singletons stats into the first AF bin, note that not all of the stats is transferred (i.e. nrd mismatches) stats->af_snps[1] += stats->af_snps[0]; stats->af_ts[1] += stats->af_ts[0]; stats->af_tv[1] += stats->af_tv[0]; stats->af_repeats[0][1] += stats->af_repeats[0][0]; stats->af_repeats[1][1] += stats->af_repeats[1][0]; stats->af_repeats[2][1] += stats->af_repeats[2][0]; } // move the singletons stats into the first AF bin, singleton stats was collected separately because of init_iaf if ( args->af_gts_snps ) { args->af_gts_snps[1].y += args->af_gts_snps[0].y; args->af_gts_snps[1].yy += args->af_gts_snps[0].yy; args->af_gts_snps[1].xx += args->af_gts_snps[0].xx; args->af_gts_snps[1].yx += args->af_gts_snps[0].yx; args->af_gts_snps[1].n += args->af_gts_snps[0].n; } if ( args->af_gts_indels ) { args->af_gts_indels[1].y += args->af_gts_indels[0].y; args->af_gts_indels[1].yy += args->af_gts_indels[0].yy; args->af_gts_indels[1].xx += args->af_gts_indels[0].xx; args->af_gts_indels[1].yx += args->af_gts_indels[0].yx; args->af_gts_indels[1].n += args->af_gts_indels[0].n; } printf("# AF, Stats by non-reference allele frequency:\n# AF\t[2]id\t[3]allele frequency\t[4]number of SNPs\t[5]number of transitions\t[6]number of transversions\t[7]number of indels\t[8]repeat-consistent\t[9]repeat-inconsistent\t[10]not applicable\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; for (i=1; im_af; i++) // note that af[1] now contains also af[0], see SiS stats output above { if ( stats->af_snps[i]+stats->af_ts[i]+stats->af_tv[i]+stats->af_repeats[0][i]+stats->af_repeats[1][i]+stats->af_repeats[2][i] == 0 ) continue; double af = args->af_bins ? (bin_get_value(args->af_bins,i)+bin_get_value(args->af_bins,i-1))*0.5 : (double)(i-1)/(args->m_af-1); printf("AF\t%d\t%f\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", id,af,stats->af_snps[i],stats->af_ts[i],stats->af_tv[i], stats->af_repeats[0][i]+stats->af_repeats[1][i]+stats->af_repeats[2][i],stats->af_repeats[0][i],stats->af_repeats[1][i],stats->af_repeats[2][i]); } } #if QUAL_STATS printf("# QUAL, Stats by quality\n# QUAL\t[2]id\t[3]Quality\t[4]number of SNPs\t[5]number of transitions (1st ALT)\t[6]number of transversions (1st ALT)\t[7]number of indels\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; int ndist_ts = dist_nbins(stats->qual_ts); int ndist_tv = dist_nbins(stats->qual_tv); int ndist_in = dist_nbins(stats->qual_indels); int ndist_max = ndist_ts; if ( ndist_max < ndist_tv ) ndist_max = ndist_tv; if ( ndist_max < ndist_in ) ndist_max = ndist_in; uint32_t beg, end; uint32_t nts, ntv, nin; for (i=0; iqual_ts, i, &beg, &end); qval = beg>0 ? 0.1*(beg - 1) : -1; } if ( i < ndist_tv ) { ntv = dist_get(stats->qual_tv, i, &beg, &end); if ( qval==-1 ) qval = beg > 0 ? 0.1*(beg - 1) : -1; } if ( i < ndist_in ) { nin = dist_get(stats->qual_indels, i, &beg, &end); if ( qval==-1 ) qval = beg > 0 ? 0.1*(beg - 1) : -1; } if ( nts+ntv+nin==0 ) continue; printf("QUAL\t%d\t",id); if ( qval==-1 ) printf("."); else printf("%.1f",qval); printf("\t%d\t%d\t%d\t%d\n",nts+ntv,nts,ntv,nin); } } #endif for (i=0; inusr; i++) { printf("# USR:%s/%d\t[2]id\t[3]%s/%d\t[4]number of SNPs\t[5]number of transitions (1st ALT)\t[6]number of transversions (1st ALT)\n", args->usr[i].tag,args->usr[i].idx,args->usr[i].tag,args->usr[i].idx); for (id=0; idnstats; id++) { user_stats_t *usr = &args->stats[id].usr[i]; int j; for (j=0; jnbins; j++) { if ( usr->vals_ts[j]+usr->vals_tv[j] == 0 ) continue; // skip empty bins float val = usr->min + (usr->max - usr->min)*j/(usr->nbins-1); const char * const fmt = usr->type==BCF_HT_REAL ? "USR:%s/%d\t%d\t%e\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"\n" : "USR:%s/%d\t%d\t%.0f\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"\n"; printf(fmt,usr->tag,usr->idx,id,val,usr->vals_ts[j]+usr->vals_tv[j],usr->vals_ts[j],usr->vals_tv[j]); } } } printf("# IDD, InDel distribution:\n# IDD\t[2]id\t[3]length (deletions negative)\t[4]number of sites\t[5]number of genotypes\t[6]mean VAF\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; for (i=stats->m_indel-1; i>=0; i--) { if ( !stats->deletions[i] ) continue; // whops, differently organized arrow, dels are together with ins int bin = stats->m_indel - i - 1; printf("IDD\t%d\t%d\t%d\t", id,-i-1,stats->deletions[i]); if ( stats->nvaf && stats->nvaf[bin] ) printf("%u\t%.2f",stats->nvaf[bin],stats->dvaf[bin]/stats->nvaf[bin]); else printf("0\t."); printf("\n"); } for (i=0; im_indel; i++) { if ( !stats->insertions[i] ) continue; int bin = stats->m_indel + i + 1; printf("IDD\t%d\t%d\t%d\t", id,i+1,stats->insertions[i]); if ( stats->nvaf && stats->nvaf[bin] ) printf("%u\t%.2f",stats->nvaf[bin],stats->dvaf[bin]/stats->nvaf[bin]); else printf("0\t."); printf("\n"); } } printf("# ST, Substitution types:\n# ST\t[2]id\t[3]type\t[4]count\n"); for (id=0; idnstats; id++) { int t; for (t=0; t<15; t++) { if ( t>>2 == (t&3) ) continue; printf("ST\t%d\t%c>%c\t%d\n", id, bcf_int2acgt(t>>2),bcf_int2acgt(t&3),args->stats[id].subst[t]); } } if ( args->files->nreaders>1 && args->files->n_smpl ) { printf("SN\t%d\tnumber of samples:\t%d\n", 2, args->files->n_smpl); int x; for (x=0; x<2; x++) // x=0: snps, x=1: indels { gtcmp_t *stats; if ( x==0 ) { printf("# GCsAF, Genotype concordance by non-reference allele frequency (SNPs)\n# GCsAF\t[2]id\t[3]allele frequency\t[4]RR Hom matches\t[5]RA Het matches\t[6]AA Hom matches\t[7]RR Hom mismatches\t[8]RA Het mismatches\t[9]AA Hom mismatches\t[10]dosage r-squared\t[11]number of genotypes\n"); stats = args->af_gts_snps; } else { printf("# GCiAF, Genotype concordance by non-reference allele frequency (indels)\n# GCiAF\t[2]id\t[3]allele frequency\t[4]RR Hom matches\t[5]RA Het matches\t[6]AA Hom matches\t[7]RR Hom mismatches\t[8]RA Het mismatches\t[9]AA Hom mismatches\t[10]dosage r-squared\t[11]number of genotypes\n"); stats = args->af_gts_indels; } uint64_t nrd_m[4] = {0,0,0,0}, nrd_mm[4] = {0,0,0,0}; // across all bins for (i=0; im_af; i++) { int n = 0; uint64_t m[4] = {0,0,0,0}, mm[4] = {0,0,0,0}; // in i-th AF bin for (j=0; j<4; j++) // rr, ra, aa hom, aa het, ./. for (k=0; k<4; k++) { n += stats[i].gt2gt[j][k]; if ( j==k ) { nrd_m[j] += stats[i].gt2gt[j][k]; m[j] += stats[i].gt2gt[j][k]; } else { nrd_mm[j] += stats[i].gt2gt[j][k]; mm[j] += stats[i].gt2gt[j][k]; } } if ( !i || !n ) continue; // skip singleton stats and empty bins // Pearson's r2 double r2 = 0; if ( stats[i].n ) { r2 = (stats[i].yx - stats[i].x*stats[i].y/stats[i].n); r2 /= sqrt((stats[i].xx - stats[i].x*stats[i].x/stats[i].n) * (stats[i].yy - stats[i].y*stats[i].y/stats[i].n)); r2 *= r2; } double af = args->af_bins ? (bin_get_value(args->af_bins,i)+bin_get_value(args->af_bins,i-1))*0.5 : (double)(i-1)/(args->m_af-1); printf("GC%cAF\t2\t%f", x==0 ? 's' : 'i', af); printf("\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"", m[T2S(GT_HOM_RR)],m[T2S(GT_HET_RA)],m[T2S(GT_HOM_AA)]); printf("\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"", mm[T2S(GT_HOM_RR)],mm[T2S(GT_HET_RA)],mm[T2S(GT_HOM_AA)]); if ( stats[i].n && !isnan(r2) ) printf("\t%f", r2); else printf("\t"NA_STRING); printf("\t%.0f\n", stats[i].n); } if ( x==0 ) { printf("# NRD and discordance is calculated as follows:\n"); printf("# m .. number of matches\n"); printf("# x .. number of mismatches\n"); printf("# NRD = 100 * (xRR + xRA + xAA) / (xRR + xRA + xAA + mRA + mAA)\n"); printf("# RR discordance = 100 * xRR / (xRR + mRR)\n"); printf("# RA discordance = 100 * xRA / (xRA + mRA)\n"); printf("# AA discordance = 100 * xAA / (xAA + mAA)\n"); printf("# Non-Reference Discordance (NRD), SNPs\n# NRDs\t[2]id\t[3]NRD\t[4]Ref/Ref discordance\t[5]Ref/Alt discordance\t[6]Alt/Alt discordance\n"); } else printf("# Non-Reference Discordance (NRD), indels\n# NRDi\t[2]id\t[3]NRD\t[4]Ref/Ref discordance\t[5]Ref/Alt discordance\t[6]Alt/Alt discordance\n"); uint64_t m = nrd_m[T2S(GT_HET_RA)] + nrd_m[T2S(GT_HOM_AA)] + nrd_m[T2S(GT_HET_AA)]; uint64_t mm = nrd_mm[T2S(GT_HOM_RR)] + nrd_mm[T2S(GT_HET_RA)] + nrd_mm[T2S(GT_HOM_AA)] + nrd_mm[T2S(GT_HET_AA)]; printf("NRD%c\t2\t%f\t%f\t%f\t%f\n", x==0 ? 's' : 'i', m+mm ? mm*100.0/(m+mm) : 0, nrd_m[T2S(GT_HOM_RR)]+nrd_mm[T2S(GT_HOM_RR)] ? nrd_mm[T2S(GT_HOM_RR)]*100.0/(nrd_m[T2S(GT_HOM_RR)]+nrd_mm[T2S(GT_HOM_RR)]) : 0, nrd_m[T2S(GT_HET_RA)]+nrd_mm[T2S(GT_HET_RA)] ? nrd_mm[T2S(GT_HET_RA)]*100.0/(nrd_m[T2S(GT_HET_RA)]+nrd_mm[T2S(GT_HET_RA)]) : 0, nrd_m[T2S(GT_HOM_AA)]+nrd_mm[T2S(GT_HOM_AA)] ? nrd_mm[T2S(GT_HOM_AA)]*100.0/(nrd_m[T2S(GT_HOM_AA)]+nrd_mm[T2S(GT_HOM_AA)]) : 0 ); } for (x=0; x<2; x++) // x=0: snps, x=1: indels { gtcmp_t *stats; if ( x==0 ) { printf("# GCsS, Genotype concordance by sample (SNPs)\n# GCsS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\t[11]dosage r-squared\n"); stats = args->smpl_gts_snps; } else { printf("# GCiS, Genotype concordance by sample (indels)\n# GCiS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\t[11]dosage r-squared\n"); stats = args->smpl_gts_indels; } for (i=0; ifiles->n_smpl; i++) { uint64_t mm = 0, m = stats[i].gt2gt[T2S(GT_HET_RA)][T2S(GT_HET_RA)] + stats[i].gt2gt[T2S(GT_HOM_AA)][T2S(GT_HOM_AA)]; for (j=0; j<3; j++) for (k=0; k<3; k++) if ( j!=k ) mm += stats[i].gt2gt[j][k]; // Pearson's r2 double r2 = 0; if ( stats[i].n ) { r2 = (stats[i].yx - stats[i].x*stats[i].y/stats[i].n); r2 /= sqrt((stats[i].xx - stats[i].x*stats[i].x/stats[i].n) * (stats[i].yy - stats[i].y*stats[i].y/stats[i].n)); r2 *= r2; } printf("GC%cS\t2\t%s\t%.3f", x==0 ? 's' : 'i', args->files->samples[i], m+mm ? mm*100.0/(m+mm) : 0); printf("\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"", stats[i].gt2gt[T2S(GT_HOM_RR)][T2S(GT_HOM_RR)], stats[i].gt2gt[T2S(GT_HET_RA)][T2S(GT_HET_RA)], stats[i].gt2gt[T2S(GT_HOM_AA)][T2S(GT_HOM_AA)]); printf("\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"", stats[i].gt2gt[T2S(GT_HOM_RR)][T2S(GT_HET_RA)] + stats[i].gt2gt[T2S(GT_HOM_RR)][T2S(GT_HOM_AA)], stats[i].gt2gt[T2S(GT_HET_RA)][T2S(GT_HOM_RR)] + stats[i].gt2gt[T2S(GT_HET_RA)][T2S(GT_HOM_AA)], stats[i].gt2gt[T2S(GT_HOM_AA)][T2S(GT_HOM_RR)] + stats[i].gt2gt[T2S(GT_HOM_AA)][T2S(GT_HET_RA)]); if ( stats[i].n && !isnan(r2) ) printf("\t%f\n", r2); else printf("\t"NA_STRING"\n"); } } for (x=0; x<2; x++) // x=0: snps, x=1: indels { //printf("# GCiS, Genotype concordance by sample (indels)\n# GCiS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\t[11]dosage r-squared\n"); gtcmp_t *stats; if ( x==0 ) { printf("# GCTs, Genotype concordance table (SNPs)\n# GCTs"); stats = args->smpl_gts_snps; } else { printf("# GCTi, Genotype concordance table (indels)\n# GCTi"); stats = args->smpl_gts_indels; } i = 1; printf("\t[%d]sample", ++i); printf("\t[%d]RR Hom -> RR Hom", ++i); printf("\t[%d]RR Hom -> RA Het", ++i); printf("\t[%d]RR Hom -> AA Hom", ++i); printf("\t[%d]RR Hom -> AA Het", ++i); printf("\t[%d]RR Hom -> missing", ++i); printf("\t[%d]RA Het -> RR Hom", ++i); printf("\t[%d]RA Het -> RA Het", ++i); printf("\t[%d]RA Het -> AA Hom", ++i); printf("\t[%d]RA Het -> AA Het", ++i); printf("\t[%d]RA Het -> missing", ++i); printf("\t[%d]AA Hom -> RR Hom", ++i); printf("\t[%d]AA Hom -> RA Het", ++i); printf("\t[%d]AA Hom -> AA Hom", ++i); printf("\t[%d]AA Hom -> AA Het", ++i); printf("\t[%d]AA Hom -> missing", ++i); printf("\t[%d]AA Het -> RR Hom", ++i); printf("\t[%d]AA Het -> RA Het", ++i); printf("\t[%d]AA Het -> AA Hom", ++i); printf("\t[%d]AA Het -> AA Het", ++i); printf("\t[%d]AA Het -> missing", ++i); printf("\t[%d]missing -> RR Hom", ++i); printf("\t[%d]missing -> RA Het", ++i); printf("\t[%d]missing -> AA Hom", ++i); printf("\t[%d]missing -> AA Het", ++i); printf("\t[%d]missing -> missing\n", ++i); for (i=0; ifiles->n_smpl; i++) { printf("GCT%c\t%s", x==0 ? 's' : 'i', args->files->samples[i]); for (j=0; j<5; j++) for (k=0; k<5; k++) printf("\t%"PRIu64, stats[i].gt2gt[j][k]); printf("\n"); } } } printf("# DP, depth:\n" "# - set id, see above\n" "# - the depth bin, corresponds to the depth (unless --depth was given)\n" "# - number of genotypes with this depth (zero unless -s/-S was given)\n" "# - fraction of genotypes with this depth (zero unless -s/-S was given)\n" "# - number of sites with this depth\n" "# - fraction of sites with this depth\n"); printf("# DP, Depth distribution\n# DP\t[2]id\t[3]bin\t[4]number of genotypes\t[5]fraction of genotypes (%%)\t[6]number of sites\t[7]fraction of sites (%%)\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; long unsigned int sum = 0, sum_sites = 0; for (i=0; idp.m_vals; i++) { sum += stats->dp.vals[i]; sum_sites += stats->dp_sites.vals[i]; } for (i=0; idp.m_vals; i++) { if ( stats->dp.vals[i]==0 && stats->dp_sites.vals[i]==0 ) continue; printf("DP\t%d\t", id); if ( i==0 ) printf("<%d", stats->dp.min); else if ( i+1==stats->dp.m_vals ) printf(">%d", stats->dp.max); else printf("%d", idist_i2bin(&stats->dp,i)); printf("\t%"PRIu64"\t%f", stats->dp.vals[i], sum ? stats->dp.vals[i]*100./sum : 0); printf("\t%"PRIu64"\t%f\n", stats->dp_sites.vals[i], sum_sites ? stats->dp_sites.vals[i]*100./sum_sites : 0); } } if ( args->files->n_smpl ) { printf("# PSC, Per-sample counts. Note that the ref/het/hom counts include only SNPs, for indels see PSI. The rest include both SNPs and indels.\n"); printf("# PSC\t[2]id\t[3]sample\t[4]nRefHom\t[5]nNonRefHom\t[6]nHets\t[7]nTransitions\t[8]nTransversions\t[9]nIndels\t[10]average depth\t[11]nSingletons" "\t[12]nHapRef\t[13]nHapAlt\t[14]nMissing\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; for (i=0; ifiles->n_smpl; i++) { float dp = stats->smpl_ndp[i] ? stats->smpl_dp[i]/(float)stats->smpl_ndp[i] : 0; printf("PSC\t%d\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%.1f\t%d\t%d\t%d\t%d\n", id,args->files->samples[i], stats->smpl_homRR[i], stats->smpl_homAA[i], stats->smpl_hets[i], stats->smpl_ts[i], stats->smpl_tv[i], stats->smpl_indels[i],dp, stats->smpl_sngl[i], stats->smpl_hapRef[i], stats->smpl_hapAlt[i], stats->smpl_missing[i]); } } printf("# PSI, Per-Sample Indels. Note that alt-het genotypes with both ins and del allele are counted twice, in both nInsHets and nDelHets.\n"); printf("# PSI\t[2]id\t[3]sample\t[4]in-frame\t[5]out-frame\t[6]not applicable\t[7]out/(in+out) ratio\t[8]nInsHets\t[9]nDelHets\t[10]nInsAltHoms\t[11]nDelAltHoms\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; for (i=0; ifiles->n_smpl; i++) { int na = 0, in = 0, out = 0; if ( args->exons ) { na = stats->smpl_frm_shifts[i*3 + 0]; in = stats->smpl_frm_shifts[i*3 + 1]; out = stats->smpl_frm_shifts[i*3 + 2]; } printf("PSI\t%d\t%s\t%d\t%d\t%d\t%.2f\t%d\t%d\t%d\t%d\n", id,args->files->samples[i], in,out,na,in+out?1.0*out/(in+out):0, stats->smpl_ins_hets[i],stats->smpl_del_hets[i],stats->smpl_ins_homs[i],stats->smpl_del_homs[i]); } } #ifdef HWE_STATS printf("# HWE\n# HWE\t[2]id\t[3]1st ALT allele frequency\t[4]Number of observations\t[5]25th percentile\t[6]median\t[7]75th percentile\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; for (i=0; inaf_hwe; i++) stats->af_hwe[i+args->naf_hwe] += stats->af_hwe[i]; // singletons for (i=1; im_af; i++) { unsigned int sum_tot = 0, sum_tmp = 0; int j, *ptr = &stats->af_hwe[i*args->naf_hwe]; for (j=0; jnaf_hwe; j++) sum_tot += ptr[j]; if ( !sum_tot ) continue; double af = args->af_bins ? (bin_get_value(args->af_bins,i)+bin_get_value(args->af_bins,i-1))*0.5 : (double)(i-1)/(args->m_af-1); int nprn = 3; printf("HWE\t%d\t%f\t%d",id,af,sum_tot); for (j=0; jnaf_hwe; j++) { sum_tmp += ptr[j]; float frac = (float)sum_tmp/sum_tot; if ( frac >= 0.75 ) { while (nprn>0) { printf("\t%f", (float)j/args->naf_hwe); nprn--; } break; } if ( frac >= 0.5 ) { while (nprn>1) { printf("\t%f", (float)j/args->naf_hwe); nprn--; } continue; } if ( frac >= 0.25 ) { while (nprn>2) { printf("\t%f", (float)j/args->naf_hwe); nprn--; } } } assert(nprn==0); printf("\n"); } } #endif } if ( args->stats[0].smpl_vaf ) { printf("# VAF, Variant Allele Frequency determined as fraction of alternate reads in FORMAT/AD\n"); printf("# VAF\t[2]id\t[3]sample\t[4]SNV VAF distribution\t[5]indel VAF distribution\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; for (i=0; ifiles->n_smpl; i++) { printf("VAF\t%d\t%s\t", id,args->files->samples[i]); for (j=0; j<21; j++) printf("%s%d",j?",":"",stats->smpl_vaf[i].snv[j]); printf("\t"); for (j=0; j<21; j++) printf("%s%d",j?",":"",stats->smpl_vaf[i].indel[j]); printf("\n"); } } } } static void usage(void) { fprintf(stderr, "\n"); fprintf(stderr, "About: Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats.\n"); fprintf(stderr, " When two files are given, the program generates separate stats for intersection\n"); fprintf(stderr, " and the complements. By default only sites are compared, -s/-S must given to include\n"); fprintf(stderr, " also sample columns.\n"); fprintf(stderr, "Usage: bcftools stats [options] []\n"); fprintf(stderr, "\n"); fprintf(stderr, "Options:\n"); fprintf(stderr, " --af-bins LIST Allele frequency bins, a list (0.1,0.5,1) or a file (0.1\\n0.5\\n1)\n"); fprintf(stderr, " --af-tag STRING Allele frequency tag to use, by default estimated from AN,AC or GT\n"); fprintf(stderr, " -1, --1st-allele-only Include only 1st allele at multiallelic sites\n"); fprintf(stderr, " -c, --collapse STRING Treat as identical records with , see man page for details [none]\n"); fprintf(stderr, " -d, --depth INT,INT,INT Depth distribution: min,max,bin size [0,500,1]\n"); fprintf(stderr, " -e, --exclude EXPR Exclude sites for which the expression is true (see man page for details)\n"); fprintf(stderr, " -E, --exons FILE.gz Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, bgzip compressed)\n"); fprintf(stderr, " -f, --apply-filters LIST Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n"); fprintf(stderr, " -F, --fasta-ref FILE Faidx indexed reference sequence file to determine INDEL context\n"); fprintf(stderr, " -i, --include EXPR Select sites for which the expression is true (see man page for details)\n"); fprintf(stderr, " -I, --split-by-ID Collect stats for sites with ID separately (known vs novel)\n"); fprintf(stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " -s, --samples LIST List of samples for sample stats, \"-\" to include all samples\n"); fprintf(stderr, " -S, --samples-file FILE File of samples to include\n"); fprintf(stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(stderr, " -u, --user-tstv TAG[:min:max:n] Collect Ts/Tv stats for any tag using the given binning [0:1:100]\n"); fprintf(stderr, " A subfield can be selected as e.g. 'PV4[0]', here the first value of the PV4 tag\n"); fprintf(stderr, " --threads INT Use multithreading with worker threads [0]\n"); fprintf(stderr, " -v, --verbose Produce verbose per-site and per-sample output\n"); fprintf(stderr, "\n"); exit(1); } int main_vcfstats(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->files = bcf_sr_init(); args->argc = argc; args->argv = argv; args->dp_min = 0; args->dp_max = 500; args->dp_step = 1; int regions_is_file = 0, targets_is_file = 0; int regions_overlap = 1; int targets_overlap = 0; static struct option loptions[] = { {"af-bins",1,0,1}, {"af-tag",1,0,2}, {"1st-allele-only",0,0,'1'}, {"include",1,0,'i'}, {"exclude",1,0,'e'}, {"help",0,0,'h'}, {"collapse",1,0,'c'}, {"regions",1,0,'r'}, {"regions-file",1,0,'R'}, {"regions-overlap",required_argument,NULL,3}, {"verbose",0,0,'v'}, {"depth",1,0,'d'}, {"apply-filters",1,0,'f'}, {"exons",1,0,'E'}, {"samples",1,0,'s'}, {"samples-file",1,0,'S'}, {"split-by-ID",0,0,'I'}, {"targets",1,0,'t'}, {"targets-file",1,0,'T'}, {"targets-overlap",required_argument,NULL,4}, {"fasta-ref",1,0,'F'}, {"user-tstv",1,0,'u'}, {"threads",1,0,9}, {0,0,0,0} }; while ((c = getopt_long(argc, argv, "hc:r:R:e:s:S:d:i:t:T:F:f:1u:vIE:",loptions,NULL)) >= 0) { switch (c) { case 1 : args->af_bins_list = optarg; break; case 2 : args->af_tag = optarg; break; case 'u': add_user_stats(args,optarg); break; case '1': args->first_allele_only = 1; break; case 'F': args->ref_fname = optarg; break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; targets_is_file = 1; break; case 'c': if ( !strcmp(optarg,"snps") ) args->files->collapse |= COLLAPSE_SNPS; else if ( !strcmp(optarg,"indels") ) args->files->collapse |= COLLAPSE_INDELS; else if ( !strcmp(optarg,"both") ) args->files->collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS; else if ( !strcmp(optarg,"any") ) args->files->collapse |= COLLAPSE_ANY; else if ( !strcmp(optarg,"all") ) args->files->collapse |= COLLAPSE_ANY; else if ( !strcmp(optarg,"some") ) args->files->collapse |= COLLAPSE_SOME; else if ( !strcmp(optarg,"none") ) args->files->collapse = COLLAPSE_NONE; else error("The --collapse string \"%s\" not recognised.\n", optarg); break; case 'v': args->verbose_sites = 1; break; case 'd': if ( sscanf(optarg,"%d,%d,%d",&args->dp_min,&args->dp_max,&args->dp_step)!=3 ) error("Could not parse --depth %s\n", optarg); if ( args->dp_min<0 || args->dp_min >= args->dp_max || args->dp_step > args->dp_max - args->dp_min + 1 ) error("Is this a typo? --depth %s\n", optarg); break; case 'f': args->files->apply_filters = optarg; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 'E': args->exons_fname = optarg; break; case 's': args->samples_list = optarg; break; case 'S': args->samples_list = optarg; args->samples_is_file = 1; break; case 'I': args->split_by_id = 1; break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 3 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 4 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 'h': case '?': usage(); break; default: error("Unknown argument: %s\n", optarg); } } char *fname = NULL; if ( optind==argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else usage(); } else fname = argv[optind]; if ( argc-optind>2 ) usage(); if ( argc-optind>1 ) { args->files->require_index = 1; if ( args->split_by_id ) error("Only one file can be given with -i.\n"); } if ( !args->samples_list ) args->files->max_unpack = BCF_UN_INFO; else args->files->max_unpack = BCF_UN_FMT; if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } if ( args->regions_list) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( args->n_threads && bcf_sr_set_threads(args->files, args->n_threads)<0) error("Failed to create threads\n"); while (fname) { if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); fname = ++optind < argc ? argv[optind] : NULL; } init_stats(args); print_header(args); do_vcf_stats(args); print_stats(args); destroy_stats(args); bcf_sr_destroy(args->files); free(args); return 0; } pysam-0.23.0/bcftools/vcfstats.c.pysam.c000066400000000000000000002571121475062545500201370ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfstats.c -- Produces stats which can be plotted using plot-vcfstats. Copyright (C) 2012-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Notes and known issues: - SN ts/tv calculation includes all non-ref alleles listed in ALT while per-sample ts/tv takes the first non-ref allele only, something to consider with many non-ref HETs. */ #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "filter.h" #include "bin.h" #include "dist.h" // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 #define HWE_STATS 1 #define QUAL_STATS 1 #define IRC_STATS 1 #define IRC_RLEN 10 #define NA_STRING "0" typedef struct { char *tag; float min, max; uint64_t *vals_ts, *vals_tv; void *val; int nbins, type, m_val, idx; } user_stats_t; typedef struct { int min, max, step, m_vals; uint64_t *vals; } idist_t; // variant allele frequency (fraction of alt allele in pileup as determined from AD) collected into 0.05 bins typedef struct { int snv[21], indel[21]; } vaf_t; typedef struct { uint64_t n_snps, n_indels, n_mnps, n_others, n_mals, n_snp_mals, n_records, n_noalts; int *af_ts, *af_tv, *af_snps; // first bin of af_* stats are singletons #if HWE_STATS int *af_hwe; #endif #if IRC_STATS int n_repeat[IRC_RLEN][4], n_repeat_na; // number of indels which are repeat-consistent, repeat-inconsistent (dels and ins), and not applicable int *af_repeats[3]; #endif int ts_alt1, tv_alt1; #if QUAL_STATS // Values are rounded to one significant digit and 1 is added (Q*10+1); missing and negative values go in the first bin // Only SNPs that are the 1st alternate allele are counted dist_t *qual_ts, *qual_tv, *qual_indels; #endif int *insertions, *deletions, m_indel; // maximum indel length int in_frame, out_frame, na_frame, in_frame_alt1, out_frame_alt1, na_frame_alt1; int subst[15]; int *smpl_hets, *smpl_homRR, *smpl_homAA, *smpl_ts, *smpl_tv, *smpl_indels, *smpl_ndp, *smpl_sngl; int *smpl_hapRef, *smpl_hapAlt, *smpl_missing; int *smpl_ins_hets, *smpl_del_hets, *smpl_ins_homs, *smpl_del_homs; int *smpl_frm_shifts; // not-applicable, in-frame, out-frame vaf_t vaf, *smpl_vaf; // total (INFO/AD) and per-sample (FMT/VAF) VAF distributions unsigned long int *smpl_dp; idist_t dp, dp_sites; int nusr; user_stats_t *usr; double *dvaf; // distribution of the mean indel-allele frequency by length: -m_indel,-(m_indel-1),...-1,0,1,..,m_indel uint32_t *nvaf; } stats_t; typedef struct { uint64_t gt2gt[5][5]; // number of RR->RR, RR->RA, etc. matches/mismatches; see type2stats /* Pearson's R^2 is used for aggregate R^2 y, yy .. sum of dosage and squared dosage in the query VCF (second file) x, xx .. sum of squared dosage in the truth VCF (first file) n .. number of genotypes */ double y, yy, x, xx, yx, n; } gtcmp_t; typedef struct { char *seq; int pos, cnt, len; } _idc1_t; typedef struct { faidx_t *ref; _idc1_t *dat; int ndat, mdat; } indel_ctx_t; typedef struct { // stats stats_t stats[3]; int *tmp_iaf, ntmp_iaf, m_af, m_qual, naf_hwe, mtmp_frm; uint8_t *tmp_frm; int dp_min, dp_max, dp_step; gtcmp_t *smpl_gts_snps, *smpl_gts_indels; gtcmp_t *af_gts_snps, *af_gts_indels; // first bin of af_* stats are singletons bin_t *af_bins; float *farr; int32_t *iarr; int mfarr, miarr; int nref_tot, nhet_tot, nalt_tot, n_nref, i_nref; // indel context indel_ctx_t *indel_ctx; char *ref_fname; // user stats int nusr; user_stats_t *usr; // other bcf_srs_t *files; bcf_sr_regions_t *exons; char **argv, *exons_fname, *regions_list, *samples_list, *targets_list, *af_bins_list, *af_tag; int argc, verbose_sites, first_allele_only, samples_is_file; int split_by_id, nstats; filter_t *filter[2]; char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE int n_threads; } args_t; static int type2dosage[6], type2ploidy[6], type2stats[7]; static void idist_init(idist_t *d, int min, int max, int step) { d->min = min; d->max = max; d->step = step; d->m_vals = 4 + (d->max - d->min)/d->step; d->vals = (uint64_t*) calloc(d->m_vals,sizeof(uint64_t)); } static void idist_destroy(idist_t *d) { if ( d->vals ) free(d->vals); } static inline uint64_t *idist(idist_t *d, int val) { if ( val < d->min ) return &d->vals[0]; if ( val > d->max ) return &d->vals[d->m_vals-1]; return &d->vals[1 + (val - d->min) / d->step]; } static inline int idist_i2bin(idist_t *d, int i) { if ( i<=0 ) return d->min; if ( i>= d->m_vals ) return d->max; return i-1+d->min; } #define IC_DBG 0 #if IC_DBG static void _indel_ctx_print1(_idc1_t *idc) { int i; fprintf(bcftools_stdout, "%d\t", idc->cnt); for (i=0; ilen; i++) fputc(idc->seq[i], bcftools_stdout); fputc('\n', bcftools_stdout); } static void _indel_ctx_print(indel_ctx_t *ctx) { int i; for (i=0; indat; i++) _indel_ctx_print1(&ctx->dat[i]); fputc('\n',bcftools_stdout); } #endif static int _indel_ctx_lookup(indel_ctx_t *ctx, char *seq, int seq_len, int *hit) { // binary search int min = 0, max = ctx->ndat - 1; while ( min<=max ) { int i = (min+max)/2; int cmp = strncmp(seq, ctx->dat[i].seq, seq_len); if ( cmp<0 ) max = i - 1; else if ( cmp>0 ) min = i + 1; else { if ( seq_len==ctx->dat[i].len ) { *hit = 1; return i; } else if ( seq_lendat[i].len ) max = i - 1; else min = i + 1; } } *hit = 0; return max; } static void _indel_ctx_insert(indel_ctx_t *ctx, char *seq, int seq_len, int pos) { int idat, hit, i; idat = _indel_ctx_lookup(ctx, seq, seq_len, &hit); if ( !hit ) { if ( pos>0 ) return; idat++; ctx->ndat++; hts_expand(_idc1_t, ctx->ndat+1, ctx->mdat, ctx->dat); if ( idatndat && ctx->ndat>1 ) memmove(&ctx->dat[idat+1], &ctx->dat[idat], (ctx->ndat - idat - 1)*sizeof(_idc1_t)); ctx->dat[idat].len = seq_len; ctx->dat[idat].cnt = 1; ctx->dat[idat].pos = pos; ctx->dat[idat].seq = (char*) malloc(sizeof(char)*(seq_len+1)); for (i=0; idat[idat].seq[i] = seq[i]; ctx->dat[idat].seq[i] = 0; return; } if ( ctx->dat[idat].pos + seq_len == pos ) { ctx->dat[idat].cnt++; ctx->dat[idat].pos = pos; } } indel_ctx_t *indel_ctx_init(char *fa_ref_fname) { indel_ctx_t *ctx = (indel_ctx_t *) calloc(1,sizeof(indel_ctx_t)); ctx->ref = fai_load(fa_ref_fname); if ( !ctx->ref ) { free(ctx); return NULL; } return ctx; } void indel_ctx_destroy(indel_ctx_t *ctx) { fai_destroy(ctx->ref); if ( ctx->mdat ) free(ctx->dat); free(ctx); } /** * indel_ctx_type() - determine indel context type * @ctx: * @chr: chromosome name * @pos: position of the first @ref base, 1-based * @ref: reference allele * @alt: alternate allele. Only first of multiple comma-separated alleles is * considered * @nrep: number of repeated elements (w) * @nlen: length of a single repeat element (w) * * Returns the INDEL length, negative for deletions, positive for insertions */ int indel_ctx_type(indel_ctx_t *ctx, char *chr, int pos, char *ref, char *alt, int *nrep, int *nlen) { const int win_size = 50; // hard-wired for now const int rep_len = IRC_RLEN; // hard-wired for now int ref_len = strlen(ref); int alt_len = 0; while ( alt[alt_len] && alt[alt_len]!=',' ) alt_len++; int i, fai_ref_len; char *fai_ref = faidx_fetch_seq(ctx->ref, chr, pos-1, pos+win_size, &fai_ref_len); for (i=0; i96 ) fai_ref[i] -= 32; // Sanity check: the reference sequence must match the REF allele for (i=0; indat = 0; for (i=0; indat; i++) { if ( max_cnt < ctx->dat[i].cnt || (max_cnt==ctx->dat[i].cnt && max_len < ctx->dat[i].len) ) { max_cnt = ctx->dat[i].cnt; max_len = ctx->dat[i].len; } free(ctx->dat[i].seq); } free(fai_ref); *nrep = max_cnt; *nlen = max_len; return alt_len - ref_len; } static void add_user_stats(args_t *args, char *str) { args->nusr++; args->usr = (user_stats_t*) realloc(args->usr,sizeof(user_stats_t)*args->nusr); user_stats_t *usr = &args->usr[args->nusr-1]; memset(usr,0,sizeof(*usr)); usr->min = 0; usr->max = 1; usr->nbins = 100; usr->idx = 0; char *tmp = str; while ( *tmp && *tmp!=':' ) tmp++; // Tag with an index or just tag? (e.g. PV4[1] vs DP) if ( tmp > str && tmp[-1]==']' ) { char *ptr = tmp; while ( ptr>str && *ptr!='[' ) ptr--; if ( *ptr=='[' ) { char *ptr2; usr->idx = strtol(ptr+1, &ptr2, 10); if ( ptr+1==ptr2 || ptr2 != tmp-1 ) error("Could not parse the index in \"%s\" (ptr=%s;ptr2=%s(%p),tmp=%s(%p),idx=%d)\n", str,ptr,ptr2,ptr2,tmp,tmp,usr->idx); if ( usr->idx<0 ) error("Error: negative index is not allowed: \"%s\"\n", str); *ptr = 0; } } usr->tag = (char*)calloc(tmp-str+2,sizeof(char)); memcpy(usr->tag,str,tmp-str); if ( *tmp ) { char *ptr = ++tmp; usr->min = strtod(tmp, &ptr); if ( tmp==ptr ) error("Could not parse %s\n", str); tmp = ptr+1; } if ( *tmp ) { char *ptr = tmp; usr->max = strtod(tmp, &ptr); if ( tmp==ptr ) error("Could not parse %s\n", str); tmp = ptr+1; } if ( *tmp ) { char *ptr = tmp; usr->nbins = strtol(tmp, &ptr, 10); if ( tmp==ptr ) error("Could not parse %s\n", str); if ( usr->nbins<=0 ) error("Number of bins does not make sense (%d): %s.\n", usr->nbins, str); } } static void init_user_stats(args_t *args, bcf_hdr_t *hdr, stats_t *stats) { stats->nusr = args->nusr; stats->usr = (user_stats_t*)malloc(sizeof(user_stats_t)*args->nusr); if (args->nusr) memcpy(stats->usr,args->usr,args->nusr*sizeof(user_stats_t)); int i; for (i=0; inusr; i++) { user_stats_t *usr = &stats->usr[i]; usr->vals_ts = (uint64_t*)calloc(usr->nbins,sizeof(uint64_t)); usr->vals_tv = (uint64_t*)calloc(usr->nbins,sizeof(uint64_t)); int id = bcf_hdr_id2int(hdr,BCF_DT_ID,usr->tag); if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,id) ) error("The INFO tag \"%s\" is not defined in the header\n", usr->tag); usr->type = bcf_hdr_id2type(hdr,BCF_HL_INFO,id); if ( usr->type!=BCF_HT_REAL && usr->type!=BCF_HT_INT ) error("The INFO tag \"%s\" is not of Float or Integer type (%d)\n", usr->tag, usr->type); } } static void init_stats(args_t *args) { int i; args->nstats = args->files->nreaders==1 ? 1 : 3; if ( args->split_by_id ) args->nstats = 2; if ( args->filter_str ) { args->filter[0] = filter_init(bcf_sr_get_header(args->files,0), args->filter_str); if ( args->files->nreaders==2 ) args->filter[1] = filter_init(bcf_sr_get_header(args->files,1), args->filter_str); args->files->max_unpack |= filter_max_unpack(args->filter[0]); } // AF corresponds to AC but is more robust to mixtures of haploid and diploid GTs if ( !args->af_bins_list ) { args->m_af = 101; for (i=0; ifiles->nreaders; i++) if ( bcf_hdr_nsamples(args->files->readers[i].header) + 1> args->m_af ) args->m_af = bcf_hdr_nsamples(args->files->readers[i].header) + 1; } else { args->af_bins = bin_init(args->af_bins_list,0,1); // m_af is used also for other af arrays, where the first bin is for // singletons. However, since the last element is unused in af_bins // (n boundaries form n-1 intervals), the m_af count is good for both. args->m_af = bin_get_size(args->af_bins); } bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0); if ( args->af_tag && !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,bcf_hdr_id2int(hdr,BCF_DT_ID,args->af_tag)) ) error("No such INFO tag: %s\n", args->af_tag); int id, has_fmt_ad = ((id=bcf_hdr_id2int(hdr,BCF_DT_ID,"AD"))>=0 && bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id)) ? 1 : 0; #if QUAL_STATS args->m_qual = 999; #endif #if HWE_STATS args->naf_hwe = 100; #endif if ( args->samples_list ) { if ( !bcf_sr_set_samples(args->files,args->samples_list,args->samples_is_file) ) { if ( !bcf_hdr_nsamples(args->files->readers[0].header) ) error("No sample columns in %s\n", args->files->readers[0].fname); error("Unable to parse the samples: \"%s\"\n", args->samples_list); } args->af_gts_snps = (gtcmp_t *) calloc(args->m_af,sizeof(gtcmp_t)); args->af_gts_indels = (gtcmp_t *) calloc(args->m_af,sizeof(gtcmp_t)); args->smpl_gts_snps = (gtcmp_t *) calloc(args->files->n_smpl,sizeof(gtcmp_t)); args->smpl_gts_indels = (gtcmp_t *) calloc(args->files->n_smpl,sizeof(gtcmp_t)); } for (i=0; instats; i++) { stats_t *stats = &args->stats[i]; stats->m_indel = 60; stats->insertions = (int*) calloc(stats->m_indel,sizeof(int)); stats->deletions = (int*) calloc(stats->m_indel,sizeof(int)); stats->af_ts = (int*) calloc(args->m_af,sizeof(int)); stats->af_tv = (int*) calloc(args->m_af,sizeof(int)); stats->af_snps = (int*) calloc(args->m_af,sizeof(int)); int j; for (j=0; j<3; j++) stats->af_repeats[j] = (int*) calloc(args->m_af,sizeof(int)); #if QUAL_STATS stats->qual_ts = dist_init(5); stats->qual_tv = dist_init(5); stats->qual_indels = dist_init(5); #endif if ( args->files->n_smpl ) { stats->smpl_missing = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_hets = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_homAA = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_homRR = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_hapRef = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_hapAlt = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_ins_hets = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_del_hets = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_ins_homs = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_del_homs = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_ts = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_tv = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_indels = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_dp = (unsigned long int *) calloc(args->files->n_smpl,sizeof(unsigned long int)); stats->smpl_ndp = (int *) calloc(args->files->n_smpl,sizeof(int)); stats->smpl_sngl = (int *) calloc(args->files->n_smpl,sizeof(int)); if ( has_fmt_ad ) stats->smpl_vaf = (vaf_t*) calloc(args->files->n_smpl,sizeof(vaf_t)); #if HWE_STATS stats->af_hwe = (int*) calloc(args->m_af*args->naf_hwe,sizeof(int)); #endif if ( args->exons_fname ) stats->smpl_frm_shifts = (int*) calloc(args->files->n_smpl*3,sizeof(int)); stats->nvaf = (uint32_t*) calloc(stats->m_indel*2+1,sizeof(*stats->nvaf)); stats->dvaf = (double*) calloc(stats->m_indel*2+1,sizeof(*stats->dvaf)); } idist_init(&stats->dp, args->dp_min,args->dp_max,args->dp_step); idist_init(&stats->dp_sites, args->dp_min,args->dp_max,args->dp_step); init_user_stats(args, i!=1 ? args->files->readers[0].header : args->files->readers[1].header, stats); } if ( args->exons_fname ) { args->exons = bcf_sr_regions_init(args->exons_fname,1,0,1,2); if ( !args->exons ) error("Error occurred while reading, was the file compressed with bgzip: %s?\n", args->exons_fname); } #if IRC_STATS if ( args->ref_fname ) args->indel_ctx = indel_ctx_init(args->ref_fname); #endif type2dosage[GT_HOM_RR] = 0; type2dosage[GT_HET_RA] = 1; type2dosage[GT_HOM_AA] = 2; type2dosage[GT_HET_AA] = 2; type2dosage[GT_HAPL_R] = 0; type2dosage[GT_HAPL_A] = 1; type2ploidy[GT_HOM_RR] = 1; type2ploidy[GT_HET_RA] = 1; type2ploidy[GT_HOM_AA] = 1; type2ploidy[GT_HET_AA] = 1; type2ploidy[GT_HAPL_R] = -1; type2ploidy[GT_HAPL_A] = -1; type2stats[GT_HOM_RR] = 0; type2stats[GT_HET_RA] = 1; type2stats[GT_HOM_AA] = 2; type2stats[GT_HET_AA] = 3; type2stats[GT_HAPL_R] = 0; type2stats[GT_HAPL_A] = 2; type2stats[GT_UNKN] = 4; } static void destroy_stats(args_t *args) { int id, j; for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; if (stats->af_ts) free(stats->af_ts); if (stats->af_tv) free(stats->af_tv); if (stats->af_snps) free(stats->af_snps); for (j=0; j<3; j++) if (stats->af_repeats[j]) free(stats->af_repeats[j]); #if QUAL_STATS if (stats->qual_ts) dist_destroy(stats->qual_ts); if (stats->qual_tv) dist_destroy(stats->qual_tv); if (stats->qual_indels) dist_destroy(stats->qual_indels); #endif #if HWE_STATS free(stats->af_hwe); #endif free(stats->insertions); free(stats->deletions); free(stats->smpl_missing); free(stats->smpl_hets); free(stats->smpl_homAA); free(stats->smpl_homRR); free(stats->smpl_hapRef); free(stats->smpl_hapAlt); free(stats->smpl_ins_homs); free(stats->smpl_del_homs); free(stats->smpl_ins_hets); free(stats->smpl_del_hets); free(stats->smpl_ts); free(stats->smpl_tv); free(stats->smpl_indels); free(stats->smpl_dp); free(stats->smpl_ndp); free(stats->smpl_sngl); free(stats->smpl_vaf); idist_destroy(&stats->dp); idist_destroy(&stats->dp_sites); for (j=0; jnusr; j++) { free(stats->usr[j].vals_ts); free(stats->usr[j].vals_tv); free(stats->usr[j].val); } free(stats->usr); if ( args->exons ) free(stats->smpl_frm_shifts); free(stats->nvaf); free(stats->dvaf); } for (j=0; jnusr; j++) free(args->usr[j].tag); if ( args->af_bins ) bin_destroy(args->af_bins); free(args->farr); free(args->iarr); free(args->usr); free(args->tmp_frm); free(args->tmp_iaf); if (args->exons) bcf_sr_regions_destroy(args->exons); free(args->af_gts_snps); free(args->af_gts_indels); free(args->smpl_gts_snps); free(args->smpl_gts_indels); if (args->indel_ctx) indel_ctx_destroy(args->indel_ctx); if (args->filter[0]) filter_destroy(args->filter[0]); if (args->filter[1]) filter_destroy(args->filter[1]); } // The arary tmp_iaf keeps the index of AF bin for each allele, the first bin is for singletons. // The number of bins, either m_af (101) or as given by the user in --af-bins static void init_iaf(args_t *args, bcf_sr_t *reader) { bcf1_t *line = reader->buffer[0]; hts_expand(int32_t,line->n_allele,args->ntmp_iaf,args->tmp_iaf); int i, ret; if ( args->af_tag ) { ret = bcf_get_info_float(reader->header, line, args->af_tag, &args->farr, &args->mfarr); if ( ret<=0 || ret!=line->n_allele-1 ) { // the AF tag is not present or wrong number of values, put in the singletons/unknown bin for (i=0; in_allele; i++) args->tmp_iaf[i] = 0; return; } args->tmp_iaf[0] = 0; for (i=1; in_allele; i++) { float af = args->farr[i-1]; if ( af<0 ) af = 0; else if ( af>1 ) af = 1; int iaf = args->af_bins ? bin_get_idx(args->af_bins,af) : af*(args->m_af-2); args->tmp_iaf[i] = iaf + 1; // the first tmp_iaf bin is reserved for singletons } return; } // tmp_iaf is first filled with AC counts in calc_ac and then transformed to // an index to af_gts_snps ret = bcf_calc_ac(reader->header, line, args->tmp_iaf, args->samples_list ? BCF_UN_INFO|BCF_UN_FMT : BCF_UN_INFO); if ( !ret ) { for (i=0; in_allele; i++) args->tmp_iaf[i] = 0; // singletons/unknown bin return; } int an = 0; for (i=0; in_allele; i++) an += args->tmp_iaf[i]; args->tmp_iaf[0] = 0; for (i=1; in_allele; i++) { if ( args->tmp_iaf[i]==1 ) args->tmp_iaf[i] = 0; // singletons into the first bin else if ( !an ) args->tmp_iaf[i] = 1; // no genotype at all, put to the AF=0 bin else { float af = (float) args->tmp_iaf[i] / an; if ( af<0 ) af = 0; else if ( af>1 ) af = 1; int iaf = args->af_bins ? bin_get_idx(args->af_bins,af) : af*(args->m_af-2); args->tmp_iaf[i] = iaf + 1; } } } static inline void do_mnp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) { stats->n_mnps++; } static inline void do_other_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) { stats->n_others++; } static void do_indel_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) { stats->n_indels++; bcf1_t *line = reader->buffer[0]; #if QUAL_STATS int iqual = (isnan(line->qual) || line->qual<0) ? 0 : 1 + (int)(line->qual*10); dist_insert(stats->qual_indels, iqual); #endif // Check if the indel is near an exon for the frameshift statistics int i, exon_overlap = 0; if ( args->exons ) { if ( !bcf_sr_regions_overlap(args->exons, bcf_seqname(reader->header,line),line->pos,line->pos) ) exon_overlap = 1; hts_expand(uint8_t,line->n_allele,args->mtmp_frm,args->tmp_frm); for (i=0; in_allele; i++) args->tmp_frm[i] = 0; } for (i=1; in_allele; i++) { if ( args->first_allele_only && i>1 ) break; int is_indel = bcf_has_variant_type(line,i,VCF_INDEL); if (is_indel < 0) error("bcf_has_variant_type() failed."); if ( !is_indel ) continue; int len = bcf_variant_length(line, i); #if IRC_STATS // Indel repeat consistency if ( args->indel_ctx ) { int nrep, nlen, ndel; ndel = indel_ctx_type(args->indel_ctx, (char*)reader->header->id[BCF_DT_CTG][line->rid].key, line->pos+1, line->d.allele[0], line->d.allele[i], &nrep, &nlen); if ( nlen<=1 || nrep<=1 ) { // not a repeat or a single base repeat stats->n_repeat_na++; stats->af_repeats[2][ args->tmp_iaf[i] ]++; } else { if ( abs(ndel) % nlen ) { // the length of the inserted/deleted sequence is not consistent with the repeat element stats->n_repeat[nlen-1][ndel<0 ? 1 : 3]++; stats->af_repeats[1][ args->tmp_iaf[i] ]++; } else { // the length consistent with the repeat stats->n_repeat[nlen-1][ndel<0 ? 0 : 2]++; stats->af_repeats[0][ args->tmp_iaf[i] ]++; } } } else stats->af_repeats[2][ args->tmp_iaf[i] ]++; #endif // Check the frameshifts int tlen = 0; if ( args->exons && exon_overlap ) // there is an exon { if ( len>0 ) { // insertion if ( args->exons->start <= line->pos && args->exons->end > line->pos ) tlen = abs(len); } else if ( args->exons->start <= line->pos + abs(len) ) { // deletion tlen = abs(len); if ( line->pos < args->exons->start ) // trim the beginning tlen -= args->exons->start - line->pos + 1; if ( args->exons->end < line->pos + abs(len) ) // trim the end tlen -= line->pos + abs(len) - args->exons->end; } } if ( tlen ) // there are some deleted/inserted bases in the exon { if ( tlen%3 ) { stats->out_frame++; args->tmp_frm[i] = 2; } else { stats->in_frame++; args->tmp_frm[i] = 1; } if ( i==1 ) { if ( tlen%3 ) stats->out_frame_alt1++; else stats->in_frame_alt1++; } } else // no exon affected { if ( i==1 ) stats->na_frame_alt1++; stats->na_frame++; } // Indel length distribution int *ptr = stats->insertions; if ( len<0 ) { len *= -1; ptr = stats->deletions; } if ( --len >= stats->m_indel ) len = stats->m_indel-1; ptr[len]++; } } static void do_user_stats(stats_t *stats, bcf_sr_t *reader, int is_ts) { int i, nval; for (i=0; inusr; i++) { user_stats_t *usr = &stats->usr[i]; uint64_t *vals = is_ts ? usr->vals_ts : usr->vals_tv; float val; if ( usr->type==BCF_HT_REAL ) { if ( (nval=bcf_get_info_float(reader->header,reader->buffer[0],usr->tag,&usr->val,&usr->m_val))<=0 ) continue; if ( usr->idx >= nval ) continue; val = ((float*)usr->val)[usr->idx]; } else { if ( (nval=bcf_get_info_int32(reader->header,reader->buffer[0],usr->tag,&usr->val,&usr->m_val))<=0 ) continue; if ( usr->idx >= nval ) continue; val = ((int32_t*)usr->val)[usr->idx]; } int idx; if ( val<=usr->min ) idx = 0; else if ( val>=usr->max ) idx = usr->nbins - 1; else idx = (val - usr->min)/(usr->max - usr->min) * (usr->nbins-1); vals[idx]++; } } static void do_snp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader) { stats->n_snps++; bcf1_t *line = reader->buffer[0]; int ref = bcf_acgt2int(*line->d.allele[0]); if ( ref<0 ) return; #if QUAL_STATS int iqual = (isnan(line->qual) || line->qual<0) ? 0 : 1 + (int)(line->qual*10); #endif int i; for (i=1; in_allele; i++) { if ( args->first_allele_only && i>1 ) break; if ( !(bcf_get_variant_type(line,i)&VCF_SNP) ) continue; int alt = bcf_acgt2int(*line->d.allele[i]); if ( alt<0 || ref==alt ) continue; stats->subst[ref<<2|alt]++; int iaf = args->tmp_iaf[i]; stats->af_snps[iaf]++; if ( abs(ref-alt)==2 ) { if (i==1) { stats->ts_alt1++; #if QUAL_STATS dist_insert(stats->qual_ts,iqual); #endif do_user_stats(stats, reader, 1); } stats->af_ts[iaf]++; } else { if (i==1) { stats->tv_alt1++; #if QUAL_STATS dist_insert(stats->qual_tv,iqual); #endif do_user_stats(stats, reader, 0); } stats->af_tv[iaf]++; } } } // Returns the max non-ref AD value static inline int get_ad(bcf1_t *line, bcf_fmt_t *ad_fmt_ptr, int ismpl, int *ial) { int iv, ad = 0; *ial = 0; #define BRANCH_INT(type_t,missing,vector_end) { \ type_t *ptr = (type_t *) (ad_fmt_ptr->p + ad_fmt_ptr->size*ismpl); \ for (iv=1; ivn && ivn_allele; iv++) \ { \ if ( ptr[iv]==vector_end ) break; \ if ( ptr[iv]==missing ) continue; \ if ( ad < ptr[iv] ) { ad = ptr[iv]; *ial = iv; }\ } \ } switch (ad_fmt_ptr->type) { case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_missing, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break; default: fprintf(bcftools_stderr, "[E::%s] todo: %d\n", __func__, ad_fmt_ptr->type); bcftools_exit(1); break; } #undef BRANCH_INT return ad; } static inline int get_iad(bcf1_t *line, bcf_fmt_t *ad_fmt_ptr, int ismpl, int ial) { #define BRANCH_INT(type_t,missing,vector_end) { \ type_t *ptr = (type_t *) (ad_fmt_ptr->p + ad_fmt_ptr->size*ismpl); \ if ( ptr[ial]==vector_end ) return 0; \ if ( ptr[ial]==missing ) return 0; \ return ptr[ial]; \ } switch (ad_fmt_ptr->type) { case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_missing, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break; default: fprintf(bcftools_stderr, "[E::%s] todo: %d\n", __func__, ad_fmt_ptr->type); bcftools_exit(1); break; } #undef BRANCH_INT } static inline void update_dvaf(stats_t *stats, bcf1_t *line, int ial, float vaf) { int len = line->d.var[ial].n; if ( len < -stats->m_indel ) len = -stats->m_indel; else if ( len > stats->m_indel ) len = stats->m_indel; int bin = stats->m_indel + len; stats->nvaf[bin]++; stats->dvaf[bin] += vaf; } #define vaf2bin(vaf) ((int)nearbyintf((vaf)/0.05)) static inline void update_vaf(vaf_t *smpl_vaf, bcf1_t *line, int ial, float vaf) { if ( vaf>=0 && vaf<=1 ) { int idx = vaf2bin(vaf); if ( bcf_get_variant_type(line,ial)==VCF_SNP ) smpl_vaf->snv[idx]++; else smpl_vaf->indel[idx]++; } } static inline int calc_sample_depth(args_t *args, int ismpl, bcf_fmt_t *ad_fmt_ptr, bcf_fmt_t *dp_fmt_ptr) { if ( dp_fmt_ptr ) { #define BRANCH_INT(type_t,missing,vector_end) { \ type_t *ptr = (type_t *) (dp_fmt_ptr->p + dp_fmt_ptr->size*ismpl); \ if ( *ptr==missing || *ptr==vector_end ) return -1; \ return *ptr; \ } switch (dp_fmt_ptr->type) { case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_missing, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break; default: fprintf(bcftools_stderr, "[E::%s] todo: %d\n", __func__, dp_fmt_ptr->type); bcftools_exit(1); break; } #undef BRANCH_INT } if ( ad_fmt_ptr ) { int iv, dp = 0, has_value = 0; #define BRANCH_INT(type_t,missing,vector_end) { \ type_t *ptr = (type_t *) (ad_fmt_ptr->p + ad_fmt_ptr->size*ismpl); \ for (iv=0; ivn; iv++) \ { \ if ( ptr[iv]==vector_end ) break; \ if ( ptr[iv]==missing ) continue; \ has_value = 1; \ dp += ptr[iv]; \ } \ } switch (ad_fmt_ptr->type) { case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_missing, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break; default: fprintf(bcftools_stderr, "[E::%s] todo: %d\n", __func__, ad_fmt_ptr->type); bcftools_exit(1); break; } #undef BRANCH_INT if ( !has_value ) return -1; return dp; } return -1; } static inline void sample_gt_stats(args_t *args, stats_t *stats, bcf1_t *line, int ismpl, int gt, int ial, int jal) { if ( gt==GT_UNKN ) { stats->smpl_missing[ismpl]++; return; } int var_type = 0; if ( ial>0 ) var_type |= bcf_get_variant_type(line,ial); if ( jal>0 ) var_type |= bcf_get_variant_type(line,jal); if ( gt==GT_HAPL_R || gt==GT_HAPL_A ) { if ( var_type&VCF_INDEL && stats->smpl_frm_shifts ) { assert( ialn_allele ); stats->smpl_frm_shifts[ismpl*3 + args->tmp_frm[ial]]++; } if ( gt == GT_HAPL_R ) stats->smpl_hapRef[ismpl]++; if ( gt == GT_HAPL_A ) stats->smpl_hapAlt[ismpl]++; return; } if ( gt != GT_HOM_RR ) { args->n_nref++; args->i_nref = ismpl; } #if HWE_STATS switch (gt) { case GT_HOM_RR: args->nref_tot++; break; case GT_HET_RA: args->nhet_tot++; break; case GT_HET_AA: case GT_HOM_AA: args->nalt_tot++; break; } #endif if ( var_type&VCF_SNP || var_type==VCF_REF ) // count ALT=. as SNP { if ( gt == GT_HET_RA ) stats->smpl_hets[ismpl]++; else if ( gt == GT_HET_AA ) stats->smpl_hets[ismpl]++; else if ( gt == GT_HOM_RR ) stats->smpl_homRR[ismpl]++; else if ( gt == GT_HOM_AA ) stats->smpl_homAA[ismpl]++; if ( gt != GT_HOM_RR && line->d.var[ial].type&VCF_SNP ) // this is safe, bcf_get_variant_types has been already called { int ref = bcf_acgt2int(*line->d.allele[0]); int alt = bcf_acgt2int(*line->d.allele[ial]); if ( alt<0 ) return; if ( abs(ref-alt)==2 ) stats->smpl_ts[ismpl]++; else stats->smpl_tv[ismpl]++; } if ( gt != GT_HOM_RR && line->d.var[jal].type&VCF_SNP && ial!=jal ) { int ref = bcf_acgt2int(*line->d.allele[0]); int alt = bcf_acgt2int(*line->d.allele[jal]); if ( alt<0 ) return; if ( abs(ref-alt)==2 ) stats->smpl_ts[ismpl]++; else stats->smpl_tv[ismpl]++; } } if ( var_type&VCF_INDEL ) { if ( gt != GT_HOM_RR ) { stats->smpl_indels[ismpl]++; if ( gt==GT_HET_RA || gt==GT_HET_AA ) { int is_ins = 0, is_del = 0; if ( bcf_get_variant_type(line,ial)&VCF_INDEL ) { if ( line->d.var[ial].n < 0 ) is_del = 1; else is_ins = 1; } if ( bcf_get_variant_type(line,jal)&VCF_INDEL ) { if ( line->d.var[jal].n < 0 ) is_del = 1; else is_ins = 1; } // Note that alt-het genotypes with both ins and del allele are counted twice!! if ( is_del ) stats->smpl_del_hets[ismpl]++; if ( is_ins ) stats->smpl_ins_hets[ismpl]++; } else if ( gt==GT_HOM_AA ) { if ( line->d.var[ial].n < 0 ) stats->smpl_del_homs[ismpl]++; else stats->smpl_ins_homs[ismpl]++; } } if ( stats->smpl_frm_shifts ) { assert( ialn_allele && jaln_allele ); stats->smpl_frm_shifts[ismpl*3 + args->tmp_frm[ial]]++; stats->smpl_frm_shifts[ismpl*3 + args->tmp_frm[jal]]++; } } } static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int matched) { bcf_srs_t *files = args->files; bcf1_t *line = reader->buffer[0]; args->nref_tot = 0; args->nhet_tot = 0; args->nalt_tot = 0; args->n_nref = 0; args->i_nref = 0; bcf_fmt_t *gt_fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"GT"); bcf_fmt_t *ad_fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"AD"); bcf_fmt_t *dp_fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"DP"); int is; for (is=0; isfiles->n_smpl; is++) { // Determine depth int dp = calc_sample_depth(args,is,ad_fmt_ptr,dp_fmt_ptr); if ( dp>0 ) { (*idist(&stats->dp, dp))++; stats->smpl_ndp[is]++; stats->smpl_dp[is] += dp; } // Determine genotype int ial, jal, gt=GT_UNKN; if ( gt_fmt_ptr ) { gt = bcf_gt_type(gt_fmt_ptr, reader->samples[is], &ial, &jal); sample_gt_stats(args,stats,line,is,gt,ial,jal); } // Determine variant allele frequency if ( dp>0 && ad_fmt_ptr ) { float iad = 0, jad = 0; if ( gt==GT_UNKN ) // GT not available { iad = get_ad(line,ad_fmt_ptr,is,&ial); } else if ( gt!=GT_UNKN ) { iad = ial==0 ? 0 : get_iad(line,ad_fmt_ptr,is,ial); jad = jal==0 ? 0 : get_iad(line,ad_fmt_ptr,is,jal); } if ( iad ) { update_dvaf(stats,line,ial,(float)iad/dp); update_vaf(&stats->smpl_vaf[is],line,ial,(float)iad/dp); } if ( jad && iad!=jad ) { update_dvaf(stats,line,jal,(float)jad/dp); update_vaf(&stats->smpl_vaf[is],line,jal,(float)jad/dp); } } } if ( args->n_nref==1 ) stats->smpl_sngl[args->i_nref]++; #if HWE_STATS if ( gt_fmt_ptr && line->n_allele > 1 && (args->nref_tot || args->nhet_tot || args->nalt_tot) ) { // Number of heterozygous genotypes observed for any given allele frequency. This is used // by plot-vcfstats to show the observed vs expected number of hets. There the expected number // of hets is calculated from the probability P(het) = 2*AF*(1-AF). // The array af_hwe is organized as follows // m_af .. number of allele frequency bins // naf_hwe .. the number of het genotype frequency bins // iallele_freq*naf_hwe + ihet_freq // float het_frac = (float)args->nhet_tot / (args->nref_tot + args->nhet_tot + args->nalt_tot); int ihet_freq = het_frac * (args->naf_hwe - 1); int idx = ihet_freq + args->tmp_iaf[1] * args->naf_hwe; stats->af_hwe[idx]++; } #endif if ( matched==3 ) { int is; bcf_fmt_t *fmt0, *fmt1; fmt0 = bcf_get_fmt(files->readers[0].header,files->readers[0].buffer[0],"GT"); if ( !fmt0 ) return; fmt1 = bcf_get_fmt(files->readers[1].header,files->readers[1].buffer[0],"GT"); if ( !fmt1 ) return; // only the first ALT allele is considered if (args->ntmp_iaf <= 1) return; // Do not consider invariate sites int iaf = args->tmp_iaf[1]; int line_type = bcf_get_variant_types(files->readers[0].buffer[0]); gtcmp_t *af_stats = line_type&VCF_SNP ? args->af_gts_snps : args->af_gts_indels; gtcmp_t *smpl_stats = line_type&VCF_SNP ? args->smpl_gts_snps : args->smpl_gts_indels; for (is=0; isn_smpl; is++) { // Simplified comparison: only 0/0, 0/1, 1/1 is looked at as the identity of // actual alleles can be enforced by running without the -c option. int gt0 = bcf_gt_type(fmt0, files->readers[0].samples[is], NULL, NULL); int gt1 = bcf_gt_type(fmt1, files->readers[1].samples[is], NULL, NULL); int idx0 = type2stats[gt0]; int idx1 = type2stats[gt1]; af_stats[iaf].gt2gt[idx0][idx1]++; smpl_stats[is].gt2gt[idx0][idx1]++; if ( gt0 == GT_UNKN || gt1 == GT_UNKN ) continue; if ( type2ploidy[gt0]*type2ploidy[gt1] == -1 ) continue; // cannot compare diploid and haploid genotypes float y = type2dosage[gt0]; float x = type2dosage[gt1]; smpl_stats[is].yx += y*x; smpl_stats[is].x += x; smpl_stats[is].xx += x*x; smpl_stats[is].y += y; smpl_stats[is].yy += y*y; smpl_stats[is].n += 1; af_stats[iaf].yx += y*x; af_stats[iaf].x += x; af_stats[iaf].xx += x*x; af_stats[iaf].y += y; af_stats[iaf].yy += y*y; af_stats[iaf].n += 1; } if ( args->verbose_sites ) { int nm = 0, nmm = 0, nrefm = 0; for (is=0; isn_smpl; is++) { int gt = bcf_gt_type(fmt0, files->readers[0].samples[is], NULL, NULL); if ( gt == GT_UNKN ) continue; int gt2 = bcf_gt_type(fmt1, files->readers[1].samples[is], NULL, NULL); if ( gt2 == GT_UNKN ) continue; if ( gt != gt2 ) { nmm++; bcf_sr_t *reader = &files->readers[0]; fprintf(bcftools_stdout, "DBG\t%s\t%"PRId64"\t%s\t%d\t%d\n",reader->header->id[BCF_DT_CTG][reader->buffer[0]->rid].key,(int64_t) reader->buffer[0]->pos+1,files->samples[is],gt,gt2); } else { if ( gt!=GT_HOM_RR ) nrefm++; nm++; } } float nrd = nrefm+nmm ? 100.*nmm/(nrefm+nmm) : 0; fprintf(bcftools_stdout, "PSD\t%s\t%"PRId64"\t%d\t%d\t%f\n", reader->header->id[BCF_DT_CTG][reader->buffer[0]->rid].key,(int64_t) reader->buffer[0]->pos+1,nm,nmm,nrd); } } } static void do_vcf_stats(args_t *args) { bcf_srs_t *files = args->files; assert( sizeof(int)>files->nreaders ); while ( bcf_sr_next_line(files) ) { bcf_sr_t *reader = NULL; bcf1_t *line = NULL; int ret = 0, i, pass = 1; for (i=0; inreaders; i++) { if ( !bcf_sr_has_line(files,i) ) continue; if ( args->filter[i] ) { int is_ok = filter_test(args->filter[i], bcf_sr_get_line(files,i), NULL); if ( args->filter_logic & FLT_EXCLUDE ) is_ok = is_ok ? 0 : 1; if ( !is_ok ) { pass = 0; break; } } ret |= 1<readers[i]; line = bcf_sr_get_line(files,i); } } if ( !pass ) continue; int line_type = bcf_get_variant_types(line); init_iaf(args, reader); stats_t *stats = &args->stats[ret-1]; if ( args->split_by_id && line->d.id[0]=='.' && !line->d.id[1] ) stats = &args->stats[1]; stats->n_records++; if ( line_type==VCF_REF ) stats->n_noalts++; if ( line_type&VCF_SNP ) do_snp_stats(args, stats, reader); if ( line_type&VCF_INDEL ) do_indel_stats(args, stats, reader); if ( line_type&VCF_MNP ) do_mnp_stats(args, stats, reader); if ( line_type&VCF_OTHER ) do_other_stats(args, stats, reader); if ( line->n_allele>2 ) { stats->n_mals++; if ( line_type == VCF_SNP ) stats->n_snp_mals++; // note: this will be fooled by C>C,T } if ( files->n_smpl ) do_sample_stats(args, stats, reader, ret); if ( bcf_get_info_int32(reader->header,line,"DP",&args->iarr,&args->miarr)==1 ) (*idist(&stats->dp_sites, args->iarr[0]))++; } } static void print_header(args_t *args) { int i; fprintf(bcftools_stdout, "# This file was produced by bcftools stats (%s+htslib-%s) and can be plotted using plot-vcfstats.\n", bcftools_version(),hts_version()); fprintf(bcftools_stdout, "# The command line was:\tbcftools %s ", args->argv[0]); for (i=1; iargc; i++) fprintf(bcftools_stdout, " %s",args->argv[i]); fprintf(bcftools_stdout, "\n#\n"); fprintf(bcftools_stdout, "# Definition of sets:\n# ID\t[2]id\t[3]tab-separated file names\n"); if ( args->files->nreaders==1 ) { const char *fname = strcmp("-",args->files->readers[0].fname) ? args->files->readers[0].fname : ""; if ( args->split_by_id ) { fprintf(bcftools_stdout, "ID\t0\t%s:known (sites with ID different from \".\")\n", fname); fprintf(bcftools_stdout, "ID\t1\t%s:novel (sites where ID column is \".\")\n", fname); } else fprintf(bcftools_stdout, "ID\t0\t%s\n", fname); } else { const char *fname0 = strcmp("-",args->files->readers[0].fname) ? args->files->readers[0].fname : ""; const char *fname1 = strcmp("-",args->files->readers[1].fname) ? args->files->readers[1].fname : ""; fprintf(bcftools_stdout, "ID\t0\t%s\n", fname0); fprintf(bcftools_stdout, "ID\t1\t%s\n", fname1); fprintf(bcftools_stdout, "ID\t2\t%s\t%s\n", fname0,fname1); if ( args->verbose_sites ) { fprintf(bcftools_stdout, "# Verbose per-site discordance output.\n" "# PSD\t[2]CHROM\t[3]POS\t[4]Number of matches\t[5]Number of mismatches\t[6]NRD\n"); fprintf(bcftools_stdout, "# Verbose per-site and per-sample output. Genotype codes: %d:HomRefRef, %d:HomAltAlt, %d:HetAltRef, %d:HetAltAlt, %d:haploidRef, %d:haploidAlt\n" "# DBG\t[2]CHROM\t[3]POS\t[4]Sample\t[5]GT in %s\t[6]GT in %s\n", GT_HOM_RR, GT_HOM_AA, GT_HET_RA, GT_HET_AA, GT_HAPL_R, GT_HAPL_A, fname0,fname1); } } } #define T2S(x) type2stats[x] static void print_stats(args_t *args) { int i, j,k, id; fprintf(bcftools_stdout, "# SN, Summary numbers:\n"); fprintf(bcftools_stdout, "# number of records .. number of data rows in the VCF\n"); fprintf(bcftools_stdout, "# number of no-ALTs .. reference-only sites, ALT is either \".\" or identical to REF\n"); fprintf(bcftools_stdout, "# number of SNPs .. number of rows with a SNP\n"); fprintf(bcftools_stdout, "# number of MNPs .. number of rows with a MNP, such as CC>TT\n"); fprintf(bcftools_stdout, "# number of indels .. number of rows with an indel\n"); fprintf(bcftools_stdout, "# number of others .. number of rows with other type, for example a symbolic allele or\n"); fprintf(bcftools_stdout, "# a complex substitution, such as ACT>TCGA\n"); fprintf(bcftools_stdout, "# number of multiallelic sites .. number of rows with multiple alternate alleles\n"); fprintf(bcftools_stdout, "# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs\n"); fprintf(bcftools_stdout, "# \n"); fprintf(bcftools_stdout, "# Note that rows containing multiple types will be counted multiple times, in each\n"); fprintf(bcftools_stdout, "# counter. For example, a row with a SNP and an indel increments both the SNP and\n"); fprintf(bcftools_stdout, "# the indel counter.\n"); fprintf(bcftools_stdout, "# \n"); fprintf(bcftools_stdout, "# SN\t[2]id\t[3]key\t[4]value\n"); for (id=0; idfiles->nreaders; id++) fprintf(bcftools_stdout, "SN\t%d\tnumber of samples:\t%d\n", id, bcf_hdr_nsamples(args->files->readers[id].header)); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; fprintf(bcftools_stdout, "SN\t%d\tnumber of records:\t%"PRIu64"\n", id, stats->n_records); fprintf(bcftools_stdout, "SN\t%d\tnumber of no-ALTs:\t%"PRIu64"\n", id, stats->n_noalts); fprintf(bcftools_stdout, "SN\t%d\tnumber of SNPs:\t%"PRIu64"\n", id, stats->n_snps); fprintf(bcftools_stdout, "SN\t%d\tnumber of MNPs:\t%"PRIu64"\n", id, stats->n_mnps); fprintf(bcftools_stdout, "SN\t%d\tnumber of indels:\t%"PRIu64"\n", id, stats->n_indels); fprintf(bcftools_stdout, "SN\t%d\tnumber of others:\t%"PRIu64"\n", id, stats->n_others); fprintf(bcftools_stdout, "SN\t%d\tnumber of multiallelic sites:\t%"PRIu64"\n", id, stats->n_mals); fprintf(bcftools_stdout, "SN\t%d\tnumber of multiallelic SNP sites:\t%"PRIu64"\n", id, stats->n_snp_mals); } fprintf(bcftools_stdout, "# TSTV, transitions/transversions\n" "# - transitions, see https://en.wikipedia.org/wiki/Transition_(genetics)\n" "# - transversions, see https://en.wikipedia.org/wiki/Transversion\n"); fprintf(bcftools_stdout, "# TSTV\t[2]id\t[3]ts\t[4]tv\t[5]ts/tv\t[6]ts (1st ALT)\t[7]tv (1st ALT)\t[8]ts/tv (1st ALT)\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; int ts=0,tv=0; for (i=0; im_af; i++) { ts += stats->af_ts[i]; tv += stats->af_tv[i]; } fprintf(bcftools_stdout, "TSTV\t%d\t%d\t%d\t%.2f\t%d\t%d\t%.2f\n", id,ts,tv,tv?(float)ts/tv:0, stats->ts_alt1,stats->tv_alt1,stats->tv_alt1?(float)stats->ts_alt1/stats->tv_alt1:0); } if ( args->exons_fname ) { fprintf(bcftools_stdout, "# FS, Indel frameshifts:\n# FS\t[2]id\t[3]in-frame\t[4]out-frame\t[5]not applicable\t[6]out/(in+out) ratio\t[7]in-frame (1st ALT)\t[8]out-frame (1st ALT)\t[9]not applicable (1st ALT)\t[10]out/(in+out) ratio (1st ALT)\n"); for (id=0; idnstats; id++) { int in=args->stats[id].in_frame, out=args->stats[id].out_frame, na=args->stats[id].na_frame; int in1=args->stats[id].in_frame_alt1, out1=args->stats[id].out_frame_alt1, na1=args->stats[id].na_frame_alt1; fprintf(bcftools_stdout, "FS\t%d\t%d\t%d\t%d\t%.2f\t%d\t%d\t%d\t%.2f\n", id, in,out,na,out?(float)out/(in+out):0,in1,out1,na1,out1?(float)out1/(in1+out1):0); } } if ( args->indel_ctx ) { fprintf(bcftools_stdout, "# ICS, Indel context:\n" "# - repeat-consistent, inconsistent and n/a: experimental and useless stats [DEPRECATED]\n"); fprintf(bcftools_stdout, "# ICS\t[2]id\t[3]repeat-consistent\t[4]repeat-inconsistent\t[5]not applicable\t[6]c/(c+i) ratio\n"); for (id=0; idnstats; id++) { int nc = 0, ni = 0, na = args->stats[id].n_repeat_na; for (i=0; istats[id].n_repeat[i][0] + args->stats[id].n_repeat[i][2]; ni += args->stats[id].n_repeat[i][1] + args->stats[id].n_repeat[i][3]; } fprintf(bcftools_stdout, "ICS\t%d\t%d\t%d\t%d\t%.4f\n", id, nc,ni,na,nc+ni ? (float)nc/(nc+ni) : 0.0); } fprintf(bcftools_stdout, "# ICL, Indel context by length:\n" "# - repeat-consistent, inconsistent and n/a: experimental and useless stats [DEPRECATED]\n"); fprintf(bcftools_stdout, "# ICL\t[2]id\t[3]length of repeat element\t[4]repeat-consistent deletions)\t[5]repeat-inconsistent deletions\t[6]consistent insertions\t[7]inconsistent insertions\t[8]c/(c+i) ratio\n"); for (id=0; idnstats; id++) { for (i=1; istats[id].n_repeat[i][0]+args->stats[id].n_repeat[i][2], ni = args->stats[id].n_repeat[i][1]+args->stats[id].n_repeat[i][3]; fprintf(bcftools_stdout, "ICL\t%d\t%d\t%d\t%d\t%d\t%d\t%.4f\n", id, i+1, args->stats[id].n_repeat[i][0],args->stats[id].n_repeat[i][1],args->stats[id].n_repeat[i][2],args->stats[id].n_repeat[i][3], nc+ni ? (float)nc/(nc+ni) : 0.0); } } } fprintf(bcftools_stdout, "# SiS, Singleton stats:\n" "# - allele count, i.e. the number of singleton genotypes (AC=1)\n" "# - number of transitions, see above\n" "# - number of transversions, see above\n" "# - repeat-consistent, inconsistent and n/a: experimental and useless stats [DEPRECATED]\n"); fprintf(bcftools_stdout, "# SiS\t[2]id\t[3]allele count\t[4]number of SNPs\t[5]number of transitions\t[6]number of transversions\t[7]number of indels\t[8]repeat-consistent\t[9]repeat-inconsistent\t[10]not applicable\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; fprintf(bcftools_stdout, "SiS\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", id,1,stats->af_snps[0],stats->af_ts[0],stats->af_tv[0], stats->af_repeats[0][0]+stats->af_repeats[1][0]+stats->af_repeats[2][0],stats->af_repeats[0][0],stats->af_repeats[1][0],stats->af_repeats[2][0]); // put the singletons stats into the first AF bin, note that not all of the stats is transferred (i.e. nrd mismatches) stats->af_snps[1] += stats->af_snps[0]; stats->af_ts[1] += stats->af_ts[0]; stats->af_tv[1] += stats->af_tv[0]; stats->af_repeats[0][1] += stats->af_repeats[0][0]; stats->af_repeats[1][1] += stats->af_repeats[1][0]; stats->af_repeats[2][1] += stats->af_repeats[2][0]; } // move the singletons stats into the first AF bin, singleton stats was collected separately because of init_iaf if ( args->af_gts_snps ) { args->af_gts_snps[1].y += args->af_gts_snps[0].y; args->af_gts_snps[1].yy += args->af_gts_snps[0].yy; args->af_gts_snps[1].xx += args->af_gts_snps[0].xx; args->af_gts_snps[1].yx += args->af_gts_snps[0].yx; args->af_gts_snps[1].n += args->af_gts_snps[0].n; } if ( args->af_gts_indels ) { args->af_gts_indels[1].y += args->af_gts_indels[0].y; args->af_gts_indels[1].yy += args->af_gts_indels[0].yy; args->af_gts_indels[1].xx += args->af_gts_indels[0].xx; args->af_gts_indels[1].yx += args->af_gts_indels[0].yx; args->af_gts_indels[1].n += args->af_gts_indels[0].n; } fprintf(bcftools_stdout, "# AF, Stats by non-reference allele frequency:\n# AF\t[2]id\t[3]allele frequency\t[4]number of SNPs\t[5]number of transitions\t[6]number of transversions\t[7]number of indels\t[8]repeat-consistent\t[9]repeat-inconsistent\t[10]not applicable\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; for (i=1; im_af; i++) // note that af[1] now contains also af[0], see SiS stats output above { if ( stats->af_snps[i]+stats->af_ts[i]+stats->af_tv[i]+stats->af_repeats[0][i]+stats->af_repeats[1][i]+stats->af_repeats[2][i] == 0 ) continue; double af = args->af_bins ? (bin_get_value(args->af_bins,i)+bin_get_value(args->af_bins,i-1))*0.5 : (double)(i-1)/(args->m_af-1); fprintf(bcftools_stdout, "AF\t%d\t%f\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", id,af,stats->af_snps[i],stats->af_ts[i],stats->af_tv[i], stats->af_repeats[0][i]+stats->af_repeats[1][i]+stats->af_repeats[2][i],stats->af_repeats[0][i],stats->af_repeats[1][i],stats->af_repeats[2][i]); } } #if QUAL_STATS fprintf(bcftools_stdout, "# QUAL, Stats by quality\n# QUAL\t[2]id\t[3]Quality\t[4]number of SNPs\t[5]number of transitions (1st ALT)\t[6]number of transversions (1st ALT)\t[7]number of indels\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; int ndist_ts = dist_nbins(stats->qual_ts); int ndist_tv = dist_nbins(stats->qual_tv); int ndist_in = dist_nbins(stats->qual_indels); int ndist_max = ndist_ts; if ( ndist_max < ndist_tv ) ndist_max = ndist_tv; if ( ndist_max < ndist_in ) ndist_max = ndist_in; uint32_t beg, end; uint32_t nts, ntv, nin; for (i=0; iqual_ts, i, &beg, &end); qval = beg>0 ? 0.1*(beg - 1) : -1; } if ( i < ndist_tv ) { ntv = dist_get(stats->qual_tv, i, &beg, &end); if ( qval==-1 ) qval = beg > 0 ? 0.1*(beg - 1) : -1; } if ( i < ndist_in ) { nin = dist_get(stats->qual_indels, i, &beg, &end); if ( qval==-1 ) qval = beg > 0 ? 0.1*(beg - 1) : -1; } if ( nts+ntv+nin==0 ) continue; fprintf(bcftools_stdout, "QUAL\t%d\t",id); if ( qval==-1 ) fprintf(bcftools_stdout, "."); else fprintf(bcftools_stdout, "%.1f",qval); fprintf(bcftools_stdout, "\t%d\t%d\t%d\t%d\n",nts+ntv,nts,ntv,nin); } } #endif for (i=0; inusr; i++) { fprintf(bcftools_stdout, "# USR:%s/%d\t[2]id\t[3]%s/%d\t[4]number of SNPs\t[5]number of transitions (1st ALT)\t[6]number of transversions (1st ALT)\n", args->usr[i].tag,args->usr[i].idx,args->usr[i].tag,args->usr[i].idx); for (id=0; idnstats; id++) { user_stats_t *usr = &args->stats[id].usr[i]; int j; for (j=0; jnbins; j++) { if ( usr->vals_ts[j]+usr->vals_tv[j] == 0 ) continue; // skip empty bins float val = usr->min + (usr->max - usr->min)*j/(usr->nbins-1); const char * const fmt = usr->type==BCF_HT_REAL ? "USR:%s/%d\t%d\t%e\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"\n" : "USR:%s/%d\t%d\t%.0f\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"\n"; fprintf(bcftools_stdout, fmt,usr->tag,usr->idx,id,val,usr->vals_ts[j]+usr->vals_tv[j],usr->vals_ts[j],usr->vals_tv[j]); } } } fprintf(bcftools_stdout, "# IDD, InDel distribution:\n# IDD\t[2]id\t[3]length (deletions negative)\t[4]number of sites\t[5]number of genotypes\t[6]mean VAF\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; for (i=stats->m_indel-1; i>=0; i--) { if ( !stats->deletions[i] ) continue; // whops, differently organized arrow, dels are together with ins int bin = stats->m_indel - i - 1; fprintf(bcftools_stdout, "IDD\t%d\t%d\t%d\t", id,-i-1,stats->deletions[i]); if ( stats->nvaf && stats->nvaf[bin] ) fprintf(bcftools_stdout, "%u\t%.2f",stats->nvaf[bin],stats->dvaf[bin]/stats->nvaf[bin]); else fprintf(bcftools_stdout, "0\t."); fprintf(bcftools_stdout, "\n"); } for (i=0; im_indel; i++) { if ( !stats->insertions[i] ) continue; int bin = stats->m_indel + i + 1; fprintf(bcftools_stdout, "IDD\t%d\t%d\t%d\t", id,i+1,stats->insertions[i]); if ( stats->nvaf && stats->nvaf[bin] ) fprintf(bcftools_stdout, "%u\t%.2f",stats->nvaf[bin],stats->dvaf[bin]/stats->nvaf[bin]); else fprintf(bcftools_stdout, "0\t."); fprintf(bcftools_stdout, "\n"); } } fprintf(bcftools_stdout, "# ST, Substitution types:\n# ST\t[2]id\t[3]type\t[4]count\n"); for (id=0; idnstats; id++) { int t; for (t=0; t<15; t++) { if ( t>>2 == (t&3) ) continue; fprintf(bcftools_stdout, "ST\t%d\t%c>%c\t%d\n", id, bcf_int2acgt(t>>2),bcf_int2acgt(t&3),args->stats[id].subst[t]); } } if ( args->files->nreaders>1 && args->files->n_smpl ) { fprintf(bcftools_stdout, "SN\t%d\tnumber of samples:\t%d\n", 2, args->files->n_smpl); int x; for (x=0; x<2; x++) // x=0: snps, x=1: indels { gtcmp_t *stats; if ( x==0 ) { fprintf(bcftools_stdout, "# GCsAF, Genotype concordance by non-reference allele frequency (SNPs)\n# GCsAF\t[2]id\t[3]allele frequency\t[4]RR Hom matches\t[5]RA Het matches\t[6]AA Hom matches\t[7]RR Hom mismatches\t[8]RA Het mismatches\t[9]AA Hom mismatches\t[10]dosage r-squared\t[11]number of genotypes\n"); stats = args->af_gts_snps; } else { fprintf(bcftools_stdout, "# GCiAF, Genotype concordance by non-reference allele frequency (indels)\n# GCiAF\t[2]id\t[3]allele frequency\t[4]RR Hom matches\t[5]RA Het matches\t[6]AA Hom matches\t[7]RR Hom mismatches\t[8]RA Het mismatches\t[9]AA Hom mismatches\t[10]dosage r-squared\t[11]number of genotypes\n"); stats = args->af_gts_indels; } uint64_t nrd_m[4] = {0,0,0,0}, nrd_mm[4] = {0,0,0,0}; // across all bins for (i=0; im_af; i++) { int n = 0; uint64_t m[4] = {0,0,0,0}, mm[4] = {0,0,0,0}; // in i-th AF bin for (j=0; j<4; j++) // rr, ra, aa hom, aa het, ./. for (k=0; k<4; k++) { n += stats[i].gt2gt[j][k]; if ( j==k ) { nrd_m[j] += stats[i].gt2gt[j][k]; m[j] += stats[i].gt2gt[j][k]; } else { nrd_mm[j] += stats[i].gt2gt[j][k]; mm[j] += stats[i].gt2gt[j][k]; } } if ( !i || !n ) continue; // skip singleton stats and empty bins // Pearson's r2 double r2 = 0; if ( stats[i].n ) { r2 = (stats[i].yx - stats[i].x*stats[i].y/stats[i].n); r2 /= sqrt((stats[i].xx - stats[i].x*stats[i].x/stats[i].n) * (stats[i].yy - stats[i].y*stats[i].y/stats[i].n)); r2 *= r2; } double af = args->af_bins ? (bin_get_value(args->af_bins,i)+bin_get_value(args->af_bins,i-1))*0.5 : (double)(i-1)/(args->m_af-1); fprintf(bcftools_stdout, "GC%cAF\t2\t%f", x==0 ? 's' : 'i', af); fprintf(bcftools_stdout, "\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"", m[T2S(GT_HOM_RR)],m[T2S(GT_HET_RA)],m[T2S(GT_HOM_AA)]); fprintf(bcftools_stdout, "\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"", mm[T2S(GT_HOM_RR)],mm[T2S(GT_HET_RA)],mm[T2S(GT_HOM_AA)]); if ( stats[i].n && !isnan(r2) ) fprintf(bcftools_stdout, "\t%f", r2); else fprintf(bcftools_stdout, "\t"NA_STRING); fprintf(bcftools_stdout, "\t%.0f\n", stats[i].n); } if ( x==0 ) { fprintf(bcftools_stdout, "# NRD and discordance is calculated as follows:\n"); fprintf(bcftools_stdout, "# m .. number of matches\n"); fprintf(bcftools_stdout, "# x .. number of mismatches\n"); fprintf(bcftools_stdout, "# NRD = 100 * (xRR + xRA + xAA) / (xRR + xRA + xAA + mRA + mAA)\n"); fprintf(bcftools_stdout, "# RR discordance = 100 * xRR / (xRR + mRR)\n"); fprintf(bcftools_stdout, "# RA discordance = 100 * xRA / (xRA + mRA)\n"); fprintf(bcftools_stdout, "# AA discordance = 100 * xAA / (xAA + mAA)\n"); fprintf(bcftools_stdout, "# Non-Reference Discordance (NRD), SNPs\n# NRDs\t[2]id\t[3]NRD\t[4]Ref/Ref discordance\t[5]Ref/Alt discordance\t[6]Alt/Alt discordance\n"); } else fprintf(bcftools_stdout, "# Non-Reference Discordance (NRD), indels\n# NRDi\t[2]id\t[3]NRD\t[4]Ref/Ref discordance\t[5]Ref/Alt discordance\t[6]Alt/Alt discordance\n"); uint64_t m = nrd_m[T2S(GT_HET_RA)] + nrd_m[T2S(GT_HOM_AA)] + nrd_m[T2S(GT_HET_AA)]; uint64_t mm = nrd_mm[T2S(GT_HOM_RR)] + nrd_mm[T2S(GT_HET_RA)] + nrd_mm[T2S(GT_HOM_AA)] + nrd_mm[T2S(GT_HET_AA)]; fprintf(bcftools_stdout, "NRD%c\t2\t%f\t%f\t%f\t%f\n", x==0 ? 's' : 'i', m+mm ? mm*100.0/(m+mm) : 0, nrd_m[T2S(GT_HOM_RR)]+nrd_mm[T2S(GT_HOM_RR)] ? nrd_mm[T2S(GT_HOM_RR)]*100.0/(nrd_m[T2S(GT_HOM_RR)]+nrd_mm[T2S(GT_HOM_RR)]) : 0, nrd_m[T2S(GT_HET_RA)]+nrd_mm[T2S(GT_HET_RA)] ? nrd_mm[T2S(GT_HET_RA)]*100.0/(nrd_m[T2S(GT_HET_RA)]+nrd_mm[T2S(GT_HET_RA)]) : 0, nrd_m[T2S(GT_HOM_AA)]+nrd_mm[T2S(GT_HOM_AA)] ? nrd_mm[T2S(GT_HOM_AA)]*100.0/(nrd_m[T2S(GT_HOM_AA)]+nrd_mm[T2S(GT_HOM_AA)]) : 0 ); } for (x=0; x<2; x++) // x=0: snps, x=1: indels { gtcmp_t *stats; if ( x==0 ) { fprintf(bcftools_stdout, "# GCsS, Genotype concordance by sample (SNPs)\n# GCsS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\t[11]dosage r-squared\n"); stats = args->smpl_gts_snps; } else { fprintf(bcftools_stdout, "# GCiS, Genotype concordance by sample (indels)\n# GCiS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\t[11]dosage r-squared\n"); stats = args->smpl_gts_indels; } for (i=0; ifiles->n_smpl; i++) { uint64_t mm = 0, m = stats[i].gt2gt[T2S(GT_HET_RA)][T2S(GT_HET_RA)] + stats[i].gt2gt[T2S(GT_HOM_AA)][T2S(GT_HOM_AA)]; for (j=0; j<3; j++) for (k=0; k<3; k++) if ( j!=k ) mm += stats[i].gt2gt[j][k]; // Pearson's r2 double r2 = 0; if ( stats[i].n ) { r2 = (stats[i].yx - stats[i].x*stats[i].y/stats[i].n); r2 /= sqrt((stats[i].xx - stats[i].x*stats[i].x/stats[i].n) * (stats[i].yy - stats[i].y*stats[i].y/stats[i].n)); r2 *= r2; } fprintf(bcftools_stdout, "GC%cS\t2\t%s\t%.3f", x==0 ? 's' : 'i', args->files->samples[i], m+mm ? mm*100.0/(m+mm) : 0); fprintf(bcftools_stdout, "\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"", stats[i].gt2gt[T2S(GT_HOM_RR)][T2S(GT_HOM_RR)], stats[i].gt2gt[T2S(GT_HET_RA)][T2S(GT_HET_RA)], stats[i].gt2gt[T2S(GT_HOM_AA)][T2S(GT_HOM_AA)]); fprintf(bcftools_stdout, "\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"", stats[i].gt2gt[T2S(GT_HOM_RR)][T2S(GT_HET_RA)] + stats[i].gt2gt[T2S(GT_HOM_RR)][T2S(GT_HOM_AA)], stats[i].gt2gt[T2S(GT_HET_RA)][T2S(GT_HOM_RR)] + stats[i].gt2gt[T2S(GT_HET_RA)][T2S(GT_HOM_AA)], stats[i].gt2gt[T2S(GT_HOM_AA)][T2S(GT_HOM_RR)] + stats[i].gt2gt[T2S(GT_HOM_AA)][T2S(GT_HET_RA)]); if ( stats[i].n && !isnan(r2) ) fprintf(bcftools_stdout, "\t%f\n", r2); else fprintf(bcftools_stdout, "\t"NA_STRING"\n"); } } for (x=0; x<2; x++) // x=0: snps, x=1: indels { //printf("# GCiS, Genotype concordance by sample (indels)\n# GCiS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\t[11]dosage r-squared\n"); gtcmp_t *stats; if ( x==0 ) { fprintf(bcftools_stdout, "# GCTs, Genotype concordance table (SNPs)\n# GCTs"); stats = args->smpl_gts_snps; } else { fprintf(bcftools_stdout, "# GCTi, Genotype concordance table (indels)\n# GCTi"); stats = args->smpl_gts_indels; } i = 1; fprintf(bcftools_stdout, "\t[%d]sample", ++i); fprintf(bcftools_stdout, "\t[%d]RR Hom -> RR Hom", ++i); fprintf(bcftools_stdout, "\t[%d]RR Hom -> RA Het", ++i); fprintf(bcftools_stdout, "\t[%d]RR Hom -> AA Hom", ++i); fprintf(bcftools_stdout, "\t[%d]RR Hom -> AA Het", ++i); fprintf(bcftools_stdout, "\t[%d]RR Hom -> missing", ++i); fprintf(bcftools_stdout, "\t[%d]RA Het -> RR Hom", ++i); fprintf(bcftools_stdout, "\t[%d]RA Het -> RA Het", ++i); fprintf(bcftools_stdout, "\t[%d]RA Het -> AA Hom", ++i); fprintf(bcftools_stdout, "\t[%d]RA Het -> AA Het", ++i); fprintf(bcftools_stdout, "\t[%d]RA Het -> missing", ++i); fprintf(bcftools_stdout, "\t[%d]AA Hom -> RR Hom", ++i); fprintf(bcftools_stdout, "\t[%d]AA Hom -> RA Het", ++i); fprintf(bcftools_stdout, "\t[%d]AA Hom -> AA Hom", ++i); fprintf(bcftools_stdout, "\t[%d]AA Hom -> AA Het", ++i); fprintf(bcftools_stdout, "\t[%d]AA Hom -> missing", ++i); fprintf(bcftools_stdout, "\t[%d]AA Het -> RR Hom", ++i); fprintf(bcftools_stdout, "\t[%d]AA Het -> RA Het", ++i); fprintf(bcftools_stdout, "\t[%d]AA Het -> AA Hom", ++i); fprintf(bcftools_stdout, "\t[%d]AA Het -> AA Het", ++i); fprintf(bcftools_stdout, "\t[%d]AA Het -> missing", ++i); fprintf(bcftools_stdout, "\t[%d]missing -> RR Hom", ++i); fprintf(bcftools_stdout, "\t[%d]missing -> RA Het", ++i); fprintf(bcftools_stdout, "\t[%d]missing -> AA Hom", ++i); fprintf(bcftools_stdout, "\t[%d]missing -> AA Het", ++i); fprintf(bcftools_stdout, "\t[%d]missing -> missing\n", ++i); for (i=0; ifiles->n_smpl; i++) { fprintf(bcftools_stdout, "GCT%c\t%s", x==0 ? 's' : 'i', args->files->samples[i]); for (j=0; j<5; j++) for (k=0; k<5; k++) fprintf(bcftools_stdout, "\t%"PRIu64, stats[i].gt2gt[j][k]); fprintf(bcftools_stdout, "\n"); } } } fprintf(bcftools_stdout, "# DP, depth:\n" "# - set id, see above\n" "# - the depth bin, corresponds to the depth (unless --depth was given)\n" "# - number of genotypes with this depth (zero unless -s/-S was given)\n" "# - fraction of genotypes with this depth (zero unless -s/-S was given)\n" "# - number of sites with this depth\n" "# - fraction of sites with this depth\n"); fprintf(bcftools_stdout, "# DP, Depth distribution\n# DP\t[2]id\t[3]bin\t[4]number of genotypes\t[5]fraction of genotypes (%%)\t[6]number of sites\t[7]fraction of sites (%%)\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; long unsigned int sum = 0, sum_sites = 0; for (i=0; idp.m_vals; i++) { sum += stats->dp.vals[i]; sum_sites += stats->dp_sites.vals[i]; } for (i=0; idp.m_vals; i++) { if ( stats->dp.vals[i]==0 && stats->dp_sites.vals[i]==0 ) continue; fprintf(bcftools_stdout, "DP\t%d\t", id); if ( i==0 ) fprintf(bcftools_stdout, "<%d", stats->dp.min); else if ( i+1==stats->dp.m_vals ) fprintf(bcftools_stdout, ">%d", stats->dp.max); else fprintf(bcftools_stdout, "%d", idist_i2bin(&stats->dp,i)); fprintf(bcftools_stdout, "\t%"PRIu64"\t%f", stats->dp.vals[i], sum ? stats->dp.vals[i]*100./sum : 0); fprintf(bcftools_stdout, "\t%"PRIu64"\t%f\n", stats->dp_sites.vals[i], sum_sites ? stats->dp_sites.vals[i]*100./sum_sites : 0); } } if ( args->files->n_smpl ) { fprintf(bcftools_stdout, "# PSC, Per-sample counts. Note that the ref/het/hom counts include only SNPs, for indels see PSI. The rest include both SNPs and indels.\n"); fprintf(bcftools_stdout, "# PSC\t[2]id\t[3]sample\t[4]nRefHom\t[5]nNonRefHom\t[6]nHets\t[7]nTransitions\t[8]nTransversions\t[9]nIndels\t[10]average depth\t[11]nSingletons" "\t[12]nHapRef\t[13]nHapAlt\t[14]nMissing\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; for (i=0; ifiles->n_smpl; i++) { float dp = stats->smpl_ndp[i] ? stats->smpl_dp[i]/(float)stats->smpl_ndp[i] : 0; fprintf(bcftools_stdout, "PSC\t%d\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%.1f\t%d\t%d\t%d\t%d\n", id,args->files->samples[i], stats->smpl_homRR[i], stats->smpl_homAA[i], stats->smpl_hets[i], stats->smpl_ts[i], stats->smpl_tv[i], stats->smpl_indels[i],dp, stats->smpl_sngl[i], stats->smpl_hapRef[i], stats->smpl_hapAlt[i], stats->smpl_missing[i]); } } fprintf(bcftools_stdout, "# PSI, Per-Sample Indels. Note that alt-het genotypes with both ins and del allele are counted twice, in both nInsHets and nDelHets.\n"); fprintf(bcftools_stdout, "# PSI\t[2]id\t[3]sample\t[4]in-frame\t[5]out-frame\t[6]not applicable\t[7]out/(in+out) ratio\t[8]nInsHets\t[9]nDelHets\t[10]nInsAltHoms\t[11]nDelAltHoms\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; for (i=0; ifiles->n_smpl; i++) { int na = 0, in = 0, out = 0; if ( args->exons ) { na = stats->smpl_frm_shifts[i*3 + 0]; in = stats->smpl_frm_shifts[i*3 + 1]; out = stats->smpl_frm_shifts[i*3 + 2]; } fprintf(bcftools_stdout, "PSI\t%d\t%s\t%d\t%d\t%d\t%.2f\t%d\t%d\t%d\t%d\n", id,args->files->samples[i], in,out,na,in+out?1.0*out/(in+out):0, stats->smpl_ins_hets[i],stats->smpl_del_hets[i],stats->smpl_ins_homs[i],stats->smpl_del_homs[i]); } } #ifdef HWE_STATS fprintf(bcftools_stdout, "# HWE\n# HWE\t[2]id\t[3]1st ALT allele frequency\t[4]Number of observations\t[5]25th percentile\t[6]median\t[7]75th percentile\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; for (i=0; inaf_hwe; i++) stats->af_hwe[i+args->naf_hwe] += stats->af_hwe[i]; // singletons for (i=1; im_af; i++) { unsigned int sum_tot = 0, sum_tmp = 0; int j, *ptr = &stats->af_hwe[i*args->naf_hwe]; for (j=0; jnaf_hwe; j++) sum_tot += ptr[j]; if ( !sum_tot ) continue; double af = args->af_bins ? (bin_get_value(args->af_bins,i)+bin_get_value(args->af_bins,i-1))*0.5 : (double)(i-1)/(args->m_af-1); int nprn = 3; fprintf(bcftools_stdout, "HWE\t%d\t%f\t%d",id,af,sum_tot); for (j=0; jnaf_hwe; j++) { sum_tmp += ptr[j]; float frac = (float)sum_tmp/sum_tot; if ( frac >= 0.75 ) { while (nprn>0) { fprintf(bcftools_stdout, "\t%f", (float)j/args->naf_hwe); nprn--; } break; } if ( frac >= 0.5 ) { while (nprn>1) { fprintf(bcftools_stdout, "\t%f", (float)j/args->naf_hwe); nprn--; } continue; } if ( frac >= 0.25 ) { while (nprn>2) { fprintf(bcftools_stdout, "\t%f", (float)j/args->naf_hwe); nprn--; } } } assert(nprn==0); fprintf(bcftools_stdout, "\n"); } } #endif } if ( args->stats[0].smpl_vaf ) { fprintf(bcftools_stdout, "# VAF, Variant Allele Frequency determined as fraction of alternate reads in FORMAT/AD\n"); fprintf(bcftools_stdout, "# VAF\t[2]id\t[3]sample\t[4]SNV VAF distribution\t[5]indel VAF distribution\n"); for (id=0; idnstats; id++) { stats_t *stats = &args->stats[id]; for (i=0; ifiles->n_smpl; i++) { fprintf(bcftools_stdout, "VAF\t%d\t%s\t", id,args->files->samples[i]); for (j=0; j<21; j++) fprintf(bcftools_stdout, "%s%d",j?",":"",stats->smpl_vaf[i].snv[j]); fprintf(bcftools_stdout, "\t"); for (j=0; j<21; j++) fprintf(bcftools_stdout, "%s%d",j?",":"",stats->smpl_vaf[i].indel[j]); fprintf(bcftools_stdout, "\n"); } } } } static void usage(void) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats.\n"); fprintf(bcftools_stderr, " When two files are given, the program generates separate stats for intersection\n"); fprintf(bcftools_stderr, " and the complements. By default only sites are compared, -s/-S must given to include\n"); fprintf(bcftools_stderr, " also sample columns.\n"); fprintf(bcftools_stderr, "Usage: bcftools stats [options] []\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Options:\n"); fprintf(bcftools_stderr, " --af-bins LIST Allele frequency bins, a list (0.1,0.5,1) or a file (0.1\\n0.5\\n1)\n"); fprintf(bcftools_stderr, " --af-tag STRING Allele frequency tag to use, by default estimated from AN,AC or GT\n"); fprintf(bcftools_stderr, " -1, --1st-allele-only Include only 1st allele at multiallelic sites\n"); fprintf(bcftools_stderr, " -c, --collapse STRING Treat as identical records with , see man page for details [none]\n"); fprintf(bcftools_stderr, " -d, --depth INT,INT,INT Depth distribution: min,max,bin size [0,500,1]\n"); fprintf(bcftools_stderr, " -e, --exclude EXPR Exclude sites for which the expression is true (see man page for details)\n"); fprintf(bcftools_stderr, " -E, --exons FILE.gz Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, bgzip compressed)\n"); fprintf(bcftools_stderr, " -f, --apply-filters LIST Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n"); fprintf(bcftools_stderr, " -F, --fasta-ref FILE Faidx indexed reference sequence file to determine INDEL context\n"); fprintf(bcftools_stderr, " -i, --include EXPR Select sites for which the expression is true (see man page for details)\n"); fprintf(bcftools_stderr, " -I, --split-by-ID Collect stats for sites with ID separately (known vs novel)\n"); fprintf(bcftools_stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(bcftools_stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n"); fprintf(bcftools_stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " -s, --samples LIST List of samples for sample stats, \"-\" to include all samples\n"); fprintf(bcftools_stderr, " -S, --samples-file FILE File of samples to include\n"); fprintf(bcftools_stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"); fprintf(bcftools_stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(bcftools_stderr, " -u, --user-tstv TAG[:min:max:n] Collect Ts/Tv stats for any tag using the given binning [0:1:100]\n"); fprintf(bcftools_stderr, " A subfield can be selected as e.g. 'PV4[0]', here the first value of the PV4 tag\n"); fprintf(bcftools_stderr, " --threads INT Use multithreading with worker threads [0]\n"); fprintf(bcftools_stderr, " -v, --verbose Produce verbose per-site and per-sample output\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int main_vcfstats(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->files = bcf_sr_init(); args->argc = argc; args->argv = argv; args->dp_min = 0; args->dp_max = 500; args->dp_step = 1; int regions_is_file = 0, targets_is_file = 0; int regions_overlap = 1; int targets_overlap = 0; static struct option loptions[] = { {"af-bins",1,0,1}, {"af-tag",1,0,2}, {"1st-allele-only",0,0,'1'}, {"include",1,0,'i'}, {"exclude",1,0,'e'}, {"help",0,0,'h'}, {"collapse",1,0,'c'}, {"regions",1,0,'r'}, {"regions-file",1,0,'R'}, {"regions-overlap",required_argument,NULL,3}, {"verbose",0,0,'v'}, {"depth",1,0,'d'}, {"apply-filters",1,0,'f'}, {"exons",1,0,'E'}, {"samples",1,0,'s'}, {"samples-file",1,0,'S'}, {"split-by-ID",0,0,'I'}, {"targets",1,0,'t'}, {"targets-file",1,0,'T'}, {"targets-overlap",required_argument,NULL,4}, {"fasta-ref",1,0,'F'}, {"user-tstv",1,0,'u'}, {"threads",1,0,9}, {0,0,0,0} }; while ((c = getopt_long(argc, argv, "hc:r:R:e:s:S:d:i:t:T:F:f:1u:vIE:",loptions,NULL)) >= 0) { switch (c) { case 1 : args->af_bins_list = optarg; break; case 2 : args->af_tag = optarg; break; case 'u': add_user_stats(args,optarg); break; case '1': args->first_allele_only = 1; break; case 'F': args->ref_fname = optarg; break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; targets_is_file = 1; break; case 'c': if ( !strcmp(optarg,"snps") ) args->files->collapse |= COLLAPSE_SNPS; else if ( !strcmp(optarg,"indels") ) args->files->collapse |= COLLAPSE_INDELS; else if ( !strcmp(optarg,"both") ) args->files->collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS; else if ( !strcmp(optarg,"any") ) args->files->collapse |= COLLAPSE_ANY; else if ( !strcmp(optarg,"all") ) args->files->collapse |= COLLAPSE_ANY; else if ( !strcmp(optarg,"some") ) args->files->collapse |= COLLAPSE_SOME; else if ( !strcmp(optarg,"none") ) args->files->collapse = COLLAPSE_NONE; else error("The --collapse string \"%s\" not recognised.\n", optarg); break; case 'v': args->verbose_sites = 1; break; case 'd': if ( sscanf(optarg,"%d,%d,%d",&args->dp_min,&args->dp_max,&args->dp_step)!=3 ) error("Could not parse --depth %s\n", optarg); if ( args->dp_min<0 || args->dp_min >= args->dp_max || args->dp_step > args->dp_max - args->dp_min + 1 ) error("Is this a typo? --depth %s\n", optarg); break; case 'f': args->files->apply_filters = optarg; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 'E': args->exons_fname = optarg; break; case 's': args->samples_list = optarg; break; case 'S': args->samples_list = optarg; args->samples_is_file = 1; break; case 'I': args->split_by_id = 1; break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 3 : regions_overlap = parse_overlap_option(optarg); if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 4 : targets_overlap = parse_overlap_option(optarg); if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 'h': case '?': usage(); break; default: error("Unknown argument: %s\n", optarg); } } char *fname = NULL; if ( optind==argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else usage(); } else fname = argv[optind]; if ( argc-optind>2 ) usage(); if ( argc-optind>1 ) { args->files->require_index = 1; if ( args->split_by_id ) error("Only one file can be given with -i.\n"); } if ( !args->samples_list ) args->files->max_unpack = BCF_UN_INFO; else args->files->max_unpack = BCF_UN_FMT; if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } if ( args->regions_list) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } if ( args->n_threads && bcf_sr_set_threads(args->files, args->n_threads)<0) error("Failed to create threads\n"); while (fname) { if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); fname = ++optind < argc ? argv[optind] : NULL; } init_stats(args); print_header(args); do_vcf_stats(args); print_stats(args); destroy_stats(args); bcf_sr_destroy(args->files); free(args); return 0; } pysam-0.23.0/bcftools/vcfview.c000066400000000000000000001167221475062545500164030ustar00rootroot00000000000000/* vcfview.c -- VCF/BCF conversion, view, subset and filter VCF/BCF files. Copyright (C) 2013-2023 Genome Research Ltd. Author: Shane McCarthy Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "filter.h" #include "htslib/khash_str2int.h" #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 #define ALLELE_NONREF 1 #define ALLELE_MINOR 2 #define ALLELE_ALT1 3 #define ALLELE_MAJOR 4 #define ALLELE_NONMAJOR 5 #define GT_NEED_HOM 1 #define GT_NEED_HET 2 #define GT_NO_HOM 3 #define GT_NO_HET 4 #define GT_NEED_MISSING 5 #define GT_NO_MISSING 6 typedef struct _args_t { filter_t *filter; char *filter_str; int filter_logic; // one of FLT_INCLUDE/FLT_EXCLUDE (-i or -e) bcf_srs_t *files; bcf_hdr_t *hdr, *hnull, *hsub; // original header, sites-only header, subset header char **argv, *format, *sample_names, *subset_fname, *targets_list, *regions_list; int regions_overlap, targets_overlap; int argc, clevel, n_threads, output_type, print_header, update_info, header_only, n_samples, *imap, calc_ac; int trim_alts, sites_only, known, novel, min_alleles, max_alleles, private_vars, uncalled, phased; int min_ac, min_ac_type, max_ac, max_ac_type, min_af_type, max_af_type, gt_type; int *ac, mac; float min_af, max_af; char *fn_ref, *fn_out, **samples; int sample_is_file, force_samples; char *include_types, *exclude_types; int include, exclude; int record_cmd_line; char *index_fn; int write_index; int trim_star_allele; htsFile *out; } args_t; static void init_data(args_t *args) { int i; args->hdr = args->files->readers[0].header; if (args->calc_ac && args->update_info) { if (bcf_hdr_append(args->hdr,"##INFO=") < 0) error_errno("[%s] Failed to add \"AC\" INFO header", __func__); if (bcf_hdr_append(args->hdr,"##INFO=") < 0) error_errno("[%s] Failed to add \"AN\" INFO header", __func__); } if (args->record_cmd_line) bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_view"); else if (bcf_hdr_sync(args->hdr) < 0) error_errno("[%s] Failed to update header", __func__); // setup sample data if (args->sample_names) { void *hdr_samples = khash_str2int_init(); for (i=0; ihdr); i++) khash_str2int_inc(hdr_samples, bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i)); void *exclude = (args->sample_names[0]=='^') ? khash_str2int_init() : NULL; int nsmpl; char **smpl = NULL; args->samples = NULL; args->n_samples = 0; smpl = hts_readlist(exclude ? &args->sample_names[1] : args->sample_names, args->sample_is_file, &nsmpl); if ( !smpl ) { error("Could not read the list: \"%s\"\n", exclude ? &args->sample_names[1] : args->sample_names); } if ( exclude ) { for (i=0; iforce_samples) { fprintf(stderr, "Warn: exclude called for sample that does not exist in header: \"%s\"... skipping\n", smpl[i]); } else { error("Error: exclude called for sample that does not exist in header: \"%s\". Use \"--force-samples\" to ignore this error.\n", smpl[i]); } } khash_str2int_inc(exclude, smpl[i]); } for (i=0; ihdr); i++) { if ( exclude && khash_str2int_has_key(exclude,bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i)) ) continue; args->samples = (char**) realloc(args->samples, (args->n_samples+1)*sizeof(const char*)); args->samples[args->n_samples++] = strdup(bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i)); } khash_str2int_destroy(exclude); } else { for (i=0; iforce_samples) { fprintf(stderr, "Warn: subset called for sample that does not exist in header: \"%s\"... skipping\n", smpl[i]); continue; } else { error("Error: subset called for sample that does not exist in header: \"%s\". Use \"--force-samples\" to ignore this error.\n", smpl[i]); } } args->samples = (char**) realloc(args->samples, (args->n_samples+1)*sizeof(const char*)); args->samples[args->n_samples++] = strdup(smpl[i]); } } for (i=0; in_samples == 0) { fprintf(stderr, "Warn: subsetting has removed all samples\n"); args->sites_only = 1; } } if (args->n_samples) args->imap = (int*)malloc(args->n_samples * sizeof(int)); // determine variant types to include/exclude if (args->include_types || args->exclude_types) { if (args->include_types && args->exclude_types) { fprintf(stderr, "Error: only supply one of --include-types, --exclude-types options\n"); exit(1); } char **type_list = 0; int m = 0, n = 0; const char *q, *p; for (q = p = args->include_types ? args->include_types : args->exclude_types;; ++p) { if (*p == ',' || *p == 0) { if (m == n) { m = m? m<<1 : 16; type_list = (char**)realloc(type_list, m * sizeof(char*)); } type_list[n] = (char*)calloc(p - q + 1, 1); strncpy(type_list[n++], q, p - q); q = p + 1; if (*p == 0) break; } } type_list = (char**)realloc(type_list, n * sizeof(char*)); if (args->include_types) { args->include = 0; for (i = 0; i < n; ++i) { if (strcmp(type_list[i], "snps") == 0) args->include |= VCF_SNP<<1; else if (strcmp(type_list[i], "indels") == 0) args->include |= VCF_INDEL<<1; else if (strcmp(type_list[i], "mnps") == 0) args->include |= VCF_MNP<<1; else if (strcmp(type_list[i], "other") == 0) args->include |= VCF_OTHER<<1; else if (strcmp(type_list[i], "ref") == 0) args->include |= VCF_OTHER<<1; else if (strcmp(type_list[i], "bnd") == 0) args->include |= VCF_BND<<1; else { fprintf(stderr, "[E::%s] unknown type\n", type_list[i]); fprintf(stderr, "Accepted types are snps, indels, mnps, other\n"); exit(1); } } } if (args->exclude_types) { args->exclude = 0; for (i = 0; i < n; ++i) { if (strcmp(type_list[i], "snps") == 0) args->exclude |= VCF_SNP<<1; else if (strcmp(type_list[i], "indels") == 0) args->exclude |= VCF_INDEL<<1; else if (strcmp(type_list[i], "mnps") == 0) args->exclude |= VCF_MNP<<1; else if (strcmp(type_list[i], "other") == 0) args->exclude |= VCF_OTHER<<1; else if (strcmp(type_list[i], "ref") == 0) args->exclude |= VCF_OTHER<<1; else if (strcmp(type_list[i], "bnd") == 0) args->exclude |= VCF_BND<<1; else { fprintf(stderr, "[E::%s] unknown type\n", type_list[i]); fprintf(stderr, "Accepted types are snps, indels, mnps, other\n"); exit(1); } } } for (i = 0; i < n; ++i) free(type_list[i]); free(type_list); } char wmode[8]; set_wmode(wmode,args->output_type,args->fn_out,args->clevel); args->out = hts_open(args->fn_out ? args->fn_out : "-", wmode); if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno)); if ( args->n_threads > 0) hts_set_opt(args->out, HTS_OPT_THREAD_POOL, args->files->p); // headers: hdr=full header, hsub=subset header, hnull=sites only header if (args->sites_only){ args->hnull = bcf_hdr_subset(args->hdr, 0, 0, 0); bcf_hdr_remove(args->hnull, BCF_HL_FMT, NULL); } if (args->n_samples > 0) { args->hsub = bcf_hdr_subset(args->hdr, args->n_samples, args->samples, args->imap); if ( !args->hsub ) error("Error occurred while subsetting samples\n"); if ( args->n_samples != bcf_hdr_nsamples(args->hsub) ) { int i; for (i=0; in_samples; i++) if ( args->imap[i]<0 ) error("Error: No such sample: \"%s\"\n", args->samples[i]); } } if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); } static void destroy_data(args_t *args) { int i; if ( args->imap ) { for (i = 0; i < args->n_samples; ++i) free(args->samples[i]); free(args->samples); free(args->imap); } if (args->hnull) bcf_hdr_destroy(args->hnull); if (args->hsub) bcf_hdr_destroy(args->hsub); if ( args->filter ) filter_destroy(args->filter); free(args->ac); } // true if all samples are phased. // haploid genotypes are considered phased // ./. => not phased, .|. => phased int bcf_all_phased(const bcf_hdr_t *header, bcf1_t *line) { bcf_unpack(line, BCF_UN_FMT); bcf_fmt_t *fmt_ptr = bcf_get_fmt(header, line, "GT"); int all_phased = 1; if ( fmt_ptr ) { int i, isample; for (isample=0; isamplen_sample; isample++) { int sample_phased = 0; #define BRANCH_INT(type_t,vector_end) { \ type_t *p = (type_t*) (fmt_ptr->p + isample*fmt_ptr->size); \ for (i=0; in; i++) \ { \ if (fmt_ptr->n == 1 || (p[i] == vector_end && i == 1)) { sample_phased = 1; break; } /* haploid phased by definition */ \ if ( p[i] == vector_end ) { break; }; /* smaller ploidy */ \ if ( bcf_gt_is_missing(p[i]) ) continue; /* missing allele */ \ if ((p[i])&1) { \ sample_phased = 1; \ break; \ } \ } \ } switch (fmt_ptr->type) { case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_vector_end); break; default: fprintf(stderr, "[E::%s] todo: fmt_type %d\n", __func__, fmt_ptr->type); exit(1); break; } #undef BRANCH_INT if (!sample_phased) { all_phased = 0; break; } } } return all_phased; } int subset_vcf(args_t *args, bcf1_t *line) { if ( args->min_alleles && line->n_allele < args->min_alleles ) return 0; // min alleles if ( args->max_alleles && line->n_allele > args->max_alleles ) return 0; // max alleles if (args->novel || args->known) { if ( args->novel && (line->d.id[0]!='.' || line->d.id[1]!=0) ) return 0; // skip sites which are known, ID != '.' if ( args->known && line->d.id[0]=='.' && line->d.id[1]==0 ) return 0; // skip sites which are novel, ID == '.' } if (args->include || args->exclude) { int line_type = bcf_get_variant_types(line); if ( args->include && !((line_type<<1) & args->include) ) return 0; // include only given variant types if ( args->exclude && (line_type<<1) & args->exclude ) return 0; // exclude given variant types } if ( args->filter ) { int ret = filter_test(args->filter, line, NULL); if ( args->filter_logic==FLT_INCLUDE ) { if ( !ret ) return 0; } else if ( ret ) return 0; } hts_expand(int, line->n_allele, args->mac, args->ac); int i, an = 0, non_ref_ac = 0; if (args->calc_ac) { bcf_calc_ac(args->hdr, line, args->ac, BCF_UN_INFO|BCF_UN_FMT); // get original AC and AN values from INFO field if available, otherwise calculate for (i=1; in_allele; i++) non_ref_ac += args->ac[i]; for (i=0; in_allele; i++) an += args->ac[i]; } int update_ac = args->calc_ac; if (args->n_samples) { int non_ref_ac_sub = 0, *ac_sub = (int*) calloc(line->n_allele,sizeof(int)); bcf_subset(args->hdr, line, args->n_samples, args->imap); if ( args->calc_ac && !bcf_get_fmt(args->hdr,line,"GT") ) update_ac = 0; if ( update_ac ) { bcf_calc_ac(args->hsub, line, ac_sub, BCF_UN_FMT); // recalculate AC and AN an = 0; for (i=0; in_allele; i++) { args->ac[i] = ac_sub[i]; an += ac_sub[i]; } for (i=1; in_allele; i++) non_ref_ac_sub += ac_sub[i]; if (args->private_vars) { if (args->private_vars == FLT_INCLUDE && !(non_ref_ac_sub > 0 && non_ref_ac == non_ref_ac_sub)) { free(ac_sub); return 0; } // select private sites if (args->private_vars == FLT_EXCLUDE && non_ref_ac_sub > 0 && non_ref_ac == non_ref_ac_sub) { free(ac_sub); return 0; } // exclude private sites } non_ref_ac = non_ref_ac_sub; } free(ac_sub); } bcf_fmt_t *gt_fmt; if ( args->gt_type && (gt_fmt=bcf_get_fmt(args->hdr,line,"GT")) ) { int nhet = 0, nhom = 0, nmiss = 0; for (i=0; ihdr); i++) { int type = bcf_gt_type(gt_fmt,i,NULL,NULL); if ( type==GT_HET_RA || type==GT_HET_AA ) { if ( args->gt_type==GT_NO_HET ) return 0; nhet = 1; } else if ( type==GT_UNKN ) { if ( args->gt_type==GT_NO_MISSING ) return 0; nmiss = 1; } else { if ( args->gt_type==GT_NO_HOM ) return 0; nhom = 1; } } if ( args->gt_type==GT_NEED_HOM && !nhom ) return 0; else if ( args->gt_type==GT_NEED_HET && !nhet ) return 0; else if ( args->gt_type==GT_NEED_MISSING && !nmiss ) return 0; } int minor_ac = 0; int major_ac = 0; if ( args->calc_ac ) { minor_ac = args->ac[0]; major_ac = args->ac[0]; for (i=1; in_allele; i++){ if (args->ac[i] < minor_ac) { minor_ac = args->ac[i]; } if (args->ac[i] > major_ac) { major_ac = args->ac[i]; } } } if (args->min_ac!=-1) { if (args->min_ac_type == ALLELE_NONREF && args->min_ac>non_ref_ac) return 0; // min AC else if (args->min_ac_type == ALLELE_MINOR && args->min_ac>minor_ac) return 0; // min minor AC else if (args->min_ac_type == ALLELE_ALT1 && args->min_ac>args->ac[1]) return 0; // min 1st alternate AC else if (args->min_ac_type == ALLELE_MAJOR && args->min_ac > major_ac) return 0; // min major AC else if (args->min_ac_type == ALLELE_NONMAJOR && args->min_ac > an-major_ac) return 0; // min non-major AC } if (args->max_ac!=-1) { if (args->max_ac_type == ALLELE_NONREF && args->max_acmax_ac_type == ALLELE_MINOR && args->max_acmax_ac_type == ALLELE_ALT1 && args->max_acac[1]) return 0; // max 1st alternate AC else if (args->max_ac_type == ALLELE_MAJOR && args->max_ac < major_ac) return 0; // max major AC else if (args->max_ac_type == ALLELE_NONMAJOR && args->max_ac < an-major_ac) return 0; // max non-major AC } if (args->min_af!=-1) { if (an == 0) return 0; // freq not defined, skip site if (args->min_af_type == ALLELE_NONREF && args->min_af>non_ref_ac/(double)an) return 0; // min AF else if (args->min_af_type == ALLELE_MINOR && args->min_af>minor_ac/(double)an) return 0; // min minor AF else if (args->min_af_type == ALLELE_ALT1 && args->min_af>args->ac[1]/(double)an) return 0; // min 1st alternate AF else if (args->min_af_type == ALLELE_MAJOR && args->min_af > major_ac/(double)an) return 0; // min major AF else if (args->min_af_type == ALLELE_NONMAJOR && args->min_af > (an-major_ac)/(double)an) return 0; // min non-major AF } if (args->max_af!=-1) { if (an == 0) return 0; // freq not defined, skip site if (args->max_af_type == ALLELE_NONREF && args->max_afmax_af_type == ALLELE_MINOR && args->max_afmax_af_type == ALLELE_ALT1 && args->max_afac[1]/(double)an) return 0; // max 1st alternate AF else if (args->max_af_type == ALLELE_MAJOR && args->max_af < major_ac/(double)an) return 0; // max major AF else if (args->max_af_type == ALLELE_NONMAJOR && args->max_af < (an-major_ac)/(double)an) return 0; // max non-major AF } if (args->uncalled) { if (args->uncalled == FLT_INCLUDE && an > 0) return 0; // select uncalled if (args->uncalled == FLT_EXCLUDE && an == 0) return 0; // skip if uncalled } if (update_ac && args->update_info) { bcf_update_info_int32(args->hdr, line, "AC", &args->ac[1], line->n_allele-1); bcf_update_info_int32(args->hdr, line, "AN", &an, 1); } if (args->trim_alts) { int ret = bcf_trim_alleles(args->hsub ? args->hsub : args->hdr, line); if ( ret<0 ) error("Error: Could not trim alleles at %s:%"PRId64"\n", bcf_seqname(args->hsub ? args->hsub : args->hdr, line), (int64_t) line->pos+1); } if (args->trim_star_allele) { int iunseen; if ( args->trim_star_allele && (line->n_allele > 2 || args->trim_star_allele > 1) && (iunseen=get_unseen_allele(line)) && iunseen>0 ) { // the unobserved star allele should be trimmed, either it is variant site or trimming of all sites was requested kbitset_t *rm_set = kbs_init(line->n_allele); kbs_insert(rm_set, iunseen); if ( bcf_remove_allele_set(args->hdr,line,rm_set) ) error("[%s] Error: failed to trim the unobserved allele at %s:%"PRIhts_pos"\n",__func__,bcf_seqname(args->hdr,line),line->pos+1); kbs_destroy(rm_set); } } if (args->phased) { int phased = bcf_all_phased(args->hdr, line); if (args->phased == FLT_INCLUDE && !phased) { return 0; } // skip unphased if (args->phased == FLT_EXCLUDE && phased) { return 0; } // skip phased } if (args->sites_only) bcf_subset(args->hsub ? args->hsub : args->hdr, line, 0, 0); return 1; } void set_allele_type (int *atype, char *atype_string) { *atype = ALLELE_NONREF; if (strcmp(atype_string, "minor") == 0) { *atype = ALLELE_MINOR; } else if (strcmp(atype_string, "alt1") == 0) { *atype = ALLELE_ALT1; } else if (strcmp(atype_string, "nref") == 0) { *atype = ALLELE_NONREF; } else if (strcmp(atype_string, "major") == 0) { *atype = ALLELE_MAJOR; } else if (strcmp(atype_string, "nonmajor") == 0) { *atype = ALLELE_NONMAJOR; } else { error("Error: allele type not recognised. Expected one of nref|alt1|minor|major|nonmajor, got \"%s\".\n", atype_string); } } static void usage(args_t *args) { fprintf(stderr, "\n"); fprintf(stderr, "About: VCF/BCF conversion, view, subset and filter VCF/BCF files.\n"); fprintf(stderr, "Usage: bcftools view [options] [region1 [...]]\n"); fprintf(stderr, "\n"); fprintf(stderr, "Output options:\n"); fprintf(stderr, " -G, --drop-genotypes Drop individual genotype information (after subsetting if -s option set)\n"); fprintf(stderr, " -h, --header-only Print only the header in VCF output (equivalent to bcftools head)\n"); fprintf(stderr, " -H, --no-header Suppress the header in VCF output\n"); fprintf(stderr, " --with-header Print both header and records in VCF output [default]\n"); fprintf(stderr, " -l, --compression-level [0-9] Compression level: 0 uncompressed, 1 best speed, 9 best compression [%d]\n", args->clevel); fprintf(stderr, " --no-version Do not append version and command line to the header\n"); fprintf(stderr, " -o, --output FILE Output file name [stdout]\n"); fprintf(stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(stderr, " -R, --regions-file FILE Restrict to regions listed in FILE\n"); fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(stderr, " -t, --targets [^]REGION Similar to -r but streams rather than index-jumps. Exclude regions with \"^\" prefix\n"); fprintf(stderr, " -T, --targets-file [^]FILE Similar to -R but streams rather than index-jumps. Exclude regions with \"^\" prefix\n"); fprintf(stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(stderr, " --threads INT Use multithreading with INT worker threads [0]\n"); fprintf(stderr, "\n"); fprintf(stderr, "Subset options:\n"); fprintf(stderr, " -A, --trim-unseen-allele Remove '<*>' or '' at variant (-A) or at all (-AA) sites\n"); fprintf(stderr, " -a, --trim-alt-alleles Trim ALT alleles not seen in the genotype fields (or their subset with -s/-S)\n"); fprintf(stderr, " -I, --no-update Do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)\n"); fprintf(stderr, " -s, --samples [^]LIST Comma separated list of samples to include (or exclude with \"^\" prefix). Be careful\n"); fprintf(stderr, " when combining filtering with sample subsetting as filtering comes (usually) first.\n"); fprintf(stderr, " If unsure, split sample subsetting and filtering in two commands, using -Ou when piping.\n"); fprintf(stderr, " -S, --samples-file [^]FILE File of samples to include (or exclude with \"^\" prefix)\n"); fprintf(stderr, " --force-samples Only warn about unknown subset samples\n"); fprintf(stderr, "\n"); fprintf(stderr, "Filter options:\n"); fprintf(stderr, " -c/C, --min-ac/--max-ac INT[:TYPE] Minimum/maximum count for non-reference (nref), 1st alternate (alt1), least frequent\n"); fprintf(stderr, " (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]\n"); fprintf(stderr, " -f, --apply-filters LIST Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n"); fprintf(stderr, " -g, --genotype [^]hom|het|miss Require one or more hom/het/missing genotype or, if prefixed with \"^\", exclude such sites\n"); fprintf(stderr, " -i/e, --include/--exclude EXPR Select/exclude sites for which the expression is true (see man page for details)\n"); fprintf(stderr, " -k/n, --known/--novel Select known/novel sites only (ID is not/is '.')\n"); fprintf(stderr, " -m/M, --min-alleles/--max-alleles INT Minimum/maximum number of alleles listed in REF and ALT (e.g. -m2 -M2 for biallelic sites)\n"); fprintf(stderr, " -p/P, --phased/--exclude-phased Select/exclude sites where all samples are phased\n"); fprintf(stderr, " -q/Q, --min-af/--max-af FLOAT[:TYPE] Minimum/maximum frequency for non-reference (nref), 1st alternate (alt1), least frequent\n"); fprintf(stderr, " (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]\n"); fprintf(stderr, " -u/U, --uncalled/--exclude-uncalled Select/exclude sites without a called genotype\n"); fprintf(stderr, " -v/V, --types/--exclude-types LIST Select/exclude comma-separated list of variant types: snps,indels,mnps,ref,bnd,other [null]\n"); fprintf(stderr, " -x/X, --private/--exclude-private Select/exclude sites where the non-reference alleles are exclusive (private) to the subset samples\n"); fprintf(stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(stderr, "\n"); exit(1); } int main_vcfview(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->files = bcf_sr_init(); args->clevel = -1; args->print_header = 1; args->update_info = 1; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->write_index = 0; args->min_ac = args->max_ac = args->min_af = args->max_af = -1; args->regions_overlap = 1; args->targets_overlap = 0; int targets_is_file = 0, regions_is_file = 0; static struct option loptions[] = { {"genotype",required_argument,NULL,'g'}, {"compression-level",required_argument,NULL,'l'}, {"threads",required_argument,NULL,9}, {"header-only",no_argument,NULL,'h'}, {"no-header",no_argument,NULL,'H'}, {"with-header",no_argument,NULL,4}, {"exclude",required_argument,NULL,'e'}, {"include",required_argument,NULL,'i'}, {"trim-alt-alleles",no_argument,NULL,'a'}, {"trim-unseen-allele",no_argument,NULL,'A'}, {"no-update",no_argument,NULL,'I'}, {"drop-genotypes",no_argument,NULL,'G'}, {"private",no_argument,NULL,'x'}, {"exclude-private",no_argument,NULL,'X'}, {"uncalled",no_argument,NULL,'u'}, {"exclude-uncalled",no_argument,NULL,'U'}, {"apply-filters",required_argument,NULL,'f'}, {"known",no_argument,NULL,'k'}, {"novel",no_argument,NULL,'n'}, {"min-alleles",required_argument,NULL,'m'}, {"max-alleles",required_argument,NULL,'M'}, {"samples",required_argument,NULL,'s'}, {"samples-file",required_argument,NULL,'S'}, {"force-samples",no_argument,NULL,1}, {"output-type",required_argument,NULL,'O'}, {"output-file",required_argument,NULL,'o'}, {"output",required_argument,NULL,'o'}, {"types",required_argument,NULL,'v'}, {"exclude-types",required_argument,NULL,'V'}, {"targets",required_argument,NULL,'t'}, {"targets-file",required_argument,NULL,'T'}, {"targets-overlap",required_argument,NULL,2}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,3}, {"min-ac",required_argument,NULL,'c'}, {"max-ac",required_argument,NULL,'C'}, {"min-af",required_argument,NULL,'q'}, {"max-af",required_argument,NULL,'Q'}, {"phased",no_argument,NULL,'p'}, {"exclude-phased",no_argument,NULL,'P'}, {"no-version",no_argument,NULL,8}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "l:t:T:r:R:o:O:s:S:Gf:knv:V:m:M:aAuUhHc:C:Ii:e:xXpPq:Q:g:W::",loptions,NULL)) >= 0) { char allele_type[9] = "nref"; switch (c) { case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } }; if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'l': args->clevel = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --compression-level %s\n", optarg); args->output_type |= FT_GZ; break; case 'o': args->fn_out = optarg; break; case 'H': args->print_header = 0; break; case 'h': args->header_only = 1; break; case 4 : args->print_header = 1; args->header_only = 0; break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; targets_is_file = 1; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 's': args->sample_names = optarg; break; case 'S': args->sample_names = optarg; args->sample_is_file = 1; break; case 1 : args->force_samples = 1; break; case 'a': args->trim_alts = 1; args->calc_ac = 1; break; case 'A': args->trim_star_allele++; break; case 'I': args->update_info = 0; break; case 'G': args->sites_only = 1; break; case 'f': args->files->apply_filters = optarg; break; case 'k': args->known = 1; break; case 'n': args->novel = 1; break; case 'm': args->min_alleles = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --min-alleles %s\n", optarg); break; case 'M': args->max_alleles = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --max-alleles %s\n", optarg); break; case 'v': args->include_types = optarg; break; case 'V': args->exclude_types = optarg; break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'c': { args->min_ac_type = ALLELE_NONREF; if ( sscanf(optarg,"%d:%8s",&args->min_ac, allele_type)!=2 && sscanf(optarg,"%d",&args->min_ac)!=1 ) error("Error: Could not parse --min-ac %s\n", optarg); set_allele_type(&args->min_ac_type, allele_type); args->calc_ac = 1; break; } case 'C': { args->max_ac_type = ALLELE_NONREF; if ( sscanf(optarg,"%d:%8s",&args->max_ac, allele_type)!=2 && sscanf(optarg,"%d",&args->max_ac)!=1 ) error("Error: Could not parse --max-ac %s\n", optarg); set_allele_type(&args->max_ac_type, allele_type); args->calc_ac = 1; break; } case 'q': { args->min_af_type = ALLELE_NONREF; if ( sscanf(optarg,"%f:%8s",&args->min_af, allele_type)!=2 && sscanf(optarg,"%f",&args->min_af)!=1 ) error("Error: Could not parse --min-af %s\n", optarg); set_allele_type(&args->min_af_type, allele_type); args->calc_ac = 1; break; } case 'Q': { args->max_af_type = ALLELE_NONREF; if ( sscanf(optarg,"%f:%8s",&args->max_af, allele_type)!=2 && sscanf(optarg,"%f",&args->max_af)!=1 ) error("Error: Could not parse --max-af %s\n", optarg); set_allele_type(&args->max_af_type, allele_type); args->calc_ac = 1; break; } case 'x': args->private_vars |= FLT_INCLUDE; args->calc_ac = 1; break; case 'X': args->private_vars |= FLT_EXCLUDE; args->calc_ac = 1; break; case 'u': args->uncalled |= FLT_INCLUDE; args->calc_ac = 1; break; case 'U': args->uncalled |= FLT_EXCLUDE; args->calc_ac = 1; break; case 'p': args->phased |= FLT_INCLUDE; break; // phased case 'P': args->phased |= FLT_EXCLUDE; break; // exclude-phased case 'g': { if ( !strcasecmp(optarg,"hom") ) args->gt_type = GT_NEED_HOM; else if ( !strcasecmp(optarg,"het") ) args->gt_type = GT_NEED_HET; else if ( !strcasecmp(optarg,"miss") ) args->gt_type = GT_NEED_MISSING; else if ( !strcasecmp(optarg,"^hom") ) args->gt_type = GT_NO_HOM; else if ( !strcasecmp(optarg,"^het") ) args->gt_type = GT_NO_HET; else if ( !strcasecmp(optarg,"^miss") ) args->gt_type = GT_NO_MISSING; else error("The argument to -g not recognised. Expected one of hom/het/miss/^hom/^het/^miss, got \"%s\".\n", optarg); break; } case 2 : args->targets_overlap = parse_overlap_option(optarg); if ( args->targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 3 : args->regions_overlap = parse_overlap_option(optarg); if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 8 : args->record_cmd_line = 0; break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case '?': usage(args); break; default: error("Unknown argument: %s\n", optarg); } } if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n"); if ( args->private_vars > FLT_EXCLUDE ) error("Only one of -x or -X can be given.\n"); if ( args->uncalled > FLT_EXCLUDE ) error("Only one of -u or -U can be given.\n"); if ( args->phased > FLT_EXCLUDE ) error("Only one of -p or -P can be given.\n"); if ( args->sample_names && args->update_info) args->calc_ac = 1; char *fname = NULL; if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else usage(args); } else fname = argv[optind]; // read in the regions from the command line if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } else if ( optind+1 < argc ) { int i; kstring_t tmp = {0,0,0}; kputs(argv[optind+1],&tmp); for (i=optind+2; ifiles, tmp.s, 0)<0 ) error("Failed to read the regions: %s\n", tmp.s); free(tmp.s); } if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,args->targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n"); if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); init_data(args); bcf_hdr_t *out_hdr = args->hnull ? args->hnull : (args->hsub ? args->hsub : args->hdr); if (args->print_header) { if ( bcf_hdr_write(args->out, out_hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->fn_out); } else if ( args->output_type & FT_BCF ) error("BCF output requires header, cannot proceed with -H\n"); if ( init_index2(args->out,out_hdr,args->fn_out, &args->index_fn, args->write_index) < 0 ) error("Error: failed to initialise index for %s\n",args->fn_out); int ret = 0; if (!args->header_only) { while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = args->files->readers[0].buffer[0]; if ( line->errcode && out_hdr!=args->hdr ) error("Undefined tags in the header, cannot proceed in the sample subset mode.\n"); if ( subset_vcf(args, line) && bcf_write1(args->out, out_hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->fn_out); } ret = args->files->errnum; if ( ret ) fprintf(stderr,"Error: %s\n", bcf_sr_strerror(args->files->errnum)); } if (args->write_index) { if (bcf_idx_save(args->out) < 0) { if ( hts_close(args->out)!=0 ) error("Error: close failed %s\n", args->fn_out?args->fn_out:"stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(args->out)!=0 ) error("Error: close failed %s\n", args->fn_out?args->fn_out:"stdout"); destroy_data(args); bcf_sr_destroy(args->files); free(args); return ret; } pysam-0.23.0/bcftools/vcfview.c.pysam.c000066400000000000000000001200701475062545500177430ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcfview.c -- VCF/BCF conversion, view, subset and filter VCF/BCF files. Copyright (C) 2013-2023 Genome Research Ltd. Author: Shane McCarthy Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "bcftools.h" #include "filter.h" #include "htslib/khash_str2int.h" #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 #define ALLELE_NONREF 1 #define ALLELE_MINOR 2 #define ALLELE_ALT1 3 #define ALLELE_MAJOR 4 #define ALLELE_NONMAJOR 5 #define GT_NEED_HOM 1 #define GT_NEED_HET 2 #define GT_NO_HOM 3 #define GT_NO_HET 4 #define GT_NEED_MISSING 5 #define GT_NO_MISSING 6 typedef struct _args_t { filter_t *filter; char *filter_str; int filter_logic; // one of FLT_INCLUDE/FLT_EXCLUDE (-i or -e) bcf_srs_t *files; bcf_hdr_t *hdr, *hnull, *hsub; // original header, sites-only header, subset header char **argv, *format, *sample_names, *subset_fname, *targets_list, *regions_list; int regions_overlap, targets_overlap; int argc, clevel, n_threads, output_type, print_header, update_info, header_only, n_samples, *imap, calc_ac; int trim_alts, sites_only, known, novel, min_alleles, max_alleles, private_vars, uncalled, phased; int min_ac, min_ac_type, max_ac, max_ac_type, min_af_type, max_af_type, gt_type; int *ac, mac; float min_af, max_af; char *fn_ref, *fn_out, **samples; int sample_is_file, force_samples; char *include_types, *exclude_types; int include, exclude; int record_cmd_line; char *index_fn; int write_index; int trim_star_allele; htsFile *out; } args_t; static void init_data(args_t *args) { int i; args->hdr = args->files->readers[0].header; if (args->calc_ac && args->update_info) { if (bcf_hdr_append(args->hdr,"##INFO=") < 0) error_errno("[%s] Failed to add \"AC\" INFO header", __func__); if (bcf_hdr_append(args->hdr,"##INFO=") < 0) error_errno("[%s] Failed to add \"AN\" INFO header", __func__); } if (args->record_cmd_line) bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_view"); else if (bcf_hdr_sync(args->hdr) < 0) error_errno("[%s] Failed to update header", __func__); // setup sample data if (args->sample_names) { void *hdr_samples = khash_str2int_init(); for (i=0; ihdr); i++) khash_str2int_inc(hdr_samples, bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i)); void *exclude = (args->sample_names[0]=='^') ? khash_str2int_init() : NULL; int nsmpl; char **smpl = NULL; args->samples = NULL; args->n_samples = 0; smpl = hts_readlist(exclude ? &args->sample_names[1] : args->sample_names, args->sample_is_file, &nsmpl); if ( !smpl ) { error("Could not read the list: \"%s\"\n", exclude ? &args->sample_names[1] : args->sample_names); } if ( exclude ) { for (i=0; iforce_samples) { fprintf(bcftools_stderr, "Warn: exclude called for sample that does not exist in header: \"%s\"... skipping\n", smpl[i]); } else { error("Error: exclude called for sample that does not exist in header: \"%s\". Use \"--force-samples\" to ignore this error.\n", smpl[i]); } } khash_str2int_inc(exclude, smpl[i]); } for (i=0; ihdr); i++) { if ( exclude && khash_str2int_has_key(exclude,bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i)) ) continue; args->samples = (char**) realloc(args->samples, (args->n_samples+1)*sizeof(const char*)); args->samples[args->n_samples++] = strdup(bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i)); } khash_str2int_destroy(exclude); } else { for (i=0; iforce_samples) { fprintf(bcftools_stderr, "Warn: subset called for sample that does not exist in header: \"%s\"... skipping\n", smpl[i]); continue; } else { error("Error: subset called for sample that does not exist in header: \"%s\". Use \"--force-samples\" to ignore this error.\n", smpl[i]); } } args->samples = (char**) realloc(args->samples, (args->n_samples+1)*sizeof(const char*)); args->samples[args->n_samples++] = strdup(smpl[i]); } } for (i=0; in_samples == 0) { fprintf(bcftools_stderr, "Warn: subsetting has removed all samples\n"); args->sites_only = 1; } } if (args->n_samples) args->imap = (int*)malloc(args->n_samples * sizeof(int)); // determine variant types to include/exclude if (args->include_types || args->exclude_types) { if (args->include_types && args->exclude_types) { fprintf(bcftools_stderr, "Error: only supply one of --include-types, --exclude-types options\n"); bcftools_exit(1); } char **type_list = 0; int m = 0, n = 0; const char *q, *p; for (q = p = args->include_types ? args->include_types : args->exclude_types;; ++p) { if (*p == ',' || *p == 0) { if (m == n) { m = m? m<<1 : 16; type_list = (char**)realloc(type_list, m * sizeof(char*)); } type_list[n] = (char*)calloc(p - q + 1, 1); strncpy(type_list[n++], q, p - q); q = p + 1; if (*p == 0) break; } } type_list = (char**)realloc(type_list, n * sizeof(char*)); if (args->include_types) { args->include = 0; for (i = 0; i < n; ++i) { if (strcmp(type_list[i], "snps") == 0) args->include |= VCF_SNP<<1; else if (strcmp(type_list[i], "indels") == 0) args->include |= VCF_INDEL<<1; else if (strcmp(type_list[i], "mnps") == 0) args->include |= VCF_MNP<<1; else if (strcmp(type_list[i], "other") == 0) args->include |= VCF_OTHER<<1; else if (strcmp(type_list[i], "ref") == 0) args->include |= VCF_OTHER<<1; else if (strcmp(type_list[i], "bnd") == 0) args->include |= VCF_BND<<1; else { fprintf(bcftools_stderr, "[E::%s] unknown type\n", type_list[i]); fprintf(bcftools_stderr, "Accepted types are snps, indels, mnps, other\n"); bcftools_exit(1); } } } if (args->exclude_types) { args->exclude = 0; for (i = 0; i < n; ++i) { if (strcmp(type_list[i], "snps") == 0) args->exclude |= VCF_SNP<<1; else if (strcmp(type_list[i], "indels") == 0) args->exclude |= VCF_INDEL<<1; else if (strcmp(type_list[i], "mnps") == 0) args->exclude |= VCF_MNP<<1; else if (strcmp(type_list[i], "other") == 0) args->exclude |= VCF_OTHER<<1; else if (strcmp(type_list[i], "ref") == 0) args->exclude |= VCF_OTHER<<1; else if (strcmp(type_list[i], "bnd") == 0) args->exclude |= VCF_BND<<1; else { fprintf(bcftools_stderr, "[E::%s] unknown type\n", type_list[i]); fprintf(bcftools_stderr, "Accepted types are snps, indels, mnps, other\n"); bcftools_exit(1); } } } for (i = 0; i < n; ++i) free(type_list[i]); free(type_list); } char wmode[8]; set_wmode(wmode,args->output_type,args->fn_out,args->clevel); args->out = hts_open(args->fn_out ? args->fn_out : "-", wmode); if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno)); if ( args->n_threads > 0) hts_set_opt(args->out, HTS_OPT_THREAD_POOL, args->files->p); // headers: hdr=full header, hsub=subset header, hnull=sites only header if (args->sites_only){ args->hnull = bcf_hdr_subset(args->hdr, 0, 0, 0); bcf_hdr_remove(args->hnull, BCF_HL_FMT, NULL); } if (args->n_samples > 0) { args->hsub = bcf_hdr_subset(args->hdr, args->n_samples, args->samples, args->imap); if ( !args->hsub ) error("Error occurred while subsetting samples\n"); if ( args->n_samples != bcf_hdr_nsamples(args->hsub) ) { int i; for (i=0; in_samples; i++) if ( args->imap[i]<0 ) error("Error: No such sample: \"%s\"\n", args->samples[i]); } } if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); } static void destroy_data(args_t *args) { int i; if ( args->imap ) { for (i = 0; i < args->n_samples; ++i) free(args->samples[i]); free(args->samples); free(args->imap); } if (args->hnull) bcf_hdr_destroy(args->hnull); if (args->hsub) bcf_hdr_destroy(args->hsub); if ( args->filter ) filter_destroy(args->filter); free(args->ac); } // true if all samples are phased. // haploid genotypes are considered phased // ./. => not phased, .|. => phased int bcf_all_phased(const bcf_hdr_t *header, bcf1_t *line) { bcf_unpack(line, BCF_UN_FMT); bcf_fmt_t *fmt_ptr = bcf_get_fmt(header, line, "GT"); int all_phased = 1; if ( fmt_ptr ) { int i, isample; for (isample=0; isamplen_sample; isample++) { int sample_phased = 0; #define BRANCH_INT(type_t,vector_end) { \ type_t *p = (type_t*) (fmt_ptr->p + isample*fmt_ptr->size); \ for (i=0; in; i++) \ { \ if (fmt_ptr->n == 1 || (p[i] == vector_end && i == 1)) { sample_phased = 1; break; } /* haploid phased by definition */ \ if ( p[i] == vector_end ) { break; }; /* smaller ploidy */ \ if ( bcf_gt_is_missing(p[i]) ) continue; /* missing allele */ \ if ((p[i])&1) { \ sample_phased = 1; \ break; \ } \ } \ } switch (fmt_ptr->type) { case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_vector_end); break; default: fprintf(bcftools_stderr, "[E::%s] todo: fmt_type %d\n", __func__, fmt_ptr->type); bcftools_exit(1); break; } #undef BRANCH_INT if (!sample_phased) { all_phased = 0; break; } } } return all_phased; } int subset_vcf(args_t *args, bcf1_t *line) { if ( args->min_alleles && line->n_allele < args->min_alleles ) return 0; // min alleles if ( args->max_alleles && line->n_allele > args->max_alleles ) return 0; // max alleles if (args->novel || args->known) { if ( args->novel && (line->d.id[0]!='.' || line->d.id[1]!=0) ) return 0; // skip sites which are known, ID != '.' if ( args->known && line->d.id[0]=='.' && line->d.id[1]==0 ) return 0; // skip sites which are novel, ID == '.' } if (args->include || args->exclude) { int line_type = bcf_get_variant_types(line); if ( args->include && !((line_type<<1) & args->include) ) return 0; // include only given variant types if ( args->exclude && (line_type<<1) & args->exclude ) return 0; // exclude given variant types } if ( args->filter ) { int ret = filter_test(args->filter, line, NULL); if ( args->filter_logic==FLT_INCLUDE ) { if ( !ret ) return 0; } else if ( ret ) return 0; } hts_expand(int, line->n_allele, args->mac, args->ac); int i, an = 0, non_ref_ac = 0; if (args->calc_ac) { bcf_calc_ac(args->hdr, line, args->ac, BCF_UN_INFO|BCF_UN_FMT); // get original AC and AN values from INFO field if available, otherwise calculate for (i=1; in_allele; i++) non_ref_ac += args->ac[i]; for (i=0; in_allele; i++) an += args->ac[i]; } int update_ac = args->calc_ac; if (args->n_samples) { int non_ref_ac_sub = 0, *ac_sub = (int*) calloc(line->n_allele,sizeof(int)); bcf_subset(args->hdr, line, args->n_samples, args->imap); if ( args->calc_ac && !bcf_get_fmt(args->hdr,line,"GT") ) update_ac = 0; if ( update_ac ) { bcf_calc_ac(args->hsub, line, ac_sub, BCF_UN_FMT); // recalculate AC and AN an = 0; for (i=0; in_allele; i++) { args->ac[i] = ac_sub[i]; an += ac_sub[i]; } for (i=1; in_allele; i++) non_ref_ac_sub += ac_sub[i]; if (args->private_vars) { if (args->private_vars == FLT_INCLUDE && !(non_ref_ac_sub > 0 && non_ref_ac == non_ref_ac_sub)) { free(ac_sub); return 0; } // select private sites if (args->private_vars == FLT_EXCLUDE && non_ref_ac_sub > 0 && non_ref_ac == non_ref_ac_sub) { free(ac_sub); return 0; } // exclude private sites } non_ref_ac = non_ref_ac_sub; } free(ac_sub); } bcf_fmt_t *gt_fmt; if ( args->gt_type && (gt_fmt=bcf_get_fmt(args->hdr,line,"GT")) ) { int nhet = 0, nhom = 0, nmiss = 0; for (i=0; ihdr); i++) { int type = bcf_gt_type(gt_fmt,i,NULL,NULL); if ( type==GT_HET_RA || type==GT_HET_AA ) { if ( args->gt_type==GT_NO_HET ) return 0; nhet = 1; } else if ( type==GT_UNKN ) { if ( args->gt_type==GT_NO_MISSING ) return 0; nmiss = 1; } else { if ( args->gt_type==GT_NO_HOM ) return 0; nhom = 1; } } if ( args->gt_type==GT_NEED_HOM && !nhom ) return 0; else if ( args->gt_type==GT_NEED_HET && !nhet ) return 0; else if ( args->gt_type==GT_NEED_MISSING && !nmiss ) return 0; } int minor_ac = 0; int major_ac = 0; if ( args->calc_ac ) { minor_ac = args->ac[0]; major_ac = args->ac[0]; for (i=1; in_allele; i++){ if (args->ac[i] < minor_ac) { minor_ac = args->ac[i]; } if (args->ac[i] > major_ac) { major_ac = args->ac[i]; } } } if (args->min_ac!=-1) { if (args->min_ac_type == ALLELE_NONREF && args->min_ac>non_ref_ac) return 0; // min AC else if (args->min_ac_type == ALLELE_MINOR && args->min_ac>minor_ac) return 0; // min minor AC else if (args->min_ac_type == ALLELE_ALT1 && args->min_ac>args->ac[1]) return 0; // min 1st alternate AC else if (args->min_ac_type == ALLELE_MAJOR && args->min_ac > major_ac) return 0; // min major AC else if (args->min_ac_type == ALLELE_NONMAJOR && args->min_ac > an-major_ac) return 0; // min non-major AC } if (args->max_ac!=-1) { if (args->max_ac_type == ALLELE_NONREF && args->max_acmax_ac_type == ALLELE_MINOR && args->max_acmax_ac_type == ALLELE_ALT1 && args->max_acac[1]) return 0; // max 1st alternate AC else if (args->max_ac_type == ALLELE_MAJOR && args->max_ac < major_ac) return 0; // max major AC else if (args->max_ac_type == ALLELE_NONMAJOR && args->max_ac < an-major_ac) return 0; // max non-major AC } if (args->min_af!=-1) { if (an == 0) return 0; // freq not defined, skip site if (args->min_af_type == ALLELE_NONREF && args->min_af>non_ref_ac/(double)an) return 0; // min AF else if (args->min_af_type == ALLELE_MINOR && args->min_af>minor_ac/(double)an) return 0; // min minor AF else if (args->min_af_type == ALLELE_ALT1 && args->min_af>args->ac[1]/(double)an) return 0; // min 1st alternate AF else if (args->min_af_type == ALLELE_MAJOR && args->min_af > major_ac/(double)an) return 0; // min major AF else if (args->min_af_type == ALLELE_NONMAJOR && args->min_af > (an-major_ac)/(double)an) return 0; // min non-major AF } if (args->max_af!=-1) { if (an == 0) return 0; // freq not defined, skip site if (args->max_af_type == ALLELE_NONREF && args->max_afmax_af_type == ALLELE_MINOR && args->max_afmax_af_type == ALLELE_ALT1 && args->max_afac[1]/(double)an) return 0; // max 1st alternate AF else if (args->max_af_type == ALLELE_MAJOR && args->max_af < major_ac/(double)an) return 0; // max major AF else if (args->max_af_type == ALLELE_NONMAJOR && args->max_af < (an-major_ac)/(double)an) return 0; // max non-major AF } if (args->uncalled) { if (args->uncalled == FLT_INCLUDE && an > 0) return 0; // select uncalled if (args->uncalled == FLT_EXCLUDE && an == 0) return 0; // skip if uncalled } if (update_ac && args->update_info) { bcf_update_info_int32(args->hdr, line, "AC", &args->ac[1], line->n_allele-1); bcf_update_info_int32(args->hdr, line, "AN", &an, 1); } if (args->trim_alts) { int ret = bcf_trim_alleles(args->hsub ? args->hsub : args->hdr, line); if ( ret<0 ) error("Error: Could not trim alleles at %s:%"PRId64"\n", bcf_seqname(args->hsub ? args->hsub : args->hdr, line), (int64_t) line->pos+1); } if (args->trim_star_allele) { int iunseen; if ( args->trim_star_allele && (line->n_allele > 2 || args->trim_star_allele > 1) && (iunseen=get_unseen_allele(line)) && iunseen>0 ) { // the unobserved star allele should be trimmed, either it is variant site or trimming of all sites was requested kbitset_t *rm_set = kbs_init(line->n_allele); kbs_insert(rm_set, iunseen); if ( bcf_remove_allele_set(args->hdr,line,rm_set) ) error("[%s] Error: failed to trim the unobserved allele at %s:%"PRIhts_pos"\n",__func__,bcf_seqname(args->hdr,line),line->pos+1); kbs_destroy(rm_set); } } if (args->phased) { int phased = bcf_all_phased(args->hdr, line); if (args->phased == FLT_INCLUDE && !phased) { return 0; } // skip unphased if (args->phased == FLT_EXCLUDE && phased) { return 0; } // skip phased } if (args->sites_only) bcf_subset(args->hsub ? args->hsub : args->hdr, line, 0, 0); return 1; } void set_allele_type (int *atype, char *atype_string) { *atype = ALLELE_NONREF; if (strcmp(atype_string, "minor") == 0) { *atype = ALLELE_MINOR; } else if (strcmp(atype_string, "alt1") == 0) { *atype = ALLELE_ALT1; } else if (strcmp(atype_string, "nref") == 0) { *atype = ALLELE_NONREF; } else if (strcmp(atype_string, "major") == 0) { *atype = ALLELE_MAJOR; } else if (strcmp(atype_string, "nonmajor") == 0) { *atype = ALLELE_NONMAJOR; } else { error("Error: allele type not recognised. Expected one of nref|alt1|minor|major|nonmajor, got \"%s\".\n", atype_string); } } static void usage(args_t *args) { fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "About: VCF/BCF conversion, view, subset and filter VCF/BCF files.\n"); fprintf(bcftools_stderr, "Usage: bcftools view [options] [region1 [...]]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Output options:\n"); fprintf(bcftools_stderr, " -G, --drop-genotypes Drop individual genotype information (after subsetting if -s option set)\n"); fprintf(bcftools_stderr, " -h, --header-only Print only the header in VCF output (equivalent to bcftools head)\n"); fprintf(bcftools_stderr, " -H, --no-header Suppress the header in VCF output\n"); fprintf(bcftools_stderr, " --with-header Print both header and records in VCF output [default]\n"); fprintf(bcftools_stderr, " -l, --compression-level [0-9] Compression level: 0 uncompressed, 1 best speed, 9 best compression [%d]\n", args->clevel); fprintf(bcftools_stderr, " --no-version Do not append version and command line to the header\n"); fprintf(bcftools_stderr, " -o, --output FILE Output file name [bcftools_stdout]\n"); fprintf(bcftools_stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n"); fprintf(bcftools_stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n"); fprintf(bcftools_stderr, " -R, --regions-file FILE Restrict to regions listed in FILE\n"); fprintf(bcftools_stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"); fprintf(bcftools_stderr, " -t, --targets [^]REGION Similar to -r but streams rather than index-jumps. Exclude regions with \"^\" prefix\n"); fprintf(bcftools_stderr, " -T, --targets-file [^]FILE Similar to -R but streams rather than index-jumps. Exclude regions with \"^\" prefix\n"); fprintf(bcftools_stderr, " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"); fprintf(bcftools_stderr, " --threads INT Use multithreading with INT worker threads [0]\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Subset options:\n"); fprintf(bcftools_stderr, " -A, --trim-unseen-allele Remove '<*>' or '' at variant (-A) or at all (-AA) sites\n"); fprintf(bcftools_stderr, " -a, --trim-alt-alleles Trim ALT alleles not seen in the genotype fields (or their subset with -s/-S)\n"); fprintf(bcftools_stderr, " -I, --no-update Do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)\n"); fprintf(bcftools_stderr, " -s, --samples [^]LIST Comma separated list of samples to include (or exclude with \"^\" prefix). Be careful\n"); fprintf(bcftools_stderr, " when combining filtering with sample subsetting as filtering comes (usually) first.\n"); fprintf(bcftools_stderr, " If unsure, split sample subsetting and filtering in two commands, using -Ou when piping.\n"); fprintf(bcftools_stderr, " -S, --samples-file [^]FILE File of samples to include (or exclude with \"^\" prefix)\n"); fprintf(bcftools_stderr, " --force-samples Only warn about unknown subset samples\n"); fprintf(bcftools_stderr, "\n"); fprintf(bcftools_stderr, "Filter options:\n"); fprintf(bcftools_stderr, " -c/C, --min-ac/--max-ac INT[:TYPE] Minimum/maximum count for non-reference (nref), 1st alternate (alt1), least frequent\n"); fprintf(bcftools_stderr, " (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]\n"); fprintf(bcftools_stderr, " -f, --apply-filters LIST Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n"); fprintf(bcftools_stderr, " -g, --genotype [^]hom|het|miss Require one or more hom/het/missing genotype or, if prefixed with \"^\", exclude such sites\n"); fprintf(bcftools_stderr, " -i/e, --include/--exclude EXPR Select/exclude sites for which the expression is true (see man page for details)\n"); fprintf(bcftools_stderr, " -k/n, --known/--novel Select known/novel sites only (ID is not/is '.')\n"); fprintf(bcftools_stderr, " -m/M, --min-alleles/--max-alleles INT Minimum/maximum number of alleles listed in REF and ALT (e.g. -m2 -M2 for biallelic sites)\n"); fprintf(bcftools_stderr, " -p/P, --phased/--exclude-phased Select/exclude sites where all samples are phased\n"); fprintf(bcftools_stderr, " -q/Q, --min-af/--max-af FLOAT[:TYPE] Minimum/maximum frequency for non-reference (nref), 1st alternate (alt1), least frequent\n"); fprintf(bcftools_stderr, " (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]\n"); fprintf(bcftools_stderr, " -u/U, --uncalled/--exclude-uncalled Select/exclude sites without a called genotype\n"); fprintf(bcftools_stderr, " -v/V, --types/--exclude-types LIST Select/exclude comma-separated list of variant types: snps,indels,mnps,ref,bnd,other [null]\n"); fprintf(bcftools_stderr, " -x/X, --private/--exclude-private Select/exclude sites where the non-reference alleles are exclusive (private) to the subset samples\n"); fprintf(bcftools_stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n"); fprintf(bcftools_stderr, "\n"); bcftools_exit(1); } int main_vcfview(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->files = bcf_sr_init(); args->clevel = -1; args->print_header = 1; args->update_info = 1; args->output_type = FT_VCF; args->n_threads = 0; args->record_cmd_line = 1; args->write_index = 0; args->min_ac = args->max_ac = args->min_af = args->max_af = -1; args->regions_overlap = 1; args->targets_overlap = 0; int targets_is_file = 0, regions_is_file = 0; static struct option loptions[] = { {"genotype",required_argument,NULL,'g'}, {"compression-level",required_argument,NULL,'l'}, {"threads",required_argument,NULL,9}, {"header-only",no_argument,NULL,'h'}, {"no-header",no_argument,NULL,'H'}, {"with-header",no_argument,NULL,4}, {"exclude",required_argument,NULL,'e'}, {"include",required_argument,NULL,'i'}, {"trim-alt-alleles",no_argument,NULL,'a'}, {"trim-unseen-allele",no_argument,NULL,'A'}, {"no-update",no_argument,NULL,'I'}, {"drop-genotypes",no_argument,NULL,'G'}, {"private",no_argument,NULL,'x'}, {"exclude-private",no_argument,NULL,'X'}, {"uncalled",no_argument,NULL,'u'}, {"exclude-uncalled",no_argument,NULL,'U'}, {"apply-filters",required_argument,NULL,'f'}, {"known",no_argument,NULL,'k'}, {"novel",no_argument,NULL,'n'}, {"min-alleles",required_argument,NULL,'m'}, {"max-alleles",required_argument,NULL,'M'}, {"samples",required_argument,NULL,'s'}, {"samples-file",required_argument,NULL,'S'}, {"force-samples",no_argument,NULL,1}, {"output-type",required_argument,NULL,'O'}, {"output-file",required_argument,NULL,'o'}, {"output",required_argument,NULL,'o'}, {"types",required_argument,NULL,'v'}, {"exclude-types",required_argument,NULL,'V'}, {"targets",required_argument,NULL,'t'}, {"targets-file",required_argument,NULL,'T'}, {"targets-overlap",required_argument,NULL,2}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,3}, {"min-ac",required_argument,NULL,'c'}, {"max-ac",required_argument,NULL,'C'}, {"min-af",required_argument,NULL,'q'}, {"max-af",required_argument,NULL,'Q'}, {"phased",no_argument,NULL,'p'}, {"exclude-phased",no_argument,NULL,'P'}, {"no-version",no_argument,NULL,8}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "l:t:T:r:R:o:O:s:S:Gf:knv:V:m:M:aAuUhHc:C:Ii:e:xXpPq:Q:g:W::",loptions,NULL)) >= 0) { char allele_type[9] = "nref"; switch (c) { case 'O': switch (optarg[0]) { case 'b': args->output_type = FT_BCF_GZ; break; case 'u': args->output_type = FT_BCF; break; case 'z': args->output_type = FT_VCF_GZ; break; case 'v': args->output_type = FT_VCF; break; default: { args->clevel = strtol(optarg,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); } }; if ( optarg[1] ) { args->clevel = strtol(optarg+1,&tmp,10); if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); } break; case 'l': args->clevel = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --compression-level %s\n", optarg); args->output_type |= FT_GZ; break; case 'o': args->fn_out = optarg; break; case 'H': args->print_header = 0; break; case 'h': args->header_only = 1; break; case 4 : args->print_header = 1; args->header_only = 0; break; case 't': args->targets_list = optarg; break; case 'T': args->targets_list = optarg; targets_is_file = 1; break; case 'r': args->regions_list = optarg; break; case 'R': args->regions_list = optarg; regions_is_file = 1; break; case 's': args->sample_names = optarg; break; case 'S': args->sample_names = optarg; args->sample_is_file = 1; break; case 1 : args->force_samples = 1; break; case 'a': args->trim_alts = 1; args->calc_ac = 1; break; case 'A': args->trim_star_allele++; break; case 'I': args->update_info = 0; break; case 'G': args->sites_only = 1; break; case 'f': args->files->apply_filters = optarg; break; case 'k': args->known = 1; break; case 'n': args->novel = 1; break; case 'm': args->min_alleles = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --min-alleles %s\n", optarg); break; case 'M': args->max_alleles = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --max-alleles %s\n", optarg); break; case 'v': args->include_types = optarg; break; case 'V': args->exclude_types = optarg; break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; case 'c': { args->min_ac_type = ALLELE_NONREF; if ( sscanf(optarg,"%d:%8s",&args->min_ac, allele_type)!=2 && sscanf(optarg,"%d",&args->min_ac)!=1 ) error("Error: Could not parse --min-ac %s\n", optarg); set_allele_type(&args->min_ac_type, allele_type); args->calc_ac = 1; break; } case 'C': { args->max_ac_type = ALLELE_NONREF; if ( sscanf(optarg,"%d:%8s",&args->max_ac, allele_type)!=2 && sscanf(optarg,"%d",&args->max_ac)!=1 ) error("Error: Could not parse --max-ac %s\n", optarg); set_allele_type(&args->max_ac_type, allele_type); args->calc_ac = 1; break; } case 'q': { args->min_af_type = ALLELE_NONREF; if ( sscanf(optarg,"%f:%8s",&args->min_af, allele_type)!=2 && sscanf(optarg,"%f",&args->min_af)!=1 ) error("Error: Could not parse --min-af %s\n", optarg); set_allele_type(&args->min_af_type, allele_type); args->calc_ac = 1; break; } case 'Q': { args->max_af_type = ALLELE_NONREF; if ( sscanf(optarg,"%f:%8s",&args->max_af, allele_type)!=2 && sscanf(optarg,"%f",&args->max_af)!=1 ) error("Error: Could not parse --max-af %s\n", optarg); set_allele_type(&args->max_af_type, allele_type); args->calc_ac = 1; break; } case 'x': args->private_vars |= FLT_INCLUDE; args->calc_ac = 1; break; case 'X': args->private_vars |= FLT_EXCLUDE; args->calc_ac = 1; break; case 'u': args->uncalled |= FLT_INCLUDE; args->calc_ac = 1; break; case 'U': args->uncalled |= FLT_EXCLUDE; args->calc_ac = 1; break; case 'p': args->phased |= FLT_INCLUDE; break; // phased case 'P': args->phased |= FLT_EXCLUDE; break; // exclude-phased case 'g': { if ( !strcasecmp(optarg,"hom") ) args->gt_type = GT_NEED_HOM; else if ( !strcasecmp(optarg,"het") ) args->gt_type = GT_NEED_HET; else if ( !strcasecmp(optarg,"miss") ) args->gt_type = GT_NEED_MISSING; else if ( !strcasecmp(optarg,"^hom") ) args->gt_type = GT_NO_HOM; else if ( !strcasecmp(optarg,"^het") ) args->gt_type = GT_NO_HET; else if ( !strcasecmp(optarg,"^miss") ) args->gt_type = GT_NO_MISSING; else error("The argument to -g not recognised. Expected one of hom/het/miss/^hom/^het/^miss, got \"%s\".\n", optarg); break; } case 2 : args->targets_overlap = parse_overlap_option(optarg); if ( args->targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; case 3 : args->regions_overlap = parse_overlap_option(optarg); if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 9 : args->n_threads = strtol(optarg, 0, 0); break; case 8 : args->record_cmd_line = 0; break; case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break; case '?': usage(args); break; default: error("Unknown argument: %s\n", optarg); } } if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n"); if ( args->private_vars > FLT_EXCLUDE ) error("Only one of -x or -X can be given.\n"); if ( args->uncalled > FLT_EXCLUDE ) error("Only one of -u or -U can be given.\n"); if ( args->phased > FLT_EXCLUDE ) error("Only one of -p or -P can be given.\n"); if ( args->sample_names && args->update_info) args->calc_ac = 1; char *fname = NULL; if ( optind>=argc ) { if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin else usage(args); } else fname = argv[optind]; // read in the regions from the command line if ( args->regions_list ) { bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap); if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions_list); } else if ( optind+1 < argc ) { int i; kstring_t tmp = {0,0,0}; kputs(argv[optind+1],&tmp); for (i=optind+2; ifiles, tmp.s, 0)<0 ) error("Failed to read the regions: %s\n", tmp.s); free(tmp.s); } if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,args->targets_overlap); if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets_list); } if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n"); if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum)); init_data(args); bcf_hdr_t *out_hdr = args->hnull ? args->hnull : (args->hsub ? args->hsub : args->hdr); if (args->print_header) { if ( bcf_hdr_write(args->out, out_hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->fn_out); } else if ( args->output_type & FT_BCF ) error("BCF output requires header, cannot proceed with -H\n"); if ( init_index2(args->out,out_hdr,args->fn_out, &args->index_fn, args->write_index) < 0 ) error("Error: failed to initialise index for %s\n",args->fn_out); int ret = 0; if (!args->header_only) { while ( bcf_sr_next_line(args->files) ) { bcf1_t *line = args->files->readers[0].buffer[0]; if ( line->errcode && out_hdr!=args->hdr ) error("Undefined tags in the header, cannot proceed in the sample subset mode.\n"); if ( subset_vcf(args, line) && bcf_write1(args->out, out_hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->fn_out); } ret = args->files->errnum; if ( ret ) fprintf(bcftools_stderr,"Error: %s\n", bcf_sr_strerror(args->files->errnum)); } if (args->write_index) { if (bcf_idx_save(args->out) < 0) { if ( hts_close(args->out)!=0 ) error("Error: close failed %s\n", args->fn_out?args->fn_out:"bcftools_stdout"); error("Error: cannot write to index %s\n", args->index_fn); } free(args->index_fn); } if ( hts_close(args->out)!=0 ) error("Error: close failed %s\n", args->fn_out?args->fn_out:"bcftools_stdout"); destroy_data(args); bcf_sr_destroy(args->files); free(args); return ret; } pysam-0.23.0/bcftools/vcmp.c000066400000000000000000000106711475062545500156730ustar00rootroot00000000000000/* vcmp.c -- reference allele utility functions. Copyright (C) 2013-2015, 2018 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "vcmp.h" struct _vcmp_t { char *dref; int ndref, mdref; // ndref: positive when ref1 longer, negative when ref2 is longer int nmatch; int *map, mmap, nmap; int *map_dip, mmap_dip, nmap_dip; }; vcmp_t *vcmp_init() { return (vcmp_t*)calloc(1,sizeof(vcmp_t)); } void vcmp_destroy(vcmp_t *vcmp) { free(vcmp->map_dip); free(vcmp->map); free(vcmp->dref); free(vcmp); } int vcmp_set_ref(vcmp_t *vcmp, char *ref1, char *ref2) { vcmp->ndref = 0; char *a = ref1, *b = ref2; while ( *a && *b && toupper(*a)==toupper(*b) ) { a++; b++; } if ( !*a && !*b ) return 0; if ( *a && *b ) return -1; // refs not compatible int i; if ( *a ) // ref1 is longer { vcmp->nmatch = b-ref2; while ( *a ) a++; vcmp->ndref = (a-ref1) - vcmp->nmatch; hts_expand(char,vcmp->ndref+1,vcmp->mdref,vcmp->dref); for (i=0; indref; i++) vcmp->dref[i] = toupper(ref1[vcmp->nmatch+i]); vcmp->dref[vcmp->ndref] = 0; return 0; } // ref2 is longer vcmp->nmatch = a-ref1; while ( *b ) b++; vcmp->ndref = (b-ref2) - vcmp->nmatch; hts_expand(char,vcmp->ndref+1,vcmp->mdref,vcmp->dref); for (i=0; indref; i++) vcmp->dref[i] = toupper(ref2[vcmp->nmatch+i]); vcmp->dref[vcmp->ndref] = 0; vcmp->ndref *= -1; return 0; } int vcmp_find_allele(vcmp_t *vcmp, char **als1, int nals1, char *al2) { int i, j; for (i=0; indref ) { if ( !*a && !*b ) break; // found continue; } // the prefixes match if ( *a ) { if ( vcmp->ndref<0 ) continue; for (j=0; jndref; j++) if ( !a[j] || toupper(a[j])!=vcmp->dref[j] ) break; if ( j!=vcmp->ndref || a[j] ) continue; break; // found } if ( vcmp->ndref>0 ) continue; for (j=0; j<-vcmp->ndref; j++) if ( !b[j] || toupper(b[j])!=vcmp->dref[j] ) break; if ( j!=-vcmp->ndref || b[j] ) continue; break; // found } if (i==nals1) return -1; return i; } int *vcmp_map_ARvalues(vcmp_t *vcmp, int n, int nals1, char **als1, int nals2, char **als2) { if ( vcmp_set_ref(vcmp,als1[0],als2[0]) < 0 ) return NULL; vcmp->nmap = n; hts_expand(int, vcmp->nmap, vcmp->mmap, vcmp->map); int i, ifrom = n==nals2 ? 0 : 1; for (i=ifrom; imap[i-ifrom] = vcmp_find_allele(vcmp, als1+ifrom, nals1-ifrom, als2[i]); } return vcmp->map; } int *vcmp_map_dipGvalues(vcmp_t *vcmp, int *nmap) { vcmp->nmap_dip = vcmp->nmap*(vcmp->nmap+1)/2; hts_expand(int, vcmp->nmap_dip, vcmp->mmap_dip, vcmp->map_dip); int i, j, k = 0; for (i=0; inmap; i++) { for (j=0; j<=i; j++) { vcmp->map_dip[k] = vcmp->map[i]>=0 && vcmp->map[j]>=0 ? bcf_alleles2gt(vcmp->map[i],vcmp->map[j]) : -1; k++; } } *nmap = k; return vcmp->map_dip; } pysam-0.23.0/bcftools/vcmp.c.pysam.c000066400000000000000000000107261475062545500172450ustar00rootroot00000000000000#include "bcftools.pysam.h" /* vcmp.c -- reference allele utility functions. Copyright (C) 2013-2015, 2018 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "vcmp.h" struct _vcmp_t { char *dref; int ndref, mdref; // ndref: positive when ref1 longer, negative when ref2 is longer int nmatch; int *map, mmap, nmap; int *map_dip, mmap_dip, nmap_dip; }; vcmp_t *vcmp_init() { return (vcmp_t*)calloc(1,sizeof(vcmp_t)); } void vcmp_destroy(vcmp_t *vcmp) { free(vcmp->map_dip); free(vcmp->map); free(vcmp->dref); free(vcmp); } int vcmp_set_ref(vcmp_t *vcmp, char *ref1, char *ref2) { vcmp->ndref = 0; char *a = ref1, *b = ref2; while ( *a && *b && toupper(*a)==toupper(*b) ) { a++; b++; } if ( !*a && !*b ) return 0; if ( *a && *b ) return -1; // refs not compatible int i; if ( *a ) // ref1 is longer { vcmp->nmatch = b-ref2; while ( *a ) a++; vcmp->ndref = (a-ref1) - vcmp->nmatch; hts_expand(char,vcmp->ndref+1,vcmp->mdref,vcmp->dref); for (i=0; indref; i++) vcmp->dref[i] = toupper(ref1[vcmp->nmatch+i]); vcmp->dref[vcmp->ndref] = 0; return 0; } // ref2 is longer vcmp->nmatch = a-ref1; while ( *b ) b++; vcmp->ndref = (b-ref2) - vcmp->nmatch; hts_expand(char,vcmp->ndref+1,vcmp->mdref,vcmp->dref); for (i=0; indref; i++) vcmp->dref[i] = toupper(ref2[vcmp->nmatch+i]); vcmp->dref[vcmp->ndref] = 0; vcmp->ndref *= -1; return 0; } int vcmp_find_allele(vcmp_t *vcmp, char **als1, int nals1, char *al2) { int i, j; for (i=0; indref ) { if ( !*a && !*b ) break; // found continue; } // the prefixes match if ( *a ) { if ( vcmp->ndref<0 ) continue; for (j=0; jndref; j++) if ( !a[j] || toupper(a[j])!=vcmp->dref[j] ) break; if ( j!=vcmp->ndref || a[j] ) continue; break; // found } if ( vcmp->ndref>0 ) continue; for (j=0; j<-vcmp->ndref; j++) if ( !b[j] || toupper(b[j])!=vcmp->dref[j] ) break; if ( j!=-vcmp->ndref || b[j] ) continue; break; // found } if (i==nals1) return -1; return i; } int *vcmp_map_ARvalues(vcmp_t *vcmp, int n, int nals1, char **als1, int nals2, char **als2) { if ( vcmp_set_ref(vcmp,als1[0],als2[0]) < 0 ) return NULL; vcmp->nmap = n; hts_expand(int, vcmp->nmap, vcmp->mmap, vcmp->map); int i, ifrom = n==nals2 ? 0 : 1; for (i=ifrom; imap[i-ifrom] = vcmp_find_allele(vcmp, als1+ifrom, nals1-ifrom, als2[i]); } return vcmp->map; } int *vcmp_map_dipGvalues(vcmp_t *vcmp, int *nmap) { vcmp->nmap_dip = vcmp->nmap*(vcmp->nmap+1)/2; hts_expand(int, vcmp->nmap_dip, vcmp->mmap_dip, vcmp->map_dip); int i, j, k = 0; for (i=0; inmap; i++) { for (j=0; j<=i; j++) { vcmp->map_dip[k] = vcmp->map[i]>=0 && vcmp->map[j]>=0 ? bcf_alleles2gt(vcmp->map[i],vcmp->map[j]) : -1; k++; } } *nmap = k; return vcmp->map_dip; } pysam-0.23.0/bcftools/vcmp.h000066400000000000000000000046061475062545500157010ustar00rootroot00000000000000/* vcmp.h -- reference allele utility functions. Copyright (C) 2013-2015 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef __VCMP_H__ #define __VCMP_H__ typedef struct _vcmp_t vcmp_t; vcmp_t *vcmp_init(void); void vcmp_destroy(vcmp_t *vcmp); /* * vcmp_set_ref() - sets and compares reference alleles * Returns 0 on success or -1 if alleles not compatible */ int vcmp_set_ref(vcmp_t *vcmp, char *ref1, char *ref2); /* * vcmp_find_allele() * @param als1: alternate alleles to ref1 above * @param al2: alternate allele to ref2 above * Returns -1 if not found or 0-based index to als1 of matching allele */ int vcmp_find_allele(vcmp_t *vcmp, char **als1, int nals1, char *al2); /* * vcmp_map_ARvalues() - Create mapping for Number=A,R tag values * @param number: nals2 for Number=R, nals2-1 for Number=A * @param nals1: number of alleles * @param als1: alleles * * Returns pointer to an array of size nals2 with mapping from als2 * to als1 or NULL if REFs (als1[0] and als2[0]) are not compatible. * If i is the index of an allele in als2, ret[i] is the index of matching * allele in als1 or -1 if als2 does not have a matching allele. * The caller must not free the array. */ int *vcmp_map_ARvalues(vcmp_t *vcmp, int number, int nals1, char **als1, int nals2, char **als2); int *vcmp_map_dipGvalues(vcmp_t *vcmp, int *nmap); #endif pysam-0.23.0/bcftools/version.c000066400000000000000000000136751475062545500164220ustar00rootroot00000000000000/* version.c -- report version numbers for plugins. Copyright (C) 2014-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "bcftools.h" #include "version.h" void version(const char **bcftools_version, const char **htslib_version) { *bcftools_version = BCFTOOLS_VERSION; *htslib_version = hts_version(); } void error(const char *format, ...) { va_list ap; va_start(ap, format); vfprintf(stderr, format, ap); va_end(ap); exit(-1); } void error_errno(const char *format, ...) { va_list ap; int e = errno; va_start(ap, format); vfprintf(stderr, format, ap); va_end(ap); if (e) { fprintf(stderr, ": %s\n", strerror(e)); } else { fprintf(stderr, "\n"); } exit(-1); } const char *hts_bcf_wmode(int file_type) { if ( file_type == FT_BCF ) return "wbu"; // uncompressed BCF if ( file_type & FT_BCF ) return "wb"; // compressed BCF if ( file_type & FT_GZ ) return "wz"; // compressed VCF return "w"; // uncompressed VCF } const char *hts_bcf_wmode2(int file_type, const char *fname) { if ( !fname ) return hts_bcf_wmode(file_type); const char *end = fname ? strstr(fname, HTS_IDX_DELIM) : NULL; if ( !end ) end = fname ? fname + strlen(fname) : fname; int len = end - fname; if ( len >= 4 && !strncasecmp(".bcf",fname+len-4,4) ) return hts_bcf_wmode(FT_BCF|FT_GZ); if ( len >= 4 && !strncasecmp(".vcf",fname+len-4,4) ) return hts_bcf_wmode(FT_VCF); if ( len >= 7 && !strncasecmp(".vcf.gz",fname+len-7,7) ) return hts_bcf_wmode(FT_VCF|FT_GZ); if ( len >= 8 && !strncasecmp(".vcf.bgz",fname+len-8,8) ) return hts_bcf_wmode(FT_VCF|FT_GZ); return hts_bcf_wmode(file_type); } void set_wmode(char dst[8], int file_type, const char *fname, int clevel) { const char *ret = NULL; const char *end = fname ? strstr(fname, HTS_IDX_DELIM) : NULL; if ( !end ) end = fname ? fname + strlen(fname) : fname; int len = end - fname; if ( len >= 4 && !strncasecmp(".bcf",fname+len-4,4) ) ret = hts_bcf_wmode(file_type & FT_BCF ? file_type : FT_BCF|FT_GZ); else if ( len >= 4 && !strncasecmp(".vcf",fname+len-4,4) ) ret = hts_bcf_wmode(FT_VCF); else if ( len >= 7 && !strncasecmp(".vcf.gz",fname+len-7,7) ) ret = hts_bcf_wmode(FT_VCF|FT_GZ); else if ( len >= 8 && !strncasecmp(".vcf.bgz",fname+len-8,8) ) ret = hts_bcf_wmode(FT_VCF|FT_GZ); else ret = hts_bcf_wmode(file_type); if ( clevel>=0 && clevel<=9 ) { if ( strchr(ret,'v') || strchr(ret,'u') ) error("Error: compression level (%d) cannot be set on uncompressed streams (%s)\n",clevel,fname); len = strlen(ret); if ( len>6 ) error("Fixme: %s\n", ret); sprintf(dst, "%s%d", ret, clevel); } else strcpy(dst, ret); } int parse_overlap_option(const char *arg) { if ( strcasecmp(arg, "pos") == 0 || strcmp(arg, "0") == 0 ) return 0; else if ( strcasecmp(arg, "record") == 0 || strcmp(arg, "1") == 0 ) return 1; else if ( strcasecmp(arg, "variant") == 0 || strcmp(arg, "2") == 0 ) return 2; else return -1; } // Used to set args->write_index in CLI. // It will be true if set correctly. // Note due to HTS_FMT_CSI being zero we have to use an additional bit. int write_index_parse(char *arg) { int fmt = HTS_FMT_CSI; if (arg) { if (strcmp(arg, "csi") == 0 || strcmp(arg, "=csi") == 0) fmt = HTS_FMT_CSI; else if (strcmp(arg, "tbi") == 0 || strcmp(arg, "=tbi") == 0) fmt = HTS_FMT_TBI; else return 0; } return 128 | fmt; } // See also samtools/sam_utils.c auto_index() int init_index2(htsFile *fh, bcf_hdr_t *hdr, const char *fname, char **idx_fname, int idx_fmt) { // Nothing to do == success. This simplifies the main code simpler. if (!idx_fmt) return 0; int min_shift; char *idx_suffix; if (idx_fmt && (idx_fmt&127) == HTS_FMT_TBI && fh->format.format == vcf) { min_shift = 0; // TBI idx_suffix = "tbi"; } else { min_shift = 14; // CSI idx_suffix = "csi"; } if ( !fname || !*fname || !strcmp(fname, "-") ) return -1; char *delim = strstr(fname, HTS_IDX_DELIM); if (delim) { delim += strlen(HTS_IDX_DELIM); *idx_fname = strdup(delim); if ( !*idx_fname ) return -1; size_t l = strlen(*idx_fname); if ( l >= 4 && strcmp(*idx_fname + l - 4, ".tbi")==0 ) min_shift = 0; } else { if ( !(*idx_fname = malloc(strlen(fname)+6)) ) return -1; sprintf(*idx_fname, "%s.%s", fname, idx_suffix); } if ( bcf_idx_init(fh, hdr, min_shift, *idx_fname) < 0 ) return -1; return 0; } int init_index(htsFile *fh, bcf_hdr_t *hdr, const char *fname, char **idx_fname) { return init_index2(fh,hdr, fname, idx_fname, HTS_FMT_CSI); } pysam-0.23.0/bcftools/version.c.pysam.c000066400000000000000000000140201475062545500177540ustar00rootroot00000000000000#include "bcftools.pysam.h" /* version.c -- report version numbers for plugins. Copyright (C) 2014-2024 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "bcftools.h" #include "version.h" void version(const char **bcftools_version, const char **htslib_version) { *bcftools_version = BCFTOOLS_VERSION; *htslib_version = hts_version(); } void error(const char *format, ...) { va_list ap; va_start(ap, format); vfprintf(bcftools_stderr, format, ap); va_end(ap); bcftools_exit(-1); } void error_errno(const char *format, ...) { va_list ap; int e = errno; va_start(ap, format); vfprintf(bcftools_stderr, format, ap); va_end(ap); if (e) { fprintf(bcftools_stderr, ": %s\n", strerror(e)); } else { fprintf(bcftools_stderr, "\n"); } bcftools_exit(-1); } const char *hts_bcf_wmode(int file_type) { if ( file_type == FT_BCF ) return "wbu"; // uncompressed BCF if ( file_type & FT_BCF ) return "wb"; // compressed BCF if ( file_type & FT_GZ ) return "wz"; // compressed VCF return "w"; // uncompressed VCF } const char *hts_bcf_wmode2(int file_type, const char *fname) { if ( !fname ) return hts_bcf_wmode(file_type); const char *end = fname ? strstr(fname, HTS_IDX_DELIM) : NULL; if ( !end ) end = fname ? fname + strlen(fname) : fname; int len = end - fname; if ( len >= 4 && !strncasecmp(".bcf",fname+len-4,4) ) return hts_bcf_wmode(FT_BCF|FT_GZ); if ( len >= 4 && !strncasecmp(".vcf",fname+len-4,4) ) return hts_bcf_wmode(FT_VCF); if ( len >= 7 && !strncasecmp(".vcf.gz",fname+len-7,7) ) return hts_bcf_wmode(FT_VCF|FT_GZ); if ( len >= 8 && !strncasecmp(".vcf.bgz",fname+len-8,8) ) return hts_bcf_wmode(FT_VCF|FT_GZ); return hts_bcf_wmode(file_type); } void set_wmode(char dst[8], int file_type, const char *fname, int clevel) { const char *ret = NULL; const char *end = fname ? strstr(fname, HTS_IDX_DELIM) : NULL; if ( !end ) end = fname ? fname + strlen(fname) : fname; int len = end - fname; if ( len >= 4 && !strncasecmp(".bcf",fname+len-4,4) ) ret = hts_bcf_wmode(file_type & FT_BCF ? file_type : FT_BCF|FT_GZ); else if ( len >= 4 && !strncasecmp(".vcf",fname+len-4,4) ) ret = hts_bcf_wmode(FT_VCF); else if ( len >= 7 && !strncasecmp(".vcf.gz",fname+len-7,7) ) ret = hts_bcf_wmode(FT_VCF|FT_GZ); else if ( len >= 8 && !strncasecmp(".vcf.bgz",fname+len-8,8) ) ret = hts_bcf_wmode(FT_VCF|FT_GZ); else ret = hts_bcf_wmode(file_type); if ( clevel>=0 && clevel<=9 ) { if ( strchr(ret,'v') || strchr(ret,'u') ) error("Error: compression level (%d) cannot be set on uncompressed streams (%s)\n",clevel,fname); len = strlen(ret); if ( len>6 ) error("Fixme: %s\n", ret); sprintf(dst, "%s%d", ret, clevel); } else strcpy(dst, ret); } int parse_overlap_option(const char *arg) { if ( strcasecmp(arg, "pos") == 0 || strcmp(arg, "0") == 0 ) return 0; else if ( strcasecmp(arg, "record") == 0 || strcmp(arg, "1") == 0 ) return 1; else if ( strcasecmp(arg, "variant") == 0 || strcmp(arg, "2") == 0 ) return 2; else return -1; } // Used to set args->write_index in CLI. // It will be true if set correctly. // Note due to HTS_FMT_CSI being zero we have to use an additional bit. int write_index_parse(char *arg) { int fmt = HTS_FMT_CSI; if (arg) { if (strcmp(arg, "csi") == 0 || strcmp(arg, "=csi") == 0) fmt = HTS_FMT_CSI; else if (strcmp(arg, "tbi") == 0 || strcmp(arg, "=tbi") == 0) fmt = HTS_FMT_TBI; else return 0; } return 128 | fmt; } // See also samtools/sam_utils.c auto_index() int init_index2(htsFile *fh, bcf_hdr_t *hdr, const char *fname, char **idx_fname, int idx_fmt) { // Nothing to do == success. This simplifies the main code simpler. if (!idx_fmt) return 0; int min_shift; char *idx_suffix; if (idx_fmt && (idx_fmt&127) == HTS_FMT_TBI && fh->format.format == vcf) { min_shift = 0; // TBI idx_suffix = "tbi"; } else { min_shift = 14; // CSI idx_suffix = "csi"; } if ( !fname || !*fname || !strcmp(fname, "-") ) return -1; char *delim = strstr(fname, HTS_IDX_DELIM); if (delim) { delim += strlen(HTS_IDX_DELIM); *idx_fname = strdup(delim); if ( !*idx_fname ) return -1; size_t l = strlen(*idx_fname); if ( l >= 4 && strcmp(*idx_fname + l - 4, ".tbi")==0 ) min_shift = 0; } else { if ( !(*idx_fname = malloc(strlen(fname)+6)) ) return -1; sprintf(*idx_fname, "%s.%s", fname, idx_suffix); } if ( bcf_idx_init(fh, hdr, min_shift, *idx_fname) < 0 ) return -1; return 0; } int init_index(htsFile *fh, bcf_hdr_t *hdr, const char *fname, char **idx_fname) { return init_index2(fh,hdr, fname, idx_fname, HTS_FMT_CSI); } pysam-0.23.0/bcftools/version.sh000077500000000000000000000027221475062545500166040ustar00rootroot00000000000000#!/bin/sh # version.sh # # Author : Petr Danecek # # Copyright (C) 2018-2021 Genome Research Ltd. # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. # Master version, for use in tarballs or non-git source copies VERSION=1.21 # If we have a git clone, then check against the current tag if [ -e .git ] then # If we ever get to 10.x this will need to be more liberal VERSION=`git describe --match '[0-9].[0-9]*' --dirty --always` fi echo $VERSION pysam-0.23.0/devtools/000077500000000000000000000000001475062545500146015ustar00rootroot00000000000000pysam-0.23.0/devtools/artifactname.py000077500000000000000000000010221475062545500176070ustar00rootroot00000000000000#!/usr/bin/env python3 import os import re import sys pattern = re.compile(r'-cp([^-]*)-cp[^-]*-([^_]*)[0-9_]*_([^.]*)') vers = set() plats = set() arches = set() for fname in sys.argv[1:]: m = pattern.search(fname) vers.add(int(m[1])) plats.add(m[2]) arches.add(m[3]) plat = '-'.join(sorted(plats)) arch = '-'.join(sorted(arches)) ver = '-'.join(map(str, sorted(vers))) tag = os.environ.get('NAMETAG', 'none') tag = f'-{tag}' if tag != 'none' else '' print(f'artifactname=wheels-{plat}-{arch}-{ver}{tag}') pysam-0.23.0/devtools/buildwheels.sh000077500000000000000000000050011475062545500174430ustar00rootroot00000000000000#!/bin/bash # # Build manylinux1 wheels for pysam. Based on the example at # # # It is best to run this in a fresh clone of the repository! # # Before running, make sure to update image: # # docker pull quay.io/pypa/manylinux1_x86_64 # # Run this within the repository root: # docker run --rm -v $(pwd):/io quay.io/pypa/manylinux1_x86_64 /io/buildwheels.sh # # The wheels will be put into the wheelhouse/ subdirectory. # # For interactive tests: # docker run -it -v $(pwd):/io quay.io/pypa/manylinux1_x86_64 /bin/bash set -xeuo pipefail # For convenience, if this script is called from outside of a docker container, # it starts a container and runs itself inside of it. if ! grep -q docker /proc/1/cgroup; then # We are not inside a container exec docker run --rm -v $(pwd):/io quay.io/pypa/manylinux1_x86_64 /io/$0 fi yum install -y zlib-devel bzip2-devel xz-devel # Without libcurl support, htslib can open files from HTTP and FTP URLs. # With libcurl support, it also supports HTTPS and S3 URLs, but libcurl needs a # current version of OpenSSL, and we do not want to be responsible for # updating the wheels as soon as there are any security issues. So disable # libcurl for now. # See also . # export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl" PYBINS="/opt/python/*/bin" echo $PYBINS for PYBIN in ${PYBINS}; do ${PYBIN}/pip install -r /io/requirements.txt ${PYBIN}/pip wheel /io/ -w wheelhouse/ done # Bundle external shared libraries into the wheels # # The '-L ""' option is a workaround. By default, auditwheel puts all external # libraries (.so files) into a .libs directory and sets the RUNPATH to $ORIGIN/.libs. # When HTSLIB_MODE is 'shared' (now the default), then all so libraries part of # pysam require that RUNPATH is set to $ORIGIN (without the .libs). It seems # auditwheel overwrites $ORIGIN with $ORIGIN/.libs. This workaround makes # auditwheel keeps the RUNPATH at "$ORIGIN" and put all the external libraries into # the pysam directory. for whl in wheelhouse/*.whl; do auditwheel repair -L "" $whl -w /io/wheelhouse/ done # mkdir -p /io/wheelhouse # cp wheelhouse/*.whl /io/wheelhouse # Created files are owned by root, so fix permissions. chown -R --reference=/io/setup.py /io/wheelhouse/ # TODO Install packages and test them for PYBIN in ${PYBINS}; do ${PYBIN}/pip install pysam --no-index -f /io/wheelhouse # smoketest (cd $HOME; ${PYBIN}/python -c 'import pysam') # todo: add more tests done pysam-0.23.0/devtools/check-platform.sh000077500000000000000000000011141475062545500200340ustar00rootroot00000000000000#!/bin/sh -e case $1 in ubuntu-*-arm) expected=arm ;; macos-13) expected=x86_64 ;; ubuntu-*) expected=x86_64 ;; macos-*) expected=arm ;; windows-*) expected=x86_64 ;; *) echo Unknown platform $1 >&2 exit 2 ;; esac arch=$(uname -m) case $arch in arm*|aarch*) actual=arm ;; x86*) actual=x86_64 ;; *) echo Unrecognized uname result $arch >&2 exit 2 ;; esac if test $actual = $expected then echo Running on $arch as expected exit 0 else echo Platform $arch is not the expected $expected >&2 exit 1 fi pysam-0.23.0/devtools/conda-recipe/000077500000000000000000000000001475062545500171325ustar00rootroot00000000000000pysam-0.23.0/devtools/conda-recipe/build.sh000066400000000000000000000003341475062545500205650ustar00rootroot00000000000000#!/bin/bash # Use internal htslib chmod a+x ./htslib/configure export CFLAGS="-I${PREFIX}/include/curl/ -I${PREFIX}/include -L${PREFIX}/lib" export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl" $PYTHON setup.py install pysam-0.23.0/devtools/conda-recipe/meta.yaml000066400000000000000000000007221475062545500207450ustar00rootroot00000000000000package: name: pysam version: 0.8.5 source: path: ../../ build: number: 0 requirements: build: - python - setuptools - zlib - cython run: - python - zlib test: imports: - pysam about: home: https://github.com/pysam-developers/pysam license: MIT summary: Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. pysam-0.23.0/devtools/environment-dev.yaml000066400000000000000000000001401475062545500206000ustar00rootroot00000000000000channels: - conda-forge - bioconda dependencies: - bzip2 - cython - setuptools - xz pysam-0.23.0/devtools/import.py000066400000000000000000000241541475062545500164730ustar00rootroot00000000000000################################################################# # Importing samtools, bcftools, and htslib # # For each package PKG: # # rm -rf PKG # python import.py PKG path/to/download/PKG-X.Y import fnmatch import os from pathlib import Path import re import itertools import shutil import sys import hashlib EXCLUDE = { "samtools": ( "test", "misc", "bgzip.c", "main.c", "calDepth.c", "bam2bed.c", "bam_tview.c", "bam_tview.h", "bam_tview_html.c", "bam_tview_curses.c", "bam2bcf.c", "bam2bcf.h", "vcf-miniview.c", ), "bcftools": ( "test", "plugins", "peakfit.c", "peakfit.h", "polysomy.c"), "htslib": ( 'annot-tsv.c', 'bgzip.c', 'htsfile.c', 'tabix.c', 'hts_probe_cc.sh', "samples", "test", "tests"), } MAIN = { "samtools": "bamtk", "bcftools": "main" } C_VERSION = { "htslib": "HTS_VERSION_TEXT", "samtools": "SAMTOOLS_VERSION", "bcftools": "BCFTOOLS_VERSION" } def locate(pattern, root=os.curdir, exclude=[], exclude_htslib=False): '''Locate all files matching supplied filename pattern (but not listed in exclude) in and below the supplied root directory. Omit any files under directories listed in exclude or (if exclude_htslib=True) matching /htslib-*/. ''' for path, dirs, files in os.walk(os.path.abspath(root)): for filename in fnmatch.filter(files, pattern): if filename not in exclude: yield os.path.join(path, filename) for dirname in exclude: if dirname in dirs: dirs.remove(dirname) if exclude_htslib: for dirname in [d for d in dirs if re.match(r"htslib-", d)]: dirs.remove(dirname) def _update_pysam_files(cf, destdir): '''update pysam files applying redirection of ouput''' basename = os.path.basename(destdir) for filename in cf: if not filename: continue dest = filename + ".pysam.c" with open(filename, encoding="utf-8") as infile: lines = "".join(infile.readlines()) with open(dest, "w", encoding="utf-8") as outfile: outfile.write('#include "{}.pysam.h"\n\n'.format(basename)) subname, _ = os.path.splitext(os.path.basename(filename)) if subname in MAIN.get(basename, []): lines = re.sub(r"int main\(", "int {}_main(".format( basename), lines) else: lines = re.sub(r"int main\(", "int {}_{}_main(".format( basename, subname), lines) lines = re.sub(r"\b({}_stdout)\b".format(basename), r"\1_internal", lines) lines = re.sub(r"\bexit\(", "{}_exit(".format(basename), lines) lines = re.sub(r"\bstderr\b", "{}_stderr".format(basename), lines) lines = re.sub(r"\bstdout\b", "{}_stdout".format(basename), lines) lines = re.sub(r" printf\(", " fprintf({}_stdout, ".format(basename), lines) lines = re.sub(r"([^kf])puts\(", r"\1{}_puts(".format(basename), lines) lines = re.sub(r"putchar\(([^)]+)\)", r"fputc(\1, {}_stdout)".format(basename), lines) fn = os.path.basename(filename) # some specific fixes: SPECIFIC_SUBSTITUTIONS = { "bam_md.c": ( 'sam_open_format("-", mode_w', 'sam_open_format({}_stdout_fn, mode_w'.format(basename)), "phase.c": ( 'putc("ACGT"[f->seq[j] == 1? (c&3, {}_stdout) : (c>>16&3)]);'.format(basename), 'putc("ACGT"[f->seq[j] == 1? (c&3) : (c>>16&3)], {}_stdout);'.format(basename)), "cut_target.c": ( 'putc(33 + (cns[j]>>8>>2, {}_stdout));'.format(basename), 'putc(33 + (cns[j]>>8>>2), {}_stdout);'.format(basename)) } if fn in SPECIFIC_SUBSTITUTIONS: lines = lines.replace( SPECIFIC_SUBSTITUTIONS[fn][0], SPECIFIC_SUBSTITUTIONS[fn][1]) if fn == "bamtk.c": lines = re.sub(r'(#include "version.h")', r'\1\n#include "samtools_config_vars.h"', lines) lines = re.sub(r'(else if.*"tview")', r'//\1', lines) lines = re.sub(r'(if[ (]*fclose)', r'if (0) { //\1', lines) outfile.write(lines) with open(os.path.join("import", "pysam.h")) as inf, \ open(os.path.join(destdir, "{}.pysam.h".format(basename)), "w") as outf: outf.write(re.sub("@pysam@", basename, inf.read())) with open(os.path.join("import", "pysam.c")) as inf, \ open(os.path.join(destdir, "{}.pysam.c".format(basename)), "w") as outf: outf.write(re.sub("@pysam@", basename, inf.read())) if len(sys.argv) >= 1: if len(sys.argv) != 3: raise ValueError("import requires dest src") dest, srcdir = sys.argv[1:3] if dest not in EXCLUDE: raise ValueError("import expected one of %s" % ",".join(EXCLUDE.keys())) exclude = EXCLUDE[dest] destdir = os.path.abspath(dest) srcdir = os.path.abspath(srcdir) if not os.path.exists(srcdir): raise IOError( "source directory `%s` does not exist." % srcdir) cfiles = locate("*.c", srcdir, exclude=exclude, exclude_htslib=True) hfiles = locate("*.h", srcdir, exclude=exclude, exclude_htslib=True) mfiles = itertools.chain(locate("README", srcdir), locate("LICENSE", srcdir), locate("version.sh", srcdir, exclude_htslib=True)) if dest == "htslib": # Add build files, including *.ac config.{guess,sub} *.in *.mk *.m4 *.sh mfiles = itertools.chain(mfiles, locate("Makefile", srcdir), locate("configure", srcdir), locate("config.*", srcdir), locate("*.[aims][cnk4h]", srcdir, exclude)) ncopied = 0 def _compareAndCopy(src, srcdir, destdir, exclude): d, f = os.path.split(src) common_prefix = os.path.commonprefix((d, srcdir)) subdir = re.sub(common_prefix, "", d)[1:] targetdir = os.path.join(destdir, subdir) if not os.path.exists(targetdir): os.makedirs(targetdir) old_file = os.path.join(targetdir, f) if os.path.exists(old_file): md5_old = hashlib.md5( "".join(open(old_file, "r", encoding="utf-8").readlines()).encode()).digest() md5_new = hashlib.md5( "".join(open(src, "r", encoding="utf-8").readlines()).encode()).digest() if md5_old != md5_new: raise ValueError( "incompatible files for %s and %s" % (old_file, src)) shutil.copy(src, targetdir) return old_file for src_file in hfiles: _compareAndCopy(src_file, srcdir, destdir, exclude) ncopied += 1 for src_file in mfiles: _compareAndCopy(src_file, srcdir, destdir, exclude) ncopied += 1 cf = [] for src_file in cfiles: cf.append(_compareAndCopy(src_file, srcdir, destdir, exclude)) ncopied += 1 sys.stdout.write( "installed latest source code from %s: " "%i files copied\n" % (srcdir, ncopied)) if dest in MAIN: # redirect stderr to pysamerr and replace bam.h with a stub. sys.stdout.write("applying stderr redirection\n") _update_pysam_files(cf, destdir) def _getVersion(srcdir): with open(os.path.join(srcdir, "version.sh"), encoding="utf-8") as inf: for line in inf: m = re.match(r"VERSION=(\S+)", line) if m: return m.group(1) raise ValueError("no VERSION line in version.sh") def _update_version_file(key, value, filename): tmpfilename = filename + ".tmp" with open(filename, encoding="utf-8") as inf: with open(tmpfilename, "w", encoding="utf-8") as outf: for line in inf: if key in line: line = re.sub(r'"[^"]*"', '"{}"'.format(value), line) outf.write(line) os.rename(tmpfilename, filename) def _update_version_doc_file(dest, value, filename): tmpfilename = filename + ".tmp" with open(filename, encoding="utf-8") as inf: with open(tmpfilename, "w", encoding="utf-8") as outf: for line in inf: if " wraps " in line: # hide the sentence's fullstop from the main regexp line = re.sub(r'\.$', ',DOT', line) line = re.sub(r'{}-[^*,]*'.format(dest), '{}-{}'.format(dest, value), line) line = re.sub(',DOT', '.', line) outf.write(line) os.rename(tmpfilename, filename) version = _getVersion(srcdir) _update_version_file("__{}_version__".format(dest), version, "pysam/version.py") _update_version_file(C_VERSION[dest], version + " (pysam)", "pysam/version.h") _update_version_doc_file(dest, version, "README.rst") _update_version_doc_file(dest, version, "doc/index.rst") if dest in MAIN: path = Path("doc/conf.py") path.write_text(re.sub(rf"doc/[\d.]*/{dest}", rf"doc/{version}/{dest}", path.read_text())) sys.exit(0) # if len(sys.argv) >= 2 and sys.argv[1] == "refresh": # sys.stdout.write("refreshing latest source code from .c to .pysam.c") # # redirect stderr to pysamerr and replace bam.h with a stub. # sys.stdout.write("applying stderr redirection") # for destdir in ('samtools', ): # pysamcfiles = locate("*.pysam.c", destdir) # for f in pysamcfiles: # os.remove(f) # cfiles = locate("*.c", destdir) # _update_pysam_files(cfiles, destdir) # sys.exit(0) pysam-0.23.0/devtools/install-CGAT-tools.sh000077500000000000000000000136041475062545500204640ustar00rootroot00000000000000#!/usr/bin/env bash # function to detect the Operating System detect_os(){ if [ -f /etc/os-release ]; then OS=$(cat /etc/os-release | awk '/VERSION_ID/ {sub("="," "); print $2;}' | sed 's/\"//g' | awk '{sub("\\."," "); print $1;}') if [ "$OS" != "12" ] ; then echo echo " Ubuntu version not supported " echo echo " Only Ubuntu 12.x has been tested so far " echo exit 1; fi OS="ubuntu" elif [ -f /etc/system-release ]; then OS=$(cat /etc/system-release | awk ' {print $4;}' | awk '{sub("\\."," "); print $1;}') if [ "$OS" != "6" ] ; then echo echo " Scientific Linux version not supported " echo echo " Only 6.x Scientific Linux has been tested so far " echo exit 1; fi OS="sl" else echo echo " Operating system not supported " echo echo " Exiting installation " echo exit 1; fi } # detect_os # message to display when the OS is not correct sanity_check_os() { echo echo " Unsupported operating system: $OS " echo " Installation aborted " echo exit 1; } # sanity_check_os # function to install operating system dependencies install_os_packages() { if [ "$OS" == "ubuntu" -o "$OS" == "travis" ] ; then echo echo " Installing packages for Ubuntu " echo apt-get install -y gcc g++ elif [ "$OS" == "sl" ] ; then echo echo " Installing packages for Scientific Linux " echo yum -y install gcc zlib-devel gcc-c++ else sanity_check_os fi # if-OS } # install_os_packages # function to install Python dependencies install_python_deps() { if [ "$OS" == "ubuntu" -o "$OS" == "sl" ] ; then echo echo " Installing Python dependencies for $1 " echo # Create virtual environment cd mkdir CGAT cd CGAT wget --no-check-certificate https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.10.1.tar.gz tar xvfz virtualenv-1.10.1.tar.gz rm virtualenv-1.10.1.tar.gz cd virtualenv-1.10.1 python virtualenv.py cgat-venv source cgat-venv/bin/activate # Install Python prerequisites pip install cython elif [ "$OS" == "travis" ] ; then # Travis-CI provides a virtualenv with Python 2.7 echo echo " Installing Python dependencies in travis " echo # Install Python prerequisites pip install cython pip install nose else sanity_check_os fi # if-OS } # install_python_deps # common set of tasks to prepare external dependencies nosetests_external_deps() { echo echo " Running nosetests for $1 " echo pushd . # create a new folder to store external tools mkdir -p $HOME/CGAT/external-tools # install samtools cd $HOME/CGAT/external-tools curl -L http://downloads.sourceforge.net/project/samtools/samtools/1.3/samtools-1.3.tar.bz2 > samtools-1.3.tar.bz2 tar xjf samtools-1.3.tar.bz2 cd samtools-1.3 make PATH=$PATH:$HOME/CGAT/external-tools/samtools-1.3 echo "installed samtools" samtools --version if [ $? != 0 ]; then exit 1 fi # install bcftools cd $HOME/CGAT/external-tools curl -L https://github.com/samtools/bcftools/releases/download/1.3/bcftools-1.3.tar.bz2 > bcftools-1.3.tar.bz2 tar xjf bcftools-1.3.tar.bz2 cd bcftools-1.3 make PATH=$PATH:$HOME/CGAT/external-tools/bcftools-1.3 echo "installed bcftools" bcftools --version if [ $? != 0 ]; then exit 1 fi popd } # nosetests_external_deps # function to run nosetests run_nosetests() { echo echo " Running nosetests for $1 " echo # prepare external dependencies nosetests_external_deps $OS # install code python setup.py install # change into tests directory. Otherwise, # 'import pysam' will import the repository, # not the installed version. This causes # problems in the compilation test. cd tests # create auxiliary data echo echo 'building test data' echo make -C pysam_data all make -C cbcf_data all make -C tabix_data all # run nosetests # -s: do not capture stdout, conflicts with pysam.dispatch # -v: verbose output nosetests -s -v } # run_nosetests # function to display help message help_message() { echo echo " Use this script as follows: " echo echo " 1) Become root and install the operating system* packages: " echo " ./install-CGAT-tools.sh --install-os-packages" echo echo " 2) Now, as a normal user (non root), install the Python dependencies**: " echo " ./install-CGAT-tools.sh --install-python-deps" echo echo " At this stage the CGAT Code Collection is ready to go and you do not need further steps. Please type the following for more information:" echo " source $HOME/CGAT/virtualenv-1.10.1/cgat-venv/bin/activate" echo " cgat --help " echo echo " The CGAT Code Collection tests the software with nosetests. If you are interested in running those, please continue with the following steps:" echo echo " 3) Become root to install external tools and set up the environment: " echo " ./install-CGAT-tools.sh --install-nosetests-deps" echo echo " 4) Then, back as a normal user (non root), run nosetests as follows:" echo " ./install-CGAT-tools.sh --run-nosetests" echo echo " NOTES: " echo " * Supported operating systems: Ubuntu 12.x and Scientific Linux 6.x " echo " ** An isolated virtual environment will be created to install Python dependencies " echo exit 1; } # the main script starts here if [ $# -eq 0 -o $# -gt 1 ] ; then help_message else if [ "$1" == "--help" ] ; then help_message elif [ "$1" == "--travis" ] ; then OS="travis" install_os_packages install_python_deps run_nosetests elif [ "$1" == "--install-os-packages" ] ; then detect_os install_os_packages elif [ "$1" == "--install-python-deps" ] ; then detect_os install_python_deps elif [ "$1" == "--install-nosetests-deps" ] ; then detect_os install_nosetests_deps elif [ "$1" == "--run-nosetests" ] ; then detect_os run_nosetests else echo echo " Incorrect input parameter: $1 " help_message fi # if argument 1 fi # if number of input parameters pysam-0.23.0/devtools/install-prerequisites.sh000077500000000000000000000023711475062545500215130ustar00rootroot00000000000000#!/bin/sh -e if test -x /usr/bin/dnf; then echo Installing prerequisites via dnf... dnf -y install epel-release dnf -y install zlib-devel bzip2-devel xz-devel curl-devel openssl-devel samtools bcftools htslib-tools elif test -x /usr/bin/yum; then if yum -y install epel-release; then echo Installing prerequisites via yum... yum -y install zlib-devel bzip2-devel xz-devel curl-devel openssl-devel samtools bcftools htslib-tools else echo Installing non-test prerequisites via yum... yum -y install zlib-devel bzip2-devel xz-devel curl-devel openssl-devel fi elif test -d /etc/dpkg; then echo Installing prerequisites via apt-get... apt-get update apt-get install -y --no-install-recommends --no-install-suggests libcurl4-openssl-dev libssl-dev zlib1g-dev libbz2-dev liblzma-dev samtools bcftools tabix elif test -x /sbin/apk; then echo Installing non-test prerequisites via apk... apk update apk add zlib-dev bzip2-dev xz-dev curl-dev openssl-dev elif test -x ${HOMEBREW_PREFIX-/usr/local}/bin/brew; then echo Installing prerequisites via brew... HOMEBREW_NO_AUTO_UPDATE=1 brew install -q samtools bcftools brew unlink xz || true else echo No package manager detected fi pysam-0.23.0/devtools/run_tests_travis.sh000077500000000000000000000070371475062545500205650ustar00rootroot00000000000000#!/usr/bin/env bash # test script for pysam. # The script performs the following tasks: # 1. Setup a conda environment and install dependencies via conda # 2. Build pysam via the conda recipe # 3. Build pysam via setup.py from repository # 4. Run tests on the setup.py version # 5. Additional build tests # 5.1 pip install with cython # 5.2 pip install without cython # 5.3 pip install without cython and without configure options pushd . WORKDIR=`pwd` #Install miniconda python if [ $TRAVIS_OS_NAME == "osx" ]; then wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O Miniconda3.sh else wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O Miniconda3.sh --no-check-certificate # Default OS versions are old and have SSL / CERT issues fi bash Miniconda3.sh -b # Create a new conda environment with the target python version ~/miniconda3/bin/conda install conda-build -y ~/miniconda3/bin/conda create -q -y --name testenv python=$CONDA_PY cython numpy pytest psutil pip # activate testenv environment source ~/miniconda3/bin/activate testenv conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge # pin versions, so that tests do not fail when pysam/htslib out of step # add htslib dependencies # NB: force conda-forge:blas due to conda/conda#7548 conda install -y "samtools>=1.11" "bcftools>=1.11" "htslib>=1.11" xz curl bzip2 "conda-forge::blas=*=openblas" # As HTSLIB_MODE is (defaulted to) 'shared', ensure we don't pick up # the external headers from the Conda-installed htslib package. mv $CONDA_PREFIX/include/htslib $CONDA_PREFIX/include/htslib-disable export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl" echo "show samtools, htslib, and bcftools versions" samtools --version htsfile --version bcftools --version # Try building conda recipe first ~/miniconda3/bin/conda-build devtools/conda-recipe/ --python=$CONDA_PY # install code from the repository via setup.py echo echo "============ installing via setup.py from repository ============" echo python setup.py install || exit # create auxiliary data echo echo 'building test data' echo make -C tests/pysam_data make -C tests/cbcf_data make -C tests/tabix_data # echo any limits that are in place ulimit -a # run tests pytest if [ $? != 0 ]; then exit 1 fi # build source tar-ball. Make sure to run 'build' target so that .pyx # files are cythonized. python setup.py build sdist if [ $? != 0 ]; then exit 1 fi # check for presence of config.h files echo "checking for presence of config.h files in tar-ball" tar -tvzf dist/pysam-*.tar.gz | grep "config.h$" if [ $? != 1 ]; then echo "ERROR: found config.h in tar-ball" tar -tvzf dist/pysam-*.tar.gz | grep "config.h%" exit 1 fi # test pip installation from tar-ball with cython echo "pip installing with cython" pip install --verbose --no-deps --no-binary=:all: dist/pysam-*.tar.gz if [ $? != 0 ]; then exit 1 fi # attempt pip installation without cython echo "pip installing without cython" ~/miniconda3/bin/conda remove -y cython ~/miniconda3/bin/conda list echo "python is" `which python` pip install --verbose --no-deps --no-binary=:all: --force-reinstall --upgrade dist/pysam-*.tar.gz if [ $? != 0 ]; then exit 1 fi # attempt pip installation without cython and without # command line options echo "pip installing without cython and no configure options" export HTSLIB_CONFIGURE_OPTIONS="" pip install --verbose --no-deps --no-binary=:all: --force-reinstall --upgrade dist/pysam-*.tar.gz if [ $? != 0 ]; then exit 1 fi pysam-0.23.0/doc/000077500000000000000000000000001475062545500135075ustar00rootroot00000000000000pysam-0.23.0/doc/Makefile000066400000000000000000000062251475062545500151540ustar00rootroot00000000000000# Makefile for Sphinx documentation # # You can set these variables from the command line. SPHINXOPTS = SPHINXBUILD = sphinx-build PAPER = # Internal variables. PAPEROPT_a4 = -D latex_paper_size=a4 PAPEROPT_letter = -D latex_paper_size=letter ALLSPHINXOPTS = -d _build/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . DIR_PUBLISH=/ifs/home/andreas/public_html/documentation/pysam .PHONY: help clean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest help: @echo "Please use \`make ' where is one of" @echo " html to make standalone HTML files" @echo " dirhtml to make HTML files named index.html in directories" @echo " pickle to make pickle files" @echo " json to make JSON files" @echo " htmlhelp to make HTML files and a HTML help project" @echo " qthelp to make HTML files and a qthelp project" @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" @echo " changes to make an overview of all changed/added/deprecated items" @echo " linkcheck to check all external links for integrity" @echo " doctest to run all doctests embedded in the documentation (if enabled)" @echo " publish to copy the HTML documentation to the server." clean: -rm -rf _build/* html: $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) _build/html @echo @echo "Build finished. The HTML pages are in _build/html." dirhtml: $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) _build/dirhtml @echo @echo "Build finished. The HTML pages are in _build/dirhtml." pickle: $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) _build/pickle @echo @echo "Build finished; now you can process the pickle files." json: $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) _build/json @echo @echo "Build finished; now you can process the JSON files." htmlhelp: $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) _build/htmlhelp @echo @echo "Build finished; now you can run HTML Help Workshop with the" \ ".hhp project file in _build/htmlhelp." qthelp: $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) _build/qthelp @echo @echo "Build finished; now you can run "qcollectiongenerator" with the" \ ".qhcp project file in _build/qthelp, like this:" @echo "# qcollectiongenerator _build/qthelp/samtools.qhcp" @echo "To view the help file:" @echo "# assistant -collectionFile _build/qthelp/samtools.qhc" latex: $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) _build/latex @echo @echo "Build finished; the LaTeX files are in _build/latex." @echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \ "run these through (pdf)latex." changes: $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) _build/changes @echo @echo "The overview file is in _build/changes." linkcheck: $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) _build/linkcheck @echo @echo "Link check complete; look for any errors in the above output " \ "or in _build/linkcheck/output.txt." doctest: $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) _build/doctest @echo "Testing of doctests in the sources finished, look at the " \ "results in _build/doctest/output.txt." publish: rm -rf $(DIR_PUBLISH) mkdir -p $(DIR_PUBLISH) cp -r _build/html/* $(DIR_PUBLISH) pysam-0.23.0/doc/api.rst000066400000000000000000000133641475062545500150210ustar00rootroot00000000000000============ Introduction ============ Pysam is a python module that makes it easy to read and manipulate mapped short read sequence data stored in SAM/BAM files. It is a lightweight wrapper of the htslib_ C-API. This page provides a quick introduction in using pysam followed by the API. See :ref:`usage` for more detailed usage instructions. To use the module to read a file in BAM format, create a :class:`~pysam.AlignmentFile` object:: import pysam samfile = pysam.AlignmentFile("ex1.bam", "rb") Once a file is opened you can iterate over all of the read mapping to a specified region using :meth:`~pysam.AlignmentFile.fetch`. Each iteration returns a :class:`~pysam.AlignedSegment` object which represents a single read along with its fields and optional tags:: for read in samfile.fetch('chr1', 100, 120): print(read) samfile.close() To give:: EAS56_57:6:190:289:82 0 99 <<<7<<<;<<<<<<<<8;;<7;4<;<;;;;;94<; 69 CTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA 0 192 1 EAS56_57:6:190:289:82 0 99 <<<<<<;<<<<<<<<<<;<<;<<<<;8<6;9;;2; 137 AGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCAC 73 64 1 EAS51_64:3:190:727:308 0 102 <<<<<<<<<<<<<<<<<<<<<<<<<<<::<<<844 99 GGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGG 99 18 1 ... You can also write to a :class:`~pysam.AlignmentFile`:: import pysam samfile = pysam.AlignmentFile("ex1.bam", "rb") pairedreads = pysam.AlignmentFile("allpaired.bam", "wb", template=samfile) for read in samfile.fetch(): if read.is_paired: pairedreads.write(read) pairedreads.close() samfile.close() An alternative way of accessing the data in a SAM file is by iterating over each base of a specified region using the :meth:`~pysam.AlignmentFile.pileup` method. Each iteration returns a :class:`~pysam.PileupColumn` which represents all the reads in the SAM file that map to a single base in the reference sequence. The list of reads are represented as :class:`~pysam.PileupRead` objects in the :attr:`PileupColumn.pileups ` property:: import pysam samfile = pysam.AlignmentFile("ex1.bam", "rb" ) for pileupcolumn in samfile.pileup("chr1", 100, 120): print("\ncoverage at base %s = %s" % (pileupcolumn.pos, pileupcolumn.n)) for pileupread in pileupcolumn.pileups: if not pileupread.is_del and not pileupread.is_refskip: # query position is None if is_del or is_refskip is set. print('\tbase in read %s = %s' % (pileupread.alignment.query_name, pileupread.alignment.query_sequence[pileupread.query_position])) samfile.close() The above code outputs:: coverage at base 99 = 1 base in read EAS56_57:6:190:289:82 = A coverage at base 100 = 1 base in read EAS56_57:6:190:289:82 = G coverage at base 101 = 1 base in read EAS56_57:6:190:289:82 = G coverage at base 102 = 2 base in read EAS56_57:6:190:289:82 = G base in read EAS51_64:3:190:727:308 = G ... Commands available in `samtools`_ are available as simple function calls. For example:: pysam.sort("-o", "output.bam", "ex1.bam") corresponds to the command line:: samtools sort -o output.bam ex1.bam Analogous to :class:`~pysam.AlignmentFile`, a :class:`~pysam.TabixFile` allows fast random access to compressed and tabix indexed tab-separated file formats with genomic data:: import pysam tabixfile = pysam.TabixFile("example.gtf.gz") for gtf in tabixfile.fetch("chr1", 1000, 2000): print(gtf.contig, gtf.start, gtf.end, gtf.gene_id) :class:`~pysam.TabixFile` implements lazy parsing in order to iterate over large tables efficiently. More detailed usage instructions is at :ref:`usage`. .. note:: Coordinates in pysam are always 0-based (following the python convention). SAM text files use 1-based coordinates. .. note:: The above examples can be run in the :file:`tests` directory of the installation directory. Type 'make' before running them. .. seealso:: https://github.com/pysam-developers/pysam The pysam code repository, containing source code and download instructions http://pysam.readthedocs.org/en/latest/ The pysam website containing documentation === API === SAM/BAM/CRAM files ================== Objects of type :class:`~pysam.AlignmentFile` allow working with BAM/SAM formatted files. .. autoclass:: pysam.AlignmentFile :members: .. autoclass:: pysam.AlignmentHeader :members: An :class:`~pysam.AlignedSegment` represents an aligned segment within a SAM/BAM file. .. autoclass:: pysam.AlignedSegment :members: .. autoclass:: pysam.PileupColumn :members: .. autoclass:: pysam.PileupRead :members: .. autoclass:: pysam.IndexedReads :members: Tabix files =========== :class:`~pysam.TabixFile` opens tabular files that have been indexed with tabix_. .. autoclass:: pysam.TabixFile :members: To iterate over tabix files, use :func:`~pysam.tabix_iterator`: .. autofunction:: pysam.tabix_iterator .. autofunction:: pysam.tabix_compress .. autofunction:: pysam.tabix_index .. autoclass:: pysam.asTuple :members: .. autoclass:: pysam.asVCF :members: .. autoclass:: pysam.asBed :members: .. autoclass:: pysam.asGTF :members: FASTA files =========== .. autoclass:: pysam.FastaFile :members: FASTQ files =========== .. autoclass:: pysam.FastxFile :members: .. autoclass:: pysam.FastqProxy :members: VCF/BCF files ============= .. autoclass:: pysam.VariantFile :members: .. autoclass:: pysam.VariantHeader :members: .. autoclass:: pysam.VariantRecord :members: .. autoclass:: pysam.VariantHeaderRecord :members: HTSFile ======= HTSFile is the base class for :class:`pysam.AlignmentFile` and :class:`pysam.VariantFile`. .. autoclass:: pysam.HTSFile :members: pysam-0.23.0/doc/benchmarking.rst000066400000000000000000000376751475062545500167130ustar00rootroot00000000000000.. _Benchmarking: ============ Benchmarking ============ Latest benchmarking results:: ------------------------------------------------------------------------------------------------------------------------ benchmark: 57 tests ------------------------------------------------------------------------------------------------------------------------ Name (time in us) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- test_set_binary_tag 93.8382 (1.0) 199.8786 (1.0) 96.1554 (1.0) 2.6241 (1.0) 95.7036 (1.0) 1.2442 (1.0) 276;303 10,399.8372 (1.0) 3170 1 test_fasta_iteration_long_sequences_without_persistence 145.3292 (1.55) 296.4940 (1.48) 176.5367 (1.84) 30.0896 (11.47) 167.2544 (1.75) 25.1532 (20.22) 840;579 5,664.5438 (0.54) 4972 1 test_fasta_iteration_long_sequences_as_file 149.0638 (1.59) 312.6319 (1.56) 177.2990 (1.84) 30.5218 (11.63) 168.6383 (1.76) 27.7516 (22.30) 669;510 5,640.1883 (0.54) 4493 1 test_fasta_iteration_long_sequences 150.3211 (1.60) 429.9153 (2.15) 176.7384 (1.84) 30.7021 (11.70) 167.5002 (1.75) 21.7482 (17.48) 682;647 5,658.0803 (0.54) 4845 1 test_fasta_iteration_short_sequences_as_file 190.6604 (2.03) 395.8736 (1.98) 216.6984 (2.25) 32.8710 (12.53) 208.9385 (2.18) 16.8057 (13.51) 291;326 4,614.7086 (0.44) 3205 1 test_read_python_uncompressed 214.1297 (2.28) 450.2051 (2.25) 234.6956 (2.44) 33.3642 (12.71) 223.4913 (2.34) 15.0129 (12.07) 140;221 4,260.8375 (0.41) 2043 1 test_fastq_iteration_short_sequences_as_file 217.5961 (2.32) 420.1643 (2.10) 238.0264 (2.48) 30.4469 (11.60) 228.8874 (2.39) 15.5573 (12.50) 209;235 4,201.2146 (0.40) 2877 1 test_iterate_file_uncompressed 225.5719 (2.40) 481.0989 (2.41) 249.7603 (2.60) 40.7266 (15.52) 239.5548 (2.50) 15.9908 (12.85) 209;327 4,003.8387 (0.38) 3627 1 test_iterate_file_compressed 257.5517 (2.74) 576.6843 (2.89) 287.2536 (2.99) 49.8803 (19.01) 277.4149 (2.90) 14.3824 (11.56) 126;248 3,481.2446 (0.33) 3023 1 test_iterate_generic_uncompressed 344.8855 (3.68) 712.5959 (3.57) 370.9369 (3.86) 46.2477 (17.62) 365.0384 (3.81) 15.7915 (12.69) 54;83 2,695.8763 (0.26) 2240 1 test_iterate_parsed_uncompressed 349.3819 (3.72) 765.3460 (3.83) 378.1446 (3.93) 54.2199 (20.66) 369.5488 (3.86) 15.4320 (12.40) 48;69 2,644.4910 (0.25) 1638 1 test_read_python_compressed 462.0645 (4.92) 836.2234 (4.18) 493.6158 (5.13) 51.2946 (19.55) 485.5469 (5.07) 11.4385 (9.19) 28;46 2,025.8670 (0.19) 906 1 test_iterate_parsed_compressed 586.5730 (6.25) 1,050.1631 (5.25) 632.5464 (6.58) 82.6438 (31.49) 608.1080 (6.35) 20.1799 (16.22) 115;143 1,580.9117 (0.15) 1474 1 test_iterate_generic_compressed 587.7707 (6.26) 1,093.4286 (5.47) 639.6830 (6.65) 85.2593 (32.49) 612.6408 (6.40) 19.9433 (16.03) 105;144 1,563.2743 (0.15) 1260 1 test_fasta_iteration_short_sequences_without_persistence 725.2563 (7.73) 1,091.6069 (5.46) 774.6549 (8.06) 53.0901 (20.23) 751.8455 (7.86) 45.0788 (36.23) 172;110 1,290.8974 (0.12) 1276 1 test_read_binary_tag 817.2598 (8.71) 1,232.0559 (6.16) 902.7002 (9.39) 87.7807 (33.45) 871.5261 (9.11) 17.4227 (14.00) 39;55 1,107.7875 (0.11) 331 1 test_fastq_iteration_short_sequences_without_persistence 840.3640 (8.96) 1,201.5756 (6.01) 870.9679 (9.06) 35.8709 (13.67) 866.1682 (9.05) 15.9768 (12.84) 53;85 1,148.1480 (0.11) 1124 1 test_count_number_lines_from_sam_with_pysam 2,755.6140 (29.37) 9,656.9806 (48.31) 2,963.2206 (30.82) 729.0077 (277.81) 2,814.3115 (29.41) 106.2388 (85.38) 8;14 337.4707 (0.03) 281 1 test_fasta_iteration_short_sequences 2,905.5942 (30.96) 3,674.1439 (18.38) 2,982.3892 (31.02) 90.9585 (34.66) 2,941.2108 (30.73) 96.1348 (77.26) 27;7 335.3016 (0.03) 302 1 test_fastq_iteration_short_sequences 3,601.3145 (38.38) 4,065.5769 (20.34) 3,671.8361 (38.19) 71.5348 (27.26) 3,635.1625 (37.98) 81.5415 (65.53) 43;10 272.3433 (0.03) 243 1 test_count_number_lines_from_bam_with_pysam 4,178.8872 (44.53) 12,063.5536 (60.35) 4,395.9713 (45.72) 794.3991 (302.73) 4,240.1757 (44.31) 67.0198 (53.86) 6;19 227.4810 (0.02) 205 1 test_build_depth_from_bam_with_pysam 6,290.2980 (67.03) 6,788.0806 (33.96) 6,420.3862 (66.77) 126.5447 (48.22) 6,357.6270 (66.43) 94.3104 (75.80) 35;29 155.7539 (0.01) 145 1 test_build_depth_with_filter_from_bam_with_pysam 6,935.8926 (73.91) 8,309.5767 (41.57) 7,085.6801 (73.69) 221.5069 (84.41) 7,005.6170 (73.20) 74.4388 (59.83) 14;27 141.1297 (0.01) 139 1 test_build_query_positions_from_bam_with_pysam 8,729.2437 (93.02) 16,836.6525 (84.23) 9,173.2902 (95.40) 1,057.4321 (402.97) 8,885.4395 (92.84) 264.7634 (212.79) 3;9 109.0121 (0.01) 103 1 test_build_mapping_qualities_from_bam_with_pysam 8,805.0570 (93.83) 15,829.8910 (79.20) 9,274.7475 (96.46) 964.6925 (367.63) 9,004.7438 (94.09) 354.9103 (285.24) 4;9 107.8196 (0.01) 106 1 test_build_query_qualities_from_bam_with_pysam 8,947.6798 (95.35) 16,756.8158 (83.83) 9,272.9117 (96.44) 1,008.7759 (384.43) 9,017.0493 (94.22) 217.2068 (174.57) 3;5 107.8410 (0.01) 94 1 test_build_query_bases_from_bam_with_samtoolspysam 9,149.0448 (97.50) 9,776.0092 (48.91) 9,208.3405 (95.77) 86.1889 (32.85) 9,190.2809 (96.03) 34.1963 (27.48) 5;7 108.5972 (0.01) 84 1 test_count_number_lines_from_bam_with_samtoolspipe 10,431.4052 (111.16) 13,431.7447 (67.20) 11,052.2360 (114.94) 445.8241 (169.90) 11,014.8042 (115.09) 492.6044 (395.91) 17;3 90.4794 (0.01) 90 1 test_count_number_lines_from_bam_with_samtools 12,057.8520 (128.50) 13,537.5429 (67.73) 12,595.0708 (130.99) 381.1799 (145.26) 12,499.5783 (130.61) 457.8107 (367.94) 25;1 79.3961 (0.01) 73 1 test_count_number_lines_from_sam_with_samtoolspipe 12,434.8756 (132.51) 14,234.1983 (71.21) 13,034.1032 (135.55) 371.0373 (141.40) 13,049.9089 (136.36) 464.8147 (373.57) 21;3 76.7218 (0.01) 72 1 test_build_query_bases_from_bam_with_pysam 12,811.6887 (136.53) 19,972.7099 (99.92) 13,268.7908 (137.99) 1,103.9459 (420.70) 13,023.1632 (136.08) 202.3596 (162.64) 4;6 75.3648 (0.01) 76 1 test_build_pileup_from_bam_with_samtoolspipe 13,480.7490 (143.66) 15,413.4836 (77.11) 13,968.3817 (145.27) 362.1282 (138.00) 13,917.4843 (145.42) 447.9736 (360.04) 12;3 71.5903 (0.01) 66 1 test_count_number_lines_from_sam_with_samtools 13,963.2300 (148.80) 15,936.2238 (79.73) 14,442.5627 (150.20) 340.4846 (129.75) 14,395.4996 (150.42) 339.3036 (272.70) 12;2 69.2398 (0.01) 59 1 test_build_pileup_from_bam_with_samtoolsshell 15,140.2969 (161.34) 16,469.8567 (82.40) 15,525.9034 (161.47) 256.0741 (97.59) 15,526.7641 (162.24) 318.5044 (255.98) 13;2 64.4085 (0.01) 51 1 test_build_depth_from_bam_with_samtoolsshell 15,291.4841 (162.96) 16,387.9916 (81.99) 15,656.5365 (162.83) 217.2420 (82.79) 15,609.9945 (163.11) 258.9412 (208.11) 16;2 63.8711 (0.01) 57 1 test_build_query_bases_from_bam_with_samtoolspipe 15,478.0652 (164.94) 17,068.8462 (85.40) 16,072.5749 (167.15) 327.6668 (124.87) 16,040.5049 (167.61) 428.1597 (344.11) 18;2 62.2178 (0.01) 60 1 test_build_query_bases_from_bam_with_samtoolsshell 15,765.5794 (168.01) 17,102.8059 (85.57) 16,305.4955 (169.57) 367.6865 (140.12) 16,256.2486 (169.86) 593.9230 (477.34) 20;0 61.3290 (0.01) 57 1 test_build_depth_from_bam_with_samtoolspipe 16,024.7944 (170.77) 25,804.2309 (129.10) 17,041.3497 (177.23) 1,522.0046 (580.01) 16,726.8887 (174.78) 767.1015 (616.52) 1;1 58.6808 (0.01) 40 1 test_build_query_qualities_from_bam_with_samtoolspipe 16,275.7467 (173.44) 18,501.0433 (92.56) 17,262.6517 (179.53) 642.2656 (244.76) 17,255.3696 (180.30) 1,060.3429 (852.20) 20;0 57.9285 (0.01) 51 1 test_build_pileup_from_bam_with_pysam 16,632.5681 (177.25) 19,306.6560 (96.59) 17,037.7162 (177.19) 531.0751 (202.38) 16,870.8330 (176.28) 279.1677 (224.37) 3;4 58.6933 (0.01) 32 1 test_build_mapping_qualities_from_bam_with_samtoolspipe 17,398.3518 (185.41) 18,481.6569 (92.46) 17,832.1261 (185.45) 294.9103 (112.39) 17,837.8206 (186.39) 511.8400 (411.37) 21;0 56.0786 (0.01) 52 1 test_build_query_names_from_bam_with_pysam 31,534.0199 (336.05) 38,316.2647 (191.70) 32,677.2804 (339.84) 1,371.6101 (522.70) 32,179.0325 (336.24) 1,392.1391 (>1000.0) 3;1 30.6023 (0.00) 30 1 test_fetch_plain 43,747.1233 (466.20) 48,690.7829 (243.60) 44,573.8085 (463.56) 1,170.8588 (446.20) 44,067.5411 (460.46) 1,436.5837 (>1000.0) 3;1 22.4347 (0.00) 22 1 test_build_query_positions_from_bam_with_samtoolspipe 46,316.5548 (493.58) 53,700.3577 (268.66) 48,235.6640 (501.64) 1,861.0317 (709.21) 47,625.2194 (497.63) 2,603.7074 (>1000.0) 6;1 20.7315 (0.00) 21 1 test_build_query_bases_with_reference_from_bam_with_samtoolspysam 51,565.1479 (549.51) 53,523.1121 (267.78) 51,778.6650 (538.49) 424.4621 (161.76) 51,656.8925 (539.76) 110.5051 (88.81) 1;4 19.3130 (0.00) 20 1 test_build_query_bases_with_reference_from_bam_with_pysam 58,850.6740 (627.15) 62,164.5451 (311.01) 60,161.6779 (625.67) 1,120.6101 (427.05) 59,595.2785 (622.71) 1,995.0196 (>1000.0) 7;0 16.6219 (0.00) 16 1 test_iterate_file_large_uncompressed 59,419.9076 (633.22) 69,053.0874 (345.48) 62,825.7126 (653.38) 3,805.1150 (>1000.0) 60,805.1391 (635.35) 6,407.6949 (>1000.0) 3;0 15.9170 (0.00) 14 1 test_iterate_file_large_compressed 63,986.9571 (681.89) 74,156.9120 (371.01) 68,370.8835 (711.05) 3,254.6200 (>1000.0) 67,221.2075 (702.39) 4,770.3525 (>1000.0) 5;0 14.6261 (0.00) 16 1 test_read_python_large_uncompressed 67,611.8080 (720.51) 89,112.1533 (445.83) 73,631.8916 (765.76) 5,978.7052 (>1000.0) 71,702.4822 (749.21) 7,856.0165 (>1000.0) 2;1 13.5811 (0.00) 13 1 test_fetch_parsed 72,237.5344 (769.81) 81,976.9856 (410.13) 74,540.4099 (775.21) 2,326.3668 (886.54) 74,016.3419 (773.39) 1,579.0667 (>1000.0) 1;1 13.4155 (0.00) 14 1 test_build_query_bases_from_bam_with_pysam_pileups 75,841.3766 (808.21) 87,975.1425 (440.14) 79,393.9784 (825.68) 3,516.2458 (>1000.0) 79,346.7313 (829.09) 5,217.5033 (>1000.0) 2;0 12.5954 (0.00) 13 1 test_build_query_bases_with_reference_from_bam_with_samtoolspipe 131,162.9396 (>1000.0) 132,858.8147 (664.70) 131,838.0199 (>1000.0) 595.6090 (226.98) 131,801.5633 (>1000.0) 956.9665 (769.11) 2;0 7.5851 (0.00) 8 1 test_iterate_parsed_large_uncompressed 132,991.8914 (>1000.0) 140,153.4099 (701.19) 134,101.5892 (>1000.0) 2,452.3161 (934.54) 133,218.1590 (>1000.0) 396.3616 (318.56) 1;1 7.4570 (0.00) 8 1 test_iterate_generic_large_uncompressed 134,743.7277 (>1000.0) 142,329.4526 (712.08) 138,167.4954 (>1000.0) 3,346.7773 (>1000.0) 136,839.1849 (>1000.0) 6,541.1879 (>1000.0) 4;0 7.2376 (0.00) 8 1 test_read_python_large_compressed 175,127.6311 (>1000.0) 190,855.1529 (954.86) 181,702.9339 (>1000.0) 5,756.2207 (>1000.0) 181,221.0185 (>1000.0) 8,577.6616 (>1000.0) 2;0 5.5035 (0.00) 6 1 test_iterate_parsed_large_compressed 231,405.7611 (>1000.0) 243,728.8519 (>1000.0) 239,037.8296 (>1000.0) 5,212.7778 (>1000.0) 241,544.3324 (>1000.0) 8,062.6113 (>1000.0) 1;0 4.1834 (0.00) 5 1 test_iterate_generic_large_compressed 235,042.3876 (>1000.0) 256,518.8371 (>1000.0) 242,535.5468 (>1000.0) 8,272.5197 (>1000.0) 240,163.0748 (>1000.0) 8,360.1568 (>1000.0) 1;0 4.1231 (0.00) 5 1 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- pysam-0.23.0/doc/conf.py000066400000000000000000000203631475062545500150120ustar00rootroot00000000000000# -*- coding: utf-8 -*- # # samtools documentation build configuration file, created by # sphinx-quickstart on Wed Aug 12 14:43:42 2009. # # This file is execfile()d with the current directory set to its containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. import sys, os, re, setuptools # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. _build_obj = setuptools.dist.Distribution().get_command_obj('build') _build_obj.ensure_finalized() _libdir = os.path.join('..', _build_obj.build_platlib) if os.path.exists(_libdir): sys.path.insert(0, os.path.abspath(_libdir)) # -- General configuration ----------------------------------------------------- # Add any Sphinx extension module names here, as strings. They can be extensions # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'sphinx.ext.extlinks', 'sphinx.ext.todo', 'sphinx.ext.ifconfig', 'sphinx.ext.intersphinx', 'sphinx.ext.napoleon'] intersphinx_mapping = {'python': ('https://docs.python.org/%d.%d' % sys.version_info[:2], None)} # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix of source filenames. source_suffix = '.rst' # The encoding of source files. #source_encoding = 'utf-8' # The master toctree document. master_doc = 'index' # General information about the project. project = u'pysam' copyright = '2009–2025 Andreas Heger, John Marshall, Kevin Jacobs, et al' # Included at the end of each rst file rst_epilog = ''' .. _pysam: https://github.com/pysam-developers/pysam .. _samtools: https://www.htslib.org/doc/1.21/samtools.html .. _bcftools: https://www.htslib.org/doc/1.21/bcftools.html .. _htslib: https://www.htslib.org/ .. _tabix: https://www.htslib.org/doc/tabix.html .. _Galaxy: https://usegalaxy.org/ .. _cython: https://cython.org/ .. _python: https://www.python.org/ .. _PyPI: https://pypi.org/ .. _pip: https://pip.pypa.io/ .. _pyximport: https://github.com/cython/cython/tree/master/pyximport .. _conda: https://conda.io/docs/ .. _bioconda: https://bioconda.github.io/ .. _sphinx: https://www.sphinx-doc.org/en/master/usage/installation.html ''' autosummary_generate = True # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # import pysam.version # The short X.Y version. version = pysam.version.__version__ # The full version, including alpha/beta/rc tags. release = version # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: # today = '' # Else, today_fmt is used as the format for a strftime call. # today_fmt = '%B %d, %Y' # List of documents that shouldn't be included in the build. # unused_docs = [] # List of directories, relative to source directory, that shouldn't be searched # for source files. exclude_trees = ['_build'] # The reST default role (used for this markup: `text`) to use for all documents. # default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. # add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). # add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. # show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. #modindex_common_prefix = [] # -- Rewrite "PR #NNN" and "#NNN" in NEWS as URL links ------------------------- extlinks = { 'issue': ('https://github.com/pysam-developers/pysam/issues/%s', '#%s'), 'pull': ('https://github.com/pysam-developers/pysam/pull/%s', 'PR #%s'), } def expand_github_references(text): text = re.sub(r'PR\s*#(\d+)', r':pull:`\1`', text) text = re.sub(r'#(\d+)', r':issue:`\1`', text) return text def include_read(app, relative_path, parent_docname, source): if relative_path.name == 'NEWS': source[0] = expand_github_references(source[0]) def setup(app): try: app.connect('include-read', include_read) except: pass # Sphinx is too old to link issues/PRs # -- Options for HTML output --------------------------------------------------- # The theme to use for HTML and HTML Help pages. Major themes that come with # Sphinx are currently 'default' and 'sphinxdoc'. html_theme = 'sphinx_rtd_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # html_theme_options = {} # Add any paths that contain custom themes here, relative to this directory. # html_theme_path = [] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". # html_title = None # A shorter title for the navigation bar. Default is the same as html_title. # html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. # html_logo = None # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. # html_favicon = None # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = [] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. # html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. # html_use_smartypants = True # Custom sidebar templates, maps document names to template names. # html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. # html_additional_pages = {} # If false, no module index is generated. # html_use_modindex = True # If false, no index is generated. # html_use_index = True # If true, the index is split into individual pages for each letter. # html_split_index = False # If true, links to the reST sources are added to the pages. # html_show_sourcelink = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. # html_use_opensearch = '' # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml"). # html_file_suffix = '' # Output file base name for HTML help builder. htmlhelp_basename = 'samtoolsdoc' # -- Options for LaTeX output -------------------------------------------------- # The paper size ('letter' or 'a4'). # latex_paper_size = 'letter' # The font size ('10pt', '11pt' or '12pt'). # latex_font_size = '10pt' # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ ('index', 'pysam.tex', u'pysam documentation', 'Andreas Heger, John Marshall, Kevin Jacobs, et al', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. # latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. # latex_use_parts = False # Additional stuff for the LaTeX preamble. # latex_preamble = '' # Documents to append as an appendix to all manuals. # latex_appendices = [] # If false, no module index is generated. # latex_use_modindex = True pysam-0.23.0/doc/developer.rst000066400000000000000000000047101475062545500162300ustar00rootroot00000000000000================= Developer's guide ================= Code organization ================= The top level directory is organized in the following directories: :file:`pysam` Code specific to pysam. :file:`doc` The documentation. To build the latest documentation, first install `Sphinx`_ and then type:: make -C doc html :file:`tests` Code and data for testing and benchmarking. :file:`htslib` Source code from `htslib`_ shipped with pysam. See :file:`import.py` about importing. :file:`samtools` Source code from `samtools`_ shipped with pysam. See :file:`import.py` about importing. :file:`bcftools` Source code from `bcftools`_ shipped with pysam. See :file:`import.py` about importing. Python language level ===================== Pysam currently requires Python 3.6 as a minimum language level. For example, this means that the following comparatively recent language features and library functions are available for use: * f-strings * ``raise ... from None`` * :meth:`str.startswith`, :meth:`str.endswith`, :meth:`str.rstrip`, etc However in particular the the following should not be used in pysam source code or infrastructure scripts: * :meth:`str.removeprefix`, :meth:`str.removesuffix` (new in 3.9) * walrus ``:=`` operator (new in 3.8) Importing new versions of htslib and samtools ============================================= See instructions in :file:`import.py` to import the latest versions of `htslib`_, `samtools`_ and `bcftools`_. Unit testing ============ Unit tests are in the :file:`tests` directory. To run all unit tests, run:: pytest tests Most tests use test data from the :file:`tests/*_data` directories. Some of these test data files are generated from other files in these directories, which is done by running ``make`` in each directory:: make -C tests/pysam_data # etc Alternatively if any :file:`tests/*_data/all.stamp` file is not already present, running the unit tests should generate that directory's data files automatically. Benchmarking ============ To run the benchmarking suite, make sure that `pytest-benchmark `_ is installed. To run all benchmarks, type:: pytest tests/*_bench.py See :ref:`Benchmarking` for more on this topic. Contributors ============ Please see Github for a list of all contributors: https://github.com/pysam-developers/pysam/graphs/contributors Many thanks to all contributors for helping in making pysam useful. pysam-0.23.0/doc/faq.rst000066400000000000000000000243521475062545500150160ustar00rootroot00000000000000=== FAQ === How should I cite pysam ======================= Pysam has not been published in print. When referring to pysam, please use the github URL: https://github.com/pysam-developers/pysam. As pysam is a wrapper around htslib and the samtools package, I suggest citing [Li.2009]_, [Bonfield.2021]_, and/or [Danecek.2021]_, as appropriate. Is pysam thread-safe? ===================== Pysam is a mix of python and C code. Instructions within python are generally made thread-safe through python's `global interpreter lock`_ (:dfn:`GIL`). This ensures that python data structures will always be in a consistent state. If an external function outside python is called, the programmer has a choice to keep the GIL in place or to release it. Keeping the GIL in place will make sure that all python threads wait until the external function has completed. This is a safe option and ensures thread-safety. Alternatively, the GIL can be released while the external function is called. This will allow other threads to run concurrently. This can be beneficial if the external function is expected to halt, for example when waiting for data to read or write. However, to achieve thread-safety, the external function needs to be implemented with thread-safety in mind. This means that there can be no shared state between threads, or if there is shared, it needs to be controlled to prevent any access conflicts. Pysam generally uses the latter option and aims to release the GIL for I/O intensive tasks. This is generally fine, but thread-safety of all parts have not been fully tested. A related issue is when different threads read from the same file object - or the same thread uses two iterators over a file. There is only a single file-position for each opened file. To prevent this from happening, use the option ``multiple_iterators=True`` when calling a fetch() method. This will return an iterator on a newly opened file. pysam coordinates are wrong =========================== pysam uses 0-based coordinates and the half-open notation for ranges as does python. Coordinates and intervals reported from pysam always follow that convention. Confusion might arise as different file formats might have different conventions. For example, the SAM format is 1-based while the BAM format is 0-based. It is important to remember that pysam will always conform to the python convention and translate to/from the file format automatically. The only exception is the :term:`region` string in the :meth:`~pysam.AlignmentFile.fetch` and :meth:`~pysam.AlignmentFile.pileup` methods. This string follows the convention of the samtools command line utilities. The same is true for any coordinates passed to the samtools command utilities directly, such as :meth:`pysam.mpileup`. Calling pysam.fetch() confuses existing iterators ================================================= The following code will cause unexpected behaviour:: samfile = pysam.AlignmentFile("pysam_ex1.bam", "rb") iter1 = samfile.fetch("chr1") print(next(iter1).reference_id) iter2 = samfile.fetch("chr2") print(next(iter2).reference_id) print(next(iter1).reference_id) This will give the following output:: 0 1 Traceback (most recent call last): File "xx.py", line 8, in print(next(iter1).reference_id) File "libcalignmentfile.pyx", line 2103, in pysam.libcalignmentfile.IteratorRowRegion.__next__ StopIteration Note how the second iterator stops as the file pointer has moved to chr2. The correct way to work with multiple iterators is:: samfile = pysam.AlignmentFile("pysam_ex1.bam", "rb") iter1 = samfile.fetch("chr1", multiple_iterators=True) print(next(iter1).reference_id) iter2 = samfile.fetch("chr2") print(next(iter2).reference_id) print(next(iter1).reference_id) Here, the output is:: 0 1 0 The reason for this behaviour is that every iterator needs to keep track of its current position in the file. Within pysam, each opened file can only keep track of one file position and hence there can only be one iterator per file. Using the option ``multiple_iterators=True`` will return an iterator within a newly opened file. This iterator will not interfere with existing iterators as it has its own file handle associated with it. Note that re-opening files incurs a performance penalty which can become severe when calling :meth:`~pysam.AlignmentFile.fetch` often. Thus, ``multiple_iterators`` is set to ``False`` by default. AlignmentFile.fetch does not show unmapped reads ================================================ By default, :meth:`~pysam.AlignmentFile.fetch` will only iterate over placed alignments in the SAM/BAM/CRAM file. Thus the following always works:: f = pysam.AlignmentFile(fname, "r") for r in f.fetch(): assert r.reference_name is not None If the file contains unaligned reads, they can be included in the iteration by adding the ``until_eof=True`` flag:: f = pysam.AlignmentFile(fname, "r") for r in f.fetch(until_eof=True): if r.is_unmapped: print("read is unmapped") See also :meth:`fetch("*") ` which iterates only over the unplaced unmapped reads at the end of the file. I can't call AlignmentFile.fetch on a file without an index =========================================================== :meth:`~pysam.AlignmentFile.fetch` requires an index when iterating over a SAM/BAM file. To iterate over a file without an index, use ``until_eof=True``:: bf = pysam.AlignmentFile(fname, "rb") for r in bf.fetch(until_eof=True): print(r) BAM files with a large number of reference sequences are slow ============================================================= If you have many reference sequences in a BAM file, the following might be slow:: track = pysam.AlignmentFile(fname, "rb") for aln in track.fetch(): pass The reason is that track.fetch() will iterate through the BAM file for each reference sequence in the order as it is defined in the header. This might require a lot of jumping around in the file. To avoid this, use:: track = pysam.AlignmentFile(fname, "rb") for aln in track.fetch(until_eof=True): pass This will iterate through reads as they appear in the file. Weirdness with spliced reads in samfile.pileup(chr,start,end) given spliced alignments from an RNA-seq bam file =============================================================================================================== Spliced reads are reported within samfile.pileup. To ignore these in your analysis, test the flags ``is_del == True and indel == 0`` in the :class:`~.PileupRead` object. I can't edit quality scores in place ==================================== Editing reads in-place generally works, though there is one quirk to be aware of. Assigning to AlignedSegment.query_sequence will invalidate any quality scores in AlignedSegment.query_qualities. The reason is that samtools manages the memory of the sequence and quality scores together and thus requires them to always be of the same length or 0. Thus, to in-place edit the sequence and quality scores, copies of the quality scores need to be taken. Consider trimming for example:: quals = read.query_qualities read.query_sequence = read.query_sequence[5:10] read.query_qualities = quals[5:10] Why is there no SNPCaller class anymore? ========================================= SNP calling is highly complex and heavily parameterized. There was a danger that the pysam implementations might show different behaviour from the samtools implementation, which would have caused a lot of confusion. The best way to use samtools SNP calling from python is to use the :meth:`pysam.mpileup` command and parse the output directly. I get an error 'PileupProxy accessed after iterator finished' ============================================================= Pysam works by providing proxy objects to objects defined within the C-samtools package. Thus, some attention must be paid to the lifetime of objects. The following to code snippets will cause an error:: s = AlignmentFile('ex1.bam') for p in s.pileup('chr1', 1000,1010): pass for pp in p.pileups: print(pp) The iteration has finished, thus the contents of ``p`` are invalid. Another variation of this:: p = next(AlignmentFile('ex1.bam').pileup('chr1', 1000, 1010)) for pp in p.pileups: print(pp) Again, the iteration finishes as the temporary iterator created by pileup goes out of scope. The solution is to keep a handle to the iterator that remains alive:: i = AlignmentFile('ex1.bam').pileup('chr1', 1000, 1010) p = next(i) for pp in p.pileups: print(pp) Pysam won't compile =================== Compiling pysam can be tricky as there are numerous variables that differ between build environments such as OS, version, python version, and compiler. It is difficult to build software that builds cleanly on all systems and the process might fail. Please see the `pysam user group `_ for common issues. If there is a build issue, read the generated output carefully - generally the cause of the problem is among the first errors to be reported. For example, you will need to have the development version of python installed that includes the header files such as :file:`Python.h`. If that file is missing, the compiler will report this at the very top of its error messages but will follow it with any unknown function or variable definition it encounters later on. General advice is to always use the latest version on python_ and cython_ when building pysam. There are some known incompatibilities: * Python 3.4 requires cython 0.20.2 or later (see `here `_) .. _global interpreter lock: https://en.wikipedia.org/wiki/Global_interpreter_lock ImportError: cannot import name csamtools ========================================= In version 0.10.0 and onwards, all pysam extension modules contain a ``lib``-prefix. This facilates linking against pysam extension modules with compilers that require to start with ``lib``. As a consequence, all code using pysam extension modules directly will need to be adapted. For example,:: cimport pysam.csamtools will become:: cimport pysam.libcsamtools pysam-0.23.0/doc/glossary.rst000066400000000000000000000114141475062545500161050ustar00rootroot00000000000000======== Glossary ======== .. glossary:: :sorted: cigar Stands for Compact Idiosyncratic Gapped Alignment Report and represents a compressed (run-length encoded) pairwise alignment format. It was first defined by the Exonerate Aligner, but was alter adapted and adopted as part of the :term:`SAM` standard and many other aligners. In the Python API, the cigar alignment is presented as a list of tuples ``(operation,length)``. For example, the tuple ``[ (0,3), (1,5), (0,2) ]`` refers to an alignment with 3 matches, 5 insertions and another 2 matches. region A genomic region, stated relative to a :term:`reference` sequence. A region consists of reference name ('chr1'), start (15000), and end (20000). Start and end can be omitted for regions spanning a whole chromosome. If ``end`` is missing, the region will span from ``start`` to the end of the chromosome. Within pysam, coordinates are 0-based half-open intervals, i.e., the first base of the reference sequence is numbered zero; and the base at position ``start`` is part of the interval, but the base at ``end`` is not. When a region is written as a single string using `samtools`_-compatible notation, e.g., 'chr1:15001-20000', the string's coordinates instead represent a 1-based closed interval, i.e., both (1-based) positions 15,001 and 20,000 are part of the interval. (This example denotes the same 5,000-base region as the example in the previous paragraph.) genotype An individual's collection of genes. It can also refer to the two alleles inherited for a particular gene. column The portion of reads aligned to a single base in the :term:`reference` sequence. tid The :term:`target` id. The target id is 0 or a positive integer mapping to entries within the sequence dictionary in the header section of a :term:`TAM` file or :term:`BAM` file. contig The sequence that a :term:`tid` refers to. For example ``chr1``, ``contig123``. reference Synonym for contig. BED Browser Extensible Data format. A text file format used to store genomic :term:`regions` as coordinates and associated notations. GTF The Gene Transfer Format is a file format used to hold information about gene structure. SAM A textual format for storing genomic alignment information. BAM Binary SAM format. BAM files are binary formatted, indexed and allow random access. CRAM CRAM is a binary format representing the same sequence alignment information as SAM and BAM, but offering significantly better lossless compression than BAM. TAM Text SAM file. TAM files are human readable files of tab-separated fields. TAM files do not allow random access. sam file A file containing aligned reads. The :term:`sam file` can either be a :term:`BAM` file or a :term:`TAM` file. pileup Pileup fetching Retrieving all mapped reads mapped to a :term:`region`. target The sequence that a read has been aligned to. Target sequences have bot a numerical identifier (:term:`tid`) and an alphanumeric name (:term:`Reference`). tabix file A sorted, compressed and indexed tab-separated file created by the command line tool :file:`tabix` or the commands :meth:`tabix_compress` and :meth:`tabix_index`. The file is indexed by chromosomal coordinates. tabix row A row in a :term:`tabix file`. Fields within a row are tab-separated. soft clipping soft clipped In alignments with soft clipping part of the query sequence are not aligned. The unaligned query sequence is still part of the alignment record. This is in difference to :term:`hard clipped` reads. hard clipping hard clipped In hard clipped reads, part of the sequence has been removed prior to alignment. That only a subsequence is aligend might be recorded in the :term:`cigar` alignment, but the removed sequence will not be part of the alignment record, in contrast to :term:`soft clipped` reads. VCF Variant Call Format. BCF Binary :term:`VCF`. FASTA Simple text format containing sequence data, with only the bare minimum of metadata. Typically used for reference sequence data. FASTQ Simple text format containing sequence data and associated base qualities. tabix Utility in the htslib package to index :term:`bgzip` compressed files. faidx Utility in the `samtools`_ package to index :term:`fasta` formatted files. bgzip Utility in the htslib package to block compress genomic data files. pysam-0.23.0/doc/index.rst000066400000000000000000000052261475062545500153550ustar00rootroot00000000000000pysam: htslib interface for python ================================== :Author: Andreas Heger, John Marshall, Kevin Jacobs, and contributors :Date: |today| :Version: |version| Pysam is a python module for reading, manipulating and writing genomic data sets. Pysam is a wrapper of the htslib_ C-API and provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the samtools_ and bcftools_ packages. The module supports compression and random access through indexing. This module provides a low-level wrapper around the htslib_ C-API as using cython and a high-level, pythonic API for convenient access to the data within genomic file formats. The current version wraps *htslib-1.21*, *samtools-1.21*, and *bcftools-1.21*. To install the latest release, type:: pip install pysam See the :ref:`Installation notes ` for details. This module is unrelated to NREL-PySAM_, which wraps the National Renewable Energy Laboratory's System Advisor Model. .. _NREL-PySAM: https://nrel-pysam.readthedocs.io/ Contents -------- .. toctree:: :maxdepth: 2 api.rst usage.rst installation.rst faq.rst developer.rst release.rst benchmarking.rst glossary.rst Indices and tables ------------------ Contents: * :ref:`genindex` * :ref:`modindex` * :ref:`search` References ---------- .. [Li.2009] *The Sequence Alignment/Map format and SAMtools.* Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. Bioinformatics. 2009 Aug 15;25(16):2078-9. Epub 2009 Jun 8 `btp352 `_. PMID: `19505943 `_. .. [Bonfield.2021] *HTSlib: C library for reading/writing high-throughput sequencing data.* Bonfield JK, Marshall J, Danecek P, Li H, Ohan V, Whitwham A, Keane T, Davies RM. GigaScience (2021) 10(2) `giab007 `_. PMID: `33594436 `_. .. [Danecek.2021] *Twelve years of SAMtools and BCFtools.* Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. GigaScience (2021) 10(2) `giab008 `_. PMID: `33590861 `_. .. seealso:: Information about htslib http://www.htslib.org The samtools homepage http://samtools.sourceforge.net The cython C-extensions for python https://cython.org/ The python language https://www.python.org pysam-0.23.0/doc/installation.rst000066400000000000000000000067011475062545500167460ustar00rootroot00000000000000.. _installation: ================ Installing pysam ================ Pysam can be installed through conda_, PyPI_ and from the repository. The recommended way to install pysam is through conda/bioconda. Conda installation ================== To install pysam in your current conda_ environment, type:: conda config --add channels r conda config --add channels bioconda conda install pysam This will install pysam from the bioconda_ channel and automatically makes sure that dependencies are installed. Also, compilation flags will be set automatically, which will potentially save a lot of trouble on OS X. PyPI installation ================= Pysam provides a python interface to the functionality contained within the htslib_ C library. There are two ways that these two can be combined, ``builtin`` and ``external``. Builtin ------- The typical installation will be through PyPI_:: pip install pysam Generally you will have the ``wheel`` package installed and this command will speedily install pysam from a pre-built wheel. Otherwise, or if you use pip's ``--no-binary`` option, this will compile the ``builtin`` htslib source code within pysam and allow the configuration facilities described below to be used. htslib_ can be configured at compilation to turn on additional features such support using encrypted configurations, enable plugins, and more. See the htslib_ project for more information on these. Pysam will attempt to configure htslib_ to turn on some advanced features. If these fail, for example due to missing library dependencies (`libcurl`, `libcrypto`), it will fall back to conservative defaults. Options can be passed to the configure script explicitly by setting the environment variable `HTSLIB_CONFIGURE_OPTIONS`. For example:: export HTSLIB_CONFIGURE_OPTIONS=--enable-plugins pip install pysam External -------- pysam can be combined with an externally installed htslib_ library. This is a good way to avoid duplication of libraries. To link against an externally installed library, set the environment variables `HTSLIB_LIBRARY_DIR` and `HTSLIB_INCLUDE_DIR` before installing:: export HTSLIB_LIBRARY_DIR=/usr/local/lib export HTSLIB_INCLUDE_DIR=/usr/local/include pip install pysam Note that the location of the file :file:`libhts.so` needs to be known to the linker once you run pysam, for example by setting the environment-varirable `LD_LIBRARY_PATH`. Note that generally the pysam and htslib version need to be compatible. See the release notes for more information. Installation from repository ============================ pysam depends on cython_ to provide the connectivity to the htslib_ C library. The installation of the source tarball (:file:`.tar.gz`) contains pre-built C-files and cython needs not be present during installation. However, when installing from the repository, cython needs to be installed beforehand. To install from repository, type:: python setup.py install For compilation options, see the section on PyPI installation above. Requirements ============ Depending on the installation method, requirements for building pysam differ. When installing through conda_, dependencies will be resolved by the package manager. The pip_ installation and installation from source require a C compiler and its standard libraries as well as all requirements for building htslib. Htslib requirements are listed in the htslib/INSTALL file. Installing from the repository will require cython_ to be installed. pysam-0.23.0/doc/make.bat000066400000000000000000000056231475062545500151220ustar00rootroot00000000000000@ECHO OFF REM Command file for Sphinx documentation set SPHINXBUILD=sphinx-build set ALLSPHINXOPTS=-d _build/doctrees %SPHINXOPTS% . if NOT "%PAPER%" == "" ( set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% ) if "%1" == "" goto help if "%1" == "help" ( :help echo.Please use `make ^` where ^ is one of echo. html to make standalone HTML files echo. dirhtml to make HTML files named index.html in directories echo. pickle to make pickle files echo. json to make JSON files echo. htmlhelp to make HTML files and a HTML help project echo. qthelp to make HTML files and a qthelp project echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter echo. changes to make an overview over all changed/added/deprecated items echo. linkcheck to check all external links for integrity echo. doctest to run all doctests embedded in the documentation if enabled goto end ) if "%1" == "clean" ( for /d %%i in (_build\*) do rmdir /q /s %%i del /q /s _build\* goto end ) if "%1" == "html" ( %SPHINXBUILD% -b html %ALLSPHINXOPTS% _build/html echo. echo.Build finished. The HTML pages are in _build/html. goto end ) if "%1" == "dirhtml" ( %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% _build/dirhtml echo. echo.Build finished. The HTML pages are in _build/dirhtml. goto end ) if "%1" == "pickle" ( %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% _build/pickle echo. echo.Build finished; now you can process the pickle files. goto end ) if "%1" == "json" ( %SPHINXBUILD% -b json %ALLSPHINXOPTS% _build/json echo. echo.Build finished; now you can process the JSON files. goto end ) if "%1" == "htmlhelp" ( %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% _build/htmlhelp echo. echo.Build finished; now you can run HTML Help Workshop with the ^ .hhp project file in _build/htmlhelp. goto end ) if "%1" == "qthelp" ( %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% _build/qthelp echo. echo.Build finished; now you can run "qcollectiongenerator" with the ^ .qhcp project file in _build/qthelp, like this: echo.^> qcollectiongenerator _build\qthelp\samtools.qhcp echo.To view the help file: echo.^> assistant -collectionFile _build\qthelp\samtools.ghc goto end ) if "%1" == "latex" ( %SPHINXBUILD% -b latex %ALLSPHINXOPTS% _build/latex echo. echo.Build finished; the LaTeX files are in _build/latex. goto end ) if "%1" == "changes" ( %SPHINXBUILD% -b changes %ALLSPHINXOPTS% _build/changes echo. echo.The overview file is in _build/changes. goto end ) if "%1" == "linkcheck" ( %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% _build/linkcheck echo. echo.Link check complete; look for any errors in the above output ^ or in _build/linkcheck/output.txt. goto end ) if "%1" == "doctest" ( %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% _build/doctest echo. echo.Testing of doctests in the sources finished, look at the ^ results in _build/doctest/output.txt. goto end ) :end pysam-0.23.0/doc/release.rst000066400000000000000000000001001475062545500156500ustar00rootroot00000000000000============= Release notes ============= .. include:: ../NEWS pysam-0.23.0/doc/requirements-rtd.txt000066400000000000000000000000461475062545500175620ustar00rootroot00000000000000sphinx==7.2.5 sphinx-rtd-theme==1.3.0 pysam-0.23.0/doc/usage.rst000066400000000000000000000414651475062545500153570ustar00rootroot00000000000000.. _Usage: ========================================= Working with BAM/CRAM/SAM-formatted files ========================================= Opening a file ============== To begin with, import the pysam module and open a :class:`pysam.AlignmentFile`:: import pysam samfile = pysam.AlignmentFile("ex1.bam", "rb") The above command opens the file :file:`ex1.bam` for reading. The ``b`` qualifier indicates that this is a :term:`BAM` file. To open a :term:`SAM` file, type:: import pysam samfile = pysam.AlignmentFile("ex1.sam", "r") :term:`CRAM` files are identified by a ``c`` qualifier:: import pysam samfile = pysam.AlignmentFile("ex1.cram", "rc") Fetching reads mapped to a :term:`region` ========================================= Reads are obtained through a call to the :meth:`pysam.AlignmentFile.fetch` method which returns an iterator. Each call to the iterator will returns a :class:`pysam.AlignedSegment` object:: iter = samfile.fetch("seq1", 10, 20) for x in iter: print(str(x)) :meth:`pysam.AlignmentFile.fetch` returns all reads overlapping a region sorted by the first aligned base in the :term:`reference` sequence. Note that it will also return reads that are only partially overlapping with the :term:`region`. Thus the reads returned might span a region that is larger than the one queried. Using the pileup-engine ======================= In contrast to :term:`fetching`, the :term:`pileup` engine returns for each base in the :term:`reference` sequence the reads that map to that particular position. In the typical view of reads stacking vertically on top of the reference sequence similar to a multiple alignment, :term:`fetching` iterates over the rows of this implied multiple alignment while a :term:`pileup` iterates over the :term:`columns`. Calling :meth:`~pysam.AlignmentFile.pileup` will return an iterator over each :term:`column` (reference base) of a specified :term:`region`. Each call to the iterator returns an object of the type :class:`pysam.PileupColumn` that provides access to all the reads aligned to that particular reference position as well as some additional information:: iter = samfile.pileup('seq1', 10, 20) for x in iter: print(str(x)) Creating BAM/CRAM/SAM files from scratch ======================================== The following example shows how a new :term:`BAM` file is constructed from scratch. The important part here is that the :class:`pysam.AlignmentFile` class needs to receive the sequence identifiers. These can be given either as a dictionary in a header structure, as lists of names and sizes, or from a template file. Here, we use a header dictionary:: header = { 'HD': {'VN': '1.0'}, 'SQ': [{'LN': 1575, 'SN': 'chr1'}, {'LN': 1584, 'SN': 'chr2'}] } with pysam.AlignmentFile(tmpfilename, "wb", header=header) as outf: a = pysam.AlignedSegment() a.query_name = "read_28833_29006_6945" a.query_sequence="AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG" a.flag = 99 a.reference_id = 0 a.reference_start = 32 a.mapping_quality = 20 a.cigar = ((0,10), (2,1), (0,25)) a.next_reference_id = 0 a.next_reference_start=199 a.template_length=167 a.query_qualities = pysam.qualitystring_to_array("<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<") a.tags = (("NM", 1), ("RG", "L1")) outf.write(a) Using streams ============= Pysam does not support reading and writing from true python file objects, but it does support reading and writing from stdin and stdout. The following example reads from stdin and writes to stdout:: infile = pysam.AlignmentFile("-", "r") outfile = pysam.AlignmentFile("-", "w", template=infile) for s in infile: outfile.write(s) It will also work with :term:`BAM` files. The following script converts a :term:`BAM` formatted file on stdin to a :term:`SAM` formatted file on stdout:: infile = pysam.AlignmentFile("-", "rb") outfile = pysam.AlignmentFile("-", "w", template=infile) for s in infile: outfile.write(s) Note that the file open mode needs to changed from ``r`` to ``rb``. ================================================== Using samtools and bcftools commands within Python ================================================== Commands available in `samtools`_ and `bcftools`_ are available as simple function calls, with command line options provided as arguments. For example:: import pysam.samtools pysam.samtools.sort("-o", "output.bam", "ex1.bam", catch_stdout=False) import pysam.bcftools pysam.bcftools.index("--csi", "ex2.vcf.gz") corresponds to the command lines:: samtools sort -o output.bam ex1.bam bcftools index --csi ex2.vcf.gz Samtools commands are also imported into the main ``pysam`` namespace. For example:: pysam.sort("-m", "1000000", "-o", "output.bam", "ex1.bam", catch_stdout=False) To make them valid Python identifiers, the functions :func:`!cram_size` and :func:`!fqimport` are spelt thus, differently from their corresponding commands. In order to get usage information, try:: print(pysam.sort.usage()) Argument errors raise a :class:`pysam.SamtoolsError`:: pysam.sort() Traceback (most recent call last): File "x.py", line 12, in pysam.sort() File "/build/lib.linux-x86_64-2.6/pysam/__init__.py", line 37, in __call__ if retval: raise SamtoolsError( "\n".join( stderr ) ) pysam.SamtoolsError: 'Usage: samtools sort [-n] [-m ] \n' Messages from `samtools`_ on stderr are captured and are available using the :meth:`~PysamDispatcher.get_messages` method:: pysam.sort.get_messages() By default, pysam captures the samtools command's standard output and returns it as the function's return value. To redirect stdout to a file instead, either use the ``save_stdout`` keyword argument, or use ``"-o", "filename"`` in the arguments and also use ``catch_stdout=False`` to prevent pysam's capturing from overriding your redirection. Finally, ``catch_stdout=False`` by itself discards standard output, which may help resolve problems in environments such as IPython notebooks:: # Return value pileup_text = pysam.samtools.mpileup("in.bam") # Save to file pysam.samtools.mpileup("in.bam", save_stdout=pileup_filename) pysam.samtools.mpileup("-o", pileup_filename, "in.bam", catch_stdout=False) # Discard standard output pysam.samtools.mpileup("in.bam", catch_stdout=False) # Returns None For each :obj:`!command` available as a `samtools`_ subcommand, the following functions are provided: .. py:function:: pysam.samtools.command(args, *, catch_stdout=True, save_stdout=None, split_lines=False) :param args: Arguments to be passed to the samtools subcommand. :param bool catch_stdout: Whether to return stdout as the function's value. :param str save_stdout: Filename to which stdout should be written. :param bool split_lines: Whether to split the return value into a list of lines. :returns: Standard output if it was caught, otherwise None. If `save_stdout` is not None, the command's standard ouput is written to the file specified and the function returns None. Otherwise, if `catch_stdout` is true, the command's standard output is captured and used as the function's return value --- either as a single :obj:`str` or as :obj:`list[str] ` according to `split_lines`. If `catch_stdout` is false, the command's standard output is discarded and the function returns None. The command's standard error is always captured and made available via :func:`~pysam.samtools.command.get_messages`. .. py:function:: pysam.samtools.command.get_messages() Returns the standard error from the most recent invocation of the particular :obj:`!command`, either as a single :obj:`str` or as :obj:`list[str] ` according to `split_lines` as specified in that invocation. .. py:function:: pysam.samtools.command.usage() Returns the command's usage/help message, as a single :obj:`str`. For each :obj:`!command` available as a `bcftools`_ subcommand, the :func:`!pysam.bcftools.command`, :func:`!pysam.bcftools.command.get_messages`, and :func:`!pysam.bcftools.command.usage` functions operate similarly. ================================ Working with tabix-indexed files ================================ To open a tabular file that has been indexed with tabix_, use :class:`~pysam.TabixFile`:: import pysam tbx = pysam.TabixFile("example.bed.gz") Similar to :class:`~pysam.AlignmentFile.fetch`, intervals within a region can be retrieved by calling :meth:`~pysam.TabixFile.fetch()`:: for row in tbx.fetch("chr1", 1000, 2000): print(str(row)) This will return a tuple-like data structure in which columns can be retrieved by numeric index:: for row in tbx.fetch("chr1", 1000, 2000): print("chromosome is", row[0]) By providing a parser to :class:`~pysam.AlignmentFile.fetch` or :class:`~pysam.TabixFile`, the data will we presented in parsed form:: for row in tbx.fetch("chr1", 1000, 2000, parser=pysam.asTuple()): print("chromosome is", row.contig) print("first field (chrom)=", row[0]) Pre-built parsers are available for :term:`bed` (:class:`~pysam.asBed`) formatted files and :term:`gtf` (:class:`~pysam.asGTF`) formatted files. Thus, additional fields become available through named access, for example:: for row in tbx.fetch("chr1", 1000, 2000, parser=pysam.asBed()): print("name is", row.name) .. Currently inactivated as pileup deprecated .. Using the samtools SNP caller .. ----------------------------- .. There are two ways to access the samtools SNP caller. The :class:`pysam.IteratorSNPCalls` .. is appropriate when calling many consecutive SNPs, while :class:`pysam.SNPCaller` is .. best when calling SNPs at non-consecutive genomic positions. Each snp caller returns objects of .. type :class:`pysam.SNPCall`. .. To use :class:`pysam.IteratorSNPCalls`, associate it with a :class:`pysam.IteratorColumn`:: .. samfile = pysam.AlignmentFile( "ex1.bam", "rb") .. fastafile = pysam.Fastafile( "ex1.fa" ) .. pileup_iter = samfile.pileup( stepper = "samtools", fastafile = fastafile ) .. sncpall_iter = pysam.IteratorSNPCalls(pileup_iter) .. for call in snpcall_iter: .. print(str(call)) .. Usage of :class:`pysam.SNPCaller` is similar:: .. samfile = pysam.AlignmentFile( "ex1.bam", "rb") .. fastafile = pysam.Fastafile( "ex1.fa" ) .. pileup_iter = samfile.pileup( stepper = "samtools", fastafile = fastafile ) .. snpcaller = pysam.SNPCaller.call(pileup_iter) .. print(snpcaller( "chr1", 100 )) .. Note the use of the option *stepper* to control which reads are included in the .. in the :term:`pileup`. The ``samtools`` stepper implements the same read selection .. and processing as in the samtools pileup command. .. Calling indels works along the same lines, using the :class:`pysam.IteratorIndelCalls` .. and :class:`pysam.IteratorIndelCaller`. ==================================== Working with VCF/BCF formatted files ==================================== To iterate through a VCF/BCF formatted file use :class:`~pysam.VariantFile`:: from pysam import VariantFile bcf_in = VariantFile("test.bcf") # auto-detect input format bcf_out = VariantFile('-', 'w', header=bcf_in.header) for rec in bcf_in.fetch('chr1', 100000, 200000): bcf_out.write(rec) :meth:`_pysam.VariantFile.fetch()` iterates over :class:`~pysam.VariantRecord` objects which provides access to simple variant attributes such as :class:`~pysam.VariantRecord.contig`, :class:`~pysam.VariantRecord.pos`, :class:`~pysam.VariantRecord.ref`:: for rec in bcf_in.fetch(): print(rec.pos) but also to complex attributes such as the contents to the :class:`~pysam.VariantRecord.info`, :class:`~pysam.VariantRecord.format` and :term:`genotype` columns. These complex attributes are views on the underlying htslib data structures and provide dictionary-like access to the data:: for rec in bcf_in.fetch(): print(rec.info) print(rec.info.keys()) print(rec.info["DP"]) The :py:attr:`~pysam.VariantFile.header` attribute (:class:`~pysam.VariantHeader`) provides access information stored in the :term:`vcf` header. The complete header can be printed:: >>> print(bcf_in.header) ##fileformat=VCFv4.2 ##FILTER= ##fileDate=20090805 ##source=myImputationProgramV3.1 ##reference=1000GenomesPilot-NCBI36 ##phasing=partial ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##contig= ##contig= ##contig= ##bcftools_viewVersion=1.3+htslib-1.3 ##bcftools_viewCommand=view -O b -o example_vcf42.bcf example_vcf42.vcf.gz #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA0000 Individual contents such as contigs, info fields, samples, formats can be retrieved as attributes from :py:attr:`~pysam.VariantFile.header`:: >>> print(bcf_in.header.contigs) To convert these views to native python types, iterate through the views:: >>> print(list((bcf_in.header.contigs))) ['M', '17', '20'] >>> print(list((bcf_in.header.filters))) ['PASS', 'q10', 's50'] >>> print(list((bcf_in.header.info))) ['NS', 'DP', 'AF', 'AA', 'DB', 'H2'] >>> print(list((bcf_in.header.samples))) ['NA00001', 'NA00002', 'NA00003'] Alternatively, it is possible to iterate through all records in the header returning objects of type :py:class:`~pysam.VariantHeaderRecord`:: :: >>> for x in bcf_in.header.records: >>> print(x) >>> print(x.type, x.key) GENERIC fileformat FILTER FILTER GENERIC fileDate GENERIC source GENERIC reference GENERIC phasing INFO INFO INFO INFO INFO INFO INFO INFO INFO INFO INFO INFO FILTER FILTER FILTER FILTER FORMAT FORMAT FORMAT FORMAT FORMAT FORMAT FORMAT FORMAT CONTIG contig CONTIG contig CONTIG contig GENERIC bcftools_viewVersion GENERIC bcftools_viewCommand =============== Extending pysam =============== Using pyximport_, it is (relatively) straight-forward to access pysam internals and the underlying `samtools`_ library. An example is provided in the :file:`tests` directory. The example emulates the samtools flagstat command and consists of three files: 1. The main script :file:`pysam_flagstat.py`. The important lines in this script are:: import pyximport pyximport.install() import _pysam_flagstat ... flag_counts = _pysam_flagstat.count(pysam_in) The first part imports, sets up pyximport_ and imports the cython module :file:`_pysam_flagstat`. The second part calls the ``count`` method in :file:`_pysam_flagstat`. 2. The cython implementation :file:`_pysam_flagstat.pyx`. This script imports the pysam API via:: from pysam.libcalignmentfile cimport AlignmentFile, AlignedSegment This statement imports, amongst others, :class:`AlignedSegment` into the namespace. Speed can be gained from declaring variables. For example, to efficiently iterate over a file, an :class:`AlignedSegment` object is declared:: # loop over samfile cdef AlignedSegment read for read in samfile: ... 3. A :file:`pyxbld` providing pyximport_ with build information. Required are the locations of the samtools and pysam header libraries of a source installation of pysam plus the :file:`csamtools.so` shared library. For example:: def make_ext(modname, pyxfilename): from distutils.extension import Extension import pysam return Extension(name=modname, sources=[pyxfilename], extra_link_args=pysam.get_libraries(), include_dirs=pysam.get_include(), define_macros=pysam.get_defines()) If the script :file:`pysam_flagstat.py` is called the first time, pyximport_ will compile the cython_ extension :file:`_pysam_flagstat.pyx` and make it available to the script. Compilation requires a working compiler and cython_ installation. Each time :file:`_pysam_flagstat.pyx` is modified, a new compilation will take place. pyximport_ comes with cython_. pysam-0.23.0/htslib/000077500000000000000000000000001475062545500142275ustar00rootroot00000000000000pysam-0.23.0/htslib/LICENSE000066400000000000000000000067241475062545500152450ustar00rootroot00000000000000[Files in this distribution outwith the cram/ subdirectory are distributed according to the terms of the following MIT/Expat license.] The MIT/Expat License Copyright (C) 2012-2024 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. [Files within the cram/ subdirectory in this distribution are distributed according to the terms of the following Modified 3-Clause BSD license.] The Modified-BSD License Copyright (C) 2012-2024 Genome Research Ltd. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. [The use of a range of years within a copyright notice in this distribution should be interpreted as being equivalent to a list of years including the first and last year specified and all consecutive years between them. For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009, 2011-2012" should be interpreted as being identical to a notice that reads "Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice that reads "Copyright (C) 2005-2012" should be interpreted as being identical to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012".] pysam-0.23.0/htslib/Makefile000066400000000000000000001362521475062545500157000ustar00rootroot00000000000000# Makefile for htslib, a C library for high-throughput sequencing data formats. # # Copyright (C) 2013-2024 Genome Research Ltd. # # Author: John Marshall # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. CC = gcc AR = ar RANLIB = ranlib # Default libraries to link if configure is not used htslib_default_libs = -lz -lm -lbz2 -llzma -lcurl CPPFLAGS = # TODO: make the 64-bit support for VCF optional via configure, for now add -DVCF_ALLOW_INT64 # to CFLAGS manually, here or in config.mk if the latter exists. # TODO: probably update cram code to make it compile cleanly with -Wc++-compat # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600 #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 CFLAGS = -g -Wall -O2 -fvisibility=hidden EXTRA_CFLAGS_PIC = -fpic TARGET_CFLAGS = LDFLAGS = -fvisibility=hidden VERSION_SCRIPT_LDFLAGS = -Wl,-version-script,$(srcprefix)htslib.map LIBS = $(htslib_default_libs) prefix = /usr/local exec_prefix = $(prefix) bindir = $(exec_prefix)/bin includedir = $(prefix)/include libdir = $(exec_prefix)/lib libexecdir = $(exec_prefix)/libexec datarootdir = $(prefix)/share mandir = $(datarootdir)/man man1dir = $(mandir)/man1 man5dir = $(mandir)/man5 man7dir = $(mandir)/man7 pkgconfigdir= $(libdir)/pkgconfig MKDIR_P = mkdir -p INSTALL = install -p INSTALL_DATA = $(INSTALL) -m 644 INSTALL_DIR = $(MKDIR_P) -m 755 LIB_PERM = 644 INSTALL_LIB = $(INSTALL) -m $(LIB_PERM) INSTALL_MAN = $(INSTALL_DATA) INSTALL_PROGRAM = $(INSTALL) # Set by config.mk if plugins are enabled plugindir = BUILT_PROGRAMS = \ annot-tsv \ bgzip \ htsfile \ tabix BUILT_TEST_PROGRAMS = \ test/hts_endian \ test/fieldarith \ test/hfile \ test/pileup \ test/pileup_mod \ test/plugins-dlhts \ test/sam \ test/test_bgzf \ test/test_expr \ test/test_faidx \ test/test_kfunc \ test/test_khash \ test/test_kstring \ test/test_mod \ test/test_nibbles \ test/test_realn \ test/test-regidx \ test/test_str2int \ test/test_time_funcs \ test/test_view \ test/test_index \ test/test-vcf-api \ test/test-vcf-sweep \ test/test-bcf-sr \ test/fuzz/hts_open_fuzzer.o \ test/test-bcf-translate \ test/test-parse-reg \ test/test_introspection \ test/test-bcf_set_variant_type BUILT_THRASH_PROGRAMS = \ test/thrash_threads1 \ test/thrash_threads2 \ test/thrash_threads3 \ test/thrash_threads4 \ test/thrash_threads5 \ test/thrash_threads6 \ test/thrash_threads7 all: lib-static lib-shared $(BUILT_PROGRAMS) plugins \ $(BUILT_TEST_PROGRAMS) htslib_static.mk htslib-uninstalled.pc # Report compiler and version cc-version: -@$(CC) --version 2>/dev/null || true -@$(CC) --qversion 2>/dev/null || true -@$(CC) -V 2>/dev/null || true ALL_CPPFLAGS = -I. $(CPPFLAGS) srcdir = . srcprefix = HTSPREFIX = # Flags for SIMD code HTS_CFLAGS_AVX2 = HTS_CFLAGS_AVX512 = HTS_CFLAGS_SSE4 = # Control building of SIMD code. Not used if configure has been run. HTS_BUILD_AVX2 = HTS_BUILD_AVX512 = HTS_BUILD_SSE4 = include htslib_vars.mk -include htscodecs.mk # If not using GNU make, you need to copy the version number from version.sh # into here. PACKAGE_VERSION := $(shell $(srcdir)/version.sh) LIBHTS_SOVERSION = 3 # Version numbers for the Mac dynamic library. Note that the leading 3 # is not strictly necessary and should be removed the next time # LIBHTS_SOVERSION is bumped (see #1144 and # https://developer.apple.com/library/archive/documentation/DeveloperTools/Conceptual/DynamicLibraries/100-Articles/DynamicLibraryDesignGuidelines.html#//apple_ref/doc/uid/TP40002013-SW23) MACH_O_COMPATIBILITY_VERSION = 3.1.21 MACH_O_CURRENT_VERSION = 3.1.21 # Force version.h to be remade if $(PACKAGE_VERSION) has changed. version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) version.h: echo '#define HTS_VERSION_TEXT "$(PACKAGE_VERSION)"' > $@ print-version: @echo $(PACKAGE_VERSION) show-version: @echo PACKAGE_VERSION = $(PACKAGE_VERSION) config_vars.h: override escape=$(subst ',\x27,$(subst ",\",$(subst \,\\,$(1)))) config_vars.h: override hts_cc_escaped=$(call escape,$(CC)) config_vars.h: override hts_cppflags_escaped=$(call escape,$(CPPFLAGS)) config_vars.h: override hts_cflags_escaped=$(call escape,$(CFLAGS)) config_vars.h: override hts_ldflags_escaped=$(call escape,$(LDFLAGS)) config_vars.h: override hts_libs_escaped=$(call escape,$(LIBS)) config_vars.h: printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ '$(hts_cc_escaped)' \ '$(hts_cppflags_escaped)' \ '$(hts_cflags_escaped)' \ '$(hts_ldflags_escaped)' \ '$(hts_libs_escaped)' > $@ .SUFFIXES: .bundle .c .cygdll .dll .o .pico .so .c.o: $(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< .c.pico: $(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $< LIBHTS_OBJS = \ kfunc.o \ kstring.o \ bcf_sr_sort.o \ bgzf.o \ errmod.o \ faidx.o \ header.o \ hfile.o \ hts.o \ hts_expr.o \ hts_os.o\ md5.o \ multipart.o \ probaln.o \ realn.o \ regidx.o \ region.o \ sam.o \ sam_mods.o \ simd.o \ synced_bcf_reader.o \ vcf_sweep.o \ tbx.o \ textutils.o \ thread_pool.o \ vcf.o \ vcfutils.o \ cram/cram_codecs.o \ cram/cram_decode.o \ cram/cram_encode.o \ cram/cram_external.o \ cram/cram_index.o \ cram/cram_io.o \ cram/cram_stats.o \ cram/mFILE.o \ cram/open_trace_file.o \ cram/pooled_alloc.o \ cram/string_alloc.o \ $(HTSCODECS_OBJS) \ $(NONCONFIGURE_OBJS) # Without configure we wish to have a rich set of default figures, # but we still need conditional inclusion as we wish to still # support ./configure --disable-blah. NONCONFIGURE_OBJS = hfile_libcurl.o PLUGIN_EXT = PLUGIN_OBJS = cram_h = cram/cram.h $(cram_samtools_h) $(header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encode.h cram/cram_decode.h cram/cram_stats.h cram/cram_codecs.h cram/cram_index.h $(htslib_cram_h) cram_io_h = cram/cram_io.h $(cram_misc_h) cram_misc_h = cram/misc.h cram_os_h = cram/os.h $(htslib_hts_endian_h) cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) cram_structs_h = cram/cram_structs.h $(htslib_thread_pool_h) $(htslib_cram_h) cram/string_alloc.h cram/mFILE.h $(htslib_khash_h) cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h bcf_sr_sort_h = bcf_sr_sort.h $(htslib_synced_bcf_reader_h) $(htslib_kbitset_h) fuzz_settings_h = fuzz_settings.h header_h = header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h) $(htslib_sam_h) hfile_internal_h = hfile_internal.h $(htslib_hts_defs_h) $(htslib_hfile_h) $(textutils_internal_h) hts_internal_h = hts_internal.h $(htslib_hts_h) $(textutils_internal_h) hts_time_funcs_h = hts_time_funcs.h sam_internal_h = sam_internal.h $(htslib_sam_h) textutils_internal_h = textutils_internal.h $(htslib_kstring_h) thread_pool_internal_h = thread_pool_internal.h $(htslib_thread_pool_h) # To be effective, config.mk needs to appear after most Makefile variables are # set but before most rules appear, so that it can both use previously-set # variables in its own rules' prerequisites and also update variables for use # in later rules' prerequisites. # If your make doesn't accept -include, change this to 'include' if you are # using the configure script or just comment the line out if you are not. -include config.mk # Usually config.h is generated by running configure or config.status, # but if those aren't used create a default config.h here. config.h: echo '/* Default config.h generated by Makefile */' > $@ echo '#ifndef _XOPEN_SOURCE' >> $@ echo '#define _XOPEN_SOURCE 600' >> $@ echo '#endif' >> $@ echo '#define HAVE_LIBBZ2 1' >> $@ echo '#define HAVE_LIBLZMA 1' >> $@ echo '#ifndef __APPLE__' >> $@ echo '#define HAVE_LZMA_H 1' >> $@ echo '#endif' >> $@ echo '#define HAVE_DRAND48 1' >> $@ echo '#define HAVE_LIBCURL 1' >> $@ if [ "x$(HTS_HAVE_CPUID)" != "x" ]; then \ echo '#define HAVE_DECL___CPUID_COUNT 1' >> $@ ; \ echo '#define HAVE_DECL___GET_CPUID_MAX 1' >> $@ ; \ fi if [ "x$(HTS_BUILD_SSE4)" != "x" ]; then \ echo '#define HAVE_POPCNT 1' >> $@ ; \ echo '#define HAVE_SSE4_1 1' >> $@ ; \ echo '#define HAVE_SSSE3 1' >> $@ ; \ echo '#if defined(HTS_ALLOW_UNALIGNED) && HTS_ALLOW_UNALIGNED == 0' >> $@ ; \ echo '#define UBSAN 1' >> $@ ; \ echo '#endif' >> $@ ; \ fi if [ "x$(HTS_BUILD_AVX2)" != "x" ] ; then \ echo '#define HAVE_AVX2 1' >> $@ ; \ fi if [ "x$(HTS_BUILD_AVX512)" != "x" ] ; then \ echo '#define HAVE_AVX512 1' >> $@ ; \ fi echo '#if defined __x86_64__ || defined __arm__ || defined __aarch64__' >> $@ echo '#define HAVE_ATTRIBUTE_CONSTRUCTOR 1' >> $@ echo '#endif' >> $@ echo '#if (defined(__x86_64__) || defined(_M_X64))' >> $@ echo '#define HAVE_ATTRIBUTE_TARGET 1' >> $@ echo '#define HAVE_BUILTIN_CPU_SUPPORT_SSSE3 1' >> $@ echo '#endif' >> $@ # And similarly for htslib.pc.tmp ("pkg-config template"). No dependency # on htslib.pc.in listed, as if that file is newer the usual way to regenerate # this target is via configure or config.status rather than this rule. htslib.pc.tmp: sed -e '/^static_libs=/s/@static_LIBS@/$(htslib_default_libs)/;s#@[^-][^@]*@##g' $(srcprefix)htslib.pc.in > $@ # Create a makefile fragment listing the libraries and LDFLAGS needed for # static linking. This can be included by projects that want to build # and link against the htslib source tree instead of an installed library. htslib_static.mk: htslib.pc.tmp sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' $< > $@ lib-static: libhts.a # $(shell), :=, and ifeq/.../endif are GNU Make-specific. If you don't have # GNU Make, comment out the parts of these conditionals that don't apply. ifneq "$(origin PLATFORM)" "file" PLATFORM := $(shell uname -s) endif ifeq "$(PLATFORM)" "Darwin" SHLIB_FLAVOUR = dylib lib-shared: libhts.dylib else ifeq "$(findstring CYGWIN,$(PLATFORM))" "CYGWIN" SHLIB_FLAVOUR = cygdll lib-shared: cyghts-$(LIBHTS_SOVERSION).dll else ifeq "$(findstring MSYS,$(PLATFORM))" "MSYS" SHLIB_FLAVOUR = dll lib-shared: hts-$(LIBHTS_SOVERSION).dll hts-$(LIBHTS_SOVERSION).def hts-$(LIBHTS_SOVERSION).lib else ifeq "$(findstring MINGW,$(PLATFORM))" "MINGW" SHLIB_FLAVOUR = dll lib-shared: hts-$(LIBHTS_SOVERSION).dll hts-$(LIBHTS_SOVERSION).def hts-$(LIBHTS_SOVERSION).lib else SHLIB_FLAVOUR = so lib-shared: libhts.so endif BUILT_PLUGINS = $(PLUGIN_OBJS:.o=$(PLUGIN_EXT)) ifneq "$(BUILT_PLUGINS)" "" plugins: lib-shared endif plugins: $(BUILT_PLUGINS) libhts.a: $(LIBHTS_OBJS) @-rm -f $@ $(AR) -rc $@ $(LIBHTS_OBJS) -$(RANLIB) $@ print-config: @echo HTS_CFLAGS_AVX2 = $(HTS_CFLAGS_AVX2) @echo HTS_CFLAGS_AVX512 = $(HTS_CFLAGS_AVX512) @echo HTS_CFLAGS_SSE4 = $(HTS_CFLAGS_SSE4) @echo LDFLAGS = $(LDFLAGS) @echo LIBHTS_OBJS = $(LIBHTS_OBJS) @echo LIBS = $(LIBS) @echo PLATFORM = $(PLATFORM) # The target here is libhts.so, as that is the built file that other rules # depend upon and that is used when -lhts appears in other program's recipes. # As a byproduct invisible to make, libhts.so.NN is also created, as it is the # file used at runtime (when $LD_LIBRARY_PATH includes the build directory). libhts.so: $(LIBHTS_OBJS:.o=.pico) $(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) $(VERSION_SCRIPT_LDFLAGS) $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) $(LIBS) -lpthread ln -sf $@ libhts.so.$(LIBHTS_SOVERSION) # Similarly this also creates libhts.NN.dylib as a byproduct, so that programs # when run can find this uninstalled shared library (when $DYLD_LIBRARY_PATH # includes this project's build directory). libhts.dylib: $(LIBHTS_OBJS) $(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(MACH_O_CURRENT_VERSION) -compatibility_version $(MACH_O_COMPATIBILITY_VERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) $(LIBS) ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib cyghts-$(LIBHTS_SOVERSION).dll libhts.dll.a: $(LIBHTS_OBJS) $(CC) -shared -Wl,--out-implib=libhts.dll.a -Wl,--enable-auto-import $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) -lpthread hts-$(LIBHTS_SOVERSION).dll hts.dll.a: $(LIBHTS_OBJS) $(CC) -shared -Wl,--out-implib=hts.dll.a -Wl,--enable-auto-import -Wl,--exclude-all-symbols $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) -lpthread hts-$(LIBHTS_SOVERSION).def: hts-$(LIBHTS_SOVERSION).dll gendef hts-$(LIBHTS_SOVERSION).dll hts-$(LIBHTS_SOVERSION).lib: hts-$(LIBHTS_SOVERSION).def dlltool -m i386:x86-64 -d hts-$(LIBHTS_SOVERSION).def -l hts-$(LIBHTS_SOVERSION).lib # Bundling libraries, binaries, dll dependencies, and licenses into a # single directory. NB: This is not needed for end-users, but a test bed # for maintainers building binary distributions. # # NOTE: only tested on the supported MSYS2/MINGW64 environment. dist-windows: DESTDIR= dist-windows: prefix=dist-windows dist-windows: install cp hts-$(LIBHTS_SOVERSION).def hts-$(LIBHTS_SOVERSION).lib dist-windows/lib cp `ldd hts-$(LIBHTS_SOVERSION).dll| awk '/mingw64/ {print $$3}'` dist-windows/bin mkdir -p dist-windows/share/licenses/htslib -cp -r /mingw64/share/licenses/mingw-w64-libraries \ /mingw64/share/licenses/brotli \ /mingw64/share/licenses/bzip2 \ /mingw64/share/licenses/gcc-libs \ /mingw64/share/licenses/libdeflate \ /mingw64/share/licenses/libpsl \ /mingw64/share/licenses/libtre \ /mingw64/share/licenses/libwinpthread \ /mingw64/share/licenses/openssl \ /mingw64/share/licenses/xz \ /mingw64/share/licenses/zlib \ /mingw64/share/licenses/zstd \ dist-windows/share/licenses/ -cp -r /usr/share/licenses/curl \ dist-windows/share/licenses/ cp LICENSE dist-windows/share/licenses/htslib/ # Target to allow htslib.mk to build all the object files before it # links the shared and static libraries. hts-object-files: $(LIBHTS_OBJS) touch $@ # On Unix dlopen("libhts.so.NN", RTLD_LAZY) may default to RTLD_LOCAL. # Hence plugins need to link to (shared) libhts.so.NN themselves, as they # may not be able to access libhts symbols via the main program's libhts # if that was dynamically loaded without an explicit RTLD_GLOBAL. %.so: %.pico libhts.so $(CC) -shared -Wl,-E $(LDFLAGS) -o $@ $< libhts.so $(LIBS) -lpthread # For programs *statically* linked to libhts.a, on macOS loading a plugin # linked to a shared libhts.NN.dylib would lead to conflicting duplicate # symbols. Fortunately macOS dlopen() defaults to RTLD_GLOBAL so there # is less need for plugins to link back to libhts themselves. %.bundle: %.o $(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS) %.cygdll: %.o libhts.dll.a $(CC) -shared $(LDFLAGS) -o $@ $< libhts.dll.a $(LIBS) %.dll: %.o hts.dll.a $(CC) -shared $(LDFLAGS) -o $@ $< hts.dll.a $(LIBS) bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_thread_pool_h) $(htslib_hts_endian_h) cram/pooled_alloc.h $(hts_internal_h) $(htslib_khash_h) errmod.o errmod.pico: errmod.c config.h $(htslib_hts_h) $(htslib_ksort_h) $(htslib_hts_os_h) kstring.o kstring.pico: kstring.c config.h $(htslib_kstring_h) header.o header.pico: header.c config.h $(textutils_internal_h) $(header_h) hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(htslib_kstring_h) $(hts_internal_h) $(htslib_khash_h) hfile_gcs.o hfile_gcs.pico: hfile_gcs.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(hfile_internal_h) hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_h) hfile_s3_write.o hfile_s3_write.pico: hfile_s3_write.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_h) hfile_s3.o hfile_s3.pico: hfile_s3.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) $(hts_time_funcs_h) hts.o hts.pico: hts.c config.h os/lzma_stub.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_hts_endian_h) version.h config_vars.h $(hts_internal_h) $(hfile_internal_h) $(sam_internal_h) $(htslib_hts_expr_h) $(htslib_hts_os_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(htslib_tbx_h) $(htscodecs_htscodecs_h) hts_expr.o hts_expr.pico: hts_expr.c config.h $(htslib_hts_expr_h) $(htslib_hts_log_h) $(textutils_internal_h) hts_os.o hts_os.pico: hts_os.c config.h $(htslib_hts_defs_h) os/rand.c vcf.o vcf.pico: vcf.c config.h $(fuzz_settings_h) $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(hts_internal_h) $(htslib_khash_str2int_h) $(htslib_kstring_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_hts_endian_h) sam.o sam.pico: sam.c config.h $(fuzz_settings_h) $(htslib_hts_defs_h) $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(sam_internal_h) $(htslib_hfile_h) $(htslib_hts_endian_h) $(htslib_hts_expr_h) $(header_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) sam_mods.o sam_mods.pico: sam_mods.c config.h $(htslib_sam_h) $(textutils_internal_h) simd.o simd.pico: simd.c config.h $(htslib_sam_h) $(sam_internal_h) tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(htslib_hts_endian_h) $(hts_internal_h) $(htslib_khash_h) faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kstring_h) $(hts_internal_h) bcf_sr_sort.o bcf_sr_sort.pico: bcf_sr_sort.c config.h $(bcf_sr_sort_h) $(htslib_khash_str2int_h) $(htslib_kbitset_h) synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h) $(htslib_thread_pool_h) $(bcf_sr_sort_h) vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h) vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h) kfunc.o kfunc.pico: kfunc.c config.h $(htslib_kfunc_h) regidx.o regidx.pico: regidx.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) $(hts_internal_h) region.o region.pico: region.c config.h $(htslib_hts_h) $(htslib_khash_h) md5.o md5.pico: md5.c config.h $(htslib_hts_h) $(htslib_hts_endian_h) multipart.o multipart.pico: multipart.c config.h $(htslib_kstring_h) $(hts_internal_h) $(hfile_internal_h) plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h) probaln.o probaln.pico: probaln.c config.h $(htslib_hts_h) realn.o realn.pico: realn.c config.h $(htslib_hts_h) $(htslib_sam_h) textutils.o textutils.pico: textutils.c config.h $(htslib_hfile_h) $(htslib_kstring_h) $(htslib_sam_h) $(hts_internal_h) cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(fuzz_settings_h) $(htslib_hts_endian_h) $(htscodecs_varint_h) $(htscodecs_pack_h) $(htscodecs_rle_h) $(cram_h) cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h) cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) $(cram_os_h) $(sam_internal_h) $(htslib_hts_h) $(htslib_hts_endian_h) $(textutils_internal_h) cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htscodecs_rANS_static4x16_h) $(htslib_hfile_h) $(cram_h) cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_bgzf_h) $(htslib_hfile_h) $(hts_internal_h) $(cram_h) $(cram_os_h) cram/cram_io.o cram/cram_io.pico: 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$(thread_pool_internal_h) $(htslib_hts_log_h) htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.pico: htscodecs/htscodecs/arith_dynamic.c config.h $(htscodecs_arith_dynamic_h) $(htscodecs_varint_h) $(htscodecs_pack_h) $(htscodecs_utils_h) $(htscodecs_c_simple_model_h) htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.pico: htscodecs/htscodecs/fqzcomp_qual.c config.h $(htscodecs_fqzcomp_qual_h) $(htscodecs_varint_h) $(htscodecs_utils_h) $(htscodecs_c_simple_model_h) htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.pico: htscodecs/htscodecs/htscodecs.c $(htscodecs_htscodecs_h) $(htscodecs_version_h) htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.pico: htscodecs/htscodecs/pack.c config.h $(htscodecs_pack_h) htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.pico: htscodecs/htscodecs/rANS_static32x16pr.c config.h $(htscodecs_rANS_word_h) $(htscodecs_rANS_static4x16_h) $(htscodecs_rANS_static16_int_h) $(htscodecs_varint_h) $(htscodecs_utils_h) htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico: htscodecs/htscodecs/rANS_static32x16pr_avx2.c config.h $(htscodecs_rANS_word_h) $(htscodecs_rANS_static4x16_h) $(htscodecs_rANS_static16_int_h) $(htscodecs_varint_h) $(htscodecs_utils_h) $(htscodecs_permute_h) htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico: htscodecs/htscodecs/rANS_static32x16pr_avx512.c config.h $(htscodecs_rANS_word_h) $(htscodecs_rANS_static4x16_h) $(htscodecs_rANS_static16_int_h) $(htscodecs_varint_h) $(htscodecs_utils_h) htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.pico: htscodecs/htscodecs/rANS_static32x16pr_neon.c config.h $(htscodecs_rANS_word_h) $(htscodecs_rANS_static4x16_h) $(htscodecs_rANS_static16_int_h) $(htscodecs_varint_h) $(htscodecs_utils_h) htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico: htscodecs/htscodecs/rANS_static32x16pr_sse4.c config.h $(htscodecs_rANS_word_h) $(htscodecs_rANS_static4x16_h) $(htscodecs_rANS_static16_int_h) $(htscodecs_varint_h) $(htscodecs_utils_h) htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.pico: htscodecs/htscodecs/rANS_static4x16pr.c config.h $(htscodecs_rANS_word_h) $(htscodecs_rANS_static4x16_h) $(htscodecs_rANS_static16_int_h) $(htscodecs_pack_h) $(htscodecs_rle_h) $(htscodecs_utils_h) $(htscodecs_rANS_static32x16pr_h) htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.pico: htscodecs/htscodecs/rANS_static.c config.h $(htscodecs_rANS_byte_h) $(htscodecs_utils_h) $(htscodecs_rANS_static_h) htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.pico: htscodecs/htscodecs/rle.c config.h $(htscodecs_varint_h) $(htscodecs_rle_h) htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.pico: htscodecs/htscodecs/tokenise_name3.c config.h $(htscodecs_pooled_alloc_h) $(htscodecs_arith_dynamic_h) $(htscodecs_rANS_static4x16_h) $(htscodecs_tokenise_name3_h) $(htscodecs_varint_h) $(htscodecs_utils_h) htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.pico: htscodecs/htscodecs/utils.c config.h $(htscodecs_utils_h) # Extra CFLAGS for specific files htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico: TARGET_CFLAGS = $(HTS_CFLAGS_AVX2) htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico: TARGET_CFLAGS = $(HTS_CFLAGS_AVX512) htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico: TARGET_CFLAGS = $(HTS_CFLAGS_SSE4) annot-tsv: annot-tsv.o libhts.a $(CC) $(LDFLAGS) -o $@ annot-tsv.o libhts.a $(LIBS) -lpthread bgzip: bgzip.o libhts.a $(CC) $(LDFLAGS) -o $@ bgzip.o libhts.a $(LIBS) -lpthread htsfile: htsfile.o libhts.a $(CC) $(LDFLAGS) -o $@ htsfile.o libhts.a $(LIBS) -lpthread tabix: tabix.o libhts.a $(CC) $(LDFLAGS) -o $@ tabix.o libhts.a $(LIBS) -lpthread annot-tsv.o: annot-tsv.c config.h $(htslib_hts_h) $(htslib_hts_defs_h) $(htslib_khash_str2int_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_regidx_h) $(textutils_internal_h) bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_hfile_h) htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h) tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_regidx_h) $(htslib_hts_defs_h) $(htslib_hts_log_h) $(htslib_thread_pool_h) # Runes to check that the htscodecs submodule is present ifdef HTSCODECS_SOURCES htscodecs/htscodecs/%.c: | htscodecs/htscodecs @if test -e htscodecs/.git && test ! -e "$@" ; then \ echo "Missing file '$@'" ; \ echo " - Do you need to update the htscodecs submodule?" ; \ false ; \ fi htscodecs/htscodecs/%.h: | htscodecs/htscodecs @if test -e htscodecs/.git && test ! -e "$@" ; then \ echo "Missing file '$@'" ; \ echo " - Do you need to update the htscodecs submodule?" ; \ false ; \ fi htscodecs/htscodecs: @if test -e .git ; then \ printf "\\n\\nError: htscodecs submodule files not present for htslib.\\n\ Try running: \\n\ git submodule update --init --recursive\\n\ in the top-level htslib directory and then re-run make.\\n\\n\\n" ; \ else \ printf "\\n\\nError: htscodecs submodule files not present and this is not a git checkout.\\n\ You have an incomplete distribution. Please try downloading one of the\\n\ official releases from https://www.htslib.org/\\n" ; \ fi @false # Build the htscodecs/htscodecs/version.h file if necessary htscodecs/htscodecs/version.h: force @if test -e $(srcdir)/htscodecs/.git && test -e $(srcdir)/htscodecs/configure.ac ; then \ vers=`cd $(srcdir)/htscodecs && git describe --always --dirty --match 'v[0-9]\.[0-9]*'` && \ case "$$vers" in \ v*) vers=$${vers#v} ;; \ *) iv=`awk '/^AC_INIT\(htscodecs,/ { match($$0, /[0-9]+(\.[0-9]+)*/); print substr($$0, RSTART, RLENGTH) }' $(srcdir)/htscodecs/configure.ac` ; vers="$$iv$${vers:+-g$$vers}" ;; \ esac ; \ if ! grep -s -q '"'"$$vers"'"' $@ ; then \ echo 'Updating $@ : #define HTSCODECS_VERSION_TEXT "'"$$vers"'"' ; \ echo '#define HTSCODECS_VERSION_TEXT "'"$$vers"'"' > $@ ; \ fi ; \ fi endif # Maintainer extra targets built # - compile public headers as C++ # Maintainer source code checks # - copyright boilerplate presence # - tab and trailing space detection maintainer-check: test/usepublic.o test/maintainer/check_copyright.pl . test/maintainer/check_spaces.pl . # Look for untracked files in the git repository. check-untracked: @if test -e .git && git status --porcelain | grep '^\?'; then \ echo 'Untracked files detected (see above). Please either clean up, add to .gitignore, or for test output files consider naming them to match *.tmp or *.tmp.*' ; \ false ; \ fi # Create a shorthand. We use $(SRC) or $(srcprefix) rather than $(srcdir)/ # for brevity in test and install rules, and so that build logs do not have # ./ sprinkled throughout. SRC = $(srcprefix) # For tests that might use it, set $REF_PATH explicitly to use only reference # areas within the test suite (or set it to ':' to use no reference areas). # # If using MSYS, avoid poor shell expansion via: # MSYS2_ARG_CONV_EXCL="*" make check check test: all $(HTSCODECS_TEST_TARGETS) test/hts_endian test/test_expr test/test_kfunc test/test_khash test/test_kstring test/test_nibbles -v test/test_str2int test/test_time_funcs test/fieldarith test/fieldarith.sam test/hfile if test "x$(BUILT_PLUGINS)" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.$(SHLIB_FLAVOUR); \ fi if test "x$(BUILT_PLUGINS)" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.$(SHLIB_FLAVOUR); \ fi test/test_bgzf test/bgziptest.txt test/test-parse-reg -t test/colons.bam cd test/faidx && ./test-faidx.sh faidx.tst cd test/sam_filter && ./filter.sh filter.tst cd test/tabix && ./test-tabix.sh tabix.tst cd test/mpileup && ./test-pileup.sh mpileup.tst cd test/fastq && ./test-fastq.sh cd test/base_mods && ./base-mods.sh base-mods.tst REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq test/test-regidx cd test && REF_PATH=: ./test.pl $${TEST_OPTS:-} test/hts_endian: test/hts_endian.o $(CC) $(LDFLAGS) -o $@ test/hts_endian.o $(LIBS) # To build the fuzzer, try: # make CC="clang16 -fsanitize=address,undefined,fuzzer" \ # CFLAGS="-g -O3 -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION" \ # test/fuzz/hts_open_fuzzer test/fuzz/hts_open_fuzzer: test/fuzz/hts_open_fuzzer.o libhts.a $(CC) $(LDFLAGS) -o $@ test/fuzz/hts_open_fuzzer.o libhts.a $(LIBS) -lpthread test/fieldarith: test/fieldarith.o libhts.a $(CC) $(LDFLAGS) -o $@ test/fieldarith.o libhts.a $(LIBS) -lpthread test/hfile: test/hfile.o libhts.a $(CC) $(LDFLAGS) -o $@ test/hfile.o libhts.a $(LIBS) -lpthread test/pileup: test/pileup.o libhts.a $(CC) $(LDFLAGS) -o $@ test/pileup.o libhts.a $(LIBS) -lpthread test/pileup_mod: test/pileup_mod.o libhts.a $(CC) $(LDFLAGS) -o $@ test/pileup_mod.o libhts.a $(LIBS) -lpthread test/plugins-dlhts: test/plugins-dlhts.o $(CC) $(LDFLAGS) -o $@ test/plugins-dlhts.o $(LIBS) test/sam: test/sam.o libhts.a $(CC) $(LDFLAGS) -o $@ test/sam.o libhts.a $(LIBS) -lpthread test/test_bgzf: test/test_bgzf.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test_bgzf.o libhts.a $(LIBS) -lpthread test/test_expr: test/test_expr.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test_expr.o libhts.a $(LIBS) -lpthread test/test_faidx: test/test_faidx.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test_faidx.o libhts.a $(LIBS) -lpthread test/test_kfunc: test/test_kfunc.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test_kfunc.o libhts.a $(LIBS) -lpthread test/test_khash: test/test_khash.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test_khash.o libhts.a $(LIBS) -lpthread test/test_kstring: test/test_kstring.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test_kstring.o libhts.a $(LIBS) -lpthread test/test_mod: test/test_mod.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test_mod.o libhts.a $(LIBS) -lpthread test/test_nibbles: test/test_nibbles.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test_nibbles.o libhts.a $(LIBS) -lpthread test/test_realn: test/test_realn.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test_realn.o libhts.a $(LIBS) -lpthread test/test-regidx: test/test-regidx.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test-regidx.o libhts.a $(LIBS) -lpthread test/test-parse-reg: test/test-parse-reg.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test-parse-reg.o libhts.a $(LIBS) -lpthread test/test_str2int: test/test_str2int.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test_str2int.o libhts.a $(LIBS) -lpthread test/test_time_funcs: test/test_time_funcs.o $(CC) $(LDFLAGS) -o $@ test/test_time_funcs.o test/test_view: test/test_view.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test_view.o libhts.a $(LIBS) -lpthread test/test_index: test/test_index.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test_index.o libhts.a $(LIBS) -lpthread test/test-vcf-api: test/test-vcf-api.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a $(LIBS) -lpthread test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a $(LIBS) -lpthread test/test-bcf-sr: test/test-bcf-sr.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test-bcf-sr.o libhts.a $(LIBS) -lpthread test/test-bcf-translate: test/test-bcf-translate.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test-bcf-translate.o libhts.a $(LIBS) -lpthread test/test_introspection: test/test_introspection.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test_introspection.o libhts.a $(LIBS) -lpthread test/test-bcf_set_variant_type: test/test-bcf_set_variant_type.o libhts.a $(CC) $(LDFLAGS) -o $@ test/test-bcf_set_variant_type.o libhts.a $(LIBS) -lpthread # Extra tests for bundled htscodecs test_htscodecs_rans4x8: htscodecs/tests/rans4x8 cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x8.test test_htscodecs_rans4x16: htscodecs/tests/rans4x16pr cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x16.test test_htscodecs_arith: htscodecs/tests/arith_dynamic cd htscodecs/tests && srcdir=. && export srcdir && ./arith.test test_htscodecs_tok3: htscodecs/tests/tokenise_name3 cd htscodecs/tests && srcdir=. && export srcdir && ./tok3.test test_htscodecs_fqzcomp: htscodecs/tests/fqzcomp_qual cd htscodecs/tests && srcdir=. && export srcdir && ./fqzcomp.test test_htscodecs_varint: htscodecs/tests/varint cd htscodecs/tests && ./varint htscodecs/tests/arith_dynamic: htscodecs/tests/arith_dynamic_test.o $(HTSCODECS_OBJS) $(CC) $(LDFLAGS) -o $@ $^ $(LIBS) -lm -lpthread htscodecs/tests/fqzcomp_qual: htscodecs/tests/fqzcomp_qual_test.o $(HTSCODECS_OBJS) $(CC) $(LDFLAGS) -o $@ $^ $(LIBS) -lm -lpthread htscodecs/tests/rans4x16pr: htscodecs/tests/rANS_static4x16pr_test.o $(HTSCODECS_OBJS) $(CC) $(LDFLAGS) -o $@ $^ $(LIBS) -lm -lpthread htscodecs/tests/rans4x8: htscodecs/tests/rANS_static_test.o $(HTSCODECS_OBJS) $(CC) $(LDFLAGS) -o $@ $^ $(LIBS) -lm -lpthread htscodecs/tests/tokenise_name3: htscodecs/tests/tokenise_name3_test.o $(HTSCODECS_OBJS) $(CC) $(LDFLAGS) -o $@ $^ $(LIBS) -lm -lpthread htscodecs/tests/varint: htscodecs/tests/varint_test.o $(HTSCODECS_OBJS) $(CC) $(LDFLAGS) -o $@ $^ $(LIBS) -lm -lpthread htscodecs/tests/arith_dynamic_test.o: CPPFLAGS += -Ihtscodecs htscodecs/tests/arith_dynamic_test.o: htscodecs/tests/arith_dynamic_test.c config.h $(htscodecs_arith_dynamic_h) htscodecs/tests/fqzcomp_qual_test.o: CPPFLAGS += -Ihtscodecs htscodecs/tests/fqzcomp_qual_test.o: htscodecs/tests/fqzcomp_qual_test.c config.h $(htscodecs_fqzcomp_qual_h) $(htscodecs_varint_h) htscodecs/tests/rANS_static4x16pr_test.o: CPPFLAGS += -Ihtscodecs htscodecs/tests/rANS_static4x16pr_test.o: htscodecs/tests/rANS_static4x16pr_test.c config.h $(htscodecs_rANS_static4x16_h) htscodecs/tests/rANS_static_test.o: CPPFLAGS += -Ihtscodecs htscodecs/tests/rANS_static_test.o: htscodecs/tests/rANS_static_test.c config.h $(htscodecs_rANS_static_h) htscodecs/tests/tokenise_name3_test.o: CPPFLAGS += -Ihtscodecs htscodecs/tests/tokenise_name3_test.o: htscodecs/tests/tokenise_name3_test.c config.h $(htscodecs_tokenise_name3_h) htscodecs/tests/varint_test.o: CPPFLAGS += -Ihtscodecs htscodecs/tests/varint_test.o: htscodecs/tests/varint_test.c config.h $(htscodecs_varint_h) test/hts_endian.o: test/hts_endian.c config.h $(htslib_hts_endian_h) test/fuzz/hts_open_fuzzer.o: test/fuzz/hts_open_fuzzer.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h) test/fieldarith.o: test/fieldarith.c config.h $(htslib_sam_h) test/hfile.o: test/hfile.c config.h $(htslib_hfile_h) $(htslib_hts_defs_h) $(htslib_kstring_h) test/pileup.o: test/pileup.c config.h $(htslib_sam_h) $(htslib_kstring_h) test/pileup_mod.o: test/pileup_mod.c config.h $(htslib_sam_h) test/plugins-dlhts.o: test/plugins-dlhts.c config.h test/sam.o: test/sam.c config.h $(htslib_hts_defs_h) $(htslib_sam_h) $(htslib_faidx_h) $(htslib_khash_h) $(htslib_hts_log_h) test/test_bgzf.o: test/test_bgzf.c config.h $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_hts_log_h) $(hfile_internal_h) test/test_expr.o: test/test_expr.c config.h $(htslib_hts_expr_h) test/test_kfunc.o: test/test_kfunc.c config.h $(htslib_kfunc_h) test/test_khash.o: test/test_khash.c config.h $(htslib_khash_h) $(htslib_kroundup_h) test/test_kstring.o: test/test_kstring.c config.h $(htslib_kstring_h) test/test_mod.o: test/test_mod.c config.h $(htslib_sam_h) test/test_nibbles.o: test/test_nibbles.c config.h $(htslib_sam_h) $(sam_internal_h) test/test-parse-reg.o: test/test-parse-reg.c config.h $(htslib_hts_h) $(htslib_sam_h) test/test_realn.o: test/test_realn.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) test/test-regidx.o: test/test-regidx.c config.h $(htslib_kstring_h) $(htslib_regidx_h) $(htslib_hts_defs_h) $(textutils_internal_h) test/test_str2int.o: test/test_str2int.c config.h $(textutils_internal_h) test/test_time_funcs.o: test/test_time_funcs.c config.h $(hts_time_funcs_h) test/test_view.o: test/test_view.c config.h $(cram_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_hts_log_h) test/test_faidx.o: test/test_faidx.c config.h $(htslib_faidx_h) test/test_index.o: test/test_index.c config.h $(htslib_sam_h) $(htslib_vcf_h) test/test-vcf-api.o: test/test-vcf-api.c config.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h) test/test-vcf-sweep.o: test/test-vcf-sweep.c config.h $(htslib_vcf_sweep_h) test/test-bcf-sr.o: test/test-bcf-sr.c config.h $(htslib_synced_bcf_reader_h) $(htslib_hts_h) $(htslib_vcf_h) test/test-bcf-translate.o: test/test-bcf-translate.c config.h $(htslib_vcf_h) test/test_introspection.o: test/test_introspection.c config.h $(htslib_hts_h) $(htslib_hfile_h) test/test-bcf_set_variant_type.o: test/test-bcf_set_variant_type.c config.h $(htslib_hts_h) vcf.c # Standalone target not added to $(BUILT_TEST_PROGRAMS) as some may not # have a compiler that compiles as C++ when given a .cpp source file. test/usepublic.o: test/usepublic.cpp config.h $(htslib_bgzf_h) $(htslib_cram_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_hts_h) $(htslib_hts_defs_h) $(htslib_hts_endian_h) $(htslib_hts_expr_h) $(htslib_hts_log_h) $(htslib_hts_os_h) $(htslib_kbitset_h) $(htslib_kfunc_h) $(htslib_khash_h) $(htslib_khash_str2int_h) $(htslib_klist_h) $(HTSPREFIX)htslib/knetfile.h $(htslib_kroundup_h) $(htslib_kseq_h) $(htslib_ksort_h) $(htslib_kstring_h) $(htslib_regidx_h) $(htslib_sam_h) $(htslib_synced_bcf_reader_h) $(htslib_tbx_h) $(htslib_thread_pool_h) $(htslib_vcf_h) $(htslib_vcf_sweep_h) $(htslib_vcfutils_h) $(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) -c -o $@ test/usepublic.cpp test/thrash_threads1: test/thrash_threads1.o libhts.a $(CC) $(LDFLAGS) -o $@ test/thrash_threads1.o libhts.a $(LIBS) -lpthread test/thrash_threads2: test/thrash_threads2.o libhts.a $(CC) $(LDFLAGS) -o $@ test/thrash_threads2.o libhts.a $(LIBS) -lpthread test/thrash_threads3: test/thrash_threads3.o libhts.a $(CC) $(LDFLAGS) -o $@ test/thrash_threads3.o libhts.a $(LIBS) -lpthread test/thrash_threads4: test/thrash_threads4.o libhts.a $(CC) $(LDFLAGS) -o $@ test/thrash_threads4.o libhts.a $(LIBS) -lpthread test/thrash_threads5: test/thrash_threads5.o libhts.a $(CC) $(LDFLAGS) -o $@ test/thrash_threads5.o libhts.a $(LIBS) -lpthread test/thrash_threads6: test/thrash_threads6.o libhts.a $(CC) $(LDFLAGS) -o $@ test/thrash_threads6.o libhts.a $(LIBS) -lpthread test/thrash_threads7: test/thrash_threads7.o libhts.a $(CC) $(LDFLAGS) -o $@ test/thrash_threads7.o libhts.a $(LIBS) -lpthread test_thrash: $(BUILT_THRASH_PROGRAMS) # Test to ensure the functions in the header files are exported by the shared # library. This currently works by comparing the output from ctags on # the headers with the list of functions exported by the shared library. # Note that functions marked as exported in the .c files and not the public # headers will be missed by this test. test-shlib-exports: header-exports.txt shlib-exports-$(SHLIB_FLAVOUR).txt @echo "Checking shared library exports" @if test ! -s header-exports.txt ; then echo "Error: header-exports.txt empty" ; false ; fi @if test ! -s shlib-exports-$(SHLIB_FLAVOUR).txt ; then echo "Error: shlib-exports-$(SHLIB_FLAVOUR).txt empty" ; false ; fi @! comm -23 header-exports.txt shlib-exports-$(SHLIB_FLAVOUR).txt | grep . || \ ( echo "Error: Found unexported symbols (listed above)" ; false ) # Extract symbols that should be exported from public headers using ctags # Filter out macros in htslib/hts_defs.h. header-exports.txt: test/header_syms.pl htslib/*.h test/header_syms.pl htslib/*.h | sort -u -o $@ shlib-exports-so.txt: libhts.so nm -D -g libhts.so | awk '$$2 == "T" { sub("@.*", "", $$3); print $$3 }' | sort -u -o $@ shlib-exports-dylib.txt: libhts.dylib nm -Ug libhts.dylib | awk '$$2 == "T" { sub("^_", "", $$3); print $$3 }' | sort -u -o $@ shlib-exports-dll.txt: hts.dll.a nm -g hts.dll.a | awk '$$2 == "T" { print $$3 }' | sort -u -o $@ $(srcprefix)htslib.map: libhts.so LC_ALL=C ; export LC_ALL; \ curr_vers=`expr 'X$(PACKAGE_VERSION)' : 'X\([0-9]*\.[0-9.]*\)'` ; \ last_vers=`awk '/^HTSLIB_[0-9](\.[0-9]+)+/ { lv = $$1 } END { print lv }' htslib.map` ; \ if test "x$$curr_vers" = 'x' || test "x$$last_vers" = 'x' ; then \ echo "Version check failed : $$curr_vers / $$las_vers" 1>&2 ; \ exit 1 ; \ fi && \ if test "HTSLIB_$$curr_vers" = "$$last_vers" ; then \ echo "Refusing to update $@ - HTSlib version not changed" 1>&2 ; \ exit 1 ; \ fi && \ nm --with-symbol-versions -D -g libhts.so | awk '$$2 ~ /^[DGRT]$$/ && $$3 ~ /@@Base$$/ && $$3 !~ /^(_init|_fini|_edata)@@/ { sub(/@@Base$$/, ";", $$3); print " " $$3 }' > $@.tmp && \ if [ -s $@.tmp ] ; then \ cat $@ > $@.new.tmp && \ printf '\n%s {\n' "HTSLIB_$$curr_vers" >> $@.new.tmp && \ cat $@.tmp >> $@.new.tmp && \ printf '} %s;\n' "$$last_vers" >> $@.new.tmp && \ rm -f $@.tmp && \ mv $@.new.tmp $@ ; \ fi ; \ else \ rm -f $@.tmp ; \ fi install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig $(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir) if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi $(INSTALL_DATA) $(SRC)htslib/*.h $(DESTDIR)$(includedir)/htslib $(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a $(INSTALL_MAN) $(SRC)annot-tsv.1 $(SRC)bgzip.1 $(SRC)htsfile.1 $(SRC)tabix.1 $(DESTDIR)$(man1dir) $(INSTALL_MAN) $(SRC)faidx.5 $(SRC)sam.5 $(SRC)vcf.5 $(DESTDIR)$(man5dir) $(INSTALL_MAN) $(SRC)htslib-s3-plugin.7 $(DESTDIR)$(man7dir) installdirs: $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(man7dir) $(DESTDIR)$(pkgconfigdir) if test -n "$(plugindir)"; then $(INSTALL_DIR) $(DESTDIR)$(plugindir); fi # After installation, the real file in $(libdir) will be libhts.so.X.Y.Z, # with symlinks libhts.so (used via -lhts during linking of client programs) # and libhts.so.NN (used by client executables at runtime). install-so: libhts.so installdirs $(INSTALL_LIB) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION) ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION) install-cygdll: cyghts-$(LIBHTS_SOVERSION).dll installdirs $(INSTALL_PROGRAM) cyghts-$(LIBHTS_SOVERSION).dll $(DESTDIR)$(bindir)/cyghts-$(LIBHTS_SOVERSION).dll $(INSTALL_PROGRAM) libhts.dll.a $(DESTDIR)$(libdir)/libhts.dll.a install-dll: hts-$(LIBHTS_SOVERSION).dll installdirs $(INSTALL_PROGRAM) hts-$(LIBHTS_SOVERSION).dll $(DESTDIR)$(bindir)/hts-$(LIBHTS_SOVERSION).dll $(INSTALL_PROGRAM) hts.dll.a $(DESTDIR)$(libdir)/hts.dll.a install-dylib: libhts.dylib installdirs $(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib # Substitute these pseudo-autoconf variables only at install time # so that "make install prefix=/prefix/path" etc continue to work. install-pkgconfig: htslib.pc.tmp installdirs sed -e 's#@-includedir@#$(includedir)#g;s#@-libdir@#$(libdir)#g;s#@-PACKAGE_VERSION@#$(PACKAGE_VERSION)#g' htslib.pc.tmp > $(DESTDIR)$(pkgconfigdir)/htslib.pc chmod 644 $(DESTDIR)$(pkgconfigdir)/htslib.pc # A pkg-config file (suitable for copying to $PKG_CONFIG_PATH) that provides # flags for building against the uninstalled library in this build directory. htslib-uninstalled.pc: htslib.pc.tmp sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > $@ testclean: -rm -f test/*.tmp test/*.tmp.* test/faidx/*.tmp* \ test/longrefs/*.tmp.* test/tabix/*.tmp.* \ test/bgzf_boundaries/*.tmp.* test/*/FAIL* \ header-exports.txt shlib-exports-$(SHLIB_FLAVOUR).txt -rm -rf htscodecs/tests/test.out # Only remove this in git checkouts DEL_HTSCODECS_VERSION := $(if $(wildcard htscodecs/.git),htscodecs/htscodecs/version.h) mostlyclean: testclean -rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM config_vars.h version.h -rm -f htscodecs/htscodecs/*.o htscodecs/htscodecs/*.pico $(DEL_HTSCODECS_VERSION) -rm -f hts-object-files -rm -f htscodecs/tests/*.o clean: mostlyclean clean-$(SHLIB_FLAVOUR) -rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS) $(BUILT_THRASH_PROGRAMS) -rm -f htscodecs/tests/rans4x8 htscodecs/tests/rans4x16pr htscodecs/tests/arith_dynamic htscodecs/tests/tokenise_name3 htscodecs/tests/fqzcomp_qual htscodecs/tests/varint distclean maintainer-clean: clean -rm -f config.cache config.h config.log config.mk config.status -rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk htscodecs.mk -rm -rf autom4te.cache clean-so: -rm -f libhts.so libhts.so.* clean-cygdll: -rm -f cyghts-*.dll libhts.dll.a clean-dll: -rm -f hts-*.dll hts.dll.a clean-dylib: -rm -f libhts.dylib libhts.*.dylib tags TAGS: ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h # We recommend libhts-using programs be built against a separate htslib # installation. However if you feel that you must bundle htslib source # code with your program, this hook enables Automake-style "make dist" # for this subdirectory. If you do bundle an htslib snapshot, please # add identifying information to $(PACKAGE_VERSION) as appropriate. # (The wildcards attempt to omit non-exported files (.git*, README.md, # etc) and other detritus that might be in the top-level directory.) distdir: @if [ -z "$(distdir)" ]; then echo "Please supply a distdir=DIR argument."; false; fi tar -c *.[ch15] [ILMNRchtv]*[ELSbcekmnth] | (cd $(distdir) && tar -x) +cd $(distdir) && $(MAKE) distclean force: .PHONY: all check check-untracked clean distclean distdir force .PHONY: install install-pkgconfig installdirs lib-shared lib-static .PHONY: maintainer-check maintainer-clean mostlyclean plugins .PHONY: print-config print-version show-version tags .PHONY: test test-shlib-exports test_thrash testclean .PHONY: clean-so install-so .PHONY: clean-cygdll install-cygdll .PHONY: clean-dll install-dll .PHONY: clean-dylib install-dylib .PHONY: test_htscodecs_rans4x8 test_htscodecs_rans4x16 test_htscodecs_arith .PHONY: test_htscodecs_tok3 test_htscodecs_fqzcomp test_htscodecs_varint .PHONY: cc-version pysam-0.23.0/htslib/README000066400000000000000000000051701475062545500151120ustar00rootroot00000000000000HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing data. It is the core library used by samtools and bcftools. See INSTALL for building and installation instructions. Please cite this paper when using HTSlib for your publications: HTSlib: C library for reading/writing high-throughput sequencing data James K Bonfield, John Marshall, Petr Danecek, Heng Li, Valeriu Ohan, Andrew Whitwham, Thomas Keane, Robert M Davies GigaScience, Volume 10, Issue 2, February 2021, giab007, https://doi.org/10.1093/gigascience/giab007 @article{10.1093/gigascience/giab007, author = {Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas and Davies, Robert M}, title = "{HTSlib: C library for reading/writing high-throughput sequencing data}", journal = {GigaScience}, volume = {10}, number = {2}, year = {2021}, month = {02}, abstract = "{Since the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on performance and robustness. The file formats themselves have become international standards under the jurisdiction of the Global Alliance for Genomics and Health.We present a software library for providing programmatic access to sequencing alignment and variant formats. It was born out of the widely used SAMtools and BCFtools applications. Considerable improvements have been made to the original code plus many new features including newer access protocols, the addition of the CRAM file format, better indexing and iterators, and better use of threading.Since the original Samtools release, performance has been considerably improved, with a BAM read-write loop running 5 times faster and BAM to SAM conversion 13 times faster (both using 16 threads, compared to Samtools 0.1.19). Widespread adoption has seen HTSlib downloaded \\>1 million times from GitHub and conda. The C library has been used directly by an estimated 900 GitHub projects and has been incorporated into Perl, Python, Rust, and R, significantly expanding the number of uses via other languages. HTSlib is open source and is freely available from htslib.org under MIT/BSD license.}", issn = {2047-217X}, doi = {10.1093/gigascience/giab007}, url = {https://doi.org/10.1093/gigascience/giab007}, note = {giab007}, eprint = {https://academic.oup.com/gigascience/article-pdf/10/2/giab007/36332285/giab007.pdf}, } pysam-0.23.0/htslib/bcf_sr_sort.c000066400000000000000000000547121475062545500167110ustar00rootroot00000000000000/* Copyright (C) 2017-2021 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include "bcf_sr_sort.h" #include "htslib/khash_str2int.h" #include "htslib/kbitset.h" #define SR_REF 1 #define SR_SNP 2 #define SR_INDEL 4 #define SR_OTHER 8 #define SR_SCORE(srt,a,b) (srt)->score[((a)<<4)|(b)] // Logical AND static inline int kbs_logical_and(kbitset_t *bs1, kbitset_t *bs2) { // General case, bitsets of unequal size: // int i, n = bs1->n < bs2->n ? bs1->n : bs2->n; int i, n = bs1->n; for (i=0; ib[i] & bs2->b[i] ) return 1; return 0; } // Bitwise OR, dst will be modified, src will be left unchanged static inline void kbs_bitwise_or(kbitset_t *dst, kbitset_t *src) { int i; for (i=0; in; i++) dst->b[i] |= src->b[i]; } static void bcf_sr_init_scores(sr_sort_t *srt) { int i,jbit,kbit; // lower number = lower priority, zero means forbidden if ( srt->pair & BCF_SR_PAIR_ANY ) srt->pair |= (BCF_SR_PAIR_SNPS | BCF_SR_PAIR_INDELS | BCF_SR_PAIR_SNP_REF | BCF_SR_PAIR_INDEL_REF); if ( srt->pair & BCF_SR_PAIR_SNPS ) SR_SCORE(srt,SR_SNP,SR_SNP) = 3; if ( srt->pair & BCF_SR_PAIR_INDELS ) SR_SCORE(srt,SR_INDEL,SR_INDEL) = 3; if ( srt->pair & BCF_SR_PAIR_SNP_REF ) { SR_SCORE(srt,SR_SNP,SR_REF) = 2; SR_SCORE(srt,SR_REF,SR_SNP) = 2; } if ( srt->pair & BCF_SR_PAIR_INDEL_REF ) { SR_SCORE(srt,SR_INDEL,SR_REF) = 2; SR_SCORE(srt,SR_REF,SR_INDEL) = 2; } if ( srt->pair & BCF_SR_PAIR_ANY ) { for (i=0; i<256; i++) if ( !srt->score[i] ) srt->score[i] = 1; } // set all combinations for (i=0; i<256; i++) { if ( srt->score[i] ) continue; // already set int max = 0; for (jbit=0; jbit<4; jbit++) // high bits { int j = 1<score[i] = max; } } static int multi_is_exact(var_t *avar, var_t *bvar) { if ( avar->nalt != bvar->nalt ) return 0; int alen = strlen(avar->str); int blen = strlen(bvar->str); if ( alen != blen ) return 0; char *abeg = avar->str; while ( *abeg ) { char *aend = abeg; while ( *aend && *aend!=',' ) aend++; char *bbeg = bvar->str; while ( *bbeg ) { char *bend = bbeg; while ( *bend && *bend!=',' ) bend++; if ( bend - bbeg == aend - abeg && !strncasecmp(abeg,bbeg,bend-bbeg) ) break; bbeg = *bend ? bend+1 : bend; } if ( !*bbeg ) return 0; abeg = *aend ? aend+1 : aend; } return 1; } static int multi_is_subset(var_t *avar, var_t *bvar) { char *abeg = avar->str; while ( *abeg ) { char *aend = abeg; while ( *aend && *aend!=',' ) aend++; char *bbeg = bvar->str; while ( *bbeg ) { char *bend = bbeg; while ( *bend && *bend!=',' ) bend++; if ( bend - bbeg == aend - abeg && !strncasecmp(abeg,bbeg,bend-bbeg) ) return 1; bbeg = *bend ? bend+1 : bend; } abeg = *aend ? aend+1 : aend; } return 0; } static uint32_t pairing_score(sr_sort_t *srt, int ivset, int jvset) { varset_t *iv = &srt->vset[ivset]; varset_t *jv = &srt->vset[jvset]; // Restrictive logic: the strictest type from a group is selected, // so that, for example, snp+ref does not lead to the inclusion of an indel int i,j; uint32_t min = UINT32_MAX; for (i=0; invar; i++) { var_t *ivar = &srt->var[iv->var[i]]; for (j=0; jnvar; j++) { var_t *jvar = &srt->var[jv->var[j]]; if ( srt->pair & BCF_SR_PAIR_EXACT ) { if ( ivar->type != jvar->type ) continue; if ( !strcmp(ivar->str,jvar->str) ) return UINT32_MAX; // exact match, best possibility if ( multi_is_exact(ivar,jvar) ) return UINT32_MAX; // identical alleles continue; } if ( ivar->type==jvar->type && !strcmp(ivar->str,jvar->str) ) return UINT32_MAX; // exact match, best possibility if ( ivar->type & jvar->type && multi_is_subset(ivar,jvar) ) return UINT32_MAX; // one of the alleles is identical uint32_t score = SR_SCORE(srt,ivar->type,jvar->type); if ( !score ) return 0; // some of the varsets in the two groups are not compatible, will not pair if ( min>score ) min = score; } } if ( srt->pair & BCF_SR_PAIR_EXACT ) return 0; assert( min!=UINT32_MAX ); uint32_t cnt = 0; for (i=0; invar; i++) cnt += srt->var[iv->var[i]].nvcf; for (j=0; jnvar; j++) cnt += srt->var[jv->var[j]].nvcf; return (1u<<(28+min)) + cnt; } static void remove_vset(sr_sort_t *srt, int jvset) { if ( jvset+1 < srt->nvset ) { varset_t tmp = srt->vset[jvset]; memmove(&srt->vset[jvset], &srt->vset[jvset+1], sizeof(varset_t)*(srt->nvset - jvset - 1)); srt->vset[srt->nvset-1] = tmp; int *jmat = srt->pmat + jvset*srt->ngrp; memmove(jmat, &jmat[srt->ngrp],sizeof(int)*(srt->nvset - jvset - 1)*srt->ngrp); memmove(&srt->cnt[jvset], &srt->cnt[jvset+1], sizeof(int)*(srt->nvset - jvset - 1)); } srt->nvset--; } static int merge_vsets(sr_sort_t *srt, int ivset, int jvset) { int i,j; if ( ivset > jvset ) { i = ivset; ivset = jvset; jvset = i; } varset_t *iv = &srt->vset[ivset]; varset_t *jv = &srt->vset[jvset]; kbs_bitwise_or(iv->mask,jv->mask); i = iv->nvar; iv->nvar += jv->nvar; hts_expand(int, iv->nvar, iv->mvar, iv->var); for (j=0; jnvar; j++,i++) iv->var[i] = jv->var[j]; int *imat = srt->pmat + ivset*srt->ngrp; int *jmat = srt->pmat + jvset*srt->ngrp; for (i=0; ingrp; i++) imat[i] += jmat[i]; srt->cnt[ivset] += srt->cnt[jvset]; remove_vset(srt, jvset); return ivset; } static int push_vset(sr_sort_t *srt, int ivset) { varset_t *iv = &srt->vset[ivset]; int i,j; for (i=0; isr->nreaders; i++) { vcf_buf_t *buf = &srt->vcf_buf[i]; buf->nrec++; hts_expand(bcf1_t*,buf->nrec,buf->mrec,buf->rec); buf->rec[buf->nrec-1] = NULL; } for (i=0; invar; i++) { var_t *var = &srt->var[ iv->var[i] ]; for (j=0; jnvcf; j++) { int jvcf = var->vcf[j]; vcf_buf_t *buf = &srt->vcf_buf[jvcf]; buf->rec[buf->nrec-1] = var->rec[j]; } } remove_vset(srt, ivset); return 0; // FIXME: check for errs in this function } static int cmpstringp(const void *p1, const void *p2) { return strcmp(* (char * const *) p1, * (char * const *) p2); } #define DEBUG_VSETS 0 #if DEBUG_VSETS void debug_vsets(sr_sort_t *srt) { int i,j,k; for (i=0; invset; i++) { fprintf(stderr,"dbg_vset %d:", i); for (j=0; jvset[i].mask->n; j++) fprintf(stderr,"%c%lu",j==0?' ':':',srt->vset[i].mask->b[j]); fprintf(stderr,"\t"); for (j=0; jvset[i].nvar; j++) { var_t *var = &srt->var[srt->vset[i].var[j]]; fprintf(stderr,"\t%s",var->str); for (k=0; knvcf; k++) fprintf(stderr,"%c%d", k==0?':':',',var->vcf[k]); } fprintf(stderr,"\n"); } } #endif #define DEBUG_VBUF 0 #if DEBUG_VBUF void debug_vbuf(sr_sort_t *srt) { int i, j; for (j=0; jvcf_buf[0].nrec; j++) { fprintf(stderr,"dbg_vbuf %d:\t", j); for (i=0; isr->nreaders; i++) { vcf_buf_t *buf = &srt->vcf_buf[i]; fprintf(stderr,"\t%"PRIhts_pos, buf->rec[j] ? buf->rec[j]->pos+1 : 0); } fprintf(stderr,"\n"); } } #endif static char *grp_create_key(sr_sort_t *srt) { if ( !srt->str.l ) return strdup(""); int i; hts_expand(char*,srt->noff,srt->mcharp,srt->charp); for (i=0; inoff; i++) { srt->charp[i] = srt->str.s + srt->off[i]; if ( i>0 ) srt->charp[i][-1] = 0; } qsort(srt->charp, srt->noff, sizeof(*srt->charp), cmpstringp); char *ret = (char*) malloc(srt->str.l + 1), *ptr = ret; for (i=0; inoff; i++) { int len = strlen(srt->charp[i]); memcpy(ptr, srt->charp[i], len); ptr += len + 1; ptr[-1] = i+1==srt->noff ? 0 : ';'; } return ret; } int bcf_sr_sort_set_active(sr_sort_t *srt, int idx) { hts_expand(int,idx+1,srt->mactive,srt->active); srt->nactive = 1; srt->active[srt->nactive - 1] = idx; return 0; // FIXME: check for errs in this function } int bcf_sr_sort_add_active(sr_sort_t *srt, int idx) { hts_expand(int,idx+1,srt->mactive,srt->active); srt->nactive++; srt->active[srt->nactive - 1] = idx; return 0; // FIXME: check for errs in this function } static int bcf_sr_sort_set(bcf_srs_t *readers, sr_sort_t *srt, const char *chr, hts_pos_t min_pos) { if ( !srt->grp_str2int ) { // first time here, initialize if ( !srt->pair ) { if ( readers->collapse==COLLAPSE_NONE ) readers->collapse = BCF_SR_PAIR_EXACT; bcf_sr_set_opt(readers, BCF_SR_PAIR_LOGIC, readers->collapse); } bcf_sr_init_scores(srt); srt->grp_str2int = khash_str2int_init(); srt->var_str2int = khash_str2int_init(); } int k; khash_t(str2int) *hash; hash = srt->grp_str2int; for (k=0; k < kh_end(hash); k++) if ( kh_exist(hash,k) ) free((char*)kh_key(hash,k)); hash = srt->var_str2int; for (k=0; k < kh_end(hash); k++) if ( kh_exist(hash,k) ) free((char*)kh_key(hash,k)); kh_clear(str2int, srt->grp_str2int); kh_clear(str2int, srt->var_str2int); srt->ngrp = srt->nvar = srt->nvset = 0; grp_t grp; memset(&grp,0,sizeof(grp_t)); // group VCFs into groups, each with a unique combination of variants in the duplicate lines int ireader,ivar,irec,igrp,ivset,iact; for (ireader=0; ireadernreaders; ireader++) srt->vcf_buf[ireader].nrec = 0; for (iact=0; iactnactive; iact++) { ireader = srt->active[iact]; bcf_sr_t *reader = &readers->readers[ireader]; int rid = bcf_hdr_name2id(reader->header, chr); grp.nvar = 0; hts_expand(int,reader->nbuffer,srt->moff,srt->off); srt->noff = 0; srt->str.l = 0; for (irec=1; irec<=reader->nbuffer; irec++) { bcf1_t *line = reader->buffer[irec]; if ( line->rid!=rid || line->pos!=min_pos ) break; if ( srt->str.l ) kputc(';',&srt->str); srt->off[srt->noff++] = srt->str.l; size_t beg = srt->str.l; int end_pos = -1; for (ivar=1; ivarn_allele; ivar++) { if ( ivar>1 ) kputc(',',&srt->str); kputs(line->d.allele[0],&srt->str); kputc('>',&srt->str); kputs(line->d.allele[ivar],&srt->str); // If symbolic allele, check also the END tag in case there are multiple events, // such as s, starting at the same positions if ( line->d.allele[ivar][0]=='<' ) { if ( end_pos==-1 ) { bcf_info_t *end_info = bcf_get_info(reader->header,line,"END"); if ( end_info ) end_pos = (int)end_info->v1.i; // this is only to create a unique id, we don't mind a potential int64 overflow else end_pos = 0; } if ( end_pos ) { kputc('/',&srt->str); kputw(end_pos, &srt->str); } } } if ( line->n_allele==1 ) { kputs(line->d.allele[0],&srt->str); kputsn(">.",2,&srt->str); } // Create new variant or attach to existing one. But careful, there can be duplicate // records with the same POS,REF,ALT (e.g. in dbSNP-b142) char *var_str = beg + srt->str.s; int ret, var_idx = 0, var_end = srt->str.l; while ( 1 ) { ret = khash_str2int_get(srt->var_str2int, var_str, &ivar); if ( ret==-1 ) break; var_t *var = &srt->var[ivar]; if ( var->vcf[var->nvcf-1] != ireader ) break; srt->str.l = var_end; kputw(var_idx, &srt->str); var_str = beg + srt->str.s; var_idx++; } if ( ret==-1 ) { ivar = srt->nvar++; hts_expand0(var_t,srt->nvar,srt->mvar,srt->var); srt->var[ivar].nvcf = 0; khash_str2int_set(srt->var_str2int, strdup(var_str), ivar); free(srt->var[ivar].str); // possible left-over from the previous position } var_t *var = &srt->var[ivar]; var->nalt = line->n_allele - 1; var->type = bcf_get_variant_types(line); srt->str.s[var_end] = 0; if ( ret==-1 ) var->str = strdup(var_str); int mvcf = var->mvcf; var->nvcf++; hts_expand0(int*, var->nvcf, var->mvcf, var->vcf); if ( mvcf != var->mvcf ) var->rec = (bcf1_t **) realloc(var->rec,sizeof(bcf1_t*)*var->mvcf); var->vcf[var->nvcf-1] = ireader; var->rec[var->nvcf-1] = line; grp.nvar++; hts_expand(var_t,grp.nvar,grp.mvar,grp.var); grp.var[grp.nvar-1] = ivar; } char *grp_key = grp_create_key(srt); int ret = khash_str2int_get(srt->grp_str2int, grp_key, &igrp); if ( ret==-1 ) { igrp = srt->ngrp++; hts_expand0(grp_t, srt->ngrp, srt->mgrp, srt->grp); free(srt->grp[igrp].var); srt->grp[igrp] = grp; srt->grp[igrp].key = grp_key; khash_str2int_set(srt->grp_str2int, grp_key, igrp); memset(&grp,0,sizeof(grp_t)); } else free(grp_key); srt->grp[igrp].nvcf++; } free(grp.var); // initialize bitmask - which groups is the variant present in for (ivar=0; ivarnvar; ivar++) { if ( kbs_resize(&srt->var[ivar].mask, srt->ngrp) < 0 ) { fprintf(stderr, "[%s:%d %s] kbs_resize failed\n", __FILE__,__LINE__,__func__); exit(1); } kbs_clear(srt->var[ivar].mask); } for (igrp=0; igrpngrp; igrp++) { for (ivar=0; ivargrp[igrp].nvar; ivar++) { int i = srt->grp[igrp].var[ivar]; kbs_insert(srt->var[i].mask, igrp); } } // create the initial list of variant sets for (ivar=0; ivarnvar; ivar++) { ivset = srt->nvset++; hts_expand0(varset_t, srt->nvset, srt->mvset, srt->vset); varset_t *vset = &srt->vset[ivset]; vset->nvar = 1; hts_expand0(var_t, vset->nvar, vset->mvar, vset->var); vset->var[vset->nvar-1] = ivar; var_t *var = &srt->var[ivar]; vset->cnt = var->nvcf; if ( kbs_resize(&vset->mask, srt->ngrp) < 0 ) { fprintf(stderr, "[%s:%d %s] kbs_resize failed\n", __FILE__,__LINE__,__func__); exit(1); } kbs_clear(vset->mask); kbs_bitwise_or(vset->mask, var->mask); int type = 0; if ( var->type==VCF_REF ) type |= SR_REF; else { if ( var->type & VCF_SNP ) type |= SR_SNP; if ( var->type & VCF_MNP ) type |= SR_SNP; if ( var->type & VCF_INDEL ) type |= SR_INDEL; if ( var->type & VCF_OTHER ) type |= SR_OTHER; } var->type = type; } #if DEBUG_VSETS debug_vsets(srt); #endif // initialize the pairing matrix hts_expand(int, srt->ngrp*srt->nvset, srt->mpmat, srt->pmat); hts_expand(int, srt->nvset, srt->mcnt, srt->cnt); memset(srt->pmat, 0, sizeof(*srt->pmat)*srt->ngrp*srt->nvset); for (ivset=0; ivsetnvset; ivset++) { varset_t *vset = &srt->vset[ivset]; for (igrp=0; igrpngrp; igrp++) srt->pmat[ivset*srt->ngrp+igrp] = 0; srt->cnt[ivset] = vset->cnt; } // pair the lines while ( srt->nvset ) { #if DEBUG_VSETS fprintf(stderr,"\n"); debug_vsets(srt); #endif int imax = 0; for (ivset=1; ivsetnvset; ivset++) if ( srt->cnt[imax] < srt->cnt[ivset] ) imax = ivset; int ipair = -1; uint32_t max_score = 0; for (ivset=0; ivsetnvset; ivset++) { if ( kbs_logical_and(srt->vset[imax].mask,srt->vset[ivset].mask) ) continue; // cannot be merged uint32_t score = pairing_score(srt, imax, ivset); // fprintf(stderr,"score: %d %d, logic=%d \t..\t %u\n", imax,ivset,srt->pair,score); if ( max_score < score ) { max_score = score; ipair = ivset; } } // merge rows creating a new variant set this way if ( ipair!=-1 && ipair!=imax ) { imax = merge_vsets(srt, imax, ipair); continue; } push_vset(srt, imax); } srt->chr = chr; srt->pos = min_pos; return 0; // FIXME: check for errs in this function } int bcf_sr_sort_next(bcf_srs_t *readers, sr_sort_t *srt, const char *chr, hts_pos_t min_pos) { int i,j; assert( srt->nactive>0 ); if ( srt->nsr != readers->nreaders ) { srt->sr = readers; if ( srt->nsr < readers->nreaders ) { srt->vcf_buf = (vcf_buf_t*) realloc(srt->vcf_buf,readers->nreaders*sizeof(vcf_buf_t)); memset(srt->vcf_buf + srt->nsr, 0, sizeof(vcf_buf_t)*(readers->nreaders - srt->nsr)); if ( srt->msr < srt->nsr ) srt->msr = srt->nsr; } srt->nsr = readers->nreaders; srt->chr = NULL; } if ( srt->nactive == 1 ) { if ( readers->nreaders>1 ) memset(readers->has_line, 0, readers->nreaders*sizeof(*readers->has_line)); bcf_sr_t *reader = &readers->readers[srt->active[0]]; assert( reader->buffer[1]->pos==min_pos ); bcf1_t *tmp = reader->buffer[0]; for (j=1; j<=reader->nbuffer; j++) reader->buffer[j-1] = reader->buffer[j]; reader->buffer[ reader->nbuffer ] = tmp; reader->nbuffer--; readers->has_line[srt->active[0]] = 1; return 1; } if ( !srt->chr || srt->pos!=min_pos || strcmp(srt->chr,chr) ) bcf_sr_sort_set(readers, srt, chr, min_pos); if ( !srt->vcf_buf[0].nrec ) return 0; #if DEBUG_VBUF debug_vbuf(srt); #endif int nret = 0; for (i=0; isr->nreaders; i++) { vcf_buf_t *buf = &srt->vcf_buf[i]; if ( buf->rec[0] ) { bcf_sr_t *reader = &srt->sr->readers[i]; for (j=1; j<=reader->nbuffer; j++) if ( reader->buffer[j] == buf->rec[0] ) break; assert( j<=reader->nbuffer ); bcf1_t *tmp = reader->buffer[0]; reader->buffer[0] = reader->buffer[j++]; for (; j<=reader->nbuffer; j++) reader->buffer[j-1] = reader->buffer[j]; reader->buffer[ reader->nbuffer ] = tmp; reader->nbuffer--; nret++; srt->sr->has_line[i] = 1; } else srt->sr->has_line[i] = 0; buf->nrec--; if ( buf->nrec > 0 ) memmove(buf->rec, &buf->rec[1], buf->nrec*sizeof(bcf1_t*)); } return nret; } void bcf_sr_sort_remove_reader(bcf_srs_t *readers, sr_sort_t *srt, int i) { //vcf_buf is allocated only in bcf_sr_sort_next //So, a call to bcf_sr_add_reader() followed immediately by bcf_sr_remove_reader() //would cause the program to crash in this segment if (srt->vcf_buf) { free(srt->vcf_buf[i].rec); if ( i+1 < srt->nsr ) memmove(&srt->vcf_buf[i], &srt->vcf_buf[i+1], (srt->nsr - i - 1)*sizeof(vcf_buf_t)); memset(srt->vcf_buf + srt->nsr - 1, 0, sizeof(vcf_buf_t)); } } sr_sort_t *bcf_sr_sort_init(sr_sort_t *srt) { if ( !srt ) return calloc(1,sizeof(sr_sort_t)); memset(srt,0,sizeof(sr_sort_t)); return srt; } void bcf_sr_sort_reset(sr_sort_t *srt) { srt->chr = NULL; } void bcf_sr_sort_destroy(sr_sort_t *srt) { free(srt->active); if ( srt->var_str2int ) khash_str2int_destroy_free(srt->var_str2int); if ( srt->grp_str2int ) khash_str2int_destroy_free(srt->grp_str2int); int i; for (i=0; insr; i++) free(srt->vcf_buf[i].rec); free(srt->vcf_buf); for (i=0; imvar; i++) { free(srt->var[i].str); free(srt->var[i].vcf); free(srt->var[i].rec); kbs_destroy(srt->var[i].mask); } free(srt->var); for (i=0; imgrp; i++) free(srt->grp[i].var); free(srt->grp); for (i=0; imvset; i++) { kbs_destroy(srt->vset[i].mask); free(srt->vset[i].var); } free(srt->vset); free(srt->str.s); free(srt->off); free(srt->charp); free(srt->cnt); free(srt->pmat); memset(srt,0,sizeof(*srt)); } pysam-0.23.0/htslib/bcf_sr_sort.h000066400000000000000000000074351475062545500167160ustar00rootroot00000000000000/* Copyright (C) 2017 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Reorder duplicate lines so that compatible variant types are returned together by bcf_sr_next_line() - readers grouped by variants. Even with many readers there will be typically only several groups */ #ifndef BCF_SR_SORT_H #define BCF_SR_SORT_H #include "htslib/synced_bcf_reader.h" #include "htslib/kbitset.h" typedef struct { int nrec, mrec; bcf1_t **rec; } vcf_buf_t; typedef struct { char *str; // "A>C" for biallelic records or "A>C,A>CC" for multiallelic records int type; // VCF_SNP, VCF_REF, etc. int nalt; // number of alternate alleles in this record int nvcf, mvcf, *vcf; // the list of readers with the same variants bcf1_t **rec; // list of VCF records in the readers kbitset_t *mask; // which groups contain the variant } var_t; typedef struct { char *key; // only for debugging int nvar, mvar, *var; // the variants and their type int nvcf; // number of readers with the same variants } grp_t; typedef struct { int nvar, mvar, *var; // list of compatible variants that can be output together int cnt; // number of readers in this group kbitset_t *mask; // which groups are populated in this set (replace with expandable bitmask) } varset_t; typedef struct { uint8_t score[256]; int nvar, mvar; var_t *var; // list of all variants from all readers int nvset, mvset; int mpmat, *pmat; // pairing matrix, i-th vset and j-th group accessible as i*ngrp+j int ngrp, mgrp; int mcnt, *cnt; // number of VCF covered by a varset grp_t *grp; // list of VCF representatives, each with a unique combination of duplicate lines varset_t *vset; // list of variant sets - combinations of compatible variants across multiple groups ready for output vcf_buf_t *vcf_buf; // records sorted in output order, for each VCF bcf_srs_t *sr; void *grp_str2int; void *var_str2int; kstring_t str; int moff, noff, *off, mcharp; char **charp; const char *chr; hts_pos_t pos; int nsr, msr; int pair; int nactive, mactive, *active; // list of readers with lines at the current pos } sr_sort_t; sr_sort_t *bcf_sr_sort_init(sr_sort_t *srt); void bcf_sr_sort_reset(sr_sort_t *srt); int bcf_sr_sort_next(bcf_srs_t *readers, sr_sort_t *srt, const char *chr, hts_pos_t pos); int bcf_sr_sort_set_active(sr_sort_t *srt, int i); int bcf_sr_sort_add_active(sr_sort_t *srt, int i); void bcf_sr_sort_destroy(sr_sort_t *srt); void bcf_sr_sort_remove_reader(bcf_srs_t *readers, sr_sort_t *srt, int i); #endif pysam-0.23.0/htslib/bgzf.c000066400000000000000000002423271475062545500153350ustar00rootroot00000000000000/* The MIT License Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology 2011, 2012 Attractive Chaos Copyright (C) 2009, 2013-2023 Genome Research Ltd Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #include #include #include #ifdef HAVE_LIBDEFLATE #include #endif #include "htslib/hts.h" #include "htslib/bgzf.h" #include "htslib/hfile.h" #include "htslib/thread_pool.h" #include "htslib/hts_endian.h" #include "cram/pooled_alloc.h" #include "hts_internal.h" #ifndef EFTYPE #define EFTYPE ENOEXEC #endif #define BGZF_CACHE #define BGZF_MT #define BLOCK_HEADER_LENGTH 18 #define BLOCK_FOOTER_LENGTH 8 /* BGZF/GZIP header (specialized from RFC 1952; little endian): +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+ | 31|139| 8| 4| 0| 0|255| 6| 66| 67| 2|BLK_LEN| +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+ BGZF extension: ^ ^ ^ ^ | | | | FLG.EXTRA XLEN B C BGZF format is compatible with GZIP. It limits the size of each compressed block to 2^16 bytes and adds and an extra "BC" field in the gzip header which records the size. */ static const uint8_t g_magic[19] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\0\0"; #ifdef BGZF_CACHE typedef struct { int size; uint8_t *block; int64_t end_offset; } cache_t; #include "htslib/khash.h" KHASH_MAP_INIT_INT64(cache, cache_t) #endif struct bgzf_cache_t { khash_t(cache) *h; khint_t last_pos; }; #ifdef BGZF_MT typedef struct bgzf_job { BGZF *fp; unsigned char comp_data[BGZF_MAX_BLOCK_SIZE]; size_t comp_len; unsigned char uncomp_data[BGZF_MAX_BLOCK_SIZE]; size_t uncomp_len; int errcode; int64_t block_address; int hit_eof; } bgzf_job; enum mtaux_cmd { NONE = 0, SEEK, SEEK_DONE, HAS_EOF, HAS_EOF_DONE, CLOSE, }; // When multi-threaded bgzf_tell won't work, so we delay the hts_idx_push // until we've written the last block. typedef struct { hts_pos_t beg, end; int tid, is_mapped; // args for hts_idx_push uint64_t offset, block_number; } hts_idx_cache_entry; typedef struct { int nentries, mentries; // used and allocated hts_idx_cache_entry *e; // hts_idx elements } hts_idx_cache_t; typedef struct bgzf_mtaux_t { // Memory pool for bgzf_job structs, to avoid many malloc/free pool_alloc_t *job_pool; bgzf_job *curr_job; // Thread pool int n_threads; int own_pool; hts_tpool *pool; // Output queue holding completed bgzf_jobs hts_tpool_process *out_queue; // I/O thread. pthread_t io_task; pthread_mutex_t job_pool_m; int jobs_pending; // number of jobs waiting int flush_pending; void *free_block; int hit_eof; // r/w entirely within main thread // Message passing to the reader thread; eg seek requests int errcode; uint64_t block_address; int eof; pthread_mutex_t command_m; // Set whenever fp is being updated pthread_cond_t command_c; enum mtaux_cmd command; // For multi-threaded on-the-fly indexing. See bgzf_idx_push below. pthread_mutex_t idx_m; hts_idx_t *hts_idx; uint64_t block_number, block_written; hts_idx_cache_t idx_cache; } mtaux_t; #endif typedef struct { uint64_t uaddr; // offset w.r.t. uncompressed data uint64_t caddr; // offset w.r.t. compressed data } bgzidx1_t; struct bgzidx_t { int noffs, moffs; // the size of the index, n:used, m:allocated bgzidx1_t *offs; // offsets uint64_t ublock_addr; // offset of the current block (uncompressed data) }; /* * Buffers up arguments to hts_idx_push for later use, once we've written all bar * this block. This is necessary when multiple blocks are in flight (threading) * and fp->block_address isn't known at the time of call as we have in-flight * blocks that haven't yet been compressed. * * NB: this only matters when we're indexing on the fly (writing). * Normal indexing is threaded reads, but we already know block sizes * so it's a simpler process * * Returns 0 on success, * -1 on failure */ int bgzf_idx_push(BGZF *fp, hts_idx_t *hidx, int tid, hts_pos_t beg, hts_pos_t end, uint64_t offset, int is_mapped) { hts_idx_cache_entry *e; mtaux_t *mt = fp->mt; if (!mt) return hts_idx_push(hidx, tid, beg, end, offset, is_mapped); // Early check for out of range positions which would fail in hts_idx_push() if (hts_idx_check_range(hidx, tid, beg, end) < 0) return -1; pthread_mutex_lock(&mt->idx_m); mt->hts_idx = hidx; hts_idx_cache_t *ic = &mt->idx_cache; if (ic->nentries >= ic->mentries) { int new_sz = ic->mentries ? ic->mentries*2 : 1024; if (!(e = realloc(ic->e, new_sz * sizeof(*ic->e)))) { pthread_mutex_unlock(&mt->idx_m); return -1; } ic->e = e; ic->mentries = new_sz; } e = &ic->e[ic->nentries++]; e->tid = tid; e->beg = beg; e->end = end; e->is_mapped = is_mapped; e->offset = offset & 0xffff; e->block_number = mt->block_number; pthread_mutex_unlock(&mt->idx_m); return 0; } static int bgzf_idx_flush(BGZF *fp, size_t block_uncomp_len, size_t block_comp_len) { mtaux_t *mt = fp->mt; if (!mt->idx_cache.e) { mt->block_written++; return 0; } pthread_mutex_lock(&mt->idx_m); hts_idx_cache_entry *e = mt->idx_cache.e; int i; assert(mt->idx_cache.nentries == 0 || mt->block_written <= e[0].block_number); for (i = 0; i < mt->idx_cache.nentries && e[i].block_number == mt->block_written; i++) { if (block_uncomp_len > 0 && e[i].offset == block_uncomp_len) { /* * If the virtual offset is at the end of the current block, * adjust it to point to the start of the next one. This * is needed when on-the-fly indexing has recorded a virtual * offset just before a new block has been started, and makes * on-the-fly and standard indexing give exactly the same results. * * In theory the two virtual offsets are equivalent, but pointing * to the end of a block is inefficient, and caused problems with * versions of HTSlib before 1.11 where bgzf_read() would * incorrectly return EOF. */ // Assert that this is the last entry for the current block_number assert(i == mt->idx_cache.nentries - 1 || e[i].block_number < e[i + 1].block_number); // Work out where the next block starts. For this entry, the // offset will be zero. uint64_t next_block_addr = mt->block_address + block_comp_len; if (hts_idx_push(mt->hts_idx, e[i].tid, e[i].beg, e[i].end, next_block_addr << 16, e[i].is_mapped) < 0) { pthread_mutex_unlock(&mt->idx_m); return -1; } // Count this entry and drop out of the loop i++; break; } if (hts_idx_push(mt->hts_idx, e[i].tid, e[i].beg, e[i].end, (mt->block_address << 16) + e[i].offset, e[i].is_mapped) < 0) { pthread_mutex_unlock(&mt->idx_m); return -1; } } memmove(&e[0], &e[i], (mt->idx_cache.nentries - i) * sizeof(*e)); mt->idx_cache.nentries -= i; mt->block_written++; pthread_mutex_unlock(&mt->idx_m); return 0; } void bgzf_index_destroy(BGZF *fp); int bgzf_index_add_block(BGZF *fp); static int mt_destroy(mtaux_t *mt); static inline void packInt16(uint8_t *buffer, uint16_t value) { buffer[0] = value; buffer[1] = value >> 8; } static inline int unpackInt16(const uint8_t *buffer) { return buffer[0] | buffer[1] << 8; } static inline void packInt32(uint8_t *buffer, uint32_t value) { buffer[0] = value; buffer[1] = value >> 8; buffer[2] = value >> 16; buffer[3] = value >> 24; } static void razf_info(hFILE *hfp, const char *filename) { uint64_t usize, csize; off_t sizes_pos; if (filename == NULL || strcmp(filename, "-") == 0) filename = "FILE"; // RAZF files end with USIZE,CSIZE stored as big-endian uint64_t if ((sizes_pos = hseek(hfp, -16, SEEK_END)) < 0) goto no_sizes; if (hread(hfp, &usize, 8) != 8 || hread(hfp, &csize, 8) != 8) goto no_sizes; if (!ed_is_big()) ed_swap_8p(&usize), ed_swap_8p(&csize); if (csize >= sizes_pos) goto no_sizes; // Very basic validity check hts_log_error( "To decompress this file, use the following commands:\n" " truncate -s %" PRIu64 " %s\n" " gunzip %s\n" "The resulting uncompressed file should be %" PRIu64 " bytes in length.\n" "If you do not have a truncate command, skip that step (though gunzip will\n" "likely produce a \"trailing garbage ignored\" message, which can be ignored).", csize, filename, filename, usize); return; no_sizes: hts_log_error( "To decompress this file, use the following command:\n" " gunzip %s\n" "This will likely produce a \"trailing garbage ignored\" message, which can\n" "usually be safely ignored.", filename); } static const char *bgzf_zerr(int errnum, z_stream *zs) { static char buffer[32]; /* Return zs->msg if available. zlib doesn't set this very reliably. Looking at the source suggests that it may get set to a useful message for deflateInit2, inflateInit2 and inflate when it returns Z_DATA_ERROR. For inflate with other return codes, deflate, deflateEnd and inflateEnd it doesn't appear to be useful. For the likely non-useful cases, the caller should pass NULL into zs. */ if (zs && zs->msg) return zs->msg; // gzerror OF((gzFile file, int *errnum) switch (errnum) { case Z_ERRNO: return strerror(errno); case Z_STREAM_ERROR: return "invalid parameter/compression level, or inconsistent stream state"; case Z_DATA_ERROR: return "invalid or incomplete IO"; case Z_MEM_ERROR: return "out of memory"; case Z_BUF_ERROR: return "progress temporarily not possible, or in() / out() returned an error"; case Z_VERSION_ERROR: return "zlib version mismatch"; case Z_NEED_DICT: return "data was compressed using a dictionary"; case Z_OK: // 0: maybe gzgets error Z_NULL default: snprintf(buffer, sizeof(buffer), "[%d] unknown", errnum); return buffer; // FIXME: Not thread-safe. } } static BGZF *bgzf_read_init(hFILE *hfpr, const char *filename) { BGZF *fp; uint8_t magic[18]; ssize_t n = hpeek(hfpr, magic, 18); if (n < 0) return NULL; fp = (BGZF*)calloc(1, sizeof(BGZF)); if (fp == NULL) return NULL; fp->is_write = 0; fp->uncompressed_block = malloc(2 * BGZF_MAX_BLOCK_SIZE); if (fp->uncompressed_block == NULL) { free(fp); return NULL; } fp->compressed_block = (char *)fp->uncompressed_block + BGZF_MAX_BLOCK_SIZE; fp->is_compressed = (n==18 && magic[0]==0x1f && magic[1]==0x8b); fp->is_gzip = ( !fp->is_compressed || ((magic[3]&4) && memcmp(&magic[12], "BC\2\0",4)==0) ) ? 0 : 1; if (fp->is_compressed && (magic[3]&4) && memcmp(&magic[12], "RAZF", 4)==0) { hts_log_error("Cannot decompress legacy RAZF format"); razf_info(hfpr, filename); free(fp->uncompressed_block); free(fp); errno = EFTYPE; return NULL; } #ifdef BGZF_CACHE if (!(fp->cache = malloc(sizeof(*fp->cache)))) { free(fp->uncompressed_block); free(fp); return NULL; } if (!(fp->cache->h = kh_init(cache))) { free(fp->uncompressed_block); free(fp->cache); free(fp); return NULL; } fp->cache->last_pos = 0; #endif return fp; } // get the compress level from the mode string: compress_level==-1 for the default level, -2 plain uncompressed static int mode2level(const char *mode) { int i, compress_level = -1; for (i = 0; mode[i]; ++i) if (mode[i] >= '0' && mode[i] <= '9') break; if (mode[i]) compress_level = (int)mode[i] - '0'; if (strchr(mode, 'u')) compress_level = -2; return compress_level; } static BGZF *bgzf_write_init(const char *mode) { BGZF *fp; fp = (BGZF*)calloc(1, sizeof(BGZF)); if (fp == NULL) goto mem_fail; fp->is_write = 1; int compress_level = mode2level(mode); if ( compress_level==-2 ) { fp->is_compressed = 0; return fp; } fp->is_compressed = 1; fp->uncompressed_block = malloc(2 * BGZF_MAX_BLOCK_SIZE); if (fp->uncompressed_block == NULL) goto mem_fail; fp->compressed_block = (char *)fp->uncompressed_block + BGZF_MAX_BLOCK_SIZE; fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1 if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION; if ( strchr(mode,'g') ) { // gzip output fp->is_gzip = 1; fp->gz_stream = (z_stream*)calloc(1,sizeof(z_stream)); if (fp->gz_stream == NULL) goto mem_fail; fp->gz_stream->zalloc = NULL; fp->gz_stream->zfree = NULL; fp->gz_stream->msg = NULL; int ret = deflateInit2(fp->gz_stream, fp->compress_level, Z_DEFLATED, 15|16, 8, Z_DEFAULT_STRATEGY); if (ret!=Z_OK) { hts_log_error("Call to deflateInit2 failed: %s", bgzf_zerr(ret, fp->gz_stream)); goto fail; } } return fp; mem_fail: hts_log_error("%s", strerror(errno)); fail: if (fp != NULL) { free(fp->uncompressed_block); free(fp->gz_stream); free(fp); } return NULL; } BGZF *bgzf_open(const char *path, const char *mode) { BGZF *fp = 0; if (strchr(mode, 'r')) { hFILE *fpr; if ((fpr = hopen(path, mode)) == 0) return 0; fp = bgzf_read_init(fpr, path); if (fp == 0) { hclose_abruptly(fpr); return NULL; } fp->fp = fpr; } else if (strchr(mode, 'w') || strchr(mode, 'a')) { hFILE *fpw; if ((fpw = hopen(path, mode)) == 0) return 0; fp = bgzf_write_init(mode); if (fp == NULL) return NULL; fp->fp = fpw; } else { errno = EINVAL; return 0; } fp->is_be = ed_is_big(); return fp; } BGZF *bgzf_dopen(int fd, const char *mode) { BGZF *fp = 0; if (strchr(mode, 'r')) { hFILE *fpr; if ((fpr = hdopen(fd, mode)) == 0) return 0; fp = bgzf_read_init(fpr, NULL); if (fp == 0) { hclose_abruptly(fpr); return NULL; } // FIXME this closes fd fp->fp = fpr; } else if (strchr(mode, 'w') || strchr(mode, 'a')) { hFILE *fpw; if ((fpw = hdopen(fd, mode)) == 0) return 0; fp = bgzf_write_init(mode); if (fp == NULL) return NULL; fp->fp = fpw; } else { errno = EINVAL; return 0; } fp->is_be = ed_is_big(); return fp; } BGZF *bgzf_hopen(hFILE *hfp, const char *mode) { BGZF *fp = NULL; if (strchr(mode, 'r')) { fp = bgzf_read_init(hfp, NULL); if (fp == NULL) return NULL; } else if (strchr(mode, 'w') || strchr(mode, 'a')) { fp = bgzf_write_init(mode); if (fp == NULL) return NULL; } else { errno = EINVAL; return 0; } fp->fp = hfp; fp->is_be = ed_is_big(); return fp; } #ifdef HAVE_LIBDEFLATE int bgzf_compress(void *_dst, size_t *dlen, const void *src, size_t slen, int level) { if (slen == 0) { // EOF block if (*dlen < 28) return -1; memcpy(_dst, "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0", 28); *dlen = 28; return 0; } uint8_t *dst = (uint8_t*)_dst; if (level == 0) { // Uncompressed data if (*dlen < slen+5 + BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH) return -1; dst[BLOCK_HEADER_LENGTH] = 1; // BFINAL=1, BTYPE=00; see RFC1951 u16_to_le(slen, &dst[BLOCK_HEADER_LENGTH+1]); // length u16_to_le(~slen, &dst[BLOCK_HEADER_LENGTH+3]); // ones-complement length memcpy(dst + BLOCK_HEADER_LENGTH+5, src, slen); *dlen = slen+5 + BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH; } else { level = level > 0 ? level : 6; // libdeflate doesn't honour -1 as default // NB levels go up to 12 here. int lvl_map[] = {0,1,2,3,5,6,7,8,10,12}; level = lvl_map[level>9 ?9 :level]; struct libdeflate_compressor *z = libdeflate_alloc_compressor(level); if (!z) return -1; // Raw deflate size_t clen = libdeflate_deflate_compress(z, src, slen, dst + BLOCK_HEADER_LENGTH, *dlen - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH); if (clen <= 0) { hts_log_error("Call to libdeflate_deflate_compress failed"); libdeflate_free_compressor(z); return -1; } *dlen = clen + BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH; libdeflate_free_compressor(z); } // write the header memcpy(dst, g_magic, BLOCK_HEADER_LENGTH); // the last two bytes are a place holder for the length of the block packInt16(&dst[16], *dlen - 1); // write the compressed length; -1 to fit 2 bytes // write the footer uint32_t crc = libdeflate_crc32(0, src, slen); packInt32((uint8_t*)&dst[*dlen - 8], crc); packInt32((uint8_t*)&dst[*dlen - 4], slen); return 0; } #else int bgzf_compress(void *_dst, size_t *dlen, const void *src, size_t slen, int level) { uint32_t crc; z_stream zs; uint8_t *dst = (uint8_t*)_dst; if (level == 0) { uncomp: // Uncompressed data if (*dlen < slen+5 + BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH) return -1; dst[BLOCK_HEADER_LENGTH] = 1; // BFINAL=1, BTYPE=00; see RFC1951 u16_to_le(slen, &dst[BLOCK_HEADER_LENGTH+1]); // length u16_to_le(~slen, &dst[BLOCK_HEADER_LENGTH+3]); // ones-complement length memcpy(dst + BLOCK_HEADER_LENGTH+5, src, slen); *dlen = slen+5 + BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH; } else { // compress the body zs.zalloc = NULL; zs.zfree = NULL; zs.msg = NULL; zs.next_in = (Bytef*)src; zs.avail_in = slen; zs.next_out = dst + BLOCK_HEADER_LENGTH; zs.avail_out = *dlen - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH; int ret = deflateInit2(&zs, level, Z_DEFLATED, -15, 8, Z_DEFAULT_STRATEGY); // -15 to disable zlib header/footer if (ret!=Z_OK) { hts_log_error("Call to deflateInit2 failed: %s", bgzf_zerr(ret, &zs)); return -1; } if ((ret = deflate(&zs, Z_FINISH)) != Z_STREAM_END) { if (ret == Z_OK && zs.avail_out == 0) { deflateEnd(&zs); goto uncomp; } else { hts_log_error("Deflate operation failed: %s", bgzf_zerr(ret, ret == Z_DATA_ERROR ? &zs : NULL)); } return -1; } // If we used up the entire output buffer, then we either ran out of // room or we *just* fitted, but either way we may as well store // uncompressed for faster decode. if (zs.avail_out == 0) { deflateEnd(&zs); goto uncomp; } if ((ret = deflateEnd(&zs)) != Z_OK) { hts_log_error("Call to deflateEnd failed: %s", bgzf_zerr(ret, NULL)); return -1; } *dlen = zs.total_out + BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH; } // write the header memcpy(dst, g_magic, BLOCK_HEADER_LENGTH); // the last two bytes are a place holder for the length of the block packInt16(&dst[16], *dlen - 1); // write the compressed length; -1 to fit 2 bytes // write the footer crc = crc32(crc32(0L, NULL, 0L), (Bytef*)src, slen); packInt32((uint8_t*)&dst[*dlen - 8], crc); packInt32((uint8_t*)&dst[*dlen - 4], slen); return 0; } #endif // HAVE_LIBDEFLATE static int bgzf_gzip_compress(BGZF *fp, void *_dst, size_t *dlen, const void *src, size_t slen, int level) { uint8_t *dst = (uint8_t*)_dst; z_stream *zs = fp->gz_stream; int flush = slen ? Z_PARTIAL_FLUSH : Z_FINISH; zs->next_in = (Bytef*)src; zs->avail_in = slen; zs->next_out = dst; zs->avail_out = *dlen; int ret = deflate(zs, flush); if (ret == Z_STREAM_ERROR) { hts_log_error("Deflate operation failed: %s", bgzf_zerr(ret, NULL)); return -1; } if (zs->avail_in != 0) { hts_log_error("Deflate block too large for output buffer"); return -1; } *dlen = *dlen - zs->avail_out; return 0; } // Deflate the block in fp->uncompressed_block into fp->compressed_block. Also adds an extra field that stores the compressed block length. static int deflate_block(BGZF *fp, int block_length) { size_t comp_size = BGZF_MAX_BLOCK_SIZE; int ret; if ( !fp->is_gzip ) ret = bgzf_compress(fp->compressed_block, &comp_size, fp->uncompressed_block, block_length, fp->compress_level); else ret = bgzf_gzip_compress(fp, fp->compressed_block, &comp_size, fp->uncompressed_block, block_length, fp->compress_level); if ( ret != 0 ) { hts_log_debug("Compression error %d", ret); fp->errcode |= BGZF_ERR_ZLIB; return -1; } fp->block_offset = 0; return comp_size; } #ifdef HAVE_LIBDEFLATE static int bgzf_uncompress(uint8_t *dst, size_t *dlen, const uint8_t *src, size_t slen, uint32_t expected_crc) { struct libdeflate_decompressor *z = libdeflate_alloc_decompressor(); if (!z) { hts_log_error("Call to libdeflate_alloc_decompressor failed"); return -1; } int ret = libdeflate_deflate_decompress(z, src, slen, dst, *dlen, dlen); libdeflate_free_decompressor(z); if (ret != LIBDEFLATE_SUCCESS) { hts_log_error("Inflate operation failed: %d", ret); return -1; } uint32_t crc = libdeflate_crc32(0, (unsigned char *)dst, *dlen); #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION // Pretend the CRC was OK so the fuzzer doesn't have to get it right crc = expected_crc; #endif if (crc != expected_crc) { hts_log_error("CRC32 checksum mismatch"); return -2; } return 0; } #else static int bgzf_uncompress(uint8_t *dst, size_t *dlen, const uint8_t *src, size_t slen, uint32_t expected_crc) { z_stream zs = { .zalloc = NULL, .zfree = NULL, .msg = NULL, .next_in = (Bytef*)src, .avail_in = slen, .next_out = (Bytef*)dst, .avail_out = *dlen }; int ret = inflateInit2(&zs, -15); if (ret != Z_OK) { hts_log_error("Call to inflateInit2 failed: %s", bgzf_zerr(ret, &zs)); return -1; } if ((ret = inflate(&zs, Z_FINISH)) != Z_STREAM_END) { hts_log_error("Inflate operation failed: %s", bgzf_zerr(ret, ret == Z_DATA_ERROR ? &zs : NULL)); if ((ret = inflateEnd(&zs)) != Z_OK) { hts_log_warning("Call to inflateEnd failed: %s", bgzf_zerr(ret, NULL)); } return -1; } if ((ret = inflateEnd(&zs)) != Z_OK) { hts_log_error("Call to inflateEnd failed: %s", bgzf_zerr(ret, NULL)); return -1; } *dlen = *dlen - zs.avail_out; uint32_t crc = crc32(crc32(0L, NULL, 0L), (unsigned char *)dst, *dlen); #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION // Pretend the CRC was OK so the fuzzer doesn't have to get it right crc = expected_crc; #endif if (crc != expected_crc) { hts_log_error("CRC32 checksum mismatch"); return -2; } return 0; } #endif // HAVE_LIBDEFLATE // Inflate the block in fp->compressed_block into fp->uncompressed_block static int inflate_block(BGZF* fp, int block_length) { size_t dlen = BGZF_MAX_BLOCK_SIZE; uint32_t crc = le_to_u32((uint8_t *)fp->compressed_block + block_length-8); int ret = bgzf_uncompress(fp->uncompressed_block, &dlen, (Bytef*)fp->compressed_block + 18, block_length - 18, crc); if (ret < 0) { if (ret == -2) fp->errcode |= BGZF_ERR_CRC; else fp->errcode |= BGZF_ERR_ZLIB; return -1; } return dlen; } // Decompress the next part of a non-blocked GZIP file. // Return the number of uncompressed bytes read, 0 on EOF, or a negative number on error. // Will fill the output buffer unless the end of the GZIP file is reached. static int inflate_gzip_block(BGZF *fp) { // we will set this to true when we detect EOF, so we don't bang against the EOF more than once per call int input_eof = 0; // write to the part of the output buffer after block_offset fp->gz_stream->next_out = (Bytef*)fp->uncompressed_block + fp->block_offset; fp->gz_stream->avail_out = BGZF_MAX_BLOCK_SIZE - fp->block_offset; while ( fp->gz_stream->avail_out != 0 ) { // until we fill the output buffer (or hit EOF) if ( !input_eof && fp->gz_stream->avail_in == 0 ) { // we are out of input data in the buffer. Get more. fp->gz_stream->next_in = fp->compressed_block; int ret = hread(fp->fp, fp->compressed_block, BGZF_BLOCK_SIZE); if ( ret < 0 ) { // hread had an error. Pass it on. return ret; } fp->gz_stream->avail_in = ret; if ( fp->gz_stream->avail_in < BGZF_BLOCK_SIZE ) { // we have reached EOF but the decompressor hasn't necessarily input_eof = 1; } } fp->gz_stream->msg = NULL; // decompress as much data as we can int ret = inflate(fp->gz_stream, Z_SYNC_FLUSH); if ( (ret < 0 && ret != Z_BUF_ERROR) || ret == Z_NEED_DICT ) { // an error occurred, other than running out of space hts_log_error("Inflate operation failed: %s", bgzf_zerr(ret, ret == Z_DATA_ERROR ? fp->gz_stream : NULL)); fp->errcode |= BGZF_ERR_ZLIB; return -1; } else if ( ret == Z_STREAM_END ) { // we finished a GZIP member // scratch for peeking to see if the file is over char c; if (fp->gz_stream->avail_in > 0 || hpeek(fp->fp, &c, 1) == 1) { // there is more data; try and read another GZIP member in the remaining data int reset_ret = inflateReset(fp->gz_stream); if (reset_ret != Z_OK) { hts_log_error("Call to inflateReset failed: %s", bgzf_zerr(reset_ret, NULL)); fp->errcode |= BGZF_ERR_ZLIB; return -1; } } else { // we consumed all the input data and hit Z_STREAM_END // so stop looping, even if we never fill the output buffer break; } } else if ( ret == Z_BUF_ERROR && input_eof && fp->gz_stream->avail_out > 0 ) { // the gzip file has ended prematurely hts_log_error("Gzip file truncated"); fp->errcode |= BGZF_ERR_IO; return -1; } } // when we get here, the buffer is full or there is an EOF after a complete gzip member return BGZF_MAX_BLOCK_SIZE - fp->gz_stream->avail_out; } // Returns: 0 on success (BGZF header); -1 on non-BGZF GZIP header; -2 on error static int check_header(const uint8_t *header) { if ( header[0] != 31 || header[1] != 139 || header[2] != 8 ) return -2; return ((header[3] & 4) != 0 && unpackInt16((uint8_t*)&header[10]) == 6 && header[12] == 'B' && header[13] == 'C' && unpackInt16((uint8_t*)&header[14]) == 2) ? 0 : -1; } #ifdef BGZF_CACHE static void free_cache(BGZF *fp) { khint_t k; if (fp->is_write) return; khash_t(cache) *h = fp->cache->h; for (k = kh_begin(h); k < kh_end(h); ++k) if (kh_exist(h, k)) free(kh_val(h, k).block); kh_destroy(cache, h); free(fp->cache); } static int load_block_from_cache(BGZF *fp, int64_t block_address) { khint_t k; cache_t *p; khash_t(cache) *h = fp->cache->h; k = kh_get(cache, h, block_address); if (k == kh_end(h)) return 0; p = &kh_val(h, k); if (fp->block_length != 0) fp->block_offset = 0; fp->block_address = block_address; fp->block_length = p->size; memcpy(fp->uncompressed_block, p->block, p->size); if ( hseek(fp->fp, p->end_offset, SEEK_SET) < 0 ) { // todo: move the error up hts_log_error("Could not hseek to %" PRId64, p->end_offset); exit(1); } return p->size; } static void cache_block(BGZF *fp, int size) { int ret; khint_t k, k_orig; uint8_t *block = NULL; cache_t *p; //fprintf(stderr, "Cache block at %llx\n", (int)fp->block_address); khash_t(cache) *h = fp->cache->h; if (BGZF_MAX_BLOCK_SIZE >= fp->cache_size) return; if (fp->block_length < 0 || fp->block_length > BGZF_MAX_BLOCK_SIZE) return; if ((kh_size(h) + 1) * BGZF_MAX_BLOCK_SIZE > (uint32_t)fp->cache_size) { /* Remove uniformly from any position in the hash by a simple * round-robin approach. An alternative strategy would be to * remove the least recently accessed block, but the round-robin * removal is simpler and is not expected to have a big impact * on performance */ if (fp->cache->last_pos >= kh_end(h)) fp->cache->last_pos = kh_begin(h); k_orig = k = fp->cache->last_pos; if (++k >= kh_end(h)) k = kh_begin(h); while (k != k_orig) { if (kh_exist(h, k)) break; if (++k == kh_end(h)) k = kh_begin(h); } fp->cache->last_pos = k; if (k != k_orig) { block = kh_val(h, k).block; kh_del(cache, h, k); } } else { block = (uint8_t*)malloc(BGZF_MAX_BLOCK_SIZE); } if (!block) return; k = kh_put(cache, h, fp->block_address, &ret); if (ret <= 0) { // kh_put failed, or in there already (shouldn't happen) free(block); return; } p = &kh_val(h, k); p->size = fp->block_length; p->end_offset = fp->block_address + size; p->block = block; memcpy(p->block, fp->uncompressed_block, p->size); } #else static void free_cache(BGZF *fp) {} static int load_block_from_cache(BGZF *fp, int64_t block_address) {return 0;} static void cache_block(BGZF *fp, int size) {} #endif /* * Absolute htell in this compressed file. * * Do not confuse with the external bgzf_tell macro which returns the virtual * offset. */ static off_t bgzf_htell(BGZF *fp) { if (fp->mt) { pthread_mutex_lock(&fp->mt->job_pool_m); off_t pos = fp->block_address + fp->block_clength; pthread_mutex_unlock(&fp->mt->job_pool_m); return pos; } else { return htell(fp->fp); } } int bgzf_read_block(BGZF *fp) { hts_tpool_result *r; if (fp->errcode) return -1; if (fp->mt) { again: if (fp->mt->hit_eof) { // Further reading at EOF will always return 0 fp->block_length = 0; return 0; } r = hts_tpool_next_result_wait(fp->mt->out_queue); bgzf_job *j = r ? (bgzf_job *)hts_tpool_result_data(r) : NULL; if (!j || j->errcode == BGZF_ERR_MT) { if (!fp->mt->free_block) { fp->uncompressed_block = malloc(2 * BGZF_MAX_BLOCK_SIZE); if (fp->uncompressed_block == NULL) return -1; fp->compressed_block = (char *)fp->uncompressed_block + BGZF_MAX_BLOCK_SIZE; } // else it's already allocated with malloc, maybe even in-use. if (mt_destroy(fp->mt) < 0) { fp->errcode = BGZF_ERR_IO; } fp->mt = NULL; hts_tpool_delete_result(r, 0); if (fp->errcode) { return -1; } goto single_threaded; } if (j->errcode) { fp->errcode = j->errcode; hts_log_error("BGZF decode jobs returned error %d " "for block offset %"PRId64, j->errcode, j->block_address); hts_tpool_delete_result(r, 0); return -1; } if (j->hit_eof) { if (!fp->last_block_eof && !fp->no_eof_block) { fp->no_eof_block = 1; hts_log_warning("EOF marker is absent. The input may be truncated"); } fp->mt->hit_eof = 1; } // Zero length blocks in the middle of a file are (wrongly) // considered as EOF by many callers. We work around this by // trying again to see if we hit a genuine EOF. if (!j->hit_eof && j->uncomp_len == 0) { fp->last_block_eof = 1; hts_tpool_delete_result(r, 0); goto again; } // block_length=0 and block_offset set by bgzf_seek. if (fp->block_length != 0) fp->block_offset = 0; if (!j->hit_eof) fp->block_address = j->block_address; fp->block_clength = j->comp_len; fp->block_length = j->uncomp_len; // bgzf_read() can change fp->block_length fp->last_block_eof = (fp->block_length == 0); if ( j->uncomp_len && j->fp->idx_build_otf ) { bgzf_index_add_block(j->fp); j->fp->idx->ublock_addr += j->uncomp_len; } // Steal the data block as it's quicker than a memcpy. // We just need to make sure we delay the pool free. if (fp->mt->curr_job) { pthread_mutex_lock(&fp->mt->job_pool_m); pool_free(fp->mt->job_pool, fp->mt->curr_job); pthread_mutex_unlock(&fp->mt->job_pool_m); } fp->uncompressed_block = j->uncomp_data; fp->mt->curr_job = j; if (fp->mt->free_block) { free(fp->mt->free_block); // clear up last non-mt block fp->mt->free_block = NULL; } hts_tpool_delete_result(r, 0); return 0; } uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block; int count, size, block_length, remaining; single_threaded: size = 0; int64_t block_address; block_address = bgzf_htell(fp); // Reading an uncompressed file if ( !fp->is_compressed ) { count = hread(fp->fp, fp->uncompressed_block, BGZF_MAX_BLOCK_SIZE); if (count < 0) // Error { hts_log_error("Failed to read uncompressed data " "at offset %"PRId64"%s%s", block_address, errno ? ": " : "", strerror(errno)); fp->errcode |= BGZF_ERR_IO; return -1; } else if (count == 0) // EOF { fp->block_length = 0; return 0; } if (fp->block_length != 0) fp->block_offset = 0; fp->block_address = block_address; fp->block_length = count; return 0; } // Reading compressed file if ( fp->is_gzip && fp->gz_stream ) // is this is an initialized gzip stream? { count = inflate_gzip_block(fp); if ( count<0 ) { hts_log_error("Reading GZIP stream failed at offset %"PRId64, block_address); fp->errcode |= BGZF_ERR_ZLIB; return -1; } fp->block_length = count; fp->block_address = block_address; return 0; } if (fp->cache_size && load_block_from_cache(fp, block_address)) return 0; // loop to skip empty bgzf blocks while (1) { count = hread(fp->fp, header, sizeof(header)); if (count == 0) { // no data read if (!fp->last_block_eof && !fp->no_eof_block && !fp->is_gzip) { fp->no_eof_block = 1; hts_log_warning("EOF marker is absent. The input may be truncated"); } fp->block_length = 0; return 0; } int ret = 0; if ( count != sizeof(header) || (ret=check_header(header))==-2 ) { fp->errcode |= BGZF_ERR_HEADER; hts_log_error("%s BGZF header at offset %"PRId64, ret ? "Invalid" : "Failed to read", block_address); return -1; } if ( ret==-1 ) { // GZIP, not BGZF uint8_t *cblock = (uint8_t*)fp->compressed_block; memcpy(cblock, header, sizeof(header)); count = hread(fp->fp, cblock+sizeof(header), BGZF_BLOCK_SIZE - sizeof(header)) + sizeof(header); fp->is_gzip = 1; fp->gz_stream = (z_stream*) calloc(1,sizeof(z_stream)); // Set up zlib, using a window size of 15, and its built-in GZIP header processing (+16). int ret = inflateInit2(fp->gz_stream, 15 + 16); if (ret != Z_OK) { hts_log_error("Call to inflateInit2 failed: %s", bgzf_zerr(ret, fp->gz_stream)); fp->errcode |= BGZF_ERR_ZLIB; return -1; } fp->gz_stream->avail_in = count; fp->gz_stream->next_in = cblock; count = inflate_gzip_block(fp); if ( count<0 ) { hts_log_error("Reading GZIP stream failed at offset %"PRId64, block_address); fp->errcode |= BGZF_ERR_ZLIB; return -1; } fp->block_length = count; fp->block_address = block_address; if ( fp->idx_build_otf ) return -1; // cannot build index for gzip return 0; } size = count; block_length = unpackInt16((uint8_t*)&header[16]) + 1; // +1 because when writing this number, we used "-1" if (block_length < BLOCK_HEADER_LENGTH) { hts_log_error("Invalid BGZF block length at offset %"PRId64, block_address); fp->errcode |= BGZF_ERR_HEADER; return -1; } compressed_block = (uint8_t*)fp->compressed_block; memcpy(compressed_block, header, BLOCK_HEADER_LENGTH); remaining = block_length - BLOCK_HEADER_LENGTH; count = hread(fp->fp, &compressed_block[BLOCK_HEADER_LENGTH], remaining); if (count != remaining) { hts_log_error("Failed to read BGZF block data at offset %"PRId64 " expected %d bytes; hread returned %d", block_address, remaining, count); fp->errcode |= BGZF_ERR_IO; return -1; } size += count; if ((count = inflate_block(fp, block_length)) < 0) { hts_log_debug("Inflate block operation failed for " "block at offset %"PRId64": %s", block_address, bgzf_zerr(count, NULL)); fp->errcode |= BGZF_ERR_ZLIB; return -1; } fp->last_block_eof = (count == 0); if ( count ) break; // otherwise an empty bgzf block block_address = bgzf_htell(fp); // update for new block start } if (fp->block_length != 0) fp->block_offset = 0; // Do not reset offset if this read follows a seek. fp->block_address = block_address; fp->block_length = count; if ( fp->idx_build_otf ) { bgzf_index_add_block(fp); fp->idx->ublock_addr += count; } cache_block(fp, size); return 0; } ssize_t bgzf_read(BGZF *fp, void *data, size_t length) { ssize_t bytes_read = 0; uint8_t *output = (uint8_t*)data; if (length <= 0) return 0; assert(fp->is_write == 0); while (bytes_read < length) { int copy_length, available = fp->block_length - fp->block_offset; uint8_t *buffer; if (available <= 0) { int ret = bgzf_read_block(fp); if (ret != 0) { hts_log_error("Read block operation failed with error %d after %zd of %zu bytes", fp->errcode, bytes_read, length); fp->errcode |= BGZF_ERR_ZLIB; return -1; } available = fp->block_length - fp->block_offset; if (available == 0) { if (fp->block_length == 0) break; // EOF // Offset was at end of block (see commit e9863a0) fp->block_address = bgzf_htell(fp); fp->block_offset = fp->block_length = 0; continue; } else if (available < 0) { // Block offset was set to an invalid coordinate hts_log_error("BGZF block offset %d set beyond block size %d", fp->block_offset, fp->block_length); fp->errcode |= BGZF_ERR_MISUSE; return -1; } } copy_length = length - bytes_read < available? length - bytes_read : available; buffer = (uint8_t*)fp->uncompressed_block; memcpy(output, buffer + fp->block_offset, copy_length); fp->block_offset += copy_length; output += copy_length; bytes_read += copy_length; // For raw gzip streams this avoids short reads. if (fp->block_offset == fp->block_length) { fp->block_address = bgzf_htell(fp); fp->block_offset = fp->block_length = 0; } } fp->uncompressed_address += bytes_read; return bytes_read; } // -1 for EOF, -2 for error, 0-255 for byte. int bgzf_peek(BGZF *fp) { int available = fp->block_length - fp->block_offset; if (available <= 0) { if (bgzf_read_block(fp) < 0) { hts_log_error("Read block operation failed with error %d", fp->errcode); fp->errcode = BGZF_ERR_ZLIB; return -2; } } available = fp->block_length - fp->block_offset; if (available) return ((unsigned char *)fp->uncompressed_block)[fp->block_offset]; return -1; } ssize_t bgzf_raw_read(BGZF *fp, void *data, size_t length) { ssize_t ret = hread(fp->fp, data, length); if (ret < 0) fp->errcode |= BGZF_ERR_IO; return ret; } #ifdef BGZF_MT /* Function to clean up when jobs are discarded (e.g. during seek) * This works for results too, as results are the same struct with * decompressed data stored in it. */ static void job_cleanup(void *arg) { bgzf_job *j = (bgzf_job *)arg; mtaux_t *mt = j->fp->mt; pthread_mutex_lock(&mt->job_pool_m); pool_free(mt->job_pool, j); pthread_mutex_unlock(&mt->job_pool_m); } static void *bgzf_encode_func(void *arg) { bgzf_job *j = (bgzf_job *)arg; j->comp_len = BGZF_MAX_BLOCK_SIZE; int ret = bgzf_compress(j->comp_data, &j->comp_len, j->uncomp_data, j->uncomp_len, j->fp->compress_level); if (ret != 0) j->errcode |= BGZF_ERR_ZLIB; return arg; } // Optimisation for compression level 0 (uncompressed deflate blocks) // Avoids memcpy of the data from uncompressed to compressed buffer. static void *bgzf_encode_level0_func(void *arg) { bgzf_job *j = (bgzf_job *)arg; uint32_t crc; j->comp_len = j->uncomp_len + BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH + 5; // Data will have already been copied in to // j->comp_data + BLOCK_HEADER_LENGTH + 5 // Add preamble memcpy(j->comp_data, g_magic, BLOCK_HEADER_LENGTH); u16_to_le(j->comp_len-1, j->comp_data + 16); // Deflate uncompressed data header j->comp_data[BLOCK_HEADER_LENGTH] = 1; // BFINAL=1, BTYPE=00; see RFC1951 u16_to_le(j->uncomp_len, j->comp_data + BLOCK_HEADER_LENGTH + 1); u16_to_le(~j->uncomp_len, j->comp_data + BLOCK_HEADER_LENGTH + 3); // Trailer (CRC, uncompressed length) #ifdef HAVE_LIBDEFLATE crc = libdeflate_crc32(0, j->comp_data + BLOCK_HEADER_LENGTH + 5, j->uncomp_len); #else crc = crc32(crc32(0L, NULL, 0L), (Bytef*)j->comp_data + BLOCK_HEADER_LENGTH + 5, j->uncomp_len); #endif u32_to_le(crc, j->comp_data + j->comp_len - 8); u32_to_le(j->uncomp_len, j->comp_data + j->comp_len - 4); return arg; } // Our input block has already been decoded by bgzf_mt_read_block(). // We need to split that into a fetch block (compressed) and make this // do the actual decompression step. static void *bgzf_decode_func(void *arg) { bgzf_job *j = (bgzf_job *)arg; j->uncomp_len = BGZF_MAX_BLOCK_SIZE; uint32_t crc = le_to_u32((uint8_t *)j->comp_data + j->comp_len-8); int ret = bgzf_uncompress(j->uncomp_data, &j->uncomp_len, j->comp_data+18, j->comp_len-18, crc); if (ret != 0) j->errcode |= BGZF_ERR_ZLIB; return arg; } /* * Nul function so we can dispatch a job with the correct serial * to mark failure or to indicate an empty read (EOF). */ static void *bgzf_nul_func(void *arg) { return arg; } /* * Takes compressed blocks off the results queue and calls hwrite to * punt them to the output stream. * * Returns NULL when no more are left, or -1 on error */ static void *bgzf_mt_writer(void *vp) { BGZF *fp = (BGZF *)vp; mtaux_t *mt = fp->mt; hts_tpool_result *r; if (fp->idx_build_otf) { fp->idx->moffs = fp->idx->noffs = 1; fp->idx->offs = (bgzidx1_t*) calloc(fp->idx->moffs, sizeof(bgzidx1_t)); if (!fp->idx->offs) goto err; } // Iterates until result queue is shutdown, where it returns NULL. while ((r = hts_tpool_next_result_wait(mt->out_queue))) { bgzf_job *j = (bgzf_job *)hts_tpool_result_data(r); assert(j); if (fp->idx_build_otf) { fp->idx->noffs++; if ( fp->idx->noffs > fp->idx->moffs ) { fp->idx->moffs = fp->idx->noffs; kroundup32(fp->idx->moffs); fp->idx->offs = (bgzidx1_t*) realloc(fp->idx->offs, fp->idx->moffs*sizeof(bgzidx1_t)); if ( !fp->idx->offs ) goto err; } fp->idx->offs[ fp->idx->noffs-1 ].uaddr = fp->idx->offs[ fp->idx->noffs-2 ].uaddr + j->uncomp_len; fp->idx->offs[ fp->idx->noffs-1 ].caddr = fp->idx->offs[ fp->idx->noffs-2 ].caddr + j->comp_len; } // Flush any cached hts_idx_push calls if (bgzf_idx_flush(fp, j->uncomp_len, j->comp_len) < 0) goto err; if (hwrite(fp->fp, j->comp_data, j->comp_len) != j->comp_len) goto err; // Update our local block_address. Cannot be fp->block_address due to no // locking in bgzf_tell. pthread_mutex_lock(&mt->idx_m); mt->block_address += j->comp_len; pthread_mutex_unlock(&mt->idx_m); /* * Periodically call hflush (which calls fsync when on a file). * This avoids the fsync being done at the bgzf_close stage, * which can sometimes cause significant delays. As this is in * a separate thread, spreading the sync delays throughout the * program execution seems better. * Frequency of 1/512 has been chosen by experimentation * across local XFS, NFS and Lustre tests. */ if (++mt->flush_pending % 512 == 0) if (hflush(fp->fp) != 0) goto err; hts_tpool_delete_result(r, 0); // Also updated by main thread pthread_mutex_lock(&mt->job_pool_m); pool_free(mt->job_pool, j); mt->jobs_pending--; pthread_mutex_unlock(&mt->job_pool_m); } if (hflush(fp->fp) != 0) goto err; hts_tpool_process_destroy(mt->out_queue); return NULL; err: hts_tpool_process_destroy(mt->out_queue); return (void *)-1; } /* * Reads a compressed block of data using hread and dispatches it to * the thread pool for decompression. This is the analogue of the old * non-threaded bgzf_read_block() function, but without modifying fp * in any way (except for the read offset). All output goes via the * supplied bgzf_job struct. * * Returns NULL when no more are left, or -1 on error */ int bgzf_mt_read_block(BGZF *fp, bgzf_job *j) { uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block; int count, block_length, remaining; // NOTE: Guaranteed to be compressed as we block multi-threading in // uncompressed mode. However it may be gzip compression instead // of bgzf. // Reading compressed file int64_t block_address; block_address = htell(fp->fp); j->block_address = block_address; // in case we exit with j->errcode if (fp->cache_size && load_block_from_cache(fp, block_address)) return 0; count = hpeek(fp->fp, header, sizeof(header)); if (count == 0) // no data read return -1; int ret; if ( count != sizeof(header) || (ret=check_header(header))==-2 ) { j->errcode |= BGZF_ERR_HEADER; return -1; } if (ret == -1) { j->errcode |= BGZF_ERR_MT; return -1; } count = hread(fp->fp, header, sizeof(header)); if (count != sizeof(header)) // no data read return -1; block_length = unpackInt16((uint8_t*)&header[16]) + 1; // +1 because when writing this number, we used "-1" if (block_length < BLOCK_HEADER_LENGTH) { j->errcode |= BGZF_ERR_HEADER; return -1; } compressed_block = (uint8_t*)j->comp_data; memcpy(compressed_block, header, BLOCK_HEADER_LENGTH); remaining = block_length - BLOCK_HEADER_LENGTH; count = hread(fp->fp, &compressed_block[BLOCK_HEADER_LENGTH], remaining); if (count != remaining) { j->errcode |= BGZF_ERR_IO; return -1; } j->comp_len = block_length; j->uncomp_len = BGZF_MAX_BLOCK_SIZE; j->block_address = block_address; j->fp = fp; j->errcode = 0; return 0; } static int bgzf_check_EOF_common(BGZF *fp) { uint8_t buf[28]; off_t offset = htell(fp->fp); if (hseek(fp->fp, -28, SEEK_END) < 0) { if (errno == ESPIPE) { hclearerr(fp->fp); return 2; } #ifdef _WIN32 if (errno == EINVAL) { hclearerr(fp->fp); return 2; } #else // Assume that EINVAL was due to the file being less than 28 bytes // long, rather than being a random error return from an hfile backend. // This should be reported as "no EOF block" rather than an error. if (errno == EINVAL) { hclearerr(fp->fp); return 0; } #endif return -1; } if ( hread(fp->fp, buf, 28) != 28 ) return -1; if ( hseek(fp->fp, offset, SEEK_SET) < 0 ) return -1; return (memcmp("\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0", buf, 28) == 0)? 1 : 0; } /* * Checks EOF from the reader thread. */ static void bgzf_mt_eof(BGZF *fp) { mtaux_t *mt = fp->mt; pthread_mutex_lock(&mt->job_pool_m); mt->eof = bgzf_check_EOF_common(fp); pthread_mutex_unlock(&mt->job_pool_m); mt->command = HAS_EOF_DONE; pthread_cond_signal(&mt->command_c); } /* * Performs the seek (called by reader thread). * * This simply drains the entire queue, throwing away blocks, seeks, * and starts it up again. Brute force, but maybe sufficient. */ static void bgzf_mt_seek(BGZF *fp) { mtaux_t *mt = fp->mt; hts_tpool_process_reset(mt->out_queue, 0); pthread_mutex_lock(&mt->job_pool_m); mt->errcode = 0; if (hseek(fp->fp, mt->block_address, SEEK_SET) < 0) mt->errcode = BGZF_ERR_IO; pthread_mutex_unlock(&mt->job_pool_m); mt->command = SEEK_DONE; pthread_cond_signal(&mt->command_c); } static void *bgzf_mt_reader(void *vp) { BGZF *fp = (BGZF *)vp; mtaux_t *mt = fp->mt; restart: pthread_mutex_lock(&mt->job_pool_m); bgzf_job *j = pool_alloc(mt->job_pool); pthread_mutex_unlock(&mt->job_pool_m); if (!j) goto err; j->errcode = 0; j->comp_len = 0; j->uncomp_len = 0; j->hit_eof = 0; j->fp = fp; while (bgzf_mt_read_block(fp, j) == 0) { // Dispatch if (hts_tpool_dispatch3(mt->pool, mt->out_queue, bgzf_decode_func, j, job_cleanup, job_cleanup, 0) < 0) { job_cleanup(j); goto err; } // Check for command pthread_mutex_lock(&mt->command_m); switch (mt->command) { case SEEK: bgzf_mt_seek(fp); // Sets mt->command to SEEK_DONE pthread_mutex_unlock(&mt->command_m); goto restart; case HAS_EOF: bgzf_mt_eof(fp); // Sets mt->command to HAS_EOF_DONE break; case SEEK_DONE: case HAS_EOF_DONE: pthread_cond_signal(&mt->command_c); break; case CLOSE: pthread_cond_signal(&mt->command_c); pthread_mutex_unlock(&mt->command_m); hts_tpool_process_destroy(mt->out_queue); return NULL; default: break; } pthread_mutex_unlock(&mt->command_m); // Allocate buffer for next block pthread_mutex_lock(&mt->job_pool_m); j = pool_alloc(mt->job_pool); pthread_mutex_unlock(&mt->job_pool_m); if (!j) { hts_tpool_process_destroy(mt->out_queue); return NULL; } j->errcode = 0; j->comp_len = 0; j->uncomp_len = 0; j->hit_eof = 0; j->fp = fp; } if (j->errcode == BGZF_ERR_MT) { // Attempt to multi-thread decode a raw gzip stream cannot be done. // We tear down the multi-threaded decoder and revert to the old code. if (hts_tpool_dispatch3(mt->pool, mt->out_queue, bgzf_nul_func, j, job_cleanup, job_cleanup, 0) < 0) { job_cleanup(j); hts_tpool_process_destroy(mt->out_queue); return NULL; } hts_tpool_process_ref_decr(mt->out_queue); return &j->errcode; } // Dispatch an empty block so EOF is spotted. // We also use this mechanism for returning errors, in which case // j->errcode is set already. j->hit_eof = 1; if (hts_tpool_dispatch3(mt->pool, mt->out_queue, bgzf_nul_func, j, job_cleanup, job_cleanup, 0) < 0) { job_cleanup(j); hts_tpool_process_destroy(mt->out_queue); return NULL; } if (j->errcode != 0) { hts_tpool_process_destroy(mt->out_queue); return &j->errcode; } // We hit EOF so can stop reading, but we may get a subsequent // seek request. In this case we need to restart the reader. // // To handle this we wait on a condition variable and then // monitor the command. (This could be either seek or close.) for (;;) { pthread_mutex_lock(&mt->command_m); if (mt->command == NONE) pthread_cond_wait(&mt->command_c, &mt->command_m); switch(mt->command) { default: pthread_mutex_unlock(&mt->command_m); break; case SEEK: bgzf_mt_seek(fp); pthread_mutex_unlock(&mt->command_m); goto restart; case HAS_EOF: bgzf_mt_eof(fp); // Sets mt->command to HAS_EOF_DONE pthread_mutex_unlock(&mt->command_m); break; case SEEK_DONE: case HAS_EOF_DONE: pthread_cond_signal(&mt->command_c); pthread_mutex_unlock(&mt->command_m); break; case CLOSE: pthread_cond_signal(&mt->command_c); pthread_mutex_unlock(&mt->command_m); hts_tpool_process_destroy(mt->out_queue); return NULL; } } err: pthread_mutex_lock(&mt->command_m); mt->command = CLOSE; pthread_cond_signal(&mt->command_c); pthread_mutex_unlock(&mt->command_m); hts_tpool_process_destroy(mt->out_queue); return NULL; } int bgzf_thread_pool(BGZF *fp, hts_tpool *pool, int qsize) { // No gain from multi-threading when not compressed if (!fp->is_compressed) return 0; mtaux_t *mt; mt = (mtaux_t*)calloc(1, sizeof(mtaux_t)); if (!mt) return -1; fp->mt = mt; mt->pool = pool; mt->n_threads = hts_tpool_size(pool); if (!qsize) qsize = mt->n_threads*2; if (!(mt->out_queue = hts_tpool_process_init(mt->pool, qsize, 0))) goto err; hts_tpool_process_ref_incr(mt->out_queue); mt->job_pool = pool_create(sizeof(bgzf_job)); if (!mt->job_pool) goto err; pthread_mutex_init(&mt->job_pool_m, NULL); pthread_mutex_init(&mt->command_m, NULL); pthread_mutex_init(&mt->idx_m, NULL); pthread_cond_init(&mt->command_c, NULL); mt->flush_pending = 0; mt->jobs_pending = 0; mt->free_block = fp->uncompressed_block; // currently in-use block mt->block_address = fp->block_address; pthread_create(&mt->io_task, NULL, fp->is_write ? bgzf_mt_writer : bgzf_mt_reader, fp); return 0; err: free(mt); fp->mt = NULL; return -1; } int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks) { // No gain from multi-threading when not compressed if (!fp->is_compressed || fp->is_gzip) return 0; if (n_threads < 1) return -1; hts_tpool *p = hts_tpool_init(n_threads); if (!p) return -1; if (bgzf_thread_pool(fp, p, 0) != 0) { hts_tpool_destroy(p); return -1; } fp->mt->own_pool = 1; return 0; } static int mt_destroy(mtaux_t *mt) { int ret = 0; // Tell the reader to shut down pthread_mutex_lock(&mt->command_m); mt->command = CLOSE; pthread_cond_signal(&mt->command_c); hts_tpool_wake_dispatch(mt->out_queue); // unstick the reader pthread_mutex_unlock(&mt->command_m); // Check for thread worker failure, indicated by is_shutdown returning 2 // It's possible really late errors might be missed, but we can live with // that. ret = -(hts_tpool_process_is_shutdown(mt->out_queue) > 1); // Destroying the queue first forces the writer to exit. // mt->out_queue is reference counted, so destroy gets called in both // this and the IO threads. The last to do it will clean up. hts_tpool_process_destroy(mt->out_queue); // IO thread will now exit. Wait for it and perform final clean-up. // If it returned non-NULL, it was not happy. void *retval = NULL; pthread_join(mt->io_task, &retval); ret = retval != NULL ? -1 : ret; pthread_mutex_destroy(&mt->job_pool_m); pthread_mutex_destroy(&mt->command_m); pthread_mutex_destroy(&mt->idx_m); pthread_cond_destroy(&mt->command_c); if (mt->curr_job) pool_free(mt->job_pool, mt->curr_job); if (mt->own_pool) hts_tpool_destroy(mt->pool); pool_destroy(mt->job_pool); if (mt->idx_cache.e) free(mt->idx_cache.e); free(mt); fflush(stderr); return ret; } static int mt_queue(BGZF *fp) { mtaux_t *mt = fp->mt; mt->block_number++; // Also updated by writer thread pthread_mutex_lock(&mt->job_pool_m); bgzf_job *j = pool_alloc(mt->job_pool); if (j) mt->jobs_pending++; pthread_mutex_unlock(&mt->job_pool_m); if (!j) return -1; j->fp = fp; j->errcode = 0; j->uncomp_len = fp->block_offset; if (fp->compress_level == 0) { memcpy(j->comp_data + BLOCK_HEADER_LENGTH + 5, fp->uncompressed_block, j->uncomp_len); if (hts_tpool_dispatch3(mt->pool, mt->out_queue, bgzf_encode_level0_func, j, job_cleanup, job_cleanup, 0) < 0) { goto fail; } } else { memcpy(j->uncomp_data, fp->uncompressed_block, j->uncomp_len); // Need non-block vers & job_pending? if (hts_tpool_dispatch3(mt->pool, mt->out_queue, bgzf_encode_func, j, job_cleanup, job_cleanup, 0) < 0) { goto fail; } } fp->block_offset = 0; return 0; fail: job_cleanup(j); pthread_mutex_lock(&mt->job_pool_m); mt->jobs_pending--; pthread_mutex_unlock(&mt->job_pool_m); return -1; } static int mt_flush_queue(BGZF *fp) { mtaux_t *mt = fp->mt; // Drain the encoder jobs. // We cannot use hts_tpool_flush here as it can cause deadlock if // the queue is full up of decoder tasks. The best solution would // be to have one input queue per type of job, but we don't right now. //hts_tpool_flush(mt->pool); pthread_mutex_lock(&mt->job_pool_m); int shutdown = 0; while (mt->jobs_pending != 0) { if ((shutdown = hts_tpool_process_is_shutdown(mt->out_queue))) break; pthread_mutex_unlock(&mt->job_pool_m); usleep(10000); // FIXME: replace by condition variable pthread_mutex_lock(&mt->job_pool_m); } pthread_mutex_unlock(&mt->job_pool_m); if (shutdown) return -1; // Wait on bgzf_mt_writer to drain the queue if (hts_tpool_process_flush(mt->out_queue) != 0) return -1; return (fp->errcode == 0)? 0 : -1; } static int lazy_flush(BGZF *fp) { if (fp->mt) return fp->block_offset ? mt_queue(fp) : 0; else return bgzf_flush(fp); } #else // ~ #ifdef BGZF_MT int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks) { return 0; } static inline int lazy_flush(BGZF *fp) { return bgzf_flush(fp); } #endif // ~ #ifdef BGZF_MT int bgzf_flush(BGZF *fp) { if (!fp->is_write) return 0; #ifdef BGZF_MT if (fp->mt) { int ret = 0; if (fp->block_offset) ret = mt_queue(fp); if (!ret) ret = mt_flush_queue(fp); // We maintain mt->block_address when threading as the // main code can call bgzf_tell without any locks. // (The result from tell are wrong, but we only care about the last // 16-bits worth except for the final flush process. pthread_mutex_lock(&fp->mt->idx_m); fp->block_address = fp->mt->block_address; pthread_mutex_unlock(&fp->mt->idx_m); return ret; } #endif if (!fp->is_compressed) { return hflush(fp->fp); } while (fp->block_offset > 0) { int block_length; if ( fp->idx_build_otf ) { bgzf_index_add_block(fp); fp->idx->ublock_addr += fp->block_offset; } block_length = deflate_block(fp, fp->block_offset); if (block_length < 0) { hts_log_debug("Deflate block operation failed: %s", bgzf_zerr(block_length, NULL)); return -1; } if (hwrite(fp->fp, fp->compressed_block, block_length) != block_length) { hts_log_error("File write failed (wrong size)"); fp->errcode |= BGZF_ERR_IO; // possibly truncated file return -1; } fp->block_address += block_length; } return 0; } int bgzf_flush_try(BGZF *fp, ssize_t size) { if (fp->block_offset + size > BGZF_BLOCK_SIZE) return lazy_flush(fp); return 0; } ssize_t bgzf_write(BGZF *fp, const void *data, size_t length) { if ( !fp->is_compressed ) { size_t push = length + (size_t) fp->block_offset; fp->block_offset = push % BGZF_MAX_BLOCK_SIZE; fp->block_address += (push - fp->block_offset); return hwrite(fp->fp, data, length); } const uint8_t *input = (const uint8_t*)data; ssize_t remaining = length; assert(fp->is_write); while (remaining > 0) { uint8_t* buffer = (uint8_t*)fp->uncompressed_block; int copy_length = BGZF_BLOCK_SIZE - fp->block_offset; if (copy_length > remaining) copy_length = remaining; memcpy(buffer + fp->block_offset, input, copy_length); fp->block_offset += copy_length; input += copy_length; remaining -= copy_length; if (fp->block_offset == BGZF_BLOCK_SIZE) { if (lazy_flush(fp) != 0) return -1; } } return length - remaining; } ssize_t bgzf_block_write(BGZF *fp, const void *data, size_t length) { if ( !fp->is_compressed ) { size_t push = length + (size_t) fp->block_offset; fp->block_offset = push % BGZF_MAX_BLOCK_SIZE; fp->block_address += (push - fp->block_offset); return hwrite(fp->fp, data, length); } const uint8_t *input = (const uint8_t*)data; ssize_t remaining = length; assert(fp->is_write); uint64_t current_block; //keep track of current block uint64_t ublock_size; // amount of uncompressed data to be fed into next block while (remaining > 0) { current_block = fp->idx->moffs - fp->idx->noffs; ublock_size = current_block + 1 < fp->idx->moffs ? fp->idx->offs[current_block+1].uaddr-fp->idx->offs[current_block].uaddr : BGZF_MAX_BLOCK_SIZE; uint8_t* buffer = (uint8_t*)fp->uncompressed_block; int copy_length = ublock_size - fp->block_offset; if (copy_length > remaining) copy_length = remaining; memcpy(buffer + fp->block_offset, input, copy_length); fp->block_offset += copy_length; input += copy_length; remaining -= copy_length; if (fp->block_offset == ublock_size) { if (lazy_flush(fp) != 0) return -1; if (fp->idx->noffs > 0) fp->idx->noffs--; // decrement noffs to track the blocks } } return length - remaining; } ssize_t bgzf_raw_write(BGZF *fp, const void *data, size_t length) { ssize_t ret = hwrite(fp->fp, data, length); if (ret < 0) fp->errcode |= BGZF_ERR_IO; return ret; } // Helper function for tidying up fp->mt and setting errcode static void bgzf_close_mt(BGZF *fp) { if (fp->mt) { if (!fp->mt->free_block) fp->uncompressed_block = NULL; if (mt_destroy(fp->mt) < 0) fp->errcode = BGZF_ERR_IO; } } int bgzf_close(BGZF* fp) { int ret, block_length; if (fp == 0) return -1; if (fp->is_write && fp->is_compressed) { if (bgzf_flush(fp) != 0) { bgzf_close_mt(fp); return -1; } fp->compress_level = -1; block_length = deflate_block(fp, 0); // write an empty block if (block_length < 0) { hts_log_debug("Deflate block operation failed: %s", bgzf_zerr(block_length, NULL)); bgzf_close_mt(fp); return -1; } if (hwrite(fp->fp, fp->compressed_block, block_length) < 0 || hflush(fp->fp) != 0) { hts_log_error("File write failed"); fp->errcode |= BGZF_ERR_IO; return -1; } } bgzf_close_mt(fp); if ( fp->is_gzip ) { if (fp->gz_stream == NULL) ret = Z_OK; else if (!fp->is_write) ret = inflateEnd(fp->gz_stream); else ret = deflateEnd(fp->gz_stream); if (ret != Z_OK) { hts_log_error("Call to inflateEnd/deflateEnd failed: %s", bgzf_zerr(ret, NULL)); } free(fp->gz_stream); } ret = hclose(fp->fp); if (ret != 0) return -1; bgzf_index_destroy(fp); free(fp->uncompressed_block); free_cache(fp); ret = fp->errcode ? -1 : 0; free(fp); return ret; } void bgzf_set_cache_size(BGZF *fp, int cache_size) { if (fp && fp->mt) return; // Not appropriate when multi-threading if (fp && fp->cache) fp->cache_size = cache_size; } int bgzf_check_EOF(BGZF *fp) { int has_eof; if (fp->mt) { pthread_mutex_lock(&fp->mt->command_m); // fp->mt->command state transitions should be: // NONE -> HAS_EOF -> HAS_EOF_DONE -> NONE // (HAS_EOF -> HAS_EOF_DONE happens in bgzf_mt_reader thread) if (fp->mt->command != CLOSE) fp->mt->command = HAS_EOF; pthread_cond_signal(&fp->mt->command_c); hts_tpool_wake_dispatch(fp->mt->out_queue); do { if (fp->mt->command == CLOSE) { // possible error in bgzf_mt_reader pthread_mutex_unlock(&fp->mt->command_m); return 0; } pthread_cond_wait(&fp->mt->command_c, &fp->mt->command_m); switch (fp->mt->command) { case HAS_EOF_DONE: break; case HAS_EOF: // Resend signal intended for bgzf_mt_reader() pthread_cond_signal(&fp->mt->command_c); break; case CLOSE: continue; default: abort(); // Should not get to any other state } } while (fp->mt->command != HAS_EOF_DONE); fp->mt->command = NONE; has_eof = fp->mt->eof; pthread_mutex_unlock(&fp->mt->command_m); } else { has_eof = bgzf_check_EOF_common(fp); } fp->no_eof_block = (has_eof == 0); return has_eof; } static inline int64_t bgzf_seek_common(BGZF* fp, int64_t block_address, int block_offset) { if (fp->mt) { // The reader runs asynchronous and does loops of: // Read block // Check & process command // Dispatch decode job // // Once at EOF it then switches to loops of // Wait for command // Process command (possibly switching back to above loop). // // To seek we therefore send the reader thread a SEEK command, // waking it up if blocked in dispatch and signalling if // waiting for a command. We then wait for the response so we // know the seek succeeded. pthread_mutex_lock(&fp->mt->command_m); fp->mt->hit_eof = 0; // fp->mt->command state transitions should be: // NONE -> SEEK -> SEEK_DONE -> NONE // (SEEK -> SEEK_DONE happens in bgzf_mt_reader thread) fp->mt->command = SEEK; fp->mt->block_address = block_address; pthread_cond_signal(&fp->mt->command_c); hts_tpool_wake_dispatch(fp->mt->out_queue); do { pthread_cond_wait(&fp->mt->command_c, &fp->mt->command_m); switch (fp->mt->command) { case SEEK_DONE: break; case SEEK: // Resend signal intended for bgzf_mt_reader() pthread_cond_signal(&fp->mt->command_c); break; default: abort(); // Should not get to any other state } } while (fp->mt->command != SEEK_DONE); fp->mt->command = NONE; fp->block_length = 0; // indicates current block has not been loaded fp->block_address = block_address; fp->block_offset = block_offset; pthread_mutex_unlock(&fp->mt->command_m); } else { if (hseek(fp->fp, block_address, SEEK_SET) < 0) { fp->errcode |= BGZF_ERR_IO; return -1; } fp->block_length = 0; // indicates current block has not been loaded fp->block_address = block_address; fp->block_offset = block_offset; } return 0; } int64_t bgzf_seek(BGZF* fp, int64_t pos, int where) { if (fp->is_write || where != SEEK_SET || fp->is_gzip) { fp->errcode |= BGZF_ERR_MISUSE; return -1; } // This is a flag to indicate we've jumped elsewhere in the stream, to act // as a hint to any other code which is wrapping up bgzf for its own // purposes. We may not be able to tell when seek happens as it can be // done on our behalf, eg by the iterator. // // This is never cleared here. Any tool that needs to handle it is also // responsible for clearing it. fp->seeked = pos; return bgzf_seek_common(fp, pos >> 16, pos & 0xFFFF); } int bgzf_is_bgzf(const char *fn) { uint8_t buf[16]; int n; hFILE *fp; if ((fp = hopen(fn, "r")) == 0) return 0; n = hread(fp, buf, 16); if (hclose(fp) < 0) return 0; if (n != 16) return 0; return check_header(buf) == 0? 1 : 0; } int bgzf_compression(BGZF *fp) { return (!fp->is_compressed)? no_compression : (fp->is_gzip)? gzip : bgzf; } int bgzf_getc(BGZF *fp) { if (fp->block_offset+1 < fp->block_length) { fp->uncompressed_address++; return ((unsigned char*)fp->uncompressed_block)[fp->block_offset++]; } int c; if (fp->block_offset >= fp->block_length) { if (bgzf_read_block(fp) != 0) return -2; /* error */ if (fp->block_length == 0) return -1; /* end-of-file */ } c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++]; if (fp->block_offset == fp->block_length) { fp->block_address = bgzf_htell(fp); fp->block_offset = 0; fp->block_length = 0; } fp->uncompressed_address++; return c; } int bgzf_getline(BGZF *fp, int delim, kstring_t *str) { int l, state = 0; str->l = 0; do { if (fp->block_offset >= fp->block_length) { if (bgzf_read_block(fp) != 0) { state = -2; break; } if (fp->block_length == 0) { state = -1; break; } } unsigned char *buf = fp->uncompressed_block; // Equivalent to a naive byte by byte search from // buf + block_offset to buf + block_length. void *e = memchr(&buf[fp->block_offset], delim, fp->block_length - fp->block_offset); l = e ? (unsigned char *)e - buf : fp->block_length; if (l < fp->block_length) state = 1; l -= fp->block_offset; if (ks_expand(str, l + 2) < 0) { state = -3; break; } memcpy(str->s + str->l, buf + fp->block_offset, l); str->l += l; fp->block_offset += l + 1; if (fp->block_offset >= fp->block_length) { fp->block_address = bgzf_htell(fp); fp->block_offset = 0; fp->block_length = 0; } } while (state == 0); if (state < -1) return state; if (str->l == 0 && state < 0) return state; fp->uncompressed_address += str->l + 1; if ( delim=='\n' && str->l>0 && str->s[str->l-1]=='\r' ) str->l--; str->s[str->l] = 0; return str->l <= INT_MAX ? (int) str->l : INT_MAX; } void bgzf_index_destroy(BGZF *fp) { if ( !fp->idx ) return; free(fp->idx->offs); free(fp->idx); fp->idx = NULL; fp->idx_build_otf = 0; } int bgzf_index_build_init(BGZF *fp) { bgzf_index_destroy(fp); fp->idx = (bgzidx_t*) calloc(1,sizeof(bgzidx_t)); if ( !fp->idx ) return -1; fp->idx_build_otf = 1; // build index on the fly return 0; } int bgzf_index_add_block(BGZF *fp) { fp->idx->noffs++; if ( fp->idx->noffs > fp->idx->moffs ) { fp->idx->moffs = fp->idx->noffs; kroundup32(fp->idx->moffs); fp->idx->offs = (bgzidx1_t*) realloc(fp->idx->offs, fp->idx->moffs*sizeof(bgzidx1_t)); if ( !fp->idx->offs ) return -1; } fp->idx->offs[ fp->idx->noffs-1 ].uaddr = fp->idx->ublock_addr; fp->idx->offs[ fp->idx->noffs-1 ].caddr = fp->block_address; return 0; } static inline int hwrite_uint64(uint64_t x, hFILE *f) { if (ed_is_big()) x = ed_swap_8(x); if (hwrite(f, &x, sizeof(x)) != sizeof(x)) return -1; return 0; } static char * get_name_suffix(const char *bname, const char *suffix) { size_t len = strlen(bname) + strlen(suffix) + 1; char *buff = malloc(len); if (!buff) return NULL; snprintf(buff, len, "%s%s", bname, suffix); return buff; } int bgzf_index_dump_hfile(BGZF *fp, struct hFILE *idx, const char *name) { // Note that the index contains one extra record when indexing files opened // for reading. The terminating record is not present when opened for writing. // This is not a bug. int i; if (!fp->idx) { hts_log_error("Called for BGZF handle with no index"); errno = EINVAL; return -1; } if (bgzf_flush(fp) != 0) return -1; // discard the entry marking the end of the file if (fp->mt && fp->idx) fp->idx->noffs--; if (hwrite_uint64(fp->idx->noffs - 1, idx) < 0) goto fail; for (i=1; iidx->noffs; i++) { if (hwrite_uint64(fp->idx->offs[i].caddr, idx) < 0) goto fail; if (hwrite_uint64(fp->idx->offs[i].uaddr, idx) < 0) goto fail; } return 0; fail: hts_log_error("Error writing to %s : %s", name ? name : "index", strerror(errno)); return -1; } int bgzf_index_dump(BGZF *fp, const char *bname, const char *suffix) { const char *name = bname, *msg = NULL; char *tmp = NULL; hFILE *idx = NULL; if (!fp->idx) { hts_log_error("Called for BGZF handle with no index"); errno = EINVAL; return -1; } if ( suffix ) { tmp = get_name_suffix(bname, suffix); if ( !tmp ) return -1; name = tmp; } idx = hopen(name, "wb"); if ( !idx ) { msg = "Error opening"; goto fail; } if (bgzf_index_dump_hfile(fp, idx, name) != 0) goto fail; if (hclose(idx) < 0) { idx = NULL; msg = "Error on closing"; goto fail; } free(tmp); return 0; fail: if (msg != NULL) { hts_log_error("%s %s : %s", msg, name, strerror(errno)); } if (idx) hclose_abruptly(idx); free(tmp); return -1; } static inline int hread_uint64(uint64_t *xptr, hFILE *f) { if (hread(f, xptr, sizeof(*xptr)) != sizeof(*xptr)) return -1; if (ed_is_big()) ed_swap_8p(xptr); return 0; } int bgzf_index_load_hfile(BGZF *fp, struct hFILE *idx, const char *name) { fp->idx = (bgzidx_t*) calloc(1,sizeof(bgzidx_t)); if (fp->idx == NULL) goto fail; uint64_t x; if (hread_uint64(&x, idx) < 0) goto fail; fp->idx->noffs = fp->idx->moffs = x + 1; fp->idx->offs = (bgzidx1_t*) malloc(fp->idx->moffs*sizeof(bgzidx1_t)); if (fp->idx->offs == NULL) goto fail; fp->idx->offs[0].caddr = fp->idx->offs[0].uaddr = 0; int i; for (i=1; iidx->noffs; i++) { if (hread_uint64(&fp->idx->offs[i].caddr, idx) < 0) goto fail; if (hread_uint64(&fp->idx->offs[i].uaddr, idx) < 0) goto fail; } return 0; fail: hts_log_error("Error reading %s : %s", name ? name : "index", strerror(errno)); if (fp->idx) { free(fp->idx->offs); free(fp->idx); fp->idx = NULL; } return -1; } int bgzf_index_load(BGZF *fp, const char *bname, const char *suffix) { const char *name = bname, *msg = NULL; char *tmp = NULL; hFILE *idx = NULL; if ( suffix ) { tmp = get_name_suffix(bname, suffix); if ( !tmp ) return -1; name = tmp; } idx = hopen(name, "rb"); if ( !idx ) { msg = "Error opening"; goto fail; } if (bgzf_index_load_hfile(fp, idx, name) != 0) goto fail; if (hclose(idx) != 0) { idx = NULL; msg = "Error closing"; goto fail; } free(tmp); return 0; fail: if (msg != NULL) { hts_log_error("%s %s : %s", msg, name, strerror(errno)); } if (idx) hclose_abruptly(idx); free(tmp); return -1; } int bgzf_useek(BGZF *fp, off_t uoffset, int where) { if (fp->is_write || where != SEEK_SET || fp->is_gzip) { fp->errcode |= BGZF_ERR_MISUSE; return -1; } if (uoffset >= fp->uncompressed_address - fp->block_offset && uoffset < fp->uncompressed_address + fp->block_length - fp->block_offset) { // Can seek into existing data fp->block_offset += uoffset - fp->uncompressed_address; fp->uncompressed_address = uoffset; return 0; } if ( !fp->is_compressed ) { if (hseek(fp->fp, uoffset, SEEK_SET) < 0) { fp->errcode |= BGZF_ERR_IO; return -1; } fp->block_length = 0; // indicates current block has not been loaded fp->block_address = uoffset; fp->block_offset = 0; if (bgzf_read_block(fp) < 0) { fp->errcode |= BGZF_ERR_IO; return -1; } fp->uncompressed_address = uoffset; return 0; } if ( !fp->idx ) { fp->errcode |= BGZF_ERR_IO; return -1; } // binary search int ilo = 0, ihi = fp->idx->noffs - 1; while ( ilo<=ihi ) { int i = (ilo+ihi)*0.5; if ( uoffset < fp->idx->offs[i].uaddr ) ihi = i - 1; else if ( uoffset >= fp->idx->offs[i].uaddr ) ilo = i + 1; else break; } int i = ilo-1; off_t offset = 0; if (bgzf_seek_common(fp, fp->idx->offs[i].caddr, 0) < 0) return -1; if ( bgzf_read_block(fp) < 0 ) { fp->errcode |= BGZF_ERR_IO; return -1; } offset = uoffset - fp->idx->offs[i].uaddr; if ( offset > 0 ) { if (offset > fp->block_length) { fp->errcode |= BGZF_ERR_IO; return -1; //offset outside the available data } fp->block_offset = offset; assert( fp->block_offset <= fp->block_length ); // todo: skipped, unindexed, blocks } fp->uncompressed_address = uoffset; return 0; } off_t bgzf_utell(BGZF *fp) { return fp->uncompressed_address; // currently maintained only when reading } /* prototype is in hfile_internal.h */ struct hFILE *bgzf_hfile(struct BGZF *fp) { return fp->fp; } pysam-0.23.0/htslib/builddir_vars.mk.in000066400000000000000000000046671475062545500200330ustar00rootroot00000000000000# Separate build directory Makefile overrides for htslib. # # Copyright (C) 2021 University of Glasgow. # # Author: John Marshall # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. # This is @configure_input@ # # When building from a separate build directory, this file is included by # HTSlib's Makefile or htslib.mk instead of htslib_vars.mk. It adjusts # variables to account for a separate source directory and then includes # the real makefile fragment. ifneq "$(HTSPREFIX)" "" # When included externally via htslib.mk, just update $(HTSSRCDIR) and hence # $(HTSPREFIX) to point to the source directory (without using any extra # unprefixed variables, which would be in the external project's namespace). # Set to $(HTSDIR)/$(srcdir) (or just $(srcdir) if that's absolute) HTSSRCDIR = @HTSDIRslash_if_relsrcdir@@srcdir@ include $(HTSSRCDIR)/htslib_vars.mk else # When included from HTSlib's Makefile, override $(srcdir) and set VPATH, # and make any other adjustments required. ($(HTSPREFIX) remains empty as # the items it prefixes will be found via VPATH instead.) srcdir = @srcdir@ VPATH = @srcdir@ srcprefix = $(srcdir)/ # Ensure that htscodecs.c can include its version.h. This -I option must come # before -I. so that these targets get this version.h rather than HTSlib's. htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.pico: ALL_CPPFLAGS = -Ihtscodecs/htscodecs -I. $(CPPFLAGS) include $(srcdir)/htslib_vars.mk endif pysam-0.23.0/htslib/config.guess000077500000000000000000001426761475062545500165670ustar00rootroot00000000000000#! /bin/sh # Attempt to guess a canonical system name. # Copyright 1992-2023 Free Software Foundation, Inc. # shellcheck disable=SC2006,SC2268 # see below for rationale timestamp='2023-08-22' # This file is free software; you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, see . # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that # program. This Exception is an additional permission under section 7 # of the GNU General Public License, version 3 ("GPLv3"). # # Originally written by Per Bothner; maintained since 2000 by Ben Elliston. # # You can get the latest version of this script from: # https://git.savannah.gnu.org/cgit/config.git/plain/config.guess # # Please send patches to . # The "shellcheck disable" line above the timestamp inhibits complaints # about features and limitations of the classic Bourne shell that were # superseded or lifted in POSIX. 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HP_ARCH=m68000 ;; 9000/[34]??) HP_ARCH=m68k ;; 9000/[678][0-9][0-9]) if test -x /usr/bin/getconf; then sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` case $sc_cpu_version in 523) HP_ARCH=hppa1.0 ;; # CPU_PA_RISC1_0 528) HP_ARCH=hppa1.1 ;; # CPU_PA_RISC1_1 532) # CPU_PA_RISC2_0 case $sc_kernel_bits in 32) HP_ARCH=hppa2.0n ;; 64) HP_ARCH=hppa2.0w ;; '') HP_ARCH=hppa2.0 ;; # HP-UX 10.20 esac ;; esac fi if test "$HP_ARCH" = ""; then set_cc_for_build sed 's/^ //' << EOF > "$dummy.c" #define _HPUX_SOURCE #include #include int main () { #if defined(_SC_KERNEL_BITS) long bits = sysconf(_SC_KERNEL_BITS); #endif long cpu = sysconf (_SC_CPU_VERSION); switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0"); break; case CPU_PA_RISC1_1: puts ("hppa1.1"); break; case CPU_PA_RISC2_0: #if defined(_SC_KERNEL_BITS) switch (bits) { case 64: puts ("hppa2.0w"); break; case 32: puts ("hppa2.0n"); break; default: puts ("hppa2.0"); break; } break; #else /* !defined(_SC_KERNEL_BITS) */ puts ("hppa2.0"); break; #endif default: puts ("hppa1.0"); break; } exit (0); } EOF (CCOPTS="" $CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null) && HP_ARCH=`"$dummy"` test -z "$HP_ARCH" && HP_ARCH=hppa fi ;; esac if test "$HP_ARCH" = hppa2.0w then set_cc_for_build # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler # generating 64-bit code. GNU and HP use different nomenclature: # # $ CC_FOR_BUILD=cc ./config.guess # => hppa2.0w-hp-hpux11.23 # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess # => hppa64-hp-hpux11.23 if echo __LP64__ | (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | grep -q __LP64__ then HP_ARCH=hppa2.0w else HP_ARCH=hppa64 fi fi GUESS=$HP_ARCH-hp-hpux$HPUX_REV ;; ia64:HP-UX:*:*) HPUX_REV=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*.[0B]*//'` GUESS=ia64-hp-hpux$HPUX_REV ;; 3050*:HI-UX:*:*) set_cc_for_build sed 's/^ //' << EOF > "$dummy.c" #include int main () { long cpu = sysconf (_SC_CPU_VERSION); /* The order matters, because CPU_IS_HP_MC68K erroneously returns true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct results, however. */ if (CPU_IS_PA_RISC (cpu)) { switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; default: puts ("hppa-hitachi-hiuxwe2"); break; } } else if (CPU_IS_HP_MC68K (cpu)) puts ("m68k-hitachi-hiuxwe2"); else puts ("unknown-hitachi-hiuxwe2"); exit (0); } EOF $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"` && { echo "$SYSTEM_NAME"; exit; } GUESS=unknown-hitachi-hiuxwe2 ;; 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:*) GUESS=hppa1.1-hp-bsd ;; 9000/8??:4.3bsd:*:*) GUESS=hppa1.0-hp-bsd ;; *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) GUESS=hppa1.0-hp-mpeix ;; hp7??:OSF1:*:* | hp8?[79]:OSF1:*:*) GUESS=hppa1.1-hp-osf ;; hp8??:OSF1:*:*) GUESS=hppa1.0-hp-osf ;; i*86:OSF1:*:*) if test -x /usr/sbin/sysversion ; then GUESS=$UNAME_MACHINE-unknown-osf1mk else GUESS=$UNAME_MACHINE-unknown-osf1 fi ;; parisc*:Lites*:*:*) GUESS=hppa1.1-hp-lites ;; C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) GUESS=c1-convex-bsd ;; C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit ;; C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) GUESS=c34-convex-bsd ;; C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) GUESS=c38-convex-bsd ;; C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) GUESS=c4-convex-bsd ;; CRAY*Y-MP:*:*:*) CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'` GUESS=ymp-cray-unicos$CRAY_REL ;; CRAY*[A-Z]90:*:*:*) echo "$UNAME_MACHINE"-cray-unicos"$UNAME_RELEASE" \ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ -e 's/\.[^.]*$/.X/' exit ;; CRAY*TS:*:*:*) CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'` GUESS=t90-cray-unicos$CRAY_REL ;; CRAY*T3E:*:*:*) CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'` GUESS=alphaev5-cray-unicosmk$CRAY_REL ;; CRAY*SV1:*:*:*) CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'` GUESS=sv1-cray-unicos$CRAY_REL ;; *:UNICOS/mp:*:*) CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'` GUESS=craynv-cray-unicosmp$CRAY_REL ;; F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) FUJITSU_PROC=`uname -m | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz` FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'` FUJITSU_REL=`echo "$UNAME_RELEASE" | sed -e 's/ /_/'` GUESS=${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL} ;; 5000:UNIX_System_V:4.*:*) FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'` FUJITSU_REL=`echo "$UNAME_RELEASE" | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/ /_/'` GUESS=sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL} ;; i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) GUESS=$UNAME_MACHINE-pc-bsdi$UNAME_RELEASE ;; sparc*:BSD/OS:*:*) GUESS=sparc-unknown-bsdi$UNAME_RELEASE ;; *:BSD/OS:*:*) GUESS=$UNAME_MACHINE-unknown-bsdi$UNAME_RELEASE ;; arm:FreeBSD:*:*) UNAME_PROCESSOR=`uname -p` set_cc_for_build if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ARM_PCS_VFP then FREEBSD_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'` GUESS=$UNAME_PROCESSOR-unknown-freebsd$FREEBSD_REL-gnueabi else FREEBSD_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'` GUESS=$UNAME_PROCESSOR-unknown-freebsd$FREEBSD_REL-gnueabihf fi ;; *:FreeBSD:*:*) UNAME_PROCESSOR=`uname -p` case $UNAME_PROCESSOR in amd64) UNAME_PROCESSOR=x86_64 ;; i386) UNAME_PROCESSOR=i586 ;; esac FREEBSD_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'` GUESS=$UNAME_PROCESSOR-unknown-freebsd$FREEBSD_REL ;; i*:CYGWIN*:*) GUESS=$UNAME_MACHINE-pc-cygwin ;; *:MINGW64*:*) GUESS=$UNAME_MACHINE-pc-mingw64 ;; *:MINGW*:*) GUESS=$UNAME_MACHINE-pc-mingw32 ;; *:MSYS*:*) GUESS=$UNAME_MACHINE-pc-msys ;; i*:PW*:*) GUESS=$UNAME_MACHINE-pc-pw32 ;; *:SerenityOS:*:*) GUESS=$UNAME_MACHINE-pc-serenity ;; *:Interix*:*) case $UNAME_MACHINE in x86) GUESS=i586-pc-interix$UNAME_RELEASE ;; authenticamd | genuineintel | EM64T) GUESS=x86_64-unknown-interix$UNAME_RELEASE ;; IA64) GUESS=ia64-unknown-interix$UNAME_RELEASE ;; esac ;; i*:UWIN*:*) GUESS=$UNAME_MACHINE-pc-uwin ;; amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*) GUESS=x86_64-pc-cygwin ;; prep*:SunOS:5.*:*) SUN_REL=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'` GUESS=powerpcle-unknown-solaris2$SUN_REL ;; *:GNU:*:*) # the GNU system GNU_ARCH=`echo "$UNAME_MACHINE" | sed -e 's,[-/].*$,,'` GNU_REL=`echo "$UNAME_RELEASE" | sed -e 's,/.*$,,'` GUESS=$GNU_ARCH-unknown-$LIBC$GNU_REL ;; *:GNU/*:*:*) # other systems with GNU libc and userland GNU_SYS=`echo "$UNAME_SYSTEM" | sed 's,^[^/]*/,,' | tr "[:upper:]" "[:lower:]"` GNU_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'` GUESS=$UNAME_MACHINE-unknown-$GNU_SYS$GNU_REL-$LIBC ;; x86_64:[Mm]anagarm:*:*|i?86:[Mm]anagarm:*:*) GUESS="$UNAME_MACHINE-pc-managarm-mlibc" ;; *:[Mm]anagarm:*:*) GUESS="$UNAME_MACHINE-unknown-managarm-mlibc" ;; *:Minix:*:*) GUESS=$UNAME_MACHINE-unknown-minix ;; aarch64:Linux:*:*) set_cc_for_build CPU=$UNAME_MACHINE LIBCABI=$LIBC if test "$CC_FOR_BUILD" != no_compiler_found; then ABI=64 sed 's/^ //' << EOF > "$dummy.c" #ifdef __ARM_EABI__ #ifdef __ARM_PCS_VFP ABI=eabihf #else ABI=eabi #endif #endif EOF cc_set_abi=`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^ABI' | sed 's, ,,g'` eval "$cc_set_abi" case $ABI in eabi | eabihf) CPU=armv8l; LIBCABI=$LIBC$ABI ;; esac fi GUESS=$CPU-unknown-linux-$LIBCABI ;; aarch64_be:Linux:*:*) UNAME_MACHINE=aarch64_be GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; alpha:Linux:*:*) case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' /proc/cpuinfo 2>/dev/null` in EV5) UNAME_MACHINE=alphaev5 ;; EV56) UNAME_MACHINE=alphaev56 ;; PCA56) UNAME_MACHINE=alphapca56 ;; PCA57) UNAME_MACHINE=alphapca56 ;; EV6) UNAME_MACHINE=alphaev6 ;; EV67) UNAME_MACHINE=alphaev67 ;; EV68*) UNAME_MACHINE=alphaev68 ;; esac objdump --private-headers /bin/sh | grep -q ld.so.1 if test "$?" = 0 ; then LIBC=gnulibc1 ; fi GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; arc:Linux:*:* | arceb:Linux:*:* | arc32:Linux:*:* | arc64:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; arm*:Linux:*:*) set_cc_for_build if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ARM_EABI__ then GUESS=$UNAME_MACHINE-unknown-linux-$LIBC else if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ARM_PCS_VFP then GUESS=$UNAME_MACHINE-unknown-linux-${LIBC}eabi else GUESS=$UNAME_MACHINE-unknown-linux-${LIBC}eabihf fi fi ;; avr32*:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; cris:Linux:*:*) GUESS=$UNAME_MACHINE-axis-linux-$LIBC ;; crisv32:Linux:*:*) GUESS=$UNAME_MACHINE-axis-linux-$LIBC ;; e2k:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; frv:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; hexagon:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; i*86:Linux:*:*) GUESS=$UNAME_MACHINE-pc-linux-$LIBC ;; ia64:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; k1om:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; kvx:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; kvx:cos:*:*) GUESS=$UNAME_MACHINE-unknown-cos ;; kvx:mbr:*:*) GUESS=$UNAME_MACHINE-unknown-mbr ;; loongarch32:Linux:*:* | loongarch64:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; m32r*:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; m68*:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; mips:Linux:*:* | mips64:Linux:*:*) set_cc_for_build IS_GLIBC=0 test x"${LIBC}" = xgnu && IS_GLIBC=1 sed 's/^ //' << EOF > "$dummy.c" #undef CPU #undef mips #undef mipsel #undef mips64 #undef mips64el #if ${IS_GLIBC} && defined(_ABI64) LIBCABI=gnuabi64 #else #if ${IS_GLIBC} && defined(_ABIN32) LIBCABI=gnuabin32 #else LIBCABI=${LIBC} #endif #endif #if ${IS_GLIBC} && defined(__mips64) && defined(__mips_isa_rev) && __mips_isa_rev>=6 CPU=mipsisa64r6 #else #if ${IS_GLIBC} && !defined(__mips64) && defined(__mips_isa_rev) && __mips_isa_rev>=6 CPU=mipsisa32r6 #else #if defined(__mips64) CPU=mips64 #else CPU=mips #endif #endif #endif #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) MIPS_ENDIAN=el #else #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) MIPS_ENDIAN= #else MIPS_ENDIAN= #endif #endif EOF cc_set_vars=`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^CPU\|^MIPS_ENDIAN\|^LIBCABI'` eval "$cc_set_vars" test "x$CPU" != x && { echo "$CPU${MIPS_ENDIAN}-unknown-linux-$LIBCABI"; exit; } ;; mips64el:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; openrisc*:Linux:*:*) GUESS=or1k-unknown-linux-$LIBC ;; or32:Linux:*:* | or1k*:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; padre:Linux:*:*) GUESS=sparc-unknown-linux-$LIBC ;; parisc64:Linux:*:* | hppa64:Linux:*:*) GUESS=hppa64-unknown-linux-$LIBC ;; parisc:Linux:*:* | hppa:Linux:*:*) # Look for CPU level case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in PA7*) GUESS=hppa1.1-unknown-linux-$LIBC ;; PA8*) GUESS=hppa2.0-unknown-linux-$LIBC ;; *) GUESS=hppa-unknown-linux-$LIBC ;; esac ;; ppc64:Linux:*:*) GUESS=powerpc64-unknown-linux-$LIBC ;; ppc:Linux:*:*) GUESS=powerpc-unknown-linux-$LIBC ;; ppc64le:Linux:*:*) GUESS=powerpc64le-unknown-linux-$LIBC ;; ppcle:Linux:*:*) GUESS=powerpcle-unknown-linux-$LIBC ;; riscv32:Linux:*:* | riscv32be:Linux:*:* | riscv64:Linux:*:* | riscv64be:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; s390:Linux:*:* | s390x:Linux:*:*) GUESS=$UNAME_MACHINE-ibm-linux-$LIBC ;; sh64*:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; sh*:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; sparc:Linux:*:* | sparc64:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; tile*:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; vax:Linux:*:*) GUESS=$UNAME_MACHINE-dec-linux-$LIBC ;; x86_64:Linux:*:*) set_cc_for_build CPU=$UNAME_MACHINE LIBCABI=$LIBC if test "$CC_FOR_BUILD" != no_compiler_found; then ABI=64 sed 's/^ //' << EOF > "$dummy.c" #ifdef __i386__ ABI=x86 #else #ifdef __ILP32__ ABI=x32 #endif #endif EOF cc_set_abi=`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^ABI' | sed 's, ,,g'` eval "$cc_set_abi" case $ABI in x86) CPU=i686 ;; x32) LIBCABI=${LIBC}x32 ;; esac fi GUESS=$CPU-pc-linux-$LIBCABI ;; xtensa*:Linux:*:*) GUESS=$UNAME_MACHINE-unknown-linux-$LIBC ;; i*86:DYNIX/ptx:4*:*) # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. # earlier versions are messed up and put the nodename in both # sysname and nodename. GUESS=i386-sequent-sysv4 ;; i*86:UNIX_SV:4.2MP:2.*) # Unixware is an offshoot of SVR4, but it has its own version # number series starting with 2... # I am not positive that other SVR4 systems won't match this, # I just have to hope. -- rms. # Use sysv4.2uw... so that sysv4* matches it. GUESS=$UNAME_MACHINE-pc-sysv4.2uw$UNAME_VERSION ;; i*86:OS/2:*:*) # If we were able to find 'uname', then EMX Unix compatibility # is probably installed. GUESS=$UNAME_MACHINE-pc-os2-emx ;; i*86:XTS-300:*:STOP) GUESS=$UNAME_MACHINE-unknown-stop ;; i*86:atheos:*:*) GUESS=$UNAME_MACHINE-unknown-atheos ;; i*86:syllable:*:*) GUESS=$UNAME_MACHINE-pc-syllable ;; i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*) GUESS=i386-unknown-lynxos$UNAME_RELEASE ;; i*86:*DOS:*:*) GUESS=$UNAME_MACHINE-pc-msdosdjgpp ;; i*86:*:4.*:*) UNAME_REL=`echo "$UNAME_RELEASE" | sed 's/\/MP$//'` if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then GUESS=$UNAME_MACHINE-univel-sysv$UNAME_REL else GUESS=$UNAME_MACHINE-pc-sysv$UNAME_REL fi ;; i*86:*:5:[678]*) # UnixWare 7.x, OpenUNIX and OpenServer 6. case `/bin/uname -X | grep "^Machine"` in *486*) UNAME_MACHINE=i486 ;; *Pentium) UNAME_MACHINE=i586 ;; *Pent*|*Celeron) UNAME_MACHINE=i686 ;; esac GUESS=$UNAME_MACHINE-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION} ;; i*86:*:3.2:*) if test -f /usr/options/cb.name; then UNAME_REL=`sed -n 's/.*Version //p' /dev/null >/dev/null ; then UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')` (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486 (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \ && UNAME_MACHINE=i586 (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \ && UNAME_MACHINE=i686 (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \ && UNAME_MACHINE=i686 GUESS=$UNAME_MACHINE-pc-sco$UNAME_REL else GUESS=$UNAME_MACHINE-pc-sysv32 fi ;; pc:*:*:*) # Left here for compatibility: # uname -m prints for DJGPP always 'pc', but it prints nothing about # the processor, so we play safe by assuming i586. # Note: whatever this is, it MUST be the same as what config.sub # prints for the "djgpp" host, or else GDB configure will decide that # this is a cross-build. GUESS=i586-pc-msdosdjgpp ;; Intel:Mach:3*:*) GUESS=i386-pc-mach3 ;; paragon:*:*:*) GUESS=i860-intel-osf1 ;; i860:*:4.*:*) # i860-SVR4 if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then GUESS=i860-stardent-sysv$UNAME_RELEASE # Stardent Vistra i860-SVR4 else # Add other i860-SVR4 vendors below as they are discovered. GUESS=i860-unknown-sysv$UNAME_RELEASE # Unknown i860-SVR4 fi ;; mini*:CTIX:SYS*5:*) # "miniframe" GUESS=m68010-convergent-sysv ;; mc68k:UNIX:SYSTEM5:3.51m) GUESS=m68k-convergent-sysv ;; M680?0:D-NIX:5.3:*) GUESS=m68k-diab-dnix ;; M68*:*:R3V[5678]*:*) test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;; 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0) OS_REL='' test -r /etc/.relid \ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4.3"$OS_REL"; exit; } /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;; 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4; exit; } ;; NCR*:*:4.2:* | MPRAS*:*:4.2:*) OS_REL='.3' test -r /etc/.relid \ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4.3"$OS_REL"; exit; } /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \ && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;; m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) GUESS=m68k-unknown-lynxos$UNAME_RELEASE ;; mc68030:UNIX_System_V:4.*:*) GUESS=m68k-atari-sysv4 ;; TSUNAMI:LynxOS:2.*:*) GUESS=sparc-unknown-lynxos$UNAME_RELEASE ;; rs6000:LynxOS:2.*:*) GUESS=rs6000-unknown-lynxos$UNAME_RELEASE ;; PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*) GUESS=powerpc-unknown-lynxos$UNAME_RELEASE ;; SM[BE]S:UNIX_SV:*:*) GUESS=mips-dde-sysv$UNAME_RELEASE ;; RM*:ReliantUNIX-*:*:*) GUESS=mips-sni-sysv4 ;; RM*:SINIX-*:*:*) GUESS=mips-sni-sysv4 ;; *:SINIX-*:*:*) if uname -p 2>/dev/null >/dev/null ; then UNAME_MACHINE=`(uname -p) 2>/dev/null` GUESS=$UNAME_MACHINE-sni-sysv4 else GUESS=ns32k-sni-sysv fi ;; PENTIUM:*:4.0*:*) # Unisys 'ClearPath HMP IX 4000' SVR4/MP effort # says GUESS=i586-unisys-sysv4 ;; *:UNIX_System_V:4*:FTX*) # From Gerald Hewes . # How about differentiating between stratus architectures? -djm GUESS=hppa1.1-stratus-sysv4 ;; *:*:*:FTX*) # From seanf@swdc.stratus.com. GUESS=i860-stratus-sysv4 ;; i*86:VOS:*:*) # From Paul.Green@stratus.com. GUESS=$UNAME_MACHINE-stratus-vos ;; *:VOS:*:*) # From Paul.Green@stratus.com. GUESS=hppa1.1-stratus-vos ;; mc68*:A/UX:*:*) GUESS=m68k-apple-aux$UNAME_RELEASE ;; news*:NEWS-OS:6*:*) GUESS=mips-sony-newsos6 ;; R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) if test -d /usr/nec; then GUESS=mips-nec-sysv$UNAME_RELEASE else GUESS=mips-unknown-sysv$UNAME_RELEASE fi ;; BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. GUESS=powerpc-be-beos ;; BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. GUESS=powerpc-apple-beos ;; BePC:BeOS:*:*) # BeOS running on Intel PC compatible. GUESS=i586-pc-beos ;; BePC:Haiku:*:*) # Haiku running on Intel PC compatible. GUESS=i586-pc-haiku ;; ppc:Haiku:*:*) # Haiku running on Apple PowerPC GUESS=powerpc-apple-haiku ;; *:Haiku:*:*) # Haiku modern gcc (not bound by BeOS compat) GUESS=$UNAME_MACHINE-unknown-haiku ;; SX-4:SUPER-UX:*:*) GUESS=sx4-nec-superux$UNAME_RELEASE ;; SX-5:SUPER-UX:*:*) GUESS=sx5-nec-superux$UNAME_RELEASE ;; SX-6:SUPER-UX:*:*) GUESS=sx6-nec-superux$UNAME_RELEASE ;; SX-7:SUPER-UX:*:*) GUESS=sx7-nec-superux$UNAME_RELEASE ;; SX-8:SUPER-UX:*:*) GUESS=sx8-nec-superux$UNAME_RELEASE ;; SX-8R:SUPER-UX:*:*) GUESS=sx8r-nec-superux$UNAME_RELEASE ;; SX-ACE:SUPER-UX:*:*) GUESS=sxace-nec-superux$UNAME_RELEASE ;; Power*:Rhapsody:*:*) GUESS=powerpc-apple-rhapsody$UNAME_RELEASE ;; *:Rhapsody:*:*) GUESS=$UNAME_MACHINE-apple-rhapsody$UNAME_RELEASE ;; arm64:Darwin:*:*) GUESS=aarch64-apple-darwin$UNAME_RELEASE ;; *:Darwin:*:*) UNAME_PROCESSOR=`uname -p` case $UNAME_PROCESSOR in unknown) UNAME_PROCESSOR=powerpc ;; esac if command -v xcode-select > /dev/null 2> /dev/null && \ ! xcode-select --print-path > /dev/null 2> /dev/null ; then # Avoid executing cc if there is no toolchain installed as # cc will be a stub that puts up a graphical alert # prompting the user to install developer tools. CC_FOR_BUILD=no_compiler_found else set_cc_for_build fi if test "$CC_FOR_BUILD" != no_compiler_found; then if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \ (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ grep IS_64BIT_ARCH >/dev/null then case $UNAME_PROCESSOR in i386) UNAME_PROCESSOR=x86_64 ;; powerpc) UNAME_PROCESSOR=powerpc64 ;; esac fi # On 10.4-10.6 one might compile for PowerPC via gcc -arch ppc if (echo '#ifdef __POWERPC__'; echo IS_PPC; echo '#endif') | \ (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ grep IS_PPC >/dev/null then UNAME_PROCESSOR=powerpc fi elif test "$UNAME_PROCESSOR" = i386 ; then # uname -m returns i386 or x86_64 UNAME_PROCESSOR=$UNAME_MACHINE fi GUESS=$UNAME_PROCESSOR-apple-darwin$UNAME_RELEASE ;; *:procnto*:*:* | *:QNX:[0123456789]*:*) UNAME_PROCESSOR=`uname -p` if test "$UNAME_PROCESSOR" = x86; then UNAME_PROCESSOR=i386 UNAME_MACHINE=pc fi GUESS=$UNAME_PROCESSOR-$UNAME_MACHINE-nto-qnx$UNAME_RELEASE ;; *:QNX:*:4*) GUESS=i386-pc-qnx ;; NEO-*:NONSTOP_KERNEL:*:*) GUESS=neo-tandem-nsk$UNAME_RELEASE ;; NSE-*:NONSTOP_KERNEL:*:*) GUESS=nse-tandem-nsk$UNAME_RELEASE ;; NSR-*:NONSTOP_KERNEL:*:*) GUESS=nsr-tandem-nsk$UNAME_RELEASE ;; NSV-*:NONSTOP_KERNEL:*:*) GUESS=nsv-tandem-nsk$UNAME_RELEASE ;; NSX-*:NONSTOP_KERNEL:*:*) GUESS=nsx-tandem-nsk$UNAME_RELEASE ;; *:NonStop-UX:*:*) GUESS=mips-compaq-nonstopux ;; BS2000:POSIX*:*:*) GUESS=bs2000-siemens-sysv ;; DS/*:UNIX_System_V:*:*) GUESS=$UNAME_MACHINE-$UNAME_SYSTEM-$UNAME_RELEASE ;; *:Plan9:*:*) # "uname -m" is not consistent, so use $cputype instead. 386 # is converted to i386 for consistency with other x86 # operating systems. if test "${cputype-}" = 386; then UNAME_MACHINE=i386 elif test "x${cputype-}" != x; then UNAME_MACHINE=$cputype fi GUESS=$UNAME_MACHINE-unknown-plan9 ;; *:TOPS-10:*:*) GUESS=pdp10-unknown-tops10 ;; *:TENEX:*:*) GUESS=pdp10-unknown-tenex ;; KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) GUESS=pdp10-dec-tops20 ;; XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) GUESS=pdp10-xkl-tops20 ;; *:TOPS-20:*:*) GUESS=pdp10-unknown-tops20 ;; *:ITS:*:*) GUESS=pdp10-unknown-its ;; SEI:*:*:SEIUX) GUESS=mips-sei-seiux$UNAME_RELEASE ;; *:DragonFly:*:*) DRAGONFLY_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'` GUESS=$UNAME_MACHINE-unknown-dragonfly$DRAGONFLY_REL ;; *:*VMS:*:*) UNAME_MACHINE=`(uname -p) 2>/dev/null` case $UNAME_MACHINE in A*) GUESS=alpha-dec-vms ;; I*) GUESS=ia64-dec-vms ;; V*) GUESS=vax-dec-vms ;; esac ;; *:XENIX:*:SysV) GUESS=i386-pc-xenix ;; i*86:skyos:*:*) SKYOS_REL=`echo "$UNAME_RELEASE" | sed -e 's/ .*$//'` GUESS=$UNAME_MACHINE-pc-skyos$SKYOS_REL ;; i*86:rdos:*:*) GUESS=$UNAME_MACHINE-pc-rdos ;; i*86:Fiwix:*:*) GUESS=$UNAME_MACHINE-pc-fiwix ;; *:AROS:*:*) GUESS=$UNAME_MACHINE-unknown-aros ;; x86_64:VMkernel:*:*) GUESS=$UNAME_MACHINE-unknown-esx ;; amd64:Isilon\ OneFS:*:*) GUESS=x86_64-unknown-onefs ;; *:Unleashed:*:*) GUESS=$UNAME_MACHINE-unknown-unleashed$UNAME_RELEASE ;; esac # Do we have a guess based on uname results? if test "x$GUESS" != x; then echo "$GUESS" exit fi # No uname command or uname output not recognized. set_cc_for_build cat > "$dummy.c" < #include #endif #if defined(ultrix) || defined(_ultrix) || defined(__ultrix) || defined(__ultrix__) #if defined (vax) || defined (__vax) || defined (__vax__) || defined(mips) || defined(__mips) || defined(__mips__) || defined(MIPS) || defined(__MIPS__) #include #if defined(_SIZE_T_) || defined(SIGLOST) #include #endif #endif #endif main () { #if defined (sony) #if defined (MIPSEB) /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed, I don't know.... */ printf ("mips-sony-bsd\n"); exit (0); #else #include printf ("m68k-sony-newsos%s\n", #ifdef NEWSOS4 "4" #else "" #endif ); exit (0); #endif #endif #if defined (NeXT) #if !defined (__ARCHITECTURE__) #define __ARCHITECTURE__ "m68k" #endif int version; version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`; if (version < 4) printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version); else printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version); exit (0); #endif #if defined (MULTIMAX) || defined (n16) #if defined (UMAXV) printf ("ns32k-encore-sysv\n"); exit (0); #else #if defined (CMU) printf ("ns32k-encore-mach\n"); exit (0); #else printf ("ns32k-encore-bsd\n"); exit (0); #endif #endif #endif #if defined (__386BSD__) printf ("i386-pc-bsd\n"); exit (0); #endif #if defined (sequent) #if defined (i386) printf ("i386-sequent-dynix\n"); exit (0); #endif #if defined (ns32000) printf ("ns32k-sequent-dynix\n"); exit (0); #endif #endif #if defined (_SEQUENT_) struct utsname un; uname(&un); if (strncmp(un.version, "V2", 2) == 0) { printf ("i386-sequent-ptx2\n"); exit (0); } if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ printf ("i386-sequent-ptx1\n"); exit (0); } printf ("i386-sequent-ptx\n"); exit (0); #endif #if defined (vax) #if !defined (ultrix) #include #if defined (BSD) #if BSD == 43 printf ("vax-dec-bsd4.3\n"); exit (0); #else #if BSD == 199006 printf ("vax-dec-bsd4.3reno\n"); exit (0); #else printf ("vax-dec-bsd\n"); exit (0); #endif #endif #else printf ("vax-dec-bsd\n"); exit (0); #endif #else #if defined(_SIZE_T_) || defined(SIGLOST) struct utsname un; uname (&un); printf ("vax-dec-ultrix%s\n", un.release); exit (0); #else printf ("vax-dec-ultrix\n"); exit (0); #endif #endif #endif #if defined(ultrix) || defined(_ultrix) || defined(__ultrix) || defined(__ultrix__) #if defined(mips) || defined(__mips) || defined(__mips__) || defined(MIPS) || defined(__MIPS__) #if defined(_SIZE_T_) || defined(SIGLOST) struct utsname *un; uname (&un); printf ("mips-dec-ultrix%s\n", un.release); exit (0); #else printf ("mips-dec-ultrix\n"); exit (0); #endif #endif #endif #if defined (alliant) && defined (i860) printf ("i860-alliant-bsd\n"); exit (0); #endif exit (1); } EOF $CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null && SYSTEM_NAME=`"$dummy"` && { echo "$SYSTEM_NAME"; exit; } # Apollos put the system type in the environment. test -d /usr/apollo && { echo "$ISP-apollo-$SYSTYPE"; exit; } echo "$0: unable to guess system type" >&2 case $UNAME_MACHINE:$UNAME_SYSTEM in mips:Linux | mips64:Linux) # If we got here on MIPS GNU/Linux, output extra information. cat >&2 <&2 <&2 </dev/null || echo unknown` uname -r = `(uname -r) 2>/dev/null || echo unknown` uname -s = `(uname -s) 2>/dev/null || echo unknown` uname -v = `(uname -v) 2>/dev/null || echo unknown` /usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null` /bin/uname -X = `(/bin/uname -X) 2>/dev/null` hostinfo = `(hostinfo) 2>/dev/null` /bin/universe = `(/bin/universe) 2>/dev/null` /usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null` /bin/arch = `(/bin/arch) 2>/dev/null` /usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null` /usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null` UNAME_MACHINE = "$UNAME_MACHINE" UNAME_RELEASE = "$UNAME_RELEASE" UNAME_SYSTEM = "$UNAME_SYSTEM" UNAME_VERSION = "$UNAME_VERSION" EOF fi exit 1 # Local variables: # eval: (add-hook 'before-save-hook 'time-stamp) # time-stamp-start: "timestamp='" # time-stamp-format: "%:y-%02m-%02d" # time-stamp-end: "'" # End: pysam-0.23.0/htslib/config.h.in000066400000000000000000000121711475062545500162540ustar00rootroot00000000000000/* config.h.in. Generated from configure.ac by autoheader. */ /* If you use configure, this file provides #defines reflecting your configuration choices. If you have not run configure, suitable conservative defaults will be used. Autoheader adds a number of items to this template file that are not used by HTSlib: STDC_HEADERS and most HAVE_*_H header file defines are immaterial, as we assume standard ISO C headers and facilities; the PACKAGE_* defines are unused and are overridden by the more accurate PACKAGE_VERSION as computed by the Makefile. */ /* Define if HTSlib should enable GCS support. */ #undef ENABLE_GCS /* Define if HTSlib should enable plugins. */ #undef ENABLE_PLUGINS /* Define if HTSlib should enable S3 support. */ #undef ENABLE_S3 /* Define if __attribute__((constructor)) is available. */ #undef HAVE_ATTRIBUTE_CONSTRUCTOR /* Define if __attribute__((target(...))) is available. */ #undef HAVE_ATTRIBUTE_TARGET /* Defined to 1 if rANS source using AVX2 can be compiled. */ #undef HAVE_AVX2 /* Defined to 1 if rANS source using AVX512F can be compiled. */ #undef HAVE_AVX512 /* Defined to 1 if __builtin_cpu_supports("ssse3") works */ #undef HAVE_BUILTIN_CPU_SUPPORT_SSSE3 /* Define if clock_gettime exists and accepts CLOCK_PROCESS_CPUTIME_ID. */ #undef HAVE_CLOCK_GETTIME_CPUTIME /* Define if you have the Common Crypto library. */ #undef HAVE_COMMONCRYPTO /* Define to 1 if you have the declaration of '__cpuid_count', and to 0 if you don't. */ #undef HAVE_DECL___CPUID_COUNT /* Define to 1 if you have the declaration of '__get_cpuid_max', and to 0 if you don't. */ #undef HAVE_DECL___GET_CPUID_MAX /* Define to 1 if you have the 'drand48' function. */ #undef HAVE_DRAND48 /* Define if using an external libhtscodecs */ #undef HAVE_EXTERNAL_LIBHTSCODECS /* Define to 1 if you have the 'fdatasync' function. */ #undef HAVE_FDATASYNC /* Define to 1 if you have the 'fsync' function. */ #undef HAVE_FSYNC /* Define to 1 if you have the 'getpagesize' function. */ #undef HAVE_GETPAGESIZE /* Define to 1 if you have the 'gmtime_r' function. */ #undef HAVE_GMTIME_R /* Define if you have libcrypto-style HMAC(). */ #undef HAVE_HMAC /* Define to 1 if you have the header file. */ #undef HAVE_INTTYPES_H /* Define to 1 if you have the 'bz2' library (-lbz2). */ #undef HAVE_LIBBZ2 /* Define if libcurl file access is enabled. */ #undef HAVE_LIBCURL /* Define if libdeflate is available. */ #undef HAVE_LIBDEFLATE /* Define to 1 if you have the 'lzma' library (-llzma). */ #undef HAVE_LIBLZMA /* Define to 1 if you have the 'z' library (-lz). */ #undef HAVE_LIBZ /* Define to 1 if you have the header file. */ #undef HAVE_LZMA_H /* Define to 1 if you have a working 'mmap' system call. */ #undef HAVE_MMAP /* Defined to 1 if rANS source using popcnt can be compiled. */ #undef HAVE_POPCNT /* Define to 1 if you have the 'srand48_deterministic' function. */ #undef HAVE_SRAND48_DETERMINISTIC /* Defined to 1 if rANS source using SSE4.1 can be compiled. */ #undef HAVE_SSE4_1 /* Defined to 1 if rANS source using SSSE3 can be compiled. */ #undef HAVE_SSSE3 /* Define to 1 if you have the header file. */ #undef HAVE_STDINT_H /* Define to 1 if you have the header file. */ #undef HAVE_STDIO_H /* Define to 1 if you have the header file. */ #undef HAVE_STDLIB_H /* Define to 1 if you have the header file. */ #undef HAVE_STRINGS_H /* Define to 1 if you have the header file. */ #undef HAVE_STRING_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_PARAM_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_STAT_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_TYPES_H /* Define to 1 if you have the header file. */ #undef HAVE_UNISTD_H /* Define to the address where bug reports for this package should be sent. */ #undef PACKAGE_BUGREPORT /* Define to the full name of this package. */ #undef PACKAGE_NAME /* Define to the full name and version of this package. */ #undef PACKAGE_STRING /* Define to the one symbol short name of this package. */ #undef PACKAGE_TARNAME /* Define to the home page for this package. */ #undef PACKAGE_URL /* Define to the version of this package. */ #undef PACKAGE_VERSION /* Platform-dependent plugin filename extension. */ #undef PLUGIN_EXT /* Define to 1 if all of the C89 standard headers exist (not just the ones required in a freestanding environment). This macro is provided for backward compatibility; new code need not use it. */ #undef STDC_HEADERS /* Prevent unaligned access in htscodecs SSE4 rANS codec */ #if defined(HTS_ALLOW_UNALIGNED) && HTS_ALLOW_UNALIGNED == 0 #undef UBSAN #endif /* Number of bits in a file offset, on hosts where this is settable. */ #undef _FILE_OFFSET_BITS /* Define to 1 on platforms where this makes off_t a 64-bit type. */ #undef _LARGE_FILES /* Number of bits in time_t, on hosts where this is settable. */ #undef _TIME_BITS /* Specify X/Open requirements */ #undef _XOPEN_SOURCE /* Define to 1 on platforms where this makes time_t a 64-bit type. */ #undef __MINGW_USE_VC2005_COMPAT pysam-0.23.0/htslib/config.mk.in000066400000000000000000000072451475062545500164420ustar00rootroot00000000000000# Optional configure Makefile overrides for htslib. # # Copyright (C) 2015-2017, 2019, 2023 Genome Research Ltd. # # Author: John Marshall # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. # This is @configure_input@ # # If you use configure, this file overrides variables and augments rules # in the Makefile to reflect your configuration choices. If you don't run # configure, the main Makefile contains suitable conservative defaults. prefix = @prefix@ exec_prefix = @exec_prefix@ bindir = @bindir@ includedir = @includedir@ libdir = @libdir@ libexecdir = @libexecdir@ datarootdir = @datarootdir@ mandir = @mandir@ CC = @CC@ RANLIB = @RANLIB@ CPPFLAGS = @CPPFLAGS@ CFLAGS = @CFLAGS@ LDFLAGS = @LDFLAGS@ VERSION_SCRIPT_LDFLAGS = @VERSION_SCRIPT_LDFLAGS@ LIBS = @LIBS@ PLATFORM = @PLATFORM@ PLUGIN_EXT = @PLUGIN_EXT@ # The default Makefile enables some of the optional files, but we blank # them so they can be controlled by configure instead. NONCONFIGURE_OBJS = # Lowercase here indicates these are "local" to config.mk plugin_OBJS = noplugin_LDFLAGS = noplugin_LIBS = # ifeq/.../endif, +=, and target-specific variables are GNU Make-specific. # If you don't have GNU Make, comment out this conditional and note that # to enable libcurl you will need to implement the following elsewhere. ifeq "libcurl-@libcurl@" "libcurl-enabled" LIBCURL_LIBS = -lcurl plugin_OBJS += hfile_libcurl.o hfile_libcurl$(PLUGIN_EXT): LIBS += $(LIBCURL_LIBS) noplugin_LIBS += $(LIBCURL_LIBS) endif ifeq "gcs-@gcs@" "gcs-enabled" plugin_OBJS += hfile_gcs.o endif ifeq "s3-@s3@" "s3-enabled" plugin_OBJS += hfile_s3.o plugin_OBJS += hfile_s3_write.o CRYPTO_LIBS = @CRYPTO_LIBS@ noplugin_LIBS += $(CRYPTO_LIBS) hfile_s3$(PLUGIN_EXT): LIBS += $(CRYPTO_LIBS) hfile_s3_write$(PLUGIN_EXT): LIBS += $(CRYPTO_LIBS) $(LIBCURL_LIBS) endif ifeq "plugins-@enable_plugins@" "plugins-yes" plugindir = @plugindir@ pluginpath = @pluginpath@ LIBHTS_OBJS += plugin.o PLUGIN_OBJS += $(plugin_OBJS) plugin.o plugin.pico: ALL_CPPFLAGS += -DPLUGINPATH=\"$(pluginpath)\" # When built as separate plugins, these record their version themselves. hfile_gcs.o hfile_gcs.pico: version.h hfile_libcurl.o hfile_libcurl.pico: version.h hfile_s3.o hfile_s3.pico: version.h hfile_s3_write.o hfile_s3_write.pico: version.h # Windows DLL plugins depend on the import library, built as a byproduct. $(plugin_OBJS:.o=.cygdll): cyghts-$(LIBHTS_SOVERSION).dll else LIBHTS_OBJS += $(plugin_OBJS) LDFLAGS += $(noplugin_LDFLAGS) LIBS += $(noplugin_LIBS) endif # Extra CFLAGS for specific files HTS_CFLAGS_AVX2 = @hts_cflags_avx2@ HTS_CFLAGS_AVX512 = @hts_cflags_avx512@ HTS_CFLAGS_SSE4 = @hts_cflags_sse4@ pysam-0.23.0/htslib/config.sub000077500000000000000000001072021475062545500162140ustar00rootroot00000000000000#! /bin/sh # Configuration validation subroutine script. # Copyright 1992-2023 Free Software Foundation, Inc. # shellcheck disable=SC2006,SC2268 # see below for rationale timestamp='2023-09-19' # This file is free software; you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, see . # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that # program. This Exception is an additional permission under section 7 # of the GNU General Public License, version 3 ("GPLv3"). # Please send patches to . # # Configuration subroutine to validate and canonicalize a configuration type. # Supply the specified configuration type as an argument. # If it is invalid, we print an error message on stderr and exit with code 1. # Otherwise, we print the canonical config type on stdout and succeed. # You can get the latest version of this script from: # https://git.savannah.gnu.org/cgit/config.git/plain/config.sub # This file is supposed to be the same for all GNU packages # and recognize all the CPU types, system types and aliases # that are meaningful with *any* GNU software. # Each package is responsible for reporting which valid configurations # it does not support. The user should be able to distinguish # a failure to support a valid configuration from a meaningless # configuration. # The goal of this file is to map all the various variations of a given # machine specification into a single specification in the form: # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM # or in some cases, the newer four-part form: # CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM # It is wrong to echo any other type of specification. # The "shellcheck disable" line above the timestamp inhibits complaints # about features and limitations of the classic Bourne shell that were # superseded or lifted in POSIX. However, this script identifies a wide # variety of pre-POSIX systems that do not have POSIX shells at all, and # even some reasonably current systems (Solaris 10 as case-in-point) still # have a pre-POSIX /bin/sh. me=`echo "$0" | sed -e 's,.*/,,'` usage="\ Usage: $0 [OPTION] CPU-MFR-OPSYS or ALIAS Canonicalize a configuration name. Options: -h, --help print this help, then exit -t, --time-stamp print date of last modification, then exit -v, --version print version number, then exit Report bugs and patches to ." version="\ GNU config.sub ($timestamp) Copyright 1992-2023 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." help=" Try '$me --help' for more information." # Parse command line while test $# -gt 0 ; do case $1 in --time-stamp | --time* | -t ) echo "$timestamp" ; exit ;; --version | -v ) echo "$version" ; exit ;; --help | --h* | -h ) echo "$usage"; exit ;; -- ) # Stop option processing shift; break ;; - ) # Use stdin as input. break ;; -* ) echo "$me: invalid option $1$help" >&2 exit 1 ;; *local*) # First pass through any local machine types. echo "$1" exit ;; * ) break ;; esac done case $# in 0) echo "$me: missing argument$help" >&2 exit 1;; 1) ;; *) echo "$me: too many arguments$help" >&2 exit 1;; esac # Split fields of configuration type # shellcheck disable=SC2162 saved_IFS=$IFS IFS="-" read field1 field2 field3 field4 <&2 exit 1 ;; *-*-*-*) basic_machine=$field1-$field2 basic_os=$field3-$field4 ;; *-*-*) # Ambiguous whether COMPANY is present, or skipped and KERNEL-OS is two # parts maybe_os=$field2-$field3 case $maybe_os in nto-qnx* | linux-* | uclinux-uclibc* \ | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* \ | netbsd*-eabi* | kopensolaris*-gnu* | cloudabi*-eabi* \ | storm-chaos* | os2-emx* | rtmk-nova* | managarm-* \ | windows-* ) basic_machine=$field1 basic_os=$maybe_os ;; 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*) basic_machine=$field1 basic_os=$field2 ;; esac ;; esac ;; *) # Convert single-component short-hands not valid as part of # multi-component configurations. case $field1 in 386bsd) basic_machine=i386-pc basic_os=bsd ;; a29khif) basic_machine=a29k-amd basic_os=udi ;; adobe68k) basic_machine=m68010-adobe basic_os=scout ;; alliant) basic_machine=fx80-alliant basic_os= ;; altos | altos3068) basic_machine=m68k-altos basic_os= ;; am29k) basic_machine=a29k-none basic_os=bsd ;; amdahl) basic_machine=580-amdahl basic_os=sysv ;; amiga) basic_machine=m68k-unknown basic_os= ;; amigaos | amigados) basic_machine=m68k-unknown basic_os=amigaos ;; amigaunix | amix) basic_machine=m68k-unknown basic_os=sysv4 ;; apollo68) basic_machine=m68k-apollo basic_os=sysv ;; apollo68bsd) basic_machine=m68k-apollo basic_os=bsd ;; aros) basic_machine=i386-pc basic_os=aros ;; aux) basic_machine=m68k-apple basic_os=aux ;; balance) basic_machine=ns32k-sequent basic_os=dynix ;; blackfin) basic_machine=bfin-unknown basic_os=linux ;; 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These examples are taken from C99 6.10.3.5. // dprintf is used instead of fprintf to avoid needing to declare // FILE and stderr. #define debug(...) dprintf (2, __VA_ARGS__) #define showlist(...) puts (#__VA_ARGS__) #define report(test,...) ((test) ? puts (#test) : printf (__VA_ARGS__)) static void test_varargs_macros (void) { int x = 1234; int y = 5678; debug ("Flag"); debug ("X = %d\n", x); showlist (The first, second, and third items.); report (x>y, "x is %d but y is %d", x, y); } // Check long long types. #define BIG64 18446744073709551615ull #define BIG32 4294967295ul #define BIG_OK (BIG64 / BIG32 == 4294967297ull && BIG64 % BIG32 == 0) #if !BIG_OK #error "your preprocessor is broken" #endif #if BIG_OK #else #error "your preprocessor is broken" #endif static long long int bignum = -9223372036854775807LL; static unsigned long long int ubignum = BIG64; struct incomplete_array { int datasize; double data[]; }; struct named_init { int number; const wchar_t *name; double average; }; typedef const char *ccp; static inline int test_restrict (ccp restrict text) { // Iterate through items via the restricted pointer. // Also check for declarations in for loops. for (unsigned int i = 0; *(text+i) != '\''\0'\''; ++i) continue; return 0; } // Check varargs and va_copy. static bool test_varargs (const char *format, ...) { va_list args; va_start (args, format); va_list args_copy; va_copy (args_copy, args); const char *str = ""; int number = 0; float fnumber = 0; while (*format) { switch (*format++) { case '\''s'\'': // string str = va_arg (args_copy, const char *); break; case '\''d'\'': // int number = va_arg (args_copy, int); break; case '\''f'\'': // float fnumber = va_arg (args_copy, double); break; default: break; } } va_end (args_copy); va_end (args); return *str && number && fnumber; } ' # Test code for whether the C compiler supports C99 (body of main). ac_c_conftest_c99_main=' // Check bool. _Bool success = false; success |= (argc != 0); // Check restrict. if (test_restrict ("String literal") == 0) success = true; char *restrict newvar = "Another string"; // Check varargs. success &= test_varargs ("s, d'\'' f .", "string", 65, 34.234); test_varargs_macros (); // Check flexible array members. struct incomplete_array *ia = malloc (sizeof (struct incomplete_array) + (sizeof (double) * 10)); ia->datasize = 10; for (int i = 0; i < ia->datasize; ++i) ia->data[i] = i * 1.234; // Work around memory leak warnings. free (ia); // Check named initializers. struct named_init ni = { .number = 34, .name = L"Test wide string", .average = 543.34343, }; ni.number = 58; int dynamic_array[ni.number]; dynamic_array[0] = argv[0][0]; dynamic_array[ni.number - 1] = 543; // work around unused variable warnings ok |= (!success || bignum == 0LL || ubignum == 0uLL || newvar[0] == '\''x'\'' || dynamic_array[ni.number - 1] != 543); ' # Test code for whether the C compiler supports C11 (global declarations) ac_c_conftest_c11_globals=' /* Does the compiler advertise C11 conformance? */ #if !defined __STDC_VERSION__ || __STDC_VERSION__ < 201112L # error "Compiler does not advertise C11 conformance" #endif // Check _Alignas. char _Alignas (double) aligned_as_double; char _Alignas (0) no_special_alignment; extern char aligned_as_int; char _Alignas (0) _Alignas (int) aligned_as_int; // Check _Alignof. enum { int_alignment = _Alignof (int), int_array_alignment = _Alignof (int[100]), char_alignment = _Alignof (char) }; _Static_assert (0 < -_Alignof (int), "_Alignof is signed"); // Check _Noreturn. int _Noreturn does_not_return (void) { for (;;) continue; } // Check _Static_assert. struct test_static_assert { int x; _Static_assert (sizeof (int) <= sizeof (long int), "_Static_assert does not work in struct"); long int y; }; // Check UTF-8 literals. #define u8 syntax error! char const utf8_literal[] = u8"happens to be ASCII" "another string"; // Check duplicate typedefs. typedef long *long_ptr; typedef long int *long_ptr; typedef long_ptr long_ptr; // Anonymous structures and unions -- taken from C11 6.7.2.1 Example 1. struct anonymous { union { struct { int i; int j; }; struct { int k; long int l; } w; }; int m; } v1; ' # Test code for whether the C compiler supports C11 (body of main). ac_c_conftest_c11_main=' _Static_assert ((offsetof (struct anonymous, i) == offsetof (struct anonymous, w.k)), "Anonymous union alignment botch"); v1.i = 2; v1.w.k = 5; ok |= v1.i != 5; ' # Test code for whether the C compiler supports C11 (complete). ac_c_conftest_c11_program="${ac_c_conftest_c89_globals} ${ac_c_conftest_c99_globals} ${ac_c_conftest_c11_globals} int main (int argc, char **argv) { int ok = 0; ${ac_c_conftest_c89_main} ${ac_c_conftest_c99_main} ${ac_c_conftest_c11_main} return ok; } " # Test code for whether the C compiler supports C99 (complete). ac_c_conftest_c99_program="${ac_c_conftest_c89_globals} ${ac_c_conftest_c99_globals} int main (int argc, char **argv) { int ok = 0; ${ac_c_conftest_c89_main} ${ac_c_conftest_c99_main} return ok; } " # Test code for whether the C compiler supports C89 (complete). ac_c_conftest_c89_program="${ac_c_conftest_c89_globals} int main (int argc, char **argv) { int ok = 0; ${ac_c_conftest_c89_main} return ok; } " as_fn_append ac_header_c_list " stdio.h stdio_h HAVE_STDIO_H" as_fn_append ac_header_c_list " stdlib.h stdlib_h HAVE_STDLIB_H" as_fn_append ac_header_c_list " string.h string_h HAVE_STRING_H" as_fn_append ac_header_c_list " inttypes.h inttypes_h HAVE_INTTYPES_H" as_fn_append ac_header_c_list " stdint.h stdint_h HAVE_STDINT_H" as_fn_append ac_header_c_list " strings.h strings_h HAVE_STRINGS_H" as_fn_append ac_header_c_list " sys/stat.h sys_stat_h HAVE_SYS_STAT_H" as_fn_append ac_header_c_list " sys/types.h sys_types_h HAVE_SYS_TYPES_H" as_fn_append ac_header_c_list " unistd.h unistd_h HAVE_UNISTD_H" as_fn_append ac_header_c_list " sys/param.h sys_param_h HAVE_SYS_PARAM_H" as_fn_append ac_func_c_list " getpagesize HAVE_GETPAGESIZE" # Auxiliary files required by this configure script. ac_aux_files="config.guess config.sub" # Locations in which to look for auxiliary files. ac_aux_dir_candidates="${srcdir}${PATH_SEPARATOR}${srcdir}/..${PATH_SEPARATOR}${srcdir}/../.." # Search for a directory containing all of the required auxiliary files, # $ac_aux_files, from the $PATH-style list $ac_aux_dir_candidates. # If we don't find one directory that contains all the files we need, # we report the set of missing files from the *first* directory in # $ac_aux_dir_candidates and give up. ac_missing_aux_files="" ac_first_candidate=: printf "%s\n" "$as_me:${as_lineno-$LINENO}: looking for aux files: $ac_aux_files" >&5 as_save_IFS=$IFS; IFS=$PATH_SEPARATOR as_found=false for as_dir in $ac_aux_dir_candidates do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac as_found=: printf "%s\n" "$as_me:${as_lineno-$LINENO}: trying $as_dir" >&5 ac_aux_dir_found=yes ac_install_sh= for ac_aux in $ac_aux_files do # As a special case, if "install-sh" is required, that requirement # can be satisfied by any of "install-sh", "install.sh", or "shtool", # and $ac_install_sh is set appropriately for whichever one is found. if test x"$ac_aux" = x"install-sh" then if test -f "${as_dir}install-sh"; then printf "%s\n" "$as_me:${as_lineno-$LINENO}: ${as_dir}install-sh found" >&5 ac_install_sh="${as_dir}install-sh -c" elif test -f "${as_dir}install.sh"; then printf "%s\n" "$as_me:${as_lineno-$LINENO}: ${as_dir}install.sh found" >&5 ac_install_sh="${as_dir}install.sh -c" elif test -f "${as_dir}shtool"; then printf "%s\n" "$as_me:${as_lineno-$LINENO}: ${as_dir}shtool found" >&5 ac_install_sh="${as_dir}shtool install -c" else ac_aux_dir_found=no if $ac_first_candidate; then ac_missing_aux_files="${ac_missing_aux_files} install-sh" else break fi fi else if test -f "${as_dir}${ac_aux}"; then printf "%s\n" "$as_me:${as_lineno-$LINENO}: ${as_dir}${ac_aux} found" >&5 else ac_aux_dir_found=no if $ac_first_candidate; then ac_missing_aux_files="${ac_missing_aux_files} ${ac_aux}" else break fi fi fi done if test "$ac_aux_dir_found" = yes; then ac_aux_dir="$as_dir" break fi ac_first_candidate=false as_found=false done IFS=$as_save_IFS if $as_found then : else case e in #( e) as_fn_error $? "cannot find required auxiliary files:$ac_missing_aux_files" "$LINENO" 5 ;; esac fi # These three variables are undocumented and unsupported, # and are intended to be withdrawn in a future Autoconf release. # They can cause serious problems if a builder's source tree is in a directory # whose full name contains unusual characters. if test -f "${ac_aux_dir}config.guess"; then ac_config_guess="$SHELL ${ac_aux_dir}config.guess" fi if test -f "${ac_aux_dir}config.sub"; then ac_config_sub="$SHELL ${ac_aux_dir}config.sub" fi if test -f "$ac_aux_dir/configure"; then ac_configure="$SHELL ${ac_aux_dir}configure" fi # Check that the precious variables saved in the cache have kept the same # value. ac_cache_corrupted=false for ac_var in $ac_precious_vars; do eval ac_old_set=\$ac_cv_env_${ac_var}_set eval ac_new_set=\$ac_env_${ac_var}_set eval ac_old_val=\$ac_cv_env_${ac_var}_value eval ac_new_val=\$ac_env_${ac_var}_value case $ac_old_set,$ac_new_set in set,) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: '$ac_var' was set to '$ac_old_val' in the previous run" >&5 printf "%s\n" "$as_me: error: '$ac_var' was set to '$ac_old_val' in the previous run" >&2;} ac_cache_corrupted=: ;; ,set) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: '$ac_var' was not set in the previous run" >&5 printf "%s\n" "$as_me: error: '$ac_var' was not set in the previous run" >&2;} ac_cache_corrupted=: ;; ,);; *) if test "x$ac_old_val" != "x$ac_new_val"; then # differences in whitespace do not lead to failure. ac_old_val_w=`echo x $ac_old_val` ac_new_val_w=`echo x $ac_new_val` if test "$ac_old_val_w" != "$ac_new_val_w"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: '$ac_var' has changed since the previous run:" >&5 printf "%s\n" "$as_me: error: '$ac_var' has changed since the previous run:" >&2;} ac_cache_corrupted=: else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in '$ac_var' since the previous run:" >&5 printf "%s\n" "$as_me: warning: ignoring whitespace changes in '$ac_var' since the previous run:" >&2;} eval $ac_var=\$ac_old_val fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: former value: '$ac_old_val'" >&5 printf "%s\n" "$as_me: former value: '$ac_old_val'" >&2;} { printf "%s\n" "$as_me:${as_lineno-$LINENO}: current value: '$ac_new_val'" >&5 printf "%s\n" "$as_me: current value: '$ac_new_val'" >&2;} fi;; esac # Pass precious variables to config.status. if test "$ac_new_set" = set; then case $ac_new_val in *\'*) ac_arg=$ac_var=`printf "%s\n" "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;; *) ac_arg=$ac_var=$ac_new_val ;; esac case " $ac_configure_args " in *" '$ac_arg' "*) ;; # Avoid dups. 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"run '${MAKE-make} distclean' and/or 'rm $cache_file' and start over" "$LINENO" 5 fi ## -------------------- ## ## Main body of script. ## ## -------------------- ## ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu ac_config_headers="$ac_config_headers config.h" # SYNOPSIS # # HTS_PROG_CC_WERROR(FLAGS_VAR) # # Set FLAGS_VAR to the flags needed to make the C compiler treat warnings # as errors. # hts_check_compile_flags_needed.m4 # # SYNOPSIS # # HTS_CHECK_COMPILE_FLAGS_NEEDED(FEATURE, FLAGS, [INPUT], [ACTION-SUCCESS], [ACTION-FAILURE], [EXTRA-FLAGS]) # # DESCRIPTION # # Check whether the given FLAGS are required to build and link INPUT with # the current language's compiler. Compilation and linking are first # tries without FLAGS. If that fails it then tries to compile and # link again with FLAGS. # # FEATURE describes the feature being tested, and is used when printing # messages and to name the cache entry (along with the tested flags). # # ACTION-SUCCESS/ACTION-FAILURE are shell commands to execute on # success/failure. In ACTION-SUCCESS, $flags_needed will be set to # either an empty string or FLAGS depending on the test results. # # If EXTRA-FLAGS is defined, it is added to the current language's default # flags (e.g. CFLAGS) when the check is done. The check is thus made with # the flags: "CFLAGS EXTRA-FLAGS FLAG". This can for example be used to # force the compiler to issue an error when a bad flag is given. # # If omitted, INPUT defaults to AC_LANG_PROGRAM(), although that probably # isn't very useful. # # NOTE: Implementation based on AX_CHECK_COMPILE_FLAG. # # LICENSE # # Copyright (c) 2008 Guido U. Draheim # Copyright (c) 2011 Maarten Bosmans # Copyright (c) 2023 Robert Davies # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice # and this notice are preserved. This file is offered as-is, without any # warranty. # HTS_CHECK_COMPILE_FLAGS_NEEDED(FEATURE, FLAGS, [INPUT], [ACTION-SUCCESS], [ACTION-FAILURE], [EXTRA-FLAGS]) # SYNOPSIS # # HTS_TEST_CC_C_LD_FLAG(FLAG, FOUND_VAR) # # Test if FLAG can be used on both CFLAGS and LDFLAGS. 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" >&6; } if test ${ac_cv_prog_cc_c11+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_cv_prog_cc_c11=no ac_save_CC=$CC cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ $ac_c_conftest_c11_program _ACEOF for ac_arg in '' -std=gnu11 do CC="$ac_save_CC $ac_arg" if ac_fn_c_try_compile "$LINENO" then : ac_cv_prog_cc_c11=$ac_arg fi rm -f core conftest.err conftest.$ac_objext conftest.beam test "x$ac_cv_prog_cc_c11" != "xno" && break done rm -f conftest.$ac_ext CC=$ac_save_CC ;; esac fi if test "x$ac_cv_prog_cc_c11" = xno then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 printf "%s\n" "unsupported" >&6; } else case e in #( e) if test "x$ac_cv_prog_cc_c11" = x then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 printf "%s\n" "none needed" >&6; } else case e in #( e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c11" >&5 printf "%s\n" "$ac_cv_prog_cc_c11" >&6; } CC="$CC $ac_cv_prog_cc_c11" ;; esac fi ac_cv_prog_cc_stdc=$ac_cv_prog_cc_c11 ac_prog_cc_stdc=c11 ;; esac fi fi if test x$ac_prog_cc_stdc = xno then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $CC option to enable C99 features" >&5 printf %s "checking for $CC option to enable C99 features... " >&6; } if test ${ac_cv_prog_cc_c99+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_cv_prog_cc_c99=no ac_save_CC=$CC cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ $ac_c_conftest_c99_program _ACEOF for ac_arg in '' -std=gnu99 -std=c99 -c99 -qlanglvl=extc1x -qlanglvl=extc99 -AC99 -D_STDC_C99= do CC="$ac_save_CC $ac_arg" if ac_fn_c_try_compile "$LINENO" then : ac_cv_prog_cc_c99=$ac_arg fi rm -f core conftest.err conftest.$ac_objext conftest.beam test "x$ac_cv_prog_cc_c99" != "xno" && break done rm -f conftest.$ac_ext CC=$ac_save_CC ;; esac fi if test "x$ac_cv_prog_cc_c99" = xno then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 printf "%s\n" "unsupported" >&6; } else case e in #( e) if test "x$ac_cv_prog_cc_c99" = x then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 printf "%s\n" "none needed" >&6; } else case e in #( e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c99" >&5 printf "%s\n" "$ac_cv_prog_cc_c99" >&6; } CC="$CC $ac_cv_prog_cc_c99" ;; esac fi ac_cv_prog_cc_stdc=$ac_cv_prog_cc_c99 ac_prog_cc_stdc=c99 ;; esac fi fi if test x$ac_prog_cc_stdc = xno then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $CC option to enable C89 features" >&5 printf %s "checking for $CC option to enable C89 features... " >&6; } if test ${ac_cv_prog_cc_c89+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_cv_prog_cc_c89=no ac_save_CC=$CC cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ $ac_c_conftest_c89_program _ACEOF for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" do CC="$ac_save_CC $ac_arg" if ac_fn_c_try_compile "$LINENO" then : ac_cv_prog_cc_c89=$ac_arg fi rm -f core conftest.err conftest.$ac_objext conftest.beam test "x$ac_cv_prog_cc_c89" != "xno" && break done rm -f conftest.$ac_ext CC=$ac_save_CC ;; esac fi if test "x$ac_cv_prog_cc_c89" = xno then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 printf "%s\n" "unsupported" >&6; } else case e in #( e) if test "x$ac_cv_prog_cc_c89" = x then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 printf "%s\n" "none needed" >&6; } else case e in #( e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5 printf "%s\n" "$ac_cv_prog_cc_c89" >&6; } CC="$CC $ac_cv_prog_cc_c89" ;; esac fi ac_cv_prog_cc_stdc=$ac_cv_prog_cc_c89 ac_prog_cc_stdc=c89 ;; esac fi fi ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. set dummy ${ac_tool_prefix}ranlib; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_prog_RANLIB+y} then : printf %s "(cached) " >&6 else case e in #( e) if test -n "$RANLIB"; then ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib" printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi ;; esac fi RANLIB=$ac_cv_prog_RANLIB if test -n "$RANLIB"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $RANLIB" >&5 printf "%s\n" "$RANLIB" >&6; } else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } fi fi if test -z "$ac_cv_prog_RANLIB"; then ac_ct_RANLIB=$RANLIB # Extract the first word of "ranlib", so it can be a program name with args. set dummy ranlib; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_prog_ac_ct_RANLIB+y} then : printf %s "(cached) " >&6 else case e in #( e) if test -n "$ac_ct_RANLIB"; then ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_RANLIB="ranlib" printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi ;; esac fi ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB if test -n "$ac_ct_RANLIB"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_ct_RANLIB" >&5 printf "%s\n" "$ac_ct_RANLIB" >&6; } else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } fi if test "x$ac_ct_RANLIB" = x; then RANLIB=":" else case $cross_compiling:$ac_tool_warned in yes:) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 printf "%s\n" "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac RANLIB=$ac_ct_RANLIB fi else RANLIB="$ac_cv_prog_RANLIB" fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5 printf %s "checking for grep that handles long lines and -e... " >&6; } if test ${ac_cv_path_GREP+y} then : printf %s "(cached) " >&6 else case e in #( e) if test -z "$GREP"; then ac_path_GREP_found=false # Loop through the user's path and test for each of PROGNAME-LIST as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac for ac_prog in grep ggrep do for ac_exec_ext in '' $ac_executable_extensions; do ac_path_GREP="$as_dir$ac_prog$ac_exec_ext" as_fn_executable_p "$ac_path_GREP" || continue # Check for GNU ac_path_GREP and select it if it is found. # Check for GNU $ac_path_GREP case `"$ac_path_GREP" --version 2>&1` in #( *GNU*) ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_found=:;; #( *) ac_count=0 printf %s 0123456789 >"conftest.in" while : do cat "conftest.in" "conftest.in" >"conftest.tmp" mv "conftest.tmp" "conftest.in" cp "conftest.in" "conftest.nl" printf "%s\n" 'GREP' >> "conftest.nl" "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break as_fn_arith $ac_count + 1 && ac_count=$as_val if test $ac_count -gt ${ac_path_GREP_max-0}; then # Best one so far, save it but keep looking for a better one ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_max=$ac_count fi # 10*(2^10) chars as input seems more than enough test $ac_count -gt 10 && break done rm -f conftest.in conftest.tmp conftest.nl conftest.out;; esac $ac_path_GREP_found && break 3 done done done IFS=$as_save_IFS if test -z "$ac_cv_path_GREP"; then as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 fi else ac_cv_path_GREP=$GREP fi ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5 printf "%s\n" "$ac_cv_path_GREP" >&6; } GREP="$ac_cv_path_GREP" # Check whether --enable-warnings was given. if test ${enable_warnings+y} then : enableval=$enable_warnings; else case e in #( e) enable_warnings=yes ;; esac fi if test "x$enable_warnings" != xno then : ansi="" if test "x$ansi" = "x" then : msg="for C compiler warning flags" else case e in #( e) msg="for C compiler warning and ANSI conformance flags" ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking $msg" >&5 printf %s "checking $msg... " >&6; } if test ${hts_cv_prog_cc_warnings+y} then : printf %s "(cached) " >&6 else case e in #( e) hts_cv_prog_cc_warnings="" if test "x$CC" != "x" then : cat > conftest.c < /dev/null 2>&1 && test -f conftest.o then : if test "x$ansi" = "x" then : hts_cv_prog_cc_warnings="-Wall" else case e in #( e) hts_cv_prog_cc_warnings="-Wall -ansi -pedantic" ;; esac fi elif # Sun Studio or Solaris C compiler "$CC" -V 2>&1 | $GREP -i -E "WorkShop|Sun C" > /dev/null 2>&1 && "$CC" -c -v -Xc conftest.c > /dev/null 2>&1 && test -f conftest.o then : if test "x$ansi" = "x" then : hts_cv_prog_cc_warnings="-v" else case e in #( e) hts_cv_prog_cc_warnings="-v -Xc" ;; esac fi elif # Digital Unix C compiler "$CC" -V 2>&1 | $GREP -i "Digital UNIX Compiler" > /dev/null 2>&1 && "$CC" -c -verbose -w0 -warnprotos -std1 conftest.c > /dev/null 2>&1 && test -f conftest.o then : if test "x$ansi" = "x" then : hts_cv_prog_cc_warnings="-verbose -w0 -warnprotos" else case e in #( e) hts_cv_prog_cc_warnings="-verbose -w0 -warnprotos -std1" ;; esac fi elif # C for AIX Compiler "$CC" 2>&1 | $GREP -i "C for AIX Compiler" > /dev/null 2>&1 && "$CC" -c -qlanglvl=ansi -qinfo=all conftest.c > /dev/null 2>&1 && test -f conftest.o then : if test "x$ansi" = "x" then : hts_cv_prog_cc_warnings="-qsrcmsg -qinfo=all:noppt:noppc:noobs:nocnd" else case e in #( e) hts_cv_prog_cc_warnings="-qsrcmsg -qinfo=all:noppt:noppc:noobs:nocnd -qlanglvl=ansi" ;; esac fi elif # IRIX C compiler "$CC" -version 2>&1 | $GREP -i "MIPSpro Compilers" > /dev/null 2>&1 && "$CC" -c -fullwarn -ansi -ansiE conftest.c > /dev/null 2>&1 && test -f conftest.o then : if test "x$ansi" = "x" then : hts_cv_prog_cc_warnings="-fullwarn" else case e in #( e) hts_cv_prog_cc_warnings="-fullwarn -ansi -ansiE" ;; esac fi elif # HP-UX C compiler what "$CC" 2>&1 | $GREP -i "HP C Compiler" > /dev/null 2>&1 && "$CC" -c -Aa +w1 conftest.c > /dev/null 2>&1 && test -f conftest.o then : if test "x$ansi" = "x" then : hts_cv_prog_cc_warnings="+w1" else case e in #( e) hts_cv_prog_cc_warnings="+w1 -Aa" ;; esac fi elif # The NEC SX series (Super-UX 10) C compiler "$CC" -V 2>&1 | $GREP "/SX" > /dev/null 2>&1 && "$CC" -c -pvctl,fullmsg -Xc conftest.c > /dev/null 2>&1 && test -f conftest.o then : if test "x$ansi" = "x" then : hts_cv_prog_cc_warnings="-pvctl,fullmsg" else case e in #( e) hts_cv_prog_cc_warnings="-pvctl,fullmsg -Xc" ;; esac fi elif # The Cray C compiler (Unicos) "$CC" -V 2>&1 | $GREP -i "Cray" > /dev/null 2>&1 && "$CC" -c -h msglevel_2 conftest.c > /dev/null 2>&1 && test -f conftest.o then : if test "x$ansi" = "x" then : hts_cv_prog_cc_warnings="-h#msglevel_2" else case e in #( e) hts_cv_prog_cc_warnings="-h#msglevel_2,conform" ;; esac fi elif # The Tiny C Compiler "$CC" -v 2>&1 | $GREP "tcc version" > /dev/null && "$CC" -Wall -c conftest.c > /dev/null 2>&1 && test -f conftest.o then : hts_cv_prog_cc_warnings="-Wall" fi rm -f conftest.* fi ;; esac fi if test "x$hts_cv_prog_cc_warnings" != "x" then : ac_arg_result=`echo "$hts_cv_prog_cc_warnings" | tr '#' ' '` { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_arg_result" >&5 printf "%s\n" "$ac_arg_result" >&6; } ac_arg_needed="" for ac_arg in $hts_cv_prog_cc_warnings do ac_arg_sp=`echo "$ac_arg" | tr '#' ' '` case " $CFLAGS " in #( *" $ac_arg_sp "*) : ;; #( *) : ac_arg_needed="$ac_arg_all $ac_arg_sp" ;; esac done CFLAGS="$ac_arg_needed $CFLAGS" else case e in #( e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: unknown" >&5 printf "%s\n" "unknown" >&6; } ;; esac fi fi # Check whether --enable-werror was given. if test ${enable_werror+y} then : enableval=$enable_werror; else case e in #( e) enable_werror=no ;; esac fi if test "x$enable_werror" != xno then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for C compiler flags to error on warnings" >&5 printf %s "checking for C compiler flags to error on warnings... " >&6; } if test ${hts_cv_prog_cc_werror+y} then : printf %s "(cached) " >&6 else case e in #( e) hts_cv_prog_cc_werror="" if test "x$CC" != "x" then : cat > conftest.c < /dev/null 2>&1 && test -f conftest.o then : hts_cv_prog_cc_werror="-Werror" elif # Sun Studio or Solaris C compiler "$CC" -V 2>&1 | $GREP -i -E "WorkShop|Sun C" > /dev/null 2>&1 && "$CC" -c -errwarn=%all conftest.c > /dev/null 2>&1 && test -f conftest.o then : hts_cv_prog_cc_werror="-errwarn=%all" elif # The Tiny C Compiler "$CC" -v 2>&1 | $GREP "tcc version" > /dev/null && "$CC" -Wall -c conftest.c > /dev/null 2>&1 && test -f conftest.o then : hts_cv_prog_cc_werror="-Werror" fi rm -f conftest.* fi ;; esac fi if test "x$hts_cv_prog_cc_werror" != x then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $hts_cv_prog_cc_werror" >&5 printf "%s\n" "$hts_cv_prog_cc_werror" >&6; } if test "xhts_late_cflags" != x then : eval hts_late_cflags="$hts_cv_prog_cc_werror" fi else case e in #( e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: unknown" >&5 printf "%s\n" "unknown" >&6; } ;; esac fi fi # HTSlib uses X/Open-only facilities (M_SQRT2 etc, drand48() etc), and # various POSIX functions that are provided by various _POSIX_C_SOURCE values # or by _XOPEN_SOURCE >= 500. It also uses usleep(), which is removed when # _XOPEN_SOURCE >= 700. Additionally, some definitions may require # _XOPEN_SOURCE >= 600 on some platforms (snprintf on MinGW, # PTHREAD_MUTEX_RECURSIVE on some Linux distributions). Hence we set it to 600. # Define _XOPEN_SOURCE unless the user has already done so via $CPPFLAGS etc. { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $CC options needed to detect all undeclared functions" >&5 printf %s "checking for $CC options needed to detect all undeclared functions... " >&6; } if test ${ac_cv_c_undeclared_builtin_options+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_save_CFLAGS=$CFLAGS ac_cv_c_undeclared_builtin_options='cannot detect' for ac_arg in '' -fno-builtin; do CFLAGS="$ac_save_CFLAGS $ac_arg" # This test program should *not* compile successfully. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main (void) { (void) strchr; ; return 0; } _ACEOF if ac_fn_c_try_compile "$LINENO" then : else case e in #( e) # This test program should compile successfully. # No library function is consistently available on # freestanding implementations, so test against a dummy # declaration. Include always-available headers on the # off chance that they somehow elicit warnings. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include #include #include extern void ac_decl (int, char *); int main (void) { (void) ac_decl (0, (char *) 0); (void) ac_decl; ; return 0; } _ACEOF if ac_fn_c_try_compile "$LINENO" then : if test x"$ac_arg" = x then : ac_cv_c_undeclared_builtin_options='none needed' else case e in #( e) ac_cv_c_undeclared_builtin_options=$ac_arg ;; esac fi break fi rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext done CFLAGS=$ac_save_CFLAGS ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_undeclared_builtin_options" >&5 printf "%s\n" "$ac_cv_c_undeclared_builtin_options" >&6; } case $ac_cv_c_undeclared_builtin_options in #( 'cannot detect') : { { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in '$ac_pwd':" >&5 printf "%s\n" "$as_me: error: in '$ac_pwd':" >&2;} as_fn_error $? "cannot make $CC report undeclared builtins See 'config.log' for more details" "$LINENO" 5; } ;; #( 'none needed') : ac_c_undeclared_builtin_options='' ;; #( *) : ac_c_undeclared_builtin_options=$ac_cv_c_undeclared_builtin_options ;; esac ac_header= ac_cache= for ac_item in $ac_header_c_list do if test $ac_cache; then ac_fn_c_check_header_compile "$LINENO" $ac_header ac_cv_header_$ac_cache "$ac_includes_default" if eval test \"x\$ac_cv_header_$ac_cache\" = xyes; then printf "%s\n" "#define $ac_item 1" >> confdefs.h fi ac_header= ac_cache= elif test $ac_header; then ac_cache=$ac_item else ac_header=$ac_item fi done if test $ac_cv_header_stdlib_h = yes && test $ac_cv_header_string_h = yes then : printf "%s\n" "#define STDC_HEADERS 1" >>confdefs.h fi ac_fn_check_decl "$LINENO" "_XOPEN_SOURCE" "ac_cv_have_decl__XOPEN_SOURCE" "$ac_includes_default" "$ac_c_undeclared_builtin_options" "CFLAGS" if test "x$ac_cv_have_decl__XOPEN_SOURCE" = xyes then : else case e in #( e) printf "%s\n" "#define _XOPEN_SOURCE 600" >>confdefs.h ;; esac fi ac_fn_check_decl "$LINENO" "__get_cpuid_max" "ac_cv_have_decl___get_cpuid_max" "#include " "$ac_c_undeclared_builtin_options" "CFLAGS" if test "x$ac_cv_have_decl___get_cpuid_max" = xyes then : ac_have_decl=1 else case e in #( e) ac_have_decl=0 ;; esac fi printf "%s\n" "#define HAVE_DECL___GET_CPUID_MAX $ac_have_decl" >>confdefs.h if test $ac_have_decl = 1 then : hts_have_cpuid=yes else case e in #( e) hts_have_cpuid=no ;; esac fi ac_fn_check_decl "$LINENO" "__cpuid_count" "ac_cv_have_decl___cpuid_count" "#include " "$ac_c_undeclared_builtin_options" "CFLAGS" if test "x$ac_cv_have_decl___cpuid_count" = xyes then : ac_have_decl=1 else case e in #( e) ac_have_decl=0 ;; esac fi printf "%s\n" "#define HAVE_DECL___CPUID_COUNT $ac_have_decl" >>confdefs.h if test $ac_have_decl = 1 then : hts_have_cpuid=yes else case e in #( e) hts_have_cpuid=no ;; esac fi if test "x$hts_have_cpuid" = "xyes" then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking C compiler flags needed for sse4.1" >&5 printf %s "checking C compiler flags needed for sse4.1... " >&6; } if test ${hts_cv_check_cflags_needed_sse4_1___msse4_1__mssse3__mpopcnt+y} then : printf %s "(cached) " >&6 else case e in #( e) cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __x86_64__ #include "x86intrin.h" #endif int main (void) { #ifdef __x86_64__ __m128i a = _mm_set_epi32(1, 2, 3, 4), b = _mm_set_epi32(4, 3, 2, 1); __m128i c = _mm_shuffle_epi8(_mm_max_epu32(a, b), b); return _mm_popcnt_u32(*((char *) &c)); #endif ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : hts_cv_check_cflags_needed_sse4_1___msse4_1__mssse3__mpopcnt=none else case e in #( e) ax_check_save_flags=$CFLAGS CFLAGS="$CFLAGS -msse4.1 -mssse3 -mpopcnt" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __x86_64__ #include "x86intrin.h" #endif int main (void) { #ifdef __x86_64__ __m128i a = _mm_set_epi32(1, 2, 3, 4), b = _mm_set_epi32(4, 3, 2, 1); __m128i c = _mm_shuffle_epi8(_mm_max_epu32(a, b), b); return _mm_popcnt_u32(*((char *) &c)); #endif ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : hts_cv_check_cflags_needed_sse4_1___msse4_1__mssse3__mpopcnt="-msse4.1 -mssse3 -mpopcnt" else case e in #( e) hts_cv_check_cflags_needed_sse4_1___msse4_1__mssse3__mpopcnt=unsupported ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext CFLAGS=$ax_check_save_flags ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $hts_cv_check_cflags_needed_sse4_1___msse4_1__mssse3__mpopcnt" >&5 printf "%s\n" "$hts_cv_check_cflags_needed_sse4_1___msse4_1__mssse3__mpopcnt" >&6; } if test "x$hts_cv_check_cflags_needed_sse4_1___msse4_1__mssse3__mpopcnt" = xunsupported then : : else case e in #( e) if test "x$hts_cv_check_cflags_needed_sse4_1___msse4_1__mssse3__mpopcnt" = xnone then : flags_needed="" else case e in #( e) flags_needed="$hts_cv_check_cflags_needed_sse4_1___msse4_1__mssse3__mpopcnt" ;; esac fi hts_cflags_sse4="$flags_needed" printf "%s\n" "#define HAVE_SSSE3 1" >>confdefs.h printf "%s\n" "#define HAVE_POPCNT 1" >>confdefs.h printf "%s\n" "#define HAVE_SSE4_1 1" >>confdefs.h printf "%s\n" "#define UBSAN 1" >>confdefs.h ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking C compiler flags needed for avx2" >&5 printf %s "checking C compiler flags needed for avx2... " >&6; } if test ${hts_cv_check_cflags_needed_avx2___mavx2__mpopcnt+y} then : printf %s "(cached) " >&6 else case e in #( e) cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __x86_64__ #include "x86intrin.h" #endif int main (void) { #ifdef __x86_64__ __m256i a = _mm256_set_epi32(1, 2, 3, 4, 5, 6, 7, 8); __m256i b = _mm256_add_epi32(a, a); long long c = _mm256_extract_epi64(b, 0); return _mm_popcnt_u32((int) c); #endif ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : hts_cv_check_cflags_needed_avx2___mavx2__mpopcnt=none else case e in #( e) ax_check_save_flags=$CFLAGS CFLAGS="$CFLAGS -mavx2 -mpopcnt" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __x86_64__ #include "x86intrin.h" #endif int main (void) { #ifdef __x86_64__ __m256i a = _mm256_set_epi32(1, 2, 3, 4, 5, 6, 7, 8); __m256i b = _mm256_add_epi32(a, a); long long c = _mm256_extract_epi64(b, 0); return _mm_popcnt_u32((int) c); #endif ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : hts_cv_check_cflags_needed_avx2___mavx2__mpopcnt="-mavx2 -mpopcnt" else case e in #( e) hts_cv_check_cflags_needed_avx2___mavx2__mpopcnt=unsupported ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext CFLAGS=$ax_check_save_flags ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $hts_cv_check_cflags_needed_avx2___mavx2__mpopcnt" >&5 printf "%s\n" "$hts_cv_check_cflags_needed_avx2___mavx2__mpopcnt" >&6; } if test "x$hts_cv_check_cflags_needed_avx2___mavx2__mpopcnt" = xunsupported then : : else case e in #( e) if test "x$hts_cv_check_cflags_needed_avx2___mavx2__mpopcnt" = xnone then : flags_needed="" else case e in #( e) flags_needed="$hts_cv_check_cflags_needed_avx2___mavx2__mpopcnt" ;; esac fi hts_cflags_avx2="$flags_needed" printf "%s\n" "#define HAVE_POPCNT 1" >>confdefs.h printf "%s\n" "#define HAVE_AVX2 1" >>confdefs.h ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking C compiler flags needed for avx512f" >&5 printf %s "checking C compiler flags needed for avx512f... " >&6; } if test ${hts_cv_check_cflags_needed_avx512f___mavx512f__mpopcnt+y} then : printf %s "(cached) " >&6 else case e in #( e) cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __x86_64__ #include "x86intrin.h" #endif int main (void) { #ifdef __x86_64__ __m512i a = _mm512_set1_epi32(1); __m512i b = _mm512_add_epi32(a, a); __m256i c = _mm512_castsi512_si256(b); __m256i d = _mm512_extracti64x4_epi64(a, 1); return _mm_popcnt_u32(*((char *) &c)) + (*(char *) &d); #endif ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : hts_cv_check_cflags_needed_avx512f___mavx512f__mpopcnt=none else case e in #( e) ax_check_save_flags=$CFLAGS CFLAGS="$CFLAGS -mavx512f -mpopcnt" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __x86_64__ #include "x86intrin.h" #endif int main (void) { #ifdef __x86_64__ __m512i a = _mm512_set1_epi32(1); __m512i b = _mm512_add_epi32(a, a); __m256i c = _mm512_castsi512_si256(b); __m256i d = _mm512_extracti64x4_epi64(a, 1); return _mm_popcnt_u32(*((char *) &c)) + (*(char *) &d); #endif ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : hts_cv_check_cflags_needed_avx512f___mavx512f__mpopcnt="-mavx512f -mpopcnt" else case e in #( e) hts_cv_check_cflags_needed_avx512f___mavx512f__mpopcnt=unsupported ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext CFLAGS=$ax_check_save_flags ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $hts_cv_check_cflags_needed_avx512f___mavx512f__mpopcnt" >&5 printf "%s\n" "$hts_cv_check_cflags_needed_avx512f___mavx512f__mpopcnt" >&6; } if test "x$hts_cv_check_cflags_needed_avx512f___mavx512f__mpopcnt" = xunsupported then : : else case e in #( e) if test "x$hts_cv_check_cflags_needed_avx512f___mavx512f__mpopcnt" = xnone then : flags_needed="" else case e in #( e) flags_needed="$hts_cv_check_cflags_needed_avx512f___mavx512f__mpopcnt" ;; esac fi hts_cflags_avx512="$flags_needed" printf "%s\n" "#define HAVE_POPCNT 1" >>confdefs.h printf "%s\n" "#define HAVE_AVX512 1" >>confdefs.h ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for working __builtin_cpu_supports(\"ssse3\")" >&5 printf %s "checking for working __builtin_cpu_supports(\"ssse3\")... " >&6; } cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main (void) { if (__builtin_cpu_supports("ssse3")) { return 0; } ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: yes" >&5 printf "%s\n" "yes" >&6; } printf "%s\n" "#define HAVE_BUILTIN_CPU_SUPPORT_SSSE3 1" >>confdefs.h else case e in #( e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for __attribute__((target))" >&5 printf %s "checking for __attribute__((target))... " >&6; } cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ __attribute__((target("ssse3"))) int zero(void) { return 0; } int main (void) { zero(); ; return 0; } _ACEOF if ac_fn_c_try_compile "$LINENO" then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: yes" >&5 printf "%s\n" "yes" >&6; } printf "%s\n" "#define HAVE_ATTRIBUTE_TARGET 1" >>confdefs.h else case e in #( e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext fi if test "x$ac_cv_env_PKG_CONFIG_set" != "xset"; then if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}pkg-config", so it can be a program name with args. set dummy ${ac_tool_prefix}pkg-config; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_path_PKG_CONFIG+y} then : printf %s "(cached) " >&6 else case e in #( e) case $PKG_CONFIG in [\\/]* | ?:[\\/]*) ac_cv_path_PKG_CONFIG="$PKG_CONFIG" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then ac_cv_path_PKG_CONFIG="$as_dir$ac_word$ac_exec_ext" printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS ;; esac ;; esac fi PKG_CONFIG=$ac_cv_path_PKG_CONFIG if test -n "$PKG_CONFIG"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $PKG_CONFIG" >&5 printf "%s\n" "$PKG_CONFIG" >&6; } else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } fi fi if test -z "$ac_cv_path_PKG_CONFIG"; then ac_pt_PKG_CONFIG=$PKG_CONFIG # Extract the first word of "pkg-config", so it can be a program name with args. set dummy pkg-config; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_path_ac_pt_PKG_CONFIG+y} then : printf %s "(cached) " >&6 else case e in #( e) case $ac_pt_PKG_CONFIG in [\\/]* | ?:[\\/]*) ac_cv_path_ac_pt_PKG_CONFIG="$ac_pt_PKG_CONFIG" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then ac_cv_path_ac_pt_PKG_CONFIG="$as_dir$ac_word$ac_exec_ext" printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS ;; esac ;; esac fi ac_pt_PKG_CONFIG=$ac_cv_path_ac_pt_PKG_CONFIG if test -n "$ac_pt_PKG_CONFIG"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_pt_PKG_CONFIG" >&5 printf "%s\n" "$ac_pt_PKG_CONFIG" >&6; } else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } fi if test "x$ac_pt_PKG_CONFIG" = x; then PKG_CONFIG="" else case $cross_compiling:$ac_tool_warned in yes:) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 printf "%s\n" "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac PKG_CONFIG=$ac_pt_PKG_CONFIG fi else PKG_CONFIG="$ac_cv_path_PKG_CONFIG" fi fi if test -n "$PKG_CONFIG"; then _pkg_min_version=0.9.0 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking pkg-config is at least version $_pkg_min_version" >&5 printf %s "checking pkg-config is at least version $_pkg_min_version... " >&6; } if $PKG_CONFIG --atleast-pkgconfig-version $_pkg_min_version; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: yes" >&5 printf "%s\n" "yes" >&6; } else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } PKG_CONFIG="" fi fi need_crypto=no pc_requires= static_LDFLAGS=$LDFLAGS static_LIBS='-lpthread -lz -lm' private_LIBS=$LDFLAGS # Check whether --enable-versioned-symbols was given. if test ${enable_versioned_symbols+y} then : enableval=$enable_versioned_symbols; else case e in #( e) enable_versioned_symbols=yes ;; esac fi # Check whether --enable-bz2 was given. if test ${enable_bz2+y} then : enableval=$enable_bz2; else case e in #( e) enable_bz2=yes ;; esac fi # Check whether --enable-gcs was given. if test ${enable_gcs+y} then : enableval=$enable_gcs; else case e in #( e) enable_gcs=check ;; esac fi # Check whether --enable-largefile was given. if test ${enable_largefile+y} then : enableval=$enable_largefile; fi if test "$enable_largefile,$enable_year2038" != no,no then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $CC option to enable large file support" >&5 printf %s "checking for $CC option to enable large file support... " >&6; } if test ${ac_cv_sys_largefile_opts+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_save_CC="$CC" ac_opt_found=no for ac_opt in "none needed" "-D_FILE_OFFSET_BITS=64" "-D_LARGE_FILES=1" "-n32"; do if test x"$ac_opt" != x"none needed" then : CC="$ac_save_CC $ac_opt" fi cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #ifndef FTYPE # define FTYPE off_t #endif /* Check that FTYPE can represent 2**63 - 1 correctly. We can't simply define LARGE_FTYPE to be 9223372036854775807, since some C++ compilers masquerading as C compilers incorrectly reject 9223372036854775807. */ #define LARGE_FTYPE (((FTYPE) 1 << 31 << 31) - 1 + ((FTYPE) 1 << 31 << 31)) int FTYPE_is_large[(LARGE_FTYPE % 2147483629 == 721 && LARGE_FTYPE % 2147483647 == 1) ? 1 : -1]; int main (void) { ; return 0; } _ACEOF if ac_fn_c_try_compile "$LINENO" then : if test x"$ac_opt" = x"none needed" then : # GNU/Linux s390x and alpha need _FILE_OFFSET_BITS=64 for wide ino_t. CC="$CC -DFTYPE=ino_t" if ac_fn_c_try_compile "$LINENO" then : else case e in #( e) CC="$CC -D_FILE_OFFSET_BITS=64" if ac_fn_c_try_compile "$LINENO" then : ac_opt='-D_FILE_OFFSET_BITS=64' fi rm -f core conftest.err conftest.$ac_objext conftest.beam ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam fi ac_cv_sys_largefile_opts=$ac_opt ac_opt_found=yes fi rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext test $ac_opt_found = no || break done CC="$ac_save_CC" test $ac_opt_found = yes || ac_cv_sys_largefile_opts="support not detected" ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sys_largefile_opts" >&5 printf "%s\n" "$ac_cv_sys_largefile_opts" >&6; } ac_have_largefile=yes case $ac_cv_sys_largefile_opts in #( "none needed") : ;; #( "supported through gnulib") : ;; #( "support not detected") : ac_have_largefile=no ;; #( "-D_FILE_OFFSET_BITS=64") : printf "%s\n" "#define _FILE_OFFSET_BITS 64" >>confdefs.h ;; #( "-D_LARGE_FILES=1") : printf "%s\n" "#define _LARGE_FILES 1" >>confdefs.h ;; #( "-n32") : CC="$CC -n32" ;; #( *) : as_fn_error $? "internal error: bad value for \$ac_cv_sys_largefile_opts" "$LINENO" 5 ;; esac if test "$enable_year2038" != no then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $CC option for timestamps after 2038" >&5 printf %s "checking for $CC option for timestamps after 2038... " >&6; } if test ${ac_cv_sys_year2038_opts+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_save_CPPFLAGS="$CPPFLAGS" ac_opt_found=no for ac_opt in "none needed" "-D_TIME_BITS=64" "-D__MINGW_USE_VC2005_COMPAT" "-U_USE_32_BIT_TIME_T -D__MINGW_USE_VC2005_COMPAT"; do if test x"$ac_opt" != x"none needed" then : CPPFLAGS="$ac_save_CPPFLAGS $ac_opt" fi cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include /* Check that time_t can represent 2**32 - 1 correctly. */ #define LARGE_TIME_T \\ ((time_t) (((time_t) 1 << 30) - 1 + 3 * ((time_t) 1 << 30))) int verify_time_t_range[(LARGE_TIME_T / 65537 == 65535 && LARGE_TIME_T % 65537 == 0) ? 1 : -1]; int main (void) { ; return 0; } _ACEOF if ac_fn_c_try_compile "$LINENO" then : ac_cv_sys_year2038_opts="$ac_opt" ac_opt_found=yes fi rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext test $ac_opt_found = no || break done CPPFLAGS="$ac_save_CPPFLAGS" test $ac_opt_found = yes || ac_cv_sys_year2038_opts="support not detected" ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sys_year2038_opts" >&5 printf "%s\n" "$ac_cv_sys_year2038_opts" >&6; } ac_have_year2038=yes case $ac_cv_sys_year2038_opts in #( "none needed") : ;; #( "support not detected") : ac_have_year2038=no ;; #( "-D_TIME_BITS=64") : printf "%s\n" "#define _TIME_BITS 64" >>confdefs.h ;; #( "-D__MINGW_USE_VC2005_COMPAT") : printf "%s\n" "#define __MINGW_USE_VC2005_COMPAT 1" >>confdefs.h ;; #( "-U_USE_32_BIT_TIME_T"*) : { { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in '$ac_pwd':" >&5 printf "%s\n" "$as_me: error: in '$ac_pwd':" >&2;} as_fn_error $? "the 'time_t' type is currently forced to be 32-bit. It will stop working after mid-January 2038. Remove _USE_32BIT_TIME_T from the compiler flags. See 'config.log' for more details" "$LINENO" 5; } ;; #( *) : as_fn_error $? "internal error: bad value for \$ac_cv_sys_year2038_opts" "$LINENO" 5 ;; esac fi fi # Check whether --enable-libcurl was given. if test ${enable_libcurl+y} then : enableval=$enable_libcurl; else case e in #( e) enable_libcurl=check ;; esac fi # Check whether --enable-lzma was given. if test ${enable_lzma+y} then : enableval=$enable_lzma; else case e in #( e) enable_lzma=yes ;; esac fi # Check whether --enable-plugins was given. if test ${enable_plugins+y} then : enableval=$enable_plugins; else case e in #( e) enable_plugins=no ;; esac fi # Check whether --with-external-htscodecs was given. if test ${with_external_htscodecs+y} then : withval=$with_external_htscodecs; else case e in #( e) with_external_htscodecs=no ;; esac fi # Check whether --with-libdeflate was given. if test ${with_libdeflate+y} then : withval=$with_libdeflate; else case e in #( e) with_libdeflate=check ;; esac fi # Check whether --with-plugin-dir was given. if test ${with_plugin_dir+y} then : withval=$with_plugin_dir; case $withval in yes|no) cat > config.mk <<'EOF' ifneq ($(MAKECMDGOALS),distclean) $(error Resolve configure error first) endif EOF as_fn_error $? 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" >&6; } if test ${hts_cv_check__xldscope_hidden+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_check_save_cflags=$CFLAGS ac_check_save_ldflags=$LDFLAGS CFLAGS="$CFLAGS -xldscope=hidden" LDFLAGS="$LDFLAGS -xldscope=hidden" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main (void) { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : hts_cv_check__xldscope_hidden=yes if test "xac_opt_found" != x then : eval ac_opt_found="-xldscope=hidden" fi else case e in #( e) hts_cv_check__xldscope_hidden=no ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext CFLAGS=$ac_check_save_cflags LDFLAGS=$ac_check_save_ldflags ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $hts_cv_check__xldscope_hidden" >&5 printf "%s\n" "$hts_cv_check__xldscope_hidden" >&6; } fi if test "x$ac_opt_found" != "xno" then : CFLAGS="$CFLAGS $ac_opt_found" LDFLAGS="$LDFLAGS $ac_opt_found" fi # Make sure we can run config.sub. $SHELL "${ac_aux_dir}config.sub" sun4 >/dev/null 2>&1 || as_fn_error $? "cannot run $SHELL ${ac_aux_dir}config.sub" "$LINENO" 5 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking build system type" >&5 printf %s "checking build system type... " >&6; } if test ${ac_cv_build+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_build_alias=$build_alias test "x$ac_build_alias" = x && ac_build_alias=`$SHELL "${ac_aux_dir}config.guess"` test "x$ac_build_alias" = x && as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5 ac_cv_build=`$SHELL "${ac_aux_dir}config.sub" $ac_build_alias` || as_fn_error $? "$SHELL ${ac_aux_dir}config.sub $ac_build_alias failed" "$LINENO" 5 ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5 printf "%s\n" "$ac_cv_build" >&6; } case $ac_cv_build in *-*-*) ;; *) as_fn_error $? "invalid value of canonical build" "$LINENO" 5;; esac build=$ac_cv_build ac_save_IFS=$IFS; IFS='-' set x $ac_cv_build shift build_cpu=$1 build_vendor=$2 shift; shift # Remember, the first character of IFS is used to create $*, # except with old shells: build_os=$* IFS=$ac_save_IFS case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking host system type" >&5 printf %s "checking host system type... " >&6; } if test ${ac_cv_host+y} then : printf %s "(cached) " >&6 else case e in #( e) if test "x$host_alias" = x; then ac_cv_host=$ac_cv_build else ac_cv_host=`$SHELL "${ac_aux_dir}config.sub" $host_alias` || as_fn_error $? "$SHELL ${ac_aux_dir}config.sub $host_alias failed" "$LINENO" 5 fi ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_host" >&5 printf "%s\n" "$ac_cv_host" >&6; } case $ac_cv_host in *-*-*) ;; *) as_fn_error $? "invalid value of canonical host" "$LINENO" 5;; esac host=$ac_cv_host ac_save_IFS=$IFS; IFS='-' set x $ac_cv_host shift host_cpu=$1 host_vendor=$2 shift; shift # Remember, the first character of IFS is used to create $*, # except with old shells: host_os=$* IFS=$ac_save_IFS case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac ac_func= for ac_item in $ac_func_c_list do if test $ac_func; then ac_fn_c_check_func "$LINENO" $ac_func ac_cv_func_$ac_func if eval test \"x\$ac_cv_func_$ac_func\" = xyes; then echo "#define $ac_item 1" >> confdefs.h fi ac_func= else ac_func=$ac_item fi done { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for working mmap" >&5 printf %s "checking for working mmap... " >&6; } if test ${ac_cv_func_mmap_fixed_mapped+y} then : printf %s "(cached) " >&6 else case e in #( e) if test "$cross_compiling" = yes then : case "$host_os" in # (( # Guess yes on platforms where we know the result. linux*) ac_cv_func_mmap_fixed_mapped=yes ;; # If we don't know, assume the worst. *) ac_cv_func_mmap_fixed_mapped=no ;; esac else case e in #( e) cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ $ac_includes_default /* malloc might have been renamed as rpl_malloc. */ #undef malloc /* Thanks to Mike Haertel and Jim Avera for this test. Here is a matrix of mmap possibilities: mmap private not fixed mmap private fixed at somewhere currently unmapped mmap private fixed at somewhere already mapped mmap shared not fixed mmap shared fixed at somewhere currently unmapped mmap shared fixed at somewhere already mapped For private mappings, we should verify that changes cannot be read() back from the file, nor mmap's back from the file at a different address. 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File must have non-zero length, otherwise we risk SIGBUS for entire page. */ fd2 = open ("conftest.txt", O_RDWR | O_CREAT | O_TRUNC, 0600); if (fd2 < 0) return 4; cdata2 = ""; if (write (fd2, cdata2, 1) != 1) return 5; data2 = (char *) mmap (0, pagesize, PROT_READ | PROT_WRITE, MAP_SHARED, fd2, 0L); if (data2 == MAP_FAILED) return 6; for (i = 0; i < pagesize; ++i) if (*(data2 + i)) return 7; close (fd2); /* 'return 8;' not currently used. */ /* Next, try to mmap the file at a fixed address which already has something else allocated at it. If we can, also make sure that we see the same garbage. */ fd = open ("conftest.mmap", O_RDWR); if (fd < 0) return 9; if (data2 != mmap (data2, pagesize, PROT_READ | PROT_WRITE, MAP_PRIVATE | MAP_FIXED, fd, 0L)) return 10; for (i = 0; i < pagesize; ++i) if (*(data + i) != *(data2 + i)) return 11; /* Finally, make sure that changes to the mapped area do not percolate back to the file as seen by read(). 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" >&6; } cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ static __attribute__((constructor)) void noop(void) {} int main (void) { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: yes" >&5 printf "%s\n" "yes" >&6; } printf "%s\n" "#define HAVE_ATTRIBUTE_CONSTRUCTOR 1" >>confdefs.h else case e in #( e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID" >&5 printf %s "checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... " >&6; } cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include int main (void) { struct timespec ts; clock_gettime(CLOCK_PROCESS_CPUTIME_ID, &ts); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: yes" >&5 printf "%s\n" "yes" >&6; } printf "%s\n" "#define HAVE_CLOCK_GETTIME_CPUTIME 1" >>confdefs.h else case e in #( e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext if test $enable_plugins != no; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for library containing dlsym" >&5 printf %s "checking for library containing dlsym... " >&6; } if test ${ac_cv_search_dlsym+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_func_search_save_LIBS=$LIBS cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. The 'extern "C"' is for builds by C++ compilers; although this is not generally supported in C code supporting it here has little cost and some practical benefit (sr 110532). */ #ifdef __cplusplus extern "C" #endif char dlsym (void); int main (void) { return dlsym (); ; return 0; } _ACEOF for ac_lib in '' dl do if test -z "$ac_lib"; then ac_res="none required" else ac_res=-l$ac_lib LIBS="-l$ac_lib $ac_func_search_save_LIBS" fi if ac_fn_c_try_link "$LINENO" then : ac_cv_search_dlsym=$ac_res fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext if test ${ac_cv_search_dlsym+y} then : break fi done if test ${ac_cv_search_dlsym+y} then : else case e in #( e) ac_cv_search_dlsym=no ;; esac fi rm conftest.$ac_ext LIBS=$ac_func_search_save_LIBS ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_dlsym" >&5 printf "%s\n" "$ac_cv_search_dlsym" >&6; } ac_res=$ac_cv_search_dlsym if test "$ac_res" != no then : test "$ac_res" = "none required" || LIBS="$ac_res $LIBS" else case e in #( e) cat > config.mk <<'EOF' ifneq ($(MAKECMDGOALS),distclean) $(error Resolve configure error first) endif EOF as_fn_error $? "dlsym() not found Plugin support requires dynamic linking facilities from the operating system. Either configure with --disable-plugins or resolve this error to build HTSlib." "$LINENO" 5 ;; esac fi # Check if the compiler understands -rdynamic # TODO Test whether this is required and/or needs tweaking per-platform { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking whether the compiler accepts -rdynamic" >&5 printf %s "checking whether the compiler accepts -rdynamic... " >&6; } if test ${hts_cv_check__rdynamic+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_check_save_cflags=$CFLAGS ac_check_save_ldflags=$LDFLAGS CFLAGS="$CFLAGS -rdynamic" LDFLAGS="$LDFLAGS -rdynamic" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main (void) { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : hts_cv_check__rdynamic=yes if test "xrdynamic_flag" != x then : eval rdynamic_flag="-rdynamic" fi else case e in #( e) hts_cv_check__rdynamic=no ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext CFLAGS=$ac_check_save_cflags LDFLAGS=$ac_check_save_ldflags ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $hts_cv_check__rdynamic" >&5 printf "%s\n" "$hts_cv_check__rdynamic" >&6; } if test x"$rdynamic_flag" != "xno" then : LDFLAGS="$LDFLAGS $rdynamic_flag" static_LDFLAGS="$static_LDFLAGS $rdynamic_flag" fi case "$ac_cv_search_dlsym" in -l*) static_LIBS="$static_LIBS $ac_cv_search_dlsym" ;; esac printf "%s\n" "#define ENABLE_PLUGINS 1" >>confdefs.h printf "%s\n" "#define PLUGIN_EXT \"$PLUGIN_EXT\"" >>confdefs.h fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for library containing log" >&5 printf %s "checking for library containing log... " >&6; } if test ${ac_cv_search_log+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_func_search_save_LIBS=$LIBS cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. The 'extern "C"' is for builds by C++ compilers; although this is not generally supported in C code supporting it here has little cost and some practical benefit (sr 110532). */ #ifdef __cplusplus extern "C" #endif char log (void); int main (void) { return log (); ; return 0; } _ACEOF for ac_lib in '' m do if test -z "$ac_lib"; then ac_res="none required" else ac_res=-l$ac_lib LIBS="-l$ac_lib $ac_func_search_save_LIBS" fi if ac_fn_c_try_link "$LINENO" then : ac_cv_search_log=$ac_res fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext if test ${ac_cv_search_log+y} then : break fi done if test ${ac_cv_search_log+y} then : else case e in #( e) ac_cv_search_log=no ;; esac fi rm conftest.$ac_ext LIBS=$ac_func_search_save_LIBS ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_log" >&5 printf "%s\n" "$ac_cv_search_log" >&6; } ac_res=$ac_cv_search_log if test "$ac_res" != no then : test "$ac_res" = "none required" || LIBS="$ac_res $LIBS" else case e in #( e) cat > config.mk <<'EOF' ifneq ($(MAKECMDGOALS),distclean) $(error Resolve configure error first) endif EOF as_fn_error $? "log() not found HTSLIB requires a working floating-point math library. FAILED. This error must be resolved in order to build HTSlib successfully." "$LINENO" 5 ;; esac fi zlib_devel=ok ac_fn_c_check_header_compile "$LINENO" "zlib.h" "ac_cv_header_zlib_h" "; " if test "x$ac_cv_header_zlib_h" = xyes then : else case e in #( e) zlib_devel=missing ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for inflate in -lz" >&5 printf %s "checking for inflate in -lz... " >&6; } if test ${ac_cv_lib_z_inflate+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_check_lib_save_LIBS=$LIBS LIBS="-lz $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. The 'extern "C"' is for builds by C++ compilers; although this is not generally supported in C code supporting it here has little cost and some practical benefit (sr 110532). */ #ifdef __cplusplus extern "C" #endif char inflate (void); int main (void) { return inflate (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : ac_cv_lib_z_inflate=yes else case e in #( e) ac_cv_lib_z_inflate=no ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_z_inflate" >&5 printf "%s\n" "$ac_cv_lib_z_inflate" >&6; } if test "x$ac_cv_lib_z_inflate" = xyes then : printf "%s\n" "#define HAVE_LIBZ 1" >>confdefs.h LIBS="-lz $LIBS" else case e in #( e) zlib_devel=missing ;; esac fi if test $zlib_devel != ok; then cat > config.mk <<'EOF' ifneq ($(MAKECMDGOALS),distclean) $(error Resolve configure error first) endif EOF as_fn_error $? "zlib development files not found HTSlib uses compression routines from the zlib library . Building HTSlib requires zlib development files to be installed on the build machine; you may need to ensure a package such as zlib1g-dev (on Debian or Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions or Cygwin) is installed. FAILED. This error must be resolved in order to build HTSlib successfully." "$LINENO" 5 fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for library containing recv" >&5 printf %s "checking for library containing recv... " >&6; } if test ${ac_cv_search_recv+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_func_search_save_LIBS=$LIBS cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. The 'extern "C"' is for builds by C++ compilers; although this is not generally supported in C code supporting it here has little cost and some practical benefit (sr 110532). */ #ifdef __cplusplus extern "C" #endif char recv (void); int main (void) { return recv (); ; return 0; } _ACEOF for ac_lib in '' socket ws2_32 do if test -z "$ac_lib"; then ac_res="none required" else ac_res=-l$ac_lib LIBS="-l$ac_lib $ac_func_search_save_LIBS" fi if ac_fn_c_try_link "$LINENO" then : ac_cv_search_recv=$ac_res fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext if test ${ac_cv_search_recv+y} then : break fi done if test ${ac_cv_search_recv+y} then : else case e in #( e) ac_cv_search_recv=no ;; esac fi rm conftest.$ac_ext LIBS=$ac_func_search_save_LIBS ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_recv" >&5 printf "%s\n" "$ac_cv_search_recv" >&6; } ac_res=$ac_cv_search_recv if test "$ac_res" != no then : test "$ac_res" = "none required" || LIBS="$ac_res $LIBS" if test "$ac_cv_search_recv" != "none required" then static_LIBS="$static_LIBS $ac_cv_search_recv" fi else case e in #( e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for library containing recv using declaration" >&5 printf %s "checking for library containing recv using declaration... " >&6; } LIBS="-lws2_32 $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include int main (void) { recv(0, 0, 0, 0); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: -lws2_32" >&5 printf "%s\n" "-lws2_32" >&6; } static_LIBS="$static_LIBS -lws2_32" else case e in #( e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } cat > config.mk <<'EOF' ifneq ($(MAKECMDGOALS),distclean) $(error Resolve configure error first) endif EOF as_fn_error $? "unable to find the recv() function" "$LINENO" 5 ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext ;; esac fi if test "$enable_bz2" != no; then bz2_devel=ok ac_fn_c_check_header_compile "$LINENO" "bzlib.h" "ac_cv_header_bzlib_h" "; " if test "x$ac_cv_header_bzlib_h" = xyes then : else case e in #( e) bz2_devel=missing ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for BZ2_bzBuffToBuffCompress in -lbz2" >&5 printf %s "checking for BZ2_bzBuffToBuffCompress in -lbz2... " >&6; } if test ${ac_cv_lib_bz2_BZ2_bzBuffToBuffCompress+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_check_lib_save_LIBS=$LIBS LIBS="-lbz2 $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. The 'extern "C"' is for builds by C++ compilers; although this is not generally supported in C code supporting it here has little cost and some practical benefit (sr 110532). */ #ifdef __cplusplus extern "C" #endif char BZ2_bzBuffToBuffCompress (void); int main (void) { return BZ2_bzBuffToBuffCompress (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : ac_cv_lib_bz2_BZ2_bzBuffToBuffCompress=yes else case e in #( e) ac_cv_lib_bz2_BZ2_bzBuffToBuffCompress=no ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_bz2_BZ2_bzBuffToBuffCompress" >&5 printf "%s\n" "$ac_cv_lib_bz2_BZ2_bzBuffToBuffCompress" >&6; } if test "x$ac_cv_lib_bz2_BZ2_bzBuffToBuffCompress" = xyes then : printf "%s\n" "#define HAVE_LIBBZ2 1" >>confdefs.h LIBS="-lbz2 $LIBS" else case e in #( e) bz2_devel=missing ;; esac fi if test $bz2_devel != ok; then cat > config.mk <<'EOF' ifneq ($(MAKECMDGOALS),distclean) $(error Resolve configure error first) endif EOF as_fn_error $? "libbzip2 development files not found The CRAM format may use bzip2 compression, which is implemented in HTSlib by using compression routines from libbzip2 . Building HTSlib requires libbzip2 development files to be installed on the build machine; you may need to ensure a package such as libbz2-dev (on Debian or Ubuntu Linux) or bzip2-devel (on RPM-based Linux distributions or Cygwin) is installed. Either configure with --disable-bz2 (which will make some CRAM files produced elsewhere unreadable) or resolve this error to build HTSlib." "$LINENO" 5 fi if test -n "$PKG_CONFIG" && "$PKG_CONFIG" --exists bzip2; then pc_requires="$pc_requires bzip2" else private_LIBS="$private_LIBS -lbz2" fi static_LIBS="$static_LIBS -lbz2" fi if test "$enable_lzma" != no; then lzma_devel=ok for ac_header in lzma.h do : ac_fn_c_check_header_compile "$LINENO" "lzma.h" "ac_cv_header_lzma_h" "; " if test "x$ac_cv_header_lzma_h" = xyes then : printf "%s\n" "#define HAVE_LZMA_H 1" >>confdefs.h else case e in #( e) lzma_devel=header-missing ;; esac fi done { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for lzma_easy_buffer_encode in -llzma" >&5 printf %s "checking for lzma_easy_buffer_encode in -llzma... " >&6; } if test ${ac_cv_lib_lzma_lzma_easy_buffer_encode+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_check_lib_save_LIBS=$LIBS LIBS="-llzma $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. The 'extern "C"' is for builds by C++ compilers; although this is not generally supported in C code supporting it here has little cost and some practical benefit (sr 110532). */ #ifdef __cplusplus extern "C" #endif char lzma_easy_buffer_encode (void); int main (void) { return lzma_easy_buffer_encode (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : ac_cv_lib_lzma_lzma_easy_buffer_encode=yes else case e in #( e) ac_cv_lib_lzma_lzma_easy_buffer_encode=no ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_lzma_lzma_easy_buffer_encode" >&5 printf "%s\n" "$ac_cv_lib_lzma_lzma_easy_buffer_encode" >&6; } if test "x$ac_cv_lib_lzma_lzma_easy_buffer_encode" = xyes then : printf "%s\n" "#define HAVE_LIBLZMA 1" >>confdefs.h LIBS="-llzma $LIBS" else case e in #( e) lzma_devel=missing ;; esac fi if test $lzma_devel = missing; then cat > config.mk <<'EOF' ifneq ($(MAKECMDGOALS),distclean) $(error Resolve configure error first) endif EOF as_fn_error $? "liblzma development files not found The CRAM format may use LZMA2 compression, which is implemented in HTSlib by using compression routines from liblzma . Building HTSlib requires liblzma development files to be installed on the build machine; you may need to ensure a package such as liblzma-dev (on Debian or Ubuntu Linux), xz-devel (on RPM-based Linux distributions or Cygwin), or xz (via Homebrew on macOS) is installed; or build XZ Utils from source. Either configure with --disable-lzma (which will make some CRAM files produced elsewhere unreadable) or resolve this error to build HTSlib." "$LINENO" 5 fi pc_requires="$pc_requires liblzma" static_LIBS="$static_LIBS -llzma" fi if test "x$with_external_htscodecs" != "xno" then : libhtscodecs=ok ac_fn_c_check_header_compile "$LINENO" "htscodecs/rANS_static4x16.h" "ac_cv_header_htscodecs_rANS_static4x16_h" "; " if test "x$ac_cv_header_htscodecs_rANS_static4x16_h" = xyes then : else case e in #( e) libhtscodecs='missing header' ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for rans_compress_bound_4x16 in -lhtscodecs" >&5 printf %s "checking for rans_compress_bound_4x16 in -lhtscodecs... " >&6; } if test ${ac_cv_lib_htscodecs_rans_compress_bound_4x16+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_check_lib_save_LIBS=$LIBS LIBS="-lhtscodecs $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. The 'extern "C"' is for builds by C++ compilers; although this is not generally supported in C code supporting it here has little cost and some practical benefit (sr 110532). */ #ifdef __cplusplus extern "C" #endif char rans_compress_bound_4x16 (void); int main (void) { return rans_compress_bound_4x16 (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : ac_cv_lib_htscodecs_rans_compress_bound_4x16=yes else case e in #( e) ac_cv_lib_htscodecs_rans_compress_bound_4x16=no ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_htscodecs_rans_compress_bound_4x16" >&5 printf "%s\n" "$ac_cv_lib_htscodecs_rans_compress_bound_4x16" >&6; } if test "x$ac_cv_lib_htscodecs_rans_compress_bound_4x16" = xyes then : : else case e in #( e) libhtscodecs='missing library' ;; esac fi if test "$libhtscodecs" = "ok" then : printf "%s\n" "#define HAVE_EXTERNAL_LIBHTSCODECS 1" >>confdefs.h LIBS="-lhtscodecs $LIBS" private_LIBS="-lhtscodecs $private_LIBS" static_LIBS="-lhtscodecs $static_LIBS" selected_htscodecs_mk="htscodecs_external.mk" else case e in #( e) cat > config.mk <<'EOF' ifneq ($(MAKECMDGOALS),distclean) $(error Resolve configure error first) endif EOF as_fn_error $? "libhtscodecs development files not found: $libhtscodecs You asked to use an external htscodecs library, but do not have the required header / library files. You either need to supply these and if necessary set CPPFLAGS and LDFLAGS so the compiler can find them; or configure using --without-external-htscodecs to build the required functions from the htscodecs submodule. " "$LINENO" 5 ;; esac fi else case e in #( e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking whether htscodecs files are present" >&5 printf %s "checking whether htscodecs files are present... " >&6; } if test -e "$srcdir/htscodecs/htscodecs/rANS_static4x16.h" then : { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: yes" >&5 printf "%s\n" "yes" >&6; } selected_htscodecs_mk="htscodecs_bundled.mk" else case e in #( e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } if test -e "$srcdir/.git" then : cat > config.mk <<'EOF' ifneq ($(MAKECMDGOALS),distclean) $(error Resolve configure error first) endif EOF as_fn_error $? "htscodecs submodule files not present. HTSlib uses some functions from the htscodecs project, which is normally included as a submodule. Try running: git submodule update --init --recursive in the top-level htslib directory to update it, and then re-run configure. " "$LINENO" 5 else case e in #( e) cat > config.mk <<'EOF' ifneq ($(MAKECMDGOALS),distclean) $(error Resolve configure error first) endif EOF as_fn_error $? "htscodecs submodule files not present. You have an incomplete distribution. Please try downloading one of the official releases from https://www.htslib.org " "$LINENO" 5 ;; esac fi ;; esac fi ;; esac fi if test "x$with_libdeflate" != "xno" then : libdeflate=ok ac_fn_c_check_header_compile "$LINENO" "libdeflate.h" "ac_cv_header_libdeflate_h" "; " if test "x$ac_cv_header_libdeflate_h" = xyes then : else case e in #( e) libdeflate='missing header' ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for libdeflate_deflate_compress in -ldeflate" >&5 printf %s "checking for libdeflate_deflate_compress in -ldeflate... " >&6; } if test ${ac_cv_lib_deflate_libdeflate_deflate_compress+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_check_lib_save_LIBS=$LIBS LIBS="-ldeflate $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. The 'extern "C"' is for builds by C++ compilers; although this is not generally supported in C code supporting it here has little cost and some practical benefit (sr 110532). */ #ifdef __cplusplus extern "C" #endif char libdeflate_deflate_compress (void); int main (void) { return libdeflate_deflate_compress (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : ac_cv_lib_deflate_libdeflate_deflate_compress=yes else case e in #( e) ac_cv_lib_deflate_libdeflate_deflate_compress=no ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_deflate_libdeflate_deflate_compress" >&5 printf "%s\n" "$ac_cv_lib_deflate_libdeflate_deflate_compress" >&6; } if test "x$ac_cv_lib_deflate_libdeflate_deflate_compress" = xyes then : : else case e in #( e) libdeflate='missing library' ;; esac fi if test "$libdeflate" = "ok" then : printf "%s\n" "#define HAVE_LIBDEFLATE 1" >>confdefs.h LIBS="-ldeflate $LIBS" private_LIBS="$private_LIBS -ldeflate" static_LIBS="$static_LIBS -ldeflate" else case e in #( e) if test "x$with_libdeflate" != "xcheck" then : cat > config.mk <<'EOF' ifneq ($(MAKECMDGOALS),distclean) $(error Resolve configure error first) endif EOF as_fn_error $? "libdeflate development files not found: $libdeflate You requested libdeflate, but do not have the required header / library files. The source for libdeflate is available from . You may have to adjust search paths in CPPFLAGS and/or LDFLAGS if the header and library are not currently on them. Either configure with --without-libdeflate or resolve this error to build HTSlib." "$LINENO" 5 fi ;; esac fi fi libcurl=disabled if test "$enable_libcurl" != no; then libcurl_devel=ok ac_fn_c_check_header_compile "$LINENO" "curl/curl.h" "ac_cv_header_curl_curl_h" "; " if test "x$ac_cv_header_curl_curl_h" = xyes then : else case e in #( e) libcurl_devel="headers not found" ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for curl_easy_pause in -lcurl" >&5 printf %s "checking for curl_easy_pause in -lcurl... " >&6; } if test ${ac_cv_lib_curl_curl_easy_pause+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_check_lib_save_LIBS=$LIBS LIBS="-lcurl $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. The 'extern "C"' is for builds by C++ compilers; although this is not generally supported in C code supporting it here has little cost and some practical benefit (sr 110532). */ #ifdef __cplusplus extern "C" #endif char curl_easy_pause (void); int main (void) { return curl_easy_pause (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : ac_cv_lib_curl_curl_easy_pause=yes else case e in #( e) ac_cv_lib_curl_curl_easy_pause=no ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_curl_curl_easy_pause" >&5 printf "%s\n" "$ac_cv_lib_curl_curl_easy_pause" >&6; } if test "x$ac_cv_lib_curl_curl_easy_pause" = xyes then : : else case e in #( e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for curl_easy_init in -lcurl" >&5 printf %s "checking for curl_easy_init in -lcurl... " >&6; } if test ${ac_cv_lib_curl_curl_easy_init+y} then : printf %s "(cached) " >&6 else case e in #( e) ac_check_lib_save_LIBS=$LIBS LIBS="-lcurl $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. The 'extern "C"' is for builds by C++ compilers; although this is not generally supported in C code supporting it here has little cost and some practical benefit (sr 110532). */ #ifdef __cplusplus extern "C" #endif char curl_easy_init (void); int main (void) { return curl_easy_init (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO" then : ac_cv_lib_curl_curl_easy_init=yes else case e in #( e) ac_cv_lib_curl_curl_easy_init=no ;; esac fi rm -f core conftest.err conftest.$ac_objext conftest.beam \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS ;; esac fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_curl_curl_easy_init" >&5 printf "%s\n" "$ac_cv_lib_curl_curl_easy_init" >&6; } if test "x$ac_cv_lib_curl_curl_easy_init" = xyes then : libcurl_devel="library is too old (7.18+ required)" else case e in #( e) libcurl_devel="library not found" ;; esac fi ;; esac fi if test "$libcurl_devel" = ok; then printf "%s\n" "#define HAVE_LIBCURL 1" >>confdefs.h libcurl=enabled elif test "$enable_libcurl" = check; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: libcurl not enabled: $libcurl_devel" >&5 printf "%s\n" "$as_me: WARNING: libcurl not enabled: $libcurl_devel" >&2;} else cat > config.mk <<'EOF' ifneq ($(MAKECMDGOALS),distclean) $(error Resolve configure error first) endif EOF as_fn_error $? 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"cannot link or copy $ac_source to $ac_file" "$LINENO" 5 fi ;; :C) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5 printf "%s\n" "$as_me: executing $ac_file commands" >&6;} ;; esac case $ac_file$ac_mode in "mkdir":C) as_dir=cram; as_fn_mkdir_p as_dir=htscodecs/htscodecs; as_fn_mkdir_p as_dir=htscodecs/tests; as_fn_mkdir_p as_dir=test/fuzz; as_fn_mkdir_p as_dir=test/longrefs; as_fn_mkdir_p as_dir=test/tabix; as_fn_mkdir_p ;; esac done # for ac_tag as_fn_exit 0 _ACEOF ac_clean_files=$ac_clean_files_save test $ac_write_fail = 0 || as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5 # configure is writing to config.log, and then calls config.status. # config.status does its own redirection, appending to config.log. # Unfortunately, on DOS this fails, as config.log is still kept open # by configure, so config.status won't be able to write to it; its # output is simply discarded. So we exec the FD to /dev/null, # effectively closing config.log, so it can be properly (re)opened and # appended to by config.status. When coming back to configure, we # need to make the FD available again. if test "$no_create" != yes; then ac_cs_success=: ac_config_status_args= test "$silent" = yes && ac_config_status_args="$ac_config_status_args --quiet" exec 5>/dev/null $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false exec 5>>config.log # Use ||, not &&, to avoid exiting from the if with $? = 1, which # would make configure fail if this is the last instruction. $ac_cs_success || as_fn_exit 1 fi if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 printf "%s\n" "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;} fi pysam-0.23.0/htslib/configure.ac000066400000000000000000000607641475062545500165320ustar00rootroot00000000000000# Configure script for htslib, a C library for high-throughput sequencing data. # # Copyright (C) 2015-2024 Genome Research Ltd. # # Author: John Marshall # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. dnl Process this file with autoconf to produce a configure script AC_INIT([HTSlib], m4_esyscmd_s([./version.sh 2>/dev/null]), [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/]) AC_PREREQ(2.63) dnl This version introduced 4-argument AC_CHECK_HEADER AC_CONFIG_SRCDIR(hts.c) AC_CONFIG_HEADERS(config.h) m4_include([m4/hts_prog_cc_warnings.m4]) m4_include([m4/hts_check_compile_flags_needed.m4]) m4_include([m4/hts_hide_dynamic_syms.m4]) m4_include([m4/pkg.m4]) dnl Copyright notice to be copied into the generated configure script AC_COPYRIGHT([Portions copyright (C) 2020-2024 Genome Research Ltd. This configure script is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.]) dnl Notes to be copied (by autoheader) into the generated config.h.in AH_TOP([/* If you use configure, this file provides @%:@defines reflecting your configuration choices. If you have not run configure, suitable conservative defaults will be used. Autoheader adds a number of items to this template file that are not used by HTSlib: STDC_HEADERS and most HAVE_*_H header file defines are immaterial, as we assume standard ISO C headers and facilities; the PACKAGE_* defines are unused and are overridden by the more accurate PACKAGE_VERSION as computed by the Makefile. */]) dnl Variant of AC_MSG_ERROR that ensures subsequent make(1) invocations fail dnl until the configuration error is resolved and configure is run again. AC_DEFUN([MSG_ERROR], [cat > config.mk <<'EOF' ifneq ($(MAKECMDGOALS),distclean) $(error Resolve configure error first) endif EOF AC_MSG_ERROR([$1], [$2])]) AC_PROG_CC AC_PROG_RANLIB dnl Turn on compiler warnings, if possible HTS_PROG_CC_WARNINGS dnl Flags to treat warnings as errors. These need to be applied to CFLAGS dnl later as they can interfere with some of the tests (notably AC_SEARCH_LIBS) HTS_PROG_CC_WERROR(hts_late_cflags) # HTSlib uses X/Open-only facilities (M_SQRT2 etc, drand48() etc), and # various POSIX functions that are provided by various _POSIX_C_SOURCE values # or by _XOPEN_SOURCE >= 500. It also uses usleep(), which is removed when # _XOPEN_SOURCE >= 700. Additionally, some definitions may require # _XOPEN_SOURCE >= 600 on some platforms (snprintf on MinGW, # PTHREAD_MUTEX_RECURSIVE on some Linux distributions). Hence we set it to 600. # Define _XOPEN_SOURCE unless the user has already done so via $CPPFLAGS etc. AC_CHECK_DECL([_XOPEN_SOURCE], [], [AC_DEFINE([_XOPEN_SOURCE], [600], [Specify X/Open requirements])], []) dnl Check that we have cpuid, and if so run the x86 SIMD checks AC_CHECK_DECLS([__get_cpuid_max, __cpuid_count], [ hts_have_cpuid=yes ], [ hts_have_cpuid=no ], [[#include ]]) AS_IF(test "x$hts_have_cpuid" = "xyes", [ dnl Options for rANS32x16 sse4.1 version - sse4.1 HTS_CHECK_COMPILE_FLAGS_NEEDED([sse4.1], [-msse4.1 -mssse3 -mpopcnt], [AC_LANG_PROGRAM([[ #ifdef __x86_64__ #include "x86intrin.h" #endif ]],[[ #ifdef __x86_64__ __m128i a = _mm_set_epi32(1, 2, 3, 4), b = _mm_set_epi32(4, 3, 2, 1); __m128i c = _mm_shuffle_epi8(_mm_max_epu32(a, b), b); return _mm_popcnt_u32(*((char *) &c)); #endif ]])], [ hts_cflags_sse4="$flags_needed" AC_DEFINE([HAVE_SSSE3],1,[Defined to 1 if rANS source using SSSE3 can be compiled.]) AC_DEFINE([HAVE_POPCNT],1,[Defined to 1 if rANS source using popcnt can be compiled.]) AC_DEFINE([HAVE_SSE4_1],1,[Defined to 1 if rANS source using SSE4.1 can be compiled. ]) dnl Propagate HTSlib's unaligned access preference to htscodecs AH_VERBATIM([UBSAN],[ /* Prevent unaligned access in htscodecs SSE4 rANS codec */ #if defined(HTS_ALLOW_UNALIGNED) && HTS_ALLOW_UNALIGNED == 0 #undef UBSAN #endif]) AC_DEFINE([UBSAN],1,[]) ]) AC_SUBST([hts_cflags_sse4]) dnl Options for rANS32x16 avx2 version HTS_CHECK_COMPILE_FLAGS_NEEDED([avx2], [-mavx2 -mpopcnt], [AC_LANG_PROGRAM([[ #ifdef __x86_64__ #include "x86intrin.h" #endif ]],[[ #ifdef __x86_64__ __m256i a = _mm256_set_epi32(1, 2, 3, 4, 5, 6, 7, 8); __m256i b = _mm256_add_epi32(a, a); long long c = _mm256_extract_epi64(b, 0); return _mm_popcnt_u32((int) c); #endif ]])], [ hts_cflags_avx2="$flags_needed" AC_SUBST([hts_cflags_avx2]) AC_DEFINE([HAVE_POPCNT],1,[Defined to 1 if rANS source using popcnt can be compiled.]) AC_DEFINE([HAVE_AVX2],1,[Defined to 1 if rANS source using AVX2 can be compiled.]) ]) dnl Options for rANS32x16 avx512 version HTS_CHECK_COMPILE_FLAGS_NEEDED([avx512f], [-mavx512f -mpopcnt], [AC_LANG_PROGRAM([[ #ifdef __x86_64__ #include "x86intrin.h" #endif ]],[[ #ifdef __x86_64__ __m512i a = _mm512_set1_epi32(1); __m512i b = _mm512_add_epi32(a, a); __m256i c = _mm512_castsi512_si256(b); __m256i d = _mm512_extracti64x4_epi64(a, 1); return _mm_popcnt_u32(*((char *) &c)) + (*(char *) &d); #endif ]])], [ hts_cflags_avx512="$flags_needed" AC_SUBST([hts_cflags_avx512]) AC_DEFINE([HAVE_POPCNT],1,[Defined to 1 if rANS source using popcnt can be compiled.]) AC_DEFINE([HAVE_AVX512],1,[Defined to 1 if rANS source using AVX512F can be compiled.]) ]) dnl Check for working __builtin_cpu_supports (ssse3 is broken on some clangs) AC_MSG_CHECKING([for working __builtin_cpu_supports("ssse3")]) AC_LINK_IFELSE([AC_LANG_PROGRAM([],[ if (__builtin_cpu_supports("ssse3")) { return 0; } ])], [ AC_MSG_RESULT([yes]) AC_DEFINE([HAVE_BUILTIN_CPU_SUPPORT_SSSE3], 1, [Defined to 1 if __builtin_cpu_supports("ssse3") works]) ], [ AC_MSG_RESULT([no]) ]) dnl Check for function attribute used in conjunction with __builtin_cpu_supports AC_MSG_CHECKING([for __attribute__((target))]) AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[ __attribute__((target("ssse3"))) int zero(void) { return 0; } ]], [[zero();]])], [ AC_MSG_RESULT([yes]) AC_DEFINE([HAVE_ATTRIBUTE_TARGET], 1, [Define if __attribute__((target(...))) is available.]) ], [ AC_MSG_RESULT([no]) ]) ]) dnl End of AS_IF(hts_have_cpuid) dnl Avoid chicken-and-egg problem where pkg-config supplies the dnl PKG_PROG_PKG_CONFIG macro, but we want to use it to check dnl for pkg-config... m4_ifdef([PKG_PROG_PKG_CONFIG], [PKG_PROG_PKG_CONFIG], [PKG_CONFIG=""]) need_crypto=no pc_requires= static_LDFLAGS=$LDFLAGS static_LIBS='-lpthread -lz -lm' private_LIBS=$LDFLAGS AC_ARG_ENABLE([versioned-symbols], [AS_HELP_STRING([--disable-versioned-symbols], [disable versioned symbols in shared library])], [], [enable_versioned_symbols=yes]) AC_ARG_ENABLE([bz2], [AS_HELP_STRING([--disable-bz2], [omit support for BZ2-compressed CRAM files])], [], [enable_bz2=yes]) AC_ARG_ENABLE([gcs], [AS_HELP_STRING([--enable-gcs], [support Google Cloud Storage URLs])], [], [enable_gcs=check]) AC_SYS_LARGEFILE AC_ARG_ENABLE([libcurl], [AS_HELP_STRING([--enable-libcurl], [enable libcurl-based support for http/https/etc URLs])], [], [enable_libcurl=check]) AC_ARG_ENABLE([lzma], [AS_HELP_STRING([--disable-lzma], [omit support for LZMA-compressed CRAM files])], [], [enable_lzma=yes]) AC_ARG_ENABLE([plugins], [AS_HELP_STRING([--enable-plugins], [enable separately-compiled plugins for file access])], [], [enable_plugins=no]) AC_SUBST(enable_plugins) AC_ARG_WITH([external-htscodecs], [AS_HELP_STRING([--with-external-htscodecs], [get htscodecs functions from a shared library])], [], [with_external_htscodecs=no]) AC_SUBST(with_external_htscodecs) AC_ARG_WITH([libdeflate], [AS_HELP_STRING([--with-libdeflate], [use libdeflate for faster crc and deflate algorithms])], [], [with_libdeflate=check]) AC_ARG_WITH([plugin-dir], [AS_HELP_STRING([--with-plugin-dir=DIR], [plugin installation location [LIBEXECDIR/htslib]])], [case $withval in yes|no) MSG_ERROR([no directory specified for --with-plugin-dir]) ;; esac], [with_plugin_dir='$(libexecdir)/htslib']) AC_SUBST([plugindir], $with_plugin_dir) AC_ARG_WITH([plugin-path], [AS_HELP_STRING([--with-plugin-path=PATH], [default HTS_PATH plugin search path [PLUGINDIR]])], [case $withval in yes) MSG_ERROR([no path specified for --with-plugin-path]) ;; no) with_plugin_path= ;; esac], [with_plugin_path=$with_plugin_dir]) AC_SUBST([pluginpath], $with_plugin_path) AC_ARG_ENABLE([s3], [AS_HELP_STRING([--enable-s3], [support Amazon AWS S3 URLs])], [], [enable_s3=check]) basic_host=${host_alias:-unknown-`uname -s`} AC_MSG_CHECKING([shared library type for $basic_host]) case $basic_host in *-cygwin* | *-CYGWIN*) host_result="Cygwin DLL" PLATFORM=CYGWIN PLUGIN_EXT=.cygdll ;; *-darwin* | *-Darwin*) host_result="Darwin dylib" PLATFORM=Darwin PLUGIN_EXT=.bundle ;; *-msys* | *-MSYS* | *-mingw* | *-MINGW*) host_result="MSYS dll" PLATFORM=MSYS PLUGIN_EXT=.dll # This also sets __USE_MINGW_ANSI_STDIO which in turn makes PRId64, # %lld and %z printf formats work. It also enforces the snprintf to # be C99 compliant so it returns the correct values (in kstring.c). # Now set by default, so no need to do it here. # CPPFLAGS="$CPPFLAGS -D_XOPEN_SOURCE=600" ;; *) host_result="plain .so" PLATFORM=default PLUGIN_EXT=.so ;; esac AC_MSG_RESULT([$host_result]) AC_SUBST([PLATFORM]) dnl Check for versioned symbol support dnl Only try for .so shared libraries as other types won't work AS_IF([test x"$PLATFORM" = xdefault && test x"$enable_versioned_symbols" = xyes], [AC_CACHE_CHECK([whether the linker supports versioned symbols], [hts_cv_have_versioned_symbols], [ save_LDFLAGS=$LDFLAGS LDFLAGS="-Wl,-version-script,$srcdir/htslib.map $LDFLAGS" AC_LINK_IFELSE([AC_LANG_PROGRAM()], [hts_cv_have_versioned_symbols=yes], [hts_cv_have_versioned_symbols=no]) LDFLAGS=$save_LDFLAGS ]) AS_IF([test "x$hts_cv_have_versioned_symbols" = xyes],[ VERSION_SCRIPT_LDFLAGS='-Wl,-version-script,$(srcprefix)htslib.map' AC_SUBST([VERSION_SCRIPT_LDFLAGS]) ]) ]) dnl Try to get more control over which symbols are exported in the shared dnl library. HTS_HIDE_DYNAMIC_SYMBOLS dnl FIXME This pulls in dozens of standard header checks AC_FUNC_MMAP AC_CHECK_FUNCS([gmtime_r fsync drand48 srand48_deterministic]) # Darwin has a dubious fdatasync() symbol, but no declaration in AC_CHECK_DECL([fdatasync(int)], [AC_CHECK_FUNCS(fdatasync)]) AC_MSG_CHECKING([for __attribute__((constructor))]) AC_LINK_IFELSE([AC_LANG_PROGRAM([[ static __attribute__((constructor)) void noop(void) {} ]], [])], [ AC_MSG_RESULT([yes]) AC_DEFINE([HAVE_ATTRIBUTE_CONSTRUCTOR], 1, [Define if __attribute__((constructor)) is available.]) ], [AC_MSG_RESULT([no])]) AC_MSG_CHECKING([for clock_gettime with CLOCK_PROCESS_CPUTIME_ID]) AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include ]], [[ struct timespec ts; clock_gettime(CLOCK_PROCESS_CPUTIME_ID, &ts); ]])], [ AC_MSG_RESULT([yes]) AC_DEFINE([HAVE_CLOCK_GETTIME_CPUTIME], 1, [Define if clock_gettime exists and accepts CLOCK_PROCESS_CPUTIME_ID.]) ], [AC_MSG_RESULT([no])]) if test $enable_plugins != no; then AC_SEARCH_LIBS([dlsym], [dl], [], [MSG_ERROR([dlsym() not found Plugin support requires dynamic linking facilities from the operating system. Either configure with --disable-plugins or resolve this error to build HTSlib.])]) # Check if the compiler understands -rdynamic # TODO Test whether this is required and/or needs tweaking per-platform HTS_TEST_CC_C_LD_FLAG([-rdynamic],[rdynamic_flag]) AS_IF([test x"$rdynamic_flag" != "xno"], [LDFLAGS="$LDFLAGS $rdynamic_flag" static_LDFLAGS="$static_LDFLAGS $rdynamic_flag"]) case "$ac_cv_search_dlsym" in -l*) static_LIBS="$static_LIBS $ac_cv_search_dlsym" ;; esac AC_DEFINE([ENABLE_PLUGINS], 1, [Define if HTSlib should enable plugins.]) AC_SUBST([PLUGIN_EXT]) AC_DEFINE_UNQUOTED([PLUGIN_EXT], ["$PLUGIN_EXT"], [Platform-dependent plugin filename extension.]) fi AC_SEARCH_LIBS([log], [m], [], [MSG_ERROR([log() not found HTSLIB requires a working floating-point math library. FAILED. This error must be resolved in order to build HTSlib successfully.])]) zlib_devel=ok dnl Set a trivial non-empty INCLUDES to avoid excess default includes tests AC_CHECK_HEADER([zlib.h], [], [zlib_devel=missing], [;]) AC_CHECK_LIB(z, inflate, [], [zlib_devel=missing]) if test $zlib_devel != ok; then MSG_ERROR([zlib development files not found HTSlib uses compression routines from the zlib library . Building HTSlib requires zlib development files to be installed on the build machine; you may need to ensure a package such as zlib1g-dev (on Debian or Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions or Cygwin) is installed. FAILED. This error must be resolved in order to build HTSlib successfully.]) fi dnl connect() etc. fns are in libc on linux, but libsocket on illumos/Solaris AC_SEARCH_LIBS([recv], [socket ws2_32], [ if test "$ac_cv_search_recv" != "none required" then static_LIBS="$static_LIBS $ac_cv_search_recv" fi], dnl on MinGW-i686, checking recv() linking requires an annotated declaration [AC_MSG_CHECKING([for library containing recv using declaration]) LIBS="-lws2_32 $LIBS" AC_LINK_IFELSE( [AC_LANG_PROGRAM([[#include ]], [[recv(0, 0, 0, 0);]])], [AC_MSG_RESULT([-lws2_32]) static_LIBS="$static_LIBS -lws2_32"], [AC_MSG_RESULT([no]) MSG_ERROR([unable to find the recv() function])])]) if test "$enable_bz2" != no; then bz2_devel=ok AC_CHECK_HEADER([bzlib.h], [], [bz2_devel=missing], [;]) AC_CHECK_LIB([bz2], [BZ2_bzBuffToBuffCompress], [], [bz2_devel=missing]) if test $bz2_devel != ok; then MSG_ERROR([libbzip2 development files not found The CRAM format may use bzip2 compression, which is implemented in HTSlib by using compression routines from libbzip2 . Building HTSlib requires libbzip2 development files to be installed on the build machine; you may need to ensure a package such as libbz2-dev (on Debian or Ubuntu Linux) or bzip2-devel (on RPM-based Linux distributions or Cygwin) is installed. Either configure with --disable-bz2 (which will make some CRAM files produced elsewhere unreadable) or resolve this error to build HTSlib.]) fi dnl Unfortunately the 'bzip2' package-cfg module is not standard. dnl Redhat/Fedora has it; Debian/Ubuntu does not. if test -n "$PKG_CONFIG" && "$PKG_CONFIG" --exists bzip2; then pc_requires="$pc_requires bzip2" else private_LIBS="$private_LIBS -lbz2" fi static_LIBS="$static_LIBS -lbz2" fi if test "$enable_lzma" != no; then lzma_devel=ok AC_CHECK_HEADERS([lzma.h], [], [lzma_devel=header-missing], [;]) AC_CHECK_LIB([lzma], [lzma_easy_buffer_encode], [], [lzma_devel=missing]) if test $lzma_devel = missing; then MSG_ERROR([liblzma development files not found The CRAM format may use LZMA2 compression, which is implemented in HTSlib by using compression routines from liblzma . Building HTSlib requires liblzma development files to be installed on the build machine; you may need to ensure a package such as liblzma-dev (on Debian or Ubuntu Linux), xz-devel (on RPM-based Linux distributions or Cygwin), or xz (via Homebrew on macOS) is installed; or build XZ Utils from source. Either configure with --disable-lzma (which will make some CRAM files produced elsewhere unreadable) or resolve this error to build HTSlib.]) fi pc_requires="$pc_requires liblzma" static_LIBS="$static_LIBS -llzma" fi AS_IF([test "x$with_external_htscodecs" != "xno"], [libhtscodecs=ok AC_CHECK_HEADER([htscodecs/rANS_static4x16.h],[], [libhtscodecs='missing header'],[;]) AC_CHECK_LIB([htscodecs],[rans_compress_bound_4x16], [:],[libhtscodecs='missing library']) AS_IF([test "$libhtscodecs" = "ok"], [AC_DEFINE([HAVE_EXTERNAL_LIBHTSCODECS], 1, [Define if using an external libhtscodecs]) LIBS="-lhtscodecs $LIBS" private_LIBS="-lhtscodecs $private_LIBS" static_LIBS="-lhtscodecs $static_LIBS" selected_htscodecs_mk="htscodecs_external.mk"], [MSG_ERROR([libhtscodecs development files not found: $libhtscodecs You asked to use an external htscodecs library, but do not have the required header / library files. You either need to supply these and if necessary set CPPFLAGS and LDFLAGS so the compiler can find them; or configure using --without-external-htscodecs to build the required functions from the htscodecs submodule. ])])], [AC_MSG_CHECKING([whether htscodecs files are present]) AS_IF([test -e "$srcdir/htscodecs/htscodecs/rANS_static4x16.h"], [AC_MSG_RESULT([yes]) selected_htscodecs_mk="htscodecs_bundled.mk"], [AC_MSG_RESULT([no]) AS_IF([test -e "$srcdir/.git"], [MSG_ERROR([htscodecs submodule files not present. HTSlib uses some functions from the htscodecs project, which is normally included as a submodule. Try running: git submodule update --init --recursive in the top-level htslib directory to update it, and then re-run configure. ])], [MSG_ERROR([htscodecs submodule files not present. You have an incomplete distribution. Please try downloading one of the official releases from https://www.htslib.org ])])])]) AS_IF([test "x$with_libdeflate" != "xno"], [libdeflate=ok AC_CHECK_HEADER([libdeflate.h],[],[libdeflate='missing header'],[;]) AC_CHECK_LIB([deflate], [libdeflate_deflate_compress],[:],[libdeflate='missing library']) AS_IF([test "$libdeflate" = "ok"], [AC_DEFINE([HAVE_LIBDEFLATE], 1, [Define if libdeflate is available.]) LIBS="-ldeflate $LIBS" private_LIBS="$private_LIBS -ldeflate" static_LIBS="$static_LIBS -ldeflate"], [AS_IF([test "x$with_libdeflate" != "xcheck"], [MSG_ERROR([libdeflate development files not found: $libdeflate You requested libdeflate, but do not have the required header / library files. The source for libdeflate is available from . You may have to adjust search paths in CPPFLAGS and/or LDFLAGS if the header and library are not currently on them. Either configure with --without-libdeflate or resolve this error to build HTSlib.])])])]) libcurl=disabled if test "$enable_libcurl" != no; then libcurl_devel=ok AC_CHECK_HEADER([curl/curl.h], [], [libcurl_devel="headers not found"], [;]) AC_CHECK_LIB([curl], [curl_easy_pause], [:], [AC_CHECK_LIB([curl], [curl_easy_init], [libcurl_devel="library is too old (7.18+ required)"], [libcurl_devel="library not found"])]) if test "$libcurl_devel" = ok; then AC_DEFINE([HAVE_LIBCURL], 1, [Define if libcurl file access is enabled.]) libcurl=enabled elif test "$enable_libcurl" = check; then AC_MSG_WARN([libcurl not enabled: $libcurl_devel]) else MSG_ERROR([libcurl $libcurl_devel Support for HTTPS and other SSL-based URLs requires routines from the libcurl library . Building HTSlib with libcurl enabled requires libcurl development files to be installed on the build machine; you may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions or Cygwin) is installed. Either configure with --disable-libcurl or resolve this error to build HTSlib.]) fi dnl -lcurl is only needed for static linking if hfile_libcurl is not a plugin if test "$libcurl" = enabled ; then if test "$enable_plugins" != yes ; then static_LIBS="$static_LIBS -lcurl" fi fi fi AC_SUBST([libcurl]) gcs=disabled if test "$enable_gcs" != no; then if test $libcurl = enabled; then AC_DEFINE([ENABLE_GCS], 1, [Define if HTSlib should enable GCS support.]) gcs=enabled else case "$enable_gcs" in check) AC_MSG_WARN([GCS support not enabled: requires libcurl support]) ;; *) MSG_ERROR([GCS support not enabled Support for Google Cloud Storage URLs requires libcurl support to be enabled in HTSlib. Configure with --enable-libcurl in order to use GCS URLs.]) ;; esac fi fi AC_SUBST([gcs]) s3=disabled if test "$enable_s3" != no; then if test $libcurl = enabled; then s3=enabled need_crypto="$enable_s3" else case "$enable_s3" in check) AC_MSG_WARN([S3 support not enabled: requires libcurl support]) ;; *) MSG_ERROR([S3 support not enabled Support for Amazon AWS S3 URLs requires libcurl support to be enabled in HTSlib. Configure with --enable-libcurl in order to use S3 URLs.]) ;; esac fi fi CRYPTO_LIBS= if test $need_crypto != no; then AC_CHECK_FUNC([CCHmac], [AC_DEFINE([HAVE_COMMONCRYPTO], 1, [Define if you have the Common Crypto library.])], [save_LIBS=$LIBS AC_SEARCH_LIBS([HMAC], [crypto], [AC_DEFINE([HAVE_HMAC], 1, [Define if you have libcrypto-style HMAC().]) case "$ac_cv_search_HMAC" in -l*) CRYPTO_LIBS=$ac_cv_search_HMAC ;; esac], [case "$need_crypto" in check) AC_MSG_WARN([S3 support not enabled: requires SSL development files]) s3=disabled ;; *) MSG_ERROR([SSL development files not found Support for AWS S3 URLs requires routines from an SSL library. Building HTSlib with libcurl enabled requires SSL development files to be installed on the build machine; you may need to ensure a package such as libgnutls-dev, libnss3-dev, or libssl-dev (on Debian or Ubuntu Linux, corresponding to the libcurl4-*-dev package installed), or openssl-devel (on RPM-based Linux distributions or Cygwin) is installed. Either configure with --disable-s3 or resolve this error to build HTSlib.]) ;; esac]) LIBS=$save_LIBS]) dnl Only need to add to static_LIBS if not building as a plugin if test "$enable_plugins" != yes ; then static_LIBS="$static_LIBS $CRYPTO_LIBS" fi fi dnl Look for regcomp in various libraries (needed on windows/mingw). AC_SEARCH_LIBS(regcomp, regex, [libregex=needed], []) dnl Look for PTHREAD_MUTEX_RECURSIVE. dnl This is normally in pthread.h except on some broken glibc implementations. dnl Now set by default dnl AC_CHECK_DECL(PTHREAD_MUTEX_RECURSIVE, [], [AC_DEFINE([_XOPEN_SOURCE],[600], [Needed for PTHREAD_MUTEX_RECURSIVE])], [[#include ]]) if test "$s3" = enabled ; then AC_DEFINE([ENABLE_S3], 1, [Define if HTSlib should enable S3 support.]) fi dnl Apply value from HTS_PROG_CC_WERROR (if set) AS_IF([test "x$hts_late_cflags" != x],[CFLAGS="$CFLAGS $hts_late_cflags"]) AC_SUBST([s3]) AC_SUBST([CRYPTO_LIBS]) AC_SUBST([pc_requires]) AC_SUBST([private_LIBS]) AC_SUBST([static_LDFLAGS]) AC_SUBST([static_LIBS]) AC_CONFIG_FILES([config.mk htslib.pc.tmp:htslib.pc.in]) AC_CONFIG_LINKS([htscodecs.mk:$selected_htscodecs_mk]) if test "$srcdir" != .; then # Set up for a separate build directory. As HTSlib uses a non-recursive # makefile, we need to create additional build subdirectories explicitly. AC_CONFIG_LINKS([Makefile:Makefile htslib.mk:htslib.mk]) AC_CONFIG_FILES([htslib_vars.mk:builddir_vars.mk.in]) AC_CONFIG_COMMANDS([mkdir], [AS_MKDIR_P([cram]) AS_MKDIR_P([htscodecs/htscodecs]) AS_MKDIR_P([htscodecs/tests]) AS_MKDIR_P([test/fuzz]) AS_MKDIR_P([test/longrefs]) AS_MKDIR_P([test/tabix])]) fi # @HTSDIRslash_if_relsrcdir@ will be empty when $srcdir is absolute case "$srcdir" in /*) HTSDIRslash_if_relsrcdir= ;; *) HTSDIRslash_if_relsrcdir='$(HTSDIR)/' ;; esac AC_SUBST([HTSDIRslash_if_relsrcdir]) AC_OUTPUT pysam-0.23.0/htslib/cram/000077500000000000000000000000001475062545500151515ustar00rootroot00000000000000pysam-0.23.0/htslib/cram/README000066400000000000000000000201521475062545500160310ustar00rootroot00000000000000CRAM encoding internals ======================= A quick summary of functions involved. The encoder works by accumulating a bunch of BAM records (via the cram_put_bam_seq function), and at a certain point (eg counter of records, or switching reference) the array of BAM records it turned into a container, which in turn creates slices, holding CRAM data-series in blocks. The function that turns an array of BAM objects into the container is below. cram_encode_container func: Validate references MD5 against header, unless no_ref mode If embed_ref <= 1, fetch ref Switch to embed_ref=2 if failed Foreach slice: If embed_ref == 2 call cram_generate_reference if failed switch to no_ref mode Foreach sequence call process_one_read to append BAM onto each data series (DS) call cram_stats_add for each DS to gather metrics call cram_encode_aux # We now have cram DS, per slice call cram_encoder_init, per DS (based on cram_stats_add data) Foreach slice: call cram_encode_slice to turn DS to blocks call cram_compess_slice call cram_encode_compression_header Threading --------- CRAM can be multi-threaded, but this brings complications. The above function is the main CPU user, so it is this bit which can be executed in parallel from multiple threads. To understand this we need to now look at how the primary loop works when writing a CRAM: Encoding main thread: repeatedly calls cram_put_bam_seq calls cram_new_container on first time through to initialise calls cram_next_container when current is full or we need to flush calls cram_flush_container_mt to flush last container pushes BAM object onto current container If non-threaded, cram_flush_container_mt does: call cram_flush_container call cram_encode_container to go from BAM to CRAM data-series call cram_flush_container2 (writes it out) If threaded, cram_flush_container_mt does: Main: Dispatch cram_flush_thread job Thread: call cram_encode_container to go from BAM to CRAM data-series Main: Call cram_flush_result to drain queue of encoded containers Main: Call cram_flush_container2 (writes it out); Decisions on when to create new containers, detection of sorted vs unsorted, switching to multi-seq mode, etc occur at the main thread in cram_put_bam_seq. We can change our mind on container parameters at any point up until the cram_encode_container call. At that point these parameters get baked into a container compression header and all data-series generated need to be in sync with the parameters. It is possible that some parameter changes can get detected while encoding the container, as it is there where we fetch references. Eg the need to enable embedded reference or switch to non-ref mode. While encoding a container, we can change the parameters for *this* container, and we can also set the default parameter for subsequent new parameters via the global cram fd to avoid spamming attempts to load a reference which doesn't exist, but we cannot change other containers that are being processed in parallel. They'll fend for themselves. References ---------- To avoid spamming the reference servers, there is a shared cache of references being currently used by all the worker threads (leading to confusing terminology of reference-counting of references). So each container fetches its section of reference, but the memory for that is handled via its own layer. The shared references and ref meta-data is held in cram_fd -> refs (a refs_t pointer): // References structure. struct refs_t { string_alloc_t *pool; // String pool for holding filenames and SN vals khash_t(refs) *h_meta; // ref_entry*, index by name ref_entry **ref_id; // ref_entry*, index by ID int nref; // number of ref_entry char *fn; // current file opened BGZF *fp; // and the hFILE* to go with it. int count; // how many cram_fd sharing this refs struct pthread_mutex_t lock; // Mutex for multi-threaded updating ref_entry *last; // Last queried sequence int last_id; // Used in cram_ref_decr_locked to delay free }; Within this, ref_entry is the per-reference information: typedef struct ref_entry { char *name; char *fn; int64_t length; int64_t offset; int bases_per_line; int line_length; int64_t count; // for shared references so we know to dealloc seq char *seq; mFILE *mf; int is_md5; // Reference comes from a raw seq found by MD5 int validated_md5; } ref_entry; Sharing of references to track use between threads is via cram_ref_incr* and cram_ref_decr* (which locked and unlocked variants). We free a reference when the usage count hits zero. To avoid spamming discard and reload in single-thread creation of a pos-sorted CRAM, we keep track of the last reference in cram_fd and delay discard by one loop iteration. There are complexities here around whether the references come from a single ref.fa file, are from a local MD5sum cache with one file per reference (mmapped), or whether they're fetched from some remote REF_PATH query such as the EBI. (This later case typically downloads to a local md5 based ref-cache first and mmaps from there.) The refs struct start off by being populated from the SAM header. We have M5 tag and name known, maybe a filename, but length is 0 and seq is NULL. This is done by cram_load_reference: cram_load_reference (cram_fd, filename): if filename non-NULL call refs_load_fai Populates ref_entry with filename, name, length, line-len, etc sanitise_SQ_lines If no refs loaded call refs_from_header populates ref_entry with name. Sets length=0 as marker for not-yet-loaded The main interface used from the code is cram_get_ref(). It takes a reference ID, start and end coordinate and returns a pointer to the relevant sub-sequence. cram_get_ref: r = fd->refs->ref_id[id]; // current ref call cram_populate_ref if stored length is 0 (ie ref.fa set) search REF_PATH / REF_CACHE call bgzf_open if local_path call open_path_mfile otherwise copy to local REF_CACHE if required (eg remote fetch) If start = 1 and end = ref-length If ref seq unknown call cram_ref_load to load entire ref and use that If ref seq now known, return it // Otherwise known via .fai or we've errored by now. call load_ref_portion to return a sub-seq from index fasta The encoder asks for the entire reference rather than a small portion of it as we're usually encoding a large amount. The decoder may be dealing with small range queries, so it only asks for the relevant sub-section of reference as specified in the cram slice headers. TODO ==== - Multi-ref mode is enabled when we have too many small containers in a row. Instead of firing off new containers when we switch reference, we could always make a new container after N records, separating off M <= N to make the container such that all M are the same reference, and shuffling any remaining N-M down as the start of the next. This means we can detect how many new containers we would create, and enable multi-ref mode straight away rather than keeping a recent history of how many small containers we've emitted. - The cache of references currently being used is a better place to track the global embed-ref and non-ref logic. Better than cram_fd. Cram_fd is a one-way change, as once we enable non-ref we'll stick with it. However if it was per-ref in the ref-cache then we'd probe and try each reference once, and then all new containers for that ref would honour the per-ref parameters. So a single missing reference in the middle of a large file wouldn't change behaviour for all subsequence references. Optionally we could still do meta-analysis on how many references are failing, and switch the global cram_fd params to avoid repeated testing of reference availability if it's becoming obvious that none of them are known. pysam-0.23.0/htslib/cram/cram.h000066400000000000000000000045641475062545500162550ustar00rootroot00000000000000/* Copyright (c) 2012-2013, 2015, 2018 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /*! \file * CRAM interface. * * Consider using the higher level hts_*() API for programs that wish to * be file format agnostic (see htslib/hts.h). * * This API should be used for CRAM specific code. The specifics of the * public API are implemented in cram_io.h, cram_encode.h and cram_decode.h * although these should not be included directly (use this file instead). */ #ifndef CRAM_ALL_H #define CRAM_ALL_H #include "cram_samtools.h" #include "../header.h" #include "cram_structs.h" #include "cram_io.h" #include "cram_encode.h" #include "cram_decode.h" #include "cram_stats.h" #include "cram_codecs.h" #include "cram_index.h" // Validate against the external cram.h, // // This contains duplicated portions from cram_io.h and cram_structs.h, // so we want to ensure that the prototypes match. #include "../htslib/cram.h" #endif pysam-0.23.0/htslib/cram/cram_codecs.c000066400000000000000000003646341475062545500175770ustar00rootroot00000000000000/* Copyright (c) 2012-2021,2023 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /* * FIXME: add checking of cram_external_type to return NULL on unsupported * {codec,type} tuples. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION #include "../fuzz_settings.h" #endif #include "../htslib/hts_endian.h" #if defined(HAVE_EXTERNAL_LIBHTSCODECS) #include #include #include #else #include "../htscodecs/htscodecs/varint.h" #include "../htscodecs/htscodecs/pack.h" #include "../htscodecs/htscodecs/rle.h" #endif #include "cram.h" /* * --------------------------------------------------------------------------- * Block bit-level I/O functions. * All defined static here to promote easy inlining by the compiler. */ #if 0 /* Get a single bit, MSB first */ static signed int get_bit_MSB(cram_block *block) { unsigned int val; if (block->byte > block->alloc) return -1; val = block->data[block->byte] >> block->bit; if (--block->bit == -1) { block->bit = 7; block->byte++; //printf("(%02X)", block->data[block->byte]); } //printf("-B%d-", val&1); return val & 1; } #endif /* * Count number of successive 0 and 1 bits */ static int get_one_bits_MSB(cram_block *block) { int n = 0, b; if (block->byte >= block->uncomp_size) return -1; do { b = block->data[block->byte] >> block->bit; if (--block->bit == -1) { block->bit = 7; block->byte++; if (block->byte == block->uncomp_size && (b&1)) return -1; } n++; } while (b&1); return n-1; } static int get_zero_bits_MSB(cram_block *block) { int n = 0, b; if (block->byte >= block->uncomp_size) return -1; do { b = block->data[block->byte] >> block->bit; if (--block->bit == -1) { block->bit = 7; block->byte++; if (block->byte == block->uncomp_size && !(b&1)) return -1; } n++; } while (!(b&1)); return n-1; } #if 0 /* Stores a single bit */ static void store_bit_MSB(cram_block *block, unsigned int bit) { if (block->byte >= block->alloc) { block->alloc = block->alloc ? block->alloc*2 : 1024; block->data = realloc(block->data, block->alloc); } if (bit) block->data[block->byte] |= (1 << block->bit); if (--block->bit == -1) { block->bit = 7; block->byte++; block->data[block->byte] = 0; } } #endif #if 0 /* Rounds to the next whole byte boundary first */ static void store_bytes_MSB(cram_block *block, char *bytes, int len) { if (block->bit != 7) { block->bit = 7; block->byte++; } while (block->byte + len >= block->alloc) { block->alloc = block->alloc ? block->alloc*2 : 1024; block->data = realloc(block->data, block->alloc); } memcpy(&block->data[block->byte], bytes, len); block->byte += len; } #endif /* Local optimised copy for inlining */ static inline int64_t get_bits_MSB(cram_block *block, int nbits) { uint64_t val = 0; int i; #if 0 // Fits within the current byte */ if (nbits <= block->bit+1) { val = (block->data[block->byte]>>(block->bit-(nbits-1))) & ((1<bit -= nbits) == -1) { block->bit = 7; block->byte++; } return val; } // partial first byte val = block->data[block->byte] & ((1<<(block->bit+1))-1); nbits -= block->bit+1; block->bit = 7; block->byte++; // whole middle bytes while (nbits >= 8) { val = (val << 8) | block->data[block->byte++]; nbits -= 8; } val <<= nbits; val |= (block->data[block->byte]>>(block->bit-(nbits-1))) & ((1<bit -= nbits; return val; #endif #if 0 /* Inefficient implementation! */ //printf("{"); for (i = 0; i < nbits; i++) //val = (val << 1) | get_bit_MSB(block); GET_BIT_MSB(block, val); #endif #if 1 /* Combination of 1st two methods */ if (nbits <= block->bit+1) { val = (block->data[block->byte]>>(block->bit-(nbits-1))) & ((1<bit -= nbits) == -1) { block->bit = 7; block->byte++; } return val; } switch(nbits) { // case 15: GET_BIT_MSB(block, val); // fall through // case 14: GET_BIT_MSB(block, val); // fall through // case 13: GET_BIT_MSB(block, val); // fall through // case 12: GET_BIT_MSB(block, val); // fall through // case 11: GET_BIT_MSB(block, val); // fall through // case 10: GET_BIT_MSB(block, val); // fall through // case 9: GET_BIT_MSB(block, val); // fall through case 8: GET_BIT_MSB(block, val); // fall through case 7: GET_BIT_MSB(block, val); // fall through case 6: GET_BIT_MSB(block, val); // fall through case 5: GET_BIT_MSB(block, val); // fall through case 4: GET_BIT_MSB(block, val); // fall through case 3: GET_BIT_MSB(block, val); // fall through case 2: GET_BIT_MSB(block, val); // fall through case 1: GET_BIT_MSB(block, val); break; default: for (i = 0; i < nbits; i++) //val = (val << 1) | get_bit_MSB(block); GET_BIT_MSB(block, val); } #endif //printf("=0x%x}", val); return val; } /* * Can store up to 24-bits worth of data encoded in an integer value * Possibly we'd want to have a less optimal store_bits function when dealing * with nbits > 24, but for now we assume the codes generated are never * that big. (Given this is only possible with 121392 or more * characters with exactly the correct frequency distribution we check * for it elsewhere.) */ static int store_bits_MSB(cram_block *block, uint64_t val, int nbits) { //fprintf(stderr, " store_bits: %02x %d\n", val, nbits); /* * Use slow mode until we tweak the huffman generator to never generate * codes longer than 24-bits. */ unsigned int mask; if (block->byte+8 >= block->alloc) { if (block->byte) { block->alloc *= 2; block->data = realloc(block->data, block->alloc + 8); if (!block->data) return -1; } else { block->alloc = 1024; block->data = realloc(block->data, block->alloc + 8); if (!block->data) return -1; block->data[0] = 0; // initialise first byte of buffer } } /* fits in current bit-field */ if (nbits <= block->bit+1) { block->data[block->byte] |= (val << (block->bit+1-nbits)); if ((block->bit-=nbits) == -1) { block->bit = 7; block->byte++; block->data[block->byte] = 0; } return 0; } block->data[block->byte] |= (val >> (nbits -= block->bit+1)); block->bit = 7; block->byte++; block->data[block->byte] = 0; mask = 1<<(nbits-1); do { if (val & mask) block->data[block->byte] |= (1 << block->bit); if (--block->bit == -1) { block->bit = 7; block->byte++; block->data[block->byte] = 0; } mask >>= 1; } while(--nbits); return 0; } /* * Returns the next 'size' bytes from a block, or NULL if insufficient * data left.This is just a pointer into the block data and not an * allocated object, so do not free the result. */ static char *cram_extract_block(cram_block *b, int size) { char *cp = (char *)b->data + b->idx; b->idx += size; if (b->idx > b->uncomp_size) return NULL; return cp; } /* * --------------------------------------------------------------------------- * EXTERNAL * * In CRAM 3.0 and earlier, E_EXTERNAL use the data type to determine the * size of the object being returned. This type is hard coded in the * spec document (changing from uint32 to uint64 requires a spec change) * and there is no data format introspection so implementations have * to determine which size to use based on version numbers. It also * doesn't support signed data. * * With CRAM 4.0 onwards the size and sign of the data is no longer stated * explicitly in the specification. Instead EXTERNAL is replaced by three * new encodings, for bytes and signed / unsigned integers which used a * variable sized encoding. * * For simplicity we use the same encode and decode functions for * bytes (CRAM4) and external (CRAM3). Given we already had code to * replace codec + type into a function pointer it makes little * difference how we ended up at that function. However we disallow * this codec to operate on integer data for CRAM4 onwards. */ int cram_external_decode_int(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { char *cp; cram_block *b; /* Find the external block */ b = cram_get_block_by_id(slice, c->u.external.content_id); if (!b) return *out_size?-1:0; cp = (char *)b->data + b->idx; // E_INT and E_LONG are guaranteed single item queries int err = 0; *(int32_t *)out = c->vv->varint_get32(&cp, (char *)b->data + b->uncomp_size, &err); b->idx = cp - (char *)b->data; *out_size = 1; return err ? -1 : 0; } int cram_external_decode_long(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { char *cp; cram_block *b; /* Find the external block */ b = cram_get_block_by_id(slice, c->u.external.content_id); if (!b) return *out_size?-1:0; cp = (char *)b->data + b->idx; // E_INT and E_LONG are guaranteed single item queries int err = 0; *(int64_t *)out = c->vv->varint_get64(&cp, (char *)b->data + b->uncomp_size, &err); b->idx = cp - (char *)b->data; *out_size = 1; return err ? -1 : 0; } int cram_external_decode_char(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { char *cp; cram_block *b; /* Find the external block */ b = cram_get_block_by_id(slice, c->u.external.content_id); if (!b) return *out_size?-1:0; cp = cram_extract_block(b, *out_size); if (!cp) return -1; if (out) memcpy(out, cp, *out_size); return 0; } static int cram_external_decode_block(cram_slice *slice, cram_codec *c, cram_block *in, char *out_, int *out_size) { char *cp; cram_block *out = (cram_block *)out_; cram_block *b = NULL; /* Find the external block */ b = cram_get_block_by_id(slice, c->u.external.content_id); if (!b) return *out_size?-1:0; cp = cram_extract_block(b, *out_size); if (!cp) return -1; BLOCK_APPEND(out, cp, *out_size); return 0; block_err: return -1; } void cram_external_decode_free(cram_codec *c) { if (c) free(c); } int cram_external_decode_size(cram_slice *slice, cram_codec *c) { cram_block *b; /* Find the external block */ b = cram_get_block_by_id(slice, c->u.external.content_id); if (!b) return -1; return b->uncomp_size; } cram_block *cram_external_get_block(cram_slice *slice, cram_codec *c) { return cram_get_block_by_id(slice, c->u.external.content_id); } int cram_external_describe(cram_codec *c, kstring_t *ks) { return ksprintf(ks, "EXTERNAL(id=%d)", c->u.external.content_id) < 0 ? -1 : 0; } cram_codec *cram_external_decode_init(cram_block_compression_hdr *hdr, char *data, int size, enum cram_encoding codec, enum cram_external_type option, int version, varint_vec *vv) { cram_codec *c = NULL; char *cp = data; if (size < 1) goto malformed; if (!(c = malloc(sizeof(*c)))) return NULL; c->codec = E_EXTERNAL; if (CRAM_MAJOR_VERS(version) >= 4) { // Version 4 does not permit integer data to be encoded as a // series of bytes. This is used purely for bytes, either // singular or declared as arrays switch (codec) { case E_EXTERNAL: if (option == E_BYTE_ARRAY_BLOCK) c->decode = cram_external_decode_block; else if (option == E_BYTE || option == E_BYTE_ARRAY) c->decode = cram_external_decode_char; else goto malformed; break; default: goto malformed; } } else { // CRAM 3 and earlier encodes integers as EXTERNAL. We need // use the option field to indicate the input data format so // we know which serialisation format to use. if (option == E_INT) c->decode = cram_external_decode_int; else if (option == E_LONG) c->decode = cram_external_decode_long; else if (option == E_BYTE_ARRAY || option == E_BYTE) c->decode = cram_external_decode_char; else c->decode = cram_external_decode_block; } c->free = cram_external_decode_free; c->size = cram_external_decode_size; c->get_block = cram_external_get_block; c->describe = cram_external_describe; c->u.external.content_id = vv->varint_get32(&cp, data+size, NULL); if (cp - data != size) goto malformed; c->u.external.type = option; return c; malformed: hts_log_error("Malformed external header stream"); free(c); return NULL; } int cram_external_encode_int(cram_slice *slice, cram_codec *c, char *in, int in_size) { uint32_t *i32 = (uint32_t *)in; return c->vv->varint_put32_blk(c->out, *i32) >= 0 ? 0 : -1; } int cram_external_encode_sint(cram_slice *slice, cram_codec *c, char *in, int in_size) { int32_t *i32 = (int32_t *)in; return c->vv->varint_put32s_blk(c->out, *i32) >= 0 ? 0 : -1; } int cram_external_encode_long(cram_slice *slice, cram_codec *c, char *in, int in_size) { uint64_t *i64 = (uint64_t *)in; return c->vv->varint_put64_blk(c->out, *i64) >= 0 ? 0 : -1; } int cram_external_encode_slong(cram_slice *slice, cram_codec *c, char *in, int in_size) { int64_t *i64 = (int64_t *)in; return c->vv->varint_put64s_blk(c->out, *i64) >= 0 ? 0 : -1; } int cram_external_encode_char(cram_slice *slice, cram_codec *c, char *in, int in_size) { BLOCK_APPEND(c->out, in, in_size); return 0; block_err: return -1; } void cram_external_encode_free(cram_codec *c) { if (!c) return; free(c); } int cram_external_encode_store(cram_codec *c, cram_block *b, char *prefix, int version) { char tmp[99], *tp = tmp, *tpend = tmp+99; int len = 0, r = 0, n; if (prefix) { size_t l = strlen(prefix); BLOCK_APPEND(b, prefix, l); len += l; } tp += c->vv->varint_put32(tp, tpend, c->u.e_external.content_id); len += (n = c->vv->varint_put32_blk(b, c->codec)); r |= n; len += (n = c->vv->varint_put32_blk(b, tp-tmp)); r |= n; BLOCK_APPEND(b, tmp, tp-tmp); len += tp-tmp; if (r > 0) return len; block_err: return -1; } cram_codec *cram_external_encode_init(cram_stats *st, enum cram_encoding codec, enum cram_external_type option, void *dat, int version, varint_vec *vv) { cram_codec *c; c = malloc(sizeof(*c)); if (!c) return NULL; c->codec = E_EXTERNAL; c->free = cram_external_encode_free; if (CRAM_MAJOR_VERS(version) >= 4) { // Version 4 does not permit integer data to be encoded as a // series of bytes. This is used purely for bytes, either // singular or declared as arrays switch (codec) { case E_EXTERNAL: if (option != E_BYTE && option != E_BYTE_ARRAY) return NULL; c->encode = cram_external_encode_char; break; default: return NULL; } } else { // CRAM 3 and earlier encodes integers as EXTERNAL. We need // use the option field to indicate the input data format so // we know which serialisation format to use. if (option == E_INT) c->encode = cram_external_encode_int; else if (option == E_LONG) c->encode = cram_external_encode_long; else if (option == E_BYTE_ARRAY || option == E_BYTE) c->encode = cram_external_encode_char; else abort(); } c->store = cram_external_encode_store; c->flush = NULL; c->u.e_external.content_id = (size_t)dat; return c; } /* * --------------------------------------------------------------------------- * VARINT * * In CRAM 3.0 and earlier, E_EXTERNAL stored both integers in ITF8 * format as well as bytes. In CRAM 4 EXTERNAL is only for bytes and * byte arrays, with two dedicated encodings for integers: * VARINT_SIGNED and VARINT_UNSIGNED. These also differ a little to * EXTERNAL with the addition of an offset field, meaning we can store * values in, say, the range -2 to 1 million without needing to use * a signed zig-zag transformation. */ int cram_varint_decode_int(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { char *cp; cram_block *b; /* Find the data block */ b = cram_get_block_by_id(slice, c->u.varint.content_id); if (!b) return *out_size?-1:0; cp = (char *)b->data + b->idx; // E_INT and E_LONG are guaranteed single item queries int err = 0; *(int32_t *)out = c->vv->varint_get32(&cp, (char *)b->data + b->uncomp_size, &err) + c->u.varint.offset; b->idx = cp - (char *)b->data; *out_size = 1; return err ? -1 : 0; } int cram_varint_decode_sint(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { char *cp; cram_block *b; /* Find the data block */ b = cram_get_block_by_id(slice, c->u.varint.content_id); if (!b) return *out_size?-1:0; cp = (char *)b->data + b->idx; // E_INT and E_LONG are guaranteed single item queries int err = 0; *(int32_t *)out = c->vv->varint_get32s(&cp, (char *)b->data + b->uncomp_size, &err) + c->u.varint.offset; b->idx = cp - (char *)b->data; *out_size = 1; return err ? -1 : 0; } int cram_varint_decode_long(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { char *cp; cram_block *b; /* Find the data block */ b = cram_get_block_by_id(slice, c->u.varint.content_id); if (!b) return *out_size?-1:0; cp = (char *)b->data + b->idx; // E_INT and E_LONG are guaranteed single item queries int err = 0; *(int64_t *)out = c->vv->varint_get64(&cp, (char *)b->data + b->uncomp_size, &err) + c->u.varint.offset; b->idx = cp - (char *)b->data; *out_size = 1; return err ? -1 : 0; } int cram_varint_decode_slong(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { char *cp; cram_block *b; /* Find the data block */ b = cram_get_block_by_id(slice, c->u.varint.content_id); if (!b) return *out_size?-1:0; cp = (char *)b->data + b->idx; // E_INT and E_LONG are guaranteed single item queries int err = 0; *(int64_t *)out = c->vv->varint_get64s(&cp, (char *)b->data + b->uncomp_size, &err) + c->u.varint.offset; b->idx = cp - (char *)b->data; *out_size = 1; return err ? -1 : 0; } void cram_varint_decode_free(cram_codec *c) { if (c) free(c); } int cram_varint_decode_size(cram_slice *slice, cram_codec *c) { cram_block *b; /* Find the data block */ b = cram_get_block_by_id(slice, c->u.varint.content_id); if (!b) return -1; return b->uncomp_size; } cram_block *cram_varint_get_block(cram_slice *slice, cram_codec *c) { return cram_get_block_by_id(slice, c->u.varint.content_id); } int cram_varint_describe(cram_codec *c, kstring_t *ks) { return ksprintf(ks, "VARINT(id=%d,offset=%"PRId64",type=%d)", c->u.varint.content_id, c->u.varint.offset, c->u.varint.type) < 0 ? -1 : 0; } cram_codec *cram_varint_decode_init(cram_block_compression_hdr *hdr, char *data, int size, enum cram_encoding codec, enum cram_external_type option, int version, varint_vec *vv) { cram_codec *c; char *cp = data, *cp_end = data+size; if (!(c = malloc(sizeof(*c)))) return NULL; c->codec = codec; // Function pointer choice is theoretically by codec type. // Given we have some vars as int32 and some as int64 we // use option too for sizing, although on disk format // does not change. switch(codec) { case E_VARINT_UNSIGNED: c->decode = (option == E_INT) ? cram_varint_decode_int : cram_varint_decode_long; break; case E_VARINT_SIGNED: c->decode = (option == E_INT) ? cram_varint_decode_sint : cram_varint_decode_slong; break; default: return NULL; } c->free = cram_varint_decode_free; c->size = cram_varint_decode_size; c->get_block = cram_varint_get_block; c->describe = cram_varint_describe; c->u.varint.content_id = vv->varint_get32 (&cp, cp_end, NULL); c->u.varint.offset = vv->varint_get64s(&cp, cp_end, NULL); if (cp - data != size) { fprintf(stderr, "Malformed varint header stream\n"); free(c); return NULL; } c->u.varint.type = option; return c; } int cram_varint_encode_int(cram_slice *slice, cram_codec *c, char *in, int in_size) { uint32_t *i32 = (uint32_t *)in; return c->vv->varint_put32_blk(c->out, *i32 - c->u.varint.offset) >= 0 ? 0 : -1; } int cram_varint_encode_sint(cram_slice *slice, cram_codec *c, char *in, int in_size) { int32_t *i32 = (int32_t *)in; return c->vv->varint_put32s_blk(c->out, *i32 - c->u.varint.offset) >= 0 ? 0 : -1; } int cram_varint_encode_long(cram_slice *slice, cram_codec *c, char *in, int in_size) { uint64_t *i64 = (uint64_t *)in; return c->vv->varint_put64_blk(c->out, *i64 - c->u.varint.offset) >= 0 ? 0 : -1; } int cram_varint_encode_slong(cram_slice *slice, cram_codec *c, char *in, int in_size) { int64_t *i64 = (int64_t *)in; return c->vv->varint_put64s_blk(c->out, *i64 - c->u.varint.offset) >= 0 ? 0 : -1; } void cram_varint_encode_free(cram_codec *c) { if (!c) return; free(c); } int cram_varint_encode_store(cram_codec *c, cram_block *b, char *prefix, int version) { char tmp[99], *tp = tmp; int len = 0; if (prefix) { size_t l = strlen(prefix); BLOCK_APPEND(b, prefix, l); len += l; } tp += c->vv->varint_put32 (tp, NULL, c->u.e_varint.content_id); tp += c->vv->varint_put64s(tp, NULL, c->u.e_varint.offset); len += c->vv->varint_put32_blk(b, c->codec); len += c->vv->varint_put32_blk(b, tp-tmp); BLOCK_APPEND(b, tmp, tp-tmp); len += tp-tmp; return len; block_err: return -1; } cram_codec *cram_varint_encode_init(cram_stats *st, enum cram_encoding codec, enum cram_external_type option, void *dat, int version, varint_vec *vv) { cram_codec *c; if (!(c = malloc(sizeof(*c)))) return NULL; c->u.e_varint.offset = 0; if (st) { // Marginal difference so far! Not worth the hassle? if (st->min_val < 0 && st->min_val >= -127 && st->max_val / -st->min_val > 100) { c->u.e_varint.offset = -st->min_val; codec = E_VARINT_UNSIGNED; } else if (st->min_val > 0) { c->u.e_varint.offset = -st->min_val; } } c->codec = codec; c->free = cram_varint_encode_free; // Function pointer choice is theoretically by codec type. // Given we have some vars as int32 and some as int64 we // use option too for sizing, although on disk format // does not change. switch (codec) { case E_VARINT_UNSIGNED: c->encode = (option == E_INT) ? cram_varint_encode_int : cram_varint_encode_long; break; case E_VARINT_SIGNED: c->encode = (option == E_INT) ? cram_varint_encode_sint : cram_varint_encode_slong; break; default: return NULL; } c->store = cram_varint_encode_store; c->flush = NULL; c->u.e_varint.content_id = (size_t)dat; return c; } /* * --------------------------------------------------------------------------- * CONST_BYTE and CONST_INT */ int cram_const_decode_byte(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int i, n; for (i = 0, n = *out_size; i < n; i++) out[i] = c->u.xconst.val; return 0; } int cram_const_decode_int(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int32_t *out_i = (int32_t *)out; int i, n; for (i = 0, n = *out_size; i < n; i++) out_i[i] = c->u.xconst.val; return 0; } int cram_const_decode_long(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int64_t *out_i = (int64_t *)out; int i, n; for (i = 0, n = *out_size; i < n; i++) out_i[i] = c->u.xconst.val; return 0; } void cram_const_decode_free(cram_codec *c) { if (c) free(c); } int cram_const_decode_size(cram_slice *slice, cram_codec *c) { return 0; } int cram_const_describe(cram_codec *c, kstring_t *ks) { return ksprintf(ks, "CONST(val=%"PRId64")", c->u.xconst.val) < 0 ? -1 : 0; } cram_codec *cram_const_decode_init(cram_block_compression_hdr *hdr, char *data, int size, enum cram_encoding codec, enum cram_external_type option, int version, varint_vec *vv) { cram_codec *c; char *cp = data; if (!(c = malloc(sizeof(*c)))) return NULL; c->codec = codec; if (codec == E_CONST_BYTE) c->decode = cram_const_decode_byte; else if (option == E_INT) c->decode = cram_const_decode_int; else c->decode = cram_const_decode_long; c->free = cram_const_decode_free; c->size = cram_const_decode_size; c->get_block = NULL; c->describe = cram_const_describe; c->u.xconst.val = vv->varint_get64s(&cp, data+size, NULL); if (cp - data != size) { fprintf(stderr, "Malformed const header stream\n"); free(c); return NULL; } return c; } int cram_const_encode(cram_slice *slice, cram_codec *c, char *in, int in_size) { return 0; } int cram_const_encode_store(cram_codec *c, cram_block *b, char *prefix, int version) { char tmp[99], *tp = tmp; int len = 0; if (prefix) { size_t l = strlen(prefix); BLOCK_APPEND(b, prefix, l); len += l; } tp += c->vv->varint_put64s(tp, NULL, c->u.xconst.val); len += c->vv->varint_put32_blk(b, c->codec); len += c->vv->varint_put32_blk(b, tp-tmp); BLOCK_APPEND(b, tmp, tp-tmp); len += tp-tmp; return len; block_err: return -1; } cram_codec *cram_const_encode_init(cram_stats *st, enum cram_encoding codec, enum cram_external_type option, void *dat, int version, varint_vec *vv) { cram_codec *c; if (!(c = malloc(sizeof(*c)))) return NULL; c->codec = codec; c->free = cram_const_decode_free; // as as decode c->encode = cram_const_encode; // a nop c->store = cram_const_encode_store; c->flush = NULL; c->u.e_xconst.val = st->min_val; return c; } /* * --------------------------------------------------------------------------- * BETA */ int cram_beta_decode_long(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int64_t *out_i = (int64_t *)out; int i, n = *out_size; if (c->u.beta.nbits) { if (cram_not_enough_bits(in, c->u.beta.nbits * n)) return -1; for (i = 0; i < n; i++) out_i[i] = get_bits_MSB(in, c->u.beta.nbits) - c->u.beta.offset; } else { for (i = 0; i < n; i++) out_i[i] = -c->u.beta.offset; } return 0; } int cram_beta_decode_int(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int32_t *out_i = (int32_t *)out; int i, n = *out_size; if (c->u.beta.nbits) { if (cram_not_enough_bits(in, c->u.beta.nbits * n)) return -1; for (i = 0; i < n; i++) out_i[i] = get_bits_MSB(in, c->u.beta.nbits) - c->u.beta.offset; } else { for (i = 0; i < n; i++) out_i[i] = -c->u.beta.offset; } return 0; } int cram_beta_decode_char(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int i, n = *out_size; if (c->u.beta.nbits) { if (cram_not_enough_bits(in, c->u.beta.nbits * n)) return -1; if (out) for (i = 0; i < n; i++) out[i] = get_bits_MSB(in, c->u.beta.nbits) - c->u.beta.offset; else for (i = 0; i < n; i++) get_bits_MSB(in, c->u.beta.nbits); } else { if (out) for (i = 0; i < n; i++) out[i] = -c->u.beta.offset; } return 0; } void cram_beta_decode_free(cram_codec *c) { if (c) free(c); } int cram_beta_describe(cram_codec *c, kstring_t *ks) { return ksprintf(ks, "BETA(offset=%d, nbits=%d)", c->u.beta.offset, c->u.beta.nbits) < 0 ? -1 : 0; } cram_codec *cram_beta_decode_init(cram_block_compression_hdr *hdr, char *data, int size, enum cram_encoding codec, enum cram_external_type option, int version, varint_vec *vv) { cram_codec *c; char *cp = data; if (!(c = malloc(sizeof(*c)))) return NULL; c->codec = E_BETA; if (option == E_INT || option == E_SINT) c->decode = cram_beta_decode_int; else if (option == E_LONG || option == E_SLONG) c->decode = cram_beta_decode_long; else if (option == E_BYTE_ARRAY || option == E_BYTE) c->decode = cram_beta_decode_char; else { hts_log_error("BYTE_ARRAYs not supported by this codec"); free(c); return NULL; } c->free = cram_beta_decode_free; c->describe = cram_beta_describe; c->u.beta.nbits = -1; c->u.beta.offset = vv->varint_get32(&cp, data + size, NULL); if (cp < data + size) // Ensure test below works c->u.beta.nbits = vv->varint_get32(&cp, data + size, NULL); if (cp - data != size || c->u.beta.nbits < 0 || c->u.beta.nbits > 8 * sizeof(int)) { hts_log_error("Malformed beta header stream"); free(c); return NULL; } return c; } int cram_beta_encode_store(cram_codec *c, cram_block *b, char *prefix, int version) { int len = 0, r = 0, n; if (prefix) { size_t l = strlen(prefix); BLOCK_APPEND(b, prefix, l); len += l; } len += (n = c->vv->varint_put32_blk(b, c->codec)); r |= n; // codec length len += (n = c->vv->varint_put32_blk(b, c->vv->varint_size(c->u.e_beta.offset) + c->vv->varint_size(c->u.e_beta.nbits))); r |= n; len += (n = c->vv->varint_put32_blk(b, c->u.e_beta.offset)); r |= n; len += (n = c->vv->varint_put32_blk(b, c->u.e_beta.nbits)); r |= n; if (r > 0) return len; block_err: return -1; } int cram_beta_encode_long(cram_slice *slice, cram_codec *c, char *in, int in_size) { int64_t *syms = (int64_t *)in; int i, r = 0; for (i = 0; i < in_size; i++) r |= store_bits_MSB(c->out, syms[i] + c->u.e_beta.offset, c->u.e_beta.nbits); return r; } int cram_beta_encode_int(cram_slice *slice, cram_codec *c, char *in, int in_size) { int *syms = (int *)in; int i, r = 0; for (i = 0; i < in_size; i++) r |= store_bits_MSB(c->out, syms[i] + c->u.e_beta.offset, c->u.e_beta.nbits); return r; } int cram_beta_encode_char(cram_slice *slice, cram_codec *c, char *in, int in_size) { unsigned char *syms = (unsigned char *)in; int i, r = 0; for (i = 0; i < in_size; i++) r |= store_bits_MSB(c->out, syms[i] + c->u.e_beta.offset, c->u.e_beta.nbits); return r; } void cram_beta_encode_free(cram_codec *c) { if (c) free(c); } cram_codec *cram_beta_encode_init(cram_stats *st, enum cram_encoding codec, enum cram_external_type option, void *dat, int version, varint_vec *vv) { cram_codec *c; hts_pos_t min_val, max_val; int len = 0; int64_t range; c = malloc(sizeof(*c)); if (!c) return NULL; c->codec = E_BETA; c->free = cram_beta_encode_free; if (option == E_INT || option == E_SINT) c->encode = cram_beta_encode_int; else if (option == E_LONG || option == E_SLONG) c->encode = cram_beta_encode_long; else c->encode = cram_beta_encode_char; c->store = cram_beta_encode_store; c->flush = NULL; if (dat) { min_val = ((hts_pos_t *)dat)[0]; max_val = ((hts_pos_t *)dat)[1]; } else { min_val = INT_MAX; max_val = INT_MIN; int i; for (i = 0; i < MAX_STAT_VAL; i++) { if (!st->freqs[i]) continue; if (min_val > i) min_val = i; max_val = i; } if (st->h) { khint_t k; for (k = kh_begin(st->h); k != kh_end(st->h); k++) { if (!kh_exist(st->h, k)) continue; i = kh_key(st->h, k); if (min_val > i) min_val = i; if (max_val < i) max_val = i; } } } if (max_val < min_val) goto err; range = (int64_t) max_val - min_val; switch (option) { case E_SINT: if (min_val < INT_MIN || range > INT_MAX) goto err; break; case E_INT: if (max_val > UINT_MAX || range > UINT_MAX) goto err; break; default: break; } c->u.e_beta.offset = -min_val; while (range) { len++; range >>= 1; } c->u.e_beta.nbits = len; return c; err: free(c); return NULL; } /* * --------------------------------------------------------------------------- * XPACK: Packing multiple values into a single byte. A fast transform that * reduces time taken by entropy encoder and may also improve compression. * * This also has the additional requirement that the data series is not * interleaved with another, permitting efficient encoding and decoding * of all elements enmasse instead of needing to only extract the bits * necessary per item. */ int cram_xpack_decode_long(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int64_t *out_i = (int64_t *)out; int i, n = *out_size; if (c->u.xpack.nbits) { for (i = 0; i < n; i++) out_i[i] = c->u.xpack.rmap[get_bits_MSB(in, c->u.xpack.nbits)]; } else { for (i = 0; i < n; i++) out_i[i] = c->u.xpack.rmap[0]; } return 0; } int cram_xpack_decode_int(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int32_t *out_i = (int32_t *)out; int i, n = *out_size; if (c->u.xpack.nbits) { if (cram_not_enough_bits(in, c->u.xpack.nbits * n)) return -1; for (i = 0; i < n; i++) out_i[i] = c->u.xpack.rmap[get_bits_MSB(in, c->u.xpack.nbits)]; } else { for (i = 0; i < n; i++) out_i[i] = c->u.xpack.rmap[0]; } return 0; } static int cram_xpack_decode_expand_char(cram_slice *slice, cram_codec *c) { cram_block *b = slice->block_by_id[512 + c->codec_id]; if (b) return 0; // get sub-codec data. cram_block *sub_b = c->u.xpack.sub_codec->get_block(slice, c->u.xpack.sub_codec); if (!sub_b) return -1; // Allocate local block to expand into b = slice->block_by_id[512 + c->codec_id] = cram_new_block(0, 0); if (!b) return -1; int n = sub_b->uncomp_size * 8/c->u.xpack.nbits; BLOCK_GROW(b, n); b->uncomp_size = n; uint8_t p[256]; int z; for (z = 0; z < 256; z++) p[z] = c->u.xpack.rmap[z]; hts_unpack(sub_b->data, sub_b->uncomp_size, b->data, b->uncomp_size, 8 / c->u.xpack.nbits, p); return 0; block_err: return -1; } int cram_xpack_decode_char(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { // FIXME: we need to ban data-series interleaving in the spec for this to work. // Remember this may be called when threaded and multi-slice per container. // Hence one cram_codec instance, multiple slices, multiple blocks. // We therefore have to cache appropriate block info in slice and not codec. // b = cram_get_block_by_id(slice, c->external.content_id); if (c->u.xpack.nval > 1) { cram_xpack_decode_expand_char(slice, c); cram_block *b = slice->block_by_id[512 + c->codec_id]; if (!b) return -1; if (out) memcpy(out, b->data + b->byte, *out_size); b->byte += *out_size; } else { memset(out, c->u.xpack.rmap[0], *out_size); } return 0; } void cram_xpack_decode_free(cram_codec *c) { if (!c) return; if (c->u.xpack.sub_codec) c->u.xpack.sub_codec->free(c->u.xpack.sub_codec); //free(slice->block_by_id[512 + c->codec_id]); //slice->block_by_id[512 + c->codec_id] = 0; free(c); } int cram_xpack_decode_size(cram_slice *slice, cram_codec *c) { cram_xpack_decode_expand_char(slice, c); return slice->block_by_id[512 + c->codec_id]->uncomp_size; } cram_block *cram_xpack_get_block(cram_slice *slice, cram_codec *c) { cram_xpack_decode_expand_char(slice, c); return slice->block_by_id[512 + c->codec_id]; } cram_codec *cram_xpack_decode_init(cram_block_compression_hdr *hdr, char *data, int size, enum cram_encoding codec, enum cram_external_type option, int version, varint_vec *vv) { cram_codec *c; char *cp = data; char *endp = data+size; if (!(c = calloc(1, sizeof(*c)))) return NULL; c->codec = E_XPACK; if (option == E_LONG) c->decode = cram_xpack_decode_long; else if (option == E_INT) c->decode = cram_xpack_decode_int; else if (option == E_BYTE_ARRAY || option == E_BYTE) c->decode = cram_xpack_decode_char; else { fprintf(stderr, "BYTE_ARRAYs not supported by this codec\n"); goto malformed; } c->free = cram_xpack_decode_free; c->size = cram_xpack_decode_size; c->get_block = cram_xpack_get_block; c->describe = NULL; c->u.xpack.nbits = vv->varint_get32(&cp, endp, NULL); c->u.xpack.nval = vv->varint_get32(&cp, endp, NULL); if (c->u.xpack.nbits >= 8 || c->u.xpack.nbits < 0 || c->u.xpack.nval > 256 || c->u.xpack.nval < 0) goto malformed; int i; for (i = 0; i < c->u.xpack.nval; i++) { uint32_t v = vv->varint_get32(&cp, endp, NULL); if (v >= 256) goto malformed; c->u.xpack.rmap[i] = v; // reverse map: e.g 0-3 to P,A,C,K } int encoding = vv->varint_get32(&cp, endp, NULL); int sub_size = vv->varint_get32(&cp, endp, NULL); if (sub_size < 0 || endp - cp < sub_size) goto malformed; c->u.xpack.sub_codec = cram_decoder_init(hdr, encoding, cp, sub_size, option, version, vv); if (c->u.xpack.sub_codec == NULL) goto malformed; cp += sub_size; if (cp - data != size || c->u.xpack.nbits < 0 || c->u.xpack.nbits > 8 * sizeof(int64_t)) { malformed: fprintf(stderr, "Malformed xpack header stream\n"); cram_xpack_decode_free(c); return NULL; } return c; } int cram_xpack_encode_flush(cram_codec *c) { // Pack the buffered up data int meta_len; uint64_t out_len; uint8_t out_meta[1024]; uint8_t *out = hts_pack(BLOCK_DATA(c->out), BLOCK_SIZE(c->out), out_meta, &meta_len, &out_len); // We now need to pass this through the next layer of transform if (c->u.e_xpack.sub_codec->encode(NULL, // also indicates flush incoming c->u.e_xpack.sub_codec, (char *)out, out_len)) return -1; int r = 0; if (c->u.e_xpack.sub_codec->flush) r = c->u.e_xpack.sub_codec->flush(c->u.e_xpack.sub_codec); free(out); return r; } int cram_xpack_encode_store(cram_codec *c, cram_block *b, char *prefix, int version) { int len = 0, r = 0, n; if (prefix) { size_t l = strlen(prefix); BLOCK_APPEND(b, prefix, l); len += l; } // Store sub-codec cram_codec *tc = c->u.e_xpack.sub_codec; cram_block *tb = cram_new_block(0, 0); if (!tb) return -1; int len2 = tc->store(tc, tb, NULL, version); len += (n = c->vv->varint_put32_blk(b, c->codec)); r |= n; // codec length int len1 = 0, i; for (i = 0; i < c->u.e_xpack.nval; i++) len1 += (n = c->vv->varint_size(c->u.e_xpack.rmap[i])), r |= n; len += (n = c->vv->varint_put32_blk(b, c->vv->varint_size(c->u.e_xpack.nbits) + c->vv->varint_size(c->u.e_xpack.nval) + len1 + len2)); r |= n; // The map and sub-codec len += (n = c->vv->varint_put32_blk(b, c->u.e_xpack.nbits)); r |= n; len += (n = c->vv->varint_put32_blk(b, c->u.e_xpack.nval)); r |= n; for (i = 0; i < c->u.e_xpack.nval; i++) len += (n = c->vv->varint_put32_blk(b, c->u.e_xpack.rmap[i])), r |= n; BLOCK_APPEND(b, BLOCK_DATA(tb), BLOCK_SIZE(tb)); cram_free_block(tb); return r > 0 ? len + len2 : -1; block_err: return -1; } // Same as cram_beta_encode_long int cram_xpack_encode_long(cram_slice *slice, cram_codec *c, char *in, int in_size) { int64_t *syms = (int64_t *)in; int i, r = 0; for (i = 0; i < in_size; i++) r |= store_bits_MSB(c->out, c->u.e_xpack.map[syms[i]], c->u.e_xpack.nbits); return r; } int cram_xpack_encode_int(cram_slice *slice, cram_codec *c, char *in, int in_size) { int *syms = (int *)in; int i, r = 0; for (i = 0; i < in_size; i++) r |= store_bits_MSB(c->out, c->u.e_xpack.map[syms[i]], c->u.e_xpack.nbits); return r; } int cram_xpack_encode_char(cram_slice *slice, cram_codec *c, char *in, int in_size) { BLOCK_APPEND(c->out, in, in_size); return 0; block_err: return -1; } void cram_xpack_encode_free(cram_codec *c) { if (!c) return; if (c->u.e_xpack.sub_codec) c->u.e_xpack.sub_codec->free(c->u.e_xpack.sub_codec); cram_free_block(c->out); free(c); } cram_codec *cram_xpack_encode_init(cram_stats *st, enum cram_encoding codec, enum cram_external_type option, void *dat, int version, varint_vec *vv) { cram_codec *c; if (!(c = malloc(sizeof(*c)))) return NULL; c->codec = E_XPACK; c->free = cram_xpack_encode_free; if (option == E_LONG) c->encode = cram_xpack_encode_long; else if (option == E_INT) c->encode = cram_xpack_encode_int; else c->encode = cram_xpack_encode_char; c->store = cram_xpack_encode_store; c->flush = cram_xpack_encode_flush; cram_xpack_encoder *e = (cram_xpack_encoder *)dat; c->u.e_xpack.nbits = e->nbits; c->u.e_xpack.nval = e->nval; c->u.e_xpack.sub_codec = cram_encoder_init(e->sub_encoding, NULL, E_BYTE_ARRAY, e->sub_codec_dat, version, vv); // Initialise fwd and rev maps memcpy(c->u.e_xpack.map, e->map, sizeof(e->map)); // P,A,C,K to 0,1,2,3 int i, n; for (i = n = 0; i < 256; i++) if (e->map[i] != -1) c->u.e_xpack.rmap[n++] = i; // 0,1,2,3 to P,A,C,K if (n != e->nval) { fprintf(stderr, "Incorrectly specified number of map items in PACK\n"); return NULL; } return c; } /* * --------------------------------------------------------------------------- * XDELTA: subtract successive values, zig-zag to turn +/- to + only, * and then var-int encode the result. * * This also has the additional requirement that the data series is not * interleaved with another, permitting efficient encoding and decoding * of all elements enmasse instead of needing to only extract the bits * necessary per item. */ static uint8_t zigzag8 (int8_t x) { return (x << 1) ^ (x >> 7); } static uint16_t zigzag16(int16_t x) { return (x << 1) ^ (x >> 15); } static uint32_t zigzag32(int32_t x) { return (x << 1) ^ (x >> 31); } //static int8_t unzigzag8 (uint8_t x) { return (x >> 1) ^ -(x & 1); } static int16_t unzigzag16(uint16_t x) { return (x >> 1) ^ -(x & 1); } static int32_t unzigzag32(uint32_t x) { return (x >> 1) ^ -(x & 1); } int cram_xdelta_decode_long(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { return -1; } int cram_xdelta_decode_int(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { // Slow value-by-value method for now uint32_t *out32 = (uint32_t *)out; int i; for (i = 0; i < *out_size; i++) { uint32_t v; int one = 1; if (c->u.e_xdelta.sub_codec->decode(slice, c->u.e_xdelta.sub_codec, in, (char *)&v, &one) < 0) return -1; uint32_t d = unzigzag32(v); c->u.xdelta.last = out32[i] = d + c->u.xdelta.last; } return 0; } static int cram_xdelta_decode_expand_char(cram_slice *slice, cram_codec *c) { return -1; } int cram_xdelta_decode_char(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { return -1; } static inline int16_t le_int2(int16_t i) { int16_t s; i16_to_le(i, (uint8_t *)&s); return s; } int cram_xdelta_decode_block(cram_slice *slice, cram_codec *c, cram_block *in, char *out_, int *out_size) { cram_block *out = (cram_block *)out_; cram_block *b = c->u.e_xdelta.sub_codec->get_block(slice, c->u.e_xdelta.sub_codec); int i = 0; const int w = c->u.xdelta.word_size; uint32_t npad = (w - *out_size%w)%w; uint32_t out_sz = *out_size + npad; c->u.xdelta.last = 0; // reset for each new array for (i = 0; i < out_sz; i += w) { uint16_t v; // Need better interface char *cp = (char *)b->data + b->byte; char *cp_end = (char *)b->data + b->uncomp_size; int err = 0; v = c->vv->varint_get32(&cp, cp_end, &err); if (err) return -1; b->byte = cp - (char *)b->data; switch(w) { case 2: { int16_t d = unzigzag16(v), z; c->u.xdelta.last = d + c->u.xdelta.last; z = le_int2(c->u.xdelta.last); BLOCK_APPEND(out, &z, 2-npad); npad = 0; break; } default: fprintf(stderr, "Unsupported word size by XDELTA\n"); return -1; } } return 0; block_err: return -1; } void cram_xdelta_decode_free(cram_codec *c) { if (!c) return; if (c->u.xdelta.sub_codec) c->u.xdelta.sub_codec->free(c->u.xdelta.sub_codec); free(c); } int cram_xdelta_decode_size(cram_slice *slice, cram_codec *c) { cram_xdelta_decode_expand_char(slice, c); return slice->block_by_id[512 + c->codec_id]->uncomp_size; } cram_block *cram_xdelta_get_block(cram_slice *slice, cram_codec *c) { cram_xdelta_decode_expand_char(slice, c); return slice->block_by_id[512 + c->codec_id]; } cram_codec *cram_xdelta_decode_init(cram_block_compression_hdr *hdr, char *data, int size, enum cram_encoding codec, enum cram_external_type option, int version, varint_vec *vv) { cram_codec *c; char *cp = data; char *endp = data+size; if (!(c = calloc(1, sizeof(*c)))) return NULL; c->codec = E_XDELTA; if (option == E_LONG) c->decode = cram_xdelta_decode_long; else if (option == E_INT) c->decode = cram_xdelta_decode_int; else if (option == E_BYTE_ARRAY || option == E_BYTE) c->decode = cram_xdelta_decode_char; else if (option == E_BYTE_ARRAY_BLOCK) { option = E_BYTE_ARRAY; c->decode = cram_xdelta_decode_block; } else { free(c); return NULL; } c->free = cram_xdelta_decode_free; c->size = cram_xdelta_decode_size; c->get_block = cram_xdelta_get_block; c->describe = NULL; c->u.xdelta.word_size = vv->varint_get32(&cp, endp, NULL); c->u.xdelta.last = 0; int encoding = vv->varint_get32(&cp, endp, NULL); int sub_size = vv->varint_get32(&cp, endp, NULL); if (sub_size < 0 || endp - cp < sub_size) goto malformed; c->u.xdelta.sub_codec = cram_decoder_init(hdr, encoding, cp, sub_size, option, version, vv); if (c->u.xdelta.sub_codec == NULL) goto malformed; cp += sub_size; if (cp - data != size) { malformed: fprintf(stderr, "Malformed xdelta header stream\n"); cram_xdelta_decode_free(c); return NULL; } return c; } int cram_xdelta_encode_flush(cram_codec *c) { int r = -1; cram_block *b = cram_new_block(0, 0); if (!b) return -1; switch (c->u.e_xdelta.word_size) { case 2: { // Delta + zigzag transform. // Subtracting two 8-bit values has a 9-bit result (-255 to 255). // However think of it as turning a wheel clockwise or anti-clockwise. // If it has 256 gradations then a -ve rotation followed by a +ve // rotation of the same amount reverses it regardless. // // Similarly the zig-zag transformation doesn't invent any extra bits, // so the entire thing can be done in-situ. This may permit faster // SIMD loops if we break apart the steps. // uint16_t last = 0, d; // for (i = 0; i < n; i++) { // d = io[i] - last; // last = io[i]; // io[i] = zigzag16(vd); // } // --- vs --- // for (i = n-1; i >= 1; i--) // io[i] -= io[i-1]; // for (i = 0; i < n; i++) // io[i] = zigzag16(io[i]); // varint: need array variant for speed here. // With zig-zag int i, n = BLOCK_SIZE(c->out)/2;; uint16_t *dat = (uint16_t *)BLOCK_DATA(c->out), last = 0; if (n*2 < BLOCK_SIZE(c->out)) { // half word last = *(uint8_t *)dat; c->vv->varint_put32_blk(b, zigzag16(last)); dat = (uint16_t *)(((uint8_t *)dat)+1); } for (i = 0; i < n; i++) { uint16_t d = dat[i] - last; // possibly unaligned last = dat[i]; c->vv->varint_put32_blk(b, zigzag16(d)); } break; } case 4: { int i, n = BLOCK_SIZE(c->out)/4;; uint32_t *dat = (uint32_t *)BLOCK_DATA(c->out), last = 0; for (i = 0; i < n; i++) { uint32_t d = dat[i] - last; last = dat[i]; c->vv->varint_put32_blk(b, zigzag32(d)); } break; } case 1: { int i, n = BLOCK_SIZE(c->out);; uint8_t *dat = (uint8_t *)BLOCK_DATA(c->out), last = 0; for (i = 0; i < n; i++) { uint32_t d = dat[i] - last; last = dat[i]; c->vv->varint_put32_blk(b, zigzag8(d)); } break; } default: goto err; } if (c->u.e_xdelta.sub_codec->encode(NULL, c->u.e_xdelta.sub_codec, (char *)b->data, b->byte)) goto err; r = 0; err: cram_free_block(b); return r; } int cram_xdelta_encode_store(cram_codec *c, cram_block *b, char *prefix, int version) { int len = 0, r = 0, n; if (prefix) { size_t l = strlen(prefix); BLOCK_APPEND(b, prefix, l); len += l; } // Store sub-codec cram_codec *tc = c->u.e_xdelta.sub_codec; cram_block *tb = cram_new_block(0, 0); if (!tb) return -1; int len2 = tc->store(tc, tb, NULL, version); len += (n = c->vv->varint_put32_blk(b, c->codec)); r |= n; // codec length len += (n = c->vv->varint_put32_blk(b, c->vv->varint_size(c->u.e_xdelta.word_size) + len2)); r |= n; // This and sub-codec len += (n = c->vv->varint_put32_blk(b, c->u.e_xdelta.word_size)); r |= n; BLOCK_APPEND(b, BLOCK_DATA(tb), BLOCK_SIZE(tb)); cram_free_block(tb); return r > 0 ? len + len2 : -1; block_err: return -1; } // Same as cram_beta_encode_long int cram_xdelta_encode_long(cram_slice *slice, cram_codec *c, char *in, int in_size) { return -1; } int cram_xdelta_encode_int(cram_slice *slice, cram_codec *c, char *in, int in_size) { return -1; } int cram_xdelta_encode_char(cram_slice *slice, cram_codec *c, char *in, int in_size) { char *dat = malloc(in_size*5); if (!dat) return -1; char *cp = dat, *cp_end = dat + in_size*5; c->u.e_xdelta.last = 0; // reset for each new array if (c->u.e_xdelta.word_size == 2) { int i, part; part = in_size%2; if (part) { uint16_t z = in[0]; c->u.e_xdelta.last = le_int2(z); cp += c->vv->varint_put32(cp, cp_end, zigzag16(c->u.e_xdelta.last)); } uint16_t *in16 = (uint16_t *)(in+part); for (i = 0; i < in_size/2; i++) { uint16_t d = le_int2(in16[i]) - c->u.e_xdelta.last; c->u.e_xdelta.last = le_int2(in16[i]); cp += c->vv->varint_put32(cp, cp_end, zigzag16(d)); } } if (c->u.e_xdelta.sub_codec->encode(slice, c->u.e_xdelta.sub_codec, (char *)dat, cp-dat)) { free(dat); return -1; } free(dat); return 0; } void cram_xdelta_encode_free(cram_codec *c) { if (!c) return; if (c->u.e_xdelta.sub_codec) c->u.e_xdelta.sub_codec->free(c->u.e_xdelta.sub_codec); cram_free_block(c->out); free(c); } cram_codec *cram_xdelta_encode_init(cram_stats *st, enum cram_encoding codec, enum cram_external_type option, void *dat, int version, varint_vec *vv) { cram_codec *c; if (!(c = malloc(sizeof(*c)))) return NULL; c->codec = E_XDELTA; c->free = cram_xdelta_encode_free; if (option == E_LONG) c->encode = cram_xdelta_encode_long; else if (option == E_INT) c->encode = cram_xdelta_encode_int; else c->encode = cram_xdelta_encode_char; c->store = cram_xdelta_encode_store; c->flush = cram_xdelta_encode_flush; cram_xdelta_encoder *e = (cram_xdelta_encoder *)dat; c->u.e_xdelta.word_size = e->word_size; c->u.e_xdelta.last = 0; c->u.e_xdelta.sub_codec = cram_encoder_init(e->sub_encoding, NULL, E_BYTE_ARRAY, e->sub_codec_dat, version, vv); return c; } /* * --------------------------------------------------------------------------- * XRLE * * This also has the additional requirement that the data series is not * interleaved with another, permitting efficient encoding and decoding * of all elements enmasse instead of needing to only extract the bits * necessary per item. */ int cram_xrle_decode_long(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { // TODO if and when needed return -1; } int cram_xrle_decode_int(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { // TODO if and when needed return -1; } // Expands an XRLE transform and caches result in slice->block_by_id[] static int cram_xrle_decode_expand_char(cram_slice *slice, cram_codec *c) { cram_block *b = slice->block_by_id[512 + c->codec_id]; if (b) return 0; b = slice->block_by_id[512 + c->codec_id] = cram_new_block(0, 0); if (!b) return -1; cram_block *lit_b = c->u.xrle.lit_codec->get_block(slice, c->u.xrle.lit_codec); if (!lit_b) return -1; unsigned char *lit_dat = lit_b->data; unsigned int lit_sz = lit_b->uncomp_size; unsigned int len_sz = c->u.xrle.len_codec->size(slice, c->u.xrle.len_codec); cram_block *len_b = c->u.xrle.len_codec->get_block(slice, c->u.xrle.len_codec); if (!len_b) return -1; unsigned char *len_dat = len_b->data; uint8_t rle_syms[256]; int rle_nsyms = 0; int i; for (i = 0; i < 256; i++) { if (c->u.xrle.rep_score[i] > 0) rle_syms[rle_nsyms++] = i; } uint64_t out_sz; int nb = var_get_u64(len_dat, len_dat+len_sz, &out_sz); if (!(b->data = malloc(out_sz))) return -1; hts_rle_decode(lit_dat, lit_sz, len_dat+nb, len_sz-nb, rle_syms, rle_nsyms, b->data, &out_sz); b->uncomp_size = out_sz; return 0; } int cram_xrle_decode_size(cram_slice *slice, cram_codec *c) { cram_xrle_decode_expand_char(slice, c); return slice->block_by_id[512 + c->codec_id]->uncomp_size; } cram_block *cram_xrle_get_block(cram_slice *slice, cram_codec *c) { cram_xrle_decode_expand_char(slice, c); return slice->block_by_id[512 + c->codec_id]; } int cram_xrle_decode_char(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int n = *out_size; cram_xrle_decode_expand_char(slice, c); cram_block *b = slice->block_by_id[512 + c->codec_id]; memcpy(out, b->data + b->idx, n); b->idx += n; return 0; // Old code when not cached while (n > 0) { if (c->u.xrle.cur_len == 0) { unsigned char lit; int one = 1; if (c->u.xrle.lit_codec->decode(slice, c->u.xrle.lit_codec, in, (char *)&lit, &one) < 0) return -1; c->u.xrle.cur_lit = lit; if (c->u.xrle.rep_score[lit] > 0) { if (c->u.xrle.len_codec->decode(slice, c->u.xrle.len_codec, in, (char *)&c->u.xrle.cur_len, &one) < 0) return -1; } // else cur_len still zero //else fprintf(stderr, "%d\n", lit); c->u.xrle.cur_len++; } if (n >= c->u.xrle.cur_len) { memset(out, c->u.xrle.cur_lit, c->u.xrle.cur_len); out += c->u.xrle.cur_len; n -= c->u.xrle.cur_len; c->u.xrle.cur_len = 0; } else { memset(out, c->u.xrle.cur_lit, n); out += n; c->u.xrle.cur_len -= n; n = 0; } } return 0; } void cram_xrle_decode_free(cram_codec *c) { if (!c) return; if (c->u.xrle.len_codec) c->u.xrle.len_codec->free(c->u.xrle.len_codec); if (c->u.xrle.lit_codec) c->u.xrle.lit_codec->free(c->u.xrle.lit_codec); free(c); } cram_codec *cram_xrle_decode_init(cram_block_compression_hdr *hdr, char *data, int size, enum cram_encoding codec, enum cram_external_type option, int version, varint_vec *vv) { cram_codec *c; char *cp = data; char *endp = data+size; int err = 0; if (!(c = calloc(1, sizeof(*c)))) return NULL; c->codec = E_XRLE; if (option == E_LONG) c->decode = cram_xrle_decode_long; else if (option == E_INT) c->decode = cram_xrle_decode_int; else if (option == E_BYTE_ARRAY || option == E_BYTE) c->decode = cram_xrle_decode_char; else { fprintf(stderr, "BYTE_ARRAYs not supported by this codec\n"); free(c); return NULL; } c->free = cram_xrle_decode_free; c->size = cram_xrle_decode_size; c->get_block = cram_xrle_get_block; c->describe = NULL; c->u.xrle.cur_len = 0; c->u.xrle.cur_lit = -1; // RLE map int i, j, nrle = vv->varint_get32(&cp, endp, &err); memset(c->u.xrle.rep_score, 0, 256*sizeof(*c->u.xrle.rep_score)); for (i = 0; i < nrle && i < 256; i++) { j = vv->varint_get32(&cp, endp, &err); if (j >= 0 && j < 256) c->u.xrle.rep_score[j] = 1; } // Length and literal sub encodings c->u.xrle.len_encoding = vv->varint_get32(&cp, endp, &err); int sub_size = vv->varint_get32(&cp, endp, &err); if (sub_size < 0 || endp - cp < sub_size) goto malformed; c->u.xrle.len_codec = cram_decoder_init(hdr, c->u.xrle.len_encoding, cp, sub_size, E_INT, version, vv); if (c->u.xrle.len_codec == NULL) goto malformed; cp += sub_size; c->u.xrle.lit_encoding = vv->varint_get32(&cp, endp, &err); sub_size = vv->varint_get32(&cp, endp, &err); if (sub_size < 0 || endp - cp < sub_size) goto malformed; c->u.xrle.lit_codec = cram_decoder_init(hdr, c->u.xrle.lit_encoding, cp, sub_size, option, version, vv); if (c->u.xrle.lit_codec == NULL) goto malformed; cp += sub_size; if (err) goto malformed; return c; malformed: fprintf(stderr, "Malformed xrle header stream\n"); cram_xrle_decode_free(c); return NULL; } int cram_xrle_encode_flush(cram_codec *c) { uint8_t *out_lit, *out_len; uint64_t out_lit_size, out_len_size; uint8_t rle_syms[256]; int rle_nsyms = 0, i; for (i = 0; i < 256; i++) if (c->u.e_xrle.rep_score[i] > 0) rle_syms[rle_nsyms++] = i; if (!c->u.e_xrle.to_flush) { c->u.e_xrle.to_flush = (char *)BLOCK_DATA(c->out); c->u.e_xrle.to_flush_size = BLOCK_SIZE(c->out); } out_len = malloc(c->u.e_xrle.to_flush_size+8); if (!out_len) return -1; int nb = var_put_u64(out_len, NULL, c->u.e_xrle.to_flush_size); out_lit = hts_rle_encode((uint8_t *)c->u.e_xrle.to_flush, c->u.e_xrle.to_flush_size, out_len+nb, &out_len_size, rle_syms, &rle_nsyms, NULL, &out_lit_size); out_len_size += nb; // TODO: can maybe "gift" the sub codec the data block, to remove // one level of memcpy. if (c->u.e_xrle.len_codec->encode(NULL, c->u.e_xrle.len_codec, (char *)out_len, out_len_size)) return -1; if (c->u.e_xrle.lit_codec->encode(NULL, c->u.e_xrle.lit_codec, (char *)out_lit, out_lit_size)) return -1; free(out_len); free(out_lit); return 0; } int cram_xrle_encode_store(cram_codec *c, cram_block *b, char *prefix, int version) { int len = 0, r = 0, n; cram_codec *tc; cram_block *b_rle, *b_len, *b_lit; if (prefix) { size_t l = strlen(prefix); BLOCK_APPEND(b, prefix, l); len += l; } // List of symbols to RLE b_rle = cram_new_block(0, 0); if (!b_rle) return -1; int i, nrle = 0, len1 = 0; for (i = 0; i < 256; i++) { if (c->u.e_xrle.rep_score[i] > 0) { nrle++; len1 += (n = c->vv->varint_put32_blk(b_rle,i)); r |= n; } } // Store length and literal sub-codecs to get encoded length tc = c->u.e_xrle.len_codec; b_len = cram_new_block(0, 0); if (!b_len) return -1; int len2 = tc->store(tc, b_len, NULL, version); tc = c->u.e_xrle.lit_codec; b_lit = cram_new_block(0, 0); if (!b_lit) return -1; int len3 = tc->store(tc, b_lit, NULL, version); len += (n = c->vv->varint_put32_blk(b, c->codec)); r |= n; len += (n = c->vv->varint_put32_blk(b, len1 + len2 + len3 + c->vv->varint_size(nrle))); r |= n; len += (n = c->vv->varint_put32_blk(b, nrle)); r |= n; BLOCK_APPEND(b, BLOCK_DATA(b_rle), BLOCK_SIZE(b_rle)); BLOCK_APPEND(b, BLOCK_DATA(b_len), BLOCK_SIZE(b_len)); BLOCK_APPEND(b, BLOCK_DATA(b_lit), BLOCK_SIZE(b_lit)); cram_free_block(b_rle); cram_free_block(b_len); cram_free_block(b_lit); if (r > 0) return len + len1 + len2 + len3; block_err: return -1; } int cram_xrle_encode_long(cram_slice *slice, cram_codec *c, char *in, int in_size) { // TODO if and when needed return -1; } int cram_xrle_encode_int(cram_slice *slice, cram_codec *c, char *in, int in_size) { // TODO if and when needed return -1; } int cram_xrle_encode_char(cram_slice *slice, cram_codec *c, char *in, int in_size) { if (c->u.e_xrle.to_flush) { if (!c->out && !(c->out = cram_new_block(0, 0))) return -1; BLOCK_APPEND(c->out, c->u.e_xrle.to_flush, c->u.e_xrle.to_flush_size); c->u.e_xrle.to_flush = NULL; c->u.e_xrle.to_flush_size = 0; } if (c->out && BLOCK_SIZE(c->out) > 0) { // Gathering data BLOCK_APPEND(c->out, in, in_size); return 0; } // else cache copy of the data we're about to send to flush instead. c->u.e_xrle.to_flush = in; c->u.e_xrle.to_flush_size = in_size; return 0; block_err: return -1; } void cram_xrle_encode_free(cram_codec *c) { if (!c) return; if (c->u.e_xrle.len_codec) c->u.e_xrle.len_codec->free(c->u.e_xrle.len_codec); if (c->u.e_xrle.lit_codec) c->u.e_xrle.lit_codec->free(c->u.e_xrle.lit_codec); cram_free_block(c->out); free(c); } cram_codec *cram_xrle_encode_init(cram_stats *st, enum cram_encoding codec, enum cram_external_type option, void *dat, int version, varint_vec *vv) { cram_codec *c; if (!(c = malloc(sizeof(*c)))) return NULL; c->codec = E_XRLE; c->free = cram_xrle_encode_free; if (option == E_LONG) c->encode = cram_xrle_encode_long; else if (option == E_INT) c->encode = cram_xrle_encode_int; else c->encode = cram_xrle_encode_char; c->store = cram_xrle_encode_store; c->flush = cram_xrle_encode_flush; cram_xrle_encoder *e = (cram_xrle_encoder *)dat; c->u.e_xrle.len_codec = cram_encoder_init(e->len_encoding, NULL, E_BYTE, e->len_dat, version, vv); c->u.e_xrle.lit_codec = cram_encoder_init(e->lit_encoding, NULL, E_BYTE, e->lit_dat, version, vv); c->u.e_xrle.cur_lit = -1; c->u.e_xrle.cur_len = -1; c->u.e_xrle.to_flush = NULL; c->u.e_xrle.to_flush_size = 0; memcpy(c->u.e_xrle.rep_score, e->rep_score, 256*sizeof(*c->u.e_xrle.rep_score)); return c; } /* * --------------------------------------------------------------------------- * SUBEXP */ int cram_subexp_decode(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int32_t *out_i = (int32_t *)out; int n, count; int k = c->u.subexp.k; for (count = 0, n = *out_size; count < n; count++) { int i = 0, tail; int val; /* Get number of 1s */ //while (get_bit_MSB(in) == 1) i++; i = get_one_bits_MSB(in); if (i < 0 || cram_not_enough_bits(in, i > 0 ? i + k - 1 : k)) return -1; /* * Val is * i > 0: 2^(k+i-1) + k+i-1 bits * i = 0: k bits */ if (i) { tail = i + k-1; val = 0; while (tail) { //val = val<<1; val |= get_bit_MSB(in); GET_BIT_MSB(in, val); tail--; } val += 1 << (i + k-1); } else { tail = k; val = 0; while (tail) { //val = val<<1; val |= get_bit_MSB(in); GET_BIT_MSB(in, val); tail--; } } out_i[count] = val - c->u.subexp.offset; } return 0; } void cram_subexp_decode_free(cram_codec *c) { if (c) free(c); } int cram_subexp_describe(cram_codec *c, kstring_t *ks) { return ksprintf(ks, "SUBEXP(offset=%d,k=%d)", c->u.subexp.offset, c->u.subexp.k) < 0 ? -1 : 0; } cram_codec *cram_subexp_decode_init(cram_block_compression_hdr *hdr, char *data, int size, enum cram_encoding codec, enum cram_external_type option, int version, varint_vec *vv) { cram_codec *c; char *cp = data; if (option != E_INT) { hts_log_error("This codec only supports INT encodings"); return NULL; } if (!(c = malloc(sizeof(*c)))) return NULL; c->codec = E_SUBEXP; c->decode = cram_subexp_decode; c->free = cram_subexp_decode_free; c->describe = cram_subexp_describe; c->u.subexp.k = -1; c->u.subexp.offset = vv->varint_get32(&cp, data + size, NULL); c->u.subexp.k = vv->varint_get32(&cp, data + size, NULL); if (cp - data != size || c->u.subexp.k < 0) { hts_log_error("Malformed subexp header stream"); free(c); return NULL; } return c; } /* * --------------------------------------------------------------------------- * GAMMA */ int cram_gamma_decode(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int32_t *out_i = (int32_t *)out; int i, n; for (i = 0, n = *out_size; i < n; i++) { int nz = 0; int val; //while (get_bit_MSB(in) == 0) nz++; nz = get_zero_bits_MSB(in); if (cram_not_enough_bits(in, nz)) return -1; val = 1; while (nz > 0) { //val <<= 1; val |= get_bit_MSB(in); GET_BIT_MSB(in, val); nz--; } out_i[i] = val - c->u.gamma.offset; } return 0; } void cram_gamma_decode_free(cram_codec *c) { if (c) free(c); } int cram_gamma_describe(cram_codec *c, kstring_t *ks) { return ksprintf(ks, "GAMMA(offset=%d)", c->u.subexp.offset) < 0 ? -1 : 0; } cram_codec *cram_gamma_decode_init(cram_block_compression_hdr *hdr, char *data, int size, enum cram_encoding codec, enum cram_external_type option, int version, varint_vec *vv) { cram_codec *c = NULL; char *cp = data; if (option != E_INT) { hts_log_error("This codec only supports INT encodings"); return NULL; } if (size < 1) goto malformed; if (!(c = malloc(sizeof(*c)))) return NULL; c->codec = E_GAMMA; c->decode = cram_gamma_decode; c->free = cram_gamma_decode_free; c->describe = cram_gamma_describe; c->u.gamma.offset = vv->varint_get32(&cp, data+size, NULL); if (cp - data != size) goto malformed; return c; malformed: hts_log_error("Malformed gamma header stream"); free(c); return NULL; } /* * --------------------------------------------------------------------------- * HUFFMAN */ static int code_sort(const void *vp1, const void *vp2) { const cram_huffman_code *c1 = (const cram_huffman_code *)vp1; const cram_huffman_code *c2 = (const cram_huffman_code *)vp2; if (c1->len != c2->len) return c1->len - c2->len; else return c1->symbol < c2->symbol ? -1 : (c1->symbol > c2->symbol ? 1 : 0); } void cram_huffman_decode_free(cram_codec *c) { if (!c) return; if (c->u.huffman.codes) free(c->u.huffman.codes); free(c); } int cram_huffman_decode_null(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { return -1; } int cram_huffman_decode_char0(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int i, n; if (!out) return 0; /* Special case of 0 length codes */ for (i = 0, n = *out_size; i < n; i++) { out[i] = c->u.huffman.codes[0].symbol; } return 0; } int cram_huffman_decode_char(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int i, n, ncodes = c->u.huffman.ncodes; const cram_huffman_code * const codes = c->u.huffman.codes; for (i = 0, n = *out_size; i < n; i++) { int idx = 0; int val = 0, len = 0, last_len = 0; for (;;) { int dlen = codes[idx].len - last_len; if (cram_not_enough_bits(in, dlen)) return -1; //val <<= dlen; //val |= get_bits_MSB(in, dlen); //last_len = (len += dlen); last_len = (len += dlen); for (; dlen; dlen--) GET_BIT_MSB(in, val); idx = val - codes[idx].p; if (idx >= ncodes || idx < 0) return -1; if (codes[idx].code == val && codes[idx].len == len) { if (out) out[i] = codes[idx].symbol; break; } } } return 0; } int cram_huffman_decode_int0(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int32_t *out_i = (int32_t *)out; int i, n; const cram_huffman_code * const codes = c->u.huffman.codes; /* Special case of 0 length codes */ for (i = 0, n = *out_size; i < n; i++) { out_i[i] = codes[0].symbol; } return 0; } int cram_huffman_decode_int(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int32_t *out_i = (int32_t *)out; int i, n, ncodes = c->u.huffman.ncodes; const cram_huffman_code * const codes = c->u.huffman.codes; for (i = 0, n = *out_size; i < n; i++) { int idx = 0; int val = 0, len = 0, last_len = 0; // Now one bit at a time for remaining checks for (;;) { int dlen = codes[idx].len - last_len; if (cram_not_enough_bits(in, dlen)) return -1; //val <<= dlen; //val |= get_bits_MSB(in, dlen); //last_len = (len += dlen); last_len = (len += dlen); for (; dlen; dlen--) GET_BIT_MSB(in, val); idx = val - codes[idx].p; if (idx >= ncodes || idx < 0) return -1; if (codes[idx].code == val && codes[idx].len == len) { out_i[i] = codes[idx].symbol; break; } } } return 0; } int cram_huffman_decode_long0(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int64_t *out_i = (int64_t *)out; int i, n; const cram_huffman_code * const codes = c->u.huffman.codes; /* Special case of 0 length codes */ for (i = 0, n = *out_size; i < n; i++) { out_i[i] = codes[0].symbol; } return 0; } int cram_huffman_decode_long(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { int64_t *out_i = (int64_t *)out; int i, n, ncodes = c->u.huffman.ncodes; const cram_huffman_code * const codes = c->u.huffman.codes; for (i = 0, n = *out_size; i < n; i++) { int idx = 0; int val = 0, len = 0, last_len = 0; // Now one bit at a time for remaining checks for (;;) { int dlen = codes[idx].len - last_len; if (cram_not_enough_bits(in, dlen)) return -1; //val <<= dlen; //val |= get_bits_MSB(in, dlen); //last_len = (len += dlen); last_len = (len += dlen); for (; dlen; dlen--) GET_BIT_MSB(in, val); idx = val - codes[idx].p; if (idx >= ncodes || idx < 0) return -1; if (codes[idx].code == val && codes[idx].len == len) { out_i[i] = codes[idx].symbol; break; } } } return 0; } int cram_huffman_describe(cram_codec *c, kstring_t *ks) { int r = 0, n; r |= ksprintf(ks, "HUFFMAN(codes={") < 0; for (n = 0; n < c->u.huffman.ncodes; n++) { r |= ksprintf(ks, "%s%"PRId64, n?",":"", c->u.huffman.codes[n].symbol); } r |= ksprintf(ks, "},lengths={") < 0; for (n = 0; n < c->u.huffman.ncodes; n++) { r |= ksprintf(ks, "%s%d", n?",":"", c->u.huffman.codes[n].len); } r |= ksprintf(ks, "})") < 0; return r; } /* * Initialises a huffman decoder from an encoding data stream. */ cram_codec *cram_huffman_decode_init(cram_block_compression_hdr *hdr, char *data, int size, enum cram_encoding codec, enum cram_external_type option, int version, varint_vec *vv) { int32_t ncodes = 0, i, j; char *cp = data, *data_end = &data[size]; cram_codec *h; cram_huffman_code *codes = NULL; int32_t val, last_len, max_len = 0; uint32_t max_val; // needs one more bit than val const int max_code_bits = sizeof(val) * 8 - 1; int err = 0; if (option == E_BYTE_ARRAY_BLOCK) { hts_log_error("BYTE_ARRAYs not supported by this codec"); return NULL; } ncodes = vv->varint_get32(&cp, data_end, &err); if (ncodes < 0) { hts_log_error("Invalid number of symbols in huffman stream"); return NULL; } if (ncodes >= SIZE_MAX / sizeof(*codes)) { errno = ENOMEM; return NULL; } #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (ncodes > FUZZ_ALLOC_LIMIT / sizeof(*codes)) { errno = ENOMEM; return NULL; } #endif h = calloc(1, sizeof(*h)); if (!h) return NULL; h->codec = E_HUFFMAN; h->free = cram_huffman_decode_free; h->u.huffman.ncodes = ncodes; h->u.huffman.option = option; if (ncodes) { codes = h->u.huffman.codes = malloc(ncodes * sizeof(*codes)); if (!codes) { free(h); return NULL; } } else { codes = h->u.huffman.codes = NULL; } /* Read symbols and bit-lengths */ if (option == E_LONG) { for (i = 0; i < ncodes; i++) codes[i].symbol = vv->varint_get64(&cp, data_end, &err); } else if (option == E_INT || option == E_BYTE) { for (i = 0; i < ncodes; i++) codes[i].symbol = vv->varint_get32(&cp, data_end, &err); } else { goto malformed; } if (err) goto malformed; i = vv->varint_get32(&cp, data_end, &err); if (i != ncodes) goto malformed; if (ncodes == 0) { /* NULL huffman stream. Ensure it returns an error if anything tries to use it. */ h->decode = cram_huffman_decode_null; return h; } for (i = 0; i < ncodes; i++) { codes[i].len = vv->varint_get32(&cp, data_end, &err); if (err) break; if (codes[i].len < 0) { hts_log_error("Huffman code length (%d) is negative", codes[i].len); goto malformed; } if (max_len < codes[i].len) max_len = codes[i].len; } if (err || cp - data != size || max_len >= ncodes) goto malformed; /* 31 is max. bits available in val */ if (max_len > max_code_bits) { hts_log_error("Huffman code length (%d) is greater " "than maximum supported (%d)", max_len, max_code_bits); goto malformed; } /* Sort by bit length and then by symbol value */ qsort(codes, ncodes, sizeof(*codes), code_sort); /* Assign canonical codes */ val = -1, last_len = 0, max_val = 0; for (i = 0; i < ncodes; i++) { val++; if (val > max_val) goto malformed; if (codes[i].len > last_len) { val <<= (codes[i].len - last_len); last_len = codes[i].len; max_val = (1U << codes[i].len) - 1; } codes[i].code = val; } /* * Compute the next starting point, offset by the i'th value. * For example if codes 10, 11, 12, 13 are 30, 31, 32, 33 then * codes[10..13].p = 30 - 10. */ last_len = 0; for (i = j = 0; i < ncodes; i++) { if (codes[i].len > last_len) { j = codes[i].code - i; last_len = codes[i].len; } codes[i].p = j; } // puts("==HUFF LEN=="); // for (i = 0; i <= last_len+1; i++) { // printf("len %d=%d prefix %d\n", i, h->u.huffman.lengths[i], h->u.huffman.prefix[i]); // } // puts("===HUFFMAN CODES==="); // for (i = 0; i < ncodes; i++) { // int j; // printf("%d: %d %d %d ", i, codes[i].symbol, codes[i].len, codes[i].code); // j = codes[i].len; // while (j) { // putchar(codes[i].code & (1 << --j) ? '1' : '0'); // } // printf(" %d\n", codes[i].code); // } if (option == E_BYTE || option == E_BYTE_ARRAY) { if (h->u.huffman.codes[0].len == 0) h->decode = cram_huffman_decode_char0; else h->decode = cram_huffman_decode_char; } else if (option == E_LONG || option == E_SLONG) { if (h->u.huffman.codes[0].len == 0) h->decode = cram_huffman_decode_long0; else h->decode = cram_huffman_decode_long; } else if (option == E_INT || option == E_SINT || option == E_BYTE) { if (h->u.huffman.codes[0].len == 0) h->decode = cram_huffman_decode_int0; else h->decode = cram_huffman_decode_int; } else { return NULL; } h->describe = cram_huffman_describe; return (cram_codec *)h; malformed: hts_log_error("Malformed huffman header stream"); free(codes); free(h); return NULL; } int cram_huffman_encode_char0(cram_slice *slice, cram_codec *c, char *in, int in_size) { return 0; } int cram_huffman_encode_char(cram_slice *slice, cram_codec *c, char *in, int in_size) { int i, code, len, r = 0; unsigned char *syms = (unsigned char *)in; while (in_size--) { int sym = *syms++; if (sym >= -1 && sym < MAX_HUFF) { i = c->u.e_huffman.val2code[sym+1]; assert(c->u.e_huffman.codes[i].symbol == sym); code = c->u.e_huffman.codes[i].code; len = c->u.e_huffman.codes[i].len; } else { /* Slow - use a lookup table for when sym < MAX_HUFF? */ for (i = 0; i < c->u.e_huffman.nvals; i++) { if (c->u.e_huffman.codes[i].symbol == sym) break; } if (i == c->u.e_huffman.nvals) return -1; code = c->u.e_huffman.codes[i].code; len = c->u.e_huffman.codes[i].len; } r |= store_bits_MSB(c->out, code, len); } return r; } int cram_huffman_encode_int0(cram_slice *slice, cram_codec *c, char *in, int in_size) { return 0; } int cram_huffman_encode_int(cram_slice *slice, cram_codec *c, char *in, int in_size) { int i, code, len, r = 0; int *syms = (int *)in; while (in_size--) { int sym = *syms++; if (sym >= -1 && sym < MAX_HUFF) { i = c->u.e_huffman.val2code[sym+1]; assert(c->u.e_huffman.codes[i].symbol == sym); code = c->u.e_huffman.codes[i].code; len = c->u.e_huffman.codes[i].len; } else { /* Slow - use a lookup table for when sym < MAX_HUFFMAN_SYM? */ for (i = 0; i < c->u.e_huffman.nvals; i++) { if (c->u.e_huffman.codes[i].symbol == sym) break; } if (i == c->u.e_huffman.nvals) return -1; code = c->u.e_huffman.codes[i].code; len = c->u.e_huffman.codes[i].len; } r |= store_bits_MSB(c->out, code, len); } return r; } int cram_huffman_encode_long0(cram_slice *slice, cram_codec *c, char *in, int in_size) { return 0; } int cram_huffman_encode_long(cram_slice *slice, cram_codec *c, char *in, int in_size) { int i, code, len, r = 0; int64_t *syms = (int64_t *)in; while (in_size--) { int sym = *syms++; if (sym >= -1 && sym < MAX_HUFF) { i = c->u.e_huffman.val2code[sym+1]; assert(c->u.e_huffman.codes[i].symbol == sym); code = c->u.e_huffman.codes[i].code; len = c->u.e_huffman.codes[i].len; } else { /* Slow - use a lookup table for when sym < MAX_HUFFMAN_SYM? */ for (i = 0; i < c->u.e_huffman.nvals; i++) { if (c->u.e_huffman.codes[i].symbol == sym) break; } if (i == c->u.e_huffman.nvals) return -1; code = c->u.e_huffman.codes[i].code; len = c->u.e_huffman.codes[i].len; } r |= store_bits_MSB(c->out, code, len); } return r; } void cram_huffman_encode_free(cram_codec *c) { if (!c) return; if (c->u.e_huffman.codes) free(c->u.e_huffman.codes); free(c); } /* * Encodes a huffman tree. * Returns number of bytes written. */ int cram_huffman_encode_store(cram_codec *c, cram_block *b, char *prefix, int version) { int i, len = 0, r = 0, n; cram_huffman_code *codes = c->u.e_huffman.codes; /* * Up to code length 127 means 2.5e+26 bytes of data required (worst * case huffman tree needs symbols with freqs matching the Fibonacci * series). So guaranteed 1 byte per code. * * Symbols themselves could be 5 bytes (eg -1 is 5 bytes in itf8). * * Therefore 6*ncodes + 5 + 5 + 1 + 5 is max memory */ char *tmp = malloc(6*c->u.e_huffman.nvals+16); char *tp = tmp, *tpend = tmp+6*c->u.e_huffman.nvals+16; if (!tmp) return -1; if (prefix) { size_t l = strlen(prefix); BLOCK_APPEND(b, prefix, l); len += l; } tp += c->vv->varint_put32(tp, tpend, c->u.e_huffman.nvals); if (c->u.e_huffman.option == E_LONG) { for (i = 0; i < c->u.e_huffman.nvals; i++) { tp += c->vv->varint_put64(tp, tpend, codes[i].symbol); } } else if (c->u.e_huffman.option == E_SLONG) { for (i = 0; i < c->u.e_huffman.nvals; i++) { tp += c->vv->varint_put64s(tp, tpend, codes[i].symbol); } } else if (c->u.e_huffman.option == E_INT || c->u.e_huffman.option == E_BYTE) { for (i = 0; i < c->u.e_huffman.nvals; i++) { tp += c->vv->varint_put32(tp, tpend, codes[i].symbol); } } else if (c->u.e_huffman.option == E_SINT) { for (i = 0; i < c->u.e_huffman.nvals; i++) { tp += c->vv->varint_put32s(tp, tpend, codes[i].symbol); } } else { return -1; } tp += c->vv->varint_put32(tp, tpend, c->u.e_huffman.nvals); for (i = 0; i < c->u.e_huffman.nvals; i++) tp += c->vv->varint_put32(tp, tpend, codes[i].len); len += (n = c->vv->varint_put32_blk(b, c->codec)); r |= n; len += (n = c->vv->varint_put32_blk(b, tp-tmp)); r |= n; BLOCK_APPEND(b, tmp, tp-tmp); len += tp-tmp; free(tmp); if (r > 0) return len; block_err: return -1; } cram_codec *cram_huffman_encode_init(cram_stats *st, enum cram_encoding codec, enum cram_external_type option, void *dat, int version, varint_vec *vv) { int *vals = NULL, *freqs = NULL, *lens = NULL, code, len; int *new_vals, *new_freqs; int i, max_val = 0, min_val = INT_MAX, k; size_t nvals, vals_alloc = 0; cram_codec *c; cram_huffman_code *codes; c = malloc(sizeof(*c)); if (!c) return NULL; c->codec = E_HUFFMAN; /* Count number of unique symbols */ for (nvals = i = 0; i < MAX_STAT_VAL; i++) { if (!st->freqs[i]) continue; if (nvals >= vals_alloc) { vals_alloc = vals_alloc ? vals_alloc*2 : 1024; new_vals = realloc(vals, vals_alloc * sizeof(int)); if (!new_vals) goto nomem; vals = new_vals; new_freqs = realloc(freqs, vals_alloc * sizeof(int)); if (!new_freqs) goto nomem; freqs = new_freqs; } vals[nvals] = i; freqs[nvals] = st->freqs[i]; assert(st->freqs[i] > 0); if (max_val < i) max_val = i; if (min_val > i) min_val = i; nvals++; } if (st->h) { khint_t k; for (k = kh_begin(st->h); k != kh_end(st->h); k++) { if (!kh_exist(st->h, k)) continue; if (nvals >= vals_alloc) { vals_alloc = vals_alloc ? vals_alloc*2 : 1024; new_vals = realloc(vals, vals_alloc * sizeof(int)); if (!new_vals) goto nomem; vals = new_vals; new_freqs = realloc(freqs, vals_alloc * sizeof(int)); if (!new_freqs) goto nomem; freqs = new_freqs; } vals[nvals]= kh_key(st->h, k); freqs[nvals] = kh_val(st->h, k); assert(freqs[nvals] > 0); if (max_val < i) max_val = i; if (min_val > i) min_val = i; nvals++; } } assert(nvals > 0); new_freqs = realloc(freqs, 2*nvals*sizeof(*freqs)); if (!new_freqs) goto nomem; freqs = new_freqs; lens = calloc(2*nvals, sizeof(*lens)); if (!lens) goto nomem; /* Inefficient, use pointers to form chain so we can insert and maintain * a sorted list? This is currently O(nvals^2) complexity. */ for (;;) { int low1 = INT_MAX, low2 = INT_MAX; int ind1 = 0, ind2 = 0; for (i = 0; i < nvals; i++) { if (freqs[i] < 0) continue; if (low1 > freqs[i]) low2 = low1, ind2 = ind1, low1 = freqs[i], ind1 = i; else if (low2 > freqs[i]) low2 = freqs[i], ind2 = i; } if (low2 == INT_MAX) break; freqs[nvals] = low1 + low2; lens[ind1] = nvals; lens[ind2] = nvals; freqs[ind1] *= -1; freqs[ind2] *= -1; nvals++; } nvals = nvals/2+1; /* Assign lengths */ for (i = 0; i < nvals; i++) { int code_len = 0; for (k = lens[i]; k; k = lens[k]) code_len++; lens[i] = code_len; freqs[i] *= -1; //fprintf(stderr, "%d / %d => %d\n", vals[i], freqs[i], lens[i]); } /* Sort, need in a struct */ if (!(codes = malloc(nvals * sizeof(*codes)))) goto nomem; for (i = 0; i < nvals; i++) { codes[i].symbol = vals[i]; codes[i].len = lens[i]; } qsort(codes, nvals, sizeof(*codes), code_sort); /* * Generate canonical codes from lengths. * Sort by length. * Start with 0. * Every new code of same length is +1. * Every new code of new length is +1 then <<1 per extra length. * * /\ * a/\ * /\/\ * bcd/\ * ef * * a 1 0 * b 3 4 (0+1)<<2 * c 3 5 * d 3 6 * e 4 14 (6+1)<<1 * f 5 15 */ code = 0; len = codes[0].len; for (i = 0; i < nvals; i++) { while (len != codes[i].len) { code<<=1; len++; } codes[i].code = code++; if (codes[i].symbol >= -1 && codes[i].symbol < MAX_HUFF) c->u.e_huffman.val2code[codes[i].symbol+1] = i; //fprintf(stderr, "sym %d, code %d, len %d\n", // codes[i].symbol, codes[i].code, codes[i].len); } free(lens); free(vals); free(freqs); c->u.e_huffman.codes = codes; c->u.e_huffman.nvals = nvals; c->u.e_huffman.option = option; c->free = cram_huffman_encode_free; if (option == E_BYTE || option == E_BYTE_ARRAY) { if (c->u.e_huffman.codes[0].len == 0) c->encode = cram_huffman_encode_char0; else c->encode = cram_huffman_encode_char; } else if (option == E_INT || option == E_SINT) { if (c->u.e_huffman.codes[0].len == 0) c->encode = cram_huffman_encode_int0; else c->encode = cram_huffman_encode_int; } else if (option == E_LONG || option == E_SLONG) { if (c->u.e_huffman.codes[0].len == 0) c->encode = cram_huffman_encode_long0; else c->encode = cram_huffman_encode_long; } else { return NULL; } c->store = cram_huffman_encode_store; c->flush = NULL; return c; nomem: hts_log_error("Out of memory"); free(vals); free(freqs); free(lens); free(c); return NULL; } /* * --------------------------------------------------------------------------- * BYTE_ARRAY_LEN */ int cram_byte_array_len_decode(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { /* Fetch length */ int32_t len = 0, one = 1; int r; r = c->u.byte_array_len.len_codec->decode(slice, c->u.byte_array_len.len_codec, in, (char *)&len, &one); //printf("ByteArray Len=%d\n", len); if (!r && c->u.byte_array_len.val_codec && len >= 0) { r = c->u.byte_array_len.val_codec->decode(slice, c->u.byte_array_len.val_codec, in, out, &len); } else { return -1; } *out_size = len; return r; } void cram_byte_array_len_decode_free(cram_codec *c) { if (!c) return; if (c->u.byte_array_len.len_codec) c->u.byte_array_len.len_codec->free(c->u.byte_array_len.len_codec); if (c->u.byte_array_len.val_codec) c->u.byte_array_len.val_codec->free(c->u.byte_array_len.val_codec); free(c); } int cram_byte_array_len_describe(cram_codec *c, kstring_t *ks) { int r = 0; r |= ksprintf(ks, "BYTE_ARRAY_LEN(len_codec={") < 0; cram_byte_array_len_decoder *l = &c->u.byte_array_len; r |= l->len_codec->describe ? l->len_codec->describe(l->len_codec, ks) : (ksprintf(ks, "?")<0); r |= ksprintf(ks, "},val_codec={") < 0; r |= l->val_codec->describe ? l->val_codec->describe(l->val_codec, ks) : (ksprintf(ks, "?")<0); r |= ksprintf(ks, "}") < 0; return r; } cram_codec *cram_byte_array_len_decode_init(cram_block_compression_hdr *hdr, char *data, int size, enum cram_encoding codec, enum cram_external_type option, int version, varint_vec *vv) { cram_codec *c; char *cp = data; char *endp = data + size; if (!(c = malloc(sizeof(*c)))) return NULL; c->codec = E_BYTE_ARRAY_LEN; c->decode = cram_byte_array_len_decode; c->free = cram_byte_array_len_decode_free; c->describe = cram_byte_array_len_describe; c->u.byte_array_len.len_codec = NULL; c->u.byte_array_len.val_codec = NULL; int encoding = vv->varint_get32(&cp, endp, NULL); int sub_size = vv->varint_get32(&cp, endp, NULL); if (sub_size < 0 || endp - cp < sub_size) goto malformed; c->u.byte_array_len.len_codec = cram_decoder_init(hdr, encoding, cp, sub_size, E_INT, version, vv); if (c->u.byte_array_len.len_codec == NULL) goto no_codec; cp += sub_size; encoding = vv->varint_get32(&cp, endp, NULL); sub_size = vv->varint_get32(&cp, endp, NULL); if (sub_size < 0 || endp - cp < sub_size) goto malformed; c->u.byte_array_len.val_codec = cram_decoder_init(hdr, encoding, cp, sub_size, option, version, vv); if (c->u.byte_array_len.val_codec == NULL) goto no_codec; cp += sub_size; if (cp - data != size) goto malformed; return c; malformed: hts_log_error("Malformed byte_array_len header stream"); no_codec: cram_byte_array_len_decode_free(c); return NULL; } int cram_byte_array_len_encode(cram_slice *slice, cram_codec *c, char *in, int in_size) { int32_t i32 = in_size; int r = 0; r |= c->u.e_byte_array_len.len_codec->encode(slice, c->u.e_byte_array_len.len_codec, (char *)&i32, 1); r |= c->u.e_byte_array_len.val_codec->encode(slice, c->u.e_byte_array_len.val_codec, in, in_size); return r; } void cram_byte_array_len_encode_free(cram_codec *c) { if (!c) return; if (c->u.e_byte_array_len.len_codec) c->u.e_byte_array_len.len_codec->free(c->u.e_byte_array_len.len_codec); if (c->u.e_byte_array_len.val_codec) c->u.e_byte_array_len.val_codec->free(c->u.e_byte_array_len.val_codec); free(c); } int cram_byte_array_len_encode_store(cram_codec *c, cram_block *b, char *prefix, int version) { int len = 0, len2, len3, r = 0, n; cram_codec *tc; cram_block *b_len = NULL, *b_val = NULL; if (prefix) { size_t l = strlen(prefix); BLOCK_APPEND(b, prefix, l); len += l; } tc = c->u.e_byte_array_len.len_codec; b_len = cram_new_block(0, 0); if (!b_len) goto block_err; len2 = tc->store(tc, b_len, NULL, version); if (len2 < 0) goto block_err; tc = c->u.e_byte_array_len.val_codec; b_val = cram_new_block(0, 0); if (!b_val) goto block_err; len3 = tc->store(tc, b_val, NULL, version); if (len3 < 0) goto block_err; len += (n = c->vv->varint_put32_blk(b, c->codec)); r |= n; len += (n = c->vv->varint_put32_blk(b, len2+len3)); r |= n; BLOCK_APPEND(b, BLOCK_DATA(b_len), BLOCK_SIZE(b_len)); BLOCK_APPEND(b, BLOCK_DATA(b_val), BLOCK_SIZE(b_val)); cram_free_block(b_len); cram_free_block(b_val); if (r > 0) return len + len2 + len3; block_err: if (b_len) cram_free_block(b_len); if (b_val) cram_free_block(b_val); return -1; } cram_codec *cram_byte_array_len_encode_init(cram_stats *st, enum cram_encoding codec, enum cram_external_type option, void *dat, int version, varint_vec *vv) { cram_codec *c; cram_byte_array_len_encoder *e = (cram_byte_array_len_encoder *)dat; c = malloc(sizeof(*c)); if (!c) return NULL; c->codec = E_BYTE_ARRAY_LEN; c->free = cram_byte_array_len_encode_free; c->encode = cram_byte_array_len_encode; c->store = cram_byte_array_len_encode_store; c->flush = NULL; c->u.e_byte_array_len.len_codec = cram_encoder_init(e->len_encoding, st, E_INT, e->len_dat, version, vv); c->u.e_byte_array_len.val_codec = cram_encoder_init(e->val_encoding, NULL, E_BYTE_ARRAY, e->val_dat, version, vv); if (!c->u.e_byte_array_len.len_codec || !c->u.e_byte_array_len.val_codec) { cram_byte_array_len_encode_free(c); return NULL; } return c; } /* * --------------------------------------------------------------------------- * BYTE_ARRAY_STOP */ static int cram_byte_array_stop_decode_char(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { char *cp, ch; cram_block *b = NULL; b = cram_get_block_by_id(slice, c->u.byte_array_stop.content_id); if (!b) return *out_size?-1:0; if (b->idx >= b->uncomp_size) return -1; cp = (char *)b->data + b->idx; if (out) { while ((ch = *cp) != (char)c->u.byte_array_stop.stop) { if (cp - (char *)b->data >= b->uncomp_size) return -1; *out++ = ch; cp++; } } else { // Consume input, but produce no output while ((ch = *cp) != (char)c->u.byte_array_stop.stop) { if (cp - (char *)b->data >= b->uncomp_size) return -1; cp++; } } *out_size = cp - (char *)(b->data + b->idx); b->idx = cp - (char *)b->data + 1; return 0; } int cram_byte_array_stop_decode_block(cram_slice *slice, cram_codec *c, cram_block *in, char *out_, int *out_size) { cram_block *b; cram_block *out = (cram_block *)out_; unsigned char *cp, *cp_end; unsigned char stop; b = cram_get_block_by_id(slice, c->u.byte_array_stop.content_id); if (!b) return *out_size?-1:0; if (b->idx >= b->uncomp_size) return -1; cp = b->data + b->idx; cp_end = b->data + b->uncomp_size; stop = c->u.byte_array_stop.stop; if (cp_end - cp < out->alloc - out->byte) { unsigned char *out_cp = BLOCK_END(out); while (cp != cp_end && *cp != stop) *out_cp++ = *cp++; BLOCK_SIZE(out) = out_cp - BLOCK_DATA(out); } else { unsigned char *cp_start; for (cp_start = cp; cp != cp_end && *cp != stop; cp++) ; BLOCK_APPEND(out, cp_start, cp - cp_start); BLOCK_GROW(out, cp - cp_start); } *out_size = cp - (b->data + b->idx); b->idx = cp - b->data + 1; return 0; block_err: return -1; } void cram_byte_array_stop_decode_free(cram_codec *c) { if (!c) return; free(c); } int cram_byte_array_stop_describe(cram_codec *c, kstring_t *ks) { return ksprintf(ks, "BYTE_ARRAY_STOP(stop=%d,id=%d)", c->u.byte_array_stop.stop, c->u.byte_array_stop.content_id) < 0 ? -1 : 0; } cram_codec *cram_byte_array_stop_decode_init(cram_block_compression_hdr *hdr, char *data, int size, enum cram_encoding codec, enum cram_external_type option, int version, varint_vec *vv) { cram_codec *c = NULL; unsigned char *cp = (unsigned char *)data; int err = 0; if (size < (CRAM_MAJOR_VERS(version) == 1 ? 5 : 2)) goto malformed; if (!(c = malloc(sizeof(*c)))) return NULL; c->codec = E_BYTE_ARRAY_STOP; switch (option) { case E_BYTE_ARRAY_BLOCK: c->decode = cram_byte_array_stop_decode_block; break; case E_BYTE_ARRAY: c->decode = cram_byte_array_stop_decode_char; break; default: hts_log_error("The byte_array_stop codec only supports BYTE_ARRAYs"); free(c); return NULL; } c->free = cram_byte_array_stop_decode_free; c->describe = cram_byte_array_stop_describe; c->u.byte_array_stop.stop = *cp++; if (CRAM_MAJOR_VERS(version) == 1) { c->u.byte_array_stop.content_id = cp[0] + (cp[1]<<8) + (cp[2]<<16) + ((unsigned int) cp[3]<<24); cp += 4; } else { c->u.byte_array_stop.content_id = vv->varint_get32((char **)&cp, data+size, &err); } if ((char *)cp - data != size || err) goto malformed; return c; malformed: hts_log_error("Malformed byte_array_stop header stream"); free(c); return NULL; } int cram_byte_array_stop_encode(cram_slice *slice, cram_codec *c, char *in, int in_size) { BLOCK_APPEND(c->out, in, in_size); BLOCK_APPEND_CHAR(c->out, c->u.e_byte_array_stop.stop); return 0; block_err: return -1; } void cram_byte_array_stop_encode_free(cram_codec *c) { if (!c) return; free(c); } int cram_byte_array_stop_encode_store(cram_codec *c, cram_block *b, char *prefix, int version) { int len = 0; char buf[20], *cp = buf; if (prefix) { size_t l = strlen(prefix); BLOCK_APPEND(b, prefix, l); len += l; } cp += c->vv->varint_put32(cp, buf+20, c->codec); if (CRAM_MAJOR_VERS(version) == 1) { cp += c->vv->varint_put32(cp, buf+20, 5); *cp++ = c->u.e_byte_array_stop.stop; *cp++ = (c->u.e_byte_array_stop.content_id >> 0) & 0xff; *cp++ = (c->u.e_byte_array_stop.content_id >> 8) & 0xff; *cp++ = (c->u.e_byte_array_stop.content_id >> 16) & 0xff; *cp++ = (c->u.e_byte_array_stop.content_id >> 24) & 0xff; } else { cp += c->vv->varint_put32(cp, buf+20, 1 + c->vv->varint_size(c->u.e_byte_array_stop.content_id)); *cp++ = c->u.e_byte_array_stop.stop; cp += c->vv->varint_put32(cp, buf+20, c->u.e_byte_array_stop.content_id); } BLOCK_APPEND(b, buf, cp-buf); len += cp-buf; return len; block_err: return -1; } cram_codec *cram_byte_array_stop_encode_init(cram_stats *st, enum cram_encoding codec, enum cram_external_type option, void *dat, int version, varint_vec *vv) { cram_codec *c; c = malloc(sizeof(*c)); if (!c) return NULL; c->codec = E_BYTE_ARRAY_STOP; c->free = cram_byte_array_stop_encode_free; c->encode = cram_byte_array_stop_encode; c->store = cram_byte_array_stop_encode_store; c->flush = NULL; c->u.e_byte_array_stop.stop = ((int *)dat)[0]; c->u.e_byte_array_stop.content_id = ((int *)dat)[1]; return c; } /* * --------------------------------------------------------------------------- */ const char *cram_encoding2str(enum cram_encoding t) { switch (t) { case E_NULL: return "NULL"; case E_EXTERNAL: return "EXTERNAL"; case E_GOLOMB: return "GOLOMB"; case E_HUFFMAN: return "HUFFMAN"; case E_BYTE_ARRAY_LEN: return "BYTE_ARRAY_LEN"; case E_BYTE_ARRAY_STOP: return "BYTE_ARRAY_STOP"; case E_BETA: return "BETA"; case E_SUBEXP: return "SUBEXP"; case E_GOLOMB_RICE: return "GOLOMB_RICE"; case E_GAMMA: return "GAMMA"; case E_VARINT_UNSIGNED: return "VARINT_UNSIGNED"; case E_VARINT_SIGNED: return "VARINT_SIGNED"; case E_CONST_BYTE: return "CONST_BYTE"; case E_CONST_INT: return "CONST_INT"; case E_NUM_CODECS: default: return "?"; } } static cram_codec *(*decode_init[])(cram_block_compression_hdr *hdr, char *data, int size, enum cram_encoding codec, enum cram_external_type option, int version, varint_vec *vv) = { // CRAM 3.0 valid codecs NULL, // null codec cram_external_decode_init, NULL, // golomb cram_huffman_decode_init, cram_byte_array_len_decode_init, cram_byte_array_stop_decode_init, cram_beta_decode_init, cram_subexp_decode_init, NULL, // golomb rice cram_gamma_decode_init, // Gap between CRAM 3 and CRAM 4; 9 to 39 inclusive NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, // was xbyte cram_varint_decode_init, // varint unsigned cram_varint_decode_init, // varint signed cram_const_decode_init, // const byte cram_const_decode_init, // const int // Gap to CRAM 4 transfomrations; 45 to 49 inclusive NULL, NULL, NULL, NULL, NULL, NULL, // xhuffman cram_xpack_decode_init, cram_xrle_decode_init, cram_xdelta_decode_init, }; cram_codec *cram_decoder_init(cram_block_compression_hdr *hdr, enum cram_encoding codec, char *data, int size, enum cram_external_type option, int version, varint_vec *vv) { if (codec >= E_NULL && codec < E_NUM_CODECS && decode_init[codec]) { cram_codec *r = decode_init[codec](hdr, data, size, codec, option, version, vv); if (r) { r->vv = vv; r->codec_id = hdr->ncodecs++; } return r; } else { hts_log_error("Unimplemented codec of type %s", cram_encoding2str(codec)); return NULL; } } static cram_codec *(*encode_init[])(cram_stats *stx, enum cram_encoding codec, enum cram_external_type option, void *opt, int version, varint_vec *vv) = { // CRAM 3.0 valid codecs NULL, // null codec cram_external_encode_init, // int/bytes in cram 3, byte only in cram 4 NULL, // golomb cram_huffman_encode_init, cram_byte_array_len_encode_init, cram_byte_array_stop_encode_init, cram_beta_encode_init, NULL, // subexponential (we support decode only) NULL, // golomb rice NULL, // gamma (we support decode only) // Gap between CRAM 3 and CRAM 4; 9 to 39 inclusive NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, // was xbyte cram_varint_encode_init, // varint unsigned cram_varint_encode_init, // varint signed cram_const_encode_init, // const byte cram_const_encode_init, // const int // Gap to CRAM 4 transfomrations; 45 to 49 inclusive NULL, NULL, NULL, NULL, NULL, NULL, // xhuffman cram_xpack_encode_init, cram_xrle_encode_init, cram_xdelta_encode_init, }; cram_codec *cram_encoder_init(enum cram_encoding codec, cram_stats *st, enum cram_external_type option, void *dat, int version, varint_vec *vv) { if (st && !st->nvals) return NULL; // cram_stats_encoding assumes integer data, but if option // is E_BYTE then tweak the requested encoding. This ought // to be fixed in cram_stats_encoding instead. if (option == E_BYTE || option == E_BYTE_ARRAY || option == E_BYTE_ARRAY_BLOCK) { if (codec == E_VARINT_SIGNED || codec == E_VARINT_UNSIGNED) codec = E_EXTERNAL; else if (codec == E_CONST_INT) codec = E_CONST_BYTE; } if (encode_init[codec]) { cram_codec *r; if ((r = encode_init[codec](st, codec, option, dat, version, vv))) r->out = NULL; if (!r) { hts_log_error("Unable to initialise codec of type %s", cram_encoding2str(codec)); return NULL; } r->vv = vv; return r; } else { hts_log_error("Unimplemented codec of type %s", cram_encoding2str(codec)); abort(); } } /* * Returns the content_id used by this codec, also in id2 if byte_array_len. * Returns -1 for the CORE block and -2 for unneeded. * id2 is only filled out for BYTE_ARRAY_LEN which uses 2 codecs. */ int cram_codec_to_id(cram_codec *c, int *id2) { int bnum1, bnum2 = -2; switch (c->codec) { case E_CONST_INT: case E_CONST_BYTE: bnum1 = -2; // no blocks used break; case E_HUFFMAN: bnum1 = c->u.huffman.ncodes == 1 ? -2 : -1; break; case E_GOLOMB: case E_BETA: case E_SUBEXP: case E_GOLOMB_RICE: case E_GAMMA: // CORE block bnum1 = -1; break; case E_EXTERNAL: case E_VARINT_UNSIGNED: case E_VARINT_SIGNED: bnum1 = c->u.external.content_id; break; case E_BYTE_ARRAY_LEN: bnum1 = cram_codec_to_id(c->u.byte_array_len.len_codec, NULL); bnum2 = cram_codec_to_id(c->u.byte_array_len.val_codec, NULL); break; case E_BYTE_ARRAY_STOP: bnum1 = c->u.byte_array_stop.content_id; break; case E_NULL: bnum1 = -2; break; default: hts_log_error("Unknown codec type %d", c->codec); bnum1 = -1; } if (id2) *id2 = bnum2; return bnum1; } /* * cram_codec structures are specialised for decoding or encoding. * Unfortunately this makes turning a decoder into an encoder (such as * when transcoding files) problematic. * * This function converts a cram decoder codec into an encoder version * in-place (ie it modifiers the codec itself). * * Returns 0 on success; * -1 on failure. */ int cram_codec_decoder2encoder(cram_fd *fd, cram_codec *c) { int j; switch (c->codec) { case E_CONST_INT: case E_CONST_BYTE: // shares struct with decode c->store = cram_const_encode_store; break; case E_EXTERNAL: // shares struct with decode c->free = cram_external_encode_free; c->store = cram_external_encode_store; if (c->decode == cram_external_decode_int) c->encode = cram_external_encode_int; else if (c->decode == cram_external_decode_long) c->encode = cram_external_encode_long; else if (c->decode == cram_external_decode_char) c->encode = cram_external_encode_char; else if (c->decode == cram_external_decode_block) c->encode = cram_external_encode_char; else return -1; break; case E_VARINT_SIGNED: case E_VARINT_UNSIGNED: // shares struct with decode c->free = cram_varint_encode_free; c->store = cram_varint_encode_store; if (c->decode == cram_varint_decode_int) c->encode = cram_varint_encode_int; else if (c->decode == cram_varint_decode_sint) c->encode = cram_varint_encode_sint; else if (c->decode == cram_varint_decode_long) c->encode = cram_varint_encode_long; else if (c->decode == cram_varint_decode_slong) c->encode = cram_varint_encode_slong; else return -1; break; case E_HUFFMAN: { // New structure, so switch. // FIXME: we huffman and e_huffman structs amended, we could // unify this. cram_codec *t = malloc(sizeof(*t)); if (!t) return -1; t->vv = c->vv; t->codec = E_HUFFMAN; t->free = cram_huffman_encode_free; t->store = cram_huffman_encode_store; t->u.e_huffman.codes = c->u.huffman.codes; t->u.e_huffman.nvals = c->u.huffman.ncodes; t->u.e_huffman.option = c->u.huffman.option; for (j = 0; j < t->u.e_huffman.nvals; j++) { int32_t sym = t->u.e_huffman.codes[j].symbol; if (sym >= -1 && sym < MAX_HUFF) t->u.e_huffman.val2code[sym+1] = j; } if (c->decode == cram_huffman_decode_char0) t->encode = cram_huffman_encode_char0; else if (c->decode == cram_huffman_decode_char) t->encode = cram_huffman_encode_char; else if (c->decode == cram_huffman_decode_int0) t->encode = cram_huffman_encode_int0; else if (c->decode == cram_huffman_decode_int) t->encode = cram_huffman_encode_int; else if (c->decode == cram_huffman_decode_long0) t->encode = cram_huffman_encode_long0; else if (c->decode == cram_huffman_decode_long) t->encode = cram_huffman_encode_long; else { free(t); return -1; } *c = *t; free(t); break; } case E_BETA: // shares struct with decode c->free = cram_beta_encode_free; c->store = cram_beta_encode_store; if (c->decode == cram_beta_decode_int) c->encode = cram_beta_encode_int; else if (c->decode == cram_beta_decode_long) c->encode = cram_beta_encode_long; else if (c->decode == cram_beta_decode_char) c->encode = cram_beta_encode_char; else return -1; break; case E_XPACK: { // shares struct with decode cram_codec t = *c; t.free = cram_xpack_encode_free; t.store = cram_xpack_encode_store; if (t.decode == cram_xpack_decode_long) t.encode = cram_xpack_encode_long; else if (t.decode == cram_xpack_decode_int) t.encode = cram_xpack_encode_int; else if (t.decode == cram_xpack_decode_char) t.encode = cram_xpack_encode_char; else return -1; t.u.e_xpack.sub_codec = t.u.xpack.sub_codec; if (cram_codec_decoder2encoder(fd, t.u.e_xpack.sub_codec) == -1) return -1; *c = t; break; } case E_BYTE_ARRAY_LEN: { cram_codec *t = malloc(sizeof(*t)); if (!t) return -1; t->vv = c->vv; t->codec = E_BYTE_ARRAY_LEN; t->free = cram_byte_array_len_encode_free; t->store = cram_byte_array_len_encode_store; t->encode = cram_byte_array_len_encode; t->u.e_byte_array_len.len_codec = c->u.byte_array_len.len_codec; t->u.e_byte_array_len.val_codec = c->u.byte_array_len.val_codec; if (cram_codec_decoder2encoder(fd, t->u.e_byte_array_len.len_codec) == -1 || cram_codec_decoder2encoder(fd, t->u.e_byte_array_len.val_codec) == -1) { t->free(t); return -1; } // {len,val}_{encoding,dat} are undefined, but unused. // Leaving them unset here means we can test that assertion. *c = *t; free(t); break; } case E_BYTE_ARRAY_STOP: // shares struct with decode c->free = cram_byte_array_stop_encode_free; c->store = cram_byte_array_stop_encode_store; c->encode = cram_byte_array_stop_encode; break; default: return -1; } return 0; } int cram_codec_describe(cram_codec *c, kstring_t *ks) { if (c && c->describe) return c->describe(c, ks); else return ksprintf(ks, "?"); } pysam-0.23.0/htslib/cram/cram_codecs.h000066400000000000000000000205541475062545500175720ustar00rootroot00000000000000/* Copyright (c) 2012-2015, 2018, 2020, 2023 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef CRAM_CODECS_H #define CRAM_CODECS_H #include #ifdef __cplusplus extern "C" { #endif struct cram_codec; /* * Slow but simple huffman decoder to start with. * Read a bit at a time, keeping track of {length, value} * eg. 1 1 0 1 => {1,1}, {2,3}, {3,6}, {4,13} * * Keep track of this through the huffman code table. * For fast scanning we have an index of where the first code of length X * appears. */ typedef struct { int64_t symbol; int32_t p; // next code start value, minus index to codes[] int32_t code; int32_t len; } cram_huffman_code; typedef struct { int ncodes; cram_huffman_code *codes; int option; } cram_huffman_decoder; #define MAX_HUFF 128 typedef struct { cram_huffman_code *codes; int nvals; int val2code[MAX_HUFF+1]; // value to code lookup for small values int option; } cram_huffman_encoder; typedef struct { int32_t offset; int32_t nbits; } cram_beta_decoder; // A PACK transform, packing multiple values into a single byte typedef struct { int32_t nbits; enum cram_encoding sub_encoding; void *sub_codec_dat; struct cram_codec *sub_codec; int nval; // number of items in maps uint32_t rmap[256]; // 0,1,2,3 -> P,A,C,K int map[256]; // P,A,C,K -> 0,1,2,3 // NB: max input is uint8_tb? Or use hash? } cram_xpack_decoder; typedef cram_xpack_decoder cram_xpack_encoder; // Transforms symbols X,Y,Z to bytes 0,1,2. typedef struct { enum cram_encoding len_encoding; enum cram_encoding lit_encoding; void *len_dat; void *lit_dat; struct cram_codec *len_codec; struct cram_codec *lit_codec; int cur_len; int cur_lit; int rep_score[256]; char *to_flush; size_t to_flush_size; } cram_xrle_decoder; typedef cram_xrle_decoder cram_xrle_encoder; // DELTA + zigzag + varint encoding typedef struct { // FIXME: define endian here too. Require little endian? int64_t last; uint8_t word_size; // 1, 2, 4, 8 //uint8_t sign; // true if input data is already signed enum cram_encoding sub_encoding; void *sub_codec_dat; struct cram_codec *sub_codec; } cram_xdelta_decoder; typedef cram_xdelta_decoder cram_xdelta_encoder; typedef struct { int32_t offset; } cram_gamma_decoder; typedef struct { int32_t offset; int32_t k; } cram_subexp_decoder; typedef struct { int32_t content_id; enum cram_external_type type; } cram_external_decoder; typedef struct { int32_t content_id; int64_t offset; enum cram_external_type type; } cram_varint_decoder; typedef struct { struct cram_codec *len_codec; struct cram_codec *val_codec; } cram_byte_array_len_decoder; typedef struct { unsigned char stop; int32_t content_id; } cram_byte_array_stop_decoder; typedef struct { enum cram_encoding len_encoding; enum cram_encoding val_encoding; void *len_dat; void *val_dat; struct cram_codec *len_codec; struct cram_codec *val_codec; } cram_byte_array_len_encoder; typedef struct { int64_t val; } cram_const_codec; /* * A generic codec structure. */ struct cram_codec { enum cram_encoding codec; cram_block *out; varint_vec *vv; int codec_id; void (*free)(struct cram_codec *codec); int (*decode)(cram_slice *slice, struct cram_codec *codec, cram_block *in, char *out, int *out_size); int (*encode)(cram_slice *slice, struct cram_codec *codec, char *in, int in_size); int (*store)(struct cram_codec *codec, cram_block *b, char *prefix, int version); int (*size)(cram_slice *slice, struct cram_codec *codec); int (*flush)(struct cram_codec *codec); cram_block *(*get_block)(cram_slice *slice, struct cram_codec *codec); int (*describe)(struct cram_codec *codec, kstring_t *ks); union { cram_huffman_decoder huffman; cram_external_decoder external; cram_beta_decoder beta; cram_gamma_decoder gamma; cram_subexp_decoder subexp; cram_byte_array_len_decoder byte_array_len; cram_byte_array_stop_decoder byte_array_stop; cram_xpack_decoder xpack; cram_xrle_decoder xrle; cram_xdelta_decoder xdelta; cram_const_codec xconst; cram_varint_decoder varint; cram_huffman_encoder e_huffman; cram_external_decoder e_external; cram_byte_array_stop_decoder e_byte_array_stop; cram_byte_array_len_encoder e_byte_array_len; cram_beta_decoder e_beta; cram_xpack_decoder e_xpack; cram_xrle_decoder e_xrle; cram_xdelta_decoder e_xdelta; cram_const_codec e_xconst; cram_varint_decoder e_varint; } u; }; const char *cram_encoding2str(enum cram_encoding t); cram_codec *cram_decoder_init(cram_block_compression_hdr *hdr, enum cram_encoding codec, char *data, int size, enum cram_external_type option, int version, varint_vec *vv); cram_codec *cram_encoder_init(enum cram_encoding codec, cram_stats *st, enum cram_external_type option, void *dat, int version, varint_vec *vv); //int cram_decode(void *codes, char *in, int in_size, char *out, int *out_size); //void cram_decoder_free(void *codes); //#define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, (--b->bit == -1) && (b->bit = 7, b->byte++)) #define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, b->byte += (--b->bit<0), b->bit&=7) /* * Check that enough bits are left in a block to satisy a bit-based decoder. * Return 0 if there are enough * 1 if not. */ static inline int cram_not_enough_bits(cram_block *blk, int nbits) { if (nbits < 0 || (blk->byte >= blk->uncomp_size && nbits > 0) || (blk->uncomp_size - blk->byte <= INT32_MAX / 8 + 1 && (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { return 1; } return 0; } /* * Returns the content_id used by this codec, also in id2 if byte_array_len. * Returns -1 for the CORE block and -2 for unneeded. * id2 is only filled out for BYTE_ARRAY_LEN which uses 2 codecs. */ int cram_codec_to_id(cram_codec *c, int *id2); /* * cram_codec structures are specialised for decoding or encoding. * Unfortunately this makes turning a decoder into an encoder (such as * when transcoding files) problematic. * * This function converts a cram decoder codec into an encoder version * in-place (ie it modifiers the codec itself). * * Returns 0 on success; * -1 on failure. */ int cram_codec_decoder2encoder(cram_fd *fd, cram_codec *c); #ifdef __cplusplus } #endif #endif /* CRAM_CODECS_H */ pysam-0.23.0/htslib/cram/cram_decode.c000066400000000000000000003650241475062545500175540ustar00rootroot00000000000000/* Copyright (c) 2012-2020, 2022-2024 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /* * - In-memory decoding of CRAM data structures. * - Iterator for reading CRAM record by record. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #include #include #include #include #include "cram.h" #include "os.h" #include "../htslib/hts.h" //Whether CIGAR has just M or uses = and X to indicate match and mismatch //#define USE_X /* ---------------------------------------------------------------------- * CRAM compression headers */ /* * Decodes the Tag Dictionary record in the preservation map * Updates the cram compression header. * * Returns number of bytes decoded on success * -1 on failure */ int cram_decode_TD(cram_fd *fd, char *cp, const char *endp, cram_block_compression_hdr *h) { char *op = cp; unsigned char *dat; cram_block *b; int32_t blk_size = 0; int nTL, i, sz, err = 0; if (!(b = cram_new_block(0, 0))) return -1; if (h->TD_blk || h->TL) { hts_log_warning("More than one TD block found in compression header"); cram_free_block(h->TD_blk); free(h->TL); h->TD_blk = NULL; h->TL = NULL; } /* Decode */ blk_size = fd->vv.varint_get32(&cp, endp, &err); if (!blk_size) { h->nTL = 0; cram_free_block(b); return cp - op; } if (err || blk_size < 0 || endp - cp < blk_size) { cram_free_block(b); return -1; } BLOCK_APPEND(b, cp, blk_size); cp += blk_size; sz = cp - op; // Force nul termination if missing if (BLOCK_DATA(b)[BLOCK_SIZE(b)-1]) BLOCK_APPEND_CHAR(b, '\0'); /* Set up TL lookup table */ dat = BLOCK_DATA(b); // Count for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { nTL++; while (dat[i]) i++; } // Copy if (!(h->TL = calloc(nTL, sizeof(*h->TL)))) { cram_free_block(b); return -1; } for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { h->TL[nTL++] = &dat[i]; while (dat[i]) i++; } h->TD_blk = b; h->nTL = nTL; return sz; block_err: cram_free_block(b); return -1; } /* * Decodes a CRAM block compression header. * Returns header ptr on success * NULL on failure */ cram_block_compression_hdr *cram_decode_compression_header(cram_fd *fd, cram_block *b) { char *cp, *endp, *cp_copy; cram_block_compression_hdr *hdr = calloc(1, sizeof(*hdr)); int i, err = 0; int32_t map_size = 0, map_count = 0; if (!hdr) return NULL; if (b->method != RAW) { if (cram_uncompress_block(b)) { free(hdr); return NULL; } } cp = (char *)b->data; endp = cp + b->uncomp_size; if (CRAM_MAJOR_VERS(fd->version) == 1) { hdr->ref_seq_id = fd->vv.varint_get32(&cp, endp, &err); if (CRAM_MAJOR_VERS(fd->version) >= 4) { hdr->ref_seq_start = fd->vv.varint_get64(&cp, endp, &err); hdr->ref_seq_span = fd->vv.varint_get64(&cp, endp, &err); } else { hdr->ref_seq_start = fd->vv.varint_get32(&cp, endp, &err); hdr->ref_seq_span = fd->vv.varint_get32(&cp, endp, &err); } hdr->num_records = fd->vv.varint_get32(&cp, endp, &err); hdr->num_landmarks = fd->vv.varint_get32(&cp, endp, &err); if (hdr->num_landmarks < 0 || hdr->num_landmarks >= SIZE_MAX / sizeof(int32_t) || endp - cp < hdr->num_landmarks) { free(hdr); return NULL; } if (!(hdr->landmark = malloc(hdr->num_landmarks * sizeof(int32_t)))) { free(hdr); return NULL; } for (i = 0; i < hdr->num_landmarks; i++) hdr->landmark[i] = fd->vv.varint_get32(&cp, endp, &err);; } hdr->preservation_map = kh_init(map); memset(hdr->rec_encoding_map, 0, CRAM_MAP_HASH * sizeof(hdr->rec_encoding_map[0])); memset(hdr->tag_encoding_map, 0, CRAM_MAP_HASH * sizeof(hdr->tag_encoding_map[0])); if (!hdr->preservation_map) { cram_free_compression_header(hdr); return NULL; } /* Initialise defaults for preservation map */ hdr->read_names_included = 0; hdr->AP_delta = 1; hdr->qs_seq_orient = 1; memcpy(hdr->substitution_matrix, "CGTNAGTNACTNACGNACGT", 20); /* Preservation map */ map_size = fd->vv.varint_get32(&cp, endp, &err); cp_copy = cp; map_count = fd->vv.varint_get32(&cp, endp, &err); for (i = 0; i < map_count; i++) { pmap_t hd; khint_t k; int r; if (endp - cp < 3) { cram_free_compression_header(hdr); return NULL; } cp += 2; switch(CRAM_KEY(cp[-2],cp[-1])) { case CRAM_KEY('M','I'): // was mapped QS included in V1.0 case CRAM_KEY('U','I'): // was unmapped QS included in V1.0 case CRAM_KEY('P','I'): // was unmapped placed in V1.0 hd.i = *cp++; break; case CRAM_KEY('R','N'): hd.i = *cp++; k = kh_put(map, hdr->preservation_map, "RN", &r); if (-1 == r) { cram_free_compression_header(hdr); return NULL; } kh_val(hdr->preservation_map, k) = hd; hdr->read_names_included = hd.i; break; case CRAM_KEY('A','P'): hd.i = *cp++; k = kh_put(map, hdr->preservation_map, "AP", &r); if (-1 == r) { cram_free_compression_header(hdr); return NULL; } kh_val(hdr->preservation_map, k) = hd; hdr->AP_delta = hd.i; break; case CRAM_KEY('R','R'): hd.i = *cp++; k = kh_put(map, hdr->preservation_map, "RR", &r); if (-1 == r) { cram_free_compression_header(hdr); return NULL; } kh_val(hdr->preservation_map, k) = hd; hdr->no_ref = !hd.i; break; case CRAM_KEY('Q','O'): hd.i = *cp++; k = kh_put(map, hdr->preservation_map, "QO", &r); if (-1 == r) { cram_free_compression_header(hdr); return NULL; } kh_val(hdr->preservation_map, k) = hd; hdr->qs_seq_orient = hd.i; break; case CRAM_KEY('S','M'): if (endp - cp < 5) { cram_free_compression_header(hdr); return NULL; } hdr->substitution_matrix[0][(cp[0]>>6)&3] = 'C'; hdr->substitution_matrix[0][(cp[0]>>4)&3] = 'G'; hdr->substitution_matrix[0][(cp[0]>>2)&3] = 'T'; hdr->substitution_matrix[0][(cp[0]>>0)&3] = 'N'; hdr->substitution_matrix[1][(cp[1]>>6)&3] = 'A'; hdr->substitution_matrix[1][(cp[1]>>4)&3] = 'G'; hdr->substitution_matrix[1][(cp[1]>>2)&3] = 'T'; hdr->substitution_matrix[1][(cp[1]>>0)&3] = 'N'; hdr->substitution_matrix[2][(cp[2]>>6)&3] = 'A'; hdr->substitution_matrix[2][(cp[2]>>4)&3] = 'C'; hdr->substitution_matrix[2][(cp[2]>>2)&3] = 'T'; hdr->substitution_matrix[2][(cp[2]>>0)&3] = 'N'; hdr->substitution_matrix[3][(cp[3]>>6)&3] = 'A'; hdr->substitution_matrix[3][(cp[3]>>4)&3] = 'C'; hdr->substitution_matrix[3][(cp[3]>>2)&3] = 'G'; hdr->substitution_matrix[3][(cp[3]>>0)&3] = 'N'; hdr->substitution_matrix[4][(cp[4]>>6)&3] = 'A'; hdr->substitution_matrix[4][(cp[4]>>4)&3] = 'C'; hdr->substitution_matrix[4][(cp[4]>>2)&3] = 'G'; hdr->substitution_matrix[4][(cp[4]>>0)&3] = 'T'; hd.p = cp; cp += 5; k = kh_put(map, hdr->preservation_map, "SM", &r); if (-1 == r) { cram_free_compression_header(hdr); return NULL; } kh_val(hdr->preservation_map, k) = hd; break; case CRAM_KEY('T','D'): { int sz = cram_decode_TD(fd, cp, endp, hdr); // tag dictionary if (sz < 0) { cram_free_compression_header(hdr); return NULL; } hd.p = cp; cp += sz; k = kh_put(map, hdr->preservation_map, "TD", &r); if (-1 == r) { cram_free_compression_header(hdr); return NULL; } kh_val(hdr->preservation_map, k) = hd; break; } default: hts_log_warning("Unrecognised preservation map key %c%c", cp[-2], cp[-1]); // guess byte; cp++; break; } } if (cp - cp_copy != map_size) { cram_free_compression_header(hdr); return NULL; } /* Record encoding map */ map_size = fd->vv.varint_get32(&cp, endp, &err); cp_copy = cp; map_count = fd->vv.varint_get32(&cp, endp, &err); int is_v4 = CRAM_MAJOR_VERS(fd->version) >= 4 ? 1 : 0; for (i = 0; i < map_count; i++) { char *key = cp; int32_t encoding = E_NULL; int32_t size = 0; ptrdiff_t offset; cram_map *m; enum cram_DS_ID ds_id; enum cram_external_type type; if (endp - cp < 4) { cram_free_compression_header(hdr); return NULL; } cp += 2; encoding = fd->vv.varint_get32(&cp, endp, &err); size = fd->vv.varint_get32(&cp, endp, &err); offset = cp - (char *)b->data; if (encoding == E_NULL) continue; if (size < 0 || endp - cp < size) { cram_free_compression_header(hdr); return NULL; } //printf("%s codes for %.2s\n", cram_encoding2str(encoding), key); /* * For CRAM1.0 CF and BF are Byte and not Int. * Practically speaking it makes no difference unless we have a * 1.0 format file that stores these in EXTERNAL as only then * does Byte vs Int matter. * * Neither this C code nor Java reference implementations did this, * so we gloss over it and treat them as int. */ ds_id = DS_CORE; if (key[0] == 'B' && key[1] == 'F') { ds_id = DS_BF; type = E_INT; } else if (key[0] == 'C' && key[1] == 'F') { ds_id = DS_CF; type = E_INT; } else if (key[0] == 'R' && key[1] == 'I') { ds_id = DS_RI; type = E_INT; } else if (key[0] == 'R' && key[1] == 'L') { ds_id = DS_RL; type = E_INT; } else if (key[0] == 'A' && key[1] == 'P') { ds_id = DS_AP; type = is_v4 ? E_SLONG : E_INT; } else if (key[0] == 'R' && key[1] == 'G') { ds_id = DS_RG; type = E_INT; } else if (key[0] == 'M' && key[1] == 'F') { ds_id = DS_MF; type = E_INT; } else if (key[0] == 'N' && key[1] == 'S') { ds_id = DS_NS; type = E_INT; } else if (key[0] == 'N' && key[1] == 'P') { ds_id = DS_NP; type = is_v4 ? E_LONG : E_INT; } else if (key[0] == 'T' && key[1] == 'S') { ds_id = DS_TS; type = is_v4 ? E_SLONG : E_INT; } else if (key[0] == 'N' && key[1] == 'F') { ds_id = DS_NF; type = E_INT; } else if (key[0] == 'T' && key[1] == 'C') { ds_id = DS_TC; type = E_BYTE; } else if (key[0] == 'T' && key[1] == 'N') { ds_id = DS_TN; type = E_INT; } else if (key[0] == 'F' && key[1] == 'N') { ds_id = DS_FN; type = E_INT; } else if (key[0] == 'F' && key[1] == 'C') { ds_id = DS_FC; type = E_BYTE; } else if (key[0] == 'F' && key[1] == 'P') { ds_id = DS_FP; type = E_INT; } else if (key[0] == 'B' && key[1] == 'S') { ds_id = DS_BS; type = E_BYTE; } else if (key[0] == 'I' && key[1] == 'N') { ds_id = DS_IN; type = E_BYTE_ARRAY; } else if (key[0] == 'S' && key[1] == 'C') { ds_id = DS_SC; type = E_BYTE_ARRAY; } else if (key[0] == 'D' && key[1] == 'L') { ds_id = DS_DL; type = E_INT; } else if (key[0] == 'B' && key[1] == 'A') { ds_id = DS_BA; type = E_BYTE; } else if (key[0] == 'B' && key[1] == 'B') { ds_id = DS_BB; type = E_BYTE_ARRAY; } else if (key[0] == 'R' && key[1] == 'S') { ds_id = DS_RS; type = E_INT; } else if (key[0] == 'P' && key[1] == 'D') { ds_id = DS_PD; type = E_INT; } else if (key[0] == 'H' && key[1] == 'C') { ds_id = DS_HC; type = E_INT; } else if (key[0] == 'M' && key[1] == 'Q') { ds_id = DS_MQ; type = E_INT; } else if (key[0] == 'R' && key[1] == 'N') { ds_id = DS_RN; type = E_BYTE_ARRAY_BLOCK; } else if (key[0] == 'Q' && key[1] == 'S') { ds_id = DS_QS; type = E_BYTE; } else if (key[0] == 'Q' && key[1] == 'Q') { ds_id = DS_QQ; type = E_BYTE_ARRAY; } else if (key[0] == 'T' && key[1] == 'L') { ds_id = DS_TL; type = E_INT; } else if (key[0] == 'T' && key[1] == 'M') { } else if (key[0] == 'T' && key[1] == 'V') { } else { hts_log_warning("Unrecognised key: %.2s", key); } if (ds_id != DS_CORE) { if (hdr->codecs[ds_id] != NULL) { hts_log_warning("Codec for key %.2s defined more than once", key); hdr->codecs[ds_id]->free(hdr->codecs[ds_id]); } hdr->codecs[ds_id] = cram_decoder_init(hdr, encoding, cp, size, type, fd->version, &fd->vv); if (!hdr->codecs[ds_id]) { cram_free_compression_header(hdr); return NULL; } } cp += size; // Fill out cram_map purely for cram_dump to dump out. m = malloc(sizeof(*m)); if (!m) { cram_free_compression_header(hdr); return NULL; } m->key = CRAM_KEY(key[0], key[1]); m->encoding = encoding; m->size = size; m->offset = offset; m->codec = NULL; m->next = hdr->rec_encoding_map[CRAM_MAP(key[0], key[1])]; hdr->rec_encoding_map[CRAM_MAP(key[0], key[1])] = m; } if (cp - cp_copy != map_size) { cram_free_compression_header(hdr); return NULL; } /* Tag encoding map */ map_size = fd->vv.varint_get32(&cp, endp, &err); cp_copy = cp; map_count = fd->vv.varint_get32(&cp, endp, &err); for (i = 0; i < map_count; i++) { int32_t encoding = E_NULL; int32_t size = 0; cram_map *m = malloc(sizeof(*m)); // FIXME: use pooled_alloc uint8_t key[3]; if (!m || endp - cp < 6) { free(m); cram_free_compression_header(hdr); return NULL; } m->key = fd->vv.varint_get32(&cp, endp, &err); key[0] = m->key>>16; key[1] = m->key>>8; key[2] = m->key; encoding = fd->vv.varint_get32(&cp, endp, &err); size = fd->vv.varint_get32(&cp, endp, &err); m->encoding = encoding; m->size = size; m->offset = cp - (char *)b->data; if (size < 0 || endp - cp < size || !(m->codec = cram_decoder_init(hdr, encoding, cp, size, E_BYTE_ARRAY_BLOCK, fd->version, &fd->vv))) { cram_free_compression_header(hdr); free(m); return NULL; } cp += size; m->next = hdr->tag_encoding_map[CRAM_MAP(key[0],key[1])]; hdr->tag_encoding_map[CRAM_MAP(key[0],key[1])] = m; } if (err || cp - cp_copy != map_size) { cram_free_compression_header(hdr); return NULL; } return hdr; } /* * Note we also need to scan through the record encoding map to * see which data series share the same block, either external or * CORE. For example if we need the BF data series but MQ and CF * are also encoded in the same block then we need to add those in * as a dependency in order to correctly decode BF. * * Returns 0 on success * -1 on failure */ int cram_dependent_data_series(cram_fd *fd, cram_block_compression_hdr *hdr, cram_slice *s) { int *block_used; int core_used = 0; int i; static int i_to_id[] = { DS_BF, DS_AP, DS_FP, DS_RL, DS_DL, DS_NF, DS_BA, DS_QS, DS_FC, DS_FN, DS_BS, DS_IN, DS_RG, DS_MQ, DS_TL, DS_RN, DS_NS, DS_NP, DS_TS, DS_MF, DS_CF, DS_RI, DS_RS, DS_PD, DS_HC, DS_SC, DS_BB, DS_QQ, }; uint32_t orig_ds; /* * Set the data_series bit field based on fd->required_fields * contents. */ if (fd->required_fields && fd->required_fields != INT_MAX) { s->data_series = 0; if (fd->required_fields & SAM_QNAME) s->data_series |= CRAM_RN; if (fd->required_fields & SAM_FLAG) s->data_series |= CRAM_BF; if (fd->required_fields & SAM_RNAME) s->data_series |= CRAM_RI | CRAM_BF; if (fd->required_fields & SAM_POS) s->data_series |= CRAM_AP | CRAM_BF; if (fd->required_fields & SAM_MAPQ) s->data_series |= CRAM_MQ; if (fd->required_fields & SAM_CIGAR) s->data_series |= CRAM_CIGAR; if (fd->required_fields & SAM_RNEXT) s->data_series |= CRAM_CF | CRAM_NF | CRAM_RI | CRAM_NS |CRAM_BF; if (fd->required_fields & SAM_PNEXT) s->data_series |= CRAM_CF | CRAM_NF | CRAM_AP | CRAM_NP | CRAM_BF; if (fd->required_fields & SAM_TLEN) s->data_series |= CRAM_CF | CRAM_NF | CRAM_AP | CRAM_TS | CRAM_BF | CRAM_MF | CRAM_RI | CRAM_CIGAR; if (fd->required_fields & SAM_SEQ) s->data_series |= CRAM_SEQ; if (!(fd->required_fields & SAM_AUX)) // No easy way to get MD/NM without other tags at present s->decode_md = 0; if (fd->required_fields & SAM_QUAL) s->data_series |= CRAM_QUAL; if (fd->required_fields & SAM_AUX) s->data_series |= CRAM_RG | CRAM_TL | CRAM_aux; if (fd->required_fields & SAM_RGAUX) s->data_series |= CRAM_RG | CRAM_BF; // Always uncompress CORE block if (cram_uncompress_block(s->block[0])) return -1; } else { s->data_series = CRAM_ALL; for (i = 0; i < s->hdr->num_blocks; i++) { if (cram_uncompress_block(s->block[i])) return -1; } return 0; } block_used = calloc(s->hdr->num_blocks+1, sizeof(int)); if (!block_used) return -1; do { /* * Also set data_series based on code prerequisites. Eg if we need * CRAM_QS then we also need to know CRAM_RL so we know how long it * is, or if we need FC/FP then we also need FN (number of features). * * It's not reciprocal though. We may be needing to decode FN * but have no need to decode FC, FP and cigar ops. */ if (s->data_series & CRAM_RS) s->data_series |= CRAM_FC|CRAM_FP; if (s->data_series & CRAM_PD) s->data_series |= CRAM_FC|CRAM_FP; if (s->data_series & CRAM_HC) s->data_series |= CRAM_FC|CRAM_FP; if (s->data_series & CRAM_QS) s->data_series |= CRAM_FC|CRAM_FP; if (s->data_series & CRAM_IN) s->data_series |= CRAM_FC|CRAM_FP; if (s->data_series & CRAM_SC) s->data_series |= CRAM_FC|CRAM_FP; if (s->data_series & CRAM_BS) s->data_series |= CRAM_FC|CRAM_FP; if (s->data_series & CRAM_DL) s->data_series |= CRAM_FC|CRAM_FP; if (s->data_series & CRAM_BA) s->data_series |= CRAM_FC|CRAM_FP; if (s->data_series & CRAM_BB) s->data_series |= CRAM_FC|CRAM_FP; if (s->data_series & CRAM_QQ) s->data_series |= CRAM_FC|CRAM_FP; // cram_decode_seq() needs seq[] array if (s->data_series & (CRAM_SEQ|CRAM_CIGAR)) s->data_series |= CRAM_RL; if (s->data_series & CRAM_FP) s->data_series |= CRAM_FC; if (s->data_series & CRAM_FC) s->data_series |= CRAM_FN; if (s->data_series & CRAM_aux) s->data_series |= CRAM_TL; if (s->data_series & CRAM_MF) s->data_series |= CRAM_CF; if (s->data_series & CRAM_MQ) s->data_series |= CRAM_BF; if (s->data_series & CRAM_BS) s->data_series |= CRAM_RI; if (s->data_series & (CRAM_MF |CRAM_NS |CRAM_NP |CRAM_TS |CRAM_NF)) s->data_series |= CRAM_CF; if (!hdr->read_names_included && s->data_series & CRAM_RN) s->data_series |= CRAM_CF | CRAM_NF; if (s->data_series & (CRAM_BA | CRAM_QS | CRAM_BB | CRAM_QQ)) s->data_series |= CRAM_BF | CRAM_CF | CRAM_RL; if (s->data_series & CRAM_FN) { // The CRAM_FN loop checks for reference length boundaries, // which needs a working seq_pos. Some fields are fixed size // irrespective of if we decode (BS), but others need to know // the size of the string fetched back (SC, IN, BB). s->data_series |= CRAM_SC | CRAM_IN | CRAM_BB; } orig_ds = s->data_series; // Find which blocks are in use. for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) { int bnum1, bnum2, j; cram_codec *c = hdr->codecs[i_to_id[i]]; if (!(s->data_series & (1<hdr->num_blocks; j++) { if (s->block[j]->content_type == EXTERNAL && s->block[j]->content_id == bnum1) { block_used[j] = 1; if (cram_uncompress_block(s->block[j])) { free(block_used); return -1; } } } break; } if (bnum2 == -2 || bnum1 == bnum2) break; bnum1 = bnum2; // 2nd pass } } // Tags too if ((fd->required_fields & SAM_AUX) || (s->data_series & CRAM_aux)) { for (i = 0; i < CRAM_MAP_HASH; i++) { int bnum1, bnum2, j; cram_map *m = hdr->tag_encoding_map[i]; while (m) { cram_codec *c = m->codec; if (!c) { m = m->next; continue; } bnum1 = cram_codec_to_id(c, &bnum2); for (;;) { switch (bnum1) { case -2: break; case -1: core_used = 1; break; default: for (j = 0; j < s->hdr->num_blocks; j++) { if (s->block[j]->content_type == EXTERNAL && s->block[j]->content_id == bnum1) { block_used[j] = 1; if (cram_uncompress_block(s->block[j])) { free(block_used); return -1; } } } break; } if (bnum2 == -2 || bnum1 == bnum2) break; bnum1 = bnum2; // 2nd pass } m = m->next; } } } // We now know which blocks are in used, so repeat and find // which other data series need to be added. for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) { int bnum1, bnum2, j; cram_codec *c = hdr->codecs[i_to_id[i]]; if (!c) continue; bnum1 = cram_codec_to_id(c, &bnum2); for (;;) { switch (bnum1) { case -2: break; case -1: if (core_used) { //printf(" + data series %08x:\n", 1<data_series |= 1<hdr->num_blocks; j++) { if (s->block[j]->content_type == EXTERNAL && s->block[j]->content_id == bnum1) { if (block_used[j]) { //printf(" + data series %08x:\n", 1<data_series |= 1<tag_encoding_map[i]; while (m) { cram_codec *c = m->codec; if (!c) { m = m->next; continue; } bnum1 = cram_codec_to_id(c, &bnum2); for (;;) { switch (bnum1) { case -2: break; case -1: //printf(" + data series %08x:\n", CRAM_aux); s->data_series |= CRAM_aux; break; default: for (j = 0; j < s->hdr->num_blocks; j++) { if (s->block[j]->content_type == EXTERNAL && s->block[j]->content_id == bnum1) { if (block_used[j]) { //printf(" + data series %08x:\n", // CRAM_aux); s->data_series |= CRAM_aux; } } } break; } if (bnum2 == -2 || bnum1 == bnum2) break; bnum1 = bnum2; // 2nd pass } m = m->next; } } } while (orig_ds != s->data_series); free(block_used); return 0; } /* * Checks whether an external block is used solely by a single data series. * Returns the codec type if so (EXTERNAL, BYTE_ARRAY_LEN, BYTE_ARRAY_STOP) * or 0 if not (E_NULL). */ static int cram_ds_unique(cram_block_compression_hdr *hdr, cram_codec *c, int id) { int i, n_id = 0; enum cram_encoding e_type = 0; for (i = 0; i < DS_END; i++) { cram_codec *c; int bnum1, bnum2, old_n_id; if (!(c = hdr->codecs[i])) continue; bnum1 = cram_codec_to_id(c, &bnum2); old_n_id = n_id; if (bnum1 == id) { n_id++; e_type = c->codec; } if (bnum2 == id) { n_id++; e_type = c->codec; } if (n_id == old_n_id+2) n_id--; // len/val in same place counts once only. } return n_id == 1 ? e_type : 0; } /* * Attempts to estimate the size of some blocks so we can preallocate them * before decoding. Although decoding will automatically grow the blocks, * it is typically more efficient to preallocate. */ void cram_decode_estimate_sizes(cram_block_compression_hdr *hdr, cram_slice *s, int *qual_size, int *name_size, int *q_id) { int bnum1, bnum2; cram_codec *cd; *qual_size = 0; *name_size = 0; /* Qual */ cd = hdr->codecs[DS_QS]; if (cd == NULL) return; bnum1 = cram_codec_to_id(cd, &bnum2); if (bnum1 < 0 && bnum2 >= 0) bnum1 = bnum2; if (cram_ds_unique(hdr, cd, bnum1)) { cram_block *b = cram_get_block_by_id(s, bnum1); if (b) *qual_size = b->uncomp_size; if (q_id && cd->codec == E_EXTERNAL) *q_id = bnum1; } /* Name */ cd = hdr->codecs[DS_RN]; if (cd == NULL) return; bnum1 = cram_codec_to_id(cd, &bnum2); if (bnum1 < 0 && bnum2 >= 0) bnum1 = bnum2; if (cram_ds_unique(hdr, cd, bnum1)) { cram_block *b = cram_get_block_by_id(s, bnum1); if (b) *name_size = b->uncomp_size; } } /* ---------------------------------------------------------------------- * CRAM slices */ /* * Decodes a CRAM (un)mapped slice header block. * Returns slice header ptr on success * NULL on failure */ cram_block_slice_hdr *cram_decode_slice_header(cram_fd *fd, cram_block *b) { cram_block_slice_hdr *hdr; unsigned char *cp; unsigned char *cp_end; int i, err = 0; if (b->method != RAW) { /* Spec. says slice header should be RAW, but we can future-proof by trying to decode it if it isn't. */ if (cram_uncompress_block(b) < 0) return NULL; } cp = (unsigned char *)BLOCK_DATA(b); cp_end = cp + b->uncomp_size; if (b->content_type != MAPPED_SLICE && b->content_type != UNMAPPED_SLICE) return NULL; if (!(hdr = calloc(1, sizeof(*hdr)))) return NULL; hdr->content_type = b->content_type; if (b->content_type == MAPPED_SLICE) { hdr->ref_seq_id = fd->vv.varint_get32s((char **)&cp, (char *)cp_end, &err); if (CRAM_MAJOR_VERS(fd->version) >= 4) { hdr->ref_seq_start = fd->vv.varint_get64((char **)&cp, (char *)cp_end, &err); hdr->ref_seq_span = fd->vv.varint_get64((char **)&cp, (char *)cp_end, &err); } else { hdr->ref_seq_start = fd->vv.varint_get32((char **)&cp, (char *)cp_end, &err); hdr->ref_seq_span = fd->vv.varint_get32((char **)&cp, (char *)cp_end, &err); } if (hdr->ref_seq_start < 0 || hdr->ref_seq_span < 0) { free(hdr); hts_log_error("Negative values not permitted for header " "sequence start or span fields"); return NULL; } } hdr->num_records = fd->vv.varint_get32((char **)&cp, (char *) cp_end, &err); hdr->record_counter = 0; if (CRAM_MAJOR_VERS(fd->version) == 2) { hdr->record_counter = fd->vv.varint_get32((char **)&cp, (char *)cp_end, &err); } else if (CRAM_MAJOR_VERS(fd->version) >= 3) { hdr->record_counter = fd->vv.varint_get64((char **)&cp, (char *)cp_end, &err); } hdr->num_blocks = fd->vv.varint_get32((char **)&cp, (char *)cp_end, &err); hdr->num_content_ids = fd->vv.varint_get32((char **)&cp, (char *)cp_end, &err); if (hdr->num_content_ids < 1 || hdr->num_content_ids >= 10000) { // Slice must have at least one data block, and there is no need // for more than 2 per possible aux-tag plus ancillary. free(hdr); return NULL; } hdr->block_content_ids = malloc(hdr->num_content_ids * sizeof(int32_t)); if (!hdr->block_content_ids) { free(hdr); return NULL; } for (i = 0; i < hdr->num_content_ids; i++) hdr->block_content_ids[i] = fd->vv.varint_get32((char **)&cp, (char *)cp_end, &err); if (err) { free(hdr->block_content_ids); free(hdr); return NULL; } if (b->content_type == MAPPED_SLICE) hdr->ref_base_id = fd->vv.varint_get32((char **)&cp, (char *) cp_end, &err); if (CRAM_MAJOR_VERS(fd->version) != 1) { if (cp_end - cp < 16) { free(hdr->block_content_ids); free(hdr); return NULL; } memcpy(hdr->md5, cp, 16); } else { memset(hdr->md5, 0, 16); } if (!err) return hdr; free(hdr->block_content_ids); free(hdr); return NULL; } #if 0 /* Returns the number of bits set in val; it the highest bit used */ static int nbits(int v) { static const int MultiplyDeBruijnBitPosition[32] = { 1, 10, 2, 11, 14, 22, 3, 30, 12, 15, 17, 19, 23, 26, 4, 31, 9, 13, 21, 29, 16, 18, 25, 8, 20, 28, 24, 7, 27, 6, 5, 32 }; v |= v >> 1; // first up to set all bits 1 after the first 1 */ v |= v >> 2; v |= v >> 4; v |= v >> 8; v |= v >> 16; // DeBruijn magic to find top bit return MultiplyDeBruijnBitPosition[(uint32_t)(v * 0x07C4ACDDU) >> 27]; } #endif #if 0 static int sort_freqs(const void *vp1, const void *vp2) { const int i1 = *(const int *)vp1; const int i2 = *(const int *)vp2; return i1-i2; } #endif /* ---------------------------------------------------------------------- * Primary CRAM sequence decoder */ static inline int add_md_char(cram_slice *s, int decode_md, char c, int32_t *md_dist) { if (decode_md) { BLOCK_APPEND_UINT(s->aux_blk, *md_dist); BLOCK_APPEND_CHAR(s->aux_blk, c); *md_dist = 0; } return 0; block_err: return -1; } /* * Internal part of cram_decode_slice(). * Generates the sequence, quality and cigar components. */ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s, cram_block *blk, cram_record *cr, sam_hdr_t *sh, int cf, char *seq, char *qual, int has_MD, int has_NM) { int prev_pos = 0, f, r = 0, out_sz = 1; int seq_pos = 1; int cig_len = 0; int64_t ref_pos = cr->apos; int32_t fn, i32; enum cigar_op cig_op = BAM_CMATCH; uint32_t *cigar = s->cigar; uint32_t ncigar = s->ncigar; uint32_t cigar_alloc = s->cigar_alloc; uint32_t nm = 0; int32_t md_dist = 0; int orig_aux = 0; // CRAM < 4.0 decode_md is off/on // CRAM >= 4.0 decode_md is auto/on (auto=on if MD* present, off otherwise) int do_md = CRAM_MAJOR_VERS(fd->version) >= 4 ? (s->decode_md > 0) : (s->decode_md != 0); int decode_md = s->ref && cr->ref_id >= 0 && ((do_md && !has_MD) || has_MD < 0); int decode_nm = s->ref && cr->ref_id >= 0 && ((do_md && !has_NM) || has_NM < 0); uint32_t ds = s->data_series; sam_hrecs_t *bfd = sh->hrecs; cram_codec **codecs = c->comp_hdr->codecs; if ((ds & CRAM_QS) && !(cf & CRAM_FLAG_PRESERVE_QUAL_SCORES)) { memset(qual, 255, cr->len); } if (cr->cram_flags & CRAM_FLAG_NO_SEQ) decode_md = decode_nm = 0; if (decode_md) { orig_aux = BLOCK_SIZE(s->aux_blk); if (has_MD == 0) BLOCK_APPEND(s->aux_blk, "MDZ", 3); } if (ds & CRAM_FN) { if (!codecs[DS_FN]) return -1; r |= codecs[DS_FN]->decode(s,codecs[DS_FN], blk, (char *)&fn, &out_sz); if (r) return r; } else { fn = 0; } ref_pos--; // count from 0 cr->cigar = ncigar; if (!(ds & (CRAM_FC | CRAM_FP))) goto skip_cigar; if (fn) { if ((ds & CRAM_FC) && !codecs[DS_FC]) return -1; if ((ds & CRAM_FP) && !codecs[DS_FP]) return -1; } for (f = 0; f < fn; f++) { int32_t pos = 0; char op; if (ncigar+2 >= cigar_alloc) { cigar_alloc = cigar_alloc ? cigar_alloc*2 : 1024; if (!(cigar = realloc(s->cigar, cigar_alloc * sizeof(*cigar)))) return -1; s->cigar = cigar; } if (ds & CRAM_FC) { r |= codecs[DS_FC]->decode(s, codecs[DS_FC], blk, &op, &out_sz); if (r) return r; } if (!(ds & CRAM_FP)) continue; r |= codecs[DS_FP]->decode(s, codecs[DS_FP], blk, (char *)&pos, &out_sz); if (r) return r; pos += prev_pos; if (pos <= 0) { hts_log_error("Feature position %d before start of read", pos); return -1; } if (pos > seq_pos) { if (pos > cr->len+1) return -1; if (s->ref && cr->ref_id >= 0) { if (ref_pos + pos - seq_pos > bfd->ref[cr->ref_id].len) { static int whinged = 0; int rlen; if (!whinged) hts_log_warning("Ref pos outside of ref sequence boundary"); whinged = 1; rlen = bfd->ref[cr->ref_id].len - ref_pos; // May miss MD/NM cases where both seq/ref are N, but this is a // malformed cram file anyway. if (rlen > 0) { if (ref_pos + rlen > s->ref_end) goto beyond_slice; memcpy(&seq[seq_pos-1], &s->ref[ref_pos - s->ref_start +1], rlen); if ((pos - seq_pos) - rlen > 0) memset(&seq[seq_pos-1+rlen], 'N', (pos - seq_pos) - rlen); } else { memset(&seq[seq_pos-1], 'N', cr->len - seq_pos + 1); } if (md_dist >= 0) md_dist += pos - seq_pos; } else { // 'N' in both ref and seq is also mismatch for NM/MD if (ref_pos + pos-seq_pos > s->ref_end) goto beyond_slice; const char *refp = s->ref + ref_pos - s->ref_start + 1; const int frag_len = pos - seq_pos; int do_cpy = 1; if (decode_md || decode_nm) { char *N = memchr(refp, 'N', frag_len); if (N) { int i; for (i = 0; i < frag_len; i++) { char base = refp[i]; if (base == 'N') { if (add_md_char(s, decode_md, 'N', &md_dist) < 0) return -1; nm++; } else { md_dist++; } seq[seq_pos-1+i] = base; } do_cpy = 0; } else { md_dist += frag_len; } } if (do_cpy) memcpy(&seq[seq_pos-1], refp, frag_len); } } #ifdef USE_X if (cig_len && cig_op != BAM_CBASE_MATCH) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } cig_op = BAM_CBASE_MATCH; #else if (cig_len && cig_op != BAM_CMATCH) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } cig_op = BAM_CMATCH; #endif cig_len += pos - seq_pos; ref_pos += pos - seq_pos; seq_pos = pos; } prev_pos = pos; if (!(ds & CRAM_FC)) goto skip_cigar; switch(op) { case 'S': { // soft clip: IN int32_t out_sz2 = 1; int have_sc = 0; if (cig_len) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } switch (CRAM_MAJOR_VERS(fd->version)) { case 1: if (ds & CRAM_IN) { r |= codecs[DS_IN] ? codecs[DS_IN]->decode(s, codecs[DS_IN], blk, cr->len ? &seq[pos-1] : NULL, &out_sz2) : (seq[pos-1] = 'N', out_sz2 = 1, 0); have_sc = 1; } break; case 2: default: if (ds & CRAM_SC) { r |= codecs[DS_SC] ? codecs[DS_SC]->decode(s, codecs[DS_SC], blk, cr->len ? &seq[pos-1] : NULL, &out_sz2) : (seq[pos-1] = 'N', out_sz2 = 1, 0); have_sc = 1; } break; //default: // r |= codecs[DS_BB] // ? codecs[DS_BB]->decode(s, codecs[DS_BB], // blk, &seq[pos-1], &out_sz2) // : (seq[pos-1] = 'N', out_sz2 = 1, 0); } if (have_sc) { if (r) return r; cigar[ncigar++] = (out_sz2<<4) + BAM_CSOFT_CLIP; cig_op = BAM_CSOFT_CLIP; seq_pos += out_sz2; } break; } case 'X': { // Substitution; BS unsigned char base; #ifdef USE_X if (cig_len && cig_op != BAM_CBASE_MISMATCH) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } if (ds & CRAM_BS) { if (!codecs[DS_BS]) return -1; r |= codecs[DS_BS]->decode(s, codecs[DS_BS], blk, (char *)&base, &out_sz); if (pos-1 < cr->len) seq[pos-1] = 'N'; // FIXME look up BS=base value } cig_op = BAM_CBASE_MISMATCH; #else int ref_base; if (cig_len && cig_op != BAM_CMATCH) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } if (ds & CRAM_BS) { if (!codecs[DS_BS]) return -1; r |= codecs[DS_BS]->decode(s, codecs[DS_BS], blk, (char *)&base, &out_sz); if (r) return -1; if (cr->ref_id < 0 || ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) { if (pos-1 < cr->len) seq[pos-1] = c->comp_hdr-> substitution_matrix[fd->L1['N']][base]; if (decode_md || decode_nm) { if (md_dist >= 0 && decode_md) BLOCK_APPEND_UINT(s->aux_blk, md_dist); md_dist = -1; nm--; } } else { unsigned char ref_call = ref_pos < s->ref_end ? (uc)s->ref[ref_pos - s->ref_start +1] : 'N'; ref_base = fd->L1[ref_call]; if (pos-1 < cr->len) seq[pos-1] = c->comp_hdr-> substitution_matrix[ref_base][base]; if (add_md_char(s, decode_md, ref_call, &md_dist) < 0) return -1; } } cig_op = BAM_CMATCH; #endif nm++; cig_len++; seq_pos++; ref_pos++; break; } case 'D': { // Deletion; DL if (cig_len && cig_op != BAM_CDEL) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } if (ds & CRAM_DL) { if (!codecs[DS_DL]) return -1; r |= codecs[DS_DL]->decode(s, codecs[DS_DL], blk, (char *)&i32, &out_sz); if (r) return r; if (decode_md || decode_nm) { if (ref_pos + i32 > s->ref_end) goto beyond_slice; if (md_dist >= 0 && decode_md) BLOCK_APPEND_UINT(s->aux_blk, md_dist); if (ref_pos + i32 <= bfd->ref[cr->ref_id].len) { if (decode_md) { BLOCK_APPEND_CHAR(s->aux_blk, '^'); BLOCK_APPEND(s->aux_blk, &s->ref[ref_pos - s->ref_start +1], i32); md_dist = 0; } nm += i32; } else { uint32_t dlen; if (bfd->ref[cr->ref_id].len >= ref_pos) { if (decode_md) { BLOCK_APPEND_CHAR(s->aux_blk, '^'); BLOCK_APPEND(s->aux_blk, &s->ref[ref_pos - s->ref_start+1], bfd->ref[cr->ref_id].len-ref_pos); BLOCK_APPEND_UINT(s->aux_blk, 0); } dlen = i32 - (bfd->ref[cr->ref_id].len - ref_pos); nm += i32 - dlen; } else { dlen = i32; } md_dist = -1; } } cig_op = BAM_CDEL; cig_len += i32; ref_pos += i32; //printf(" %d: DL = %d (ret %d)\n", f, i32, r); } break; } case 'I': { // Insertion (several bases); IN int32_t out_sz2 = 1; if (cig_len && cig_op != BAM_CINS) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } if (ds & CRAM_IN) { if (!codecs[DS_IN]) return -1; r |= codecs[DS_IN]->decode(s, codecs[DS_IN], blk, cr->len ? &seq[pos-1] : NULL, &out_sz2); if (r) return r; cig_op = BAM_CINS; cig_len += out_sz2; seq_pos += out_sz2; nm += out_sz2; //printf(" %d: IN(I) = %.*s (ret %d, out_sz %d)\n", f, out_sz2, dat, r, out_sz2); } break; } case 'i': { // Insertion (single base); BA if (cig_len && cig_op != BAM_CINS) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } if (ds & CRAM_BA) { if (!codecs[DS_BA]) return -1; r |= codecs[DS_BA]->decode(s, codecs[DS_BA], blk, cr->len ? &seq[pos-1] : NULL, &out_sz); if (r) return r; } cig_op = BAM_CINS; cig_len++; seq_pos++; nm++; break; } case 'b': { // Several bases int32_t len = 1; if (cig_len && cig_op != BAM_CMATCH) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } if (ds & CRAM_BB) { if (!codecs[DS_BB]) return -1; r |= codecs[DS_BB]->decode(s, codecs[DS_BB], blk, cr->len ? &seq[pos-1] : NULL, &len); if (r) return r; if (decode_md || decode_nm) { int x; if (md_dist >= 0 && decode_md) BLOCK_APPEND_UINT(s->aux_blk, md_dist); for (x = 0; x < len; x++) { if (x && decode_md) BLOCK_APPEND_UINT(s->aux_blk, 0); if (ref_pos+x >= bfd->ref[cr->ref_id].len || !s->ref) { md_dist = -1; break; } else { if (decode_md) { if (ref_pos + x > s->ref_end) goto beyond_slice; char r = s->ref[ref_pos+x-s->ref_start +1]; BLOCK_APPEND_CHAR(s->aux_blk, r); } } } nm += x; md_dist = 0; } } cig_op = BAM_CMATCH; cig_len+=len; seq_pos+=len; ref_pos+=len; //prev_pos+=len; break; } case 'q': { // Several quality values int32_t len = 1; if (cig_len && cig_op != BAM_CMATCH) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } if (ds & CRAM_QQ) { if (!codecs[DS_QQ]) return -1; if ((ds & CRAM_QS) && !(cf & CRAM_FLAG_PRESERVE_QUAL_SCORES) && (unsigned char)*qual == 255) memset(qual, 30, cr->len); // ? r |= codecs[DS_QQ]->decode(s, codecs[DS_QQ], blk, (char *)&qual[pos-1], &len); if (r) return r; } cig_op = BAM_CMATCH; //prev_pos+=len; break; } case 'B': { // Read base; BA, QS #ifdef USE_X if (cig_len && cig_op != BAM_CBASE_MISMATCH) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } #else if (cig_len && cig_op != BAM_CMATCH) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } #endif if (ds & CRAM_BA) { if (!codecs[DS_BA]) return -1; r |= codecs[DS_BA]->decode(s, codecs[DS_BA], blk, cr->len ? &seq[pos-1] : NULL, &out_sz); if (decode_md || decode_nm) { if (md_dist >= 0 && decode_md) BLOCK_APPEND_UINT(s->aux_blk, md_dist); if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) { md_dist = -1; } else { if (decode_md) { if (ref_pos > s->ref_end) goto beyond_slice; BLOCK_APPEND_CHAR(s->aux_blk, s->ref[ref_pos-s->ref_start +1]); } nm++; md_dist = 0; } } } if (ds & CRAM_QS) { if (!codecs[DS_QS]) return -1; if (!(cf & CRAM_FLAG_PRESERVE_QUAL_SCORES) && (unsigned char)*qual == 255) memset(qual, 30, cr->len); // ASCII ?. Same as htsjdk r |= codecs[DS_QS]->decode(s, codecs[DS_QS], blk, (char *)&qual[pos-1], &out_sz); } #ifdef USE_X cig_op = BAM_CBASE_MISMATCH; #else cig_op = BAM_CMATCH; #endif cig_len++; seq_pos++; ref_pos++; //printf(" %d: BA/QS(B) = %c/%d (ret %d)\n", f, i32, qc, r); break; } case 'Q': { // Quality score; QS if (ds & CRAM_QS) { if (!codecs[DS_QS]) return -1; if (!(cf & CRAM_FLAG_PRESERVE_QUAL_SCORES) && (unsigned char)*qual == 255) memset(qual, 30, cr->len); // ? r |= codecs[DS_QS]->decode(s, codecs[DS_QS], blk, (char *)&qual[pos-1], &out_sz); //printf(" %d: QS = %d (ret %d)\n", f, qc, r); } break; } case 'H': { // hard clip; HC if (cig_len && cig_op != BAM_CHARD_CLIP) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } if (ds & CRAM_HC) { if (!codecs[DS_HC]) return -1; r |= codecs[DS_HC]->decode(s, codecs[DS_HC], blk, (char *)&i32, &out_sz); if (r) return r; cig_op = BAM_CHARD_CLIP; cig_len += i32; } break; } case 'P': { // padding; PD if (cig_len && cig_op != BAM_CPAD) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } if (ds & CRAM_PD) { if (!codecs[DS_PD]) return -1; r |= codecs[DS_PD]->decode(s, codecs[DS_PD], blk, (char *)&i32, &out_sz); if (r) return r; cig_op = BAM_CPAD; cig_len += i32; } break; } case 'N': { // Ref skip; RS if (cig_len && cig_op != BAM_CREF_SKIP) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } if (ds & CRAM_RS) { if (!codecs[DS_RS]) return -1; r |= codecs[DS_RS]->decode(s, codecs[DS_RS], blk, (char *)&i32, &out_sz); if (r) return r; cig_op = BAM_CREF_SKIP; cig_len += i32; ref_pos += i32; } break; } default: hts_log_error("Unknown feature code '%c'", op); return -1; } } if (!(ds & CRAM_FC)) goto skip_cigar; /* An implicit match op for any unaccounted for bases */ if ((ds & CRAM_FN) && cr->len >= seq_pos) { if (s->ref && cr->ref_id >= 0) { if (ref_pos + cr->len - seq_pos + 1 > bfd->ref[cr->ref_id].len) { static int whinged = 0; int rlen; if (!whinged) hts_log_warning("Ref pos outside of ref sequence boundary"); whinged = 1; rlen = bfd->ref[cr->ref_id].len - ref_pos; // May miss MD/NM cases where both seq/ref are N, but this is a // malformed cram file anyway. if (rlen > 0) { if (seq_pos-1 + rlen < cr->len) memcpy(&seq[seq_pos-1], &s->ref[ref_pos - s->ref_start +1], rlen); if ((cr->len - seq_pos + 1) - rlen > 0) memset(&seq[seq_pos-1+rlen], 'N', (cr->len - seq_pos + 1) - rlen); } else { if (cr->len - seq_pos + 1 > 0) memset(&seq[seq_pos-1], 'N', cr->len - seq_pos + 1); } if (md_dist >= 0) md_dist += cr->len - seq_pos + 1; } else { if (cr->len - seq_pos + 1 > 0) { if (ref_pos + cr->len-seq_pos +1 > s->ref_end) goto beyond_slice; int remainder = cr->len - (seq_pos-1); int j = ref_pos - s->ref_start + 1; if (decode_md || decode_nm) { int i; char *N = memchr(&s->ref[j], 'N', remainder); if (!N) { // short cut the common case md_dist += cr->len - (seq_pos-1); } else { char *refp = &s->ref[j-(seq_pos-1)]; md_dist += N-&s->ref[j]; int i_start = seq_pos-1 + (N - &s->ref[j]); for (i = i_start; i < cr->len; i++) { char base = refp[i]; if (base == 'N') { if (add_md_char(s, decode_md, 'N', &md_dist) < 0) return -1; nm++; } else { md_dist++; } } } } memcpy(&seq[seq_pos-1], &s->ref[j], remainder); } ref_pos += cr->len - seq_pos + 1; } } else if (cr->ref_id >= 0) { // So alignment end can be computed even when not decoding sequence ref_pos += cr->len - seq_pos + 1; } if (ncigar+1 >= cigar_alloc) { cigar_alloc = cigar_alloc ? cigar_alloc*2 : 1024; if (!(cigar = realloc(s->cigar, cigar_alloc * sizeof(*cigar)))) return -1; s->cigar = cigar; } #ifdef USE_X if (cig_len && cig_op != BAM_CBASE_MATCH) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } cig_op = BAM_CBASE_MATCH; #else if (cig_len && cig_op != BAM_CMATCH) { cigar[ncigar++] = (cig_len<<4) + cig_op; cig_len = 0; } cig_op = BAM_CMATCH; #endif cig_len += cr->len - seq_pos+1; } skip_cigar: if ((ds & CRAM_FN) && decode_md) { if (md_dist >= 0) BLOCK_APPEND_UINT(s->aux_blk, md_dist); } if (cig_len) { if (ncigar >= cigar_alloc) { cigar_alloc = cigar_alloc ? cigar_alloc*2 : 1024; if (!(cigar = realloc(s->cigar, cigar_alloc * sizeof(*cigar)))) return -1; s->cigar = cigar; } cigar[ncigar++] = (cig_len<<4) + cig_op; } cr->ncigar = ncigar - cr->cigar; cr->aend = ref_pos > cr->apos ? ref_pos : cr->apos; //printf("2: %.*s %d .. %d\n", cr->name_len, DSTRING_STR(name_ds) + cr->name, cr->apos, ref_pos); if (ds & CRAM_MQ) { if (!codecs[DS_MQ]) return -1; r |= codecs[DS_MQ]->decode(s, codecs[DS_MQ], blk, (char *)&cr->mqual, &out_sz); } else { cr->mqual = 40; } if ((ds & CRAM_QS) && (cf & CRAM_FLAG_PRESERVE_QUAL_SCORES)) { int32_t out_sz2 = cr->len; if (!codecs[DS_QS]) return -1; r |= codecs[DS_QS]->decode(s, codecs[DS_QS], blk, qual, &out_sz2); } s->cigar = cigar; s->cigar_alloc = cigar_alloc; s->ncigar = ncigar; if (cr->cram_flags & CRAM_FLAG_NO_SEQ) cr->len = 0; if (decode_md) { BLOCK_APPEND_CHAR(s->aux_blk, '\0'); // null terminate MD:Z: size_t sz = BLOCK_SIZE(s->aux_blk) - orig_aux; if (has_MD < 0) { // has_MD < 0; already have MDZ allocated in aux at -has_MD, // but wrote MD to end of aux (at orig_aux). // We need some memmoves to shuffle it around. char tmp_MD_[1024], *tmp_MD = tmp_MD_; unsigned char *orig_aux_p = BLOCK_DATA(s->aux_blk) + orig_aux; if (sz > 1024) { tmp_MD = malloc(sz); if (!tmp_MD) return -1; } memcpy(tmp_MD, orig_aux_p, sz); memmove(&BLOCK_DATA(s->aux_blk)[-has_MD] + sz, &BLOCK_DATA(s->aux_blk)[-has_MD], orig_aux_p - &BLOCK_DATA(s->aux_blk)[-has_MD]); memcpy(&BLOCK_DATA(s->aux_blk)[-has_MD], tmp_MD, sz); if (tmp_MD != tmp_MD_) free(tmp_MD); if (-has_NM > -has_MD) // we inserted before NM, so move it up a bit has_NM -= sz; } // else has_MD == 0 and we've already appended MD to the end. cr->aux_size += sz; } if (decode_nm) { if (has_NM == 0) { char buf[7]; size_t buf_size; buf[0] = 'N'; buf[1] = 'M'; if (nm <= UINT8_MAX) { buf_size = 4; buf[2] = 'C'; buf[3] = (nm>> 0) & 0xff; } else if (nm <= UINT16_MAX) { buf_size = 5; buf[2] = 'S'; buf[3] = (nm>> 0) & 0xff; buf[4] = (nm>> 8) & 0xff; } else { buf_size = 7; buf[2] = 'I'; buf[3] = (nm>> 0) & 0xff; buf[4] = (nm>> 8) & 0xff; buf[5] = (nm>>16) & 0xff; buf[6] = (nm>>24) & 0xff; } BLOCK_APPEND(s->aux_blk, buf, buf_size); cr->aux_size += buf_size; } else { // Preallocated space for NM at -has_NM into aux block unsigned char *buf = BLOCK_DATA(s->aux_blk) + -has_NM; buf[0] = (nm>> 0) & 0xff; buf[1] = (nm>> 8) & 0xff; buf[2] = (nm>>16) & 0xff; buf[3] = (nm>>24) & 0xff; } } return r; beyond_slice: // Cramtools can create CRAMs that have sequence features outside the // stated range of the container & slice reference extents (start + span). // We have to check for these in many places, but for brevity have the // error reporting in only one. hts_log_error("CRAM CIGAR extends beyond slice reference extents"); return -1; block_err: return -1; } /* * Quick and simple hash lookup for cram_map arrays */ static cram_map *map_find(cram_map **map, unsigned char *key, int id) { cram_map *m; m = map[CRAM_MAP(key[0],key[1])]; while (m && m->key != id) m= m->next; return m; } //#define map_find(M,K,I) M[CRAM_MAP(K[0],K[1])];while (m && m->key != I);m= m->next static int cram_decode_aux_1_0(cram_container *c, cram_slice *s, cram_block *blk, cram_record *cr) { int i, r = 0, out_sz = 1; unsigned char ntags; if (!c->comp_hdr->codecs[DS_TC]) return -1; r |= c->comp_hdr->codecs[DS_TC]->decode(s, c->comp_hdr->codecs[DS_TC], blk, (char *)&ntags, &out_sz); cr->ntags = ntags; //printf("TC=%d\n", cr->ntags); cr->aux_size = 0; cr->aux = BLOCK_SIZE(s->aux_blk); for (i = 0; i < cr->ntags; i++) { int32_t id, out_sz = 1; unsigned char tag_data[3]; cram_map *m; //printf("Tag %d/%d\n", i+1, cr->ntags); if (!c->comp_hdr->codecs[DS_TN]) return -1; r |= c->comp_hdr->codecs[DS_TN]->decode(s, c->comp_hdr->codecs[DS_TN], blk, (char *)&id, &out_sz); if (out_sz == 3) { // Tag name stored as 3 chars instead of an int? memcpy(tag_data, &id, 3); } else { tag_data[0] = (id>>16) & 0xff; tag_data[1] = (id>>8) & 0xff; tag_data[2] = id & 0xff; } m = map_find(c->comp_hdr->tag_encoding_map, tag_data, id); if (!m) return -1; BLOCK_APPEND(s->aux_blk, (char *)tag_data, 3); if (!m->codec) return -1; r |= m->codec->decode(s, m->codec, blk, (char *)s->aux_blk, &out_sz); cr->aux_size += out_sz + 3; } return r; block_err: return -1; } // has_MD and has_NM are filled out with 0 for none present, // 1 for present and verbatim, and -pos for present as placeholder // (MD*, NM*) to be generated and filled out at offset +pos. static int cram_decode_aux(cram_fd *fd, cram_container *c, cram_slice *s, cram_block *blk, cram_record *cr, int *has_MD, int *has_NM) { int i, r = 0, out_sz = 1; int32_t TL = 0; unsigned char *TN; uint32_t ds = s->data_series; if (!(ds & (CRAM_TL|CRAM_aux))) { cr->aux = 0; cr->aux_size = 0; return 0; } if (!c->comp_hdr->codecs[DS_TL]) return -1; r |= c->comp_hdr->codecs[DS_TL]->decode(s, c->comp_hdr->codecs[DS_TL], blk, (char *)&TL, &out_sz); if (r || TL < 0 || TL >= c->comp_hdr->nTL) return -1; TN = c->comp_hdr->TL[TL]; cr->ntags = strlen((char *)TN)/3; // optimise to remove strlen //printf("TC=%d\n", cr->ntags); cr->aux_size = 0; cr->aux = BLOCK_SIZE(s->aux_blk); if (!(ds & CRAM_aux)) return 0; for (i = 0; i < cr->ntags; i++) { int32_t id, out_sz = 1; unsigned char tag_data[7]; cram_map *m; if (TN[0] == 'M' && TN[1] == 'D' && has_MD) *has_MD = (BLOCK_SIZE(s->aux_blk)+3) * (TN[2] == '*' ? -1 : 1); if (TN[0] == 'N' && TN[1] == 'M' && has_NM) *has_NM = (BLOCK_SIZE(s->aux_blk)+3) * (TN[2] == '*' ? -1 : 1);; //printf("Tag %d/%d\n", i+1, cr->ntags); tag_data[0] = TN[0]; tag_data[1] = TN[1]; tag_data[2] = TN[2]; id = (tag_data[0]<<16) | (tag_data[1]<<8) | tag_data[2]; if (CRAM_MAJOR_VERS(fd->version) >= 4 && TN[2] == '*') { // Place holder, fill out contents later. int tag_data_size; if (TN[0] == 'N' && TN[1] == 'M') { // Use a fixed size, so we can allocate room for it now. memcpy(&tag_data[2], "I\0\0\0\0", 5); tag_data_size = 7; } else if (TN[0] == 'R' && TN[1] == 'G') { // RG is variable size, but known already. Insert now TN += 3; // Equiv to fd->header->hrecs->rg[cr->rg], but this is the // new header API equivalent. const char *rg = sam_hdr_line_name(fd->header, "RG", cr->rg); if (!rg) continue; size_t rg_len = strlen(rg); tag_data[2] = 'Z'; BLOCK_APPEND(s->aux_blk, (char *)tag_data, 3); BLOCK_APPEND(s->aux_blk, rg, rg_len); BLOCK_APPEND_CHAR(s->aux_blk, '\0'); cr->aux_size += 3 + rg_len + 1; cr->rg = -1; // prevents auto-add later continue; } else { // Unknown size. We'll insert MD into stream later. tag_data[2] = 'Z'; tag_data_size = 3; } BLOCK_APPEND(s->aux_blk, (char *)tag_data, tag_data_size); cr->aux_size += tag_data_size; TN += 3; } else { TN += 3; m = map_find(c->comp_hdr->tag_encoding_map, tag_data, id); if (!m) return -1; BLOCK_APPEND(s->aux_blk, (char *)tag_data, 3); if (!m->codec) return -1; r |= m->codec->decode(s, m->codec, blk, (char *)s->aux_blk, &out_sz); if (r) break; cr->aux_size += out_sz + 3; // cF CRAM flags. if (TN[-3]=='c' && TN[-2]=='F' && TN[-1]=='C' && out_sz == 1) { // Remove cF tag uint8_t cF = BLOCK_END(s->aux_blk)[-1]; BLOCK_SIZE(s->aux_blk) -= out_sz+3; cr->aux_size -= out_sz+3; // bit 1 => don't auto-decode MD. // Pretend MD is present verbatim, so we don't auto-generate if ((cF & 1) && has_MD && *has_MD == 0) *has_MD = 1; // bit 1 => don't auto-decode NM if ((cF & 2) && has_NM && *has_NM == 0) *has_NM = 1; } } // We could go to 2^32 fine, but we shouldn't be hitting this anyway, // and it's protecting against memory hogs too. if (BLOCK_SIZE(s->aux_blk) > (1u<<31)) { hts_log_error("CRAM->BAM aux block size overflow"); goto block_err; } } return r; block_err: return -1; } /* Resolve mate pair cross-references between recs within this slice */ static int cram_decode_slice_xref(cram_slice *s, int required_fields) { int rec; if (!(required_fields & (SAM_RNEXT | SAM_PNEXT | SAM_TLEN))) { for (rec = 0; rec < s->hdr->num_records; rec++) { cram_record *cr = &s->crecs[rec]; cr->tlen = 0; cr->mate_pos = 0; cr->mate_ref_id = -1; } return 0; } for (rec = 0; rec < s->hdr->num_records; rec++) { cram_record *cr = &s->crecs[rec]; if (cr->mate_line >= 0) { if (cr->mate_line < s->hdr->num_records) { /* * On the first read, loop through computing lengths. * It's not perfect as we have one slice per reference so we * cannot detect when TLEN should be zero due to seqs that * map to multiple references. * * We also cannot set tlen correct when it spans a slice for * other reasons. This may make tlen too small. Should we * fix this by forcing TLEN to be stored verbatim in such cases? * * Or do we just admit defeat and output 0 for tlen? It's the * safe option... */ if (cr->tlen == INT64_MIN) { int id1 = rec, id2 = rec; int64_t aleft = cr->apos, aright = cr->aend; int64_t tlen; int ref = cr->ref_id; // number of segments starting at the same point. int left_cnt = 0; do { if (aleft > s->crecs[id2].apos) aleft = s->crecs[id2].apos, left_cnt = 1; else if (aleft == s->crecs[id2].apos) left_cnt++; if (aright < s->crecs[id2].aend) aright = s->crecs[id2].aend; if (s->crecs[id2].mate_line == -1) { s->crecs[id2].mate_line = rec; break; } if (s->crecs[id2].mate_line <= id2 || s->crecs[id2].mate_line >= s->hdr->num_records) return -1; id2 = s->crecs[id2].mate_line; if (s->crecs[id2].ref_id != ref) ref = -1; } while (id2 != id1); if (ref != -1) { tlen = aright - aleft + 1; id1 = id2 = rec; /* * When we have two seqs with identical start and * end coordinates, set +/- tlen based on 1st/last * bit flags instead, as a tie breaker. */ if (s->crecs[id2].apos == aleft) { if (left_cnt == 1 || (s->crecs[id2].flags & BAM_FREAD1)) s->crecs[id2].tlen = tlen; else s->crecs[id2].tlen = -tlen; } else { s->crecs[id2].tlen = -tlen; } id2 = s->crecs[id2].mate_line; while (id2 != id1) { if (s->crecs[id2].apos == aleft) { if (left_cnt == 1 || (s->crecs[id2].flags & BAM_FREAD1)) s->crecs[id2].tlen = tlen; else s->crecs[id2].tlen = -tlen; } else { s->crecs[id2].tlen = -tlen; } id2 = s->crecs[id2].mate_line; } } else { id1 = id2 = rec; s->crecs[id2].tlen = 0; id2 = s->crecs[id2].mate_line; while (id2 != id1) { s->crecs[id2].tlen = 0; id2 = s->crecs[id2].mate_line; } } } cr->mate_pos = s->crecs[cr->mate_line].apos; cr->mate_ref_id = s->crecs[cr->mate_line].ref_id; // paired cr->flags |= BAM_FPAIRED; // set mate unmapped if needed if (s->crecs[cr->mate_line].flags & BAM_FUNMAP) { cr->flags |= BAM_FMUNMAP; cr->tlen = 0; } if (cr->flags & BAM_FUNMAP) { cr->tlen = 0; } // set mate reversed if needed if (s->crecs[cr->mate_line].flags & BAM_FREVERSE) cr->flags |= BAM_FMREVERSE; } else { hts_log_error("Mate line out of bounds: %d vs [0, %d]", cr->mate_line, s->hdr->num_records-1); } /* FIXME: construct read names here too if needed */ } else { if (cr->mate_flags & CRAM_M_REVERSE) { cr->flags |= BAM_FPAIRED | BAM_FMREVERSE; } if (cr->mate_flags & CRAM_M_UNMAP) { cr->flags |= BAM_FMUNMAP; //cr->mate_ref_id = -1; } if (!(cr->flags & BAM_FPAIRED)) cr->mate_ref_id = -1; } if (cr->tlen == INT64_MIN) cr->tlen = 0; // Just incase } for (rec = 0; rec < s->hdr->num_records; rec++) { cram_record *cr = &s->crecs[rec]; if (cr->explicit_tlen != INT64_MIN) cr->tlen = cr->explicit_tlen; } return 0; } static char *md5_print(unsigned char *md5, char *out) { int i; for (i = 0; i < 16; i++) { out[i*2+0] = "0123456789abcdef"[md5[i]>>4]; out[i*2+1] = "0123456789abcdef"[md5[i]&15]; } out[32] = 0; return out; } /* * Utility function to decode tlen (ISIZE), as it's called * in multiple places. * * Returns codec return value (0 on success). */ static int cram_decode_tlen(cram_fd *fd, cram_container *c, cram_slice *s, cram_block *blk, int64_t *tlen) { int out_sz = 1, r = 0; if (!c->comp_hdr->codecs[DS_TS]) return -1; if (CRAM_MAJOR_VERS(fd->version) < 4) { int32_t i32; r |= c->comp_hdr->codecs[DS_TS] ->decode(s, c->comp_hdr->codecs[DS_TS], blk, (char *)&i32, &out_sz); *tlen = i32; } else { r |= c->comp_hdr->codecs[DS_TS] ->decode(s, c->comp_hdr->codecs[DS_TS], blk, (char *)tlen, &out_sz); } return r; } /* * Decode an entire slice from container blocks. Fills out s->crecs[] array. * Returns 0 on success * -1 on failure */ int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s, sam_hdr_t *sh) { cram_block *blk = s->block[0]; int32_t bf, ref_id; unsigned char cf; int out_sz, r = 0; int rec; char *seq = NULL, *qual = NULL; int unknown_rg = -1; int embed_ref; char **refs = NULL; uint32_t ds; sam_hrecs_t *bfd = sh->hrecs; if (cram_dependent_data_series(fd, c->comp_hdr, s) != 0) return -1; ds = s->data_series; blk->bit = 7; // MSB first // Study the blocks and estimate approx sizes to preallocate. // This looks to speed up decoding by around 8-9%. // We can always shrink back down at the end if we overestimated. // However it's likely that this also saves memory as own growth // factor (*=1.5) is never applied. { int qsize, nsize, q_id; cram_decode_estimate_sizes(c->comp_hdr, s, &qsize, &nsize, &q_id); //fprintf(stderr, "qsize=%d nsize=%d\n", qsize, nsize); if (qsize && (ds & CRAM_RL)) BLOCK_RESIZE_EXACT(s->seqs_blk, qsize+1); if (qsize && (ds & CRAM_RL)) BLOCK_RESIZE_EXACT(s->qual_blk, qsize+1); if (nsize && (ds & CRAM_NS)) BLOCK_RESIZE_EXACT(s->name_blk, nsize+1); // To do - consider using q_id here to usurp the quality block and // avoid a memcpy during decode. // Specifically when quality is an external block uniquely used by // DS_QS only, then we can set s->qual_blk directly to this // block and save the codec->decode() calls. (Approx 3% cpu saving) } /* Look for unknown RG, added as last by Java CRAM? */ if (bfd->nrg > 0 && bfd->rg[bfd->nrg-1].name != NULL && !strcmp(bfd->rg[bfd->nrg-1].name, "UNKNOWN")) unknown_rg = bfd->nrg-1; if (blk->content_type != CORE) return -1; if (s->crecs) free(s->crecs); if (!(s->crecs = malloc(s->hdr->num_records * sizeof(*s->crecs)))) return -1; ref_id = s->hdr->ref_seq_id; if (CRAM_MAJOR_VERS(fd->version) < 4) embed_ref = s->hdr->ref_base_id >= 0 ? 1 : 0; else embed_ref = s->hdr->ref_base_id > 0 ? 1 : 0; if (ref_id >= 0) { if (embed_ref) { cram_block *b; if (s->hdr->ref_base_id < 0) { hts_log_error("No reference specified and no embedded reference is available" " at #%d:%"PRId64"-%"PRId64, ref_id, s->hdr->ref_seq_start, s->hdr->ref_seq_start + s->hdr->ref_seq_span-1); return -1; } b = cram_get_block_by_id(s, s->hdr->ref_base_id); if (!b) return -1; if (cram_uncompress_block(b) != 0) return -1; s->ref = (char *)BLOCK_DATA(b); s->ref_start = s->hdr->ref_seq_start; s->ref_end = s->hdr->ref_seq_start + s->hdr->ref_seq_span-1; if (s->hdr->ref_seq_span > b->uncomp_size) { hts_log_error("Embedded reference is too small at #%d:%"PRIhts_pos"-%"PRIhts_pos, ref_id, s->ref_start, s->ref_end); return -1; } } else if (!c->comp_hdr->no_ref) { //// Avoid Java cramtools bug by loading entire reference seq //s->ref = cram_get_ref(fd, s->hdr->ref_seq_id, 1, 0); //s->ref_start = 1; if (fd->required_fields & SAM_SEQ) { s->ref = cram_get_ref(fd, s->hdr->ref_seq_id, s->hdr->ref_seq_start, s->hdr->ref_seq_start + s->hdr->ref_seq_span -1); } s->ref_start = s->hdr->ref_seq_start; s->ref_end = s->hdr->ref_seq_start + s->hdr->ref_seq_span-1; /* Sanity check */ if (s->ref_start < 0) { hts_log_warning("Slice starts before base 1" " at #%d:%"PRId64"-%"PRId64, ref_id, s->hdr->ref_seq_start, s->hdr->ref_seq_start + s->hdr->ref_seq_span-1); s->ref_start = 0; } pthread_mutex_lock(&fd->ref_lock); pthread_mutex_lock(&fd->refs->lock); if ((fd->required_fields & SAM_SEQ) && ref_id < fd->refs->nref && fd->refs->ref_id && s->ref_end > fd->refs->ref_id[ref_id]->length) { s->ref_end = fd->refs->ref_id[ref_id]->length; } pthread_mutex_unlock(&fd->refs->lock); pthread_mutex_unlock(&fd->ref_lock); } } if ((fd->required_fields & SAM_SEQ) && s->ref == NULL && s->hdr->ref_seq_id >= 0 && !c->comp_hdr->no_ref) { hts_log_error("Unable to fetch reference #%d:%"PRId64"-%"PRId64"\n", ref_id, s->hdr->ref_seq_start, s->hdr->ref_seq_start + s->hdr->ref_seq_span-1); return -1; } if (CRAM_MAJOR_VERS(fd->version) != 1 && (fd->required_fields & SAM_SEQ) && s->hdr->ref_seq_id >= 0 && !fd->ignore_md5 && memcmp(s->hdr->md5, "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0", 16)) { hts_md5_context *md5; unsigned char digest[16]; if (s->ref && s->hdr->ref_seq_id >= 0) { int start, len; if (s->hdr->ref_seq_start >= s->ref_start) { start = s->hdr->ref_seq_start - s->ref_start; } else { hts_log_warning("Slice starts before base 1 at #%d:%"PRIhts_pos"-%"PRIhts_pos, ref_id, s->ref_start, s->ref_end); start = 0; } if (s->hdr->ref_seq_span <= s->ref_end - s->ref_start + 1) { len = s->hdr->ref_seq_span; } else { hts_log_warning("Slice ends beyond reference end at #%d:%"PRIhts_pos"-%"PRIhts_pos, ref_id, s->ref_start, s->ref_end); len = s->ref_end - s->ref_start + 1; } if (!(md5 = hts_md5_init())) return -1; if (start + len > s->ref_end - s->ref_start + 1) len = s->ref_end - s->ref_start + 1 - start; if (len >= 0) hts_md5_update(md5, s->ref + start, len); hts_md5_final(digest, md5); hts_md5_destroy(md5); } else if (!s->ref && s->hdr->ref_base_id >= 0) { cram_block *b = cram_get_block_by_id(s, s->hdr->ref_base_id); if (b) { if (!(md5 = hts_md5_init())) return -1; hts_md5_update(md5, b->data, b->uncomp_size); hts_md5_final(digest, md5); hts_md5_destroy(md5); } } if (!c->comp_hdr->no_ref && ((!s->ref && s->hdr->ref_base_id < 0) || memcmp(digest, s->hdr->md5, 16) != 0)) { char M[33]; const char *rname = sam_hdr_tid2name(sh, ref_id); if (!rname) rname="?"; // cannot happen normally hts_log_error("MD5 checksum reference mismatch at %s:%"PRIhts_pos"-%"PRIhts_pos, rname, s->ref_start, s->ref_end); hts_log_error("CRAM : %s", md5_print(s->hdr->md5, M)); hts_log_error("Ref : %s", md5_print(digest, M)); kstring_t ks = KS_INITIALIZE; if (sam_hdr_find_tag_id(sh, "SQ", "SN", rname, "M5", &ks) == 0) hts_log_error("@SQ M5: %s", ks.s); hts_log_error("Please check the reference given is correct"); ks_free(&ks); return -1; } } if (ref_id == -2) { pthread_mutex_lock(&fd->ref_lock); pthread_mutex_lock(&fd->refs->lock); refs = calloc(fd->refs->nref, sizeof(char *)); pthread_mutex_unlock(&fd->refs->lock); pthread_mutex_unlock(&fd->ref_lock); if (!refs) return -1; } int last_ref_id = -9; // Arbitrary -ve marker for not-yet-set for (rec = 0; rec < s->hdr->num_records; rec++) { cram_record *cr = &s->crecs[rec]; int has_MD, has_NM; //fprintf(stderr, "Decode seq %d, %d/%d\n", rec, blk->byte, blk->bit); cr->s = s; out_sz = 1; /* decode 1 item */ if (ds & CRAM_BF) { if (!c->comp_hdr->codecs[DS_BF]) goto block_err; r |= c->comp_hdr->codecs[DS_BF] ->decode(s, c->comp_hdr->codecs[DS_BF], blk, (char *)&bf, &out_sz); if (r || bf < 0 || bf >= sizeof(fd->bam_flag_swap)/sizeof(*fd->bam_flag_swap)) goto block_err; bf = fd->bam_flag_swap[bf]; cr->flags = bf; } else { cr->flags = bf = 0x4; // unmapped } if (ds & CRAM_CF) { if (CRAM_MAJOR_VERS(fd->version) == 1) { /* CF is byte in 1.0, int32 in 2.0 */ if (!c->comp_hdr->codecs[DS_CF]) goto block_err; r |= c->comp_hdr->codecs[DS_CF] ->decode(s, c->comp_hdr->codecs[DS_CF], blk, (char *)&cf, &out_sz); if (r) goto block_err; cr->cram_flags = cf; } else { if (!c->comp_hdr->codecs[DS_CF]) goto block_err; r |= c->comp_hdr->codecs[DS_CF] ->decode(s, c->comp_hdr->codecs[DS_CF], blk, (char *)&cr->cram_flags, &out_sz); if (r) goto block_err; cf = cr->cram_flags; } } else { cf = cr->cram_flags = 0; } if (CRAM_MAJOR_VERS(fd->version) != 1 && ref_id == -2) { if (ds & CRAM_RI) { if (!c->comp_hdr->codecs[DS_RI]) goto block_err; r |= c->comp_hdr->codecs[DS_RI] ->decode(s, c->comp_hdr->codecs[DS_RI], blk, (char *)&cr->ref_id, &out_sz); if (r) goto block_err; if ((fd->required_fields & (SAM_SEQ|SAM_TLEN)) && cr->ref_id >= 0 && cr->ref_id != last_ref_id) { if (!c->comp_hdr->no_ref) { // Range(fd): seq >= 0, unmapped -1, unspecified -2 // Slice(s): seq >= 0, unmapped -1, multiple refs -2 // Record(cr): seq >= 0, unmapped -1 pthread_mutex_lock(&fd->range_lock); int need_ref = (fd->range.refid == -2 || cr->ref_id == fd->range.refid); pthread_mutex_unlock(&fd->range_lock); if (need_ref) { if (!refs[cr->ref_id]) refs[cr->ref_id] = cram_get_ref(fd, cr->ref_id, 1, 0); if (!(s->ref = refs[cr->ref_id])) goto block_err; } else { // For multi-ref containers, we don't need to fetch all // refs if we're only querying one. s->ref = NULL; } pthread_mutex_lock(&fd->range_lock); int discard_last_ref = (last_ref_id >= 0 && refs[last_ref_id] && (fd->range.refid == -2 || last_ref_id == fd->range.refid)); pthread_mutex_unlock(&fd->range_lock); if (discard_last_ref) { pthread_mutex_lock(&fd->ref_lock); discard_last_ref = !fd->unsorted; pthread_mutex_unlock(&fd->ref_lock); } if (discard_last_ref) { cram_ref_decr(fd->refs, last_ref_id); refs[last_ref_id] = NULL; } } s->ref_start = 1; pthread_mutex_lock(&fd->ref_lock); pthread_mutex_lock(&fd->refs->lock); s->ref_end = fd->refs->ref_id[cr->ref_id]->length; pthread_mutex_unlock(&fd->refs->lock); pthread_mutex_unlock(&fd->ref_lock); last_ref_id = cr->ref_id; } } else { cr->ref_id = -1; } } else { cr->ref_id = ref_id; // Forced constant in CRAM 1.0 } if (cr->ref_id < -1 || cr->ref_id >= bfd->nref) { hts_log_error("Requested unknown reference ID %d", cr->ref_id); goto block_err; } if (ds & CRAM_RL) { if (!c->comp_hdr->codecs[DS_RL]) goto block_err; r |= c->comp_hdr->codecs[DS_RL] ->decode(s, c->comp_hdr->codecs[DS_RL], blk, (char *)&cr->len, &out_sz); if (r) goto block_err; if (cr->len < 0) { hts_log_error("Read has negative length"); goto block_err; } } if (ds & CRAM_AP) { if (!c->comp_hdr->codecs[DS_AP]) goto block_err; if (CRAM_MAJOR_VERS(fd->version) >= 4) { r |= c->comp_hdr->codecs[DS_AP] ->decode(s, c->comp_hdr->codecs[DS_AP], blk, (char *)&cr->apos, &out_sz); } else { int32_t i32; r |= c->comp_hdr->codecs[DS_AP] ->decode(s, c->comp_hdr->codecs[DS_AP], blk, (char *)&i32, &out_sz); cr->apos = i32; } if (r) goto block_err;; if (c->comp_hdr->AP_delta) { if (cr->apos < 0 && c->unsorted == 0) { // cache locally in c->unsorted so we don't have an // excessive number of locks pthread_mutex_lock(&fd->ref_lock); c->unsorted = fd->unsorted = 1; pthread_mutex_unlock(&fd->ref_lock); } cr->apos += s->last_apos; } s->last_apos= cr->apos; } else { cr->apos = c->ref_seq_start; } if (ds & CRAM_RG) { if (!c->comp_hdr->codecs[DS_RG]) goto block_err; r |= c->comp_hdr->codecs[DS_RG] ->decode(s, c->comp_hdr->codecs[DS_RG], blk, (char *)&cr->rg, &out_sz); if (r) goto block_err; if (cr->rg == unknown_rg) cr->rg = -1; } else { cr->rg = -1; } cr->name_len = 0; if (c->comp_hdr->read_names_included) { int32_t out_sz2 = 1; // Read directly into name cram_block cr->name = BLOCK_SIZE(s->name_blk); if (ds & CRAM_RN) { if (!c->comp_hdr->codecs[DS_RN]) goto block_err; r |= c->comp_hdr->codecs[DS_RN] ->decode(s, c->comp_hdr->codecs[DS_RN], blk, (char *)s->name_blk, &out_sz2); if (r) goto block_err; cr->name_len = out_sz2; } } cr->mate_pos = 0; cr->mate_line = -1; cr->mate_ref_id = -1; cr->explicit_tlen = INT64_MIN; if ((ds & CRAM_CF) && (cf & CRAM_FLAG_DETACHED)) { if (ds & CRAM_MF) { if (CRAM_MAJOR_VERS(fd->version) == 1) { /* MF is byte in 1.0, int32 in 2.0 */ unsigned char mf; if (!c->comp_hdr->codecs[DS_MF]) goto block_err; r |= c->comp_hdr->codecs[DS_MF] ->decode(s, c->comp_hdr->codecs[DS_MF], blk, (char *)&mf, &out_sz); if (r) goto block_err; cr->mate_flags = mf; } else { if (!c->comp_hdr->codecs[DS_MF]) goto block_err; r |= c->comp_hdr->codecs[DS_MF] ->decode(s, c->comp_hdr->codecs[DS_MF], blk, (char *)&cr->mate_flags, &out_sz); if (r) goto block_err; } } else { cr->mate_flags = 0; } if (!c->comp_hdr->read_names_included) { int32_t out_sz2 = 1; // Read directly into name cram_block cr->name = BLOCK_SIZE(s->name_blk); if (ds & CRAM_RN) { if (!c->comp_hdr->codecs[DS_RN]) goto block_err; r |= c->comp_hdr->codecs[DS_RN] ->decode(s, c->comp_hdr->codecs[DS_RN], blk, (char *)s->name_blk, &out_sz2); if (r) goto block_err; cr->name_len = out_sz2; } } if (ds & CRAM_NS) { if (!c->comp_hdr->codecs[DS_NS]) goto block_err; r |= c->comp_hdr->codecs[DS_NS] ->decode(s, c->comp_hdr->codecs[DS_NS], blk, (char *)&cr->mate_ref_id, &out_sz); if (r) goto block_err; } // Skip as mate_ref of "*" is legit. It doesn't mean unmapped, just unknown. // if (cr->mate_ref_id == -1 && cr->flags & 0x01) { // /* Paired, but unmapped */ // cr->flags |= BAM_FMUNMAP; // } if (ds & CRAM_NP) { if (!c->comp_hdr->codecs[DS_NP]) goto block_err;; if (CRAM_MAJOR_VERS(fd->version) < 4) { int32_t i32; r |= c->comp_hdr->codecs[DS_NP] ->decode(s, c->comp_hdr->codecs[DS_NP], blk, (char *)&i32, &out_sz); cr->mate_pos = i32; } else { r |= c->comp_hdr->codecs[DS_NP] ->decode(s, c->comp_hdr->codecs[DS_NP], blk, (char *)&cr->mate_pos, &out_sz); } if (r) goto block_err; } if (ds & CRAM_TS) { if (!c->comp_hdr->codecs[DS_TS]) goto block_err; r = cram_decode_tlen(fd, c, s, blk, &cr->tlen); if (r) goto block_err; } else { cr->tlen = INT64_MIN; } } else if ((ds & CRAM_CF) && (cf & CRAM_FLAG_MATE_DOWNSTREAM)) { // else not detached if (ds & CRAM_NF) { if (!c->comp_hdr->codecs[DS_NF]) goto block_err; r |= c->comp_hdr->codecs[DS_NF] ->decode(s, c->comp_hdr->codecs[DS_NF], blk, (char *)&cr->mate_line, &out_sz); if (r) goto block_err; cr->mate_line += rec + 1; //cr->name_len = sprintf(name, "%d", name_id++); //cr->name = DSTRING_LEN(name_ds); //dstring_nappend(name_ds, name, cr->name_len); cr->mate_ref_id = -1; cr->tlen = INT64_MIN; cr->mate_pos = 0; } else { cr->mate_flags = 0; cr->tlen = INT64_MIN; } if ((ds & CRAM_CF) && (cf & CRAM_FLAG_EXPLICIT_TLEN)) { if (ds & CRAM_TS) { r = cram_decode_tlen(fd, c, s, blk, &cr->explicit_tlen); if (r) return r; } else { cr->mate_flags = 0; cr->tlen = INT64_MIN; } } } else if ((ds & CRAM_CF) && (cf & CRAM_FLAG_EXPLICIT_TLEN)) { if (ds & CRAM_TS) { r = cram_decode_tlen(fd, c, s, blk, &cr->explicit_tlen); if (r) return r; } else { cr->mate_flags = 0; cr->tlen = INT64_MIN; } } else { cr->mate_flags = 0; cr->tlen = INT64_MIN; } /* else if (!name[0]) { //name[0] = '?'; name[1] = 0; //cr->name_len = 1; //cr->name= DSTRING_LEN(s->name_ds); //dstring_nappend(s->name_ds, "?", 1); cr->mate_ref_id = -1; cr->tlen = 0; cr->mate_pos = 0; } */ /* Auxiliary tags */ has_MD = has_NM = 0; if (CRAM_MAJOR_VERS(fd->version) == 1) r |= cram_decode_aux_1_0(c, s, blk, cr); else r |= cram_decode_aux(fd, c, s, blk, cr, &has_MD, &has_NM); if (r) goto block_err; /* Fake up dynamic string growth and appending */ if (ds & CRAM_RL) { cr->seq = BLOCK_SIZE(s->seqs_blk); BLOCK_GROW(s->seqs_blk, cr->len); seq = (char *)BLOCK_END(s->seqs_blk); BLOCK_SIZE(s->seqs_blk) += cr->len; if (!seq) goto block_err; cr->qual = BLOCK_SIZE(s->qual_blk); BLOCK_GROW(s->qual_blk, cr->len); qual = (char *)BLOCK_END(s->qual_blk); BLOCK_SIZE(s->qual_blk) += cr->len; if (!s->ref) memset(seq, '=', cr->len); } if (!(bf & BAM_FUNMAP)) { if ((ds & CRAM_AP) && cr->apos <= 0) { hts_log_error("Read has alignment position %"PRId64 " but no unmapped flag", cr->apos); goto block_err; } /* Decode sequence and generate CIGAR */ if (ds & (CRAM_SEQ | CRAM_MQ)) { r |= cram_decode_seq(fd, c, s, blk, cr, sh, cf, seq, qual, has_MD, has_NM); if (r) goto block_err; } else { cr->cigar = 0; cr->ncigar = 0; cr->aend = cr->apos; cr->mqual = 0; } } else { int out_sz2 = cr->len; //puts("Unmapped"); cr->cigar = 0; cr->ncigar = 0; cr->aend = cr->apos; cr->mqual = 0; if (ds & CRAM_BA && cr->len) { if (!c->comp_hdr->codecs[DS_BA]) goto block_err; r |= c->comp_hdr->codecs[DS_BA] ->decode(s, c->comp_hdr->codecs[DS_BA], blk, (char *)seq, &out_sz2); if (r) goto block_err; } if ((ds & CRAM_CF) && (cf & CRAM_FLAG_PRESERVE_QUAL_SCORES)) { out_sz2 = cr->len; if (ds & CRAM_QS && cr->len >= 0) { if (!c->comp_hdr->codecs[DS_QS]) goto block_err; r |= c->comp_hdr->codecs[DS_QS] ->decode(s, c->comp_hdr->codecs[DS_QS], blk, qual, &out_sz2); if (r) goto block_err; } } else { if (ds & CRAM_RL) memset(qual, 255, cr->len); } } if (!c->comp_hdr->qs_seq_orient && (ds & CRAM_QS) && (cr->flags & BAM_FREVERSE)) { int i, j; for (i = 0, j = cr->len-1; i < j; i++, j--) { unsigned char c; c = qual[i]; qual[i] = qual[j]; qual[j] = c; } } } pthread_mutex_lock(&fd->ref_lock); if (refs) { int i; for (i = 0; i < fd->refs->nref; i++) { if (refs[i]) cram_ref_decr(fd->refs, i); } free(refs); refs = NULL; } else if (ref_id >= 0 && s->ref != fd->ref_free && !embed_ref) { cram_ref_decr(fd->refs, ref_id); } pthread_mutex_unlock(&fd->ref_lock); /* Resolve mate pair cross-references between recs within this slice */ r |= cram_decode_slice_xref(s, fd->required_fields); // Free the original blocks as we no longer need these. { int i; for (i = 0; i < s->hdr->num_blocks; i++) { cram_block *b = s->block[i]; cram_free_block(b); s->block[i] = NULL; } } // Also see initial BLOCK_RESIZE_EXACT at top of function. // As we grow blocks we overallocate by up to 50%. So shrink // back to their final sizes here. // //fprintf(stderr, "%d %d // %d %d // %d %d // %d %d\n", // (int)s->seqs_blk->byte, (int)s->seqs_blk->alloc, // (int)s->qual_blk->byte, (int)s->qual_blk->alloc, // (int)s->name_blk->byte, (int)s->name_blk->alloc, // (int)s->aux_blk->byte, (int)s->aux_blk->alloc); BLOCK_RESIZE_EXACT(s->seqs_blk, BLOCK_SIZE(s->seqs_blk)+1); BLOCK_RESIZE_EXACT(s->qual_blk, BLOCK_SIZE(s->qual_blk)+1); BLOCK_RESIZE_EXACT(s->name_blk, BLOCK_SIZE(s->name_blk)+1); BLOCK_RESIZE_EXACT(s->aux_blk, BLOCK_SIZE(s->aux_blk)+1); return r; block_err: if (refs) { int i; pthread_mutex_lock(&fd->ref_lock); for (i = 0; i < fd->refs->nref; i++) { if (refs[i]) cram_ref_decr(fd->refs, i); } free(refs); pthread_mutex_unlock(&fd->ref_lock); } return -1; } typedef struct { cram_fd *fd; cram_container *c; cram_slice *s; sam_hdr_t *h; int exit_code; } cram_decode_job; void *cram_decode_slice_thread(void *arg) { cram_decode_job *j = (cram_decode_job *)arg; j->exit_code = cram_decode_slice(j->fd, j->c, j->s, j->h); return j; } /* * Spawn a multi-threaded version of cram_decode_slice(). */ int cram_decode_slice_mt(cram_fd *fd, cram_container *c, cram_slice *s, sam_hdr_t *bfd) { cram_decode_job *j; int nonblock; if (!fd->pool) return cram_decode_slice(fd, c, s, bfd); if (!(j = malloc(sizeof(*j)))) return -1; j->fd = fd; j->c = c; j->s = s; j->h = bfd; nonblock = hts_tpool_process_sz(fd->rqueue) ? 1 : 0; int saved_errno = errno; errno = 0; if (-1 == hts_tpool_dispatch2(fd->pool, fd->rqueue, cram_decode_slice_thread, j, nonblock)) { /* Would block */ if (errno != EAGAIN) return -1; fd->job_pending = j; } else { fd->job_pending = NULL; } errno = saved_errno; // flush too return 0; } /* ---------------------------------------------------------------------- * CRAM sequence iterators. */ /* * Converts a cram in-memory record into a bam in-memory record. We * pass a pointer to a bam_seq_t pointer along with the a pointer to * the allocated size. These can initially be pointers to NULL and zero. * * This function will reallocate the bam buffer as required and update * (*bam)->alloc accordingly, allowing it to be used within a loop * efficiently without needing to allocate new bam objects over and * over again. * * Returns the used size of the bam record on success * -1 on failure. */ int cram_to_bam(sam_hdr_t *sh, cram_fd *fd, cram_slice *s, cram_record *cr, int rec, bam_seq_t **bam) { int ret, rg_len; char name_a[1024], *name; int name_len; char *aux; char *seq, *qual; sam_hrecs_t *bfd = sh->hrecs; /* Assign names if not explicitly set */ if (fd->required_fields & SAM_QNAME) { if (cr->name_len) { name = (char *)BLOCK_DATA(s->name_blk) + cr->name; name_len = cr->name_len; } else { name = name_a; if (cr->mate_line >= 0 && cr->mate_line < s->max_rec && s->crecs[cr->mate_line].name_len > 0) { // Copy our mate if non-zero. memcpy(name_a, BLOCK_DATA(s->name_blk)+s->crecs[cr->mate_line].name, s->crecs[cr->mate_line].name_len); name = name_a + s->crecs[cr->mate_line].name_len; } else { // Otherwise generate a name based on prefix name_len = strlen(fd->prefix); memcpy(name, fd->prefix, name_len); name += name_len; *name++ = ':'; if (cr->mate_line >= 0 && cr->mate_line < rec) { name = (char *)append_uint64((unsigned char *)name, s->hdr->record_counter + cr->mate_line + 1); } else { name = (char *)append_uint64((unsigned char *)name, s->hdr->record_counter + rec + 1); } } name_len = name - name_a; name = name_a; } } else { name = "?"; name_len = 1; } /* Generate BAM record */ if (cr->rg < -1 || cr->rg >= bfd->nrg) return -1; rg_len = (cr->rg != -1) ? bfd->rg[cr->rg].name_len + 4 : 0; if (fd->required_fields & (SAM_SEQ | SAM_QUAL)) { if (!BLOCK_DATA(s->seqs_blk)) return -1; seq = (char *)BLOCK_DATA(s->seqs_blk) + cr->seq; } else { seq = "*"; cr->len = 0; } if (fd->required_fields & SAM_QUAL) { if (!BLOCK_DATA(s->qual_blk)) return -1; qual = (char *)BLOCK_DATA(s->qual_blk) + cr->qual; } else { qual = NULL; } ret = bam_set1(*bam, name_len, name, cr->flags, cr->ref_id, cr->apos - 1, cr->mqual, cr->ncigar, &s->cigar[cr->cigar], cr->mate_ref_id, cr->mate_pos - 1, cr->tlen, cr->len, seq, qual, cr->aux_size + rg_len); if (ret < 0) { return ret; } aux = (char *)bam_aux(*bam); /* Auxiliary strings */ if (cr->aux_size != 0) { memcpy(aux, BLOCK_DATA(s->aux_blk) + cr->aux, cr->aux_size); aux += cr->aux_size; (*bam)->l_data += cr->aux_size; } /* RG:Z: */ if (rg_len > 0) { *aux++ = 'R'; *aux++ = 'G'; *aux++ = 'Z'; int len = bfd->rg[cr->rg].name_len; memcpy(aux, bfd->rg[cr->rg].name, len); aux += len; *aux++ = 0; (*bam)->l_data += rg_len; } return (*bam)->l_data; } /* * Here be dragons! The multi-threading code in this is crufty beyond belief. */ /* * Load first container. * Called when fd->ctr is NULL> * * Returns container on success * NULL on failure. */ static cram_container *cram_first_slice(cram_fd *fd) { cram_container *c; do { if (fd->ctr) cram_free_container(fd->ctr); if (!(c = fd->ctr = cram_read_container(fd))) return NULL; c->curr_slice_mt = c->curr_slice; } while (c->length == 0); /* * The first container may be a result of a sub-range query. * In which case it may still not be the optimal starting point * due to skipped containers/slices in the index. */ // No need for locks here as we're in the main thread. if (fd->range.refid != -2) { while (c->ref_seq_id != -2 && (c->ref_seq_id < fd->range.refid || (fd->range.refid >= 0 && c->ref_seq_id == fd->range.refid && c->ref_seq_start + c->ref_seq_span-1 < fd->range.start))) { if (0 != cram_seek(fd, c->length, SEEK_CUR)) return NULL; cram_free_container(fd->ctr); do { if (!(c = fd->ctr = cram_read_container(fd))) return NULL; } while (c->length == 0); } if (c->ref_seq_id != -2 && c->ref_seq_id != fd->range.refid) { fd->eof = 1; return NULL; } } if (!(c->comp_hdr_block = cram_read_block(fd))) return NULL; if (c->comp_hdr_block->content_type != COMPRESSION_HEADER) return NULL; c->comp_hdr = cram_decode_compression_header(fd, c->comp_hdr_block); if (!c->comp_hdr) return NULL; if (!c->comp_hdr->AP_delta && sam_hrecs_sort_order(fd->header->hrecs) != ORDER_COORD) { pthread_mutex_lock(&fd->ref_lock); fd->unsorted = 1; pthread_mutex_unlock(&fd->ref_lock); } return c; } cram_slice *cram_next_slice(cram_fd *fd, cram_container **cp) { cram_container *c_curr; // container being consumed via cram_get_seq() cram_slice *s_curr = NULL; // Populate the first container if unknown. if (!(c_curr = fd->ctr)) { if (!(c_curr = cram_first_slice(fd))) return NULL; } // Discard previous slice if ((s_curr = c_curr->slice)) { c_curr->slice = NULL; cram_free_slice(s_curr); s_curr = NULL; } // If we've consumed all slices in this container, also discard // the container too. if (c_curr->curr_slice == c_curr->max_slice) { if (fd->ctr == c_curr) fd->ctr = NULL; if (fd->ctr_mt == c_curr) fd->ctr_mt = NULL; cram_free_container(c_curr); c_curr = NULL; } if (!fd->ctr_mt) fd->ctr_mt = c_curr; // Fetch the next slice (and the container if necessary). // // If single threaded this loop bails out as soon as it finds // a slice in range. In this case c_next and c_curr end up being // the same thing. // // If multi-threaded, we loop until we have filled out // thread pool input queue. Here c_next and c_curr *may* differ, as // can fd->ctr and fd->ctr_mt. for (;;) { cram_container *c_next = fd->ctr_mt; cram_slice *s_next = NULL; // Next slice; either from the last job we failed to push // to the input queue or via more I/O. if (fd->job_pending) { cram_decode_job *j = (cram_decode_job *)fd->job_pending; c_next = j->c; s_next = j->s; free(fd->job_pending); fd->job_pending = NULL; } else if (!fd->ooc) { empty_container: if (!c_next || c_next->curr_slice_mt == c_next->max_slice) { // new container for(;;) { if (!(c_next = cram_read_container(fd))) { if (fd->pool) { fd->ooc = 1; break; } return NULL; } c_next->curr_slice_mt = c_next->curr_slice; if (c_next->length != 0) break; cram_free_container(c_next); } if (fd->ooc) break; /* Skip containers not yet spanning our range */ if (fd->range.refid != -2 && c_next->ref_seq_id != -2) { // ref_id beyond end of range; bail out if (c_next->ref_seq_id != fd->range.refid) { cram_free_container(c_next); fd->ctr_mt = NULL; fd->ooc = 1; break; } // position beyond end of range; bail out if (fd->range.refid != -1 && c_next->ref_seq_start > fd->range.end) { cram_free_container(c_next); fd->ctr_mt = NULL; fd->ooc = 1; break; } // before start of range; skip to next container if (fd->range.refid != -1 && c_next->ref_seq_start + c_next->ref_seq_span-1 < fd->range.start) { c_next->curr_slice_mt = c_next->max_slice; cram_seek(fd, c_next->length, SEEK_CUR); cram_free_container(c_next); c_next = NULL; continue; } } // Container is valid range, so remember it for restarting // this function. fd->ctr_mt = c_next; if (!(c_next->comp_hdr_block = cram_read_block(fd))) return NULL; if (c_next->comp_hdr_block->content_type != COMPRESSION_HEADER) return NULL; c_next->comp_hdr = cram_decode_compression_header(fd, c_next->comp_hdr_block); if (!c_next->comp_hdr) return NULL; if (!c_next->comp_hdr->AP_delta && sam_hrecs_sort_order(fd->header->hrecs) != ORDER_COORD) { pthread_mutex_lock(&fd->ref_lock); fd->unsorted = 1; pthread_mutex_unlock(&fd->ref_lock); } } if (c_next->num_records == 0) { if (fd->ctr == c_next) fd->ctr = NULL; if (c_curr == c_next) c_curr = NULL; if (fd->ctr_mt == c_next) fd->ctr_mt = NULL; cram_free_container(c_next); c_next = NULL; goto empty_container; } if (!(s_next = c_next->slice = cram_read_slice(fd))) return NULL; s_next->slice_num = ++c_next->curr_slice_mt; s_next->curr_rec = 0; s_next->max_rec = s_next->hdr->num_records; s_next->last_apos = s_next->hdr->ref_seq_start; // We know the container overlaps our range, but with multi-slice // containers we may have slices that do not. Skip these also. if (fd->range.refid != -2 && s_next->hdr->ref_seq_id != -2) { // ref_id beyond end of range; bail out if (s_next->hdr->ref_seq_id != fd->range.refid) { fd->ooc = 1; cram_free_slice(s_next); c_next->slice = s_next = NULL; break; } // position beyond end of range; bail out if (fd->range.refid != -1 && s_next->hdr->ref_seq_start > fd->range.end) { fd->ooc = 1; cram_free_slice(s_next); c_next->slice = s_next = NULL; break; } // before start of range; skip to next slice if (fd->range.refid != -1 && s_next->hdr->ref_seq_start + s_next->hdr->ref_seq_span-1 < fd->range.start) { cram_free_slice(s_next); c_next->slice = s_next = NULL; continue; } } } // end: if (!fd->ooc) if (!c_next || !s_next) break; // Decode the slice, either right now (non-threaded) or by pushing // it to the a decode queue (threaded). if (cram_decode_slice_mt(fd, c_next, s_next, fd->header) != 0) { hts_log_error("Failure to decode slice"); cram_free_slice(s_next); c_next->slice = NULL; return NULL; } // No thread pool, so don't loop again if (!fd->pool) { c_curr = c_next; s_curr = s_next; break; } // With thread pool, but we have a job pending so our decode queue // is full. if (fd->job_pending) break; // Otherwise we're threaded with room in the decode input queue, so // keep reading slices for decode. // Push it a bit far, to qsize in queue rather than pending arrival, // as cram tends to be a bit bursty in decode timings. if (hts_tpool_process_len(fd->rqueue) > hts_tpool_process_qsize(fd->rqueue)) break; } // end of for(;;) // When not threaded we've already have c_curr and s_curr. // Otherwise we need get them by pulling off the decode output queue. if (fd->pool) { hts_tpool_result *res; cram_decode_job *j; if (fd->ooc && hts_tpool_process_empty(fd->rqueue)) { fd->eof = 1; return NULL; } res = hts_tpool_next_result_wait(fd->rqueue); if (!res || !hts_tpool_result_data(res)) { hts_log_error("Call to hts_tpool_next_result failed"); return NULL; } j = (cram_decode_job *)hts_tpool_result_data(res); c_curr = j->c; s_curr = j->s; if (j->exit_code != 0) { hts_log_error("Slice decode failure"); fd->eof = 0; hts_tpool_delete_result(res, 1); return NULL; } hts_tpool_delete_result(res, 1); } *cp = c_curr; // Update current slice being processed (as opposed to current // slice in the multi-threaded reahead. fd->ctr = c_curr; if (c_curr) { c_curr->slice = s_curr; if (s_curr) c_curr->curr_slice = s_curr->slice_num; } if (s_curr) s_curr->curr_rec = 0; else fd->eof = 1; return s_curr; } /* * Read the next cram record and return it. * Note that to decode cram_record the caller will need to look up some data * in the current slice, pointed to by fd->ctr->slice. This is valid until * the next call to cram_get_seq (which may invalidate it). * * Returns record pointer on success (do not free) * NULL on failure */ cram_record *cram_get_seq(cram_fd *fd) { cram_container *c; cram_slice *s; for (;;) { c = fd->ctr; if (c && c->slice && c->slice->curr_rec < c->slice->max_rec) { s = c->slice; } else { if (!(s = cram_next_slice(fd, &c))) return NULL; continue; /* In case slice contains no records */ } // No need to lock here as get_seq is running in the main thread, // which is also the same one that does the range modifications. if (fd->range.refid != -2) { if (fd->range.refid == -1 && s->crecs[s->curr_rec].ref_id != -1) { // Special case when looking for unmapped blocks at end. // If these are mixed in with mapped data (c->ref_id == -2) // then we need skip until we find the unmapped data, if at all s->curr_rec++; continue; } if (s->crecs[s->curr_rec].ref_id < fd->range.refid && s->crecs[s->curr_rec].ref_id != -1) { // Looking for a mapped read, but not there yet. Special case // as -1 (unmapped) shouldn't be considered < refid. s->curr_rec++; continue; } if (s->crecs[s->curr_rec].ref_id != fd->range.refid) { fd->eof = 1; cram_free_slice(s); c->slice = NULL; return NULL; } if (fd->range.refid != -1 && s->crecs[s->curr_rec].apos > fd->range.end) { fd->eof = 1; cram_free_slice(s); c->slice = NULL; return NULL; } if (fd->range.refid != -1 && s->crecs[s->curr_rec].aend < fd->range.start) { s->curr_rec++; continue; } } break; } fd->ctr = c; c->slice = s; return &s->crecs[s->curr_rec++]; } /* * Read the next cram record and convert it to a bam_seq_t struct. * * Returns >= 0 success (number of bytes written to *bam) * -1 on EOF or failure (check fd->err) */ int cram_get_bam_seq(cram_fd *fd, bam_seq_t **bam) { cram_record *cr; cram_container *c; cram_slice *s; if (!(cr = cram_get_seq(fd))) return -1; c = fd->ctr; s = c->slice; return cram_to_bam(fd->header, fd, s, cr, s->curr_rec-1, bam); } /* * Drains and frees the decode read-queue for a multi-threaded reader. */ void cram_drain_rqueue(cram_fd *fd) { cram_container *lc = NULL; if (!fd->pool || !fd->rqueue) return; // drain queue of any in-flight decode jobs while (!hts_tpool_process_empty(fd->rqueue)) { hts_tpool_result *r = hts_tpool_next_result_wait(fd->rqueue); if (!r) break; cram_decode_job *j = (cram_decode_job *)hts_tpool_result_data(r); if (j->c->slice == j->s) j->c->slice = NULL; if (j->c != lc) { if (lc) { if (fd->ctr == lc) fd->ctr = NULL; if (fd->ctr_mt == lc) fd->ctr_mt = NULL; cram_free_container(lc); } lc = j->c; } cram_free_slice(j->s); hts_tpool_delete_result(r, 1); } // Also tidy up any pending decode job that we didn't submit to the workers // due to the input queue being full. if (fd->job_pending) { cram_decode_job *j = (cram_decode_job *)fd->job_pending; if (j->c->slice == j->s) j->c->slice = NULL; if (j->c != lc) { if (lc) { if (fd->ctr == lc) fd->ctr = NULL; if (fd->ctr_mt == lc) fd->ctr_mt = NULL; cram_free_container(lc); } lc = j->c; } cram_free_slice(j->s); free(j); fd->job_pending = NULL; } if (lc) { if (fd->ctr == lc) fd->ctr = NULL; if (fd->ctr_mt == lc) fd->ctr_mt = NULL; cram_free_container(lc); } } pysam-0.23.0/htslib/cram/cram_decode.h000066400000000000000000000107341475062545500175540ustar00rootroot00000000000000/* Copyright (c) 2012-2013, 2018, 2024 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /*! \file * Include cram.h instead. * * This is an internal part of the CRAM system and is automatically included * when you #include cram.h. * * Implements the decoding portion of CRAM I/O. Also see * cram_codecs.[ch] for the actual encoding functions themselves. */ #ifndef CRAM_DECODE_H #define CRAM_DECODE_H #ifdef __cplusplus extern "C" { #endif /* ---------------------------------------------------------------------- * CRAM sequence iterators. */ /*! Read the next cram record and return it as a cram_record. * * Note that to decode cram_record the caller will need to look up some data * in the current slice, pointed to by fd->ctr->slice. This is valid until * the next call to cram_get_seq (which may invalidate it). * * @return * Returns record pointer on success (do not free); * NULL on failure */ cram_record *cram_get_seq(cram_fd *fd); /*! Read the next cram record and convert it to a bam_seq_t struct. * * @return * Returns 0 on success; * -1 on EOF or failure (check fd->err) */ int cram_get_bam_seq(cram_fd *fd, bam_seq_t **bam); /* ---------------------------------------------------------------------- * Internal functions */ /*! INTERNAL: * Decodes a CRAM block compression header. * * @return * Returns header ptr on success; * NULL on failure */ cram_block_compression_hdr *cram_decode_compression_header(cram_fd *fd, cram_block *b); /*! INTERNAL: * Decodes a CRAM (un)mapped slice header block. * * @return * Returns slice header ptr on success; * NULL on failure */ cram_block_slice_hdr *cram_decode_slice_header(cram_fd *fd, cram_block *b); /*! INTERNAL: * Loads and decodes the next slice worth of data. * * @return * Returns cram slice pointer on success; * NULL on failure */ cram_slice *cram_next_slice(cram_fd *fd, cram_container **cp); /*! INTERNAL: * Decode an entire slice from container blocks. Fills out s->crecs[] array. * * @return * Returns 0 on success; * -1 on failure */ int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s, sam_hdr_t *hdr); /*! INTERNAL: * Converts a cram in-memory record into a bam in-memory record. We * pass a pointer to a bam_seq_t pointer along with the a pointer to * the allocated size. These can initially be pointers to NULL and zero. * * This function will reallocate the bam buffer as required and update * (*bam)->alloc accordingly, allowing it to be used within a loop * efficiently without needing to allocate new bam objects over and * over again. * * Returns the used size of the bam record on success * -1 on failure. */ int cram_to_bam(sam_hdr_t *sh, cram_fd *fd, cram_slice *s, cram_record *cr, int rec, bam_seq_t **bam); /* * Drains and frees the decode read-queue for a multi-threaded reader. */ void cram_drain_rqueue(cram_fd *fd); #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/cram/cram_encode.c000066400000000000000000004437201475062545500175660ustar00rootroot00000000000000/* Copyright (c) 2012-2020, 2022-2024 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #include #include #include #include #include #include "cram.h" #include "os.h" #include "../sam_internal.h" // for nibble2base #include "../htslib/hts.h" #include "../htslib/hts_endian.h" #include "../textutils_internal.h" KHASH_MAP_INIT_STR(m_s2u64, uint64_t) #define Z_CRAM_STRAT Z_FILTERED //#define Z_CRAM_STRAT Z_RLE //#define Z_CRAM_STRAT Z_HUFFMAN_ONLY //#define Z_CRAM_STRAT Z_DEFAULT_STRATEGY static int process_one_read(cram_fd *fd, cram_container *c, cram_slice *s, cram_record *cr, bam_seq_t *b, int rnum, kstring_t *MD, int embed_ref, int no_ref); /* * Returns index of val into key. * Basically strchr(key, val)-key; */ static int sub_idx(char *key, char val) { int i; for (i = 0; i < 4 && *key++ != val; i++); return i; } /* * Encodes a compression header block into a generic cram_block structure. * * Returns cram_block ptr on success * NULL on failure */ cram_block *cram_encode_compression_header(cram_fd *fd, cram_container *c, cram_block_compression_hdr *h, int embed_ref) { cram_block *cb = cram_new_block(COMPRESSION_HEADER, 0); cram_block *map = cram_new_block(COMPRESSION_HEADER, 0); int i, mc, r = 0; int no_ref = c->no_ref; if (!cb || !map) return NULL; /* * This is a concatenation of several blocks of data: * header + landmarks, preservation map, read encoding map, and the tag * encoding map. * All 4 are variable sized and we need to know how large these are * before creating the compression header itself as this starts with * the total size (stored as a variable length string). */ // Duplicated from container itself, and removed in 1.1 if (CRAM_MAJOR_VERS(fd->version) == 1) { r |= itf8_put_blk(cb, h->ref_seq_id); r |= itf8_put_blk(cb, h->ref_seq_start); r |= itf8_put_blk(cb, h->ref_seq_span); r |= itf8_put_blk(cb, h->num_records); r |= itf8_put_blk(cb, h->num_landmarks); for (i = 0; i < h->num_landmarks; i++) { r |= itf8_put_blk(cb, h->landmark[i]); } } if (h->preservation_map) { kh_destroy(map, h->preservation_map); h->preservation_map = NULL; } /* Create in-memory preservation map */ /* FIXME: should create this when we create the container */ if (c->num_records > 0) { khint_t k; int r; if (!(h->preservation_map = kh_init(map))) return NULL; k = kh_put(map, h->preservation_map, "RN", &r); if (-1 == r) return NULL; kh_val(h->preservation_map, k).i = !fd->lossy_read_names; if (CRAM_MAJOR_VERS(fd->version) == 1) { k = kh_put(map, h->preservation_map, "PI", &r); if (-1 == r) return NULL; kh_val(h->preservation_map, k).i = 0; k = kh_put(map, h->preservation_map, "UI", &r); if (-1 == r) return NULL; kh_val(h->preservation_map, k).i = 1; k = kh_put(map, h->preservation_map, "MI", &r); if (-1 == r) return NULL; kh_val(h->preservation_map, k).i = 1; } else { // Technically SM was in 1.0, but wasn't in Java impl. k = kh_put(map, h->preservation_map, "SM", &r); if (-1 == r) return NULL; kh_val(h->preservation_map, k).i = 0; k = kh_put(map, h->preservation_map, "TD", &r); if (-1 == r) return NULL; kh_val(h->preservation_map, k).i = 0; k = kh_put(map, h->preservation_map, "AP", &r); if (-1 == r) return NULL; kh_val(h->preservation_map, k).i = h->AP_delta; if (CRAM_MAJOR_VERS(fd->version) >= 4) { k = kh_put(map, h->preservation_map, "QO", &r); if (-1 == r) return NULL; kh_val(h->preservation_map, k).i = h->qs_seq_orient; } if (no_ref || embed_ref>0) { // Reference Required == No k = kh_put(map, h->preservation_map, "RR", &r); if (-1 == r) return NULL; kh_val(h->preservation_map, k).i = 0; } } } /* Encode preservation map; could collapse this and above into one */ mc = 0; BLOCK_SIZE(map) = 0; if (h->preservation_map) { khint_t k; for (k = kh_begin(h->preservation_map); k != kh_end(h->preservation_map); k++) { const char *key; khash_t(map) *pmap = h->preservation_map; if (!kh_exist(pmap, k)) continue; key = kh_key(pmap, k); BLOCK_APPEND(map, key, 2); switch(CRAM_KEY(key[0], key[1])) { case CRAM_KEY('M','I'): case CRAM_KEY('U','I'): case CRAM_KEY('P','I'): case CRAM_KEY('A','P'): case CRAM_KEY('R','N'): case CRAM_KEY('R','R'): case CRAM_KEY('Q','O'): BLOCK_APPEND_CHAR(map, kh_val(pmap, k).i); break; case CRAM_KEY('S','M'): { char smat[5], *mp = smat; // Output format is for order ACGTN (minus ref base) // to store the code value 0-3 for each symbol. // // Note this is different to storing the symbols in order // that the codes occur from 0-3, which is what we used to // do. (It didn't matter as we always had a fixed table in // the order.) *mp++ = (sub_idx(h->substitution_matrix[0], 'C') << 6) | (sub_idx(h->substitution_matrix[0], 'G') << 4) | (sub_idx(h->substitution_matrix[0], 'T') << 2) | (sub_idx(h->substitution_matrix[0], 'N') << 0); *mp++ = (sub_idx(h->substitution_matrix[1], 'A') << 6) | (sub_idx(h->substitution_matrix[1], 'G') << 4) | (sub_idx(h->substitution_matrix[1], 'T') << 2) | (sub_idx(h->substitution_matrix[1], 'N') << 0); *mp++ = (sub_idx(h->substitution_matrix[2], 'A') << 6) | (sub_idx(h->substitution_matrix[2], 'C') << 4) | (sub_idx(h->substitution_matrix[2], 'T') << 2) | (sub_idx(h->substitution_matrix[2], 'N') << 0); *mp++ = (sub_idx(h->substitution_matrix[3], 'A') << 6) | (sub_idx(h->substitution_matrix[3], 'C') << 4) | (sub_idx(h->substitution_matrix[3], 'G') << 2) | (sub_idx(h->substitution_matrix[3], 'N') << 0); *mp++ = (sub_idx(h->substitution_matrix[4], 'A') << 6) | (sub_idx(h->substitution_matrix[4], 'C') << 4) | (sub_idx(h->substitution_matrix[4], 'G') << 2) | (sub_idx(h->substitution_matrix[4], 'T') << 0); BLOCK_APPEND(map, smat, 5); break; } case CRAM_KEY('T','D'): { r |= (fd->vv.varint_put32_blk(map, BLOCK_SIZE(h->TD_blk)) <= 0); BLOCK_APPEND(map, BLOCK_DATA(h->TD_blk), BLOCK_SIZE(h->TD_blk)); break; } default: hts_log_warning("Unknown preservation key '%.2s'", key); break; } mc++; } } r |= (fd->vv.varint_put32_blk(cb, BLOCK_SIZE(map) + fd->vv.varint_size(mc)) <= 0); r |= (fd->vv.varint_put32_blk(cb, mc) <= 0); BLOCK_APPEND(cb, BLOCK_DATA(map), BLOCK_SIZE(map)); /* rec encoding map */ mc = 0; BLOCK_SIZE(map) = 0; if (h->codecs[DS_BF]) { if (-1 == h->codecs[DS_BF]->store(h->codecs[DS_BF], map, "BF", fd->version)) return NULL; mc++; } if (h->codecs[DS_CF]) { if (-1 == h->codecs[DS_CF]->store(h->codecs[DS_CF], map, "CF", fd->version)) return NULL; mc++; } if (h->codecs[DS_RL]) { if (-1 == h->codecs[DS_RL]->store(h->codecs[DS_RL], map, "RL", fd->version)) return NULL; mc++; } if (h->codecs[DS_AP]) { if (-1 == h->codecs[DS_AP]->store(h->codecs[DS_AP], map, "AP", fd->version)) return NULL; mc++; } if (h->codecs[DS_RG]) { if (-1 == h->codecs[DS_RG]->store(h->codecs[DS_RG], map, "RG", fd->version)) return NULL; mc++; } if (h->codecs[DS_MF]) { if (-1 == h->codecs[DS_MF]->store(h->codecs[DS_MF], map, "MF", fd->version)) return NULL; mc++; } if (h->codecs[DS_NS]) { if (-1 == h->codecs[DS_NS]->store(h->codecs[DS_NS], map, "NS", fd->version)) return NULL; mc++; } if (h->codecs[DS_NP]) { if (-1 == h->codecs[DS_NP]->store(h->codecs[DS_NP], map, "NP", fd->version)) return NULL; mc++; } if (h->codecs[DS_TS]) { if (-1 == h->codecs[DS_TS]->store(h->codecs[DS_TS], map, "TS", fd->version)) return NULL; mc++; } if (h->codecs[DS_NF]) { if (-1 == h->codecs[DS_NF]->store(h->codecs[DS_NF], map, "NF", fd->version)) return NULL; mc++; } if (h->codecs[DS_TC]) { if (-1 == h->codecs[DS_TC]->store(h->codecs[DS_TC], map, "TC", fd->version)) return NULL; mc++; } if (h->codecs[DS_TN]) { if (-1 == h->codecs[DS_TN]->store(h->codecs[DS_TN], map, "TN", fd->version)) return NULL; mc++; } if (h->codecs[DS_TL]) { if (-1 == h->codecs[DS_TL]->store(h->codecs[DS_TL], map, "TL", fd->version)) return NULL; mc++; } if (h->codecs[DS_FN]) { if (-1 == h->codecs[DS_FN]->store(h->codecs[DS_FN], map, "FN", fd->version)) return NULL; mc++; } if (h->codecs[DS_FC]) { if (-1 == h->codecs[DS_FC]->store(h->codecs[DS_FC], map, "FC", fd->version)) return NULL; mc++; } if (h->codecs[DS_FP]) { if (-1 == h->codecs[DS_FP]->store(h->codecs[DS_FP], map, "FP", fd->version)) return NULL; mc++; } if (h->codecs[DS_BS]) { if (-1 == h->codecs[DS_BS]->store(h->codecs[DS_BS], map, "BS", fd->version)) return NULL; mc++; } if (h->codecs[DS_IN]) { if (-1 == h->codecs[DS_IN]->store(h->codecs[DS_IN], map, "IN", fd->version)) return NULL; mc++; } if (h->codecs[DS_DL]) { if (-1 == h->codecs[DS_DL]->store(h->codecs[DS_DL], map, "DL", fd->version)) return NULL; mc++; } if (h->codecs[DS_BA]) { if (-1 == h->codecs[DS_BA]->store(h->codecs[DS_BA], map, "BA", fd->version)) return NULL; mc++; } if (h->codecs[DS_BB]) { if (-1 == h->codecs[DS_BB]->store(h->codecs[DS_BB], map, "BB", fd->version)) return NULL; mc++; } if (h->codecs[DS_MQ]) { if (-1 == h->codecs[DS_MQ]->store(h->codecs[DS_MQ], map, "MQ", fd->version)) return NULL; mc++; } if (h->codecs[DS_RN]) { if (-1 == h->codecs[DS_RN]->store(h->codecs[DS_RN], map, "RN", fd->version)) return NULL; mc++; } if (h->codecs[DS_QS]) { if (-1 == h->codecs[DS_QS]->store(h->codecs[DS_QS], map, "QS", fd->version)) return NULL; mc++; } if (h->codecs[DS_QQ]) { if (-1 == h->codecs[DS_QQ]->store(h->codecs[DS_QQ], map, "QQ", fd->version)) return NULL; mc++; } if (h->codecs[DS_RI]) { if (-1 == h->codecs[DS_RI]->store(h->codecs[DS_RI], map, "RI", fd->version)) return NULL; mc++; } if (CRAM_MAJOR_VERS(fd->version) != 1) { if (h->codecs[DS_SC]) { if (-1 == h->codecs[DS_SC]->store(h->codecs[DS_SC], map, "SC", fd->version)) return NULL; mc++; } if (h->codecs[DS_RS]) { if (-1 == h->codecs[DS_RS]->store(h->codecs[DS_RS], map, "RS", fd->version)) return NULL; mc++; } if (h->codecs[DS_PD]) { if (-1 == h->codecs[DS_PD]->store(h->codecs[DS_PD], map, "PD", fd->version)) return NULL; mc++; } if (h->codecs[DS_HC]) { if (-1 == h->codecs[DS_HC]->store(h->codecs[DS_HC], map, "HC", fd->version)) return NULL; mc++; } } if (h->codecs[DS_TM]) { if (-1 == h->codecs[DS_TM]->store(h->codecs[DS_TM], map, "TM", fd->version)) return NULL; mc++; } if (h->codecs[DS_TV]) { if (-1 == h->codecs[DS_TV]->store(h->codecs[DS_TV], map, "TV", fd->version)) return NULL; mc++; } r |= (fd->vv.varint_put32_blk(cb, BLOCK_SIZE(map) + fd->vv.varint_size(mc)) <= 0); r |= (fd->vv.varint_put32_blk(cb, mc) <= 0); BLOCK_APPEND(cb, BLOCK_DATA(map), BLOCK_SIZE(map)); /* tag encoding map */ mc = 0; BLOCK_SIZE(map) = 0; if (c->tags_used) { khint_t k; for (k = kh_begin(c->tags_used); k != kh_end(c->tags_used); k++) { int key; if (!kh_exist(c->tags_used, k)) continue; key = kh_key(c->tags_used, k); cram_codec *cd = kh_val(c->tags_used, k)->codec; r |= (fd->vv.varint_put32_blk(map, key) <= 0); if (-1 == cd->store(cd, map, NULL, fd->version)) return NULL; mc++; } } r |= (fd->vv.varint_put32_blk(cb, BLOCK_SIZE(map) + fd->vv.varint_size(mc)) <= 0); r |= (fd->vv.varint_put32_blk(cb, mc) <= 0); BLOCK_APPEND(cb, BLOCK_DATA(map), BLOCK_SIZE(map)); hts_log_info("Wrote compression block header in %d bytes", (int)BLOCK_SIZE(cb)); BLOCK_UPLEN(cb); cram_free_block(map); if (r >= 0) return cb; block_err: return NULL; } /* * Encodes a slice compression header. * * Returns cram_block on success * NULL on failure */ cram_block *cram_encode_slice_header(cram_fd *fd, cram_slice *s) { char *buf; char *cp; cram_block *b = cram_new_block(MAPPED_SLICE, 0); int j; if (!b) return NULL; cp = buf = malloc(22+16+5*(8+s->hdr->num_blocks)); if (NULL == buf) { cram_free_block(b); return NULL; } cp += fd->vv.varint_put32s(cp, NULL, s->hdr->ref_seq_id); if (CRAM_MAJOR_VERS(fd->version) >= 4) { cp += fd->vv.varint_put64(cp, NULL, s->hdr->ref_seq_start); cp += fd->vv.varint_put64(cp, NULL, s->hdr->ref_seq_span); } else { if (s->hdr->ref_seq_start < 0 || s->hdr->ref_seq_start > INT_MAX) { hts_log_error("Reference position too large for CRAM 3"); cram_free_block(b); free(buf); return NULL; } cp += fd->vv.varint_put32(cp, NULL, s->hdr->ref_seq_start); cp += fd->vv.varint_put32(cp, NULL, s->hdr->ref_seq_span); } cp += fd->vv.varint_put32(cp, NULL, s->hdr->num_records); if (CRAM_MAJOR_VERS(fd->version) == 2) cp += fd->vv.varint_put32(cp, NULL, s->hdr->record_counter); else if (CRAM_MAJOR_VERS(fd->version) >= 3) cp += fd->vv.varint_put64(cp, NULL, s->hdr->record_counter); cp += fd->vv.varint_put32(cp, NULL, s->hdr->num_blocks); cp += fd->vv.varint_put32(cp, NULL, s->hdr->num_content_ids); for (j = 0; j < s->hdr->num_content_ids; j++) { cp += fd->vv.varint_put32(cp, NULL, s->hdr->block_content_ids[j]); } if (s->hdr->content_type == MAPPED_SLICE) cp += fd->vv.varint_put32(cp, NULL, s->hdr->ref_base_id); if (CRAM_MAJOR_VERS(fd->version) != 1) { memcpy(cp, s->hdr->md5, 16); cp += 16; } assert(cp-buf <= 22+16+5*(8+s->hdr->num_blocks)); b->data = (unsigned char *)buf; b->comp_size = b->uncomp_size = cp-buf; return b; } /* * Encodes a single read. * * Returns 0 on success * -1 on failure */ static int cram_encode_slice_read(cram_fd *fd, cram_container *c, cram_block_compression_hdr *h, cram_slice *s, cram_record *cr, int64_t *last_pos) { int r = 0; int32_t i32; int64_t i64; unsigned char uc; //fprintf(stderr, "Encode seq %d, %d/%d FN=%d, %s\n", rec, core->byte, core->bit, cr->nfeature, s->name_ds->str + cr->name); //printf("BF=0x%x\n", cr->flags); // bf = cram_flag_swap[cr->flags]; i32 = fd->cram_flag_swap[cr->flags & 0xfff]; r |= h->codecs[DS_BF]->encode(s, h->codecs[DS_BF], (char *)&i32, 1); i32 = cr->cram_flags & CRAM_FLAG_MASK; r |= h->codecs[DS_CF]->encode(s, h->codecs[DS_CF], (char *)&i32, 1); if (CRAM_MAJOR_VERS(fd->version) != 1 && s->hdr->ref_seq_id == -2) r |= h->codecs[DS_RI]->encode(s, h->codecs[DS_RI], (char *)&cr->ref_id, 1); r |= h->codecs[DS_RL]->encode(s, h->codecs[DS_RL], (char *)&cr->len, 1); if (c->pos_sorted) { if (CRAM_MAJOR_VERS(fd->version) >= 4) { i64 = cr->apos - *last_pos; r |= h->codecs[DS_AP]->encode(s, h->codecs[DS_AP], (char *)&i64, 1); } else { i32 = cr->apos - *last_pos; r |= h->codecs[DS_AP]->encode(s, h->codecs[DS_AP], (char *)&i32, 1); } *last_pos = cr->apos; } else { if (CRAM_MAJOR_VERS(fd->version) >= 4) { i64 = cr->apos; r |= h->codecs[DS_AP]->encode(s, h->codecs[DS_AP], (char *)&i64, 1); } else { i32 = cr->apos; r |= h->codecs[DS_AP]->encode(s, h->codecs[DS_AP], (char *)&i32, 1); } } r |= h->codecs[DS_RG]->encode(s, h->codecs[DS_RG], (char *)&cr->rg, 1); if (cr->cram_flags & CRAM_FLAG_DETACHED) { i32 = cr->mate_flags; r |= h->codecs[DS_MF]->encode(s, h->codecs[DS_MF], (char *)&i32, 1); r |= h->codecs[DS_NS]->encode(s, h->codecs[DS_NS], (char *)&cr->mate_ref_id, 1); if (CRAM_MAJOR_VERS(fd->version) >= 4) { r |= h->codecs[DS_NP]->encode(s, h->codecs[DS_NP], (char *)&cr->mate_pos, 1); r |= h->codecs[DS_TS]->encode(s, h->codecs[DS_TS], (char *)&cr->tlen, 1); } else { i32 = cr->mate_pos; r |= h->codecs[DS_NP]->encode(s, h->codecs[DS_NP], (char *)&i32, 1); i32 = cr->tlen; r |= h->codecs[DS_TS]->encode(s, h->codecs[DS_TS], (char *)&i32, 1); } } else { if (cr->cram_flags & CRAM_FLAG_MATE_DOWNSTREAM) { r |= h->codecs[DS_NF]->encode(s, h->codecs[DS_NF], (char *)&cr->mate_line, 1); } if (cr->cram_flags & CRAM_FLAG_EXPLICIT_TLEN) { if (CRAM_MAJOR_VERS(fd->version) >= 4) { r |= h->codecs[DS_TS]->encode(s, h->codecs[DS_TS], (char *)&cr->tlen, 1); } } } /* Aux tags */ if (CRAM_MAJOR_VERS(fd->version) == 1) { int j; uc = cr->ntags; r |= h->codecs[DS_TC]->encode(s, h->codecs[DS_TC], (char *)&uc, 1); for (j = 0; j < cr->ntags; j++) { uint32_t i32 = s->TN[cr->TN_idx + j]; // id r |= h->codecs[DS_TN]->encode(s, h->codecs[DS_TN], (char *)&i32, 1); } } else { r |= h->codecs[DS_TL]->encode(s, h->codecs[DS_TL], (char *)&cr->TL, 1); } // qual // QS codec : Already stored in block[2]. // features (diffs) if (!(cr->flags & BAM_FUNMAP)) { int prev_pos = 0, j; r |= h->codecs[DS_FN]->encode(s, h->codecs[DS_FN], (char *)&cr->nfeature, 1); for (j = 0; j < cr->nfeature; j++) { cram_feature *f = &s->features[cr->feature + j]; uc = f->X.code; r |= h->codecs[DS_FC]->encode(s, h->codecs[DS_FC], (char *)&uc, 1); i32 = f->X.pos - prev_pos; r |= h->codecs[DS_FP]->encode(s, h->codecs[DS_FP], (char *)&i32, 1); prev_pos = f->X.pos; switch(f->X.code) { //char *seq; case 'X': //fprintf(stderr, " FC=%c FP=%d base=%d\n", f->X.code, i32, f->X.base); uc = f->X.base; r |= h->codecs[DS_BS]->encode(s, h->codecs[DS_BS], (char *)&uc, 1); break; case 'S': // Already done //r |= h->codecs[DS_SC]->encode(s, h->codecs[DS_SC], // BLOCK_DATA(s->soft_blk) + f->S.seq_idx, // f->S.len); //if (CRAM_MAJOR_VERS(fd->version) >= 3) { // r |= h->codecs[DS_BB]->encode(s, h->codecs[DS_BB], // BLOCK_DATA(s->seqs_blk) + f->S.seq_idx, // f->S.len); //} break; case 'I': //seq = DSTRING_STR(s->seqs_ds) + f->S.seq_idx; //r |= h->codecs[DS_IN]->encode(s, h->codecs[DS_IN], // seq, f->S.len); //if (CRAM_MAJOR_VERS(fd->version) >= 3) { // r |= h->codecs[DS_BB]->encode(s, h->codecs[DS_BB], // BLOCK_DATA(s->seqs_blk) + f->I.seq_idx, // f->I.len); //} break; case 'i': uc = f->i.base; r |= h->codecs[DS_BA]->encode(s, h->codecs[DS_BA], (char *)&uc, 1); //seq = DSTRING_STR(s->seqs_ds) + f->S.seq_idx; //r |= h->codecs[DS_IN]->encode(s, h->codecs[DS_IN], // seq, 1); break; case 'D': i32 = f->D.len; r |= h->codecs[DS_DL]->encode(s, h->codecs[DS_DL], (char *)&i32, 1); break; case 'B': // // Used when we try to store a non ACGTN base or an N // // that aligns against a non ACGTN reference uc = f->B.base; r |= h->codecs[DS_BA]->encode(s, h->codecs[DS_BA], (char *)&uc, 1); // Already added // uc = f->B.qual; // r |= h->codecs[DS_QS]->encode(s, h->codecs[DS_QS], // (char *)&uc, 1); break; case 'b': // string of bases r |= h->codecs[DS_BB]->encode(s, h->codecs[DS_BB], (char *)BLOCK_DATA(s->seqs_blk) + f->b.seq_idx, f->b.len); break; case 'Q': // Already added // uc = f->B.qual; // r |= h->codecs[DS_QS]->encode(s, h->codecs[DS_QS], // (char *)&uc, 1); break; case 'N': i32 = f->N.len; r |= h->codecs[DS_RS]->encode(s, h->codecs[DS_RS], (char *)&i32, 1); break; case 'P': i32 = f->P.len; r |= h->codecs[DS_PD]->encode(s, h->codecs[DS_PD], (char *)&i32, 1); break; case 'H': i32 = f->H.len; r |= h->codecs[DS_HC]->encode(s, h->codecs[DS_HC], (char *)&i32, 1); break; default: hts_log_error("Unhandled feature code %c", f->X.code); return -1; } } r |= h->codecs[DS_MQ]->encode(s, h->codecs[DS_MQ], (char *)&cr->mqual, 1); } else { char *seq = (char *)BLOCK_DATA(s->seqs_blk) + cr->seq; if (cr->len) r |= h->codecs[DS_BA]->encode(s, h->codecs[DS_BA], seq, cr->len); } return r ? -1 : 0; } /* * Applies various compression methods to specific blocks, depending on * known observations of how data series compress. * * Returns 0 on success * -1 on failure */ static int cram_compress_slice(cram_fd *fd, cram_container *c, cram_slice *s) { int level = fd->level, i; int method = 1<version >= (3<<8)+1); /* Compress the CORE Block too, with minimal zlib level */ if (level > 5 && s->block[0]->uncomp_size > 500) cram_compress_block2(fd, s, s->block[0], NULL, 1<use_bz2) method |= 1<use_rans) { method_ranspr = (1< 1) method_ranspr |= (1< 5) method_ranspr |= (1<use_rans) { methodF |= v31_or_above ? method_ranspr : method_rans; method |= v31_or_above ? method_ranspr : method_rans; } int method_arith = 0; if (fd->use_arith) { method_arith = (1< 1) method_arith |= (1<use_arith && v31_or_above) { methodF |= method_arith; method |= method_arith; } if (fd->use_lzma) method |= (1<= 5) { method |= 1<use_fqz) { qmethod |= 1<level > 4) { qmethod |= 1<level > 6) { qmethod |= (1<metrics_lock); for (i = 0; i < DS_END; i++) if (c->stats[i] && c->stats[i]->nvals > 16) fd->m[i]->unpackable = 1; pthread_mutex_unlock(&fd->metrics_lock); /* Specific compression methods for certain block types */ if (cram_compress_block2(fd, s, s->block[DS_IN], fd->m[DS_IN], //IN (seq) method, level)) return -1; if (fd->level == 0) { /* Do nothing */ } else if (fd->level == 1) { if (cram_compress_block2(fd, s, s->block[DS_QS], fd->m[DS_QS], qmethodF, 1)) return -1; for (i = DS_aux; i <= DS_aux_oz; i++) { if (s->block[i]) if (cram_compress_block2(fd, s, s->block[i], fd->m[i], method, 1)) return -1; } } else if (fd->level < 3) { if (cram_compress_block2(fd, s, s->block[DS_QS], fd->m[DS_QS], qmethod, 1)) return -1; if (cram_compress_block2(fd, s, s->block[DS_BA], fd->m[DS_BA], method, 1)) return -1; if (s->block[DS_BB]) if (cram_compress_block2(fd, s, s->block[DS_BB], fd->m[DS_BB], method, 1)) return -1; for (i = DS_aux; i <= DS_aux_oz; i++) { if (s->block[i]) if (cram_compress_block2(fd, s, s->block[i], fd->m[i], method, level)) return -1; } } else { if (cram_compress_block2(fd, s, s->block[DS_QS], fd->m[DS_QS], qmethod, level)) return -1; if (cram_compress_block2(fd, s, s->block[DS_BA], fd->m[DS_BA], method, level)) return -1; if (s->block[DS_BB]) if (cram_compress_block2(fd, s, s->block[DS_BB], fd->m[DS_BB], method, level)) return -1; for (i = DS_aux; i <= DS_aux_oz; i++) { if (s->block[i]) if (cram_compress_block2(fd, s, s->block[i], fd->m[i], method, level)) return -1; } } // NAME: best is generally xz, bzip2, zlib then rans1 int method_rn = method & ~(method_rans | method_ranspr | 1<version >= (3<<8)+1 && fd->use_tok) method_rn |= fd->use_arith ? (1<block[DS_RN], fd->m[DS_RN], method_rn, level)) return -1; // NS shows strong local correlation as rearrangements are localised if (s->block[DS_NS] && s->block[DS_NS] != s->block[0]) if (cram_compress_block2(fd, s, s->block[DS_NS], fd->m[DS_NS], method, level)) return -1; /* * Compress any auxiliary tags with their own per-tag metrics */ { int i; for (i = DS_END /*num_blk - naux_blk*/; i < s->hdr->num_blocks; i++) { if (!s->block[i] || s->block[i] == s->block[0]) continue; if (s->block[i]->method != RAW) continue; if (cram_compress_block2(fd, s, s->block[i], s->block[i]->m, method, level)) return -1; } } /* * Minimal compression of any block still uncompressed, bar CORE */ { int i; for (i = 1; i < s->hdr->num_blocks && i < DS_END; i++) { if (!s->block[i] || s->block[i] == s->block[0]) continue; if (s->block[i]->method != RAW) continue; if (cram_compress_block2(fd, s, s->block[i], fd->m[i], methodF, level)) return -1; } } return 0; } /* * Allocates a block associated with the cram codec associated with * data series ds_id or the internal codec_id (depending on codec * type). * * The ds_ids are what end up written to disk as an external block. * The c_ids are internal and used when daisy-chaining transforms * such as MAP and RLE. These blocks are also allocated, but * are ephemeral in nature. (The codecs themselves cannot allocate * these as the same codec pointer may be operating on multiple slices * if we're using a multi-slice container.) * * Returns 0 on success * -1 on failure */ static int cram_allocate_block(cram_codec *codec, cram_slice *s, int ds_id) { if (!codec) return 0; switch(codec->codec) { // Codecs which are hard-coded to use the CORE block case E_GOLOMB: case E_HUFFMAN: case E_BETA: case E_SUBEXP: case E_GOLOMB_RICE: case E_GAMMA: codec->out = s->block[0]; break; // Codecs which don't use external blocks case E_CONST_BYTE: case E_CONST_INT: codec->out = NULL; break; // Codecs that emit directly to external blocks case E_EXTERNAL: case E_VARINT_UNSIGNED: case E_VARINT_SIGNED: if (!(s->block[ds_id] = cram_new_block(EXTERNAL, ds_id))) return -1; codec->u.external.content_id = ds_id; codec->out = s->block[ds_id]; break; case E_BYTE_ARRAY_STOP: // Why no sub-codec? if (!(s->block[ds_id] = cram_new_block(EXTERNAL, ds_id))) return -1; codec->u.byte_array_stop.content_id = ds_id; codec->out = s->block[ds_id]; break; // Codecs that contain sub-codecs which may in turn emit to external blocks case E_BYTE_ARRAY_LEN: { cram_codec *bal = codec->u.e_byte_array_len.len_codec; if (cram_allocate_block(bal, s, bal->u.external.content_id)) return -1; bal = codec->u.e_byte_array_len.val_codec; if (cram_allocate_block(bal, s, bal->u.external.content_id)) return -1; break; } case E_XRLE: if (cram_allocate_block(codec->u.e_xrle.len_codec, s, ds_id)) //ds_id == DS_QS ? DS_QS_len : ds_id)) return -1; if (cram_allocate_block(codec->u.e_xrle.lit_codec, s, ds_id)) return -1; break; case E_XPACK: if (cram_allocate_block(codec->u.e_xpack.sub_codec, s, ds_id)) return -1; codec->out = cram_new_block(0, 0); // ephemeral if (!codec->out) return -1; break; case E_XDELTA: if (cram_allocate_block(codec->u.e_xdelta.sub_codec, s, ds_id)) return -1; codec->out = cram_new_block(0, 0); // ephemeral if (!codec->out) return -1; break; default: break; } return 0; } /* * Encodes a single slice from a container * * Returns 0 on success * -1 on failure */ static int cram_encode_slice(cram_fd *fd, cram_container *c, cram_block_compression_hdr *h, cram_slice *s, int embed_ref) { int rec, r = 0; int64_t last_pos; enum cram_DS_ID id; /* * Slice external blocks: * ID 0 => base calls (insertions, soft-clip) * ID 1 => qualities * ID 2 => names * ID 3 => TS (insert size), NP (next frag) * ID 4 => tag values * ID 6 => tag IDs (TN), if CRAM_V1.0 * ID 7 => TD tag dictionary, if !CRAM_V1.0 */ /* Create cram slice header */ s->hdr->ref_base_id = embed_ref>0 && s->hdr->ref_seq_span > 0 ? DS_ref : (CRAM_MAJOR_VERS(fd->version) >= 4 ? 0 : -1); s->hdr->record_counter = c->num_records + c->record_counter; c->num_records += s->hdr->num_records; int ntags = c->tags_used ? c->tags_used->n_occupied : 0; s->block = calloc(DS_END + ntags*2, sizeof(s->block[0])); s->hdr->block_content_ids = malloc(DS_END * sizeof(int32_t)); if (!s->block || !s->hdr->block_content_ids) return -1; // Create first fixed blocks, always external. // CORE if (!(s->block[0] = cram_new_block(CORE, 0))) return -1; // TN block for CRAM v1 if (CRAM_MAJOR_VERS(fd->version) == 1) { if (h->codecs[DS_TN]->codec == E_EXTERNAL) { if (!(s->block[DS_TN] = cram_new_block(EXTERNAL,DS_TN))) return -1; h->codecs[DS_TN]->u.external.content_id = DS_TN; } else { s->block[DS_TN] = s->block[0]; } } // Embedded reference if (embed_ref>0) { if (!(s->block[DS_ref] = cram_new_block(EXTERNAL, DS_ref))) return -1; s->ref_id = DS_ref; // needed? BLOCK_APPEND(s->block[DS_ref], c->ref + s->hdr->ref_seq_start - c->ref_start, s->hdr->ref_seq_span); } /* * All the data-series blocks if appropriate. */ for (id = DS_QS; id < DS_TN; id++) { if (cram_allocate_block(h->codecs[id], s, id) < 0) return -1; } /* * Add in the external tag blocks too. */ if (c->tags_used) { int n; s->hdr->num_blocks = DS_END; for (n = 0; n < s->naux_block; n++) { s->block[s->hdr->num_blocks++] = s->aux_block[n]; s->aux_block[n] = NULL; } } /* Encode reads */ last_pos = s->hdr->ref_seq_start; for (rec = 0; rec < s->hdr->num_records; rec++) { cram_record *cr = &s->crecs[rec]; if (cram_encode_slice_read(fd, c, h, s, cr, &last_pos) == -1) return -1; } s->block[0]->uncomp_size = s->block[0]->byte + (s->block[0]->bit < 7); s->block[0]->comp_size = s->block[0]->uncomp_size; // Make sure the fixed blocks point to the correct sources if (s->block[DS_IN]) cram_free_block(s->block[DS_IN]); s->block[DS_IN] = s->base_blk; s->base_blk = NULL; if (s->block[DS_QS]) cram_free_block(s->block[DS_QS]); s->block[DS_QS] = s->qual_blk; s->qual_blk = NULL; if (s->block[DS_RN]) cram_free_block(s->block[DS_RN]); s->block[DS_RN] = s->name_blk; s->name_blk = NULL; if (s->block[DS_SC]) cram_free_block(s->block[DS_SC]); s->block[DS_SC] = s->soft_blk; s->soft_blk = NULL; // Finalise any data transforms. for (id = DS_QS; id < DS_TN; id++) { if (h->codecs[id] && h->codecs[id]->flush) h->codecs[id]->flush(h->codecs[id]); } // Ensure block sizes are up to date. for (id = 1; id < s->hdr->num_blocks; id++) { if (!s->block[id] || s->block[id] == s->block[0]) continue; if (s->block[id]->uncomp_size == 0) BLOCK_UPLEN(s->block[id]); } // Compress it all if (cram_compress_slice(fd, c, s) == -1) return -1; // Collapse empty blocks and create hdr_block { int i, j; s->hdr->block_content_ids = realloc(s->hdr->block_content_ids, s->hdr->num_blocks * sizeof(int32_t)); if (!s->hdr->block_content_ids) return -1; for (i = j = 1; i < s->hdr->num_blocks; i++) { if (!s->block[i] || s->block[i] == s->block[0]) continue; if (s->block[i]->uncomp_size == 0) { cram_free_block(s->block[i]); s->block[i] = NULL; continue; } s->block[j] = s->block[i]; s->hdr->block_content_ids[j-1] = s->block[i]->content_id; j++; } s->hdr->num_content_ids = j-1; s->hdr->num_blocks = j; if (!(s->hdr_block = cram_encode_slice_header(fd, s))) return -1; } return r ? -1 : 0; block_err: return -1; } static inline const char *bam_data_end(bam1_t *b) { return (const char *)b->data + b->l_data; } /* * A bounds checking version of bam_aux2i. */ static inline int bam_aux2i_end(const uint8_t *aux, const uint8_t *aux_end) { int type = *aux++; switch (type) { case 'c': if (aux_end - aux < 1) { errno = EINVAL; return 0; } return *(int8_t *)aux; case 'C': if (aux_end - aux < 1) { errno = EINVAL; return 0; } return *aux; case 's': if (aux_end - aux < 2) { errno = EINVAL; return 0; } return le_to_i16(aux); case 'S': if (aux_end - aux < 2) { errno = EINVAL; return 0; } return le_to_u16(aux); case 'i': if (aux_end - aux < 4) { errno = EINVAL; return 0; } return le_to_i32(aux); case 'I': if (aux_end - aux < 4) { errno = EINVAL; return 0; } return le_to_u32(aux); default: errno = EINVAL; } return 0; } /* * Returns the number of expected read names for this record. */ static int expected_template_count(bam_seq_t *b) { int expected = bam_flag(b) & BAM_FPAIRED ? 2 : 1; uint8_t *TC = (uint8_t *)bam_aux_get(b, "TC"); if (TC) { int n = bam_aux2i_end(TC, (uint8_t *)bam_data_end(b)); if (expected < n) expected = n; } if (!TC && bam_aux_get(b, "SA")) { // We could count the semicolons, but we'd have to do this for // read1, read2 and read(not-1-or-2) combining the results // together. This is a cheap and safe alternative for now. expected = INT_MAX; } return expected; } /* * Lossily reject read names. * * The rule here is that if all reads for this template reside in the * same slice then we can lose the name. Otherwise we keep them as we * do not know when (or if) the other reads will turn up. * * Note there may be only 1 read (non-paired library) or more than 2 * reads (paired library with supplementary reads), or other weird * setups. We need to know how many are expected. Ways to guess: * * - Flags (0x1 - has > 1 read) * - TC aux field (not mandatory) * - SA tags (count semicolons, NB per fragment so sum - hard) * - RNEXT/PNEXT uniqueness count. (not implemented, tricky) * * Returns 0 on success * -1 on failure */ static int lossy_read_names(cram_fd *fd, cram_container *c, cram_slice *s, int bam_start) { int r1, r2, ret = -1; // Initialise cram_flags for (r2 = 0; r2 < s->hdr->num_records; r2++) s->crecs[r2].cram_flags = 0; if (!fd->lossy_read_names) return 0; khash_t(m_s2u64) *names = kh_init(m_s2u64); if (!names) goto fail; // 1: Iterate through names to count frequency for (r1 = bam_start, r2 = 0; r2 < s->hdr->num_records; r1++, r2++) { //cram_record *cr = &s->crecs[r2]; bam_seq_t *b = c->bams[r1]; khint_t k; int n; uint64_t e; union { uint64_t i64; struct { int32_t e,c; // expected & observed counts. } counts; } u; e = expected_template_count(b); u.counts.e = e; u.counts.c = 1; k = kh_put(m_s2u64, names, bam_name(b), &n); if (n == -1) goto fail; if (n == 0) { // not a new name u.i64 = kh_val(names, k); if (u.counts.e != e) { // different expectation or already hit the max //fprintf(stderr, "Err computing no. %s recs\n", bam_name(b)); kh_val(names, k) = 0; } else { u.counts.c++; if (u.counts.e == u.counts.c) { // Reached expected count. kh_val(names, k) = -1; } else { kh_val(names, k) = u.i64; } } } else { // new name kh_val(names, k) = u.i64; } } // 2: Remove names if all present (hd.i == -1) for (r1 = bam_start, r2 = 0; r2 < s->hdr->num_records; r1++, r2++) { cram_record *cr = &s->crecs[r2]; bam_seq_t *b = c->bams[r1]; khint_t k; k = kh_get(m_s2u64, names, bam_name(b)); if (k == kh_end(names)) goto fail; if (kh_val(names, k) == -1) cr->cram_flags = CRAM_FLAG_DISCARD_NAME; } ret = 0; fail: // ret==-1 if (names) kh_destroy(m_s2u64, names); return ret; } /* * Adds the reading names. We do this here as a separate pass rather * than per record in the process_one_read calls as that function can * go back and change the CRAM_FLAG_DETACHED status of a previously * processed read if it subsequently determines the TLEN field is * incorrect. Given DETACHED reads always try to decode read names, * we need to know their status before generating the read-name block. * * Output is an update s->name_blk, and cr->name / cr->name_len * fields. */ static int add_read_names(cram_fd *fd, cram_container *c, cram_slice *s, int bam_start) { int r1, r2; int keep_names = !fd->lossy_read_names; for (r1 = bam_start, r2 = 0; r1 < c->curr_c_rec && r2 < s->hdr->num_records; r1++, r2++) { cram_record *cr = &s->crecs[r2]; bam_seq_t *b = c->bams[r1]; cr->name = BLOCK_SIZE(s->name_blk); if ((cr->cram_flags & CRAM_FLAG_DETACHED) || keep_names) { if (CRAM_MAJOR_VERS(fd->version) >= 4 && (cr->cram_flags & CRAM_FLAG_MATE_DOWNSTREAM) && cr->mate_line) { // Dedup read names in V4 BLOCK_APPEND(s->name_blk, "\0", 1); cr->name_len = 1; } else { BLOCK_APPEND(s->name_blk, bam_name(b), bam_name_len(b)); cr->name_len = bam_name_len(b); } } else { // Can only discard duplicate names if not detached cr->name_len = 0; } if (cram_stats_add(c->stats[DS_RN], cr->name_len) < 0) goto block_err; } return 0; block_err: return -1; } // CRAM version >= 3.1 #define CRAM_ge31(v) ((v) >= 0x301) // Returns the next cigar op code: one of the BAM_C* codes, // or -1 if no more are present. static inline int next_cigar_op(uint32_t *cigar, uint32_t ncigar, int *skip, int *spos, uint32_t *cig_ind, uint32_t *cig_op, uint32_t *cig_len) { for(;;) { while (*cig_len == 0) { if (*cig_ind < ncigar) { *cig_op = cigar[*cig_ind] & BAM_CIGAR_MASK; *cig_len = cigar[*cig_ind] >> BAM_CIGAR_SHIFT; (*cig_ind)++; } else { return -1; } } if (skip[*cig_op]) { *spos += (bam_cigar_type(*cig_op)&1) * *cig_len; *cig_len = 0; continue; } (*cig_len)--; break; } return *cig_op; } // Ensure ref and hist are large enough. static inline int extend_ref(char **ref, uint32_t (**hist)[5], hts_pos_t pos, hts_pos_t ref_start, hts_pos_t *ref_end) { if (pos < ref_start) return -1; if (pos < *ref_end) return 0; // realloc if (pos - ref_start > UINT_MAX) return -2; // protect overflow in new_end calculation hts_pos_t old_end = *ref_end ? *ref_end : ref_start; hts_pos_t new_end = ref_start + 1000 + (pos-ref_start)*1.5; // Refuse to work on excessively large blocks. // We'll just switch to referenceless encoding, which is probably better // here as this must be very sparse data anyway. if (new_end - ref_start > UINT_MAX/sizeof(**hist)/2) return -2; char *tmp = realloc(*ref, new_end-ref_start+1); if (!tmp) return -1; *ref = tmp; uint32_t (*tmp5)[5] = realloc(**hist, (new_end - ref_start)*sizeof(**hist)); if (!tmp5) return -1; *hist = tmp5; *ref_end = new_end; // initialise old_end -= ref_start; new_end -= ref_start; memset(&(*ref)[old_end], 0, new_end-old_end); memset(&(*hist)[old_end], 0, (new_end-old_end)*sizeof(**hist)); return 0; } // Walk through MD + seq to generate ref // Returns 1 on success, <0 on failure static int cram_add_to_ref_MD(bam1_t *b, char **ref, uint32_t (**hist)[5], hts_pos_t ref_start, hts_pos_t *ref_end, const uint8_t *MD) { uint8_t *seq = bam_get_seq(b); uint32_t *cigar = bam_get_cigar(b); uint32_t ncigar = b->core.n_cigar; uint32_t cig_op = 0, cig_len = 0, cig_ind = 0; int iseq = 0, next_op; hts_pos_t iref = b->core.pos - ref_start; // Skip INS, REF_SKIP, *CLIP, PAD. and BACK. static int cig_skip[16] = {0,1,0,1,1,1,1,0,0,1,1,1,1,1,1,1}; while (iseq < b->core.l_qseq && *MD) { if (isdigit(*MD)) { // match int overflow = 0; int len = hts_str2uint((char *)MD, (char **)&MD, 31, &overflow); if (overflow || extend_ref(ref, hist, iref+ref_start + len, ref_start, ref_end) < 0) return -1; while (iseq < b->core.l_qseq && len) { // rewrite to have internal loops? if ((next_op = next_cigar_op(cigar, ncigar, cig_skip, &iseq, &cig_ind, &cig_op, &cig_len)) < 0) return -1; if (next_op != BAM_CMATCH && next_op != BAM_CEQUAL) { hts_log_info("MD:Z and CIGAR are incompatible for " "record %s", bam_get_qname(b)); return -1; } // Short-cut loop over same cigar op for efficiency cig_len++; do { cig_len--; (*ref)[iref++] = seq_nt16_str[bam_seqi(seq, iseq)]; iseq++; len--; } while (cig_len && iseq < b->core.l_qseq && len); } if (len > 0) return -1; // MD is longer than seq } else if (*MD == '^') { // deletion MD++; while (isalpha(*MD)) { if (extend_ref(ref, hist, iref+ref_start, ref_start, ref_end) < 0) return -1; if ((next_op = next_cigar_op(cigar, ncigar, cig_skip, &iseq, &cig_ind, &cig_op, &cig_len)) < 0) return -1; if (next_op != BAM_CDEL) { hts_log_info("MD:Z and CIGAR are incompatible"); return -1; } (*ref)[iref++] = *MD++ & ~0x20; } } else { // substitution if (extend_ref(ref, hist, iref+ref_start, ref_start, ref_end) < 0) return -1; if ((next_op = next_cigar_op(cigar, ncigar, cig_skip, &iseq, &cig_ind, &cig_op, &cig_len)) < 0) return -1; if (next_op != BAM_CMATCH && next_op != BAM_CDIFF) { hts_log_info("MD:Z and CIGAR are incompatible"); return -1; } (*ref)[iref++] = *MD++ & ~0x20; iseq++; } } return 1; } // Append a sequence to a ref/consensus structure. // We maintain both an absolute refefence (ACGTN where MD:Z is // present) and a 5-way frequency array for when no MD:Z is known. // We then subsequently convert the 5-way frequencies to a consensus // ref in a second pass. // // Returns >=0 on success, // -1 on failure (eg inconsistent data) static int cram_add_to_ref(bam1_t *b, char **ref, uint32_t (**hist)[5], hts_pos_t ref_start, hts_pos_t *ref_end) { const uint8_t *MD = bam_aux_get(b, "MD"); int ret = 0; if (MD && *MD == 'Z') { // We can use MD to directly compute the reference int ret = cram_add_to_ref_MD(b, ref, hist, ref_start, ref_end, MD+1); if (ret > 0) return ret; } // Otherwise we just use SEQ+CIGAR and build a consensus which we later // turn into a fake reference uint32_t *cigar = bam_get_cigar(b); uint32_t ncigar = b->core.n_cigar; uint32_t i, j; hts_pos_t iseq = 0, iref = b->core.pos - ref_start; uint8_t *seq = bam_get_seq(b); for (i = 0; i < ncigar; i++) { switch (bam_cigar_op(cigar[i])) { case BAM_CSOFT_CLIP: case BAM_CINS: iseq += bam_cigar_oplen(cigar[i]); break; case BAM_CMATCH: case BAM_CEQUAL: case BAM_CDIFF: { int len = bam_cigar_oplen(cigar[i]); // Maps an nt16 (A=1 C=2 G=4 T=8 bits) to 0123 plus N=4 static uint8_t L16[16] = {4,0,1,4, 2,4,4,4, 3,4,4,4, 4,4,4,4}; if (extend_ref(ref, hist, iref+ref_start + len, ref_start, ref_end) < 0) return -1; if (iseq + len <= b->core.l_qseq) { // Nullify failed MD:Z if appropriate if (ret < 0) memset(&(*ref)[iref], 0, len); for (j = 0; j < len; j++, iref++, iseq++) (*hist)[iref][L16[bam_seqi(seq, iseq)]]++; } else { // Probably a 2ndary read with seq "*" iseq += len; iref += len; } break; } case BAM_CDEL: case BAM_CREF_SKIP: iref += bam_cigar_oplen(cigar[i]); } } return 1; } // Automatically generates the reference and stashed it in c->ref, also // setting c->ref_start and c->ref_end. // // If we have MD:Z tags then we use them to directly infer the reference, // along with SEQ + CIGAR. Otherwise we use SEQ/CIGAR only to build up // a consensus and then assume the reference as the majority rule. // // In this latter scenario we need to be wary of auto-generating MD and NM // during decode, but that's handled elsewhere via an additional aux tag. // // Returns 0 on success, // -1 on failure static int cram_generate_reference(cram_container *c, cram_slice *s, int r1) { // TODO: if we can find an external reference then use it, even if the // user told us to do embed_ref=2. char *ref = NULL; uint32_t (*hist)[5] = NULL; hts_pos_t ref_start = c->bams[r1]->core.pos, ref_end = 0; if (ref_start < 0) return -1; // cannot build consensus from unmapped data // initial allocation if (extend_ref(&ref, &hist, c->bams[r1 + s->hdr->num_records-1]->core.pos + c->bams[r1 + s->hdr->num_records-1]->core.l_qseq, ref_start, &ref_end) < 0) return -1; // Add each bam file to the reference/consensus arrays int r2; hts_pos_t last_pos = -1; for (r2 = 0; r1 < c->curr_c_rec && r2 < s->hdr->num_records; r1++, r2++) { if (c->bams[r1]->core.pos < last_pos) { hts_log_error("Cannot build reference with unsorted data"); goto err; } last_pos = c->bams[r1]->core.pos; if (cram_add_to_ref(c->bams[r1], &ref, &hist, ref_start, &ref_end) < 0) goto err; } // Compute the consensus hts_pos_t i; for (i = 0; i < ref_end-ref_start; i++) { if (!ref[i]) { int max_v = 0, max_j = 4, j; for (j = 0; j < 4; j++) // don't call N (j==4) unless no coverage if (max_v < hist[i][j]) max_v = hist[i][j], max_j = j; ref[i] = "ACGTN"[max_j]; } } free(hist); // Put the reference in place so it appears to be an external // ref file. c->ref = ref; c->ref_start = ref_start+1; c->ref_end = ref_end+1; c->ref_free = 1; return 0; err: free(ref); free(hist); return -1; } // Check if the SQ M5 tag matches the reference we've loaded. static int validate_md5(cram_fd *fd, int ref_id) { if (fd->ignore_md5 || ref_id < 0 || ref_id >= fd->refs->nref) return 0; // Have we already checked this ref? if (fd->refs->ref_id[ref_id]->validated_md5) return 0; // Check if we have the MD5 known. // We should, but maybe we're using embedded references? sam_hrecs_t *hrecs = fd->header->hrecs; sam_hrec_type_t *ty = sam_hrecs_find_type_id(hrecs, "SQ", "SN", hrecs->ref[ref_id].name); if (!ty) return 0; sam_hrec_tag_t *m5tag = sam_hrecs_find_key(ty, "M5", NULL); if (!m5tag) return 0; // It's known, so compute md5 on the loaded reference sequence. char *ref = fd->refs->ref_id[ref_id]->seq; int64_t len = fd->refs->ref_id[ref_id]->length; hts_md5_context *md5; char unsigned buf[16]; char buf2[33]; if (!(md5 = hts_md5_init())) return -1; hts_md5_update(md5, ref, len); hts_md5_final(buf, md5); hts_md5_destroy(md5); hts_md5_hex(buf2, buf); // Compare it to header @SQ M5 tag if (strcmp(m5tag->str+3, buf2)) { hts_log_error("SQ header M5 tag discrepancy for reference '%s'", hrecs->ref[ref_id].name); hts_log_error("Please use the correct reference, or " "consider using embed_ref=2"); return -1; } fd->refs->ref_id[ref_id]->validated_md5 = 1; return 0; } /* * Encodes all slices in a container into blocks. * Returns 0 on success * -1 on failure */ int cram_encode_container(cram_fd *fd, cram_container *c) { int i, j, slice_offset; cram_block_compression_hdr *h = c->comp_hdr; cram_block *c_hdr; int multi_ref = 0; int r1, r2, sn, nref, embed_ref, no_ref; spare_bams *spares; if (!c->bams) goto err; if (CRAM_MAJOR_VERS(fd->version) == 1) goto err; //#define goto_err {fprintf(stderr, "ERR at %s:%d\n", __FILE__, __LINE__);goto err;} #define goto_err goto err // Don't try embed ref if we repeatedly fail pthread_mutex_lock(&fd->ref_lock); int failed_embed = (fd->no_ref_counter >= 5); // maximum 5 tries if (!failed_embed && c->embed_ref == -2) { hts_log_warning("Retrying embed_ref=2 mode for #%d/5", fd->no_ref_counter); fd->no_ref = c->no_ref = 0; fd->embed_ref = c->embed_ref = 2; } else if (failed_embed && c->embed_ref == -2) { // We've tried several times, so this time give up for good hts_log_warning("Keeping non-ref mode from now on"); fd->embed_ref = c->embed_ref = 0; } pthread_mutex_unlock(&fd->ref_lock); restart: /* Cache references up-front if we have unsorted access patterns */ pthread_mutex_lock(&fd->ref_lock); nref = fd->refs->nref; pthread_mutex_unlock(&fd->ref_lock); embed_ref = c->embed_ref; no_ref = c->no_ref; /* To create M5 strings */ /* Fetch reference sequence */ if (!no_ref) { if (!c->bams || !c->curr_c_rec || !c->bams[0]) goto_err; bam_seq_t *b = c->bams[0]; if (embed_ref <= 1) { char *ref = cram_get_ref(fd, bam_ref(b), 1, 0); if (!ref && bam_ref(b) >= 0) { if (!c->pos_sorted) { // TODO: maybe also check fd->no_ref? hts_log_warning("Failed to load reference #%d", bam_ref(b)); hts_log_warning("Switching to non-ref mode"); pthread_mutex_lock(&fd->ref_lock); c->embed_ref = fd->embed_ref = 0; c->no_ref = fd->no_ref = 1; pthread_mutex_unlock(&fd->ref_lock); goto restart; } if (c->multi_seq || embed_ref == 0) { hts_log_error("Failed to load reference #%d", bam_ref(b)); return -1; } hts_log_warning("Failed to load reference #%d", bam_ref(b)); hts_log_warning("Enabling embed_ref=2 mode to auto-generate" " reference"); if (embed_ref <= 0) hts_log_warning("NOTE: the CRAM file will be bigger than" " using an external reference"); pthread_mutex_lock(&fd->ref_lock); embed_ref = c->embed_ref = fd->embed_ref = 2; pthread_mutex_unlock(&fd->ref_lock); goto auto_ref; } else if (ref) { if (validate_md5(fd, c->ref_seq_id) < 0) goto_err; } if ((c->ref_id = bam_ref(b)) >= 0) { c->ref_seq_id = c->ref_id; c->ref = fd->refs->ref_id[c->ref_seq_id]->seq; c->ref_start = 1; c->ref_end = fd->refs->ref_id[c->ref_seq_id]->length; } } else { auto_ref: // Auto-embed ref. // This starts as 'N' and is amended on-the-fly as we go // based on MD:Z tags. if ((c->ref_id = bam_ref(b)) >= 0) { c->ref = NULL; // c->ref_free is boolean; whether to free c->ref. In this // case c->ref will be our auto-embedded sequence instead of // a "global" portion of reference from fd->refs. // Do not confuse with fd->ref_free which is a pointer to a // reference string to free. c->ref_free = 1; } } c->ref_seq_id = c->ref_id; } else { c->ref_id = bam_ref(c->bams[0]); cram_ref_incr(fd->refs, c->ref_id); c->ref_seq_id = c->ref_id; } if (!no_ref && c->refs_used) { for (i = 0; i < nref; i++) { if (c->refs_used[i]) { if (cram_get_ref(fd, i, 1, 0)) { if (validate_md5(fd, i) < 0) goto_err; } else { hts_log_warning("Failed to find reference, " "switching to non-ref mode"); no_ref = c->no_ref = 1; } } } } /* Turn bams into cram_records and gather basic stats */ for (r1 = sn = 0; r1 < c->curr_c_rec; sn++) { cram_slice *s = c->slices[sn]; int64_t first_base = INT64_MAX, last_base = INT64_MIN; int r1_start = r1; assert(sn < c->curr_slice); // Discover which read names *may* be safely removed. // Ie which ones have all their records in this slice. if (lossy_read_names(fd, c, s, r1_start) != 0) return -1; // Tracking of MD tags so we can spot when the auto-generated values // will differ from the current stored ones. The kstring here is // simply to avoid excessive malloc and free calls. All initialisation // is done within process_one_read(). kstring_t MD = {0}; // Embed consensus / MD-generated ref if (embed_ref == 2) { if (cram_generate_reference(c, s, r1) < 0) { // Should this be a permanent thing via fd->no_ref? // Doing so means we cannot easily switch back again should // things fix themselves later on. This is likely not a // concern though as failure to generate a reference implies // unsorted data which is rarely recovered from. // Only if sn == 0. We're hosed if we're on the 2nd slice and // the first worked, as no-ref is a container global param. if (sn > 0) { hts_log_error("Failed to build reference, " "switching to non-ref mode"); return -1; } else { hts_log_warning("Failed to build reference, " "switching to non-ref mode"); } pthread_mutex_lock(&fd->ref_lock); c->embed_ref = fd->embed_ref = -2; // was previously embed_ref c->no_ref = fd->no_ref = 1; fd->no_ref_counter++; // more likely to keep permanent action pthread_mutex_unlock(&fd->ref_lock); failed_embed = 1; goto restart; } else { pthread_mutex_lock(&fd->ref_lock); fd->no_ref_counter -= (fd->no_ref_counter > 0); pthread_mutex_unlock(&fd->ref_lock); } } // Iterate through records creating the cram blocks for some // fields and just gathering stats for others. for (r2 = 0; r1 < c->curr_c_rec && r2 < s->hdr->num_records; r1++, r2++) { cram_record *cr = &s->crecs[r2]; bam_seq_t *b = c->bams[r1]; /* If multi-ref we need to cope with changing reference per seq */ if (c->multi_seq && !no_ref) { if (bam_ref(b) != c->ref_seq_id && bam_ref(b) >= 0) { if (c->ref_seq_id >= 0) cram_ref_decr(fd->refs, c->ref_seq_id); if (!cram_get_ref(fd, bam_ref(b), 1, 0)) { hts_log_error("Failed to load reference #%d", bam_ref(b)); free(MD.s); return -1; } if (validate_md5(fd, bam_ref(b)) < 0) return -1; c->ref_seq_id = bam_ref(b); // overwritten later by -2 if (!fd->refs->ref_id[c->ref_seq_id]->seq) return -1; c->ref = fd->refs->ref_id[c->ref_seq_id]->seq; c->ref_start = 1; c->ref_end = fd->refs->ref_id[c->ref_seq_id]->length; } } if (process_one_read(fd, c, s, cr, b, r2, &MD, embed_ref, no_ref) != 0) { free(MD.s); return -1; } if (first_base > cr->apos) first_base = cr->apos; if (last_base < cr->aend) last_base = cr->aend; } free(MD.s); // Process_one_read doesn't add read names as it can change // its mind during the loop on the CRAM_FLAG_DETACHED setting // of earlier records (if it detects the auto-generation of // TLEN is incorrect). This affects which read-names can be // lossily compressed, so we do these in another pass. if (add_read_names(fd, c, s, r1_start) < 0) return -1; if (c->multi_seq) { s->hdr->ref_seq_id = -2; s->hdr->ref_seq_start = 0; s->hdr->ref_seq_span = 0; } else if (c->ref_id == -1 && CRAM_ge31(fd->version)) { // Spec states span=0, but it broke our range queries. // See commit message for this and prior. s->hdr->ref_seq_id = -1; s->hdr->ref_seq_start = 0; s->hdr->ref_seq_span = 0; } else { s->hdr->ref_seq_id = c->ref_id; s->hdr->ref_seq_start = first_base; s->hdr->ref_seq_span = MAX(0, last_base - first_base + 1); } s->hdr->num_records = r2; // Processed a slice, now stash the aux blocks so the next // slice can start aggregating them from the start again. if (c->tags_used->n_occupied) { int ntags = c->tags_used->n_occupied; s->aux_block = calloc(ntags*2, sizeof(*s->aux_block)); if (!s->aux_block) return -1; khint_t k; s->naux_block = 0; for (k = kh_begin(c->tags_used); k != kh_end(c->tags_used); k++) { if (!kh_exist(c->tags_used, k)) continue; cram_tag_map *tm = kh_val(c->tags_used, k); if (!tm) goto_err; if (!tm->blk) continue; s->aux_block[s->naux_block++] = tm->blk; tm->blk = NULL; if (!tm->blk2) continue; s->aux_block[s->naux_block++] = tm->blk2; tm->blk2 = NULL; } assert(s->naux_block <= 2*c->tags_used->n_occupied); } } if (c->multi_seq && !no_ref) { if (c->ref_seq_id >= 0) cram_ref_decr(fd->refs, c->ref_seq_id); } /* Link our bams[] array onto the spare bam list for reuse */ spares = malloc(sizeof(*spares)); if (!spares) goto_err; pthread_mutex_lock(&fd->bam_list_lock); spares->bams = c->bams; spares->next = fd->bl; fd->bl = spares; pthread_mutex_unlock(&fd->bam_list_lock); c->bams = NULL; /* Detect if a multi-seq container */ cram_stats_encoding(fd, c->stats[DS_RI]); multi_ref = c->stats[DS_RI]->nvals > 1; pthread_mutex_lock(&fd->metrics_lock); fd->last_RI_count = c->stats[DS_RI]->nvals; pthread_mutex_unlock(&fd->metrics_lock); if (multi_ref) { hts_log_info("Multi-ref container"); c->ref_seq_id = -2; c->ref_seq_start = 0; c->ref_seq_span = 0; } /* Compute MD5s */ no_ref = c->no_ref; int is_v4 = CRAM_MAJOR_VERS(fd->version) >= 4 ? 1 : 0; for (i = 0; i < c->curr_slice; i++) { cram_slice *s = c->slices[i]; if (CRAM_MAJOR_VERS(fd->version) != 1) { if (s->hdr->ref_seq_id >= 0 && c->multi_seq == 0 && !no_ref) { hts_md5_context *md5 = hts_md5_init(); if (!md5) return -1; hts_md5_update(md5, c->ref + s->hdr->ref_seq_start - c->ref_start, s->hdr->ref_seq_span); hts_md5_final(s->hdr->md5, md5); hts_md5_destroy(md5); } else { memset(s->hdr->md5, 0, 16); } } } c->num_records = 0; c->num_blocks = 1; // cram_block_compression_hdr c->length = 0; //fprintf(stderr, "=== BF ===\n"); h->codecs[DS_BF] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_BF]), c->stats[DS_BF], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_BF]->nvals && !h->codecs[DS_BF]) goto_err; //fprintf(stderr, "=== CF ===\n"); h->codecs[DS_CF] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_CF]), c->stats[DS_CF], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_CF]->nvals && !h->codecs[DS_CF]) goto_err; //fprintf(stderr, "=== RN ===\n"); //h->codecs[DS_RN] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_RN]), // c->stats[DS_RN], E_BYTE_ARRAY, NULL, // fd->version); //fprintf(stderr, "=== AP ===\n"); if (c->pos_sorted || CRAM_MAJOR_VERS(fd->version) >= 4) { if (c->pos_sorted) h->codecs[DS_AP] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_AP]), c->stats[DS_AP], is_v4 ? E_LONG : E_INT, NULL, fd->version, &fd->vv); else // Unsorted data has no stats, but hard-code VARINT_SIGNED / EXT. h->codecs[DS_AP] = cram_encoder_init(is_v4 ? E_VARINT_SIGNED : E_EXTERNAL, NULL, is_v4 ? E_LONG : E_INT, NULL, fd->version, &fd->vv); } else { // Removed BETA in v4.0. // Should we consider dropping use of it for 3.0 too? hts_pos_t p[2] = {0, c->max_apos}; h->codecs[DS_AP] = cram_encoder_init(E_BETA, NULL, is_v4 ? E_LONG : E_INT, p, fd->version, &fd->vv); // cram_xdelta_encoder e; // e.word_size = is_v4 ? 8 : 4; // e.sub_encoding = E_EXTERNAL; // e.sub_codec_dat = (void *)DS_AP; // // h->codecs[DS_AP] = cram_encoder_init(E_XDELTA, NULL, // is_v4 ? E_LONG : E_INT, // &e, fd->version, &fd->vv); } if (!h->codecs[DS_AP]) goto_err; //fprintf(stderr, "=== RG ===\n"); h->codecs[DS_RG] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_RG]), c->stats[DS_RG], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_RG]->nvals && !h->codecs[DS_RG]) goto_err; //fprintf(stderr, "=== MQ ===\n"); h->codecs[DS_MQ] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_MQ]), c->stats[DS_MQ], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_MQ]->nvals && !h->codecs[DS_MQ]) goto_err; //fprintf(stderr, "=== NS ===\n"); h->codecs[DS_NS] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_NS]), c->stats[DS_NS], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_NS]->nvals && !h->codecs[DS_NS]) goto_err; //fprintf(stderr, "=== MF ===\n"); h->codecs[DS_MF] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_MF]), c->stats[DS_MF], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_MF]->nvals && !h->codecs[DS_MF]) goto_err; //fprintf(stderr, "=== TS ===\n"); h->codecs[DS_TS] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_TS]), c->stats[DS_TS], is_v4 ? E_LONG : E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_TS]->nvals && !h->codecs[DS_TS]) goto_err; //fprintf(stderr, "=== NP ===\n"); h->codecs[DS_NP] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_NP]), c->stats[DS_NP], is_v4 ? E_LONG : E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_NP]->nvals && !h->codecs[DS_NP]) goto_err; //fprintf(stderr, "=== NF ===\n"); h->codecs[DS_NF] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_NF]), c->stats[DS_NF], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_NF]->nvals && !h->codecs[DS_NF]) goto_err; //fprintf(stderr, "=== RL ===\n"); h->codecs[DS_RL] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_RL]), c->stats[DS_RL], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_RL]->nvals && !h->codecs[DS_RL]) goto_err; //fprintf(stderr, "=== FN ===\n"); h->codecs[DS_FN] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_FN]), c->stats[DS_FN], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_FN]->nvals && !h->codecs[DS_FN]) goto_err; //fprintf(stderr, "=== FC ===\n"); h->codecs[DS_FC] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_FC]), c->stats[DS_FC], E_BYTE, NULL, fd->version, &fd->vv); if (c->stats[DS_FC]->nvals && !h->codecs[DS_FC]) goto_err; //fprintf(stderr, "=== FP ===\n"); h->codecs[DS_FP] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_FP]), c->stats[DS_FP], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_FP]->nvals && !h->codecs[DS_FP]) goto_err; //fprintf(stderr, "=== DL ===\n"); h->codecs[DS_DL] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_DL]), c->stats[DS_DL], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_DL]->nvals && !h->codecs[DS_DL]) goto_err; //fprintf(stderr, "=== BA ===\n"); h->codecs[DS_BA] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_BA]), c->stats[DS_BA], E_BYTE, NULL, fd->version, &fd->vv); if (c->stats[DS_BA]->nvals && !h->codecs[DS_BA]) goto_err; if (CRAM_MAJOR_VERS(fd->version) >= 3) { cram_byte_array_len_encoder e; e.len_encoding = CRAM_MAJOR_VERS(fd->version) >= 4 ? E_VARINT_UNSIGNED : E_EXTERNAL; e.len_dat = (void *)DS_BB_len; //e.len_dat = (void *)DS_BB; e.val_encoding = E_EXTERNAL; e.val_dat = (void *)DS_BB; h->codecs[DS_BB] = cram_encoder_init(E_BYTE_ARRAY_LEN, NULL, E_BYTE_ARRAY, (void *)&e, fd->version, &fd->vv); if (!h->codecs[DS_BB]) goto_err; } else { h->codecs[DS_BB] = NULL; } //fprintf(stderr, "=== BS ===\n"); h->codecs[DS_BS] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_BS]), c->stats[DS_BS], E_BYTE, NULL, fd->version, &fd->vv); if (c->stats[DS_BS]->nvals && !h->codecs[DS_BS]) goto_err; if (CRAM_MAJOR_VERS(fd->version) == 1) { h->codecs[DS_TL] = NULL; h->codecs[DS_RI] = NULL; h->codecs[DS_RS] = NULL; h->codecs[DS_PD] = NULL; h->codecs[DS_HC] = NULL; h->codecs[DS_SC] = NULL; //fprintf(stderr, "=== TC ===\n"); h->codecs[DS_TC] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_TC]), c->stats[DS_TC], E_BYTE, NULL, fd->version, &fd->vv); if (c->stats[DS_TC]->nvals && !h->codecs[DS_TC]) goto_err; //fprintf(stderr, "=== TN ===\n"); h->codecs[DS_TN] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_TN]), c->stats[DS_TN], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_TN]->nvals && !h->codecs[DS_TN]) goto_err; } else { h->codecs[DS_TC] = NULL; h->codecs[DS_TN] = NULL; //fprintf(stderr, "=== TL ===\n"); h->codecs[DS_TL] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_TL]), c->stats[DS_TL], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_TL]->nvals && !h->codecs[DS_TL]) goto_err; //fprintf(stderr, "=== RI ===\n"); h->codecs[DS_RI] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_RI]), c->stats[DS_RI], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_RI]->nvals && !h->codecs[DS_RI]) goto_err; //fprintf(stderr, "=== RS ===\n"); h->codecs[DS_RS] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_RS]), c->stats[DS_RS], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_RS]->nvals && !h->codecs[DS_RS]) goto_err; //fprintf(stderr, "=== PD ===\n"); h->codecs[DS_PD] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_PD]), c->stats[DS_PD], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_PD]->nvals && !h->codecs[DS_PD]) goto_err; //fprintf(stderr, "=== HC ===\n"); h->codecs[DS_HC] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_HC]), c->stats[DS_HC], E_INT, NULL, fd->version, &fd->vv); if (c->stats[DS_HC]->nvals && !h->codecs[DS_HC]) goto_err; //fprintf(stderr, "=== SC ===\n"); if (1) { int i2[2] = {0, DS_SC}; h->codecs[DS_SC] = cram_encoder_init(E_BYTE_ARRAY_STOP, NULL, E_BYTE_ARRAY, (void *)i2, fd->version, &fd->vv); } else { // Appears to be no practical benefit to using this method, // but it may work better if we start mixing SC, IN and BB // elements into the same external block. cram_byte_array_len_encoder e; e.len_encoding = CRAM_MAJOR_VERS(fd->version) >= 4 ? E_VARINT_UNSIGNED : E_EXTERNAL; e.len_dat = (void *)DS_SC_len; e.val_encoding = E_EXTERNAL; e.val_dat = (void *)DS_SC; h->codecs[DS_SC] = cram_encoder_init(E_BYTE_ARRAY_LEN, NULL, E_BYTE_ARRAY, (void *)&e, fd->version, &fd->vv); } if (!h->codecs[DS_SC]) goto_err; } //fprintf(stderr, "=== IN ===\n"); { int i2[2] = {0, DS_IN}; h->codecs[DS_IN] = cram_encoder_init(E_BYTE_ARRAY_STOP, NULL, E_BYTE_ARRAY, (void *)i2, fd->version, &fd->vv); if (!h->codecs[DS_IN]) goto_err; } h->codecs[DS_QS] = cram_encoder_init(E_EXTERNAL, NULL, E_BYTE, (void *)DS_QS, fd->version, &fd->vv); if (!h->codecs[DS_QS]) goto_err; { int i2[2] = {0, DS_RN}; h->codecs[DS_RN] = cram_encoder_init(E_BYTE_ARRAY_STOP, NULL, E_BYTE_ARRAY, (void *)i2, fd->version, &fd->vv); if (!h->codecs[DS_RN]) goto_err; } /* Encode slices */ for (i = 0; i < c->curr_slice; i++) { hts_log_info("Encode slice %d", i); int local_embed_ref = embed_ref>0 && c->slices[i]->hdr->ref_seq_id != -1 ? 1 : 0; if (cram_encode_slice(fd, c, h, c->slices[i], local_embed_ref) != 0) return -1; } /* Create compression header */ { h->ref_seq_id = c->ref_seq_id; h->ref_seq_start = c->ref_seq_start; h->ref_seq_span = c->ref_seq_span; h->num_records = c->num_records; h->qs_seq_orient = c->qs_seq_orient; // slight misnomer - sorted or treat as-if sorted (ap_delta force to 1) h->AP_delta = c->pos_sorted; memcpy(h->substitution_matrix, CRAM_SUBST_MATRIX, 20); if (!(c_hdr = cram_encode_compression_header(fd, c, h, embed_ref))) return -1; } /* Compute landmarks */ /* Fill out slice landmarks */ c->num_landmarks = c->curr_slice; c->landmark = malloc(c->num_landmarks * sizeof(*c->landmark)); if (!c->landmark) return -1; /* * Slice offset starts after the first block, so we need to simulate * writing it to work out the correct offset */ { slice_offset = c_hdr->method == RAW ? c_hdr->uncomp_size : c_hdr->comp_size; slice_offset += 2 + 4*(CRAM_MAJOR_VERS(fd->version) >= 3) + fd->vv.varint_size(c_hdr->content_id) + fd->vv.varint_size(c_hdr->comp_size) + fd->vv.varint_size(c_hdr->uncomp_size); } c->ref_seq_id = c->slices[0]->hdr->ref_seq_id; if (c->ref_seq_id == -1 && CRAM_ge31(fd->version)) { // Spec states span=0, but it broke our range queries. // See commit message for this and prior. c->ref_seq_start = 0; c->ref_seq_span = 0; } else { c->ref_seq_start = c->slices[0]->hdr->ref_seq_start; c->ref_seq_span = c->slices[0]->hdr->ref_seq_span; } for (i = 0; i < c->curr_slice; i++) { cram_slice *s = c->slices[i]; c->num_blocks += s->hdr->num_blocks + 1; // slice header c->landmark[i] = slice_offset; if (s->hdr->ref_seq_start + s->hdr->ref_seq_span > c->ref_seq_start + c->ref_seq_span) { c->ref_seq_span = s->hdr->ref_seq_start + s->hdr->ref_seq_span - c->ref_seq_start; } slice_offset += s->hdr_block->method == RAW ? s->hdr_block->uncomp_size : s->hdr_block->comp_size; slice_offset += 2 + 4*(CRAM_MAJOR_VERS(fd->version) >= 3) + fd->vv.varint_size(s->hdr_block->content_id) + fd->vv.varint_size(s->hdr_block->comp_size) + fd->vv.varint_size(s->hdr_block->uncomp_size); for (j = 0; j < s->hdr->num_blocks; j++) { slice_offset += 2 + 4*(CRAM_MAJOR_VERS(fd->version) >= 3) + fd->vv.varint_size(s->block[j]->content_id) + fd->vv.varint_size(s->block[j]->comp_size) + fd->vv.varint_size(s->block[j]->uncomp_size); slice_offset += s->block[j]->method == RAW ? s->block[j]->uncomp_size : s->block[j]->comp_size; } } c->length += slice_offset; // just past the final slice c->comp_hdr_block = c_hdr; if (c->ref_seq_id >= 0) { if (c->ref_free) { free(c->ref); c->ref = NULL; } else { cram_ref_decr(fd->refs, c->ref_seq_id); } } /* Cache references up-front if we have unsorted access patterns */ if (!no_ref && c->refs_used) { for (i = 0; i < fd->refs->nref; i++) { if (c->refs_used[i]) cram_ref_decr(fd->refs, i); } } return 0; err: return -1; } /* * Adds a feature code to a read within a slice. For purposes of minimising * memory allocations and fragmentation we have one array of features for all * reads within the slice. We return the index into this array for this new * feature. * * Returns feature index on success * -1 on failure. */ static int cram_add_feature(cram_container *c, cram_slice *s, cram_record *r, cram_feature *f) { if (s->nfeatures >= s->afeatures) { s->afeatures = s->afeatures ? s->afeatures*2 : 1024; s->features = realloc(s->features, s->afeatures*sizeof(*s->features)); if (!s->features) return -1; } if (!r->nfeature++) { r->feature = s->nfeatures; if (cram_stats_add(c->stats[DS_FP], f->X.pos) < 0) return -1; } else { if (cram_stats_add(c->stats[DS_FP], f->X.pos - s->features[r->feature + r->nfeature-2].X.pos) < 0) return -1; } if (cram_stats_add(c->stats[DS_FC], f->X.code) < 0) return -1; s->features[s->nfeatures++] = *f; return 0; } static int cram_add_substitution(cram_fd *fd, cram_container *c, cram_slice *s, cram_record *r, int pos, char base, char qual, char ref) { cram_feature f; // seq=ACGTN vs ref=ACGT or seq=ACGT vs ref=ACGTN if (fd->L2[(uc)base]<4 || (fd->L2[(uc)base]<5 && fd->L2[(uc)ref]<4)) { f.X.pos = pos+1; f.X.code = 'X'; f.X.base = fd->cram_sub_matrix[ref&0x1f][base&0x1f]; if (cram_stats_add(c->stats[DS_BS], f.X.base) < 0) return -1; } else { f.B.pos = pos+1; f.B.code = 'B'; f.B.base = base; f.B.qual = qual; if (cram_stats_add(c->stats[DS_BA], f.B.base) < 0) return -1; if (cram_stats_add(c->stats[DS_QS], f.B.qual) < 0) return -1; BLOCK_APPEND_CHAR(s->qual_blk, qual); } return cram_add_feature(c, s, r, &f); block_err: return -1; } static int cram_add_bases(cram_fd *fd, cram_container *c, cram_slice *s, cram_record *r, int pos, int len, char *base) { cram_feature f; f.b.pos = pos+1; f.b.code = 'b'; f.b.seq_idx = base - (char *)BLOCK_DATA(s->seqs_blk); f.b.len = len; return cram_add_feature(c, s, r, &f); } static int cram_add_base(cram_fd *fd, cram_container *c, cram_slice *s, cram_record *r, int pos, char base, char qual) { cram_feature f; f.B.pos = pos+1; f.B.code = 'B'; f.B.base = base; f.B.qual = qual; if (cram_stats_add(c->stats[DS_BA], base) < 0) return -1; if (cram_stats_add(c->stats[DS_QS], qual) < 0) return -1; BLOCK_APPEND_CHAR(s->qual_blk, qual); return cram_add_feature(c, s, r, &f); block_err: return -1; } static int cram_add_quality(cram_fd *fd, cram_container *c, cram_slice *s, cram_record *r, int pos, char qual) { cram_feature f; f.Q.pos = pos+1; f.Q.code = 'Q'; f.Q.qual = qual; if (cram_stats_add(c->stats[DS_QS], qual) < 0) return -1; BLOCK_APPEND_CHAR(s->qual_blk, qual); return cram_add_feature(c, s, r, &f); block_err: return -1; } static int cram_add_deletion(cram_container *c, cram_slice *s, cram_record *r, int pos, int len, char *base) { cram_feature f; f.D.pos = pos+1; f.D.code = 'D'; f.D.len = len; if (cram_stats_add(c->stats[DS_DL], len) < 0) return -1; return cram_add_feature(c, s, r, &f); } static int cram_add_softclip(cram_container *c, cram_slice *s, cram_record *r, int pos, int len, char *base, int version) { cram_feature f; f.S.pos = pos+1; f.S.code = 'S'; f.S.len = len; switch (CRAM_MAJOR_VERS(version)) { case 1: f.S.seq_idx = BLOCK_SIZE(s->base_blk); BLOCK_APPEND(s->base_blk, base, len); BLOCK_APPEND_CHAR(s->base_blk, '\0'); break; case 2: default: f.S.seq_idx = BLOCK_SIZE(s->soft_blk); if (base) { BLOCK_APPEND(s->soft_blk, base, len); } else { int i; for (i = 0; i < len; i++) BLOCK_APPEND_CHAR(s->soft_blk, 'N'); } BLOCK_APPEND_CHAR(s->soft_blk, '\0'); break; //default: // // v3.0 onwards uses BB data-series // f.S.seq_idx = BLOCK_SIZE(s->soft_blk); } return cram_add_feature(c, s, r, &f); block_err: return -1; } static int cram_add_hardclip(cram_container *c, cram_slice *s, cram_record *r, int pos, int len, char *base) { cram_feature f; f.S.pos = pos+1; f.S.code = 'H'; f.S.len = len; if (cram_stats_add(c->stats[DS_HC], len) < 0) return -1; return cram_add_feature(c, s, r, &f); } static int cram_add_skip(cram_container *c, cram_slice *s, cram_record *r, int pos, int len, char *base) { cram_feature f; f.S.pos = pos+1; f.S.code = 'N'; f.S.len = len; if (cram_stats_add(c->stats[DS_RS], len) < 0) return -1; return cram_add_feature(c, s, r, &f); } static int cram_add_pad(cram_container *c, cram_slice *s, cram_record *r, int pos, int len, char *base) { cram_feature f; f.S.pos = pos+1; f.S.code = 'P'; f.S.len = len; if (cram_stats_add(c->stats[DS_PD], len) < 0) return -1; return cram_add_feature(c, s, r, &f); } static int cram_add_insertion(cram_container *c, cram_slice *s, cram_record *r, int pos, int len, char *base) { cram_feature f; f.I.pos = pos+1; if (len == 1) { char b = base ? *base : 'N'; f.i.code = 'i'; f.i.base = b; if (cram_stats_add(c->stats[DS_BA], b) < 0) return -1; } else { f.I.code = 'I'; f.I.len = len; f.S.seq_idx = BLOCK_SIZE(s->base_blk); if (base) { BLOCK_APPEND(s->base_blk, base, len); } else { int i; for (i = 0; i < len; i++) BLOCK_APPEND_CHAR(s->base_blk, 'N'); } BLOCK_APPEND_CHAR(s->base_blk, '\0'); } return cram_add_feature(c, s, r, &f); block_err: return -1; } /* * Encodes auxiliary data. Largely duplicated from above, but done so to * keep it simple and avoid a myriad of version ifs. * * Returns the RG header line pointed to by the BAM aux fields on success, * NULL on failure or no rg present, also sets "*err" to non-zero */ static sam_hrec_rg_t *cram_encode_aux(cram_fd *fd, bam_seq_t *b, cram_container *c, cram_slice *s, cram_record *cr, int verbatim_NM, int verbatim_MD, int NM, kstring_t *MD, int cf_tag, int no_ref, int *err) { char *aux, *orig; sam_hrec_rg_t *brg = NULL; int aux_size = bam_get_l_aux(b); const char *aux_end = bam_data_end(b); cram_block *td_b = c->comp_hdr->TD_blk; int TD_blk_size = BLOCK_SIZE(td_b), new; char *key; khint_t k; if (err) *err = 1; orig = aux = (char *)bam_aux(b); // cF:i => Extra CRAM bit flags. // 1: Don't auto-decode MD (may be invalid) // 2: Don't auto-decode NM (may be invalid) if (cf_tag && CRAM_MAJOR_VERS(fd->version) < 4) { // Temporary copy of aux so we can ammend it. aux = malloc(aux_size+4); if (!aux) return NULL; memcpy(aux, orig, aux_size); aux[aux_size++] = 'c'; aux[aux_size++] = 'F'; aux[aux_size++] = 'C'; aux[aux_size++] = cf_tag; orig = aux; aux_end = aux + aux_size; } // Copy aux keys to td_b and aux values to slice aux blocks while (aux_end - aux >= 1 && aux[0] != 0) { int r; // Room for code + type + at least 1 byte of data if (aux - orig >= aux_size - 3) goto err; // RG:Z if (aux[0] == 'R' && aux[1] == 'G' && aux[2] == 'Z') { char *rg = &aux[3]; aux = rg; while (aux < aux_end && *aux++); if (aux == aux_end && aux[-1] != '\0') { hts_log_error("Unterminated RG:Z tag for read \"%s\"", bam_get_qname(b)); goto err; } brg = sam_hrecs_find_rg(fd->header->hrecs, rg); if (brg) { if (CRAM_MAJOR_VERS(fd->version) >= 4) BLOCK_APPEND(td_b, "RG*", 3); continue; } else { // RG:Z tag will be stored verbatim hts_log_warning("Missing @RG header for RG \"%s\"", rg); aux = rg - 3; } } // MD:Z if (aux[0] == 'M' && aux[1] == 'D' && aux[2] == 'Z') { if (cr->len && !no_ref && !(cr->flags & BAM_FUNMAP) && !verbatim_MD) { if (MD && MD->s && strncasecmp(MD->s, aux+3, orig + aux_size - (aux+3)) == 0) { while (aux < aux_end && *aux++); if (aux == aux_end && aux[-1] != '\0') { hts_log_error("Unterminated MD:Z tag for read \"%s\"", bam_get_qname(b)); goto err; } if (CRAM_MAJOR_VERS(fd->version) >= 4) BLOCK_APPEND(td_b, "MD*", 3); continue; } } } // NM:i if (aux[0] == 'N' && aux[1] == 'M') { if (cr->len && !no_ref && !(cr->flags & BAM_FUNMAP) && !verbatim_NM) { int NM_ = bam_aux2i_end((uint8_t *)aux+2, (uint8_t *)aux_end); if (NM_ == NM) { switch(aux[2]) { case 'A': case 'C': case 'c': aux+=4; break; case 'S': case 's': aux+=5; break; case 'I': case 'i': case 'f': aux+=7; break; default: hts_log_error("Unhandled type code for NM tag"); goto err; } if (CRAM_MAJOR_VERS(fd->version) >= 4) BLOCK_APPEND(td_b, "NM*", 3); continue; } } } BLOCK_APPEND(td_b, aux, 3); // Container level tags_used, for TD series // Maps integer key ('X0i') to cram_tag_map struct. int key = (((unsigned char *) aux)[0]<<16 | ((unsigned char *) aux)[1]<<8 | ((unsigned char *) aux)[2]); k = kh_put(m_tagmap, c->tags_used, key, &r); if (-1 == r) goto err; else if (r != 0) kh_val(c->tags_used, k) = NULL; if (r == 1) { khint_t k_global; // Global tags_used for cram_metrics support pthread_mutex_lock(&fd->metrics_lock); k_global = kh_put(m_metrics, fd->tags_used, key, &r); if (-1 == r) { pthread_mutex_unlock(&fd->metrics_lock); goto err; } if (r >= 1) { kh_val(fd->tags_used, k_global) = cram_new_metrics(); if (!kh_val(fd->tags_used, k_global)) { kh_del(m_metrics, fd->tags_used, k_global); pthread_mutex_unlock(&fd->metrics_lock); goto err; } } pthread_mutex_unlock(&fd->metrics_lock); int i2[2] = {'\t',key}; size_t sk = key; cram_tag_map *m = calloc(1, sizeof(*m)); if (!m) goto_err; kh_val(c->tags_used, k) = m; cram_codec *c; // Use a block content id based on the tag id. // Codec type depends on tag data type. switch(aux[2]) { case 'Z': case 'H': // string as byte_array_stop c = cram_encoder_init(E_BYTE_ARRAY_STOP, NULL, E_BYTE_ARRAY, (void *)i2, fd->version, &fd->vv); break; case 'A': case 'c': case 'C': { // byte array len, 1 byte cram_byte_array_len_encoder e; cram_stats st; if (CRAM_MAJOR_VERS(fd->version) <= 3) { e.len_encoding = E_HUFFMAN; e.len_dat = NULL; // will get codes from st } else { e.len_encoding = E_CONST_INT; e.len_dat = NULL; // will get codes from st } memset(&st, 0, sizeof(st)); if (cram_stats_add(&st, 1) < 0) goto block_err; cram_stats_encoding(fd, &st); e.val_encoding = E_EXTERNAL; e.val_dat = (void *)sk; c = cram_encoder_init(E_BYTE_ARRAY_LEN, &st, E_BYTE_ARRAY, (void *)&e, fd->version, &fd->vv); break; } case 's': case 'S': { // byte array len, 2 byte cram_byte_array_len_encoder e; cram_stats st; if (CRAM_MAJOR_VERS(fd->version) <= 3) { e.len_encoding = E_HUFFMAN; e.len_dat = NULL; // will get codes from st } else { e.len_encoding = E_CONST_INT; e.len_dat = NULL; // will get codes from st } memset(&st, 0, sizeof(st)); if (cram_stats_add(&st, 2) < 0) goto block_err; cram_stats_encoding(fd, &st); e.val_encoding = E_EXTERNAL; e.val_dat = (void *)sk; c = cram_encoder_init(E_BYTE_ARRAY_LEN, &st, E_BYTE_ARRAY, (void *)&e, fd->version, &fd->vv); break; } case 'i': case 'I': case 'f': { // byte array len, 4 byte cram_byte_array_len_encoder e; cram_stats st; if (CRAM_MAJOR_VERS(fd->version) <= 3) { e.len_encoding = E_HUFFMAN; e.len_dat = NULL; // will get codes from st } else { e.len_encoding = E_CONST_INT; e.len_dat = NULL; // will get codes from st } memset(&st, 0, sizeof(st)); if (cram_stats_add(&st, 4) < 0) goto block_err; cram_stats_encoding(fd, &st); e.val_encoding = E_EXTERNAL; e.val_dat = (void *)sk; c = cram_encoder_init(E_BYTE_ARRAY_LEN, &st, E_BYTE_ARRAY, (void *)&e, fd->version, &fd->vv); break; } case 'B': { // Byte array of variable size, but we generate our tag // byte stream at the wrong stage (during reading and not // after slice header construction). So we use // BYTE_ARRAY_LEN with the length codec being external // too. cram_byte_array_len_encoder e; e.len_encoding = CRAM_MAJOR_VERS(fd->version) >= 4 ? E_VARINT_UNSIGNED : E_EXTERNAL; e.len_dat = (void *)sk; // or key+128 for len? e.val_encoding = E_EXTERNAL; e.val_dat = (void *)sk; c = cram_encoder_init(E_BYTE_ARRAY_LEN, NULL, E_BYTE_ARRAY, (void *)&e, fd->version, &fd->vv); break; } default: hts_log_error("Unsupported SAM aux type '%c'", aux[2]); c = NULL; } if (!c) goto_err; m->codec = c; // Link to fd-global tag metrics pthread_mutex_lock(&fd->metrics_lock); m->m = k_global ? (cram_metrics *)kh_val(fd->tags_used, k_global) : NULL; pthread_mutex_unlock(&fd->metrics_lock); } cram_tag_map *tm = (cram_tag_map *)kh_val(c->tags_used, k); if (!tm) goto_err; cram_codec *codec = tm->codec; if (!tm->codec) goto_err; switch(aux[2]) { case 'A': case 'C': case 'c': if (aux_end - aux < 3+1) goto err; if (!tm->blk) { if (!(tm->blk = cram_new_block(EXTERNAL, key))) goto err; codec->u.e_byte_array_len.val_codec->out = tm->blk; } aux+=3; //codec->encode(s, codec, aux, 1); // Functionally equivalent, but less code. BLOCK_APPEND_CHAR(tm->blk, *aux); aux++; break; case 'S': case 's': if (aux_end - aux < 3+2) goto err; if (!tm->blk) { if (!(tm->blk = cram_new_block(EXTERNAL, key))) goto err; codec->u.e_byte_array_len.val_codec->out = tm->blk; } aux+=3; //codec->encode(s, codec, aux, 2); BLOCK_APPEND(tm->blk, aux, 2); aux+=2; break; case 'I': case 'i': case 'f': if (aux_end - aux < 3+4) goto err; if (!tm->blk) { if (!(tm->blk = cram_new_block(EXTERNAL, key))) goto err; codec->u.e_byte_array_len.val_codec->out = tm->blk; } aux+=3; //codec->encode(s, codec, aux, 4); BLOCK_APPEND(tm->blk, aux, 4); aux+=4; break; case 'd': if (aux_end - aux < 3+8) goto err; if (!tm->blk) { if (!(tm->blk = cram_new_block(EXTERNAL, key))) goto err; codec->u.e_byte_array_len.val_codec->out = tm->blk; } aux+=3; //*tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; //codec->encode(s, codec, aux, 8); BLOCK_APPEND(tm->blk, aux, 8); aux+=8; break; case 'Z': case 'H': { if (aux_end - aux < 3) goto err; if (!tm->blk) { if (!(tm->blk = cram_new_block(EXTERNAL, key))) goto err; codec->out = tm->blk; } char *aux_s; aux += 3; aux_s = aux; while (aux < aux_end && *aux++); if (aux == aux_end && aux[-1] != '\0') { hts_log_error("Unterminated %c%c:%c tag for read \"%s\"", aux_s[-3], aux_s[-2], aux_s[-1], bam_get_qname(b)); goto err; } if (codec->encode(s, codec, aux_s, aux - aux_s) < 0) goto err; break; } case 'B': { if (aux_end - aux < 4+4) goto err; int type = aux[3]; uint64_t count = (((uint64_t)((unsigned char *)aux)[4]) << 0 | ((uint64_t)((unsigned char *)aux)[5]) << 8 | ((uint64_t)((unsigned char *)aux)[6]) <<16 | ((uint64_t)((unsigned char *)aux)[7]) <<24); uint64_t blen; if (!tm->blk) { if (!(tm->blk = cram_new_block(EXTERNAL, key))) goto err; if (codec->u.e_byte_array_len.val_codec->codec == E_XDELTA) { if (!(tm->blk2 = cram_new_block(EXTERNAL, key+128))) goto err; codec->u.e_byte_array_len.len_codec->out = tm->blk2; codec->u.e_byte_array_len.val_codec->u.e_xdelta.sub_codec->out = tm->blk; } else { codec->u.e_byte_array_len.len_codec->out = tm->blk; codec->u.e_byte_array_len.val_codec->out = tm->blk; } } // skip TN field aux+=3; // We use BYTE_ARRAY_LEN with external length, so store that first switch (type) { case 'c': case 'C': blen = count; break; case 's': case 'S': blen = 2*count; break; case 'i': case 'I': case 'f': blen = 4*count; break; default: hts_log_error("Unknown sub-type '%c' for aux type 'B'", type); goto err; } blen += 5; // sub-type & length if (aux_end - aux < blen || blen > INT_MAX) goto err; if (codec->encode(s, codec, aux, (int) blen) < 0) goto err; aux += blen; break; } default: hts_log_error("Unknown aux type '%c'", aux_end - aux < 2 ? '?' : aux[2]); goto err; } tm->blk->m = tm->m; } // FIXME: sort BLOCK_DATA(td_b) by char[3] triples // And and increment TD hash entry BLOCK_APPEND_CHAR(td_b, 0); // Duplicate key as BLOCK_DATA() can be realloced to a new pointer. key = string_ndup(c->comp_hdr->TD_keys, (char *)BLOCK_DATA(td_b) + TD_blk_size, BLOCK_SIZE(td_b) - TD_blk_size); if (!key) goto block_err; k = kh_put(m_s2i, c->comp_hdr->TD_hash, key, &new); if (new < 0) { goto err; } else if (new == 0) { BLOCK_SIZE(td_b) = TD_blk_size; } else { kh_val(c->comp_hdr->TD_hash, k) = c->comp_hdr->nTL; c->comp_hdr->nTL++; } cr->TL = kh_val(c->comp_hdr->TD_hash, k); if (cram_stats_add(c->stats[DS_TL], cr->TL) < 0) goto block_err; if (orig != (char *)bam_aux(b)) free(orig); if (err) *err = 0; return brg; err: block_err: if (orig != (char *)bam_aux(b)) free(orig); return NULL; } /* * During cram_next_container or before the final flush at end of * file, we update the current slice headers and increment the slice * number to the next slice. * * See cram_next_container() and cram_close(). */ void cram_update_curr_slice(cram_container *c, int version) { cram_slice *s = c->slice; if (c->multi_seq) { s->hdr->ref_seq_id = -2; s->hdr->ref_seq_start = 0; s->hdr->ref_seq_span = 0; } else if (c->curr_ref == -1 && CRAM_ge31(version)) { // Spec states span=0, but it broke our range queries. // See commit message for this and prior. s->hdr->ref_seq_id = -1; s->hdr->ref_seq_start = 0; s->hdr->ref_seq_span = 0; } else { s->hdr->ref_seq_id = c->curr_ref; s->hdr->ref_seq_start = c->first_base; s->hdr->ref_seq_span = MAX(0, c->last_base - c->first_base + 1); } s->hdr->num_records = c->curr_rec; if (c->curr_slice == 0) { if (c->ref_seq_id != s->hdr->ref_seq_id) c->ref_seq_id = s->hdr->ref_seq_id; c->ref_seq_start = c->first_base; } c->curr_slice++; } /* * Handles creation of a new container or new slice, flushing any * existing containers when appropriate. * * Really this is next slice, which may or may not lead to a new container. * * Returns cram_container pointer on success * NULL on failure. */ static cram_container *cram_next_container(cram_fd *fd, bam_seq_t *b) { cram_container *c = fd->ctr; int i; /* First occurrence */ if (c->curr_ref == -2) c->curr_ref = bam_ref(b); if (c->slice) cram_update_curr_slice(c, fd->version); /* Flush container */ if (c->curr_slice == c->max_slice || (bam_ref(b) != c->curr_ref && !c->multi_seq)) { c->ref_seq_span = fd->last_base - c->ref_seq_start + 1; hts_log_info("Flush container %d/%"PRId64"..%"PRId64, c->ref_seq_id, c->ref_seq_start, c->ref_seq_start + c->ref_seq_span -1); /* Encode slices */ if (-1 == cram_flush_container_mt(fd, c)) return NULL; if (!fd->pool) { // Move to sep func, as we need cram_flush_container for // the closing phase to flush the partial container. for (i = 0; i < c->max_slice; i++) { cram_free_slice(c->slices[i]); c->slices[i] = NULL; } c->slice = NULL; c->curr_slice = 0; /* Easy approach for purposes of freeing stats */ cram_free_container(c); } c = fd->ctr = cram_new_container(fd->seqs_per_slice, fd->slices_per_container); if (!c) return NULL; pthread_mutex_lock(&fd->ref_lock); c->no_ref = fd->no_ref; c->embed_ref = fd->embed_ref; c->record_counter = fd->record_counter; pthread_mutex_unlock(&fd->ref_lock); c->curr_ref = bam_ref(b); } c->last_pos = c->first_base = c->last_base = bam_pos(b)+1; /* New slice */ c->slice = c->slices[c->curr_slice] = cram_new_slice(MAPPED_SLICE, c->max_rec); if (!c->slice) return NULL; if (c->multi_seq) { c->slice->hdr->ref_seq_id = -2; c->slice->hdr->ref_seq_start = 0; c->slice->last_apos = 1; } else { c->slice->hdr->ref_seq_id = bam_ref(b); // wrong for unsorted data, will fix during encoding. c->slice->hdr->ref_seq_start = bam_pos(b)+1; c->slice->last_apos = bam_pos(b)+1; } c->curr_rec = 0; c->s_num_bases = 0; c->n_mapped = 0; // QO field: 0 implies original orientation, 1 implies sequence orientation // 1 is often preferable for NovaSeq, but impact is slight. ~0.5% diff. // Conversely other data sets it's often better than 1% saving for 0. // Short of trying both and learning, for now we use use 0 for V4, 1 for V3. c->qs_seq_orient = CRAM_MAJOR_VERS(fd->version) >= 4 ? 0 : 1; return c; } /* * Converts a single bam record into a cram record. * Possibly used within a thread. * * Returns 0 on success; * -1 on failure */ static int process_one_read(cram_fd *fd, cram_container *c, cram_slice *s, cram_record *cr, bam_seq_t *b, int rnum, kstring_t *MD, int embed_ref, int no_ref) { int i, fake_qual = -1, NM = 0; char *cp; char *ref, *seq, *qual; // Any places with N in seq and/or reference can lead to ambiguous // interpretation of the SAM NM:i tag. So we store these verbatim // to ensure valid data round-trips the same regardless of who // defines it as valid. // Similarly when alignments go beyond end of the reference. int verbatim_NM = fd->store_nm; int verbatim_MD = fd->store_md; // FIXME: multi-ref containers cr->flags = bam_flag(b); cr->len = bam_seq_len(b); uint8_t *md; if (!(md = bam_aux_get(b, "MD"))) MD = NULL; else MD->l = 0; int cf_tag = 0; if (embed_ref == 2) { cf_tag = MD ? 0 : 1; // No MD cf_tag |= bam_aux_get(b, "NM") ? 0 : 2; // No NM } //fprintf(stderr, "%s => %d\n", rg ? rg : "\"\"", cr->rg); ref = c->ref ? c->ref - (c->ref_start-1) : NULL; cr->ref_id = bam_ref(b); if (cram_stats_add(c->stats[DS_RI], cr->ref_id) < 0) goto block_err; if (cram_stats_add(c->stats[DS_BF], fd->cram_flag_swap[cr->flags & 0xfff]) < 0) goto block_err; // Non reference based encoding means storing the bases verbatim as features, which in // turn means every base also has a quality already stored. if (!no_ref || CRAM_MAJOR_VERS(fd->version) >= 3) cr->cram_flags |= CRAM_FLAG_PRESERVE_QUAL_SCORES; if (cr->len <= 0 && CRAM_MAJOR_VERS(fd->version) >= 3) cr->cram_flags |= CRAM_FLAG_NO_SEQ; //cram_stats_add(c->stats[DS_CF], cr->cram_flags & CRAM_FLAG_MASK); c->num_bases += cr->len; cr->apos = bam_pos(b)+1; if (cr->apos < 0 || cr->apos > INT64_MAX/2) goto err; if (c->pos_sorted) { if (cr->apos < s->last_apos && !fd->ap_delta) { c->pos_sorted = 0; } else { if (cram_stats_add(c->stats[DS_AP], cr->apos - s->last_apos) < 0) goto block_err; s->last_apos = cr->apos; } } else { //cram_stats_add(c->stats[DS_AP], cr->apos); } c->max_apos += (cr->apos > c->max_apos) * (cr->apos - c->max_apos); /* * This seqs_ds is largely pointless and it could reuse the same memory * over and over. * s->base_blk is what we need for encoding. */ cr->seq = BLOCK_SIZE(s->seqs_blk); cr->qual = BLOCK_SIZE(s->qual_blk); BLOCK_GROW(s->seqs_blk, cr->len+1); BLOCK_GROW(s->qual_blk, cr->len); // Convert BAM nibble encoded sequence to string of base pairs seq = cp = (char *)BLOCK_END(s->seqs_blk); *seq = 0; nibble2base(bam_seq(b), cp, cr->len); BLOCK_SIZE(s->seqs_blk) += cr->len; qual = cp = (char *)bam_qual(b); /* Copy and parse */ if (!(cr->flags & BAM_FUNMAP)) { uint32_t *cig_to, *cig_from; int64_t apos = cr->apos-1, spos = 0; int64_t MD_last = apos; // last position of edit in MD tag if (apos < 0) { hts_log_error("Mapped read with position <= 0 is disallowed"); return -1; } cr->cigar = s->ncigar; cr->ncigar = bam_cigar_len(b); while (cr->cigar + cr->ncigar >= s->cigar_alloc) { s->cigar_alloc = s->cigar_alloc ? s->cigar_alloc*2 : 1024; s->cigar = realloc(s->cigar, s->cigar_alloc * sizeof(*s->cigar)); if (!s->cigar) return -1; } cig_to = (uint32_t *)s->cigar; cig_from = (uint32_t *)bam_cigar(b); cr->feature = 0; cr->nfeature = 0; for (i = 0; i < cr->ncigar; i++) { enum cigar_op cig_op = cig_from[i] & BAM_CIGAR_MASK; uint32_t cig_len = cig_from[i] >> BAM_CIGAR_SHIFT; cig_to[i] = cig_from[i]; /* Can also generate events from here for CRAM diffs */ switch (cig_op) { int l; // Don't trust = and X ops to be correct. case BAM_CMATCH: case BAM_CBASE_MATCH: case BAM_CBASE_MISMATCH: //fprintf(stderr, "\nBAM_CMATCH\nR: %.*s\nS: %.*s\n", // cig_len, &ref[apos], cig_len, &seq[spos]); l = 0; if (!no_ref && cr->len) { int end = cig_len+apos < c->ref_end ? cig_len : c->ref_end - apos; char *sp = &seq[spos]; char *rp = &ref[apos]; char *qp = &qual[spos]; if (end > cr->len) { hts_log_error("CIGAR and query sequence are of different length"); return -1; } for (l = 0; l < end; l++) { // This case is just too disputed and different tools // interpret these in different ways. We give up and // store verbatim. if (rp[l] == 'N' && sp[l] == 'N') verbatim_NM = verbatim_MD = 1; if (rp[l] != sp[l]) { // Build our own MD tag if one is on the sequence, so // we can ensure it matches and thus can be discarded. if (MD && ref) { if (kputuw(apos+l - MD_last, MD) < 0) goto err; if (kputc(rp[l], MD) < 0) goto err; MD_last = apos+l+1; } NM++; if (!sp[l]) break; if (0 && CRAM_MAJOR_VERS(fd->version) >= 3) { #if 0 // Disabled for the time being as it doesn't // seem to gain us much. int ol=l; while (l 1) { if (cram_add_bases(fd, c, s, cr, spos+ol, l-ol, &seq[spos+ol])) return -1; l--; } else { l = ol; if (cram_add_substitution(fd, c, s, cr, spos+l, sp[l], qp[l], rp[l])) return -1; } #else // With urmap pushed to the limit and lots // of unaligned data (should be soft-clipped) // this saves ~2-7%. Worth it? int nl = l; int max_end = nl, max_score = 0, score = 0; while (nl < end) { if (rp[nl] != sp[nl]) { score += 3; if (max_score < score) { max_score = score; max_end = nl; } } else { score--; if (score < -2 || max_score - score > 7) break; } nl++; } if (max_score > 20) { cram_add_bases(fd, c, s, cr, spos+l, max_end-l, &seq[spos+l]); l = max_end-1; } else { while (l < nl) { if (rp[l] != sp[l]) cram_add_substitution(fd, c, s, cr, spos+l, sp[l], qp[l], rp[l]); l++; } l--; } #endif } else { if (cram_add_substitution(fd, c, s, cr, spos+l, sp[l], qp[l], rp[l])) return -1; } } } spos += l; apos += l; } if (l < cig_len && cr->len) { if (no_ref) { if (CRAM_MAJOR_VERS(fd->version) == 3) { if (cram_add_bases(fd, c, s, cr, spos, cig_len-l, &seq[spos])) return -1; spos += cig_len-l; } else { for (; l < cig_len && seq[spos]; l++, spos++) { if (cram_add_base(fd, c, s, cr, spos, seq[spos], qual[spos])) return -1; } } } else { /* off end of sequence or non-ref based output */ verbatim_NM = verbatim_MD = 1; for (; l < cig_len && seq[spos]; l++, spos++) { if (cram_add_base(fd, c, s, cr, spos, seq[spos], qual[spos])) return -1; } } apos += cig_len; } else if (!cr->len) { /* Seq "*" */ verbatim_NM = verbatim_MD = 1; apos += cig_len; spos += cig_len; } break; case BAM_CDEL: if (MD && ref) { if (kputuw(apos - MD_last, MD) < 0) goto err; if (apos < c->ref_end) { if (kputc_('^', MD) < 0) goto err; if (kputsn(&ref[apos], MIN(c->ref_end - apos, cig_len), MD) < 0) goto err; } } NM += cig_len; if (cram_add_deletion(c, s, cr, spos, cig_len, &seq[spos])) return -1; apos += cig_len; MD_last = apos; break; case BAM_CREF_SKIP: if (cram_add_skip(c, s, cr, spos, cig_len, &seq[spos])) return -1; apos += cig_len; MD_last += cig_len; break; case BAM_CINS: if (cram_add_insertion(c, s, cr, spos, cig_len, cr->len ? &seq[spos] : NULL)) return -1; if (no_ref && cr->len) { for (l = 0; l < cig_len; l++, spos++) { cram_add_quality(fd, c, s, cr, spos, qual[spos]); } } else { spos += cig_len; } NM += cig_len; break; case BAM_CSOFT_CLIP: if (cram_add_softclip(c, s, cr, spos, cig_len, cr->len ? &seq[spos] : NULL, fd->version)) return -1; if (no_ref && !(cr->cram_flags & CRAM_FLAG_PRESERVE_QUAL_SCORES)) { if (cr->len) { for (l = 0; l < cig_len; l++, spos++) { cram_add_quality(fd, c, s, cr, spos, qual[spos]); } } else { for (l = 0; l < cig_len; l++, spos++) { cram_add_quality(fd, c, s, cr, spos, -1); } } } else { spos += cig_len; } break; case BAM_CHARD_CLIP: if (cram_add_hardclip(c, s, cr, spos, cig_len, &seq[spos])) return -1; break; case BAM_CPAD: if (cram_add_pad(c, s, cr, spos, cig_len, &seq[spos])) return -1; break; default: hts_log_error("Unknown CIGAR op code %d", cig_op); return -1; } } if (cr->len && spos != cr->len) { hts_log_error("CIGAR and query sequence are of different length"); return -1; } fake_qual = spos; cr->aend = no_ref ? apos : MIN(apos, c->ref_end); if (cram_stats_add(c->stats[DS_FN], cr->nfeature) < 0) goto block_err; if (MD && ref) if (kputuw(apos - MD_last, MD) < 0) goto err; } else { // Unmapped cr->cram_flags |= CRAM_FLAG_PRESERVE_QUAL_SCORES; cr->cigar = 0; cr->ncigar = 0; cr->nfeature = 0; cr->aend = MIN(cr->apos, c->ref_end); for (i = 0; i < cr->len; i++) if (cram_stats_add(c->stats[DS_BA], seq[i]) < 0) goto block_err; fake_qual = 0; } cr->ntags = 0; //cram_stats_add(c->stats[DS_TC], cr->ntags); int err = 0; sam_hrec_rg_t *brg = cram_encode_aux(fd, b, c, s, cr, verbatim_NM, verbatim_MD, NM, MD, cf_tag, no_ref, &err); if (err) goto block_err; /* Read group, identified earlier */ if (brg) { cr->rg = brg->id; } else if (CRAM_MAJOR_VERS(fd->version) == 1) { sam_hrec_rg_t *brg = sam_hrecs_find_rg(fd->header->hrecs, "UNKNOWN"); if (!brg) goto block_err; cr->rg = brg->id; } else { cr->rg = -1; } if (cram_stats_add(c->stats[DS_RG], cr->rg) < 0) goto block_err; /* * Append to the qual block now. We do this here as * cram_add_substitution() can generate BA/QS events which need to * be in the qual block before we append the rest of the data. */ if (cr->cram_flags & CRAM_FLAG_PRESERVE_QUAL_SCORES) { /* Special case of seq "*" */ if (cr->len == 0) { cr->len = fake_qual; BLOCK_GROW(s->qual_blk, cr->len); cp = (char *)BLOCK_END(s->qual_blk); memset(cp, 255, cr->len); } else { BLOCK_GROW(s->qual_blk, cr->len); cp = (char *)BLOCK_END(s->qual_blk); char *from = (char *)&bam_qual(b)[0]; char *to = &cp[0]; memcpy(to, from, cr->len); // Store quality in original orientation for better compression. if (!c->qs_seq_orient) { if (cr->flags & BAM_FREVERSE) { int i, j; for (i = 0, j = cr->len-1; i < j; i++, j--) { unsigned char c; c = to[i]; to[i] = to[j]; to[j] = c; } } } } BLOCK_SIZE(s->qual_blk) += cr->len; } else { if (cr->len == 0) cr->len = fake_qual >= 0 ? fake_qual : cr->aend - cr->apos + 1; } if (cram_stats_add(c->stats[DS_RL], cr->len) < 0) goto block_err; /* Now we know apos and aend both, update mate-pair information */ { int new; khint_t k; int sec = (cr->flags & BAM_FSECONDARY) ? 1 : 0; //fprintf(stderr, "Checking %"PRId64"/%.*s\t", rnum, // cr->name_len, DSTRING_STR(s->name_ds)+cr->name); if (cr->flags & BAM_FPAIRED) { char *key = string_ndup(s->pair_keys, bam_name(b), bam_name_len(b)); if (!key) return -1; k = kh_put(m_s2i, s->pair[sec], key, &new); if (-1 == new) return -1; else if (new > 0) kh_val(s->pair[sec], k) = rnum; } else { new = 1; k = 0; // Prevents false-positive warning from gcc -Og } if (new == 0) { cram_record *p = &s->crecs[kh_val(s->pair[sec], k)]; int64_t aleft, aright; int sign; aleft = MIN(cr->apos, p->apos); aright = MAX(cr->aend, p->aend); if (cr->apos < p->apos) { sign = 1; } else if (cr->apos > p->apos) { sign = -1; } else if (cr->flags & BAM_FREAD1) { sign = 1; } else { sign = -1; } // This vs p: tlen, matepos, flags. Permit TLEN 0 and/or TLEN +/- // a small amount, if appropriate options set. if ((!fd->tlen_zero && MAX(bam_mate_pos(b)+1, 0) != p->apos) && !(fd->tlen_zero && bam_mate_pos(b) == 0)) goto detached; if (((bam_flag(b) & BAM_FMUNMAP) != 0) != ((p->flags & BAM_FUNMAP) != 0)) goto detached; if (((bam_flag(b) & BAM_FMREVERSE) != 0) != ((p->flags & BAM_FREVERSE) != 0)) goto detached; // p vs this: tlen, matepos, flags if (p->ref_id != cr->ref_id && !(fd->tlen_zero && p->ref_id == -1)) goto detached; if (p->mate_pos != cr->apos && !(fd->tlen_zero && p->mate_pos == 0)) goto detached; if (((p->flags & BAM_FMUNMAP) != 0) != ((p->mate_flags & CRAM_M_UNMAP) != 0)) goto detached; if (((p->flags & BAM_FMREVERSE) != 0) != ((p->mate_flags & CRAM_M_REVERSE) != 0)) goto detached; // Supplementary reads are just too ill defined if ((cr->flags & BAM_FSUPPLEMENTARY) || (p->flags & BAM_FSUPPLEMENTARY)) goto detached; // When in lossy name mode, if a read isn't detached we // cannot store the name. The corollary is that when we // must store the name, it must be detached (inefficient). if (fd->lossy_read_names && (!(cr->cram_flags & CRAM_FLAG_DISCARD_NAME) || !((p->cram_flags & CRAM_FLAG_DISCARD_NAME)))) goto detached; // Now check TLEN. We do this last as sometimes it's the // only thing that differs. In CRAM4 we have a better way // of handling this that doesn't break detached status int explicit_tlen = 0; int tflag1 = ((bam_ins_size(b) && llabs(bam_ins_size(b) - sign*(aright-aleft+1)) > fd->tlen_approx) || (!bam_ins_size(b) && !fd->tlen_zero)); int tflag2 = ((p->tlen && llabs(p->tlen - -sign*(aright-aleft+1)) > fd->tlen_approx) || (!p->tlen && !fd->tlen_zero)); if (tflag1 || tflag2) { if (CRAM_MAJOR_VERS(fd->version) >= 4) { explicit_tlen = CRAM_FLAG_EXPLICIT_TLEN; } else { // Stil do detached for unmapped data in CRAM4 as this // also impacts RNEXT calculation. goto detached; } } /* * The fields below are unused when encoding this read as it is * no longer detached. In theory they may get referred to when * processing a 3rd or 4th read in this template?, so we set them * here just to be sure. * * They do not need cram_stats_add() calls those as they are * not emitted. */ cr->mate_pos = p->apos; cram_stats_add(c->stats[DS_NP], cr->mate_pos); cr->tlen = explicit_tlen ? bam_ins_size(b) : sign*(aright-aleft+1); cram_stats_add(c->stats[DS_TS], cr->tlen); cr->mate_flags = ((p->flags & BAM_FMUNMAP) == BAM_FMUNMAP) * CRAM_M_UNMAP + ((p->flags & BAM_FMREVERSE) == BAM_FMREVERSE) * CRAM_M_REVERSE; // Decrement statistics aggregated earlier if (p->cram_flags & CRAM_FLAG_STATS_ADDED) { cram_stats_del(c->stats[DS_NP], p->mate_pos); cram_stats_del(c->stats[DS_MF], p->mate_flags); if (!(p->cram_flags & CRAM_FLAG_EXPLICIT_TLEN)) cram_stats_del(c->stats[DS_TS], p->tlen); cram_stats_del(c->stats[DS_NS], p->mate_ref_id); } /* Similarly we could correct the p-> values too, but these will no * longer have any code that refers back to them as the new 'p' * for this template is our current 'cr'. */ //p->mate_pos = cr->apos; //p->mate_flags = // ((cr->flags & BAM_FMUNMAP) == BAM_FMUNMAP) * CRAM_M_UNMAP + // ((cr->flags & BAM_FMREVERSE) == BAM_FMREVERSE)* CRAM_M_REVERSE; //p->tlen = p->apos - cr->aend; // Clear detached from cr flags cr->cram_flags &= ~CRAM_FLAG_DETACHED; cr->cram_flags |= explicit_tlen; if (cram_stats_add(c->stats[DS_CF], cr->cram_flags & CRAM_FLAG_MASK) < 0) goto block_err; // Clear detached from p flags and set downstream if (p->cram_flags & CRAM_FLAG_STATS_ADDED) { cram_stats_del(c->stats[DS_CF], p->cram_flags & CRAM_FLAG_MASK); p->cram_flags &= ~CRAM_FLAG_STATS_ADDED; } p->cram_flags &= ~CRAM_FLAG_DETACHED; p->cram_flags |= CRAM_FLAG_MATE_DOWNSTREAM | explicit_tlen;; if (cram_stats_add(c->stats[DS_CF], p->cram_flags & CRAM_FLAG_MASK) < 0) goto block_err; p->mate_line = rnum - (kh_val(s->pair[sec], k) + 1); if (cram_stats_add(c->stats[DS_NF], p->mate_line) < 0) goto block_err; kh_val(s->pair[sec], k) = rnum; } else { detached: //fprintf(stderr, "unpaired\n"); /* Derive mate flags from this flag */ cr->mate_flags = 0; if (bam_flag(b) & BAM_FMUNMAP) cr->mate_flags |= CRAM_M_UNMAP; if (bam_flag(b) & BAM_FMREVERSE) cr->mate_flags |= CRAM_M_REVERSE; if (cram_stats_add(c->stats[DS_MF], cr->mate_flags) < 0) goto block_err; cr->mate_pos = MAX(bam_mate_pos(b)+1, 0); if (cram_stats_add(c->stats[DS_NP], cr->mate_pos) < 0) goto block_err; cr->tlen = bam_ins_size(b); if (cram_stats_add(c->stats[DS_TS], cr->tlen) < 0) goto block_err; cr->cram_flags |= CRAM_FLAG_DETACHED; if (cram_stats_add(c->stats[DS_CF], cr->cram_flags & CRAM_FLAG_MASK) < 0) goto block_err; if (cram_stats_add(c->stats[DS_NS], bam_mate_ref(b)) < 0) goto block_err; cr->cram_flags |= CRAM_FLAG_STATS_ADDED; } } cr->mqual = bam_map_qual(b); if (cram_stats_add(c->stats[DS_MQ], cr->mqual) < 0) goto block_err; cr->mate_ref_id = bam_mate_ref(b); if (!(bam_flag(b) & BAM_FUNMAP)) { if (c->first_base > cr->apos) c->first_base = cr->apos; if (c->last_base < cr->aend) c->last_base = cr->aend; } return 0; block_err: err: return -1; } /* * Write iterator: put BAM format sequences into a CRAM file. * We buffer up a containers worth of data at a time. * * Returns 0 on success * -1 on failure */ int cram_put_bam_seq(cram_fd *fd, bam_seq_t *b) { cram_container *c; if (!fd->ctr) { fd->ctr = cram_new_container(fd->seqs_per_slice, fd->slices_per_container); if (!fd->ctr) return -1; fd->ctr->record_counter = fd->record_counter; pthread_mutex_lock(&fd->ref_lock); fd->ctr->no_ref = fd->no_ref; fd->ctr->embed_ref = fd->embed_ref; pthread_mutex_unlock(&fd->ref_lock); } c = fd->ctr; int embed_ref = c->embed_ref; if (!c->slice || c->curr_rec == c->max_rec || (bam_ref(b) != c->curr_ref && c->curr_ref >= -1) || (c->s_num_bases + c->s_aux_bytes >= fd->bases_per_slice)) { int slice_rec, curr_rec, multi_seq = fd->multi_seq == 1; int curr_ref = c->slice ? c->curr_ref : bam_ref(b); /* * Start packing slices when we routinely have under 1/4tr full. * * This option isn't available if we choose to embed references * since we can only have one per slice. * * The multi_seq var here refers to our intention for the next slice. * This slice has already been encoded so we output as-is. */ if (fd->multi_seq == -1 && c->curr_rec < c->max_rec/4+10 && fd->last_slice && fd->last_slice < c->max_rec/4+10 && embed_ref<=0) { if (!c->multi_seq) hts_log_info("Multi-ref enabled for next container"); multi_seq = 1; } else if (fd->multi_seq == 1) { pthread_mutex_lock(&fd->metrics_lock); if (fd->last_RI_count <= c->max_slice && fd->multi_seq_user != 1) { multi_seq = 0; hts_log_info("Multi-ref disabled for next container"); } pthread_mutex_unlock(&fd->metrics_lock); } slice_rec = c->slice_rec; curr_rec = c->curr_rec; if (CRAM_MAJOR_VERS(fd->version) == 1 || c->curr_rec == c->max_rec || fd->multi_seq != 1 || !c->slice || c->s_num_bases + c->s_aux_bytes >= fd->bases_per_slice) { if (NULL == (c = cram_next_container(fd, b))) { if (fd->ctr) { // prevent cram_close attempting to flush fd->ctr_mt = fd->ctr; // delay free when threading fd->ctr = NULL; } return -1; } } /* * Due to our processing order, some things we've already done we * cannot easily undo. So when we first notice we should be packing * multiple sequences per container we emit the small partial * container as-is and then start a fresh one in a different mode. */ if (multi_seq == 0 && fd->multi_seq == 1 && fd->multi_seq_user == -1) { // User selected auto-mode, we're currently using multi-seq, but // have detected we don't need to. Switch back to auto. fd->multi_seq = -1; } else if (multi_seq) { // We detected we need multi-seq fd->multi_seq = 1; c->multi_seq = 1; c->pos_sorted = 0; // Cram_next_container may end up flushing an existing one and // triggering fd->embed_ref=2 if no reference is found. // Embedded refs are incompatible with multi-seq, so we bail // out and switch to no_ref in this scenario. We do this // within the container only, as multi_seq may be temporary // and we switch back away from it again. pthread_mutex_lock(&fd->ref_lock); if (fd->embed_ref > 0 && c->curr_rec == 0 && c->curr_slice == 0) { hts_log_warning("Changing from embed_ref to no_ref mode"); // Should we update fd->embed_ref and no_ref here too? // Doing so means if we go into multi-seq and back out // again, eg due a cluster of tiny refs in the middle of // much larger ones, then we bake in no-ref mode. // // However for unsorted data we're realistically not // going to switch back. c->embed_ref = fd->embed_ref = 0; // or -1 for auto? c->no_ref = fd->no_ref = 1; } pthread_mutex_unlock(&fd->ref_lock); if (!c->refs_used) { pthread_mutex_lock(&fd->ref_lock); c->refs_used = calloc(fd->refs->nref, sizeof(int)); pthread_mutex_unlock(&fd->ref_lock); if (!c->refs_used) return -1; } } fd->last_slice = curr_rec - slice_rec; c->slice_rec = c->curr_rec; // Have we seen this reference before? if (bam_ref(b) >= 0 && curr_ref >= 0 && bam_ref(b) != curr_ref && embed_ref<=0 && !fd->unsorted && multi_seq) { if (!c->refs_used) { pthread_mutex_lock(&fd->ref_lock); c->refs_used = calloc(fd->refs->nref, sizeof(int)); pthread_mutex_unlock(&fd->ref_lock); if (!c->refs_used) return -1; } else if (c->refs_used && c->refs_used[bam_ref(b)]) { pthread_mutex_lock(&fd->ref_lock); fd->unsorted = 1; fd->multi_seq = 1; pthread_mutex_unlock(&fd->ref_lock); } } c->curr_ref = bam_ref(b); if (c->refs_used && c->curr_ref >= 0) c->refs_used[c->curr_ref]++; } if (!c->bams) { /* First time through, allocate a set of bam pointers */ pthread_mutex_lock(&fd->bam_list_lock); if (fd->bl) { spare_bams *spare = fd->bl; c->bams = spare->bams; fd->bl = spare->next; free(spare); } else { c->bams = calloc(c->max_c_rec, sizeof(bam_seq_t *)); if (!c->bams) { pthread_mutex_unlock(&fd->bam_list_lock); return -1; } } pthread_mutex_unlock(&fd->bam_list_lock); } /* Copy or alloc+copy the bam record, for later encoding */ if (c->bams[c->curr_c_rec]) { if (bam_copy1(c->bams[c->curr_c_rec], b) == NULL) return -1; } else { c->bams[c->curr_c_rec] = bam_dup1(b); if (c->bams[c->curr_c_rec] == NULL) return -1; } if (bam_seq_len(b)) { c->s_num_bases += bam_seq_len(b); } else { // No sequence in BAM record. CRAM doesn't directly support this // case, it ends up being stored as a string of N's for each query // consuming CIGAR operation. As this can become very inefficient // in time and memory, data where the query length is excessively // long are rejected. hts_pos_t qlen = bam_cigar2qlen(b->core.n_cigar, bam_get_cigar(b)); if (qlen > 100000000) { hts_log_error("CIGAR query length %"PRIhts_pos " for read \"%s\" is too long", qlen, bam_get_qname(b)); return -1; } c->s_num_bases += qlen; } c->curr_rec++; c->curr_c_rec++; c->s_aux_bytes += bam_get_l_aux(b); c->n_mapped += (bam_flag(b) & BAM_FUNMAP) ? 0 : 1; fd->record_counter++; return 0; } pysam-0.23.0/htslib/cram/cram_encode.h000066400000000000000000000071651475062545500175720ustar00rootroot00000000000000/* Copyright (c) 2012-2013, 2018 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /*! \file * Include cram.h instead. * * This is an internal part of the CRAM system and is automatically included * when you #include cram.h. * * Implements the encoding portion of CRAM I/O. Also see * cram_codecs.[ch] for the actual encoding functions themselves. */ #ifndef CRAM_ENCODE_H #define CRAM_ENCODE_H #ifdef __cplusplus extern "C" { #endif /* ---------------------------------------------------------------------- * CRAM sequence iterators. */ /*! Write iterator: put BAM format sequences into a CRAM file. * * We buffer up a containers worth of data at a time. * * FIXME: break this into smaller pieces. * * @return * Returns 0 on success; * -1 on failure */ int cram_put_bam_seq(cram_fd *fd, bam_seq_t *b); /* ---------------------------------------------------------------------- * Internal functions */ /*! INTERNAL: * Encodes a compression header block into a generic cram_block structure. * * @return * Returns cram_block ptr on success; * NULL on failure */ cram_block *cram_encode_compression_header(cram_fd *fd, cram_container *c, cram_block_compression_hdr *h, int embed_ref); /*! INTERNAL: * Encodes a slice compression header. * * @return * Returns cram_block on success; * NULL on failure */ cram_block *cram_encode_slice_header(cram_fd *fd, cram_slice *s); /*! INTERNAL: * Encodes all slices in a container into blocks. * * @return * Returns 0 on success; * -1 on failure * * FIXME: separate into encode_container and write_container. Ideally * we should be able to do read_container / write_container or * decode_container / encode_container. */ int cram_encode_container(cram_fd *fd, cram_container *c); /*! INTERNAL: * * During cram_next_container or before the final flush at end of * file, we update the current slice headers and increment the slice * number to the next slice. * * See cram_next_container() and cram_close(). */ void cram_update_curr_slice(cram_container *c, int version); #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/cram/cram_external.c000066400000000000000000001007661475062545500201530ustar00rootroot00000000000000/* Copyright (c) 2015, 2018-2020, 2022-2024 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /*! \file * External CRAM interface. * * Internally we're happy to use macros and to grub around in the cram * structures. This isn't very sustainable for an externally usable * ABI though, so we have anonymous structs and accessor functions too * to permit software such as samtools reheader to manipulate cram * containers and blocks in a robust manner. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #if defined(HAVE_EXTERNAL_LIBHTSCODECS) #include #else #include "../htscodecs/htscodecs/rANS_static4x16.h" #endif #include "../htslib/hfile.h" #include "cram.h" /* *----------------------------------------------------------------------------- * cram_fd */ sam_hdr_t *cram_fd_get_header(cram_fd *fd) { return fd->header; } void cram_fd_set_header(cram_fd *fd, sam_hdr_t *hdr) { fd->header = hdr; } int cram_fd_get_version(cram_fd *fd) { return fd->version; } void cram_fd_set_version(cram_fd *fd, int vers) { fd->version = vers; } int cram_major_vers(cram_fd *fd) { return CRAM_MAJOR_VERS(fd->version); } int cram_minor_vers(cram_fd *fd) { return CRAM_MINOR_VERS(fd->version); } hFILE *cram_fd_get_fp(cram_fd *fd) { return fd->fp; } void cram_fd_set_fp(cram_fd *fd, hFILE *fp) { fd->fp = fp; } /* *----------------------------------------------------------------------------- * cram_container */ int32_t cram_container_get_length(cram_container *c) { return c->length; } void cram_container_set_length(cram_container *c, int32_t length) { c->length = length; } int32_t cram_container_get_num_blocks(cram_container *c) { return c->num_blocks; } void cram_container_set_num_blocks(cram_container *c, int32_t num_blocks) { c->num_blocks = num_blocks; } int32_t cram_container_get_num_records(cram_container *c) { return c->num_records; } int64_t cram_container_get_num_bases(cram_container *c) { return c->num_bases; } /* Returns the landmarks[] array and the number of elements * in num_landmarks. */ int32_t *cram_container_get_landmarks(cram_container *c, int32_t *num_landmarks) { *num_landmarks = c->num_landmarks; return c->landmark; } /* Sets the landmarks[] array (pointer copy, not a memory dup) and * num_landmarks value. */ void cram_container_set_landmarks(cram_container *c, int32_t num_landmarks, int32_t *landmarks) { c->num_landmarks = num_landmarks; c->landmark = landmarks; } /* Returns true if the container is empty (EOF marker) */ int cram_container_is_empty(cram_fd *fd) { return fd->empty_container; } void cram_container_get_coords(cram_container *c, int *refid, hts_pos_t *start, hts_pos_t *span) { if (refid) *refid = c->ref_seq_id; if (start) *start = c->ref_seq_start; if (span) *span = c->ref_seq_span; } /* *----------------------------------------------------------------------------- * cram_block_compression_hdr */ /* * Utility function to edit an RG id. * This is only possible if there is one single RG value used and it * is in the container compression header using HUFFMAN or BETA * codec. In this case it is essentially hard coded and needs no * editing of external (or worse, CORE) blocks. * * Returns 0 on success * -1 on failure */ // Or arbitrary set compression header constant? static int cram_block_compression_hdr_set_DS(cram_block_compression_hdr *ch, int ds, int new_rg) { if (!ch || !ch->codecs[ds]) return -1; switch (ch->codecs[ds]->codec) { case E_HUFFMAN: if (ch->codecs[ds]->u.huffman.ncodes != 1) return -1; ch->codecs[ds]->u.huffman.codes[0].symbol = new_rg; return 0; case E_BETA: if (ch->codecs[ds]->u.beta.nbits != 0) return -1; ch->codecs[ds]->u.beta.offset = -new_rg; return 0; default: break; } return -1; } int cram_block_compression_hdr_set_rg(cram_block_compression_hdr *ch, int new_rg) { return cram_block_compression_hdr_set_DS(ch, DS_RG, new_rg); } /* * Converts a cram_block_compression_hdr struct used for decoding to * one used for encoding. Maybe this should be a transparent * operation applied on-demand. * * Returns 0 on success * -1 on failure */ int cram_block_compression_hdr_decoder2encoder(cram_fd *fd, cram_block_compression_hdr *ch) { int i; if (!ch) return -1; for (i = 0; i < DS_END; i++) { cram_codec *co = ch->codecs[i]; if (!co) continue; if (-1 == cram_codec_decoder2encoder(fd, co)) return -1; } return 0; } typedef struct { cram_block_compression_hdr *hdr; cram_map *curr_map; int idx; int is_tag; // phase 2 using tag_encoding_map } cram_codec_iter; static void cram_codec_iter_init(cram_block_compression_hdr *hdr, cram_codec_iter *iter) { iter->hdr = hdr; iter->curr_map = NULL; iter->idx = 0; iter->is_tag = 0; } // See enum cram_DS_ID in cram/cram_structs static int cram_ds_to_key(enum cram_DS_ID ds) { switch(ds) { case DS_RN: return 256*'R'+'N'; case DS_QS: return 256*'Q'+'S'; case DS_IN: return 256*'I'+'N'; case DS_SC: return 256*'S'+'C'; case DS_BF: return 256*'B'+'F'; case DS_CF: return 256*'C'+'F'; case DS_AP: return 256*'A'+'P'; case DS_RG: return 256*'R'+'G'; case DS_MQ: return 256*'M'+'Q'; case DS_NS: return 256*'N'+'S'; case DS_MF: return 256*'M'+'F'; case DS_TS: return 256*'T'+'S'; case DS_NP: return 256*'N'+'P'; case DS_NF: return 256*'N'+'F'; case DS_RL: return 256*'R'+'L'; case DS_FN: return 256*'F'+'N'; case DS_FC: return 256*'F'+'C'; case DS_FP: return 256*'F'+'P'; case DS_DL: return 256*'D'+'L'; case DS_BA: return 256*'B'+'A'; case DS_BS: return 256*'B'+'S'; case DS_TL: return 256*'T'+'L'; case DS_RI: return 256*'R'+'I'; case DS_RS: return 256*'R'+'S'; case DS_PD: return 256*'P'+'D'; case DS_HC: return 256*'H'+'C'; case DS_BB: return 256*'B'+'B'; case DS_QQ: return 256*'Q'+'Q'; case DS_TN: return 256*'T'+'N'; case DS_TC: return 256*'T'+'C'; case DS_TM: return 256*'T'+'M'; case DS_TV: return 256*'T'+'V'; default: break; } return -1; // unknown } static cram_codec *cram_codec_iter_next(cram_codec_iter *iter, int *key) { cram_codec *cc = NULL; cram_block_compression_hdr *hdr = iter->hdr; if (!iter->is_tag) { // 1: Iterating through main data-series do { cc = hdr->codecs[iter->idx++]; } while(!cc && iter->idx < DS_END); if (cc) { *key = cram_ds_to_key(iter->idx-1); return cc; } // Reset index for phase 2 iter->idx = 0; iter->is_tag = 1; } do { if (!iter->curr_map) iter->curr_map = hdr->tag_encoding_map[iter->idx++]; cc = iter->curr_map ? iter->curr_map->codec : NULL; if (cc) { *key = iter->curr_map->key; iter->curr_map = iter->curr_map->next; return cc; } } while (iter->idx < CRAM_MAP_HASH); // End of codecs return NULL; } /* * A list of data-series, used to create a linked list threaded through * a single array. */ typedef struct ds_list { int data_series; int next; } ds_list; KHASH_MAP_INIT_INT(cid, int64_t) // Opaque struct for the CRAM block content-id -> data-series map. struct cram_cid2ds_t { ds_list *ds; // array of data-series with linked lists threading through it int ds_size; int ds_idx; khash_t(cid) *hash; // key=content_id, value=index to ds array int *ds_a; // serialised array of data-series returned by queries. }; void cram_cid2ds_free(cram_cid2ds_t *cid2ds) { if (cid2ds) { if (cid2ds->hash) kh_destroy(cid, cid2ds->hash); free(cid2ds->ds); free(cid2ds->ds_a); free(cid2ds); } } /* * Map cram block numbers to data-series. It's normally a 1:1 mapping, * but in rare cases it can be 1:many (or even many:many). * The key is the block number and the value is an index into the data-series * array, which we iterate over until reaching a negative value. * * Provide cid2ds as NULL to allocate a new map or pass in an existing one * to append to this map. The new (or existing) map is returned. * * Returns the cid2ds (newly allocated or as provided) on success, * NULL on failure. */ cram_cid2ds_t *cram_update_cid2ds_map(cram_block_compression_hdr *hdr, cram_cid2ds_t *cid2ds) { cram_cid2ds_t *c2d = cid2ds; if (!c2d) { c2d = calloc(1, sizeof(*c2d)); if (!c2d) return NULL; c2d->hash = kh_init(cid); if (!c2d->hash) goto err; } // Iterate through codecs. Initially primary two-left ones in // rec_encoding_map, and then the three letter in tag_encoding_map. cram_codec_iter citer; cram_codec_iter_init(hdr, &citer); cram_codec *codec; int key; while ((codec = cram_codec_iter_next(&citer, &key))) { // Having got a codec, we can then use cram_codec_to_id to get // the block IDs utilised by that codec. This is then our // map for allocating data blocks to data series, but for shared // blocks we can't separate out how much is used by each DS. int bnum[2]; cram_codec_get_content_ids(codec, bnum); khiter_t k; int ret, i; for (i = 0; i < 2; i++) { if (bnum[i] > -2) { k = kh_put(cid, c2d->hash, bnum[i], &ret); if (ret < 0) goto err; if (c2d->ds_idx >= c2d->ds_size) { c2d->ds_size += 100; c2d->ds_size *= 2; ds_list *ds_new = realloc(c2d->ds, c2d->ds_size * sizeof(*ds_new)); if (!ds_new) goto err; c2d->ds = ds_new; } if (ret == 0) { // Shared content_id, so add to list of DS // Maybe data-series should be part of the hash key? // // So top-32 bit is content-id, bot-32 bit is key. // Sort hash by key and then can group all the data-series // known together. ?? // // Brute force for now, scan to see if recorded. // Typically this is minimal effort as we almost always // have 1 data-series per block content-id, so the list to // search is of size 1. int dsi = kh_value(c2d->hash, k); while (dsi >= 0) { if (c2d->ds[dsi].data_series == key) break; dsi = c2d->ds[dsi].next; } if (dsi == -1) { // Block content_id seen before, but not with this DS c2d->ds[c2d->ds_idx].data_series = key; c2d->ds[c2d->ds_idx].next = kh_value(c2d->hash, k); kh_value(c2d->hash, k) = c2d->ds_idx; c2d->ds_idx++; } } else { // First time this content id has been used c2d->ds[c2d->ds_idx].data_series = key; c2d->ds[c2d->ds_idx].next = -1; kh_value(c2d->hash, k) = c2d->ds_idx; c2d->ds_idx++; } } } } return c2d; err: if (c2d != cid2ds) cram_cid2ds_free(c2d); return NULL; } /* * Return a list of data series observed as belonging to a block with * the specified content_id. *n is the number of data series * returned, or 0 if block is unused. * Block content_id of -1 is used to indicate the CORE block. * * The pointer returned is owned by the cram_cid2ds state and should * not be freed by the caller. */ int *cram_cid2ds_query(cram_cid2ds_t *c2d, int content_id, int *n) { *n = 0; if (!c2d || !c2d->hash) return NULL; khiter_t k = kh_get(cid, c2d->hash, content_id); if (k == kh_end(c2d->hash)) return NULL; if (!c2d->ds_a) { c2d->ds_a = malloc(c2d->ds_idx * sizeof(int)); if (!c2d->ds_a) return NULL; } int dsi = kh_value(c2d->hash, k); // initial ds array index from hash int idx = 0; while (dsi >= 0) { c2d->ds_a[idx++] = c2d->ds[dsi].data_series; dsi = c2d->ds[dsi].next; // iterate over list within ds array } *n = idx; return c2d->ds_a; } /* * Produces a description of the record and tag encodings held within * a compression header and appends to 'ks'. * * Returns 0 on success, * <0 on failure. */ int cram_describe_encodings(cram_block_compression_hdr *hdr, kstring_t *ks) { cram_codec_iter citer; cram_codec_iter_init(hdr, &citer); cram_codec *codec; int key, r = 0; while ((codec = cram_codec_iter_next(&citer, &key))) { char key_s[4] = {0}; int key_i = 0; if (key>>16) key_s[key_i++] = key>>16; key_s[key_i++] = (key>>8)&0xff; key_s[key_i++] = key&0xff; r |= ksprintf(ks, "\t%s\t", key_s) < 0; r |= cram_codec_describe(codec, ks) < 0; r |= kputc('\n', ks) < 0; } return r ? -1 : 0; } /* *----------------------------------------------------------------------------- * cram_slice */ int32_t cram_slice_hdr_get_num_blocks(cram_block_slice_hdr *hdr) { return hdr->num_blocks; } int cram_slice_hdr_get_embed_ref_id(cram_block_slice_hdr *h) { return h->ref_base_id; } void cram_slice_hdr_get_coords(cram_block_slice_hdr *h, int *refid, hts_pos_t *start, hts_pos_t *span) { if (refid) *refid = h->ref_seq_id; if (start) *start = h->ref_seq_start; if (span) *span = h->ref_seq_span; } /* *----------------------------------------------------------------------------- * cram_block */ int32_t cram_block_get_content_id(cram_block *b) { return b->content_type == CORE ? -1 : b->content_id; } int32_t cram_block_get_comp_size(cram_block *b) { return b->comp_size; } int32_t cram_block_get_uncomp_size(cram_block *b) { return b->uncomp_size; } int32_t cram_block_get_crc32(cram_block *b) { return b->crc32; } void * cram_block_get_data(cram_block *b) { return BLOCK_DATA(b); } int32_t cram_block_get_size(cram_block *b) { return BLOCK_SIZE(b); } enum cram_block_method cram_block_get_method(cram_block *b) { return (enum cram_block_method)b->orig_method; } enum cram_content_type cram_block_get_content_type(cram_block *b) { return b->content_type; } void cram_block_set_content_id(cram_block *b, int32_t id) { b->content_id = id; } void cram_block_set_comp_size(cram_block *b, int32_t size) { b->comp_size = size; } void cram_block_set_uncomp_size(cram_block *b, int32_t size) { b->uncomp_size = size; } void cram_block_set_crc32(cram_block *b, int32_t crc) { b->crc32 = crc; } void cram_block_set_data(cram_block *b, void *data) { BLOCK_DATA(b) = data; } void cram_block_set_size(cram_block *b, int32_t size) { BLOCK_SIZE(b) = size; } int cram_block_append(cram_block *b, const void *data, int size) { BLOCK_APPEND(b, data, size); return 0; block_err: return -1; } void cram_block_update_size(cram_block *b) { BLOCK_UPLEN(b); } // Offset is known as "size" internally, but it can be confusing. size_t cram_block_get_offset(cram_block *b) { return BLOCK_SIZE(b); } void cram_block_set_offset(cram_block *b, size_t offset) { BLOCK_SIZE(b) = offset; } /* * Given a compressed block of data in a specified compression method, * fill out the 'cm' field with meta-data gleaned from the compressed * block. * * If comp is CRAM_COMP_UNKNOWN, we attempt to auto-detect the compression * format, but this doesn't work for all methods. * * Retuns the detected or specified comp method, and fills out *cm * if non-NULL. */ cram_method_details *cram_expand_method(uint8_t *data, int32_t size, enum cram_block_method comp) { cram_method_details *cm = calloc(1, sizeof(*cm)); if (!cm) return NULL; const char *xz_header = "\xFD""7zXZ"; // including nul if (comp == CRAM_COMP_UNKNOWN) { // Auto-detect if (size > 1 && data[0] == 0x1f && data[1] == 0x8b) comp = CRAM_COMP_GZIP; else if (size > 3 && data[1] == 'B' && data[2] == 'Z' && data[3] == 'h') comp = CRAM_COMP_BZIP2; else if (size > 6 && memcmp(xz_header, data, 6) == 0) comp = CRAM_COMP_LZMA; else comp = CRAM_COMP_UNKNOWN; } cm->method = comp; // Interrogate the compressed data stream to fill out additional fields. switch (comp) { case CRAM_COMP_GZIP: if (size > 8) { if (data[8] == 4) cm->level = 1; else if (data[8] == 2) cm->level = 9; else cm->level = 5; } break; case CRAM_COMP_BZIP2: if (size > 3 && data[3] >= '1' && data[3] <= '9') cm->level = data[3]-'0'; break; case CRAM_COMP_RANS4x8: cm->Nway = 4; if (size > 0 && data[0] == 1) cm->order = 1; else cm->order = 0; break; case CRAM_COMP_RANSNx16: if (size > 0) { cm->order = data[0] & 1; cm->Nway = data[0] & RANS_ORDER_X32 ? 32 : 4; cm->rle = data[0] & RANS_ORDER_RLE ? 1 : 0; cm->pack = data[0] & RANS_ORDER_PACK ? 1 : 0; cm->cat = data[0] & RANS_ORDER_CAT ? 1 : 0; cm->stripe = data[0] & RANS_ORDER_STRIPE ? 1 : 0; cm->nosz = data[0] & RANS_ORDER_NOSZ ? 1 : 0; } break; case CRAM_COMP_ARITH: if (size > 0) { // Not in a public header, but the same transforms as rANSNx16 cm->order = data[0] & 3; cm->rle = data[0] & RANS_ORDER_RLE ? 1 : 0; cm->pack = data[0] & RANS_ORDER_PACK ? 1 : 0; cm->cat = data[0] & RANS_ORDER_CAT ? 1 : 0; cm->stripe = data[0] & RANS_ORDER_STRIPE ? 1 : 0; cm->nosz = data[0] & RANS_ORDER_NOSZ ? 1 : 0; cm->ext = data[0] & 4 /*external*/ ? 1 : 0; } break; case CRAM_COMP_TOK3: if (size > 8) { if (data[8] == 1) cm->level = 11; else if (data[8] == 0) cm->level = 1; } break; default: break; } return cm; } /* *----------------------------------------------------------------------------- * cram_codecs */ // -2 is unused. // -1 is CORE // >= 0 is the block with that Content ID void cram_codec_get_content_ids(cram_codec *c, int ids[2]) { ids[0] = cram_codec_to_id(c, &ids[1]); } /* *----------------------------------------------------------------------------- * Utility functions */ /* * Copies the blocks representing the next num_slice slices from a * container from 'in' to 'out'. It is expected that the file pointer * is just after the read of the cram_container and cram compression * header. * * Returns 0 on success * -1 on failure */ int cram_copy_slice(cram_fd *in, cram_fd *out, int32_t num_slice) { int32_t i, j; for (i = 0; i < num_slice; i++) { cram_block *blk; cram_block_slice_hdr *hdr; if (!(blk = cram_read_block(in))) return -1; if (!(hdr = cram_decode_slice_header(in, blk))) { cram_free_block(blk); return -1; } if (cram_write_block(out, blk) != 0) { cram_free_block(blk); return -1; } cram_free_block(blk); int num_blocks = cram_slice_hdr_get_num_blocks(hdr); for (j = 0; j < num_blocks; j++) { blk = cram_read_block(in); if (!blk || cram_write_block(out, blk) != 0) { if (blk) cram_free_block(blk); return -1; } cram_free_block(blk); } cram_free_slice_header(hdr); } return 0; } /* * Discards the next containers worth of data. * Only the cram structure has been read so far. * * Returns 0 on success, * -1 on failure */ static int cram_skip_container(cram_fd *in, cram_container *c) { // Compression header cram_block *blk; if (!(blk = cram_read_block(in))) return -1; cram_free_block(blk); int i; for (i = 0; i < c->num_landmarks; i++) { cram_block_slice_hdr *hdr; if (!(blk = cram_read_block(in))) return -1; if (!(hdr = cram_decode_slice_header(in, blk))) { cram_free_block(blk); return -1; } cram_free_block(blk); int num_blocks = cram_slice_hdr_get_num_blocks(hdr), j; for (j = 0; j < num_blocks; j++) { blk = cram_read_block(in); if (!blk) { cram_free_slice_header(hdr); return -1; } cram_free_block(blk); } cram_free_slice_header(hdr); } return 0; } /* * Copies a container, but filtering it down to a specific region, * which has already been set on the 'in' fd. * * This is used in e.g. samtools cat where we specified a region and discover * that a region doesn't entirely span the container, so we have to select * which reads we need to copy out of it. * * If ref_id is non-NULL we also return the last ref_id we filtered. * This can be -2 if it's multi-ref and we observe more than one reference, * and actual ref_id >= -1 if it's multi-ref and we observe just one ref or * it's fixed reference. * * Returns 0 on success * -1 on error */ int cram_filter_container(cram_fd *in, cram_fd *out, cram_container *c, int *ref_id) { int err = 0, fixed_ref = -3; if (ref_id) *ref_id = c->ref_seq_id; int rid = in->range.refid == -2 ? -1 : in->range.refid; if (rid != c->ref_seq_id || in->range.start > c->ref_seq_start + c->ref_seq_span-1) // Except for multi-ref cases if (c->ref_seq_id != -2) return cram_skip_container(in, c); // Container compression header cram_block *blk = cram_read_block(in); if (!blk) return -1; c->comp_hdr = cram_decode_compression_header(in, blk); in->ctr = c; // If it's multi-ref but a constant ref-id, then we can still do // basic level chromosome filtering. Similarly multi-ref where we're // _already_ in ref "*" (unmapped) means we can just copy the container // as there are no positions to filter on and "*" sorts to the end. // TODO: how to tell "already in" though? if (c->ref_seq_id == -2) { cram_codec *cd = c->comp_hdr->codecs[DS_RI]; if (cd && cd->codec == E_HUFFMAN && cd->u.huffman.ncodes == 1 && // this check should be always true anyway rid == cd->u.huffman.codes[0].symbol) // We're in multi-ref mode, but actually the entire container // matches. So if we're in whole-chromosome mode we can just // copy. if (in->range.start <= 1 && in->range.end >= (INT64_MAX&(0xffffffffULL<<32))) { if (ref_id) *ref_id = rid; err |= cram_write_container(out, c) < 0; err |= cram_write_block(out, blk); return cram_copy_slice(in, out, c->num_landmarks) | -err; } } // A simple read-write loop with region filtering automatically due to // an earlier CRAM_OPT_RANGE request. // // We can hit EOF when reaching the end of the range, but we still need // to manually check we don't attempt to read beyond this single container. cram_range rng_copy = in->range; in->range.start = INT64_MIN; in->range.end = INT64_MAX; bam1_t *b = bam_init1(); while ((c->curr_slice < c->max_slice || c->slice->curr_rec < c->slice->max_rec)) { cram_slice *s; if (c->slice && c->slice->curr_rec < c->slice->max_rec) s = c->slice; else if (c->curr_slice < c->max_slice) s = cram_next_slice(in, &c); else break; // end of container c->slice = s; // This is more efficient if we check as a cram record instead of a // bam record as we don't have to parse CIGAR end. cram_record *cr = &c->slice->crecs[c->slice->curr_rec]; if (fixed_ref == -3) fixed_ref = cr->ref_id; else if (fixed_ref != cr->ref_id) fixed_ref = -2; if (rng_copy.refid != cr->ref_id) { if (rng_copy.refid == -2) { if (cr->ref_id > -1) { // Want unmapped, but have mapped c->slice->curr_rec++; continue; } } else { if (rng_copy.refid > cr->ref_id || rng_copy.refid == -1) { // multi-ref and not at the correct ref yet c->slice->curr_rec++; continue; } else { // multi-ref and beyond the desired ref break; } } } // Correct ref, but check the desired region if (cr->aend < rng_copy.start) { c->slice->curr_rec++; continue; } if (cr->apos > rng_copy.end) break; // Broadly rquivalent to cram_get_bam_seq, but starting from 'cr' err |= cram_to_bam(in->header, in, s, cr, s->curr_rec++, &b) < 0; if (cram_put_bam_seq(out, b) < 0) { err |= 1; break; } } bam_destroy1(b); if (ref_id) *ref_id = fixed_ref; in->range = rng_copy; // Avoids double frees as we stole the container from our other // file descriptor. in->ctr = NULL; in->ctr_mt = NULL; err |= cram_flush(out); cram_free_block(blk); return -err; } /* * Renumbers RG numbers in a cram compression header. * * CRAM stores RG as the Nth number in the header, rather than a * string holding the ID: tag. This is smaller in space, but means * "samtools cat" to join files together that contain single but * different RG lines needs a way of renumbering them. * * The file descriptor is expected to be immediately after the * cram_container structure (ie before the cram compression header). * Due to the nature of the CRAM format, this needs to read and write * the blocks itself. Note that there may be multiple slices within * the container, meaning multiple compression headers to manipulate. * Changing RG may change the size of the compression header and * therefore the length field in the container. Hence we rewrite all * blocks just in case and also emit the adjusted container. * * The current implementation can only cope with renumbering a single * RG (and only then if it is using HUFFMAN or BETA codecs). In * theory it *may* be possible to renumber multiple RGs if they use * HUFFMAN to the CORE block or use an external block unshared by any * other data series. So we have an API that can be upgraded to * support this, but do not implement it for now. An example * implementation of RG as an EXTERNAL block would be to find that * block and rewrite it, returning the number of blocks consumed. * * Returns 0 on success; * -1 if unable to edit; * -2 on other errors (eg I/O). */ int cram_transcode_rg(cram_fd *in, cram_fd *out, cram_container *c, int nrg, int *in_rg, int *out_rg) { int new_rg = *out_rg, old_size, new_size; cram_block *o_blk, *n_blk; cram_block_compression_hdr *ch; if (nrg != 1) { hts_log_error("CRAM transcode supports only a single RG"); return -2; } // Produce a new block holding the updated compression header, // with RG transcoded to a new value. (Single only supported.) o_blk = cram_read_block(in); old_size = cram_block_size(o_blk); ch = cram_decode_compression_header(in, o_blk); if (cram_block_compression_hdr_set_rg(ch, new_rg) != 0) return -1; if (cram_block_compression_hdr_decoder2encoder(in, ch) != 0) return -1; n_blk = cram_encode_compression_header(in, c, ch, in->embed_ref); cram_free_compression_header(ch); /* * Warning: this has internal knowledge of the cram compression * header format. * * The decoder doesn't set c->tags_used, so the encoder puts a two * byte blank segment. This means n_blk is too short. We skip * through the decoded old block (o_blk) and copy from there. */ char *cp = cram_block_get_data(o_blk); char *op = cp; char *endp = cp + cram_block_get_uncomp_size(o_blk); //fprintf(stderr, "sz = %d\n", (int)(endp-cp)); int32_t i32, err = 0; i32 = in->vv.varint_get32(&cp, endp, &err); cp += i32; i32 = in->vv.varint_get32(&cp, endp, &err); cp += i32; op = cp; i32 = in->vv.varint_get32(&cp, endp, &err); i32 += (cp-op); if (err) return -2; //fprintf(stderr, "remaining %d bytes\n", i32); cram_block_set_size(n_blk, cram_block_get_size(n_blk)-2); cram_block_append(n_blk, op, i32); cram_block_update_size(n_blk); new_size = cram_block_size(n_blk); //fprintf(stderr, "size %d -> %d\n", old_size, new_size); // Now we've constructedthe updated compression header, // amend the container too (it may have changed size). int32_t *landmarks, num_landmarks; landmarks = cram_container_get_landmarks(c, &num_landmarks); if (old_size != new_size) { int diff = new_size - old_size, j; for (j = 0; j < num_landmarks; j++) landmarks[j] += diff; //cram_container_set_landmarks(c, num_landmarks, landmarks); cram_container_set_length(c, cram_container_get_length(c) + diff); } // Finally write it all out; container, compression header, // and then all the remaining slice blocks. if (cram_write_container(out, c) != 0) return -2; cram_write_block(out, n_blk); cram_free_block(o_blk); cram_free_block(n_blk); // Container num_blocks can be invalid, due to a bug. // Instead we iterate in slice context instead. return cram_copy_slice(in, out, num_landmarks); } /*! * Returns the refs_t structure used by a cram file handle. * * This may be used in conjunction with option CRAM_OPT_SHARED_REF to * share reference memory between multiple file handles. * * @return * Returns NULL if none exists or the file handle is not a CRAM file. */ refs_t *cram_get_refs(htsFile *fd) { return fd->format.format == cram ? fd->fp.cram->refs : NULL; } pysam-0.23.0/htslib/cram/cram_index.c000066400000000000000000000716111475062545500174340ustar00rootroot00000000000000/* Copyright (c) 2013-2020, 2023-2024 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /* * The index is a gzipped tab-delimited text file with one line per slice. * The columns are: * 1: reference number (0 to N-1, as per BAM ref_id) * 2: reference position of 1st read in slice (1..?) * 3: number of reads in slice * 4: offset of container start (relative to end of SAM header, so 1st * container is offset 0). * 5: slice number within container (ie which landmark). * * In memory, we hold this in a nested containment list. Each list element is * a cram_index struct. Each element in turn can contain its own list of * cram_index structs. * * Any start..end range which is entirely contained within another (and * earlier as it is sorted) range will be held within it. This ensures that * the outer list will never have containments and we can safely do a * binary search to find the first range which overlaps any given coordinate. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #include #include #include #include "../htslib/bgzf.h" #include "../htslib/hfile.h" #include "../hts_internal.h" #include "cram.h" #include "os.h" #if 0 static void dump_index_(cram_index *e, int level) { int i, n; n = printf("%*s%d / %d .. %d, ", level*4, "", e->refid, e->start, e->end); printf("%*soffset %"PRId64" %p %p\n", MAX(0,50-n), "", e->offset, e, e->e_next); for (i = 0; i < e->nslice; i++) { dump_index_(&e->e[i], level+1); } } static void dump_index(cram_fd *fd) { int i; for (i = 0; i < fd->index_sz; i++) { dump_index_(&fd->index[i], 0); } } #endif // Thread a linked list through the nested containment list. // This makes navigating it and finding the "next" index entry // trivial. static cram_index *link_index_(cram_index *e, cram_index *e_last) { int i; if (e_last) e_last->e_next = e; // We don't want to link in the top-level cram_index with // offset=0 and start/end = INT_MIN/INT_MAX. if (e->offset) e_last = e; for (i = 0; i < e->nslice; i++) e_last = link_index_(&e->e[i], e_last); return e_last; } static void link_index(cram_fd *fd) { int i; cram_index *e_last = NULL; for (i = 0; i < fd->index_sz; i++) { e_last = link_index_(&fd->index[i], e_last); } if (e_last) e_last->e_next = NULL; } static int kget_int32(kstring_t *k, size_t *pos, int32_t *val_p) { int sign = 1; int32_t val = 0; size_t p = *pos; while (p < k->l && (k->s[p] == ' ' || k->s[p] == '\t')) p++; if (p < k->l && k->s[p] == '-') sign = -1, p++; if (p >= k->l || !(k->s[p] >= '0' && k->s[p] <= '9')) return -1; while (p < k->l && k->s[p] >= '0' && k->s[p] <= '9') { int digit = k->s[p++]-'0'; val = val*10 + digit; } *pos = p; *val_p = sign*val; return 0; } static int kget_int64(kstring_t *k, size_t *pos, int64_t *val_p) { int sign = 1; int64_t val = 0; size_t p = *pos; while (p < k->l && (k->s[p] == ' ' || k->s[p] == '\t')) p++; if (p < k->l && k->s[p] == '-') sign = -1, p++; if (p >= k->l || !(k->s[p] >= '0' && k->s[p] <= '9')) return -1; while (p < k->l && k->s[p] >= '0' && k->s[p] <= '9') { int digit = k->s[p++]-'0'; val = val*10 + digit; } *pos = p; *val_p = sign*val; return 0; } /* * Loads a CRAM .crai index into memory. * * Returns 0 for success * -1 for failure */ int cram_index_load(cram_fd *fd, const char *fn, const char *fn_idx) { char *tfn_idx = NULL; char buf[65536]; ssize_t len; kstring_t kstr = {0}; hFILE *fp; cram_index *idx; cram_index **idx_stack = NULL, *ep, e; int idx_stack_alloc = 0, idx_stack_ptr = 0; size_t pos = 0; /* Check if already loaded */ if (fd->index) return 0; fd->index = calloc((fd->index_sz = 1), sizeof(*fd->index)); if (!fd->index) return -1; idx = &fd->index[0]; idx->refid = -1; idx->start = INT_MIN; idx->end = INT_MAX; idx_stack = calloc(++idx_stack_alloc, sizeof(*idx_stack)); if (!idx_stack) goto fail; idx_stack[idx_stack_ptr] = idx; // Support pathX.cram##idx##pathY.crai const char *fn_delim = strstr(fn, HTS_IDX_DELIM); if (fn_delim && !fn_idx) fn_idx = fn_delim + strlen(HTS_IDX_DELIM); if (!fn_idx) { if (hts_idx_check_local(fn, HTS_FMT_CRAI, &tfn_idx) == 0 && hisremote(fn)) tfn_idx = hts_idx_getfn(fn, ".crai"); if (!tfn_idx) { hts_log_error("Could not retrieve index file for '%s'", fn); goto fail; } fn_idx = tfn_idx; } if (!(fp = hopen(fn_idx, "r"))) { hts_log_error("Could not open index file '%s'", fn_idx); goto fail; } // Load the file into memory while ((len = hread(fp, buf, sizeof(buf))) > 0) { if (kputsn(buf, len, &kstr) < 0) goto fail; } if (len < 0 || kstr.l < 2) goto fail; if (hclose(fp) < 0) goto fail; // Uncompress if required if (kstr.s[0] == 31 && (uc)kstr.s[1] == 139) { size_t l = 0; char *s = zlib_mem_inflate(kstr.s, kstr.l, &l); if (!s) goto fail; free(kstr.s); kstr.s = s; kstr.l = l; kstr.m = l; // conservative estimate of the size allocated if (kputsn("", 0, &kstr) < 0) // ensure kstr.s is NUL-terminated goto fail; } // Parse it line at a time while (pos < kstr.l) { /* 1.1 layout */ if (kget_int32(&kstr, &pos, &e.refid) == -1) goto fail; if (kget_int32(&kstr, &pos, &e.start) == -1) goto fail; if (kget_int32(&kstr, &pos, &e.end) == -1) goto fail; if (kget_int64(&kstr, &pos, &e.offset) == -1) goto fail; if (kget_int32(&kstr, &pos, &e.slice) == -1) goto fail; if (kget_int32(&kstr, &pos, &e.len) == -1) goto fail; e.end += e.start-1; //printf("%d/%d..%d-offset=%" PRIu64 ",len=%d,slice=%d\n", e.refid, e.start, e.end, e.offset, e.len, e.slice); if (e.refid < -1) { hts_log_error("Malformed index file, refid %d", e.refid); goto fail; } if (e.refid != idx->refid) { if (fd->index_sz < e.refid+2) { cram_index *new_idx; int new_sz = e.refid+2; size_t index_end = fd->index_sz * sizeof(*fd->index); new_idx = realloc(fd->index, new_sz * sizeof(*fd->index)); if (!new_idx) goto fail; fd->index = new_idx; fd->index_sz = new_sz; memset(((char *)fd->index) + index_end, 0, fd->index_sz * sizeof(*fd->index) - index_end); } idx = &fd->index[e.refid+1]; idx->refid = e.refid; idx->start = INT_MIN; idx->end = INT_MAX; idx->nslice = idx->nalloc = 0; idx->e = NULL; idx_stack[(idx_stack_ptr = 0)] = idx; } while (!(e.start >= idx->start && e.end <= idx->end) || (idx->start == 0 && idx->refid == -1)) { idx = idx_stack[--idx_stack_ptr]; } // Now contains, so append if (idx->nslice+1 >= idx->nalloc) { cram_index *new_e; idx->nalloc = idx->nalloc ? idx->nalloc*2 : 16; new_e = realloc(idx->e, idx->nalloc * sizeof(*idx->e)); if (!new_e) goto fail; idx->e = new_e; } e.nalloc = e.nslice = 0; e.e = NULL; *(ep = &idx->e[idx->nslice++]) = e; idx = ep; if (++idx_stack_ptr >= idx_stack_alloc) { cram_index **new_stack; idx_stack_alloc *= 2; new_stack = realloc(idx_stack, idx_stack_alloc*sizeof(*idx_stack)); if (!new_stack) goto fail; idx_stack = new_stack; } idx_stack[idx_stack_ptr] = idx; while (pos < kstr.l && kstr.s[pos] != '\n') pos++; pos++; } free(idx_stack); free(kstr.s); free(tfn_idx); // Convert NCList to linear linked list link_index(fd); //dump_index(fd); return 0; fail: free(kstr.s); free(idx_stack); free(tfn_idx); cram_index_free(fd); // Also sets fd->index = NULL return -1; } static void cram_index_free_recurse(cram_index *e) { if (e->e) { int i; for (i = 0; i < e->nslice; i++) { cram_index_free_recurse(&e->e[i]); } free(e->e); } } void cram_index_free(cram_fd *fd) { int i; if (!fd->index) return; for (i = 0; i < fd->index_sz; i++) { cram_index_free_recurse(&fd->index[i]); } free(fd->index); fd->index = NULL; } /* * Searches the index for the first slice overlapping a reference ID * and position, or one immediately preceding it if none is found in * the index to overlap this position. (Our index may have missing * entries, but we require at least one per reference.) * * If the index finds multiple slices overlapping this position we * return the first one only. Subsequent calls should specify * "from" as the last slice we checked to find the next one. Otherwise * set "from" to be NULL to find the first one. * * Refid can also be any of the special HTS_IDX_ values. * For backwards compatibility, refid -1 is equivalent to HTS_IDX_NOCOOR. * * Returns the cram_index pointer on success * NULL on failure */ cram_index *cram_index_query(cram_fd *fd, int refid, hts_pos_t pos, cram_index *from) { int i, j, k; cram_index *e; if (from) { // Continue from a previous search. // We switch to just scanning the linked list, as the nested // lists are typically short. if (refid == HTS_IDX_NOCOOR) refid = -1; e = from->e_next; if (e && e->refid == refid && e->start <= pos) return e; else return NULL; } switch(refid) { case HTS_IDX_NONE: case HTS_IDX_REST: // fail, or already there, dealt with elsewhere. return NULL; case -1: case HTS_IDX_NOCOOR: refid = -1; pos = 0; break; case HTS_IDX_START: { int64_t min_idx = INT64_MAX; for (i = 0, j = -1; i < fd->index_sz; i++) { if (fd->index[i].e && fd->index[i].e[0].offset < min_idx) { min_idx = fd->index[i].e[0].offset; j = i; } } if (j < 0) return NULL; return fd->index[j].e; } default: if (refid < HTS_IDX_NONE || refid+1 >= fd->index_sz) return NULL; } from = &fd->index[refid+1]; // Ref with nothing aligned against it. if (!from->e) return NULL; // This sequence is covered by the index, so binary search to find // the optimal starting block. i = 0, j = fd->index[refid+1].nslice-1; for (k = j/2; k != i; k = (j-i)/2 + i) { if (from->e[k].refid > refid) { j = k; continue; } if (from->e[k].refid < refid) { i = k; continue; } if (from->e[k].start >= pos) { j = k; continue; } if (from->e[k].start < pos) { i = k; continue; } } // i==j or i==j-1. Check if j is better. if (j >= 0 && from->e[j].start < pos && from->e[j].refid == refid) i = j; /* The above found *a* bin overlapping, but not necessarily the first */ while (i > 0 && from->e[i-1].end >= pos) i--; /* We may be one bin before the optimum, so check */ while (i+1 < from->nslice && (from->e[i].refid < refid || from->e[i].end < pos)) i++; e = &from->e[i]; return e; } // Return the index entry for last slice on a specific reference. cram_index *cram_index_last(cram_fd *fd, int refid, cram_index *from) { int slice; if (refid+1 < 0 || refid+1 >= fd->index_sz) return NULL; if (!from) from = &fd->index[refid+1]; // Ref with nothing aligned against it. if (!from->e) return NULL; slice = fd->index[refid+1].nslice - 1; // e is the last entry in the nested containment list, but it may // contain further slices within it. cram_index *e = &from->e[slice]; while (e->e_next) e = e->e_next; return e; } /* * Find the last container overlapping pos 'end', and the file offset of * its end (equivalent to the start offset of the container following it). */ cram_index *cram_index_query_last(cram_fd *fd, int refid, hts_pos_t end) { cram_index *e = NULL, *prev_e; do { prev_e = e; e = cram_index_query(fd, refid, end, prev_e); } while (e); if (!prev_e) return NULL; e = prev_e; // Note: offset of e and e->e_next may be the same if we're using a // multi-ref container where a single container generates multiple // index entries. // // We need to keep iterating until offset differs in order to find // the genuine file offset for the end of container. do { prev_e = e; e = e->e_next; } while (e && e->offset == prev_e->offset); return prev_e; } /* * Skips to a container overlapping the start coordinate listed in * cram_range. * * In theory we call cram_index_query multiple times, once per slice * overlapping the range. However slices may be absent from the index * which makes this problematic. Instead we find the left-most slice * and then read from then on, skipping decoding of slices and/or * whole containers when they don't overlap the specified cram_range. * * This function also updates the cram_fd range field. * * Returns 0 on success * -1 on general failure * -2 on no-data (empty chromosome) */ int cram_seek_to_refpos(cram_fd *fd, cram_range *r) { int ret = 0; cram_index *e; if (r->refid == HTS_IDX_NONE) { ret = -2; goto err; } // Ideally use an index, so see if we have one. if ((e = cram_index_query(fd, r->refid, r->start, NULL))) { if (0 != cram_seek(fd, e->offset, SEEK_SET)) { if (0 != cram_seek(fd, e->offset - fd->first_container, SEEK_CUR)) { ret = -1; goto err; } } } else { // Absent from index, but this most likely means it simply has no data. ret = -2; goto err; } pthread_mutex_lock(&fd->range_lock); fd->range = *r; if (r->refid == HTS_IDX_NOCOOR) { fd->range.refid = -1; fd->range.start = 0; } else if (r->refid == HTS_IDX_START || r->refid == HTS_IDX_REST) { fd->range.refid = -2; // special case in cram_next_slice } pthread_mutex_unlock(&fd->range_lock); if (fd->ctr) { cram_free_container(fd->ctr); if (fd->ctr_mt && fd->ctr_mt != fd->ctr) cram_free_container(fd->ctr_mt); fd->ctr = NULL; fd->ctr_mt = NULL; fd->ooc = 0; fd->eof = 0; } return 0; err: // It's unlikely fd->range will be accessed after EOF or error, // but this maintains identical behaviour to the previous code. pthread_mutex_lock(&fd->range_lock); fd->range = *r; pthread_mutex_unlock(&fd->range_lock); return ret; } /* * A specialised form of cram_index_build (below) that deals with slices * having multiple references in this (ref_id -2). In this scenario we * decode the slice to look at the RI data series instead. * * Returns 0 on success * -1 on read failure * -2 on wrong sort order * -4 on write failure */ static int cram_index_build_multiref(cram_fd *fd, cram_container *c, cram_slice *s, BGZF *fp, off_t cpos, int32_t landmark, int sz) { int i, ref = -2; int64_t ref_start = 0, ref_end; char buf[1024]; if (fd->mode != 'w') { if (0 != cram_decode_slice(fd, c, s, fd->header)) return -1; } ref_end = INT_MIN; int32_t last_ref = -9; int32_t last_pos = -9; for (i = 0; i < s->hdr->num_records; i++) { if (s->crecs[i].ref_id == last_ref && s->crecs[i].apos < last_pos) { hts_log_error("CRAM file is not sorted by chromosome / position"); return -2; } last_ref = s->crecs[i].ref_id; last_pos = s->crecs[i].apos; if (s->crecs[i].ref_id == ref) { if (ref_end < s->crecs[i].aend) ref_end = s->crecs[i].aend; continue; } if (ref != -2) { snprintf(buf, sizeof(buf), "%d\t%"PRId64"\t%"PRId64"\t%"PRId64"\t%d\t%d\n", ref, ref_start, ref_end - ref_start + 1, (int64_t)cpos, landmark, sz); if (bgzf_write(fp, buf, strlen(buf)) < 0) return -4; } ref = s->crecs[i].ref_id; ref_start = s->crecs[i].apos; ref_end = s->crecs[i].aend; } if (ref != -2) { snprintf(buf, sizeof(buf), "%d\t%"PRId64"\t%"PRId64"\t%"PRId64"\t%d\t%d\n", ref, ref_start, ref_end - ref_start + 1, (int64_t)cpos, landmark, sz); if (bgzf_write(fp, buf, strlen(buf)) < 0) return -4; } return 0; } /* * Adds a single slice to the index. */ int cram_index_slice(cram_fd *fd, cram_container *c, cram_slice *s, BGZF *fp, off_t cpos, off_t spos, // relative to cpos off_t sz) { int ret; char buf[1024]; if (sz > INT_MAX) { hts_log_error("CRAM slice is too big (%"PRId64" bytes)", (int64_t) sz); return -1; } if (s->hdr->ref_seq_id == -2) { ret = cram_index_build_multiref(fd, c, s, fp, cpos, spos, sz); } else { snprintf(buf, sizeof(buf), "%d\t%"PRId64"\t%"PRId64"\t%"PRId64"\t%d\t%d\n", s->hdr->ref_seq_id, s->hdr->ref_seq_start, s->hdr->ref_seq_span, (int64_t)cpos, (int)spos, (int)sz); ret = (bgzf_write(fp, buf, strlen(buf)) >= 0)? 0 : -4; } return ret; } /* * Adds a single container to the index. */ static int cram_index_container(cram_fd *fd, cram_container *c, BGZF *fp, off_t cpos) { int j; off_t spos; // 2.0 format for (j = 0; j < c->num_landmarks; j++) { cram_slice *s; off_t sz; int ret; spos = htell(fd->fp); if (spos - cpos - (off_t) c->offset != c->landmark[j]) { hts_log_error("CRAM slice offset %"PRId64" does not match" " landmark %d in container header (%"PRId32")", (int64_t) (spos - cpos - (off_t) c->offset), j, c->landmark[j]); return -1; } if (!(s = cram_read_slice(fd))) { return -1; } sz = htell(fd->fp) - spos; ret = cram_index_slice(fd, c, s, fp, cpos, c->landmark[j], sz); cram_free_slice(s); if (ret < 0) { return ret; } } return 0; } /* * Builds an index file. * * fd is a newly opened cram file that we wish to index. * fn_base is the filename of the associated CRAM file. * fn_idx is the filename of the index file to be written; * if NULL, we add ".crai" to fn_base to get the index filename. * * Returns 0 on success, * negative on failure (-1 for read failure, -4 for write failure) */ int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx) { cram_container *c; off_t cpos, hpos; BGZF *fp; kstring_t fn_idx_str = {0}; int64_t last_ref = -9, last_start = -9; // Useful for cram_index_build_multiref cram_set_option(fd, CRAM_OPT_REQUIRED_FIELDS, SAM_RNAME | SAM_POS | SAM_CIGAR); if (! fn_idx) { kputs(fn_base, &fn_idx_str); kputs(".crai", &fn_idx_str); fn_idx = fn_idx_str.s; } if (!(fp = bgzf_open(fn_idx, "wg"))) { perror(fn_idx); free(fn_idx_str.s); return -4; } free(fn_idx_str.s); cpos = htell(fd->fp); while ((c = cram_read_container(fd))) { if (fd->err) { perror("Cram container read"); return -1; } hpos = htell(fd->fp); if (!(c->comp_hdr_block = cram_read_block(fd))) return -1; assert(c->comp_hdr_block->content_type == COMPRESSION_HEADER); c->comp_hdr = cram_decode_compression_header(fd, c->comp_hdr_block); if (!c->comp_hdr) return -1; if (c->ref_seq_id == last_ref && c->ref_seq_start < last_start) { hts_log_error("CRAM file is not sorted by chromosome / position"); return -2; } last_ref = c->ref_seq_id; last_start = c->ref_seq_start; if (cram_index_container(fd, c, fp, cpos) < 0) { bgzf_close(fp); return -1; } off_t next_cpos = htell(fd->fp); if (next_cpos != hpos + c->length) { hts_log_error("Length %"PRId32" in container header at offset %lld does not match block lengths (%lld)", c->length, (long long) cpos, (long long) next_cpos - hpos); return -1; } cpos = next_cpos; cram_free_container(c); } if (fd->err) { bgzf_close(fp); return -1; } return (bgzf_close(fp) >= 0)? 0 : -4; } // internal recursive step static int64_t cram_num_containers_between_(cram_index *e, int64_t *last_pos, int64_t nct, off_t cstart, off_t cend, int64_t *first, int64_t *last) { int64_t nc = 0, i; if (e->offset) { if (e->offset != *last_pos) { if (e->offset >= cstart && (!cend || e->offset <= cend)) { if (first && *first < 0) *first = nct; if (last) *last = nct; } nc++; } // else a new multi-ref in same container *last_pos = e->offset; } for (i = 0; i < e->nslice; i++) nc += cram_num_containers_between_(&e->e[i], last_pos, nc + nct, cstart, cend, first, last); return nc; } /*! Returns the number of containers in the CRAM file within given offsets. * * The cstart and cend offsets are the locations of the start of containers * as returned by index_container_offset. * * If non-NULL, first and last will hold the inclusive range of container * numbers, counting from zero. * * @return * Returns the number of containers, equivalent to *last-*first+1. */ int64_t cram_num_containers_between(cram_fd *fd, off_t cstart, off_t cend, int64_t *first, int64_t *last) { int64_t nc = 0, i; int64_t last_pos = -99; int64_t l_first = -1, l_last = -1; for (i = 0; i < fd->index_sz; i++) { int j = i+1 == fd->index_sz ? 0 : i+1; // maps "*" to end nc += cram_num_containers_between_(&fd->index[j], &last_pos, nc, cstart, cend, &l_first, &l_last); } if (first) *first = l_first; if (last) *last = l_last; return l_last - l_first + 1; } /* * Queries the total number of distinct containers in the index. * Note there may be more containers in the file than in the index, as we * are not required to have an index entry for every one. */ int64_t cram_num_containers(cram_fd *fd) { return cram_num_containers_between(fd, 0, 0, NULL, NULL); } /*! Returns the byte offset for the start of the n^th container. * * The index must have previously been loaded, otherwise <0 is returned. */ static cram_index *cram_container_num2offset_(cram_index *e, int num, int64_t *last_pos, int *nc) { if (e->offset) { if (e->offset != *last_pos) { if (*nc == num) return e; (*nc)++; } // else a new multi-ref in same container *last_pos = e->offset; } int i; for (i = 0; i < e->nslice; i++) { cram_index *tmp = cram_container_num2offset_(&e->e[i], num, last_pos, nc); if (tmp) return tmp; } return NULL; } off_t cram_container_num2offset(cram_fd *fd, int64_t num) { int nc = 0, i; int64_t last_pos = -9; cram_index *e = NULL; for (i = 0; i < fd->index_sz; i++) { int j = i+1 == fd->index_sz ? 0 : i+1; // maps "*" to end if (!fd->index[j].nslice) continue; if ((e = cram_container_num2offset_(&fd->index[j], num, &last_pos, &nc))) break; } return e ? e->offset : -1; } /*! Returns the container number for the first container at offset >= pos. * * The index must have previously been loaded, otherwise <0 is returned. */ static cram_index *cram_container_offset2num_(cram_index *e, off_t pos, int64_t *last_pos, int *nc) { if (e->offset) { if (e->offset != *last_pos) { if (e->offset >= pos) return e; (*nc)++; } // else a new multi-ref in same container *last_pos = e->offset; } int i; for (i = 0; i < e->nslice; i++) { cram_index *tmp = cram_container_offset2num_(&e->e[i], pos, last_pos, nc); if (tmp) return tmp; } return NULL; } int64_t cram_container_offset2num(cram_fd *fd, off_t pos) { int nc = 0, i; int64_t last_pos = -9; cram_index *e = NULL; for (i = 0; i < fd->index_sz; i++) { int j = i+1 == fd->index_sz ? 0 : i+1; // maps "*" to end if (!fd->index[j].nslice) continue; if ((e = cram_container_offset2num_(&fd->index[j], pos, &last_pos, &nc))) break; } return e ? nc : -1; } /*! * Returns the file offsets of CRAM containers covering a specific region * query. Note both offsets are the START of the container. * * first will point to the start of the first overlapping container * last will point to the start of the last overlapping container * * Returns 0 on success * <0 on failure */ int cram_index_extents(cram_fd *fd, int refid, hts_pos_t start, hts_pos_t end, off_t *first, off_t *last) { cram_index *ci; if (first) { if (!(ci = cram_index_query(fd, refid, start, NULL))) return -1; *first = ci->offset; } if (last) { if (!(ci = cram_index_query_last(fd, refid, end))) return -1; *last = ci->offset; } return 0; } pysam-0.23.0/htslib/cram/cram_index.h000066400000000000000000000074321475062545500174410ustar00rootroot00000000000000/* Copyright (c) 2013, 2018 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef CRAM_INDEX_H #define CRAM_INDEX_H #ifdef __cplusplus extern "C" { #endif /* * Loads a CRAM .crai index into memory. * Returns 0 for success * -1 for failure */ int cram_index_load(cram_fd *fd, const char *fn, const char *fn_idx); void cram_index_free(cram_fd *fd); /* * Searches the index for the first slice overlapping a reference ID * and position. * * Returns the cram_index pointer on success * NULL on failure */ cram_index *cram_index_query(cram_fd *fd, int refid, hts_pos_t pos, cram_index *frm); cram_index *cram_index_last(cram_fd *fd, int refid, cram_index *from); cram_index *cram_index_query_last(cram_fd *fd, int refid, hts_pos_t end); /* * Skips to a container overlapping the start coordinate listed in * cram_range. * * Returns 0 on success * -1 on failure */ int cram_seek_to_refpos(cram_fd *fd, cram_range *r); void cram_index_free(cram_fd *fd); /* * Skips to a container overlapping the start coordinate listed in * cram_range. * * In theory we call cram_index_query multiple times, once per slice * overlapping the range. However slices may be absent from the index * which makes this problematic. Instead we find the left-most slice * and then read from then on, skipping decoding of slices and/or * whole containers when they don't overlap the specified cram_range. * * Returns 0 on success * -1 on failure */ int cram_seek_to_refpos(cram_fd *fd, cram_range *r); /* * Builds an index file. * * fd is a newly opened cram file that we wish to index. * fn_base is the filename of the associated CRAM file. * fn_idx is the filename of the index file to be written; * if NULL, we add ".crai" to fn_base to get the index filename. * * Returns 0 on success, * negative on failure (-1 for read failure, -4 for write failure) */ int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx); /* * Adds a single slice to the index. * * Returns 0 on success, * -1 on failure */ int cram_index_slice(cram_fd *fd, cram_container *c, cram_slice *s, BGZF *fp, off_t cpos, off_t spos, // relative to cpos off_t sz); #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/cram/cram_io.c000066400000000000000000005312671475062545500167440ustar00rootroot00000000000000/* Copyright (c) 2012-2024 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /* * CRAM I/O primitives. * * - ITF8 encoding and decoding. * - Block based I/O * - Zlib inflating and deflating (memory) * - CRAM basic data structure reading and writing * - File opening / closing * - Reference sequence handling */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #ifdef HAVE_LIBBZ2 #include #endif #ifdef HAVE_LIBLZMA #ifdef HAVE_LZMA_H #include #else #include "../os/lzma_stub.h" #endif #endif #include #include #include #include #ifdef HAVE_LIBDEFLATE #include #define crc32(a,b,c) libdeflate_crc32((a),(b),(c)) #endif #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION #include "../fuzz_settings.h" #endif #include "cram.h" #include "os.h" #include "../htslib/hts.h" #include "open_trace_file.h" #if defined(HAVE_EXTERNAL_LIBHTSCODECS) #include #include #include #include #include #include // CRAM v4.0 variable-size integers #else #include "../htscodecs/htscodecs/rANS_static.h" #include "../htscodecs/htscodecs/rANS_static4x16.h" #include "../htscodecs/htscodecs/arith_dynamic.h" #include "../htscodecs/htscodecs/tokenise_name3.h" #include "../htscodecs/htscodecs/fqzcomp_qual.h" #include "../htscodecs/htscodecs/varint.h" #endif //#define REF_DEBUG #ifdef REF_DEBUG #include #define gettid() (int)syscall(SYS_gettid) #define RP(...) fprintf (stderr, __VA_ARGS__) #else #define RP(...) #endif #include "../htslib/hfile.h" #include "../htslib/bgzf.h" #include "../htslib/faidx.h" #include "../hts_internal.h" #ifndef PATH_MAX #define PATH_MAX FILENAME_MAX #endif #define TRIAL_SPAN 70 #define NTRIALS 3 #define CRAM_DEFAULT_LEVEL 5 /* ---------------------------------------------------------------------- * ITF8 encoding and decoding. * * Also see the itf8_get and itf8_put macros in cram_io.h */ /* * LEGACY: consider using itf8_decode_crc. * * Reads an integer in ITF-8 encoding from 'cp' and stores it in * *val. * * Returns the number of bytes read on success * -1 on failure */ int itf8_decode(cram_fd *fd, int32_t *val_p) { static int nbytes[16] = { 0,0,0,0, 0,0,0,0, // 0000xxxx - 0111xxxx 1,1,1,1, // 1000xxxx - 1011xxxx 2,2, // 1100xxxx - 1101xxxx 3, // 1110xxxx 4, // 1111xxxx }; static int nbits[16] = { 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, // 0000xxxx - 0111xxxx 0x3f, 0x3f, 0x3f, 0x3f, // 1000xxxx - 1011xxxx 0x1f, 0x1f, // 1100xxxx - 1101xxxx 0x0f, // 1110xxxx 0x0f, // 1111xxxx }; int32_t val = hgetc(fd->fp); if (val == -1) return -1; int i = nbytes[val>>4]; val &= nbits[val>>4]; switch(i) { case 0: *val_p = val; return 1; case 1: val = (val<<8) | (unsigned char)hgetc(fd->fp); *val_p = val; return 2; case 2: val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); *val_p = val; return 3; case 3: val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); *val_p = val; return 4; case 4: // really 3.5 more, why make it different? val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<4) | (((unsigned char)hgetc(fd->fp)) & 0x0f); *val_p = val; } return 5; } int itf8_decode_crc(cram_fd *fd, int32_t *val_p, uint32_t *crc) { static int nbytes[16] = { 0,0,0,0, 0,0,0,0, // 0000xxxx - 0111xxxx 1,1,1,1, // 1000xxxx - 1011xxxx 2,2, // 1100xxxx - 1101xxxx 3, // 1110xxxx 4, // 1111xxxx }; static int nbits[16] = { 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, // 0000xxxx - 0111xxxx 0x3f, 0x3f, 0x3f, 0x3f, // 1000xxxx - 1011xxxx 0x1f, 0x1f, // 1100xxxx - 1101xxxx 0x0f, // 1110xxxx 0x0f, // 1111xxxx }; unsigned char c[5]; int32_t val = hgetc(fd->fp); if (val == -1) return -1; c[0]=val; int i = nbytes[val>>4]; val &= nbits[val>>4]; if (i > 0) { if (hread(fd->fp, &c[1], i) < i) return -1; } switch(i) { case 0: *val_p = val; *crc = crc32(*crc, c, 1); return 1; case 1: val = (val<<8) | c[1]; *val_p = val; *crc = crc32(*crc, c, 2); return 2; case 2: val = (val<<8) | c[1]; val = (val<<8) | c[2]; *val_p = val; *crc = crc32(*crc, c, 3); return 3; case 3: val = (val<<8) | c[1]; val = (val<<8) | c[2]; val = (val<<8) | c[3]; *val_p = val; *crc = crc32(*crc, c, 4); return 4; case 4: // really 3.5 more, why make it different? { uint32_t uv = val; uv = (uv<<8) | c[1]; uv = (uv<<8) | c[2]; uv = (uv<<8) | c[3]; uv = (uv<<4) | (c[4] & 0x0f); // Avoid implementation-defined behaviour on negative values *val_p = uv < 0x80000000UL ? (int32_t) uv : -((int32_t) (0xffffffffUL - uv)) - 1; *crc = crc32(*crc, c, 5); } } return 5; } /* * Stores a value to memory in ITF-8 format. * * Returns the number of bytes required to store the number. * This is a maximum of 5 bytes. */ static inline int itf8_put(char *cp, int32_t val) { unsigned char *up = (unsigned char *)cp; if (!(val & ~0x00000007f)) { // 1 byte *up = val; return 1; } else if (!(val & ~0x00003fff)) { // 2 byte *up++ = (val >> 8 ) | 0x80; *up = val & 0xff; return 2; } else if (!(val & ~0x01fffff)) { // 3 byte *up++ = (val >> 16) | 0xc0; *up++ = (val >> 8 ) & 0xff; *up = val & 0xff; return 3; } else if (!(val & ~0x0fffffff)) { // 4 byte *up++ = (val >> 24) | 0xe0; *up++ = (val >> 16) & 0xff; *up++ = (val >> 8 ) & 0xff; *up = val & 0xff; return 4; } else { // 5 byte *up++ = 0xf0 | ((val>>28) & 0xff); *up++ = (val >> 20) & 0xff; *up++ = (val >> 12) & 0xff; *up++ = (val >> 4 ) & 0xff; *up = val & 0x0f; return 5; } } /* 64-bit itf8 variant */ static inline int ltf8_put(char *cp, int64_t val) { unsigned char *up = (unsigned char *)cp; if (!(val & ~((1LL<<7)-1))) { *up = val; return 1; } else if (!(val & ~((1LL<<(6+8))-1))) { *up++ = (val >> 8 ) | 0x80; *up = val & 0xff; return 2; } else if (!(val & ~((1LL<<(5+2*8))-1))) { *up++ = (val >> 16) | 0xc0; *up++ = (val >> 8 ) & 0xff; *up = val & 0xff; return 3; } else if (!(val & ~((1LL<<(4+3*8))-1))) { *up++ = (val >> 24) | 0xe0; *up++ = (val >> 16) & 0xff; *up++ = (val >> 8 ) & 0xff; *up = val & 0xff; return 4; } else if (!(val & ~((1LL<<(3+4*8))-1))) { *up++ = (val >> 32) | 0xf0; *up++ = (val >> 24) & 0xff; *up++ = (val >> 16) & 0xff; *up++ = (val >> 8 ) & 0xff; *up = val & 0xff; return 5; } else if (!(val & ~((1LL<<(2+5*8))-1))) { *up++ = (val >> 40) | 0xf8; *up++ = (val >> 32) & 0xff; *up++ = (val >> 24) & 0xff; *up++ = (val >> 16) & 0xff; *up++ = (val >> 8 ) & 0xff; *up = val & 0xff; return 6; } else if (!(val & ~((1LL<<(1+6*8))-1))) { *up++ = (val >> 48) | 0xfc; *up++ = (val >> 40) & 0xff; *up++ = (val >> 32) & 0xff; *up++ = (val >> 24) & 0xff; *up++ = (val >> 16) & 0xff; *up++ = (val >> 8 ) & 0xff; *up = val & 0xff; return 7; } else if (!(val & ~((1LL<<(7*8))-1))) { *up++ = (val >> 56) | 0xfe; *up++ = (val >> 48) & 0xff; *up++ = (val >> 40) & 0xff; *up++ = (val >> 32) & 0xff; *up++ = (val >> 24) & 0xff; *up++ = (val >> 16) & 0xff; *up++ = (val >> 8 ) & 0xff; *up = val & 0xff; return 8; } else { *up++ = 0xff; *up++ = (val >> 56) & 0xff; *up++ = (val >> 48) & 0xff; *up++ = (val >> 40) & 0xff; *up++ = (val >> 32) & 0xff; *up++ = (val >> 24) & 0xff; *up++ = (val >> 16) & 0xff; *up++ = (val >> 8 ) & 0xff; *up = val & 0xff; return 9; } } /* * Encodes and writes a single integer in ITF-8 format. * Returns 0 on success * -1 on failure */ int itf8_encode(cram_fd *fd, int32_t val) { char buf[5]; int len = itf8_put(buf, val); return hwrite(fd->fp, buf, len) == len ? 0 : -1; } const int itf8_bytes[16] = { 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 4, 5 }; const int ltf8_bytes[256] = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 7, 7, 8, 9 }; /* * LEGACY: consider using ltf8_decode_crc. */ int ltf8_decode(cram_fd *fd, int64_t *val_p) { int c = hgetc(fd->fp); int64_t val = (unsigned char)c; if (c == -1) return -1; if (val < 0x80) { *val_p = val; return 1; } else if (val < 0xc0) { val = (val<<8) | (unsigned char)hgetc(fd->fp); *val_p = val & (((1LL<<(6+8)))-1); return 2; } else if (val < 0xe0) { val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); *val_p = val & ((1LL<<(5+2*8))-1); return 3; } else if (val < 0xf0) { val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); *val_p = val & ((1LL<<(4+3*8))-1); return 4; } else if (val < 0xf8) { val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); *val_p = val & ((1LL<<(3+4*8))-1); return 5; } else if (val < 0xfc) { val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); *val_p = val & ((1LL<<(2+5*8))-1); return 6; } else if (val < 0xfe) { val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); *val_p = val & ((1LL<<(1+6*8))-1); return 7; } else if (val < 0xff) { val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); *val_p = val & ((1LL<<(7*8))-1); return 8; } else { val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); val = (val<<8) | (unsigned char)hgetc(fd->fp); *val_p = val; } return 9; } int ltf8_decode_crc(cram_fd *fd, int64_t *val_p, uint32_t *crc) { unsigned char c[9]; int64_t val = hgetc(fd->fp); if (val < 0) return -1; c[0] = val; if (val < 0x80) { *val_p = val; *crc = crc32(*crc, c, 1); return 1; } else if (val < 0xc0) { int v = hgetc(fd->fp); if (v < 0) return -1; val = (val<<8) | (c[1]=v); *val_p = val & (((1LL<<(6+8)))-1); *crc = crc32(*crc, c, 2); return 2; } else if (val < 0xe0) { if (hread(fd->fp, &c[1], 2) < 2) return -1; val = (val<<8) | c[1]; val = (val<<8) | c[2]; *val_p = val & ((1LL<<(5+2*8))-1); *crc = crc32(*crc, c, 3); return 3; } else if (val < 0xf0) { if (hread(fd->fp, &c[1], 3) < 3) return -1; val = (val<<8) | c[1]; val = (val<<8) | c[2]; val = (val<<8) | c[3]; *val_p = val & ((1LL<<(4+3*8))-1); *crc = crc32(*crc, c, 4); return 4; } else if (val < 0xf8) { if (hread(fd->fp, &c[1], 4) < 4) return -1; val = (val<<8) | c[1]; val = (val<<8) | c[2]; val = (val<<8) | c[3]; val = (val<<8) | c[4]; *val_p = val & ((1LL<<(3+4*8))-1); *crc = crc32(*crc, c, 5); return 5; } else if (val < 0xfc) { if (hread(fd->fp, &c[1], 5) < 5) return -1; val = (val<<8) | c[1]; val = (val<<8) | c[2]; val = (val<<8) | c[3]; val = (val<<8) | c[4]; val = (val<<8) | c[5]; *val_p = val & ((1LL<<(2+5*8))-1); *crc = crc32(*crc, c, 6); return 6; } else if (val < 0xfe) { if (hread(fd->fp, &c[1], 6) < 6) return -1; val = (val<<8) | c[1]; val = (val<<8) | c[2]; val = (val<<8) | c[3]; val = (val<<8) | c[4]; val = (val<<8) | c[5]; val = (val<<8) | c[6]; *val_p = val & ((1LL<<(1+6*8))-1); *crc = crc32(*crc, c, 7); return 7; } else if (val < 0xff) { uint64_t uval = val; if (hread(fd->fp, &c[1], 7) < 7) return -1; uval = (uval<<8) | c[1]; uval = (uval<<8) | c[2]; uval = (uval<<8) | c[3]; uval = (uval<<8) | c[4]; uval = (uval<<8) | c[5]; uval = (uval<<8) | c[6]; uval = (uval<<8) | c[7]; *val_p = uval & ((1ULL<<(7*8))-1); *crc = crc32(*crc, c, 8); return 8; } else { uint64_t uval; if (hread(fd->fp, &c[1], 8) < 8) return -1; uval = c[1]; uval = (uval<<8) | c[2]; uval = (uval<<8) | c[3]; uval = (uval<<8) | c[4]; uval = (uval<<8) | c[5]; uval = (uval<<8) | c[6]; uval = (uval<<8) | c[7]; uval = (uval<<8) | c[8]; *crc = crc32(*crc, c, 9); // Avoid implementation-defined behaviour on negative values *val_p = c[1] < 0x80 ? (int64_t) uval : -((int64_t) (0xffffffffffffffffULL - uval)) - 1; } return 9; } /* * Pushes a value in ITF8 format onto the end of a block. * This shouldn't be used for high-volume data as it is not the fastest * method. * * Returns the number of bytes written */ int itf8_put_blk(cram_block *blk, int32_t val) { char buf[5]; int sz; sz = itf8_put(buf, val); BLOCK_APPEND(blk, buf, sz); return sz; block_err: return -1; } int ltf8_put_blk(cram_block *blk, int64_t val) { char buf[9]; int sz; sz = ltf8_put(buf, val); BLOCK_APPEND(blk, buf, sz); return sz; block_err: return -1; } static int64_t safe_itf8_get(char **cp, const char *endp, int *err) { const unsigned char *up = (unsigned char *)*cp; if (endp && endp - *cp < 5 && (*cp >= endp || endp - *cp < itf8_bytes[up[0]>>4])) { if (err) *err = 1; return 0; } if (up[0] < 0x80) { (*cp)++; return up[0]; } else if (up[0] < 0xc0) { (*cp)+=2; return ((up[0] <<8) | up[1]) & 0x3fff; } else if (up[0] < 0xe0) { (*cp)+=3; return ((up[0]<<16) | (up[1]<< 8) | up[2]) & 0x1fffff; } else if (up[0] < 0xf0) { (*cp)+=4; uint32_t uv = (((uint32_t)up[0]<<24) | (up[1]<<16) | (up[2]<<8) | up[3]) & 0x0fffffff; return (int32_t)uv; } else { (*cp)+=5; uint32_t uv = (((uint32_t)up[0] & 0x0f)<<28) | (up[1]<<20) | (up[2]<<12) | (up[3]<<4) | (up[4] & 0x0f); return (int32_t)uv; } } static int64_t safe_ltf8_get(char **cp, const char *endp, int *err) { unsigned char *up = (unsigned char *)*cp; if (endp && endp - *cp < 9 && (*cp >= endp || endp - *cp < ltf8_bytes[up[0]])) { if (err) *err = 1; return 0; } if (up[0] < 0x80) { (*cp)++; return up[0]; } else if (up[0] < 0xc0) { (*cp)+=2; return (((uint64_t)up[0]<< 8) | (uint64_t)up[1]) & (((1LL<<(6+8)))-1); } else if (up[0] < 0xe0) { (*cp)+=3; return (((uint64_t)up[0]<<16) | ((uint64_t)up[1]<< 8) | (uint64_t)up[2]) & ((1LL<<(5+2*8))-1); } else if (up[0] < 0xf0) { (*cp)+=4; return (((uint64_t)up[0]<<24) | ((uint64_t)up[1]<<16) | ((uint64_t)up[2]<< 8) | (uint64_t)up[3]) & ((1LL<<(4+3*8))-1); } else if (up[0] < 0xf8) { (*cp)+=5; return (((uint64_t)up[0]<<32) | ((uint64_t)up[1]<<24) | ((uint64_t)up[2]<<16) | ((uint64_t)up[3]<< 8) | (uint64_t)up[4]) & ((1LL<<(3+4*8))-1); } else if (up[0] < 0xfc) { (*cp)+=6; return (((uint64_t)up[0]<<40) | ((uint64_t)up[1]<<32) | ((uint64_t)up[2]<<24) | ((uint64_t)up[3]<<16) | ((uint64_t)up[4]<< 8) | (uint64_t)up[5]) & ((1LL<<(2+5*8))-1); } else if (up[0] < 0xfe) { (*cp)+=7; return (((uint64_t)up[0]<<48) | ((uint64_t)up[1]<<40) | ((uint64_t)up[2]<<32) | ((uint64_t)up[3]<<24) | ((uint64_t)up[4]<<16) | ((uint64_t)up[5]<< 8) | (uint64_t)up[6]) & ((1LL<<(1+6*8))-1); } else if (up[0] < 0xff) { (*cp)+=8; return (((uint64_t)up[1]<<48) | ((uint64_t)up[2]<<40) | ((uint64_t)up[3]<<32) | ((uint64_t)up[4]<<24) | ((uint64_t)up[5]<<16) | ((uint64_t)up[6]<< 8) | (uint64_t)up[7]) & ((1LL<<(7*8))-1); } else { (*cp)+=9; return (((uint64_t)up[1]<<56) | ((uint64_t)up[2]<<48) | ((uint64_t)up[3]<<40) | ((uint64_t)up[4]<<32) | ((uint64_t)up[5]<<24) | ((uint64_t)up[6]<<16) | ((uint64_t)up[7]<< 8) | (uint64_t)up[8]); } } // Wrapper for now static int safe_itf8_put(char *cp, char *cp_end, int32_t val) { return itf8_put(cp, val); } static int safe_ltf8_put(char *cp, char *cp_end, int64_t val) { return ltf8_put(cp, val); } static int itf8_size(int64_t v) { return ((!((v)&~0x7f))?1:(!((v)&~0x3fff))?2:(!((v)&~0x1fffff))?3:(!((v)&~0xfffffff))?4:5); } //----------------------------------------------------------------------------- // CRAM v4.0 onwards uses a different variable sized integer encoding // that is size agnostic. // Local interface to varint.h inline version, so we can use in func ptr. // Note a lot of these use the unsigned interface but take signed int64_t. // This is because the old CRAM ITF8 inteface had signed -1 as unsigned // 0xffffffff. static int uint7_size(int64_t v) { return var_size_u64(v); } static int64_t uint7_get_32(char **cp, const char *endp, int *err) { uint32_t val; int nb = var_get_u32((uint8_t *)(*cp), (const uint8_t *)endp, &val); (*cp) += nb; if (!nb && err) *err = 1; return val; } static int64_t sint7_get_32(char **cp, const char *endp, int *err) { int32_t val; int nb = var_get_s32((uint8_t *)(*cp), (const uint8_t *)endp, &val); (*cp) += nb; if (!nb && err) *err = 1; return val; } static int64_t uint7_get_64(char **cp, const char *endp, int *err) { uint64_t val; int nb = var_get_u64((uint8_t *)(*cp), (const uint8_t *)endp, &val); (*cp) += nb; if (!nb && err) *err = 1; return val; } static int64_t sint7_get_64(char **cp, const char *endp, int *err) { int64_t val; int nb = var_get_s64((uint8_t *)(*cp), (const uint8_t *)endp, &val); (*cp) += nb; if (!nb && err) *err = 1; return val; } static int uint7_put_32(char *cp, char *endp, int32_t val) { return var_put_u32((uint8_t *)cp, (uint8_t *)endp, val); } static int sint7_put_32(char *cp, char *endp, int32_t val) { return var_put_s32((uint8_t *)cp, (uint8_t *)endp, val); } static int uint7_put_64(char *cp, char *endp, int64_t val) { return var_put_u64((uint8_t *)cp, (uint8_t *)endp, val); } static int sint7_put_64(char *cp, char *endp, int64_t val) { return var_put_s64((uint8_t *)cp, (uint8_t *)endp, val); } // Put direct to to cram_block static int uint7_put_blk_32(cram_block *blk, int32_t v) { uint8_t buf[10]; int sz = var_put_u32(buf, buf+10, v); BLOCK_APPEND(blk, buf, sz); return sz; block_err: return -1; } static int sint7_put_blk_32(cram_block *blk, int32_t v) { uint8_t buf[10]; int sz = var_put_s32(buf, buf+10, v); BLOCK_APPEND(blk, buf, sz); return sz; block_err: return -1; } static int uint7_put_blk_64(cram_block *blk, int64_t v) { uint8_t buf[10]; int sz = var_put_u64(buf, buf+10, v); BLOCK_APPEND(blk, buf, sz); return sz; block_err: return -1; } static int sint7_put_blk_64(cram_block *blk, int64_t v) { uint8_t buf[10]; int sz = var_put_s64(buf, buf+10, v); BLOCK_APPEND(blk, buf, sz); return sz; block_err: return -1; } // Decode 32-bits with CRC update from cram_fd static int uint7_decode_crc32(cram_fd *fd, int32_t *val_p, uint32_t *crc) { uint8_t b[5], i = 0; int c; uint32_t v = 0; #ifdef VARINT2 b[0] = hgetc(fd->fp); if (b[0] < 177) { } else if (b[0] < 241) { b[1] = hgetc(fd->fp); } else if (b[0] < 249) { b[1] = hgetc(fd->fp); b[2] = hgetc(fd->fp); } else { int n = b[0]+2, z = 1; while (n-- >= 249) b[z++] = hgetc(fd->fp); } i = var_get_u32(b, NULL, &v); #else // // Little endian // int s = 0; // do { // b[i++] = c = hgetc(fd->fp); // if (c < 0) // return -1; // v |= (c & 0x7f) << s; // s += 7; // } while (i < 5 && (c & 0x80)); // Big endian, see also htscodecs/varint.h do { b[i++] = c = hgetc(fd->fp); if (c < 0) return -1; v = (v<<7) | (c & 0x7f); } while (i < 5 && (c & 0x80)); #endif *crc = crc32(*crc, b, i); *val_p = v; return i; } // Decode 32-bits with CRC update from cram_fd static int sint7_decode_crc32(cram_fd *fd, int32_t *val_p, uint32_t *crc) { uint8_t b[5], i = 0; int c; uint32_t v = 0; #ifdef VARINT2 b[0] = hgetc(fd->fp); if (b[0] < 177) { } else if (b[0] < 241) { b[1] = hgetc(fd->fp); } else if (b[0] < 249) { b[1] = hgetc(fd->fp); b[2] = hgetc(fd->fp); } else { int n = b[0]+2, z = 1; while (n-- >= 249) b[z++] = hgetc(fd->fp); } i = var_get_u32(b, NULL, &v); #else // // Little endian // int s = 0; // do { // b[i++] = c = hgetc(fd->fp); // if (c < 0) // return -1; // v |= (c & 0x7f) << s; // s += 7; // } while (i < 5 && (c & 0x80)); // Big endian, see also htscodecs/varint.h do { b[i++] = c = hgetc(fd->fp); if (c < 0) return -1; v = (v<<7) | (c & 0x7f); } while (i < 5 && (c & 0x80)); #endif *crc = crc32(*crc, b, i); *val_p = (v>>1) ^ -(v&1); return i; } // Decode 64-bits with CRC update from cram_fd static int uint7_decode_crc64(cram_fd *fd, int64_t *val_p, uint32_t *crc) { uint8_t b[10], i = 0; int c; uint64_t v = 0; #ifdef VARINT2 b[0] = hgetc(fd->fp); if (b[0] < 177) { } else if (b[0] < 241) { b[1] = hgetc(fd->fp); } else if (b[0] < 249) { b[1] = hgetc(fd->fp); b[2] = hgetc(fd->fp); } else { int n = b[0]+2, z = 1; while (n-- >= 249) b[z++] = hgetc(fd->fp); } i = var_get_u64(b, NULL, &v); #else // // Little endian // int s = 0; // do { // b[i++] = c = hgetc(fd->fp); // if (c < 0) // return -1; // v |= (c & 0x7f) << s; // s += 7; // } while (i < 10 && (c & 0x80)); // Big endian, see also htscodecs/varint.h do { b[i++] = c = hgetc(fd->fp); if (c < 0) return -1; v = (v<<7) | (c & 0x7f); } while (i < 5 && (c & 0x80)); #endif *crc = crc32(*crc, b, i); *val_p = v; return i; } //----------------------------------------------------------------------------- /* * Decodes a 32-bit little endian value from fd and stores in val. * * Returns the number of bytes read on success * -1 on failure */ static int int32_decode(cram_fd *fd, int32_t *val) { int32_t i; if (4 != hread(fd->fp, &i, 4)) return -1; *val = le_int4(i); return 4; } /* * Encodes a 32-bit little endian value 'val' and writes to fd. * * Returns the number of bytes written on success * -1 on failure */ static int int32_encode(cram_fd *fd, int32_t val) { uint32_t v = le_int4(val); if (4 != hwrite(fd->fp, &v, 4)) return -1; return 4; } /* As int32_decoded/encode, but from/to blocks instead of cram_fd */ int int32_get_blk(cram_block *b, int32_t *val) { if (b->uncomp_size - BLOCK_SIZE(b) < 4) return -1; uint32_t v = ((uint32_t) b->data[b->byte ]) | (((uint32_t) b->data[b->byte+1]) << 8) | (((uint32_t) b->data[b->byte+2]) << 16) | (((uint32_t) b->data[b->byte+3]) << 24); // Avoid implementation-defined behaviour on negative values *val = v < 0x80000000U ? (int32_t) v : -((int32_t) (0xffffffffU - v)) - 1; BLOCK_SIZE(b) += 4; return 4; } /* As int32_decoded/encode, but from/to blocks instead of cram_fd */ int int32_put_blk(cram_block *b, int32_t val) { unsigned char cp[4]; uint32_t v = val; cp[0] = ( v & 0xff); cp[1] = ((v>>8) & 0xff); cp[2] = ((v>>16) & 0xff); cp[3] = ((v>>24) & 0xff); BLOCK_APPEND(b, cp, 4); return 0; block_err: return -1; } #ifdef HAVE_LIBDEFLATE /* ---------------------------------------------------------------------- * libdeflate compression code, with interface to match * zlib_mem_{in,de}flate for simplicity elsewhere. */ // Named the same as the version that uses zlib as we always use libdeflate for // decompression when available. char *zlib_mem_inflate(char *cdata, size_t csize, size_t *size) { struct libdeflate_decompressor *z = libdeflate_alloc_decompressor(); if (!z) { hts_log_error("Call to libdeflate_alloc_decompressor failed"); return NULL; } uint8_t *data = NULL, *new_data; if (!*size) *size = csize*2; for(;;) { new_data = realloc(data, *size); if (!new_data) { hts_log_error("Memory allocation failure"); goto fail; } data = new_data; int ret = libdeflate_gzip_decompress(z, cdata, csize, data, *size, size); // Auto grow output buffer size if needed and try again. // Fortunately for all bar one call of this we know the size already. if (ret == LIBDEFLATE_INSUFFICIENT_SPACE) { (*size) *= 1.5; continue; } if (ret != LIBDEFLATE_SUCCESS) { hts_log_error("Inflate operation failed: %d", ret); goto fail; } else { break; } } libdeflate_free_decompressor(z); return (char *)data; fail: libdeflate_free_decompressor(z); free(data); return NULL; } // Named differently as we use both zlib/libdeflate for compression. static char *libdeflate_deflate(char *data, size_t size, size_t *cdata_size, int level, int strat) { level = level > 0 ? level : 6; // libdeflate doesn't honour -1 as default level *= 1.23; // NB levels go up to 12 here; 5 onwards is +1 level += level>=8; // 5,6,7->6,7,8 8->10 9->12 if (level > 12) level = 12; if (strat == Z_RLE) // not supported by libdeflate level = 1; struct libdeflate_compressor *z = libdeflate_alloc_compressor(level); if (!z) { hts_log_error("Call to libdeflate_alloc_compressor failed"); return NULL; } unsigned char *cdata = NULL; /* Compressed output */ size_t cdata_alloc; cdata = malloc(cdata_alloc = size*1.05+100); if (!cdata) { hts_log_error("Memory allocation failure"); libdeflate_free_compressor(z); return NULL; } *cdata_size = libdeflate_gzip_compress(z, data, size, cdata, cdata_alloc); libdeflate_free_compressor(z); if (*cdata_size == 0) { hts_log_error("Call to libdeflate_gzip_compress failed"); free(cdata); return NULL; } return (char *)cdata; } #else /* ---------------------------------------------------------------------- * zlib compression code - from Gap5's tg_iface_g.c * They're static here as they're only used within the cram_compress_block * and cram_uncompress_block functions, which are the external interface. */ char *zlib_mem_inflate(char *cdata, size_t csize, size_t *size) { z_stream s; unsigned char *data = NULL; /* Uncompressed output */ int data_alloc = 0; int err; /* Starting point at uncompressed size, and scale after that */ data = malloc(data_alloc = csize*1.2+100); if (!data) return NULL; /* Initialise zlib stream */ s.zalloc = Z_NULL; /* use default allocation functions */ s.zfree = Z_NULL; s.opaque = Z_NULL; s.next_in = (unsigned char *)cdata; s.avail_in = csize; s.total_in = 0; s.next_out = data; s.avail_out = data_alloc; s.total_out = 0; //err = inflateInit(&s); err = inflateInit2(&s, 15 + 32); if (err != Z_OK) { hts_log_error("Call to zlib inflateInit failed: %s", s.msg); free(data); return NULL; } /* Decode to 'data' array */ for (;s.avail_in;) { unsigned char *data_tmp; int alloc_inc; s.next_out = &data[s.total_out]; err = inflate(&s, Z_NO_FLUSH); if (err == Z_STREAM_END) break; if (err != Z_OK) { hts_log_error("Call to zlib inflate failed: %s", s.msg); free(data); inflateEnd(&s); return NULL; } /* More to come, so realloc based on growth so far */ alloc_inc = (double)s.avail_in/s.total_in * s.total_out + 100; data = realloc((data_tmp = data), data_alloc += alloc_inc); if (!data) { free(data_tmp); inflateEnd(&s); return NULL; } s.avail_out += alloc_inc; } inflateEnd(&s); *size = s.total_out; return (char *)data; } #endif #if !defined(HAVE_LIBDEFLATE) || LIBDEFLATE_VERSION_MAJOR < 1 || (LIBDEFLATE_VERSION_MAJOR == 1 && LIBDEFLATE_VERSION_MINOR <= 8) static char *zlib_mem_deflate(char *data, size_t size, size_t *cdata_size, int level, int strat) { z_stream s; unsigned char *cdata = NULL; /* Compressed output */ int cdata_alloc = 0; int cdata_pos = 0; int err; cdata = malloc(cdata_alloc = size*1.05+100); if (!cdata) return NULL; cdata_pos = 0; /* Initialise zlib stream */ s.zalloc = Z_NULL; /* use default allocation functions */ s.zfree = Z_NULL; s.opaque = Z_NULL; s.next_in = (unsigned char *)data; s.avail_in = size; s.total_in = 0; s.next_out = cdata; s.avail_out = cdata_alloc; s.total_out = 0; s.data_type = Z_BINARY; err = deflateInit2(&s, level, Z_DEFLATED, 15|16, 9, strat); if (err != Z_OK) { hts_log_error("Call to zlib deflateInit2 failed: %s", s.msg); return NULL; } /* Encode to 'cdata' array */ for (;s.avail_in;) { s.next_out = &cdata[cdata_pos]; s.avail_out = cdata_alloc - cdata_pos; if (cdata_alloc - cdata_pos <= 0) { hts_log_error("Deflate produced larger output than expected"); return NULL; } err = deflate(&s, Z_NO_FLUSH); cdata_pos = cdata_alloc - s.avail_out; if (err != Z_OK) { hts_log_error("Call to zlib deflate failed: %s", s.msg); break; } } if (deflate(&s, Z_FINISH) != Z_STREAM_END) { hts_log_error("Call to zlib deflate failed: %s", s.msg); } *cdata_size = s.total_out; if (deflateEnd(&s) != Z_OK) { hts_log_error("Call to zlib deflate failed: %s", s.msg); } return (char *)cdata; } #endif #ifdef HAVE_LIBLZMA /* ------------------------------------------------------------------------ */ /* * Data compression routines using liblzma (xz) * * On a test set this shrunk the main db from 136157104 bytes to 114796168, but * caused tg_index to grow from 2m43.707s to 15m3.961s. Exporting as bfastq * went from 18.3s to 36.3s. So decompression suffers too, but not as bad * as compression times. * * For now we disable this functionality. If it's to be reenabled make sure you * improve the mem_inflate implementation as it's just a test hack at the * moment. */ static char *lzma_mem_deflate(char *data, size_t size, size_t *cdata_size, int level) { char *out; size_t out_size = lzma_stream_buffer_bound(size); *cdata_size = 0; out = malloc(out_size); /* Single call compression */ if (LZMA_OK != lzma_easy_buffer_encode(level, LZMA_CHECK_CRC32, NULL, (uint8_t *)data, size, (uint8_t *)out, cdata_size, out_size)) return NULL; return out; } static char *lzma_mem_inflate(char *cdata, size_t csize, size_t *size) { lzma_stream strm = LZMA_STREAM_INIT; size_t out_size = 0, out_pos = 0; char *out = NULL, *new_out; int r; /* Initiate the decoder */ if (LZMA_OK != lzma_stream_decoder(&strm, lzma_easy_decoder_memusage(9), 0)) return NULL; /* Decode loop */ strm.avail_in = csize; strm.next_in = (uint8_t *)cdata; for (;strm.avail_in;) { if (strm.avail_in > out_size - out_pos) { out_size += strm.avail_in * 4 + 32768; new_out = realloc(out, out_size); if (!new_out) goto fail; out = new_out; } strm.avail_out = out_size - out_pos; strm.next_out = (uint8_t *)&out[out_pos]; r = lzma_code(&strm, LZMA_RUN); if (LZMA_OK != r && LZMA_STREAM_END != r) { hts_log_error("LZMA decode failure (error %d)", r); goto fail; } out_pos = strm.total_out; if (r == LZMA_STREAM_END) break; } /* finish up any unflushed data; necessary? */ r = lzma_code(&strm, LZMA_FINISH); if (r != LZMA_OK && r != LZMA_STREAM_END) { hts_log_error("Call to lzma_code failed with error %d", r); goto fail; } new_out = realloc(out, strm.total_out > 0 ? strm.total_out : 1); if (new_out) out = new_out; *size = strm.total_out; lzma_end(&strm); return out; fail: lzma_end(&strm); free(out); return NULL; } #endif /* ---------------------------------------------------------------------- * CRAM blocks - the dynamically growable data block. We have code to * create, update, (un)compress and read/write. * * These are derived from the deflate_interlaced.c blocks, but with the * CRAM extension of content types and IDs. */ /* * Allocates a new cram_block structure with a specified content_type and * id. * * Returns block pointer on success * NULL on failure */ cram_block *cram_new_block(enum cram_content_type content_type, int content_id) { cram_block *b = malloc(sizeof(*b)); if (!b) return NULL; b->method = b->orig_method = RAW; b->content_type = content_type; b->content_id = content_id; b->comp_size = 0; b->uncomp_size = 0; b->data = NULL; b->alloc = 0; b->byte = 0; b->bit = 7; // MSB b->crc32 = 0; b->idx = 0; b->m = NULL; return b; } /* * Reads a block from a cram file. * Returns cram_block pointer on success. * NULL on failure */ cram_block *cram_read_block(cram_fd *fd) { cram_block *b = malloc(sizeof(*b)); unsigned char c; uint32_t crc = 0; if (!b) return NULL; //fprintf(stderr, "Block at %d\n", (int)ftell(fd->fp)); if (-1 == (b->method = hgetc(fd->fp))) { free(b); return NULL; } c = b->method; crc = crc32(crc, &c, 1); if (-1 == (b->content_type= hgetc(fd->fp))) { free(b); return NULL; } c = b->content_type; crc = crc32(crc, &c, 1); if (-1 == fd->vv.varint_decode32_crc(fd, &b->content_id, &crc)) { free(b); return NULL; } if (-1 == fd->vv.varint_decode32_crc(fd, &b->comp_size, &crc)) { free(b); return NULL; } if (-1 == fd->vv.varint_decode32_crc(fd, &b->uncomp_size, &crc)) { free(b); return NULL; } //fprintf(stderr, " method %d, ctype %d, cid %d, csize %d, ucsize %d\n", // b->method, b->content_type, b->content_id, b->comp_size, b->uncomp_size); if (b->method == RAW) { if (b->uncomp_size < 0 || b->comp_size != b->uncomp_size) { free(b); return NULL; } b->alloc = b->uncomp_size; if (!(b->data = malloc(b->uncomp_size))){ free(b); return NULL; } if (b->uncomp_size != hread(fd->fp, b->data, b->uncomp_size)) { free(b->data); free(b); return NULL; } } else { if (b->comp_size < 0 || b->uncomp_size < 0) { free(b); return NULL; } b->alloc = b->comp_size; if (!(b->data = malloc(b->comp_size))) { free(b); return NULL; } if (b->comp_size != hread(fd->fp, b->data, b->comp_size)) { free(b->data); free(b); return NULL; } } if (CRAM_MAJOR_VERS(fd->version) >= 3) { if (-1 == int32_decode(fd, (int32_t *)&b->crc32)) { free(b->data); free(b); return NULL; } b->crc32_checked = fd->ignore_md5; b->crc_part = crc; } else { b->crc32_checked = 1; // CRC not present } b->orig_method = b->method; b->idx = 0; b->byte = 0; b->bit = 7; // MSB return b; } /* * Computes the size of a cram block, including the block * header itself. */ uint32_t cram_block_size(cram_block *b) { unsigned char dat[100], *cp = dat;; uint32_t sz; *cp++ = b->method; *cp++ = b->content_type; cp += itf8_put((char*)cp, b->content_id); cp += itf8_put((char*)cp, b->comp_size); cp += itf8_put((char*)cp, b->uncomp_size); sz = cp-dat + 4; sz += b->method == RAW ? b->uncomp_size : b->comp_size; return sz; } /* * Writes a CRAM block. * Returns 0 on success * -1 on failure */ int cram_write_block(cram_fd *fd, cram_block *b) { char vardata[100]; int vardata_o = 0; assert(b->method != RAW || (b->comp_size == b->uncomp_size)); if (hputc(b->method, fd->fp) == EOF) return -1; if (hputc(b->content_type, fd->fp) == EOF) return -1; vardata_o += fd->vv.varint_put32(vardata , vardata+100, b->content_id); vardata_o += fd->vv.varint_put32(vardata+vardata_o, vardata+100, b->comp_size); vardata_o += fd->vv.varint_put32(vardata+vardata_o, vardata+100, b->uncomp_size); if (vardata_o != hwrite(fd->fp, vardata, vardata_o)) return -1; if (b->data) { if (b->method == RAW) { if (b->uncomp_size != hwrite(fd->fp, b->data, b->uncomp_size)) return -1; } else { if (b->comp_size != hwrite(fd->fp, b->data, b->comp_size)) return -1; } } else { // Absent blocks should be size 0 assert(b->method == RAW && b->uncomp_size == 0); } if (CRAM_MAJOR_VERS(fd->version) >= 3) { char dat[100], *cp = (char *)dat; uint32_t crc; *cp++ = b->method; *cp++ = b->content_type; cp += fd->vv.varint_put32(cp, dat+100, b->content_id); cp += fd->vv.varint_put32(cp, dat+100, b->comp_size); cp += fd->vv.varint_put32(cp, dat+100, b->uncomp_size); crc = crc32(0L, (uc *)dat, cp-dat); if (b->method == RAW) { b->crc32 = crc32(crc, b->data ? b->data : (uc*)"", b->uncomp_size); } else { b->crc32 = crc32(crc, b->data ? b->data : (uc*)"", b->comp_size); } if (-1 == int32_encode(fd, b->crc32)) return -1; } return 0; } /* * Frees a CRAM block, deallocating internal data too. */ void cram_free_block(cram_block *b) { if (!b) return; if (b->data) free(b->data); free(b); } /* * Uncompresses a CRAM block, if compressed. */ int cram_uncompress_block(cram_block *b) { char *uncomp; size_t uncomp_size = 0; #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION // Pretend the CRC was OK so the fuzzer doesn't have to get it right b->crc32_checked = 1; #endif if (b->crc32_checked == 0) { uint32_t crc = crc32(b->crc_part, b->data ? b->data : (uc *)"", b->alloc); b->crc32_checked = 1; if (crc != b->crc32) { hts_log_error("Block CRC32 failure"); return -1; } } if (b->uncomp_size == 0) { // blank block b->method = RAW; return 0; } assert(b->uncomp_size >= 0); // cram_read_block should ensure this switch (b->method) { case RAW: return 0; case GZIP: uncomp_size = b->uncomp_size; uncomp = zlib_mem_inflate((char *)b->data, b->comp_size, &uncomp_size); if (!uncomp) return -1; if (uncomp_size != b->uncomp_size) { free(uncomp); return -1; } free(b->data); b->data = (unsigned char *)uncomp; b->alloc = uncomp_size; b->method = RAW; break; #ifdef HAVE_LIBBZ2 case BZIP2: { unsigned int usize = b->uncomp_size; if (!(uncomp = malloc(usize))) return -1; if (BZ_OK != BZ2_bzBuffToBuffDecompress(uncomp, &usize, (char *)b->data, b->comp_size, 0, 0)) { free(uncomp); return -1; } free(b->data); b->data = (unsigned char *)uncomp; b->alloc = usize; b->method = RAW; b->uncomp_size = usize; // Just in case it differs break; } #else case BZIP2: hts_log_error("Bzip2 compression is not compiled into this version. Please rebuild and try again"); return -1; #endif #ifdef HAVE_LIBLZMA case LZMA: uncomp = lzma_mem_inflate((char *)b->data, b->comp_size, &uncomp_size); if (!uncomp) return -1; if (uncomp_size != b->uncomp_size) { free(uncomp); return -1; } free(b->data); b->data = (unsigned char *)uncomp; b->alloc = uncomp_size; b->method = RAW; break; #else case LZMA: hts_log_error("Lzma compression is not compiled into this version. Please rebuild and try again"); return -1; break; #endif case RANS: { unsigned int usize = b->uncomp_size, usize2; uncomp = (char *)rans_uncompress(b->data, b->comp_size, &usize2); if (!uncomp) return -1; if (usize != usize2) { free(uncomp); return -1; } free(b->data); b->data = (unsigned char *)uncomp; b->alloc = usize2; b->method = RAW; b->uncomp_size = usize2; // Just in case it differs //fprintf(stderr, "Expanded %d to %d\n", b->comp_size, b->uncomp_size); break; } case FQZ: { uncomp_size = b->uncomp_size; uncomp = fqz_decompress((char *)b->data, b->comp_size, &uncomp_size, NULL, 0); if (!uncomp) return -1; free(b->data); b->data = (unsigned char *)uncomp; b->alloc = uncomp_size; b->method = RAW; b->uncomp_size = uncomp_size; break; } case RANS_PR0: { unsigned int usize = b->uncomp_size, usize2; uncomp = (char *)rans_uncompress_4x16(b->data, b->comp_size, &usize2); if (!uncomp) return -1; if (usize != usize2) { free(uncomp); return -1; } b->orig_method = RANS_PR0 + (b->data[0]&1) + 2*((b->data[0]&0x40)>0) + 4*((b->data[0]&0x80)>0); free(b->data); b->data = (unsigned char *)uncomp; b->alloc = usize2; b->method = RAW; b->uncomp_size = usize2; // Just incase it differs //fprintf(stderr, "Expanded %d to %d\n", b->comp_size, b->uncomp_size); break; } case ARITH_PR0: { unsigned int usize = b->uncomp_size, usize2; uncomp = (char *)arith_uncompress_to(b->data, b->comp_size, NULL, &usize2); if (!uncomp) return -1; if (usize != usize2) { free(uncomp); return -1; } b->orig_method = ARITH_PR0 + (b->data[0]&1) + 2*((b->data[0]&0x40)>0) + 4*((b->data[0]&0x80)>0); free(b->data); b->data = (unsigned char *)uncomp; b->alloc = usize2; b->method = RAW; b->uncomp_size = usize2; // Just incase it differs //fprintf(stderr, "Expanded %d to %d\n", b->comp_size, b->uncomp_size); break; } case TOK3: { uint32_t out_len; uint8_t *cp = tok3_decode_names(b->data, b->comp_size, &out_len); if (!cp) return -1; b->orig_method = TOK3; b->method = RAW; free(b->data); b->data = cp; b->alloc = out_len; b->uncomp_size = out_len; break; } default: return -1; } return 0; } static char *cram_compress_by_method(cram_slice *s, char *in, size_t in_size, int content_id, size_t *out_size, enum cram_block_method_int method, int level, int strat) { switch (method) { case GZIP: case GZIP_RLE: case GZIP_1: // Read names bizarrely benefit from zlib over libdeflate for // mid-range compression levels. Focusing purely of ratio or // speed, libdeflate still wins. It also seems to win for // other data series too. // // Eg RN at level 5; libdeflate=55.9MB zlib=51.6MB #ifdef HAVE_LIBDEFLATE # if (LIBDEFLATE_VERSION_MAJOR < 1 || (LIBDEFLATE_VERSION_MAJOR == 1 && LIBDEFLATE_VERSION_MINOR <= 8)) if (content_id == DS_RN && level >= 4 && level <= 7) return zlib_mem_deflate(in, in_size, out_size, level, strat); else # endif return libdeflate_deflate(in, in_size, out_size, level, strat); #else return zlib_mem_deflate(in, in_size, out_size, level, strat); #endif case BZIP2: { #ifdef HAVE_LIBBZ2 unsigned int comp_size = in_size*1.01 + 600; char *comp = malloc(comp_size); if (!comp) return NULL; if (BZ_OK != BZ2_bzBuffToBuffCompress(comp, &comp_size, in, in_size, level, 0, 30)) { free(comp); return NULL; } *out_size = comp_size; return comp; #else return NULL; #endif } case FQZ: case FQZ_b: case FQZ_c: case FQZ_d: { // Extract the necessary portion of the slice into an fqz_slice struct. // These previously were the same thing, but this permits us to detach // the codec from the rest of this CRAM implementation. fqz_slice *f = malloc(2*s->hdr->num_records * sizeof(uint32_t) + sizeof(fqz_slice)); if (!f) return NULL; f->num_records = s->hdr->num_records; f->len = (uint32_t *)(((char *)f) + sizeof(fqz_slice)); f->flags = f->len + s->hdr->num_records; int i; for (i = 0; i < s->hdr->num_records; i++) { f->flags[i] = s->crecs[i].flags; f->len[i] = (i+1 < s->hdr->num_records ? s->crecs[i+1].qual - s->crecs[i].qual : s->block[DS_QS]->uncomp_size - s->crecs[i].qual); } char *comp = fqz_compress(strat & 0xff /* cram vers */, f, in, in_size, out_size, strat >> 8, NULL); free(f); return comp; } case LZMA: #ifdef HAVE_LIBLZMA return lzma_mem_deflate(in, in_size, out_size, level); #else return NULL; #endif case RANS0: case RANS1: { unsigned int out_size_i; unsigned char *cp; cp = rans_compress((unsigned char *)in, in_size, &out_size_i, method == RANS0 ? 0 : 1); *out_size = out_size_i; return (char *)cp; } case RANS_PR0: case RANS_PR1: case RANS_PR64: case RANS_PR9: case RANS_PR128: case RANS_PR129: case RANS_PR192: case RANS_PR193: { unsigned int out_size_i; unsigned char *cp; // see enum cram_block. We map RANS_* methods to order bit-fields static int methmap[] = { 1, 64,9, 128,129, 192,193 }; int m = method == RANS_PR0 ? 0 : methmap[method - RANS_PR1]; cp = rans_compress_4x16((unsigned char *)in, in_size, &out_size_i, m | RANS_ORDER_SIMD_AUTO); *out_size = out_size_i; return (char *)cp; } case ARITH_PR0: case ARITH_PR1: case ARITH_PR64: case ARITH_PR9: case ARITH_PR128: case ARITH_PR129: case ARITH_PR192: case ARITH_PR193: { unsigned int out_size_i; unsigned char *cp; // see enum cram_block. We map ARITH_* methods to order bit-fields static int methmap[] = { 1, 64,9, 128,129, 192,193 }; cp = arith_compress_to((unsigned char *)in, in_size, NULL, &out_size_i, method == ARITH_PR0 ? 0 : methmap[method - ARITH_PR1]); *out_size = out_size_i; return (char *)cp; } case TOK3: case TOKA: { int out_len; int lev = level; if (method == TOK3 && lev > 3) lev = 3; uint8_t *cp = tok3_encode_names(in, in_size, lev, strat, &out_len, NULL); *out_size = out_len; return (char *)cp; } case RAW: break; default: return NULL; } return NULL; } /* * Compresses a block using one of two different zlib strategies. If we only * want one choice set strat2 to be -1. * * The logic here is that sometimes Z_RLE does a better job than Z_FILTERED * or Z_DEFAULT_STRATEGY on quality data. If so, we'd rather use it as it is * significantly faster. * * Method and level -1 implies defaults, as specified in cram_fd. */ int cram_compress_block2(cram_fd *fd, cram_slice *s, cram_block *b, cram_metrics *metrics, int method, int level) { if (!b) return 0; char *comp = NULL; size_t comp_size = 0; int strat; // Internally we have parameterised methods that externally map // to the same CRAM method value. // See enum_cram_block_method_int in cram_structs.h. int methmap[] = { // Externally defined values RAW, GZIP, BZIP2, LZMA, RANS, RANSPR, ARITH, FQZ, TOK3, // Reserved for possible expansion 0, 0, // Internally parameterised versions matching back to above // external values GZIP, GZIP, FQZ, FQZ, FQZ, RANS, RANSPR, RANSPR, RANSPR, RANSPR, RANSPR, RANSPR, RANSPR, TOK3, ARITH, ARITH, ARITH, ARITH, ARITH, ARITH, ARITH, }; if (b->method != RAW) { // Maybe already compressed if s->block[0] was compressed and // we have e.g. s->block[DS_BA] set to s->block[0] due to only // one base type present and hence using E_HUFFMAN on block 0. // A second explicit attempt to compress the same block then // occurs. return 0; } if (method == -1) { method = 1<use_bz2) method |= 1<use_lzma) method |= 1<level; //fprintf(stderr, "IN: block %d, sz %d\n", b->content_id, b->uncomp_size); if (method == RAW || level == 0 || b->uncomp_size == 0) { b->method = RAW; b->comp_size = b->uncomp_size; //fprintf(stderr, "Skip block id %d\n", b->content_id); return 0; } #ifndef ABS # define ABS(a) ((a)>=0?(a):-(a)) #endif if (metrics) { pthread_mutex_lock(&fd->metrics_lock); // Sudden changes in size trigger a retrial. These are mainly // triggered when switching to sorted / unsorted, where the number // of elements in a slice radically changes. // // We also get large fluctuations based on genome coordinate for // e.g. SA:Z and SC series, but we consider the typical scale of // delta between blocks and use this to look for abnormality. // Equivalent to (but minus possible integer overflow) // (b->uncomp_size + 1000)/4 > metrics->input_avg_sz+1000 || // b->uncomp_size + 1000 < (metrics->input_avg_sz+1000)/4) if (metrics->input_avg_sz && (b->uncomp_size/4 - 750 > metrics->input_avg_sz || b->uncomp_size < metrics->input_avg_sz/4 - 750) && ABS(b->uncomp_size-metrics->input_avg_sz)/10 > metrics->input_avg_delta) { metrics->next_trial = 0; } if (metrics->trial > 0 || --metrics->next_trial <= 0) { int m, unpackable = metrics->unpackable; size_t sz_best = b->uncomp_size; size_t sz[CRAM_MAX_METHOD] = {0}; int method_best = 0; // RAW char *c_best = NULL, *c = NULL; metrics->input_avg_delta = 0.9 * (metrics->input_avg_delta + ABS(b->uncomp_size - metrics->input_avg_sz)); metrics->input_avg_sz += b->uncomp_size*.2; metrics->input_avg_sz *= 0.8; if (metrics->revised_method) method = metrics->revised_method; else metrics->revised_method = method; if (metrics->next_trial <= 0) { metrics->next_trial = TRIAL_SPAN; metrics->trial = NTRIALS; for (m = 0; m < CRAM_MAX_METHOD; m++) metrics->sz[m] /= 2; metrics->unpackable = 0; } // Compress this block using the best method if (unpackable && CRAM_MAJOR_VERS(fd->version) > 3) { // No point trying bit-pack if 17+ symbols. if (method & (1<metrics_lock); for (m = 0; m < CRAM_MAX_METHOD; m++) { if (method & (1u<version); break; case FQZ_b: strat = CRAM_MAJOR_VERS(fd->version)+256; break; case FQZ_c: strat = CRAM_MAJOR_VERS(fd->version)+2*256; break; case FQZ_d: strat = CRAM_MAJOR_VERS(fd->version)+3*256; break; case TOK3: strat = 0; break; case TOKA: strat = 1; break; default: strat = 0; } c = cram_compress_by_method(s, (char *)b->data, b->uncomp_size, b->content_id, &sz[m], m, lvl, strat); if (c && sz_best > sz[m]) { sz_best = sz[m]; method_best = m; if (c_best) free(c_best); c_best = c; } else if (c) { free(c); } else { sz[m] = UINT_MAX; // arbitrarily worse than raw } } else { sz[m] = UINT_MAX; // arbitrarily worse than raw } } if (c_best) { free(b->data); b->data = (unsigned char *)c_best; b->method = method_best; // adjusted to methmap[method_best] later b->comp_size = sz_best; } // Accumulate stats for all methods tried pthread_mutex_lock(&fd->metrics_lock); for (m = 0; m < CRAM_MAX_METHOD; m++) // don't be overly sure on small blocks. // +2000 means eg bzip2 vs gzip (1.07 to 1.04) or gz vs rans1 // needs to be at least 60 bytes smaller to overcome the // fixed size addition. metrics->sz[m] += sz[m]+2000; // When enough trials performed, find the best on average if (--metrics->trial == 0) { int best_method = RAW; int best_sz = INT_MAX; // Relative costs of methods. See enum_cram_block_method_int // and methmap double meth_cost[32] = { // Externally defined methods 1, // 0 raw 1.04, // 1 gzip (Z_FILTERED) 1.07, // 2 bzip2 1.08, // 3 lzma 1.00, // 4 rans (O0) 1.00, // 5 ranspr (O0) 1.04, // 6 arithpr (O0) 1.05, // 7 fqz 1.05, // 8 tok3 (rans) 1.00, 1.00, // 9,10 reserved // Paramterised versions of above 1.01, // gzip rle 1.01, // gzip -1 1.05, 1.05, 1.05, // FQZ_b,c,d 1.01, // rans O1 1.01, // rans_pr1 1.00, // rans_pr64; if smaller, usually fast 1.03, // rans_pr65/9 1.00, // rans_pr128 1.01, // rans_pr129 1.00, // rans_pr192 1.01, // rans_pr193 1.07, // tok3 arith 1.04, // arith_pr1 1.04, // arith_pr64 1.04, // arith_pr9 1.03, // arith_pr128 1.04, // arith_pr129 1.04, // arith_pr192 1.04, // arith_pr193 }; // Scale methods by cost based on compression level if (fd->level <= 1) { for (m = 0; m < CRAM_MAX_METHOD; m++) metrics->sz[m] *= 1+(meth_cost[m]-1)*4; } else if (fd->level <= 3) { for (m = 0; m < CRAM_MAX_METHOD; m++) metrics->sz[m] *= 1+(meth_cost[m]-1); } else if (fd->level <= 6) { for (m = 0; m < CRAM_MAX_METHOD; m++) metrics->sz[m] *= 1+(meth_cost[m]-1)/2; } else if (fd->level <= 7) { for (m = 0; m < CRAM_MAX_METHOD; m++) metrics->sz[m] *= 1+(meth_cost[m]-1)/3; } // else cost is ignored // Ensure these are never used; BSC and ZSTD metrics->sz[9] = metrics->sz[10] = INT_MAX; for (m = 0; m < CRAM_MAX_METHOD; m++) { if ((!metrics->sz[m]) || (!(method & (1u< metrics->sz[m]) best_sz = metrics->sz[m], best_method = m; } if (best_method != metrics->method) { //metrics->trial = (NTRIALS+1)/2; // be sure //metrics->next_trial /= 1.5; metrics->consistency = 0; } else { metrics->next_trial *= MIN(2, 1+metrics->consistency/4.0); metrics->consistency++; } metrics->method = best_method; switch (best_method) { case GZIP: strat = Z_FILTERED; break; case GZIP_1: strat = Z_DEFAULT_STRATEGY; break; case GZIP_RLE: strat = Z_RLE; break; case FQZ: strat = CRAM_MAJOR_VERS(fd->version); break; case FQZ_b: strat = CRAM_MAJOR_VERS(fd->version)+256; break; case FQZ_c: strat = CRAM_MAJOR_VERS(fd->version)+2*256; break; case FQZ_d: strat = CRAM_MAJOR_VERS(fd->version)+3*256; break; case TOK3: strat = 0; break; case TOKA: strat = 1; break; default: strat = 0; } metrics->strat = strat; // If we see at least MAXFAIL trials in a row for a specific // compression method with more than MAXDELTA aggregate // size then we drop this from the list of methods used // for this block type. #define MAXDELTA 0.20 #define MAXFAILS 4 for (m = 0; m < CRAM_MAX_METHOD; m++) { if (best_method == m) { metrics->cnt[m] = 0; metrics->extra[m] = 0; } else if (best_sz < metrics->sz[m]) { double r = (double)metrics->sz[m] / best_sz - 1; int mul = 1+(fd->level>=7); if (++metrics->cnt[m] >= MAXFAILS*mul && (metrics->extra[m] += r) >= MAXDELTA*mul) method &= ~(1u<sz[m] > best_sz) method &= ~(1u<verbose > 1 && method != metrics->revised_method) // fprintf(stderr, "%d: revising method from %x to %x\n", // b->content_id, metrics->revised_method, method); metrics->revised_method = method; } pthread_mutex_unlock(&fd->metrics_lock); } else { metrics->input_avg_delta = 0.9 * (metrics->input_avg_delta + ABS(b->uncomp_size - metrics->input_avg_sz)); metrics->input_avg_sz += b->uncomp_size*.2; metrics->input_avg_sz *= 0.8; strat = metrics->strat; method = metrics->method; pthread_mutex_unlock(&fd->metrics_lock); comp = cram_compress_by_method(s, (char *)b->data, b->uncomp_size, b->content_id, &comp_size, method, method == GZIP_1 ? 1 : level, strat); if (!comp) return -1; if (comp_size < b->uncomp_size) { free(b->data); b->data = (unsigned char *)comp; b->comp_size = comp_size; b->method = method; } else { free(comp); } } } else { // no cached metrics, so just do zlib? comp = cram_compress_by_method(s, (char *)b->data, b->uncomp_size, b->content_id, &comp_size, GZIP, level, Z_FILTERED); if (!comp) { hts_log_error("Compression failed!"); return -1; } if (comp_size < b->uncomp_size) { free(b->data); b->data = (unsigned char *)comp; b->comp_size = comp_size; b->method = GZIP; } else { free(comp); } strat = Z_FILTERED; } hts_log_info("Compressed block ID %d from %d to %d by method %s", b->content_id, b->uncomp_size, b->comp_size, cram_block_method2str(b->method)); b->method = methmap[b->method]; return 0; } int cram_compress_block(cram_fd *fd, cram_block *b, cram_metrics *metrics, int method, int level) { return cram_compress_block2(fd, NULL, b, metrics, method, level); } cram_metrics *cram_new_metrics(void) { cram_metrics *m = calloc(1, sizeof(*m)); if (!m) return NULL; m->trial = NTRIALS-1; m->next_trial = TRIAL_SPAN/2; // learn quicker at start m->method = RAW; m->strat = 0; m->revised_method = 0; m->unpackable = 0; return m; } char *cram_block_method2str(enum cram_block_method_int m) { switch(m) { case RAW: return "RAW"; case GZIP: return "GZIP"; case BZIP2: return "BZIP2"; case LZMA: return "LZMA"; case RANS0: return "RANS0"; case RANS1: return "RANS1"; case GZIP_RLE: return "GZIP_RLE"; case GZIP_1: return "GZIP_1"; case FQZ: return "FQZ"; case FQZ_b: return "FQZ_b"; case FQZ_c: return "FQZ_c"; case FQZ_d: return "FQZ_d"; case RANS_PR0: return "RANS_PR0"; case RANS_PR1: return "RANS_PR1"; case RANS_PR64: return "RANS_PR64"; case RANS_PR9: return "RANS_PR9"; case RANS_PR128: return "RANS_PR128"; case RANS_PR129: return "RANS_PR129"; case RANS_PR192: return "RANS_PR192"; case RANS_PR193: return "RANS_PR193"; case TOK3: return "TOK3_R"; case TOKA: return "TOK3_A"; case ARITH_PR0: return "ARITH_PR0"; case ARITH_PR1: return "ARITH_PR1"; case ARITH_PR64: return "ARITH_PR64"; case ARITH_PR9: return "ARITH_PR9"; case ARITH_PR128: return "ARITH_PR128"; case ARITH_PR129: return "ARITH_PR129"; case ARITH_PR192: return "ARITH_PR192"; case ARITH_PR193: return "ARITH_PR193"; case BM_ERROR: break; } return "?"; } char *cram_content_type2str(enum cram_content_type t) { switch (t) { case FILE_HEADER: return "FILE_HEADER"; case COMPRESSION_HEADER: return "COMPRESSION_HEADER"; case MAPPED_SLICE: return "MAPPED_SLICE"; case UNMAPPED_SLICE: return "UNMAPPED_SLICE"; case EXTERNAL: return "EXTERNAL"; case CORE: return "CORE"; case CT_ERROR: break; } return "?"; } /* ---------------------------------------------------------------------- * Reference sequence handling * * These revolve around the refs_t structure, which may potentially be * shared between multiple cram_fd. * * We start with refs_create() to allocate an empty refs_t and then * populate it with @SQ line data using refs_from_header(). This is done on * cram_open(). Also at start up we can call cram_load_reference() which * is used with "scramble -r foo.fa". This replaces the fd->refs with the * new one specified. In either case refs2id() is then called which * maps ref_entry names to @SQ ids (refs_t->ref_id[]). * * Later, possibly within a thread, we will want to know the actual ref * seq itself, obtained by calling cram_get_ref(). This may use the * UR: or M5: fields or the filename specified in the original * cram_load_reference() call. * * Given the potential for multi-threaded reference usage, we have * reference counting (sorry for the confusing double use of "ref") to * track the number of callers interested in any specific reference. */ /* * Frees/unmaps a reference sequence and associated file handles. */ static void ref_entry_free_seq(ref_entry *e) { if (e->mf) mfclose(e->mf); if (e->seq && !e->mf) free(e->seq); e->seq = NULL; e->mf = NULL; } void refs_free(refs_t *r) { RP("refs_free()\n"); if (--r->count > 0) return; if (!r) return; if (r->pool) string_pool_destroy(r->pool); if (r->h_meta) { khint_t k; for (k = kh_begin(r->h_meta); k != kh_end(r->h_meta); k++) { ref_entry *e; if (!kh_exist(r->h_meta, k)) continue; if (!(e = kh_val(r->h_meta, k))) continue; ref_entry_free_seq(e); free(e); } kh_destroy(refs, r->h_meta); } if (r->ref_id) free(r->ref_id); if (r->fp) bgzf_close(r->fp); pthread_mutex_destroy(&r->lock); free(r); } static refs_t *refs_create(void) { refs_t *r = calloc(1, sizeof(*r)); RP("refs_create()\n"); if (!r) return NULL; if (!(r->pool = string_pool_create(8192))) goto err; r->ref_id = NULL; // see refs2id() to populate. r->count = 1; r->last = NULL; r->last_id = -1; if (!(r->h_meta = kh_init(refs))) goto err; pthread_mutex_init(&r->lock, NULL); return r; err: refs_free(r); return NULL; } /* * Opens a reference fasta file as a BGZF stream, allowing for * compressed files. It automatically builds a .fai file if * required and if compressed a .gzi bgzf index too. * * Returns a BGZF handle on success; * NULL on failure. */ static BGZF *bgzf_open_ref(char *fn, char *mode, int is_md5) { BGZF *fp; if (!is_md5 && !hisremote(fn)) { char fai_file[PATH_MAX]; snprintf(fai_file, PATH_MAX, "%s.fai", fn); if (access(fai_file, R_OK) != 0) if (fai_build(fn) != 0) return NULL; } if (!(fp = bgzf_open(fn, mode))) { perror(fn); return NULL; } if (fp->is_compressed == 1 && bgzf_index_load(fp, fn, ".gzi") < 0) { hts_log_error("Unable to load .gzi index '%s.gzi'", fn); bgzf_close(fp); return NULL; } return fp; } /* * Loads a FAI file for a reference.fasta. * "is_err" indicates whether failure to load is worthy of emitting an * error message. In some cases (eg with embedded references) we * speculatively load, just in case, and silently ignore errors. * * Returns the refs_t struct on success (maybe newly allocated); * NULL on failure */ static refs_t *refs_load_fai(refs_t *r_orig, const char *fn, int is_err) { hFILE *fp = NULL; char fai_fn[PATH_MAX]; char line[8192]; refs_t *r = r_orig; size_t fn_l = strlen(fn); int id = 0, id_alloc = 0; RP("refs_load_fai %s\n", fn); if (!r) if (!(r = refs_create())) goto err; if (r->fp) if (bgzf_close(r->fp) != 0) goto err; r->fp = NULL; /* Look for a FASTA##idx##FAI format */ char *fn_delim = strstr(fn, HTS_IDX_DELIM); if (fn_delim) { if (!(r->fn = string_ndup(r->pool, fn, fn_delim - fn))) goto err; fn_delim += strlen(HTS_IDX_DELIM); snprintf(fai_fn, PATH_MAX, "%s", fn_delim); } else { /* An index file was provided, instead of the actual reference file */ if (fn_l > 4 && strcmp(&fn[fn_l-4], ".fai") == 0) { if (!r->fn) { if (!(r->fn = string_ndup(r->pool, fn, fn_l-4))) goto err; } snprintf(fai_fn, PATH_MAX, "%s", fn); } else { /* Only the reference file provided. Get the index file name from it */ if (!(r->fn = string_dup(r->pool, fn))) goto err; snprintf(fai_fn, PATH_MAX, "%.*s.fai", PATH_MAX-5, fn); } } if (!(r->fp = bgzf_open_ref(r->fn, "r", 0))) { hts_log_error("Failed to open reference file '%s'", r->fn); goto err; } if (!(fp = hopen(fai_fn, "r"))) { hts_log_error("Failed to open index file '%s'", fai_fn); if (is_err) perror(fai_fn); goto err; } while (hgets(line, 8192, fp) != NULL) { ref_entry *e = malloc(sizeof(*e)); char *cp; int n; khint_t k; if (!e) return NULL; // id for (cp = line; *cp && !isspace_c(*cp); cp++) ; *cp++ = 0; e->name = string_dup(r->pool, line); // length while (*cp && isspace_c(*cp)) cp++; e->length = strtoll(cp, &cp, 10); // offset while (*cp && isspace_c(*cp)) cp++; e->offset = strtoll(cp, &cp, 10); // bases per line while (*cp && isspace_c(*cp)) cp++; e->bases_per_line = strtol(cp, &cp, 10); // line length while (*cp && isspace_c(*cp)) cp++; e->line_length = strtol(cp, &cp, 10); // filename e->fn = r->fn; e->count = 0; e->seq = NULL; e->mf = NULL; e->is_md5 = 0; e->validated_md5 = 0; k = kh_put(refs, r->h_meta, e->name, &n); if (-1 == n) { free(e); return NULL; } if (n) { kh_val(r->h_meta, k) = e; } else { ref_entry *re = kh_val(r->h_meta, k); if (re && (re->count != 0 || re->length != 0)) { /* Keep old */ free(e); } else { /* Replace old */ if (re) free(re); kh_val(r->h_meta, k) = e; } } if (id >= id_alloc) { ref_entry **new_refs; int x; id_alloc = id_alloc ?id_alloc*2 : 16; new_refs = realloc(r->ref_id, id_alloc * sizeof(*r->ref_id)); if (!new_refs) goto err; r->ref_id = new_refs; for (x = id; x < id_alloc; x++) r->ref_id[x] = NULL; } r->ref_id[id] = e; r->nref = ++id; } if(hclose(fp) < 0) goto err; return r; err: if (fp) hclose_abruptly(fp); if (!r_orig) refs_free(r); return NULL; } /* * Verifies that the CRAM @SQ lines and .fai files match. */ static void sanitise_SQ_lines(cram_fd *fd) { int i; if (!fd->header || !fd->header->hrecs) return; if (!fd->refs || !fd->refs->h_meta) return; for (i = 0; i < fd->header->hrecs->nref; i++) { const char *name = fd->header->hrecs->ref[i].name; khint_t k = kh_get(refs, fd->refs->h_meta, name); ref_entry *r; // We may have @SQ lines which have no known .fai, but do not // in themselves pose a problem because they are unused in the file. if (k == kh_end(fd->refs->h_meta)) continue; if (!(r = (ref_entry *)kh_val(fd->refs->h_meta, k))) continue; if (r->length && r->length != fd->header->hrecs->ref[i].len) { assert(strcmp(r->name, fd->header->hrecs->ref[i].name) == 0); // Should we also check MD5sums here to ensure the correct // reference was given? hts_log_warning("Header @SQ length mismatch for ref %s, %"PRIhts_pos" vs %d", r->name, fd->header->hrecs->ref[i].len, (int)r->length); // Fixing the parsed @SQ header will make MD:Z: strings work // and also stop it producing N for the sequence. fd->header->hrecs->ref[i].len = r->length; } } } /* * Indexes references by the order they appear in a BAM file. This may not * necessarily be the same order they appear in the fasta reference file. * * Returns 0 on success * -1 on failure */ int refs2id(refs_t *r, sam_hdr_t *hdr) { int i; sam_hrecs_t *h = hdr->hrecs; if (r->ref_id) free(r->ref_id); if (r->last) r->last = NULL; r->ref_id = calloc(h->nref, sizeof(*r->ref_id)); if (!r->ref_id) return -1; r->nref = h->nref; for (i = 0; i < h->nref; i++) { khint_t k = kh_get(refs, r->h_meta, h->ref[i].name); if (k != kh_end(r->h_meta)) { r->ref_id[i] = kh_val(r->h_meta, k); } else { hts_log_warning("Unable to find ref name '%s'", h->ref[i].name); } } return 0; } /* * Generates refs_t entries based on @SQ lines in the header. * Returns 0 on success * -1 on failure */ static int refs_from_header(cram_fd *fd) { if (!fd) return -1; refs_t *r = fd->refs; if (!r) return -1; sam_hdr_t *h = fd->header; if (!h) return 0; if (!h->hrecs) { if (-1 == sam_hdr_fill_hrecs(h)) return -1; } if (h->hrecs->nref == 0) return 0; //fprintf(stderr, "refs_from_header for %p mode %c\n", fd, fd->mode); /* Existing refs are fine, as long as they're compatible with the hdr. */ ref_entry **new_ref_id = realloc(r->ref_id, (r->nref + h->hrecs->nref) * sizeof(*r->ref_id)); if (!new_ref_id) return -1; r->ref_id = new_ref_id; int i, j; /* Copy info from h->ref[i] over to r */ for (i = 0, j = r->nref; i < h->hrecs->nref; i++) { sam_hrec_type_t *ty; sam_hrec_tag_t *tag; khint_t k; int n; k = kh_get(refs, r->h_meta, h->hrecs->ref[i].name); if (k != kh_end(r->h_meta)) // Ref already known about continue; if (!(r->ref_id[j] = calloc(1, sizeof(ref_entry)))) return -1; if (!h->hrecs->ref[i].name) return -1; r->ref_id[j]->name = string_dup(r->pool, h->hrecs->ref[i].name); if (!r->ref_id[j]->name) return -1; r->ref_id[j]->length = 0; // marker for not yet loaded /* Initialise likely filename if known */ if ((ty = sam_hrecs_find_type_id(h->hrecs, "SQ", "SN", h->hrecs->ref[i].name))) { if ((tag = sam_hrecs_find_key(ty, "M5", NULL))) { r->ref_id[j]->fn = string_dup(r->pool, tag->str+3); //fprintf(stderr, "Tagging @SQ %s / %s\n", r->ref_id[h]->name, r->ref_id[h]->fn); } } k = kh_put(refs, r->h_meta, r->ref_id[j]->name, &n); if (n <= 0) // already exists or error return -1; kh_val(r->h_meta, k) = r->ref_id[j]; j++; } r->nref = j; return 0; } /* * Attaches a header to a cram_fd. * * This should be used when creating a new cram_fd for writing where * we have a header already constructed (eg from a file we've read * in). */ int cram_set_header2(cram_fd *fd, const sam_hdr_t *hdr) { if (!fd || !hdr ) return -1; if (fd->header != hdr) { if (fd->header) sam_hdr_destroy(fd->header); fd->header = sam_hdr_dup(hdr); if (!fd->header) return -1; } return refs_from_header(fd); } int cram_set_header(cram_fd *fd, sam_hdr_t *hdr) { return cram_set_header2(fd, hdr); } /* * Returns whether the path refers to a directory. */ static int is_directory(char *fn) { struct stat buf; if ( stat(fn,&buf) ) return 0; return S_ISDIR(buf.st_mode); } /* * Converts a directory and a filename into an expanded path, replacing %s * in directory with the filename and %[0-9]+s with portions of the filename * Any remaining parts of filename are added to the end with /%s. */ static int expand_cache_path(char *path, char *dir, const char *fn) { char *cp, *start = path; size_t len; size_t sz = PATH_MAX; while ((cp = strchr(dir, '%'))) { if (cp-dir >= sz) return -1; strncpy(path, dir, cp-dir); path += cp-dir; sz -= cp-dir; if (*++cp == 's') { len = strlen(fn); if (len >= sz) return -1; strcpy(path, fn); path += len; sz -= len; fn += len; cp++; } else if (*cp >= '0' && *cp <= '9') { char *endp; long l; l = strtol(cp, &endp, 10); l = MIN(l, strlen(fn)); if (*endp == 's') { if (l >= sz) return -1; strncpy(path, fn, l); path += l; fn += l; sz -= l; *path = 0; cp = endp+1; } else { if (sz < 3) return -1; *path++ = '%'; *path++ = *cp++; } } else { if (sz < 3) return -1; *path++ = '%'; *path++ = *cp++; } dir = cp; } len = strlen(dir); if (len >= sz) return -1; strcpy(path, dir); path += len; sz -= len; len = strlen(fn) + ((*fn && path > start && path[-1] != '/') ? 1 : 0); if (len >= sz) return -1; if (*fn && path > start && path[-1] != '/') *path++ = '/'; strcpy(path, fn); return 0; } /* * Make the directory containing path and any prefix directories. */ static void mkdir_prefix(char *path, int mode) { char *cp = strrchr(path, '/'); if (!cp) return; *cp = 0; if (is_directory(path)) { *cp = '/'; return; } if (mkdir(path, mode) == 0) { chmod(path, mode); *cp = '/'; return; } mkdir_prefix(path, mode); mkdir(path, mode); chmod(path, mode); *cp = '/'; } /* * Return the cache directory to use, based on the first of these * environment variables to be set to a non-empty value. */ static const char *get_cache_basedir(const char **extra) { char *base; *extra = ""; base = getenv("XDG_CACHE_HOME"); if (base && *base) return base; base = getenv("HOME"); if (base && *base) { *extra = "/.cache"; return base; } base = getenv("TMPDIR"); if (base && *base) return base; base = getenv("TEMP"); if (base && *base) return base; return "/tmp"; } /* * Queries the M5 string from the header and attempts to populate the * reference from this using the REF_PATH environment. * * Returns 0 on success * -1 on failure */ static int cram_populate_ref(cram_fd *fd, int id, ref_entry *r) { char *ref_path = getenv("REF_PATH"); sam_hrec_type_t *ty; sam_hrec_tag_t *tag; char path[PATH_MAX]; kstring_t path_tmp = KS_INITIALIZE; char cache[PATH_MAX], cache_root[PATH_MAX]; char *local_cache = getenv("REF_CACHE"); mFILE *mf; int local_path = 0; hts_log_info("Running cram_populate_ref on fd %p, id %d", (void *)fd, id); cache_root[0] = '\0'; if (!ref_path || *ref_path == '\0') { /* * If we have no ref path, we use the EBI server. * However to avoid spamming it we require a local ref cache too. */ ref_path = "https://www.ebi.ac.uk/ena/cram/md5/%s"; if (!local_cache || *local_cache == '\0') { const char *extra; const char *base = get_cache_basedir(&extra); snprintf(cache_root, PATH_MAX, "%s%s/hts-ref", base, extra); snprintf(cache,PATH_MAX, "%s%s/hts-ref/%%2s/%%2s/%%s", base, extra); local_cache = cache; hts_log_info("Populating local cache: %s", local_cache); } } if (!r->name) return -1; if (!(ty = sam_hrecs_find_type_id(fd->header->hrecs, "SQ", "SN", r->name))) return -1; if (!(tag = sam_hrecs_find_key(ty, "M5", NULL))) goto no_M5; hts_log_info("Querying ref %s", tag->str+3); /* Use cache if available */ if (local_cache && *local_cache) { if (expand_cache_path(path, local_cache, tag->str+3) == 0) local_path = 1; } #ifndef HAVE_MMAP char *path2; /* Search local files in REF_PATH; we can open them and return as above */ if (!local_path && (path2 = find_path(tag->str+3, ref_path))) { int len = snprintf(path, PATH_MAX, "%s", path2); free(path2); if (len > 0 && len < PATH_MAX) // in case it's too long local_path = 1; } #endif /* Found via REF_CACHE or local REF_PATH file */ if (local_path) { struct stat sb; BGZF *fp; if (0 == stat(path, &sb) && S_ISREG(sb.st_mode) && (fp = bgzf_open(path, "r"))) { r->length = sb.st_size; r->offset = r->line_length = r->bases_per_line = 0; r->fn = string_dup(fd->refs->pool, path); if (fd->refs->fp) if (bgzf_close(fd->refs->fp) != 0) return -1; fd->refs->fp = fp; fd->refs->fn = r->fn; r->is_md5 = 1; r->validated_md5 = 1; // Fall back to cram_get_ref() where it'll do the actual // reading of the file. return 0; } } /* Otherwise search full REF_PATH; slower as loads entire file */ if ((mf = open_path_mfile(tag->str+3, ref_path, NULL))) { size_t sz; r->seq = mfsteal(mf, &sz); if (r->seq) { r->mf = NULL; } else { // keep mf around as we couldn't detach r->seq = mf->data; r->mf = mf; } r->length = sz; r->is_md5 = 1; r->validated_md5 = 1; } else { refs_t *refs; const char *fn; no_M5: /* Failed to find in search path or M5 cache, see if @SQ UR: tag? */ if (!(tag = sam_hrecs_find_key(ty, "UR", NULL))) return -1; fn = (strncmp(tag->str+3, "file:", 5) == 0) ? tag->str+8 : tag->str+3; if (fd->refs->fp) { if (bgzf_close(fd->refs->fp) != 0) return -1; fd->refs->fp = NULL; } if (!(refs = refs_load_fai(fd->refs, fn, 0))) return -1; sanitise_SQ_lines(fd); fd->refs = refs; if (fd->refs->fp) { if (bgzf_close(fd->refs->fp) != 0) return -1; fd->refs->fp = NULL; } if (!fd->refs->fn) return -1; if (-1 == refs2id(fd->refs, fd->header)) return -1; if (!fd->refs->ref_id || !fd->refs->ref_id[id]) return -1; // Local copy already, so fall back to cram_get_ref(). return 0; } /* Populate the local disk cache if required */ if (local_cache && *local_cache) { hFILE *fp; if (*cache_root && !is_directory(cache_root)) { hts_log_warning("Creating reference cache directory %s\n" "This may become large; see the samtools(1) manual page REF_CACHE discussion", cache_root); } if (expand_cache_path(path, local_cache, tag->str+3) < 0) { return 0; // Not fatal - we have the data already so keep going. } hts_log_info("Writing cache file '%s'", path); mkdir_prefix(path, 01777); fp = hts_open_tmpfile(path, "wx", &path_tmp); if (!fp) { perror(path_tmp.s); free(path_tmp.s); // Not fatal - we have the data already so keep going. return 0; } // Check md5sum hts_md5_context *md5; char unsigned md5_buf1[16]; char md5_buf2[33]; if (!(md5 = hts_md5_init())) { hclose_abruptly(fp); unlink(path_tmp.s); free(path_tmp.s); return -1; } hts_md5_update(md5, r->seq, r->length); hts_md5_final(md5_buf1, md5); hts_md5_destroy(md5); hts_md5_hex(md5_buf2, md5_buf1); if (strncmp(tag->str+3, md5_buf2, 32) != 0) { hts_log_error("Mismatching md5sum for downloaded reference"); hclose_abruptly(fp); unlink(path_tmp.s); free(path_tmp.s); return -1; } ssize_t length_written = hwrite(fp, r->seq, r->length); if (hclose(fp) < 0 || length_written != r->length || chmod(path_tmp.s, 0444) < 0 || rename(path_tmp.s, path) < 0) { hts_log_error("Creating reference at %s failed: %s", path, strerror(errno)); unlink(path_tmp.s); } } free(path_tmp.s); return 0; } static void cram_ref_incr_locked(refs_t *r, int id) { RP("%d INC REF %d, %d %p\n", gettid(), id, (int)(id>=0 && r->ref_id[id]?r->ref_id[id]->count+1:-999), id>=0 && r->ref_id[id]?r->ref_id[id]->seq:(char *)1); if (id < 0 || !r->ref_id[id] || !r->ref_id[id]->seq) return; if (r->last_id == id) r->last_id = -1; ++r->ref_id[id]->count; } void cram_ref_incr(refs_t *r, int id) { pthread_mutex_lock(&r->lock); cram_ref_incr_locked(r, id); pthread_mutex_unlock(&r->lock); } static void cram_ref_decr_locked(refs_t *r, int id) { RP("%d DEC REF %d, %d %p\n", gettid(), id, (int)(id>=0 && r->ref_id[id]?r->ref_id[id]->count-1:-999), id>=0 && r->ref_id[id]?r->ref_id[id]->seq:(char *)1); if (id < 0 || !r->ref_id[id] || !r->ref_id[id]->seq) { return; } if (--r->ref_id[id]->count <= 0) { assert(r->ref_id[id]->count == 0); if (r->last_id >= 0) { if (r->ref_id[r->last_id]->count <= 0 && r->ref_id[r->last_id]->seq) { RP("%d FREE REF %d (%p)\n", gettid(), r->last_id, r->ref_id[r->last_id]->seq); ref_entry_free_seq(r->ref_id[r->last_id]); if (r->ref_id[r->last_id]->is_md5) r->ref_id[r->last_id]->length = 0; } } r->last_id = id; } } void cram_ref_decr(refs_t *r, int id) { pthread_mutex_lock(&r->lock); cram_ref_decr_locked(r, id); pthread_mutex_unlock(&r->lock); } /* * Used by cram_ref_load and cram_get_ref. The file handle will have * already been opened, so we can catch it. The ref_entry *e informs us * of whether this is a multi-line fasta file or a raw MD5 style file. * Either way we create a single contiguous sequence. * * Returns all or part of a reference sequence on success (malloced); * NULL on failure. */ static char *load_ref_portion(BGZF *fp, ref_entry *e, hts_pos_t start, hts_pos_t end) { off_t offset, len; char *seq; if (end < start) end = start; /* * Compute locations in file. This is trivial for the MD5 files, but * is still necessary for the fasta variants. * * Note the offset here, as with faidx, has the assumption that white- * space (the diff between line_length and bases_per_line) only occurs * at the end of a line of text. */ offset = e->line_length ? e->offset + (start-1)/e->bases_per_line * e->line_length + (start-1) % e->bases_per_line : start-1; len = (e->line_length ? e->offset + (end-1)/e->bases_per_line * e->line_length + (end-1) % e->bases_per_line : end-1) - offset + 1; if (bgzf_useek(fp, offset, SEEK_SET) < 0) { perror("bgzf_useek() on reference file"); return NULL; } if (len == 0 || !(seq = malloc(len))) { return NULL; } if (len != bgzf_read(fp, seq, len)) { perror("bgzf_read() on reference file"); free(seq); return NULL; } /* Strip white-space if required. */ if (len != end-start+1) { hts_pos_t i, j; char *cp = seq; char *cp_to; // Copy up to the first white-space, and then repeatedly just copy // bases_per_line verbatim, and use the slow method to end again. // // This may seem excessive, but this code can be a significant // portion of total CRAM decode CPU time for shallow data sets. for (i = j = 0; i < len; i++) { if (!isspace_c(cp[i])) cp[j++] = cp[i] & ~0x20; else break; } while (i < len && isspace_c(cp[i])) i++; while (i < len - e->line_length) { hts_pos_t j_end = j + e->bases_per_line; while (j < j_end) cp[j++] = cp[i++] & ~0x20; // toupper equiv i += e->line_length - e->bases_per_line; } for (; i < len; i++) { if (!isspace_c(cp[i])) cp[j++] = cp[i] & ~0x20; } cp_to = cp+j; if (cp_to - seq != end-start+1) { hts_log_error("Malformed reference file"); free(seq); return NULL; } } else { int i; for (i = 0; i < len; i++) { seq[i] = toupper_c(seq[i]); } } return seq; } /* * Load the entire reference 'id'. * This also increments the reference count by 1. * * Returns ref_entry on success; * NULL on failure */ ref_entry *cram_ref_load(refs_t *r, int id, int is_md5) { ref_entry *e = r->ref_id[id]; hts_pos_t start = 1, end = e->length; char *seq; if (e->seq) { return e; } assert(e->count == 0); if (r->last) { #ifdef REF_DEBUG int idx = 0; for (idx = 0; idx < r->nref; idx++) if (r->last == r->ref_id[idx]) break; RP("%d cram_ref_load DECR %d\n", gettid(), idx); #endif assert(r->last->count > 0); if (--r->last->count <= 0) { RP("%d FREE REF %d (%p)\n", gettid(), id, r->ref_id[id]->seq); if (r->last->seq) ref_entry_free_seq(r->last); } } if (!r->fn) return NULL; /* Open file if it's not already the current open reference */ if (strcmp(r->fn, e->fn) || r->fp == NULL) { if (r->fp) if (bgzf_close(r->fp) != 0) return NULL; r->fn = e->fn; if (!(r->fp = bgzf_open_ref(r->fn, "r", is_md5))) return NULL; } RP("%d Loading ref %d (%d..%d)\n", gettid(), id, start, end); if (!(seq = load_ref_portion(r->fp, e, start, end))) { return NULL; } RP("%d Loaded ref %d (%d..%d) = %p\n", gettid(), id, start, end, seq); RP("%d INC REF %d, %"PRId64"\n", gettid(), id, (e->count+1)); e->seq = seq; e->mf = NULL; e->count++; /* * Also keep track of last used ref so incr/decr loops on the same * sequence don't cause load/free loops. */ RP("%d cram_ref_load INCR %d => %"PRId64"\n", gettid(), id, e->count+1); r->last = e; e->count++; return e; } /* * Returns a portion of a reference sequence from start to end inclusive. * The returned pointer is owned by either the cram_file fd or by the * internal refs_t structure and should not be freed by the caller. * * The difference is whether or not this refs_t is in use by just the one * cram_fd or by multiples, or whether we have multiple threads accessing * references. In either case fd->shared will be true and we start using * reference counting to track the number of users of a specific reference * sequence. * * Otherwise the ref seq returned is allocated as part of cram_fd itself * and will be freed up on the next call to cram_get_ref or cram_close. * * To return the entire reference sequence, specify start as 1 and end * as 0. * * To cease using a reference, call cram_ref_decr(). * * Returns reference on success, * NULL on failure */ char *cram_get_ref(cram_fd *fd, int id, hts_pos_t start, hts_pos_t end) { ref_entry *r; char *seq; int ostart = start; if (id == -1 || start < 1) return NULL; /* FIXME: axiomatic query of r->seq being true? * Or shortcut for unsorted data where we load once and never free? */ //fd->shared_ref = 1; // hard code for now to simplify things pthread_mutex_lock(&fd->ref_lock); RP("%d cram_get_ref on fd %p, id %d, range %d..%d\n", gettid(), fd, id, start, end); /* * Unsorted data implies we want to fetch an entire reference at a time. * We just deal with this at the moment by claiming we're sharing * references instead, which has the same requirement. */ if (fd->unsorted) fd->shared_ref = 1; /* Sanity checking: does this ID exist? */ if (id >= fd->refs->nref) { hts_log_error("No reference found for id %d", id); pthread_mutex_unlock(&fd->ref_lock); return NULL; } if (!fd->refs || !fd->refs->ref_id[id]) { hts_log_error("No reference found for id %d", id); pthread_mutex_unlock(&fd->ref_lock); return NULL; } if (!(r = fd->refs->ref_id[id])) { hts_log_error("No reference found for id %d", id); pthread_mutex_unlock(&fd->ref_lock); return NULL; } /* * It has an entry, but may not have been populated yet. * Any manually loaded .fai files have their lengths known. * A ref entry computed from @SQ lines (M5 or UR field) will have * r->length == 0 unless it's been loaded once and verified that we have * an on-disk filename for it. * * 19 Sep 2013: Moved the lock here as the cram_populate_ref code calls * open_path_mfile and libcurl, which isn't multi-thread safe unless I * rewrite my code to have one curl handle per thread. */ pthread_mutex_lock(&fd->refs->lock); if (r->length == 0) { if (fd->ref_fn) hts_log_warning("Reference file given, but ref '%s' not present", r->name); if (cram_populate_ref(fd, id, r) == -1) { hts_log_warning("Failed to populate reference for id %d", id); pthread_mutex_unlock(&fd->refs->lock); pthread_mutex_unlock(&fd->ref_lock); return NULL; } r = fd->refs->ref_id[id]; if (fd->unsorted) cram_ref_incr_locked(fd->refs, id); } /* * We now know that we the filename containing the reference, so check * for limits. If it's over half the reference we'll load all of it in * memory as this will speed up subsequent calls. */ if (end < 1) end = r->length; if (end >= r->length) end = r->length; if (end - start >= 0.5*r->length || fd->shared_ref) { start = 1; end = r->length; } /* * Maybe we have it cached already? If so use it. * * Alternatively if we don't have the sequence but we're sharing * references and/or are asking for the entire length of it, then * load the full reference into the refs structure and return * a pointer to that one instead. */ if (fd->shared_ref || r->seq || (start == 1 && end == r->length)) { char *cp; if (id >= 0) { if (r->seq) { cram_ref_incr_locked(fd->refs, id); } else { ref_entry *e; if (!(e = cram_ref_load(fd->refs, id, r->is_md5))) { pthread_mutex_unlock(&fd->refs->lock); pthread_mutex_unlock(&fd->ref_lock); return NULL; } /* unsorted data implies cache ref indefinitely, to avoid * continually loading and unloading. */ if (fd->unsorted) cram_ref_incr_locked(fd->refs, id); } fd->ref = NULL; /* We never access it directly */ fd->ref_start = 1; fd->ref_end = r->length; fd->ref_id = id; cp = fd->refs->ref_id[id]->seq + ostart-1; } else { fd->ref = NULL; cp = NULL; } RP("%d cram_get_ref returning for id %d, count %d\n", gettid(), id, (int)r->count); pthread_mutex_unlock(&fd->refs->lock); pthread_mutex_unlock(&fd->ref_lock); return cp; } /* * Otherwise we're not sharing, we don't have a copy of it already and * we're only asking for a small portion of it. * * In this case load up just that segment ourselves, freeing any old * small segments in the process. */ /* Unmapped ref ID */ if (id < 0 || !fd->refs->fn) { if (fd->ref_free) { free(fd->ref_free); fd->ref_free = NULL; } fd->ref = NULL; fd->ref_id = id; pthread_mutex_unlock(&fd->refs->lock); pthread_mutex_unlock(&fd->ref_lock); return NULL; } /* Open file if it's not already the current open reference */ if (strcmp(fd->refs->fn, r->fn) || fd->refs->fp == NULL) { if (fd->refs->fp) if (bgzf_close(fd->refs->fp) != 0) return NULL; fd->refs->fn = r->fn; if (!(fd->refs->fp = bgzf_open_ref(fd->refs->fn, "r", r->is_md5))) { pthread_mutex_unlock(&fd->refs->lock); pthread_mutex_unlock(&fd->ref_lock); return NULL; } } if (!(fd->ref = load_ref_portion(fd->refs->fp, r, start, end))) { pthread_mutex_unlock(&fd->refs->lock); pthread_mutex_unlock(&fd->ref_lock); return NULL; } if (fd->ref_free) free(fd->ref_free); fd->ref_id = id; fd->ref_start = start; fd->ref_end = end; fd->ref_free = fd->ref; seq = fd->ref; pthread_mutex_unlock(&fd->refs->lock); pthread_mutex_unlock(&fd->ref_lock); return seq ? seq + ostart - start : NULL; } /* * If fd has been opened for reading, it may be permitted to specify 'fn' * as NULL and let the code auto-detect the reference by parsing the * SAM header @SQ lines. */ int cram_load_reference(cram_fd *fd, char *fn) { int ret = 0; if (fn) { fd->refs = refs_load_fai(fd->refs, fn, !(fd->embed_ref>0 && fd->mode == 'r')); fn = fd->refs ? fd->refs->fn : NULL; if (!fn) ret = -1; sanitise_SQ_lines(fd); } fd->ref_fn = fn; if ((!fd->refs || (fd->refs->nref == 0 && !fn)) && fd->header) { if (fd->refs) refs_free(fd->refs); if (!(fd->refs = refs_create())) return -1; if (-1 == refs_from_header(fd)) return -1; } if (fd->header) if (-1 == refs2id(fd->refs, fd->header)) return -1; return ret; } /* ---------------------------------------------------------------------- * Containers */ /* * Creates a new container, specifying the maximum number of slices * and records permitted. * * Returns cram_container ptr on success * NULL on failure */ cram_container *cram_new_container(int nrec, int nslice) { cram_container *c = calloc(1, sizeof(*c)); enum cram_DS_ID id; if (!c) return NULL; c->curr_ref = -2; c->max_c_rec = nrec * nslice; c->curr_c_rec = 0; c->max_rec = nrec; c->record_counter = 0; c->num_bases = 0; c->s_num_bases = 0; c->max_slice = nslice; c->curr_slice = 0; c->pos_sorted = 1; c->max_apos = 0; c->multi_seq = 0; c->qs_seq_orient = 1; c->no_ref = 0; c->embed_ref = -1; // automatic selection c->bams = NULL; if (!(c->slices = calloc(nslice != 0 ? nslice : 1, sizeof(cram_slice *)))) goto err; c->slice = NULL; if (!(c->comp_hdr = cram_new_compression_header())) goto err; c->comp_hdr_block = NULL; for (id = DS_RN; id < DS_TN; id++) if (!(c->stats[id] = cram_stats_create())) goto err; //c->aux_B_stats = cram_stats_create(); if (!(c->tags_used = kh_init(m_tagmap))) goto err; c->refs_used = 0; c->ref_free = 0; return c; err: if (c) { if (c->slices) free(c->slices); free(c); } return NULL; } static void free_bam_list(bam_seq_t **bams, int max_rec) { int i; for (i = 0; i < max_rec; i++) bam_free(bams[i]); free(bams); } void cram_free_container(cram_container *c) { enum cram_DS_ID id; int i; if (!c) return; if (c->refs_used) free(c->refs_used); if (c->landmark) free(c->landmark); if (c->comp_hdr) cram_free_compression_header(c->comp_hdr); if (c->comp_hdr_block) cram_free_block(c->comp_hdr_block); // Free the slices; filled out by encoder only if (c->slices) { for (i = 0; i < c->max_slice; i++) { if (c->slices[i]) cram_free_slice(c->slices[i]); if (c->slices[i] == c->slice) c->slice = NULL; } free(c->slices); } // Free the current slice; set by both encoder & decoder if (c->slice) { cram_free_slice(c->slice); c->slice = NULL; } for (id = DS_RN; id < DS_TN; id++) if (c->stats[id]) cram_stats_free(c->stats[id]); //if (c->aux_B_stats) cram_stats_free(c->aux_B_stats); if (c->tags_used) { khint_t k; for (k = kh_begin(c->tags_used); k != kh_end(c->tags_used); k++) { if (!kh_exist(c->tags_used, k)) continue; cram_tag_map *tm = (cram_tag_map *)kh_val(c->tags_used, k); if (tm) { cram_codec *c = tm->codec; if (c) c->free(c); // If tm->blk or tm->blk2 is set, then we haven't yet got to // cram_encode_container which copies the blocks to s->aux_block // and NULLifies tm->blk*. In this case we failed to complete // the container construction, so we have to free up our partially // converted CRAM. cram_free_block(tm->blk); cram_free_block(tm->blk2); free(tm); } } kh_destroy(m_tagmap, c->tags_used); } if (c->ref_free) free(c->ref); if (c->bams) free_bam_list(c->bams, c->max_c_rec); free(c); } /* * Reads a container header. * * Returns cram_container on success * NULL on failure or no container left (fd->err == 0). */ cram_container *cram_read_container(cram_fd *fd) { cram_container c2, *c; int i, s; size_t rd = 0; uint32_t crc = 0; fd->err = 0; fd->eof = 0; memset(&c2, 0, sizeof(c2)); if (CRAM_MAJOR_VERS(fd->version) == 1) { if ((s = fd->vv.varint_decode32_crc(fd, &c2.length, &crc)) == -1) { fd->eof = fd->empty_container ? 1 : 2; return NULL; } else { rd+=s; } } else if (CRAM_MAJOR_VERS(fd->version) < 4) { uint32_t len; if ((s = int32_decode(fd, &c2.length)) == -1) { if (CRAM_MAJOR_VERS(fd->version) == 2 && CRAM_MINOR_VERS(fd->version) == 0) fd->eof = 1; // EOF blocks arrived in v2.1 else fd->eof = fd->empty_container ? 1 : 2; return NULL; } else { rd+=s; } len = le_int4(c2.length); crc = crc32(0L, (unsigned char *)&len, 4); } else { if ((s = fd->vv.varint_decode32_crc(fd, &c2.length, &crc)) == -1) { fd->eof = fd->empty_container ? 1 : 2; return NULL; } else { rd+=s; } } if ((s = fd->vv.varint_decode32s_crc(fd, &c2.ref_seq_id, &crc)) == -1) return NULL; else rd+=s; if (CRAM_MAJOR_VERS(fd->version) >= 4) { int64_t i64; if ((s = fd->vv.varint_decode64_crc(fd, &i64, &crc))== -1) return NULL; else rd+=s; c2.ref_seq_start = i64; if ((s = fd->vv.varint_decode64_crc(fd, &i64, &crc)) == -1) return NULL; else rd+=s; c2.ref_seq_span = i64; } else { int32_t i32; if ((s = fd->vv.varint_decode32_crc(fd, &i32, &crc))== -1) return NULL; else rd+=s; c2.ref_seq_start = i32; if ((s = fd->vv.varint_decode32_crc(fd, &i32, &crc)) == -1) return NULL; else rd+=s; c2.ref_seq_span = i32; } if ((s = fd->vv.varint_decode32_crc(fd, &c2.num_records, &crc)) == -1) return NULL; else rd+=s; if (CRAM_MAJOR_VERS(fd->version) == 1) { c2.record_counter = 0; c2.num_bases = 0; } else { if (CRAM_MAJOR_VERS(fd->version) >= 3) { if ((s = fd->vv.varint_decode64_crc(fd, &c2.record_counter, &crc)) == -1) return NULL; else rd += s; } else { int32_t i32; if ((s = fd->vv.varint_decode32_crc(fd, &i32, &crc)) == -1) return NULL; else rd += s; c2.record_counter = i32; } if ((s = fd->vv.varint_decode64_crc(fd, &c2.num_bases, &crc))== -1) return NULL; else rd += s; } if ((s = fd->vv.varint_decode32_crc(fd, &c2.num_blocks, &crc)) == -1) return NULL; else rd+=s; if ((s = fd->vv.varint_decode32_crc(fd, &c2.num_landmarks, &crc))== -1) return NULL; else rd+=s; if (c2.num_landmarks < 0 || c2.num_landmarks >= SIZE_MAX / sizeof(int32_t)) return NULL; if (!(c = calloc(1, sizeof(*c)))) return NULL; *c = c2; #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (c->num_landmarks > FUZZ_ALLOC_LIMIT/sizeof(int32_t)) { fd->err = errno = ENOMEM; cram_free_container(c); return NULL; } #endif if (c->num_landmarks && !(c->landmark = malloc(c->num_landmarks * sizeof(int32_t)))) { fd->err = errno; cram_free_container(c); return NULL; } for (i = 0; i < c->num_landmarks; i++) { if ((s = fd->vv.varint_decode32_crc(fd, &c->landmark[i], &crc)) == -1) { cram_free_container(c); return NULL; } else { rd += s; } } if (CRAM_MAJOR_VERS(fd->version) >= 3) { if (-1 == int32_decode(fd, (int32_t *)&c->crc32)) { cram_free_container(c); return NULL; } else { rd+=4; } #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION // Pretend the CRC was OK so the fuzzer doesn't have to get it right crc = c->crc32; #endif if (crc != c->crc32) { hts_log_error("Container header CRC32 failure"); cram_free_container(c); return NULL; } } c->offset = rd; c->slices = NULL; c->slice = NULL; c->curr_slice = 0; c->max_slice = c->num_landmarks; c->slice_rec = 0; c->curr_rec = 0; c->max_rec = 0; if (c->ref_seq_id == -2) { c->multi_seq = 1; fd->multi_seq = 1; } fd->empty_container = (c->num_records == 0 && c->ref_seq_id == -1 && c->ref_seq_start == 0x454f46 /* EOF */) ? 1 : 0; return c; } /* MAXIMUM storage size needed for the container. */ int cram_container_size(cram_container *c) { return 55 + 5*c->num_landmarks; } /* * Stores the container structure in dat and returns *size as the * number of bytes written to dat[]. The input size of dat is also * held in *size and should be initialised to cram_container_size(c). * * Returns 0 on success; * -1 on failure */ int cram_store_container(cram_fd *fd, cram_container *c, char *dat, int *size) { char *cp = (char *)dat; int i; // Check the input buffer is large enough according to our stated // requirements. (NOTE: it may actually take less.) if (cram_container_size(c) > *size) return -1; if (CRAM_MAJOR_VERS(fd->version) == 1) { cp += itf8_put(cp, c->length); } else { *(int32_t *)cp = le_int4(c->length); cp += 4; } if (c->multi_seq) { cp += fd->vv.varint_put32(cp, NULL, -2); cp += fd->vv.varint_put32(cp, NULL, 0); cp += fd->vv.varint_put32(cp, NULL, 0); } else { cp += fd->vv.varint_put32s(cp, NULL, c->ref_seq_id); if (CRAM_MAJOR_VERS(fd->version) >= 4) { cp += fd->vv.varint_put64(cp, NULL, c->ref_seq_start); cp += fd->vv.varint_put64(cp, NULL, c->ref_seq_span); } else { cp += fd->vv.varint_put32(cp, NULL, c->ref_seq_start); cp += fd->vv.varint_put32(cp, NULL, c->ref_seq_span); } } cp += fd->vv.varint_put32(cp, NULL, c->num_records); if (CRAM_MAJOR_VERS(fd->version) == 2) { cp += fd->vv.varint_put64(cp, NULL, c->record_counter); } else if (CRAM_MAJOR_VERS(fd->version) >= 3) { cp += fd->vv.varint_put32(cp, NULL, c->record_counter); } cp += fd->vv.varint_put64(cp, NULL, c->num_bases); cp += fd->vv.varint_put32(cp, NULL, c->num_blocks); cp += fd->vv.varint_put32(cp, NULL, c->num_landmarks); for (i = 0; i < c->num_landmarks; i++) cp += fd->vv.varint_put32(cp, NULL, c->landmark[i]); if (CRAM_MAJOR_VERS(fd->version) >= 3) { c->crc32 = crc32(0L, (uc *)dat, cp-dat); cp[0] = c->crc32 & 0xff; cp[1] = (c->crc32 >> 8) & 0xff; cp[2] = (c->crc32 >> 16) & 0xff; cp[3] = (c->crc32 >> 24) & 0xff; cp += 4; } *size = cp-dat; // actual used size return 0; } /* * Writes a container structure. * * Returns 0 on success * -1 on failure */ int cram_write_container(cram_fd *fd, cram_container *c) { char buf_a[1024], *buf = buf_a, *cp; int i; if (61 + c->num_landmarks * 10 >= 1024) { buf = malloc(61 + c->num_landmarks * 10); if (!buf) return -1; } cp = buf; if (CRAM_MAJOR_VERS(fd->version) == 1) { cp += itf8_put(cp, c->length); } else if (CRAM_MAJOR_VERS(fd->version) <= 3) { *(int32_t *)cp = le_int4(c->length); cp += 4; } else { cp += fd->vv.varint_put32(cp, NULL, c->length); } if (c->multi_seq) { cp += fd->vv.varint_put32(cp, NULL, (uint32_t)-2); cp += fd->vv.varint_put32(cp, NULL, 0); cp += fd->vv.varint_put32(cp, NULL, 0); } else { cp += fd->vv.varint_put32s(cp, NULL, c->ref_seq_id); if (CRAM_MAJOR_VERS(fd->version) >= 4) { cp += fd->vv.varint_put64(cp, NULL, c->ref_seq_start); cp += fd->vv.varint_put64(cp, NULL, c->ref_seq_span); } else { cp += fd->vv.varint_put32(cp, NULL, c->ref_seq_start); cp += fd->vv.varint_put32(cp, NULL, c->ref_seq_span); } } cp += fd->vv.varint_put32(cp, NULL, c->num_records); if (CRAM_MAJOR_VERS(fd->version) >= 3) cp += fd->vv.varint_put64(cp, NULL, c->record_counter); else cp += fd->vv.varint_put32(cp, NULL, c->record_counter); cp += fd->vv.varint_put64(cp, NULL, c->num_bases); cp += fd->vv.varint_put32(cp, NULL, c->num_blocks); cp += fd->vv.varint_put32(cp, NULL, c->num_landmarks); for (i = 0; i < c->num_landmarks; i++) cp += fd->vv.varint_put32(cp, NULL, c->landmark[i]); if (CRAM_MAJOR_VERS(fd->version) >= 3) { c->crc32 = crc32(0L, (uc *)buf, cp-buf); cp[0] = c->crc32 & 0xff; cp[1] = (c->crc32 >> 8) & 0xff; cp[2] = (c->crc32 >> 16) & 0xff; cp[3] = (c->crc32 >> 24) & 0xff; cp += 4; } if (cp-buf != hwrite(fd->fp, buf, cp-buf)) { if (buf != buf_a) free(buf); return -1; } if (buf != buf_a) free(buf); return 0; } // common component shared by cram_flush_container{,_mt} static int cram_flush_container2(cram_fd *fd, cram_container *c) { int i, j; if (c->curr_slice > 0 && !c->slices) return -1; //fprintf(stderr, "Writing container %d, sum %u\n", c->record_counter, sum); off_t c_offset = htell(fd->fp); // File offset of container /* Write the container struct itself */ if (0 != cram_write_container(fd, c)) return -1; off_t hdr_size = htell(fd->fp) - c_offset; /* And the compression header */ if (0 != cram_write_block(fd, c->comp_hdr_block)) return -1; /* Followed by the slice blocks */ off_t file_offset = htell(fd->fp); for (i = 0; i < c->curr_slice; i++) { cram_slice *s = c->slices[i]; off_t spos = file_offset - c_offset - hdr_size; if (0 != cram_write_block(fd, s->hdr_block)) return -1; for (j = 0; j < s->hdr->num_blocks; j++) { if (0 != cram_write_block(fd, s->block[j])) return -1; } file_offset = htell(fd->fp); off_t sz = file_offset - c_offset - hdr_size - spos; if (fd->idxfp) { if (cram_index_slice(fd, c, s, fd->idxfp, c_offset, spos, sz) < 0) return -1; } } return 0; } /* * Flushes a completely or partially full container to disk, writing * container structure, header and blocks. This also calls the encoder * functions. * * Returns 0 on success * -1 on failure */ int cram_flush_container(cram_fd *fd, cram_container *c) { /* Encode the container blocks and generate compression header */ if (0 != cram_encode_container(fd, c)) return -1; return cram_flush_container2(fd, c); } typedef struct { cram_fd *fd; cram_container *c; } cram_job; void *cram_flush_thread(void *arg) { cram_job *j = (cram_job *)arg; /* Encode the container blocks and generate compression header */ if (0 != cram_encode_container(j->fd, j->c)) { hts_log_error("Call to cram_encode_container failed"); return NULL; } return arg; } static int cram_flush_result(cram_fd *fd) { int i, ret = 0; hts_tpool_result *r; cram_container *lc = NULL; // NB: we can have one result per slice, not per container, // so we need to free the container only after all slices // within it have been freed. (Automatic via reference counting.) while ((r = hts_tpool_next_result(fd->rqueue))) { cram_job *j = (cram_job *)hts_tpool_result_data(r); cram_container *c; if (!j) { hts_tpool_delete_result(r, 0); return -1; } fd = j->fd; c = j->c; if (fd->mode == 'w') if (0 != cram_flush_container2(fd, c)) return -1; // Free the slices; filled out by encoder only if (c->slices) { for (i = 0; i < c->max_slice; i++) { if (c->slices[i]) cram_free_slice(c->slices[i]); if (c->slices[i] == c->slice) c->slice = NULL; c->slices[i] = NULL; } } // Free the current slice; set by both encoder & decoder if (c->slice) { cram_free_slice(c->slice); c->slice = NULL; } c->curr_slice = 0; // Our jobs will be in order, so we free the last // container when our job has switched to a new one. if (c != lc) { if (lc) { if (fd->ctr == lc) fd->ctr = NULL; if (fd->ctr_mt == lc) fd->ctr_mt = NULL; cram_free_container(lc); } lc = c; } hts_tpool_delete_result(r, 1); } if (lc) { if (fd->ctr == lc) fd->ctr = NULL; if (fd->ctr_mt == lc) fd->ctr_mt = NULL; cram_free_container(lc); } return ret; } // Note: called while metrics_lock is held. // Will be left in this state too, but may temporarily unlock. void reset_metrics(cram_fd *fd) { int i; if (fd->pool) { // If multi-threaded we have multiple blocks being // compressed already and several on the to-do list // (fd->rqueue->pending). It's tricky to reset the // metrics exactly the correct point, so instead we // just flush the pool, reset, and then continue again. // Don't bother starting a new trial before then though. for (i = 0; i < DS_END; i++) { cram_metrics *m = fd->m[i]; if (!m) continue; m->next_trial = 999; } pthread_mutex_unlock(&fd->metrics_lock); hts_tpool_process_flush(fd->rqueue); pthread_mutex_lock(&fd->metrics_lock); } for (i = 0; i < DS_END; i++) { cram_metrics *m = fd->m[i]; if (!m) continue; m->trial = NTRIALS; m->next_trial = TRIAL_SPAN; m->revised_method = 0; m->unpackable = 0; memset(m->sz, 0, sizeof(m->sz)); } } int cram_flush_container_mt(cram_fd *fd, cram_container *c) { cram_job *j; // At the junction of mapped to unmapped data the compression // methods may need to change due to very different statistical // properties; particularly BA if minhash sorted. // // However with threading we'll have several in-flight blocks // arriving out of order. // // So we do one trial reset of NThreads to last for NThreads // duration to get us over this transition period, followed // by another retrial of the usual ntrials & trial span. pthread_mutex_lock(&fd->metrics_lock); if (c->n_mapped < 0.3*c->curr_rec && fd->last_mapped > 0.7*c->max_rec) { reset_metrics(fd); } fd->last_mapped = c->n_mapped * (c->max_rec+1)/(c->curr_rec+1) ; pthread_mutex_unlock(&fd->metrics_lock); if (!fd->pool) return cram_flush_container(fd, c); if (!(j = malloc(sizeof(*j)))) return -1; j->fd = fd; j->c = c; // Flush the job. Note our encoder queue may be full, so we // either have to keep trying in non-blocking mode (what we do) or // use a dedicated separate thread for draining the queue. for (;;) { errno = 0; hts_tpool_dispatch2(fd->pool, fd->rqueue, cram_flush_thread, j, 1); int pending = (errno == EAGAIN); if (cram_flush_result(fd) != 0) return -1; if (!pending) break; usleep(1000); } return 0; } /* ---------------------------------------------------------------------- * Compression headers; the first part of the container */ /* * Creates a new blank container compression header * * Returns header ptr on success * NULL on failure */ cram_block_compression_hdr *cram_new_compression_header(void) { cram_block_compression_hdr *hdr = calloc(1, sizeof(*hdr)); if (!hdr) return NULL; if (!(hdr->TD_blk = cram_new_block(CORE, 0))) { free(hdr); return NULL; } if (!(hdr->TD_hash = kh_init(m_s2i))) { cram_free_block(hdr->TD_blk); free(hdr); return NULL; } if (!(hdr->TD_keys = string_pool_create(8192))) { kh_destroy(m_s2i, hdr->TD_hash); cram_free_block(hdr->TD_blk); free(hdr); return NULL; } return hdr; } void cram_free_compression_header(cram_block_compression_hdr *hdr) { int i; if (hdr->landmark) free(hdr->landmark); if (hdr->preservation_map) kh_destroy(map, hdr->preservation_map); for (i = 0; i < CRAM_MAP_HASH; i++) { cram_map *m, *m2; for (m = hdr->rec_encoding_map[i]; m; m = m2) { m2 = m->next; if (m->codec) m->codec->free(m->codec); free(m); } } for (i = 0; i < CRAM_MAP_HASH; i++) { cram_map *m, *m2; for (m = hdr->tag_encoding_map[i]; m; m = m2) { m2 = m->next; if (m->codec) m->codec->free(m->codec); free(m); } } for (i = 0; i < DS_END; i++) { if (hdr->codecs[i]) hdr->codecs[i]->free(hdr->codecs[i]); } if (hdr->TL) free(hdr->TL); if (hdr->TD_blk) cram_free_block(hdr->TD_blk); if (hdr->TD_hash) kh_destroy(m_s2i, hdr->TD_hash); if (hdr->TD_keys) string_pool_destroy(hdr->TD_keys); free(hdr); } /* ---------------------------------------------------------------------- * Slices and slice headers */ void cram_free_slice_header(cram_block_slice_hdr *hdr) { if (!hdr) return; if (hdr->block_content_ids) free(hdr->block_content_ids); free(hdr); return; } void cram_free_slice(cram_slice *s) { if (!s) return; if (s->hdr_block) cram_free_block(s->hdr_block); if (s->block) { int i; if (s->hdr) { for (i = 0; i < s->hdr->num_blocks; i++) { if (i > 0 && s->block[i] == s->block[0]) continue; cram_free_block(s->block[i]); } } free(s->block); } { // Normally already copied into s->block[], but potentially still // here if we error part way through cram_encode_slice. int i; for (i = 0; i < s->naux_block; i++) cram_free_block(s->aux_block[i]); } if (s->block_by_id) free(s->block_by_id); if (s->hdr) cram_free_slice_header(s->hdr); if (s->seqs_blk) cram_free_block(s->seqs_blk); if (s->qual_blk) cram_free_block(s->qual_blk); if (s->name_blk) cram_free_block(s->name_blk); if (s->aux_blk) cram_free_block(s->aux_blk); if (s->base_blk) cram_free_block(s->base_blk); if (s->soft_blk) cram_free_block(s->soft_blk); if (s->cigar) free(s->cigar); if (s->crecs) free(s->crecs); if (s->features) free(s->features); if (s->TN) free(s->TN); if (s->pair_keys) string_pool_destroy(s->pair_keys); if (s->pair[0]) kh_destroy(m_s2i, s->pair[0]); if (s->pair[1]) kh_destroy(m_s2i, s->pair[1]); if (s->aux_block) free(s->aux_block); free(s); } /* * Creates a new empty slice in memory, for subsequent writing to * disk. * * Returns cram_slice ptr on success * NULL on failure */ cram_slice *cram_new_slice(enum cram_content_type type, int nrecs) { cram_slice *s = calloc(1, sizeof(*s)); if (!s) return NULL; if (!(s->hdr = (cram_block_slice_hdr *)calloc(1, sizeof(*s->hdr)))) goto err; s->hdr->content_type = type; s->hdr_block = NULL; s->block = NULL; s->block_by_id = NULL; s->last_apos = 0; if (!(s->crecs = malloc(nrecs * sizeof(cram_record)))) goto err; s->cigar_alloc = 1024; if (!(s->cigar = malloc(s->cigar_alloc * sizeof(*s->cigar)))) goto err; s->ncigar = 0; if (!(s->seqs_blk = cram_new_block(EXTERNAL, 0))) goto err; if (!(s->qual_blk = cram_new_block(EXTERNAL, DS_QS))) goto err; if (!(s->name_blk = cram_new_block(EXTERNAL, DS_RN))) goto err; if (!(s->aux_blk = cram_new_block(EXTERNAL, DS_aux))) goto err; if (!(s->base_blk = cram_new_block(EXTERNAL, DS_IN))) goto err; if (!(s->soft_blk = cram_new_block(EXTERNAL, DS_SC))) goto err; s->features = NULL; s->nfeatures = s->afeatures = 0; #ifndef TN_external s->TN = NULL; s->nTN = s->aTN = 0; #endif // Volatile keys as we do realloc in dstring if (!(s->pair_keys = string_pool_create(8192))) goto err; if (!(s->pair[0] = kh_init(m_s2i))) goto err; if (!(s->pair[1] = kh_init(m_s2i))) goto err; #ifdef BA_external s->BA_len = 0; #endif return s; err: if (s) cram_free_slice(s); return NULL; } /* * Loads an entire slice. * FIXME: In 1.0 the native unit of slices within CRAM is broken * as slices contain references to objects in other slices. * To work around this while keeping the slice oriented outer loop * we read all slices and stitch them together into a fake large * slice instead. * * Returns cram_slice ptr on success * NULL on failure */ cram_slice *cram_read_slice(cram_fd *fd) { cram_block *b = cram_read_block(fd); cram_slice *s = calloc(1, sizeof(*s)); int i, n, max_id, min_id; if (!b || !s) goto err; s->hdr_block = b; switch (b->content_type) { case MAPPED_SLICE: case UNMAPPED_SLICE: if (!(s->hdr = cram_decode_slice_header(fd, b))) goto err; break; default: hts_log_error("Unexpected block of type %s", cram_content_type2str(b->content_type)); goto err; } if (s->hdr->num_blocks < 1) { hts_log_error("Slice does not include any data blocks"); goto err; } s->block = calloc(n = s->hdr->num_blocks, sizeof(*s->block)); if (!s->block) goto err; for (max_id = i = 0, min_id = INT_MAX; i < n; i++) { if (!(s->block[i] = cram_read_block(fd))) goto err; if (s->block[i]->content_type == EXTERNAL) { if (max_id < s->block[i]->content_id) max_id = s->block[i]->content_id; if (min_id > s->block[i]->content_id) min_id = s->block[i]->content_id; } } if (!(s->block_by_id = calloc(512, sizeof(s->block[0])))) goto err; for (i = 0; i < n; i++) { if (s->block[i]->content_type != EXTERNAL) continue; uint32_t v = s->block[i]->content_id; if (v >= 256) v = 256 + v % 251; s->block_by_id[v] = s->block[i]; } /* Initialise encoding/decoding tables */ s->cigar_alloc = 1024; if (!(s->cigar = malloc(s->cigar_alloc * sizeof(*s->cigar)))) goto err; s->ncigar = 0; if (!(s->seqs_blk = cram_new_block(EXTERNAL, 0))) goto err; if (!(s->qual_blk = cram_new_block(EXTERNAL, DS_QS))) goto err; if (!(s->name_blk = cram_new_block(EXTERNAL, DS_RN))) goto err; if (!(s->aux_blk = cram_new_block(EXTERNAL, DS_aux))) goto err; if (!(s->base_blk = cram_new_block(EXTERNAL, DS_IN))) goto err; if (!(s->soft_blk = cram_new_block(EXTERNAL, DS_SC))) goto err; s->crecs = NULL; s->last_apos = s->hdr->ref_seq_start; s->decode_md = fd->decode_md; return s; err: if (b) cram_free_block(b); if (s) { s->hdr_block = NULL; cram_free_slice(s); } return NULL; } /* ---------------------------------------------------------------------- * CRAM file definition (header) */ /* * Reads a CRAM file definition structure. * Returns file_def ptr on success * NULL on failure */ cram_file_def *cram_read_file_def(cram_fd *fd) { cram_file_def *def = malloc(sizeof(*def)); if (!def) return NULL; if (26 != hread(fd->fp, &def->magic[0], 26)) { free(def); return NULL; } if (memcmp(def->magic, "CRAM", 4) != 0) { free(def); return NULL; } if (def->major_version > 4) { hts_log_error("CRAM version number mismatch. Expected 1.x, 2.x, 3.x or 4.x, got %d.%d", def->major_version, def->minor_version); free(def); return NULL; } fd->first_container += 26; fd->curr_position = fd->first_container; fd->last_slice = 0; return def; } /* * Writes a cram_file_def structure to cram_fd. * Returns 0 on success * -1 on failure */ int cram_write_file_def(cram_fd *fd, cram_file_def *def) { return (hwrite(fd->fp, &def->magic[0], 26) == 26) ? 0 : -1; } void cram_free_file_def(cram_file_def *def) { if (def) free(def); } /* ---------------------------------------------------------------------- * SAM header I/O */ /* * Reads the SAM header from the first CRAM data block. * Also performs minimal parsing to extract read-group * and sample information. * Returns SAM hdr ptr on success * NULL on failure */ sam_hdr_t *cram_read_SAM_hdr(cram_fd *fd) { int32_t header_len; char *header; sam_hdr_t *hdr; /* 1.1 onwards stores the header in the first block of a container */ if (CRAM_MAJOR_VERS(fd->version) == 1) { /* Length */ if (-1 == int32_decode(fd, &header_len)) return NULL; #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (header_len > FUZZ_ALLOC_LIMIT) return NULL; #endif /* Alloc and read */ if (header_len < 0 || NULL == (header = malloc((size_t) header_len+1))) return NULL; if (header_len != hread(fd->fp, header, header_len)) { free(header); return NULL; } header[header_len] = '\0'; fd->first_container += 4 + header_len; } else { cram_container *c = cram_read_container(fd); cram_block *b; int i; int64_t len; if (!c) return NULL; fd->first_container += c->length + c->offset; fd->curr_position = fd->first_container; if (c->num_blocks < 1) { cram_free_container(c); return NULL; } if (!(b = cram_read_block(fd))) { cram_free_container(c); return NULL; } if (cram_uncompress_block(b) != 0) { cram_free_container(c); cram_free_block(b); return NULL; } len = b->comp_size + 2 + 4*(CRAM_MAJOR_VERS(fd->version) >= 3) + fd->vv.varint_size(b->content_id) + fd->vv.varint_size(b->uncomp_size) + fd->vv.varint_size(b->comp_size); /* Extract header from 1st block */ if (-1 == int32_get_blk(b, &header_len) || header_len < 0 || /* Spec. says signed... why? */ b->uncomp_size - 4 < header_len) { cram_free_container(c); cram_free_block(b); return NULL; } if (NULL == (header = malloc((size_t) header_len+1))) { cram_free_container(c); cram_free_block(b); return NULL; } memcpy(header, BLOCK_END(b), header_len); header[header_len] = '\0'; cram_free_block(b); /* Consume any remaining blocks */ for (i = 1; i < c->num_blocks; i++) { if (!(b = cram_read_block(fd))) { cram_free_container(c); free(header); return NULL; } len += b->comp_size + 2 + 4*(CRAM_MAJOR_VERS(fd->version) >= 3) + fd->vv.varint_size(b->content_id) + fd->vv.varint_size(b->uncomp_size) + fd->vv.varint_size(b->comp_size); cram_free_block(b); } if (c->length > 0 && len > 0 && c->length > len) { // Consume padding char *pads = malloc(c->length - len); if (!pads) { cram_free_container(c); free(header); return NULL; } if (c->length - len != hread(fd->fp, pads, c->length - len)) { cram_free_container(c); free(header); free(pads); return NULL; } free(pads); } cram_free_container(c); } /* Parse */ hdr = sam_hdr_init(); if (!hdr) { free(header); return NULL; } if (-1 == sam_hdr_add_lines(hdr, header, header_len)) { free(header); sam_hdr_destroy(hdr); return NULL; } hdr->l_text = header_len; hdr->text = header; return hdr; } /* * Converts 'in' to a full pathname to store in out. * Out must be at least PATH_MAX bytes long. */ static void full_path(char *out, char *in) { size_t in_l = strlen(in); if (hisremote(in)) { if (in_l > PATH_MAX) { hts_log_error("Reference path is longer than %d", PATH_MAX); return; } strncpy(out, in, PATH_MAX-1); out[PATH_MAX-1] = 0; return; } if (*in == '/' || // Windows paths (in_l > 3 && toupper_c(*in) >= 'A' && toupper_c(*in) <= 'Z' && in[1] == ':' && (in[2] == '/' || in[2] == '\\'))) { strncpy(out, in, PATH_MAX-1); out[PATH_MAX-1] = 0; } else { size_t len; // unable to get dir or out+in is too long if (!getcwd(out, PATH_MAX) || (len = strlen(out))+1+strlen(in) >= PATH_MAX) { strncpy(out, in, PATH_MAX-1); out[PATH_MAX-1] = 0; return; } snprintf(out+len, PATH_MAX - len, "/%s", in); // FIXME: cope with `pwd`/../../../foo.fa ? } } /* * Writes a CRAM SAM header. * Returns 0 on success * -1 on failure */ int cram_write_SAM_hdr(cram_fd *fd, sam_hdr_t *hdr) { size_t header_len; int blank_block = (CRAM_MAJOR_VERS(fd->version) >= 3); /* Write CRAM MAGIC if not yet written. */ if (fd->file_def->major_version == 0) { fd->file_def->major_version = CRAM_MAJOR_VERS(fd->version); fd->file_def->minor_version = CRAM_MINOR_VERS(fd->version); if (0 != cram_write_file_def(fd, fd->file_def)) return -1; } /* 1.0 requires an UNKNOWN read-group */ if (CRAM_MAJOR_VERS(fd->version) == 1) { if (!sam_hrecs_find_rg(hdr->hrecs, "UNKNOWN")) if (sam_hdr_add_line(hdr, "RG", "ID", "UNKNOWN", "SM", "UNKNOWN", NULL)) return -1; } if (-1 == refs_from_header(fd)) return -1; if (-1 == refs2id(fd->refs, fd->header)) return -1; /* Fix M5 strings */ if (fd->refs && !fd->no_ref && fd->embed_ref <= 1) { int i; for (i = 0; i < hdr->hrecs->nref; i++) { sam_hrec_type_t *ty; char *ref; if (!(ty = sam_hrecs_find_type_id(hdr->hrecs, "SQ", "SN", hdr->hrecs->ref[i].name))) return -1; if (!sam_hrecs_find_key(ty, "M5", NULL)) { char unsigned buf[16]; char buf2[33]; hts_pos_t rlen; hts_md5_context *md5; if (!fd->refs || !fd->refs->ref_id || !fd->refs->ref_id[i]) { return -1; } rlen = fd->refs->ref_id[i]->length; ref = cram_get_ref(fd, i, 1, rlen); if (NULL == ref) { if (fd->embed_ref == -1) { // auto embed-ref hts_log_warning("No M5 tags present and could not " "find reference"); hts_log_warning("Enabling embed_ref=2 option"); hts_log_warning("NOTE: the CRAM file will be bigger " "than using an external reference"); pthread_mutex_lock(&fd->ref_lock); fd->embed_ref = 2; pthread_mutex_unlock(&fd->ref_lock); break; } return -1; } rlen = fd->refs->ref_id[i]->length; /* In case it just loaded */ if (!(md5 = hts_md5_init())) return -1; if (HTS_POS_MAX <= ULONG_MAX) { // Platforms with 64-bit unsigned long update in one go hts_md5_update(md5, ref, rlen); } else { // Those with 32-bit ulong (Windows) may have to loop // over epic references hts_pos_t pos = 0; while (rlen - pos > ULONG_MAX) { hts_md5_update(md5, ref + pos, ULONG_MAX); pos += ULONG_MAX; } hts_md5_update(md5, ref + pos, (unsigned long)(rlen - pos)); } hts_md5_final(buf, md5); hts_md5_destroy(md5); cram_ref_decr(fd->refs, i); hts_md5_hex(buf2, buf); fd->refs->ref_id[i]->validated_md5 = 1; if (sam_hdr_update_line(hdr, "SQ", "SN", hdr->hrecs->ref[i].name, "M5", buf2, NULL)) return -1; } if (fd->ref_fn) { char ref_fn[PATH_MAX]; full_path(ref_fn, fd->ref_fn); if (sam_hdr_update_line(hdr, "SQ", "SN", hdr->hrecs->ref[i].name, "UR", ref_fn, NULL)) return -1; } } } /* Length */ header_len = sam_hdr_length(hdr); if (header_len > INT32_MAX) { hts_log_error("Header is too long for CRAM format"); return -1; } if (CRAM_MAJOR_VERS(fd->version) == 1) { if (-1 == int32_encode(fd, header_len)) return -1; /* Text data */ if (header_len != hwrite(fd->fp, sam_hdr_str(hdr), header_len)) return -1; } else { /* Create block(s) inside a container */ cram_block *b = cram_new_block(FILE_HEADER, 0); cram_container *c = cram_new_container(0, 0); int padded_length; char *pads; int is_cram_3 = (CRAM_MAJOR_VERS(fd->version) >= 3); if (!b || !c) { if (b) cram_free_block(b); if (c) cram_free_container(c); return -1; } if (int32_put_blk(b, header_len) < 0) return -1; if (header_len) BLOCK_APPEND(b, sam_hdr_str(hdr), header_len); BLOCK_UPLEN(b); // Compress header block if V3.0 and above if (CRAM_MAJOR_VERS(fd->version) >= 3) if (cram_compress_block(fd, b, NULL, -1, -1) < 0) return -1; if (blank_block) { c->length = b->comp_size + 2 + 4*is_cram_3 + fd->vv.varint_size(b->content_id) + fd->vv.varint_size(b->uncomp_size) + fd->vv.varint_size(b->comp_size); c->num_blocks = 2; c->num_landmarks = 2; if (!(c->landmark = malloc(2*sizeof(*c->landmark)))) { cram_free_block(b); cram_free_container(c); return -1; } c->landmark[0] = 0; c->landmark[1] = c->length; // Plus extra storage for uncompressed secondary blank block padded_length = MIN(c->length*.5, 10000); c->length += padded_length + 2 + 4*is_cram_3 + fd->vv.varint_size(b->content_id) + fd->vv.varint_size(padded_length)*2; } else { // Pad the block instead. c->num_blocks = 1; c->num_landmarks = 1; if (!(c->landmark = malloc(sizeof(*c->landmark)))) return -1; c->landmark[0] = 0; padded_length = MAX(c->length*1.5, 10000) - c->length; c->length = b->comp_size + padded_length + 2 + 4*is_cram_3 + fd->vv.varint_size(b->content_id) + fd->vv.varint_size(b->uncomp_size) + fd->vv.varint_size(b->comp_size); if (NULL == (pads = calloc(1, padded_length))) { cram_free_block(b); cram_free_container(c); return -1; } BLOCK_APPEND(b, pads, padded_length); BLOCK_UPLEN(b); free(pads); } if (-1 == cram_write_container(fd, c)) { cram_free_block(b); cram_free_container(c); return -1; } if (-1 == cram_write_block(fd, b)) { cram_free_block(b); cram_free_container(c); return -1; } if (blank_block) { BLOCK_RESIZE(b, padded_length); memset(BLOCK_DATA(b), 0, padded_length); BLOCK_SIZE(b) = padded_length; BLOCK_UPLEN(b); b->method = RAW; if (-1 == cram_write_block(fd, b)) { cram_free_block(b); cram_free_container(c); return -1; } } cram_free_block(b); cram_free_container(c); } if (0 != hflush(fd->fp)) return -1; RP("=== Finishing saving header ===\n"); return 0; block_err: return -1; } /* ---------------------------------------------------------------------- * The top-level cram opening, closing and option handling */ /* * Sets CRAM variable sized integer decode function tables. * CRAM 1, 2, and 3.x all used ITF8 for uint32 and UTF8 for uint64. * CRAM 4.x uses the same encoding mechanism for 32-bit and 64-bit * (or anything inbetween), but also now supports signed values. * * Version is the CRAM major version number. * vv is the vector table (probably &cram_fd->vv) */ static void cram_init_varint(varint_vec *vv, int version) { if (version >= 4) { vv->varint_get32 = uint7_get_32; // FIXME: varint.h API should be size agnostic vv->varint_get32s = sint7_get_32; vv->varint_get64 = uint7_get_64; vv->varint_get64s = sint7_get_64; vv->varint_put32 = uint7_put_32; vv->varint_put32s = sint7_put_32; vv->varint_put64 = uint7_put_64; vv->varint_put64s = sint7_put_64; vv->varint_put32_blk = uint7_put_blk_32; vv->varint_put32s_blk = sint7_put_blk_32; vv->varint_put64_blk = uint7_put_blk_64; vv->varint_put64s_blk = sint7_put_blk_64; vv->varint_size = uint7_size; vv->varint_decode32_crc = uint7_decode_crc32; vv->varint_decode32s_crc = sint7_decode_crc32; vv->varint_decode64_crc = uint7_decode_crc64; } else { vv->varint_get32 = safe_itf8_get; vv->varint_get32s = safe_itf8_get; vv->varint_get64 = safe_ltf8_get; vv->varint_get64s = safe_ltf8_get; vv->varint_put32 = safe_itf8_put; vv->varint_put32s = safe_itf8_put; vv->varint_put64 = safe_ltf8_put; vv->varint_put64s = safe_ltf8_put; vv->varint_put32_blk = itf8_put_blk; vv->varint_put32s_blk = itf8_put_blk; vv->varint_put64_blk = ltf8_put_blk; vv->varint_put64s_blk = ltf8_put_blk; vv->varint_size = itf8_size; vv->varint_decode32_crc = itf8_decode_crc; vv->varint_decode32s_crc = itf8_decode_crc; vv->varint_decode64_crc = ltf8_decode_crc; } } /* * Initialises the lookup tables. These could be global statics, but they're * clumsy to setup in a multi-threaded environment unless we generate * verbatim code and include that. */ static void cram_init_tables(cram_fd *fd) { int i; memset(fd->L1, 4, 256); fd->L1['A'] = 0; fd->L1['a'] = 0; fd->L1['C'] = 1; fd->L1['c'] = 1; fd->L1['G'] = 2; fd->L1['g'] = 2; fd->L1['T'] = 3; fd->L1['t'] = 3; memset(fd->L2, 5, 256); fd->L2['A'] = 0; fd->L2['a'] = 0; fd->L2['C'] = 1; fd->L2['c'] = 1; fd->L2['G'] = 2; fd->L2['g'] = 2; fd->L2['T'] = 3; fd->L2['t'] = 3; fd->L2['N'] = 4; fd->L2['n'] = 4; if (CRAM_MAJOR_VERS(fd->version) == 1) { for (i = 0; i < 0x200; i++) { int f = 0; if (i & CRAM_FPAIRED) f |= BAM_FPAIRED; if (i & CRAM_FPROPER_PAIR) f |= BAM_FPROPER_PAIR; if (i & CRAM_FUNMAP) f |= BAM_FUNMAP; if (i & CRAM_FREVERSE) f |= BAM_FREVERSE; if (i & CRAM_FREAD1) f |= BAM_FREAD1; if (i & CRAM_FREAD2) f |= BAM_FREAD2; if (i & CRAM_FSECONDARY) f |= BAM_FSECONDARY; if (i & CRAM_FQCFAIL) f |= BAM_FQCFAIL; if (i & CRAM_FDUP) f |= BAM_FDUP; fd->bam_flag_swap[i] = f; } for (i = 0; i < 0x1000; i++) { int g = 0; if (i & BAM_FPAIRED) g |= CRAM_FPAIRED; if (i & BAM_FPROPER_PAIR) g |= CRAM_FPROPER_PAIR; if (i & BAM_FUNMAP) g |= CRAM_FUNMAP; if (i & BAM_FREVERSE) g |= CRAM_FREVERSE; if (i & BAM_FREAD1) g |= CRAM_FREAD1; if (i & BAM_FREAD2) g |= CRAM_FREAD2; if (i & BAM_FSECONDARY) g |= CRAM_FSECONDARY; if (i & BAM_FQCFAIL) g |= CRAM_FQCFAIL; if (i & BAM_FDUP) g |= CRAM_FDUP; fd->cram_flag_swap[i] = g; } } else { /* NOP */ for (i = 0; i < 0x1000; i++) fd->bam_flag_swap[i] = i; for (i = 0; i < 0x1000; i++) fd->cram_flag_swap[i] = i; } memset(fd->cram_sub_matrix, 4, 32*32); for (i = 0; i < 32; i++) { fd->cram_sub_matrix[i]['A'&0x1f]=0; fd->cram_sub_matrix[i]['C'&0x1f]=1; fd->cram_sub_matrix[i]['G'&0x1f]=2; fd->cram_sub_matrix[i]['T'&0x1f]=3; fd->cram_sub_matrix[i]['N'&0x1f]=4; } for (i = 0; i < 20; i+=4) { int j; for (j = 0; j < 20; j++) { fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]=3; fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]=3; fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]=3; fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]=3; } fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][CRAM_SUBST_MATRIX[i+0]&0x1f]=0; fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][CRAM_SUBST_MATRIX[i+1]&0x1f]=1; fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][CRAM_SUBST_MATRIX[i+2]&0x1f]=2; fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][CRAM_SUBST_MATRIX[i+3]&0x1f]=3; } cram_init_varint(&fd->vv, CRAM_MAJOR_VERS(fd->version)); } // Default version numbers for CRAM static int major_version = 3; static int minor_version = 0; /* * Opens a CRAM file for read (mode "rb") or write ("wb"). * The filename may be "-" to indicate stdin or stdout. * * Returns file handle on success * NULL on failure. */ cram_fd *cram_open(const char *filename, const char *mode) { hFILE *fp; cram_fd *fd; char fmode[3]= { mode[0], '\0', '\0' }; if (strlen(mode) > 1 && (mode[1] == 'b' || mode[1] == 'c')) { fmode[1] = 'b'; } fp = hopen(filename, fmode); if (!fp) return NULL; fd = cram_dopen(fp, filename, mode); if (!fd) hclose_abruptly(fp); return fd; } /* Opens an existing stream for reading or writing. * * Returns file handle on success; * NULL on failure. */ cram_fd *cram_dopen(hFILE *fp, const char *filename, const char *mode) { int i; char *cp; cram_fd *fd = calloc(1, sizeof(*fd)); if (!fd) return NULL; fd->level = CRAM_DEFAULT_LEVEL; for (i = 0; mode[i]; i++) { if (mode[i] >= '0' && mode[i] <= '9') { fd->level = mode[i] - '0'; break; } } fd->fp = fp; fd->mode = *mode; fd->first_container = 0; fd->curr_position = 0; if (fd->mode == 'r') { /* Reader */ if (!(fd->file_def = cram_read_file_def(fd))) goto err; fd->version = fd->file_def->major_version * 256 + fd->file_def->minor_version; cram_init_tables(fd); if (!(fd->header = cram_read_SAM_hdr(fd))) { cram_free_file_def(fd->file_def); goto err; } } else { /* Writer */ cram_file_def *def = calloc(1, sizeof(*def)); if (!def) return NULL; fd->file_def = def; def->magic[0] = 'C'; def->magic[1] = 'R'; def->magic[2] = 'A'; def->magic[3] = 'M'; def->major_version = 0; // Indicator to write file def later. def->minor_version = 0; memset(def->file_id, 0, 20); strncpy(def->file_id, filename, 20); fd->version = major_version * 256 + minor_version; cram_init_tables(fd); /* SAM header written later along with this file_def */ } fd->prefix = strdup((cp = strrchr(filename, '/')) ? cp+1 : filename); if (!fd->prefix) goto err; fd->first_base = fd->last_base = -1; fd->record_counter = 0; fd->ctr = NULL; fd->ctr_mt = NULL; fd->refs = refs_create(); if (!fd->refs) goto err; fd->ref_id = -2; fd->ref = NULL; fd->decode_md = 0; fd->seqs_per_slice = SEQS_PER_SLICE; fd->bases_per_slice = BASES_PER_SLICE; fd->slices_per_container = SLICE_PER_CNT; fd->embed_ref = -1; // automatic selection fd->no_ref = 0; fd->no_ref_counter = 0; fd->ap_delta = 0; fd->ignore_md5 = 0; fd->lossy_read_names = 0; fd->use_bz2 = 0; fd->use_rans = (CRAM_MAJOR_VERS(fd->version) >= 3); fd->use_tok = (CRAM_MAJOR_VERS(fd->version) >= 3) && (CRAM_MINOR_VERS(fd->version) >= 1); fd->use_lzma = 0; fd->multi_seq = -1; fd->multi_seq_user = -1; fd->unsorted = 0; fd->shared_ref = 0; fd->store_md = 0; fd->store_nm = 0; fd->last_RI_count = 0; fd->index = NULL; fd->own_pool = 0; fd->pool = NULL; fd->rqueue = NULL; fd->job_pending = NULL; fd->ooc = 0; fd->required_fields = INT_MAX; pthread_mutex_init(&fd->metrics_lock, NULL); pthread_mutex_init(&fd->ref_lock, NULL); pthread_mutex_init(&fd->range_lock, NULL); pthread_mutex_init(&fd->bam_list_lock, NULL); for (i = 0; i < DS_END; i++) { fd->m[i] = cram_new_metrics(); if (!fd->m[i]) goto err; } if (!(fd->tags_used = kh_init(m_metrics))) goto err; fd->range.refid = -2; // no ref. fd->eof = 1; // See samtools issue #150 fd->ref_fn = NULL; fd->bl = NULL; /* Initialise dummy refs from the @SQ headers */ if (-1 == refs_from_header(fd)) goto err; return fd; err: if (fd) free(fd); return NULL; } /* * Seek within a CRAM file. * * Returns 0 on success * -1 on failure */ int cram_seek(cram_fd *fd, off_t offset, int whence) { char buf[65536]; fd->ooc = 0; cram_drain_rqueue(fd); if (hseek(fd->fp, offset, whence) >= 0) { return 0; } if (!(whence == SEEK_CUR && offset >= 0)) return -1; /* Couldn't fseek, but we're in SEEK_CUR mode so read instead */ while (offset > 0) { int len = MIN(65536, offset); if (len != hread(fd->fp, buf, len)) return -1; offset -= len; } return 0; } /* * Flushes a CRAM file. * Useful for when writing to stdout without wishing to close the stream. * * Returns 0 on success * -1 on failure */ int cram_flush(cram_fd *fd) { if (!fd) return -1; int ret = 0; if (fd->mode == 'w' && fd->ctr) { if(fd->ctr->slice) cram_update_curr_slice(fd->ctr, fd->version); if (-1 == cram_flush_container_mt(fd, fd->ctr)) ret = -1; cram_free_container(fd->ctr); if (fd->ctr_mt == fd->ctr) fd->ctr_mt = NULL; fd->ctr = NULL; } return ret; } /* * Writes an EOF block to a CRAM file. * * Returns 0 on success * -1 on failure */ int cram_write_eof_block(cram_fd *fd) { // EOF block is a container with special values to aid detection if (CRAM_MAJOR_VERS(fd->version) >= 2) { // Empty container with // ref_seq_id -1 // start pos 0x454f46 ("EOF") // span 0 // nrec 0 // counter 0 // nbases 0 // 1 block (landmark 0) // (CRC32) cram_container c; memset(&c, 0, sizeof(c)); c.ref_seq_id = -1; c.ref_seq_start = 0x454f46; // "EOF" c.ref_seq_span = 0; c.record_counter = 0; c.num_bases = 0; c.num_blocks = 1; int32_t land[1] = {0}; c.landmark = land; // An empty compression header block with // method raw (0) // type comp header (1) // content id 0 // block contents size 6 // raw size 6 // empty preservation map (01 00) // empty data series map (01 00) // empty tag map (01 00) // block CRC cram_block_compression_hdr ch; memset(&ch, 0, sizeof(ch)); c.comp_hdr_block = cram_encode_compression_header(fd, &c, &ch, 0); c.length = c.comp_hdr_block->byte // Landmark[0] + 5 // block struct + 4*(CRAM_MAJOR_VERS(fd->version) >= 3); // CRC if (cram_write_container(fd, &c) < 0 || cram_write_block(fd, c.comp_hdr_block) < 0) { cram_close(fd); cram_free_block(c.comp_hdr_block); return -1; } if (ch.preservation_map) kh_destroy(map, ch.preservation_map); cram_free_block(c.comp_hdr_block); // V2.1 bytes // 0b 00 00 00 ff ff ff ff 0f // Cont HDR: size, ref seq id // e0 45 4f 46 00 00 00 // Cont HDR: pos, span, nrec, counter // 00 01 00 // Cont HDR: nbase, nblk, landmark // 00 01 00 06 06 // Comp.HDR blk // 01 00 01 00 01 00 // Comp.HDR blk // V3.0 bytes: // 0f 00 00 00 ff ff ff ff 0f // Cont HDR: size, ref seq id // e0 45 4f 46 00 00 00 // Cont HDR: pos, span, nrec, counter // 00 01 00 // Cont HDR: nbase, nblk, landmark // 05 bd d9 4f // CRC32 // 00 01 00 06 06 // Comp.HDR blk // 01 00 01 00 01 00 // Comp.HDR blk // ee 63 01 4b // CRC32 // V4.0 bytes: // 0f 00 00 00 8f ff ff ff // Cont HDR: size, ref seq id // 82 95 9e 46 00 00 00 // Cont HDR: pos, span, nrec, counter // 00 01 00 // Cont HDR: nbase, nblk, landmark // ac d6 05 bc // CRC32 // 00 01 00 06 06 // Comp.HDR blk // 01 00 01 00 01 00 // Comp.HDR blk // ee 63 01 4b // CRC32 } return 0; } /* * Closes a CRAM file. * Returns 0 on success * -1 on failure */ int cram_close(cram_fd *fd) { spare_bams *bl, *next; int i, ret = 0; if (!fd) return -1; if (fd->mode == 'w' && fd->ctr) { if(fd->ctr->slice) cram_update_curr_slice(fd->ctr, fd->version); if (-1 == cram_flush_container_mt(fd, fd->ctr)) ret = -1; } if (fd->mode != 'w') cram_drain_rqueue(fd); if (fd->pool && fd->eof >= 0 && fd->rqueue) { hts_tpool_process_flush(fd->rqueue); if (0 != cram_flush_result(fd)) ret = -1; if (fd->mode == 'w') fd->ctr = NULL; // prevent double freeing //fprintf(stderr, "CRAM: destroy queue %p\n", fd->rqueue); hts_tpool_process_destroy(fd->rqueue); } pthread_mutex_destroy(&fd->metrics_lock); pthread_mutex_destroy(&fd->ref_lock); pthread_mutex_destroy(&fd->range_lock); pthread_mutex_destroy(&fd->bam_list_lock); if (ret == 0 && fd->mode == 'w') { /* Write EOF block */ if (0 != cram_write_eof_block(fd)) ret = -1; } for (bl = fd->bl; bl; bl = next) { int max_rec = fd->seqs_per_slice * fd->slices_per_container; next = bl->next; free_bam_list(bl->bams, max_rec); free(bl); } if (hclose(fd->fp) != 0) ret = -1; if (fd->file_def) cram_free_file_def(fd->file_def); if (fd->header) sam_hdr_destroy(fd->header); free(fd->prefix); if (fd->ctr) cram_free_container(fd->ctr); if (fd->ctr_mt && fd->ctr_mt != fd->ctr) cram_free_container(fd->ctr_mt); if (fd->refs) refs_free(fd->refs); if (fd->ref_free) free(fd->ref_free); for (i = 0; i < DS_END; i++) if (fd->m[i]) free(fd->m[i]); if (fd->tags_used) { khint_t k; for (k = kh_begin(fd->tags_used); k != kh_end(fd->tags_used); k++) { if (kh_exist(fd->tags_used, k)) free(kh_val(fd->tags_used, k)); } kh_destroy(m_metrics, fd->tags_used); } if (fd->index) cram_index_free(fd); if (fd->own_pool && fd->pool) hts_tpool_destroy(fd->pool); if (fd->idxfp) if (bgzf_close(fd->idxfp) < 0) ret = -1; free(fd); return ret; } /* * Returns 1 if we hit an EOF while reading. */ int cram_eof(cram_fd *fd) { return fd->eof; } /* * Sets options on the cram_fd. See CRAM_OPT_* definitions in cram_structs.h. * Use this immediately after opening. * * Returns 0 on success * -1 on failure */ int cram_set_option(cram_fd *fd, enum hts_fmt_option opt, ...) { int r; va_list args; va_start(args, opt); r = cram_set_voption(fd, opt, args); va_end(args); return r; } /* * Sets options on the cram_fd. See CRAM_OPT_* definitions in cram_structs.h. * Use this immediately after opening. * * Returns 0 on success * -1 on failure */ int cram_set_voption(cram_fd *fd, enum hts_fmt_option opt, va_list args) { refs_t *refs; if (!fd) { errno = EBADF; return -1; } switch (opt) { case CRAM_OPT_DECODE_MD: fd->decode_md = va_arg(args, int); break; case CRAM_OPT_PREFIX: if (fd->prefix) free(fd->prefix); if (!(fd->prefix = strdup(va_arg(args, char *)))) return -1; break; case CRAM_OPT_VERBOSITY: break; case CRAM_OPT_SEQS_PER_SLICE: fd->seqs_per_slice = va_arg(args, int); if (fd->bases_per_slice == BASES_PER_SLICE) fd->bases_per_slice = fd->seqs_per_slice * 500; break; case CRAM_OPT_BASES_PER_SLICE: fd->bases_per_slice = va_arg(args, int); break; case CRAM_OPT_SLICES_PER_CONTAINER: fd->slices_per_container = va_arg(args, int); break; case CRAM_OPT_EMBED_REF: fd->embed_ref = va_arg(args, int); break; case CRAM_OPT_NO_REF: fd->no_ref = va_arg(args, int); break; case CRAM_OPT_POS_DELTA: fd->ap_delta = va_arg(args, int); break; case CRAM_OPT_IGNORE_MD5: fd->ignore_md5 = va_arg(args, int); break; case CRAM_OPT_LOSSY_NAMES: fd->lossy_read_names = va_arg(args, int); // Currently lossy read names required paired (attached) reads. // TLEN 0 or being 1 out causes read pairs to be detached, breaking // the lossy read name compression, so we have extra options to // slacken the exact TLEN round-trip checks. fd->tlen_approx = fd->lossy_read_names; fd->tlen_zero = fd->lossy_read_names; break; case CRAM_OPT_USE_BZIP2: fd->use_bz2 = va_arg(args, int); break; case CRAM_OPT_USE_RANS: fd->use_rans = va_arg(args, int); break; case CRAM_OPT_USE_TOK: fd->use_tok = va_arg(args, int); break; case CRAM_OPT_USE_FQZ: fd->use_fqz = va_arg(args, int); break; case CRAM_OPT_USE_ARITH: fd->use_arith = va_arg(args, int); break; case CRAM_OPT_USE_LZMA: fd->use_lzma = va_arg(args, int); break; case CRAM_OPT_SHARED_REF: fd->shared_ref = 1; refs = va_arg(args, refs_t *); if (refs != fd->refs) { if (fd->refs) refs_free(fd->refs); fd->refs = refs; fd->refs->count++; } break; case CRAM_OPT_RANGE: { int r = cram_seek_to_refpos(fd, va_arg(args, cram_range *)); pthread_mutex_lock(&fd->range_lock); if (fd->range.refid != -2) fd->required_fields |= SAM_POS; pthread_mutex_unlock(&fd->range_lock); return r; } case CRAM_OPT_RANGE_NOSEEK: { // As per CRAM_OPT_RANGE, but no seeking pthread_mutex_lock(&fd->range_lock); cram_range *r = va_arg(args, cram_range *); fd->range = *r; if (r->refid == HTS_IDX_NOCOOR) { fd->range.refid = -1; fd->range.start = 0; } else if (r->refid == HTS_IDX_START || r->refid == HTS_IDX_REST) { fd->range.refid = -2; // special case in cram_next_slice } if (fd->range.refid != -2) fd->required_fields |= SAM_POS; fd->ooc = 0; fd->eof = 0; pthread_mutex_unlock(&fd->range_lock); return 0; } case CRAM_OPT_REFERENCE: return cram_load_reference(fd, va_arg(args, char *)); case CRAM_OPT_VERSION: { int major, minor; char *s = va_arg(args, char *); if (2 != sscanf(s, "%d.%d", &major, &minor)) { hts_log_error("Malformed version string %s", s); return -1; } if (!((major == 1 && minor == 0) || (major == 2 && (minor == 0 || minor == 1)) || (major == 3 && (minor == 0 || minor == 1)) || (major == 4 && minor == 0))) { hts_log_error("Unknown version string; use 1.0, 2.0, 2.1, 3.0, 3.1 or 4.0"); errno = EINVAL; return -1; } if (major > 3 || (major == 3 && minor > 1)) { hts_log_warning( "CRAM version %s is still a draft and subject to change.\n" "This is a technology demonstration that should not be " "used for archival data.", s); } fd->version = major*256 + minor; fd->use_rans = (CRAM_MAJOR_VERS(fd->version) >= 3) ? 1 : 0; fd->use_tok = ((CRAM_MAJOR_VERS(fd->version) == 3 && CRAM_MINOR_VERS(fd->version) >= 1) || CRAM_MAJOR_VERS(fd->version) >= 4) ? 1 : 0; cram_init_tables(fd); break; } case CRAM_OPT_MULTI_SEQ_PER_SLICE: fd->multi_seq_user = fd->multi_seq = va_arg(args, int); break; case CRAM_OPT_NTHREADS: { int nthreads = va_arg(args, int); if (nthreads >= 1) { if (!(fd->pool = hts_tpool_init(nthreads))) return -1; fd->rqueue = hts_tpool_process_init(fd->pool, nthreads*2, 0); fd->shared_ref = 1; fd->own_pool = 1; } break; } case CRAM_OPT_THREAD_POOL: { htsThreadPool *p = va_arg(args, htsThreadPool *); fd->pool = p ? p->pool : NULL; if (fd->pool) { fd->rqueue = hts_tpool_process_init(fd->pool, p->qsize ? p->qsize : hts_tpool_size(fd->pool)*2, 0); } fd->shared_ref = 1; // Needed to avoid clobbering ref between threads fd->own_pool = 0; //fd->qsize = 1; //fd->decoded = calloc(fd->qsize, sizeof(cram_container *)); //hts_tpool_dispatch(fd->pool, cram_decoder_thread, fd); break; } case CRAM_OPT_REQUIRED_FIELDS: fd->required_fields = va_arg(args, int); if (fd->range.refid != -2) fd->required_fields |= SAM_POS; break; case CRAM_OPT_STORE_MD: fd->store_md = va_arg(args, int); break; case CRAM_OPT_STORE_NM: fd->store_nm = va_arg(args, int); break; case HTS_OPT_COMPRESSION_LEVEL: fd->level = va_arg(args, int); break; case HTS_OPT_PROFILE: { enum hts_profile_option prof = va_arg(args, int); switch (prof) { case HTS_PROFILE_FAST: if (fd->level == CRAM_DEFAULT_LEVEL) fd->level = 1; fd->use_tok = 0; fd->seqs_per_slice = 10000; break; case HTS_PROFILE_NORMAL: break; case HTS_PROFILE_SMALL: if (fd->level == CRAM_DEFAULT_LEVEL) fd->level = 6; fd->use_bz2 = 1; fd->use_fqz = 1; fd->seqs_per_slice = 25000; break; case HTS_PROFILE_ARCHIVE: if (fd->level == CRAM_DEFAULT_LEVEL) fd->level = 7; fd->use_bz2 = 1; fd->use_fqz = 1; fd->use_arith = 1; if (fd->level > 7) fd->use_lzma = 1; fd->seqs_per_slice = 100000; break; } if (fd->bases_per_slice == BASES_PER_SLICE) fd->bases_per_slice = fd->seqs_per_slice * 500; break; } default: hts_log_error("Unknown CRAM option code %d", opt); errno = EINVAL; return -1; } return 0; } int cram_check_EOF(cram_fd *fd) { // Byte 9 in these templates is & with 0x0f to resolve differences // between ITF-8 interpretations between early Java and C // implementations of CRAM static const unsigned char TEMPLATE_2_1[30] = { 0x0b, 0x00, 0x00, 0x00, 0xff, 0xff, 0xff, 0xff, 0x0f, 0xe0, 0x45, 0x4f, 0x46, 0x00, 0x00, 0x00, 0x00, 0x01, 0x00, 0x00, 0x01, 0x00, 0x06, 0x06, 0x01, 0x00, 0x01, 0x00, 0x01, 0x00 }; static const unsigned char TEMPLATE_3[38] = { 0x0f, 0x00, 0x00, 0x00, 0xff, 0xff, 0xff, 0xff, 0x0f, 0xe0, 0x45, 0x4f, 0x46, 0x00, 0x00, 0x00, 0x00, 0x01, 0x00, 0x05, 0xbd, 0xd9, 0x4f, 0x00, 0x01, 0x00, 0x06, 0x06, 0x01, 0x00, 0x01, 0x00, 0x01, 0x00, 0xee, 0x63, 0x01, 0x4b }; unsigned char buf[38]; // max(sizeof TEMPLATE_*) uint8_t major = CRAM_MAJOR_VERS(fd->version); uint8_t minor = CRAM_MINOR_VERS(fd->version); const unsigned char *template; ssize_t template_len; if ((major < 2) || (major == 2 && minor == 0)) { return 3; // No EOF support in cram versions less than 2.1 } else if (major == 2 && minor == 1) { template = TEMPLATE_2_1; template_len = sizeof TEMPLATE_2_1; } else { template = TEMPLATE_3; template_len = sizeof TEMPLATE_3; } off_t offset = htell(fd->fp); if (hseek(fd->fp, -template_len, SEEK_END) < 0) { if (errno == ESPIPE) { hclearerr(fd->fp); return 2; } else { return -1; } } if (hread(fd->fp, buf, template_len) != template_len) return -1; if (hseek(fd->fp, offset, SEEK_SET) < 0) return -1; buf[8] &= 0x0f; return (memcmp(template, buf, template_len) == 0)? 1 : 0; } pysam-0.23.0/htslib/cram/cram_io.h000066400000000000000000000434201475062545500167360ustar00rootroot00000000000000/* Copyright (c) 2012-2020 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /*! \file * Include cram.h instead. * * This is an internal part of the CRAM system and is automatically included * when you #include cram.h. * * Implements the low level CRAM I/O primitives. * This includes basic data types such as byte, int, ITF-8, * maps, bitwise I/O, etc. */ #ifndef CRAM_IO_H #define CRAM_IO_H #include #include "misc.h" #ifdef __cplusplus extern "C" { #endif /**@{ ---------------------------------------------------------------------- * ITF8 encoding and decoding. * * Also see the itf8_get and itf8_put macros. */ /*! INTERNAL: Converts two characters into an integer for use in switch{} */ #define CRAM_KEY(a,b) ((((unsigned char) a)<<8)|(((unsigned char) b))) /*! Reads an integer in ITF-8 encoding from 'fd' and stores it in * *val. * * @return * Returns the number of bytes read on success; * -1 on failure */ int itf8_decode(cram_fd *fd, int32_t *val); extern const int itf8_bytes[16]; extern const int ltf8_bytes[256]; /*! Pushes a value in ITF8 format onto the end of a block. * * This shouldn't be used for high-volume data as it is not the fastest * method. * * @return * Returns the number of bytes written */ int itf8_put_blk(cram_block *blk, int32_t val); int ltf8_put_blk(cram_block *blk, int64_t val); /*! Pulls a literal 32-bit value from a block. * * @returns the number of bytes decoded; * -1 on failure. */ int int32_get_blk(cram_block *b, int32_t *val); /*! Pushes a literal 32-bit value onto the end of a block. * * @return * Returns 0 on success; * -1 on failure. */ int int32_put_blk(cram_block *blk, int32_t val); /**@}*/ /**@{ ---------------------------------------------------------------------- * CRAM blocks - the dynamically growable data block. We have code to * create, update, (un)compress and read/write. * * These are derived from the deflate_interlaced.c blocks, but with the * CRAM extension of content types and IDs. */ /*! Allocates a new cram_block structure with a specified content_type and * id. * * @return * Returns block pointer on success; * NULL on failure */ cram_block *cram_new_block(enum cram_content_type content_type, int content_id); /*! Reads a block from a cram file. * * @return * Returns cram_block pointer on success; * NULL on failure */ cram_block *cram_read_block(cram_fd *fd); /*! Writes a CRAM block. * * @return * Returns 0 on success; * -1 on failure */ int cram_write_block(cram_fd *fd, cram_block *b); /*! Frees a CRAM block, deallocating internal data too. */ void cram_free_block(cram_block *b); /*! Uncompress a memory block using Zlib. * * @return * Returns 0 on success; * -1 on failure */ char *zlib_mem_inflate(char *cdata, size_t csize, size_t *size); /*! Uncompresses a CRAM block, if compressed. * * @return * Returns 0 on success; * -1 on failure */ int cram_uncompress_block(cram_block *b); /*! Compresses a block. * * Compresses a block using one of two different zlib strategies. If we only * want one choice set strat2 to be -1. * * The logic here is that sometimes Z_RLE does a better job than Z_FILTERED * or Z_DEFAULT_STRATEGY on quality data. If so, we'd rather use it as it is * significantly faster. * * @return * Returns 0 on success; * -1 on failure */ int cram_compress_block(cram_fd *fd, cram_block *b, cram_metrics *metrics, int method, int level); int cram_compress_block2(cram_fd *fd, cram_slice *s, cram_block *b, cram_metrics *metrics, int method, int level); cram_metrics *cram_new_metrics(void); char *cram_block_method2str(enum cram_block_method_int m); char *cram_content_type2str(enum cram_content_type t); /* * Find an external block by its content_id */ static inline cram_block *cram_get_block_by_id(cram_slice *slice, int id) { //fprintf(stderr, "%d\t%p\n", id, slice->block_by_id); uint32_t v = id; if (slice->block_by_id && v < 256) { return slice->block_by_id[v]; } else { v = 256 + v % 251; if (slice->block_by_id && slice->block_by_id[v] && slice->block_by_id[v]->content_id == id) return slice->block_by_id[v]; // Otherwise a linear search in case of collision int i; for (i = 0; i < slice->hdr->num_blocks; i++) { cram_block *b = slice->block[i]; if (b && b->content_type == EXTERNAL && b->content_id == id) return b; } } return NULL; } /* --- Accessor macros for manipulating blocks on a byte by byte basis --- */ /* Block size and data pointer. */ #define BLOCK_SIZE(b) ((b)->byte) #define BLOCK_DATA(b) ((b)->data) /* Returns the address one past the end of the block */ #define BLOCK_END(b) (&(b)->data[(b)->byte]) /* Make block exactly 'l' bytes long */ static inline int block_resize_exact(cram_block *b, size_t len) { unsigned char *tmp = realloc(b->data, len); if (!tmp) return -1; b->alloc = len; b->data = tmp; return 0; } /* Request block to be at least 'l' bytes long */ static inline int block_resize(cram_block *b, size_t len) { if (b->alloc > len) return 0; size_t alloc = b->alloc+800; alloc = MAX(alloc + (alloc>>2), len); return block_resize_exact(b, alloc); } /* Ensure the block can hold at least another 'l' bytes */ static inline int block_grow(cram_block *b, size_t len) { return block_resize(b, BLOCK_SIZE(b) + len); } /* Append string 's' of length 'l'. */ static inline int block_append(cram_block *b, const void *s, size_t len) { if (block_grow(b, len) < 0) return -1; if (len) { memcpy(BLOCK_END(b), s, len); BLOCK_SIZE(b) += len; } return 0; } /* Append as single character 'c' */ static inline int block_append_char(cram_block *b, char c) { if (block_grow(b, 1) < 0) return -1; b->data[b->byte++] = c; return 0; } /* Append a single unsigned integer */ static inline unsigned char *append_uint32(unsigned char *cp, uint32_t i); static inline int block_append_uint(cram_block *b, unsigned int i) { if (block_grow(b, 11) < 0) return -1; unsigned char *cp = &b->data[b->byte]; b->byte += append_uint32(cp, i) - cp; return 0; } // Versions of above with built in goto block_err calls. #define BLOCK_RESIZE_EXACT(b,l) if (block_resize_exact((b),(l))<0) goto block_err #define BLOCK_RESIZE(b,l) if (block_resize((b),(l)) <0) goto block_err #define BLOCK_GROW(b,l) if (block_grow((b),(l)) <0) goto block_err #define BLOCK_APPEND(b,s,l) if (block_append((b),(s),(l)) <0) goto block_err #define BLOCK_APPEND_CHAR(b,c) if (block_append_char((b),(c)) <0) goto block_err #define BLOCK_APPEND_UINT(b,i) if (block_append_uint((b),(i)) <0) goto block_err static inline unsigned char *append_uint32(unsigned char *cp, uint32_t i) { uint32_t j; if (i == 0) { *cp++ = '0'; return cp; } if (i < 100) goto b1; if (i < 10000) goto b3; if (i < 1000000) goto b5; if (i < 100000000) goto b7; if ((j = i / 1000000000)) {*cp++ = j + '0'; i -= j*1000000000; goto x8;} if ((j = i / 100000000)) {*cp++ = j + '0'; i -= j*100000000; goto x7;} b7:if ((j = i / 10000000)) {*cp++ = j + '0'; i -= j*10000000; goto x6;} if ((j = i / 1000000)) {*cp++ = j + '0', i -= j*1000000; goto x5;} b5:if ((j = i / 100000)) {*cp++ = j + '0', i -= j*100000; goto x4;} if ((j = i / 10000)) {*cp++ = j + '0', i -= j*10000; goto x3;} b3:if ((j = i / 1000)) {*cp++ = j + '0', i -= j*1000; goto x2;} if ((j = i / 100)) {*cp++ = j + '0', i -= j*100; goto x1;} b1:if ((j = i / 10)) {*cp++ = j + '0', i -= j*10; goto x0;} if (i) *cp++ = i + '0'; return cp; x8: *cp++ = i / 100000000 + '0', i %= 100000000; x7: *cp++ = i / 10000000 + '0', i %= 10000000; x6: *cp++ = i / 1000000 + '0', i %= 1000000; x5: *cp++ = i / 100000 + '0', i %= 100000; x4: *cp++ = i / 10000 + '0', i %= 10000; x3: *cp++ = i / 1000 + '0', i %= 1000; x2: *cp++ = i / 100 + '0', i %= 100; x1: *cp++ = i / 10 + '0', i %= 10; x0: *cp++ = i + '0'; return cp; } static inline unsigned char *append_sub32(unsigned char *cp, uint32_t i) { *cp++ = i / 100000000 + '0', i %= 100000000; *cp++ = i / 10000000 + '0', i %= 10000000; *cp++ = i / 1000000 + '0', i %= 1000000; *cp++ = i / 100000 + '0', i %= 100000; *cp++ = i / 10000 + '0', i %= 10000; *cp++ = i / 1000 + '0', i %= 1000; *cp++ = i / 100 + '0', i %= 100; *cp++ = i / 10 + '0', i %= 10; *cp++ = i + '0'; return cp; } static inline unsigned char *append_uint64(unsigned char *cp, uint64_t i) { uint64_t j; if (i <= 0xffffffff) return append_uint32(cp, i); if ((j = i/1000000000) > 1000000000) { cp = append_uint32(cp, j/1000000000); j %= 1000000000; cp = append_sub32(cp, j); } else { cp = append_uint32(cp, i / 1000000000); } cp = append_sub32(cp, i % 1000000000); return cp; } #define BLOCK_UPLEN(b) \ (b)->comp_size = (b)->uncomp_size = BLOCK_SIZE((b)) /**@}*/ /**@{ ---------------------------------------------------------------------- * Reference sequence handling */ /*! Loads a reference set from fn and stores in the cram_fd. * * @return * Returns 0 on success; * -1 on failure */ int cram_load_reference(cram_fd *fd, char *fn); /*! Generates a lookup table in refs based on the SQ headers in sam_hdr_t. * * Indexes references by the order they appear in a BAM file. This may not * necessarily be the same order they appear in the fasta reference file. * * @return * Returns 0 on success; * -1 on failure */ int refs2id(refs_t *r, sam_hdr_t *hdr); void refs_free(refs_t *r); /*! Returns a portion of a reference sequence from start to end inclusive. * * The returned pointer is owned by the cram_file fd and should not be freed * by the caller. It is valid only until the next cram_get_ref is called * with the same fd parameter (so is thread-safe if given multiple files). * * To return the entire reference sequence, specify start as 1 and end * as 0. * * @return * Returns reference on success; * NULL on failure */ char *cram_get_ref(cram_fd *fd, int id, hts_pos_t start, hts_pos_t end); void cram_ref_incr(refs_t *r, int id); void cram_ref_decr(refs_t *r, int id); /**@}*/ /**@{ ---------------------------------------------------------------------- * Containers */ /*! Creates a new container, specifying the maximum number of slices * and records permitted. * * @return * Returns cram_container ptr on success; * NULL on failure */ cram_container *cram_new_container(int nrec, int nslice); void cram_free_container(cram_container *c); /*! Reads a container header. * * @return * Returns cram_container on success; * NULL on failure or no container left (fd->err == 0). */ cram_container *cram_read_container(cram_fd *fd); /*! Writes a container structure. * * @return * Returns 0 on success; * -1 on failure */ int cram_write_container(cram_fd *fd, cram_container *h); /*! Flushes a container to disk. * * Flushes a completely or partially full container to disk, writing * container structure, header and blocks. This also calls the encoder * functions. * * @return * Returns 0 on success; * -1 on failure */ int cram_flush_container(cram_fd *fd, cram_container *c); int cram_flush_container_mt(cram_fd *fd, cram_container *c); /**@}*/ /**@{ ---------------------------------------------------------------------- * Compression headers; the first part of the container */ /*! Creates a new blank container compression header * * @return * Returns header ptr on success; * NULL on failure */ cram_block_compression_hdr *cram_new_compression_header(void); /*! Frees a cram_block_compression_hdr */ void cram_free_compression_header(cram_block_compression_hdr *hdr); /**@}*/ /**@{ ---------------------------------------------------------------------- * Slices and slice headers */ /*! Frees a slice header */ void cram_free_slice_header(cram_block_slice_hdr *hdr); /*! Frees a slice */ void cram_free_slice(cram_slice *s); /*! Creates a new empty slice in memory, for subsequent writing to * disk. * * @return * Returns cram_slice ptr on success; * NULL on failure */ cram_slice *cram_new_slice(enum cram_content_type type, int nrecs); /*! Loads an entire slice. * * FIXME: In 1.0 the native unit of slices within CRAM is broken * as slices contain references to objects in other slices. * To work around this while keeping the slice oriented outer loop * we read all slices and stitch them together into a fake large * slice instead. * * @return * Returns cram_slice ptr on success; * NULL on failure */ cram_slice *cram_read_slice(cram_fd *fd); /**@}*/ /**@{ ---------------------------------------------------------------------- * CRAM file definition (header) */ /*! Reads a CRAM file definition structure. * * @return * Returns file_def ptr on success; * NULL on failure */ cram_file_def *cram_read_file_def(cram_fd *fd); /*! Writes a cram_file_def structure to cram_fd. * * @return * Returns 0 on success; * -1 on failure */ int cram_write_file_def(cram_fd *fd, cram_file_def *def); /*! Frees a cram_file_def structure. */ void cram_free_file_def(cram_file_def *def); /**@}*/ /**@{ ---------------------------------------------------------------------- * SAM header I/O */ /*! Reads the SAM header from the first CRAM data block. * * Also performs minimal parsing to extract read-group * and sample information. * * @return * Returns SAM hdr ptr on success; * NULL on failure */ sam_hdr_t *cram_read_SAM_hdr(cram_fd *fd); /*! Writes a CRAM SAM header. * * @return * Returns 0 on success; * -1 on failure */ int cram_write_SAM_hdr(cram_fd *fd, sam_hdr_t *hdr); /**@}*/ /**@{ ---------------------------------------------------------------------- * The top-level cram opening, closing and option handling */ /*! Opens a CRAM file for read (mode "rb") or write ("wb"). * * The filename may be "-" to indicate stdin or stdout. * * @return * Returns file handle on success; * NULL on failure. */ cram_fd *cram_open(const char *filename, const char *mode); /*! Opens an existing stream for reading or writing. * * @return * Returns file handle on success; * NULL on failure. */ cram_fd *cram_dopen(struct hFILE *fp, const char *filename, const char *mode); /*! Closes a CRAM file. * * @return * Returns 0 on success; * -1 on failure */ int cram_close(cram_fd *fd); /* * Seek within a CRAM file. * * Returns 0 on success * -1 on failure */ int cram_seek(cram_fd *fd, off_t offset, int whence); /* * Flushes a CRAM file. * Useful for when writing to stdout without wishing to close the stream. * * Returns 0 on success * -1 on failure */ int cram_flush(cram_fd *fd); /*! Checks for end of file on a cram_fd stream. * * @return * Returns 0 if not at end of file * 1 if we hit an expected EOF (end of range or EOF block) * 2 for other EOF (end of stream without EOF block) */ int cram_eof(cram_fd *fd); /*! Sets options on the cram_fd. * * See CRAM_OPT_* definitions in cram_structs.h. * Use this immediately after opening. * * @return * Returns 0 on success; * -1 on failure */ int cram_set_option(cram_fd *fd, enum hts_fmt_option opt, ...); /*! Sets options on the cram_fd. * * See CRAM_OPT_* definitions in cram_structs.h. * Use this immediately after opening. * * @return * Returns 0 on success; * -1 on failure */ int cram_set_voption(cram_fd *fd, enum hts_fmt_option opt, va_list args); /*! * Attaches a header to a cram_fd. * * This should be used when creating a new cram_fd for writing where * we have an sam_hdr_t already constructed (eg from a file we've read * in). * * @return * Returns 0 on success; * -1 on failure */ int cram_set_header2(cram_fd *fd, const sam_hdr_t *hdr); /*! * Returns the hFILE connected to a cram_fd. */ static inline struct hFILE *cram_hfile(cram_fd *fd) { return fd->fp; } #ifdef __cplusplus } #endif #endif /* CRAM_IO_H */ pysam-0.23.0/htslib/cram/cram_samtools.h000066400000000000000000000055371475062545500201770ustar00rootroot00000000000000/* Copyright (c) 2010-2013, 2018, 2020 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef CRAM_SAMTOOLS_H #define CRAM_SAMTOOLS_H /* Samtools compatible API */ #define bam_blk_size(b) ((b)->l_data) #define bam_set_blk_size(b,v) ((b)->data_len = (v)) #define bam_ref(b) (b)->core.tid #define bam_pos(b) (b)->core.pos #define bam_mate_pos(b) (b)->core.mpos #define bam_mate_ref(b) (b)->core.mtid #define bam_ins_size(b) (b)->core.isize #define bam_seq_len(b) (b)->core.l_qseq #define bam_cigar_len(b) (b)->core.n_cigar #define bam_flag(b) (b)->core.flag #define bam_bin(b) (b)->core.bin #define bam_map_qual(b) (b)->core.qual #define bam_name_len(b) ((b)->core.l_qname - (b)->core.l_extranul) #define bam_name(b) bam_get_qname((b)) #define bam_qual(b) bam_get_qual((b)) #define bam_seq(b) bam_get_seq((b)) #define bam_cigar(b) bam_get_cigar((b)) #define bam_aux(b) bam_get_aux((b)) #define bam_free(b) bam_destroy1((b)) #define bam_reg2bin(beg,end) hts_reg2bin((beg),(end),14,5) #include "../htslib/sam.h" enum cigar_op { BAM_CMATCH_=BAM_CMATCH, BAM_CINS_=BAM_CINS, BAM_CDEL_=BAM_CDEL, BAM_CREF_SKIP_=BAM_CREF_SKIP, BAM_CSOFT_CLIP_=BAM_CSOFT_CLIP, BAM_CHARD_CLIP_=BAM_CHARD_CLIP, BAM_CPAD_=BAM_CPAD, BAM_CBASE_MATCH=BAM_CEQUAL, BAM_CBASE_MISMATCH=BAM_CDIFF }; typedef bam1_t bam_seq_t; #endif /* CRAM_SAMTOOLS_H */ pysam-0.23.0/htslib/cram/cram_stats.c000066400000000000000000000156171475062545500174670ustar00rootroot00000000000000/* Copyright (c) 2012-2014, 2016, 2018, 2020 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #include #include #include #include "cram.h" #include "os.h" cram_stats *cram_stats_create(void) { return calloc(1, sizeof(cram_stats)); } int cram_stats_add(cram_stats *st, int64_t val) { st->nsamp++; //assert(val >= 0); if (val < MAX_STAT_VAL && val >= 0) { st->freqs[val]++; } else { khint_t k; int r; if (!st->h) { st->h = kh_init(m_i2i); if (!st->h) return -1; } k = kh_put(m_i2i, st->h, val, &r); if (r == 0) kh_val(st->h, k)++; else if (r != -1) kh_val(st->h, k) = 1; else return -1; } return 0; } void cram_stats_del(cram_stats *st, int64_t val) { st->nsamp--; //assert(val >= 0); if (val < MAX_STAT_VAL && val >= 0) { st->freqs[val]--; assert(st->freqs[val] >= 0); } else if (st->h) { khint_t k = kh_get(m_i2i, st->h, val); if (k != kh_end(st->h)) { if (--kh_val(st->h, k) == 0) kh_del(m_i2i, st->h, k); } else { hts_log_warning("Failed to remove val %"PRId64" from cram_stats", val); st->nsamp++; } } else { hts_log_warning("Failed to remove val %"PRId64" from cram_stats", val); st->nsamp++; } } #if DEBUG_CRAM_STATS void cram_stats_dump(cram_stats *st) { int i; fprintf(stderr, "cram_stats:\n"); for (i = 0; i < MAX_STAT_VAL; i++) { if (!st->freqs[i]) continue; fprintf(stderr, "\t%d\t%d\n", i, st->freqs[i]); } if (st->h) { khint_t k; for (k = kh_begin(st->h); k != kh_end(st->h); k++) { if (!kh_exist(st->h, k)) continue; fprintf(stderr, "\t%d\t%d\n", kh_key(st->h, k), kh_val(st->h, k)); } } } #endif /* * Computes entropy from integer frequencies for various encoding methods and * picks the best encoding. * * FIXME: we could reuse some of the code here for the actual encoding * parameters too. Eg the best 'k' for SUBEXP or the code lengths for huffman. * * Returns the best codec to use. */ enum cram_encoding cram_stats_encoding(cram_fd *fd, cram_stats *st) { int nvals, i, max_val = 0, min_val = INT_MAX; int *vals = NULL, *freqs = NULL, vals_alloc = 0; int ntot HTS_UNUSED = 0; #if DEBUG_CRAM_STATS cram_stats_dump(st); #endif /* Count number of unique symbols */ for (nvals = i = 0; i < MAX_STAT_VAL; i++) { if (!st->freqs[i]) continue; if (nvals >= vals_alloc) { vals_alloc = vals_alloc ? vals_alloc*2 : 1024; int *vals_tmp = realloc(vals, vals_alloc * sizeof(int)); int *freqs_tmp = realloc(freqs, vals_alloc * sizeof(int)); if (!vals_tmp || !freqs_tmp) { free(vals_tmp ? vals_tmp : vals); free(freqs_tmp ? freqs_tmp : freqs); return E_HUFFMAN; // Cannot do much else atm } vals = vals_tmp; freqs = freqs_tmp; } vals[nvals] = i; freqs[nvals] = st->freqs[i]; ntot += freqs[nvals]; if (max_val < i) max_val = i; if (min_val > i) min_val = i; nvals++; } if (st->h) { khint_t k; int i; for (k = kh_begin(st->h); k != kh_end(st->h); k++) { if (!kh_exist(st->h, k)) continue; if (nvals >= vals_alloc) { vals_alloc = vals_alloc ? vals_alloc*2 : 1024; int *vals_tmp = realloc(vals, vals_alloc * sizeof(int)); int *freqs_tmp = realloc(freqs, vals_alloc * sizeof(int)); if (!vals_tmp || !freqs_tmp) { free(vals_tmp ? vals_tmp : vals); free(freqs_tmp ? freqs_tmp : freqs); return E_HUFFMAN; // Cannot do much else atm } vals = vals_tmp; freqs = freqs_tmp; } i = kh_key(st->h, k); vals[nvals]=i; freqs[nvals] = kh_val(st->h, k); ntot += freqs[nvals]; if (max_val < i) max_val = i; if (min_val > i) min_val = i; nvals++; } } st->nvals = nvals; st->min_val = min_val; st->max_val = max_val; assert(ntot == st->nsamp); free(vals); free(freqs); /* * Simple policy that everything is external unless it can be * encoded using zero bits as a unary item huffman table. */ if (CRAM_MAJOR_VERS(fd->version) >= 4) { // Note, we're assuming integer data here as we don't have the // type passed in. Cram_encoder_init does know the type and // will convert to E_CONST_BYTE or E_EXTERNAL as appropriate. if (nvals == 1) return E_CONST_INT; else if (nvals == 0 || min_val < 0) return E_VARINT_SIGNED; else return E_VARINT_UNSIGNED; } else { return nvals <= 1 ? E_HUFFMAN : E_EXTERNAL; } } void cram_stats_free(cram_stats *st) { if (st->h) kh_destroy(m_i2i, st->h); free(st); } pysam-0.23.0/htslib/cram/cram_stats.h000066400000000000000000000043411475062545500174640ustar00rootroot00000000000000/* Copyright (c) 2012-2013, 2018 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef CRAM_STATS_H #define CRAM_STATS_H #ifdef __cplusplus extern "C" { #endif cram_stats *cram_stats_create(void); int cram_stats_add(cram_stats *st, int64_t val); void cram_stats_del(cram_stats *st, int64_t val); void cram_stats_dump(cram_stats *st); void cram_stats_free(cram_stats *st); /* * Computes entropy from integer frequencies for various encoding methods and * picks the best encoding. * * FIXME: we could reuse some of the code here for the actual encoding * parameters too. Eg the best 'k' for SUBEXP or the code lengths for huffman. * * Returns the best codec to use. */ enum cram_encoding cram_stats_encoding(cram_fd *fd, cram_stats *st); #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/cram/cram_structs.h000066400000000000000000000717411475062545500200450ustar00rootroot00000000000000/* Copyright (c) 2012-2016, 2018-2020, 2023 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef HTSLIB_CRAM_STRUCTS_H #define HTSLIB_CRAM_STRUCTS_H /* * Defines in-memory structs for the basic file-format objects in the * CRAM format. * * The basic file format is: * File-def SAM-hdr Container Container ... * * Container: * Service-block data-block data-block ... * * Multiple blocks in a container are grouped together as slices, * also sometimes referred to as landmarks in the spec. */ #include #include #include #include "../htslib/thread_pool.h" #include "../htslib/cram.h" #include "string_alloc.h" #include "mFILE.h" #include "../htslib/khash.h" #ifdef __cplusplus extern "C" { #endif // Generic hash-map integer -> integer KHASH_MAP_INIT_INT64(m_i2i, int) // Generic hash-set integer -> (existence) KHASH_SET_INIT_INT(s_i2i) // For brevity typedef unsigned char uc; /* * A union for the preservation map. Required for khash. */ typedef union { int i; char *p; } pmap_t; // Generates static functions here which isn't ideal, but we have no way // currently to declare the kh_map_t structure here without also declaring a // duplicate in the .c files due to the nature of the KHASH macros. KHASH_MAP_INIT_STR(map, pmap_t) struct hFILE; #define SEQS_PER_SLICE 10000 #define BASES_PER_SLICE (SEQS_PER_SLICE*500) #define SLICE_PER_CNT 1 #define CRAM_SUBST_MATRIX "CGTNGTANCATNGCANACGT" #define MAX_STAT_VAL 1024 //#define MAX_STAT_VAL 16 typedef struct cram_stats { int freqs[MAX_STAT_VAL]; khash_t(m_i2i) *h; int nsamp; // total number of values added int nvals; // total number of unique values added int64_t min_val, max_val; } cram_stats; /* NB: matches java impl, not the spec */ enum cram_encoding { E_NULL = 0, E_EXTERNAL = 1, // Only for BYTE type in CRAM 4 E_GOLOMB = 2, // Not in CRAM 4 E_HUFFMAN = 3, // Not in CRAM 4 E_BYTE_ARRAY_LEN = 4, E_BYTE_ARRAY_STOP = 5, E_BETA = 6, // Not in CRAM 4 E_SUBEXP = 7, // Not in CRAM 4 E_GOLOMB_RICE = 8, // Not in CRAM 4 E_GAMMA = 9, // Not in CRAM 4 // CRAM 4 specific codecs E_VARINT_UNSIGNED = 41, // Specialisation of EXTERNAL E_VARINT_SIGNED = 42, // Specialisation of EXTERNAL E_CONST_BYTE = 43, // Alternative to HUFFMAN with 1 symbol E_CONST_INT = 44, // Alternative to HUFFMAN with 1 symbol // More experimental ideas, not documented in spec yet E_XHUFFMAN = 50, // To external block E_XPACK = 51, // Transform to sub-codec E_XRLE = 52, // Transform to sub-codec E_XDELTA = 53, // Transform to sub-codec // Total number of codecs, not a real one. E_NUM_CODECS, }; enum cram_external_type { E_INT = 1, E_LONG = 2, E_BYTE = 3, E_BYTE_ARRAY = 4, E_BYTE_ARRAY_BLOCK = 5, E_SINT = 6, // signed INT E_SLONG = 7, // signed LONG }; /* External IDs used by this implementation (only assumed during writing) */ enum cram_DS_ID { DS_CORE = 0, DS_aux = 1, // aux_blk DS_aux_OQ = 2, DS_aux_BQ = 3, DS_aux_BD = 4, DS_aux_BI = 5, DS_aux_FZ = 6, // also ZM:B DS_aux_oq = 7, // other qualities DS_aux_os = 8, // other sequences DS_aux_oz = 9, // other strings DS_ref, DS_RN, // name_blk DS_QS, // qual_blk DS_IN, // base_blk DS_SC, // soft_blk DS_BF, // start loop DS_CF, DS_AP, DS_RG, DS_MQ, DS_NS, DS_MF, DS_TS, DS_NP, DS_NF, DS_RL, DS_FN, DS_FC, DS_FP, DS_DL, DS_BA, DS_BS, DS_TL, DS_RI, DS_RS, DS_PD, DS_HC, DS_BB, DS_QQ, DS_TN, // end loop DS_RN_len, DS_SC_len, DS_BB_len, DS_QQ_len, DS_TC, // CRAM v1.0 tags DS_TM, // test DS_TV, // test DS_END, }; /* "File Definition Structure" */ struct cram_file_def { char magic[4]; uint8_t major_version; uint8_t minor_version; char file_id[20] HTS_NONSTRING; // Filename or SHA1 checksum }; #define CRAM_MAJOR_VERS(v) ((v) >> 8) #define CRAM_MINOR_VERS(v) ((v) & 0xff) struct cram_slice; // Internal version of htslib/cram.h enum. // Note these have to match the laout of methmap and methcost in // cram_io.c:cram_compress_block2 enum cram_block_method_int { // Public methods as defined in the CRAM spec. BM_ERROR = -1, // CRAM 2.x and 3.0 RAW = 0, GZIP = 1, BZIP2 = 2, LZMA = 3, RANS = 4, RANS0 = RANS, // CRAM 3.1 onwards RANSPR = 5, RANS_PR0 = RANSPR, ARITH = 6, ARITH_PR0 = ARITH, FQZ = 7, TOK3 = 8, // BSC = 9, ZSTD = 10 // Methods not externalised, but used in metrics. // Externally they become one of the above methods. GZIP_RLE = 11, GZIP_1, // Z_DEFAULT_STRATEGY level 1, NB: not externalised in CRAM FQZ_b, FQZ_c, FQZ_d, // Various preset FQZ methods //RANS0, // Order 0 RANS1, //RANS_PR0, // Order 0 RANS_PR1, // Order 1 RANS_PR64, // O0 + RLE RANS_PR9, // O1 + X4 RANS_PR128, // O0 + Pack RANS_PR129, // O1 + Pack RANS_PR192, // O0 + RLE + pack RANS_PR193, // O1 + RLE + pack //TOK3, // tok+rans TOKA, // tok+arith //ARITH_PR0, // Order 0 ARITH_PR1, // Order 1 ARITH_PR64, // O0 + RLE ARITH_PR9, // O1 + X4 ARITH_PR128, // O0 + Pack ARITH_PR129, // O1 + Pack ARITH_PR192, // O0 + RLE + pack ARITH_PR193, // O1 + RLE + pack // NB: must end on no more than 31 unless we change to a // 64-bit method type. }; /* Now in htslib/cram.h enum cram_content_type { CT_ERROR = -1, FILE_HEADER = 0, COMPRESSION_HEADER = 1, MAPPED_SLICE = 2, UNMAPPED_SLICE = 3, // CRAM V1.0 only EXTERNAL = 4, CORE = 5, }; */ /* Maximum simultaneous codecs allowed, 1 per bit */ #define CRAM_MAX_METHOD 32 /* Compression metrics */ struct cram_metrics { // number of trials and time to next trial int trial; int next_trial; int consistency; // aggregate sizes during trials int sz[CRAM_MAX_METHOD]; int input_avg_sz, input_avg_delta; // resultant method from trials int method, revised_method; int strat; // Revisions of method, to allow culling of continually failing ones. int cnt[CRAM_MAX_METHOD]; double extra[CRAM_MAX_METHOD]; // Not amenable to rANS bit-packing techniques; cardinality > 16 int unpackable; }; // Hash aux key (XX:i) to cram_metrics KHASH_MAP_INIT_INT(m_metrics, cram_metrics*) /* Block */ struct cram_block { enum cram_block_method_int method, orig_method; enum cram_content_type content_type; int32_t content_id; int32_t comp_size; int32_t uncomp_size; uint32_t crc32; int32_t idx; /* offset into data */ unsigned char *data; // For bit I/O size_t alloc; size_t byte; int bit; // To aid compression cram_metrics *m; // used to track aux block compression only int crc32_checked; uint32_t crc_part; }; struct cram_codec; /* defined in cram_codecs.h */ struct cram_map; #define CRAM_MAP_HASH 32 #define CRAM_MAP(a,b) (((a)*3+(b))&(CRAM_MAP_HASH-1)) /* Compression header block */ struct cram_block_compression_hdr { int32_t ref_seq_id; int64_t ref_seq_start; int64_t ref_seq_span; int32_t num_records; int32_t num_landmarks; int32_t *landmark; /* Flags from preservation map */ int read_names_included; int AP_delta; // indexed by ref-base and subst. code char substitution_matrix[5][4]; int no_ref; int qs_seq_orient; // 1 => same as seq. 0 => original orientation // TD Dictionary as a concatenated block cram_block *TD_blk; // Tag Dictionary int nTL; // number of TL entries in TD unsigned char **TL; // array of size nTL, pointer into TD_blk. khash_t(m_s2i) *TD_hash; // Keyed on TD strings, map to TL[] indices string_alloc_t *TD_keys; // Pooled keys for TD hash. khash_t(map) *preservation_map; struct cram_map *rec_encoding_map[CRAM_MAP_HASH]; struct cram_map *tag_encoding_map[CRAM_MAP_HASH]; struct cram_codec *codecs[DS_END]; char *uncomp; // A single block of uncompressed data size_t uncomp_size, uncomp_alloc; // Total codec count, used for index to block_by_id for transforms int ncodecs; }; typedef struct cram_map { int key; /* 0xe0 + 3 bytes */ enum cram_encoding encoding; int offset; /* Offset into a single block of memory */ int size; /* Size */ struct cram_codec *codec; struct cram_map *next; // for noddy internal hash } cram_map; typedef struct cram_tag_map { struct cram_codec *codec; cram_block *blk; cram_block *blk2; cram_metrics *m; } cram_tag_map; // Hash aux key (XX:i) to cram_tag_map KHASH_MAP_INIT_INT(m_tagmap, cram_tag_map*) /* Mapped or unmapped slice header block */ struct cram_block_slice_hdr { enum cram_content_type content_type; int32_t ref_seq_id; /* if content_type == MAPPED_SLICE */ int64_t ref_seq_start; /* if content_type == MAPPED_SLICE */ int64_t ref_seq_span; /* if content_type == MAPPED_SLICE */ int32_t num_records; int64_t record_counter; int32_t num_blocks; int32_t num_content_ids; int32_t *block_content_ids; int32_t ref_base_id; /* if content_type == MAPPED_SLICE */ unsigned char md5[16]; }; struct ref_entry; /* * Container. * * Conceptually a container is split into slices, and slices into blocks. * However on disk it's just a list of blocks and we need to query the * block types to identify the start/end points of the slices. * * OR... are landmarks the start/end points of slices? */ struct cram_container { int32_t length; int32_t ref_seq_id; int64_t ref_seq_start; int64_t ref_seq_span; int64_t record_counter; int64_t num_bases; int32_t num_records; int32_t num_blocks; int32_t num_landmarks; int32_t *landmark; /* Size of container header above */ size_t offset; /* Compression header is always the first block? */ cram_block_compression_hdr *comp_hdr; cram_block *comp_hdr_block; /* For construction purposes */ int max_slice, curr_slice; // maximum number of slices int curr_slice_mt; // Curr_slice when reading ahead (via threads) int max_rec, curr_rec; // current and max recs per slice int max_c_rec, curr_c_rec; // current and max recs per container int slice_rec; // rec no. for start of this slice int curr_ref; // current ref ID. -2 for no previous int64_t last_pos; // last record position struct cram_slice **slices, *slice; int pos_sorted; // boolean, 1=>position sorted data int64_t max_apos; // maximum position, used if pos_sorted==0 int last_slice; // number of reads in last slice (0 for 1st) int multi_seq; // true if packing multi seqs per cont/slice int unsorted; // true is AP_delta is 0. int qs_seq_orient; // 1 => same as seq. 0 => original orientation /* Copied from fd before encoding, to allow multi-threading */ int ref_id; hts_pos_t ref_start, first_base, last_base, ref_end; char *ref; int embed_ref; // 1 if embedding ref, 2 if embedding cons int no_ref; // true if referenceless //struct ref_entry *ref; /* For multi-threading */ bam_seq_t **bams; /* Statistics for encoding */ cram_stats *stats[DS_END]; khash_t(m_tagmap) *tags_used; // set of tag types in use, for tag encoding map int *refs_used; // array of frequency of ref seq IDs uint32_t crc32; // CRC32 uint64_t s_num_bases; // number of bases in this slice uint64_t s_aux_bytes; // number of bytes of aux in BAM uint32_t n_mapped; // Number of mapped reads int ref_free; // whether 'ref' is owned by us and must be freed. }; /* * A single cram record */ typedef struct cram_record { struct cram_slice *s; // Filled out by cram_decode only int32_t ref_id; // fixed for all recs in slice? int32_t flags; // BF int32_t cram_flags; // CF int32_t len; // RL int64_t apos; // AP int32_t rg; // RG int32_t name; // RN; idx to s->names_blk int32_t name_len; int32_t mate_line; // index to another cram_record int32_t mate_ref_id; int64_t mate_pos; // NP int64_t tlen; // TS int64_t explicit_tlen;// TS, but PNEXT/RNEXT still need auto-computing // Auxiliary data int32_t ntags; // TC uint32_t aux; // idx to s->aux_blk uint32_t aux_size; // total size of packed ntags in aux_blk #ifndef TN_external int32_t TN_idx; // TN; idx to s->TN; #else int32_t tn; // idx to s->tn_blk #endif int TL; uint32_t seq; // idx to s->seqs_blk uint32_t qual; // idx to s->qual_blk uint32_t cigar; // idx to s->cigar int32_t ncigar; int64_t aend; // alignment end int32_t mqual; // MQ uint32_t feature; // idx to s->feature uint32_t nfeature; // number of features int32_t mate_flags; // MF } cram_record; // Accessor macros as an analogue of the bam ones #define cram_qname(c) (&(c)->s->name_blk->data[(c)->name]) #define cram_seq(c) (&(c)->s->seqs_blk->data[(c)->seq]) #define cram_qual(c) (&(c)->s->qual_blk->data[(c)->qual]) #define cram_aux(c) (&(c)->s->aux_blk->data[(c)->aux]) #define cram_seqi(c,i) (cram_seq((c))[(i)]) #define cram_name_len(c) ((c)->name_len) #define cram_strand(c) (((c)->flags & BAM_FREVERSE) != 0) #define cram_mstrand(c) (((c)->flags & BAM_FMREVERSE) != 0) #define cram_cigar(c) (&((cr)->s->cigar)[(c)->cigar]) /* * A feature is a base difference, used for the sequence reference encoding. * (We generate these internally when writing CRAM.) */ typedef union cram_feature { struct { int pos; int code; int base; // substitution code } X; struct { int pos; int code; int base; // actual base & qual int qual; } B; struct { int pos; int code; int seq_idx; // index to s->seqs_blk int len; } b; struct { int pos; int code; int qual; } Q; struct { int pos; int code; int len; int seq_idx; // soft-clip multiple bases } S; struct { int pos; int code; int len; int seq_idx; // insertion multiple bases } I; struct { int pos; int code; int base; // insertion single base } i; struct { int pos; int code; int len; } D; struct { int pos; int code; int len; } N; struct { int pos; int code; int len; } P; struct { int pos; int code; int len; } H; } cram_feature; /* * A slice is really just a set of blocks, but it * is the logical unit for decoding a number of * sequences. */ struct cram_slice { cram_block_slice_hdr *hdr; cram_block *hdr_block; cram_block **block; cram_block **block_by_id; /* State used during encoding/decoding */ int64_t last_apos, max_apos; /* Array of decoded cram records */ cram_record *crecs; /* An dynamically growing buffers for data pointed * to by crecs[] array. */ uint32_t *cigar; uint32_t cigar_alloc; uint32_t ncigar; cram_feature *features; uint32_t nfeatures; uint32_t afeatures; // allocated size of features #ifndef TN_external // TN field (Tag Name) uint32_t *TN; int nTN, aTN; // used and allocated size for TN[] #else cram_block *tn_blk; int tn_id; #endif // For variable sized elements which are always external blocks. cram_block *name_blk; cram_block *seqs_blk; cram_block *qual_blk; cram_block *base_blk; cram_block *soft_blk; cram_block *aux_blk; // BAM aux block, created while decoding CRAM string_alloc_t *pair_keys; // Pooled keys for pair hash. khash_t(m_s2i) *pair[2]; // for identifying read-pairs in this slice. char *ref; // slice of current reference hts_pos_t ref_start; // start position of current reference; hts_pos_t ref_end; // end position of current reference; int ref_id; // For going from BAM to CRAM; an array of auxiliary blocks per type int naux_block; cram_block **aux_block; unsigned int data_series; // See cram_fields enum int decode_md; int max_rec, curr_rec; // current and max recs per slice int slice_num; // To be copied into c->curr_slice in decode }; /*----------------------------------------------------------------------------- * Consider moving reference handling to cram_refs.[ch] */ // from fa.fai / samtools faidx files typedef struct ref_entry { char *name; char *fn; int64_t length; int64_t offset; int bases_per_line; int line_length; int64_t count; // for shared references so we know to dealloc seq char *seq; mFILE *mf; int is_md5; // Reference comes from a raw seq found by MD5 int validated_md5; } ref_entry; KHASH_MAP_INIT_STR(refs, ref_entry*) // References structure. struct refs_t { string_alloc_t *pool; // String pool for holding filenames and SN vals khash_t(refs) *h_meta; // ref_entry*, index by name ref_entry **ref_id; // ref_entry*, index by ID int nref; // number of ref_entry char *fn; // current file opened BGZF *fp; // and the hFILE* to go with it. int count; // how many cram_fd sharing this refs struct pthread_mutex_t lock; // Mutex for multi-threaded updating ref_entry *last; // Last queried sequence int last_id; // Used in cram_ref_decr_locked to delay free }; /*----------------------------------------------------------------------------- * CRAM index * * Detect format by number of entries per line. * 5 => 1.0 (refid, start, nseq, C offset, slice) * 6 => 1.1 (refid, start, span, C offset, S offset, S size) * * Indices are stored in a nested containment list, which is trivial to set * up as the indices are on sorted data so we're appending to the nclist * in sorted order. Basically if a slice entirely fits within a previous * slice then we append to that slices list. This is done recursively. * * Lists are sorted on two dimensions: ref id + slice coords. */ typedef struct cram_index { int nslice, nalloc; // total number of slices struct cram_index *e; // array of size nslice int refid; // 1.0 1.1 int start; // 1.0 1.1 int end; // 1.1 int nseq; // 1.0 - undocumented int slice; // 1.0 landmark index, 1.1 landmark value int len; // 1.1 - size of slice in bytes int64_t offset; // 1.0 1.1 // Linked list of cram_index entries. Used to convert recursive // NCList back to a linear list. struct cram_index *e_next; } cram_index; typedef struct { int refid; int64_t start; int64_t end; } cram_range; /*----------------------------------------------------------------------------- */ /* CRAM File handle */ typedef struct spare_bams { bam_seq_t **bams; struct spare_bams *next; } spare_bams; struct cram_fd; typedef struct varint_vec { // Returns number of bytes decoded from fd, 0 on error int (*varint_decode32_crc)(struct cram_fd *fd, int32_t *val_p, uint32_t *crc); int (*varint_decode32s_crc)(struct cram_fd *fd, int32_t *val_p, uint32_t *crc); int (*varint_decode64_crc)(struct cram_fd *fd, int64_t *val_p, uint32_t *crc); // Returns the value and increments *cp. Sets err to 1 iff an error occurs. // NOTE: Does not set err to 0 on success. int64_t (*varint_get32) (char **cp, const char *endp, int *err); int64_t (*varint_get32s)(char **cp, const char *endp, int *err); int64_t (*varint_get64) (char **cp, const char *endp, int *err); int64_t (*varint_get64s)(char **cp, const char *endp, int *err); // Returns the number of bytes written, <= 0 on error. int (*varint_put32) (char *cp, char *endp, int32_t val_p); int (*varint_put32s)(char *cp, char *endp, int32_t val_p); int (*varint_put64) (char *cp, char *endp, int64_t val_p); int (*varint_put64s)(char *cp, char *endp, int64_t val_p); // Returns the number of bytes written, <= 0 on error. int (*varint_put32_blk) (cram_block *blk, int32_t val_p); int (*varint_put32s_blk)(cram_block *blk, int32_t val_p); int (*varint_put64_blk) (cram_block *blk, int64_t val_p); int (*varint_put64s_blk)(cram_block *blk, int64_t val_p); // Returns number of bytes needed to encode 'val' int (*varint_size)(int64_t val); } varint_vec; struct cram_fd { struct hFILE *fp; int mode; // 'r' or 'w' int version; cram_file_def *file_def; sam_hdr_t *header; char *prefix; int64_t record_counter; int err; // Most recent compression header decoded //cram_block_compression_hdr *comp_hdr; //cram_block_slice_hdr *slice_hdr; // Current container being processed cram_container *ctr; // Current container used for decoder threads cram_container *ctr_mt; // positions for encoding or decoding int first_base, last_base; // copied to container // cached reference portion refs_t *refs; // ref meta-data structure char *ref, *ref_free; // current portion held in memory int ref_id; // copied to container hts_pos_t ref_start; // copied to container hts_pos_t ref_end; // copied to container char *ref_fn; // reference fasta filename // compression level and metrics int level; cram_metrics *m[DS_END]; khash_t(m_metrics) *tags_used; // cram_metrics[], per tag types in use. // options int decode_md; // Whether to export MD and NM tags int seqs_per_slice; int bases_per_slice; int slices_per_container; int embed_ref; // copied to container int no_ref; // copied to container int no_ref_counter; // decide if permanent switch int ignore_md5; int use_bz2; int use_rans; int use_lzma; int use_fqz; int use_tok; int use_arith; int shared_ref; unsigned int required_fields; int store_md; int store_nm; cram_range range; // lookup tables, stored here so we can be trivially multi-threaded unsigned int bam_flag_swap[0x1000]; // cram -> bam flags unsigned int cram_flag_swap[0x1000];// bam -> cram flags unsigned char L1[256]; // ACGT{*} ->0123{4} unsigned char L2[256]; // ACGTN{*}->01234{5} char cram_sub_matrix[32][32]; // base substitution codes int index_sz; cram_index *index; // array, sizeof index_sz off_t first_container; off_t curr_position; int eof; int last_slice; // number of recs encoded in last slice int last_RI_count; // number of references encoded in last container int multi_seq; // -1 is auto, 0 is one ref per container, 1 is multi... int multi_seq_user; // Original user setting (CRAM_OPT_MULTI_SEQ_PER_SLICE) int unsorted; int last_mapped; // number of mapped reads in last container int empty_container; // Marker for EOF block // thread pool int own_pool; hts_tpool *pool; hts_tpool_process *rqueue; pthread_mutex_t metrics_lock; pthread_mutex_t ref_lock; pthread_mutex_t range_lock; spare_bams *bl; pthread_mutex_t bam_list_lock; void *job_pending; int ooc; // out of containers. int lossy_read_names; // boolean int tlen_approx; // max TLEN calculation offset. int tlen_zero; // If true, permit tlen 0 (=> tlen calculated) BGZF *idxfp; // File pointer for on-the-fly index creation // variable integer decoding callbacks. // This changed in CRAM4.0 to a data-size agnostic encoding. varint_vec vv; // Force AP delta even on non positional sorted data. // This can be beneficial for pairs where pairs are nearby each other. // We suffer with delta to unrelated things (previous pair), but gain // in delta between them. (Ideal would be a per read setting.) int ap_delta; }; // Translation of required fields to cram data series enum cram_fields { CRAM_BF = 0x00000001, CRAM_AP = 0x00000002, CRAM_FP = 0x00000004, CRAM_RL = 0x00000008, CRAM_DL = 0x00000010, CRAM_NF = 0x00000020, CRAM_BA = 0x00000040, CRAM_QS = 0x00000080, CRAM_FC = 0x00000100, CRAM_FN = 0x00000200, CRAM_BS = 0x00000400, CRAM_IN = 0x00000800, CRAM_RG = 0x00001000, CRAM_MQ = 0x00002000, CRAM_TL = 0x00004000, CRAM_RN = 0x00008000, CRAM_NS = 0x00010000, CRAM_NP = 0x00020000, CRAM_TS = 0x00040000, CRAM_MF = 0x00080000, CRAM_CF = 0x00100000, CRAM_RI = 0x00200000, CRAM_RS = 0x00400000, CRAM_PD = 0x00800000, CRAM_HC = 0x01000000, CRAM_SC = 0x02000000, CRAM_BB = 0x04000000, CRAM_BB_len = 0x08000000, CRAM_QQ = 0x10000000, CRAM_QQ_len = 0x20000000, CRAM_aux= 0x40000000, CRAM_ALL= 0x7fffffff, }; // A CIGAR opcode, but not necessarily the implications of it. Eg FC/FP may // encode a base difference, but we don't need to know what it is for CIGAR. // If we have a soft-clip or insertion, we do need SC/IN though to know how // long that array is. #define CRAM_CIGAR (CRAM_FN | CRAM_FP | CRAM_FC | CRAM_DL | CRAM_IN | \ CRAM_SC | CRAM_HC | CRAM_PD | CRAM_RS | CRAM_RL | CRAM_BF) #define CRAM_SEQ (CRAM_CIGAR | CRAM_BA | CRAM_BS | \ CRAM_RL | CRAM_AP | CRAM_BB) #define CRAM_QUAL (CRAM_CIGAR | CRAM_RL | CRAM_AP | CRAM_QS | CRAM_QQ) /* BF bitfields */ /* Corrected in 1.1. Use bam_flag_swap[bf] and BAM_* macros for 1.0 & 1.1 */ #define CRAM_FPAIRED 256 #define CRAM_FPROPER_PAIR 128 #define CRAM_FUNMAP 64 #define CRAM_FREVERSE 32 #define CRAM_FREAD1 16 #define CRAM_FREAD2 8 #define CRAM_FSECONDARY 4 #define CRAM_FQCFAIL 2 #define CRAM_FDUP 1 #define DS_aux_S "\001" #define DS_aux_OQ_S "\002" #define DS_aux_BQ_S "\003" #define DS_aux_BD_S "\004" #define DS_aux_BI_S "\005" #define DS_aux_FZ_S "\006" #define DS_aux_oq_S "\007" #define DS_aux_os_S "\010" #define DS_aux_oz_S "\011" #define CRAM_M_REVERSE 1 #define CRAM_M_UNMAP 2 /* CF bitfields */ #define CRAM_FLAG_PRESERVE_QUAL_SCORES (1<<0) #define CRAM_FLAG_DETACHED (1<<1) #define CRAM_FLAG_MATE_DOWNSTREAM (1<<2) #define CRAM_FLAG_NO_SEQ (1<<3) #define CRAM_FLAG_EXPLICIT_TLEN (1<<4) #define CRAM_FLAG_MASK ((1<<5)-1) /* Internal only */ #define CRAM_FLAG_STATS_ADDED (1<<30) #define CRAM_FLAG_DISCARD_NAME (1U<<31) #ifdef __cplusplus } #endif #endif /* HTSLIB_CRAM_STRUCTS_H */ pysam-0.23.0/htslib/cram/mFILE.c000066400000000000000000000415211475062545500162140ustar00rootroot00000000000000/* Copyright (c) 2005-2006, 2008-2009, 2013, 2015, 2017-2019 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #include #include #include "../htslib/hts_log.h" #include "os.h" #include "mFILE.h" #ifdef HAVE_MMAP #include #endif /* * This file contains memory-based versions of the most commonly used * (by io_lib) stdio functions. * * Actual file IO takes place either on opening or closing an mFILE. * * Coupled to this are a bunch of rather scary macros which can be obtained * by including stdio_hack.h. It is recommended though that you use mFILE.h * instead and replace fopen with mfopen (etc). This is more or less * mandatory if you wish to use both FILE and mFILE structs in a single file. */ static mFILE *m_channel[3]; /* stdin, stdout and stderr fakes */ /* * Reads the entirety of fp into memory. If 'fn' exists it is the filename * associated with fp. This will be used for more optimal reading (via a * stat to identify the size and a single read). Otherwise we use successive * reads until EOF. * * Returns a malloced buffer on success of length *size * NULL on failure */ static char *mfload(FILE *fp, const char *fn, size_t *size, int binary) { struct stat sb; char *data = NULL; size_t allocated = 0, used = 0; int bufsize = 8192; #ifdef _WIN32 if (binary) _setmode(_fileno(fp), _O_BINARY); else _setmode(_fileno(fp), _O_TEXT); #endif if (fn && -1 != stat(fn, &sb)) { data = malloc(allocated = sb.st_size); if (!data) return NULL; bufsize = sb.st_size; } else { fn = NULL; } do { size_t len; if (used + bufsize > allocated) { allocated += bufsize; char *datan = realloc(data, allocated); if (datan) { data = datan; } else { free(data); return NULL; } } len = fread(data + used, 1, allocated - used, fp); if (len > 0) used += len; } while (!feof(fp) && (fn == NULL || used < sb.st_size)); *size = used; return data; } #ifdef HAVE_MMAP /* * mmaps in the file, but only for reading currently. * * Returns 0 on success * -1 on failure */ int mfmmap(mFILE *mf, FILE *fp, const char *fn) { struct stat sb; if (stat(fn, &sb) != 0) return -1; mf->size = sb.st_size; mf->data = mmap(NULL, mf->size, PROT_READ, MAP_SHARED, fileno(fp), 0); if (!mf->data || mf->data == (void *)-1) return -1; mf->alloced = 0; return 0; } #endif /* * Creates and returns m_channel[0]. * We initialise this on the first attempted read, which then slurps in * all of stdin until EOF is met. */ mFILE *mstdin(void) { if (m_channel[0]) return m_channel[0]; m_channel[0] = mfcreate(NULL, 0); if (NULL == m_channel[0]) return NULL; m_channel[0]->fp = stdin; return m_channel[0]; } static void init_mstdin(void) { static int done_stdin = 0; if (done_stdin) return; m_channel[0]->data = mfload(stdin, NULL, &m_channel[0]->size, 1); m_channel[0]->mode = MF_READ; done_stdin = 1; } /* * Creates and returns m_channel[1]. This is the fake for stdout. It starts as * an empty buffer which is physically written out only when mfflush or * mfclose are called. */ mFILE *mstdout(void) { if (m_channel[1]) return m_channel[1]; m_channel[1] = mfcreate(NULL, 0); if (NULL == m_channel[1]) return NULL; m_channel[1]->fp = stdout; m_channel[1]->mode = MF_WRITE; return m_channel[1]; } /* * Stderr as an mFILE. * The code handles stderr by returning m_channel[2], but also checking * for stderr in fprintf (the common usage of it) to auto-flush. */ mFILE *mstderr(void) { if (m_channel[2]) return m_channel[2]; m_channel[2] = mfcreate(NULL, 0); if (NULL == m_channel[2]) return NULL; m_channel[2]->fp = stderr; m_channel[2]->mode = MF_WRITE; return m_channel[2]; } /* * For creating existing mFILE pointers directly from memory buffers. */ mFILE *mfcreate(char *data, int size) { mFILE *mf = (mFILE *)malloc(sizeof(*mf)); if (NULL == mf) return NULL; mf->fp = NULL; mf->data = data; mf->alloced = size; mf->size = size; mf->eof = 0; mf->offset = 0; mf->flush_pos = 0; mf->mode = MF_READ | MF_WRITE; return mf; } /* * Recreate an existing mFILE to house new data/size. * It also rewinds the file. */ void mfrecreate(mFILE *mf, char *data, int size) { if (mf->data) free(mf->data); mf->data = data; mf->size = size; mf->alloced = size; mf->eof = 0; mf->offset = 0; mf->flush_pos = 0; } /* * Creates a new mFILE to contain the contents of the FILE pointer. * This mFILE is purely for in-memory operations and has no links to the * original FILE* it came from. It also doesn't close the FILE pointer. * Consider using mfreopen() is you need different behaviour. * * Returns mFILE * on success * NULL on failure. */ mFILE *mfcreate_from(const char *path, const char *mode_str, FILE *fp) { mFILE *mf; /* Open using mfreopen() */ if (NULL == (mf = mfreopen(path, mode_str, fp))) return NULL; /* Disassociate from the input stream */ mf->fp = NULL; return mf; } /* * Converts a FILE * to an mFILE *. * Use this for wrapper functions to turn external prototypes requiring * FILE * as an argument into internal code using mFILE *. */ mFILE *mfreopen(const char *path, const char *mode_str, FILE *fp) { mFILE *mf; int r = 0, w = 0, a = 0, b = 0, x = 0, mode = 0; /* Parse mode: * r = read file contents (if truncated => don't read) * w = write on close * a = position at end of buffer * x = position at same location as the original fp, don't seek on flush * + = for update (read and write) * m = mmap (read only) */ if (strchr(mode_str, 'r')) r = 1, mode |= MF_READ; if (strchr(mode_str, 'w')) w = 1, mode |= MF_WRITE | MF_TRUNC; if (strchr(mode_str, 'a')) w = a = 1, mode |= MF_WRITE | MF_APPEND; if (strchr(mode_str, 'b')) b = 1, mode |= MF_BINARY; if (strchr(mode_str, 'x')) x = 1; if (strchr(mode_str, '+')) { w = 1, mode |= MF_READ | MF_WRITE; if (a) r = 1; } #ifdef HAVE_MMAP if (strchr(mode_str, 'm')) if (!w) mode |= MF_MMAP; #endif if (r) { mf = mfcreate(NULL, 0); if (NULL == mf) return NULL; if (!(mode & MF_TRUNC)) { #ifdef HAVE_MMAP if (mode & MF_MMAP) { if (mfmmap(mf, fp, path) == -1) { mf->data = NULL; mode &= ~MF_MMAP; } } #endif if (!mf->data) { mf->data = mfload(fp, path, &mf->size, b); if (!mf->data) { free(mf); return NULL; } mf->alloced = mf->size; if (!a) fseek(fp, 0, SEEK_SET); } } } else if (w) { /* Write - initialise the data structures */ mf = mfcreate(NULL, 0); if (NULL == mf) return NULL; } else { hts_log_error("Must specify either r, w or a for mode"); return NULL; } mf->fp = fp; mf->mode = mode; if (x) { mf->mode |= MF_MODEX; } if (a) { mf->flush_pos = mf->size; fseek(fp, 0, SEEK_END); } return mf; } /* * Opens a file. If we have read access (r or a+) then it loads the entire * file into memory. If We have write access then the pathname is stored. * We do not actually write until an mfclose, which then checks this pathname. */ mFILE *mfopen(const char *path, const char *mode) { FILE *fp; if (NULL == (fp = fopen(path, mode))) return NULL; return mfreopen(path, mode, fp); } /* * Closes an mFILE. If the filename is known (implying write access) then this * also writes the data to disk. * * Stdout is handled by calling mfflush which writes to stdout if appropriate. */ int mfclose(mFILE *mf) { if (!mf) return -1; mfflush(mf); #ifdef HAVE_MMAP if ((mf->mode & MF_MMAP) && mf->data) { /* Mmaped */ munmap(mf->data, mf->size); mf->data = NULL; } #endif if (mf->fp) fclose(mf->fp); mfdestroy(mf); return 0; } /* * Closes the file pointer contained within the mFILE without destroying * the in-memory data. * * Attempting to do this on an mmaped buffer is an error. */ int mfdetach(mFILE *mf) { if (!mf) return -1; mfflush(mf); if (mf->mode & MF_MMAP) return -1; if (mf->fp) { fclose(mf->fp); mf->fp = NULL; } return 0; } /* * Destroys an mFILE structure but does not flush or close it */ int mfdestroy(mFILE *mf) { if (!mf) return -1; if (mf->data) free(mf->data); free(mf); return 0; } /* * Steals that data out of an mFILE. The mFILE itself will be closed. * It is up to the caller to free the stolen buffer. If size_out is * not NULL, mf->size will be stored in it. * This is more-or-less the opposite of mfcreate(). * * Note, we cannot steal the allocated buffer from an mmaped mFILE. */ void *mfsteal(mFILE *mf, size_t *size_out) { void *data; if (!mf) return NULL; data = mf->data; if (NULL != size_out) *size_out = mf->size; if (mfdetach(mf) != 0) return NULL; mf->data = NULL; mfdestroy(mf); return data; } /* * Seek/tell functions. Nothing more than updating and reporting an * in-memory index. NB we can seek on stdin or stdout even provided we * haven't been flushing. */ int mfseek(mFILE *mf, long offset, int whence) { switch (whence) { case SEEK_SET: mf->offset = offset; break; case SEEK_CUR: mf->offset += offset; break; case SEEK_END: mf->offset = mf->size + offset; break; default: errno = EINVAL; return -1; } mf->eof = 0; return 0; } long mftell(mFILE *mf) { return mf->offset; } void mrewind(mFILE *mf) { mf->offset = 0; mf->eof = 0; } /* * mftruncate is not directly a translation of ftruncate as the latter * takes a file descriptor instead of a FILE *. It performs the analogous * role though. * * If offset is -1 then the file is truncated to be the current file * offset. */ void mftruncate(mFILE *mf, long offset) { mf->size = offset != -1 ? offset : mf->offset; if (mf->offset > mf->size) mf->offset = mf->size; } int mfeof(mFILE *mf) { return mf->eof; } /* * mFILE read/write functions. Basically these turn fread/fwrite syntax * into memcpy statements, with appropriate memory handling for writing. */ size_t mfread(void *ptr, size_t size, size_t nmemb, mFILE *mf) { size_t len; char *cptr = (char *)ptr; if (mf == m_channel[0]) init_mstdin(); if (mf->size <= mf->offset) return 0; len = size * nmemb <= mf->size - mf->offset ? size * nmemb : mf->size - mf->offset; if (!size) return 0; memcpy(cptr, &mf->data[mf->offset], len); mf->offset += len; if (len != size * nmemb) { mf->eof = 1; } return len / size; } size_t mfwrite(void *ptr, size_t size, size_t nmemb, mFILE *mf) { if (!(mf->mode & MF_WRITE)) return 0; /* Append mode => forced all writes to end of file */ if (mf->mode & MF_APPEND) mf->offset = mf->size; /* Make sure we have enough room */ while (size * nmemb + mf->offset > mf->alloced) { size_t new_alloced = mf->alloced ? mf->alloced * 2 : 1024; void * new_data = realloc(mf->data, new_alloced); if (NULL == new_data) return 0; mf->alloced = new_alloced; mf->data = new_data; } /* Record where we need to reflush from */ if (mf->offset < mf->flush_pos) mf->flush_pos = mf->offset; /* Copy the data over */ memcpy(&mf->data[mf->offset], ptr, size * nmemb); mf->offset += size * nmemb; if (mf->size < mf->offset) mf->size = mf->offset; return nmemb; } int mfgetc(mFILE *mf) { if (mf == m_channel[0]) init_mstdin(); if (mf->offset < mf->size) { return (unsigned char)mf->data[mf->offset++]; } mf->eof = 1; return -1; } int mungetc(int c, mFILE *mf) { if (mf->offset > 0) { mf->data[--mf->offset] = c; return c; } mf->eof = 1; return -1; } char *mfgets(char *s, int size, mFILE *mf) { int i; if (mf == m_channel[0]) init_mstdin(); *s = 0; for (i = 0; i < size-1;) { if (mf->offset < mf->size) { s[i] = mf->data[mf->offset++]; if (s[i++] == '\n') break; } else { mf->eof = 1; break; } } s[i] = 0; return i ? s : NULL; } /* * Flushes an mFILE. If this is a real open of a file in write mode then * mFILE->fp will be set. We then write out any new data in mFILE since the * last flush. We cannot tell what may have been modified as we don't keep * track of that, so we typically rewrite out the entire file contents between * the last flush_pos and the end of file. * * For stderr/stdout we also reset the offsets so we cannot modify things * we've already output. */ int mfflush(mFILE *mf) { if (!mf->fp) return 0; /* FIXME: only do this when opened in write mode */ if (mf == m_channel[1] || mf == m_channel[2]) { if (mf->flush_pos < mf->size) { size_t bytes = mf->size - mf->flush_pos; if (fwrite(mf->data + mf->flush_pos, 1, bytes, mf->fp) < bytes) return -1; if (0 != fflush(mf->fp)) return -1; } /* Stdout & stderr are non-seekable streams so throw away the data */ mf->offset = mf->size = mf->flush_pos = 0; } /* only flush when opened in write mode */ if (mf->mode & MF_WRITE) { if (mf->flush_pos < mf->size) { size_t bytes = mf->size - mf->flush_pos; if (!(mf->mode & MF_MODEX)) { fseek(mf->fp, mf->flush_pos, SEEK_SET); } if (fwrite(mf->data + mf->flush_pos, 1, bytes, mf->fp) < bytes) return -1; if (0 != fflush(mf->fp)) return -1; } if (ftell(mf->fp) != -1 && ftruncate(fileno(mf->fp), ftell(mf->fp)) == -1) return -1; mf->flush_pos = mf->size; } return 0; } /* * Converts an mFILE from binary to ascii mode by replacing all * cr-nl with nl. * * Primarily used on windows when we've uncompressed a binary file which * happens to be a text file (eg Experiment File). Previously we would have * seeked back to the start and used _setmode(fileno(fp), _O_TEXT). * * Side effect: resets offset and flush_pos back to the start. */ void mfascii(mFILE *mf) { size_t p1, p2; for (p1 = p2 = 1; p1 < mf->size; p1++, p2++) { if (mf->data[p1] == '\n' && mf->data[p1-1] == '\r') { p2--; /* delete the \r */ } mf->data[p2] = mf->data[p1]; } mf->size = p2; mf->offset = mf->flush_pos = 0; } pysam-0.23.0/htslib/cram/mFILE.h000066400000000000000000000060031475062545500162150ustar00rootroot00000000000000/* Copyright (c) 2005-2006, 2008-2009, 2013, 2018 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef CRAM_MFILE_H #define CRAM_MFILE_H #include #ifdef __cplusplus extern "C" { #endif typedef struct { FILE *fp; char *data; size_t alloced; int eof; int mode; /* open mode in MF_?? define bit pattern */ size_t size; size_t offset; size_t flush_pos; } mFILE; // Work around a clash with winuser.h #ifdef MF_APPEND # undef MF_APPEND #endif #define MF_READ 1 #define MF_WRITE 2 #define MF_APPEND 4 #define MF_BINARY 8 #define MF_TRUNC 16 #define MF_MODEX 32 #define MF_MMAP 64 mFILE *mfreopen(const char *path, const char *mode, FILE *fp); mFILE *mfopen(const char *path, const char *mode); int mfdetach(mFILE *mf); int mfclose(mFILE *mf); int mfdestroy(mFILE *mf); int mfseek(mFILE *mf, long offset, int whence); long mftell(mFILE *mf); void mrewind(mFILE *mf); void mftruncate(mFILE *mf, long offset); int mfeof(mFILE *mf); size_t mfread(void *ptr, size_t size, size_t nmemb, mFILE *mf); size_t mfwrite(void *ptr, size_t size, size_t nmemb, mFILE *mf); int mfgetc(mFILE *mf); int mungetc(int c, mFILE *mf); mFILE *mfcreate(char *data, int size); mFILE *mfcreate_from(const char *path, const char *mode_str, FILE *fp); void mfrecreate(mFILE *mf, char *data, int size); void *mfsteal(mFILE *mf, size_t *size_out); char *mfgets(char *s, int size, mFILE *mf); int mfflush(mFILE *mf); mFILE *mstdin(void); mFILE *mstdout(void); mFILE *mstderr(void); void mfascii(mFILE *mf); #ifdef __cplusplus } #endif #endif /* CRAM_MFILE_H */ pysam-0.23.0/htslib/cram/misc.h000066400000000000000000000064531475062545500162650ustar00rootroot00000000000000/* Copyright (c) 1994-1997, 2001-2002 MEDICAL RESEARCH COUNCIL All rights reserved Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1 Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2 Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /* Copyright (c) 2003-2013, 2018-2019 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef CRAM_MISC_H #define CRAM_MISC_H #ifdef __cplusplus extern "C" { #endif #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) #define MAX(A,B) ( ( (A) > (B) ) ? (A) : (B) ) #ifdef __cplusplus } #endif #endif /* CRAM_MISC_H */ pysam-0.23.0/htslib/cram/open_trace_file.c000066400000000000000000000332521475062545500204400ustar00rootroot00000000000000/* Author: James Bonfield Copyright (c) 2000-2001 MEDICAL RESEARCH COUNCIL All rights reserved Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /* Copyright (c) 2008, 2009, 2013, 2014-2015, 2018-2020 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #include #include "os.h" #ifndef PATH_MAX # define PATH_MAX 1024 #endif #include "open_trace_file.h" #include "misc.h" #include "../htslib/hfile.h" #include "../htslib/hts_log.h" #include "../htslib/hts.h" /* * Returns whether the path refers to a regular file. */ static int is_file(char *fn) { struct stat buf; if ( stat(fn,&buf) ) return 0; return S_ISREG(buf.st_mode); } /* * Tokenises the search path splitting on colons (unix) or semicolons * (windows). * We also explicitly add a "./" to the end of the search path * * Returns: A new search path with items separated by nul chars. Two nul * chars in a row represent the end of the tokenised path. * Returns NULL for a failure. * * The returned data has been malloced. It is up to the caller to free this * memory. */ char *tokenise_search_path(const char *searchpath) { char *newsearch; unsigned int i, j; size_t len; char path_sep = HTS_PATH_SEPARATOR_CHAR; if (!searchpath) searchpath=""; newsearch = (char *)malloc((len = strlen(searchpath))+5); if (!newsearch) return NULL; for (i = 0, j = 0; i < len; i++) { /* "::" => ":". Used for escaping colons in http://foo */ if (i < len-1 && searchpath[i] == ':' && searchpath[i+1] == ':') { newsearch[j++] = ':'; i++; continue; } /* Handle http:// and ftp:// too without :: */ if (path_sep == ':') { if ((i == 0 || (i > 0 && searchpath[i-1] == ':')) && (!strncmp(&searchpath[i], "http:", 5) || !strncmp(&searchpath[i], "https:", 6) || !strncmp(&searchpath[i], "ftp:", 4) || !strncmp(&searchpath[i], "|http:", 6) || !strncmp(&searchpath[i], "|https:", 7) || !strncmp(&searchpath[i], "|ftp:", 5) || !strncmp(&searchpath[i], "URL=http:", 9) || !strncmp(&searchpath[i], "URL=https:",10)|| !strncmp(&searchpath[i], "URL=ftp:", 8))) { do { newsearch[j++] = searchpath[i]; } while (i 0) { if (mfwrite(buf, len, 1, mf) <= 0) { hclose_abruptly(hf); goto fail; } } if (hclose(hf) < 0 || len < 0) { hts_log_warning("Failed to read reference \"%s\": %s", path, strerror(errno)); goto fail; } free(path); mrewind(mf); return mf; fail: mfdestroy(mf); free(path); return NULL; } /* * Takes a dirname possibly including % rules and appends the filename * to it. * * Returns expanded pathname or NULL for malloc failure. */ static char *expand_path(const char *file, char *dirname, int max_s_digits) { size_t len = strlen(dirname); size_t lenf = strlen(file); char *cp, *path; path = malloc(len+lenf+2); // worst expansion DIR/FILE if (!path) { hts_log_error("Out of memory"); return NULL; } if (dirname[len-1] == '/') len--; /* Special case for "./" or absolute filenames */ if (*file == '/' || (len==1 && *dirname == '.')) { memcpy(path, file, lenf + 1); } else { /* Handle %[0-9]*s expansions, if required */ char *path_end = path; *path = 0; while ((cp = strchr(dirname, '%'))) { char *endp; long l = strtol(cp+1, &endp, 10); if (*endp != 's' || endp - cp - 1 > max_s_digits) { strncpy(path_end, dirname, (endp+1)-dirname); path_end += (endp+1)-dirname; dirname = endp+1; continue; } strncpy(path_end, dirname, cp-dirname); path_end += cp-dirname; if (l) { strncpy(path_end, file, l); path_end += MIN(strlen(file), l); file += MIN(strlen(file), l); } else { strcpy(path_end, file); path_end += strlen(file); file += strlen(file); } len -= (endp+1) - dirname; dirname = endp+1; } strncpy(path_end, dirname, len); path_end += MIN(strlen(dirname), len); *path_end = 0; if (*file) { *path_end++ = '/'; strcpy(path_end, file); } } //fprintf(stderr, "*PATH=\"%s\"\n", path); return path; } /* * Searches for file in the directory 'dirname'. If it finds it, it opens * it. This also searches for compressed versions of the file in dirname * too. * * Returns mFILE pointer if found * NULL if not */ static mFILE *find_file_dir(const char *file, char *dirname) { char *path; mFILE *mf = NULL; path = expand_path(file, dirname, INT_MAX); if (!path) return NULL; if (is_file(path)) mf = mfopen(path, "rbm"); free(path); return mf; } /* * ------------------------------------------------------------------------ * Public functions below. */ /* * Opens a trace file named 'file'. This is initially looked for as a * pathname relative to a file named "relative_to". This may (for * example) be the name of an experiment file referencing the trace * file. In this case by passing relative_to as the experiment file * filename the trace file will be picked up in the same directory as * the experiment file. Relative_to may be supplied as NULL. * * 'file' is looked for at relative_to, then the current directory, and then * all of the locations listed in 'path' (which is a colon separated list). * If 'path' is NULL it uses the RAWDATA environment variable instead. * * Returns a mFILE pointer when found. * NULL otherwise. */ mFILE *open_path_mfile(const char *file, char *path, char *relative_to) { char *newsearch; char *ele; mFILE *fp; /* Use path first */ if (!path) path = getenv("RAWDATA"); if (NULL == (newsearch = tokenise_search_path(path))) return NULL; /* * Step through the search path testing out each component. * We now look through each path element treating some prefixes as * special, otherwise we treat the element as a directory. */ for (ele = newsearch; *ele; ele += strlen(ele)+1) { char *ele2; /* * '|' prefixing a path component indicates that we do not * wish to perform the compression extension searching in that * location. * * NB: this has been removed from the htslib implementation. */ if (*ele == '|') { ele2 = ele+1; } else { ele2 = ele; } if (0 == strncmp(ele2, "URL=", 4)) { if ((fp = find_file_url(file, ele2+4))) { free(newsearch); return fp; } } else if (!strncmp(ele2, "http:", 5) || !strncmp(ele2, "https:", 6) || !strncmp(ele2, "ftp:", 4)) { if ((fp = find_file_url(file, ele2))) { free(newsearch); return fp; } } else if ((fp = find_file_dir(file, ele2))) { free(newsearch); return fp; } } free(newsearch); /* Look in the same location as the incoming 'relative_to' filename */ if (relative_to) { char *cp; char relative_path[PATH_MAX+1]; strcpy(relative_path, relative_to); if ((cp = strrchr(relative_path, '/'))) *cp = 0; if ((fp = find_file_dir(file, relative_path))) return fp; } return NULL; } /* * As per open_path_mfile, but searching only for local filenames. * This is useful as we may avoid doing a full mfopen and loading * the entire file into memory. * * Returns the expanded pathname if found. * NULL if not */ char *find_path(const char *file, const char *path) { char *newsearch; char *ele; char *outpath = NULL; /* Use path first */ if (!path) path = getenv("RAWDATA"); if (NULL == (newsearch = tokenise_search_path(path))) return NULL; for (ele = newsearch; *ele; ele += strlen(ele)+1) { char *ele2 = (*ele == '|') ? ele+1 : ele; if (!strncmp(ele2, "URL=", 4) || !strncmp(ele2, "http:", 5) || !strncmp(ele2, "https:", 6) || !strncmp(ele2, "ftp:", 4)) { continue; } else { outpath = expand_path(file, ele2, INT_MAX); if (is_file(outpath)) { free(newsearch); return outpath; } else { free(outpath); } } } free(newsearch); return NULL; } pysam-0.23.0/htslib/cram/open_trace_file.h000066400000000000000000000116431475062545500204450ustar00rootroot00000000000000/* Author: James Bonfield Copyright (c) 2000-2001 MEDICAL RESEARCH COUNCIL All rights reserved Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /* Copyright (c) 2008, 2009, 2013, 2018 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef OPEN_TRACE_FILE_H #define OPEN_TRACE_FILE_H #include "mFILE.h" #ifdef __cplusplus extern "C" { #endif /* * Tokenises the search path splitting on colons (unix) or semicolons * (windows). * We also explicitly add a "./" to the end of the search path * * Returns: A new search path with items separated by nul chars. Two nul * chars in a row represent the end of the tokenised path. * Returns NULL for a failure. * * The returned data has been malloced. It is up to the caller to free this * memory. */ char *tokenise_search_path(const char *searchpath); /* * Opens a trace file named 'file'. This is initially looked for as a * pathname relative to a file named "relative_to". This may (for * example) be the name of an experiment file referencing the trace * file. In this case by passing relative_to as the experiment file * filename the trace file will be picked up in the same directory as * the experiment file. Relative_to may be supplied as NULL. * * 'file' is looked for at relative_to, then the current directory, and then * all of the locations listed in 'path' (which is a colon separated list). * If 'path' is NULL it uses the RAWDATA environment variable instead. * * Returns a mFILE pointer when found. * NULL otherwise. */ mFILE *open_path_mfile(const char *file, char *path, char *relative_to); /* * Returns a mFILE containing the entire contents of the url; * NULL on failure. */ mFILE *find_file_url(const char *file, char *url); /* * As per open_path_mfile, but searching only for local filenames. * This is useful as we may avoid doing a full mfopen and loading * the entire file into memory. * * Returns the expanded pathname if found. * NULL if not */ char *find_path(const char *file, const char *path); #ifdef __cplusplus } #endif #endif /* OPEN_TRACE_FILE_H */ pysam-0.23.0/htslib/cram/os.h000066400000000000000000000152401475062545500157450ustar00rootroot00000000000000/* Copyright (c) 1993, 1995-2002 MEDICAL RESEARCH COUNCIL All rights reserved Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1 Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2 Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /* Copyright (c) 2004, 2006, 2009-2011, 2013, 2017-2018 Genome Research Ltd. Author: James Bonfield Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /* * File: os.h * * Author: * MRC Laboratory of Molecular Biology * Hills Road * Cambridge CB2 2QH * United Kingdom * * Description: operating system specific type definitions * */ #ifndef CRAM_OS_H #define CRAM_OS_H #include #include #include "../htslib/hts_endian.h" #ifdef __cplusplus extern "C" { #endif /*----------------------------------------------------------------------------- * Byte swapping macros */ /* * Our new swap runs at the same speed on Ultrix, but substantially faster * (300% for swap_int4, ~50% for swap_int2) on an Alpha (due to the lack of * decent 'char' support). * * They also have the ability to swap in situ (src == dst). Newer code now * relies on this so don't change back! */ #define iswap_int8(x) \ (((x & 0x00000000000000ffLL) << 56) + \ ((x & 0x000000000000ff00LL) << 40) + \ ((x & 0x0000000000ff0000LL) << 24) + \ ((x & 0x00000000ff000000LL) << 8) + \ ((x & 0x000000ff00000000LL) >> 8) + \ ((x & 0x0000ff0000000000LL) >> 24) + \ ((x & 0x00ff000000000000LL) >> 40) + \ ((x & 0xff00000000000000LL) >> 56)) #define iswap_int4(x) \ (((x & 0x000000ff) << 24) + \ ((x & 0x0000ff00) << 8) + \ ((x & 0x00ff0000) >> 8) + \ ((x & 0xff000000) >> 24)) #define iswap_int2(x) \ (((x & 0x00ff) << 8) + \ ((x & 0xff00) >> 8)) /* * Linux systems may use byteswap.h to get assembly versions of byte-swap * on intel systems. This can be as trivial as the bswap opcode, which works * out at over 2-times faster than iswap_int4 above. */ #if 0 #if defined(__linux__) # include # undef iswap_int8 # undef iswap_int4 # undef iswap_int2 # define iswap_int8 bswap_64 # define iswap_int4 bswap_32 # define iswap_int2 bswap_16 #endif #endif /* * Macros to specify that data read in is of a particular endianness. * The macros here swap to the appropriate order for the particular machine * running the macro and return the new answer. These may also be used when * writing to a file to specify that we wish to write in (eg) big endian * format. * * This leads to efficient code as most of the time these macros are * trivial. */ #if defined(HTS_BIG_ENDIAN) #define le_int4(x) iswap_int4((x)) #define le_int2(x) iswap_int2((x)) #elif defined(HTS_LITTLE_ENDIAN) #define le_int4(x) (x) #define le_int2(x) (x) #else static inline uint32_t le_int4(uint32_t x) { return le_to_u32((uint8_t *) &x); } static inline uint16_t le_int2(uint16_t x) { return le_to_u16((uint8_t *) &x); } #endif /*----------------------------------------------------------------------------- * Operating system specifics. * These ought to be done by autoconf, but are legacy code. */ /* * SunOS 4.x * Even though we use the ANSI gcc, we make use the the standard SunOS 4.x * libraries and include files, which are non-ansi */ #if defined(__sun__) && !defined(__svr4__) #define SEEK_SET 0 #define SEEK_CUR 1 #define SEEK_END 2 #endif /* * Microsoft Visual C++ * Windows */ #if defined(_MSC_VER) #define popen _popen #define pclose _pclose #define ftruncate(fd,len) _chsize(fd,len) #endif /* * Microsoft Windows running MinGW */ #if defined(__MINGW32__) #include #define mkdir(filename,mode) mkdir((filename)) #define sysconf(x) 512 #ifndef ftruncate # define ftruncate(fd,len) _chsize(fd,len) #endif #endif #ifdef __cplusplus } #endif #endif /* CRAM_OS_H */ pysam-0.23.0/htslib/cram/pooled_alloc.c000066400000000000000000000116711475062545500177570ustar00rootroot00000000000000/* Copyright (c) 2009, 2013, 2015, 2018-2019 Genome Research Ltd. Author: Rob Davies Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include "pooled_alloc.h" #include "misc.h" //#define DISABLE_POOLED_ALLOC //#define TEST_MAIN #define PSIZE 1024*1024 // credit to http://graphics.stanford.edu/~seander/bithacks.html static int next_power_2(unsigned int v) { v--; v |= v >> 1; v |= v >> 2; v |= v >> 4; v |= v >> 8; v |= v >> 16; v++; return v; } /* * Creates a pool. * Pool allocations are approx minimum of 1024*dsize or PSIZE. * (Assumes we're not trying to use pools for >= 2Gb or more) */ pool_alloc_t *pool_create(size_t dsize) { pool_alloc_t *p; if (NULL == (p = (pool_alloc_t *)malloc(sizeof(*p)))) return NULL; /* Minimum size is a pointer, for free list */ dsize = (dsize + sizeof(void *) - 1) & ~(sizeof(void *)-1); if (dsize < sizeof(void *)) dsize = sizeof(void *); p->dsize = dsize; p->psize = MIN(PSIZE, next_power_2(p->dsize*1024)); p->npools = 0; p->pools = NULL; p->free = NULL; return p; } void pool_destroy(pool_alloc_t *p) { size_t i; for (i = 0; i < p->npools; i++) { free(p->pools[i].pool); } free(p->pools); free(p); } #ifndef DISABLE_POOLED_ALLOC static pool_t *new_pool(pool_alloc_t *p) { size_t n = p->psize / p->dsize; pool_t *pool; pool = realloc(p->pools, (p->npools + 1) * sizeof(*p->pools)); if (NULL == pool) return NULL; p->pools = pool; pool = &p->pools[p->npools]; pool->pool = malloc(n * p->dsize); if (NULL == pool->pool) return NULL; pool->used = 0; p->npools++; return pool; } void *pool_alloc(pool_alloc_t *p) { pool_t *pool; void *ret; /* Look on free list */ if (NULL != p->free) { ret = p->free; p->free = *((void **)p->free); return ret; } /* Look for space in the last pool */ if (p->npools) { pool = &p->pools[p->npools - 1]; if (pool->used + p->dsize < p->psize) { ret = ((char *) pool->pool) + pool->used; pool->used += p->dsize; return ret; } } /* Need a new pool */ pool = new_pool(p); if (NULL == pool) return NULL; pool->used = p->dsize; return pool->pool; } void pool_free(pool_alloc_t *p, void *ptr) { *(void **)ptr = p->free; p->free = ptr; } #else void *pool_alloc(pool_alloc_t *p) { return malloc(p->dsize); } void pool_free(pool_alloc_t *p, void *ptr) { free(ptr); } #endif #ifdef TEST_MAIN typedef struct { int x, y, z; } xyz; #define NP 10000 int main(void) { int i; xyz *item; xyz **items; pool_alloc_t *p = pool_create(sizeof(xyz)); items = (xyz **)malloc(NP * sizeof(*items)); for (i = 0; i < NP; i++) { item = pool_alloc(p); item->x = i; item->y = i+1; item->z = i+2; items[i] = item; } for (i = 0; i < NP; i++) { item = items[i]; if (i % 3) pool_free(p, item); } for (i = 0; i < NP; i++) { item = pool_alloc(p); item->x = 1000000+i; item->y = 1000000+i+1; item->z = 1000000+i+2; } for (i = 0; i < NP; i++) { item = items[i]; printf("%d\t%d\t%d\t%d\n", i, item->x, item->y, item->z); pool_free(p, item); } free(items); return 0; } #endif pysam-0.23.0/htslib/cram/pooled_alloc.h000066400000000000000000000042111475062545500177540ustar00rootroot00000000000000/* Copyright (c) 2009, 2013, 2018 Genome Research Ltd. Author: Rob Davies Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef POOLED_ALLOC_H #define POOLED_ALLOC_H #include #ifdef __cplusplus extern "C" { #endif /* * Implements a pooled block allocator where all items are the same size, * but we need many of them. */ typedef struct { void *pool; size_t used; } pool_t; typedef struct { size_t dsize; size_t psize; size_t npools; pool_t *pools; void *free; } pool_alloc_t; pool_alloc_t *pool_create(size_t dsize); void pool_destroy(pool_alloc_t *p); void *pool_alloc(pool_alloc_t *p); void pool_free(pool_alloc_t *p, void *ptr); #ifdef __cplusplus } #endif #endif /* POOLED_ALLOC_H */ pysam-0.23.0/htslib/cram/string_alloc.c000066400000000000000000000105061475062545500177770ustar00rootroot00000000000000/* Copyright (c) 2010, 2013, 2018-2019 Genome Research Ltd. Author: Andrew Whitwham Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /* A pooled string allocator intended to cut down on the memory overhead of many small string allocations. Andrew Whitwham, September 2010. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include "string_alloc.h" #define MIN_STR_SIZE 1024 /* creates the string pool. max_length is the initial size a single string can be. The max_length can grow as needed */ string_alloc_t *string_pool_create(size_t max_length) { string_alloc_t *a_str; if (NULL == (a_str = (string_alloc_t *)malloc(sizeof(*a_str)))) { return NULL; } if (max_length < MIN_STR_SIZE) max_length = MIN_STR_SIZE; a_str->nstrings = 0; a_str->max_strings = 0; a_str->max_length = max_length; a_str->strings = NULL; return a_str; } /* internal function to do the actual memory allocation */ static string_t *new_string_pool(string_alloc_t *a_str) { string_t *str; if (a_str->nstrings == a_str->max_strings) { size_t new_max = (a_str->max_strings | (a_str->max_strings >> 2)) + 1; str = realloc(a_str->strings, new_max * sizeof(*a_str->strings)); if (NULL == str) return NULL; a_str->strings = str; a_str->max_strings = new_max; } str = &a_str->strings[a_str->nstrings]; str->str = malloc(a_str->max_length); if (NULL == str->str) return NULL; str->used = 0; a_str->nstrings++; return str; } /* free allocated memory */ void string_pool_destroy(string_alloc_t *a_str) { size_t i; for (i = 0; i < a_str->nstrings; i++) { free(a_str->strings[i].str); } free(a_str->strings); free(a_str); } /* allocate space for a string */ char *string_alloc(string_alloc_t *a_str, size_t length) { string_t *str; char *ret; if (length <= 0) return NULL; // add to last string pool if we have space if (a_str->nstrings) { str = &a_str->strings[a_str->nstrings - 1]; if (str->used + length < a_str->max_length) { ret = str->str + str->used; str->used += length; return ret; } } // increase the max length if needs be if (length > a_str->max_length) a_str->max_length = length; // need a new string pool str = new_string_pool(a_str); if (NULL == str) return NULL; str->used = length; return str->str; } /* equivalent to strdup */ char *string_dup(string_alloc_t *a_str, const char *instr) { return string_ndup(a_str, instr, strlen(instr)); } char *string_ndup(string_alloc_t *a_str, const char *instr, size_t len) { char *str = string_alloc(a_str, len + 1); if (NULL == str) return NULL; memcpy(str, instr, len); str[len] = 0; return str; } pysam-0.23.0/htslib/cram/string_alloc.h000066400000000000000000000044641475062545500200120ustar00rootroot00000000000000/* Copyright (c) 2010, 2013, 2018 Genome Research Ltd. Author: Andrew Whitwham Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef STRING_ALLOC_H #define STRING_ALLOC_H #include #ifdef __cplusplus extern "C" { #endif /* * A pooled string allocator intended to cut down on the * memory overhead of many small string allocations. * * Andrew Whitwham, September 2010. */ typedef struct { char *str; size_t used; } string_t; typedef struct { size_t max_length; size_t nstrings; size_t max_strings; string_t *strings; } string_alloc_t; string_alloc_t *string_pool_create(size_t max_length); void string_pool_destroy(string_alloc_t *a_str); char *string_alloc(string_alloc_t *a_str, size_t length); char *string_dup(string_alloc_t *a_str, const char *instr); char *string_ndup(string_alloc_t *a_str, const char *instr, size_t len); #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/errmod.c000066400000000000000000000151451475062545500156710ustar00rootroot00000000000000/* errmod.c -- revised MAQ error model. Copyright (C) 2010 Broad Institute. Copyright (C) 2012, 2013, 2016-2017, 2019 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include "htslib/hts.h" #include "htslib/ksort.h" #include "htslib/hts_os.h" // for drand48 KSORT_INIT_STATIC_GENERIC(uint16_t) struct errmod_t { double depcorr; /* table of constants generated for given depcorr and eta */ double *fk, *beta, *lhet; }; typedef struct { double fsum[16], bsum[16]; uint32_t c[16]; } call_aux_t; /* \Gamma(n) = (n-1)! */ #define lfact(n) lgamma(n+1) /* generates a success * trials table of bionomial probability densities (log transformed) */ static double* logbinomial_table( const int n_size ) { /* prob distribution for binom var is p(k) = {n! \over k! (n-k)! } p^k (1-p)^{n-k} */ /* this calcs p(k) = {log(n!) - log(k!) - log((n-k)!) */ int k, n; double *logbinom = (double*)calloc(n_size * n_size, sizeof(double)); if (!logbinom) return NULL; for (n = 1; n < n_size; ++n) { double lfn = lfact(n); for (k = 1; k <= n; ++k) logbinom[n<<8|k] = lfn - lfact(k) - lfact(n-k); } return logbinom; } static int cal_coef(errmod_t *em, double depcorr, double eta) { int k, n, q; double sum, sum1; double *lC; // initialize ->fk em->fk = (double*)calloc(256, sizeof(double)); if (!em->fk) return -1; em->fk[0] = 1.0; for (n = 1; n < 256; ++n) em->fk[n] = pow(1. - depcorr, n) * (1.0 - eta) + eta; // initialize ->beta em->beta = (double*)calloc(256 * 256 * 64, sizeof(double)); if (!em->beta) return -1; lC = logbinomial_table( 256 ); if (!lC) return -1; for (q = 1; q < 64; ++q) { double e = pow(10.0, -q/10.0); double le = log(e); double le1 = log(1.0 - e); for (n = 1; n <= 255; ++n) { double *beta = em->beta + (q<<16|n<<8); sum1 = lC[n<<8|n] + n*le; beta[n] = HUGE_VAL; for (k = n - 1; k >= 0; --k, sum1 = sum) { sum = sum1 + log1p(exp(lC[n<<8|k] + k*le + (n-k)*le1 - sum1)); beta[k] = -10. / M_LN10 * (sum1 - sum); } } } // initialize ->lhet em->lhet = (double*)calloc(256 * 256, sizeof(double)); if (!em->lhet) { free(lC); return -1; } for (n = 0; n < 256; ++n) for (k = 0; k < 256; ++k) em->lhet[n<<8|k] = lC[n<<8|k] - M_LN2 * n; free(lC); return 0; } /** * Create errmod_t object with obj.depcorr set to depcorr and initialise */ errmod_t *errmod_init(double depcorr) { errmod_t *em; em = (errmod_t*)calloc(1, sizeof(errmod_t)); if (!em) return NULL; em->depcorr = depcorr; cal_coef(em, depcorr, 0.03); return em; } /** * Deallocate an errmod_t object */ void errmod_destroy(errmod_t *em) { if (em == 0) return; free(em->lhet); free(em->fk); free(em->beta); free(em); } // // em: error model to fit to data // m: number of alleles across all samples // n: number of bases observed in sample // bases[i]: bases observed in pileup [6 bit quality|1 bit strand|4 bit base] // q[i*m+j]: (Output) phred-scaled likelihood of each genotype (i,j) int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q) { // Aux // aux.c is total count of each base observed (ignoring strand) call_aux_t aux; // Loop variables int i, j, k; // The total count of each base observed per strand int w[32]; memset(q, 0, m * m * sizeof(float)); // initialise q to 0 if (n == 0) return 0; // This section randomly downsamples to 255 depth so as not to go beyond our precalculated matrix if (n > 255) { // if we exceed 255 bases observed then shuffle them to sample and only keep the first 255 ks_shuffle(uint16_t, n, bases); n = 255; } ks_introsort(uint16_t, n, bases); /* zero out w and aux */ memset(w, 0, 32 * sizeof(int)); memset(&aux, 0, sizeof(call_aux_t)); for (j = n - 1; j >= 0; --j) { // calculate esum and fsum uint16_t b = bases[j]; /* extract quality and cap at 63 */ int qual = b>>5 < 4? 4 : b>>5; if (qual > 63) qual = 63; /* extract base ORed with strand */ int basestrand = b&0x1f; /* extract base */ int base = b&0xf; aux.fsum[base] += em->fk[w[basestrand]]; aux.bsum[base] += em->fk[w[basestrand]] * em->beta[qual<<16|n<<8|aux.c[base]]; ++aux.c[base]; ++w[basestrand]; } // generate likelihood for (j = 0; j < m; ++j) { float tmp1, tmp3; int tmp2; // homozygous for (k = 0, tmp1 = tmp3 = 0.0, tmp2 = 0; k < m; ++k) { if (k == j) continue; tmp1 += aux.bsum[k]; tmp2 += aux.c[k]; tmp3 += aux.fsum[k]; } if (tmp2) { q[j*m+j] = tmp1; } // heterozygous for (k = j + 1; k < m; ++k) { int cjk = aux.c[j] + aux.c[k]; for (i = 0, tmp2 = 0, tmp1 = tmp3 = 0.0; i < m; ++i) { if (i == j || i == k) continue; tmp1 += aux.bsum[i]; tmp2 += aux.c[i]; tmp3 += aux.fsum[i]; } if (tmp2) { q[j*m+k] = q[k*m+j] = -4.343 * em->lhet[cjk<<8|aux.c[k]] + tmp1; } else q[j*m+k] = q[k*m+j] = -4.343 * em->lhet[cjk<<8|aux.c[k]]; // all the bases are either j or k } /* clamp to greater than 0 */ for (k = 0; k < m; ++k) if (q[j*m+k] < 0.0) q[j*m+k] = 0.0; } return 0; } pysam-0.23.0/htslib/faidx.c000066400000000000000000000744061475062545500155010ustar00rootroot00000000000000/* faidx.c -- FASTA and FASTQ random access. Copyright (C) 2008, 2009, 2013-2020, 2022, 2024 Genome Research Ltd. Portions copyright (C) 2011 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #include #include #include "htslib/bgzf.h" #include "htslib/faidx.h" #include "htslib/hfile.h" #include "htslib/khash.h" #include "htslib/kstring.h" #include "hts_internal.h" // Faster isgraph; assumes ASCII static inline int isgraph_(unsigned char c) { return c > ' ' && c <= '~'; } #ifdef isgraph # undef isgraph #endif #define isgraph isgraph_ // An optimised bgzf_getc. // We could consider moving this to bgzf.h, but our own code uses it here only. static inline int bgzf_getc_(BGZF *fp) { if (fp->block_offset+1 < fp->block_length) { int c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++]; fp->uncompressed_address++; return c; } return bgzf_getc(fp); } #define bgzf_getc bgzf_getc_ typedef struct { int id; // faidx_t->name[id] is for this struct. uint32_t line_len, line_blen; uint64_t len; uint64_t seq_offset; uint64_t qual_offset; } faidx1_t; KHASH_MAP_INIT_STR(s, faidx1_t) struct faidx_t { BGZF *bgzf; int n, m; char **name; khash_t(s) *hash; enum fai_format_options format; }; static int fai_name2id(void *v, const char *ref) { faidx_t *fai = (faidx_t *)v; khint_t k = kh_get(s, fai->hash, ref); return k == kh_end(fai->hash) ? -1 : kh_val(fai->hash, k).id; } static inline int fai_insert_index(faidx_t *idx, const char *name, uint64_t len, uint32_t line_len, uint32_t line_blen, uint64_t seq_offset, uint64_t qual_offset) { if (!name) { hts_log_error("Malformed line"); return -1; } char *name_key = strdup(name); int absent; khint_t k = kh_put(s, idx->hash, name_key, &absent); faidx1_t *v = &kh_value(idx->hash, k); if (! absent) { hts_log_warning("Ignoring duplicate sequence \"%s\" at byte offset %" PRIu64, name, seq_offset); free(name_key); return 0; } if (idx->n == idx->m) { char **tmp; idx->m = idx->m? idx->m<<1 : 16; if (!(tmp = (char**)realloc(idx->name, sizeof(char*) * idx->m))) { hts_log_error("Out of memory"); return -1; } idx->name = tmp; } v->id = idx->n; idx->name[idx->n++] = name_key; v->len = len; v->line_len = line_len; v->line_blen = line_blen; v->seq_offset = seq_offset; v->qual_offset = qual_offset; return 0; } static faidx_t *fai_build_core(BGZF *bgzf) { kstring_t name = { 0, 0, NULL }; int c, read_done, line_num; faidx_t *idx; uint64_t seq_offset, qual_offset; uint64_t seq_len, qual_len; uint64_t char_len, cl, line_len, ll; enum read_state {OUT_READ, IN_NAME, IN_SEQ, SEQ_END, IN_QUAL} state; idx = (faidx_t*)calloc(1, sizeof(faidx_t)); idx->hash = kh_init(s); idx->format = FAI_NONE; state = OUT_READ, read_done = 0, line_num = 1; seq_offset = qual_offset = seq_len = qual_len = char_len = cl = line_len = ll = 0; while ((c = bgzf_getc(bgzf)) >= 0) { switch (state) { case OUT_READ: switch (c) { case '>': if (idx->format == FAI_FASTQ) { hts_log_error("Found '>' in a FASTQ file, error at line %d", line_num); goto fail; } idx->format = FAI_FASTA; state = IN_NAME; break; case '@': if (idx->format == FAI_FASTA) { hts_log_error("Found '@' in a FASTA file, error at line %d", line_num); goto fail; } idx->format = FAI_FASTQ; state = IN_NAME; break; case '\r': // Blank line with cr-lf ending? if ((c = bgzf_getc(bgzf)) == '\n') { line_num++; } else { hts_log_error("Format error, carriage return not followed by new line at line %d", line_num); goto fail; } break; case '\n': // just move onto the next line line_num++; break; default: { char s[4] = { '"', c, '"', '\0' }; hts_log_error("Format error, unexpected %s at line %d", isprint(c) ? s : "character", line_num); goto fail; } } break; case IN_NAME: if (read_done) { if (fai_insert_index(idx, name.s, seq_len, line_len, char_len, seq_offset, qual_offset) != 0) goto fail; read_done = 0; } name.l = 0; do { if (!isspace(c)) { kputc(c, &name); } else if (name.l > 0 || c == '\n') { break; } } while ((c = bgzf_getc(bgzf)) >= 0); kputsn("", 0, &name); if (c < 0) { hts_log_error("The last entry '%s' has no sequence at line %d", name.s, line_num); goto fail; } // read the rest of the line if necessary if (c != '\n') while ((c = bgzf_getc(bgzf)) >= 0 && c != '\n'); state = IN_SEQ; seq_len = qual_len = char_len = line_len = 0; seq_offset = bgzf_utell(bgzf); line_num++; break; case IN_SEQ: if (idx->format == FAI_FASTA) { if (c == '\n') { state = OUT_READ; line_num++; continue; } else if (c == '>') { state = IN_NAME; continue; } } else if (idx->format == FAI_FASTQ) { if (c == '+') { state = IN_QUAL; if (c != '\n') while ((c = bgzf_getc(bgzf)) >= 0 && c != '\n'); qual_offset = bgzf_utell(bgzf); line_num++; continue; } else if (c == '\n') { hts_log_error("Inlined empty line is not allowed in sequence '%s' at line %d", name.s, line_num); goto fail; } } ll = cl = 0; if (idx->format == FAI_FASTA) read_done = 1; do { ll++; if (isgraph(c)) cl++; } while ((c = bgzf_getc(bgzf)) >= 0 && c != '\n'); ll++; seq_len += cl; if (line_len == 0) { line_len = ll; char_len = cl; } else if (line_len > ll) { if (idx->format == FAI_FASTA) state = OUT_READ; else state = SEQ_END; } else if (line_len < ll) { hts_log_error("Different line length in sequence '%s' at line %d", name.s, line_num); goto fail; } line_num++; break; case SEQ_END: if (c == '+') { state = IN_QUAL; while ((c = bgzf_getc(bgzf)) >= 0 && c != '\n'); qual_offset = bgzf_utell(bgzf); line_num++; } else { hts_log_error("Format error, expecting '+', got '%c' at line %d", c, line_num); goto fail; } break; case IN_QUAL: if (c == '\n') { if (!read_done) { hts_log_error("Inlined empty line is not allowed in quality of sequence '%s' at line %d", name.s, line_num); goto fail; } state = OUT_READ; line_num++; continue; } else if (c == '@' && read_done) { state = IN_NAME; continue; } ll = cl = 0; do { ll++; if (isgraph(c)) cl++; } while ((c = bgzf_getc(bgzf)) >= 0 && c != '\n'); ll++; qual_len += cl; if (line_len < ll) { hts_log_error("Quality line length too long in '%s' at line %d", name.s, line_num); goto fail; } else if (qual_len == seq_len) { read_done = 1; } else if (qual_len > seq_len) { hts_log_error("Quality length longer than sequence in '%s' at line %d", name.s, line_num); goto fail; } else if (line_len > ll) { hts_log_error("Quality line length too short in '%s' at line %d", name.s, line_num); goto fail; } line_num++; break; } } if (read_done) { if (fai_insert_index(idx, name.s, seq_len, line_len, char_len, seq_offset, qual_offset) != 0) goto fail; } else { hts_log_error("File truncated at line %d", line_num); goto fail; } free(name.s); return idx; fail: free(name.s); fai_destroy(idx); return NULL; } static int fai_save(const faidx_t *fai, hFILE *fp) { khint_t k; int i; char buf[96]; // Must be big enough for format below. for (i = 0; i < fai->n; ++i) { faidx1_t x; k = kh_get(s, fai->hash, fai->name[i]); assert(k < kh_end(fai->hash)); x = kh_value(fai->hash, k); if (fai->format == FAI_FASTA) { snprintf(buf, sizeof(buf), "\t%"PRIu64"\t%"PRIu64"\t%"PRIu32"\t%"PRIu32"\n", x.len, x.seq_offset, x.line_blen, x.line_len); } else { snprintf(buf, sizeof(buf), "\t%"PRIu64"\t%"PRIu64"\t%"PRIu32"\t%"PRIu32"\t%"PRIu64"\n", x.len, x.seq_offset, x.line_blen, x.line_len, x.qual_offset); } if (hputs(fai->name[i], fp) != 0) return -1; if (hputs(buf, fp) != 0) return -1; } return 0; } static faidx_t *fai_read(hFILE *fp, const char *fname, int format) { faidx_t *fai; char *buf = NULL, *p; ssize_t l, lnum = 1; fai = (faidx_t*)calloc(1, sizeof(faidx_t)); if (!fai) return NULL; fai->hash = kh_init(s); if (!fai->hash) goto fail; buf = (char*)calloc(0x10000, 1); if (!buf) goto fail; while ((l = hgetln(buf, 0x10000, fp)) > 0) { uint32_t line_len, line_blen, n; uint64_t len; uint64_t seq_offset; uint64_t qual_offset = 0; for (p = buf; *p && !isspace_c(*p); ++p); if (p - buf < l) { *p = 0; ++p; } if (format == FAI_FASTA) { n = sscanf(p, "%"SCNu64"%"SCNu64"%"SCNu32"%"SCNu32, &len, &seq_offset, &line_blen, &line_len); if (n != 4) { hts_log_error("Could not understand FASTA index %s line %zd", fname, lnum); goto fail; } } else { n = sscanf(p, "%"SCNu64"%"SCNu64"%"SCNu32"%"SCNu32"%"SCNu64, &len, &seq_offset, &line_blen, &line_len, &qual_offset); if (n != 5) { if (n == 4) { hts_log_error("Possibly this is a FASTA index, try using faidx. Problem in %s line %zd", fname, lnum); } else { hts_log_error("Could not understand FASTQ index %s line %zd", fname, lnum); } goto fail; } } if (fai_insert_index(fai, buf, len, line_len, line_blen, seq_offset, qual_offset) != 0) { goto fail; } if (buf[l - 1] == '\n') ++lnum; } if (l < 0) { hts_log_error("Error while reading %s: %s", fname, strerror(errno)); goto fail; } free(buf); return fai; fail: free(buf); fai_destroy(fai); return NULL; } void fai_destroy(faidx_t *fai) { int i; if (!fai) return; for (i = 0; i < fai->n; ++i) free(fai->name[i]); free(fai->name); kh_destroy(s, fai->hash); if (fai->bgzf) bgzf_close(fai->bgzf); free(fai); } static int fai_build3_core(const char *fn, const char *fnfai, const char *fngzi) { kstring_t fai_kstr = { 0, 0, NULL }; kstring_t gzi_kstr = { 0, 0, NULL }; BGZF *bgzf = NULL; hFILE *fp = NULL; faidx_t *fai = NULL; int save_errno, res; char *file_type; bgzf = bgzf_open(fn, "r"); if ( !bgzf ) { hts_log_error("Failed to open the file %s : %s", fn, strerror(errno)); goto fail; } if ( bgzf->is_compressed ) { if (bgzf_index_build_init(bgzf) != 0) { hts_log_error("Failed to allocate bgzf index"); goto fail; } } fai = fai_build_core(bgzf); if ( !fai ) { if (bgzf->is_compressed && bgzf->is_gzip) { hts_log_error("Cannot index files compressed with gzip, please use bgzip"); } goto fail; } if (fai->format == FAI_FASTA) { file_type = "FASTA"; } else { file_type = "FASTQ"; } if (!fnfai) { if (ksprintf(&fai_kstr, "%s.fai", fn) < 0) goto fail; fnfai = fai_kstr.s; } if (!fngzi) { if (ksprintf(&gzi_kstr, "%s.gzi", fn) < 0) goto fail; fngzi = gzi_kstr.s; } if ( bgzf->is_compressed ) { if (bgzf_index_dump(bgzf, fngzi, NULL) < 0) { hts_log_error("Failed to make bgzf index %s", fngzi); goto fail; } } res = bgzf_close(bgzf); bgzf = NULL; if (res < 0) { hts_log_error("Error on closing %s : %s", fn, strerror(errno)); goto fail; } fp = hopen(fnfai, "wb"); if ( !fp ) { hts_log_error("Failed to open %s index %s : %s", file_type, fnfai, strerror(errno)); goto fail; } if (fai_save(fai, fp) != 0) { hts_log_error("Failed to write %s index %s : %s", file_type, fnfai, strerror(errno)); goto fail; } if (hclose(fp) != 0) { hts_log_error("Failed on closing %s index %s : %s", file_type, fnfai, strerror(errno)); goto fail; } free(fai_kstr.s); free(gzi_kstr.s); fai_destroy(fai); return 0; fail: save_errno = errno; free(fai_kstr.s); free(gzi_kstr.s); bgzf_close(bgzf); fai_destroy(fai); errno = save_errno; return -1; } int fai_build3(const char *fn, const char *fnfai, const char *fngzi) { return fai_build3_core(fn, fnfai, fngzi); } int fai_build(const char *fn) { return fai_build3(fn, NULL, NULL); } static faidx_t *fai_load3_core(const char *fn, const char *fnfai, const char *fngzi, int flags, int format) { kstring_t fai_kstr = { 0, 0, NULL }; kstring_t gzi_kstr = { 0, 0, NULL }; hFILE *fp = NULL; faidx_t *fai = NULL; int res, gzi_index_needed = 0; char *file_type; if (format == FAI_FASTA) { file_type = "FASTA"; } else { file_type = "FASTQ"; } if (fn == NULL) return NULL; if (fnfai == NULL) { if (ksprintf(&fai_kstr, "%s.fai", fn) < 0) goto fail; fnfai = fai_kstr.s; } if (fngzi == NULL) { if (ksprintf(&gzi_kstr, "%s.gzi", fn) < 0) goto fail; fngzi = gzi_kstr.s; } fp = hopen(fnfai, "rb"); if (fp) { // index file present, check if a compressed index is needed hFILE *gz = NULL; BGZF *bgzf = bgzf_open(fn, "rb"); if (bgzf == 0) { hts_log_error("Failed to open %s file %s", file_type, fn); goto fail; } if (bgzf_compression(bgzf) == 2) { // BGZF compression if ((gz = hopen(fngzi, "rb")) == 0) { if (!(flags & FAI_CREATE) || errno != ENOENT) { hts_log_error("Failed to open %s index %s: %s", file_type, fngzi, strerror(errno)); bgzf_close(bgzf); goto fail; } gzi_index_needed = 1; res = hclose(fp); // closed as going to be re-indexed if (res < 0) { hts_log_error("Failed on closing %s index %s : %s", file_type, fnfai, strerror(errno)); goto fail; } } else { res = hclose(gz); if (res < 0) { hts_log_error("Failed on closing %s index %s : %s", file_type, fngzi, strerror(errno)); goto fail; } } } bgzf_close(bgzf); } if (fp == 0 || gzi_index_needed) { if (!(flags & FAI_CREATE) || errno != ENOENT) { hts_log_error("Failed to open %s index %s: %s", file_type, fnfai, strerror(errno)); goto fail; } hts_log_info("Build %s index", file_type); if (fai_build3_core(fn, fnfai, fngzi) < 0) { goto fail; } fp = hopen(fnfai, "rb"); if (fp == 0) { hts_log_error("Failed to open %s index %s: %s", file_type, fnfai, strerror(errno)); goto fail; } } fai = fai_read(fp, fnfai, format); if (fai == NULL) { hts_log_error("Failed to read %s index %s", file_type, fnfai); goto fail; } res = hclose(fp); fp = NULL; if (res < 0) { hts_log_error("Failed on closing %s index %s : %s", file_type, fnfai, strerror(errno)); goto fail; } fai->bgzf = bgzf_open(fn, "rb"); if (fai->bgzf == 0) { hts_log_error("Failed to open %s file %s", file_type, fn); goto fail; } if ( fai->bgzf->is_compressed==1 ) { if ( bgzf_index_load(fai->bgzf, fngzi, NULL) < 0 ) { hts_log_error("Failed to load .gzi index: %s", fngzi); goto fail; } } free(fai_kstr.s); free(gzi_kstr.s); return fai; fail: if (fai) fai_destroy(fai); if (fp) hclose_abruptly(fp); free(fai_kstr.s); free(gzi_kstr.s); return NULL; } faidx_t *fai_load3(const char *fn, const char *fnfai, const char *fngzi, int flags) { return fai_load3_core(fn, fnfai, fngzi, flags, FAI_FASTA); } faidx_t *fai_load(const char *fn) { return fai_load3(fn, NULL, NULL, FAI_CREATE); } faidx_t *fai_load3_format(const char *fn, const char *fnfai, const char *fngzi, int flags, enum fai_format_options format) { return fai_load3_core(fn, fnfai, fngzi, flags, format); } faidx_t *fai_load_format(const char *fn, enum fai_format_options format) { return fai_load3_format(fn, NULL, NULL, FAI_CREATE, format); } static char *fai_retrieve(const faidx_t *fai, const faidx1_t *val, uint64_t offset, hts_pos_t beg, hts_pos_t end, hts_pos_t *len) { char *buffer, *s; ssize_t nread, remaining, firstline_len, firstline_blen; int ret; if ((uint64_t) end - (uint64_t) beg >= SIZE_MAX - 2) { hts_log_error("Range %"PRId64"..%"PRId64" too big", beg, end); *len = -1; return NULL; } if (val->line_blen <= 0) { hts_log_error("Invalid line length in index: %d", val->line_blen); *len = -1; return NULL; } ret = bgzf_useek(fai->bgzf, offset + beg / val->line_blen * val->line_len + beg % val->line_blen, SEEK_SET); if (ret < 0) { *len = -1; hts_log_error("Failed to retrieve block. (Seeking in a compressed, .gzi unindexed, file?)"); return NULL; } // Over-allocate so there is extra space for one end-of-line sequence buffer = (char*)malloc((size_t) end - beg + val->line_len - val->line_blen + 1); if (!buffer) { *len = -1; return NULL; } remaining = *len = end - beg; firstline_blen = val->line_blen - beg % val->line_blen; // Special case when the entire interval requested is within a single FASTA/Q line if (remaining <= firstline_blen) { nread = bgzf_read_small(fai->bgzf, buffer, remaining); if (nread < remaining) goto error; buffer[nread] = '\0'; return buffer; } s = buffer; firstline_len = val->line_len - beg % val->line_blen; // Read the (partial) first line and its line terminator, but increment s past the // line contents only, so the terminator characters will be overwritten by the next line. nread = bgzf_read_small(fai->bgzf, s, firstline_len); if (nread < firstline_len) goto error; s += firstline_blen; remaining -= firstline_blen; // Similarly read complete lines and their line terminator characters, but overwrite the latter. while (remaining > val->line_blen) { nread = bgzf_read_small(fai->bgzf, s, val->line_len); if (nread < (ssize_t) val->line_len) goto error; s += val->line_blen; remaining -= val->line_blen; } if (remaining > 0) { nread = bgzf_read_small(fai->bgzf, s, remaining); if (nread < remaining) goto error; s += remaining; } *s = '\0'; return buffer; error: hts_log_error("Failed to retrieve block: %s", (nread == 0)? "unexpected end of file" : "error reading file"); free(buffer); *len = -1; return NULL; } static int fai_get_val(const faidx_t *fai, const char *str, hts_pos_t *len, faidx1_t *val, hts_pos_t *fbeg, hts_pos_t *fend) { khiter_t iter; khash_t(s) *h; int id; hts_pos_t beg, end; if (!fai_parse_region(fai, str, &id, &beg, &end, 0)) { hts_log_warning("Reference %s not found in FASTA file, returning empty sequence", str); *len = -2; return 1; } h = fai->hash; iter = kh_get(s, h, faidx_iseq(fai, id)); if (iter >= kh_end(h)) { // should have already been caught above abort(); } *val = kh_value(h, iter); if (beg >= val->len) beg = val->len; if (end >= val->len) end = val->len; if (beg > end) beg = end; *fbeg = beg; *fend = end; return 0; } /* * The internal still has line_blen as uint32_t, but our references * can be longer, so for future proofing we use hts_pos_t. We also needed * a signed value so we can return negatives as an error. */ hts_pos_t fai_line_length(const faidx_t *fai, const char *str) { faidx1_t val; int64_t beg, end; hts_pos_t len; if (fai_get_val(fai, str, &len, &val, &beg, &end)) return -1; else return val.line_blen; } char *fai_fetch64(const faidx_t *fai, const char *str, hts_pos_t *len) { faidx1_t val; int64_t beg, end; if (fai_get_val(fai, str, len, &val, &beg, &end)) { return NULL; } // now retrieve the sequence return fai_retrieve(fai, &val, val.seq_offset, beg, end, len); } char *fai_fetch(const faidx_t *fai, const char *str, int *len) { hts_pos_t len64; char *ret = fai_fetch64(fai, str, &len64); *len = len64 < INT_MAX ? len64 : INT_MAX; // trunc return ret; } char *fai_fetchqual64(const faidx_t *fai, const char *str, hts_pos_t *len) { faidx1_t val; int64_t beg, end; if (fai_get_val(fai, str, len, &val, &beg, &end)) { return NULL; } // now retrieve the sequence return fai_retrieve(fai, &val, val.qual_offset, beg, end, len); } char *fai_fetchqual(const faidx_t *fai, const char *str, int *len) { hts_pos_t len64; char *ret = fai_fetchqual64(fai, str, &len64); *len = len64 < INT_MAX ? len64 : INT_MAX; // trunc return ret; } int faidx_fetch_nseq(const faidx_t *fai) { return fai->n; } int faidx_nseq(const faidx_t *fai) { return fai->n; } const char *faidx_iseq(const faidx_t *fai, int i) { return fai->name[i]; } hts_pos_t faidx_seq_len64(const faidx_t *fai, const char *seq) { khint_t k = kh_get(s, fai->hash, seq); if ( k == kh_end(fai->hash) ) return -1; return kh_val(fai->hash, k).len; } int faidx_seq_len(const faidx_t *fai, const char *seq) { hts_pos_t len = faidx_seq_len64(fai, seq); return len < INT_MAX ? len : INT_MAX; } static int faidx_adjust_position(const faidx_t *fai, int end_adjust, faidx1_t *val_out, const char *c_name, hts_pos_t *p_beg_i, hts_pos_t *p_end_i, hts_pos_t *len) { khiter_t iter; faidx1_t *val; // Adjust position iter = kh_get(s, fai->hash, c_name); if (iter == kh_end(fai->hash)) { if (len) *len = -2; hts_log_error("The sequence \"%s\" was not found", c_name); return 1; } val = &kh_value(fai->hash, iter); if (val_out) *val_out = *val; if(*p_end_i < *p_beg_i) *p_beg_i = *p_end_i; if(*p_beg_i < 0) *p_beg_i = 0; else if(val->len <= *p_beg_i) *p_beg_i = val->len; if(*p_end_i < 0) *p_end_i = 0; else if(val->len <= *p_end_i) *p_end_i = val->len - end_adjust; return 0; } int fai_adjust_region(const faidx_t *fai, int tid, hts_pos_t *beg, hts_pos_t *end) { hts_pos_t orig_beg, orig_end; if (!fai || !beg || !end || tid < 0 || tid >= fai->n) return -1; orig_beg = *beg; orig_end = *end; if (faidx_adjust_position(fai, 0, NULL, fai->name[tid], beg, end, NULL) != 0) { hts_log_error("Inconsistent faidx internal state - couldn't find \"%s\"", fai->name[tid]); return -1; } return ((orig_beg != *beg ? 1 : 0) | (orig_end != *end && orig_end < HTS_POS_MAX ? 2 : 0)); } char *faidx_fetch_seq64(const faidx_t *fai, const char *c_name, hts_pos_t p_beg_i, hts_pos_t p_end_i, hts_pos_t *len) { faidx1_t val; // Adjust position if (faidx_adjust_position(fai, 1, &val, c_name, &p_beg_i, &p_end_i, len)) { return NULL; } // Now retrieve the sequence return fai_retrieve(fai, &val, val.seq_offset, p_beg_i, p_end_i + 1, len); } char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len) { hts_pos_t len64; char *ret = faidx_fetch_seq64(fai, c_name, p_beg_i, p_end_i, &len64); *len = len64 < INT_MAX ? len64 : INT_MAX; // trunc return ret; } char *faidx_fetch_qual64(const faidx_t *fai, const char *c_name, hts_pos_t p_beg_i, hts_pos_t p_end_i, hts_pos_t *len) { faidx1_t val; // Adjust position if (faidx_adjust_position(fai, 1, &val, c_name, &p_beg_i, &p_end_i, len)) { return NULL; } // Now retrieve the sequence return fai_retrieve(fai, &val, val.qual_offset, p_beg_i, p_end_i + 1, len); } char *faidx_fetch_qual(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len) { hts_pos_t len64; char *ret = faidx_fetch_qual64(fai, c_name, p_beg_i, p_end_i, &len64); *len = len64 < INT_MAX ? len64 : INT_MAX; // trunc return ret; } int faidx_has_seq(const faidx_t *fai, const char *seq) { khiter_t iter = kh_get(s, fai->hash, seq); if (iter == kh_end(fai->hash)) return 0; return 1; } const char *fai_parse_region(const faidx_t *fai, const char *s, int *tid, hts_pos_t *beg, hts_pos_t *end, int flags) { return hts_parse_region(s, tid, beg, end, (hts_name2id_f)fai_name2id, (void *)fai, flags); } void fai_set_cache_size(faidx_t *fai, int cache_size) { bgzf_set_cache_size(fai->bgzf, cache_size); } // Adds a thread pool to the underlying BGZF layer. int fai_thread_pool(faidx_t *fai, struct hts_tpool *pool, int qsize) { return bgzf_thread_pool(fai->bgzf, pool, qsize); } char *fai_path(const char *fa) { char *fai = NULL; if (!fa) { hts_log_error("No reference file specified"); } else { char *fai_tmp = strstr(fa, HTS_IDX_DELIM); if (fai_tmp) { fai_tmp += strlen(HTS_IDX_DELIM); fai = strdup(fai_tmp); if (!fai) hts_log_error("Failed to allocate memory"); } else { if (hisremote(fa)) { fai = hts_idx_locatefn(fa, ".fai"); // get the remote fai file name, if any, but do not download the file if (!fai) hts_log_error("Failed to locate index file for remote reference file '%s'", fa); } else{ if (hts_idx_check_local(fa, HTS_FMT_FAI, &fai) == 0 && fai) { if (fai_build3(fa, fai, NULL) == -1) { // create local fai file by indexing local fasta hts_log_error("Failed to build index file for reference file '%s'", fa); free(fai); fai = NULL; } } } } } return fai; } pysam-0.23.0/htslib/fuzz_settings.h000066400000000000000000000026421475062545500173220ustar00rootroot00000000000000/* fuzz_settings.h -- fuzz-tester specific definitions Copyright (C) 2023 Genome Research Ltd. Author: Rob Davies Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTSLIB_FUZZ_SETTINGS_H #define HTSLIB_FUZZ_SETTINGS_H #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION #ifndef FUZZ_ALLOC_LIMIT // By default libfuzzer reports out-of-memory on allocations > 2 Gbytes #define FUZZ_ALLOC_LIMIT 2000000000ULL #endif #endif #endif pysam-0.23.0/htslib/header.c000066400000000000000000002377611475062545500156430ustar00rootroot00000000000000/* Copyright (c) 2018-2020, 2023 Genome Research Ltd. Authors: James Bonfield , Valeriu Ohan Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include "textutils_internal.h" #include "header.h" // Hash table for removing multiple lines from the header KHASH_SET_INIT_STR(rm) // Used for long refs in SAM files KHASH_DECLARE(s2i, kh_cstr_t, int64_t) typedef khash_t(rm) rmhash_t; static int sam_hdr_link_pg(sam_hdr_t *bh); static int sam_hrecs_vupdate(sam_hrecs_t *hrecs, sam_hrec_type_t *type, va_list ap); static int sam_hrecs_update(sam_hrecs_t *hrecs, sam_hrec_type_t *type, ...); #define MAX_ERROR_QUOTE 320 // Prevent over-long error messages static void sam_hrecs_error(const char *msg, const char *line, size_t len, size_t lno) { int j; if (len > MAX_ERROR_QUOTE) len = MAX_ERROR_QUOTE; for (j = 0; j < len && line[j] != '\n'; j++) ; hts_log_error("%s at line %zd: \"%.*s\"", msg, lno, j, line); } /* ==== Static methods ==== */ static int sam_hrecs_init_type_order(sam_hrecs_t *hrecs, char *type_list) { if (!hrecs) return -1; if (!type_list) { hrecs->type_count = 5; hrecs->type_order = calloc(hrecs->type_count, 3); if (!hrecs->type_order) return -1; memcpy(hrecs->type_order[0], "HD", 2); memcpy(hrecs->type_order[1], "SQ", 2); memcpy(hrecs->type_order[2], "RG", 2); memcpy(hrecs->type_order[3], "PG", 2); memcpy(hrecs->type_order[4], "CO", 2); } return 0; } static int sam_hrecs_add_ref_altnames(sam_hrecs_t *hrecs, int nref, const char *list) { const char *token; ks_tokaux_t aux; if (!list) return 0; for (token = kstrtok(list, ",", &aux); token; token = kstrtok(NULL, NULL, &aux)) { if (aux.p == token) continue; char *name = string_ndup(hrecs->str_pool, token, aux.p - token); if (!name) return -1; int r; khint_t k = kh_put(m_s2i, hrecs->ref_hash, name, &r); if (r < 0) return -1; if (r > 0) kh_val(hrecs->ref_hash, k) = nref; else if (kh_val(hrecs->ref_hash, k) != nref) hts_log_warning("Duplicate entry AN:\"%s\" in sam header", name); } return 0; } static void sam_hrecs_remove_ref_altnames(sam_hrecs_t *hrecs, int expected, const char *list) { const char *token, *sn; ks_tokaux_t aux; kstring_t str = KS_INITIALIZE; if (expected < 0 || expected >= hrecs->nref) return; sn = hrecs->ref[expected].name; for (token = kstrtok(list, ",", &aux); token; token = kstrtok(NULL, NULL, &aux)) { kputsn(token, aux.p - token, ks_clear(&str)); khint_t k = kh_get(m_s2i, hrecs->ref_hash, str.s); if (k != kh_end(hrecs->ref_hash) && kh_val(hrecs->ref_hash, k) == expected && strcmp(sn, str.s) != 0) kh_del(m_s2i, hrecs->ref_hash, k); } free(str.s); } /* Updates the hash tables in the sam_hrecs_t structure. * * Returns 0 on success; * -1 on failure */ static int sam_hrecs_update_hashes(sam_hrecs_t *hrecs, khint32_t type, sam_hrec_type_t *h_type) { /* Add to reference hash? */ if (type == TYPEKEY("SQ")) { sam_hrec_tag_t *tag = h_type->tag; int nref = hrecs->nref; const char *name = NULL; const char *altnames = NULL; hts_pos_t len = -1; int r; khint_t k; while (tag) { if (tag->str[0] == 'S' && tag->str[1] == 'N') { assert(tag->len >= 3); name = tag->str+3; } else if (tag->str[0] == 'L' && tag->str[1] == 'N') { assert(tag->len >= 3); len = strtoll(tag->str+3, NULL, 10); } else if (tag->str[0] == 'A' && tag->str[1] == 'N') { assert(tag->len >= 3); altnames = tag->str+3; } tag = tag->next; } if (!name) { hts_log_error("Header includes @SQ line with no SN: tag"); return -1; // SN should be present, according to spec. } if (len == -1) { hts_log_error("Header includes @SQ line \"%s\" with no LN: tag", name); return -1; // LN should be present, according to spec. } // Seen already? k = kh_get(m_s2i, hrecs->ref_hash, name); if (k < kh_end(hrecs->ref_hash)) { nref = kh_val(hrecs->ref_hash, k); int ref_changed_flag = 0; // Check for hash entry added by sam_hrecs_refs_from_targets_array() if (hrecs->ref[nref].ty == NULL) { // Attach header line to existing stub entry. hrecs->ref[nref].ty = h_type; // Check lengths match; correct if not. if (len != hrecs->ref[nref].len) { char tmp[32]; snprintf(tmp, sizeof(tmp), "%" PRIhts_pos, hrecs->ref[nref].len); if (sam_hrecs_update(hrecs, h_type, "LN", tmp, NULL) < 0) return -1; ref_changed_flag = 1; } if (sam_hrecs_add_ref_altnames(hrecs, nref, altnames) < 0) return -1; if (ref_changed_flag && (hrecs->refs_changed < 0 || hrecs->refs_changed > nref)) hrecs->refs_changed = nref; return 0; } // Check to see if an existing entry is being updated if (hrecs->ref[nref].ty == h_type) { if (hrecs->ref[nref].len != len) { hrecs->ref[nref].len = len; ref_changed_flag = 1; } if (!hrecs->ref[nref].name || strcmp(hrecs->ref[nref].name, name)) { hrecs->ref[nref].name = name; ref_changed_flag = 1; } if (sam_hrecs_add_ref_altnames(hrecs, nref, altnames) < 0) return -1; if (ref_changed_flag && (hrecs->refs_changed < 0 || hrecs->refs_changed > nref)) hrecs->refs_changed = nref; return 0; } // If here, the name is a duplicate. // Check to see if it matches the SN: tag from the earlier record. if (strcmp(hrecs->ref[nref].name, name) == 0) { hts_log_error("Duplicate entry \"%s\" in sam header", name); return -1; } // Clash with an already-seen altname // As SN: should be preferred to AN: add this as a new // record and update the hash entry to point to it. hts_log_warning("Ref name SN:\"%s\" is a duplicate of an existing AN key", name); nref = hrecs->nref; } if (nref == hrecs->ref_sz) { size_t new_sz = hrecs->ref_sz >= 4 ? hrecs->ref_sz + (hrecs->ref_sz / 4) : 32; sam_hrec_sq_t *new_ref = realloc(hrecs->ref, sizeof(*hrecs->ref) * new_sz); if (!new_ref) return -1; hrecs->ref = new_ref; hrecs->ref_sz = new_sz; } hrecs->ref[nref].name = name; hrecs->ref[nref].len = len; hrecs->ref[nref].ty = h_type; k = kh_put(m_s2i, hrecs->ref_hash, hrecs->ref[nref].name, &r); if (-1 == r) return -1; kh_val(hrecs->ref_hash, k) = nref; if (sam_hrecs_add_ref_altnames(hrecs, nref, altnames) < 0) return -1; if (hrecs->refs_changed < 0 || hrecs->refs_changed > hrecs->nref) hrecs->refs_changed = hrecs->nref; hrecs->nref++; } /* Add to read-group hash? */ if (type == TYPEKEY("RG")) { sam_hrec_tag_t *tag = sam_hrecs_find_key(h_type, "ID", NULL); int nrg = hrecs->nrg, r; khint_t k; if (!tag) { hts_log_error("Header includes @RG line with no ID: tag"); return -1; // ID should be present, according to spec. } assert(tag->str && tag->len >= 3); // Seen already? k = kh_get(m_s2i, hrecs->rg_hash, tag->str + 3); if (k < kh_end(hrecs->rg_hash)) { nrg = kh_val(hrecs->rg_hash, k); assert(hrecs->rg[nrg].ty != NULL); if (hrecs->rg[nrg].ty != h_type) { hts_log_warning("Duplicate entry \"%s\" in sam header", tag->str + 3); } else { hrecs->rg[nrg].name = tag->str + 3; hrecs->rg[nrg].name_len = tag->len - 3; } return 0; } if (nrg == hrecs->rg_sz) { size_t new_sz = hrecs->rg_sz >= 4 ? hrecs->rg_sz + hrecs->rg_sz / 4 : 4; sam_hrec_rg_t *new_rg = realloc(hrecs->rg, sizeof(*hrecs->rg) * new_sz); if (!new_rg) return -1; hrecs->rg = new_rg; hrecs->rg_sz = new_sz; } hrecs->rg[nrg].name = tag->str + 3; hrecs->rg[nrg].name_len = tag->len - 3; hrecs->rg[nrg].ty = h_type; hrecs->rg[nrg].id = nrg; k = kh_put(m_s2i, hrecs->rg_hash, hrecs->rg[nrg].name, &r); if (-1 == r) return -1; kh_val(hrecs->rg_hash, k) = nrg; hrecs->nrg++; } /* Add to program hash? */ if (type == TYPEKEY("PG")) { sam_hrec_tag_t *tag; sam_hrec_pg_t *new_pg; int npg = hrecs->npg; if (npg == hrecs->pg_sz) { size_t new_sz = hrecs->pg_sz >= 4 ? hrecs->pg_sz + hrecs->pg_sz / 4 : 4; new_pg = realloc(hrecs->pg, sizeof(*hrecs->pg) * new_sz); if (!new_pg) return -1; hrecs->pg = new_pg; hrecs->pg_sz = new_sz; } tag = h_type->tag; hrecs->pg[npg].name = NULL; hrecs->pg[npg].name_len = 0; hrecs->pg[npg].ty = h_type; hrecs->pg[npg].id = npg; hrecs->pg[npg].prev_id = -1; while (tag) { if (tag->str[0] == 'I' && tag->str[1] == 'D') { /* Avoid duplicate ID tags coming from other applications */ if (!hrecs->pg[npg].name) { assert(tag->len >= 3); hrecs->pg[npg].name = tag->str + 3; hrecs->pg[npg].name_len = tag->len - 3; } else { hts_log_warning("PG line with multiple ID tags. The first encountered was preferred - ID:%s", hrecs->pg[npg].name); } } else if (tag->str[0] == 'P' && tag->str[1] == 'P') { // Resolve later if needed khint_t k; k = kh_get(m_s2i, hrecs->pg_hash, tag->str+3); if (k != kh_end(hrecs->pg_hash)) { int p_id = kh_val(hrecs->pg_hash, k); hrecs->pg[npg].prev_id = hrecs->pg[p_id].id; /* Unmark previous entry as a PG termination */ if (hrecs->npg_end > 0 && hrecs->pg_end[hrecs->npg_end-1] == p_id) { hrecs->npg_end--; } else { int i; for (i = 0; i < hrecs->npg_end; i++) { if (hrecs->pg_end[i] == p_id) { memmove(&hrecs->pg_end[i], &hrecs->pg_end[i+1], (hrecs->npg_end-i-1)*sizeof(*hrecs->pg_end)); hrecs->npg_end--; } } } } else { hrecs->pg[npg].prev_id = -1; } } tag = tag->next; } if (hrecs->pg[npg].name) { khint_t k; int r; k = kh_put(m_s2i, hrecs->pg_hash, hrecs->pg[npg].name, &r); if (-1 == r) return -1; kh_val(hrecs->pg_hash, k) = npg; } else { return -1; // ID should be present, according to spec. } /* Add to npg_end[] array. Remove later if we find a PP line */ if (hrecs->npg_end >= hrecs->npg_end_alloc) { int *new_pg_end; int new_alloc = hrecs->npg_end_alloc ? hrecs->npg_end_alloc*2 : 4; new_pg_end = realloc(hrecs->pg_end, new_alloc * sizeof(int)); if (!new_pg_end) return -1; hrecs->npg_end_alloc = new_alloc; hrecs->pg_end = new_pg_end; } hrecs->pg_end[hrecs->npg_end++] = npg; hrecs->npg++; } return 0; } static int sam_hrecs_remove_hash_entry(sam_hrecs_t *hrecs, khint32_t type, sam_hrec_type_t *h_type) { if (!hrecs || !h_type) return -1; sam_hrec_tag_t *tag; const char *key = NULL; khint_t k; /* Remove name and any alternative names from reference hash */ if (type == TYPEKEY("SQ")) { const char *altnames = NULL; tag = h_type->tag; while (tag) { if (tag->str[0] == 'S' && tag->str[1] == 'N') { assert(tag->len >= 3); key = tag->str + 3; } else if (tag->str[0] == 'A' && tag->str[1] == 'N') { assert(tag->len >= 3); altnames = tag->str + 3; } tag = tag->next; } if (key) { k = kh_get(m_s2i, hrecs->ref_hash, key); if (k != kh_end(hrecs->ref_hash)) { int idx = kh_val(hrecs->ref_hash, k); if (idx + 1 < hrecs->nref) memmove(&hrecs->ref[idx], &hrecs->ref[idx+1], sizeof(sam_hrec_sq_t)*(hrecs->nref - idx - 1)); if (altnames) sam_hrecs_remove_ref_altnames(hrecs, idx, altnames); kh_del(m_s2i, hrecs->ref_hash, k); hrecs->nref--; if (hrecs->refs_changed < 0 || hrecs->refs_changed > idx) hrecs->refs_changed = idx; for (k = 0; k < kh_end(hrecs->ref_hash); k++) { if (kh_exist(hrecs->ref_hash, k) && kh_value(hrecs->ref_hash, k) > idx) { kh_value(hrecs->ref_hash, k)--; } } } } } /* Remove from read-group hash */ if (type == TYPEKEY("RG")) { tag = h_type->tag; while (tag) { if (tag->str[0] == 'I' && tag->str[1] == 'D') { assert(tag->len >= 3); key = tag->str + 3; k = kh_get(m_s2i, hrecs->rg_hash, key); if (k != kh_end(hrecs->rg_hash)) { int idx = kh_val(hrecs->rg_hash, k); if (idx + 1 < hrecs->nrg) memmove(&hrecs->rg[idx], &hrecs->rg[idx+1], sizeof(sam_hrec_rg_t)*(hrecs->nrg - idx - 1)); kh_del(m_s2i, hrecs->rg_hash, k); hrecs->nrg--; for (k = 0; k < kh_end(hrecs->rg_hash); k++) { if (kh_exist(hrecs->rg_hash, k) && kh_value(hrecs->rg_hash, k) > idx) { kh_value(hrecs->rg_hash, k)--; } } } break; } tag = tag->next; } } return 0; } /** Add a header record to the global line ordering * * If @p after is not NULL, the new record will be inserted after this one, * otherwise it will go at the end. * * An exception is an HD record, which will always be put first unless * one is already present. */ static void sam_hrecs_global_list_add(sam_hrecs_t *hrecs, sam_hrec_type_t *h_type, sam_hrec_type_t *after) { const khint32_t hd_type = TYPEKEY("HD"); int update_first_line = 0; // First line seen if (!hrecs->first_line) { hrecs->first_line = h_type->global_next = h_type->global_prev = h_type; return; } // @HD goes at the top (unless there's one already) if (h_type->type == hd_type && hrecs->first_line->type != hd_type) { after = hrecs->first_line->global_prev; update_first_line = 1; } // If no instructions given, put it at the end if (!after) after = hrecs->first_line->global_prev; h_type->global_prev = after; h_type->global_next = after->global_next; h_type->global_prev->global_next = h_type; h_type->global_next->global_prev = h_type; if (update_first_line) hrecs->first_line = h_type; } /*! Add header record with a va_list interface. * * Adds a single record to a SAM header. * * This takes a header record type, a va_list argument and one or more * key,value pairs, ending with the NULL key. * * Eg. sam_hrecs_vadd(h, "SQ", args, "ID", "foo", "LN", "100", NULL). * * The purpose of the additional va_list parameter is to permit other * varargs functions to call this while including their own additional * parameters; an example is in sam_hdr_add_pg(). * * Note: this function invokes va_arg at least once, making the value * of ap indeterminate after the return. The caller should call * va_start/va_end before/after calling this function or use va_copy. * * @return * Returns >= 0 on success; * -1 on failure */ static int sam_hrecs_vadd(sam_hrecs_t *hrecs, const char *type, va_list ap, ...) { va_list args; sam_hrec_type_t *h_type; sam_hrec_tag_t *h_tag, *last=NULL; int new; khint32_t type_i = TYPEKEY(type), k; if (!strncmp(type, "HD", 2) && (h_type = sam_hrecs_find_type_id(hrecs, "HD", NULL, NULL))) return sam_hrecs_vupdate(hrecs, h_type, ap); if (!(h_type = pool_alloc(hrecs->type_pool))) return -1; k = kh_put(sam_hrecs_t, hrecs->h, type_i, &new); if (new < 0) return -1; h_type->type = type_i; // Form the ring, either with self or other lines of this type if (!new) { sam_hrec_type_t *t = kh_val(hrecs->h, k), *p; p = t->prev; assert(p->next == t); p->next = h_type; h_type->prev = p; t->prev = h_type; h_type->next = t; } else { kh_val(hrecs->h, k) = h_type; h_type->prev = h_type->next = h_type; } h_type->tag = NULL; // Add to global line ordering after any existing line of the same type, // or at the end if no line of this type exists yet. sam_hrecs_global_list_add(hrecs, h_type, !new ? h_type->prev : NULL); // Check linked-list invariants assert(h_type->prev->next == h_type); assert(h_type->next->prev == h_type); assert(h_type->global_prev->global_next == h_type); assert(h_type->global_next->global_prev == h_type); // Any ... varargs va_start(args, ap); for (;;) { char *key, *val = NULL, *str; if (!(key = (char *)va_arg(args, char *))) break; if (strncmp(type, "CO", 2) && !(val = (char *)va_arg(args, char *))) break; if (*val == '\0') continue; if (!(h_tag = pool_alloc(hrecs->tag_pool))) return -1; if (strncmp(type, "CO", 2)) { h_tag->len = 3 + strlen(val); str = string_alloc(hrecs->str_pool, h_tag->len+1); if (!str || snprintf(str, h_tag->len+1, "%2.2s:%s", key, val) < 0) return -1; h_tag->str = str; } else { h_tag->len = strlen(key); h_tag->str = string_ndup(hrecs->str_pool, key, h_tag->len); if (!h_tag->str) return -1; } h_tag->next = NULL; if (last) last->next = h_tag; else h_type->tag = h_tag; last = h_tag; } va_end(args); // Plus the specified va_list params for (;;) { char *key, *val = NULL, *str; if (!(key = (char *)va_arg(ap, char *))) break; if (strncmp(type, "CO", 2) && !(val = (char *)va_arg(ap, char *))) break; if (!(h_tag = pool_alloc(hrecs->tag_pool))) return -1; if (strncmp(type, "CO", 2)) { h_tag->len = 3 + strlen(val); str = string_alloc(hrecs->str_pool, h_tag->len+1); if (!str || snprintf(str, h_tag->len+1, "%2.2s:%s", key, val) < 0) return -1; h_tag->str = str; } else { h_tag->len = strlen(key); h_tag->str = string_ndup(hrecs->str_pool, key, h_tag->len); if (!h_tag->str) return -1; } h_tag->next = NULL; if (last) last->next = h_tag; else h_type->tag = h_tag; last = h_tag; } if (-1 == sam_hrecs_update_hashes(hrecs, TYPEKEY(type), h_type)) return -1; if (!strncmp(type, "PG", 2)) hrecs->pgs_changed = 1; hrecs->dirty = 1; return 0; } // As sam_hrecs_vadd(), but without the extra va_list parameter static int sam_hrecs_add(sam_hrecs_t *hrecs, const char *type, ...) { va_list args; int res; va_start(args, type); res = sam_hrecs_vadd(hrecs, type, args, NULL); va_end(args); return res; } /* * Function for deallocating a list of tags */ static void sam_hrecs_free_tags(sam_hrecs_t *hrecs, sam_hrec_tag_t *tag) { if (!hrecs || !tag) return; if (tag->next) sam_hrecs_free_tags(hrecs, tag->next); pool_free(hrecs->tag_pool, tag); } static int sam_hrecs_remove_line(sam_hrecs_t *hrecs, const char *type_name, sam_hrec_type_t *type_found, int remove_hash) { if (!hrecs || !type_name || !type_found) return -1; khint32_t itype = TYPEKEY(type_name); khint_t k = kh_get(sam_hrecs_t, hrecs->h, itype); if (k == kh_end(hrecs->h)) return -1; // Remove from global list (remembering it could be the only line) if (hrecs->first_line == type_found) { hrecs->first_line = (type_found->global_next != type_found ? type_found->global_next : NULL); } type_found->global_next->global_prev = type_found->global_prev; type_found->global_prev->global_next = type_found->global_next; /* single element in the list */ if (type_found->prev == type_found || type_found->next == type_found) { kh_del(sam_hrecs_t, hrecs->h, k); } else { type_found->prev->next = type_found->next; type_found->next->prev = type_found->prev; if (kh_val(hrecs->h, k) == type_found) { //first element kh_val(hrecs->h, k) = type_found->next; } } if (remove_hash && (!strncmp(type_name, "SQ", 2) || !strncmp(type_name, "RG", 2))) sam_hrecs_remove_hash_entry(hrecs, itype, type_found); sam_hrecs_free_tags(hrecs, type_found->tag); pool_free(hrecs->type_pool, type_found); hrecs->dirty = 1; return 0; } // Paste together a line from the parsed data structures static int build_header_line(const sam_hrec_type_t *ty, kstring_t *ks) { sam_hrec_tag_t *tag; int r = 0; char c[2]= { ty->type >> 8, ty->type & 0xff }; r |= (kputc_('@', ks) == EOF); r |= (kputsn(c, 2, ks) == EOF); for (tag = ty->tag; tag; tag = tag->next) { r |= (kputc_('\t', ks) == EOF); r |= (kputsn(tag->str, tag->len, ks) == EOF); } return r; } static int sam_hrecs_rebuild_lines(const sam_hrecs_t *hrecs, kstring_t *ks) { const sam_hrec_type_t *t1, *t2; if (!hrecs->first_line) return kputsn("", 0, ks) >= 0 ? 0 : -1; t1 = t2 = hrecs->first_line; do { if (build_header_line(t1, ks) != 0) return -1; if (kputc('\n', ks) < 0) return -1; t1 = t1->global_next; } while (t1 != t2); return 0; } static int sam_hrecs_parse_lines(sam_hrecs_t *hrecs, const char *hdr, size_t len) { size_t i, lno; if (!hrecs || len > SSIZE_MAX) return -1; if (!len) len = strlen(hdr); if (len < 3) { if (len == 0 || *hdr == '\0') return 0; sam_hrecs_error("Header line too short", hdr, len, 1); return -1; } for (i = 0, lno = 1; i < len - 3 && hdr[i] != '\0'; i++, lno++) { khint32_t type; khint_t k; int l_start = i, new; sam_hrec_type_t *h_type; sam_hrec_tag_t *h_tag, *last; if (hdr[i] != '@') { sam_hrecs_error("Header line does not start with '@'", &hdr[l_start], len - l_start, lno); return -1; } if (!isalpha_c(hdr[i+1]) || !isalpha_c(hdr[i+2])) { sam_hrecs_error("Header line does not have a two character key", &hdr[l_start], len - l_start, lno); return -1; } type = TYPEKEY(&hdr[i+1]); i += 3; if (i == len || hdr[i] == '\n') continue; // Add the header line type if (!(h_type = pool_alloc(hrecs->type_pool))) return -1; k = kh_put(sam_hrecs_t, hrecs->h, type, &new); if (new < 0) return -1; h_type->type = type; // Add to end of global list sam_hrecs_global_list_add(hrecs, h_type, NULL); // Form the ring, either with self or other lines of this type if (!new) { sam_hrec_type_t *t = kh_val(hrecs->h, k), *p; p = t->prev; assert(p->next == t); p->next = h_type; h_type->prev = p; t->prev = h_type; h_type->next = t; } else { kh_val(hrecs->h, k) = h_type; h_type->prev = h_type->next = h_type; } // Parse the tags on this line last = NULL; if (type == TYPEKEY("CO")) { size_t j; if (i == len || hdr[i] != '\t') { sam_hrecs_error("Missing tab", &hdr[l_start], len - l_start, lno); return -1; } for (j = ++i; j < len && hdr[j] != '\0' && hdr[j] != '\n'; j++) ; if (!(h_type->tag = h_tag = pool_alloc(hrecs->tag_pool))) return -1; h_tag->str = string_ndup(hrecs->str_pool, &hdr[i], j-i); h_tag->len = j-i; h_tag->next = NULL; if (!h_tag->str) return -1; i = j; } else { do { size_t j; if (i == len || hdr[i] != '\t') { sam_hrecs_error("Missing tab", &hdr[l_start], len - l_start, lno); return -1; } for (j = ++i; j < len && hdr[j] != '\0' && hdr[j] != '\n' && hdr[j] != '\t'; j++) ; if (j - i < 3 || hdr[i + 2] != ':') { sam_hrecs_error("Malformed key:value pair", &hdr[l_start], len - l_start, lno); return -1; } if (!(h_tag = pool_alloc(hrecs->tag_pool))) return -1; h_tag->str = string_ndup(hrecs->str_pool, &hdr[i], j-i); h_tag->len = j-i; h_tag->next = NULL; if (!h_tag->str) return -1; if (last) last->next = h_tag; else h_type->tag = h_tag; last = h_tag; i = j; } while (i < len && hdr[i] != '\0' && hdr[i] != '\n'); } /* Update RG/SQ hashes */ if (-1 == sam_hrecs_update_hashes(hrecs, type, h_type)) return -1; } return 0; } /*! Update sam_hdr_t target_name and target_len arrays * * @return 0 on success; -1 on failure */ int sam_hdr_update_target_arrays(sam_hdr_t *bh, const sam_hrecs_t *hrecs, int refs_changed) { if (!bh || !hrecs) return -1; if (refs_changed < 0) return 0; // Grow arrays if necessary if (bh->n_targets < hrecs->nref) { char **new_names = realloc(bh->target_name, hrecs->nref * sizeof(*new_names)); if (!new_names) return -1; bh->target_name = new_names; uint32_t *new_lens = realloc(bh->target_len, hrecs->nref * sizeof(*new_lens)); if (!new_lens) return -1; bh->target_len = new_lens; } // Update names and lengths where changed // hrecs->refs_changed is the first ref that has been updated, so ones // before that can be skipped. int i; khint_t k; khash_t(s2i) *long_refs = (khash_t(s2i) *) bh->sdict; for (i = refs_changed; i < hrecs->nref; i++) { if (i >= bh->n_targets || strcmp(bh->target_name[i], hrecs->ref[i].name) != 0) { if (i < bh->n_targets) free(bh->target_name[i]); bh->target_name[i] = strdup(hrecs->ref[i].name); if (!bh->target_name[i]) return -1; } if (hrecs->ref[i].len < UINT32_MAX) { bh->target_len[i] = hrecs->ref[i].len; if (!long_refs) continue; // Check if we have an old length, if so remove it. k = kh_get(s2i, long_refs, bh->target_name[i]); if (k < kh_end(long_refs)) kh_del(s2i, long_refs, k); } else { bh->target_len[i] = UINT32_MAX; if (bh->hrecs != hrecs) { // Called from sam_hdr_dup; need to add sdict entries if (!long_refs) { if (!(bh->sdict = long_refs = kh_init(s2i))) return -1; } // Add / update length int absent; k = kh_put(s2i, long_refs, bh->target_name[i], &absent); if (absent < 0) return -1; kh_val(long_refs, k) = hrecs->ref[i].len; } } } // Free up any names that have been removed for (; i < bh->n_targets; i++) { if (long_refs) { k = kh_get(s2i, long_refs, bh->target_name[i]); if (k < kh_end(long_refs)) kh_del(s2i, long_refs, k); } free(bh->target_name[i]); } bh->n_targets = hrecs->nref; return 0; } static int rebuild_target_arrays(sam_hdr_t *bh) { if (!bh || !bh->hrecs) return -1; sam_hrecs_t *hrecs = bh->hrecs; if (hrecs->refs_changed < 0) return 0; if (sam_hdr_update_target_arrays(bh, hrecs, hrecs->refs_changed) != 0) return -1; hrecs->refs_changed = -1; return 0; } /// Populate hrecs refs array from header target_name, target_len arrays /** * @return 0 on success; -1 on failure * * Pre-fills the refs hash from the target arrays. For BAM files this * will ensure that they are in the correct order as the target arrays * are the canonical source for converting target ids to names and lengths. * * The added entries do not link to a header line. sam_hrecs_update_hashes() * will add the links later for lines found in the text header. * * This should be called before the text header is parsed. */ static int sam_hrecs_refs_from_targets_array(sam_hrecs_t *hrecs, const sam_hdr_t *bh) { int32_t tid = 0; if (!hrecs || !bh) return -1; // This should always be called before parsing the text header // so the ref array should start off empty, and we don't have to try // to reconcile any existing data. if (hrecs->nref > 0) { hts_log_error("Called with non-empty ref array"); return -1; } if (hrecs->ref_sz < bh->n_targets) { sam_hrec_sq_t *new_ref = realloc(hrecs->ref, bh->n_targets * sizeof(*new_ref)); if (!new_ref) return -1; hrecs->ref = new_ref; hrecs->ref_sz = bh->n_targets; } for (tid = 0; tid < bh->n_targets; tid++) { khint_t k; int r; hrecs->ref[tid].name = string_dup(hrecs->str_pool, bh->target_name[tid]); if (!hrecs->ref[tid].name) goto fail; if (bh->target_len[tid] < UINT32_MAX || !bh->sdict) { hrecs->ref[tid].len = bh->target_len[tid]; } else { khash_t(s2i) *long_refs = (khash_t(s2i) *) bh->sdict; k = kh_get(s2i, long_refs, hrecs->ref[tid].name); if (k < kh_end(long_refs)) { hrecs->ref[tid].len = kh_val(long_refs, k); } else { hrecs->ref[tid].len = UINT32_MAX; } } hrecs->ref[tid].ty = NULL; k = kh_put(m_s2i, hrecs->ref_hash, hrecs->ref[tid].name, &r); if (r < 0) goto fail; if (r == 0) { hts_log_error("Duplicate entry \"%s\" in target list", hrecs->ref[tid].name); return -1; } else { kh_val(hrecs->ref_hash, k) = tid; } } hrecs->nref = bh->n_targets; return 0; fail: { int32_t i; hts_log_error("%s", strerror(errno)); for (i = 0; i < tid; i++) { khint_t k; if (!hrecs->ref[i].name) continue; k = kh_get(m_s2i, hrecs->ref_hash, hrecs->ref[tid].name); if (k < kh_end(hrecs->ref_hash)) kh_del(m_s2i, hrecs->ref_hash, k); } hrecs->nref = 0; return -1; } } /* * Add SQ header records for any references in the hrecs->ref array that * were added by sam_hrecs_refs_from_targets_array() but have not * been linked to an @SQ line by sam_hrecs_update_hashes() yet. * * This may be needed either because: * * - A bam file was read that had entries in its refs list with no * corresponding @SQ line. * * - A program constructed a sam_hdr_t which has target_name and target_len * array entries with no corresponding @SQ line in text. */ static int add_stub_ref_sq_lines(sam_hrecs_t *hrecs) { int tid; char len[32]; for (tid = 0; tid < hrecs->nref; tid++) { if (hrecs->ref[tid].ty == NULL) { snprintf(len, sizeof(len), "%"PRIhts_pos, hrecs->ref[tid].len); if (sam_hrecs_add(hrecs, "SQ", "SN", hrecs->ref[tid].name, "LN", len, NULL) != 0) return -1; // Check that the stub has actually been filled if(hrecs->ref[tid].ty == NULL) { hts_log_error("Reference stub with tid=%d, name=\"%s\", len=%"PRIhts_pos" could not be filled", tid, hrecs->ref[tid].name, hrecs->ref[tid].len); return -1; } } } return 0; } int sam_hdr_fill_hrecs(sam_hdr_t *bh) { sam_hrecs_t *hrecs = sam_hrecs_new(); if (!hrecs) return -1; if (bh->target_name && bh->target_len && bh->n_targets > 0) { if (sam_hrecs_refs_from_targets_array(hrecs, bh) != 0) { sam_hrecs_free(hrecs); return -1; } } // Parse existing header text if (bh->text && bh->l_text > 0) { if (sam_hrecs_parse_lines(hrecs, bh->text, bh->l_text) != 0) { sam_hrecs_free(hrecs); return -1; } } if (add_stub_ref_sq_lines(hrecs) < 0) { sam_hrecs_free(hrecs); return -1; } bh->hrecs = hrecs; if (hrecs->refs_changed >= 0 && rebuild_target_arrays(bh) != 0) return -1; return 0; } /** Remove outdated header text @param bh BAM header This is called when API functions have changed the header so that the text version is no longer valid. */ static void redact_header_text(sam_hdr_t *bh) { assert(bh->hrecs && bh->hrecs->dirty); bh->l_text = 0; free(bh->text); bh->text = NULL; } /** Find nth header record of a given type @param type Header type (SQ, RG etc.) @param idx 0-based index @return sam_hrec_type_t pointer to the record on success NULL if no record exists with the given type and index */ static sam_hrec_type_t *sam_hrecs_find_type_pos(sam_hrecs_t *hrecs, const char *type, int idx) { sam_hrec_type_t *first, *itr; if (idx < 0) return NULL; if (type[0] == 'S' && type[1] == 'Q') return idx < hrecs->nref ? hrecs->ref[idx].ty : NULL; if (type[0] == 'R' && type[1] == 'G') return idx < hrecs->nrg ? hrecs->rg[idx].ty : NULL; if (type[0] == 'P' && type[1] == 'G') return idx < hrecs->npg ? hrecs->pg[idx].ty : NULL; first = itr = sam_hrecs_find_type_id(hrecs, type, NULL, NULL); if (!first) return NULL; while (idx > 0) { itr = itr->next; if (itr == first) break; --idx; } return idx == 0 ? itr : NULL; } /* ==== Public methods ==== */ size_t sam_hdr_length(sam_hdr_t *bh) { if (!bh || -1 == sam_hdr_rebuild(bh)) return SIZE_MAX; return bh->l_text; } const char *sam_hdr_str(sam_hdr_t *bh) { if (!bh || -1 == sam_hdr_rebuild(bh)) return NULL; return bh->text; } int sam_hdr_nref(const sam_hdr_t *bh) { if (!bh) return -1; return bh->hrecs ? bh->hrecs->nref : bh->n_targets; } /* * Reconstructs the text representation from the header hash table. * Returns 0 on success * -1 on failure */ int sam_hdr_rebuild(sam_hdr_t *bh) { sam_hrecs_t *hrecs; if (!bh) return -1; if (!(hrecs = bh->hrecs)) return bh->text ? 0 : -1; if (hrecs->refs_changed >= 0) { if (rebuild_target_arrays(bh) < 0) { hts_log_error("Header target array rebuild has failed"); return -1; } } /* If header text wasn't changed or header is empty, don't rebuild it. */ if (!hrecs->dirty) return 0; if (hrecs->pgs_changed && sam_hdr_link_pg(bh) < 0) { hts_log_error("Linking @PG lines has failed"); return -1; } kstring_t ks = KS_INITIALIZE; if (sam_hrecs_rebuild_text(hrecs, &ks) != 0) { ks_free(&ks); hts_log_error("Header text rebuild has failed"); return -1; } hrecs->dirty = 0; /* Sync */ free(bh->text); bh->l_text = ks_len(&ks); bh->text = ks_release(&ks); return 0; } /* * Appends a formatted line to an existing SAM header. * Line is a full SAM header record, eg "@SQ\tSN:foo\tLN:100", with * optional new-line. If it contains more than 1 line then multiple lines * will be added in order. * * Input text is of maximum length len or as terminated earlier by a NUL. * len may be 0 if unknown, in which case lines must be NUL-terminated. * * Returns 0 on success * -1 on failure */ int sam_hdr_add_lines(sam_hdr_t *bh, const char *lines, size_t len) { sam_hrecs_t *hrecs; if (!bh || !lines) return -1; if (len == 0 && *lines == '\0') return 0; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return -1; hrecs = bh->hrecs; } if (sam_hrecs_parse_lines(hrecs, lines, len) != 0) return -1; if (hrecs->refs_changed >= 0 && rebuild_target_arrays(bh) != 0) return -1; hrecs->dirty = 1; redact_header_text(bh); return 0; } /* * Adds a single line to a SAM header. * Specify type and one or more key,value pairs, ending with the NULL key. * Eg. sam_hdr_add_line(h, "SQ", "ID", "foo", "LN", "100", NULL). * * Returns 0 on success * -1 on failure */ int sam_hdr_add_line(sam_hdr_t *bh, const char *type, ...) { va_list args; sam_hrecs_t *hrecs; if (!bh || !type) return -1; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return -1; hrecs = bh->hrecs; } va_start(args, type); int ret = sam_hrecs_vadd(hrecs, type, args, NULL); va_end(args); if (ret == 0) { if (hrecs->refs_changed >= 0 && rebuild_target_arrays(bh) != 0) return -1; if (hrecs->dirty) redact_header_text(bh); } return ret; } /* * Returns a complete line of formatted text for a specific head type/ID * combination. If ID_key is NULL then it returns the first line of the specified * type. */ int sam_hdr_find_line_id(sam_hdr_t *bh, const char *type, const char *ID_key, const char *ID_val, kstring_t *ks) { sam_hrecs_t *hrecs; if (!bh || !type) return -2; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return -2; hrecs = bh->hrecs; } sam_hrec_type_t *ty = sam_hrecs_find_type_id(hrecs, type, ID_key, ID_val); if (!ty) return -1; ks->l = 0; if (build_header_line(ty, ks) < 0) { return -2; } return 0; } int sam_hdr_find_line_pos(sam_hdr_t *bh, const char *type, int pos, kstring_t *ks) { sam_hrecs_t *hrecs; if (!bh || !type) return -2; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return -2; hrecs = bh->hrecs; } sam_hrec_type_t *ty = sam_hrecs_find_type_pos(hrecs, type, pos); if (!ty) return -1; ks->l = 0; if (build_header_line(ty, ks) < 0) { return -2; } return 0; } /* * Remove a line from the header by specifying a tag:value that uniquely * identifies a line, i.e. the @SQ line containing "SN:ref1". * @SQ line is uniquely identified by SN tag. * @RG line is uniquely identified by ID tag. * @PG line is uniquely identified by ID tag. * * Returns 0 on success and -1 on error */ int sam_hdr_remove_line_id(sam_hdr_t *bh, const char *type, const char *ID_key, const char *ID_value) { sam_hrecs_t *hrecs; if (!bh || !type) return -1; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return -1; hrecs = bh->hrecs; } if (!strncmp(type, "PG", 2)) { hts_log_warning("Removing PG lines is not supported!"); return -1; } sam_hrec_type_t *type_found = sam_hrecs_find_type_id(hrecs, type, ID_key, ID_value); if (!type_found) return 0; int ret = sam_hrecs_remove_line(hrecs, type, type_found, 1); if (ret == 0) { if (hrecs->refs_changed >= 0 && rebuild_target_arrays(bh) != 0) return -1; if (hrecs->dirty) redact_header_text(bh); } return ret; } /* * Remove a line from the header by specifying the position in the type * group, i.e. 3rd @SQ line. * * Returns 0 on success and -1 on error */ int sam_hdr_remove_line_pos(sam_hdr_t *bh, const char *type, int position) { sam_hrecs_t *hrecs; if (!bh || !type || position <= 0) return -1; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return -1; hrecs = bh->hrecs; } if (!strncmp(type, "PG", 2)) { hts_log_warning("Removing PG lines is not supported!"); return -1; } sam_hrec_type_t *type_found = sam_hrecs_find_type_pos(hrecs, type, position); if (!type_found) return -1; int ret = sam_hrecs_remove_line(hrecs, type, type_found, 1); if (ret == 0) { if (hrecs->refs_changed >= 0 && rebuild_target_arrays(bh) != 0) return -1; if (hrecs->dirty) redact_header_text(bh); } return ret; } /* * Check if sam_hdr_update_line() is being used to change the name of * a record, and if the new name is going to clash with an existing one. * * If ap includes repeated keys, we go with the last one as sam_hrecs_vupdate() * will go through them all and leave the final one in place. * * Returns 0 if the name does not change * 1 if the name changes but does not clash * -1 if the name changes and the new one is already in use */ static int check_for_name_update(sam_hrecs_t *hrecs, sam_hrec_type_t *rec, va_list ap, const char **old_name, const char **new_name, char id_tag_out[3], khash_t(m_s2i) **hash_out) { char *key, *val; const char *id_tag; sam_hrec_tag_t *tag, *prev; khash_t(m_s2i) *hash; khint_t k; int ret = 0; if (rec->type == TYPEKEY("SQ")) { id_tag = "SN"; hash = hrecs->ref_hash; } else if (rec->type == TYPEKEY("RG")) { id_tag = "ID"; hash = hrecs->rg_hash; } else if (rec->type == TYPEKEY("PG")) { id_tag = "ID"; hash = hrecs->pg_hash; } else { return 0; } memcpy(id_tag_out, id_tag, 3); *hash_out = hash; tag = sam_hrecs_find_key(rec, id_tag, &prev); if (!tag) return 0; assert(tag->len >= 3); *old_name = tag->str + 3; while ((key = va_arg(ap, char *)) != NULL) { val = va_arg(ap, char *); if (!val) val = ""; if (strcmp(key, id_tag) != 0) continue; if (strcmp(val, tag->str + 3) == 0) { ret = 0; continue; } k = kh_get(m_s2i, hash, val); ret = k < kh_end(hash) ? -1 : 1; *new_name = val; } return ret; } int sam_hdr_update_line(sam_hdr_t *bh, const char *type, const char *ID_key, const char *ID_value, ...) { sam_hrecs_t *hrecs; if (!bh) return -1; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return -1; hrecs = bh->hrecs; } int ret, rename; sam_hrec_type_t *ty = sam_hrecs_find_type_id(hrecs, type, ID_key, ID_value); if (!ty) return -1; va_list args; const char *old_name = "?", *new_name = "?"; char id_tag[3]; khash_t(m_s2i) *hash = NULL; va_start(args, ID_value); rename = check_for_name_update(hrecs, ty, args, &old_name, &new_name, id_tag, &hash); va_end(args); if (rename < 0) { hts_log_error("Cannot rename @%s \"%s\" to \"%s\" : already exists", type, old_name, new_name); return -1; } if (rename > 0 && TYPEKEY(type) == TYPEKEY("PG")) { // This is just too complicated hts_log_error("Renaming @PG records is not supported"); return -1; } va_start(args, ID_value); ret = sam_hrecs_vupdate(hrecs, ty, args); va_end(args); if (ret) return ret; // TODO Account for @SQ-AN altnames if (rename) { // Adjust the hash table to point to the new name // sam_hrecs_update_hashes() should sort out everything else khint_t k = kh_get(m_s2i, hash, old_name); sam_hrec_tag_t *new_tag = sam_hrecs_find_key(ty, id_tag, NULL); int r, pos; assert(k < kh_end(hash)); // Or we wouldn't have found it earlier assert(new_tag && new_tag->str); // id_tag should exist assert(new_tag->len > 3); pos = kh_val(hash, k); kh_del(m_s2i, hash, k); k = kh_put(m_s2i, hash, new_tag->str + 3, &r); if (r < 1) { hts_log_error("Failed to rename item in hash table"); return -1; } kh_val(hash, k) = pos; } ret = sam_hrecs_update_hashes(hrecs, TYPEKEY(type), ty); if (!ret && hrecs->refs_changed >= 0) ret = rebuild_target_arrays(bh); if (!ret && hrecs->dirty) redact_header_text(bh); return ret; } static int rebuild_hash(sam_hrecs_t *hrecs, const char *type) { sam_hrec_type_t *head, *step; khiter_t k; if (strncmp(type, "SQ", 2) == 0) { hrecs->nref = 0; kh_clear(m_s2i, hrecs->ref_hash); } else if (strncmp(type, "RG", 2) == 0) { hrecs->nrg = 0; kh_clear(m_s2i, hrecs->rg_hash); } k = kh_get(sam_hrecs_t, hrecs->h, TYPEKEY(type)); if (k != kh_end(hrecs->h)) { // something to rebuild head = kh_val(hrecs->h, k); step = head; do { if (sam_hrecs_update_hashes(hrecs, TYPEKEY(type), step) == -1) { hts_log_error("Unable to rebuild hashes"); return -1; } step = step->next; } while (step != head); } return 0; } int sam_hdr_remove_except(sam_hdr_t *bh, const char *type, const char *ID_key, const char *ID_value) { sam_hrecs_t *hrecs; if (!bh || !type) return -1; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return -1; hrecs = bh->hrecs; } sam_hrec_type_t *step; int ret = 1, remove_all = (ID_key == NULL); if (!strncmp(type, "PG", 2) || !strncmp(type, "CO", 2)) { hts_log_warning("Removing PG or CO lines is not supported!"); return -1; } sam_hrec_type_t *type_found = sam_hrecs_find_type_id(hrecs, type, ID_key, ID_value); if (!type_found) { // remove all line of this type khint_t k = kh_get(sam_hrecs_t, hrecs->h, TYPEKEY(type)); if (k == kh_end(hrecs->h)) return 0; type_found = kh_val(hrecs->h, k); if (!type_found) return 0; remove_all = 1; } step = type_found->next; while (step != type_found) { sam_hrec_type_t *to_remove = step; step = step->next; ret &= sam_hrecs_remove_line(hrecs, type, to_remove, 0); } if (remove_all) ret &= sam_hrecs_remove_line(hrecs, type, type_found, 0); /* if RG or SQ, delete then rebuild the hashes (as it is faster to rebuild than delete one by one). */ if ((strncmp(type, "SQ", 2) == 0) || (strncmp(type, "RG", 2) == 0)) { if (rebuild_hash(hrecs, type)) { return -1; } } if (!ret && hrecs->dirty) redact_header_text(bh); return 0; } int sam_hdr_remove_lines(sam_hdr_t *bh, const char *type, const char *id, void *vrh) { sam_hrecs_t *hrecs; rmhash_t *rh = (rmhash_t *)vrh; if (!bh || !type) return -1; if (!rh) // remove all lines return sam_hdr_remove_except(bh, type, NULL, NULL); if (!id) return -1; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return -1; hrecs = bh->hrecs; } khint_t k = kh_get(sam_hrecs_t, hrecs->h, TYPEKEY(type)); if (k == kh_end(hrecs->h)) // nothing to remove from return 0; sam_hrec_type_t *head = kh_val(hrecs->h, k); if (!head) { hts_log_error("Header inconsistency"); return -1; } int ret = 0; sam_hrec_type_t *step = head->next; while (step != head) { sam_hrec_tag_t *tag = sam_hrecs_find_key(step, id, NULL); if (tag && tag->str && tag->len >= 3) { k = kh_get(rm, rh, tag->str+3); if (k == kh_end(rh)) { // value is not in the hash table, so remove sam_hrec_type_t *to_remove = step; step = step->next; ret |= sam_hrecs_remove_line(hrecs, type, to_remove, 0); } else { step = step->next; } } else { // tag is not on the line, so skip to next line step = step->next; } } // process the first line sam_hrec_tag_t * tag = sam_hrecs_find_key(head, id, NULL); if (tag && tag->str && tag->len >= 3) { k = kh_get(rm, rh, tag->str+3); if (k == kh_end(rh)) { // value is not in the hash table, so remove sam_hrec_type_t *to_remove = head; head = head->next; ret |= sam_hrecs_remove_line(hrecs, type, to_remove, 0); } } /* if RG or SQ, delete then rebuild the hashes (as it is faster to rebuild than delete one by one). */ if ((strncmp(type, "SQ", 2) == 0) || (strncmp(type, "RG", 2) == 0)) { if (rebuild_hash(hrecs, type)) { return -1; } } if (!ret && hrecs->dirty) redact_header_text(bh); return ret; } int sam_hdr_count_lines(sam_hdr_t *bh, const char *type) { int count; sam_hrec_type_t *first_ty, *itr_ty; if (!bh || !type) return -1; if (!bh->hrecs) { if (sam_hdr_fill_hrecs(bh) != 0) return -1; } // Deal with types that have counts switch (type[0]) { case 'S': if (type[1] == 'Q') return bh->hrecs->nref; break; case 'R': if (type[1] == 'G') return bh->hrecs->nrg; break; case 'P': if (type[1] == 'G') return bh->hrecs->npg; break; default: break; } first_ty = sam_hrecs_find_type_id(bh->hrecs, type, NULL, NULL); if (!first_ty) return 0; count = 1; for (itr_ty = first_ty->next; itr_ty && itr_ty != first_ty; itr_ty = itr_ty->next) { count++; } return count; } int sam_hdr_line_index(sam_hdr_t *bh, const char *type, const char *key) { sam_hrecs_t *hrecs; if (!bh || !type || !key) return -2; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return -2; hrecs = bh->hrecs; } khint_t k; int idx = -1; switch (type[0]) { case 'S': if (type[1] == 'Q') { k = kh_get(m_s2i, hrecs->ref_hash, key); if (k != kh_end(hrecs->ref_hash)) idx = kh_val(hrecs->ref_hash, k); } else { hts_log_warning("Type '%s' not supported. Only @SQ, @RG and @PG lines are indexed", type); } break; case 'R': if (type[1] == 'G') { k = kh_get(m_s2i, hrecs->rg_hash, key); if (k != kh_end(hrecs->rg_hash)) idx = kh_val(hrecs->rg_hash, k); } else { hts_log_warning("Type '%s' not supported. Only @SQ, @RG and @PG lines are indexed", type); } break; case 'P': if (type[1] == 'G') { k = kh_get(m_s2i, hrecs->pg_hash, key); if (k != kh_end(hrecs->pg_hash)) idx = kh_val(hrecs->pg_hash, k); } else { hts_log_warning("Type '%s' not supported. Only @SQ, @RG and @PG lines are indexed", type); } break; default: hts_log_warning("Type '%s' not supported. Only @SQ, @RG and @PG lines are indexed", type); } return idx; } const char *sam_hdr_line_name(sam_hdr_t *bh, const char *type, int pos) { sam_hrecs_t *hrecs; if (!bh || !type || pos < 0) return NULL; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return NULL; hrecs = bh->hrecs; } switch (type[0]) { case 'S': if (type[1] == 'Q') { if (pos < hrecs->nref) return hrecs->ref[pos].name; } else { hts_log_warning("Type '%s' not supported. Only @SQ, @RG and @PG lines are indexed", type); } break; case 'R': if (type[1] == 'G') { if (pos < hrecs->nrg) return hrecs->rg[pos].name; } else { hts_log_warning("Type '%s' not supported. Only @SQ, @RG and @PG lines are indexed", type); } break; case 'P': if (type[1] == 'G') { if (pos < hrecs->npg) return hrecs->pg[pos].name; } else { hts_log_warning("Type '%s' not supported. Only @SQ, @RG and @PG lines are indexed", type); } break; default: hts_log_warning("Type '%s' not supported. Only @SQ, @RG and @PG lines are indexed", type); } return NULL; } /* ==== Key:val level methods ==== */ int sam_hdr_find_tag_id(sam_hdr_t *bh, const char *type, const char *ID_key, const char *ID_value, const char *key, kstring_t *ks) { sam_hrecs_t *hrecs; if (!bh || !type || !key) return -2; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return -2; hrecs = bh->hrecs; } sam_hrec_type_t *ty = sam_hrecs_find_type_id(hrecs, type, ID_key, ID_value); if (!ty) return -1; sam_hrec_tag_t *tag = sam_hrecs_find_key(ty, key, NULL); if (!tag || !tag->str || tag->len < 4) return -1; ks->l = 0; if (kputsn(tag->str+3, tag->len-3, ks) == EOF) { return -2; } return 0; } int sam_hdr_find_tag_pos(sam_hdr_t *bh, const char *type, int pos, const char *key, kstring_t *ks) { sam_hrecs_t *hrecs; if (!bh || !type || !key) return -2; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return -2; hrecs = bh->hrecs; } sam_hrec_type_t *ty = sam_hrecs_find_type_pos(hrecs, type, pos); if (!ty) return -1; sam_hrec_tag_t *tag = sam_hrecs_find_key(ty, key, NULL); if (!tag || !tag->str || tag->len < 4) return -1; ks->l = 0; if (kputsn(tag->str+3, tag->len-3, ks) == EOF) { return -2; } return 0; } int sam_hdr_remove_tag_id(sam_hdr_t *bh, const char *type, const char *ID_key, const char *ID_value, const char *key) { sam_hrecs_t *hrecs; if (!bh || !type || !key) return -1; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return -1; hrecs = bh->hrecs; } sam_hrec_type_t *ty = sam_hrecs_find_type_id(hrecs, type, ID_key, ID_value); if (!ty) return -1; int ret = sam_hrecs_remove_key(hrecs, ty, key); if (!ret && hrecs->dirty) redact_header_text(bh); return ret; } /* * Reconstructs a kstring from the header hash table. * Returns 0 on success * -1 on failure */ int sam_hrecs_rebuild_text(const sam_hrecs_t *hrecs, kstring_t *ks) { ks->l = 0; if (!hrecs->h || !hrecs->h->size) { return kputsn("", 0, ks) >= 0 ? 0 : -1; } if (sam_hrecs_rebuild_lines(hrecs, ks) != 0) return -1; return 0; } /* * Looks up a reference sequence by name and returns the numerical ID. * Returns -1 if unknown reference; -2 if header could not be parsed. */ int sam_hdr_name2tid(sam_hdr_t *bh, const char *ref) { sam_hrecs_t *hrecs; khint_t k; if (!bh) return -1; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return -2; hrecs = bh->hrecs; } if (!hrecs->ref_hash) return -1; k = kh_get(m_s2i, hrecs->ref_hash, ref); return k == kh_end(hrecs->ref_hash) ? -1 : kh_val(hrecs->ref_hash, k); } const char *sam_hdr_tid2name(const sam_hdr_t *h, int tid) { sam_hrecs_t *hrecs; if (!h || tid < 0) return NULL; if ((hrecs = h->hrecs) != NULL && tid < hrecs->nref) { return hrecs->ref[tid].name; } else { if (tid < h->n_targets) return h->target_name[tid]; } return NULL; } hts_pos_t sam_hdr_tid2len(const sam_hdr_t *h, int tid) { sam_hrecs_t *hrecs; if (!h || tid < 0) return 0; if ((hrecs = h->hrecs) != NULL && tid < hrecs->nref) { return hrecs->ref[tid].len; } else { if (tid < h->n_targets) { if (h->target_len[tid] < UINT32_MAX || !h->sdict) { return h->target_len[tid]; } else { khash_t(s2i) *long_refs = (khash_t(s2i) *) h->sdict; khint_t k = kh_get(s2i, long_refs, h->target_name[tid]); if (k < kh_end(long_refs)) { return kh_val(long_refs, k); } else { return UINT32_MAX; } } } } return 0; } /* * Fixes any PP links in @PG headers. * If the entries are in order then this doesn't need doing, but in case * our header is out of order this goes through the hrecs->pg[] array * setting the prev_id field. * * Note we can have multiple complete chains. This code should identify the * tails of these chains as these are the entries we have to link to in * subsequent PP records. * * Returns 0 on success * -1 on failure (indicating broken PG/PP records) */ static int sam_hdr_link_pg(sam_hdr_t *bh) { sam_hrecs_t *hrecs; int i, j, ret = 0, *new_pg_end; if (!bh) return -1; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return -1; hrecs = bh->hrecs; } if (!hrecs->pgs_changed || !hrecs->npg) return 0; hrecs->npg_end_alloc = hrecs->npg; new_pg_end = realloc(hrecs->pg_end, hrecs->npg * sizeof(*new_pg_end)); if (!new_pg_end) return -1; hrecs->pg_end = new_pg_end; int *chain_size = calloc(hrecs->npg, sizeof(int)); if (!chain_size) return -1; for (i = 0; i < hrecs->npg; i++) hrecs->pg_end[i] = i; for (i = 0; i < hrecs->npg; i++) { khint_t k; sam_hrec_tag_t *tag; assert(hrecs->pg[i].ty != NULL); for (tag = hrecs->pg[i].ty->tag; tag; tag = tag->next) { if (tag->str[0] == 'P' && tag->str[1] == 'P') break; } if (!tag) { /* Chain start points */ continue; } k = kh_get(m_s2i, hrecs->pg_hash, tag->str+3); if (k == kh_end(hrecs->pg_hash)) { hts_log_warning("PG line with ID:%s has a PP link to missing program '%s'", hrecs->pg[i].name, tag->str+3); continue; } int pp_idx = kh_val(hrecs->pg_hash, k); if (pp_idx == i) { hts_log_warning("PG line with ID:%s has a PP link to itself", hrecs->pg[i].name); continue; } hrecs->pg[i].prev_id = hrecs->pg[pp_idx].id; hrecs->pg_end[pp_idx] = -1; chain_size[i] = chain_size[pp_idx]+1; } int last_end = -1; for (i = j = 0; i < hrecs->npg; i++) { if (hrecs->pg_end[i] != -1) { last_end = hrecs->pg_end[i]; if (chain_size[i] > 0) hrecs->pg_end[j++] = hrecs->pg_end[i]; } } /* Only leafs? Choose the last one! */ if (!j && hrecs->npg_end > 0 && last_end >= 0) { hrecs->pg_end[0] = last_end; j = 1; } hrecs->npg_end = j; hrecs->pgs_changed = 0; /* mark as dirty or empty for rebuild */ hrecs->dirty = 1; redact_header_text(bh); free(chain_size); return ret; } /* * Returns a unique ID from a base name. * * The value returned is valid until the next call to * this function. */ const char *sam_hdr_pg_id(sam_hdr_t *bh, const char *name) { sam_hrecs_t *hrecs; size_t name_len; const size_t name_extra = 17; if (!bh || !name) return NULL; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return NULL; hrecs = bh->hrecs; } khint_t k = kh_get(m_s2i, hrecs->pg_hash, name); if (k == kh_end(hrecs->pg_hash)) return name; name_len = strlen(name); if (name_len > 1000) name_len = 1000; if (hrecs->ID_buf_sz < name_len + name_extra) { char *new_ID_buf = realloc(hrecs->ID_buf, name_len + name_extra); if (new_ID_buf == NULL) return NULL; hrecs->ID_buf = new_ID_buf; hrecs->ID_buf_sz = name_len + name_extra; } do { snprintf(hrecs->ID_buf, hrecs->ID_buf_sz, "%.1000s.%d", name, hrecs->ID_cnt++); k = kh_get(m_s2i, hrecs->pg_hash, hrecs->ID_buf); } while (k != kh_end(hrecs->pg_hash)); return hrecs->ID_buf; } /* * Add an @PG line. * * If we wish complete control over this use sam_hdr_add_line() directly. This * function uses that, but attempts to do a lot of tedious house work for * you too. * * - It will generate a suitable ID if the supplied one clashes. * - It will generate multiple @PG records if we have multiple PG chains. * * Call it as per sam_hdr_add_line() with a series of key,value pairs ending * in NULL. * * Returns 0 on success * -1 on failure */ int sam_hdr_add_pg(sam_hdr_t *bh, const char *name, ...) { sam_hrecs_t *hrecs; const char *specified_id = NULL, *specified_pn = NULL, *specified_pp = NULL; const char *key, *val; if (!bh) return -1; if (!(hrecs = bh->hrecs)) { if (sam_hdr_fill_hrecs(bh) != 0) return -1; hrecs = bh->hrecs; } bh->hrecs->pgs_changed = 1; if (sam_hdr_link_pg(bh) < 0) { hts_log_error("Error linking @PG lines"); return -1; } va_list args; // Check for ID / PN / PP tags in varargs list va_start(args, name); while ((key = va_arg(args, const char *)) != NULL) { val = va_arg(args, const char *); if (!val) break; if (strcmp(key, "PN") == 0 && *val != '\0') specified_pn = val; else if (strcmp(key, "PP") == 0 && *val != '\0') specified_pp = val; else if (strcmp(key, "ID") == 0 && *val != '\0') specified_id = val; } va_end(args); if (specified_id && hrecs->pg_hash) { khint_t k = kh_get(m_s2i, hrecs->pg_hash, specified_id); if (k != kh_end(hrecs->pg_hash)) { hts_log_error("Header @PG ID:%s already present", specified_id); return -1; } } if (specified_pp && hrecs->pg_hash) { khint_t k = kh_get(m_s2i, hrecs->pg_hash, specified_pp); if (k == kh_end(hrecs->pg_hash)) { hts_log_error("Header @PG ID:%s referred to by PP tag not present", specified_pp); return -1; } } if (!specified_pp && hrecs->npg_end) { /* Copy ends array to avoid us looping while modifying it */ int *end = malloc(hrecs->npg_end * sizeof(int)); int i, nends = hrecs->npg_end; if (!end) return -1; memcpy(end, hrecs->pg_end, nends * sizeof(*end)); for (i = 0; i < nends; i++) { const char *id = !specified_id ? sam_hdr_pg_id(bh, name) : ""; if (!id) { free(end); return -1; } assert(end[i] >= 0 && end[i] < hrecs->npg); va_start(args, name); if (-1 == sam_hrecs_vadd(hrecs, "PG", args, "ID", id, "PN", !specified_pn ? name : "", "PP", hrecs->pg[end[i]].name, NULL)) { free(end); return -1; } va_end(args); } free(end); } else { const char *id = !specified_id ? sam_hdr_pg_id(bh, name) : ""; if (!id) return -1; va_start(args, name); if (-1 == sam_hrecs_vadd(hrecs, "PG", args, "ID", id, "PN", !specified_pn ? name : "", NULL)) return -1; va_end(args); } hrecs->dirty = 1; redact_header_text(bh); return 0; } /*! Increments a reference count on bh. * * This permits multiple files to share the same header, all calling * sam_hdr_destroy when done, without causing errors for other open files. */ void sam_hdr_incr_ref(sam_hdr_t *bh) { if (!bh) return; bh->ref_count++; } /* ==== Internal methods ==== */ /* * Creates an empty SAM header. Allocates space for the SAM header * structures (hash tables) ready to be populated. * * Returns a sam_hrecs_t struct on success (free with sam_hrecs_free()) * NULL on failure */ sam_hrecs_t *sam_hrecs_new(void) { sam_hrecs_t *hrecs = calloc(1, sizeof(*hrecs)); if (!hrecs) return NULL; hrecs->h = kh_init(sam_hrecs_t); if (!hrecs->h) goto err; hrecs->ID_cnt = 1; hrecs->nref = 0; hrecs->ref_sz = 0; hrecs->ref = NULL; if (!(hrecs->ref_hash = kh_init(m_s2i))) goto err; hrecs->refs_changed = -1; hrecs->nrg = 0; hrecs->rg_sz = 0; hrecs->rg = NULL; if (!(hrecs->rg_hash = kh_init(m_s2i))) goto err; hrecs->npg = 0; hrecs->pg_sz = 0; hrecs->pg = NULL; hrecs->npg_end = hrecs->npg_end_alloc = 0; hrecs->pg_end = NULL; if (!(hrecs->pg_hash = kh_init(m_s2i))) goto err; if (!(hrecs->tag_pool = pool_create(sizeof(sam_hrec_tag_t)))) goto err; if (!(hrecs->type_pool = pool_create(sizeof(sam_hrec_type_t)))) goto err; if (!(hrecs->str_pool = string_pool_create(65536))) goto err; if (sam_hrecs_init_type_order(hrecs, NULL)) goto err; return hrecs; err: if (hrecs->h) kh_destroy(sam_hrecs_t, hrecs->h); if (hrecs->tag_pool) pool_destroy(hrecs->tag_pool); if (hrecs->type_pool) pool_destroy(hrecs->type_pool); if (hrecs->str_pool) string_pool_destroy(hrecs->str_pool); free(hrecs); return NULL; } #if 0 /* * Produces a duplicate copy of source and returns it. * Returns NULL on failure */ sam_hrecs_t *sam_hrecs_dup(sam_hrecs_t *source) { return NULL; } #endif /*! Deallocates all storage used by a sam_hrecs_t struct. * * This also decrements the header reference count. If after decrementing * it is still non-zero then the header is assumed to be in use by another * caller and the free is not done. * */ void sam_hrecs_free(sam_hrecs_t *hrecs) { if (!hrecs) return; if (hrecs->h) kh_destroy(sam_hrecs_t, hrecs->h); if (hrecs->ref_hash) kh_destroy(m_s2i, hrecs->ref_hash); if (hrecs->ref) free(hrecs->ref); if (hrecs->rg_hash) kh_destroy(m_s2i, hrecs->rg_hash); if (hrecs->rg) free(hrecs->rg); if (hrecs->pg_hash) kh_destroy(m_s2i, hrecs->pg_hash); if (hrecs->pg) free(hrecs->pg); if (hrecs->pg_end) free(hrecs->pg_end); if (hrecs->type_pool) pool_destroy(hrecs->type_pool); if (hrecs->tag_pool) pool_destroy(hrecs->tag_pool); if (hrecs->str_pool) string_pool_destroy(hrecs->str_pool); if (hrecs->type_order) free(hrecs->type_order); if (hrecs->ID_buf) free(hrecs->ID_buf); free(hrecs); } /* * Internal method already used by the CRAM code * Returns the first header item matching 'type'. If ID is non-NULL it checks * for the tag ID: and compares against the specified ID. * * Returns NULL if no type/ID is found */ sam_hrec_type_t *sam_hrecs_find_type_id(sam_hrecs_t *hrecs, const char *type, const char *ID_key, const char *ID_value) { if (!hrecs || !type) return NULL; sam_hrec_type_t *t1, *t2; khint_t k; /* Special case for types we have prebuilt hashes on */ if (ID_key) { if (!ID_value) return NULL; if (type[0] == 'S' && type[1] == 'Q' && ID_key[0] == 'S' && ID_key[1] == 'N') { k = kh_get(m_s2i, hrecs->ref_hash, ID_value); return k != kh_end(hrecs->ref_hash) ? hrecs->ref[kh_val(hrecs->ref_hash, k)].ty : NULL; } if (type[0] == 'R' && type[1] == 'G' && ID_key[0] == 'I' && ID_key[1] == 'D') { k = kh_get(m_s2i, hrecs->rg_hash, ID_value); return k != kh_end(hrecs->rg_hash) ? hrecs->rg[kh_val(hrecs->rg_hash, k)].ty : NULL; } if (type[0] == 'P' && type[1] == 'G' && ID_key[0] == 'I' && ID_key[1] == 'D') { k = kh_get(m_s2i, hrecs->pg_hash, ID_value); return k != kh_end(hrecs->pg_hash) ? hrecs->pg[kh_val(hrecs->pg_hash, k)].ty : NULL; } } k = kh_get(sam_hrecs_t, hrecs->h, TYPEKEY(type)); if (k == kh_end(hrecs->h)) return NULL; if (!ID_key) return kh_val(hrecs->h, k); t1 = t2 = kh_val(hrecs->h, k); do { sam_hrec_tag_t *tag; for (tag = t1->tag; tag; tag = tag->next) { if (tag->str[0] == ID_key[0] && tag->str[1] == ID_key[1]) { const char *cp1 = tag->str+3; const char *cp2 = ID_value; while (*cp1 && *cp1 == *cp2) cp1++, cp2++; if (*cp2 || *cp1) continue; return t1; } } t1 = t1->next; } while (t1 != t2); return NULL; } /* * Adds or updates tag key,value pairs in a header line. * Eg for adding M5 tags to @SQ lines or updating sort order for the * @HD line. * * va_list contains multiple key,value pairs ending in NULL. * * Returns 0 on success * -1 on failure */ int sam_hrecs_vupdate(sam_hrecs_t *hrecs, sam_hrec_type_t *type, va_list ap) { if (!hrecs) return -1; for (;;) { char *k, *v, *str; sam_hrec_tag_t *tag, *prev = NULL; if (!(k = (char *)va_arg(ap, char *))) break; if (!(v = va_arg(ap, char *))) v = ""; tag = sam_hrecs_find_key(type, k, &prev); if (!tag) { if (!(tag = pool_alloc(hrecs->tag_pool))) return -1; if (prev) prev->next = tag; else type->tag = tag; tag->next = NULL; } tag->len = 3 + strlen(v); str = string_alloc(hrecs->str_pool, tag->len+1); if (!str) return -1; if (snprintf(str, tag->len+1, "%2.2s:%s", k, v) < 0) return -1; tag->str = str; } hrecs->dirty = 1; //mark text as dirty and force a rebuild return 0; } /* * Adds or updates tag key,value pairs in a header line. * Eg for adding M5 tags to @SQ lines or updating sort order for the * @HD line. * * Specify multiple key,value pairs ending in NULL. * * Returns 0 on success * -1 on failure */ static int sam_hrecs_update(sam_hrecs_t *hrecs, sam_hrec_type_t *type, ...) { va_list args; int res; va_start(args, type); res = sam_hrecs_vupdate(hrecs, type, args); va_end(args); return res; } /* * Looks for a specific key in a single sam header line identified by *type. * If prev is non-NULL it also fills this out with the previous tag, to * permit use in key removal. *prev is set to NULL when the tag is the first * key in the list. When a tag isn't found, prev (if non NULL) will be the last * tag in the existing list. * * Returns the tag pointer on success * NULL on failure */ sam_hrec_tag_t *sam_hrecs_find_key(sam_hrec_type_t *type, const char *key, sam_hrec_tag_t **prev) { sam_hrec_tag_t *tag, *p = NULL; if (!type) return NULL; for (tag = type->tag; tag; p = tag, tag = tag->next) { if (tag->str[0] == key[0] && tag->str[1] == key[1]) { if (prev) *prev = p; return tag; } } if (prev) *prev = p; return NULL; } int sam_hrecs_remove_key(sam_hrecs_t *hrecs, sam_hrec_type_t *type, const char *key) { sam_hrec_tag_t *tag, *prev; if (!hrecs) return -1; tag = sam_hrecs_find_key(type, key, &prev); if (!tag) return 0; // Not there anyway if (type->type == TYPEKEY("SQ") && tag->str[0] == 'A' && tag->str[1] == 'N') { assert(tag->len >= 3); sam_hrec_tag_t *sn_tag = sam_hrecs_find_key(type, "SN", NULL); if (sn_tag) { assert(sn_tag->len >= 3); khint_t k = kh_get(m_s2i, hrecs->ref_hash, sn_tag->str + 3); if (k != kh_end(hrecs->ref_hash)) sam_hrecs_remove_ref_altnames(hrecs, kh_val(hrecs->ref_hash, k), tag->str + 3); } } if (!prev) { //first tag type->tag = tag->next; } else { prev->next = tag->next; } pool_free(hrecs->tag_pool, tag); hrecs->dirty = 1; //mark text as dirty and force a rebuild return 1; } /* * Looks up a read-group by name and returns a pointer to the start of the * associated tag list. * * Returns NULL on failure */ sam_hrec_rg_t *sam_hrecs_find_rg(sam_hrecs_t *hrecs, const char *rg) { khint_t k = kh_get(m_s2i, hrecs->rg_hash, rg); return k == kh_end(hrecs->rg_hash) ? NULL : &hrecs->rg[kh_val(hrecs->rg_hash, k)]; } #if DEBUG_HEADER void sam_hrecs_dump(sam_hrecs_t *hrecs) { khint_t k; int i; printf("===DUMP===\n"); for (k = kh_begin(hrecs->h); k != kh_end(hrecs->h); k++) { sam_hrec_type_t *t1, *t2; char c[2]; int idx = 0; if (!kh_exist(hrecs->h, k)) continue; t1 = t2 = kh_val(hrecs->h, k); c[0] = kh_key(hrecs->h, k)>>8; c[1] = kh_key(hrecs->h, k)&0xff; printf("Type %.2s\n", c); do { sam_hrec_tag_t *tag; printf(">>>%d ", idx++); for (tag = t1->tag; tag; tag=tag->next) { if (strncmp(c, "CO", 2)) printf("\"%.2s\":\"%.*s\"\t", tag->str, tag->len-3, tag->str+3); else printf("%s", tag->str); } putchar('\n'); t1 = t1->next; } while (t1 != t2); } /* Dump out PG chains */ printf("\n@PG chains:\n"); for (i = 0; i < hrecs->npg_end; i++) { int j; printf(" %d:", i); for (j = hrecs->pg_end[i]; j != -1; j = hrecs->pg[j].prev_id) { printf("%s%d(%.*s)", j == hrecs->pg_end[i] ? " " : "->", j, hrecs->pg[j].name_len, hrecs->pg[j].name); } printf("\n"); } puts("===END DUMP==="); } #endif /* * Returns the sort order: */ enum sam_sort_order sam_hrecs_sort_order(sam_hrecs_t *hrecs) { khint_t k; enum sam_sort_order so; so = ORDER_UNKNOWN; k = kh_get(sam_hrecs_t, hrecs->h, TYPEKEY("HD")); if (k != kh_end(hrecs->h)) { sam_hrec_type_t *ty = kh_val(hrecs->h, k); sam_hrec_tag_t *tag; for (tag = ty->tag; tag; tag = tag->next) { if (tag->str[0] == 'S' && tag->str[1] == 'O') { if (strcmp(tag->str+3, "unsorted") == 0) so = ORDER_UNSORTED; else if (strcmp(tag->str+3, "queryname") == 0) so = ORDER_NAME; else if (strcmp(tag->str+3, "coordinate") == 0) so = ORDER_COORD; else if (strcmp(tag->str+3, "unknown") != 0) hts_log_error("Unknown sort order field: %s", tag->str+3); } } } return so; } enum sam_group_order sam_hrecs_group_order(sam_hrecs_t *hrecs) { khint_t k; enum sam_group_order go; go = ORDER_NONE; k = kh_get(sam_hrecs_t, hrecs->h, TYPEKEY("HD")); if (k != kh_end(hrecs->h)) { sam_hrec_type_t *ty = kh_val(hrecs->h, k); sam_hrec_tag_t *tag; for (tag = ty->tag; tag; tag = tag->next) { if (tag->str[0] == 'G' && tag->str[1] == 'O') { if (strcmp(tag->str+3, "query") == 0) go = ORDER_QUERY; else if (strcmp(tag->str+3, "reference") == 0) go = ORDER_REFERENCE; } } } return go; } pysam-0.23.0/htslib/header.h000066400000000000000000000243421475062545500156350ustar00rootroot00000000000000/* Copyright (c) 2013-2019 Genome Research Ltd. Authors: James Bonfield , Valeriu Ohan Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /*! \file * SAM header parsing. * * These functions can be shared between SAM, BAM and CRAM file * formats as all three internally use the same string encoding for * header fields. */ #ifndef HEADER_H_ #define HEADER_H_ #include #include "cram/string_alloc.h" #include "cram/pooled_alloc.h" #include "htslib/khash.h" #include "htslib/kstring.h" #include "htslib/sam.h" #ifdef __cplusplus extern "C" { #endif /*! Make a single integer out of a two-letter type code */ static inline khint32_t TYPEKEY(const char *type) { unsigned int u0 = (unsigned char) type[0]; unsigned int u1 = (unsigned char) type[1]; return (u0 << 8) | u1; } /* * Proposed new SAM header parsing 1 @SQ ID:foo LN:100 2 @SQ ID:bar LN:200 3 @SQ ID:ram LN:300 UR:xyz 4 @RG ID:r ... 5 @RG ID:s ... Hash table for 2-char @keys without dup entries. If dup lines, we form a circular linked list. Ie hash keys = {RG, SQ}. HASH("SQ")--\ | (3) <-> 1 <-> 2 <-> 3 <-> (1) HASH("RG")--\ | (5) <-> 4 <-> 5 <-> (4) Items stored in the hash values also form their own linked lists: Ie SQ->ID(foo)->LN(100) SQ->ID(bar)->LN(200) SQ->ID(ram)->LN(300)->UR(xyz) RG->ID(r) */ /*! A single key:value pair on a header line * * These form a linked list and hold strings. The strings are * allocated from a string_alloc_t pool referenced in the master * sam_hrecs_t structure. Do not attempt to free, malloc or manipulate * these strings directly. */ typedef struct sam_hrec_tag_s { struct sam_hrec_tag_s *next; const char *str; int len; } sam_hrec_tag_t; /*! The parsed version of the SAM header string. * * Each header type (SQ, RG, HD, etc) points to its own sam_hdr_type * struct via the main hash table h in the sam_hrecs_t struct. * * These in turn consist of circular bi-directional linked lists (ie * rings) to hold the multiple instances of the same header type * code. For example if we have 5 \@SQ lines the primary hash table * will key on \@SQ pointing to the first sam_hdr_type and that in turn * will be part of a ring of 5 elements. * * For each sam_hdr_type structure we also point to a sam_hdr_tag * structure which holds the tokenised attributes; the tab separated * key:value pairs per line. */ typedef struct sam_hrec_type_s { struct sam_hrec_type_s *next; // circular list of this type struct sam_hrec_type_s *prev; // circular list of this type struct sam_hrec_type_s *global_next; // circular list of all lines struct sam_hrec_type_s *global_prev; // circular list of all lines sam_hrec_tag_t *tag; // first tag khint32_t type; // Two-letter type code as an int } sam_hrec_type_t; /*! Parsed \@SQ lines */ typedef struct { const char *name; hts_pos_t len; sam_hrec_type_t *ty; } sam_hrec_sq_t; /*! Parsed \@RG lines */ typedef struct { const char *name; sam_hrec_type_t *ty; int name_len; int id; // numerical ID } sam_hrec_rg_t; /*! Parsed \@PG lines */ typedef struct { const char *name; sam_hrec_type_t *ty; int name_len; int id; // numerical ID int prev_id; // -1 if none } sam_hrec_pg_t; /*! Sort order parsed from @HD line */ enum sam_sort_order { ORDER_UNKNOWN =-1, ORDER_UNSORTED = 0, ORDER_NAME = 1, ORDER_COORD = 2 //ORDER_COLLATE = 3 // maybe one day! }; enum sam_group_order { ORDER_NONE =-1, ORDER_QUERY = 0, ORDER_REFERENCE = 1 }; KHASH_MAP_INIT_INT(sam_hrecs_t, sam_hrec_type_t*) KHASH_MAP_INIT_STR(m_s2i, int) /*! Primary structure for header manipulation * * The initial header text is held in the text kstring_t, but is also * parsed out into SQ, RG and PG arrays. These have a hash table * associated with each to allow lookup by ID or SN fields instead of * their numeric array indices. Additionally PG has an array to hold * the linked list start points (the last in a PP chain). * * Use the appropriate sam_hdr_* functions to edit the header, and * call sam_hdr_rebuild() any time the textual form needs to be * updated again. */ struct sam_hrecs_t { khash_t(sam_hrecs_t) *h; sam_hrec_type_t *first_line; //!< First line (usually @HD) string_alloc_t *str_pool; //!< Pool of sam_hdr_tag->str strings pool_alloc_t *type_pool;//!< Pool of sam_hdr_type structs pool_alloc_t *tag_pool; //!< Pool of sam_hdr_tag structs // @SQ lines / references int nref; //!< Number of \@SQ lines int ref_sz; //!< Number of entries available in ref[] sam_hrec_sq_t *ref; //!< Array of parsed \@SQ lines khash_t(m_s2i) *ref_hash; //!< Maps SQ SN field to ref[] index // @RG lines / read-groups int nrg; //!< Number of \@RG lines int rg_sz; //!< number of entries available in rg[] sam_hrec_rg_t *rg; //!< Array of parsed \@RG lines khash_t(m_s2i) *rg_hash; //!< Maps RG ID field to rg[] index // @PG lines / programs int npg; //!< Number of \@PG lines int pg_sz; //!< Number of entries available in pg[] int npg_end; //!< Number of terminating \@PG lines int npg_end_alloc; //!< Size of pg_end field sam_hrec_pg_t *pg; //!< Array of parsed \@PG lines khash_t(m_s2i) *pg_hash; //!< Maps PG ID field to pg[] index int *pg_end; //!< \@PG chain termination IDs // @cond internal char *ID_buf; // temporary buffer for sam_hdr_pg_id uint32_t ID_buf_sz; int ID_cnt; // @endcond int dirty; // marks the header as modified, so it can be rebuilt int refs_changed; // Index of first changed ref (-1 if unchanged) int pgs_changed; // New PG line added int type_count; char (*type_order)[3]; }; /*! * Method for parsing the header text and populating the * internal hash tables. After calling this method, the * parsed representation becomes the single source of truth. * * @param bh Header structure, previously initialised by a * sam_hdr_init call * @return 0 on success, -1 on failure */ int sam_hdr_fill_hrecs(sam_hdr_t *bh); /*! * Reconstructs the text representation of the header from * the hash table data after a change has been performed on * the header. * * @return 0 on success, -1 on failure */ int sam_hdr_rebuild(sam_hdr_t *bh); /*! Creates an empty SAM header, ready to be populated. * * @return * Returns a sam_hrecs_t struct on success (free with sam_hrecs_free()) * NULL on failure */ sam_hrecs_t *sam_hrecs_new(void); /*! Produces a duplicate copy of hrecs and returns it. * @return * Returns NULL on failure */ sam_hrecs_t *sam_hrecs_dup(sam_hrecs_t *hrecs); /*! Update sam_hdr_t target_name and target_len arrays * * sam_hdr_t and sam_hrecs_t are specified separately so that sam_hdr_dup * can use it to construct target arrays from the source header. * * @return 0 on success; -1 on failure */ int sam_hdr_update_target_arrays(sam_hdr_t *bh, const sam_hrecs_t *hrecs, int refs_changed); /*! Reconstructs a kstring from the header hash table. * * @return * Returns 0 on success * -1 on failure */ int sam_hrecs_rebuild_text(const sam_hrecs_t *hrecs, kstring_t *ks); /*! Deallocates all storage used by a sam_hrecs_t struct. * * This also decrements the header reference count. If after decrementing * it is still non-zero then the header is assumed to be in use by another * caller and the free is not done. */ void sam_hrecs_free(sam_hrecs_t *hrecs); /*! * @return * Returns the first header item matching 'type'. If ID is non-NULL it checks * for the tag ID: and compares against the specified ID. * * Returns NULL if no type/ID is found */ sam_hrec_type_t *sam_hrecs_find_type_id(sam_hrecs_t *hrecs, const char *type, const char *ID_key, const char *ID_value); sam_hrec_tag_t *sam_hrecs_find_key(sam_hrec_type_t *type, const char *key, sam_hrec_tag_t **prev); int sam_hrecs_remove_key(sam_hrecs_t *hrecs, sam_hrec_type_t *type, const char *key); /*! Looks up a read-group by name and returns a pointer to the start of the * associated tag list. * * @return * Returns NULL on failure */ sam_hrec_rg_t *sam_hrecs_find_rg(sam_hrecs_t *hrecs, const char *rg); /*! Returns the sort order from the @HD SO: field */ enum sam_sort_order sam_hrecs_sort_order(sam_hrecs_t *hrecs); /*! Returns the group order from the @HD SO: field */ enum sam_group_order sam_hrecs_group_order(sam_hrecs_t *hrecs); #ifdef __cplusplus } #endif #endif /* HEADER_H_ */ pysam-0.23.0/htslib/hfile.c000066400000000000000000001177261475062545500155000ustar00rootroot00000000000000/* hfile.c -- buffered low-level input/output streams. Copyright (C) 2013-2021, 2023-2024 Genome Research Ltd. Author: John Marshall Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #ifdef ENABLE_PLUGINS #if defined(_WIN32) || defined(__CYGWIN__) || defined(__MSYS__) #define USING_WINDOWS_PLUGIN_DLLS #include #endif #endif #include "htslib/hfile.h" #include "hfile_internal.h" #include "htslib/kstring.h" #ifndef ENOTSUP #define ENOTSUP EINVAL #endif #ifndef EOVERFLOW #define EOVERFLOW ERANGE #endif #ifndef EPROTONOSUPPORT #define EPROTONOSUPPORT ENOSYS #endif #ifndef SSIZE_MAX /* SSIZE_MAX is POSIX 1 */ #define SSIZE_MAX LONG_MAX #endif /* hFILE fields are used as follows: char *buffer; // Pointer to the start of the I/O buffer char *begin; // First not-yet-read character / unused position char *end; // First unfilled/unfillable position char *limit; // Pointer to the first position past the buffer const hFILE_backend *backend; // Methods to refill/flush I/O buffer off_t offset; // Offset within the stream of buffer position 0 unsigned at_eof:1;// For reading, whether EOF has been seen unsigned mobile:1;// Buffer is a mobile window or fixed full contents unsigned readonly:1;// Whether opened as "r" rather than "r+"/"w"/"a" int has_errno; // Error number from the last failure on this stream For reading, begin is the first unread character in the buffer and end is the first unfilled position: -----------ABCDEFGHIJKLMNO--------------- ^buffer ^begin ^end ^limit For writing, begin is the first unused position and end is unused so remains equal to buffer: ABCDEFGHIJKLMNOPQRSTUVWXYZ--------------- ^buffer ^begin ^limit ^end Thus if begin > end then there is a non-empty write buffer, if begin < end then there is a non-empty read buffer, and if begin == end then both buffers are empty. In all cases, the stream's file position indicator corresponds to the position pointed to by begin. The above is the normal scenario of a mobile window. For in-memory streams (eg via hfile_init_fixed) the buffer can be used as the full contents without any separate backend behind it. These always have at_eof set, offset set to 0, need no read() method, and should just return EINVAL for seek(): abcdefghijkLMNOPQRSTUVWXYZ------ ^buffer ^begin ^end ^limit */ HTSLIB_EXPORT hFILE *hfile_init(size_t struct_size, const char *mode, size_t capacity) { hFILE *fp = (hFILE *) malloc(struct_size); if (fp == NULL) goto error; if (capacity == 0) capacity = 32768; // FIXME For now, clamp input buffer sizes so mpileup doesn't eat memory if (strchr(mode, 'r') && capacity > 32768) capacity = 32768; fp->buffer = (char *) malloc(capacity); if (fp->buffer == NULL) goto error; fp->begin = fp->end = fp->buffer; fp->limit = &fp->buffer[capacity]; fp->offset = 0; fp->at_eof = 0; fp->mobile = 1; fp->readonly = (strchr(mode, 'r') && ! strchr(mode, '+')); fp->preserve = 0; fp->has_errno = 0; return fp; error: hfile_destroy(fp); return NULL; } hFILE *hfile_init_fixed(size_t struct_size, const char *mode, char *buffer, size_t buf_filled, size_t buf_size) { hFILE *fp = (hFILE *) malloc(struct_size); if (fp == NULL) return NULL; fp->buffer = fp->begin = buffer; fp->end = &fp->buffer[buf_filled]; fp->limit = &fp->buffer[buf_size]; fp->offset = 0; fp->at_eof = 1; fp->mobile = 0; fp->readonly = (strchr(mode, 'r') && ! strchr(mode, '+')); fp->preserve = 0; fp->has_errno = 0; return fp; } static const struct hFILE_backend mem_backend; HTSLIB_EXPORT void hfile_destroy(hFILE *fp) { int save = errno; if (fp) free(fp->buffer); free(fp); errno = save; } static inline int writebuffer_is_nonempty(hFILE *fp) { return fp->begin > fp->end; } /* Refills the read buffer from the backend (once, so may only partially fill the buffer), returning the number of additional characters read (which might be 0), or negative when an error occurred. */ static ssize_t refill_buffer(hFILE *fp) { ssize_t n; // Move any unread characters to the start of the buffer if (fp->mobile && fp->begin > fp->buffer) { fp->offset += fp->begin - fp->buffer; memmove(fp->buffer, fp->begin, fp->end - fp->begin); fp->end = &fp->buffer[fp->end - fp->begin]; fp->begin = fp->buffer; } // Read into the available buffer space at fp->[end,limit) if (fp->at_eof || fp->end == fp->limit) n = 0; else { n = fp->backend->read(fp, fp->end, fp->limit - fp->end); if (n < 0) { fp->has_errno = errno; return n; } else if (n == 0) fp->at_eof = 1; } fp->end += n; return n; } /* * Changes the buffer size for an hFILE. Ideally this is done * immediately after opening. If performed later, this function may * fail if we are reducing the buffer size and the current offset into * the buffer is beyond the new capacity. * * Returns 0 on success; * -1 on failure. */ HTSLIB_EXPORT int hfile_set_blksize(hFILE *fp, size_t bufsiz) { char *buffer; ptrdiff_t curr_used; if (!fp) return -1; curr_used = (fp->begin > fp->end ? fp->begin : fp->end) - fp->buffer; if (bufsiz == 0) bufsiz = 32768; // Ensure buffer resize will not erase live data if (bufsiz < curr_used) return -1; if (!(buffer = (char *) realloc(fp->buffer, bufsiz))) return -1; fp->begin = buffer + (fp->begin - fp->buffer); fp->end = buffer + (fp->end - fp->buffer); fp->buffer = buffer; fp->limit = &fp->buffer[bufsiz]; return 0; } /* Called only from hgetc(), when our buffer is empty. */ HTSLIB_EXPORT int hgetc2(hFILE *fp) { return (refill_buffer(fp) > 0)? (unsigned char) *(fp->begin++) : EOF; } ssize_t hgetdelim(char *buffer, size_t size, int delim, hFILE *fp) { char *found; size_t n, copied = 0; ssize_t got; if (size < 1 || size > SSIZE_MAX) { fp->has_errno = errno = EINVAL; return -1; } if (writebuffer_is_nonempty(fp)) { fp->has_errno = errno = EBADF; return -1; } --size; /* to allow space for the NUL terminator */ do { n = fp->end - fp->begin; if (n > size - copied) n = size - copied; /* Look in the hFILE buffer for the delimiter */ found = memchr(fp->begin, delim, n); if (found != NULL) { n = found - fp->begin + 1; memcpy(buffer + copied, fp->begin, n); buffer[n + copied] = '\0'; fp->begin += n; return n + copied; } /* No delimiter yet, copy as much as we can and refill if necessary */ memcpy(buffer + copied, fp->begin, n); fp->begin += n; copied += n; if (copied == size) { /* Output buffer full */ buffer[copied] = '\0'; return copied; } got = refill_buffer(fp); } while (got > 0); if (got < 0) return -1; /* Error on refill. */ buffer[copied] = '\0'; /* EOF, return anything that was copied. */ return copied; } char *hgets(char *buffer, int size, hFILE *fp) { if (size < 1) { fp->has_errno = errno = EINVAL; return NULL; } return hgetln(buffer, size, fp) > 0 ? buffer : NULL; } ssize_t hpeek(hFILE *fp, void *buffer, size_t nbytes) { size_t n = fp->end - fp->begin; while (n < nbytes) { ssize_t ret = refill_buffer(fp); if (ret < 0) return ret; else if (ret == 0) break; else n += ret; } if (n > nbytes) n = nbytes; memcpy(buffer, fp->begin, n); return n; } /* Called only from hread(); when called, our buffer is empty and nread bytes have already been placed in the destination buffer. */ HTSLIB_EXPORT ssize_t hread2(hFILE *fp, void *destv, size_t nbytes, size_t nread) { const size_t capacity = fp->limit - fp->buffer; int buffer_invalidated = 0; char *dest = (char *) destv; dest += nread, nbytes -= nread; // Read large requests directly into the destination buffer while (nbytes * 2 >= capacity && !fp->at_eof) { ssize_t n = fp->backend->read(fp, dest, nbytes); if (n < 0) { fp->has_errno = errno; return n; } else if (n == 0) fp->at_eof = 1; else buffer_invalidated = 1; fp->offset += n; dest += n, nbytes -= n; nread += n; } if (buffer_invalidated) { // Our unread buffer is empty, so begin == end, but our already-read // buffer [buffer,begin) is likely non-empty and is no longer valid as // its contents are no longer adjacent to the file position indicator. // Discard it so that hseek() can't try to take advantage of it. fp->offset += fp->begin - fp->buffer; fp->begin = fp->end = fp->buffer; } while (nbytes > 0 && !fp->at_eof) { size_t n; ssize_t ret = refill_buffer(fp); if (ret < 0) return ret; n = fp->end - fp->begin; if (n > nbytes) n = nbytes; memcpy(dest, fp->begin, n); fp->begin += n; dest += n, nbytes -= n; nread += n; } return nread; } /* Flushes the write buffer, fp->[buffer,begin), out through the backend returning 0 on success or negative if an error occurred. */ static ssize_t flush_buffer(hFILE *fp) { const char *buffer = fp->buffer; while (buffer < fp->begin) { ssize_t n = fp->backend->write(fp, buffer, fp->begin - buffer); if (n < 0) { fp->has_errno = errno; return n; } buffer += n; fp->offset += n; } fp->begin = fp->buffer; // Leave the buffer empty return 0; } int hflush(hFILE *fp) { if (flush_buffer(fp) < 0) return EOF; if (fp->backend->flush) { if (fp->backend->flush(fp) < 0) { fp->has_errno = errno; return EOF; } } return 0; } /* Called only from hputc(), when our buffer is already full. */ HTSLIB_EXPORT int hputc2(int c, hFILE *fp) { if (flush_buffer(fp) < 0) return EOF; *(fp->begin++) = c; return c; } /* Called only from hwrite() and hputs2(); when called, our buffer is either full and ncopied bytes from the source have already been copied to our buffer; or completely empty, ncopied is zero and totalbytes is greater than the buffer size. */ HTSLIB_EXPORT ssize_t hwrite2(hFILE *fp, const void *srcv, size_t totalbytes, size_t ncopied) { const char *src = (const char *) srcv; ssize_t ret; const size_t capacity = fp->limit - fp->buffer; size_t remaining = totalbytes - ncopied; src += ncopied; ret = flush_buffer(fp); if (ret < 0) return ret; // Write large blocks out directly from the source buffer while (remaining * 2 >= capacity) { ssize_t n = fp->backend->write(fp, src, remaining); if (n < 0) { fp->has_errno = errno; return n; } fp->offset += n; src += n, remaining -= n; } // Just buffer any remaining characters memcpy(fp->begin, src, remaining); fp->begin += remaining; return totalbytes; } /* Called only from hputs(), when our buffer is already full. */ HTSLIB_EXPORT int hputs2(const char *text, size_t totalbytes, size_t ncopied, hFILE *fp) { return (hwrite2(fp, text, totalbytes, ncopied) >= 0)? 0 : EOF; } off_t hseek(hFILE *fp, off_t offset, int whence) { off_t curpos, pos; if (writebuffer_is_nonempty(fp) && fp->mobile) { int ret = flush_buffer(fp); if (ret < 0) return ret; } curpos = htell(fp); // Relative offsets are given relative to the hFILE's stream position, // which may differ from the backend's physical position due to buffering // read-ahead. Correct for this by converting to an absolute position. if (whence == SEEK_CUR) { if (curpos + offset < 0) { // Either a negative offset resulted in a position before the // start of the file, or we overflowed when given a positive offset fp->has_errno = errno = (offset < 0)? EINVAL : EOVERFLOW; return -1; } whence = SEEK_SET; offset = curpos + offset; } // For fixed immobile buffers, convert everything else to SEEK_SET too // so that seeking can be avoided for all (within range) requests. else if (! fp->mobile && whence == SEEK_END) { size_t length = fp->end - fp->buffer; if (offset > 0 || -offset > length) { fp->has_errno = errno = EINVAL; return -1; } whence = SEEK_SET; offset = length + offset; } // Avoid seeking if the desired position is within our read buffer. // (But not when the next operation may be a write on a mobile buffer.) if (whence == SEEK_SET && (! fp->mobile || fp->readonly) && offset >= fp->offset && offset - fp->offset <= fp->end - fp->buffer) { fp->begin = &fp->buffer[offset - fp->offset]; return offset; } pos = fp->backend->seek(fp, offset, whence); if (pos < 0) { fp->has_errno = errno; return pos; } // Seeking succeeded, so discard any non-empty read buffer fp->begin = fp->end = fp->buffer; fp->at_eof = 0; fp->offset = pos; return pos; } int hclose(hFILE *fp) { int err = fp->has_errno; if (writebuffer_is_nonempty(fp) && hflush(fp) < 0) err = fp->has_errno; if (!fp->preserve) { if (fp->backend->close(fp) < 0) err = errno; hfile_destroy(fp); } if (err) { errno = err; return EOF; } else return 0; } void hclose_abruptly(hFILE *fp) { int save = errno; if (fp->preserve) return; if (fp->backend->close(fp) < 0) { /* Ignore subsequent errors */ } hfile_destroy(fp); errno = save; } /*************************** * File descriptor backend * ***************************/ #ifndef _WIN32 #include #include #define HAVE_STRUCT_STAT_ST_BLKSIZE #else #include #define HAVE_CLOSESOCKET #define HAVE_SETMODE #endif #include #include /* For Unix, it doesn't matter whether a file descriptor is a socket. However Windows insists on send()/recv() and its own closesocket() being used when fd happens to be a socket. */ typedef struct { hFILE base; int fd; unsigned is_socket:1, is_shared:1; } hFILE_fd; static ssize_t fd_read(hFILE *fpv, void *buffer, size_t nbytes) { hFILE_fd *fp = (hFILE_fd *) fpv; ssize_t n; do { n = fp->is_socket? recv(fp->fd, buffer, nbytes, 0) : read(fp->fd, buffer, nbytes); } while (n < 0 && errno == EINTR); return n; } static ssize_t fd_write(hFILE *fpv, const void *buffer, size_t nbytes) { hFILE_fd *fp = (hFILE_fd *) fpv; ssize_t n; do { n = fp->is_socket? send(fp->fd, buffer, nbytes, 0) : write(fp->fd, buffer, nbytes); } while (n < 0 && errno == EINTR); #ifdef _WIN32 // On windows we have no SIGPIPE. Instead write returns // EINVAL. We check for this and our fd being a pipe. // If so, we raise SIGTERM instead of SIGPIPE. It's not // ideal, but I think the only alternative is extra checking // in every single piece of code. if (n < 0 && errno == EINVAL && GetLastError() == ERROR_NO_DATA && GetFileType((HANDLE)_get_osfhandle(fp->fd)) == FILE_TYPE_PIPE) { raise(SIGTERM); } #endif return n; } static off_t fd_seek(hFILE *fpv, off_t offset, int whence) { hFILE_fd *fp = (hFILE_fd *) fpv; #ifdef _WIN32 // On windows lseek can return non-zero values even on a pipe. Instead // it's likely to seek somewhere within the pipe memory buffer. // This breaks bgzf_check_EOF among other things. if (GetFileType((HANDLE)_get_osfhandle(fp->fd)) == FILE_TYPE_PIPE) { errno = ESPIPE; return -1; } #endif return lseek(fp->fd, offset, whence); } static int fd_flush(hFILE *fpv) { int ret = 0; do { #ifdef HAVE_FDATASYNC hFILE_fd *fp = (hFILE_fd *) fpv; ret = fdatasync(fp->fd); #elif defined(HAVE_FSYNC) hFILE_fd *fp = (hFILE_fd *) fpv; ret = fsync(fp->fd); #endif // Ignore invalid-for-fsync(2) errors due to being, e.g., a pipe, // and operation-not-supported errors (Mac OS X) if (ret < 0 && (errno == EINVAL || errno == ENOTSUP)) ret = 0; } while (ret < 0 && errno == EINTR); return ret; } static int fd_close(hFILE *fpv) { hFILE_fd *fp = (hFILE_fd *) fpv; int ret; // If we don't own the fd, return successfully without actually closing it if (fp->is_shared) return 0; do { #ifdef HAVE_CLOSESOCKET ret = fp->is_socket? closesocket(fp->fd) : close(fp->fd); #else ret = close(fp->fd); #endif } while (ret < 0 && errno == EINTR); return ret; } static const struct hFILE_backend fd_backend = { fd_read, fd_write, fd_seek, fd_flush, fd_close }; static size_t blksize(int fd) { #ifdef HAVE_STRUCT_STAT_ST_BLKSIZE struct stat sbuf; if (fstat(fd, &sbuf) != 0) return 0; return sbuf.st_blksize; #else return 0; #endif } static hFILE *hopen_fd(const char *filename, const char *mode) { hFILE_fd *fp = NULL; int fd = open(filename, hfile_oflags(mode), 0666); if (fd < 0) goto error; fp = (hFILE_fd *) hfile_init(sizeof (hFILE_fd), mode, blksize(fd)); if (fp == NULL) goto error; fp->fd = fd; fp->is_socket = 0; fp->is_shared = 0; fp->base.backend = &fd_backend; return &fp->base; error: if (fd >= 0) { int save = errno; (void) close(fd); errno = save; } hfile_destroy((hFILE *) fp); return NULL; } // Loads the contents of filename to produced a read-only, in memory, // immobile hfile. fp is the already opened file. We always close this // input fp, irrespective of whether we error or whether we return a new // immobile hfile. static hFILE *hpreload(hFILE *fp) { hFILE *mem_fp; char *buf = NULL; off_t buf_sz = 0, buf_a = 0, buf_inc = 8192, len; for (;;) { if (buf_a - buf_sz < 5000) { buf_a += buf_inc; char *t = realloc(buf, buf_a); if (!t) goto err; buf = t; if (buf_inc < 1000000) buf_inc *= 1.3; } len = hread(fp, buf+buf_sz, buf_a-buf_sz); if (len > 0) buf_sz += len; else break; } if (len < 0) goto err; mem_fp = hfile_init_fixed(sizeof(hFILE), "r", buf, buf_sz, buf_a); if (!mem_fp) goto err; mem_fp->backend = &mem_backend; if (hclose(fp) < 0) { hclose_abruptly(mem_fp); goto err; } return mem_fp; err: free(buf); hclose_abruptly(fp); return NULL; } static int is_preload_url_remote(const char *url){ return hisremote(url + 8); // len("preload:") = 8 } static hFILE *hopen_preload(const char *url, const char *mode){ hFILE* fp = hopen(url + 8, mode); return fp ? hpreload(fp) : NULL; } hFILE *hdopen(int fd, const char *mode) { hFILE_fd *fp = (hFILE_fd*) hfile_init(sizeof (hFILE_fd), mode, blksize(fd)); if (fp == NULL) return NULL; fp->fd = fd; fp->is_socket = (strchr(mode, 's') != NULL); fp->is_shared = (strchr(mode, 'S') != NULL); fp->base.backend = &fd_backend; return &fp->base; } static hFILE *hopen_fd_fileuri(const char *url, const char *mode) { if (strncmp(url, "file://localhost/", 17) == 0) url += 16; else if (strncmp(url, "file:///", 8) == 0) url += 7; else { errno = EPROTONOSUPPORT; return NULL; } #if defined(_WIN32) || defined(__MSYS__) // For cases like C:/foo if (url[0] == '/' && url[1] && url[2] == ':' && url[3] == '/') url++; #endif return hopen_fd(url, mode); } static hFILE *hopen_fd_stdinout(const char *mode) { int fd = (strchr(mode, 'r') != NULL)? STDIN_FILENO : STDOUT_FILENO; char mode_shared[101]; snprintf(mode_shared, sizeof mode_shared, "S%s", mode); #if defined HAVE_SETMODE && defined O_BINARY if (setmode(fd, O_BINARY) < 0) return NULL; #endif return hdopen(fd, mode_shared); } HTSLIB_EXPORT int hfile_oflags(const char *mode) { int rdwr = 0, flags = 0; const char *s; for (s = mode; *s; s++) switch (*s) { case 'r': rdwr = O_RDONLY; break; case 'w': rdwr = O_WRONLY; flags |= O_CREAT | O_TRUNC; break; case 'a': rdwr = O_WRONLY; flags |= O_CREAT | O_APPEND; break; case '+': rdwr = O_RDWR; break; #ifdef O_CLOEXEC case 'e': flags |= O_CLOEXEC; break; #endif #ifdef O_EXCL case 'x': flags |= O_EXCL; break; #endif default: break; } #ifdef O_BINARY flags |= O_BINARY; #endif return rdwr | flags; } /********************* * In-memory backend * *********************/ #include "hts_internal.h" typedef struct { hFILE base; } hFILE_mem; static off_t mem_seek(hFILE *fpv, off_t offset, int whence) { errno = EINVAL; return -1; } static int mem_close(hFILE *fpv) { return 0; } static const struct hFILE_backend mem_backend = { NULL, NULL, mem_seek, NULL, mem_close }; static int cmp_prefix(const char *key, const char *s) { while (*key) if (tolower_c(*s) != *key) return +1; else s++, key++; return 0; } static hFILE *create_hfile_mem(char* buffer, const char* mode, size_t buf_filled, size_t buf_size) { hFILE_mem *fp = (hFILE_mem *) hfile_init_fixed(sizeof(hFILE_mem), mode, buffer, buf_filled, buf_size); if (fp == NULL) return NULL; fp->base.backend = &mem_backend; return &fp->base; } static hFILE *hopen_mem(const char *url, const char *mode) { size_t length, size; char *buffer; const char *data, *comma = strchr(url, ','); if (comma == NULL) { errno = EINVAL; return NULL; } data = comma+1; // TODO Implement write modes if (strchr(mode, 'r') == NULL) { errno = EROFS; return NULL; } if (comma - url >= 7 && cmp_prefix(";base64", &comma[-7]) == 0) { size = hts_base64_decoded_length(strlen(data)); buffer = malloc(size); if (buffer == NULL) return NULL; hts_decode_base64(buffer, &length, data); } else { size = strlen(data) + 1; buffer = malloc(size); if (buffer == NULL) return NULL; hts_decode_percent(buffer, &length, data); } hFILE* hf; if(!(hf = create_hfile_mem(buffer, mode, length, size))){ free(buffer); return NULL; } return hf; } static hFILE *hopenv_mem(const char *filename, const char *mode, va_list args) { char* buffer = va_arg(args, char*); size_t sz = va_arg(args, size_t); va_end(args); hFILE* hf; if(!(hf = create_hfile_mem(buffer, mode, sz, sz))){ free(buffer); return NULL; } return hf; } char *hfile_mem_get_buffer(hFILE *file, size_t *length) { if (file->backend != &mem_backend) { errno = EINVAL; return NULL; } if (length) *length = file->buffer - file->limit; return file->buffer; } char *hfile_mem_steal_buffer(hFILE *file, size_t *length) { char *buf = hfile_mem_get_buffer(file, length); if (buf) file->buffer = NULL; return buf; } // open() stub for mem: which only works with the vopen() interface // Use 'data:,' for data encoded in the URL static hFILE *hopen_not_supported(const char *fname, const char *mode) { errno = EINVAL; return NULL; } int hfile_plugin_init_mem(struct hFILE_plugin *self) { // mem files are declared remote so they work with a tabix index static const struct hFILE_scheme_handler handler = {hopen_not_supported, hfile_always_remote, "mem", 2000 + 50, hopenv_mem}; self->name = "mem"; hfile_add_scheme_handler("mem", &handler); return 0; } /********************************************************************** * Dummy crypt4gh plug-in. Does nothing apart from advise how to get * * the real one. It will be overridden by the actual plug-in. * **********************************************************************/ static hFILE *crypt4gh_needed(const char *url, const char *mode) { const char *u = strncmp(url, "crypt4gh:", 9) == 0 ? url + 9 : url; #if defined(ENABLE_PLUGINS) const char *enable_plugins = ""; #else const char *enable_plugins = "You also need to rebuild HTSlib with plug-ins enabled.\n"; #endif hts_log_error("Accessing \"%s\" needs the crypt4gh plug-in.\n" "It can be found at " "https://github.com/samtools/htslib-crypt4gh\n" "%s" "If you have the plug-in, please ensure it can be " "found on your HTS_PATH.", u, enable_plugins); errno = EPROTONOSUPPORT; return NULL; } int hfile_plugin_init_crypt4gh_needed(struct hFILE_plugin *self) { static const struct hFILE_scheme_handler handler = { crypt4gh_needed, hfile_always_local, "crypt4gh-needed", 0, NULL }; self->name = "crypt4gh-needed"; hfile_add_scheme_handler("crypt4gh", &handler); return 0; } /***************************************** * Plugin and hopen() backend dispatcher * *****************************************/ #include "htslib/khash.h" KHASH_MAP_INIT_STR(scheme_string, const struct hFILE_scheme_handler *) static khash_t(scheme_string) *schemes = NULL; struct hFILE_plugin_list { struct hFILE_plugin plugin; struct hFILE_plugin_list *next; }; static struct hFILE_plugin_list *plugins = NULL; static pthread_mutex_t plugins_lock = PTHREAD_MUTEX_INITIALIZER; void hfile_shutdown(int do_close_plugin) { pthread_mutex_lock(&plugins_lock); if (schemes) { kh_destroy(scheme_string, schemes); schemes = NULL; } while (plugins != NULL) { struct hFILE_plugin_list *p = plugins; if (p->plugin.destroy) p->plugin.destroy(); #ifdef ENABLE_PLUGINS if (p->plugin.obj && do_close_plugin) close_plugin(p->plugin.obj); #endif plugins = p->next; free(p); } pthread_mutex_unlock(&plugins_lock); } static void hfile_exit(void) { hfile_shutdown(0); pthread_mutex_destroy(&plugins_lock); } static inline int priority(const struct hFILE_scheme_handler *handler) { return handler->priority % 1000; } #ifdef USING_WINDOWS_PLUGIN_DLLS /* * Work-around for Windows plug-in dlls where the plug-in could be * using a different HTSlib library to the executable (for example * because the latter was build against a static libhts.a). When this * happens, the plug-in can call the wrong copy of hfile_add_scheme_handler(). * If this is detected, it calls this function which attempts to fix the * problem by redirecting to the hfile_add_scheme_handler() in the main * executable. */ static int try_exe_add_scheme_handler(const char *scheme, const struct hFILE_scheme_handler *handler) { static void (*add_scheme_handler)(const char *scheme, const struct hFILE_scheme_handler *handler); if (!add_scheme_handler) { // dlopen the main executable and resolve hfile_add_scheme_handler void *exe_handle = dlopen(NULL, RTLD_LAZY); if (!exe_handle) return -1; *(void **) (&add_scheme_handler) = dlsym(exe_handle, "hfile_add_scheme_handler"); dlclose(exe_handle); } // Check that the symbol was obtained and isn't the one in this copy // of the library (to avoid infinite recursion) if (!add_scheme_handler || add_scheme_handler == hfile_add_scheme_handler) return -1; add_scheme_handler(scheme, handler); return 0; } #else static int try_exe_add_scheme_handler(const char *scheme, const struct hFILE_scheme_handler *handler) { return -1; } #endif HTSLIB_EXPORT void hfile_add_scheme_handler(const char *scheme, const struct hFILE_scheme_handler *handler) { int absent; if (handler->open == NULL || handler->isremote == NULL) { hts_log_warning("Couldn't register scheme handler for %s: missing method", scheme); return; } if (!schemes) { if (try_exe_add_scheme_handler(scheme, handler) != 0) { hts_log_warning("Couldn't register scheme handler for %s", scheme); } return; } khint_t k = kh_put(scheme_string, schemes, scheme, &absent); if (absent < 0) { hts_log_warning("Couldn't register scheme handler for %s : %s", scheme, strerror(errno)); return; } if (absent || priority(handler) > priority(kh_value(schemes, k))) { kh_value(schemes, k) = handler; } } static int init_add_plugin(void *obj, int (*init)(struct hFILE_plugin *), const char *pluginname) { struct hFILE_plugin_list *p = malloc (sizeof (struct hFILE_plugin_list)); if (p == NULL) { hts_log_debug("Failed to allocate memory for plugin \"%s\"", pluginname); return -1; } p->plugin.api_version = 1; p->plugin.obj = obj; p->plugin.name = NULL; p->plugin.destroy = NULL; int ret = (*init)(&p->plugin); if (ret != 0) { hts_log_debug("Initialisation failed for plugin \"%s\": %d", pluginname, ret); free(p); return ret; } hts_log_debug("Loaded \"%s\"", pluginname); p->next = plugins, plugins = p; return 0; } /* * Returns 0 on success, * <0 on failure */ static int load_hfile_plugins(void) { static const struct hFILE_scheme_handler data = { hopen_mem, hfile_always_local, "built-in", 80 }, file = { hopen_fd_fileuri, hfile_always_local, "built-in", 80 }, preload = { hopen_preload, is_preload_url_remote, "built-in", 80 }; schemes = kh_init(scheme_string); if (schemes == NULL) return -1; hfile_add_scheme_handler("data", &data); hfile_add_scheme_handler("file", &file); hfile_add_scheme_handler("preload", &preload); init_add_plugin(NULL, hfile_plugin_init_mem, "mem"); init_add_plugin(NULL, hfile_plugin_init_crypt4gh_needed, "crypt4gh-needed"); #ifdef ENABLE_PLUGINS struct hts_path_itr path; const char *pluginname; hts_path_itr_setup(&path, NULL, NULL, "hfile_", 6, NULL, 0); while ((pluginname = hts_path_itr_next(&path)) != NULL) { void *obj; int (*init)(struct hFILE_plugin *) = (int (*)(struct hFILE_plugin *)) load_plugin(&obj, pluginname, "hfile_plugin_init"); if (init) { if (init_add_plugin(obj, init, pluginname) != 0) close_plugin(obj); } } #else #ifdef HAVE_LIBCURL init_add_plugin(NULL, hfile_plugin_init_libcurl, "libcurl"); #endif #ifdef ENABLE_GCS init_add_plugin(NULL, hfile_plugin_init_gcs, "gcs"); #endif #ifdef ENABLE_S3 init_add_plugin(NULL, hfile_plugin_init_s3, "s3"); init_add_plugin(NULL, hfile_plugin_init_s3_write, "s3w"); #endif #endif // In the unlikely event atexit() fails, it's better to succeed here and // carry on; then eventually when the program exits, we'll merely close // down the plugins uncleanly, as if we had aborted. (void) atexit(hfile_exit); return 0; } /* A filename like "foo:bar" in which we don't recognise the scheme is either an ordinary file or an indication of a missing or broken plugin. Try to open it as an ordinary file; but if there's no such file, set errno distinctively to make the plugin issue apparent. */ static hFILE *hopen_unknown_scheme(const char *fname, const char *mode) { hFILE *fp = hopen_fd(fname, mode); if (fp == NULL && errno == ENOENT) errno = EPROTONOSUPPORT; return fp; } /* Returns the appropriate handler, or NULL if the string isn't an URL. */ static const struct hFILE_scheme_handler *find_scheme_handler(const char *s) { static const struct hFILE_scheme_handler unknown_scheme = { hopen_unknown_scheme, hfile_always_local, "built-in", 0 }; char scheme[12]; int i; for (i = 0; i < sizeof scheme; i++) if (isalnum_c(s[i]) || s[i] == '+' || s[i] == '-' || s[i] == '.') scheme[i] = tolower_c(s[i]); else if (s[i] == ':') break; else return NULL; // 1 byte schemes are likely windows C:/foo pathnames if (i <= 1 || i >= sizeof scheme) return NULL; scheme[i] = '\0'; pthread_mutex_lock(&plugins_lock); if (!schemes && load_hfile_plugins() < 0) { pthread_mutex_unlock(&plugins_lock); return NULL; } pthread_mutex_unlock(&plugins_lock); khint_t k = kh_get(scheme_string, schemes, scheme); return (k != kh_end(schemes))? kh_value(schemes, k) : &unknown_scheme; } /*************************** * Library introspection functions ***************************/ /* * Fills out sc_list[] with the list of known URL schemes. * This can be restricted to just ones from a specific plugin, * or all (plugin == NULL). * * Returns number of schemes found on success; * -1 on failure. */ HTSLIB_EXPORT int hfile_list_schemes(const char *plugin, const char *sc_list[], int *nschemes) { pthread_mutex_lock(&plugins_lock); if (!schemes && load_hfile_plugins() < 0) { pthread_mutex_unlock(&plugins_lock); return -1; } pthread_mutex_unlock(&plugins_lock); khiter_t k; int ns = 0; for (k = kh_begin(schemes); k != kh_end(schemes); k++) { if (!kh_exist(schemes, k)) continue; const struct hFILE_scheme_handler *s = kh_value(schemes, k); if (plugin && strcmp(s->provider, plugin) != 0) continue; if (ns < *nschemes) sc_list[ns] = kh_key(schemes, k); ns++; } if (*nschemes > ns) *nschemes = ns; return ns; } /* * Fills out plist[] with the list of known hFILE plugins. * * Returns number of schemes found on success; * -1 on failure */ HTSLIB_EXPORT int hfile_list_plugins(const char *plist[], int *nplugins) { pthread_mutex_lock(&plugins_lock); if (!schemes && load_hfile_plugins() < 0) { pthread_mutex_unlock(&plugins_lock); return -1; } pthread_mutex_unlock(&plugins_lock); int np = 0; if (*nplugins) plist[np++] = "built-in"; struct hFILE_plugin_list *p = plugins; while (p) { if (np < *nplugins) plist[np] = p->plugin.name; p = p->next; np++; } if (*nplugins > np) *nplugins = np; return np; } /* * Tests for the presence of a specific hFILE plugin. * * Returns 1 if true * 0 otherwise */ HTSLIB_EXPORT int hfile_has_plugin(const char *name) { pthread_mutex_lock(&plugins_lock); if (!schemes && load_hfile_plugins() < 0) { pthread_mutex_unlock(&plugins_lock); return -1; } pthread_mutex_unlock(&plugins_lock); struct hFILE_plugin_list *p = plugins; while (p) { if (strcmp(p->plugin.name, name) == 0) return 1; p = p->next; } return 0; } /*************************** * hFILE interface proper ***************************/ hFILE *hopen(const char *fname, const char *mode, ...) { const struct hFILE_scheme_handler *handler = find_scheme_handler(fname); if (handler) { if (strchr(mode, ':') == NULL || handler->priority < 2000 || handler->vopen == NULL) { return handler->open(fname, mode); } else { hFILE *fp; va_list arg; va_start(arg, mode); fp = handler->vopen(fname, mode, arg); va_end(arg); return fp; } } else if (strcmp(fname, "-") == 0) return hopen_fd_stdinout(mode); else return hopen_fd(fname, mode); } HTSLIB_EXPORT int hfile_always_local (const char *fname) { return 0; } HTSLIB_EXPORT int hfile_always_remote(const char *fname) { return 1; } int hisremote(const char *fname) { const struct hFILE_scheme_handler *handler = find_scheme_handler(fname); return handler? handler->isremote(fname) : 0; } // Remove an extension, if any, from the basename part of [start,limit). // Note: Doesn't notice percent-encoded '.' and '/' characters. Don't do that. static const char *strip_extension(const char *start, const char *limit) { const char *s = limit; while (s > start) { --s; if (*s == '.') return s; else if (*s == '/') break; } return limit; } char *haddextension(struct kstring_t *buffer, const char *filename, int replace, const char *new_extension) { const char *trailing, *end; if (find_scheme_handler(filename)) { // URL, so alter extensions before any trailing query or fragment parts // Allow # symbols in s3 URLs trailing = filename + ((strncmp(filename, "s3://", 5) && strncmp(filename, "s3+http://", 10) && strncmp(filename, "s3+https://", 11)) ? strcspn(filename, "?#") : strcspn(filename, "?")); } else { // Local path, so alter extensions at the end of the filename trailing = strchr(filename, '\0'); } end = replace? strip_extension(filename, trailing) : trailing; buffer->l = 0; if (kputsn(filename, end - filename, buffer) >= 0 && kputs(new_extension, buffer) >= 0 && kputs(trailing, buffer) >= 0) return buffer->s; else return NULL; } /* * ---------------------------------------------------------------------- * Minimal stub functions for knet, added after the removal of * hfile_net.c and knetfile.c. * * They exist purely for ABI compatibility, but are simply wrappers to * hFILE. API should be compatible except knet_fileno (unused?). * * CULL THESE and knetfile.h at the next .so version bump. */ typedef struct knetFile_s { // As per htslib/knetfile.h. Duplicated here as we don't wish to // have any dependence on the deprecated knetfile.h interface, plus // it's hopefully only temporary. int type, fd; int64_t offset; char *host, *port; int ctrl_fd, pasv_ip[4], pasv_port, max_response, no_reconnect, is_ready; char *response, *retr, *size_cmd; int64_t seek_offset; int64_t file_size; char *path, *http_host; // Our local addition hFILE *hf; } knetFile; HTSLIB_EXPORT knetFile *knet_open(const char *fn, const char *mode) { knetFile *fp = calloc(1, sizeof(*fp)); if (!fp) return NULL; if (!(fp->hf = hopen(fn, mode))) { free(fp); return NULL; } // FD backend is the only one implementing knet_fileno fp->fd = fp->hf->backend == &fd_backend ? ((hFILE_fd *)fp->hf)->fd : -1; return fp; } HTSLIB_EXPORT knetFile *knet_dopen(int fd, const char *mode) { knetFile *fp = calloc(1, sizeof(*fp)); if (!fp) return NULL; if (!(fp->hf = hdopen(fd, mode))) { free(fp); return NULL; } fp->fd = fd; return fp; } HTSLIB_EXPORT ssize_t knet_read(knetFile *fp, void *buf, size_t len) { ssize_t r = hread(fp->hf, buf, len); fp->offset += r>0?r:0; return r; } HTSLIB_EXPORT off_t knet_seek(knetFile *fp, off_t off, int whence) { off_t r = hseek(fp->hf, off, whence); if (r >= 0) fp->offset = r; return r; } HTSLIB_EXPORT int knet_close(knetFile *fp) { int r = hclose(fp->hf); free(fp); return r; } pysam-0.23.0/htslib/hfile_gcs.c000066400000000000000000000120231475062545500163140ustar00rootroot00000000000000/* hfile_gcs.c -- Google Cloud Storage backend for low-level file streams. Copyright (C) 2016, 2021 Genome Research Ltd. Author: John Marshall Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include "htslib/hts.h" #include "htslib/kstring.h" #include "hfile_internal.h" #ifdef ENABLE_PLUGINS #include "version.h" #endif static hFILE * gcs_rewrite(const char *gsurl, const char *mode, int mode_has_colon, va_list *argsp) { const char *bucket, *path, *access_token, *requester_pays_project; kstring_t mode_colon = { 0, 0, NULL }; kstring_t url = { 0, 0, NULL }; kstring_t auth_hdr = { 0, 0, NULL }; kstring_t requester_pays_hdr = { 0, 0, NULL }; hFILE *fp = NULL; // GCS URL format is gs[+SCHEME]://BUCKET/PATH if (gsurl[2] == '+') { bucket = strchr(gsurl, ':') + 1; kputsn(&gsurl[3], bucket - &gsurl[3], &url); } else { kputs("https:", &url); bucket = &gsurl[3]; } while (*bucket == '/') kputc(*bucket++, &url); path = bucket + strcspn(bucket, "/?#"); kputsn(bucket, path - bucket, &url); if (strchr(mode, 'r')) kputs(".storage-download", &url); else if (strchr(mode, 'w')) kputs(".storage-upload", &url); else kputs(".storage", &url); kputs(".googleapis.com", &url); kputs(path, &url); if (hts_verbose >= 8) fprintf(stderr, "[M::gcs_open] rewrote URL as %s\n", url.s); // TODO Find the access token in a more standard way access_token = getenv("GCS_OAUTH_TOKEN"); if (access_token) { kputs("Authorization: Bearer ", &auth_hdr); kputs(access_token, &auth_hdr); } requester_pays_project = getenv("GCS_REQUESTER_PAYS_PROJECT"); if (requester_pays_project) { kputs("X-Goog-User-Project: ", &requester_pays_hdr); kputs(requester_pays_project, &requester_pays_hdr); } if (argsp || mode_has_colon || auth_hdr.l > 0 || requester_pays_hdr.l > 0) { if (! mode_has_colon) { kputs(mode, &mode_colon); kputc(':', &mode_colon); mode = mode_colon.s; } if (auth_hdr.l > 0 && requester_pays_hdr.l > 0) { fp = hopen( url.s, mode, "va_list", argsp, "httphdr:l", auth_hdr.s, requester_pays_hdr.s, NULL, NULL ); } else { fp = hopen(url.s, mode, "va_list", argsp, "httphdr", (auth_hdr.l > 0)? auth_hdr.s : NULL, NULL); } } else fp = hopen(url.s, mode); free(mode_colon.s); free(url.s); free(auth_hdr.s); free(requester_pays_hdr.s); return fp; } static hFILE *gcs_open(const char *url, const char *mode) { return gcs_rewrite(url, mode, 0, NULL); } static hFILE *gcs_vopen(const char *url, const char *mode_colon, va_list args0) { // Need to use va_copy() as we can only take the address of an actual // va_list object, not that of a parameter as its type may have decayed. va_list args; va_copy(args, args0); hFILE *fp = gcs_rewrite(url, mode_colon, 1, &args); va_end(args); return fp; } int PLUGIN_GLOBAL(hfile_plugin_init,_gcs)(struct hFILE_plugin *self) { static const struct hFILE_scheme_handler handler = { gcs_open, hfile_always_remote, "Google Cloud Storage", 2000 + 50, gcs_vopen }; #ifdef ENABLE_PLUGINS // Embed version string for examination via strings(1) or what(1) static const char id[] = "@(#)hfile_gcs plugin (htslib)\t" HTS_VERSION_TEXT; if (hts_verbose >= 9) fprintf(stderr, "[M::hfile_gcs.init] version %s\n", strchr(id, '\t')+1); #endif self->name = "Google Cloud Storage"; hfile_add_scheme_handler("gs", &handler); hfile_add_scheme_handler("gs+http", &handler); hfile_add_scheme_handler("gs+https", &handler); return 0; } pysam-0.23.0/htslib/hfile_internal.h000066400000000000000000000176601475062545500173750ustar00rootroot00000000000000/* hfile_internal.h -- internal parts of low-level input/output streams. Copyright (C) 2013-2016, 2019 Genome Research Ltd. Author: John Marshall Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HFILE_INTERNAL_H #define HFILE_INTERNAL_H #include #include "htslib/hts_defs.h" #include "htslib/hfile.h" #include "textutils_internal.h" #ifdef __cplusplus extern "C" { #endif /*! @abstract Resizes the buffer within an hFILE. @notes Changes the buffer size for an hFILE. Ideally this is done immediately after opening. If performed later, this function may fail if we are reducing the buffer size and the current offset into the buffer is beyond the new capacity. @param fp The file stream @param bufsiz The size of the new buffer @return Returns 0 on success, -1 on failure. */ int hfile_set_blksize(hFILE *fp, size_t bufsiz); struct BGZF; /*! @abstract Return the hFILE connected to a BGZF */ struct hFILE *bgzf_hfile(struct BGZF *fp); /*! @abstract Closes all hFILE plugins that have been loaded */ void hfile_shutdown(int do_close_plugin); struct hFILE_backend { /* As per read(2), returning the number of bytes read (possibly 0) or negative (and setting errno) on errors. Front-end code will call this repeatedly if necessary to attempt to get the desired byte count. */ ssize_t (*read)(hFILE *fp, void *buffer, size_t nbytes) HTS_RESULT_USED; /* As per write(2), returning the number of bytes written or negative (and setting errno) on errors. Front-end code will call this repeatedly if necessary until the desired block is written or an error occurs. */ ssize_t (*write)(hFILE *fp, const void *buffer, size_t nbytes) HTS_RESULT_USED; /* As per lseek(2), returning the resulting offset within the stream or negative (and setting errno) on errors. */ off_t (*seek)(hFILE *fp, off_t offset, int whence) HTS_RESULT_USED; /* Performs low-level flushing, if any, e.g., fsync(2); for writing streams only. Returns 0 for success or negative (and sets errno) on errors. */ int (*flush)(hFILE *fp) HTS_RESULT_USED; /* Closes the underlying stream (for output streams, the buffer will already have been flushed), returning 0 for success or negative (and setting errno) on errors, as per close(2). */ int (*close)(hFILE *fp) HTS_RESULT_USED; }; /* May be called by hopen_*() functions to decode a fopen()-style mode into open(2)-style flags. */ HTSLIB_EXPORT int hfile_oflags(const char *mode); /* Must be called by hopen_*() functions to allocate the hFILE struct and set up its base. Capacity is a suggested buffer size (e.g., via fstat(2)) or 0 for a default-sized buffer. */ HTSLIB_EXPORT hFILE *hfile_init(size_t struct_size, const char *mode, size_t capacity); /* Alternative to hfile_init() for in-memory backends for which the base buffer is the only storage. Buffer is already allocated via malloc(2) of size buf_size and with buf_filled bytes already filled. Ownership of the buffer is transferred to the resulting hFILE. */ hFILE *hfile_init_fixed(size_t struct_size, const char *mode, char *buffer, size_t buf_filled, size_t buf_size); /* May be called by hopen_*() functions to undo the effects of hfile_init() in the event opening the stream subsequently fails. (This is safe to use even if fp is NULL. This takes care to preserve errno.) */ HTSLIB_EXPORT void hfile_destroy(hFILE *fp); struct hFILE_scheme_handler { /* Opens a stream when dispatched by hopen(); should call hfile_init() to malloc a struct "derived" from hFILE and initialise it appropriately, including setting base.backend to its own backend vector. */ hFILE *(*open)(const char *filename, const char *mode) HTS_RESULT_USED; /* Returns whether the URL denotes remote storage when dispatched by hisremote(). For simple cases, use one of hfile_always_*() below. */ int (*isremote)(const char *filename) HTS_RESULT_USED; /* The name of the plugin or other code providing this handler. */ const char *provider; /* If multiple handlers are registered for the same scheme, the one with the highest priority is used; range is 0 (lowest) to 100 (highest). This field is used modulo 1000 as a priority; thousands indicate later revisions to this structure, as noted below. */ int priority; /* Fields below are present when priority >= 2000. */ /* Same as the open() method, used when extra arguments have been given to hopen(). */ hFILE *(*vopen)(const char *filename, const char *mode, va_list args) HTS_RESULT_USED; }; /* May be used as an isremote() function in simple cases. */ HTSLIB_EXPORT extern int hfile_always_local (const char *fname); HTSLIB_EXPORT extern int hfile_always_remote(const char *fname); /* Should be called by plugins for each URL scheme they wish to handle. */ HTSLIB_EXPORT void hfile_add_scheme_handler(const char *scheme, const struct hFILE_scheme_handler *handler); struct hFILE_plugin { /* On entry, HTSlib's plugin API version (currently 1). */ int api_version; /* On entry, the plugin's handle as returned by dlopen() etc. */ void *obj; /* The plugin should fill this in with its (human-readable) name. */ const char *name; /* The plugin may wish to fill in a function to be called on closing. */ void (*destroy)(void); }; #ifdef ENABLE_PLUGINS #define PLUGIN_GLOBAL(identifier,suffix) identifier /* Plugins must define an entry point with this signature. */ HTSLIB_EXPORT extern int hfile_plugin_init(struct hFILE_plugin *self); #else #define PLUGIN_GLOBAL(identifier,suffix) identifier##suffix /* Only plugins distributed within the HTSlib source that might be built even with --disable-plugins need to use PLUGIN_GLOBAL and be listed here; others can simply define hfile_plugin_init(). */ extern int hfile_plugin_init_gcs(struct hFILE_plugin *self); extern int hfile_plugin_init_libcurl(struct hFILE_plugin *self); extern int hfile_plugin_init_s3(struct hFILE_plugin *self); extern int hfile_plugin_init_s3_write(struct hFILE_plugin *self); #endif // Callback to allow headers to be set in http connections. Currently used // to allow s3 to renew tokens when seeking. Kept internal for now, // although we may consider exposing it in the API later. typedef int (* hts_httphdr_callback) (void *cb_data, char ***hdrs); /** Callback for handling 3xx redirect responses from http connections. @param data is passed to the callback @param response http response code (e.g. 301) @param headers http response headers @param new_url the callback should write the url to switch to in here Currently used by s3 to handle switching region endpoints. */ typedef int (*redirect_callback) (void *data, long response, kstring_t *headers, kstring_t *new_url); #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/hfile_libcurl.c000066400000000000000000001415451475062545500172100ustar00rootroot00000000000000/* hfile_libcurl.c -- libcurl backend for low-level file streams. Copyright (C) 2015-2017, 2019-2020 Genome Research Ltd. Author: John Marshall Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #ifndef _WIN32 # include #endif #include #include #include "hfile_internal.h" #ifdef ENABLE_PLUGINS #include "version.h" #endif #include "htslib/hts.h" // for hts_version() and hts_verbose #include "htslib/kstring.h" #include "htslib/khash.h" #include // Number of seconds to take off auth_token expiry, to allow for clock skew // and slow servers #define AUTH_REFRESH_EARLY_SECS 60 // Minimum number of bytes to skip when seeking forward. Seeks less than // this will just read the data and throw it away. The optimal value // depends on how long it takes to make a new connection compared // to how fast the data arrives. #define MIN_SEEK_FORWARD 1000000 typedef struct { char *path; char *token; time_t expiry; int failed; pthread_mutex_t lock; } auth_token; // For the authorization header cache KHASH_MAP_INIT_STR(auth_map, auth_token *) // Curl-compatible header linked list typedef struct { struct curl_slist *list; unsigned int num; unsigned int size; } hdrlist; typedef struct { hdrlist fixed; // List of headers supplied at hopen() hdrlist extra; // List of headers from callback hts_httphdr_callback callback; // Callback to get more headers void *callback_data; // Data to pass to httphdr callback auth_token *auth; // Authentication token int auth_hdr_num; // Location of auth_token in hdrlist extra // If -1, Authorization header is in fixed // -2, it came from the callback // -3, "auth_token_enabled", "false" // passed to hopen() redirect_callback redirect; // Callback to handle 3xx redirects void *redirect_data; // Data to pass to redirect_callback long *http_response_ptr; // Location to store http response code. int fail_on_error; // Open fails on >400 response code // (default true) } http_headers; typedef struct { hFILE base; CURL *easy; CURLM *multi; off_t file_size; struct { union { char *rd; const char *wr; } ptr; size_t len; } buffer; CURLcode final_result; // easy result code for finished transfers // Flags for communicating with libcurl callbacks: unsigned paused : 1; // callback tells us that it has paused transfer unsigned closing : 1; // informs callback that hclose() has been invoked unsigned finished : 1; // wait_perform() tells us transfer is complete unsigned perform_again : 1; unsigned is_read : 1; // Opened in read mode unsigned can_seek : 1; // Can (attempt to) seek on this handle unsigned is_recursive:1; // Opened by hfile_libcurl itself unsigned tried_seek : 1; // At least one seek has been attempted int nrunning; http_headers headers; off_t delayed_seek; // Location to seek to before reading off_t last_offset; // Location we're seeking from char *preserved; // Preserved buffer content on seek size_t preserved_bytes; // Number of preserved bytes size_t preserved_size; // Size of preserved buffer } hFILE_libcurl; static off_t libcurl_seek(hFILE *fpv, off_t offset, int whence); static int restart_from_position(hFILE_libcurl *fp, off_t pos); static int http_status_errno(int status) { if (status >= 500) switch (status) { case 501: return ENOSYS; case 503: return EBUSY; case 504: return ETIMEDOUT; default: return EIO; } else if (status >= 400) switch (status) { case 401: return EPERM; case 403: return EACCES; case 404: return ENOENT; case 405: return EROFS; case 407: return EPERM; case 408: return ETIMEDOUT; case 410: return ENOENT; default: return EINVAL; } else return 0; } static int easy_errno(CURL *easy, CURLcode err) { long lval; switch (err) { case CURLE_OK: return 0; case CURLE_UNSUPPORTED_PROTOCOL: case CURLE_URL_MALFORMAT: return EINVAL; #if LIBCURL_VERSION_NUM >= 0x071505 case CURLE_NOT_BUILT_IN: return ENOSYS; #endif case CURLE_COULDNT_RESOLVE_PROXY: case CURLE_COULDNT_RESOLVE_HOST: case CURLE_FTP_CANT_GET_HOST: return EDESTADDRREQ; // Lookup failure case CURLE_COULDNT_CONNECT: case CURLE_SEND_ERROR: case CURLE_RECV_ERROR: if (curl_easy_getinfo(easy, CURLINFO_OS_ERRNO, &lval) == CURLE_OK) return lval; else return ECONNABORTED; case CURLE_REMOTE_ACCESS_DENIED: case CURLE_LOGIN_DENIED: case CURLE_TFTP_PERM: return EACCES; case CURLE_PARTIAL_FILE: return EPIPE; case CURLE_HTTP_RETURNED_ERROR: if (curl_easy_getinfo(easy, CURLINFO_RESPONSE_CODE, &lval) == CURLE_OK) return http_status_errno(lval); else return EIO; case CURLE_OUT_OF_MEMORY: return ENOMEM; case CURLE_OPERATION_TIMEDOUT: return ETIMEDOUT; case CURLE_RANGE_ERROR: return ESPIPE; case CURLE_SSL_CONNECT_ERROR: // TODO return SSL error buffer messages return ECONNABORTED; case CURLE_FILE_COULDNT_READ_FILE: case CURLE_TFTP_NOTFOUND: return ENOENT; case CURLE_TOO_MANY_REDIRECTS: return ELOOP; case CURLE_FILESIZE_EXCEEDED: return EFBIG; case CURLE_REMOTE_DISK_FULL: return ENOSPC; case CURLE_REMOTE_FILE_EXISTS: return EEXIST; default: hts_log_error("Libcurl reported error %d (%s)", (int) err, curl_easy_strerror(err)); return EIO; } } static int multi_errno(CURLMcode errm) { switch (errm) { case CURLM_CALL_MULTI_PERFORM: case CURLM_OK: return 0; case CURLM_BAD_HANDLE: case CURLM_BAD_EASY_HANDLE: case CURLM_BAD_SOCKET: return EBADF; case CURLM_OUT_OF_MEMORY: return ENOMEM; default: hts_log_error("Libcurl reported error %d (%s)", (int) errm, curl_multi_strerror(errm)); return EIO; } } static struct { kstring_t useragent; CURLSH *share; char *auth_path; khash_t(auth_map) *auth_map; int allow_unencrypted_auth_header; pthread_mutex_t auth_lock; pthread_mutex_t share_lock; } curl = { { 0, 0, NULL }, NULL, NULL, NULL, 0, PTHREAD_MUTEX_INITIALIZER, PTHREAD_MUTEX_INITIALIZER }; static void share_lock(CURL *handle, curl_lock_data data, curl_lock_access access, void *userptr) { pthread_mutex_lock(&curl.share_lock); } static void share_unlock(CURL *handle, curl_lock_data data, void *userptr) { pthread_mutex_unlock(&curl.share_lock); } static void free_auth(auth_token *tok) { if (!tok) return; if (pthread_mutex_destroy(&tok->lock)) abort(); free(tok->path); free(tok->token); free(tok); } static void libcurl_exit(void) { if (curl_share_cleanup(curl.share) == CURLSHE_OK) curl.share = NULL; free(curl.useragent.s); curl.useragent.l = curl.useragent.m = 0; curl.useragent.s = NULL; free(curl.auth_path); curl.auth_path = NULL; if (curl.auth_map) { khiter_t i; for (i = kh_begin(curl.auth_map); i != kh_end(curl.auth_map); ++i) { if (kh_exist(curl.auth_map, i)) { free_auth(kh_value(curl.auth_map, i)); kh_key(curl.auth_map, i) = NULL; kh_value(curl.auth_map, i) = NULL; } } kh_destroy(auth_map, curl.auth_map); curl.auth_map = NULL; } curl_global_cleanup(); } static int append_header(hdrlist *hdrs, const char *data, int dup) { if (hdrs->num == hdrs->size) { unsigned int new_sz = hdrs->size ? hdrs->size * 2 : 4, i; struct curl_slist *new_list = realloc(hdrs->list, new_sz * sizeof(*new_list)); if (!new_list) return -1; hdrs->size = new_sz; hdrs->list = new_list; for (i = 1; i < hdrs->num; i++) hdrs->list[i-1].next = &hdrs->list[i]; } // Annoyingly, libcurl doesn't declare the char * as const... hdrs->list[hdrs->num].data = dup ? strdup(data) : (char *) data; if (!hdrs->list[hdrs->num].data) return -1; if (hdrs->num > 0) hdrs->list[hdrs->num - 1].next = &hdrs->list[hdrs->num]; hdrs->list[hdrs->num].next = NULL; hdrs->num++; return 0; } static void free_headers(hdrlist *hdrs, int completely) { unsigned int i; for (i = 0; i < hdrs->num; i++) { free(hdrs->list[i].data); hdrs->list[i].data = NULL; hdrs->list[i].next = NULL; } hdrs->num = 0; if (completely) { free(hdrs->list); hdrs->size = 0; hdrs->list = NULL; } } static struct curl_slist * get_header_list(hFILE_libcurl *fp) { if (fp->headers.fixed.num > 0) return &fp->headers.fixed.list[0]; if (fp->headers.extra.num > 0) return &fp->headers.extra.list[0]; return 0; } static inline int is_authorization(const char *hdr) { return (strncasecmp("authorization:", hdr, 14) == 0); } static int add_callback_headers(hFILE_libcurl *fp) { char **hdrs = NULL, **hdr; if (!fp->headers.callback) return 0; // Get the headers from the callback if (fp->headers.callback(fp->headers.callback_data, &hdrs) != 0) { return -1; } if (!hdrs) // No change return 0; // Remove any old callback headers if (fp->headers.fixed.num > 0) { // Unlink lists fp->headers.fixed.list[fp->headers.fixed.num - 1].next = NULL; } free_headers(&fp->headers.extra, 0); if (fp->headers.auth_hdr_num > 0 || fp->headers.auth_hdr_num == -2) fp->headers.auth_hdr_num = 0; // Just removed it... // Convert to libcurl-suitable form for (hdr = hdrs; *hdr; hdr++) { if (append_header(&fp->headers.extra, *hdr, 0) < 0) { goto cleanup; } if (is_authorization(*hdr) && !fp->headers.auth_hdr_num) fp->headers.auth_hdr_num = -2; } for (hdr = hdrs; *hdr; hdr++) *hdr = NULL; if (fp->headers.fixed.num > 0 && fp->headers.extra.num > 0) { // Relink lists fp->headers.fixed.list[fp->headers.fixed.num - 1].next = &fp->headers.extra.list[0]; } return 0; cleanup: while (hdr && *hdr) { free(*hdr); *hdr = NULL; } return -1; } /* * Read an OAUTH2-style Bearer access token (see * https://tools.ietf.org/html/rfc6750#section-4). * Returns 'v' for valid; 'i' for invalid (token missing or wrong sort); * '?' for a JSON parse error; 'm' if it runs out of memory. */ static int read_auth_json(auth_token *tok, hFILE *auth_fp) { hts_json_token *t = hts_json_alloc_token(); kstring_t str = {0, 0, NULL}; char *token = NULL, *type = NULL, *expiry = NULL; int ret = 'i'; if (!t) goto error; if ((ret = hts_json_fnext(auth_fp, t, &str)) != '{') goto error; while (hts_json_fnext(auth_fp, t, &str) != '}') { char *key; if (hts_json_token_type(t) != 's') { ret = '?'; goto error; } key = hts_json_token_str(t); if (!key) goto error; if (strcmp(key, "access_token") == 0) { if ((ret = hts_json_fnext(auth_fp, t, &str)) != 's') goto error; token = ks_release(&str); } else if (strcmp(key, "token_type") == 0) { if ((ret = hts_json_fnext(auth_fp, t, &str)) != 's') goto error; type = ks_release(&str); } else if (strcmp(key, "expires_in") == 0) { if ((ret = hts_json_fnext(auth_fp, t, &str)) != 'n') goto error; expiry = ks_release(&str); } else if (hts_json_fskip_value(auth_fp, '\0') != 'v') { ret = '?'; goto error; } } if (!token || (type && strcmp(type, "Bearer") != 0)) { ret = 'i'; goto error; } ret = 'm'; str.l = 0; if (kputs("Authorization: Bearer ", &str) < 0) goto error; if (kputs(token, &str) < 0) goto error; free(tok->token); tok->token = ks_release(&str); if (expiry) { long exp = strtol(expiry, NULL, 10); if (exp < 0) exp = 0; tok->expiry = time(NULL) + exp; } else { tok->expiry = 0; } ret = 'v'; error: free(token); free(type); free(expiry); free(str.s); hts_json_free_token(t); return ret; } static int read_auth_plain(auth_token *tok, hFILE *auth_fp) { kstring_t line = {0, 0, NULL}; kstring_t token = {0, 0, NULL}; const char *start, *end; if (kgetline(&line, (char * (*)(char *, int, void *)) hgets, auth_fp) < 0) goto error; if (kputc('\0', &line) < 0) goto error; for (start = line.s; *start && isspace_c(*start); start++) {} for (end = start; *end && !isspace_c(*end); end++) {} if (end > start) { if (kputs("Authorization: Bearer ", &token) < 0) goto error; if (kputsn(start, end - start, &token) < 0) goto error; } free(tok->token); tok->token = ks_release(&token); tok->expiry = 0; free(line.s); return 0; error: free(line.s); free(token.s); return -1; } static int renew_auth_token(auth_token *tok, int *changed) { hFILE *auth_fp = NULL; char buffer[16]; ssize_t len; *changed = 0; if (tok->expiry == 0 || time(NULL) + AUTH_REFRESH_EARLY_SECS < tok->expiry) return 0; // Still valid if (tok->failed) return -1; *changed = 1; auth_fp = hopen(tok->path, "rR"); if (!auth_fp) { // Not worried about missing files; other errors are bad. if (errno != ENOENT) goto fail; tok->expiry = 0; // Prevent retry free(tok->token); // Just in case it was set return 0; } len = hpeek(auth_fp, buffer, sizeof(buffer)); if (len < 0) goto fail; if (memchr(buffer, '{', len) != NULL) { if (read_auth_json(tok, auth_fp) != 'v') goto fail; } else { if (read_auth_plain(tok, auth_fp) < 0) goto fail; } return hclose(auth_fp) < 0 ? -1 : 0; fail: tok->failed = 1; if (auth_fp) hclose_abruptly(auth_fp); return -1; } static int add_auth_header(hFILE_libcurl *fp) { int changed = 0; if (fp->headers.auth_hdr_num < 0) return 0; // Have an Authorization header from open or header callback if (!fp->headers.auth) return 0; // Nothing to add pthread_mutex_lock(&fp->headers.auth->lock); if (renew_auth_token(fp->headers.auth, &changed) < 0) goto unlock_fail; if (!changed && fp->headers.auth_hdr_num > 0) { pthread_mutex_unlock(&fp->headers.auth->lock); return 0; } if (fp->headers.auth_hdr_num > 0) { // Had a previous header, so swap in the new one char *header = fp->headers.auth->token; char *header_copy = header ? strdup(header) : NULL; int idx = fp->headers.auth_hdr_num - 1; if (header && !header_copy) goto unlock_fail; if (header_copy) { free(fp->headers.extra.list[idx].data); fp->headers.extra.list[idx].data = header_copy; } else { unsigned int j; // More complicated case - need to get rid of the old header // and tidy up linked lists free(fp->headers.extra.list[idx].data); for (j = idx + 1; j < fp->headers.extra.num; j++) { fp->headers.extra.list[j - 1] = fp->headers.extra.list[j]; fp->headers.extra.list[j - 1].next = &fp->headers.extra.list[j]; } fp->headers.extra.num--; if (fp->headers.extra.num > 0) { fp->headers.extra.list[fp->headers.extra.num-1].next = NULL; } else if (fp->headers.fixed.num > 0) { fp->headers.fixed.list[fp->headers.fixed.num - 1].next = NULL; } fp->headers.auth_hdr_num = 0; } } else if (fp->headers.auth->token) { // Add new header and remember where it is if (append_header(&fp->headers.extra, fp->headers.auth->token, 1) < 0) { goto unlock_fail; } fp->headers.auth_hdr_num = fp->headers.extra.num; } pthread_mutex_unlock(&fp->headers.auth->lock); return 0; unlock_fail: pthread_mutex_unlock(&fp->headers.auth->lock); return -1; } static int get_auth_token(hFILE_libcurl *fp, const char *url) { const char *host = NULL, *p, *q; kstring_t name = {0, 0, NULL}; size_t host_len = 0; khiter_t idx; auth_token *tok = NULL; // Nothing to do if: // curl.auth_path has not been set // fp was made by hfile_libcurl (e.g. auth_path is a http:// url) // we already have an Authorization header if (!curl.auth_path || fp->is_recursive || fp->headers.auth_hdr_num != 0) return 0; // Insist on having a secure connection unless the user insists harder if (!curl.allow_unencrypted_auth_header && strncmp(url, "https://", 8) != 0) return 0; host = strstr(url, "://"); if (host) { host += 3; host_len = strcspn(host, "/"); } p = curl.auth_path; while ((q = strstr(p, "%h")) != NULL) { if (q - p > INT_MAX || host_len > INT_MAX) goto error; if (kputsn_(p, q - p, &name) < 0) goto error; if (kputsn_(host, host_len, &name) < 0) goto error; p = q + 2; } if (kputs(p, &name) < 0) goto error; pthread_mutex_lock(&curl.auth_lock); idx = kh_get(auth_map, curl.auth_map, name.s); if (idx < kh_end(curl.auth_map)) { tok = kh_value(curl.auth_map, idx); } else { tok = calloc(1, sizeof(*tok)); if (tok && pthread_mutex_init(&tok->lock, NULL) != 0) { free(tok); tok = NULL; } if (tok) { int ret = -1; tok->path = ks_release(&name); tok->token = NULL; tok->expiry = 1; // Force refresh idx = kh_put(auth_map, curl.auth_map, tok->path, &ret); if (ret < 0) { free_auth(tok); tok = NULL; } kh_value(curl.auth_map, idx) = tok; } } pthread_mutex_unlock(&curl.auth_lock); fp->headers.auth = tok; free(name.s); return add_auth_header(fp); error: free(name.s); return -1; } static void process_messages(hFILE_libcurl *fp) { CURLMsg *msg; int remaining; while ((msg = curl_multi_info_read(fp->multi, &remaining)) != NULL) { switch (msg->msg) { case CURLMSG_DONE: fp->finished = 1; fp->final_result = msg->data.result; break; default: break; } } } static int wait_perform(hFILE_libcurl *fp) { fd_set rd, wr, ex; int maxfd, nrunning; long timeout; CURLMcode errm; if (!fp->perform_again) { FD_ZERO(&rd); FD_ZERO(&wr); FD_ZERO(&ex); if (curl_multi_fdset(fp->multi, &rd, &wr, &ex, &maxfd) != CURLM_OK) maxfd = -1, timeout = 1000; else { if (curl_multi_timeout(fp->multi, &timeout) != CURLM_OK) timeout = 1000; else if (timeout < 0) { timeout = 10000; // as recommended by curl_multi_timeout(3) } } if (maxfd < 0) { if (timeout > 100) timeout = 100; // as recommended by curl_multi_fdset(3) #ifdef _WIN32 /* Windows ignores the first argument of select, so calling select * with maxfd=-1 does not give the expected result of sleeping for * timeout milliseconds in the conditional block below. * So sleep here and skip the next block. */ Sleep(timeout); timeout = 0; #endif } if (timeout > 0) { struct timeval tval; tval.tv_sec = (timeout / 1000); tval.tv_usec = (timeout % 1000) * 1000; if (select(maxfd + 1, &rd, &wr, &ex, &tval) < 0) return -1; } } errm = curl_multi_perform(fp->multi, &nrunning); fp->perform_again = 0; if (errm == CURLM_CALL_MULTI_PERFORM) fp->perform_again = 1; else if (errm != CURLM_OK) { errno = multi_errno(errm); return -1; } if (nrunning < fp->nrunning) process_messages(fp); return 0; } static size_t recv_callback(char *ptr, size_t size, size_t nmemb, void *fpv) { hFILE_libcurl *fp = (hFILE_libcurl *) fpv; size_t n = size * nmemb; if (n > fp->buffer.len) { fp->paused = 1; return CURL_WRITEFUNC_PAUSE; } else if (n == 0) return 0; memcpy(fp->buffer.ptr.rd, ptr, n); fp->buffer.ptr.rd += n; fp->buffer.len -= n; return n; } static size_t header_callback(void *contents, size_t size, size_t nmemb, void *userp) { size_t realsize = size * nmemb; kstring_t *resp = (kstring_t *)userp; if (kputsn((const char *)contents, realsize, resp) == EOF) { return 0; } return realsize; } static ssize_t libcurl_read(hFILE *fpv, void *bufferv, size_t nbytes) { hFILE_libcurl *fp = (hFILE_libcurl *) fpv; char *buffer = (char *) bufferv; off_t to_skip = -1; ssize_t got = 0; CURLcode err; if (fp->delayed_seek >= 0) { assert(fp->base.offset == fp->delayed_seek); if (fp->preserved && fp->last_offset > fp->delayed_seek && fp->last_offset - fp->preserved_bytes <= fp->delayed_seek) { // Can use buffer contents copied when seeking started, to // avoid having to re-read data discarded by hseek(). // Note fp->last_offset is the offset of the *end* of the // preserved buffer. size_t n = fp->last_offset - fp->delayed_seek; char *start = fp->preserved + (fp->preserved_bytes - n); size_t bytes = n <= nbytes ? n : nbytes; memcpy(buffer, start, bytes); if (bytes < n) { // Part of the preserved buffer still left fp->delayed_seek += bytes; } else { fp->last_offset = fp->delayed_seek = -1; } return bytes; } if (fp->last_offset >= 0 && fp->delayed_seek > fp->last_offset && fp->delayed_seek - fp->last_offset < MIN_SEEK_FORWARD) { // If not seeking far, just read the data and throw it away. This // is likely to be quicker than opening a new stream to_skip = fp->delayed_seek - fp->last_offset; } else { if (restart_from_position(fp, fp->delayed_seek) < 0) { return -1; } } fp->delayed_seek = -1; fp->last_offset = -1; fp->preserved_bytes = 0; } do { fp->buffer.ptr.rd = buffer; fp->buffer.len = nbytes; fp->paused = 0; if (!fp->finished) { err = curl_easy_pause(fp->easy, CURLPAUSE_CONT); if (err != CURLE_OK) { errno = easy_errno(fp->easy, err); return -1; } } while (! fp->paused && ! fp->finished) { if (wait_perform(fp) < 0) return -1; } got = fp->buffer.ptr.rd - buffer; if (to_skip >= 0) { // Skipping over a small seek if (got <= to_skip) { // Need to skip more data to_skip -= got; } else { got -= to_skip; if (got > 0) { // If enough was skipped, return the rest memmove(buffer, buffer + to_skip, got); to_skip = -1; } } } } while (to_skip >= 0 && ! fp->finished); fp->buffer.ptr.rd = NULL; fp->buffer.len = 0; if (fp->finished && fp->final_result != CURLE_OK) { errno = easy_errno(fp->easy, fp->final_result); return -1; } return got; } static size_t send_callback(char *ptr, size_t size, size_t nmemb, void *fpv) { hFILE_libcurl *fp = (hFILE_libcurl *) fpv; size_t n = size * nmemb; if (fp->buffer.len == 0) { // Send buffer is empty; normally pause, or signal EOF if we're closing if (fp->closing) return 0; else { fp->paused = 1; return CURL_READFUNC_PAUSE; } } if (n > fp->buffer.len) n = fp->buffer.len; memcpy(ptr, fp->buffer.ptr.wr, n); fp->buffer.ptr.wr += n; fp->buffer.len -= n; return n; } static ssize_t libcurl_write(hFILE *fpv, const void *bufferv, size_t nbytes) { hFILE_libcurl *fp = (hFILE_libcurl *) fpv; const char *buffer = (const char *) bufferv; CURLcode err; fp->buffer.ptr.wr = buffer; fp->buffer.len = nbytes; fp->paused = 0; err = curl_easy_pause(fp->easy, CURLPAUSE_CONT); if (err != CURLE_OK) { errno = easy_errno(fp->easy, err); return -1; } while (! fp->paused && ! fp->finished) if (wait_perform(fp) < 0) return -1; nbytes = fp->buffer.ptr.wr - buffer; fp->buffer.ptr.wr = NULL; fp->buffer.len = 0; if (fp->finished && fp->final_result != CURLE_OK) { errno = easy_errno(fp->easy, fp->final_result); return -1; } return nbytes; } static void preserve_buffer_content(hFILE_libcurl *fp) { if (fp->base.begin == fp->base.end) { fp->preserved_bytes = 0; return; } if (!fp->preserved || fp->preserved_size < fp->base.limit - fp->base.buffer) { fp->preserved = malloc(fp->base.limit - fp->base.buffer); if (!fp->preserved) return; fp->preserved_size = fp->base.limit - fp->base.buffer; } assert(fp->base.end - fp->base.begin <= fp->preserved_size); memcpy(fp->preserved, fp->base.begin, fp->base.end - fp->base.begin); fp->preserved_bytes = fp->base.end - fp->base.begin; return; } static off_t libcurl_seek(hFILE *fpv, off_t offset, int whence) { hFILE_libcurl *fp = (hFILE_libcurl *) fpv; off_t origin, pos; if (!fp->is_read || !fp->can_seek) { // Cowardly refuse to seek when writing or a previous seek failed. errno = ESPIPE; return -1; } switch (whence) { case SEEK_SET: origin = 0; break; case SEEK_CUR: errno = ENOSYS; return -1; case SEEK_END: if (fp->file_size < 0) { errno = ESPIPE; return -1; } origin = fp->file_size; break; default: errno = EINVAL; return -1; } // Check 0 <= origin+offset < fp->file_size carefully, avoiding overflow if ((offset < 0)? origin + offset < 0 : (fp->file_size >= 0 && offset > fp->file_size - origin)) { errno = EINVAL; return -1; } pos = origin + offset; if (fp->tried_seek) { /* Seeking has worked at least once, so now we can delay doing the actual work until the next read. This avoids lots of pointless http or ftp reconnections if the caller does lots of seeks without any intervening reads. */ if (fp->delayed_seek < 0) { fp->last_offset = fp->base.offset + (fp->base.end - fp->base.buffer); // Stash the current hFILE buffer content in case it's useful later preserve_buffer_content(fp); } fp->delayed_seek = pos; return pos; } if (restart_from_position(fp, pos) < 0) { /* This value for errno may not be entirely true, but the caller may be able to carry on with the existing handle. */ errno = ESPIPE; return -1; } fp->tried_seek = 1; return pos; } static int restart_from_position(hFILE_libcurl *fp, off_t pos) { hFILE_libcurl temp_fp; CURLcode err; CURLMcode errm; int update_headers = 0; int save_errno = 0; // TODO If we seem to be doing random access, use CURLOPT_RANGE to do // limited reads (e.g. about a BAM block!) so seeking can reuse the // existing connection more often. // Get new headers from the callback (if defined). This changes the // headers in fp before it gets duplicated, but they should be have been // sent by now. if (fp->headers.callback) { if (add_callback_headers(fp) != 0) return -1; update_headers = 1; } if (fp->headers.auth_hdr_num > 0 && fp->headers.auth) { if (add_auth_header(fp) != 0) return -1; update_headers = 1; } if (update_headers) { struct curl_slist *list = get_header_list(fp); if (list) { err = curl_easy_setopt(fp->easy, CURLOPT_HTTPHEADER, list); if (err != CURLE_OK) { errno = easy_errno(fp->easy,err); return -1; } } } /* Duplicate the easy handle, and use CURLOPT_RESUME_FROM_LARGE to open a new request to the server, reading from the location that we want to seek to. If the new request works and returns the correct data, the original easy handle in *fp is closed and replaced with the new one. If not, we close the new handle and leave *fp unchanged. */ memcpy(&temp_fp, fp, sizeof(temp_fp)); temp_fp.buffer.len = 0; temp_fp.buffer.ptr.rd = NULL; temp_fp.easy = curl_easy_duphandle(fp->easy); if (!temp_fp.easy) goto early_error; err = curl_easy_setopt(temp_fp.easy, CURLOPT_RESUME_FROM_LARGE,(curl_off_t)pos); err |= curl_easy_setopt(temp_fp.easy, CURLOPT_PRIVATE, &temp_fp); err |= curl_easy_setopt(temp_fp.easy, CURLOPT_WRITEDATA, &temp_fp); if (err != CURLE_OK) { save_errno = easy_errno(temp_fp.easy, err); goto error; } temp_fp.buffer.len = 0; // Ensures we only read the response headers temp_fp.paused = temp_fp.finished = 0; // fp->multi and temp_fp.multi are the same. errm = curl_multi_add_handle(fp->multi, temp_fp.easy); if (errm != CURLM_OK) { save_errno = multi_errno(errm); goto error; } temp_fp.nrunning = ++fp->nrunning; while (! temp_fp.paused && ! temp_fp.finished) if (wait_perform(&temp_fp) < 0) { save_errno = errno; goto error_remove; } if (temp_fp.finished && temp_fp.final_result != CURLE_OK) { save_errno = easy_errno(temp_fp.easy, temp_fp.final_result); goto error_remove; } // We've got a good response, close the original connection and // replace it with the new one. errm = curl_multi_remove_handle(fp->multi, fp->easy); if (errm != CURLM_OK) { // Clean up as much as possible curl_easy_reset(temp_fp.easy); if (curl_multi_remove_handle(fp->multi, temp_fp.easy) == CURLM_OK) { fp->nrunning--; curl_easy_cleanup(temp_fp.easy); } save_errno = multi_errno(errm); goto early_error; } fp->nrunning--; curl_easy_cleanup(fp->easy); fp->easy = temp_fp.easy; err = curl_easy_setopt(fp->easy, CURLOPT_WRITEDATA, fp); err |= curl_easy_setopt(fp->easy, CURLOPT_PRIVATE, fp); if (err != CURLE_OK) { save_errno = easy_errno(fp->easy, err); curl_easy_reset(fp->easy); errno = save_errno; return -1; } fp->buffer.len = 0; fp->paused = temp_fp.paused; fp->finished = temp_fp.finished; fp->perform_again = temp_fp.perform_again; fp->final_result = temp_fp.final_result; return 0; error_remove: curl_easy_reset(temp_fp.easy); // Ensure no pointers to on-stack temp_fp errm = curl_multi_remove_handle(fp->multi, temp_fp.easy); if (errm != CURLM_OK) { errno = multi_errno(errm); return -1; } fp->nrunning--; error: curl_easy_cleanup(temp_fp.easy); early_error: fp->can_seek = 0; // Don't try to seek again if (save_errno) errno = save_errno; return -1; } static int libcurl_close(hFILE *fpv) { hFILE_libcurl *fp = (hFILE_libcurl *) fpv; CURLcode err; CURLMcode errm; int save_errno = 0; // Before closing the file, unpause it and perform on it so that uploads // have the opportunity to signal EOF to the server -- see send_callback(). fp->buffer.len = 0; fp->closing = 1; fp->paused = 0; if (!fp->finished) { err = curl_easy_pause(fp->easy, CURLPAUSE_CONT); if (err != CURLE_OK) save_errno = easy_errno(fp->easy, err); } while (save_errno == 0 && ! fp->paused && ! fp->finished) if (wait_perform(fp) < 0) save_errno = errno; if (fp->finished && fp->final_result != CURLE_OK) save_errno = easy_errno(fp->easy, fp->final_result); errm = curl_multi_remove_handle(fp->multi, fp->easy); if (errm != CURLM_OK && save_errno == 0) save_errno = multi_errno(errm); fp->nrunning--; curl_easy_cleanup(fp->easy); curl_multi_cleanup(fp->multi); if (fp->headers.callback) // Tell callback to free any data it needs to fp->headers.callback(fp->headers.callback_data, NULL); free_headers(&fp->headers.fixed, 1); free_headers(&fp->headers.extra, 1); free(fp->preserved); if (save_errno) { errno = save_errno; return -1; } else return 0; } static const struct hFILE_backend libcurl_backend = { libcurl_read, libcurl_write, libcurl_seek, NULL, libcurl_close }; static hFILE * libcurl_open(const char *url, const char *modes, http_headers *headers) { hFILE_libcurl *fp; struct curl_slist *list; char mode; const char *s; CURLcode err; CURLMcode errm; int save, is_recursive; kstring_t in_header = {0, 0, NULL}; long response; is_recursive = strchr(modes, 'R') != NULL; if ((s = strpbrk(modes, "rwa+")) != NULL) { mode = *s; if (strpbrk(&s[1], "rwa+")) mode = 'e'; } else mode = '\0'; if (mode != 'r' && mode != 'w') { errno = EINVAL; goto early_error; } fp = (hFILE_libcurl *) hfile_init(sizeof (hFILE_libcurl), modes, 0); if (fp == NULL) goto early_error; if (headers) { fp->headers = *headers; } else { memset(&fp->headers, 0, sizeof(fp->headers)); fp->headers.fail_on_error = 1; } fp->file_size = -1; fp->buffer.ptr.rd = NULL; fp->buffer.len = 0; fp->final_result = (CURLcode) -1; fp->paused = fp->closing = fp->finished = fp->perform_again = 0; fp->can_seek = 1; fp->tried_seek = 0; fp->delayed_seek = fp->last_offset = -1; fp->preserved = NULL; fp->preserved_bytes = fp->preserved_size = 0; fp->is_recursive = is_recursive; fp->nrunning = 0; fp->easy = NULL; fp->multi = curl_multi_init(); if (fp->multi == NULL) { errno = ENOMEM; goto error; } fp->easy = curl_easy_init(); if (fp->easy == NULL) { errno = ENOMEM; goto error; } // Make a route to the hFILE_libcurl* given just a CURL* easy handle err = curl_easy_setopt(fp->easy, CURLOPT_PRIVATE, fp); // Avoid many repeated CWD calls with FTP, instead requesting the filename // by full path (but not strictly compliant with RFC1738). err |= curl_easy_setopt(fp->easy, CURLOPT_FTP_FILEMETHOD, CURLFTPMETHOD_NOCWD); if (mode == 'r') { err |= curl_easy_setopt(fp->easy, CURLOPT_WRITEFUNCTION, recv_callback); err |= curl_easy_setopt(fp->easy, CURLOPT_WRITEDATA, fp); fp->is_read = 1; } else { err |= curl_easy_setopt(fp->easy, CURLOPT_READFUNCTION, send_callback); err |= curl_easy_setopt(fp->easy, CURLOPT_READDATA, fp); err |= curl_easy_setopt(fp->easy, CURLOPT_UPLOAD, 1L); if (append_header(&fp->headers.fixed, "Transfer-Encoding: chunked", 1) < 0) goto error; fp->is_read = 0; } err |= curl_easy_setopt(fp->easy, CURLOPT_SHARE, curl.share); err |= curl_easy_setopt(fp->easy, CURLOPT_URL, url); { char* env_curl_ca_bundle = getenv("CURL_CA_BUNDLE"); if (env_curl_ca_bundle) { err |= curl_easy_setopt(fp->easy, CURLOPT_CAINFO, env_curl_ca_bundle); } #if defined __linux__ && defined BUILDING_WHEEL else { // Linux wheels are (currently) built on AlmaLinux, so the libcurl.so bundled // into the wheel follows Alma/Red Hat/Fedora conventions for the location of // its certificate bundle. This fails when the wheel is used on a Debian/Ubuntu // platform with a different convention for this location. When not overridden // by $CURL_CA_BUNDLE, work around this by specifying the expected Debian bundle // location if the Red Hat one isn't present. struct stat st; if (stat("/etc/pki", &st) < 0 && errno == ENOENT) err |= curl_easy_setopt(fp->easy, CURLOPT_CAINFO, "/etc/ssl/certs/ca-certificates.crt"); } #endif } err |= curl_easy_setopt(fp->easy, CURLOPT_USERAGENT, curl.useragent.s); if (fp->headers.callback) { if (add_callback_headers(fp) != 0) goto error; } if (get_auth_token(fp, url) < 0) goto error; if ((list = get_header_list(fp)) != NULL) err |= curl_easy_setopt(fp->easy, CURLOPT_HTTPHEADER, list); if (hts_verbose <= 8 && fp->headers.fail_on_error) err |= curl_easy_setopt(fp->easy, CURLOPT_FAILONERROR, 1L); if (hts_verbose >= 8) err |= curl_easy_setopt(fp->easy, CURLOPT_VERBOSE, 1L); if (fp->headers.redirect) { err |= curl_easy_setopt(fp->easy, CURLOPT_HEADERFUNCTION, header_callback); err |= curl_easy_setopt(fp->easy, CURLOPT_HEADERDATA, (void *)&in_header); } else { err |= curl_easy_setopt(fp->easy, CURLOPT_FOLLOWLOCATION, 1L); } if (err != 0) { errno = ENOSYS; goto error; } errm = curl_multi_add_handle(fp->multi, fp->easy); if (errm != CURLM_OK) { errno = multi_errno(errm); goto error; } fp->nrunning++; while (! fp->paused && ! fp->finished) { if (wait_perform(fp) < 0) goto error_remove; } curl_easy_getinfo(fp->easy, CURLINFO_RESPONSE_CODE, &response); if (fp->headers.http_response_ptr) { *fp->headers.http_response_ptr = response; } if (fp->finished && fp->final_result != CURLE_OK) { errno = easy_errno(fp->easy, fp->final_result); goto error_remove; } if (fp->headers.redirect) { if (response >= 300 && response < 400) { // redirection kstring_t new_url = {0, 0, NULL}; if (fp->headers.redirect(fp->headers.redirect_data, response, &in_header, &new_url)) { errno = ENOSYS; goto error; } err |= curl_easy_setopt(fp->easy, CURLOPT_URL, new_url.s); err |= curl_easy_setopt(fp->easy, CURLOPT_HEADERFUNCTION, NULL); err |= curl_easy_setopt(fp->easy, CURLOPT_HEADERDATA, NULL); free(ks_release(&in_header)); if (err != 0) { errno = ENOSYS; goto error; } free(ks_release(&new_url)); if (restart_from_position(fp, 0) < 0) { goto error_remove; } if (fp->headers.http_response_ptr) { curl_easy_getinfo(fp->easy, CURLINFO_RESPONSE_CODE, fp->headers.http_response_ptr); } if (fp->finished && fp->final_result != CURLE_OK) { errno = easy_errno(fp->easy, fp->final_result); goto error_remove; } } else { // we no longer need to look at the headers err |= curl_easy_setopt(fp->easy, CURLOPT_HEADERFUNCTION, NULL); err |= curl_easy_setopt(fp->easy, CURLOPT_HEADERDATA, NULL); free(ks_release(&in_header)); if (err != 0) { errno = ENOSYS; goto error; } } } if (mode == 'r') { #if LIBCURL_VERSION_NUM >= 0x073700 // 7.55.0 curl_off_t offset; if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD_T, &offset) == CURLE_OK && offset > 0) fp->file_size = (off_t) offset; #else double dval; if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD, &dval) == CURLE_OK && dval >= 0.0) fp->file_size = (off_t) (dval + 0.1); #endif } fp->base.backend = &libcurl_backend; return &fp->base; error_remove: save = errno; (void) curl_multi_remove_handle(fp->multi, fp->easy); fp->nrunning--; errno = save; error: if (fp->headers.redirect) free(in_header.s); save = errno; if (fp->easy) curl_easy_cleanup(fp->easy); if (fp->multi) curl_multi_cleanup(fp->multi); free_headers(&fp->headers.extra, 1); hfile_destroy((hFILE *) fp); errno = save; return NULL; early_error: return NULL; } static hFILE *hopen_libcurl(const char *url, const char *modes) { return libcurl_open(url, modes, NULL); } static int parse_va_list(http_headers *headers, va_list args) { const char *argtype; while ((argtype = va_arg(args, const char *)) != NULL) if (strcmp(argtype, "httphdr:v") == 0) { const char **hdr; for (hdr = va_arg(args, const char **); *hdr; hdr++) { if (append_header(&headers->fixed, *hdr, 1) < 0) return -1; if (is_authorization(*hdr)) headers->auth_hdr_num = -1; } } else if (strcmp(argtype, "httphdr:l") == 0) { const char *hdr; while ((hdr = va_arg(args, const char *)) != NULL) { if (append_header(&headers->fixed, hdr, 1) < 0) return -1; if (is_authorization(hdr)) headers->auth_hdr_num = -1; } } else if (strcmp(argtype, "httphdr") == 0) { const char *hdr = va_arg(args, const char *); if (hdr) { if (append_header(&headers->fixed, hdr, 1) < 0) return -1; if (is_authorization(hdr)) headers->auth_hdr_num = -1; } } else if (strcmp(argtype, "httphdr_callback") == 0) { headers->callback = va_arg(args, const hts_httphdr_callback); } else if (strcmp(argtype, "httphdr_callback_data") == 0) { headers->callback_data = va_arg(args, void *); } else if (strcmp(argtype, "va_list") == 0) { va_list *args2 = va_arg(args, va_list *); if (args2) { if (parse_va_list(headers, *args2) < 0) return -1; } } else if (strcmp(argtype, "auth_token_enabled") == 0) { const char *flag = va_arg(args, const char *); if (strcmp(flag, "false") == 0) headers->auth_hdr_num = -3; } else if (strcmp(argtype, "redirect_callback") == 0) { headers->redirect = va_arg(args, const redirect_callback); } else if (strcmp(argtype, "redirect_callback_data") == 0) { headers->redirect_data = va_arg(args, void *); } else if (strcmp(argtype, "http_response_ptr") == 0) { headers->http_response_ptr = va_arg(args, long *); } else if (strcmp(argtype, "fail_on_error") == 0) { headers->fail_on_error = va_arg(args, int); } else { errno = EINVAL; return -1; } return 0; } /* HTTP headers to be added to the request can be passed in as extra arguments to hopen(). The headers can be specified as follows: * Single header: hopen(url, mode, "httphdr", "X-Hdr-1: text", NULL); * Multiple headers in the argument list: hopen(url, mode, "httphdr:l", "X-Hdr-1: text", "X-Hdr-2: text", NULL, NULL); * Multiple headers in a char* array: hopen(url, mode, "httphdr:v", hdrs, NULL); where `hdrs` is a char **. The list ends with a NULL pointer. * A callback function hopen(url, mode, "httphdr_callback", func, "httphdr_callback_data", arg, NULL); `func` has type int (* hts_httphdr_callback) (void *cb_data, char ***hdrs); `arg` is passed to the callback as a void *. The function is called at file open, and when attempting to seek (which opens a new HTTP request). This allows, for example, access tokens that may have gone stale to be regenerated. The function is also called (with `hdrs` == NULL) on file close so that the callback can free any memory that it needs to. The callback should return 0 on success, non-zero on failure. It should return in *hdrs a list of strings containing the new headers (terminated with a NULL pointer). These will replace any headers previously supplied by the callback. If no changes are necessary, it can return NULL in *hdrs, in which case the previous headers will be left unchanged. Ownership of the strings in the header list passes to hfile_libcurl, so the callback should not attempt to use or free them itself. The memory containing the array belongs to the callback and will not be freed by hfile_libcurl. Headers supplied by the callback are appended after any specified using the "httphdr", "httphdr:l" or "httphdr:v" methods. No attempt is made to replace these headers (even if a key is repeated) so anything that is expected to vary needs to come from the callback. */ static hFILE *vhopen_libcurl(const char *url, const char *modes, va_list args) { hFILE *fp = NULL; http_headers headers = { .fail_on_error = 1 }; if (parse_va_list(&headers, args) == 0) { fp = libcurl_open(url, modes, &headers); } if (!fp) { free_headers(&headers.fixed, 1); } return fp; } int PLUGIN_GLOBAL(hfile_plugin_init,_libcurl)(struct hFILE_plugin *self) { static const struct hFILE_scheme_handler handler = { hopen_libcurl, hfile_always_remote, "libcurl", 2000 + 50, vhopen_libcurl }; #ifdef ENABLE_PLUGINS // Embed version string for examination via strings(1) or what(1) static const char id[] = "@(#)hfile_libcurl plugin (htslib)\t" HTS_VERSION_TEXT; const char *version = strchr(id, '\t')+1; #else const char *version = hts_version(); #endif const curl_version_info_data *info; const char * const *protocol; const char *auth; CURLcode err; CURLSHcode errsh; err = curl_global_init(CURL_GLOBAL_ALL); if (err != CURLE_OK) { errno = easy_errno(NULL, err); return -1; } curl.share = curl_share_init(); if (curl.share == NULL) { curl_global_cleanup(); errno = EIO; return -1; } errsh = curl_share_setopt(curl.share, CURLSHOPT_LOCKFUNC, share_lock); errsh |= curl_share_setopt(curl.share, CURLSHOPT_UNLOCKFUNC, share_unlock); errsh |= curl_share_setopt(curl.share, CURLSHOPT_SHARE, CURL_LOCK_DATA_DNS); if (errsh != 0) { curl_share_cleanup(curl.share); curl_global_cleanup(); errno = EIO; return -1; } if ((auth = getenv("HTS_AUTH_LOCATION")) != NULL) { curl.auth_path = strdup(auth); curl.auth_map = kh_init(auth_map); if (!curl.auth_path || !curl.auth_map) { int save_errno = errno; free(curl.auth_path); kh_destroy(auth_map, curl.auth_map); curl_share_cleanup(curl.share); curl_global_cleanup(); errno = save_errno; return -1; } } if ((auth = getenv("HTS_ALLOW_UNENCRYPTED_AUTHORIZATION_HEADER")) != NULL && strcmp(auth, "I understand the risks") == 0) { curl.allow_unencrypted_auth_header = 1; } info = curl_version_info(CURLVERSION_NOW); ksprintf(&curl.useragent, "htslib/%s libcurl/%s", version, info->version); self->name = "libcurl"; self->destroy = libcurl_exit; for (protocol = info->protocols; *protocol; protocol++) hfile_add_scheme_handler(*protocol, &handler); return 0; } pysam-0.23.0/htslib/hfile_s3.c000066400000000000000000001204201475062545500160660ustar00rootroot00000000000000/* hfile_s3.c -- Amazon S3 backend for low-level file streams. Copyright (C) 2015-2017, 2019-2024 Genome Research Ltd. Author: John Marshall Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #include "hfile_internal.h" #ifdef ENABLE_PLUGINS #include "version.h" #endif #include "htslib/hts.h" // for hts_version() and hts_verbose #include "htslib/kstring.h" #include "hts_time_funcs.h" typedef struct s3_auth_data { kstring_t id; kstring_t token; kstring_t secret; kstring_t region; kstring_t canonical_query_string; kstring_t user_query_string; kstring_t host; kstring_t profile; enum {s3_auto, s3_virtual, s3_path} url_style; time_t creds_expiry_time; char *bucket; kstring_t auth_hdr; time_t auth_time; char date[40]; char date_long[17]; char date_short[9]; kstring_t date_html; char mode; char *headers[5]; int refcount; } s3_auth_data; #define AUTH_LIFETIME 60 // Regenerate auth headers if older than this #define CREDENTIAL_LIFETIME 60 // Seconds before expiry to reread credentials #if defined HAVE_COMMONCRYPTO #include #define DIGEST_BUFSIZ CC_SHA1_DIGEST_LENGTH #define SHA256_DIGEST_BUFSIZE CC_SHA256_DIGEST_LENGTH #define HASH_LENGTH_SHA256 (SHA256_DIGEST_BUFSIZE * 2) + 1 static size_t s3_sign(unsigned char *digest, kstring_t *key, kstring_t *message) { CCHmac(kCCHmacAlgSHA1, key->s, key->l, message->s, message->l, digest); return CC_SHA1_DIGEST_LENGTH; } static void s3_sha256(const unsigned char *in, size_t length, unsigned char *out) { CC_SHA256(in, length, out); } static void s3_sign_sha256(const void *key, int key_len, const unsigned char *d, int n, unsigned char *md, unsigned int *md_len) { CCHmac(kCCHmacAlgSHA256, key, key_len, d, n, md); *md_len = CC_SHA256_DIGEST_LENGTH; } #elif defined HAVE_HMAC #include #include #define DIGEST_BUFSIZ EVP_MAX_MD_SIZE #define SHA256_DIGEST_BUFSIZE SHA256_DIGEST_LENGTH #define HASH_LENGTH_SHA256 (SHA256_DIGEST_BUFSIZE * 2) + 1 static size_t s3_sign(unsigned char *digest, kstring_t *key, kstring_t *message) { unsigned int len; HMAC(EVP_sha1(), key->s, key->l, (unsigned char *) message->s, message->l, digest, &len); return len; } static void s3_sha256(const unsigned char *in, size_t length, unsigned char *out) { SHA256(in, length, out); } static void s3_sign_sha256(const void *key, int key_len, const unsigned char *d, int n, unsigned char *md, unsigned int *md_len) { HMAC(EVP_sha256(), key, key_len, d, n, md, md_len); } #else #error No HMAC() routine found by configure #endif static void urldecode_kput(const char *s, int len, kstring_t *str) { char buf[3]; int i = 0; while (i < len) if (s[i] == '%' && i+2 < len) { buf[0] = s[i+1], buf[1] = s[i+2], buf[2] = '\0'; kputc(strtol(buf, NULL, 16), str); i += 3; } else kputc(s[i++], str); } static void base64_kput(const unsigned char *data, size_t len, kstring_t *str) { static const char base64[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/"; size_t i = 0; unsigned x = 0; int bits = 0, pad = 0; while (bits || i < len) { if (bits < 6) { x <<= 8, bits += 8; if (i < len) x |= data[i++]; else pad++; } bits -= 6; kputc(base64[(x >> bits) & 63], str); } str->l -= pad; kputsn("==", pad, str); } static int is_dns_compliant(const char *s0, const char *slim, int is_https) { int has_nondigit = 0, len = 0; const char *s; for (s = s0; s < slim; len++, s++) if (islower_c(*s)) has_nondigit = 1; else if (*s == '-') { has_nondigit = 1; if (s == s0 || s+1 == slim) return 0; } else if (isdigit_c(*s)) ; else if (*s == '.') { if (is_https) return 0; if (s == s0 || ! isalnum_c(s[-1])) return 0; if (s+1 == slim || ! isalnum_c(s[1])) return 0; } else return 0; return has_nondigit && len >= 3 && len <= 63; } static FILE *expand_tilde_open(const char *fname, const char *mode) { FILE *fp; if (strncmp(fname, "~/", 2) == 0) { kstring_t full_fname = { 0, 0, NULL }; const char *home = getenv("HOME"); if (! home) return NULL; kputs(home, &full_fname); kputs(&fname[1], &full_fname); fp = fopen(full_fname.s, mode); free(full_fname.s); } else fp = fopen(fname, mode); return fp; } static void parse_ini(const char *fname, const char *section, ...) { kstring_t line = { 0, 0, NULL }; int active = 1; // Start active, so global properties are accepted char *s; FILE *fp = expand_tilde_open(fname, "r"); if (fp == NULL) return; while (line.l = 0, kgetline(&line, (kgets_func *) fgets, fp) >= 0) if (line.s[0] == '[' && (s = strchr(line.s, ']')) != NULL) { *s = '\0'; active = (strcmp(&line.s[1], section) == 0); } else if (active && (s = strpbrk(line.s, ":=")) != NULL) { const char *key = line.s, *value = &s[1], *akey; va_list args; while (isspace_c(*key)) key++; while (s > key && isspace_c(s[-1])) s--; *s = '\0'; while (isspace_c(*value)) value++; while (line.l > 0 && isspace_c(line.s[line.l-1])) line.s[--line.l] = '\0'; va_start(args, section); while ((akey = va_arg(args, const char *)) != NULL) { kstring_t *avar = va_arg(args, kstring_t *); if (strcmp(key, akey) == 0) { avar->l = 0; kputs(value, avar); break; } } va_end(args); } fclose(fp); free(line.s); } static void parse_simple(const char *fname, kstring_t *id, kstring_t *secret) { kstring_t text = { 0, 0, NULL }; char *s; size_t len; FILE *fp = expand_tilde_open(fname, "r"); if (fp == NULL) return; while (kgetline(&text, (kgets_func *) fgets, fp) >= 0) kputc(' ', &text); fclose(fp); s = text.s; while (isspace_c(*s)) s++; kputsn(s, len = strcspn(s, " \t"), id); s += len; while (isspace_c(*s)) s++; kputsn(s, strcspn(s, " \t"), secret); free(text.s); } static int copy_auth_headers(s3_auth_data *ad, char ***hdrs) { char **hdr = &ad->headers[0]; int idx = 0; *hdrs = hdr; hdr[idx] = strdup(ad->date); if (!hdr[idx]) return -1; idx++; if (ad->token.l) { kstring_t token_hdr = KS_INITIALIZE; kputs("X-Amz-Security-Token: ", &token_hdr); kputs(ad->token.s, &token_hdr); if (token_hdr.s) { hdr[idx++] = token_hdr.s; } else { goto fail; } } if (ad->auth_hdr.l) { hdr[idx] = strdup(ad->auth_hdr.s); if (!hdr[idx]) goto fail; idx++; } hdr[idx] = NULL; return 0; fail: for (--idx; idx >= 0; --idx) free(hdr[idx]); return -1; } static void free_auth_data(s3_auth_data *ad) { if (ad->refcount > 0) { --ad->refcount; return; } free(ad->profile.s); free(ad->id.s); free(ad->token.s); free(ad->secret.s); free(ad->region.s); free(ad->canonical_query_string.s); free(ad->user_query_string.s); free(ad->host.s); free(ad->bucket); free(ad->auth_hdr.s); free(ad->date_html.s); free(ad); } static time_t parse_rfc3339_date(kstring_t *datetime) { int offset = 0; time_t when; int num; char should_be_t = '\0', timezone[10] = { '\0' }; unsigned int year, mon, day, hour, min, sec; if (!datetime->s) return 0; // It should be possible to do this with strptime(), but it seems // to not get on with our feature definitions. num = sscanf(datetime->s, "%4u-%2u-%2u%c%2u:%2u:%2u%9s", &year, &mon, &day, &should_be_t, &hour, &min, &sec, timezone); if (num < 8) return 0; if (should_be_t != 'T' && should_be_t != 't' && should_be_t != ' ') return 0; struct tm parsed = { sec, min, hour, day, mon - 1, year - 1900, 0, 0, 0 }; switch (timezone[0]) { case 'Z': case 'z': case '\0': break; case '+': case '-': { unsigned hr_off, min_off; if (sscanf(timezone + 1, "%2u:%2u", &hr_off, &min_off)) { if (hr_off < 24 && min_off <= 60) { offset = ((hr_off * 60 + min_off) * (timezone[0] == '+' ? -60 : 60)); } } break; } default: return 0; } when = hts_time_gm(&parsed); return when >= 0 ? when + offset : 0; } static void refresh_auth_data(s3_auth_data *ad) { // Basically a copy of the AWS_SHARED_CREDENTIALS_FILE part of // setup_auth_data(), but this only reads the authorisation parts. const char *v = getenv("AWS_SHARED_CREDENTIALS_FILE"); kstring_t expiry_time = KS_INITIALIZE; parse_ini(v? v : "~/.aws/credentials", ad->profile.s, "aws_access_key_id", &ad->id, "aws_secret_access_key", &ad->secret, "aws_session_token", &ad->token, "expiry_time", &expiry_time); if (expiry_time.l) { ad->creds_expiry_time = parse_rfc3339_date(&expiry_time); } ks_free(&expiry_time); } static int auth_header_callback(void *ctx, char ***hdrs) { s3_auth_data *ad = (s3_auth_data *) ctx; time_t now = time(NULL); #ifdef HAVE_GMTIME_R struct tm tm_buffer; struct tm *tm = gmtime_r(&now, &tm_buffer); #else struct tm *tm = gmtime(&now); #endif kstring_t message = { 0, 0, NULL }; unsigned char digest[DIGEST_BUFSIZ]; size_t digest_len; if (!hdrs) { // Closing connection free_auth_data(ad); return 0; } if (ad->creds_expiry_time > 0 && ad->creds_expiry_time - now < CREDENTIAL_LIFETIME) { refresh_auth_data(ad); } else if (now - ad->auth_time < AUTH_LIFETIME) { // Last auth string should still be valid *hdrs = NULL; return 0; } strftime(ad->date, sizeof(ad->date), "Date: %a, %d %b %Y %H:%M:%S GMT", tm); if (!ad->id.l || !ad->secret.l) { ad->auth_time = now; return copy_auth_headers(ad, hdrs); } if (ksprintf(&message, "%s\n\n\n%s\n%s%s%s%s", ad->mode == 'r' ? "GET" : "PUT", ad->date + 6, ad->token.l ? "x-amz-security-token:" : "", ad->token.l ? ad->token.s : "", ad->token.l ? "\n" : "", ad->bucket) < 0) { return -1; } digest_len = s3_sign(digest, &ad->secret, &message); ad->auth_hdr.l = 0; if (ksprintf(&ad->auth_hdr, "Authorization: AWS %s:", ad->id.s) < 0) goto fail; base64_kput(digest, digest_len, &ad->auth_hdr); free(message.s); ad->auth_time = now; return copy_auth_headers(ad, hdrs); fail: free(message.s); return -1; } /* like a escape path but for query strings '=' and '&' are untouched */ static char *escape_query(const char *qs) { size_t i, j = 0, length, alloced; char *escaped; length = strlen(qs); alloced = length * 3 + 1; if ((escaped = malloc(alloced)) == NULL) { return NULL; } for (i = 0; i < length; i++) { int c = qs[i]; if ((c >= '0' && c <= '9') || (c >= 'A' && c <= 'Z') || (c >= 'a' && c <= 'z') || c == '_' || c == '-' || c == '~' || c == '.' || c == '/' || c == '=' || c == '&') { escaped[j++] = c; } else { snprintf(escaped + j, alloced - j, "%%%02X", c); j += 3; } } escaped[j] = '\0'; return escaped; } static char *escape_path(const char *path) { size_t i, j = 0, length, alloced; char *escaped; length = strlen(path); alloced = length * 3 + 1; if ((escaped = malloc(alloced)) == NULL) { return NULL; } for (i = 0; i < length; i++) { int c = path[i]; if (c == '?') break; // don't escape ? or beyond if ((c >= '0' && c <= '9') || (c >= 'A' && c <= 'Z') || (c >= 'a' && c <= 'z') || c == '_' || c == '-' || c == '~' || c == '.' || c == '/') { escaped[j++] = c; } else { snprintf(escaped + j, alloced - j, "%%%02X", c); j += 3; } } if (i != length) { // in the case of a '?' copy the rest of the path across unchanged strcpy(escaped + j, path + i); } else { escaped[j] = '\0'; } return escaped; } static int is_escaped(const char *str) { const char *c = str; int escaped = 0; int needs_escape = 0; while (*c != '\0') { if (*c == '%' && c[1] != '\0' && c[2] != '\0') { if (isxdigit_c(c[1]) && isxdigit_c(c[2])) { escaped = 1; c += 3; continue; } else { // only escaped if all % signs are escaped escaped = 0; } } if (!((*c >= '0' && *c <= '9') || (*c >= 'A' && *c <= 'Z') || (*c >= 'a' && *c <= 'z') || *c == '_' || *c == '-' || *c == '~' || *c == '.' || *c == '/')) { needs_escape = 1; } c++; } return escaped || !needs_escape; } static int redirect_endpoint_callback(void *auth, long response, kstring_t *header, kstring_t *url) { s3_auth_data *ad = (s3_auth_data *)auth; char *new_region; char *end; int ret = -1; // get the new region from the reply header if ((new_region = strstr(header->s, "x-amz-bucket-region: "))) { new_region += strlen("x-amz-bucket-region: "); end = new_region; while (isalnum_c(*end) || ispunct_c(*end)) end++; *end = 0; if (strstr(ad->host.s, "amazonaws.com")) { ad->region.l = 0; kputs(new_region, &ad->region); ad->host.l = 0; if (ad->url_style == s3_path) { // Path style https://s3.{region-code}.amazonaws.com/{bucket-name}/{key-name} ksprintf(&ad->host, "s3.%s.amazonaws.com", new_region); } else { // Virtual https://{bucket-name}.s3.{region-code}.amazonaws.com/{key-name} // Extract the {bucket-name} from {ad->host} to include in subdomain kstring_t url_prefix = KS_INITIALIZE; kputsn(ad->host.s, strcspn(ad->host.s, "."), &url_prefix); ksprintf(&ad->host, "%s.s3.%s.amazonaws.com", url_prefix.s, new_region); free(url_prefix.s); } if (ad->region.l && ad->host.l) { int e = 0; url->l = 0; e |= kputs("https://", url) < 0; e |= kputs(ad->host.s, url) < 0; e |= kputsn(ad->bucket, strlen(ad->bucket), url) < 0; if (!e) ret = 0; } if (ad->user_query_string.l) { kputc('?', url); kputsn(ad->user_query_string.s, ad->user_query_string.l, url); } } } return ret; } static s3_auth_data * setup_auth_data(const char *s3url, const char *mode, int sigver, kstring_t *url) { s3_auth_data *ad = calloc(1, sizeof(*ad)); const char *bucket, *path; char *escaped = NULL; size_t url_path_pos; ptrdiff_t bucket_len; int is_https = 1, dns_compliant; char *query_start; if (!ad) return NULL; ad->mode = strchr(mode, 'r') ? 'r' : 'w'; ad->url_style = s3_auto; // Our S3 URL format is s3[+SCHEME]://[ID[:SECRET[:TOKEN]]@]BUCKET/PATH if (s3url[2] == '+') { bucket = strchr(s3url, ':') + 1; if (bucket == NULL) { free(ad); return NULL; } kputsn(&s3url[3], bucket - &s3url[3], url); is_https = strncmp(url->s, "https:", 6) == 0; } else { kputs("https:", url); bucket = &s3url[3]; } while (*bucket == '/') kputc(*bucket++, url); path = bucket + strcspn(bucket, "/?#@"); if (*path == '@') { const char *colon = strpbrk(bucket, ":@"); if (*colon != ':') { urldecode_kput(bucket, colon - bucket, &ad->profile); } else { const char *colon2 = strpbrk(&colon[1], ":@"); urldecode_kput(bucket, colon - bucket, &ad->id); urldecode_kput(&colon[1], colon2 - &colon[1], &ad->secret); if (*colon2 == ':') urldecode_kput(&colon2[1], path - &colon2[1], &ad->token); } bucket = &path[1]; path = bucket + strcspn(bucket, "/?#"); } else { // If the URL has no ID[:SECRET]@, consider environment variables. const char *v; if ((v = getenv("AWS_ACCESS_KEY_ID")) != NULL) kputs(v, &ad->id); if ((v = getenv("AWS_SECRET_ACCESS_KEY")) != NULL) kputs(v, &ad->secret); if ((v = getenv("AWS_SESSION_TOKEN")) != NULL) kputs(v, &ad->token); if ((v = getenv("AWS_DEFAULT_REGION")) != NULL) kputs(v, &ad->region); if ((v = getenv("HTS_S3_HOST")) != NULL) kputs(v, &ad->host); if ((v = getenv("AWS_DEFAULT_PROFILE")) != NULL) kputs(v, &ad->profile); else if ((v = getenv("AWS_PROFILE")) != NULL) kputs(v, &ad->profile); else kputs("default", &ad->profile); if ((v = getenv("HTS_S3_ADDRESS_STYLE")) != NULL) { if (strcasecmp(v, "virtual") == 0) { ad->url_style = s3_virtual; } else if (strcasecmp(v, "path") == 0) { ad->url_style = s3_path; } } } if (ad->id.l == 0) { kstring_t url_style = KS_INITIALIZE; kstring_t expiry_time = KS_INITIALIZE; const char *v = getenv("AWS_SHARED_CREDENTIALS_FILE"); parse_ini(v? v : "~/.aws/credentials", ad->profile.s, "aws_access_key_id", &ad->id, "aws_secret_access_key", &ad->secret, "aws_session_token", &ad->token, "region", &ad->region, "addressing_style", &url_style, "expiry_time", &expiry_time, NULL); if (url_style.l) { if (strcmp(url_style.s, "virtual") == 0) { ad->url_style = s3_virtual; } else if (strcmp(url_style.s, "path") == 0) { ad->url_style = s3_path; } else { ad->url_style = s3_auto; } } if (expiry_time.l) { // Not a real part of the AWS configuration file, but it allows // support for short-term credentials like those for the IAM // service. The botocore library uses the key "expiry_time" // internally for this purpose. // See https://github.com/boto/botocore/blob/develop/botocore/credentials.py ad->creds_expiry_time = parse_rfc3339_date(&expiry_time); } ks_free(&url_style); ks_free(&expiry_time); } if (ad->id.l == 0) { kstring_t url_style = KS_INITIALIZE; const char *v = getenv("HTS_S3_S3CFG"); parse_ini(v? v : "~/.s3cfg", ad->profile.s, "access_key", &ad->id, "secret_key", &ad->secret, "access_token", &ad->token, "host_base", &ad->host, "bucket_location", &ad->region, "host_bucket", &url_style, NULL); if (url_style.l) { // Conforming to s3cmd's GitHub PR#416, host_bucket without the "%(bucket)s" string // indicates use of path style adressing. if (strstr(url_style.s, "%(bucket)s") == NULL) { ad->url_style = s3_path; } else { ad->url_style = s3_auto; } } ks_free(&url_style); } if (ad->id.l == 0) parse_simple("~/.awssecret", &ad->id, &ad->secret); // if address_style is set, force the dns_compliant setting if (ad->url_style == s3_virtual) { dns_compliant = 1; } else if (ad->url_style == s3_path) { dns_compliant = 0; } else { dns_compliant = is_dns_compliant(bucket, path, is_https); } if (ad->host.l == 0) kputs("s3.amazonaws.com", &ad->host); if (!dns_compliant && ad->region.l > 0 && strcmp(ad->host.s, "s3.amazonaws.com") == 0) { // Can avoid a redirection by including the region in the host name // (assuming the right one has been specified) ad->host.l = 0; ksprintf(&ad->host, "s3.%s.amazonaws.com", ad->region.s); } if (ad->region.l == 0) kputs("us-east-1", &ad->region); if (!is_escaped(path)) { escaped = escape_path(path); if (escaped == NULL) { goto error; } } bucket_len = path - bucket; // Use virtual hosted-style access if possible, otherwise path-style. if (dns_compliant) { size_t url_host_pos = url->l; // Append "bucket.host" to url kputsn_(bucket, bucket_len, url); kputc('.', url); kputsn(ad->host.s, ad->host.l, url); url_path_pos = url->l; if (sigver == 4) { // Copy back to ad->host to use when making the signature ad->host.l = 0; kputsn(url->s + url_host_pos, url->l - url_host_pos, &ad->host); } } else { // Append "host/bucket" to url kputsn(ad->host.s, ad->host.l, url); url_path_pos = url->l; kputc('/', url); kputsn(bucket, bucket_len, url); } kputs(escaped == NULL ? path : escaped, url); if (sigver == 4 || !dns_compliant) { ad->bucket = malloc(url->l - url_path_pos + 1); if (ad->bucket == NULL) { goto error; } memcpy(ad->bucket, url->s + url_path_pos, url->l - url_path_pos + 1); } else { ad->bucket = malloc(url->l - url_path_pos + bucket_len + 2); if (ad->bucket == NULL) { goto error; } ad->bucket[0] = '/'; memcpy(ad->bucket + 1, bucket, bucket_len); memcpy(ad->bucket + bucket_len + 1, url->s + url_path_pos, url->l - url_path_pos + 1); } // write any query strings to its own place to use later if ((query_start = strchr(ad->bucket, '?'))) { kputs(query_start + 1, &ad->user_query_string); *query_start = 0; } free(escaped); return ad; error: free(escaped); free_auth_data(ad); return NULL; } static hFILE * s3_rewrite(const char *s3url, const char *mode, va_list *argsp) { kstring_t url = { 0, 0, NULL }; s3_auth_data *ad = setup_auth_data(s3url, mode, 2, &url); if (!ad) return NULL; hFILE *fp = hopen(url.s, mode, "va_list", argsp, "httphdr_callback", auth_header_callback, "httphdr_callback_data", ad, "redirect_callback", redirect_endpoint_callback, "redirect_callback_data", ad, NULL); if (!fp) goto fail; free(url.s); return fp; fail: free(url.s); free_auth_data(ad); return NULL; } /*************************************************************** AWS S3 sig version 4 writing code ****************************************************************/ static void hash_string(char *in, size_t length, char *out, size_t out_len) { unsigned char hashed[SHA256_DIGEST_BUFSIZE]; int i, j; s3_sha256((const unsigned char *)in, length, hashed); for (i = 0, j = 0; i < SHA256_DIGEST_BUFSIZE; i++, j+= 2) { snprintf(out + j, out_len - j, "%02x", hashed[i]); } } static void ksinit(kstring_t *s) { s->l = 0; s->m = 0; s->s = NULL; } static void ksfree(kstring_t *s) { free(s->s); ksinit(s); } static int make_signature(s3_auth_data *ad, kstring_t *string_to_sign, char *signature_string, size_t sig_string_len) { unsigned char date_key[SHA256_DIGEST_BUFSIZE]; unsigned char date_region_key[SHA256_DIGEST_BUFSIZE]; unsigned char date_region_service_key[SHA256_DIGEST_BUFSIZE]; unsigned char signing_key[SHA256_DIGEST_BUFSIZE]; unsigned char signature[SHA256_DIGEST_BUFSIZE]; const unsigned char service[] = "s3"; const unsigned char request[] = "aws4_request"; kstring_t secret_access_key = KS_INITIALIZE; unsigned int len; unsigned int i, j; ksprintf(&secret_access_key, "AWS4%s", ad->secret.s); if (secret_access_key.l == 0) { return -1; } s3_sign_sha256(secret_access_key.s, secret_access_key.l, (const unsigned char *)ad->date_short, strlen(ad->date_short), date_key, &len); s3_sign_sha256(date_key, len, (const unsigned char *)ad->region.s, ad->region.l, date_region_key, &len); s3_sign_sha256(date_region_key, len, service, 2, date_region_service_key, &len); s3_sign_sha256(date_region_service_key, len, request, 12, signing_key, &len); s3_sign_sha256(signing_key, len, (const unsigned char *)string_to_sign->s, string_to_sign->l, signature, &len); for (i = 0, j = 0; i < len; i++, j+= 2) { snprintf(signature_string + j, sig_string_len - j, "%02x", signature[i]); } ksfree(&secret_access_key); return 0; } static int make_authorisation(s3_auth_data *ad, char *http_request, char *content, kstring_t *auth) { kstring_t signed_headers = KS_INITIALIZE; kstring_t canonical_headers = KS_INITIALIZE; kstring_t canonical_request = KS_INITIALIZE; kstring_t scope = KS_INITIALIZE; kstring_t string_to_sign = KS_INITIALIZE; char cr_hash[HASH_LENGTH_SHA256]; char signature_string[HASH_LENGTH_SHA256]; int ret = -1; if (!ad->token.l) { kputs("host;x-amz-content-sha256;x-amz-date", &signed_headers); } else { kputs("host;x-amz-content-sha256;x-amz-date;x-amz-security-token", &signed_headers); } if (signed_headers.l == 0) { return -1; } if (!ad->token.l) { ksprintf(&canonical_headers, "host:%s\nx-amz-content-sha256:%s\nx-amz-date:%s\n", ad->host.s, content, ad->date_long); } else { ksprintf(&canonical_headers, "host:%s\nx-amz-content-sha256:%s\nx-amz-date:%s\nx-amz-security-token:%s\n", ad->host.s, content, ad->date_long, ad->token.s); } if (canonical_headers.l == 0) { goto cleanup; } // bucket == canonical_uri ksprintf(&canonical_request, "%s\n%s\n%s\n%s\n%s\n%s", http_request, ad->bucket, ad->canonical_query_string.s, canonical_headers.s, signed_headers.s, content); if (canonical_request.l == 0) { goto cleanup; } hash_string(canonical_request.s, canonical_request.l, cr_hash, sizeof(cr_hash)); ksprintf(&scope, "%s/%s/s3/aws4_request", ad->date_short, ad->region.s); if (scope.l == 0) { goto cleanup; } ksprintf(&string_to_sign, "AWS4-HMAC-SHA256\n%s\n%s\n%s", ad->date_long, scope.s, cr_hash); if (string_to_sign.l == 0) { goto cleanup; } if (make_signature(ad, &string_to_sign, signature_string, sizeof(signature_string))) { goto cleanup; } ksprintf(auth, "Authorization: AWS4-HMAC-SHA256 Credential=%s/%s/%s/s3/aws4_request,SignedHeaders=%s,Signature=%s", ad->id.s, ad->date_short, ad->region.s, signed_headers.s, signature_string); if (auth->l == 0) { goto cleanup; } ret = 0; cleanup: ksfree(&signed_headers); ksfree(&canonical_headers); ksfree(&canonical_request); ksfree(&scope); ksfree(&string_to_sign); return ret; } static int update_time(s3_auth_data *ad, time_t now) { int ret = -1; #ifdef HAVE_GMTIME_R struct tm tm_buffer; struct tm *tm = gmtime_r(&now, &tm_buffer); #else struct tm *tm = gmtime(&now); #endif if (now - ad->auth_time > AUTH_LIFETIME) { // update timestamp ad->auth_time = now; if (strftime(ad->date_long, 17, "%Y%m%dT%H%M%SZ", tm) != 16) { return -1; } if (strftime(ad->date_short, 9, "%Y%m%d", tm) != 8) { return -1;; } ad->date_html.l = 0; ksprintf(&ad->date_html, "x-amz-date: %s", ad->date_long); } if (ad->date_html.l) ret = 0; return ret; } static int query_cmp(const void *p1, const void *p2) { char **q1 = (char **)p1; char **q2 = (char **)p2; return strcmp(*q1, *q2); } /* Query strings must be in alphabetical order for authorisation */ static int order_query_string(kstring_t *qs) { int *query_offset = NULL; int num_queries, i; char **queries = NULL; kstring_t ordered = KS_INITIALIZE; char *escaped = NULL; int ret = -1; if ((query_offset = ksplit(qs, '&', &num_queries)) == NULL) { return -1; } if ((queries = malloc(num_queries * sizeof(char*))) == NULL) goto err; for (i = 0; i < num_queries; i++) { queries[i] = qs->s + query_offset[i]; } qsort(queries, num_queries, sizeof(char *), query_cmp); for (i = 0; i < num_queries; i++) { if (i) { kputs("&", &ordered); } kputs(queries[i], &ordered); } if ((escaped = escape_query(ordered.s)) == NULL) goto err; qs->l = 0; kputs(escaped, qs); ret = 0; err: free(ordered.s); free(queries); free(query_offset); free(escaped); return ret; } static int write_authorisation_callback(void *auth, char *request, kstring_t *content, char *cqs, kstring_t *hash, kstring_t *auth_str, kstring_t *date, kstring_t *token, int uqs) { s3_auth_data *ad = (s3_auth_data *)auth; char content_hash[HASH_LENGTH_SHA256]; time_t now; if (request == NULL) { // signal to free auth data free_auth_data(ad); return 0; } now = time(NULL); if (update_time(ad, now)) { return -1; } if (ad->creds_expiry_time > 0 && ad->creds_expiry_time - now < CREDENTIAL_LIFETIME) { refresh_auth_data(ad); } if (content) { hash_string(content->s, content->l, content_hash, sizeof(content_hash)); } else { // empty hash hash_string("", 0, content_hash, sizeof(content_hash)); } ad->canonical_query_string.l = 0; kputs(cqs, &ad->canonical_query_string); if (ad->canonical_query_string.l == 0) { return -1; } /* add a user provided query string, normally only useful on upload initiation */ if (uqs) { kputs("&", &ad->canonical_query_string); kputs(ad->user_query_string.s, &ad->canonical_query_string); if (order_query_string(&ad->canonical_query_string)) { return -1; } } if (make_authorisation(ad, request, content_hash, auth_str)) { return -1; } kputs(ad->date_html.s, date); kputsn(content_hash, HASH_LENGTH_SHA256, hash); if (date->l == 0 || hash->l == 0) { return -1; } if (ad->token.l) { ksprintf(token, "x-amz-security-token: %s", ad->token.s); } return 0; } static int v4_auth_header_callback(void *ctx, char ***hdrs) { s3_auth_data *ad = (s3_auth_data *) ctx; char content_hash[HASH_LENGTH_SHA256]; kstring_t content = KS_INITIALIZE; kstring_t authorisation = KS_INITIALIZE; kstring_t token_hdr = KS_INITIALIZE; char *date_html = NULL; time_t now; int idx; if (!hdrs) { // Closing connection free_auth_data(ad); return 0; } now = time(NULL); if (update_time(ad, now)) { return -1; } if (ad->creds_expiry_time > 0 && ad->creds_expiry_time - now < CREDENTIAL_LIFETIME) { refresh_auth_data(ad); } if (!ad->id.l || !ad->secret.l) { return copy_auth_headers(ad, hdrs); } hash_string("", 0, content_hash, sizeof(content_hash)); // empty hash ad->canonical_query_string.l = 0; if (ad->user_query_string.l > 0) { kputs(ad->user_query_string.s, &ad->canonical_query_string); if (order_query_string(&ad->canonical_query_string)) { return -1; } } else { kputs("", &ad->canonical_query_string); } if (make_authorisation(ad, "GET", content_hash, &authorisation)) { return -1; } ksprintf(&content, "x-amz-content-sha256: %s", content_hash); date_html = strdup(ad->date_html.s); if (ad->token.l > 0) { kputs("X-Amz-Security-Token: ", &token_hdr); kputs(ad->token.s, &token_hdr); } if (content.l == 0 || date_html == NULL) { ksfree(&authorisation); ksfree(&content); ksfree(&token_hdr); free(date_html); return -1; } *hdrs = &ad->headers[0]; idx = 0; ad->headers[idx++] = ks_release(&authorisation); ad->headers[idx++] = date_html; ad->headers[idx++] = ks_release(&content); if (token_hdr.s) ad->headers[idx++] = ks_release(&token_hdr); ad->headers[idx++] = NULL; return 0; } static int handle_400_response(hFILE *fp, s3_auth_data *ad) { // v4 signatures in virtual hosted mode return 400 Bad Request if the // wrong region is used to make the signature. The response is an xml // document which includes the name of the correct region. This can // be extracted and used to generate a corrected signature. // As the xml is fairly simple, go with something "good enough" instead // of trying to parse it properly. char buffer[1024], *region, *reg_end; ssize_t bytes; bytes = hread(fp, buffer, sizeof(buffer) - 1); if (bytes < 0) { return -1; } buffer[bytes] = '\0'; region = strstr(buffer, ""); if (region == NULL) { return -1; } region += 8; while (isspace((unsigned char) *region)) ++region; reg_end = strchr(region, '<'); if (reg_end == NULL || strncmp(reg_end + 1, "/Region>", 8) != 0) { return -1; } while (reg_end > region && isspace((unsigned char) reg_end[-1])) --reg_end; ad->region.l = 0; kputsn(region, reg_end - region, &ad->region); if (ad->region.l == 0) { return -1; } return 0; } static int set_region(void *adv, kstring_t *region) { s3_auth_data *ad = (s3_auth_data *) adv; ad->region.l = 0; return kputsn(region->s, region->l, &ad->region) < 0; } static int http_status_errno(int status) { if (status >= 500) switch (status) { case 501: return ENOSYS; case 503: return EBUSY; case 504: return ETIMEDOUT; default: return EIO; } else if (status >= 400) switch (status) { case 401: return EPERM; case 403: return EACCES; case 404: return ENOENT; case 405: return EROFS; case 407: return EPERM; case 408: return ETIMEDOUT; case 410: return ENOENT; default: return EINVAL; } else return 0; } static hFILE *s3_open_v4(const char *s3url, const char *mode, va_list *argsp) { kstring_t url = { 0, 0, NULL }; s3_auth_data *ad = setup_auth_data(s3url, mode, 4, &url); hFILE *fp = NULL; if (ad == NULL) { return NULL; } if (ad->mode == 'r') { long http_response = 0; fp = hopen(url.s, mode, "va_list", argsp, "httphdr_callback", v4_auth_header_callback, "httphdr_callback_data", ad, "redirect_callback", redirect_endpoint_callback, "redirect_callback_data", ad, "http_response_ptr", &http_response, "fail_on_error", 0, NULL); if (fp == NULL) goto error; if (http_response == 307) { // Follow additional redirect. ad->refcount = 1; hclose_abruptly(fp); url.l = 0; ksprintf(&url, "https://%s%s", ad->host.s, ad->bucket); fp = hopen(url.s, mode, "va_list", argsp, "httphdr_callback", v4_auth_header_callback, "httphdr_callback_data", ad, "redirect_callback", redirect_endpoint_callback, "redirect_callback_data", ad, "http_response_ptr", &http_response, "fail_on_error", 0, NULL); } if (http_response == 400) { ad->refcount = 1; if (handle_400_response(fp, ad) != 0) { goto error; } hclose_abruptly(fp); fp = hopen(url.s, mode, "va_list", argsp, "httphdr_callback", v4_auth_header_callback, "httphdr_callback_data", ad, "redirect_callback", redirect_endpoint_callback, "redirect_callback_data", ad, NULL); } else if (http_response > 400) { ad->refcount = 1; errno = http_status_errno(http_response); goto error; } if (fp == NULL) goto error; } else { kstring_t final_url = KS_INITIALIZE; // add the scheme marker ksprintf(&final_url, "s3w+%s", url.s); if(final_url.l == 0) goto error; fp = hopen(final_url.s, mode, "va_list", argsp, "s3_auth_callback", write_authorisation_callback, "s3_auth_callback_data", ad, "redirect_callback", redirect_endpoint_callback, "set_region_callback", set_region, NULL); free(final_url.s); if (fp == NULL) goto error; } free(url.s); return fp; error: if (fp) hclose_abruptly(fp); free(url.s); free_auth_data(ad); return NULL; } static hFILE *s3_open(const char *url, const char *mode) { hFILE *fp; kstring_t mode_colon = { 0, 0, NULL }; kputs(mode, &mode_colon); kputc(':', &mode_colon); if (getenv("HTS_S3_V2") == NULL) { // Force the v2 signature code fp = s3_open_v4(url, mode_colon.s, NULL); } else { fp = s3_rewrite(url, mode_colon.s, NULL); } free(mode_colon.s); return fp; } static hFILE *s3_vopen(const char *url, const char *mode_colon, va_list args0) { hFILE *fp; // Need to use va_copy() as we can only take the address of an actual // va_list object, not that of a parameter whose type may have decayed. va_list args; va_copy(args, args0); if (getenv("HTS_S3_V2") == NULL) { // Force the v2 signature code fp = s3_open_v4(url, mode_colon, &args); } else { fp = s3_rewrite(url, mode_colon, &args); } va_end(args); return fp; } int PLUGIN_GLOBAL(hfile_plugin_init,_s3)(struct hFILE_plugin *self) { static const struct hFILE_scheme_handler handler = { s3_open, hfile_always_remote, "Amazon S3", 2000 + 50, s3_vopen }; #ifdef ENABLE_PLUGINS // Embed version string for examination via strings(1) or what(1) static const char id[] = "@(#)hfile_s3 plugin (htslib)\t" HTS_VERSION_TEXT; if (hts_verbose >= 9) fprintf(stderr, "[M::hfile_s3.init] version %s\n", strchr(id, '\t')+1); #endif self->name = "Amazon S3"; hfile_add_scheme_handler("s3", &handler); hfile_add_scheme_handler("s3+http", &handler); hfile_add_scheme_handler("s3+https", &handler); return 0; } pysam-0.23.0/htslib/hfile_s3_write.c000066400000000000000000000571361475062545500173150ustar00rootroot00000000000000/* hfile_s3_write.c - Code to handle multipart uploading to S3. Copyright (C) 2019 Genome Research Ltd. Author: Andrew Whitwham Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE S3 Multipart Upload ------------------- There are several steps in the Mulitipart upload. 1) Initiate Upload ------------------ Initiate the upload and get an upload ID. This ID is used in all other steps. 2) Upload Part -------------- Upload a part of the data. 5Mb minimum part size (except for the last part). Each part is numbered and a successful upload returns an Etag header value that needs to used for the completion step. Step repeated till all data is uploaded. 3) Completion ------------- Complete the upload by sending all the part numbers along with their associated Etag values. Optional - Abort ---------------- If something goes wrong this instructs the server to delete all the partial uploads and abandon the upload process. Andrew Whitwham, January 2019 */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #ifdef __MSYS__ #include #endif #include #include #include "hfile_internal.h" #ifdef ENABLE_PLUGINS #include "version.h" #endif #include "htslib/hts.h" #include "htslib/kstring.h" #include "htslib/khash.h" #include #define MINIMUM_S3_WRITE_SIZE 5242880 #define S3_MOVED_PERMANENTLY 301 #define S3_BAD_REQUEST 400 // Lets the part memory size grow to about 1Gb giving a 2.5Tb max file size. // Max. parts allowed by AWS is 10000, so use ceil(10000.0/9.0) #define EXPAND_ON 1112 static struct { kstring_t useragent; CURLSH *share; pthread_mutex_t share_lock; } curl = { { 0, 0, NULL }, NULL, PTHREAD_MUTEX_INITIALIZER }; static void share_lock(CURL *handle, curl_lock_data data, curl_lock_access access, void *userptr) { pthread_mutex_lock(&curl.share_lock); } static void share_unlock(CURL *handle, curl_lock_data data, void *userptr) { pthread_mutex_unlock(&curl.share_lock); } typedef int (*s3_auth_callback) (void *auth_data, char *, kstring_t*, char*, kstring_t*, kstring_t*, kstring_t*, kstring_t*, int); typedef int (*set_region_callback) (void *auth_data, kstring_t *region); typedef struct { s3_auth_callback callback; redirect_callback redirect_callback; set_region_callback set_region_callback; void *callback_data; } s3_authorisation; typedef struct { hFILE base; CURL *curl; CURLcode ret; s3_authorisation *au; kstring_t buffer; kstring_t url; kstring_t upload_id; kstring_t completion_message; int part_no; int aborted; size_t index; long verbose; int part_size; int expand; } hFILE_s3_write; static void ksinit(kstring_t *s) { s->l = 0; s->m = 0; s->s = NULL; } static void ksfree(kstring_t *s) { free(s->s); ksinit(s); } static size_t response_callback(void *contents, size_t size, size_t nmemb, void *userp) { size_t realsize = size * nmemb; kstring_t *resp = (kstring_t *)userp; if (kputsn((const char *)contents, realsize, resp) == EOF) { return 0; } return realsize; } static int get_entry(char *in, char *start_tag, char *end_tag, kstring_t *out) { char *start; char *end; if (!in) { return EOF; } start = strstr(in, start_tag); if (!start) return EOF; start += strlen(start_tag); end = strstr(start, end_tag); if (!end) return EOF; return kputsn(start, end - start, out); } static void cleanup_local(hFILE_s3_write *fp) { ksfree(&fp->buffer); ksfree(&fp->url); ksfree(&fp->upload_id); ksfree(&fp->completion_message); curl_easy_cleanup(fp->curl); free(fp->au); } static void cleanup(hFILE_s3_write *fp) { // free up authorisation data fp->au->callback(fp->au->callback_data, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0); cleanup_local(fp); } static struct curl_slist *set_html_headers(hFILE_s3_write *fp, kstring_t *auth, kstring_t *date, kstring_t *content, kstring_t *token) { struct curl_slist *headers = NULL; headers = curl_slist_append(headers, "Content-Type:"); // get rid of this headers = curl_slist_append(headers, "Expect:"); // and this headers = curl_slist_append(headers, auth->s); headers = curl_slist_append(headers, date->s); headers = curl_slist_append(headers, content->s); if (token->l) { headers = curl_slist_append(headers, token->s); } curl_easy_setopt(fp->curl, CURLOPT_HTTPHEADER, headers); return headers; } /* The partially uploaded file will hang around unless the delete command is sent. */ static int abort_upload(hFILE_s3_write *fp) { kstring_t content_hash = {0, 0, NULL}; kstring_t authorisation = {0, 0, NULL}; kstring_t url = {0, 0, NULL}; kstring_t content = {0, 0, NULL}; kstring_t canonical_query_string = {0, 0, NULL}; kstring_t date = {0, 0, NULL}; kstring_t token = {0, 0, NULL}; int ret = -1; struct curl_slist *headers = NULL; char http_request[] = "DELETE"; if (ksprintf(&canonical_query_string, "uploadId=%s", fp->upload_id.s) < 0) { goto out; } if (fp->au->callback(fp->au->callback_data, http_request, NULL, canonical_query_string.s, &content_hash, &authorisation, &date, &token, 0) != 0) { goto out; } if (ksprintf(&url, "%s?%s", fp->url.s, canonical_query_string.s) < 0) { goto out; } if (ksprintf(&content, "x-amz-content-sha256: %s", content_hash.s) < 0) { goto out; } curl_easy_reset(fp->curl); curl_easy_setopt(fp->curl, CURLOPT_CUSTOMREQUEST, http_request); curl_easy_setopt(fp->curl, CURLOPT_USERAGENT, curl.useragent.s); curl_easy_setopt(fp->curl, CURLOPT_URL, url.s); curl_easy_setopt(fp->curl, CURLOPT_VERBOSE, fp->verbose); headers = set_html_headers(fp, &authorisation, &date, &content, &token); fp->ret = curl_easy_perform(fp->curl); if (fp->ret == CURLE_OK) { ret = 0; } out: ksfree(&authorisation); ksfree(&content); ksfree(&content_hash); ksfree(&url); ksfree(&date); ksfree(&canonical_query_string); ksfree(&token); curl_slist_free_all(headers); fp->aborted = 1; cleanup(fp); return ret; } static int complete_upload(hFILE_s3_write *fp, kstring_t *resp) { kstring_t content_hash = {0, 0, NULL}; kstring_t authorisation = {0, 0, NULL}; kstring_t url = {0, 0, NULL}; kstring_t content = {0, 0, NULL}; kstring_t canonical_query_string = {0, 0, NULL}; kstring_t date = {0, 0, NULL}; kstring_t token = {0, 0, NULL}; int ret = -1; struct curl_slist *headers = NULL; char http_request[] = "POST"; if (ksprintf(&canonical_query_string, "uploadId=%s", fp->upload_id.s) < 0) { return -1; } // finish off the completion reply if (kputs("\n", &fp->completion_message) < 0) { goto out; } if (fp->au->callback(fp->au->callback_data, http_request, &fp->completion_message, canonical_query_string.s, &content_hash, &authorisation, &date, &token, 0) != 0) { goto out; } if (ksprintf(&url, "%s?%s", fp->url.s, canonical_query_string.s) < 0) { goto out; } if (ksprintf(&content, "x-amz-content-sha256: %s", content_hash.s) < 0) { goto out; } curl_easy_reset(fp->curl); curl_easy_setopt(fp->curl, CURLOPT_POST, 1L); curl_easy_setopt(fp->curl, CURLOPT_POSTFIELDS, fp->completion_message.s); curl_easy_setopt(fp->curl, CURLOPT_POSTFIELDSIZE, (long) fp->completion_message.l); curl_easy_setopt(fp->curl, CURLOPT_WRITEFUNCTION, response_callback); curl_easy_setopt(fp->curl, CURLOPT_WRITEDATA, (void *)resp); curl_easy_setopt(fp->curl, CURLOPT_URL, url.s); curl_easy_setopt(fp->curl, CURLOPT_USERAGENT, curl.useragent.s); curl_easy_setopt(fp->curl, CURLOPT_VERBOSE, fp->verbose); headers = set_html_headers(fp, &authorisation, &date, &content, &token); fp->ret = curl_easy_perform(fp->curl); if (fp->ret == CURLE_OK) { ret = 0; } out: ksfree(&authorisation); ksfree(&content); ksfree(&content_hash); ksfree(&url); ksfree(&date); ksfree(&token); ksfree(&canonical_query_string); curl_slist_free_all(headers); return ret; } static size_t upload_callback(void *ptr, size_t size, size_t nmemb, void *stream) { size_t realsize = size * nmemb; hFILE_s3_write *fp = (hFILE_s3_write *)stream; size_t read_length; if (realsize > (fp->buffer.l - fp->index)) { read_length = fp->buffer.l - fp->index; } else { read_length = realsize; } memcpy(ptr, fp->buffer.s + fp->index, read_length); fp->index += read_length; return read_length; } static int upload_part(hFILE_s3_write *fp, kstring_t *resp) { kstring_t content_hash = {0, 0, NULL}; kstring_t authorisation = {0, 0, NULL}; kstring_t url = {0, 0, NULL}; kstring_t content = {0, 0, NULL}; kstring_t canonical_query_string = {0, 0, NULL}; kstring_t date = {0, 0, NULL}; kstring_t token = {0, 0, NULL}; int ret = -1; struct curl_slist *headers = NULL; char http_request[] = "PUT"; if (ksprintf(&canonical_query_string, "partNumber=%d&uploadId=%s", fp->part_no, fp->upload_id.s) < 0) { return -1; } if (fp->au->callback(fp->au->callback_data, http_request, &fp->buffer, canonical_query_string.s, &content_hash, &authorisation, &date, &token, 0) != 0) { goto out; } if (ksprintf(&url, "%s?%s", fp->url.s, canonical_query_string.s) < 0) { goto out; } fp->index = 0; if (ksprintf(&content, "x-amz-content-sha256: %s", content_hash.s) < 0) { goto out; } curl_easy_reset(fp->curl); curl_easy_setopt(fp->curl, CURLOPT_UPLOAD, 1L); curl_easy_setopt(fp->curl, CURLOPT_READFUNCTION, upload_callback); curl_easy_setopt(fp->curl, CURLOPT_READDATA, fp); curl_easy_setopt(fp->curl, CURLOPT_INFILESIZE_LARGE, (curl_off_t)fp->buffer.l); curl_easy_setopt(fp->curl, CURLOPT_HEADERFUNCTION, response_callback); curl_easy_setopt(fp->curl, CURLOPT_HEADERDATA, (void *)resp); curl_easy_setopt(fp->curl, CURLOPT_URL, url.s); curl_easy_setopt(fp->curl, CURLOPT_USERAGENT, curl.useragent.s); curl_easy_setopt(fp->curl, CURLOPT_VERBOSE, fp->verbose); headers = set_html_headers(fp, &authorisation, &date, &content, &token); fp->ret = curl_easy_perform(fp->curl); if (fp->ret == CURLE_OK) { ret = 0; } out: ksfree(&authorisation); ksfree(&content); ksfree(&content_hash); ksfree(&url); ksfree(&date); ksfree(&token); ksfree(&canonical_query_string); curl_slist_free_all(headers); return ret; } static ssize_t s3_write(hFILE *fpv, const void *bufferv, size_t nbytes) { hFILE_s3_write *fp = (hFILE_s3_write *)fpv; const char *buffer = (const char *)bufferv; if (kputsn(buffer, nbytes, &fp->buffer) == EOF) { return -1; } if (fp->buffer.l > fp->part_size) { // time to write out our data kstring_t response = {0, 0, NULL}; int ret; ret = upload_part(fp, &response); if (!ret) { long response_code; kstring_t etag = {0, 0, NULL}; curl_easy_getinfo(fp->curl, CURLINFO_RESPONSE_CODE, &response_code); if (response_code > 200) { ret = -1; } else { if (get_entry(response.s, "ETag: \"", "\"", &etag) == EOF) { ret = -1; } else { ksprintf(&fp->completion_message, "\t\n\t\t%d\n\t\t%s\n\t\n", fp->part_no, etag.s); ksfree(&etag); } } } ksfree(&response); if (ret) { abort_upload(fp); return -1; } fp->part_no++; fp->buffer.l = 0; if (fp->expand && (fp->part_no % EXPAND_ON == 0)) { fp->part_size *= 2; } } return nbytes; } static int s3_close(hFILE *fpv) { hFILE_s3_write *fp = (hFILE_s3_write *)fpv; kstring_t response = {0, 0, NULL}; int ret = 0; if (!fp->aborted) { if (fp->buffer.l) { // write the last part ret = upload_part(fp, &response); if (!ret) { long response_code; kstring_t etag = {0, 0, NULL}; curl_easy_getinfo(fp->curl, CURLINFO_RESPONSE_CODE, &response_code); if (response_code > 200) { ret = -1; } else { if (get_entry(response.s, "ETag: \"", "\"", &etag) == EOF) { ret = -1; } else { ksprintf(&fp->completion_message, "\t\n\t\t%d\n\t\t%s\n\t\n", fp->part_no, etag.s); ksfree(&etag); } } } ksfree(&response); if (ret) { abort_upload(fp); return -1; } fp->part_no++; } if (fp->part_no > 1) { ret = complete_upload(fp, &response); if (!ret) { if (strstr(response.s, "CompleteMultipartUploadResult") == NULL) { ret = -1; } } } else { ret = -1; } if (ret) { abort_upload(fp); } else { cleanup(fp); } } ksfree(&response); return ret; } static int redirect_endpoint(hFILE_s3_write *fp, kstring_t *head) { int ret = -1; if (fp->au->redirect_callback) { ret = fp->au->redirect_callback(fp->au->callback_data, 301, head, &fp->url); } return ret; } static int handle_bad_request(hFILE_s3_write *fp, kstring_t *resp) { kstring_t region = {0, 0, NULL}; int ret = -1; if (fp->au->set_region_callback) { if (get_entry(resp->s, "", "", ®ion) == EOF) { return -1; } ret = fp->au->set_region_callback(fp->au->callback_data, ®ion); ksfree(®ion); } return ret; } static int initialise_upload(hFILE_s3_write *fp, kstring_t *head, kstring_t *resp, int user_query) { kstring_t content_hash = {0, 0, NULL}; kstring_t authorisation = {0, 0, NULL}; kstring_t url = {0, 0, NULL}; kstring_t content = {0, 0, NULL}; kstring_t date = {0, 0, NULL}; kstring_t token = {0, 0, NULL}; int ret = -1; struct curl_slist *headers = NULL; char http_request[] = "POST"; char delimiter = '?'; if (user_query) { delimiter = '&'; } if (fp->au->callback(fp->au->callback_data, http_request, NULL, "uploads=", &content_hash, &authorisation, &date, &token, user_query) != 0) { goto out; } if (ksprintf(&url, "%s%cuploads", fp->url.s, delimiter) < 0) { goto out; } if (ksprintf(&content, "x-amz-content-sha256: %s", content_hash.s) < 0) { goto out; } curl_easy_setopt(fp->curl, CURLOPT_URL, url.s); curl_easy_setopt(fp->curl, CURLOPT_POST, 1L); curl_easy_setopt(fp->curl, CURLOPT_POSTFIELDS, ""); // send no data curl_easy_setopt(fp->curl, CURLOPT_WRITEFUNCTION, response_callback); curl_easy_setopt(fp->curl, CURLOPT_WRITEDATA, (void *)resp); curl_easy_setopt(fp->curl, CURLOPT_HEADERFUNCTION, response_callback); curl_easy_setopt(fp->curl, CURLOPT_HEADERDATA, (void *)head); curl_easy_setopt(fp->curl, CURLOPT_USERAGENT, curl.useragent.s); curl_easy_setopt(fp->curl, CURLOPT_VERBOSE, fp->verbose); headers = set_html_headers(fp, &authorisation, &date, &content, &token); fp->ret = curl_easy_perform(fp->curl); if (fp->ret == CURLE_OK) { ret = 0; } out: ksfree(&authorisation); ksfree(&content); ksfree(&content_hash); ksfree(&url); ksfree(&date); ksfree(&token); curl_slist_free_all(headers); return ret; } static int get_upload_id(hFILE_s3_write *fp, kstring_t *resp) { int ret = 0; ksinit(&fp->upload_id); if (get_entry(resp->s, "", "", &fp->upload_id) == EOF) { ret = -1; } return ret; } static const struct hFILE_backend s3_write_backend = { NULL, s3_write, NULL, NULL, s3_close }; static hFILE *s3_write_open(const char *url, s3_authorisation *auth) { hFILE_s3_write *fp; kstring_t response = {0, 0, NULL}; kstring_t header = {0, 0, NULL}; int ret, has_user_query = 0; char *query_start; const char *env; if (!auth || !auth->callback || !auth->callback_data) { return NULL; } fp = (hFILE_s3_write *)hfile_init(sizeof(hFILE_s3_write), "w", 0); if (fp == NULL) { return NULL; } if ((fp->curl = curl_easy_init()) == NULL) { errno = ENOMEM; goto error; } if ((fp->au = calloc(1, sizeof(s3_authorisation))) == NULL) { goto error; } memcpy(fp->au, auth, sizeof(s3_authorisation)); ksinit(&fp->buffer); ksinit(&fp->url); ksinit(&fp->completion_message); fp->aborted = 0; fp->part_size = MINIMUM_S3_WRITE_SIZE; fp->expand = 1; if ((env = getenv("HTS_S3_PART_SIZE")) != NULL) { int part_size = atoi(env) * 1024 * 1024; if (part_size > fp->part_size) fp->part_size = part_size; fp->expand = 0; } if (hts_verbose >= 8) { fp->verbose = 1L; } else { fp->verbose = 0L; } kputs(url + 4, &fp->url); if ((query_start = strchr(fp->url.s, '?'))) { has_user_query = 1;; } ret = initialise_upload(fp, &header, &response, has_user_query); if (ret == 0) { long response_code; curl_easy_getinfo(fp->curl, CURLINFO_RESPONSE_CODE, &response_code); if (response_code == S3_MOVED_PERMANENTLY) { if (redirect_endpoint(fp, &header) == 0) { ksfree(&response); ksfree(&header); ret = initialise_upload(fp, &header, &response, has_user_query); } } else if (response_code == S3_BAD_REQUEST) { if (handle_bad_request(fp, &response) == 0) { ksfree(&response); ksfree(&header); ret = initialise_upload(fp, &header, &response, has_user_query); } } ksfree(&header); // no longer needed } if (ret) goto error; if (get_upload_id(fp, &response)) goto error; // start the completion message (a formatted list of parts) ksinit(&fp->completion_message); if (kputs("\n", &fp->completion_message) == EOF) { goto error; } fp->part_no = 1; // user query string no longer a useful part of the URL if (query_start) *query_start = '\0'; fp->base.backend = &s3_write_backend; ksfree(&response); return &fp->base; error: ksfree(&response); cleanup_local(fp); hfile_destroy((hFILE *)fp); return NULL; } static hFILE *hopen_s3_write(const char *url, const char *mode) { if (hts_verbose >= 1) { fprintf(stderr, "[E::%s] s3w:// URLs should not be used directly; use s3:// instead.\n", __func__); } return NULL; } static int parse_va_list(s3_authorisation *auth, va_list args) { const char *argtype; while ((argtype = va_arg(args, const char *)) != NULL) { if (strcmp(argtype, "s3_auth_callback") == 0) { auth->callback = va_arg(args, s3_auth_callback); } else if (strcmp(argtype, "s3_auth_callback_data") == 0) { auth->callback_data = va_arg(args, void *); } else if (strcmp(argtype, "redirect_callback") == 0) { auth->redirect_callback = va_arg(args, redirect_callback); } else if (strcmp(argtype, "set_region_callback") == 0) { auth->set_region_callback = va_arg(args, set_region_callback); } else if (strcmp(argtype, "va_list") == 0) { va_list *args2 = va_arg(args, va_list *); if (args2) { if (parse_va_list(auth, *args2) < 0) return -1; } } else { errno = EINVAL; return -1; } } return 0; } static hFILE *vhopen_s3_write(const char *url, const char *mode, va_list args) { hFILE *fp = NULL; s3_authorisation auth = {NULL, NULL, NULL}; if (parse_va_list(&auth, args) == 0) { fp = s3_write_open(url, &auth); } return fp; } static void s3_write_exit(void) { if (curl_share_cleanup(curl.share) == CURLSHE_OK) curl.share = NULL; free(curl.useragent.s); curl.useragent.l = curl.useragent.m = 0; curl.useragent.s = NULL; curl_global_cleanup(); } int PLUGIN_GLOBAL(hfile_plugin_init,_s3_write)(struct hFILE_plugin *self) { static const struct hFILE_scheme_handler handler = { hopen_s3_write, hfile_always_remote, "S3 Multipart Upload", 2000 + 50, vhopen_s3_write }; #ifdef ENABLE_PLUGINS // Embed version string for examination via strings(1) or what(1) static const char id[] = "@(#)hfile_s3_write plugin (htslib)\t" HTS_VERSION_TEXT; const char *version = strchr(id, '\t') + 1; if (hts_verbose >= 9) fprintf(stderr, "[M::hfile_s3_write.init] version %s\n", version); #else const char *version = hts_version(); #endif const curl_version_info_data *info; CURLcode err; CURLSHcode errsh; err = curl_global_init(CURL_GLOBAL_ALL); if (err != CURLE_OK) { // look at putting in an errno here return -1; } curl.share = curl_share_init(); if (curl.share == NULL) { curl_global_cleanup(); errno = EIO; return -1; } errsh = curl_share_setopt(curl.share, CURLSHOPT_LOCKFUNC, share_lock); errsh |= curl_share_setopt(curl.share, CURLSHOPT_UNLOCKFUNC, share_unlock); errsh |= curl_share_setopt(curl.share, CURLSHOPT_SHARE, CURL_LOCK_DATA_DNS); if (errsh != 0) { curl_share_cleanup(curl.share); curl_global_cleanup(); errno = EIO; return -1; } info = curl_version_info(CURLVERSION_NOW); ksprintf(&curl.useragent, "htslib/%s libcurl/%s", version, info->version); self->name = "S3 Multipart Upload"; self->destroy = s3_write_exit; hfile_add_scheme_handler("s3w", &handler); hfile_add_scheme_handler("s3w+http", &handler); hfile_add_scheme_handler("s3w+https", &handler); return 0; } pysam-0.23.0/htslib/hts.c000066400000000000000000005121451475062545500152010ustar00rootroot00000000000000/* hts.c -- format-neutral I/O, indexing, and iterator API functions. Copyright (C) 2008, 2009, 2012-2024 Genome Research Ltd. Copyright (C) 2012, 2013 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #ifdef HAVE_LIBLZMA #ifdef HAVE_LZMA_H #include #else #include "os/lzma_stub.h" #endif #endif #include "htslib/hts.h" #include "htslib/bgzf.h" #include "cram/cram.h" #include "htslib/hfile.h" #include "htslib/hts_endian.h" #include "version.h" #include "config_vars.h" #include "hts_internal.h" #include "hfile_internal.h" #include "sam_internal.h" #include "htslib/hts_expr.h" #include "htslib/hts_os.h" // drand48 #include "htslib/khash.h" #include "htslib/kseq.h" #include "htslib/ksort.h" #include "htslib/tbx.h" #if defined(HAVE_EXTERNAL_LIBHTSCODECS) #include #else #include "htscodecs/htscodecs/htscodecs.h" #endif #ifndef EFTYPE #define EFTYPE ENOEXEC #endif KHASH_INIT2(s2i,, kh_cstr_t, int64_t, 1, kh_str_hash_func, kh_str_hash_equal) HTSLIB_EXPORT int hts_verbose = HTS_LOG_WARNING; const char *hts_version(void) { return HTS_VERSION_TEXT; } unsigned int hts_features(void) { unsigned int feat = HTS_FEATURE_HTSCODECS; // Always present #ifdef PACKAGE_URL feat |= HTS_FEATURE_CONFIGURE; #endif #ifdef ENABLE_PLUGINS feat |= HTS_FEATURE_PLUGINS; #endif #ifdef HAVE_LIBCURL feat |= HTS_FEATURE_LIBCURL; #endif #ifdef ENABLE_S3 feat |= HTS_FEATURE_S3; #endif #ifdef ENABLE_GCS feat |= HTS_FEATURE_GCS; #endif #ifdef HAVE_LIBDEFLATE feat |= HTS_FEATURE_LIBDEFLATE; #endif #ifdef HAVE_LIBLZMA feat |= HTS_FEATURE_LZMA; #endif #ifdef HAVE_LIBBZ2 feat |= HTS_FEATURE_BZIP2; #endif return feat; } const char *hts_test_feature(unsigned int id) { unsigned int feat = hts_features(); switch (id) { case HTS_FEATURE_CONFIGURE: return feat & HTS_FEATURE_CONFIGURE ? "yes" : NULL; case HTS_FEATURE_PLUGINS: return feat & HTS_FEATURE_PLUGINS ? "yes" : NULL; case HTS_FEATURE_LIBCURL: return feat & HTS_FEATURE_LIBCURL ? "yes" : NULL; case HTS_FEATURE_S3: return feat & HTS_FEATURE_S3 ? "yes" : NULL; case HTS_FEATURE_GCS: return feat & HTS_FEATURE_GCS ? "yes" : NULL; case HTS_FEATURE_LIBDEFLATE: return feat & HTS_FEATURE_LIBDEFLATE ? "yes" : NULL; case HTS_FEATURE_BZIP2: return feat & HTS_FEATURE_BZIP2 ? "yes" : NULL; case HTS_FEATURE_LZMA: return feat & HTS_FEATURE_LZMA ? "yes" : NULL; case HTS_FEATURE_HTSCODECS: return htscodecs_version(); case HTS_FEATURE_CC: return HTS_CC; case HTS_FEATURE_CFLAGS: return HTS_CFLAGS; case HTS_FEATURE_LDFLAGS: return HTS_LDFLAGS; case HTS_FEATURE_CPPFLAGS: return HTS_CPPFLAGS; default: fprintf(stderr, "Unknown feature code: %u\n", id); } return NULL; } // Note this implementation also means we can just "strings" the library // to find the configuration parameters. const char *hts_feature_string(void) { static char config[1200]; const char *flags= #ifdef PACKAGE_URL "build=configure " #else "build=Makefile " #endif #ifdef HAVE_LIBCURL "libcurl=yes " #else "libcurl=no " #endif #ifdef ENABLE_S3 "S3=yes " #else "S3=no " #endif #ifdef ENABLE_GCS "GCS=yes " #else "GCS=no " #endif #ifdef HAVE_LIBDEFLATE "libdeflate=yes " #else "libdeflate=no " #endif #ifdef HAVE_LIBLZMA "lzma=yes " #else "lzma=no " #endif #ifdef HAVE_LIBBZ2 "bzip2=yes " #else "bzip2=no " #endif // "plugins=" must stay at the end as it is followed by "plugin-path=" #ifdef ENABLE_PLUGINS "plugins=yes"; #else "plugins=no"; #endif #ifdef ENABLE_PLUGINS snprintf(config, sizeof(config), "%s plugin-path=%.1000s htscodecs=%.40s", flags, hts_plugin_path(), htscodecs_version()); #else snprintf(config, sizeof(config), "%s htscodecs=%.40s", flags, htscodecs_version()); #endif return config; } HTSLIB_EXPORT const unsigned char seq_nt16_table[256] = { 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15, 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15, 15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15, 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15, 15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15 }; HTSLIB_EXPORT const char seq_nt16_str[] = "=ACMGRSVTWYHKDBN"; HTSLIB_EXPORT const int seq_nt16_int[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 }; /********************** *** Basic file I/O *** **********************/ static enum htsFormatCategory format_category(enum htsExactFormat fmt) { switch (fmt) { case bam: case sam: case cram: case fastq_format: case fasta_format: return sequence_data; case vcf: case bcf: return variant_data; case bai: case crai: case csi: case fai_format: case fqi_format: case gzi: case tbi: return index_file; case bed: case d4_format: return region_list; case htsget: case hts_crypt4gh_format: return unknown_category; case unknown_format: case binary_format: case text_format: case empty_format: case format_maximum: break; } return unknown_category; } // Decompress several hundred bytes by peeking at the file, which must be // positioned at the start of a GZIP block. static ssize_t decompress_peek_gz(hFILE *fp, unsigned char *dest, size_t destsize) { unsigned char buffer[2048]; z_stream zs; ssize_t npeek = hpeek(fp, buffer, sizeof buffer); if (npeek < 0) return -1; zs.zalloc = NULL; zs.zfree = NULL; zs.next_in = buffer; zs.avail_in = npeek; zs.next_out = dest; zs.avail_out = destsize; if (inflateInit2(&zs, 31) != Z_OK) return -1; int ret; const unsigned char *last_in = buffer; while (zs.avail_out > 0) { ret = inflate(&zs, Z_SYNC_FLUSH); if (ret == Z_STREAM_END) { if (last_in == zs.next_in) break; // Paranoia to avoid potential looping. Shouldn't happen else last_in = zs.next_in; inflateReset(&zs); } else if (ret != Z_OK) { // eg Z_BUF_ERROR due to avail_in/out becoming zero break; } } // NB: zs.total_out is changed by inflateReset, so use pointer diff instead destsize = zs.next_out - dest; inflateEnd(&zs); return destsize; } #ifdef HAVE_LIBLZMA // Similarly decompress a portion by peeking at the file, which must be // positioned at the start of the file. static ssize_t decompress_peek_xz(hFILE *fp, unsigned char *dest, size_t destsize) { unsigned char buffer[2048]; ssize_t npeek = hpeek(fp, buffer, sizeof buffer); if (npeek < 0) return -1; lzma_stream ls = LZMA_STREAM_INIT; if (lzma_stream_decoder(&ls, lzma_easy_decoder_memusage(9), 0) != LZMA_OK) return -1; ls.next_in = buffer; ls.avail_in = npeek; ls.next_out = dest; ls.avail_out = destsize; int r = lzma_code(&ls, LZMA_RUN); if (! (r == LZMA_OK || r == LZMA_STREAM_END)) { lzma_end(&ls); return -1; } destsize = ls.total_out; lzma_end(&ls); return destsize; } #endif // Parse "x.y" text, taking care because the string is not NUL-terminated // and filling in major/minor only when the digits are followed by a delimiter, // so we don't misread "1.10" as "1.1" due to reaching the end of the buffer. static void parse_version(htsFormat *fmt, const unsigned char *u, const unsigned char *ulim) { const char *s = (const char *) u; const char *slim = (const char *) ulim; short v; fmt->version.major = fmt->version.minor = -1; for (v = 0; s < slim && isdigit_c(*s); s++) v = 10 * v + *s - '0'; if (s < slim) { fmt->version.major = v; if (*s == '.') { s++; for (v = 0; s < slim && isdigit_c(*s); s++) v = 10 * v + *s - '0'; if (s < slim) fmt->version.minor = v; } else fmt->version.minor = 0; } } static int cmp_nonblank(const char *key, const unsigned char *u, const unsigned char *ulim) { const unsigned char *ukey = (const unsigned char *) key; while (*ukey) if (u >= ulim) return +1; else if (isspace_c(*u)) u++; else if (*u != *ukey) return (*ukey < *u)? -1 : +1; else u++, ukey++; return 0; } static int is_text_only(const unsigned char *u, const unsigned char *ulim) { for (; u < ulim; u++) if (! (*u >= ' ' || *u == '\t' || *u == '\r' || *u == '\n')) return 0; return 1; } static inline int alternate_zeros(const unsigned char *u, const unsigned char *ulim) { for (; u < ulim; u += 2) if (*u != '\0') return 0; return 1; } static int is_utf16_text(const unsigned char *u, const unsigned char *ulim) { if (ulim - u >= 6 && ((u[0] == 0xfe && u[1] == 0xff && alternate_zeros(u+2, ulim)) || (u[0] == 0xff && u[1] == 0xfe && alternate_zeros(u+3, ulim)))) return 2; else if (ulim - u >= 8 && (alternate_zeros(u, ulim) || alternate_zeros(u+1, ulim))) return 1; else return 0; } static int is_fastaq(const unsigned char *u, const unsigned char *ulim) { const unsigned char *eol = memchr(u, '\n', ulim - u); // Check that the first line is entirely textual if (! is_text_only(u, eol? eol : ulim)) return 0; // If the first line is very long, consider the file to indeed be FASTA/Q if (eol == NULL) return 1; u = eol+1; // Now points to the first character of the second line // Scan over all base-encoding letters (including 'N' but not SEQ's '=') while (u < ulim && (seq_nt16_table[*u] != 15 || toupper(*u) == 'N')) { if (*u == '=') return 0; u++; } return (u == ulim || *u == '\r' || *u == '\n')? 1 : 0; } // Parse tab-delimited text, filling in a string of column types and returning // the number of columns spotted (within [u,ulim), and up to column_len) or -1 // if non-printable characters were seen. Column types: // i: integer, s: strand sign, C: CIGAR, O: SAM optional field, Z: anything static int parse_tabbed_text(char *columns, int column_len, const unsigned char *u, const unsigned char *ulim, int *complete) { const char *str = (const char *) u; const char *slim = (const char *) ulim; const char *s; int ncolumns = 0; enum { digit = 1, leading_sign = 2, cigar_operator = 4, other = 8 }; unsigned seen = 0; *complete = 0; for (s = str; s < slim; s++) if (*s >= ' ') { if (isdigit_c(*s)) seen |= digit; else if ((*s == '+' || *s == '-') && s == str) seen |= leading_sign; else if (strchr(BAM_CIGAR_STR, *s) && s > str && isdigit_c(s[-1])) seen |= cigar_operator; else seen |= other; } else if (*s == '\t' || *s == '\r' || *s == '\n') { size_t len = s - str; char type; if (seen == digit || seen == (leading_sign|digit)) type = 'i'; else if (seen == (digit|cigar_operator)) type = 'C'; else if (len == 1) switch (str[0]) { case '*': type = 'C'; break; case '+': case '-': case '.': type = 's'; break; default: type = 'Z'; break; } else if (len >= 5 && str[2] == ':' && str[4] == ':') type = 'O'; else type = 'Z'; columns[ncolumns++] = type; if (*s != '\t' || ncolumns >= column_len - 1) { *complete = 1; // finished the line or more columns than needed break; } str = s + 1; seen = 0; } else return -1; columns[ncolumns] = '\0'; return ncolumns; } // Match COLUMNS as a prefix against PATTERN (so COLUMNS may run out first). // Returns len(COLUMNS) (modulo '+'), or 0 if there is a mismatched entry. static int colmatch(const char *columns, const char *pattern) { int i; for (i = 0; columns[i] != '\0'; i++) { if (pattern[i] == '+') return i; if (! (columns[i] == pattern[i] || pattern[i] == 'Z')) return 0; } return i; } int hts_detect_format(hFILE *hfile, htsFormat *fmt) { return hts_detect_format2(hfile, NULL, fmt); } int hts_detect_format2(hFILE *hfile, const char *fname, htsFormat *fmt) { char extension[HTS_MAX_EXT_LEN], columns[24]; unsigned char s[1024]; int complete = 0; ssize_t len = hpeek(hfile, s, 18); if (len < 0) return -1; fmt->category = unknown_category; fmt->format = unknown_format; fmt->version.major = fmt->version.minor = -1; fmt->compression = no_compression; fmt->compression_level = -1; fmt->specific = NULL; if (len >= 2 && s[0] == 0x1f && s[1] == 0x8b) { // The stream is either gzip-compressed or BGZF-compressed. // Determine which, and decompress the first few records or lines. fmt->compression = gzip; if (len >= 18 && (s[3] & 4)) { if (memcmp(&s[12], "BC\2\0", 4) == 0) fmt->compression = bgzf; else if (memcmp(&s[12], "RAZF", 4) == 0) fmt->compression = razf_compression; } if (len >= 9 && s[2] == 8) fmt->compression_level = (s[8] == 2)? 9 : (s[8] == 4)? 1 : -1; len = decompress_peek_gz(hfile, s, sizeof s); } else if (len >= 10 && memcmp(s, "BZh", 3) == 0 && (memcmp(&s[4], "\x31\x41\x59\x26\x53\x59", 6) == 0 || memcmp(&s[4], "\x17\x72\x45\x38\x50\x90", 6) == 0)) { fmt->compression = bzip2_compression; fmt->compression_level = s[3] - '0'; // Decompressing via libbz2 produces no output until it has a whole // block (of size 100Kb x level), which is too large for peeking. // So unfortunately we can recognise bzip2 but not the contents, // except that \x1772... magic indicates the stream is empty. if (s[4] == '\x31') return 0; else len = 0; } else if (len >= 6 && memcmp(s, "\xfd""7zXZ\0", 6) == 0) { fmt->compression = xz_compression; #ifdef HAVE_LIBLZMA len = decompress_peek_xz(hfile, s, sizeof s); #else // Without liblzma, we can't recognise the decompressed contents. return 0; #endif } else if (len >= 4 && memcmp(s, "\x28\xb5\x2f\xfd", 4) == 0) { fmt->compression = zstd_compression; return 0; } else { len = hpeek(hfile, s, sizeof s); } if (len < 0) return -1; if (len == 0) { fmt->format = empty_format; return 0; } // We avoid using filename extensions wherever possible (as filenames are // not always available), but in a few cases they must be considered: // - FASTA/Q indexes are simply tab-separated text; files that match these // patterns but not the fai/fqi extension are usually generic BED files // - GZI indexes have no magic numbers so can only be detected by filename if (fname && strcmp(fname, "-") != 0) { char *s; if (find_file_extension(fname, extension) < 0) extension[0] = '\0'; for (s = extension; *s; s++) *s = tolower_c(*s); } else extension[0] = '\0'; if (len >= 6 && memcmp(s,"CRAM",4) == 0 && s[4]>=1 && s[4]<=7 && s[5]<=7) { fmt->category = sequence_data; fmt->format = cram; fmt->version.major = s[4], fmt->version.minor = s[5]; fmt->compression = custom; return 0; } else if (len >= 4 && s[3] <= '\4') { if (memcmp(s, "BAM\1", 4) == 0) { fmt->category = sequence_data; fmt->format = bam; // TODO Decompress enough to pick version from @HD-VN header fmt->version.major = 1, fmt->version.minor = -1; return 0; } else if (memcmp(s, "BAI\1", 4) == 0) { fmt->category = index_file; fmt->format = bai; fmt->version.major = -1, fmt->version.minor = -1; return 0; } else if (memcmp(s, "BCF\4", 4) == 0) { fmt->category = variant_data; fmt->format = bcf; fmt->version.major = 1, fmt->version.minor = -1; return 0; } else if (memcmp(s, "BCF\2", 4) == 0) { fmt->category = variant_data; fmt->format = bcf; fmt->version.major = s[3]; fmt->version.minor = (len >= 5 && s[4] <= 2)? s[4] : 0; return 0; } else if (memcmp(s, "CSI\1", 4) == 0) { fmt->category = index_file; fmt->format = csi; fmt->version.major = 1, fmt->version.minor = -1; return 0; } else if (memcmp(s, "TBI\1", 4) == 0) { fmt->category = index_file; fmt->format = tbi; return 0; } // GZI indexes have no magic numbers, so must be recognised solely by // filename extension. else if (strcmp(extension, "gzi") == 0) { fmt->category = index_file; fmt->format = gzi; return 0; } } else if (len >= 16 && memcmp(s, "##fileformat=VCF", 16) == 0) { fmt->category = variant_data; fmt->format = vcf; if (len >= 21 && s[16] == 'v') parse_version(fmt, &s[17], &s[len]); return 0; } else if (len >= 4 && s[0] == '@' && (memcmp(s, "@HD\t", 4) == 0 || memcmp(s, "@SQ\t", 4) == 0 || memcmp(s, "@RG\t", 4) == 0 || memcmp(s, "@PG\t", 4) == 0 || memcmp(s, "@CO\t", 4) == 0)) { fmt->category = sequence_data; fmt->format = sam; // @HD-VN is not guaranteed to be the first tag, but then @HD is // not guaranteed to be present at all... if (len >= 9 && memcmp(s, "@HD\tVN:", 7) == 0) parse_version(fmt, &s[7], &s[len]); else fmt->version.major = 1, fmt->version.minor = -1; return 0; } else if (len >= 8 && memcmp(s, "d4\xdd\xdd", 4) == 0) { fmt->category = region_list; fmt->format = d4_format; // How to decode the D4 Format Version bytes is not yet specified // so we don't try to set fmt->version.{major,minor}. return 0; } else if (cmp_nonblank("{\"htsget\":", s, &s[len]) == 0) { fmt->category = unknown_category; fmt->format = htsget; return 0; } else if (len > 8 && memcmp(s, "crypt4gh", 8) == 0) { fmt->category = unknown_category; fmt->format = hts_crypt4gh_format; return 0; } else if (len >= 1 && s[0] == '>' && is_fastaq(s, &s[len])) { fmt->category = sequence_data; fmt->format = fasta_format; return 0; } else if (len >= 1 && s[0] == '@' && is_fastaq(s, &s[len])) { fmt->category = sequence_data; fmt->format = fastq_format; return 0; } else if (parse_tabbed_text(columns, sizeof columns, s, &s[len], &complete) > 0) { // A complete SAM line is at least 11 columns. On unmapped long reads may // be missing two. (On mapped long reads we must have an @ header so long // CIGAR is irrelevant.) if (colmatch(columns, "ZiZiiCZiiZZOOOOOOOOOOOOOOOOOOOO+") >= 9 + 2*complete) { fmt->category = sequence_data; fmt->format = sam; fmt->version.major = 1, fmt->version.minor = -1; return 0; } else if (fmt->compression == gzip && colmatch(columns, "iiiiii") == 6) { fmt->category = index_file; fmt->format = crai; return 0; } else if (strstr(extension, "fqi") && colmatch(columns, "Ziiiii") == 6) { fmt->category = index_file; fmt->format = fqi_format; return 0; } else if (strstr(extension, "fai") && colmatch(columns, "Ziiii") == 5) { fmt->category = index_file; fmt->format = fai_format; return 0; } else if (colmatch(columns, "Zii+") >= 3) { fmt->category = region_list; fmt->format = bed; return 0; } } // Arbitrary text files can be read using hts_getline(). if (is_text_only(s, &s[len])) fmt->format = text_format; // Nothing recognised: leave unset fmt-> fields as unknown. return 0; } char *hts_format_description(const htsFormat *format) { kstring_t str = { 0, 0, NULL }; switch (format->format) { case sam: kputs("SAM", &str); break; case bam: kputs("BAM", &str); break; case cram: kputs("CRAM", &str); break; case fasta_format: kputs("FASTA", &str); break; case fastq_format: kputs("FASTQ", &str); break; case vcf: kputs("VCF", &str); break; case bcf: if (format->version.major == 1) kputs("Legacy BCF", &str); else kputs("BCF", &str); break; case bai: kputs("BAI", &str); break; case crai: kputs("CRAI", &str); break; case csi: kputs("CSI", &str); break; case fai_format: kputs("FASTA-IDX", &str); break; case fqi_format: kputs("FASTQ-IDX", &str); break; case gzi: kputs("GZI", &str); break; case tbi: kputs("Tabix", &str); break; case bed: kputs("BED", &str); break; case d4_format: kputs("D4", &str); break; case htsget: kputs("htsget", &str); break; case hts_crypt4gh_format: kputs("crypt4gh", &str); break; case empty_format: kputs("empty", &str); break; default: kputs("unknown", &str); break; } if (format->version.major >= 0) { kputs(" version ", &str); kputw(format->version.major, &str); if (format->version.minor >= 0) { kputc('.', &str); kputw(format->version.minor, &str); } } switch (format->compression) { case bzip2_compression: kputs(" bzip2-compressed", &str); break; case razf_compression: kputs(" legacy-RAZF-compressed", &str); break; case xz_compression: kputs(" XZ-compressed", &str); break; case zstd_compression: kputs(" Zstandard-compressed", &str); break; case custom: kputs(" compressed", &str); break; case gzip: kputs(" gzip-compressed", &str); break; case bgzf: switch (format->format) { case bam: case bcf: case csi: case tbi: // These are by definition BGZF, so just use the generic term kputs(" compressed", &str); break; default: kputs(" BGZF-compressed", &str); break; } break; case no_compression: switch (format->format) { case bam: case bcf: case cram: case csi: case tbi: // These are normally compressed, so emphasise that this one isn't kputs(" uncompressed", &str); break; default: break; } break; default: break; } switch (format->category) { case sequence_data: kputs(" sequence", &str); break; case variant_data: kputs(" variant calling", &str); break; case index_file: kputs(" index", &str); break; case region_list: kputs(" genomic region", &str); break; default: break; } if (format->compression == no_compression) switch (format->format) { case text_format: case sam: case crai: case vcf: case bed: case fai_format: case fqi_format: case fasta_format: case fastq_format: case htsget: kputs(" text", &str); break; case empty_format: break; default: kputs(" data", &str); break; } else kputs(" data", &str); return ks_release(&str); } htsFile *hts_open_format(const char *fn, const char *mode, const htsFormat *fmt) { char smode[101], *cp, *cp2, *mode_c, *uncomp = NULL; htsFile *fp = NULL; hFILE *hfile = NULL; char fmt_code = '\0'; // see enum htsExactFormat in htslib/hts.h const char format_to_mode[] = "\0g\0\0b\0c\0\0b\0g\0\0\0\0\0Ff\0\0"; strncpy(smode, mode, 99); smode[99]=0; if ((cp = strchr(smode, ','))) *cp = '\0'; // Migrate format code (b or c) to the end of the smode buffer. for (cp2 = cp = smode; *cp; cp++) { if (*cp == 'b') fmt_code = 'b'; else if (*cp == 'c') fmt_code = 'c'; else { *cp2++ = *cp; // Cache the uncompress flag 'u' pos if present if (!uncomp && (*cp == 'u')) { uncomp = cp2 - 1; } } } mode_c = cp2; *cp2++ = fmt_code; *cp2++ = 0; // Set or reset the format code if opts->format is used if (fmt && fmt->format > unknown_format && fmt->format < sizeof(format_to_mode)) { *mode_c = format_to_mode[fmt->format]; } // Uncompressed bam/bcf is not supported, change 'u' to '0' on write if (uncomp && *mode_c == 'b' && (strchr(smode, 'w') || strchr(smode, 'a'))) { *uncomp = '0'; } // If we really asked for a compressed text format then mode_c above will // point to nul. We set to 'z' to enable bgzf. if (strchr(mode, 'w') && fmt && fmt->compression == bgzf) { if (fmt->format == sam || fmt->format == vcf || fmt->format == text_format) *mode_c = 'z'; } char *rmme = NULL, *fnidx = strstr(fn, HTS_IDX_DELIM); if ( fnidx ) { rmme = strdup(fn); if ( !rmme ) goto error; rmme[fnidx-fn] = 0; fn = rmme; } hfile = hopen(fn, smode); if (hfile == NULL) goto error; fp = hts_hopen(hfile, fn, smode); if (fp == NULL) goto error; // Compensate for the loss of exactness in htsExactFormat. // hts_hopen returns generics such as binary or text, but we // have been given something explicit here so use that instead. if (fp->is_write && fmt && (fmt->format == bam || fmt->format == sam || fmt->format == vcf || fmt->format == bcf || fmt->format == bed || fmt->format == fasta_format || fmt->format == fastq_format)) fp->format.format = fmt->format; if (fmt && fmt->specific) { if (hts_opt_apply(fp, fmt->specific) != 0) { if (((hts_opt*)fmt->specific)->opt == CRAM_OPT_REFERENCE && (errno == ENOENT || errno == EIO || errno == EBADF || errno == EACCES || errno == EISDIR)) { /* error during reference file operation for these specific errors, set the error as EINVAL */ errno = EINVAL; } goto error; } } if ( rmme ) free(rmme); return fp; error: hts_log_error("Failed to open file \"%s\"%s%s", fn, errno ? " : " : "", errno ? strerror(errno) : ""); if ( rmme ) free(rmme); if (hfile) hclose_abruptly(hfile); return NULL; } htsFile *hts_open(const char *fn, const char *mode) { return hts_open_format(fn, mode, NULL); } /* * Splits str into a prefix, delimiter ('\0' or delim), and suffix, writing * the prefix in lowercase into buf and returning a pointer to the suffix. * On return, buf is always NUL-terminated; thus assumes that the "keyword" * prefix should be one of several known values of maximum length buflen-2. * (If delim is not found, returns a pointer to the '\0'.) */ static const char * scan_keyword(const char *str, char delim, char *buf, size_t buflen) { size_t i = 0; while (*str && *str != delim) { if (i < buflen-1) buf[i++] = tolower_c(*str); str++; } buf[i] = '\0'; return *str? str+1 : str; } /* * Parses arg and appends it to the option list. * * Returns 0 on success; * -1 on failure. */ int hts_opt_add(hts_opt **opts, const char *c_arg) { hts_opt *o, *t; char *val; /* * IMPORTANT!!! * If you add another string option here, don't forget to also add * it to the case statement in hts_opt_apply. */ if (!c_arg) return -1; if (!(o = malloc(sizeof(*o)))) return -1; if (!(o->arg = strdup(c_arg))) { free(o); return -1; } if (!(val = strchr(o->arg, '='))) val = "1"; // assume boolean else *val++ = '\0'; if (strcmp(o->arg, "decode_md") == 0 || strcmp(o->arg, "DECODE_MD") == 0) o->opt = CRAM_OPT_DECODE_MD, o->val.i = atoi(val); else if (strcmp(o->arg, "verbosity") == 0 || strcmp(o->arg, "VERBOSITY") == 0) o->opt = CRAM_OPT_VERBOSITY, o->val.i = atoi(val); else if (strcmp(o->arg, "seqs_per_slice") == 0 || strcmp(o->arg, "SEQS_PER_SLICE") == 0) o->opt = CRAM_OPT_SEQS_PER_SLICE, o->val.i = atoi(val); else if (strcmp(o->arg, "bases_per_slice") == 0 || strcmp(o->arg, "BASES_PER_SLICE") == 0) o->opt = CRAM_OPT_BASES_PER_SLICE, o->val.i = atoi(val); else if (strcmp(o->arg, "slices_per_container") == 0 || strcmp(o->arg, "SLICES_PER_CONTAINER") == 0) o->opt = CRAM_OPT_SLICES_PER_CONTAINER, o->val.i = atoi(val); else if (strcmp(o->arg, "embed_ref") == 0 || strcmp(o->arg, "EMBED_REF") == 0) o->opt = CRAM_OPT_EMBED_REF, o->val.i = atoi(val); else if (strcmp(o->arg, "no_ref") == 0 || strcmp(o->arg, "NO_REF") == 0) o->opt = CRAM_OPT_NO_REF, o->val.i = atoi(val); else if (strcmp(o->arg, "pos_delta") == 0 || strcmp(o->arg, "POS_DELTA") == 0) o->opt = CRAM_OPT_POS_DELTA, o->val.i = atoi(val); else if (strcmp(o->arg, "ignore_md5") == 0 || strcmp(o->arg, "IGNORE_MD5") == 0) o->opt = CRAM_OPT_IGNORE_MD5, o->val.i = atoi(val); else if (strcmp(o->arg, "use_bzip2") == 0 || strcmp(o->arg, "USE_BZIP2") == 0) o->opt = CRAM_OPT_USE_BZIP2, o->val.i = atoi(val); else if (strcmp(o->arg, "use_rans") == 0 || strcmp(o->arg, "USE_RANS") == 0) o->opt = CRAM_OPT_USE_RANS, o->val.i = atoi(val); else if (strcmp(o->arg, "use_lzma") == 0 || strcmp(o->arg, "USE_LZMA") == 0) o->opt = CRAM_OPT_USE_LZMA, o->val.i = atoi(val); else if (strcmp(o->arg, "use_tok") == 0 || strcmp(o->arg, "USE_TOK") == 0) o->opt = CRAM_OPT_USE_TOK, o->val.i = atoi(val); else if (strcmp(o->arg, "use_fqz") == 0 || strcmp(o->arg, "USE_FQZ") == 0) o->opt = CRAM_OPT_USE_FQZ, o->val.i = atoi(val); else if (strcmp(o->arg, "use_arith") == 0 || strcmp(o->arg, "USE_ARITH") == 0) o->opt = CRAM_OPT_USE_ARITH, o->val.i = atoi(val); else if (strcmp(o->arg, "fast") == 0 || strcmp(o->arg, "FAST") == 0) o->opt = HTS_OPT_PROFILE, o->val.i = HTS_PROFILE_FAST; else if (strcmp(o->arg, "normal") == 0 || strcmp(o->arg, "NORMAL") == 0) o->opt = HTS_OPT_PROFILE, o->val.i = HTS_PROFILE_NORMAL; else if (strcmp(o->arg, "small") == 0 || strcmp(o->arg, "SMALL") == 0) o->opt = HTS_OPT_PROFILE, o->val.i = HTS_PROFILE_SMALL; else if (strcmp(o->arg, "archive") == 0 || strcmp(o->arg, "ARCHIVE") == 0) o->opt = HTS_OPT_PROFILE, o->val.i = HTS_PROFILE_ARCHIVE; else if (strcmp(o->arg, "reference") == 0 || strcmp(o->arg, "REFERENCE") == 0) o->opt = CRAM_OPT_REFERENCE, o->val.s = val; else if (strcmp(o->arg, "version") == 0 || strcmp(o->arg, "VERSION") == 0) o->opt = CRAM_OPT_VERSION, o->val.s =val; else if (strcmp(o->arg, "multi_seq_per_slice") == 0 || strcmp(o->arg, "MULTI_SEQ_PER_SLICE") == 0) o->opt = CRAM_OPT_MULTI_SEQ_PER_SLICE, o->val.i = atoi(val); else if (strcmp(o->arg, "nthreads") == 0 || strcmp(o->arg, "NTHREADS") == 0) o->opt = HTS_OPT_NTHREADS, o->val.i = atoi(val); else if (strcmp(o->arg, "cache_size") == 0 || strcmp(o->arg, "CACHE_SIZE") == 0) { char *endp; o->opt = HTS_OPT_CACHE_SIZE; o->val.i = strtol(val, &endp, 0); // NB: Doesn't support floats, eg 1.5g // TODO: extend hts_parse_decimal? See also samtools sort. switch (*endp) { case 'g': case 'G': o->val.i *= 1024; // fall through case 'm': case 'M': o->val.i *= 1024; // fall through case 'k': case 'K': o->val.i *= 1024; break; case '\0': break; default: hts_log_error("Unrecognised cache size suffix '%c'", *endp); free(o->arg); free(o); return -1; } } else if (strcmp(o->arg, "required_fields") == 0 || strcmp(o->arg, "REQUIRED_FIELDS") == 0) o->opt = CRAM_OPT_REQUIRED_FIELDS, o->val.i = strtol(val, NULL, 0); else if (strcmp(o->arg, "lossy_names") == 0 || strcmp(o->arg, "LOSSY_NAMES") == 0) o->opt = CRAM_OPT_LOSSY_NAMES, o->val.i = strtol(val, NULL, 0); else if (strcmp(o->arg, "name_prefix") == 0 || strcmp(o->arg, "NAME_PREFIX") == 0) o->opt = CRAM_OPT_PREFIX, o->val.s = val; else if (strcmp(o->arg, "store_md") == 0 || strcmp(o->arg, "store_md") == 0) o->opt = CRAM_OPT_STORE_MD, o->val.i = atoi(val); else if (strcmp(o->arg, "store_nm") == 0 || strcmp(o->arg, "store_nm") == 0) o->opt = CRAM_OPT_STORE_NM, o->val.i = atoi(val); else if (strcmp(o->arg, "block_size") == 0 || strcmp(o->arg, "BLOCK_SIZE") == 0) o->opt = HTS_OPT_BLOCK_SIZE, o->val.i = strtol(val, NULL, 0); else if (strcmp(o->arg, "level") == 0 || strcmp(o->arg, "LEVEL") == 0) o->opt = HTS_OPT_COMPRESSION_LEVEL, o->val.i = strtol(val, NULL, 0); else if (strcmp(o->arg, "filter") == 0 || strcmp(o->arg, "FILTER") == 0) o->opt = HTS_OPT_FILTER, o->val.s = val; else if (strcmp(o->arg, "fastq_aux") == 0 || strcmp(o->arg, "FASTQ_AUX") == 0) o->opt = FASTQ_OPT_AUX, o->val.s = val; else if (strcmp(o->arg, "fastq_barcode") == 0 || strcmp(o->arg, "FASTQ_BARCODE") == 0) o->opt = FASTQ_OPT_BARCODE, o->val.s = val; else if (strcmp(o->arg, "fastq_rnum") == 0 || strcmp(o->arg, "FASTQ_RNUM") == 0) o->opt = FASTQ_OPT_RNUM, o->val.i = 1; else if (strcmp(o->arg, "fastq_casava") == 0 || strcmp(o->arg, "FASTQ_CASAVA") == 0) o->opt = FASTQ_OPT_CASAVA, o->val.i = 1; else if (strcmp(o->arg, "fastq_name2") == 0 || strcmp(o->arg, "FASTQ_NAME2") == 0) o->opt = FASTQ_OPT_NAME2, o->val.i = 1; else { hts_log_error("Unknown option '%s'", o->arg); free(o->arg); free(o); return -1; } o->next = NULL; // Append; assumes small list. if (*opts) { t = *opts; while (t->next) t = t->next; t->next = o; } else { *opts = o; } return 0; } /* * Applies an hts_opt option list to a given htsFile. * * Returns 0 on success * -1 on failure */ int hts_opt_apply(htsFile *fp, hts_opt *opts) { hts_opt *last = NULL; for (; opts; opts = (last=opts)->next) { switch (opts->opt) { case CRAM_OPT_REFERENCE: if (!(fp->fn_aux = strdup(opts->val.s))) return -1; // fall through case CRAM_OPT_VERSION: case CRAM_OPT_PREFIX: case HTS_OPT_FILTER: case FASTQ_OPT_AUX: case FASTQ_OPT_BARCODE: if (hts_set_opt(fp, opts->opt, opts->val.s) != 0) return -1; break; default: if (hts_set_opt(fp, opts->opt, opts->val.i) != 0) return -1; break; } } return 0; } /* * Frees an hts_opt list. */ void hts_opt_free(hts_opt *opts) { hts_opt *last = NULL; while (opts) { opts = (last=opts)->next; free(last->arg); free(last); } } /* * Tokenise options as (key(=value)?,)*(key(=value)?)? * NB: No provision for ',' appearing in the value! * Add backslashing rules? * * This could be used as part of a general command line option parser or * as a string concatenated onto the file open mode. * * Returns 0 on success * -1 on failure. */ int hts_parse_opt_list(htsFormat *fmt, const char *str) { while (str && *str) { const char *str_start; int len; char arg[8001]; while (*str && *str == ',') str++; for (str_start = str; *str && *str != ','; str++); len = str - str_start; // Produce a nul terminated copy of the option strncpy(arg, str_start, len < 8000 ? len : 8000); arg[len < 8000 ? len : 8000] = '\0'; if (hts_opt_add((hts_opt **)&fmt->specific, arg) != 0) return -1; if (*str) str++; } return 0; } /* * Accepts a string file format (sam, bam, cram, vcf, bam) optionally * followed by a comma separated list of key=value options and splits * these up into the fields of htsFormat struct. * * format is assumed to be already initialised, either to blank * "unknown" values or via previous hts_opt_add calls. * * Returns 0 on success * -1 on failure. */ int hts_parse_format(htsFormat *format, const char *str) { char fmt[9]; const char *cp = scan_keyword(str, ',', fmt, sizeof fmt); format->version.minor = 0; // unknown format->version.major = 0; // unknown if (strcmp(fmt, "sam") == 0) { format->category = sequence_data; format->format = sam; format->compression = no_compression; format->compression_level = 0; } else if (strcmp(fmt, "sam.gz") == 0) { format->category = sequence_data; format->format = sam; format->compression = bgzf; format->compression_level = -1; } else if (strcmp(fmt, "bam") == 0) { format->category = sequence_data; format->format = bam; format->compression = bgzf; format->compression_level = -1; } else if (strcmp(fmt, "cram") == 0) { format->category = sequence_data; format->format = cram; format->compression = custom; format->compression_level = -1; } else if (strcmp(fmt, "vcf") == 0) { format->category = variant_data; format->format = vcf; format->compression = no_compression; format->compression_level = 0; } else if (strcmp(fmt, "bcf") == 0) { format->category = variant_data; format->format = bcf; format->compression = bgzf; format->compression_level = -1; } else if (strcmp(fmt, "fastq") == 0 || strcmp(fmt, "fq") == 0) { format->category = sequence_data; format->format = fastq_format; format->compression = no_compression; format->compression_level = 0; } else if (strcmp(fmt, "fastq.gz") == 0 || strcmp(fmt, "fq.gz") == 0) { format->category = sequence_data; format->format = fastq_format; format->compression = bgzf; format->compression_level = 0; } else if (strcmp(fmt, "fasta") == 0 || strcmp(fmt, "fa") == 0) { format->category = sequence_data; format->format = fasta_format; format->compression = no_compression; format->compression_level = 0; } else if (strcmp(fmt, "fasta.gz") == 0 || strcmp(fmt, "fa.gz") == 0) { format->category = sequence_data; format->format = fasta_format; format->compression = bgzf; format->compression_level = 0; } else { return -1; } return hts_parse_opt_list(format, cp); } /* * Tokenise options as (key(=value)?,)*(key(=value)?)? * NB: No provision for ',' appearing in the value! * Add backslashing rules? * * This could be used as part of a general command line option parser or * as a string concatenated onto the file open mode. * * Returns 0 on success * -1 on failure. */ static int hts_process_opts(htsFile *fp, const char *opts) { htsFormat fmt; fmt.specific = NULL; if (hts_parse_opt_list(&fmt, opts) != 0) return -1; if (hts_opt_apply(fp, fmt.specific) != 0) { hts_opt_free(fmt.specific); return -1; } hts_opt_free(fmt.specific); return 0; } static int hts_crypt4gh_redirect(const char *fn, const char *mode, hFILE **hfile_ptr, htsFile *fp) { hFILE *hfile1 = *hfile_ptr; hFILE *hfile2 = NULL; char fn_buf[512], *fn2 = fn_buf; char mode2[102]; // Size set by sizeof(simple_mode) in hts_hopen() const char *prefix = "crypt4gh:"; size_t fn2_len = strlen(prefix) + strlen(fn) + 1; int ret = -1; if (fn2_len > sizeof(fn_buf)) { if (fn2_len >= INT_MAX) // Silence gcc format-truncation warning return -1; fn2 = malloc(fn2_len); if (!fn2) return -1; } // Reopen fn using the crypt4gh plug-in (if available) snprintf(fn2, fn2_len, "%s%s", prefix, fn); snprintf(mode2, sizeof(mode2), "%s%s", mode, strchr(mode, ':') ? "" : ":"); hfile2 = hopen(fn2, mode2, "parent", hfile1, NULL); if (hfile2) { // Replace original hfile with the new one. The original is now // enclosed within hfile2 *hfile_ptr = hfile2; ret = 0; } if (fn2 != fn_buf) free(fn2); return ret; } htsFile *hts_hopen(hFILE *hfile, const char *fn, const char *mode) { hFILE *hfile_orig = hfile; hFILE *hfile_cleanup = hfile; htsFile *fp = (htsFile*)calloc(1, sizeof(htsFile)); char simple_mode[101], *cp, *opts; simple_mode[100] = '\0'; if (fp == NULL) goto error; fp->fn = strdup(fn); fp->is_be = ed_is_big(); // Split mode into simple_mode,opts strings if ((cp = strchr(mode, ','))) { strncpy(simple_mode, mode, cp-mode <= 100 ? cp-mode : 100); simple_mode[cp-mode] = '\0'; opts = cp+1; } else { strncpy(simple_mode, mode, 100); opts = NULL; } if (strchr(simple_mode, 'r')) { const int max_loops = 5; // Should be plenty int loops = 0; if (hts_detect_format2(hfile, fn, &fp->format) < 0) goto error; // Deal with formats that re-direct an underlying file via a plug-in. // Loops as we may have crypt4gh served via htsget, or // crypt4gh-in-crypt4gh. while (fp->format.format == htsget || fp->format.format == hts_crypt4gh_format) { // Ensure we don't get stuck in an endless redirect loop if (++loops > max_loops) { errno = ELOOP; goto error; } if (fp->format.format == htsget) { hFILE *hfile2 = hopen_htsget_redirect(hfile, simple_mode); if (hfile2 == NULL) goto error; if (hfile != hfile_cleanup) { // Close the result of an earlier redirection hclose_abruptly(hfile); } hfile = hfile2; } else if (fp->format.format == hts_crypt4gh_format) { int should_preserve = (hfile == hfile_orig); int update_cleanup = (hfile == hfile_cleanup); if (hts_crypt4gh_redirect(fn, simple_mode, &hfile, fp) < 0) goto error; if (should_preserve) { // The original hFILE is now contained in a crypt4gh // wrapper. Should we need to close the wrapper due // to a later error, we need to prevent the wrapped // handle from being closed as the caller will see // this function return NULL and try to clean up itself. hfile_orig->preserve = 1; } if (update_cleanup) { // Update handle to close at the end if redirected by htsget hfile_cleanup = hfile; } } // Re-detect format against the result of the redirection if (hts_detect_format2(hfile, fn, &fp->format) < 0) goto error; } } else if (strchr(simple_mode, 'w') || strchr(simple_mode, 'a')) { htsFormat *fmt = &fp->format; fp->is_write = 1; if (strchr(simple_mode, 'b')) fmt->format = binary_format; else if (strchr(simple_mode, 'c')) fmt->format = cram; else if (strchr(simple_mode, 'f')) fmt->format = fastq_format; else if (strchr(simple_mode, 'F')) fmt->format = fasta_format; else fmt->format = text_format; if (strchr(simple_mode, 'z')) fmt->compression = bgzf; else if (strchr(simple_mode, 'g')) fmt->compression = gzip; else if (strchr(simple_mode, 'u')) fmt->compression = no_compression; else { // No compression mode specified, set to the default for the format switch (fmt->format) { case binary_format: fmt->compression = bgzf; break; case cram: fmt->compression = custom; break; case fastq_format: fmt->compression = no_compression; break; case fasta_format: fmt->compression = no_compression; break; case text_format: fmt->compression = no_compression; break; default: abort(); } } // Fill in category (if determinable; e.g. 'b' could be BAM or BCF) fmt->category = format_category(fmt->format); fmt->version.major = fmt->version.minor = -1; fmt->compression_level = -1; fmt->specific = NULL; } else { errno = EINVAL; goto error; } switch (fp->format.format) { case binary_format: case bam: case bcf: fp->fp.bgzf = bgzf_hopen(hfile, simple_mode); if (fp->fp.bgzf == NULL) goto error; fp->is_bin = fp->is_bgzf = 1; break; case cram: fp->fp.cram = cram_dopen(hfile, fn, simple_mode); if (fp->fp.cram == NULL) goto error; if (!fp->is_write) cram_set_option(fp->fp.cram, CRAM_OPT_DECODE_MD, -1); // auto fp->is_cram = 1; break; case empty_format: case text_format: case bed: case fasta_format: case fastq_format: case sam: case vcf: if (fp->format.compression != no_compression) { fp->fp.bgzf = bgzf_hopen(hfile, simple_mode); if (fp->fp.bgzf == NULL) goto error; fp->is_bgzf = 1; } else fp->fp.hfile = hfile; break; default: errno = EFTYPE; goto error; } if (opts) hts_process_opts(fp, opts); // Allow original file to close if it was preserved earlier by crypt4gh hfile_orig->preserve = 0; // If redirecting via htsget, close the original hFILE now (pedantically // we would instead close it in hts_close(), but this a simplifying // optimisation) if (hfile != hfile_cleanup) hclose_abruptly(hfile_cleanup); return fp; error: hts_log_error("Failed to open file %s", fn); // If redirecting, close the failed redirection hFILE that we have opened if (hfile != hfile_orig) hclose_abruptly(hfile); hfile_orig->preserve = 0; // Allow caller to close the original hfile if (fp) { free(fp->fn); free(fp->fn_aux); free(fp); } return NULL; } static int hts_idx_close_otf_fp(hts_idx_t *idx); int hts_close(htsFile *fp) { int ret = 0, save; if (!fp) { errno = EINVAL; return -1; } switch (fp->format.format) { case binary_format: case bam: case bcf: ret = bgzf_close(fp->fp.bgzf); break; case cram: if (!fp->is_write) { switch (cram_eof(fp->fp.cram)) { case 2: hts_log_warning("EOF marker is absent. The input is probably truncated"); break; case 0: /* not at EOF, but may not have wanted all seqs */ default: /* case 1, expected EOF */ break; } } ret = cram_close(fp->fp.cram); break; case empty_format: case text_format: case bed: case fasta_format: case fastq_format: case sam: case vcf: if (fp->format.format == sam) ret = sam_state_destroy(fp); else if (fp->format.format == fastq_format || fp->format.format == fasta_format) fastq_state_destroy(fp); if (fp->format.compression != no_compression) ret |= bgzf_close(fp->fp.bgzf); else ret |= hclose(fp->fp.hfile); break; default: ret = -1; break; } if (fp->idx) { // Close deferred index file handle, if present. // Unfortunately this means errors on the index will get mixed with // those on the main file, but as we only have the EOF block left to // write it hopefully won't happen that often. ret |= hts_idx_close_otf_fp(fp->idx); } save = errno; sam_hdr_destroy(fp->bam_header); hts_idx_destroy(fp->idx); hts_filter_free(fp->filter); free(fp->fn); free(fp->fn_aux); free(fp->line.s); free(fp); errno = save; return ret; } int hts_flush(htsFile *fp) { if (fp == NULL) return 0; switch (fp->format.format) { case binary_format: case bam: case bcf: return bgzf_flush(fp->fp.bgzf); case cram: return cram_flush(fp->fp.cram); case empty_format: case text_format: case bed: case fasta_format: case fastq_format: case sam: case vcf: if (fp->format.compression != no_compression) return bgzf_flush(fp->fp.bgzf); else return hflush(fp->fp.hfile); default: break; } return 0; } const htsFormat *hts_get_format(htsFile *fp) { return fp? &fp->format : NULL; } const char *hts_format_file_extension(const htsFormat *format) { if (!format) return "?"; switch (format->format) { case sam: return "sam"; case bam: return "bam"; case bai: return "bai"; case cram: return "cram"; case crai: return "crai"; case vcf: return "vcf"; case bcf: return "bcf"; case csi: return "csi"; case fai_format: return "fai"; case fqi_format: return "fqi"; case gzi: return "gzi"; case tbi: return "tbi"; case bed: return "bed"; case d4_format: return "d4"; case fasta_format: return "fa"; case fastq_format: return "fq"; default: return "?"; } } static hFILE *hts_hfile(htsFile *fp) { switch (fp->format.format) { case binary_format:// fall through case bcf: // fall through case bam: return bgzf_hfile(fp->fp.bgzf); case cram: return cram_hfile(fp->fp.cram); case text_format: // fall through case vcf: // fall through case fastq_format: // fall through case fasta_format: // fall through case sam: return fp->format.compression != no_compression ? bgzf_hfile(fp->fp.bgzf) : fp->fp.hfile; default: return NULL; } } int hts_set_opt(htsFile *fp, enum hts_fmt_option opt, ...) { int r; va_list args; switch (opt) { case HTS_OPT_NTHREADS: { va_start(args, opt); int nthreads = va_arg(args, int); va_end(args); return hts_set_threads(fp, nthreads); } case HTS_OPT_BLOCK_SIZE: { hFILE *hf = hts_hfile(fp); if (hf) { va_start(args, opt); if (hfile_set_blksize(hf, va_arg(args, int)) != 0) hts_log_warning("Failed to change block size"); va_end(args); } else { // To do - implement for vcf/bcf. hts_log_warning("Cannot change block size for this format"); } return 0; } case HTS_OPT_THREAD_POOL: { va_start(args, opt); htsThreadPool *p = va_arg(args, htsThreadPool *); va_end(args); return hts_set_thread_pool(fp, p); } case HTS_OPT_CACHE_SIZE: { va_start(args, opt); int cache_size = va_arg(args, int); va_end(args); hts_set_cache_size(fp, cache_size); return 0; } case FASTQ_OPT_CASAVA: case FASTQ_OPT_RNUM: case FASTQ_OPT_NAME2: if (fp->format.format == fastq_format || fp->format.format == fasta_format) return fastq_state_set(fp, opt); return 0; case FASTQ_OPT_AUX: if (fp->format.format == fastq_format || fp->format.format == fasta_format) { va_start(args, opt); char *list = va_arg(args, char *); va_end(args); return fastq_state_set(fp, opt, list); } return 0; case FASTQ_OPT_BARCODE: if (fp->format.format == fastq_format || fp->format.format == fasta_format) { va_start(args, opt); char *bc = va_arg(args, char *); va_end(args); return fastq_state_set(fp, opt, bc); } return 0; // Options below here flow through to cram_set_voption case HTS_OPT_COMPRESSION_LEVEL: { va_start(args, opt); int level = va_arg(args, int); va_end(args); if (fp->is_bgzf) fp->fp.bgzf->compress_level = level; else if (fp->format.format == cram) return cram_set_option(fp->fp.cram, opt, level); return 0; } case HTS_OPT_FILTER: { va_start(args, opt); char *expr = va_arg(args, char *); va_end(args); return hts_set_filter_expression(fp, expr); } case HTS_OPT_PROFILE: { va_start(args, opt); enum hts_profile_option prof = va_arg(args, int); va_end(args); if (fp->is_bgzf) { switch (prof) { #ifdef HAVE_LIBDEFLATE case HTS_PROFILE_FAST: fp->fp.bgzf->compress_level = 2; break; case HTS_PROFILE_NORMAL: fp->fp.bgzf->compress_level = -1; break; case HTS_PROFILE_SMALL: fp->fp.bgzf->compress_level = 10; break; case HTS_PROFILE_ARCHIVE: fp->fp.bgzf->compress_level = 12; break; #else case HTS_PROFILE_FAST: fp->fp.bgzf->compress_level = 1; break; case HTS_PROFILE_NORMAL: fp->fp.bgzf->compress_level = -1; break; case HTS_PROFILE_SMALL: fp->fp.bgzf->compress_level = 8; break; case HTS_PROFILE_ARCHIVE: fp->fp.bgzf->compress_level = 9; break; #endif } } // else CRAM manages this in its own way break; } default: break; } if (fp->format.format != cram) return 0; va_start(args, opt); r = cram_set_voption(fp->fp.cram, opt, args); va_end(args); return r; } BGZF *hts_get_bgzfp(htsFile *fp); int hts_set_threads(htsFile *fp, int n) { if (fp->format.format == sam) { return sam_set_threads(fp, n); } else if (fp->format.compression == bgzf) { return bgzf_mt(hts_get_bgzfp(fp), n, 256/*unused*/); } else if (fp->format.format == cram) { return hts_set_opt(fp, CRAM_OPT_NTHREADS, n); } else return 0; } int hts_set_thread_pool(htsFile *fp, htsThreadPool *p) { if (fp->format.format == sam || fp->format.format == text_format) { return sam_set_thread_pool(fp, p); } else if (fp->format.compression == bgzf) { return bgzf_thread_pool(hts_get_bgzfp(fp), p->pool, p->qsize); } else if (fp->format.format == cram) { return hts_set_opt(fp, CRAM_OPT_THREAD_POOL, p); } else return 0; } void hts_set_cache_size(htsFile *fp, int n) { if (fp->format.compression == bgzf) bgzf_set_cache_size(hts_get_bgzfp(fp), n); } int hts_set_fai_filename(htsFile *fp, const char *fn_aux) { free(fp->fn_aux); if (fn_aux) { fp->fn_aux = strdup(fn_aux); if (fp->fn_aux == NULL) return -1; } else fp->fn_aux = NULL; if (fp->format.format == cram) if (cram_set_option(fp->fp.cram, CRAM_OPT_REFERENCE, fp->fn_aux)) return -1; return 0; } int hts_set_filter_expression(htsFile *fp, const char *expr) { if (fp->filter) hts_filter_free(fp->filter); if (!expr) return 0; return (fp->filter = hts_filter_init(expr)) ? 0 : -1; } hFILE *hts_open_tmpfile(const char *fname, const char *mode, kstring_t *tmpname) { int pid = (int) getpid(); unsigned ptr = (uintptr_t) tmpname; int n = 0; hFILE *fp = NULL; do { // Attempt to further uniquify the temporary filename unsigned t = ((unsigned) time(NULL)) ^ ((unsigned) clock()) ^ ptr; n++; ks_clear(tmpname); if (ksprintf(tmpname, "%s.tmp_%d_%d_%u", fname, pid, n, t) < 0) break; fp = hopen(tmpname->s, mode); } while (fp == NULL && errno == EEXIST && n < 100); return fp; } int hts_is_utf16_text(const kstring_t *str) { const unsigned char *u = (const unsigned char *) (str->s); return (str->l > 0 && str->s)? is_utf16_text(u, u + str->l) : 0; } // For VCF/BCF backward sweeper. Not exposing these functions because their // future is uncertain. Things will probably have to change with hFILE... BGZF *hts_get_bgzfp(htsFile *fp) { if (fp->is_bgzf) return fp->fp.bgzf; else return NULL; } int hts_useek(htsFile *fp, off_t uoffset, int where) { if (fp->is_bgzf) return bgzf_useek(fp->fp.bgzf, uoffset, where); else return (hseek(fp->fp.hfile, uoffset, SEEK_SET) >= 0)? 0 : -1; } off_t hts_utell(htsFile *fp) { if (fp->is_bgzf) return bgzf_utell(fp->fp.bgzf); else return htell(fp->fp.hfile); } int hts_getline(htsFile *fp, int delimiter, kstring_t *str) { int ret; if (! (delimiter == KS_SEP_LINE || delimiter == '\n')) { hts_log_error("Unexpected delimiter %d", delimiter); abort(); } switch (fp->format.compression) { case no_compression: str->l = 0; ret = kgetline2(str, (kgets_func2 *) hgetln, fp->fp.hfile); if (ret >= 0) ret = (str->l <= INT_MAX)? (int) str->l : INT_MAX; else if (herrno(fp->fp.hfile)) ret = -2, errno = herrno(fp->fp.hfile); else ret = -1; break; case gzip: case bgzf: ret = bgzf_getline(fp->fp.bgzf, '\n', str); break; default: abort(); } ++fp->lineno; return ret; } char **hts_readlist(const char *string, int is_file, int *_n) { unsigned int m = 0, n = 0; char **s = 0, **s_new; if ( is_file ) { BGZF *fp = bgzf_open(string, "r"); if ( !fp ) return NULL; kstring_t str; int ret; str.s = 0; str.l = str.m = 0; while ((ret = bgzf_getline(fp, '\n', &str)) >= 0) { if (str.l == 0) continue; if (n == 0 && hts_is_utf16_text(&str)) hts_log_warning("'%s' appears to be encoded as UTF-16", string); if (hts_resize(char*, n + 1, &m, &s, 0) < 0) goto err; s[n] = strdup(str.s); if (!s[n]) goto err; n++; } if (ret < -1) // Read error goto err; bgzf_close(fp); free(str.s); } else { const char *q = string, *p = string; while ( 1 ) { if (*p == ',' || *p == 0) { if (hts_resize(char*, n + 1, &m, &s, 0) < 0) goto err; s[n] = (char*)calloc(p - q + 1, 1); if (!s[n]) goto err; strncpy(s[n++], q, p - q); q = p + 1; } if ( !*p ) break; p++; } } // Try to shrink s to the minimum size needed s_new = (char**)realloc(s, n * sizeof(char*)); if (!s_new) goto err; s = s_new; assert(n < INT_MAX); // hts_resize() should ensure this *_n = n; return s; err: for (m = 0; m < n; m++) free(s[m]); free(s); return NULL; } char **hts_readlines(const char *fn, int *_n) { unsigned int m = 0, n = 0; char **s = 0, **s_new; BGZF *fp = bgzf_open(fn, "r"); if ( fp ) { // read from file kstring_t str; int ret; str.s = 0; str.l = str.m = 0; while ((ret = bgzf_getline(fp, '\n', &str)) >= 0) { if (str.l == 0) continue; if (n == 0 && hts_is_utf16_text(&str)) hts_log_warning("'%s' appears to be encoded as UTF-16", fn); if (hts_resize(char *, n + 1, &m, &s, 0) < 0) goto err; s[n] = strdup(str.s); if (!s[n]) goto err; n++; } if (ret < -1) // Read error goto err; bgzf_close(fp); free(str.s); } else if (*fn == ':') { // read from string const char *q, *p; for (q = p = fn + 1;; ++p) if (*p == ',' || *p == 0) { if (hts_resize(char *, n + 1, &m, &s, 0) < 0) goto err; s[n] = (char*)calloc(p - q + 1, 1); if (!s[n]) goto err; strncpy(s[n++], q, p - q); q = p + 1; if (*p == 0) break; } } else return 0; // Try to shrink s to the minimum size needed s_new = (char**)realloc(s, n * sizeof(char*)); if (!s_new) goto err; s = s_new; assert(n < INT_MAX); // hts_resize() should ensure this *_n = n; return s; err: for (m = 0; m < n; m++) free(s[m]); free(s); return NULL; } // DEPRECATED: To be removed in a future HTSlib release int hts_file_type(const char *fname) { int len = strlen(fname); if ( !strcasecmp(".vcf.gz",fname+len-7) ) return FT_VCF_GZ; if ( !strcasecmp(".vcf",fname+len-4) ) return FT_VCF; if ( !strcasecmp(".bcf",fname+len-4) ) return FT_BCF_GZ; if ( !strcmp("-",fname) ) return FT_STDIN; hFILE *f = hopen(fname, "r"); if (f == NULL) return 0; htsFormat fmt; if (hts_detect_format2(f, fname, &fmt) < 0) { hclose_abruptly(f); return 0; } if (hclose(f) < 0) return 0; switch (fmt.format) { case vcf: return (fmt.compression == no_compression)? FT_VCF : FT_VCF_GZ; case bcf: return (fmt.compression == no_compression)? FT_BCF : FT_BCF_GZ; default: return 0; } } int hts_check_EOF(htsFile *fp) { if (fp->format.compression == bgzf) return bgzf_check_EOF(hts_get_bgzfp(fp)); else if (fp->format.format == cram) return cram_check_EOF(fp->fp.cram); else return 3; } /**************** *** Indexing *** ****************/ #define HTS_MIN_MARKER_DIST 0x10000 // Finds the special meta bin // ((1<<(3 * n_lvls + 3)) - 1) / 7 + 1 #define META_BIN(idx) ((idx)->n_bins + 1) #define pair64_lt(a,b) ((a).u < (b).u) #define pair64max_lt(a,b) ((a).u < (b).u || \ ((a).u == (b).u && (a).max < (b).max)) KSORT_INIT_STATIC(_off, hts_pair64_t, pair64_lt) KSORT_INIT_STATIC(_off_max, hts_pair64_max_t, pair64max_lt) typedef struct { int32_t m, n; uint64_t loff; hts_pair64_t *list; } bins_t; KHASH_MAP_INIT_INT(bin, bins_t) typedef khash_t(bin) bidx_t; typedef struct { hts_pos_t n, m; uint64_t *offset; } lidx_t; struct hts_idx_t { int fmt, min_shift, n_lvls, n_bins; uint32_t l_meta; int32_t n, m; uint64_t n_no_coor; bidx_t **bidx; lidx_t *lidx; uint8_t *meta; // MUST have a terminating NUL on the end int tbi_n, last_tbi_tid; struct { uint32_t last_bin, save_bin; hts_pos_t last_coor; int last_tid, save_tid, finished; uint64_t last_off, save_off; uint64_t off_beg, off_end; uint64_t n_mapped, n_unmapped; } z; // keep internal states BGZF *otf_fp; // Index on-the-fly output file }; static char * idx_format_name(int fmt) { switch (fmt) { case HTS_FMT_CSI: return "csi"; case HTS_FMT_BAI: return "bai"; case HTS_FMT_TBI: return "tbi"; case HTS_FMT_CRAI: return "crai"; default: return "unknown"; } } #ifdef DEBUG_INDEX static void idx_dump(const hts_idx_t *idx) { int i; int64_t j; if (!idx) fprintf(stderr, "Null index\n"); fprintf(stderr, "format='%s', min_shift=%d, n_lvls=%d, n_bins=%d, l_meta=%u ", idx_format_name(idx->fmt), idx->min_shift, idx->n_lvls, idx->n_bins, idx->l_meta); fprintf(stderr, "n=%d, m=%d, n_no_coor=%"PRIu64"\n", idx->n, idx->m, idx->n_no_coor); for (i = 0; i < idx->n; i++) { bidx_t *bidx = idx->bidx[i]; lidx_t *lidx = &idx->lidx[i]; if (bidx) { fprintf(stderr, "======== BIN Index - tid=%d, n_buckets=%d, size=%d\n", i, bidx->n_buckets, bidx->size); int b; for (b = 0; b < META_BIN(idx); b++) { khint_t k; if ((k = kh_get(bin, bidx, b)) != kh_end(bidx)) { bins_t *entries = &kh_value(bidx, k); int l = hts_bin_level(b); int64_t bin_width = 1LL << ((idx->n_lvls - l) * 3 + idx->min_shift); fprintf(stderr, "\tbin=%d, level=%d, parent=%d, n_chunks=%d, loff=%"PRIu64", interval=[%"PRId64" - %"PRId64"]\n", b, l, hts_bin_parent(b), entries->n, entries->loff, (b-hts_bin_first(l))*bin_width+1, (b+1-hts_bin_first(l))*bin_width); for (j = 0; j < entries->n; j++) fprintf(stderr, "\t\tchunk=%"PRId64", u=%"PRIu64", v=%"PRIu64"\n", j, entries->list[j].u, entries->list[j].v); } } } if (lidx) { fprintf(stderr, "======== LINEAR Index - tid=%d, n_values=%"PRId64"\n", i, lidx->n); for (j = 0; j < lidx->n; j++) { fprintf(stderr, "\t\tentry=%"PRId64", offset=%"PRIu64", interval=[%"PRId64" - %"PRId64"]\n", j, lidx->offset[j], j*(1<min_shift)+1, (j+1)*(1<min_shift)); } } } } #endif static inline int insert_to_b(bidx_t *b, int bin, uint64_t beg, uint64_t end) { khint_t k; bins_t *l; int absent; k = kh_put(bin, b, bin, &absent); if (absent < 0) return -1; // Out of memory l = &kh_value(b, k); if (absent) { l->m = 1; l->n = 0; l->list = (hts_pair64_t*)calloc(l->m, sizeof(hts_pair64_t)); if (!l->list) { kh_del(bin, b, k); return -1; } } else if (l->n == l->m) { uint32_t new_m = l->m ? l->m << 1 : 1; hts_pair64_t *new_list = realloc(l->list, new_m * sizeof(hts_pair64_t)); if (!new_list) return -1; l->list = new_list; l->m = new_m; } l->list[l->n].u = beg; l->list[l->n++].v = end; return 0; } static inline int insert_to_l(lidx_t *l, int64_t _beg, int64_t _end, uint64_t offset, int min_shift) { int i; hts_pos_t beg, end; beg = _beg >> min_shift; end = (_end - 1) >> min_shift; if (l->m < end + 1) { size_t new_m = l->m * 2 > end + 1 ? l->m * 2 : end + 1; uint64_t *new_offset; new_offset = (uint64_t*)realloc(l->offset, new_m * sizeof(uint64_t)); if (!new_offset) return -1; // fill unused memory with (uint64_t)-1 memset(new_offset + l->m, 0xff, sizeof(uint64_t) * (new_m - l->m)); l->m = new_m; l->offset = new_offset; } for (i = beg; i <= end; ++i) { if (l->offset[i] == (uint64_t)-1) l->offset[i] = offset; } if (l->n < end + 1) l->n = end + 1; return 0; } hts_idx_t *hts_idx_init(int n, int fmt, uint64_t offset0, int min_shift, int n_lvls) { hts_idx_t *idx; idx = (hts_idx_t*)calloc(1, sizeof(hts_idx_t)); if (idx == NULL) return NULL; idx->fmt = fmt; idx->min_shift = min_shift; idx->n_lvls = n_lvls; idx->n_bins = ((1<<(3 * n_lvls + 3)) - 1) / 7; idx->z.save_tid = idx->z.last_tid = -1; idx->z.save_bin = idx->z.last_bin = 0xffffffffu; idx->z.save_off = idx->z.last_off = idx->z.off_beg = idx->z.off_end = offset0; idx->z.last_coor = 0xffffffffu; if (n) { idx->n = idx->m = n; idx->bidx = (bidx_t**)calloc(n, sizeof(bidx_t*)); if (idx->bidx == NULL) { free(idx); return NULL; } idx->lidx = (lidx_t*) calloc(n, sizeof(lidx_t)); if (idx->lidx == NULL) { free(idx->bidx); free(idx); return NULL; } } idx->tbi_n = -1; idx->last_tbi_tid = -1; idx->otf_fp = NULL; return idx; } static void update_loff(hts_idx_t *idx, int i, int free_lidx) { bidx_t *bidx = idx->bidx[i]; lidx_t *lidx = &idx->lidx[i]; khint_t k; int l; // the last entry is always valid for (l=lidx->n-2; l >= 0; l--) { if (lidx->offset[l] == (uint64_t)-1) lidx->offset[l] = lidx->offset[l+1]; } if (bidx == 0) return; for (k = kh_begin(bidx); k != kh_end(bidx); ++k) // set loff if (kh_exist(bidx, k)) { if ( kh_key(bidx, k) < idx->n_bins ) { int bot_bin = hts_bin_bot(kh_key(bidx, k), idx->n_lvls); // disable linear index if bot_bin out of bounds kh_val(bidx, k).loff = bot_bin < lidx->n ? lidx->offset[bot_bin] : 0; } else kh_val(bidx, k).loff = 0; } if (free_lidx) { free(lidx->offset); lidx->m = lidx->n = 0; lidx->offset = 0; } } static int compress_binning(hts_idx_t *idx, int i) { bidx_t *bidx = idx->bidx[i]; khint_t k; int l, m; if (bidx == 0) return 0; // merge a bin to its parent if the bin is too small for (l = idx->n_lvls; l > 0; --l) { unsigned start = hts_bin_first(l); for (k = kh_begin(bidx); k != kh_end(bidx); ++k) { bins_t *p, *q; if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue; p = &kh_value(bidx, k); if (l < idx->n_lvls && p->n > 1) ks_introsort(_off, p->n, p->list); if ((p->list[p->n - 1].v>>16) - (p->list[0].u>>16) < HTS_MIN_MARKER_DIST) { khint_t kp; kp = kh_get(bin, bidx, hts_bin_parent(kh_key(bidx, k))); if (kp == kh_end(bidx)) continue; q = &kh_val(bidx, kp); if (q->n + p->n > q->m) { uint32_t new_m = q->n + p->n; hts_pair64_t *new_list; kroundup32(new_m); if (new_m > INT32_MAX) return -1; // Limited by index format new_list = realloc(q->list, new_m * sizeof(*new_list)); if (!new_list) return -1; q->m = new_m; q->list = new_list; } memcpy(q->list + q->n, p->list, p->n * sizeof(hts_pair64_t)); q->n += p->n; free(p->list); kh_del(bin, bidx, k); } } } k = kh_get(bin, bidx, 0); if (k != kh_end(bidx)) ks_introsort(_off, kh_val(bidx, k).n, kh_val(bidx, k).list); // merge adjacent chunks that start from the same BGZF block for (k = kh_begin(bidx); k != kh_end(bidx); ++k) { bins_t *p; if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue; p = &kh_value(bidx, k); for (l = 1, m = 0; l < p->n; ++l) { if (p->list[m].v>>16 >= p->list[l].u>>16) { if (p->list[m].v < p->list[l].v) p->list[m].v = p->list[l].v; } else p->list[++m] = p->list[l]; } p->n = m + 1; } return 0; } int hts_idx_finish(hts_idx_t *idx, uint64_t final_offset) { int i, ret = 0; if (idx == NULL || idx->z.finished) return 0; // do not run this function on an empty index or multiple times if (idx->z.save_tid >= 0) { ret |= insert_to_b(idx->bidx[idx->z.save_tid], idx->z.save_bin, idx->z.save_off, final_offset); ret |= insert_to_b(idx->bidx[idx->z.save_tid], META_BIN(idx), idx->z.off_beg, final_offset); ret |= insert_to_b(idx->bidx[idx->z.save_tid], META_BIN(idx), idx->z.n_mapped, idx->z.n_unmapped); } for (i = 0; i < idx->n; ++i) { update_loff(idx, i, (idx->fmt == HTS_FMT_CSI)); ret |= compress_binning(idx, i); } idx->z.finished = 1; return ret; } static inline hts_pos_t hts_idx_maxpos(const hts_idx_t *idx) { return hts_bin_maxpos(idx->min_shift, idx->n_lvls); } int hts_idx_check_range(hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end) { hts_pos_t maxpos = hts_idx_maxpos(idx); if (tid < 0 || (beg <= maxpos && end <= maxpos)) return 0; if (idx->fmt == HTS_FMT_CSI) { hts_log_error("Region %"PRIhts_pos"..%"PRIhts_pos" " "cannot be stored in a csi index with these parameters. " "Please use a larger min_shift or depth", beg, end); } else { hts_log_error("Region %"PRIhts_pos"..%"PRIhts_pos " cannot be stored in a %s index. Try using a csi index", beg, end, idx_format_name(idx->fmt)); } errno = ERANGE; return -1; } int hts_idx_push(hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, uint64_t offset, int is_mapped) { int bin; if (tid<0) beg = -1, end = 0; if (hts_idx_check_range(idx, tid, beg, end) < 0) return -1; if (tid >= idx->m) { // enlarge the index uint32_t new_m = idx->m * 2 > tid + 1 ? idx->m * 2 : tid + 1; bidx_t **new_bidx; lidx_t *new_lidx; new_bidx = (bidx_t**)realloc(idx->bidx, new_m * sizeof(bidx_t*)); if (!new_bidx) return -1; idx->bidx = new_bidx; new_lidx = (lidx_t*) realloc(idx->lidx, new_m * sizeof(lidx_t)); if (!new_lidx) return -1; idx->lidx = new_lidx; memset(&idx->bidx[idx->m], 0, (new_m - idx->m) * sizeof(bidx_t*)); memset(&idx->lidx[idx->m], 0, (new_m - idx->m) * sizeof(lidx_t)); idx->m = new_m; } if (idx->n < tid + 1) idx->n = tid + 1; if (idx->z.finished) return 0; if (idx->z.last_tid != tid || (idx->z.last_tid >= 0 && tid < 0)) { // change of chromosome if ( tid>=0 && idx->n_no_coor ) { hts_log_error("NO_COOR reads not in a single block at the end %d %d", tid, idx->z.last_tid); return -1; } if (tid>=0 && idx->bidx[tid] != 0) { hts_log_error("Chromosome blocks not continuous"); return -1; } idx->z.last_tid = tid; idx->z.last_bin = 0xffffffffu; } else if (tid >= 0 && idx->z.last_coor > beg) { // test if positions are out of order hts_log_error("Unsorted positions on sequence #%d: %"PRIhts_pos" followed by %"PRIhts_pos, tid+1, idx->z.last_coor+1, beg+1); return -1; } if (end < beg) { // Malformed ranges are errors. (Empty ranges (beg==end) are unusual but acceptable.) hts_log_error("Invalid record on sequence #%d: end %"PRId64" < begin %"PRId64, tid+1, end, beg+1); return -1; } if ( tid>=0 ) { if (idx->bidx[tid] == 0) idx->bidx[tid] = kh_init(bin); // shoehorn [-1,0) (VCF POS=0) into the leftmost bottom-level bin if (beg < 0) beg = 0; if (end <= 0) end = 1; // idx->z.last_off points to the start of the current record if (insert_to_l(&idx->lidx[tid], beg, end, idx->z.last_off, idx->min_shift) < 0) return -1; } else idx->n_no_coor++; bin = hts_reg2bin(beg, end, idx->min_shift, idx->n_lvls); if ((int)idx->z.last_bin != bin) { // then possibly write the binning index if (idx->z.save_bin != 0xffffffffu) { // save_bin==0xffffffffu only happens to the first record if (insert_to_b(idx->bidx[idx->z.save_tid], idx->z.save_bin, idx->z.save_off, idx->z.last_off) < 0) return -1; } if (idx->z.last_bin == 0xffffffffu && idx->z.save_bin != 0xffffffffu) { // change of chr; keep meta information idx->z.off_end = idx->z.last_off; if (insert_to_b(idx->bidx[idx->z.save_tid], META_BIN(idx), idx->z.off_beg, idx->z.off_end) < 0) return -1; if (insert_to_b(idx->bidx[idx->z.save_tid], META_BIN(idx), idx->z.n_mapped, idx->z.n_unmapped) < 0) return -1; idx->z.n_mapped = idx->z.n_unmapped = 0; idx->z.off_beg = idx->z.off_end; } idx->z.save_off = idx->z.last_off; idx->z.save_bin = idx->z.last_bin = bin; idx->z.save_tid = tid; } if (is_mapped) ++idx->z.n_mapped; else ++idx->z.n_unmapped; idx->z.last_off = offset; idx->z.last_coor = beg; return 0; } // Needed for TBI only. Ensure 'tid' with 'name' is in the index meta data. // idx->meta needs to have been initialised first with an appropriate Tabix // configuration via hts_idx_set_meta. // // NB number of references (first 4 bytes of tabix header) aren't in // idx->meta, but held in idx->n instead. int hts_idx_tbi_name(hts_idx_t *idx, int tid, const char *name) { // Horrid - we have to map incoming tid to a tbi alternative tid. // This is because TBI counts tids by "covered" refs while everything // else counts by Nth SQ/contig record in header. if (tid == idx->last_tbi_tid || tid < 0 || !name) return idx->tbi_n; uint32_t len = strlen(name)+1; uint8_t *tmp = (uint8_t *)realloc(idx->meta, idx->l_meta + len); if (!tmp) return -1; // Append name idx->meta = tmp; strcpy((char *)idx->meta + idx->l_meta, name); idx->l_meta += len; // Update seq length u32_to_le(le_to_u32(idx->meta+24)+len, idx->meta+24); idx->last_tbi_tid = tid; return ++idx->tbi_n; } // When doing samtools index we have a read_bam / hts_idx_push(bgzf_tell()) // loop. idx->z.last_off is the previous bzgf_tell location, so we know // the location the current bam record started at as well as where it ends. // // When building an index on the fly via a write_bam / hts_idx_push loop, // this isn't quite identical as we may amend the virtual coord returned // by bgzf_tell to the start of a new block if the next bam struct doesn't // fit. It's essentially the same thing, but for bit-identical indices // we need to amend the idx->z.last_off when we know we're starting a new // block. void hts_idx_amend_last(hts_idx_t *idx, uint64_t offset) { idx->z.last_off = offset; } void hts_idx_destroy(hts_idx_t *idx) { khint_t k; int i; if (idx == 0) return; // For HTS_FMT_CRAI, idx actually points to a different type -- see sam.c if (idx->fmt == HTS_FMT_CRAI) { hts_cram_idx_t *cidx = (hts_cram_idx_t *) idx; cram_index_free(cidx->cram); free(cidx); return; } for (i = 0; i < idx->m; ++i) { bidx_t *bidx = idx->bidx[i]; free(idx->lidx[i].offset); if (bidx == 0) continue; for (k = kh_begin(bidx); k != kh_end(bidx); ++k) if (kh_exist(bidx, k)) free(kh_value(bidx, k).list); kh_destroy(bin, bidx); } free(idx->bidx); free(idx->lidx); free(idx->meta); free(idx); } int hts_idx_fmt(hts_idx_t *idx) { return idx->fmt; } // The optimizer eliminates these ed_is_big() calls; still it would be good to // TODO Determine endianness at configure- or compile-time static inline ssize_t HTS_RESULT_USED idx_write_int32(BGZF *fp, int32_t x) { if (ed_is_big()) x = ed_swap_4(x); return bgzf_write(fp, &x, sizeof x); } static inline ssize_t HTS_RESULT_USED idx_write_uint32(BGZF *fp, uint32_t x) { if (ed_is_big()) x = ed_swap_4(x); return bgzf_write(fp, &x, sizeof x); } static inline ssize_t HTS_RESULT_USED idx_write_uint64(BGZF *fp, uint64_t x) { if (ed_is_big()) x = ed_swap_8(x); return bgzf_write(fp, &x, sizeof x); } static inline void swap_bins(bins_t *p) { int i; for (i = 0; i < p->n; ++i) { ed_swap_8p(&p->list[i].u); ed_swap_8p(&p->list[i].v); } } static int need_idx_ugly_delay_hack(const hts_idx_t *idx) { // Ugly hack for on-the-fly BAI indexes. As these are uncompressed, // we need to delay writing a few bytes of data until file close // so that we have something to force a modification time update. // // (For compressed indexes like CSI, the BGZF EOF block serves the same // purpose). return idx->otf_fp && !idx->otf_fp->is_compressed; } static int idx_save_core(const hts_idx_t *idx, BGZF *fp, int fmt) { int32_t i, j; #define check(ret) if ((ret) < 0) return -1 // VCF TBI/CSI only writes IDs for non-empty bins (ie covered references) // // NOTE: CSI meta is undefined in spec, so this code has an assumption // that we're only using it for Tabix data. int nids = idx->n; if (idx->meta && idx->l_meta >= 4 && le_to_u32(idx->meta) == TBX_VCF) { for (i = nids = 0; i < idx->n; ++i) { if (idx->bidx[i]) nids++; } } check(idx_write_int32(fp, nids)); if (fmt == HTS_FMT_TBI && idx->l_meta) check(bgzf_write(fp, idx->meta, idx->l_meta)); for (i = 0; i < idx->n; ++i) { khint_t k; bidx_t *bidx = idx->bidx[i]; lidx_t *lidx = &idx->lidx[i]; // write binning index if (nids == idx->n || bidx) check(idx_write_int32(fp, bidx? kh_size(bidx) : 0)); if (bidx) for (k = kh_begin(bidx); k != kh_end(bidx); ++k) if (kh_exist(bidx, k)) { bins_t *p = &kh_value(bidx, k); check(idx_write_uint32(fp, kh_key(bidx, k))); if (fmt == HTS_FMT_CSI) check(idx_write_uint64(fp, p->loff)); //int j;for(j=0;jn;++j)fprintf(stderr,"%d,%llx,%d,%llx:%llx\n",kh_key(bidx,k),kh_val(bidx, k).loff,j,p->list[j].u,p->list[j].v); check(idx_write_int32(fp, p->n)); for (j = 0; j < p->n; ++j) { //fprintf(stderr, "\t%ld\t%ld\n", p->list[j].u, p->list[j].v); check(idx_write_uint64(fp, p->list[j].u)); check(idx_write_uint64(fp, p->list[j].v)); } } // write linear index if (fmt != HTS_FMT_CSI) { check(idx_write_int32(fp, lidx->n)); for (j = 0; j < lidx->n; ++j) check(idx_write_uint64(fp, lidx->offset[j])); } } if (!need_idx_ugly_delay_hack(idx)) { // Write this for compressed (CSI) indexes, but for BAI we // need to save a bit for later. See hts_idx_close_otf_fp() check(idx_write_uint64(fp, idx->n_no_coor)); } #ifdef DEBUG_INDEX idx_dump(idx); #endif return 0; #undef check } int hts_idx_save(const hts_idx_t *idx, const char *fn, int fmt) { int ret, save; if (idx == NULL || fn == NULL) { errno = EINVAL; return -1; } char *fnidx = (char*)calloc(1, strlen(fn) + 5); if (fnidx == NULL) return -1; strcpy(fnidx, fn); switch (fmt) { case HTS_FMT_BAI: strcat(fnidx, ".bai"); break; case HTS_FMT_CSI: strcat(fnidx, ".csi"); break; case HTS_FMT_TBI: strcat(fnidx, ".tbi"); break; default: abort(); } ret = hts_idx_save_as(idx, fn, fnidx, fmt); save = errno; free(fnidx); errno = save; return ret; } static int hts_idx_write_out(const hts_idx_t *idx, BGZF *fp, int fmt) { #define check(ret) if ((ret) < 0) return -1 if (fmt == HTS_FMT_CSI) { check(bgzf_write(fp, "CSI\1", 4)); check(idx_write_int32(fp, idx->min_shift)); check(idx_write_int32(fp, idx->n_lvls)); check(idx_write_uint32(fp, idx->l_meta)); if (idx->l_meta) check(bgzf_write(fp, idx->meta, idx->l_meta)); } else if (fmt == HTS_FMT_TBI) { check(bgzf_write(fp, "TBI\1", 4)); } else if (fmt == HTS_FMT_BAI) { check(bgzf_write(fp, "BAI\1", 4)); } else abort(); check(idx_save_core(idx, fp, fmt)); #undef check return 0; } int hts_idx_save_as(const hts_idx_t *idx, const char *fn, const char *fnidx, int fmt) { BGZF *fp; if (fnidx == NULL) return hts_idx_save(idx, fn, fmt); fp = bgzf_open(fnidx, (fmt == HTS_FMT_BAI)? "wu" : "w"); if (fp == NULL) return -1; if (hts_idx_write_out(idx, fp, fmt) < 0) { int save_errno = errno; bgzf_close(fp); errno = save_errno; return -1; } return bgzf_close(fp); } // idx_save for on-the-fly indexes. Mostly duplicated from above, except // idx is not const because we want to store the file handle in it, and // the index file handle is not closed. This allows the index file to be // closed after the EOF block on the indexed file has been written out, // so the modification times on the two files will be in the correct order. int hts_idx_save_but_not_close(hts_idx_t *idx, const char *fnidx, int fmt) { idx->otf_fp = bgzf_open(fnidx, (fmt == HTS_FMT_BAI)? "wu" : "w"); if (idx->otf_fp == NULL) return -1; if (hts_idx_write_out(idx, idx->otf_fp, fmt) < 0) { int save_errno = errno; bgzf_close(idx->otf_fp); idx->otf_fp = NULL; errno = save_errno; return -1; } return bgzf_flush(idx->otf_fp); } static int hts_idx_close_otf_fp(hts_idx_t *idx) { if (idx && idx->otf_fp) { int ret = 0; if (need_idx_ugly_delay_hack(idx)) { // BAI index - write out the bytes we deferred earlier ret = idx_write_uint64(idx->otf_fp, idx->n_no_coor) < 0; } ret |= bgzf_close(idx->otf_fp) < 0; idx->otf_fp = NULL; return ret == 0 ? 0 : -1; } return 0; } static int idx_read_core(hts_idx_t *idx, BGZF *fp, int fmt) { int32_t i, n, is_be; is_be = ed_is_big(); if (idx == NULL) return -4; for (i = 0; i < idx->n; ++i) { bidx_t *h; lidx_t *l = &idx->lidx[i]; uint32_t key; int j, absent; bins_t *p; h = idx->bidx[i] = kh_init(bin); if (bgzf_read(fp, &n, 4) != 4) return -1; if (is_be) ed_swap_4p(&n); if (n < 0) return -3; for (j = 0; j < n; ++j) { khint_t k; if (bgzf_read(fp, &key, 4) != 4) return -1; if (is_be) ed_swap_4p(&key); k = kh_put(bin, h, key, &absent); if (absent < 0) return -2; // No memory if (absent == 0) return -3; // Duplicate bin number p = &kh_val(h, k); if (fmt == HTS_FMT_CSI) { if (bgzf_read(fp, &p->loff, 8) != 8) return -1; if (is_be) ed_swap_8p(&p->loff); } else p->loff = 0; if (bgzf_read(fp, &p->n, 4) != 4) return -1; if (is_be) ed_swap_4p(&p->n); if (p->n < 0) return -3; if ((size_t) p->n > SIZE_MAX / sizeof(hts_pair64_t)) return -2; p->m = p->n; p->list = (hts_pair64_t*)malloc(p->m * sizeof(hts_pair64_t)); if (p->list == NULL) return -2; if (bgzf_read(fp, p->list, ((size_t) p->n)<<4) != ((size_t) p->n)<<4) return -1; if (is_be) swap_bins(p); } if (fmt != HTS_FMT_CSI) { // load linear index int j, k; uint32_t x; if (bgzf_read(fp, &x, 4) != 4) return -1; if (is_be) ed_swap_4p(&x); l->n = x; if (l->n < 0) return -3; if ((size_t) l->n > SIZE_MAX / sizeof(uint64_t)) return -2; l->m = l->n; l->offset = (uint64_t*)malloc(l->n * sizeof(uint64_t)); if (l->offset == NULL) return -2; if (bgzf_read(fp, l->offset, l->n << 3) != l->n << 3) return -1; if (is_be) for (j = 0; j < l->n; ++j) ed_swap_8p(&l->offset[j]); for (k = j = 0; j < l->n && l->offset[j] == 0; k = ++j); // stop at the first non-zero entry for (j = l->n-1; j > k; j--) // fill missing values; may happen given older samtools and tabix if (l->offset[j-1] == 0) l->offset[j-1] = l->offset[j]; update_loff(idx, i, 0); } } if (bgzf_read(fp, &idx->n_no_coor, 8) != 8) idx->n_no_coor = 0; if (is_be) ed_swap_8p(&idx->n_no_coor); #ifdef DEBUG_INDEX idx_dump(idx); #endif return 0; } static hts_idx_t *idx_read(const char *fn) { uint8_t magic[4]; int i, is_be; hts_idx_t *idx = NULL; uint8_t *meta = NULL; BGZF *fp = bgzf_open(fn, "r"); if (fp == NULL) return NULL; is_be = ed_is_big(); if (bgzf_read(fp, magic, 4) != 4) goto fail; if (memcmp(magic, "CSI\1", 4) == 0) { uint32_t x[3], n; if (bgzf_read(fp, x, 12) != 12) goto fail; if (is_be) for (i = 0; i < 3; ++i) ed_swap_4p(&x[i]); if (x[2]) { if (SIZE_MAX - x[2] < 1) goto fail; // Prevent possible overflow if ((meta = (uint8_t*)malloc((size_t) x[2] + 1)) == NULL) goto fail; if (bgzf_read(fp, meta, x[2]) != x[2]) goto fail; // Prevent possible strlen past the end in tbx_index_load2 meta[x[2]] = '\0'; } if (bgzf_read(fp, &n, 4) != 4) goto fail; if (is_be) ed_swap_4p(&n); if (n > INT32_MAX) goto fail; if ((idx = hts_idx_init(n, HTS_FMT_CSI, 0, x[0], x[1])) == NULL) goto fail; idx->l_meta = x[2]; idx->meta = meta; meta = NULL; if (idx_read_core(idx, fp, HTS_FMT_CSI) < 0) goto fail; } else if (memcmp(magic, "TBI\1", 4) == 0) { uint8_t x[8 * 4]; uint32_t n; // Read file header if (bgzf_read(fp, x, sizeof(x)) != sizeof(x)) goto fail; n = le_to_u32(&x[0]); // location of n_ref if (n > INT32_MAX) goto fail; if ((idx = hts_idx_init(n, HTS_FMT_TBI, 0, 14, 5)) == NULL) goto fail; n = le_to_u32(&x[7*4]); // location of l_nm if (n > UINT32_MAX - 29) goto fail; // Prevent possible overflow idx->l_meta = 28 + n; if ((idx->meta = (uint8_t*)malloc(idx->l_meta + 1)) == NULL) goto fail; // copy format, col_seq, col_beg, col_end, meta, skip, l_nm // N.B. left in little-endian byte order. memcpy(idx->meta, &x[1*4], 28); // Read in sequence names. if (bgzf_read(fp, idx->meta + 28, n) != n) goto fail; // Prevent possible strlen past the end in tbx_index_load2 idx->meta[idx->l_meta] = '\0'; if (idx_read_core(idx, fp, HTS_FMT_TBI) < 0) goto fail; } else if (memcmp(magic, "BAI\1", 4) == 0) { uint32_t n; if (bgzf_read(fp, &n, 4) != 4) goto fail; if (is_be) ed_swap_4p(&n); if (n > INT32_MAX) goto fail; if ((idx = hts_idx_init(n, HTS_FMT_BAI, 0, 14, 5)) == NULL) goto fail; if (idx_read_core(idx, fp, HTS_FMT_BAI) < 0) goto fail; } else { errno = EINVAL; goto fail; } bgzf_close(fp); return idx; fail: bgzf_close(fp); hts_idx_destroy(idx); free(meta); return NULL; } int hts_idx_set_meta(hts_idx_t *idx, uint32_t l_meta, uint8_t *meta, int is_copy) { uint8_t *new_meta = meta; if (is_copy) { size_t l = l_meta; if (l > SIZE_MAX - 1) { errno = ENOMEM; return -1; } new_meta = malloc(l + 1); if (!new_meta) return -1; memcpy(new_meta, meta, l); // Prevent possible strlen past the end in tbx_index_load2 new_meta[l] = '\0'; } if (idx->meta) free(idx->meta); idx->l_meta = l_meta; idx->meta = new_meta; return 0; } uint8_t *hts_idx_get_meta(hts_idx_t *idx, uint32_t *l_meta) { *l_meta = idx->l_meta; return idx->meta; } const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr) { if ( !idx || !idx->n ) { *n = 0; return NULL; } int tid = 0, i; const char **names = (const char**) calloc(idx->n,sizeof(const char*)); for (i=0; in; i++) { bidx_t *bidx = idx->bidx[i]; if ( !bidx ) continue; names[tid++] = getid(hdr,i); } *n = tid; return names; } int hts_idx_nseq(const hts_idx_t *idx) { if (!idx) return -1; return idx->n; } int hts_idx_get_stat(const hts_idx_t* idx, int tid, uint64_t* mapped, uint64_t* unmapped) { if (!idx) return -1; if ( idx->fmt == HTS_FMT_CRAI ) { *mapped = 0; *unmapped = 0; return -1; } bidx_t *h = idx->bidx[tid]; if (!h) return -1; khint_t k = kh_get(bin, h, META_BIN(idx)); if (k != kh_end(h)) { *mapped = kh_val(h, k).list[1].u; *unmapped = kh_val(h, k).list[1].v; return 0; } else { *mapped = 0; *unmapped = 0; return -1; } } uint64_t hts_idx_get_n_no_coor(const hts_idx_t* idx) { if (idx->fmt == HTS_FMT_CRAI) return 0; return idx->n_no_coor; } /**************** *** Iterator *** ****************/ // Note: even with 32-bit hts_pos_t, end needs to be 64-bit here due to 1LL<>s); e = t + (end>>s); for (i = b; i <= e; ++i) { if (kh_get(bin, bidx, i) != kh_end(bidx)) { assert(itr->bins.n < itr->bins.m); itr->bins.a[itr->bins.n++] = i; } } } return itr->bins.n; } static inline int reg2bins_wide(int64_t beg, int64_t end, hts_itr_t *itr, int min_shift, int n_lvls, bidx_t *bidx) { khint_t i; hts_pos_t max_shift = 3 * n_lvls + min_shift; --end; if (beg < 0) beg = 0; for (i = kh_begin(bidx); i != kh_end(bidx); i++) { if (!kh_exist(bidx, i)) continue; hts_pos_t bin = (hts_pos_t) kh_key(bidx, i); int level = hts_bin_level(bin); if (level > n_lvls) continue; // Dodgy index? hts_pos_t first = hts_bin_first(level); hts_pos_t beg_at_level = first + (beg >> (max_shift - 3 * level)); hts_pos_t end_at_level = first + (end >> (max_shift - 3 * level)); if (beg_at_level <= bin && bin <= end_at_level) { assert(itr->bins.n < itr->bins.m); itr->bins.a[itr->bins.n++] = bin; } } return itr->bins.n; } static inline int reg2bins(int64_t beg, int64_t end, hts_itr_t *itr, int min_shift, int n_lvls, bidx_t *bidx) { int l, t, s = min_shift + (n_lvls<<1) + n_lvls; size_t reg_bin_count = 0, hash_bin_count = kh_n_buckets(bidx), max_bins; hts_pos_t end1; if (end >= 1LL<= end) return 0; end1 = end - 1; // Count bins to see if it's faster to iterate through the hash table // or the set of bins covering the region for (l = 0, t = 0; l <= n_lvls; s -= 3, t += 1<<((l<<1)+l), ++l) { reg_bin_count += (end1 >> s) - (beg >> s) + 1; } max_bins = reg_bin_count < kh_size(bidx) ? reg_bin_count : kh_size(bidx); if (itr->bins.m - itr->bins.n < max_bins) { // Worst-case memory usage. May be wasteful on very sparse // data, but the bin list usually won't be too big anyway. size_t new_m = max_bins + itr->bins.n; if (new_m > INT_MAX || new_m > SIZE_MAX / sizeof(int)) { errno = ENOMEM; return -1; } int *new_a = realloc(itr->bins.a, new_m * sizeof(*new_a)); if (!new_a) return -1; itr->bins.a = new_a; itr->bins.m = new_m; } if (reg_bin_count < hash_bin_count) { return reg2bins_narrow(beg, end, itr, min_shift, n_lvls, bidx); } else { return reg2bins_wide(beg, end, itr, min_shift, n_lvls, bidx); } } static inline int add_to_interval(hts_itr_t *iter, bins_t *bin, int tid, uint32_t interval, uint64_t min_off, uint64_t max_off) { hts_pair64_max_t *off; int j; if (!bin->n) return 0; off = realloc(iter->off, (iter->n_off + bin->n) * sizeof(*off)); if (!off) return -2; iter->off = off; for (j = 0; j < bin->n; ++j) { if (bin->list[j].v > min_off && bin->list[j].u < max_off) { iter->off[iter->n_off].u = min_off > bin->list[j].u ? min_off : bin->list[j].u; iter->off[iter->n_off].v = max_off < bin->list[j].v ? max_off : bin->list[j].v; // hts_pair64_max_t::max is now used to link // file offsets to region list entries. // The iterator can use this to decide if it // can skip some file regions. iter->off[iter->n_off].max = ((uint64_t) tid << 32) | interval; iter->n_off++; } } return 0; } static inline int reg2intervals_narrow(hts_itr_t *iter, const bidx_t *bidx, int tid, int64_t beg, int64_t end, uint32_t interval, uint64_t min_off, uint64_t max_off, int min_shift, int n_lvls) { int l, t, s = min_shift + n_lvls * 3; hts_pos_t b, e, i; for (--end, l = 0, t = 0; l <= n_lvls; s -= 3, t += 1<<((l<<1)+l), ++l) { b = t + (beg>>s); e = t + (end>>s); for (i = b; i <= e; ++i) { khint_t k = kh_get(bin, bidx, i); if (k != kh_end(bidx)) { bins_t *bin = &kh_value(bidx, k); int res = add_to_interval(iter, bin, tid, interval, min_off, max_off); if (res < 0) return res; } } } return 0; } static inline int reg2intervals_wide(hts_itr_t *iter, const bidx_t *bidx, int tid, int64_t beg, int64_t end, uint32_t interval, uint64_t min_off, uint64_t max_off, int min_shift, int n_lvls) { khint_t i; hts_pos_t max_shift = 3 * n_lvls + min_shift; --end; if (beg < 0) beg = 0; for (i = kh_begin(bidx); i != kh_end(bidx); i++) { if (!kh_exist(bidx, i)) continue; hts_pos_t bin = (hts_pos_t) kh_key(bidx, i); int level = hts_bin_level(bin); if (level > n_lvls) continue; // Dodgy index? hts_pos_t first = hts_bin_first(level); hts_pos_t beg_at_level = first + (beg >> (max_shift - 3 * level)); hts_pos_t end_at_level = first + (end >> (max_shift - 3 * level)); if (beg_at_level <= bin && bin <= end_at_level) { bins_t *bin = &kh_value(bidx, i); int res = add_to_interval(iter, bin, tid, interval, min_off, max_off); if (res < 0) return res; } } return 0; } static inline int reg2intervals(hts_itr_t *iter, const hts_idx_t *idx, int tid, int64_t beg, int64_t end, uint32_t interval, uint64_t min_off, uint64_t max_off, int min_shift, int n_lvls) { int l, t, s; int i, j; hts_pos_t end1; bidx_t *bidx; int start_n_off; size_t reg_bin_count = 0, hash_bin_count; int res; if (!iter || !idx || (bidx = idx->bidx[tid]) == NULL || beg > end) return -1; hash_bin_count = kh_n_buckets(bidx); s = min_shift + (n_lvls<<1) + n_lvls; if (end >= 1LL<> s) - (beg >> s) + 1; } start_n_off = iter->n_off; // Populate iter->off with the intervals for this region if (reg_bin_count < hash_bin_count) { res = reg2intervals_narrow(iter, bidx, tid, beg, end, interval, min_off, max_off, min_shift, n_lvls); } else { res = reg2intervals_wide(iter, bidx, tid, beg, end, interval, min_off, max_off, min_shift, n_lvls); } if (res < 0) return res; if (iter->n_off - start_n_off > 1) { ks_introsort(_off_max, iter->n_off - start_n_off, iter->off + start_n_off); for (i = start_n_off, j = start_n_off + 1; j < iter->n_off; j++) { if (iter->off[i].v >= iter->off[j].u) { if (iter->off[i].v < iter->off[j].v) iter->off[i].v = iter->off[j].v; } else { i++; if (i < j) iter->off[i] = iter->off[j]; } } iter->n_off = i + 1; } return iter->n_off; } static int compare_regions(const void *r1, const void *r2) { hts_reglist_t *reg1 = (hts_reglist_t *)r1; hts_reglist_t *reg2 = (hts_reglist_t *)r2; if (reg1->tid < 0 && reg2->tid >= 0) return 1; else if (reg1->tid >= 0 && reg2->tid < 0) return -1; else return reg1->tid - reg2->tid; } uint64_t hts_itr_off(const hts_idx_t* idx, int tid) { int i; bidx_t* bidx; uint64_t off0 = (uint64_t) -1; khint_t k; switch (tid) { case HTS_IDX_START: // Find the smallest offset, note that sequence ids may not be ordered sequentially for (i = 0; i < idx->n; i++) { bidx = idx->bidx[i]; k = kh_get(bin, bidx, META_BIN(idx)); if (k == kh_end(bidx)) continue; if (off0 > kh_val(bidx, k).list[0].u) off0 = kh_val(bidx, k).list[0].u; } if (off0 == (uint64_t) -1 && idx->n_no_coor) off0 = 0; // only no-coor reads in this bam break; case HTS_IDX_NOCOOR: /* No-coor reads sort after all of the mapped reads. The position is not stored in the index itself, so need to find the end offset for the last mapped read. A loop is needed here in case references at the end of the file have no mapped reads, or sequence ids are not ordered sequentially. See issue samtools#568 and commits b2aab8, 60c22d and cc207d. */ for (i = 0; i < idx->n; i++) { bidx = idx->bidx[i]; k = kh_get(bin, bidx, META_BIN(idx)); if (k != kh_end(bidx)) { if (off0 == (uint64_t) -1 || off0 < kh_val(bidx, k).list[0].v) { off0 = kh_val(bidx, k).list[0].v; } } } if (off0 == (uint64_t) -1 && idx->n_no_coor) off0 = 0; // only no-coor reads in this bam break; case HTS_IDX_REST: off0 = 0; break; case HTS_IDX_NONE: off0 = 0; break; } return off0; } hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, hts_readrec_func *readrec) { int i, n_off, l, bin; hts_pair64_max_t *off; khint_t k; bidx_t *bidx; uint64_t min_off, max_off; hts_pos_t idx_maxpos; hts_itr_t *iter; uint32_t unmapped = 0, rel_off; // It's possible to call this function with NULL idx iff // tid is one of the special values HTS_IDX_REST or HTS_IDX_NONE if (!idx && !(tid == HTS_IDX_REST || tid == HTS_IDX_NONE)) { errno = EINVAL; return NULL; } iter = (hts_itr_t*)calloc(1, sizeof(hts_itr_t)); if (iter) { if (tid < 0) { uint64_t off = hts_itr_off(idx, tid); if (off != (uint64_t) -1) { iter->read_rest = 1; iter->curr_off = off; iter->readrec = readrec; if (tid == HTS_IDX_NONE) iter->finished = 1; } else { free(iter); iter = NULL; } } else if (tid >= idx->n || (bidx = idx->bidx[tid]) == NULL) { iter->finished = 1; } else { if (beg < 0) beg = 0; if (end < beg) { free(iter); return NULL; } k = kh_get(bin, bidx, META_BIN(idx)); if (k != kh_end(bidx)) unmapped = kh_val(bidx, k).list[1].v; else unmapped = 1; iter->tid = tid, iter->beg = beg, iter->end = end; iter->i = -1; iter->readrec = readrec; if ( !kh_size(bidx) ) { iter->finished = 1; return iter; } idx_maxpos = hts_idx_maxpos(idx); if (beg >= idx_maxpos) { iter->finished = 1; return iter; } rel_off = beg>>idx->min_shift; // compute min_off bin = hts_bin_first(idx->n_lvls) + rel_off; do { int first; k = kh_get(bin, bidx, bin); if (k != kh_end(bidx)) break; first = (hts_bin_parent(bin)<<3) + 1; if (bin > first) --bin; else bin = hts_bin_parent(bin); } while (bin); if (bin == 0) k = kh_get(bin, bidx, bin); min_off = k != kh_end(bidx)? kh_val(bidx, k).loff : 0; // min_off can be calculated more accurately if the // linear index is available if (idx->lidx[tid].offset && rel_off < idx->lidx[tid].n) { if (min_off < idx->lidx[tid].offset[rel_off]) min_off = idx->lidx[tid].offset[rel_off]; if (unmapped) { // unmapped reads are not covered by the linear index, // so search backwards for a smaller offset int tmp_off; for (tmp_off = rel_off-1; tmp_off >= 0; tmp_off--) { if (idx->lidx[tid].offset[tmp_off] < min_off) { min_off = idx->lidx[tid].offset[tmp_off]; break; } } // if the search went too far back or no satisfactory entry // was found, revert to the bin index loff value if (k != kh_end(bidx) && (min_off < kh_val(bidx, k).loff || tmp_off < 0)) min_off = kh_val(bidx, k).loff; } } else if (unmapped) { //CSI index if (k != kh_end(bidx)) min_off = kh_val(bidx, k).loff; } // compute max_off: a virtual offset from a bin to the right of end // First check if end lies within the range of the index (it won't // if it's HTS_POS_MAX) if (end <= idx_maxpos) { bin = hts_bin_first(idx->n_lvls) + ((end-1) >> idx->min_shift) + 1; if (bin >= idx->n_bins) bin = 0; while (1) { // search for an extant bin by moving right, but moving up to the // parent whenever we get to a first child (which also covers falling // off the RHS, which wraps around and immediately goes up to bin 0) while (bin % 8 == 1) bin = hts_bin_parent(bin); if (bin == 0) { max_off = UINT64_MAX; break; } k = kh_get(bin, bidx, bin); if (k != kh_end(bidx) && kh_val(bidx, k).n > 0) { max_off = kh_val(bidx, k).list[0].u; break; } bin++; } } else { // Searching to end of reference max_off = UINT64_MAX; } // retrieve bins if (reg2bins(beg, end, iter, idx->min_shift, idx->n_lvls, bidx) < 0) { hts_itr_destroy(iter); return NULL; } for (i = n_off = 0; i < iter->bins.n; ++i) if ((k = kh_get(bin, bidx, iter->bins.a[i])) != kh_end(bidx)) n_off += kh_value(bidx, k).n; if (n_off == 0) { // No overlapping bins means the iterator has already finished. iter->finished = 1; return iter; } off = calloc(n_off, sizeof(*off)); for (i = n_off = 0; i < iter->bins.n; ++i) { if ((k = kh_get(bin, bidx, iter->bins.a[i])) != kh_end(bidx)) { int j; bins_t *p = &kh_value(bidx, k); for (j = 0; j < p->n; ++j) if (p->list[j].v > min_off && p->list[j].u < max_off) { off[n_off].u = min_off > p->list[j].u ? min_off : p->list[j].u; off[n_off].v = max_off < p->list[j].v ? max_off : p->list[j].v; // hts_pair64_max_t::max is now used to link // file offsets to region list entries. // The iterator can use this to decide if it // can skip some file regions. off[n_off].max = ((uint64_t) tid << 32) | j; n_off++; } } } if (n_off == 0) { free(off); iter->finished = 1; return iter; } ks_introsort(_off_max, n_off, off); // resolve completely contained adjacent blocks for (i = 1, l = 0; i < n_off; ++i) if (off[l].v < off[i].v) off[++l] = off[i]; n_off = l + 1; // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing for (i = 1; i < n_off; ++i) if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u; // merge adjacent blocks for (i = 1, l = 0; i < n_off; ++i) { if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v; else off[++l] = off[i]; } n_off = l + 1; iter->n_off = n_off; iter->off = off; } } return iter; } int hts_itr_multi_bam(const hts_idx_t *idx, hts_itr_t *iter) { int i, j, bin; khint_t k; bidx_t *bidx; uint64_t min_off, max_off, t_off = (uint64_t)-1; int tid; hts_pos_t beg, end, idx_maxpos; hts_reglist_t *curr_reg; uint32_t unmapped = 0, rel_off; if (!idx || !iter || !iter->multi) return -1; iter->i = -1; for (i=0; in_reg; i++) { curr_reg = &iter->reg_list[i]; tid = curr_reg->tid; if (tid < 0) { t_off = hts_itr_off(idx, tid); if (t_off != (uint64_t)-1) { switch (tid) { case HTS_IDX_NONE: iter->finished = 1; // fall through case HTS_IDX_START: case HTS_IDX_REST: iter->curr_off = t_off; iter->n_reg = 0; iter->reg_list = NULL; iter->read_rest = 1; return 0; case HTS_IDX_NOCOOR: iter->nocoor = 1; iter->nocoor_off = t_off; } } } else { if (tid >= idx->n || (bidx = idx->bidx[tid]) == NULL || !kh_size(bidx)) continue; k = kh_get(bin, bidx, META_BIN(idx)); if (k != kh_end(bidx)) unmapped = kh_val(bidx, k).list[1].v; else unmapped = 1; idx_maxpos = hts_idx_maxpos(idx); for(j=0; jcount; j++) { hts_pair32_t *curr_intv = &curr_reg->intervals[j]; if (curr_intv->end < curr_intv->beg) continue; beg = curr_intv->beg; end = curr_intv->end; if (beg >= idx_maxpos) continue; rel_off = beg>>idx->min_shift; /* Compute 'min_off' by searching the lowest level bin containing 'beg'. If the computed bin is not in the index, try the next bin to the left, belonging to the same parent. If it is the first sibling bin, try the parent bin. */ bin = hts_bin_first(idx->n_lvls) + rel_off; do { int first; k = kh_get(bin, bidx, bin); if (k != kh_end(bidx)) break; first = (hts_bin_parent(bin)<<3) + 1; if (bin > first) --bin; else bin = hts_bin_parent(bin); } while (bin); if (bin == 0) k = kh_get(bin, bidx, bin); min_off = k != kh_end(bidx)? kh_val(bidx, k).loff : 0; // min_off can be calculated more accurately if the // linear index is available if (idx->lidx[tid].offset && rel_off < idx->lidx[tid].n) { if (min_off < idx->lidx[tid].offset[rel_off]) min_off = idx->lidx[tid].offset[rel_off]; if (unmapped) { int tmp_off; for (tmp_off = rel_off-1; tmp_off >= 0; tmp_off--) { if (idx->lidx[tid].offset[tmp_off] < min_off) { min_off = idx->lidx[tid].offset[tmp_off]; break; } } if (k != kh_end(bidx) && (min_off < kh_val(bidx, k).loff || tmp_off < 0)) min_off = kh_val(bidx, k).loff; } } else if (unmapped) { //CSI index if (k != kh_end(bidx)) min_off = kh_val(bidx, k).loff; } // compute max_off: a virtual offset from a bin to the right of end // First check if end lies within the range of the index (it // won't if it's HTS_POS_MAX) if (end <= idx_maxpos) { bin = hts_bin_first(idx->n_lvls) + ((end-1) >> idx->min_shift) + 1; if (bin >= idx->n_bins) bin = 0; while (1) { // search for an extant bin by moving right, but moving up to the // parent whenever we get to a first child (which also covers falling // off the RHS, which wraps around and immediately goes up to bin 0) while (bin % 8 == 1) bin = hts_bin_parent(bin); if (bin == 0) { max_off = UINT64_MAX; break; } k = kh_get(bin, bidx, bin); if (k != kh_end(bidx) && kh_val(bidx, k).n > 0) { max_off = kh_val(bidx, k).list[0].u; break; } bin++; } } else { // Searching to end of reference max_off = UINT64_MAX; } //convert coordinates to file offsets if (reg2intervals(iter, idx, tid, beg, end, j, min_off, max_off, idx->min_shift, idx->n_lvls) < 0) { return -1; } } } } if (iter->n_off > 1) ks_introsort(_off_max, iter->n_off, iter->off); if(!iter->n_off && !iter->nocoor) iter->finished = 1; return 0; } int hts_itr_multi_cram(const hts_idx_t *idx, hts_itr_t *iter) { const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx; int tid, i, n_off = 0; uint32_t j; hts_pos_t beg, end; hts_reglist_t *curr_reg; hts_pair32_t *curr_intv; hts_pair64_max_t *off = NULL, *tmp; cram_index *e = NULL; if (!cidx || !iter || !iter->multi) return -1; iter->is_cram = 1; iter->read_rest = 0; iter->off = NULL; iter->n_off = 0; iter->curr_off = 0; iter->i = -1; for (i=0; in_reg; i++) { curr_reg = &iter->reg_list[i]; tid = curr_reg->tid; if (tid >= 0) { tmp = realloc(off, (n_off + curr_reg->count) * sizeof(*off)); if (!tmp) goto err; off = tmp; for (j=0; j < curr_reg->count; j++) { curr_intv = &curr_reg->intervals[j]; if (curr_intv->end < curr_intv->beg) continue; beg = curr_intv->beg; end = curr_intv->end; /* First, fetch the container overlapping 'beg' and assign its file offset to u, then * find the container overlapping 'end' and assign the relative end of the slice to v. * The cram_ptell function will adjust with the container offset, which is not stored * in the index. */ e = cram_index_query(cidx->cram, tid, beg+1, NULL); if (e) { off[n_off].u = e->offset; // hts_pair64_max_t::max is now used to link // file offsets to region list entries. // The iterator can use this to decide if it // can skip some file regions. off[n_off].max = ((uint64_t) tid << 32) | j; if (end >= HTS_POS_MAX) { e = cram_index_last(cidx->cram, tid, NULL); } else { e = cram_index_query_last(cidx->cram, tid, end+1); } if (e) { off[n_off++].v = e->e_next ? e->e_next->offset : e->offset + e->slice + e->len; } else { hts_log_warning("Could not set offset end for region %d:%"PRIhts_pos"-%"PRIhts_pos". Skipping", tid, beg, end); } } } } else { switch (tid) { case HTS_IDX_NOCOOR: e = cram_index_query(cidx->cram, tid, 1, NULL); if (e) { iter->nocoor = 1; iter->nocoor_off = e->offset; } else { hts_log_warning("No index entry for NOCOOR region"); } break; case HTS_IDX_START: e = cram_index_query(cidx->cram, tid, 1, NULL); if (e) { iter->read_rest = 1; tmp = realloc(off, sizeof(*off)); if (!tmp) goto err; off = tmp; off[0].u = e->offset; off[0].v = 0; n_off=1; } else { hts_log_warning("No index entries"); } break; case HTS_IDX_REST: break; case HTS_IDX_NONE: iter->finished = 1; break; default: hts_log_error("Query with tid=%d not implemented for CRAM files", tid); } } } if (n_off) { ks_introsort(_off_max, n_off, off); iter->n_off = n_off; iter->off = off; } if(!n_off && !iter->nocoor) iter->finished = 1; return 0; err: free(off); return -1; } void hts_itr_destroy(hts_itr_t *iter) { if (iter) { if (iter->multi) { hts_reglist_free(iter->reg_list, iter->n_reg); } else { free(iter->bins.a); } if (iter->off) free(iter->off); free(iter); } } static inline unsigned long long push_digit(unsigned long long i, char c) { // ensure subtraction occurs first, avoiding overflow for >= MAX-48 or so int digit = c - '0'; return 10 * i + digit; } long long hts_parse_decimal(const char *str, char **strend, int flags) { unsigned long long n = 0; int digits = 0, decimals = 0, e = 0, lost = 0; char sign = '+', esign = '+'; const char *s, *str_orig = str; while (isspace_c(*str)) str++; s = str; if (*s == '+' || *s == '-') sign = *s++; while (*s) if (isdigit_c(*s)) digits++, n = push_digit(n, *s++); else if (*s == ',' && (flags & HTS_PARSE_THOUSANDS_SEP)) s++; else break; if (*s == '.') { s++; while (isdigit_c(*s)) decimals++, digits++, n = push_digit(n, *s++); } switch (*s) { case 'e': case 'E': s++; if (*s == '+' || *s == '-') esign = *s++; while (isdigit_c(*s)) e = push_digit(e, *s++); if (esign == '-') e = -e; break; case 'k': case 'K': e += 3; s++; break; case 'm': case 'M': e += 6; s++; break; case 'g': case 'G': e += 9; s++; break; } e -= decimals; while (e > 0) n *= 10, e--; while (e < 0) lost += n % 10, n /= 10, e++; if (lost > 0) { hts_log_warning("Discarding fractional part of %.*s", (int)(s - str), str); } if (strend) { // Set to the original input str pointer if not valid number syntax *strend = (digits > 0)? (char *)s : (char *)str_orig; } else if (digits == 0) { hts_log_warning("Invalid numeric value %.8s[truncated]", str); } else if (*s) { if ((flags & HTS_PARSE_THOUSANDS_SEP) || (!(flags & HTS_PARSE_THOUSANDS_SEP) && *s != ',')) hts_log_warning("Ignoring unknown characters after %.*s[%s]", (int)(s - str), str, s); } return (sign == '+')? n : -n; } static void *hts_memrchr(const void *s, int c, size_t n) { size_t i; unsigned char *u = (unsigned char *)s; for (i = n; i > 0; i--) { if (u[i-1] == c) return u+i-1; } return NULL; } /* * A variant of hts_parse_reg which is reference-id aware. It uses * the iterator name2id callbacks to validate the region tokenisation works. * * This is necessary due to GRCh38 HLA additions which have reference names * like "HLA-DRB1*12:17". * * All parameters are mandatory. * * To work around ambiguous parsing issues, eg both "chr1" and "chr1:100-200" * are reference names, we may quote using curly braces. * Thus "{chr1}:100-200" and "{chr1:100-200}" disambiguate the above example. * * Flags are used to control how parsing works, and can be one of the below. * * HTS_PARSE_LIST: * If present, the region is assmed to be a comma separated list and * position parsing will not contain commas (this implicitly * clears HTS_PARSE_THOUSANDS_SEP in the call to hts_parse_decimal). * On success the return pointer will be the start of the next region, ie * the character after the comma. (If *ret != '\0' then the caller can * assume another region is present in the list.) * * If not set then positions may contain commas. In this case the return * value should point to the end of the string, or NULL on failure. * * HTS_PARSE_ONE_COORD: * If present, X:100 is treated as the single base pair region X:100-100. * In this case X:-100 is shorthand for X:1-100 and X:100- is X:100-. * (This is the standard bcftools region convention.) * * When not set X:100 is considered to be X:100- where is * the end of chromosome X (set to HTS_POS_MAX here). X:100- and X:-100 * are invalid. * (This is the standard samtools region convention.) * * Note the supplied string expects 1 based inclusive coordinates, but the * returned coordinates start from 0 and are half open, so pos0 is valid * for use in e.g. "for (pos0 = beg; pos0 < end; pos0++) {...}" * * On success a pointer to the byte after the end of the entire region * specifier is returned (plus any trailing comma), and tid, * beg & end will be set. * On failure NULL is returned. */ const char *hts_parse_region(const char *s, int *tid, hts_pos_t *beg, hts_pos_t *end, hts_name2id_f getid, void *hdr, int flags) { if (!s || !tid || !beg || !end || !getid) return NULL; size_t s_len = strlen(s); kstring_t ks = { 0, 0, NULL }; const char *colon = NULL, *comma = NULL; int quoted = 0; if (flags & HTS_PARSE_LIST) flags &= ~HTS_PARSE_THOUSANDS_SEP; else flags |= HTS_PARSE_THOUSANDS_SEP; const char *s_end = s + s_len; // Braced quoting of references is permitted to resolve ambiguities. if (*s == '{') { const char *close = memchr(s, '}', s_len); if (!close) { hts_log_error("Mismatching braces in \"%s\"", s); *tid = -1; return NULL; } s++; s_len--; if (close[1] == ':') colon = close+1; quoted = 1; // number of trailing characters to trim // Truncate to this item only, if appropriate. if (flags & HTS_PARSE_LIST) { comma = strchr(close, ','); if (comma) { s_len = comma-s; s_end = comma+1; } } } else { // Truncate to this item only, if appropriate. if (flags & HTS_PARSE_LIST) { comma = strchr(s, ','); if (comma) { s_len = comma-s; s_end = comma+1; } } colon = hts_memrchr(s, ':', s_len); } // No colon is simplest case; just check and return. if (colon == NULL) { *beg = 0; *end = HTS_POS_MAX; kputsn(s, s_len-quoted, &ks); // convert to nul terminated string if (!ks.s) { *tid = -2; return NULL; } *tid = getid(hdr, ks.s); free(ks.s); return *tid >= 0 ? s_end : NULL; } // Has a colon, but check whole name first. if (!quoted) { *beg = 0; *end = HTS_POS_MAX; kputsn(s, s_len, &ks); // convert to nul terminated string if (!ks.s) { *tid = -2; return NULL; } if ((*tid = getid(hdr, ks.s)) >= 0) { // Entire name matches, but also check this isn't // ambiguous. eg we have ref chr1 and ref chr1:100-200 // both present. ks.l = 0; kputsn(s, colon-s, &ks); // convert to nul terminated string if (!ks.s) { *tid = -2; return NULL; } if (getid(hdr, ks.s) >= 0) { free(ks.s); *tid = -1; hts_log_error("Range is ambiguous. " "Use {%s} or {%.*s}%s instead", s, (int)(colon-s), s, colon); return NULL; } free(ks.s); return s_end; } if (*tid < -1) // Failed to parse header return NULL; } // Quoted, or unquoted and whole string isn't a name. // Check the pre-colon part is valid. ks.l = 0; kputsn(s, colon-s-quoted, &ks); // convert to nul terminated string if (!ks.s) { *tid = -2; return NULL; } *tid = getid(hdr, ks.s); free(ks.s); if (*tid < 0) return NULL; // Finally parse the post-colon coordinates char *hyphen; *beg = hts_parse_decimal(colon+1, &hyphen, flags) - 1; if (*beg < 0) { if (*beg != -1 && *hyphen == '-' && colon[1] != '\0') { // User specified zero, but we're 1-based. hts_log_error("Coordinates must be > 0"); return NULL; } if (isdigit_c(*hyphen) || *hyphen == '\0' || *hyphen == ',') { // interpret chr:-100 as chr:1-100 *end = *beg==-1 ? HTS_POS_MAX : -(*beg+1); *beg = 0; return s_end; } else if (*beg < -1) { hts_log_error("Unexpected string \"%s\" after region", hyphen); return NULL; } } if (*hyphen == '\0' || ((flags & HTS_PARSE_LIST) && *hyphen == ',')) { *end = flags & HTS_PARSE_ONE_COORD ? *beg+1 : HTS_POS_MAX; } else if (*hyphen == '-') { *end = hts_parse_decimal(hyphen+1, &hyphen, flags); if (*hyphen != '\0' && *hyphen != ',') { hts_log_error("Unexpected string \"%s\" after region", hyphen); return NULL; } } else { hts_log_error("Unexpected string \"%s\" after region", hyphen); return NULL; } if (*end == 0) *end = HTS_POS_MAX; // interpret chr:100- as chr:100- if (*beg >= *end) return NULL; return s_end; } // Next release we should mark this as deprecated? // Use hts_parse_region above instead. const char *hts_parse_reg64(const char *s, hts_pos_t *beg, hts_pos_t *end) { char *hyphen; const char *colon = strrchr(s, ':'); if (colon == NULL) { *beg = 0; *end = HTS_POS_MAX; return s + strlen(s); } *beg = hts_parse_decimal(colon+1, &hyphen, HTS_PARSE_THOUSANDS_SEP) - 1; if (*beg < 0) *beg = 0; if (*hyphen == '\0') *end = HTS_POS_MAX; else if (*hyphen == '-') *end = hts_parse_decimal(hyphen+1, NULL, HTS_PARSE_THOUSANDS_SEP); else return NULL; if (*beg >= *end) return NULL; return colon; } const char *hts_parse_reg(const char *s, int *beg, int *end) { hts_pos_t beg64 = 0, end64 = 0; const char *colon = hts_parse_reg64(s, &beg64, &end64); if (beg64 > INT_MAX) { hts_log_error("Position %"PRId64" too large", beg64); return NULL; } if (end64 > INT_MAX) { if (end64 == HTS_POS_MAX) { end64 = INT_MAX; } else { hts_log_error("Position %"PRId64" too large", end64); return NULL; } } *beg = beg64; *end = end64; return colon; } hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec) { int tid; hts_pos_t beg, end; if (strcmp(reg, ".") == 0) return itr_query(idx, HTS_IDX_START, 0, 0, readrec); else if (strcmp(reg, "*") == 0) return itr_query(idx, HTS_IDX_NOCOOR, 0, 0, readrec); if (!hts_parse_region(reg, &tid, &beg, &end, getid, hdr, HTS_PARSE_THOUSANDS_SEP)) return NULL; return itr_query(idx, tid, beg, end, readrec); } hts_itr_t *hts_itr_regions(const hts_idx_t *idx, hts_reglist_t *reglist, int count, hts_name2id_f getid, void *hdr, hts_itr_multi_query_func *itr_specific, hts_readrec_func *readrec, hts_seek_func *seek, hts_tell_func *tell) { int i; if (!reglist) return NULL; hts_itr_t *itr = (hts_itr_t*)calloc(1, sizeof(hts_itr_t)); if (itr) { itr->n_reg = count; itr->readrec = readrec; itr->seek = seek; itr->tell = tell; itr->reg_list = reglist; itr->finished = 0; itr->nocoor = 0; itr->multi = 1; for (i = 0; i < itr->n_reg; i++) { if (itr->reg_list[i].reg) { if (!strcmp(itr->reg_list[i].reg, ".")) { itr->reg_list[i].tid = HTS_IDX_START; continue; } if (!strcmp(itr->reg_list[i].reg, "*")) { itr->reg_list[i].tid = HTS_IDX_NOCOOR; continue; } itr->reg_list[i].tid = getid(hdr, reglist[i].reg); if (itr->reg_list[i].tid < 0) { if (itr->reg_list[i].tid < -1) { hts_log_error("Failed to parse header"); hts_itr_destroy(itr); return NULL; } else { hts_log_warning("Region '%s' specifies an unknown reference name. Continue anyway", reglist[i].reg); } } } } qsort(itr->reg_list, itr->n_reg, sizeof(hts_reglist_t), compare_regions); if (itr_specific(idx, itr) != 0) { hts_log_error("Failed to create the multi-region iterator!"); hts_itr_destroy(itr); itr = NULL; } } return itr; } int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, void *data) { int ret, tid; hts_pos_t beg, end; if (iter == NULL || iter->finished) return -1; if (iter->read_rest) { if (iter->curr_off) { // seek to the start if (bgzf_seek(fp, iter->curr_off, SEEK_SET) < 0) { hts_log_error("Failed to seek to offset %"PRIu64"%s%s", iter->curr_off, errno ? ": " : "", strerror(errno)); return -2; } iter->curr_off = 0; // only seek once } ret = iter->readrec(fp, data, r, &tid, &beg, &end); if (ret < 0) iter->finished = 1; iter->curr_tid = tid; iter->curr_beg = beg; iter->curr_end = end; return ret; } // A NULL iter->off should always be accompanied by iter->finished. assert(iter->off != NULL); for (;;) { if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk if (iter->i == iter->n_off - 1) { ret = -1; break; } // no more chunks if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek if (bgzf_seek(fp, iter->off[iter->i+1].u, SEEK_SET) < 0) { hts_log_error("Failed to seek to offset %"PRIu64"%s%s", iter->off[iter->i+1].u, errno ? ": " : "", strerror(errno)); return -2; } iter->curr_off = bgzf_tell(fp); } ++iter->i; } if ((ret = iter->readrec(fp, data, r, &tid, &beg, &end)) >= 0) { iter->curr_off = bgzf_tell(fp); if (tid != iter->tid || beg >= iter->end) { // no need to proceed ret = -1; break; } else if (end > iter->beg && iter->end > beg) { iter->curr_tid = tid; iter->curr_beg = beg; iter->curr_end = end; return ret; } } else break; // end of file or error } iter->finished = 1; return ret; } int hts_itr_multi_next(htsFile *fd, hts_itr_t *iter, void *r) { void *fp; int ret, tid, i, cr, ci; hts_pos_t beg, end; hts_reglist_t *found_reg; if (iter == NULL || iter->finished) return -1; if (iter->is_cram) { fp = fd->fp.cram; } else { fp = fd->fp.bgzf; } if (iter->read_rest) { if (iter->curr_off) { // seek to the start if (iter->seek(fp, iter->curr_off, SEEK_SET) < 0) { hts_log_error("Seek at offset %" PRIu64 " failed.", iter->curr_off); return -1; } iter->curr_off = 0; // only seek once } ret = iter->readrec(fp, fd, r, &tid, &beg, &end); if (ret < 0) iter->finished = 1; iter->curr_tid = tid; iter->curr_beg = beg; iter->curr_end = end; return ret; } // A NULL iter->off should always be accompanied by iter->finished. assert(iter->off != NULL || iter->nocoor != 0); int next_range = 0; for (;;) { // Note that due to the way bam indexing works, iter->off may contain // file chunks that are not actually needed as they contain data // beyond the end of the requested region. These are filtered out // by comparing the tid and index into hts_reglist_t::intervals // (packed for reasons of convenience into iter->off[iter->i].max) // associated with the file region with iter->curr_tid and // iter->curr_intv. if (next_range || iter->curr_off == 0 || iter->i >= iter->n_off || iter->curr_off >= iter->off[iter->i].v || (iter->off[iter->i].max >> 32 == iter->curr_tid && (iter->off[iter->i].max & 0xffffffff) < iter->curr_intv)) { // Jump to the next chunk. It may be necessary to skip more // than one as the iter->off list can include overlapping entries. do { iter->i++; } while (iter->i < iter->n_off && (iter->curr_off >= iter->off[iter->i].v || (iter->off[iter->i].max >> 32 == iter->curr_tid && (iter->off[iter->i].max & 0xffffffff) < iter->curr_intv))); if (iter->is_cram && iter->i < iter->n_off) { // Ensure iter->curr_reg is correct. // // We need this for CRAM as we shortcut some of the later // logic by getting an end-of-range and continuing to the // next offset. // // We cannot do this for BAM (and fortunately do not need to // either) because in BAM world a query to genomic positions // GX and GY leading to a seek offsets PX and PY may have // GX > GY and PX < PY. (This is due to the R-tree and falling // between intervals, bumping up to a higher bin.) // CRAM strictly follows PX >= PY if GX >= GY, so this logic // works. int want_tid = iter->off[iter->i].max >> 32; if (!(iter->curr_reg < iter->n_reg && iter->reg_list[iter->curr_reg].tid == want_tid)) { int j; for (j = 0; j < iter->n_reg; j++) if (iter->reg_list[j].tid == want_tid) break; if (j == iter->n_reg) return -1; iter->curr_reg = j; iter->curr_tid = iter->reg_list[iter->curr_reg].tid; }; iter->curr_intv = iter->off[iter->i].max & 0xffffffff; } if (iter->i >= iter->n_off) { // no more chunks, except NOCOORs if (iter->nocoor) { next_range = 0; if (iter->seek(fp, iter->nocoor_off, SEEK_SET) < 0) { hts_log_error("Seek at offset %" PRIu64 " failed.", iter->nocoor_off); return -1; } if (iter->is_cram) { cram_range r = { HTS_IDX_NOCOOR }; cram_set_option(fp, CRAM_OPT_RANGE_NOSEEK, &r); } // The first slice covering the unmapped reads might // contain a few mapped reads, so scroll // forward until finding the first unmapped read. do { ret = iter->readrec(fp, fd, r, &tid, &beg, &end); } while (tid >= 0 && ret >=0); if (ret < 0) iter->finished = 1; else iter->read_rest = 1; iter->curr_off = 0; // don't seek any more iter->curr_tid = tid; iter->curr_beg = beg; iter->curr_end = end; return ret; } else { ret = -1; break; } } else if (iter->i < iter->n_off) { // New chunk may overlap the last one, so ensure we // only seek forwards. if (iter->curr_off < iter->off[iter->i].u || next_range) { iter->curr_off = iter->off[iter->i].u; // CRAM has the capability of setting an end location. // This means multi-threaded decodes can stop once they // reach that point, rather than pointlessly decoding // more slices than we'll be using. // // We have to be careful here. Whenever we set the cram // range we need a corresponding seek in order to ensure // we can safely decode at that offset. We use next_range // var to ensure this is always true; this is set on // end-of-range condition. It's never modified for BAM. if (iter->is_cram) { // Next offset.[uv] tuple, but it's already been // included in our cram range, so don't seek and don't // reset range so we can efficiently multi-thread. if (next_range || iter->curr_off >= iter->end) { if (iter->seek(fp, iter->curr_off, SEEK_SET) < 0) { hts_log_error("Seek at offset %" PRIu64 " failed.", iter->curr_off); return -1; } // Find the genomic range matching this interval. int j; hts_reglist_t *rl = &iter->reg_list[iter->curr_reg]; cram_range r = { rl->tid, rl->intervals[iter->curr_intv].beg, rl->intervals[iter->curr_intv].end }; // Expand it up to cover neighbouring intervals. // Note we can only have a single chromosome in a // range, so if we detect our blocks span chromosomes // or we have a multi-ref mode slice, we just use // HTS_IDX_START refid instead. This doesn't actually // seek (due to CRAM_OPT_RANGE_NOSEEK) and is simply // and indicator of decoding with no end limit. // // That isn't as efficient as it could be, but it's // no poorer than before and it works. int tid = r.refid; int64_t end = r.end; int64_t v = iter->off[iter->i].v; j = iter->i+1; while (j < iter->n_off) { if (iter->off[j].u > v) break; uint64_t max = iter->off[j].max; if ((max>>32) != tid) { tid = HTS_IDX_START; // => no range limit } else { if (end < rl->intervals[max & 0xffffffff].end) end = rl->intervals[max & 0xffffffff].end; } if (v < iter->off[j].v) v = iter->off[j].v; j++; } r.refid = tid; r.end = end; // Remember maximum 'v' here so we don't do // unnecessary subsequent seeks for the next // regions. We can't change curr_off, but // beg/end are used only by single region iterator so // we cache it there to avoid changing the struct. iter->end = v; cram_set_option(fp, CRAM_OPT_RANGE_NOSEEK, &r); next_range = 0; } } else { // Not CRAM if (iter->seek(fp, iter->curr_off, SEEK_SET) < 0) { hts_log_error("Seek at offset %" PRIu64 " failed.", iter->curr_off); return -1; } } } } } ret = iter->readrec(fp, fd, r, &tid, &beg, &end); if (ret < 0) { if (iter->is_cram && cram_eof(fp)) { // Skip to end of range // // We should never be adjusting curr_off manually unless // we also can guarantee we'll be doing a seek after to // a new location. Otherwise we'll be reading wrong offset // for the next container. // // We ensure this by adjusting our CRAM_OPT_RANGE // accordingly above, but to double check we also // set the skipped_block flag to enforce a seek also. iter->curr_off = iter->off[iter->i].v; next_range = 1; // Next region if (++iter->curr_intv >= iter->reg_list[iter->curr_reg].count){ if (++iter->curr_reg >= iter->n_reg) break; iter->curr_intv = 0; iter->curr_tid = iter->reg_list[iter->curr_reg].tid; } continue; } else { break; } } iter->curr_off = iter->tell(fp); if (tid != iter->curr_tid) { hts_reglist_t key; key.tid = tid; found_reg = (hts_reglist_t *)bsearch(&key, iter->reg_list, iter->n_reg, sizeof(hts_reglist_t), compare_regions); if (!found_reg) continue; iter->curr_reg = (found_reg - iter->reg_list); iter->curr_tid = tid; iter->curr_intv = 0; } cr = iter->curr_reg; ci = iter->curr_intv; for (i = ci; i < iter->reg_list[cr].count; i++) { if (end > iter->reg_list[cr].intervals[i].beg && iter->reg_list[cr].intervals[i].end > beg) { iter->curr_beg = beg; iter->curr_end = end; iter->curr_intv = i; return ret; } // Check if the read starts beyond intervals[i].end // If so, the interval is finished so move on to the next. if (beg > iter->reg_list[cr].intervals[i].end) iter->curr_intv = i + 1; // No need to keep searching if the read ends before intervals[i].beg if (end < iter->reg_list[cr].intervals[i].beg) break; } } iter->finished = 1; return ret; } /********************** *** Retrieve index *** **********************/ // Local_fn and local_len will return a sub-region of 'fn'. // Eg http://elsewhere/dir/foo.bam.bai?a=b may return // foo.bam.bai via local_fn and local_len. // // Returns -1 if index couldn't be opened. // -2 on other errors static int idx_test_and_fetch(const char *fn, const char **local_fn, int *local_len, int download) { hFILE *remote_hfp = NULL; hFILE *local_fp = NULL; int save_errno; htsFormat fmt; kstring_t s = KS_INITIALIZE; kstring_t tmps = KS_INITIALIZE; if (hisremote(fn)) { const int buf_size = 1 * 1024 * 1024; int l; const char *p, *e; // Ignore ?# params: eg any file.fmt?param=val, except for S3 URLs e = fn + ((strncmp(fn, "s3://", 5) && strncmp(fn, "s3+http://", 10) && strncmp(fn, "s3+https://", 11)) ? strcspn(fn, "?#") : strcspn(fn, "?")); // Find the previous slash from there. p = e; while (p > fn && *p != '/') p--; if (*p == '/') p++; // Attempt to open local file first kputsn(p, e-p, &s); if (access(s.s, R_OK) == 0) { free(s.s); *local_fn = p; *local_len = e-p; return 0; } // Attempt to open remote file. Stay quiet on failure, it is OK to fail when trying first .csi then .bai or .tbi index. if ((remote_hfp = hopen(fn, "r")) == 0) { hts_log_info("Failed to open index file '%s'", fn); free(s.s); return -1; } if (hts_detect_format2(remote_hfp, fn, &fmt)) { hts_log_error("Failed to detect format of index file '%s'", fn); goto fail; } if (fmt.category != index_file || (fmt.format != bai && fmt.format != csi && fmt.format != tbi && fmt.format != crai && fmt.format != fai_format)) { hts_log_error("Format of index file '%s' is not supported", fn); goto fail; } if (download) { if ((local_fp = hts_open_tmpfile(s.s, "wx", &tmps)) == NULL) { hts_log_error("Failed to create file %s in the working directory", p); goto fail; } hts_log_info("Downloading file %s to local directory", fn); uint8_t *buf = (uint8_t*)calloc(buf_size, 1); if (!buf) { hts_log_error("%s", strerror(errno)); goto fail; } while ((l = hread(remote_hfp, buf, buf_size)) > 0) { if (hwrite(local_fp, buf, l) != l) { hts_log_error("Failed to write data to %s : %s", fn, strerror(errno)); free(buf); goto fail; } } free(buf); if (l < 0) { hts_log_error("Error reading \"%s\"", fn); goto fail; } if (hclose(local_fp) < 0) { hts_log_error("Error closing %s : %s", fn, strerror(errno)); local_fp = NULL; goto fail; } local_fp = NULL; if (rename(tmps.s, s.s) < 0) { hts_log_error("Error renaming %s : %s", tmps.s, strerror(errno)); goto fail; } ks_clear(&tmps); *local_fn = p; *local_len = e-p; } else { *local_fn = fn; *local_len = e-fn; } if (hclose(remote_hfp) != 0) { hts_log_error("Failed to close remote file %s", fn); } free(tmps.s); free(s.s); return 0; } else { hFILE *local_hfp; if ((local_hfp = hopen(fn, "r")) == 0) return -1; hclose_abruptly(local_hfp); *local_fn = fn; *local_len = strlen(fn); return 0; } fail: save_errno = errno; if (remote_hfp) hclose_abruptly(remote_hfp); if (local_fp) hclose_abruptly(local_fp); if (tmps.l > 0) unlink(tmps.s); free(tmps.s); free(s.s); errno = save_errno; return -2; } /* * Check the existence of a local index file using part of the alignment * file name. * * For a filename fn of fn.fmt (eg fn.bam or fn.cram) the order of checks is * fn.fmt.csi, fn.csi, * fn.fmt.bai, fn.bai - if fmt is HTS_FMT_BAI * fn.fmt.tbi, fn.tbi - if fmt is HTS_FMT_TBI * fn.fmt.crai, fn.crai - if fmt is HTS_FMT_CRAI * fn.fmt.fai - if fmt is HTS_FMT_FAI * also .gzi if fmt is ".gz" * * @param fn - pointer to the file name * @param fmt - one of the HTS_FMT index formats * @param fnidx - pointer to the index file name placeholder * @return 1 for success, 0 for failure */ int hts_idx_check_local(const char *fn, int fmt, char **fnidx) { int i, l_fn, l_ext; const char *fn_tmp = NULL; char *fnidx_tmp; const char *csi_ext = ".csi"; const char *bai_ext = ".bai"; const char *tbi_ext = ".tbi"; const char *crai_ext = ".crai"; const char *fai_ext = ".fai"; const char *gzi_ext = ".gzi"; if (!fn) return 0; if (hisremote(fn)) { for (i = strlen(fn) - 1; i >= 0; --i) if (fn[i] == '/') { fn_tmp = (char *)&fn[i+1]; break; } } else { // Borrowed from hopen_fd_fileuri() if (strncmp(fn, "file://localhost/", 17) == 0) fn_tmp = fn + 16; else if (strncmp(fn, "file:///", 8) == 0) fn_tmp = fn + 7; else fn_tmp = fn; #if defined(_WIN32) || defined(__MSYS__) // For cases like C:/foo if (fn_tmp[0] == '/' && fn_tmp[1] && fn_tmp[2] == ':' && fn_tmp[3] == '/') fn_tmp++; #endif } if (!fn_tmp) return 0; hts_log_info("Using alignment file '%s'", fn_tmp); l_fn = strlen(fn_tmp); l_ext = 5; fnidx_tmp = (char*)calloc(l_fn + l_ext + 1, 1); if (!fnidx_tmp) return 0; struct stat sbuf; // Try alignment.bam.csi first strcpy(fnidx_tmp, fn_tmp); strcpy(fnidx_tmp + l_fn, csi_ext); if(stat(fnidx_tmp, &sbuf) == 0) { *fnidx = fnidx_tmp; return 1; } else { // Then try alignment.csi for (i = l_fn - 1; i > 0; --i) if (fnidx_tmp[i] == '.') { strcpy(fnidx_tmp + i, csi_ext); if(stat(fnidx_tmp, &sbuf) == 0) { *fnidx = fnidx_tmp; return 1; } break; } } if (fmt == HTS_FMT_BAI) { // Next, try alignment.bam.bai strcpy(fnidx_tmp, fn_tmp); strcpy(fnidx_tmp + l_fn, bai_ext); if(stat(fnidx_tmp, &sbuf) == 0) { *fnidx = fnidx_tmp; return 1; } else { // And finally, try alignment.bai for (i = l_fn - 1; i > 0; --i) if (fnidx_tmp[i] == '.') { strcpy(fnidx_tmp + i, bai_ext); if(stat(fnidx_tmp, &sbuf) == 0) { *fnidx = fnidx_tmp; return 1; } break; } } } else if (fmt == HTS_FMT_TBI) { // Or .tbi strcpy(fnidx_tmp, fn_tmp); strcpy(fnidx_tmp + l_fn, tbi_ext); if(stat(fnidx_tmp, &sbuf) == 0) { *fnidx = fnidx_tmp; return 1; } else { for (i = l_fn - 1; i > 0; --i) if (fnidx_tmp[i] == '.') { strcpy(fnidx_tmp + i, tbi_ext); if(stat(fnidx_tmp, &sbuf) == 0) { *fnidx = fnidx_tmp; return 1; } break; } } } else if (fmt == HTS_FMT_CRAI) { // Or .crai strcpy(fnidx_tmp, fn_tmp); strcpy(fnidx_tmp + l_fn, crai_ext); if(stat(fnidx_tmp, &sbuf) == 0) { *fnidx = fnidx_tmp; return 1; } else { for (i = l_fn - 1; i > 0; --i) if (fnidx_tmp[i] == '.') { strcpy(fnidx_tmp + i, crai_ext); if(stat(fnidx_tmp, &sbuf) == 0) { *fnidx = fnidx_tmp; return 1; } break; } } } else if (fmt == HTS_FMT_FAI) { // Or .fai // Check .gzi if we have a .gz file strcpy(fnidx_tmp, fn_tmp); int gzi_ok = 1; if ((l_fn > 3 && strcmp(fn_tmp+l_fn-3, ".gz") == 0) || (l_fn > 5 && strcmp(fn_tmp+l_fn-5, ".bgzf") == 0)) { strcpy(fnidx_tmp + l_fn, gzi_ext); gzi_ok = stat(fnidx_tmp, &sbuf)==0; } // Now check for .fai. Occurs second as we're returning this // in *fnidx irrespective of whether we did gzi check. strcpy(fnidx_tmp + l_fn, fai_ext); *fnidx = fnidx_tmp; if (stat(fnidx_tmp, &sbuf) == 0) return gzi_ok; else return 0; } free(fnidx_tmp); return 0; } static char *idx_filename(const char *fn, const char *ext, int download) { int ret, local_len; char *fnidx; const char *local_fn = NULL; kstring_t buffer = KS_INITIALIZE; // First try : append `ext` to `fn` if (!(fnidx = haddextension(&buffer, fn, 0, ext))) { free(buffer.s); return NULL; } if ((ret = idx_test_and_fetch(fnidx, &local_fn, &local_len, download)) == -1) { // Second try : replace suffix of `fn` with `ext` if (!(fnidx = haddextension(&buffer, fn, 1, ext))) { free(buffer.s); return NULL; } ret = idx_test_and_fetch(fnidx, &local_fn, &local_len, download); } if (ret < 0) { free(buffer.s); return NULL; } memmove(fnidx, local_fn, local_len); fnidx[local_len] = 0; return fnidx; } char *hts_idx_getfn(const char *fn, const char *ext) { return idx_filename(fn, ext, HTS_IDX_SAVE_REMOTE); } char *hts_idx_locatefn(const char *fn, const char *ext) { return idx_filename(fn, ext, 0); } static hts_idx_t *idx_find_and_load(const char *fn, int fmt, int flags) { char *fnidx = strstr(fn, HTS_IDX_DELIM); hts_idx_t *idx; if ( fnidx ) { char *fn2 = strdup(fn); if (!fn2) { hts_log_error("%s", strerror(errno)); return NULL; } fn2[fnidx - fn] = '\0'; fnidx += strlen(HTS_IDX_DELIM); idx = hts_idx_load3(fn2, fnidx, fmt, flags); free(fn2); return idx; } if (hts_idx_check_local(fn, fmt, &fnidx) == 0 && hisremote(fn)) { if (flags & HTS_IDX_SAVE_REMOTE) { fnidx = idx_filename(fn, ".csi", HTS_IDX_SAVE_REMOTE); if (!fnidx) { switch (fmt) { case HTS_FMT_BAI: fnidx = idx_filename(fn, ".bai", HTS_IDX_SAVE_REMOTE); break; case HTS_FMT_TBI: fnidx = idx_filename(fn, ".tbi", HTS_IDX_SAVE_REMOTE); break; default: break; } } } else { fnidx = idx_filename(fn, ".csi", 0); if (!fnidx) { switch (fmt) { case HTS_FMT_BAI: fnidx = idx_filename(fn, ".bai", 0); break; case HTS_FMT_TBI: fnidx = idx_filename(fn, ".tbi", 0); break; default: break; } } } } if (!fnidx) { if (!(flags & HTS_IDX_SILENT_FAIL)) hts_log_error("Could not retrieve index file for '%s'", fn); return 0; } if (flags & HTS_IDX_SAVE_REMOTE) idx = hts_idx_load3(fn, fnidx, fmt, flags); else idx = idx_read(fnidx); free(fnidx); return idx; } hts_idx_t *hts_idx_load(const char *fn, int fmt) { return idx_find_and_load(fn, fmt, 1); } hts_idx_t *hts_idx_load2(const char *fn, const char *fnidx) { return hts_idx_load3(fn, fnidx, 0, 0); } hts_idx_t *hts_idx_load3(const char *fn, const char *fnidx, int fmt, int flags) { const char *local_fn = NULL; char *local_fnidx = NULL; int local_len; if (!fnidx) return idx_find_and_load(fn, fmt, flags); // Check that the index file is up to date, the main file might have changed struct stat stat_idx,stat_main; int remote_fn = hisremote(fn), remote_fnidx = hisremote(fnidx); if ( !remote_fn && !remote_fnidx && !stat(fn, &stat_main) && !stat(fnidx, &stat_idx) ) { if ( stat_idx.st_mtime < stat_main.st_mtime ) hts_log_warning("The index file is older than the data file: %s", fnidx); } if (remote_fnidx && (flags & HTS_IDX_SAVE_REMOTE)) { int ret = idx_test_and_fetch(fnidx, &local_fn, &local_len, 1); if (ret == 0) { local_fnidx = strdup(local_fn); if (local_fnidx) { local_fnidx[local_len] = '\0'; fnidx = local_fnidx; } } } hts_idx_t *idx = idx_read(fnidx); if (!idx && !(flags & HTS_IDX_SILENT_FAIL)) hts_log_error("Could not load local index file '%s'%s%s", fnidx, errno ? " : " : "", errno ? strerror(errno) : ""); free(local_fnidx); return idx; } /********************** *** Memory *** **********************/ /* For use with hts_expand macros *only* */ HTSLIB_EXPORT size_t hts_realloc_or_die(size_t n, size_t m, size_t m_sz, size_t size, int clear, void **ptr, const char *func) { /* If new_m and size are both below this limit, multiplying them together can't overflow */ const size_t safe = (size_t) 1 << (sizeof(size_t) * 4); void *new_ptr; size_t bytes, new_m; new_m = n; kroundup_size_t(new_m); bytes = size * new_m; /* Check for overflow. Both ensure that new_m will fit in m (we make the pessimistic assumption that m is signed), and that bytes has not wrapped around. */ if (new_m > (((size_t) 1 << (m_sz * 8 - 1)) - 1) || ((size > safe || new_m > safe) && bytes / new_m != size)) { errno = ENOMEM; goto die; } new_ptr = realloc(*ptr, bytes); if (new_ptr == NULL) goto die; if (clear) { if (new_m > m) { memset((char *) new_ptr + m * size, 0, (new_m - m) * size); } } *ptr = new_ptr; return new_m; die: hts_log_error("%s", strerror(errno)); exit(1); } /* * Companion to hts_resize() macro that does the actual allocation. * * Somewhat complicated as hts_resize() needs to write the new allocated * size back into *size_in_out, and the value pointed to may either be * int32_t, uint32_t or size_t depending on which array is being resized. * This is solved by making `size_in_out` a void pointer, getting the macro * to pass in the size of the item pointed to (in `size_sz`) and then using * an appropriate cast (based on the value of size_sz). The function * ensures that the maximum size will be storable in a signed type of * the given size so storing to an int32_t should work correctly. * * Assumes that sizeof(uint32_t) and sizeof(int32_t) is 4, * sizeof(uint64_t) and sizeof(int64_t) is 8 and sizeof(size_t) is * either 4 or 8. It also assumes casting from unsigned to signed will * work as long as the top bit isn't set. */ int hts_resize_array_(size_t item_size, size_t num, size_t size_sz, void *size_in_out, void **ptr_in_out, int flags, const char *func) { /* If new_size and item_size are both below this limit, multiplying them together can't overflow */ const size_t safe = (size_t) 1 << (sizeof(size_t) * 4); void *new_ptr; size_t bytes, new_size; new_size = num; kroundup_size_t(new_size); bytes = item_size * new_size; /* Check for overflow. Both ensure that alloc will fit in alloc_in_out (we make the pessimistic assumption that *alloc_in_out is signed), and that bytes has not wrapped around. */ if ((new_size > (((size_t) 1 << (size_sz * 8 - 1)) - 1)) || (((item_size > safe) || (new_size > safe)) && bytes / new_size != item_size)) { hts_log(HTS_LOG_ERROR, func, "Memory allocation too large"); errno = ENOMEM; return -1; } new_ptr = realloc(*ptr_in_out, bytes); if (new_ptr == NULL) { int save_errno = errno; hts_log(HTS_LOG_ERROR, func, "%s", strerror(errno)); errno = save_errno; return -1; } if (flags & HTS_RESIZE_CLEAR) { size_t old_size; switch (size_sz) { case 4: old_size = *((uint32_t *) size_in_out); break; case 8: old_size = *((uint64_t *) size_in_out); break; default: abort(); } if (new_size > old_size) { memset((char *) new_ptr + old_size * item_size, 0, (new_size - old_size) * item_size); } } switch (size_sz) { case 4: *((uint32_t *) size_in_out) = new_size; break; case 8: *((uint64_t *) size_in_out) = new_size; break; default: abort(); } *ptr_in_out = new_ptr; return 0; } void hts_lib_shutdown(void) { hfile_shutdown(1); } void hts_free(void *ptr) { free(ptr); } void hts_set_log_level(enum htsLogLevel level) { hts_verbose = level; } enum htsLogLevel hts_get_log_level(void) { return hts_verbose; } static char get_severity_tag(enum htsLogLevel severity) { switch (severity) { case HTS_LOG_ERROR: return 'E'; case HTS_LOG_WARNING: return 'W'; case HTS_LOG_INFO: return 'I'; case HTS_LOG_DEBUG: return 'D'; case HTS_LOG_TRACE: return 'T'; default: break; } return '*'; } void hts_log(enum htsLogLevel severity, const char *context, const char *format, ...) { int save_errno = errno; if (severity <= hts_verbose) { va_list argptr; fprintf(stderr, "[%c::%s] ", get_severity_tag(severity), context); va_start(argptr, format); vfprintf(stderr, format, argptr); va_end(argptr); fprintf(stderr, "\n"); } errno = save_errno; } pysam-0.23.0/htslib/hts_expr.c000066400000000000000000000675251475062545500162460ustar00rootroot00000000000000/* hts_expr.c -- filter expression parsing and processing. Copyright (C) 2020-2022, 2024 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notices and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ // TODO: // - ?: operator for conditionals? #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #include #include "htslib/hts_expr.h" #include "htslib/hts_log.h" #include "textutils_internal.h" // Could also cache hts_expr_val_t stack here for kstring reuse? #define MAX_REGEX 10 struct hts_filter_t { char *str; int parsed; int curr_regex, max_regex; regex_t preg[MAX_REGEX]; }; /* * This is designed to be mostly C like with mostly same the precedence rules, * with the exception of bit operators (widely considered as a mistake in C). * It's not full C (eg no bit-shifting), but good enough for our purposes. * * Supported syntax, in order of precedence: * * Grouping: (, ), eg "(1+2)*3" * Values: integers, floats, strings or variables * Unary ops: +, -, !, ~ eg -10 +10, !10 (0), ~5 (bitwise not) * Math ops: *, /, % [TODO: add // for floor division?] * Math ops: +, - * Bit-wise: &, ^, | [NB as 3 precedence levels, in that order] * Conditionals: >, >=, <, <=, * Equality: ==, !=, =~, !~ * Boolean: &&, || */ // Skip to start of term static char *ws(char *str) { while (*str && (*str == ' ' || *str == '\t')) str++; return str; } static int expression(hts_filter_t *filt, void *data, hts_expr_sym_func *fn, char *str, char **end, hts_expr_val_t *res); /* * Simple functions operating on strings only. * length, min, max, avg. * * All return 0 on success, * -1 on failure */ static int expr_func_length(hts_expr_val_t *res) { if (!res->is_str) return -1; res->is_str = 0; res->d = res->s.l; return 0; } static int expr_func_min(hts_expr_val_t *res) { if (!res->is_str) return -1; size_t l = res->s.l; int v = INT_MAX; const uint8_t *x = (uint8_t *)res->s.s; for (l = 0; l < res->s.l; l++) if (v > x[l]) v = x[l]; res->is_str = 0; res->d = v == INT_MAX ? NAN : v; return 0; } static int expr_func_max(hts_expr_val_t *res) { if (!res->is_str) return -1; size_t l = res->s.l; int v = INT_MIN; const uint8_t *x = (uint8_t *)res->s.s; for (l = 0; l < res->s.l; l++) if (v < x[l]) v = x[l]; res->is_str = 0; res->d = v == INT_MIN ? NAN : v; return 0; } static int expr_func_avg(hts_expr_val_t *res) { if (!res->is_str) return -1; size_t l = res->s.l; double v = 0; const uint8_t *x = (uint8_t *)res->s.s; for (l = 0; l < res->s.l; l++) v += x[l]; if (l) v /= l; res->is_str = 0; res->d = v; return 0; } /* * functions: FUNC(expr). * Note for simplicity of parsing, the "(" must immediately follow FUNC, * so "FUNC (x)" is invalid. */ static int func_expr(hts_filter_t *filt, void *data, hts_expr_sym_func *fn, char *str, char **end, hts_expr_val_t *res) { int func_ok = -1; switch (*str) { case 'a': if (strncmp(str, "avg(", 4) == 0) { if (expression(filt, data, fn, str+4, end, res)) return -1; func_ok = expr_func_avg(res); } break; case 'd': if (strncmp(str, "default(", 8) == 0) { if (expression(filt, data, fn, str+8, end, res)) return -1; if (**end != ',') return -1; (*end)++; hts_expr_val_t val = HTS_EXPR_VAL_INIT; if (expression(filt, data, fn, ws(*end), end, &val)) return -1; func_ok = 1; if (!hts_expr_val_existsT(res)) { kstring_t swap = res->s; *res = val; val.s = swap; hts_expr_val_free(&val); } } break; case 'e': if (strncmp(str, "exists(", 7) == 0) { if (expression(filt, data, fn, str+7, end, res)) return -1; func_ok = 1; res->is_true = res->d = hts_expr_val_existsT(res); res->is_str = 0; } else if (strncmp(str, "exp(", 4) == 0) { if (expression(filt, data, fn, str+4, end, res)) return -1; func_ok = 1; res->d = exp(res->d); res->is_str = 0; if (isnan(res->d)) hts_expr_val_undef(res); } break; case 'l': if (strncmp(str, "length(", 7) == 0) { if (expression(filt, data, fn, str+7, end, res)) return -1; func_ok = expr_func_length(res); } else if (strncmp(str, "log(", 4) == 0) { if (expression(filt, data, fn, str+4, end, res)) return -1; func_ok = 1; res->d = log(res->d); res->is_str = 0; if (isnan(res->d)) hts_expr_val_undef(res); } break; case 'm': if (strncmp(str, "min(", 4) == 0) { if (expression(filt, data, fn, str+4, end, res)) return -1; func_ok = expr_func_min(res); } else if (strncmp(str, "max(", 4) == 0) { if (expression(filt, data, fn, str+4, end, res)) return -1; func_ok = expr_func_max(res); } break; case 'p': if (strncmp(str, "pow(", 4) == 0) { if (expression(filt, data, fn, str+4, end, res)) return -1; func_ok = 1; if (**end != ',') return -1; (*end)++; hts_expr_val_t val = HTS_EXPR_VAL_INIT; if (expression(filt, data, fn, ws(*end), end, &val)) return -1; if (!hts_expr_val_exists(res) || !hts_expr_val_exists(&val)) { hts_expr_val_undef(res); } else if (res->is_str || val.is_str) { hts_expr_val_free(&val); // arith on strings return -1; } else { func_ok = 1; res->d = pow(res->d, val.d); hts_expr_val_free(&val); res->is_str = 0; } if (isnan(res->d)) hts_expr_val_undef(res); } break; case 's': if (strncmp(str, "sqrt(", 5) == 0) { if (expression(filt, data, fn, str+5, end, res)) return -1; func_ok = 1; res->d = sqrt(res->d); res->is_str = 0; if (isnan(res->d)) hts_expr_val_undef(res); } break; } if (func_ok < 0) return -1; str = ws(*end); if (*str != ')') { fprintf(stderr, "Missing ')'\n"); return -1; } *end = str+1; return 0; } /* * simple_expr * : identifier * | constant * | string * | func_expr * | '(' expression ')' */ static int simple_expr(hts_filter_t *filt, void *data, hts_expr_sym_func *fn, char *str, char **end, hts_expr_val_t *res) { // Main recursion step str = ws(str); if (*str == '(') { if (expression(filt, data, fn, str+1, end, res)) return -1; str = ws(*end); if (*str != ')') { fprintf(stderr, "Missing ')'\n"); return -1; } *end = str+1; return 0; } // Otherwise a basic element. int fail = 0; double d = hts_str2dbl(str, end, &fail); if (str != *end) { res->is_str = 0; res->d = d; } else { // Not valid floating point syntax. // TODO: add function call names in here; len(), sqrt(), pow(), etc if (*str == '"') { res->is_str = 1; char *e = str+1; int backslash = 0; while (*e && *e != '"') { if (*e == '\\') backslash=1, e+=1+(e[1]!='\0'); else e++; } kputsn(str+1, e-(str+1), ks_clear(&res->s)); if (backslash) { size_t i, j; for (i = j = 0; i < res->s.l; i++) { res->s.s[j++] = res->s.s[i]; if (res->s.s[i] == '\\') { switch (res->s.s[++i]) { case '"': res->s.s[j-1] = '"'; break; case '\\':res->s.s[j-1] = '\\'; break; case 't': res->s.s[j-1] = '\t'; break; case 'n': res->s.s[j-1] = '\n'; break; case 'r': res->s.s[j-1] = '\r'; break; default: res->s.s[j++] = res->s.s[i]; } } } res->s.s[j] = 0; res->s.l = j; } if (*e != '"') return -1; *end = e+1; } else if (fn) { // Try lookup as variable, if not as function if (fn(data, str, end, res) == 0) return 0; else return func_expr(filt, data, fn, str, end, res); } else { return -1; } } return 0; } /* * unary_expr * : simple_expr * | '+' simple_expr * | '-' simple_expr * | '!' unary_expr // higher precedence * | '~' unary_expr // higher precedence */ static int unary_expr(hts_filter_t *filt, void *data, hts_expr_sym_func *fn, char *str, char **end, hts_expr_val_t *res) { int err; str = ws(str); if (*str == '+' || *str == '-') { err = simple_expr(filt, data, fn, str+1, end, res); if (!hts_expr_val_exists(res)) { hts_expr_val_undef(res); } else { err |= res->is_str; if (*str == '-') res->d = -res->d; res->is_true = res->d != 0; } } else if (*str == '!') { err = unary_expr(filt, data, fn, str+1, end, res); if (res->is_true) { // Any explicitly true value becomes false res->d = res->is_true = 0; } else if (!hts_expr_val_exists(res)) { // We can also still negate undef values by toggling the // is_true override value. res->d = res->is_true = !res->is_true; } else if (res->is_str) { // !null = true, !"foo" = false, NOTE: !"" = false also res->d = res->is_true = (res->s.s == NULL); } else { res->d = !(int64_t)res->d; res->is_true = res->d != 0; } res->is_str = 0; } else if (*str == '~') { err = unary_expr(filt, data, fn, str+1, end, res); if (!hts_expr_val_exists(res)) { hts_expr_val_undef(res); } else { err |= res->is_str; if (!hts_expr_val_exists(res)) { hts_expr_val_undef(res); } else { res->d = ~(int64_t)res->d; res->is_true = res->d != 0; } } } else { err = simple_expr(filt, data, fn, str, end, res); } return err ? -1 : 0; } /* * mul_expr * : unary_expr ( * '*' unary_expr * | '/' unary_expr * | '%' unary_expr * )* */ static int mul_expr(hts_filter_t *filt, void *data, hts_expr_sym_func *fn, char *str, char **end, hts_expr_val_t *res) { if (unary_expr(filt, data, fn, str, end, res)) return -1; str = *end; hts_expr_val_t val = HTS_EXPR_VAL_INIT; while (*str) { str = ws(str); if (*str == '*' || *str == '/' || *str == '%') { if (unary_expr(filt, data, fn, str+1, end, &val)) return -1; if (!hts_expr_val_exists(&val) || !hts_expr_val_exists(res)) { hts_expr_val_undef(res); } else if (val.is_str || res->is_str) { hts_expr_val_free(&val); return -1; // arith on strings } } if (*str == '*') res->d *= val.d; else if (*str == '/') res->d /= val.d; else if (*str == '%') { if (val.d) res->d = (int64_t)res->d % (int64_t)val.d; else hts_expr_val_undef(res); } else break; res->is_true = hts_expr_val_exists(res) && (res->d != 0); str = *end; } hts_expr_val_free(&val); return 0; } /* * add_expr * : mul_expr ( * '+' mul_expr * | '-' mul_expr * )* */ static int add_expr(hts_filter_t *filt, void *data, hts_expr_sym_func *fn, char *str, char **end, hts_expr_val_t *res) { if (mul_expr(filt, data, fn, str, end, res)) return -1; str = *end; hts_expr_val_t val = HTS_EXPR_VAL_INIT; while (*str) { str = ws(str); int undef = 0; if (*str == '+' || *str == '-') { if (mul_expr(filt, data, fn, str+1, end, &val)) return -1; if (!hts_expr_val_exists(&val) || !hts_expr_val_exists(res)) { undef = 1; } else if (val.is_str || res->is_str) { hts_expr_val_free(&val); return -1; // arith on strings } } if (*str == '+') res->d += val.d; else if (*str == '-') res->d -= val.d; else break; if (undef) hts_expr_val_undef(res); else res->is_true = res->d != 0; str = *end; } hts_expr_val_free(&val); return 0; } /* * bitand_expr * : add_expr * | bitand_expr '&' add_expr */ static int bitand_expr(hts_filter_t *filt, void *data, hts_expr_sym_func *fn, char *str, char **end, hts_expr_val_t *res) { if (add_expr(filt, data, fn, str, end, res)) return -1; hts_expr_val_t val = HTS_EXPR_VAL_INIT; int undef = 0; for (;;) { str = ws(*end); if (*str == '&' && str[1] != '&') { if (add_expr(filt, data, fn, str+1, end, &val)) return -1; if (!hts_expr_val_exists(&val) || !hts_expr_val_exists(res)) { undef = 1; } else if (res->is_str || val.is_str) { hts_expr_val_free(&val); return -1; } else { res->is_true = (res->d = ((int64_t)res->d & (int64_t)val.d)) != 0; } } else { break; } } hts_expr_val_free(&val); if (undef) hts_expr_val_undef(res); return 0; } /* * bitxor_expr * : bitand_expr * | bitxor_expr '^' bitand_expr */ static int bitxor_expr(hts_filter_t *filt, void *data, hts_expr_sym_func *fn, char *str, char **end, hts_expr_val_t *res) { if (bitand_expr(filt, data, fn, str, end, res)) return -1; hts_expr_val_t val = HTS_EXPR_VAL_INIT; int undef = 0; for (;;) { str = ws(*end); if (*str == '^') { if (bitand_expr(filt, data, fn, str+1, end, &val)) return -1; if (!hts_expr_val_exists(&val) || !hts_expr_val_exists(res)) { undef = 1; } else if (res->is_str || val.is_str) { hts_expr_val_free(&val); return -1; } else { res->is_true = (res->d = ((int64_t)res->d ^ (int64_t)val.d)) != 0; } } else { break; } } hts_expr_val_free(&val); if (undef) hts_expr_val_undef(res); return 0; } /* * bitor_expr * : bitxor_expr * | bitor_expr '|' bitxor_expr */ static int bitor_expr(hts_filter_t *filt, void *data, hts_expr_sym_func *fn, char *str, char **end, hts_expr_val_t *res) { if (bitxor_expr(filt, data, fn, str, end, res)) return -1; hts_expr_val_t val = HTS_EXPR_VAL_INIT; int undef = 0; for (;;) { str = ws(*end); if (*str == '|' && str[1] != '|') { if (bitxor_expr(filt, data, fn, str+1, end, &val)) return -1; if (!hts_expr_val_exists(&val) || !hts_expr_val_exists(res)) { undef = 1; } else if (res->is_str || val.is_str) { hts_expr_val_free(&val); return -1; } else { res->is_true = (res->d = ((int64_t)res->d | (int64_t)val.d)) != 0; } } else { break; } } hts_expr_val_free(&val); if (undef) hts_expr_val_undef(res); return 0; } /* * cmp_expr * : bitor_expr * | cmp_expr '<=' bitor_expr * | cmp_expr '<' bitor_expr * | cmp_expr '>=' bitor_expr * | cmp_expr '>' bitor_expr */ static int cmp_expr(hts_filter_t *filt, void *data, hts_expr_sym_func *fn, char *str, char **end, hts_expr_val_t *res) { if (bitor_expr(filt, data, fn, str, end, res)) return -1; str = ws(*end); hts_expr_val_t val = HTS_EXPR_VAL_INIT; int err = 0, cmp_done = 0; if (*str == '>' && str[1] == '=') { cmp_done = 1; err = cmp_expr(filt, data, fn, str+2, end, &val); if (!hts_expr_val_exists(res) || !hts_expr_val_exists(&val)) { hts_expr_val_undef(res); } else { res->is_true=res->d = res->is_str && res->s.s && val.is_str && val.s.s ? strcmp(res->s.s, val.s.s) >= 0 : !res->is_str && !val.is_str && res->d >= val.d; res->is_str = 0; } } else if (*str == '>') { cmp_done = 1; err = cmp_expr(filt, data, fn, str+1, end, &val); if (!hts_expr_val_exists(res) || !hts_expr_val_exists(&val)) { hts_expr_val_undef(res); } else { res->is_true=res->d = res->is_str && res->s.s && val.is_str && val.s.s ? strcmp(res->s.s, val.s.s) > 0 : !res->is_str && !val.is_str && res->d > val.d; res->is_str = 0; } } else if (*str == '<' && str[1] == '=') { cmp_done = 1; err = cmp_expr(filt, data, fn, str+2, end, &val); if (!hts_expr_val_exists(res) || !hts_expr_val_exists(&val)) { hts_expr_val_undef(res); } else { res->is_true=res->d = res->is_str && res->s.s && val.is_str && val.s.s ? strcmp(res->s.s, val.s.s) <= 0 : !res->is_str && !val.is_str && res->d <= val.d; res->is_str = 0; } } else if (*str == '<') { cmp_done = 1; err = cmp_expr(filt, data, fn, str+1, end, &val); if (!hts_expr_val_exists(res) || !hts_expr_val_exists(&val)) { hts_expr_val_undef(res); } else { res->is_true=res->d = res->is_str && res->s.s && val.is_str && val.s.s ? strcmp(res->s.s, val.s.s) < 0 : !res->is_str && !val.is_str && res->d < val.d; res->is_str = 0; } } if (cmp_done && (!hts_expr_val_exists(&val) || !hts_expr_val_exists(res))) hts_expr_val_undef(res); hts_expr_val_free(&val); return err ? -1 : 0; } /* * eq_expr * : cmp_expr * | eq_expr '==' cmp_expr * | eq_expr '!=' cmp_expr * | eq_expr '=~' cmp_expr * | eq_expr '!~' cmp_expr */ static int eq_expr(hts_filter_t *filt, void *data, hts_expr_sym_func *fn, char *str, char **end, hts_expr_val_t *res) { if (cmp_expr(filt, data, fn, str, end, res)) return -1; str = ws(*end); int err = 0, eq_done = 0; hts_expr_val_t val = HTS_EXPR_VAL_INIT; // numeric vs numeric comparison is as expected // string vs string comparison is as expected // numeric vs string is false if (str[0] == '=' && str[1] == '=') { eq_done = 1; if ((err = eq_expr(filt, data, fn, str+2, end, &val))) { res->is_true = res->d = 0; } else { if (!hts_expr_val_exists(res) || !hts_expr_val_exists(&val)) { hts_expr_val_undef(res); } else { res->is_true = res->d = res->is_str ? (res->s.s && val.s.s ?strcmp(res->s.s, val.s.s)==0 :0) : !res->is_str && !val.is_str && res->d == val.d; } } res->is_str = 0; } else if (str[0] == '!' && str[1] == '=') { eq_done = 1; if ((err = eq_expr(filt, data, fn, str+2, end, &val))) { res->is_true = res->d = 0; } else { if (!hts_expr_val_exists(res) || !hts_expr_val_exists(&val)) { hts_expr_val_undef(res); } else { res->is_true = res->d = res->is_str ? (res->s.s && val.s.s ?strcmp(res->s.s, val.s.s) != 0 :1) : res->is_str != val.is_str || res->d != val.d; } } res->is_str = 0; } else if ((str[0] == '=' && str[1] == '~') || (str[0] == '!' && str[1] == '~')) { eq_done = 1; err = eq_expr(filt, data, fn, str+2, end, &val); if (!val.is_str || !res->is_str) { hts_expr_val_free(&val); return -1; } if (val.s.s && res->s.s && val.is_true >= 0 && res->is_true >= 0) { regex_t preg_, *preg; if (filt->curr_regex >= filt->max_regex) { // Compile regex if not seen before if (filt->curr_regex >= MAX_REGEX) { preg = &preg_; } else { preg = &filt->preg[filt->curr_regex]; filt->max_regex++; } int ec = regcomp(preg, val.s.s, REG_EXTENDED | REG_NOSUB); if (ec != 0) { char errbuf[1024]; regerror(ec, preg, errbuf, 1024); fprintf(stderr, "Failed regex: %.1024s\n", errbuf); hts_expr_val_free(&val); return -1; } } else { preg = &filt->preg[filt->curr_regex]; } res->is_true = res->d = regexec(preg, res->s.s, 0, NULL, 0) == 0 ? *str == '=' // matcn : *str == '!'; // no-match if (preg == &preg_) regfree(preg); filt->curr_regex++; } else { // nul regexp or input is considered false res->is_true = 0; } res->is_str = 0; } if (eq_done && ((!hts_expr_val_exists(&val)) || !hts_expr_val_exists(res))) hts_expr_val_undef(res); hts_expr_val_free(&val); return err ? -1 : 0; } /* * and_expr * : eq_expr * | and_expr 'and' eq_expr * | and_expr 'or' eq_expr */ static int and_expr(hts_filter_t *filt, void *data, hts_expr_sym_func *fn, char *str, char **end, hts_expr_val_t *res) { if (eq_expr(filt, data, fn, str, end, res)) return -1; for (;;) { hts_expr_val_t val = HTS_EXPR_VAL_INIT; str = ws(*end); if (str[0] == '&' && str[1] == '&') { if (eq_expr(filt, data, fn, str+2, end, &val)) return -1; if (!hts_expr_val_existsT(res) || !hts_expr_val_existsT(&val)) { hts_expr_val_undef(res); res->d = 0; } else { res->is_true = res->d = (res->is_true || (res->is_str && res->s.s) || res->d) && (val.is_true || (val.is_str && val.s.s) || val.d); res->is_str = 0; } } else if (str[0] == '|' && str[1] == '|') { if (eq_expr(filt, data, fn, str+2, end, &val)) return -1; if (!hts_expr_val_existsT(res) && !hts_expr_val_existsT(&val)) { // neither defined hts_expr_val_undef(res); res->d = 0; } else if (!hts_expr_val_existsT(res) && !(val.is_true || (val.is_str && val.s.s ) || val.d)) { // LHS undef and RHS false hts_expr_val_undef(res); res->d = 0; } else if (!hts_expr_val_existsT(&val) && !(res->is_true || (res->is_str && res->s.s) || res->d)){ // RHS undef and LHS false hts_expr_val_undef(res); res->d = 0; } else { res->is_true = res->d = res->is_true || (res->is_str && res->s.s) || res->d || val.is_true || (val.is_str && val.s.s ) || val.d; res->is_str = 0; } } else { break; } hts_expr_val_free(&val); } return 0; } static int expression(hts_filter_t *filt, void *data, hts_expr_sym_func *fn, char *str, char **end, hts_expr_val_t *res) { return and_expr(filt, data, fn, str, end, res); } hts_filter_t *hts_filter_init(const char *str) { hts_filter_t *f = calloc(1, sizeof(*f)); if (!f) return NULL; // Oversize to permit faster comparisons with memcmp over strcmp size_t len = strlen(str)+100; if (!(f->str = malloc(len))) { free(f); return NULL; } strcpy(f->str, str); return f; } void hts_filter_free(hts_filter_t *filt) { if (!filt) return; int i; for (i = 0; i < filt->max_regex; i++) regfree(&filt->preg[i]); free(filt->str); free(filt); } static int hts_filter_eval_(hts_filter_t *filt, void *data, hts_expr_sym_func *fn, hts_expr_val_t *res) { char *end = NULL; filt->curr_regex = 0; if (expression(filt, data, fn, filt->str, &end, res)) return -1; if (end && *ws(end)) { fprintf(stderr, "Unable to parse expression at %s\n", filt->str); return -1; } // Strings evaluate to true. An empty string is also true, but an // absent (null) string is false, unless overriden by is_true. An // empty string has kstring length of zero, but a pointer as it's // nul-terminated. if (res->is_str) { res->is_true |= res->s.s != NULL; res->d = res->is_true; } else if (hts_expr_val_exists(res)) { res->is_true |= res->d != 0; } return 0; } int hts_filter_eval(hts_filter_t *filt, void *data, hts_expr_sym_func *fn, hts_expr_val_t *res) { if (res->s.l != 0 || res->s.m != 0 || res->s.s != NULL) { // As *res is cleared below, it's not safe to call this function // with res->s.s set, as memory would be leaked. It's also not // possible to know is res was initialised correctly, so in // either case we fail. hts_log_error("Results structure must be cleared before calling this function"); return -1; } memset(res, 0, sizeof(*res)); return hts_filter_eval_(filt, data, fn, res); } int hts_filter_eval2(hts_filter_t *filt, void *data, hts_expr_sym_func *fn, hts_expr_val_t *res) { ks_free(&res->s); memset(res, 0, sizeof(*res)); return hts_filter_eval_(filt, data, fn, res); } pysam-0.23.0/htslib/hts_internal.h000066400000000000000000000130551475062545500170760ustar00rootroot00000000000000/* hts_internal.h -- internal functions; not part of the public API. Copyright (C) 2015-2016, 2018-2020 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTSLIB_HTS_INTERNAL_H #define HTSLIB_HTS_INTERNAL_H #include #include #include "htslib/hts.h" #include "textutils_internal.h" #define HTS_MAX_EXT_LEN 9 #ifdef __cplusplus extern "C" { #endif struct hFILE; struct hts_json_token { char type; ///< Token type char *str; ///< Value as a C string (filled in for all token types) // TODO Add other fields to fill in for particular data types, e.g. // int inum; // float fnum; }; struct cram_fd; /* * Check the existence of a local index file using part of the alignment file name. * The order is alignment.bam.csi, alignment.csi, alignment.bam.bai, alignment.bai * @param fn - pointer to the file name * @param fnidx - pointer to the index file name placeholder * @return 1 for success, 0 for failure */ int hts_idx_check_local(const char *fn, int fmt, char **fnidx); // Retrieve the name of the index file and also download it, if it is remote char *hts_idx_getfn(const char *fn, const char *ext); // Retrieve the name of the index file, but do not download it, if it is remote char *hts_idx_locatefn(const char *fn, const char *ext); // Used for on-the-fly indexing. See the comments in hts.c. void hts_idx_amend_last(hts_idx_t *idx, uint64_t offset); int hts_idx_fmt(hts_idx_t *idx); // Internal interface to save on-the-fly indexes. The index file handle // is kept open so hts_close() can close if after writing out the EOF // block for its own file. int hts_idx_save_but_not_close(hts_idx_t *idx, const char *fnidx, int fmt); // Construct a unique filename based on fname and open it. struct hFILE *hts_open_tmpfile(const char *fname, const char *mode, kstring_t *tmpname); // Check that index is capable of storing items in range beg..end int hts_idx_check_range(hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end); // The CRAM implementation stores the loaded index within the cram_fd rather // than separately as is done elsewhere in htslib. So if p is a pointer to // an hts_idx_t with p->fmt == HTS_FMT_CRAI, then it actually points to an // hts_cram_idx_t and should be cast accordingly. typedef struct hts_cram_idx_t { int fmt; struct cram_fd *cram; } hts_cram_idx_t; // Determine whether the string's contents appear to be UTF-16-encoded text. // Returns 1 if they are, 2 if there is also a BOM, or 0 otherwise. int hts_is_utf16_text(const kstring_t *str); // Entry point to hFILE_multipart backend. struct hFILE *hopen_htsget_redirect(struct hFILE *hfile, const char *mode); struct hts_path_itr { kstring_t path, entry; void *dirv; // DIR * privately const char *pathdir, *prefix, *suffix; size_t prefix_len, suffix_len, entry_dir_l; }; void hts_path_itr_setup(struct hts_path_itr *itr, const char *path, const char *builtin_path, const char *prefix, size_t prefix_len, const char *suffix, size_t suffix_len); const char *hts_path_itr_next(struct hts_path_itr *itr); typedef void plugin_void_func(void); plugin_void_func *load_plugin(void **pluginp, const char *filename, const char *symbol); void *plugin_sym(void *plugin, const char *name, const char **errmsg); plugin_void_func *plugin_func(void *plugin, const char *name, const char **errmsg); void close_plugin(void *plugin); const char *hts_plugin_path(void); /* * Buffers up arguments to hts_idx_push for later use, once we've written all bar * this block. This is necessary when multiple blocks are in flight (threading). * * Returns 0 on success, * -1 on failure */ int bgzf_idx_push(BGZF *fp, hts_idx_t *hidx, int tid, hts_pos_t beg, hts_pos_t end, uint64_t offset, int is_mapped); static inline int find_file_extension(const char *fn, char ext_out[static HTS_MAX_EXT_LEN]) { const char *delim = fn ? strstr(fn, HTS_IDX_DELIM) : NULL, *ext; if (!fn) return -1; if (!delim) delim = fn + strlen(fn); for (ext = delim; ext > fn && *ext != '.' && *ext != '/'; --ext) {} if (*ext == '.' && ((delim - ext == 3 && ext[1] == 'g' && ext[2] == 'z') || // permit .sam.gz as a valid file extension (delim - ext == 4 && ext[1] == 'b' && ext[2] == 'g' && ext[3] == 'z'))) // permit .vcf.bgz as a valid file extension { for (ext--; ext > fn && *ext != '.' && *ext != '/'; --ext) {} } if (*ext != '.' || delim - ext > HTS_MAX_EXT_LEN || delim - ext < 3) return -1; memcpy(ext_out, ext + 1, delim - ext - 1); ext_out[delim - ext - 1] = '\0'; return 0; } #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/hts_os.c000066400000000000000000000036751475062545500157050ustar00rootroot00000000000000/// @file hts_os.c /// Operating System specific tweaks, for compatibility with POSIX. /* Copyright (C) 2017, 2019-2020 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include "htslib/hts_defs.h" // Windows (maybe more) lack a drand48 implementation. #ifndef HAVE_DRAND48 #include "os/rand.c" #else #include HTSLIB_EXPORT void hts_srand48(long seed) { #ifdef HAVE_SRAND48_DETERMINISTIC srand48_deterministic(seed); #else srand48(seed); #endif } HTSLIB_EXPORT double hts_erand48(unsigned short xseed[3]) { return erand48(xseed); } HTSLIB_EXPORT double hts_drand48(void) { return drand48(); } HTSLIB_EXPORT long hts_lrand48(void) { return lrand48(); } #endif // // On Windows when using the MSYS or Cygwin terminals, isatty fails // #ifdef _WIN32 // #define USE_FILEEXTD // #include "os/iscygpty.c" // #endif pysam-0.23.0/htslib/hts_time_funcs.h000066400000000000000000000133761475062545500174240ustar00rootroot00000000000000/* hts_time_funcs.h -- Implementations of non-standard time functions Copyright (C) 2022 Genome Research Ltd. Author: Rob Davies Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* This mainly exists because timegm() is not a standard function, and so Cannot be used in portable code. Unfortunately the standard one (mktime) always takes the local timezone into accout so doing a UTC conversion with it involves changing the TZ environment variable, which is rather messy and not likely to go well with threaded code. The code here is a much simplified version of the BSD timegm() implementation. It currently rejects dates before 1970, avoiding problems with -ve time_t. It also works strictly in UTC, so doesn't have to worry about tm_isdst which makes the calculation much easier. Some of this is derived from BSD sources, for example https://github.com/NetBSD/src/blob/trunk/lib/libc/time/localtime.c which state: ** This file is in the public domain, so clarified as of ** 1996-06-05 by Arthur David Olson. Non-derived code is copyright as above. */ #include #include #include #include static inline int hts_time_normalise(int *tens, int *units, int base) { if (*units < 0 || *units >= base) { int delta = *units >= 0 ? *units / base : (-1 - (-1 - *units) / base); int64_t tmp = (int64_t) (*tens) + delta; if (tmp < INT_MIN || tmp > INT_MAX) return 1; *tens = tmp; *units -= delta * base; } return 0; } static inline int hts_year_is_leap(int64_t year) { return ((year % 4 == 0) && (year % 100 != 0)) || (year % 400 == 0); } // Number of leap years to start of year // Only works for year >= 1. static inline int64_t hts_leaps_to_year_start(int64_t year) { --year; return year / 4 - year / 100 + year / 400; } static inline int hts_time_normalise_tm(struct tm *t) { const int days_per_mon[2][12] = { { 31, 28, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31 }, { 31, 29, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31 } }; const int year_days[2] = { 365, 366 }; int overflow = 0; int64_t year; if (t->tm_sec > 62) { overflow |= hts_time_normalise(&t->tm_min, &t->tm_sec, 60); } overflow |= hts_time_normalise(&t->tm_hour, &t->tm_min, 60); overflow |= hts_time_normalise(&t->tm_mday, &t->tm_hour, 24); overflow |= hts_time_normalise(&t->tm_year, &t->tm_mon, 12); if (overflow) return 1; year = (int64_t) t->tm_year + 1900LL; while (t->tm_mday <= 0) { --year; t->tm_mday += year_days[hts_year_is_leap(year + (1 < t->tm_mon))]; } while (t->tm_mday > 366) { t->tm_mday -= year_days[hts_year_is_leap(year + (1 < t->tm_mon))]; ++year; } for (;;) { int mdays = days_per_mon[hts_year_is_leap(year)][t->tm_mon]; if (t->tm_mday <= mdays) break; t->tm_mday -= mdays; t->tm_mon++; if (t->tm_mon >= 12) { year++; t->tm_mon = 0; } } year -= 1900; if (year != t->tm_year) { if (year < INT_MIN || year > INT_MAX) return 1; t->tm_year = year; } return 0; } /** * Convert broken-down time to an equivalent time_t value * @param target Target broken-down time structure * @return Equivalent time_t value on success; -1 on failure * * This function first normalises the time in @p target so that the * structure members are in the valid range. It then calculates the * number of seconds (ignoring leap seconds) between midnight Jan 1st 1970 * and the target date. * * If @p target is outside the range that can be represented in a time_t, * or tm_year is less than 70 (which would return a negative value) then * it returns -1 and sets errno to EOVERFLOW. */ static inline time_t hts_time_gm(struct tm *target) { int month_start[2][12] = { { 0, 31, 59, 90, 120, 151, 181, 212, 243, 273, 304, 334 }, { 0, 31, 60, 91, 121, 152, 182, 213, 244, 274, 305, 335 } }; int years_from_epoch, leaps, days; int64_t secs; if (hts_time_normalise_tm(target) != 0) goto overflow; if (target->tm_year < 70) goto overflow; years_from_epoch = target->tm_year - 70; leaps = (hts_leaps_to_year_start(target->tm_year + 1900) - hts_leaps_to_year_start(1970)); days = ((365 * (years_from_epoch - leaps) + 366 * leaps) + month_start[hts_year_is_leap(target->tm_year + 1900)][target->tm_mon] + target->tm_mday - 1); secs = ((int64_t) days * 86400LL + target->tm_hour * 3600 + target->tm_min * 60 + target->tm_sec); if (sizeof(time_t) < 8 && secs > INT_MAX) goto overflow; return (time_t) secs; overflow: errno = EOVERFLOW; return (time_t) -1; } pysam-0.23.0/htslib/htscodecs/000077500000000000000000000000001475062545500162065ustar00rootroot00000000000000pysam-0.23.0/htslib/htscodecs/htscodecs/000077500000000000000000000000001475062545500201655ustar00rootroot00000000000000pysam-0.23.0/htslib/htscodecs/htscodecs/arith_dynamic.c000066400000000000000000001106101475062545500231430ustar00rootroot00000000000000/* * Copyright (c) 2019-2022 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ // As per standard rANS_static but using optional RLE or bit-packing // techniques prior to entropy encoding. This is a significant // reduction in some data sets. // top bits in order byte #define X_PACK 0x80 // Pack 2,4,8 or infinite symbols into a byte. #define X_RLE 0x40 // Run length encoding with runs & lits encoded separately #define X_CAT 0x20 // Nop; for tiny segments where rANS overhead is too big #define X_NOSZ 0x10 // Don't store the original size; used by STRIPE mode #define X_STRIPE 0x08 // For 4-byte integer data; rotate & encode 4 streams. #define X_EXT 0x04 // External compression codec via magic num (gz, xz, bz2) #define X_ORDER 0x03 // Mask to obtain order #include "config.h" #ifdef HAVE_LIBBZ2 #include #endif #include #include #include #include #include #include #include #include #include "arith_dynamic.h" #include "varint.h" #include "pack.h" #include "utils.h" #define MIN(a,b) ((a)<(b)?(a):(b)) /*----------------------------------------------------------------------------- * Memory to memory compression functions. * * These are original versions without any manual loop unrolling. They * are easier to understand, but can be up to 2x slower. */ #define MAGIC 8 unsigned int arith_compress_bound(unsigned int size, int order) { int N = (order>>8) & 0xff; if (!N) N=4; return (order == 0 ? 1.05*size + 257*3 + 4 : 1.05*size + 257*257*3 + 4 + 257*3+4) + 5 + ((order & X_PACK) ? 1 : 0) + ((order & X_RLE) ? 1 + 257*3+4: 0) + ((order & X_STRIPE) ? 7 + 5*N: 0); } #ifndef MODEL_256 // see fqzcomp_qual_fuzz.c #define NSYM 256 #include "c_simple_model.h" #endif // Compresses in_size bytes from 'in' to *out_size bytes in 'out'. // // NB: The output buffer does not hold the original size, so it is up to // the caller to store this. static unsigned char *arith_compress_O0(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { int i, bound = arith_compress_bound(in_size,0)-5; // -5 for order/size unsigned char *out_free = NULL; if (!out) { *out_size = bound; out_free = out = malloc(*out_size); } if (!out || bound > *out_size) return NULL; unsigned int m = 0; for (i = 0; i < in_size; i++) if (m < in[i]) m = in[i]; m++; *out = m; SIMPLE_MODEL(256,_) byte_model; SIMPLE_MODEL(256,_init)(&byte_model, m); RangeCoder rc; RC_SetOutput(&rc, (char *)out+1); RC_SetOutputEnd(&rc, (char *)out + *out_size); RC_StartEncode(&rc); for (i = 0; i < in_size; i++) SIMPLE_MODEL(256, _encodeSymbol)(&byte_model, &rc, in[i]); if (RC_FinishEncode(&rc) < 0) { free(out_free); return NULL; } // Finalise block size and return it *out_size = RC_OutSize(&rc)+1; return out; } static unsigned char *arith_uncompress_O0(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { RangeCoder rc; int i; unsigned int m = in[0] ? in[0] : 256; SIMPLE_MODEL(256,_) byte_model; SIMPLE_MODEL(256,_init)(&byte_model, m); unsigned char *out_free = NULL; if (!out) out_free = out = malloc(out_sz); if (!out) return NULL; RC_SetInput(&rc, (char *)in+1, (char *)in+in_size); RC_StartDecode(&rc); for (i = 0; i < out_sz; i++) out[i] = SIMPLE_MODEL(256, _decodeSymbol)(&byte_model, &rc); if (RC_FinishDecode(&rc) < 0) { free(out_free); return NULL; } return out; } //----------------------------------------------------------------------------- static unsigned char *arith_compress_O1(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { int i, bound = arith_compress_bound(in_size,0)-5; // -5 for order/size unsigned char *out_free = NULL; if (!out) { *out_size = bound; out_free = out = malloc(*out_size); } if (!out || bound > *out_size) return NULL; SIMPLE_MODEL(256,_) *byte_model = htscodecs_tls_alloc(256 * sizeof(*byte_model)); if (!byte_model) { free(out_free); return NULL; } unsigned int m = 0; if (1 || in_size > 1000) { for (i = 0; i < in_size; i++) if (m < in[i]) m = in[i]; //fprintf(stderr, "%d max %d\n", in_size, m); m++; } *out = m; for (i = 0; i < 256; i++) SIMPLE_MODEL(256,_init)(&byte_model[i], m); RangeCoder rc; RC_SetOutput(&rc, (char *)out+1); RC_SetOutputEnd(&rc, (char *)out + *out_size); RC_StartEncode(&rc); uint8_t last = 0; for (i = 0; i < in_size; i++) { SIMPLE_MODEL(256, _encodeSymbol)(&byte_model[last], &rc, in[i]); last = in[i]; } if (RC_FinishEncode(&rc) < 0) { free(out_free); htscodecs_tls_free(byte_model); return NULL; } // Finalise block size and return it *out_size = RC_OutSize(&rc)+1; htscodecs_tls_free(byte_model); return out; } static unsigned char *arith_uncompress_O1(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { RangeCoder rc; unsigned char *out_free = NULL; if (!out) out_free = out = malloc(out_sz); if (!out) return NULL; SIMPLE_MODEL(256,_) *byte_model = htscodecs_tls_alloc(256 * sizeof(*byte_model)); if (!byte_model) { free(out_free); return NULL; } unsigned int m = in[0] ? in[0] : 256, i; for (i = 0; i < 256; i++) SIMPLE_MODEL(256,_init)(&byte_model[i], m); RC_SetInput(&rc, (char *)in+1, (char *)in+in_size); RC_StartDecode(&rc); unsigned char last = 0; for (i = 0; i < out_sz; i++) { out[i] = SIMPLE_MODEL(256, _decodeSymbol)(&byte_model[last], &rc); last = out[i]; } if (RC_FinishDecode(&rc) < 0) { htscodecs_tls_free(byte_model); free(out_free); return NULL; } htscodecs_tls_free(byte_model); return out; } //----------------------------------------------------------------------------- // Disable O2 for now #if 0 #if 0 unsigned char *arith_compress_O2(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { fprintf(stderr, "WARNING: using undocumented O2 arith\n"); int i, j; int bound = arith_compress_bound(in_size,0)-5; // -5 for order/size unsigned char *out_free = NULL; if (!out) { *out_size = bound; out_free = out = malloc(*out_size); } if (!out || bound > *out_size) return NULL; unsigned int m = 0; if (1 || in_size > 1000) { for (i = 0; i < in_size; i++) if (m < in[i]) m = in[i]; //fprintf(stderr, "%d max %d\n", in_size, m); m++; } *out = m; SIMPLE_MODEL(256,_) *byte_model; byte_model = malloc(256*256*sizeof(*byte_model)); for (i = 0; i < 256; i++) for (j = 0; j < 256; j++) SIMPLE_MODEL(256,_init)(&byte_model[i*256+j], m); RangeCoder rc; RC_SetOutput(&rc, (char *)out+1); RC_SetOutputEnd(&rc, (char *)out + *out_size); RC_StartEncode(&rc); unsigned char last1 = 0, last2 = 0; for (i = 0; i < in_size; i++) { SIMPLE_MODEL(256, _encodeSymbol)(&byte_model[last1*256 + last2], &rc, in[i]); last2 = last1; last1 = in[i]; } free(byte_model); if (RC_FinishEncode(&rc) < 0) { free(out_free); return NULL; } // Finalise block size and return it *out_size = RC_OutSize(&rc)+1; return out; } #else unsigned char *arith_compress_O2(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { fprintf(stderr, "WARNING: using undocumented O2 arith\n"); int i, j; int bound = arith_compress_bound(in_size,0)-5; // -5 for order/size unsigned char *out_free = NULL; if (!out) { *out_size = bound; out_free = out = malloc(*out_size); } if (!out || bound > *out_size) return NULL; unsigned int m = 0; if (1 || in_size > 1000) { for (i = 0; i < in_size; i++) if (m < in[i]) m = in[i]; //fprintf(stderr, "%d max %d\n", in_size, m); m++; } *out = m; SIMPLE_MODEL(256,_) *byte_model; byte_model = malloc(256*256*sizeof(*byte_model)); for (i = 0; i < 256; i++) for (j = 0; j < 256; j++) SIMPLE_MODEL(256,_init)(&byte_model[i*256+j], m); SIMPLE_MODEL(256,_) byte_model1[256]; for (i = 0; i < 256; i++) SIMPLE_MODEL(256,_init)(&byte_model1[i], m); RangeCoder rc; RC_SetOutput(&rc, (char *)out+1); RC_SetOutputEnd(&rc, (char *)out + *out_size); RC_StartEncode(&rc); unsigned char last1 = 0, last2 = 0; for (i = 0; i < in_size; i++) { // Use Order-1 is order-2 isn't sufficiently advanced yet (75+ symbols) if (byte_model[last1*256+last2].TotFreq <= m+75*16) { SIMPLE_MODEL(256, _encodeSymbol)(&byte_model1[last1], &rc, in[i]); SIMPLE_MODEL(256, _updateSymbol)(&byte_model[last1*256 + last2], &rc, in[i]); } else { SIMPLE_MODEL(256, _encodeSymbol)(&byte_model[last1*256 + last2], &rc, in[i]); //SIMPLE_MODEL(256, _updateSymbol)(&byte_model1[last1], &rc, in[i]); } last2 = last1; last1 = in[i]; } free(byte_model); if (RC_FinishEncode(&rc) < 0) { free(out_free); return NULL; } // Finalise block size and return it *out_size = RC_OutSize(&rc)+1; return out; } #endif unsigned char *arith_uncompress_O2(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { RangeCoder rc; SIMPLE_MODEL(256,_) *byte_model; byte_model = malloc(256*256*sizeof(*byte_model)); unsigned int m = in[0] ? in[0] : 256, i, j; for (i = 0; i < 256; i++) for (j = 0; j < 256; j++) SIMPLE_MODEL(256,_init)(&byte_model[i*256+j], m); unsigned char *out_free = NULL; if (!out) out_free = out = malloc(out_sz); if (!out) return NULL; RC_SetInput(&rc, (char *)in+1, (char *)in+in_size); RC_StartDecode(&rc); unsigned char last1 = 0, last2 = 0; for (i = 0; i < out_sz; i++) { out[i] = SIMPLE_MODEL(256, _decodeSymbol)(&byte_model[last1*256 + last2], &rc); last2 = last1; last1 = out[i]; } free(byte_model); if (RC_FinishDecode(&rc) < 0) { free(out_free); return NULL; } return out; } #endif // Disable O2 /*----------------------------------------------------------------------------- */ #undef NSYM #define NSYM 258 #include "c_simple_model.h" #define MAX_RUN 4 static unsigned char *arith_compress_O0_RLE(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { int i, bound = arith_compress_bound(in_size,0)-5; // -5 for order/size unsigned char *out_free = NULL; if (!out) { *out_size = bound; out_free = out = malloc(*out_size); } if (!out || bound > *out_size) return NULL; unsigned int m = 0; for (i = 0; i < in_size; i++) if (m < in[i]) m = in[i]; m++; *out = m; SIMPLE_MODEL(256,_) byte_model; SIMPLE_MODEL(256,_init)(&byte_model, m); SIMPLE_MODEL(NSYM,_) *run_model = htscodecs_tls_alloc(NSYM * sizeof(*run_model)); if (!run_model) { free(out_free); return NULL; } for (i = 0; i < NSYM; i++) SIMPLE_MODEL(NSYM,_init)(&run_model[i], MAX_RUN); RangeCoder rc; RC_SetOutput(&rc, (char *)out+1); RC_SetOutputEnd(&rc, (char *)out + *out_size); RC_StartEncode(&rc); unsigned char last = 0; for (i = 0; i < in_size;) { //SIMPLE_MODEL(256, _encodeSymbol)(&byte_model, &rc, in[i]); SIMPLE_MODEL(256, _encodeSymbol)(&byte_model, &rc, in[i]); //fprintf(stderr, "lit %c (ctx %c)\n", in[i], last); int run = 0; last = in[i++]; while (i < in_size && in[i] == last/* && run < MAX_RUN-1*/) run++, i++; int rctx = last; do { int c = run < MAX_RUN ? run : MAX_RUN-1; SIMPLE_MODEL(NSYM, _encodeSymbol)(&run_model[rctx], &rc, c); run -= c; if (rctx == last) rctx = 256; else rctx += (rctx < NSYM-1); if (c == MAX_RUN-1 && run == 0) SIMPLE_MODEL(NSYM, _encodeSymbol)(&run_model[rctx], &rc, 0); } while (run); } if (RC_FinishEncode(&rc) < 0) { htscodecs_tls_free(run_model); free(out_free); return NULL; } // Finalise block size and return it *out_size = RC_OutSize(&rc)+1; //fprintf(stderr, "RLE %d to %d\n", in_size, *out_size); htscodecs_tls_free(run_model); return out; } static unsigned char *arith_uncompress_O0_RLE(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { RangeCoder rc; int i; unsigned int m = in[0] ? in[0] : 256; unsigned char *out_free = NULL; if (!out) out_free = out = malloc(out_sz); if (!out) return NULL; SIMPLE_MODEL(256,_) byte_model; SIMPLE_MODEL(256,_init)(&byte_model, m); SIMPLE_MODEL(NSYM,_) *run_model = htscodecs_tls_alloc(NSYM * sizeof(*run_model)); if (!run_model) { free(out_free); return NULL; } for (i = 0; i < NSYM; i++) SIMPLE_MODEL(NSYM,_init)(&run_model[i], MAX_RUN); RC_SetInput(&rc, (char *)in+1, (char *)in+in_size); RC_StartDecode(&rc); for (i = 0; i < out_sz; i++) { unsigned char last; last = out[i] = SIMPLE_MODEL(256, _decodeSymbol)(&byte_model, &rc); //fprintf(stderr, "lit %c\n", last); int run = 0, r = 0, rctx = out[i]; do { r = SIMPLE_MODEL(NSYM, _decodeSymbol)(&run_model[rctx], &rc); if (rctx == last) rctx = 256; else rctx += (rctx < NSYM-1); //fprintf(stderr, "run %d (ctx %d, %d)\n", r, last, l); run += r; } while (r == MAX_RUN-1 && run < out_sz); while (run-- && i+1 < out_sz) out[++i] = last; } if (RC_FinishDecode(&rc) < 0) { htscodecs_tls_free(run_model); free(out_free); return NULL; } htscodecs_tls_free(run_model); return out; } static unsigned char *arith_compress_O1_RLE(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { int i, bound = arith_compress_bound(in_size,0)-5; // -5 for order/size unsigned char *out_free = NULL; if (!out) { *out_size = bound; out_free = out = malloc(*out_size); } if (!out || bound > *out_size) return NULL; unsigned int m = 0; for (i = 0; i < in_size; i++) if (m < in[i]) m = in[i]; m++; *out = m; SIMPLE_MODEL(256,_) *byte_model = htscodecs_tls_alloc(256 * sizeof(*byte_model)); if (!byte_model) { free(out_free); return NULL; } for (i = 0; i < 256; i++) SIMPLE_MODEL(256,_init)(&byte_model[i], m); SIMPLE_MODEL(NSYM,_) *run_model = htscodecs_tls_alloc(NSYM * sizeof(*run_model)); if (!run_model) { htscodecs_tls_free(byte_model); free(out_free); return NULL; } for (i = 0; i < NSYM; i++) SIMPLE_MODEL(NSYM,_init)(&run_model[i], MAX_RUN); RangeCoder rc; RC_SetOutput(&rc, (char *)out+1); RC_SetOutputEnd(&rc, (char *)out + *out_size); RC_StartEncode(&rc); unsigned char last = 0; for (i = 0; i < in_size;) { //SIMPLE_MODEL(256, _encodeSymbol)(&byte_model, &rc, in[i]); SIMPLE_MODEL(256, _encodeSymbol)(&byte_model[last], &rc, in[i]); //fprintf(stderr, "lit %c (ctx %c)\n", in[i], last); int run = 0; last = in[i++]; while (i < in_size && in[i] == last/* && run < MAX_RUN-1*/) run++, i++; int rctx = last; do { int c = run < MAX_RUN ? run : MAX_RUN-1; SIMPLE_MODEL(NSYM, _encodeSymbol)(&run_model[rctx], &rc, c); run -= c; if (rctx == last) rctx = 256; else rctx += (rctx < NSYM-1); if (c == MAX_RUN-1 && run == 0) SIMPLE_MODEL(NSYM, _encodeSymbol)(&run_model[rctx], &rc, 0); } while (run); } if (RC_FinishEncode(&rc) < 0) { htscodecs_tls_free(byte_model); htscodecs_tls_free(run_model); free(out_free); return NULL; } // Finalise block size and return it *out_size = RC_OutSize(&rc)+1; //fprintf(stderr, "RLE %d to %d\n", in_size, *out_size); htscodecs_tls_free(byte_model); htscodecs_tls_free(run_model); return out; } static unsigned char *arith_uncompress_O1_RLE(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { RangeCoder rc; int i; unsigned int m = in[0] ? in[0] : 256; unsigned char *out_free = NULL; if (!out) out_free = out = malloc(out_sz); if (!out) return NULL; SIMPLE_MODEL(256,_) *byte_model = htscodecs_tls_alloc(256 * sizeof(*byte_model)); if (!byte_model) { free(out_free); return NULL; } for (i = 0; i < 256; i++) SIMPLE_MODEL(256,_init)(&byte_model[i], m); SIMPLE_MODEL(NSYM,_) *run_model = htscodecs_tls_alloc(NSYM * sizeof(*run_model)); if (!run_model) { htscodecs_tls_free(byte_model); free(out_free); return NULL; } for (i = 0; i < NSYM; i++) SIMPLE_MODEL(NSYM,_init)(&run_model[i], MAX_RUN); RC_SetInput(&rc, (char *)in+1, (char *)in+in_size); RC_StartDecode(&rc); unsigned char last = 0; for (i = 0; i < out_sz; i++) { out[i] = SIMPLE_MODEL(256, _decodeSymbol)(&byte_model[last], &rc); //fprintf(stderr, "lit %c (ctx %c)\n", out[i], last); last = out[i]; int run = 0, r = 0, rctx = last; do { r = SIMPLE_MODEL(NSYM, _decodeSymbol)(&run_model[rctx], &rc); if (rctx == last) rctx = 256; else rctx += (rctx < NSYM-1); run += r; } while (r == MAX_RUN-1 && run < out_sz); while (run-- && i+1 < out_sz) out[++i] = last; } if (RC_FinishDecode(&rc) < 0) { htscodecs_tls_free(byte_model); htscodecs_tls_free(run_model); free(out_free); return NULL; } htscodecs_tls_free(byte_model); htscodecs_tls_free(run_model); return out; } /*----------------------------------------------------------------------------- * Simple interface to the order-0 vs order-1 encoders and decoders. * * Smallest is method, , so worst case 2 bytes longer. */ unsigned char *arith_compress_to(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size, int order) { unsigned int c_meta_len; uint8_t *rle = NULL, *packed = NULL; if (in_size > INT_MAX) { *out_size = 0; return NULL; } if (!out) { *out_size = arith_compress_bound(in_size, order); if (!(out = malloc(*out_size))) return NULL; } unsigned char *out_end = out + *out_size; if (in_size <= 20) order &= ~X_STRIPE; if (order & X_CAT) { out[0] = X_CAT; c_meta_len = 1 + var_put_u32(&out[1], out_end, in_size); memcpy(out+c_meta_len, in, in_size); *out_size = in_size+c_meta_len; } if (order & X_STRIPE) { int N = (order>>8); if (N == 0) N = 4; // default for compatibility with old tests if (N > 255) return NULL; unsigned char *transposed = malloc(in_size); unsigned int part_len[256]; unsigned int idx[256]; if (!transposed) return NULL; int i, j, x; for (i = 0; i < N; i++) { part_len[i] = in_size / N + ((in_size % N) > i); idx[i] = i ? idx[i-1] + part_len[i-1] : 0; // cumulative index } for (i = x = 0; i < in_size-N; i += N, x++) { for (j = 0; j < N; j++) transposed[idx[j]+x] = in[i+j]; } for (; i < in_size; i += N, x++) { for (j = 0; i+j < in_size; j++) transposed[idx[j]+x] = in[i+j]; } unsigned int olen2; unsigned char *out2, *out2_start; c_meta_len = 1; *out = order & ~X_NOSZ; c_meta_len += var_put_u32(out+c_meta_len, out_end, in_size); out[c_meta_len++] = N; out2_start = out2 = out+7+5*N; // shares a buffer with c_meta for (i = 0; i < N; i++) { // Brute force try all methods. // FIXME: optimise this bit. Maybe learn over time? int j, best_j = 0, best_sz = INT_MAX; // Works OK with read names. The first byte is the most important, // as it has most variability (little-endian). After that it's // often quite predictable. // // Do we gain in any other context in CRAM? Aux tags maybe? int m[][4] = {{3, 1,64,0}, {2, 1,0}, {2, 1,128}, {2, 1,128}}; // int m[][6] = {{4, 1,64,2,0}, //test of adding in an order-2 codec // {3, 1,2,0}, // {3, 1,2,128}, // {3, 1,2,128}}; // Other possibilities for methods to try. // int m[][10] = {{8, 1,128,129,64,65,192,193,4,0}, // {8, 1,128,129,64,65,192,193,4,0}, // {8, 1,128,129,64,65,192,193,4,0}, // {8, 1,128,129,64,65,192,193,4,0}}; // int m[][9] = {{5, 1,128,64,65,0}, // {5, 1,128,64,65,0}, // {5, 1,128,64,65,0}, // {5, 1,128,64,65,0}}; // int m[][6] = {{4, 0,1,128,64}, // {5, 0,1,128,65,193}, // {3, 0,1,128}, // {3, 0,1,128}}; // int m[][6] = {{4, 1,128,64,0}, // {4, 1,128,65,0}, // {2, 128,0}, // {2, 128,0}}; // int m[][6] = {{2, 64,0}, // {1, 0}, // {1, 128}, // {1, 128}}; // int m[][6] = {{1, 0}, // {2, 128,0}, // {1, 128}, // {1, 128}}; for (j = 1; j <= m[MIN(i,3)][0]; j++) { olen2 = *out_size - (out2 - out); //fprintf(stderr, "order=%d m=%d\n", order&3, m[MIN(i,4)][j]); if ((order&3) == 0 && (m[MIN(i,3)][j]&1)) continue; arith_compress_to(transposed+idx[i], part_len[i], out2, &olen2, m[MIN(i,3)][j] | X_NOSZ); if (best_sz > olen2) { best_sz = olen2; best_j = j; } } // if (best_j == 0) // none desireable // return NULL; if (best_j != j-1) { olen2 = *out_size - (out2 - out); arith_compress_to(transposed+idx[i], part_len[i], out2, &olen2, m[MIN(i,3)][best_j] | X_NOSZ); } out2 += olen2; c_meta_len += var_put_u32(out+c_meta_len, out_end, olen2); } memmove(out+c_meta_len, out2_start, out2-out2_start); free(transposed); *out_size = c_meta_len + out2-out2_start; return out; } int do_pack = order & X_PACK; int do_rle = order & X_RLE; int no_size = order & X_NOSZ; int do_ext = order & X_EXT; out[0] = order; c_meta_len = 1; if (!no_size) c_meta_len += var_put_u32(&out[1], out_end, in_size); order &= 0x3; // Format is compressed meta-data, compressed data. // Meta-data can be empty, pack, rle lengths, or pack + rle lengths. // Data is either the original data, bit-packed packed, rle literals or // packed + rle literals. if (do_pack && in_size) { // PACK 2, 4 or 8 symbols into one byte. int pmeta_len; uint64_t packed_len; packed = hts_pack(in, in_size, out+c_meta_len, &pmeta_len, &packed_len); if (!packed) { out[0] &= ~X_PACK; do_pack = 0; free(packed); packed = NULL; } else { in = packed; in_size = packed_len; c_meta_len += pmeta_len; // Could derive this rather than storing verbatim. // Orig size * 8/nbits (+1 if not multiple of 8/n) int sz = var_put_u32(out+c_meta_len, out_end, in_size); c_meta_len += sz; *out_size -= sz; } } else if (do_pack) { out[0] &= ~X_PACK; } if (do_rle && !in_size) { out[0] &= ~X_RLE; } *out_size -= c_meta_len; if (order && in_size < 8) { out[0] &= ~3; order &= ~3; } if (do_ext) { // Use an external compression library instead. // For now, bzip2 #ifdef HAVE_LIBBZ2 if (BZ_OK != BZ2_bzBuffToBuffCompress((char *)out+c_meta_len, out_size, (char *)in, in_size, 9, 0, 30)) *out_size = in_size; // Didn't fit with bz2; force X_CAT below instead #else fprintf(stderr, "Htscodecs has been compiled without libbz2 support\n"); free(out); return NULL; #endif // // lzma doesn't help generally, at least not for the name tokeniser // size_t lzma_size = 0; // lzma_easy_buffer_encode(9, LZMA_CHECK_CRC32, NULL, // in, in_size, out+c_meta_len, &lzma_size, // *out_size); // *out_size = lzma_size; } else { if (do_rle) { if (order == 0) arith_compress_O0_RLE(in, in_size, out+c_meta_len, out_size); else arith_compress_O1_RLE(in, in_size, out+c_meta_len, out_size); } else { //if (order == 2) // arith_compress_O2(in, in_size, out+c_meta_len, out_size); //else if (order == 1) arith_compress_O1(in, in_size, out+c_meta_len, out_size); else arith_compress_O0(in, in_size, out+c_meta_len, out_size); } } if (*out_size >= in_size) { out[0] &= ~(3|X_EXT); // no entropy encoding, but keep e.g. PACK out[0] |= X_CAT | no_size; memcpy(out+c_meta_len, in, in_size); *out_size = in_size; } free(rle); free(packed); *out_size += c_meta_len; return out; } unsigned char *arith_compress(unsigned char *in, unsigned int in_size, unsigned int *out_size, int order) { return arith_compress_to(in, in_size, NULL, out_size, order); } unsigned char *arith_uncompress_to(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { unsigned char *in_end = in + in_size; unsigned char *out_free = NULL; unsigned char *tmp_free = NULL; if (in_size == 0) return NULL; if (*in & X_STRIPE) { unsigned int ulen, olen, c_meta_len = 1; int i; uint64_t clen_tot = 0; // Decode lengths c_meta_len += var_get_u32(in+c_meta_len, in_end, &ulen); if (c_meta_len >= in_size) return NULL; unsigned int N = in[c_meta_len++]; if (N < 1) // Must be at least one stripe return NULL; unsigned int clenN[256], ulenN[256], idxN[256]; if (!out) { if (ulen >= INT_MAX) return NULL; if (!(out_free = out = malloc(ulen))) { return NULL; } *out_size = ulen; } if (ulen != *out_size) { free(out_free); return NULL; } for (i = 0; i < N; i++) { ulenN[i] = ulen / N + ((ulen % N) > i); idxN[i] = i ? idxN[i-1] + ulenN[i-1] : 0; c_meta_len += var_get_u32(in+c_meta_len, in_end, &clenN[i]); clen_tot += clenN[i]; if (c_meta_len > in_size || clenN[i] > in_size || clenN[i] < 1) { free(out_free); return NULL; } } // We can call this with a larger buffer, but once we've determined // how much we really use we limit it so the recursion becomes easier // to limit. if (c_meta_len + clen_tot > in_size) { free(out_free); return NULL; } in_size = c_meta_len + clen_tot; //fprintf(stderr, " stripe meta %d\n", c_meta_len); //c-size // Uncompress the N streams unsigned char *outN = malloc(ulen); if (!outN) { free(out_free); return NULL; } for (i = 0; i < N; i++) { olen = ulenN[i]; if (in_size < c_meta_len) { free(out_free); free(outN); return NULL; } if (!arith_uncompress_to(in+c_meta_len, in_size-c_meta_len, outN + idxN[i], &olen) || olen != ulenN[i]) { free(out_free); free(outN); return NULL; } c_meta_len += clenN[i]; } unstripe(out, outN, ulen, N, idxN); free(outN); *out_size = ulen; return out; } int order = *in++; in_size--; int do_pack = order & X_PACK; int do_rle = order & X_RLE; int do_cat = order & X_CAT; int no_size = order & X_NOSZ; int do_ext = order & X_EXT; order &= 3; int sz = 0; unsigned int osz; if (!no_size) sz = var_get_u32(in, in_end, &osz); else sz = 0, osz = *out_size; in += sz; in_size -= sz; if (osz >= INT_MAX) return NULL; #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION // Limit maximum size to get fast turnaround on fuzzing test cases if (osz > 100000) goto err; #endif if (no_size && !out) return NULL; // Need one or the other if (!out) { *out_size = osz; if (!(out_free = out = malloc(*out_size))) return NULL; } else { if (*out_size < osz) return NULL; *out_size = osz; } uint32_t c_meta_size = 0; unsigned int tmp1_size = *out_size; unsigned int tmp2_size = *out_size; unsigned char *tmp1 = NULL, *tmp2 = NULL, *tmp = NULL; // Need In, Out and Tmp buffers with temporary buffer of the same size // as output. Our entropy decode is either arithmetic (with/without RLE) // or external (bz2, gzip, lzma) but with an optional unPACK transform // at the end. // // To avoid pointless memcpy when unpacking we switch around which // buffers we're writing to accordingly. // Format is pack meta data if present, followed by compressed data. if (do_pack) { if (!(tmp_free = tmp = malloc(*out_size))) goto err; tmp1 = tmp; // uncompress tmp2 = out; // unpack } else { // no pack tmp = NULL; tmp1 = out; // uncompress tmp2 = out; // NOP } // Decode the bit-packing map. uint8_t map[16] = {0}; int npacked_sym = 0; uint64_t unpacked_sz = 0; // FIXME: rename to packed_per_byte if (do_pack) { c_meta_size = hts_unpack_meta(in, in_size, *out_size, map, &npacked_sym); if (c_meta_size == 0) goto err; unpacked_sz = osz; in += c_meta_size; in_size -= c_meta_size; // New unpacked size. We could derive this bit from *out_size // and npacked_sym. unsigned int osz; sz = var_get_u32(in, in_end, &osz); in += sz; in_size -= sz; if (osz > tmp1_size) goto err; tmp1_size = osz; } //fprintf(stderr, " meta_size %d bytes\n", (int)(in - orig_in)); //c-size // uncompress RLE data. in -> tmp1 if (in_size) { #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION // Limit maximum size to get fast turnaround on fuzzing test cases if (tmp1_size > 100000) goto err; #endif if (do_cat) { //fprintf(stderr, " CAT %d\n", tmp1_size); //c-size if (tmp1_size > in_size) goto err; if (tmp1_size > *out_size) goto err; memcpy(tmp1, in, tmp1_size); } else if (do_ext) { #ifdef HAVE_LIBBZ2 if (BZ_OK != BZ2_bzBuffToBuffDecompress((char *)tmp1, &tmp1_size, (char *)in, in_size, 0, 0)) goto err; #else fprintf(stderr, "Htscodecs has been compiled without libbz2 support\n"); goto err; #endif } else { // in -> tmp1 if (do_rle) { tmp1 = order == 1 ? arith_uncompress_O1_RLE(in, in_size, tmp1, tmp1_size) : arith_uncompress_O0_RLE(in, in_size, tmp1, tmp1_size); } else { //if (order == 2) // tmp1 = arith_uncompress_O2(in, in_size, tmp1, tmp1_size) //else tmp1 = order == 1 ? arith_uncompress_O1(in, in_size, tmp1, tmp1_size) : arith_uncompress_O0(in, in_size, tmp1, tmp1_size); } if (!tmp1) goto err; } } else { tmp1_size = 0; } if (do_pack) { // Unpack bits via pack-map. tmp1 -> tmp2 if (npacked_sym == 1) unpacked_sz = tmp1_size; //uint8_t *porig = unpack(tmp2, tmp2_size, unpacked_sz, npacked_sym, map); //memcpy(tmp3, porig, unpacked_sz); if (!hts_unpack(tmp1, tmp1_size, tmp2, unpacked_sz, npacked_sym, map)) goto err; tmp2_size = unpacked_sz; } else { tmp2_size = tmp1_size; } if (tmp) free(tmp); *out_size = tmp2_size; return tmp2; err: free(tmp_free); free(out_free); return NULL; } unsigned char *arith_uncompress(unsigned char *in, unsigned int in_size, unsigned int *out_size) { return arith_uncompress_to(in, in_size, NULL, out_size); } pysam-0.23.0/htslib/htscodecs/htscodecs/arith_dynamic.h000066400000000000000000000047101475062545500231530ustar00rootroot00000000000000/* * Copyright (c) 2019 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef ARITH_DYNAMIC_H #define ARITH_DYNAMIC_H #ifdef __cplusplus extern "C" { #endif unsigned char *arith_compress(unsigned char *in, unsigned int in_size, unsigned int *out_size, int order); unsigned char *arith_uncompress(unsigned char *in, unsigned int in_size, unsigned int *out_size); unsigned char *arith_compress_to(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size, int order); unsigned char *arith_uncompress_to(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_sz); unsigned int arith_compress_bound(unsigned int size, int order); #ifdef __cplusplus } #endif #endif /* ARITH_DYNAMIC_H */ pysam-0.23.0/htslib/htscodecs/htscodecs/c_range_coder.h000066400000000000000000000105601475062545500231120ustar00rootroot00000000000000// Copyright Eugene Shelwien. // Release into public domain. // Modifications by James Bonfield (2019) /* * Note it is up to the calling code to ensure that no overruns on input and * output buffers occur. * * Call the input() and output() functions to set and query the current * buffer locations. * */ #ifndef C_RANGER_CODER_H #define C_RANGER_CODER_H #define DO(n) int _;for (_=0; _out_buf = rc->in_buf = (uc *)in; rc->in_end = (uc *)in_end; } // NB: call RC_SetOutput first, and then RC_SetOutputEnd static inline void RC_SetOutput(RangeCoder *rc, char *out) { rc->in_buf = rc->out_buf = (uc *)out; rc->out_end = NULL;} static inline void RC_SetOutputEnd(RangeCoder *rc, char *out_end) { rc->out_end = (uc *)out_end; } static inline char *RC_GetInput(RangeCoder *rc) { return (char *)rc->in_buf; } static inline char *RC_GetOutput(RangeCoder *rc) { return (char *)rc->out_buf; } static inline size_t RC_OutSize(RangeCoder *rc) { return rc->out_buf - rc->in_buf; } static inline size_t RC_InSize(RangeCoder *rc) { return rc->in_buf - rc->out_buf; } static inline void RC_StartEncode(RangeCoder *rc) { rc->range = 0xFFFFFFFF; rc->low = 0; rc->FFNum = 0; rc->Carry = 0; rc->Cache = 0; rc->code = 0; rc->err = 0; } static inline void RC_StartDecode(RangeCoder *rc) { rc->range = 0xFFFFFFFF; rc->low = 0; rc->FFNum = 0; rc->Carry = 0; rc->Cache = 0; rc->code = 0; rc->err = 0; if (rc->in_buf+5 > rc->in_end) { rc->in_buf = rc->in_end; // prevent decode return; } DO(5) rc->code = (rc->code<<8) | *rc->in_buf++; } static inline void RC_ShiftLowCheck(RangeCoder *rc) { if (rc->low < Thres || rc->Carry) { if (rc->out_end && rc->FFNum >= rc->out_end - rc->out_buf) { rc->err = -1; return; } *rc->out_buf++ = rc->Cache + rc->Carry; // Flush any stored FFs while (rc->FFNum) { *rc->out_buf++ = rc->Carry-1; // (Carry-1)&255; rc->FFNum--; } // Take copy of top byte ready for next flush rc->Cache = rc->low >> 24; rc->Carry = 0; } else { // Low if FFxx xxxx. Bump FF count and shift in as before rc->FFNum++; } rc->low = rc->low<<8; } static inline void RC_ShiftLow(RangeCoder *rc) { if (rc->low < Thres || rc->Carry) { *rc->out_buf++ = rc->Cache + rc->Carry; // Flush any stored FFs while (rc->FFNum) { *rc->out_buf++ = rc->Carry-1; // (Carry-1)&255; rc->FFNum--; } // Take copy of top byte ready for next flush rc->Cache = rc->low >> 24; rc->Carry = 0; } else { // Low if FFxx xxxx. Bump FF count and shift in as before rc->FFNum++; } rc->low = rc->low<<8; } static inline int RC_FinishEncode(RangeCoder *rc) { DO(5) RC_ShiftLowCheck(rc); return rc->err; } static inline int RC_FinishDecode(RangeCoder *rc) { return rc->err; } static inline void RC_Encode (RangeCoder *rc, uint32_t cumFreq, uint32_t freq, uint32_t totFreq) { uint32_t tmp = rc->low; rc->low += cumFreq * (rc->range/= totFreq); rc->range*= freq; rc->Carry += rc->lowrange < TOP) { rc->range <<= 8; RC_ShiftLowCheck(rc); } } static inline uint32_t RC_GetFreq (RangeCoder *rc, uint32_t totFreq) { //return rc->code/(rc->range/=totFreq); return (totFreq && rc->range >= totFreq) ? rc->code/(rc->range/=totFreq) : 0; } static inline void RC_Decode (RangeCoder *rc, uint32_t cumFreq, uint32_t freq, uint32_t totFreq) { rc->code -= cumFreq * rc->range; rc->range *= freq; while (rc->range < TOP) { if (rc->in_buf >= rc->in_end) { rc->err = -1; return; } rc->code = (rc->code<<8) + *rc->in_buf++; rc->range <<= 8; } } #endif /* C_RANGER_CODER_H */ pysam-0.23.0/htslib/htscodecs/htscodecs/c_simple_model.h000066400000000000000000000126601475062545500233160ustar00rootroot00000000000000/* * Copyright (c) 2012, 2018-2019 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #include #include "c_range_coder.h" /* *-------------------------------------------------------------------------- * A simple frequency model. * * Define NSYM to be an integer value before including this file. * It will then generate types and functions specific to that * maximum number of symbols. * * This keeps a list of symbols and their frequencies, approximately * sorted by symbol frequency. We allow for a single symbol to periodically * move up the list when emitted, effectively doing a single step of * bubble sort periodically. This means it's largely the same complexity * irrespective of alphabet size. * It's more efficient on strongly biased distributions than random data. * * There is no escape symbol, so the model is tailored to relatively * stationary samples (although we do have occasional normalisation to * avoid frequency counters getting too high). *-------------------------------------------------------------------------- */ //----------------------------------------------------------------------------- // Bits we want included once only - constants, types, etc #ifndef C_SIMPLE_MODEL_H #define C_SIMPLE_MODEL_H #define MAX_FREQ (1<<16)-17 #define PASTE3(a,b,c) a##b##c #define SIMPLE_MODEL(a,b) PASTE3(SIMPLE_MODEL,a,b) #define STEP 16 typedef struct { uint16_t Freq; uint16_t Symbol; } SymFreqs; #endif /* C_SIMPLE_MODEL_H */ //----------------------------------------------------------------------------- // Bits we regenerate for each NSYM value. typedef struct { uint32_t TotFreq; // Total frequency // Array of Symbols approximately sorted by Freq. SymFreqs sentinel, F[NSYM+1], terminal; } SIMPLE_MODEL(NSYM,_); static inline void SIMPLE_MODEL(NSYM,_init)(SIMPLE_MODEL(NSYM,_) *m, int max_sym) { int i; for (i=0; iF[i].Symbol = i; m->F[i].Freq = 1; } for (; iF[i].Symbol = i; m->F[i].Freq = 0; } m->TotFreq = max_sym; m->sentinel.Symbol = 0; m->sentinel.Freq = MAX_FREQ; // Always first; simplifies sorting. m->terminal.Symbol = 0; m->terminal.Freq = MAX_FREQ; m->F[NSYM].Freq = 0; // terminates normalize() loop. See below. } static inline void SIMPLE_MODEL(NSYM,_normalize)(SIMPLE_MODEL(NSYM,_) *m) { SymFreqs *s; /* Faster than F[i].Freq for 0 <= i < NSYM */ m->TotFreq=0; for (s = m->F; s->Freq; s++) { s->Freq -= s->Freq>>1; m->TotFreq += s->Freq; } } static inline void SIMPLE_MODEL(NSYM,_encodeSymbol)(SIMPLE_MODEL(NSYM,_) *m, RangeCoder *rc, uint16_t sym) { SymFreqs *s = m->F; uint32_t AccFreq = 0; while (s->Symbol != sym) AccFreq += s++->Freq; RC_Encode(rc, AccFreq, s->Freq, m->TotFreq); s->Freq += STEP; m->TotFreq += STEP; if (m->TotFreq > MAX_FREQ) SIMPLE_MODEL(NSYM,_normalize)(m); /* Keep approx sorted */ if (s[0].Freq > s[-1].Freq) { SymFreqs t = s[0]; s[0] = s[-1]; s[-1] = t; } } static inline uint16_t SIMPLE_MODEL(NSYM,_decodeSymbol)(SIMPLE_MODEL(NSYM,_) *m, RangeCoder *rc) { SymFreqs* s = m->F; uint32_t freq = RC_GetFreq(rc, m->TotFreq); uint32_t AccFreq; if (freq > MAX_FREQ) return 0; // error for (AccFreq = 0; (AccFreq += s->Freq) <= freq; s++) ; if (s - m->F > NSYM) return 0; // error AccFreq -= s->Freq; RC_Decode(rc, AccFreq, s->Freq, m->TotFreq); s->Freq += STEP; m->TotFreq += STEP; if (m->TotFreq > MAX_FREQ) SIMPLE_MODEL(NSYM,_normalize)(m); /* Keep approx sorted */ if (s[0].Freq > s[-1].Freq) { SymFreqs t = s[0]; s[0] = s[-1]; s[-1] = t; return t.Symbol; } return s->Symbol; } pysam-0.23.0/htslib/htscodecs/htscodecs/fqzcomp_qual.c000066400000000000000000001423661475062545500230460ustar00rootroot00000000000000/* * Copyright (c) 2011-2013, 2018-2022 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ // We use generic maps to turn 0-M into 0-N where N <= M // before adding these into the context. These are used // for positions, running-diffs and quality values. // // This can be used as a simple divisor, eg pos/24 to get // 2 bits of positional data for each quarter along a 100bp // read, or it can be tailored for specific such as noting // the first 5 cycles are poor, then we have stability and // a gradual drop off in the last 20 or so. Perhaps we then // map pos 0-4=0, 5-79=1, 80-89=2, 90-99=3. // // We don't need to specify how many bits of data we are // using (2 in the above example), as that is just implicit // in the values in the map. Specify not to use a map simply // disables that context type (our map is essentially 0-M -> 0). // Example of command line usage: // // f=~/scratch/data/q4 // cc -Wall -DTEST_MAIN -O3 -g fqzcomp_qual2.c -lm // ./a.out $f > /tmp/_ && ./a.out -d < /tmp/_ > /tmp/__ && cmp /tmp/__ $f #include "config.h" #include #include #include #include #include #include #include #include #include #include #include "fqzcomp_qual.h" #include "varint.h" #include "utils.h" #define CTX_BITS 16 #define CTX_SIZE (1<(b)?(a):(b)) #endif #define QMAX 256 #define QBITS 12 #define QSIZE (1< 255 therefore means we need to repeatedly read to find // the actual run length. // Alternatively we could bit-encode instead of byte encode, eg BETA. static int store_array(unsigned char *out, unsigned int *array, int size) { unsigned char tmp[2048]; int i, j, k; for (i = j = k = 0; i < size; j++) { int run_len = i; while (i < size && array[i] == j) i++; run_len = i-run_len; int r; do { r = MIN(255, run_len); tmp[k++] = r; run_len -= r; } while (r == 255); } while (i < size) tmp[k++] = 0, j++; // RLE on out. // 1 2 3 3 3 3 3 4 4 5 // => 1 2 3 3 +3... 4 4 +0 5 int last = -1; for (i = j = 0; j < k; i++) { out[i] = tmp[j++]; if (out[i] == last) { int n = j; while (j < k && tmp[j] == last) j++; out[++i] = j-n; } else { last = out[i]; } } k = i; // fprintf(stderr, "Store_array %d => %d {", size, k); // for (i = 0; i < k; i++) // fprintf(stderr, "%d,", out[i]); // fprintf(stderr, "}\n"); return k; } static int read_array(unsigned char *in, size_t in_size, unsigned int *array, int size) { unsigned char R[1024]; int i, j, z, last = -1, nb = 0; size = MIN(1024, size); // Remove level one of run-len encoding for (i = j = z = 0; z < size && i < in_size; i++) { int run = in[i]; R[j++] = run; z += run; if (run == last) { if (i+1 >= in_size) return -1; int copy = in[++i]; z += run * copy; while (copy-- && z <= size && j < 1024) R[j++] = run; } if (j >= 1024) return -1; last = run; } nb = i; // Now expand inner level of run-length encoding int R_max = j; for (i = j = z = 0; j < size; i++) { int run_len = 0; int run_part; if (z >= R_max) return -1; do { run_part = R[z++]; run_len += run_part; } while (run_part == 255 && z < R_max); if (run_part == 255) return -1; while (run_len && j < size) run_len--, array[j++] = i; } return nb; } // FIXME: how to auto-tune these rather than trial and error? // r2 = READ2 // qa = qual avg (0, 2, 4) static int strat_opts[][12] = { // qb qs pb ps db ds ql sl pl dl r2 qa {10, 5, 4,-1, 2, 1, 0, 14, 10, 14, 0,-1}, // basic options (level < 7) {8, 5, 7, 0, 0, 0, 0, 14, 8, 14, 1,-1}, // e.g. HiSeq 2000 {12, 6, 2, 0, 2, 3, 0, 9, 12, 14, 0, 0}, // e.g. MiSeq {12, 6, 0, 0, 0, 0, 0, 12, 0, 0, 0, 0}, // e.g. IonTorrent; adaptive O1 {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // custom }; static int nstrats = sizeof(strat_opts) / sizeof(*strat_opts); #ifdef HAVE_BUILTIN_PREFETCH static inline void mm_prefetch(void *x) { __builtin_prefetch(x); } #else static inline void mm_prefetch(void *x) { // Fetch and discard is quite close to a genuine prefetch *(volatile int *)x; } #endif typedef struct { unsigned int qctx; // quality sub-context unsigned int p; // pos (bytes remaining) unsigned int delta; // delta running total unsigned int prevq; // previous quality unsigned int s; // selector unsigned int qtot, qlen; unsigned int first_len; unsigned int last_len; ssize_t rec; unsigned int ctx; } fqz_state; static void dump_table(unsigned int *tab, int size, char *name) { int i, last = -99, run = 0; fprintf(stderr, "\t%s\t{", name); for (i = 0; i < size; i++) { if (tab[i] == last) { run++; } else if (run == 1 && tab[i] == last+1) { int first = last; do { last = tab[i]; i++; } while (i < size && tab[i] == last+1); i--; // Want 0,1,2,3,3,3 as 0..2 3x3, not 0..3 3x2 if (tab[i] == tab[i+1]) i--; if (tab[i] != first) fprintf(stderr, "..%d", tab[i]); run = 1; last = -99; } else { if (run > 1) fprintf(stderr, " x %d%s%d", run, i?", ":"", tab[i]); else fprintf(stderr, "%s%d", i?", ":"", tab[i]); run = 1; last = tab[i]; } } if (run > 1) fprintf(stderr, " x %d", run); fprintf(stderr, "}\n"); } static void dump_map(unsigned int *map, int size, char *name) { int i, c = 0; fprintf(stderr, "\t%s\t{", name); for (i = 0; i < size; i++) if (map[i] != INT_MAX) fprintf(stderr, "%s%d=%d", c++?", ":"", i, map[i]); fprintf(stderr, "}\n"); } #pragma GCC diagnostic ignored "-Wunused-function" static void dump_params(fqz_gparams *gp) { fprintf(stderr, "Global params = {\n"); fprintf(stderr, "\tvers\t%d\n", gp->vers); fprintf(stderr, "\tgflags\t0x%02x\n", gp->gflags); fprintf(stderr, "\tnparam\t%d\n", gp->nparam); fprintf(stderr, "\tmax_sel\t%d\n", gp->max_sel); fprintf(stderr, "\tmax_sym\t%d\n", gp->max_sym); if (gp->gflags & GFLAG_HAVE_STAB) dump_table(gp->stab, 256, "stab"); fprintf(stderr, "}\n"); int i; for (i = 0; i < gp->nparam; i++) { fqz_param *pm = &gp->p[i]; fprintf(stderr, "\nParam[%d] = {\n", i); fprintf(stderr, "\tcontext\t0x%04x\n", pm->context); fprintf(stderr, "\tpflags\t0x%02x\n", pm->pflags); fprintf(stderr, "\tmax_sym\t%d\n", pm->max_sym); fprintf(stderr, "\tqbits\t%d\n", pm->qbits); fprintf(stderr, "\tqshift\t%d\n", pm->qshift); fprintf(stderr, "\tqloc\t%d\n", pm->qloc); fprintf(stderr, "\tsloc\t%d\n", pm->sloc); fprintf(stderr, "\tploc\t%d\n", pm->ploc); fprintf(stderr, "\tdloc\t%d\n", pm->dloc); if (pm->pflags & PFLAG_HAVE_QMAP) dump_map(pm->qmap, 256, "qmap"); if (pm->pflags & PFLAG_HAVE_QTAB) dump_table(pm->qtab, 256, "qtab"); if (pm->pflags & PFLAG_HAVE_PTAB) dump_table(pm->ptab, 1024, "ptab"); if (pm->pflags & PFLAG_HAVE_DTAB) dump_table(pm->dtab, 256, "dtab"); fprintf(stderr, "}\n"); } } typedef struct { SIMPLE_MODEL(QMAX,_) *qual; SIMPLE_MODEL(256,_) len[4]; SIMPLE_MODEL(2,_) revcomp; SIMPLE_MODEL(256,_) sel; SIMPLE_MODEL(2,_) dup; } fqz_model; static int fqz_create_models(fqz_model *m, fqz_gparams *gp) { int i; if (!(m->qual = htscodecs_tls_alloc(sizeof(*m->qual) * CTX_SIZE))) return -1; for (i = 0; i < CTX_SIZE; i++) SIMPLE_MODEL(QMAX,_init)(&m->qual[i], gp->max_sym+1); for (i = 0; i < 4; i++) SIMPLE_MODEL(256,_init)(&m->len[i],256); SIMPLE_MODEL(2,_init)(&m->revcomp,2); SIMPLE_MODEL(2,_init)(&m->dup,2); if (gp->max_sel > 0) SIMPLE_MODEL(256,_init)(&m->sel, gp->max_sel+1); return 0; } static void fqz_destroy_models(fqz_model *m) { htscodecs_tls_free(m->qual); } static inline unsigned int fqz_update_ctx(fqz_param *pm, fqz_state *state, int q) { unsigned int last = 0; // pm->context state->qctx = (state->qctx << pm->qshift) + pm->qtab[q]; last += (state->qctx & pm->qmask) << pm->qloc; // The final shifts have been factored into the tables already. last += pm->ptab[MIN(1023, state->p)]; // << pm->ploc last += pm->dtab[MIN(255, state->delta)]; // << pm->dloc last += state->s << pm->sloc; // On the fly average is slow work. // However it can be slightly better than using a selector bit // as it's something we can compute on the fly and thus doesn't // consume output bits for storing the selector itself. // // Q4 (novaseq.bam) // qtot+=q*q -DQ1=8.84 -DQ2=8.51 -DQ3=7.70; 7203598 (-0.7%) // qtot+=q -DQ1=2.96 -DQ2=2.85 -DQ3=2.69; 7207315 // vs old delta; 7255614 (default params) // vs 2 bit selector (no delta) 7203006 (-x 0x8261000e80) // vs 2 bit selector (no delta) 7199153 (-x 0x7270000e70) -0.8% // vs 2 bit selector (no delta) 7219668 (-x 0xa243000ea0) //{ // double qa = state->qtot / (state->qlen+.01); // //fprintf(stderr, "%f\n", qa); // int x = 0; // if (qa>=Q1) x=3; // else if (qa>=Q2) x=2; // else if (qa>=Q3) x=1; // else x=0; // last += x << pm->dloc; // tmp reuse of delta pos // state->qtot += q*q; // state->qlen++; //} // Only update delta after 1st base. state->delta += (state->prevq != q); state->prevq = q; state->p--; return last & (CTX_SIZE-1); } // Build quality stats for qhist and set nsym, do_dedup and do_sel params. // One_param is -1 to gather stats on all data, or >= 0 to gather data // on one specific selector parameter. Used only in TEST_MAIN via // fqz_manual_parameters at the moment. void fqz_qual_stats(fqz_slice *s, unsigned char *in, size_t in_size, fqz_param *pm, uint32_t qhist[256], int one_param) { #define NP 32 uint32_t qhistb[NP][256] = {{0}}; // both uint32_t qhist1[NP][256] = {{0}}; // READ1 only uint32_t qhist2[NP][256] = {{0}}; // READ2 only uint64_t t1[NP] = {0}; // Count for READ1 uint64_t t2[NP] = {0}; // COUNT for READ2 uint32_t avg[2560] = {0}; // Avg qual *and later* avg-to-selector map. int dir = 0; int last_len = 0; int do_dedup = 0; size_t rec; size_t i, j; int num_rec = 0; // See what info we've been given. // Do we have READ1 / READ2? // Do we have selector hidden in the top bits of flag? int max_sel = 0; int has_r2 = 0; for (rec = 0; rec < s->num_records; rec++) { if (one_param >= 0 && (s->flags[rec] >> 16) != one_param) continue; num_rec++; if (max_sel < (s->flags[rec] >> 16)) max_sel = (s->flags[rec] >> 16); if (s->flags[rec] & FQZ_FREAD2) has_r2 = 1; } // Dedup detection and histogram stats gathering int *avg_qual = calloc((s->num_records+1), sizeof(int)); if (!avg_qual) return; rec = i = j = 0; while (i < in_size) { if (one_param >= 0 && (s->flags[rec] >> 16) != one_param) { avg_qual[rec] = 0; i += s->len[rec++]; continue; } if (rec < s->num_records) { j = s->len[rec]; dir = s->flags[rec] & FQZ_FREAD2 ? 1 : 0; if (i > 0 && j == last_len && !memcmp(in+i-last_len, in+i, j)) do_dedup++; // cache which records are dup? } else { j = in_size - i; dir = 0; } last_len = j; uint32_t (*qh)[256] = dir ? qhist2 : qhist1; uint64_t *th = dir ? t2 : t1; uint32_t tot = 0; for (; i < in_size && j > 0; i++, j--) { tot += in[i]; qhist[in[i]]++; qhistb[j & (NP-1)][in[i]]++; qh[j & (NP-1)][in[i]]++; th[j & (NP-1)]++; } tot = last_len ? (tot*10.0)/last_len+.5 : 0; avg_qual[rec] = tot; avg[MIN(2559, tot)]++; rec++; } pm->do_dedup = ((rec+1)/(do_dedup+1) < 500); last_len = 0; // Unique symbol count for (i = pm->max_sym = pm->nsym = 0; i < 256; i++) { if (qhist[i]) pm->max_sym = i, pm->nsym++; } // Auto tune: does average quality helps us? if (pm->do_qa != 0) { // Histogram of average qual in avg[] // NB: we convert avg[] from count to selector index // Few symbols means high compression which means // selector bits become more significant fraction. // Reduce selector bits by skewing the distribution // to not be even binning. double qf0 = pm->nsym > 8 ? 0.2 : 0.05; double qf1 = pm->nsym > 8 ? 0.5 : 0.22; double qf2 = pm->nsym > 8 ? 0.8 : 0.60; int total = 0; i = 0; while (i < 2560) { total += avg[i]; if (total > qf0 * num_rec) { //fprintf(stderr, "Q1=%d\n", (int)i); break; } avg[i++] = 0; } while (i < 2560) { total += avg[i]; if (total > qf1 * num_rec) { //fprintf(stderr, "Q2=%d\n", (int)i); break; } avg[i++] = 1; } while (i < 2560) { total += avg[i]; if (total > qf2 * num_rec) { //fprintf(stderr, "Q3=%d\n", (int)i); break; } avg[i++] = 2; } while (i < 2560) avg[i++] = 3; // Compute simple entropy of merged signal vs split signal. i = 0; rec = 0; int qbin4[4][NP][256] = {{{0}}}; int qbin2[2][NP][256] = {{{0}}}; int qbin1 [NP][256] = {{0}}; int qcnt4[4][NP] = {{0}}; int qcnt2[4][NP] = {{0}}; int qcnt1 [NP] = {0}; while (i < in_size) { if (one_param >= 0 && (s->flags[rec] >> 16) != one_param) { i += s->len[rec++]; continue; } if ((rec & 7) && rec < s->num_records) { // subsample for speed i += s->len[rec++]; continue; } if (rec < s->num_records) j = s->len[rec]; else j = in_size - i; last_len = j; uint32_t tot = avg_qual[rec]; int qb4 = avg[MIN(2559, tot)]; int qb2 = qb4/2; for (; i < in_size && j > 0; i++, j--) { int x = j & (NP-1); qbin4[qb4][x][in[i]]++; qcnt4[qb4][x]++; qbin2[qb2][x][in[i]]++; qcnt2[qb2][x]++; qbin1 [x][in[i]]++; qcnt1 [x]++; } rec++; } double e1 = 0, e2 = 0, e4 = 0; for (j = 0; j < NP; j++) { for (i = 0; i < 256; i++) { if (qbin1 [j][i]) e1 += qbin1 [j][i] * fast_log(qbin1 [j][i] / (double)qcnt1 [j]); if (qbin2[0][j][i]) e2 += qbin2[0][j][i] * fast_log(qbin2[0][j][i] / (double)qcnt2[0][j]); if (qbin2[1][j][i]) e2 += qbin2[1][j][i] * fast_log(qbin2[1][j][i] / (double)qcnt2[1][j]); if (qbin4[0][j][i]) e4 += qbin4[0][j][i] * fast_log(qbin4[0][j][i] / (double)qcnt4[0][j]); if (qbin4[1][j][i]) e4 += qbin4[1][j][i] * fast_log(qbin4[1][j][i] / (double)qcnt4[1][j]); if (qbin4[2][j][i]) e4 += qbin4[2][j][i] * fast_log(qbin4[2][j][i] / (double)qcnt4[2][j]); if (qbin4[3][j][i]) e4 += qbin4[3][j][i] * fast_log(qbin4[3][j][i] / (double)qcnt4[3][j]); } } e1 /= -log(2)/8; e2 /= -log(2)/8; e4 /= -log(2)/8; //fprintf(stderr, "E1=%f E2=%f E4=%f %f\n", e1, e2+s->num_records/8, e4+s->num_records/4, (e4+s->num_records/4)/(e2+s->num_records/8)); // Note by using the selector we're robbing bits from elsewhere in // the context, which may reduce compression better. // We don't know how much by, so this is basically a guess! // For now we just say need 5% saving here. double qm = pm->do_qa > 0 ? 1 : 0.98; if ((pm->do_qa == -1 || pm->do_qa >= 4) && e4 + s->num_records/4 < e2*qm + s->num_records/8 && e4 + s->num_records/4 < e1*qm) { //fprintf(stderr, "do q4\n"); for (i = 0; i < s->num_records; i++) { //fprintf(stderr, "%d -> %d -> %d, %d\n", (int)i, avg_qual[i], avg[MIN(2559, avg_qual[i])], s->flags[i]>>16); s->flags[i] |= avg[MIN(2559, avg_qual[i])] <<16; } pm->do_sel = 1; max_sel = 3; } else if ((pm->do_qa == -1 || pm->do_qa >= 2) && e2 + s->num_records/8 < e1*qm) { //fprintf(stderr, "do q2\n"); for (i = 0; i < s->num_records; i++) s->flags[i] |= (avg[MIN(2559, avg_qual[i])]>>1) <<16; pm->do_sel = 1; max_sel = 1; } if (pm->do_qa == -1) { // assume qual, pos, delta in that order. if (pm->pbits > 0 && pm->dbits > 0) { // 1 from pos/delta pm->sloc = pm->dloc-1; pm->pbits--; pm->dbits--; pm->dloc++; } else if (pm->dbits >= 2) { // 2 from delta pm->sloc = pm->dloc; pm->dbits -= 2; pm->dloc += 2; } else if (pm->qbits >= 2) { pm->qbits -= 2; pm->ploc -= 2; pm->sloc = 16-2 - pm->do_r2; if (pm->qbits == 6 && pm->qshift == 5) pm->qbits--; } pm->do_qa = 4; } } // Auto tune: does splitting up READ1 and READ2 help us? if (has_r2 || pm->do_r2) { // FIXME: && but debug for now double e1 = 0, e2 = 0; // entropy sum for (j = 0; j < NP; j++) { if (!t1[j] || !t2[j]) continue; for (i = 0; i < 256; i++) { if (!qhistb[j][i]) continue; e1 -= (qhistb[j][i])*log(qhistb[j][i] / (double)(t1[j]+t2[j])); if (qhist1[j][i]) e2 -= qhist1[j][i] * log(qhist1[j][i] / (double)t1[j]); if (qhist2[j][i]) e2 -= qhist2[j][i] * log(qhist2[j][i] / (double)t2[j]); } } e1 /= log(2)*8; // bytes e2 /= log(2)*8; //fprintf(stderr, "read1/2 entropy merge %f split %f\n", e1, e2); // Note by using the selector we're robbing bits from elsewhere in // the context, which may reduce compression better. // We don't know how much by, so this is basically a guess! // For now we just say need 5% saving here. double qm = pm->do_r2 > 0 ? 1 : 0.95; if (e2 + (8+s->num_records/8) < e1*qm) { for (rec = 0; rec < s->num_records; rec++) { if (one_param >= 0 && (s->flags[rec] >> 16) != one_param) continue; int sel = s->flags[rec] >> 16; s->flags[rec] = (s->flags[rec] & 0xffff) | ((s->flags[rec] & FQZ_FREAD2) ? ((sel*2)+1) << 16 : ((sel*2)+0) << 16); if (max_sel < (s->flags[rec]>>16)) max_sel = (s->flags[rec]>>16); } } } // We provided explicit selector data or auto-tuned it if (max_sel > 0) { pm->do_sel = 1; pm->max_sel = max_sel; } free(avg_qual); } static inline int fqz_store_parameters1(fqz_param *pm, unsigned char *comp) { int comp_idx = 0, i, j; // Starting context comp[comp_idx++] = pm->context; comp[comp_idx++] = pm->context >> 8; comp[comp_idx++] = pm->pflags; comp[comp_idx++] = pm->max_sym; comp[comp_idx++] = (pm->qbits<<4)|pm->qshift; comp[comp_idx++] = (pm->qloc<<4)|pm->sloc; comp[comp_idx++] = (pm->ploc<<4)|pm->dloc; if (pm->store_qmap) { for (i = j = 0; i < 256; i++) if (pm->qmap[i] != INT_MAX) comp[comp_idx++] = i; } if (pm->qbits && pm->use_qtab) // custom qtab comp_idx += store_array(comp+comp_idx, pm->qtab, 256); if (pm->pbits && pm->use_ptab) // custom ptab comp_idx += store_array(comp+comp_idx, pm->ptab, 1024); if (pm->dbits && pm->use_dtab) // custom dtab comp_idx += store_array(comp+comp_idx, pm->dtab, 256); return comp_idx; } static int fqz_store_parameters(fqz_gparams *gp, unsigned char *comp) { int comp_idx = 0; comp[comp_idx++] = gp->vers; // Format number comp[comp_idx++] = gp->gflags; if (gp->gflags & GFLAG_MULTI_PARAM) comp[comp_idx++] = gp->nparam; if (gp->gflags & GFLAG_HAVE_STAB) { comp[comp_idx++] = gp->max_sel; comp_idx += store_array(comp+comp_idx, gp->stab, 256); } int i; for (i = 0; i < gp->nparam; i++) comp_idx += fqz_store_parameters1(&gp->p[i], comp+comp_idx); //fprintf(stderr, "Encoded %d bytes of param\n", comp_idx); return comp_idx; } // Choose a set of parameters based on quality statistics and // some predefined options (selected via "strat"). static inline int fqz_pick_parameters(fqz_gparams *gp, int vers, int strat, fqz_slice *s, unsigned char *in, size_t in_size) { //approx sqrt(delta), must be sequential int dsqr[] = { 0, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7 }; uint32_t qhist[256] = {0}; if (strat >= nstrats) strat = nstrats-1; // Start with 1 set of parameters. // FIXME: add support for multiple params later. memset(gp, 0, sizeof(*gp)); gp->vers = FQZ_VERS; if (!(gp->p = calloc(1, sizeof(fqz_param)))) return -1; gp->nparam = 1; gp->max_sel = 0; if (vers == 3) // V3.0 doesn't store qual in original orientation gp->gflags |= GFLAG_DO_REV; fqz_param *pm = gp->p; // Programmed strategies, which we then amend based on our // statistical analysis of the quality stream. pm->qbits = strat_opts[strat][0]; pm->qshift = strat_opts[strat][1]; pm->pbits = strat_opts[strat][2]; pm->pshift = strat_opts[strat][3]; pm->dbits = strat_opts[strat][4]; pm->dshift = strat_opts[strat][5]; pm->qloc = strat_opts[strat][6]; pm->sloc = strat_opts[strat][7]; pm->ploc = strat_opts[strat][8]; pm->dloc = strat_opts[strat][9]; // Params for controlling behaviour here. pm->do_r2 = strat_opts[strat][10]; pm->do_qa = strat_opts[strat][11]; // Validity check input lengths and buffer size size_t tlen = 0, i; for (i = 0; i < s->num_records; i++) { if (tlen + s->len[i] > in_size) // Oversized buffer s->len[i] = in_size - tlen; tlen += s->len[i]; } if (s->num_records > 0 && tlen < in_size) // Undersized buffer s->len[s->num_records-1] += in_size - tlen; // Quality metrics, for all recs fqz_qual_stats(s, in, in_size, pm, qhist, -1); pm->store_qmap = (pm->nsym <= 8 && pm->nsym*2 < pm->max_sym); // Check for fixed length. uint32_t first_len = s->len[0]; for (i = 1; i < s->num_records; i++) { if (s->len[i] != first_len) break; } pm->fixed_len = (i == s->num_records); pm->use_qtab = 0; // unused by current encoder if (strat >= nstrats-1) goto manually_set; // used in TEST_MAIN for debugging if (pm->pshift < 0) pm->pshift = MAX(0, log((double)s->len[0]/(1<pbits))/log(2)+.5); if (pm->nsym <= 4) { // NovaSeq pm->qshift = 2; // qmax 64, although we can store up to 256 if needed if (in_size < 5000000) { pm->pbits =2; pm->pshift=5; } } else if (pm->nsym <= 8) { // HiSeqX pm->qbits =MIN(pm->qbits,9); pm->qshift=3; if (in_size < 5000000) pm->qbits =6; } if (in_size < 300000) { pm->qbits=pm->qshift; pm->dbits=2; } manually_set: // fprintf(stderr, "-x 0x%x%x%x%x%x%x%x%x%x%x%x%x\n", // pm->qbits, pm->qshift, // pm->pbits, pm->pshift, // pm->dbits, pm->dshift, // pm->qloc, pm->sloc, pm->ploc, pm->dloc, // pm->do_r2, pm->do_qa); for (i = 0; i < sizeof(dsqr)/sizeof(*dsqr); i++) if (dsqr[i] > (1<dbits)-1) dsqr[i] = (1<dbits)-1; if (pm->store_qmap) { int j; for (i = j = 0; i < 256; i++) if (qhist[i]) pm->qmap[i] = j++; else pm->qmap[i] = INT_MAX; pm->max_sym = pm->nsym; } else { pm->nsym = 255; for (i = 0; i < 256; i++) pm->qmap[i] = i; } if (gp->max_sym < pm->max_sym) gp->max_sym = pm->max_sym; // Produce ptab from pshift. if (pm->qbits) { for (i = 0; i < 256; i++) { pm->qtab[i] = i; // 1:1 // Alternative mappings: //qtab[i] = i > 30 ? MIN(max_sym,i)-15 : i/2; // eg for 9827 BAM } } pm->qmask = (1<qbits)-1; if (pm->pbits) { for (i = 0; i < 1024; i++) pm->ptab[i] = MIN((1<pbits)-1, i>>pm->pshift); // Alternatively via analysis of quality distributions we // may select a bunch of positions that are special and // have a non-uniform ptab[]. // Manual experimentation on a NovaSeq run saved 2.8% here. } if (pm->dbits) { for (i = 0; i < 256; i++) pm->dtab[i] = dsqr[MIN(sizeof(dsqr)/sizeof(*dsqr)-1, i>>pm->dshift)]; } pm->use_ptab = (pm->pbits > 0); pm->use_dtab = (pm->dbits > 0); pm->pflags = (pm->use_qtab ?PFLAG_HAVE_QTAB :0)| (pm->use_dtab ?PFLAG_HAVE_DTAB :0)| (pm->use_ptab ?PFLAG_HAVE_PTAB :0)| (pm->do_sel ?PFLAG_DO_SEL :0)| (pm->fixed_len ?PFLAG_DO_LEN :0)| (pm->do_dedup ?PFLAG_DO_DEDUP :0)| (pm->store_qmap ?PFLAG_HAVE_QMAP :0); gp->max_sel = 0; if (pm->do_sel) { // 2 selectors values, but 1 parameter block. // We'll use the sloc instead to encode the selector bits into // the context. gp->max_sel = 1; // indicator to check recs gp->gflags |= GFLAG_HAVE_STAB; // NB: stab is already all zero } if (gp->max_sel && s->num_records) { int max = 0; for (i = 0; i < s->num_records; i++) { if (max < (s->flags[i] >> 16)) max = (s->flags[i] >> 16); } gp->max_sel = max; } return 0; } static void fqz_free_parameters(fqz_gparams *gp) { if (gp && gp->p) free(gp->p); } static int compress_new_read(fqz_slice *s, fqz_state *state, fqz_gparams *gp, fqz_param *pm, fqz_model *model, RangeCoder *rc, unsigned char *in, size_t *in_i, // in[in_i], unsigned int *last) { ssize_t rec = state->rec; size_t i = *in_i; if (pm->do_sel || (gp->gflags & GFLAG_MULTI_PARAM)) { state->s = rec < s->num_records ? s->flags[rec] >> 16 // reuse spare bits : 0; SIMPLE_MODEL(256,_encodeSymbol)(&model->sel, rc, state->s); } else { state->s = 0; } int x = (gp->gflags & GFLAG_HAVE_STAB) ? gp->stab[state->s] : state->s; pm = &gp->p[x]; int len = s->len[rec]; if (!pm->fixed_len || state->first_len) { SIMPLE_MODEL(256,_encodeSymbol)(&model->len[0], rc, (len>> 0) & 0xff); SIMPLE_MODEL(256,_encodeSymbol)(&model->len[1], rc, (len>> 8) & 0xff); SIMPLE_MODEL(256,_encodeSymbol)(&model->len[2], rc, (len>>16) & 0xff); SIMPLE_MODEL(256,_encodeSymbol)(&model->len[3], rc, (len>>24) & 0xff); state->first_len = 0; } if (gp->gflags & GFLAG_DO_REV) { // no need to reverse complement for V4.0 as the core format // already has this feature. if (s->flags[rec] & FQZ_FREVERSE) SIMPLE_MODEL(2,_encodeSymbol)(&model->revcomp, rc, 1); else SIMPLE_MODEL(2,_encodeSymbol)(&model->revcomp, rc, 0); } state->rec++; state->qtot = 0; state->qlen = 0; state->p = len; state->delta = 0; state->qctx = 0; state->prevq = 0; *last = pm->context; if (pm->do_dedup) { // Possible dup of previous read? if (i && len == state->last_len && !memcmp(in+i-state->last_len, in+i, len)) { SIMPLE_MODEL(2,_encodeSymbol)(&model->dup, rc, 1); i += len-1; state->p = 0; *in_i = i; return 1; // is a dup } else { SIMPLE_MODEL(2,_encodeSymbol)(&model->dup, rc, 0); } state->last_len = len; } *in_i = i; return 0; // not dup } static unsigned char *compress_block_fqz2f(int vers, int strat, fqz_slice *s, unsigned char *in, size_t in_size, size_t *out_size, fqz_gparams *gp) { fqz_gparams local_gp; int free_params = 0; unsigned int last = 0; size_t i, j; ssize_t rec = 0; int comp_idx = 0; RangeCoder rc; // Pick and store params if (!gp) { gp = &local_gp; if (fqz_pick_parameters(gp, vers, strat, s, in, in_size) < 0) return NULL; free_params = 1; } // Worst case scenario assuming random input data and no way to compress // is NBytes*growth for some small growth factor (arith_dynamic uses 1.05), // plus fixed overheads for the header / params. Growth can be high // here as we're modelling things and pathological cases may trigger a // bad probability model. // // Per read is 4-byte len if not fixed length (but less if avg smaller) // up to 1 byte for selection state (log2(max_sel) bits) // 1-bit for reverse flag // 1-bit for dup-last flag (but then no quals) // Per qual is 1-byte (assuming QMAX==256) // // Header size is total guess, as depends on params, but it's almost // always tiny, so a few K extra should be sufficient. // // => Total of (s->num_records*4.25 + in_size)*growth + hdr int sel_bits = 0, sel = gp->max_sel; while (sel) { sel_bits++; sel >>= 1; } double len_sz = gp->p[0].fixed_len ? 0.25 : 4.25; len_sz += sel_bits / 8.0; size_t comp_sz = (s->num_records*len_sz + in_size)*1.1 + 10000; unsigned char *comp = (unsigned char *)malloc(comp_sz); unsigned char *compe = comp + (size_t)comp_sz; if (!comp) return NULL; //dump_params(gp); comp_idx = var_put_u32(comp, compe, in_size); comp_idx += fqz_store_parameters(gp, comp+comp_idx); fqz_param *pm; // Optimise tables to remove shifts in loop (NB: cannot do this in next vers) for (j = 0; j < gp->nparam; j++) { pm = &gp->p[j]; for (i = 0; i < 1024; i++) pm->ptab[i] <<= pm->ploc; for (i = 0; i < 256; i++) pm->dtab[i] <<= pm->dloc; } // Create models and initialise range coder fqz_model model; if (fqz_create_models(&model, gp) < 0) return NULL; RC_SetOutput(&rc, (char *)comp+comp_idx); RC_SetOutputEnd(&rc, (char *)comp+comp_sz); RC_StartEncode(&rc); // For CRAM3.1, reverse upfront if needed pm = &gp->p[0]; if (gp->gflags & GFLAG_DO_REV) { i = rec = j = 0; while (i < in_size) { int len = rec < s->num_records-1 ? s->len[rec] : in_size - i; if (s->flags[rec] & FQZ_FREVERSE) { // Reverse complement sequence - note: modifies buffer int I,J; unsigned char *cp = in+i; for (I = 0, J = len-1; I < J; I++, J--) { unsigned char c; c = cp[I]; cp[I] = cp[J]; cp[J] = c; } } i += len; rec++; } rec = 0; } fqz_state state = {0}; pm = &gp->p[0]; state.p = 0; state.first_len = 1; state.last_len = 0; state.rec = rec; for (i = 0; i < in_size; i++) { if (state.p == 0) { if (state.rec >= s->num_records || s->len[state.rec] <= 0) { free(comp); comp = NULL; goto err; } if (compress_new_read(s, &state, gp, pm, &model, &rc, in, &i, /*&rec,*/ &last)) continue; } #if 0 // fqz_qual_stats imp. // q40 6.876 6.852 5.96 // q4 6.566 5.07 // _Q 1.383 1.11 unsigned char q = in[i]; unsigned char qm = pm->qmap[q]; SIMPLE_MODEL(QMAX,_encodeSymbol)(&model.qual[last], &rc, qm); last = fqz_update_ctx(pm, &state, qm); #else // gcc clang gcc+fqz_qual_stats imp. // q40 5.033 5.026 -27% 4.137 -38% // q4 5.595 -15% 4.011 -36% // _Q 1.225 -11% 0.956 int j = -1; while (state.p >= 4 && i+j+4 < in_size) { int l1 = last, l2, l3, l4; // Model has symbols sorted by frequency, so most common are at // start. So while model is approx 1Kb, the first cache line is // a big win. mm_prefetch(&model.qual[l1]); unsigned char qm1 = pm->qmap[in[i + ++j]]; last = fqz_update_ctx(pm, &state, qm1); l2 = last; mm_prefetch(&model.qual[l2]); unsigned char qm2 = pm->qmap[in[i + ++j]]; last = fqz_update_ctx(pm, &state, qm2); l3 = last; mm_prefetch(&model.qual[l3]); unsigned char qm3 = pm->qmap[in[i + ++j]]; last = fqz_update_ctx(pm, &state, qm3); l4 = last; mm_prefetch(&model.qual[l4]); unsigned char qm4 = pm->qmap[in[i + ++j]]; last = fqz_update_ctx(pm, &state, qm4); SIMPLE_MODEL(QMAX,_encodeSymbol)(&model.qual[l1], &rc, qm1); SIMPLE_MODEL(QMAX,_encodeSymbol)(&model.qual[l2], &rc, qm2); SIMPLE_MODEL(QMAX,_encodeSymbol)(&model.qual[l3], &rc, qm3); SIMPLE_MODEL(QMAX,_encodeSymbol)(&model.qual[l4], &rc, qm4); } while (state.p > 0) { int l2 = last; mm_prefetch(&model.qual[last]); unsigned char qm = pm->qmap[in[i + ++j]]; last = fqz_update_ctx(pm, &state, qm); SIMPLE_MODEL(QMAX,_encodeSymbol)(&model.qual[l2], &rc, qm); } i += j; #endif } if (RC_FinishEncode(&rc) < 0) { free(comp); comp = NULL; *out_size = 0; goto err; } // For CRAM3.1, undo our earlier reversal step rec = state.rec; if (gp->gflags & GFLAG_DO_REV) { i = rec = j = 0; while (i < in_size) { int len = rec < s->num_records-1 ? s->len[rec] : in_size - i; if (s->flags[rec] & FQZ_FREVERSE) { // Reverse complement sequence - note: modifies buffer int I,J; unsigned char *cp = in+i; for (I = 0, J = len-1; I < J; I++, J--) { unsigned char c; c = cp[I]; cp[I] = cp[J]; cp[J] = c; } } i += len; rec++; } } // Clear selector abuse of flags for (rec = 0; rec < s->num_records; rec++) s->flags[rec] &= 0xffff; *out_size = comp_idx + RC_OutSize(&rc); //fprintf(stderr, "%d -> %d\n", (int)in_size, (int)*out_size); err: fqz_destroy_models(&model); if (free_params) fqz_free_parameters(gp); return comp; } // Read fqz paramaters. // // FIXME: pass in and check in_size. // // Returns number of bytes read on success, // -1 on failure. static inline int fqz_read_parameters1(fqz_param *pm, unsigned char *in, size_t in_size) { int in_idx = 0; size_t i; if (in_size < 7) return -1; // Starting context pm->context = in[in_idx] + (in[in_idx+1]<<8); in_idx += 2; // Bit flags pm->pflags = in[in_idx++]; pm->use_qtab = pm->pflags & PFLAG_HAVE_QTAB; pm->use_dtab = pm->pflags & PFLAG_HAVE_DTAB; pm->use_ptab = pm->pflags & PFLAG_HAVE_PTAB; pm->do_sel = pm->pflags & PFLAG_DO_SEL; pm->fixed_len = pm->pflags & PFLAG_DO_LEN; pm->do_dedup = pm->pflags & PFLAG_DO_DEDUP; pm->store_qmap = pm->pflags & PFLAG_HAVE_QMAP; pm->max_sym = in[in_idx++]; // Sub-context sizes and locations pm->qbits = in[in_idx]>>4; pm->qmask = (1<qbits)-1; pm->qshift = in[in_idx++]&15; pm->qloc = in[in_idx]>>4; pm->sloc = in[in_idx++]&15; pm->ploc = in[in_idx]>>4; pm->dloc = in[in_idx++]&15; // Maps and tables if (pm->store_qmap) { for (i = 0; i < 256; i++) pm->qmap[i] = INT_MAX; // so dump_map works if (in_idx + pm->max_sym > in_size) return -1; for (i = 0; i < pm->max_sym; i++) pm->qmap[i] = in[in_idx++]; } else { for (i = 0; i < 256; i++) pm->qmap[i] = i; } if (pm->qbits) { if (pm->use_qtab) { int used = read_array(in+in_idx, in_size-in_idx, pm->qtab, 256); if (used < 0) return -1; in_idx += used; } else { for (i = 0; i < 256; i++) pm->qtab[i] = i; } } if (pm->use_ptab) { int used = read_array(in+in_idx, in_size-in_idx, pm->ptab, 1024); if (used < 0) return -1; in_idx += used; } else { for (i = 0; i < 1024; i++) pm->ptab[i] = 0; } if (pm->use_dtab) { int used = read_array(in+in_idx, in_size-in_idx, pm->dtab, 256); if (used < 0) return -1; in_idx += used; } else { for (i = 0; i < 256; i++) pm->dtab[i] = 0; } return in_idx; } static int fqz_read_parameters(fqz_gparams *gp, unsigned char *in, size_t in_size) { int in_idx = 0; int i; if (in_size < 10) return -1; // Format version gp->vers = in[in_idx++]; if (gp->vers != FQZ_VERS) return -1; // Global glags gp->gflags = in[in_idx++]; // Number of param blocks and param selector details gp->nparam = (gp->gflags & GFLAG_MULTI_PARAM) ? in[in_idx++] : 1; if (gp->nparam <= 0) return -1; gp->max_sel = gp->nparam > 1 ? gp->nparam : 0; if (gp->gflags & GFLAG_HAVE_STAB) { gp->max_sel = in[in_idx++]; int used = read_array(in+in_idx, in_size-in_idx, gp->stab, 256); if (used < 0) goto err; in_idx += used; } else { for (i = 0; i < gp->nparam; i++) gp->stab[i] = i; for (; i < 256; i++) gp->stab[i] = gp->nparam-1; } // Load the individual parameter locks if (!(gp->p = malloc(gp->nparam * sizeof(*gp->p)))) return -1; gp->max_sym = 0; for (i = 0; i < gp->nparam; i++) { int e = fqz_read_parameters1(&gp->p[i], in + in_idx, in_size-in_idx); if (e < 0) goto err; if (gp->p[i].do_sel && gp->max_sel == 0) goto err; // Inconsistent in_idx += e; if (gp->max_sym < gp->p[i].max_sym) gp->max_sym = gp->p[i].max_sym; } //fprintf(stderr, "Decoded %d bytes of param\n", in_idx); return in_idx; err: fqz_free_parameters(gp); gp->nparam = 0; return -1; } // Handles the state.p==0 section of uncompress_block_fqz2f static int decompress_new_read(fqz_slice *s, fqz_state *state, fqz_gparams *gp, fqz_param *pm, fqz_model *model, RangeCoder *rc, unsigned char *in, ssize_t *in_i, // in[in_i], unsigned char *uncomp, size_t *out_size, int *rev, char *rev_a, int *len_a, int *lengths, int nlengths) { size_t i = *in_i; ssize_t rec = state->rec; if (pm->do_sel) { state->s = SIMPLE_MODEL(256,_decodeSymbol)(&model->sel, rc); } else { state->s = 0; } int x = (gp->gflags & GFLAG_HAVE_STAB) ? gp->stab[MIN(255, state->s)] : state->s; if (x >= gp->nparam) return -1; pm = &gp->p[x]; unsigned int len = state->last_len; if (!pm->fixed_len || state->first_len) { len = SIMPLE_MODEL(256,_decodeSymbol)(&model->len[0], rc); len |= SIMPLE_MODEL(256,_decodeSymbol)(&model->len[1], rc)<<8; len |= SIMPLE_MODEL(256,_decodeSymbol)(&model->len[2], rc)<<16; len |= ((unsigned)SIMPLE_MODEL(256,_decodeSymbol)(&model->len[3], rc))<<24; state->first_len = 0; state->last_len = len; } if (len > *out_size-i || len <= 0) return -1; if (lengths && rec < nlengths) lengths[rec] = len; if (gp->gflags & GFLAG_DO_REV) { *rev = SIMPLE_MODEL(2,_decodeSymbol)(&model->revcomp, rc); rev_a[rec] = *rev; len_a[rec] = len; } if (pm->do_dedup) { if (SIMPLE_MODEL(2,_decodeSymbol)(&model->dup, rc)) { // Dup of last line if (len > i) return -1; memcpy(uncomp+i, uncomp+i-len, len); i += len; state->p = 0; state->rec++; *in_i = i; return 1; // dup => continue } } state->rec++; state->p = len; state->delta = 0; state->prevq = 0; state->qctx = 0; state->ctx = pm->context; *in_i = i; return 0; } static unsigned char *uncompress_block_fqz2f(fqz_slice *s, unsigned char *in, size_t in_size, size_t *out_size, int *lengths, int nlengths) { fqz_gparams gp; fqz_param *pm; char *rev_a = NULL; int *len_a = NULL; memset(&gp, 0, sizeof(gp)); uint32_t len; ssize_t i, rec = 0, in_idx; in_idx = var_get_u32(in, in+in_size, &len); *out_size = len; #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (len > 100000) return NULL; #endif unsigned char *uncomp = NULL; RangeCoder rc; unsigned int last = 0; // Decode parameter blocks if ((i = fqz_read_parameters(&gp, in+in_idx, in_size-in_idx)) < 0) return NULL; //dump_params(&gp); in_idx += i; // Optimisations to remove shifts from main loop for (i = 0; i < gp.nparam; i++) { int j; pm = &gp.p[i]; for (j = 0; j < 1024; j++) pm->ptab[j] <<= pm->ploc; for (j = 0; j < 256; j++) pm->dtab[j] <<= pm->dloc; } // Initialise models and entropy coder fqz_model model; if (fqz_create_models(&model, &gp) < 0) return NULL; RC_SetInput(&rc, (char *)in+in_idx, (char *)in+in_size); RC_StartDecode(&rc); // Allocate buffers uncomp = (unsigned char *)malloc(*out_size); if (!uncomp) goto err; int nrec = 1000; rev_a = malloc(nrec); len_a = malloc(nrec * sizeof(int)); if (!rev_a || !len_a) goto err; // Main decode loop fqz_state state; state.delta = 0; state.prevq = 0; state.qctx = 0; state.p = 0; state.s = 0; state.first_len = 1; state.last_len = 0; state.rec = 0; state.ctx = last; int rev = 0; int x = 0; pm = &gp.p[x]; for (i = 0; i < len; ) { if (state.rec >= nrec) { nrec *= 2; rev_a = realloc(rev_a, nrec); len_a = realloc(len_a, nrec*sizeof(int)); if (!rev_a || !len_a) goto err; } if (state.p == 0) { int r = decompress_new_read(s, &state, &gp, pm, &model, &rc, in, &i, uncomp, out_size, &rev, rev_a, len_a, lengths, nlengths); if (r < 0) goto err; if (r > 0) continue; last = state.ctx; } // Decode and update context do { unsigned char Q = SIMPLE_MODEL(QMAX,_decodeSymbol) (&model.qual[last], &rc); last = fqz_update_ctx(pm, &state, Q); uncomp[i++] = pm->qmap[Q]; } while (state.p != 0 && i < len); } rec = state.rec; if (rec >= nrec) { nrec *= 2; rev_a = realloc(rev_a, nrec); len_a = realloc(len_a, nrec*sizeof(int)); if (!rev_a || !len_a) goto err; } rev_a[rec] = rev; len_a[rec] = len; if (gp.gflags & GFLAG_DO_REV) { for (i = rec = 0; i < len && rec < nrec; i += len_a[rec++]) { if (!rev_a[rec]) continue; int I, J; unsigned char *cp = uncomp+i; for (I = 0, J = len_a[rec]-1; I < J; I++, J--) { unsigned char c; c = cp[I]; cp[I] = cp[J]; cp[J] = c; } } } if (RC_FinishDecode(&rc) < 0) goto err; fqz_destroy_models(&model); free(rev_a); free(len_a); fqz_free_parameters(&gp); #ifdef TEST_MAIN s->num_records = rec; #endif return uncomp; err: fqz_destroy_models(&model); free(rev_a); free(len_a); fqz_free_parameters(&gp); free(uncomp); return NULL; } char *fqz_compress(int vers, fqz_slice *s, char *in, size_t uncomp_size, size_t *comp_size, int strat, fqz_gparams *gp) { if (uncomp_size > INT_MAX) { *comp_size = 0; return NULL; } return (char *)compress_block_fqz2f(vers, strat, s, (unsigned char *)in, uncomp_size, comp_size, gp); } char *fqz_decompress(char *in, size_t comp_size, size_t *uncomp_size, int *lengths, int nlengths) { return (char *)uncompress_block_fqz2f(NULL, (unsigned char *)in, comp_size, uncomp_size, lengths, nlengths); } pysam-0.23.0/htslib/htscodecs/htscodecs/fqzcomp_qual.h000066400000000000000000000141371475062545500230450ustar00rootroot00000000000000/* * Copyright (c) 2011-2013, 2018-2019 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef FQZ_COMP_QUAL_H #define FQZ_COMP_QUAL_H #ifdef __cplusplus extern "C" { #endif #include /* Bit flags, deliberately mirroring BAM ones */ #define FQZ_FREVERSE 16 #define FQZ_FREAD2 128 /* Current FQZ format version */ #define FQZ_VERS 5 #define FQZ_MAX_STRAT 3 /* * Minimal per-record information taken from a cram slice. * * To compress we need to know the junction from one quality string to * the next (len), whether it is first/second read and whether it is * reverse complemented (flags). */ typedef struct { int num_records; uint32_t *len; // of size num_records uint32_t *flags; // of size num_records } fqz_slice; // Global flags static const int GFLAG_MULTI_PARAM = 1; static const int GFLAG_HAVE_STAB = 2; static const int GFLAG_DO_REV = 4; // Param flags // Add PFLAG_HAVE_DMAP and a dmap[] for delta incr? static const int PFLAG_DO_DEDUP = 2; static const int PFLAG_DO_LEN = 4; static const int PFLAG_DO_SEL = 8; static const int PFLAG_HAVE_QMAP = 16; static const int PFLAG_HAVE_PTAB = 32; static const int PFLAG_HAVE_DTAB = 64; static const int PFLAG_HAVE_QTAB = 128; /* * FQZ parameters. These may be simply passed in as NULL to fqz_compress * and it'll automatically choose, but if we wish to have complete control * then this (long) struct contains all the details. * * TODO: document all this! */ // A single parameter block typedef struct { // Starting context value uint16_t context; // flags unsigned int pflags; unsigned int do_sel, do_dedup, store_qmap, fixed_len; unsigned char use_qtab, use_dtab, use_ptab; // context bits and locations unsigned int qbits, qloc; unsigned int pbits, ploc; unsigned int dbits, dloc; unsigned int sbits, sloc; // models int max_sym, nsym, max_sel; // tables / maps unsigned int qmap[256]; unsigned int qtab[256]; unsigned int ptab[1024]; unsigned int dtab[256]; // Not stored paramters, but computed as part of encoder // parameterisation. int qshift; int pshift; int dshift; int sshift; unsigned int qmask; // (1< #include #include #include #include "pack.h" //----------------------------------------------------------------------------- /* * Packs multiple symbols into a single byte if the total alphabet of symbols * used is <= 16. Each new symbol takes up 1, 2, 4 or 8 bits, or 0 if the * alphabet used is 1 (constant). * * If successful, out_meta/out_meta_len are set to hold the mapping table * to be used during decompression. * * Returns the packed buffer on success with new length in out_len, * NULL of failure */ uint8_t *hts_pack(uint8_t *data, int64_t len, uint8_t *out_meta, int *out_meta_len, uint64_t *out_len) { int p[256] = {0}, n; uint64_t i, j; // count syms for (i = 0; i < len; i++) p[data[i]]=1; for (i = n = 0; i < 256; i++) { if (p[i]) { p[i] = n++; // p[i] is now the code number out_meta[n] = i; } } out_meta[0] = n; // 256 wraps to 0 j = n+1; // 1 value per byte if (n > 16) return NULL; uint8_t *out = malloc(len+1); if (!out) return NULL; // Work out how many values per byte to encode. int val_per_byte; if (n > 4) val_per_byte = 2; else if (n > 2) val_per_byte = 4; else if (n > 1) val_per_byte = 8; else val_per_byte = 0; // infinite *out_meta_len = j; j = 0; switch (val_per_byte) { case 2: for (i = 0; i < (len & ~1); i+=2) out[j++] = (p[data[i]]<<0) | (p[data[i+1]]<<4); switch (len-i) { case 1: out[j++] = p[data[i]]; } *out_len = j; return out; case 4: { for (i = 0; i < (len & ~3); i+=4) out[j++] = (p[data[i]]<<0) | (p[data[i+1]]<<2) | (p[data[i+2]]<<4) | (p[data[i+3]]<<6); out[j] = 0; int s = len-i, x = 0; switch (s) { case 3: out[j] |= p[data[i++]] << x; x+=2; // fall-through case 2: out[j] |= p[data[i++]] << x; x+=2; // fall-through case 1: out[j] |= p[data[i++]] << x; x+=2; j++; } *out_len = j; return out; } case 8: { for (i = 0; i < (len & ~7); i+=8) out[j++] = (p[data[i+0]]<<0) | (p[data[i+1]]<<1) | (p[data[i+2]]<<2) | (p[data[i+3]]<<3) | (p[data[i+4]]<<4) | (p[data[i+5]]<<5) | (p[data[i+6]]<<6) | (p[data[i+7]]<<7); out[j] = 0; int s = len-i, x = 0; switch (s) { case 7: out[j] |= p[data[i++]] << x++; // fall-through case 6: out[j] |= p[data[i++]] << x++; // fall-through case 5: out[j] |= p[data[i++]] << x++; // fall-through case 4: out[j] |= p[data[i++]] << x++; // fall-through case 3: out[j] |= p[data[i++]] << x++; // fall-through case 2: out[j] |= p[data[i++]] << x++; // fall-through case 1: out[j] |= p[data[i++]] << x++; j++; } *out_len = j; return out; } case 0: *out_len = j; return out; } return NULL; } /* * Unpacks the meta-data portions of the hts_pack algorithm. * This consists of the count of symbols and their values. * * The "map" array is filled out with the used symbols. * "nsym" is set to contain the number of symbols per byte; * 0, 1, 2, 4 or 8. * * Returns number of bytes of data[] consumed on success, * zero on failure. */ uint8_t hts_unpack_meta(uint8_t *data, uint32_t data_len, uint64_t udata_len, uint8_t *map, int *nsym) { if (data_len == 0) return 0; // Number of symbols used unsigned int n = data[0]; if (n == 0) n = 256; // Symbols per byte if (n <= 1) *nsym = 0; else if (n <= 2) *nsym = 8; else if (n <= 4) *nsym = 4; else if (n <= 16) *nsym = 2; else { *nsym = 1; // no packing return 1; } if (data_len <= 1) return 0; int j = 1, c = 0; do { map[c++] = data[j++]; } while (c < n && j < data_len); return c < n ? 0 : j; } /* * Unpacks a packed data steam (given the unpacked meta-data). * * "map" is the pack map, mapping 0->n to the expanded symbols. * The "out" buffer must be preallocated by the caller to be the correct * size. For error checking purposes, out_len is set to the size of * this buffer. * * Returns uncompressed data (out) on success, * NULL on failure. */ uint8_t *hts_unpack(uint8_t *data, int64_t len, uint8_t *out, uint64_t out_len, int nsym, uint8_t *p) { //uint8_t *out; uint8_t c = 0; int64_t i, j = 0, olen; if (nsym == 1) { // raw data; FIXME: shortcut the need for malloc & memcpy here memcpy(out, data, len); return out; } switch(nsym) { case 8: { union { uint64_t w; uint8_t c[8]; } map[256]; int x; for (x = 0; x < 256; x++) { map[x].c[0] = p[x>>0&1]; map[x].c[1] = p[x>>1&1]; map[x].c[2] = p[x>>2&1]; map[x].c[3] = p[x>>3&1]; map[x].c[4] = p[x>>4&1]; map[x].c[5] = p[x>>5&1]; map[x].c[6] = p[x>>6&1]; map[x].c[7] = p[x>>7&1]; } if ((out_len+7)/8 > len) return NULL; olen = out_len & ~7; for (i = 0; i < olen; i+=8) memcpy(&out[i], &map[data[j++]].w, 8); if (out_len != olen) { c = data[j++]; while (i < out_len) { out[i++] = p[c & 1]; c >>= 1; } } break; } case 4: { union { uint32_t w; uint8_t c[4]; } map[256]; int x, y, z, _, P=0; for (x = 0; x < 4; x++) for (y = 0; y < 4; y++) for (z = 0; z < 4; z++) for (_ = 0; _ < 4; _++, P++) { map[P].c[0] = p[_]; map[P].c[1] = p[z]; map[P].c[2] = p[y]; map[P].c[3] = p[x]; } if ((out_len+3)/4 > len) return NULL; olen = out_len & ~3; for (i = 0; i < olen-12; i+=16) { uint32_t w[] = { map[data[j+0]].w, map[data[j+1]].w, map[data[j+2]].w, map[data[j+3]].w }; j += 4; memcpy(&out[i], &w, 16); } for (; i < olen; i+=4) memcpy(&out[i], &map[data[j++]].w, 4); if (out_len != olen) { c = data[j++]; while (i < out_len) { out[i++] = p[c & 3]; c >>= 2; } } break; } case 2: { union { uint16_t w; uint8_t c[2]; } map[256]; int x, y; for (x = 0; x < 16; x++) { for (y = 0; y < 16; y++) { map[x*16+y].c[0] = p[y]; map[x*16+y].c[1] = p[x]; } } if ((out_len+1)/2 > len) return NULL; olen = out_len & ~1; for (i = j = 0; i+2 < olen; i+=4) { uint16_t w[] = { map[data[j+0]].w, map[data[j+1]].w }; memcpy(&out[i], &w, 4); j += 2; } for (; i < olen; i+=2) memcpy(&out[i], &map[data[j++]].w, 2); if (out_len != olen) { c = data[j++]; out[i+0] = p[c&15]; } break; } case 0: memset(out, p[0], out_len); break; default: return NULL; } return out; } uint8_t *hts_unpack_(uint8_t *data, int64_t len, uint8_t *out, uint64_t out_len, int nsym, uint8_t *p) { //uint8_t *out; uint8_t c = 0; int64_t i, j = 0, olen; if (nsym == 1) { // raw data; FIXME: shortcut the need for malloc & memcpy here memcpy(out, data, len); return out; } switch(nsym) { case 2: { uint16_t map[256], x, y; for (x = 0; x < 16; x++) for (y = 0; y < 16; y++) map[x*16+y] = p[x]*256+p[y]; if ((out_len+1)/2 > len) return NULL; olen = out_len & ~1; uint16_t *o16 = (uint16_t *)out; for (i = 0; i+4 < olen/2; i+=4) { int k; for (k = 0; k < 4; k++) o16[i+k] = map[data[i+k]]; } j = i; i *= 2; for (; i < olen; i+=2) { uint16_t w1 = map[data[j++]]; *(uint16_t *)&out[i] = w1; } if (out_len != olen) { c = data[j++]; out[i+0] = p[c&15]; } break; } default: return NULL; } return out; } pysam-0.23.0/htslib/htscodecs/htscodecs/pack.h000066400000000000000000000063341475062545500212620ustar00rootroot00000000000000/* * Copyright (c) 2019 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef HTS_PACK_H #define HTS_PACK_H #ifdef __cplusplus extern "C" { #endif /* * Packs multiple symbols into a single byte if the total alphabet of symbols * used is <= 16. Each new symbol takes up 1, 2, 4 or 8 bits, or 0 if the * alphabet used is 1 (constant). * * If successful, out_meta/out_meta_len are set to hold the mapping table * to be used during decompression. * * Returns the packed buffer on success with new length in out_len, * NULL of failure */ uint8_t *hts_pack(uint8_t *data, int64_t len, uint8_t *out_meta, int *out_meta_len, uint64_t *out_len); /* * Unpacks the meta-data portions of the hts_pack algorithm. * This consists of the count of symbols and their values. * * The "map" array is filled out with the used symbols. * "nsym" is set to contain the number of symbols per byte; * 0, 1, 2, 4 or 8. * * Returns number of bytes of data[] consumed on success, * zero on failure. */ uint8_t hts_unpack_meta(uint8_t *data, uint32_t data_len, uint64_t udata_len, uint8_t *map, int *nsym); /* * Unpacks a packed data steam (given the unpacked meta-data). * * "map" is the pack map, mapping 0->n to the expanded symbols. * The "out" buffer must be preallocated by the caller to be the correct * size. For error checking purposes, out_len is set to the size of * this buffer. * * Returns uncompressed data (out) on success, * NULL on failure. */ uint8_t *hts_unpack(uint8_t *data, int64_t len, uint8_t *out, uint64_t out_len, int nsym, uint8_t *map); #ifdef __cplusplus } #endif #endif /* HTS_PACK_H */ pysam-0.23.0/htslib/htscodecs/htscodecs/permute.h000066400000000000000000000336761475062545500220360ustar00rootroot00000000000000#ifdef MAIN #include /* * Shuffle based on input bits. * So bit N true => keep Nth byte. * bit N false => skip Nth byte. */ int main(void) { int i, j; FILE *fp = fopen(__FILE__, "r"); char line[8192]; while(fgets(line, 8192, fp)) { printf("%s", line); } close(fp); printf("\n"); // Decode table; distributes N adjacent values across lanes printf("#define _ 9\n"); printf("static uint32_t permute[256][8] = { // reverse binary bit order\n"); for (i = 0; i < 256; i++) { int b = 0; int v[8] = {0}; for (j = 0; j < 8; j++) { if (i & (1<= 0 && v[j]) printf("%d,", v[j]-1); else printf("_,"); } printf("},\n"); } printf("};\n"); return 0; } #endif /* * These tables are 8k. On older systems with small L1 cache, this may be * a problem. * * #define PM(a,b,c,d,e,f,g,h) ((a<<0)|(b<<4)|(c<<8)|(d<<12)|(e<<16)|(f<<20)|(g<<24)|(h<<28)) * * Instead of permute via * __m256i idx1 = _mm256_load_si256((const __m256i*)permute[imask1]); * * we can pack the indices and shift them back again * __m256i idx1 = _mm256_srlv_epi32(_mm256_set1_epi32(permute2[imask1]), * _mm256_set_epi32(28,24,20,16,12,8,4,0)); * * However on my Haswell system this slows down r32x16b_avx2 from 1440 to * 1200 MB/s decode speeds. * It's much closer for order-1 decoder, but still doesn't help. * * The encoder side seems to make no difference either way or be very marginal. */ #define _ 9 static uint32_t permute[256][8] __attribute__((aligned(32))) = { // reverse binary bit order { _,_,_,_,_,_,_,_,}, { 0,_,_,_,_,_,_,_,}, { _,0,_,_,_,_,_,_,}, { 0,1,_,_,_,_,_,_,}, { _,_,0,_,_,_,_,_,}, { 0,_,1,_,_,_,_,_,}, { _,0,1,_,_,_,_,_,}, { 0,1,2,_,_,_,_,_,}, { _,_,_,0,_,_,_,_,}, { 0,_,_,1,_,_,_,_,}, { _,0,_,1,_,_,_,_,}, { 0,1,_,2,_,_,_,_,}, { _,_,0,1,_,_,_,_,}, { 0,_,1,2,_,_,_,_,}, { _,0,1,2,_,_,_,_,}, { 0,1,2,3,_,_,_,_,}, { _,_,_,_,0,_,_,_,}, { 0,_,_,_,1,_,_,_,}, { _,0,_,_,1,_,_,_,}, { 0,1,_,_,2,_,_,_,}, { _,_,0,_,1,_,_,_,}, { 0,_,1,_,2,_,_,_,}, { _,0,1,_,2,_,_,_,}, { 0,1,2,_,3,_,_,_,}, { _,_,_,0,1,_,_,_,}, { 0,_,_,1,2,_,_,_,}, { _,0,_,1,2,_,_,_,}, { 0,1,_,2,3,_,_,_,}, { _,_,0,1,2,_,_,_,}, { 0,_,1,2,3,_,_,_,}, { _,0,1,2,3,_,_,_,}, { 0,1,2,3,4,_,_,_,}, { _,_,_,_,_,0,_,_,}, { 0,_,_,_,_,1,_,_,}, { _,0,_,_,_,1,_,_,}, { 0,1,_,_,_,2,_,_,}, { _,_,0,_,_,1,_,_,}, { 0,_,1,_,_,2,_,_,}, { _,0,1,_,_,2,_,_,}, { 0,1,2,_,_,3,_,_,}, { _,_,_,0,_,1,_,_,}, { 0,_,_,1,_,2,_,_,}, { _,0,_,1,_,2,_,_,}, { 0,1,_,2,_,3,_,_,}, { _,_,0,1,_,2,_,_,}, { 0,_,1,2,_,3,_,_,}, { _,0,1,2,_,3,_,_,}, { 0,1,2,3,_,4,_,_,}, { _,_,_,_,0,1,_,_,}, { 0,_,_,_,1,2,_,_,}, { _,0,_,_,1,2,_,_,}, { 0,1,_,_,2,3,_,_,}, { _,_,0,_,1,2,_,_,}, { 0,_,1,_,2,3,_,_,}, { _,0,1,_,2,3,_,_,}, { 0,1,2,_,3,4,_,_,}, { _,_,_,0,1,2,_,_,}, { 0,_,_,1,2,3,_,_,}, { _,0,_,1,2,3,_,_,}, { 0,1,_,2,3,4,_,_,}, { _,_,0,1,2,3,_,_,}, { 0,_,1,2,3,4,_,_,}, { _,0,1,2,3,4,_,_,}, { 0,1,2,3,4,5,_,_,}, { _,_,_,_,_,_,0,_,}, { 0,_,_,_,_,_,1,_,}, { _,0,_,_,_,_,1,_,}, { 0,1,_,_,_,_,2,_,}, { _,_,0,_,_,_,1,_,}, { 0,_,1,_,_,_,2,_,}, { _,0,1,_,_,_,2,_,}, { 0,1,2,_,_,_,3,_,}, { _,_,_,0,_,_,1,_,}, { 0,_,_,1,_,_,2,_,}, { _,0,_,1,_,_,2,_,}, { 0,1,_,2,_,_,3,_,}, { _,_,0,1,_,_,2,_,}, { 0,_,1,2,_,_,3,_,}, { _,0,1,2,_,_,3,_,}, { 0,1,2,3,_,_,4,_,}, { _,_,_,_,0,_,1,_,}, { 0,_,_,_,1,_,2,_,}, { _,0,_,_,1,_,2,_,}, { 0,1,_,_,2,_,3,_,}, { _,_,0,_,1,_,2,_,}, { 0,_,1,_,2,_,3,_,}, { _,0,1,_,2,_,3,_,}, { 0,1,2,_,3,_,4,_,}, { _,_,_,0,1,_,2,_,}, { 0,_,_,1,2,_,3,_,}, { _,0,_,1,2,_,3,_,}, { 0,1,_,2,3,_,4,_,}, { _,_,0,1,2,_,3,_,}, { 0,_,1,2,3,_,4,_,}, { _,0,1,2,3,_,4,_,}, { 0,1,2,3,4,_,5,_,}, { _,_,_,_,_,0,1,_,}, { 0,_,_,_,_,1,2,_,}, { _,0,_,_,_,1,2,_,}, { 0,1,_,_,_,2,3,_,}, { _,_,0,_,_,1,2,_,}, { 0,_,1,_,_,2,3,_,}, { _,0,1,_,_,2,3,_,}, { 0,1,2,_,_,3,4,_,}, { _,_,_,0,_,1,2,_,}, { 0,_,_,1,_,2,3,_,}, { _,0,_,1,_,2,3,_,}, { 0,1,_,2,_,3,4,_,}, { _,_,0,1,_,2,3,_,}, { 0,_,1,2,_,3,4,_,}, { _,0,1,2,_,3,4,_,}, { 0,1,2,3,_,4,5,_,}, { _,_,_,_,0,1,2,_,}, { 0,_,_,_,1,2,3,_,}, { _,0,_,_,1,2,3,_,}, { 0,1,_,_,2,3,4,_,}, { _,_,0,_,1,2,3,_,}, { 0,_,1,_,2,3,4,_,}, { _,0,1,_,2,3,4,_,}, { 0,1,2,_,3,4,5,_,}, { _,_,_,0,1,2,3,_,}, { 0,_,_,1,2,3,4,_,}, { _,0,_,1,2,3,4,_,}, { 0,1,_,2,3,4,5,_,}, { _,_,0,1,2,3,4,_,}, { 0,_,1,2,3,4,5,_,}, { _,0,1,2,3,4,5,_,}, { 0,1,2,3,4,5,6,_,}, { _,_,_,_,_,_,_,0,}, { 0,_,_,_,_,_,_,1,}, { _,0,_,_,_,_,_,1,}, { 0,1,_,_,_,_,_,2,}, { _,_,0,_,_,_,_,1,}, { 0,_,1,_,_,_,_,2,}, { _,0,1,_,_,_,_,2,}, { 0,1,2,_,_,_,_,3,}, { _,_,_,0,_,_,_,1,}, { 0,_,_,1,_,_,_,2,}, { _,0,_,1,_,_,_,2,}, { 0,1,_,2,_,_,_,3,}, { _,_,0,1,_,_,_,2,}, { 0,_,1,2,_,_,_,3,}, { _,0,1,2,_,_,_,3,}, { 0,1,2,3,_,_,_,4,}, { _,_,_,_,0,_,_,1,}, { 0,_,_,_,1,_,_,2,}, { _,0,_,_,1,_,_,2,}, { 0,1,_,_,2,_,_,3,}, { _,_,0,_,1,_,_,2,}, { 0,_,1,_,2,_,_,3,}, { _,0,1,_,2,_,_,3,}, { 0,1,2,_,3,_,_,4,}, { _,_,_,0,1,_,_,2,}, { 0,_,_,1,2,_,_,3,}, { _,0,_,1,2,_,_,3,}, { 0,1,_,2,3,_,_,4,}, { _,_,0,1,2,_,_,3,}, { 0,_,1,2,3,_,_,4,}, { _,0,1,2,3,_,_,4,}, { 0,1,2,3,4,_,_,5,}, { _,_,_,_,_,0,_,1,}, { 0,_,_,_,_,1,_,2,}, { _,0,_,_,_,1,_,2,}, { 0,1,_,_,_,2,_,3,}, { _,_,0,_,_,1,_,2,}, { 0,_,1,_,_,2,_,3,}, { _,0,1,_,_,2,_,3,}, { 0,1,2,_,_,3,_,4,}, { _,_,_,0,_,1,_,2,}, { 0,_,_,1,_,2,_,3,}, { _,0,_,1,_,2,_,3,}, { 0,1,_,2,_,3,_,4,}, { _,_,0,1,_,2,_,3,}, { 0,_,1,2,_,3,_,4,}, { _,0,1,2,_,3,_,4,}, { 0,1,2,3,_,4,_,5,}, { _,_,_,_,0,1,_,2,}, { 0,_,_,_,1,2,_,3,}, { _,0,_,_,1,2,_,3,}, { 0,1,_,_,2,3,_,4,}, { _,_,0,_,1,2,_,3,}, { 0,_,1,_,2,3,_,4,}, { _,0,1,_,2,3,_,4,}, { 0,1,2,_,3,4,_,5,}, { _,_,_,0,1,2,_,3,}, { 0,_,_,1,2,3,_,4,}, { _,0,_,1,2,3,_,4,}, { 0,1,_,2,3,4,_,5,}, { _,_,0,1,2,3,_,4,}, { 0,_,1,2,3,4,_,5,}, { _,0,1,2,3,4,_,5,}, { 0,1,2,3,4,5,_,6,}, { _,_,_,_,_,_,0,1,}, { 0,_,_,_,_,_,1,2,}, { _,0,_,_,_,_,1,2,}, { 0,1,_,_,_,_,2,3,}, { _,_,0,_,_,_,1,2,}, { 0,_,1,_,_,_,2,3,}, { _,0,1,_,_,_,2,3,}, { 0,1,2,_,_,_,3,4,}, { _,_,_,0,_,_,1,2,}, { 0,_,_,1,_,_,2,3,}, { _,0,_,1,_,_,2,3,}, { 0,1,_,2,_,_,3,4,}, { _,_,0,1,_,_,2,3,}, { 0,_,1,2,_,_,3,4,}, { _,0,1,2,_,_,3,4,}, { 0,1,2,3,_,_,4,5,}, { _,_,_,_,0,_,1,2,}, { 0,_,_,_,1,_,2,3,}, { _,0,_,_,1,_,2,3,}, { 0,1,_,_,2,_,3,4,}, { _,_,0,_,1,_,2,3,}, { 0,_,1,_,2,_,3,4,}, { _,0,1,_,2,_,3,4,}, { 0,1,2,_,3,_,4,5,}, { _,_,_,0,1,_,2,3,}, { 0,_,_,1,2,_,3,4,}, { _,0,_,1,2,_,3,4,}, { 0,1,_,2,3,_,4,5,}, { _,_,0,1,2,_,3,4,}, { 0,_,1,2,3,_,4,5,}, { _,0,1,2,3,_,4,5,}, { 0,1,2,3,4,_,5,6,}, { _,_,_,_,_,0,1,2,}, { 0,_,_,_,_,1,2,3,}, { _,0,_,_,_,1,2,3,}, { 0,1,_,_,_,2,3,4,}, { _,_,0,_,_,1,2,3,}, { 0,_,1,_,_,2,3,4,}, { _,0,1,_,_,2,3,4,}, { 0,1,2,_,_,3,4,5,}, { _,_,_,0,_,1,2,3,}, { 0,_,_,1,_,2,3,4,}, { _,0,_,1,_,2,3,4,}, { 0,1,_,2,_,3,4,5,}, { _,_,0,1,_,2,3,4,}, { 0,_,1,2,_,3,4,5,}, { _,0,1,2,_,3,4,5,}, { 0,1,2,3,_,4,5,6,}, { _,_,_,_,0,1,2,3,}, { 0,_,_,_,1,2,3,4,}, { _,0,_,_,1,2,3,4,}, { 0,1,_,_,2,3,4,5,}, { _,_,0,_,1,2,3,4,}, { 0,_,1,_,2,3,4,5,}, { _,0,1,_,2,3,4,5,}, { 0,1,2,_,3,4,5,6,}, { _,_,_,0,1,2,3,4,}, { 0,_,_,1,2,3,4,5,}, { _,0,_,1,2,3,4,5,}, { 0,1,_,2,3,4,5,6,}, { _,_,0,1,2,3,4,5,}, { 0,_,1,2,3,4,5,6,}, { _,0,1,2,3,4,5,6,}, { 0,1,2,3,4,5,6,7,}, }; static uint32_t permutec[256][8] __attribute__((aligned(32))) = { // reverse binary bit order { _,_,_,_,_,_,_,_,}, { _,_,_,_,_,_,_,0,}, { _,_,_,_,_,_,_,1,}, { _,_,_,_,_,_,0,1,}, { _,_,_,_,_,_,_,2,}, { _,_,_,_,_,_,0,2,}, { _,_,_,_,_,_,1,2,}, { _,_,_,_,_,0,1,2,}, { _,_,_,_,_,_,_,3,}, { _,_,_,_,_,_,0,3,}, { _,_,_,_,_,_,1,3,}, { _,_,_,_,_,0,1,3,}, { _,_,_,_,_,_,2,3,}, { _,_,_,_,_,0,2,3,}, { _,_,_,_,_,1,2,3,}, { _,_,_,_,0,1,2,3,}, { _,_,_,_,_,_,_,4,}, { _,_,_,_,_,_,0,4,}, { _,_,_,_,_,_,1,4,}, { _,_,_,_,_,0,1,4,}, { _,_,_,_,_,_,2,4,}, { _,_,_,_,_,0,2,4,}, { _,_,_,_,_,1,2,4,}, { _,_,_,_,0,1,2,4,}, { _,_,_,_,_,_,3,4,}, { _,_,_,_,_,0,3,4,}, { _,_,_,_,_,1,3,4,}, { _,_,_,_,0,1,3,4,}, { _,_,_,_,_,2,3,4,}, { _,_,_,_,0,2,3,4,}, { _,_,_,_,1,2,3,4,}, { _,_,_,0,1,2,3,4,}, { _,_,_,_,_,_,_,5,}, { _,_,_,_,_,_,0,5,}, { _,_,_,_,_,_,1,5,}, { _,_,_,_,_,0,1,5,}, { _,_,_,_,_,_,2,5,}, { _,_,_,_,_,0,2,5,}, { _,_,_,_,_,1,2,5,}, { _,_,_,_,0,1,2,5,}, { _,_,_,_,_,_,3,5,}, { _,_,_,_,_,0,3,5,}, { _,_,_,_,_,1,3,5,}, { _,_,_,_,0,1,3,5,}, { _,_,_,_,_,2,3,5,}, { _,_,_,_,0,2,3,5,}, { _,_,_,_,1,2,3,5,}, { _,_,_,0,1,2,3,5,}, { _,_,_,_,_,_,4,5,}, { _,_,_,_,_,0,4,5,}, { _,_,_,_,_,1,4,5,}, { _,_,_,_,0,1,4,5,}, { _,_,_,_,_,2,4,5,}, { _,_,_,_,0,2,4,5,}, { _,_,_,_,1,2,4,5,}, { _,_,_,0,1,2,4,5,}, { _,_,_,_,_,3,4,5,}, { _,_,_,_,0,3,4,5,}, { _,_,_,_,1,3,4,5,}, { _,_,_,0,1,3,4,5,}, { _,_,_,_,2,3,4,5,}, { _,_,_,0,2,3,4,5,}, { _,_,_,1,2,3,4,5,}, { _,_,0,1,2,3,4,5,}, { _,_,_,_,_,_,_,6,}, { _,_,_,_,_,_,0,6,}, { _,_,_,_,_,_,1,6,}, { _,_,_,_,_,0,1,6,}, { _,_,_,_,_,_,2,6,}, { _,_,_,_,_,0,2,6,}, { _,_,_,_,_,1,2,6,}, { _,_,_,_,0,1,2,6,}, { _,_,_,_,_,_,3,6,}, { _,_,_,_,_,0,3,6,}, { _,_,_,_,_,1,3,6,}, { _,_,_,_,0,1,3,6,}, { _,_,_,_,_,2,3,6,}, { _,_,_,_,0,2,3,6,}, { _,_,_,_,1,2,3,6,}, { _,_,_,0,1,2,3,6,}, { _,_,_,_,_,_,4,6,}, { _,_,_,_,_,0,4,6,}, { _,_,_,_,_,1,4,6,}, { _,_,_,_,0,1,4,6,}, { _,_,_,_,_,2,4,6,}, { _,_,_,_,0,2,4,6,}, { _,_,_,_,1,2,4,6,}, { _,_,_,0,1,2,4,6,}, { _,_,_,_,_,3,4,6,}, { _,_,_,_,0,3,4,6,}, { _,_,_,_,1,3,4,6,}, { _,_,_,0,1,3,4,6,}, { _,_,_,_,2,3,4,6,}, { _,_,_,0,2,3,4,6,}, { _,_,_,1,2,3,4,6,}, { _,_,0,1,2,3,4,6,}, { _,_,_,_,_,_,5,6,}, { _,_,_,_,_,0,5,6,}, { _,_,_,_,_,1,5,6,}, { _,_,_,_,0,1,5,6,}, { _,_,_,_,_,2,5,6,}, { _,_,_,_,0,2,5,6,}, { _,_,_,_,1,2,5,6,}, { _,_,_,0,1,2,5,6,}, { _,_,_,_,_,3,5,6,}, { _,_,_,_,0,3,5,6,}, { _,_,_,_,1,3,5,6,}, { _,_,_,0,1,3,5,6,}, { _,_,_,_,2,3,5,6,}, { _,_,_,0,2,3,5,6,}, { _,_,_,1,2,3,5,6,}, { _,_,0,1,2,3,5,6,}, { _,_,_,_,_,4,5,6,}, { _,_,_,_,0,4,5,6,}, { _,_,_,_,1,4,5,6,}, { _,_,_,0,1,4,5,6,}, { _,_,_,_,2,4,5,6,}, { _,_,_,0,2,4,5,6,}, { _,_,_,1,2,4,5,6,}, { _,_,0,1,2,4,5,6,}, { _,_,_,_,3,4,5,6,}, { _,_,_,0,3,4,5,6,}, { _,_,_,1,3,4,5,6,}, { _,_,0,1,3,4,5,6,}, { _,_,_,2,3,4,5,6,}, { _,_,0,2,3,4,5,6,}, { _,_,1,2,3,4,5,6,}, { _,0,1,2,3,4,5,6,}, { _,_,_,_,_,_,_,7,}, { _,_,_,_,_,_,0,7,}, { _,_,_,_,_,_,1,7,}, { _,_,_,_,_,0,1,7,}, { _,_,_,_,_,_,2,7,}, { _,_,_,_,_,0,2,7,}, { _,_,_,_,_,1,2,7,}, { _,_,_,_,0,1,2,7,}, { _,_,_,_,_,_,3,7,}, { _,_,_,_,_,0,3,7,}, { _,_,_,_,_,1,3,7,}, { _,_,_,_,0,1,3,7,}, { _,_,_,_,_,2,3,7,}, { _,_,_,_,0,2,3,7,}, { _,_,_,_,1,2,3,7,}, { _,_,_,0,1,2,3,7,}, { _,_,_,_,_,_,4,7,}, { _,_,_,_,_,0,4,7,}, { _,_,_,_,_,1,4,7,}, { _,_,_,_,0,1,4,7,}, { _,_,_,_,_,2,4,7,}, { _,_,_,_,0,2,4,7,}, { _,_,_,_,1,2,4,7,}, { _,_,_,0,1,2,4,7,}, { _,_,_,_,_,3,4,7,}, { _,_,_,_,0,3,4,7,}, { _,_,_,_,1,3,4,7,}, { _,_,_,0,1,3,4,7,}, { _,_,_,_,2,3,4,7,}, { _,_,_,0,2,3,4,7,}, { _,_,_,1,2,3,4,7,}, { _,_,0,1,2,3,4,7,}, { _,_,_,_,_,_,5,7,}, { _,_,_,_,_,0,5,7,}, { _,_,_,_,_,1,5,7,}, { _,_,_,_,0,1,5,7,}, { _,_,_,_,_,2,5,7,}, { _,_,_,_,0,2,5,7,}, { _,_,_,_,1,2,5,7,}, { _,_,_,0,1,2,5,7,}, { _,_,_,_,_,3,5,7,}, { _,_,_,_,0,3,5,7,}, { _,_,_,_,1,3,5,7,}, { _,_,_,0,1,3,5,7,}, { _,_,_,_,2,3,5,7,}, { _,_,_,0,2,3,5,7,}, { _,_,_,1,2,3,5,7,}, { _,_,0,1,2,3,5,7,}, { _,_,_,_,_,4,5,7,}, { _,_,_,_,0,4,5,7,}, { _,_,_,_,1,4,5,7,}, { _,_,_,0,1,4,5,7,}, { _,_,_,_,2,4,5,7,}, { _,_,_,0,2,4,5,7,}, { _,_,_,1,2,4,5,7,}, { _,_,0,1,2,4,5,7,}, { _,_,_,_,3,4,5,7,}, { _,_,_,0,3,4,5,7,}, { _,_,_,1,3,4,5,7,}, { _,_,0,1,3,4,5,7,}, { _,_,_,2,3,4,5,7,}, { _,_,0,2,3,4,5,7,}, { _,_,1,2,3,4,5,7,}, { _,0,1,2,3,4,5,7,}, { _,_,_,_,_,_,6,7,}, { _,_,_,_,_,0,6,7,}, { _,_,_,_,_,1,6,7,}, { _,_,_,_,0,1,6,7,}, { _,_,_,_,_,2,6,7,}, { _,_,_,_,0,2,6,7,}, { _,_,_,_,1,2,6,7,}, { _,_,_,0,1,2,6,7,}, { _,_,_,_,_,3,6,7,}, { _,_,_,_,0,3,6,7,}, { _,_,_,_,1,3,6,7,}, { _,_,_,0,1,3,6,7,}, { _,_,_,_,2,3,6,7,}, { _,_,_,0,2,3,6,7,}, { _,_,_,1,2,3,6,7,}, { _,_,0,1,2,3,6,7,}, { _,_,_,_,_,4,6,7,}, { _,_,_,_,0,4,6,7,}, { _,_,_,_,1,4,6,7,}, { _,_,_,0,1,4,6,7,}, { _,_,_,_,2,4,6,7,}, { _,_,_,0,2,4,6,7,}, { _,_,_,1,2,4,6,7,}, { _,_,0,1,2,4,6,7,}, { _,_,_,_,3,4,6,7,}, { _,_,_,0,3,4,6,7,}, { _,_,_,1,3,4,6,7,}, { _,_,0,1,3,4,6,7,}, { _,_,_,2,3,4,6,7,}, { _,_,0,2,3,4,6,7,}, { _,_,1,2,3,4,6,7,}, { _,0,1,2,3,4,6,7,}, { _,_,_,_,_,5,6,7,}, { _,_,_,_,0,5,6,7,}, { _,_,_,_,1,5,6,7,}, { _,_,_,0,1,5,6,7,}, { _,_,_,_,2,5,6,7,}, { _,_,_,0,2,5,6,7,}, { _,_,_,1,2,5,6,7,}, { _,_,0,1,2,5,6,7,}, { _,_,_,_,3,5,6,7,}, { _,_,_,0,3,5,6,7,}, { _,_,_,1,3,5,6,7,}, { _,_,0,1,3,5,6,7,}, { _,_,_,2,3,5,6,7,}, { _,_,0,2,3,5,6,7,}, { _,_,1,2,3,5,6,7,}, { _,0,1,2,3,5,6,7,}, { _,_,_,_,4,5,6,7,}, { _,_,_,0,4,5,6,7,}, { _,_,_,1,4,5,6,7,}, { _,_,0,1,4,5,6,7,}, { _,_,_,2,4,5,6,7,}, { _,_,0,2,4,5,6,7,}, { _,_,1,2,4,5,6,7,}, { _,0,1,2,4,5,6,7,}, { _,_,_,3,4,5,6,7,}, { _,_,0,3,4,5,6,7,}, { _,_,1,3,4,5,6,7,}, { _,0,1,3,4,5,6,7,}, { _,_,2,3,4,5,6,7,}, { _,0,2,3,4,5,6,7,}, { _,1,2,3,4,5,6,7,}, { 0,1,2,3,4,5,6,7,}, }; pysam-0.23.0/htslib/htscodecs/htscodecs/pooled_alloc.h000066400000000000000000000076741475062545500230100ustar00rootroot00000000000000/* * Copyright (c) 2009-2010, 2013 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ // Defined static here as we only use in one file for now and don't // want to pollute the library name space (io_lib has the same named // functions). #ifndef _POOLED_ALLOC_H_ #define _POOLED_ALLOC_H_ #include #include #include /* * Implements a pooled block allocator where all items are the same size, * but we need many of them. */ typedef struct { void *pool; size_t used; } pool_t; typedef struct { size_t dsize; size_t npools; pool_t *pools; void *free; } pool_alloc_t; #define PSIZE 1024*1024 static pool_alloc_t *pool_create(size_t dsize) { pool_alloc_t *p; if (NULL == (p = (pool_alloc_t *)malloc(sizeof(*p)))) return NULL; /* Minimum size is a pointer, for free list */ dsize = (dsize + sizeof(void *) - 1) & ~(sizeof(void *)-1); if (dsize < sizeof(void *)) dsize = sizeof(void *); p->dsize = dsize; p->npools = 0; p->pools = NULL; p->free = NULL; return p; } static pool_t *new_pool(pool_alloc_t *p) { size_t n = PSIZE / p->dsize; pool_t *pool; pool = realloc(p->pools, (p->npools + 1) * sizeof(*p->pools)); if (NULL == pool) return NULL; p->pools = pool; pool = &p->pools[p->npools]; pool->pool = malloc(n * p->dsize); if (NULL == pool->pool) return NULL; pool->used = 0; p->npools++; return pool; } static void pool_destroy(pool_alloc_t *p) { size_t i; for (i = 0; i < p->npools; i++) { free(p->pools[i].pool); } free(p->pools); free(p); } static void *pool_alloc(pool_alloc_t *p) { pool_t *pool; void *ret; /* Look on free list */ if (NULL != p->free) { ret = p->free; p->free = *((void **)p->free); return ret; } /* Look for space in the last pool */ if (p->npools) { pool = &p->pools[p->npools - 1]; if (pool->used + p->dsize < PSIZE) { ret = ((char *) pool->pool) + pool->used; pool->used += p->dsize; return ret; } } /* Need a new pool */ pool = new_pool(p); if (NULL == pool) return NULL; pool->used = p->dsize; return pool->pool; } // static void pool_free(pool_alloc_t *p, void *ptr) { // *(void **)ptr = p->free; // p->free = ptr; // } #endif /*_POOLED_ALLOC_H_*/ pysam-0.23.0/htslib/htscodecs/htscodecs/rANS_byte.h000066400000000000000000000442301475062545500221670ustar00rootroot00000000000000/* rans_byte.h originally from https://github.com/rygorous/ryg_rans * * This is a public-domain implementation of several rANS variants. rANS is an * entropy coder from the ANS family, as described in Jarek Duda's paper * "Asymmetric numeral systems" (http://arxiv.org/abs/1311.2540). */ /*-------------------------------------------------------------------------- */ /* rans_byte.h from https://github.com/rygorous/ryg_rans */ // Simple byte-aligned rANS encoder/decoder - public domain - Fabian 'ryg' Giesen 2014 // // Not intended to be "industrial strength"; just meant to illustrate the general // idea. #ifndef RANS_BYTE_HEADER #define RANS_BYTE_HEADER #include #include #include #include "utils.h" #ifdef assert #define RansAssert assert #else #define RansAssert(x) #endif // READ ME FIRST: // // This is designed like a typical arithmetic coder API, but there's three // twists you absolutely should be aware of before you start hacking: // // 1. You need to encode data in *reverse* - last symbol first. rANS works // like a stack: last in, first out. // 2. Likewise, the encoder outputs bytes *in reverse* - that is, you give // it a pointer to the *end* of your buffer (exclusive), and it will // slowly move towards the beginning as more bytes are emitted. // 3. Unlike basically any other entropy coder implementation you might // have used, you can interleave data from multiple independent rANS // encoders into the same bytestream without any extra signaling; // you can also just write some bytes by yourself in the middle if // you want to. This is in addition to the usual arithmetic encoder // property of being able to switch models on the fly. Writing raw // bytes can be useful when you have some data that you know is // incompressible, and is cheaper than going through the rANS encode // function. Using multiple rANS coders on the same byte stream wastes // a few bytes compared to using just one, but execution of two // independent encoders can happen in parallel on superscalar and // Out-of-Order CPUs, so this can be *much* faster in tight decoding // loops. // // This is why all the rANS functions take the write pointer as an // argument instead of just storing it in some context struct. // -------------------------------------------------------------------------- // L ('l' in the paper) is the lower bound of our normalization interval. // Between this and our byte-aligned emission, we use 31 (not 32!) bits. // This is done intentionally because exact reciprocals for 31-bit uints // fit in 32-bit uints: this permits some optimizations during encoding. #define RANS_BYTE_L (1u << 23) // lower bound of our normalization interval // State for a rANS encoder. Yep, that's all there is to it. typedef uint32_t RansState; // Initialize a rANS encoder. static inline void RansEncInit(RansState* r) { *r = RANS_BYTE_L; } #if 0 /* Curently unused */ // Renormalize the encoder. Internal function. static inline RansState RansEncRenorm(RansState x, uint8_t** pptr, uint32_t freq, uint32_t scale_bits) { uint32_t x_max = ((RANS_BYTE_L >> scale_bits) << 8) * freq; // this turns into a shift. if (x >= x_max) { uint8_t* ptr = *pptr; do { *--ptr = (uint8_t) (x & 0xff); x >>= 8; } while (x >= x_max); *pptr = ptr; } return x; } // Encodes a single symbol with range start "start" and frequency "freq". // All frequencies are assumed to sum to "1 << scale_bits", and the // resulting bytes get written to ptr (which is updated). // // NOTE: With rANS, you need to encode symbols in *reverse order*, i.e. from // beginning to end! Likewise, the output bytestream is written *backwards*: // ptr starts pointing at the end of the output buffer and keeps decrementing. static inline void RansEncPut(RansState* r, uint8_t** pptr, uint32_t start, uint32_t freq, uint32_t scale_bits) { // renormalize RansState x = RansEncRenorm(*r, pptr, freq, scale_bits); // x = C(s,x) *r = ((x / freq) << scale_bits) + (x % freq) + start; } #endif /* Curently unused */ // Flushes the rANS encoder. static inline void RansEncFlush(RansState* r, uint8_t** pptr) { uint32_t x = *r; uint8_t* ptr = *pptr; ptr -= 4; ptr[0] = (uint8_t) (x >> 0); ptr[1] = (uint8_t) (x >> 8); ptr[2] = (uint8_t) (x >> 16); ptr[3] = (uint8_t) (x >> 24); *pptr = ptr; } // Initializes a rANS decoder. // Unlike the encoder, the decoder works forwards as you'd expect. static inline void RansDecInit(RansState* r, uint8_t** pptr) { uint32_t x; uint8_t* ptr = *pptr; x = ptr[0] << 0; x |= ptr[1] << 8; x |= ptr[2] << 16; x |= ((uint32_t)ptr[3]) << 24; ptr += 4; *pptr = ptr; *r = x; } // Returns the current cumulative frequency (map it to a symbol yourself!) static inline uint32_t RansDecGet(RansState* r, uint32_t scale_bits) { return *r & ((1u << scale_bits) - 1); } // Advances in the bit stream by "popping" a single symbol with range start // "start" and frequency "freq". All frequencies are assumed to sum to "1 << scale_bits", // and the resulting bytes get written to ptr (which is updated). static inline void RansDecAdvance(RansState* r, uint8_t** pptr, uint32_t start, uint32_t freq, uint32_t scale_bits) { uint32_t mask = (1u << scale_bits) - 1; // s, x = D(x) uint32_t x = *r; x = freq * (x >> scale_bits) + (x & mask) - start; // renormalize if (x < RANS_BYTE_L) { uint8_t* ptr = *pptr; do x = (x << 8) | *ptr++; while (x < RANS_BYTE_L); *pptr = ptr; } *r = x; } // -------------------------------------------------------------------------- // That's all you need for a full encoder; below here are some utility // functions with extra convenience or optimizations. // Encoder symbol description // This (admittedly odd) selection of parameters was chosen to make // RansEncPutSymbol as cheap as possible. typedef struct { uint32_t x_max; // (Exclusive) upper bound of pre-normalization interval uint32_t rcp_freq; // Fixed-point reciprocal frequency uint32_t bias; // Bias uint16_t cmpl_freq; // Complement of frequency: (1 << scale_bits) - freq uint16_t rcp_shift; // Reciprocal shift } RansEncSymbol; // Decoder symbols are straightforward. // 32-bit means more memory, but oddly faster on old gcc? Why? // 322MB/s vs 309MB/s for order-1. typedef struct { uint16_t freq; // Symbol frequency. uint16_t start; // Start of range. } RansDecSymbol; typedef struct { uint32_t freq; // Symbol frequency. uint32_t start; // Start of range. } RansDecSymbol32; // Initializes an encoder symbol to start "start" and frequency "freq" static inline void RansEncSymbolInit(RansEncSymbol* s, uint32_t start, uint32_t freq, uint32_t scale_bits) { RansAssert(scale_bits <= 16); RansAssert(start <= (1u << scale_bits)); RansAssert(freq <= (1u << scale_bits) - start); // Say M := 1 << scale_bits. // // The original encoder does: // x_new = (x/freq)*M + start + (x%freq) // // The fast encoder does (schematically): // q = mul_hi(x, rcp_freq) >> rcp_shift (division) // r = x - q*freq (remainder) // x_new = q*M + bias + r (new x) // plugging in r into x_new yields: // x_new = bias + x + q*(M - freq) // =: bias + x + q*cmpl_freq (*) // // and we can just precompute cmpl_freq. Now we just need to // set up our parameters such that the original encoder and // the fast encoder agree. s->x_max = ((RANS_BYTE_L >> scale_bits) << 8) * freq; s->cmpl_freq = (uint16_t) ((1 << scale_bits) - freq); if (freq < 2) { // freq=0 symbols are never valid to encode, so it doesn't matter what // we set our values to. // // freq=1 is tricky, since the reciprocal of 1 is 1; unfortunately, // our fixed-point reciprocal approximation can only multiply by values // smaller than 1. // // So we use the "next best thing": rcp_freq=0xffffffff, rcp_shift=0. // This gives: // q = mul_hi(x, rcp_freq) >> rcp_shift // = mul_hi(x, (1<<32) - 1)) >> 0 // = floor(x - x/(2^32)) // = x - 1 if 1 <= x < 2^32 // and we know that x>0 (x=0 is never in a valid normalization interval). // // So we now need to choose the other parameters such that // x_new = x*M + start // plug it in: // x*M + start (desired result) // = bias + x + q*cmpl_freq (*) // = bias + x + (x - 1)*(M - 1) (plug in q=x-1, cmpl_freq) // = bias + 1 + (x - 1)*M // = x*M + (bias + 1 - M) // // so we have start = bias + 1 - M, or equivalently // bias = start + M - 1. s->rcp_freq = ~0u; s->rcp_shift = 0; s->bias = start + (1 << scale_bits) - 1; } else { // Alverson, "Integer Division using reciprocals" // shift=ceil(log2(freq)) uint32_t shift = 0; while (freq > (1u << shift)) shift++; s->rcp_freq = (uint32_t) (((1ull << (shift + 31)) + freq-1) / freq); s->rcp_shift = shift - 1; // With these values, 'q' is the correct quotient, so we // have bias=start. s->bias = start; } s->rcp_shift += 32; // Avoid the extra >>32 in RansEncPutSymbol } // Initialize a decoder symbol to start "start" and frequency "freq" static inline void RansDecSymbolInit(RansDecSymbol* s, uint32_t start, uint32_t freq) { RansAssert(start <= (1 << 16)); RansAssert(freq <= (1 << 16) - start); s->start = (uint16_t) start; s->freq = (uint16_t) freq; } // Encodes a given symbol. This is faster than straight RansEnc since we can do // multiplications instead of a divide. // // See RansEncSymbolInit for a description of how this works. static inline void RansEncPutSymbol(RansState* r, uint8_t** pptr, RansEncSymbol const* sym) { RansAssert(sym->x_max != 0); // can't encode symbol with freq=0 // renormalize uint32_t x = *r; uint32_t x_max = sym->x_max; // This is better for 40-qual illumina (3.7% quicker overall CRAM). // The old method was better for low complexity data such as NovaSeq // quals (2.6% quicker overall CRAM). int o = x >= x_max; uint8_t* ptr = *pptr; ptr[-1] = x & 0xff; ptr -= o; x >>= o*8; if (unlikely(x >= x_max)) { *--ptr = (uint8_t) (x & 0xff); x >>= 8; } *pptr = ptr; //uint32_t q = (uint32_t) (((uint64_t)x * sym->rcp_freq) >> sym->rcp_shift); //*r = q * sym->cmpl_freq + x + sym->bias; // x = C(s,x) // NOTE: written this way so we get a 32-bit "multiply high" when // available. If you're on a 64-bit platform with cheap multiplies // (e.g. x64), just bake the +32 into rcp_shift. //uint32_t q = (uint32_t) (((uint64_t)x * sym->rcp_freq) >> 32) >> sym->rcp_shift; // The extra >>32 has already been added to RansEncSymbolInit uint32_t q = (uint32_t) (((uint64_t)x * sym->rcp_freq) >> sym->rcp_shift); *r = q * sym->cmpl_freq + x + sym->bias; } // A 4-way version of RansEncPutSymbol, renormalising 4 states // simulatenously with their results written to the same ptr buffer. // (This is perhaps a failing as it makes optmisation tricky.) static inline void RansEncPutSymbol4(RansState *r0, RansState *r1, RansState *r2, RansState *r3, uint8_t** pptr, RansEncSymbol const *sym0, RansEncSymbol const *sym1, RansEncSymbol const *sym2, RansEncSymbol const *sym3) { RansAssert(sym0->x_max != 0); // can't encode symbol with freq=0 RansAssert(sym1->x_max != 0); // can't encode symbol with freq=0 RansAssert(sym2->x_max != 0); // can't encode symbol with freq=0 RansAssert(sym3->x_max != 0); // can't encode symbol with freq=0 // renormalize uint32_t x0, x1, x2, x3; uint8_t* ptr = *pptr; int o; uint32_t m[4] = { sym0->x_max, sym1->x_max, sym2->x_max, sym3->x_max }; x0 = *r0; o = x0 >= m[0]; ptr[-1] = x0; ptr -= o; x0 >>= o*8; if (x0 >= m[0]) { *--ptr = x0; x0 >>= 8; } x1 = *r1; o = x1 >= m[1]; ptr[-1] = x1; ptr -= o; x1 >>= o*8; if (x1 >= m[1]) { *--ptr = x1; x1 >>= 8; } x2 = *r2; o = x2 >= m[2]; ptr[-1] = x2; ptr -= o; x2 >>= o*8; if (x2 >= m[2]) { *--ptr = x2; x2 >>= 8; } x3 = *r3; o = x3 >= m[3]; ptr[-1] = x3; ptr -= o; x3 >>= o*8; if (x3 >= m[3]) { *--ptr = x3; x3 >>= 8; } *pptr = ptr; // x = C(s,x) uint32_t qa, qb; qa = (uint32_t) (((uint64_t)x0 * sym0->rcp_freq) >> sym0->rcp_shift); uint32_t X0 = qa * sym0->cmpl_freq; qb = (uint32_t) (((uint64_t)x1 * sym1->rcp_freq) >> sym1->rcp_shift); uint32_t X1 = qb * sym1->cmpl_freq; *r0 = X0 + x0 + sym0->bias; *r1 = X1 + x1 + sym1->bias; qa = (uint32_t) (((uint64_t)x2 * sym2->rcp_freq) >> sym2->rcp_shift); uint32_t X2 = qa * sym2->cmpl_freq; qb = (uint32_t) (((uint64_t)x3 * sym3->rcp_freq) >> sym3->rcp_shift); uint32_t X3 = qb * sym3->cmpl_freq; *r2 = X2 + x2 + sym2->bias; *r3 = X3 + x3 + sym3->bias; } // Equivalent to RansDecAdvance that takes a symbol. static inline void RansDecAdvanceSymbol(RansState* r, uint8_t** pptr, RansDecSymbol const* sym, uint32_t scale_bits) { RansDecAdvance(r, pptr, sym->start, sym->freq, scale_bits); } // Advances in the bit stream by "popping" a single symbol with range start // "start" and frequency "freq". All frequencies are assumed to sum to "1 << scale_bits". // No renormalization or output happens. static inline void RansDecAdvanceStep(RansState* r, uint32_t start, uint32_t freq, uint32_t scale_bits) { uint32_t mask = (1u << scale_bits) - 1; // s, x = D(x) uint32_t x = *r; *r = freq * (x >> scale_bits) + (x & mask) - start; } // Equivalent to RansDecAdvanceStep that takes a symbol. static inline void RansDecAdvanceSymbolStep(RansState* r, RansDecSymbol const* sym, uint32_t scale_bits) { RansDecAdvanceStep(r, sym->start, sym->freq, scale_bits); } // Renormalize. #if defined(__x86_64) && !defined(__ILP32__) /* * Assembly variants of the RansDecRenorm code. * These are based on joint ideas from Rob Davies and from looking at * the clang assembly output. */ static inline void RansDecRenorm(RansState* r, uint8_t** pptr) { uint32_t x = *r; uint8_t *ptr = *pptr; __asm__ ("movzbl (%0), %%eax\n\t" "mov %1, %%edx\n\t" "shl $0x8,%%edx\n\t" "or %%eax,%%edx\n\t" "cmp $0x800000,%1\n\t" "cmovb %%edx,%1\n\t" "adc $0x0,%0\n\t" : "=r" (ptr), "=r" (x) : "0" (ptr), "1" (x) : "eax", "edx" ); if (x < 0x800000) x = (x << 8) | *ptr++; *pptr = ptr; *r = x; } /* * A variant that normalises two rans states. * The only minor tweak here is to adjust the reorder a few opcodes * to reduce dependency delays. */ static inline void RansDecRenorm2(RansState* r1, RansState* r2, uint8_t** pptr) { uint32_t x1 = *r1; uint32_t x2 = *r2; uint8_t *ptr = *pptr; __asm__ ("movzbl (%0), %%eax\n\t" "mov %1, %%edx\n\t" "shl $0x8, %%edx\n\t" "or %%eax, %%edx\n\t" "cmp $0x800000, %1\n\t" "cmovb %%edx, %1\n\t" "adc $0x0, %0\n\t" "mov %2, %%edx\n\t" "shl $0x8, %%edx\n\t" "cmp $0x800000, %1\n\t" "jae 1f\n\t" "movzbl (%0), %%eax\n\t" "shl $0x8, %1\n\t" "or %%eax, %1\n\t" "add $0x1, %0\n\t" "1:\n\t" "movzbl (%0), %%eax\n\t" "or %%eax, %%edx\n\t" "cmp $0x800000, %2\n\t" "cmovb %%edx, %2\n\t" "adc $0x0, %0\n\t" "cmp $0x800000, %2\n\t" "jae 2f\n\t" "movzbl (%0), %%eax\n\t" "shl $0x8, %2\n\t" "or %%eax, %2\n\t" "add $0x1, %0\n\t" "2:\n\t" : "=r" (ptr), "=r" (x1), "=r" (x2) : "0" (ptr), "1" (x1), "2" (x2) : "eax", "edx" ); *pptr = ptr; *r1 = x1; *r2 = x2; } #else /* __x86_64 */ static inline void RansDecRenorm(RansState* r, uint8_t** pptr) { // renormalize uint32_t x = *r; #ifdef __clang__ // Generates cmov instructions on clang, but alas not gcc uint8_t* ptr = *pptr; uint32_t y = (x << 8) | *ptr; uint32_t cond = x < RANS_BYTE_L; x = cond ? y : x; ptr += cond ? 1 : 0; if (x < RANS_BYTE_L) x = (x<<8) | *ptr++; *pptr = ptr; #else if (x >= RANS_BYTE_L) return; uint8_t* ptr = *pptr; x = (x << 8) | *ptr++; if (x < RANS_BYTE_L) x = (x << 8) | *ptr++; *pptr = ptr; #endif /* __clang__ */ *r = x; } static inline void RansDecRenorm2(RansState* r1, RansState* r2, uint8_t** pptr) { RansDecRenorm(r1, pptr); RansDecRenorm(r2, pptr); } #endif /* __x86_64 */ static inline void RansDecRenormSafe(RansState* r, uint8_t** pptr, uint8_t *ptr_end) { uint32_t x = *r; uint8_t* ptr = *pptr; if (x >= RANS_BYTE_L || ptr >= ptr_end) return; x = (x << 8) | *ptr++; if (x < RANS_BYTE_L && ptr < ptr_end) x = (x << 8) | *ptr++; *pptr = ptr; *r = x; } static inline void RansDecSymbolInit32(RansDecSymbol32* s, uint32_t start, uint32_t freq) { RansAssert(start <= (1 << 16)); RansAssert(freq <= (1 << 16) - start); s->start = (uint16_t) start; s->freq = (uint16_t) freq; } static inline void RansDecAdvanceSymbol32(RansState* r, uint8_t** pptr, RansDecSymbol32 const* sym, uint32_t scale_bits) { RansDecAdvance(r, pptr, sym->start, sym->freq, scale_bits); } #endif // RANS_BYTE_HEADER pysam-0.23.0/htslib/htscodecs/htscodecs/rANS_static.c000066400000000000000000000610471475062545500225130ustar00rootroot00000000000000/* * Copyright (c) 2014-2022 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #include "config.h" // Use 11 for order-1? #define TF_SHIFT 12 #define TOTFREQ (1< #include #include #include #include #include #include #include #ifndef NO_THREADS #include #endif #include "rANS_static.h" #define ABS(a) ((a)>0?(a):-(a)) /*----------------------------------------------------------------------------- * Memory to memory compression functions. * * These are original versions without any manual loop unrolling. They * are easier to understand, but can be up to 2x slower. */ static unsigned char *rans_compress_O0(unsigned char *in, unsigned int in_size, unsigned int *out_size) { unsigned char *out_buf = malloc(1.05*in_size + 257*257*3 + 9); unsigned char *cp, *out_end; RansEncSymbol syms[256]; RansState rans0; RansState rans2; RansState rans1; RansState rans3; uint8_t* ptr; int F[256+MAGIC] = {0}, i, j, tab_size, rle, x, fsum = 0; int m = 0, M = 0; uint64_t tr; if (!out_buf) return NULL; ptr = out_end = out_buf + (uint32_t)(1.05*in_size) + 257*257*3 + 9; // Compute statistics if (hist8(in, in_size, (uint32_t *)F) < 0) { free(out_buf); return NULL; } tr = in_size ? ((uint64_t)TOTFREQ<<31)/in_size + (1<<30)/in_size : 0; normalise_harder: // Normalise so T[i] == TOTFREQ for (fsum = m = M = j = 0; j < 256; j++) { if (!F[j]) continue; if (m < F[j]) m = F[j], M = j; if ((F[j] = (F[j]*tr)>>31) == 0) F[j] = 1; fsum += F[j]; } fsum++; if (fsum < TOTFREQ) { F[M] += TOTFREQ-fsum; } else if (fsum-TOTFREQ > F[M]/2) { // Corner case to avoid excessive frequency reduction tr = 2104533975; goto normalise_harder; // equiv to *0.98. } else { F[M] -= fsum-TOTFREQ; } //printf("F[%d]=%d\n", M, F[M]); assert(F[M]>0); // Encode statistics. cp = out_buf+9; for (x = rle = j = 0; j < 256; j++) { if (F[j]) { // j if (rle) { rle--; } else { *cp++ = j; if (!rle && j && F[j-1]) { for(rle=j+1; rle<256 && F[rle]; rle++) ; rle -= j+1; *cp++ = rle; } //fprintf(stderr, "%d: %d %d\n", j, rle, N[j]); } // F[j] if (F[j]<128) { *cp++ = F[j]; } else { *cp++ = 128 | (F[j]>>8); *cp++ = F[j]&0xff; } RansEncSymbolInit(&syms[j], x, F[j], TF_SHIFT); x += F[j]; } } *cp++ = 0; //write(2, out_buf+4, cp-(out_buf+4)); tab_size = cp-out_buf; RansEncInit(&rans0); RansEncInit(&rans1); RansEncInit(&rans2); RansEncInit(&rans3); switch (i=(in_size&3)) { case 3: RansEncPutSymbol(&rans2, &ptr, &syms[in[in_size-(i-2)]]); // fall-through case 2: RansEncPutSymbol(&rans1, &ptr, &syms[in[in_size-(i-1)]]); // fall-through case 1: RansEncPutSymbol(&rans0, &ptr, &syms[in[in_size-(i-0)]]); // fall-through case 0: break; } for (i=(in_size &~3); likely(i>0); i-=4) { RansEncSymbol *s3 = &syms[in[i-1]]; RansEncSymbol *s2 = &syms[in[i-2]]; RansEncSymbol *s1 = &syms[in[i-3]]; RansEncSymbol *s0 = &syms[in[i-4]]; RansEncPutSymbol(&rans3, &ptr, s3); RansEncPutSymbol(&rans2, &ptr, s2); RansEncPutSymbol(&rans1, &ptr, s1); RansEncPutSymbol(&rans0, &ptr, s0); } RansEncFlush(&rans3, &ptr); RansEncFlush(&rans2, &ptr); RansEncFlush(&rans1, &ptr); RansEncFlush(&rans0, &ptr); // Finalise block size and return it *out_size = (out_end - ptr) + tab_size; cp = out_buf; *cp++ = 0; // order *cp++ = ((*out_size-9)>> 0) & 0xff; *cp++ = ((*out_size-9)>> 8) & 0xff; *cp++ = ((*out_size-9)>>16) & 0xff; *cp++ = ((*out_size-9)>>24) & 0xff; *cp++ = (in_size>> 0) & 0xff; *cp++ = (in_size>> 8) & 0xff; *cp++ = (in_size>>16) & 0xff; *cp++ = (in_size>>24) & 0xff; memmove(out_buf + tab_size, ptr, out_end-ptr); return out_buf; } typedef struct { unsigned char R[TOTFREQ]; } ari_decoder; static unsigned char *rans_uncompress_O0(unsigned char *in, unsigned int in_size, unsigned int *out_size) { /* Load in the static tables */ unsigned char *cp = in + 9; unsigned char *cp_end = in + in_size; const uint32_t mask = (1u << TF_SHIFT)-1; int i, j, rle; unsigned int x, y; unsigned int out_sz, in_sz; char *out_buf; RansState R[4]; RansState m[4]; uint16_t sfreq[TOTFREQ+32]; uint16_t ssym [TOTFREQ+32]; // faster, but only needs uint8_t uint32_t sbase[TOTFREQ+16]; // faster, but only needs uint16_t if (in_size < 26) // Need at least this many bytes just to start return NULL; if (*in++ != 0) // Order-0 check return NULL; in_sz = ((in[0])<<0) | ((in[1])<<8) | ((in[2])<<16) | (((uint32_t)in[3])<<24); out_sz = ((in[4])<<0) | ((in[5])<<8) | ((in[6])<<16) | (((uint32_t)in[7])<<24); if (in_sz != in_size-9) return NULL; if (out_sz >= INT_MAX) return NULL; // protect against some overflow cases // For speeding up the fuzzer only. // Small input can lead to large uncompressed data. // We reject this as it just slows things up instead of testing more code // paths (once we've verified a few times for large data). #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (out_sz > 100000) return NULL; #endif out_buf = malloc(out_sz); if (!out_buf) return NULL; //fprintf(stderr, "out_sz=%d\n", out_sz); // Precompute reverse lookup of frequency. rle = x = y = 0; j = *cp++; do { int F, C; if (cp > cp_end - 16) goto cleanup; // Not enough input bytes left if ((F = *cp++) >= 128) { F &= ~128; F = ((F & 127) << 8) | *cp++; } C = x; if (x + F > TOTFREQ) goto cleanup; for (y = 0; y < F; y++) { ssym [y + C] = j; sfreq[y + C] = F; sbase[y + C] = y; } x += F; if (!rle && j+1 == *cp) { j = *cp++; rle = *cp++; } else if (rle) { rle--; j++; if (j > 255) goto cleanup; } else { j = *cp++; } } while(j); if (x < TOTFREQ-1 || x > TOTFREQ) goto cleanup; if (x != TOTFREQ) { // Protection against accessing uninitialised memory in the case // where SUM(freqs) == 4095 and not 4096. ssym [x] = ssym [x-1]; sfreq[x] = sfreq[x-1]; sbase[x] = sbase[x-1]+1; } // 16 bytes of cp here. Also why cp - 16 in above loop. if (cp > cp_end - 16) goto cleanup; // Not enough input bytes left RansDecInit(&R[0], &cp); if (R[0] < RANS_BYTE_L) goto cleanup; RansDecInit(&R[1], &cp); if (R[1] < RANS_BYTE_L) goto cleanup; RansDecInit(&R[2], &cp); if (R[2] < RANS_BYTE_L) goto cleanup; RansDecInit(&R[3], &cp); if (R[3] < RANS_BYTE_L) goto cleanup; int out_end = (out_sz&~3); cp_end -= 8; // within 8 for simplicity of loop below // 2 x likely() here harms gcc 7.5 by about 8% rate drop, but only in O2 for (i=0; likely(i < out_end); i+=4) { // /curr code // gcc7 O2 513/497 562/556++ 556/547 ok // gcc7 O3 566/552 569/553 581/563+ // gcc10 O2 544/538 563/547 541/537-? // gcc10 O3 531/519 546/530 575/546+ // gcc11 O2 512/490 588/540 540/535 mid // gcc11 O3 482/471 553/541 549/535 // gcc12 O2 533/526 544/534 539/535 // gcc12 O3 548/533 502/497-- 553/527 ok // clang10 555/542 564/549 560/541 // clang13 560/553 572/559 556/559 m[0] = R[0] & mask; R[0] = sfreq[m[0]] * (R[0] >> TF_SHIFT) + sbase[m[0]]; m[1] = R[1] & mask; R[1] = sfreq[m[1]] * (R[1] >> TF_SHIFT) + sbase[m[1]]; m[2] = R[2] & mask; R[2] = sfreq[m[2]] * (R[2] >> TF_SHIFT) + sbase[m[2]]; m[3] = R[3] & mask; R[3] = sfreq[m[3]] * (R[3] >> TF_SHIFT) + sbase[m[3]]; // likely() here harms gcc12 -O3 if (cp>2)]]++; F[0][in[2*(in_size>>2)]]++; F[0][in[3*(in_size>>2)]]++; T[0]+=3; // Normalise so T[i] == TOTFREQ for (rle_i = i = 0; i < 256; i++) { int t2, m, M; unsigned int x; if (T[i] == 0) continue; //uint64_t p = (TOTFREQ * TOTFREQ) / t; double p = ((double)TOTFREQ)/T[i]; normalise_harder: for (t2 = m = M = j = 0; j < 256; j++) { if (!F[i][j]) continue; if (m < F[i][j]) m = F[i][j], M = j; //if ((F[i][j] = (F[i][j] * p) / TOTFREQ) == 0) if ((F[i][j] *= p) == 0) F[i][j] = 1; t2 += F[i][j]; } t2++; if (t2 < TOTFREQ) { F[i][M] += TOTFREQ-t2; } else if (t2-TOTFREQ >= F[i][M]/2) { // Corner case to avoid excessive frequency reduction p = .98; goto normalise_harder; } else { F[i][M] -= t2-TOTFREQ; } // Store frequency table // i if (rle_i) { rle_i--; } else { *cp++ = i; // FIXME: could use order-0 statistics to observe which alphabet // symbols are present and base RLE on that ordering instead. if (i && T[i-1]) { for(rle_i=i+1; rle_i<256 && T[rle_i]; rle_i++) ; rle_i -= i+1; *cp++ = rle_i; } } int *F_i_ = F[i]; x = 0; rle_j = 0; for (j = 0; j < 256; j++) { if (F_i_[j]) { //fprintf(stderr, "F[%d][%d]=%d, x=%d\n", i, j, F_i_[j], x); // j if (rle_j) { rle_j--; } else { *cp++ = j; if (!rle_j && j && F_i_[j-1]) { for(rle_j=j+1; rle_j<256 && F_i_[rle_j]; rle_j++) ; rle_j -= j+1; *cp++ = rle_j; } } // F_i_[j] if (F_i_[j]<128) { *cp++ = F_i_[j]; } else { *cp++ = 128 | (F_i_[j]>>8); *cp++ = F_i_[j]&0xff; } RansEncSymbolInit(&syms[i][j], x, F_i_[j], TF_SHIFT); x += F_i_[j]; } } *cp++ = 0; } *cp++ = 0; //write(2, out_buf+4, cp-(out_buf+4)); tab_size = cp - out_buf; assert(tab_size < 257*257*3); RansState rans0, rans1, rans2, rans3; RansEncInit(&rans0); RansEncInit(&rans1); RansEncInit(&rans2); RansEncInit(&rans3); uint8_t* ptr = out_end; int isz4 = in_size>>2; int i0 = 1*isz4-2; int i1 = 2*isz4-2; int i2 = 3*isz4-2; int i3 = 4*isz4-2; unsigned char l0 = in[i0+1]; unsigned char l1 = in[i1+1]; unsigned char l2 = in[i2+1]; unsigned char l3 = in[i3+1]; // Deal with the remainder l3 = in[in_size-1]; for (i3 = in_size-2; i3 > 4*isz4-2; i3--) { unsigned char c3 = in[i3]; RansEncPutSymbol(&rans3, &ptr, &syms[c3][l3]); l3 = c3; } for (; likely(i0 >= 0); i0--, i1--, i2--, i3--) { unsigned char c3 = in[i3]; unsigned char c2 = in[i2]; unsigned char c1 = in[i1]; unsigned char c0 = in[i0]; RansEncSymbol *s3 = &syms[c3][l3]; RansEncSymbol *s2 = &syms[c2][l2]; RansEncSymbol *s1 = &syms[c1][l1]; RansEncSymbol *s0 = &syms[c0][l0]; RansEncPutSymbol4(&rans3, &rans2, &rans1, &rans0, &ptr, s3, s2, s1, s0); l3 = c3; l2 = c2; l1 = c1; l0 = c0; } RansEncPutSymbol(&rans3, &ptr, &syms[0][l3]); RansEncPutSymbol(&rans2, &ptr, &syms[0][l2]); RansEncPutSymbol(&rans1, &ptr, &syms[0][l1]); RansEncPutSymbol(&rans0, &ptr, &syms[0][l0]); RansEncFlush(&rans3, &ptr); RansEncFlush(&rans2, &ptr); RansEncFlush(&rans1, &ptr); RansEncFlush(&rans0, &ptr); *out_size = (out_end - ptr) + tab_size; cp = out_buf; *cp++ = 1; // order *cp++ = ((*out_size-9)>> 0) & 0xff; *cp++ = ((*out_size-9)>> 8) & 0xff; *cp++ = ((*out_size-9)>>16) & 0xff; *cp++ = ((*out_size-9)>>24) & 0xff; *cp++ = (in_size>> 0) & 0xff; *cp++ = (in_size>> 8) & 0xff; *cp++ = (in_size>>16) & 0xff; *cp++ = (in_size>>24) & 0xff; memmove(out_buf + tab_size, ptr, out_end-ptr); cleanup: htscodecs_tls_free(syms); return out_buf; } static unsigned char *rans_uncompress_O1(unsigned char *in, unsigned int in_size, unsigned int *out_size) { /* Load in the static tables */ unsigned char *cp = in + 9; unsigned char *ptr_end = in + in_size; int i, j = -999, rle_i, rle_j; unsigned int x; unsigned int out_sz, in_sz; char *out_buf = NULL; // Sanity checking if (in_size < 27) // Need at least this many bytes to start return NULL; if (*in++ != 1) // Order-1 check return NULL; in_sz = ((in[0])<<0) | ((in[1])<<8) | ((in[2])<<16) | (((uint32_t)in[3])<<24); out_sz = ((in[4])<<0) | ((in[5])<<8) | ((in[6])<<16) | (((uint32_t)in[7])<<24); if (in_sz != in_size-9) return NULL; if (out_sz >= INT_MAX) return NULL; // protect against some overflow cases // For speeding up the fuzzer only. // Small input can lead to large uncompressed data. // We reject this as it just slows things up instead of testing more code // paths (once we've verified a few times for large data). #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (out_sz > 100000) return NULL; #endif // Allocate decoding lookup tables RansDecSymbol32 (*syms)[256]; uint8_t *mem = htscodecs_tls_calloc(256, sizeof(ari_decoder) + sizeof(*syms)); if (!mem) return NULL; ari_decoder *const D = (ari_decoder *)mem; syms = (RansDecSymbol32 (*)[256])(mem + 256*sizeof(ari_decoder)); int16_t map[256], map_i = 0; memset(map, -1, 256*sizeof(*map)); if (!D) goto cleanup; /* These memsets prevent illegal memory access in syms due to broken compressed data. As D is calloc'd, all illegal transitions will end up in either row or column 0 of syms. */ memset(&syms[0], 0, sizeof(syms[0])); for (i = 0; i < 256; i++) memset(&syms[i][0], 0, sizeof(syms[0][0])); //fprintf(stderr, "out_sz=%d\n", out_sz); //i = *cp++; rle_i = 0; i = *cp++; do { // Map arbitrary a,b,c to 0,1,2 to improve cache locality. if (map[i] == -1) map[i] = map_i++; int m_i = map[i]; rle_j = x = 0; j = *cp++; do { if (map[j] == -1) map[j] = map_i++; int F, C; if (cp > ptr_end - 16) goto cleanup; // Not enough input bytes left if ((F = *cp++) >= 128) { F &= ~128; F = ((F & 127) << 8) | *cp++; } C = x; //fprintf(stderr, "i=%d j=%d F=%d C=%d\n", i, j, F, C); if (unlikely(!F)) F = TOTFREQ; RansDecSymbolInit32(&syms[m_i][j], C, F); /* Build reverse lookup table */ //if (!D[i].R) D[i].R = (unsigned char *)malloc(TOTFREQ); if (x + F > TOTFREQ) goto cleanup; memset(&D[m_i].R[x], j, F); x += F; if (!rle_j && j+1 == *cp) { j = *cp++; rle_j = *cp++; } else if (rle_j) { rle_j--; j++; if (j > 255) goto cleanup; } else { j = *cp++; } } while(j); if (x < TOTFREQ-1 || x > TOTFREQ) goto cleanup; if (x < TOTFREQ) // historically we fill 4095, not 4096 D[i].R[x] = D[i].R[x-1]; if (!rle_i && i+1 == *cp) { i = *cp++; rle_i = *cp++; } else if (rle_i) { rle_i--; i++; if (i > 255) goto cleanup; } else { i = *cp++; } } while (i); for (i = 0; i < 256; i++) if (map[i] == -1) map[i] = 0; RansState rans0, rans1, rans2, rans3; uint8_t *ptr = cp; if (cp > ptr_end - 16) goto cleanup; // Not enough input bytes left RansDecInit(&rans0, &ptr); if (rans0 < RANS_BYTE_L) goto cleanup; RansDecInit(&rans1, &ptr); if (rans1 < RANS_BYTE_L) goto cleanup; RansDecInit(&rans2, &ptr); if (rans2 < RANS_BYTE_L) goto cleanup; RansDecInit(&rans3, &ptr); if (rans3 < RANS_BYTE_L) goto cleanup; RansState R[4]; R[0] = rans0; R[1] = rans1; R[2] = rans2; R[3] = rans3; unsigned int isz4 = out_sz>>2; uint32_t l0 = 0; uint32_t l1 = 0; uint32_t l2 = 0; uint32_t l3 = 0; unsigned int i4[] = {0*isz4, 1*isz4, 2*isz4, 3*isz4}; /* Allocate output buffer */ out_buf = malloc(out_sz); if (!out_buf) goto cleanup; uint8_t cc0 = D[map[l0]].R[R[0] & ((1u << TF_SHIFT)-1)]; uint8_t cc1 = D[map[l1]].R[R[1] & ((1u << TF_SHIFT)-1)]; uint8_t cc2 = D[map[l2]].R[R[2] & ((1u << TF_SHIFT)-1)]; uint8_t cc3 = D[map[l3]].R[R[3] & ((1u << TF_SHIFT)-1)]; ptr_end -= 8; for (; likely(i4[0] < isz4); i4[0]++, i4[1]++, i4[2]++, i4[3]++) { // seq4-head2: file q40b // O3 O2 // gcc7 296/291 290/260 // gcc10 292/292 290/261 // gcc11 293/293 290/265 // gcc12 293/290 291/266 // clang10 293/290 296/272 // clang13 300/290 290/266 out_buf[i4[0]] = cc0; out_buf[i4[1]] = cc1; out_buf[i4[2]] = cc2; out_buf[i4[3]] = cc3; RansDecSymbol32 s[4] = { syms[l0][cc0], syms[l1][cc1], syms[l2][cc2], syms[l3][cc3], }; RansDecAdvanceStep(&R[0], s[0].start, s[0].freq, TF_SHIFT); RansDecAdvanceStep(&R[1], s[1].start, s[1].freq, TF_SHIFT); RansDecAdvanceStep(&R[2], s[2].start, s[2].freq, TF_SHIFT); RansDecAdvanceStep(&R[3], s[3].start, s[3].freq, TF_SHIFT); // Likely here helps speed of high-entropy data by 10-11%, // but harms low entropy-data speed by 3-4%. if ((ptr < ptr_end)) { RansDecRenorm2(&R[0], &R[1], &ptr); RansDecRenorm2(&R[2], &R[3], &ptr); } else { RansDecRenormSafe(&R[0], &ptr, ptr_end+8); RansDecRenormSafe(&R[1], &ptr, ptr_end+8); RansDecRenormSafe(&R[2], &ptr, ptr_end+8); RansDecRenormSafe(&R[3], &ptr, ptr_end+8); } l0 = map[cc0]; l1 = map[cc1]; l2 = map[cc2]; l3 = map[cc3]; cc0 = D[l0].R[R[0] & ((1u << TF_SHIFT)-1)]; cc1 = D[l1].R[R[1] & ((1u << TF_SHIFT)-1)]; cc2 = D[l2].R[R[2] & ((1u << TF_SHIFT)-1)]; cc3 = D[l3].R[R[3] & ((1u << TF_SHIFT)-1)]; } // Remainder for (; i4[3] < out_sz; i4[3]++) { unsigned char c3 = D[l3].R[RansDecGet(&R[3], TF_SHIFT)]; out_buf[i4[3]] = c3; uint32_t m = R[3] & ((1u << TF_SHIFT)-1); R[3] = syms[l3][c3].freq * (R[3]>>TF_SHIFT) + m - syms[l3][c3].start; RansDecRenormSafe(&R[3], &ptr, ptr_end+8); l3 = map[c3]; } *out_size = out_sz; cleanup: htscodecs_tls_free(D); return (unsigned char *)out_buf; } /*----------------------------------------------------------------------------- * Simple interface to the order-0 vs order-1 encoders and decoders. */ unsigned char *rans_compress(unsigned char *in, unsigned int in_size, unsigned int *out_size, int order) { if (in_size > INT_MAX) { *out_size = 0; return NULL; } return order ? rans_compress_O1(in, in_size, out_size) : rans_compress_O0(in, in_size, out_size); } unsigned char *rans_uncompress(unsigned char *in, unsigned int in_size, unsigned int *out_size) { /* Both rans_uncompress functions need to be able to read at least 9 bytes. */ if (in_size < 9) return NULL; return in[0] ? rans_uncompress_O1(in, in_size, out_size) : rans_uncompress_O0(in, in_size, out_size); } pysam-0.23.0/htslib/htscodecs/htscodecs/rANS_static.h000066400000000000000000000040371475062545500225140ustar00rootroot00000000000000/* * Copyright (c) 2014-2019 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef RANS_STATIC_H #define RANS_STATIC_H #ifdef __cplusplus extern "C" { #endif unsigned char *rans_compress(unsigned char *in, unsigned int in_size, unsigned int *out_size, int order); unsigned char *rans_uncompress(unsigned char *in, unsigned int in_size, unsigned int *out_size); #ifdef __cplusplus } #endif #endif /* RANS_STATIC_H */ pysam-0.23.0/htslib/htscodecs/htscodecs/rANS_static16_int.h000066400000000000000000000456401475062545500235420ustar00rootroot00000000000000#ifndef RANS_INTERNAL_H #define RANS_INTERNAL_H #include "config.h" #include "varint.h" #include "utils.h" /* * Copyright (c) 2017-2022 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ // Internal: common parts to all the rANSNx16pr implementations. // As per standard rANS_static but using optional RLE or bit-packing // techniques prior to entropy encoding. This is a significant // reduction in some data sets. // top bits in order byte #define X_PACK 0x80 // Pack 2,4,8 or infinite symbols into a byte. #define X_RLE 0x40 // Run length encoding with runs & lits encoded separately #define X_CAT 0x20 // Nop; for tiny segments where rANS overhead is too big #define X_NOSZ 0x10 // Don't store the original size; used by STRIPE mode #define X_STRIPE 0x08 // For N-byte integer data; rotate & encode N streams. #define X_32 0x04 // 32-way unrolling instead of 4-way // Not part of the file format, but used to direct the encoder #define X_SIMD_AUTO 0x100 // automatically enable X_32 if we deem it worthy #define X_SW32_ENC 0x200 // forcibly use the software version of X_32 #define X_SW32_DEC 0x400 // forcibly use the software version of X_32 #define X_NO_AVX512 0x800 // turn off avx512, but permits AVX2 #define TF_SHIFT 12 #define TOTFREQ (1<> 1; v |= v >> 2; v |= v >> 4; v |= v >> 8; v |= v >> 16; v++; return v; } static inline int normalise_freq(uint32_t *F, int size, uint32_t tot) { int m, M, j, loop = 0; uint64_t tr; if (!size) return 0; again: tr = ((uint64_t)tot<<31)/size + (1<<30)/size; for (size = m = M = j = 0; j < 256; j++) { if (!F[j]) continue; if (m < F[j]) m = F[j], M = j; if ((F[j] = (F[j]*tr)>>31) == 0) F[j] = 1; size += F[j]; // if (F[j] == tot) // F[j]--; } int adjust = tot - size; if (adjust > 0) { F[M] += adjust; } else if (adjust < 0) { if (F[M] > -adjust && (loop == 1 || F[M]/2 >= -adjust)) { F[M] += adjust; } else { if (loop < 1) { loop++; goto again; } adjust += F[M]-1; F[M] = 1; for (j = 0; adjust && j < 256; j++) { if (F[j] < 2) continue; int d = F[j] > -adjust; int m = d ? adjust : 1-F[j]; F[j] += m; adjust -= m; } } } //printf("F[%d]=%d\n", M, F[M]); return F[M]>0 ? 0 : -1; } // A specialised version of normalise_freq_shift where the input size // is already normalised to a power of 2, meaning we can just perform // shifts instead of hard to define multiplications and adjustments. static inline void normalise_freq_shift(uint32_t *F, uint32_t size, uint32_t max_tot) { if (size == 0 || size == max_tot) return; int shift = 0, i; while (size < max_tot) size*=2, shift++; for (i = 0; i < 256; i++) F[i] <<= shift; } // symbols only static inline int encode_alphabet(uint8_t *cp, uint32_t *F) { uint8_t *op = cp; int rle, j; for (rle = j = 0; j < 256; j++) { if (F[j]) { // j if (rle) { rle--; } else { *cp++ = j; if (!rle && j && F[j-1]) { for(rle=j+1; rle<256 && F[rle]; rle++) ; rle -= j+1; *cp++ = rle; } //fprintf(stderr, "%d: %d %d\n", j, rle, N[j]); } } } *cp++ = 0; return cp - op; } static inline int decode_alphabet(uint8_t *cp, uint8_t *cp_end, uint32_t *F) { if (cp == cp_end) return 0; uint8_t *op = cp; int rle = 0; int j = *cp++; if (cp+2 >= cp_end) goto carefully; do { F[j] = 1; if (!rle && j+1 == *cp) { j = *cp++; rle = *cp++; } else if (rle) { rle--; j++; if (j > 255) return 0; } else { j = *cp++; } } while(j && cp+2 < cp_end); carefully: if (j) { do { F[j] = 1; if(cp >= cp_end) return 0; if (!rle && j+1 == *cp) { if (cp+1 >= cp_end) return 0; j = *cp++; rle = *cp++; } else if (rle) { rle--; j++; if (j > 255) return 0; } else { if (cp >= cp_end) return 0; j = *cp++; } } while(j && cp < cp_end); } return cp - op; } static inline int encode_freq(uint8_t *cp, uint32_t *F) { uint8_t *op = cp; int j; cp += encode_alphabet(cp, F); for (j = 0; j < 256; j++) { if (F[j]) cp += var_put_u32(cp, NULL, F[j]); } return cp - op; } static inline int decode_freq(uint8_t *cp, uint8_t *cp_end, uint32_t *F, uint32_t *fsum) { if (cp == cp_end) return 0; uint8_t *op = cp; cp += decode_alphabet(cp, cp_end, F); int j, tot = 0; for (j = 0; j < 256; j++) { if (F[j]) { cp += var_get_u32(cp, cp_end, (unsigned int *)&F[j]); tot += F[j]; } } *fsum = tot; return cp - op; } // Use the order-0 freqs in F0 to encode the order-1 stats in F. // All symbols present in F are present in F0, but some in F0 will // be empty in F. Thus we run-length encode the 0 frequencies. static inline int encode_freq_d(uint8_t *cp, uint32_t *F0, uint32_t *F) { uint8_t *op = cp; int j, dz; for (dz = j = 0; j < 256; j++) { if (F0[j]) { if (F[j] != 0) { if (dz) { // Replace dz zeros with zero + dz-1 run length cp -= dz-1; *cp++ = dz-1; } dz = 0; cp += var_put_u32(cp, NULL, F[j]); } else { //fprintf(stderr, "2: j=%d F0[j]=%d, F[j]=%d, dz=%d\n", j, F0[j], F[j], dz); dz++; *cp++ = 0; } } } if (dz) { cp -= dz-1; *cp++ = dz-1; } return cp - op; } // Normalise frequency total T[i] to match TOTFREQ_O1 and encode. // Also initialises the RansEncSymbol structs. // // Returns the desired TF_SHIFT; 10 or 12 bit, or -1 on error. static inline int encode_freq1(uint8_t *in, uint32_t in_size, int Nway, RansEncSymbol syms[256][256], uint8_t **cp_p) { int i, j, z; uint8_t *out = *cp_p, *cp = out; // Compute O1 frequency statistics uint32_t (*F)[256] = htscodecs_tls_calloc(256, (sizeof(*F))); if (!F) return -1; uint32_t T[256+MAGIC] = {0}; int isz4 = in_size/Nway; if (hist1_4(in, in_size, F, T) < 0) goto err; for (z = 1; z < Nway; z++) F[0][in[z*isz4]]++; T[0]+=Nway-1; // Potential fix for the wrap-around bug in AVX2 O1 encoder with shift=12. // This occurs when we have one single symbol, giving freq=4096. // We fix it elsewhere for now by looking for the wrap-around. // See "if (1)" statements in the AVX2 code, which is an alternative // to the "if (0)" here. // if (0) { // int x = -1, y = -1; // int n1, n2; // for (x = 0; x < 256; x++) { // n1 = n2 = -1; // for (y = 0; y < 256; y++) { // if (F[x][y]) // n2 = n1, n1 = y; // } // if (n2!=-1 || n1 == -1) // continue; // // for (y = 0; y < 256; y++) // if (!F[x][y]) // break; // assert(y<256); // F[x][y]++; // F[0][y]++; T[y]++; F0[y]=1; // F[0][x]++; T[x]++; F0[x]=1; // } // } // Encode the order-0 stats int tmp_T0 = T[0]; T[0] = 1; *cp++ = 0; // marker for uncompressed (may change) cp += encode_alphabet(cp, T); T[0] = tmp_T0; // Decide between 10-bit and 12-bit freqs. // Fills out S[] to hold the new scaled maximum value. uint32_t S[256] = {0}; int shift = rans_compute_shift(T, F, T, S); // Normalise so T[i] == TOTFREQ_O1 for (i = 0; i < 256; i++) { unsigned int x; if (T[i] == 0) continue; uint32_t max_val = S[i]; if (shift == TF_SHIFT_O1_FAST && max_val > TOTFREQ_O1_FAST) max_val = TOTFREQ_O1_FAST; if (normalise_freq(F[i], T[i], max_val) < 0) goto err; T[i]=max_val; // Encode our frequency array cp += encode_freq_d(cp, T, F[i]); normalise_freq_shift(F[i], T[i], 1< 1000) { uint8_t *op = out; // try rans0 compression of header unsigned int u_freq_sz = cp-(op+1); unsigned int c_freq_sz; unsigned char *c_freq = rans_compress_O0_4x16(op+1, u_freq_sz, NULL, &c_freq_sz); if (c_freq && c_freq_sz + 6 < cp-op) { *op++ |= 1; // compressed op += var_put_u32(op, NULL, u_freq_sz); op += var_put_u32(op, NULL, c_freq_sz); memcpy(op, c_freq, c_freq_sz); cp = op+c_freq_sz; } free(c_freq); } *cp_p = cp; htscodecs_tls_free(F); return shift; err: htscodecs_tls_free(F); return -1; } // Part of decode_freq1 below. This decodes an order-1 frequency table // using an order-0 table to determine which stats may be stored. static inline int decode_freq_d(uint8_t *cp, uint8_t *cp_end, uint32_t *F0, uint32_t *F, uint32_t *total) { if (cp == cp_end) return 0; uint8_t *op = cp; int j, dz, T = 0; for (j = dz = 0; j < 256 && cp < cp_end; j++) { //if (F0[j]) fprintf(stderr, "F0[%d]=%d\n", j, F0[j]); if (!F0[j]) continue; uint32_t f; if (dz) { f = 0; dz--; } else { if (cp >= cp_end) return 0; cp += var_get_u32(cp, cp_end, &f); if (f == 0) { if (cp >= cp_end) return 0; dz = *cp++; } } F[j] = f; T += f; } if (total) *total = T; return cp - op; } typedef struct { uint16_t f; uint16_t b; } fb_t; // Decode order-1 frequency table, filling out various lookup tables // in the process. (Which will depend on shift and which values have // been passed in.) // // Returns the number of bytes decoded. static inline int decode_freq1(uint8_t *cp, uint8_t *cp_end, int shift, uint32_t s3 [256][TOTFREQ_O1], uint32_t s3F[256][TOTFREQ_O1_FAST], uint8_t *sfb[256], fb_t fb[256][256]) { uint8_t *cp_start = cp; int i, j, x; uint32_t F0[256] = {0}; int fsz = decode_alphabet(cp, cp_end, F0); if (!fsz) goto err; cp += fsz; if (cp >= cp_end) goto err; // silence false gcc warnings if (fb) {fb [0][0].b= 0;} if (s3) {s3 [0][0] = 0;} if (s3F){s3F[0][0] = 0;} for (i = 0; i < 256; i++) { if (F0[i] == 0) continue; uint32_t F[256] = {0}, T = 0; fsz = decode_freq_d(cp, cp_end, F0, F, &T); if (!fsz) goto err; cp += fsz; if (!T) { //fprintf(stderr, "No freq for F_%d\n", i); continue; } normalise_freq_shift(F, T, 1< (1< // Our own implementation of _mm256_set_m128i as it's not there on older // gcc implementations. This is basically the same thing. static inline __m256i _mm256_set_m128ix(__m128i H, __m128i L) { return _mm256_insertf128_si256(_mm256_castsi128_si256(L), H, 1); } static inline void rot32_simd(uint8_t t[32][32], uint8_t *out, int iN[32]) { int z; __m256i lh8[32]; for (z = 0; z < 32/2; z+=2) { __m256i a, b, c, d; a = _mm256_loadu_si256((__m256i *)&t[z*2+0]); b = _mm256_loadu_si256((__m256i *)&t[z*2+1]); c = _mm256_loadu_si256((__m256i *)&t[z*2+2]); d = _mm256_loadu_si256((__m256i *)&t[z*2+3]); lh8[z+0] = _mm256_unpacklo_epi8(a, b); lh8[z+16] = _mm256_unpackhi_epi8(a, b); lh8[z+1] = _mm256_unpacklo_epi8(c, d); lh8[z+17] = _mm256_unpackhi_epi8(c, d); } __m256i lh32[32]; for (z = 0; z < 32/4; z+=2) { __m256i a, b, c, d; a = _mm256_unpacklo_epi16(lh8[z*4+0], lh8[z*4+1]); b = _mm256_unpacklo_epi16(lh8[z*4+2], lh8[z*4+3]); c = _mm256_unpackhi_epi16(lh8[z*4+0], lh8[z*4+1]); d = _mm256_unpackhi_epi16(lh8[z*4+2], lh8[z*4+3]); __m256i e, f, g, h; e = _mm256_unpacklo_epi16(lh8[(z+1)*4+0], lh8[(z+1)*4+1]); f = _mm256_unpacklo_epi16(lh8[(z+1)*4+2], lh8[(z+1)*4+3]); g = _mm256_unpackhi_epi16(lh8[(z+1)*4+0], lh8[(z+1)*4+1]); h = _mm256_unpackhi_epi16(lh8[(z+1)*4+2], lh8[(z+1)*4+3]); lh32[z+0] = _mm256_unpacklo_epi32(a,b); lh32[z+8] = _mm256_unpacklo_epi32(c,d); lh32[z+16] = _mm256_unpackhi_epi32(a,b); lh32[z+24] = _mm256_unpackhi_epi32(c,d); lh32[z+1+0] = _mm256_unpacklo_epi32(e,f); lh32[z+1+8] = _mm256_unpacklo_epi32(g,h); lh32[z+1+16] = _mm256_unpackhi_epi32(e,f); lh32[z+1+24] = _mm256_unpackhi_epi32(g,h); } // Final unpack 64 and store int idx[] = {0, 8, 4, 12, 2, 10, 6, 14}; for (z = 0; z < 8; z++) { int i = idx[z]; // Putting this here doesn't soeed things up __m256i a = _mm256_unpacklo_epi64(lh32[i*2+0], lh32[i*2+1]); __m256i b = _mm256_unpacklo_epi64(lh32[i*2+2], lh32[i*2+3]); __m256i c = _mm256_unpackhi_epi64(lh32[i*2+0], lh32[i*2+1]); __m256i d = _mm256_unpackhi_epi64(lh32[i*2+2], lh32[i*2+3]); __m256i p = _mm256_set_m128ix(_mm256_extracti128_si256(b,0), _mm256_extracti128_si256(a,0)); __m256i q = _mm256_set_m128ix(_mm256_extracti128_si256(d,0), _mm256_extracti128_si256(c,0)); __m256i r = _mm256_set_m128ix(_mm256_extracti128_si256(b,1), _mm256_extracti128_si256(a,1)); __m256i s = _mm256_set_m128ix(_mm256_extracti128_si256(d,1), _mm256_extracti128_si256(c,1)); _mm256_storeu_si256((__m256i *)(&out[iN[z*2+0]]), p); _mm256_storeu_si256((__m256i *)(&out[iN[z*2+1]]), q); _mm256_storeu_si256((__m256i *)(&out[iN[z*2+16]]), r); _mm256_storeu_si256((__m256i *)(&out[iN[z*2+17]]), s); } // Store for (z = 0; z < 32; z++) iN[z] += 32; } #endif #endif // RANS_INTERNAL_H pysam-0.23.0/htslib/htscodecs/htscodecs/rANS_static32x16pr.c000066400000000000000000000604401475062545500235550ustar00rootroot00000000000000/* * Copyright (c) 2017-2023 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #include "config.h" #include #include #include #include #include #include #include "rANS_word.h" #include "rANS_static4x16.h" #include "rANS_static16_int.h" #include "varint.h" #include "utils.h" #define TF_SHIFT 12 #define TOTFREQ (1< *out_size) return NULL; // If "out" isn't word aligned, tweak out_end/ptr to ensure it is. // We already added more round in bound to allow for this. if (((size_t)out)&1) bound--; ptr = out_end = out + bound; if (in_size == 0) goto empty; // Compute statistics double e = hist8e(in, in_size, F); int low_ent = e < 2; // Normalise so frequences sum to power of 2 uint32_t fsum = in_size; uint32_t max_val = round2(fsum); if (max_val > TOTFREQ) max_val = TOTFREQ; if (normalise_freq(F, fsum, max_val) < 0) { free(out_free); return NULL; } fsum=max_val; cp = out; cp += encode_freq(cp, F); tab_size = cp-out; //write(2, out+4, cp-(out+4)); if (normalise_freq(F, fsum, TOTFREQ) < 0) { free(out_free); return NULL; } // Encode statistics. for (x = j = 0; j < 256; j++) { if (F[j]) { RansEncSymbolInit(&syms[j], x, F[j], TF_SHIFT); x += F[j]; } } for (z = 0; z < NX; z++) RansEncInit(&ransN[z]); z = i = in_size&(NX-1); while (z-- > 0) RansEncPutSymbol(&ransN[z], &ptr, &syms[in[in_size-(i-z)]]); if (low_ent) { // orig // gcc 446 // clang 427 for (i=(in_size &~(NX-1)); likely(i>0); i-=NX) { for (z = NX-1; z >= 0; z-=4) { RansEncSymbol *s0 = &syms[in[i-(NX-z+0)]]; RansEncSymbol *s1 = &syms[in[i-(NX-z+1)]]; RansEncSymbol *s2 = &syms[in[i-(NX-z+2)]]; RansEncSymbol *s3 = &syms[in[i-(NX-z+3)]]; RansEncPutSymbol_branched(&ransN[z-0], &ptr, s0); RansEncPutSymbol_branched(&ransN[z-1], &ptr, s1); RansEncPutSymbol_branched(&ransN[z-2], &ptr, s2); RansEncPutSymbol_branched(&ransN[z-3], &ptr, s3); if (NX%8 == 0) { z -= 4; RansEncSymbol *s0 = &syms[in[i-(NX-z+0)]]; RansEncSymbol *s1 = &syms[in[i-(NX-z+1)]]; RansEncSymbol *s2 = &syms[in[i-(NX-z+2)]]; RansEncSymbol *s3 = &syms[in[i-(NX-z+3)]]; RansEncPutSymbol_branched(&ransN[z-0], &ptr, s0); RansEncPutSymbol_branched(&ransN[z-1], &ptr, s1); RansEncPutSymbol_branched(&ransN[z-2], &ptr, s2); RansEncPutSymbol_branched(&ransN[z-3], &ptr, s3); } } if (z < -1) abort(); } } else { // Branchless version optimises poorly with gcc unless we have // AVX2 capability, so have a custom rewrite of it. uint16_t* ptr16 = (uint16_t *)ptr; for (i=(in_size &~(NX-1)); likely(i>0); i-=NX) { // Unrolled copy of below, because gcc doesn't optimise this // well in the original form. // // Gcc11: 328 MB/s (this) vs 208 MB/s (orig) // Clang10: 352 MB/s (this) vs 340 MB/s (orig) // // for (z = NX-1; z >= 0; z-=4) { // RansEncSymbol *s0 = &syms[in[i-(NX-z+0)]]; // RansEncSymbol *s1 = &syms[in[i-(NX-z+1)]]; // RansEncSymbol *s2 = &syms[in[i-(NX-z+2)]]; // RansEncSymbol *s3 = &syms[in[i-(NX-z+3)]]; // RansEncPutSymbol(&ransN[z-0], &ptr, s0); // RansEncPutSymbol(&ransN[z-1], &ptr, s1); // RansEncPutSymbol(&ransN[z-2], &ptr, s2); // RansEncPutSymbol(&ransN[z-3], &ptr, s3); // } for (z = NX-1; z >= 0; z-=4) { // RansEncPutSymbol added in-situ RansState *rp = &ransN[z]-3; RansEncSymbol *sy[4]; uint8_t *C = &in[i-(NX-z)]-3; sy[0] = &syms[C[3]]; sy[1] = &syms[C[2]]; int c0 = rp[3-0] > sy[0]->x_max; int c1 = rp[3-1] > sy[1]->x_max; #ifdef HTSCODECS_LITTLE_ENDIAN ptr16[-1] = rp[3-0]; ptr16 -= c0; ptr16[-1] = rp[3-1]; ptr16 -= c1; #else ((uint8_t *)&ptr16[-1])[0] = rp[3-0]; ((uint8_t *)&ptr16[-1])[1] = rp[3-0]>>8; ptr16 -= c0; ((uint8_t *)&ptr16[-1])[0] = rp[3-1]; ((uint8_t *)&ptr16[-1])[1] = rp[3-1]>>8; ptr16 -= c1; #endif rp[3-0] = c0 ? rp[3-0]>>16 : rp[3-0]; rp[3-1] = c1 ? rp[3-1]>>16 : rp[3-1]; sy[2] = &syms[C[1]]; sy[3] = &syms[C[0]]; int c2 = rp[3-2] > sy[2]->x_max; int c3 = rp[3-3] > sy[3]->x_max; #ifdef HTSCODECS_LITTLE_ENDIAN ptr16[-1] = rp[3-2]; ptr16 -= c2; ptr16[-1] = rp[3-3]; ptr16 -= c3; #else ((uint8_t *)&ptr16[-1])[0] = rp[3-2]; ((uint8_t *)&ptr16[-1])[1] = rp[3-2]>>8; ptr16 -= c2; ((uint8_t *)&ptr16[-1])[0] = rp[3-3]; ((uint8_t *)&ptr16[-1])[1] = rp[3-3]>>8; ptr16 -= c3; #endif rp[3-2] = c2 ? rp[3-2]>>16 : rp[3-2]; rp[3-3] = c3 ? rp[3-3]>>16 : rp[3-3]; int k; for (k = 0; k < 4; k++) { uint64_t r64 = (uint64_t)rp[3-k]; uint32_t q = (r64 * sy[k]->rcp_freq) >> sy[k]->rcp_shift; rp[3-k] += sy[k]->bias + q*sy[k]->cmpl_freq; } } if (z < -1) abort(); } ptr = (uint8_t *)ptr16; } for (z = NX-1; z >= 0; z--) RansEncFlush(&ransN[z], &ptr); empty: // Finalise block size and return it *out_size = (out_end - ptr) + tab_size; memmove(out + tab_size, ptr, out_end-ptr); return out; } unsigned char *rans_uncompress_O0_32x16(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { if (in_size < 16) // 4-states at least return NULL; if (out_sz >= INT_MAX) return NULL; // protect against some overflow cases #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (out_sz > 100000) return NULL; #endif /* Load in the static tables */ unsigned char *cp = in, *out_free = NULL; unsigned char *cp_end = in + in_size; int i; uint32_t s3[TOTFREQ]; // For TF_SHIFT <= 12 if (!out) out_free = out = malloc(out_sz); if (!out) return NULL; // Precompute reverse lookup of frequency. uint32_t F[256] = {0}, fsum; int fsz = decode_freq(cp, cp_end, F, &fsum); if (!fsz) goto err; cp += fsz; normalise_freq_shift(F, fsum, TOTFREQ); // Build symbols; fixme, do as part of decode, see the _d variant if (rans_F_to_s3(F, TF_SHIFT, s3)) goto err; if (cp_end - cp < NX * 4) goto err; int z; RansState R[NX]; for (z = 0; z < NX; z++) { RansDecInit(&R[z], &cp); if (R[z] < RANS_BYTE_L) goto err; } int out_end = (out_sz&~(NX-1)); const uint32_t mask = (1u << TF_SHIFT)-1; cp_end -= NX*2; // worst case for renorm bytes // assume NX is divisible by 4 assert(NX%4==0); // Unsafe loop with no ptr overflow checking within loop itself for (i=0; likely(i < out_end && cp < cp_end); i+=NX) { for (z = 0; z < NX; z+=4) { uint32_t S[4]; S[0] = s3[R[z+0] & mask]; S[1] = s3[R[z+1] & mask]; S[2] = s3[R[z+2] & mask]; S[3] = s3[R[z+3] & mask]; R[z+0] = (S[0]>>(TF_SHIFT+8)) * (R[z+0] >> TF_SHIFT) + ((S[0]>>8) & mask); R[z+1] = (S[1]>>(TF_SHIFT+8)) * (R[z+1] >> TF_SHIFT) + ((S[1]>>8) & mask); R[z+2] = (S[2]>>(TF_SHIFT+8)) * (R[z+2] >> TF_SHIFT) + ((S[2]>>8) & mask); R[z+3] = (S[3]>>(TF_SHIFT+8)) * (R[z+3] >> TF_SHIFT) + ((S[3]>>8) & mask); out[i+z+0] = S[0]; out[i+z+1] = S[1]; out[i+z+2] = S[2]; out[i+z+3] = S[3]; RansDecRenorm(&R[z+0], &cp); RansDecRenorm(&R[z+1], &cp); RansDecRenorm(&R[z+2], &cp); RansDecRenorm(&R[z+3], &cp); if (NX%8==0) { z += 4; S[0] = s3[R[z+0] & mask]; S[1] = s3[R[z+1] & mask]; S[2] = s3[R[z+2] & mask]; S[3] = s3[R[z+3] & mask]; R[z+0] = (S[0]>>(TF_SHIFT+8)) * (R[z+0] >> TF_SHIFT) + ((S[0]>>8) & mask); R[z+1] = (S[1]>>(TF_SHIFT+8)) * (R[z+1] >> TF_SHIFT) + ((S[1]>>8) & mask); R[z+2] = (S[2]>>(TF_SHIFT+8)) * (R[z+2] >> TF_SHIFT) + ((S[2]>>8) & mask); R[z+3] = (S[3]>>(TF_SHIFT+8)) * (R[z+3] >> TF_SHIFT) + ((S[3]>>8) & mask); out[i+z+0] = S[0]; out[i+z+1] = S[1]; out[i+z+2] = S[2]; out[i+z+3] = S[3]; RansDecRenorm(&R[z+0], &cp); RansDecRenorm(&R[z+1], &cp); RansDecRenorm(&R[z+2], &cp); RansDecRenorm(&R[z+3], &cp); } } } // Safe loop for (; i < out_end; i+=NX) { for (z = 0; z < NX; z+=4) { uint32_t S[4]; S[0] = s3[R[z+0] & mask]; S[1] = s3[R[z+1] & mask]; S[2] = s3[R[z+2] & mask]; S[3] = s3[R[z+3] & mask]; R[z+0] = (S[0]>>(TF_SHIFT+8)) * (R[z+0] >> TF_SHIFT) + ((S[0]>>8) & mask); R[z+1] = (S[1]>>(TF_SHIFT+8)) * (R[z+1] >> TF_SHIFT) + ((S[1]>>8) & mask); R[z+2] = (S[2]>>(TF_SHIFT+8)) * (R[z+2] >> TF_SHIFT) + ((S[2]>>8) & mask); R[z+3] = (S[3]>>(TF_SHIFT+8)) * (R[z+3] >> TF_SHIFT) + ((S[3]>>8) & mask); out[i+z+0] = S[0]; out[i+z+1] = S[1]; out[i+z+2] = S[2]; out[i+z+3] = S[3]; RansDecRenormSafe(&R[z+0], &cp, cp_end+NX*2); RansDecRenormSafe(&R[z+1], &cp, cp_end+NX*2); RansDecRenormSafe(&R[z+2], &cp, cp_end+NX*2); RansDecRenormSafe(&R[z+3], &cp, cp_end+NX*2); } } for (z = out_sz & (NX-1); z-- > 0; ) out[out_end + z] = s3[R[z] & mask]; //fprintf(stderr, " 0 Decoded %d bytes\n", (int)(cp-in)); //c-size return out; err: free(out_free); return NULL; } //----------------------------------------------------------------------------- unsigned char *rans_compress_O1_32x16(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { unsigned char *cp, *out_end, *out_free = NULL; unsigned int tab_size; int bound = rans_compress_bound_4x16(in_size,1)-20, z; RansState ransN[NX]; if (in_size < NX) // force O0 instead return NULL; if (!out) { *out_size = bound; out_free = out = malloc(*out_size); } if (!out || bound > *out_size) return NULL; if (((size_t)out)&1) bound--; out_end = out + bound; RansEncSymbol (*syms)[256] = htscodecs_tls_alloc(256 * (sizeof(*syms))); if (!syms) { free(out_free); return NULL; } cp = out; int shift = encode_freq1(in, in_size, 32, syms, &cp); if (shift < 0) { free(out_free); htscodecs_tls_free(syms); return NULL; } tab_size = cp - out; for (z = 0; z < NX; z++) RansEncInit(&ransN[z]); uint8_t* ptr = out_end; int iN[NX], isz4 = in_size/NX, i; for (z = 0; z < NX; z++) iN[z] = (z+1)*isz4-2; unsigned char lN[NX]; for (z = 0; z < NX; z++) lN[z] = in[iN[z]+1]; // Deal with the remainder z = NX-1; lN[z] = in[in_size-1]; for (iN[z] = in_size-2; iN[z] > NX*isz4-2; iN[z]--) { unsigned char c = in[iN[z]]; RansEncPutSymbol(&ransN[z], &ptr, &syms[c][lN[z]]); lN[z] = c; } unsigned char *i32[NX]; for (i = 0; i < NX; i++) i32[i] = &in[iN[i]]; for (; likely(i32[0] >= in); ) { uint16_t *ptr16 = (uint16_t *)ptr; for (z = NX-1; z >= 0; z-=4) { RansEncSymbol *sy[4]; int k; for (k = 0; k < 4; k++) { sy[k] = &syms[*i32[z-k]][lN[z-k]]; lN[z-k] = *i32[z-k]--; } // RansEncPutSymbol added in-situ for (k = 0; k < 4; k++) { int c = ransN[z-k] > sy[k]->x_max; #ifdef HTSCODECS_LITTLE_ENDIAN ptr16[-1] = ransN[z-k]; #else ((uint8_t *)&ptr16[-1])[0] = ransN[z-k]; ((uint8_t *)&ptr16[-1])[1] = ransN[z-k]>>8; #endif ptr16 -= c; //ransN[z-k] >>= c<<4; ransN[z-k] = c ? ransN[z-k]>>16 : ransN[z-k]; } for (k = 0; k < 4; k++) { uint64_t r64 = ransN[z-k]; uint32_t q = (r64 * sy[k]->rcp_freq) >> sy[k]->rcp_shift; ransN[z-k] += sy[k]->bias + q*sy[k]->cmpl_freq; } } ptr = (uint8_t *)ptr16; } for (z = NX-1; z>=0; z--) RansEncPutSymbol(&ransN[z], &ptr, &syms[0][lN[z]]); for (z = NX-1; z>=0; z--) RansEncFlush(&ransN[z], &ptr); *out_size = (out_end - ptr) + tab_size; cp = out; memmove(out + tab_size, ptr, out_end-ptr); htscodecs_tls_free(syms); return out; } //#define MAGIC2 111 #define MAGIC2 179 //#define MAGIC2 0 unsigned char *rans_uncompress_O1_32x16(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { if (in_size < NX*4) // 4-states at least return NULL; if (out_sz >= INT_MAX) return NULL; // protect against some overflow cases #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (out_sz > 100000) return NULL; #endif /* Load in the static tables */ unsigned char *cp = in, *cp_end = in+in_size, *out_free = NULL; unsigned char *c_freq = NULL; int i; /* * Somewhat complex memory layout. * With shift==12 (TF_SHIFT_O1) we fill out use both sfb and fb. * With shift==10 (...O1_FAST) we fill out and use s3 only. * * sfb+fb is larger, therefore we allocate this much memory. */ uint8_t *sfb_ = htscodecs_tls_alloc(256* ((TOTFREQ_O1+MAGIC2)*sizeof(*sfb_) +256 * sizeof(fb_t))); if (!sfb_) return NULL; // sfb and fb are consecutive uint8_t *sfb[257]; if ((*cp >> 4) == TF_SHIFT_O1) { for (i = 0; i <= 256; i++) sfb[i]= sfb_ + i*(TOTFREQ_O1+MAGIC2); } else { for (i = 0; i <= 256; i++) sfb[i]= sfb_ + i*(TOTFREQ_O1_FAST+MAGIC2); } fb_t (*fb)[256] = (fb_t (*)[256]) sfb[256]; // NOTE: s3 overlaps sfb/fb uint32_t (*s3)[TOTFREQ_O1_FAST] = (uint32_t (*)[TOTFREQ_O1_FAST])sfb_; if (!out) out_free = out = malloc(out_sz); if (!out) goto err; //fprintf(stderr, "out_sz=%d\n", out_sz); // compressed header? If so uncompress it unsigned char *tab_end = NULL; unsigned char *c_freq_end = cp_end; unsigned int shift = *cp >> 4; if (*cp++ & 1) { uint32_t u_freq_sz, c_freq_sz; cp += var_get_u32(cp, cp_end, &u_freq_sz); cp += var_get_u32(cp, cp_end, &c_freq_sz); if (c_freq_sz > cp_end - cp) goto err; tab_end = cp + c_freq_sz; if (!(c_freq = rans_uncompress_O0_4x16(cp, c_freq_sz, NULL,u_freq_sz))) goto err; cp = c_freq; c_freq_end = c_freq + u_freq_sz; } // Decode order-0 symbol list; avoids needing in order-1 tables cp += decode_freq1(cp, c_freq_end, shift, NULL, s3, sfb, fb); if (tab_end) cp = tab_end; free(c_freq); c_freq = NULL; if (cp_end - cp < NX * 4) goto err; RansState R[NX]; uint8_t *ptr = cp, *ptr_end = in + in_size - 2*NX; int z; for (z = 0; z < NX; z++) { RansDecInit(&R[z], &ptr); if (R[z] < RANS_BYTE_L) goto err; } int isz4 = out_sz/NX; int i4[NX], l[NX] = {0}; for (z = 0; z < NX; z++) i4[z] = z*isz4; const int low_ent = in_size < 0.2 * out_sz; // Around 15% faster to specialise for 10/12 than to have one // loop with shift as a variable. if (shift == TF_SHIFT_O1) { // TF_SHIFT_O1 = 12 const uint32_t mask = ((1u << TF_SHIFT_O1)-1); for (; likely(i4[0] < isz4);) { for (z = 0; z < NX; z+=4) { uint16_t m[4], c[4]; c[0] = sfb[l[z+0]][m[0] = R[z+0] & mask]; c[1] = sfb[l[z+1]][m[1] = R[z+1] & mask]; c[2] = sfb[l[z+2]][m[2] = R[z+2] & mask]; c[3] = sfb[l[z+3]][m[3] = R[z+3] & mask]; R[z+0] = fb[l[z+0]][c[0]].f * (R[z+0]>>TF_SHIFT_O1); R[z+0] += m[0] - fb[l[z+0]][c[0]].b; R[z+1] = fb[l[z+1]][c[1]].f * (R[z+1]>>TF_SHIFT_O1); R[z+1] += m[1] - fb[l[z+1]][c[1]].b; R[z+2] = fb[l[z+2]][c[2]].f * (R[z+2]>>TF_SHIFT_O1); R[z+2] += m[2] - fb[l[z+2]][c[2]].b; R[z+3] = fb[l[z+3]][c[3]].f * (R[z+3]>>TF_SHIFT_O1); R[z+3] += m[3] - fb[l[z+3]][c[3]].b; out[i4[z+0]++] = l[z+0] = c[0]; out[i4[z+1]++] = l[z+1] = c[1]; out[i4[z+2]++] = l[z+2] = c[2]; out[i4[z+3]++] = l[z+3] = c[3]; if (!low_ent && likely(ptr < ptr_end)) { RansDecRenorm(&R[z+0], &ptr); RansDecRenorm(&R[z+1], &ptr); RansDecRenorm(&R[z+2], &ptr); RansDecRenorm(&R[z+3], &ptr); } else { RansDecRenormSafe(&R[z+0], &ptr, ptr_end+2*NX); RansDecRenormSafe(&R[z+1], &ptr, ptr_end+2*NX); RansDecRenormSafe(&R[z+2], &ptr, ptr_end+2*NX); RansDecRenormSafe(&R[z+3], &ptr, ptr_end+2*NX); } } } // Remainder for (; i4[NX-1] < out_sz; i4[NX-1]++) { uint32_t m = R[NX-1] & ((1u<>TF_SHIFT_O1) + m - fb[l[NX-1]][c].b; RansDecRenormSafe(&R[NX-1], &ptr, ptr_end + 2*NX); l[NX-1] = c; } } else { // TF_SHIFT_O1 = 10 const uint32_t mask = ((1u << TF_SHIFT_O1_FAST)-1); for (; likely(i4[0] < isz4);) { for (z = 0; z < NX; z+=4) { // Merged sfb and fb into single s3 lookup. // The m[4] array completely vanishes in this method. uint32_t S[4] = { s3[l[z+0]][R[z+0] & mask], s3[l[z+1]][R[z+1] & mask], s3[l[z+2]][R[z+2] & mask], s3[l[z+3]][R[z+3] & mask], }; l[z+0] = out[i4[z+0]++] = S[0]; l[z+1] = out[i4[z+1]++] = S[1]; l[z+2] = out[i4[z+2]++] = S[2]; l[z+3] = out[i4[z+3]++] = S[3]; uint32_t F[4] = { S[0]>>(TF_SHIFT_O1_FAST+8), S[1]>>(TF_SHIFT_O1_FAST+8), S[2]>>(TF_SHIFT_O1_FAST+8), S[3]>>(TF_SHIFT_O1_FAST+8), }; uint32_t B[4] = { (S[0]>>8) & mask, (S[1]>>8) & mask, (S[2]>>8) & mask, (S[3]>>8) & mask, }; R[z+0] = F[0] * (R[z+0]>>TF_SHIFT_O1_FAST) + B[0]; R[z+1] = F[1] * (R[z+1]>>TF_SHIFT_O1_FAST) + B[1]; R[z+2] = F[2] * (R[z+2]>>TF_SHIFT_O1_FAST) + B[2]; R[z+3] = F[3] * (R[z+3]>>TF_SHIFT_O1_FAST) + B[3]; if (!low_ent && (ptr < ptr_end)) { // branchless & asm RansDecRenorm(&R[z+0], &ptr); RansDecRenorm(&R[z+1], &ptr); RansDecRenorm(&R[z+2], &ptr); RansDecRenorm(&R[z+3], &ptr); } else { // branched, but better when predictable RansDecRenormSafe(&R[z+0], &ptr, ptr_end+2*NX); RansDecRenormSafe(&R[z+1], &ptr, ptr_end+2*NX); RansDecRenormSafe(&R[z+2], &ptr, ptr_end+2*NX); RansDecRenormSafe(&R[z+3], &ptr, ptr_end+2*NX); } } } // Remainder for (; i4[NX-1] < out_sz; i4[NX-1]++) { uint32_t S = s3[l[NX-1]][R[NX-1] & ((1u<>(TF_SHIFT_O1_FAST+8)) * (R[NX-1]>>TF_SHIFT_O1_FAST) + ((S>>8) & ((1u< #include #include #include #include #include #include "rANS_word.h" #include "rANS_static4x16.h" #define ROT32_SIMD #include "rANS_static16_int.h" #include "varint.h" #include "utils.h" #include "permute.h" #define NX 32 #define LOAD1(a,b) __m256i a##1 = _mm256_load_si256((__m256i *)&b[0]); #define LOAD2(a,b) __m256i a##2 = _mm256_load_si256((__m256i *)&b[8]); #define LOAD3(a,b) __m256i a##3 = _mm256_load_si256((__m256i *)&b[16]); #define LOAD4(a,b) __m256i a##4 = _mm256_load_si256((__m256i *)&b[24]); #define LOAD(a,b) LOAD1(a,b);LOAD2(a,b);LOAD3(a,b);LOAD4(a,b) #define STORE1(a,b) _mm256_store_si256((__m256i *)&b[0], a##1); #define STORE2(a,b) _mm256_store_si256((__m256i *)&b[8], a##2); #define STORE3(a,b) _mm256_store_si256((__m256i *)&b[16], a##3); #define STORE4(a,b) _mm256_store_si256((__m256i *)&b[24], a##4); #define STORE(a,b) STORE1(a,b);STORE2(a,b);STORE3(a,b);STORE4(a,b) // _mm256__mul_epu32 is: // -b -d -f -h //* -q -s -u -w //= BQ DS FU HW where BQ=b*q etc // // We want // abcd efgh (a) // *pqrs tuvw (b) // =ABCD EFGH // // a mul b => BQ DS FU HW // >>= 8 => -B QD SF UH // & => -B -D -F -H (1) // a>>8 mul b>>8 => AP CR ET GV // & => A- C- E- G- // | with (1) => AB CD EF GH #if 0 static __m256i _mm256_mulhi_epu32(__m256i a, __m256i b) { __m256i ab_lm = _mm256_mul_epu32(a, b); ab_lm = _mm256_srli_epi64(ab_lm, 32); a = _mm256_srli_epi64(a, 32); ab_lm = _mm256_and_si256(ab_lm, _mm256_set1_epi64x(0xffffffff)); b = _mm256_srli_epi64(b, 32); __m256i ab_hm = _mm256_mul_epu32(a, b); //return _mm256_blend_epi32(ab_lm, ab_hm, 0xaa); ab_hm = _mm256_and_si256(ab_hm, _mm256_set1_epi64x((uint64_t)0xffffffff00000000)); ab_hm = _mm256_or_si256(ab_hm, ab_lm); return ab_hm; } #else static inline __m256i _mm256_mulhi_epu32(__m256i a, __m256i b) { // Multiply bottom 4 items and top 4 items together. __m256i ab_hm = _mm256_mul_epu32(_mm256_srli_epi64(a, 32), _mm256_srli_epi64(b, 32)); __m256i ab_lm = _mm256_srli_epi64(_mm256_mul_epu32(a, b), 32); return _mm256_blend_epi32(ab_lm, ab_hm, 0xaa); // // // Shift to get hi 32-bit of each 64-bit product // ab_hm = _mm256_and_si256(ab_hm, // _mm256_set1_epi64x((uint64_t)0xffffffff00000000)); // // return _mm256_or_si256(ab_lm, ab_hm); } #endif #ifndef USE_GATHER // Simulated gather. This is sometimes faster if gathers are slow, either // due to the particular implementation (maybe on Zen4) or because of // a microcode patch such as Intel's Downfall fix. static inline __m256i _mm256_i32gather_epi32x(int *b, __m256i idx, int size) { volatile // force the store to happen, hence forcing scalar loads int c[8] __attribute__((aligned(32))); _mm256_store_si256((__m256i *)c, idx); // Fast with modern gccs, and no change with clang. // Equivalent to: // return _mm256_set_epi32(b[c[7]], b[c[6]], b[c[5]], b[c[4]], // b[c[3]], b[c[2]], b[c[1]], b[c[0]]); register int bc1 = b[c[1]]; register int bc3 = b[c[3]]; register int bc5 = b[c[5]]; register int bc7 = b[c[7]]; __m128i x0a = _mm_cvtsi32_si128(b[c[0]]); __m128i x1a = _mm_cvtsi32_si128(b[c[2]]); __m128i x2a = _mm_cvtsi32_si128(b[c[4]]); __m128i x3a = _mm_cvtsi32_si128(b[c[6]]); __m128i x0 = _mm_insert_epi32(x0a, bc1, 1); __m128i x1 = _mm_insert_epi32(x1a, bc3, 1); __m128i x2 = _mm_insert_epi32(x2a, bc5, 1); __m128i x3 = _mm_insert_epi32(x3a, bc7, 1); __m128i x01 = _mm_unpacklo_epi64(x0, x1); __m128i x23 = _mm_unpacklo_epi64(x2, x3); __m256i y =_mm256_castsi128_si256(x01); return _mm256_inserti128_si256(y, x23, 1); } #else #define _mm256_i32gather_epi32x _mm256_i32gather_epi32 #endif unsigned char *rans_compress_O0_32x16_avx2(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { unsigned char *cp, *out_end; RansEncSymbol syms[256]; RansState ransN[NX] __attribute__((aligned(32))); uint8_t* ptr; uint32_t F[256+MAGIC] = {0}; int i, j, tab_size = 0, x, z; // -20 for order/size/meta uint32_t bound = rans_compress_bound_4x16(in_size,0)-20; if (!out) { *out_size = bound; out = malloc(*out_size); } if (!out || bound > *out_size) return NULL; // If "out" isn't word aligned, tweak out_end/ptr to ensure it is. // We already added more round in bound to allow for this. if (((size_t)out)&1) bound--; ptr = out_end = out + bound; if (in_size == 0) goto empty; // Compute statistics if (hist8(in, in_size, F) < 0) return NULL; // Normalise so frequences sum to power of 2 uint32_t fsum = in_size; uint32_t max_val = round2(fsum); if (max_val > TOTFREQ) max_val = TOTFREQ; if (normalise_freq(F, fsum, max_val) < 0) return NULL; fsum=max_val; cp = out; cp += encode_freq(cp, F); tab_size = cp-out; //write(2, out+4, cp-(out+4)); if (normalise_freq(F, fsum, TOTFREQ) < 0) return NULL; // Encode statistics. for (x = j = 0; j < 256; j++) { if (F[j]) { RansEncSymbolInit(&syms[j], x, F[j], TF_SHIFT); x += F[j]; } } for (z = 0; z < NX; z++) RansEncInit(&ransN[z]); z = i = in_size&(NX-1); while (z-- > 0) RansEncPutSymbol(&ransN[z], &ptr, &syms[in[in_size-(i-z)]]); uint16_t *ptr16 = (uint16_t *)ptr; LOAD(Rv, ransN); for (i=(in_size &~(NX-1)); i>0; i-=NX) { // We need to gather sym[curr_char][last_char] structs. // These hold 4 32-bit values, so are 128 bit each, and // are loaded from 32 distinct addresses. // // We load them into 32 128-bit lanes and then combine to get // 16 avx-256 registers. // These are now ABCD ABCD ABCD ABCD... orientation // We can then "gather" from these registers via a combination // of shuffle / permutes / and / or operations. This is less // IO than repeating 4 sets of gathers/loads 32-times over. // DCBA holding 4 elements in a syms[] array // -> 4-way rotate via shuffles // [0] DCBA 11 10 01 00 E4 // [1] CBAD 10 01 00 11 93 // [2] BADC 01 00 11 10 4E // [3] ADCB 00 11 10 01 39 // // Then AND to select relevant lanes and OR // [0] ......A0 // [1] ....A1.. // [2] ..A2.... // [3] A3...... OR to get A3A2A1A0 // // or: // [0] ....B0.. // [1] ..B1.... // [2] B2...... // [3] ......B3 OR to get B2B1B0B3 and shuffle to B3B2B1B0 __m256i sh[16]; for (z = 0; z < 16; z+=4) { int Z = i - NX + z*2; #define m128_to_256 _mm256_castsi128_si256 __m256i t0, t1, t2, t3; __m128i *s0, *s1, *s2, *s3; s0 = (__m128i *)(&syms[in[Z+0]]); s1 = (__m128i *)(&syms[in[Z+4]]); s2 = (__m128i *)(&syms[in[Z+1]]); s3 = (__m128i *)(&syms[in[Z+5]]); // FIXME: try load instead of loadu, as 128-bit aligned. t0 = _mm256_shuffle_epi32(m128_to_256(_mm_loadu_si128(s0)), 0xE4); t1 = _mm256_shuffle_epi32(m128_to_256(_mm_loadu_si128(s1)), 0xE4); t2 = _mm256_shuffle_epi32(m128_to_256(_mm_loadu_si128(s2)), 0x93); t3 = _mm256_shuffle_epi32(m128_to_256(_mm_loadu_si128(s3)), 0x93); sh[z+0] = _mm256_permute2x128_si256(t0, t1, 0x20); sh[z+1] = _mm256_permute2x128_si256(t2, t3, 0x20); s0 = (__m128i *)(&syms[in[Z+2]]); s1 = (__m128i *)(&syms[in[Z+6]]); s2 = (__m128i *)(&syms[in[Z+3]]); s3 = (__m128i *)(&syms[in[Z+7]]); t0 = _mm256_shuffle_epi32(m128_to_256(_mm_loadu_si128(s0)), 0x4E); t1 = _mm256_shuffle_epi32(m128_to_256(_mm_loadu_si128(s1)), 0x4E); t2 = _mm256_shuffle_epi32(m128_to_256(_mm_loadu_si128(s2)), 0x39); t3 = _mm256_shuffle_epi32(m128_to_256(_mm_loadu_si128(s3)), 0x39); sh[z+2] = _mm256_permute2x128_si256(t0, t1, 0x20); sh[z+3] = _mm256_permute2x128_si256(t2, t3, 0x20); // potential to set xmax, rf, bias, and SD in-situ here, removing // the need to hold sh[] in regs. Doing so doesn't seem to speed // things up though. } __m256i xA = _mm256_set_epi32(0,0,0,-1, 0,0,0,-1); __m256i xB = _mm256_set_epi32(0,0,-1,0, 0,0,-1,0); __m256i xC = _mm256_set_epi32(0,-1,0,0, 0,-1,0,0); __m256i xD = _mm256_set_epi32(-1,0,0,0, -1,0,0,0); #define SYM_LOAD(x, A, B, C, D) \ _mm256_or_si256(_mm256_or_si256(_mm256_and_si256(sh[x+0], A), \ _mm256_and_si256(sh[x+1], B)), \ _mm256_or_si256(_mm256_and_si256(sh[x+2], C), \ _mm256_and_si256(sh[x+3], D))) // Renorm: // if (x > x_max) {*--ptr16 = x & 0xffff; x >>= 16;} __m256i xmax1 = SYM_LOAD( 0, xA, xB, xC, xD); __m256i xmax2 = SYM_LOAD( 4, xA, xB, xC, xD); __m256i xmax3 = SYM_LOAD( 8, xA, xB, xC, xD); __m256i xmax4 = SYM_LOAD(12, xA, xB, xC, xD); __m256i cv1 = _mm256_cmpgt_epi32(Rv1, xmax1); __m256i cv2 = _mm256_cmpgt_epi32(Rv2, xmax2); __m256i cv3 = _mm256_cmpgt_epi32(Rv3, xmax3); __m256i cv4 = _mm256_cmpgt_epi32(Rv4, xmax4); // Store bottom 16-bits at ptr16 unsigned int imask1 = _mm256_movemask_ps((__m256)cv1); unsigned int imask2 = _mm256_movemask_ps((__m256)cv2); unsigned int imask3 = _mm256_movemask_ps((__m256)cv3); unsigned int imask4 = _mm256_movemask_ps((__m256)cv4); __m256i idx1 = _mm256_load_si256((const __m256i*)permutec[imask1]); __m256i idx2 = _mm256_load_si256((const __m256i*)permutec[imask2]); __m256i idx3 = _mm256_load_si256((const __m256i*)permutec[imask3]); __m256i idx4 = _mm256_load_si256((const __m256i*)permutec[imask4]); // Permute; to gather together the rans states that need flushing __m256i V1, V2, V3, V4; V1 = _mm256_permutevar8x32_epi32(_mm256_and_si256(Rv1, cv1), idx1); V2 = _mm256_permutevar8x32_epi32(_mm256_and_si256(Rv2, cv2), idx2); V3 = _mm256_permutevar8x32_epi32(_mm256_and_si256(Rv3, cv3), idx3); V4 = _mm256_permutevar8x32_epi32(_mm256_and_si256(Rv4, cv4), idx4); // We only flush bottom 16 bits, to squash 32-bit states into 16 bit. V1 = _mm256_and_si256(V1, _mm256_set1_epi32(0xffff)); V2 = _mm256_and_si256(V2, _mm256_set1_epi32(0xffff)); V3 = _mm256_and_si256(V3, _mm256_set1_epi32(0xffff)); V4 = _mm256_and_si256(V4, _mm256_set1_epi32(0xffff)); __m256i V12 = _mm256_packus_epi32(V1, V2); __m256i V34 = _mm256_packus_epi32(V3, V4); // It's BAba order, want BbAa so shuffle. V12 = _mm256_permute4x64_epi64(V12, 0xd8); V34 = _mm256_permute4x64_epi64(V34, 0xd8); // Now we have bottom N 16-bit values in each V12/V34 to flush __m128i f = _mm256_extractf128_si256(V34, 1); _mm_storeu_si128((__m128i *)(ptr16-8), f); ptr16 -= _mm_popcnt_u32(imask4); f = _mm256_extractf128_si256(V34, 0); _mm_storeu_si128((__m128i *)(ptr16-8), f); ptr16 -= _mm_popcnt_u32(imask3); f = _mm256_extractf128_si256(V12, 1); _mm_storeu_si128((__m128i *)(ptr16-8), f); ptr16 -= _mm_popcnt_u32(imask2); f = _mm256_extractf128_si256(V12, 0); _mm_storeu_si128((__m128i *)(ptr16-8), f); ptr16 -= _mm_popcnt_u32(imask1); __m256i Rs; Rs = _mm256_srli_epi32(Rv1,16); Rv1 = _mm256_blendv_epi8(Rv1, Rs, cv1); Rs = _mm256_srli_epi32(Rv2,16); Rv2 = _mm256_blendv_epi8(Rv2, Rs, cv2); Rs = _mm256_srli_epi32(Rv3,16); Rv3 = _mm256_blendv_epi8(Rv3, Rs, cv3); Rs = _mm256_srli_epi32(Rv4,16); Rv4 = _mm256_blendv_epi8(Rv4, Rs, cv4); // Cannot trivially replace the multiply as mulhi_epu32 doesn't // exist (only mullo). // However we can use _mm256_mul_epu32 twice to get 64bit results // (half our lanes) and shift/or to get the answer. // // (AVX512 allows us to hold it all in 64-bit lanes and use mullo_epi64 // plus a shift. KNC has mulhi_epi32, but not sure if this is // available.) __m256i rfv1 = _mm256_shuffle_epi32(SYM_LOAD( 0, xB, xC, xD, xA),0x39); __m256i rfv2 = _mm256_shuffle_epi32(SYM_LOAD( 4, xB, xC, xD, xA),0x39); __m256i rfv3 = _mm256_shuffle_epi32(SYM_LOAD( 8, xB, xC, xD, xA),0x39); __m256i rfv4 = _mm256_shuffle_epi32(SYM_LOAD(12, xB, xC, xD, xA),0x39); rfv1 = _mm256_mulhi_epu32(Rv1, rfv1); rfv2 = _mm256_mulhi_epu32(Rv2, rfv2); rfv3 = _mm256_mulhi_epu32(Rv3, rfv3); rfv4 = _mm256_mulhi_epu32(Rv4, rfv4); __m256i SDv1 = _mm256_shuffle_epi32(SYM_LOAD( 0, xD, xA, xB, xC),0x93); __m256i SDv2 = _mm256_shuffle_epi32(SYM_LOAD( 4, xD, xA, xB, xC),0x93); __m256i SDv3 = _mm256_shuffle_epi32(SYM_LOAD( 8, xD, xA, xB, xC),0x93); __m256i SDv4 = _mm256_shuffle_epi32(SYM_LOAD(12, xD, xA, xB, xC),0x93); __m256i shiftv1 = _mm256_srli_epi32(SDv1, 16); __m256i shiftv2 = _mm256_srli_epi32(SDv2, 16); __m256i shiftv3 = _mm256_srli_epi32(SDv3, 16); __m256i shiftv4 = _mm256_srli_epi32(SDv4, 16); shiftv1 = _mm256_sub_epi32(shiftv1, _mm256_set1_epi32(32)); shiftv2 = _mm256_sub_epi32(shiftv2, _mm256_set1_epi32(32)); shiftv3 = _mm256_sub_epi32(shiftv3, _mm256_set1_epi32(32)); shiftv4 = _mm256_sub_epi32(shiftv4, _mm256_set1_epi32(32)); __m256i qv1 = _mm256_srlv_epi32(rfv1, shiftv1); __m256i qv2 = _mm256_srlv_epi32(rfv2, shiftv2); __m256i freqv1 = _mm256_and_si256(SDv1, _mm256_set1_epi32(0xffff)); __m256i freqv2 = _mm256_and_si256(SDv2, _mm256_set1_epi32(0xffff)); qv1 = _mm256_mullo_epi32(qv1, freqv1); qv2 = _mm256_mullo_epi32(qv2, freqv2); __m256i qv3 = _mm256_srlv_epi32(rfv3, shiftv3); __m256i qv4 = _mm256_srlv_epi32(rfv4, shiftv4); __m256i freqv3 = _mm256_and_si256(SDv3, _mm256_set1_epi32(0xffff)); __m256i freqv4 = _mm256_and_si256(SDv4, _mm256_set1_epi32(0xffff)); qv3 = _mm256_mullo_epi32(qv3, freqv3); qv4 = _mm256_mullo_epi32(qv4, freqv4); __m256i biasv1=_mm256_shuffle_epi32(SYM_LOAD( 0, xC, xD, xA, xB),0x4E); __m256i biasv2=_mm256_shuffle_epi32(SYM_LOAD( 4, xC, xD, xA, xB),0x4E); __m256i biasv3=_mm256_shuffle_epi32(SYM_LOAD( 8, xC, xD, xA, xB),0x4E); __m256i biasv4=_mm256_shuffle_epi32(SYM_LOAD(12, xC, xD, xA, xB),0x4E); qv1 = _mm256_add_epi32(qv1, biasv1); qv2 = _mm256_add_epi32(qv2, biasv2); qv3 = _mm256_add_epi32(qv3, biasv3); qv4 = _mm256_add_epi32(qv4, biasv4); Rv1 = _mm256_add_epi32(Rv1, qv1); Rv2 = _mm256_add_epi32(Rv2, qv2); Rv3 = _mm256_add_epi32(Rv3, qv3); Rv4 = _mm256_add_epi32(Rv4, qv4); } STORE(Rv, ransN); ptr = (uint8_t *)ptr16; for (z = NX-1; z >= 0; z--) RansEncFlush(&ransN[z], &ptr); empty: // Finalise block size and return it *out_size = (out_end - ptr) + tab_size; // cp = out; // *cp++ = (in_size>> 0) & 0xff; // *cp++ = (in_size>> 8) & 0xff; // *cp++ = (in_size>>16) & 0xff; // *cp++ = (in_size>>24) & 0xff; memmove(out + tab_size, ptr, out_end-ptr); return out; } unsigned char *rans_uncompress_O0_32x16_avx2(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { if (in_size < 16) // 4-states at least return NULL; if (out_sz >= INT_MAX) return NULL; // protect against some overflow cases #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (out_sz > 100000) return NULL; #endif /* Load in the static tables */ unsigned char *cp = in, *out_free = NULL; unsigned char *cp_end = in + in_size; int i; uint32_t s3[TOTFREQ] __attribute__((aligned(32))); // For TF_SHIFT <= 12 if (!out) out_free = out = malloc(out_sz); if (!out) return NULL; // Precompute reverse lookup of frequency. uint32_t F[256] = {0}, fsum; int fsz = decode_freq(cp, cp_end, F, &fsum); if (!fsz) goto err; cp += fsz; normalise_freq_shift(F, fsum, TOTFREQ); // Build symbols; fixme, do as part of decode, see the _d variant if (rans_F_to_s3(F, TF_SHIFT, s3)) goto err; if (cp_end - cp < NX * 4) goto err; int z; RansState R[NX] __attribute__((aligned(32))); for (z = 0; z < NX; z++) { RansDecInit(&R[z], &cp); if (R[z] < RANS_BYTE_L) goto err; } uint16_t *sp = (uint16_t *)cp; uint8_t overflow[64+64] = {0}; cp_end -= 64; // Protect against running off the end of in buffer. // We copy it to a worst-case local buffer when near the end. if ((uint8_t *)sp > cp_end) { memmove(overflow, sp, cp_end+64 - (uint8_t *)sp); sp = (uint16_t *)overflow; cp_end = overflow + sizeof(overflow) - 64; } int out_end = (out_sz&~(NX-1)); const uint32_t mask = (1u << TF_SHIFT)-1; __m256i maskv = _mm256_set1_epi32(mask); // set mask in all lanes LOAD(Rv, R); for (i=0; i < out_end; i+=NX) { //for (z = 0; z < NX; z++) // m[z] = R[z] & mask; __m256i masked1 = _mm256_and_si256(Rv1, maskv); __m256i masked2 = _mm256_and_si256(Rv2, maskv); __m256i masked3 = _mm256_and_si256(Rv3, maskv); __m256i masked4 = _mm256_and_si256(Rv4, maskv); // S[z] = s3[m[z]]; __m256i Sv1 = _mm256_i32gather_epi32x((int *)s3, masked1, sizeof(*s3)); __m256i Sv2 = _mm256_i32gather_epi32x((int *)s3, masked2, sizeof(*s3)); __m256i Sv3 = _mm256_i32gather_epi32x((int *)s3, masked3, sizeof(*s3)); __m256i Sv4 = _mm256_i32gather_epi32x((int *)s3, masked4, sizeof(*s3)); // f[z] = S[z]>>(TF_SHIFT+8); __m256i fv1 = _mm256_srli_epi32(Sv1, TF_SHIFT+8); __m256i fv2 = _mm256_srli_epi32(Sv2, TF_SHIFT+8); // b[z] = (S[z]>>8) & mask; __m256i bv1 = _mm256_and_si256(_mm256_srli_epi32(Sv1, 8), maskv); __m256i bv2 = _mm256_and_si256(_mm256_srli_epi32(Sv2, 8), maskv); // s[z] = S[z] & 0xff; __m256i sv1 = _mm256_and_si256(Sv1, _mm256_set1_epi32(0xff)); __m256i sv2 = _mm256_and_si256(Sv2, _mm256_set1_epi32(0xff)); // R[z] = f[z] * (R[z] >> TF_SHIFT) + b[z]; Rv1 = _mm256_add_epi32( _mm256_mullo_epi32( _mm256_srli_epi32(Rv1,TF_SHIFT), fv1), bv1); Rv2 = _mm256_add_epi32( _mm256_mullo_epi32( _mm256_srli_epi32(Rv2,TF_SHIFT), fv2), bv2); // Tricky one: out[i+z] = s[z]; // ---h---g ---f---e ---d---c ---b---a // ---p---o ---n---m ---l---k ---j---i // packs_epi32 -p-o-n-m -h-g-f-e -l-k-j-i -d-c-b-a // permute4x64 -p-o-n-m -l-k-j-i -h-g-f-e -d-c-b-a // packs_epi16 ponmlkji ponmlkji hgfedcba hgfedcba sv1 = _mm256_packus_epi32(sv1, sv2); sv1 = _mm256_permute4x64_epi64(sv1, 0xd8); // Protect against running off the end of in buffer. // We copy it to a worst-case local buffer when near the end. if ((uint8_t *)sp > cp_end) { memmove(overflow, sp, cp_end+64 - (uint8_t *)sp); sp = (uint16_t *)overflow; cp_end = overflow + sizeof(overflow) - 64; } __m256i Vv1 = _mm256_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); sv1 = _mm256_packus_epi16(sv1, sv1); // c = R[z] < RANS_BYTE_L; // The lack of unsigned comparisons means we have to jump through hoops. // in AVX2 land the second version comes out best (and first in SSE land). //#define _mm256_cmplt_epu32_imm(a,b) _mm256_andnot_si256(_mm256_cmpeq_epi32(_mm256_max_epu32((a),_mm256_set1_epi32(b)), (a)), _mm256_set1_epi32(-1)); #define _mm256_cmplt_epu32_imm(a,b) _mm256_cmpgt_epi32(_mm256_set1_epi32((b)-0x80000000), _mm256_xor_si256((a), _mm256_set1_epi32(0x80000000))) __m256i renorm_mask1, renorm_mask2; renorm_mask1 = _mm256_cmplt_epu32_imm(Rv1, RANS_BYTE_L); renorm_mask2 = _mm256_cmplt_epu32_imm(Rv2, RANS_BYTE_L); // y = (R[z] << 16) | V[z]; unsigned int imask1 = _mm256_movemask_ps((__m256)renorm_mask1); __m256i idx1 = _mm256_load_si256((const __m256i*)permute[imask1]); __m256i Yv1 = _mm256_slli_epi32(Rv1, 16); Vv1 = _mm256_permutevar8x32_epi32(Vv1, idx1); __m256i Yv2 = _mm256_slli_epi32(Rv2, 16); // Shuffle the renorm values to correct lanes and incr sp pointer unsigned int imask2 = _mm256_movemask_ps((__m256)renorm_mask2); sp += _mm_popcnt_u32(imask1); __m256i idx2 = _mm256_load_si256((const __m256i*)permute[imask2]); __m256i Vv2 = _mm256_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); sp += _mm_popcnt_u32(imask2); Yv1 = _mm256_or_si256(Yv1, Vv1); Vv2 = _mm256_permutevar8x32_epi32(Vv2, idx2); Yv2 = _mm256_or_si256(Yv2, Vv2); // R[z] = c ? Y[z] : R[z]; Rv1 = _mm256_blendv_epi8(Rv1, Yv1, renorm_mask1); Rv2 = _mm256_blendv_epi8(Rv2, Yv2, renorm_mask2); // ------------------------------------------------------------ // f[z] = S[z]>>(TF_SHIFT+8); __m256i fv3 = _mm256_srli_epi32(Sv3, TF_SHIFT+8); __m256i fv4 = _mm256_srli_epi32(Sv4, TF_SHIFT+8); // b[z] = (S[z]>>8) & mask; __m256i bv3 = _mm256_and_si256(_mm256_srli_epi32(Sv3, 8), maskv); __m256i bv4 = _mm256_and_si256(_mm256_srli_epi32(Sv4, 8), maskv); // s[z] = S[z] & 0xff; __m256i sv3 = _mm256_and_si256(Sv3, _mm256_set1_epi32(0xff)); __m256i sv4 = _mm256_and_si256(Sv4, _mm256_set1_epi32(0xff)); // R[z] = f[z] * (R[z] >> TF_SHIFT) + b[z]; Rv3 = _mm256_add_epi32(_mm256_mullo_epi32(_mm256_srli_epi32(Rv3,TF_SHIFT),fv3),bv3); Rv4 = _mm256_add_epi32(_mm256_mullo_epi32(_mm256_srli_epi32(Rv4,TF_SHIFT),fv4),bv4); // Tricky one: out[i+z] = s[z]; // ---h---g ---f---e ---d---c ---b---a // ---p---o ---n---m ---l---k ---j---i // packs_epi32 -p-o-n-m -h-g-f-e -l-k-j-i -d-c-b-a // permute4x64 -p-o-n-m -l-k-j-i -h-g-f-e -d-c-b-a // packs_epi16 ponmlkji ponmlkji hgfedcba hgfedcba sv3 = _mm256_packus_epi32(sv3, sv4); sv3 = _mm256_permute4x64_epi64(sv3, 0xd8); // c = R[z] < RANS_BYTE_L; __m256i renorm_mask3, renorm_mask4; renorm_mask3 = _mm256_cmplt_epu32_imm(Rv3, RANS_BYTE_L); sv3 = _mm256_packus_epi16(sv3, sv3); renorm_mask4 = _mm256_cmplt_epu32_imm(Rv4, RANS_BYTE_L); // y = (R[z] << 16) | V[z]; __m256i Vv3 = _mm256_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); *(uint64_t *)&out[i+0] = _mm256_extract_epi64(sv1, 0); *(uint64_t *)&out[i+8] = _mm256_extract_epi64(sv1, 2); *(uint64_t *)&out[i+16] = _mm256_extract_epi64(sv3, 0); *(uint64_t *)&out[i+24] = _mm256_extract_epi64(sv3, 2); __m256i Yv3 = _mm256_slli_epi32(Rv3, 16); unsigned int imask3 = _mm256_movemask_ps((__m256)renorm_mask3); __m256i idx3 = _mm256_load_si256((const __m256i*)permute[imask3]); // Shuffle the renorm values to correct lanes and incr sp pointer Vv3 = _mm256_permutevar8x32_epi32(Vv3, idx3); __m256i Yv4 = _mm256_slli_epi32(Rv4, 16); unsigned int imask4 = _mm256_movemask_ps((__m256)renorm_mask4); sp += _mm_popcnt_u32(imask3); __m256i idx4 = _mm256_load_si256((const __m256i*)permute[imask4]); __m256i Vv4 = _mm256_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); //Vv = _mm256_and_si256(Vv, renorm_mask); (blend does the AND anyway) Yv3 = _mm256_or_si256(Yv3, Vv3); Vv4 = _mm256_permutevar8x32_epi32(Vv4, idx4); Yv4 = _mm256_or_si256(Yv4, Vv4); sp += _mm_popcnt_u32(imask4); // R[z] = c ? Y[z] : R[z]; Rv3 = _mm256_blendv_epi8(Rv3, Yv3, renorm_mask3); Rv4 = _mm256_blendv_epi8(Rv4, Yv4, renorm_mask4); } STORE(Rv, R); //_mm256_store_si256((__m256i *)&R[0], Rv1); //_mm256_store_si256((__m256i *)&R[8], Rv2); //_mm256_store_si256((__m256i *)&R[16], Rv3); //_mm256_store_si256((__m256i *)&R[24], Rv4); for (z = out_sz & (NX-1); z-- > 0; ) out[out_end + z] = s3[R[z] & mask]; //fprintf(stderr, " 0 Decoded %d bytes\n", (int)(cp-in)); //c-size return out; err: free(out_free); return NULL; } //----------------------------------------------------------------------------- unsigned char *rans_compress_O1_32x16_avx2(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { unsigned char *cp, *out_end, *out_free = NULL; unsigned int tab_size; uint32_t bound = rans_compress_bound_4x16(in_size,1)-20; int z; RansState ransN[NX] __attribute__((aligned(32))); if (in_size < NX) // force O0 instead return NULL; if (!out) { *out_size = bound; out = malloc(*out_size); } if (!out || bound > *out_size) return NULL; if (((size_t)out)&1) bound--; out_end = out + bound; RansEncSymbol (*syms)[256] = htscodecs_tls_alloc(256 * (sizeof(*syms))); if (!syms) { free(out_free); return NULL; } cp = out; int shift = encode_freq1(in, in_size, 32, syms, &cp); if (shift < 0) { free(out_free); htscodecs_tls_free(syms); return NULL; } tab_size = cp - out; for (z = 0; z < NX; z++) RansEncInit(&ransN[z]); uint8_t* ptr = out_end; int iN[NX], isz4 = in_size/NX; for (z = 0; z < NX; z++) iN[z] = (z+1)*isz4-2; unsigned char lN[NX]; for (z = 0; z < NX; z++) lN[z] = in[iN[z]+1]; // Deal with the remainder z = NX-1; lN[z] = in[in_size-1]; for (iN[z] = in_size-2; iN[z] > NX*isz4-2; iN[z]--) { unsigned char c = in[iN[z]]; RansEncPutSymbol(&ransN[z], &ptr, &syms[c][lN[z]]); lN[z] = c; } uint16_t *ptr16 = (uint16_t *)ptr; // clang16 clang10 gcc7 gcc13 // 587 435 381 588 438 403 504 386 415 527 381 394 // simT 611 432 402 475 401 367 472 422 386 486 353 324 LOAD(Rv, ransN); for (; iN[0] >= 0; ) { // We need to gather sym[curr_char][last_char] structs. // These hold 4 32-bit values, so are 128 bit each, and // are loaded from 32 distinct addresses. // // We load them into 32 128-bit lanes and then combine to get // 16 avx-256 registers. // These are now ABCD ABCD ABCD ABCD... orientation // Code we can then "gather" from these registers via a combination // of shuffle / permutes / and / or operations. This is less // IO than repeating 4 sets of gathers/loads 32-times over. // DCBA holding 4 elements in a syms[] array // -> 4-way rotate via shuffles // [0] DCBA 11 10 01 00 E4 // [1] CBAD 10 01 00 11 93 // [2] BADC 01 00 11 10 4E // [3] ADCB 00 11 10 01 39 // // Then AND to select relevant lanes and OR // [0] ......A0 // [1] ....A1.. // [2] ..A2.... // [3] A3...... OR to get A3A2A1A0 // // or: // [0] ....B0.. // [1] ..B1.... // [2] B2...... // [3] ......B3 OR to get B2B1B0B3 and shuffle to B3B2B1B0 __m256i xmaxv[4]; __m256i rfv[4]; __m256i SDv[4]; __m256i biasv[4]; const __m256i xA = _mm256_set_epi32(0,0,0,-1, 0,0,0,-1); const __m256i xB = _mm256_set_epi32(0,0,-1,0, 0,0,-1,0); const __m256i xC = _mm256_set_epi32(0,-1,0,0, 0,-1,0,0); const __m256i xD = _mm256_set_epi32(-1,0,0,0, -1,0,0,0); for (z = 0; z < 32; z += 8) { #define m128_to_256 _mm256_castsi128_si256 __m128i *s0 = (__m128i *)(&syms[in[iN[z+0]]][lN[z+0]]); __m128i *s1 = (__m128i *)(&syms[in[iN[z+4]]][lN[z+4]]); __m128i *s2 = (__m128i *)(&syms[in[iN[z+1]]][lN[z+1]]); __m128i *s3 = (__m128i *)(&syms[in[iN[z+5]]][lN[z+5]]); __m256i t0, t1, t2, t3; t0 = _mm256_shuffle_epi32(m128_to_256(_mm_loadu_si128(s0)), 0xE4); t1 = _mm256_shuffle_epi32(m128_to_256(_mm_loadu_si128(s1)), 0xE4); t2 = _mm256_shuffle_epi32(m128_to_256(_mm_loadu_si128(s2)), 0x93); t3 = _mm256_shuffle_epi32(m128_to_256(_mm_loadu_si128(s3)), 0x93); __m256i sh0 = _mm256_permute2x128_si256(t0, t1, 0x20); __m256i sh1 = _mm256_permute2x128_si256(t2, t3, 0x20); lN[z+0] = in[iN[z+0]]; lN[z+4] = in[iN[z+4]]; lN[z+1] = in[iN[z+1]]; lN[z+5] = in[iN[z+5]]; // Initialise first half of xmax, rf, SD and bias vectors __m128i *s4 = (__m128i *)(&syms[in[iN[z+2]]][lN[z+2]]); __m128i *s5 = (__m128i *)(&syms[in[iN[z+6]]][lN[z+6]]); __m128i *s6 = (__m128i *)(&syms[in[iN[z+3]]][lN[z+3]]); __m128i *s7 = (__m128i *)(&syms[in[iN[z+7]]][lN[z+7]]); __m256i t4, t5, t6, t7; t4 = _mm256_shuffle_epi32(m128_to_256(_mm_loadu_si128(s4)), 0x4E); t5 = _mm256_shuffle_epi32(m128_to_256(_mm_loadu_si128(s5)), 0x4E); t6 = _mm256_shuffle_epi32(m128_to_256(_mm_loadu_si128(s6)), 0x39); t7 = _mm256_shuffle_epi32(m128_to_256(_mm_loadu_si128(s7)), 0x39); __m256i sh2 = _mm256_permute2x128_si256(t4, t5, 0x20); __m256i sh3 = _mm256_permute2x128_si256(t6, t7, 0x20); lN[z+2] = in[iN[z+2]]; lN[z+6] = in[iN[z+6]]; lN[z+3] = in[iN[z+3]]; lN[z+7] = in[iN[z+7]]; #define SH_LOAD(A, B, C, D) \ _mm256_or_si256(_mm256_or_si256(_mm256_and_si256(sh0, A), \ _mm256_and_si256(sh1, B)),\ _mm256_or_si256(_mm256_and_si256(sh2, C), \ _mm256_and_si256(sh3, D))) xmaxv[z/8] = SH_LOAD(xA, xB, xC, xD); rfv [z/8] = SH_LOAD(xB, xC, xD, xA); SDv [z/8] = SH_LOAD(xD, xA, xB, xC); biasv[z/8] = SH_LOAD(xC, xD, xA, xB); rfv [z/8] = _mm256_shuffle_epi32(rfv [z/8], 0x39); SDv [z/8] = _mm256_shuffle_epi32(SDv [z/8], 0x93); biasv[z/8] = _mm256_shuffle_epi32(biasv[z/8],0x4E); } // ------------------------------------------------------------ // for (z = NX-1; z >= 0; z--) { // if (ransN[z] >= x_max[z]) { // *--ptr16 = ransN[z] & 0xffff; // ransN[z] >>= 16; // } // } __m256i cv1 = _mm256_cmpgt_epi32(Rv1, xmaxv[0]); __m256i cv2 = _mm256_cmpgt_epi32(Rv2, xmaxv[1]); __m256i cv3 = _mm256_cmpgt_epi32(Rv3, xmaxv[2]); __m256i cv4 = _mm256_cmpgt_epi32(Rv4, xmaxv[3]); // Store bottom 16-bits at ptr16 // // for (z = NX-1; z >= 0; z--) { // if (cond[z]) *--ptr16 = (uint16_t )(ransN[z] & 0xffff); // } unsigned int imask1 = _mm256_movemask_ps((__m256)cv1); unsigned int imask2 = _mm256_movemask_ps((__m256)cv2); unsigned int imask3 = _mm256_movemask_ps((__m256)cv3); unsigned int imask4 = _mm256_movemask_ps((__m256)cv4); __m256i idx1 = _mm256_load_si256((const __m256i*)permutec[imask1]); __m256i idx2 = _mm256_load_si256((const __m256i*)permutec[imask2]); __m256i idx3 = _mm256_load_si256((const __m256i*)permutec[imask3]); __m256i idx4 = _mm256_load_si256((const __m256i*)permutec[imask4]); // Permute; to gather together the rans states that need flushing __m256i V1, V2, V3, V4; V1 = _mm256_permutevar8x32_epi32(_mm256_and_si256(Rv1, cv1), idx1); V2 = _mm256_permutevar8x32_epi32(_mm256_and_si256(Rv2, cv2), idx2); V3 = _mm256_permutevar8x32_epi32(_mm256_and_si256(Rv3, cv3), idx3); V4 = _mm256_permutevar8x32_epi32(_mm256_and_si256(Rv4, cv4), idx4); // We only flush bottom 16 bits, to squash 32-bit states into 16 bit. V1 = _mm256_and_si256(V1, _mm256_set1_epi32(0xffff)); V2 = _mm256_and_si256(V2, _mm256_set1_epi32(0xffff)); V3 = _mm256_and_si256(V3, _mm256_set1_epi32(0xffff)); V4 = _mm256_and_si256(V4, _mm256_set1_epi32(0xffff)); __m256i V12 = _mm256_packus_epi32(V1, V2); __m256i V34 = _mm256_packus_epi32(V3, V4); // It's BAba order, want BbAa so shuffle. V12 = _mm256_permute4x64_epi64(V12, 0xd8); V34 = _mm256_permute4x64_epi64(V34, 0xd8); // Now we have bottom N 16-bit values in each V12/V34 to flush __m128i f = _mm256_extractf128_si256(V34, 1); _mm_storeu_si128((__m128i *)(ptr16-8), f); ptr16 -= _mm_popcnt_u32(imask4); f = _mm256_extractf128_si256(V34, 0); _mm_storeu_si128((__m128i *)(ptr16-8), f); ptr16 -= _mm_popcnt_u32(imask3); f = _mm256_extractf128_si256(V12, 1); _mm_storeu_si128((__m128i *)(ptr16-8), f); ptr16 -= _mm_popcnt_u32(imask2); f = _mm256_extractf128_si256(V12, 0); _mm_storeu_si128((__m128i *)(ptr16-8), f); ptr16 -= _mm_popcnt_u32(imask1); __m256i Rs1, Rs2, Rs3, Rs4; Rs1 = _mm256_srli_epi32(Rv1,16); Rs2 = _mm256_srli_epi32(Rv2,16); Rs3 = _mm256_srli_epi32(Rv3,16); Rs4 = _mm256_srli_epi32(Rv4,16); Rv1 = _mm256_blendv_epi8(Rv1, Rs1, cv1); Rv2 = _mm256_blendv_epi8(Rv2, Rs2, cv2); Rv3 = _mm256_blendv_epi8(Rv3, Rs3, cv3); Rv4 = _mm256_blendv_epi8(Rv4, Rs4, cv4); // ------------------------------------------------------------ // uint32_t q = (uint32_t) (((uint64_t)ransN[z] * // rcp_freq[z]) >> rcp_shift[z]); // ransN[z] = ransN[z] + bias[z] + q * cmpl_freq[z]; // Cannot trivially replace the multiply as mulhi_epu32 doesn't exist // (only mullo). However we can use _mm256_mul_epu32 twice to get // 64bit results (half our lanes) and shift/or to get the answer. // // (AVX512 allows us to hold it all in 64-bit lanes and use mullo_epi64 // plus a shift. KNC has mulhi_epi32, but not sure if this is // available.) rfv[0] = _mm256_mulhi_epu32(Rv1, rfv[0]); rfv[1] = _mm256_mulhi_epu32(Rv2, rfv[1]); rfv[2] = _mm256_mulhi_epu32(Rv3, rfv[2]); rfv[3] = _mm256_mulhi_epu32(Rv4, rfv[3]); __m256i shiftv1 = _mm256_srli_epi32(SDv[0], 16); __m256i shiftv2 = _mm256_srli_epi32(SDv[1], 16); __m256i shiftv3 = _mm256_srli_epi32(SDv[2], 16); __m256i shiftv4 = _mm256_srli_epi32(SDv[3], 16); shiftv1 = _mm256_sub_epi32(shiftv1, _mm256_set1_epi32(32)); shiftv2 = _mm256_sub_epi32(shiftv2, _mm256_set1_epi32(32)); shiftv3 = _mm256_sub_epi32(shiftv3, _mm256_set1_epi32(32)); shiftv4 = _mm256_sub_epi32(shiftv4, _mm256_set1_epi32(32)); __m256i qv1 = _mm256_srlv_epi32(rfv[0], shiftv1); __m256i qv2 = _mm256_srlv_epi32(rfv[1], shiftv2); __m256i freqv1 = _mm256_and_si256(SDv[0], _mm256_set1_epi32(0xffff)); __m256i freqv2 = _mm256_and_si256(SDv[1], _mm256_set1_epi32(0xffff)); qv1 = _mm256_mullo_epi32(qv1, freqv1); qv2 = _mm256_mullo_epi32(qv2, freqv2); __m256i qv3 = _mm256_srlv_epi32(rfv[2], shiftv3); __m256i qv4 = _mm256_srlv_epi32(rfv[3], shiftv4); __m256i freqv3 = _mm256_and_si256(SDv[2], _mm256_set1_epi32(0xffff)); __m256i freqv4 = _mm256_and_si256(SDv[3], _mm256_set1_epi32(0xffff)); qv3 = _mm256_mullo_epi32(qv3, freqv3); qv4 = _mm256_mullo_epi32(qv4, freqv4); qv1 = _mm256_add_epi32(qv1, biasv[0]); qv2 = _mm256_add_epi32(qv2, biasv[1]); qv3 = _mm256_add_epi32(qv3, biasv[2]); qv4 = _mm256_add_epi32(qv4, biasv[3]); for (z = 0; z < NX; z++) iN[z]--; Rv1 = _mm256_add_epi32(Rv1, qv1); Rv2 = _mm256_add_epi32(Rv2, qv2); Rv3 = _mm256_add_epi32(Rv3, qv3); Rv4 = _mm256_add_epi32(Rv4, qv4); } STORE(Rv, ransN); ptr = (uint8_t *)ptr16; for (z = NX-1; z>=0; z--) RansEncPutSymbol(&ransN[z], &ptr, &syms[0][lN[z]]); for (z = NX-1; z>=0; z--) RansEncFlush(&ransN[z], &ptr); *out_size = (out_end - ptr) + tab_size; cp = out; memmove(out + tab_size, ptr, out_end-ptr); htscodecs_tls_free(syms); return out; } /* * A 32 x 32 matrix transpose and serialise from t[][] to out. * Storing in the other orientation speeds up the decoder, and we * can then flush to out in 1KB blocks. */ static inline void transpose_and_copy(uint8_t *out, int iN[32], uint8_t t[32][32]) { // int z; // for (z = 0; z < NX; z++) { // int k; // for (k = 0; k < 32; k++) // out[iN[z]+k] = t[k][z]; // iN[z] += 32; // } rot32_simd(t, out, iN); } unsigned char *rans_uncompress_O1_32x16_avx2(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { if (in_size < NX*4) // 4-states at least return NULL; if (out_sz >= INT_MAX) return NULL; // protect against some overflow cases #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (out_sz > 100000) return NULL; #endif /* Load in the static tables */ unsigned char *cp = in, *cp_end = in+in_size, *out_free = NULL; unsigned char *c_freq = NULL; uint32_t (*s3)[TOTFREQ_O1] = htscodecs_tls_alloc(256*TOTFREQ_O1*4); if (!s3) return NULL; //uint32_t s3[256][TOTFREQ_O1] __attribute__((aligned(32))); uint32_t (*s3F)[TOTFREQ_O1_FAST] = (uint32_t (*)[TOTFREQ_O1_FAST])s3; if (!out) out_free = out = malloc(out_sz); if (!out) goto err; //fprintf(stderr, "out_sz=%d\n", out_sz); // compressed header? If so uncompress it unsigned char *tab_end = NULL; unsigned char *c_freq_end = cp_end; unsigned int shift = *cp >> 4; if (*cp++ & 1) { uint32_t u_freq_sz, c_freq_sz; cp += var_get_u32(cp, cp_end, &u_freq_sz); cp += var_get_u32(cp, cp_end, &c_freq_sz); if (c_freq_sz > cp_end - cp) goto err; tab_end = cp + c_freq_sz; if (!(c_freq = rans_uncompress_O0_4x16(cp, c_freq_sz, NULL, u_freq_sz))) goto err; cp = c_freq; c_freq_end = c_freq + u_freq_sz; } // Decode order-0 symbol list; avoids needing in order-1 tables cp += decode_freq1(cp, c_freq_end, shift, s3, s3F, NULL, NULL); if (tab_end) cp = tab_end; free(c_freq); c_freq = NULL; if (cp_end - cp < NX * 4) goto err; RansState R[NX] __attribute__((aligned(32))); uint8_t *ptr = cp, *ptr_end = in + in_size; int z; for (z = 0; z < NX; z++) { RansDecInit(&R[z], &ptr); if (R[z] < RANS_BYTE_L) goto err; } int isz4 = out_sz/NX; int iN[NX], lN[NX] __attribute__((aligned(32))) = {0}; for (z = 0; z < NX; z++) iN[z] = z*isz4; uint16_t *sp = (uint16_t *)ptr; const uint32_t mask = (1u << shift)-1; __m256i maskv = _mm256_set1_epi32(mask); LOAD(Rv, R); LOAD(Lv, lN); union { unsigned char tbuf[32][32]; uint64_t tbuf64[32][4]; } u __attribute__((aligned(32))); unsigned int tidx = 0; if (0) { int z; for (z = 0; z < 32; z++) iN[z] = iN[z] & ~31; } if (shift == TF_SHIFT_O1) { isz4 -= 64; for (; iN[0] < isz4 && (uint8_t *)sp+64 < ptr_end; ) { // m[z] = R[z] & mask; __m256i masked1 = _mm256_and_si256(Rv1, maskv); __m256i masked2 = _mm256_and_si256(Rv2, maskv); // S[z] = s3[lN[z]][m[z]]; Lv1 = _mm256_slli_epi32(Lv1, TF_SHIFT_O1); masked1 = _mm256_add_epi32(masked1, Lv1); Lv2 = _mm256_slli_epi32(Lv2, TF_SHIFT_O1); masked2 = _mm256_add_epi32(masked2, Lv2); __m256i masked3 = _mm256_and_si256(Rv3, maskv); __m256i masked4 = _mm256_and_si256(Rv4, maskv); Lv3 = _mm256_slli_epi32(Lv3, TF_SHIFT_O1); masked3 = _mm256_add_epi32(masked3, Lv3); Lv4 = _mm256_slli_epi32(Lv4, TF_SHIFT_O1); masked4 = _mm256_add_epi32(masked4, Lv4); __m256i Sv1 = _mm256_i32gather_epi32x((int *)&s3[0][0], masked1, sizeof(s3[0][0])); __m256i Sv2 = _mm256_i32gather_epi32x((int *)&s3[0][0], masked2, sizeof(s3[0][0])); // f[z] = S[z]>>(TF_SHIFT_O1+8); __m256i fv1 = _mm256_srli_epi32(Sv1, TF_SHIFT_O1+8); __m256i fv2 = _mm256_srli_epi32(Sv2, TF_SHIFT_O1+8); __m256i Sv3 = _mm256_i32gather_epi32x((int *)&s3[0][0], masked3, sizeof(s3[0][0])); __m256i Sv4 = _mm256_i32gather_epi32x((int *)&s3[0][0], masked4, sizeof(s3[0][0])); __m256i fv3 = _mm256_srli_epi32(Sv3, TF_SHIFT_O1+8); __m256i fv4 = _mm256_srli_epi32(Sv4, TF_SHIFT_O1+8); // b[z] = (S[z]>>8) & mask; __m256i bv1 = _mm256_and_si256(_mm256_srli_epi32(Sv1, 8), maskv); __m256i bv2 = _mm256_and_si256(_mm256_srli_epi32(Sv2, 8), maskv); __m256i bv3 = _mm256_and_si256(_mm256_srli_epi32(Sv3, 8), maskv); __m256i bv4 = _mm256_and_si256(_mm256_srli_epi32(Sv4, 8), maskv); // s[z] = S[z] & 0xff; __m256i sv1 = _mm256_and_si256(Sv1, _mm256_set1_epi32(0xff)); __m256i sv2 = _mm256_and_si256(Sv2, _mm256_set1_epi32(0xff)); __m256i sv3 = _mm256_and_si256(Sv3, _mm256_set1_epi32(0xff)); __m256i sv4 = _mm256_and_si256(Sv4, _mm256_set1_epi32(0xff)); if (1) { // A maximum frequency of 4096 doesn't fit in our s3 array. // as it's 12 bit + 12 bit + 8 bit. It wraps around to zero. // (We don't have this issue for TOTFREQ_O1_FAST.) // // Solution 1 is to change to spec to forbid freq of 4096. // Easy hack is to add an extra symbol so it sums correctly. // => 572 MB/s on q40 (deskpro). // // Solution 2 implemented here is to look for the wrap around // and fix it. // => 556 MB/s on q40 // cope with max freq of 4096. Only 3% hit __m256i max_freq = _mm256_set1_epi32(TOTFREQ_O1); __m256i zero = _mm256_setzero_si256(); __m256i cmp1 = _mm256_cmpeq_epi32(fv1, zero); fv1 = _mm256_blendv_epi8(fv1, max_freq, cmp1); __m256i cmp2 = _mm256_cmpeq_epi32(fv2, zero); fv2 = _mm256_blendv_epi8(fv2, max_freq, cmp2); } // R[z] = f[z] * (R[z] >> TF_SHIFT_O1) + b[z]; Rv1 = _mm256_add_epi32( _mm256_mullo_epi32( _mm256_srli_epi32(Rv1,TF_SHIFT_O1), fv1), bv1); Rv2 = _mm256_add_epi32( _mm256_mullo_epi32( _mm256_srli_epi32(Rv2,TF_SHIFT_O1), fv2), bv2); //for (z = 0; z < NX; z++) lN[z] = c[z]; Lv1 = sv1; Lv2 = sv2; sv1 = _mm256_packus_epi32(sv1, sv2); sv1 = _mm256_permute4x64_epi64(sv1, 0xd8); // Start loading next batch of normalised states __m256i Vv1 = _mm256_cvtepu16_epi32( _mm_loadu_si128((__m128i *)sp)); sv1 = _mm256_packus_epi16(sv1, sv1); // out[iN[z]] = c[z]; // simulate scatter // RansDecRenorm(&R[z], &ptr); __m256i renorm_mask1, renorm_mask2; renorm_mask1 = _mm256_xor_si256(Rv1,_mm256_set1_epi32(0x80000000)); renorm_mask2 = _mm256_xor_si256(Rv2,_mm256_set1_epi32(0x80000000)); renorm_mask1 = _mm256_cmpgt_epi32( _mm256_set1_epi32(RANS_BYTE_L-0x80000000), renorm_mask1); renorm_mask2 = _mm256_cmpgt_epi32( _mm256_set1_epi32(RANS_BYTE_L-0x80000000), renorm_mask2); unsigned int imask1 = _mm256_movemask_ps((__m256)renorm_mask1); __m256i idx1 = _mm256_load_si256((const __m256i*)permute[imask1]); __m256i Yv1 = _mm256_slli_epi32(Rv1, 16); __m256i Yv2 = _mm256_slli_epi32(Rv2, 16); unsigned int imask2 = _mm256_movemask_ps((__m256)renorm_mask2); Vv1 = _mm256_permutevar8x32_epi32(Vv1, idx1); sp += _mm_popcnt_u32(imask1); __m256i idx2 = _mm256_load_si256((const __m256i*)permute[imask2]); __m256i Vv2 = _mm256_cvtepu16_epi32( _mm_loadu_si128((__m128i *)sp)); sp += _mm_popcnt_u32(imask2); Vv2 = _mm256_permutevar8x32_epi32(Vv2, idx2); Yv1 = _mm256_or_si256(Yv1, Vv1); Yv2 = _mm256_or_si256(Yv2, Vv2); Rv1 = _mm256_blendv_epi8(Rv1, Yv1, renorm_mask1); Rv2 = _mm256_blendv_epi8(Rv2, Yv2, renorm_mask2); ////////////////////////////////////////////////////////////////// // Start loading next batch of normalised states __m256i Vv3 = _mm256_cvtepu16_epi32( _mm_loadu_si128((__m128i *)sp)); if (1) { // cope with max freq of 4096 __m256i max_freq = _mm256_set1_epi32(TOTFREQ_O1); __m256i zero = _mm256_setzero_si256(); __m256i cmp3 = _mm256_cmpeq_epi32(fv3, zero); fv3 = _mm256_blendv_epi8(fv3, max_freq, cmp3); __m256i cmp4 = _mm256_cmpeq_epi32(fv4, zero); fv4 = _mm256_blendv_epi8(fv4, max_freq, cmp4); } // R[z] = f[z] * (R[z] >> TF_SHIFT_O1) + b[z]; Rv3 = _mm256_add_epi32( _mm256_mullo_epi32( _mm256_srli_epi32(Rv3,TF_SHIFT_O1), fv3), bv3); Rv4 = _mm256_add_epi32( _mm256_mullo_epi32( _mm256_srli_epi32(Rv4,TF_SHIFT_O1), fv4), bv4); //for (z = 0; z < NX; z++) lN[z] = c[z]; Lv3 = sv3; Lv4 = sv4; // out[iN[z]] = c[z]; // simulate scatter // RansDecRenorm(&R[z], &ptr); __m256i renorm_mask3, renorm_mask4; renorm_mask3 = _mm256_xor_si256(Rv3,_mm256_set1_epi32(0x80000000)); renorm_mask4 = _mm256_xor_si256(Rv4,_mm256_set1_epi32(0x80000000)); renorm_mask3 = _mm256_cmpgt_epi32( _mm256_set1_epi32(RANS_BYTE_L-0x80000000), renorm_mask3); renorm_mask4 = _mm256_cmpgt_epi32( _mm256_set1_epi32(RANS_BYTE_L-0x80000000), renorm_mask4); __m256i Yv3 = _mm256_slli_epi32(Rv3, 16); __m256i Yv4 = _mm256_slli_epi32(Rv4, 16); unsigned int imask3 = _mm256_movemask_ps((__m256)renorm_mask3); unsigned int imask4 = _mm256_movemask_ps((__m256)renorm_mask4); __m256i idx3 = _mm256_load_si256((const __m256i*)permute[imask3]); sp += _mm_popcnt_u32(imask3); Vv3 = _mm256_permutevar8x32_epi32(Vv3, idx3); sv3 = _mm256_packus_epi32(sv3, sv4); sv3 = _mm256_permute4x64_epi64(sv3, 0xd8); sv3 = _mm256_packus_epi16(sv3, sv3); u.tbuf64[tidx][0] = _mm256_extract_epi64(sv1, 0); u.tbuf64[tidx][1] = _mm256_extract_epi64(sv1, 2); u.tbuf64[tidx][2] = _mm256_extract_epi64(sv3, 0); u.tbuf64[tidx][3] = _mm256_extract_epi64(sv3, 2); iN[0]++; if (++tidx == 32) { iN[0]-=32; transpose_and_copy(out, iN, u.tbuf); tidx = 0; } __m256i idx4 = _mm256_load_si256((const __m256i*)permute[imask4]); __m256i Vv4 = _mm256_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); //Vv = _mm256_and_si256(Vv, renorm_mask); (blend does the AND anyway) Yv3 = _mm256_or_si256(Yv3, Vv3); Vv4 = _mm256_permutevar8x32_epi32(Vv4, idx4); Yv4 = _mm256_or_si256(Yv4, Vv4); sp += _mm_popcnt_u32(imask4); Rv3 = _mm256_blendv_epi8(Rv3, Yv3, renorm_mask3); Rv4 = _mm256_blendv_epi8(Rv4, Yv4, renorm_mask4); } isz4 += 64; STORE(Rv, R); STORE(Lv, lN); ptr = (uint8_t *)sp; if (1) { iN[0]-=tidx; int T; for (z = 0; z < NX; z++) for (T = 0; T < tidx; T++) out[iN[z]++] = u.tbuf[T][z]; } // Scalar version for close to the end of in[] array so we don't // do SIMD loads beyond the end of the buffer for (; iN[0] < isz4;) { for (z = 0; z < NX; z++) { uint32_t m = R[z] & ((1u<>(TF_SHIFT_O1+8); R[z] = (F?F:4096) * (R[z]>>TF_SHIFT_O1) + ((S>>8) & ((1u<>(TF_SHIFT_O1+8); R[z] = (F?F:4096) * (R[z]>>TF_SHIFT_O1) + ((S>>8) & ((1u<>(TF_SHIFT_O1+8); __m256i fv1 = _mm256_srli_epi32(Sv1, TF_SHIFT_O1_FAST+8); __m256i fv2 = _mm256_srli_epi32(Sv2, TF_SHIFT_O1_FAST+8); __m256i Sv3 = _mm256_i32gather_epi32x((int *)&s3F[0][0], masked3, sizeof(s3F[0][0])); __m256i Sv4 = _mm256_i32gather_epi32x((int *)&s3F[0][0], masked4, sizeof(s3F[0][0])); __m256i fv3 = _mm256_srli_epi32(Sv3, TF_SHIFT_O1_FAST+8); __m256i fv4 = _mm256_srli_epi32(Sv4, TF_SHIFT_O1_FAST+8); // b[z] = (S[z]>>8) & mask; __m256i bv1 = _mm256_and_si256(_mm256_srli_epi32(Sv1, 8), maskv); __m256i bv2 = _mm256_and_si256(_mm256_srli_epi32(Sv2, 8), maskv); __m256i bv3 = _mm256_and_si256(_mm256_srli_epi32(Sv3, 8), maskv); __m256i bv4 = _mm256_and_si256(_mm256_srli_epi32(Sv4, 8), maskv); // s[z] = S[z] & 0xff; __m256i sv1 = _mm256_and_si256(Sv1, _mm256_set1_epi32(0xff)); __m256i sv2 = _mm256_and_si256(Sv2, _mm256_set1_epi32(0xff)); __m256i sv3 = _mm256_and_si256(Sv3, _mm256_set1_epi32(0xff)); __m256i sv4 = _mm256_and_si256(Sv4, _mm256_set1_epi32(0xff)); // R[z] = f[z] * (R[z] >> TF_SHIFT_O1) + b[z]; Rv1 = _mm256_add_epi32( _mm256_mullo_epi32( _mm256_srli_epi32(Rv1,TF_SHIFT_O1_FAST), fv1), bv1); Rv2 = _mm256_add_epi32( _mm256_mullo_epi32( _mm256_srli_epi32(Rv2,TF_SHIFT_O1_FAST), fv2), bv2); //for (z = 0; z < NX; z++) lN[z] = c[z]; Lv1 = sv1; Lv2 = sv2; sv1 = _mm256_packus_epi32(sv1, sv2); sv1 = _mm256_permute4x64_epi64(sv1, 0xd8); // Start loading next batch of normalised states __m256i Vv1 = _mm256_cvtepu16_epi32( _mm_loadu_si128((__m128i *)sp)); sv1 = _mm256_packus_epi16(sv1, sv1); // out[iN[z]] = c[z]; // simulate scatter // RansDecRenorm(&R[z], &ptr); __m256i renorm_mask1, renorm_mask2; renorm_mask1 = _mm256_xor_si256(Rv1,_mm256_set1_epi32(0x80000000)); renorm_mask2 = _mm256_xor_si256(Rv2,_mm256_set1_epi32(0x80000000)); renorm_mask1 = _mm256_cmpgt_epi32( _mm256_set1_epi32(RANS_BYTE_L-0x80000000), renorm_mask1); renorm_mask2 = _mm256_cmpgt_epi32( _mm256_set1_epi32(RANS_BYTE_L-0x80000000), renorm_mask2); unsigned int imask1 = _mm256_movemask_ps((__m256)renorm_mask1); __m256i idx1 = _mm256_load_si256((const __m256i*)permute[imask1]); __m256i Yv1 = _mm256_slli_epi32(Rv1, 16); __m256i Yv2 = _mm256_slli_epi32(Rv2, 16); unsigned int imask2 = _mm256_movemask_ps((__m256)renorm_mask2); Vv1 = _mm256_permutevar8x32_epi32(Vv1, idx1); sp += _mm_popcnt_u32(imask1); __m256i idx2 = _mm256_load_si256((const __m256i*)permute[imask2]); __m256i Vv2 = _mm256_cvtepu16_epi32( _mm_loadu_si128((__m128i *)sp)); sp += _mm_popcnt_u32(imask2); Vv2 = _mm256_permutevar8x32_epi32(Vv2, idx2); Yv1 = _mm256_or_si256(Yv1, Vv1); Yv2 = _mm256_or_si256(Yv2, Vv2); Rv1 = _mm256_blendv_epi8(Rv1, Yv1, renorm_mask1); Rv2 = _mm256_blendv_epi8(Rv2, Yv2, renorm_mask2); ///////////////////////////////////////////////////////////////// // Start loading next batch of normalised states __m256i Vv3 = _mm256_cvtepu16_epi32( _mm_loadu_si128((__m128i *)sp)); // R[z] = f[z] * (R[z] >> TF_SHIFT_O1) + b[z]; Rv3 = _mm256_add_epi32( _mm256_mullo_epi32( _mm256_srli_epi32(Rv3,TF_SHIFT_O1_FAST), fv3), bv3); Rv4 = _mm256_add_epi32( _mm256_mullo_epi32( _mm256_srli_epi32(Rv4,TF_SHIFT_O1_FAST), fv4), bv4); //for (z = 0; z < NX; z++) lN[z] = c[z]; Lv3 = sv3; Lv4 = sv4; // out[iN[z]] = c[z]; // simulate scatter // RansDecRenorm(&R[z], &ptr); __m256i renorm_mask3, renorm_mask4; renorm_mask3 = _mm256_xor_si256(Rv3,_mm256_set1_epi32(0x80000000)); renorm_mask4 = _mm256_xor_si256(Rv4,_mm256_set1_epi32(0x80000000)); renorm_mask3 = _mm256_cmpgt_epi32( _mm256_set1_epi32(RANS_BYTE_L-0x80000000), renorm_mask3); renorm_mask4 = _mm256_cmpgt_epi32( _mm256_set1_epi32(RANS_BYTE_L-0x80000000), renorm_mask4); __m256i Yv3 = _mm256_slli_epi32(Rv3, 16); __m256i Yv4 = _mm256_slli_epi32(Rv4, 16); unsigned int imask3 = _mm256_movemask_ps((__m256)renorm_mask3); unsigned int imask4 = _mm256_movemask_ps((__m256)renorm_mask4); __m256i idx3 = _mm256_load_si256((const __m256i*)permute[imask3]); sp += _mm_popcnt_u32(imask3); Vv3 = _mm256_permutevar8x32_epi32(Vv3, idx3); // sv3 sv4 are 32-bit ints with lowest bit being char sv3 = _mm256_packus_epi32(sv3, sv4); // 32 to 16; ABab sv3 = _mm256_permute4x64_epi64(sv3, 0xd8); // shuffle; AaBb sv3 = _mm256_packus_epi16(sv3, sv3); // 16 to 8 u.tbuf64[tidx][0] = _mm256_extract_epi64(sv1, 0); u.tbuf64[tidx][1] = _mm256_extract_epi64(sv1, 2); u.tbuf64[tidx][2] = _mm256_extract_epi64(sv3, 0); u.tbuf64[tidx][3] = _mm256_extract_epi64(sv3, 2); iN[0]++; if (++tidx == 32) { iN[0]-=32; // We have tidx[x][y] which we want to store in // memory in out[y][z] instead. This is an unrolled // transposition. // // A straight memcpy (obviously wrong) decodes my test // data in around 1030MB/s vs 930MB/s for this transpose, // giving an idea of the time spent in this portion. transpose_and_copy(out, iN, u.tbuf); tidx = 0; } __m256i idx4 = _mm256_load_si256((const __m256i*)permute[imask4]); __m256i Vv4 = _mm256_cvtepu16_epi32( _mm_loadu_si128((__m128i *)sp)); Yv3 = _mm256_or_si256(Yv3, Vv3); Vv4 = _mm256_permutevar8x32_epi32(Vv4, idx4); Yv4 = _mm256_or_si256(Yv4, Vv4); sp += _mm_popcnt_u32(imask4); Rv3 = _mm256_blendv_epi8(Rv3, Yv3, renorm_mask3); Rv4 = _mm256_blendv_epi8(Rv4, Yv4, renorm_mask4); } isz4 += 64; STORE(Rv, R); STORE(Lv, lN); ptr = (uint8_t *)sp; if (1) { iN[0]-=tidx; int T; for (z = 0; z < NX; z++) for (T = 0; T < tidx; T++) out[iN[z]++] = u.tbuf[T][z]; } // Scalar version for close to the end of in[] array so we don't // do SIMD loads beyond the end of the buffer for (; iN[0] < isz4;) { for (z = 0; z < NX; z++) { uint32_t m = R[z] & ((1u<>(TF_SHIFT_O1_FAST+8)) * (R[z]>>TF_SHIFT_O1_FAST) + ((S>>8) & ((1u<>(TF_SHIFT_O1_FAST+8)) * (R[z]>>TF_SHIFT_O1_FAST) + ((S>>8) & ((1u< #include #include #include #include #include #include "rANS_word.h" #include "rANS_static4x16.h" #define ROT32_SIMD #include "rANS_static16_int.h" #include "varint.h" #include "utils.h" #ifndef USE_GATHER // Speds with Downfall mitigation Off/On and Zen4. // <------ AVX512 ---------> <------- AVX2 --------> // -o4: IntelOff IntelOn AMDZen4 // gcc7 544/1673 562/1711 448/1818 649/1515 645/1525 875/1624 // gcc13 557/1672 576/1711 582/1761 630/1623 629/1652 866/1762 // clang10 541/1547 564/1630 807/1912 620/1456 637/1481 837/1606 // clang16 533/1431 555/1510 890/1611 629/1370 627/1406 996/1432 // // Zen4 encode is particularly slow with gcc, but AVX2 encode is // faster and we use that already. static inline __m512i _mm512_i32gather_epi32x(__m512i idx, void *v, int size) { uint32_t *b = (uint32_t *)v; #ifndef __clang__ volatile #endif int c[16] __attribute__((aligned(32))); //_mm512_store_si512((__m512i *)c, idx); // equivalent, but slower _mm256_store_si256((__m256i *)(c), _mm512_castsi512_si256(idx)); _mm256_store_si256((__m256i *)(c+8), _mm512_extracti64x4_epi64(idx, 1)); __m128i x0 = _mm_insert_epi32(_mm_cvtsi32_si128(b[c[0]]), b[c[1]], 1); __m128i x1 = _mm_insert_epi32(_mm_cvtsi32_si128(b[c[2]]), b[c[3]], 1); __m128i x2 = _mm_insert_epi32(_mm_cvtsi32_si128(b[c[4]]), b[c[5]], 1); __m128i x3 = _mm_insert_epi32(_mm_cvtsi32_si128(b[c[6]]), b[c[7]], 1); __m128i x01 = _mm_unpacklo_epi64(x0, x1); __m128i x23 = _mm_unpacklo_epi64(x2, x3); __m256i y0 =_mm256_castsi128_si256(x01); __m128i x4 = _mm_insert_epi32(_mm_cvtsi32_si128(b[c[ 8]]), b[c[ 9]], 1); __m128i x5 = _mm_insert_epi32(_mm_cvtsi32_si128(b[c[10]]), b[c[11]], 1); __m128i x6 = _mm_insert_epi32(_mm_cvtsi32_si128(b[c[12]]), b[c[13]], 1); __m128i x7 = _mm_insert_epi32(_mm_cvtsi32_si128(b[c[14]]), b[c[15]], 1); __m128i x45 = _mm_unpacklo_epi64(x4, x5); __m128i x67 = _mm_unpacklo_epi64(x6, x7); __m256i y1 =_mm256_castsi128_si256(x45); y0 = _mm256_inserti128_si256(y0, x23, 1); y1 = _mm256_inserti128_si256(y1, x67, 1); return _mm512_inserti64x4(_mm512_castsi256_si512(y0), y1, 1); } // 32-bit indices, 8-bit quantities into 32-bit lanes static inline __m512i _mm512_i32gather_epi32x1(__m512i idx, void *v) { uint8_t *b = (uint8_t *)v; volatile int c[16] __attribute__((aligned(32))); //_mm512_store_si512((__m512i *)c, idx); // equivalent, but slower _mm256_store_si256((__m256i *)(c), _mm512_castsi512_si256(idx)); _mm256_store_si256((__m256i *)(c+8), _mm512_extracti64x4_epi64(idx, 1)); return _mm512_set_epi32(b[c[15]], b[c[14]], b[c[13]], b[c[12]], b[c[11]], b[c[10]], b[c[9]], b[c[8]], b[c[7]], b[c[6]], b[c[5]], b[c[4]], b[c[3]], b[c[2]], b[c[1]], b[c[0]]); } #else // real gathers #define _mm512_i32gather_epi32x _mm512_i32gather_epi32 #endif unsigned char *rans_compress_O0_32x16_avx512(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { unsigned char *cp, *out_end; RansEncSymbol syms[256]; RansState ransN[32] __attribute__((aligned(64))); uint8_t* ptr; uint32_t F[256+MAGIC] = {0}; int i, j, tab_size = 0, x, z; // -20 for order/size/meta uint32_t bound = rans_compress_bound_4x16(in_size,0)-20; if (!out) { *out_size = bound; out = malloc(*out_size); } if (!out || bound > *out_size) return NULL; // If "out" isn't word aligned, tweak out_end/ptr to ensure it is. // We already added more round in bound to allow for this. if (((size_t)out)&1) bound--; ptr = out_end = out + bound; if (in_size == 0) goto empty; // Compute statistics if (hist8(in, in_size, F) < 0) return NULL; // Normalise so frequences sum to power of 2 uint32_t fsum = in_size; uint32_t max_val = round2(fsum); if (max_val > TOTFREQ) max_val = TOTFREQ; if (normalise_freq(F, fsum, max_val) < 0) return NULL; fsum=max_val; cp = out; cp += encode_freq(cp, F); tab_size = cp-out; //write(2, out+4, cp-(out+4)); if (normalise_freq(F, fsum, TOTFREQ) < 0) return NULL; // Encode statistics and build lookup tables for SIMD encoding. uint32_t SB[256], SA[256], SD[256], SC[256]; for (x = j = 0; j < 256; j++) { if (F[j]) { RansEncSymbolInit(&syms[j], x, F[j], TF_SHIFT); SB[j] = syms[j].x_max; SA[j] = syms[j].rcp_freq; SD[j] = (syms[j].cmpl_freq<<0) | ((syms[j].rcp_shift-32)<<16); SC[j] = syms[j].bias; x += F[j]; } } for (z = 0; z < 32; z++) RansEncInit(&ransN[z]); z = i = in_size&(32-1); while (z-- > 0) RansEncPutSymbol(&ransN[z], &ptr, &syms[in[in_size-(i-z)]]); #define LOAD512(a,b) \ __m512i a##1 = _mm512_load_si512((__m512i *)&b[0]); \ __m512i a##2 = _mm512_load_si512((__m512i *)&b[16]); #define STORE512(a,b) \ _mm512_store_si512((__m256i *)&b[0], a##1); \ _mm512_store_si512((__m256i *)&b[16], a##2); LOAD512(Rv, ransN); uint16_t *ptr16 = (uint16_t *)ptr; for (i=(in_size &~(32-1)); i>0; i-=32) { uint8_t *c = &in[i-32]; // GATHER versions // Much faster now we have an efficient loadu mechanism in place, // BUT... // Try this for avx2 variant too? Better way to populate the mm256 // regs for mix of avx2 and avx512 opcodes. __m256i c12 = _mm256_loadu_si256((__m256i const *)c); __m512i c1 = _mm512_cvtepu8_epi32(_mm256_extracti128_si256(c12,0)); __m512i c2 = _mm512_cvtepu8_epi32(_mm256_extracti128_si256(c12,1)); #define SET512(a,b) \ __m512i a##1 = _mm512_i32gather_epi32x(c1, b, 4); \ __m512i a##2 = _mm512_i32gather_epi32x(c2, b, 4) SET512(xmax, SB); uint16_t gt_mask1 = _mm512_cmpgt_epi32_mask(Rv1, xmax1); int pc1 = _mm_popcnt_u32(gt_mask1); __m512i Rp1 = _mm512_and_si512(Rv1, _mm512_set1_epi32(0xffff)); __m512i Rp2 = _mm512_and_si512(Rv2, _mm512_set1_epi32(0xffff)); uint16_t gt_mask2 = _mm512_cmpgt_epi32_mask(Rv2, xmax2); SET512(SDv, SD); int pc2 = _mm_popcnt_u32(gt_mask2); Rp1 = _mm512_maskz_compress_epi32(gt_mask1, Rp1); Rp2 = _mm512_maskz_compress_epi32(gt_mask2, Rp2); _mm512_mask_cvtepi32_storeu_epi16(ptr16-pc2, (1<= 0; z--) RansEncFlush(&ransN[z], &ptr); empty: // Finalise block size and return it *out_size = (out_end - ptr) + tab_size; memmove(out + tab_size, ptr, out_end-ptr); return out; } unsigned char *rans_uncompress_O0_32x16_avx512(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { if (in_size < 32*4) // 32-states at least return NULL; if (out_sz >= INT_MAX) return NULL; // protect against some overflow cases /* Load in the static tables */ unsigned char *cp = in, *out_free = NULL; unsigned char *cp_end = in + in_size; int i; uint32_t s3[TOTFREQ] __attribute__((aligned(64))); // For TF_SHIFT <= 12 if (!out) out_free = out = malloc(out_sz); if (!out) return NULL; // Precompute reverse lookup of frequency. uint32_t F[256] = {0}, fsum; int fsz = decode_freq(cp, cp_end, F, &fsum); if (!fsz) goto err; cp += fsz; normalise_freq_shift(F, fsum, TOTFREQ); // Build symbols; fixme, do as part of decode, see the _d variant if (rans_F_to_s3(F, TF_SHIFT, s3)) goto err; if (cp_end - cp < 32 * 4) goto err; int z; RansState Rv[32] __attribute__((aligned(64))); for (z = 0; z < 32; z++) { RansDecInit(&Rv[z], &cp); if (Rv[z] < RANS_BYTE_L) goto err; } uint16_t *sp = (uint16_t *)cp; int out_end = (out_sz&~(32-1)); const uint32_t mask = (1u << TF_SHIFT)-1; __m512i maskv = _mm512_set1_epi32(mask); // set mask in all lanes __m512i R1 = _mm512_load_epi32(&Rv[0]); __m512i R2 = _mm512_load_epi32(&Rv[16]); // Start of the first loop iteration, which we do move to the end of the // loop for the next cycle so we can remove some of the instr. latency. __m512i masked1 = _mm512_and_epi32(R1, maskv); __m512i masked2 = _mm512_and_epi32(R2, maskv); __m512i S1 = _mm512_i32gather_epi32x(masked1, (int *)s3, sizeof(*s3)); __m512i S2 = _mm512_i32gather_epi32x(masked2, (int *)s3, sizeof(*s3)); uint8_t overflow[64+64] = {0}; for (i=0; i < out_end; i+=32) { //for (z = 0; z < 16; z++) { // Protect against running off the end of in buffer. // We copy it to a worst-case local buffer when near the end. if ((uint8_t *)sp+64 > cp_end) { memmove(overflow, sp, cp_end - (uint8_t *)sp); sp = (uint16_t *)overflow; cp_end = overflow + sizeof(overflow); } //uint32_t S = s3[R[z] & mask]; __m512i renorm_words1 = _mm512_cvtepu16_epi32(_mm256_loadu_si256((const __m256i *)sp)); // next 16 words //uint16_t f = S>>(TF_SHIFT+8), b = (S>>8) & mask; __m512i f1 = _mm512_srli_epi32(S1, TF_SHIFT+8); __m512i f2 = _mm512_srli_epi32(S2, TF_SHIFT+8); __m512i b1 = _mm512_and_epi32(_mm512_srli_epi32(S1, 8), maskv); __m512i b2 = _mm512_and_epi32(_mm512_srli_epi32(S2, 8), maskv); //R[z] = f * (R[z] >> TF_SHIFT) + b; // approx 10 cycle latency on mullo. R1 = _mm512_add_epi32( _mm512_mullo_epi32( _mm512_srli_epi32(R1, TF_SHIFT), f1), b1); __mmask16 renorm_mask1, renorm_mask2; renorm_mask1=_mm512_cmplt_epu32_mask(R1, _mm512_set1_epi32(RANS_BYTE_L)); R2 = _mm512_add_epi32( _mm512_mullo_epi32( _mm512_srli_epi32(R2, TF_SHIFT), f2), b2); // renorm. this is the interesting part: renorm_mask2=_mm512_cmplt_epu32_mask(R2, _mm512_set1_epi32(RANS_BYTE_L)); // advance by however many words we actually read sp += _mm_popcnt_u32(renorm_mask1); __m512i renorm_words2 = _mm512_cvtepu16_epi32(_mm256_loadu_si256( (const __m256i *)sp)); // select masked only __m512i renorm_vals1, renorm_vals2; renorm_vals1 = _mm512_mask_expand_epi32(R1, renorm_mask1, renorm_words1); renorm_vals2 = _mm512_mask_expand_epi32(R2, renorm_mask2, renorm_words2); // For start of next loop iteration. This has been moved here // (and duplicated to before the loop starts) so we can do something // with the latency period of gather, such as finishing up the // renorm offset and writing the results. __m512i S1_ = S1; // temporary copy for use in out[]=S later __m512i S2_ = S2; masked1 = _mm512_and_epi32(renorm_vals1, maskv); S1 = _mm512_i32gather_epi32x(masked1, (int *)s3, sizeof(*s3)); masked2 = _mm512_and_epi32(renorm_vals2, maskv); S2 = _mm512_i32gather_epi32x(masked2, (int *)s3, sizeof(*s3)); R1 = _mm512_mask_slli_epi32(R1, renorm_mask1, R1, 16); R2 = _mm512_mask_slli_epi32(R2, renorm_mask2, R2, 16); __m512i m16 = _mm512_set1_epi32(0xffff); renorm_vals1 = _mm512_maskz_and_epi32(renorm_mask1, renorm_vals1, m16); renorm_vals2 = _mm512_maskz_and_epi32(renorm_mask2, renorm_vals2, m16); // advance by however many words we actually read sp += _mm_popcnt_u32(renorm_mask2); R1 = _mm512_add_epi32(R1, renorm_vals1); R2 = _mm512_add_epi32(R2, renorm_vals2); //out[i+z] = S; _mm_storeu_si128((__m128i *)(out+i), _mm512_cvtepi32_epi8(S1_)); _mm_storeu_si128((__m128i *)(out+i+16), _mm512_cvtepi32_epi8(S2_)); } _mm512_store_epi32(&Rv[ 0], R1); _mm512_store_epi32(&Rv[16], R2); for (z = out_sz & (32-1); z-- > 0; ) out[out_end + z] = s3[Rv[z] & mask]; return out; err: free(out_free); return NULL; } #define TBUF8 #ifdef TBUF8 // 15% quicker overall O1 decode now due to rot32_simd below. // NB: This uses AVX2 though and we could rewrite using AVX512 for // further speed gains. static inline void transpose_and_copy(uint8_t *out, int iN[32], uint8_t t[32][32]) { // int z; // for (z = 0; z < 32; z++) { // int k; // for (k = 0; k < 32; k++) // out[iN[z]+k] = t[k][z]; // iN[z] += 32; // } rot32_simd(t, out, iN); } #else // Implemented using AVX512 gathers. // This is faster than a naive scalar implementation, but doesn't beat the // AVX2 vectorised 32x32 transpose function. static inline void transpose_and_copy_avx512(uint8_t *out, int iN[32], uint32_t t32[32][32]) { int z; // for (z = 0; z < 32; z++) { // int k; // for (k = 0; k < 32; k++) // out[iN[z]+k] = t32[k][z]; // iN[z] += 32; // } __m512i v1 = _mm512_set_epi32(15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0); v1 = _mm512_slli_epi32(v1, 5); for (z = 0; z < 32; z++) { __m512i t1 = _mm512_i32gather_epi32x(v1, &t32[ 0][z], 4); __m512i t2 = _mm512_i32gather_epi32x(v1, &t32[16][z], 4); _mm_storeu_si128((__m128i*)(&out[iN[z] ]), _mm512_cvtepi32_epi8(t1)); _mm_storeu_si128((__m128i*)(&out[iN[z]+16]), _mm512_cvtepi32_epi8(t2)); iN[z] += 32; } } #endif // TBUF unsigned char *rans_compress_O1_32x16_avx512(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { unsigned char *cp, *out_end, *out_free = NULL; unsigned int tab_size; uint32_t bound = rans_compress_bound_4x16(in_size,1)-20; int z; RansState ransN[32] __attribute__((aligned(64))); if (in_size < 32) // force O0 instead return NULL; if (!out) { *out_size = bound; out = malloc(*out_size); } if (!out || bound > *out_size) return NULL; if (((size_t)out)&1) bound--; out_end = out + bound; RansEncSymbol (*syms)[256] = htscodecs_tls_alloc(256 * (sizeof(*syms))); if (!syms) { free(out_free); return NULL; } cp = out; int shift = encode_freq1(in, in_size, 32, syms, &cp); if (shift < 0) { free(out_free); htscodecs_tls_free(syms); return NULL; } tab_size = cp - out; for (z = 0; z < 32; z++) RansEncInit(&ransN[z]); uint8_t* ptr = out_end; int iN[32] __attribute__((aligned(64))); int isz4 = in_size/32; for (z = 0; z < 32; z++) iN[z] = (z+1)*isz4-2; uint32_t lN[32] __attribute__((aligned(64))); for (z = 0; z < 32; z++) lN[z] = in[iN[z]+1]; // Deal with the remainder z = 32-1; lN[z] = in[in_size-1]; for (iN[z] = in_size-2; iN[z] > 32*isz4-2; iN[z]--) { unsigned char c = in[iN[z]]; RansEncPutSymbol(&ransN[z], &ptr, &syms[c][lN[z]]); lN[z] = c; } LOAD512(Rv, ransN); uint16_t *ptr16 = (uint16_t *)ptr; LOAD512(iN, iN); LOAD512(last, lN); __m512i c1 = _mm512_i32gather_epi32x1(iN1, in); __m512i c2 = _mm512_i32gather_epi32x1(iN2, in); // We cache the next 64-bytes locally and transpose. // This means we can load 32 ints from t32[x] with load instructions // instead of gathers. The copy, transpose and expand is easier done // in scalar code. #define BATCH 64 uint8_t t32[BATCH][32] __attribute__((aligned(64))); int next_batch; if (iN[0] > BATCH) { int i, j; for (i = 0; i < BATCH; i++) // memcpy(c[i], &in[iN[i]-32], 32); fast mode for (j = 0; j < 32; j++) t32[BATCH-1-i][j] = in[iN[j]-1-i]; next_batch = BATCH; } else { next_batch = -1; } for (; iN[0] >= 0; iN[0]--) { // Note, consider doing the same approach for the AVX2 encoder. // Maybe we can also get gather working well there? // Gather here is still a major latency bottleneck, consuming // around 40% of CPU cycles overall. // FIXME: maybe we need to cope with in[31] read over-flow // on loop cycles 0, 1, 2 where gather reads 32-bits instead of // 8 bits. Use set instead there on c2? // index into syms[0][0] array, used for x_max, rcp_freq, and bias __m512i vidx1 = _mm512_slli_epi32(c1, 8); __m512i vidx2 = _mm512_slli_epi32(c2, 8); vidx1 = _mm512_add_epi32(vidx1, last1); vidx2 = _mm512_add_epi32(vidx2, last2); vidx1 = _mm512_slli_epi32(vidx1, 2); vidx2 = _mm512_slli_epi32(vidx2, 2); // ------------------------------------------------------------ // for (z = NX-1; z >= 0; z--) { // if (ransN[z] >= x_max[z]) { // *--ptr16 = ransN[z] & 0xffff; // ransN[z] >>= 16; // } // } #define SET512x(a,x) \ __m512i a##1 = _mm512_i32gather_epi32x(vidx1, &syms[0][0].x, 4); \ __m512i a##2 = _mm512_i32gather_epi32x(vidx2, &syms[0][0].x, 4) // Start of next loop, moved here to remove latency. // last[z] = c[z] // iN[z]-- // c[z] = in[iN[z]] last1 = c1; last2 = c2; iN1 = _mm512_sub_epi32(iN1, _mm512_set1_epi32(1)); iN2 = _mm512_sub_epi32(iN2, _mm512_set1_epi32(1)); // Code below is equivalent to this: // c1 = _mm512_i32gather_epi32(iN1, in, 1); // c2 = _mm512_i32gather_epi32(iN2, in, 1); // Better when we have a power of 2 if (next_batch >= 0) { if (--next_batch < 0 && iN[0] > BATCH) { // Load 32 BATCH blocks of data. // Executed once every BATCH cycles int i, j; uint8_t c[32][BATCH]; iN[0] += BATCH; for (j = 0; j < 32; j++) { iN[j] -= BATCH; memcpy(c[j], &in[iN[j]-BATCH], BATCH); } // transpose matrix from 32xBATCH to BATCHx32 for (j = 0; j < 32; j++) { for (i = 0; i < BATCH; i+=16) { int z; for (z = 0; z < 16; z++) t32[i+z][j] = c[j][i+z]; } } next_batch = BATCH-1; } if (next_batch >= 0) { // Copy from our of our pre-loaded BATCHx32 tables // Executed every cycles __m128i c1_ = _mm_load_si128((__m128i *)&t32[next_batch][0]); __m128i c2_ = _mm_load_si128((__m128i *)&t32[next_batch][16]); c1 = _mm512_cvtepu8_epi32(c1_); c2 = _mm512_cvtepu8_epi32(c2_); } } if (next_batch < 0 && iN[0]) { // no pre-loaded data as within BATCHx32 of input end c1 = _mm512_i32gather_epi32x1(iN1, in); c2 = _mm512_i32gather_epi32x1(iN2, in); // Speeds up clang, even though not needed any more. // Harmless to leave here. c1 = _mm512_and_si512(c1, _mm512_set1_epi32(0xff)); c2 = _mm512_and_si512(c2, _mm512_set1_epi32(0xff)); } // End of "equivalent to" code block SET512x(xmax, x_max); // high latency uint16_t gt_mask1 = _mm512_cmpgt_epi32_mask(Rv1, xmax1); int pc1 = _mm_popcnt_u32(gt_mask1); __m512i Rp1 = _mm512_and_si512(Rv1, _mm512_set1_epi32(0xffff)); __m512i Rp2 = _mm512_and_si512(Rv2, _mm512_set1_epi32(0xffff)); uint16_t gt_mask2 = _mm512_cmpgt_epi32_mask(Rv2, xmax2); SET512x(SDv, cmpl_freq); // good int pc2 = _mm_popcnt_u32(gt_mask2); Rp1 = _mm512_maskz_compress_epi32(gt_mask1, Rp1); Rp2 = _mm512_maskz_compress_epi32(gt_mask2, Rp2); _mm512_mask_cvtepi32_storeu_epi16(ptr16-pc2, (1<> rcp_shift[z]); // ransN[z] = ransN[z] + bias[z] + q * cmpl_freq[z]; SET512x(rfv, rcp_freq); // good-ish __m512i rf1_hm = _mm512_mul_epu32(_mm512_srli_epi64(Rv1, 32), _mm512_srli_epi64(rfv1, 32)); __m512i rf2_hm = _mm512_mul_epu32(_mm512_srli_epi64(Rv2, 32), _mm512_srli_epi64(rfv2, 32)); __m512i rf1_lm = _mm512_srli_epi64(_mm512_mul_epu32(Rv1, rfv1), 32); __m512i rf2_lm = _mm512_srli_epi64(_mm512_mul_epu32(Rv2, rfv2), 32); const __m512i top32 = _mm512_set1_epi64((uint64_t)0xffffffff00000000); rf1_hm = _mm512_and_epi32(rf1_hm, top32); rf2_hm = _mm512_and_epi32(rf2_hm, top32); rfv1 = _mm512_or_epi32(rf1_lm, rf1_hm); rfv2 = _mm512_or_epi32(rf2_lm, rf2_hm); SET512x(biasv, bias); // good __m512i shiftv1 = _mm512_srli_epi32(SDv1, 16); __m512i shiftv2 = _mm512_srli_epi32(SDv2, 16); shiftv1 = _mm512_sub_epi32(shiftv1, _mm512_set1_epi32(32)); shiftv2 = _mm512_sub_epi32(shiftv2, _mm512_set1_epi32(32)); __m512i qv1 = _mm512_srlv_epi32(rfv1, shiftv1); __m512i qv2 = _mm512_srlv_epi32(rfv2, shiftv2); const __m512i bot16 = _mm512_set1_epi32(0xffff); qv1 = _mm512_mullo_epi32(qv1, _mm512_and_si512(SDv1, bot16)); qv2 = _mm512_mullo_epi32(qv2, _mm512_and_si512(SDv2, bot16)); qv1 = _mm512_add_epi32(qv1, biasv1); Rv1 = _mm512_add_epi32(Rv1, qv1); qv2 = _mm512_add_epi32(qv2, biasv2); Rv2 = _mm512_add_epi32(Rv2, qv2); } STORE512(Rv, ransN); STORE512(last, lN); ptr = (uint8_t *)ptr16; for (z = 32-1; z>=0; z--) RansEncPutSymbol(&ransN[z], &ptr, &syms[0][lN[z]]); for (z = 32-1; z >= 0; z--) RansEncFlush(&ransN[z], &ptr); // Finalise block size and return it *out_size = (out_end - ptr) + tab_size; // cp = out; // *cp++ = (in_size>> 0) & 0xff; // *cp++ = (in_size>> 8) & 0xff; // *cp++ = (in_size>>16) & 0xff; // *cp++ = (in_size>>24) & 0xff; memmove(out + tab_size, ptr, out_end-ptr); htscodecs_tls_free(syms); return out; } #define NX 32 unsigned char *rans_uncompress_O1_32x16_avx512(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { if (in_size < NX*4) // 4-states at least return NULL; if (out_sz >= INT_MAX) return NULL; // protect against some overflow cases /* Load in the static tables */ unsigned char *cp = in, *cp_end = in+in_size, *out_free = NULL; unsigned char *c_freq = NULL; uint32_t (*s3)[TOTFREQ_O1] = htscodecs_tls_alloc(256*TOTFREQ_O1*4); if (!s3) return NULL; uint32_t (*s3F)[TOTFREQ_O1_FAST] = (uint32_t (*)[TOTFREQ_O1_FAST])s3; if (!out) out_free = out = malloc(out_sz); if (!out) goto err; //fprintf(stderr, "out_sz=%d\n", out_sz); // compressed header? If so uncompress it unsigned char *tab_end = NULL; unsigned char *c_freq_end = cp_end; unsigned int shift = *cp >> 4; if (*cp++ & 1) { uint32_t u_freq_sz, c_freq_sz; cp += var_get_u32(cp, cp_end, &u_freq_sz); cp += var_get_u32(cp, cp_end, &c_freq_sz); if (c_freq_sz > cp_end - cp) goto err; tab_end = cp + c_freq_sz; if (!(c_freq = rans_uncompress_O0_4x16(cp, c_freq_sz, NULL, u_freq_sz))) goto err; cp = c_freq; c_freq_end = c_freq + u_freq_sz; } // Decode order-0 symbol list; avoids needing in order-1 tables cp += decode_freq1(cp, c_freq_end, shift, s3, s3F, NULL, NULL); if (tab_end) cp = tab_end; free(c_freq); c_freq = NULL; if (cp_end - cp < NX * 4) goto err; RansState R[NX] __attribute__((aligned(64))); uint8_t *ptr = cp, *ptr_end = in + in_size; int z; for (z = 0; z < NX; z++) { RansDecInit(&R[z], &ptr); if (R[z] < RANS_BYTE_L) goto err; } int isz4 = out_sz/NX; int iN[NX], lN[NX] __attribute__((aligned(64))) = {0}; for (z = 0; z < NX; z++) iN[z] = z*isz4; uint16_t *sp = (uint16_t *)ptr; const uint32_t mask = (1u << shift)-1; __m512i _maskv = _mm512_set1_epi32(mask); LOAD512(_Rv, R); LOAD512(_Lv, lN); #ifdef TBUF8 union { unsigned char tbuf[32][32]; uint64_t tbuf64[32][4]; } u __attribute__((aligned(32))); #else uint32_t tbuf[32][32]; #endif unsigned int tidx = 0; if (shift == TF_SHIFT_O1) { isz4 -= 64; for (; iN[0] < isz4 && (uint8_t *)sp+64 < ptr_end; ) { // m[z] = R[z] & mask; __m512i _masked1 = _mm512_and_si512(_Rv1, _maskv); __m512i _masked2 = _mm512_and_si512(_Rv2, _maskv); // S[z] = s3[lN[z]][m[z]]; _Lv1 = _mm512_slli_epi32(_Lv1, TF_SHIFT_O1); _Lv2 = _mm512_slli_epi32(_Lv2, TF_SHIFT_O1); _masked1 = _mm512_add_epi32(_masked1, _Lv1); _masked2 = _mm512_add_epi32(_masked2, _Lv2); // This is the biggest bottleneck __m512i _Sv1 = _mm512_i32gather_epi32x(_masked1, (int *)&s3F[0][0], sizeof(s3F[0][0])); __m512i _Sv2 = _mm512_i32gather_epi32x(_masked2, (int *)&s3F[0][0], sizeof(s3F[0][0])); // f[z] = S[z]>>(TF_SHIFT_O1+8); __m512i _fv1 = _mm512_srli_epi32(_Sv1, TF_SHIFT_O1+8); __m512i _fv2 = _mm512_srli_epi32(_Sv2, TF_SHIFT_O1+8); // b[z] = (S[z]>>8) & mask; __m512i _bv1 = _mm512_and_si512(_mm512_srli_epi32(_Sv1,8), _maskv); __m512i _bv2 = _mm512_and_si512(_mm512_srli_epi32(_Sv2,8), _maskv); // s[z] = S[z] & 0xff; __m512i _sv1 = _mm512_and_si512(_Sv1, _mm512_set1_epi32(0xff)); __m512i _sv2 = _mm512_and_si512(_Sv2, _mm512_set1_epi32(0xff)); // A maximum frequency of 4096 doesn't fit in our s3 array. // as it's 12 bit + 12 bit + 8 bit. It wraps around to zero. // (We don't have this issue for TOTFREQ_O1_FAST.) // // Solution 1 is to change to spec to forbid freq of 4096. // Easy hack is to add an extra symbol so it sums correctly. // => 572 MB/s on q40 (deskpro). // // Solution 2 implemented here is to look for the wrap around // and fix it. // => 556 MB/s on q40 // cope with max freq of 4096. Only 3% hit __m512i max_freq = _mm512_set1_epi32(TOTFREQ_O1); __m512i zero = _mm512_setzero_si512(); __mmask16 cmp1 = _mm512_cmpeq_epi32_mask(_fv1, zero); __mmask16 cmp2 = _mm512_cmpeq_epi32_mask(_fv2, zero); _fv1 = _mm512_mask_blend_epi32(cmp1, _fv1, max_freq); _fv2 = _mm512_mask_blend_epi32(cmp2, _fv2, max_freq); // R[z] = f[z] * (R[z] >> TF_SHIFT_O1) + b[z]; _Rv1 = _mm512_add_epi32( _mm512_mullo_epi32( _mm512_srli_epi32(_Rv1,TF_SHIFT_O1), _fv1), _bv1); _Rv2 = _mm512_add_epi32( _mm512_mullo_epi32( _mm512_srli_epi32(_Rv2,TF_SHIFT_O1), _fv2), _bv2); //for (z = 0; z < NX; z++) lN[z] = c[z]; _Lv1 = _sv1; _Lv2 = _sv2; // RansDecRenorm(&R[z], &ptr); __m512i _renorm_mask1 = _mm512_xor_si512(_Rv1, _mm512_set1_epi32(0x80000000)); __m512i _renorm_mask2 = _mm512_xor_si512(_Rv2, _mm512_set1_epi32(0x80000000)); int _imask1 =_mm512_cmpgt_epi32_mask (_mm512_set1_epi32(RANS_BYTE_L-0x80000000), _renorm_mask1); int _imask2 = _mm512_cmpgt_epi32_mask (_mm512_set1_epi32(RANS_BYTE_L-0x80000000), _renorm_mask2); __m512i renorm_words1 = _mm512_cvtepu16_epi32 (_mm256_loadu_si256((const __m256i *)sp)); sp += _mm_popcnt_u32(_imask1); __m512i renorm_words2 = _mm512_cvtepu16_epi32 (_mm256_loadu_si256((const __m256i *)sp)); sp += _mm_popcnt_u32(_imask2); __m512i _renorm_vals1 = _mm512_maskz_expand_epi32(_imask1, renorm_words1); __m512i _renorm_vals2 = _mm512_maskz_expand_epi32(_imask2, renorm_words2); _Rv1 = _mm512_mask_slli_epi32(_Rv1, _imask1, _Rv1, 16); _Rv2 = _mm512_mask_slli_epi32(_Rv2, _imask2, _Rv2, 16); _Rv1 = _mm512_add_epi32(_Rv1, _renorm_vals1); _Rv2 = _mm512_add_epi32(_Rv2, _renorm_vals2); #ifdef TBUF8 _mm_storeu_si128((__m128i *)(&u.tbuf64[tidx][0]), _mm512_cvtepi32_epi8(_Sv1)); // or _sv1? _mm_storeu_si128((__m128i *)(&u.tbuf64[tidx][2]), _mm512_cvtepi32_epi8(_Sv2)); #else _mm512_storeu_si512((__m512i *)(&tbuf[tidx][ 0]), _sv1); _mm512_storeu_si512((__m512i *)(&tbuf[tidx][16]), _sv2); #endif iN[0]++; if (++tidx == 32) { iN[0]-=32; // We have tidx[x][y] which we want to store in // memory in out[y][z] instead. This is an unrolled // transposition. #ifdef TBUF8 transpose_and_copy(out, iN, u.tbuf); #else transpose_and_copy_avx512(out, iN, tbuf); #endif tidx = 0; } } isz4 += 64; STORE512(_Rv, R); STORE512(_Lv, lN); ptr = (uint8_t *)sp; if (1) { iN[0]-=tidx; int T; for (z = 0; z < NX; z++) for (T = 0; T < tidx; T++) #ifdef TBUF8 out[iN[z]++] = u.tbuf[T][z]; #else out[iN[z]++] = tbuf[T][z]; #endif } // Scalar version for close to the end of in[] array so we don't // do SIMD loads beyond the end of the buffer for (; iN[0] < isz4;) { for (z = 0; z < NX; z++) { uint32_t m = R[z] & ((1u<>(TF_SHIFT_O1+8); R[z] = (F?F:4096) * (R[z]>>TF_SHIFT_O1) + ((S>>8) & ((1u<>(TF_SHIFT_O1+8); R[z] = (F?F:4096) * (R[z]>>TF_SHIFT_O1) + ((S>>8) & ((1u<>(TF_SHIFT_O1+8); __m512i _fv1 = _mm512_srli_epi32(_Sv1, TF_SHIFT_O1_FAST+8); __m512i _fv2 = _mm512_srli_epi32(_Sv2, TF_SHIFT_O1_FAST+8); // b[z] = (S[z]>>8) & mask; __m512i _bv1 = _mm512_and_si512(_mm512_srli_epi32(_Sv1,8), _maskv); __m512i _bv2 = _mm512_and_si512(_mm512_srli_epi32(_Sv2,8), _maskv); // s[z] = S[z] & 0xff; __m512i _sv1 = _mm512_and_si512(_Sv1, _mm512_set1_epi32(0xff)); __m512i _sv2 = _mm512_and_si512(_Sv2, _mm512_set1_epi32(0xff)); // R[z] = f[z] * (R[z] >> TF_SHIFT_O1) + b[z]; _Rv1 = _mm512_add_epi32( _mm512_mullo_epi32( _mm512_srli_epi32(_Rv1,TF_SHIFT_O1_FAST), _fv1), _bv1); _Rv2 = _mm512_add_epi32( _mm512_mullo_epi32( _mm512_srli_epi32(_Rv2,TF_SHIFT_O1_FAST), _fv2), _bv2); //for (z = 0; z < NX; z++) lN[z] = c[z]; _Lv1 = _sv1; _Lv2 = _sv2; // RansDecRenorm(&R[z], &ptr); __m512i _renorm_mask1 = _mm512_xor_si512(_Rv1, _mm512_set1_epi32(0x80000000)); __m512i _renorm_mask2 = _mm512_xor_si512(_Rv2, _mm512_set1_epi32(0x80000000)); int _imask1 =_mm512_cmpgt_epi32_mask (_mm512_set1_epi32(RANS_BYTE_L-0x80000000), _renorm_mask1); int _imask2 = _mm512_cmpgt_epi32_mask (_mm512_set1_epi32(RANS_BYTE_L-0x80000000), _renorm_mask2); __m512i renorm_words1 = _mm512_cvtepu16_epi32 (_mm256_loadu_si256((const __m256i *)sp)); sp += _mm_popcnt_u32(_imask1); __m512i renorm_words2 = _mm512_cvtepu16_epi32 (_mm256_loadu_si256((const __m256i *)sp)); sp += _mm_popcnt_u32(_imask2); __m512i _renorm_vals1 = _mm512_maskz_expand_epi32(_imask1, renorm_words1); __m512i _renorm_vals2 = _mm512_maskz_expand_epi32(_imask2, renorm_words2); _Rv1 = _mm512_mask_slli_epi32(_Rv1, _imask1, _Rv1, 16); _Rv2 = _mm512_mask_slli_epi32(_Rv2, _imask2, _Rv2, 16); _Rv1 = _mm512_add_epi32(_Rv1, _renorm_vals1); _Rv2 = _mm512_add_epi32(_Rv2, _renorm_vals2); #ifdef TBUF8 _mm_storeu_si128((__m128i *)(&u.tbuf64[tidx][0]), _mm512_cvtepi32_epi8(_Sv1)); // or _sv1? _mm_storeu_si128((__m128i *)(&u.tbuf64[tidx][2]), _mm512_cvtepi32_epi8(_Sv2)); #else _mm512_storeu_si512((__m512i *)(&tbuf[tidx][ 0]), _sv1); _mm512_storeu_si512((__m512i *)(&tbuf[tidx][16]), _sv2); #endif iN[0]++; if (++tidx == 32) { iN[0]-=32; #ifdef TBUF8 transpose_and_copy(out, iN, u.tbuf); #else transpose_and_copy_avx512(out, iN, tbuf); #endif tidx = 0; } } isz4 += 64; STORE512(_Rv, R); STORE512(_Lv, lN); ptr = (uint8_t *)sp; if (1) { iN[0]-=tidx; int T; for (z = 0; z < NX; z++) for (T = 0; T < tidx; T++) #ifdef TBUF8 out[iN[z]++] = u.tbuf[T][z]; #else out[iN[z]++] = tbuf[T][z]; #endif } // Scalar version for close to the end of in[] array so we don't // do SIMD loads beyond the end of the buffer for (; iN[0] < isz4;) { for (z = 0; z < NX; z++) { uint32_t m = R[z] & ((1u<>(TF_SHIFT_O1_FAST+8)) * (R[z]>>TF_SHIFT_O1_FAST) + ((S>>8) & ((1u<>(TF_SHIFT_O1_FAST+8)) * (R[z]>>TF_SHIFT_O1_FAST) + ((S>>8) & ((1u< #include #include #include "rANS_word.h" #include "rANS_static4x16.h" #include "rANS_static16_int.h" #include "varint.h" #include "utils.h" #define NX 32 // TODO: get access to MVE architecture so we can tune for the newer // SIMD instructions. // // #if __ARM_FEATURE_MVE & 1 // #include // Helium, eg for use of vcreateq_u32 // #endif #define _ 99 static uint8x8_t vtab[16] = { {_,_, _,_, _,_, _,_ }, {_,_, _,_, _,_, 12,13}, {_,_, _,_, _,_, 8,9 }, {_,_, _,_, 8,9, 12,13}, {_,_, _,_, _,_, 4,5 }, {_,_, _,_, 4,5, 12,13}, {_,_, _,_, 4,5, 8,9 }, {_,_, 4,5, 8,9, 12,13}, {_,_, _,_, _,_, 0,1 }, {_,_, _,_, 0,1, 12,13}, {_,_, _,_, 0,1, 8,9 }, {_,_, 0,1 , 8,9, 12,13}, {_,_, _,_, 0,1, 4,5 }, {_,_, 0,1, 4,5, 12,13}, {_,_, 0,1, 4,5, 8,9 }, {0,1, 4,5, 8,9, 12,13}, }; #undef _ unsigned char *rans_compress_O0_32x16_neon(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { unsigned char *cp, *out_end; RansEncSymbol syms[256]; RansState R[NX]; uint8_t* ptr; uint32_t F[256+MAGIC] = {0}; int i, j, tab_size = 0, x, z; // -20 for order/size/meta uint32_t bound = rans_compress_bound_4x16(in_size,0)-20; if (!out) { *out_size = bound; out = malloc(*out_size); } if (!out || bound > *out_size) return NULL; // If "out" isn't word aligned, tweak out_end/ptr to ensure it is. // We already added more round in bound to allow for this. if (((size_t)out)&1) bound--; ptr = out_end = out + bound; if (in_size == 0) goto empty; // Compute statistics if (hist8(in, in_size, F) < 0) return NULL; // Normalise so frequences sum to power of 2 uint32_t fsum = in_size; uint32_t max_val = round2(fsum); if (max_val > TOTFREQ) max_val = TOTFREQ; if (normalise_freq(F, fsum, max_val) < 0) return NULL; fsum=max_val; cp = out; cp += encode_freq(cp, F); tab_size = cp-out; //write(2, out+4, cp-(out+4)); if (normalise_freq(F, fsum, TOTFREQ) < 0) return NULL; // Encode statistics. for (x = j = 0; j < 256; j++) { if (F[j]) { RansEncSymbolInit(&syms[j], x, F[j], TF_SHIFT); x += F[j]; } } for (z = 0; z < NX; z++) RansEncInit(&R[z]); z = i = in_size&(NX-1); while (z-- > 0) RansEncPutSymbol(&R[z], &ptr, &syms[in[in_size-(i-z)]]); for (i=(in_size &~(NX-1)); i>0; i-=NX) { // // Scalar equivalent // for (z = NX-1; z >= 0; z-=4) { // // 327 / 272 // RansEncSymbol *s0 = &syms[in[i-(NX-z+0)]]; // RansEncSymbol *s1 = &syms[in[i-(NX-z+1)]]; // RansEncSymbol *s2 = &syms[in[i-(NX-z+2)]]; // RansEncSymbol *s3 = &syms[in[i-(NX-z+3)]]; // // RansEncPutSymbol(&R[z-0], &ptr, s0); // RansEncPutSymbol(&R[z-1], &ptr, s1); // RansEncPutSymbol(&R[z-2], &ptr, s2); // RansEncPutSymbol(&R[z-3], &ptr, s3); // } // SIMD with 16-way unrolling for (z = NX-1; z >= 0; z-=8) { RansEncSymbol *s0 = &syms[in[i-(NX-z+0)]]; RansEncSymbol *s1 = &syms[in[i-(NX-z+1)]]; RansEncSymbol *s2 = &syms[in[i-(NX-z+2)]]; RansEncSymbol *s3 = &syms[in[i-(NX-z+3)]]; RansEncSymbol *s4 = &syms[in[i-(NX-z+4)]]; RansEncSymbol *s5 = &syms[in[i-(NX-z+5)]]; RansEncSymbol *s6 = &syms[in[i-(NX-z+6)]]; RansEncSymbol *s7 = &syms[in[i-(NX-z+7)]]; uint32x4_t Rv1 = vld1q_u32(&R[z-3]); uint32x4_t Rv2 = vld1q_u32(&R[z-7]); // Sym bit sizes = 128bits // 32: x_max // 32: rcp_freq // 32: bias // 16: cmpl_freq // 16: rcp_shift // Load and shuffle around // A <---Xmax---><---RFreq--><---Bias---><-cf-><-rs-> // B <---Xmax---><---RFreq--><---Bias---><-cf-><-rs-> // C <---Xmax---><---RFreq--><---Bias---><-cf-><-rs-> // D <---Xmax---><---RFreq--><---Bias---><-cf-><-rs-> // vtrn1q_u32 vtrn2q_u32 (A1 = A+B) // A1 <---Xmax---><---Xmax---><---Bias---><---Bias---> // C1 <---Xmax---><---Xmax---><---Bias---><---Bias---> // A2 <---RFreq--><---RFreq--><-cf-><-rs-><-cf-><-rs-> // C2 <---RFreq--><---RFreq--><-cf-><-rs-><-cf-><-rs-> // vtrn1q_u64 vtrn2q_u64 (A11 = A1+C1) // A11 <---Xmax---><---Xmax---><---Xmax---><---Xmax---> // A12 <---Bias---><---Bias---><---Bias---><---Bias---> // A21 <---RFreq--><---RFreq--><---RFreq--><---RFreq--> // A22 <-cf-><-rs-><-cf-><-rs-><-cf-><-rs-><-cf-><-rs-> uint32x4_t A_1 = vld1q_u32((void *)s3); uint32x4_t B_1 = vld1q_u32((void *)s2); uint32x4_t C_1 = vld1q_u32((void *)s1); uint32x4_t D_1 = vld1q_u32((void *)s0); uint32x4_t A1_1 = vtrn1q_u32(A_1, B_1); uint32x4_t C1_1 = vtrn1q_u32(C_1, D_1); uint32x4_t A2_1 = vtrn2q_u32(A_1, B_1); uint32x4_t C2_1 = vtrn2q_u32(C_1, D_1); #define u32_u64(x) vreinterpretq_u32_u64((x)) #define u64_u32(x) vreinterpretq_u64_u32((x)) uint32x4_t Xmaxv1=u32_u64(vtrn1q_u64(u64_u32(A1_1),u64_u32(C1_1))); uint32x4_t Biasv1=u32_u64(vtrn2q_u64(u64_u32(A1_1),u64_u32(C1_1))); uint32x4_t RFv1 =u32_u64(vtrn1q_u64(u64_u32(A2_1),u64_u32(C2_1))); uint32x4_t FSv1 =u32_u64(vtrn2q_u64(u64_u32(A2_1),u64_u32(C2_1))); uint32x4_t A_2 = vld1q_u32((void *)s7); uint32x4_t B_2 = vld1q_u32((void *)s6); uint32x4_t C_2 = vld1q_u32((void *)s5); uint32x4_t D_2 = vld1q_u32((void *)s4); uint32x4_t A1_2 = vtrn1q_u32(A_2, B_2); uint32x4_t C1_2 = vtrn1q_u32(C_2, D_2); uint32x4_t A2_2 = vtrn2q_u32(A_2, B_2); uint32x4_t C2_2 = vtrn2q_u32(C_2, D_2); uint32x4_t Xmaxv2=u32_u64(vtrn1q_u64(u64_u32(A1_2),u64_u32(C1_2))); uint32x4_t Biasv2=u32_u64(vtrn2q_u64(u64_u32(A1_2),u64_u32(C1_2))); uint32x4_t RFv2 =u32_u64(vtrn1q_u64(u64_u32(A2_2),u64_u32(C2_2))); uint32x4_t FSv2 =u32_u64(vtrn2q_u64(u64_u32(A2_2),u64_u32(C2_2))); // Turn multi R>16 uint32x4_t Rv1_r = vshrq_n_u32(Rv1, 16); uint32x4_t Rv2_r = vshrq_n_u32(Rv2, 16); // Blend R and R' based on Cv. Rv1 = vbslq_u32(Cv1, Rv1_r, Rv1); Rv2 = vbslq_u32(Cv2, Rv2_r, Rv2); // R -> R' update // q = (uint32_t) (((uint64_t)x * rcp_freq) >> rcp_shift); // R' = R + sym->bias + q * sym->cmpl_freq; // Mix SIMD (mul) & scalar (shift). 365MB/s // We do 32 x 32 mul to get 64-bit, but then extract this // a 64-bit quantity and shift as scalar, before // recreating the 32x4 result. Despite SIMD-scalar-SIMD reg // it's slightly quicker. uint64x2_t qvl1 = vmull_u32(vget_low_u32(Rv1), vget_low_u32(RFv1)); uint64x2_t qvh1 = vmull_high_u32(Rv1, RFv1); uint64x2_t qvl2 = vmull_u32(vget_low_u32(Rv2), vget_low_u32(RFv2)); uint64x2_t qvh2 = vmull_high_u32(Rv2, RFv2); uint32x2_t qv1a = vcreate_u32(vgetq_lane_u64(qvl1, 1) >> s2->rcp_shift << 32 | vgetq_lane_u64(qvl1, 0) >> s3->rcp_shift); uint32x2_t qv1b = vcreate_u32(vgetq_lane_u64(qvh1, 1) >> s0->rcp_shift << 32 | vgetq_lane_u64(qvh1, 0) >> s1->rcp_shift); uint32x2_t qv2a = vcreate_u32(vgetq_lane_u64(qvl2, 1) >> s6->rcp_shift << 32 | vgetq_lane_u64(qvl2, 0) >> s7->rcp_shift); uint32x2_t qv2b = vcreate_u32(vgetq_lane_u64(qvh2, 1) >> s4->rcp_shift << 32 | vgetq_lane_u64(qvh2, 0) >> s5->rcp_shift); uint32x4_t qv1 = vcombine_u32(qv1a, qv1b); uint32x4_t qv2 = vcombine_u32(qv2a, qv2b); FSv1 = vandq_u32(FSv1, vdupq_n_u32(0xffff)); // cmpl_freq FSv2 = vandq_u32(FSv2, vdupq_n_u32(0xffff)); qv1 = vmlaq_u32(Biasv1, qv1, FSv1); qv2 = vmlaq_u32(Biasv2, qv2, FSv2); Rv1 = vaddq_u32(Rv1, qv1); Rv2 = vaddq_u32(Rv2, qv2); vst1q_u32(&R[z-3], Rv1); vst1q_u32(&R[z-7], Rv2); } if (z < -1) abort(); } for (z = NX-1; z >= 0; z--) RansEncFlush(&R[z], &ptr); empty: // Finalise block size and return it *out_size = (out_end - ptr) + tab_size; memmove(out + tab_size, ptr, out_end-ptr); return out; } #define _ 99 static uint8x8_t idx[16] = { { _,_,_,_,_,_,_,_ }, // 0000 { _,_,_,_,_,_,0,1 }, // 0001 { _,_,_,_,0,1,_,_ }, // 0010 { _,_,_,_,0,1,2,3 }, // 0011 { _,_,0,1,_,_,_,_ }, // 0100 { _,_,0,1,_,_,2,3 }, // 0101 { _,_,0,1,2,3,_,_ }, // 0110 { _,_,0,1,2,3,4,5 }, // 0111 { 0,1,_,_,_,_,_,_ }, // 1000 { 0,1,_,_,_,_,2,3 }, // 1001 { 0,1,_,_,2,3,_,_ }, // 1010 { 0,1,_,_,2,3,4,5 }, // 1011 { 0,1,2,3,_,_,_,_ }, // 1100 { 0,1,2,3,_,_,4,5 }, // 1101 { 0,1,2,3,4,5,_,_ }, // 1110 { 0,1,2,3,4,5,6,7 }, // 1111 }; // norm2 with norm1 in top 4 bits already consumed static uint8x8_t idx2[256] = { { _, _, _, _, _, _, _, _, }, { _, _, _, _, _, _, 0, 1, }, { _, _, _, _, 0, 1, _, _, }, { _, _, _, _, 0, 1, 2, 3, }, { _, _, 0, 1, _, _, _, _, }, { _, _, 0, 1, _, _, 2, 3, }, { _, _, 0, 1, 2, 3, _, _, }, { _, _, 0, 1, 2, 3, 4, 5, }, { 0, 1, _, _, _, _, _, _, }, { 0, 1, _, _, _, _, 2, 3, }, { 0, 1, _, _, 2, 3, _, _, }, { 0, 1, _, _, 2, 3, 4, 5, }, { 0, 1, 2, 3, _, _, _, _, }, { 0, 1, 2, 3, _, _, 4, 5, }, { 0, 1, 2, 3, 4, 5, _, _, }, { 0, 1, 2, 3, 4, 5, 6, 7, }, { _, _, _, _, _, _, _, _, }, { _, _, _, _, _, _, 2, 3, }, { _, _, _, _, 2, 3, _, _, }, { _, _, _, _, 2, 3, 4, 5, }, { _, _, 2, 3, _, _, _, _, }, { _, _, 2, 3, _, _, 4, 5, }, { _, _, 2, 3, 4, 5, _, _, }, { _, _, 2, 3, 4, 5, 6, 7, }, { 2, 3, _, _, _, _, _, _, }, { 2, 3, _, _, _, _, 4, 5, }, { 2, 3, _, _, 4, 5, _, _, }, { 2, 3, _, _, 4, 5, 6, 7, }, { 2, 3, 4, 5, _, _, _, _, }, { 2, 3, 4, 5, _, _, 6, 7, }, { 2, 3, 4, 5, 6, 7, _, _, }, { 2, 3, 4, 5, 6, 7, 8, 9, }, { _, _, _, _, _, _, _, _, }, { _, _, _, _, _, _, 2, 3, }, { _, _, _, _, 2, 3, _, _, }, { _, _, _, _, 2, 3, 4, 5, }, { _, _, 2, 3, _, _, _, _, }, { _, _, 2, 3, _, _, 4, 5, }, { _, _, 2, 3, 4, 5, _, _, }, { _, _, 2, 3, 4, 5, 6, 7, }, { 2, 3, _, _, _, _, _, _, }, { 2, 3, _, _, _, _, 4, 5, }, { 2, 3, _, _, 4, 5, _, _, }, { 2, 3, _, _, 4, 5, 6, 7, }, { 2, 3, 4, 5, _, _, _, _, }, { 2, 3, 4, 5, _, _, 6, 7, }, { 2, 3, 4, 5, 6, 7, _, _, }, { 2, 3, 4, 5, 6, 7, 8, 9, }, { _, _, _, _, _, _, _, _, }, { _, _, _, _, _, _, 4, 5, }, { _, _, _, _, 4, 5, _, _, }, { _, _, _, _, 4, 5, 6, 7, }, { _, _, 4, 5, _, _, _, _, }, { _, _, 4, 5, _, _, 6, 7, }, { _, _, 4, 5, 6, 7, _, _, }, { _, _, 4, 5, 6, 7, 8, 9, }, { 4, 5, _, _, _, _, _, _, }, { 4, 5, _, _, _, _, 6, 7, }, { 4, 5, _, _, 6, 7, _, _, }, { 4, 5, _, _, 6, 7, 8, 9, }, { 4, 5, 6, 7, _, _, _, _, }, { 4, 5, 6, 7, _, _, 8, 9, }, { 4, 5, 6, 7, 8, 9, _, _, }, { 4, 5, 6, 7, 8, 9,10,11, }, { _, _, _, _, _, _, _, _, }, { _, _, _, _, _, _, 2, 3, }, { _, _, _, _, 2, 3, _, _, }, { _, _, _, _, 2, 3, 4, 5, }, { _, _, 2, 3, _, _, _, _, }, { _, _, 2, 3, _, _, 4, 5, }, { _, _, 2, 3, 4, 5, _, _, }, { _, _, 2, 3, 4, 5, 6, 7, }, { 2, 3, _, _, _, _, _, _, }, { 2, 3, _, _, _, _, 4, 5, }, { 2, 3, _, _, 4, 5, _, _, }, { 2, 3, _, _, 4, 5, 6, 7, }, { 2, 3, 4, 5, _, _, _, _, }, { 2, 3, 4, 5, _, _, 6, 7, }, { 2, 3, 4, 5, 6, 7, _, _, }, { 2, 3, 4, 5, 6, 7, 8, 9, }, { _, _, _, _, _, _, _, _, }, { _, _, _, _, _, _, 4, 5, }, { _, _, _, _, 4, 5, _, _, }, { _, _, _, _, 4, 5, 6, 7, }, { _, _, 4, 5, _, _, _, _, }, { _, _, 4, 5, _, _, 6, 7, }, { _, _, 4, 5, 6, 7, _, _, }, { _, _, 4, 5, 6, 7, 8, 9, }, { 4, 5, _, _, _, _, _, _, }, { 4, 5, _, _, _, _, 6, 7, }, { 4, 5, _, _, 6, 7, _, _, }, { 4, 5, _, _, 6, 7, 8, 9, }, { 4, 5, 6, 7, _, _, _, _, }, { 4, 5, 6, 7, _, _, 8, 9, }, { 4, 5, 6, 7, 8, 9, _, _, }, { 4, 5, 6, 7, 8, 9,10,11, }, { _, _, _, _, _, _, _, _, }, { _, _, _, _, _, _, 4, 5, }, { _, _, _, _, 4, 5, _, _, }, { _, _, _, _, 4, 5, 6, 7, }, { _, _, 4, 5, _, _, _, _, }, { _, _, 4, 5, _, _, 6, 7, }, { _, _, 4, 5, 6, 7, _, _, }, { _, _, 4, 5, 6, 7, 8, 9, }, { 4, 5, _, _, _, _, _, _, }, { 4, 5, _, _, _, _, 6, 7, }, { 4, 5, _, _, 6, 7, _, _, }, { 4, 5, _, _, 6, 7, 8, 9, }, { 4, 5, 6, 7, _, _, _, _, }, { 4, 5, 6, 7, _, _, 8, 9, }, { 4, 5, 6, 7, 8, 9, _, _, }, { 4, 5, 6, 7, 8, 9,10,11, }, { _, _, _, _, _, _, _, _, }, { _, _, _, _, _, _, 6, 7, }, { _, _, _, _, 6, 7, _, _, }, { _, _, _, _, 6, 7, 8, 9, }, { _, _, 6, 7, _, _, _, _, }, { _, _, 6, 7, _, _, 8, 9, }, { _, _, 6, 7, 8, 9, _, _, }, { _, _, 6, 7, 8, 9,10,11, }, { 6, 7, _, _, _, _, _, _, }, { 6, 7, _, _, _, _, 8, 9, }, { 6, 7, _, _, 8, 9, _, _, }, { 6, 7, _, _, 8, 9,10,11, }, { 6, 7, 8, 9, _, _, _, _, }, { 6, 7, 8, 9, _, _,10,11, }, { 6, 7, 8, 9,10,11, _, _, }, { 6, 7, 8, 9,10,11,12,13, }, { _, _, _, _, _, _, _, _, }, { _, _, _, _, _, _, 2, 3, }, { _, _, _, _, 2, 3, _, _, }, { _, _, _, _, 2, 3, 4, 5, }, { _, _, 2, 3, _, _, _, _, }, { _, _, 2, 3, _, _, 4, 5, }, { _, _, 2, 3, 4, 5, _, _, }, { _, _, 2, 3, 4, 5, 6, 7, }, { 2, 3, _, _, _, _, _, _, }, { 2, 3, _, _, _, _, 4, 5, }, { 2, 3, _, _, 4, 5, _, _, }, { 2, 3, _, _, 4, 5, 6, 7, }, { 2, 3, 4, 5, _, _, _, _, }, { 2, 3, 4, 5, _, _, 6, 7, }, { 2, 3, 4, 5, 6, 7, _, _, }, { 2, 3, 4, 5, 6, 7, 8, 9, }, { _, _, _, _, _, _, _, _, }, { _, _, _, _, _, _, 4, 5, }, { _, _, _, _, 4, 5, _, _, }, { _, _, _, _, 4, 5, 6, 7, }, { _, _, 4, 5, _, _, _, _, }, { _, _, 4, 5, _, _, 6, 7, }, { _, _, 4, 5, 6, 7, _, _, }, { _, _, 4, 5, 6, 7, 8, 9, }, { 4, 5, _, _, _, _, _, _, }, { 4, 5, _, _, _, _, 6, 7, }, { 4, 5, _, _, 6, 7, _, _, }, { 4, 5, _, _, 6, 7, 8, 9, }, { 4, 5, 6, 7, _, _, _, _, }, { 4, 5, 6, 7, _, _, 8, 9, }, { 4, 5, 6, 7, 8, 9, _, _, }, { 4, 5, 6, 7, 8, 9,10,11, }, { _, _, _, _, _, _, _, _, }, { _, _, _, _, _, _, 4, 5, }, { _, _, _, _, 4, 5, _, _, }, { _, _, _, _, 4, 5, 6, 7, }, { _, _, 4, 5, _, _, _, _, }, { _, _, 4, 5, _, _, 6, 7, }, { _, _, 4, 5, 6, 7, _, _, }, { _, _, 4, 5, 6, 7, 8, 9, }, { 4, 5, _, _, _, _, _, _, }, { 4, 5, _, _, _, _, 6, 7, }, { 4, 5, _, _, 6, 7, _, _, }, { 4, 5, _, _, 6, 7, 8, 9, }, { 4, 5, 6, 7, _, _, _, _, }, { 4, 5, 6, 7, _, _, 8, 9, }, { 4, 5, 6, 7, 8, 9, _, _, }, { 4, 5, 6, 7, 8, 9,10,11, }, { _, _, _, _, _, _, _, _, }, { _, _, _, _, _, _, 6, 7, }, { _, _, _, _, 6, 7, _, _, }, { _, _, _, _, 6, 7, 8, 9, }, { _, _, 6, 7, _, _, _, _, }, { _, _, 6, 7, _, _, 8, 9, }, { _, _, 6, 7, 8, 9, _, _, }, { _, _, 6, 7, 8, 9,10,11, }, { 6, 7, _, _, _, _, _, _, }, { 6, 7, _, _, _, _, 8, 9, }, { 6, 7, _, _, 8, 9, _, _, }, { 6, 7, _, _, 8, 9,10,11, }, { 6, 7, 8, 9, _, _, _, _, }, { 6, 7, 8, 9, _, _,10,11, }, { 6, 7, 8, 9,10,11, _, _, }, { 6, 7, 8, 9,10,11,12,13, }, { _, _, _, _, _, _, _, _, }, { _, _, _, _, _, _, 4, 5, }, { _, _, _, _, 4, 5, _, _, }, { _, _, _, _, 4, 5, 6, 7, }, { _, _, 4, 5, _, _, _, _, }, { _, _, 4, 5, _, _, 6, 7, }, { _, _, 4, 5, 6, 7, _, _, }, { _, _, 4, 5, 6, 7, 8, 9, }, { 4, 5, _, _, _, _, _, _, }, { 4, 5, _, _, _, _, 6, 7, }, { 4, 5, _, _, 6, 7, _, _, }, { 4, 5, _, _, 6, 7, 8, 9, }, { 4, 5, 6, 7, _, _, _, _, }, { 4, 5, 6, 7, _, _, 8, 9, }, { 4, 5, 6, 7, 8, 9, _, _, }, { 4, 5, 6, 7, 8, 9,10,11, }, { _, _, _, _, _, _, _, _, }, { _, _, _, _, _, _, 6, 7, }, { _, _, _, _, 6, 7, _, _, }, { _, _, _, _, 6, 7, 8, 9, }, { _, _, 6, 7, _, _, _, _, }, { _, _, 6, 7, _, _, 8, 9, }, { _, _, 6, 7, 8, 9, _, _, }, { _, _, 6, 7, 8, 9,10,11, }, { 6, 7, _, _, _, _, _, _, }, { 6, 7, _, _, _, _, 8, 9, }, { 6, 7, _, _, 8, 9, _, _, }, { 6, 7, _, _, 8, 9,10,11, }, { 6, 7, 8, 9, _, _, _, _, }, { 6, 7, 8, 9, _, _,10,11, }, { 6, 7, 8, 9,10,11, _, _, }, { 6, 7, 8, 9,10,11,12,13, }, { _, _, _, _, _, _, _, _, }, { _, _, _, _, _, _, 6, 7, }, { _, _, _, _, 6, 7, _, _, }, { _, _, _, _, 6, 7, 8, 9, }, { _, _, 6, 7, _, _, _, _, }, { _, _, 6, 7, _, _, 8, 9, }, { _, _, 6, 7, 8, 9, _, _, }, { _, _, 6, 7, 8, 9,10,11, }, { 6, 7, _, _, _, _, _, _, }, { 6, 7, _, _, _, _, 8, 9, }, { 6, 7, _, _, 8, 9, _, _, }, { 6, 7, _, _, 8, 9,10,11, }, { 6, 7, 8, 9, _, _, _, _, }, { 6, 7, 8, 9, _, _,10,11, }, { 6, 7, 8, 9,10,11, _, _, }, { 6, 7, 8, 9,10,11,12,13, }, { _, _, _, _, _, _, _, _, }, { _, _, _, _, _, _, 8, 9, }, { _, _, _, _, 8, 9, _, _, }, { _, _, _, _, 8, 9,10,11, }, { _, _, 8, 9, _, _, _, _, }, { _, _, 8, 9, _, _,10,11, }, { _, _, 8, 9,10,11, _, _, }, { _, _, 8, 9,10,11,12,13, }, { 8, 9, _, _, _, _, _, _, }, { 8, 9, _, _, _, _,10,11, }, { 8, 9, _, _,10,11, _, _, }, { 8, 9, _, _,10,11,12,13, }, { 8, 9,10,11, _, _, _, _, }, { 8, 9,10,11, _, _,12,13, }, { 8, 9,10,11,12,13, _, _, }, { 8, 9,10,11,12,13,14,15, }, }; // SIMD: 650MB/s unsigned char *rans_uncompress_O0_32x16_neon(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { if (in_size < 16) // 4-states at least return NULL; if (out_sz >= INT_MAX) return NULL; // protect against some overflow cases /* Load in the static tables */ unsigned char *cp = in, *out_free = NULL; unsigned char *cp_end = in + in_size; int i; uint32_t s3[TOTFREQ]; // For TF_SHIFT <= 12 if (!out) out_free = out = malloc(out_sz); if (!out) return NULL; // Precompute reverse lookup of frequency. uint32_t F[256] = {0}, fsum; int fsz = decode_freq(cp, cp_end, F, &fsum); if (!fsz) goto err; cp += fsz; normalise_freq_shift(F, fsum, TOTFREQ); // Build symbols; fixme, do as part of decode, see the _d variant if (rans_F_to_s3(F, TF_SHIFT, s3)) goto err; if (cp_end - cp < NX * 4) goto err; int z; RansState R[NX]; for (z = 0; z < NX; z++) { RansDecInit(&R[z], &cp); if (R[z] < RANS_BYTE_L) goto err; } int out_end = (out_sz&~(NX-1)); const uint32_t mask = (1u << TF_SHIFT)-1; uint32x4_t maskv = vdupq_n_u32((1u << TF_SHIFT)-1); // assume NX is divisible by 4 assert(NX%4==0); uint32x4_t Rv1 = vld1q_u32(&R[0]); uint32x4_t Rv2 = vld1q_u32(&R[4]); uint32x4_t Rv3 = vld1q_u32(&R[8]); uint32x4_t Rv4 = vld1q_u32(&R[12]); uint32x4_t Rv5 = vld1q_u32(&R[16]); uint32x4_t Rv6 = vld1q_u32(&R[20]); uint32x4_t Rv7 = vld1q_u32(&R[24]); uint32x4_t Rv8 = vld1q_u32(&R[28]); // Note this has a considerable amount of manual instruction reordering // to avoid latency. We have 8 lanes of 4 rans states, but process 4 // lanes at a time with the two sets of 4-lane steps interleaved to // ensure best use of processor pipeline units and latency removal. // // Unfortunately this is still poor with Clang-10. Gcc more or less // honours this order and on my test set operates at ~675MB/s decode. // Clang without the manual reordering was at 440MB/s and with it at // 500MB/s. Clang does a lot of reordering of this code, removing some // of the manual tuning benefits. Short of dropping to assembly, for now // I would recommend using gcc to compile this file. uint16_t *sp = (uint16_t *)cp; uint8_t overflow[64+64] = {0}; for (i=0; i < out_end; i+=NX) { // Decode freq, bias and symbol from s3 lookups uint32x4_t Sv1, Sv2, Sv3, Sv4, Sv5, Sv6, Sv7, Sv8; uint32x4_t Fv1, Fv2, Fv3, Fv4, Fv5, Fv6, Fv7, Fv8; uint32x4_t Bv1, Bv2, Bv3, Bv4, Bv5, Bv6, Bv7, Bv8; // Note we could check __ARM_FEATURE_MVE & 1 and use // vcreateq_u32 here, but I don't have a system to test with // so cannot validate if the code works. uint32x2_t s1a, s1b, s2a, s2b, s3a, s3b, s4a, s4b; s1a = vcreate_u32((uint64_t)(s3[R[ 1]&mask])<<32 | (s3[R[ 0]&mask])); s2a = vcreate_u32((uint64_t)(s3[R[ 5]&mask])<<32 | (s3[R[ 4]&mask])); s1b = vcreate_u32((uint64_t)(s3[R[ 3]&mask])<<32 | (s3[R[ 2]&mask])); s2b = vcreate_u32((uint64_t)(s3[R[ 7]&mask])<<32 | (s3[R[ 6]&mask])); s3a = vcreate_u32((uint64_t)(s3[R[ 9]&mask])<<32 | (s3[R[ 8]&mask])); s3b = vcreate_u32((uint64_t)(s3[R[11]&mask])<<32 | (s3[R[10]&mask])); s4a = vcreate_u32((uint64_t)(s3[R[13]&mask])<<32 | (s3[R[12]&mask])); s4b = vcreate_u32((uint64_t)(s3[R[15]&mask])<<32 | (s3[R[14]&mask])); Sv1 = vcombine_u32(s1a, s1b); Sv2 = vcombine_u32(s2a, s2b); Sv3 = vcombine_u32(s3a, s3b); Sv4 = vcombine_u32(s4a, s4b); Fv1 = vshrq_n_u32(Sv1, TF_SHIFT+8); // Freq = S >> TF_SHIFT+8 Fv2 = vshrq_n_u32(Sv2, TF_SHIFT+8); Fv3 = vshrq_n_u32(Sv3, TF_SHIFT+8); Fv4 = vshrq_n_u32(Sv4, TF_SHIFT+8); uint32x2_t s5a, s5b, s6a, s6b, s7a, s7b, s8a, s8b; s5a = vcreate_u32((uint64_t)(s3[R[17]&mask])<<32 | (s3[R[16]&mask])); s5b = vcreate_u32((uint64_t)(s3[R[19]&mask])<<32 | (s3[R[18]&mask])); s6a = vcreate_u32((uint64_t)(s3[R[21]&mask])<<32 | (s3[R[20]&mask])); s6b = vcreate_u32((uint64_t)(s3[R[23]&mask])<<32 | (s3[R[22]&mask])); s7a = vcreate_u32((uint64_t)(s3[R[25]&mask])<<32 | (s3[R[24]&mask])); s7b = vcreate_u32((uint64_t)(s3[R[27]&mask])<<32 | (s3[R[26]&mask])); s8a = vcreate_u32((uint64_t)(s3[R[29]&mask])<<32 | (s3[R[28]&mask])); s8b = vcreate_u32((uint64_t)(s3[R[31]&mask])<<32 | (s3[R[30]&mask])); Bv1 = vshrq_n_u32(Sv1, 8); // Bias = (S >> 8) Bv2 = vshrq_n_u32(Sv2, 8); Bv3 = vshrq_n_u32(Sv3, 8); Bv4 = vshrq_n_u32(Sv4, 8); // R[0] = (freq * (R[0] >> TF_SHIFT) + bias; Rv1 = vshrq_n_u32(Rv1, TF_SHIFT); // R >> TF_SHIFT Rv2 = vshrq_n_u32(Rv2, TF_SHIFT); Rv3 = vshrq_n_u32(Rv3, TF_SHIFT); Rv4 = vshrq_n_u32(Rv4, TF_SHIFT); Sv5 = vcombine_u32(s5a, s5b); Sv6 = vcombine_u32(s6a, s6b); Sv7 = vcombine_u32(s7a, s7b); Sv8 = vcombine_u32(s8a, s8b); Bv1 = vandq_u32(Bv1, maskv); // & mask Bv2 = vandq_u32(Bv2, maskv); Bv3 = vandq_u32(Bv3, maskv); Bv4 = vandq_u32(Bv4, maskv); Fv5 = vshrq_n_u32(Sv5, TF_SHIFT+8); Fv6 = vshrq_n_u32(Sv6, TF_SHIFT+8); Fv7 = vshrq_n_u32(Sv7, TF_SHIFT+8); Fv8 = vshrq_n_u32(Sv8, TF_SHIFT+8); // A mix of mul+add and mla instructions seems to win. //Rv1 = vmulq_u32(Fv1, Rv1); Rv1 = vaddq_u32(Rv1, Bv1); Rv1 = vmlaq_u32(Bv1, Fv1, Rv1); // R = R*Freq + Bias Rv2 = vmulq_u32(Fv2, Rv2); Rv2 = vaddq_u32(Rv2, Bv2); //Rv2 = vmlaq_u32(Bv2, Fv2, Rv2); //Rv3 = vmulq_u32(Fv3, Rv3); Rv3 = vaddq_u32(Rv3, Bv3); Rv3 = vmlaq_u32(Bv3, Fv3, Rv3); Rv4 = vmulq_u32(Fv4, Rv4); Rv4 = vaddq_u32(Rv4, Bv4); //Rv4 = vmlaq_u32(Bv4, Fv4, Rv4); Bv5 = vshrq_n_u32(Sv5, 8); Bv6 = vshrq_n_u32(Sv6, 8); Bv7 = vshrq_n_u32(Sv7, 8); Bv8 = vshrq_n_u32(Sv8, 8); // Renorm uint32x4_t Rlt1 = vcltq_u32(Rv1, vdupq_n_u32(RANS_BYTE_L)); // R cp_end) { memmove(overflow, sp, cp_end - (uint8_t *)sp); sp = (uint16_t *)overflow; cp_end = overflow + sizeof(overflow); } uint16x8_t norm12 = vld1q_u16(sp); sp += nbits[imask1] + nbits[imask2]; uint16x8_t norm34 = vld1q_u16(sp); sp += nbits[imask3] + nbits[imask4]; Bv5 = vandq_u32(Bv5, maskv); Bv6 = vandq_u32(Bv6, maskv); Bv7 = vandq_u32(Bv7, maskv); Bv8 = vandq_u32(Bv8, maskv); // Shuffle norm to the corresponding R lanes, via imask //Rv5 = vmulq_u32(Fv5, Rv5); Rv5 = vaddq_u32(Rv5, Bv5); Rv5 = vmlaq_u32(Bv5, Fv5, Rv5); Rv6 = vmulq_u32(Fv6, Rv6); Rv6 = vaddq_u32(Rv6, Bv6); //Rv6 = vmlaq_u32(Bv6, Fv6, Rv6); //Rv7 = vmulq_u32(Fv7, Rv7); Rv7 = vaddq_u32(Rv7, Bv7); Rv7 = vmlaq_u32(Bv7, Fv7, Rv7); Rv8 = vmulq_u32(Fv8, Rv8); Rv8 = vaddq_u32(Rv8, Bv8); //Rv8 = vmlaq_u32(Bv8, Fv8, Rv8); uint32_t imask12 = (imask1<<4)|imask2; uint32_t imask34 = (imask3<<4)|imask4; // #define for brevity and formatting #define cast_u16_u8 vreinterpret_u16_u8 #define cast_u8_u16 vreinterpretq_u8_u16 uint16x4_t norm1, norm2, norm3, norm4, norm5, norm6, norm7, norm8; norm1 = cast_u16_u8(vqtbl1_u8(cast_u8_u16(norm12),idx [imask1])); norm2 = cast_u16_u8(vqtbl1_u8(cast_u8_u16(norm12),idx2[imask12])); norm3 = cast_u16_u8(vqtbl1_u8(cast_u8_u16(norm34),idx [imask3])); norm4 = cast_u16_u8(vqtbl1_u8(cast_u8_u16(norm34),idx2[imask34])); uint32x4_t Rlt5 = vcltq_u32(Rv5, vdupq_n_u32(RANS_BYTE_L)); uint32x4_t Rlt6 = vcltq_u32(Rv6, vdupq_n_u32(RANS_BYTE_L)); uint32x4_t Rlt7 = vcltq_u32(Rv7, vdupq_n_u32(RANS_BYTE_L)); uint32x4_t Rlt8 = vcltq_u32(Rv8, vdupq_n_u32(RANS_BYTE_L)); // Add norm to R<<16 (Rsl) and blend back in with R uint32x4_t Rsl1 = vshlq_n_u32(Rv1, 16); // Rsl = R << 16 uint32x4_t Rsl2 = vshlq_n_u32(Rv2, 16); uint32x4_t Rsl3 = vshlq_n_u32(Rv3, 16); uint32x4_t Rsl4 = vshlq_n_u32(Rv4, 16); uint16x8_t norm56 = vld1q_u16(sp); uint32_t imask5 = vaddvq_u32(vandq_u32(Rlt5, bit)); uint32_t imask6 = vaddvq_u32(vandq_u32(Rlt6, bit)); uint32_t imask7 = vaddvq_u32(vandq_u32(Rlt7, bit)); uint32_t imask8 = vaddvq_u32(vandq_u32(Rlt8, bit)); sp += nbits[imask5] + nbits[imask6]; uint16x8_t norm78 = vld1q_u16(sp); sp += nbits[imask7] + nbits[imask8]; Rsl1 = vaddw_u16(Rsl1, norm1); // Rsl += norm Rsl2 = vaddw_u16(Rsl2, norm2); Rsl3 = vaddw_u16(Rsl3, norm3); Rsl4 = vaddw_u16(Rsl4, norm4); uint32_t imask56 = (imask5<<4)|imask6; uint32_t imask78 = (imask7<<4)|imask8; Rv1 = vbslq_u32(Rlt1, Rsl1, Rv1); // R = R 0; ) out[out_end + z] = s3[R[z] & mask]; //fprintf(stderr, " 0 Decoded %d bytes\n", (int)(cp-in)); //c-size return out; err: free(out_free); return NULL; } //----------------------------------------------------------------------------- unsigned char *rans_compress_O1_32x16_neon(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { unsigned char *cp, *out_end, *out_free = NULL; unsigned int tab_size; uint32_t bound = rans_compress_bound_4x16(in_size,1)-20; int z; RansState ransN[NX]; if (in_size < NX) // force O0 instead return NULL; if (!out) { *out_size = bound; out_free = out = malloc(*out_size); } if (!out || bound > *out_size) return NULL; if (((size_t)out)&1) bound--; out_end = out + bound; RansEncSymbol (*syms)[256] = htscodecs_tls_alloc(256 * (sizeof(*syms))); if (!syms) { free(out_free); return NULL; } cp = out; int shift = encode_freq1(in, in_size, 32, syms, &cp); if (shift < 0) { free(out_free); htscodecs_tls_free(syms); return NULL; } tab_size = cp - out; for (z = 0; z < NX; z++) RansEncInit(&ransN[z]); uint8_t* ptr = out_end; int iN[NX], isz4 = in_size/NX; for (z = 0; z < NX; z++) iN[z] = (z+1)*isz4-2; unsigned char lN[NX]; for (z = 0; z < NX; z++) lN[z] = in[iN[z]+1]; // Deal with the remainder z = NX-1; lN[z] = in[in_size-1]; for (iN[z] = in_size-2; iN[z] > NX*isz4-2; iN[z]--) { unsigned char c = in[iN[z]]; RansEncPutSymbol(&ransN[z], &ptr, &syms[c][lN[z]]); lN[z] = c; } #if 0 // Scalar code equivalent for (; iN[0] >= 0; ) { for (z = NX-1; z >= 0; z-=4) { unsigned char c0; unsigned char c1; unsigned char c2; unsigned char c3; RansEncSymbol *s0 = &syms[c0=in[iN[z-0]--]][lN[z-0]]; lN[z-0] = c0; RansEncSymbol *s1 = &syms[c1=in[iN[z-1]--]][lN[z-1]]; lN[z-1] = c1; RansEncSymbol *s2 = &syms[c2=in[iN[z-2]--]][lN[z-2]]; lN[z-2] = c2; RansEncSymbol *s3 = &syms[c3=in[iN[z-3]--]][lN[z-3]]; lN[z-3] = c3; RansEncPutSymbol(&ransN[z-0], &ptr, s0); RansEncPutSymbol(&ransN[z-1], &ptr, s1); RansEncPutSymbol(&ransN[z-2], &ptr, s2); RansEncPutSymbol(&ransN[z-3], &ptr, s3); } } #else // SIMD code for (; iN[0] >= 0; ) { for (z = NX-1; z >= 0; z-=16) { unsigned char c; RansEncSymbol *s0 = &syms[c=in[iN[z- 0]--]][lN[z- 0]]; lN[z- 0]=c; RansEncSymbol *s1 = &syms[c=in[iN[z- 1]--]][lN[z- 1]]; lN[z- 1]=c; RansEncSymbol *s2 = &syms[c=in[iN[z- 2]--]][lN[z- 2]]; lN[z- 2]=c; RansEncSymbol *s3 = &syms[c=in[iN[z- 3]--]][lN[z- 3]]; lN[z- 3]=c; uint32x4_t Rv1 = vld1q_u32(&ransN[z-3]); uint32x4_t Rv2 = vld1q_u32(&ransN[z-7]); uint32x4_t Rv3 = vld1q_u32(&ransN[z-11]); uint32x4_t Rv4 = vld1q_u32(&ransN[z-15]); RansEncSymbol *s4 = &syms[c=in[iN[z- 4]--]][lN[z- 4]]; lN[z- 4]=c; RansEncSymbol *s5 = &syms[c=in[iN[z- 5]--]][lN[z- 5]]; lN[z- 5]=c; RansEncSymbol *s6 = &syms[c=in[iN[z- 6]--]][lN[z- 6]]; lN[z- 6]=c; RansEncSymbol *s7 = &syms[c=in[iN[z- 7]--]][lN[z- 7]]; lN[z- 7]=c; uint32x4_t A_1 = vld1q_u32((void *)s3); uint32x4_t B_1 = vld1q_u32((void *)s2); uint32x4_t C_1 = vld1q_u32((void *)s1); uint32x4_t D_1 = vld1q_u32((void *)s0); uint32x4_t A1_1 = vtrn1q_u32(A_1, B_1); uint32x4_t C1_1 = vtrn1q_u32(C_1, D_1); uint32x4_t A2_1 = vtrn2q_u32(A_1, B_1); uint32x4_t C2_1 = vtrn2q_u32(C_1, D_1); uint32x4_t Xmaxv1=u32_u64(vtrn1q_u64(u64_u32(A1_1),u64_u32(C1_1))); uint32x4_t Biasv1=u32_u64(vtrn2q_u64(u64_u32(A1_1),u64_u32(C1_1))); uint32x4_t RFv1 =u32_u64(vtrn1q_u64(u64_u32(A2_1),u64_u32(C2_1))); uint32x4_t FSv1 =u32_u64(vtrn2q_u64(u64_u32(A2_1),u64_u32(C2_1))); uint32x4_t A_2 = vld1q_u32((void *)s7); uint32x4_t B_2 = vld1q_u32((void *)s6); uint32x4_t C_2 = vld1q_u32((void *)s5); uint32x4_t D_2 = vld1q_u32((void *)s4); uint32x4_t A1_2 = vtrn1q_u32(A_2, B_2); uint32x4_t C1_2 = vtrn1q_u32(C_2, D_2); uint32x4_t A2_2 = vtrn2q_u32(A_2, B_2); uint32x4_t C2_2 = vtrn2q_u32(C_2, D_2); uint32x4_t Xmaxv2=u32_u64(vtrn1q_u64(u64_u32(A1_2),u64_u32(C1_2))); uint32x4_t Biasv2=u32_u64(vtrn2q_u64(u64_u32(A1_2),u64_u32(C1_2))); uint32x4_t RFv2 =u32_u64(vtrn1q_u64(u64_u32(A2_2),u64_u32(C2_2))); uint32x4_t FSv2 =u32_u64(vtrn2q_u64(u64_u32(A2_2),u64_u32(C2_2))); uint32x4_t Cv1 = vcgtq_u32(Rv1, Xmaxv1); uint32x4_t Cv2 = vcgtq_u32(Rv2, Xmaxv2); uint32x4_t bit = {8,4,2,1}; uint32_t imask1 = vaddvq_u32(vandq_u32(Cv1, bit)); uint32_t imask2 = vaddvq_u32(vandq_u32(Cv2, bit)); RansEncSymbol *s8 = &syms[c=in[iN[z- 8]--]][lN[z- 8]]; lN[z- 8]=c; RansEncSymbol *s9 = &syms[c=in[iN[z- 9]--]][lN[z- 9]]; lN[z- 9]=c; RansEncSymbol *s10= &syms[c=in[iN[z-10]--]][lN[z-10]]; lN[z-10]=c; RansEncSymbol *s11= &syms[c=in[iN[z-11]--]][lN[z-11]]; lN[z-11]=c; RansEncSymbol *s12= &syms[c=in[iN[z-12]--]][lN[z-12]]; lN[z-12]=c; RansEncSymbol *s13= &syms[c=in[iN[z-13]--]][lN[z-13]]; lN[z-13]=c; RansEncSymbol *s14= &syms[c=in[iN[z-14]--]][lN[z-14]]; lN[z-14]=c; RansEncSymbol *s15= &syms[c=in[iN[z-15]--]][lN[z-15]]; lN[z-15]=c; uint32x4_t A_3 = vld1q_u32((void *)s11); uint32x4_t B_3 = vld1q_u32((void *)s10); uint32x4_t C_3 = vld1q_u32((void *)s9); uint32x4_t D_3 = vld1q_u32((void *)s8); uint32x4_t A1_3 = vtrn1q_u32(A_3, B_3); uint32x4_t C1_3 = vtrn1q_u32(C_3, D_3); uint32x4_t A2_3 = vtrn2q_u32(A_3, B_3); uint32x4_t C2_3 = vtrn2q_u32(C_3, D_3); uint32x4_t Xmaxv3=u32_u64(vtrn1q_u64(u64_u32(A1_3),u64_u32(C1_3))); uint32x4_t Biasv3=u32_u64(vtrn2q_u64(u64_u32(A1_3),u64_u32(C1_3))); uint32x4_t RFv3 =u32_u64(vtrn1q_u64(u64_u32(A2_3),u64_u32(C2_3))); uint32x4_t FSv3 =u32_u64(vtrn2q_u64(u64_u32(A2_3),u64_u32(C2_3))); uint32x4_t A_4 = vld1q_u32((void *)s15); uint32x4_t B_4 = vld1q_u32((void *)s14); uint32x4_t C_4 = vld1q_u32((void *)s13); uint32x4_t D_4 = vld1q_u32((void *)s12); uint32x4_t A1_4 = vtrn1q_u32(A_4, B_4); uint32x4_t C1_4 = vtrn1q_u32(C_4, D_4); uint32x4_t A2_4 = vtrn2q_u32(A_4, B_4); uint32x4_t C2_4 = vtrn2q_u32(C_4, D_4); uint32x4_t Xmaxv4=u32_u64(vtrn1q_u64(u64_u32(A1_4),u64_u32(C1_4))); uint32x4_t Biasv4=u32_u64(vtrn2q_u64(u64_u32(A1_4),u64_u32(C1_4))); uint32x4_t RFv4 =u32_u64(vtrn1q_u64(u64_u32(A2_4),u64_u32(C2_4))); uint32x4_t FSv4 =u32_u64(vtrn2q_u64(u64_u32(A2_4),u64_u32(C2_4))); uint32x4_t Cv3 = vcgtq_u32(Rv3, Xmaxv3); uint32x4_t Cv4 = vcgtq_u32(Rv4, Xmaxv4); uint32_t imask3 = vaddvq_u32(vandq_u32(Cv3, bit)); uint32_t imask4 = vaddvq_u32(vandq_u32(Cv4, bit)); // Select low 16-bits from Rv based on imask, using tbl uint8x8_t norm1, norm2, norm3, norm4; static int nbits[16] = { 0,2,2,4, 2,4,4,6, 2,4,4,6, 4,6,6,8 }; norm1 = vqtbl1_u8(vreinterpretq_u8_u32(Rv1),vtab[imask1]); norm2 = vqtbl1_u8(vreinterpretq_u8_u32(Rv2),vtab[imask2]); vst1_u8(ptr-8, norm1); ptr -= nbits[imask1]; vst1_u8(ptr-8, norm2); ptr -= nbits[imask2]; norm3 = vqtbl1_u8(vreinterpretq_u8_u32(Rv3),vtab[imask3]); norm4 = vqtbl1_u8(vreinterpretq_u8_u32(Rv4),vtab[imask4]); vst1_u8(ptr-8, norm3); ptr -= nbits[imask3]; vst1_u8(ptr-8, norm4); ptr -= nbits[imask4]; // R' = R>>16 uint32x4_t Rv1_r = vshrq_n_u32(Rv1, 16); uint32x4_t Rv2_r = vshrq_n_u32(Rv2, 16); uint32x4_t Rv3_r = vshrq_n_u32(Rv3, 16); uint32x4_t Rv4_r = vshrq_n_u32(Rv4, 16); // Blend R and R' based on Cv. Rv1 = vbslq_u32(Cv1, Rv1_r, Rv1); Rv2 = vbslq_u32(Cv2, Rv2_r, Rv2); Rv3 = vbslq_u32(Cv3, Rv3_r, Rv3); Rv4 = vbslq_u32(Cv4, Rv4_r, Rv4); uint64x2_t qvl1 = vmull_u32(vget_low_u32(Rv1), vget_low_u32(RFv1)); uint64x2_t qvh1 = vmull_high_u32(Rv1, RFv1); uint64x2_t qvl2 = vmull_u32(vget_low_u32(Rv2), vget_low_u32(RFv2)); uint64x2_t qvh2 = vmull_high_u32(Rv2, RFv2); int32x4_t RSv1 = vnegq_s32(vreinterpretq_s32_u32( vshrq_n_u32(FSv1, 16))); int32x4_t RSv2 = vnegq_s32(vreinterpretq_s32_u32( vshrq_n_u32(FSv2, 16))); uint64x2_t qvl3 = vmull_u32(vget_low_u32(Rv3), vget_low_u32(RFv3)); uint64x2_t qvh3 = vmull_high_u32(Rv3, RFv3); uint64x2_t qvl4 = vmull_u32(vget_low_u32(Rv4), vget_low_u32(RFv4)); uint64x2_t qvh4 = vmull_high_u32(Rv4, RFv4); int32x4_t RSv3 = vnegq_s32(vreinterpretq_s32_u32( vshrq_n_u32(FSv3, 16))); int32x4_t RSv4 = vnegq_s32(vreinterpretq_s32_u32( vshrq_n_u32(FSv4, 16))); qvl1 = vreinterpretq_u64_s64( vshlq_s64(vreinterpretq_s64_u64(qvl1), vmovl_s32(vget_low_s32(RSv1)))); qvh1 = vreinterpretq_u64_s64( vshlq_s64(vreinterpretq_s64_u64(qvh1), vmovl_s32(vget_high_s32(RSv1)))); qvl2 = vreinterpretq_u64_s64( vshlq_s64(vreinterpretq_s64_u64(qvl2), vmovl_s32(vget_low_s32(RSv2)))); qvh2 = vreinterpretq_u64_s64( vshlq_s64(vreinterpretq_s64_u64(qvh2), vmovl_s32(vget_high_s32(RSv2)))); uint32x4_t qv1 = vcombine_u32(vmovn_u64(qvl1), vmovn_u64(qvh1)); uint32x4_t qv2 = vcombine_u32(vmovn_u64(qvl2), vmovn_u64(qvh2)); qvl3 = vreinterpretq_u64_s64( vshlq_s64(vreinterpretq_s64_u64(qvl3), vmovl_s32(vget_low_s32(RSv3)))); qvh3 = vreinterpretq_u64_s64( vshlq_s64(vreinterpretq_s64_u64(qvh3), vmovl_s32(vget_high_s32(RSv3)))); qvl4 = vreinterpretq_u64_s64( vshlq_s64(vreinterpretq_s64_u64(qvl4), vmovl_s32(vget_low_s32(RSv4)))); qvh4 = vreinterpretq_u64_s64( vshlq_s64(vreinterpretq_s64_u64(qvh4), vmovl_s32(vget_high_s32(RSv4)))); uint32x4_t qv3 = vcombine_u32(vmovn_u64(qvl3), vmovn_u64(qvh3)); uint32x4_t qv4 = vcombine_u32(vmovn_u64(qvl4), vmovn_u64(qvh4)); FSv1 = vandq_u32(FSv1, vdupq_n_u32(0xffff)); // cmpl_freq FSv2 = vandq_u32(FSv2, vdupq_n_u32(0xffff)); FSv3 = vandq_u32(FSv3, vdupq_n_u32(0xffff)); FSv4 = vandq_u32(FSv4, vdupq_n_u32(0xffff)); qv1 = vmlaq_u32(Biasv1, qv1, FSv1); qv2 = vmlaq_u32(Biasv2, qv2, FSv2); qv3 = vmlaq_u32(Biasv3, qv3, FSv3); qv4 = vmlaq_u32(Biasv4, qv4, FSv4); Rv1 = vaddq_u32(Rv1, qv1); Rv2 = vaddq_u32(Rv2, qv2); Rv3 = vaddq_u32(Rv3, qv3); Rv4 = vaddq_u32(Rv4, qv4); vst1q_u32(&ransN[z-3], Rv1); vst1q_u32(&ransN[z-7], Rv2); vst1q_u32(&ransN[z-11],Rv3); vst1q_u32(&ransN[z-15],Rv4); } } #endif for (z = NX-1; z>=0; z--) RansEncPutSymbol(&ransN[z], &ptr, &syms[0][lN[z]]); for (z = NX-1; z>=0; z--) RansEncFlush(&ransN[z], &ptr); *out_size = (out_end - ptr) + tab_size; cp = out; memmove(out + tab_size, ptr, out_end-ptr); htscodecs_tls_free(syms); return out; } //#define MAGIC2 111 #define MAGIC2 179 //#define MAGIC2 0 typedef struct { union { struct { uint16_t f; uint16_t b; } s; uint32_t fb; } u; } bf_t; static inline void transpose_and_copy(uint8_t *out, int iN[32], uint8_t t[32][32]) { int z; // for (z = 0; z < NX; z++) { // int k; // for (k = 0; k < 32; k++) // out[iN[z]+k] = t[k][z]; // iN[z] += 32; // } for (z = 0; z < NX; z+=4) { *(uint64_t *)&out[iN[z]] = ((uint64_t)(t[0][z])<< 0) + ((uint64_t)(t[1][z])<< 8) + ((uint64_t)(t[2][z])<<16) + ((uint64_t)(t[3][z])<<24) + ((uint64_t)(t[4][z])<<32) + ((uint64_t)(t[5][z])<<40) + ((uint64_t)(t[6][z])<<48) + ((uint64_t)(t[7][z])<<56); *(uint64_t *)&out[iN[z+1]] = ((uint64_t)(t[0][z+1])<< 0) + ((uint64_t)(t[1][z+1])<< 8) + ((uint64_t)(t[2][z+1])<<16) + ((uint64_t)(t[3][z+1])<<24) + ((uint64_t)(t[4][z+1])<<32) + ((uint64_t)(t[5][z+1])<<40) + ((uint64_t)(t[6][z+1])<<48) + ((uint64_t)(t[7][z+1])<<56); *(uint64_t *)&out[iN[z+2]] = ((uint64_t)(t[0][z+2])<< 0) + ((uint64_t)(t[1][z+2])<< 8) + ((uint64_t)(t[2][z+2])<<16) + ((uint64_t)(t[3][z+2])<<24) + ((uint64_t)(t[4][z+2])<<32) + ((uint64_t)(t[5][z+2])<<40) + ((uint64_t)(t[6][z+2])<<48) + ((uint64_t)(t[7][z+2])<<56); *(uint64_t *)&out[iN[z+3]] = ((uint64_t)(t[0][z+3])<< 0) + ((uint64_t)(t[1][z+3])<< 8) + ((uint64_t)(t[2][z+3])<<16) + ((uint64_t)(t[3][z+3])<<24) + ((uint64_t)(t[4][z+3])<<32) + ((uint64_t)(t[5][z+3])<<40) + ((uint64_t)(t[6][z+3])<<48) + ((uint64_t)(t[7][z+3])<<56); *(uint64_t *)&out[iN[z]+8] = ((uint64_t)(t[8+0][z])<< 0) + ((uint64_t)(t[8+1][z])<< 8) + ((uint64_t)(t[8+2][z])<<16) + ((uint64_t)(t[8+3][z])<<24) + ((uint64_t)(t[8+4][z])<<32) + ((uint64_t)(t[8+5][z])<<40) + ((uint64_t)(t[8+6][z])<<48) + ((uint64_t)(t[8+7][z])<<56); *(uint64_t *)&out[iN[z+1]+8] = ((uint64_t)(t[8+0][z+1])<< 0) + ((uint64_t)(t[8+1][z+1])<< 8) + ((uint64_t)(t[8+2][z+1])<<16) + ((uint64_t)(t[8+3][z+1])<<24) + ((uint64_t)(t[8+4][z+1])<<32) + ((uint64_t)(t[8+5][z+1])<<40) + ((uint64_t)(t[8+6][z+1])<<48) + ((uint64_t)(t[8+7][z+1])<<56); *(uint64_t *)&out[iN[z+2]+8] = ((uint64_t)(t[8+0][z+2])<< 0) + ((uint64_t)(t[8+1][z+2])<< 8) + ((uint64_t)(t[8+2][z+2])<<16) + ((uint64_t)(t[8+3][z+2])<<24) + ((uint64_t)(t[8+4][z+2])<<32) + ((uint64_t)(t[8+5][z+2])<<40) + ((uint64_t)(t[8+6][z+2])<<48) + ((uint64_t)(t[8+7][z+2])<<56); *(uint64_t *)&out[iN[z+3]+8] = ((uint64_t)(t[8+0][z+3])<< 0) + ((uint64_t)(t[8+1][z+3])<< 8) + ((uint64_t)(t[8+2][z+3])<<16) + ((uint64_t)(t[8+3][z+3])<<24) + ((uint64_t)(t[8+4][z+3])<<32) + ((uint64_t)(t[8+5][z+3])<<40) + ((uint64_t)(t[8+6][z+3])<<48) + ((uint64_t)(t[8+7][z+3])<<56); *(uint64_t *)&out[iN[z]+16] = ((uint64_t)(t[16+0][z])<< 0) + ((uint64_t)(t[16+1][z])<< 8) + ((uint64_t)(t[16+2][z])<<16) + ((uint64_t)(t[16+3][z])<<24) + ((uint64_t)(t[16+4][z])<<32) + ((uint64_t)(t[16+5][z])<<40) + ((uint64_t)(t[16+6][z])<<48) + ((uint64_t)(t[16+7][z])<<56); *(uint64_t *)&out[iN[z+1]+16] = ((uint64_t)(t[16+0][z+1])<< 0) + ((uint64_t)(t[16+1][z+1])<< 8) + ((uint64_t)(t[16+2][z+1])<<16) + ((uint64_t)(t[16+3][z+1])<<24) + ((uint64_t)(t[16+4][z+1])<<32) + ((uint64_t)(t[16+5][z+1])<<40) + ((uint64_t)(t[16+6][z+1])<<48) + ((uint64_t)(t[16+7][z+1])<<56); *(uint64_t *)&out[iN[z+2]+16] = ((uint64_t)(t[16+0][z+2])<< 0) + ((uint64_t)(t[16+1][z+2])<< 8) + ((uint64_t)(t[16+2][z+2])<<16) + ((uint64_t)(t[16+3][z+2])<<24) + ((uint64_t)(t[16+4][z+2])<<32) + ((uint64_t)(t[16+5][z+2])<<40) + ((uint64_t)(t[16+6][z+2])<<48) + ((uint64_t)(t[16+7][z+2])<<56); *(uint64_t *)&out[iN[z+3]+16] = ((uint64_t)(t[16+0][z+3])<< 0) + ((uint64_t)(t[16+1][z+3])<< 8) + ((uint64_t)(t[16+2][z+3])<<16) + ((uint64_t)(t[16+3][z+3])<<24) + ((uint64_t)(t[16+4][z+3])<<32) + ((uint64_t)(t[16+5][z+3])<<40) + ((uint64_t)(t[16+6][z+3])<<48) + ((uint64_t)(t[16+7][z+3])<<56); *(uint64_t *)&out[iN[z]+24] = ((uint64_t)(t[24+0][z])<< 0) + ((uint64_t)(t[24+1][z])<< 8) + ((uint64_t)(t[24+2][z])<<16) + ((uint64_t)(t[24+3][z])<<24) + ((uint64_t)(t[24+4][z])<<32) + ((uint64_t)(t[24+5][z])<<40) + ((uint64_t)(t[24+6][z])<<48) + ((uint64_t)(t[24+7][z])<<56); *(uint64_t *)&out[iN[z+1]+24] = ((uint64_t)(t[24+0][z+1])<< 0) + ((uint64_t)(t[24+1][z+1])<< 8) + ((uint64_t)(t[24+2][z+1])<<16) + ((uint64_t)(t[24+3][z+1])<<24) + ((uint64_t)(t[24+4][z+1])<<32) + ((uint64_t)(t[24+5][z+1])<<40) + ((uint64_t)(t[24+6][z+1])<<48) + ((uint64_t)(t[24+7][z+1])<<56); *(uint64_t *)&out[iN[z+2]+24] = ((uint64_t)(t[24+0][z+2])<< 0) + ((uint64_t)(t[24+1][z+2])<< 8) + ((uint64_t)(t[24+2][z+2])<<16) + ((uint64_t)(t[24+3][z+2])<<24) + ((uint64_t)(t[24+4][z+2])<<32) + ((uint64_t)(t[24+5][z+2])<<40) + ((uint64_t)(t[24+6][z+2])<<48) + ((uint64_t)(t[24+7][z+2])<<56); *(uint64_t *)&out[iN[z+3]+24] = ((uint64_t)(t[24+0][z+3])<< 0) + ((uint64_t)(t[24+1][z+3])<< 8) + ((uint64_t)(t[24+2][z+3])<<16) + ((uint64_t)(t[24+3][z+3])<<24) + ((uint64_t)(t[24+4][z+3])<<32) + ((uint64_t)(t[24+5][z+3])<<40) + ((uint64_t)(t[24+6][z+3])<<48) + ((uint64_t)(t[24+7][z+3])<<56); iN[z+0] += 32; iN[z+1] += 32; iN[z+2] += 32; iN[z+3] += 32; } } unsigned char *rans_uncompress_O1_32x16_neon(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { if (in_size < NX*4) // 4-states at least return NULL; if (out_sz >= INT_MAX) return NULL; // protect against some overflow cases #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (out_sz > 100000) return NULL; #endif /* Load in the static tables */ unsigned char *cp = in, *cp_end = in+in_size, *out_free = NULL; unsigned char *c_freq = NULL; int i, j = -999; unsigned int x; uint8_t *sfb_ = htscodecs_tls_alloc(256*(TOTFREQ_O1+MAGIC2)*sizeof(*sfb_)); uint32_t s3[256][TOTFREQ_O1_FAST]; if (!sfb_) return NULL; bf_t fb[256][256]; uint8_t *sfb[256]; if ((*cp >> 4) == TF_SHIFT_O1) { for (i = 0; i < 256; i++) sfb[i]= sfb_ + i*(TOTFREQ_O1+MAGIC2); } else { for (i = 0; i < 256; i++) sfb[i]= sfb_ + i*(TOTFREQ_O1_FAST+MAGIC2); } if (!out) out_free = out = malloc(out_sz); if (!out) goto err; //fprintf(stderr, "out_sz=%d\n", out_sz); // compressed header? If so uncompress it unsigned char *tab_end = NULL; unsigned char *c_freq_end = cp_end; unsigned int shift = *cp >> 4; if (*cp++ & 1) { uint32_t u_freq_sz, c_freq_sz; cp += var_get_u32(cp, cp_end, &u_freq_sz); cp += var_get_u32(cp, cp_end, &c_freq_sz); if (c_freq_sz > cp_end - cp) goto err; tab_end = cp + c_freq_sz; if (!(c_freq = rans_uncompress_O0_4x16(cp, c_freq_sz, NULL, u_freq_sz))) goto err; cp = c_freq; c_freq_end = c_freq + u_freq_sz; } // Decode order-0 symbol list; avoids needing in order-1 tables #if 0 // Disable inline for now as this is ~10% slower under gcc. Why? cp += decode_freq1(cp, c_freq_end, shift, NULL, s3, sfb, fb); #else uint32_t F0[256] = {0}; int fsz = decode_alphabet(cp, c_freq_end, F0); if (!fsz) goto err; cp += fsz; if (cp >= c_freq_end) goto err; for (i = 0; i < 256; i++) { if (F0[i] == 0) continue; uint32_t F[256] = {0}, T = 0; fsz = decode_freq_d(cp, c_freq_end, F0, F, &T); if (!fsz) goto err; cp += fsz; if (!T) { //fprintf(stderr, "No freq for F_%d\n", i); continue; } normalise_freq_shift(F, T, 1< (1<>TF_SHIFT_O1) + m - fb[l[z]][c].u.s.b; RansDecRenormSafe(&R[z], &ptr, ptr_end); l[z] = c; } } // Remainder for (; i4[NX-1] < out_sz; i4[NX-1]++) { uint32_t m = R[NX-1] & ((1u<>TF_SHIFT_O1) + m - fb[l[NX-1]][c].u.s.b; RansDecRenormSafe(&R[NX-1], &ptr, ptr_end); l[NX-1] = c; } } else { // TF_SHIFT_O1 = 10 const uint32_t mask = ((1u << TF_SHIFT_O1_FAST)-1); uint32x4_t maskv = vdupq_n_u32((1u << TF_SHIFT_O1_FAST)-1); // FIXME: plus room for "safe" renorm. // Follow with 2nd copy doing scalar code instead? unsigned char tbuf[32][32]; int tidx = 0; uint32x4_t RV[8] = { vld1q_u32(&R[0]), vld1q_u32(&R[4]), vld1q_u32(&R[8]), vld1q_u32(&R[12]), vld1q_u32(&R[16]), vld1q_u32(&R[20]), vld1q_u32(&R[24]), vld1q_u32(&R[28]), }; // uint32x4_t MV[8] = { // vandq_u32(RV[0], maskv), // vandq_u32(RV[1], maskv), // vandq_u32(RV[2], maskv), // vandq_u32(RV[3], maskv), // vandq_u32(RV[4], maskv), // vandq_u32(RV[5], maskv), // vandq_u32(RV[6], maskv), // vandq_u32(RV[7], maskv), // }; uint32_t m[NX]; for (z = 0; z < NX; z++) m[z] = l[z]*TOTFREQ_O1_FAST + (R[z] & mask); uint32_t *S3 = (uint32_t *)s3; for (; i4[0] < isz4 && ptr+64 < ptr_end;) { int Z = 0; for (z = 0; z < NX; z+=16, Z+=4) { // streamline these. Could swap between two banks and pre-load uint32x4_t Sv1, Sv2, Sv3, Sv4; uint32x4_t Fv1, Fv2, Fv3, Fv4; uint32x4_t Bv1, Bv2, Bv3, Bv4; uint32x2_t s1a, s1b, s2a, s2b, s3a, s3b, s4a, s4b; s1a = vcreate_u32((uint64_t)(S3[m[z+1]])<<32 | (S3[m[z+0]])); s1b = vcreate_u32((uint64_t)(S3[m[z+3]])<<32 | (S3[m[z+2]])); s2a = vcreate_u32((uint64_t)(S3[m[z+5]])<<32 | (S3[m[z+4]])); s2b = vcreate_u32((uint64_t)(S3[m[z+7]])<<32 | (S3[m[z+6]])); s3a = vcreate_u32((uint64_t)(S3[m[z+9]])<<32 | (S3[m[z+8]])); s3b = vcreate_u32((uint64_t)(S3[m[z+11]])<<32 | (S3[m[z+10]])); s4a = vcreate_u32((uint64_t)(S3[m[z+13]])<<32 | (S3[m[z+12]])); s4b = vcreate_u32((uint64_t)(S3[m[z+15]])<<32 | (S3[m[z+14]])); Sv1 = vcombine_u32(s1a, s1b); Sv2 = vcombine_u32(s2a, s2b); Sv3 = vcombine_u32(s3a, s3b); Sv4 = vcombine_u32(s4a, s4b); uint16x4_t p16_1 = vmovn_u32(Sv1); uint16x4_t p16_2 = vmovn_u32(Sv2); uint16x4_t p16_3 = vmovn_u32(Sv3); uint16x4_t p16_4 = vmovn_u32(Sv4); uint8x8_t p8_12 = vmovn_u16(vcombine_u16(p16_1,p16_2)); uint8x8_t p8_34 = vmovn_u16(vcombine_u16(p16_3,p16_4)); uint8x16_t p8_a = vcombine_u8(p8_12, p8_34); vst1q_u8(l+z, p8_a); Fv1 = vshrq_n_u32(Sv1, TF_SHIFT_O1_FAST+8); Fv2 = vshrq_n_u32(Sv2, TF_SHIFT_O1_FAST+8); Fv3 = vshrq_n_u32(Sv3, TF_SHIFT_O1_FAST+8); Fv4 = vshrq_n_u32(Sv4, TF_SHIFT_O1_FAST+8); Bv1 = vandq_u32(vshrq_n_u32(Sv1, 8), maskv); Bv2 = vandq_u32(vshrq_n_u32(Sv2, 8), maskv); Bv3 = vandq_u32(vshrq_n_u32(Sv3, 8), maskv); Bv4 = vandq_u32(vshrq_n_u32(Sv4, 8), maskv); // Add in transpose here. memcpy(&tbuf[tidx][z], &l[z], 16); RV[Z+0] = vshrq_n_u32(RV[Z+0], TF_SHIFT_O1_FAST); RV[Z+1] = vshrq_n_u32(RV[Z+1], TF_SHIFT_O1_FAST); RV[Z+2] = vshrq_n_u32(RV[Z+2], TF_SHIFT_O1_FAST); RV[Z+3] = vshrq_n_u32(RV[Z+3], TF_SHIFT_O1_FAST); // Ready for use in S3[] offset Sv1 = vshlq_n_u32(vandq_u32(Sv1, vdupq_n_u32(0xff)), TF_SHIFT_O1_FAST); Sv2 = vshlq_n_u32(vandq_u32(Sv2, vdupq_n_u32(0xff)), TF_SHIFT_O1_FAST); Sv3 = vshlq_n_u32(vandq_u32(Sv3, vdupq_n_u32(0xff)), TF_SHIFT_O1_FAST); Sv4 = vshlq_n_u32(vandq_u32(Sv4, vdupq_n_u32(0xff)), TF_SHIFT_O1_FAST); RV[Z+0] = vmlaq_u32(Bv1, Fv1, RV[Z+0]); RV[Z+1] = vmlaq_u32(Bv2, Fv2, RV[Z+1]); RV[Z+2] = vmlaq_u32(Bv3, Fv3, RV[Z+2]); RV[Z+3] = vmlaq_u32(Bv4, Fv4, RV[Z+3]); // Renorm uint32x4_t Rlt1 = vcltq_u32(RV[Z+0], vdupq_n_u32(RANS_BYTE_L)); uint32x4_t Rlt2 = vcltq_u32(RV[Z+1], vdupq_n_u32(RANS_BYTE_L)); uint32x4_t Rlt3 = vcltq_u32(RV[Z+2], vdupq_n_u32(RANS_BYTE_L)); uint32x4_t Rlt4 = vcltq_u32(RV[Z+3], vdupq_n_u32(RANS_BYTE_L)); // Compute lookup table index static int nbits[16] = { 0,2,2,4, 2,4,4,6, 2,4,4,6, 4,6,6,8 }; uint32x4_t bit = {8,4,2,1}; uint32_t imask1 = vaddvq_u32(vandq_u32(Rlt1, bit)); uint32_t imask2 = vaddvq_u32(vandq_u32(Rlt2, bit)); uint32_t imask3 = vaddvq_u32(vandq_u32(Rlt3, bit)); uint32_t imask4 = vaddvq_u32(vandq_u32(Rlt4, bit)); // load 8 lanes of renorm data uint16x8_t norm12 = vld1q_u16((uint16_t *)ptr); // move ptr by no. renorm lanes used ptr += nbits[imask1] + nbits[imask2]; uint16x8_t norm34 = vld1q_u16((uint16_t *)ptr); ptr += nbits[imask3] + nbits[imask4]; uint32_t imask12 = (imask1<<4)|imask2; uint32_t imask34 = (imask3<<4)|imask4; // Shuffle norm to the corresponding R lanes, via imask // #define for brevity and formatting uint16x4_t norm1, norm2, norm3, norm4; norm1 = cast_u16_u8(vqtbl1_u8(cast_u8_u16(norm12),idx [imask1])); norm2 = cast_u16_u8(vqtbl1_u8(cast_u8_u16(norm12),idx2[imask12])); norm3 = cast_u16_u8(vqtbl1_u8(cast_u8_u16(norm34),idx [imask3])); norm4 = cast_u16_u8(vqtbl1_u8(cast_u8_u16(norm34),idx2[imask34])); // Add norm to R<<16 and blend back in with R uint32x4_t Rsl1 = vshlq_n_u32(RV[Z+0], 16); // Rsl = R << 16 uint32x4_t Rsl2 = vshlq_n_u32(RV[Z+1], 16); uint32x4_t Rsl3 = vshlq_n_u32(RV[Z+2], 16); uint32x4_t Rsl4 = vshlq_n_u32(RV[Z+3], 16); Rsl1 = vaddw_u16(Rsl1, norm1); // Rsl += norm Rsl2 = vaddw_u16(Rsl2, norm2); Rsl3 = vaddw_u16(Rsl3, norm3); Rsl4 = vaddw_u16(Rsl4, norm4); RV[Z+0] = vbslq_u32(Rlt1, Rsl1, RV[Z+0]); // R = R s3 + l*TOTFREQ_O1_FAST + c. uint32x4_t off1 = vandq_u32(RV[Z+0], maskv); uint32x4_t off2 = vandq_u32(RV[Z+1], maskv); uint32x4_t off3 = vandq_u32(RV[Z+2], maskv); uint32x4_t off4 = vandq_u32(RV[Z+3], maskv); off1 = vaddq_u32(off1, Sv1); off2 = vaddq_u32(off2, Sv2); off3 = vaddq_u32(off3, Sv3); off4 = vaddq_u32(off4, Sv4); vst1q_u32(&m[z+ 0], off1); vst1q_u32(&m[z+ 4], off2); vst1q_u32(&m[z+ 8], off3); vst1q_u32(&m[z+12], off4); } i4[0]++; if (++tidx == 32) { i4[0] -= 32; transpose_and_copy(out, i4, tbuf); tidx = 0; } } vst1q_u32(&R[ 0], RV[0]); vst1q_u32(&R[ 4], RV[1]); vst1q_u32(&R[ 8], RV[2]); vst1q_u32(&R[12], RV[3]); vst1q_u32(&R[16], RV[4]); vst1q_u32(&R[20], RV[5]); vst1q_u32(&R[24], RV[6]); vst1q_u32(&R[28], RV[7]); i4[0]-=tidx; int T; for (z = 0; z < NX; z++) for (T = 0; T < tidx; T++) out[i4[z]++] = tbuf[T][z]; // Scalar version for close to end of in[] array so we don't do // SIMD loads beyond the end of the buffer for (; i4[0] < isz4; ) { for (z = 0; z < NX; z++) { uint32_t m = R[z] & ((1u<>(TF_SHIFT_O1_FAST+8)) * (R[z]>>TF_SHIFT_O1_FAST) + ((S>>8) & ((1u<>(TF_SHIFT_O1_FAST+8)) * (R[NX-1]>>TF_SHIFT_O1_FAST) + ((S>>8) & ((1u< #include #include #include #include #include #include "rANS_word.h" #include "rANS_static4x16.h" #include "rANS_static16_int.h" #include "varint.h" #include "utils.h" /* Uses: SSE, SSE2, SSSE3, SSE4.1 and POPCNT SSE: _mm_movemask_ps SSE2: _mm_load_si128 _mm_store_si128 _mm_set_epi32 _mm_set1_epi32 _mm_and_si128 _mm_or_si128 _mm_srli_epi32 _mm_slli_epi32 _mm_srli_epi64 _mm_set1_epi64x _mm_add_epi32 _mm_packus_epi32 _mm_andnot_si128 _mm_cmpeq_epi32 _mm_mul_epu32 _mm_shuffle_epi32 SSSE3: _mm_shuffle_epi8 SSE4.1: _mm_mullo_epi32 _mm_packus_epi32 _mm_max_epu32 _mm_cvtepu16_epi32 _mm_blendv_epi8 POPCNT: _mm_popcnt_u32 */ #define NX 32 #define LOAD128(a,b) \ __m128i a##1 = _mm_load_si128((__m128i *)&b[0]); \ __m128i a##2 = _mm_load_si128((__m128i *)&b[4]); \ __m128i a##3 = _mm_load_si128((__m128i *)&b[8]); \ __m128i a##4 = _mm_load_si128((__m128i *)&b[12]); \ __m128i a##5 = _mm_load_si128((__m128i *)&b[16]); \ __m128i a##6 = _mm_load_si128((__m128i *)&b[20]); \ __m128i a##7 = _mm_load_si128((__m128i *)&b[24]); \ __m128i a##8 = _mm_load_si128((__m128i *)&b[28]); #define STORE128(a,b) \ _mm_store_si128((__m128i *)&b[ 0], a##1); \ _mm_store_si128((__m128i *)&b[ 4], a##2); \ _mm_store_si128((__m128i *)&b[ 8], a##3); \ _mm_store_si128((__m128i *)&b[12], a##4); \ _mm_store_si128((__m128i *)&b[16], a##5); \ _mm_store_si128((__m128i *)&b[20], a##6); \ _mm_store_si128((__m128i *)&b[24], a##7); \ _mm_store_si128((__m128i *)&b[28], a##8); static inline __m128i _mm_i32gather_epi32x(int *b, __m128i idx, int size) { int c[4] __attribute__((aligned(32))); _mm_store_si128((__m128i *)c, idx); return _mm_set_epi32(b[c[3]], b[c[2]], b[c[1]], b[c[0]]); } // SSE4 implementation of the Order-0 encoder is poorly performing. // Disabled for now. #if 0 #define LOAD128v(a,b) \ __m128i a[8]; \ a[0] = _mm_load_si128((__m128i *)&b[0]); \ a[1] = _mm_load_si128((__m128i *)&b[4]); \ a[2] = _mm_load_si128((__m128i *)&b[8]); \ a[3] = _mm_load_si128((__m128i *)&b[12]); \ a[4] = _mm_load_si128((__m128i *)&b[16]); \ a[5] = _mm_load_si128((__m128i *)&b[20]); \ a[6] = _mm_load_si128((__m128i *)&b[24]); \ a[7] = _mm_load_si128((__m128i *)&b[28]); #define STORE128v(a,b) \ _mm_store_si128((__m128i *)&b[ 0], a[0]); \ _mm_store_si128((__m128i *)&b[ 4], a[1]); \ _mm_store_si128((__m128i *)&b[ 8], a[2]); \ _mm_store_si128((__m128i *)&b[12], a[3]); \ _mm_store_si128((__m128i *)&b[16], a[4]); \ _mm_store_si128((__m128i *)&b[20], a[5]); \ _mm_store_si128((__m128i *)&b[24], a[6]); \ _mm_store_si128((__m128i *)&b[28], a[7]); static inline __m128i _mm_mulhi_epu32(__m128i a, __m128i b) { // Multiply bottom 4 items and top 4 items together. __m128i ab_hm = _mm_mul_epu32(_mm_srli_epi64(a, 32),_mm_srli_epi64(b, 32)); __m128i ab_lm = _mm_srli_epi64(_mm_mul_epu32(a, b), 32); // Blend or and/or seems to make no difference. return _mm_blend_epi16(ab_lm, ab_hm, 0xcc); // // Shift to get hi 32-bit of each 64-bit product // ab_hm = _mm_and_si128(ab_hm,_mm_set1_epi64x((uint64_t)0xffffffff00000000)); // // return _mm_or_si128(ab_lm, ab_hm); } // Shift A>>B for non-constant B exists in AVX2, but not SSE world. // We simulate this for now by store, shift, and load. Ugly! static inline __m128i _mm_srlv_epi32x(__m128i a, __m128i b) { // Extract and inline shift. Slowest clang, joint fastest gcc // return _mm_set_epi32(_mm_extract_epi32(a,3)>>_mm_extract_epi32(b,3), // _mm_extract_epi32(a,2)>>_mm_extract_epi32(b,2), // _mm_extract_epi32(a,1)>>_mm_extract_epi32(b,1), // _mm_extract_epi32(a,0)>>_mm_extract_epi32(b,0)); // Half store and inline shift; Fastest gcc, comparable to others below clang // uint32_t A[4]; // _mm_storeu_si128((__m128i *)&A, a); // // return _mm_set_epi32(A[3]>>_mm_extract_epi32(b,3), // A[2]>>_mm_extract_epi32(b,2), // A[1]>>_mm_extract_epi32(b,1), // A[0]>>_mm_extract_epi32(b,0)); // Other half uint32_t B[4]; _mm_storeu_si128((__m128i *)&B, b); return _mm_set_epi32(_mm_extract_epi32(a,3)>>B[3], _mm_extract_epi32(a,2)>>B[2], _mm_extract_epi32(a,1)>>B[1], _mm_extract_epi32(a,0)>>B[0]); // Check if all b[] match, and constant shift if so. // Too costly, even on q4 where it's common for all shift to be identical. // __m128i cmp = _mm_cmpeq_epi32(b, _mm_shuffle_epi32(b, 0x39)); // if (_mm_movemask_ps((__m128)cmp) == 15) { // return _mm_srl_epi32(a, _mm_set1_epi64x(_mm_extract_epi32(b,0))); // //_mm_storeu_si128((__m128i *)&B,_mm_set1_epi32(_mm_extract_epi32(b,0))); // } else { // uint32_t B[4]; // _mm_storeu_si128((__m128i *)&B, b); // return _mm_set_epi32(_mm_extract_epi32(a,3)>>B[3], // _mm_extract_epi32(a,2)>>B[2], // _mm_extract_epi32(a,1)>>B[1], // _mm_extract_epi32(a,0)>>B[0]); // } // Full store and inline shift // uint32_t A[4], B[4] __attribute__((aligned(16))); // _mm_storeu_si128((__m128i *)&A, a); // _mm_storeu_si128((__m128i *)&B, b); // // return _mm_set_epi32(A[3]>>B[3], A[2]>>B[2], A[1]>>B[1], A[0]>>B[0]); // Full store, shift and load // uint32_t A[4], B[4] __attribute__((aligned(16))); // _mm_storeu_si128((__m128i *)&A, a); // _mm_storeu_si128((__m128i *)&B, b); // A[0]>>=B[0]; // A[1]>>=B[1]; // A[2]>>=B[2]; // A[3]>>=B[3]; // return _mm_loadu_si128((__m128i *)A); } unsigned char *rans_compress_O0_32x16_sse4(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { unsigned char *cp, *out_end; RansEncSymbol syms[256]; RansState ransN[NX]; uint8_t* ptr; uint32_t F[256+MAGIC] = {0}; int i, j, tab_size = 0, x, z; // -20 for order/size/meta uint32_t bound = rans_compress_bound_4x16(in_size,0)-20; if (!out) { *out_size = bound; out = malloc(*out_size); } if (!out || bound > *out_size) return NULL; // If "out" isn't word aligned, tweak out_end/ptr to ensure it is. // We already added more round in bound to allow for this. if (((size_t)out)&1) bound--; ptr = out_end = out + bound; if (in_size == 0) goto empty; // Compute statistics if (hist8(in, in_size, F) < 0) return NULL; // Normalise so frequences sum to power of 2 uint32_t fsum = in_size; uint32_t max_val = round2(fsum); if (max_val > TOTFREQ) max_val = TOTFREQ; if (normalise_freq(F, fsum, max_val) < 0) return NULL; fsum=max_val; cp = out; cp += encode_freq(cp, F); tab_size = cp-out; //write(2, out+4, cp-(out+4)); if (normalise_freq(F, fsum, TOTFREQ) < 0) return NULL; // Encode statistics. for (x = j = 0; j < 256; j++) { if (F[j]) { RansEncSymbolInit(&syms[j], x, F[j], TF_SHIFT); x += F[j]; } } for (z = 0; z < NX; z++) RansEncInit(&ransN[z]); z = i = in_size&(NX-1); while (z-- > 0) RansEncPutSymbol(&ransN[z], &ptr, &syms[in[in_size-(i-z)]]); uint32_t SB[256], SA[256], SD[256], SC[256]; // Build lookup tables for SIMD encoding uint16_t *ptr16 = (uint16_t *)ptr; for (i = 0; i < 256; i++) { SB[i] = syms[i].x_max; SA[i] = syms[i].rcp_freq; SD[i] = (syms[i].cmpl_freq<<0) | (syms[i].rcp_shift<<16); SC[i] = syms[i].bias; } LOAD128v(Rv, ransN); const __m128i shuf = _mm_set_epi8(0x80, 0x80, 0x80, 0x80, 0x80, 0x80, 0x80, 0x80, 0x0d, 0x0c, 0x09, 0x08, 0x05, 0x04, 0x01, 0x00); // FIXME: slower! // q40: 340 (scalar) vs 300 (this) // q4: 430 (scalar) vs 304 (this) for (i=(in_size &~(NX-1)); i>0; i-=NX) { uint8_t *c = &in[i-NX]; int h; // Slightly better in 4x8 instead of 2x16 cycles with clang, // but the reverse with gcc. //for (h=24; h >= 0; h -= 8) { for (h=16; h >= 0; h -= 16) { int H = h/4; // rans index uint8_t *C = &in[i-NX+h]; #define SET(i,a) _mm_set_epi32(a[C[i+3]],a[C[i+2]],a[C[i+1]],a[C[i+0]]) __m128i xmax8 = SET(12, SB); __m128i xmax7 = SET( 8, SB); __m128i xmax6 = SET( 4, SB); __m128i xmax5 = SET( 0, SB); __m128i cv8 = _mm_cmpgt_epi32(Rv[H+3], xmax8); __m128i cv7 = _mm_cmpgt_epi32(Rv[H+2], xmax7); __m128i cv6 = _mm_cmpgt_epi32(Rv[H+1], xmax6); __m128i cv5 = _mm_cmpgt_epi32(Rv[H+0], xmax5); // Store bottom 16-bits at ptr16 unsigned int imask8 = _mm_movemask_ps((__m128)cv8); unsigned int imask7 = _mm_movemask_ps((__m128)cv7); unsigned int imask6 = _mm_movemask_ps((__m128)cv6); unsigned int imask5 = _mm_movemask_ps((__m128)cv5); #define X(A) 4*A,4*A+1,0x80,0x80 #define _ 0x80,0x80,0x80,0x80 uint8_t permutec[16][16] __attribute__((aligned(16))) = { { _ , _ , _ , _ }, { _ , _ , _ ,X(0)}, { _ , _ , _ ,X(1)}, { _ , _ ,X(0),X(1)}, { _ , _ , _ ,X(2)}, { _ , _ ,X(0),X(2)}, { _ , _ ,X(1),X(2)}, { _ ,X(0),X(1),X(2)}, { _ , _ , _ ,X(3)}, { _ , _ ,X(0),X(3)}, { _ , _ ,X(1),X(3)}, { _ ,X(0),X(1),X(3)}, { _ , _ ,X(2),X(3)}, { _ ,X(0),X(2),X(3)}, { _ ,X(1),X(2),X(3)}, {X(0),X(1),X(2),X(3)}, }; #undef X #undef _ __m128i idx8 = _mm_load_si128((__m128i *)permutec[imask8]); __m128i idx7 = _mm_load_si128((__m128i *)permutec[imask7]); __m128i idx6 = _mm_load_si128((__m128i *)permutec[imask6]); __m128i idx5 = _mm_load_si128((__m128i *)permutec[imask5]); // Permute; to gather together the rans states that need flushing __m128i V1, V2, V3, V4, V5, V6, V7, V8; V8 = _mm_shuffle_epi8(_mm_and_si128(Rv[H+3], cv8), idx8); V7 = _mm_shuffle_epi8(_mm_and_si128(Rv[H+2], cv7), idx7); V6 = _mm_shuffle_epi8(_mm_and_si128(Rv[H+1], cv6), idx6); V5 = _mm_shuffle_epi8(_mm_and_si128(Rv[H+0], cv5), idx5); // Shuffle alternating shorts together to collect low 16-bit // elements together. ... 9 8 5 4 1 0. // Or as with avx2 code use packus instead. V8 = _mm_shuffle_epi8(V8, shuf); V7 = _mm_shuffle_epi8(V7, shuf); V6 = _mm_shuffle_epi8(V6, shuf); V5 = _mm_shuffle_epi8(V5, shuf); _mm_storeu_si64(ptr16-4, V8); ptr16 -= _mm_popcnt_u32(imask8); _mm_storeu_si64(ptr16-4, V7); ptr16 -= _mm_popcnt_u32(imask7); _mm_storeu_si64(ptr16-4, V6); ptr16 -= _mm_popcnt_u32(imask6); _mm_storeu_si64(ptr16-4, V5); ptr16 -= _mm_popcnt_u32(imask5); Rv[H+3] = _mm_blendv_epi8(Rv[H+3], _mm_srli_epi32(Rv[H+3], 16), cv8); Rv[H+2] = _mm_blendv_epi8(Rv[H+2], _mm_srli_epi32(Rv[H+2], 16), cv7); Rv[H+1] = _mm_blendv_epi8(Rv[H+1], _mm_srli_epi32(Rv[H+1], 16), cv6); Rv[H+0] = _mm_blendv_epi8(Rv[H+0], _mm_srli_epi32(Rv[H+0], 16), cv5); // Cannot trivially replace the multiply as mulhi_epu32 doesn't // exist (only mullo). // However we can use _mm_mul_epu32 twice to get 64bit results // (h our lanes) and shift/or to get the answer. // // (AVX512 allows us to hold it all in 64-bit lanes and use mullo_epi64 // plus a shift. KNC has mulhi_epi32, but not sure if this is // available.) __m128i rfv8 = SET(12, SA); __m128i rfv7 = SET( 8, SA); __m128i rfv6 = SET( 4, SA); __m128i rfv5 = SET( 0, SA); rfv8 = _mm_mulhi_epu32(Rv[H+3], rfv8); rfv7 = _mm_mulhi_epu32(Rv[H+2], rfv7); rfv6 = _mm_mulhi_epu32(Rv[H+1], rfv6); rfv5 = _mm_mulhi_epu32(Rv[H+0], rfv5); __m128i SDv8 = SET(12, SD); __m128i SDv7 = SET( 8, SD); __m128i SDv6 = SET( 4, SD); __m128i SDv5 = SET( 0, SD); __m128i shiftv8 = _mm_srli_epi32(SDv8, 16); __m128i shiftv7 = _mm_srli_epi32(SDv7, 16); __m128i shiftv6 = _mm_srli_epi32(SDv6, 16); __m128i shiftv5 = _mm_srli_epi32(SDv5, 16); __m128i freqv8 = _mm_and_si128(SDv8, _mm_set1_epi32(0xffff)); __m128i freqv7 = _mm_and_si128(SDv7, _mm_set1_epi32(0xffff)); __m128i freqv6 = _mm_and_si128(SDv6, _mm_set1_epi32(0xffff)); __m128i freqv5 = _mm_and_si128(SDv5, _mm_set1_epi32(0xffff)); // Bake this into the tabel to start with? shiftv8 = _mm_sub_epi32(shiftv8, _mm_set1_epi32(32)); shiftv7 = _mm_sub_epi32(shiftv7, _mm_set1_epi32(32)); shiftv6 = _mm_sub_epi32(shiftv6, _mm_set1_epi32(32)); shiftv5 = _mm_sub_epi32(shiftv5, _mm_set1_epi32(32)); // No way to shift by varying amounts. Store, shift, load? Simulated __m128i qv8 = _mm_srlv_epi32x(rfv8, shiftv8); __m128i qv7 = _mm_srlv_epi32x(rfv7, shiftv7); __m128i qv6 = _mm_srlv_epi32x(rfv6, shiftv6); __m128i qv5 = _mm_srlv_epi32x(rfv5, shiftv5); qv8 = _mm_mullo_epi32(qv8, freqv8); qv7 = _mm_mullo_epi32(qv7, freqv7); qv6 = _mm_mullo_epi32(qv6, freqv6); qv5 = _mm_mullo_epi32(qv5, freqv5); qv8 = _mm_add_epi32(qv8, SET(12, SC)); qv7 = _mm_add_epi32(qv7, SET( 8, SC)); qv6 = _mm_add_epi32(qv6, SET( 4, SC)); qv5 = _mm_add_epi32(qv5, SET( 0, SC)); Rv[H+3] = _mm_add_epi32(Rv[H+3], qv8); Rv[H+2] = _mm_add_epi32(Rv[H+2], qv7); Rv[H+1] = _mm_add_epi32(Rv[H+1], qv6); Rv[H+0] = _mm_add_epi32(Rv[H+0], qv5); } } STORE128v(Rv, ransN); ptr = (uint8_t *)ptr16; for (z = NX-1; z >= 0; z--) RansEncFlush(&ransN[z], &ptr); empty: // Finalise block size and return it *out_size = (out_end - ptr) + tab_size; // cp = out; // *cp++ = (in_size>> 0) & 0xff; // *cp++ = (in_size>> 8) & 0xff; // *cp++ = (in_size>>16) & 0xff; // *cp++ = (in_size>>24) & 0xff; memmove(out + tab_size, ptr, out_end-ptr); return out; } #endif // disable SSE4 encoder unsigned char *rans_uncompress_O0_32x16_sse4(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { if (in_size < 16) // 4-states at least return NULL; if (out_sz >= INT_MAX) return NULL; // protect against some overflow cases #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (out_sz > 100000) return NULL; #endif /* Load in the static tables */ unsigned char *cp = in, *out_free = NULL; unsigned char *cp_end = in + in_size; int i; uint32_t s3[TOTFREQ] __attribute__((aligned(32))); // For TF_SHIFT <= 12 if (!out) out_free = out = malloc(out_sz); if (!out) return NULL; // Precompute reverse lookup of frequency. uint32_t F[256] = {0}, fsum; int fsz = decode_freq(cp, cp_end, F, &fsum); if (!fsz) goto err; cp += fsz; normalise_freq_shift(F, fsum, TOTFREQ); // Build symbols; fixme, do as part of decode, see the _d variant if (rans_F_to_s3(F, TF_SHIFT, s3)) goto err; if (cp_end - cp < NX * 4) goto err; int z; RansState R[NX] __attribute__((aligned(32))); for (z = 0; z < NX; z++) { RansDecInit(&R[z], &cp); if (R[z] < RANS_BYTE_L) goto err; } uint16_t *sp = (uint16_t *)cp; int out_end = (out_sz&~(NX-1)); const uint32_t mask = (1u << TF_SHIFT)-1; __m128i maskv = _mm_set1_epi32(mask); // set mask in all lanes LOAD128(Rv, R); uint8_t overflow[72+64] = {0}; for (i=0; i < out_end; i+=NX) { //for (z = 0; z < NX; z++) // m[z] = R[z] & mask; __m128i masked1 = _mm_and_si128(Rv1, maskv); __m128i masked2 = _mm_and_si128(Rv2, maskv); __m128i masked3 = _mm_and_si128(Rv3, maskv); __m128i masked4 = _mm_and_si128(Rv4, maskv); // S[z] = s3[m[z]]; __m128i Sv1 = _mm_i32gather_epi32x((int *)s3, masked1, sizeof(*s3)); __m128i Sv2 = _mm_i32gather_epi32x((int *)s3, masked2, sizeof(*s3)); __m128i Sv3 = _mm_i32gather_epi32x((int *)s3, masked3, sizeof(*s3)); __m128i Sv4 = _mm_i32gather_epi32x((int *)s3, masked4, sizeof(*s3)); // f[z] = S[z]>>(TF_SHIFT+8); __m128i fv1 = _mm_srli_epi32(Sv1, TF_SHIFT+8); __m128i fv2 = _mm_srli_epi32(Sv2, TF_SHIFT+8); __m128i fv3 = _mm_srli_epi32(Sv3, TF_SHIFT+8); __m128i fv4 = _mm_srli_epi32(Sv4, TF_SHIFT+8); // b[z] = (S[z]>>8) & mask; __m128i bv1 = _mm_and_si128(_mm_srli_epi32(Sv1, 8), maskv); __m128i bv2 = _mm_and_si128(_mm_srli_epi32(Sv2, 8), maskv); __m128i bv3 = _mm_and_si128(_mm_srli_epi32(Sv3, 8), maskv); __m128i bv4 = _mm_and_si128(_mm_srli_epi32(Sv4, 8), maskv); // s[z] = S[z] & 0xff; __m128i sv1 = _mm_and_si128(Sv1, _mm_set1_epi32(0xff)); __m128i sv2 = _mm_and_si128(Sv2, _mm_set1_epi32(0xff)); __m128i sv3 = _mm_and_si128(Sv3, _mm_set1_epi32(0xff)); __m128i sv4 = _mm_and_si128(Sv4, _mm_set1_epi32(0xff)); // R[z] = f[z] * (R[z] >> TF_SHIFT) + b[z]; Rv1 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv1,TF_SHIFT), fv1), bv1); Rv2 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv2,TF_SHIFT), fv2), bv2); Rv3 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv3,TF_SHIFT), fv3), bv3); Rv4 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv4,TF_SHIFT), fv4), bv4); // Tricky one: out[i+z] = s[z]; // ---d---c ---b---a sv1 // ---h---g ---f---e sv2 // packs_epi32 -h-g-f-e -d-c-b-a sv1(2) // packs_epi16 ponmlkji hgfedcba sv1(2) / sv3(4) sv1 = _mm_packus_epi32(sv1, sv2); sv3 = _mm_packus_epi32(sv3, sv4); sv1 = _mm_packus_epi16(sv1, sv3); // c = R[z] < RANS_BYTE_L; // A little tricky as we only have signed comparisons. // See https://stackoverflow.com/questions/32945410/sse2-intrinsics-comparing-unsigned-integers #define _mm_cmplt_epu32_imm(a,b) _mm_andnot_si128(_mm_cmpeq_epi32(_mm_max_epu32((a),_mm_set1_epi32(b)), (a)), _mm_set1_epi32(-1)); //#define _mm_cmplt_epu32_imm(a,b) _mm_cmpgt_epi32(_mm_set1_epi32((b)-0x80000000), _mm_xor_si128((a), _mm_set1_epi32(0x80000000))) __m128i renorm_mask1, renorm_mask2, renorm_mask3, renorm_mask4; renorm_mask1 = _mm_cmplt_epu32_imm(Rv1, RANS_BYTE_L); renorm_mask2 = _mm_cmplt_epu32_imm(Rv2, RANS_BYTE_L); renorm_mask3 = _mm_cmplt_epu32_imm(Rv3, RANS_BYTE_L); renorm_mask4 = _mm_cmplt_epu32_imm(Rv4, RANS_BYTE_L); //#define P(A,B,C,D) ((A)+((B)<<2) + ((C)<<4) + ((D)<<6)) #define P(A,B,C,D) \ { A+0,A+1,A+2,A+3, \ B+0,B+1,B+2,B+3, \ C+0,C+1,C+2,C+3, \ D+0,D+1,D+2,D+3} #ifdef _ #undef _ #endif #define _ 0x80 uint8_t pidx[16][16] = { P(_,_,_,_), P(0,_,_,_), P(_,0,_,_), P(0,4,_,_), P(_,_,0,_), P(0,_,4,_), P(_,0,4,_), P(0,4,8,_), P(_,_,_,0), P(0,_,_,4), P(_,0,_,4), P(0,4,_,8), P(_,_,0,4), P(0,_,4,8), P(_,0,4,8), P(0,4,8,12), }; #undef _ // Protect against running off the end of in buffer. // We copy it to a worst-case local buffer when near the end. // 72 = 7*8(imask1..7) + 16; worse case for 8th _mm_loadu_si128 call. // An extra 64 bytes is to avoid triggering this multiple times // after we swap sp/cp_end over. if ((uint8_t *)sp+72 > cp_end) { memmove(overflow, sp, cp_end - (uint8_t *)sp); sp = (uint16_t *)overflow; cp_end = (uint8_t *)overflow + sizeof(overflow); } // Shuffle the renorm values to correct lanes and incr sp pointer __m128i Vv1 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask1 = _mm_movemask_ps((__m128)renorm_mask1); Vv1 = _mm_shuffle_epi8(Vv1, _mm_load_si128((__m128i*)pidx[imask1])); sp += _mm_popcnt_u32(imask1); __m128i Vv2 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask2 = _mm_movemask_ps((__m128)renorm_mask2); sp += _mm_popcnt_u32(imask2); Vv2 = _mm_shuffle_epi8(Vv2, _mm_load_si128((__m128i*)pidx[imask2])); __m128i Vv3 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask3 = _mm_movemask_ps((__m128)renorm_mask3); Vv3 = _mm_shuffle_epi8(Vv3, _mm_load_si128((__m128i*)pidx[imask3])); sp += _mm_popcnt_u32(imask3); __m128i Vv4 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask4 = _mm_movemask_ps((__m128)renorm_mask4); sp += _mm_popcnt_u32(imask4); Vv4 = _mm_shuffle_epi8(Vv4, _mm_load_si128((__m128i*)pidx[imask4])); __m128i Yv1 = _mm_slli_epi32(Rv1, 16); __m128i Yv2 = _mm_slli_epi32(Rv2, 16); __m128i Yv3 = _mm_slli_epi32(Rv3, 16); __m128i Yv4 = _mm_slli_epi32(Rv4, 16); // y = (R[z] << 16) | V[z]; Yv1 = _mm_or_si128(Yv1, Vv1); Yv2 = _mm_or_si128(Yv2, Vv2); Yv3 = _mm_or_si128(Yv3, Vv3); Yv4 = _mm_or_si128(Yv4, Vv4); // R[z] = c ? Y[z] : R[z]; Rv1 = _mm_blendv_epi8(Rv1, Yv1, renorm_mask1); Rv2 = _mm_blendv_epi8(Rv2, Yv2, renorm_mask2); Rv3 = _mm_blendv_epi8(Rv3, Yv3, renorm_mask3); Rv4 = _mm_blendv_epi8(Rv4, Yv4, renorm_mask4); // ------------------------------------------------------------ // m[z] = R[z] & mask; __m128i masked5 = _mm_and_si128(Rv5, maskv); __m128i masked6 = _mm_and_si128(Rv6, maskv); __m128i masked7 = _mm_and_si128(Rv7, maskv); __m128i masked8 = _mm_and_si128(Rv8, maskv); // S[z] = s3[m[z]]; __m128i Sv5 = _mm_i32gather_epi32x((int *)s3, masked5, sizeof(*s3)); __m128i Sv6 = _mm_i32gather_epi32x((int *)s3, masked6, sizeof(*s3)); __m128i Sv7 = _mm_i32gather_epi32x((int *)s3, masked7, sizeof(*s3)); __m128i Sv8 = _mm_i32gather_epi32x((int *)s3, masked8, sizeof(*s3)); // f[z] = S[z]>>(TF_SHIFT+8); __m128i fv5 = _mm_srli_epi32(Sv5, TF_SHIFT+8); __m128i fv6 = _mm_srli_epi32(Sv6, TF_SHIFT+8); __m128i fv7 = _mm_srli_epi32(Sv7, TF_SHIFT+8); __m128i fv8 = _mm_srli_epi32(Sv8, TF_SHIFT+8); // b[z] = (S[z]>>8) & mask; __m128i bv5 = _mm_and_si128(_mm_srli_epi32(Sv5, 8), maskv); __m128i bv6 = _mm_and_si128(_mm_srli_epi32(Sv6, 8), maskv); __m128i bv7 = _mm_and_si128(_mm_srli_epi32(Sv7, 8), maskv); __m128i bv8 = _mm_and_si128(_mm_srli_epi32(Sv8, 8), maskv); // s[z] = S[z] & 0xff; __m128i sv5 = _mm_and_si128(Sv5, _mm_set1_epi32(0xff)); __m128i sv6 = _mm_and_si128(Sv6, _mm_set1_epi32(0xff)); __m128i sv7 = _mm_and_si128(Sv7, _mm_set1_epi32(0xff)); __m128i sv8 = _mm_and_si128(Sv8, _mm_set1_epi32(0xff)); // R[z] = f[z] * (R[z] >> TF_SHIFT) + b[z]; Rv5 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv5,TF_SHIFT), fv5), bv5); Rv6 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv6,TF_SHIFT), fv6), bv6); Rv7 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv7,TF_SHIFT), fv7), bv7); Rv8 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv8,TF_SHIFT), fv8), bv8); // Tricky one: out[i+z] = s[z]; // ---d---c ---b---a sv1 // ---h---g ---f---e sv2 // packs_epi32 -h-g-f-e -d-c-b-a sv1(2) // packs_epi16 ponmlkji hgfedcba sv1(2) / sv3(4) sv5 = _mm_packus_epi32(sv5, sv6); sv7 = _mm_packus_epi32(sv7, sv8); sv5 = _mm_packus_epi16(sv5, sv7); // c = R[z] < RANS_BYTE_L; __m128i renorm_mask5, renorm_mask6, renorm_mask7, renorm_mask8; renorm_mask5 = _mm_cmplt_epu32_imm(Rv5, RANS_BYTE_L); renorm_mask6 = _mm_cmplt_epu32_imm(Rv6, RANS_BYTE_L); renorm_mask7 = _mm_cmplt_epu32_imm(Rv7, RANS_BYTE_L); renorm_mask8 = _mm_cmplt_epu32_imm(Rv8, RANS_BYTE_L); // Shuffle the renorm values to correct lanes and incr sp pointer __m128i Vv5 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask5 = _mm_movemask_ps((__m128)renorm_mask5); Vv5 = _mm_shuffle_epi8(Vv5, _mm_load_si128((__m128i*)pidx[imask5])); sp += _mm_popcnt_u32(imask5); __m128i Vv6 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask6 = _mm_movemask_ps((__m128)renorm_mask6); sp += _mm_popcnt_u32(imask6); Vv6 = _mm_shuffle_epi8(Vv6, _mm_load_si128((__m128i*)pidx[imask6])); __m128i Vv7 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask7 = _mm_movemask_ps((__m128)renorm_mask7); Vv7 = _mm_shuffle_epi8(Vv7, _mm_load_si128((__m128i*)pidx[imask7])); sp += _mm_popcnt_u32(imask7); __m128i Vv8 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask8 = _mm_movemask_ps((__m128)renorm_mask8); sp += _mm_popcnt_u32(imask8); Vv8 = _mm_shuffle_epi8(Vv8, _mm_load_si128((__m128i*)pidx[imask8])); __m128i Yv5 = _mm_slli_epi32(Rv5, 16); __m128i Yv6 = _mm_slli_epi32(Rv6, 16); __m128i Yv7 = _mm_slli_epi32(Rv7, 16); __m128i Yv8 = _mm_slli_epi32(Rv8, 16); // y = (R[z] << 16) | V[z]; Yv5 = _mm_or_si128(Yv5, Vv5); Yv6 = _mm_or_si128(Yv6, Vv6); Yv7 = _mm_or_si128(Yv7, Vv7); Yv8 = _mm_or_si128(Yv8, Vv8); // R[z] = c ? Y[z] : R[z]; Rv5 = _mm_blendv_epi8(Rv5, Yv5, renorm_mask5); Rv6 = _mm_blendv_epi8(Rv6, Yv6, renorm_mask6); Rv7 = _mm_blendv_epi8(Rv7, Yv7, renorm_mask7); Rv8 = _mm_blendv_epi8(Rv8, Yv8, renorm_mask8); // Maybe just a store128 instead? _mm_storeu_si128((__m128i *)&out[i+ 0], sv1); _mm_storeu_si128((__m128i *)&out[i+16], sv5); // *(uint64_t *)&out[i+ 0] = _mm_extract_epi64(sv1, 0); // *(uint64_t *)&out[i+ 8] = _mm_extract_epi64(sv1, 1); // *(uint64_t *)&out[i+16] = _mm_extract_epi64(sv5, 0); // *(uint64_t *)&out[i+24] = _mm_extract_epi64(sv5, 1); } STORE128(Rv, R); for (z = out_sz & (NX-1); z-- > 0; ) out[out_end + z] = s3[R[z] & mask]; //fprintf(stderr, " 0 Decoded %d bytes\n", (int)(cp-in)); //c-size return out; err: free(out_free); return NULL; } //#define MAGIC2 111 #define MAGIC2 179 //#define MAGIC2 0 /* * A 32 x 32 matrix transpose and serialise from t[][] to out. * Storing in the other orientation speeds up the decoder, and we * can then flush to out in 1KB blocks. */ static inline void transpose_and_copy(uint8_t *out, int iN[32], uint8_t t[32][32]) { int z; // Simplified version from below. // This is pretty good with zig cc, but slow on clang and very slow on // gcc, even with -O3 /* for (z = 0; z < NX; z++) { int k; for (k = 0; k < 32; k++) out[iN[z]+k] = t[k][z]; iN[z] += 32; } */ // A better approach for clang and gcc can be had with some manual // restructuring to attempt to do the two loops in explcit blocks. // With gcc -O3 or -O2 -ftree-vectorize this is quite fast, as is clang // and zig but neither beat the version below (or, for zig, the basic // code above). // // It's left here incase we ever want to move to tidier code and // to understand what auto-vectorises and what doesn't. /* #define NZ 2 #define NK 8 for (z = 0; z < 32; z+=NZ) { for (int k = 0; k < 32; k+=NK) { for (int z0 = z; z0 < z+NZ; z0++) { uint8_t tmp[NK];// __attribute__((aligned(32))); //uint8_t (*RESTRICT t0)[32] = &t[k]; for (int k0 = 0; k0 < NK; k0++) //tmp[k0] = t0[k0][z0]; tmp[k0] = t[k+k0][z0]; memcpy(&out[iN[z0]+k], tmp, NK); } } for (int z0 = z; z0 < z+NZ; z0++) iN[z0] += 32; } */ // Manually unrolled code. // This is fastest on gcc and clang and not far behind with zig cc. // It also doesn't need aggressive gcc optimisation levels to be // efficient. // // It works by constructing 64-bit ints and copying them with a single // memory write. The fixed size memcpys just boil down to a memory write, // but unlike the earlier versions that did this direct, this isn't // exploiting undefined behaviour. for (z = 0; z < 32; z+=4) { uint64_t i64; i64 = ((uint64_t)(t[0][z])<< 0) + ((uint64_t)(t[1][z])<< 8) + ((uint64_t)(t[2][z])<<16) + ((uint64_t)(t[3][z])<<24) + ((uint64_t)(t[4][z])<<32) + ((uint64_t)(t[5][z])<<40) + ((uint64_t)(t[6][z])<<48) + ((uint64_t)(t[7][z])<<56); memcpy(&out[iN[z]], &i64, 8); i64 = ((uint64_t)(t[0][z+1])<< 0) + ((uint64_t)(t[1][z+1])<< 8) + ((uint64_t)(t[2][z+1])<<16) + ((uint64_t)(t[3][z+1])<<24) + ((uint64_t)(t[4][z+1])<<32) + ((uint64_t)(t[5][z+1])<<40) + ((uint64_t)(t[6][z+1])<<48) + ((uint64_t)(t[7][z+1])<<56); memcpy(&out[iN[z+1]], &i64, 8); i64 = ((uint64_t)(t[0][z+2])<< 0) + ((uint64_t)(t[1][z+2])<< 8) + ((uint64_t)(t[2][z+2])<<16) + ((uint64_t)(t[3][z+2])<<24) + ((uint64_t)(t[4][z+2])<<32) + ((uint64_t)(t[5][z+2])<<40) + ((uint64_t)(t[6][z+2])<<48) + ((uint64_t)(t[7][z+2])<<56); memcpy(&out[iN[z+2]], &i64, 8); i64 = ((uint64_t)(t[0][z+3])<< 0) + ((uint64_t)(t[1][z+3])<< 8) + ((uint64_t)(t[2][z+3])<<16) + ((uint64_t)(t[3][z+3])<<24) + ((uint64_t)(t[4][z+3])<<32) + ((uint64_t)(t[5][z+3])<<40) + ((uint64_t)(t[6][z+3])<<48) + ((uint64_t)(t[7][z+3])<<56); memcpy(&out[iN[z+3]], &i64, 8); i64 = ((uint64_t)(t[8+0][z])<< 0) + ((uint64_t)(t[8+1][z])<< 8) + ((uint64_t)(t[8+2][z])<<16) + ((uint64_t)(t[8+3][z])<<24) + ((uint64_t)(t[8+4][z])<<32) + ((uint64_t)(t[8+5][z])<<40) + ((uint64_t)(t[8+6][z])<<48) + ((uint64_t)(t[8+7][z])<<56); memcpy(&out[iN[z]+8], &i64, 8); i64 = ((uint64_t)(t[8+0][z+1])<< 0) + ((uint64_t)(t[8+1][z+1])<< 8) + ((uint64_t)(t[8+2][z+1])<<16) + ((uint64_t)(t[8+3][z+1])<<24) + ((uint64_t)(t[8+4][z+1])<<32) + ((uint64_t)(t[8+5][z+1])<<40) + ((uint64_t)(t[8+6][z+1])<<48) + ((uint64_t)(t[8+7][z+1])<<56); memcpy(&out[iN[z+1]+8], &i64, 8); i64 = ((uint64_t)(t[8+0][z+2])<< 0) + ((uint64_t)(t[8+1][z+2])<< 8) + ((uint64_t)(t[8+2][z+2])<<16) + ((uint64_t)(t[8+3][z+2])<<24) + ((uint64_t)(t[8+4][z+2])<<32) + ((uint64_t)(t[8+5][z+2])<<40) + ((uint64_t)(t[8+6][z+2])<<48) + ((uint64_t)(t[8+7][z+2])<<56); memcpy(&out[iN[z+2]+8], &i64, 8); i64 = ((uint64_t)(t[8+0][z+3])<< 0) + ((uint64_t)(t[8+1][z+3])<< 8) + ((uint64_t)(t[8+2][z+3])<<16) + ((uint64_t)(t[8+3][z+3])<<24) + ((uint64_t)(t[8+4][z+3])<<32) + ((uint64_t)(t[8+5][z+3])<<40) + ((uint64_t)(t[8+6][z+3])<<48) + ((uint64_t)(t[8+7][z+3])<<56); memcpy(&out[iN[z+3]+8], &i64, 8); i64 = ((uint64_t)(t[16+0][z])<< 0) + ((uint64_t)(t[16+1][z])<< 8) + ((uint64_t)(t[16+2][z])<<16) + ((uint64_t)(t[16+3][z])<<24) + ((uint64_t)(t[16+4][z])<<32) + ((uint64_t)(t[16+5][z])<<40) + ((uint64_t)(t[16+6][z])<<48) + ((uint64_t)(t[16+7][z])<<56); memcpy(&out[iN[z]+16], &i64, 8); i64 = ((uint64_t)(t[16+0][z+1])<< 0) + ((uint64_t)(t[16+1][z+1])<< 8) + ((uint64_t)(t[16+2][z+1])<<16) + ((uint64_t)(t[16+3][z+1])<<24) + ((uint64_t)(t[16+4][z+1])<<32) + ((uint64_t)(t[16+5][z+1])<<40) + ((uint64_t)(t[16+6][z+1])<<48) + ((uint64_t)(t[16+7][z+1])<<56); memcpy(&out[iN[z+1]+16], &i64, 8); i64 = ((uint64_t)(t[16+0][z+2])<< 0) + ((uint64_t)(t[16+1][z+2])<< 8) + ((uint64_t)(t[16+2][z+2])<<16) + ((uint64_t)(t[16+3][z+2])<<24) + ((uint64_t)(t[16+4][z+2])<<32) + ((uint64_t)(t[16+5][z+2])<<40) + ((uint64_t)(t[16+6][z+2])<<48) + ((uint64_t)(t[16+7][z+2])<<56); memcpy(&out[iN[z+2]+16], &i64, 8); i64 = ((uint64_t)(t[16+0][z+3])<< 0) + ((uint64_t)(t[16+1][z+3])<< 8) + ((uint64_t)(t[16+2][z+3])<<16) + ((uint64_t)(t[16+3][z+3])<<24) + ((uint64_t)(t[16+4][z+3])<<32) + ((uint64_t)(t[16+5][z+3])<<40) + ((uint64_t)(t[16+6][z+3])<<48) + ((uint64_t)(t[16+7][z+3])<<56); memcpy(&out[iN[z+3]+16], &i64, 8); i64 = ((uint64_t)(t[24+0][z])<< 0) + ((uint64_t)(t[24+1][z])<< 8) + ((uint64_t)(t[24+2][z])<<16) + ((uint64_t)(t[24+3][z])<<24) + ((uint64_t)(t[24+4][z])<<32) + ((uint64_t)(t[24+5][z])<<40) + ((uint64_t)(t[24+6][z])<<48) + ((uint64_t)(t[24+7][z])<<56); memcpy(&out[iN[z]+24], &i64, 8); i64 = ((uint64_t)(t[24+0][z+1])<< 0) + ((uint64_t)(t[24+1][z+1])<< 8) + ((uint64_t)(t[24+2][z+1])<<16) + ((uint64_t)(t[24+3][z+1])<<24) + ((uint64_t)(t[24+4][z+1])<<32) + ((uint64_t)(t[24+5][z+1])<<40) + ((uint64_t)(t[24+6][z+1])<<48) + ((uint64_t)(t[24+7][z+1])<<56); memcpy(&out[iN[z+1]+24], &i64, 8); i64 = ((uint64_t)(t[24+0][z+2])<< 0) + ((uint64_t)(t[24+1][z+2])<< 8) + ((uint64_t)(t[24+2][z+2])<<16) + ((uint64_t)(t[24+3][z+2])<<24) + ((uint64_t)(t[24+4][z+2])<<32) + ((uint64_t)(t[24+5][z+2])<<40) + ((uint64_t)(t[24+6][z+2])<<48) + ((uint64_t)(t[24+7][z+2])<<56); memcpy(&out[iN[z+2]+24], &i64, 8); i64 = ((uint64_t)(t[24+0][z+3])<< 0) + ((uint64_t)(t[24+1][z+3])<< 8) + ((uint64_t)(t[24+2][z+3])<<16) + ((uint64_t)(t[24+3][z+3])<<24) + ((uint64_t)(t[24+4][z+3])<<32) + ((uint64_t)(t[24+5][z+3])<<40) + ((uint64_t)(t[24+6][z+3])<<48) + ((uint64_t)(t[24+7][z+3])<<56); memcpy(&out[iN[z+3]+24], &i64, 8); iN[z+0] += 32; iN[z+1] += 32; iN[z+2] += 32; iN[z+3] += 32; } } unsigned char *rans_uncompress_O1_32x16_sse4(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { if (in_size < NX*4) // 4-states at least return NULL; if (out_sz >= INT_MAX) return NULL; // protect against some overflow cases #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (out_sz > 100000) return NULL; #endif /* Load in the static tables */ unsigned char *cp = in, *cp_end = in+in_size, *out_free = NULL; unsigned char *c_freq = NULL; uint32_t (*s3)[TOTFREQ_O1] = htscodecs_tls_alloc(256*TOTFREQ_O1*4); if (!s3) return NULL; uint32_t (*s3F)[TOTFREQ_O1_FAST] = (uint32_t (*)[TOTFREQ_O1_FAST])s3; if (!out) out_free = out = malloc(out_sz); if (!out) goto err; //fprintf(stderr, "out_sz=%d\n", out_sz); // compressed header? If so uncompress it unsigned char *tab_end = NULL; unsigned char *c_freq_end = cp_end; unsigned int shift = *cp >> 4; if (*cp++ & 1) { uint32_t u_freq_sz, c_freq_sz; cp += var_get_u32(cp, cp_end, &u_freq_sz); cp += var_get_u32(cp, cp_end, &c_freq_sz); if (c_freq_sz > cp_end - cp) goto err; tab_end = cp + c_freq_sz; if (!(c_freq = rans_uncompress_O0_4x16(cp, c_freq_sz, NULL,u_freq_sz))) goto err; cp = c_freq; c_freq_end = c_freq + u_freq_sz; } // Decode order-0 symbol list; avoids needing in order-1 tables cp += decode_freq1(cp, c_freq_end, shift, s3, s3F, NULL, NULL); if (tab_end) cp = tab_end; free(c_freq); c_freq = NULL; if (cp_end - cp < NX * 4) goto err; RansState R[NX]; uint8_t *ptr = cp, *ptr_end = in + in_size; int z; for (z = 0; z < NX; z++) { RansDecInit(&R[z], &ptr); if (R[z] < RANS_BYTE_L) goto err; } int isz4 = out_sz/NX; int i4[NX], l[NX] = {0}; for (z = 0; z < NX; z++) i4[z] = z*isz4; // Around 15% faster to specialise for 10/12 than to have one // loop with shift as a variable. if (shift == TF_SHIFT_O1) { // TF_SHIFT_O1 = 12 uint16_t *sp = (uint16_t *)ptr; const uint32_t mask = ((1u << TF_SHIFT_O1)-1); __m128i maskv = _mm_set1_epi32(mask); // set mask in all lanes uint8_t tbuf[32][32]; int tidx = 0; LOAD128(Rv, R); LOAD128(Lv, l); isz4 -= 64; for (; i4[0] < isz4 && (uint8_t *)sp+72 < ptr_end; ) { //for (z = 0; z < NX; z++) // m[z] = R[z] & mask; __m128i masked1 = _mm_and_si128(Rv1, maskv); __m128i masked2 = _mm_and_si128(Rv2, maskv); __m128i masked3 = _mm_and_si128(Rv3, maskv); __m128i masked4 = _mm_and_si128(Rv4, maskv); Lv1 = _mm_slli_epi32(Lv1, TF_SHIFT_O1); Lv2 = _mm_slli_epi32(Lv2, TF_SHIFT_O1); Lv3 = _mm_slli_epi32(Lv3, TF_SHIFT_O1); Lv4 = _mm_slli_epi32(Lv4, TF_SHIFT_O1); masked1 = _mm_add_epi32(masked1, Lv1); masked2 = _mm_add_epi32(masked2, Lv2); masked3 = _mm_add_epi32(masked3, Lv3); masked4 = _mm_add_epi32(masked4, Lv4); // S[z] = s3[l[z]][m[z]]; __m128i Sv1 = _mm_i32gather_epi32x((int *)s3, masked1, sizeof(*s3)); __m128i Sv2 = _mm_i32gather_epi32x((int *)s3, masked2, sizeof(*s3)); __m128i Sv3 = _mm_i32gather_epi32x((int *)s3, masked3, sizeof(*s3)); __m128i Sv4 = _mm_i32gather_epi32x((int *)s3, masked4, sizeof(*s3)); // f[z] = S[z]>>(TF_SHIFT+8); __m128i fv1 = _mm_srli_epi32(Sv1, TF_SHIFT_O1+8); __m128i fv2 = _mm_srli_epi32(Sv2, TF_SHIFT_O1+8); __m128i fv3 = _mm_srli_epi32(Sv3, TF_SHIFT_O1+8); __m128i fv4 = _mm_srli_epi32(Sv4, TF_SHIFT_O1+8); // b[z] = (S[z]>>8) & mask; __m128i bv1 = _mm_and_si128(_mm_srli_epi32(Sv1, 8), maskv); __m128i bv2 = _mm_and_si128(_mm_srli_epi32(Sv2, 8), maskv); __m128i bv3 = _mm_and_si128(_mm_srli_epi32(Sv3, 8), maskv); __m128i bv4 = _mm_and_si128(_mm_srli_epi32(Sv4, 8), maskv); // s[z] = S[z] & 0xff; __m128i sv1 = _mm_and_si128(Sv1, _mm_set1_epi32(0xff)); __m128i sv2 = _mm_and_si128(Sv2, _mm_set1_epi32(0xff)); __m128i sv3 = _mm_and_si128(Sv3, _mm_set1_epi32(0xff)); __m128i sv4 = _mm_and_si128(Sv4, _mm_set1_epi32(0xff)); // A maximum frequency of 4096 doesn't fit in our s3 array. // as it's 12 bit + 12 bit + 8 bit. It wraps around to zero. // (We don't have this issue for TOTFREQ_O1_FAST.) // // Solution 1 is to change to spec to forbid freq of 4096. // Easy hack is to add an extra symbol so it sums correctly. // // Solution 2 implemented here is to look for the wrap around // and fix it. __m128i max_freq = _mm_set1_epi32(TOTFREQ_O1); __m128i zero = _mm_set1_epi32(0); __m128i cmp1 = _mm_cmpeq_epi32(fv1, zero); fv1 = _mm_blendv_epi8(fv1, max_freq, cmp1); __m128i cmp2 = _mm_cmpeq_epi32(fv2, zero); fv2 = _mm_blendv_epi8(fv2, max_freq, cmp2); __m128i cmp3 = _mm_cmpeq_epi32(fv3, zero); fv3 = _mm_blendv_epi8(fv3, max_freq, cmp3); __m128i cmp4 = _mm_cmpeq_epi32(fv4, zero); fv4 = _mm_blendv_epi8(fv4, max_freq, cmp4); // R[z] = f[z] * (R[z] >> TF_SHIFT_O1) + b[z]; Rv1 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv1,TF_SHIFT_O1), fv1), bv1); Rv2 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv2,TF_SHIFT_O1), fv2), bv2); Rv3 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv3,TF_SHIFT_O1), fv3), bv3); Rv4 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv4,TF_SHIFT_O1), fv4), bv4); Lv1 = sv1; Lv2 = sv2; Lv3 = sv3; Lv4 = sv4; // Tricky one: out[i+z] = s[z]; // ---d---c ---b---a sv1 // ---h---g ---f---e sv2 // packs_epi32 -h-g-f-e -d-c-b-a sv1(2) // packs_epi16 ponmlkji hgfedcba sv1(2) / sv3(4) sv1 = _mm_packus_epi32(sv1, sv2); sv3 = _mm_packus_epi32(sv3, sv4); sv1 = _mm_packus_epi16(sv1, sv3); // c = R[z] < RANS_BYTE_L; // A little tricky as we only have signed comparisons. // See https://stackoverflow.com/questions/32945410/sse2-intrinsics-comparing-unsigned-integers //#define _mm_cmplt_epu32_imm(a,b) _mm_andnot_si128(_mm_cmpeq_epi32(_mm_max_epu32((a),_mm_set1_epi32(b)), (a)), _mm_set1_epi32(-1)); //#define _mm_cmplt_epu32_imm(a,b) _mm_cmpgt_epi32(_mm_set1_epi32((b)-0x80000000), _mm_xor_si128((a), _mm_set1_epi32(0x80000000))) __m128i renorm_mask1, renorm_mask2, renorm_mask3, renorm_mask4; renorm_mask1 = _mm_cmplt_epu32_imm(Rv1, RANS_BYTE_L); renorm_mask2 = _mm_cmplt_epu32_imm(Rv2, RANS_BYTE_L); renorm_mask3 = _mm_cmplt_epu32_imm(Rv3, RANS_BYTE_L); renorm_mask4 = _mm_cmplt_epu32_imm(Rv4, RANS_BYTE_L); //#define P(A,B,C,D) ((A)+((B)<<2) + ((C)<<4) + ((D)<<6)) #define P(A,B,C,D) \ { A+0,A+1,A+2,A+3, \ B+0,B+1,B+2,B+3, \ C+0,C+1,C+2,C+3, \ D+0,D+1,D+2,D+3} #ifdef _ #undef _ #endif #define _ 0x80 uint8_t pidx[16][16] = { P(_,_,_,_), P(0,_,_,_), P(_,0,_,_), P(0,4,_,_), P(_,_,0,_), P(0,_,4,_), P(_,0,4,_), P(0,4,8,_), P(_,_,_,0), P(0,_,_,4), P(_,0,_,4), P(0,4,_,8), P(_,_,0,4), P(0,_,4,8), P(_,0,4,8), P(0,4,8,12), }; #undef _ // Shuffle the renorm values to correct lanes and incr sp pointer __m128i Vv1 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask1 = _mm_movemask_ps((__m128)renorm_mask1); Vv1 = _mm_shuffle_epi8(Vv1, _mm_load_si128((__m128i*)pidx[imask1])); sp += _mm_popcnt_u32(imask1); __m128i Vv2 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask2 = _mm_movemask_ps((__m128)renorm_mask2); sp += _mm_popcnt_u32(imask2); Vv2 = _mm_shuffle_epi8(Vv2, _mm_load_si128((__m128i*)pidx[imask2])); __m128i Vv3 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask3 = _mm_movemask_ps((__m128)renorm_mask3); Vv3 = _mm_shuffle_epi8(Vv3, _mm_load_si128((__m128i*)pidx[imask3])); sp += _mm_popcnt_u32(imask3); __m128i Vv4 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask4 = _mm_movemask_ps((__m128)renorm_mask4); sp += _mm_popcnt_u32(imask4); Vv4 = _mm_shuffle_epi8(Vv4, _mm_load_si128((__m128i*)pidx[imask4])); __m128i Yv1 = _mm_slli_epi32(Rv1, 16); __m128i Yv2 = _mm_slli_epi32(Rv2, 16); __m128i Yv3 = _mm_slli_epi32(Rv3, 16); __m128i Yv4 = _mm_slli_epi32(Rv4, 16); // y = (R[z] << 16) | V[z]; Yv1 = _mm_or_si128(Yv1, Vv1); Yv2 = _mm_or_si128(Yv2, Vv2); Yv3 = _mm_or_si128(Yv3, Vv3); Yv4 = _mm_or_si128(Yv4, Vv4); // R[z] = c ? Y[z] : R[z]; Rv1 = _mm_blendv_epi8(Rv1, Yv1, renorm_mask1); Rv2 = _mm_blendv_epi8(Rv2, Yv2, renorm_mask2); Rv3 = _mm_blendv_epi8(Rv3, Yv3, renorm_mask3); Rv4 = _mm_blendv_epi8(Rv4, Yv4, renorm_mask4); // ------------------------------------------------------------ // m[z] = R[z] & mask; __m128i masked5 = _mm_and_si128(Rv5, maskv); __m128i masked6 = _mm_and_si128(Rv6, maskv); __m128i masked7 = _mm_and_si128(Rv7, maskv); __m128i masked8 = _mm_and_si128(Rv8, maskv); Lv5 = _mm_slli_epi32(Lv5, TF_SHIFT_O1); Lv6 = _mm_slli_epi32(Lv6, TF_SHIFT_O1); Lv7 = _mm_slli_epi32(Lv7, TF_SHIFT_O1); Lv8 = _mm_slli_epi32(Lv8, TF_SHIFT_O1); masked5 = _mm_add_epi32(masked5, Lv5); masked6 = _mm_add_epi32(masked6, Lv6); masked7 = _mm_add_epi32(masked7, Lv7); masked8 = _mm_add_epi32(masked8, Lv8); // S[z] = s3[m[z]]; __m128i Sv5 = _mm_i32gather_epi32x((int *)s3, masked5, sizeof(*s3)); __m128i Sv6 = _mm_i32gather_epi32x((int *)s3, masked6, sizeof(*s3)); __m128i Sv7 = _mm_i32gather_epi32x((int *)s3, masked7, sizeof(*s3)); __m128i Sv8 = _mm_i32gather_epi32x((int *)s3, masked8, sizeof(*s3)); // f[z] = S[z]>>(TF_SHIFT_O1+8); __m128i fv5 = _mm_srli_epi32(Sv5, TF_SHIFT_O1+8); __m128i fv6 = _mm_srli_epi32(Sv6, TF_SHIFT_O1+8); __m128i fv7 = _mm_srli_epi32(Sv7, TF_SHIFT_O1+8); __m128i fv8 = _mm_srli_epi32(Sv8, TF_SHIFT_O1+8); // b[z] = (S[z]>>8) & mask; __m128i bv5 = _mm_and_si128(_mm_srli_epi32(Sv5, 8), maskv); __m128i bv6 = _mm_and_si128(_mm_srli_epi32(Sv6, 8), maskv); __m128i bv7 = _mm_and_si128(_mm_srli_epi32(Sv7, 8), maskv); __m128i bv8 = _mm_and_si128(_mm_srli_epi32(Sv8, 8), maskv); // s[z] = S[z] & 0xff; __m128i sv5 = _mm_and_si128(Sv5, _mm_set1_epi32(0xff)); __m128i sv6 = _mm_and_si128(Sv6, _mm_set1_epi32(0xff)); __m128i sv7 = _mm_and_si128(Sv7, _mm_set1_epi32(0xff)); __m128i sv8 = _mm_and_si128(Sv8, _mm_set1_epi32(0xff)); // A maximum frequency of 4096 doesn't fit in our s3 array. Fix __m128i cmp5 = _mm_cmpeq_epi32(fv5, zero); fv5 = _mm_blendv_epi8(fv5, max_freq, cmp5); __m128i cmp6 = _mm_cmpeq_epi32(fv6, zero); fv6 = _mm_blendv_epi8(fv6, max_freq, cmp6); __m128i cmp7 = _mm_cmpeq_epi32(fv7, zero); fv7 = _mm_blendv_epi8(fv7, max_freq, cmp7); __m128i cmp8 = _mm_cmpeq_epi32(fv8, zero); fv8 = _mm_blendv_epi8(fv8, max_freq, cmp8); // R[z] = f[z] * (R[z] >> TF_SHIFT_O1) + b[z]; Rv5 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv5,TF_SHIFT_O1), fv5), bv5); Rv6 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv6,TF_SHIFT_O1), fv6), bv6); Rv7 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv7,TF_SHIFT_O1), fv7), bv7); Rv8 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv8,TF_SHIFT_O1), fv8), bv8); Lv5 = sv5; Lv6 = sv6; Lv7 = sv7; Lv8 = sv8; // Tricky one: out[i+z] = s[z]; // ---d---c ---b---a sv1 // ---h---g ---f---e sv2 // packs_epi32 -h-g-f-e -d-c-b-a sv1(2) // packs_epi16 ponmlkji hgfedcba sv1(2) / sv3(4) sv5 = _mm_packus_epi32(sv5, sv6); sv7 = _mm_packus_epi32(sv7, sv8); sv5 = _mm_packus_epi16(sv5, sv7); // c = R[z] < RANS_BYTE_L; __m128i renorm_mask5, renorm_mask6, renorm_mask7, renorm_mask8; renorm_mask5 = _mm_cmplt_epu32_imm(Rv5, RANS_BYTE_L); renorm_mask6 = _mm_cmplt_epu32_imm(Rv6, RANS_BYTE_L); renorm_mask7 = _mm_cmplt_epu32_imm(Rv7, RANS_BYTE_L); renorm_mask8 = _mm_cmplt_epu32_imm(Rv8, RANS_BYTE_L); // Shuffle the renorm values to correct lanes and incr sp pointer __m128i Vv5 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask5 = _mm_movemask_ps((__m128)renorm_mask5); Vv5 = _mm_shuffle_epi8(Vv5, _mm_load_si128((__m128i*)pidx[imask5])); sp += _mm_popcnt_u32(imask5); __m128i Vv6 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask6 = _mm_movemask_ps((__m128)renorm_mask6); sp += _mm_popcnt_u32(imask6); Vv6 = _mm_shuffle_epi8(Vv6, _mm_load_si128((__m128i*)pidx[imask6])); __m128i Vv7 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask7 = _mm_movemask_ps((__m128)renorm_mask7); Vv7 = _mm_shuffle_epi8(Vv7, _mm_load_si128((__m128i*)pidx[imask7])); sp += _mm_popcnt_u32(imask7); __m128i Vv8 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask8 = _mm_movemask_ps((__m128)renorm_mask8); sp += _mm_popcnt_u32(imask8); Vv8 = _mm_shuffle_epi8(Vv8, _mm_load_si128((__m128i*)pidx[imask8])); __m128i Yv5 = _mm_slli_epi32(Rv5, 16); __m128i Yv6 = _mm_slli_epi32(Rv6, 16); __m128i Yv7 = _mm_slli_epi32(Rv7, 16); __m128i Yv8 = _mm_slli_epi32(Rv8, 16); // y = (R[z] << 16) | V[z]; Yv5 = _mm_or_si128(Yv5, Vv5); Yv6 = _mm_or_si128(Yv6, Vv6); Yv7 = _mm_or_si128(Yv7, Vv7); Yv8 = _mm_or_si128(Yv8, Vv8); // R[z] = c ? Y[z] : R[z]; Rv5 = _mm_blendv_epi8(Rv5, Yv5, renorm_mask5); Rv6 = _mm_blendv_epi8(Rv6, Yv6, renorm_mask6); Rv7 = _mm_blendv_epi8(Rv7, Yv7, renorm_mask7); Rv8 = _mm_blendv_epi8(Rv8, Yv8, renorm_mask8); // Maybe just a store128 instead? _mm_store_si128((__m128i *)&tbuf[tidx][ 0], sv1); _mm_store_si128((__m128i *)&tbuf[tidx][16], sv5); // *(uint64_t *)&out[i+ 0] = _mm_extract_epi64(sv1, 0); // *(uint64_t *)&out[i+ 8] = _mm_extract_epi64(sv1, 1); // *(uint64_t *)&out[i+16] = _mm_extract_epi64(sv5, 0); // *(uint64_t *)&out[i+24] = _mm_extract_epi64(sv5, 1); // WRONG - need to reorder these periodically. i4[0]++; if (++tidx == 32) { i4[0]-=32; transpose_and_copy(out, i4, tbuf); tidx = 0; } } isz4 += 64; STORE128(Rv, R); STORE128(Lv, l); ptr = (uint8_t *)sp; i4[0]-=tidx; int T; for (z = 0; z < NX; z++) for (T = 0; T < tidx; T++) out[i4[z]++] = tbuf[T][z]; // Scalar version for close to the end of in[] array so we don't // do SIMD loads beyond the end of the buffer for (; i4[0] < isz4;) { for (z = 0; z < NX; z++) { uint32_t m = R[z] & ((1u<>(TF_SHIFT_O1+8); R[z] = (F?F:4096) * (R[z]>>TF_SHIFT_O1) + ((S>>8) & ((1u<>(TF_SHIFT_O1+8)); if (f == 0) f = 4096; R[z] = f * (R[z]>>TF_SHIFT_O1) + ((S>>8) & ((1u<>(TF_SHIFT+8); __m128i fv1 = _mm_srli_epi32(Sv1, TF_SHIFT_O1_FAST+8); __m128i fv2 = _mm_srli_epi32(Sv2, TF_SHIFT_O1_FAST+8); __m128i fv3 = _mm_srli_epi32(Sv3, TF_SHIFT_O1_FAST+8); __m128i fv4 = _mm_srli_epi32(Sv4, TF_SHIFT_O1_FAST+8); // b[z] = (S[z]>>8) & mask; __m128i bv1 = _mm_and_si128(_mm_srli_epi32(Sv1, 8), maskv); __m128i bv2 = _mm_and_si128(_mm_srli_epi32(Sv2, 8), maskv); __m128i bv3 = _mm_and_si128(_mm_srli_epi32(Sv3, 8), maskv); __m128i bv4 = _mm_and_si128(_mm_srli_epi32(Sv4, 8), maskv); // s[z] = S[z] & 0xff; __m128i sv1 = _mm_and_si128(Sv1, _mm_set1_epi32(0xff)); __m128i sv2 = _mm_and_si128(Sv2, _mm_set1_epi32(0xff)); __m128i sv3 = _mm_and_si128(Sv3, _mm_set1_epi32(0xff)); __m128i sv4 = _mm_and_si128(Sv4, _mm_set1_epi32(0xff)); // R[z] = f[z] * (R[z] >> TF_SHIFT_O1_FAST) + b[z]; Rv1 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv1,TF_SHIFT_O1_FAST), fv1), bv1); Rv2 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv2,TF_SHIFT_O1_FAST), fv2), bv2); Rv3 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv3,TF_SHIFT_O1_FAST), fv3), bv3); Rv4 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv4,TF_SHIFT_O1_FAST), fv4), bv4); Lv1 = sv1; Lv2 = sv2; Lv3 = sv3; Lv4 = sv4; // Tricky one: out[i+z] = s[z]; // ---d---c ---b---a sv1 // ---h---g ---f---e sv2 // packs_epi32 -h-g-f-e -d-c-b-a sv1(2) // packs_epi16 ponmlkji hgfedcba sv1(2) / sv3(4) sv1 = _mm_packus_epi32(sv1, sv2); sv3 = _mm_packus_epi32(sv3, sv4); sv1 = _mm_packus_epi16(sv1, sv3); // c = R[z] < RANS_BYTE_L; // A little tricky as we only have signed comparisons. // See https://stackoverflow.com/questions/32945410/sse2-intrinsics-comparing-unsigned-integers //#define _mm_cmplt_epu32_imm(a,b) _mm_andnot_si128(_mm_cmpeq_epi32(_mm_max_epu32((a),_mm_set1_epi32(b)), (a)), _mm_set1_epi32(-1)); //#define _mm_cmplt_epu32_imm(a,b) _mm_cmpgt_epi32(_mm_set1_epi32((b)-0x80000000), _mm_xor_si128((a), _mm_set1_epi32(0x80000000))) __m128i renorm_mask1, renorm_mask2, renorm_mask3, renorm_mask4; renorm_mask1 = _mm_cmplt_epu32_imm(Rv1, RANS_BYTE_L); renorm_mask2 = _mm_cmplt_epu32_imm(Rv2, RANS_BYTE_L); renorm_mask3 = _mm_cmplt_epu32_imm(Rv3, RANS_BYTE_L); renorm_mask4 = _mm_cmplt_epu32_imm(Rv4, RANS_BYTE_L); //#define P(A,B,C,D) ((A)+((B)<<2) + ((C)<<4) + ((D)<<6)) #define P(A,B,C,D) \ { A+0,A+1,A+2,A+3, \ B+0,B+1,B+2,B+3, \ C+0,C+1,C+2,C+3, \ D+0,D+1,D+2,D+3} #ifdef _ #undef _ #endif #define _ 0x80 uint8_t pidx[16][16] = { P(_,_,_,_), P(0,_,_,_), P(_,0,_,_), P(0,4,_,_), P(_,_,0,_), P(0,_,4,_), P(_,0,4,_), P(0,4,8,_), P(_,_,_,0), P(0,_,_,4), P(_,0,_,4), P(0,4,_,8), P(_,_,0,4), P(0,_,4,8), P(_,0,4,8), P(0,4,8,12), }; #undef _ // Shuffle the renorm values to correct lanes and incr sp pointer __m128i Vv1 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask1 = _mm_movemask_ps((__m128)renorm_mask1); Vv1 = _mm_shuffle_epi8(Vv1, _mm_load_si128((__m128i*)pidx[imask1])); sp += _mm_popcnt_u32(imask1); __m128i Vv2 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask2 = _mm_movemask_ps((__m128)renorm_mask2); sp += _mm_popcnt_u32(imask2); Vv2 = _mm_shuffle_epi8(Vv2, _mm_load_si128((__m128i*)pidx[imask2])); __m128i Vv3 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask3 = _mm_movemask_ps((__m128)renorm_mask3); Vv3 = _mm_shuffle_epi8(Vv3, _mm_load_si128((__m128i*)pidx[imask3])); sp += _mm_popcnt_u32(imask3); __m128i Vv4 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask4 = _mm_movemask_ps((__m128)renorm_mask4); sp += _mm_popcnt_u32(imask4); Vv4 = _mm_shuffle_epi8(Vv4, _mm_load_si128((__m128i*)pidx[imask4])); __m128i Yv1 = _mm_slli_epi32(Rv1, 16); __m128i Yv2 = _mm_slli_epi32(Rv2, 16); __m128i Yv3 = _mm_slli_epi32(Rv3, 16); __m128i Yv4 = _mm_slli_epi32(Rv4, 16); // y = (R[z] << 16) | V[z]; Yv1 = _mm_or_si128(Yv1, Vv1); Yv2 = _mm_or_si128(Yv2, Vv2); Yv3 = _mm_or_si128(Yv3, Vv3); Yv4 = _mm_or_si128(Yv4, Vv4); // R[z] = c ? Y[z] : R[z]; Rv1 = _mm_blendv_epi8(Rv1, Yv1, renorm_mask1); Rv2 = _mm_blendv_epi8(Rv2, Yv2, renorm_mask2); Rv3 = _mm_blendv_epi8(Rv3, Yv3, renorm_mask3); Rv4 = _mm_blendv_epi8(Rv4, Yv4, renorm_mask4); // ------------------------------------------------------------ // m[z] = R[z] & mask; __m128i masked5 = _mm_and_si128(Rv5, maskv); __m128i masked6 = _mm_and_si128(Rv6, maskv); __m128i masked7 = _mm_and_si128(Rv7, maskv); __m128i masked8 = _mm_and_si128(Rv8, maskv); Lv5 = _mm_slli_epi32(Lv5, TF_SHIFT_O1_FAST); Lv6 = _mm_slli_epi32(Lv6, TF_SHIFT_O1_FAST); Lv7 = _mm_slli_epi32(Lv7, TF_SHIFT_O1_FAST); Lv8 = _mm_slli_epi32(Lv8, TF_SHIFT_O1_FAST); masked5 = _mm_add_epi32(masked5, Lv5); masked6 = _mm_add_epi32(masked6, Lv6); masked7 = _mm_add_epi32(masked7, Lv7); masked8 = _mm_add_epi32(masked8, Lv8); // S[z] = s3[m[z]]; __m128i Sv5 = _mm_i32gather_epi32x((int *)s3F, masked5, sizeof(*s3)); __m128i Sv6 = _mm_i32gather_epi32x((int *)s3F, masked6, sizeof(*s3)); __m128i Sv7 = _mm_i32gather_epi32x((int *)s3F, masked7, sizeof(*s3)); __m128i Sv8 = _mm_i32gather_epi32x((int *)s3F, masked8, sizeof(*s3)); // f[z] = S[z]>>(TF_SHIFT_O1_FAST+8); __m128i fv5 = _mm_srli_epi32(Sv5, TF_SHIFT_O1_FAST+8); __m128i fv6 = _mm_srli_epi32(Sv6, TF_SHIFT_O1_FAST+8); __m128i fv7 = _mm_srli_epi32(Sv7, TF_SHIFT_O1_FAST+8); __m128i fv8 = _mm_srli_epi32(Sv8, TF_SHIFT_O1_FAST+8); // b[z] = (S[z]>>8) & mask; __m128i bv5 = _mm_and_si128(_mm_srli_epi32(Sv5, 8), maskv); __m128i bv6 = _mm_and_si128(_mm_srli_epi32(Sv6, 8), maskv); __m128i bv7 = _mm_and_si128(_mm_srli_epi32(Sv7, 8), maskv); __m128i bv8 = _mm_and_si128(_mm_srli_epi32(Sv8, 8), maskv); // s[z] = S[z] & 0xff; __m128i sv5 = _mm_and_si128(Sv5, _mm_set1_epi32(0xff)); __m128i sv6 = _mm_and_si128(Sv6, _mm_set1_epi32(0xff)); __m128i sv7 = _mm_and_si128(Sv7, _mm_set1_epi32(0xff)); __m128i sv8 = _mm_and_si128(Sv8, _mm_set1_epi32(0xff)); // R[z] = f[z] * (R[z] >> TF_SHIFT_O1_FAST) + b[z]; Rv5 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv5,TF_SHIFT_O1_FAST), fv5), bv5); Rv6 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv6,TF_SHIFT_O1_FAST), fv6), bv6); Rv7 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv7,TF_SHIFT_O1_FAST), fv7), bv7); Rv8 = _mm_add_epi32( _mm_mullo_epi32( _mm_srli_epi32(Rv8,TF_SHIFT_O1_FAST), fv8), bv8); Lv5 = sv5; Lv6 = sv6; Lv7 = sv7; Lv8 = sv8; // Tricky one: out[i+z] = s[z]; // ---d---c ---b---a sv1 // ---h---g ---f---e sv2 // packs_epi32 -h-g-f-e -d-c-b-a sv1(2) // packs_epi16 ponmlkji hgfedcba sv1(2) / sv3(4) sv5 = _mm_packus_epi32(sv5, sv6); sv7 = _mm_packus_epi32(sv7, sv8); sv5 = _mm_packus_epi16(sv5, sv7); // c = R[z] < RANS_BYTE_L; __m128i renorm_mask5, renorm_mask6, renorm_mask7, renorm_mask8; renorm_mask5 = _mm_cmplt_epu32_imm(Rv5, RANS_BYTE_L); renorm_mask6 = _mm_cmplt_epu32_imm(Rv6, RANS_BYTE_L); renorm_mask7 = _mm_cmplt_epu32_imm(Rv7, RANS_BYTE_L); renorm_mask8 = _mm_cmplt_epu32_imm(Rv8, RANS_BYTE_L); // Shuffle the renorm values to correct lanes and incr sp pointer __m128i Vv5 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask5 = _mm_movemask_ps((__m128)renorm_mask5); Vv5 = _mm_shuffle_epi8(Vv5, _mm_load_si128((__m128i*)pidx[imask5])); sp += _mm_popcnt_u32(imask5); __m128i Vv6 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask6 = _mm_movemask_ps((__m128)renorm_mask6); sp += _mm_popcnt_u32(imask6); Vv6 = _mm_shuffle_epi8(Vv6, _mm_load_si128((__m128i*)pidx[imask6])); __m128i Vv7 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask7 = _mm_movemask_ps((__m128)renorm_mask7); Vv7 = _mm_shuffle_epi8(Vv7, _mm_load_si128((__m128i*)pidx[imask7])); sp += _mm_popcnt_u32(imask7); __m128i Vv8 = _mm_cvtepu16_epi32(_mm_loadu_si128((__m128i *)sp)); unsigned int imask8 = _mm_movemask_ps((__m128)renorm_mask8); sp += _mm_popcnt_u32(imask8); Vv8 = _mm_shuffle_epi8(Vv8, _mm_load_si128((__m128i*)pidx[imask8])); __m128i Yv5 = _mm_slli_epi32(Rv5, 16); __m128i Yv6 = _mm_slli_epi32(Rv6, 16); __m128i Yv7 = _mm_slli_epi32(Rv7, 16); __m128i Yv8 = _mm_slli_epi32(Rv8, 16); // y = (R[z] << 16) | V[z]; Yv5 = _mm_or_si128(Yv5, Vv5); Yv6 = _mm_or_si128(Yv6, Vv6); Yv7 = _mm_or_si128(Yv7, Vv7); Yv8 = _mm_or_si128(Yv8, Vv8); // R[z] = c ? Y[z] : R[z]; Rv5 = _mm_blendv_epi8(Rv5, Yv5, renorm_mask5); Rv6 = _mm_blendv_epi8(Rv6, Yv6, renorm_mask6); Rv7 = _mm_blendv_epi8(Rv7, Yv7, renorm_mask7); Rv8 = _mm_blendv_epi8(Rv8, Yv8, renorm_mask8); // Maybe just a store128 instead? _mm_store_si128((__m128i *)&tbuf[tidx][ 0], sv1); _mm_store_si128((__m128i *)&tbuf[tidx][16], sv5); // *(uint64_t *)&out[i+ 0] = _mm_extract_epi64(sv1, 0); // *(uint64_t *)&out[i+ 8] = _mm_extract_epi64(sv1, 1); // *(uint64_t *)&out[i+16] = _mm_extract_epi64(sv5, 0); // *(uint64_t *)&out[i+24] = _mm_extract_epi64(sv5, 1); // WRONG - need to reorder these periodically. i4[0]++; if (++tidx == 32) { i4[0]-=32; transpose_and_copy(out, i4, tbuf); tidx = 0; } } isz4 += 64; STORE128(Rv, R); STORE128(Lv, l); ptr = (uint8_t *)sp; i4[0]-=tidx; int T; for (z = 0; z < NX; z++) for (T = 0; T < tidx; T++) out[i4[z]++] = tbuf[T][z]; // Scalar version for close to the end of in[] array so we don't // do SIMD loads beyond the end of the buffer for (; i4[0] < isz4;) { for (z = 0; z < NX; z++) { uint32_t m = R[z] & ((1u<>(TF_SHIFT_O1_FAST+8)) * (R[z]>>TF_SHIFT_O1_FAST) + ((S>>8) & ((1u<>(TF_SHIFT_O1_FAST+8)) * (R[z]>>TF_SHIFT_O1_FAST) + ((S>>8) & ((1u< #include #include #include #include #include #include #include #include #ifndef NO_THREADS #include #endif #include "rANS_word.h" #include "rANS_static4x16.h" #include "rANS_static16_int.h" #include "pack.h" #include "rle.h" #include "utils.h" #define TF_SHIFT 12 #define TOTFREQ (1<>8) & 0xff; if (!N) N=4; order &= 0xff; unsigned int sz = (order == 0 ? 1.05*size + 257*3 + 4 : 1.05*size + 257*257*3 + 4 + 257*3+4) + ((order & RANS_ORDER_PACK) ? 1 : 0) + ((order & RANS_ORDER_RLE) ? 1 + 257*3+4: 0) + 20 + ((order & RANS_ORDER_X32) ? (32-4)*4 : 0) + ((order & RANS_ORDER_STRIPE) ? 7 + 5*N: 0); return sz + (sz&1) + 2; // make this even so buffers are word aligned } // Compresses in_size bytes from 'in' to *out_size bytes in 'out'. // // NB: The output buffer does not hold the original size, so it is up to // the caller to store this. unsigned char *rans_compress_O0_4x16(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { unsigned char *cp, *out_end; RansEncSymbol syms[256]; RansState rans0; RansState rans2; RansState rans1; RansState rans3; uint8_t* ptr; uint32_t F[256+MAGIC] = {0}; int i, j, tab_size = 0, rle, x; // -20 for order/size/meta uint32_t bound = rans_compress_bound_4x16(in_size,0)-20; if (!out) { *out_size = bound; out = malloc(*out_size); } if (!out || bound > *out_size) return NULL; // If "out" isn't word aligned, tweak out_end/ptr to ensure it is. // We already added more round in bound to allow for this. if (((size_t)out)&1) bound--; ptr = out_end = out + bound; if (in_size == 0) goto empty; // Compute statistics if (hist8(in, in_size, F) < 0) return NULL; // Normalise so frequences sum to power of 2 uint32_t fsum = in_size; uint32_t max_val = round2(fsum); if (max_val > TOTFREQ) max_val = TOTFREQ; if (normalise_freq(F, fsum, max_val) < 0) return NULL; fsum=max_val; cp = out; cp += encode_freq(cp, F); tab_size = cp-out; //write(2, out+4, cp-(out+4)); if (normalise_freq(F, fsum, TOTFREQ) < 0) return NULL; // Encode statistics. for (x = rle = j = 0; j < 256; j++) { if (F[j]) { RansEncSymbolInit(&syms[j], x, F[j], TF_SHIFT); x += F[j]; } } RansEncInit(&rans0); RansEncInit(&rans1); RansEncInit(&rans2); RansEncInit(&rans3); switch (i=(in_size&3)) { case 3: RansEncPutSymbol(&rans2, &ptr, &syms[in[in_size-(i-2)]]); // fall-through case 2: RansEncPutSymbol(&rans1, &ptr, &syms[in[in_size-(i-1)]]); // fall-through case 1: RansEncPutSymbol(&rans0, &ptr, &syms[in[in_size-(i-0)]]); // fall-through case 0: break; } for (i=(in_size &~3); i>0; i-=4) { RansEncSymbol *s3 = &syms[in[i-1]]; RansEncSymbol *s2 = &syms[in[i-2]]; RansEncSymbol *s1 = &syms[in[i-3]]; RansEncSymbol *s0 = &syms[in[i-4]]; #if 1 RansEncPutSymbol(&rans3, &ptr, s3); RansEncPutSymbol(&rans2, &ptr, s2); RansEncPutSymbol(&rans1, &ptr, s1); RansEncPutSymbol(&rans0, &ptr, s0); #else // Slightly beter on gcc, much better on clang uint16_t *ptr16 = (uint16_t *)ptr; if (rans3 >= s3->x_max) *--ptr16 = (uint16_t)rans3, rans3 >>= 16; if (rans2 >= s2->x_max) *--ptr16 = (uint16_t)rans2, rans2 >>= 16; uint32_t q3 = (uint32_t) (((uint64_t)rans3 * s3->rcp_freq) >> s3->rcp_shift); uint32_t q2 = (uint32_t) (((uint64_t)rans2 * s2->rcp_freq) >> s2->rcp_shift); rans3 += s3->bias + q3 * s3->cmpl_freq; rans2 += s2->bias + q2 * s2->cmpl_freq; if (rans1 >= s1->x_max) *--ptr16 = (uint16_t)rans1, rans1 >>= 16; if (rans0 >= s0->x_max) *--ptr16 = (uint16_t)rans0, rans0 >>= 16; uint32_t q1 = (uint32_t) (((uint64_t)rans1 * s1->rcp_freq) >> s1->rcp_shift); uint32_t q0 = (uint32_t) (((uint64_t)rans0 * s0->rcp_freq) >> s0->rcp_shift); rans1 += s1->bias + q1 * s1->cmpl_freq; rans0 += s0->bias + q0 * s0->cmpl_freq; ptr = (uint8_t *)ptr16; #endif } RansEncFlush(&rans3, &ptr); RansEncFlush(&rans2, &ptr); RansEncFlush(&rans1, &ptr); RansEncFlush(&rans0, &ptr); empty: // Finalise block size and return it *out_size = (out_end - ptr) + tab_size; memmove(out + tab_size, ptr, out_end-ptr); return out; } unsigned char *rans_uncompress_O0_4x16(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { if (in_size < 16) // 4-states at least return NULL; if (out_sz >= INT_MAX) return NULL; // protect against some overflow cases #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (out_sz > 100000) return NULL; #endif /* Load in the static tables */ unsigned char *cp = in, *out_free = NULL; unsigned char *cp_end = in + in_size - 8; // within 8 => be extra safe int i, j; unsigned int x, y; uint16_t sfreq[TOTFREQ+32]; uint16_t sbase[TOTFREQ+32]; // faster to use 32-bit on clang uint8_t ssym [TOTFREQ+64]; // faster to use 16-bit on clang if (!out) out_free = out = malloc(out_sz); if (!out) return NULL; // Precompute reverse lookup of frequency. uint32_t F[256] = {0}, fsum; int fsz = decode_freq(cp, cp_end, F, &fsum); if (!fsz) goto err; cp += fsz; normalise_freq_shift(F, fsum, TOTFREQ); // Build symbols; fixme, do as part of decode, see the _d variant for (j = x = 0; j < 256; j++) { if (F[j]) { if (F[j] > TOTFREQ - x) goto err; for (y = 0; y < F[j]; y++) { ssym [y + x] = j; sfreq[y + x] = F[j]; sbase[y + x] = y; } x += F[j]; } } if (x != TOTFREQ) goto err; if (cp+16 > cp_end+8) goto err; RansState R[4]; RansDecInit(&R[0], &cp); if (R[0] < RANS_BYTE_L) goto err; RansDecInit(&R[1], &cp); if (R[1] < RANS_BYTE_L) goto err; RansDecInit(&R[2], &cp); if (R[2] < RANS_BYTE_L) goto err; RansDecInit(&R[3], &cp); if (R[3] < RANS_BYTE_L) goto err; // Simple version is comparable to below, but only with -O3 // // for (i = 0; cp < cp_end-8 && i < (out_sz&~7); i+=8) { // for(j=0; j<8;j++) { // RansState m = RansDecGet(&R[j%4], TF_SHIFT); // R[j%4] = sfreq[m] * (R[j%4] >> TF_SHIFT) + sbase[m]; // out[i+j] = ssym[m]; // RansDecRenorm(&R[j%4], &cp); // } // } for (i = 0; cp < cp_end-8 && i < (out_sz&~7); i+=8) { for (j = 0; j < 8; j+=4) { RansState m0 = RansDecGet(&R[0], TF_SHIFT); RansState m1 = RansDecGet(&R[1], TF_SHIFT); out[i+j+0] = ssym[m0]; out[i+j+1] = ssym[m1]; R[0] = sfreq[m0] * (R[0] >> TF_SHIFT) + sbase[m0]; R[1] = sfreq[m1] * (R[1] >> TF_SHIFT) + sbase[m1]; RansState m2 = RansDecGet(&R[2], TF_SHIFT); RansState m3 = RansDecGet(&R[3], TF_SHIFT); RansDecRenorm(&R[0], &cp); RansDecRenorm(&R[1], &cp); R[2] = sfreq[m2] * (R[2] >> TF_SHIFT) + sbase[m2]; R[3] = sfreq[m3] * (R[3] >> TF_SHIFT) + sbase[m3]; RansDecRenorm(&R[2], &cp); RansDecRenorm(&R[3], &cp); out[i+j+2] = ssym[m2]; out[i+j+3] = ssym[m3]; } } // remainder for (; i < out_sz; i++) { RansState m = RansDecGet(&R[i%4], TF_SHIFT); R[i%4] = sfreq[m] * (R[i%4] >> TF_SHIFT) + sbase[m]; out[i] = ssym[m]; RansDecRenormSafe(&R[i%4], &cp, cp_end+8); } //fprintf(stderr, " 0 Decoded %d bytes\n", (int)(cp-in)); //c-size return out; err: free(out_free); return NULL; } //----------------------------------------------------------------------------- // Compute the entropy of 12-bit vs 10-bit frequency tables. // 10 bit means smaller memory footprint when decoding and // more speed due to cache hits, but it *may* be a poor // compression fit. int rans_compute_shift(uint32_t *F0, uint32_t (*F)[256], uint32_t *T, uint32_t *S) { int i, j; double e10 = 0, e12 = 0; int max_tot = 0; for (i = 0; i < 256; i++) { if (F0[i] == 0) continue; unsigned int max_val = round2(T[i]); int ns = 0; #define MAX(a,b) ((a)>(b)?(a):(b)) // Number of samples that get their freq bumped to 1 int sm10 = 0, sm12 = 0; for (j = 0; j < 256; j++) { if (F[i][j] && max_val / F[i][j] > TOTFREQ_O1_FAST) sm10++; if (F[i][j] && max_val / F[i][j] > TOTFREQ_O1) sm12++; } double l10 = log(TOTFREQ_O1_FAST + sm10); double l12 = log(TOTFREQ_O1 + sm12); double T_slow = (double)TOTFREQ_O1/T[i]; double T_fast = (double)TOTFREQ_O1_FAST/T[i]; for (j = 0; j < 256; j++) { if (F[i][j]) { ns++; e10 -= F[i][j] * (fast_log(MAX(F[i][j]*T_fast,1)) - l10); e12 -= F[i][j] * (fast_log(MAX(F[i][j]*T_slow,1)) - l12); // Estimation of compressed symbol freq table too. e10 += 1.3; e12 += 4.7; } } // Order-1 frequencies often end up totalling under TOTFREQ. // In this case it's smaller to output the real frequencies // prior to normalisation and normalise after (with an extra // normalisation step needed in the decoder too). // // Thus we normalise to a power of 2 only, store those, // and renormalise later here (and in decoder) by bit-shift // to get to the fixed size. if (ns < 64 && max_val > 128) max_val /= 2; if (max_val > 1024) max_val /= 2; if (max_val > TOTFREQ_O1) max_val = TOTFREQ_O1; S[i] = max_val; // scale to max this if (max_tot < max_val) max_tot = max_val; } int shift = e10/e12 < 1.01 || max_tot <= TOTFREQ_O1_FAST ? TF_SHIFT_O1_FAST : TF_SHIFT_O1; // fprintf(stderr, "e10/12 = %f %f %f, shift %d\n", // e10/log(256), e12/log(256), e10/e12, shift); return shift; } static unsigned char *rans_compress_O1_4x16(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { unsigned char *cp, *out_end, *out_free = NULL; unsigned int tab_size; // -20 for order/size/meta uint32_t bound = rans_compress_bound_4x16(in_size,1)-20; if (!out) { *out_size = bound; out_free = out = malloc(*out_size); } if (!out || bound > *out_size) return NULL; if (((size_t)out)&1) bound--; out_end = out + bound; RansEncSymbol (*syms)[256] = htscodecs_tls_alloc(256 * (sizeof(*syms))); if (!syms) { free(out_free); return NULL; } cp = out; int shift = encode_freq1(in, in_size, 4, syms, &cp); if (shift < 0) { htscodecs_tls_free(syms); return NULL; } tab_size = cp - out; RansState rans0, rans1, rans2, rans3; RansEncInit(&rans0); RansEncInit(&rans1); RansEncInit(&rans2); RansEncInit(&rans3); uint8_t* ptr = out_end; int isz4 = in_size>>2; int i0 = 1*isz4-2; int i1 = 2*isz4-2; int i2 = 3*isz4-2; int i3 = 4*isz4-2; unsigned char l0 = in[i0+1]; unsigned char l1 = in[i1+1]; unsigned char l2 = in[i2+1]; unsigned char l3 = in[i3+1]; // Deal with the remainder l3 = in[in_size-1]; for (i3 = in_size-2; i3 > 4*isz4-2; i3--) { unsigned char c3 = in[i3]; RansEncPutSymbol(&rans3, &ptr, &syms[c3][l3]); l3 = c3; } for (; i0 >= 0; i0--, i1--, i2--, i3--) { unsigned char c0, c1, c2, c3; RansEncSymbol *s3 = &syms[c3 = in[i3]][l3]; RansEncSymbol *s2 = &syms[c2 = in[i2]][l2]; RansEncSymbol *s1 = &syms[c1 = in[i1]][l1]; RansEncSymbol *s0 = &syms[c0 = in[i0]][l0]; RansEncPutSymbol(&rans3, &ptr, s3); RansEncPutSymbol(&rans2, &ptr, s2); RansEncPutSymbol(&rans1, &ptr, s1); RansEncPutSymbol(&rans0, &ptr, s0); l0 = c0; l1 = c1; l2 = c2; l3 = c3; } RansEncPutSymbol(&rans3, &ptr, &syms[0][l3]); RansEncPutSymbol(&rans2, &ptr, &syms[0][l2]); RansEncPutSymbol(&rans1, &ptr, &syms[0][l1]); RansEncPutSymbol(&rans0, &ptr, &syms[0][l0]); RansEncFlush(&rans3, &ptr); RansEncFlush(&rans2, &ptr); RansEncFlush(&rans1, &ptr); RansEncFlush(&rans0, &ptr); *out_size = (out_end - ptr) + tab_size; cp = out; memmove(out + tab_size, ptr, out_end-ptr); htscodecs_tls_free(syms); return out; } //#define MAGIC2 111 #define MAGIC2 179 //#define MAGIC2 0 static unsigned char *rans_uncompress_O1_4x16(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_sz) { if (in_size < 16) // 4-states at least return NULL; if (out_sz >= INT_MAX) return NULL; // protect against some overflow cases #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (out_sz > 100000) return NULL; #endif /* Load in the static tables */ unsigned char *cp = in, *cp_end = in+in_size, *out_free = NULL; unsigned char *c_freq = NULL; int i, j = -999; unsigned int x; uint8_t *sfb_ = htscodecs_tls_alloc(256*(TOTFREQ_O1+MAGIC2)*sizeof(*sfb_)); uint32_t (*s3)[TOTFREQ_O1_FAST] = (uint32_t (*)[TOTFREQ_O1_FAST])sfb_; // reuse the same memory for the fast mode lookup, but this only works // if we're on e.g. 12-bit freqs vs 10-bit freqs as needs 4x larger array. //uint32_t s3[256][TOTFREQ_O1_FAST]; if (!sfb_) return NULL; fb_t (*fb)[256] = htscodecs_tls_alloc(256 * sizeof(*fb)); if (!fb) goto err; uint8_t *sfb[256]; if ((*cp >> 4) == TF_SHIFT_O1) { for (i = 0; i < 256; i++) sfb[i]= sfb_ + i*(TOTFREQ_O1+MAGIC2); } else { for (i = 0; i < 256; i++) sfb[i]= sfb_ + i*(TOTFREQ_O1_FAST+MAGIC2); } if (!out) out_free = out = malloc(out_sz); if (!out) goto err; //fprintf(stderr, "out_sz=%d\n", out_sz); // compressed header? If so uncompress it unsigned char *tab_end = NULL; unsigned char *c_freq_end = cp_end; unsigned int shift = *cp >> 4; if (*cp++ & 1) { uint32_t u_freq_sz, c_freq_sz; cp += var_get_u32(cp, cp_end, &u_freq_sz); cp += var_get_u32(cp, cp_end, &c_freq_sz); if (c_freq_sz > cp_end - cp) goto err; tab_end = cp + c_freq_sz; if (!(c_freq = rans_uncompress_O0_4x16(cp, c_freq_sz, NULL, u_freq_sz))) goto err; cp = c_freq; c_freq_end = c_freq + u_freq_sz; } // Decode order-0 symbol list; avoids needing in order-1 tables uint32_t F0[256] = {0}; int fsz = decode_alphabet(cp, c_freq_end, F0); if (!fsz) goto err; cp += fsz; if (cp >= c_freq_end) goto err; const int s3_fast_on = in_size >= 100000; for (i = 0; i < 256; i++) { if (F0[i] == 0) continue; uint32_t F[256] = {0}, T = 0; fsz = decode_freq_d(cp, c_freq_end, F0, F, &T); if (!fsz) goto err; cp += fsz; if (!T) { //fprintf(stderr, "No freq for F_%d\n", i); continue; } normalise_freq_shift(F, T, 1< (1< cp_end) goto err; RansState rans0, rans1, rans2, rans3; uint8_t *ptr = cp, *ptr_end = in + in_size - 8; RansDecInit(&rans0, &ptr); if (rans0 < RANS_BYTE_L) goto err; RansDecInit(&rans1, &ptr); if (rans1 < RANS_BYTE_L) goto err; RansDecInit(&rans2, &ptr); if (rans2 < RANS_BYTE_L) goto err; RansDecInit(&rans3, &ptr); if (rans3 < RANS_BYTE_L) goto err; unsigned int isz4 = out_sz>>2; int l0 = 0, l1 = 0, l2 = 0, l3 = 0; unsigned int i4[] = {0*isz4, 1*isz4, 2*isz4, 3*isz4}; RansState R[4]; R[0] = rans0; R[1] = rans1; R[2] = rans2; R[3] = rans3; // Around 15% faster to specialise for 10/12 than to have one // loop with shift as a variable. if (shift == TF_SHIFT_O1) { // TF_SHIFT_O1 = 12 const uint32_t mask = ((1u << TF_SHIFT_O1)-1); for (; i4[0] < isz4; i4[0]++, i4[1]++, i4[2]++, i4[3]++) { uint16_t m, c; c = sfb[l0][m = R[0] & mask]; R[0] = fb[l0][c].f * (R[0]>>TF_SHIFT_O1) + m - fb[l0][c].b; out[i4[0]] = l0 = c; c = sfb[l1][m = R[1] & mask]; R[1] = fb[l1][c].f * (R[1]>>TF_SHIFT_O1) + m - fb[l1][c].b; out[i4[1]] = l1 = c; c = sfb[l2][m = R[2] & mask]; R[2] = fb[l2][c].f * (R[2]>>TF_SHIFT_O1) + m - fb[l2][c].b; out[i4[2]] = l2 = c; c = sfb[l3][m = R[3] & mask]; R[3] = fb[l3][c].f * (R[3]>>TF_SHIFT_O1) + m - fb[l3][c].b; out[i4[3]] = l3 = c; if (ptr < ptr_end) { RansDecRenorm(&R[0], &ptr); RansDecRenorm(&R[1], &ptr); RansDecRenorm(&R[2], &ptr); RansDecRenorm(&R[3], &ptr); } else { RansDecRenormSafe(&R[0], &ptr, ptr_end+8); RansDecRenormSafe(&R[1], &ptr, ptr_end+8); RansDecRenormSafe(&R[2], &ptr, ptr_end+8); RansDecRenormSafe(&R[3], &ptr, ptr_end+8); } } // Remainder for (; i4[3] < out_sz; i4[3]++) { uint32_t m3 = R[3] & ((1u<>TF_SHIFT_O1) + m3 - fb[l3][c3].b; RansDecRenormSafe(&R[3], &ptr, ptr_end + 8); l3 = c3; } } else if (!s3_fast_on) { // TF_SHIFT_O1 = 10 with sfb[256][1024] & fb[256]256] array lookup // Slightly faster for -o193 on q4 (high comp), but also less // initialisation cost for smaller data const uint32_t mask = ((1u << TF_SHIFT_O1_FAST)-1); for (; i4[0] < isz4; i4[0]++, i4[1]++, i4[2]++, i4[3]++) { uint16_t m, c; c = sfb[l0][m = R[0] & mask]; R[0] = fb[l0][c].f * (R[0]>>TF_SHIFT_O1_FAST) + m - fb[l0][c].b; out[i4[0]] = l0 = c; c = sfb[l1][m = R[1] & mask]; R[1] = fb[l1][c].f * (R[1]>>TF_SHIFT_O1_FAST) + m - fb[l1][c].b; out[i4[1]] = l1 = c; c = sfb[l2][m = R[2] & mask]; R[2] = fb[l2][c].f * (R[2]>>TF_SHIFT_O1_FAST) + m - fb[l2][c].b; out[i4[2]] = l2 = c; c = sfb[l3][m = R[3] & mask]; R[3] = fb[l3][c].f * (R[3]>>TF_SHIFT_O1_FAST) + m - fb[l3][c].b; out[i4[3]] = l3 = c; if (ptr < ptr_end) { RansDecRenorm(&R[0], &ptr); RansDecRenorm(&R[1], &ptr); RansDecRenorm(&R[2], &ptr); RansDecRenorm(&R[3], &ptr); } else { RansDecRenormSafe(&R[0], &ptr, ptr_end+8); RansDecRenormSafe(&R[1], &ptr, ptr_end+8); RansDecRenormSafe(&R[2], &ptr, ptr_end+8); RansDecRenormSafe(&R[3], &ptr, ptr_end+8); } } // Remainder for (; i4[3] < out_sz; i4[3]++) { uint32_t m3 = R[3] & ((1u<>TF_SHIFT_O1_FAST) + m3 - fb[l3][c3].b; RansDecRenormSafe(&R[3], &ptr, ptr_end + 8); l3 = c3; } } else { // TF_SHIFT_O1_FAST. // Significantly faster for -o1 on q40 (low comp). // Higher initialisation cost, so only use if big blocks. const uint32_t mask = ((1u << TF_SHIFT_O1_FAST)-1); for (; i4[0] < isz4; i4[0]++, i4[1]++, i4[2]++, i4[3]++) { uint32_t S0 = s3[l0][R[0] & mask]; uint32_t S1 = s3[l1][R[1] & mask]; l0 = out[i4[0]] = S0; l1 = out[i4[1]] = S1; uint16_t F0 = S0>>(TF_SHIFT_O1_FAST+8); uint16_t F1 = S1>>(TF_SHIFT_O1_FAST+8); uint16_t B0 = (S0>>8) & mask; uint16_t B1 = (S1>>8) & mask; R[0] = F0 * (R[0]>>TF_SHIFT_O1_FAST) + B0; R[1] = F1 * (R[1]>>TF_SHIFT_O1_FAST) + B1; uint32_t S2 = s3[l2][R[2] & mask]; uint32_t S3 = s3[l3][R[3] & mask]; l2 = out[i4[2]] = S2; l3 = out[i4[3]] = S3; uint16_t F2 = S2>>(TF_SHIFT_O1_FAST+8); uint16_t F3 = S3>>(TF_SHIFT_O1_FAST+8); uint16_t B2 = (S2>>8) & mask; uint16_t B3 = (S3>>8) & mask; R[2] = F2 * (R[2]>>TF_SHIFT_O1_FAST) + B2; R[3] = F3 * (R[3]>>TF_SHIFT_O1_FAST) + B3; if (ptr < ptr_end) { RansDecRenorm(&R[0], &ptr); RansDecRenorm(&R[1], &ptr); RansDecRenorm(&R[2], &ptr); RansDecRenorm(&R[3], &ptr); } else { RansDecRenormSafe(&R[0], &ptr, ptr_end+8); RansDecRenormSafe(&R[1], &ptr, ptr_end+8); RansDecRenormSafe(&R[2], &ptr, ptr_end+8); RansDecRenormSafe(&R[3], &ptr, ptr_end+8); } } // Remainder for (; i4[3] < out_sz; i4[3]++) { uint32_t S = s3[l3][R[3] & ((1u<>(TF_SHIFT_O1_FAST+8)) * (R[3]>>TF_SHIFT_O1_FAST) + ((S>>8) & ((1u< #if defined(__clang__) && defined(__has_attribute) # if __has_attribute(unused) # define UNUSED __attribute__((unused)) # else # define UNUSED # endif #elif defined(__GNUC__) && __GNUC__ >= 3 # define UNUSED __attribute__((unused)) #else # define UNUSED #endif // CPU detection is performed once. NB this has an assumption that we're // not migrating between processes with different instruction stes, but // to date the only systems I know of that support this don't have different // capabilities (that we use) per core. #ifndef NO_THREADS static pthread_once_t rans_cpu_once = PTHREAD_ONCE_INIT; #endif static int have_ssse3 UNUSED = 0; static int have_sse4_1 UNUSED = 0; static int have_popcnt UNUSED = 0; static int have_avx2 UNUSED = 0; static int have_avx512f UNUSED = 0; static int is_amd UNUSED = 0; #define HAVE_HTSCODECS_TLS_CPU_INIT static void htscodecs_tls_cpu_init(void) { unsigned int eax = 0, ebx = 0, ecx = 0, edx = 0; // These may be unused, depending on HAVE_* config.h macros int level = __get_cpuid_max(0, NULL); __cpuid_count(0, 0, eax, ebx, ecx, edx); is_amd = (ecx == 0x444d4163); if (level >= 1) { __cpuid_count(1, 0, eax, ebx, ecx, edx); #if defined(bit_SSSE3) have_ssse3 = ecx & bit_SSSE3; #endif #if defined(bit_POPCNT) have_popcnt = ecx & bit_POPCNT; #endif #if defined(bit_SSE4_1) have_sse4_1 = ecx & bit_SSE4_1; #endif } if (level >= 7) { __cpuid_count(7, 0, eax, ebx, ecx, edx); #if defined(bit_AVX2) have_avx2 = ebx & bit_AVX2; #endif #if defined(bit_AVX512F) have_avx512f = ebx & bit_AVX512F; #endif } if (!have_popcnt) have_avx512f = have_avx2 = have_sse4_1 = 0; if (!have_ssse3) have_sse4_1 = 0; } static inline unsigned char *(*rans_enc_func(int do_simd, int order)) (unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { int have_e_sse4_1 = have_sse4_1; int have_e_avx2 = have_avx2; int have_e_avx512f = have_avx512f; if (!(rans_cpu & RANS_CPU_ENC_AVX512)) have_e_avx512f = 0; if (!(rans_cpu & RANS_CPU_ENC_AVX2)) have_e_avx2 = 0; if (!(rans_cpu & RANS_CPU_ENC_SSE4)) have_e_sse4_1 = 0; if (!do_simd) { // SIMD disabled return order & 1 ? rans_compress_O1_4x16 : rans_compress_O0_4x16; } #ifdef NO_THREADS htscodecs_tls_cpu_init(); #else int err = pthread_once(&rans_cpu_once, htscodecs_tls_cpu_init); if (err != 0) { fprintf(stderr, "Initialising TLS data failed: pthread_once: %s\n", strerror(err)); fprintf(stderr, "Using scalar code only\n"); } #endif if (order & 1) { // With simulated gathers, the AVX512 is now slower than AVX2, so // we avoid using it unless asking for the real avx512 gather. // Note for testing we do -c 0x0404 to enable AVX512 and disable AVX2. // We then need to call the avx512 func regardless. int use_gather; #ifdef USE_GATHER use_gather = 1; #else use_gather = !have_e_avx2; #endif #if defined(HAVE_AVX512) if (have_e_avx512f && (!is_amd || !have_e_avx2) && use_gather) return rans_compress_O1_32x16_avx512; #endif #if defined(HAVE_AVX2) if (have_e_avx2) return rans_compress_O1_32x16_avx2; #endif #if defined(HAVE_SSE4_1) && defined(HAVE_SSSE3) && defined(HAVE_POPCNT) if (have_e_sse4_1) return rans_compress_O1_32x16; #endif return rans_compress_O1_32x16; } else { #if defined(HAVE_AVX512) if (have_e_avx512f && (!is_amd || !have_e_avx2)) return rans_compress_O0_32x16_avx512; #endif #if defined(HAVE_AVX2) if (have_e_avx2) return rans_compress_O0_32x16_avx2; #endif #if defined(HAVE_SSE4_1) && defined(HAVE_SSSE3) && defined(HAVE_POPCNT) if (have_e_sse4_1) return rans_compress_O0_32x16; #endif return rans_compress_O0_32x16; } } static inline unsigned char *(*rans_dec_func(int do_simd, int order)) (unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_size) { int have_d_sse4_1 = have_sse4_1; int have_d_avx2 = have_avx2; int have_d_avx512f = have_avx512f; if (!(rans_cpu & RANS_CPU_DEC_AVX512)) have_d_avx512f = 0; if (!(rans_cpu & RANS_CPU_DEC_AVX2)) have_d_avx2 = 0; if (!(rans_cpu & RANS_CPU_DEC_SSE4)) have_d_sse4_1 = 0; if (!do_simd) { // SIMD disabled return order & 1 ? rans_uncompress_O1_4x16 : rans_uncompress_O0_4x16; } #ifdef NO_THREADS htscodecs_tls_cpu_init(); #else int err = pthread_once(&rans_cpu_once, htscodecs_tls_cpu_init); if (err != 0) { fprintf(stderr, "Initialising TLS data failed: pthread_once: %s\n", strerror(err)); fprintf(stderr, "Using scalar code only\n"); } #endif if (order & 1) { #if defined(HAVE_AVX512) if (have_d_avx512f) return rans_uncompress_O1_32x16_avx512; #endif #if defined(HAVE_AVX2) if (have_d_avx2) return rans_uncompress_O1_32x16_avx2; #endif #if defined(HAVE_SSE4_1) && defined(HAVE_SSSE3) && defined(HAVE_POPCNT) if (have_d_sse4_1) return rans_uncompress_O1_32x16_sse4; #endif return rans_uncompress_O1_32x16; } else { #if defined(HAVE_AVX512) if (have_d_avx512f) return rans_uncompress_O0_32x16_avx512; #endif #if defined(HAVE_AVX2) if (have_d_avx2) return rans_uncompress_O0_32x16_avx2; #endif #if defined(HAVE_SSE4_1) && defined(HAVE_SSSE3) && defined(HAVE_POPCNT) if (have_d_sse4_1) return rans_uncompress_O0_32x16_sse4; #endif return rans_uncompress_O0_32x16; } } #elif defined(__ARM_NEON) && defined(__aarch64__) #if defined(__linux__) || defined(__FreeBSD__) #include #elif defined(_WIN32) #include #endif static inline int have_neon(void) { #if defined(__linux__) && defined(__arm__) return (getauxval(AT_HWCAP) & HWCAP_NEON) != 0; #elif defined(__linux__) && defined(__aarch64__) && defined(HWCAP_ASIMD) return (getauxval(AT_HWCAP) & HWCAP_ASIMD) != 0; #elif defined(__APPLE__) return 1; #elif defined(__FreeBSD__) && defined(__arm__) unsigned long cap; if (elf_aux_info(AT_HWCAP, &cap, sizeof cap) != 0) return 0; return (cap & HWCAP_NEON) != 0; #elif defined(__FreeBSD__) && defined(__aarch64__) && defined(HWCAP_ASIMD) unsigned long cap; if (elf_aux_info(AT_HWCAP, &cap, sizeof cap) != 0) return 0; return (cap & HWCAP_ASIMD) != 0; #elif defined(_WIN32) return IsProcessorFeaturePresent(PF_ARM_V8_INSTRUCTIONS_AVAILABLE) != 0; #else return 0; #endif } static inline unsigned char *(*rans_enc_func(int do_simd, int order)) (unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { if (do_simd) { if ((rans_cpu & RANS_CPU_ENC_NEON) && have_neon()) return order & 1 ? rans_compress_O1_32x16_neon : rans_compress_O0_32x16_neon; else return order & 1 ? rans_compress_O1_32x16 : rans_compress_O0_32x16; } else { return order & 1 ? rans_compress_O1_4x16 : rans_compress_O0_4x16; } } static inline unsigned char *(*rans_dec_func(int do_simd, int order)) (unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_size) { if (do_simd) { if ((rans_cpu & RANS_CPU_DEC_NEON) && have_neon()) return order & 1 ? rans_uncompress_O1_32x16_neon : rans_uncompress_O0_32x16_neon; else return order & 1 ? rans_uncompress_O1_32x16 : rans_uncompress_O0_32x16; } else { return order & 1 ? rans_uncompress_O1_4x16 : rans_uncompress_O0_4x16; } } #else // !(defined(__GNUC__) && defined(__x86_64__)) && !defined(__ARM_NEON) static inline unsigned char *(*rans_enc_func(int do_simd, int order)) (unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { if (do_simd) { return order & 1 ? rans_compress_O1_32x16 : rans_compress_O0_32x16; } else { return order & 1 ? rans_compress_O1_4x16 : rans_compress_O0_4x16; } } static inline unsigned char *(*rans_dec_func(int do_simd, int order)) (unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int out_size) { if (do_simd) { return order & 1 ? rans_uncompress_O1_32x16 : rans_uncompress_O0_32x16; } else { return order & 1 ? rans_uncompress_O1_4x16 : rans_uncompress_O0_4x16; } } #endif // Test interface for restricting the auto-detection methods so we // can forcibly compare different implementations on the same machine. // See RANS_CPU_ defines in rANS_static4x16.h void rans_set_cpu(int opts) { rans_cpu = opts; #ifdef HAVE_HTSCODECS_TLS_CPU_INIT htscodecs_tls_cpu_init(); #endif } /*----------------------------------------------------------------------------- * Simple interface to the order-0 vs order-1 encoders and decoders. * * Smallest is method, , so worst case 2 bytes longer. */ unsigned char *rans_compress_to_4x16(unsigned char *in, unsigned int in_size, unsigned char *out,unsigned int *out_size, int order) { if (in_size > INT_MAX) { *out_size = 0; return NULL; } unsigned int c_meta_len; uint8_t *meta = NULL, *rle = NULL, *packed = NULL; uint8_t *out_free = NULL; if (!out) { *out_size = rans_compress_bound_4x16(in_size, order); if (*out_size == 0) return NULL; if (!(out_free = out = malloc(*out_size))) return NULL; } unsigned char *out_end = out + *out_size; // Permit 32-way unrolling for large blocks, paving the way for // AVX2 and AVX512 SIMD variants. if ((order & RANS_ORDER_SIMD_AUTO) && in_size >= 50000 && !(order & RANS_ORDER_STRIPE)) order |= X_32; if (in_size <= 20) order &= ~RANS_ORDER_STRIPE; #ifndef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (in_size <= 1000) order &= ~RANS_ORDER_X32; #endif if (order & RANS_ORDER_STRIPE) { int N = (order>>8) & 0xff; if (N == 0) N = 4; // default for compatibility with old tests unsigned char *transposed = malloc(in_size); unsigned int part_len[256]; unsigned int idx[256]; if (!transposed) { free(out_free); return NULL; } int i, j, x; for (i = 0; i < N; i++) { part_len[i] = in_size / N + ((in_size % N) > i); idx[i] = i ? idx[i-1] + part_len[i-1] : 0; // cumulative index } #define KN 8 i = x = 0; if (in_size >= N*KN) { for (; i < in_size-N*KN;) { int k; unsigned char *ink = in+i; for (j = 0; j < N; j++) for (k = 0; k < KN; k++) transposed[idx[j]+x+k] = ink[j+N*k]; x += KN; i+=N*KN; } } #undef KN for (; i < in_size-N; i += N, x++) { for (j = 0; j < N; j++) transposed[idx[j]+x] = in[i+j]; } for (; i < in_size; i += N, x++) { for (j = 0; i+j < in_size; j++) transposed[idx[j]+x] = in[i+j]; } unsigned int olen2; unsigned char *out2, *out2_start; c_meta_len = 1; *out = order & ~RANS_ORDER_NOSZ; c_meta_len += var_put_u32(out+c_meta_len, out_end, in_size); out[c_meta_len++] = N; unsigned char *out_best = NULL; unsigned int out_best_len = 0; out2_start = out2 = out+7+5*N; // shares a buffer with c_meta for (i = 0; i < N; i++) { // Brute force try all methods. int j, m[] = {1,64,128,0}, best_j = 0, best_sz = in_size+10; for (j = 0; j < sizeof(m)/sizeof(*m); j++) { if ((order & m[j]) != m[j]) continue; // order-1 *only*; bit check above cannot elide order-0 if ((order & RANS_ORDER_STRIPE_NO0) && (m[j]&1) == 0) continue; olen2 = *out_size - (out2 - out); rans_compress_to_4x16(transposed+idx[i], part_len[i], out2, &olen2, m[j] | RANS_ORDER_NOSZ | (order&RANS_ORDER_X32)); if (best_sz > olen2) { best_sz = olen2; best_j = j; if (j < sizeof(m)/sizeof(*m) && olen2 > out_best_len) { unsigned char *tmp = realloc(out_best, olen2); if (!tmp) { free(out_free); return NULL; } out_best = tmp; out_best_len = olen2; } // Cache a copy of the best so far memcpy(out_best, out2, olen2); } } if (best_j < sizeof(m)/sizeof(*m)) { // Copy the best compression to output buffer if not current memcpy(out2, out_best, best_sz); olen2 = best_sz; } out2 += olen2; c_meta_len += var_put_u32(out+c_meta_len, out_end, olen2); } if (out_best) free(out_best); memmove(out+c_meta_len, out2_start, out2-out2_start); free(transposed); *out_size = c_meta_len + out2-out2_start; return out; } if (order & RANS_ORDER_CAT) { out[0] = RANS_ORDER_CAT; c_meta_len = 1; c_meta_len += var_put_u32(&out[1], out_end, in_size); if (in_size) memcpy(out+c_meta_len, in, in_size); *out_size = c_meta_len + in_size; return out; } int do_pack = order & RANS_ORDER_PACK; int do_rle = order & RANS_ORDER_RLE; int no_size = order & RANS_ORDER_NOSZ; int do_simd = order & RANS_ORDER_X32; out[0] = order; c_meta_len = 1; if (!no_size) c_meta_len += var_put_u32(&out[1], out_end, in_size); order &= 3; // Format is compressed meta-data, compressed data. // Meta-data can be empty, pack, rle lengths, or pack + rle lengths. // Data is either the original data, bit-packed packed, rle literals or // packed + rle literals. if (do_pack && in_size) { // PACK 2, 4 or 8 symbols into one byte. int pmeta_len; uint64_t packed_len; packed = hts_pack(in, in_size, out+c_meta_len, &pmeta_len, &packed_len); if (!packed) { out[0] &= ~RANS_ORDER_PACK; do_pack = 0; free(packed); packed = NULL; } else { in = packed; in_size = packed_len; c_meta_len += pmeta_len; // Could derive this rather than storing verbatim. // Orig size * 8/nbits (+1 if not multiple of 8/n) int sz = var_put_u32(out+c_meta_len, out_end, in_size); c_meta_len += sz; *out_size -= sz; } } else if (do_pack) { out[0] &= ~RANS_ORDER_PACK; } if (do_rle && in_size) { // RLE 'in' -> rle_length + rle_literals arrays unsigned int rmeta_len, c_rmeta_len; uint64_t rle_len; c_rmeta_len = in_size+257; if (!(meta = malloc(c_rmeta_len))) { free(out_free); return NULL; } uint8_t rle_syms[256]; int rle_nsyms = 0; uint64_t rmeta_len64; rle = hts_rle_encode(in, in_size, meta, &rmeta_len64, rle_syms, &rle_nsyms, NULL, &rle_len); memmove(meta+1+rle_nsyms, meta, rmeta_len64); meta[0] = rle_nsyms; memcpy(meta+1, rle_syms, rle_nsyms); rmeta_len = rmeta_len64 + rle_nsyms+1; if (!rle || rle_len + rmeta_len >= .99*in_size) { // Not worth the speed hit. out[0] &= ~RANS_ORDER_RLE; do_rle = 0; free(rle); rle = NULL; } else { // Compress lengths with O0 and literals with O0/O1 ("order" param) int sz = var_put_u32(out+c_meta_len, out_end, rmeta_len*2), sz2; sz += var_put_u32(out+c_meta_len+sz, out_end, rle_len); c_rmeta_len = *out_size - (c_meta_len+sz+5); rans_enc_func(do_simd, 0)(meta, rmeta_len, out+c_meta_len+sz+5, &c_rmeta_len); if (c_rmeta_len < rmeta_len) { sz2 = var_put_u32(out+c_meta_len+sz, out_end, c_rmeta_len); memmove(out+c_meta_len+sz+sz2, out+c_meta_len+sz+5, c_rmeta_len); } else { // Uncompressed RLE meta-data as too small sz = var_put_u32(out+c_meta_len, out_end, rmeta_len*2+1); sz2 = var_put_u32(out+c_meta_len+sz, out_end, rle_len); memcpy(out+c_meta_len+sz+sz2, meta, rmeta_len); c_rmeta_len = rmeta_len; } c_meta_len += sz + sz2 + c_rmeta_len; in = rle; in_size = rle_len; } free(meta); } else if (do_rle) { out[0] &= ~RANS_ORDER_RLE; } *out_size -= c_meta_len; if (order && in_size < 8) { out[0] &= ~1; order &= ~1; } rans_enc_func(do_simd, order)(in, in_size, out+c_meta_len, out_size); if (*out_size >= in_size) { out[0] &= ~3; out[0] |= RANS_ORDER_CAT | no_size; if (in_size) memcpy(out+c_meta_len, in, in_size); *out_size = in_size; } free(rle); free(packed); *out_size += c_meta_len; return out; } unsigned char *rans_compress_4x16(unsigned char *in, unsigned int in_size, unsigned int *out_size, int order) { return rans_compress_to_4x16(in, in_size, NULL, out_size, order); } unsigned char *rans_uncompress_to_4x16(unsigned char *in, unsigned int in_size, unsigned char *out, unsigned int *out_size) { unsigned char *in_end = in + in_size; unsigned char *out_free = NULL, *tmp_free = NULL, *meta_free = NULL; if (in_size == 0) return NULL; if (*in & RANS_ORDER_STRIPE) { unsigned int ulen, olen, c_meta_len = 1; int i; uint64_t clen_tot = 0; // Decode lengths c_meta_len += var_get_u32(in+c_meta_len, in_end, &ulen); if (c_meta_len >= in_size) return NULL; unsigned int N = in[c_meta_len++]; if (N < 1) // Must be at least one stripe return NULL; unsigned int clenN[256], ulenN[256], idxN[256]; if (!out) { if (ulen >= INT_MAX) return NULL; #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (ulen > 100000) return NULL; #endif if (!(out_free = out = malloc(ulen))) { return NULL; } *out_size = ulen; } if (ulen != *out_size) { free(out_free); return NULL; } for (i = 0; i < N; i++) { ulenN[i] = ulen / N + ((ulen % N) > i); idxN[i] = i ? idxN[i-1] + ulenN[i-1] : 0; c_meta_len += var_get_u32(in+c_meta_len, in_end, &clenN[i]); clen_tot += clenN[i]; if (c_meta_len > in_size || clenN[i] > in_size || clenN[i] < 1) { free(out_free); return NULL; } } // We can call this with a larger buffer, but once we've determined // how much we really use we limit it so the recursion becomes easier // to limit. if (c_meta_len + clen_tot > in_size) { free(out_free); return NULL; } in_size = c_meta_len + clen_tot; //fprintf(stderr, " stripe meta %d\n", c_meta_len); //c-size // Uncompress the N streams unsigned char *outN = malloc(ulen); if (!outN) { free(out_free); return NULL; } for (i = 0; i < N; i++) { olen = ulenN[i]; if (in_size < c_meta_len) { free(out_free); free(outN); return NULL; } if (!rans_uncompress_to_4x16(in+c_meta_len, in_size-c_meta_len, outN + idxN[i], &olen) || olen != ulenN[i]) { free(out_free); free(outN); return NULL; } c_meta_len += clenN[i]; } unstripe(out, outN, ulen, N, idxN); free(outN); *out_size = ulen; return out; } int order = *in++; in_size--; int do_pack = order & RANS_ORDER_PACK; int do_rle = order & RANS_ORDER_RLE; int do_cat = order & RANS_ORDER_CAT; int no_size = order & RANS_ORDER_NOSZ; int do_simd = order & RANS_ORDER_X32; order &= 1; int sz = 0; unsigned int osz; if (!no_size) { sz = var_get_u32(in, in_end, &osz); } else sz = 0, osz = *out_size; in += sz; in_size -= sz; #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (osz > 100000) return NULL; #endif if (no_size && !out) goto err; // Need one or the other if (!out) { *out_size = osz; if (!(out = out_free = malloc(*out_size))) return NULL; } else { if (*out_size < osz) goto err; *out_size = osz; } // if (do_pack || do_rle) { // in += sz; // size field not needed when pure rANS // in_size -= sz; // } uint32_t c_meta_size = 0; unsigned int tmp1_size = *out_size; unsigned int tmp2_size = *out_size; unsigned int tmp3_size = *out_size; unsigned char *tmp1 = NULL, *tmp2 = NULL, *tmp3 = NULL, *tmp = NULL; // Need In, Out and Tmp buffers with temporary buffer of the same size // as output. All use rANS, but with optional transforms (none, RLE, // Pack, or both). // // rans unrle unpack // If none: in -> out // If RLE: in -> tmp -> out // If Pack: in -> tmp -> out // If RLE+Pack: in -> out -> tmp -> out // tmp1 tmp2 tmp3 // // So rans is in -> tmp1 // RLE is tmp1 -> tmp2 // Unpack is tmp2 -> tmp3 // Format is meta data (Pack and RLE in that order if present), // followed by rANS compressed data. if (do_pack || do_rle) { if (!(tmp = tmp_free = malloc(*out_size))) goto err; if (do_pack && do_rle) { tmp1 = out; tmp2 = tmp; tmp3 = out; } else if (do_pack) { tmp1 = tmp; tmp2 = tmp1; tmp3 = out; } else if (do_rle) { tmp1 = tmp; tmp2 = out; tmp3 = out; } } else { // neither tmp = NULL; tmp1 = out; tmp2 = out; tmp3 = out; } // Decode the bit-packing map. uint8_t map[16] = {0}; int npacked_sym = 0; uint64_t unpacked_sz = 0; // FIXME: rename to packed_per_byte if (do_pack) { c_meta_size = hts_unpack_meta(in, in_size, *out_size, map, &npacked_sym); if (c_meta_size == 0) goto err; unpacked_sz = osz; in += c_meta_size; in_size -= c_meta_size; // New unpacked size. We could derive this bit from *out_size // and npacked_sym. unsigned int osz; sz = var_get_u32(in, in_end, &osz); in += sz; in_size -= sz; if (osz > tmp1_size) goto err; tmp1_size = osz; } uint8_t *meta = NULL; uint32_t u_meta_size = 0; if (do_rle) { // Uncompress meta data uint32_t c_meta_size, rle_len, sz; sz = var_get_u32(in, in_end, &u_meta_size); sz += var_get_u32(in+sz, in_end, &rle_len); if (rle_len > tmp1_size) // should never grow goto err; if (u_meta_size & 1) { meta = in + sz; u_meta_size = u_meta_size/2 > (in_end-meta) ? (in_end-meta) : u_meta_size/2; c_meta_size = u_meta_size; } else { sz += var_get_u32(in+sz, in_end, &c_meta_size); u_meta_size /= 2; meta_free = meta = rans_dec_func(do_simd, 0)(in+sz, in_size-sz, NULL, u_meta_size); if (!meta) goto err; } if (c_meta_size+sz > in_size) goto err; in += c_meta_size+sz; in_size -= c_meta_size+sz; tmp1_size = rle_len; } //fprintf(stderr, " meta_size %d bytes\n", (int)(in - orig_in)); //c-size // uncompress RLE data. in -> tmp1 if (in_size) { if (do_cat) { //fprintf(stderr, " CAT %d\n", tmp1_size); //c-size if (tmp1_size > in_size) goto err; if (tmp1_size > *out_size) goto err; memcpy(tmp1, in, tmp1_size); } else { tmp1 = rans_dec_func(do_simd, order)(in, in_size, tmp1, tmp1_size); if (!tmp1) goto err; } } else { tmp1_size = 0; } tmp2_size = tmp3_size = tmp1_size; if (do_rle) { // Unpack RLE. tmp1 -> tmp2. if (u_meta_size == 0) goto err; uint64_t unrle_size = *out_size; int rle_nsyms = *meta ? *meta : 256; if (u_meta_size < 1+rle_nsyms) goto err; if (!hts_rle_decode(tmp1, tmp1_size, meta+1+rle_nsyms, u_meta_size-(1+rle_nsyms), meta+1, rle_nsyms, tmp2, &unrle_size)) goto err; tmp3_size = tmp2_size = unrle_size; free(meta_free); meta_free = NULL; } if (do_pack) { // Unpack bits via pack-map. tmp2 -> tmp3 if (npacked_sym == 1) unpacked_sz = tmp2_size; //uint8_t *porig = unpack(tmp2, tmp2_size, unpacked_sz, npacked_sym, map); //memcpy(tmp3, porig, unpacked_sz); if (!hts_unpack(tmp2, tmp2_size, tmp3, unpacked_sz, npacked_sym, map)) goto err; tmp3_size = unpacked_sz; } if (tmp) free(tmp); *out_size = tmp3_size; return tmp3; err: free(meta_free); free(out_free); free(tmp_free); return NULL; } unsigned char *rans_uncompress_4x16(unsigned char *in, unsigned int in_size, unsigned int *out_size) { return rans_uncompress_to_4x16(in, in_size, NULL, out_size); } pysam-0.23.0/htslib/htscodecs/htscodecs/rANS_word.h000066400000000000000000000401251475062545500221760ustar00rootroot00000000000000/* rans_byte.h originally from https://github.com/rygorous/ryg_rans * * This is a public-domain implementation of several rANS variants. rANS is an * entropy coder from the ANS family, as described in Jarek Duda's paper * "Asymmetric numeral systems" (http://arxiv.org/abs/1311.2540). */ /*-------------------------------------------------------------------------- */ /* rans_byte.h from https://github.com/rygorous/ryg_rans */ // Simple byte-aligned rANS encoder/decoder - public domain - Fabian 'ryg' Giesen 2014 // // Not intended to be "industrial strength"; just meant to illustrate the general // idea. #ifndef RANS_WORD_HEADER #define RANS_WORD_HEADER #include #include #include #include #include "htscodecs_endian.h" #ifdef assert #define RansAssert assert #else #define RansAssert(x) #endif // READ ME FIRST: // // This is designed like a typical arithmetic coder API, but there's three // twists you absolutely should be aware of before you start hacking: // // 1. You need to encode data in *reverse* - last symbol first. rANS works // like a stack: last in, first out. // 2. Likewise, the encoder outputs bytes *in reverse* - that is, you give // it a pointer to the *end* of your buffer (exclusive), and it will // slowly move towards the beginning as more bytes are emitted. // 3. Unlike basically any other entropy coder implementation you might // have used, you can interleave data from multiple independent rANS // encoders into the same bytestream without any extra signaling; // you can also just write some bytes by yourself in the middle if // you want to. This is in addition to the usual arithmetic encoder // property of being able to switch models on the fly. Writing raw // bytes can be useful when you have some data that you know is // incompressible, and is cheaper than going through the rANS encode // function. Using multiple rANS coders on the same byte stream wastes // a few bytes compared to using just one, but execution of two // independent encoders can happen in parallel on superscalar and // Out-of-Order CPUs, so this can be *much* faster in tight decoding // loops. // // This is why all the rANS functions take the write pointer as an // argument instead of just storing it in some context struct. // -------------------------------------------------------------------------- // L ('l' in the paper) is the lower bound of our normalization interval. // Between this and our byte-aligned emission, we use 31 (not 32!) bits. // This is done intentionally because exact reciprocals for 31-bit uints // fit in 32-bit uints: this permits some optimizations during encoding. #define RANS_BYTE_L (1u << 15) // lower bound of our normalization interval // State for a rANS encoder. Yep, that's all there is to it. typedef uint32_t RansState; // Initialize a rANS encoder. static inline void RansEncInit(RansState* r) { *r = RANS_BYTE_L; } // Renormalize the encoder. Internal function. static inline RansState RansEncRenorm(RansState x, uint8_t** pptr, uint32_t freq, uint32_t scale_bits) { uint32_t x_max = ((RANS_BYTE_L >> scale_bits) << 16) * freq-1; // this turns into a shift. if (x > x_max) { uint16_t* ptr = (uint16_t *)*pptr; *--ptr = (uint16_t) (x & 0xffff); x >>= 16; *pptr = (uint8_t *)ptr; } return x; } // Encodes a single symbol with range start "start" and frequency "freq". // All frequencies are assumed to sum to "1 << scale_bits", and the // resulting bytes get written to ptr (which is updated). // // NOTE: With rANS, you need to encode symbols in *reverse order*, i.e. from // beginning to end! Likewise, the output bytestream is written *backwards*: // ptr starts pointing at the end of the output buffer and keeps decrementing. static inline void RansEncPut(RansState* r, uint8_t** pptr, uint32_t start, uint32_t freq, uint32_t scale_bits) { // renormalize RansState x = RansEncRenorm(*r, pptr, freq, scale_bits); // x = C(s,x) *r = ((x / freq) << scale_bits) + (x % freq) + start; } // Flushes the rANS encoder. static inline void RansEncFlush(RansState* r, uint8_t** pptr) { uint32_t x = *r; uint8_t* ptr = *pptr; ptr -= 4; ptr[0] = (uint8_t) (x >> 0); ptr[1] = (uint8_t) (x >> 8); ptr[2] = (uint8_t) (x >> 16); ptr[3] = (uint8_t) (x >> 24); *pptr = ptr; } // Initializes a rANS decoder. // Unlike the encoder, the decoder works forwards as you'd expect. static inline void RansDecInit(RansState* r, uint8_t** pptr) { uint32_t x; uint8_t* ptr = *pptr; x = ptr[0] << 0; x |= ptr[1] << 8; x |= ptr[2] << 16; x |= ((uint32_t)ptr[3]) << 24; ptr += 4; *pptr = ptr; *r = x; } // Returns the current cumulative frequency (map it to a symbol yourself!) static inline uint32_t RansDecGet(RansState* r, uint32_t scale_bits) { return *r & ((1u << scale_bits) - 1); } // Advances in the bit stream by "popping" a single symbol with range start // "start" and frequency "freq". All frequencies are assumed to sum to "1 << scale_bits", // and the resulting bytes get written to ptr (which is updated). static inline void RansDecAdvance(RansState* r, uint8_t** pptr, uint32_t start, uint32_t freq, uint32_t scale_bits) { uint32_t mask = (1u << scale_bits) - 1; // s, x = D(x) uint32_t x = *r; x = freq * (x >> scale_bits) + (x & mask) - start; // renormalize if (x < RANS_BYTE_L) { uint8_t* ptr = *pptr; do x = (x << 8) | *ptr++; while (x < RANS_BYTE_L); *pptr = ptr; } *r = x; } // -------------------------------------------------------------------------- // That's all you need for a full encoder; below here are some utility // functions with extra convenience or optimizations. // Encoder symbol description // This (admittedly odd) selection of parameters was chosen to make // RansEncPutSymbol as cheap as possible. typedef struct { uint32_t x_max; // (Exclusive) upper bound of pre-normalization interval uint32_t rcp_freq; // Fixed-point reciprocal frequency uint32_t bias; // Bias // NB: This pair are read as a 32-bit value by the SIMD o1 encoder. uint16_t cmpl_freq; // Complement of frequency: (1 << scale_bits) - freq uint16_t rcp_shift; // Reciprocal shift } RansEncSymbol; // As above, but with cmpl_freq and rcp_shift combined into // a single value. This could be done with a cast, but it avoids // a type punning error. We could use a union, but anonymous unions // are C11 only (still that's 10 year old!). For now we just cheat // instead. typedef struct { uint32_t x_max; // (Exclusive) upper bound of pre-normalization interval uint32_t rcp_freq; // Fixed-point reciprocal frequency uint32_t bias; // Bias uint32_t cmpl_freq; // cmpl_freq+rcp_shift } RansEncSymbol_simd; // Decoder symbols are straightforward. typedef struct { uint16_t start; // Start of range. uint16_t freq; // Symbol frequency. } RansDecSymbol; // Initializes an encoder symbol to start "start" and frequency "freq" static inline void RansEncSymbolInit(RansEncSymbol* s, uint32_t start, uint32_t freq, uint32_t scale_bits) { RansAssert(scale_bits <= 16); RansAssert(start <= (1u << scale_bits)); RansAssert(freq <= (1u << scale_bits) - start); // Say M := 1 << scale_bits. // // The original encoder does: // x_new = (x/freq)*M + start + (x%freq) // // The fast encoder does (schematically): // q = mul_hi(x, rcp_freq) >> rcp_shift (division) // r = x - q*freq (remainder) // x_new = q*M + bias + r (new x) // plugging in r into x_new yields: // x_new = bias + x + q*(M - freq) // =: bias + x + q*cmpl_freq (*) // // and we can just precompute cmpl_freq. Now we just need to // set up our parameters such that the original encoder and // the fast encoder agree. s->x_max = ((RANS_BYTE_L >> scale_bits) << 16) * freq -1; s->cmpl_freq = (uint16_t) ((1 << scale_bits) - freq); if (freq < 2) { // freq=0 symbols are never valid to encode, so it doesn't matter what // we set our values to. // // freq=1 is tricky, since the reciprocal of 1 is 1; unfortunately, // our fixed-point reciprocal approximation can only multiply by values // smaller than 1. // // So we use the "next best thing": rcp_freq=0xffffffff, rcp_shift=0. // This gives: // q = mul_hi(x, rcp_freq) >> rcp_shift // = mul_hi(x, (1<<32) - 1)) >> 0 // = floor(x - x/(2^32)) // = x - 1 if 1 <= x < 2^32 // and we know that x>0 (x=0 is never in a valid normalization interval). // // So we now need to choose the other parameters such that // x_new = x*M + start // plug it in: // x*M + start (desired result) // = bias + x + q*cmpl_freq (*) // = bias + x + (x - 1)*(M - 1) (plug in q=x-1, cmpl_freq) // = bias + 1 + (x - 1)*M // = x*M + (bias + 1 - M) // // so we have start = bias + 1 - M, or equivalently // bias = start + M - 1. s->rcp_freq = ~0u; s->rcp_shift = 0; s->bias = start + (1 << scale_bits) - 1; } else { // Alverson, "Integer Division using reciprocals" // shift=ceil(log2(freq)) uint32_t shift = 0; while (freq > (1u << shift)) shift++; s->rcp_freq = (uint32_t) (((1ull << (shift + 31)) + freq-1) / freq); s->rcp_shift = shift - 1; // With these values, 'q' is the correct quotient, so we // have bias=start. s->bias = start; } s->rcp_shift += 32; // Avoid the extra >>32 in RansEncPutSymbol } // Initialize a decoder symbol to start "start" and frequency "freq" static inline void RansDecSymbolInit(RansDecSymbol* s, uint32_t start, uint32_t freq) { RansAssert(start <= (1 << 16)); RansAssert(freq <= (1 << 16) - start); s->start = (uint16_t) start; s->freq = (uint16_t) freq; } // Encodes a given symbol. This is faster than straight RansEnc since we can do // multiplications instead of a divide. // // See RansEncSymbolInit for a description of how this works. static inline void RansEncPutSymbol(RansState* r, uint8_t** pptr, RansEncSymbol const* sym) { //RansAssert(sym->x_max != 0); // can't encode symbol with freq=0 // renormalize uint32_t x = *r; uint32_t x_max = sym->x_max; #ifdef HTSCODECS_LITTLE_ENDIAN // Branchless renorm. // // This works best on high entropy data where branch prediction // is poor. // // Note the bit-packing and RLE modes are more likely to be used on // low entropy data, making this assertion generally true. See // RansEncPutSymbol_branched for a low-entropy optimised function. // NB: "(x > x_max)*2" turns back into branched code with gcc. int c = (x > x_max); c*=2; memcpy(*pptr-2, &x, 2); x >>= c*8; *pptr = *pptr - c; #else if (x > x_max) { uint8_t* ptr = *pptr; ptr -= 2; ptr[0] = x & 0xff; ptr[1] = (x >> 8) & 0xff; x >>= 16; *pptr = ptr; } #endif // x = C(s,x) // NOTE: written this way so we get a 32-bit "multiply high" when // available. If you're on a 64-bit platform with cheap multiplies // (e.g. x64), just bake the +32 into rcp_shift. //uint32_t q = (uint32_t) (((uint64_t)x * sym->rcp_freq) >> 32) >> sym->rcp_shift; // Slow method, but robust // *r = ((x / sym->freq) << sym->scale_bits) + (x % sym->freq) + sym->start; // return; // The extra >>32 has already been added to RansEncSymbolInit uint32_t q = (uint32_t) (((uint64_t)x * sym->rcp_freq) >> sym->rcp_shift); *r = x + sym->bias + q * sym->cmpl_freq; // assert(((x / sym->freq) << sym->scale_bits) + (x % sym->freq) + sym->start == *r); } static inline void RansEncPutSymbol_branched(RansState* r, uint8_t** pptr, RansEncSymbol const* sym) { //RansAssert(sym->x_max != 0); // can't encode symbol with freq=0 // renormalize uint32_t x = *r; uint32_t x_max = sym->x_max; #ifdef HTSCODECS_LITTLE_ENDIAN // The old non-branchless method if (x > x_max) { (*pptr) -= 2; memcpy(*pptr, &x, 2); x >>= 16; } #else if (x > x_max) { uint8_t* ptr = *pptr; ptr -= 2; ptr[0] = x & 0xff; ptr[1] = (x >> 8) & 0xff; x >>= 16; *pptr = ptr; } #endif // x = C(s,x) // NOTE: written this way so we get a 32-bit "multiply high" when // available. If you're on a 64-bit platform with cheap multiplies // (e.g. x64), just bake the +32 into rcp_shift. //uint32_t q = (uint32_t) (((uint64_t)x * sym->rcp_freq) >> 32) >> sym->rcp_shift; // Slow method, but robust // *r = ((x / sym->freq) << sym->scale_bits) + (x % sym->freq) + sym->start; // return; // The extra >>32 has already been added to RansEncSymbolInit uint32_t q = (uint32_t) (((uint64_t)x * sym->rcp_freq) >> sym->rcp_shift); *r = x + sym->bias + q * sym->cmpl_freq; // assert(((x / sym->freq) << sym->scale_bits) + (x % sym->freq) + sym->start == *r); } // Equivalent to RansDecAdvance that takes a symbol. static inline void RansDecAdvanceSymbol(RansState* r, uint8_t** pptr, RansDecSymbol const* sym, uint32_t scale_bits) { RansDecAdvance(r, pptr, sym->start, sym->freq, scale_bits); } // Advances in the bit stream by "popping" a single symbol with range start // "start" and frequency "freq". All frequencies are assumed to sum to "1 << scale_bits". // No renormalization or output happens. static inline void RansDecAdvanceStep(RansState* r, uint32_t start, uint32_t freq, uint32_t scale_bits) { uint32_t mask = (1u << scale_bits) - 1; // s, x = D(x) uint32_t x = *r; *r = freq * (x >> scale_bits) + (x & mask) - start; } // Equivalent to RansDecAdvanceStep that takes a symbol. static inline void RansDecAdvanceSymbolStep(RansState* r, RansDecSymbol const* sym, uint32_t scale_bits) { RansDecAdvanceStep(r, sym->start, sym->freq, scale_bits); } // Renormalize. #if defined(__x86_64) && !defined(__ILP32__) /* * Assembly variants of the RansDecRenorm code. * These are based on joint ideas from Rob Davies and from looking at * the clang assembly output. */ static inline void RansDecRenorm(RansState* r, uint8_t** pptr) { // q4 q40 // clang 730/608 717/467 // gcc8 733/588 737/458 uint32_t x = *r; uint8_t *ptr = *pptr; __asm__ ("movzwl (%0), %%eax\n\t" "mov %1, %%edx\n\t" "shl $0x10, %%edx\n\t" "or %%eax, %%edx\n\t" "xor %%eax, %%eax\n\t" "cmp $0x8000,%1\n\t" "cmovb %%edx, %1\n\t" "lea 2(%0), %%rax\n\t" "cmovb %%rax, %0\n\t" : "=r" (ptr), "=r" (x) : "0" (ptr), "1" (x) : "eax", "edx" ); *pptr = (uint8_t *)ptr; *r = x; } #else /* __x86_64 */ static inline void RansDecRenorm(RansState* r, uint8_t** pptr) { // renormalize, branchless uint32_t x = *r; int cmp = (x < RANS_BYTE_L)*2; uint32_t y = (*pptr)[0] + ((*pptr)[1]<<8); uint32_t x2 = (x << 16) | y; x = cmp ? x2 : x; (*pptr) += cmp; *r = x; // // renormalize, branched. Faster on low-complexity data, but generally // // that is best compressed with PACK and/or RLE which turns it back // // into high complexity data. // uint32_t x = *r; // uint32_t y = (*pptr)[0] | ((*pptr)[1]<<8); // // if (x < RANS_BYTE_L) // (*pptr)+=2; // if (x < RANS_BYTE_L) // x = (x << 16) | y; // // *r = x; } #endif /* __x86_64 */ // Note the data may not be word aligned here. // This function is only used sparingly, for the last few bytes in the buffer, // so speed isn't critical. static inline void RansDecRenormSafe(RansState* r, uint8_t** pptr, uint8_t *ptr_end) { uint32_t x = *r; if (x >= RANS_BYTE_L || *pptr+1 >= ptr_end) return; uint16_t y = (*pptr)[0] + ((*pptr)[1]<<8); x = (x << 16) | y; (*pptr) += 2; *r = x; } #endif // RANS_WORD_HEADER pysam-0.23.0/htslib/htscodecs/htscodecs/rle.c000066400000000000000000000151501475062545500211150ustar00rootroot00000000000000/* * Copyright (c) 2019-2021 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #include "config.h" #include #include #include #include #include "varint.h" #include "rle.h" #define MAGIC 8 //----------------------------------------------------------------------------- // Auto compute rle_syms / rle_nsyms static void rle_find_syms(uint8_t *data, uint64_t data_len, int64_t *saved, // dim >= 256 uint8_t *rle_syms, int *rle_nsyms) { int last = -1, n; uint64_t i; if (data_len > 256) { // 186/450 // Interleaved buffers to avoid cache collisions int64_t saved2[256+MAGIC] = {0}; int64_t saved3[256+MAGIC] = {0}; int64_t saved4[256+MAGIC] = {0}; int64_t len4 = data_len&~3; for (i = 0; i < len4; i+=4) { int d1 = (data[i+0] == last) <<1; int d2 = (data[i+1] == data[i+0])<<1; int d3 = (data[i+2] == data[i+1])<<1; int d4 = (data[i+3] == data[i+2])<<1; last = data[i+3]; saved [data[i+0]] += d1-1; saved2[data[i+1]] += d2-1; saved3[data[i+2]] += d3-1; saved4[data[i+3]] += d4-1; } while (i < data_len) { int d = (data[i] == last)<<1; saved[data[i]] += d - 1; last = data[i]; i++; } for (i = 0; i < 256; i++) saved[i] += saved2[i] + saved3[i] + saved4[i]; } else { // 163/391 for (i = 0; i < data_len; i++) { if (data[i] == last) { saved[data[i]]++; } else { saved[data[i]]--; last = data[i]; } } } // Map back to a list for (i = n = 0; i < 256; i++) { if (saved[i] > 0) rle_syms[n++] = i; } *rle_nsyms = n; } uint8_t *hts_rle_encode(uint8_t *data, uint64_t data_len, uint8_t *run, uint64_t *run_len, uint8_t *rle_syms, int *rle_nsyms, uint8_t *out, uint64_t *out_len) { uint64_t i, j, k; if (!out) if (!(out = malloc(data_len*2))) return NULL; // Two pass: Firstly compute which symbols are worth using RLE on. int64_t saved[256+MAGIC] = {0}; if (*rle_nsyms) { for (i = 0; i < *rle_nsyms; i++) saved[rle_syms[i]] = 1; } else { // Writes back to rle_syms and rle_nsyms rle_find_syms(data, data_len, saved, rle_syms, rle_nsyms); } // 2nd pass: perform RLE itself to out[] and run[] arrays. for (i = j = k = 0; i < data_len; i++) { out[k++] = data[i]; if (saved[data[i]] > 0) { int rlen = i; int last = data[i]; while (i < data_len && data[i] == last) i++; i--; rlen = i-rlen; j += var_put_u32(&run[j], NULL, rlen); } } *run_len = j; *out_len = k; return out; } // On input *out_len holds the allocated size of out[]. // On output it holds the used size of out[]. uint8_t *hts_rle_decode(uint8_t *lit, uint64_t lit_len, uint8_t *run, uint64_t run_len, uint8_t *rle_syms, int rle_nsyms, uint8_t *out, uint64_t *out_len) { uint64_t j; uint8_t *run_end = run + run_len; #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (*out_len > 100000) return NULL; #endif int saved[256] = {0}; for (j = 0; j < rle_nsyms; j++) saved[rle_syms[j]] = 1; uint8_t *lit_end = lit + lit_len; uint8_t *out_end = out + *out_len; uint8_t *outp = out; while (lit < lit_end) { if (outp >= out_end) goto err; uint8_t b = *lit; if (saved[b]) { uint32_t rlen; run += var_get_u32(run, run_end, &rlen); if (rlen) { if (outp + rlen >= out_end) goto err; memset(outp, b, rlen+1); outp += rlen+1; } else { *outp++ = b; } } else { *outp++ = b; } lit++; } *out_len = outp-out; return out; err: return NULL; } // Deprecated interface; to remove when we next to an ABI breakage uint8_t *rle_encode(uint8_t *data, uint64_t data_len, uint8_t *run, uint64_t *run_len, uint8_t *rle_syms, int *rle_nsyms, uint8_t *out, uint64_t *out_len) { return hts_rle_encode(data, data_len, run, run_len, rle_syms, rle_nsyms, out, out_len); } // Deprecated interface; to remove when we next to an ABI breakage uint8_t *rle_decode(uint8_t *lit, uint64_t lit_len, uint8_t *run, uint64_t run_len, uint8_t *rle_syms, int rle_nsyms, uint8_t *out, uint64_t *out_len) { return hts_rle_decode(lit, lit_len, run, run_len, rle_syms, rle_nsyms, out, out_len); } pysam-0.23.0/htslib/htscodecs/htscodecs/rle.h000066400000000000000000000073361475062545500211310ustar00rootroot00000000000000/* * Copyright (c) 2019 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef HTS_RLE_H #define HTS_RLE_H #ifdef __cplusplus extern "C" { #endif /* * Performs run length encoding of a byte stream, turning it into a * list of lengths and a list of literals. * * The method used is a bit different to traditional run length * encoding. It always outputs run-lengths for symbols in the * 'rle_syms' list (even if that length is +0 more), and never outputs * lengths for symbols not in that list. * * "run" should be preallocated to be large enough; * e.g at least data_len bytes long as a worse case. * "rle_syms" should be allocated to be at least 256 bytes. * * If *rle_nsyms is zero this function will survey the input data * first to choose symbols automatically, writing back to rle_syms and * rle_nsyms. * * The "out" buffer may be passed in as NULL in which case it is * allocated and returned (and is up to the caller to free). * Otherwise if specified as non-NULL it will be written to, but * it is up to the caller to ensure the buffer size is large enough. * A worst case scenario is 2*data_len. * * Returns the literal buffer on success with new length in out_len, * also fills out run buffer and run_len, and potentially * updates rle_syms / rle_nsyms too. * Returns NULL of failure */ uint8_t *hts_rle_encode(uint8_t *data, uint64_t data_len, uint8_t *run, uint64_t *run_len, uint8_t *rle_syms, int *rle_nsyms, uint8_t *out, uint64_t *out_len); /* * Expands a run lengthed data steam from a pair of literal and * run-length buffers. * * On input *out_len holds the length of the supplied out * buffer. On exit, it holds the used portion of this buffer. * * Returns uncompressed data (out) on success, * NULL on failure. */ uint8_t *hts_rle_decode(uint8_t *lit, uint64_t lit_len, uint8_t *run, uint64_t run_len, uint8_t *rle_syms, int rle_nsyms, uint8_t *out, uint64_t *out_len); // TODO: Add rle scanning func to compute rle_syms. #ifdef __cplusplus } #endif #endif /* HTS_RLE_H */ pysam-0.23.0/htslib/htscodecs/htscodecs/tokenise_name3.c000066400000000000000000001710611475062545500232430ustar00rootroot00000000000000/* * Copyright (c) 2016-2022 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ // cc -O3 -g -DTEST_TOKENISER tokenise_name3.c arith_dynamic.c rANS_static4x16pr.c pooled_alloc.c -I.. -I. -lbz2 -pthread // Name tokeniser. // It generates a series of byte streams (per token) and compresses these // either using static rANS or dynamic arithmetic coding. Arith coding is // typically 1-5% smaller, but around 50-100% slower. We only envisage it // being used at the higher compression levels. // TODO // // - Is it better when encoding 1, 2, 3, 3, 4, 5, 5, 6, 7, 9, 9, 10 to encode // this as a mixture of MATCH and DELTA ops, or as entirely as DELTA ops // with some delta values being zero? I suspect the latter, but it is // not implemented here. See "last_token_delta" comments in code. // // - Consider variable size string implementations. // Pascal style strings (length + str), // C style strings (nul terminated), // Or split blocks: length block and string contents block. // // - Is this one token-block or many serialised token-blocks? // A) Lots of different models but feeding one bit-buffer emitted to // by the entropy encoder => one block (fqzcomp). // B) Lots of different models each feeding their own bit-buffers // => many blocks. // // - multiple integer types depending on size; 1, 2, 4 byte long. // // - Consider token choice for isalnum instead of isalpha. Sometimes better. // // - Consider token synchronisation (eg on matching chr symbols?) incase of // variable number. Eg consider foo:0999, foo:1000, foo:1001 (the leading // zero adds an extra token). // // - Optimisation of tokens. Eg: // HS25_09827:2:2102:11274:80442#49 // HS25_09827:2:2109:12941:31311#49 // // We'll have tokens for HS 25 _ 09827 : 2 : that are entirely // after the initial token. These 7 tokens could be one ALPHA instead // of 7 distinct tokens, with 1 MATCH instead of 7. This is both a speed // improvement for decoding as well as a space saving (fewer token-blocks // and associated overhead). // // - XOR. Like ALPHA, but used when previous symbol is ALPHA or XOR // and string lengths match. Useful when names are similar, eg: // the sequence in 07.names: // // @VP2-06:112:H7LNDMCVY:1:1105:26919:1172 1:N:0:ATTCAGAA+AGGAGAAG // @VP2-06:112:H7LNDMCVY:1:1105:27100:1172 1:N:0:ATTCAGAA+AGGCGAAG // @VP2-06:112:H7LNDMCVY:1:1105:27172:1172 1:N:0:ATTCAGAA+AGGCTAAG #include "config.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "pooled_alloc.h" #include "arith_dynamic.h" #include "rANS_static4x16.h" #include "tokenise_name3.h" #include "varint.h" #include "utils.h" // 128 is insufficient for SAM names (max 256 bytes) as // we may alternate a0a0a0a0a0 etc. However if we fail, // we just give up and switch to another codec, so this // isn't a serious limit. Maybe up to 256 to permit all // SAM names? #define MAX_TOKENS 128 #define MAX_TBLOCKS (MAX_TOKENS<<4) // Number of names per block #define MAX_NAMES 1000000 enum name_type {N_ERR = -1, N_TYPE = 0, N_ALPHA, N_CHAR, N_DIGITS0, N_DZLEN, N_DUP, N_DIFF, N_DIGITS, N_DDELTA, N_DDELTA0, N_MATCH, N_NOP, N_END, N_ALL}; typedef struct trie { struct trie *next, *sibling; int count; uint32_t c:8; uint32_t n:24; // Nth line } trie_t; typedef struct { enum name_type token_type; int token_int; int token_str; } last_context_tok; typedef struct { char *last_name; int last_ntok; last_context_tok *last; // [last_ntok] } last_context; typedef struct { uint8_t *buf; size_t buf_a, buf_l; // alloc and used length. int tnum, ttype; int dup_from; } descriptor; typedef struct { last_context *lc; // For finding entire line dups int counter; // Trie used in encoder only trie_t *t_head; pool_alloc_t *pool; // token blocks descriptor desc[MAX_TBLOCKS]; // summary stats per token int token_dcount[MAX_TOKENS]; int token_icount[MAX_TOKENS]; //int token_zcount[MAX_TOKENS]; int max_tok; // tracks which desc/[id]count elements have been initialised int max_names; } name_context; static name_context *create_context(int max_names) { if (max_names <= 0) return NULL; #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (max_names > 100000) return NULL; #endif // An arbitrary limit to prevent malformed data from consuming excessive // amounts of memory. Consider upping this if we have genuine use cases // for larger blocks. if (max_names > 1e7) { fprintf(stderr, "Name codec currently has a max of 10 million rec.\n"); return NULL; } name_context *ctx = htscodecs_tls_alloc(sizeof(*ctx) + ++max_names*sizeof(*ctx->lc)); if (!ctx) return NULL; ctx->max_names = max_names; ctx->counter = 0; ctx->t_head = NULL; ctx->lc = (last_context *)(((char *)ctx) + sizeof(*ctx)); ctx->pool = NULL; memset(&ctx->desc[0], 0, 2*16 * sizeof(ctx->desc[0])); memset(&ctx->token_dcount[0], 0, sizeof(int)); memset(&ctx->token_icount[0], 0, sizeof(int)); memset(&ctx->lc[0], 0, max_names*sizeof(ctx->lc[0])); ctx->max_tok = 1; ctx->lc[0].last_ntok = 0; return ctx; } static void free_context(name_context *ctx) { if (!ctx) return; if (ctx->t_head) free(ctx->t_head); if (ctx->pool) pool_destroy(ctx->pool); int i; for (i = 0; i < ctx->max_tok*16; i++) free(ctx->desc[i].buf); for (i = 0; i < ctx->max_names; i++) free(ctx->lc[i].last); htscodecs_tls_free(ctx); } //----------------------------------------------------------------------------- // Fast unsigned integer printing code. // Returns number of bytes written. static int append_uint32_fixed(char *cp, uint32_t i, uint8_t l) { switch (l) { case 9:*cp++ = i / 100000000 + '0', i %= 100000000; // fall-through case 8:*cp++ = i / 10000000 + '0', i %= 10000000; // fall-through case 7:*cp++ = i / 1000000 + '0', i %= 1000000; // fall-through case 6:*cp++ = i / 100000 + '0', i %= 100000; // fall-through case 5:*cp++ = i / 10000 + '0', i %= 10000; // fall-through case 4:*cp++ = i / 1000 + '0', i %= 1000; // fall-through case 3:*cp++ = i / 100 + '0', i %= 100; // fall-through case 2:*cp++ = i / 10 + '0', i %= 10; // fall-through case 1:*cp++ = i + '0'; // fall-throuhg case 0:break; } return l; } static int append_uint32_var(char *cp, uint32_t i) { char *op = cp; uint32_t j; //if (i < 10) goto b0; if (i < 100) goto b1; //if (i < 1000) goto b2; if (i < 10000) goto b3; //if (i < 100000) goto b4; if (i < 1000000) goto b5; //if (i < 10000000) goto b6; if (i < 100000000) goto b7; if ((j = i / 1000000000)) {*cp++ = j + '0'; i -= j*1000000000; goto x8;} if ((j = i / 100000000)) {*cp++ = j + '0'; i -= j*100000000; goto x7;} b7:if ((j = i / 10000000)) {*cp++ = j + '0'; i -= j*10000000; goto x6;} if ((j = i / 1000000)) {*cp++ = j + '0', i -= j*1000000; goto x5;} b5:if ((j = i / 100000)) {*cp++ = j + '0', i -= j*100000; goto x4;} if ((j = i / 10000)) {*cp++ = j + '0', i -= j*10000; goto x3;} b3:if ((j = i / 1000)) {*cp++ = j + '0', i -= j*1000; goto x2;} if ((j = i / 100)) {*cp++ = j + '0', i -= j*100; goto x1;} b1:if ((j = i / 10)) {*cp++ = j + '0', i -= j*10; goto x0;} if (i) *cp++ = i + '0'; return cp-op; x8:*cp++ = i / 100000000 + '0', i %= 100000000; x7:*cp++ = i / 10000000 + '0', i %= 10000000; x6:*cp++ = i / 1000000 + '0', i %= 1000000; x5:*cp++ = i / 100000 + '0', i %= 100000; x4:*cp++ = i / 10000 + '0', i %= 10000; x3:*cp++ = i / 1000 + '0', i %= 1000; x2:*cp++ = i / 100 + '0', i %= 100; x1:*cp++ = i / 10 + '0', i %= 10; x0:*cp++ = i + '0'; return cp-op; } //----------------------------------------------------------------------------- // Example descriptor encoding and IO. // // Here we just append to a buffer so we can dump out the results. // These could then be passed through a static entropy encoder that // encodes the entire buffer. // // Alternatively an adaptive entropy encoder could be place inline // here to encode as it goes using additional knowledge from the // supplied context. // Ensure room for sz more bytes. static int descriptor_grow(descriptor *fd, uint32_t sz) { while (fd->buf_l + sz > fd->buf_a) { size_t buf_a = fd->buf_a ? fd->buf_a*2 : 65536; unsigned char *buf = realloc(fd->buf, buf_a); if (!buf) return -1; fd->buf = buf; fd->buf_a = buf_a; } return 0; } static int encode_token_type(name_context *ctx, int ntok, enum name_type type) { int id = ntok<<4; if (descriptor_grow(&ctx->desc[id], 1) < 0) return -1; ctx->desc[id].buf[ctx->desc[id].buf_l++] = type; return 0; } static int encode_token_match(name_context *ctx, int ntok) { return encode_token_type(ctx, ntok, N_MATCH); } static int encode_token_end(name_context *ctx, int ntok) { return encode_token_type(ctx, ntok, N_END); } static enum name_type decode_token_type(name_context *ctx, int ntok) { int id = ntok<<4; if (ctx->desc[id].buf_l >= ctx->desc[id].buf_a) return -1; return ctx->desc[id].buf[ctx->desc[id].buf_l++]; } // int stored as 32-bit quantities static int encode_token_int(name_context *ctx, int ntok, enum name_type type, uint32_t val) { int id = (ntok<<4) | type; if (encode_token_type(ctx, ntok, type) < 0) return -1; if (descriptor_grow(&ctx->desc[id], 4) < 0) return -1; uint8_t *cp = &ctx->desc[id].buf[ctx->desc[id].buf_l]; cp[0] = (val >> 0) & 0xff; cp[1] = (val >> 8) & 0xff; cp[2] = (val >> 16) & 0xff; cp[3] = (val >> 24) & 0xff; ctx->desc[id].buf_l += 4; return 0; } // Return 0 on success, -1 on failure; static int decode_token_int(name_context *ctx, int ntok, enum name_type type, uint32_t *val) { int id = (ntok<<4) | type; if (ctx->desc[id].buf_l + 4 > ctx->desc[id].buf_a) return -1; uint8_t *cp = ctx->desc[id].buf + ctx->desc[id].buf_l; *val = (cp[0]) + (cp[1]<<8) + (cp[2]<<16) + ((uint32_t)cp[3]<<24); ctx->desc[id].buf_l += 4; return 0; } // 8 bit integer quantity static int encode_token_int1(name_context *ctx, int ntok, enum name_type type, uint32_t val) { int id = (ntok<<4) | type; if (encode_token_type(ctx, ntok, type) < 0) return -1; if (descriptor_grow(&ctx->desc[id], 1) < 0) return -1; ctx->desc[id].buf[ctx->desc[id].buf_l++] = val; return 0; } static int encode_token_int1_(name_context *ctx, int ntok, enum name_type type, uint32_t val) { int id = (ntok<<4) | type; if (descriptor_grow(&ctx->desc[id], 1) < 0) return -1; ctx->desc[id].buf[ctx->desc[id].buf_l++] = val; return 0; } // Return 0 on success, -1 on failure; static int decode_token_int1(name_context *ctx, int ntok, enum name_type type, uint32_t *val) { int id = (ntok<<4) | type; if (ctx->desc[id].buf_l >= ctx->desc[id].buf_a) return -1; *val = ctx->desc[id].buf[ctx->desc[id].buf_l++]; return 0; } // Basic C-string style for now. // // Maybe XOR with previous string as context? // This permits partial match to be encoded efficiently. static int encode_token_alpha(name_context *ctx, int ntok, char *str, int len) { int id = (ntok<<4) | N_ALPHA; if (encode_token_type(ctx, ntok, N_ALPHA) < 0) return -1; if (descriptor_grow(&ctx->desc[id], len+1) < 0) return -1; memcpy(&ctx->desc[id].buf[ctx->desc[id].buf_l], str, len); ctx->desc[id].buf[ctx->desc[id].buf_l+len] = 0; ctx->desc[id].buf_l += len+1; return 0; } // FIXME: need limit on string length for security. // Return length on success, -1 on failure; static int decode_token_alpha(name_context *ctx, int ntok, char *str, int max_len) { int id = (ntok<<4) | N_ALPHA; char c; int len = 0; if (ctx->desc[id].buf_l >= ctx->desc[id].buf_a) return -1; do { c = ctx->desc[id].buf[ctx->desc[id].buf_l++]; str[len++] = c; } while(c && len < max_len && ctx->desc[id].buf_l < ctx->desc[id].buf_a); return len-1; } static int encode_token_char(name_context *ctx, int ntok, char c) { int id = (ntok<<4) | N_CHAR; if (encode_token_type(ctx, ntok, N_CHAR) < 0) return -1; if (descriptor_grow(&ctx->desc[id], 1) < 0) return -1; ctx->desc[id].buf[ctx->desc[id].buf_l++] = c; return 0; } // FIXME: need limit on string length for security // Return length on success, -1 on failure; static int decode_token_char(name_context *ctx, int ntok, char *str) { int id = (ntok<<4) | N_CHAR; if (ctx->desc[id].buf_l >= ctx->desc[id].buf_a) return -1; *str = ctx->desc[id].buf[ctx->desc[id].buf_l++]; return 1; } // A duplicated name static int encode_token_dup(name_context *ctx, uint32_t val) { return encode_token_int(ctx, 0, N_DUP, val); } // Which read to delta against static int encode_token_diff(name_context *ctx, uint32_t val) { return encode_token_int(ctx, 0, N_DIFF, val); } //----------------------------------------------------------------------------- // Trie implementation for tracking common name prefixes. static int build_trie(name_context *ctx, char *data, size_t len, int n) { int nlines = 0; size_t i; trie_t *t; if (!ctx->t_head) { ctx->t_head = calloc(1, sizeof(*ctx->t_head)); if (!ctx->t_head) return -1; } // Build our trie, also counting input lines for (nlines = i = 0; i < len; i++, nlines++) { t = ctx->t_head; t->count++; while (i < len && (unsigned char)data[i] > '\n') { unsigned char c = data[i++]; if (c & 0x80) //fprintf(stderr, "8-bit ASCII is unsupported\n"); return -1; c &= 127; trie_t *x = t->next, *l = NULL; while (x && x->c != c) { l = x; x = x->sibling; } if (!x) { if (!ctx->pool) ctx->pool = pool_create(sizeof(trie_t)); if (!(x = (trie_t *)pool_alloc(ctx->pool))) return -1; memset(x, 0, sizeof(*x)); if (!l) x = t->next = x; else x = l->sibling = x; x->n = n; x->c = c; } t = x; t->c = c; t->count++; } } return 0; } #if 0 void dump_trie(trie_t *t, int depth) { if (depth == 0) { printf("graph x_%p {\n splines = ortho\n ranksep=2\n", t); printf(" p_%p [label=\"\"];\n", t); dump_trie(t, 1); printf("}\n"); } else { int j, k, count;//, cj; char label[100], *cp; trie_t *tp = t; // patricia: // for (count = j = 0; j < 128; j++) // if (t->next[j]) // count++, cj=j; // // if (count == 1) { // t = t->next[cj]; // *cp++ = cj; // goto patricia; // } trie_t *x; for (x = t->next; x; x = x->sibling) { printf(" p_%p [label=\"%c\"];\n", x, x->c); printf(" p_%p -- p_%p [label=\"%d\", penwidth=\"%f\"];\n", tp, x, x->count, MAX((log(x->count)-3)*2,1)); //if (depth <= 11) dump_trie(x, depth+1); } #if 0 for (j = 0; j < 128; j++) { trie_t *tn; if (!t->next[j]) continue; cp = label; tn = t->next[j]; *cp++ = j; // patricia: for (count = k = 0; k < 128; k++) if (tn->next[k]) count++;//, cj=k; // if (count == 1) { // tn = tn->next[cj]; // *cp++ = cj; // goto patricia; // } *cp++ = 0; printf(" p_%p [label=\"%s\"];\n", tn, label); printf(" p_%p -- p_%p [label=\"%d\", penwidth=\"%f\"];\n", tp, tn, tn->count, MAX((log(tn->count)-3)*2,1)); if (depth <= 11) dump_trie(tn, depth+1); } #endif } } #endif static int search_trie(name_context *ctx, char *data, size_t len, int n, int *exact, int *is_fixed, int *fixed_len) { int nlines = 0; size_t i; trie_t *t; int from = -1, p3 = -1; *exact = 0; *fixed_len = 0; *is_fixed = 0; // Horrid hack for the encoder only. // We optimise per known name format here. int prefix_len; char *d = *data == '@' ? data+1 : data; int l = *data == '@' ? len-1 : len; int f = (*data == '>') ? 1 : 0; if (l > 70 && d[f+0] == 'm' && d[7] == '_' && d[f+14] == '_' && d[f+61] == '/') { prefix_len = 60; // PacBio *is_fixed = 0; } else if (l == 17 && d[f+5] == ':' && d[f+11] == ':') { prefix_len = 6; // IonTorrent *fixed_len = 6; *is_fixed = 1; } else if (l > 37 && d[f+8] == '-' && d[f+13] == '-' && d[f+18] == '-' && d[f+23] == '-' && ((d[f+0] >= '0' && d[f+0] <='9') || (d[f+0] >= 'a' && d[f+0] <= 'f')) && ((d[f+35] >= '0' && d[f+35] <='9') || (d[f+35] >= 'a' && d[f+35] <= 'f'))) { // ONT: f33d30d5-6eb8-4115-8f46-154c2620a5da_Basecall_1D_template... prefix_len = 37; *fixed_len = 37; *is_fixed = 1; } else { // Check Illumina and trim back to lane:tile:x:y. int colons = 0; for (i = 0; i < len && data[i] > ' '; i++) ; while (i > 0 && colons < 4) if (data[--i] == ':') colons++; if (colons == 4) { // Constant illumina prefix *fixed_len = i+1; prefix_len = i+1; *is_fixed = 1; } else { // Unknown, don't use a fixed len, but still search // for any exact matches. prefix_len = INT_MAX; *is_fixed = 0; } } //prefix_len = INT_MAX; if (!ctx->t_head) { ctx->t_head = calloc(1, sizeof(*ctx->t_head)); if (!ctx->t_head) return -1; } // Find an item in the trie for (nlines = i = 0; i < len; i++, nlines++) { t = ctx->t_head; while (i < len && data[i] > '\n') { unsigned char c = data[i++]; if (c & 0x80) //fprintf(stderr, "8-bit ASCII is unsupported\n"); return -1; c &= 127; trie_t *x = t->next; while (x && x->c != c) x = x->sibling; t = x; // t = t->next[c]; // if (!t) // return -1; from = t->n; if (i == prefix_len) p3 = t->n; //if (t->count >= .0035*ctx->t_head->count && t->n != n) p3 = t->n; // pacbio //if (i == 60) p3 = t->n; // pacbio //if (i == 7) p3 = t->n; // iontorrent t->n = n; } } //printf("Looked for %d, found %d, prefix %d\n", n, from, p3); *exact = (n != from) && len; return *exact ? from : p3; } //----------------------------------------------------------------------------- // Name encoder /* * Tokenises a read name using ctx as context as the previous * tokenisation. * * Parsed elements are then emitted for encoding by calling the * encode_token() function with the context, token number (Nth token * in line), token type and token value. * * Returns 0 on success; * -1 on failure. */ static int encode_name(name_context *ctx, char *name, int len, int mode) { int i, is_fixed, fixed_len; int exact; int cnum = ctx->counter++; int pnum = search_trie(ctx, name, len, cnum, &exact, &is_fixed, &fixed_len); if (pnum < 0) pnum = cnum ? cnum-1 : 0; //pnum = pnum & (MAX_NAMES-1); //cnum = cnum & (MAX_NAMES-1); //if (pnum == cnum) {pnum = cnum ? cnum-1 : 0;} #ifdef ENC_DEBUG fprintf(stderr, "%d: pnum=%d (%d), exact=%d\n%s\n%s\n", ctx->counter, pnum, cnum-pnum, exact, ctx->lc[pnum].last_name, name); #endif // Return DUP or DIFF switch, plus the distance. if (exact && len == strlen(ctx->lc[pnum].last_name)) { encode_token_dup(ctx, cnum-pnum); ctx->lc[cnum].last_name = name; ctx->lc[cnum].last_ntok = ctx->lc[pnum].last_ntok; int nc = ctx->lc[cnum].last_ntok ? ctx->lc[cnum].last_ntok : MAX_TOKENS; ctx->lc[cnum].last = malloc(nc * sizeof(*ctx->lc[cnum].last)); if (!ctx->lc[cnum].last) return -1; memcpy(ctx->lc[cnum].last, ctx->lc[pnum].last, ctx->lc[cnum].last_ntok * sizeof(*ctx->lc[cnum].last)); return 0; } ctx->lc[cnum].last = malloc(MAX_TOKENS * sizeof(*ctx->lc[cnum].last)); if (!ctx->lc[cnum].last) return -1; encode_token_diff(ctx, cnum-pnum); int ntok = 1; i = 0; if (is_fixed) { if (ntok >= ctx->max_tok) { memset(&ctx->desc[ctx->max_tok << 4], 0, 16*sizeof(ctx->desc[0])); memset(&ctx->token_dcount[ctx->max_tok], 0, sizeof(int)); memset(&ctx->token_icount[ctx->max_tok], 0, sizeof(int)); ctx->max_tok = ntok+1; } if (pnum < cnum && ntok < ctx->lc[pnum].last_ntok && ctx->lc[pnum].last[ntok].token_type == N_ALPHA) { if (ctx->lc[pnum].last[ntok].token_int == fixed_len && memcmp(name, ctx->lc[pnum].last_name, fixed_len) == 0) { encode_token_match(ctx, ntok); } else { encode_token_alpha(ctx, ntok, name, fixed_len); } } else { encode_token_alpha(ctx, ntok, name, fixed_len); } ctx->lc[cnum].last[ntok].token_int = fixed_len; ctx->lc[cnum].last[ntok].token_str = 0; ctx->lc[cnum].last[ntok++].token_type = N_ALPHA; i = fixed_len; } for (; i < len; i++) { if (ntok >= ctx->max_tok) { if (ctx->max_tok >= MAX_TOKENS) return -1; memset(&ctx->desc[ctx->max_tok << 4], 0, 16*sizeof(ctx->desc[0])); memset(&ctx->token_dcount[ctx->max_tok], 0, sizeof(int)); memset(&ctx->token_icount[ctx->max_tok], 0, sizeof(int)); ctx->max_tok = ntok+1; } /* Determine data type of this segment */ if (isalpha((uint8_t)name[i])) { int s = i+1; // int S = i+1; // // FIXME: try which of these is best. alnum is good sometimes. // while (s < len && isalpha((uint8_t)name[s])) while (s < len && (isalpha((uint8_t)name[s]) || ispunct((uint8_t)name[s]))) // while (s < len && name[s] != ':') // while (s < len && !isdigit((uint8_t)name[s]) && name[s] != ':') s++; // if (!is_fixed) { // while (S < len && isalnum((uint8_t)name[S])) // S++; // if (s < S) // s = S; // } // Single byte strings are better encoded as chars. if (s-i == 1) goto n_char; if (pnum < cnum && ntok < ctx->lc[pnum].last_ntok && ctx->lc[pnum].last[ntok].token_type == N_ALPHA) { if (s-i == ctx->lc[pnum].last[ntok].token_int && memcmp(&name[i], &ctx->lc[pnum].last_name[ctx->lc[pnum].last[ntok].token_str], s-i) == 0) { #ifdef ENC_DEBUG fprintf(stderr, "Tok %d (alpha-mat, %.*s)\n", N_MATCH, s-i, &name[i]); #endif if (encode_token_match(ctx, ntok) < 0) return -1; } else { #ifdef ENC_DEBUG fprintf(stderr, "Tok %d (alpha, %.*s / %.*s)\n", N_ALPHA, s-i, &ctx->lc[pnum].last_name[ctx->lc[pnum].last[ntok].token_str], s-i, &name[i]); #endif // same token/length, but mismatches if (encode_token_alpha(ctx, ntok, &name[i], s-i) < 0) return -1; } } else { #ifdef ENC_DEBUG fprintf(stderr, "Tok %d (new alpha, %.*s)\n", N_ALPHA, s-i, &name[i]); #endif if (encode_token_alpha(ctx, ntok, &name[i], s-i) < 0) return -1; } ctx->lc[cnum].last[ntok].token_int = s-i; ctx->lc[cnum].last[ntok].token_str = i; ctx->lc[cnum].last[ntok].token_type = N_ALPHA; i = s-1; } else if (name[i] == '0') digits0: { // Digits starting with zero; encode length + value uint32_t s = i; uint32_t v = 0; int d = 0; while (s < len && isdigit((uint8_t)name[s]) && s-i < 9) { v = v*10 + name[s] - '0'; //putchar(name[s]); s++; } // TODO: optimise choice over whether to switch from DIGITS to DELTA // regularly vs all DIGITS, also MATCH vs DELTA 0. if (pnum < cnum && ntok < ctx->lc[pnum].last_ntok && ctx->lc[pnum].last[ntok].token_type == N_DIGITS0) { d = v - ctx->lc[pnum].last[ntok].token_int; if (d == 0 && ctx->lc[pnum].last[ntok].token_str == s-i) { #ifdef ENC_DEBUG fprintf(stderr, "Tok %d (dig-mat, %d)\n", N_MATCH, v); #endif if (encode_token_match(ctx, ntok) < 0) return -1; //ctx->lc[pnum].last[ntok].token_delta=0; } else if (mode == 1 && d < 256 && d >= 0 && ctx->lc[pnum].last[ntok].token_str == s-i) { #ifdef ENC_DEBUG fprintf(stderr, "Tok %d (dig0-delta, %d / %d)\n", N_DDELTA0, ctx->lc[pnum].last[ntok].token_int, v); #endif //if (encode_token_int1_(ctx, ntok, N_DZLEN, s-i) < 0) return -1; if (encode_token_int1(ctx, ntok, N_DDELTA0, d) < 0) return -1; //ctx->lc[pnum].last[ntok].token_delta=1; } else { #ifdef ENC_DEBUG fprintf(stderr, "Tok %d (dig0, %d / %d len %d)\n", N_DIGITS0, ctx->lc[pnum].last[ntok].token_int, v, s-i); #endif if (encode_token_int1_(ctx, ntok, N_DZLEN, s-i) < 0) return -1; if (encode_token_int(ctx, ntok, N_DIGITS0, v) < 0) return -1; //ctx->lc[pnum].last[ntok].token_delta=0; } } else { #ifdef ENC_DEBUG fprintf(stderr, "Tok %d (new dig0, %d len %d)\n", N_DIGITS0, v, s-i); #endif if (encode_token_int1_(ctx, ntok, N_DZLEN, s-i) < 0) return -1; if (encode_token_int(ctx, ntok, N_DIGITS0, v) < 0) return -1; //ctx->lc[pnum].last[ntok].token_delta=0; } ctx->lc[cnum].last[ntok].token_str = s-i; // length ctx->lc[cnum].last[ntok].token_int = v; ctx->lc[cnum].last[ntok].token_type = N_DIGITS0; i = s-1; } else if (isdigit((uint8_t)name[i])) { // digits starting 1-9; encode value uint32_t s = i; uint32_t v = 0; int d = 0; while (s < len && isdigit((uint8_t)name[s]) && s-i < 9) { v = v*10 + name[s] - '0'; //putchar(name[s]); s++; } // dataset/10/K562_cytosol_LID8465_TopHat_v2.names // col 4 is Illumina lane - we don't want match & delta in there // as it has multiple lanes (so not ALL match) and delta is just // random chance, increasing entropy instead. // if (ntok == 4 || ntok == 8 || ntok == 10) { // encode_token_int(ctx, ntok, N_DIGITS, v); // } else { // If the last token was DIGITS0 and we are the same length, then encode // using that method instead as it seems likely the entire column is fixed // width, sometimes with leading zeros. if (pnum < cnum && ntok < ctx->lc[pnum].last_ntok && ctx->lc[pnum].last[ntok].token_type == N_DIGITS0 && ctx->lc[pnum].last[ntok].token_str == s-i) goto digits0; // TODO: optimise choice over whether to switch from DIGITS to DELTA // regularly vs all DIGITS, also MATCH vs DELTA 0. if (pnum < cnum && ntok < ctx->lc[pnum].last_ntok && ctx->lc[pnum].last[ntok].token_type == N_DIGITS) { d = v - ctx->lc[pnum].last[ntok].token_int; if (d == 0) { #ifdef ENC_DEBUG fprintf(stderr, "Tok %d (dig-mat, %d)\n", N_MATCH, v); #endif if (encode_token_match(ctx, ntok) < 0) return -1; //ctx->lc[pnum].last[ntok].token_delta=0; //ctx->token_zcount[ntok]++; } else if (mode == 1 && d < 256 && d >= 0 //&& (10+ctx->token_dcount[ntok]) > (ctx->token_icount[ntok]+ctx->token_zcount[ntok]) && (5+ctx->token_dcount[ntok]) > ctx->token_icount[ntok] ) { #ifdef ENC_DEBUG fprintf(stderr, "Tok %d (dig-delta, %d / %d)\n", N_DDELTA, ctx->lc[pnum].last[ntok].token_int, v); #endif if (encode_token_int1(ctx, ntok, N_DDELTA, d) < 0) return -1; //ctx->lc[pnum].last[ntok].token_delta=1; ctx->token_dcount[ntok]++; } else { #ifdef ENC_DEBUG fprintf(stderr, "Tok %d (dig, %d / %d)\n", N_DIGITS, ctx->lc[pnum].last[ntok].token_int, v); #endif if (encode_token_int(ctx, ntok, N_DIGITS, v) < 0) return -1; //ctx->lc[pnum].last[ntok].token_delta=0; ctx->token_icount[ntok]++; } } else { #ifdef ENC_DEBUG fprintf(stderr, "Tok %d (new dig, %d)\n", N_DIGITS, v); #endif if (encode_token_int(ctx, ntok, N_DIGITS, v) < 0) return -1; //ctx->lc[pnum].last[ntok].token_delta=0; } // } ctx->lc[cnum].last[ntok].token_int = v; ctx->lc[cnum].last[ntok].token_type = N_DIGITS; i = s-1; } else { n_char: //if (!isalpha((uint8_t)name[i])) putchar(name[i]); if (pnum < cnum && ntok < ctx->lc[pnum].last_ntok && ctx->lc[pnum].last[ntok].token_type == N_CHAR) { if (name[i] == ctx->lc[pnum].last[ntok].token_int) { #ifdef ENC_DEBUG fprintf(stderr, "Tok %d (chr-mat, %c)\n", N_MATCH, name[i]); #endif if (encode_token_match(ctx, ntok) < 0) return -1; } else { #ifdef ENC_DEBUG fprintf(stderr, "Tok %d (chr, %c / %c)\n", N_CHAR, ctx->lc[pnum].last[ntok].token_int, name[i]); #endif if (encode_token_char(ctx, ntok, name[i]) < 0) return -1; } } else { #ifdef ENC_DEBUG fprintf(stderr, "Tok %d (new chr, %c)\n", N_CHAR, name[i]); #endif if (encode_token_char(ctx, ntok, name[i]) < 0) return -1; } ctx->lc[cnum].last[ntok].token_int = name[i]; ctx->lc[cnum].last[ntok].token_type = N_CHAR; } ntok++; //putchar(' '); } #ifdef ENC_DEBUG fprintf(stderr, "Tok %d (end)\n", N_END); #endif if (ntok >= ctx->max_tok) { if (ctx->max_tok >= MAX_TOKENS) return -1; memset(&ctx->desc[ctx->max_tok << 4], 0, 16*sizeof(ctx->desc[0])); memset(&ctx->token_dcount[ctx->max_tok], 0, sizeof(int)); memset(&ctx->token_icount[ctx->max_tok], 0, sizeof(int)); ctx->max_tok = ntok+1; } if (encode_token_end(ctx, ntok) < 0) return -1; #ifdef ENC_DEBUG fprintf(stderr, "ntok=%d max_tok=%d\n", ntok, ctx->max_tok); #endif //printf("Encoded %.*s with %d tokens\n", len, name, ntok); ctx->lc[cnum].last_name = name; ctx->lc[cnum].last_ntok = ntok; last_context_tok *shrunk = realloc(ctx->lc[cnum].last, (ntok+1) * sizeof(*ctx->lc[cnum].last)); if (shrunk) ctx->lc[cnum].last = shrunk; if (!ctx->lc[cnum].last) return -1; return 0; } //----------------------------------------------------------------------------- // Name decoder static int decode_name(name_context *ctx, char *name, int name_len) { int t0 = decode_token_type(ctx, 0); uint32_t dist; int pnum, cnum = ctx->counter++; if (cnum >= ctx->max_names) return -1; if (t0 < 0 || t0 >= ctx->max_tok*16) return 0; if (decode_token_int(ctx, 0, t0, &dist) < 0 || dist > cnum) return -1; if ((pnum = cnum - dist) < 0) pnum = 0; //fprintf(stderr, "t0=%d, dist=%d, pnum=%d, cnum=%d\n", t0, dist, pnum, cnum); if (t0 == N_DUP) { if (pnum == cnum) return -1; if (strlen(ctx->lc[pnum].last_name) +1 >= name_len) return -1; strcpy(name, ctx->lc[pnum].last_name); // FIXME: optimise this ctx->lc[cnum].last_name = name; ctx->lc[cnum].last_ntok = ctx->lc[pnum].last_ntok; int nc = ctx->lc[cnum].last_ntok ? ctx->lc[cnum].last_ntok : MAX_TOKENS; ctx->lc[cnum].last = malloc(nc * sizeof(*ctx->lc[cnum].last)); if (!ctx->lc[cnum].last) return -1; memcpy(ctx->lc[cnum].last, ctx->lc[pnum].last, ctx->lc[cnum].last_ntok * sizeof(*ctx->lc[cnum].last)); return strlen(name)+1; } *name = 0; int ntok, len = 0, len2; ctx->lc[cnum].last = malloc(MAX_TOKENS * sizeof(*ctx->lc[cnum].last)); if (!ctx->lc[cnum].last) return -1; for (ntok = 1; ntok < MAX_TOKENS && ntok < ctx->max_tok; ntok++) { uint32_t v, vl; enum name_type tok; tok = decode_token_type(ctx, ntok); //fprintf(stderr, "Tok %d = %d\n", ntok, tok); ctx->lc[cnum].last_ntok = 0; switch (tok) { case N_CHAR: if (len+1 >= name_len) return -1; if (decode_token_char(ctx, ntok, &name[len]) < 0) return -1; //fprintf(stderr, "Tok %d CHAR %c\n", ntok, name[len]); ctx->lc[cnum].last[ntok].token_type = N_CHAR; ctx->lc[cnum].last[ntok].token_int = name[len++]; break; case N_ALPHA: if ((len2 = decode_token_alpha(ctx, ntok, &name[len], name_len - len)) < 0) return -1; //fprintf(stderr, "Tok %d ALPHA %.*s\n", ntok, len2, &name[len]); ctx->lc[cnum].last[ntok].token_type = N_ALPHA; ctx->lc[cnum].last[ntok].token_str = len; ctx->lc[cnum].last[ntok].token_int = len2; len += len2; break; case N_DIGITS0: // [0-9]* if (decode_token_int1(ctx, ntok, N_DZLEN, &vl) < 0) return -1; if (decode_token_int(ctx, ntok, N_DIGITS0, &v) < 0) return -1; if (len+20+vl >= name_len) return -1; len += append_uint32_fixed(&name[len], v, vl); //fprintf(stderr, "Tok %d DIGITS0 %0*d\n", ntok, vl, v); ctx->lc[cnum].last[ntok].token_type = N_DIGITS0; ctx->lc[cnum].last[ntok].token_int = v; ctx->lc[cnum].last[ntok].token_str = vl; break; case N_DDELTA0: if (ntok >= ctx->lc[pnum].last_ntok) return -1; if (decode_token_int1(ctx, ntok, N_DDELTA0, &v) < 0) return -1; v += ctx->lc[pnum].last[ntok].token_int; if (len+ctx->lc[pnum].last[ntok].token_str+1 >= name_len) return -1; len += append_uint32_fixed(&name[len], v, ctx->lc[pnum].last[ntok].token_str); //fprintf(stderr, "Tok %d DELTA0 %0*d\n", ntok, ctx->lc[pnum].last[ntok].token_str, v); ctx->lc[cnum].last[ntok].token_type = N_DIGITS0; ctx->lc[cnum].last[ntok].token_int = v; ctx->lc[cnum].last[ntok].token_str = ctx->lc[pnum].last[ntok].token_str; break; case N_DIGITS: // [1-9][0-9]* if (decode_token_int(ctx, ntok, N_DIGITS, &v) < 0) return -1; if (len+20 >= name_len) return -1; len += append_uint32_var(&name[len], v); //fprintf(stderr, "Tok %d DIGITS %d\n", ntok, v); ctx->lc[cnum].last[ntok].token_type = N_DIGITS; ctx->lc[cnum].last[ntok].token_int = v; break; case N_DDELTA: if (ntok >= ctx->lc[pnum].last_ntok) return -1; if (decode_token_int1(ctx, ntok, N_DDELTA, &v) < 0) return -1; v += ctx->lc[pnum].last[ntok].token_int; if (len+20 >= name_len) return -1; len += append_uint32_var(&name[len], v); //fprintf(stderr, "Tok %d DELTA %d\n", ntok, v); ctx->lc[cnum].last[ntok].token_type = N_DIGITS; ctx->lc[cnum].last[ntok].token_int = v; break; case N_NOP: ctx->lc[cnum].last[ntok].token_type = N_NOP; break; case N_MATCH: if (ntok >= ctx->lc[pnum].last_ntok) return -1; switch (ctx->lc[pnum].last[ntok].token_type) { case N_CHAR: if (len+1 >= name_len) return -1; name[len++] = ctx->lc[pnum].last[ntok].token_int; //fprintf(stderr, "Tok %d MATCH CHAR %c\n", ntok, ctx->lc[pnum].last[ntok].token_int); ctx->lc[cnum].last[ntok].token_type = N_CHAR; ctx->lc[cnum].last[ntok].token_int = ctx->lc[pnum].last[ntok].token_int; break; case N_ALPHA: if (ctx->lc[pnum].last[ntok].token_int < 0 || len+ctx->lc[pnum].last[ntok].token_int >= name_len) return -1; memcpy(&name[len], &ctx->lc[pnum].last_name[ctx->lc[pnum].last[ntok].token_str], ctx->lc[pnum].last[ntok].token_int); //fprintf(stderr, "Tok %d MATCH ALPHA %.*s\n", ntok, ctx->lc[pnum].last[ntok].token_int, &name[len]); ctx->lc[cnum].last[ntok].token_type = N_ALPHA; ctx->lc[cnum].last[ntok].token_str = len; ctx->lc[cnum].last[ntok].token_int = ctx->lc[pnum].last[ntok].token_int; len += ctx->lc[pnum].last[ntok].token_int; break; case N_DIGITS: if (len+20 >= name_len) return -1; len += append_uint32_var(&name[len], ctx->lc[pnum].last[ntok].token_int); //fprintf(stderr, "Tok %d MATCH DIGITS %d\n", ntok, ctx->lc[pnum].last[ntok].token_int); ctx->lc[cnum].last[ntok].token_type = N_DIGITS; ctx->lc[cnum].last[ntok].token_int = ctx->lc[pnum].last[ntok].token_int; break; case N_DIGITS0: if (len+ctx->lc[pnum].last[ntok].token_str >= name_len) return -1; len += append_uint32_fixed(&name[len], ctx->lc[pnum].last[ntok].token_int, ctx->lc[pnum].last[ntok].token_str); //fprintf(stderr, "Tok %d MATCH DIGITS %0*d\n", ntok, ctx->lc[pnum].last[ntok].token_str, ctx->lc[pnum].last[ntok].token_int); ctx->lc[cnum].last[ntok].token_type = N_DIGITS0; ctx->lc[cnum].last[ntok].token_int = ctx->lc[pnum].last[ntok].token_int; ctx->lc[cnum].last[ntok].token_str = ctx->lc[pnum].last[ntok].token_str; break; default: return -1; } break; default: // an elided N_END case N_END: if (len+1 >= name_len) return -1; name[len++] = 0; ctx->lc[cnum].last[ntok].token_type = N_END; ctx->lc[cnum].last_name = name; ctx->lc[cnum].last_ntok = ntok; last_context_tok *shrunk = realloc(ctx->lc[cnum].last, (ntok+1) * sizeof(*ctx->lc[cnum].last)); if (shrunk) ctx->lc[cnum].last = shrunk; if (!ctx->lc[cnum].last) return -1; return len; } } return -1; } //----------------------------------------------------------------------------- // arith adaptive codec or static rANS 4x16pr codec static int arith_encode(uint8_t *in, uint64_t in_len, uint8_t *out, uint64_t *out_len, int method) { unsigned int olen = *out_len-6, nb; if (arith_compress_to(in, in_len, out+6, &olen, method) == NULL) return -1; nb = var_put_u32(out, out + *out_len, olen); memmove(out+nb, out+6, olen); *out_len = olen+nb; return 0; } // Returns number of bytes read from 'in' on success, // -1 on failure. static int64_t arith_decode(uint8_t *in, uint64_t in_len, uint8_t *out, uint64_t *out_len) { unsigned int olen = *out_len; uint32_t clen; int nb = var_get_u32(in, in+in_len, &clen); //fprintf(stderr, "Arith decode %x\n", in[nb]); if (arith_uncompress_to(in+nb, in_len-nb, out, &olen) == NULL) return -1; //fprintf(stderr, " Stored clen=%d\n", (int)clen); *out_len = olen; return clen+nb; } static int rans_encode(uint8_t *in, uint64_t in_len, uint8_t *out, uint64_t *out_len, int method) { unsigned int olen = *out_len-6, nb; if (rans_compress_to_4x16(in, in_len, out+6, &olen, method) == NULL) return -1; nb = var_put_u32(out, out + *out_len, olen); memmove(out+nb, out+6, olen); *out_len = olen+nb; return 0; } // Returns number of bytes read from 'in' on success, // -1 on failure. static int64_t rans_decode(uint8_t *in, uint64_t in_len, uint8_t *out, uint64_t *out_len) { unsigned int olen = *out_len; uint32_t clen; int nb = var_get_u32(in, in+in_len, &clen); //fprintf(stderr, "Arith decode %x\n", in[nb]); if (rans_uncompress_to_4x16(in+nb, in_len-nb, out, &olen) == NULL) return -1; //fprintf(stderr, " Stored clen=%d\n", (int)clen); *out_len = olen; return clen+nb; } static int compress(uint8_t *in, uint64_t in_len, enum name_type type, int level, int use_arith, uint8_t *out, uint64_t *out_len) { uint64_t best_sz = UINT64_MAX; uint64_t olen = *out_len; int ret = -1; // Map levels 1-9 to 0-4, for parameter lookup in R[] below level = (level-1)/2; if (level<0) level=0; if (level>4) level=4; // rANS4x16pr and arith_dynamic parameters to explore. // We brute force these, so fast levels test 1 setting and slow test more int R[5][N_ALL][7] = { { // -1 /* TYPE */ {1, 128}, /* ALPHA */ {1, 129}, /* CHAR */ {1, 0}, /* DIGITS0 */ {1, 8}, /* DZLEN */ {1, 0}, /* DUP */ {1, 8}, /* DIFF */ {1, 8}, /* DIGITS */ {1, 8}, /* DDELTA */ {1, 0}, /* DDELTA0 */ {1, 128}, /* MATCH */ {1, 0}, /* NOP */ {1, 0}, /* END */ {1, 0} }, { // -3 /* TYPE */ {2, 192,0}, /* ALPHA */ {2, 129,1}, /* CHAR */ {1, 0}, /* DIGITS0 */ {2, 128+8,0}, // size%4==0 /* DZLEN */ {1, 0}, /* DUP */ {1, 192+8}, // size%4==0 /* DIFF */ {1, 128+8}, // size%4==0 /* DIGITS */ {1, 192+8}, // size%4==0 /* DDELTA */ {1, 0}, /* DDELTA0 */ {1, 128}, /* MATCH */ {1, 0}, /* NOP */ {1, 0}, /* END */ {1, 0} }, { // -5 /* TYPE */ {2, 192,0}, /* ALPHA */ {4, 1,128,0,129}, /* CHAR */ {1, 0}, /* DIGITS0 */ {2, 200,0}, /* DZLEN */ {1, 0}, /* DUP */ {1, 200}, /* DIFF */ {2, 192,200}, /* DIGITS */ {2, 132,201}, /* DDELTA */ {1, 0}, /* DDELTA0 */ {1, 128}, /* MATCH */ {1, 0}, /* NOP */ {1, 0}, /* END */ {1, 0} }, { // -7 /* TYPE */ {3, 193,0,1}, /* ALPHA */ {5, 128, 1,128,0,129}, /* CHAR */ {2, 1,0}, /* DIGITS0 */ {2, 200,0}, // or 201,0 /* DZLEN */ {1, 0}, /* DUP */ {1, 201}, /* DIFF */ {2, 192,200}, // or 192,201 /* DIGITS */ {2, 132, 201}, // +bz2 here and -9 /* DDELTA */ {1, 0}, /* DDELTA0 */ {1, 128}, /* MATCH */ {1, 0}, /* NOP */ {1, 0}, /* END */ {1, 0} }, { // -9 /* TYPE */ {6, 192,0,1, 65, 193,132}, /* ALPHA */ {4, 132, 1, 0,129}, /* CHAR */ {3, 1,0,192}, /* DIGITS0 */ {4, 201,0, 192,64}, /* DZLEN */ {3, 0,128,1}, /* DUP */ {1, 201}, /* DIFF */ {3, 192, 201,65}, /* DIGITS */ {6, 132, 201,1, 192,129, 193}, /* DDELTA */ {3, 1,0, 192}, /* DDELTA0 */ {3, 192,1, 0}, /* MATCH */ {1, 0}, /* NOP */ {1, 0}, /* END */ {1, 0} }, }; // Minor tweak to level 3 DIGITS if arithmetic, to use O(201) instead. if (use_arith) R[1][N_DIGITS][1]=201; int *meth = R[level][type]; int last = 0, m; uint8_t best_static[8192]; uint8_t *best_dat = best_static; for (m = 1; m <= meth[0]; m++) { *out_len = olen; if (!use_arith && (meth[m] & 4)) meth[m] &= ~4; if (in_len % 4 != 0 && (meth[m] & 8)) continue; last = 0; if (use_arith) { if (arith_encode(in, in_len, out, out_len, meth[m]) <0) goto err; } else { if (rans_encode(in, in_len, out, out_len, meth[m]) < 0) goto err; } if (best_sz > *out_len) { best_sz = *out_len; last = 1; if (m+1 > meth[0]) // no need to memcpy if we're not going to overwrite out break; if (best_sz > 8192 && best_dat == best_static) { // No need to realloc as best_sz only ever decreases best_dat = malloc(best_sz); if (!best_dat) return -1; } memcpy(best_dat, out, best_sz); } } if (!last) memcpy(out, best_dat, best_sz); *out_len = best_sz; ret = 0; err: if (best_dat != best_static) free(best_dat); return ret; } static uint64_t uncompressed_size(uint8_t *in, uint64_t in_len) { uint32_t clen, ulen; // in[0] in part of buffer written by us int nb = var_get_u32(in, in+in_len, &clen); // in[nb] is part of buffer written to by arith_dynamic. var_get_u32(in+nb+1, in+in_len, &ulen); return ulen; } static int uncompress(int use_arith, uint8_t *in, uint64_t in_len, uint8_t *out, uint64_t *out_len) { uint32_t clen; var_get_u32(in, in+in_len, &clen); return use_arith ? arith_decode(in, in_len, out, out_len) : rans_decode(in, in_len, out, out_len); } //----------------------------------------------------------------------------- /* * Converts a line or \0 separated block of reading names to a compressed buffer. * The code can only encode whole lines and will not attempt a partial line. * Use the "last_start_p" return value to identify the partial line start * offset, for continuation purposes. * * Returns a malloced buffer holding compressed data of size *out_len, * or NULL on failure */ uint8_t *tok3_encode_names(char *blk, int len, int level, int use_arith, int *out_len, int *last_start_p) { int last_start = 0, i, j, nreads; if (len < 0) { *out_len = 0; return NULL; } // Count lines for (nreads = i = 0; i < len; i++) if (blk[i] <= '\n') // \n or \0 separated entries nreads++; name_context *ctx = create_context(nreads); if (!ctx) return NULL; // Construct trie int ctr = 0; for (i = j = 0; i < len; j=++i) { while (i < len && blk[i] > '\n') i++; if (i >= len) break; //blk[i] = '\0'; last_start = i+1; if (build_trie(ctx, &blk[j], i-j, ctr++) < 0) { free_context(ctx); return NULL; } } if (last_start_p) *last_start_p = last_start; //fprintf(stderr, "Processed %d of %d in block, line %d\n", last_start, len, ctr); // Encode name for (i = j = 0; i < len; j=++i) { while (i < len && (signed char)blk[i] >= ' ') // non-ASCII check i++; if (i >= len) break; if (blk[i] != '\0' && blk[i] != '\n') { // Names must be 7-bit ASCII printable free_context(ctx); return NULL; } blk[i] = '\0'; // try both 0 and 1 and pick best? if (encode_name(ctx, &blk[j], i-j, 1) < 0) { free_context(ctx); return NULL; } } #if 0 for (i = 0; i < ctx->max_tok*16; i++) { char fn[1024]; if (!ctx->desc[i].buf_l) continue; sprintf(fn, "_tok.%02d_%02d.%d", i>>4,i&15,i); FILE *fp = fopen(fn, "w"); fwrite(ctx->desc[i].buf, 1, ctx->desc[i].buf_l, fp); fclose(fp); } #endif //dump_trie(t_head, 0); // FIXME: merge descriptors // // If we see foo7:1 foo7:12 foo7:7 etc then foo: is constant, // but it's encoded as alpha+dig<7>+char<:> instead of alpha. // Any time token type 0 is all match beyond the first location we have // a candidate for merging in string form. // // This saves around .1 to 1.3 percent on varying data sets. // Cruder hack is dedicated prefix/suffix matching to short-cut this. // Drop N_TYPE blocks if they all contain matches bar the first item, // as we can regenerate these from the subsequent blocks types during // decode. for (i = 0; i < ctx->max_tok*16; i+=16) { if (!ctx->desc[i].buf_l) continue; int z; for (z=1; zdesc[i].buf_l; z++) { if (ctx->desc[i].buf[z] != N_MATCH) break; } if (z == ctx->desc[i].buf_l) { int k; for (k=1; k<16; k++) if (ctx->desc[i+k].buf_l) break; if (k < 16) { ctx->desc[i].buf_l = 0; free(ctx->desc[i].buf); ctx->desc[i].buf = NULL; } } } // Serialise descriptors uint32_t tot_size = 9; for (i = 0; i < ctx->max_tok*16; i++) { if (!ctx->desc[i].buf_l) continue; int tnum = i>>4; int ttype = i&15; uint64_t out_len = 1.5 * arith_compress_bound(ctx->desc[i].buf_l, 1); // guesswork uint8_t *out = malloc(out_len); if (!out) { free_context(ctx); return NULL; } if (compress(ctx->desc[i].buf, ctx->desc[i].buf_l, i&0xf, level, use_arith, out, &out_len) < 0) { free_context(ctx); return NULL; } free(ctx->desc[i].buf); ctx->desc[i].buf = out; ctx->desc[i].buf_l = out_len; ctx->desc[i].tnum = tnum; ctx->desc[i].ttype = ttype; // Find dups int j; for (j = 0; j < i; j++) { if (!ctx->desc[j].buf) continue; if (ctx->desc[i].buf_l != ctx->desc[j].buf_l || ctx->desc[i].buf_l <= 4) continue; if (memcmp(ctx->desc[i].buf, ctx->desc[j].buf, ctx->desc[i].buf_l) == 0) break; } if (j < i) { ctx->desc[i].dup_from = j; tot_size += 3; // flag, dup_from, ttype } else { ctx->desc[i].dup_from = -1; tot_size += out_len + 1; // ttype } } #if 0 for (i = 0; i < ctx->max_tok*16; i++) { char fn[1024]; if (!ctx->desc[i].buf_l && ctx->desc[i].dup_from == -1) continue; sprintf(fn, "_tok.%02d_%02d.%d.comp", i>>4,i&15,i); FILE *fp = fopen(fn, "w"); fwrite(ctx->desc[i].buf, 1, ctx->desc[i].buf_l, fp); fclose(fp); } #endif // Write uint8_t *out = malloc(tot_size+13); if (!out) { free_context(ctx); return NULL; } uint8_t *cp = out; *out_len = tot_size; // *(uint32_t *)cp = last_start; cp += 4; // *(uint32_t *)cp = nreads; cp += 4; *cp++ = (last_start >> 0) & 0xff; *cp++ = (last_start >> 8) & 0xff; *cp++ = (last_start >> 16) & 0xff; *cp++ = (last_start >> 24) & 0xff; *cp++ = (nreads >> 0) & 0xff; *cp++ = (nreads >> 8) & 0xff; *cp++ = (nreads >> 16) & 0xff; *cp++ = (nreads >> 24) & 0xff; *cp++ = use_arith; //write(1, &nreads, 4); int last_tnum = -1; for (i = 0; i < ctx->max_tok*16; i++) { if (!ctx->desc[i].buf_l) continue; uint8_t ttype8 = ctx->desc[i].ttype; if (ctx->desc[i].tnum != last_tnum) { ttype8 |= 128; last_tnum = ctx->desc[i].tnum; } if (ctx->desc[i].dup_from >= 0) { //fprintf(stderr, "Dup %d from %d, sz %d\n", i, ctx->desc[i].dup_from, ctx->desc[i].buf_l); *cp++ = ttype8 | 64; *cp++ = ctx->desc[i].dup_from >> 4; *cp++ = ctx->desc[i].dup_from & 15; } else { *cp++ = ttype8; memcpy(cp, ctx->desc[i].buf, ctx->desc[i].buf_l); cp += ctx->desc[i].buf_l; } } //assert(cp-out == tot_size); free_context(ctx); return out; } // Deprecated interface; to remove when we next to an ABI breakage uint8_t *encode_names(char *blk, int len, int level, int use_arith, int *out_len, int *last_start_p) { return tok3_encode_names(blk, len, level, use_arith, out_len, last_start_p); } /* * Decodes a compressed block of read names into \0 separated names. * The size of the data returned (malloced) is in *out_len. * * Returns NULL on failure. */ uint8_t *tok3_decode_names(uint8_t *in, uint32_t sz, uint32_t *out_len) { if (sz < 9) return NULL; int i, o = 9; //int ulen = *(uint32_t *)in; int ulen = (in[0]<<0) | (in[1]<<8) | (in[2]<<16) | (((uint32_t)in[3])<<24); if (ulen < 0 || ulen >= INT_MAX-1024) return NULL; #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION // Speed up fuzzing by blocking excessive sizes if (ulen > 100000) return NULL; #endif //int nreads = *(uint32_t *)(in+4); int nreads = (in[4]<<0) | (in[5]<<8) | (in[6]<<16) | (((uint32_t)in[7])<<24); int use_arith = in[8]; name_context *ctx = create_context(nreads); if (!ctx) return NULL; // Unpack descriptors int tnum = -1; while (o < sz) { uint8_t ttype = in[o++]; if (ttype & 64) { if (o+2 > sz) goto err; int j = in[o++]<<4; j += in[o++]; if (ttype & 128) { tnum++; if (tnum >= MAX_TOKENS) goto err; ctx->max_tok = tnum+1; memset(&ctx->desc[tnum<<4], 0, 16*sizeof(ctx->desc[tnum])); } if ((ttype & 15) != 0 && (ttype & 128)) { if (tnum < 0) goto err; ctx->desc[tnum<<4].buf = malloc(nreads); if (!ctx->desc[tnum<<4].buf) goto err; ctx->desc[tnum<<4].buf_l = 0; ctx->desc[tnum<<4].buf_a = nreads; ctx->desc[tnum<<4].buf[0] = ttype&15; memset(&ctx->desc[tnum<<4].buf[1], N_MATCH, nreads-1); } if (tnum < 0) goto err; i = (tnum<<4) | (ttype&15); if (j >= i) goto err; if (!ctx->desc[j].buf) goto err; // Attempt to copy a non-existent stream ctx->desc[i].buf_l = 0; ctx->desc[i].buf_a = ctx->desc[j].buf_a; if (ctx->desc[i].buf) free(ctx->desc[i].buf); ctx->desc[i].buf = malloc(ctx->desc[i].buf_a); if (!ctx->desc[i].buf) goto err; memcpy(ctx->desc[i].buf, ctx->desc[j].buf, ctx->desc[i].buf_a); //fprintf(stderr, "Copy ttype %d, i=%d,j=%d, size %d\n", ttype, i, j, (int)ctx->desc[i].buf_a); continue; } //if (ttype == 0) if (ttype & 128) { tnum++; if (tnum >= MAX_TOKENS) goto err; ctx->max_tok = tnum+1; memset(&ctx->desc[tnum<<4], 0, 16*sizeof(ctx->desc[tnum])); } if ((ttype & 15) != 0 && (ttype & 128)) { if (tnum < 0) goto err; if (ctx->desc[tnum<<4].buf) free(ctx->desc[tnum<<4].buf); ctx->desc[tnum<<4].buf = malloc(nreads); if (!ctx->desc[tnum<<4].buf) goto err; ctx->desc[tnum<<4].buf_l = 0; ctx->desc[tnum<<4].buf_a = nreads; ctx->desc[tnum<<4].buf[0] = ttype&15; memset(&ctx->desc[tnum<<4].buf[1], N_MATCH, nreads-1); } //fprintf(stderr, "Read %02x\n", c); // Load compressed block int64_t clen, ulen = uncompressed_size(&in[o], sz-o); if (ulen < 0 || ulen >= INT_MAX) goto err; if (tnum < 0) goto err; i = (tnum<<4) | (ttype&15); if (i >= MAX_TBLOCKS || i < 0) goto err; ctx->desc[i].buf_l = 0; if (ctx->desc[i].buf) free(ctx->desc[i].buf); ctx->desc[i].buf = malloc(ulen); if (!ctx->desc[i].buf) goto err; ctx->desc[i].buf_a = ulen; uint64_t usz = ctx->desc[i].buf_a; // convert from size_t for 32-bit sys clen = uncompress(use_arith, &in[o], sz-o, ctx->desc[i].buf, &usz); ctx->desc[i].buf_a = usz; if (clen < 0 || ctx->desc[i].buf_a != ulen) goto err; // fprintf(stderr, "%d: Decode tnum %d type %d clen %d ulen %d via %d\n", // o, tnum, ttype, (int)clen, (int)ctx->desc[i].buf_a, ctx->desc[i].buf[0]); o += clen; // Encode tnum 0 type 0 ulen 100000 clen 12530 via 2 // Encode tnum 0 type 6 ulen 196800 clen 43928 via 3 // Encode tnum 0 type 7 ulen 203200 clen 17531 via 3 // Encode tnum 1 type 0 ulen 50800 clen 10 via 1 // Encode tnum 1 type 1 ulen 3 clen 5 via 0 // Encode tnum 2 type 0 ulen 50800 clen 10 via 1 // } int ret; ulen += 1024; // for easy coding in decode_name. uint8_t *out = malloc(ulen); if (!out) goto err; size_t out_sz = 0; while ((ret = decode_name(ctx, (char *)out+out_sz, ulen)) > 0) { out_sz += ret; ulen -= ret; } if (ret < 0) free(out); free_context(ctx); *out_len = out_sz; return ret == 0 ? out : NULL; err: free_context(ctx); return NULL; } // Deprecated interface; to remove when we next to an ABI breakage uint8_t *decode_names(uint8_t *in, uint32_t sz, uint32_t *out_len) { return tok3_decode_names(in, sz, out_len); } pysam-0.23.0/htslib/htscodecs/htscodecs/tokenise_name3.h000066400000000000000000000050321475062545500232420ustar00rootroot00000000000000/* * Copyright (c) 2017, 2019 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef _TOKENISE_NAME3_H_ #define _TOKENISE_NAME3_H_ #ifdef __cplusplus extern "C" { #endif /* * Converts a line or \0 separated block of reading names to a compressed buffer. * The code can only encode whole lines and will not attempt a partial line. * Use the "last_start_p" return value to identify the partial line start * offset, for continuation purposes. * * Returns a malloced buffer holding compressed data of size *out_len, * or NULL on failure */ uint8_t *tok3_encode_names(char *blk, int len, int level, int use_arith, int *out_len, int *last_start_p); /* * Decodes a compressed block of read names into \0 separated names. * The size of the data returned (malloced) is in *out_len. * * Returns NULL on failure. */ uint8_t *tok3_decode_names(uint8_t *in, uint32_t sz, uint32_t *out_len); #ifdef __cplusplus } #endif #endif /* _TOKENISE_NAME3_H_ */ pysam-0.23.0/htslib/htscodecs/htscodecs/utils.c000066400000000000000000000166501475062545500215010ustar00rootroot00000000000000/* * Copyright (c) 2022 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #include "config.h" #include #include #include #include #include "utils.h" #ifndef NO_THREADS #include #endif //#define TLS_DEBUG #ifndef NO_THREADS /* * Thread local storage per thread in the pool. * * We have some large memory blocks for rANS which we cannot store on the * stack due to various system limitations. Allocaitng them can be * expensive as some OSes use mmap and will pass the pages back to the OS * on each free. This unfortunately then means zeroing the pages out again * on each new malloc, plus additional switching into the kernel. * * Instead where available, we use pthread_once to allocate a small arena * of memory buffers and we continually reuse these same buffers. We don't * need to memset it (calloc equivalent) either as we're sure that any * leakage of data is simply an earlier set of precomputed frequency * lookups, and not something more sinister such as an encryption key. * * If we don't have pthreads, then we have to fall back to the slow * traditional calloc instead. */ #define MAX_TLS_BUFS 10 typedef struct { void *bufs[MAX_TLS_BUFS]; size_t sizes[MAX_TLS_BUFS]; int used[MAX_TLS_BUFS]; } tls_pool; static pthread_once_t rans_once = PTHREAD_ONCE_INIT; static pthread_key_t rans_key; /* * Frees all local storage for this thread. * Note: this isn't a function to free a specific allocated item. */ static void htscodecs_tls_free_all(void *ptr) { tls_pool *tls = (tls_pool *)ptr; if (!tls) return; int i; for (i = 0; i < MAX_TLS_BUFS; i++) { #ifdef TLS_DEBUG if (tls->bufs[i]) fprintf(stderr, "Free %ld = %p\n", tls->sizes[i], tls->bufs[i]); #endif if (tls->used[i]) { fprintf(stderr, "Closing thread while TLS data is in use\n"); } free(tls->bufs[i]); } free(tls); } static void htscodecs_tls_init(void) { pthread_key_create(&rans_key, htscodecs_tls_free_all); } /* * Allocates size bytes from the global Thread Local Storage pool. * This is shared by all subsequent calls within this thread. * * An simpler alternative could be possible where we have a fixed number * of types of alloc, say 5, and specify the correct label when allocating. * Eg histogram, name_context, fqzcomp, rans. We can have multiple types * in use in different stack frames (such name_context + hist + rans), but * the number is very limited. That then paves the way to simply check and * realloc without needing to keep track of use status or overflowing * the maximum number permitted. */ void *htscodecs_tls_alloc(size_t size) { int i; int err = pthread_once(&rans_once, htscodecs_tls_init); if (err != 0) { fprintf(stderr, "Initialising TLS data failed: pthread_once: %s\n", strerror(err)); return NULL; } // Initialise tls_pool on first usage tls_pool *tls = pthread_getspecific(rans_key); if (!tls) { if (!(tls = calloc(1, sizeof(*tls)))) return NULL; pthread_setspecific(rans_key, tls); } // Query pool for size int avail = -1; for (i = 0; i < MAX_TLS_BUFS; i++) { if (!tls->used[i]) { if (size <= tls->sizes[i]) { tls->used[i] = 1; #ifdef TLS_DEBUG fprintf(stderr, "Reuse %d: %ld/%ld = %p\n", i, size, tls->sizes[i], tls->bufs[i]); #endif return tls->bufs[i]; } else if (avail == -1) { avail = i; } } } if (i == MAX_TLS_BUFS && avail == -1) { // Shouldn't happen given our very limited use of this function fprintf(stderr, "Error: out of rans_tls_alloc slots\n"); return NULL; } if (tls->bufs[avail]) free(tls->bufs[avail]); if (!(tls->bufs[avail] = calloc(1, size))) return NULL; #ifdef TLS_DEBUG fprintf(stderr, "Alloc %d: %ld = %p\n", avail, size, tls->bufs[avail]); #endif tls->sizes[avail] = size; tls->used[avail] = 1; return tls->bufs[avail]; } void *htscodecs_tls_calloc(size_t nmemb, size_t size) { #ifdef TLS_DEBUG fprintf(stderr, "htscodecs_tls_calloc(%ld)\n", nmemb*size); #endif void *ptr = htscodecs_tls_alloc(nmemb * size); if (ptr) memset(ptr, 0, nmemb * size); return ptr; } void htscodecs_tls_free(void *ptr) { if (!ptr) return; tls_pool *tls = pthread_getspecific(rans_key); int i; for (i = 0; i < MAX_TLS_BUFS; i++) { if (tls->bufs[i] == ptr) break; } #ifdef TLS_DEBUG fprintf(stderr, "Fake free %d size %ld ptr %p\n", i, tls->sizes[i], tls->bufs[i]); #endif if (i == MAX_TLS_BUFS) { fprintf(stderr, "Attempt to htscodecs_tls_free a buffer not allocated" " with htscodecs_tls_alloc\n"); return; } if (!tls->used[i]) { fprintf(stderr, "Attempt to htscodecs_tls_free a buffer twice\n"); return; } tls->used[i] = 0; } #else /* * Calloc/free equivalents instead. * * We use calloc instead of malloc as a sufficiently malformed set of input * frequencies may not sum to the expected total frequency size, leaving * some elements uninitialised. It's unlikely, but potentially a crafty * attacker could somehow exploit this to pull out parts of this allocated * buffer and leak them into the decompressed data stream, potentially * compromising previous buffers such as encryption keys. (Although * frankly any well-written crypto library should be zeroing such memory * before freeing it to ensure it's never visible to a subsequent malloc.) */ void *htscodecs_tls_alloc(size_t size) { return calloc(1, size); } void *htscodecs_tls_calloc(size_t nmemb, size_t size) { return calloc(nmemb, size); } void htscodecs_tls_free(void *ptr) { free(ptr); } #endif pysam-0.23.0/htslib/htscodecs/htscodecs/utils.h000066400000000000000000000270231475062545500215020ustar00rootroot00000000000000/* * Copyright (c) 2019-2022 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef RANS_UTILS_H #define RANS_UTILS_H #include #include #include #if defined(__GNUC__) || defined(__clang__) # if !defined(__clang__) && __GNUC__ >= 100 // better still on gcc10 for O1 decode of old rans 4x8 // gcc 10=246/205 11=243/205 12=230/197 # define likely(x) __builtin_expect_with_probability((x), 1, 0.99) # else // gcc 10=193/168 11=195/161 12=199/176 # define likely(x) __builtin_expect((x), 1) # endif # define unlikely(x) __builtin_expect((x), 0) #else # define likely(x) (x) # define unlikely(x) (x) #endif /* * Allocates size bytes from the global Thread Local Storage pool. * This is shared by all subsequent calls within this thread. * * Note this is NOT a general purpose allocator and usage outside of this * library is not advised due to assumptions and limitations in the design. */ void *htscodecs_tls_alloc(size_t size); void *htscodecs_tls_calloc(size_t nmemb, size_t size); void htscodecs_tls_free(void *ptr); /* Fast approximate log base 2 */ static inline double fast_log(double a) { union { double d; long long x; } u = { a }; return (u.x - 4606921278410026770) * 1.539095918623324e-16; /* 1 / 6497320848556798.0; */ } /* * Data transpose by N. Common to rANS4x16 and arith_dynamic decoders. * * Tuned for specific common cases of N. */ static inline void unstripe(unsigned char *out, unsigned char *outN, unsigned int ulen, unsigned int N, unsigned int idxN[256]) { int j = 0, k; if (ulen >= N) { switch (N) { case 4: #define LLN 16 if (ulen >= 4*LLN) { while (j < ulen-4*LLN) { int l; for (l = 0; l < LLN; l++) { for (k = 0; k < 4; k++) out[j+k+l*4] = outN[idxN[k]+l]; } for (k = 0; k < 4; k++) idxN[k] += LLN; j += 4*LLN; } } while (j < ulen-4) { for (k = 0; k < 4; k++) out[j++] = outN[idxN[k]++]; } #undef LLN break; case 2: #define LLN 4 if (ulen >= 2*LLN) { while (j < ulen-2*LLN) { int l; for (l = 0; l < LLN; l++) { for (k = 0; k < 2; k++) out[j++] = outN[idxN[k]+l]; } for (k = 0; k < 2; k++) idxN[k] += l; } } while (j < ulen-2) { for (k = 0; k < 2; k++) out[j++] = outN[idxN[k]++]; } #undef LLN break; default: // General case, around 25% slower overall decode while (j < ulen-N) { for (k = 0; k < N; k++) out[j++] = outN[idxN[k]++]; } break; } } for (k = 0; j < ulen; k++) out[j++] = outN[idxN[k]++]; } #define MAGIC 8 /* * Order 0 histogram construction. 8-way unrolled to avoid cache collisions. */ static inline int hist8(unsigned char *in, unsigned int in_size, uint32_t F0[256]) { if (in_size > 500000) { uint32_t *f0 = htscodecs_tls_calloc((65536+37)*3, sizeof(*f0)); if (f0 == NULL) return -1; uint32_t *f1 = f0 + 65536+37; uint32_t *f2 = f1 + 65536+37; uint32_t i, i8 = in_size & ~15; for (i = 0; i < i8; i+=16) { uint16_t i16a[4], i16b[4]; memcpy(i16a, in+i, 8); f0[i16a[0]]++; f1[i16a[1]]++; f2[i16a[2]]++; f0[i16a[3]]++; memcpy(i16b, in+i+8, 8); f1[i16b[0]]++; f0[i16b[1]]++; f1[i16b[2]]++; f2[i16b[3]]++; } while (i < in_size) F0[in[i++]]++; for (i = 0; i < 65536; i++) { F0[i & 0xff] += f0[i] + f1[i] + f2[i]; F0[i >> 8 ] += f0[i] + f1[i] + f2[i]; } htscodecs_tls_free(f0); } else { uint32_t F1[256+MAGIC] = {0}, F2[256+MAGIC] = {0}, F3[256+MAGIC] = {0}; uint32_t i, i8 = in_size & ~7; for (i = 0; i < i8; i+=8) { F0[in[i+0]]++; F1[in[i+1]]++; F2[in[i+2]]++; F3[in[i+3]]++; F0[in[i+4]]++; F1[in[i+5]]++; F2[in[i+6]]++; F3[in[i+7]]++; } while (i < in_size) F0[in[i++]]++; for (i = 0; i < 256; i++) F0[i] += F1[i] + F2[i] + F3[i]; } return 0; } // Hist8 with a crude entropy (bits / byte) estimator. static inline double hist8e(unsigned char *in, unsigned int in_size, uint32_t F0[256]) { uint32_t F1[256+MAGIC] = {0}, F2[256+MAGIC] = {0}, F3[256+MAGIC] = {0}; uint32_t F4[256+MAGIC] = {0}, F5[256+MAGIC] = {0}, F6[256+MAGIC] = {0}; uint32_t F7[256+MAGIC] = {0}; #ifdef __GNUC__ double e = 0, in_size_r2 = log(1.0/in_size)/log(2); #else double e = 0, in_size_r2 = log(1.0/in_size); #endif unsigned int i, i8 = in_size & ~7; for (i = 0; i < i8; i+=8) { F0[in[i+0]]++; F1[in[i+1]]++; F2[in[i+2]]++; F3[in[i+3]]++; F4[in[i+4]]++; F5[in[i+5]]++; F6[in[i+6]]++; F7[in[i+7]]++; } while (i < in_size) F0[in[i++]]++; for (i = 0; i < 256; i++) { F0[i] += F1[i] + F2[i] + F3[i] + F4[i] + F5[i] + F6[i] + F7[i]; #ifdef __GNUC__ e -= F0[i] * (32 - __builtin_clz(F0[i]|1) + in_size_r2); #else e -= F0[i] * (fast_log(F0[i]) + in_size_r2); #endif } #ifndef __GNUC__ e /= log(2); #endif return e/in_size; } /* * A variant of hist8 that simply marks the presence of a symbol rather * than its frequency. */ static inline void present8(unsigned char *in, unsigned int in_size, uint32_t F0[256]) { uint32_t F1[256+MAGIC] = {0}, F2[256+MAGIC] = {0}, F3[256+MAGIC] = {0}; uint32_t F4[256+MAGIC] = {0}, F5[256+MAGIC] = {0}, F6[256+MAGIC] = {0}; uint32_t F7[256+MAGIC] = {0}; unsigned int i, i8 = in_size & ~7; for (i = 0; i < i8; i+=8) { F0[in[i+0]]=1; F1[in[i+1]]=1; F2[in[i+2]]=1; F3[in[i+3]]=1; F4[in[i+4]]=1; F5[in[i+5]]=1; F6[in[i+6]]=1; F7[in[i+7]]=1; } while (i < in_size) F0[in[i++]]=1; for (i = 0; i < 256; i++) F0[i] += F1[i] + F2[i] + F3[i] + F4[i] + F5[i] + F6[i] + F7[i]; } /* * Order 1 histogram construction. 4-way unrolled to avoid cache collisions. */ #if 1 static inline int hist1_4(unsigned char *in, unsigned int in_size, uint32_t F0[256][256], uint32_t *T0) { unsigned char l = 0, c; unsigned char *in_end = in + in_size; unsigned char cc[5] = {0}; if (in_size > 500000) { uint32_t (*F1)[259] = htscodecs_tls_calloc(256, sizeof(*F1)); if (F1 == NULL) return -1; while (in < in_end-8) { memcpy(cc, in, 4); in += 4; F0[cc[4]][cc[0]]++; F1[cc[0]][cc[1]]++; F0[cc[1]][cc[2]]++; F1[cc[2]][cc[3]]++; cc[4] = cc[3]; memcpy(cc, in, 4); in += 4; F0[cc[4]][cc[0]]++; F1[cc[0]][cc[1]]++; F0[cc[1]][cc[2]]++; F1[cc[2]][cc[3]]++; cc[4] = cc[3]; } l = cc[3]; while (in < in_end) { F0[l][c = *in++]++; l = c; } T0[l]++; int i, j; for (i = 0; i < 256; i++) { int tt = 0; for (j = 0; j < 256; j++) { F0[i][j] += F1[i][j]; tt += F0[i][j]; } T0[i]+=tt; } htscodecs_tls_free(F1); } else { while (in < in_end-8) { memcpy(cc, in, 4); in += 4; F0[cc[4]][cc[0]]++; F0[cc[0]][cc[1]]++; F0[cc[1]][cc[2]]++; F0[cc[2]][cc[3]]++; cc[4] = cc[3]; memcpy(cc, in, 4); in += 4; F0[cc[4]][cc[0]]++; F0[cc[0]][cc[1]]++; F0[cc[1]][cc[2]]++; F0[cc[2]][cc[3]]++; cc[4] = cc[3]; } l = cc[3]; while (in < in_end) { F0[l][c = *in++]++; l = c; } T0[l]++; int i, j; for (i = 0; i < 256; i++) { int tt = 0; for (j = 0; j < 256; j++) tt += F0[i][j]; T0[i]+=tt; } } return 0; } #else // 16 bit mode, similar to O0 freq. // This is better on some low entropy data, but generally we prefer to do // bit-packing and/or RLE to turn it into higher-entropy data first. // // Kept here for posterity incase we need it again, as it's quick tricky. static inline int hist1_4(unsigned char *in, unsigned int in_size, uint32_t F0[256][256], uint32_t *T0) { uint32_t f0[65536+MAGIC] = {0}; uint32_t f1[65536+MAGIC] = {0}; uint32_t i, i8 = (in_size-1) & ~15; T0[0]++; f0[in[0]<<8]++; for (i = 0; i < i8; i+=16) { uint16_t i16a[16]; memcpy(i16a, in+i, 16); // faster in 2 as gcc recognises this memcpy(i16a+8, in+i+1, 16); // faster in 2 as gcc recognises this f0[i16a[0]]++; f1[i16a[1]]++; f0[i16a[2]]++; f1[i16a[3]]++; f0[i16a[4]]++; f1[i16a[5]]++; f0[i16a[6]]++; f1[i16a[7]]++; f0[i16a[8]]++; f1[i16a[9]]++; f0[i16a[10]]++; f1[i16a[11]]++; f0[i16a[12]]++; f1[i16a[13]]++; f0[i16a[14]]++; f1[i16a[15]]++; } while (i < in_size-1) { F0[in[i]][in[i+1]]++; T0[in[i+1]]++; i++; } for (i = 0; i < 65536; i++) { F0[i&0xff][i>>8] += f0[i] + f1[i]; T0[i>>8] += f0[i] + f1[i]; } return 0; } #endif #endif /* RANS_UTILS_H */ pysam-0.23.0/htslib/htscodecs/htscodecs/varint.h000066400000000000000000000302341475062545500216430ustar00rootroot00000000000000// FIXME: make get functions const uint8_t * /* * Copyright (c) 2019-2021 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef VARINT_H #define VARINT_H #include #ifdef VARINT2 #include "varint2.h" #else // General API scheme is var_{get,put}_{s,u}{32,64} // s/u for signed/unsigned; 32/64 for integer size. // FIXME: consider returning the value and having nbytes passed in by // reference instead of vice-versa. // // ie uint64_t var_get_u64(uint8_t *cp, int *nbytes) // vs int var_get_u64(uint8_t *cp, uint64_t *val) // // The return value can then be assigned to 32-bit or 64-bit type // without need of a new function name. The cost is we can't then // do "cp += var_get_u32(cp, endp, &u_freq_sz);". Maybe we can't do // overflow detection with former? (Want 32-bit but got, say, 40 bit) // Big endian. // Harder for encoding, but a simpler and faster decoder. #define BIG_END #ifdef BIG_END static inline int var_put_u64_safe(uint8_t *cp, const uint8_t *endp, uint64_t i) { uint8_t *op = cp; int s = 0; uint64_t X = i; // safe method when we're near end of buffer do { s += 7; X >>= 7; } while (X); if (endp && (endp-cp)*7 < s) return 0; int n; for (n = 0; n < 10; n++) { s -= 7; *cp++ = ((i>>s) & 0x7f) + (s?128:0); if (!s) break; } return cp-op; } // This can be optimised further with __builtin_clzl(i) and goto various // bits of the if/else-if structure, but it's not a vast improvement and // we are dominated by small values. Simplicity wins for now static inline int var_put_u64(uint8_t *cp, const uint8_t *endp, uint64_t i) { if (endp && (endp-cp) < 10) return var_put_u64_safe(cp, endp, i); // maximum of 10 bytes written if (i < (1<<7)) { *cp = i; return 1; } else if (i < (1<<14)) { *cp++ = ((i>> 7) & 0x7f) | 128; *cp++ = i & 0x7f; return 2; } else if (i < (1<<21)) { *cp++ = ((i>>14) & 0x7f) | 128; *cp++ = ((i>> 7) & 0x7f) | 128; *cp++ = i & 0x7f; return 3; } else if (i < (1<<28)) { *cp++ = ((i>>21) & 0x7f) | 128; *cp++ = ((i>>14) & 0x7f) | 128; *cp++ = ((i>> 7) & 0x7f) | 128; *cp++ = i & 0x7f; return 4; } else if (i < (1ULL<<35)) { *cp++ = ((i>>28) & 0x7f) | 128; *cp++ = ((i>>21) & 0x7f) | 128; *cp++ = ((i>>14) & 0x7f) | 128; *cp++ = ((i>> 7) & 0x7f) | 128; *cp++ = i & 0x7f; return 5; } else if (i < (1ULL<<42)) { *cp++ = ((i>>35) & 0x7f) | 128; *cp++ = ((i>>28) & 0x7f) | 128; *cp++ = ((i>>21) & 0x7f) | 128; *cp++ = ((i>>14) & 0x7f) | 128; *cp++ = ((i>> 7) & 0x7f) | 128; *cp++ = i & 0x7f; return 6; } else if (i < (1ULL<<49)) { *cp++ = ((i>>42) & 0x7f) | 128; *cp++ = ((i>>35) & 0x7f) | 128; *cp++ = ((i>>28) & 0x7f) | 128; *cp++ = ((i>>21) & 0x7f) | 128; *cp++ = ((i>>14) & 0x7f) | 128; *cp++ = ((i>> 7) & 0x7f) | 128; *cp++ = i & 0x7f; return 7; } else if (i < (1ULL<<56)) { *cp++ = ((i>>49) & 0x7f) | 128; *cp++ = ((i>>42) & 0x7f) | 128; *cp++ = ((i>>35) & 0x7f) | 128; *cp++ = ((i>>28) & 0x7f) | 128; *cp++ = ((i>>21) & 0x7f) | 128; *cp++ = ((i>>14) & 0x7f) | 128; *cp++ = ((i>> 7) & 0x7f) | 128; *cp++ = i & 0x7f; return 8; } else if (i < (1ULL<<63)) { *cp++ = ((i>>56) & 0x7f) | 128; *cp++ = ((i>>49) & 0x7f) | 128; *cp++ = ((i>>42) & 0x7f) | 128; *cp++ = ((i>>35) & 0x7f) | 128; *cp++ = ((i>>28) & 0x7f) | 128; *cp++ = ((i>>21) & 0x7f) | 128; *cp++ = ((i>>14) & 0x7f) | 128; *cp++ = ((i>> 7) & 0x7f) | 128; *cp++ = i & 0x7f; return 9; } else { *cp++ = ((i>>63) & 0x7f) | 128; *cp++ = ((i>>56) & 0x7f) | 128; *cp++ = ((i>>49) & 0x7f) | 128; *cp++ = ((i>>42) & 0x7f) | 128; *cp++ = ((i>>35) & 0x7f) | 128; *cp++ = ((i>>28) & 0x7f) | 128; *cp++ = ((i>>21) & 0x7f) | 128; *cp++ = ((i>>14) & 0x7f) | 128; *cp++ = ((i>> 7) & 0x7f) | 128; *cp++ = i & 0x7f; } return 10; } static inline int var_put_u32_safe(uint8_t *cp, const uint8_t *endp, uint32_t i) { uint8_t *op = cp; int s = 0; uint32_t X = i; // safe method when we're near end of buffer do { s += 7; X >>= 7; } while (X); if (endp && (endp-cp)*7 < s) return 0; int n; for (n = 0; n < 5; n++) { s -= 7; *cp++ = ((i>>s) & 0x7f) + (s?128:0); if (!s) break; } return cp-op; } static inline int var_put_u32(uint8_t *cp, const uint8_t *endp, uint32_t i) { if (endp && (endp-cp) < 5) return var_put_u32_safe(cp, endp, i); if (i < (1<<7)) { *cp = i; return 1; } else if (i < (1<<14)) { *cp++ = ((i>> 7) & 0x7f) | 128; *cp++ = i & 0x7f; return 2; } else if (i < (1<<21)) { *cp++ = ((i>>14) & 0x7f) | 128; *cp++ = ((i>> 7) & 0x7f) | 128; *cp++ = i & 0x7f; return 3; } else if (i < (1<<28)) { *cp++ = ((i>>21) & 0x7f) | 128; *cp++ = ((i>>14) & 0x7f) | 128; *cp++ = ((i>> 7) & 0x7f) | 128; *cp++ = i & 0x7f; return 4; } else { *cp++ = ((i>>28) & 0x7f) | 128; *cp++ = ((i>>21) & 0x7f) | 128; *cp++ = ((i>>14) & 0x7f) | 128; *cp++ = ((i>> 7) & 0x7f) | 128; *cp++ = i & 0x7f; } return 5; } static inline int var_get_u64(uint8_t *cp, const uint8_t *endp, uint64_t *i) { uint8_t *op = cp, c; uint64_t j = 0; if (!endp || endp - cp >= 11) { int n = 10; do { c = *cp++; j = (j<<7) | (c & 0x7f); } while ((c & 0x80) && n-- > 0); } else { if (cp >= endp) { *i = 0; return 0; } do { c = *cp++; j = (j<<7) | (c & 0x7f); } while ((c & 0x80) && cp < endp); } *i = j; return cp-op; } static inline int var_get_u32(uint8_t *cp, const uint8_t *endp, uint32_t *i) { uint8_t *op = cp, c; uint32_t j = 0; if (!endp || endp - cp >= 6) { // Known maximum loop count helps optimiser. // NB: this helps considerably at -O3 level, but may harm -O2. // (However we optimise for those that want optimal code.) int n = 5; do { c = *cp++; j = (j<<7) | (c & 0x7f); } while ((c & 0x80) && n-- > 0); } else { if (cp >= endp) { *i = 0; return 0; } if (*cp < 128) { *i = *cp; return 1; } do { c = *cp++; j = (j<<7) | (c & 0x7f); } while ((c & 0x80) && cp < endp); } *i = j; return cp-op; } //----------------------------------------------------------------------------- #else // BIG_END // Little endian 7-bit variable sized integer encoding. // The unsigned value is equivalent to LEB128 encoding. // For signed, see below. // This is also the Google Protocol Buffer and WebAssembly format. static inline int var_put_u64(uint8_t *cp, const uint8_t *endp, uint64_t i) { uint8_t *op = cp; if (!endp || (endp-cp)*7 >= 10) { // Unsafe or big-enough anyway do { *cp++ = (i&0x7f) + ((i>=0x80)<<7); i >>= 7; } while (i); } else if (cp < endp) { // End checked variant do { *cp++ = (i&0x7f) + ((i>=0x80)<<7); i >>= 7; } while (i && cp < endp); } return cp-op; } static inline int var_put_u32(uint8_t *cp, const uint8_t *endp, uint32_t i) { uint8_t *op = cp; if (!endp || (endp-cp)*7 >= 5) { // Unsafe or big-enough anyway do { *cp++ = (i&0x7f) + ((i>=0x80)<<7); i >>= 7; } while (i); } else if (cp < endp) { // End checked variant do { *cp++ = (i&0x7f) + ((i>=0x80)<<7); i >>= 7; } while (i && cp < endp); } return cp-op; } static inline int var_get_u64(uint8_t *cp, const uint8_t *endp, uint64_t *i) { uint8_t *op = cp, c; uint64_t j = 0, s = 0; if (endp) { // Safe variant if (cp >= endp) { *i = 0; return 0; } do { c = *cp++; j |= (c & 0x7f) << s; s += 7; } while ((c & 0x80) && cp < endp); } else { // Unsafe variant do { c = *cp++; j |= (c & 0x7f) << s; s += 7; } while ((c & 0x80)); } *i = j; return cp-op; } static inline int var_get_u32(uint8_t *cp, const uint8_t *endp, uint32_t *i) { uint8_t *op = cp, c; uint32_t j = 0, s = 0; if (endp) { // Safe variant if (cp >= endp) { *i = 0; return 0; } do { c = *cp++; j |= (c & 0x7f) << s; s += 7; } while ((c & 0x80) && cp < endp); } else { // Unsafe variant do { c = *cp++; j |= (c & 0x7f) << s; s += 7; } while ((c & 0x80)); } *i = j; return cp-op; } #endif // BIG_END //----------------------------------------------------------------------------- // Signed versions of the above using zig-zag integer encoding. // This folds the sign bit into the bottom bit so we iterate // 0, -1, +1, -2, +2, etc. static inline int var_put_s32(uint8_t *cp, const uint8_t *endp, int32_t i) { return var_put_u32(cp, endp, ((uint32_t)i << 1) ^ (i >> 31)); } static inline int var_put_s64(uint8_t *cp, const uint8_t *endp, int64_t i) { return var_put_u64(cp, endp, ((uint64_t)i << 1) ^ (i >> 63)); } static inline int var_get_s32(uint8_t *cp, const uint8_t *endp, int32_t *i) { int b = var_get_u32(cp, endp, (uint32_t *)i); *i = ((uint32_t)*i >> 1) ^ -(int32_t)(*i & 1); return b; } static inline int var_get_s64(uint8_t *cp, const uint8_t *endp, int64_t *i) { int b = var_get_u64(cp, endp, (uint64_t *)i); *i = ((uint64_t)*i >> 1) ^ -(int64_t)(*i & 1); return b; } static inline int var_size_u64(uint64_t v) { int i = 0; do { i++; v >>= 7; } while (v); return i; } #define var_size_u32 var_size_u64 static inline int var_size_s64(int64_t v) { return var_size_u64(((uint64_t)v << 1) ^ (v >> 63)); } #define var_size_s32 var_size_s64 #endif /* VARINT2 */ #endif /* VARINT_H */ pysam-0.23.0/htslib/htscodecs/htscodecs/varint2.h000066400000000000000000000227631475062545500217350ustar00rootroot00000000000000//#include // FIXME: make get functions const uint8_t * /* * Copyright (c) 2019 Genome Research Ltd. * Author(s): James Bonfield * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * 1. Redistributions of source code must retain the above copyright notice, * this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger * Institute nor the names of its contributors may be used to endorse * or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef VARINT2_H #define VARINT2_H #include // General API scheme is var_{get,put}_{s,u}{32,64} // s/u for signed/unsigned; 32/64 for integer size. // The ideas here are taken from the vbenc code in TurboPFor // (https://github.com/powturbo/TurboPFor) with analysis at // https://github.com/stoklund/varint. // Unlike the ITF8 and standard 7-bit at a time encodings, this // tries to ensure a larger portion of small numbers still fit in 1 byte. // This trades more space for long integers with less space for short ones, // which seems like a good tradeoff given the typical distribution curves. // // Like ITF8 and LTF8, the first byte also indicates the total number of // bytes we need to decode, but unlike those it uses the same format for // both meaning changing data type doesn't change encoding. // // Size comparison examples. // // Max value // Bytes ITF8/7bit This // 1 127 176 // 2 16,383 16,560 // 3 2,097,151 540,848 // 4 268,435,455 16,777,215 // 5 34,359,738,368 4,294,967,296 // 6 4,398,046,511,104 1,099,511,627,776 // ... // // The format is as follows: // 0-176 1 byte: 0 + 8 bit // 177-16560 (14 bit range) 2 bytes: 177 + 6bit, 0 + 8bit, for x-177 // 16561-540848 (19 bits) 3 bytes: 241 + 3bit, 0+8, 0+8, for x-16561 // 540849-16777215 (~24 bit) 4 bytes: 249, 0+8, 0+8, 0+8, for x // 2^24 - 2^32-1 5 bytes: 250, 0+8 x4 // 2^32 - 2^40-1 6 bytes: 251, 0+8 x5 // 2^40 - 2^48-1 7 bytes: 252, 0+8 x6 // 2^48 - 2^56-1 8 bytes: 253, 0+8 x7 // 2^56 - 2^64-1 9 bytes: 254, 0+8 x8 // // Hence first byte value 255 is not possible and permits future // escape code. // FIXME: consider returning the value and having nbytes passed in by // reference instead of vice-versa. // // ie uint64_t var_get_u64(uint8_t *cp, int *nbytes) // vs int var_get_u64(uint8_t *cp, uint64_t *val) // // The return value can then be assigned to 32-bit or 64-bit type // without need of a new function name. The cost is we can't then // do "cp += var_get_u32(cp, endp, &u_freq_sz);". Maybe we can't do // overflow detection with former? (Want 32-bit but got, say, 40 bit) // static inline char *var_dump(const uint8_t *cp, int n) { // static char buf[1000]; // int i, o = 0; // for (i = 0; i < n; i++) // o += sprintf(&buf[o], " %d", cp[i]); // return buf; // } static inline int var_put_u64(uint8_t *cp, const uint8_t *endp, uint64_t x) { uint8_t *op = cp; if (x < 177) { if (endp && endp - cp < 1) return 0; // 0 to 176 in single byte as-is *cp++ = x; } else if (x < 16561) { if (endp && endp - cp < 2) return 0; *cp++ = ((x-177)>>8)+177; *cp++ = x-177; } else if (x < 540849) { if (endp && endp - cp < 3) return 0; *cp++ = ((x-16561)>>16)+241; *cp++ = (x-16561)>>8; *cp++ = x-16561; } else if (x < (1<<24)) { if (endp && endp - cp < 4) return 0; *cp++ = 249; *cp++ = x>>16; *cp++ = x>>8; *cp++ = x; } else if (x < (1LL<<32)) { if (endp && endp - cp < 5) return 0; *cp++ = 250; *cp++ = x>>24; *cp++ = x>>16; *cp++ = x>>8; *cp++ = x; } else if (x < (1LL<<40)) { if (endp && endp - cp < 6) return 0; *cp++ = 251; *cp++ = x>>32; *cp++ = x>>24; *cp++ = x>>16; *cp++ = x>>8; *cp++ = x; } else if (x < (1LL<<48)) { if (endp && endp - cp < 7) return 0; *cp++ = 252; *cp++ = x>>40; *cp++ = x>>32; *cp++ = x>>24; *cp++ = x>>16; *cp++ = x>>8; *cp++ = x; } else if (x < (1LL<<56)) { if (endp && endp - cp < 8) return 0; *cp++ = 253; *cp++ = x>>48; *cp++ = x>>40; *cp++ = x>>32; *cp++ = x>>24; *cp++ = x>>16; *cp++ = x>>8; *cp++ = x; } else { if (endp && endp - cp < 9) return 0; *cp++ = 254; *cp++ = x>>56; *cp++ = x>>48; *cp++ = x>>40; *cp++ = x>>32; *cp++ = x>>24; *cp++ = x>>16; *cp++ = x>>8; *cp++ = x; } // fprintf(stderr, "Put64 %d (%s)\n", x, var_dump(op, cp-op)); return cp-op; } static inline int var_put_u32(uint8_t *cp, const uint8_t *endp, uint32_t x) { uint8_t *op = cp; if (x < 177) { if (endp && endp - cp < 1) abort();//return 0; // 0 to 176 in single byte as-is *cp++ = x; } else if (x < 16561) { if (endp && endp - cp < 2) abort();//return 0; *cp++ = ((x-177)>>8)+177; *cp++ = x-177; } else if (x < 540849) { if (endp && endp - cp < 3) abort();//return 0; *cp++ = ((x-16561)>>16)+241; *cp++ = (x-16561)>>8; *cp++ = x-16561; } else if (x < (1<<24)) { if (endp && endp - cp < 4) abort();//return 0; *cp++ = 249; *cp++ = x>>16; *cp++ = x>>8; *cp++ = x; } else { if (endp && endp - cp < 5) abort();//return 0; *cp++ = 250; *cp++ = x>>24; *cp++ = x>>16; *cp++ = x>>8; *cp++ = x; } // fprintf(stderr, "Put32 %d (%s)\n", x, var_dump(op, cp-op)); return cp-op; } static inline int var_get_u64(uint8_t *cp, const uint8_t *endp, uint64_t *i) { uint8_t *op = cp; uint64_t j = 0; if (endp && cp >= endp) { *i = 0; return 0; } if (*cp < 177) { j = *cp++; } else if (*cp < 241) { j = ((cp[0] - 177)<<8) + cp[1] + 177; cp += 2; } else if (*cp < 249) { j = ((cp[0] - 241)<<16) + (cp[1]<<8) + cp[2] + 16561; cp += 3; } else { int n = *cp++ - 249 + 3; while (n--) j = (j<<8) + *cp++; } // fprintf(stderr, "Get64 %ld (%s)\n", j, var_dump(op, cp-op)); *i = j; return cp-op; } static inline int var_get_u32(uint8_t *cp, const uint8_t *endp, uint32_t *i) { uint8_t *op = cp; uint32_t j = 0; if (endp && cp >= endp) { *i = 0; return 0; } if (*cp < 177) { j = *cp++; } else if (*cp < 241) { j = ((cp[0] - 177)<<8) + cp[1] + 177; cp += 2; } else if (*cp < 249) { j = ((cp[0] - 241)<<16) + (cp[1]<<8) + cp[2] + 16561; cp += 3; } else { int n = *cp++ - 249 + 3; while (n--) j = (j<<8) + *cp++; } // fprintf(stderr, "Get32 %d (%s)\n", j, var_dump(op, cp-op)); *i = j; return cp-op; } // Signed versions of the above using zig-zag integer encoding. // This folds the sign bit into the bottom bit so we iterate // 0, -1, +1, -2, +2, etc. static inline int var_put_s32(uint8_t *cp, const uint8_t *endp, int32_t i) { return var_put_u32(cp, endp, (i << 1) ^ (i >> 31)); } static inline int var_put_s64(uint8_t *cp, const uint8_t *endp, int64_t i) { return var_put_u64(cp, endp, (i << 1) ^ (i >> 63)); } static inline int var_get_s32(uint8_t *cp, const uint8_t *endp, int32_t *i) { int b = var_get_u32(cp, endp, (uint32_t *)i); *i = (*i >> 1) ^ -(*i & 1); return b; } static inline int var_get_s64(uint8_t *cp, const uint8_t *endp, int64_t *i) { int b = var_get_u64(cp, endp, (uint64_t *)i); *i = (*i >> 1) ^ -(*i & 1); return b; } static inline int var_size_u64(uint64_t v) { if (v < 177) return 1; else if (v < 16561) return 2; else if (v < 540849) return 3; int i = 0; do { v >>= 8; i++; } while (v); // fprintf(stderr, "Size %ld (%d)\n", v, i+1); return i+1; } #define var_size_u32 var_size_u64 static inline int var_size_s64(int64_t v) { return var_size_u64((v >> 63) ^ (v << 1)); } #define var_size_s32 var_size_s64 #endif /* VARINT2_H */ pysam-0.23.0/htslib/htscodecs/htscodecs/version.h000066400000000000000000000000471475062545500220240ustar00rootroot00000000000000#define HTSCODECS_VERSION_TEXT "1.6.1" pysam-0.23.0/htslib/htscodecs_bundled.mk000066400000000000000000000071331475062545500202400ustar00rootroot00000000000000# Makefile fragment to add settings needed when bundling htscodecs functions # # Copyright (C) 2021-2022 Genome Research Ltd. # # Author: Rob Davies # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. HTSCODECS_SOURCES = $(HTSPREFIX)htscodecs/htscodecs/arith_dynamic.c \ $(HTSPREFIX)htscodecs/htscodecs/fqzcomp_qual.c \ $(HTSPREFIX)htscodecs/htscodecs/htscodecs.c \ $(HTSPREFIX)htscodecs/htscodecs/pack.c \ $(HTSPREFIX)htscodecs/htscodecs/rANS_static4x16pr.c \ $(HTSPREFIX)htscodecs/htscodecs/rANS_static32x16pr_avx2.c \ $(HTSPREFIX)htscodecs/htscodecs/rANS_static32x16pr_avx512.c \ $(HTSPREFIX)htscodecs/htscodecs/rANS_static32x16pr_sse4.c \ $(HTSPREFIX)htscodecs/htscodecs/rANS_static32x16pr_neon.c \ $(HTSPREFIX)htscodecs/htscodecs/rANS_static32x16pr.c \ $(HTSPREFIX)htscodecs/htscodecs/rANS_static.c \ $(HTSPREFIX)htscodecs/htscodecs/rle.c \ $(HTSPREFIX)htscodecs/htscodecs/tokenise_name3.c \ $(HTSPREFIX)htscodecs/htscodecs/utils.c HTSCODECS_OBJS = $(HTSCODECS_SOURCES:.c=.o) # htscodecs public headers htscodecs_arith_dynamic_h = htscodecs/htscodecs/arith_dynamic.h htscodecs_fqzcomp_qual_h = htscodecs/htscodecs/fqzcomp_qual.h htscodecs_htscodecs_h = htscodecs/htscodecs/htscodecs.h $(htscodecs_version_h) htscodecs_pack_h = htscodecs/htscodecs/pack.h htscodecs_rANS_static_h = htscodecs/htscodecs/rANS_static.h htscodecs_rANS_static4x16_h = htscodecs/htscodecs/rANS_static4x16.h htscodecs_rle_h = htscodecs/htscodecs/rle.h htscodecs_tokenise_name3_h = htscodecs/htscodecs/tokenise_name3.h htscodecs_varint_h = htscodecs/htscodecs/varint.h # htscodecs internal headers htscodecs_htscodecs_endian_h = htscodecs/htscodecs/htscodecs_endian.h htscodecs_c_range_coder_h = htscodecs/htscodecs/c_range_coder.h htscodecs_c_simple_model_h = htscodecs/htscodecs/c_simple_model.h $(htscodecs_c_range_coder_h) htscodecs_permute_h = htscodecs/htscodecs/permute.h htscodecs_pooled_alloc_h = htscodecs/htscodecs/pooled_alloc.h htscodecs_rANS_byte_h = htscodecs/htscodecs/rANS_byte.h htscodecs_rANS_static16_int_h = htscodecs/htscodecs/rANS_static16_int.h $(htscodecs_varint_h) $(htscodecs_utils_h) htscodecs_rANS_static32x16pr_h = htscodecs/htscodecs/rANS_static32x16pr.h htscodecs_rANS_word_h = htscodecs/htscodecs/rANS_word.h $(htscodecs_htscodecs_endian_h) htscodecs_utils_h = htscodecs/htscodecs/utils.h htscodecs_version_h = htscodecs/htscodecs/version.h # Add htscodecs tests into the HTSlib test framework HTSCODECS_TEST_TARGETS = test_htscodecs_rans4x8 \ test_htscodecs_rans4x16 test_htscodecs_arith test_htscodecs_tok3 \ test_htscodecs_fqzcomp test_htscodecs_varint pysam-0.23.0/htslib/htscodecs_external.mk000066400000000000000000000032561475062545500204470ustar00rootroot00000000000000# Makefile fragment for use when linking to an external libhtscodecs # # Copyright (C) 2021 Genome Research Ltd. # # Author: Rob Davies # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. HTSCODECS_SOURCES = HTSCODECS_OBJS = HTSCODECS_TEST_TARGETS = htscodecs_arith_dynamic_h = htscodecs_fqzcomp_qual_h = htscodecs_htscodecs_h = htscodecs_pack_h = htscodecs_rANS_static_h = htscodecs_rANS_static4x16_h = htscodecs_rle_h = htscodecs_tokenise_name3_h = htscodecs_varint_h = htscodecs_htscodecs_endian_h = htscodecs_c_range_coder_h = htscodecs_c_simple_model_h = htscodecs_pooled_alloc_h = htscodecs_rANS_byte_h = htscodecs_rANS_word_h = htscodecs_utils_h = htscodecs_version_h = pysam-0.23.0/htslib/htslib.mk000066400000000000000000000155001475062545500160460ustar00rootroot00000000000000# Makefile rules useful for third-party code using htslib's public API. # # Copyright (C) 2013-2017, 2019, 2021 Genome Research Ltd. # # Author: John Marshall # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. # The makefile fragment included below provides variables that can be used # to express dependencies on headers supplied by an in-development htslib. # If your source file foo.c #includes and , # you can write the correct prerequisites for foo.o as: # # HTSDIR = # include $(HTSDIR)/htslib.mk # # foo.o: foo.c $(htslib_hts_h) $(htslib_kstring_h) HTSSRCDIR = $(HTSDIR) HTSPREFIX = $(HTSSRCDIR)/ include $(HTSDIR)/htslib_vars.mk # This file provides the HTSCODECS_SOURCES variable. It may not be present # in a freshly checked-out htslib, so is only included if available. The # absence is unlikely to cause a problem as there will be plenty of other # missing files that will trigger a build in htslib, and when that happens # htslib's makefile will create it. -include $(HTSDIR)/htscodecs.mk # Rules for rebuilding an in-development htslib's static and shared libraries. # If your program foo links with libhts, adding the appropriate prerequisite # will cause the library to be rebuilt as necessary: # # foo: foo.o $(HTSDIR)/libhts.a # # or similarly if your target requires any of the tools supplied: # # bar.bed.bgz.tbi: bar.bed.bgz $(HTSDIR)/tabix # $(HTSDIR)/tabix -p bed bar.bed.bgz HTSLIB_PUBLIC_HEADERS = \ $(HTSSRCDIR)/htslib/bgzf.h \ $(HTSSRCDIR)/htslib/cram.h \ $(HTSSRCDIR)/htslib/faidx.h \ $(HTSSRCDIR)/htslib/hfile.h \ $(HTSSRCDIR)/htslib/hts.h \ $(HTSSRCDIR)/htslib/hts_defs.h \ $(HTSSRCDIR)/htslib/hts_endian.h \ $(HTSSRCDIR)/htslib/hts_expr.h \ $(HTSSRCDIR)/htslib/hts_log.h \ $(HTSSRCDIR)/htslib/hts_os.h \ $(HTSSRCDIR)/htslib/kbitset.h \ $(HTSSRCDIR)/htslib/kfunc.h \ $(HTSSRCDIR)/htslib/khash.h \ $(HTSSRCDIR)/htslib/khash_str2int.h \ $(HTSSRCDIR)/htslib/klist.h \ $(HTSSRCDIR)/htslib/kseq.h \ $(HTSSRCDIR)/htslib/ksort.h \ $(HTSSRCDIR)/htslib/kstring.h \ $(HTSSRCDIR)/htslib/regidx.h \ $(HTSSRCDIR)/htslib/sam.h \ $(HTSSRCDIR)/htslib/synced_bcf_reader.h \ $(HTSSRCDIR)/htslib/tbx.h \ $(HTSSRCDIR)/htslib/thread_pool.h \ $(HTSSRCDIR)/htslib/vcf.h \ $(HTSSRCDIR)/htslib/vcf_sweep.h \ $(HTSSRCDIR)/htslib/vcfutils.h HTSLIB_ALL = \ $(HTSLIB_PUBLIC_HEADERS) \ $(HTSSRCDIR)/bcf_sr_sort.c \ $(HTSSRCDIR)/bcf_sr_sort.h \ $(HTSSRCDIR)/bgzf.c \ $(HTSDIR)/config.h \ $(HTSSRCDIR)/errmod.c \ $(HTSSRCDIR)/faidx.c \ $(HTSSRCDIR)/header.c \ $(HTSSRCDIR)/header.h \ $(HTSSRCDIR)/hfile_internal.h \ $(HTSSRCDIR)/hfile.c \ $(HTSSRCDIR)/hfile_gcs.c \ $(HTSSRCDIR)/hfile_libcurl.c \ $(HTSSRCDIR)/hfile_s3.c \ $(HTSSRCDIR)/hfile_s3_write.c \ $(HTSSRCDIR)/hts.c \ $(HTSSRCDIR)/hts_expr.c \ $(HTSSRCDIR)/hts_internal.h \ $(HTSSRCDIR)/hts_os.c \ $(HTSSRCDIR)/kfunc.c \ $(HTSSRCDIR)/kstring.c \ $(HTSSRCDIR)/md5.c \ $(HTSSRCDIR)/multipart.c \ $(HTSSRCDIR)/plugin.c \ $(HTSSRCDIR)/probaln.c \ $(HTSSRCDIR)/realn.c \ $(HTSSRCDIR)/regidx.c \ $(HTSSRCDIR)/region.c \ $(HTSSRCDIR)/sam.c \ $(HTSSRCDIR)/sam_internal.h \ $(HTSSRCDIR)/synced_bcf_reader.c \ $(HTSSRCDIR)/tbx.c \ $(HTSSRCDIR)/textutils.c \ $(HTSSRCDIR)/textutils_internal.h \ $(HTSSRCDIR)/thread_pool.c \ $(HTSSRCDIR)/thread_pool_internal.h \ $(HTSSRCDIR)/vcf.c \ $(HTSSRCDIR)/vcf_sweep.c \ $(HTSSRCDIR)/vcfutils.c \ $(HTSSRCDIR)/cram/cram.h \ $(HTSSRCDIR)/cram/cram_codecs.c \ $(HTSSRCDIR)/cram/cram_codecs.h \ $(HTSSRCDIR)/cram/cram_decode.c \ $(HTSSRCDIR)/cram/cram_decode.h \ $(HTSSRCDIR)/cram/cram_encode.c \ $(HTSSRCDIR)/cram/cram_encode.h \ $(HTSSRCDIR)/cram/cram_external.c \ $(HTSSRCDIR)/cram/cram_index.c \ $(HTSSRCDIR)/cram/cram_index.h \ $(HTSSRCDIR)/cram/cram_io.c \ $(HTSSRCDIR)/cram/cram_io.h \ $(HTSSRCDIR)/cram/cram_samtools.h \ $(HTSSRCDIR)/cram/cram_stats.c \ $(HTSSRCDIR)/cram/cram_stats.h \ $(HTSSRCDIR)/cram/cram_structs.h \ $(HTSSRCDIR)/cram/mFILE.c \ $(HTSSRCDIR)/cram/mFILE.h \ $(HTSSRCDIR)/cram/misc.h \ $(HTSSRCDIR)/cram/open_trace_file.c \ $(HTSSRCDIR)/cram/open_trace_file.h \ $(HTSSRCDIR)/cram/os.h \ $(HTSSRCDIR)/cram/pooled_alloc.c \ $(HTSSRCDIR)/cram/pooled_alloc.h \ $(HTSSRCDIR)/cram/string_alloc.c \ $(HTSSRCDIR)/cram/string_alloc.h \ $(HTSSRCDIR)/os/lzma_stub.h \ $(HTSSRCDIR)/os/rand.c \ $(HTSCODECS_SOURCES) $(HTSDIR)/config.h: +cd $(HTSDIR) && $(MAKE) config.h $(HTSDIR)/hts-object-files : $(HTSLIB_ALL) +cd $(HTSDIR) && $(MAKE) hts-object-files $(HTSDIR)/libhts.a: $(HTSDIR)/hts-object-files +cd $(HTSDIR) && $(MAKE) lib-static $(HTSDIR)/libhts.so: $(HTSLIB_ALL) +cd $(HTSDIR) && $(MAKE) lib-shared $(HTSDIR)/libhts.dylib $(HTSDIR)/libhts.dll.a $(HTSDIR)/hts.dll.a: $(HTSDIR)/hts-object-files +cd $(HTSDIR) && $(MAKE) lib-shared $(HTSDIR)/bgzip: $(HTSSRCDIR)/bgzip.c $(HTSLIB_PUBLIC_HEADERS) $(HTSDIR)/libhts.a +cd $(HTSDIR) && $(MAKE) bgzip $(HTSDIR)/htsfile: $(HTSSRCDIR)/htsfile.c $(HTSLIB_PUBLIC_HEADERS) $(HTSDIR)/libhts.a +cd $(HTSDIR) && $(MAKE) htsfile $(HTSDIR)/tabix: $(HTSSRCDIR)/tabix.c $(HTSLIB_PUBLIC_HEADERS) $(HTSDIR)/libhts.a +cd $(HTSDIR) && $(MAKE) tabix $(HTSDIR)/annot-tsv: $(HTSSRCDIR)/annot-tsv.c $(HTSLIB_PUBLIC_HEADERS) $(HTSDIR)/libhts.a +cd $(HTSDIR) && $(MAKE) annot-tsv $(HTSDIR)/htslib_static.mk: $(HTSDIR)/htslib.pc.tmp +cd $(HTSDIR) && $(MAKE) htslib_static.mk $(HTSDIR)/htslib.pc.tmp: +cd $(HTSDIR) && $(MAKE) htslib.pc.tmp # Rules for phony targets. You may wish to have your corresponding phony # targets invoke these in addition to their own recipes: # # clean: clean-htslib all-htslib check-htslib clean-htslib distclean-htslib install-htslib mostlyclean-htslib plugins-htslib test-htslib testclean-htslib: +cd $(HTSDIR) && $(MAKE) $(@:-htslib=) .PHONY: all-htslib check-htslib clean-htslib distclean-htslib install-htslib .PHONY: mostlyclean-htslib plugins-htslib test-htslib testclean-htslib pysam-0.23.0/htslib/htslib.pc.in000066400000000000000000000007521475062545500164510ustar00rootroot00000000000000includedir=@-includedir@ libdir=@-libdir@ # Flags and libraries needed when linking against a static libhts.a # (used by manual and semi-manual pkg-config(1)-style enquiries). static_ldflags=@static_LDFLAGS@ static_libs=@static_LIBS@ Name: htslib Description: C library for high-throughput sequencing data formats Version: @-PACKAGE_VERSION@ Cflags: -I${includedir} Libs: -L${libdir} -lhts Libs.private: -L${libdir} @private_LIBS@ -lhts -lm -lpthread Requires.private: zlib @pc_requires@ pysam-0.23.0/htslib/htslib/000077500000000000000000000000001475062545500155145ustar00rootroot00000000000000pysam-0.23.0/htslib/htslib/bgzf.h000066400000000000000000000426331475062545500166250ustar00rootroot00000000000000/// @file htslib/bgzf.h /// Low-level routines for direct BGZF operations. /* Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology 2011, 2012 Attractive Chaos Copyright (C) 2009, 2013, 2014, 2017, 2018-2019, 2022-2024 Genome Research Ltd Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* The BGZF library was originally written by Bob Handsaker from the Broad * Institute. It was later improved by the SAMtools developers. */ #ifndef HTSLIB_BGZF_H #define HTSLIB_BGZF_H #include #include #include #include "hts_defs.h" // Ensure ssize_t exists within this header. All #includes must precede this, // and ssize_t must be undefined again at the end of this header. #if defined _MSC_VER && defined _INTPTR_T_DEFINED && !defined _SSIZE_T_DEFINED && !defined ssize_t #define HTSLIB_SSIZE_T #define ssize_t intptr_t #endif #ifdef __cplusplus extern "C" { #endif #define BGZF_BLOCK_SIZE 0xff00 // make sure compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE #define BGZF_MAX_BLOCK_SIZE 0x10000 #define BGZF_ERR_ZLIB 1 #define BGZF_ERR_HEADER 2 #define BGZF_ERR_IO 4 #define BGZF_ERR_MISUSE 8 #define BGZF_ERR_MT 16 // stream cannot be multi-threaded #define BGZF_ERR_CRC 32 struct hFILE; struct hts_tpool; struct kstring_t; struct bgzf_mtaux_t; typedef struct bgzidx_t bgzidx_t; typedef struct bgzf_cache_t bgzf_cache_t; struct z_stream_s; struct BGZF { // Reserved bits should be written as 0; read as "don't care" unsigned errcode:16, reserved:1, is_write:1, no_eof_block:1, is_be:1; signed compress_level:9; unsigned last_block_eof:1, is_compressed:1, is_gzip:1; int cache_size; int block_length, block_clength, block_offset; int64_t block_address, uncompressed_address; void *uncompressed_block, *compressed_block; bgzf_cache_t *cache; struct hFILE *fp; // actual file handle struct bgzf_mtaux_t *mt; // only used for multi-threading bgzidx_t *idx; // BGZF index int idx_build_otf; // build index on the fly, set by bgzf_index_build_init() struct z_stream_s *gz_stream; // for gzip-compressed files int64_t seeked; // virtual offset of last seek }; #ifndef HTS_BGZF_TYPEDEF typedef struct BGZF BGZF; #define HTS_BGZF_TYPEDEF #endif /****************** * Basic routines * ******************/ /** * Open an existing file descriptor for reading or writing. * * @param fd file descriptor * Note that the file must be opened in binary mode, or else * there will be problems on platforms that make a difference * between text and binary mode. * @param mode mode matching /[rwag][u0-9]+/: 'r' for reading, 'w' for * writing, 'a' for appending, 'g' for gzip rather than BGZF * compression (with 'w' only), and digit specifies the zlib * compression level. * Note that there is a distinction between 'u' and '0': the * first yields plain uncompressed output whereas the latter * outputs uncompressed data wrapped in the zlib format. * @return BGZF file handler; 0 on error */ HTSLIB_EXPORT BGZF* bgzf_dopen(int fd, const char *mode); #define bgzf_fdopen(fd, mode) bgzf_dopen((fd), (mode)) // for backward compatibility /** * Open the specified file for reading or writing. */ HTSLIB_EXPORT BGZF* bgzf_open(const char* path, const char *mode); /** * Open an existing hFILE stream for reading or writing. */ HTSLIB_EXPORT BGZF* bgzf_hopen(struct hFILE *fp, const char *mode); /** * Close the BGZF and free all associated resources. * * @param fp BGZF file handler * @return 0 on success and -1 on error */ HTSLIB_EXPORT int bgzf_close(BGZF *fp); /** * Read up to _length_ bytes from the file storing into _data_. * * @param fp BGZF file handler * @param data data array to read into * @param length size of data to read * @return number of bytes actually read; 0 on end-of-file and -1 on error */ HTSLIB_EXPORT ssize_t bgzf_read(BGZF *fp, void *data, size_t length) HTS_RESULT_USED; /** * bgzf_read optimised for small quantities, as a static inline * See bgzf_read() normal function for return values. */ static inline ssize_t bgzf_read_small(BGZF *fp, void *data, size_t length) { // A block length of 0 implies current block isn't loaded (see // bgzf_seek_common). That gives negative available so careful on types if ((ssize_t)length < fp->block_length - fp->block_offset) { // Short cut the common and easy mode memcpy((uint8_t *)data, (uint8_t *)fp->uncompressed_block + fp->block_offset, length); fp->block_offset += length; fp->uncompressed_address += length; return length; } else { return bgzf_read(fp, data, length); } } /** * Write _length_ bytes from _data_ to the file. If no I/O errors occur, * the complete _length_ bytes will be written (or queued for writing). * * @param fp BGZF file handler * @param data data array to write * @param length size of data to write * @return number of bytes written (i.e., _length_); negative on error */ HTSLIB_EXPORT ssize_t bgzf_write(BGZF *fp, const void *data, size_t length) HTS_RESULT_USED; /** * bgzf_write optimised for small quantities, as a static inline * See bgzf_write() normal function for return values. */ static inline ssize_t bgzf_write_small(BGZF *fp, const void *data, size_t length) { if (fp->is_compressed && (size_t) (BGZF_BLOCK_SIZE - fp->block_offset) > length) { // Short cut the common and easy mode memcpy((uint8_t *)fp->uncompressed_block + fp->block_offset, data, length); fp->block_offset += length; return length; } else { return bgzf_write(fp, data, length); } } /** * Write _length_ bytes from _data_ to the file, the index will be used to * decide the amount of uncompressed data to be written to each bgzip block. * If no I/O errors occur, the complete _length_ bytes will be written (or * queued for writing). * @param fp BGZF file handler * @param data data array to write * @param length size of data to write * @return number of bytes written (i.e., _length_); negative on error */ HTSLIB_EXPORT ssize_t bgzf_block_write(BGZF *fp, const void *data, size_t length); /** * Returns the next byte in the file without consuming it. * @param fp BGZF file handler * @return -1 on EOF, * -2 on error, * otherwise the unsigned byte value. */ HTSLIB_EXPORT int bgzf_peek(BGZF *fp); /** * Read up to _length_ bytes directly from the underlying stream without * decompressing. Bypasses BGZF blocking, so must be used with care in * specialised circumstances only. * * @param fp BGZF file handler * @param data data array to read into * @param length number of raw bytes to read * @return number of bytes actually read; 0 on end-of-file and -1 on error */ HTSLIB_EXPORT ssize_t bgzf_raw_read(BGZF *fp, void *data, size_t length) HTS_RESULT_USED; /** * Write _length_ bytes directly to the underlying stream without * compressing. Bypasses BGZF blocking, so must be used with care * in specialised circumstances only. * * @param fp BGZF file handler * @param data data array to write * @param length number of raw bytes to write * @return number of bytes actually written; -1 on error */ HTSLIB_EXPORT ssize_t bgzf_raw_write(BGZF *fp, const void *data, size_t length) HTS_RESULT_USED; /** * Write the data in the buffer to the file. * * @param fp BGZF file handle * @return 0 on success and -1 on error */ HTSLIB_EXPORT int bgzf_flush(BGZF *fp) HTS_RESULT_USED; /** * Return a virtual file pointer to the current location in the file. * No interpretation of the value should be made, other than a subsequent * call to bgzf_seek can be used to position the file at the same point. * Return value is non-negative on success. */ #define bgzf_tell(fp) (((fp)->block_address << 16) | ((fp)->block_offset & 0xFFFF)) /** * Set the file to read from the location specified by _pos_. * * @param fp BGZF file handler * @param pos virtual file offset returned by bgzf_tell() * @param whence must be SEEK_SET * @return 0 on success and -1 on error * * @note It is not permitted to seek on files open for writing, * or files compressed with gzip (as opposed to bgzip). */ HTSLIB_EXPORT int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence) HTS_RESULT_USED; /** * Check if the BGZF end-of-file (EOF) marker is present * * @param fp BGZF file handler opened for reading * @return 1 if the EOF marker is present and correct; * 2 if it can't be checked, e.g., because fp isn't seekable; * 0 if the EOF marker is absent; * -1 (with errno set) on error */ HTSLIB_EXPORT int bgzf_check_EOF(BGZF *fp); /** Return the file's compression format * * @param fp BGZF file handle * @return A small integer matching the corresponding * `enum htsCompression` value: * - 0 / `no_compression` if the file is uncompressed * - 1 / `gzip` if the file is plain GZIP-compressed * - 2 / `bgzf` if the file is BGZF-compressed * @since 1.4 */ HTSLIB_EXPORT int bgzf_compression(BGZF *fp); /** * Check if a file is in the BGZF format * * @param fn file name * @return 1 if _fn_ is BGZF; 0 if not or on I/O error */ HTSLIB_EXPORT int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead"); /********************* * Advanced routines * *********************/ /** * Set the cache size. Only effective when compiled with -DBGZF_CACHE. * * @param fp BGZF file handler * @param size size of cache in bytes; 0 to disable caching (default) */ HTSLIB_EXPORT void bgzf_set_cache_size(BGZF *fp, int size); /** * Flush the file if the remaining buffer size is smaller than _size_ * @return 0 if flushing succeeded or was not needed; negative on error */ HTSLIB_EXPORT int bgzf_flush_try(BGZF *fp, ssize_t size) HTS_RESULT_USED; /** * Read one byte from a BGZF file. It is faster than bgzf_read() * @param fp BGZF file handler * @return byte read; -1 on end-of-file or error */ HTSLIB_EXPORT int bgzf_getc(BGZF *fp); /** * Read one line from a BGZF file. It is faster than bgzf_getc() * * @param fp BGZF file handler * @param delim delimiter * @param str string to write to; must be initialized * @return length of the string (capped at INT_MAX); * -1 on end-of-file; <= -2 on error */ HTSLIB_EXPORT int bgzf_getline(BGZF *fp, int delim, struct kstring_t *str); /** * Read the next BGZF block. */ HTSLIB_EXPORT int bgzf_read_block(BGZF *fp) HTS_RESULT_USED; /** * Enable multi-threading via a shared thread pool. This means * both encoder and decoder can balance usage across a single pool * of worker jobs. * * @param fp BGZF file handler * @param pool The thread pool (see hts_create_threads) * @param qsize The size of the job queue. If 0 this is twice the * number of threads in the pool. */ HTSLIB_EXPORT int bgzf_thread_pool(BGZF *fp, struct hts_tpool *pool, int qsize); /** * Enable multi-threading * * @param fp BGZF file handler * @param n_threads #threads used for reading / writing * @param n_sub_blks Unused (was #blocks processed by each thread) */ HTSLIB_EXPORT int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks); /** * Compress a single BGZF block. * * @param dst output buffer (must have size >= BGZF_MAX_BLOCK_SIZE) * @param dlen size of output buffer; updated on return to the number * of bytes actually written to dst * @param src buffer to be compressed * @param slen size of data to compress (must be <= BGZF_BLOCK_SIZE) * @param level compression level * @return 0 on success and negative on error */ HTSLIB_EXPORT int bgzf_compress(void *dst, size_t *dlen, const void *src, size_t slen, int level); /******************* * bgzidx routines * *******************/ /** * Position BGZF at the uncompressed offset * * @param fp BGZF file handler; must be opened for reading * @param uoffset file offset in the uncompressed data * @param where must be SEEK_SET * * Returns 0 on success and -1 on error. * * @note It is not permitted to seek on files open for writing, * or files compressed with gzip (as opposed to bgzip). */ HTSLIB_EXPORT int bgzf_useek(BGZF *fp, off_t uoffset, int where) HTS_RESULT_USED; /** * Position in uncompressed BGZF * * @param fp BGZF file handler; must be opened for reading * * Returns the current offset on success and -1 on error. */ HTSLIB_EXPORT off_t bgzf_utell(BGZF *fp); /** * Tell BGZF to build index while compressing. * * @param fp BGZF file handler; can be opened for reading or writing. * * Returns 0 on success and -1 on error. * * @note This function must be called before any data has been read or * written, and in particular before calling bgzf_mt() on the same * file handle (as threads may start reading data before the index * has been set up). */ HTSLIB_EXPORT int bgzf_index_build_init(BGZF *fp); /// Load BGZF index /** * @param fp BGZF file handler * @param bname base name * @param suffix suffix to add to bname (can be NULL) * @return 0 on success and -1 on error. */ HTSLIB_EXPORT int bgzf_index_load(BGZF *fp, const char *bname, const char *suffix) HTS_RESULT_USED; /// Load BGZF index from an hFILE /** * @param fp BGZF file handle * @param idx hFILE to read from * @param name file name (for error reporting only; can be NULL) * @return 0 on success and -1 on error. * * Populates @p fp with index data read from the hFILE handle @p idx. * The file pointer to @idx should point to the start of the index * data when this function is called. * * The file name can optionally be passed in the @p name parameter. This * is only used for printing error messages; if NULL the word "index" is * used instead. */ HTSLIB_EXPORT int bgzf_index_load_hfile(BGZF *fp, struct hFILE *idx, const char *name) HTS_RESULT_USED; /// Save BGZF index /** * @param fp BGZF file handler * @param bname base name * @param suffix suffix to add to bname (can be NULL) * @return 0 on success and -1 on error. */ HTSLIB_EXPORT int bgzf_index_dump(BGZF *fp, const char *bname, const char *suffix) HTS_RESULT_USED; /// Write a BGZF index to an hFILE /** * @param fp BGZF file handle * @param idx hFILE to write to * @param name file name (for error reporting only, can be NULL) * @return 0 on success and -1 on error. * * Write index data from @p fp to the file @p idx. * * The file name can optionally be passed in the @p name parameter. This * is only used for printing error messages; if NULL the word "index" is * used instead. */ HTSLIB_EXPORT int bgzf_index_dump_hfile(BGZF *fp, struct hFILE *idx, const char *name) HTS_RESULT_USED; #ifdef __cplusplus } #endif #ifdef HTSLIB_SSIZE_T #undef HTSLIB_SSIZE_T #undef ssize_t #endif #endif pysam-0.23.0/htslib/htslib/cram.h000066400000000000000000000600461475062545500166150ustar00rootroot00000000000000/// @file htslib/cram.h /// CRAM format-specific API functions. /* Copyright (C) 2015, 2016, 2018-2020, 2022-2024 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /** @file * Consider using the higher level hts_*() API for programs that wish to * be file format agnostic (see htslib/hts.h). * * This API should be used for CRAM specific code. The specifics of the * public API are implemented in cram_io.h, cram_encode.h and cram_decode.h * although these should not be included directly (use this file instead). */ #ifndef HTSLIB_CRAM_H #define HTSLIB_CRAM_H #include #include #include #include "hts_defs.h" #include "hts.h" #include "sam.h" #ifdef __cplusplus extern "C" { #endif // see cram/cram_structs.h for an internal more complete copy of this enum // Htslib 1.11 had these listed without any hts prefix, and included // some internal values such as RANS1 and GZIP_RLE (which shouldn't have ever // been public). // // We can't find evidence of these being used and the data type occurs // nowhere in functions or structures meaning using it would be pointless. // However for safety, if you absolute need the API to not change then // define HTS_COMPAT to 101100 (XYYYZZ for X.Y[.Z], meaning 1.11). #if defined(HTS_COMPAT) && HTS_COMPAT <= 101100 enum cram_block_method { // Public methods as defined in the CRAM spec. BM_ERROR = -1, // CRAM 2.x and 3.0 RAW = 0, GZIP = 1, BZIP2 = 2, LZMA = 3, RANS = 4, // NB: the subsequent numbers may change. They're simply here for // compatibility with the old API, but may have no bearing on the // internal way htslib works. DO NOT USE RANS0 = 4, RANS1 = 10, GZIP_RLE = 11, }; #else // Values as defined in the CRAM specifications. // See cram/cram_structs.h cram_block_method_int for an expanded version of // this with local specialisations assigned to codes. enum cram_block_method { CRAM_COMP_UNKNOWN = -1, // CRAM 2.x and 3.0 CRAM_COMP_RAW = 0, CRAM_COMP_GZIP = 1, CRAM_COMP_BZIP2 = 2, // CRAM 3.0 CRAM_COMP_LZMA = 3, CRAM_COMP_RANS4x8 = 4, // 4-way interleaving, 8-bit renormalisation // CRAM 3.1 CRAM_COMP_RANSNx16 = 5, // both 4x16 and 32x16 variants, plus transforms CRAM_COMP_ARITH = 6, // aka Range coding CRAM_COMP_FQZ = 7, // FQZComp CRAM_COMP_TOK3 = 8, // Name tokeniser }; #endif /* NOTE this structure may be expanded in future releases by appending * additional fields. * * Do not assume the size is fixed and avoid using arrays of this struct. */ typedef struct { enum cram_block_method method; // Generic compression level if known (0 if not). // 1 or 9 for gzip min/max flag (else 5). 1-9 for bzip2 // 1 or 11 for for tok3 (rans/arith encoder). int level; // For rans* and arith codecs int order; // ransNx16/arith specific int rle; int pack; int stripe; int cat; int nosz; int Nway; // Arithmetic coder only int ext; // external: use gz, xz or bzip2 } cram_method_details; enum cram_content_type { CT_ERROR = -1, FILE_HEADER = 0, COMPRESSION_HEADER = 1, MAPPED_SLICE = 2, UNMAPPED_SLICE = 3, // CRAM V1.0 only EXTERNAL = 4, CORE = 5, }; // Opaque data types, see cram_structs for the fully fledged versions. typedef struct cram_file_def cram_file_def; typedef struct cram_fd cram_fd; typedef struct cram_container cram_container; typedef struct cram_block cram_block; typedef struct cram_slice cram_slice; typedef struct cram_metrics cram_metrics; typedef struct cram_block_slice_hdr cram_block_slice_hdr; typedef struct cram_block_compression_hdr cram_block_compression_hdr; typedef struct cram_codec cram_codec; typedef struct refs_t refs_t; struct hFILE; // Accessor functions /* *----------------------------------------------------------------------------- * cram_fd */ HTSLIB_EXPORT sam_hdr_t *cram_fd_get_header(cram_fd *fd); HTSLIB_EXPORT void cram_fd_set_header(cram_fd *fd, sam_hdr_t *hdr); HTSLIB_EXPORT int cram_fd_get_version(cram_fd *fd); HTSLIB_EXPORT void cram_fd_set_version(cram_fd *fd, int vers); HTSLIB_EXPORT int cram_major_vers(cram_fd *fd); HTSLIB_EXPORT int cram_minor_vers(cram_fd *fd); HTSLIB_EXPORT struct hFILE *cram_fd_get_fp(cram_fd *fd); HTSLIB_EXPORT void cram_fd_set_fp(cram_fd *fd, struct hFILE *fp); /* *----------------------------------------------------------------------------- * cram_container */ HTSLIB_EXPORT int32_t cram_container_get_length(cram_container *c); HTSLIB_EXPORT void cram_container_set_length(cram_container *c, int32_t length); HTSLIB_EXPORT int32_t cram_container_get_num_blocks(cram_container *c); HTSLIB_EXPORT void cram_container_set_num_blocks(cram_container *c, int32_t num_blocks); HTSLIB_EXPORT int32_t *cram_container_get_landmarks(cram_container *c, int32_t *num_landmarks); HTSLIB_EXPORT void cram_container_set_landmarks(cram_container *c, int32_t num_landmarks, int32_t *landmarks); HTSLIB_EXPORT int32_t cram_container_get_num_records(cram_container *c); HTSLIB_EXPORT int64_t cram_container_get_num_bases(cram_container *c); /* Returns true if the container is empty (EOF marker) */ HTSLIB_EXPORT int cram_container_is_empty(cram_fd *fd); /* Returns chromosome and start/span from container struct */ HTSLIB_EXPORT void cram_container_get_coords(cram_container *c, int *refid, hts_pos_t *start, hts_pos_t *span); /* *----------------------------------------------------------------------------- * cram_block */ HTSLIB_EXPORT int32_t cram_block_get_content_id(cram_block *b); HTSLIB_EXPORT int32_t cram_block_get_comp_size(cram_block *b); HTSLIB_EXPORT int32_t cram_block_get_uncomp_size(cram_block *b); HTSLIB_EXPORT int32_t cram_block_get_crc32(cram_block *b); HTSLIB_EXPORT void * cram_block_get_data(cram_block *b); HTSLIB_EXPORT enum cram_content_type cram_block_get_content_type(cram_block *b); HTSLIB_EXPORT enum cram_block_method cram_block_get_method(cram_block *b); HTSLIB_EXPORT cram_method_details *cram_expand_method(uint8_t *data, int32_t size, enum cram_block_method comp); HTSLIB_EXPORT void cram_block_set_content_id(cram_block *b, int32_t id); HTSLIB_EXPORT void cram_block_set_comp_size(cram_block *b, int32_t size); HTSLIB_EXPORT void cram_block_set_uncomp_size(cram_block *b, int32_t size); HTSLIB_EXPORT void cram_block_set_crc32(cram_block *b, int32_t crc); HTSLIB_EXPORT void cram_block_set_data(cram_block *b, void *data); HTSLIB_EXPORT int cram_block_append(cram_block *b, const void *data, int size); HTSLIB_EXPORT void cram_block_update_size(cram_block *b); // Offset is known as "size" internally, but it can be confusing. HTSLIB_EXPORT size_t cram_block_get_offset(cram_block *b); HTSLIB_EXPORT void cram_block_set_offset(cram_block *b, size_t offset); /* * Computes the size of a cram block, including the block * header itself. */ HTSLIB_EXPORT uint32_t cram_block_size(cram_block *b); /* * Returns the Block Content ID values referred to by a cram_codec in * ids[2]. * * -2 is unused. * -1 is CORE * >= 0 is the block with that Content ID */ HTSLIB_EXPORT void cram_codec_get_content_ids(cram_codec *c, int ids[2]); /* * Produces a human readable description of the codec parameters. * This is appended to an existing kstring 'ks'. * * Returns 0 on succes, * <0 on failure */ HTSLIB_EXPORT int cram_codec_describe(cram_codec *c, kstring_t *ks); /* * Renumbers RG numbers in a cram compression header. * * CRAM stores RG as the Nth number in the header, rather than a * string holding the ID: tag. This is smaller in space, but means * "samtools cat" to join files together that contain single but * different RG lines needs a way of renumbering them. * * The file descriptor is expected to be immediately after the * cram_container structure (ie before the cram compression header). * Due to the nature of the CRAM format, this needs to read and write * the blocks itself. Note that there may be multiple slices within * the container, meaning multiple compression headers to manipulate. * Changing RG may change the size of the compression header and * therefore the length field in the container. Hence we rewrite all * blocks just in case and also emit the adjusted container. * * The current implementation can only cope with renumbering a single * RG (and only then if it is using HUFFMAN or BETA codecs). In * theory it *may* be possible to renumber multiple RGs if they use * HUFFMAN to the CORE block or use an external block unshared by any * other data series. So we have an API that can be upgraded to * support this, but do not implement it for now. An example * implementation of RG as an EXTERNAL block would be to find that * block and rewrite it, returning the number of blocks consumed. * * Returns 0 on success; * -1 if unable to edit; * -2 on other errors (eg I/O). */ HTSLIB_EXPORT int cram_transcode_rg(cram_fd *in, cram_fd *out, cram_container *c, int nrg, int *in_rg, int *out_rg); /* * Copies the blocks representing the next num_slice slices from a * container from 'in' to 'out'. It is expected that the file pointer * is just after the read of the cram_container and cram compression * header. * * Returns 0 on success * -1 on failure */ HTSLIB_EXPORT int cram_copy_slice(cram_fd *in, cram_fd *out, int32_t num_slice); /* * Copies a container, but filtering it down to a specific region (as * already specified in 'in' * * Returns 0 on success * -1 on EOF * -2 on error */ HTSLIB_EXPORT int cram_filter_container(cram_fd *in, cram_fd *out, cram_container *c, int *ref_id); /* * Decodes a CRAM block compression header. * Returns header ptr on success * NULL on failure */ HTSLIB_EXPORT cram_block_compression_hdr *cram_decode_compression_header(cram_fd *fd, cram_block *b); /* * Frees a cram_block_compression_hdr structure. */ HTSLIB_EXPORT void cram_free_compression_header(cram_block_compression_hdr *hdr); typedef struct cram_cid2ds_t cram_cid2ds_t; /* * Map cram block numbers to data-series. It's normally a 1:1 mapping, * but in rare cases it can be 1:many (or even many:many). * The key is the block number and the value is an index into the data-series * array, which we iterate over until reaching a negative value. * * Provide cid2ds as NULL to allocate a new map or pass in an existing one * to append to this map. The new (or existing) map is returned. * * Returns the cid2ds (newly allocated or as provided) on success, * NULL on failure. */ HTSLIB_EXPORT cram_cid2ds_t *cram_update_cid2ds_map(cram_block_compression_hdr *hdr, cram_cid2ds_t *cid2ds); /* * Return a list of data series observed as belonging to a block with * the specified content_id. *n is the number of data series * returned, or 0 if block is unused. * Block content_id of -1 is used to indicate the CORE block. * * The pointer returned is owned by the cram_cid2ds state and should * not be freed by the caller. */ HTSLIB_EXPORT int *cram_cid2ds_query(cram_cid2ds_t *c2d, int content_id, int *n); /* * Frees a cram_cid2ds_t allocated by cram_update_cid2ds_map */ HTSLIB_EXPORT void cram_cid2ds_free(cram_cid2ds_t *cid2ds); /* * Produces a description of the record and tag encodings held within * a compression header and appends to 'ks'. * * Returns 0 on success, * <0 on failure. */ HTSLIB_EXPORT int cram_describe_encodings(cram_block_compression_hdr *hdr, kstring_t *ks); /* *----------------------------------------------------------------------------- * cram slice interrogation */ /* * Returns the number of cram blocks within this slice. */ HTSLIB_EXPORT int32_t cram_slice_hdr_get_num_blocks(cram_block_slice_hdr *hdr); /* * Returns the block content_id for the block containing an embedded reference * sequence. If none is present, -1 is returned. */ HTSLIB_EXPORT int cram_slice_hdr_get_embed_ref_id(cram_block_slice_hdr *h); /* * Returns slice reference ID, start and span (length) coordinates. * Return parameters may be NULL in which case they are ignored. */ HTSLIB_EXPORT void cram_slice_hdr_get_coords(cram_block_slice_hdr *h, int *refid, hts_pos_t *start, hts_pos_t *span); /* * Decodes a slice header from a cram block. * Returns the opaque cram_block_slice_hdr pointer on success, * NULL on failure. */ HTSLIB_EXPORT cram_block_slice_hdr *cram_decode_slice_header(cram_fd *fd, cram_block *b); /* * Frees a cram_block_slice_hdr structure. */ HTSLIB_EXPORT void cram_free_slice_header(cram_block_slice_hdr *hdr); /* *----------------------------------------------------------------------------- * cram_io basics */ /**@{ ---------------------------------------------------------------------- * CRAM blocks - the dynamically growable data block. We have code to * create, update, (un)compress and read/write. * * These are derived from the deflate_interlaced.c blocks, but with the * CRAM extension of content types and IDs. */ /*! Allocates a new cram_block structure with a specified content_type and * id. * * @return * Returns block pointer on success; * NULL on failure * * The cram_block struct returned by a successful call should be freed * via cram_free_block() when it is no longer needed. */ HTSLIB_EXPORT cram_block *cram_new_block(enum cram_content_type content_type, int content_id); /*! Reads a block from a cram file. * * @return * Returns cram_block pointer on success; * NULL on failure * * The cram_block struct returned by a successful call should be freed * via cram_free_block() when it is no longer needed. */ HTSLIB_EXPORT cram_block *cram_read_block(cram_fd *fd); /*! Writes a CRAM block. * * @return * Returns 0 on success; * -1 on failure */ HTSLIB_EXPORT int cram_write_block(cram_fd *fd, cram_block *b); /*! Frees a CRAM block, deallocating internal data too. */ HTSLIB_EXPORT void cram_free_block(cram_block *b); /*! Uncompresses a CRAM block, if compressed. * * @return * Returns 0 on success; * -1 on failure */ HTSLIB_EXPORT int cram_uncompress_block(cram_block *b); /*! Compresses a block. * * Compresses a block using one of two different zlib strategies. If we only * want one choice set strat2 to be -1. * * The logic here is that sometimes Z_RLE does a better job than Z_FILTERED * or Z_DEFAULT_STRATEGY on quality data. If so, we'd rather use it as it is * significantly faster. * * @return * Returns 0 on success; * -1 on failure */ HTSLIB_EXPORT int cram_compress_block(cram_fd *fd, cram_block *b, cram_metrics *metrics, int method, int level); int cram_compress_block2(cram_fd *fd, cram_slice *s, cram_block *b, cram_metrics *metrics, int method, int level); /**@}*/ /**@{ ---------------------------------------------------------------------- * Containers */ /*! Creates a new container, specifying the maximum number of slices * and records permitted. * * @return * Returns cram_container ptr on success; * NULL on failure * * The cram_container struct returned by a successful call should be freed * via cram_free_container() when it is no longer needed. */ HTSLIB_EXPORT cram_container *cram_new_container(int nrec, int nslice); HTSLIB_EXPORT void cram_free_container(cram_container *c); /*! Reads a container header. * * @return * Returns cram_container on success; * NULL on failure or no container left (fd->err == 0). * * The cram_container struct returned by a successful call should be freed * via cram_free_container() when it is no longer needed. */ HTSLIB_EXPORT cram_container *cram_read_container(cram_fd *fd); /*! Writes a container structure. * * @return * Returns 0 on success; * -1 on failure */ HTSLIB_EXPORT int cram_write_container(cram_fd *fd, cram_container *h); /* * Stores the container structure in dat and returns *size as the * number of bytes written to dat[]. The input size of dat is also * held in *size and should be initialised to cram_container_size(c). * * Returns 0 on success; * -1 on failure */ HTSLIB_EXPORT int cram_store_container(cram_fd *fd, cram_container *c, char *dat, int *size); HTSLIB_EXPORT int cram_container_size(cram_container *c); /**@}*/ /**@{ ---------------------------------------------------------------------- * The top-level cram opening, closing and option handling */ /*! Opens a CRAM file for read (mode "rb") or write ("wb"). * * The filename may be "-" to indicate stdin or stdout. * * @return * Returns file handle on success; * NULL on failure. */ HTSLIB_EXPORT cram_fd *cram_open(const char *filename, const char *mode); /*! Opens an existing stream for reading or writing. * * @return * Returns file handle on success; * NULL on failure. */ HTSLIB_EXPORT cram_fd *cram_dopen(struct hFILE *fp, const char *filename, const char *mode); /*! Closes a CRAM file. * * @return * Returns 0 on success; * -1 on failure */ HTSLIB_EXPORT int cram_close(cram_fd *fd); /* * Seek within a CRAM file. * * Returns 0 on success * -1 on failure */ HTSLIB_EXPORT int cram_seek(cram_fd *fd, off_t offset, int whence); /* * Flushes a CRAM file. * Useful for when writing to stdout without wishing to close the stream. * * Returns 0 on success * -1 on failure */ HTSLIB_EXPORT int cram_flush(cram_fd *fd); /*! Checks for end of file on a cram_fd stream. * * @return * Returns 0 if not at end of file * 1 if we hit an expected EOF (end of range or EOF block) * 2 for other EOF (end of stream without EOF block) */ HTSLIB_EXPORT int cram_eof(cram_fd *fd); /*! Sets options on the cram_fd. * * See CRAM_OPT_* definitions in hts.h. * Use this immediately after opening. * * @return * Returns 0 on success; * -1 on failure */ HTSLIB_EXPORT int cram_set_option(cram_fd *fd, enum hts_fmt_option opt, ...); /*! Sets options on the cram_fd. * * See CRAM_OPT_* definitions in hts.h. * Use this immediately after opening. * * @return * Returns 0 on success; * -1 on failure */ HTSLIB_EXPORT int cram_set_voption(cram_fd *fd, enum hts_fmt_option opt, va_list args); /*! * Attaches a header to a cram_fd. * * This should be used when creating a new cram_fd for writing where * we have an SAM_hdr already constructed (eg from a file we've read * in). * * @return * Returns 0 on success; * -1 on failure */ HTSLIB_EXPORT int cram_set_header(cram_fd *fd, sam_hdr_t *hdr); /*! Check if this file has a proper EOF block * * @return * Returns 3 if the file is a version of CRAM that does not contain EOF blocks * 2 if the file is a stream and thus unseekable * 1 if the file contains an EOF block * 0 if the file does not contain an EOF block * -1 if an error occurred whilst reading the file or we could not seek back to where we were * */ HTSLIB_EXPORT int cram_check_EOF(cram_fd *fd); /* As int32_decoded/encode, but from/to blocks instead of cram_fd */ HTSLIB_EXPORT int int32_put_blk(cram_block *b, int32_t val); /**@}*/ /**@{ ------------------------------------------------------------------- * Old typedef and function names for compatibility with existing code. * Header functionality is now provided by sam.h's sam_hdr_t functions. */ typedef sam_hdr_t SAM_hdr; /*! Tokenises a SAM header into a hash table. * * Also extracts a few bits on specific data types, such as @RG lines. * * @return * Returns a SAM_hdr struct on success (free with sam_hdr_free()); * NULL on failure */ static inline SAM_hdr *sam_hdr_parse_(const char *hdr, size_t len) { return sam_hdr_parse(len, hdr); } /*! Deallocates all storage used by a SAM_hdr struct. * * This also decrements the header reference count. If after decrementing * it is still non-zero then the header is assumed to be in use by another * caller and the free is not done. */ static inline void sam_hdr_free(SAM_hdr *hdr) { sam_hdr_destroy(hdr); } /* sam_hdr_length() and sam_hdr_str() are now provided by sam.h. */ /*! Add an @PG line. * * If we wish complete control over this use sam_hdr_add_line() directly. This * function uses that, but attempts to do a lot of tedious house work for * you too. * * - It will generate a suitable ID if the supplied one clashes. * - It will generate multiple @PG records if we have multiple PG chains. * * Call it as per sam_hdr_add_line() with a series of key,value pairs ending * in NULL. * * @return * Returns 0 on success; * -1 on failure */ #define sam_hdr_add_PG sam_hdr_add_pg /**@{ -------------------------------------------------------------------*/ /*! * Returns the refs_t structure used by a cram file handle. * * This may be used in conjunction with option CRAM_OPT_SHARED_REF to * share reference memory between multiple file handles. * * @return * Returns NULL if none exists or the file handle is not a CRAM file. */ HTSLIB_EXPORT refs_t *cram_get_refs(htsFile *fd); /*! * Returns the file offsets of CRAM slices covering a specific region * query. Note both offsets are the START of the slice. * * first will point to the start of the first overlapping slice * last will point to the start of the last overlapping slice * * @return * Returns 0 on success * <0 on failure */ HTSLIB_EXPORT int cram_index_extents(cram_fd *fd, int refid, hts_pos_t start, hts_pos_t end, off_t *first, off_t *last); /*! Returns the total number of containers in the CRAM index. * * Note the index is not required to have an entry for every container, but it * will always have an index entry for the start of each chromosome. * (Although in practice our indices do container one entry per container.) * * This is equivalent to cram_num_containers_between(fd, 0, 0, NULL, NULL) */ HTSLIB_EXPORT int64_t cram_num_containers(cram_fd *fd); /*! Returns the number of containers in the CRAM index within given offsets. * * The cstart and cend offsets are the locations of the start of containers * as returned by index_container_offset. * * If non-NULL, first and last will hold the inclusive range of container * numbers, counting from zero. * * @return * Returns the number of containers, equivalent to *last-*first+1. */ HTSLIB_EXPORT int64_t cram_num_containers_between(cram_fd *fd, off_t cstart, off_t cend, int64_t *first, int64_t *last); /*! Returns the byte offset for the start of the n^th container. * * The index must have previously been loaded, otherwise <0 is returned. */ HTSLIB_EXPORT off_t cram_container_num2offset(cram_fd *fd, int64_t n); /*! Returns the container number for the first container at offset >= pos. * * The index must have previously been loaded, otherwise <0 is returned. */ HTSLIB_EXPORT int64_t cram_container_offset2num(cram_fd *fd, off_t pos); /**@}*/ #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/htslib/faidx.h000066400000000000000000000354221475062545500167660ustar00rootroot00000000000000/// @file htslib/faidx.h /// FASTA random access. /* Copyright (C) 2008, 2009, 2013, 2014, 2016, 2017-2020, 2022-2023 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTSLIB_FAIDX_H #define HTSLIB_FAIDX_H #include #include "hts_defs.h" #include "hts.h" #ifdef __cplusplus extern "C" { #endif /** @file Index FASTA or FASTQ files and extract subsequence. The fai file index columns for FASTA are: - chromosome name - chromosome length: number of bases - offset: number of bytes to skip to get to the first base from the beginning of the file, including the length of the sequence description string (`>chr ..\n`) - line length: number of bases per line (excluding `\n`) - binary line length: number of bytes, including `\n` The index for FASTQ is similar to above: - chromosome name - chromosome length: number of bases - sequence offset: number of bytes to skip to get to the first base from the beginning of the file, including the length of the sequence description string (`@chr ..\n`) - line length: number of bases per line (excluding `\n`) - binary line length: number of bytes, including `\n` - quality offset: number of bytes to skip from the beginning of the file to get to the first quality value in the indexed entry. The FASTQ version of the index uses line length and binary line length for both the sequence and the quality values, so they must be line wrapped in the same way. */ struct faidx_t; /// Opaque structure representing FASTA index typedef struct faidx_t faidx_t; /// Opaque structure; sole item needed from htslib/thread_pool.h struct hts_tpool; /// File format to be dealing with. enum fai_format_options { FAI_NONE, FAI_FASTA, FAI_FASTQ }; /// Build index for a FASTA or FASTQ or bgzip-compressed FASTA or FASTQ file. /** @param fn FASTA/FASTQ file name @param fnfai Name of .fai file to build. @param fngzi Name of .gzi file to build (if fn is bgzip-compressed). @return 0 on success; or -1 on failure If fnfai is NULL, ".fai" will be appended to fn to make the FAI file name. If fngzi is NULL, ".gzi" will be appended to fn for the GZI file. The GZI file will only be built if fn is bgzip-compressed. */ HTSLIB_EXPORT int fai_build3(const char *fn, const char *fnfai, const char *fngzi) HTS_RESULT_USED; /// Build index for a FASTA or FASTQ or bgzip-compressed FASTA or FASTQ file. /** @param fn FASTA/FASTQ file name @return 0 on success; or -1 on failure File "fn.fai" will be generated. This function is equivalent to fai_build3(fn, NULL, NULL); */ HTSLIB_EXPORT int fai_build(const char *fn) HTS_RESULT_USED; /// Destroy a faidx_t struct HTSLIB_EXPORT void fai_destroy(faidx_t *fai); enum fai_load_options { FAI_CREATE = 0x01, }; /// Load FASTA indexes. /** @param fn File name of the FASTA file (can be compressed with bgzip). @param fnfai File name of the FASTA index. @param fngzi File name of the bgzip index. @param flags Option flags to control index file caching and creation. @return Pointer to a faidx_t struct on success, NULL on failure. If fnfai is NULL, ".fai" will be appended to fn to make the FAI file name. If fngzi is NULL, ".gzi" will be appended to fn for the bgzip index name. The bgzip index is only needed if fn is compressed. If (flags & FAI_CREATE) is true, the index files will be built using fai_build3() if they are not already present. The struct returned by a successful call should be freed via fai_destroy() when it is no longer needed. */ HTSLIB_EXPORT faidx_t *fai_load3(const char *fn, const char *fnfai, const char *fngzi, int flags); /// Load index from "fn.fai". /** @param fn File name of the FASTA file @return Pointer to a faidx_t struct on success, NULL on failure. This function is equivalent to fai_load3(fn, NULL, NULL, FAI_CREATE|FAI_CACHE); */ HTSLIB_EXPORT faidx_t *fai_load(const char *fn); /// Load FASTA or FASTQ indexes. /** @param fn File name of the FASTA/FASTQ file (can be compressed with bgzip). @param fnfai File name of the FASTA/FASTQ index. @param fngzi File name of the bgzip index. @param flags Option flags to control index file caching and creation. @param format FASTA or FASTQ file format @return Pointer to a faidx_t struct on success, NULL on failure. If fnfai is NULL, ".fai" will be appended to fn to make the FAI file name. If fngzi is NULL, ".gzi" will be appended to fn for the bgzip index name. The bgzip index is only needed if fn is compressed. If (flags & FAI_CREATE) is true, the index files will be built using fai_build3() if they are not already present. The struct returned by a successful call should be freed via fai_destroy() when it is no longer needed. */ HTSLIB_EXPORT faidx_t *fai_load3_format(const char *fn, const char *fnfai, const char *fngzi, int flags, enum fai_format_options format); /// Load index from "fn.fai". /** @param fn File name of the FASTA/FASTQ file @param format FASTA or FASTQ file format @return Pointer to a faidx_t struct on success, NULL on failure. This function is equivalent to fai_load3_format(fn, NULL, NULL, FAI_CREATE|FAI_CACHE, format); */ HTSLIB_EXPORT faidx_t *fai_load_format(const char *fn, enum fai_format_options format); /// Fetch the sequence in a region /** @param fai Pointer to the faidx_t struct @param reg Region in the format "chr2:20,000-30,000" @param len Length of the region; -2 if seq not present, -1 general error @return Pointer to the sequence; `NULL` on failure The returned sequence is allocated by `malloc()` family and should be destroyed by end users by calling `free()` on it. To work around ambiguous parsing issues, eg both "chr1" and "chr1:100-200" are reference names, quote using curly braces. Thus "{chr1}:100-200" and "{chr1:100-200}" disambiguate the above example. */ HTSLIB_EXPORT char *fai_fetch(const faidx_t *fai, const char *reg, int *len); HTSLIB_EXPORT char *fai_fetch64(const faidx_t *fai, const char *reg, hts_pos_t *len); /// Query the line-wrap length for a chromosome specified as part of a region /** @param fai Pointer to the faidx_t struct @param reg Region in the format "chr2:20,000-30,000" @return The line length (excluding newline), negative on error. */ HTSLIB_EXPORT hts_pos_t fai_line_length(const faidx_t *fai, const char *reg); /// Fetch the quality string for a region for FASTQ files /** @param fai Pointer to the faidx_t struct @param reg Region in the format "chr2:20,000-30,000" @param len Length of the region; -2 if seq not present, -1 general error @return Pointer to the quality string; null on failure The returned quality string is allocated by `malloc()` family and should be destroyed by end users by calling `free()` on it. Region names can be quoted with curly braces, as for fai_fetch(). */ HTSLIB_EXPORT char *fai_fetchqual(const faidx_t *fai, const char *reg, int *len); HTSLIB_EXPORT char *fai_fetchqual64(const faidx_t *fai, const char *reg, hts_pos_t *len); /// Fetch the number of sequences /** @param fai Pointer to the faidx_t struct @return The number of sequences */ HTSLIB_EXPORT int faidx_fetch_nseq(const faidx_t *fai) HTS_DEPRECATED("Please use faidx_nseq instead"); /// Fetch the sequence in a region /** @param fai Pointer to the faidx_t struct @param c_name Region name @param p_beg_i Beginning position number (zero-based) @param p_end_i End position number (zero-based) @param len Length of the region; -2 if c_name not present, -1 general error @return Pointer to the sequence; null on failure The returned sequence is allocated by `malloc()` family and should be destroyed by end users by calling `free()` on it. */ HTSLIB_EXPORT char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len); /// Fetch the sequence in a region /** @param fai Pointer to the faidx_t struct @param c_name Region name @param p_beg_i Beginning position number (zero-based) @param p_end_i End position number (zero-based) @param len Length of the region; -2 if c_name not present, -1 general error @return Pointer to the sequence; null on failure The returned sequence is allocated by `malloc()` family and should be destroyed by end users by calling `free()` on it. */ HTSLIB_EXPORT char *faidx_fetch_seq64(const faidx_t *fai, const char *c_name, hts_pos_t p_beg_i, hts_pos_t p_end_i, hts_pos_t *len); /// Fetch the quality string in a region for FASTQ files /** @param fai Pointer to the faidx_t struct @param c_name Region name @param p_beg_i Beginning position number (zero-based) @param p_end_i End position number (zero-based) @param len Length of the region; -2 if c_name not present, -1 general error @return Pointer to the sequence; null on failure The returned sequence is allocated by `malloc()` family and should be destroyed by end users by calling `free()` on it. */ HTSLIB_EXPORT char *faidx_fetch_qual(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len); /// Fetch the quality string in a region for FASTQ files /** @param fai Pointer to the faidx_t struct @param c_name Region name @param p_beg_i Beginning position number (zero-based) @param p_end_i End position number (zero-based) @param len Length of the region; -2 if c_name not present, -1 general error @return Pointer to the sequence; null on failure The returned sequence is allocated by `malloc()` family and should be destroyed by end users by calling `free()` on it. */ HTSLIB_EXPORT char *faidx_fetch_qual64(const faidx_t *fai, const char *c_name, hts_pos_t p_beg_i, hts_pos_t p_end_i, hts_pos_t *len); /// Query if sequence is present /** @param fai Pointer to the faidx_t struct @param seq Sequence name @return 1 if present or 0 if absent */ HTSLIB_EXPORT int faidx_has_seq(const faidx_t *fai, const char *seq); /// Return number of sequences in fai index HTSLIB_EXPORT int faidx_nseq(const faidx_t *fai); /// Return name of i-th sequence HTSLIB_EXPORT const char *faidx_iseq(const faidx_t *fai, int i); /// Return sequence length /** @param fai Pointer to the faidx_t struct @param seq Name of the sequence @return Sequence length, or -1 if not present */ HTSLIB_EXPORT hts_pos_t faidx_seq_len64(const faidx_t *fai, const char *seq); /// Return sequence length /** @param fai Pointer to the faidx_t struct @param seq Name of the sequence @return Sequence length, or -1 if not present @deprecated This funtion cannot handle very long sequences. Use faidx_seq_len64() instead. */ HTSLIB_EXPORT int faidx_seq_len(const faidx_t *fai, const char *seq); /// Parses a region string. /** @param fai Pointer to the faidx_t struct @param s Region string @param tid Returns which i-th sequence is described in the region. @param beg Returns the start of the region (0 based) @param end Returns the one past last of the region (0 based) @param flags Parsing method, see HTS_PARSE_* in hts.h. @return Pointer to end of parsed s if successful, NULL if not. To work around ambiguous parsing issues, eg both "chr1" and "chr1:100-200" are reference names, quote using curly braces. Thus "{chr1}:100-200" and "{chr1:100-200}" disambiguate the above example. */ HTSLIB_EXPORT const char *fai_parse_region(const faidx_t *fai, const char *s, int *tid, hts_pos_t *beg, hts_pos_t *end, int flags); /// Adjust region to the actual sequence length /** @param fai Pointer to the faidx_t struct @param tid Sequence index, as returned by fai_parse_region() @param beg[in,out] The start of the region (0 based) @param end[in,out] One past end of the region (0 based) @return 1, 2, or 3 if @p beg, @p end, or both are adjusted, 0 if @p beg and @p end are unchanged -1 on error Looks up the length of @p tid, and then adjusts the values of @p beg and @p end if they fall outside the boundaries of the sequence. If @p beg > @p end, it will be set to @p end. The return value indicates which, if any, of the inputs have been adjusted. -1 will be returned if @p tid is not a valid sequence index. */ HTSLIB_EXPORT int fai_adjust_region(const faidx_t *fai, int tid, hts_pos_t *beg, hts_pos_t *end); /// Sets the cache size of the underlying BGZF compressed file /** @param fai Pointer to the faidx_t struct * @param cache_size Selected cache size in bytes */ HTSLIB_EXPORT void fai_set_cache_size(faidx_t *fai, int cache_size); /// Adds a thread pool to the underlying BGZF layer. /** @param fai FAI file handler * @param pool The thread pool (see hts_create_threads) * @param qsize The size of the job queue. If 0 this is twice the * number of threads in the pool. */ HTSLIB_EXPORT int fai_thread_pool(faidx_t *fai, struct hts_tpool *pool, int qsize); /// Determines the path to the reference index file /** @param fa String with the path to the reference file * @return String with the path to the reference index file, or NULL on failure If the reference path has the format reference.fa##idx##index.fa.fai, the index path is taken directly from it as index.fa.fai. If the reference file is local and the index file cannot be found, it will be created alongside the reference file. If the reference file is remote and the index file cannot be found, the method returns NULL. The returned string has to be freed by the user at the end of its scope. */ HTSLIB_EXPORT char *fai_path(const char *fa); #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/htslib/hfile.h000066400000000000000000000324121475062545500167560ustar00rootroot00000000000000/// @file htslib/hfile.h /// Buffered low-level input/output streams. /* Copyright (C) 2013-2022 Genome Research Ltd. Author: John Marshall Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTSLIB_HFILE_H #define HTSLIB_HFILE_H #include #include #include "hts_defs.h" // Ensure ssize_t exists within this header. All #includes must precede this, // and ssize_t must be undefined again at the end of this header. #if defined _MSC_VER && defined _INTPTR_T_DEFINED && !defined _SSIZE_T_DEFINED && !defined ssize_t #define HTSLIB_SSIZE_T #define ssize_t intptr_t #endif #ifdef __cplusplus extern "C" { #endif struct hFILE_backend; struct kstring_t; /// Low-level input/output stream handle /** The fields of this structure are declared here solely for the benefit of the hFILE-related inline functions. They may change in future releases. User code should not use them directly; you should imagine that hFILE is an opaque incomplete type. */ typedef struct hFILE { // @cond internal char *buffer, *begin, *end, *limit; const struct hFILE_backend *backend; off_t offset; unsigned at_eof:1, mobile:1, readonly:1, preserve:1; int has_errno; // @endcond } hFILE; /// Open the named file or URL as a stream /** @return An hFILE pointer, or `NULL` (with _errno_ set) if an error occurred. The usual `fopen(3)` _mode_ letters are supported: one of `r` (read), `w` (write), `a` (append), optionally followed by any of `+` (update), `e` (close on `exec(2)`), `x` (create exclusively), `:` (indicates scheme-specific variable arguments follow). */ HTSLIB_EXPORT hFILE *hopen(const char *filename, const char *mode, ...) HTS_RESULT_USED; /// Associate a stream with an existing open file descriptor /** @return An hFILE pointer, or `NULL` (with _errno_ set) if an error occurred. Note that the file must be opened in binary mode, or else there will be problems on platforms that make a difference between text and binary mode. By default, the returned hFILE "takes ownership" of the file descriptor and _fd_ will be closed by hclose(). When _mode_ contains `S` (shared fd), hclose() will destroy the hFILE but not close the underlying _fd_. For socket descriptors (on Windows), _mode_ should contain `s`. */ HTSLIB_EXPORT hFILE *hdopen(int fd, const char *mode) HTS_RESULT_USED; /// Report whether the file name or URL denotes remote storage /** @return 0 if local, 1 if remote. "Remote" means involving e.g. explicit network access, with the implication that callers may wish to cache such files' contents locally. */ HTSLIB_EXPORT int hisremote(const char *filename) HTS_RESULT_USED; /// Append an extension or replace an existing extension /** @param buffer The kstring to be used to store the modified filename @param filename The filename to be (copied and) adjusted @param replace If non-zero, one extension (if any) is removed first @param extension The extension to be added (e.g. ".csi") @return The modified filename (i.e., `buffer->s`), or NULL on error. @since 1.10 If _filename_ is an URL, alters extensions at the end of the `hier-part`, leaving any trailing `?query` or `#fragment` unchanged. */ HTSLIB_EXPORT char *haddextension(struct kstring_t *buffer, const char *filename, int replace, const char *extension) HTS_RESULT_USED; /// Flush (for output streams) and close the stream /** @return 0 if successful, or `EOF` (with _errno_ set) if an error occurred. */ HTSLIB_EXPORT int hclose(hFILE *fp) HTS_RESULT_USED; /// Close the stream, without flushing or propagating errors /** For use while cleaning up after an error only. Preserves _errno_. */ HTSLIB_EXPORT void hclose_abruptly(hFILE *fp); /// Return the stream's error indicator /** @return Non-zero (in fact, an _errno_ value) if an error has occurred. This would be called `herror()` and return true/false to parallel `ferror(3)`, but a networking-related `herror(3)` function already exists. */ static inline int herrno(hFILE *fp) { return fp->has_errno; } /// Clear the stream's error indicator static inline void hclearerr(hFILE *fp) { fp->has_errno = 0; } /// Reposition the read/write stream offset /** @return The resulting offset within the stream (as per `lseek(2)`), or negative if an error occurred. */ HTSLIB_EXPORT off_t hseek(hFILE *fp, off_t offset, int whence) HTS_RESULT_USED; /// Report the current stream offset /** @return The offset within the stream, starting from zero. */ static inline off_t htell(hFILE *fp) { return fp->offset + (fp->begin - fp->buffer); } /// Read one character from the stream /** @return The character read, or `EOF` on end-of-file or error. */ static inline int hgetc(hFILE *fp) { HTSLIB_EXPORT extern int hgetc2(hFILE *); return (fp->end > fp->begin)? (unsigned char) *(fp->begin++) : hgetc2(fp); } /// Read from the stream until the delimiter, up to a maximum length /** @param buffer The buffer into which bytes will be written @param size The size of the buffer @param delim The delimiter (interpreted as an `unsigned char`) @param fp The file stream @return The number of bytes read, or negative on error. @since 1.4 Bytes will be read into the buffer up to and including a delimiter, until EOF is reached, or _size-1_ bytes have been written, whichever comes first. The string will then be terminated with a NUL byte (`\0`). */ HTSLIB_EXPORT ssize_t hgetdelim(char *buffer, size_t size, int delim, hFILE *fp) HTS_RESULT_USED; /// Read a line from the stream, up to a maximum length /** @param buffer The buffer into which bytes will be written @param size The size of the buffer @param fp The file stream @return The number of bytes read, or negative on error. @since 1.4 Specialization of hgetdelim() for a `\n` delimiter. */ static inline ssize_t HTS_RESULT_USED hgetln(char *buffer, size_t size, hFILE *fp) { return hgetdelim(buffer, size, '\n', fp); } /// Read a line from the stream, up to a maximum length /** @param buffer The buffer into which bytes will be written @param size The size of the buffer (must be > 1 to be useful) @param fp The file stream @return _buffer_ on success, or `NULL` if an error occurred. @since 1.4 This function can be used as a replacement for `fgets(3)`, or together with kstring's `kgetline()` to read arbitrarily-long lines into a _kstring_t_. */ HTSLIB_EXPORT char *hgets(char *buffer, int size, hFILE *fp) HTS_RESULT_USED; /// Peek at characters to be read without removing them from buffers /** @param fp The file stream @param buffer The buffer to which the peeked bytes will be written @param nbytes The number of bytes to peek at; limited by the size of the internal buffer, which could be as small as 4K. @return The number of bytes peeked, which may be less than _nbytes_ if EOF is encountered; or negative, if there was an I/O error. The characters peeked at remain in the stream's internal buffer, and will be returned by later hread() etc calls. */ HTSLIB_EXPORT ssize_t hpeek(hFILE *fp, void *buffer, size_t nbytes) HTS_RESULT_USED; /// Read a block of characters from the file /** @return The number of bytes read, or negative if an error occurred. The full _nbytes_ requested will be returned, except as limited by EOF or I/O errors. */ static inline ssize_t HTS_RESULT_USED hread(hFILE *fp, void *buffer, size_t nbytes) { HTSLIB_EXPORT extern ssize_t hread2(hFILE *, void *, size_t, size_t); size_t n = fp->end - fp->begin; if (n > nbytes) n = nbytes; memcpy(buffer, fp->begin, n); fp->begin += n; return (n == nbytes || !fp->mobile)? (ssize_t) n : hread2(fp, buffer, nbytes, n); } /// Write a character to the stream /** @return The character written, or `EOF` if an error occurred. */ static inline int hputc(int c, hFILE *fp) { HTSLIB_EXPORT extern int hputc2(int, hFILE *); if (fp->begin < fp->limit) *(fp->begin++) = c; else c = hputc2(c, fp); return c; } /// Write a string to the stream /** @return 0 if successful, or `EOF` if an error occurred. */ static inline int hputs(const char *text, hFILE *fp) { HTSLIB_EXPORT extern int hputs2(const char *, size_t, size_t, hFILE *); size_t nbytes = strlen(text), n = fp->limit - fp->begin; if (n > nbytes) n = nbytes; memcpy(fp->begin, text, n); fp->begin += n; return (n == nbytes)? 0 : hputs2(text, nbytes, n, fp); } /// Write a block of characters to the file /** @return Either _nbytes_, or negative if an error occurred. In the absence of I/O errors, the full _nbytes_ will be written. */ static inline ssize_t HTS_RESULT_USED hwrite(hFILE *fp, const void *buffer, size_t nbytes) { HTSLIB_EXPORT extern ssize_t hwrite2(hFILE *, const void *, size_t, size_t); HTSLIB_EXPORT extern int hfile_set_blksize(hFILE *fp, size_t bufsiz); if (!fp->mobile) { size_t n = fp->limit - fp->begin; if (n < nbytes) { hfile_set_blksize(fp, fp->limit - fp->buffer + nbytes); fp->end = fp->limit; } } size_t n = fp->limit - fp->begin; if (nbytes >= n && fp->begin == fp->buffer) { // Go straight to hwrite2 if the buffer is empty and the request // won't fit. return hwrite2(fp, buffer, nbytes, 0); } if (n > nbytes) n = nbytes; memcpy(fp->begin, buffer, n); fp->begin += n; return (n==nbytes)? (ssize_t) n : hwrite2(fp, buffer, nbytes, n); } /// For writing streams, flush buffered output to the underlying stream /** @return 0 if successful, or `EOF` if an error occurred. This includes low-level flushing such as via `fdatasync(2)`. */ HTSLIB_EXPORT int hflush(hFILE *fp) HTS_RESULT_USED; /// For hfile_mem: get the internal buffer and it's size from a hfile /** @return buffer if successful, or NULL if an error occurred The buffer returned should not be freed as this will happen when the hFILE is closed. */ HTSLIB_EXPORT char *hfile_mem_get_buffer(hFILE *file, size_t *length); /// For hfile_mem: get the internal buffer and it's size from a hfile. /** @return buffer if successful, or NULL if an error occurred This is similar to hfile_mem_get_buffer except that ownership of the buffer is granted to the caller, who now has responsibility for freeing it. From this point onwards, the hFILE should not be used for any purpose other than closing. */ HTSLIB_EXPORT char *hfile_mem_steal_buffer(hFILE *file, size_t *length); /// Fills out sc_list[] with the list of known URL schemes. /** * @param plugin [in] Restricts schemes to only those from 'plugin. * @param sc_list [out] Filled out with the scheme names * @param nschemes [in/out] Size of sc_list (in) and number returned (out) * * Plugin may be passed in as NULL in which case all schemes are returned. * Use plugin "built-in" to list the built in schemes. * The size of sc_list is determined by the input value of *nschemes. * This is updated to return the output size. It is up to the caller to * determine whether to call again with a larger number if this is too small. * * The return value represents the total number found matching plugin, which * may be larger than *nschemes if too small a value was specified. * * @return the number of schemes found on success. * -1 on failure */ HTSLIB_EXPORT int hfile_list_schemes(const char *plugin, const char *sc_list[], int *nschemes); /// Fills out plist[] with the list of known hFILE plugins. /* * @param plist [out] Filled out with the plugin names * @param nplugins [in/out] Size of plist (in) and number returned (out) * * The size of plist is determined by the input value of *nplugins. * This is updated to return the output size. It is up to the caller to * determine whether to call again with a larger number if this is too small. * * The return value represents the total number found, which may be * larger than *nplugins if too small a value was specified. * * @return the number of plugins found on success. * -1 on failure */ HTSLIB_EXPORT int hfile_list_plugins(const char *plist[], int *nplugins); /// Tests for the presence of a specific hFILE plugin. /* * @param name The name of the plugin to query. * * @return 1 if found, 0 otherwise. */ HTSLIB_EXPORT int hfile_has_plugin(const char *name); #ifdef __cplusplus } #endif #ifdef HTSLIB_SSIZE_T #undef HTSLIB_SSIZE_T #undef ssize_t #endif #endif pysam-0.23.0/htslib/htslib/hts.h000066400000000000000000001603541475062545500164740ustar00rootroot00000000000000/// @file htslib/hts.h /// Format-neutral I/O, indexing, and iterator API functions. /* Copyright (C) 2012-2022 Genome Research Ltd. Copyright (C) 2010, 2012 Broad Institute. Portions copyright (C) 2003-2006, 2008-2010 by Heng Li Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTSLIB_HTS_H #define HTSLIB_HTS_H #include #include #include #include "hts_defs.h" #include "hts_log.h" #include "kstring.h" #include "kroundup.h" #ifdef __cplusplus extern "C" { #endif // Separator used to split HTS_PATH (for plugins); REF_PATH (cram references) #if defined(_WIN32) || defined(__MSYS__) #define HTS_PATH_SEPARATOR_CHAR ';' #define HTS_PATH_SEPARATOR_STR ";" #else #define HTS_PATH_SEPARATOR_CHAR ':' #define HTS_PATH_SEPARATOR_STR ":" #endif #ifndef HTS_BGZF_TYPEDEF typedef struct BGZF BGZF; #define HTS_BGZF_TYPEDEF #endif struct cram_fd; struct hFILE; struct hts_tpool; struct sam_hdr_t; /** * @hideinitializer * Deprecated macro to expand a dynamic array of a given type * * @param type_t The type of the array elements * @param[in] n Requested number of elements of type type_t * @param[in,out] m Size of memory allocated * @param[in,out] ptr Pointer to the array * * @discussion * Do not use this macro. Use hts_resize() instead as allows allocation * failures to be handled more gracefully. * * The array *ptr will be expanded if necessary so that it can hold @p n * or more elements. If the array is expanded then the new size will be * written to @p m and the value in @p ptr may change. * * It must be possible to take the address of @p ptr and @p m must be usable * as an lvalue. * * @bug * If the memory allocation fails, this will call exit(1). This is * not ideal behaviour in a library. */ #define hts_expand(type_t, n, m, ptr) do { \ if ((n) > (m)) { \ size_t hts_realloc_or_die(size_t, size_t, size_t, size_t, \ int, void **, const char *); \ (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \ sizeof(type_t), 0, \ (void **)&(ptr), __func__); \ } \ } while (0) /** * @hideinitializer * Macro to expand a dynamic array, zeroing any newly-allocated memory * * @param type_t The type of the array elements * @param[in] n Requested number of elements of type type_t * @param[in,out] m Size of memory allocated * @param[in,out] ptr Pointer to the array * * @discussion * Do not use this macro. Use hts_resize() instead as allows allocation * failures to be handled more gracefully. * * As for hts_expand(), except the bytes that make up the array elements * between the old and new values of @p m are set to zero using memset(). * * @bug * If the memory allocation fails, this will call exit(1). This is * not ideal behaviour in a library. */ #define hts_expand0(type_t, n, m, ptr) do { \ if ((n) > (m)) { \ size_t hts_realloc_or_die(size_t, size_t, size_t, size_t, \ int, void **, const char *); \ (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \ sizeof(type_t), 1, \ (void **)&(ptr), __func__); \ } \ } while (0) // For internal use (by hts_resize()) only HTSLIB_EXPORT int hts_resize_array_(size_t, size_t, size_t, void *, void **, int, const char *); #define HTS_RESIZE_CLEAR 1 /** * @hideinitializer * Macro to expand a dynamic array of a given type * * @param type_t The type of the array elements * @param[in] num Requested number of elements of type type_t * @param[in,out] size_ptr Pointer to where the size (in elements) of the array is stored. * @param[in,out] ptr Location of the pointer to the array * @param[in] flags Option flags * * @return 0 for success, or negative if an error occurred. * * @discussion * The array *ptr will be expanded if necessary so that it can hold @p num * or more elements. If the array is expanded then the new size will be * written to @p *size_ptr and the value in @p *ptr may change. * * If ( @p flags & HTS_RESIZE_CLEAR ) is set, any newly allocated memory will * be cleared. */ #define hts_resize(type_t, num, size_ptr, ptr, flags) \ ((num) > (*(size_ptr)) \ ? hts_resize_array_(sizeof(type_t), (num), \ sizeof(*(size_ptr)), (size_ptr), \ (void **)(ptr), (flags), __func__) \ : 0) /// Release resources when dlclosing a dynamically loaded HTSlib /** @discussion * Normally HTSlib cleans up automatically when your program exits, * whether that is via exit(3) or returning from main(). However if you * have dlopen(3)ed HTSlib and wish to close it before your main program * exits, you must call hts_lib_shutdown() before dlclose(3). */ HTSLIB_EXPORT void hts_lib_shutdown(void); /** * Wrapper function for free(). Enables memory deallocation across DLL * boundary. Should be used by all applications, which are compiled * with a different standard library than htslib and call htslib * methods that return dynamically allocated data. */ HTSLIB_EXPORT void hts_free(void *ptr); /************ * File I/O * ************/ // Add new entries only at the end (but before the *_maximum entry) // of these enums, as their numbering is part of the htslib ABI. enum htsFormatCategory { unknown_category, sequence_data, // Sequence data -- SAM, BAM, CRAM, etc variant_data, // Variant calling data -- VCF, BCF, etc index_file, // Index file associated with some data file region_list, // Coordinate intervals or regions -- BED, etc category_maximum = 32767 }; enum htsExactFormat { unknown_format, binary_format, text_format, sam, bam, bai, cram, crai, vcf, bcf, csi, gzi, tbi, bed, htsget, json HTS_DEPRECATED_ENUM("Use htsExactFormat 'htsget' instead") = htsget, empty_format, // File is empty (or empty after decompression) fasta_format, fastq_format, fai_format, fqi_format, hts_crypt4gh_format, d4_format, format_maximum = 32767 }; enum htsCompression { no_compression, gzip, bgzf, custom, bzip2_compression, razf_compression, xz_compression, zstd_compression, compression_maximum = 32767 }; typedef struct htsFormat { enum htsFormatCategory category; enum htsExactFormat format; struct { short major, minor; } version; enum htsCompression compression; short compression_level; // currently unused void *specific; // format specific options; see struct hts_opt. } htsFormat; struct hts_idx_t; typedef struct hts_idx_t hts_idx_t; struct hts_filter_t; /** * @brief File handle returned by hts_open() etc. * This structure should be considered opaque by end users. There should be * no need to access most fields directly in user code, and in cases where * it is desirable accessor functions such as hts_get_format() are provided. */ // Maintainers note htsFile cannot be an incomplete struct because some of its // fields are part of libhts.so's ABI (hence these fields must not be moved): // - fp is used in the public sam_itr_next()/etc macros // - is_bin is used directly in samtools <= 1.1 and bcftools <= 1.1 // - is_write and is_cram are used directly in samtools <= 1.1 // - fp is used directly in samtools (up to and including current develop) // - line is used directly in bcftools (up to and including current develop) // - is_bgzf and is_cram flags indicate which fp union member to use. // Note is_bgzf being set does not indicate the flag is BGZF compressed, // nor even whether it is compressed at all (eg on naked BAMs). typedef struct htsFile { uint32_t is_bin:1, is_write:1, is_be:1, is_cram:1, is_bgzf:1, dummy:27; int64_t lineno; kstring_t line; char *fn, *fn_aux; union { BGZF *bgzf; struct cram_fd *cram; struct hFILE *hfile; } fp; void *state; // format specific state information htsFormat format; hts_idx_t *idx; const char *fnidx; struct sam_hdr_t *bam_header; struct hts_filter_t *filter; } htsFile; // A combined thread pool and queue allocation size. // The pool should already be defined, but qsize may be zero to // indicate an appropriate queue size is taken from the pool. // // Reasons for explicitly setting it could be where many more file // descriptors are in use than threads, so keeping memory low is // important. typedef struct htsThreadPool { struct hts_tpool *pool; // The shared thread pool itself int qsize; // Size of I/O queue to use for this fp } htsThreadPool; // REQUIRED_FIELDS enum sam_fields { SAM_QNAME = 0x00000001, SAM_FLAG = 0x00000002, SAM_RNAME = 0x00000004, SAM_POS = 0x00000008, SAM_MAPQ = 0x00000010, SAM_CIGAR = 0x00000020, SAM_RNEXT = 0x00000040, SAM_PNEXT = 0x00000080, SAM_TLEN = 0x00000100, SAM_SEQ = 0x00000200, SAM_QUAL = 0x00000400, SAM_AUX = 0x00000800, SAM_RGAUX = 0x00001000, }; // Mostly CRAM only, but this could also include other format options enum hts_fmt_option { // CRAM specific CRAM_OPT_DECODE_MD, CRAM_OPT_PREFIX, CRAM_OPT_VERBOSITY, // obsolete, use hts_set_log_level() instead CRAM_OPT_SEQS_PER_SLICE, CRAM_OPT_SLICES_PER_CONTAINER, CRAM_OPT_RANGE, CRAM_OPT_VERSION, // rename to cram_version? CRAM_OPT_EMBED_REF, CRAM_OPT_IGNORE_MD5, CRAM_OPT_REFERENCE, // make general CRAM_OPT_MULTI_SEQ_PER_SLICE, CRAM_OPT_NO_REF, CRAM_OPT_USE_BZIP2, CRAM_OPT_SHARED_REF, CRAM_OPT_NTHREADS, // deprecated, use HTS_OPT_NTHREADS CRAM_OPT_THREAD_POOL,// make general CRAM_OPT_USE_LZMA, CRAM_OPT_USE_RANS, CRAM_OPT_REQUIRED_FIELDS, CRAM_OPT_LOSSY_NAMES, CRAM_OPT_BASES_PER_SLICE, CRAM_OPT_STORE_MD, CRAM_OPT_STORE_NM, CRAM_OPT_RANGE_NOSEEK, // CRAM_OPT_RANGE minus the seek CRAM_OPT_USE_TOK, CRAM_OPT_USE_FQZ, CRAM_OPT_USE_ARITH, CRAM_OPT_POS_DELTA, // force delta for AP, even on non-pos sorted data // General purpose HTS_OPT_COMPRESSION_LEVEL = 100, HTS_OPT_NTHREADS, HTS_OPT_THREAD_POOL, HTS_OPT_CACHE_SIZE, HTS_OPT_BLOCK_SIZE, HTS_OPT_FILTER, HTS_OPT_PROFILE, // Fastq // Boolean. // Read / Write CASAVA 1.8 format. // See https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq_letterbooklet_15038058brpmi.pdf // // The CASAVA tag matches \d:[YN]:\d+:[ACGTN]+ // The first \d is read 1/2 (1 or 2), [YN] is QC-PASS/FAIL flag, // \d+ is a control number, and the sequence at the end is // for barcode sequence. Barcodes are read into the aux tag defined // by FASTQ_OPT_BARCODE ("BC" by default). FASTQ_OPT_CASAVA = 1000, // String. // Whether to read / write extra SAM format aux tags from the fastq // identifier line. For reading this can simply be "1" to request // decoding aux tags. For writing it is a comma separated list of aux // tag types to be written out. FASTQ_OPT_AUX, // Boolean. // Whether to add /1 and /2 to read identifiers when writing FASTQ. // These come from the BAM_FREAD1 or BAM_FREAD2 flags. // (Detecting the /1 and /2 is automatic when reading fastq.) FASTQ_OPT_RNUM, // Two character string. // Barcode aux tag for CASAVA; defaults to "BC". FASTQ_OPT_BARCODE, // Process SRA and ENA read names which pointlessly move the original // name to the second field and insert a constructed . // name in its place. FASTQ_OPT_NAME2, }; // Profile options for encoding; primarily used at present in CRAM // but also usable in BAM as a synonym for deflate compression levels. enum hts_profile_option { HTS_PROFILE_FAST, HTS_PROFILE_NORMAL, HTS_PROFILE_SMALL, HTS_PROFILE_ARCHIVE, }; // For backwards compatibility #define cram_option hts_fmt_option typedef struct hts_opt { char *arg; // string form, strdup()ed enum hts_fmt_option opt; // tokenised key union { // ... and value int i; char *s; } val; struct hts_opt *next; } hts_opt; #define HTS_FILE_OPTS_INIT {{0},0} /* * Explicit index file name delimiter, see below */ #define HTS_IDX_DELIM "##idx##" /********************** * Exported functions * **********************/ /* * Parses arg and appends it to the option list. * * Returns 0 on success; * -1 on failure. */ HTSLIB_EXPORT int hts_opt_add(hts_opt **opts, const char *c_arg); /* * Applies an hts_opt option list to a given htsFile. * * Returns 0 on success * -1 on failure */ HTSLIB_EXPORT int hts_opt_apply(htsFile *fp, hts_opt *opts); /* * Frees an hts_opt list. */ HTSLIB_EXPORT void hts_opt_free(hts_opt *opts); /* * Accepts a string file format (sam, bam, cram, vcf, bam) optionally * followed by a comma separated list of key=value options and splits * these up into the fields of htsFormat struct. * * Returns 0 on success * -1 on failure. */ HTSLIB_EXPORT int hts_parse_format(htsFormat *opt, const char *str); /* * Tokenise options as (key(=value)?,)*(key(=value)?)? * NB: No provision for ',' appearing in the value! * Add backslashing rules? * * This could be used as part of a general command line option parser or * as a string concatenated onto the file open mode. * * Returns 0 on success * -1 on failure. */ HTSLIB_EXPORT int hts_parse_opt_list(htsFormat *opt, const char *str); /*! @abstract Table for converting a nucleotide character to 4-bit encoding. The input character may be either an IUPAC ambiguity code, '=' for 0, or '0'/'1'/'2'/'3' for a result of 1/2/4/8. The result is encoded as 1/2/4/8 for A/C/G/T or combinations of these bits for ambiguous bases. */ HTSLIB_EXPORT extern const unsigned char seq_nt16_table[256]; /*! @abstract Table for converting a 4-bit encoded nucleotide to an IUPAC ambiguity code letter (or '=' when given 0). */ HTSLIB_EXPORT extern const char seq_nt16_str[]; /*! @abstract Table for converting a 4-bit encoded nucleotide to about 2 bits. Returns 0/1/2/3 for 1/2/4/8 (i.e., A/C/G/T), or 4 otherwise (0 or ambiguous). */ HTSLIB_EXPORT extern const int seq_nt16_int[]; /*! @abstract Get the htslib version number @return For released versions, a string like "N.N[.N]"; or git describe output if using a library built within a Git repository. */ HTSLIB_EXPORT const char *hts_version(void); /*! @abstract Compile-time HTSlib version number, for use in #if checks @return For released versions X.Y[.Z], an integer of the form XYYYZZ; useful for preprocessor conditionals such as #if HTS_VERSION >= 101000 // Check for v1.10 or later */ // Maintainers: Bump this in the final stage of preparing a new release. // Immediately after release, bump ZZ to 90 to distinguish in-development // Git repository builds from the release; you may wish to increment this // further when significant features are merged. #define HTS_VERSION 102100 /*! @abstract Introspection on the features enabled in htslib * * @return a bitfield of HTS_FEATURE_* macros. */ HTSLIB_EXPORT unsigned int hts_features(void); HTSLIB_EXPORT const char *hts_test_feature(unsigned int id); /*! @abstract Introspection on the features enabled in htslib, string form * * @return a string describing htslib build features */ HTSLIB_EXPORT const char *hts_feature_string(void); // Whether ./configure was used or vanilla Makefile #define HTS_FEATURE_CONFIGURE 1 // Whether --enable-plugins was used #define HTS_FEATURE_PLUGINS 2 // Transport specific #define HTS_FEATURE_LIBCURL (1u<<10) #define HTS_FEATURE_S3 (1u<<11) #define HTS_FEATURE_GCS (1u<<12) // Compression options #define HTS_FEATURE_LIBDEFLATE (1u<<20) #define HTS_FEATURE_LZMA (1u<<21) #define HTS_FEATURE_BZIP2 (1u<<22) #define HTS_FEATURE_HTSCODECS (1u<<23) // htscodecs library version // Build params #define HTS_FEATURE_CC (1u<<27) #define HTS_FEATURE_CFLAGS (1u<<28) #define HTS_FEATURE_CPPFLAGS (1u<<29) #define HTS_FEATURE_LDFLAGS (1u<<30) /*! @abstract Determine format by peeking at the start of a file @param fp File opened for reading, positioned at the beginning @param fmt Format structure that will be filled out on return @return 0 for success, or negative if an error occurred. Equivalent to hts_detect_format2(fp, NULL, fmt). */ HTSLIB_EXPORT int hts_detect_format(struct hFILE *fp, htsFormat *fmt); /*! @abstract Determine format primarily by peeking at the start of a file @param fp File opened for reading, positioned at the beginning @param fname Name of the file, or NULL if not available @param fmt Format structure that will be filled out on return @return 0 for success, or negative if an error occurred. @since 1.15 Some formats are only recognised if the filename is available and has the expected extension, as otherwise more generic files may be misrecognised. In particular: - FASTA/Q indexes must have .fai/.fqi extensions; without this requirement, some similar BED files would be misrecognised as indexes. */ HTSLIB_EXPORT int hts_detect_format2(struct hFILE *fp, const char *fname, htsFormat *fmt); /*! @abstract Get a human-readable description of the file format @param fmt Format structure holding type, version, compression, etc. @return Description string, to be freed by the caller after use. */ HTSLIB_EXPORT char *hts_format_description(const htsFormat *format); /*! @abstract Open a sequence data (SAM/BAM/CRAM) or variant data (VCF/BCF) or possibly-compressed textual line-orientated file @param fn The file name or "-" for stdin/stdout. For indexed files with a non-standard naming, the file name can include the name of the index file delimited with HTS_IDX_DELIM @param mode Mode matching / [rwa][bcefFguxz0-9]* / @discussion With 'r' opens for reading; any further format mode letters are ignored as the format is detected by checking the first few bytes or BGZF blocks of the file. With 'w' or 'a' opens for writing or appending, with format specifier letters: b binary format (BAM, BCF, etc) rather than text (SAM, VCF, etc) c CRAM format f FASTQ format F FASTA format g gzip compressed u uncompressed z bgzf compressed [0-9] zlib compression level and with non-format option letters (for any of 'r'/'w'/'a'): e close the file on exec(2) (opens with O_CLOEXEC, where supported) x create the file exclusively (opens with O_EXCL, where supported) Note that there is a distinction between 'u' and '0': the first yields plain uncompressed output whereas the latter outputs uncompressed data wrapped in the zlib format. @example [rw]b .. compressed BCF, BAM, FAI [rw]bu .. uncompressed BCF [rw]z .. compressed VCF [rw] .. uncompressed VCF */ HTSLIB_EXPORT htsFile *hts_open(const char *fn, const char *mode); /*! @abstract Open a SAM/BAM/CRAM/VCF/BCF/etc file @param fn The file name or "-" for stdin/stdout @param mode Open mode, as per hts_open() @param fmt Optional format specific parameters @discussion See hts_open() for description of fn and mode. // TODO Update documentation for s/opts/fmt/ Opts contains a format string (sam, bam, cram, vcf, bcf) which will, if defined, override mode. Opts also contains a linked list of hts_opt structures to apply to the open file handle. These can contain things like pointers to the reference or information on compression levels, block sizes, etc. */ HTSLIB_EXPORT htsFile *hts_open_format(const char *fn, const char *mode, const htsFormat *fmt); /*! @abstract Open an existing stream as a SAM/BAM/CRAM/VCF/BCF/etc file @param fn The already-open file handle @param mode Open mode, as per hts_open() */ HTSLIB_EXPORT htsFile *hts_hopen(struct hFILE *fp, const char *fn, const char *mode); /*! @abstract For output streams, flush any buffered data @param fp The file handle to be flushed @return 0 for success, or negative if an error occurred. @since 1.14 */ HTSLIB_EXPORT int hts_flush(htsFile *fp); /*! @abstract Close a file handle, flushing buffered data for output streams @param fp The file handle to be closed @return 0 for success, or negative if an error occurred. */ HTSLIB_EXPORT int hts_close(htsFile *fp); /*! @abstract Returns the file's format information @param fp The file handle @return Read-only pointer to the file's htsFormat. */ HTSLIB_EXPORT const htsFormat *hts_get_format(htsFile *fp); /*! @ abstract Returns a string containing the file format extension. @ param format Format structure containing the file type. @ return A string ("sam", "bam", etc) or "?" for unknown formats. */ HTSLIB_EXPORT const char *hts_format_file_extension(const htsFormat *format); /*! @abstract Sets a specified CRAM option on the open file handle. @param fp The file handle open the open file. @param opt The CRAM_OPT_* option. @param ... Optional arguments, dependent on the option used. @return 0 for success, or negative if an error occurred. */ HTSLIB_EXPORT int hts_set_opt(htsFile *fp, enum hts_fmt_option opt, ...); /*! @abstract Read a line (and its \n or \r\n terminator) from a file @param fp The file handle @param delimiter Unused, but must be '\n' (or KS_SEP_LINE) @param str The line (not including the terminator) is written here @return Length of the string read (capped at INT_MAX); -1 on end-of-file; <= -2 on error */ HTSLIB_EXPORT int hts_getline(htsFile *fp, int delimiter, kstring_t *str); HTSLIB_EXPORT char **hts_readlines(const char *fn, int *_n); /*! @abstract Parse comma-separated list or read list from a file @param list File name or comma-separated list @param is_file @param _n Size of the output array (number of items read) @return NULL on failure or pointer to newly allocated array of strings */ HTSLIB_EXPORT char **hts_readlist(const char *fn, int is_file, int *_n); /*! @abstract Create extra threads to aid compress/decompression for this file @param fp The file handle @param n The number of worker threads to create @return 0 for success, or negative if an error occurred. @notes This function creates non-shared threads for use solely by fp. The hts_set_thread_pool function is the recommended alternative. */ HTSLIB_EXPORT int hts_set_threads(htsFile *fp, int n); /*! @abstract Create extra threads to aid compress/decompression for this file @param fp The file handle @param p A pool of worker threads, previously allocated by hts_create_threads(). @return 0 for success, or negative if an error occurred. */ HTSLIB_EXPORT int hts_set_thread_pool(htsFile *fp, htsThreadPool *p); /*! @abstract Adds a cache of decompressed blocks, potentially speeding up seeks. This may not work for all file types (currently it is bgzf only). @param fp The file handle @param n The size of cache, in bytes */ HTSLIB_EXPORT void hts_set_cache_size(htsFile *fp, int n); /*! @abstract Set .fai filename for a file opened for reading @return 0 for success, negative on failure @discussion Called before *_hdr_read(), this provides the name of a .fai file used to provide a reference list if the htsFile contains no @SQ headers. */ HTSLIB_EXPORT int hts_set_fai_filename(htsFile *fp, const char *fn_aux); /*! @abstract Sets a filter expression @return 0 for success, negative on failure @discussion To clear an existing filter, specifying expr as NULL. */ HTSLIB_EXPORT int hts_set_filter_expression(htsFile *fp, const char *expr); /*! @abstract Determine whether a given htsFile contains a valid EOF block @return 3 for a non-EOF checkable filetype; 2 for an unseekable file type where EOF cannot be checked; 1 for a valid EOF block; 0 for if the EOF marker is absent when it should be present; -1 (with errno set) on failure @discussion Check if the BGZF end-of-file (EOF) marker is present */ HTSLIB_EXPORT int hts_check_EOF(htsFile *fp); /************ * Indexing * ************/ /*! These HTS_IDX_* macros are used as special tid values for hts_itr_query()/etc, producing iterators operating as follows: - HTS_IDX_NOCOOR iterates over unmapped reads sorted at the end of the file - HTS_IDX_START iterates over the entire file - HTS_IDX_REST iterates from the current position to the end of the file - HTS_IDX_NONE always returns "no more alignment records" When one of these special tid values is used, beg and end are ignored. When REST or NONE is used, idx is also ignored and may be NULL. */ #define HTS_IDX_NOCOOR (-2) #define HTS_IDX_START (-3) #define HTS_IDX_REST (-4) #define HTS_IDX_NONE (-5) #define HTS_FMT_CSI 0 #define HTS_FMT_BAI 1 #define HTS_FMT_TBI 2 #define HTS_FMT_CRAI 3 #define HTS_FMT_FAI 4 // Almost INT64_MAX, but when cast into a 32-bit int it's // also INT_MAX instead of -1. This avoids bugs with old code // using the new hts_pos_t data type. #define HTS_POS_MAX ((((int64_t)INT_MAX)<<32)|INT_MAX) #define HTS_POS_MIN INT64_MIN #define PRIhts_pos PRId64 typedef int64_t hts_pos_t; // For comparison with previous release: // // #define HTS_POS_MAX INT_MAX // #define HTS_POS_MIN INT_MIN // #define PRIhts_pos PRId32 // typedef int32_t hts_pos_t; typedef struct hts_pair_pos_t { hts_pos_t beg, end; } hts_pair_pos_t; typedef hts_pair_pos_t hts_pair32_t; // For backwards compatibility typedef struct hts_pair64_t { uint64_t u, v; } hts_pair64_t; typedef struct hts_pair64_max_t { uint64_t u, v; uint64_t max; } hts_pair64_max_t; typedef struct hts_reglist_t { const char *reg; hts_pair_pos_t *intervals; int tid; uint32_t count; hts_pos_t min_beg, max_end; } hts_reglist_t; typedef int hts_readrec_func(BGZF *fp, void *data, void *r, int *tid, hts_pos_t *beg, hts_pos_t *end); typedef int hts_seek_func(void *fp, int64_t offset, int where); typedef int64_t hts_tell_func(void *fp); /** * @brief File iterator that can handle multiple target regions. * This structure should be considered opaque by end users. * It does both the stepping inside the file and the filtering of alignments. * It can operate in single or multi-region mode, and depending on this, * it uses different fields. * * read_rest (1) - read everything from the current offset, without filtering * finished (1) - no more iterations * is_cram (1) - current file has CRAM format * nocoor (1) - read all unmapped reads * * multi (1) - multi-region moode * reg_list - List of target regions * n_reg - Size of the above list * curr_reg - List index of the current region of search * curr_intv - Interval index inside the current region; points to a (beg, end) * end - Used for CRAM files, to preserve the max end coordinate * * multi (0) - single-region mode * tid - Reference id of the target region * beg - Start position of the target region * end - End position of the target region * * Common fields: * off - List of file offsets computed from the index * n_off - Size of the above list * i - List index of the current file offset * curr_off - File offset for the next file read * curr_tid - Reference id of the current alignment * curr_beg - Start position of the current alignment * curr_end - End position of the current alignment * nocoor_off - File offset where the unmapped reads start * * readrec - File specific function that reads an alignment * seek - File specific function for changing the file offset * tell - File specific function for indicating the file offset */ typedef struct hts_itr_t { uint32_t read_rest:1, finished:1, is_cram:1, nocoor:1, multi:1, dummy:27; int tid, n_off, i, n_reg; hts_pos_t beg, end; hts_reglist_t *reg_list; int curr_tid, curr_reg, curr_intv; hts_pos_t curr_beg, curr_end; uint64_t curr_off, nocoor_off; hts_pair64_max_t *off; hts_readrec_func *readrec; hts_seek_func *seek; hts_tell_func *tell; struct { int n, m; int *a; } bins; } hts_itr_t; typedef hts_itr_t hts_itr_multi_t; /// Compute the first bin on a given level #define hts_bin_first(l) (((1<<(((l)<<1) + (l))) - 1) / 7) /// Compute the parent bin of a given bin #define hts_bin_parent(b) (((b) - 1) >> 3) /////////////////////////////////////////////////////////// // Low-level API for building indexes. /// Create a BAI/CSI/TBI type index structure /** @param n Initial number of targets @param fmt Format, one of HTS_FMT_CSI, HTS_FMT_BAI or HTS_FMT_TBI @param offset0 Initial file offset @param min_shift Number of bits for the minimal interval @param n_lvls Number of levels in the binning index @return An initialised hts_idx_t struct on success; NULL on failure The struct returned by a successful call should be freed via hts_idx_destroy() when it is no longer needed. */ HTSLIB_EXPORT hts_idx_t *hts_idx_init(int n, int fmt, uint64_t offset0, int min_shift, int n_lvls); /// Free a BAI/CSI/TBI type index /** @param idx Index structure to free */ HTSLIB_EXPORT void hts_idx_destroy(hts_idx_t *idx); /// Push an index entry /** @param idx Index @param tid Target id @param beg Range start (zero-based) @param end Range end (zero-based, half-open) @param offset File offset @param is_mapped Range corresponds to a mapped read @return 0 on success; -1 on failure The @p is_mapped parameter is used to update the n_mapped / n_unmapped counts stored in the meta-data bin. */ HTSLIB_EXPORT int hts_idx_push(hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, uint64_t offset, int is_mapped); /// Finish building an index /** @param idx Index @param final_offset Last file offset @return 0 on success; non-zero on failure. */ HTSLIB_EXPORT int hts_idx_finish(hts_idx_t *idx, uint64_t final_offset); /// Returns index format /** @param idx Index @return One of HTS_FMT_CSI, HTS_FMT_BAI or HTS_FMT_TBI */ HTSLIB_EXPORT int hts_idx_fmt(hts_idx_t *idx); /// Add name to TBI index meta-data /** @param idx Index @param tid Target identifier @param name Target name @return Index number of name in names list on success; -1 on failure. */ HTSLIB_EXPORT int hts_idx_tbi_name(hts_idx_t *idx, int tid, const char *name); // Index loading and saving /// Save an index to a file /** @param idx Index to be written @param fn Input BAM/BCF/etc filename, to which .bai/.csi/etc will be added @param fmt One of the HTS_FMT_* index formats @return 0 if successful, or negative if an error occurred. */ HTSLIB_EXPORT int hts_idx_save(const hts_idx_t *idx, const char *fn, int fmt) HTS_RESULT_USED; /// Save an index to a specific file /** @param idx Index to be written @param fn Input BAM/BCF/etc filename @param fnidx Output filename, or NULL to add .bai/.csi/etc to @a fn @param fmt One of the HTS_FMT_* index formats @return 0 if successful, or negative if an error occurred. */ HTSLIB_EXPORT int hts_idx_save_as(const hts_idx_t *idx, const char *fn, const char *fnidx, int fmt) HTS_RESULT_USED; /// Load an index file /** @param fn BAM/BCF/etc filename, to which .bai/.csi/etc will be added or the extension substituted, to search for an existing index file. In case of a non-standard naming, the file name can include the name of the index file delimited with HTS_IDX_DELIM. @param fmt One of the HTS_FMT_* index formats @return The index, or NULL if an error occurred. If @p fn contains the string "##idx##" (HTS_IDX_DELIM), the part before the delimiter will be used as the name of the data file and the part after it will be used as the name of the index. Otherwise, this function tries to work out the index name as follows: It will try appending ".csi" to @p fn It will try substituting an existing suffix (e.g. .bam, .vcf) with ".csi" Then, if @p fmt is HTS_FMT_BAI: It will try appending ".bai" to @p fn To will substituting the existing suffix (e.g. .bam) with ".bai" else if @p fmt is HTS_FMT_TBI: It will try appending ".tbi" to @p fn To will substituting the existing suffix (e.g. .vcf) with ".tbi" If the index file is remote (served over a protocol like https), first a check is made to see is a locally cached copy is available. This is done for all of the possible names listed above. If a cached copy is not available then the index will be downloaded and stored in the current working directory, with the same name as the remote index. Equivalent to hts_idx_load3(fn, NULL, fmt, HTS_IDX_SAVE_REMOTE); */ HTSLIB_EXPORT hts_idx_t *hts_idx_load(const char *fn, int fmt); /// Load a specific index file /** @param fn Input BAM/BCF/etc filename @param fnidx The input index filename @return The index, or NULL if an error occurred. Equivalent to hts_idx_load3(fn, fnidx, 0, 0); This function will not attempt to save index files locally. */ HTSLIB_EXPORT hts_idx_t *hts_idx_load2(const char *fn, const char *fnidx); /// Load a specific index file /** @param fn Input BAM/BCF/etc filename @param fnidx The input index filename @param fmt One of the HTS_FMT_* index formats @param flags Flags to alter behaviour (see description) @return The index, or NULL if an error occurred. If @p fnidx is NULL, the index name will be derived from @p fn in the same way as hts_idx_load(). If @p fnidx is not NULL, @p fmt is ignored. The @p flags parameter can be set to a combination of the following values: HTS_IDX_SAVE_REMOTE Save a local copy of any remote indexes HTS_IDX_SILENT_FAIL Fail silently if the index is not present The index struct returned by a successful call should be freed via hts_idx_destroy() when it is no longer needed. */ HTSLIB_EXPORT hts_idx_t *hts_idx_load3(const char *fn, const char *fnidx, int fmt, int flags); /// Flags for hts_idx_load3() ( and also sam_idx_load3(), tbx_idx_load3() ) #define HTS_IDX_SAVE_REMOTE 1 #define HTS_IDX_SILENT_FAIL 2 /////////////////////////////////////////////////////////// // Functions for accessing meta-data stored in indexes typedef const char *(*hts_id2name_f)(void*, int); /// Get extra index meta-data /** @param idx The index @param l_meta Pointer to where the length of the extra data is stored @return Pointer to the extra data if present; NULL otherwise Indexes (both .tbi and .csi) made by tabix include extra data about the indexed file. The returns a pointer to this data. Note that the data is stored exactly as it is in the index. Callers need to interpret the results themselves, including knowing what sort of data to expect; byte swapping etc. */ HTSLIB_EXPORT uint8_t *hts_idx_get_meta(hts_idx_t *idx, uint32_t *l_meta); /// Set extra index meta-data /** @param idx The index @param l_meta Length of data @param meta Pointer to the extra data @param is_copy If not zero, a copy of the data is taken @return 0 on success; -1 on failure (out of memory). Sets the data that is returned by hts_idx_get_meta(). If is_copy != 0, a copy of the input data is taken. If not, ownership of the data pointed to by *meta passes to the index. */ HTSLIB_EXPORT int hts_idx_set_meta(hts_idx_t *idx, uint32_t l_meta, uint8_t *meta, int is_copy); /// Get number of mapped and unmapped reads from an index /** @param idx Index @param tid Target ID @param[out] mapped Location to store number of mapped reads @param[out] unmapped Location to store number of unmapped reads @return 0 on success; -1 on failure (data not available) BAI and CSI indexes store information on the number of reads for each target that were mapped or unmapped (unmapped reads will generally have a paired read that is mapped to the target). This function returns this information if it is available. @note Cram CRAI indexes do not include this information. */ HTSLIB_EXPORT int hts_idx_get_stat(const hts_idx_t* idx, int tid, uint64_t* mapped, uint64_t* unmapped); /// Return the number of unplaced reads from an index /** @param idx Index @return Unplaced reads count Unplaced reads are not linked to any reference (e.g. RNAME is '*' in SAM files). */ HTSLIB_EXPORT uint64_t hts_idx_get_n_no_coor(const hts_idx_t* idx); /// Return a list of target names from an index /** @param idx Index @param[out] n Location to store the number of targets @param getid Callback function to get the name for a target ID @param hdr Header from indexed file @return An array of pointers to the names on success; NULL on failure @note The names are pointers into the header data structure. When cleaning up, only the array should be freed, not the names. */ HTSLIB_EXPORT const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values /// Return the number of targets from an index /** @param idx Index @return The number of targets */ HTSLIB_EXPORT int hts_idx_nseq(const hts_idx_t *idx); /////////////////////////////////////////////////////////// // Region parsing #define HTS_PARSE_THOUSANDS_SEP 1 ///< Ignore ',' separators within numbers #define HTS_PARSE_ONE_COORD 2 ///< chr:pos means chr:pos-pos and not chr:pos-end #define HTS_PARSE_LIST 4 ///< Expect a comma separated list of regions. (Disables HTS_PARSE_THOUSANDS_SEP) /// Parse a numeric string /** The number may be expressed in scientific notation, and optionally may contain commas in the integer part (before any decimal point or E notation). @param str String to be parsed @param strend If non-NULL, set on return to point to the first character in @a str after those forming the parsed number @param flags Or'ed-together combination of HTS_PARSE_* flags @return Integer value of the parsed number, or 0 if no valid number The input string is parsed as: optional whitespace; an optional '+' or '-' sign; decimal digits possibly including ',' characters (if @a flags includes HTS_PARSE_THOUSANDS_SEP) and a '.' decimal point; and an optional case-insensitive suffix, which may be either 'k', 'M', 'G', or scientific notation consisting of 'e'/'E' followed by an optional '+' or '-' sign and decimal digits. To be considered a valid numeric value, the main part (not including any suffix or scientific notation) must contain at least one digit (either before or after the decimal point). When @a strend is NULL, @a str is expected to contain only (optional whitespace followed by) the numeric value. A warning will be printed (if hts_verbose is HTS_LOG_WARNING or more) if no valid parsable number is found or if there are any unused characters after the number. When @a strend is non-NULL, @a str starts with (optional whitespace followed by) the numeric value. On return, @a strend is set to point to the first unused character after the numeric value, or to @a str if no valid parsable number is found. */ HTSLIB_EXPORT long long hts_parse_decimal(const char *str, char **strend, int flags); typedef int (*hts_name2id_f)(void*, const char*); /// Parse a "CHR:START-END"-style region string /** @param str String to be parsed @param beg Set on return to the 0-based start of the region @param end Set on return to the 1-based end of the region @return Pointer to the colon or '\0' after the reference sequence name, or NULL if @a str could not be parsed. NOTE: For compatibility with hts_parse_reg only. Please use hts_parse_region instead. */ HTSLIB_EXPORT const char *hts_parse_reg64(const char *str, hts_pos_t *beg, hts_pos_t *end); /// Parse a "CHR:START-END"-style region string /** @param str String to be parsed @param beg Set on return to the 0-based start of the region @param end Set on return to the 1-based end of the region @return Pointer to the colon or '\0' after the reference sequence name, or NULL if @a str could not be parsed. */ HTSLIB_EXPORT const char *hts_parse_reg(const char *str, int *beg, int *end); /// Parse a "CHR:START-END"-style region string /** @param str String to be parsed @param tid Set on return (if not NULL) to be reference index (-1 if invalid) @param beg Set on return to the 0-based start of the region @param end Set on return to the 1-based end of the region @param getid Function pointer. Called if not NULL to set tid. @param hdr Caller data passed to getid. @param flags Bitwise HTS_PARSE_* flags listed above. @return Pointer to the byte after the end of the entire region specifier (including any trailing comma) on success, or NULL if @a str could not be parsed. A variant of hts_parse_reg which is reference-id aware. It uses the iterator name2id callbacks to validate the region tokenisation works. This is necessary due to GRCh38 HLA additions which have reference names like "HLA-DRB1*12:17". To work around ambiguous parsing issues, eg both "chr1" and "chr1:100-200" are reference names, quote using curly braces. Thus "{chr1}:100-200" and "{chr1:100-200}" disambiguate the above example. Flags are used to control how parsing works, and can be one of the below. HTS_PARSE_THOUSANDS_SEP: Ignore commas in numbers. For example with this flag 1,234,567 is interpreted as 1234567. HTS_PARSE_LIST: If present, the region is assmed to be a comma separated list and position parsing will not contain commas (this implicitly clears HTS_PARSE_THOUSANDS_SEP in the call to hts_parse_decimal). On success the return pointer will be the start of the next region, ie the character after the comma. (If *ret != '\0' then the caller can assume another region is present in the list.) If not set then positions may contain commas. In this case the return value should point to the end of the string, or NULL on failure. HTS_PARSE_ONE_COORD: If present, X:100 is treated as the single base pair region X:100-100. In this case X:-100 is shorthand for X:1-100 and X:100- is X:100-. (This is the standard bcftools region convention.) When not set X:100 is considered to be X:100- where is the end of chromosome X (set to INT_MAX here). X:100- and X:-100 are invalid. (This is the standard samtools region convention.) Note the supplied string expects 1 based inclusive coordinates, but the returned coordinates start from 0 and are half open, so pos0 is valid for use in e.g. "for (pos0 = beg; pos0 < end; pos0++) {...}" If NULL is returned, the value in tid mat give additional information about the error: -2 Failed to parse @p hdr; or out of memory -1 The reference in @p str has mismatched braces, or does not exist in @p hdr >= 0 The specified range in @p str could not be parsed */ HTSLIB_EXPORT const char *hts_parse_region(const char *s, int *tid, hts_pos_t *beg, hts_pos_t *end, hts_name2id_f getid, void *hdr, int flags); /////////////////////////////////////////////////////////// // Generic iterators // // These functions provide the low-level infrastructure for iterators. // Wrappers around these are used to make iterators for specific file types. // See: // htslib/sam.h for SAM/BAM/CRAM iterators // htslib/vcf.h for VCF/BCF iterators // htslib/tbx.h for files indexed by tabix /// Create a single-region iterator /** @param idx Index @param tid Target ID @param beg Start of region @param end End of region @param readrec Callback to read a record from the input file @return An iterator on success; NULL on failure The iterator struct returned by a successful call should be freed via hts_itr_destroy() when it is no longer needed. */ HTSLIB_EXPORT hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, hts_readrec_func *readrec); /// Free an iterator /** @param iter Iterator to free */ HTSLIB_EXPORT void hts_itr_destroy(hts_itr_t *iter); typedef hts_itr_t *hts_itr_query_func(const hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, hts_readrec_func *readrec); /// Create a single-region iterator from a text region specification /** @param idx Index @param reg Region specifier @param getid Callback function to return the target ID for a name @param hdr Input file header @param itr_query Callback function returning an iterator for a numeric tid, start and end position @param readrec Callback to read a record from the input file @return An iterator on success; NULL on error The iterator struct returned by a successful call should be freed via hts_itr_destroy() when it is no longer needed. */ HTSLIB_EXPORT hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec); /// Return the next record from an iterator /** @param fp Input file handle @param iter Iterator @param r Pointer to record placeholder @param data Data passed to the readrec callback @return >= 0 on success, -1 when there is no more data, < -1 on error */ HTSLIB_EXPORT int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, void *data) HTS_RESULT_USED; /********************************** * Iterator with multiple regions * **********************************/ typedef int hts_itr_multi_query_func(const hts_idx_t *idx, hts_itr_t *itr); HTSLIB_EXPORT int hts_itr_multi_bam(const hts_idx_t *idx, hts_itr_t *iter); HTSLIB_EXPORT int hts_itr_multi_cram(const hts_idx_t *idx, hts_itr_t *iter); /// Create a multi-region iterator from a region list /** @param idx Index @param reglist Region list @param count Number of items in region list @param getid Callback to convert names to target IDs @param hdr Indexed file header (passed to getid) @param itr_specific Filetype-specific callback function @param readrec Callback to read an input file record @param seek Callback to seek in the input file @param tell Callback to return current input file location @return An iterator on success; NULL on failure The iterator struct returned by a successful call should be freed via hts_itr_destroy() when it is no longer needed. */ HTSLIB_EXPORT hts_itr_t *hts_itr_regions(const hts_idx_t *idx, hts_reglist_t *reglist, int count, hts_name2id_f getid, void *hdr, hts_itr_multi_query_func *itr_specific, hts_readrec_func *readrec, hts_seek_func *seek, hts_tell_func *tell); /// Return the next record from an iterator /** @param fp Input file handle @param iter Iterator @param r Pointer to record placeholder @return >= 0 on success, -1 when there is no more data, < -1 on error */ HTSLIB_EXPORT int hts_itr_multi_next(htsFile *fd, hts_itr_t *iter, void *r); /// Create a region list from a char array /** @param argv Char array of target:interval elements, e.g. chr1:2500-3600, chr1:5100, chr2 @param argc Number of items in the array @param r_count Pointer to the number of items in the resulting region list @param hdr Header for the sam/bam/cram file @param getid Callback to convert target names to target ids. @return A region list on success, NULL on failure The hts_reglist_t struct returned by a successful call should be freed via hts_reglist_free() when it is no longer needed. */ HTSLIB_EXPORT hts_reglist_t *hts_reglist_create(char **argv, int argc, int *r_count, void *hdr, hts_name2id_f getid); /// Free a region list /** @param reglist Region list @param count Number of items in the list */ HTSLIB_EXPORT void hts_reglist_free(hts_reglist_t *reglist, int count); /// Free a multi-region iterator /** @param iter Iterator to free */ #define hts_itr_multi_destroy(iter) hts_itr_destroy(iter) /** * hts_file_type() - Convenience function to determine file type * DEPRECATED: This function has been replaced by hts_detect_format(). * It and these FT_* macros will be removed in a future HTSlib release. */ #define FT_UNKN 0 #define FT_GZ 1 #define FT_VCF 2 #define FT_VCF_GZ (FT_GZ|FT_VCF) #define FT_BCF (1<<2) #define FT_BCF_GZ (FT_GZ|FT_BCF) #define FT_STDIN (1<<3) HTSLIB_EXPORT int hts_file_type(const char *fname); /*************************** * Revised MAQ error model * ***************************/ struct errmod_t; typedef struct errmod_t errmod_t; HTSLIB_EXPORT errmod_t *errmod_init(double depcorr); HTSLIB_EXPORT void errmod_destroy(errmod_t *em); /* n: number of bases m: maximum base bases[i]: qual:6, strand:1, base:4 q[i*m+j]: phred-scaled likelihood of (i,j) */ HTSLIB_EXPORT int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q); /***************************************************** * Probabilistic banded glocal alignment * * See https://doi.org/10.1093/bioinformatics/btr076 * *****************************************************/ typedef struct probaln_par_t { float d, e; int bw; } probaln_par_t; /// Perform probabilistic banded glocal alignment /** @param ref Reference sequence @param l_ref Length of reference @param query Query sequence @param l_query Length of query sequence @param iqual Query base qualities @param c Alignment parameters @param[out] state Output alignment @param[out] q Phred scaled posterior probability of state[i] being wrong @return Phred-scaled likelihood score, or INT_MIN on failure. The reference and query sequences are coded using integers 0,1,2,3,4 for bases A,C,G,T,N respectively (N here is for any ambiguity code). On output, state and q are arrays of length l_query. The higher 30 bits give the reference position the query base is matched to and the lower two bits can be 0 (an alignment match) or 1 (an insertion). q[i] gives the phred scaled posterior probability of state[i] being wrong. On failure, errno will be set to EINVAL if the values of l_ref or l_query were invalid; or ENOMEM if a memory allocation failed. */ HTSLIB_EXPORT int probaln_glocal(const uint8_t *ref, int l_ref, const uint8_t *query, int l_query, const uint8_t *iqual, const probaln_par_t *c, int *state, uint8_t *q); /********************** * MD5 implementation * **********************/ struct hts_md5_context; typedef struct hts_md5_context hts_md5_context; /*! @abstract Initialises an MD5 context. * @discussion * The expected use is to allocate an hts_md5_context using * hts_md5_init(). This pointer is then passed into one or more calls * of hts_md5_update() to compute successive internal portions of the * MD5 sum, which can then be externalised as a full 16-byte MD5sum * calculation by calling hts_md5_final(). This can then be turned * into ASCII via hts_md5_hex(). * * To dealloate any resources created by hts_md5_init() call the * hts_md5_destroy() function. * * @return hts_md5_context pointer on success, NULL otherwise. */ HTSLIB_EXPORT hts_md5_context *hts_md5_init(void); /*! @abstract Updates the context with the MD5 of the data. */ HTSLIB_EXPORT void hts_md5_update(hts_md5_context *ctx, const void *data, unsigned long size); /*! @abstract Computes the final 128-bit MD5 hash from the given context */ HTSLIB_EXPORT void hts_md5_final(unsigned char *digest, hts_md5_context *ctx); /*! @abstract Resets an md5_context to the initial state, as returned * by hts_md5_init(). */ HTSLIB_EXPORT void hts_md5_reset(hts_md5_context *ctx); /*! @abstract Converts a 128-bit MD5 hash into a 33-byte nul-termninated * hex string. */ HTSLIB_EXPORT void hts_md5_hex(char *hex, const unsigned char *digest); /*! @abstract Deallocates any memory allocated by hts_md5_init. */ HTSLIB_EXPORT void hts_md5_destroy(hts_md5_context *ctx); static inline int hts_reg2bin(hts_pos_t beg, hts_pos_t end, int min_shift, int n_lvls) { int l, s = min_shift, t = ((1<<((n_lvls<<1) + n_lvls)) - 1) / 7; for (--end, l = n_lvls; l > 0; --l, s += 3, t -= 1<<((l<<1)+l)) if (beg>>s == end>>s) return t + (beg>>s); return 0; } /// Compute the level of a bin in a binning index static inline int hts_bin_level(int bin) { int l, b; for (l = 0, b = bin; b; ++l, b = hts_bin_parent(b)); return l; } //! Compute the corresponding entry into the linear index of a given bin from //! a binning index /*! * @param bin The bin number * @param n_lvls The index depth (number of levels - 0 based) * @return The integer offset into the linear index * * Explanation of the return value formula: * Each bin on level l covers exp(2, (n_lvls - l)*3 + min_shift) base pairs. * A linear index entry covers exp(2, min_shift) base pairs. */ static inline int hts_bin_bot(int bin, int n_lvls) { int l = hts_bin_level(bin); return (bin - hts_bin_first(l)) << (n_lvls - l) * 3; } /// Compute the (0-based exclusive) maximum position covered by a binning index static inline hts_pos_t hts_bin_maxpos(int min_shift, int n_lvls) { hts_pos_t one = 1; return one << (min_shift + n_lvls * 3); } /************** * Endianness * **************/ static inline int ed_is_big(void) { long one= 1; return !(*((char *)(&one))); } static inline uint16_t ed_swap_2(uint16_t v) { return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8)); } static inline void *ed_swap_2p(void *x) { *(uint16_t*)x = ed_swap_2(*(uint16_t*)x); return x; } static inline uint32_t ed_swap_4(uint32_t v) { v = ((v & 0x0000FFFFU) << 16) | (v >> 16); return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8); } static inline void *ed_swap_4p(void *x) { *(uint32_t*)x = ed_swap_4(*(uint32_t*)x); return x; } static inline uint64_t ed_swap_8(uint64_t v) { v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32); v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16); return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8); } static inline void *ed_swap_8p(void *x) { *(uint64_t*)x = ed_swap_8(*(uint64_t*)x); return x; } #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/htslib/hts_defs.h000066400000000000000000000105431475062545500174670ustar00rootroot00000000000000/* hts_defs.h -- Miscellaneous definitions. Copyright (C) 2013-2015,2017, 2019-2020, 2024 Genome Research Ltd. Author: John Marshall Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTSLIB_HTS_DEFS_H #define HTSLIB_HTS_DEFS_H #if defined __MINGW32__ #include // For __MINGW_PRINTF_FORMAT macro #endif #ifdef __clang__ #ifdef __has_attribute #define HTS_COMPILER_HAS(attribute) __has_attribute(attribute) #endif #elif defined __GNUC__ #define HTS_GCC_AT_LEAST(major, minor) \ (__GNUC__ > (major) || (__GNUC__ == (major) && __GNUC_MINOR__ >= (minor))) #endif #ifndef HTS_COMPILER_HAS #define HTS_COMPILER_HAS(attribute) 0 #endif #ifndef HTS_GCC_AT_LEAST #define HTS_GCC_AT_LEAST(major, minor) 0 #endif #if HTS_COMPILER_HAS(__nonstring__) || HTS_GCC_AT_LEAST(8,1) #define HTS_NONSTRING __attribute__ ((__nonstring__)) #else #define HTS_NONSTRING #endif #if HTS_COMPILER_HAS(__noreturn__) || HTS_GCC_AT_LEAST(3,0) #define HTS_NORETURN __attribute__ ((__noreturn__)) #else #define HTS_NORETURN #endif // Enable optimisation level 3, especially for gcc. To be used // where we want to force vectorisation in hot loops and the default -O2 // just doesn't cut it. #if HTS_COMPILER_HAS(optimize) || HTS_GCC_AT_LEAST(4,4) #define HTS_OPT3 __attribute__((optimize("O3"))) #else #define HTS_OPT3 #endif #if HTS_COMPILER_HAS(aligned) || HTS_GCC_AT_LEAST(4,3) #define HTS_ALIGN32 __attribute__((aligned(32))) #else #define HTS_ALIGN32 #endif // GCC introduced warn_unused_result in 3.4 but added -Wno-unused-result later #if HTS_COMPILER_HAS(__warn_unused_result__) || HTS_GCC_AT_LEAST(4,5) #define HTS_RESULT_USED __attribute__ ((__warn_unused_result__)) #else #define HTS_RESULT_USED #endif #if HTS_COMPILER_HAS(__unused__) || HTS_GCC_AT_LEAST(3,0) #define HTS_UNUSED __attribute__ ((__unused__)) #else #define HTS_UNUSED #endif #if HTS_COMPILER_HAS(__deprecated__) || HTS_GCC_AT_LEAST(4,5) #define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message))) #elif HTS_GCC_AT_LEAST(3,1) #define HTS_DEPRECATED(message) __attribute__ ((__deprecated__)) #else #define HTS_DEPRECATED(message) #endif #if (HTS_COMPILER_HAS(__deprecated__) || HTS_GCC_AT_LEAST(6,4)) && !defined(__ICC) #define HTS_DEPRECATED_ENUM(message) __attribute__ ((__deprecated__ (message))) #else #define HTS_DEPRECATED_ENUM(message) #endif // On mingw the "printf" format type doesn't work. It needs "gnu_printf" // in order to check %lld and %z, otherwise it defaults to checking against // the Microsoft library printf format options despite linking against the // GNU posix implementation of printf. The __MINGW_PRINTF_FORMAT macro // expands to printf or gnu_printf as required, but obviously may not // exist #ifdef __MINGW_PRINTF_FORMAT #define HTS_PRINTF_FMT __MINGW_PRINTF_FORMAT #else #define HTS_PRINTF_FMT printf #endif #if HTS_COMPILER_HAS(__format__) || HTS_GCC_AT_LEAST(3,0) #define HTS_FORMAT(type, idx, first) __attribute__((__format__ (type, idx, first))) #else #define HTS_FORMAT(type, idx, first) #endif #if defined(_WIN32) || defined(__CYGWIN__) #if defined(HTS_BUILDING_LIBRARY) #define HTSLIB_EXPORT __declspec(dllexport) #else #define HTSLIB_EXPORT #endif #elif HTS_COMPILER_HAS(__visibility__) || HTS_GCC_AT_LEAST(4,0) #define HTSLIB_EXPORT __attribute__((__visibility__("default"))) #elif defined(__SUNPRO_C) && __SUNPRO_C >= 0x550 #define HTSLIB_EXPORT __global #else #define HTSLIB_EXPORT #endif #endif pysam-0.23.0/htslib/htslib/hts_endian.h000066400000000000000000000267211475062545500200110ustar00rootroot00000000000000/// @file hts_endian.h /// Byte swapping and unaligned access functions. /* Copyright (C) 2017 Genome Research Ltd. Author: Rob Davies Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTS_ENDIAN_H #define HTS_ENDIAN_H #include /* * Compile-time endianness tests. * * Note that these tests may fail. They should only be used to enable * faster versions of endian-neutral implementations. The endian-neutral * version should always be available as a fall-back. * * See https://sourceforge.net/p/predef/wiki/Endianness/ */ /* Save typing as both endian and unaligned tests want to know about x86 */ #if (defined(__i386__) || defined(__i386) || defined(__amd64__) || defined(__amd64) || defined(__x86_64__) || defined(__x86_64) || defined(__i686__) || defined(__i686)) && !defined(HTS_x86) # define HTS_x86 /* x86 and x86_64 platform */ #endif /** @def HTS_LITTLE_ENDIAN * @brief Defined if platform is known to be little-endian */ #ifndef HTS_LITTLE_ENDIAN # if (defined(__BYTE_ORDER__) && __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__) \ || defined(__LITTLE_ENDIAN__) \ || defined(HTS_x86) \ || defined(__ARMEL__) || defined(__THUMBEL__) || defined(__AARCH64EL__) \ || defined(_MIPSEL) || defined(__MIPSEL) || defined(__MIPSEL__) # define HTS_LITTLE_ENDIAN # endif #endif /** @def HTS_BIG_ENDIAN * @brief Defined if platform is known to be big-endian */ #ifndef HTS_BIG_ENDIAN # if (defined(__BYTE_ORDER__) && __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__) \ || defined(__BIG_ENDIAN__) \ || defined(__ARMEB__) || defined(__THUMBEB__) || defined(__AAARCHEB__) \ || defined(_MIPSEB) || defined(__MIPSEB) || defined(__MIPSEB__) # define HTS_BIG_ENDIAN # endif #endif /** @def HTS_ENDIAN_NEUTRAL * @brief Define this to disable any endian-specific optimizations */ #if defined(HTS_ENDIAN_NEUTRAL) || (defined(HTS_LITTLE_ENDIAN) && defined(HTS_BIG_ENDIAN)) /* Disable all endian-specific code. */ # undef HTS_LITTLE_ENDIAN # undef HTS_BIG_ENDIAN #endif /** @def HTS_ALLOW_UNALIGNED * @brief Control use of unaligned memory access. * * Defining HTS_ALLOW_UNALIGNED=1 converts shift-and-or to simple casts on * little-endian platforms that can tolerate unaligned access (notably Intel * x86). * * Defining HTS_ALLOW_UNALIGNED=0 forces shift-and-or. */ // Consider using AX_CHECK_ALIGNED_ACCESS_REQUIRED in autoconf. #ifndef HTS_ALLOW_UNALIGNED # if defined(HTS_x86) # define HTS_ALLOW_UNALIGNED 1 # else # define HTS_ALLOW_UNALIGNED 0 # endif #endif #if HTS_ALLOW_UNALIGNED != 0 # if defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3)) || defined(__clang__) // This prevents problems with gcc's vectoriser generating the wrong // instructions for unaligned data. typedef uint16_t uint16_u __attribute__ ((__aligned__ (1))); typedef uint32_t uint32_u __attribute__ ((__aligned__ (1))); typedef uint64_t uint64_u __attribute__ ((__aligned__ (1))); #else typedef uint16_t uint16_u; typedef uint32_t uint32_u; typedef uint64_t uint64_u; # endif #endif /// Get a uint8_t value from an unsigned byte array /** @param buf Pointer to source byte, may be unaligned * @return An 8-bit unsigned integer */ static inline uint8_t le_to_u8(const uint8_t *buf) { return *buf; } /// Get a uint16_t value from an unsigned byte array /** @param buf Pointer to source byte, may be unaligned * @return A 16 bit unsigned integer * The input is read in little-endian byte order. */ static inline uint16_t le_to_u16(const uint8_t *buf) { #if defined(HTS_LITTLE_ENDIAN) && HTS_ALLOW_UNALIGNED != 0 return *((uint16_u *) buf); #else return (uint16_t) buf[0] | ((uint16_t) buf[1] << 8); #endif } /// Get a uint32_t value from an unsigned byte array /** @param buf Pointer to source byte array, may be unaligned * @return A 32 bit unsigned integer * The input is read in little-endian byte order. */ static inline uint32_t le_to_u32(const uint8_t *buf) { #if defined(HTS_LITTLE_ENDIAN) && HTS_ALLOW_UNALIGNED != 0 return *((uint32_u *) buf); #else return ((uint32_t) buf[0] | ((uint32_t) buf[1] << 8) | ((uint32_t) buf[2] << 16) | ((uint32_t) buf[3] << 24)); #endif } /// Get a uint64_t value from an unsigned byte array /** @param buf Pointer to source byte array, may be unaligned * @return A 64 bit unsigned integer * The input is read in little-endian byte order. */ static inline uint64_t le_to_u64(const uint8_t *buf) { #if defined(HTS_LITTLE_ENDIAN) && HTS_ALLOW_UNALIGNED != 0 return *((uint64_u *) buf); #else return ((uint64_t) buf[0] | ((uint64_t) buf[1] << 8) | ((uint64_t) buf[2] << 16) | ((uint64_t) buf[3] << 24) | ((uint64_t) buf[4] << 32) | ((uint64_t) buf[5] << 40) | ((uint64_t) buf[6] << 48) | ((uint64_t) buf[7] << 56)); #endif } /// Store a uint16_t value in little-endian byte order /** @param val The value to store * @param buf Where to store it (may be unaligned) */ static inline void u16_to_le(uint16_t val, uint8_t *buf) { #if defined(HTS_LITTLE_ENDIAN) && HTS_ALLOW_UNALIGNED != 0 *((uint16_u *) buf) = val; #else buf[0] = val & 0xff; buf[1] = (val >> 8) & 0xff; #endif } /// Store a uint32_t value in little-endian byte order /** @param val The value to store * @param buf Where to store it (may be unaligned) */ static inline void u32_to_le(uint32_t val, uint8_t *buf) { #if defined(HTS_LITTLE_ENDIAN) && HTS_ALLOW_UNALIGNED != 0 *((uint32_u *) buf) = val; #else buf[0] = val & 0xff; buf[1] = (val >> 8) & 0xff; buf[2] = (val >> 16) & 0xff; buf[3] = (val >> 24) & 0xff; #endif } /// Store a uint64_t value in little-endian byte order /** @param val The value to store * @param buf Where to store it (may be unaligned) */ static inline void u64_to_le(uint64_t val, uint8_t *buf) { #if defined(HTS_LITTLE_ENDIAN) && HTS_ALLOW_UNALIGNED != 0 *((uint64_u *) buf) = val; #else buf[0] = val & 0xff; buf[1] = (val >> 8) & 0xff; buf[2] = (val >> 16) & 0xff; buf[3] = (val >> 24) & 0xff; buf[4] = (val >> 32) & 0xff; buf[5] = (val >> 40) & 0xff; buf[6] = (val >> 48) & 0xff; buf[7] = (val >> 56) & 0xff; #endif } /* Signed values. Grab the data as unsigned, then convert to signed without * triggering undefined behaviour. On any sensible platform, the conversion * should optimise away to nothing. */ /// Get an int8_t value from an unsigned byte array /** @param buf Pointer to source byte array, may be unaligned * @return A 8 bit signed integer * The input data is interpreted as 2's complement representation. */ static inline int8_t le_to_i8(const uint8_t *buf) { return *buf < 0x80 ? (int8_t) *buf : -((int8_t) (0xff - *buf)) - 1; } /// Get an int16_t value from an unsigned byte array /** @param buf Pointer to source byte array, may be unaligned * @return A 16 bit signed integer * The input data is interpreted as 2's complement representation in * little-endian byte order. */ static inline int16_t le_to_i16(const uint8_t *buf) { uint16_t v = le_to_u16(buf); return v < 0x8000 ? (int16_t) v : -((int16_t) (0xffff - v)) - 1; } /// Get an int32_t value from an unsigned byte array /** @param buf Pointer to source byte array, may be unaligned * @return A 32 bit signed integer * The input data is interpreted as 2's complement representation in * little-endian byte order. */ static inline int32_t le_to_i32(const uint8_t *buf) { uint32_t v = le_to_u32(buf); return v < 0x80000000U ? (int32_t) v : -((int32_t) (0xffffffffU - v)) - 1; } /// Get an int64_t value from an unsigned byte array /** @param buf Pointer to source byte array, may be unaligned * @return A 64 bit signed integer * The input data is interpreted as 2's complement representation in * little-endian byte order. */ static inline int64_t le_to_i64(const uint8_t *buf) { uint64_t v = le_to_u64(buf); return (v < 0x8000000000000000ULL ? (int64_t) v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); } // Converting the other way is easier as signed -> unsigned is well defined. /// Store a uint16_t value in little-endian byte order /** @param val The value to store * @param buf Where to store it (may be unaligned) */ static inline void i16_to_le(int16_t val, uint8_t *buf) { u16_to_le(val, buf); } /// Store a uint32_t value in little-endian byte order /** @param val The value to store * @param buf Where to store it (may be unaligned) */ static inline void i32_to_le(int32_t val, uint8_t *buf) { u32_to_le(val, buf); } /// Store a uint64_t value in little-endian byte order /** @param val The value to store * @param buf Where to store it (may be unaligned) */ static inline void i64_to_le(int64_t val, uint8_t *buf) { u64_to_le(val, buf); } /* Floating point. Assumptions: * Platform uses IEEE 754 format * sizeof(float) == sizeof(uint32_t) * sizeof(double) == sizeof(uint64_t) * Endian-ness is the same for both floating point and integer * Type-punning via a union is allowed */ /// Get a float value from an unsigned byte array /** @param buf Pointer to source byte array, may be unaligned * @return A 32 bit floating point value * The input is interpreted as an IEEE 754 format float in little-endian * byte order. */ static inline float le_to_float(const uint8_t *buf) { union { uint32_t u; float f; } convert; convert.u = le_to_u32(buf); return convert.f; } /// Get a double value from an unsigned byte array /** @param buf Pointer to source byte array, may be unaligned * @return A 64 bit floating point value * The input is interpreted as an IEEE 754 format double in little-endian * byte order. */ static inline double le_to_double(const uint8_t *buf) { union { uint64_t u; double f; } convert; convert.u = le_to_u64(buf); return convert.f; } /// Store a float value in little-endian byte order /** @param val The value to store * @param buf Where to store it (may be unaligned) */ static inline void float_to_le(float val, uint8_t *buf) { union { uint32_t u; float f; } convert; convert.f = val; u32_to_le(convert.u, buf); } /// Store a double value in little-endian byte order /** @param val The value to store * @param buf Where to store it (may be unaligned) */ static inline void double_to_le(double val, uint8_t *buf) { union { uint64_t u; double f; } convert; convert.f = val; u64_to_le(convert.u, buf); } #endif /* HTS_ENDIAN_H */ pysam-0.23.0/htslib/htslib/hts_expr.h000066400000000000000000000135471475062545500175330ustar00rootroot00000000000000/* expr.c -- filter expression parsing and processing. Copyright (C) 2020, 2022 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notices and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTS_EXPR_H #define HTS_EXPR_H #include #include "kstring.h" #include "hts_defs.h" /// Holds a filter variable. This is also used to return the results. /** * The expression language has 3-states of string, numeric, and unknown. * The unknown state is either a NaN numeric or a null string, with both * internally considered to have the same "unknown" meaning. * * These largely match the IEE 754 semantics for NaN comparisons: <, >, ==, * != all fail, (even NaN == NaN). Similarly arithmetic (+,-,/,*,%) with * unknown values are still unknown (and false). * * The departure from NaN semantics though is that our unknown/null state is * considered to be false while NaN in C is true. Similarly the false nature * of our unknown state meants !val becomes true, !!val is once again false, * val && 1 is false, val || 0 is false, and val || 1 is true along with * !val || 0 and !val && 1. * * Note it is possible for empty strings and zero numbers to also be true. * An example of this is the aux string '[NM]' which returns true if the * NM tag is found, regardless of whether it is also zero. However the * better approach added in 1.16 is 'exists([NM])'. */ typedef struct hts_expr_val_t { char is_str; // Use .s vs .d char is_true; // Force true if even zero kstring_t s; // is_str and empty s permitted (eval as false) double d; // otherwise this } hts_expr_val_t; /// Returns true if an hts_expr_val_t is defined. /* An example usage of this is in the SAM expression filter where an * [X0] aux tag will be the value of X0 (string or numeric) if set, or * a false nul-string (not the same as an empty one) when not set. */ static inline int hts_expr_val_exists(hts_expr_val_t *v) { return v && !(v->is_str == 1 && v->s.s == NULL) && !(v->is_str == 0 && isnan(v->d)); } /// Returns true if an hts_expr_val_t is defined or is undef-but-true static inline int hts_expr_val_existsT(hts_expr_val_t *v) { return (v && v->is_true) || hts_expr_val_exists(v); } /// Set a value to be undefined (nan). static inline void hts_expr_val_undef(hts_expr_val_t *v) { ks_clear(&v->s); v->is_true = 0; v->is_str = 0; v->d = NAN; } /// Frees a hts_expr_val_t type. static inline void hts_expr_val_free(hts_expr_val_t *f) { ks_free(&f->s); } /// Opaque hts_filter_t type. Definition in hts_expr.c typedef struct hts_filter_t hts_filter_t; /// For static initialisation of hts_expr_val_t values #define HTS_EXPR_VAL_INIT {0, 0, KS_INITIALIZE, 0} /// Creates a filter for expression "str". /** @param str The filter expression * @return A pointer on success, NULL on failure */ HTSLIB_EXPORT hts_filter_t *hts_filter_init(const char *str); /// Frees an hts_filter_t created via hts_filter_init /** @param filt The filter pointer. */ HTSLIB_EXPORT void hts_filter_free(hts_filter_t *filt); /// Type for expression symbol lookups; name -> value. typedef int (hts_expr_sym_func)(void *data, char *str, char **end, hts_expr_val_t *res); /// Evaluates a filter expression and returns the value /** @param filt The filter, produced by hts_filter_init * @param data Arbitrary caller data, passed into sym_func * @param sym_func Callback function to lookup variables. * @param res Filled out with the result of the filter evaluation * @return Returns 0 on success, -1 on failure * * sym_func and data may be NULL if the caller does not need its own data * pointer or if it has no variables to lookup. * * The type of the returned result may be numeric of string, as defined by * the is_str member. It can also be explicitly defined to be true even * for a null value. This may be used to check for the existence of * something, irrespective of whether that something evaluates to zero. * * @p res must be initialized using HTS_EXPR_VAL_INIT before passing it * to this function for the first time. */ HTSLIB_EXPORT int hts_filter_eval2(hts_filter_t *filt, void *data, hts_expr_sym_func *sym_func, hts_expr_val_t *res); /// Evaluate a filter expression (derecated API) /** * @copydetails hts_filter_eval2() * * If calling this function more than once with the same @p res * parameter, hts_expr_val_free(res) must be used between invocations * to clear any allocated memory prior to reuse. * * @deprecated This function has been replaced by hts_filter_eval2(), * which clears @p res properly itself. */ HTSLIB_EXPORT int hts_filter_eval(hts_filter_t *filt, void *data, hts_expr_sym_func *sym_func, hts_expr_val_t *res) HTS_DEPRECATED("Please use hts_filter_eval2 instead"); #endif /* HTS_EXPR_H */ pysam-0.23.0/htslib/htslib/hts_log.h000066400000000000000000000075661475062545500173420ustar00rootroot00000000000000/// \file htslib/hts_log.h /// Configuration of log levels. /* The MIT License Copyright (C) 2017 Genome Research Ltd. Author: Anders Kaplan Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTS_LOG_H #define HTS_LOG_H #include "hts_defs.h" #ifdef __cplusplus extern "C" { #endif /// Log levels. enum htsLogLevel { HTS_LOG_OFF, ///< All logging disabled. HTS_LOG_ERROR, ///< Logging of errors only. HTS_LOG_WARNING = 3, ///< Logging of errors and warnings. HTS_LOG_INFO, ///< Logging of errors, warnings, and normal but significant events. HTS_LOG_DEBUG, ///< Logging of all except the most detailed debug events. HTS_LOG_TRACE ///< All logging enabled. }; /// Sets the selected log level. HTSLIB_EXPORT void hts_set_log_level(enum htsLogLevel level); /// Gets the selected log level. HTSLIB_EXPORT enum htsLogLevel hts_get_log_level(void); /// Selected log level. /*! * One of the HTS_LOG_* values. The default is HTS_LOG_WARNING. * \note Avoid direct use of this variable. Use hts_set_log_level and hts_get_log_level instead. */ HTSLIB_EXPORT extern int hts_verbose; /*! Logs an event. * \param severity Severity of the event: * - HTS_LOG_ERROR means that something went wrong so that a task could not be completed. * - HTS_LOG_WARNING means that something unexpected happened, but that execution can continue, perhaps in a degraded mode. * - HTS_LOG_INFO means that something normal but significant happened. * - HTS_LOG_DEBUG means that something normal and insignificant happened. * - HTS_LOG_TRACE means that something happened that might be of interest when troubleshooting. * \param context Context where the event occurred. Typically set to "__func__". * \param format Format string with placeholders, like printf. */ HTSLIB_EXPORT void hts_log(enum htsLogLevel severity, const char *context, const char *format, ...) HTS_FORMAT(HTS_PRINTF_FMT, 3, 4); /*! Logs an event with severity HTS_LOG_ERROR and default context. Parameters: format, ... */ #define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__) /*! Logs an event with severity HTS_LOG_WARNING and default context. Parameters: format, ... */ #define hts_log_warning(...) hts_log(HTS_LOG_WARNING, __func__, __VA_ARGS__) /*! Logs an event with severity HTS_LOG_INFO and default context. Parameters: format, ... */ #define hts_log_info(...) hts_log(HTS_LOG_INFO, __func__, __VA_ARGS__) /*! Logs an event with severity HTS_LOG_DEBUG and default context. Parameters: format, ... */ #define hts_log_debug(...) hts_log(HTS_LOG_DEBUG, __func__, __VA_ARGS__) /*! Logs an event with severity HTS_LOG_TRACE and default context. Parameters: format, ... */ #define hts_log_trace(...) hts_log(HTS_LOG_TRACE, __func__, __VA_ARGS__) #ifdef __cplusplus } #endif #endif // #ifndef HTS_LOG_H pysam-0.23.0/htslib/htslib/hts_os.h000066400000000000000000000054321475062545500171700ustar00rootroot00000000000000/// @file hts_os.h /// Operating System specific tweaks, for compatibility with POSIX. /* Copyright (C) 2017, 2019-2020 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTSLIB_HTS_OS_H #define HTSLIB_HTS_OS_H #include "hts_defs.h" #ifdef __cplusplus extern "C" { #endif /* This is srand48_deterministic() on platforms that provide it, or srand48() otherwise (or our own POSIX srand48() on platforms that provide neither). Hence calling hts_srand48() will always set up the same POSIX-determined sequence of pseudo-random numbers on any platform, while calling srand48() may (e.g., on OpenBSD) set up a different non-deterministic sequence. */ HTSLIB_EXPORT void hts_srand48(long seed); HTSLIB_EXPORT double hts_erand48(unsigned short xseed[3]); HTSLIB_EXPORT double hts_drand48(void); HTSLIB_EXPORT long hts_lrand48(void); #if defined(_WIN32) && !defined(__CYGWIN__) // Windows usually lacks *rand48(), but cygwin provides them. #define srand48(S) hts_srand48((S)) #define erand48(X) hts_erand48((X)) #define drand48() hts_drand48() #define lrand48() hts_lrand48() #endif #if 0 /* def _WIN32 - disabled for now, not currently used */ /* Check if the fd is a cygwin/msys's pty. */ extern int is_cygpty(int fd); #endif #ifdef __cplusplus } #endif #if defined(__MINGW32__) #include #define mkdir(filename,mode) mkdir((filename)) #endif #ifdef _WIN32 #include #define srandom srand #define random rand #endif /* MSVC does not provide ssize_t in its . This ensures the type is available (unless suppressed by defining HTS_NO_SSIZE_T first). */ #if defined _MSC_VER && defined _INTPTR_T_DEFINED && !defined _SSIZE_T_DEFINED && !defined HTS_NO_SSIZE_T && !defined ssize_t #define ssize_t intptr_t #endif #endif // HTSLIB_HTS_OS_H pysam-0.23.0/htslib/htslib/kbitset.h000066400000000000000000000127451475062545500173430ustar00rootroot00000000000000/* The MIT License Copyright (C) 2015, 2018 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef KBITSET_H #define KBITSET_H /* Example of using kbitset_t, which represents a subset of {0,..., N-1}, where N is the size specified in kbs_init(). kbitset_t *bset = kbs_init(100); kbs_insert(bset, 5); kbs_insert(bset, 68); kbs_delete(bset, 37); // ... if (kbs_exists(bset, 68)) printf("68 present\n"); kbitset_iter_t itr; int i; kbs_start(&itr); while ((i = kbs_next(bset, &itr)) >= 0) printf("%d present\n", i); kbs_destroy(bset); Example of declaring a kbitset_t-using function in a header file, so that only source files that actually use process() need to include : struct kbitset_t; void process(struct kbitset_t *bset); */ #include #include #include #define KBS_ELTBITS (CHAR_BIT * sizeof (unsigned long)) #define KBS_ELT(i) ((i) / KBS_ELTBITS) #define KBS_MASK(i) (1UL << ((i) % KBS_ELTBITS)) typedef struct kbitset_t { size_t n, n_max; unsigned long b[1]; } kbitset_t; // (For internal use only.) Returns a mask (like 00011111) showing // which bits are in use in the last slot (for the given ni) set. static inline unsigned long kbs_last_mask(size_t ni) { unsigned long mask = KBS_MASK(ni) - 1; return mask? mask : ~0UL; } // Initialise a bit set capable of holding ni integers, 0 <= i < ni. // The set returned is empty if fill == 0, or all of [0,ni) otherwise. static inline kbitset_t *kbs_init2(size_t ni, int fill) { size_t n = (ni + KBS_ELTBITS-1) / KBS_ELTBITS; kbitset_t *bs = (kbitset_t *) malloc(sizeof(kbitset_t) + n * sizeof(unsigned long)); if (bs == NULL) return NULL; bs->n = bs->n_max = n; memset(bs->b, fill? ~0 : 0, n * sizeof (unsigned long)); // b[n] is always non-zero (a fact used by kbs_next()). bs->b[n] = kbs_last_mask(ni); if (fill) bs->b[n-1] &= bs->b[n]; return bs; } // Initialise an empty bit set capable of holding ni integers, 0 <= i < ni. static inline kbitset_t *kbs_init(size_t ni) { return kbs_init2(ni, 0); } // Resize an existing bit set to be capable of holding ni_new integers. // Elements in [ni_old,ni_new) are added to the set if fill != 0. static inline int kbs_resize2(kbitset_t **bsp, size_t ni_new, int fill) { kbitset_t *bs = *bsp; size_t n = bs? bs->n : 0; size_t n_new = (ni_new + KBS_ELTBITS-1) / KBS_ELTBITS; if (bs == NULL || n_new > bs->n_max) { bs = (kbitset_t *) realloc(*bsp, sizeof(kbitset_t) + n_new * sizeof(unsigned long)); if (bs == NULL) return -1; bs->n_max = n_new; *bsp = bs; } bs->n = n_new; if (n_new >= n) memset(&bs->b[n], fill? ~0 : 0, (n_new - n) * sizeof (unsigned long)); bs->b[n_new] = kbs_last_mask(ni_new); // Need to clear excess bits when fill!=0 or n_newb[n_new-1] &= bs->b[n_new]; return 0; } // Resize an existing bit set to be capable of holding ni_new integers. // Returns negative on error. static inline int kbs_resize(kbitset_t **bsp, size_t ni_new) { return kbs_resize2(bsp, ni_new, 0); } // Destroy a bit set. static inline void kbs_destroy(kbitset_t *bs) { free(bs); } // Reset the bit set to empty. static inline void kbs_clear(kbitset_t *bs) { memset(bs->b, 0, bs->n * sizeof (unsigned long)); } // Reset the bit set to all of [0,ni). static inline void kbs_insert_all(kbitset_t *bs) { memset(bs->b, ~0, bs->n * sizeof (unsigned long)); bs->b[bs->n-1] &= bs->b[bs->n]; } // Insert an element into the bit set. static inline void kbs_insert(kbitset_t *bs, int i) { bs->b[KBS_ELT(i)] |= KBS_MASK(i); } // Remove an element from the bit set. static inline void kbs_delete(kbitset_t *bs, int i) { bs->b[KBS_ELT(i)] &= ~KBS_MASK(i); } // Test whether the bit set contains the element. static inline int kbs_exists(const kbitset_t *bs, int i) { return (bs->b[KBS_ELT(i)] & KBS_MASK(i)) != 0; } typedef struct kbitset_iter_t { unsigned long mask; size_t elt; int i; } kbitset_iter_t; // Initialise or reset a bit set iterator. static inline void kbs_start(kbitset_iter_t *itr) { itr->mask = 1; itr->elt = 0; itr->i = 0; } // Return the next element contained in the bit set, or -1 if there are no more. static inline int kbs_next(const kbitset_t *bs, kbitset_iter_t *itr) { unsigned long b = bs->b[itr->elt]; for (;;) { if (itr->mask == 0) { while ((b = bs->b[++itr->elt]) == 0) itr->i += KBS_ELTBITS; if (itr->elt == bs->n) return -1; itr->mask = 1; } if (b & itr->mask) break; itr->i++; itr->mask <<= 1; } itr->mask <<= 1; return itr->i++; } #endif pysam-0.23.0/htslib/htslib/kfunc.h000066400000000000000000000054141475062545500167770ustar00rootroot00000000000000/* The MIT License Copyright (C) 2010, 2013-2014 Genome Research Ltd. Copyright (C) 2011 Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTSLIB_KFUNC_H #define HTSLIB_KFUNC_H #include "hts_defs.h" #ifdef __cplusplus extern "C" { #endif /* Log gamma function * \log{\Gamma(z)} * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245 */ HTSLIB_EXPORT double kf_lgamma(double z); /* complementary error function * \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2} dt * AS66, 2nd algorithm, http://lib.stat.cmu.edu/apstat/66 */ HTSLIB_EXPORT double kf_erfc(double x); /* The following computes regularized incomplete gamma functions. * Formulas are taken from Wiki, with additional input from Numerical * Recipes in C (for modified Lentz's algorithm) and AS245 * (http://lib.stat.cmu.edu/apstat/245). * * A good online calculator is available at: * * http://www.danielsoper.com/statcalc/calc23.aspx * * It calculates upper incomplete gamma function, which equals * kf_gammaq(s,z)*tgamma(s). */ HTSLIB_EXPORT double kf_gammap(double s, double z); HTSLIB_EXPORT double kf_gammaq(double s, double z); /* Regularized incomplete beta function. The method is taken from * Numerical Recipe in C, 2nd edition, section 6.4. The following web * page calculates the incomplete beta function, which equals * kf_betai(a,b,x) * gamma(a) * gamma(b) / gamma(a+b): * * http://www.danielsoper.com/statcalc/calc36.aspx */ HTSLIB_EXPORT double kf_betai(double a, double b, double x); /* * n11 n12 | n1_ * n21 n22 | n2_ * -----------+---- * n_1 n_2 | n */ HTSLIB_EXPORT double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two); #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/htslib/khash.h000066400000000000000000000640371475062545500167750ustar00rootroot00000000000000/* The MIT License Copyright (c) 2008, 2009, 2011 by Attractive Chaos Copyright (C) 2014-2015, 2018, 2024 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* An example: #include "khash.h" KHASH_MAP_INIT_INT(32, char) int main() { int ret, is_missing; khiter_t k; khash_t(32) *h = kh_init(32); k = kh_put(32, h, 5, &ret); kh_value(h, k) = 10; k = kh_get(32, h, 10); is_missing = (k == kh_end(h)); k = kh_get(32, h, 5); kh_del(32, h, k); for (k = kh_begin(h); k != kh_end(h); ++k) if (kh_exist(h, k)) kh_value(h, k) = 1; kh_destroy(32, h); return 0; } */ /* 2013-05-02 (0.2.8): * Use quadratic probing. When the capacity is power of 2, stepping function i*(i+1)/2 guarantees to traverse each bucket. It is better than double hashing on cache performance and is more robust than linear probing. In theory, double hashing should be more robust than quadratic probing. However, my implementation is probably not for large hash tables, because the second hash function is closely tied to the first hash function, which reduce the effectiveness of double hashing. Reference: http://research.cs.vt.edu/AVresearch/hashing/quadratic.php 2011-12-29 (0.2.7): * Minor code clean up; no actual effect. 2011-09-16 (0.2.6): * The capacity is a power of 2. This seems to dramatically improve the speed for simple keys. Thank Zilong Tan for the suggestion. Reference: - http://code.google.com/p/ulib/ - http://nothings.org/computer/judy/ * Allow to optionally use linear probing which usually has better performance for random input. Double hashing is still the default as it is more robust to certain non-random input. * Added Wang's integer hash function (not used by default). This hash function is more robust to certain non-random input. 2011-02-14 (0.2.5): * Allow to declare global functions. 2009-09-26 (0.2.4): * Improve portability 2008-09-19 (0.2.3): * Corrected the example * Improved interfaces 2008-09-11 (0.2.2): * Improved speed a little in kh_put() 2008-09-10 (0.2.1): * Added kh_clear() * Fixed a compiling error 2008-09-02 (0.2.0): * Changed to token concatenation which increases flexibility. 2008-08-31 (0.1.2): * Fixed a bug in kh_get(), which has not been tested previously. 2008-08-31 (0.1.1): * Added destructor */ #ifndef __AC_KHASH_H #define __AC_KHASH_H /*! @header Generic hash table library. */ #define AC_VERSION_KHASH_H "0.2.8" #include #include #include #include "kstring.h" #include "kroundup.h" /* compiler specific configuration */ #if UINT_MAX == 0xffffffffu typedef unsigned int khint32_t; #elif ULONG_MAX == 0xffffffffu typedef unsigned long khint32_t; #endif #if ULONG_MAX == ULLONG_MAX typedef unsigned long khint64_t; #else typedef unsigned long long khint64_t; #endif #ifndef kh_inline #ifdef _MSC_VER #define kh_inline __inline #else #define kh_inline inline #endif #endif /* kh_inline */ #ifndef klib_unused #if (defined __clang__ && __clang_major__ >= 3) || (defined __GNUC__ && __GNUC__ >= 3) #define klib_unused __attribute__ ((__unused__)) #else #define klib_unused #endif #endif /* klib_unused */ typedef khint32_t khint_t; typedef khint_t khiter_t; #define __ac_isempty(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&2) #define __ac_isdel(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&1) #define __ac_iseither(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&3) #define __ac_set_isdel_false(flag, i) (flag[i>>4]&=~(1ul<<((i&0xfU)<<1))) #define __ac_set_isempty_false(flag, i) (flag[i>>4]&=~(2ul<<((i&0xfU)<<1))) #define __ac_set_isboth_false(flag, i) (flag[i>>4]&=~(3ul<<((i&0xfU)<<1))) #define __ac_set_isdel_true(flag, i) (flag[i>>4]|=1ul<<((i&0xfU)<<1)) #define __ac_fsize(m) ((m) < 16? 1 : (m)>>4) #ifndef kroundup32 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif #ifndef kcalloc #define kcalloc(N,Z) calloc(N,Z) #endif #ifndef kmalloc #define kmalloc(Z) malloc(Z) #endif #ifndef krealloc #define krealloc(P,Z) realloc(P,Z) #endif #ifndef kfree #define kfree(P) free(P) #endif static const double __ac_HASH_UPPER = 0.77; #define __KHASH_TYPE(name, khkey_t, khval_t) \ typedef struct kh_##name##_s { \ khint_t n_buckets, size, n_occupied, upper_bound; \ khint32_t *flags; \ khkey_t *keys; \ khval_t *vals; \ } kh_##name##_t; #define __KHASH_PROTOTYPES(name, khkey_t, khval_t) \ extern kh_##name##_t *kh_init_##name(void); \ extern void kh_destroy_##name(kh_##name##_t *h); \ extern void kh_clear_##name(kh_##name##_t *h); \ extern khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key); \ extern int kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets); \ extern khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret); \ extern void kh_del_##name(kh_##name##_t *h, khint_t x); #define __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \ SCOPE kh_##name##_t *kh_init_##name(void) { \ return (kh_##name##_t*)kcalloc(1, sizeof(kh_##name##_t)); \ } \ SCOPE void kh_destroy_##name(kh_##name##_t *h) \ { \ if (h) { \ kfree((void *)h->keys); kfree(h->flags); \ kfree((void *)h->vals); \ kfree(h); \ } \ } \ SCOPE void kh_clear_##name(kh_##name##_t *h) \ { \ if (h && h->flags) { \ memset(h->flags, 0xaa, __ac_fsize(h->n_buckets) * sizeof(khint32_t)); \ h->size = h->n_occupied = 0; \ } \ } \ SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ { \ if (h->n_buckets) { \ khint_t k, i, last, mask, step = 0; \ mask = h->n_buckets - 1; \ k = __hash_func(key); i = k & mask; \ last = i; \ while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \ i = (i + (++step)) & mask; \ if (i == last) return h->n_buckets; \ } \ return __ac_iseither(h->flags, i)? h->n_buckets : i; \ } else return 0; \ } \ SCOPE int kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \ { /* This function uses 0.25*n_buckets bytes of working space instead of [sizeof(key_t+val_t)+.25]*n_buckets. */ \ khint32_t *new_flags = 0; \ khint_t j = 1; \ { \ kroundup32(new_n_buckets); \ if (new_n_buckets < 4) new_n_buckets = 4; \ if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0; /* requested size is too small */ \ else { /* hash table size to be changed (shrink or expand); rehash */ \ new_flags = (khint32_t*)kmalloc(__ac_fsize(new_n_buckets) * sizeof(khint32_t)); \ if (!new_flags) return -1; \ memset(new_flags, 0xaa, __ac_fsize(new_n_buckets) * sizeof(khint32_t)); \ if (h->n_buckets < new_n_buckets) { /* expand */ \ khkey_t *new_keys = (khkey_t*)krealloc((void *)h->keys, new_n_buckets * sizeof(khkey_t)); \ if (!new_keys) { kfree(new_flags); return -1; } \ h->keys = new_keys; \ if (kh_is_map) { \ khval_t *new_vals = (khval_t*)krealloc((void *)h->vals, new_n_buckets * sizeof(khval_t)); \ if (!new_vals) { kfree(new_flags); return -1; } \ h->vals = new_vals; \ } \ } /* otherwise shrink */ \ } \ } \ if (j) { /* rehashing is needed */ \ for (j = 0; j != h->n_buckets; ++j) { \ if (__ac_iseither(h->flags, j) == 0) { \ khkey_t key = h->keys[j]; \ khval_t val; \ khint_t new_mask; \ new_mask = new_n_buckets - 1; \ if (kh_is_map) val = h->vals[j]; \ __ac_set_isdel_true(h->flags, j); \ while (1) { /* kick-out process; sort of like in Cuckoo hashing */ \ khint_t k, i, step = 0; \ k = __hash_func(key); \ i = k & new_mask; \ while (!__ac_isempty(new_flags, i)) i = (i + (++step)) & new_mask; \ __ac_set_isempty_false(new_flags, i); \ if (i < h->n_buckets && __ac_iseither(h->flags, i) == 0) { /* kick out the existing element */ \ { khkey_t tmp = h->keys[i]; h->keys[i] = key; key = tmp; } \ if (kh_is_map) { khval_t tmp = h->vals[i]; h->vals[i] = val; val = tmp; } \ __ac_set_isdel_true(h->flags, i); /* mark it as deleted in the old hash table */ \ } else { /* write the element and jump out of the loop */ \ h->keys[i] = key; \ if (kh_is_map) h->vals[i] = val; \ break; \ } \ } \ } \ } \ if (h->n_buckets > new_n_buckets) { /* shrink the hash table */ \ h->keys = (khkey_t*)krealloc((void *)h->keys, new_n_buckets * sizeof(khkey_t)); \ if (kh_is_map) h->vals = (khval_t*)krealloc((void *)h->vals, new_n_buckets * sizeof(khval_t)); \ } \ kfree(h->flags); /* free the working space */ \ h->flags = new_flags; \ h->n_buckets = new_n_buckets; \ h->n_occupied = h->size; \ h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \ } \ return 0; \ } \ SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ { \ khint_t x; \ if (h->n_occupied >= h->upper_bound) { /* update the hash table */ \ if (h->n_buckets > (h->size<<1)) { \ if (kh_resize_##name(h, h->n_buckets - 1) < 0) { /* clear "deleted" elements */ \ *ret = -1; return h->n_buckets; \ } \ } else if (kh_resize_##name(h, h->n_buckets + 1) < 0) { /* expand the hash table */ \ *ret = -1; return h->n_buckets; \ } \ } /* TODO: to implement automatically shrinking; resize() already support shrinking */ \ { \ khint_t k, i, site, last, mask = h->n_buckets - 1, step = 0; \ x = site = h->n_buckets; k = __hash_func(key); i = k & mask; \ if (__ac_isempty(h->flags, i)) x = i; /* for speed up */ \ else { \ last = i; \ while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \ if (__ac_isdel(h->flags, i)) site = i; \ i = (i + (++step)) & mask; \ if (i == last) { x = site; break; } \ } \ if (x == h->n_buckets) { \ if (__ac_isempty(h->flags, i) && site != h->n_buckets) x = site; \ else x = i; \ } \ } \ } \ if (__ac_isempty(h->flags, x)) { /* not present at all */ \ h->keys[x] = key; \ __ac_set_isboth_false(h->flags, x); \ ++h->size; ++h->n_occupied; \ *ret = 1; \ } else if (__ac_isdel(h->flags, x)) { /* deleted */ \ h->keys[x] = key; \ __ac_set_isboth_false(h->flags, x); \ ++h->size; \ *ret = 2; \ } else *ret = 0; /* Don't touch h->keys[x] if present and not deleted */ \ return x; \ } \ SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ { \ if (x != h->n_buckets && !__ac_iseither(h->flags, x)) { \ __ac_set_isdel_true(h->flags, x); \ --h->size; \ } \ } \ SCOPE int kh_stats_##name(kh_##name##_t *h, khint_t *empty, \ khint_t *deleted, khint_t *hist_size, \ khint_t **hist_out) \ { \ khint_t i, *hist = NULL, dist_max = 0, k, dist, step; \ khint_t mask = h->n_buckets - 1; \ *empty = *deleted = *hist_size = 0; \ hist = (khint_t *) calloc(1, sizeof(*hist)); \ if (!hist) { return -1; } \ for (i = kh_begin(h); i < kh_end(h); ++i) { \ if (__ac_isempty(h->flags, i)) { (*empty)++; continue; } \ if (__ac_isdel(h->flags, i)) { (*deleted)++; continue; } \ k = __hash_func(h->keys[i]) & (h->n_buckets - 1); \ dist = 0; \ step = 0; \ while (k != i) { \ dist++; \ k = (k + (++step)) & mask; \ } \ if (dist_max <= dist) { \ khint_t *new_hist = (khint_t *) realloc(hist, sizeof(*new_hist) * (dist + 1)); \ if (!new_hist) { free(hist); return -1; } \ for (k = dist_max + 1; k <= dist; k++) new_hist[k] = 0; \ hist = new_hist; \ dist_max = dist; \ } \ hist[dist]++; \ } \ *hist_out = hist; \ *hist_size = dist_max + 1; \ return 0; \ } #define KHASH_DECLARE(name, khkey_t, khval_t) \ __KHASH_TYPE(name, khkey_t, khval_t) \ __KHASH_PROTOTYPES(name, khkey_t, khval_t) #define KHASH_INIT2(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \ __KHASH_TYPE(name, khkey_t, khval_t) \ __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) #define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \ KHASH_INIT2(name, static kh_inline klib_unused, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) /* --- BEGIN OF HASH FUNCTIONS --- */ /*! @function @abstract Integer hash function @param key The integer [khint32_t] @return The hash value [khint_t] */ #define kh_int_hash_func(key) (khint32_t)(key) /*! @function @abstract Integer comparison function */ #define kh_int_hash_equal(a, b) ((a) == (b)) /*! @function @abstract 64-bit integer hash function @param key The integer [khint64_t] @return The hash value [khint_t] */ #define kh_int64_hash_func(key) (khint32_t)((key)>>33^(key)^(key)<<11) /*! @function @abstract 64-bit integer comparison function */ #define kh_int64_hash_equal(a, b) ((a) == (b)) /*! @function @abstract const char* hash function @param s Pointer to a null terminated string @return The hash value */ static kh_inline khint_t __ac_X31_hash_string(const char *s) { khint_t h = (khint_t)*s; if (h) for (++s ; *s; ++s) h = (h << 5) - h + (khint_t)*s; return h; } /*! @function @abstract const char* FNV1a hash function @param s Pointer to a null terminated string @return The hash value */ static kh_inline khint_t __ac_FNV1a_hash_string(const char *s) { const khint_t offset_basis = 2166136261; const khint_t FNV_prime = 16777619; khint_t h = offset_basis; for (; *s; ++s) h = (h ^ (uint8_t) *s) * FNV_prime; return h; } /*! @function @abstract Another interface to const char* hash function @param key Pointer to a nul terminated string [const char*] @return The hash value [khint_t] */ #define kh_str_hash_func(key) __ac_FNV1a_hash_string(key) /*! @function @abstract Const char* comparison function */ #define kh_str_hash_equal(a, b) (strcmp(a, b) == 0) /*! @function @abstract Kstring hash function @param s Pointer to a kstring @return The hash value */ static kh_inline khint_t __ac_X31_hash_kstring(const kstring_t ks) { khint_t h = 0; size_t i; for (i = 0; i < ks.l; i++) h = (h << 5) - h + (khint_t)ks.s[i]; return h; } /*! @function @abstract Kstring hash function @param s Pointer to a kstring @return The hash value */ static kh_inline khint_t __ac_FNV1a_hash_kstring(const kstring_t ks) { const khint_t offset_basis = 2166136261; const khint_t FNV_prime = 16777619; khint_t h = offset_basis; size_t i; for (i = 0; i < ks.l; i++) h = (h ^ (uint8_t) ks.s[i]) * FNV_prime; return h; } /*! @function @abstract Interface to kstring hash function. @param key Pointer to a khash; permits hashing on non-nul terminated strings. @return The hash value [khint_t] */ #define kh_kstr_hash_func(key) __ac_FNV1a_hash_kstring(key) /*! @function @abstract kstring comparison function */ #define kh_kstr_hash_equal(a, b) ((a).l == (b).l && strncmp((a).s, (b).s, (a).l) == 0) static kh_inline khint_t __ac_Wang_hash(khint_t key) { key += ~(key << 15); key ^= (key >> 10); key += (key << 3); key ^= (key >> 6); key += ~(key << 11); key ^= (key >> 16); return key; } #define kh_int_hash_func2(key) __ac_Wang_hash((khint_t)(key)) /* --- END OF HASH FUNCTIONS --- */ /* Other convenient macros... */ /*! @abstract Type of the hash table. @param name Name of the hash table [symbol] */ #define khash_t(name) kh_##name##_t /*! @function @abstract Initiate a hash table. @param name Name of the hash table [symbol] @return Pointer to the hash table [khash_t(name)*] */ #define kh_init(name) kh_init_##name() /*! @function @abstract Destroy a hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] */ #define kh_destroy(name, h) kh_destroy_##name(h) /*! @function @abstract Reset a hash table without deallocating memory. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] */ #define kh_clear(name, h) kh_clear_##name(h) /*! @function @abstract Resize a hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param s New size [khint_t] */ #define kh_resize(name, h, s) kh_resize_##name(h, s) /*! @function @abstract Insert a key to the hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param k Key [type of keys] @param r Extra return code: -1 if the operation failed; 0 if the key is present in the hash table; 1 if the bucket is empty (never used); 2 if the element in the bucket has been deleted [int*] @return Iterator to the inserted element [khint_t] */ #define kh_put(name, h, k, r) kh_put_##name(h, k, r) /*! @function @abstract Retrieve a key from the hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param k Key [type of keys] @return Iterator to the found element, or kh_end(h) if the element is absent [khint_t] */ #define kh_get(name, h, k) kh_get_##name(h, k) /*! @function @abstract Remove a key from the hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param k Iterator to the element to be deleted [khint_t] */ #define kh_del(name, h, k) kh_del_##name(h, k) /*! @function @abstract Test whether a bucket contains data. @param h Pointer to the hash table [khash_t(name)*] @param x Iterator to the bucket [khint_t] @return 1 if containing data; 0 otherwise [int] */ #define kh_exist(h, x) (!__ac_iseither((h)->flags, (x))) /*! @function @abstract Get key given an iterator @param h Pointer to the hash table [khash_t(name)*] @param x Iterator to the bucket [khint_t] @return Key [type of keys] */ #define kh_key(h, x) ((h)->keys[x]) /*! @function @abstract Get value given an iterator @param h Pointer to the hash table [khash_t(name)*] @param x Iterator to the bucket [khint_t] @return Value [type of values] @discussion For hash sets, calling this results in segfault. */ #define kh_val(h, x) ((h)->vals[x]) /*! @function @abstract Alias of kh_val() */ #define kh_value(h, x) ((h)->vals[x]) /*! @function @abstract Get the start iterator @param h Pointer to the hash table [khash_t(name)*] @return The start iterator [khint_t] */ #define kh_begin(h) (khint_t)(0) /*! @function @abstract Get the end iterator @param h Pointer to the hash table [khash_t(name)*] @return The end iterator [khint_t] */ #define kh_end(h) ((h)->n_buckets) /*! @function @abstract Get the number of elements in the hash table @param h Pointer to the hash table [khash_t(name)*] @return Number of elements in the hash table [khint_t] */ #define kh_size(h) ((h)->size) /*! @function @abstract Get the number of buckets in the hash table @param h Pointer to the hash table [khash_t(name)*] @return Number of buckets in the hash table [khint_t] */ #define kh_n_buckets(h) ((h)->n_buckets) /*! @function @abstract Iterate over the entries in the hash table @param h Pointer to the hash table [khash_t(name)*] @param kvar Variable to which key will be assigned @param vvar Variable to which value will be assigned @param code Block of code to execute */ #define kh_foreach(h, kvar, vvar, code) { khint_t __i; \ for (__i = kh_begin(h); __i != kh_end(h); ++__i) { \ if (!kh_exist(h,__i)) continue; \ (kvar) = kh_key(h,__i); \ (vvar) = kh_val(h,__i); \ code; \ } } /*! @function @abstract Iterate over the values in the hash table @param h Pointer to the hash table [khash_t(name)*] @param vvar Variable to which value will be assigned @param code Block of code to execute */ #define kh_foreach_value(h, vvar, code) { khint_t __i; \ for (__i = kh_begin(h); __i != kh_end(h); ++__i) { \ if (!kh_exist(h,__i)) continue; \ (vvar) = kh_val(h,__i); \ code; \ } } /*! @function @abstract Gather hash table statistics @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param empty[out] Number of empty hash bins @param deleted[out] Number of hash bins with the deleted flag @param hist_size[out] Size of @p hist array @param hist[out] Probe count histogram @return 0 on success; -1 on failure */ #define kh_stats(name, h, empty, deleted, hist_size, hist) \ kh_stats_##name(h, empty, deleted, hist_size, hist) /* More convenient interfaces */ /*! @function @abstract Instantiate a hash set containing integer keys @param name Name of the hash table [symbol] */ #define KHASH_SET_INIT_INT(name) \ KHASH_INIT(name, khint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal) /*! @function @abstract Instantiate a hash map containing integer keys @param name Name of the hash table [symbol] @param khval_t Type of values [type] */ #define KHASH_MAP_INIT_INT(name, khval_t) \ KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) /*! @function @abstract Instantiate a hash set containing 64-bit integer keys @param name Name of the hash table [symbol] */ #define KHASH_SET_INIT_INT64(name) \ KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) /*! @function @abstract Instantiate a hash map containing 64-bit integer keys @param name Name of the hash table [symbol] @param khval_t Type of values [type] */ #define KHASH_MAP_INIT_INT64(name, khval_t) \ KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) typedef const char *kh_cstr_t; /*! @function @abstract Instantiate a hash set containing const char* keys @param name Name of the hash table [symbol] */ #define KHASH_SET_INIT_STR(name) \ KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) /*! @function @abstract Instantiate a hash map containing const char* keys @param name Name of the hash table [symbol] @param khval_t Type of values [type] */ #define KHASH_MAP_INIT_STR(name, khval_t) \ KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) /*! @function @abstract Instantiate a hash set containing kstring_t keys @param name Name of the hash table [symbol] */ #define KHASH_SET_INIT_KSTR(name) \ KHASH_INIT(name, kstring_t, char, 0, kh_kstr_hash_func, kh_kstr_hash_equal) /*! @function @abstract Instantiate a hash map containing kstring_t keys @param name Name of the hash table [symbol] @param khval_t Type of values [type] */ #define KHASH_MAP_INIT_KSTR(name, khval_t) \ KHASH_INIT(name, kstring_t, khval_t, 1, kh_kstr_hash_func, kh_kstr_hash_equal) #endif /* __AC_KHASH_H */ pysam-0.23.0/htslib/htslib/khash_str2int.h000066400000000000000000000077221475062545500204600ustar00rootroot00000000000000/* khash_str2int.h -- C-string to integer hash table. Copyright (C) 2013-2014,2020 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTSLIB_KHASH_STR2INT_H #define HTSLIB_KHASH_STR2INT_H #include "khash.h" KHASH_MAP_INIT_STR(str2int, int) /* * Wrappers for khash dictionaries used by mpileup. */ static inline void *khash_str2int_init(void) { return kh_init(str2int); } /* * Destroy the hash structure, but not the keys */ static inline void khash_str2int_destroy(void *_hash) { khash_t(str2int) *hash = (khash_t(str2int)*)_hash; if (hash) kh_destroy(str2int, hash); // Note that strings are not freed. } /* * Destroys both the hash structure and the keys */ static inline void khash_str2int_destroy_free(void *_hash) { khash_t(str2int) *hash = (khash_t(str2int)*)_hash; khint_t k; if (hash == 0) return; for (k = 0; k < kh_end(hash); ++k) if (kh_exist(hash, k)) free((char*)kh_key(hash, k)); kh_destroy(str2int, hash); } /* * Returns 1 if key exists or 0 if not */ static inline int khash_str2int_has_key(void *_hash, const char *str) { khash_t(str2int) *hash = (khash_t(str2int)*)_hash; khint_t k = kh_get(str2int, hash, str); if ( k == kh_end(hash) ) return 0; return 1; } /* * Returns 0 on success and -1 when the key is not present. On success, * *value is set, unless NULL is passed. */ static inline int khash_str2int_get(void *_hash, const char *str, int *value) { khash_t(str2int) *hash = (khash_t(str2int)*)_hash; khint_t k; if ( !hash ) return -1; k = kh_get(str2int, hash, str); if ( k == kh_end(hash) ) return -1; if ( !value ) return 0; *value = kh_val(hash, k); return 0; } /* * Add a new string to the dictionary, auto-incrementing the value. * On success returns the newly inserted integer id, on error -1 * is returned. Note that the key must continue to exist throughout * the whole life of _hash. */ static inline int khash_str2int_inc(void *_hash, const char *str) { khint_t k; int ret; khash_t(str2int) *hash = (khash_t(str2int)*)_hash; if ( !hash ) return -1; k = kh_put(str2int, hash, str, &ret); if (ret < 0) return -1; if (ret == 0) return kh_val(hash, k); kh_val(hash, k) = kh_size(hash) - 1; return kh_val(hash, k); } /* * Set a new key,value pair. On success returns the bin index, on * error -1 is returned. Note that the key must continue to exist * throughout the whole life of _hash. */ static inline int khash_str2int_set(void *_hash, const char *str, int value) { khint_t k; int ret; khash_t(str2int) *hash = (khash_t(str2int)*)_hash; if ( !hash ) return -1; k = kh_put(str2int, hash, str, &ret); if (ret < 0) return -1; kh_val(hash,k) = value; return k; } /* * Return the number of keys in the hash table. */ static inline int khash_str2int_size(void *_hash) { khash_t(str2int) *hash = (khash_t(str2int)*)_hash; return kh_size(hash); } #endif pysam-0.23.0/htslib/htslib/klist.h000066400000000000000000000121051475062545500170120ustar00rootroot00000000000000/* The MIT License Copyright (c) 2008-2009, by Attractive Chaos Copyright (C) 2013, 2015 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef _AC_KLIST_H #define _AC_KLIST_H #include #ifndef klib_unused #if (defined __clang__ && __clang_major__ >= 3) || (defined __GNUC__ && __GNUC__ >= 3) #define klib_unused __attribute__ ((__unused__)) #else #define klib_unused #endif #endif /* klib_unused */ #define KMEMPOOL_INIT2(SCOPE, name, kmptype_t, kmpfree_f) \ typedef struct { \ size_t cnt, n, max; \ kmptype_t **buf; \ } kmp_##name##_t; \ SCOPE kmp_##name##_t *kmp_init_##name(void) { \ return (kmp_##name##_t *)calloc(1, sizeof(kmp_##name##_t)); \ } \ SCOPE void kmp_destroy_##name(kmp_##name##_t *mp) { \ size_t k; \ for (k = 0; k < mp->n; ++k) { \ kmpfree_f(mp->buf[k]); free(mp->buf[k]); \ } \ free(mp->buf); free(mp); \ } \ SCOPE kmptype_t *kmp_alloc_##name(kmp_##name##_t *mp) { \ ++mp->cnt; \ if (mp->n == 0) return (kmptype_t *)calloc(1, sizeof(kmptype_t)); \ return mp->buf[--mp->n]; \ } \ SCOPE void kmp_free_##name(kmp_##name##_t *mp, kmptype_t *p) { \ --mp->cnt; \ if (mp->n == mp->max) { \ mp->max = mp->max? mp->max<<1 : 16; \ mp->buf = (kmptype_t **)realloc(mp->buf, sizeof(kmptype_t *) * mp->max); \ } \ mp->buf[mp->n++] = p; \ } #define KMEMPOOL_INIT(name, kmptype_t, kmpfree_f) \ KMEMPOOL_INIT2(static inline klib_unused, name, kmptype_t, kmpfree_f) #define kmempool_t(name) kmp_##name##_t #define kmp_init(name) kmp_init_##name() #define kmp_destroy(name, mp) kmp_destroy_##name(mp) #define kmp_alloc(name, mp) kmp_alloc_##name(mp) #define kmp_free(name, mp, p) kmp_free_##name(mp, p) #define KLIST_INIT2(SCOPE, name, kltype_t, kmpfree_t) \ struct __kl1_##name { \ kltype_t data; \ struct __kl1_##name *next; \ }; \ typedef struct __kl1_##name kl1_##name; \ KMEMPOOL_INIT2(SCOPE, name, kl1_##name, kmpfree_t) \ typedef struct { \ kl1_##name *head, *tail; \ kmp_##name##_t *mp; \ size_t size; \ } kl_##name##_t; \ SCOPE kl_##name##_t *kl_init_##name(void) { \ kl_##name##_t *kl = (kl_##name##_t *)calloc(1, sizeof(kl_##name##_t)); \ kl->mp = kmp_init(name); \ kl->head = kl->tail = kmp_alloc(name, kl->mp); \ kl->head->next = 0; \ return kl; \ } \ SCOPE void kl_destroy_##name(kl_##name##_t *kl) { \ kl1_##name *p; \ for (p = kl->head; p != kl->tail; p = p->next) \ kmp_free(name, kl->mp, p); \ kmp_free(name, kl->mp, p); \ kmp_destroy(name, kl->mp); \ free(kl); \ } \ SCOPE kltype_t *kl_pushp_##name(kl_##name##_t *kl) { \ kl1_##name *q, *p = kmp_alloc(name, kl->mp); \ q = kl->tail; p->next = 0; kl->tail->next = p; kl->tail = p; \ ++kl->size; \ return &q->data; \ } \ SCOPE int kl_shift_##name(kl_##name##_t *kl, kltype_t *d) { \ kl1_##name *p; \ if (kl->head->next == 0) return -1; \ --kl->size; \ p = kl->head; kl->head = kl->head->next; \ if (d) *d = p->data; \ kmp_free(name, kl->mp, p); \ return 0; \ } #define KLIST_INIT(name, kltype_t, kmpfree_t) \ KLIST_INIT2(static inline klib_unused, name, kltype_t, kmpfree_t) #define kliter_t(name) kl1_##name #define klist_t(name) kl_##name##_t #define kl_val(iter) ((iter)->data) #define kl_next(iter) ((iter)->next) #define kl_begin(kl) ((kl)->head) #define kl_end(kl) ((kl)->tail) #define kl_init(name) kl_init_##name() #define kl_destroy(name, kl) kl_destroy_##name(kl) #define kl_pushp(name, kl) kl_pushp_##name(kl) #define kl_shift(name, kl, d) kl_shift_##name(kl, d) #endif pysam-0.23.0/htslib/htslib/knetfile.h000066400000000000000000000072251475062545500174740ustar00rootroot00000000000000/* The MIT License Copyright (c) 2008, 2012, 2014, 2021-2022 Genome Research Ltd (GRL). 2010 by Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef KNETFILE_H #define KNETFILE_H #include #include #include #include "hts_defs.h" #ifndef _WIN32 #define netread(fd, ptr, len) read(fd, ptr, len) #define netwrite(fd, ptr, len) write(fd, ptr, len) #define netclose(fd) close(fd) #else #include #define netread(fd, ptr, len) recv(fd, ptr, len, 0) #define netwrite(fd, ptr, len) send(fd, ptr, len, 0) #define netclose(fd) closesocket(fd) #endif // Ensure ssize_t exists within this header. All #includes must precede this, // and ssize_t must be undefined again at the end of this header. #if defined _MSC_VER && defined _INTPTR_T_DEFINED && !defined _SSIZE_T_DEFINED && !defined ssize_t #define HTSLIB_SSIZE_T #define ssize_t intptr_t #endif // FIXME: currently I/O is unbuffered #define KNF_TYPE_LOCAL 1 #define KNF_TYPE_FTP 2 #define KNF_TYPE_HTTP 3 // Kept for API/ABI compatability only. Do not use directly! typedef struct knetFile_s { int type, fd; int64_t offset; char *host, *port; // the following are for FTP only int ctrl_fd, pasv_ip[4], pasv_port, max_response, no_reconnect, is_ready; char *response, *retr, *size_cmd; int64_t seek_offset; // for lazy seek int64_t file_size; // the following are for HTTP only char *path, *http_host; } knetFile; #define knet_tell(fp) ((fp)->offset) #define knet_fileno(fp) ((fp)->fd) #ifdef __cplusplus extern "C" { #endif HTSLIB_EXPORT knetFile *knet_open(const char *fn, const char *mode) HTS_DEPRECATED("Please use hopen instead"); /* This only works with local files. */ HTSLIB_EXPORT knetFile *knet_dopen(int fd, const char *mode) HTS_DEPRECATED("Please use hdopen instead"); /* If ->is_ready==0, this routine updates ->fd; otherwise, it simply reads from ->fd. */ HTSLIB_EXPORT ssize_t knet_read(knetFile *fp, void *buf, size_t len) HTS_DEPRECATED("Please use hread instead"); /* This routine only sets ->offset and ->is_ready=0. It does not communicate with the FTP server. */ HTSLIB_EXPORT off_t knet_seek(knetFile *fp, off_t off, int whence) HTS_DEPRECATED("Please use hseek instead"); HTSLIB_EXPORT int knet_close(knetFile *fp) HTS_DEPRECATED("Please use hclose instead"); #ifdef __cplusplus } #endif #ifdef HTSLIB_SSIZE_T #undef HTSLIB_SSIZE_T #undef ssize_t #endif #endif pysam-0.23.0/htslib/htslib/kroundup.h000066400000000000000000000063371475062545500175450ustar00rootroot00000000000000/* The MIT License Copyright (C) 2020 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef KROUNDUP_H #define KROUNDUP_H // Value of this macro is 1 if x is a signed type; 0 if unsigned #define k_signed_type(x) (!(-((x) * 0 + 1) > 0)) /* Macro with value 1 if the highest bit in x is set for any integer type This is written avoiding conditionals (?: operator) to reduce the likelihood of gcc attempting jump thread optimisations for code paths where (x) is large. These optimisations can cause gcc to issue warnings about excessively large memory allocations when the kroundup64() macro below is used with malloc(). Such warnings can be misleading as they imply only the large allocation happens when it's actually working fine for normal values of (x). See https://developers.redhat.com/blog/2019/03/13/understanding-gcc-warnings-part-2/ */ #define k_high_bit_set(x) ((((x) >> (sizeof(x) * 8 - 1 - k_signed_type(x))) & 1)) /*! @hideinitializer @abstract Round up to next power of two @discussion This macro will work for unsigned types up to uint64_t. If the next power of two does not fit in the given type, it will set the largest value that does. */ #define kroundup64(x) ((x) > 0 ? \ (--(x), \ (x)|=(x)>>(sizeof(x)/8), \ (x)|=(x)>>(sizeof(x)/4), \ (x)|=(x)>>(sizeof(x)/2), \ (x)|=(x)>>(sizeof(x)), \ (x)|=(x)>>(sizeof(x)*2), \ (x)|=(x)>>(sizeof(x)*4), \ (x) += !k_high_bit_set(x), \ (x)) \ : 0) // Historic interfaces for 32-bit and size_t values. The macro above // works for both (as long as size_t is no more than 64 bits). #ifndef kroundup32 #define kroundup32(x) kroundup64(x) #endif #ifndef kroundup_size_t #define kroundup_size_t(x) kroundup64(x) #endif #endif pysam-0.23.0/htslib/htslib/kseq.h000066400000000000000000000222151475062545500166320ustar00rootroot00000000000000/* The MIT License Copyright (c) 2008, 2009, 2011 Attractive Chaos Copyright (C) 2013, 2018, 2020, 2023 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef AC_KSEQ_H #define AC_KSEQ_H #include #include #include #include "kstring.h" #ifndef klib_unused #if (defined __clang__ && __clang_major__ >= 3) || (defined __GNUC__ && __GNUC__ >= 3) #define klib_unused __attribute__ ((__unused__)) #else #define klib_unused #endif #endif /* klib_unused */ #define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r #define KS_SEP_TAB 1 // isspace() && !' ' #define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows) #define KS_SEP_MAX 2 #define __KS_TYPE(type_t) \ typedef struct __kstream_t { \ int begin, end; \ int is_eof:2, bufsize:30; \ uint64_t seek_pos; \ type_t f; \ unsigned char *buf; \ } kstream_t; #define ks_err(ks) ((ks)->end == -1) #define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end) #define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0) #define __KS_BASIC(SCOPE, type_t, __bufsize) \ SCOPE kstream_t *ks_init(type_t f) \ { \ kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \ ks->f = f; ks->bufsize = __bufsize; \ ks->buf = (unsigned char*)malloc(__bufsize); \ return ks; \ } \ SCOPE void ks_destroy(kstream_t *ks) \ { \ if (!ks) return; \ free(ks->buf); \ free(ks); \ } #define __KS_INLINED(__read) \ static inline klib_unused int ks_getc(kstream_t *ks) \ { \ if (ks_err(ks)) return -3; \ if (ks->is_eof && ks->begin >= ks->end) return -1; \ if (ks->begin >= ks->end) { \ ks->begin = 0; \ ks->end = __read(ks->f, ks->buf, ks->bufsize); \ if (ks->end == 0) { ks->is_eof = 1; return -1; } \ if (ks->end == -1) { ks->is_eof = 1; return -3; } \ } \ ks->seek_pos++; \ return (int)ks->buf[ks->begin++]; \ } \ static inline klib_unused int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \ { return ks_getuntil2(ks, delimiter, str, dret, 0); } #define __KS_GETUNTIL(SCOPE, __read) \ SCOPE int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \ { \ int gotany = 0; \ if (dret) *dret = 0; \ str->l = append? str->l : 0; \ uint64_t seek_pos = str->l; \ for (;;) { \ int i; \ if (ks_err(ks)) return -3; \ if (ks->begin >= ks->end) { \ if (!ks->is_eof) { \ ks->begin = 0; \ ks->end = __read(ks->f, ks->buf, ks->bufsize); \ if (ks->end == 0) { ks->is_eof = 1; break; } \ if (ks->end == -1) { ks->is_eof = 1; return -3; } \ } else break; \ } \ if (delimiter == KS_SEP_LINE) { \ unsigned char *sep = (unsigned char *)memchr(ks->buf + ks->begin, '\n', ks->end - ks->begin); \ i = sep != NULL ? sep - ks->buf : ks->end; \ } else if (delimiter > KS_SEP_MAX) { \ unsigned char *sep = (unsigned char *)memchr(ks->buf + ks->begin, delimiter, ks->end - ks->begin); \ i = sep != NULL ? sep - ks->buf : ks->end; \ } else if (delimiter == KS_SEP_SPACE) { \ for (i = ks->begin; i < ks->end; ++i) \ if (isspace(ks->buf[i])) break; \ } else if (delimiter == KS_SEP_TAB) { \ for (i = ks->begin; i < ks->end; ++i) \ if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \ } else i = 0; /* never come to here! */ \ (void) ks_expand(str, i - ks->begin + 1); \ seek_pos += i - ks->begin; if ( i < ks->end ) seek_pos++; \ gotany = 1; \ memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \ str->l = str->l + (i - ks->begin); \ ks->begin = i + 1; \ if (i < ks->end) { \ if (dret) *dret = ks->buf[i]; \ break; \ } \ } \ if (!gotany && ks_eof(ks)) return -1; \ ks->seek_pos += seek_pos; \ if (str->s == 0) { \ str->m = 1; \ str->s = (char*)calloc(1, 1); \ } else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l-1] == '\r') --str->l; \ str->s[str->l] = '\0'; \ return str->l; \ } #define KSTREAM_INIT2(SCOPE, type_t, __read, __bufsize) \ __KS_TYPE(type_t) \ __KS_BASIC(SCOPE, type_t, __bufsize) \ __KS_GETUNTIL(SCOPE, __read) \ __KS_INLINED(__read) #define KSTREAM_INIT(type_t, __read, __bufsize) KSTREAM_INIT2(static, type_t, __read, __bufsize) #define KSTREAM_DECLARE(type_t, __read) \ __KS_TYPE(type_t) \ extern int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append); \ extern kstream_t *ks_init(type_t f); \ extern void ks_destroy(kstream_t *ks); \ __KS_INLINED(__read) /****************** * FASTA/Q parser * ******************/ #define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0) #define __KSEQ_BASIC(SCOPE, type_t) \ SCOPE kseq_t *kseq_init(type_t fd) \ { \ kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \ s->f = ks_init(fd); \ return s; \ } \ SCOPE void kseq_destroy(kseq_t *ks) \ { \ if (!ks) return; \ free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \ ks_destroy(ks->f); \ free(ks); \ } /* Return value: >=0 length of the sequence (normal) -1 end-of-file -2 truncated quality string -3 error reading stream -4 overflow error */ #define __KSEQ_READ(SCOPE) \ SCOPE int kseq_read(kseq_t *seq) \ { \ int c,r; \ kstream_t *ks = seq->f; \ if (seq->last_char == 0) { /* then jump to the next header line */ \ while ((c = ks_getc(ks)) >= 0 && c != '>' && c != '@'); \ if (c < 0) return c; /* end of file or error */ \ seq->last_char = c; \ } /* else: the first header char has been read in the previous call */ \ seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \ if ((r=ks_getuntil(ks, 0, &seq->name, &c)) < 0) return r; /* normal exit: EOF or error */ \ if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \ if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \ seq->seq.m = 256; \ seq->seq.s = (char*)malloc(seq->seq.m); \ } \ while ((c = ks_getc(ks)) >= 0 && c != '>' && c != '+' && c != '@') { \ if (c == '\n') continue; /* skip empty lines */ \ seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \ ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \ } \ if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \ if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \ seq->seq.m = seq->seq.l + 2; \ kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \ if (seq->seq.l + 1 >= seq->seq.m) return -4; /* error: adjusting m overflowed */ \ seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \ } \ seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \ if (c != '+') return seq->seq.l; /* FASTA */ \ if (seq->qual.m < seq->seq.m) { /* allocate memory for qual in case insufficient */ \ seq->qual.m = seq->seq.m; \ seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \ } \ while ((c = ks_getc(ks)) >= 0 && c != '\n'); /* skip the rest of '+' line */ \ if (c == -1) return -2; /* error: no quality string */ \ while ((c = ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1)) >= 0 && seq->qual.l < seq->seq.l); \ if (c == -3) return -3; /* stream error */ \ seq->last_char = 0; /* we have not come to the next header line */ \ if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \ return seq->seq.l; \ } #define __KSEQ_TYPE(type_t) \ typedef struct { \ kstring_t name, comment, seq, qual; \ int last_char; \ kstream_t *f; \ } kseq_t; #define KSEQ_INIT2(SCOPE, type_t, __read) \ KSTREAM_INIT(type_t, __read, 16384) \ __KSEQ_TYPE(type_t) \ __KSEQ_BASIC(SCOPE, type_t) \ __KSEQ_READ(SCOPE) #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) #define KSEQ_DECLARE(type_t) \ __KS_TYPE(type_t) \ __KSEQ_TYPE(type_t) \ extern kseq_t *kseq_init(type_t fd); \ void kseq_destroy(kseq_t *ks); \ int kseq_read(kseq_t *seq); #endif pysam-0.23.0/htslib/htslib/ksort.h000066400000000000000000000263631475062545500170410ustar00rootroot00000000000000/* The MIT License Copyright (c) 2008, 2012-2013, 2017-2019 Genome Research Ltd (GRL). Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Contact: Heng Li */ /* 2012-12-11 (0.1.4): * Defined __ks_insertsort_##name as static to compile with C99. 2008-11-16 (0.1.4): * Fixed a bug in introsort() that happens in rare cases. 2008-11-05 (0.1.3): * Fixed a bug in introsort() for complex comparisons. * Fixed a bug in mergesort(). The previous version is not stable. 2008-09-15 (0.1.2): * Accelerated introsort. On my Mac (not on another Linux machine), my implementation is as fast as the C++ standard library's sort() on random input. * Added combsort and in introsort, switch to combsort if the recursion is too deep. 2008-09-13 (0.1.1): * Added k-small algorithm 2008-09-05 (0.1.0): * Initial version */ #ifndef AC_KSORT_H #define AC_KSORT_H #include #include #include "hts_defs.h" #ifndef klib_unused #if (defined __clang__ && __clang_major__ >= 3) || (defined __GNUC__ && __GNUC__ >= 3) #define klib_unused __attribute__ ((__unused__)) #else #define klib_unused #endif #endif /* klib_unused */ #ifdef __cplusplus extern "C" { #endif // Use our own drand48() symbol (used by ks_shuffle) to avoid portability // problems on Windows. Don't include htslib/hts_os.h for this as it // may not get on with older attempts to fix this in code that includes // this file. HTSLIB_EXPORT extern double hts_drand48(void); typedef struct { void *left, *right; int depth; } ks_isort_stack_t; #define KSORT_SWAP(type_t, a, b) { type_t t=(a); (a)=(b); (b)=t; } #define KSORT_INIT(name, type_t, __sort_lt) KSORT_INIT_(_ ## name, , type_t, __sort_lt) #define KSORT_INIT_STATIC(name, type_t, __sort_lt) KSORT_INIT_(_ ## name, static klib_unused, type_t, __sort_lt) #define KSORT_INIT2(name, SCOPE, type_t, __sort_lt) KSORT_INIT_(_ ## name, SCOPE, type_t, __sort_lt) #define KSORT_INIT_(name, SCOPE, type_t, __sort_lt) \ SCOPE int ks_mergesort##name(size_t n, type_t array[], type_t temp[]) \ { \ type_t *a2[2], *a, *b; \ int curr, shift; \ \ a2[0] = array; \ a2[1] = temp? temp : (type_t*)malloc(sizeof(type_t) * n); \ for (curr = 0, shift = 0; (1ul<> 1) - 1; i != (size_t)(-1); --i) \ ks_heapadjust##name(i, lsize, l); \ } \ SCOPE void ks_heapsort##name(size_t lsize, type_t l[]) \ { \ size_t i; \ for (i = lsize - 1; i > 0; --i) { \ type_t tmp; \ tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust##name(0, i, l); \ } \ } \ static inline void __ks_insertsort##name(type_t *s, type_t *t) \ { \ type_t *i, *j, swap_tmp; \ for (i = s + 1; i < t; ++i) \ for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) { \ swap_tmp = *j; *j = *(j-1); *(j-1) = swap_tmp; \ } \ } \ SCOPE void ks_combsort##name(size_t n, type_t a[]) \ { \ const double shrink_factor = 1.2473309501039786540366528676643; \ int do_swap; \ size_t gap = n; \ type_t tmp, *i, *j; \ do { \ if (gap > 2) { \ gap = (size_t)(gap / shrink_factor); \ if (gap == 9 || gap == 10) gap = 11; \ } \ do_swap = 0; \ for (i = a; i < a + n - gap; ++i) { \ j = i + gap; \ if (__sort_lt(*j, *i)) { \ tmp = *i; *i = *j; *j = tmp; \ do_swap = 1; \ } \ } \ } while (do_swap || gap > 2); \ if (gap != 1) __ks_insertsort##name(a, a + n); \ } \ SCOPE int ks_introsort##name(size_t n, type_t a[]) \ { \ int d; \ ks_isort_stack_t *top, *stack; \ type_t rp, swap_tmp; \ type_t *s, *t, *i, *j, *k; \ \ if (n < 1) return 0; \ else if (n == 2) { \ if (__sort_lt(a[1], a[0])) { swap_tmp = a[0]; a[0] = a[1]; a[1] = swap_tmp; } \ return 0; \ } \ for (d = 2; 1ul<>1) + 1; \ if (__sort_lt(*k, *i)) { \ if (__sort_lt(*k, *j)) k = j; \ } else k = __sort_lt(*j, *i)? i : j; \ rp = *k; \ if (k != t) { swap_tmp = *k; *k = *t; *t = swap_tmp; } \ for (;;) { \ do ++i; while (__sort_lt(*i, rp)); \ do --j; while (i <= j && __sort_lt(rp, *j)); \ if (j <= i) break; \ swap_tmp = *i; *i = *j; *j = swap_tmp; \ } \ swap_tmp = *i; *i = *t; *t = swap_tmp; \ if (i-s > t-i) { \ if (i-s > 16) { top->left = s; top->right = i-1; top->depth = d; ++top; } \ s = t-i > 16? i+1 : t; \ } else { \ if (t-i > 16) { top->left = i+1; top->right = t; top->depth = d; ++top; } \ t = i-s > 16? i-1 : s; \ } \ } else { \ if (top == stack) { \ free(stack); \ __ks_insertsort##name(a, a+n); \ return 0; \ } else { --top; s = (type_t*)top->left; t = (type_t*)top->right; d = top->depth; } \ } \ } \ return 0; \ } \ /* This function is adapted from: http://ndevilla.free.fr/median/ */ \ /* 0 <= kk < n */ \ SCOPE type_t ks_ksmall##name(size_t n, type_t arr[], size_t kk) \ { \ type_t *low, *high, *k, *ll, *hh, *mid; \ low = arr; high = arr + n - 1; k = arr + kk; \ for (;;) { \ if (high <= low) return *k; \ if (high == low + 1) { \ if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ return *k; \ } \ mid = low + (high - low) / 2; \ if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ KSORT_SWAP(type_t, *mid, *(low+1)); \ ll = low + 1; hh = high; \ for (;;) { \ do ++ll; while (__sort_lt(*ll, *low)); \ do --hh; while (__sort_lt(*low, *hh)); \ if (hh < ll) break; \ KSORT_SWAP(type_t, *ll, *hh); \ } \ KSORT_SWAP(type_t, *low, *hh); \ if (hh <= k) low = ll; \ if (hh >= k) high = hh - 1; \ } \ } \ SCOPE void ks_shuffle##name(size_t n, type_t a[]) \ { \ int i, j; \ for (i = n; i > 1; --i) { \ type_t tmp; \ j = (int)(hts_drand48() * i); \ tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp; \ } \ } #define ks_mergesort(name, n, a, t) ks_mergesort_##name(n, a, t) #define ks_introsort(name, n, a) ks_introsort_##name(n, a) #define ks_combsort(name, n, a) ks_combsort_##name(n, a) #define ks_heapsort(name, n, a) ks_heapsort_##name(n, a) #define ks_heapmake(name, n, a) ks_heapmake_##name(n, a) #define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a) #define ks_ksmall(name, n, a, k) ks_ksmall_##name(n, a, k) #define ks_shuffle(name, n, a) ks_shuffle_##name(n, a) #define ks_lt_generic(a, b) ((a) < (b)) #define ks_lt_str(a, b) (strcmp((a), (b)) < 0) typedef const char *ksstr_t; #define KSORT_INIT_GENERIC(type_t) KSORT_INIT_(_ ## type_t, , type_t, ks_lt_generic) #define KSORT_INIT_STR KSORT_INIT(str, ksstr_t, ks_lt_str) #define KSORT_INIT_STATIC_GENERIC(type_t) KSORT_INIT_(_ ## type_t, static klib_unused, type_t, ks_lt_generic) #define KSORT_INIT_STATIC_STR KSORT_INIT_STATIC(str, ksstr_t, ks_lt_str) #define KSORT_INIT2_GENERIC(type_t, SCOPE) KSORT_INIT_(_ ## type_t, SCOPE, type_t, ks_lt_generic) #define KSORT_INIT2_STR KSORT_INIT2(str, SCOPE, ksstr_t, ks_lt_str) #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/htslib/kstring.h000066400000000000000000000303271475062545500173530ustar00rootroot00000000000000/* The MIT License Copyright (C) 2011 by Attractive Chaos Copyright (C) 2013-2014, 2016, 2018-2020, 2022, 2024 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef KSTRING_H #define KSTRING_H #include #include #include #include #include #include #include #include #include "hts_defs.h" #include "kroundup.h" #if defined __GNUC__ && (__GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ > 4)) #ifdef __MINGW_PRINTF_FORMAT #define KS_ATTR_PRINTF(fmt, arg) __attribute__((__format__ (__MINGW_PRINTF_FORMAT, fmt, arg))) #else #define KS_ATTR_PRINTF(fmt, arg) __attribute__((__format__ (__printf__, fmt, arg))) #endif // __MINGW_PRINTF_FORMAT #else #define KS_ATTR_PRINTF(fmt, arg) #endif #ifndef HAVE___BUILTIN_CLZ #if defined __GNUC__ && (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) #define HAVE___BUILTIN_CLZ 1 #endif #endif // Ensure ssize_t exists within this header. All #includes must precede this, // and ssize_t must be undefined again at the end of this header. #if defined _MSC_VER && defined _INTPTR_T_DEFINED && !defined _SSIZE_T_DEFINED && !defined ssize_t #define HTSLIB_SSIZE_T #define ssize_t intptr_t #endif /* kstring_t is a simple non-opaque type whose fields are likely to be * used directly by user code (but see also ks_str() and ks_len() below). * A kstring_t object is initialised by either of * kstring_t str = KS_INITIALIZE; * kstring_t str; ...; ks_initialize(&str); * and either ownership of the underlying buffer should be given away before * the object disappears (see ks_release() below) or the kstring_t should be * destroyed with ks_free(&str) or free(str.s) */ #ifndef KSTRING_T #define KSTRING_T kstring_t typedef struct kstring_t { size_t l, m; char *s; } kstring_t; #endif typedef struct ks_tokaux_t { uint64_t tab[4]; int sep, finished; const char *p; // end of the current token } ks_tokaux_t; #ifdef __cplusplus extern "C" { #endif HTSLIB_EXPORT int kvsprintf(kstring_t *s, const char *fmt, va_list ap) KS_ATTR_PRINTF(2,0); HTSLIB_EXPORT int ksprintf(kstring_t *s, const char *fmt, ...) KS_ATTR_PRINTF(2,3); HTSLIB_EXPORT int kputd(double d, kstring_t *s); // custom %g only handler HTSLIB_EXPORT int ksplit_core(char *s, int delimiter, int *_max, int **_offsets); HTSLIB_EXPORT char *kstrstr(const char *str, const char *pat, int **_prep); HTSLIB_EXPORT char *kstrnstr(const char *str, const char *pat, int n, int **_prep); HTSLIB_EXPORT void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep); /* kstrtok() is similar to strtok_r() except that str is not * modified and both str and sep can be NULL. For efficiency, it is * actually recommended to set both to NULL in the subsequent calls * if sep is not changed. */ HTSLIB_EXPORT char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux); /* kgetline() uses the supplied fgets()-like function to read a "\n"- * or "\r\n"-terminated line from fp. The line read is appended to the * kstring without its terminator and 0 is returned; EOF is returned at * EOF or on error (determined by querying fp, as per fgets()). */ typedef char *kgets_func(char *, int, void *); HTSLIB_EXPORT int kgetline(kstring_t *s, kgets_func *fgets_fn, void *fp); /* kgetline2() uses the supplied hgetln()-like function to read a "\n"- * or "\r\n"-terminated line from fp. The line read is appended to the * ksring without its terminator and 0 is returned; EOF is returned at * EOF or on error (determined by querying fp, as per fgets()). */ typedef ssize_t kgets_func2(char *, size_t, void *); HTSLIB_EXPORT int kgetline2(kstring_t *s, kgets_func2 *fgets_fn, void *fp); #ifdef __cplusplus } #endif /// kstring initializer for structure assignment #define KS_INITIALIZE { 0, 0, NULL } /// kstring initializer for pointers /** @note Not to be used if the buffer has been allocated. Use ks_release() or ks_clear() instead. */ static inline void ks_initialize(kstring_t *s) { s->l = s->m = 0; s->s = NULL; } /// Resize a kstring to a given capacity static inline int ks_resize(kstring_t *s, size_t size) { if (s->m < size) { char *tmp; size = (size > (SIZE_MAX>>2)) ? size : size + (size >> 1); tmp = (char*)realloc(s->s, size); if (!tmp) return -1; s->s = tmp; s->m = size; } return 0; } /// Increase kstring capacity by a given number of bytes static inline int ks_expand(kstring_t *s, size_t expansion) { size_t new_size = s->l + expansion; if (new_size < s->l) // Overflow check return -1; return ks_resize(s, new_size); } /// Returns the kstring buffer static inline char *ks_str(kstring_t *s) { return s->s; } /// Returns the kstring buffer, or an empty string if l == 0 /** * Unlike ks_str(), this function will never return NULL. If the kstring is * empty it will return a read-only empty string. As the returned value * may be read-only, the caller should not attempt to modify it. */ static inline const char *ks_c_str(kstring_t *s) { return s->l && s->s ? s->s : ""; } static inline size_t ks_len(kstring_t *s) { return s->l; } /// Reset kstring length to zero /** @return The kstring itself Example use: kputsn(string, len, ks_clear(s)) */ static inline kstring_t *ks_clear(kstring_t *s) { s->l = 0; return s; } // Give ownership of the underlying buffer away to something else (making // that something else responsible for freeing it), leaving the kstring_t // empty and ready to be used again, or ready to go out of scope without // needing free(str.s) to prevent a memory leak. static inline char *ks_release(kstring_t *s) { char *ss = s->s; s->l = s->m = 0; s->s = NULL; return ss; } /// Safely free the underlying buffer in a kstring. static inline void ks_free(kstring_t *s) { if (s) { free(s->s); ks_initialize(s); } } static inline int kputsn(const char *p, size_t l, kstring_t *s) { size_t new_sz = s->l + l + 2; if (new_sz <= s->l || ks_resize(s, new_sz) < 0) return EOF; memcpy(s->s + s->l, p, l); s->l += l; s->s[s->l] = 0; return l; } static inline int kputs(const char *p, kstring_t *s) { if (!p) { errno = EFAULT; return -1; } return kputsn(p, strlen(p), s); } static inline int kputc(int c, kstring_t *s) { if (ks_resize(s, s->l + 2) < 0) return EOF; s->s[s->l++] = c; s->s[s->l] = 0; return (unsigned char)c; } static inline int kputc_(int c, kstring_t *s) { if (ks_resize(s, s->l + 1) < 0) return EOF; s->s[s->l++] = c; return 1; } static inline int kputsn_(const void *p, size_t l, kstring_t *s) { size_t new_sz = s->l + l; if (new_sz < s->l || ks_resize(s, new_sz ? new_sz : 1) < 0) return EOF; memcpy(s->s + s->l, p, l); s->l += l; return l; } static inline int kputuw(unsigned x, kstring_t *s) { #if HAVE___BUILTIN_CLZ && UINT_MAX == 4294967295U static const unsigned int kputuw_num_digits[32] = { 10, 10, 10, 9, 9, 9, 8, 8, 8, 7, 7, 7, 7, 6, 6, 6, 5, 5, 5, 4, 4, 4, 4, 3, 3, 3, 2, 2, 2, 1, 1, 1 }; static const unsigned int kputuw_thresholds[32] = { 0, 0, 1000000000U, 0, 0, 100000000U, 0, 0, 10000000, 0, 0, 0, 1000000, 0, 0, 100000, 0, 0, 10000, 0, 0, 0, 1000, 0, 0, 100, 0, 0, 10, 0, 0, 0 }; #else uint64_t m; #endif static const char kputuw_dig2r[] = "00010203040506070809" "10111213141516171819" "20212223242526272829" "30313233343536373839" "40414243444546474849" "50515253545556575859" "60616263646566676869" "70717273747576777879" "80818283848586878889" "90919293949596979899"; unsigned int l, j; char *cp; // Trivial case - also prevents __builtin_clz(0), which is undefined if (x < 10) { if (ks_resize(s, s->l + 2) < 0) return EOF; s->s[s->l++] = '0'+x; s->s[s->l] = 0; return 0; } // Find out how many digits are to be printed. #if HAVE___BUILTIN_CLZ && UINT_MAX == 4294967295U /* * Table method - should be quick if clz can be done in hardware. * Find the most significant bit of the value to print and look * up in a table to find out how many decimal digits are needed. * This number needs to be adjusted by 1 for cases where the decimal * length could vary for a given number of bits (for example, * a four bit number could be between 8 and 15). */ l = __builtin_clz(x); l = kputuw_num_digits[l] - (x < kputuw_thresholds[l]); #else // Fallback for when clz is not available m = 1; l = 0; do { l++; m *= 10; } while (x >= m); #endif if (ks_resize(s, s->l + l + 2) < 0) return EOF; // Add digits two at a time j = l; cp = s->s + s->l; while (x >= 10) { const char *d = &kputuw_dig2r[2*(x%100)]; x /= 100; memcpy(&cp[j-=2], d, 2); } // Last one (if necessary). We know that x < 10 by now. if (j == 1) cp[0] = x + '0'; s->l += l; s->s[s->l] = 0; return 0; } static inline int kputw(int c, kstring_t *s) { unsigned int x = c; if (c < 0) { x = -x; if (ks_resize(s, s->l + 3) < 0) return EOF; s->s[s->l++] = '-'; } return kputuw(x, s); } static inline int kputll(long long c, kstring_t *s) { // Worst case expansion. One check reduces function size // and aids inlining chance. Memory overhead is minimal. if (ks_resize(s, s->l + 23) < 0) return EOF; unsigned long long x = c; if (c < 0) { x = -x; s->s[s->l++] = '-'; } if (x <= UINT32_MAX) return kputuw(x, s); static const char kputull_dig2r[] = "00010203040506070809" "10111213141516171819" "20212223242526272829" "30313233343536373839" "40414243444546474849" "50515253545556575859" "60616263646566676869" "70717273747576777879" "80818283848586878889" "90919293949596979899"; unsigned int l, j; char *cp; // Find out how long the number is (could consider clzll) uint64_t m = 1; l = 0; if (sizeof(long long)==sizeof(uint64_t) && x >= 10000000000000000000ULL) { // avoids overflow below l = 20; } else { do { l++; m *= 10; } while (x >= m); } // Add digits two at a time j = l; cp = s->s + s->l; while (x >= 10) { const char *d = &kputull_dig2r[2*(x%100)]; x /= 100; memcpy(&cp[j-=2], d, 2); } // Last one (if necessary). We know that x < 10 by now. if (j == 1) cp[0] = x + '0'; s->l += l; s->s[s->l] = 0; return 0; } static inline int kputl(long c, kstring_t *s) { return kputll(c, s); } /* * Returns 's' split by delimiter, with *n being the number of components; * NULL on failure. */ static inline int *ksplit(kstring_t *s, int delimiter, int *n) { int max = 0, *offsets = 0; *n = ksplit_core(s->s, delimiter, &max, &offsets); return offsets; } #ifdef HTSLIB_SSIZE_T #undef HTSLIB_SSIZE_T #undef ssize_t #endif #endif pysam-0.23.0/htslib/htslib/regidx.h000066400000000000000000000212611475062545500171510ustar00rootroot00000000000000/// @file htslib/regidx.h /// Region indexing. /* Copyright (C) 2014-2019 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Region indexing with an optional payload. Example of usage: // Init the parser and print regions. In this example the payload is a // pointer to a string. For the description of parse_custom and // free_custom functions, see regidx_parse_f and regidx_free_f below, // and for working example see test/test-regidx.c. regidx_t *idx = regidx_init(in_fname,parse_custom,free_custom,sizeof(char*),NULL); // Query overlap with chr:beg-end (beg,end are 1-based coordinates) regitr_t *itr = regitr_init(idx); if ( regidx_overlap(idx, chr,beg-1,end-1, itr) ) printf("There is an overlap!\n"); while ( regitr_overlap(itr) ) { printf("[%"PRIhts_pos",%"PRIhts_pos"] overlaps with [%"PRIhts_pos",%"PRIhts_pos"], payload=%s\n", beg, end, itr->beg+1, itr->end+1, regitr_payload(itr,char*)); } regidx_destroy(idx); regitr_destroy(itr); Another example, loop over all regions: regidx_t *idx = regidx_init(in_fname,NULL,NULL,0,NULL); regitr_t *itr = regitr_init(idx); while ( regitr_loop(itr) ) printf("chr=%s beg=%d end=%d\n", itr->seq, itr->beg+1, itr->end+1); regidx_destroy(idx); regitr_destroy(itr); */ #ifndef HTSLIB_REGIDX_H #define HTSLIB_REGIDX_H #include "hts.h" #ifdef __cplusplus extern "C" { #endif // maximum regidx position (0-based). Used to represent the end point of // regions which do not explicitly set one. regidx_push() also limits // positions passed to it to be no bigger than this. // Limit is set to ensure some internal values used by regidx keep within 32 // bits and to stop the index from getting too big. #define REGIDX_MAX (1ULL << 35) typedef struct regidx_t regidx_t; typedef struct regitr_t { hts_pos_t beg,end; void *payload; char *seq; void *itr; } regitr_t; #define regitr_payload(itr,type_t) (*((type_t*)(itr)->payload)) // Old API for backwards compatibility #define REGITR_START(itr) (itr).beg #define REGITR_END(itr) (itr).end #define REGITR_PAYLOAD(itr,type_t) ((type_t*)(itr).payload) #define REGITR_OVERLAP(itr,from,to) regidx_overlap((itr)); /* * regidx_parse_f - Function to parse one input line, such as regidx_parse_bed * or regidx_parse_tab below. The function is expected to set `chr_from` and * `chr_to` to point to first and last character of chromosome name and set * coordinates `beg` and `end` (0-based, inclusive). If regidx_init() was * called with non-zero payload_size, the `payload` points to a memory * location of the payload_size and `usr` is the data passed to regidx_init(). * Any memory allocated by the function will be freed by regidx_free_f called * by regidx_destroy(). * * Return value: 0 on success, -1 to skip a record, -2 on fatal error. */ typedef int (*regidx_parse_f)(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr); typedef void (*regidx_free_f)(void *payload); /* * A note about the parsers: * - leading spaces are ignored * - lines starting with "#" are ignored */ HTSLIB_EXPORT int regidx_parse_bed(const char*,char**,char**,hts_pos_t*,hts_pos_t*,void*,void*); // CHROM or whitespace-sepatated CHROM,FROM,TO (0-based,right-open) HTSLIB_EXPORT int regidx_parse_tab(const char*,char**,char**,hts_pos_t*,hts_pos_t*,void*,void*); // CHROM or whitespace-separated CHROM,POS (1-based, inclusive) HTSLIB_EXPORT int regidx_parse_reg(const char*,char**,char**,hts_pos_t*,hts_pos_t*,void*,void*); // CHROM, CHROM:POS, CHROM:FROM-TO, CHROM:FROM- (1-based, inclusive) HTSLIB_EXPORT int regidx_parse_vcf(const char*,char**,char**,hts_pos_t*,hts_pos_t*,void*,void*); /* * regidx_init() - creates new index * regidx_init_string() - creates new index, from a string rather than from a file * * @param fname: input file name or NULL if regions will be added one-by-one via regidx_insert() * @param parsef: regidx_parse_bed, regidx_parse_tab or see description of regidx_parse_f. If NULL, * the format will be autodected, currently either regidx_parse_tab (the default) or * regidx_parse_bed (file must be named 'bed' or 'bed.gz') will be used. Note that * the exact autodetection algorithm will change. * @param freef: NULL or see description of regidx_parse_f * @param payload_size: 0 with regidx_parse_bed, regidx_parse_tab or see regidx_parse_f * @param usr: optional user data passed to regidx_parse_f * * Returns index on success or NULL on error. * * The regidx_t index struct returned by a successful call should be freed * via regidx_destroy() when it is no longer needed. */ HTSLIB_EXPORT regidx_t *regidx_init(const char *fname, regidx_parse_f parsef, regidx_free_f freef, size_t payload_size, void *usr); HTSLIB_EXPORT regidx_t *regidx_init_string(const char *string, regidx_parse_f parsef, regidx_free_f freef, size_t payload_size, void *usr); /* * regidx_destroy() - free memory allocated by regidx_init */ HTSLIB_EXPORT void regidx_destroy(regidx_t *idx); /* * regidx_overlap() - check overlap of the location chr:from-to with regions * @param beg,end: 0-based start, end coordinate (inclusive) * @param itr: pointer to iterator, can be NULL if regidx_loop not needed * * Returns 0 if there is no overlap or 1 if overlap is found. The overlapping * regions can be iterated as shown in the example above. */ HTSLIB_EXPORT int regidx_overlap(regidx_t *idx, const char *chr, hts_pos_t beg, hts_pos_t end, regitr_t *itr); /* * regidx_insert() - add a new region. * regidx_insert_list() - add new regions from a list * regidx_push() - low level insertion of a new region * * Returns 0 on success or -1 on error. */ HTSLIB_EXPORT int regidx_insert(regidx_t *idx, char *line); HTSLIB_EXPORT int regidx_insert_list(regidx_t *idx, char *line, char delim); HTSLIB_EXPORT int regidx_push(regidx_t *idx, char *chr_beg, char *chr_end, hts_pos_t beg, hts_pos_t end, void *payload); /* * regidx_seq_names() - return list of all sequence names */ HTSLIB_EXPORT char **regidx_seq_names(regidx_t *idx, int *n); /* * regidx_seq_nregs() - number of regions * regidx_nregs() - total number of regions */ HTSLIB_EXPORT int regidx_seq_nregs(regidx_t *idx, const char *seq); HTSLIB_EXPORT int regidx_nregs(regidx_t *idx); /* * regitr_init() - initialize an iterator. The idx parameter is required only * with regitr_loop. If only regitr_overlap is called, NULL * can be given. * * The regitr_t struct returned by a successful regitr_init() * call should be freed via regitr_destroy() when it is no * longer needed. * * regitr_reset() - initialize an iterator for a repeated regitr_loop cycle. * Not required with regitr_overlap. */ HTSLIB_EXPORT regitr_t *regitr_init(regidx_t *idx); HTSLIB_EXPORT void regitr_destroy(regitr_t *itr); HTSLIB_EXPORT void regitr_reset(regidx_t *idx, regitr_t *itr); /* * regitr_overlap() - next overlapping region * Returns 0 when done or 1 when itr is set to next region */ HTSLIB_EXPORT int regitr_overlap(regitr_t *itr); /* * regitr_loop() - loop over all regions * Returns 0 when done or 1 when itr is set to next region */ HTSLIB_EXPORT int regitr_loop(regitr_t *itr); /* * regitr_copy() - create a copy of an iterator for a repeated iteration with regitr_loop */ HTSLIB_EXPORT void regitr_copy(regitr_t *dst, regitr_t *src); #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/htslib/sam.h000066400000000000000000002637041475062545500164610ustar00rootroot00000000000000/// @file htslib/sam.h /// High-level SAM/BAM/CRAM sequence file operations. /* Copyright (C) 2008, 2009, 2013-2023 Genome Research Ltd. Copyright (C) 2010, 2012, 2013 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTSLIB_SAM_H #define HTSLIB_SAM_H #include #include #include #include "hts.h" #include "hts_endian.h" // Ensure ssize_t exists within this header. All #includes must precede this, // and ssize_t must be undefined again at the end of this header. #if defined _MSC_VER && defined _INTPTR_T_DEFINED && !defined _SSIZE_T_DEFINED && !defined ssize_t #define HTSLIB_SSIZE_T #define ssize_t intptr_t #endif #ifdef __cplusplus extern "C" { #endif /// Highest SAM format version supported by this library #define SAM_FORMAT_VERSION "1.6" /*************************** *** SAM/BAM/CRAM header *** ***************************/ /*! @typedef * @abstract Header extension structure, grouping a collection * of hash tables that contain the parsed header data. */ typedef struct sam_hrecs_t sam_hrecs_t; /*! @typedef @abstract Structure for the alignment header. @field n_targets number of reference sequences @field l_text length of the plain text in the header (may be zero if the header has been edited) @field target_len lengths of the reference sequences @field target_name names of the reference sequences @field text plain text (may be NULL if the header has been edited) @field sdict header dictionary @field hrecs pointer to the extended header struct (internal use only) @field ref_count reference count @note The text and l_text fields are included for backwards compatibility. These fields may be set to NULL and zero respectively as a side-effect of calling some header API functions. New code that needs to access the header text should use the sam_hdr_str() and sam_hdr_length() functions instead of these fields. */ typedef struct sam_hdr_t { int32_t n_targets, ignore_sam_err; size_t l_text; uint32_t *target_len; const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); char **target_name; char *text; void *sdict; sam_hrecs_t *hrecs; uint32_t ref_count; } sam_hdr_t; /*! @typedef * @abstract Old name for compatibility with existing code. */ typedef sam_hdr_t bam_hdr_t; /**************************** *** CIGAR related macros *** ****************************/ #define BAM_CMATCH 0 #define BAM_CINS 1 #define BAM_CDEL 2 #define BAM_CREF_SKIP 3 #define BAM_CSOFT_CLIP 4 #define BAM_CHARD_CLIP 5 #define BAM_CPAD 6 #define BAM_CEQUAL 7 #define BAM_CDIFF 8 #define BAM_CBACK 9 #define BAM_CIGAR_STR "MIDNSHP=XB" #define BAM_CIGAR_SHIFT 4 #define BAM_CIGAR_MASK 0xf #define BAM_CIGAR_TYPE 0x3C1A7 /*! @abstract Table for converting a CIGAR operator character to BAM_CMATCH etc. Result is operator code or -1. Be sure to cast the index if it is a plain char: int op = bam_cigar_table[(unsigned char) ch]; */ HTSLIB_EXPORT extern const int8_t bam_cigar_table[256]; #define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK) #define bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT) // Note that BAM_CIGAR_STR is padded to length 16 bytes below so that // the array look-up will not fall off the end. '?' is chosen as the // padding character so it's easy to spot if one is emitted, and will // result in a parsing failure (in sam_parse1(), at least) if read. #define bam_cigar_opchr(c) (BAM_CIGAR_STR "??????" [bam_cigar_op(c)]) #define bam_cigar_gen(l, o) ((l)<>((o)<<1)&3) // bit 1: consume query; bit 2: consume reference /*! @abstract the read is paired in sequencing, no matter whether it is mapped in a pair */ #define BAM_FPAIRED 1 /*! @abstract the read is mapped in a proper pair */ #define BAM_FPROPER_PAIR 2 /*! @abstract the read itself is unmapped; conflictive with BAM_FPROPER_PAIR */ #define BAM_FUNMAP 4 /*! @abstract the mate is unmapped */ #define BAM_FMUNMAP 8 /*! @abstract the read is mapped to the reverse strand */ #define BAM_FREVERSE 16 /*! @abstract the mate is mapped to the reverse strand */ #define BAM_FMREVERSE 32 /*! @abstract this is read1 */ #define BAM_FREAD1 64 /*! @abstract this is read2 */ #define BAM_FREAD2 128 /*! @abstract not primary alignment */ #define BAM_FSECONDARY 256 /*! @abstract QC failure */ #define BAM_FQCFAIL 512 /*! @abstract optical or PCR duplicate */ #define BAM_FDUP 1024 /*! @abstract supplementary alignment */ #define BAM_FSUPPLEMENTARY 2048 /************************* *** Alignment records *** *************************/ /* * Assumptions made here. While pos can be 64-bit, no sequence * itself is that long, but due to ref skip CIGAR fields it * may span more than that. (CIGAR itself is 28-bit len + 4 bit * type, but in theory we can combine multiples together.) * * Mate position and insert size also need to be 64-bit, but * we won't accept more than 32-bit for tid. * * The bam1_core_t structure is the *in memory* layout and not * the same as the on-disk format. 64-bit changes here permit * SAM to work with very long chromosomes and permit BAM and CRAM * to seamlessly update in the future without further API/ABI * revisions. */ /*! @typedef @abstract Structure for core alignment information. @field pos 0-based leftmost coordinate @field tid chromosome ID, defined by sam_hdr_t @field bin bin calculated by bam_reg2bin() @field qual mapping quality @field l_extranul length of extra NULs between qname & cigar (for alignment) @field flag bitwise flag @field l_qname length of the query name @field n_cigar number of CIGAR operations @field l_qseq length of the query sequence (read) @field mtid chromosome ID of next read in template, defined by sam_hdr_t @field mpos 0-based leftmost coordinate of next read in template @field isize observed template length ("insert size") */ typedef struct bam1_core_t { hts_pos_t pos; int32_t tid; uint16_t bin; // NB: invalid on 64-bit pos uint8_t qual; uint8_t l_extranul; uint16_t flag; uint16_t l_qname; uint32_t n_cigar; int32_t l_qseq; int32_t mtid; hts_pos_t mpos; hts_pos_t isize; } bam1_core_t; /*! @typedef @abstract Structure for one alignment. @field core core information about the alignment @field id @field data all variable-length data, concatenated; structure: qname-cigar-seq-qual-aux @field l_data current length of bam1_t::data @field m_data maximum length of bam1_t::data @field mempolicy memory handling policy, see bam_set_mempolicy() @discussion Notes: 1. The data blob should be accessed using bam_get_qname, bam_get_cigar, bam_get_seq, bam_get_qual and bam_get_aux macros. These returns pointers to the start of each type of data. 2. qname is terminated by one to four NULs, so that the following cigar data is 32-bit aligned; core.l_qname includes these trailing NULs, while core.l_extranul counts the excess NULs (so 0 <= l_extranul <= 3). 3. Cigar data is encoded 4 bytes per CIGAR operation. See the bam_cigar_* macros for manipulation. 4. seq is nibble-encoded according to bam_nt16_table. See the bam_seqi macro for retrieving individual bases. 5. Per base qualities are stored in the Phred scale with no +33 offset. Ie as per the BAM specification and not the SAM ASCII printable method. */ typedef struct bam1_t { bam1_core_t core; uint64_t id; uint8_t *data; int l_data; uint32_t m_data; uint32_t mempolicy:2, :30 /* Reserved */; } bam1_t; /*! @function @abstract Get whether the query is on the reverse strand @param b pointer to an alignment @return boolean true if query is on the reverse strand */ #define bam_is_rev(b) (((b)->core.flag&BAM_FREVERSE) != 0) /*! @function @abstract Get whether the query's mate is on the reverse strand @param b pointer to an alignment @return boolean true if query's mate on the reverse strand */ #define bam_is_mrev(b) (((b)->core.flag&BAM_FMREVERSE) != 0) /*! @function @abstract Get the name of the query @param b pointer to an alignment @return pointer to the name string, null terminated */ #define bam_get_qname(b) ((char*)(b)->data) /*! @function @abstract Get the CIGAR array @param b pointer to an alignment @return pointer to the CIGAR array @discussion In the CIGAR array, each element is a 32-bit integer. The lower 4 bits gives a CIGAR operation and the higher 28 bits keep the length of a CIGAR. */ #define bam_get_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname)) /*! @function @abstract Get query sequence @param b pointer to an alignment @return pointer to sequence @discussion Each base is encoded in 4 bits: 1 for A, 2 for C, 4 for G, 8 for T and 15 for N. Two bases are packed in one byte with the base at the higher 4 bits having smaller coordinate on the read. It is recommended to use bam_seqi() macro to get the base. */ #define bam_get_seq(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname) /*! @function @abstract Get query quality @param b pointer to an alignment @return pointer to quality string */ #define bam_get_qual(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1)) /*! @function @abstract Get auxiliary data @param b pointer to an alignment @return pointer to the concatenated auxiliary data */ #define bam_get_aux(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1) + (b)->core.l_qseq) /*! @function @abstract Get length of auxiliary data @param b pointer to an alignment @return length of the concatenated auxiliary data */ #define bam_get_l_aux(b) ((b)->l_data - ((b)->core.n_cigar<<2) - (b)->core.l_qname - (b)->core.l_qseq - (((b)->core.l_qseq + 1)>>1)) /*! @function @abstract Get a base on read @param s Query sequence returned by bam_get_seq() @param i The i-th position, 0-based @return 4-bit integer representing the base. */ #define bam_seqi(s, i) ((s)[(i)>>1] >> ((~(i)&1)<<2) & 0xf) /*! @abstract Modifies a single base in the bam structure. @param s Query sequence returned by bam_get_seq() @param i The i-th position, 0-based @param b Base in nt16 nomenclature (see seq_nt16_table) */ #define bam_set_seqi(s,i,b) ((s)[(i)>>1] = ((s)[(i)>>1] & (0xf0 >> ((~(i)&1)<<2))) | ((b)<<((~(i)&1)<<2))) /************************** *** Exported functions *** **************************/ /*************** *** BAM I/O *** ***************/ /* Header */ /// Generates a new unpopulated header structure. /*! * * @return A valid pointer to new header on success, NULL on failure * * The sam_hdr_t struct returned by a successful call should be freed * via sam_hdr_destroy() when it is no longer needed. */ HTSLIB_EXPORT sam_hdr_t *sam_hdr_init(void); /// Read the header from a BAM compressed file. /*! * @param fp File pointer * @return A valid pointer to new header on success, NULL on failure * * This function only works with BAM files. It is usually better to use * sam_hdr_read(), which works on SAM, BAM and CRAM files. * * The sam_hdr_t struct returned by a successful call should be freed * via sam_hdr_destroy() when it is no longer needed. */ HTSLIB_EXPORT sam_hdr_t *bam_hdr_read(BGZF *fp); /// Writes the header to a BAM file. /*! * @param fp File pointer * @param h Header pointer * @return 0 on success, -1 on failure * * This function only works with BAM files. Use sam_hdr_write() to * write in any of the SAM, BAM or CRAM formats. */ HTSLIB_EXPORT int bam_hdr_write(BGZF *fp, const sam_hdr_t *h) HTS_RESULT_USED; /*! * Frees the resources associated with a header. */ HTSLIB_EXPORT void sam_hdr_destroy(sam_hdr_t *h); /// Duplicate a header structure. /*! * @return A valid pointer to new header on success, NULL on failure * * The sam_hdr_t struct returned by a successful call should be freed * via sam_hdr_destroy() when it is no longer needed. */ HTSLIB_EXPORT sam_hdr_t *sam_hdr_dup(const sam_hdr_t *h0); /*! * @abstract Old names for compatibility with existing code. */ static inline sam_hdr_t *bam_hdr_init(void) { return sam_hdr_init(); } static inline void bam_hdr_destroy(sam_hdr_t *h) { sam_hdr_destroy(h); } static inline sam_hdr_t *bam_hdr_dup(const sam_hdr_t *h0) { return sam_hdr_dup(h0); } typedef htsFile samFile; /// Create a header from existing text. /*! * @param l_text Length of text * @param text Header text * @return A populated sam_hdr_t structure on success; NULL on failure. * @note The text field of the returned header will be NULL, and the l_text * field will be zero. * * The sam_hdr_t struct returned by a successful call should be freed * via sam_hdr_destroy() when it is no longer needed. */ HTSLIB_EXPORT sam_hdr_t *sam_hdr_parse(size_t l_text, const char *text); /// Read a header from a SAM, BAM or CRAM file. /*! * @param fp Pointer to a SAM, BAM or CRAM file handle * @return A populated sam_hdr_t struct on success; NULL on failure. * * The sam_hdr_t struct returned by a successful call should be freed * via sam_hdr_destroy() when it is no longer needed. */ HTSLIB_EXPORT sam_hdr_t *sam_hdr_read(samFile *fp); /// Write a header to a SAM, BAM or CRAM file. /*! * @param fp SAM, BAM or CRAM file header * @param h Header structure to write * @return 0 on success; -1 on failure */ HTSLIB_EXPORT int sam_hdr_write(samFile *fp, const sam_hdr_t *h) HTS_RESULT_USED; /// Returns the current length of the header text. /*! * @return >= 0 on success, SIZE_MAX on failure */ HTSLIB_EXPORT size_t sam_hdr_length(sam_hdr_t *h); /// Returns the text representation of the header. /*! * @return valid char pointer on success, NULL on failure * * The returned string is part of the header structure. It will remain * valid until a call to a header API function causes the string to be * invalidated, or the header is destroyed. * * The caller should not attempt to free or realloc this pointer. */ HTSLIB_EXPORT const char *sam_hdr_str(sam_hdr_t *h); /// Returns the number of references in the header. /*! * @return >= 0 on success, -1 on failure */ HTSLIB_EXPORT int sam_hdr_nref(const sam_hdr_t *h); /* ==== Line level methods ==== */ /// Add formatted lines to an existing header. /*! * @param lines Full SAM header record, eg "@SQ\tSN:foo\tLN:100", with * optional new-line. If it contains more than 1 line then * multiple lines will be added in order * @param len The maximum length of lines (if an early NUL is not * encountered). len may be 0 if unknown, in which case * lines must be NUL-terminated * @return 0 on success, -1 on failure * * The lines will be appended to the end of the existing header * (apart from HD, which always comes first). */ HTSLIB_EXPORT int sam_hdr_add_lines(sam_hdr_t *h, const char *lines, size_t len); /// Adds a single line to an existing header. /*! * Specify type and one or more key,value pairs, ending with the NULL key. * Eg. sam_hdr_add_line(h, "SQ", "SN", "foo", "LN", "100", NULL). * * @param type Type of the added line. Eg. "SQ" * @return 0 on success, -1 on failure * * The new line will be added immediately after any others of the same * type, or at the end of the existing header if no lines of the * given type currently exist. The exception is HD lines, which always * come first. If an HD line already exists, it will be replaced. */ HTSLIB_EXPORT int sam_hdr_add_line(sam_hdr_t *h, const char *type, ...); /// Returns a complete line of formatted text for a given type and ID. /*! * @param type Type of the searched line. Eg. "SQ" * @param ID_key Tag key defining the line. Eg. "SN" * @param ID_value Tag value associated with the key above. Eg. "ref1" * @param ks kstring to hold the result * @return 0 on success; * -1 if no matching line is found * -2 on other failures * * Puts a complete line of formatted text for a specific header type/ID * combination into @p ks. If ID_key is NULL then it returns the first line of * the specified type. * * Any existing content in @p ks will be overwritten. */ HTSLIB_EXPORT int sam_hdr_find_line_id(sam_hdr_t *h, const char *type, const char *ID_key, const char *ID_val, kstring_t *ks); /// Returns a complete line of formatted text for a given type and index. /*! * @param type Type of the searched line. Eg. "SQ" * @param position Index in lines of this type (zero-based) * @param ks kstring to hold the result * @return 0 on success; * -1 if no matching line is found * -2 on other failures * * Puts a complete line of formatted text for a specific line into @p ks. * The header line is selected using the @p type and @p position parameters. * * Any existing content in @p ks will be overwritten. */ HTSLIB_EXPORT int sam_hdr_find_line_pos(sam_hdr_t *h, const char *type, int pos, kstring_t *ks); /// Remove a line with given type / id from a header /*! * @param type Type of the searched line. Eg. "SQ" * @param ID_key Tag key defining the line. Eg. "SN" * @param ID_value Tag value associated with the key above. Eg. "ref1" * @return 0 on success, -1 on error * * Remove a line from the header by specifying a tag:value that uniquely * identifies the line, i.e. the @SQ line containing "SN:ref1". * * \@SQ line is uniquely identified by the SN tag. * \@RG line is uniquely identified by the ID tag. * \@PG line is uniquely identified by the ID tag. * Eg. sam_hdr_remove_line_id(h, "SQ", "SN", "ref1") * * If no key:value pair is specified, the type MUST be followed by a NULL argument and * the first line of the type will be removed, if any. * Eg. sam_hdr_remove_line_id(h, "SQ", NULL, NULL) * * @note Removing \@PG lines is currently unsupported. */ HTSLIB_EXPORT int sam_hdr_remove_line_id(sam_hdr_t *h, const char *type, const char *ID_key, const char *ID_value); /// Remove nth line of a given type from a header /*! * @param type Type of the searched line. Eg. "SQ" * @param position Index in lines of this type (zero-based). E.g. 3 * @return 0 on success, -1 on error * * Remove a line from the header by specifying the position in the type * group, i.e. 3rd @SQ line. */ HTSLIB_EXPORT int sam_hdr_remove_line_pos(sam_hdr_t *h, const char *type, int position); /// Add or update tag key,value pairs in a header line. /*! * @param type Type of the searched line. Eg. "SQ" * @param ID_key Tag key defining the line. Eg. "SN" * @param ID_value Tag value associated with the key above. Eg. "ref1" * @return 0 on success, -1 on error * * Adds or updates tag key,value pairs in a header line. * Eg. for adding M5 tags to @SQ lines or updating sort order for the * @HD line. * * Specify multiple key,value pairs ending in NULL. Eg. * sam_hdr_update_line(h, "RG", "ID", "rg1", "DS", "description", "PG", "samtools", NULL) * * Attempting to update the record name (i.e. @SQ SN or @RG ID) will * work as long as the new name is not already in use, however doing this * on a file opened for reading may produce unexpected results. * * Renaming an @RG record in this way will only change the header. Alignment * records written later will not be updated automatically even if they * reference the old read group name. * * Attempting to change an @PG ID tag is not permitted. */ HTSLIB_EXPORT int sam_hdr_update_line(sam_hdr_t *h, const char *type, const char *ID_key, const char *ID_value, ...); /// Remove all lines of a given type from a header, except the one matching an ID /*! * @param type Type of the searched line. Eg. "SQ" * @param ID_key Tag key defining the line. Eg. "SN" * @param ID_value Tag value associated with the key above. Eg. "ref1" * @return 0 on success, -1 on failure * * Remove all lines of type from the header, except the one * specified by tag:value, i.e. the @SQ line containing "SN:ref1". * * If no line matches the key:value ID, all lines of the given type are removed. * To remove all lines of a given type, use NULL for both ID_key and ID_value. */ HTSLIB_EXPORT int sam_hdr_remove_except(sam_hdr_t *h, const char *type, const char *ID_key, const char *ID_value); /// Remove header lines of a given type, except those in a given ID set /*! * @param type Type of the searched line. Eg. "RG" * @param id Tag key defining the line. Eg. "ID" * @param rh Hash set initialised by the caller with the values to be kept. * See description for how to create this. If @p rh is NULL, all * lines of this type will be removed. * @return 0 on success, -1 on failure * * Remove all lines of type @p type from the header, except the ones * specified in the hash set @p rh. If @p rh is NULL, all lines of * this type will be removed. * Declaration of @p rh is done using KHASH_SET_INIT_STR macro. Eg. * @code{.c} * #include "htslib/khash.h" * KHASH_SET_INIT_STR(keep) * typedef khash_t(keep) *keephash_t; * * void your_method() { * samFile *sf = sam_open("alignment.bam", "r"); * sam_hdr_t *h = sam_hdr_read(sf); * keephash_t rh = kh_init(keep); * int ret = 0; * kh_put(keep, rh, strdup("chr2"), &ret); * kh_put(keep, rh, strdup("chr3"), &ret); * if (sam_hdr_remove_lines(h, "SQ", "SN", rh) == -1) * fprintf(stderr, "Error removing lines\n"); * khint_t k; * for (k = 0; k < kh_end(rh); ++k) * if (kh_exist(rh, k)) free((char*)kh_key(rh, k)); * kh_destroy(keep, rh); * sam_hdr_destroy(h); * sam_close(sf); * } * @endcode * */ HTSLIB_EXPORT int sam_hdr_remove_lines(sam_hdr_t *h, const char *type, const char *id, void *rh); /// Count the number of lines for a given header type /*! * @param h BAM header * @param type Header type to count. Eg. "RG" * @return Number of lines of this type on success; -1 on failure */ HTSLIB_EXPORT int sam_hdr_count_lines(sam_hdr_t *h, const char *type); /// Index of the line for the types that have dedicated look-up tables (SQ, RG, PG) /*! * @param h BAM header * @param type Type of the searched line. Eg. "RG" * @param key The value of the identifying key. Eg. "rg1" * @return 0-based index on success; -1 if line does not exist; -2 on failure */ HTSLIB_EXPORT int sam_hdr_line_index(sam_hdr_t *bh, const char *type, const char *key); /// Id key of the line for the types that have dedicated look-up tables (SQ, RG, PG) /*! * @param h BAM header * @param type Type of the searched line. Eg. "RG" * @param pos Zero-based index inside the type group. Eg. 2 (for the third RG line) * @return Valid key string on success; NULL on failure */ HTSLIB_EXPORT const char *sam_hdr_line_name(sam_hdr_t *bh, const char *type, int pos); /* ==== Key:val level methods ==== */ /// Return the value associated with a key for a header line identified by ID_key:ID_val /*! * @param type Type of the line to which the tag belongs. Eg. "SQ" * @param ID_key Tag key defining the line. Eg. "SN". Can be NULL, if looking for the first line. * @param ID_value Tag value associated with the key above. Eg. "ref1". Can be NULL, if ID_key is NULL. * @param key Key of the searched tag. Eg. "LN" * @param ks kstring where the value will be written * @return 0 on success * -1 if the requested tag does not exist * -2 on other errors * * Looks for a specific key in a single SAM header line and writes the * associated value into @p ks. The header line is selected using the ID_key * and ID_value parameters. Any pre-existing content in @p ks will be * overwritten. */ HTSLIB_EXPORT int sam_hdr_find_tag_id(sam_hdr_t *h, const char *type, const char *ID_key, const char *ID_value, const char *key, kstring_t *ks); /// Return the value associated with a key for a header line identified by position /*! * @param type Type of the line to which the tag belongs. Eg. "SQ" * @param position Index in lines of this type (zero-based). E.g. 3 * @param key Key of the searched tag. Eg. "LN" * @param ks kstring where the value will be written * @return 0 on success * -1 if the requested tag does not exist * -2 on other errors * * Looks for a specific key in a single SAM header line and writes the * associated value into @p ks. The header line is selected using the @p type * and @p position parameters. Any pre-existing content in @p ks will be * overwritten. */ HTSLIB_EXPORT int sam_hdr_find_tag_pos(sam_hdr_t *h, const char *type, int pos, const char *key, kstring_t *ks); /// Remove the key from the line identified by type, ID_key and ID_value. /*! * @param type Type of the line to which the tag belongs. Eg. "SQ" * @param ID_key Tag key defining the line. Eg. "SN" * @param ID_value Tag value associated with the key above. Eg. "ref1" * @param key Key of the targeted tag. Eg. "M5" * @return 1 if the key was removed; 0 if it was not present; -1 on error */ HTSLIB_EXPORT int sam_hdr_remove_tag_id(sam_hdr_t *h, const char *type, const char *ID_key, const char *ID_value, const char *key); /// Get the target id for a given reference sequence name /*! * @param ref Reference name * @return Positive value on success, * -1 if unknown reference, * -2 if the header could not be parsed * * Looks up a reference sequence by name in the reference hash table * and returns the numerical target id. */ HTSLIB_EXPORT int sam_hdr_name2tid(sam_hdr_t *h, const char *ref); /// Get the reference sequence name from a target index /*! * @param tid Target index * @return Valid reference name on success, NULL on failure * * Fetch the reference sequence name from the target name array, * using the numerical target id. */ HTSLIB_EXPORT const char *sam_hdr_tid2name(const sam_hdr_t *h, int tid); /// Get the reference sequence length from a target index /*! * @param tid Target index * @return Strictly positive value on success, 0 on failure * * Fetch the reference sequence length from the target length array, * using the numerical target id. */ HTSLIB_EXPORT hts_pos_t sam_hdr_tid2len(const sam_hdr_t *h, int tid); /// Alias of sam_hdr_name2tid(), for backwards compatibility. /*! * @param ref Reference name * @return Positive value on success, * -1 if unknown reference, * -2 if the header could not be parsed */ static inline int bam_name2id(sam_hdr_t *h, const char *ref) { return sam_hdr_name2tid(h, ref); } /// Generate a unique \@PG ID: value /*! * @param name Name of the program. Eg. samtools * @return Valid ID on success, NULL on failure * * Returns a unique ID from a base name. The string returned will remain * valid until the next call to this function, or the header is destroyed. * The caller should not attempt to free() or realloc() it. */ HTSLIB_EXPORT const char *sam_hdr_pg_id(sam_hdr_t *h, const char *name); /// Add an \@PG line. /*! * @param name Name of the program. Eg. samtools * @return 0 on success, -1 on failure * * If we wish complete control over this use sam_hdr_add_line() directly. This * function uses that, but attempts to do a lot of tedious house work for * you too. * * - It will generate a suitable ID if the supplied one clashes. * - It will generate multiple \@PG records if we have multiple PG chains. * * Call it as per sam_hdr_add_line() with a series of key,value pairs ending * in NULL. */ HTSLIB_EXPORT int sam_hdr_add_pg(sam_hdr_t *h, const char *name, ...); /*! * A function to help with construction of CL tags in @PG records. * Takes an argc, argv pair and returns a single space-separated string. * This string should be deallocated by the calling function. * * @return * Returns malloced char * on success; * NULL on failure */ HTSLIB_EXPORT char *stringify_argv(int argc, char *argv[]); /// Increments the reference count on a header /*! * This permits multiple files to share the same header, all calling * sam_hdr_destroy when done, without causing errors for other open files. */ HTSLIB_EXPORT void sam_hdr_incr_ref(sam_hdr_t *h); /* * Macros for changing the \@HD line. They eliminate the need to use NULL method arguments. */ /// Returns the SAM formatted text of the \@HD header line #define sam_hdr_find_hd(h, ks) sam_hdr_find_line_id((h), "HD", NULL, NULL, (ks)) /// Returns the value associated with a given \@HD line tag #define sam_hdr_find_tag_hd(h, key, ks) sam_hdr_find_tag_id((h), "HD", NULL, NULL, (key), (ks)) /// Adds or updates tags on the header \@HD line #define sam_hdr_update_hd(h, ...) sam_hdr_update_line((h), "HD", NULL, NULL, __VA_ARGS__, NULL) /// Removes the \@HD line tag with the given key #define sam_hdr_remove_tag_hd(h, key) sam_hdr_remove_tag_id((h), "HD", NULL, NULL, (key)) /* Alignment */ /// Create a new bam1_t alignment structure /** @return An empty bam1_t structure on success, NULL on failure The bam1_t struct returned by a successful call should be freed via bam_destroy1() when it is no longer needed. */ HTSLIB_EXPORT bam1_t *bam_init1(void); /// Destroy a bam1_t structure /** @param b structure to destroy Does nothing if @p b is NULL. If not, all memory associated with @p b will be freed, along with the structure itself. @p b should not be accessed after calling this function. */ HTSLIB_EXPORT void bam_destroy1(bam1_t *b); #define BAM_USER_OWNS_STRUCT 1 #define BAM_USER_OWNS_DATA 2 /// Set alignment record memory policy /** @param b Alignment record @param policy Desired policy Allows the way HTSlib reallocates and frees bam1_t data to be changed. @policy can be set to the bitwise-or of the following values: \li \c BAM_USER_OWNS_STRUCT If this is set then bam_destroy1() will not try to free the bam1_t struct. \li \c BAM_USER_OWNS_DATA If this is set, bam_destroy1() will not free the bam1_t::data pointer. Also, functions which need to expand bam1_t::data memory will change behaviour. Instead of calling realloc() on the pointer, they will allocate a new data buffer and copy any existing content in to it. The existing memory will \b not be freed. bam1_t::data will be set to point to the new memory and the BAM_USER_OWNS_DATA flag will be cleared. BAM_USER_OWNS_STRUCT allows bam_destroy1() to be called on bam1_t structures that are members of an array. BAM_USER_OWNS_DATA can be used by applications that want more control over where the variable-length parts of the bam record will be stored. By preventing calls to free() and realloc(), it allows bam1_t::data to hold pointers to memory that cannot be passed to those functions. Example: Read a block of alignment records, storing the variable-length data in a single buffer and the records in an array. Stop when either the array or the buffer is full. \code{.c} #define MAX_RECS 1000 #define REC_LENGTH 400 // Average length estimate, to get buffer size size_t bufsz = MAX_RECS * REC_LENGTH, nrecs, buff_used = 0; bam1_t *recs = calloc(MAX_RECS, sizeof(bam1_t)); uint8_t *buffer = malloc(bufsz); int res = 0, result = EXIT_FAILURE; uint32_t new_m_data; if (!recs || !buffer) goto cleanup; for (nrecs = 0; nrecs < MAX_RECS; nrecs++) { bam_set_mempolicy(&recs[nrecs], BAM_USER_OWNS_STRUCT|BAM_USER_OWNS_DATA); // Set data pointer to unused part of buffer recs[nrecs].data = &buffer[buff_used]; // Set m_data to size of unused part of buffer. On 64-bit platforms it // will be necessary to limit this to UINT32_MAX due to the size of // bam1_t::m_data (not done here as our buffer is only 400K). recs[nrecs].m_data = bufsz - buff_used; // Read the record res = sam_read1(file_handle, header, &recs[nrecs]); if (res <= 0) break; // EOF or error // Check if the record data didn't fit - if not, stop reading if ((bam_get_mempolicy(&recs[nrecs]) & BAM_USER_OWNS_DATA) == 0) { nrecs++; // Include last record in count break; } // Adjust m_data to the space actually used. If space is available, // round up to eight bytes so the next record aligns nicely. new_m_data = ((uint32_t) recs[nrecs].l_data + 7) & (~7U); if (new_m_data < recs[nrecs].m_data) recs[nrecs].m_data = new_m_data; buff_used += recs[nrecs].m_data; } if (res < 0) goto cleanup; result = EXIT_SUCCESS; // ... use data ... cleanup: if (recs) { for (size_t i = 0; i < nrecs; i++) bam_destroy1(&recs[i]); free(recs); } free(buffer); \endcode */ static inline void bam_set_mempolicy(bam1_t *b, uint32_t policy) { b->mempolicy = policy; } /// Get alignment record memory policy /** @param b Alignment record See bam_set_mempolicy() */ static inline uint32_t bam_get_mempolicy(bam1_t *b) { return b->mempolicy; } /// Read a BAM format alignment record /** @param fp BGZF file being read @param b Destination for the alignment data @return number of bytes read on success -1 at end of file < -1 on failure This function can only read BAM format files. Most code should use sam_read1() instead, which can be used with BAM, SAM and CRAM formats. */ HTSLIB_EXPORT int bam_read1(BGZF *fp, bam1_t *b) HTS_RESULT_USED; /// Write a BAM format alignment record /** @param fp BGZF file being written @param b Alignment record to write @return number of bytes written on success -1 on error This function can only write BAM format files. Most code should use sam_write1() instead, which can be used with BAM, SAM and CRAM formats. */ HTSLIB_EXPORT int bam_write1(BGZF *fp, const bam1_t *b) HTS_RESULT_USED; /// Copy alignment record data /** @param bdst Destination alignment record @param bsrc Source alignment record @return bdst on success; NULL on failure */ HTSLIB_EXPORT bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc) HTS_RESULT_USED; /// Create a duplicate alignment record /** @param bsrc Source alignment record @return Pointer to a new alignment record on success; NULL on failure The bam1_t struct returned by a successful call should be freed via bam_destroy1() when it is no longer needed. */ HTSLIB_EXPORT bam1_t *bam_dup1(const bam1_t *bsrc); /// Sets all components of an alignment structure /** @param bam Target alignment structure. Must be initialized by a call to bam_init1(). The data field will be reallocated automatically as needed. @param l_qname Length of the query name. If set to 0, the placeholder query name "*" will be used. @param qname Query name, may be NULL if l_qname = 0 @param flag Bitwise flag, a combination of the BAM_F* constants. @param tid Chromosome ID, defined by sam_hdr_t (a.k.a. RNAME). @param pos 0-based leftmost coordinate. @param mapq Mapping quality. @param n_cigar Number of CIGAR operations. @param cigar CIGAR data, may be NULL if n_cigar = 0. @param mtid Chromosome ID of next read in template, defined by sam_hdr_t (a.k.a. RNEXT). @param mpos 0-based leftmost coordinate of next read in template (a.k.a. PNEXT). @param isize Observed template length ("insert size") (a.k.a. TLEN). @param l_seq Length of the query sequence (read) and sequence quality string. @param seq Sequence, may be NULL if l_seq = 0. @param qual Sequence quality, may be NULL. @param l_aux Length to be reserved for auxiliary field data, may be 0. @return >= 0 on success (number of bytes written to bam->data), negative (with errno set) on failure. */ HTSLIB_EXPORT int bam_set1(bam1_t *bam, size_t l_qname, const char *qname, uint16_t flag, int32_t tid, hts_pos_t pos, uint8_t mapq, size_t n_cigar, const uint32_t *cigar, int32_t mtid, hts_pos_t mpos, hts_pos_t isize, size_t l_seq, const char *seq, const char *qual, size_t l_aux); /// Calculate query length from CIGAR data /** @param n_cigar Number of items in @p cigar @param cigar CIGAR data @return Query length CIGAR data is stored as in the BAM format, i.e. (op_len << 4) | op where op_len is the length in bases and op is a value between 0 and 8 representing one of the operations "MIDNSHP=X" (M = 0; X = 8) This function returns the sum of the lengths of the M, I, S, = and X operations in @p cigar (these are the operations that "consume" query bases). All other operations (including invalid ones) are ignored. @note This return type of this function is hts_pos_t so that it can correctly return the length of CIGAR sequences including many long operations without overflow. However, other restrictions (notably the sizes of bam1_core_t::l_qseq and bam1_t::data) limit the maximum query sequence length supported by HTSlib to fewer than INT_MAX bases. */ HTSLIB_EXPORT hts_pos_t bam_cigar2qlen(int n_cigar, const uint32_t *cigar); /// Calculate reference length from CIGAR data /** @param n_cigar Number of items in @p cigar @param cigar CIGAR data @return Reference length CIGAR data is stored as in the BAM format, i.e. (op_len << 4) | op where op_len is the length in bases and op is a value between 0 and 8 representing one of the operations "MIDNSHP=X" (M = 0; X = 8) This function returns the sum of the lengths of the M, D, N, = and X operations in @p cigar (these are the operations that "consume" reference bases). All other operations (including invalid ones) are ignored. */ HTSLIB_EXPORT hts_pos_t bam_cigar2rlen(int n_cigar, const uint32_t *cigar); /*! @abstract Calculate the rightmost base position of an alignment on the reference genome. @param b pointer to an alignment @return the coordinate of the first base after the alignment, 0-based @discussion For a mapped read, this is just b->core.pos + bam_cigar2rlen. For an unmapped read (either according to its flags or if it has no cigar string) or a read whose cigar string consumes no reference bases at all, we return b->core.pos + 1 by convention. */ HTSLIB_EXPORT hts_pos_t bam_endpos(const bam1_t *b); HTSLIB_EXPORT int bam_str2flag(const char *str); /** returns negative value on error */ HTSLIB_EXPORT char *bam_flag2str(int flag); /** The string must be freed by the user */ /*! @function @abstract Set the name of the query @param b pointer to an alignment @return 0 on success, -1 on failure */ HTSLIB_EXPORT int bam_set_qname(bam1_t *b, const char *qname); /*! @function @abstract Parse a CIGAR string into a uint32_t array @param in [in] pointer to the source string @param end [out] address of the pointer to the new end of the input string can be NULL @param a_cigar [in/out] address of the destination uint32_t buffer @param a_mem [in/out] address of the allocated number of buffer elements @return number of processed CIGAR operators; -1 on error */ HTSLIB_EXPORT ssize_t sam_parse_cigar(const char *in, char **end, uint32_t **a_cigar, size_t *a_mem); /*! @function @abstract Parse a CIGAR string into a bam1_t struct @param in [in] pointer to the source string @param end [out] address of the pointer to the new end of the input string can be NULL @param b [in/out] address of the destination bam1_t struct @return number of processed CIGAR operators; -1 on error @discussion The BAM record may be partial and empty of existing cigar, seq and quality, as is the case during SAM parsing, or it may be an existing BAM record in which case this function replaces the existing CIGAR field and shuffles data accordingly. A CIGAR of "*" will remove the CIGAR, returning zero. */ HTSLIB_EXPORT ssize_t bam_parse_cigar(const char *in, char **end, bam1_t *b); /************************* *** BAM/CRAM indexing *** *************************/ // These BAM iterator functions work only on BAM files. To work with either // BAM or CRAM files use the sam_index_load() & sam_itr_*() functions. #define bam_itr_destroy(iter) hts_itr_destroy(iter) #define bam_itr_queryi(idx, tid, beg, end) sam_itr_queryi(idx, tid, beg, end) #define bam_itr_querys(idx, hdr, region) sam_itr_querys(idx, hdr, region) #define bam_itr_next(htsfp, itr, r) sam_itr_next((htsfp), (itr), (r)) // Load/build .csi or .bai BAM index file. Does not work with CRAM. // It is recommended to use the sam_index_* functions below instead. #define bam_index_load(fn) hts_idx_load((fn), HTS_FMT_BAI) #define bam_index_build(fn, min_shift) (sam_index_build((fn), (min_shift))) /// Initialise fp->idx for the current format type for SAM, BAM and CRAM types . /** @param fp File handle for the data file being written. @param h Bam header structured (needed for BAI and CSI). @param min_shift 0 for BAI, or larger for CSI (CSI defaults to 14). @param fnidx Filename to write index to. This pointer must remain valid until after sam_idx_save is called. @return 0 on success, <0 on failure. @note This must be called after the header has been written, but before any other data. */ HTSLIB_EXPORT int sam_idx_init(htsFile *fp, sam_hdr_t *h, int min_shift, const char *fnidx); /// Writes the index initialised with sam_idx_init to disk. /** @param fp File handle for the data file being written. @return 0 on success, <0 on failure. */ HTSLIB_EXPORT int sam_idx_save(htsFile *fp) HTS_RESULT_USED; /// Load a BAM (.csi or .bai) or CRAM (.crai) index file /** @param fp File handle of the data file whose index is being opened @param fn BAM/CRAM/etc filename to search alongside for the index file @return The index, or NULL if an error occurred. Equivalent to sam_index_load3(fp, fn, NULL, HTS_IDX_SAVE_REMOTE); */ HTSLIB_EXPORT hts_idx_t *sam_index_load(htsFile *fp, const char *fn); /// Load a specific BAM (.csi or .bai) or CRAM (.crai) index file /** @param fp File handle of the data file whose index is being opened @param fn BAM/CRAM/etc data file filename @param fnidx Index filename, or NULL to search alongside @a fn @return The index, or NULL if an error occurred. Equivalent to sam_index_load3(fp, fn, fnidx, HTS_IDX_SAVE_REMOTE); */ HTSLIB_EXPORT hts_idx_t *sam_index_load2(htsFile *fp, const char *fn, const char *fnidx); /// Load or stream a BAM (.csi or .bai) or CRAM (.crai) index file /** @param fp File handle of the data file whose index is being opened @param fn BAM/CRAM/etc data file filename @param fnidx Index filename, or NULL to search alongside @a fn @param flags Flags to alter behaviour (see description) @return The index, or NULL if an error occurred. The @p flags parameter can be set to a combination of the following values: HTS_IDX_SAVE_REMOTE Save a local copy of any remote indexes HTS_IDX_SILENT_FAIL Fail silently if the index is not present Note that HTS_IDX_SAVE_REMOTE has no effect for remote CRAM indexes. They are always downloaded and never cached locally. The index struct returned by a successful call should be freed via hts_idx_destroy() when it is no longer needed. */ HTSLIB_EXPORT hts_idx_t *sam_index_load3(htsFile *fp, const char *fn, const char *fnidx, int flags); /// Generate and save an index file /** @param fn Input BAM/etc filename, to which .csi/etc will be added @param min_shift Positive to generate CSI, or 0 to generate BAI @return 0 if successful, or negative if an error occurred (usually -1; or -2: opening fn failed; -3: format not indexable; -4: failed to create and/or save the index) */ HTSLIB_EXPORT int sam_index_build(const char *fn, int min_shift) HTS_RESULT_USED; /// Generate and save an index to a specific file /** @param fn Input BAM/CRAM/etc filename @param fnidx Output filename, or NULL to add .bai/.csi/etc to @a fn @param min_shift Positive to generate CSI, or 0 to generate BAI @return 0 if successful, or negative if an error occurred (see sam_index_build for error codes) */ HTSLIB_EXPORT int sam_index_build2(const char *fn, const char *fnidx, int min_shift) HTS_RESULT_USED; /// Generate and save an index to a specific file /** @param fn Input BAM/CRAM/etc filename @param fnidx Output filename, or NULL to add .bai/.csi/etc to @a fn @param min_shift Positive to generate CSI, or 0 to generate BAI @param nthreads Number of threads to use when building the index @return 0 if successful, or negative if an error occurred (see sam_index_build for error codes) */ HTSLIB_EXPORT int sam_index_build3(const char *fn, const char *fnidx, int min_shift, int nthreads) HTS_RESULT_USED; /// Free a SAM iterator /// @param iter Iterator to free #define sam_itr_destroy(iter) hts_itr_destroy(iter) /// Create a BAM/CRAM iterator /** @param idx Index @param tid Target id @param beg Start position in target @param end End position in target @return An iterator on success; NULL on failure The following special values (defined in htslib/hts.h)can be used for @p tid. When using one of these values, @p beg and @p end are ignored. HTS_IDX_NOCOOR iterates over unmapped reads sorted at the end of the file HTS_IDX_START iterates over the entire file HTS_IDX_REST iterates from the current position to the end of the file HTS_IDX_NONE always returns "no more alignment records" When using HTS_IDX_REST or HTS_IDX_NONE, NULL can be passed in to @p idx. */ HTSLIB_EXPORT hts_itr_t *sam_itr_queryi(const hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end); /// Create a SAM/BAM/CRAM iterator /** @param idx Index @param hdr Header @param region Region specification @return An iterator on success; NULL on failure Regions are parsed by hts_parse_reg(), and take one of the following forms: region | Outputs --------------- | ------------- REF | All reads with RNAME REF REF: | All reads with RNAME REF REF:START | Reads with RNAME REF overlapping START to end of REF REF:-END | Reads with RNAME REF overlapping start of REF to END REF:START-END | Reads with RNAME REF overlapping START to END . | All reads from the start of the file * | Unmapped reads at the end of the file (RNAME '*' in SAM) The form `REF:` should be used when the reference name itself contains a colon. Note that SAM files must be bgzf-compressed for iterators to work. */ HTSLIB_EXPORT hts_itr_t *sam_itr_querys(const hts_idx_t *idx, sam_hdr_t *hdr, const char *region); /// Create a multi-region iterator /** @param idx Index @param hdr Header @param reglist Array of regions to iterate over @param regcount Number of items in reglist Each @p reglist entry should have the reference name in the `reg` field, an array of regions for that reference in `intervals` and the number of items in `intervals` should be stored in `count`. No other fields need to be filled in. The iterator will return all reads overlapping the given regions. If a read overlaps more than one region, it will only be returned once. */ HTSLIB_EXPORT hts_itr_t *sam_itr_regions(const hts_idx_t *idx, sam_hdr_t *hdr, hts_reglist_t *reglist, unsigned int regcount); /// Create a multi-region iterator /** @param idx Index @param hdr Header @param regarray Array of ref:interval region specifiers @param regcount Number of items in regarray Each @p regarray entry is parsed by hts_parse_reg(), and takes one of the following forms: region | Outputs --------------- | ------------- REF | All reads with RNAME REF REF: | All reads with RNAME REF REF:START | Reads with RNAME REF overlapping START to end of REF REF:-END | Reads with RNAME REF overlapping start of REF to END REF:START-END | Reads with RNAME REF overlapping START to END . | All reads from the start of the file * | Unmapped reads at the end of the file (RNAME '*' in SAM) The form `REF:` should be used when the reference name itself contains a colon. The iterator will return all reads overlapping the given regions. If a read overlaps more than one region, it will only be returned once. */ HTSLIB_EXPORT hts_itr_t *sam_itr_regarray(const hts_idx_t *idx, sam_hdr_t *hdr, char **regarray, unsigned int regcount); /// Get the next read from a SAM/BAM/CRAM iterator /** @param htsfp Htsfile pointer for the input file @param itr Iterator @param r Pointer to a bam1_t struct @return >= 0 on success; -1 when there is no more data; < -1 on error */ static inline int sam_itr_next(htsFile *htsfp, hts_itr_t *itr, bam1_t *r) { if (!htsfp->is_bgzf && !htsfp->is_cram) { hts_log_error("%s not BGZF compressed", htsfp->fn ? htsfp->fn : "File"); return -2; } if (!itr) { hts_log_error("Null iterator"); return -2; } if (itr->multi) return hts_itr_multi_next(htsfp, itr, r); else return hts_itr_next(htsfp->is_bgzf ? htsfp->fp.bgzf : NULL, itr, r, htsfp); } /// Get the next read from a BAM/CRAM multi-iterator /** @param htsfp Htsfile pointer for the input file @param itr Iterator @param r Pointer to a bam1_t struct @return >= 0 on success; -1 when there is no more data; < -1 on error */ #define sam_itr_multi_next(htsfp, itr, r) sam_itr_next(htsfp, itr, r) HTSLIB_EXPORT const char *sam_parse_region(sam_hdr_t *h, const char *s, int *tid, hts_pos_t *beg, hts_pos_t *end, int flags); /*************** *** SAM I/O *** ***************/ #define sam_open(fn, mode) (hts_open((fn), (mode))) #define sam_open_format(fn, mode, fmt) (hts_open_format((fn), (mode), (fmt))) #define sam_flush(fp) hts_flush((fp)) #define sam_close(fp) hts_close(fp) HTSLIB_EXPORT int sam_open_mode(char *mode, const char *fn, const char *format); // A version of sam_open_mode that can handle ,key=value options. // The format string is allocated and returned, to be freed by the caller. // Prefix should be "r" or "w", HTSLIB_EXPORT char *sam_open_mode_opts(const char *fn, const char *mode, const char *format); HTSLIB_EXPORT int sam_hdr_change_HD(sam_hdr_t *h, const char *key, const char *val); HTSLIB_EXPORT int sam_parse1(kstring_t *s, sam_hdr_t *h, bam1_t *b) HTS_RESULT_USED; HTSLIB_EXPORT int sam_format1(const sam_hdr_t *h, const bam1_t *b, kstring_t *str) HTS_RESULT_USED; /// sam_read1 - Read a record from a file /** @param fp Pointer to the source file * @param h Pointer to the header previously read (fully or partially) * @param b Pointer to the record placeholder * @return >= 0 on successfully reading a new record, -1 on end of stream, < -1 on error */ HTSLIB_EXPORT int sam_read1(samFile *fp, sam_hdr_t *h, bam1_t *b) HTS_RESULT_USED; /// sam_write1 - Write a record to a file /** @param fp Pointer to the destination file * @param h Pointer to the header structure previously read * @param b Pointer to the record to be written * @return >= 0 on successfully writing the record, -ve on error */ HTSLIB_EXPORT int sam_write1(samFile *fp, const sam_hdr_t *h, const bam1_t *b) HTS_RESULT_USED; // Forward declaration, see hts_expr.h for full. struct hts_filter_t; /// sam_passes_filter - Checks whether a record passes an hts_filter. /** @param h Pointer to the header structure previously read * @param b Pointer to the BAM record to be checked * @param filt Pointer to the filter, created from hts_filter_init. * @return 1 if passes, 0 if not, and <0 on error. */ HTSLIB_EXPORT int sam_passes_filter(const sam_hdr_t *h, const bam1_t *b, struct hts_filter_t *filt); /************************************* *** Manipulating auxiliary fields *** *************************************/ /// Converts a BAM aux tag to SAM format /* * @param key Two letter tag key * @param type Single letter type code: ACcSsIifHZB. * @param tag Tag data pointer, in BAM format * @param end Pointer to end of bam record (largest extent of tag) * @param ks kstring to write the formatted tag to * * @return pointer to end of tag on success, * NULL on failure. * * @discussion The three separate parameters key, type, tag may be * derived from a s=bam_aux_get() query as s-2, *s and s+1. However * it is recommended to use bam_aux_get_str in this situation. * The desire to split these parameters up is for potential processing * of non-BAM formats that encode using a BAM type mechanism * (such as the internal CRAM representation). */ static inline const uint8_t *sam_format_aux1(const uint8_t *key, const uint8_t type, const uint8_t *tag, const uint8_t *end, kstring_t *ks) { int r = 0; const uint8_t *s = tag; // brevity and consistency with other code. r |= kputsn_((char*)key, 2, ks) < 0; r |= kputc_(':', ks) < 0; if (type == 'C') { r |= kputsn_("i:", 2, ks) < 0; r |= kputw(*s, ks) < 0; ++s; } else if (type == 'c') { r |= kputsn_("i:", 2, ks) < 0; r |= kputw(*(int8_t*)s, ks) < 0; ++s; } else if (type == 'S') { if (end - s >= 2) { r |= kputsn_("i:", 2, ks) < 0; r |= kputuw(le_to_u16(s), ks) < 0; s += 2; } else goto bad_aux; } else if (type == 's') { if (end - s >= 2) { r |= kputsn_("i:", 2, ks) < 0; r |= kputw(le_to_i16(s), ks) < 0; s += 2; } else goto bad_aux; } else if (type == 'I') { if (end - s >= 4) { r |= kputsn_("i:", 2, ks) < 0; r |= kputuw(le_to_u32(s), ks) < 0; s += 4; } else goto bad_aux; } else if (type == 'i') { if (end - s >= 4) { r |= kputsn_("i:", 2, ks) < 0; r |= kputw(le_to_i32(s), ks) < 0; s += 4; } else goto bad_aux; } else if (type == 'A') { r |= kputsn_("A:", 2, ks) < 0; r |= kputc_(*s, ks) < 0; ++s; } else if (type == 'f') { if (end - s >= 4) { // cast to avoid triggering -Wdouble-promotion ksprintf(ks, "f:%g", (double)le_to_float(s)); s += 4; } else goto bad_aux; } else if (type == 'd') { // NB: "d" is not an official type in the SAM spec. // However for unknown reasons samtools has always supported this. // We believe, HOPE, it is not in general usage and we do not // encourage it. if (end - s >= 8) { ksprintf(ks, "d:%g", le_to_double(s)); s += 8; } else goto bad_aux; } else if (type == 'Z' || type == 'H') { r |= kputc_(type, ks) < 0; r |= kputc_(':', ks) < 0; while (s < end && *s) r |= kputc_(*s++, ks) < 0; r |= kputsn("", 0, ks) < 0; //ensures NUL termination if (s >= end) goto bad_aux; ++s; } else if (type == 'B') { uint8_t sub_type = *(s++); unsigned sub_type_size; // or externalise sam.c's aux_type2size function? switch (sub_type) { case 'A': case 'c': case 'C': sub_type_size = 1; break; case 's': case 'S': sub_type_size = 2; break; case 'i': case 'I': case 'f': sub_type_size = 4; break; default: sub_type_size = 0; break; } uint32_t i, n; if (sub_type_size == 0 || end - s < 4) goto bad_aux; n = le_to_u32(s); s += 4; // now points to the start of the array if ((size_t)(end - s) / sub_type_size < n) goto bad_aux; r |= kputsn_("B:", 2, ks) < 0; r |= kputc(sub_type, ks) < 0; // write the type switch (sub_type) { case 'c': if (ks_expand(ks, n*2) < 0) goto mem_err; for (i = 0; i < n; ++i) { ks->s[ks->l++] = ','; r |= kputw(*(int8_t*)s, ks) < 0; ++s; } break; case 'C': if (ks_expand(ks, n*2) < 0) goto mem_err; for (i = 0; i < n; ++i) { ks->s[ks->l++] = ','; r |= kputuw(*(uint8_t*)s, ks) < 0; ++s; } break; case 's': if (ks_expand(ks, n*4) < 0) goto mem_err; for (i = 0; i < n; ++i) { ks->s[ks->l++] = ','; r |= kputw(le_to_i16(s), ks) < 0; s += 2; } break; case 'S': if (ks_expand(ks, n*4) < 0) goto mem_err; for (i = 0; i < n; ++i) { ks->s[ks->l++] = ','; r |= kputuw(le_to_u16(s), ks) < 0; s += 2; } break; case 'i': if (ks_expand(ks, n*6) < 0) goto mem_err; for (i = 0; i < n; ++i) { ks->s[ks->l++] = ','; r |= kputw(le_to_i32(s), ks) < 0; s += 4; } break; case 'I': if (ks_expand(ks, n*6) < 0) goto mem_err; for (i = 0; i < n; ++i) { ks->s[ks->l++] = ','; r |= kputuw(le_to_u32(s), ks) < 0; s += 4; } break; case 'f': if (ks_expand(ks, n*8) < 0) goto mem_err; for (i = 0; i < n; ++i) { ks->s[ks->l++] = ','; // cast to avoid triggering -Wdouble-promotion r |= kputd((double)le_to_float(s), ks) < 0; s += 4; } break; default: goto bad_aux; } } else { // Unknown type goto bad_aux; } return r ? NULL : s; bad_aux: errno = EINVAL; return NULL; mem_err: hts_log_error("Out of memory"); errno = ENOMEM; return NULL; } /// Return a pointer to a BAM record's first aux field /** @param b Pointer to the BAM record @return Aux field pointer, or NULL if the record has none When NULL is returned, errno will also be set to ENOENT. ("Aux field pointers" point to the TYPE byte within the auxiliary data for that field; but in general it is unnecessary for user code to be aware of this.) */ HTSLIB_EXPORT uint8_t *bam_aux_first(const bam1_t *b); /// Return a pointer to a BAM record's next aux field /** @param b Pointer to the BAM record @param s Aux field pointer, as returned by bam_aux_first()/_next()/_get() @return Pointer to the next aux field, or NULL if no next field or error Whenever NULL is returned, errno will also be set: ENOENT if @p s was the record's last aux field; otherwise EINVAL, indicating that the BAM record's aux data is corrupt. */ HTSLIB_EXPORT uint8_t *bam_aux_next(const bam1_t *b, const uint8_t *s); /// Return a pointer to an aux record /** @param b Pointer to the bam record @param tag Desired aux tag @return Pointer to the tag data, or NULL if tag is not present or on error If the tag is not present, this function returns NULL and sets errno to ENOENT. If the bam record's aux data is corrupt (either a tag has an invalid type, or the last record is incomplete) then errno is set to EINVAL and NULL is returned. */ HTSLIB_EXPORT uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]); /// Return the aux field's 2-character tag /** @param s Aux field pointer, as returned by bam_aux_first()/_next()/_get() @return Pointer to the tag characters, NOT NUL-terminated */ static inline const char *bam_aux_tag(const uint8_t *s) { return (const char *) (s-2); } /// Return the aux field's type character /** @param s Aux field pointer, as returned by bam_aux_first()/_next()/_get() @return The type character: one of cCsSiI/fd/A/Z/H/B */ static inline char bam_aux_type(const uint8_t *s) { return *s; } /// Return a SAM formatting string containing a BAM tag /** @param b Pointer to the bam record @param tag Desired aux tag @param s The kstring to write to. @return 1 on success, 0 on no tag found with errno = ENOENT, -1 on error (errno will be either EINVAL or ENOMEM). */ static inline int bam_aux_get_str(const bam1_t *b, const char tag[2], kstring_t *s) { const uint8_t *t = bam_aux_get(b, tag); if (!t) return errno == ENOENT ? 0 : -1; if (!sam_format_aux1(t-2, *t, t+1, b->data + b->l_data, s)) return -1; return 1; } /// Get an integer aux value /** @param s Pointer to the tag data, as returned by bam_aux_get() @return The value, or 0 if the tag was not an integer type If the tag is not an integer type, errno is set to EINVAL. This function will not return the value of floating-point tags. */ HTSLIB_EXPORT int64_t bam_aux2i(const uint8_t *s); /// Get a float aux value /** @param s Pointer to the tag data, as returned by bam_aux_get() @return The value, or 0 if the tag was not a float type If the tag is not an numeric type, errno is set to EINVAL. The value of the float will be returned cast to a double. */ HTSLIB_EXPORT double bam_aux2f(const uint8_t *s); /// Get a character aux value /** @param s Pointer to the tag data, as returned by bam_aux_get(). @return The value, or 0 if the tag was not a character ('A') type If the tag is not a character type, errno is set to EINVAL. */ HTSLIB_EXPORT char bam_aux2A(const uint8_t *s); /// Get a string aux value /** @param s Pointer to the tag data, as returned by bam_aux_get(). @return Pointer to the string, or NULL if the tag was not a string type If the tag is not a string type ('Z' or 'H'), errno is set to EINVAL. */ HTSLIB_EXPORT char *bam_aux2Z(const uint8_t *s); /// Get the length of an array-type ('B') tag /** @param s Pointer to the tag data, as returned by bam_aux_get(). @return The length of the array, or 0 if the tag is not an array type. If the tag is not an array type, errno is set to EINVAL. */ HTSLIB_EXPORT uint32_t bam_auxB_len(const uint8_t *s); /// Get an integer value from an array-type tag /** @param s Pointer to the tag data, as returned by bam_aux_get(). @param idx 0-based Index into the array @return The idx'th value, or 0 on error. If the array is not an integer type, errno is set to EINVAL. If idx is greater than or equal to the value returned by bam_auxB_len(s), errno is set to ERANGE. In both cases, 0 will be returned. */ HTSLIB_EXPORT int64_t bam_auxB2i(const uint8_t *s, uint32_t idx); /// Get a floating-point value from an array-type tag /** @param s Pointer to the tag data, as returned by bam_aux_get(). @param idx 0-based Index into the array @return The idx'th value, or 0.0 on error. If the array is not a numeric type, errno is set to EINVAL. This can only actually happen if the input record has an invalid type field. If idx is greater than or equal to the value returned by bam_auxB_len(s), errno is set to ERANGE. In both cases, 0.0 will be returned. */ HTSLIB_EXPORT double bam_auxB2f(const uint8_t *s, uint32_t idx); /// Append tag data to a bam record /* @param b The bam record to append to. @param tag Tag identifier @param type Tag data type @param len Length of the data in bytes @param data The data to append @return 0 on success; -1 on failure. If there is not enough space to store the additional tag, errno is set to ENOMEM. If the type is invalid, errno may be set to EINVAL. errno is also set to EINVAL if the bam record's aux data is corrupt. */ HTSLIB_EXPORT int bam_aux_append(bam1_t *b, const char tag[2], char type, int len, const uint8_t *data); /// Delete tag data from a bam record /** @param b The BAM record to update @param s Pointer to the aux field to delete, as returned by bam_aux_get() Must not be NULL @return 0 on success; -1 on failure If the BAM record's aux data is corrupt, errno is set to EINVAL and this function returns -1. */ HTSLIB_EXPORT int bam_aux_del(bam1_t *b, uint8_t *s); /// Delete an aux field from a BAM record /** @param b The BAM record to update @param s Pointer to the aux field to delete, as returned by bam_aux_first()/_next()/_get(); must not be NULL @return Pointer to the following aux field, or NULL if none or on error Identical to @c bam_aux_del() apart from the return value, which is an aux iterator suitable for use with @c bam_aux_next()/etc. Whenever NULL is returned, errno will also be set: ENOENT if the aux field deleted was the record's last one; otherwise EINVAL, indicating that the BAM record's aux data is corrupt. */ HTSLIB_EXPORT uint8_t *bam_aux_remove(bam1_t *b, uint8_t *s); /// Update or add a string-type tag /* @param b The bam record to update @param tag Tag identifier @param len The length of the new string @param data The new string @return 0 on success, -1 on failure This function will not change the ordering of tags in the bam record. New tags will be appended to any existing aux records. If @p len is less than zero, the length of the input string will be calculated using strlen(). Otherwise exactly @p len bytes will be copied from @p data to make the new tag. If these bytes do not include a terminating NUL character, one will be added. (Note that versions of HTSlib up to 1.10.2 had different behaviour here and simply copied @p len bytes from data. To generate a valid tag it was necessary to ensure the last character was a NUL, and include it in @p len.) On failure, errno may be set to one of the following values: EINVAL: The bam record's aux data is corrupt or an existing tag with the given ID is not of type 'Z'. ENOMEM: The bam data needs to be expanded and either the attempt to reallocate the data buffer failed or the resulting buffer would be longer than the maximum size allowed in a bam record (2Gbytes). */ HTSLIB_EXPORT int bam_aux_update_str(bam1_t *b, const char tag[2], int len, const char *data); /// Update or add an integer tag /* @param b The bam record to update @param tag Tag identifier @param val The new value @return 0 on success, -1 on failure This function will not change the ordering of tags in the bam record. New tags will be appended to any existing aux records. On failure, errno may be set to one of the following values: EINVAL: The bam record's aux data is corrupt or an existing tag with the given ID is not of an integer type (c, C, s, S, i or I). EOVERFLOW (or ERANGE on systems that do not have EOVERFLOW): val is outside the range that can be stored in an integer bam tag (-2147483647 to 4294967295). ENOMEM: The bam data needs to be expanded and either the attempt to reallocate the data buffer failed or the resulting buffer would be longer than the maximum size allowed in a bam record (2Gbytes). */ HTSLIB_EXPORT int bam_aux_update_int(bam1_t *b, const char tag[2], int64_t val); /// Update or add a floating-point tag /* @param b The bam record to update @param tag Tag identifier @param val The new value @return 0 on success, -1 on failure This function will not change the ordering of tags in the bam record. New tags will be appended to any existing aux records. On failure, errno may be set to one of the following values: EINVAL: The bam record's aux data is corrupt or an existing tag with the given ID is not of a float type. ENOMEM: The bam data needs to be expanded and either the attempt to reallocate the data buffer failed or the resulting buffer would be longer than the maximum size allowed in a bam record (2Gbytes). */ HTSLIB_EXPORT int bam_aux_update_float(bam1_t *b, const char tag[2], float val); /// Update or add an array tag /* @param b The bam record to update @param tag Tag identifier @param type Data type (one of c, C, s, S, i, I or f) @param items Number of items @param data Pointer to data @return 0 on success, -1 on failure The type parameter indicates the how the data is interpreted: Letter code | Data type | Item Size (bytes) ----------- | --------- | ----------------- c | int8_t | 1 C | uint8_t | 1 s | int16_t | 2 S | uint16_t | 2 i | int32_t | 4 I | uint32_t | 4 f | float | 4 This function will not change the ordering of tags in the bam record. New tags will be appended to any existing aux records. The bam record will grow or shrink in order to accommodate the new data. The data parameter must not point to any data in the bam record itself or undefined behaviour may result. On failure, errno may be set to one of the following values: EINVAL: The bam record's aux data is corrupt, an existing tag with the given ID is not of an array type or the type parameter is not one of the values listed above. ENOMEM: The bam data needs to be expanded and either the attempt to reallocate the data buffer failed or the resulting buffer would be longer than the maximum size allowed in a bam record (2Gbytes). */ HTSLIB_EXPORT int bam_aux_update_array(bam1_t *b, const char tag[2], uint8_t type, uint32_t items, void *data); /************************** *** Pileup and Mpileup *** **************************/ #if !defined(BAM_NO_PILEUP) /*! @typedef @abstract Generic pileup 'client data'. @discussion The pileup iterator allows setting a constructor and destructor function, which will be called every time a sequence is fetched and discarded. This permits caching of per-sequence data in a tidy manner during the pileup process. This union is the cached data to be manipulated by the "client" (the caller of pileup). */ typedef union { void *p; int64_t i; double f; } bam_pileup_cd; /*! @typedef @abstract Structure for one alignment covering the pileup position. @field b pointer to the alignment @field qpos position of the read base at the pileup site, 0-based @field indel indel length; 0 for no indel, positive for ins and negative for del @field level the level of the read in the "viewer" mode @field is_del 1 iff the base on the padded read is a deletion @field is_head 1 iff this is the first base in the query sequence @field is_tail 1 iff this is the last base in the query sequence @field is_refskip 1 iff the base on the padded read is part of CIGAR N op @field aux (used by bcf_call_gap_prep()) @field cigar_ind index of the CIGAR operator that has just been processed @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The difference between the two functions is that the former does not set bam_pileup1_t::level, while the later does. Level helps the implementation of alignment viewers, but calculating this has some overhead. */ typedef struct bam_pileup1_t { bam1_t *b; int32_t qpos; int indel, level; uint32_t is_del:1, is_head:1, is_tail:1, is_refskip:1, /* reserved */ :1, aux:27; bam_pileup_cd cd; // generic per-struct data, owned by caller. int cigar_ind; } bam_pileup1_t; typedef int (*bam_plp_auto_f)(void *data, bam1_t *b); struct bam_plp_s; typedef struct bam_plp_s *bam_plp_t; struct bam_mplp_s; typedef struct bam_mplp_s *bam_mplp_t; /** * bam_plp_init() - sets an iterator over multiple * @func: see mplp_func in bam_plcmd.c in samtools for an example. Expected return * status: 0 on success, -1 on end, < -1 on non-recoverable errors * @data: user data to pass to @func * * The struct returned by a successful call should be freed * via bam_plp_destroy() when it is no longer needed. */ HTSLIB_EXPORT bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data); HTSLIB_EXPORT void bam_plp_destroy(bam_plp_t iter); HTSLIB_EXPORT int bam_plp_push(bam_plp_t iter, const bam1_t *b); HTSLIB_EXPORT const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp); HTSLIB_EXPORT const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp); HTSLIB_EXPORT const bam_pileup1_t *bam_plp64_next(bam_plp_t iter, int *_tid, hts_pos_t *_pos, int *_n_plp); HTSLIB_EXPORT const bam_pileup1_t *bam_plp64_auto(bam_plp_t iter, int *_tid, hts_pos_t *_pos, int *_n_plp); HTSLIB_EXPORT void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt); HTSLIB_EXPORT void bam_plp_reset(bam_plp_t iter); /** * bam_plp_constructor() - sets a callback to initialise any per-pileup1_t fields. * @plp: The bam_plp_t initialised using bam_plp_init. * @func: The callback function itself. When called, it is given * the data argument (specified in bam_plp_init), the bam * structure and a pointer to a locally allocated * bam_pileup_cd union. This union will also be present in * each bam_pileup1_t created. * The callback function should have a negative return * value to indicate an error. (Similarly for destructor.) */ HTSLIB_EXPORT void bam_plp_constructor(bam_plp_t plp, int (*func)(void *data, const bam1_t *b, bam_pileup_cd *cd)); HTSLIB_EXPORT void bam_plp_destructor(bam_plp_t plp, int (*func)(void *data, const bam1_t *b, bam_pileup_cd *cd)); /// Get pileup padded insertion sequence /** * @param p pileup data * @param ins the kstring where the insertion sequence will be written * @param del_len location for deletion length * @return the length of insertion string on success; -1 on failure. * * Fills out the kstring with the padded insertion sequence for the current * location in 'p'. If this is not an insertion site, the string is blank. * * If del_len is not NULL, the location pointed to is set to the length of * any deletion immediately following the insertion, or zero if none. */ HTSLIB_EXPORT int bam_plp_insertion(const bam_pileup1_t *p, kstring_t *ins, int *del_len) HTS_RESULT_USED; /*! @typedef @abstract An opaque type used for caching base modification state between successive calls to bam_mods_* functions. */ typedef struct hts_base_mod_state hts_base_mod_state; /// Get pileup padded insertion sequence, including base modifications /** * @param p pileup data * @param m state data for the base modification finder * @param ins the kstring where the insertion sequence will be written * @param del_len location for deletion length * @return the number of insertion string on success, with string length * being accessable via ins->l; -1 on failure. * * Fills out the kstring with the padded insertion sequence for the current * location in 'p'. If this is not an insertion site, the string is blank. * * The modification state needs to have been previously initialised using * bam_parse_basemod. It is permitted to be passed in as NULL, in which * case this function outputs identically to bam_plp_insertion. * * If del_len is not NULL, the location pointed to is set to the length of * any deletion immediately following the insertion, or zero if none. */ HTSLIB_EXPORT int bam_plp_insertion_mod(const bam_pileup1_t *p, hts_base_mod_state *m, kstring_t *ins, int *del_len) HTS_RESULT_USED; /// Create a new bam_mplp_t structure /** The struct returned by a successful call should be freed * via bam_mplp_destroy() when it is no longer needed. */ HTSLIB_EXPORT bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data); /// Set up mpileup overlap detection /** * @param iter mpileup iterator * @return 0 on success; a negative value on error * * If called, mpileup will detect overlapping * read pairs and for each base pair set the base quality of the * lower-quality base to zero, thus effectively discarding it from * calling. If the two bases are identical, the quality of the other base * is increased to the sum of their qualities (capped at 200), otherwise * it is multiplied by 0.8. */ HTSLIB_EXPORT int bam_mplp_init_overlaps(bam_mplp_t iter); HTSLIB_EXPORT void bam_mplp_destroy(bam_mplp_t iter); HTSLIB_EXPORT void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt); HTSLIB_EXPORT int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); HTSLIB_EXPORT int bam_mplp64_auto(bam_mplp_t iter, int *_tid, hts_pos_t *_pos, int *n_plp, const bam_pileup1_t **plp); HTSLIB_EXPORT void bam_mplp_reset(bam_mplp_t iter); HTSLIB_EXPORT void bam_mplp_constructor(bam_mplp_t iter, int (*func)(void *data, const bam1_t *b, bam_pileup_cd *cd)); HTSLIB_EXPORT void bam_mplp_destructor(bam_mplp_t iter, int (*func)(void *data, const bam1_t *b, bam_pileup_cd *cd)); #endif // ~!defined(BAM_NO_PILEUP) /*********************************** * BAQ calculation and realignment * ***********************************/ HTSLIB_EXPORT int sam_cap_mapq(bam1_t *b, const char *ref, hts_pos_t ref_len, int thres); // Used as flag parameter in sam_prob_realn. enum htsRealnFlags { BAQ_APPLY = 1, BAQ_EXTEND = 2, BAQ_REDO = 4, // Platform subfield, in bit position 3 onwards BAQ_AUTO = 0<<3, BAQ_ILLUMINA = 1<<3, BAQ_PACBIOCCS = 2<<3, BAQ_PACBIO = 3<<3, BAQ_ONT = 4<<3, BAQ_GENAPSYS = 5<<3 }; /// Calculate BAQ scores /** @param b BAM record @param ref Reference sequence @param ref_len Reference sequence length @param flag Flags, see description @return 0 on success \n -1 if the read was unmapped, zero length, had no quality values, did not have at least one M, X or = CIGAR operator, or included a reference skip. \n -3 if BAQ alignment has already been done and does not need to be applied, or has already been applied. \n -4 if alignment failed (most likely due to running out of memory) This function calculates base alignment quality (BAQ) values using the method described in "Improving SNP discovery by base alignment quality", Heng Li, Bioinformatics, Volume 27, Issue 8 (https://doi.org/10.1093/bioinformatics/btr076). The @param flag value can be generated using the htsRealnFlags enum, but for backwards compatibilty reasons is retained as an "int". An example usage of the enum could be this, equivalent to flag 19: sam_prob_realn(b, ref, len, BAQ_APPLY | BAQ_EXTEND | BAQ_PACBIOCCS); The following @param flag bits can be used: Bit 0 (BAQ_APPLY): Adjust the quality values using the BAQ values If set, the data in the BQ:Z tag is used to adjust the quality values, and the BQ:Z tag is renamed to ZQ:Z. If clear, and a ZQ:Z tag is present, the quality values are reverted using the data in the tag, and the tag is renamed to BQ:Z. Bit 1 (BAQ_EXTEND): Use "extended" BAQ. Changes the BAQ calculation to increase sensitivity at the expense of reduced specificity. Bit 2 (BAQ_REDO): Recalculate BAQ, even if a BQ tag is present. Force BAQ to be recalculated. Note that a ZQ:Z tag will always disable recalculation. Bits 3-10: Choose parameters tailored to a specific instrument type. One of BAQ_AUTO, BAQ_ILLUMINA, BAQ_PACBIOCCS, BAQ_PACBIO, BAQ_ONT and BAQ_GENAPSYS. The BAQ parameter tuning are still a work in progress and at the time of writing mainly consist of Illumina vs long-read technology adjustments. @bug If the input read has both BQ:Z and ZQ:Z tags, the ZQ:Z one will be removed. Depending on what previous processing happened, this may or may not be the correct thing to do. It would be wise to avoid this situation if possible. */ HTSLIB_EXPORT int sam_prob_realn(bam1_t *b, const char *ref, hts_pos_t ref_len, int flag); // --------------------------- // Base modification retrieval /*! @typedef @abstract Holds a single base modification. @field modified_base The short base code (m, h, etc) or -ChEBI (negative) @field canonical_base The canonical base referred to in the MM tag. One of A, C, G, T or N. Note this may not be the explicit base recorded in the SEQ column (esp. if N). @field strand 0 or 1, indicating + or - strand from MM tag. @field qual Quality code (256*probability), or -1 if unknown @discussion Note this doesn't hold any location data or information on which other modifications may be possible at this site. */ typedef struct hts_base_mod { int modified_base; int canonical_base; int strand; int qual; } hts_base_mod; #define HTS_MOD_UNKNOWN -1 // In MM but not ML #define HTS_MOD_UNCHECKED -2 // Not in MM and in explicit mode // Flags for bam_parse_basemod2 #define HTS_MOD_REPORT_UNCHECKED 1 /// Allocates an hts_base_mode_state. /** * @return An hts_base_mode_state pointer on success, * NULL on failure. * * This just allocates the memory. The initialisation of the contents is * done using bam_parse_basemod. Successive calls may be made to that * without the need to free and allocate a new state. * * The state be destroyed using the hts_base_mode_state_free function. */ HTSLIB_EXPORT hts_base_mod_state *hts_base_mod_state_alloc(void); /// Destroys an hts_base_mode_state. /** * @param state The base modification state pointer. * * The should have previously been created by hts_base_mode_state_alloc. */ HTSLIB_EXPORT void hts_base_mod_state_free(hts_base_mod_state *state); /// Parses the MM and ML tags out of a bam record. /** * @param b BAM alignment record * @param state The base modification state pointer. * @return 0 on success, * -1 on failure. * * This fills out the contents of the modification state, resetting the * iterator location to the first sequence base. * (Parses the draft Mm/Ml tags instead if MM and/or ML are not present.) */ HTSLIB_EXPORT int bam_parse_basemod(const bam1_t *b, hts_base_mod_state *state); /// Parses the MM and ML tags out of a bam record. /** * @param b BAM alignment record * @param state The base modification state pointer. * @param flags A bit-field controlling base modification processing * * @return 0 on success, * -1 on failure. * * This fills out the contents of the modification state, resetting the * iterator location to the first sequence base. * (Parses the draft Mm/Ml tags instead if MM and/or ML are not present.) */ HTSLIB_EXPORT int bam_parse_basemod2(const bam1_t *b, hts_base_mod_state *state, uint32_t flags); /// Returns modification status for the next base position in the query seq. /** * @param b BAM alignment record * @param state The base modification state pointer. * @param mods A supplied array for returning base modifications * @param n_mods The size of the mods array * @return The number of modifications found on success, * -1 on failure. * * This is intended to be used as an iterator, with one call per location * along the query sequence. * * If no modifications are found, the returned value is zero. * If more than n_mods modifications are found, the total found is returned. * Note this means the caller needs to check whether this is higher than * n_mods. */ HTSLIB_EXPORT int bam_mods_at_next_pos(const bam1_t *b, hts_base_mod_state *state, hts_base_mod *mods, int n_mods); /// Finds the next location containing base modifications and returns them /** * @param b BAM alignment record * @param state The base modification state pointer. * @param mods A supplied array for returning base modifications * @param n_mods The size of the mods array * @param pos Pointer holding position of modification in sequence * @return The number of modifications found on success, * 0 if no more modifications are present, * -1 on failure. * * Unlike bam_mods_at_next_pos this skips ahead to the next site * with modifications. * * If more than n_mods modifications are found, the total found is returned. * Note this means the caller needs to check whether this is higher than * n_mods. */ HTSLIB_EXPORT int bam_next_basemod(const bam1_t *b, hts_base_mod_state *state, hts_base_mod *mods, int n_mods, int *pos); /// Returns modification status for a specific query position. /** * @param b BAM alignment record * @param state The base modification state pointer. * @param mods A supplied array for returning base modifications * @param n_mods The size of the mods array * @return The number of modifications found on success, * -1 on failure. * * Note if called multipled times, qpos must be higher than the previous call. * Hence this is suitable for use from a pileup iterator. If more random * access is required, bam_parse_basemod must be called each time to reset * the state although this has an efficiency cost. * * If no modifications are found, the returned value is zero. * If more than n_mods modifications are found, the total found is returned. * Note this means the caller needs to check whether this is higher than * n_mods. */ HTSLIB_EXPORT int bam_mods_at_qpos(const bam1_t *b, int qpos, hts_base_mod_state *state, hts_base_mod *mods, int n_mods); /// Returns data about a specific modification type for the alignment record. /** * @param b BAM alignment record * @param state The base modification state pointer. * @param code Modification code. If positive this is a character code, * if negative it is a -ChEBI code. * * @param strand Boolean for top (0) or bottom (1) strand * @param implicit Boolean for whether unlisted positions should be * implicitly assumed to be unmodified, or require an * explicit score and should be considered as unknown. * Returned. * @param canonical Canonical base type associated with this modification * Returned. * * @return 0 on success or -1 if not found. The strand, implicit and canonical * fields are filled out if passed in as non-NULL pointers. */ HTSLIB_EXPORT int bam_mods_query_type(hts_base_mod_state *state, int code, int *strand, int *implicit, char *canonical); /// Returns data about the i^th modification type for the alignment record. /** * @param b BAM alignment record * @param state The base modification state pointer. * @param i Modification index, from 0 to ntype-1 * @param strand Boolean for top (0) or bottom (1) strand * @param implicit Boolean for whether unlisted positions should be * implicitly assumed to be unmodified, or require an * explicit score and should be considered as unknown. * Returned. * @param canonical Canonical base type associated with this modification * Returned. * * @return 0 on success or -1 if not found. The strand, implicit and canonical * fields are filled out if passed in as non-NULL pointers. */ HTSLIB_EXPORT int bam_mods_queryi(hts_base_mod_state *state, int i, int *strand, int *implicit, char *canonical); /// Returns the list of base modification codes provided for this /// alignment record as an array of character codes (+ve) or ChEBI numbers /// (negative). /* * @param b BAM alignment record * @param state The base modification state pointer. * @param ntype Filled out with the number of array elements returned * * @return the type array, with *ntype filled out with the size. * The array returned should not be freed. * It is a valid pointer until the state is freed using * hts_base_mod_free(). */ HTSLIB_EXPORT int *bam_mods_recorded(hts_base_mod_state *state, int *ntype); #ifdef __cplusplus } #endif #ifdef HTSLIB_SSIZE_T #undef HTSLIB_SSIZE_T #undef ssize_t #endif #endif pysam-0.23.0/htslib/htslib/synced_bcf_reader.h000066400000000000000000000403101475062545500213040ustar00rootroot00000000000000/// @file htslib/synced_bcf_reader.h /// Stream through multiple VCF files. /* Copyright (C) 2012-2017, 2019-2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* The synced_bcf_reader allows to keep multiple VCFs open and stream them using the next_line iterator in a seamless matter without worrying about chromosomes and synchronizing the sites. This is used by vcfcheck to compare multiple VCFs simultaneously and is used also for merging, creating intersections, etc. The synced_bcf_reader also provides API for reading indexed BCF/VCF, hiding differences in BCF/VCF opening, indexing and reading. Example of usage: bcf_srs_t *sr = bcf_sr_init(); bcf_sr_set_opt(sr, BCF_SR_PAIR_LOGIC, BCF_SR_PAIR_BOTH_REF); bcf_sr_set_opt(sr, BCF_SR_REQUIRE_IDX); for (i=0; ierrnum ) error("Error: %s\n", bcf_sr_strerror(sr->errnum)); bcf_sr_destroy(sr); */ #ifndef HTSLIB_SYNCED_BCF_READER_H #define HTSLIB_SYNCED_BCF_READER_H #include "hts.h" #include "vcf.h" #include "tbx.h" #ifdef __cplusplus extern "C" { #endif /* When reading multiple files in parallel, duplicate records within each file will be reordered and offered in intuitive order. For example, when reading two files, each with unsorted SNP and indel record, the reader should return the SNP records together and the indel records together. The logic of compatible records can vary depending on the application and can be set using the PAIR_* defined below. The COLLAPSE_* definitions will be deprecated in future versions, please use the PAIR_* definitions instead. */ #define COLLAPSE_NONE 0 // require the exact same set of alleles in all files #define COLLAPSE_SNPS 1 // allow different alleles, as long as they all are SNPs #define COLLAPSE_INDELS 2 // the same as above, but with indels #define COLLAPSE_ANY 4 // any combination of alleles can be returned by bcf_sr_next_line() #define COLLAPSE_SOME 8 // at least some of the ALTs must match #define COLLAPSE_BOTH (COLLAPSE_SNPS|COLLAPSE_INDELS) #define BCF_SR_PAIR_SNPS (1<<0) // allow different alleles, as long as they all are SNPs #define BCF_SR_PAIR_INDELS (1<<1) // the same as above, but with indels #define BCF_SR_PAIR_ANY (1<<2) // any combination of alleles can be returned by bcf_sr_next_line() #define BCF_SR_PAIR_SOME (1<<3) // at least some of multiallelic ALTs must match. Implied by all the others with the exception of EXACT #define BCF_SR_PAIR_SNP_REF (1<<4) // allow REF-only records with SNPs #define BCF_SR_PAIR_INDEL_REF (1<<5) // allow REF-only records with indels #define BCF_SR_PAIR_EXACT (1<<6) // require the exact same set of alleles in all files #define BCF_SR_PAIR_BOTH (BCF_SR_PAIR_SNPS|BCF_SR_PAIR_INDELS) #define BCF_SR_PAIR_BOTH_REF (BCF_SR_PAIR_SNPS|BCF_SR_PAIR_INDELS|BCF_SR_PAIR_SNP_REF|BCF_SR_PAIR_INDEL_REF) typedef enum { BCF_SR_REQUIRE_IDX, BCF_SR_PAIR_LOGIC, // combination of the PAIR_* values above BCF_SR_ALLOW_NO_IDX, // allow to proceed even if required index is not present (at the user's risk) BCF_SR_REGIONS_OVERLAP, // include overlapping records with POS outside the regions: 0=no, 1=VCF line overlap, 2=true variant overlap [1] BCF_SR_TARGETS_OVERLAP // include overlapping records with POS outside the targets: 0=no, 1=VCF line overlap, 2=true variant overlap [0] } bcf_sr_opt_t; struct bcf_sr_region_t; typedef struct bcf_sr_regions_t { // for reading from tabix-indexed file (big data) tbx_t *tbx; // tabix index hts_itr_t *itr; // tabix iterator kstring_t line; // holder of the current line, set only when reading from tabix-indexed files htsFile *file; char *fname; int is_bin; // is open in binary mode (tabix access) char **als; // parsed alleles if targets_als set and _regions_match_alleles called kstring_t als_str; // block of parsed alleles int nals, mals; // number of set alleles and the size of allocated array int als_type; // alleles type, currently VCF_SNP or VCF_INDEL // user handler to deal with skipped regions without a counterpart in VCFs void (*missed_reg_handler)(struct bcf_sr_regions_t *, void *); void *missed_reg_data; // for in-memory regions (small data) struct bcf_sr_region_t *regs; // the regions // shared by both tabix-index and in-memory regions void *seq_hash; // keys: sequence names, values: index to seqs char **seq_names; // sequence names int nseqs; // number of sequences (chromosomes) in the file int iseq; // current position: chr name, index to snames hts_pos_t start, end; // current position: start, end of the region (0-based) int prev_seq; hts_pos_t prev_start, prev_end; int overlap; // see BCF_SR_REGIONS_OVERLAP/BCF_SR_TARGETS_OVERLAP } bcf_sr_regions_t; typedef struct bcf_sr_t { htsFile *file; tbx_t *tbx_idx; hts_idx_t *bcf_idx; bcf_hdr_t *header; hts_itr_t *itr; char *fname; bcf1_t **buffer; // cached VCF records. First is the current record synced across the reader int nbuffer, mbuffer; // number of cached records (including the current record); number of allocated records int nfilter_ids, *filter_ids; // -1 for ".", otherwise filter id as returned by bcf_hdr_id2int int *samples, n_smpl; // list of columns in the order consistent with bcf_srs_t.samples } bcf_sr_t; typedef enum { open_failed, not_bgzf, idx_load_failed, file_type_error, api_usage_error, header_error, no_eof, no_memory, vcf_parse_error, bcf_read_error, noidx_error } bcf_sr_error; typedef struct bcf_srs_t { // Parameters controlling the logic int collapse; // Do not access directly, use bcf_sr_set_pairing_logic() instead char *apply_filters; // If set, sites where none of the FILTER strings is listed // will be skipped. Active only at the time of // initialization, that is during the add_reader() // calls. Therefore, each reader can be initialized with different // filters. int require_index; // Some tools do not need random access int max_unpack; // When reading VCFs and knowing some fields will not be needed, boost performance of vcf_parse1 int *has_line; // Corresponds to return value of bcf_sr_next_line but is not limited by sizeof(int). Use bcf_sr_has_line macro to query. bcf_sr_error errnum; // Auxiliary data bcf_sr_t *readers; int nreaders; int streaming; // reading mode: index-jumping or streaming int explicit_regs; // was the list of regions se by bcf_sr_set_regions or guessed from tabix index? char **samples; // List of samples bcf_sr_regions_t *regions, *targets; // see bcf_sr_set_[targets|regions] for description int targets_als; // subset to targets not only by position but also by alleles? int targets_exclude; kstring_t tmps; int n_smpl; int n_threads; // Simple multi-threaded decoding / encoding. htsThreadPool *p; // Our pool, but it can be used by others if needed. void *aux; // Opaque auxiliary data } bcf_srs_t; /** Allocate and initialize a bcf_srs_t struct. * * The bcf_srs_t struct returned by a successful call should be freed * via bcf_sr_destroy() when it is no longer needed. */ HTSLIB_EXPORT bcf_srs_t *bcf_sr_init(void); /** Destroy a bcf_srs_t struct */ HTSLIB_EXPORT void bcf_sr_destroy(bcf_srs_t *readers); HTSLIB_EXPORT char *bcf_sr_strerror(int errnum); HTSLIB_EXPORT int bcf_sr_set_opt(bcf_srs_t *readers, bcf_sr_opt_t opt, ...); /** * bcf_sr_set_threads() - allocates a thread-pool for use by the synced reader. * @n_threads: size of thread pool * * Returns 0 if the call succeeded, or <0 on error. */ HTSLIB_EXPORT int bcf_sr_set_threads(bcf_srs_t *files, int n_threads); /** Deallocates thread memory, if owned by us. */ HTSLIB_EXPORT void bcf_sr_destroy_threads(bcf_srs_t *files); /** * bcf_sr_add_reader() - open new reader * @readers: holder of the open readers * @fname: the VCF file * * Returns 1 if the call succeeded, or 0 on error. * * See also the bcf_srs_t data structure for parameters controlling * the reader's logic. */ HTSLIB_EXPORT int bcf_sr_add_reader(bcf_srs_t *readers, const char *fname); HTSLIB_EXPORT void bcf_sr_remove_reader(bcf_srs_t *files, int i); /** * bcf_sr_next_line() - the iterator * @readers: holder of the open readers * * Returns the number of readers which have the current line * (bcf_sr_t.buffer[0]) set at this position. Use the bcf_sr_has_line macro to * determine which of the readers are set. */ HTSLIB_EXPORT int bcf_sr_next_line(bcf_srs_t *readers); #define bcf_sr_has_line(readers, i) (readers)->has_line[i] #define bcf_sr_get_line(_readers, i) ((_readers)->has_line[i] ? ((_readers)->readers[i].buffer[0]) : (bcf1_t *) NULL) #define bcf_sr_swap_line(_readers, i, lieu) { bcf1_t *tmp = lieu; lieu = (_readers)->readers[i].buffer[0]; (_readers)->readers[i].buffer[0] = tmp; } #define bcf_sr_region_done(_readers,i) (!(_readers)->has_line[i] && !(_readers)->readers[i].nbuffer ? 1 : 0) #define bcf_sr_get_header(_readers, i) (_readers)->readers[i].header #define bcf_sr_get_reader(_readers, i) &((_readers)->readers[i]) /** * bcf_sr_seek() - set all readers to selected position * @seq: sequence name; NULL to seek to start * @pos: 0-based coordinate */ HTSLIB_EXPORT int bcf_sr_seek(bcf_srs_t *readers, const char *seq, hts_pos_t pos); /** * bcf_sr_set_samples() - sets active samples * @readers: holder of the open readers * @samples: this can be one of: file name with one sample per line; * or column-separated list of samples; or '-' for a list of * samples shared by all files. If first character is the * exclamation mark, all but the listed samples are included. * @is_file: 0: list of samples; 1: file with sample names * * Returns 1 if the call succeeded, or 0 on error. */ HTSLIB_EXPORT int bcf_sr_set_samples(bcf_srs_t *readers, const char *samples, int is_file); /** * bcf_sr_set_targets(), bcf_sr_set_regions() - init targets/regions * @readers: holder of the open readers * @targets: list of regions, one-based and inclusive. * @is_fname: 0: targets is a comma-separated list of regions (chr,chr:from-to) * 1: targets is a tabix indexed file with a list of regions * ( or ) * * Returns 0 if the call succeeded, or -1 on error. * * Both functions behave the same way, unlisted positions will be skipped by * bcf_sr_next_line(). However, there is an important difference: regions use * index to jump to desired positions while targets streams the whole files * and merely skip unlisted positions. * * Moreover, bcf_sr_set_targets() accepts an optional parameter $alleles which * is interpreted as a 1-based column index in the tab-delimited file where * alleles are listed. This in principle enables to perform the COLLAPSE_* * logic also with tab-delimited files. However, the current implementation * considers the alleles merely as a suggestion for prioritizing one of possibly * duplicate VCF lines. It is up to the caller to examine targets->als if * perfect match is sought after. Note that the duplicate positions in targets * file are currently not supported. * Targets (but not regions) can be prefixed with "^" to request logical complement, * for example "^X,Y,MT" indicates that sequences X, Y and MT should be skipped. * * API notes: * - bcf_sr_set_targets MUST be called before the first call to bcf_sr_add_reader() * - calling bcf_sr_set_regions AFTER readers have been initialized will * reposition the readers and discard all previous regions. */ HTSLIB_EXPORT int bcf_sr_set_targets(bcf_srs_t *readers, const char *targets, int is_file, int alleles); HTSLIB_EXPORT int bcf_sr_set_regions(bcf_srs_t *readers, const char *regions, int is_file); /* * bcf_sr_regions_init() * @regions: regions can be either a comma-separated list of regions * (chr|chr:pos|chr:from-to|chr:from-) or VCF, BED, or * tab-delimited file (the default). Uncompressed files * are stored in memory while bgzip-compressed and tabix-indexed * region files are streamed. * @is_file: 0: regions is a comma-separated list of regions * (chr|chr:pos|chr:from-to|chr:from-) * 1: VCF, BED or tab-delimited file * @chr, from, to: * Column indexes of chromosome, start position and end position * in the tab-delimited file. The positions are 1-based and * inclusive. * These parameters are ignored when reading from VCF, BED or * tabix-indexed files. When end position column is not present, * supply 'from' in place of 'to'. When 'to' is negative, first * abs(to) will be attempted and if that fails, 'from' will be used * instead. * If chromosome name contains the characters ':' or '-', it should * be put in curly brackets, for example as "{weird-chr-name:1-2}:1000-2000" * * The bcf_sr_regions_t struct returned by a successful call should be freed * via bcf_sr_regions_destroy() when it is no longer needed. */ HTSLIB_EXPORT bcf_sr_regions_t *bcf_sr_regions_init(const char *regions, int is_file, int chr, int from, int to); HTSLIB_EXPORT void bcf_sr_regions_destroy(bcf_sr_regions_t *regions); /* * bcf_sr_regions_seek() - seek to the chromosome block * * Returns 0 on success or -1 on failure. Sets reg->seq appropriately and * reg->start,reg->end to -1. */ HTSLIB_EXPORT int bcf_sr_regions_seek(bcf_sr_regions_t *regions, const char *chr); /* * bcf_sr_regions_next() - retrieves next region. Returns 0 on success and -1 * when all regions have been read. The fields reg->seq, reg->start and * reg->end are filled with the genomic coordinates on success or with * NULL,-1,-1 when no region is available. The coordinates are 0-based, * inclusive. */ HTSLIB_EXPORT int bcf_sr_regions_next(bcf_sr_regions_t *reg); /* * bcf_sr_regions_overlap() - checks if the interval overlaps any of * the regions, the coordinates are 0-based, inclusive. The coordinate queries * must come in ascending order. * * Returns 0 if the position is in regions; -1 if the position is not in the * regions and more regions exist; -2 if not in the regions and there are no more * regions left. */ HTSLIB_EXPORT int bcf_sr_regions_overlap(bcf_sr_regions_t *reg, const char *seq, hts_pos_t start, hts_pos_t end); /* * bcf_sr_regions_flush() - calls repeatedly regs->missed_reg_handler() until * all remaining records are processed. * Returns 0 on success, <0 on error. */ HTSLIB_EXPORT int bcf_sr_regions_flush(bcf_sr_regions_t *regs); #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/htslib/tbx.h000066400000000000000000000116001475062545500164600ustar00rootroot00000000000000/// @file htslib/tbx.h /// Tabix API functions. /* Copyright (C) 2009, 2012-2015, 2019 Genome Research Ltd. Copyright (C) 2010, 2012 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTSLIB_TBX_H #define HTSLIB_TBX_H #include "hts.h" #ifdef __cplusplus extern "C" { #endif #define TBX_MAX_SHIFT 31 #define TBX_GENERIC 0 #define TBX_SAM 1 #define TBX_VCF 2 #define TBX_GAF 3 #define TBX_UCSC 0x10000 typedef struct tbx_conf_t { int32_t preset; int32_t sc, bc, ec; // seq col., beg col. and end col. int32_t meta_char, line_skip; } tbx_conf_t; typedef struct tbx_t { tbx_conf_t conf; hts_idx_t *idx; void *dict; } tbx_t; HTSLIB_EXPORT extern const tbx_conf_t tbx_conf_gff, tbx_conf_bed, tbx_conf_psltbl, tbx_conf_sam, tbx_conf_vcf, tbx_conf_gaf; #define tbx_itr_destroy(iter) hts_itr_destroy(iter) #define tbx_itr_queryi(tbx, tid, beg, end) hts_itr_query((tbx)->idx, (tid), (beg), (end), tbx_readrec) #define tbx_itr_querys(tbx, s) hts_itr_querys((tbx)->idx, (s), (hts_name2id_f)(tbx_name2id), (tbx), hts_itr_query, tbx_readrec) #define tbx_itr_next(htsfp, tbx, itr, r) hts_itr_next(hts_get_bgzfp(htsfp), (itr), (r), (tbx)) #define tbx_bgzf_itr_next(bgzfp, tbx, itr, r) hts_itr_next((bgzfp), (itr), (r), (tbx)) HTSLIB_EXPORT int tbx_name2id(tbx_t *tbx, const char *ss); /* Internal helper function used by tbx_itr_next() */ HTSLIB_EXPORT BGZF *hts_get_bgzfp(htsFile *fp); HTSLIB_EXPORT int tbx_readrec(BGZF *fp, void *tbxv, void *sv, int *tid, hts_pos_t *beg, hts_pos_t *end); /// Build an index of the lines in a BGZF-compressed file /** The index struct returned by a successful call should be freed via tbx_destroy() when it is no longer needed. */ HTSLIB_EXPORT tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf); /* * All tbx_index_build* methods return: 0 (success), -1 (general failure) or -2 (compression not BGZF) */ HTSLIB_EXPORT int tbx_index_build(const char *fn, int min_shift, const tbx_conf_t *conf); HTSLIB_EXPORT int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf); HTSLIB_EXPORT int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_conf_t *conf); /// Load or stream a .tbi or .csi index /** @param fn Name of the data file corresponding to the index Equivalent to tbx_index_load3(fn, NULL, HTS_IDX_SAVE_REMOTE); */ HTSLIB_EXPORT tbx_t *tbx_index_load(const char *fn); /// Load or stream a .tbi or .csi index /** @param fn Name of the data file corresponding to the index @param fnidx Name of the indexed file @return The index, or NULL if an error occurred If @p fnidx is NULL, the index name will be derived from @p fn. Equivalent to tbx_index_load3(fn, fnidx, HTS_IDX_SAVE_REMOTE); */ HTSLIB_EXPORT tbx_t *tbx_index_load2(const char *fn, const char *fnidx); /// Load or stream a .tbi or .csi index /** @param fn Name of the data file corresponding to the index @param fnidx Name of the indexed file @param flags Flags to alter behaviour (see description) @return The index, or NULL if an error occurred If @p fnidx is NULL, the index name will be derived from @p fn. The @p flags parameter can be set to a combination of the following values: HTS_IDX_SAVE_REMOTE Save a local copy of any remote indexes HTS_IDX_SILENT_FAIL Fail silently if the index is not present The index struct returned by a successful call should be freed via tbx_destroy() when it is no longer needed. */ HTSLIB_EXPORT tbx_t *tbx_index_load3(const char *fn, const char *fnidx, int flags); HTSLIB_EXPORT const char **tbx_seqnames(tbx_t *tbx, int *n); // free the array but not the values HTSLIB_EXPORT void tbx_destroy(tbx_t *tbx); #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/htslib/thread_pool.h000066400000000000000000000307131475062545500201710ustar00rootroot00000000000000/// @file htslib/thread_pool.h /// Thread pool for multi-threading applications. /* Copyright (c) 2013-2017, 2019, 2020 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* * This file implements a thread pool for multi-threading applications. It * consists of two distinct interfaces: thread pools and thread process * queues (a queue of both jobs to-do and of the results of completed jobs). * Do not confuse "process" here with a unix PID; rather it is analogous to a * program reading a stream of data blocks, processing them in some manner, * and outputting a stream of new data blocks. * * The pool of threads is given a function pointer and void* data to pass in. * This means the pool can run jobs of multiple types, albeit first come * first served with no job scheduling except to pick tasks for the * processes that have room to store the result. * * Upon completion, the return value from the function pointer is * added to back to the process result queue if required. We may have * multiple "processes" in use for the one pool. * * To see example usage, please look at the #ifdef TEST_MAIN code in * thread_pool.c. */ #ifndef HTSLIB_THREAD_POOL_H #define HTSLIB_THREAD_POOL_H #include "hts_defs.h" #ifdef __cplusplus extern "C" { #endif /*----------------------------------------------------------------------------- * Opaque data types. * * Actual definitions are in thread_pool_internal.h, but these should only * be used by thread_pool.c itself. */ /* * An hts_tpool_process implements a queue of input jobs to process and a * queue of resulting output post-processing. Internally it consists of two * buffered queues, analogous to the pipes in a unix pipeline: * ...input | process | output... * * Both input and output queues have size limits to prevent either queue from * growing too large and serial numbers to ensure sequential consumption of * the output. * * The thread pool may have many heterogeneous tasks, each using its own * process mixed into the same thread pool. */ typedef struct hts_tpool_process hts_tpool_process; /* * The single pool structure itself. * * This knows nothing about the nature of the jobs or where their output is * going, but it maintains a list of process-queues associated with this pool * from which the jobs are taken. */ typedef struct hts_tpool hts_tpool; /* * An output, after job has executed. */ typedef struct hts_tpool_result hts_tpool_result; /*----------------------------------------------------------------------------- * Thread pool external functions */ /* * Creates a worker pool with n worker threads. * * Returns pool pointer on success; * NULL on failure * * The hts_tpool struct returned by a successful call should be freed * via hts_tpool_destroy() when it is no longer needed. */ HTSLIB_EXPORT hts_tpool *hts_tpool_init(int n); /* * Returns the number of requested threads for a pool. */ HTSLIB_EXPORT int hts_tpool_size(hts_tpool *p); /// Add an item to the work pool. /** * @param p Thread pool * @param q Process queue * @param func Function run by the thread pool * @param arg Data for use by func() * @return 0 on success * -1 on failure */ // FIXME: should this drop the hts_tpool*p argument? It's just q->p HTSLIB_EXPORT int hts_tpool_dispatch(hts_tpool *p, hts_tpool_process *q, void *(*func)(void *arg), void *arg); /// Add an item to the work pool, with nonblocking option. /** * @param p Thread pool * @param q Process queue * @param func Function run by the thread pool * @param arg Data for use by func() * @param nonblock Non-blocking flag (see description) * @return 0 on success * -1 on failure * * The @p nonblock parameter can take one of the following values: * 0 => block if input queue is full * +1 => don't block if input queue is full, but do not add task * -1 => add task regardless of whether queue is full (over-size) * * If @p nonblock is +1 and the queue is full, -1 will be returned and * `errno` is set to `EAGAIN`. */ HTSLIB_EXPORT int hts_tpool_dispatch2(hts_tpool *p, hts_tpool_process *q, void *(*func)(void *arg), void *arg, int nonblock); /// Add an item to the work pool, with nonblocking and cleanup callbacks. /** * @param p Thread pool * @param q Process queue * @param exec_func Function run by the thread pool * @param arg Data for use by func() * @param job_cleanup Callback to clean up when discarding jobs * @param result_cleanup Callback to clean up when discarding result data * @param nonblock Non-blocking flag (see description) * @return 0 on success * -1 on failure * * The @p nonblock parameter can take one of the following values: * 0 => block if input queue is full * +1 => don't block if input queue is full, but do not add task * -1 => add task regardless of whether queue is full (over-size) * * If @p nonblock is +1 and the queue is full, -1 will be returned and * `errno` is set to `EAGAIN`. * * The job_cleanup() and result_cleanup() callbacks are used when discarding * data from a queue, for example when calling hts_tpool_process_reset() * or hts_tpool_process_destroy(). * * If not NULL, job_cleanup() will be called for each pending job with the * value of @p arg that was set for that job. This can be used to free * any data associated with @p arg, and also @p arg itself. * * Similarly, result_cleanup() can be used to free any results left by * jobs that had started before hts_tpool_process_reset() was called. * The argument passed to result_cleanup() is the pointer that would * have been returned by calling hts_tpool_result_data() on the result * when pulled from the queue. * * job_cleanup() and result_cleanup() are only called when discarding jobs. * For jobs that are processed normally, it is the responsibility of * exec_func() and / or consumers of any results to do any cleaning up * necessary. */ HTSLIB_EXPORT int hts_tpool_dispatch3(hts_tpool *p, hts_tpool_process *q, void *(*exec_func)(void *arg), void *arg, void (*job_cleanup)(void *arg), void (*result_cleanup)(void *data), int nonblock); /* * Wakes up a single thread stuck in dispatch and make it return with * errno EAGAIN. */ HTSLIB_EXPORT void hts_tpool_wake_dispatch(hts_tpool_process *q); /* * Flushes the process-queue, but doesn't exit. This simply drains the queue * and ensures all worker threads have finished their current tasks * associated with this process. * * NOT: This does not mean the worker threads are not executing jobs in * another process-queue. * * Returns 0 on success; * -1 on failure */ HTSLIB_EXPORT int hts_tpool_process_flush(hts_tpool_process *q); /* * Resets a process to the initial state. * * This removes any queued up input jobs, disables any notification of * new results/output, flushes what is left and then discards any * queued output. Anything consumer stuck in a wait on results to * appear should stay stuck and will only wake up when new data is * pushed through the queue. * * Returns 0 on success; * -1 on failure */ HTSLIB_EXPORT int hts_tpool_process_reset(hts_tpool_process *q, int free_results); /* Returns the process queue size */ HTSLIB_EXPORT int hts_tpool_process_qsize(hts_tpool_process *q); /* * Destroys a thread pool. The threads are joined into the main * thread so they will finish their current work load. */ HTSLIB_EXPORT void hts_tpool_destroy(hts_tpool *p); /* * Destroys a thread pool without waiting on jobs to complete. * Use hts_tpool_kill(p) to quickly exit after a fatal error. */ HTSLIB_EXPORT void hts_tpool_kill(hts_tpool *p); /* * Pulls the next item off the process result queue. The caller should free * it (and any internals as appropriate) after use. This doesn't wait for a * result to be present. * * Results will be returned in strict order. * * Returns hts_tpool_result pointer if a result is ready. * NULL if not. */ HTSLIB_EXPORT hts_tpool_result *hts_tpool_next_result(hts_tpool_process *q); /* * Pulls the next item off the process result queue. The caller should free * it (and any internals as appropriate) after use. This will wait for * a result to be present if none are currently available. * * Results will be returned in strict order. * * Returns hts_tpool_result pointer if a result is ready. * NULL on error or during shutdown. */ HTSLIB_EXPORT hts_tpool_result *hts_tpool_next_result_wait(hts_tpool_process *q); /* * Frees a result 'r' and if free_data is true also frees * the internal r->data result too. */ HTSLIB_EXPORT void hts_tpool_delete_result(hts_tpool_result *r, int free_data); /* * Returns the data portion of a hts_tpool_result, corresponding * to the actual "result" itself. */ HTSLIB_EXPORT void *hts_tpool_result_data(hts_tpool_result *r); /* * Initialises a thread process-queue. * * In_only, if true, indicates that the process generates does not need to * hold any output. Otherwise an output queue is used to store the results * of processing each input job. * * Results hts_tpool_process pointer on success; * NULL on failure * * The hts_tpool_process struct returned by a successful call should be freed * via hts_tpool_process_destroy() when it is no longer needed. */ HTSLIB_EXPORT hts_tpool_process *hts_tpool_process_init(hts_tpool *p, int qsize, int in_only); /* Deallocates memory for a thread process-queue. * Must be called before the thread pool is destroyed. */ HTSLIB_EXPORT void hts_tpool_process_destroy(hts_tpool_process *q); /* * Returns true if there are no items in the process results queue and * also none still pending. */ HTSLIB_EXPORT int hts_tpool_process_empty(hts_tpool_process *q); /* * Returns the number of completed jobs in the process results queue. */ HTSLIB_EXPORT int hts_tpool_process_len(hts_tpool_process *q); /* * Returns the number of completed jobs in the process results queue plus the * number running and queued up to run. */ HTSLIB_EXPORT int hts_tpool_process_sz(hts_tpool_process *q); /* * Shutdown a process. * * This sets the shutdown flag and wakes any threads waiting on process * condition variables. */ HTSLIB_EXPORT void hts_tpool_process_shutdown(hts_tpool_process *q); /* * Returns whether this process queue has been shutdown. * Return value of 1 signifies normal shutdown while >1 signifies it * was shutdown due to an error condition. */ HTSLIB_EXPORT int hts_tpool_process_is_shutdown(hts_tpool_process *q); /* * Attach and detach a thread process-queue with / from the thread pool * scheduler. * * We need to do attach after making a thread process, but may also wish * to temporarily detach if we wish to stop running jobs on a specific * process while permitting other process to continue. */ HTSLIB_EXPORT void hts_tpool_process_attach(hts_tpool *p, hts_tpool_process *q); HTSLIB_EXPORT void hts_tpool_process_detach(hts_tpool *p, hts_tpool_process *q); /* * Increment and decrement the reference count in a process-queue. * If the queue is being driven from two external (non thread-pool) * threads, eg "main" and a "reader", this permits each end to * decrement its use of the process-queue independently. */ HTSLIB_EXPORT void hts_tpool_process_ref_incr(hts_tpool_process *q); HTSLIB_EXPORT void hts_tpool_process_ref_decr(hts_tpool_process *q); #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/htslib/vcf.h000066400000000000000000002065551475062545500164600ustar00rootroot00000000000000/// @file htslib/vcf.h /// High-level VCF/BCF variant calling file operations. /* Copyright (C) 2012, 2013 Broad Institute. Copyright (C) 2012-2020, 2022-2023 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* todo: - make the function names consistent - provide calls to abstract away structs as much as possible */ #ifndef HTSLIB_VCF_H #define HTSLIB_VCF_H #include #include #include #include "hts.h" #include "kstring.h" #include "hts_defs.h" #include "hts_endian.h" /* Included only for backwards compatibility with e.g. bcftools 1.10 */ #include #ifdef __cplusplus extern "C" { #endif /***************** * Header struct * *****************/ #define BCF_HL_FLT 0 // header line #define BCF_HL_INFO 1 #define BCF_HL_FMT 2 #define BCF_HL_CTG 3 #define BCF_HL_STR 4 // structured header line TAG= #define BCF_HL_GEN 5 // generic header line #define BCF_HT_FLAG 0 // header type #define BCF_HT_INT 1 #define BCF_HT_REAL 2 #define BCF_HT_STR 3 #define BCF_HT_LONG (BCF_HT_INT | 0x100) // BCF_HT_INT, but for int64_t values; VCF only! #define BCF_VL_FIXED 0 // variable length #define BCF_VL_VAR 1 #define BCF_VL_A 2 #define BCF_VL_G 3 #define BCF_VL_R 4 /* === Dictionary === The header keeps three dictionaries. The first keeps IDs in the "FILTER/INFO/FORMAT" lines, the second keeps the sequence names and lengths in the "contig" lines and the last keeps the sample names. bcf_hdr_t::dict[] is the actual hash table, which is opaque to the end users. In the hash table, the key is the ID or sample name as a C string and the value is a bcf_idinfo_t struct. bcf_hdr_t::id[] points to key-value pairs in the hash table in the order that they appear in the VCF header. bcf_hdr_t::n[] is the size of the hash table or, equivalently, the length of the id[] arrays. */ #define BCF_DT_ID 0 // dictionary type #define BCF_DT_CTG 1 #define BCF_DT_SAMPLE 2 // Complete textual representation of a header line typedef struct bcf_hrec_t { int type; // One of the BCF_HL_* type char *key; // The part before '=', i.e. FILTER/INFO/FORMAT/contig/fileformat etc. char *value; // Set only for generic lines, NULL for FILTER/INFO, etc. int nkeys; // Number of structured fields char **keys, **vals; // The key=value pairs } bcf_hrec_t; typedef struct bcf_idinfo_t { uint64_t info[3]; // stores Number:20, var:4, Type:4, ColType:4 in info[0..2] // for BCF_HL_FLT,INFO,FMT and contig length in info[0] for BCF_HL_CTG bcf_hrec_t *hrec[3]; int id; } bcf_idinfo_t; typedef struct bcf_idpair_t { const char *key; const bcf_idinfo_t *val; } bcf_idpair_t; // Note that bcf_hdr_t structs must always be created via bcf_hdr_init() typedef struct bcf_hdr_t { int32_t n[3]; // n:the size of the dictionary block in use, (allocated size, m, is below to preserve ABI) bcf_idpair_t *id[3]; void *dict[3]; // ID dictionary, contig dict and sample dict char **samples; bcf_hrec_t **hrec; int nhrec, dirty; int ntransl, *transl[2]; // for bcf_translate() int nsamples_ori; // for bcf_hdr_set_samples() uint8_t *keep_samples; kstring_t mem; int32_t m[3]; // m: allocated size of the dictionary block in use (see n above) } bcf_hdr_t; HTSLIB_EXPORT extern uint8_t bcf_type_shift[]; /************** * VCF record * **************/ #define BCF_BT_NULL 0 #define BCF_BT_INT8 1 #define BCF_BT_INT16 2 #define BCF_BT_INT32 3 #define BCF_BT_INT64 4 // Unofficial, for internal use only. #define BCF_BT_FLOAT 5 #define BCF_BT_CHAR 7 #define VCF_REF 0 #define VCF_SNP (1<<0) #define VCF_MNP (1<<1) #define VCF_INDEL (1<<2) #define VCF_OTHER (1<<3) #define VCF_BND (1<<4) // breakend #define VCF_OVERLAP (1<<5) // overlapping deletion, ALT=* #define VCF_INS (1<<6) // implies VCF_INDEL #define VCF_DEL (1<<7) // implies VCF_INDEL #define VCF_ANY (VCF_SNP|VCF_MNP|VCF_INDEL|VCF_OTHER|VCF_BND|VCF_OVERLAP|VCF_INS|VCF_DEL) // any variant type (but not VCF_REF) typedef struct bcf_variant_t { int type, n; // variant type and the number of bases affected, negative for deletions } bcf_variant_t; typedef struct bcf_fmt_t { int id; // id: numeric tag id, the corresponding string is bcf_hdr_t::id[BCF_DT_ID][$id].key int n, size, type; // n: number of values per-sample; size: number of bytes per-sample; type: one of BCF_BT_* types uint8_t *p; // same as vptr and vptr_* in bcf_info_t below uint32_t p_len; uint32_t p_off:31, p_free:1; } bcf_fmt_t; typedef struct bcf_info_t { int key; // key: numeric tag id, the corresponding string is bcf_hdr_t::id[BCF_DT_ID][$key].key int type; // type: one of BCF_BT_* types union { int64_t i; // integer value float f; // float value } v1; // only set if $len==1; for easier access uint8_t *vptr; // pointer to data array in bcf1_t->shared.s, excluding the size+type and tag id bytes uint32_t vptr_len; // length of the vptr block or, when set, of the vptr_mod block, excluding offset uint32_t vptr_off:31, // vptr offset, i.e., the size of the INFO key plus size+type bytes vptr_free:1; // indicates that vptr-vptr_off must be freed; set only when modified and the new // data block is bigger than the original int len; // vector length, 1 for scalars } bcf_info_t; #define BCF1_DIRTY_ID 1 #define BCF1_DIRTY_ALS 2 #define BCF1_DIRTY_FLT 4 #define BCF1_DIRTY_INF 8 typedef struct bcf_dec_t { int m_fmt, m_info, m_id, m_als, m_allele, m_flt; // allocated size (high-water mark); do not change int n_flt; // Number of FILTER fields int *flt; // FILTER keys in the dictionary char *id, *als; // ID and REF+ALT block (\0-separated) char **allele; // allele[0] is the REF (allele[] pointers to the als block); all null terminated bcf_info_t *info; // INFO bcf_fmt_t *fmt; // FORMAT and individual sample bcf_variant_t *var; // $var and $var_type set only when set_variant_types called int n_var, var_type; int shared_dirty; // if set, shared.s must be recreated on BCF output int indiv_dirty; // if set, indiv.s must be recreated on BCF output } bcf_dec_t; #define BCF_ERR_CTG_UNDEF 1 #define BCF_ERR_TAG_UNDEF 2 #define BCF_ERR_NCOLS 4 #define BCF_ERR_LIMITS 8 #define BCF_ERR_CHAR 16 #define BCF_ERR_CTG_INVALID 32 #define BCF_ERR_TAG_INVALID 64 /// Get error description for bcf error code /** @param errorcode The error code which is to be described @param buffer The buffer in which description to be added @param maxbuffer The size of buffer passed @return NULL on invalid buffer; buffer on other cases The buffer will be an empty string when @p errorcode is 0. Description of errors present in code will be appended to @p buffer with ',' separation. The buffer has to be at least 4 characters long. NULL will be returned if it is smaller or when buffer is NULL. '...' will be appended if the description doesn't fit in the given buffer. */ HTSLIB_EXPORT const char *bcf_strerror(int errorcode, char *buffer, size_t maxbuffer); /* The bcf1_t structure corresponds to one VCF/BCF line. Reading from VCF file is slower because the string is first to be parsed, packed into BCF line (done in vcf_parse), then unpacked into internal bcf1_t structure. If it is known in advance that some of the fields will not be required (notably the sample columns), parsing of these can be skipped by setting max_unpack appropriately. Similarly, it is fast to output a BCF line because the columns (kept in shared.s, indiv.s, etc.) are written directly by bcf_write, whereas a VCF line must be formatted in vcf_format. */ typedef struct bcf1_t { hts_pos_t pos; // POS hts_pos_t rlen; // length of REF int32_t rid; // CHROM float qual; // QUAL uint32_t n_info:16, n_allele:16; uint32_t n_fmt:8, n_sample:24; kstring_t shared, indiv; bcf_dec_t d; // lazy evaluation: $d is not generated by bcf_read(), but by explicitly calling bcf_unpack() int max_unpack; // Set to BCF_UN_STR, BCF_UN_FLT, or BCF_UN_INFO to boost performance of vcf_parse when some of the fields won't be needed int unpacked; // remember what has been unpacked to allow calling bcf_unpack() repeatedly without redoing the work int unpack_size[3]; // the original block size of ID, REF+ALT and FILTER int errcode; // one of BCF_ERR_* codes } bcf1_t; /******* * API * *******/ /*********************************************************************** * BCF and VCF I/O * * A note about naming conventions: htslib internally represents VCF * records as bcf1_t data structures, therefore most functions are * prefixed with bcf_. There are a few exceptions where the functions must * be aware of both BCF and VCF worlds, such as bcf_parse vs vcf_parse. In * these cases, functions prefixed with bcf_ are more general and work * with both BCF and VCF. * ***********************************************************************/ /** These macros are defined only for consistency with other parts of htslib */ #define bcf_init1() bcf_init() #define bcf_read1(fp,h,v) bcf_read((fp),(h),(v)) #define vcf_read1(fp,h,v) vcf_read((fp),(h),(v)) #define bcf_write1(fp,h,v) bcf_write((fp),(h),(v)) #define vcf_write1(fp,h,v) vcf_write((fp),(h),(v)) #define bcf_destroy1(v) bcf_destroy(v) #define bcf_empty1(v) bcf_empty(v) #define vcf_parse1(s,h,v) vcf_parse((s),(h),(v)) #define bcf_clear1(v) bcf_clear(v) #define vcf_format1(h,v,s) vcf_format((h),(v),(s)) /** * bcf_hdr_init() - create an empty BCF header. * @param mode "r" or "w" * * When opened for writing, the mandatory fileFormat and * FILTER=PASS lines are added automatically. * * The bcf_hdr_t struct returned by a successful call should be freed * via bcf_hdr_destroy() when it is no longer needed. */ HTSLIB_EXPORT bcf_hdr_t *bcf_hdr_init(const char *mode); /** Destroy a BCF header struct */ HTSLIB_EXPORT void bcf_hdr_destroy(bcf_hdr_t *h); /** Allocate and initialize a bcf1_t object. * * The bcf1_t struct returned by a successful call should be freed * via bcf_destroy() when it is no longer needed. */ HTSLIB_EXPORT bcf1_t *bcf_init(void); /** Deallocate a bcf1_t object */ HTSLIB_EXPORT void bcf_destroy(bcf1_t *v); /** * Same as bcf_destroy() but frees only the memory allocated by bcf1_t, * not the bcf1_t object itself. */ HTSLIB_EXPORT void bcf_empty(bcf1_t *v); /** * Make the bcf1_t object ready for next read. Intended mostly for * internal use, the user should rarely need to call this function * directly. */ HTSLIB_EXPORT void bcf_clear(bcf1_t *v); /** bcf_open and vcf_open mode: please see hts_open() in hts.h */ typedef htsFile vcfFile; #define bcf_open(fn, mode) hts_open((fn), (mode)) #define vcf_open(fn, mode) hts_open((fn), (mode)) #define bcf_flush(fp) hts_flush((fp)) #define bcf_close(fp) hts_close(fp) #define vcf_close(fp) hts_close(fp) /// Read a VCF or BCF header /** @param fp The file to read the header from @return Pointer to a populated header structure on success; NULL on failure The bcf_hdr_t struct returned by a successful call should be freed via bcf_hdr_destroy() when it is no longer needed. */ HTSLIB_EXPORT bcf_hdr_t *bcf_hdr_read(htsFile *fp) HTS_RESULT_USED; /** * bcf_hdr_set_samples() - for more efficient VCF parsing when only one/few samples are needed * @param samples samples to include or exclude from file or as a comma-separated string. * LIST|FILE .. select samples in list/file * ^LIST|FILE .. exclude samples from list/file * - .. include all samples * NULL .. exclude all samples * @param is_file @p samples is a file (1) or a comma-separated list (0) * * The bottleneck of VCF reading is parsing of genotype fields. If the * reader knows in advance that only subset of samples is needed (possibly * no samples at all), the performance of bcf_read() can be significantly * improved by calling bcf_hdr_set_samples after bcf_hdr_read(). * The function bcf_read() will subset the VCF/BCF records automatically * with the notable exception when reading records via bcf_itr_next(). * In this case, bcf_subset_format() must be called explicitly, because * bcf_readrec() does not see the header. * * Returns 0 on success, -1 on error or a positive integer if the list * contains samples not present in the VCF header. In such a case, the * return value is the index of the offending sample. */ HTSLIB_EXPORT int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file) HTS_RESULT_USED; HTSLIB_EXPORT int bcf_subset_format(const bcf_hdr_t *hdr, bcf1_t *rec); /// Write a VCF or BCF header /** @param fp Output file @param h The header to write @return 0 on success; -1 on failure */ HTSLIB_EXPORT int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h) HTS_RESULT_USED; /** * Parse VCF line contained in kstring and populate the bcf1_t struct * The line must not end with \n or \r characters. */ HTSLIB_EXPORT int vcf_parse(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v); /** * Complete the file opening mode, according to its extension. * @param mode Preallocated mode string to be completed. * @param fn File name to be opened. * @param format Format string (vcf|bcf|vcf.gz) * @return 0 on success; -1 on failure */ HTSLIB_EXPORT int vcf_open_mode(char *mode, const char *fn, const char *format); /** The opposite of vcf_parse. It should rarely be called directly, see vcf_write */ HTSLIB_EXPORT int vcf_format(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s); /// Read next VCF or BCF record /** @param fp The file to read the record from @param h The header for the vcf/bcf file @param v The bcf1_t structure to populate @return 0 on success; -1 on end of file; < -1 on critical error On errors which are not critical for reading, such as missing header definitions in vcf files, zero will be returned but v->errcode will have been set to one of BCF_ERR* codes and must be checked before calling bcf_write(). */ HTSLIB_EXPORT int bcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) HTS_RESULT_USED; /** * bcf_unpack() - unpack/decode a BCF record (fills the bcf1_t::d field) * * Note that bcf_unpack() must be called even when reading VCF. It is safe * to call the function repeatedly, it will not unpack the same field * twice. */ #define BCF_UN_STR 1 // up to ALT inclusive #define BCF_UN_FLT 2 // up to FILTER #define BCF_UN_INFO 4 // up to INFO #define BCF_UN_SHR (BCF_UN_STR|BCF_UN_FLT|BCF_UN_INFO) // all shared information #define BCF_UN_FMT 8 // unpack format and each sample #define BCF_UN_IND BCF_UN_FMT // a synonym of BCF_UN_FMT #define BCF_UN_ALL (BCF_UN_SHR|BCF_UN_FMT) // everything HTSLIB_EXPORT int bcf_unpack(bcf1_t *b, int which); /* * bcf_dup() - create a copy of BCF record. * * Note that bcf_unpack() must be called on the returned copy as if it was * obtained from bcf_read(). Also note that bcf_dup() calls bcf_sync1(src) * internally to reflect any changes made by bcf_update_* functions. * * The bcf1_t struct returned by a successful call should be freed * via bcf_destroy() when it is no longer needed. */ HTSLIB_EXPORT bcf1_t *bcf_dup(bcf1_t *src); HTSLIB_EXPORT bcf1_t *bcf_copy(bcf1_t *dst, bcf1_t *src); /// Write one VCF or BCF record. The type is determined at the open() call. /** @param fp The file to write to @param h The header for the vcf/bcf file @param v The bcf1_t structure to write @return 0 on success; -1 on error */ HTSLIB_EXPORT int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v) HTS_RESULT_USED; /** * The following functions work only with VCFs and should rarely be called * directly. Usually one wants to use their bcf_* alternatives, which work * transparently with both VCFs and BCFs. */ /// Read a VCF format header /** @param fp The file to read the header from @return Pointer to a populated header structure on success; NULL on failure Use bcf_hdr_read() instead. The bcf_hdr_t struct returned by a successful call should be freed via bcf_hdr_destroy() when it is no longer needed. */ HTSLIB_EXPORT bcf_hdr_t *vcf_hdr_read(htsFile *fp) HTS_RESULT_USED; /// Write a VCF format header /** @param fp Output file @param h The header to write @return 0 on success; -1 on failure Use bcf_hdr_write() instead */ HTSLIB_EXPORT int vcf_hdr_write(htsFile *fp, const bcf_hdr_t *h) HTS_RESULT_USED; /// Read a record from a VCF file /** @param fp The file to read the record from @param h The header for the vcf file @param v The bcf1_t structure to populate @return 0 on success; -1 on end of file; < -1 on error Use bcf_read() instead */ HTSLIB_EXPORT int vcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) HTS_RESULT_USED; /// Write a record to a VCF file /** @param fp The file to write to @param h The header for the vcf file @param v The bcf1_t structure to write @return 0 on success; -1 on error Use bcf_write() instead */ HTSLIB_EXPORT int vcf_write(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) HTS_RESULT_USED; /** Helper function for the bcf_itr_next() macro; internal use, ignore it */ HTSLIB_EXPORT int bcf_readrec(BGZF *fp, void *null, void *v, int *tid, hts_pos_t *beg, hts_pos_t *end); /// Write a line to a VCF file /** @param line Line to write @param fp File to write it to @return 0 on success; -1 on failure @note No checks are done on the line being added, apart from ensuring that it ends with a newline. This function should therefore be used with care. */ HTSLIB_EXPORT int vcf_write_line(htsFile *fp, kstring_t *line); /************************************************************************** * Header querying and manipulation routines **************************************************************************/ /** Create a new header using the supplied template * * The bcf_hdr_t struct returned by a successful call should be freed * via bcf_hdr_destroy() when it is no longer needed. * @return NULL on failure, header otherwise */ HTSLIB_EXPORT bcf_hdr_t *bcf_hdr_dup(const bcf_hdr_t *hdr); /** * Copy header lines from src to dst if not already present in dst. See also bcf_translate(). * Returns 0 on success or sets a bit on error: * 1 .. conflicting definitions of tag length * // todo */ HTSLIB_EXPORT int bcf_hdr_combine(bcf_hdr_t *dst, const bcf_hdr_t *src) HTS_DEPRECATED("Please use bcf_hdr_merge instead"); /** * bcf_hdr_merge() - copy header lines from src to dst, see also bcf_translate() * @param dst: the destination header to be merged into, NULL on the first pass * @param src: the source header * @return NULL on failure, header otherwise * * Notes: * - use as: * bcf_hdr_t *dst = NULL; * for (i=0; in[BCF_DT_SAMPLE] /** The following functions are for internal use and should rarely be called directly */ HTSLIB_EXPORT int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt); /// Synchronize internal header structures /** @param h Header @return 0 on success, -1 on failure This function updates the id, sample and contig arrays in the bcf_hdr_t structure so that they point to the same locations as the id, sample and contig dictionaries. */ HTSLIB_EXPORT int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED; /** * bcf_hdr_parse_line() - parse a single line of VCF textual header * @param h BCF header struct * @param line One or more lines of header text * @param len Filled out with length data parsed from 'line'. * @return bcf_hrec_t* on success; * NULL on error or on end of header text. * NB: to distinguish error from end-of-header, check *len: * *len == 0 indicates @p line did not start with "##" * *len == -1 indicates failure, likely due to out of memory * *len > 0 indicates a malformed header line * * If *len > 0 on exit, it will contain the full length of the line * including any trailing newline (this includes cases where NULL was * returned due to a malformed line). Callers can use this to skip to * the next header line. */ HTSLIB_EXPORT bcf_hrec_t *bcf_hdr_parse_line(const bcf_hdr_t *h, const char *line, int *len); /// Convert a bcf header record to string form /** * @param hrec Header record * @param str Destination kstring * @return 0 on success; < 0 on error */ HTSLIB_EXPORT int bcf_hrec_format(const bcf_hrec_t *hrec, kstring_t *str); /// Add a header record into a header /** * @param hdr Destination header * @param hrec Header record * @return 0 on success, -1 on failure * * If this function returns success, ownership of @p hrec will have * been transferred to the header structure. It may also have been * freed if it was a duplicate of a record already in the header. * Therefore the @p hrec pointer should not be used after a successful * return from this function. * * If this function returns failure, ownership will not have been taken * and the caller is responsible for cleaning up @p hrec. */ HTSLIB_EXPORT int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec); /** * bcf_hdr_get_hrec() - get header line info * @param type: one of the BCF_HL_* types: FLT,INFO,FMT,CTG,STR,GEN * @param key: the header key for generic lines (e.g. "fileformat"), any field * for structured lines, typically "ID". * @param value: the value which pairs with key. Can be be NULL for BCF_HL_GEN * @param str_class: the class of BCF_HL_STR line (e.g. "ALT" or "SAMPLE"), otherwise NULL */ HTSLIB_EXPORT bcf_hrec_t *bcf_hdr_get_hrec(const bcf_hdr_t *hdr, int type, const char *key, const char *value, const char *str_class); /// Duplicate a header record /** @param hrec Header record to copy @return A new header record on success; NULL on failure The bcf_hrec_t struct returned by a successful call should be freed via bcf_hrec_destroy() when it is no longer needed. */ HTSLIB_EXPORT bcf_hrec_t *bcf_hrec_dup(bcf_hrec_t *hrec); /// Add a new header record key /** @param hrec Header record @param str Key name @param len Length of @p str @return 0 on success; -1 on failure */ HTSLIB_EXPORT int bcf_hrec_add_key(bcf_hrec_t *hrec, const char *str, size_t len) HTS_RESULT_USED; /// Set a header record value /** @param hrec Header record @param i Index of value @param str Value to set @param len Length of @p str @param is_quoted Value should be quoted @return 0 on success; -1 on failure */ HTSLIB_EXPORT int bcf_hrec_set_val(bcf_hrec_t *hrec, int i, const char *str, size_t len, int is_quoted) HTS_RESULT_USED; HTSLIB_EXPORT int bcf_hrec_find_key(bcf_hrec_t *hrec, const char *key); /// Add an IDX header record /** @param hrec Header record @param idx IDX value to add @return 0 on success; -1 on failure */ HTSLIB_EXPORT int hrec_add_idx(bcf_hrec_t *hrec, int idx) HTS_RESULT_USED; /// Free up a header record and associated structures /** @param hrec Header record */ HTSLIB_EXPORT void bcf_hrec_destroy(bcf_hrec_t *hrec); /************************************************************************** * Individual record querying and manipulation routines **************************************************************************/ /** See the description of bcf_hdr_subset() */ HTSLIB_EXPORT int bcf_subset(const bcf_hdr_t *h, bcf1_t *v, int n, int *imap); /** * bcf_translate() - translate tags ids to be consistent with different header. This function * is useful when lines from multiple VCF need to be combined. * @dst_hdr: the destination header, to be used in bcf_write(), see also bcf_hdr_combine() * @src_hdr: the source header, used in bcf_read() * @src_line: line obtained by bcf_read() */ HTSLIB_EXPORT int bcf_translate(const bcf_hdr_t *dst_hdr, bcf_hdr_t *src_hdr, bcf1_t *src_line); /// Get variant types in a BCF record /** * @param rec BCF/VCF record * @return Types of variant present * * The return value will be a bitwise-or of VCF_SNP, VCF_MNP, * VCF_INDEL, VCF_OTHER, VCF_BND or VCF_OVERLAP. If will return * VCF_REF (i.e. 0) if none of the other types is present. * @deprecated Please use bcf_has_variant_types() instead */ HTSLIB_EXPORT int bcf_get_variant_types(bcf1_t *rec); /// Get variant type in a BCF record, for a given allele /** * @param rec BCF/VCF record * @param ith_allele Allele to check * @return Type of variant present * * The return value will be one of VCF_REF, VCF_SNP, VCF_MNP, * VCF_INDEL, VCF_OTHER, VCF_BND or VCF_OVERLAP. * @deprecated Please use bcf_has_variant_type() instead */ HTSLIB_EXPORT int bcf_get_variant_type(bcf1_t *rec, int ith_allele); /// Match mode for bcf_has_variant_types() enum bcf_variant_match { bcf_match_exact, ///< Types present exactly match tested for bcf_match_overlap, ///< At least one variant type in common bcf_match_subset, ///< Test set is a subset of types present }; /// Check for presence of variant types in a BCF record /** * @param rec BCF/VCF record * @param bitmask Set of variant types to test for * @param mode Match mode * @return >0 if the variant types are present, * 0 if not present, * -1 on error * * @p bitmask should be the bitwise-or of the variant types (VCF_SNP, * VCF_MNP, etc.) to test for. * * The return value is the bitwise-and of the set of types present * and @p bitmask. Callers that want to check for the presence of more * than one type can avoid function call overhead by passing all the * types to be checked for in a single call to this function, in * bcf_match_overlap mode, and then check for them individually in the * returned value. * * As VCF_REF is represented by 0 (i.e. the absence of other variants) * it should be tested for using * bcf_has_variant_types(rec, VCF_REF, bcf_match_exact) * which will return 1 if no other variant type is present, otherwise 0. */ HTSLIB_EXPORT int bcf_has_variant_types(bcf1_t *rec, uint32_t bitmask, enum bcf_variant_match mode); /// Check for presence of variant types in a BCF record, for a given allele /** * @param rec BCF/VCF record * @param ith_allele Allele to check * @param bitmask Set of variant types to test for * @return >0 if one of the variant types is present, * 0 if not present, * -1 on error * * @p bitmask should be the bitwise-or of the variant types (VCF_SNP, * VCF_MNP, etc.) to test for, or VCF_REF on its own. * * The return value is the bitwise-and of the set of types present * and @p bitmask. Callers that want to check for the presence of more * than one type can avoid function call overhead by passing all the * types to be checked for in a single call to this function, and then * check for them individually in the returned value. * * As a special case, if @p bitmask is VCF_REF (i.e. 0), the function * tests for an exact match. The return value will be 1 if the * variant type calculated for the allele is VCF_REF, otherwise if * any other type is present it will be 0. */ HTSLIB_EXPORT int bcf_has_variant_type(bcf1_t *rec, int ith_allele, uint32_t bitmask); /// Return the number of bases affected by a variant, for a given allele /** * @param rec BCF/VCF record * @param ith_allele Allele index * @return The number of bases affected (negative for deletions), * or bcf_int32_missing on error. */ HTSLIB_EXPORT int bcf_variant_length(bcf1_t *rec, int ith_allele); HTSLIB_EXPORT int bcf_is_snp(bcf1_t *v); /** * bcf_update_filter() - sets the FILTER column * @flt_ids: The filter IDs to set, numeric IDs returned by bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS") * @n: Number of filters. If n==0, all filters are removed */ HTSLIB_EXPORT int bcf_update_filter(const bcf_hdr_t *hdr, bcf1_t *line, int *flt_ids, int n); /** * bcf_add_filter() - adds to the FILTER column * @flt_id: filter ID to add, numeric ID returned by bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS") * * If flt_id is PASS, all existing filters are removed first. If other than PASS, existing PASS is removed. */ HTSLIB_EXPORT int bcf_add_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id); /** * bcf_remove_filter() - removes from the FILTER column * @flt_id: filter ID to remove, numeric ID returned by bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS") * @pass: when set to 1 and no filters are present, set to PASS */ HTSLIB_EXPORT int bcf_remove_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id, int pass); /** * Returns 1 if present, 0 if absent, or -1 if filter does not exist. "PASS" and "." can be used interchangeably. */ HTSLIB_EXPORT int bcf_has_filter(const bcf_hdr_t *hdr, bcf1_t *line, char *filter); /** * bcf_update_alleles() and bcf_update_alleles_str() - update REF and ALT column * @alleles: Array of alleles * @nals: Number of alleles * @alleles_string: Comma-separated alleles, starting with the REF allele */ HTSLIB_EXPORT int bcf_update_alleles(const bcf_hdr_t *hdr, bcf1_t *line, const char **alleles, int nals); HTSLIB_EXPORT int bcf_update_alleles_str(const bcf_hdr_t *hdr, bcf1_t *line, const char *alleles_string); /** * bcf_update_id() - sets new ID string * bcf_add_id() - adds to the ID string checking for duplicates */ HTSLIB_EXPORT int bcf_update_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id); HTSLIB_EXPORT int bcf_add_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id); /** * bcf_update_info_*() - functions for updating INFO fields * @param hdr: the BCF header * @param line: VCF line to be edited * @param key: the INFO tag to be updated * @param values: pointer to the array of values. Pass NULL to remove the tag. * @param n: number of values in the array. When set to 0, the INFO tag is removed * @return 0 on success or negative value on error. * * The @p string in bcf_update_info_flag() is optional, * @p n indicates whether the flag is set or removed. * * Note that updating an END info tag will cause line->rlen to be * updated as a side-effect (removing the tag will set it to the * string length of the REF allele). If line->pos is being changed as * well, it is important that this is done before calling * bcf_update_info_int32() to update the END tag, otherwise rlen will be * set incorrectly. If the new END value is less than or equal to * line->pos, a warning will be printed and line->rlen will be set to * the length of the REF allele. */ #define bcf_update_info_int32(hdr,line,key,values,n) bcf_update_info((hdr),(line),(key),(values),(n),BCF_HT_INT) #define bcf_update_info_float(hdr,line,key,values,n) bcf_update_info((hdr),(line),(key),(values),(n),BCF_HT_REAL) #define bcf_update_info_flag(hdr,line,key,string,n) bcf_update_info((hdr),(line),(key),(string),(n),BCF_HT_FLAG) #define bcf_update_info_string(hdr,line,key,string) bcf_update_info((hdr),(line),(key),(string),1,BCF_HT_STR) HTSLIB_EXPORT int bcf_update_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type); /// Set or update 64-bit integer INFO values /** * @param hdr: the BCF header * @param line: VCF line to be edited * @param key: the INFO tag to be updated * @param values: pointer to the array of values. Pass NULL to remove the tag. * @param n: number of values in the array. When set to 0, the INFO tag is removed * @return 0 on success or negative value on error. * * This function takes an int64_t values array as input. The data * actually stored will be shrunk to the minimum size that can * accept all of the values. * * INFO values outside of the range BCF_MIN_BT_INT32 to BCF_MAX_BT_INT32 * can only be written to VCF files. */ static inline int bcf_update_info_int64(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const int64_t *values, int n) { return bcf_update_info(hdr, line, key, values, n, BCF_HT_LONG); } /* * bcf_update_format_*() - functions for updating FORMAT fields * @values: pointer to the array of values, the same number of elements * is expected for each sample. Missing values must be padded * with bcf_*_missing or bcf_*_vector_end values. * @n: number of values in the array. If n==0, existing tag is removed. * * The function bcf_update_format_string() is a higher-level (slower) variant of * bcf_update_format_char(). The former accepts array of \0-terminated strings * whereas the latter requires that the strings are collapsed into a single array * of fixed-length strings. In case of strings with variable length, shorter strings * can be \0-padded. Note that the collapsed strings passed to bcf_update_format_char() * are not \0-terminated. * * Returns 0 on success or negative value on error. */ #define bcf_update_format_int32(hdr,line,key,values,n) bcf_update_format((hdr),(line),(key),(values),(n),BCF_HT_INT) #define bcf_update_format_float(hdr,line,key,values,n) bcf_update_format((hdr),(line),(key),(values),(n),BCF_HT_REAL) #define bcf_update_format_char(hdr,line,key,values,n) bcf_update_format((hdr),(line),(key),(values),(n),BCF_HT_STR) #define bcf_update_genotypes(hdr,line,gts,n) bcf_update_format((hdr),(line),"GT",(gts),(n),BCF_HT_INT) // See bcf_gt_ macros below HTSLIB_EXPORT int bcf_update_format_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const char **values, int n); HTSLIB_EXPORT int bcf_update_format(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type); // Macros for setting genotypes correctly, for use with bcf_update_genotypes only; idx corresponds // to VCF's GT (1-based index to ALT or 0 for the reference allele) and val is the opposite, obtained // from bcf_get_genotypes() below. #define bcf_gt_phased(idx) (((idx)+1)<<1|1) #define bcf_gt_unphased(idx) (((idx)+1)<<1) #define bcf_gt_missing 0 #define bcf_gt_is_missing(val) ((val)>>1 ? 0 : 1) #define bcf_gt_is_phased(idx) ((idx)&1) #define bcf_gt_allele(val) (((val)>>1)-1) /** Conversion between alleles indexes to Number=G genotype index (assuming diploid, all 0-based) */ #define bcf_alleles2gt(a,b) ((a)>(b)?((a)*((a)+1)/2+(b)):((b)*((b)+1)/2+(a))) static inline void bcf_gt2alleles(int igt, int *a, int *b) { int k = 0, dk = 1; while ( k=0 on success * -1 .. no such INFO tag defined in the header * -2 .. clash between types defined in the header and encountered in the VCF record * -3 .. tag is not present in the VCF record * -4 .. the operation could not be completed (e.g. out of memory) * * Returns negative value on error or the number of values (including * missing values) put in *dst on success. bcf_get_info_string() returns * on success the number of characters stored excluding the nul- * terminating byte. bcf_get_info_flag() does not store anything in *dst * but returns 1 if the flag is set or 0 if not. * * *dst will be reallocated if it is not big enough (i.e. *ndst is too * small) or NULL on entry. The new size will be stored in *ndst. */ #define bcf_get_info_int32(hdr,line,tag,dst,ndst) bcf_get_info_values(hdr,line,tag,(void**)(dst),ndst,BCF_HT_INT) #define bcf_get_info_float(hdr,line,tag,dst,ndst) bcf_get_info_values(hdr,line,tag,(void**)(dst),ndst,BCF_HT_REAL) #define bcf_get_info_string(hdr,line,tag,dst,ndst) bcf_get_info_values(hdr,line,tag,(void**)(dst),ndst,BCF_HT_STR) #define bcf_get_info_flag(hdr,line,tag,dst,ndst) bcf_get_info_values(hdr,line,tag,(void**)(dst),ndst,BCF_HT_FLAG) HTSLIB_EXPORT int bcf_get_info_values(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, void **dst, int *ndst, int type); /// Put integer INFO values into an int64_t array /** * @param hdr: BCF header * @param line: BCF record * @param tag: INFO tag to retrieve * @param dst: *dst is pointer to a memory location, can point to NULL * @param ndst: pointer to the size of allocated memory * @return >=0 on success * -1 .. no such INFO tag defined in the header * -2 .. clash between types defined in the header and encountered in the VCF record * -3 .. tag is not present in the VCF record * -4 .. the operation could not be completed (e.g. out of memory) * * Returns negative value on error or the number of values (including * missing values) put in *dst on success. * * *dst will be reallocated if it is not big enough (i.e. *ndst is too * small) or NULL on entry. The new size will be stored in *ndst. */ static inline int bcf_get_info_int64(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, int64_t **dst, int *ndst) { return bcf_get_info_values(hdr, line, tag, (void **) dst, ndst, BCF_HT_LONG); } /** * bcf_get_format_*() - same as bcf_get_info*() above * * The function bcf_get_format_string() is a higher-level (slower) variant of bcf_get_format_char(). * see the description of bcf_update_format_string() and bcf_update_format_char() above. * Unlike other bcf_get_format__*() functions, bcf_get_format_string() allocates two arrays: * a single block of \0-terminated strings collapsed into a single array and an array of pointers * to these strings. Both arrays must be cleaned by the user. * * Returns negative value on error or the number of written values on success. * * Use the returned number of written values for accessing valid entries of dst, as ndst is only a * watermark that can be higher than the returned value, i.e. the end of dst can contain carry-over * values from previous calls to bcf_get_format_*() on lines with more values per sample. * * Example: * int ndst = 0; char **dst = NULL; * if ( bcf_get_format_string(hdr, line, "XX", &dst, &ndst) > 0 ) * for (i=0; iid[type][int_id].key) /** * bcf_hdr_name2id() - Translates sequence names (chromosomes) into numeric ID * bcf_hdr_id2name() - Translates numeric ID to sequence name */ static inline int bcf_hdr_name2id(const bcf_hdr_t *hdr, const char *id) { return bcf_hdr_id2int(hdr, BCF_DT_CTG, id); } static inline const char *bcf_hdr_id2name(const bcf_hdr_t *hdr, int rid) { if ( !hdr || rid<0 || rid>=hdr->n[BCF_DT_CTG] ) return NULL; return hdr->id[BCF_DT_CTG][rid].key; } static inline const char *bcf_seqname(const bcf_hdr_t *hdr, const bcf1_t *rec) { return bcf_hdr_id2name(hdr, rec ? rec->rid : -1); } /** Return CONTIG name, or "(unknown)" Like bcf_seqname(), but this function will never return NULL. If the contig name cannot be found (either because @p hdr was not supplied or rec->rid was out of range) it returns the string "(unknown)". */ static inline const char *bcf_seqname_safe(const bcf_hdr_t *hdr, const bcf1_t *rec) { const char *name = bcf_seqname(hdr, rec); return name ? name : "(unknown)"; } /** * bcf_hdr_id2*() - Macros for accessing bcf_idinfo_t * @type: one of BCF_HL_FLT, BCF_HL_INFO, BCF_HL_FMT * @int_id: return value of bcf_hdr_id2int, must be >=0 * * The returned values are: * bcf_hdr_id2length .. whether the number of values is fixed or variable, one of BCF_VL_* * bcf_hdr_id2number .. the number of values, 0xfffff for variable length fields * bcf_hdr_id2type .. the field type, one of BCF_HT_* * bcf_hdr_id2coltype .. the column type, one of BCF_HL_* * * Notes: Prior to using the macros, the presence of the info should be * tested with bcf_hdr_idinfo_exists(). */ #define bcf_hdr_id2length(hdr,type,int_id) ((hdr)->id[BCF_DT_ID][int_id].val->info[type]>>8 & 0xf) #define bcf_hdr_id2number(hdr,type,int_id) ((hdr)->id[BCF_DT_ID][int_id].val->info[type]>>12) #define bcf_hdr_id2type(hdr,type,int_id) (uint32_t)((hdr)->id[BCF_DT_ID][int_id].val->info[type]>>4 & 0xf) #define bcf_hdr_id2coltype(hdr,type,int_id) (uint32_t)((hdr)->id[BCF_DT_ID][int_id].val->info[type] & 0xf) #define bcf_hdr_idinfo_exists(hdr,type,int_id) ((int_id)>=0 && (int_id)<(hdr)->n[BCF_DT_ID] && (hdr)->id[BCF_DT_ID][int_id].val && bcf_hdr_id2coltype((hdr),(type),(int_id))!=0xf) #define bcf_hdr_id2hrec(hdr,dict_type,col_type,int_id) ((hdr)->id[(dict_type)==BCF_DT_CTG?BCF_DT_CTG:BCF_DT_ID][int_id].val->hrec[(dict_type)==BCF_DT_CTG?0:(col_type)]) /// Convert BCF FORMAT data to string form /** * @param s kstring to write into * @param n number of items in @p data * @param type type of items in @p data * @param data BCF format data * @return 0 on success * -1 if out of memory */ HTSLIB_EXPORT int bcf_fmt_array(kstring_t *s, int n, int type, void *data); HTSLIB_EXPORT uint8_t *bcf_fmt_sized_array(kstring_t *s, uint8_t *ptr); /// Encode a variable-length char array in BCF format /** * @param s kstring to write into * @param l length of input * @param a input data to encode * @return 0 on success; < 0 on error */ HTSLIB_EXPORT int bcf_enc_vchar(kstring_t *s, int l, const char *a); /// Encode a variable-length integer array in BCF format /** * @param s kstring to write into * @param n total number of items in @p a (<= 0 to encode BCF_BT_NULL) * @param a input data to encode * @param wsize vector length (<= 0 is equivalent to @p n) * @return 0 on success; < 0 on error * @note @p n should be an exact multiple of @p wsize */ HTSLIB_EXPORT int bcf_enc_vint(kstring_t *s, int n, int32_t *a, int wsize); /// Encode a variable-length float array in BCF format /** * @param s kstring to write into * @param n total number of items in @p a (<= 0 to encode BCF_BT_NULL) * @param a input data to encode * @return 0 on success; < 0 on error */ HTSLIB_EXPORT int bcf_enc_vfloat(kstring_t *s, int n, float *a); /************************************************************************** * BCF index * * Note that these functions work with BCFs only. See synced_bcf_reader.h * which provides (amongst other things) an API to work transparently with * both indexed BCFs and VCFs. **************************************************************************/ #define bcf_itr_destroy(iter) hts_itr_destroy(iter) #define bcf_itr_queryi(idx, tid, beg, end) hts_itr_query((idx), (tid), (beg), (end), bcf_readrec) #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec) static inline int bcf_itr_next(htsFile *htsfp, hts_itr_t *itr, void *r) { if (htsfp->is_bgzf) return hts_itr_next(htsfp->fp.bgzf, itr, r, 0); hts_log_error("Only bgzf compressed files can be used with iterators"); errno = EINVAL; return -2; } /// Load a BCF index /** @param fn BCF file name @return The index, or NULL if an error occurred. @note This only works for BCF files. Consider synced_bcf_reader instead which works for both BCF and VCF. */ #define bcf_index_load(fn) hts_idx_load(fn, HTS_FMT_CSI) #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr)) /// Load a BCF index from a given index file name /** @param fn Input BAM/BCF/etc filename @param fnidx The input index filename @return The index, or NULL if an error occurred. @note This only works for BCF files. Consider synced_bcf_reader instead which works for both BCF and VCF. */ HTSLIB_EXPORT hts_idx_t *bcf_index_load2(const char *fn, const char *fnidx); /// Load a BCF index from a given index file name /** @param fn Input BAM/BCF/etc filename @param fnidx The input index filename @param flags Flags to alter behaviour (see description) @return The index, or NULL if an error occurred. @note This only works for BCF files. Consider synced_bcf_reader instead which works for both BCF and VCF. The @p flags parameter can be set to a combination of the following values: HTS_IDX_SAVE_REMOTE Save a local copy of any remote indexes HTS_IDX_SILENT_FAIL Fail silently if the index is not present Equivalent to hts_idx_load3(fn, fnidx, HTS_FMT_CSI, flags); */ HTSLIB_EXPORT hts_idx_t *bcf_index_load3(const char *fn, const char *fnidx, int flags); /** * bcf_index_build() - Generate and save an index file * @fn: Input VCF(compressed)/BCF filename * @min_shift: log2(width of the smallest bin), e.g. a value of 14 * imposes a 16k base lower limit on the width of index bins. * Positive to generate CSI, or 0 to generate TBI. However, a small * value of min_shift would create a large index, which would lead to * reduced performance when using the index. A recommended value is 14. * For BCF files, only the CSI index can be generated. * * Returns 0 if successful, or negative if an error occurred. * * List of error codes: * -1 .. indexing failed * -2 .. opening @fn failed * -3 .. format not indexable * -4 .. failed to create and/or save the index */ HTSLIB_EXPORT int bcf_index_build(const char *fn, int min_shift); /** * bcf_index_build2() - Generate and save an index to a specific file * @fn: Input VCF/BCF filename * @fnidx: Output filename, or NULL to add .csi/.tbi to @fn * @min_shift: Positive to generate CSI, or 0 to generate TBI * * Returns 0 if successful, or negative if an error occurred. * * List of error codes: * -1 .. indexing failed * -2 .. opening @fn failed * -3 .. format not indexable * -4 .. failed to create and/or save the index */ HTSLIB_EXPORT int bcf_index_build2(const char *fn, const char *fnidx, int min_shift); /** * bcf_index_build3() - Generate and save an index to a specific file * @fn: Input VCF/BCF filename * @fnidx: Output filename, or NULL to add .csi/.tbi to @fn * @min_shift: Positive to generate CSI, or 0 to generate TBI * @n_threads: Number of VCF/BCF decoder threads * * Returns 0 if successful, or negative if an error occurred. * * List of error codes: * -1 .. indexing failed * -2 .. opening @fn failed * -3 .. format not indexable * -4 .. failed to create and/or save the index */ HTSLIB_EXPORT int bcf_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads); /// Initialise fp->idx for the current format type, for VCF and BCF files. /** @param fp File handle for the data file being written. @param h BCF header structured (needed for BAI and CSI). @param min_shift CSI bin size (CSI default is 14). @param fnidx Filename to write index to. This pointer must remain valid until after bcf_idx_save is called. @return 0 on success, <0 on failure. @note This must be called after the header has been written, but before any other data. */ HTSLIB_EXPORT int bcf_idx_init(htsFile *fp, bcf_hdr_t *h, int min_shift, const char *fnidx); /// Writes the index initialised with bcf_idx_init to disk. /** @param fp File handle for the data file being written. @return 0 on success, <0 on failure. */ HTSLIB_EXPORT int bcf_idx_save(htsFile *fp); /******************* * Typed value I/O * *******************/ /* Note that in contrast with BCFv2.1 specification, HTSlib implementation allows missing values in vectors. For integer types, the values 0x80, 0x8000, 0x80000000 are interpreted as missing values and 0x81, 0x8001, 0x80000001 as end-of-vector indicators. Similarly for floats, the value of 0x7F800001 is interpreted as a missing value and 0x7F800002 as an end-of-vector indicator. Note that the end-of-vector byte is not part of the vector. This trial BCF version (v2.2) is compatible with the VCF specification and enables to handle correctly vectors with different ploidy in presence of missing values. */ #define bcf_int8_vector_end (-127) /* INT8_MIN + 1 */ #define bcf_int16_vector_end (-32767) /* INT16_MIN + 1 */ #define bcf_int32_vector_end (-2147483647) /* INT32_MIN + 1 */ #define bcf_int64_vector_end (-9223372036854775807LL) /* INT64_MIN + 1 */ #define bcf_str_vector_end 0 #define bcf_int8_missing (-128) /* INT8_MIN */ #define bcf_int16_missing (-32767-1) /* INT16_MIN */ #define bcf_int32_missing (-2147483647-1) /* INT32_MIN */ #define bcf_int64_missing (-9223372036854775807LL - 1LL) /* INT64_MIN */ // All of the above are values, which may occur multiple times in lists of // integers or lists of floating point. Strings in VCF don't have // lists - a list of strings is just another (comma-separated) string. // // Hence bcf_str_missing is the whole string being missing rather than // an element of a list. Ie a string of length zero: (0<<4)|BCF_BT_CHAR. #define bcf_str_missing BCF_BT_CHAR // Limits on BCF values stored in given types. Max values are the same // as for the underlying type. Min values are slightly different as // the last 8 values for each type were reserved by BCFv2.2. #define BCF_MAX_BT_INT8 (0x7f) /* INT8_MAX */ #define BCF_MAX_BT_INT16 (0x7fff) /* INT16_MAX */ #define BCF_MAX_BT_INT32 (0x7fffffff) /* INT32_MAX */ #define BCF_MIN_BT_INT8 (-120) /* INT8_MIN + 8 */ #define BCF_MIN_BT_INT16 (-32760) /* INT16_MIN + 8 */ #define BCF_MIN_BT_INT32 (-2147483640) /* INT32_MIN + 8 */ HTSLIB_EXPORT extern uint32_t bcf_float_vector_end; HTSLIB_EXPORT extern uint32_t bcf_float_missing; static inline void bcf_float_set(float *ptr, uint32_t value) { union { uint32_t i; float f; } u; u.i = value; *ptr = u.f; } #define bcf_float_set_vector_end(x) bcf_float_set(&(x),bcf_float_vector_end) #define bcf_float_set_missing(x) bcf_float_set(&(x),bcf_float_missing) static inline int bcf_float_is_missing(float f) { union { uint32_t i; float f; } u; u.f = f; return u.i==bcf_float_missing ? 1 : 0; } static inline int bcf_float_is_vector_end(float f) { union { uint32_t i; float f; } u; u.f = f; return u.i==bcf_float_vector_end ? 1 : 0; } static inline int bcf_format_gt(bcf_fmt_t *fmt, int isample, kstring_t *str) { uint32_t e = 0; #define BRANCH(type_t, convert, missing, vector_end) { \ uint8_t *ptr = fmt->p + isample*fmt->size; \ int i; \ for (i=0; in; i++, ptr += sizeof(type_t)) \ { \ type_t val = convert(ptr); \ if ( val == vector_end ) break; \ if ( i ) e |= kputc("/|"[val&1], str) < 0; \ if ( !(val>>1) ) e |= kputc('.', str) < 0; \ else e |= kputw((val>>1) - 1, str) < 0; \ } \ if (i == 0) e |= kputc('.', str) < 0; \ } switch (fmt->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, bcf_int8_missing, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, bcf_int16_missing, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, bcf_int32_missing, bcf_int32_vector_end); break; case BCF_BT_NULL: e |= kputc('.', str) < 0; break; default: hts_log_error("Unexpected type %d", fmt->type); return -2; } #undef BRANCH return e == 0 ? 0 : -1; } static inline int bcf_enc_size(kstring_t *s, int size, int type) { // Most common case is first if (size < 15) { if (ks_resize(s, s->l + 1) < 0) return -1; uint8_t *p = (uint8_t *)s->s + s->l; *p++ = (size<<4) | type; s->l++; return 0; } if (ks_resize(s, s->l + 6) < 0) return -1; uint8_t *p = (uint8_t *)s->s + s->l; *p++ = 15<<4|type; if (size < 128) { *p++ = 1<<4|BCF_BT_INT8; *p++ = size; s->l += 3; } else { if (size < 32768) { *p++ = 1<<4|BCF_BT_INT16; i16_to_le(size, p); s->l += 4; } else { *p++ = 1<<4|BCF_BT_INT32; i32_to_le(size, p); s->l += 6; } } return 0; } static inline int bcf_enc_inttype(long x) { if (x <= BCF_MAX_BT_INT8 && x >= BCF_MIN_BT_INT8) return BCF_BT_INT8; if (x <= BCF_MAX_BT_INT16 && x >= BCF_MIN_BT_INT16) return BCF_BT_INT16; return BCF_BT_INT32; } static inline int bcf_enc_int1(kstring_t *s, int32_t x) { if (ks_resize(s, s->l + 5) < 0) return -1; uint8_t *p = (uint8_t *)s->s + s->l; if (x == bcf_int32_vector_end) { // An inline implementation of bcf_enc_size with size==1 and // memory allocation already accounted for. *p = (1<<4) | BCF_BT_INT8; p[1] = bcf_int8_vector_end; s->l+=2; } else if (x == bcf_int32_missing) { *p = (1<<4) | BCF_BT_INT8; p[1] = bcf_int8_missing; s->l+=2; } else if (x <= BCF_MAX_BT_INT8 && x >= BCF_MIN_BT_INT8) { *p = (1<<4) | BCF_BT_INT8; p[1] = x; s->l+=2; } else if (x <= BCF_MAX_BT_INT16 && x >= BCF_MIN_BT_INT16) { *p = (1<<4) | BCF_BT_INT16; i16_to_le(x, p+1); s->l+=3; } else { *p = (1<<4) | BCF_BT_INT32; i32_to_le(x, p+1); s->l+=5; } return 0; } /// Return the value of a single typed integer. /** @param p Pointer to input data block. @param type One of the BCF_BT_INT* type codes @param[out] q Location to store an updated value for p @return The integer value, or zero if @p type is not valid. If @p type is not one of BCF_BT_INT8, BCF_BT_INT16, BCF_BT_INT32 or BCF_BT_INT64, zero will be returned and @p *q will not be updated. Otherwise, the integer value will be returned and @p *q will be set to the memory location immediately following the integer value. Cautious callers can detect invalid type codes by checking that *q has actually been updated. */ static inline int64_t bcf_dec_int1(const uint8_t *p, int type, uint8_t **q) { if (type == BCF_BT_INT8) { *q = (uint8_t*)p + 1; return le_to_i8(p); } else if (type == BCF_BT_INT16) { *q = (uint8_t*)p + 2; return le_to_i16(p); } else if (type == BCF_BT_INT32) { *q = (uint8_t*)p + 4; return le_to_i32(p); } else if (type == BCF_BT_INT64) { *q = (uint8_t*)p + 8; return le_to_i64(p); } else { // Invalid type. return 0; } } /// Return the value of a single typed integer from a byte stream. /** @param p Pointer to input data block. @param[out] q Location to store an updated value for p @return The integer value, or zero if the type code was not valid. Reads a one-byte type code from @p p, and uses it to decode an integer value from the following bytes in @p p. If the type is not one of BCF_BT_INT8, BCF_BT_INT16 or BCF_BT_INT32, zero will be returned and @p *q will unchanged. Otherwise, the integer value will be returned and @p *q will be set to the memory location immediately following the integer value. Cautious callers can detect invalid type codes by checking that *q has actually been updated. */ static inline int64_t bcf_dec_typed_int1(const uint8_t *p, uint8_t **q) { return bcf_dec_int1(p + 1, *p&0xf, q); } static inline int32_t bcf_dec_size(const uint8_t *p, uint8_t **q, int *type) { *type = *p & 0xf; if (*p>>4 != 15) { *q = (uint8_t*)p + 1; return *p>>4; } else return bcf_dec_typed_int1(p + 1, q); } #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/htslib/vcf_sweep.h000066400000000000000000000032261475062545500176510ustar00rootroot00000000000000/// @file htslib/vcf_sweep.h /// Forward/reverse sweep API. /* Copyright (C) 2013-2015, 2019 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTSLIB_VCF_SWEEP_H #define HTSLIB_VCF_SWEEP_H #include "hts.h" #include "vcf.h" #ifdef __cplusplus extern "C" { #endif typedef struct bcf_sweep_t bcf_sweep_t; HTSLIB_EXPORT bcf_sweep_t *bcf_sweep_init(const char *fname); HTSLIB_EXPORT void bcf_sweep_destroy(bcf_sweep_t *sw); HTSLIB_EXPORT bcf_hdr_t *bcf_sweep_hdr(bcf_sweep_t *sw); HTSLIB_EXPORT bcf1_t *bcf_sweep_fwd(bcf_sweep_t *sw); HTSLIB_EXPORT bcf1_t *bcf_sweep_bwd(bcf_sweep_t *sw); #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/htslib/vcfutils.h000066400000000000000000000114671475062545500175350ustar00rootroot00000000000000/// @file htslib/vcfutils.h /// Allele-related utility functions. /* Copyright (C) 2012, 2013, 2015-2016 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTSLIB_VCFUTILS_H #define HTSLIB_VCFUTILS_H #include "vcf.h" #ifdef __cplusplus extern "C" { #endif struct kbitset_t; /** * bcf_trim_alleles() - remove ALT alleles unused in genotype fields * @header: for access to BCF_DT_ID dictionary * @line: VCF line obtain from vcf_parse1 * * Returns the number of removed alleles on success or negative * on error: * -1 .. some allele index is out of bounds * -2 .. could not remove alleles */ HTSLIB_EXPORT int bcf_trim_alleles(const bcf_hdr_t *header, bcf1_t *line); /** * bcf_remove_alleles() - remove ALT alleles according to bitmask @mask * @header: for access to BCF_DT_ID dictionary * @line: VCF line obtained from vcf_parse1 * @mask: alleles to remove * * If you have more than 31 alleles, then the integer bit mask will * overflow, so use bcf_remove_allele_set instead * Returns 0 on success, <0 on error */ HTSLIB_EXPORT int bcf_remove_alleles(const bcf_hdr_t *header, bcf1_t *line, int mask) HTS_DEPRECATED("Please use bcf_remove_allele_set instead"); /** * bcf_remove_allele_set() - remove ALT alleles according to bitset @rm_set * @header: for access to BCF_DT_ID dictionary * @line: VCF line obtained from vcf_parse1 * @rm_set: pointer to kbitset_t object with bits set for allele * indexes to remove * * Returns 0 on success or -1 on failure * * Number=A,R,G INFO and FORMAT fields will be updated accordingly. */ HTSLIB_EXPORT int bcf_remove_allele_set(const bcf_hdr_t *header, bcf1_t *line, const struct kbitset_t *rm_set); /** * bcf_calc_ac() - calculate the number of REF and ALT alleles * @header: for access to BCF_DT_ID dictionary * @line: VCF line obtained from vcf_parse1 * @ac: array of length line->n_allele * @which: determine if INFO/AN,AC and indv fields be used * * Returns 1 if the call succeeded, or 0 if the value could not * be determined. * * The value of @which determines if existing INFO/AC,AN can be * used (BCF_UN_INFO) and and if indv fields can be split (BCF_UN_FMT). */ HTSLIB_EXPORT int bcf_calc_ac(const bcf_hdr_t *header, bcf1_t *line, int *ac, int which); /** * bcf_gt_type() - determines type of the genotype * @fmt_ptr: the GT format field as set for example by set_fmt_ptr * @isample: sample index (starting from 0) * @ial: index of the 1st non-reference allele (starting from 1) * @jal: index of the 2nd non-reference allele (starting from 1) * * Returns the type of the genotype (one of GT_HOM_RR, GT_HET_RA, * GT_HOM_AA, GT_HET_AA, GT_HAPL_R, GT_HAPL_A or GT_UNKN). If $ial * is not NULL and the genotype has one or more non-reference * alleles, $ial will be set. In case of GT_HET_AA, $ial is the * position of the allele which appeared first in ALT. If $jal is * not null and the genotype is GT_HET_AA, $jal will be set and is * the position of the second allele in ALT. */ #define GT_HOM_RR 0 // note: the actual value of GT_* matters, used in dosage r2 calculation #define GT_HOM_AA 1 #define GT_HET_RA 2 #define GT_HET_AA 3 #define GT_HAPL_R 4 #define GT_HAPL_A 5 #define GT_UNKN 6 HTSLIB_EXPORT int bcf_gt_type(bcf_fmt_t *fmt_ptr, int isample, int *ial, int *jal); static inline int bcf_acgt2int(char c) { if ( (int)c>96 ) c -= 32; if ( c=='A' ) return 0; if ( c=='C' ) return 1; if ( c=='G' ) return 2; if ( c=='T' ) return 3; return -1; } #define bcf_int2acgt(i) "ACGT"[i] /** * bcf_ij2G() - common task: allele indexes to Number=G index (diploid) * @i,j: allele indexes, 0-based, i<=j * * Returns index to the Number=G diploid array */ #define bcf_ij2G(i, j) ((j)*((j)+1)/2+(i)) #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/htslib_vars.mk000066400000000000000000000064051475062545500171050ustar00rootroot00000000000000# Makefile variables useful for third-party code using htslib's public API. # # Copyright (C) 2013-2017, 2019-2020 Genome Research Ltd. # # Author: John Marshall # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. # These variables can be used to express dependencies on htslib headers. # See htslib.mk for details. htslib_bgzf_h = $(HTSPREFIX)htslib/bgzf.h $(htslib_hts_defs_h) htslib_cram_h = $(HTSPREFIX)htslib/cram.h $(htslib_hts_defs_h) $(htslib_hts_h) $(htslib_sam_h) htslib_faidx_h = $(HTSPREFIX)htslib/faidx.h $(htslib_hts_defs_h) $(htslib_hts_h) htslib_hfile_h = $(HTSPREFIX)htslib/hfile.h $(htslib_hts_defs_h) htslib_hts_h = $(HTSPREFIX)htslib/hts.h $(htslib_hts_defs_h) $(htslib_hts_log_h) $(htslib_kstring_h) $(htslib_kroundup_h) htslib_hts_defs_h = $(HTSPREFIX)htslib/hts_defs.h htslib_hts_endian_h = $(HTSPREFIX)htslib/hts_endian.h htslib_hts_expr_h = $(HTSPREFIX)htslib/hts_expr.h $(htslib_kstring_h) $(htslib_hts_defs_h) htslib_hts_log_h = $(HTSPREFIX)htslib/hts_log.h $(htslib_hts_defs_h) htslib_hts_os_h = $(HTSPREFIX)htslib/hts_os.h $(htslib_hts_defs_h) htslib_kbitset_h = $(HTSPREFIX)htslib/kbitset.h htslib_kfunc_h = $(HTSPREFIX)htslib/kfunc.h $(htslib_hts_defs_h) htslib_khash_h = $(HTSPREFIX)htslib/khash.h $(htslib_kstring_h) $(htslib_kroundup_h) htslib_khash_str2int_h = $(HTSPREFIX)htslib/khash_str2int.h $(htslib_khash_h) htslib_klist_h = $(HTSPREFIX)htslib/klist.h htslib_kroundup_h = $(HTSPREFIX)htslib/kroundup.h htslib_kseq_h = $(HTSPREFIX)htslib/kseq.h htslib_ksort_h = $(HTSPREFIX)htslib/ksort.h $(htslib_hts_defs_h) htslib_kstring_h = $(HTSPREFIX)htslib/kstring.h $(htslib_hts_defs_h) $(htslib_kroundup_h) htslib_regidx_h = $(HTSPREFIX)htslib/regidx.h $(htslib_hts_h) htslib_sam_h = $(HTSPREFIX)htslib/sam.h $(htslib_hts_h) $(htslib_hts_endian_h) htslib_synced_bcf_reader_h = $(HTSPREFIX)htslib/synced_bcf_reader.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_tbx_h) htslib_tbx_h = $(HTSPREFIX)htslib/tbx.h $(htslib_hts_h) htslib_thread_pool_h = $(HTSPREFIX)htslib/thread_pool.h $(htslib_hts_defs_h) htslib_vcf_h = $(HTSPREFIX)htslib/vcf.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_hts_defs_h) $(htslib_hts_endian_h) htslib_vcf_sweep_h = $(HTSPREFIX)htslib/vcf_sweep.h $(htslib_hts_h) $(htslib_vcf_h) htslib_vcfutils_h = $(HTSPREFIX)htslib/vcfutils.h $(htslib_vcf_h) pysam-0.23.0/htslib/kfunc.c000066400000000000000000000251771475062545500155150ustar00rootroot00000000000000/* The MIT License Copyright (C) 2010, 2013-2014, 2020 Genome Research Ltd. Copyright (C) 2011 Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include "htslib/kfunc.h" /* Log gamma function * \log{\Gamma(z)} * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245 */ double kf_lgamma(double z) { double x = 0; x += 0.1659470187408462e-06 / (z+7); x += 0.9934937113930748e-05 / (z+6); x -= 0.1385710331296526 / (z+5); x += 12.50734324009056 / (z+4); x -= 176.6150291498386 / (z+3); x += 771.3234287757674 / (z+2); x -= 1259.139216722289 / (z+1); x += 676.5203681218835 / z; x += 0.9999999999995183; return log(x) - 5.58106146679532777 - z + (z-0.5) * log(z+6.5); } /* complementary error function * \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2} dt * AS66, 2nd algorithm, http://lib.stat.cmu.edu/apstat/66 */ double kf_erfc(double x) { const double p0 = 220.2068679123761; const double p1 = 221.2135961699311; const double p2 = 112.0792914978709; const double p3 = 33.912866078383; const double p4 = 6.37396220353165; const double p5 = .7003830644436881; const double p6 = .03526249659989109; const double q0 = 440.4137358247522; const double q1 = 793.8265125199484; const double q2 = 637.3336333788311; const double q3 = 296.5642487796737; const double q4 = 86.78073220294608; const double q5 = 16.06417757920695; const double q6 = 1.755667163182642; const double q7 = .08838834764831844; double expntl, z, p; z = fabs(x) * M_SQRT2; if (z > 37.) return x > 0.? 0. : 2.; expntl = exp(z * z * - .5); if (z < 10. / M_SQRT2) // for small z p = expntl * ((((((p6 * z + p5) * z + p4) * z + p3) * z + p2) * z + p1) * z + p0) / (((((((q7 * z + q6) * z + q5) * z + q4) * z + q3) * z + q2) * z + q1) * z + q0); else p = expntl / 2.506628274631001 / (z + 1. / (z + 2. / (z + 3. / (z + 4. / (z + .65))))); return x > 0.? 2. * p : 2. * (1. - p); } /* The following computes regularized incomplete gamma functions. * Formulas are taken from Wiki, with additional input from Numerical * Recipes in C (for modified Lentz's algorithm) and AS245 * (http://lib.stat.cmu.edu/apstat/245). * * A good online calculator is available at: * * http://www.danielsoper.com/statcalc/calc23.aspx * * It calculates upper incomplete gamma function, which equals * kf_gammaq(s,z)*tgamma(s). */ #define KF_GAMMA_EPS 1e-14 #define KF_TINY 1e-290 // regularized lower incomplete gamma function, by series expansion static double _kf_gammap(double s, double z) { double sum, x; int k; for (k = 1, sum = x = 1.; k < 100; ++k) { sum += (x *= z / (s + k)); if (x / sum < KF_GAMMA_EPS) break; } return exp(s * log(z) - z - kf_lgamma(s + 1.) + log(sum)); } // regularized upper incomplete gamma function, by continued fraction static double _kf_gammaq(double s, double z) { int j; double C, D, f; f = 1. + z - s; C = f; D = 0.; // Modified Lentz's algorithm for computing continued fraction // See Numerical Recipes in C, 2nd edition, section 5.2 for (j = 1; j < 100; ++j) { double a = j * (s - j), b = (j<<1) + 1 + z - s, d; D = b + a * D; if (D < KF_TINY) D = KF_TINY; C = b + a / C; if (C < KF_TINY) C = KF_TINY; D = 1. / D; d = C * D; f *= d; if (fabs(d - 1.) < KF_GAMMA_EPS) break; } return exp(s * log(z) - z - kf_lgamma(s) - log(f)); } double kf_gammap(double s, double z) { return z <= 1. || z < s? _kf_gammap(s, z) : 1. - _kf_gammaq(s, z); } double kf_gammaq(double s, double z) { return z <= 1. || z < s? 1. - _kf_gammap(s, z) : _kf_gammaq(s, z); } /* Regularized incomplete beta function. The method is taken from * Numerical Recipe in C, 2nd edition, section 6.4. The following web * page calculates the incomplete beta function, which equals * kf_betai(a,b,x) * gamma(a) * gamma(b) / gamma(a+b): * * http://www.danielsoper.com/statcalc/calc36.aspx */ static double kf_betai_aux(double a, double b, double x) { double C, D, f; int j; if (x == 0.) return 0.; if (x == 1.) return 1.; f = 1.; C = f; D = 0.; // Modified Lentz's algorithm for computing continued fraction for (j = 1; j < 200; ++j) { double aa, d; int m = j>>1; aa = (j&1)? -(a + m) * (a + b + m) * x / ((a + 2*m) * (a + 2*m + 1)) : m * (b - m) * x / ((a + 2*m - 1) * (a + 2*m)); D = 1. + aa * D; if (D < KF_TINY) D = KF_TINY; C = 1. + aa / C; if (C < KF_TINY) C = KF_TINY; D = 1. / D; d = C * D; f *= d; if (fabs(d - 1.) < KF_GAMMA_EPS) break; } return exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b) + a * log(x) + b * log(1.-x)) / a / f; } double kf_betai(double a, double b, double x) { return x < (a + 1.) / (a + b + 2.)? kf_betai_aux(a, b, x) : 1. - kf_betai_aux(b, a, 1. - x); } #ifdef KF_MAIN #include int main(int argc, char *argv[]) { double x = 5.5, y = 3; double a, b; printf("erfc(%lg): %lg, %lg\n", x, erfc(x), kf_erfc(x)); printf("upper-gamma(%lg,%lg): %lg\n", x, y, kf_gammaq(y, x)*tgamma(y)); a = 2; b = 2; x = 0.5; printf("incomplete-beta(%lg,%lg,%lg): %lg\n", a, b, x, kf_betai(a, b, x) / exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b))); return 0; } #endif // log\binom{n}{k} static double lbinom(int n, int k) { if (k == 0 || n == k) return 0; return lgamma(n+1) - lgamma(k+1) - lgamma(n-k+1); } // n11 n12 | n1_ // n21 n22 | n2_ //-----------+---- // n_1 n_2 | n // hypergeometric distribution static double hypergeo(int n11, int n1_, int n_1, int n) { return exp(lbinom(n1_, n11) + lbinom(n-n1_, n_1-n11) - lbinom(n, n_1)); } typedef struct { int n11, n1_, n_1, n; double p; } hgacc_t; // incremental version of hypergenometric distribution static double hypergeo_acc(int n11, int n1_, int n_1, int n, hgacc_t *aux) { if (n1_ || n_1 || n) { aux->n11 = n11; aux->n1_ = n1_; aux->n_1 = n_1; aux->n = n; } else { // then only n11 changed; the rest fixed if (n11%11 && n11 + aux->n - aux->n1_ - aux->n_1) { if (n11 == aux->n11 + 1) { // incremental aux->p *= (double)(aux->n1_ - aux->n11) / n11 * (aux->n_1 - aux->n11) / (n11 + aux->n - aux->n1_ - aux->n_1); aux->n11 = n11; return aux->p; } if (n11 == aux->n11 - 1) { // incremental aux->p *= (double)aux->n11 / (aux->n1_ - n11) * (aux->n11 + aux->n - aux->n1_ - aux->n_1) / (aux->n_1 - n11); aux->n11 = n11; return aux->p; } } aux->n11 = n11; } aux->p = hypergeo(aux->n11, aux->n1_, aux->n_1, aux->n); return aux->p; } double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two) { int i, j, max, min; double p, q, left, right; hgacc_t aux; int n1_, n_1, n; n1_ = n11 + n12; n_1 = n11 + n21; n = n11 + n12 + n21 + n22; // calculate n1_, n_1 and n max = (n_1 < n1_) ? n_1 : n1_; // max n11, for right tail min = n1_ + n_1 - n; // not sure why n11-n22 is used instead of min(n_1,n1_) if (min < 0) min = 0; // min n11, for left tail *two = *_left = *_right = 1.; if (min == max) return 1.; // no need to do test q = hypergeo_acc(n11, n1_, n_1, n, &aux); // the probability of the current table if (q == 0.0) { /* If here, the calculated probablility is so small it can't be stored in a double, which is possible when the table contains fairly large numbers. If this happens, most of the calculation can be skipped as 'left', 'right' and '*two' will be (to a good approximation) 0.0. The returned values '*_left' and '*_right' depend on which side of the hypergeometric PDF 'n11' sits. This can be found by comparing with the mode of the distribution, the formula for which can be found at: https://en.wikipedia.org/wiki/Hypergeometric_distribution Note that in the comparison we multiply through by the denominator of the mode (n + 2) to avoid a division. */ if ((int64_t) n11 * ((int64_t) n + 2) < ((int64_t) n_1 + 1) * ((int64_t) n1_ + 1)) { // Peak to right of n11, so probability will be lower for all // of the region from min to n11 and higher for at least some // of the region from n11 to max; hence abs(i-n11) will be 0, // abs(j-n11) will be > 0 and: *_left = 0.0; *_right = 1.0; *two = 0.0; return 0.0; } else { // Peak to left of n11, so probability will be lower for all // of the region from n11 to max and higher for at least some // of the region from min to n11; hence abs(i-n11) will be > 0, // abs(j-n11) will be 0 and: *_left = 1.0; *_right = 0.0; *two = 0.0; return 0.0; } } // left tail p = hypergeo_acc(min, 0, 0, 0, &aux); for (left = 0., i = min + 1; p < 0.99999999 * q && i<=max; ++i) // loop until underflow left += p, p = hypergeo_acc(i, 0, 0, 0, &aux); --i; if (p < 1.00000001 * q) left += p; else --i; // right tail p = hypergeo_acc(max, 0, 0, 0, &aux); for (right = 0., j = max - 1; p < 0.99999999 * q && j>=0; --j) // loop until underflow right += p, p = hypergeo_acc(j, 0, 0, 0, &aux); ++j; if (p < 1.00000001 * q) right += p; else ++j; // two-tail *two = left + right; if (*two > 1.) *two = 1.; // adjust left and right if (abs(i - n11) < abs(j - n11)) right = 1. - left + q; else left = 1.0 - right + q; *_left = left; *_right = right; return q; } pysam-0.23.0/htslib/kstring.c000066400000000000000000000270751475062545500160670ustar00rootroot00000000000000/* The MIT License Copyright (C) 2011 by Attractive Chaos Copyright (C) 2013-2018, 2020-2021, 2023 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include "htslib/kstring.h" int kputd(double d, kstring_t *s) { int len = 0; char buf[21], *cp = buf+20, *ep; if (d == 0) { if (signbit(d)) { kputsn("-0",2,s); return 2; } else { kputsn("0",1,s); return 1; } } if (d < 0) { kputc('-',s); len = 1; d=-d; } if (!(d >= 0.0001 && d <= 999999)) { if (ks_resize(s, s->l + 50) < 0) return EOF; // We let stdio handle the exponent cases int s2 = snprintf(s->s + s->l, s->m - s->l, "%g", d); len += s2; s->l += s2; return len; } // Correction for rounding - rather ugly // Optimised for small numbers. uint32_t i; if (d<0.001) i = rint(d*1000000000), cp -= 1; else if (d < 0.01) i = rint(d*100000000), cp -= 2; else if (d < 0.1) i = rint(d*10000000), cp -= 3; else if (d < 1) i = rint(d*1000000), cp -= 4; else if (d < 10) i = rint(d*100000), cp -= 5; else if (d < 100) i = rint(d*10000), cp -= 6; else if (d < 1000) i = rint(d*1000), cp -= 7; else if (d < 10000) i = rint(d*100), cp -= 8; else if (d < 100000) i = rint(d*10), cp -= 9; else i = rint(d), cp -= 10; // integer i is always 6 digits, so print it 2 at a time. static const char kputuw_dig2r[] = "00010203040506070809" "10111213141516171819" "20212223242526272829" "30313233343536373839" "40414243444546474849" "50515253545556575859" "60616263646566676869" "70717273747576777879" "80818283848586878889" "90919293949596979899"; memcpy(cp-=2, &kputuw_dig2r[2*(i%100)], 2); i /= 100; memcpy(cp-=2, &kputuw_dig2r[2*(i%100)], 2); i /= 100; memcpy(cp-=2, &kputuw_dig2r[2*(i%100)], 2); // Except when it rounds up (d=0.009999999 is i=1000000) if (i >= 100) *--cp = '0' + (i/100); int p = buf+20-cp; if (p <= 10) { /* d < 1 */ // 0.00123 is 123, so add leading zeros and 0. ep = cp+5; // 6 precision while (p < 10) { // aka d < 1 *--cp = '0'; p++; } *--cp = '.'; *--cp = '0'; } else { // 123.001 is 123001 with p==13, so move 123 down and add "." // Equiv to memmove(cp-1, cp, p-10); cp--; char *xp = --cp; ep = cp+6; while (p > 10) { xp[0] = xp[1]; xp++; p--; } xp[0] = '.'; } // Cull trailing zeros while (*ep == '0' && ep > cp) ep--; // End can be 1 out due to the mostly-6 but occasionally 7 (i==1) case. // Also code with "123." which should be "123" if (*ep && *ep != '.') ep++; *ep = 0; int sl = ep-cp; len += sl; kputsn(cp, sl, s); return len; } int kvsprintf(kstring_t *s, const char *fmt, va_list ap) { va_list args; int l; va_copy(args, ap); if (fmt[0] == '%' && fmt[1] == 'g' && fmt[2] == 0) { double d = va_arg(args, double); l = kputd(d, s); va_end(args); return l; } if (!s->s) { const size_t sz = 64; s->s = malloc(sz); if (!s->s) return -1; s->m = sz; s->l = 0; } l = vsnprintf(s->s + s->l, s->m - s->l, fmt, args); // This line does not work with glibc 2.0. See `man snprintf'. va_end(args); if (l + 1 > s->m - s->l) { if (ks_resize(s, s->l + l + 2) < 0) return -1; va_copy(args, ap); l = vsnprintf(s->s + s->l, s->m - s->l, fmt, args); va_end(args); } s->l += l; return l; } int ksprintf(kstring_t *s, const char *fmt, ...) { va_list ap; int l; va_start(ap, fmt); l = kvsprintf(s, fmt, ap); va_end(ap); return l; } char *kstrtok(const char *str, const char *sep_in, ks_tokaux_t *aux) { const unsigned char *p, *start, *sep = (unsigned char *) sep_in; if (sep) { // set up the table if (str == 0 && aux->finished) return 0; // no need to set up if we have finished aux->finished = 0; if (sep[0] && sep[1]) { aux->sep = -1; aux->tab[0] = aux->tab[1] = aux->tab[2] = aux->tab[3] = 0; for (p = sep; *p; ++p) aux->tab[*p>>6] |= 1ull<<(*p&0x3f); } else aux->sep = sep[0]; } if (aux->finished) return 0; else if (str) start = (unsigned char *) str, aux->finished = 0; else start = (unsigned char *) aux->p + 1; if (aux->sep < 0) { for (p = start; *p; ++p) if (aux->tab[*p>>6]>>(*p&0x3f)&1) break; } else { // Using strchr is fast for next token, but slower for // last token due to extra pass from strlen. Overall // on a VCF parse this func was 146% faster with // strchr. // Equiv to: // for (p = start; *p; ++p) if (*p == aux->sep) break; // NB: We could use strchrnul() here from glibc if detected, // which is ~40% faster again, but it's not so portable. // i.e. p = (uint8_t *)strchrnul((char *)start, aux->sep); uint8_t *p2 = (uint8_t *)strchr((char *)start, aux->sep); p = p2 ? p2 : start + strlen((char *)start); } aux->p = (const char *) p; // end of token if (*p == 0) aux->finished = 1; // no more tokens return (char*)start; } // s MUST BE a null terminated string; l = strlen(s) int ksplit_core(char *s, int delimiter, int *_max, int **_offsets) { int i, n, max, last_char, last_start, *offsets, l; n = 0; max = *_max; offsets = *_offsets; l = strlen(s); #define __ksplit_aux do { \ if (_offsets) { \ s[i] = 0; \ if (n == max) { \ int *tmp; \ max = max? max<<1 : 2; \ if ((tmp = (int*)realloc(offsets, sizeof(int) * max))) { \ offsets = tmp; \ } else { \ free(offsets); \ *_offsets = NULL; \ return 0; \ } \ } \ offsets[n++] = last_start; \ } else ++n; \ } while (0) for (i = 0, last_char = last_start = 0; i <= l; ++i) { if (delimiter == 0) { if (isspace((int)((unsigned char) s[i])) || s[i] == 0) { if (isgraph(last_char)) __ksplit_aux; // the end of a field } else { if (isspace(last_char) || last_char == 0) last_start = i; } } else { if (s[i] == delimiter || s[i] == 0) { if (last_char != 0 && last_char != delimiter) __ksplit_aux; // the end of a field } else { if (last_char == delimiter || last_char == 0) last_start = i; } } last_char = (int)((unsigned char)s[i]); } *_max = max; *_offsets = offsets; return n; } int kgetline(kstring_t *s, kgets_func *fgets_fn, void *fp) { size_t l0 = s->l; while (s->l == l0 || s->s[s->l-1] != '\n') { if (s->m - s->l < 200) { if (ks_resize(s, s->m + 200) < 0) return EOF; } if (fgets_fn(s->s + s->l, s->m - s->l, fp) == NULL) break; s->l += strlen(s->s + s->l); } if (s->l == l0) return EOF; if (s->l > l0 && s->s[s->l-1] == '\n') { s->l--; if (s->l > l0 && s->s[s->l-1] == '\r') s->l--; } s->s[s->l] = '\0'; return 0; } int kgetline2(kstring_t *s, kgets_func2 *fgets_fn, void *fp) { size_t l0 = s->l; while (s->l == l0 || s->s[s->l-1] != '\n') { if (s->m - s->l < 200) { // We return EOF for both EOF and error and the caller // needs to check for errors in fp, and we haven't // even got there yet. // // The only way of propagating memory errors is to // deliberately call something that we know triggers // and error so fp is also set. This works for // hgets, but not for gets where reading <= 0 bytes // isn't an error. if (ks_resize(s, s->m + 200) < 0) { fgets_fn(s->s + s->l, 0, fp); return EOF; } } ssize_t len = fgets_fn(s->s + s->l, s->m - s->l, fp); if (len <= 0) break; s->l += len; } if (s->l == l0) return EOF; if (s->l > l0 && s->s[s->l-1] == '\n') { s->l--; if (s->l > l0 && s->s[s->l-1] == '\r') s->l--; } s->s[s->l] = '\0'; return 0; } /********************** * Boyer-Moore search * **********************/ typedef unsigned char ubyte_t; // reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html static int *ksBM_prep(const ubyte_t *pat, int m) { int i, *suff, *prep, *bmGs, *bmBc; prep = (int*)calloc(m + 256, sizeof(int)); if (!prep) return NULL; bmGs = prep; bmBc = prep + m; { // preBmBc() for (i = 0; i < 256; ++i) bmBc[i] = m; for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1; } suff = (int*)calloc(m, sizeof(int)); if (!suff) { free(prep); return NULL; } { // suffixes() int f = 0, g; suff[m - 1] = m; g = m - 1; for (i = m - 2; i >= 0; --i) { if (i > g && suff[i + m - 1 - f] < i - g) suff[i] = suff[i + m - 1 - f]; else { if (i < g) g = i; f = i; while (g >= 0 && pat[g] == pat[g + m - 1 - f]) --g; suff[i] = f - g; } } } { // preBmGs() int j = 0; for (i = 0; i < m; ++i) bmGs[i] = m; for (i = m - 1; i >= 0; --i) if (suff[i] == i + 1) for (; j < m - 1 - i; ++j) if (bmGs[j] == m) bmGs[j] = m - 1 - i; for (i = 0; i <= m - 2; ++i) bmGs[m - 1 - suff[i]] = m - 1 - i; } free(suff); return prep; } void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep) { int i, j, *prep = 0, *bmGs, *bmBc; const ubyte_t *str, *pat; str = (const ubyte_t*)_str; pat = (const ubyte_t*)_pat; prep = (_prep == 0 || *_prep == 0)? ksBM_prep(pat, m) : *_prep; if (!prep) return NULL; if (_prep && *_prep == 0) *_prep = prep; bmGs = prep; bmBc = prep + m; j = 0; while (j <= n - m) { for (i = m - 1; i >= 0 && pat[i] == str[i+j]; --i); if (i >= 0) { int max = bmBc[str[i+j]] - m + 1 + i; if (max < bmGs[i]) max = bmGs[i]; j += max; } else return (void*)(str + j); } if (_prep == 0) free(prep); return 0; } char *kstrstr(const char *str, const char *pat, int **_prep) { return (char*)kmemmem(str, strlen(str), pat, strlen(pat), _prep); } char *kstrnstr(const char *str, const char *pat, int n, int **_prep) { return (char*)kmemmem(str, n, pat, strlen(pat), _prep); } /*********************** * The main() function * ***********************/ #ifdef KSTRING_MAIN #include int main() { kstring_t *s; int *fields, n, i; ks_tokaux_t aux; char *p; s = (kstring_t*)calloc(1, sizeof(kstring_t)); // test ksprintf() ksprintf(s, " abcdefg: %d ", 100); printf("'%s'\n", s->s); // test ksplit() fields = ksplit(s, 0, &n); for (i = 0; i < n; ++i) printf("field[%d] = '%s'\n", i, s->s + fields[i]); // test kstrtok() s->l = 0; for (p = kstrtok("ab:cde:fg/hij::k", ":/", &aux); p; p = kstrtok(0, 0, &aux)) { kputsn(p, aux.p - p, s); kputc('\n', s); } printf("%s", s->s); // free free(s->s); free(s); free(fields); { static char *str = "abcdefgcdgcagtcakcdcd"; static char *pat = "cd"; char *ret, *s = str; int *prep = 0; while ((ret = kstrstr(s, pat, &prep)) != 0) { printf("match: %s\n", ret); s = ret + prep[0]; } free(prep); } return 0; } #endif pysam-0.23.0/htslib/m4/000077500000000000000000000000001475062545500145475ustar00rootroot00000000000000pysam-0.23.0/htslib/m4/hts_check_compile_flags_needed.m4000066400000000000000000000051401475062545500231340ustar00rootroot00000000000000# hts_check_compile_flags_needed.m4 # # SYNOPSIS # # HTS_CHECK_COMPILE_FLAGS_NEEDED(FEATURE, FLAGS, [INPUT], [ACTION-SUCCESS], [ACTION-FAILURE], [EXTRA-FLAGS]) # # DESCRIPTION # # Check whether the given FLAGS are required to build and link INPUT with # the current language's compiler. Compilation and linking are first # tries without FLAGS. If that fails it then tries to compile and # link again with FLAGS. # # FEATURE describes the feature being tested, and is used when printing # messages and to name the cache entry (along with the tested flags). # # ACTION-SUCCESS/ACTION-FAILURE are shell commands to execute on # success/failure. In ACTION-SUCCESS, $flags_needed will be set to # either an empty string or FLAGS depending on the test results. # # If EXTRA-FLAGS is defined, it is added to the current language's default # flags (e.g. CFLAGS) when the check is done. The check is thus made with # the flags: "CFLAGS EXTRA-FLAGS FLAG". This can for example be used to # force the compiler to issue an error when a bad flag is given. # # If omitted, INPUT defaults to AC_LANG_PROGRAM(), although that probably # isn't very useful. # # NOTE: Implementation based on AX_CHECK_COMPILE_FLAG. # # LICENSE # # Copyright (c) 2008 Guido U. Draheim # Copyright (c) 2011 Maarten Bosmans # Copyright (c) 2023 Robert Davies # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice # and this notice are preserved. This file is offered as-is, without any # warranty. # HTS_CHECK_COMPILE_FLAGS_NEEDED(FEATURE, FLAGS, [INPUT], [ACTION-SUCCESS], [ACTION-FAILURE], [EXTRA-FLAGS]) AC_DEFUN([HTS_CHECK_COMPILE_FLAGS_NEEDED], [AC_PREREQ(2.64)dnl for _AC_LANG_PREFIX and AS_VAR_IF AS_VAR_PUSHDEF([CACHEVAR],[hts_cv_check_[]_AC_LANG_ABBREV[]flags_needed_$1_$6_$2])dnl AC_CACHE_CHECK([_AC_LANG compiler flags needed for $1], CACHEVAR, [ AC_LINK_IFELSE([m4_default([$3],[AC_LANG_PROGRAM()])], [AS_VAR_SET(CACHEVAR,[none])], [ax_check_save_flags=$[]_AC_LANG_PREFIX[]FLAGS _AC_LANG_PREFIX[]FLAGS="$[]_AC_LANG_PREFIX[]FLAGS $6 $2" AC_LINK_IFELSE([m4_default([$3],[AC_LANG_PROGRAM()])], [AS_VAR_SET(CACHEVAR,["$2"])], [AS_VAR_SET(CACHEVAR,[unsupported])]) _AC_LANG_PREFIX[]FLAGS=$ax_check_save_flags])]) AS_VAR_IF(CACHEVAR,unsupported, [ m4_default([$5], :) ], [ AS_VAR_IF(CACHEVAR,none,[flags_needed=""], [flags_needed="$CACHEVAR"]) m4_default([$4], :) ]) AS_VAR_POPDEF([CACHEVAR])dnl ])dnl HTS_CHECK_COMPILE_FLAGS_NEEDED pysam-0.23.0/htslib/m4/hts_hide_dynamic_syms.m4000066400000000000000000000050541475062545500213630ustar00rootroot00000000000000dnl @synopsis HTS_HIDE_DYNAMIC_SYMBOLS dnl dnl Turn on compiler options that prevent unwanted symbols from being exported dnl by shared libraries. dnl dnl @author Rob Davies dnl @license MIT/Expat dnl dnl Copyright (C) 2018 Genome Research Ltd. dnl dnl Permission is hereby granted, free of charge, to any person obtaining a copy dnl of this software and associated documentation files (the "Software"), to dnl deal in the Software without restriction, including without limitation the dnl rights to use, copy, modify, merge, publish, distribute, sublicense, and/or dnl sell copies of the Software, and to permit persons to whom the Software is dnl furnished to do so, subject to the following conditions: dnl dnl The above copyright notice and this permission notice shall be included in dnl all copies or substantial portions of the Software. dnl dnl THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR dnl IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, dnl FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL dnl THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER dnl LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING dnl FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER dnl DEALINGS IN THE SOFTWARE. # SYNOPSIS # # HTS_TEST_CC_C_LD_FLAG(FLAG, FOUND_VAR) # # Test if FLAG can be used on both CFLAGS and LDFLAGS. It it works, # variable FOUND_VAR is set to FLAG. AC_DEFUN([HTS_TEST_CC_C_LD_FLAG], [AS_VAR_PUSHDEF([hts_cv_check_flag],[hts_cv_check_$1])dnl AC_CACHE_CHECK([whether the compiler accepts $1], [hts_cv_check_flag], [ac_check_save_cflags=$CFLAGS ac_check_save_ldflags=$LDFLAGS CFLAGS="$CFLAGS $1" LDFLAGS="$LDFLAGS $1" AC_LINK_IFELSE([AC_LANG_PROGRAM()], [AS_VAR_SET([hts_cv_check_flag],[yes]) AS_IF([test "x$2" != x],[eval AS_TR_SH([$2])="$1"])], [AS_VAR_SET([hts_cv_check_flag],[no])]) CFLAGS=$ac_check_save_cflags LDFLAGS=$ac_check_save_ldflags]) AS_VAR_POPDEF([hts_cv_check_flag])dnl ]) AC_DEFUN([HTS_HIDE_DYNAMIC_SYMBOLS], [ # Test for flags to set default shared library visibility to hidden # -fvisibility=hidden : GCC compatible # -xldscope=hidden : SunStudio ac_opt_found=no m4_foreach_w([ac_opt],[-fvisibility=hidden -xldscope=hidden], [AS_IF([test "x$ac_opt_found" = "xno"], [HTS_TEST_CC_C_LD_FLAG(ac_opt,[ac_opt_found])]) ]) AS_IF([test "x$ac_opt_found" != "xno"], [CFLAGS="$CFLAGS $ac_opt_found" LDFLAGS="$LDFLAGS $ac_opt_found"]) ]) pysam-0.23.0/htslib/m4/hts_prog_cc_warnings.m4000066400000000000000000000201211475062545500212070ustar00rootroot00000000000000dnl @synopsis HTS_PROG_CC_WARNINGS([ANSI]) dnl dnl Derived from dnl http://ac-archive.sourceforge.net/ac-archive/vl_prog_cc_warnings.html dnl dnl Enables a reasonable set of warnings for the C compiler. dnl Optionally, if the first argument is nonempty, turns on flags which dnl enforce and/or enable proper ANSI C if such are known with the dnl compiler used. dnl dnl Currently this macro knows about GCC, Solaris C compiler, Digital dnl Unix C compiler, C for AIX Compiler, HP-UX C compiler, IRIX C dnl compiler, NEC SX-5 (Super-UX 10) C compiler, and Cray J90 (Unicos dnl 10.0.0.8) C compiler. dnl dnl @category C dnl @author Ville Laurikari dnl Updated by Rob Davies for HTSlib dnl @license AllPermissive dnl Copying and distribution of this file, with or without modification, dnl are permitted in any medium without royalty provided the copyright notice dnl and this notice are preserved. Users of this software should generally dnl follow the principles of the MIT License including its disclaimer. dnl Original Copyright (c) Ville Laurikari 2002 dnl Modifications Copyright (c) Genome Research Limited 2015,2017 AC_DEFUN([HTS_PROG_CC_WARNINGS], [ AC_ARG_ENABLE([warnings], [AS_HELP_STRING([--disable-warnings], [turn off compiler warnings])], [], [enable_warnings=yes]) AS_IF([test "x$enable_warnings" != xno],[ AC_REQUIRE([AC_PROG_GREP]) ansi="$1" AS_IF([test "x$ansi" = "x"], [msg="for C compiler warning flags"], [msg="for C compiler warning and ANSI conformance flags"]) AC_MSG_CHECKING($msg) AC_CACHE_VAL(hts_cv_prog_cc_warnings, [dnl hts_cv_prog_cc_warnings="" AS_IF([test "x$CC" != "x"],[ cat > conftest.c < /dev/null 2>&1 && test -f conftest.o],[dnl AS_IF([test "x$ansi" = "x"], [hts_cv_prog_cc_warnings="-Wall"], [hts_cv_prog_cc_warnings="-Wall -ansi -pedantic"]) ], # Sun Studio or Solaris C compiler ["$CC" -V 2>&1 | $GREP -i -E "WorkShop|Sun C" > /dev/null 2>&1 && "$CC" -c -v -Xc conftest.c > /dev/null 2>&1 && test -f conftest.o],[dnl AS_IF([test "x$ansi" = "x"], [hts_cv_prog_cc_warnings="-v"], [hts_cv_prog_cc_warnings="-v -Xc"]) ], # Digital Unix C compiler ["$CC" -V 2>&1 | $GREP -i "Digital UNIX Compiler" > /dev/null 2>&1 && "$CC" -c -verbose -w0 -warnprotos -std1 conftest.c > /dev/null 2>&1 && test -f conftest.o], [dnl AS_IF([test "x$ansi" = "x"], [hts_cv_prog_cc_warnings="-verbose -w0 -warnprotos"], [hts_cv_prog_cc_warnings="-verbose -w0 -warnprotos -std1"]) ], # C for AIX Compiler ["$CC" 2>&1 | $GREP -i "C for AIX Compiler" > /dev/null 2>&1 && "$CC" -c -qlanglvl=ansi -qinfo=all conftest.c > /dev/null 2>&1 && test -f conftest.o],[dnl AS_IF([test "x$ansi" = "x"], [hts_cv_prog_cc_warnings="-qsrcmsg -qinfo=all:noppt:noppc:noobs:nocnd"], [hts_cv_prog_cc_warnings="-qsrcmsg -qinfo=all:noppt:noppc:noobs:nocnd -qlanglvl=ansi"]) ], # IRIX C compiler ["$CC" -version 2>&1 | $GREP -i "MIPSpro Compilers" > /dev/null 2>&1 && "$CC" -c -fullwarn -ansi -ansiE conftest.c > /dev/null 2>&1 && test -f conftest.o],[dnl AS_IF([test "x$ansi" = "x"], [hts_cv_prog_cc_warnings="-fullwarn"], [hts_cv_prog_cc_warnings="-fullwarn -ansi -ansiE"]) ], # HP-UX C compiler [what "$CC" 2>&1 | $GREP -i "HP C Compiler" > /dev/null 2>&1 && "$CC" -c -Aa +w1 conftest.c > /dev/null 2>&1 && test -f conftest.o],[dnl AS_IF([test "x$ansi" = "x"], [hts_cv_prog_cc_warnings="+w1"], [hts_cv_prog_cc_warnings="+w1 -Aa"]) ], # The NEC SX series (Super-UX 10) C compiler ["$CC" -V 2>&1 | $GREP "/SX" > /dev/null 2>&1 && "$CC" -c -pvctl[,]fullmsg -Xc conftest.c > /dev/null 2>&1 && test -f conftest.o],[ AS_IF([test "x$ansi" = "x"], [hts_cv_prog_cc_warnings="-pvctl[,]fullmsg"], [hts_cv_prog_cc_warnings="-pvctl[,]fullmsg -Xc"]) ], # The Cray C compiler (Unicos) ["$CC" -V 2>&1 | $GREP -i "Cray" > /dev/null 2>&1 && "$CC" -c -h msglevel_2 conftest.c > /dev/null 2>&1 && test -f conftest.o],[dnl AS_IF([test "x$ansi" = "x"], [hts_cv_prog_cc_warnings="-h#msglevel_2"], [hts_cv_prog_cc_warnings="-h#msglevel_2,conform"]) ], # The Tiny C Compiler ["$CC" -v 2>&1 | $GREP "tcc version" > /dev/null && "$CC" -Wall -c conftest.c > /dev/null 2>&1 && test -f conftest.o],[dnl hts_cv_prog_cc_warnings="-Wall" ]) rm -f conftest.* ]) ]) AS_IF([test "x$hts_cv_prog_cc_warnings" != "x"],[ dnl Print result, with underscores as spaces ac_arg_result=`echo "$hts_cv_prog_cc_warnings" | tr '#' ' '` AC_MSG_RESULT($ac_arg_result) dnl Add options to CFLAGS only if they are not already present ac_arg_needed="" for ac_arg in $hts_cv_prog_cc_warnings do ac_arg_sp=`echo "$ac_arg" | tr '#' ' '` AS_CASE([" $CFLAGS "], [*" $ac_arg_sp "*], [], [ac_arg_needed="$ac_arg_all $ac_arg_sp"]) done CFLAGS="$ac_arg_needed $CFLAGS"],[dnl AC_MSG_RESULT(unknown) ]) ]) ])dnl HTS_PROG_CC_WARNINGS # SYNOPSIS # # HTS_PROG_CC_WERROR(FLAGS_VAR) # # Set FLAGS_VAR to the flags needed to make the C compiler treat warnings # as errors. AC_DEFUN([HTS_PROG_CC_WERROR], [ AC_ARG_ENABLE([werror], [AS_HELP_STRING([--enable-werror], [change warnings into errors, where supported])], [], [enable_werror=no]) AS_IF([test "x$enable_werror" != xno],[ AC_MSG_CHECKING([for C compiler flags to error on warnings]) AC_CACHE_VAL(hts_cv_prog_cc_werror, [dnl hts_cv_prog_cc_werror="" AS_IF([test "x$CC" != "x"],[ cat > conftest.c < /dev/null 2>&1 && test -f conftest.o],[hts_cv_prog_cc_werror="-Werror"], # Sun Studio or Solaris C compiler ["$CC" -V 2>&1 | $GREP -i -E "WorkShop|Sun C" > /dev/null 2>&1 && "$CC" -c -errwarn=%all conftest.c > /dev/null 2>&1 && test -f conftest.o],[hts_cv_prog_cc_werror="-errwarn=%all"], # The Tiny C Compiler ["$CC" -v 2>&1 | $GREP "tcc version" > /dev/null && "$CC" -Wall -c conftest.c > /dev/null 2>&1 && test -f conftest.o],[hts_cv_prog_cc_werror="-Werror"] dnl TODO: Add more compilers ) rm -f conftest.* ]) ]) AS_IF([test "x$hts_cv_prog_cc_werror" != x],[ AC_MSG_RESULT($hts_cv_prog_cc_werror) AS_IF([test "x$1" != x],[eval AS_TR_SH([$1])="$hts_cv_prog_cc_werror"]) ],[dnl AC_MSG_RESULT(unknown) ]) ]) ])dnl HTS_PROG_CC_WERROR pysam-0.23.0/htslib/m4/pkg.m4000066400000000000000000000240041475062545500155720ustar00rootroot00000000000000# pkg.m4 - Macros to locate and use pkg-config. -*- Autoconf -*- # serial 12 (pkg-config-0.29.2) dnl Copyright © 2004 Scott James Remnant . dnl Copyright © 2012-2015 Dan Nicholson dnl dnl This program is free software; you can redistribute it and/or modify dnl it under the terms of the GNU General Public License as published by dnl the Free Software Foundation; either version 2 of the License, or dnl (at your option) any later version. dnl dnl This program is distributed in the hope that it will be useful, but dnl WITHOUT ANY WARRANTY; without even the implied warranty of dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU dnl General Public License for more details. dnl dnl You should have received a copy of the GNU General Public License dnl along with this program; if not, write to the Free Software dnl Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA dnl 02111-1307, USA. dnl dnl As a special exception to the GNU General Public License, if you dnl distribute this file as part of a program that contains a dnl configuration script generated by Autoconf, you may include it under dnl the same distribution terms that you use for the rest of that dnl program. dnl PKG_PREREQ(MIN-VERSION) dnl ----------------------- dnl Since: 0.29 dnl dnl Verify that the version of the pkg-config macros are at least dnl MIN-VERSION. Unlike PKG_PROG_PKG_CONFIG, which checks the user's dnl installed version of pkg-config, this checks the developer's version dnl of pkg.m4 when generating configure. dnl dnl To ensure that this macro is defined, also add: dnl m4_ifndef([PKG_PREREQ], dnl [m4_fatal([must install pkg-config 0.29 or later before running autoconf/autogen])]) dnl dnl See the "Since" comment for each macro you use to see what version dnl of the macros you require. m4_defun([PKG_PREREQ], [m4_define([PKG_MACROS_VERSION], [0.29.2]) m4_if(m4_version_compare(PKG_MACROS_VERSION, [$1]), -1, [m4_fatal([pkg.m4 version $1 or higher is required but ]PKG_MACROS_VERSION[ found])]) ])dnl PKG_PREREQ dnl PKG_PROG_PKG_CONFIG([MIN-VERSION]) dnl ---------------------------------- dnl Since: 0.16 dnl dnl Search for the pkg-config tool and set the PKG_CONFIG variable to dnl first found in the path. Checks that the version of pkg-config found dnl is at least MIN-VERSION. If MIN-VERSION is not specified, 0.9.0 is dnl used since that's the first version where most current features of dnl pkg-config existed. AC_DEFUN([PKG_PROG_PKG_CONFIG], [m4_pattern_forbid([^_?PKG_[A-Z_]+$]) m4_pattern_allow([^PKG_CONFIG(_(PATH|LIBDIR|SYSROOT_DIR|ALLOW_SYSTEM_(CFLAGS|LIBS)))?$]) m4_pattern_allow([^PKG_CONFIG_(DISABLE_UNINSTALLED|TOP_BUILD_DIR|DEBUG_SPEW)$]) AC_ARG_VAR([PKG_CONFIG], [path to pkg-config utility]) AC_ARG_VAR([PKG_CONFIG_PATH], [directories to add to pkg-config's search path]) AC_ARG_VAR([PKG_CONFIG_LIBDIR], [path overriding pkg-config's built-in search path]) if test "x$ac_cv_env_PKG_CONFIG_set" != "xset"; then AC_PATH_TOOL([PKG_CONFIG], [pkg-config]) fi if test -n "$PKG_CONFIG"; then _pkg_min_version=m4_default([$1], [0.9.0]) AC_MSG_CHECKING([pkg-config is at least version $_pkg_min_version]) if $PKG_CONFIG --atleast-pkgconfig-version $_pkg_min_version; then AC_MSG_RESULT([yes]) else AC_MSG_RESULT([no]) PKG_CONFIG="" fi fi[]dnl ])dnl PKG_PROG_PKG_CONFIG dnl PKG_CHECK_EXISTS(MODULES, [ACTION-IF-FOUND], [ACTION-IF-NOT-FOUND]) dnl ------------------------------------------------------------------- dnl Since: 0.18 dnl dnl Check to see whether a particular set of modules exists. Similar to dnl PKG_CHECK_MODULES(), but does not set variables or print errors. dnl dnl Please remember that m4 expands AC_REQUIRE([PKG_PROG_PKG_CONFIG]) dnl only at the first occurrence in configure.ac, so if the first place dnl it's called might be skipped (such as if it is within an "if", you dnl have to call PKG_CHECK_EXISTS manually AC_DEFUN([PKG_CHECK_EXISTS], [AC_REQUIRE([PKG_PROG_PKG_CONFIG])dnl if test -n "$PKG_CONFIG" && \ AC_RUN_LOG([$PKG_CONFIG --exists --print-errors "$1"]); then m4_default([$2], [:]) m4_ifvaln([$3], [else $3])dnl fi]) dnl _PKG_CONFIG([VARIABLE], [COMMAND], [MODULES]) dnl --------------------------------------------- dnl Internal wrapper calling pkg-config via PKG_CONFIG and setting dnl pkg_failed based on the result. m4_define([_PKG_CONFIG], [if test -n "$$1"; then pkg_cv_[]$1="$$1" elif test -n "$PKG_CONFIG"; then PKG_CHECK_EXISTS([$3], [pkg_cv_[]$1=`$PKG_CONFIG --[]$2 "$3" 2>/dev/null` test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes]) else pkg_failed=untried fi[]dnl ])dnl _PKG_CONFIG dnl _PKG_SHORT_ERRORS_SUPPORTED dnl --------------------------- dnl Internal check to see if pkg-config supports short errors. AC_DEFUN([_PKG_SHORT_ERRORS_SUPPORTED], [AC_REQUIRE([PKG_PROG_PKG_CONFIG]) if $PKG_CONFIG --atleast-pkgconfig-version 0.20; then _pkg_short_errors_supported=yes else _pkg_short_errors_supported=no fi[]dnl ])dnl _PKG_SHORT_ERRORS_SUPPORTED dnl PKG_CHECK_MODULES(VARIABLE-PREFIX, MODULES, [ACTION-IF-FOUND], dnl [ACTION-IF-NOT-FOUND]) dnl -------------------------------------------------------------- dnl Since: 0.4.0 dnl dnl Note that if there is a possibility the first call to dnl PKG_CHECK_MODULES might not happen, you should be sure to include an dnl explicit call to PKG_PROG_PKG_CONFIG in your configure.ac AC_DEFUN([PKG_CHECK_MODULES], [AC_REQUIRE([PKG_PROG_PKG_CONFIG])dnl AC_ARG_VAR([$1][_CFLAGS], [C compiler flags for $1, overriding pkg-config])dnl AC_ARG_VAR([$1][_LIBS], [linker flags for $1, overriding pkg-config])dnl pkg_failed=no AC_MSG_CHECKING([for $2]) _PKG_CONFIG([$1][_CFLAGS], [cflags], [$2]) _PKG_CONFIG([$1][_LIBS], [libs], [$2]) m4_define([_PKG_TEXT], [Alternatively, you may set the environment variables $1[]_CFLAGS and $1[]_LIBS to avoid the need to call pkg-config. See the pkg-config man page for more details.]) if test $pkg_failed = yes; then AC_MSG_RESULT([no]) _PKG_SHORT_ERRORS_SUPPORTED if test $_pkg_short_errors_supported = yes; then $1[]_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "$2" 2>&1` else $1[]_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "$2" 2>&1` fi # Put the nasty error message in config.log where it belongs echo "$$1[]_PKG_ERRORS" >&AS_MESSAGE_LOG_FD m4_default([$4], [AC_MSG_ERROR( [Package requirements ($2) were not met: $$1_PKG_ERRORS Consider adjusting the PKG_CONFIG_PATH environment variable if you installed software in a non-standard prefix. _PKG_TEXT])[]dnl ]) elif test $pkg_failed = untried; then AC_MSG_RESULT([no]) m4_default([$4], [AC_MSG_FAILURE( [The pkg-config script could not be found or is too old. Make sure it is in your PATH or set the PKG_CONFIG environment variable to the full path to pkg-config. _PKG_TEXT To get pkg-config, see .])[]dnl ]) else $1[]_CFLAGS=$pkg_cv_[]$1[]_CFLAGS $1[]_LIBS=$pkg_cv_[]$1[]_LIBS AC_MSG_RESULT([yes]) $3 fi[]dnl ])dnl PKG_CHECK_MODULES dnl PKG_CHECK_MODULES_STATIC(VARIABLE-PREFIX, MODULES, [ACTION-IF-FOUND], dnl [ACTION-IF-NOT-FOUND]) dnl --------------------------------------------------------------------- dnl Since: 0.29 dnl dnl Checks for existence of MODULES and gathers its build flags with dnl static libraries enabled. Sets VARIABLE-PREFIX_CFLAGS from --cflags dnl and VARIABLE-PREFIX_LIBS from --libs. dnl dnl Note that if there is a possibility the first call to dnl PKG_CHECK_MODULES_STATIC might not happen, you should be sure to dnl include an explicit call to PKG_PROG_PKG_CONFIG in your dnl configure.ac. AC_DEFUN([PKG_CHECK_MODULES_STATIC], [AC_REQUIRE([PKG_PROG_PKG_CONFIG])dnl _save_PKG_CONFIG=$PKG_CONFIG PKG_CONFIG="$PKG_CONFIG --static" PKG_CHECK_MODULES($@) PKG_CONFIG=$_save_PKG_CONFIG[]dnl ])dnl PKG_CHECK_MODULES_STATIC dnl PKG_INSTALLDIR([DIRECTORY]) dnl ------------------------- dnl Since: 0.27 dnl dnl Substitutes the variable pkgconfigdir as the location where a module dnl should install pkg-config .pc files. By default the directory is dnl $libdir/pkgconfig, but the default can be changed by passing dnl DIRECTORY. The user can override through the --with-pkgconfigdir dnl parameter. AC_DEFUN([PKG_INSTALLDIR], [m4_pushdef([pkg_default], [m4_default([$1], ['${libdir}/pkgconfig'])]) m4_pushdef([pkg_description], [pkg-config installation directory @<:@]pkg_default[@:>@]) AC_ARG_WITH([pkgconfigdir], [AS_HELP_STRING([--with-pkgconfigdir], pkg_description)],, [with_pkgconfigdir=]pkg_default) AC_SUBST([pkgconfigdir], [$with_pkgconfigdir]) m4_popdef([pkg_default]) m4_popdef([pkg_description]) ])dnl PKG_INSTALLDIR dnl PKG_NOARCH_INSTALLDIR([DIRECTORY]) dnl -------------------------------- dnl Since: 0.27 dnl dnl Substitutes the variable noarch_pkgconfigdir as the location where a dnl module should install arch-independent pkg-config .pc files. By dnl default the directory is $datadir/pkgconfig, but the default can be dnl changed by passing DIRECTORY. The user can override through the dnl --with-noarch-pkgconfigdir parameter. AC_DEFUN([PKG_NOARCH_INSTALLDIR], [m4_pushdef([pkg_default], [m4_default([$1], ['${datadir}/pkgconfig'])]) m4_pushdef([pkg_description], [pkg-config arch-independent installation directory @<:@]pkg_default[@:>@]) AC_ARG_WITH([noarch-pkgconfigdir], [AS_HELP_STRING([--with-noarch-pkgconfigdir], pkg_description)],, [with_noarch_pkgconfigdir=]pkg_default) AC_SUBST([noarch_pkgconfigdir], [$with_noarch_pkgconfigdir]) m4_popdef([pkg_default]) m4_popdef([pkg_description]) ])dnl PKG_NOARCH_INSTALLDIR dnl PKG_CHECK_VAR(VARIABLE, MODULE, CONFIG-VARIABLE, dnl [ACTION-IF-FOUND], [ACTION-IF-NOT-FOUND]) dnl ------------------------------------------- dnl Since: 0.28 dnl dnl Retrieves the value of the pkg-config variable for the given module. AC_DEFUN([PKG_CHECK_VAR], [AC_REQUIRE([PKG_PROG_PKG_CONFIG])dnl AC_ARG_VAR([$1], [value of $3 for $2, overriding pkg-config])dnl _PKG_CONFIG([$1], [variable="][$3]["], [$2]) AS_VAR_COPY([$1], [pkg_cv_][$1]) AS_VAR_IF([$1], [""], [$5], [$4])dnl ])dnl PKG_CHECK_VAR pysam-0.23.0/htslib/md5.c000066400000000000000000000246401475062545500150660ustar00rootroot00000000000000/* * Trivial amendments by James Bonfield to provide an * HTSlib interface. 2015. * * Externally our API uses an opaque hts_md5_context structure. * * Internally either this gets defined and used with the routines here * or it remains incomplete and is cast to the OpenSSL MD5_CTX structure * and used by routines from OpenSSL. */ /* * This is an OpenSSL-compatible implementation of the RSA Data Security, Inc. * MD5 Message-Digest Algorithm (RFC 1321). * * Homepage: * http://openwall.info/wiki/people/solar/software/public-domain-source-code/md5 * * Author: * Alexander Peslyak, better known as Solar Designer * * This software was written by Alexander Peslyak in 2001. No copyright is * claimed, and the software is hereby placed in the public domain. * In case this attempt to disclaim copyright and place the software in the * public domain is deemed null and void, then the software is * Copyright (c) 2001 Alexander Peslyak and it is hereby released to the * general public under the following terms: * * Redistribution and use in source and binary forms, with or without * modification, are permitted. * * There's ABSOLUTELY NO WARRANTY, express or implied. * * (This is a heavily cut-down "BSD license".) * * This differs from Colin Plumb's older public domain implementation in that * no exactly 32-bit integer data type is required (any 32-bit or wider * unsigned integer data type will do), there's no compile-time endianness * configuration, and the function prototypes match OpenSSL's. No code from * Colin Plumb's implementation has been reused; this comment merely compares * the properties of the two independent implementations. * * The primary goals of this implementation are portability and ease of use. * It is meant to be fast, but not as fast as possible. Some known * optimizations are not included to reduce source code size and avoid * compile-time configuration. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include "htslib/hts.h" #include "htslib/hts_endian.h" #ifndef HAVE_OPENSSL #include /* Any 32-bit or wider unsigned integer data type will do */ typedef unsigned int hts_md5_u32plus; struct hts_md5_context { hts_md5_u32plus lo, hi; hts_md5_u32plus a, b, c, d; unsigned char buffer[64]; hts_md5_u32plus block[16]; }; /* * The basic MD5 functions. * * F and G are optimized compared to their RFC 1321 definitions for * architectures that lack an AND-NOT instruction, just like in Colin Plumb's * implementation. */ #define F(x, y, z) ((z) ^ ((x) & ((y) ^ (z)))) #define G(x, y, z) ((y) ^ ((z) & ((x) ^ (y)))) #define H(x, y, z) (((x) ^ (y)) ^ (z)) #define H2(x, y, z) ((x) ^ ((y) ^ (z))) #define I(x, y, z) ((y) ^ ((x) | ~(z))) /* * The MD5 transformation for all four rounds. */ #define STEP(f, a, b, c, d, x, t, s) \ (a) += f((b), (c), (d)) + (x) + (t); \ (a) = (((a) << (s)) | (((a) & 0xffffffff) >> (32 - (s)))); \ (a) += (b); /* * SET reads 4 input bytes in little-endian byte order and stores them * in a properly aligned word in host byte order. * * The check for little-endian architectures that tolerate unaligned * memory accesses is just an optimization. Nothing will break if it * doesn't work. */ #if defined(HTS_LITTLE_ENDIAN) && HTS_ALLOW_UNALIGNED != 0 #define SET(n) \ (*(hts_md5_u32plus *)&ptr[(n) * 4]) #define GET(n) \ SET(n) #else #define SET(n) \ (ctx->block[(n)] = \ (hts_md5_u32plus)ptr[(n) * 4] | \ ((hts_md5_u32plus)ptr[(n) * 4 + 1] << 8) | \ ((hts_md5_u32plus)ptr[(n) * 4 + 2] << 16) | \ ((hts_md5_u32plus)ptr[(n) * 4 + 3] << 24)) #define GET(n) \ (ctx->block[(n)]) #endif /* * This processes one or more 64-byte data blocks, but does NOT update * the bit counters. There are no alignment requirements. */ static const void *body(hts_md5_context *ctx, const void *data, unsigned long size) { const unsigned char *ptr; hts_md5_u32plus a, b, c, d; hts_md5_u32plus saved_a, saved_b, saved_c, saved_d; ptr = (const unsigned char *)data; a = ctx->a; b = ctx->b; c = ctx->c; d = ctx->d; do { saved_a = a; saved_b = b; saved_c = c; saved_d = d; /* Round 1 */ STEP(F, a, b, c, d, SET(0), 0xd76aa478, 7) STEP(F, d, a, b, c, SET(1), 0xe8c7b756, 12) STEP(F, c, d, a, b, SET(2), 0x242070db, 17) STEP(F, b, c, d, a, SET(3), 0xc1bdceee, 22) STEP(F, a, b, c, d, SET(4), 0xf57c0faf, 7) STEP(F, d, a, b, c, SET(5), 0x4787c62a, 12) STEP(F, c, d, a, b, SET(6), 0xa8304613, 17) STEP(F, b, c, d, a, SET(7), 0xfd469501, 22) STEP(F, a, b, c, d, SET(8), 0x698098d8, 7) STEP(F, d, a, b, c, SET(9), 0x8b44f7af, 12) STEP(F, c, d, a, b, SET(10), 0xffff5bb1, 17) STEP(F, b, c, d, a, SET(11), 0x895cd7be, 22) STEP(F, a, b, c, d, SET(12), 0x6b901122, 7) STEP(F, d, a, b, c, SET(13), 0xfd987193, 12) STEP(F, c, d, a, b, SET(14), 0xa679438e, 17) STEP(F, b, c, d, a, SET(15), 0x49b40821, 22) /* Round 2 */ STEP(G, a, b, c, d, GET(1), 0xf61e2562, 5) STEP(G, d, a, b, c, GET(6), 0xc040b340, 9) STEP(G, c, d, a, b, GET(11), 0x265e5a51, 14) STEP(G, b, c, d, a, GET(0), 0xe9b6c7aa, 20) STEP(G, a, b, c, d, GET(5), 0xd62f105d, 5) STEP(G, d, a, b, c, GET(10), 0x02441453, 9) STEP(G, c, d, a, b, GET(15), 0xd8a1e681, 14) STEP(G, b, c, d, a, GET(4), 0xe7d3fbc8, 20) STEP(G, a, b, c, d, GET(9), 0x21e1cde6, 5) STEP(G, d, a, b, c, GET(14), 0xc33707d6, 9) STEP(G, c, d, a, b, GET(3), 0xf4d50d87, 14) STEP(G, b, c, d, a, GET(8), 0x455a14ed, 20) STEP(G, a, b, c, d, GET(13), 0xa9e3e905, 5) STEP(G, d, a, b, c, GET(2), 0xfcefa3f8, 9) STEP(G, c, d, a, b, GET(7), 0x676f02d9, 14) STEP(G, b, c, d, a, GET(12), 0x8d2a4c8a, 20) /* Round 3 */ STEP(H, a, b, c, d, GET(5), 0xfffa3942, 4) STEP(H2, d, a, b, c, GET(8), 0x8771f681, 11) STEP(H, c, d, a, b, GET(11), 0x6d9d6122, 16) STEP(H2, b, c, d, a, GET(14), 0xfde5380c, 23) STEP(H, a, b, c, d, GET(1), 0xa4beea44, 4) STEP(H2, d, a, b, c, GET(4), 0x4bdecfa9, 11) STEP(H, c, d, a, b, GET(7), 0xf6bb4b60, 16) STEP(H2, b, c, d, a, GET(10), 0xbebfbc70, 23) STEP(H, a, b, c, d, GET(13), 0x289b7ec6, 4) STEP(H2, d, a, b, c, GET(0), 0xeaa127fa, 11) STEP(H, c, d, a, b, GET(3), 0xd4ef3085, 16) STEP(H2, b, c, d, a, GET(6), 0x04881d05, 23) STEP(H, a, b, c, d, GET(9), 0xd9d4d039, 4) STEP(H2, d, a, b, c, GET(12), 0xe6db99e5, 11) STEP(H, c, d, a, b, GET(15), 0x1fa27cf8, 16) STEP(H2, b, c, d, a, GET(2), 0xc4ac5665, 23) /* Round 4 */ STEP(I, a, b, c, d, GET(0), 0xf4292244, 6) STEP(I, d, a, b, c, GET(7), 0x432aff97, 10) STEP(I, c, d, a, b, GET(14), 0xab9423a7, 15) STEP(I, b, c, d, a, GET(5), 0xfc93a039, 21) STEP(I, a, b, c, d, GET(12), 0x655b59c3, 6) STEP(I, d, a, b, c, GET(3), 0x8f0ccc92, 10) STEP(I, c, d, a, b, GET(10), 0xffeff47d, 15) STEP(I, b, c, d, a, GET(1), 0x85845dd1, 21) STEP(I, a, b, c, d, GET(8), 0x6fa87e4f, 6) STEP(I, d, a, b, c, GET(15), 0xfe2ce6e0, 10) STEP(I, c, d, a, b, GET(6), 0xa3014314, 15) STEP(I, b, c, d, a, GET(13), 0x4e0811a1, 21) STEP(I, a, b, c, d, GET(4), 0xf7537e82, 6) STEP(I, d, a, b, c, GET(11), 0xbd3af235, 10) STEP(I, c, d, a, b, GET(2), 0x2ad7d2bb, 15) STEP(I, b, c, d, a, GET(9), 0xeb86d391, 21) a += saved_a; b += saved_b; c += saved_c; d += saved_d; ptr += 64; } while (size -= 64); ctx->a = a; ctx->b = b; ctx->c = c; ctx->d = d; return ptr; } void hts_md5_reset(hts_md5_context *ctx) { ctx->a = 0x67452301; ctx->b = 0xefcdab89; ctx->c = 0x98badcfe; ctx->d = 0x10325476; ctx->lo = 0; ctx->hi = 0; } void hts_md5_update(hts_md5_context *ctx, const void *data, unsigned long size) { hts_md5_u32plus saved_lo; unsigned long used, available; saved_lo = ctx->lo; if ((ctx->lo = (saved_lo + size) & 0x1fffffff) < saved_lo) ctx->hi++; ctx->hi += size >> 29; used = saved_lo & 0x3f; if (used) { available = 64 - used; if (size < available) { memcpy(&ctx->buffer[used], data, size); return; } memcpy(&ctx->buffer[used], data, available); data = (const unsigned char *)data + available; size -= available; body(ctx, ctx->buffer, 64); } if (size >= 64) { data = body(ctx, data, size & ~(unsigned long)0x3f); size &= 0x3f; } memcpy(ctx->buffer, data, size); } void hts_md5_final(unsigned char *result, hts_md5_context *ctx) { unsigned long used, available; used = ctx->lo & 0x3f; ctx->buffer[used++] = 0x80; available = 64 - used; if (available < 8) { memset(&ctx->buffer[used], 0, available); body(ctx, ctx->buffer, 64); used = 0; available = 64; } memset(&ctx->buffer[used], 0, available - 8); ctx->lo <<= 3; ctx->buffer[56] = ctx->lo; ctx->buffer[57] = ctx->lo >> 8; ctx->buffer[58] = ctx->lo >> 16; ctx->buffer[59] = ctx->lo >> 24; ctx->buffer[60] = ctx->hi; ctx->buffer[61] = ctx->hi >> 8; ctx->buffer[62] = ctx->hi >> 16; ctx->buffer[63] = ctx->hi >> 24; body(ctx, ctx->buffer, 64); result[0] = ctx->a; result[1] = ctx->a >> 8; result[2] = ctx->a >> 16; result[3] = ctx->a >> 24; result[4] = ctx->b; result[5] = ctx->b >> 8; result[6] = ctx->b >> 16; result[7] = ctx->b >> 24; result[8] = ctx->c; result[9] = ctx->c >> 8; result[10] = ctx->c >> 16; result[11] = ctx->c >> 24; result[12] = ctx->d; result[13] = ctx->d >> 8; result[14] = ctx->d >> 16; result[15] = ctx->d >> 24; memset(ctx, 0, sizeof(*ctx)); } hts_md5_context *hts_md5_init(void) { hts_md5_context *ctx = malloc(sizeof(*ctx)); if (!ctx) return NULL; hts_md5_reset(ctx); return ctx; } #else #include #include /* * Wrappers around the OpenSSL libcrypto.so MD5 implementation. * * These are here to ensure they end up in the symbol table of the * library regardless of the static inline in the headers. */ hts_md5_context *hts_md5_init(void) { MD5_CTX *ctx = malloc(sizeof(*ctx)); if (!ctx) return NULL; MD5_Init(ctx); return (hts_md5_context *)ctx; } void hts_md5_reset(hts_md5_context *ctx) { MD5_Init((MD5_CTX *)ctx); } void hts_md5_update(hts_md5_context *ctx, const void *data, unsigned long size) { MD5_Update((MD5_CTX *)ctx, data, size); } void hts_md5_final(unsigned char *result, hts_md5_context *ctx) { MD5_Final(result, (MD5_CTX *)ctx); } #endif void hts_md5_destroy(hts_md5_context *ctx) { if (!ctx) return; free(ctx); } void hts_md5_hex(char *hex, const unsigned char *digest) { int i; for (i = 0; i < 16; i++) { hex[i*2+0] = "0123456789abcdef"[(digest[i]>>4)&0xf]; hex[i*2+1] = "0123456789abcdef"[digest[i]&0xf]; } hex[32] = 0; } pysam-0.23.0/htslib/multipart.c000066400000000000000000000204501475062545500164150ustar00rootroot00000000000000/* multipart.c -- GA4GH redirection and multipart backend for file streams. Copyright (C) 2016-2017 Genome Research Ltd. Author: John Marshall Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include "htslib/kstring.h" #include "hts_internal.h" #include "hfile_internal.h" #ifndef EPROTO #define EPROTO ENOEXEC #endif typedef struct hfile_part { char *url; char **headers; } hfile_part; typedef struct { hFILE base; hfile_part *parts; size_t nparts, maxparts, current; hFILE *currentfp; } hFILE_multipart; static void free_part(hfile_part *p) { free(p->url); if (p->headers) { char **hdr; for (hdr = p->headers; *hdr; hdr++) free(*hdr); free(p->headers); } p->url = NULL; p->headers = NULL; } static void free_all_parts(hFILE_multipart *fp) { size_t i; for (i = 0; i < fp->nparts; i++) free_part(&fp->parts[i]); free(fp->parts); } static ssize_t multipart_read(hFILE *fpv, void *buffer, size_t nbytes) { hFILE_multipart *fp = (hFILE_multipart *) fpv; size_t n; open_next: if (fp->currentfp == NULL) { if (fp->current < fp->nparts) { const hfile_part *p = &fp->parts[fp->current]; hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"", fp->current+1, fp->nparts, p->url, (strlen(p->url) > 120)? "..." : ""); fp->currentfp = p->headers? hopen(p->url, "r:", "httphdr:v", p->headers, "auth_token_enabled", "false", NULL) : hopen(p->url, "r:", "auth_token_enabled", "false", NULL); if (fp->currentfp == NULL) return -1; } else return 0; // No more parts, so we're truly at EOF } n = fp->currentfp->mobile? fp->currentfp->backend->read(fp->currentfp, buffer, nbytes) : hread(fp->currentfp, buffer, nbytes); if (n == 0) { // We're at EOF on this part, so set up the next part hFILE *prevfp = fp->currentfp; free_part(&fp->parts[fp->current]); fp->current++; fp->currentfp = NULL; if (hclose(prevfp) < 0) return -1; goto open_next; } return n; // Number of bytes read by (or an error from) fp->currentfp } static ssize_t multipart_write(hFILE *fpv, const void *buffer, size_t nbytes) { errno = EROFS; return -1; } static off_t multipart_seek(hFILE *fpv, off_t offset, int whence) { errno = ESPIPE; return -1; } static int multipart_close(hFILE *fpv) { hFILE_multipart *fp = (hFILE_multipart *) fpv; free_all_parts(fp); if (fp->currentfp) { if (hclose(fp->currentfp) < 0) return -1; } return 0; } static const struct hFILE_backend multipart_backend = { multipart_read, multipart_write, multipart_seek, NULL, multipart_close }; // Returns 'v' (valid value), 'i' (invalid; required GA4GH field missing), // or upon encountering an unexpected token, that token's type. // Explicit `return '?'` means a JSON parsing error, typically a member key // that is not a string. An unexpected token may be a valid token that was // not the type expected for a particular GA4GH field, or it may be '?' or // '\0' which should be propagated. static char parse_ga4gh_body_json(hFILE_multipart *fp, hFILE *json, kstring_t *b, kstring_t *header) { hts_json_token t; if (hts_json_fnext(json, &t, b) != '{') return t.type; while (hts_json_fnext(json, &t, b) != '}') { if (t.type != 's') return '?'; if (strcmp(t.str, "urls") == 0) { if (hts_json_fnext(json, &t, b) != '[') return t.type; while (hts_json_fnext(json, &t, b) != ']') { hfile_part *part; size_t n = 0, max = 0; hts_expand(hfile_part, fp->nparts+1, fp->maxparts, fp->parts); part = &fp->parts[fp->nparts++]; part->url = NULL; part->headers = NULL; if (t.type != '{') return t.type; while (hts_json_fnext(json, &t, b) != '}') { if (t.type != 's') return '?'; if (strcmp(t.str, "url") == 0) { if (hts_json_fnext(json, &t, b) != 's') return t.type; part->url = ks_release(b); } else if (strcmp(t.str, "headers") == 0) { if (hts_json_fnext(json, &t, b) != '{') return t.type; while (hts_json_fnext(json, &t, header) != '}') { if (t.type != 's') return '?'; if (hts_json_fnext(json, &t, b) != 's') return t.type; kputs(": ", header); kputs(t.str, header); n++; hts_expand(char *, n+1, max, part->headers); part->headers[n-1] = ks_release(header); part->headers[n] = NULL; } } else if (hts_json_fskip_value(json, '\0') != 'v') return '?'; } if (! part->url) return 'i'; } } else if (strcmp(t.str, "format") == 0) { if (hts_json_fnext(json, &t, b) != 's') return t.type; hts_log_debug("GA4GH JSON redirection to multipart %s data", t.str); } else if (hts_json_fskip_value(json, '\0') != 'v') return '?'; } return 'v'; } // Returns 'v' (valid value), 'i' (invalid; required GA4GH field missing), // or upon encountering an unexpected token, that token's type. // Explicit `return '?'` means a JSON parsing error, typically a member key // that is not a string. An unexpected token may be a valid token that was // not the type expected for a particular GA4GH field, or it may be '?' or // '\0' which should be propagated. static char parse_ga4gh_redirect_json(hFILE_multipart *fp, hFILE *json, kstring_t *b, kstring_t *header) { hts_json_token t; if (hts_json_fnext(json, &t, b) != '{') return t.type; while (hts_json_fnext(json, &t, b) != '}') { if (t.type != 's') return '?'; if (strcmp(t.str, "htsget") == 0) { char ret = parse_ga4gh_body_json(fp, json, b, header); if (ret != 'v') return ret; } else return '?'; } if (hts_json_fnext(json, &t, b) != '\0') return '?'; return 'v'; } hFILE *hopen_htsget_redirect(hFILE *hfile, const char *mode) { hFILE_multipart *fp; kstring_t s1 = { 0, 0, NULL }, s2 = { 0, 0, NULL }; char ret; fp = (hFILE_multipart *) hfile_init(sizeof (hFILE_multipart), mode, 0); if (fp == NULL) return NULL; fp->parts = NULL; fp->nparts = fp->maxparts = 0; ret = parse_ga4gh_redirect_json(fp, hfile, &s1, &s2); free(s1.s); free(s2.s); if (ret != 'v') { free_all_parts(fp); hfile_destroy((hFILE *) fp); errno = (ret == '?' || ret == '\0')? EPROTO : EINVAL; return NULL; } fp->current = 0; fp->currentfp = NULL; fp->base.backend = &multipart_backend; return &fp->base; } pysam-0.23.0/htslib/os/000077500000000000000000000000001475062545500146505ustar00rootroot00000000000000pysam-0.23.0/htslib/os/lzma_stub.h000066400000000000000000000044511475062545500170250ustar00rootroot00000000000000#ifndef LZMA_STUB_H #define LZMA_STUB_H /* Some platforms, notably macOS, ship a usable liblzma shared library but do not ship any LZMA header files. The and header files that come with the library contain the following statement: * * Author: Lasse Collin * * This file has been put into the public domain. * You can do whatever you want with this file. * Accordingly the following declarations have been copied and distilled from and (primarily) and are sufficient to compile cram/cram_io.c in the absence of proper LZMA headers. This file, lzma_stub.h, remains in the public domain. */ #include #ifdef __cplusplus extern "C" { #endif typedef enum { LZMA_OK = 0, LZMA_STREAM_END = 1 } lzma_ret; typedef enum { LZMA_RUN = 0, LZMA_FINISH = 3 } lzma_action; typedef enum { LZMA_CHECK_CRC32 = 1 } lzma_check; typedef enum { LZMA_RESERVED_ENUM = 0 } lzma_reserved_enum; struct lzma_allocator; struct lzma_internal; typedef struct { const uint8_t *next_in; size_t avail_in; uint64_t total_in; uint8_t *next_out; size_t avail_out; uint64_t total_out; const struct lzma_allocator *allocator; struct lzma_internal *internal; void *reserved_ptr1; void *reserved_ptr2; void *reserved_ptr3; void *reserved_ptr4; uint64_t reserved_int1; uint64_t reserved_int2; size_t reserved_int3; size_t reserved_int4; lzma_reserved_enum reserved_enum1; lzma_reserved_enum reserved_enum2; } lzma_stream; #define LZMA_STREAM_INIT \ { NULL, 0, 0, NULL, 0, 0, NULL, NULL, \ NULL, NULL, NULL, NULL, 0, 0, 0, 0, \ LZMA_RESERVED_ENUM, LZMA_RESERVED_ENUM } extern size_t lzma_stream_buffer_bound(size_t uncompressed_size); extern lzma_ret lzma_easy_buffer_encode( uint32_t preset, lzma_check check, const struct lzma_allocator *allocator, const uint8_t *in, size_t in_size, uint8_t *out, size_t *out_pos, size_t out_size); extern lzma_ret lzma_stream_decoder( lzma_stream *strm, uint64_t memlimit, uint32_t flags); extern uint64_t lzma_easy_decoder_memusage(uint32_t preset); extern lzma_ret lzma_code(lzma_stream *strm, lzma_action action); extern void lzma_end(lzma_stream *strm); #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/os/rand.c000066400000000000000000000052201475062545500157370ustar00rootroot00000000000000/* rand.c -- drand48 implementation from the FreeBSD source tree. */ // This file is an amalgamation of the many small files in FreeBSD to do with // drand48 and friends implementations. // It comprises _rand48.c, rand48.h, srand48.c, drand48.c, erand48.c, lrand48.c /* * Copyright (c) 1993 Martin Birgmeier * All rights reserved. * * You may redistribute unmodified or modified versions of this source * code provided that the above copyright notice and this and the * following conditions are retained. * * This software is provided ``as is'', and comes with no warranties * of any kind. I shall in no event be liable for anything that happens * to anyone/anything when using this software. */ //#include //__FBSDID("$FreeBSD: src/lib/libc/gen/_rand48.c,v 1.2 2002/03/22 21:52:05 obrien Exp $"); #include #define RAND48_SEED_0 (0x330e) #define RAND48_SEED_1 (0xabcd) #define RAND48_SEED_2 (0x1234) #define RAND48_MULT_0 (0xe66d) #define RAND48_MULT_1 (0xdeec) #define RAND48_MULT_2 (0x0005) #define RAND48_ADD (0x000b) static unsigned short _rand48_seed[3] = { RAND48_SEED_0, RAND48_SEED_1, RAND48_SEED_2 }; static unsigned short _rand48_mult[3] = { RAND48_MULT_0, RAND48_MULT_1, RAND48_MULT_2 }; static unsigned short _rand48_add = RAND48_ADD; static void _dorand48(unsigned short xseed[3]) { unsigned long accu; unsigned short temp[2]; accu = (unsigned long) _rand48_mult[0] * (unsigned long) xseed[0] + (unsigned long) _rand48_add; temp[0] = (unsigned short) accu; /* lower 16 bits */ accu >>= sizeof(unsigned short) * 8; accu += (unsigned long) _rand48_mult[0] * (unsigned long) xseed[1] + (unsigned long) _rand48_mult[1] * (unsigned long) xseed[0]; temp[1] = (unsigned short) accu; /* middle 16 bits */ accu >>= sizeof(unsigned short) * 8; accu += _rand48_mult[0] * xseed[2] + _rand48_mult[1] * xseed[1] + _rand48_mult[2] * xseed[0]; xseed[0] = temp[0]; xseed[1] = temp[1]; xseed[2] = (unsigned short) accu; } HTSLIB_EXPORT void hts_srand48(long seed) { _rand48_seed[0] = RAND48_SEED_0; _rand48_seed[1] = (unsigned short) seed; _rand48_seed[2] = (unsigned short) (seed >> 16); _rand48_mult[0] = RAND48_MULT_0; _rand48_mult[1] = RAND48_MULT_1; _rand48_mult[2] = RAND48_MULT_2; _rand48_add = RAND48_ADD; } HTSLIB_EXPORT double hts_erand48(unsigned short xseed[3]) { _dorand48(xseed); return ldexp((double) xseed[0], -48) + ldexp((double) xseed[1], -32) + ldexp((double) xseed[2], -16); } HTSLIB_EXPORT double hts_drand48(void) { return hts_erand48(_rand48_seed); } HTSLIB_EXPORT long hts_lrand48(void) { _dorand48(_rand48_seed); return ((long) _rand48_seed[2] << 15) + ((long) _rand48_seed[1] >> 1); } pysam-0.23.0/htslib/plugin.c000066400000000000000000000145611475062545500157000ustar00rootroot00000000000000/* plugin.c -- low-level path parsing and plugin functions. Copyright (C) 2015-2016, 2020 Genome Research Ltd. Author: John Marshall Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "hts_internal.h" #include "htslib/kstring.h" #ifndef PLUGINPATH #define PLUGINPATH "" #endif static DIR *open_nextdir(struct hts_path_itr *itr) { DIR *dir; while (1) { const char *colon = strchr(itr->pathdir, HTS_PATH_SEPARATOR_CHAR); if (colon == NULL) return NULL; itr->entry.l = 0; kputsn(itr->pathdir, colon - itr->pathdir, &itr->entry); itr->pathdir = &colon[1]; if (itr->entry.l == 0) continue; dir = opendir(itr->entry.s); if (dir) break; if (hts_verbose >= 4) fprintf(stderr, "[W::hts_path_itr] can't scan directory \"%s\": %s\n", itr->entry.s, strerror(errno)); } if (itr->entry.s[itr->entry.l-1] != '/') kputc('/', &itr->entry); itr->entry_dir_l = itr->entry.l; return dir; } void hts_path_itr_setup(struct hts_path_itr *itr, const char *path, const char *builtin_path, const char *prefix, size_t prefix_len, const char *suffix, size_t suffix_len) { itr->prefix = prefix; itr->prefix_len = prefix_len; if (suffix) itr->suffix = suffix, itr->suffix_len = suffix_len; else itr->suffix = PLUGIN_EXT, itr->suffix_len = strlen(PLUGIN_EXT); itr->path.l = itr->path.m = 0; itr->path.s = NULL; itr->entry.l = itr->entry.m = 0; itr->entry.s = NULL; if (! builtin_path) builtin_path = PLUGINPATH; if (! path) { path = getenv("HTS_PATH"); if (! path) path = ""; } while (1) { size_t len = strcspn(path, HTS_PATH_SEPARATOR_STR); if (len == 0) kputs(builtin_path, &itr->path); else kputsn(path, len, &itr->path); kputc(HTS_PATH_SEPARATOR_CHAR, &itr->path); path += len; if (*path == HTS_PATH_SEPARATOR_CHAR) path++; else break; } // Note that ':' now terminates entries rather than separates them itr->pathdir = itr->path.s; itr->dirv = open_nextdir(itr); } const char *hts_path_itr_next(struct hts_path_itr *itr) { while (itr->dirv) { struct dirent *e; while ((e = readdir((DIR *) itr->dirv)) != NULL) { size_t d_name_len = strlen(e->d_name); if (strncmp(e->d_name, itr->prefix, itr->prefix_len) == 0 && d_name_len >= itr->suffix_len && strncmp(e->d_name + d_name_len - itr->suffix_len, itr->suffix, itr->suffix_len) == 0) { itr->entry.l = itr->entry_dir_l; kputs(e->d_name, &itr->entry); return itr->entry.s; } } closedir((DIR *) itr->dirv); itr->dirv = open_nextdir(itr); } itr->pathdir = NULL; free(itr->path.s); itr->path.s = NULL; free(itr->entry.s); itr->entry.s = NULL; return NULL; } #ifndef RTLD_NOLOAD #define RTLD_NOLOAD 0 #endif plugin_void_func *load_plugin(void **pluginp, const char *filename, const char *symbol) { void *lib = dlopen(filename, RTLD_NOW | RTLD_LOCAL); if (lib == NULL) goto error; plugin_void_func *sym; *(void **) &sym = dlsym(lib, symbol); if (sym == NULL) { // Reopen the plugin with RTLD_GLOBAL and check for uniquified symbol void *libg = dlopen(filename, RTLD_NOLOAD | RTLD_NOW | RTLD_GLOBAL); if (libg == NULL) goto error; dlclose(lib); lib = libg; kstring_t symbolg = { 0, 0, NULL }; kputs(symbol, &symbolg); kputc('_', &symbolg); const char *slash = strrchr(filename, '/'); const char *basename = slash? slash+1 : filename; kputsn(basename, strcspn(basename, ".-+"), &symbolg); *(void **) &sym = dlsym(lib, symbolg.s); free(symbolg.s); if (sym == NULL) goto error; } *pluginp = lib; return sym; error: if (hts_verbose >= 4) fprintf(stderr, "[W::%s] can't load plugin \"%s\": %s\n", __func__, filename, dlerror()); if (lib) dlclose(lib); return NULL; } void *plugin_sym(void *plugin, const char *name, const char **errmsg) { void *sym = dlsym(plugin, name); if (sym == NULL) *errmsg = dlerror(); return sym; } plugin_void_func *plugin_func(void *plugin, const char *name, const char **errmsg) { plugin_void_func *sym; *(void **) &sym = plugin_sym(plugin, name, errmsg); return sym; } void close_plugin(void *plugin) { if (dlclose(plugin) != 0) { if (hts_verbose >= 4) fprintf(stderr, "[W::%s] dlclose() failed: %s\n", __func__, dlerror()); } } const char *hts_plugin_path(void) { #ifdef ENABLE_PLUGINS char *path = getenv("HTS_PATH"); if (!path) path = ""; kstring_t ks = {0}; while(1) { size_t len = strcspn(path, HTS_PATH_SEPARATOR_STR); if (len == 0) kputs(PLUGINPATH, &ks); else kputsn(path, len, &ks); kputc(HTS_PATH_SEPARATOR_CHAR, &ks); path += len; if (*path == HTS_PATH_SEPARATOR_CHAR) path++; else break; } static char s_path[1024]; snprintf(s_path, sizeof(s_path), "%s", ks.s ? ks.s : ""); free(ks.s); return s_path; #else return NULL; #endif } pysam-0.23.0/htslib/probaln.c000066400000000000000000000416041475062545500160350ustar00rootroot00000000000000/* The MIT License Copyright (C) 2003-2006, 2008-2010 by Heng Li Copyright (C) 2016-2017, 2020, 2023 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #include "htslib/hts.h" /***************************************** * Probabilistic banded glocal alignment * *****************************************/ #define EI .25 #define EM .33333333333 static float g_qual2prob[256]; #define set_u(u, b, i, k) { int x=(i)-(b); x=x>0?x:0; (u)=((k)-x+1)*3; } /* The topology of the profile HMM: /\ /\ /\ /\ I[1] I[k-1] I[k] I[L] ^ \ \ ^ \ ^ \ \ ^ | \ \ | \ | \ \ | M[0] M[1] -> ... -> M[k-1] -> M[k] -> ... -> M[L] M[L+1] \ \/ \/ \/ / \ /\ /\ /\ / -> D[k-1] -> D[k] -> M[0] points to every {M,I}[k] and every {M,I}[k] points to M[L+1]. On input, ref is the reference sequence and query is the query sequence. Both are sequences of 0/1/2/3/4 where 4 stands for an ambiguous residue. iqual is the base quality. c sets the gap open probability, gap extension probability and band width. On output, state and q are arrays of length l_query. The higher 30 bits give the reference position the query base is matched to and the lower two bits can be 0 (an alignment match) or 1 (an insertion). q[i] gives the phred scaled posterior probability of state[i] being wrong. Returns phred-scaled likelihood score, or INT_MIN on failure. */ int probaln_glocal(const uint8_t *ref, int l_ref, const uint8_t *query, int l_query, const uint8_t *iqual, const probaln_par_t *c, int *state, uint8_t *q) { double *f = NULL, *b = NULL, *s = NULL, m[9], sI, sM, bI, bM; float *qual = NULL; int bw, bw2, i, k, is_backward = 1, Pr; if ( l_ref<0 || l_query<0 || l_query >= INT_MAX - 2) { errno = EINVAL; return INT_MIN; } if (l_ref==0 || l_query==0) return 0; // Is this actually invalid?? /*** initialization ***/ is_backward = state && q? 1 : 0; bw = l_ref > l_query? l_ref : l_query; if (bw > c->bw) bw = c->bw; if (bw < abs(l_ref - l_query)) bw = abs(l_ref - l_query); bw2 = bw * 2 + 1; size_t i_dim = bw2 < l_ref ? (size_t) bw2*3+6 : (size_t) l_ref*3+6; // allocate the forward and backward matrices f[][] and b[][] // and the scaling array s[] // Ideally these callocs would be mallocs + initialisation of // the few bits needed. if (SIZE_MAX / (l_query+1) / i_dim < sizeof(double)) { errno = ENOMEM; // Allocation would fail return INT_MIN; } f = calloc((l_query+1)*i_dim, sizeof(double)); if (!f) goto fail; if (is_backward) { b = calloc((l_query+1)*i_dim, sizeof(double)); if (!b) goto fail; } // s[] is the scaling factor to avoid underflow s = malloc((l_query+2) * sizeof(double)); if (!s) goto fail; // initialize qual qual = malloc(l_query * sizeof(float)); if (!qual) goto fail; if (g_qual2prob[0] == 0) for (i = 0; i < 256; ++i) g_qual2prob[i] = pow(10, -i/10.); qual[0] = 0.0; // Should be unused for (i = 0; i < l_query; ++i) qual[i] = g_qual2prob[iqual? iqual[i] : 30]; // initialize transition probability // the value here seems not to affect results; FIXME: need proof sM = sI = 1. / (2 * l_query + 2); m[0*3+0] = (1 - c->d - c->d) * (1 - sM); m[0*3+1] = m[0*3+2] = c->d * (1 - sM); m[1*3+0] = (1 - c->e) * (1 - sI); m[1*3+1] = c->e * (1 - sI); m[1*3+2] = 0.; m[2*3+0] = 1 - c->e; m[2*3+1] = 0.; m[2*3+2] = c->e; bM = (1 - c->d) / l_ref; // (bM+bI)*l_ref==1 bI = c->d / l_ref; // f[] and b[] are 2-d arrays of three scores, with rows along the // query and columns across the band. The first query base and // first band position appear at index 1 allowing edge conditions // to be stored in index 0. Hence the loops below appear to use // 1-based indexing instead of 0-based as you'd normally expect in C, // and the sequences are accessed using query[i - 1] and ref[k - 1]. /*** forward ***/ // f[0] set_u(k, bw, 0, 0); f[0*i_dim+k] = s[0] = 1.; { // f[1] double *fi = &f[1*i_dim], sum; int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1; for (k = beg, sum = 0.; k <= end; ++k) { int u; double e = (ref[k - 1] > 3 || query[0] > 3)? 1. : ref[k - 1] == query[0]? 1. - qual[0] : qual[0] * EM; set_u(u, bw, 1, k); fi[u+0] = e * bM; fi[u+1] = EI * bI; sum += fi[u] + fi[u+1]; } s[1] = sum; } // f[2..l_query] for (i = 2; i <= l_query; ++i) { double *fi = &f[i*i_dim], *fi1 = &f[(i-1)*i_dim], sum, qli = qual[i-1]; int beg = 1, end = l_ref, x; uint8_t qyi = query[i - 1]; x = i - bw; beg = beg > x? beg : x; // band start x = i + bw; end = end < x? end : x; // band end // NB end-beg is almost always 14 (99.9% of the time) // Hence not a large volume to parallelise. // // Maybe stripe in diagonal doing 14 lines together? // // Consider rotation? 150x14 vs 14x150 so inner loop // takes longer. double E[] = { qli * EM, // 00 1. - qli, // 01 1., // 10 1., // 11 }; double M = 1./s[i-1]; // Note this code has the original version listed here (albeit // with improved formatting), but we do not compile using // -DPROBALN_ORIG. The purpose of this code is to act as an // easier(?) to understand version of the heavily optimised // version following it and as an easy validation path in case // of any differences in results. #ifdef PROBALN_ORIG for (k = beg, sum = 0.; k <= end; ++k) { int u, v11, v01, v10; double e; e = E[(ref[k - 1] > 3 || qyi > 3)*2 + (ref[k - 1] == qyi)]; set_u(u, bw, i, k); set_u(v11, bw, i-1, k-1); set_u(v10, bw, i-1, k); set_u(v01, bw, i, k-1); fi[u+0] = e * (m[0] * M*fi1[v11+0] + m[3] * M*fi1[v11+1] + m[6] * M*fi1[v11+2]); fi[u+1] = EI * (m[1] * M*fi1[v10+0] + m[4] * M*fi1[v10+1]); fi[u+2] = m[2] * fi[v01+0] + m[8] * fi[v01+2]; sum += fi[u] + fi[u+1] + fi[u+2]; } #else // We use EI*(M*m[1]*? + M*m[4]*?) a lot. So factor it out here. double xm[5]; xm[0] = M*m[0]; xm[1] = M*m[3]; xm[2] = M*m[6]; xm[3] = EI*M*m[1]; xm[4] = EI*M*m[4]; { int u, v11; set_u(u, bw, i, beg); set_u(v11, bw, i-1, beg-1); // Rather than recompute k->{u,v01,v10,v11} each loop // we just increment the pointers. double *xi = &fi[u]; double *yi = &fi1[v11]; // Derived from xi[0,2] in previous loop iter. double l_x0 = m[2]*xi[0]; double l_x2 = m[8]*xi[2]; for (k = beg, sum = 0.; k <= end; ++k, xi+=3, yi+=3) { int cond = (ref[k-1] > 3 || qyi > 3)*2 + (ref[k-1] == qyi); double z0 = xm[0]*yi[0]; double z1 = xm[1]*yi[1]; double z2 = xm[2]*yi[2]; double z3 = xm[3]*yi[3]; double z4 = xm[4]*yi[4]; xi[0] = E[cond] * (z0+z1+z2); xi[1] = z3 + z4; xi[2] = l_x0 + l_x2; sum += xi[0] + xi[1] + xi[2]; l_x0 = m[2]*xi[0]; l_x2 = m[8]*xi[2]; } } #endif s[i] = sum; } { // f[l_query+1] double sum; double M = 1./s[l_query]; // Note that this goes from 1 to l_ref inclusive, but as the // alignment is banded not all of the values will have been // calculated (the rest are taken as 0), so the summation // actually goes over the values set in the last iteration of // the previous loop (when i = l_query). For some reason lost to // time this is done by looking for valid values of 'u' instead of // working out 'beg' and 'end'. // From HTSlib 1.8 to 1.17, the endpoint was incorrectly set // to i_dim - 3. When l_query <= bandwidth, this caused the last // column to be missed, and if l_ref == l_query then a match at the end // could incorrectly be reported as an insertion. See #1605. for (k = 1, sum = 0.; k <= l_ref; ++k) { int u; set_u(u, bw, l_query, k); if (u < 3 || u >= i_dim) continue; sum += M*f[l_query*i_dim + u+0] * sM + M*f[l_query*i_dim + u+1] * sI; } s[l_query+1] = sum; // the last scaling factor } { // compute likelihood double p = 1., Pr1 = 0.; for (i = 0; i <= l_query + 1; ++i) { p *= s[i]; if (p < 1e-100) Pr1 += -4.343 * log(p), p = 1.; } Pr1 += -4.343 * log(p * l_ref * l_query); Pr = (int)(Pr1 + .499); if (!is_backward) { // skip backward and MAP free(f); free(s); free(qual); return Pr; } } /*** backward ***/ // b[l_query] (b[l_query+1][0]=1 and thus \tilde{b}[][]=1/s[l_query+1]; this is where s[l_query+1] comes from) for (k = 1; k <= l_ref; ++k) { int u; double *bi = &b[l_query*i_dim]; set_u(u, bw, l_query, k); if (u < 3 || u >= i_dim) continue; bi[u+0] = sM / s[l_query] / s[l_query+1]; bi[u+1] = sI / s[l_query] / s[l_query+1]; } // b[l_query-1..1] for (i = l_query - 1; i >= 1; --i) { int beg = 1, end = l_ref, x; double *bi = &b[i*i_dim], *bi1 = &b[(i+1)*i_dim], y = (i > 1), qli1 = qual[i]; uint8_t qyi1 = query[i]; x = i - bw; beg = beg > x? beg : x; x = i + bw; end = end < x? end : x; double E[] = { qli1 * EM, //000 1. - qli1, //001 1., //010 1., //011 //0,0,0,0 //1xx }; #ifdef PROBALN_ORIG for (k = end; k >= beg; --k) { int u, v11, v01, v10; double e; set_u(u, bw, i, k); set_u(v11, bw, i+1, k+1); set_u(v10, bw, i+1, k); set_u(v01, bw, i, k+1); e = (k>=l_ref)?0 :E[(ref[k] > 3 || qyi1 > 3)*2 + (ref[k] == qyi1)] * bi1[v11]; bi[u+0] = e * m[0] + EI * m[1] * bi1[v10+1] + m[2] * bi[v01+2]; // bi1[v11] has been foled into e. bi[u+1] = e * m[3] + EI * m[4] * bi1[v10+1]; bi[u+2] = (e * m[6] + m[8] * bi[v01+2]) * y; // fprintf(stderr, "B (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, bi[u], bi[u+1], bi[u+2]); // DEBUG } // rescale int _beg, _end; set_u(_beg, bw, i, beg); set_u(_end, bw, i, end); _end += 2; for (k = _beg, y = 1./s[i]; k <= _end; ++k) bi[k] *= y; #else { int u, v10; set_u(u, bw, i, end); set_u(v10, bw, i+1, end); // Rather than recompute k->{u,v01,v10,v11} each loop // we just increment the pointers. double *xi = &bi[u]; double *yi = &bi1[v10]; // NB xi[5] is equiv to v01+2. double xi_5 = xi[5]; // Manual loop invariant removal double e1 = EI*m[1]; double e4 = EI*m[4]; // Do renorm too in the same pass. double n = 1./s[i]; for (k = end; k >= beg; --k, xi -= 3, yi -= 3) { double e = (k>=l_ref) ? 0 : E[(ref[k]>3 || qyi1>3)*2 + (ref[k] == qyi1)] * yi[3]; xi[1] = e * m[3] + e4 * yi[1]; xi[0] = e * m[0] + e1 * yi[1] + m[2] * xi_5; xi[2] = (e * m[6] + m[8] * xi_5) * y; // bi[u+2] from this iter becomes bi[v01+2] in next iter xi_5 = xi[2]; // rescale xi[1] *= n; xi[0] *= n; xi[2] *= n; } } #endif } { // b[0] int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1; double sum = 0.; for (k = end; k >= beg; --k) { int u; double e = (ref[k - 1] > 3 || query[0] > 3)? 1. : ref[k - 1] == query[0]? 1. - qual[0] : qual[0] * EM; set_u(u, bw, 1, k); if (u < 3 || u >= i_dim) continue; sum += e * b[1*i_dim + u+0] * bM + EI * b[1*i_dim + u+1] * bI; } set_u(k, bw, 0, 0); b[0*i_dim + k] = sum / s[0]; // if everything works as is expected, b[0][k] == 1.0 } /*** MAP ***/ for (i = 1; i <= l_query; ++i) { double sum = 0., *fi = &f[i*i_dim], *bi = &b[i*i_dim], max = 0.; int beg = 1, end = l_ref, x, max_k = -1; x = i - bw; beg = beg > x? beg : x; x = i + bw; end = end < x? end : x; double M = 1./s[i]; #ifdef PROBALN_ORIG for (k = beg; k <= end; ++k) { int u; double z; set_u(u, bw, i, k); z = M*fi[u+0] * bi[u+0]; if (z > max) max = z, max_k = (k-1)<<2 | 0; sum += z; z = M*fi[u+1] * bi[u+1]; if (z > max) max = z, max_k = (k-1)<<2 | 1; sum += z; } #else { int u; set_u(u, bw, i, beg); for (k = beg; k <= end; ++k, u+=3) { double z1, z2; z1 = M*fi[u+0] * bi[u+0]; z2 = M*fi[u+1] * bi[u+1]; int which = z2 > z1; // strictly z2 >= z1 matches old code double zm = which ? z2 : z1; if (zm > max) { max = zm; max_k = (k-1)<<2 | which; } sum += z1 + z2; } } #endif max /= sum; sum *= s[i]; // if everything works as is expected, sum == 1.0 if (state) state[i-1] = max_k; if (q) k = (int)(-4.343 * log(1. - max) + .499), q[i-1] = k > 100? 99 : k; #ifdef PROBALN_MAIN k = 0; set_u(k, bw, 0, 0); fprintf(stderr, "(%.10lg,%.10lg) (%d,%d:%c,%c:%d) %lg\n", b[0][k], sum, i-1, max_k>>2, "ACGT"[query[i - 1]], "ACGT"[ref[(max_k>>2)]], max_k&3, max); // DEBUG #endif } /*** free ***/ free(f); free(b); free(s); free(qual); return Pr; fail: free(f); free(b); free(s); free(qual); return INT_MIN; } #ifdef PROBALN_MAIN #include int main(int argc, char *argv[]) { uint8_t conv[256], *iqual, *ref, *query; probaln_par_t par = { 0.001, 0.1, 10 }; int c, l_ref, l_query, i, q = 30, b = 10, P; while ((c = getopt(argc, argv, "b:q:")) >= 0) { switch (c) { case 'b': b = atoi(optarg); break; case 'q': q = atoi(optarg); break; } } if (optind + 2 > argc) { fprintf(stderr, "Usage: %s [-q %d] [-b %d] \n", argv[0], q, b); // example: acttc attc return 1; } memset(conv, 4, 256); conv['a'] = conv['A'] = 0; conv['c'] = conv['C'] = 1; conv['g'] = conv['G'] = 2; conv['t'] = conv['T'] = 3; ref = (uint8_t*)argv[optind]; query = (uint8_t*)argv[optind+1]; l_ref = strlen((char*)ref); l_query = strlen((char*)query); for (i = 0; i < l_ref; ++i) ref[i] = conv[ref[i]]; for (i = 0; i < l_query; ++i) query[i] = conv[query[i]]; iqual = malloc(l_query); memset(iqual, q, l_query); par.bw = b; P = probaln_glocal(ref, l_ref, query, l_query, iqual, &par, 0, 0); fprintf(stderr, "%d\n", P); free(iqual); return 0; } #endif pysam-0.23.0/htslib/realn.c000066400000000000000000000316421475062545500155020ustar00rootroot00000000000000/* realn.c -- BAQ calculation and realignment. Copyright (C) 2009-2011, 2014-2016, 2018, 2021, 2023 Genome Research Ltd. Portions copyright (C) 2009-2011 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #include "htslib/hts.h" #include "htslib/sam.h" int sam_cap_mapq(bam1_t *b, const char *ref, hts_pos_t ref_len, int thres) { uint8_t *seq = bam_get_seq(b), *qual = bam_get_qual(b); uint32_t *cigar = bam_get_cigar(b); bam1_core_t *c = &b->core; int i, y, mm, q, len, clip_l, clip_q; hts_pos_t x; double t; if (thres < 0) thres = 40; // set the default mm = q = len = clip_l = clip_q = 0; for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) { int j, l = cigar[i]>>4, op = cigar[i]&0xf; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { for (j = 0; j < l; ++j) { int c1, c2, z = y + j; if (x+j >= ref_len || ref[x+j] == '\0') break; // out of bounds c1 = bam_seqi(seq, z), c2 = seq_nt16_table[(unsigned char)ref[x+j]]; if (c2 != 15 && c1 != 15 && qual[z] >= 13) { // not ambiguous ++len; if (c1 && c1 != c2 && qual[z] >= 13) { // mismatch ++mm; q += qual[z] > 33? 33 : qual[z]; } } } if (j < l) break; x += l; y += l; len += l; } else if (op == BAM_CDEL) { for (j = 0; j < l; ++j) if (x+j >= ref_len || ref[x+j] == '\0') break; if (j < l) break; x += l; } else if (op == BAM_CSOFT_CLIP) { for (j = 0; j < l; ++j) clip_q += qual[y+j]; clip_l += l; y += l; } else if (op == BAM_CHARD_CLIP) { clip_q += 13 * l; clip_l += l; } else if (op == BAM_CINS) y += l; else if (op == BAM_CREF_SKIP) x += l; } for (i = 0, t = 1; i < mm; ++i) t *= (double)len / (i+1); t = q - 4.343 * log(t) + clip_q / 5.; if (t > thres) return -1; if (t < 0) t = 0; t = sqrt((thres - t) / thres) * thres; //fprintf(stderr, "%s %lf %d\n", bam_get_qname(b), t, q); return (int)(t + .499); } static int realn_check_tag(const uint8_t *tg, enum htsLogLevel severity, const char *type, const bam1_t *b) { if (*tg != 'Z') { hts_log(severity, __func__, "Incorrect %s tag type (%c) for read %s", type, *tg, bam_get_qname(b)); return -1; } if (b->core.l_qseq != strlen((const char *) tg + 1)) { hts_log(severity, __func__, "Read %s %s tag is wrong length", bam_get_qname(b), type); return -1; } return 0; } int sam_prob_realn(bam1_t *b, const char *ref, hts_pos_t ref_len, int flag) { int k, bw, y, yb, ye, xb, xe, fix_bq = 0, apply_baq = flag & BAQ_APPLY, extend_baq = flag & BAQ_EXTEND, redo_baq = flag & BAQ_REDO; enum htsRealnFlags system = flag & (0xff << 3); hts_pos_t i, x; uint32_t *cigar = bam_get_cigar(b); bam1_core_t *c = &b->core; // d(I) e(M) band probaln_par_t conf = { 0.001, 0.1, 10 }; // Illumina if (b->core.l_qseq > 1000 || system > BAQ_ILLUMINA) { // Params that work well on PacBio CCS 15k. Unknown if they // help other long-read platforms yet, but likely better than // the short-read tuned ones. // // This function has no access to the SAM header. // Ideally the calling function would check for e.g. // @RG PL = "PACBIO" and DS contains "READTYPE=CCS". // // In the absense of this, we simply auto-detect via a crude // short vs long strategy. conf.d = 1e-7; conf.e = 1e-1; } uint8_t *bq = NULL, *zq = NULL, *qual = bam_get_qual(b); int *state = NULL; if ((c->flag & BAM_FUNMAP) || b->core.l_qseq == 0 || qual[0] == (uint8_t)-1) return -1; // do nothing // test if BQ or ZQ is present, and make sanity checks if ((bq = bam_aux_get(b, "BQ")) != NULL) { if (!redo_baq) { if (realn_check_tag(bq, HTS_LOG_WARNING, "BQ", b) < 0) fix_bq = 1; } ++bq; } if ((zq = bam_aux_get(b, "ZQ")) != NULL) { if (realn_check_tag(zq, HTS_LOG_ERROR, "ZQ", b) < 0) return -4; ++zq; } if (bq && redo_baq) { bam_aux_del(b, bq-1); bq = 0; } if (bq && zq) { // remove the ZQ tag bam_aux_del(b, zq-1); zq = 0; } if (!zq && fix_bq) { // Need to fix invalid BQ tag (by realigning) assert(bq != NULL); bam_aux_del(b, bq-1); bq = 0; } if (bq || zq) { if ((apply_baq && zq) || (!apply_baq && bq)) return -3; // in both cases, do nothing if (bq && apply_baq) { // then convert BQ to ZQ for (i = 0; i < c->l_qseq; ++i) qual[i] = qual[i] + 64 < bq[i]? 0 : qual[i] - ((int)bq[i] - 64); *(bq - 3) = 'Z'; } else if (zq && !apply_baq) { // then convert ZQ to BQ for (i = 0; i < c->l_qseq; ++i) qual[i] += (int)zq[i] - 64; *(zq - 3) = 'B'; } return 0; } // find the start and end of the alignment x = c->pos, y = 0, yb = ye = xb = xe = -1; for (k = 0; k < c->n_cigar; ++k) { int op, l; op = cigar[k]&0xf; l = cigar[k]>>4; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { if (yb < 0) yb = y; if (xb < 0) xb = x; ye = y + l; xe = x + l; x += l; y += l; } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l; else if (op == BAM_CDEL) x += l; else if (op == BAM_CREF_SKIP) return -1; // do nothing if there is a reference skip } if (xb == -1) // No matches in CIGAR. return -1; // set bandwidth and the start and the end bw = 7; if (abs((xe - xb) - (ye - yb)) > bw) bw = abs((xe - xb) - (ye - yb)) + 3; conf.bw = bw; xb -= yb + bw/2; if (xb < 0) xb = 0; xe += c->l_qseq - ye + bw/2; if (xe - xb - c->l_qseq > bw) xb += (xe - xb - c->l_qseq - bw) / 2, xe -= (xe - xb - c->l_qseq - bw) / 2; { // glocal uint8_t *seq = bam_get_seq(b); uint8_t *tseq; // translated seq A=>0,C=>1,G=>2,T=>3,other=>4 uint8_t *tref; // translated ref uint8_t *q; // Probability of incorrect alignment from probaln_glocal() size_t lref = xe > xb ? xe - xb : 1; size_t align_lqseq; if (extend_baq && lref < c->l_qseq) lref = c->l_qseq; // So we can recycle tseq,tref for left,rght below // Try to make q,tref,tseq reasonably well aligned align_lqseq = ((c->l_qseq + 1) | 0xf) + 1; // Overflow check - 3 for *bq, sizeof(int) for *state if ((SIZE_MAX - lref) / (3 + sizeof(int)) < align_lqseq) { errno = ENOMEM; goto fail; } assert(bq == NULL); // bq was used above, but should now be NULL bq = malloc(align_lqseq * 3 + lref); if (!bq) goto fail; q = bq + align_lqseq; tseq = q + align_lqseq; tref = tseq + align_lqseq; memcpy(bq, qual, c->l_qseq); bq[c->l_qseq] = 0; for (i = 0; i < c->l_qseq; ++i) tseq[i] = seq_nt16_int[bam_seqi(seq, i)]; for (i = xb; i < xe; ++i) { if (i >= ref_len || ref[i] == '\0') { xe = i; break; } tref[i-xb] = seq_nt16_int[seq_nt16_table[(unsigned char)ref[i]]]; } state = malloc(c->l_qseq * sizeof(int)); if (!state) goto fail; if (probaln_glocal(tref, xe-xb, tseq, c->l_qseq, qual, &conf, state, q) == INT_MIN) { goto fail; } if (!extend_baq) { // in this block, bq[] is capped by base quality qual[] for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) { int op = cigar[k]&0xf, l = cigar[k]>>4; if (l == 0) continue; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { // Sanity check running off the end of the sequence // Can only happen if the alignment is broken if (l > c->l_qseq - y) l = c->l_qseq - y; for (i = y; i < y + l; ++i) { if ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y)) bq[i] = 0; else bq[i] = bq[i] < q[i]? bq[i] : q[i]; } x += l; y += l; } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) { // Need sanity check here too. if (l > c->l_qseq - y) l = c->l_qseq - y; y += l; } else if (op == BAM_CDEL) { x += l; } } for (i = 0; i < c->l_qseq; ++i) bq[i] = qual[i] - bq[i] + 64; // finalize BQ } else { // in this block, bq[] is BAQ that can be larger than qual[] (different from the above!) // tseq,tref are no longer needed, so we can steal them to avoid mallocs uint8_t *left = tseq; uint8_t *rght = tref; int len = 0; for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) { int op = cigar[k]&0xf, l = cigar[k]>>4; // concatenate alignment matches (including sequence (mis)matches) // otherwise 50M50M gives a different result to 100M if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { if ((k + 1) < c->n_cigar) { int next_op = bam_cigar_op(cigar[k + 1]); if (next_op == BAM_CMATCH || next_op == BAM_CEQUAL || next_op == BAM_CDIFF) { len += l; continue; } } // last of M/X/= ops l += len; len = 0; } if (l == 0) continue; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { // Sanity check running off the end of the sequence // Can only happen if the alignment is broken if (l > c->l_qseq - y) l = c->l_qseq - y; for (i = y; i < y + l; ++i) bq[i] = ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y))? 0 : q[i]; for (left[y] = bq[y], i = y + 1; i < y + l; ++i) left[i] = bq[i] > left[i-1]? bq[i] : left[i-1]; for (rght[y+l-1] = bq[y+l-1], i = y + l - 2; i >= y; --i) rght[i] = bq[i] > rght[i+1]? bq[i] : rght[i+1]; for (i = y; i < y + l; ++i) bq[i] = left[i] < rght[i]? left[i] : rght[i]; x += l; y += l; } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) { // Need sanity check here too. if (l > c->l_qseq - y) l = c->l_qseq - y; y += l; } else if (op == BAM_CDEL) { x += l; } } for (i = 0; i < c->l_qseq; ++i) bq[i] = 64 + (qual[i] <= bq[i]? 0 : qual[i] - bq[i]); // finalize BQ } if (apply_baq) { for (i = 0; i < c->l_qseq; ++i) qual[i] -= bq[i] - 64; // modify qual bam_aux_append(b, "ZQ", 'Z', c->l_qseq + 1, bq); } else bam_aux_append(b, "BQ", 'Z', c->l_qseq + 1, bq); free(bq); free(state); } return 0; fail: free(bq); free(state); return -4; } pysam-0.23.0/htslib/regidx.c000066400000000000000000000470411475062545500156630ustar00rootroot00000000000000/* Copyright (C) 2014-2019 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include "htslib/hts.h" #include "htslib/kstring.h" #include "htslib/kseq.h" #include "htslib/khash_str2int.h" #include "htslib/regidx.h" #include "hts_internal.h" #define MAX_COOR_0 REGIDX_MAX // CSI and hts_itr_query limit, 0-based #define iBIN(x) ((x)>>13) typedef struct { hts_pos_t beg, end; } reg_t; typedef struct { hts_pos_t pos; // position uint32_t ireg; // index to reglist.reg and reglist.dat } pos_t; typedef struct reglist_t reglist_t; typedef struct { hts_pos_t beg, end; // query region uint32_t ireg; // index of active region regidx_t *ridx; reglist_t *list; int active; } itr_t_; // List of regions for one chromosome. struct reglist_t { uint32_t *idx, nidx; // index to list.reg+1 uint32_t nreg, mreg; // n:used, m:allocated reg_t *reg; // regions uint8_t *dat; // payload data char *seq; // sequence name int unsorted; }; // Container of all sequences struct regidx_t { int nseq, mseq; // n:used, m:alloced reglist_t *seq; // regions for each sequence void *seq2regs; // hash for fast lookup from chr name to regions char **seq_names; regidx_free_f free; // function to free any data allocated by regidx_parse_f regidx_parse_f parse; // parse one input line void *usr; // user data to pass to regidx_parse_f int payload_size; void *payload; // temporary payload data set by regidx_parse_f (sequence is not known beforehand) kstring_t str; }; int regidx_seq_nregs(regidx_t *idx, const char *seq) { int iseq; if ( khash_str2int_get(idx->seq2regs, seq, &iseq)!=0 ) return 0; // no such sequence return idx->seq[iseq].nreg; } int regidx_nregs(regidx_t *idx) { int i, nreg = 0; for (i=0; inseq; i++) nreg += idx->seq[i].nreg; return nreg; } char **regidx_seq_names(regidx_t *idx, int *n) { *n = idx->nseq; return idx->seq_names; } int regidx_insert_list(regidx_t *idx, char *line, char delim) { kstring_t tmp = KS_INITIALIZE; char *ss = line; while ( *ss ) { char *se = ss; while ( *se && *se!=delim ) se++; kputsn(ss, se-ss, ks_clear(&tmp)); if ( regidx_insert(idx,tmp.s) < 0 ) { ks_free(&tmp); return -1; } if ( !*se ) break; ss = se+1; } ks_free(&tmp); return 0; } static inline int cmp_regs(reg_t *a, reg_t *b) { if ( a->beg < b->beg ) return -1; if ( a->beg > b->beg ) return 1; if ( a->end < b->end ) return 1; // longer intervals come first if ( a->end > b->end ) return -1; if ( a < b ) return -1; // this is are just for qsort reproducibility across platforms if ( a > b ) return 1; return 0; } static int cmp_reg_ptrs(const void *a, const void *b) { return cmp_regs((reg_t*)a,(reg_t*)b); } static int cmp_reg_ptrs2(const void *a, const void *b) { return cmp_regs(*((reg_t**)a),*((reg_t**)b)); } int regidx_push(regidx_t *idx, char *chr_beg, char *chr_end, hts_pos_t beg, hts_pos_t end, void *payload) { if (beg < 0) beg = 0; if (end < 0) end = 0; if ( beg > MAX_COOR_0 ) beg = MAX_COOR_0; if ( end > MAX_COOR_0 ) end = MAX_COOR_0; int rid; if (kputsn(chr_beg, chr_end-chr_beg+1, ks_clear(&idx->str)) < 0) return -1; if ( khash_str2int_get(idx->seq2regs, idx->str.s, &rid)!=0 ) { // new chromosome int m_tmp = idx->mseq; if (hts_resize(char*, idx->nseq + 1, &m_tmp, &idx->seq_names, HTS_RESIZE_CLEAR) < 0) { return -1; } if (hts_resize(reglist_t, idx->nseq + 1, &idx->mseq, &idx->seq, HTS_RESIZE_CLEAR) < 0) { return -1; } assert(m_tmp == idx->mseq); idx->seq_names[idx->nseq] = strdup(idx->str.s); rid = khash_str2int_inc(idx->seq2regs, idx->seq_names[idx->nseq]); idx->nseq++; } reglist_t *list = &idx->seq[rid]; list->seq = idx->seq_names[rid]; int mreg = list->mreg; if (hts_resize(reg_t, list->nreg + 1, &list->mreg, &list->reg, 0) < 0) return -1; list->reg[list->nreg].beg = beg; list->reg[list->nreg].end = end; if ( idx->payload_size ) { if ( mreg != list->mreg ) { uint8_t *new_dat = realloc(list->dat, idx->payload_size*list->mreg); if (!new_dat) return -1; list->dat = new_dat; } memcpy(list->dat + idx->payload_size*list->nreg, payload, idx->payload_size); } list->nreg++; if ( !list->unsorted && list->nreg>1 && cmp_regs(&list->reg[list->nreg-2],&list->reg[list->nreg-1])>0 ) list->unsorted = 1; return 0; } int regidx_insert(regidx_t *idx, char *line) { if ( !line ) return 0; char *chr_from, *chr_to; hts_pos_t beg,end; int ret = idx->parse(line,&chr_from,&chr_to,&beg,&end,idx->payload,idx->usr); if ( ret==-2 ) return -1; // error if ( ret==-1 ) return 0; // skip the line return regidx_push(idx, chr_from,chr_to,beg,end,idx->payload); } regidx_t *regidx_init_string(const char *str, regidx_parse_f parser, regidx_free_f free_f, size_t payload_size, void *usr_dat) { kstring_t tmp = KS_INITIALIZE; regidx_t *idx = (regidx_t*) calloc(1,sizeof(regidx_t)); if ( !idx ) return NULL; idx->free = free_f; idx->parse = parser ? parser : regidx_parse_tab; idx->usr = usr_dat; idx->seq2regs = khash_str2int_init(); if (!idx->seq2regs) goto fail; idx->payload_size = payload_size; if ( payload_size ) { idx->payload = malloc(payload_size); if (!idx->payload) goto fail; } const char *ss = str; while ( *ss ) { while ( *ss && isspace_c(*ss) ) ss++; const char *se = ss; while ( *se && *se!='\r' && *se!='\n' ) se++; if (kputsn(ss, se-ss, ks_clear(&tmp)) < 0) goto fail; if (regidx_insert(idx, tmp.s) < 0) goto fail; while ( *se && isspace_c(*se) ) se++; ss = se; } ks_free(&tmp); return idx; fail: regidx_destroy(idx); ks_free(&tmp); return NULL; } regidx_t *regidx_init(const char *fname, regidx_parse_f parser, regidx_free_f free_f, size_t payload_size, void *usr_dat) { if ( !parser ) { if ( !fname ) parser = regidx_parse_tab; else { int len = strlen(fname); if ( len>=7 && !strcasecmp(".bed.gz",fname+len-7) ) parser = regidx_parse_bed; else if ( len>=8 && !strcasecmp(".bed.bgz",fname+len-8) ) parser = regidx_parse_bed; else if ( len>=4 && !strcasecmp(".bed",fname+len-4) ) parser = regidx_parse_bed; else if ( len>=4 && !strcasecmp(".vcf",fname+len-4) ) parser = regidx_parse_vcf; else if ( len>=7 && !strcasecmp(".vcf.gz",fname+len-7) ) parser = regidx_parse_vcf; else parser = regidx_parse_tab; } } kstring_t str = KS_INITIALIZE; htsFile *fp = NULL; int ret; regidx_t *idx = (regidx_t*) calloc(1,sizeof(regidx_t)); if (!idx) return NULL; idx->free = free_f; idx->parse = parser; idx->usr = usr_dat; idx->seq2regs = khash_str2int_init(); if (!idx->seq2regs) goto error; idx->payload_size = payload_size; if ( payload_size ) { idx->payload = malloc(payload_size); if (!idx->payload) goto error; } if ( !fname ) return idx; fp = hts_open(fname,"r"); if ( !fp ) goto error; while ((ret = hts_getline(fp, KS_SEP_LINE, &str)) > 0 ) { if ( regidx_insert(idx, str.s) ) goto error; } if (ret < -1) goto error; ret = hts_close(fp); fp = NULL; if ( ret != 0 ) { hts_log_error("Close failed .. %s", fname); goto error; } ks_free(&str); return idx; error: ks_free(&str); if ( fp ) hts_close(fp); regidx_destroy(idx); return NULL; } void regidx_destroy(regidx_t *idx) { int i, j; if (!idx) return; for (i=0; inseq; i++) { reglist_t *list = &idx->seq[i]; if ( idx->free ) { for (j=0; jnreg; j++) idx->free((char *)list->dat + idx->payload_size*j); } free(list->dat); free(list->reg); free(list->idx); } free(idx->seq_names); free(idx->seq); free(idx->str.s); free(idx->payload); khash_str2int_destroy_free(idx->seq2regs); free(idx); } static int reglist_build_index_(regidx_t *regidx, reglist_t *list) { int i; if ( list->unsorted ) { if ( !regidx->payload_size ) { qsort(list->reg,list->nreg,sizeof(reg_t),cmp_reg_ptrs); } else { reg_t **ptr = malloc(sizeof(*ptr)*list->nreg); if (!ptr) return -1; for (i=0; inreg; i++) ptr[i] = list->reg + i; qsort(ptr,list->nreg,sizeof(*ptr),cmp_reg_ptrs2); uint8_t *tmp_dat = malloc(regidx->payload_size*list->nreg); if (!tmp_dat) { free(ptr); return -1; } for (i=0; inreg; i++) { size_t iori = ptr[i] - list->reg; memcpy(tmp_dat+i*regidx->payload_size, list->dat+iori*regidx->payload_size, regidx->payload_size); } free(list->dat); list->dat = tmp_dat; reg_t *tmp_reg = (reg_t*) malloc(sizeof(reg_t)*list->nreg); if (!tmp_reg) { free(ptr); return -1; } for (i=0; inreg; i++) { size_t iori = ptr[i] - list->reg; tmp_reg[i] = list->reg[iori]; } free(ptr); free(list->reg); list->reg = tmp_reg; list->mreg = list->nreg; } list->unsorted = 0; } list->nidx = 0; uint32_t j,k, midx = 0; // Find highest index bin. It's possible that we could just look at // the last region, but go through the list in case some entries overlap. for (j=0; jnreg; j++) { int iend = iBIN(list->reg[j].end); if (midx <= iend) midx = iend; } midx++; uint32_t *new_idx = calloc(midx, sizeof(uint32_t)); if (!new_idx) return -1; free(list->idx); // Should be NULL on entry, but just in case... list->idx = new_idx; list->nidx = midx; for (j=0; jnreg; j++) { int ibeg = iBIN(list->reg[j].beg); int iend = iBIN(list->reg[j].end); if ( ibeg==iend ) { if ( !list->idx[ibeg] ) list->idx[ibeg] = j + 1; } else { for (k=ibeg; k<=iend; k++) if ( !list->idx[k] ) list->idx[k] = j + 1; } } return 0; } int regidx_overlap(regidx_t *regidx, const char *chr, hts_pos_t beg, hts_pos_t end, regitr_t *regitr) { if ( regitr ) regitr->seq = NULL; int iseq, ireg; if ( khash_str2int_get(regidx->seq2regs, chr, &iseq)!=0 ) return 0; // no such sequence reglist_t *list = ®idx->seq[iseq]; if ( !list->nreg ) return 0; if ( list->nreg==1 ) { if ( beg > list->reg[0].end ) return 0; if ( end < list->reg[0].beg ) return 0; ireg = 0; } else { if ( !list->idx ) { if (reglist_build_index_(regidx,list) < 0) return -1; } int ibeg = iBIN(beg); if ( ibeg >= list->nidx ) return 0; // beg is too big // find a matching region uint32_t i = list->idx[ibeg]; if ( !i ) { int iend = iBIN(end); if ( iend > list->nidx ) iend = list->nidx; for (i=ibeg; i<=iend; i++) if ( list->idx[i] ) break; if ( i>iend ) return 0; i = list->idx[i]; } for (ireg=i-1; iregnreg; ireg++) { if ( list->reg[ireg].beg > end ) return 0; // no match, past the query region if ( list->reg[ireg].end >= beg && list->reg[ireg].beg <= end ) break; // found } if ( ireg >= list->nreg ) return 0; // no match } if ( !regitr ) return 1; // match, but no more info to save // may need to iterate over the matching regions later itr_t_ *itr = (itr_t_*)regitr->itr; itr->ridx = regidx; itr->list = list; itr->beg = beg; itr->end = end; itr->ireg = ireg; itr->active = 0; regitr->seq = list->seq; regitr->beg = list->reg[ireg].beg; regitr->end = list->reg[ireg].end; if ( regidx->payload_size ) regitr->payload = list->dat + regidx->payload_size*ireg; return 1; } int regidx_parse_bed(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr) { char *ss = (char*) line; while ( *ss && isspace_c(*ss) ) ss++; if ( !*ss ) return -1; // skip blank lines if ( *ss=='#' ) return -1; // skip comments char *se = ss; while ( *se && !isspace_c(*se) ) se++; *chr_beg = ss; *chr_end = se-1; if ( !*se ) { // just the chromosome name *beg = 0; *end = MAX_COOR_0; return 0; } ss = se+1; *beg = hts_parse_decimal(ss, &se, 0); if ( ss==se ) { hts_log_error("Could not parse bed line: %s", line); return -2; } ss = se+1; *end = hts_parse_decimal(ss, &se, 0) - 1; if ( ss==se ) { hts_log_error("Could not parse bed line: %s", line); return -2; } return 0; } int regidx_parse_tab(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr) { char *ss = (char*) line; while ( *ss && isspace_c(*ss) ) ss++; if ( !*ss ) return -1; // skip blank lines if ( *ss=='#' ) return -1; // skip comments char *se = ss; while ( *se && !isspace_c(*se) ) se++; *chr_beg = ss; *chr_end = se-1; if ( !*se ) { // just the chromosome name *beg = 0; *end = MAX_COOR_0; return 0; } ss = se+1; *beg = hts_parse_decimal(ss, &se, 0); if ( ss==se ) { hts_log_error("Could not parse tab line: %s", line); return -2; } if ( *beg==0 ) { hts_log_error("Could not parse tab line, expected 1-based coordinate: %s", line); return -2; } (*beg)--; if ( !se[0] || !se[1] ) *end = *beg; else { ss = se+1; *end = hts_parse_decimal(ss, &se, 0); if ( ss==se || (*se && !isspace_c(*se)) ) *end = *beg; else if ( *end==0 ) { hts_log_error("Could not parse tab line, expected 1-based coordinate: %s", line); return -2; } else (*end)--; } return 0; } int regidx_parse_vcf(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr) { int ret = regidx_parse_tab(line, chr_beg, chr_end, beg, end, payload, usr); if ( !ret ) *end = *beg; return ret; } int regidx_parse_reg(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr) { char *ss = (char*) line; while ( *ss && isspace_c(*ss) ) ss++; if ( !*ss ) return -1; // skip blank lines if ( *ss=='#' ) return -1; // skip comments char *se = ss; while ( *se && *se!=':' ) se++; *chr_beg = ss; *chr_end = se-1; if ( !*se ) { *beg = 0; *end = MAX_COOR_0; return 0; } ss = se+1; *beg = hts_parse_decimal(ss, &se, 0); if ( ss==se ) { hts_log_error("Could not parse reg line: %s", line); return -2; } if ( *beg==0 ) { hts_log_error("Could not parse reg line, expected 1-based coordinate: %s", line); return -2; } (*beg)--; if ( !se[0] || !se[1] ) *end = se[0]=='-' ? MAX_COOR_0 : *beg; else { ss = se+1; *end = hts_parse_decimal(ss, &se, 0); if ( ss==se ) *end = *beg; else if ( *end==0 ) { hts_log_error("Could not parse reg line, expected 1-based coordinate: %s", line); return -2; } else (*end)--; } return 0; } regitr_t *regitr_init(regidx_t *regidx) { regitr_t *regitr = (regitr_t*) calloc(1,sizeof(regitr_t)); if (!regitr) return NULL; regitr->itr = (itr_t_*) calloc(1,sizeof(itr_t_)); if (!regitr->itr) { free(regitr); return NULL; } itr_t_ *itr = (itr_t_*) regitr->itr; itr->ridx = regidx; itr->list = NULL; return regitr; } void regitr_reset(regidx_t *regidx, regitr_t *regitr) { itr_t_ *itr = (itr_t_*) regitr->itr; memset(itr,0,sizeof(itr_t_)); itr->ridx = regidx; } void regitr_destroy(regitr_t *regitr) { free(regitr->itr); free(regitr); } int regitr_overlap(regitr_t *regitr) { if ( !regitr || !regitr->seq || !regitr->itr ) return 0; itr_t_ *itr = (itr_t_*) regitr->itr; if ( !itr->active ) { // is this the first call after regidx_overlap? itr->active = 1; itr->ireg++; return 1; } reglist_t *list = itr->list; int i; for (i=itr->ireg; inreg; i++) { if ( list->reg[i].beg > itr->end ) return 0; // no match, past the query region if ( list->reg[i].end >= itr->beg && list->reg[i].beg <= itr->end ) break; // found } if ( i >= list->nreg ) return 0; // no match itr->ireg = i + 1; regitr->seq = list->seq; regitr->beg = list->reg[i].beg; regitr->end = list->reg[i].end; if ( itr->ridx->payload_size ) regitr->payload = (char *)list->dat + itr->ridx->payload_size*i; return 1; } int regitr_loop(regitr_t *regitr) { if ( !regitr || !regitr->itr ) return 0; itr_t_ *itr = (itr_t_*) regitr->itr; regidx_t *regidx = itr->ridx; if ( !itr->list ) // first time here { itr->list = regidx->seq; itr->ireg = 0; } size_t iseq = itr->list - regidx->seq; if ( iseq >= regidx->nseq ) return 0; if ( itr->ireg >= itr->list->nreg ) { iseq++; if ( iseq >= regidx->nseq ) return 0; // no more sequences, done itr->ireg = 0; itr->list = ®idx->seq[iseq]; } regitr->seq = itr->list->seq; regitr->beg = itr->list->reg[itr->ireg].beg; regitr->end = itr->list->reg[itr->ireg].end; if ( regidx->payload_size ) regitr->payload = (char *)itr->list->dat + regidx->payload_size*itr->ireg; itr->ireg++; return 1; } void regitr_copy(regitr_t *dst, regitr_t *src) { itr_t_ *dst_itr = (itr_t_*) dst->itr; itr_t_ *src_itr = (itr_t_*) src->itr; *dst_itr = *src_itr; *dst = *src; dst->itr = dst_itr; } pysam-0.23.0/htslib/region.c000066400000000000000000000171001475062545500156550ustar00rootroot00000000000000/* region.c -- Functions to create and free region lists Copyright (C) 2019 Genome Research Ltd. Author: Valeriu Ohan Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include "htslib/hts.h" #include "htslib/khash.h" typedef struct reglist { uint32_t n, m; hts_pair_pos_t *a; int tid; } reglist_t; KHASH_MAP_INIT_INT(reg, reglist_t) typedef kh_reg_t reghash_t; static int compare_hts_pair_pos_t (const void *av, const void *bv) { hts_pair_pos_t *a = (hts_pair_pos_t *) av; hts_pair_pos_t *b = (hts_pair_pos_t *) bv; if (a->beg < b->beg) return -1; if (a->beg > b->beg) return 1; if (a->end < b->end) return -1; if (a->end > b->end) return 1; return 0; } #if 0 /** * Good to have around for debugging */ static void reg_print(reghash_t *h) { reglist_t *p; khint_t k; uint32_t i; khint32_t key; if (!h) { fprintf(stderr, "Hash table is empty!\n"); return; } for (k = kh_begin(h); k < kh_end(h); k++) { if (kh_exist(h,k)) { key = kh_key(h,k); fprintf(stderr, "Region: key %u tid %d\n", key, p->tid); if ((p = &kh_val(h,k)) != NULL && p->n > 0) { for (i=0; in; i++) { fprintf(stderr, "\tinterval[%d]: %"PRIhts_pos"-%"PRIhts_pos"\n", i, p->a[i].beg, p->a[i].end); } } else { fprintf(stderr, "Region key %u has no intervals!\n", key); } } } } #endif /** * Sort and merge overlapping or adjacent intervals. */ static int reg_compact(reghash_t *h) { khint_t i; uint32_t j, new_n; reglist_t *p; int count = 0; if (!h) return 0; for (i = kh_begin(h); i < kh_end(h); i++) { if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || !(p->n)) continue; qsort(p->a, p->n, sizeof(p->a[0]), compare_hts_pair_pos_t); for (new_n = 0, j = 1; j < p->n; j++) { if (p->a[new_n].end < p->a[j].beg) { p->a[++new_n].beg = p->a[j].beg; p->a[new_n].end = p->a[j].end; } else { if (p->a[new_n].end < p->a[j].end) p->a[new_n].end = p->a[j].end; } } ++new_n; if (p->n > new_n) { // Shrink array to required size. hts_pair_pos_t *new_a = realloc(p->a, new_n * sizeof(p->a[0])); if (new_a) p->a = new_a; } p->n = new_n; count++; } return count; } static int reg_insert(reghash_t *h, int tid, hts_pos_t beg, hts_pos_t end) { khint_t k; reglist_t *p; if (!h) return -1; // Put reg in the hash table if not already there k = kh_get(reg, h, tid); if (k == kh_end(h)) { // absent from the hash table int ret; k = kh_put(reg, h, tid, &ret); if (-1 == ret) { return -1; } memset(&kh_val(h, k), 0, sizeof(reglist_t)); kh_val(h, k).tid = tid; } p = &kh_val(h, k); // Add beg and end to the list if (p->n == p->m) { uint32_t new_m = p->m ? p->m<<1 : 4; if (new_m == 0) return -1; hts_pair_pos_t *new_a = realloc(p->a, new_m * sizeof(p->a[0])); if (new_a == NULL) return -1; p->m = new_m; p->a = new_a; } p->a[p->n].beg = beg; p->a[p->n++].end = end; return 0; } static void reg_destroy(reghash_t *h) { khint_t k; if (!h) return; for (k = 0; k < kh_end(h); ++k) { if (kh_exist(h, k)) { free(kh_val(h, k).a); } } kh_destroy(reg, h); } /** * Take a char array of reg:interval elements and produce a hts_reglis_t with r_count elements. */ hts_reglist_t *hts_reglist_create(char **argv, int argc, int *r_count, void *hdr, hts_name2id_f getid) { if (!argv || argc < 1) return NULL; reghash_t *h = NULL; reglist_t *p; hts_reglist_t *h_reglist = NULL; khint_t k; int i, l_count = 0, tid; const char *q; hts_pos_t beg, end; /* First, transform the char array into a hash table */ h = kh_init(reg); if (!h) { hts_log_error("Error when creating the region hash table"); return NULL; } for (i=0; itid; h_reglist[l_count].intervals = p->a; h_reglist[l_count].count = p->n; p->a = NULL; // As we stole it. // After reg_compact(), list is ordered and non-overlapping, so... if (p->n > 0) { h_reglist[l_count].min_beg = h_reglist[l_count].intervals[0].beg; h_reglist[l_count].max_end = h_reglist[l_count].intervals[p->n - 1].end; } else { h_reglist[l_count].min_beg = 0; h_reglist[l_count].max_end = 0; } l_count++; } reg_destroy(h); return h_reglist; fail: reg_destroy(h); if(h_reglist) hts_reglist_free(h_reglist, l_count); return NULL; } void hts_reglist_free(hts_reglist_t *reglist, int count) { int i; if(reglist) { for (i = 0; i < count; i++) { if (reglist[i].intervals) free(reglist[i].intervals); } free(reglist); } } pysam-0.23.0/htslib/sam.c000066400000000000000000006175441475062545500151740ustar00rootroot00000000000000/* sam.c -- SAM and BAM file I/O and manipulation. Copyright (C) 2008-2010, 2012-2024 Genome Research Ltd. Copyright (C) 2010, 2012, 2013 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #include #include #include #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION #include "fuzz_settings.h" #endif // Suppress deprecation message for cigar_tab, which we initialise #include "htslib/hts_defs.h" #undef HTS_DEPRECATED #define HTS_DEPRECATED(message) #include "htslib/sam.h" #include "htslib/bgzf.h" #include "cram/cram.h" #include "hts_internal.h" #include "sam_internal.h" #include "htslib/hfile.h" #include "htslib/hts_endian.h" #include "htslib/hts_expr.h" #include "header.h" #include "htslib/khash.h" KHASH_DECLARE(s2i, kh_cstr_t, int64_t) KHASH_SET_INIT_INT(tag) #ifndef EFTYPE #define EFTYPE ENOEXEC #endif #ifndef EOVERFLOW #define EOVERFLOW ERANGE #endif /********************** *** BAM header I/O *** **********************/ HTSLIB_EXPORT const int8_t bam_cigar_table[256] = { // 0 .. 47 -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, // 48 .. 63 (including =) -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, BAM_CEQUAL, -1, -1, // 64 .. 79 (including MIDNHB) -1, -1, BAM_CBACK, -1, BAM_CDEL, -1, -1, -1, BAM_CHARD_CLIP, BAM_CINS, -1, -1, -1, BAM_CMATCH, BAM_CREF_SKIP, -1, // 80 .. 95 (including SPX) BAM_CPAD, -1, -1, BAM_CSOFT_CLIP, -1, -1, -1, -1, BAM_CDIFF, -1, -1, -1, -1, -1, -1, -1, // 96 .. 127 -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, // 128 .. 255 -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 }; sam_hdr_t *sam_hdr_init(void) { sam_hdr_t *bh = (sam_hdr_t*)calloc(1, sizeof(sam_hdr_t)); if (bh == NULL) return NULL; bh->cigar_tab = bam_cigar_table; return bh; } void sam_hdr_destroy(sam_hdr_t *bh) { int32_t i; if (bh == NULL) return; if (bh->ref_count > 0) { --bh->ref_count; return; } if (bh->target_name) { for (i = 0; i < bh->n_targets; ++i) free(bh->target_name[i]); free(bh->target_name); free(bh->target_len); } free(bh->text); if (bh->hrecs) sam_hrecs_free(bh->hrecs); if (bh->sdict) kh_destroy(s2i, (khash_t(s2i) *) bh->sdict); free(bh); } // Copy the sam_hdr_t::sdict hash, used to store the real lengths of long // references before sam_hdr_t::hrecs is populated int sam_hdr_dup_sdict(const sam_hdr_t *h0, sam_hdr_t *h) { const khash_t(s2i) *src_long_refs = (khash_t(s2i) *) h0->sdict; khash_t(s2i) *dest_long_refs = kh_init(s2i); int i; if (!dest_long_refs) return -1; for (i = 0; i < h->n_targets; i++) { int ret; khiter_t ksrc, kdest; if (h->target_len[i] < UINT32_MAX) continue; ksrc = kh_get(s2i, src_long_refs, h->target_name[i]); if (ksrc == kh_end(src_long_refs)) continue; kdest = kh_put(s2i, dest_long_refs, h->target_name[i], &ret); if (ret < 0) { kh_destroy(s2i, dest_long_refs); return -1; } kh_val(dest_long_refs, kdest) = kh_val(src_long_refs, ksrc); } h->sdict = dest_long_refs; return 0; } sam_hdr_t *sam_hdr_dup(const sam_hdr_t *h0) { if (h0 == NULL) return NULL; sam_hdr_t *h; if ((h = sam_hdr_init()) == NULL) return NULL; // copy the simple data h->n_targets = 0; h->ignore_sam_err = h0->ignore_sam_err; h->l_text = 0; // Then the pointery stuff if (!h0->hrecs) { h->target_len = (uint32_t*)calloc(h0->n_targets, sizeof(uint32_t)); if (!h->target_len) goto fail; h->target_name = (char**)calloc(h0->n_targets, sizeof(char*)); if (!h->target_name) goto fail; int i; for (i = 0; i < h0->n_targets; ++i) { h->target_len[i] = h0->target_len[i]; h->target_name[i] = strdup(h0->target_name[i]); if (!h->target_name[i]) break; } h->n_targets = i; if (i < h0->n_targets) goto fail; if (h0->sdict) { if (sam_hdr_dup_sdict(h0, h) < 0) goto fail; } } if (h0->hrecs) { kstring_t tmp = { 0, 0, NULL }; if (sam_hrecs_rebuild_text(h0->hrecs, &tmp) != 0) { free(ks_release(&tmp)); goto fail; } h->l_text = tmp.l; h->text = ks_release(&tmp); if (sam_hdr_update_target_arrays(h, h0->hrecs, 0) != 0) goto fail; } else { h->l_text = h0->l_text; h->text = malloc(h->l_text + 1); if (!h->text) goto fail; memcpy(h->text, h0->text, h->l_text); h->text[h->l_text] = '\0'; } return h; fail: sam_hdr_destroy(h); return NULL; } sam_hdr_t *bam_hdr_read(BGZF *fp) { sam_hdr_t *h; uint8_t buf[4]; int magic_len, has_EOF; int32_t i, name_len, num_names = 0; size_t bufsize; ssize_t bytes; // check EOF has_EOF = bgzf_check_EOF(fp); if (has_EOF < 0) { perror("[W::bam_hdr_read] bgzf_check_EOF"); } else if (has_EOF == 0) { hts_log_warning("EOF marker is absent. The input is probably truncated"); } // read "BAM1" magic_len = bgzf_read(fp, buf, 4); if (magic_len != 4 || memcmp(buf, "BAM\1", 4)) { hts_log_error("Invalid BAM binary header"); return 0; } h = sam_hdr_init(); if (!h) goto nomem; // read plain text and the number of reference sequences bytes = bgzf_read(fp, buf, 4); if (bytes != 4) goto read_err; h->l_text = le_to_u32(buf); bufsize = h->l_text + 1; if (bufsize < h->l_text) goto nomem; // so large that adding 1 overflowed #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (bufsize > FUZZ_ALLOC_LIMIT) goto nomem; #endif h->text = (char*)malloc(bufsize); if (!h->text) goto nomem; h->text[h->l_text] = 0; // make sure it is NULL terminated bytes = bgzf_read(fp, h->text, h->l_text); if (bytes != h->l_text) goto read_err; bytes = bgzf_read(fp, &h->n_targets, 4); if (bytes != 4) goto read_err; if (fp->is_be) ed_swap_4p(&h->n_targets); if (h->n_targets < 0) goto invalid; // read reference sequence names and lengths #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (h->n_targets > (FUZZ_ALLOC_LIMIT - bufsize)/(sizeof(char*)+sizeof(uint32_t))) goto nomem; #endif if (h->n_targets > 0) { h->target_name = (char**)calloc(h->n_targets, sizeof(char*)); if (!h->target_name) goto nomem; h->target_len = (uint32_t*)calloc(h->n_targets, sizeof(uint32_t)); if (!h->target_len) goto nomem; } else { h->target_name = NULL; h->target_len = NULL; } for (i = 0; i != h->n_targets; ++i) { bytes = bgzf_read(fp, &name_len, 4); if (bytes != 4) goto read_err; if (fp->is_be) ed_swap_4p(&name_len); if (name_len <= 0) goto invalid; h->target_name[i] = (char*)malloc(name_len); if (!h->target_name[i]) goto nomem; num_names++; bytes = bgzf_read(fp, h->target_name[i], name_len); if (bytes != name_len) goto read_err; if (h->target_name[i][name_len - 1] != '\0') { /* Fix missing NUL-termination. Is this being too nice? We could alternatively bail out with an error. */ char *new_name; if (name_len == INT32_MAX) goto invalid; new_name = realloc(h->target_name[i], name_len + 1); if (new_name == NULL) goto nomem; h->target_name[i] = new_name; h->target_name[i][name_len] = '\0'; } bytes = bgzf_read(fp, &h->target_len[i], 4); if (bytes != 4) goto read_err; if (fp->is_be) ed_swap_4p(&h->target_len[i]); } return h; nomem: hts_log_error("Out of memory"); goto clean; read_err: if (bytes < 0) { hts_log_error("Error reading BGZF stream"); } else { hts_log_error("Truncated BAM header"); } goto clean; invalid: hts_log_error("Invalid BAM binary header"); clean: if (h != NULL) { h->n_targets = num_names; // ensure we free only allocated target_names sam_hdr_destroy(h); } return NULL; } int bam_hdr_write(BGZF *fp, const sam_hdr_t *h) { int32_t i, name_len, x; kstring_t hdr_ks = { 0, 0, NULL }; char *text; uint32_t l_text; if (!h) return -1; if (h->hrecs) { if (sam_hrecs_rebuild_text(h->hrecs, &hdr_ks) != 0) return -1; if (hdr_ks.l > UINT32_MAX) { hts_log_error("Header too long for BAM format"); free(hdr_ks.s); return -1; } else if (hdr_ks.l > INT32_MAX) { hts_log_warning("Header too long for BAM specification (>2GB)"); hts_log_warning("Output file may not be portable"); } text = hdr_ks.s; l_text = hdr_ks.l; } else { if (h->l_text > UINT32_MAX) { hts_log_error("Header too long for BAM format"); return -1; } else if (h->l_text > INT32_MAX) { hts_log_warning("Header too long for BAM specification (>2GB)"); hts_log_warning("Output file may not be portable"); } text = h->text; l_text = h->l_text; } // write "BAM1" if (bgzf_write(fp, "BAM\1", 4) < 0) { free(hdr_ks.s); return -1; } // write plain text and the number of reference sequences if (fp->is_be) { x = ed_swap_4(l_text); if (bgzf_write(fp, &x, 4) < 0) { free(hdr_ks.s); return -1; } if (l_text) { if (bgzf_write(fp, text, l_text) < 0) { free(hdr_ks.s); return -1; } } x = ed_swap_4(h->n_targets); if (bgzf_write(fp, &x, 4) < 0) { free(hdr_ks.s); return -1; } } else { if (bgzf_write(fp, &l_text, 4) < 0) { free(hdr_ks.s); return -1; } if (l_text) { if (bgzf_write(fp, text, l_text) < 0) { free(hdr_ks.s); return -1; } } if (bgzf_write(fp, &h->n_targets, 4) < 0) { free(hdr_ks.s); return -1; } } free(hdr_ks.s); // write sequence names and lengths for (i = 0; i != h->n_targets; ++i) { char *p = h->target_name[i]; name_len = strlen(p) + 1; if (fp->is_be) { x = ed_swap_4(name_len); if (bgzf_write(fp, &x, 4) < 0) return -1; } else { if (bgzf_write(fp, &name_len, 4) < 0) return -1; } if (bgzf_write(fp, p, name_len) < 0) return -1; if (fp->is_be) { x = ed_swap_4(h->target_len[i]); if (bgzf_write(fp, &x, 4) < 0) return -1; } else { if (bgzf_write(fp, &h->target_len[i], 4) < 0) return -1; } } if (bgzf_flush(fp) < 0) return -1; return 0; } const char *sam_parse_region(sam_hdr_t *h, const char *s, int *tid, hts_pos_t *beg, hts_pos_t *end, int flags) { return hts_parse_region(s, tid, beg, end, (hts_name2id_f)bam_name2id, h, flags); } /************************* *** BAM alignment I/O *** *************************/ bam1_t *bam_init1(void) { return (bam1_t*)calloc(1, sizeof(bam1_t)); } int sam_realloc_bam_data(bam1_t *b, size_t desired) { uint32_t new_m_data; uint8_t *new_data; new_m_data = desired; kroundup32(new_m_data); // next power of 2 new_m_data += 32; // reduces malloc arena migrations? if (new_m_data < desired) { errno = ENOMEM; // Not strictly true but we can't store the size return -1; } #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (new_m_data > FUZZ_ALLOC_LIMIT) { errno = ENOMEM; return -1; } #endif if ((bam_get_mempolicy(b) & BAM_USER_OWNS_DATA) == 0) { new_data = realloc(b->data, new_m_data); } else { if ((new_data = malloc(new_m_data)) != NULL) { if (b->l_data > 0) memcpy(new_data, b->data, b->l_data < b->m_data ? b->l_data : b->m_data); bam_set_mempolicy(b, bam_get_mempolicy(b) & (~BAM_USER_OWNS_DATA)); } } if (!new_data) return -1; b->data = new_data; b->m_data = new_m_data; return 0; } void bam_destroy1(bam1_t *b) { if (b == 0) return; if ((bam_get_mempolicy(b) & BAM_USER_OWNS_DATA) == 0) { free(b->data); if ((bam_get_mempolicy(b) & BAM_USER_OWNS_STRUCT) != 0) { // In case of reuse b->data = NULL; b->m_data = 0; b->l_data = 0; } } if ((bam_get_mempolicy(b) & BAM_USER_OWNS_STRUCT) == 0) free(b); } bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc) { if (realloc_bam_data(bdst, bsrc->l_data) < 0) return NULL; memcpy(bdst->data, bsrc->data, bsrc->l_data); // copy var-len data memcpy(&bdst->core, &bsrc->core, sizeof(bsrc->core)); // copy the rest bdst->l_data = bsrc->l_data; bdst->id = bsrc->id; return bdst; } bam1_t *bam_dup1(const bam1_t *bsrc) { if (bsrc == NULL) return NULL; bam1_t *bdst = bam_init1(); if (bdst == NULL) return NULL; if (bam_copy1(bdst, bsrc) == NULL) { bam_destroy1(bdst); return NULL; } return bdst; } static void bam_cigar2rqlens(int n_cigar, const uint32_t *cigar, hts_pos_t *rlen, hts_pos_t *qlen) { int k; *rlen = *qlen = 0; for (k = 0; k < n_cigar; ++k) { int type = bam_cigar_type(bam_cigar_op(cigar[k])); int len = bam_cigar_oplen(cigar[k]); if (type & 1) *qlen += len; if (type & 2) *rlen += len; } } static int subtract_check_underflow(size_t length, size_t *limit) { if (length <= *limit) { *limit -= length; return 0; } return -1; } int bam_set1(bam1_t *bam, size_t l_qname, const char *qname, uint16_t flag, int32_t tid, hts_pos_t pos, uint8_t mapq, size_t n_cigar, const uint32_t *cigar, int32_t mtid, hts_pos_t mpos, hts_pos_t isize, size_t l_seq, const char *seq, const char *qual, size_t l_aux) { // use a default qname "*" if none is provided if (l_qname == 0) { l_qname = 1; qname = "*"; } // note: the qname is stored nul terminated and padded as described in the // documentation for the bam1_t struct. size_t qname_nuls = 4 - l_qname % 4; // the aligment length, needed for bam_reg2bin(), is calculated as in bam_endpos(). // can't use bam_endpos() directly as some fields not yet set up. hts_pos_t rlen = 0, qlen = 0; if (!(flag & BAM_FUNMAP)) { bam_cigar2rqlens((int)n_cigar, cigar, &rlen, &qlen); } if (rlen == 0) { rlen = 1; } // validate parameters if (l_qname > 254) { hts_log_error("Query name too long"); errno = EINVAL; return -1; } if (HTS_POS_MAX - rlen <= pos) { hts_log_error("Read ends beyond highest supported position"); errno = EINVAL; return -1; } if (!(flag & BAM_FUNMAP) && l_seq > 0 && n_cigar == 0) { hts_log_error("Mapped query must have a CIGAR"); errno = EINVAL; return -1; } if (!(flag & BAM_FUNMAP) && l_seq > 0 && l_seq != qlen) { hts_log_error("CIGAR and query sequence are of different length"); errno = EINVAL; return -1; } size_t limit = INT32_MAX; int u = subtract_check_underflow(l_qname + qname_nuls, &limit); u += subtract_check_underflow(n_cigar * 4, &limit); u += subtract_check_underflow((l_seq + 1) / 2, &limit); u += subtract_check_underflow(l_seq, &limit); u += subtract_check_underflow(l_aux, &limit); if (u != 0) { hts_log_error("Size overflow"); errno = EINVAL; return -1; } // re-allocate the data buffer as needed. size_t data_len = l_qname + qname_nuls + n_cigar * 4 + (l_seq + 1) / 2 + l_seq; if (realloc_bam_data(bam, data_len + l_aux) < 0) { return -1; } bam->l_data = (int)data_len; bam->core.pos = pos; bam->core.tid = tid; bam->core.bin = bam_reg2bin(pos, pos + rlen); bam->core.qual = mapq; bam->core.l_extranul = (uint8_t)(qname_nuls - 1); bam->core.flag = flag; bam->core.l_qname = (uint16_t)(l_qname + qname_nuls); bam->core.n_cigar = (uint32_t)n_cigar; bam->core.l_qseq = (int32_t)l_seq; bam->core.mtid = mtid; bam->core.mpos = mpos; bam->core.isize = isize; uint8_t *cp = bam->data; strncpy((char *)cp, qname, l_qname); int i; for (i = 0; i < qname_nuls; i++) { cp[l_qname + i] = '\0'; } cp += l_qname + qname_nuls; if (n_cigar > 0) { memcpy(cp, cigar, n_cigar * 4); } cp += n_cigar * 4; #define NN 16 const uint8_t *useq = (uint8_t *)seq; for (i = 0; i + NN < l_seq; i += NN) { int j; const uint8_t *u2 = useq+i; for (j = 0; j < NN/2; j++) cp[j] = (seq_nt16_table[u2[j*2]]<<4) | seq_nt16_table[u2[j*2+1]]; cp += NN/2; } for (; i + 1 < l_seq; i += 2) { *cp++ = (seq_nt16_table[useq[i]] << 4) | seq_nt16_table[useq[i + 1]]; } for (; i < l_seq; i++) { *cp++ = seq_nt16_table[(unsigned char)seq[i]] << 4; } if (qual) { memcpy(cp, qual, l_seq); } else { memset(cp, '\xff', l_seq); } return (int)data_len; } hts_pos_t bam_cigar2qlen(int n_cigar, const uint32_t *cigar) { int k; hts_pos_t l; for (k = l = 0; k < n_cigar; ++k) if (bam_cigar_type(bam_cigar_op(cigar[k]))&1) l += bam_cigar_oplen(cigar[k]); return l; } hts_pos_t bam_cigar2rlen(int n_cigar, const uint32_t *cigar) { int k; hts_pos_t l; for (k = l = 0; k < n_cigar; ++k) if (bam_cigar_type(bam_cigar_op(cigar[k]))&2) l += bam_cigar_oplen(cigar[k]); return l; } hts_pos_t bam_endpos(const bam1_t *b) { hts_pos_t rlen = (b->core.flag & BAM_FUNMAP)? 0 : bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(b)); if (rlen == 0) rlen = 1; return b->core.pos + rlen; } static int bam_tag2cigar(bam1_t *b, int recal_bin, int give_warning) // return 0 if CIGAR is untouched; 1 if CIGAR is updated with CG { bam1_core_t *c = &b->core; // Bail out as fast as possible for the easy case uint32_t test_CG = BAM_CSOFT_CLIP | (c->l_qseq << BAM_CIGAR_SHIFT); if (c->n_cigar == 0 || test_CG != *bam_get_cigar(b)) return 0; // The above isn't fool proof - we may have old CIGAR tags that aren't used, // but this is much less likely so do as a secondary check. if (c->tid < 0 || c->pos < 0) return 0; // Do we have a CG tag? uint8_t *CG = bam_aux_get(b, "CG"); int saved_errno = errno; if (!CG) { if (errno != ENOENT) return -1; // Bad aux data errno = saved_errno; // restore errno on expected no-CG-tag case return 0; } // Now we start with the serious work migrating CG to CIGAR uint32_t cigar_st, n_cigar4, CG_st, CG_en, ori_len = b->l_data, *cigar0, CG_len, fake_bytes; cigar0 = bam_get_cigar(b); fake_bytes = c->n_cigar * 4; if (CG[0] != 'B' || !(CG[1] == 'I' || CG[1] == 'i')) return 0; // not of type B,I CG_len = le_to_u32(CG + 2); // don't move if the real CIGAR length is shorter than the fake cigar length if (CG_len < c->n_cigar || CG_len >= 1U<<29) return 0; // move from the CG tag to the right position cigar_st = (uint8_t*)cigar0 - b->data; c->n_cigar = CG_len; n_cigar4 = c->n_cigar * 4; CG_st = CG - b->data - 2; CG_en = CG_st + 8 + n_cigar4; if (possibly_expand_bam_data(b, n_cigar4 - fake_bytes) < 0) return -1; // we need c->n_cigar-fake_bytes bytes to swap CIGAR to the right place b->l_data = b->l_data - fake_bytes + n_cigar4; // insert c->n_cigar-fake_bytes empty space to make room memmove(b->data + cigar_st + n_cigar4, b->data + cigar_st + fake_bytes, ori_len - (cigar_st + fake_bytes)); // copy the real CIGAR to the right place; -fake_bytes for the fake CIGAR memcpy(b->data + cigar_st, b->data + (n_cigar4 - fake_bytes) + CG_st + 8, n_cigar4); if (ori_len > CG_en) // move data after the CG tag memmove(b->data + CG_st + n_cigar4 - fake_bytes, b->data + CG_en + n_cigar4 - fake_bytes, ori_len - CG_en); b->l_data -= n_cigar4 + 8; // 8: CGBI (4 bytes) and CGBI length (4) if (recal_bin) b->core.bin = hts_reg2bin(b->core.pos, bam_endpos(b), 14, 5); if (give_warning) hts_log_warning("%s encodes a CIGAR with %d operators at the CG tag", bam_get_qname(b), c->n_cigar); return 1; } static inline int aux_type2size(uint8_t type) { switch (type) { case 'A': case 'c': case 'C': return 1; case 's': case 'S': return 2; case 'i': case 'I': case 'f': return 4; case 'd': return 8; case 'Z': case 'H': case 'B': return type; default: return 0; } } static void swap_data(const bam1_core_t *c, int l_data, uint8_t *data, int is_host) { uint32_t *cigar = (uint32_t*)(data + c->l_qname); uint32_t i; for (i = 0; i < c->n_cigar; ++i) ed_swap_4p(&cigar[i]); } // Fix bad records where qname is not terminated correctly. static int fixup_missing_qname_nul(bam1_t *b) { bam1_core_t *c = &b->core; // Note this is called before c->l_extranul is added to c->l_qname if (c->l_extranul > 0) { b->data[c->l_qname++] = '\0'; c->l_extranul--; } else { if (b->l_data > INT_MAX - 4) return -1; if (realloc_bam_data(b, b->l_data + 4) < 0) return -1; b->l_data += 4; b->data[c->l_qname++] = '\0'; c->l_extranul = 3; } return 0; } /* * Note a second interface that returns a bam pointer instead would avoid bam_copy1 * in multi-threaded handling. This may be worth considering for htslib2. */ int bam_read1(BGZF *fp, bam1_t *b) { bam1_core_t *c = &b->core; int32_t block_len, ret, i; uint32_t new_l_data; uint8_t tmp[32], *x; b->l_data = 0; if ((ret = bgzf_read_small(fp, &block_len, 4)) != 4) { if (ret == 0) return -1; // normal end-of-file else return -2; // truncated } if (fp->is_be) ed_swap_4p(&block_len); if (block_len < 32) return -4; // block_len includes core data if (fp->block_length - fp->block_offset > 32) { // Avoid bgzf_read and a temporary copy to a local buffer x = (uint8_t *)fp->uncompressed_block + fp->block_offset; fp->block_offset += 32; } else { x = tmp; if (bgzf_read(fp, x, 32) != 32) return -3; } c->tid = le_to_u32(x); c->pos = le_to_i32(x+4); uint32_t x2 = le_to_u32(x+8); c->bin = x2>>16; c->qual = x2>>8&0xff; c->l_qname = x2&0xff; c->l_extranul = (c->l_qname%4 != 0)? (4 - c->l_qname%4) : 0; uint32_t x3 = le_to_u32(x+12); c->flag = x3>>16; c->n_cigar = x3&0xffff; c->l_qseq = le_to_u32(x+16); c->mtid = le_to_u32(x+20); c->mpos = le_to_i32(x+24); c->isize = le_to_i32(x+28); new_l_data = block_len - 32 + c->l_extranul; if (new_l_data > INT_MAX || c->l_qseq < 0 || c->l_qname < 1) return -4; if (((uint64_t) c->n_cigar << 2) + c->l_qname + c->l_extranul + (((uint64_t) c->l_qseq + 1) >> 1) + c->l_qseq > (uint64_t) new_l_data) return -4; if (realloc_bam_data(b, new_l_data) < 0) return -4; b->l_data = new_l_data; if (bgzf_read_small(fp, b->data, c->l_qname) != c->l_qname) return -4; if (b->data[c->l_qname - 1] != '\0') { // try to fix missing nul termination if (fixup_missing_qname_nul(b) < 0) return -4; } for (i = 0; i < c->l_extranul; ++i) b->data[c->l_qname+i] = '\0'; c->l_qname += c->l_extranul; if (b->l_data < c->l_qname || bgzf_read_small(fp, b->data + c->l_qname, b->l_data - c->l_qname) != b->l_data - c->l_qname) return -4; if (fp->is_be) swap_data(c, b->l_data, b->data, 0); if (bam_tag2cigar(b, 0, 0) < 0) return -4; // TODO: consider making this conditional if (c->n_cigar > 0) { // recompute "bin" and check CIGAR-qlen consistency hts_pos_t rlen, qlen; bam_cigar2rqlens(c->n_cigar, bam_get_cigar(b), &rlen, &qlen); if ((b->core.flag & BAM_FUNMAP) || rlen == 0) rlen = 1; b->core.bin = hts_reg2bin(b->core.pos, b->core.pos + rlen, 14, 5); // Sanity check for broken CIGAR alignments if (c->l_qseq > 0 && !(c->flag & BAM_FUNMAP) && qlen != c->l_qseq) { hts_log_error("CIGAR and query sequence lengths differ for %s", bam_get_qname(b)); return -4; } } return 4 + block_len; } int bam_write1(BGZF *fp, const bam1_t *b) { const bam1_core_t *c = &b->core; uint32_t x[8], block_len = b->l_data - c->l_extranul + 32, y; int i, ok; if (c->l_qname - c->l_extranul > 255) { hts_log_error("QNAME \"%s\" is longer than 254 characters", bam_get_qname(b)); errno = EOVERFLOW; return -1; } if (c->n_cigar > 0xffff) block_len += 16; // "16" for "CGBI", 4-byte tag length and 8-byte fake CIGAR if (c->pos > INT_MAX || c->mpos > INT_MAX || c->isize < INT_MIN || c->isize > INT_MAX) { hts_log_error("Positional data is too large for BAM format"); return -1; } x[0] = c->tid; x[1] = c->pos; x[2] = (uint32_t)c->bin<<16 | c->qual<<8 | (c->l_qname - c->l_extranul); if (c->n_cigar > 0xffff) x[3] = (uint32_t)c->flag << 16 | 2; else x[3] = (uint32_t)c->flag << 16 | (c->n_cigar & 0xffff); x[4] = c->l_qseq; x[5] = c->mtid; x[6] = c->mpos; x[7] = c->isize; ok = (bgzf_flush_try(fp, 4 + block_len) >= 0); if (fp->is_be) { for (i = 0; i < 8; ++i) ed_swap_4p(x + i); y = block_len; if (ok) ok = (bgzf_write_small(fp, ed_swap_4p(&y), 4) >= 0); swap_data(c, b->l_data, b->data, 1); } else { if (ok) ok = (bgzf_write_small(fp, &block_len, 4) >= 0); } if (ok) ok = (bgzf_write_small(fp, x, 32) >= 0); if (ok) ok = (bgzf_write_small(fp, b->data, c->l_qname - c->l_extranul) >= 0); if (c->n_cigar <= 0xffff) { // no long CIGAR; write normally if (ok) ok = (bgzf_write_small(fp, b->data + c->l_qname, b->l_data - c->l_qname) >= 0); } else { // with long CIGAR, insert a fake CIGAR record and move the real CIGAR to the CG:B,I tag uint8_t buf[8]; uint32_t cigar_st, cigar_en, cigar[2]; hts_pos_t cigreflen = bam_cigar2rlen(c->n_cigar, bam_get_cigar(b)); if (cigreflen >= (1<<28)) { // Length of reference covered is greater than the biggest // CIGAR operation currently allowed. hts_log_error("Record %s with %d CIGAR ops and ref length %"PRIhts_pos " cannot be written in BAM. Try writing SAM or CRAM instead.\n", bam_get_qname(b), c->n_cigar, cigreflen); return -1; } cigar_st = (uint8_t*)bam_get_cigar(b) - b->data; cigar_en = cigar_st + c->n_cigar * 4; cigar[0] = (uint32_t)c->l_qseq << 4 | BAM_CSOFT_CLIP; cigar[1] = (uint32_t)cigreflen << 4 | BAM_CREF_SKIP; u32_to_le(cigar[0], buf); u32_to_le(cigar[1], buf + 4); if (ok) ok = (bgzf_write_small(fp, buf, 8) >= 0); // write cigar: SN if (ok) ok = (bgzf_write_small(fp, &b->data[cigar_en], b->l_data - cigar_en) >= 0); // write data after CIGAR if (ok) ok = (bgzf_write_small(fp, "CGBI", 4) >= 0); // write CG:B,I u32_to_le(c->n_cigar, buf); if (ok) ok = (bgzf_write_small(fp, buf, 4) >= 0); // write the true CIGAR length if (ok) ok = (bgzf_write_small(fp, &b->data[cigar_st], c->n_cigar * 4) >= 0); // write the real CIGAR } if (fp->is_be) swap_data(c, b->l_data, b->data, 0); return ok? 4 + block_len : -1; } /* * Write a BAM file and append to the in-memory index simultaneously. */ static int bam_write_idx1(htsFile *fp, const sam_hdr_t *h, const bam1_t *b) { BGZF *bfp = fp->fp.bgzf; if (!fp->idx) return bam_write1(bfp, b); uint32_t block_len = b->l_data - b->core.l_extranul + 32; if (bgzf_flush_try(bfp, 4 + block_len) < 0) return -1; if (!bfp->mt) hts_idx_amend_last(fp->idx, bgzf_tell(bfp)); int ret = bam_write1(bfp, b); if (ret < 0) return -1; if (bgzf_idx_push(bfp, fp->idx, b->core.tid, b->core.pos, bam_endpos(b), bgzf_tell(bfp), !(b->core.flag&BAM_FUNMAP)) < 0) { hts_log_error("Read '%s' with ref_name='%s', ref_length=%"PRIhts_pos", flags=%d, pos=%"PRIhts_pos" cannot be indexed", bam_get_qname(b), sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), b->core.flag, b->core.pos+1); ret = -1; } return ret; } /* * Set the qname in a BAM record */ int bam_set_qname(bam1_t *rec, const char *qname) { if (!rec) return -1; if (!qname || !*qname) return -1; size_t old_len = rec->core.l_qname; size_t new_len = strlen(qname) + 1; if (new_len < 1 || new_len > 255) return -1; int extranul = (new_len%4 != 0) ? (4 - new_len%4) : 0; size_t new_data_len = rec->l_data - old_len + new_len + extranul; if (realloc_bam_data(rec, new_data_len) < 0) return -1; // Make room if (new_len + extranul != rec->core.l_qname) memmove(rec->data + new_len + extranul, rec->data + rec->core.l_qname, rec->l_data - rec->core.l_qname); // Copy in new name and pad if needed memcpy(rec->data, qname, new_len); int n; for (n = 0; n < extranul; n++) rec->data[new_len + n] = '\0'; rec->l_data = new_data_len; rec->core.l_qname = new_len + extranul; rec->core.l_extranul = extranul; return 0; } /******************** *** BAM indexing *** ********************/ static hts_idx_t *sam_index(htsFile *fp, int min_shift) { int n_lvls, i, fmt, ret; bam1_t *b; hts_idx_t *idx; sam_hdr_t *h; h = sam_hdr_read(fp); if (h == NULL) return NULL; if (min_shift > 0) { hts_pos_t max_len = 0, s; for (i = 0; i < h->n_targets; ++i) { hts_pos_t len = sam_hdr_tid2len(h, i); if (max_len < len) max_len = len; } max_len += 256; for (n_lvls = 0, s = 1< s; ++n_lvls, s <<= 3); fmt = HTS_FMT_CSI; } else min_shift = 14, n_lvls = 5, fmt = HTS_FMT_BAI; idx = hts_idx_init(h->n_targets, fmt, bgzf_tell(fp->fp.bgzf), min_shift, n_lvls); b = bam_init1(); while ((ret = sam_read1(fp, h, b)) >= 0) { ret = hts_idx_push(idx, b->core.tid, b->core.pos, bam_endpos(b), bgzf_tell(fp->fp.bgzf), !(b->core.flag&BAM_FUNMAP)); if (ret < 0) { // unsorted or doesn't fit hts_log_error("Read '%s' with ref_name='%s', ref_length=%"PRIhts_pos", flags=%d, pos=%"PRIhts_pos" cannot be indexed", bam_get_qname(b), sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), b->core.flag, b->core.pos+1); goto err; } } if (ret < -1) goto err; // corrupted BAM file hts_idx_finish(idx, bgzf_tell(fp->fp.bgzf)); sam_hdr_destroy(h); bam_destroy1(b); return idx; err: bam_destroy1(b); hts_idx_destroy(idx); return NULL; } int sam_index_build3(const char *fn, const char *fnidx, int min_shift, int nthreads) { hts_idx_t *idx; htsFile *fp; int ret = 0; if ((fp = hts_open(fn, "r")) == 0) return -2; if (nthreads) hts_set_threads(fp, nthreads); switch (fp->format.format) { case cram: ret = cram_index_build(fp->fp.cram, fn, fnidx); break; case bam: case sam: if (fp->format.compression != bgzf) { hts_log_error("%s file \"%s\" not BGZF compressed", fp->format.format == bam ? "BAM" : "SAM", fn); ret = -1; break; } idx = sam_index(fp, min_shift); if (idx) { ret = hts_idx_save_as(idx, fn, fnidx, (min_shift > 0)? HTS_FMT_CSI : HTS_FMT_BAI); if (ret < 0) ret = -4; hts_idx_destroy(idx); } else ret = -1; break; default: ret = -3; break; } hts_close(fp); return ret; } int sam_index_build2(const char *fn, const char *fnidx, int min_shift) { return sam_index_build3(fn, fnidx, min_shift, 0); } int sam_index_build(const char *fn, int min_shift) { return sam_index_build3(fn, NULL, min_shift, 0); } // Provide bam_index_build() symbol for binary compatibility with earlier HTSlib #undef bam_index_build int bam_index_build(const char *fn, int min_shift) { return sam_index_build2(fn, NULL, min_shift); } // Initialise fp->idx for the current format type. // This must be called after the header has been written but no other data. int sam_idx_init(htsFile *fp, sam_hdr_t *h, int min_shift, const char *fnidx) { fp->fnidx = fnidx; if (fp->format.format == bam || fp->format.format == bcf || (fp->format.format == sam && fp->format.compression == bgzf)) { int n_lvls, fmt = HTS_FMT_CSI; if (min_shift > 0) { int64_t max_len = 0, s; int i; for (i = 0; i < h->n_targets; ++i) if (max_len < h->target_len[i]) max_len = h->target_len[i]; max_len += 256; for (n_lvls = 0, s = 1< s; ++n_lvls, s <<= 3); } else min_shift = 14, n_lvls = 5, fmt = HTS_FMT_BAI; fp->idx = hts_idx_init(h->n_targets, fmt, bgzf_tell(fp->fp.bgzf), min_shift, n_lvls); return fp->idx ? 0 : -1; } if (fp->format.format == cram) { fp->fp.cram->idxfp = bgzf_open(fnidx, "wg"); return fp->fp.cram->idxfp ? 0 : -1; } return -1; } // Finishes an index. Call after the last record has been written. // Returns 0 on success, <0 on failure. int sam_idx_save(htsFile *fp) { if (fp->format.format == bam || fp->format.format == bcf || fp->format.format == vcf || fp->format.format == sam) { int ret; if ((ret = sam_state_destroy(fp)) < 0) { errno = -ret; return -1; } if (!fp->is_bgzf || bgzf_flush(fp->fp.bgzf) < 0) return -1; hts_idx_amend_last(fp->idx, bgzf_tell(fp->fp.bgzf)); if (hts_idx_finish(fp->idx, bgzf_tell(fp->fp.bgzf)) < 0) return -1; return hts_idx_save_but_not_close(fp->idx, fp->fnidx, hts_idx_fmt(fp->idx)); } else if (fp->format.format == cram) { // flushed and closed by cram_close } return 0; } static int sam_readrec(BGZF *ignored, void *fpv, void *bv, int *tid, hts_pos_t *beg, hts_pos_t *end) { htsFile *fp = (htsFile *)fpv; bam1_t *b = bv; fp->line.l = 0; int ret = sam_read1(fp, fp->bam_header, b); if (ret >= 0) { *tid = b->core.tid; *beg = b->core.pos; *end = bam_endpos(b); } return ret; } // This is used only with read_rest=1 iterators, so need not set tid/beg/end. static int sam_readrec_rest(BGZF *ignored, void *fpv, void *bv, int *tid, hts_pos_t *beg, hts_pos_t *end) { htsFile *fp = (htsFile *)fpv; bam1_t *b = bv; fp->line.l = 0; int ret = sam_read1(fp, fp->bam_header, b); return ret; } // Internal (for now) func used by bam_sym_lookup. This is copied from // samtools/bam.c. static const char *bam_get_library(const bam_hdr_t *h, const bam1_t *b) { const char *rg; kstring_t lib = { 0, 0, NULL }; rg = (char *)bam_aux_get(b, "RG"); if (!rg) return NULL; else rg++; if (sam_hdr_find_tag_id((bam_hdr_t *)h, "RG", "ID", rg, "LB", &lib) < 0) return NULL; static char LB_text[1024]; int len = lib.l < sizeof(LB_text) - 1 ? lib.l : sizeof(LB_text) - 1; memcpy(LB_text, lib.s, len); LB_text[len] = 0; free(lib.s); return LB_text; } // Bam record pointer and SAM header combined typedef struct { const sam_hdr_t *h; const bam1_t *b; } hb_pair; // Looks up variable names in str and replaces them with their value. // Also supports aux tags. // // Note the expression parser deliberately overallocates str size so it // is safe to use memcmp over strcmp. static int bam_sym_lookup(void *data, char *str, char **end, hts_expr_val_t *res) { hb_pair *hb = (hb_pair *)data; const bam1_t *b = hb->b; res->is_str = 0; switch(*str) { case 'c': if (memcmp(str, "cigar", 5) == 0) { *end = str+5; res->is_str = 1; ks_clear(&res->s); uint32_t *cigar = bam_get_cigar(b); int i, n = b->core.n_cigar, r = 0; if (n) { for (i = 0; i < n; i++) { r |= kputw (bam_cigar_oplen(cigar[i]), &res->s) < 0; r |= kputc_(bam_cigar_opchr(cigar[i]), &res->s) < 0; } r |= kputs("", &res->s) < 0; } else { r |= kputs("*", &res->s) < 0; } return r ? -1 : 0; } break; case 'e': if (memcmp(str, "endpos", 6) == 0) { *end = str+6; res->d = bam_endpos(b); return 0; } break; case 'f': if (memcmp(str, "flag", 4) == 0) { str = *end = str+4; if (*str != '.') { res->d = b->core.flag; return 0; } else { str++; if (!memcmp(str, "paired", 6)) { *end = str+6; res->d = b->core.flag & BAM_FPAIRED; return 0; } else if (!memcmp(str, "proper_pair", 11)) { *end = str+11; res->d = b->core.flag & BAM_FPROPER_PAIR; return 0; } else if (!memcmp(str, "unmap", 5)) { *end = str+5; res->d = b->core.flag & BAM_FUNMAP; return 0; } else if (!memcmp(str, "munmap", 6)) { *end = str+6; res->d = b->core.flag & BAM_FMUNMAP; return 0; } else if (!memcmp(str, "reverse", 7)) { *end = str+7; res->d = b->core.flag & BAM_FREVERSE; return 0; } else if (!memcmp(str, "mreverse", 8)) { *end = str+8; res->d = b->core.flag & BAM_FMREVERSE; return 0; } else if (!memcmp(str, "read1", 5)) { *end = str+5; res->d = b->core.flag & BAM_FREAD1; return 0; } else if (!memcmp(str, "read2", 5)) { *end = str+5; res->d = b->core.flag & BAM_FREAD2; return 0; } else if (!memcmp(str, "secondary", 9)) { *end = str+9; res->d = b->core.flag & BAM_FSECONDARY; return 0; } else if (!memcmp(str, "qcfail", 6)) { *end = str+6; res->d = b->core.flag & BAM_FQCFAIL; return 0; } else if (!memcmp(str, "dup", 3)) { *end = str+3; res->d = b->core.flag & BAM_FDUP; return 0; } else if (!memcmp(str, "supplementary", 13)) { *end = str+13; res->d = b->core.flag & BAM_FSUPPLEMENTARY; return 0; } else { hts_log_error("Unrecognised flag string"); return -1; } } } break; case 'h': if (memcmp(str, "hclen", 5) == 0) { int hclen = 0; uint32_t *cigar = bam_get_cigar(b); uint32_t ncigar = b->core.n_cigar; // left if (ncigar > 0 && bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) hclen = bam_cigar_oplen(cigar[0]); // right if (ncigar > 1 && bam_cigar_op(cigar[ncigar-1]) == BAM_CHARD_CLIP) hclen += bam_cigar_oplen(cigar[ncigar-1]); *end = str+5; res->d = hclen; return 0; } break; case 'l': if (memcmp(str, "library", 7) == 0) { *end = str+7; res->is_str = 1; const char *lib = bam_get_library(hb->h, b); kputs(lib ? lib : "", ks_clear(&res->s)); return 0; } break; case 'm': if (memcmp(str, "mapq", 4) == 0) { *end = str+4; res->d = b->core.qual; return 0; } else if (memcmp(str, "mpos", 4) == 0) { *end = str+4; res->d = b->core.mpos+1; return 0; } else if (memcmp(str, "mrname", 6) == 0) { *end = str+6; res->is_str = 1; const char *rn = sam_hdr_tid2name(hb->h, b->core.mtid); kputs(rn ? rn : "*", ks_clear(&res->s)); return 0; } else if (memcmp(str, "mrefid", 6) == 0) { *end = str+6; res->d = b->core.mtid; return 0; } break; case 'n': if (memcmp(str, "ncigar", 6) == 0) { *end = str+6; res->d = b->core.n_cigar; return 0; } break; case 'p': if (memcmp(str, "pos", 3) == 0) { *end = str+3; res->d = b->core.pos+1; return 0; } else if (memcmp(str, "pnext", 5) == 0) { *end = str+5; res->d = b->core.mpos+1; return 0; } break; case 'q': if (memcmp(str, "qlen", 4) == 0) { *end = str+4; res->d = bam_cigar2qlen(b->core.n_cigar, bam_get_cigar(b)); return 0; } else if (memcmp(str, "qname", 5) == 0) { *end = str+5; res->is_str = 1; kputs(bam_get_qname(b), ks_clear(&res->s)); return 0; } else if (memcmp(str, "qual", 4) == 0) { *end = str+4; ks_clear(&res->s); if (ks_resize(&res->s, b->core.l_qseq+1) < 0) return -1; memcpy(res->s.s, bam_get_qual(b), b->core.l_qseq); res->s.l = b->core.l_qseq; res->is_str = 1; return 0; } break; case 'r': if (memcmp(str, "rlen", 4) == 0) { *end = str+4; res->d = bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(b)); return 0; } else if (memcmp(str, "rname", 5) == 0) { *end = str+5; res->is_str = 1; const char *rn = sam_hdr_tid2name(hb->h, b->core.tid); kputs(rn ? rn : "*", ks_clear(&res->s)); return 0; } else if (memcmp(str, "rnext", 5) == 0) { *end = str+5; res->is_str = 1; const char *rn = sam_hdr_tid2name(hb->h, b->core.mtid); kputs(rn ? rn : "*", ks_clear(&res->s)); return 0; } else if (memcmp(str, "refid", 5) == 0) { *end = str+5; res->d = b->core.tid; return 0; } break; case 's': if (memcmp(str, "seq", 3) == 0) { *end = str+3; ks_clear(&res->s); if (ks_resize(&res->s, b->core.l_qseq+1) < 0) return -1; nibble2base(bam_get_seq(b), res->s.s, b->core.l_qseq); res->s.s[b->core.l_qseq] = 0; res->s.l = b->core.l_qseq; res->is_str = 1; return 0; } else if (memcmp(str, "sclen", 5) == 0) { int sclen = 0; uint32_t *cigar = bam_get_cigar(b); int ncigar = b->core.n_cigar; int left = 0; // left if (ncigar > 0 && bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) left = 0, sclen += bam_cigar_oplen(cigar[0]); else if (ncigar > 1 && bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) left = 1, sclen += bam_cigar_oplen(cigar[1]); // right if (ncigar-1 > left && bam_cigar_op(cigar[ncigar-1]) == BAM_CSOFT_CLIP) sclen += bam_cigar_oplen(cigar[ncigar-1]); else if (ncigar-2 > left && bam_cigar_op(cigar[ncigar-1]) == BAM_CHARD_CLIP && bam_cigar_op(cigar[ncigar-2]) == BAM_CSOFT_CLIP) sclen += bam_cigar_oplen(cigar[ncigar-2]); *end = str+5; res->d = sclen; return 0; } break; case 't': if (memcmp(str, "tlen", 4) == 0) { *end = str+4; res->d = b->core.isize; return 0; } break; case '[': if (*str == '[' && str[1] && str[2] && str[3] == ']') { /* aux tags */ *end = str+4; uint8_t *aux = bam_aux_get(b, str+1); if (aux) { // we define the truth of a tag to be its presence, even if 0. res->is_true = 1; switch (*aux) { case 'Z': case 'H': res->is_str = 1; kputs((char *)aux+1, ks_clear(&res->s)); break; case 'A': res->is_str = 1; kputsn((char *)aux+1, 1, ks_clear(&res->s)); break; case 'i': case 'I': case 's': case 'S': case 'c': case 'C': res->is_str = 0; res->d = bam_aux2i(aux); break; case 'f': case 'd': res->is_str = 0; res->d = bam_aux2f(aux); break; default: hts_log_error("Aux type '%c not yet supported by filters", *aux); return -1; } return 0; } else { // hence absent tags are always false (and strings) res->is_str = 1; res->s.l = 0; res->d = 0; res->is_true = 0; return 0; } } break; } // All successful matches in switch should return 0. // So if we didn't match, it's a parse error. return -1; } // Returns 1 when accepted by the filter, 0 if not, -1 on error. int sam_passes_filter(const sam_hdr_t *h, const bam1_t *b, hts_filter_t *filt) { hb_pair hb = {h, b}; hts_expr_val_t res = HTS_EXPR_VAL_INIT; if (hts_filter_eval2(filt, &hb, bam_sym_lookup, &res)) { hts_log_error("Couldn't process filter expression"); hts_expr_val_free(&res); return -1; } int t = res.is_true; hts_expr_val_free(&res); return t; } static int cram_readrec(BGZF *ignored, void *fpv, void *bv, int *tid, hts_pos_t *beg, hts_pos_t *end) { htsFile *fp = fpv; bam1_t *b = bv; int pass_filter, ret; do { ret = cram_get_bam_seq(fp->fp.cram, &b); if (ret < 0) return cram_eof(fp->fp.cram) ? -1 : -2; if (bam_tag2cigar(b, 1, 1) < 0) return -2; *tid = b->core.tid; *beg = b->core.pos; *end = bam_endpos(b); if (fp->filter) { pass_filter = sam_passes_filter(fp->bam_header, b, fp->filter); if (pass_filter < 0) return -2; } else { pass_filter = 1; } } while (pass_filter == 0); return ret; } static int cram_pseek(void *fp, int64_t offset, int whence) { cram_fd *fd = (cram_fd *)fp; if ((0 != cram_seek(fd, offset, SEEK_SET)) && (0 != cram_seek(fd, offset - fd->first_container, SEEK_CUR))) return -1; fd->curr_position = offset; if (fd->ctr) { cram_free_container(fd->ctr); if (fd->ctr_mt && fd->ctr_mt != fd->ctr) cram_free_container(fd->ctr_mt); fd->ctr = NULL; fd->ctr_mt = NULL; fd->ooc = 0; } return 0; } /* * cram_ptell is a pseudo-tell function, because it matches the position of the disk cursor only * after a fresh seek call. Otherwise it indicates that the read takes place inside the buffered * container previously fetched. It was designed like this to integrate with the functionality * of the iterator stepping logic. */ static int64_t cram_ptell(void *fp) { cram_fd *fd = (cram_fd *)fp; cram_container *c; cram_slice *s; int64_t ret = -1L; if (fd) { if ((c = fd->ctr) != NULL) { if ((s = c->slice) != NULL && s->max_rec) { if ((c->curr_slice + s->curr_rec/s->max_rec) >= (c->max_slice + 1)) fd->curr_position += c->offset + c->length; } } ret = fd->curr_position; } return ret; } static int bam_pseek(void *fp, int64_t offset, int whence) { BGZF *fd = (BGZF *)fp; return bgzf_seek(fd, offset, whence); } static int64_t bam_ptell(void *fp) { BGZF *fd = (BGZF *)fp; if (!fd) return -1L; return bgzf_tell(fd); } static hts_idx_t *index_load(htsFile *fp, const char *fn, const char *fnidx, int flags) { switch (fp->format.format) { case bam: case sam: return hts_idx_load3(fn, fnidx, HTS_FMT_BAI, flags); case cram: { if (cram_index_load(fp->fp.cram, fn, fnidx) < 0) return NULL; // Cons up a fake "index" just pointing at the associated cram_fd: hts_cram_idx_t *idx = malloc(sizeof (hts_cram_idx_t)); if (idx == NULL) return NULL; idx->fmt = HTS_FMT_CRAI; idx->cram = fp->fp.cram; return (hts_idx_t *) idx; } default: return NULL; // TODO Would use tbx_index_load if it returned hts_idx_t } } hts_idx_t *sam_index_load3(htsFile *fp, const char *fn, const char *fnidx, int flags) { return index_load(fp, fn, fnidx, flags); } hts_idx_t *sam_index_load2(htsFile *fp, const char *fn, const char *fnidx) { return index_load(fp, fn, fnidx, HTS_IDX_SAVE_REMOTE); } hts_idx_t *sam_index_load(htsFile *fp, const char *fn) { return index_load(fp, fn, NULL, HTS_IDX_SAVE_REMOTE); } static hts_itr_t *cram_itr_query(const hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, hts_readrec_func *readrec) { const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx; hts_itr_t *iter = (hts_itr_t *) calloc(1, sizeof(hts_itr_t)); if (iter == NULL) return NULL; // Cons up a dummy iterator for which hts_itr_next() will simply invoke // the readrec function: iter->is_cram = 1; iter->read_rest = 1; iter->off = NULL; iter->bins.a = NULL; iter->readrec = readrec; if (tid >= 0 || tid == HTS_IDX_NOCOOR || tid == HTS_IDX_START) { cram_range r = { tid, beg+1, end }; int ret = cram_set_option(cidx->cram, CRAM_OPT_RANGE, &r); iter->curr_off = 0; // The following fields are not required by hts_itr_next(), but are // filled in in case user code wants to look at them. iter->tid = tid; iter->beg = beg; iter->end = end; switch (ret) { case 0: break; case -2: // No data vs this ref, so mark iterator as completed. // Same as HTS_IDX_NONE. iter->finished = 1; break; default: free(iter); return NULL; } } else switch (tid) { case HTS_IDX_REST: iter->curr_off = 0; break; case HTS_IDX_NONE: iter->curr_off = 0; iter->finished = 1; break; default: hts_log_error("Query with tid=%d not implemented for CRAM files", tid); abort(); break; } return iter; } hts_itr_t *sam_itr_queryi(const hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end) { const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx; if (idx == NULL) return hts_itr_query(NULL, tid, beg, end, sam_readrec_rest); else if (cidx->fmt == HTS_FMT_CRAI) return cram_itr_query(idx, tid, beg, end, sam_readrec); else return hts_itr_query(idx, tid, beg, end, sam_readrec); } static int cram_name2id(void *fdv, const char *ref) { cram_fd *fd = (cram_fd *) fdv; return sam_hdr_name2tid(fd->header, ref); } hts_itr_t *sam_itr_querys(const hts_idx_t *idx, sam_hdr_t *hdr, const char *region) { const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx; return hts_itr_querys(idx, region, (hts_name2id_f)(bam_name2id), hdr, cidx->fmt == HTS_FMT_CRAI ? cram_itr_query : hts_itr_query, sam_readrec); } hts_itr_t *sam_itr_regarray(const hts_idx_t *idx, sam_hdr_t *hdr, char **regarray, unsigned int regcount) { const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx; hts_reglist_t *r_list = NULL; int r_count = 0; if (!cidx || !hdr) return NULL; hts_itr_t *itr = NULL; if (cidx->fmt == HTS_FMT_CRAI) { r_list = hts_reglist_create(regarray, regcount, &r_count, cidx->cram, cram_name2id); if (!r_list) return NULL; itr = hts_itr_regions(idx, r_list, r_count, cram_name2id, cidx->cram, hts_itr_multi_cram, cram_readrec, cram_pseek, cram_ptell); } else { r_list = hts_reglist_create(regarray, regcount, &r_count, hdr, (hts_name2id_f)(bam_name2id)); if (!r_list) return NULL; itr = hts_itr_regions(idx, r_list, r_count, (hts_name2id_f)(bam_name2id), hdr, hts_itr_multi_bam, sam_readrec, bam_pseek, bam_ptell); } if (!itr) hts_reglist_free(r_list, r_count); return itr; } hts_itr_t *sam_itr_regions(const hts_idx_t *idx, sam_hdr_t *hdr, hts_reglist_t *reglist, unsigned int regcount) { const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx; if(!cidx || !hdr || !reglist) return NULL; if (cidx->fmt == HTS_FMT_CRAI) return hts_itr_regions(idx, reglist, regcount, cram_name2id, cidx->cram, hts_itr_multi_cram, cram_readrec, cram_pseek, cram_ptell); else return hts_itr_regions(idx, reglist, regcount, (hts_name2id_f)(bam_name2id), hdr, hts_itr_multi_bam, sam_readrec, bam_pseek, bam_ptell); } /********************** *** SAM header I/O *** **********************/ #include "htslib/kseq.h" #include "htslib/kstring.h" sam_hdr_t *sam_hdr_parse(size_t l_text, const char *text) { sam_hdr_t *bh = sam_hdr_init(); if (!bh) return NULL; if (sam_hdr_add_lines(bh, text, l_text) != 0) { sam_hdr_destroy(bh); return NULL; } return bh; } static int valid_sam_header_type(const char *s) { if (s[0] != '@') return 0; switch (s[1]) { case 'H': return s[2] == 'D' && s[3] == '\t'; case 'S': return s[2] == 'Q' && s[3] == '\t'; case 'R': case 'P': return s[2] == 'G' && s[3] == '\t'; case 'C': return s[2] == 'O'; } return 0; } // Minimal sanitisation of a header to ensure. // - null terminated string. // - all lines start with @ (also implies no blank lines). // // Much more could be done, but currently is not, including: // - checking header types are known (HD, SQ, etc). // - syntax (eg checking tab separated fields). // - validating n_targets matches @SQ records. // - validating target lengths against @SQ records. static sam_hdr_t *sam_hdr_sanitise(sam_hdr_t *h) { if (!h) return NULL; // Special case for empty headers. if (h->l_text == 0) return h; size_t i; unsigned int lnum = 0; char *cp = h->text, last = '\n'; for (i = 0; i < h->l_text; i++) { // NB: l_text excludes terminating nul. This finds early ones. if (cp[i] == 0) break; // Error on \n[^@], including duplicate newlines if (last == '\n') { lnum++; if (cp[i] != '@') { hts_log_error("Malformed SAM header at line %u", lnum); sam_hdr_destroy(h); return NULL; } } last = cp[i]; } if (i < h->l_text) { // Early nul found. Complain if not just padding. size_t j = i; while (j < h->l_text && cp[j] == '\0') j++; if (j < h->l_text) hts_log_warning("Unexpected NUL character in header. Possibly truncated"); } // Add trailing newline and/or trailing nul if required. if (last != '\n') { hts_log_warning("Missing trailing newline on SAM header. Possibly truncated"); if (h->l_text < 2 || i >= h->l_text - 2) { if (h->l_text >= SIZE_MAX - 2) { hts_log_error("No room for extra newline"); sam_hdr_destroy(h); return NULL; } cp = realloc(h->text, (size_t) h->l_text+2); if (!cp) { sam_hdr_destroy(h); return NULL; } h->text = cp; } cp[i++] = '\n'; // l_text may be larger already due to multiple nul padding if (h->l_text < i) h->l_text = i; cp[h->l_text] = '\0'; } return h; } static void known_stderr(const char *tool, const char *advice) { hts_log_warning("SAM file corrupted by embedded %s error/log message", tool); hts_log_warning("%s", advice); } static void warn_if_known_stderr(const char *line) { if (strstr(line, "M::bwa_idx_load_from_disk") != NULL) known_stderr("bwa", "Use `bwa mem -o file.sam ...` or `bwa sampe -f file.sam ...` instead of `bwa ... > file.sam`"); else if (strstr(line, "M::mem_pestat") != NULL) known_stderr("bwa", "Use `bwa mem -o file.sam ...` instead of `bwa mem ... > file.sam`"); else if (strstr(line, "loaded/built the index") != NULL) known_stderr("minimap2", "Use `minimap2 -o file.sam ...` instead of `minimap2 ... > file.sam`"); } static sam_hdr_t *sam_hdr_create(htsFile* fp) { kstring_t str = { 0, 0, NULL }; khint_t k; sam_hdr_t* h = sam_hdr_init(); const char *q, *r; char* sn = NULL; khash_t(s2i) *d = kh_init(s2i); khash_t(s2i) *long_refs = NULL; if (!h || !d) goto error; int ret, has_SQ = 0; int next_c = '@'; while (next_c == '@' && (ret = hts_getline(fp, KS_SEP_LINE, &fp->line)) >= 0) { if (fp->line.s[0] != '@') break; if (fp->line.l > 3 && strncmp(fp->line.s, "@SQ", 3) == 0) { has_SQ = 1; hts_pos_t ln = -1; for (q = fp->line.s + 4;; ++q) { if (strncmp(q, "SN:", 3) == 0) { q += 3; for (r = q;*r != '\t' && *r != '\n' && *r != '\0';++r); if (sn) { hts_log_warning("SQ header line has more than one SN: tag"); free(sn); } sn = (char*)calloc(r - q + 1, 1); if (!sn) goto error; strncpy(sn, q, r - q); q = r; } else { if (strncmp(q, "LN:", 3) == 0) ln = strtoll(q + 3, (char**)&q, 10); } while (*q != '\t' && *q != '\n' && *q != '\0') ++q; if (*q == '\0' || *q == '\n') break; } if (sn) { if (ln >= 0) { int absent; k = kh_put(s2i, d, sn, &absent); if (absent < 0) goto error; if (!absent) { hts_log_warning("Duplicated sequence \"%s\" in file \"%s\"", sn, fp->fn); free(sn); } else { sn = NULL; if (ln >= UINT32_MAX) { // Stash away ref length that // doesn't fit in target_len array int k2; if (!long_refs) { long_refs = kh_init(s2i); if (!long_refs) goto error; } k2 = kh_put(s2i, long_refs, kh_key(d, k), &absent); if (absent < 0) goto error; kh_val(long_refs, k2) = ln; kh_val(d, k) = ((int64_t) (kh_size(d) - 1) << 32 | UINT32_MAX); } else { kh_val(d, k) = (int64_t) (kh_size(d) - 1) << 32 | ln; } } } else { hts_log_warning("Ignored @SQ SN:%s : bad or missing LN tag", sn); warn_if_known_stderr(fp->line.s); free(sn); } } else { hts_log_warning("Ignored @SQ line with missing SN: tag"); warn_if_known_stderr(fp->line.s); } sn = NULL; } else if (!valid_sam_header_type(fp->line.s)) { hts_log_error("Invalid header line: must start with @HD/@SQ/@RG/@PG/@CO"); warn_if_known_stderr(fp->line.s); goto error; } if (kputsn(fp->line.s, fp->line.l, &str) < 0) goto error; if (kputc('\n', &str) < 0) goto error; if (fp->is_bgzf) { next_c = bgzf_peek(fp->fp.bgzf); } else { unsigned char nc; ssize_t pret = hpeek(fp->fp.hfile, &nc, 1); next_c = pret > 0 ? nc : pret - 1; } if (next_c < -1) goto error; } if (next_c != '@') fp->line.l = 0; if (ret < -1) goto error; if (!has_SQ && fp->fn_aux) { kstring_t line = { 0, 0, NULL }; /* The reference index (.fai) is actually needed here */ char *fai_fn = fp->fn_aux; char *fn_delim = strstr(fp->fn_aux, HTS_IDX_DELIM); if (fn_delim) fai_fn = fn_delim + strlen(HTS_IDX_DELIM); hFILE* f = hopen(fai_fn, "r"); int e = 0, absent; if (f == NULL) goto error; while (line.l = 0, kgetline(&line, (kgets_func*) hgets, f) >= 0) { char* tab = strchr(line.s, '\t'); hts_pos_t ln; if (tab == NULL) continue; sn = (char*)calloc(tab-line.s+1, 1); if (!sn) { e = 1; break; } memcpy(sn, line.s, tab-line.s); k = kh_put(s2i, d, sn, &absent); if (absent < 0) { e = 1; break; } ln = strtoll(tab, NULL, 10); if (!absent) { hts_log_warning("Duplicated sequence \"%s\" in the file \"%s\"", sn, fai_fn); free(sn); sn = NULL; } else { sn = NULL; if (ln >= UINT32_MAX) { // Stash away ref length that // doesn't fit in target_len array khint_t k2; int absent = -1; if (!long_refs) { long_refs = kh_init(s2i); if (!long_refs) { e = 1; break; } } k2 = kh_put(s2i, long_refs, kh_key(d, k), &absent); if (absent < 0) { e = 1; break; } kh_val(long_refs, k2) = ln; kh_val(d, k) = ((int64_t) (kh_size(d) - 1) << 32 | UINT32_MAX); } else { kh_val(d, k) = (int64_t) (kh_size(d) - 1) << 32 | ln; } has_SQ = 1; } e |= kputs("@SQ\tSN:", &str) < 0; e |= kputsn(line.s, tab - line.s, &str) < 0; e |= kputs("\tLN:", &str) < 0; e |= kputll(ln, &str) < 0; e |= kputc('\n', &str) < 0; if (e) break; } ks_free(&line); if (hclose(f) != 0) { hts_log_error("Error on closing %s", fai_fn); e = 1; } if (e) goto error; } if (has_SQ) { // Populate the targets array h->n_targets = kh_size(d); h->target_name = (char**) malloc(sizeof(char*) * h->n_targets); if (!h->target_name) { h->n_targets = 0; goto error; } h->target_len = (uint32_t*) malloc(sizeof(uint32_t) * h->n_targets); if (!h->target_len) { h->n_targets = 0; goto error; } for (k = kh_begin(d); k != kh_end(d); ++k) { if (!kh_exist(d, k)) continue; h->target_name[kh_val(d, k) >> 32] = (char*) kh_key(d, k); h->target_len[kh_val(d, k) >> 32] = kh_val(d, k) & 0xffffffffUL; kh_val(d, k) >>= 32; } } // Repurpose sdict to hold any references longer than UINT32_MAX h->sdict = long_refs; kh_destroy(s2i, d); if (str.l == 0) kputsn("", 0, &str); h->l_text = str.l; h->text = ks_release(&str); fp->bam_header = sam_hdr_sanitise(h); fp->bam_header->ref_count = 1; return fp->bam_header; error: if (h && d && (!h->target_name || !h->target_len)) { for (k = kh_begin(d); k != kh_end(d); ++k) if (kh_exist(d, k)) free((void *)kh_key(d, k)); } sam_hdr_destroy(h); ks_free(&str); kh_destroy(s2i, d); kh_destroy(s2i, long_refs); if (sn) free(sn); return NULL; } sam_hdr_t *sam_hdr_read(htsFile *fp) { if (!fp) { errno = EINVAL; return NULL; } switch (fp->format.format) { case bam: return sam_hdr_sanitise(bam_hdr_read(fp->fp.bgzf)); case cram: return sam_hdr_sanitise(sam_hdr_dup(fp->fp.cram->header)); case sam: return sam_hdr_create(fp); case fastq_format: case fasta_format: return sam_hdr_init(); case empty_format: errno = EPIPE; return NULL; default: errno = EFTYPE; return NULL; } } int sam_hdr_write(htsFile *fp, const sam_hdr_t *h) { if (!fp || !h) { errno = EINVAL; return -1; } switch (fp->format.format) { case binary_format: fp->format.category = sequence_data; fp->format.format = bam; /* fall-through */ case bam: if (bam_hdr_write(fp->fp.bgzf, h) < 0) return -1; break; case cram: { cram_fd *fd = fp->fp.cram; if (cram_set_header2(fd, h) < 0) return -1; if (fp->fn_aux) cram_load_reference(fd, fp->fn_aux); if (cram_write_SAM_hdr(fd, fd->header) < 0) return -1; } break; case text_format: fp->format.category = sequence_data; fp->format.format = sam; /* fall-through */ case sam: { if (!h->hrecs && !h->text) return 0; char *text; kstring_t hdr_ks = { 0, 0, NULL }; size_t l_text; ssize_t bytes; int r = 0, no_sq = 0; if (h->hrecs) { if (sam_hrecs_rebuild_text(h->hrecs, &hdr_ks) != 0) return -1; text = hdr_ks.s; l_text = hdr_ks.l; } else { const char *p = NULL; do { const char *q = p == NULL ? h->text : p + 4; p = strstr(q, "@SQ\t"); } while (!(p == NULL || p == h->text || *(p - 1) == '\n')); no_sq = p == NULL; text = h->text; l_text = h->l_text; } if (fp->is_bgzf) { bytes = bgzf_write(fp->fp.bgzf, text, l_text); } else { bytes = hwrite(fp->fp.hfile, text, l_text); } free(hdr_ks.s); if (bytes != l_text) return -1; if (no_sq) { int i; for (i = 0; i < h->n_targets; ++i) { fp->line.l = 0; r |= kputsn("@SQ\tSN:", 7, &fp->line) < 0; r |= kputs(h->target_name[i], &fp->line) < 0; r |= kputsn("\tLN:", 4, &fp->line) < 0; r |= kputw(h->target_len[i], &fp->line) < 0; r |= kputc('\n', &fp->line) < 0; if (r != 0) return -1; if (fp->is_bgzf) { bytes = bgzf_write(fp->fp.bgzf, fp->line.s, fp->line.l); } else { bytes = hwrite(fp->fp.hfile, fp->line.s, fp->line.l); } if (bytes != fp->line.l) return -1; } } if (fp->is_bgzf) { if (bgzf_flush(fp->fp.bgzf) != 0) return -1; } else { if (hflush(fp->fp.hfile) != 0) return -1; } } break; case fastq_format: case fasta_format: // Nothing to output; FASTQ has no file headers. break; default: errno = EBADF; return -1; } return 0; } static int old_sam_hdr_change_HD(sam_hdr_t *h, const char *key, const char *val) { char *p, *q, *beg = NULL, *end = NULL, *newtext; size_t new_l_text; if (!h || !key) return -1; if (h->l_text > 3) { if (strncmp(h->text, "@HD", 3) == 0) { //@HD line exists if ((p = strchr(h->text, '\n')) == 0) return -1; *p = '\0'; // for strstr call char tmp[5] = { '\t', key[0], key[0] ? key[1] : '\0', ':', '\0' }; if ((q = strstr(h->text, tmp)) != 0) { // key exists *p = '\n'; // change back // mark the key:val beg = q; for (q += 4; *q != '\n' && *q != '\t'; ++q); end = q; if (val && (strncmp(beg + 4, val, end - beg - 4) == 0) && strlen(val) == end - beg - 4) return 0; // val is the same, no need to change } else { beg = end = p; *p = '\n'; } } } if (beg == NULL) { // no @HD new_l_text = h->l_text; if (new_l_text > SIZE_MAX - strlen(SAM_FORMAT_VERSION) - 9) return -1; new_l_text += strlen(SAM_FORMAT_VERSION) + 8; if (val) { if (new_l_text > SIZE_MAX - strlen(val) - 5) return -1; new_l_text += strlen(val) + 4; } newtext = (char*)malloc(new_l_text + 1); if (!newtext) return -1; if (val) snprintf(newtext, new_l_text + 1, "@HD\tVN:%s\t%s:%s\n%s", SAM_FORMAT_VERSION, key, val, h->text); else snprintf(newtext, new_l_text + 1, "@HD\tVN:%s\n%s", SAM_FORMAT_VERSION, h->text); } else { // has @HD but different or no key new_l_text = (beg - h->text) + (h->text + h->l_text - end); if (val) { if (new_l_text > SIZE_MAX - strlen(val) - 5) return -1; new_l_text += strlen(val) + 4; } newtext = (char*)malloc(new_l_text + 1); if (!newtext) return -1; if (val) { snprintf(newtext, new_l_text + 1, "%.*s\t%s:%s%s", (int) (beg - h->text), h->text, key, val, end); } else { //delete key snprintf(newtext, new_l_text + 1, "%.*s%s", (int) (beg - h->text), h->text, end); } } free(h->text); h->text = newtext; h->l_text = new_l_text; return 0; } int sam_hdr_change_HD(sam_hdr_t *h, const char *key, const char *val) { if (!h || !key) return -1; if (!h->hrecs) return old_sam_hdr_change_HD(h, key, val); if (val) { if (sam_hdr_update_line(h, "HD", NULL, NULL, key, val, NULL) != 0) return -1; } else { if (sam_hdr_remove_tag_id(h, "HD", NULL, NULL, key) != 0) return -1; } return sam_hdr_rebuild(h); } /********************** *** SAM record I/O *** **********************/ // The speed of this code can vary considerably depending on minor code // changes elsewhere as some of the tight loops are particularly prone to // speed changes when the instruction blocks are split over a 32-byte // boundary. To protect against this, we explicitly specify an alignment // for this function. If this is insufficient, we may also wish to // consider alignment of blocks within this function via // __attribute__((optimize("align-loops=5"))) (gcc) or clang equivalents. // However it's not very portable. // Instead we break into separate functions so we can explicitly specify // use __attribute__((aligned(32))) instead and force consistent loop // alignment. static inline int64_t grow_B_array(bam1_t *b, uint32_t *n, size_t size) { // Avoid overflow on 32-bit platforms, but it breaks BAM anyway if (*n > INT32_MAX*0.666) { errno = ENOMEM; return -1; } size_t bytes = (size_t)size * (size_t)(*n>>1); if (possibly_expand_bam_data(b, bytes) < 0) { hts_log_error("Out of memory"); return -1; } (*n)+=*n>>1; return 0; } // This ensures that q always ends up at the next comma after // reading a number even if it's followed by junk. It // prevents the possibility of trying to read more than n items. #define skip_to_comma_(q) do { while (*(q) > '\t' && *(q) != ',') (q)++; } while (0) HTS_ALIGN32 static char *sam_parse_Bc_vals(bam1_t *b, char *q, uint32_t *nused, uint32_t *nalloc, int *overflow) { while (*q == ',') { if ((*nused)++ >= (*nalloc)) { if (grow_B_array(b, nalloc, 1) < 0) return NULL; } *(b->data + b->l_data) = hts_str2int(q + 1, &q, 8, overflow); b->l_data++; } return q; } HTS_ALIGN32 static char *sam_parse_BC_vals(bam1_t *b, char *q, uint32_t *nused, uint32_t *nalloc, int *overflow) { while (*q == ',') { if ((*nused)++ >= (*nalloc)) { if (grow_B_array(b, nalloc, 1) < 0) return NULL; } if (q[1] != '-') { *(b->data + b->l_data) = hts_str2uint(q + 1, &q, 8, overflow); b->l_data++; } else { *overflow = 1; q++; skip_to_comma_(q); } } return q; } HTS_ALIGN32 static char *sam_parse_Bs_vals(bam1_t *b, char *q, uint32_t *nused, uint32_t *nalloc, int *overflow) { while (*q == ',') { if ((*nused)++ >= (*nalloc)) { if (grow_B_array(b, nalloc, 2) < 0) return NULL; } i16_to_le(hts_str2int(q + 1, &q, 16, overflow), b->data + b->l_data); b->l_data += 2; } return q; } HTS_ALIGN32 static char *sam_parse_BS_vals(bam1_t *b, char *q, uint32_t *nused, uint32_t *nalloc, int *overflow) { while (*q == ',') { if ((*nused)++ >= (*nalloc)) { if (grow_B_array(b, nalloc, 2) < 0) return NULL; } if (q[1] != '-') { u16_to_le(hts_str2uint(q + 1, &q, 16, overflow), b->data + b->l_data); b->l_data += 2; } else { *overflow = 1; q++; skip_to_comma_(q); } } return q; } HTS_ALIGN32 static char *sam_parse_Bi_vals(bam1_t *b, char *q, uint32_t *nused, uint32_t *nalloc, int *overflow) { while (*q == ',') { if ((*nused)++ >= (*nalloc)) { if (grow_B_array(b, nalloc, 4) < 0) return NULL; } i32_to_le(hts_str2int(q + 1, &q, 32, overflow), b->data + b->l_data); b->l_data += 4; } return q; } HTS_ALIGN32 static char *sam_parse_BI_vals(bam1_t *b, char *q, uint32_t *nused, uint32_t *nalloc, int *overflow) { while (*q == ',') { if ((*nused)++ >= (*nalloc)) { if (grow_B_array(b, nalloc, 4) < 0) return NULL; } if (q[1] != '-') { u32_to_le(hts_str2uint(q + 1, &q, 32, overflow), b->data + b->l_data); b->l_data += 4; } else { *overflow = 1; q++; skip_to_comma_(q); } } return q; } HTS_ALIGN32 static char *sam_parse_Bf_vals(bam1_t *b, char *q, uint32_t *nused, uint32_t *nalloc, int *overflow) { while (*q == ',') { if ((*nused)++ >= (*nalloc)) { if (grow_B_array(b, nalloc, 4) < 0) return NULL; } float_to_le(strtod(q + 1, &q), b->data + b->l_data); b->l_data += 4; } return q; } HTS_ALIGN32 static int sam_parse_B_vals_r(char type, uint32_t nalloc, char *in, char **end, bam1_t *b, int *ctr) { // Protect against infinite recursion when dealing with invalid input. // An example string is "XX:B:C,-". The lack of a number means min=0, // but it overflowed due to "-" and so we repeat ad-infinitum. // // Loop detection is the safest solution incase there are other // strange corner cases with malformed inputs. if (++(*ctr) > 2) { hts_log_error("Malformed data in B:%c array", type); return -1; } int orig_l = b->l_data; char *q = in; int32_t size; size_t bytes; int overflow = 0; size = aux_type2size(type); if (size <= 0 || size > 4) { hts_log_error("Unrecognized type B:%c", type); return -1; } // Ensure space for type + values. // The first pass through here we don't know the number of entries and // nalloc == 0. We start with a small working set and then parse the // data, growing as needed. // // If we have a second pass through we do know the number of entries // and nalloc is already known. We have no need to expand the bam data. if (!nalloc) nalloc=7; // Ensure allocated memory is big enough (for current nalloc estimate) bytes = (size_t) nalloc * (size_t) size; if (bytes / size != nalloc || possibly_expand_bam_data(b, bytes + 2 + sizeof(uint32_t))) { hts_log_error("Out of memory"); return -1; } uint32_t nused = 0; b->data[b->l_data++] = 'B'; b->data[b->l_data++] = type; // 32-bit B-array length is inserted later once we know it. int b_len_idx = b->l_data; b->l_data += sizeof(uint32_t); if (type == 'c') { if (!(q = sam_parse_Bc_vals(b, q, &nused, &nalloc, &overflow))) return -1; } else if (type == 'C') { if (!(q = sam_parse_BC_vals(b, q, &nused, &nalloc, &overflow))) return -1; } else if (type == 's') { if (!(q = sam_parse_Bs_vals(b, q, &nused, &nalloc, &overflow))) return -1; } else if (type == 'S') { if (!(q = sam_parse_BS_vals(b, q, &nused, &nalloc, &overflow))) return -1; } else if (type == 'i') { if (!(q = sam_parse_Bi_vals(b, q, &nused, &nalloc, &overflow))) return -1; } else if (type == 'I') { if (!(q = sam_parse_BI_vals(b, q, &nused, &nalloc, &overflow))) return -1; } else if (type == 'f') { if (!(q = sam_parse_Bf_vals(b, q, &nused, &nalloc, &overflow))) return -1; } if (*q != '\t' && *q != '\0') { // Unknown B array type or junk in the numbers hts_log_error("Malformed B:%c", type); return -1; } i32_to_le(nused, b->data + b_len_idx); if (!overflow) { *end = q; return 0; } else { int64_t max = 0, min = 0, val; // Given type was incorrect. Try to rescue the situation. char *r = q; q = in; overflow = 0; b->l_data = orig_l; // Find out what range of values is present while (q < r) { val = hts_str2int(q + 1, &q, 64, &overflow); if (max < val) max = val; if (min > val) min = val; skip_to_comma_(q); } // Retry with appropriate type if (!overflow) { if (min < 0) { if (min >= INT8_MIN && max <= INT8_MAX) { return sam_parse_B_vals_r('c', nalloc, in, end, b, ctr); } else if (min >= INT16_MIN && max <= INT16_MAX) { return sam_parse_B_vals_r('s', nalloc, in, end, b, ctr); } else if (min >= INT32_MIN && max <= INT32_MAX) { return sam_parse_B_vals_r('i', nalloc, in, end, b, ctr); } } else { if (max < UINT8_MAX) { return sam_parse_B_vals_r('C', nalloc, in, end, b, ctr); } else if (max <= UINT16_MAX) { return sam_parse_B_vals_r('S', nalloc, in, end, b, ctr); } else if (max <= UINT32_MAX) { return sam_parse_B_vals_r('I', nalloc, in, end, b, ctr); } } } // If here then at least one of the values is too big to store hts_log_error("Numeric value in B array out of allowed range"); return -1; } #undef skip_to_comma_ } HTS_ALIGN32 static int sam_parse_B_vals(char type, char *in, char **end, bam1_t *b) { int ctr = 0; uint32_t nalloc = 0; return sam_parse_B_vals_r(type, nalloc, in, end, b, &ctr); } static inline unsigned int parse_sam_flag(char *v, char **rv, int *overflow) { if (*v >= '1' && *v <= '9') { return hts_str2uint(v, rv, 16, overflow); } else if (*v == '0') { // handle single-digit "0" directly; otherwise it's hex or octal if (v[1] == '\t') { *rv = v+1; return 0; } else { unsigned long val = strtoul(v, rv, 0); if (val > 65535) { *overflow = 1; return 65535; } return val; } } else { // TODO implement symbolic flag letters *rv = v; return 0; } } // Parse tag line and append to bam object b. // Shared by both SAM and FASTQ parsers. // // The difference between the two is how lenient we are to recognising // non-compliant strings. The FASTQ parser glosses over arbitrary // non-SAM looking strings. static inline int aux_parse(char *start, char *end, bam1_t *b, int lenient, khash_t(tag) *tag_whitelist) { int overflow = 0; int checkpoint; char logbuf[40]; char *q = start, *p = end; #define _parse_err(cond, ...) \ do { \ if (cond) { \ if (lenient) { \ while (q < p && !isspace_c(*q)) \ q++; \ while (q < p && isspace_c(*q)) \ q++; \ b->l_data = checkpoint; \ goto loop; \ } else { \ hts_log_error(__VA_ARGS__); \ goto err_ret; \ } \ } \ } while (0) while (q < p) loop: { char type; checkpoint = b->l_data; if (p - q < 5) { if (lenient) { break; } else { hts_log_error("Incomplete aux field"); goto err_ret; } } _parse_err(q[0] < '!' || q[1] < '!', "invalid aux tag id"); if (lenient && (q[2] | q[4]) != ':') { while (q < p && !isspace_c(*q)) q++; while (q < p && isspace_c(*q)) q++; continue; } if (tag_whitelist) { int tt = q[0]*256 + q[1]; if (kh_get(tag, tag_whitelist, tt) == kh_end(tag_whitelist)) { while (q < p && *q != '\t') q++; continue; } } // Copy over id if (possibly_expand_bam_data(b, 2) < 0) goto err_ret; memcpy(b->data + b->l_data, q, 2); b->l_data += 2; q += 3; type = *q++; ++q; // q points to value if (type != 'Z' && type != 'H') // the only zero length acceptable fields _parse_err(*q <= '\t', "incomplete aux field"); // Ensure enough space for a double + type allocated. if (possibly_expand_bam_data(b, 16) < 0) goto err_ret; if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { b->data[b->l_data++] = 'A'; b->data[b->l_data++] = *q++; } else if (type == 'i' || type == 'I') { if (*q == '-') { int32_t x = hts_str2int(q, &q, 32, &overflow); if (x >= INT8_MIN) { b->data[b->l_data++] = 'c'; b->data[b->l_data++] = x; } else if (x >= INT16_MIN) { b->data[b->l_data++] = 's'; i16_to_le(x, b->data + b->l_data); b->l_data += 2; } else { b->data[b->l_data++] = 'i'; i32_to_le(x, b->data + b->l_data); b->l_data += 4; } } else { uint32_t x = hts_str2uint(q, &q, 32, &overflow); if (x <= UINT8_MAX) { b->data[b->l_data++] = 'C'; b->data[b->l_data++] = x; } else if (x <= UINT16_MAX) { b->data[b->l_data++] = 'S'; u16_to_le(x, b->data + b->l_data); b->l_data += 2; } else { b->data[b->l_data++] = 'I'; u32_to_le(x, b->data + b->l_data); b->l_data += 4; } } } else if (type == 'f') { b->data[b->l_data++] = 'f'; float_to_le(strtod(q, &q), b->data + b->l_data); b->l_data += sizeof(float); } else if (type == 'd') { b->data[b->l_data++] = 'd'; double_to_le(strtod(q, &q), b->data + b->l_data); b->l_data += sizeof(double); } else if (type == 'Z' || type == 'H') { char *end = strchr(q, '\t'); if (!end) end = q + strlen(q); _parse_err(type == 'H' && ((end-q)&1) != 0, "hex field does not have an even number of digits"); b->data[b->l_data++] = type; if (possibly_expand_bam_data(b, end - q + 1) < 0) goto err_ret; memcpy(b->data + b->l_data, q, end - q); b->l_data += end - q; b->data[b->l_data++] = '\0'; q = end; } else if (type == 'B') { type = *q++; // q points to the first ',' following the typing byte _parse_err(*q && *q != ',' && *q != '\t', "B aux field type not followed by ','"); if (sam_parse_B_vals(type, q, &q, b) < 0) goto err_ret; } else _parse_err(1, "unrecognized type %s", hts_strprint(logbuf, sizeof logbuf, '\'', &type, 1)); while (*q > '\t') { q++; } // Skip any junk to next tab q++; } _parse_err(!lenient && overflow != 0, "numeric value out of allowed range"); #undef _parse_err return 0; err_ret: return -2; } int sam_parse1(kstring_t *s, sam_hdr_t *h, bam1_t *b) { #define _read_token(_p) (_p); do { char *tab = strchr((_p), '\t'); if (!tab) goto err_ret; *tab = '\0'; (_p) = tab + 1; } while (0) #if HTS_ALLOW_UNALIGNED != 0 && ULONG_MAX == 0xffffffffffffffff // Macro that operates on 64-bits at a time. #define COPY_MINUS_N(to,from,n,l,failed) \ do { \ uint64_u *from8 = (uint64_u *)(from); \ uint64_u *to8 = (uint64_u *)(to); \ uint64_t uflow = 0; \ size_t l8 = (l)>>3, i; \ for (i = 0; i < l8; i++) { \ to8[i] = from8[i] - (n)*0x0101010101010101UL; \ uflow |= to8[i]; \ } \ for (i<<=3; i < (l); ++i) { \ to[i] = from[i] - (n); \ uflow |= to[i]; \ } \ failed = (uflow & 0x8080808080808080UL) > 0; \ } while (0) #else // Basic version which operates a byte at a time #define COPY_MINUS_N(to,from,n,l,failed) do { \ uint8_t uflow = 0; \ for (i = 0; i < (l); ++i) { \ (to)[i] = (from)[i] - (n); \ uflow |= (uint8_t) (to)[i]; \ } \ failed = (uflow & 0x80) > 0; \ } while (0) #endif #define _get_mem(type_t, x, b, l) if (possibly_expand_bam_data((b), (l)) < 0) goto err_ret; *(x) = (type_t*)((b)->data + (b)->l_data); (b)->l_data += (l) #define _parse_err(cond, ...) do { if (cond) { hts_log_error(__VA_ARGS__); goto err_ret; } } while (0) #define _parse_warn(cond, ...) do { if (cond) { hts_log_warning(__VA_ARGS__); } } while (0) uint8_t *t; char *p = s->s, *q; int i, overflow = 0; char logbuf[40]; hts_pos_t cigreflen; bam1_core_t *c = &b->core; b->l_data = 0; memset(c, 0, 32); // qname q = _read_token(p); _parse_warn(p - q <= 1, "empty query name"); _parse_err(p - q > 255, "query name too long"); // resize large enough for name + extranul if (possibly_expand_bam_data(b, (p - q) + 4) < 0) goto err_ret; memcpy(b->data + b->l_data, q, p-q); b->l_data += p-q; c->l_extranul = (4 - (b->l_data & 3)) & 3; memcpy(b->data + b->l_data, "\0\0\0\0", c->l_extranul); b->l_data += c->l_extranul; c->l_qname = p - q + c->l_extranul; // flag c->flag = parse_sam_flag(p, &p, &overflow); if (*p++ != '\t') goto err_ret; // malformated flag // chr q = _read_token(p); if (strcmp(q, "*")) { _parse_err(h->n_targets == 0, "no SQ lines present in the header"); c->tid = bam_name2id(h, q); _parse_err(c->tid < -1, "failed to parse header"); _parse_warn(c->tid < 0, "unrecognized reference name %s; treated as unmapped", hts_strprint(logbuf, sizeof logbuf, '"', q, SIZE_MAX)); } else c->tid = -1; // pos c->pos = hts_str2uint(p, &p, 62, &overflow) - 1; if (*p++ != '\t') goto err_ret; if (c->pos < 0 && c->tid >= 0) { _parse_warn(1, "mapped query cannot have zero coordinate; treated as unmapped"); c->tid = -1; } if (c->tid < 0) c->flag |= BAM_FUNMAP; // mapq c->qual = hts_str2uint(p, &p, 8, &overflow); if (*p++ != '\t') goto err_ret; // cigar if (*p != '*') { uint32_t *cigar = NULL; int old_l_data = b->l_data; int n_cigar = bam_parse_cigar(p, &p, b); if (n_cigar < 1 || *p++ != '\t') goto err_ret; cigar = (uint32_t *)(b->data + old_l_data); // can't use bam_endpos() directly as some fields not yet set up cigreflen = (!(c->flag&BAM_FUNMAP))? bam_cigar2rlen(c->n_cigar, cigar) : 1; if (cigreflen == 0) cigreflen = 1; } else { _parse_warn(!(c->flag&BAM_FUNMAP), "mapped query must have a CIGAR; treated as unmapped"); c->flag |= BAM_FUNMAP; q = _read_token(p); cigreflen = 1; } _parse_err(HTS_POS_MAX - cigreflen <= c->pos, "read ends beyond highest supported position"); c->bin = hts_reg2bin(c->pos, c->pos + cigreflen, 14, 5); // mate chr q = _read_token(p); if (strcmp(q, "=") == 0) { c->mtid = c->tid; } else if (strcmp(q, "*") == 0) { c->mtid = -1; } else { c->mtid = bam_name2id(h, q); _parse_err(c->mtid < -1, "failed to parse header"); _parse_warn(c->mtid < 0, "unrecognized mate reference name %s; treated as unmapped", hts_strprint(logbuf, sizeof logbuf, '"', q, SIZE_MAX)); } // mpos c->mpos = hts_str2uint(p, &p, 62, &overflow) - 1; if (*p++ != '\t') goto err_ret; if (c->mpos < 0 && c->mtid >= 0) { _parse_warn(1, "mapped mate cannot have zero coordinate; treated as unmapped"); c->mtid = -1; } // tlen c->isize = hts_str2int(p, &p, 63, &overflow); if (*p++ != '\t') goto err_ret; _parse_err(overflow, "number outside allowed range"); // seq q = _read_token(p); if (strcmp(q, "*")) { _parse_err(p - q - 1 > INT32_MAX, "read sequence is too long"); c->l_qseq = p - q - 1; hts_pos_t ql = bam_cigar2qlen(c->n_cigar, (uint32_t*)(b->data + c->l_qname)); _parse_err(c->n_cigar && ql != c->l_qseq, "CIGAR and query sequence are of different length"); i = (c->l_qseq + 1) >> 1; _get_mem(uint8_t, &t, b, i); unsigned int lqs2 = c->l_qseq&~1, i; for (i = 0; i < lqs2; i+=2) t[i>>1] = (seq_nt16_table[(unsigned char)q[i]] << 4) | seq_nt16_table[(unsigned char)q[i+1]]; for (; i < c->l_qseq; ++i) t[i>>1] = seq_nt16_table[(unsigned char)q[i]] << ((~i&1)<<2); } else c->l_qseq = 0; // qual _get_mem(uint8_t, &t, b, c->l_qseq); if (p[0] == '*' && (p[1] == '\t' || p[1] == '\0')) { memset(t, 0xff, c->l_qseq); p += 2; } else { int failed = 0; _parse_err(s->l - (p - s->s) < c->l_qseq || (p[c->l_qseq] != '\t' && p[c->l_qseq] != '\0'), "SEQ and QUAL are of different length"); COPY_MINUS_N(t, p, 33, c->l_qseq, failed); _parse_err(failed, "invalid QUAL character"); p += c->l_qseq + 1; } // aux if (aux_parse(p, s->s + s->l, b, 0, NULL) < 0) goto err_ret; if (bam_tag2cigar(b, 1, 1) < 0) return -2; return 0; #undef _parse_warn #undef _parse_err #undef _get_mem #undef _read_token err_ret: return -2; } static uint32_t read_ncigar(const char *q) { uint32_t n_cigar = 0; for (; *q && *q != '\t'; ++q) if (!isdigit_c(*q)) ++n_cigar; if (!n_cigar) { hts_log_error("No CIGAR operations"); return 0; } if (n_cigar >= 2147483647) { hts_log_error("Too many CIGAR operations"); return 0; } return n_cigar; } /*! @function @abstract Parse a CIGAR string into preallocated a uint32_t array @param in [in] pointer to the source string @param a_cigar [out] address of the destination uint32_t buffer @return number of processed input characters; 0 on error */ static int parse_cigar(const char *in, uint32_t *a_cigar, uint32_t n_cigar) { int i, overflow = 0; const char *p = in; for (i = 0; i < n_cigar; i++) { uint32_t len; int op; char *q; len = hts_str2uint(p, &q, 28, &overflow)< *a_mem) { uint32_t *a_tmp = realloc(*a_cigar, n_cigar*sizeof(**a_cigar)); if (a_tmp) { *a_cigar = a_tmp; *a_mem = n_cigar; } else { hts_log_error("Memory allocation error"); return -1; } } if (!(diff = parse_cigar(in, *a_cigar, n_cigar))) return -1; if (end) *end = (char *)in+diff; return n_cigar; } ssize_t bam_parse_cigar(const char *in, char **end, bam1_t *b) { size_t n_cigar = 0; int diff; if (!in || !b) { hts_log_error("NULL pointer arguments"); return -1; } if (end) *end = (char *)in; n_cigar = (*in == '*') ? 0 : read_ncigar(in); if (!n_cigar && b->core.n_cigar == 0) { if (end) *end = (char *)in+1; return 0; } ssize_t cig_diff = n_cigar - b->core.n_cigar; if (cig_diff > 0 && possibly_expand_bam_data(b, cig_diff * sizeof(uint32_t)) < 0) { hts_log_error("Memory allocation error"); return -1; } uint32_t *cig = bam_get_cigar(b); if ((uint8_t *)cig != b->data + b->l_data) { // Modifying an BAM existing BAM record uint8_t *seq = bam_get_seq(b); memmove(cig + n_cigar, seq, (b->data + b->l_data) - seq); } if (n_cigar) { if (!(diff = parse_cigar(in, cig, n_cigar))) return -1; } else { diff = 1; // handle "*" } b->l_data += cig_diff * sizeof(uint32_t); b->core.n_cigar = n_cigar; if (end) *end = (char *)in + diff; return n_cigar; } /* * ----------------------------------------------------------------------------- * SAM threading */ // Size of SAM text block (reading) #define SAM_NBYTES 240000 // Number of BAM records (writing, up to NB_mem in size) #define SAM_NBAM 1000 struct SAM_state; // Output job - a block of BAM records typedef struct sp_bams { struct sp_bams *next; int serial; bam1_t *bams; int nbams, abams; // used and alloc for bams[] array size_t bam_mem; // very approximate total size struct SAM_state *fd; } sp_bams; // Input job - a block of SAM text typedef struct sp_lines { struct sp_lines *next; int serial; char *data; int data_size; int alloc; struct SAM_state *fd; sp_bams *bams; } sp_lines; enum sam_cmd { SAM_NONE = 0, SAM_CLOSE, SAM_CLOSE_DONE, }; typedef struct SAM_state { sam_hdr_t *h; hts_tpool *p; int own_pool; pthread_mutex_t lines_m; hts_tpool_process *q; pthread_t dispatcher; int dispatcher_set; sp_lines *lines; sp_bams *bams; sp_bams *curr_bam; int curr_idx; int serial; // Be warned: moving these mutexes around in this struct can reduce // threading performance by up to 70%! pthread_mutex_t command_m; pthread_cond_t command_c; enum sam_cmd command; // One of the E* errno codes int errcode; htsFile *fp; } SAM_state; // Returns a SAM_state struct from a generic hFILE. // // Returns NULL on failure. static SAM_state *sam_state_create(htsFile *fp) { // Ideally sam_open wouldn't be a #define to hts_open but instead would // be a redirect call with an additional 'S' mode. This in turn would // correctly set the designed format to sam instead of a generic // text_format. if (fp->format.format != sam && fp->format.format != text_format) return NULL; SAM_state *fd = calloc(1, sizeof(*fd)); if (!fd) return NULL; fp->state = fd; fd->fp = fp; return fd; } static int sam_format1_append(const bam_hdr_t *h, const bam1_t *b, kstring_t *str); static void *sam_format_worker(void *arg); static void sam_state_err(SAM_state *fd, int errcode) { pthread_mutex_lock(&fd->command_m); if (!fd->errcode) fd->errcode = errcode; pthread_mutex_unlock(&fd->command_m); } static void sam_free_sp_bams(sp_bams *b) { if (!b) return; if (b->bams) { int i; for (i = 0; i < b->abams; i++) { if (b->bams[i].data) free(b->bams[i].data); } free(b->bams); } free(b); } // Destroys the state produce by sam_state_create. int sam_state_destroy(htsFile *fp) { int ret = 0; if (!fp->state) return 0; SAM_state *fd = fp->state; if (fd->p) { if (fd->h) { // Notify sam_dispatcher we're closing pthread_mutex_lock(&fd->command_m); if (fd->command != SAM_CLOSE_DONE) fd->command = SAM_CLOSE; pthread_cond_signal(&fd->command_c); ret = -fd->errcode; if (fd->q) hts_tpool_wake_dispatch(fd->q); // unstick the reader if (!fp->is_write && fd->q && fd->dispatcher_set) { for (;;) { // Avoid deadlocks with dispatcher if (fd->command == SAM_CLOSE_DONE) break; hts_tpool_wake_dispatch(fd->q); pthread_mutex_unlock(&fd->command_m); usleep(10000); pthread_mutex_lock(&fd->command_m); } } pthread_mutex_unlock(&fd->command_m); if (fp->is_write) { // Dispatch the last partial block. sp_bams *gb = fd->curr_bam; if (!ret && gb && gb->nbams > 0 && fd->q) ret = hts_tpool_dispatch(fd->p, fd->q, sam_format_worker, gb); // Flush and drain output if (fd->q) hts_tpool_process_flush(fd->q); pthread_mutex_lock(&fd->command_m); if (!ret) ret = -fd->errcode; pthread_mutex_unlock(&fd->command_m); while (!ret && fd->q && !hts_tpool_process_empty(fd->q)) { usleep(10000); pthread_mutex_lock(&fd->command_m); ret = -fd->errcode; // not empty but shutdown implies error if (hts_tpool_process_is_shutdown(fd->q) && !ret) ret = EIO; pthread_mutex_unlock(&fd->command_m); } if (fd->q) hts_tpool_process_shutdown(fd->q); } // Wait for it to acknowledge if (fd->dispatcher_set) pthread_join(fd->dispatcher, NULL); if (!ret) ret = -fd->errcode; } // Tidy up memory if (fd->q) hts_tpool_process_destroy(fd->q); if (fd->own_pool && fp->format.compression == no_compression) { hts_tpool_destroy(fd->p); fd->p = NULL; } pthread_mutex_destroy(&fd->lines_m); pthread_mutex_destroy(&fd->command_m); pthread_cond_destroy(&fd->command_c); sp_lines *l = fd->lines; while (l) { sp_lines *n = l->next; free(l->data); free(l); l = n; } sp_bams *b = fd->bams; while (b) { if (fd->curr_bam == b) fd->curr_bam = NULL; sp_bams *n = b->next; sam_free_sp_bams(b); b = n; } if (fd->curr_bam) sam_free_sp_bams(fd->curr_bam); // Decrement counter by one, maybe destroying too. // This is to permit the caller using bam_hdr_destroy // before sam_close without triggering decode errors // in the background threads. bam_hdr_destroy(fd->h); } free(fp->state); fp->state = NULL; return ret; } // Cleanup function - job for sam_parse_worker; result for sam_format_worker static void cleanup_sp_lines(void *arg) { sp_lines *gl = (sp_lines *)arg; if (!gl) return; // Should always be true for lines passed to / from thread workers. assert(gl->next == NULL); free(gl->data); sam_free_sp_bams(gl->bams); free(gl); } // Run from one of the worker threads. // Convert a passed in array of lines to array of BAMs, returning // the result back to the thread queue. static void *sam_parse_worker(void *arg) { sp_lines *gl = (sp_lines *)arg; sp_bams *gb = NULL; char *lines = gl->data; int i; bam1_t *b; SAM_state *fd = gl->fd; // Use a block of BAM structs we had earlier if available. pthread_mutex_lock(&fd->lines_m); if (fd->bams) { gb = fd->bams; fd->bams = gb->next; } pthread_mutex_unlock(&fd->lines_m); if (gb == NULL) { gb = calloc(1, sizeof(*gb)); if (!gb) { return NULL; } gb->abams = 100; gb->bams = b = calloc(gb->abams, sizeof(*b)); if (!gb->bams) { sam_state_err(fd, ENOMEM); goto err; } gb->nbams = 0; gb->bam_mem = 0; } gb->serial = gl->serial; gb->next = NULL; b = (bam1_t *)gb->bams; if (!b) { sam_state_err(fd, ENOMEM); goto err; } i = 0; char *cp = lines, *cp_end = lines + gl->data_size; while (cp < cp_end) { if (i >= gb->abams) { int old_abams = gb->abams; gb->abams *= 2; b = (bam1_t *)realloc(gb->bams, gb->abams*sizeof(bam1_t)); if (!b) { gb->abams /= 2; sam_state_err(fd, ENOMEM); goto err; } memset(&b[old_abams], 0, (gb->abams - old_abams)*sizeof(*b)); gb->bams = b; } // Ideally we'd get sam_parse1 to return the number of // bytes decoded and to be able to stop on newline as // well as \0. // // We can then avoid the additional strchr loop. // It's around 6% of our CPU cost, albeit threadable. // // However this is an API change so for now we copy. char *nl = strchr(cp, '\n'); char *line_end; if (nl) { line_end = nl; if (line_end > cp && *(line_end - 1) == '\r') line_end--; nl++; } else { nl = line_end = cp_end; } *line_end = '\0'; kstring_t ks = { line_end - cp, gl->alloc, cp }; if (sam_parse1(&ks, fd->h, &b[i]) < 0) { sam_state_err(fd, errno ? errno : EIO); cleanup_sp_lines(gl); goto err; } cp = nl; i++; } gb->nbams = i; pthread_mutex_lock(&fd->lines_m); gl->next = fd->lines; fd->lines = gl; pthread_mutex_unlock(&fd->lines_m); return gb; err: sam_free_sp_bams(gb); return NULL; } static void *sam_parse_eof(void *arg) { return NULL; } // Cleanup function - result for sam_parse_worker; job for sam_format_worker static void cleanup_sp_bams(void *arg) { sam_free_sp_bams((sp_bams *) arg); } // Runs in its own thread. // Reads a block of text (SAM) and sends a new job to the thread queue to // translate this to BAM. static void *sam_dispatcher_read(void *vp) { htsFile *fp = vp; kstring_t line = {0}; int line_frag = 0; SAM_state *fd = fp->state; sp_lines *l = NULL; // Pre-allocate buffer for left-over bits of line (exact size doesn't // matter as it will grow if necessary). if (ks_resize(&line, 1000) < 0) goto err; for (;;) { // Check for command pthread_mutex_lock(&fd->command_m); switch (fd->command) { case SAM_CLOSE: pthread_cond_signal(&fd->command_c); pthread_mutex_unlock(&fd->command_m); hts_tpool_process_shutdown(fd->q); goto tidyup; default: break; } pthread_mutex_unlock(&fd->command_m); pthread_mutex_lock(&fd->lines_m); if (fd->lines) { // reuse existing line buffer l = fd->lines; fd->lines = l->next; } pthread_mutex_unlock(&fd->lines_m); if (l == NULL) { // none to reuse, to create a new one l = calloc(1, sizeof(*l)); if (!l) goto err; l->alloc = SAM_NBYTES; l->data = malloc(l->alloc+8); // +8 for optimisation in sam_parse1 if (!l->data) { free(l); l = NULL; goto err; } l->fd = fd; } l->next = NULL; if (l->alloc < line_frag+SAM_NBYTES/2) { char *rp = realloc(l->data, line_frag+SAM_NBYTES/2 +8); if (!rp) goto err; l->alloc = line_frag+SAM_NBYTES/2; l->data = rp; } memcpy(l->data, line.s, line_frag); l->data_size = line_frag; ssize_t nbytes; longer_line: if (fp->is_bgzf) nbytes = bgzf_read(fp->fp.bgzf, l->data + line_frag, l->alloc - line_frag); else nbytes = hread(fp->fp.hfile, l->data + line_frag, l->alloc - line_frag); if (nbytes < 0) { sam_state_err(fd, errno ? errno : EIO); goto err; } else if (nbytes == 0) break; // EOF l->data_size += nbytes; // trim to last \n. Maybe \r\n, but that's still fine if (nbytes == l->alloc - line_frag) { char *cp_end = l->data + l->data_size; char *cp = cp_end-1; while (cp > (char *)l->data && *cp != '\n') cp--; // entire buffer is part of a single line if (cp == l->data) { line_frag = l->data_size; char *rp = realloc(l->data, l->alloc * 2 + 8); if (!rp) goto err; l->alloc *= 2; l->data = rp; assert(l->alloc >= l->data_size); assert(l->alloc >= line_frag); assert(l->alloc >= l->alloc - line_frag); goto longer_line; } cp++; // line holds the remainder of our line. if (ks_resize(&line, cp_end - cp) < 0) goto err; memcpy(line.s, cp, cp_end - cp); line_frag = cp_end - cp; l->data_size = l->alloc - line_frag; } else { // out of buffer line_frag = 0; } l->serial = fd->serial++; //fprintf(stderr, "Dispatching %p, %d bytes, serial %d\n", l, l->data_size, l->serial); if (hts_tpool_dispatch3(fd->p, fd->q, sam_parse_worker, l, cleanup_sp_lines, cleanup_sp_bams, 0) < 0) goto err; pthread_mutex_lock(&fd->command_m); if (fd->command == SAM_CLOSE) { pthread_mutex_unlock(&fd->command_m); l = NULL; goto tidyup; } l = NULL; // Now "owned" by sam_parse_worker() pthread_mutex_unlock(&fd->command_m); } if (hts_tpool_dispatch(fd->p, fd->q, sam_parse_eof, NULL) < 0) goto err; // At EOF, wait for close request. // (In future if we add support for seek, this is where we need to catch it.) for (;;) { pthread_mutex_lock(&fd->command_m); if (fd->command == SAM_NONE) pthread_cond_wait(&fd->command_c, &fd->command_m); switch (fd->command) { case SAM_CLOSE: pthread_cond_signal(&fd->command_c); pthread_mutex_unlock(&fd->command_m); hts_tpool_process_shutdown(fd->q); goto tidyup; default: pthread_mutex_unlock(&fd->command_m); break; } } tidyup: pthread_mutex_lock(&fd->command_m); fd->command = SAM_CLOSE_DONE; pthread_cond_signal(&fd->command_c); pthread_mutex_unlock(&fd->command_m); if (l) { pthread_mutex_lock(&fd->lines_m); l->next = fd->lines; fd->lines = l; pthread_mutex_unlock(&fd->lines_m); } free(line.s); return NULL; err: sam_state_err(fd, errno ? errno : ENOMEM); hts_tpool_process_shutdown(fd->q); goto tidyup; } // Runs in its own thread. // Takes encoded blocks of SAM off the thread results queue and writes them // to our output stream. static void *sam_dispatcher_write(void *vp) { htsFile *fp = vp; SAM_state *fd = fp->state; hts_tpool_result *r; // Iterates until result queue is shutdown, where it returns NULL. while ((r = hts_tpool_next_result_wait(fd->q))) { sp_lines *gl = (sp_lines *)hts_tpool_result_data(r); if (!gl) { sam_state_err(fd, ENOMEM); goto err; } if (fp->idx) { sp_bams *gb = gl->bams; int i = 0, count = 0; while (i < gl->data_size) { int j = i; while (i < gl->data_size && gl->data[i] != '\n') i++; if (i < gl->data_size) i++; if (fp->is_bgzf) { if (bgzf_flush_try(fp->fp.bgzf, i-j) < 0) goto err; if (bgzf_write(fp->fp.bgzf, &gl->data[j], i-j) != i-j) goto err; } else { if (hwrite(fp->fp.hfile, &gl->data[j], i-j) != i-j) goto err; } bam1_t *b = &gb->bams[count++]; if (fp->format.compression == bgzf) { if (bgzf_idx_push(fp->fp.bgzf, fp->idx, b->core.tid, b->core.pos, bam_endpos(b), bgzf_tell(fp->fp.bgzf), !(b->core.flag&BAM_FUNMAP)) < 0) { sam_state_err(fd, errno ? errno : ENOMEM); hts_log_error("Read '%s' with ref_name='%s', ref_length=%"PRIhts_pos", flags=%d, pos=%"PRIhts_pos" cannot be indexed", bam_get_qname(b), sam_hdr_tid2name(fd->h, b->core.tid), sam_hdr_tid2len(fd->h, b->core.tid), b->core.flag, b->core.pos+1); goto err; } } else { if (hts_idx_push(fp->idx, b->core.tid, b->core.pos, bam_endpos(b), bgzf_tell(fp->fp.bgzf), !(b->core.flag&BAM_FUNMAP)) < 0) { sam_state_err(fd, errno ? errno : ENOMEM); hts_log_error("Read '%s' with ref_name='%s', ref_length=%"PRIhts_pos", flags=%d, pos=%"PRIhts_pos" cannot be indexed", bam_get_qname(b), sam_hdr_tid2name(fd->h, b->core.tid), sam_hdr_tid2len(fd->h, b->core.tid), b->core.flag, b->core.pos+1); goto err; } } } assert(count == gb->nbams); // Add bam array to free-list pthread_mutex_lock(&fd->lines_m); gb->next = fd->bams; fd->bams = gl->bams; gl->bams = NULL; pthread_mutex_unlock(&fd->lines_m); } else { if (fp->is_bgzf) { // We keep track of how much in the current block we have // remaining => R. We look for the last newline in input // [i] to [i+R], backwards => position N. // // If we find a newline, we write out bytes i to N. // We know we cannot fit the next record in this bgzf block, // so we flush what we have and copy input N to i+R into // the start of a new block, and recompute a new R for that. // // If we don't find a newline (i==N) then we cannot extend // the current block at all, so flush whatever is in it now // if it ends on a newline. // We still copy i(==N) to i+R to the next block and // continue as before with a new R. // // The only exception on the flush is when we run out of // data in the input. In that case we skip it as we don't // yet know if the next record will fit. // // Both conditions share the same code here: // - Look for newline (pos N) // - Write i to N (which maybe 0) // - Flush if block ends on newline and not end of input // - write N to i+R int i = 0; BGZF *fb = fp->fp.bgzf; while (i < gl->data_size) { // remaining space in block int R = BGZF_BLOCK_SIZE - fb->block_offset; int eod = 0; if (R > gl->data_size-i) R = gl->data_size-i, eod = 1; // Find last newline in input data int N = i + R; while (--N > i) { if (gl->data[N] == '\n') break; } if (N != i) { // Found a newline N++; if (bgzf_write(fb, &gl->data[i], N-i) != N-i) goto err; } // Flush bgzf block int b_off = fb->block_offset; if (!eod && b_off && ((char *)fb->uncompressed_block)[b_off-1] == '\n') if (bgzf_flush_try(fb, BGZF_BLOCK_SIZE) < 0) goto err; // Copy from N onwards into next block if (i+R > N) if (bgzf_write(fb, &gl->data[N], i+R - N) != i+R - N) goto err; i = i+R; } } else { if (hwrite(fp->fp.hfile, gl->data, gl->data_size) != gl->data_size) goto err; } } hts_tpool_delete_result(r, 0); // Also updated by main thread pthread_mutex_lock(&fd->lines_m); gl->next = fd->lines; fd->lines = gl; pthread_mutex_unlock(&fd->lines_m); } sam_state_err(fd, 0); // success hts_tpool_process_shutdown(fd->q); return NULL; err: sam_state_err(fd, errno ? errno : EIO); return (void *)-1; } // Run from one of the worker threads. // Convert a passed in array of BAMs (sp_bams) and converts to a block // of text SAM records (sp_lines). static void *sam_format_worker(void *arg) { sp_bams *gb = (sp_bams *)arg; sp_lines *gl = NULL; int i; SAM_state *fd = gb->fd; htsFile *fp = fd->fp; // Use a block of SAM strings we had earlier if available. pthread_mutex_lock(&fd->lines_m); if (fd->lines) { gl = fd->lines; fd->lines = gl->next; } pthread_mutex_unlock(&fd->lines_m); if (gl == NULL) { gl = calloc(1, sizeof(*gl)); if (!gl) { sam_state_err(fd, ENOMEM); return NULL; } gl->alloc = gl->data_size = 0; gl->data = NULL; } gl->serial = gb->serial; gl->next = NULL; kstring_t ks = {0, gl->alloc, gl->data}; for (i = 0; i < gb->nbams; i++) { if (sam_format1_append(fd->h, &gb->bams[i], &ks) < 0) { sam_state_err(fd, errno ? errno : EIO); goto err; } kputc('\n', &ks); } pthread_mutex_lock(&fd->lines_m); gl->data_size = ks.l; gl->alloc = ks.m; gl->data = ks.s; if (fp->idx) { // Keep hold of the bam array a little longer as // sam_dispatcher_write needs to use them for building the index. gl->bams = gb; } else { // Add bam array to free-list gb->next = fd->bams; fd->bams = gb; } pthread_mutex_unlock(&fd->lines_m); return gl; err: // Possible race between this and fd->curr_bam. // Easier to not free and leave it on the input list so it // gets freed there instead? // sam_free_sp_bams(gb); if (gl) { free(gl->data); free(gl); } return NULL; } int sam_set_thread_pool(htsFile *fp, htsThreadPool *p) { if (fp->state) return 0; if (!(fp->state = sam_state_create(fp))) return -1; SAM_state *fd = (SAM_state *)fp->state; pthread_mutex_init(&fd->lines_m, NULL); pthread_mutex_init(&fd->command_m, NULL); pthread_cond_init(&fd->command_c, NULL); fd->p = p->pool; int qsize = p->qsize; if (!qsize) qsize = 2*hts_tpool_size(fd->p); fd->q = hts_tpool_process_init(fd->p, qsize, 0); if (!fd->q) { sam_state_destroy(fp); return -1; } if (fp->format.compression == bgzf) return bgzf_thread_pool(fp->fp.bgzf, p->pool, p->qsize); return 0; } int sam_set_threads(htsFile *fp, int nthreads) { if (nthreads <= 0) return 0; htsThreadPool p; p.pool = hts_tpool_init(nthreads); p.qsize = nthreads*2; int ret = sam_set_thread_pool(fp, &p); if (ret < 0) return ret; SAM_state *fd = (SAM_state *)fp->state; fd->own_pool = 1; return 0; } typedef struct { kstring_t name; kstring_t comment; // NB: pointer into name, do not free kstring_t seq; kstring_t qual; int casava; int aux; int rnum; char BC[3]; // aux tag ID for barcode khash_t(tag) *tags; // which aux tags to use (if empty, use all). char nprefix; int sra_names; } fastq_state; // Initialise fastq state. // Name char of '@' or '>' distinguishes fastq vs fasta variant static fastq_state *fastq_state_init(int name_char) { fastq_state *x = (fastq_state *)calloc(1, sizeof(*x)); if (!x) return NULL; strcpy(x->BC, "BC"); x->nprefix = name_char; return x; } void fastq_state_destroy(htsFile *fp) { if (fp->state) { fastq_state *x = (fastq_state *)fp->state; if (x->tags) kh_destroy(tag, x->tags); ks_free(&x->name); ks_free(&x->seq); ks_free(&x->qual); free(fp->state); } } int fastq_state_set(samFile *fp, enum hts_fmt_option opt, ...) { va_list args; if (!fp) return -1; if (!fp->state) if (!(fp->state = fastq_state_init(fp->format.format == fastq_format ? '@' : '>'))) return -1; fastq_state *x = (fastq_state *)fp->state; switch (opt) { case FASTQ_OPT_CASAVA: x->casava = 1; break; case FASTQ_OPT_NAME2: x->sra_names = 1; break; case FASTQ_OPT_AUX: { va_start(args, opt); x->aux = 1; char *tag = va_arg(args, char *); va_end(args); if (tag && strcmp(tag, "1") != 0) { if (!x->tags) if (!(x->tags = kh_init(tag))) return -1; size_t i, tlen = strlen(tag); for (i = 0; i+3 <= tlen+1; i += 3) { if (tag[i+0] == ',' || tag[i+1] == ',' || !(tag[i+2] == ',' || tag[i+2] == '\0')) { hts_log_warning("Bad tag format '%.3s'; skipping option", tag+i); break; } int ret, tcode = tag[i+0]*256 + tag[i+1]; kh_put(tag, x->tags, tcode, &ret); if (ret < 0) return -1; } } break; } case FASTQ_OPT_BARCODE: { va_start(args, opt); char *bc = va_arg(args, char *); va_end(args); strncpy(x->BC, bc, 2); x->BC[2] = 0; break; } case FASTQ_OPT_RNUM: x->rnum = 1; break; default: break; } return 0; } static int fastq_parse1(htsFile *fp, bam1_t *b) { fastq_state *x = (fastq_state *)fp->state; size_t i, l; int ret = 0; if (fp->format.format == fasta_format && fp->line.s) { // For FASTA we've already read the >name line; steal it // Not the most efficient, but we don't optimise for fasta reading. if (fp->line.l == 0) return -1; // EOF free(x->name.s); x->name = fp->line; fp->line.l = fp->line.m = 0; fp->line.s = NULL; } else { // Read a FASTQ format entry. ret = hts_getline(fp, KS_SEP_LINE, &x->name); if (ret == -1) return -1; // EOF else if (ret < -1) return ret; // ERR } // Name if (*x->name.s != x->nprefix) return -2; // Reverse the SRA strangeness of putting the run_name.number before // the read name. i = 0; char *name = x->name.s+1; if (x->sra_names) { char *cp = strpbrk(x->name.s, " \t"); if (cp) { while (*cp == ' ' || *cp == '\t') cp++; *--cp = '@'; i = cp - x->name.s; name = cp+1; } } l = x->name.l; char *s = x->name.s; while (i < l && !isspace_c(s[i])) i++; if (i < l) { s[i] = 0; x->name.l = i++; } // Comment; a kstring struct, but pointer into name line. (Do not free) while (i < l && isspace_c(s[i])) i++; x->comment.s = s+i; x->comment.l = l - i; // Seq x->seq.l = 0; for (;;) { if ((ret = hts_getline(fp, KS_SEP_LINE, &fp->line)) < 0) if (fp->format.format == fastq_format || ret < -1) return -2; if (ret == -1 || *fp->line.s == (fp->format.format == fastq_format ? '+' : '>')) break; if (kputsn(fp->line.s, fp->line.l, &x->seq) < 0) return -2; } // Qual if (fp->format.format == fastq_format) { size_t remainder = x->seq.l; x->qual.l = 0; do { if (hts_getline(fp, KS_SEP_LINE, &fp->line) < 0) return -2; if (fp->line.l > remainder) return -2; if (kputsn(fp->line.s, fp->line.l, &x->qual) < 0) return -2; remainder -= fp->line.l; } while (remainder > 0); // Decr qual for (i = 0; i < x->qual.l; i++) x->qual.s[i] -= '!'; } int flag = BAM_FUNMAP; int pflag = BAM_FMUNMAP | BAM_FPAIRED; if (x->name.l > 2 && x->name.s[x->name.l-2] == '/' && isdigit_c(x->name.s[x->name.l-1])) { switch(x->name.s[x->name.l-1]) { case '1': flag |= BAM_FREAD1 | pflag; break; case '2': flag |= BAM_FREAD2 | pflag; break; default : flag |= BAM_FREAD1 | BAM_FREAD2 | pflag; break; } x->name.s[x->name.l-=2] = 0; } // Convert to BAM ret = bam_set1(b, x->name.s + x->name.l - name, name, flag, -1, -1, 0, // ref '*', pos, mapq, 0, NULL, // no cigar, -1, -1, 0, // mate x->seq.l, x->seq.s, x->qual.s, 0); // Identify Illumina CASAVA strings. // ::: char *barcode = NULL; int barcode_len = 0; kstring_t *kc = &x->comment; char *endptr; if (x->casava && // \d:[YN]:\d+:[ACGTN]+ kc->l > 6 && (kc->s[1] | kc->s[3]) == ':' && isdigit_c(kc->s[0]) && strtol(kc->s+4, &endptr, 10) >= 0 && endptr != kc->s+4 && *endptr == ':') { // read num switch(kc->s[0]) { case '1': b->core.flag |= BAM_FREAD1 | pflag; break; case '2': b->core.flag |= BAM_FREAD2 | pflag; break; default : b->core.flag |= BAM_FREAD1 | BAM_FREAD2 | pflag; break; } if (kc->s[2] == 'Y') b->core.flag |= BAM_FQCFAIL; // Barcode, maybe numeric in which case we skip it if (!isdigit_c(endptr[1])) { barcode = endptr+1; for (i = barcode - kc->s; i < kc->l; i++) if (isspace_c(kc->s[i])) break; kc->s[i] = 0; barcode_len = i+1-(barcode - kc->s); } } if (ret >= 0 && barcode_len) if (bam_aux_append(b, x->BC, 'Z', barcode_len, (uint8_t *)barcode) < 0) ret = -2; if (!x->aux) return ret; // Identify any SAM style aux tags in comments too. if (aux_parse(&kc->s[barcode_len], kc->s + kc->l, b, 1, x->tags) < 0) ret = -2; return ret; } // Internal component of sam_read1 below static inline int sam_read1_bam(htsFile *fp, sam_hdr_t *h, bam1_t *b) { int ret = bam_read1(fp->fp.bgzf, b); if (h && ret >= 0) { if (b->core.tid >= h->n_targets || b->core.tid < -1 || b->core.mtid >= h->n_targets || b->core.mtid < -1) { errno = ERANGE; return -3; } } return ret; } // Internal component of sam_read1 below static inline int sam_read1_cram(htsFile *fp, sam_hdr_t *h, bam1_t **b) { int ret = cram_get_bam_seq(fp->fp.cram, b); if (ret < 0) return cram_eof(fp->fp.cram) ? -1 : -2; if (bam_tag2cigar(*b, 1, 1) < 0) return -2; return ret; } // Internal component of sam_read1 below static inline int sam_read1_sam(htsFile *fp, sam_hdr_t *h, bam1_t *b) { int ret; // Consume 1st line after header parsing as it wasn't using peek if (fp->line.l != 0) { ret = sam_parse1(&fp->line, h, b); fp->line.l = 0; return ret; } if (fp->state) { SAM_state *fd = (SAM_state *)fp->state; if (fp->format.compression == bgzf && fp->fp.bgzf->seeked) { // We don't support multi-threaded SAM parsing with seeks yet. int ret; if ((ret = sam_state_destroy(fp)) < 0) { errno = -ret; return -2; } if (bgzf_seek(fp->fp.bgzf, fp->fp.bgzf->seeked, SEEK_SET) < 0) return -1; fp->fp.bgzf->seeked = 0; goto err_recover; } if (!fd->h) { fd->h = h; fd->h->ref_count++; // Ensure hrecs is initialised now as we don't want multiple // threads trying to do this simultaneously. if (!fd->h->hrecs && sam_hdr_fill_hrecs(fd->h) < 0) return -2; // We can only do this once we've got a header if (pthread_create(&fd->dispatcher, NULL, sam_dispatcher_read, fp) != 0) return -2; fd->dispatcher_set = 1; } if (fd->h != h) { hts_log_error("SAM multi-threaded decoding does not support changing header"); return -1; } sp_bams *gb = fd->curr_bam; if (!gb) { if (fd->errcode) { // In case reader failed errno = fd->errcode; return -2; } hts_tpool_result *r = hts_tpool_next_result_wait(fd->q); if (!r) return -2; fd->curr_bam = gb = (sp_bams *)hts_tpool_result_data(r); hts_tpool_delete_result(r, 0); } if (!gb) return fd->errcode ? -2 : -1; bam1_t *b_array = (bam1_t *)gb->bams; if (fd->curr_idx < gb->nbams) if (!bam_copy1(b, &b_array[fd->curr_idx++])) return -2; if (fd->curr_idx == gb->nbams) { pthread_mutex_lock(&fd->lines_m); gb->next = fd->bams; fd->bams = gb; pthread_mutex_unlock(&fd->lines_m); fd->curr_bam = NULL; fd->curr_idx = 0; // Consider prefetching next record? I.e. // } else { // __builtin_prefetch(&b_array[fd->curr_idx], 0, 3); } ret = 0; } else { err_recover: ret = hts_getline(fp, KS_SEP_LINE, &fp->line); if (ret < 0) return ret; ret = sam_parse1(&fp->line, h, b); fp->line.l = 0; if (ret < 0) { hts_log_warning("Parse error at line %lld", (long long)fp->lineno); if (h && h->ignore_sam_err) goto err_recover; } } return ret; } // Returns 0 on success, // -1 on EOF, // <-1 on error int sam_read1(htsFile *fp, sam_hdr_t *h, bam1_t *b) { int ret, pass_filter; do { switch (fp->format.format) { case bam: ret = sam_read1_bam(fp, h, b); break; case cram: ret = sam_read1_cram(fp, h, &b); break; case sam: ret = sam_read1_sam(fp, h, b); break; case fasta_format: case fastq_format: { fastq_state *x = (fastq_state *)fp->state; if (!x) { if (!(fp->state = fastq_state_init(fp->format.format == fastq_format ? '@' : '>'))) return -2; } return fastq_parse1(fp, b); } case empty_format: errno = EPIPE; return -3; default: errno = EFTYPE; return -3; } pass_filter = (ret >= 0 && fp->filter) ? sam_passes_filter(h, b, fp->filter) : 1; } while (pass_filter == 0); return pass_filter < 0 ? -2 : ret; } // With gcc, -O3 or -ftree-loop-vectorize is really key here as otherwise // this code isn't vectorised and runs far slower than is necessary (even // with the restrict keyword being used). static inline void HTS_OPT3 add33(uint8_t *a, const uint8_t * b, int32_t len) { uint32_t i; for (i = 0; i < len; i++) a[i] = b[i]+33; } static int sam_format1_append(const bam_hdr_t *h, const bam1_t *b, kstring_t *str) { int i, r = 0; uint8_t *s, *end; const bam1_core_t *c = &b->core; if (c->l_qname == 0) return -1; r |= kputsn_(bam_get_qname(b), c->l_qname-1-c->l_extranul, str); r |= kputc_('\t', str); // query name r |= kputw(c->flag, str); r |= kputc_('\t', str); // flag if (c->tid >= 0) { // chr r |= kputs(h->target_name[c->tid] , str); r |= kputc_('\t', str); } else r |= kputsn_("*\t", 2, str); r |= kputll(c->pos + 1, str); r |= kputc_('\t', str); // pos r |= kputw(c->qual, str); r |= kputc_('\t', str); // qual if (c->n_cigar) { // cigar uint32_t *cigar = bam_get_cigar(b); for (i = 0; i < c->n_cigar; ++i) { r |= kputw(bam_cigar_oplen(cigar[i]), str); r |= kputc_(bam_cigar_opchr(cigar[i]), str); } } else r |= kputc_('*', str); r |= kputc_('\t', str); if (c->mtid < 0) r |= kputsn_("*\t", 2, str); // mate chr else if (c->mtid == c->tid) r |= kputsn_("=\t", 2, str); else { r |= kputs(h->target_name[c->mtid], str); r |= kputc_('\t', str); } r |= kputll(c->mpos + 1, str); r |= kputc_('\t', str); // mate pos r |= kputll(c->isize, str); r |= kputc_('\t', str); // template len if (c->l_qseq) { // seq and qual uint8_t *s = bam_get_seq(b); if (ks_resize(str, str->l+2+2*c->l_qseq) < 0) goto mem_err; char *cp = str->s + str->l; // Sequence, 2 bases at a time nibble2base(s, cp, c->l_qseq); cp[c->l_qseq] = '\t'; cp += c->l_qseq+1; // Quality s = bam_get_qual(b); i = 0; if (s[0] == 0xff) { cp[i++] = '*'; } else { add33((uint8_t *)cp, s, c->l_qseq); // cp[i] = s[i]+33; i = c->l_qseq; } cp[i] = 0; cp += i; str->l = cp - str->s; } else r |= kputsn_("*\t*", 3, str); s = bam_get_aux(b); // aux end = b->data + b->l_data; while (end - s >= 4) { r |= kputc_('\t', str); if ((s = (uint8_t *)sam_format_aux1(s, s[2], s+3, end, str)) == NULL) goto bad_aux; } r |= kputsn("", 0, str); // nul terminate if (r < 0) goto mem_err; return str->l; bad_aux: hts_log_error("Corrupted aux data for read %.*s flag %d", b->core.l_qname, bam_get_qname(b), b->core.flag); errno = EINVAL; return -1; mem_err: hts_log_error("Out of memory"); errno = ENOMEM; return -1; } int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str) { str->l = 0; return sam_format1_append(h, b, str); } static inline uint8_t *skip_aux(uint8_t *s, uint8_t *end); int fastq_format1(fastq_state *x, const bam1_t *b, kstring_t *str) { unsigned flag = b->core.flag; int i, e = 0, len = b->core.l_qseq; uint8_t *seq, *qual; str->l = 0; // Name if (kputc(x->nprefix, str) == EOF || kputs(bam_get_qname(b), str) == EOF) return -1; // /1 or /2 suffix if (x && x->rnum && (flag & BAM_FPAIRED)) { int r12 = flag & (BAM_FREAD1 | BAM_FREAD2); if (r12 == BAM_FREAD1) { if (kputs("/1", str) == EOF) return -1; } else if (r12 == BAM_FREAD2) { if (kputs("/2", str) == EOF) return -1; } } // Illumina CASAVA tag. // This is ::: if (x && x->casava) { int rnum = (flag & BAM_FREAD1)? 1 : (flag & BAM_FREAD2)? 2 : 0; char filtered = (flag & BAM_FQCFAIL)? 'Y' : 'N'; uint8_t *bc = bam_aux_get(b, x->BC); if (ksprintf(str, " %d:%c:0:%s", rnum, filtered, bc ? (char *)bc+1 : "0") < 0) return -1; if (bc && (*bc != 'Z' || (!isupper_c(bc[1]) && !islower_c(bc[1])))) { hts_log_warning("BC tag starts with non-sequence base; using '0'"); str->l -= strlen((char *)bc)-2; // limit to 1 char str->s[str->l-1] = '0'; str->s[str->l] = 0; bc = NULL; } // Replace any non-alpha with '+'. Ie seq-seq to seq+seq if (bc) { int l = strlen((char *)bc+1); char *c = (char *)str->s + str->l - l; for (i = 0; i < l; i++) { if (!isalpha_c(c[i])) c[i] = '+'; else if (islower_c(c[i])) c[i] = toupper_c(c[i]); } } } // Aux tags if (x && x->aux) { uint8_t *s = bam_get_aux(b), *end = b->data + b->l_data; while (s && end - s >= 4) { int tt = s[0]*256 + s[1]; if (x->tags == NULL || kh_get(tag, x->tags, tt) != kh_end(x->tags)) { e |= kputc_('\t', str) < 0; if (!(s = (uint8_t *)sam_format_aux1(s, s[2], s+3, end, str))) return -1; } else { s = skip_aux(s+2, end); } } e |= kputsn("", 0, str) < 0; // nul terminate } if (ks_resize(str, str->l + 1 + len+1 + 2 + len+1 + 1) < 0) return -1; e |= kputc_('\n', str) < 0; // Seq line seq = bam_get_seq(b); if (flag & BAM_FREVERSE) for (i = len-1; i >= 0; i--) e |= kputc_("!TGKCYSBAWRDMHVN"[bam_seqi(seq, i)], str) < 0; else for (i = 0; i < len; i++) e |= kputc_(seq_nt16_str[bam_seqi(seq, i)], str) < 0; // Qual line if (x->nprefix == '@') { kputsn("\n+\n", 3, str); qual = bam_get_qual(b); if (qual[0] == 0xff) for (i = 0; i < len; i++) e |= kputc_('B', str) < 0; else if (flag & BAM_FREVERSE) for (i = len-1; i >= 0; i--) e |= kputc_(33 + qual[i], str) < 0; else for (i = 0; i < len; i++) e |= kputc_(33 + qual[i], str) < 0; } e |= kputc('\n', str) < 0; return e ? -1 : str->l; } // Sadly we need to be able to modify the bam_hdr here so we can // reference count the structure. int sam_write1(htsFile *fp, const sam_hdr_t *h, const bam1_t *b) { switch (fp->format.format) { case binary_format: fp->format.category = sequence_data; fp->format.format = bam; /* fall-through */ case bam: return bam_write_idx1(fp, h, b); case cram: return cram_put_bam_seq(fp->fp.cram, (bam1_t *)b); case text_format: fp->format.category = sequence_data; fp->format.format = sam; /* fall-through */ case sam: if (fp->state) { SAM_state *fd = (SAM_state *)fp->state; // Threaded output if (!fd->h) { // NB: discard const. We don't actually modify sam_hdr_t here, // just data pointed to by it (which is a bit weasely still), // but out cached pointer must be non-const as we want to // destroy it later on and sam_hdr_destroy takes non-const. // // We do this because some tools do sam_hdr_destroy; sam_close // while others do sam_close; sam_hdr_destroy. The former is // an issue as we need the header still when flushing. fd->h = (sam_hdr_t *)h; fd->h->ref_count++; if (pthread_create(&fd->dispatcher, NULL, sam_dispatcher_write, fp) != 0) return -2; fd->dispatcher_set = 1; } if (fd->h != h) { hts_log_error("SAM multi-threaded decoding does not support changing header"); return -2; } // Find a suitable BAM array to copy to sp_bams *gb = fd->curr_bam; if (!gb) { pthread_mutex_lock(&fd->lines_m); if (fd->bams) { fd->curr_bam = gb = fd->bams; fd->bams = gb->next; gb->next = NULL; gb->nbams = 0; gb->bam_mem = 0; pthread_mutex_unlock(&fd->lines_m); } else { pthread_mutex_unlock(&fd->lines_m); if (!(gb = calloc(1, sizeof(*gb)))) return -1; if (!(gb->bams = calloc(SAM_NBAM, sizeof(*gb->bams)))) { free(gb); return -1; } gb->nbams = 0; gb->abams = SAM_NBAM; gb->bam_mem = 0; gb->fd = fd; fd->curr_idx = 0; fd->curr_bam = gb; } } if (!bam_copy1(&gb->bams[gb->nbams++], b)) return -2; gb->bam_mem += b->l_data + sizeof(*b); // Dispatch if full if (gb->nbams == SAM_NBAM || gb->bam_mem > SAM_NBYTES*0.8) { gb->serial = fd->serial++; pthread_mutex_lock(&fd->command_m); if (fd->errcode != 0) { pthread_mutex_unlock(&fd->command_m); return -fd->errcode; } if (hts_tpool_dispatch3(fd->p, fd->q, sam_format_worker, gb, cleanup_sp_bams, cleanup_sp_lines, 0) < 0) { pthread_mutex_unlock(&fd->command_m); return -1; } pthread_mutex_unlock(&fd->command_m); fd->curr_bam = NULL; } // Dummy value as we don't know how long it really is. // We could track file sizes via a SAM_state field, but I don't think // it is necessary. return 1; } else { if (sam_format1(h, b, &fp->line) < 0) return -1; kputc('\n', &fp->line); if (fp->is_bgzf) { if (bgzf_flush_try(fp->fp.bgzf, fp->line.l) < 0) return -1; if ( bgzf_write(fp->fp.bgzf, fp->line.s, fp->line.l) != fp->line.l ) return -1; } else { if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; } if (fp->idx) { if (fp->format.compression == bgzf) { if (bgzf_idx_push(fp->fp.bgzf, fp->idx, b->core.tid, b->core.pos, bam_endpos(b), bgzf_tell(fp->fp.bgzf), !(b->core.flag&BAM_FUNMAP)) < 0) { hts_log_error("Read '%s' with ref_name='%s', ref_length=%"PRIhts_pos", flags=%d, pos=%"PRIhts_pos" cannot be indexed", bam_get_qname(b), sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), b->core.flag, b->core.pos+1); return -1; } } else { if (hts_idx_push(fp->idx, b->core.tid, b->core.pos, bam_endpos(b), bgzf_tell(fp->fp.bgzf), !(b->core.flag&BAM_FUNMAP)) < 0) { hts_log_error("Read '%s' with ref_name='%s', ref_length=%"PRIhts_pos", flags=%d, pos=%"PRIhts_pos" cannot be indexed", bam_get_qname(b), sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), b->core.flag, b->core.pos+1); return -1; } } } return fp->line.l; } case fasta_format: case fastq_format: { fastq_state *x = (fastq_state *)fp->state; if (!x) { if (!(fp->state = fastq_state_init(fp->format.format == fastq_format ? '@' : '>'))) return -2; } if (fastq_format1(fp->state, b, &fp->line) < 0) return -1; if (fp->is_bgzf) { if (bgzf_flush_try(fp->fp.bgzf, fp->line.l) < 0) return -1; if (bgzf_write(fp->fp.bgzf, fp->line.s, fp->line.l) != fp->line.l) return -1; } else { if (hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l) return -1; } return fp->line.l; } default: errno = EBADF; return -1; } } /************************ *** Auxiliary fields *** ************************/ #ifndef HTS_LITTLE_ENDIAN static int aux_to_le(char type, uint8_t *out, const uint8_t *in, size_t len) { int tsz = aux_type2size(type); if (tsz >= 2 && tsz <= 8 && (len & (tsz - 1)) != 0) return -1; switch (tsz) { case 'H': case 'Z': case 1: // Trivial memcpy(out, in, len); break; #define aux_val_to_le(type_t, store_le) do { \ type_t v; \ size_t i; \ for (i = 0; i < len; i += sizeof(type_t), out += sizeof(type_t)) { \ memcpy(&v, in + i, sizeof(type_t)); \ store_le(v, out); \ } \ } while (0) case 2: aux_val_to_le(uint16_t, u16_to_le); break; case 4: aux_val_to_le(uint32_t, u32_to_le); break; case 8: aux_val_to_le(uint64_t, u64_to_le); break; #undef aux_val_to_le case 'B': { // Recurse! uint32_t n; if (len < 5) return -1; memcpy(&n, in + 1, 4); out[0] = in[0]; u32_to_le(n, out + 1); return aux_to_le(in[0], out + 5, in + 5, len - 5); } default: // Unknown type code return -1; } return 0; } #endif int bam_aux_append(bam1_t *b, const char tag[2], char type, int len, const uint8_t *data) { uint32_t new_len; assert(b->l_data >= 0); new_len = b->l_data + 3 + len; if (new_len > INT32_MAX || new_len < b->l_data) goto nomem; if (realloc_bam_data(b, new_len) < 0) return -1; b->data[b->l_data] = tag[0]; b->data[b->l_data + 1] = tag[1]; b->data[b->l_data + 2] = type; #ifdef HTS_LITTLE_ENDIAN memcpy(b->data + b->l_data + 3, data, len); #else if (aux_to_le(type, b->data + b->l_data + 3, data, len) != 0) { errno = EINVAL; return -1; } #endif b->l_data = new_len; return 0; nomem: errno = ENOMEM; return -1; } static inline uint8_t *skip_aux(uint8_t *s, uint8_t *end) { int size; uint32_t n; if (s >= end) return end; size = aux_type2size(*s); ++s; // skip type switch (size) { case 'Z': case 'H': while (s < end && *s) ++s; return s < end ? s + 1 : end; case 'B': if (end - s < 5) return NULL; size = aux_type2size(*s); ++s; n = le_to_u32(s); s += 4; if (size == 0 || end - s < size * n) return NULL; return s + size * n; case 0: return NULL; default: if (end - s < size) return NULL; return s + size; } } uint8_t *bam_aux_first(const bam1_t *b) { uint8_t *s = bam_get_aux(b); uint8_t *end = b->data + b->l_data; if (end - s <= 2) { errno = ENOENT; return NULL; } return s+2; } uint8_t *bam_aux_next(const bam1_t *b, const uint8_t *s) { uint8_t *end = b->data + b->l_data; uint8_t *next = s? skip_aux((uint8_t *) s, end) : end; if (next == NULL) goto bad_aux; if (end - next <= 2) { errno = ENOENT; return NULL; } return next+2; bad_aux: hts_log_error("Corrupted aux data for read %s flag %d", bam_get_qname(b), b->core.flag); errno = EINVAL; return NULL; } uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]) { uint8_t *s; for (s = bam_aux_first(b); s; s = bam_aux_next(b, s)) if (s[-2] == tag[0] && s[-1] == tag[1]) { // Check the tag value is valid and complete uint8_t *e = skip_aux(s, b->data + b->l_data); if (e == NULL) goto bad_aux; if ((*s == 'Z' || *s == 'H') && *(e - 1) != '\0') goto bad_aux; return s; } // errno now as set by bam_aux_first()/bam_aux_next() return NULL; bad_aux: hts_log_error("Corrupted aux data for read %s flag %d", bam_get_qname(b), b->core.flag); errno = EINVAL; return NULL; } int bam_aux_del(bam1_t *b, uint8_t *s) { s = bam_aux_remove(b, s); return (s || errno == ENOENT)? 0 : -1; } uint8_t *bam_aux_remove(bam1_t *b, uint8_t *s) { uint8_t *end = b->data + b->l_data; uint8_t *next = skip_aux(s, end); if (next == NULL) goto bad_aux; b->l_data -= next - (s-2); if (next >= end) { errno = ENOENT; return NULL; } memmove(s-2, next, end - next); return s; bad_aux: hts_log_error("Corrupted aux data for read %s flag %d", bam_get_qname(b), b->core.flag); errno = EINVAL; return NULL; } int bam_aux_update_str(bam1_t *b, const char tag[2], int len, const char *data) { // FIXME: This is not at all efficient! size_t ln = len >= 0 ? len : strlen(data) + 1; size_t old_ln = 0; int need_nul = ln == 0 || data[ln - 1] != '\0'; int save_errno = errno; int new_tag = 0; uint8_t *s = bam_aux_get(b,tag), *e; if (s) { // Replacing existing tag char type = *s; if (type != 'Z') { hts_log_error("Called bam_aux_update_str for type '%c' instead of 'Z'", type); errno = EINVAL; return -1; } s++; e = memchr(s, '\0', b->data + b->l_data - s); old_ln = (e ? e - s : b->data + b->l_data - s) + 1; s -= 3; } else { if (errno != ENOENT) { // Invalid aux data, give up return -1; } else { // Tag doesn't exist - put it on the end errno = save_errno; s = b->data + b->l_data; new_tag = 3; } } if (old_ln < ln + need_nul + new_tag) { ptrdiff_t s_offset = s - b->data; if (possibly_expand_bam_data(b, ln + need_nul + new_tag - old_ln) < 0) return -1; s = b->data + s_offset; } if (!new_tag) { memmove(s + 3 + ln + need_nul, s + 3 + old_ln, b->l_data - (s + 3 - b->data) - old_ln); } b->l_data += new_tag + ln + need_nul - old_ln; s[0] = tag[0]; s[1] = tag[1]; s[2] = 'Z'; memmove(s+3,data,ln); if (need_nul) s[3 + ln] = '\0'; return 0; } int bam_aux_update_int(bam1_t *b, const char tag[2], int64_t val) { uint32_t sz, old_sz = 0, new = 0; uint8_t *s, type; if (val < INT32_MIN || val > UINT32_MAX) { errno = EOVERFLOW; return -1; } if (val < INT16_MIN) { type = 'i'; sz = 4; } else if (val < INT8_MIN) { type = 's'; sz = 2; } else if (val < 0) { type = 'c'; sz = 1; } else if (val < UINT8_MAX) { type = 'C'; sz = 1; } else if (val < UINT16_MAX) { type = 'S'; sz = 2; } else { type = 'I'; sz = 4; } s = bam_aux_get(b, tag); if (s) { // Tag present - how big was the old one? switch (*s) { case 'c': case 'C': old_sz = 1; break; case 's': case 'S': old_sz = 2; break; case 'i': case 'I': old_sz = 4; break; default: errno = EINVAL; return -1; // Not an integer } } else { if (errno == ENOENT) { // Tag doesn't exist - add a new one s = b->data + b->l_data; new = 1; } else { // Invalid aux data, give up. return -1; } } if (new || old_sz < sz) { // Make room for new tag ptrdiff_t s_offset = s - b->data; if (possibly_expand_bam_data(b, (new ? 3 : 0) + sz - old_sz) < 0) return -1; s = b->data + s_offset; if (new) { // Add tag id *s++ = tag[0]; *s++ = tag[1]; } else { // Shift following data so we have space memmove(s + sz, s + old_sz, b->l_data - s_offset - old_sz); } } else { // Reuse old space. Data value may be bigger than necessary but // we avoid having to move everything else sz = old_sz; type = (val < 0 ? "\0cs\0i" : "\0CS\0I")[old_sz]; assert(type > 0); } *s++ = type; #ifdef HTS_LITTLE_ENDIAN memcpy(s, &val, sz); #else switch (sz) { case 4: u32_to_le(val, s); break; case 2: u16_to_le(val, s); break; default: *s = val; break; } #endif b->l_data += (new ? 3 : 0) + sz - old_sz; return 0; } int bam_aux_update_float(bam1_t *b, const char tag[2], float val) { uint8_t *s = bam_aux_get(b, tag); int shrink = 0, new = 0; if (s) { // Tag present - what was it? switch (*s) { case 'f': break; case 'd': shrink = 1; break; default: errno = EINVAL; return -1; // Not a float } } else { if (errno == ENOENT) { // Tag doesn't exist - add a new one new = 1; } else { // Invalid aux data, give up. return -1; } } if (new) { // Ensure there's room if (possibly_expand_bam_data(b, 3 + 4) < 0) return -1; s = b->data + b->l_data; *s++ = tag[0]; *s++ = tag[1]; } else if (shrink) { // Convert non-standard double tag to float memmove(s + 5, s + 9, b->l_data - ((s + 9) - b->data)); b->l_data -= 4; } *s++ = 'f'; float_to_le(val, s); if (new) b->l_data += 7; return 0; } int bam_aux_update_array(bam1_t *b, const char tag[2], uint8_t type, uint32_t items, void *data) { uint8_t *s = bam_aux_get(b, tag); size_t old_sz = 0, new_sz; int new = 0; if (s) { // Tag present if (*s != 'B') { errno = EINVAL; return -1; } old_sz = aux_type2size(s[1]); if (old_sz < 1 || old_sz > 4) { errno = EINVAL; return -1; } old_sz *= le_to_u32(s + 2); } else { if (errno == ENOENT) { // Tag doesn't exist - add a new one s = b->data + b->l_data; new = 1; } else { // Invalid aux data, give up. return -1; } } new_sz = aux_type2size(type); if (new_sz < 1 || new_sz > 4) { errno = EINVAL; return -1; } if (items > INT32_MAX / new_sz) { errno = ENOMEM; return -1; } new_sz *= items; if (new || old_sz < new_sz) { // Make room for new tag ptrdiff_t s_offset = s - b->data; if (possibly_expand_bam_data(b, (new ? 8 : 0) + new_sz - old_sz) < 0) return -1; s = b->data + s_offset; } if (new) { // Add tag id and type *s++ = tag[0]; *s++ = tag[1]; *s = 'B'; b->l_data += 8 + new_sz; } else if (old_sz != new_sz) { // shift following data if necessary memmove(s + 6 + new_sz, s + 6 + old_sz, b->l_data - ((s + 6 + old_sz) - b->data)); b->l_data -= old_sz; b->l_data += new_sz; } s[1] = type; u32_to_le(items, s + 2); #ifdef HTS_LITTLE_ENDIAN memcpy(s + 6, data, new_sz); return 0; #else return aux_to_le(type, s + 6, data, new_sz); #endif } static inline int64_t get_int_aux_val(uint8_t type, const uint8_t *s, uint32_t idx) { switch (type) { case 'c': return le_to_i8(s + idx); case 'C': return s[idx]; case 's': return le_to_i16(s + 2 * idx); case 'S': return le_to_u16(s + 2 * idx); case 'i': return le_to_i32(s + 4 * idx); case 'I': return le_to_u32(s + 4 * idx); default: errno = EINVAL; return 0; } } int64_t bam_aux2i(const uint8_t *s) { int type; type = *s++; return get_int_aux_val(type, s, 0); } double bam_aux2f(const uint8_t *s) { int type; type = *s++; if (type == 'd') return le_to_double(s); else if (type == 'f') return le_to_float(s); else return get_int_aux_val(type, s, 0); } char bam_aux2A(const uint8_t *s) { int type; type = *s++; if (type == 'A') return *(char*)s; errno = EINVAL; return 0; } char *bam_aux2Z(const uint8_t *s) { int type; type = *s++; if (type == 'Z' || type == 'H') return (char*)s; errno = EINVAL; return 0; } uint32_t bam_auxB_len(const uint8_t *s) { if (s[0] != 'B') { errno = EINVAL; return 0; } return le_to_u32(s + 2); } int64_t bam_auxB2i(const uint8_t *s, uint32_t idx) { uint32_t len = bam_auxB_len(s); if (idx >= len) { errno = ERANGE; return 0; } return get_int_aux_val(s[1], s + 6, idx); } double bam_auxB2f(const uint8_t *s, uint32_t idx) { uint32_t len = bam_auxB_len(s); if (idx >= len) { errno = ERANGE; return 0.0; } if (s[1] == 'f') return le_to_float(s + 6 + 4 * idx); else return get_int_aux_val(s[1], s + 6, idx); } int sam_open_mode(char *mode, const char *fn, const char *format) { // TODO Parse "bam5" etc for compression level if (format == NULL) { // Try to pick a format based on the filename extension char extension[HTS_MAX_EXT_LEN]; if (find_file_extension(fn, extension) < 0) return -1; return sam_open_mode(mode, fn, extension); } else if (strcasecmp(format, "bam") == 0) strcpy(mode, "b"); else if (strcasecmp(format, "cram") == 0) strcpy(mode, "c"); else if (strcasecmp(format, "sam") == 0) strcpy(mode, ""); else if (strcasecmp(format, "sam.gz") == 0) strcpy(mode, "z"); else if (strcasecmp(format, "fastq") == 0 || strcasecmp(format, "fq") == 0) strcpy(mode, "f"); else if (strcasecmp(format, "fastq.gz") == 0 || strcasecmp(format, "fq.gz") == 0) strcpy(mode, "fz"); else if (strcasecmp(format, "fasta") == 0 || strcasecmp(format, "fa") == 0) strcpy(mode, "F"); else if (strcasecmp(format, "fasta.gz") == 0 || strcasecmp(format, "fa.gz") == 0) strcpy(mode, "Fz"); else return -1; return 0; } // A version of sam_open_mode that can handle ,key=value options. // The format string is allocated and returned, to be freed by the caller. // Prefix should be "r" or "w", char *sam_open_mode_opts(const char *fn, const char *mode, const char *format) { char *mode_opts = malloc((format ? strlen(format) : 1) + (mode ? strlen(mode) : 1) + 12); char *opts, *cp; int format_len; if (!mode_opts) return NULL; strcpy(mode_opts, mode ? mode : "r"); cp = mode_opts + strlen(mode_opts); if (format == NULL) { // Try to pick a format based on the filename extension char extension[HTS_MAX_EXT_LEN]; if (find_file_extension(fn, extension) < 0) { free(mode_opts); return NULL; } if (sam_open_mode(cp, fn, extension) == 0) { return mode_opts; } else { free(mode_opts); return NULL; } } if ((opts = strchr(format, ','))) { format_len = opts-format; } else { opts=""; format_len = strlen(format); } if (strncmp(format, "bam", format_len) == 0) { *cp++ = 'b'; } else if (strncmp(format, "cram", format_len) == 0) { *cp++ = 'c'; } else if (strncmp(format, "cram2", format_len) == 0) { *cp++ = 'c'; strcpy(cp, ",VERSION=2.1"); cp += 12; } else if (strncmp(format, "cram3", format_len) == 0) { *cp++ = 'c'; strcpy(cp, ",VERSION=3.0"); cp += 12; } else if (strncmp(format, "sam", format_len) == 0) { ; // format mode="" } else if (strncmp(format, "sam.gz", format_len) == 0) { *cp++ = 'z'; } else if (strncmp(format, "fastq", format_len) == 0 || strncmp(format, "fq", format_len) == 0) { *cp++ = 'f'; } else if (strncmp(format, "fastq.gz", format_len) == 0 || strncmp(format, "fq.gz", format_len) == 0) { *cp++ = 'f'; *cp++ = 'z'; } else if (strncmp(format, "fasta", format_len) == 0 || strncmp(format, "fa", format_len) == 0) { *cp++ = 'F'; } else if (strncmp(format, "fasta.gz", format_len) == 0 || strncmp(format, "fa", format_len) == 0) { *cp++ = 'F'; *cp++ = 'z'; } else { free(mode_opts); return NULL; } strcpy(cp, opts); return mode_opts; } #define STRNCMP(a,b,n) (strncasecmp((a),(b),(n)) || strlen(a)!=(n)) int bam_str2flag(const char *str) { char *end, *beg = (char*) str; long int flag = strtol(str, &end, 0); if ( end!=str ) return flag; // the conversion was successful flag = 0; while ( *str ) { end = beg; while ( *end && *end!=',' ) end++; if ( !STRNCMP("PAIRED",beg,end-beg) ) flag |= BAM_FPAIRED; else if ( !STRNCMP("PROPER_PAIR",beg,end-beg) ) flag |= BAM_FPROPER_PAIR; else if ( !STRNCMP("UNMAP",beg,end-beg) ) flag |= BAM_FUNMAP; else if ( !STRNCMP("MUNMAP",beg,end-beg) ) flag |= BAM_FMUNMAP; else if ( !STRNCMP("REVERSE",beg,end-beg) ) flag |= BAM_FREVERSE; else if ( !STRNCMP("MREVERSE",beg,end-beg) ) flag |= BAM_FMREVERSE; else if ( !STRNCMP("READ1",beg,end-beg) ) flag |= BAM_FREAD1; else if ( !STRNCMP("READ2",beg,end-beg) ) flag |= BAM_FREAD2; else if ( !STRNCMP("SECONDARY",beg,end-beg) ) flag |= BAM_FSECONDARY; else if ( !STRNCMP("QCFAIL",beg,end-beg) ) flag |= BAM_FQCFAIL; else if ( !STRNCMP("DUP",beg,end-beg) ) flag |= BAM_FDUP; else if ( !STRNCMP("SUPPLEMENTARY",beg,end-beg) ) flag |= BAM_FSUPPLEMENTARY; else return -1; if ( !*end ) break; beg = end + 1; } return flag; } char *bam_flag2str(int flag) { kstring_t str = {0,0,0}; if ( flag&BAM_FPAIRED ) ksprintf(&str,"%s%s", str.l?",":"","PAIRED"); if ( flag&BAM_FPROPER_PAIR ) ksprintf(&str,"%s%s", str.l?",":"","PROPER_PAIR"); if ( flag&BAM_FUNMAP ) ksprintf(&str,"%s%s", str.l?",":"","UNMAP"); if ( flag&BAM_FMUNMAP ) ksprintf(&str,"%s%s", str.l?",":"","MUNMAP"); if ( flag&BAM_FREVERSE ) ksprintf(&str,"%s%s", str.l?",":"","REVERSE"); if ( flag&BAM_FMREVERSE ) ksprintf(&str,"%s%s", str.l?",":"","MREVERSE"); if ( flag&BAM_FREAD1 ) ksprintf(&str,"%s%s", str.l?",":"","READ1"); if ( flag&BAM_FREAD2 ) ksprintf(&str,"%s%s", str.l?",":"","READ2"); if ( flag&BAM_FSECONDARY ) ksprintf(&str,"%s%s", str.l?",":"","SECONDARY"); if ( flag&BAM_FQCFAIL ) ksprintf(&str,"%s%s", str.l?",":"","QCFAIL"); if ( flag&BAM_FDUP ) ksprintf(&str,"%s%s", str.l?",":"","DUP"); if ( flag&BAM_FSUPPLEMENTARY ) ksprintf(&str,"%s%s", str.l?",":"","SUPPLEMENTARY"); if ( str.l == 0 ) kputsn("", 0, &str); return str.s; } /************************** *** Pileup and Mpileup *** **************************/ #if !defined(BAM_NO_PILEUP) #include /******************* *** Memory pool *** *******************/ typedef struct { int k, y; hts_pos_t x, end; } cstate_t; static cstate_t g_cstate_null = { -1, 0, 0, 0 }; typedef struct __linkbuf_t { bam1_t b; hts_pos_t beg, end; cstate_t s; struct __linkbuf_t *next; bam_pileup_cd cd; } lbnode_t; typedef struct { int cnt, n, max; lbnode_t **buf; } mempool_t; static mempool_t *mp_init(void) { mempool_t *mp; mp = (mempool_t*)calloc(1, sizeof(mempool_t)); return mp; } static void mp_destroy(mempool_t *mp) { int k; for (k = 0; k < mp->n; ++k) { free(mp->buf[k]->b.data); free(mp->buf[k]); } free(mp->buf); free(mp); } static inline lbnode_t *mp_alloc(mempool_t *mp) { ++mp->cnt; if (mp->n == 0) return (lbnode_t*)calloc(1, sizeof(lbnode_t)); else return mp->buf[--mp->n]; } static inline void mp_free(mempool_t *mp, lbnode_t *p) { --mp->cnt; p->next = 0; // clear lbnode_t::next here if (mp->n == mp->max) { mp->max = mp->max? mp->max<<1 : 256; mp->buf = (lbnode_t**)realloc(mp->buf, sizeof(lbnode_t*) * mp->max); } mp->buf[mp->n++] = p; } /********************** *** CIGAR resolver *** **********************/ /* s->k: the index of the CIGAR operator that has just been processed. s->x: the reference coordinate of the start of s->k s->y: the query coordinate of the start of s->k */ static inline int resolve_cigar2(bam_pileup1_t *p, hts_pos_t pos, cstate_t *s) { #define _cop(c) ((c)&BAM_CIGAR_MASK) #define _cln(c) ((c)>>BAM_CIGAR_SHIFT) bam1_t *b = p->b; bam1_core_t *c = &b->core; uint32_t *cigar = bam_get_cigar(b); int k; // determine the current CIGAR operation //fprintf(stderr, "%s\tpos=%ld\tend=%ld\t(%d,%ld,%d)\n", bam_get_qname(b), pos, s->end, s->k, s->x, s->y); if (s->k == -1) { // never processed p->qpos = 0; if (c->n_cigar == 1) { // just one operation, save a loop if (_cop(cigar[0]) == BAM_CMATCH || _cop(cigar[0]) == BAM_CEQUAL || _cop(cigar[0]) == BAM_CDIFF) s->k = 0, s->x = c->pos, s->y = 0; } else { // find the first match or deletion for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) { int op = _cop(cigar[k]); int l = _cln(cigar[k]); if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) break; else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l; } assert(k < c->n_cigar); s->k = k; } } else { // the read has been processed before int op, l = _cln(cigar[s->k]); if (pos - s->x >= l) { // jump to the next operation assert(s->k < c->n_cigar); // otherwise a bug: this function should not be called in this case op = _cop(cigar[s->k+1]); if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) { // jump to the next without a loop if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l; s->x += l; ++s->k; } else { // find the next M/D/N/=/X if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l; s->x += l; for (k = s->k + 1; k < c->n_cigar; ++k) { op = _cop(cigar[k]), l = _cln(cigar[k]); if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) break; else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l; } s->k = k; } assert(s->k < c->n_cigar); // otherwise a bug } // else, do nothing } { // collect pileup information int op, l; op = _cop(cigar[s->k]); l = _cln(cigar[s->k]); p->is_del = p->indel = p->is_refskip = 0; if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation int op2 = _cop(cigar[s->k+1]); int l2 = _cln(cigar[s->k+1]); if (op2 == BAM_CDEL && op != BAM_CDEL) { // At start of a new deletion, merge e.g. 1D2D to 3D. // Within a deletion (the 2D in 1D2D) we keep p->indel=0 // and rely on is_del=1 as we would for 3D. p->indel = -(int)l2; for (k = s->k+2; k < c->n_cigar; ++k) { op2 = _cop(cigar[k]); l2 = _cln(cigar[k]); if (op2 == BAM_CDEL) p->indel -= l2; else break; } } else if (op2 == BAM_CINS) { p->indel = l2; for (k = s->k+2; k < c->n_cigar; ++k) { op2 = _cop(cigar[k]); l2 = _cln(cigar[k]); if (op2 == BAM_CINS) p->indel += l2; else if (op2 != BAM_CPAD) break; } } else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { int l3 = 0; for (k = s->k + 2; k < c->n_cigar; ++k) { op2 = _cop(cigar[k]); l2 = _cln(cigar[k]); if (op2 == BAM_CINS) l3 += l2; else if (op2 == BAM_CDEL || op2 == BAM_CMATCH || op2 == BAM_CREF_SKIP || op2 == BAM_CEQUAL || op2 == BAM_CDIFF) break; } if (l3 > 0) p->indel = l3; } } if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { p->qpos = s->y + (pos - s->x); } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) { p->is_del = 1; p->qpos = s->y; // FIXME: distinguish D and N!!!!! p->is_refskip = (op == BAM_CREF_SKIP); } // cannot be other operations; otherwise a bug p->is_head = (pos == c->pos); p->is_tail = (pos == s->end); } p->cigar_ind = s->k; return 1; } /******************************* *** Expansion of insertions *** *******************************/ /* * Fills out the kstring with the padded insertion sequence for the current * location in 'p'. If this is not an insertion site, the string is blank. * * This variant handles base modifications, but only when "m" is non-NULL. * * Returns the number of inserted base on success, with string length being * accessable via ins->l; * -1 on failure. */ int bam_plp_insertion_mod(const bam_pileup1_t *p, hts_base_mod_state *m, kstring_t *ins, int *del_len) { int j, k, indel, nb = 0; uint32_t *cigar; if (p->indel <= 0) { if (ks_resize(ins, 1) < 0) return -1; ins->l = 0; ins->s[0] = '\0'; return 0; } if (del_len) *del_len = 0; // Measure indel length including pads indel = 0; k = p->cigar_ind+1; cigar = bam_get_cigar(p->b); while (k < p->b->core.n_cigar) { switch (cigar[k] & BAM_CIGAR_MASK) { case BAM_CPAD: case BAM_CINS: indel += (cigar[k] >> BAM_CIGAR_SHIFT); break; default: k = p->b->core.n_cigar; break; } k++; } nb = ins->l = indel; // Produce sequence if (ks_resize(ins, indel+1) < 0) return -1; indel = 0; k = p->cigar_ind+1; j = 1; while (k < p->b->core.n_cigar) { int l, c; switch (cigar[k] & BAM_CIGAR_MASK) { case BAM_CPAD: for (l = 0; l < (cigar[k]>>BAM_CIGAR_SHIFT); l++) ins->s[indel++] = '*'; break; case BAM_CINS: for (l = 0; l < (cigar[k]>>BAM_CIGAR_SHIFT); l++, j++) { c = p->qpos + j - p->is_del < p->b->core.l_qseq ? seq_nt16_str[bam_seqi(bam_get_seq(p->b), p->qpos + j - p->is_del)] : 'N'; ins->s[indel++] = c; int nm; hts_base_mod mod[256]; if (m && (nm = bam_mods_at_qpos(p->b, p->qpos + j - p->is_del, m, mod, 256)) > 0) { int o_indel = indel; if (ks_resize(ins, ins->l + nm*16+3) < 0) return -1; ins->s[indel++] = '['; int j; for (j = 0; j < nm; j++) { char qual[20]; if (mod[j].qual >= 0) snprintf(qual, sizeof(qual), "%d", mod[j].qual); else *qual=0; if (mod[j].modified_base < 0) // ChEBI indel += snprintf(&ins->s[indel], ins->m - indel, "%c(%d)%s", "+-"[mod[j].strand], -mod[j].modified_base, qual); else indel += snprintf(&ins->s[indel], ins->m - indel, "%c%c%s", "+-"[mod[j].strand], mod[j].modified_base, qual); } ins->s[indel++] = ']'; ins->l += indel - o_indel; // grow by amount we used } } break; case BAM_CDEL: // eg cigar 1M2I1D gives mpileup output in T+2AA-1C style if (del_len) *del_len = cigar[k]>>BAM_CIGAR_SHIFT; // fall through default: k = p->b->core.n_cigar; break; } k++; } ins->s[indel] = '\0'; ins->l = indel; // string length return nb; // base length } /* * Fills out the kstring with the padded insertion sequence for the current * location in 'p'. If this is not an insertion site, the string is blank. * * This is the original interface with no capability for reporting base * modifications. * * Returns the length of insertion string on success; * -1 on failure. */ int bam_plp_insertion(const bam_pileup1_t *p, kstring_t *ins, int *del_len) { return bam_plp_insertion_mod(p, NULL, ins, del_len); } /*********************** *** Pileup iterator *** ***********************/ // Dictionary of overlapping reads KHASH_MAP_INIT_STR(olap_hash, lbnode_t *) typedef khash_t(olap_hash) olap_hash_t; struct bam_plp_s { mempool_t *mp; lbnode_t *head, *tail; int32_t tid, max_tid; hts_pos_t pos, max_pos; int is_eof, max_plp, error, maxcnt; uint64_t id; bam_pileup1_t *plp; // for the "auto" interface only bam1_t *b; bam_plp_auto_f func; void *data; olap_hash_t *overlaps; // For notification of creation and destruction events // and associated client-owned pointer. int (*plp_construct)(void *data, const bam1_t *b, bam_pileup_cd *cd); int (*plp_destruct )(void *data, const bam1_t *b, bam_pileup_cd *cd); }; bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data) { bam_plp_t iter; iter = (bam_plp_t)calloc(1, sizeof(struct bam_plp_s)); iter->mp = mp_init(); iter->head = iter->tail = mp_alloc(iter->mp); iter->max_tid = iter->max_pos = -1; iter->maxcnt = 8000; if (func) { iter->func = func; iter->data = data; iter->b = bam_init1(); } return iter; } int bam_plp_init_overlaps(bam_plp_t iter) { iter->overlaps = kh_init(olap_hash); // hash for tweaking quality of bases in overlapping reads return iter->overlaps ? 0 : -1; } void bam_plp_destroy(bam_plp_t iter) { lbnode_t *p, *pnext; if ( iter->overlaps ) kh_destroy(olap_hash, iter->overlaps); for (p = iter->head; p != NULL; p = pnext) { if (iter->plp_destruct && p != iter->tail) iter->plp_destruct(iter->data, &p->b, &p->cd); pnext = p->next; mp_free(iter->mp, p); } mp_destroy(iter->mp); if (iter->b) bam_destroy1(iter->b); free(iter->plp); free(iter); } void bam_plp_constructor(bam_plp_t plp, int (*func)(void *data, const bam1_t *b, bam_pileup_cd *cd)) { plp->plp_construct = func; } void bam_plp_destructor(bam_plp_t plp, int (*func)(void *data, const bam1_t *b, bam_pileup_cd *cd)) { plp->plp_destruct = func; } //--------------------------------- //--- Tweak overlapping reads //--------------------------------- /** * cigar_iref2iseq_set() - find the first CMATCH setting the ref and the read index * cigar_iref2iseq_next() - get the next CMATCH base * @cigar: pointer to current cigar block (rw) * @cigar_max: pointer just beyond the last cigar block * @icig: position within the current cigar block (rw) * @iseq: position in the sequence (rw) * @iref: position with respect to the beginning of the read (iref_pos - b->core.pos) (rw) * * Returns BAM_CMATCH, -1 when there is no more cigar to process or the requested position is not covered, * or -2 on error. */ static inline int cigar_iref2iseq_set(const uint32_t **cigar, const uint32_t *cigar_max, hts_pos_t *icig, hts_pos_t *iseq, hts_pos_t *iref) { hts_pos_t pos = *iref; if ( pos < 0 ) return -1; *icig = 0; *iseq = 0; *iref = 0; while ( *cigar> BAM_CIGAR_SHIFT; if ( cig==BAM_CSOFT_CLIP ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } if ( cig==BAM_CHARD_CLIP || cig==BAM_CPAD ) { (*cigar)++; *icig = 0; continue; } if ( cig==BAM_CMATCH || cig==BAM_CEQUAL || cig==BAM_CDIFF ) { pos -= ncig; if ( pos < 0 ) { *icig = ncig + pos; *iseq += *icig; *iref += *icig; return BAM_CMATCH; } (*cigar)++; *iseq += ncig; *icig = 0; *iref += ncig; continue; } if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } if ( cig==BAM_CDEL || cig==BAM_CREF_SKIP ) { pos -= ncig; if ( pos<0 ) pos = 0; (*cigar)++; *icig = 0; *iref += ncig; continue; } hts_log_error("Unexpected cigar %d", cig); return -2; } *iseq = -1; return -1; } static inline int cigar_iref2iseq_next(const uint32_t **cigar, const uint32_t *cigar_max, hts_pos_t *icig, hts_pos_t *iseq, hts_pos_t *iref) { while ( *cigar < cigar_max ) { int cig = (**cigar) & BAM_CIGAR_MASK; int ncig = (**cigar) >> BAM_CIGAR_SHIFT; if ( cig==BAM_CMATCH || cig==BAM_CEQUAL || cig==BAM_CDIFF ) { if ( *icig >= ncig - 1 ) { *icig = -1; (*cigar)++; continue; } (*iseq)++; (*icig)++; (*iref)++; return BAM_CMATCH; } if ( cig==BAM_CDEL || cig==BAM_CREF_SKIP ) { (*cigar)++; (*iref) += ncig; *icig = -1; continue; } if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = -1; continue; } if ( cig==BAM_CSOFT_CLIP ) { (*cigar)++; *iseq += ncig; *icig = -1; continue; } if ( cig==BAM_CHARD_CLIP || cig==BAM_CPAD ) { (*cigar)++; *icig = -1; continue; } hts_log_error("Unexpected cigar %d", cig); return -2; } *iseq = -1; *iref = -1; return -1; } // Given overlapping read 'a' (left) and 'b' (right) on the same // template, adjust quality values to zero for either a or b. // Note versions 1.12 and earlier always removed quality from 'b' for // matching bases. Now we select a or b semi-randomly based on name hash. // Returns 0 on success, // -1 on failure static int tweak_overlap_quality(bam1_t *a, bam1_t *b) { const uint32_t *a_cigar = bam_get_cigar(a), *a_cigar_max = a_cigar + a->core.n_cigar; const uint32_t *b_cigar = bam_get_cigar(b), *b_cigar_max = b_cigar + b->core.n_cigar; hts_pos_t a_icig = 0, a_iseq = 0; hts_pos_t b_icig = 0, b_iseq = 0; uint8_t *a_qual = bam_get_qual(a), *b_qual = bam_get_qual(b); uint8_t *a_seq = bam_get_seq(a), *b_seq = bam_get_seq(b); hts_pos_t iref = b->core.pos; hts_pos_t a_iref = iref - a->core.pos; hts_pos_t b_iref = iref - b->core.pos; int a_ret = cigar_iref2iseq_set(&a_cigar, a_cigar_max, &a_icig, &a_iseq, &a_iref); if ( a_ret<0 ) // no overlap or error return a_ret<-1 ? -1:0; int b_ret = cigar_iref2iseq_set(&b_cigar, b_cigar_max, &b_icig, &b_iseq, &b_iref); if ( b_ret<0 ) // no overlap or error return b_ret<-1 ? -1:0; // Determine which seq is the one getting modified qualities. uint8_t amul, bmul; if (__ac_Wang_hash(__ac_X31_hash_string(bam_get_qname(a))) & 1) { amul = 1; bmul = 0; } else { amul = 0; bmul = 1; } // Loop over the overlapping region nulling qualities in either // seq a or b. int err = 0; while ( 1 ) { // Step to next matching reference position in a and b while ( a_ret >= 0 && a_iref>=0 && a_iref < iref - a->core.pos ) a_ret = cigar_iref2iseq_next(&a_cigar, a_cigar_max, &a_icig, &a_iseq, &a_iref); if ( a_ret<0 ) { // done err = a_ret<-1?-1:0; break; } while ( b_ret >= 0 && b_iref>=0 && b_iref < iref - b->core.pos ) b_ret = cigar_iref2iseq_next(&b_cigar, b_cigar_max, &b_icig, &b_iseq, &b_iref); if ( b_ret<0 ) { // done err = b_ret<-1?-1:0; break; } if ( iref < a_iref + a->core.pos ) iref = a_iref + a->core.pos; if ( iref < b_iref + b->core.pos ) iref = b_iref + b->core.pos; iref++; // If A or B has a deletion then we catch up the other to this point. // We also amend quality values using the same rules for mismatch. if (a_iref+a->core.pos != b_iref+b->core.pos) { if (a_iref+a->core.pos < b_iref+b->core.pos && b_cigar > bam_get_cigar(b) && bam_cigar_op(b_cigar[-1]) == BAM_CDEL) { // Del in B means it's moved on further than A do { a_qual[a_iseq] = amul ? a_qual[a_iseq]*0.8 : 0; a_ret = cigar_iref2iseq_next(&a_cigar, a_cigar_max, &a_icig, &a_iseq, &a_iref); if (a_ret < 0) return -(a_ret<-1); // 0 or -1 } while (a_iref + a->core.pos < b_iref+b->core.pos); } else if (a_cigar > bam_get_cigar(a) && bam_cigar_op(a_cigar[-1]) == BAM_CDEL) { // Del in A means it's moved on further than B do { b_qual[b_iseq] = bmul ? b_qual[b_iseq]*0.8 : 0; b_ret = cigar_iref2iseq_next(&b_cigar, b_cigar_max, &b_icig, &b_iseq, &b_iref); if (b_ret < 0) return -(b_ret<-1); // 0 or -1 } while (b_iref + b->core.pos < a_iref+a->core.pos); } else { // Anything else, eg ref-skip, we don't support here continue; } } // fprintf(stderr, "a_cig=%ld,%ld b_cig=%ld,%ld iref=%ld " // "a_iref=%ld b_iref=%ld a_iseq=%ld b_iseq=%ld\n", // a_cigar-bam_get_cigar(a), a_icig, // b_cigar-bam_get_cigar(b), b_icig, // iref, a_iref+a->core.pos+1, b_iref+b->core.pos+1, // a_iseq, b_iseq); if (a_iseq > a->core.l_qseq || b_iseq > b->core.l_qseq) // Fell off end of sequence, bad CIGAR? return -1; // We're finally at the same ref base in both a and b. // Check if the bases match (confident) or mismatch // (not so confident). if ( bam_seqi(a_seq,a_iseq) == bam_seqi(b_seq,b_iseq) ) { // We are very confident about this base. Use sum of quals int qual = a_qual[a_iseq] + b_qual[b_iseq]; a_qual[a_iseq] = amul * (qual>200 ? 200 : qual); b_qual[b_iseq] = bmul * (qual>200 ? 200 : qual);; } else { // Not so confident about anymore given the mismatch. // Reduce qual for lowest quality base. if ( a_qual[a_iseq] > b_qual[b_iseq] ) { // A highest qual base; keep a_qual[a_iseq] = 0.8 * a_qual[a_iseq]; b_qual[b_iseq] = 0; } else if (a_qual[a_iseq] < b_qual[b_iseq] ) { // B highest qual base; keep b_qual[b_iseq] = 0.8 * b_qual[b_iseq]; a_qual[a_iseq] = 0; } else { // Both equal, so pick randomly a_qual[a_iseq] = amul * 0.8 * a_qual[a_iseq]; b_qual[b_iseq] = bmul * 0.8 * b_qual[b_iseq]; } } } return err; } // Fix overlapping reads. Simple soft-clipping did not give good results. // Lowering qualities of unwanted bases is more selective and works better. // // Returns 0 on success, -1 on failure static int overlap_push(bam_plp_t iter, lbnode_t *node) { if ( !iter->overlaps ) return 0; // mapped mates and paired reads only if ( node->b.core.flag&BAM_FMUNMAP || !(node->b.core.flag&BAM_FPROPER_PAIR) ) return 0; // no overlap possible, unless some wild cigar if ( (node->b.core.mtid >= 0 && node->b.core.tid != node->b.core.mtid) || (llabs(node->b.core.isize) >= 2*node->b.core.l_qseq && node->b.core.mpos >= node->end) // for those wild cigars ) return 0; khiter_t kitr = kh_get(olap_hash, iter->overlaps, bam_get_qname(&node->b)); if ( kitr==kh_end(iter->overlaps) ) { // Only add reads where the mate is still to arrive if (node->b.core.mpos >= node->b.core.pos || ((node->b.core.flag & BAM_FPAIRED) && node->b.core.mpos == -1)) { int ret; kitr = kh_put(olap_hash, iter->overlaps, bam_get_qname(&node->b), &ret); if (ret < 0) return -1; kh_value(iter->overlaps, kitr) = node; } } else { lbnode_t *a = kh_value(iter->overlaps, kitr); int err = tweak_overlap_quality(&a->b, &node->b); kh_del(olap_hash, iter->overlaps, kitr); assert(a->end-1 == a->s.end); return err; } return 0; } static void overlap_remove(bam_plp_t iter, const bam1_t *b) { if ( !iter->overlaps ) return; khiter_t kitr; if ( b ) { kitr = kh_get(olap_hash, iter->overlaps, bam_get_qname(b)); if ( kitr!=kh_end(iter->overlaps) ) kh_del(olap_hash, iter->overlaps, kitr); } else { // remove all for (kitr = kh_begin(iter->overlaps); kitroverlaps); kitr++) if ( kh_exist(iter->overlaps, kitr) ) kh_del(olap_hash, iter->overlaps, kitr); } } // Prepares next pileup position in bam records collected by bam_plp_auto -> user func -> bam_plp_push. Returns // pointer to the piled records if next position is ready or NULL if there is not enough records in the // buffer yet (the current position is still the maximum position across all buffered reads). const bam_pileup1_t *bam_plp64_next(bam_plp_t iter, int *_tid, hts_pos_t *_pos, int *_n_plp) { if (iter->error) { *_n_plp = -1; return NULL; } *_n_plp = 0; if (iter->is_eof && iter->head == iter->tail) return NULL; while (iter->is_eof || iter->max_tid > iter->tid || (iter->max_tid == iter->tid && iter->max_pos > iter->pos)) { int n_plp = 0; // write iter->plp at iter->pos lbnode_t **pptr = &iter->head; while (*pptr != iter->tail) { lbnode_t *p = *pptr; if (p->b.core.tid < iter->tid || (p->b.core.tid == iter->tid && p->end <= iter->pos)) { // then remove overlap_remove(iter, &p->b); if (iter->plp_destruct) iter->plp_destruct(iter->data, &p->b, &p->cd); *pptr = p->next; mp_free(iter->mp, p); } else { if (p->b.core.tid == iter->tid && p->beg <= iter->pos) { // here: p->end > pos; then add to pileup if (n_plp == iter->max_plp) { // then double the capacity iter->max_plp = iter->max_plp? iter->max_plp<<1 : 256; iter->plp = (bam_pileup1_t*)realloc(iter->plp, sizeof(bam_pileup1_t) * iter->max_plp); } iter->plp[n_plp].b = &p->b; iter->plp[n_plp].cd = p->cd; if (resolve_cigar2(iter->plp + n_plp, iter->pos, &p->s)) ++n_plp; // actually always true... } pptr = &(*pptr)->next; } } *_n_plp = n_plp; *_tid = iter->tid; *_pos = iter->pos; // update iter->tid and iter->pos if (iter->head != iter->tail) { if (iter->tid > iter->head->b.core.tid) { hts_log_error("Unsorted input. Pileup aborts"); iter->error = 1; *_n_plp = -1; return NULL; } } if (iter->tid < iter->head->b.core.tid) { // come to a new reference sequence iter->tid = iter->head->b.core.tid; iter->pos = iter->head->beg; // jump to the next reference } else if (iter->pos < iter->head->beg) { // here: tid == head->b.core.tid iter->pos = iter->head->beg; // jump to the next position } else ++iter->pos; // scan contiguously // return if (n_plp) return iter->plp; if (iter->is_eof && iter->head == iter->tail) break; } return NULL; } const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp) { hts_pos_t pos64 = 0; const bam_pileup1_t *p = bam_plp64_next(iter, _tid, &pos64, _n_plp); if (pos64 < INT_MAX) { *_pos = pos64; } else { hts_log_error("Position %"PRId64" too large", pos64); *_pos = INT_MAX; iter->error = 1; *_n_plp = -1; return NULL; } return p; } int bam_plp_push(bam_plp_t iter, const bam1_t *b) { if (iter->error) return -1; if (b) { if (b->core.tid < 0) { overlap_remove(iter, b); return 0; } // Skip only unmapped reads here, any additional filtering must be done in iter->func if (b->core.flag & BAM_FUNMAP) { overlap_remove(iter, b); return 0; } if (iter->tid == b->core.tid && iter->pos == b->core.pos && iter->mp->cnt > iter->maxcnt) { overlap_remove(iter, b); return 0; } if (bam_copy1(&iter->tail->b, b) == NULL) return -1; iter->tail->b.id = iter->id++; iter->tail->beg = b->core.pos; // Use raw rlen rather than bam_endpos() which adjusts rlen=0 to rlen=1 iter->tail->end = b->core.pos + bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(b)); iter->tail->s = g_cstate_null; iter->tail->s.end = iter->tail->end - 1; // initialize cstate_t if (b->core.tid < iter->max_tid) { hts_log_error("The input is not sorted (chromosomes out of order)"); iter->error = 1; return -1; } if ((b->core.tid == iter->max_tid) && (iter->tail->beg < iter->max_pos)) { hts_log_error("The input is not sorted (reads out of order)"); iter->error = 1; return -1; } iter->max_tid = b->core.tid; iter->max_pos = iter->tail->beg; if (iter->tail->end > iter->pos || iter->tail->b.core.tid > iter->tid) { lbnode_t *next = mp_alloc(iter->mp); if (!next) { iter->error = 1; return -1; } if (iter->plp_construct) { if (iter->plp_construct(iter->data, &iter->tail->b, &iter->tail->cd) < 0) { mp_free(iter->mp, next); iter->error = 1; return -1; } } if (overlap_push(iter, iter->tail) < 0) { mp_free(iter->mp, next); iter->error = 1; return -1; } iter->tail->next = next; iter->tail = iter->tail->next; } } else iter->is_eof = 1; return 0; } const bam_pileup1_t *bam_plp64_auto(bam_plp_t iter, int *_tid, hts_pos_t *_pos, int *_n_plp) { const bam_pileup1_t *plp; if (iter->func == 0 || iter->error) { *_n_plp = -1; return 0; } if ((plp = bam_plp64_next(iter, _tid, _pos, _n_plp)) != 0) return plp; else { // no pileup line can be obtained; read alignments *_n_plp = 0; if (iter->is_eof) return 0; int ret; while ( (ret=iter->func(iter->data, iter->b)) >= 0) { if (bam_plp_push(iter, iter->b) < 0) { *_n_plp = -1; return 0; } if ((plp = bam_plp64_next(iter, _tid, _pos, _n_plp)) != 0) return plp; // otherwise no pileup line can be returned; read the next alignment. } if ( ret < -1 ) { iter->error = ret; *_n_plp = -1; return 0; } if (bam_plp_push(iter, 0) < 0) { *_n_plp = -1; return 0; } if ((plp = bam_plp64_next(iter, _tid, _pos, _n_plp)) != 0) return plp; return 0; } } const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp) { hts_pos_t pos64 = 0; const bam_pileup1_t *p = bam_plp64_auto(iter, _tid, &pos64, _n_plp); if (pos64 < INT_MAX) { *_pos = pos64; } else { hts_log_error("Position %"PRId64" too large", pos64); *_pos = INT_MAX; iter->error = 1; *_n_plp = -1; return NULL; } return p; } void bam_plp_reset(bam_plp_t iter) { overlap_remove(iter, NULL); iter->max_tid = iter->max_pos = -1; iter->tid = iter->pos = 0; iter->is_eof = 0; while (iter->head != iter->tail) { lbnode_t *p = iter->head; iter->head = p->next; mp_free(iter->mp, p); } } void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt) { iter->maxcnt = maxcnt; } /************************ *** Mpileup iterator *** ************************/ struct bam_mplp_s { int n; int32_t min_tid, *tid; hts_pos_t min_pos, *pos; bam_plp_t *iter; int *n_plp; const bam_pileup1_t **plp; }; bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data) { int i; bam_mplp_t iter; iter = (bam_mplp_t)calloc(1, sizeof(struct bam_mplp_s)); iter->pos = (hts_pos_t*)calloc(n, sizeof(hts_pos_t)); iter->tid = (int32_t*)calloc(n, sizeof(int32_t)); iter->n_plp = (int*)calloc(n, sizeof(int)); iter->plp = (const bam_pileup1_t**)calloc(n, sizeof(bam_pileup1_t*)); iter->iter = (bam_plp_t*)calloc(n, sizeof(bam_plp_t)); iter->n = n; iter->min_pos = HTS_POS_MAX; iter->min_tid = (uint32_t)-1; for (i = 0; i < n; ++i) { iter->iter[i] = bam_plp_init(func, data[i]); iter->pos[i] = iter->min_pos; iter->tid[i] = iter->min_tid; } return iter; } int bam_mplp_init_overlaps(bam_mplp_t iter) { int i, r = 0; for (i = 0; i < iter->n; ++i) r |= bam_plp_init_overlaps(iter->iter[i]); return r == 0 ? 0 : -1; } void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt) { int i; for (i = 0; i < iter->n; ++i) iter->iter[i]->maxcnt = maxcnt; } void bam_mplp_destroy(bam_mplp_t iter) { int i; for (i = 0; i < iter->n; ++i) bam_plp_destroy(iter->iter[i]); free(iter->iter); free(iter->pos); free(iter->tid); free(iter->n_plp); free(iter->plp); free(iter); } int bam_mplp64_auto(bam_mplp_t iter, int *_tid, hts_pos_t *_pos, int *n_plp, const bam_pileup1_t **plp) { int i, ret = 0; hts_pos_t new_min_pos = HTS_POS_MAX; uint32_t new_min_tid = (uint32_t)-1; for (i = 0; i < iter->n; ++i) { if (iter->pos[i] == iter->min_pos && iter->tid[i] == iter->min_tid) { int tid; hts_pos_t pos; iter->plp[i] = bam_plp64_auto(iter->iter[i], &tid, &pos, &iter->n_plp[i]); if ( iter->iter[i]->error ) return -1; if (iter->plp[i]) { iter->tid[i] = tid; iter->pos[i] = pos; } else { iter->tid[i] = 0; iter->pos[i] = 0; } } if (iter->plp[i]) { if (iter->tid[i] < new_min_tid) { new_min_tid = iter->tid[i]; new_min_pos = iter->pos[i]; } else if (iter->tid[i] == new_min_tid && iter->pos[i] < new_min_pos) { new_min_pos = iter->pos[i]; } } } iter->min_pos = new_min_pos; iter->min_tid = new_min_tid; if (new_min_pos == HTS_POS_MAX) return 0; *_tid = new_min_tid; *_pos = new_min_pos; for (i = 0; i < iter->n; ++i) { if (iter->pos[i] == iter->min_pos && iter->tid[i] == iter->min_tid) { n_plp[i] = iter->n_plp[i], plp[i] = iter->plp[i]; ++ret; } else n_plp[i] = 0, plp[i] = 0; } return ret; } int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp) { hts_pos_t pos64 = 0; int ret = bam_mplp64_auto(iter, _tid, &pos64, n_plp, plp); if (ret >= 0) { if (pos64 < INT_MAX) { *_pos = pos64; } else { hts_log_error("Position %"PRId64" too large", pos64); *_pos = INT_MAX; return -1; } } return ret; } void bam_mplp_reset(bam_mplp_t iter) { int i; iter->min_pos = HTS_POS_MAX; iter->min_tid = (uint32_t)-1; for (i = 0; i < iter->n; ++i) { bam_plp_reset(iter->iter[i]); iter->pos[i] = HTS_POS_MAX; iter->tid[i] = (uint32_t)-1; iter->n_plp[i] = 0; iter->plp[i] = NULL; } } void bam_mplp_constructor(bam_mplp_t iter, int (*func)(void *arg, const bam1_t *b, bam_pileup_cd *cd)) { int i; for (i = 0; i < iter->n; ++i) bam_plp_constructor(iter->iter[i], func); } void bam_mplp_destructor(bam_mplp_t iter, int (*func)(void *arg, const bam1_t *b, bam_pileup_cd *cd)) { int i; for (i = 0; i < iter->n; ++i) bam_plp_destructor(iter->iter[i], func); } #endif // ~!defined(BAM_NO_PILEUP) pysam-0.23.0/htslib/sam_internal.h000066400000000000000000000076321475062545500170640ustar00rootroot00000000000000/* sam_internal.h -- internal functions; not part of the public API. Copyright (C) 2019-2020, 2023-2024 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTSLIB_SAM_INTERNAL_H #define HTSLIB_SAM_INTERNAL_H #include #include #include "htslib/sam.h" #ifdef __cplusplus extern "C" { #endif // Used internally in the SAM format multi-threading. int sam_state_destroy(samFile *fp); int sam_set_thread_pool(htsFile *fp, htsThreadPool *p); int sam_set_threads(htsFile *fp, int nthreads); // Fastq state int fastq_state_set(samFile *fp, enum hts_fmt_option opt, ...); void fastq_state_destroy(samFile *fp); // bam1_t data (re)allocation int sam_realloc_bam_data(bam1_t *b, size_t desired); static inline int realloc_bam_data(bam1_t *b, size_t desired) { if (desired <= b->m_data) return 0; return sam_realloc_bam_data(b, desired); } static inline int possibly_expand_bam_data(bam1_t *b, size_t bytes) { size_t new_len = (size_t) b->l_data + bytes; if (new_len > INT32_MAX || new_len < bytes) { // Too big or overflow errno = ENOMEM; return -1; } if (new_len <= b->m_data) return 0; return sam_realloc_bam_data(b, new_len); } /* * Convert a nibble encoded BAM sequence to a string of bases. * * We do this 2 bp at a time for speed. Equiv to: * * for (i = 0; i < len; i++) * seq[i] = seq_nt16_str[bam_seqi(nib, i)]; */ static inline void nibble2base_default(uint8_t *nib, char *seq, int len) { static const char code2base[512] = "===A=C=M=G=R=S=V=T=W=Y=H=K=D=B=N" "A=AAACAMAGARASAVATAWAYAHAKADABAN" "C=CACCCMCGCRCSCVCTCWCYCHCKCDCBCN" "M=MAMCMMMGMRMSMVMTMWMYMHMKMDMBMN" "G=GAGCGMGGGRGSGVGTGWGYGHGKGDGBGN" "R=RARCRMRGRRRSRVRTRWRYRHRKRDRBRN" "S=SASCSMSGSRSSSVSTSWSYSHSKSDSBSN" "V=VAVCVMVGVRVSVVVTVWVYVHVKVDVBVN" "T=TATCTMTGTRTSTVTTTWTYTHTKTDTBTN" "W=WAWCWMWGWRWSWVWTWWWYWHWKWDWBWN" "Y=YAYCYMYGYRYSYVYTYWYYYHYKYDYBYN" "H=HAHCHMHGHRHSHVHTHWHYHHHKHDHBHN" "K=KAKCKMKGKRKSKVKTKWKYKHKKKDKBKN" "D=DADCDMDGDRDSDVDTDWDYDHDKDDDBDN" "B=BABCBMBGBRBSBVBTBWBYBHBKBDBBBN" "N=NANCNMNGNRNSNVNTNWNYNHNKNDNBNN"; int i, len2 = len/2; seq[0] = 0; for (i = 0; i < len2; i++) // Note size_t cast helps gcc optimiser. memcpy(&seq[i*2], &code2base[(size_t)nib[i]*2], 2); if ((i *= 2) < len) seq[i] = seq_nt16_str[bam_seqi(nib, i)]; } #if defined HAVE_ATTRIBUTE_CONSTRUCTOR && \ ((defined __x86_64__ && defined HAVE_ATTRIBUTE_TARGET && defined HAVE_BUILTIN_CPU_SUPPORT_SSSE3) || \ (defined __ARM_NEON)) #define BUILDING_SIMD_NIBBLE2BASE #endif static inline void nibble2base(uint8_t *nib, char *seq, int len) { #ifdef BUILDING_SIMD_NIBBLE2BASE extern void (*htslib_nibble2base)(uint8_t *nib, char *seq, int len); htslib_nibble2base(nib, seq, len); #else nibble2base_default(nib, seq, len); #endif } #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/sam_mods.c000066400000000000000000000622771475062545500162130ustar00rootroot00000000000000/* sam_mods.c -- Base modification handling in SAM and BAM. Copyright (C) 2020-2024 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include "htslib/sam.h" #include "textutils_internal.h" // --------------------------- // Base Modification retrieval // // These operate by recording state in an opaque type, allocated and freed // via the functions below. // // Initially we call bam_parse_basemod to process the tags and record the // modifications in the state structure, and then functions such as // bam_next_basemod can iterate over this cached state. /* Overview of API. We start by allocating an hts_base_mod_state and parsing the MM, ML and MN tags into it. This has optional flags controlling how we report base modifications in "explicit" coordinates. See below hts_base_mod_state *m = hts_base_mod_state_alloc(); bam_parse_basemod2(b, m, HTS_MOD_REPORT_UNCHECKED); // Or: bam_parse_basemod(b, m), which is equiv to flags==0 //... do something ... hts_base_mod_state_free(m); In the default implicit MM coordinate system, any location not reported is implicitly assumed to contain no modification. We only report the places we think are likely modified. Some tools however only look for base modifications in particular contexts, eg CpG islands. Here we need to distinguish between not-looked-for and looked-for-but-didn't-find. These calls have an explicit coordinate system, where we only know information about the coordinates explicitly listed and everything else is considered to be unverified. By default we don't get reports on the other coordinates in an explicit MM tag, but the HTS_MOD_REPORT_UNCHECKED flag will report them (with quality HTS_MOD_UNCHECKED) meaning we can do consensus modification analysis with accurate counting when dealing with a mixture of explicit and implicit records. We have different ways of processing the base modifications. We can iterate either mod-by-mod or position-by-position, or we can simply query a specific coordinate as may be done when processing a pileup. To check for base modifications as a specific location within a sequence we can use bam_mods_at_qpos. This provides complete random access within the MM string. However currently this is inefficiently implemented so should only be used for occasional analysis or as a way to start iterating at a specific location. It modifies the state position, so after the first use we can then switch to bam_mods_at_next_pos to iterate position by position from then on. hts_base_mod mods[10]; int n = bam_mods_at_qpos(b, pos, m, mods, 10); For base by base, we have bam_mods_at_next_pos. This strictly starts at the first base and reports entries one at a time. It's more efficient than a loop repeatedly calling ...at-pos. hts_base_mod mods[10]; int n = bam_mods_at_next_pos(b, m, mods, 10); for (int i = 0; i < n; i++) { // report mod i of n } Iterating over modifications instead of coordinates is simpler and more efficient as it skips reporting of unmodified bases. This is done with bam_next_basemod. hts_base_mod mods[10]; while ((n=bam_next_basemod(b, m, mods, 10, &pos)) > 0) { for (j = 0; j < n; j++) { // Report 'n'th mod at sequence position 'pos' } } There are also functions that query meta-data about the MM line rather than per-site information. bam_mods_recorded returns an array of ints holding the +ve code ('m') or -ve CHEBI numeric values. int ntypes, *types = bam_mods_recorded(m, &ntype); We can then query a specific modification type to get further information on the strand it is operating on, whether it has implicit or explicit coordinates, and what it's corresponding canonical base it is (The "C" in "C+m"). bam_mods_query_type does this by code name, while bam_mods_queryi does this by numeric i^{th} type (from 0 to ntype-1). bam_mods_query_type(m, 'c', &strand, &implicit, &canonical); bam_mods_queryi(m, 2, &strand, &implicit, &canonical); */ /* * Base modification are stored in MM/Mm tags as defined as * * ::= | "" * ::= * * ::= "A" | "C" | "G" | "T" | "N". * * ::= "+" | "-". * * ::= | * ::= | * ::= * ::= * * ::= "," | ";" * * We do not allocate additional memory other than the fixed size * state, thus we track up to 256 pointers to different locations * within the MM and ML tags. Each pointer is for a distinct * modification code (simple or ChEBI), meaning some may point to the * same delta-list when multiple codes are combined together * (e.g. "C+mh,1,5,18,3;"). This is the MM[] array. * * Each numeric in the delta-list is tracked in MMcount[], counted * down until it hits zero in which case the next delta is fetched. * * ML array similarly holds the locations in the quality (ML) tag per * type, but these are interleaved so C+mhfc,10,15 will have 4 types * all pointing to the same delta position, but in ML we store * Q(m0)Q(h0)Q(f0)Q(c0) followed by Q(m1)Q(h1)Q(f1)Q(c1). This ML * also has MLstride indicating how many positions along ML to jump * each time we consume a base. (4 in our above example, but usually 1 * for the simple case). * * One complexity of the base modification system is that mods are * always stored in the original DNA orientation. This is so that * tools that may reverse-complement a sequence (eg "samtools fastq -T * MM,ML") can pass through these modification tags irrespective of * whether they have any knowledge of their internal workings. * * Because we don't wish to allocate extra memory, we cannot simply * reverse the MM and ML tags. Sadly this means we have to manage the * reverse complementing ourselves on-the-fly. * For reversed reads we start at the right end of MM and no longer * stop at the semicolon. Instead we use MMend[] array to mark the * termination point. */ #define MAX_BASE_MOD 256 struct hts_base_mod_state { int type[MAX_BASE_MOD]; // char or minus-CHEBI int canonical[MAX_BASE_MOD];// canonical base, as seqi (1,2,4,8,15) char strand[MAX_BASE_MOD]; // strand of modification; + or - int MMcount[MAX_BASE_MOD]; // no. canonical bases left until next mod char *MM[MAX_BASE_MOD]; // next pos delta (string) char *MMend[MAX_BASE_MOD]; // end of pos-delta string uint8_t *ML[MAX_BASE_MOD]; // next qual int MLstride[MAX_BASE_MOD]; // bytes between quals for this type int implicit[MAX_BASE_MOD]; // treat unlisted positions as non-modified? int seq_pos; // current position along sequence int nmods; // used array size (0 to MAX_BASE_MOD-1). uint32_t flags; // Bit-field: see HTS_MOD_REPORT_UNCHECKED }; hts_base_mod_state *hts_base_mod_state_alloc(void) { return calloc(1, sizeof(hts_base_mod_state)); } void hts_base_mod_state_free(hts_base_mod_state *state) { free(state); } /* * Count frequency of A, C, G, T and N canonical bases in the sequence */ static void seq_freq(const bam1_t *b, int freq[16]) { int i; memset(freq, 0, 16*sizeof(*freq)); uint8_t *seq = bam_get_seq(b); for (i = 0; i < b->core.l_qseq; i++) freq[bam_seqi(seq, i)]++; freq[15] = b->core.l_qseq; // all bases count as N for base mods } //0123456789ABCDEF //=ACMGRSVTWYHKDBN aka seq_nt16_str[] //=TGKCYSBAWRDMHVN comp1ement of seq_nt16_str //084C2A6E195D3B7F static int seqi_rc[] = { 0,8,4,12,2,10,6,14,1,9,5,13,3,11,7,15 }; /* * Parse the MM and ML tags to populate the base mod state. * This structure will have been previously allocated via * hts_base_mod_state_alloc, but it does not need to be repeatedly * freed and allocated for each new bam record. (Although obviously * it requires a new call to this function.) * * Flags are copied into the state and used to control reporting functions. * Currently the only flag is HTS_MOD_REPORT_UNCHECKED, to control whether * explicit "C+m?" mods report quality HTS_MOD_UNCHECKED for the bases * outside the explicitly reported region. */ int bam_parse_basemod2(const bam1_t *b, hts_base_mod_state *state, uint32_t flags) { // Reset position, else upcoming calls may fail on // seq pos - length comparison state->seq_pos = 0; state->nmods = 0; state->flags = flags; // Read MM and ML tags uint8_t *mm = bam_aux_get(b, "MM"); if (!mm) mm = bam_aux_get(b, "Mm"); if (!mm) return 0; if (mm[0] != 'Z') { hts_log_error("%s: MM tag is not of type Z", bam_get_qname(b)); return -1; } uint8_t *mi = bam_aux_get(b, "MN"); if (mi && bam_aux2i(mi) != b->core.l_qseq && b->core.l_qseq) { // bam_aux2i with set errno = EINVAL and return 0 if the tag // isn't integer, but 0 will be a seq-length mismatch anyway so // triggers an error here too. hts_log_error("%s: MM/MN data length is incompatible with" " SEQ length", bam_get_qname(b)); return -1; } uint8_t *ml = bam_aux_get(b, "ML"); if (!ml) ml = bam_aux_get(b, "Ml"); if (ml && (ml[0] != 'B' || ml[1] != 'C')) { hts_log_error("%s: ML tag is not of type B,C", bam_get_qname(b)); return -1; } uint8_t *ml_end = ml ? ml+6 + le_to_u32(ml+2) : NULL; if (ml) ml += 6; // Aggregate freqs of ACGTN if reversed, to get final-delta (later) int freq[16]; if (b->core.flag & BAM_FREVERSE) seq_freq(b, freq); char *cp = (char *)mm+1; int mod_num = 0; int implicit = 1; while (*cp) { for (; *cp; cp++) { // cp should be [ACGTNU][+-]([a-zA-Z]+|[0-9]+)[.?]?(,\d+)*; unsigned char btype = *cp++; if (btype != 'A' && btype != 'C' && btype != 'G' && btype != 'T' && btype != 'U' && btype != 'N') return -1; if (btype == 'U') btype = 'T'; btype = seq_nt16_table[btype]; // Strand if (*cp != '+' && *cp != '-') return -1; // malformed char strand = *cp++; // List of modification types char *ms = cp, *me; // mod code start and end char *cp_end = NULL; int chebi = 0; if (isdigit_c(*cp)) { chebi = strtol(cp, &cp_end, 10); cp = cp_end; ms = cp-1; } else { while (*cp && isalpha_c(*cp)) cp++; if (*cp == '\0') return -1; } me = cp; // Optional explicit vs implicit marker implicit = 1; if (*cp == '.') { // default is implicit = 1; cp++; } else if (*cp == '?') { implicit = 0; cp++; } else if (*cp != ',' && *cp != ';') { // parse error return -1; } long delta; int n = 0; // nth symbol in a multi-mod string int stride = me-ms; int ndelta = 0; if (b->core.flag & BAM_FREVERSE) { // We process the sequence in left to right order, // but delta is successive count of bases to skip // counting right to left. This also means the number // of bases to skip at left edge is unrecorded (as it's // the remainder). // // To output mods in left to right, we step through the // MM list in reverse and need to identify the left-end // "remainder" delta. int total_seq = 0; for (;;) { cp += (*cp == ','); if (*cp == 0 || *cp == ';') break; delta = strtol(cp, &cp_end, 10); if (cp_end == cp) { hts_log_error("%s: Hit end of MM tag. Missing " "semicolon?", bam_get_qname(b)); return -1; } cp = cp_end; total_seq += delta+1; ndelta++; } delta = freq[seqi_rc[btype]] - total_seq; // remainder } else { delta = *cp == ',' ? strtol(cp+1, &cp_end, 10) : 0; if (!cp_end) { // empty list delta = INT_MAX; cp_end = cp; } } // Now delta is first in list or computed remainder, // and cp_end is either start or end of the MM list. while (ms < me) { state->type [mod_num] = chebi ? -chebi : *ms; state->strand [mod_num] = (strand == '-'); state->canonical[mod_num] = btype; state->MLstride [mod_num] = stride; state->implicit [mod_num] = implicit; if (delta < 0) { hts_log_error("%s: MM tag refers to bases beyond sequence " "length", bam_get_qname(b)); return -1; } state->MMcount [mod_num] = delta; if (b->core.flag & BAM_FREVERSE) { state->MM [mod_num] = me+1; state->MMend[mod_num] = cp_end; state->ML [mod_num] = ml ? ml+n +(ndelta-1)*stride: NULL; } else { state->MM [mod_num] = cp_end; state->MMend[mod_num] = NULL; state->ML [mod_num] = ml ? ml+n : NULL; } if (++mod_num >= MAX_BASE_MOD) { hts_log_error("%s: Too many base modification types", bam_get_qname(b)); return -1; } ms++; n++; } // Skip modification deltas if (ml) { if (b->core.flag & BAM_FREVERSE) { ml += ndelta*stride; } else { while (*cp && *cp != ';') { if (*cp == ',') ml+=stride; cp++; } } if (ml > ml_end) { hts_log_error("%s: Insufficient number of entries in ML " "tag", bam_get_qname(b)); return -1; } } else { // cp_end already known if FREVERSE if (cp_end && (b->core.flag & BAM_FREVERSE)) cp = cp_end; else while (*cp && *cp != ';') cp++; } if (!*cp) { hts_log_error("%s: Hit end of MM tag. Missing semicolon?", bam_get_qname(b)); return -1; } } } if (ml && ml != ml_end) { hts_log_error("%s: Too many entries in ML tag", bam_get_qname(b)); return -1; } state->nmods = mod_num; return 0; } int bam_parse_basemod(const bam1_t *b, hts_base_mod_state *state) { return bam_parse_basemod2(b, state, 0); } /* * Fills out mods[] with the base modifications found. * Returns the number found (0 if none), which may be more than * the size of n_mods if more were found than reported. * Returns <= -1 on error. * * This always marches left to right along sequence, irrespective of * reverse flag or modification strand. */ int bam_mods_at_next_pos(const bam1_t *b, hts_base_mod_state *state, hts_base_mod *mods, int n_mods) { if (b->core.flag & BAM_FREVERSE) { if (state->seq_pos < 0) return -1; } else { if (state->seq_pos >= b->core.l_qseq) return -1; } int i, j, n = 0; unsigned char base = bam_seqi(bam_get_seq(b), state->seq_pos); state->seq_pos++; if (b->core.flag & BAM_FREVERSE) base = seqi_rc[base]; for (i = 0; i < state->nmods; i++) { int unchecked = 0; if (state->canonical[i] != base && state->canonical[i] != 15/*N*/) continue; if (state->MMcount[i]-- > 0) { if (!state->implicit[i] && (state->flags & HTS_MOD_REPORT_UNCHECKED)) unchecked = 1; else continue; } char *MMptr = state->MM[i]; if (n < n_mods) { mods[n].modified_base = state->type[i]; mods[n].canonical_base = seq_nt16_str[state->canonical[i]]; mods[n].strand = state->strand[i]; mods[n].qual = unchecked ? HTS_MOD_UNCHECKED : (state->ML[i] ? *state->ML[i] : HTS_MOD_UNKNOWN); } n++; if (unchecked) continue; if (state->ML[i]) state->ML[i] += (b->core.flag & BAM_FREVERSE) ? -state->MLstride[i] : +state->MLstride[i]; if (b->core.flag & BAM_FREVERSE) { // process MM list backwards char *cp; if (state->MMend[i]-1 < state->MM[i]) { // Should be impossible to hit if coding is correct hts_log_error("Assert failed while processing base modification states"); return -1; } for (cp = state->MMend[i]-1; cp != state->MM[i]; cp--) if (*cp == ',') break; state->MMend[i] = cp; if (cp != state->MM[i]) state->MMcount[i] = strtol(cp+1, NULL, 10); else state->MMcount[i] = INT_MAX; } else { if (*state->MM[i] == ',') state->MMcount[i] = strtol(state->MM[i]+1, &state->MM[i], 10); else state->MMcount[i] = INT_MAX; } // Multiple mods at the same coords. for (j=i+1; j < state->nmods && state->MM[j] == MMptr; j++) { if (n < n_mods) { mods[n].modified_base = state->type[j]; mods[n].canonical_base = seq_nt16_str[state->canonical[j]]; mods[n].strand = state->strand[j]; mods[n].qual = state->ML[j] ? *state->ML[j] : -1; } n++; state->MMcount[j] = state->MMcount[i]; state->MM[j] = state->MM[i]; if (state->ML[j]) state->ML[j] += (b->core.flag & BAM_FREVERSE) ? -state->MLstride[j] : +state->MLstride[j]; } i = j-1; } return n; } /* * Return data at the next modified location. * * bam_mods_at_next_pos does quite a bit of work, so we don't want to * repeatedly call it for every location until we find a mod. Instead * we check how many base types we can consume before the next mod, * and scan through the sequence looking for them. Once we're at that * site, we defer back to bam_mods_at_next_pos for the return values. */ int bam_next_basemod(const bam1_t *b, hts_base_mod_state *state, hts_base_mod *mods, int n_mods, int *pos) { // Look through state->MMcount arrays to see when the next lowest is // per base type; int next[16], freq[16] = {0}, i; memset(next, 0x7f, 16*sizeof(*next)); const int unchecked = state->flags & HTS_MOD_REPORT_UNCHECKED; if (b->core.flag & BAM_FREVERSE) { for (i = 0; i < state->nmods; i++) { if (unchecked && !state->implicit[i]) next[seqi_rc[state->canonical[i]]] = 1; else if (next[seqi_rc[state->canonical[i]]] > state->MMcount[i]) next[seqi_rc[state->canonical[i]]] = state->MMcount[i]; } } else { for (i = 0; i < state->nmods; i++) { if (unchecked && !state->implicit[i]) next[state->canonical[i]] = 0; else if (next[state->canonical[i]] > state->MMcount[i]) next[state->canonical[i]] = state->MMcount[i]; } } // Now step through the sequence counting off base types. for (i = state->seq_pos; i < b->core.l_qseq; i++) { unsigned char bc = bam_seqi(bam_get_seq(b), i); if (next[bc] <= freq[bc] || next[15] <= freq[15]) break; freq[bc]++; if (bc != 15) // N freq[15]++; } *pos = state->seq_pos = i; if (b->core.flag & BAM_FREVERSE) { for (i = 0; i < state->nmods; i++) state->MMcount[i] -= freq[seqi_rc[state->canonical[i]]]; } else { for (i = 0; i < state->nmods; i++) state->MMcount[i] -= freq[state->canonical[i]]; } if (b->core.l_qseq && state->seq_pos >= b->core.l_qseq && !(b->core.flag & BAM_FREVERSE)) { // Spots +ve orientation run-overs. // The -ve orientation is spotted in bam_parse_basemod2 int i; for (i = 0; i < state->nmods; i++) { // Check if any remaining items in MM after hitting the end // of the sequence. if (state->MMcount[i] < 0x7f000000 || (*state->MM[i]!=0 && *state->MM[i]!=';')) { hts_log_warning("MM tag refers to bases beyond sequence length"); return -1; } } return 0; } int r = bam_mods_at_next_pos(b, state, mods, n_mods); return r > 0 ? r : 0; } /* * As per bam_mods_at_next_pos, but at a specific qpos >= the previous qpos. * This can only march forwards along the read, but can do so by more than * one base-pair. * * This makes it useful for calling from pileup iterators where qpos may * start part way through a read for the first occurrence of that record. */ int bam_mods_at_qpos(const bam1_t *b, int qpos, hts_base_mod_state *state, hts_base_mod *mods, int n_mods) { // FIXME: for now this is inefficient in implementation. int r = 0; while (state->seq_pos <= qpos) if ((r = bam_mods_at_next_pos(b, state, mods, n_mods)) < 0) break; return r; } /* * Returns the list of base modification codes provided for this * alignment record as an array of character codes (+ve) or ChEBI numbers * (negative). * * Returns the array, with *ntype filled out with the size. * The array returned should not be freed. * It is a valid pointer until the state is freed using * hts_base_mod_free(). */ int *bam_mods_recorded(hts_base_mod_state *state, int *ntype) { *ntype = state->nmods; return state->type; } /* * Returns data about a specific modification type for the alignment record. * Code is either positive (eg 'm') or negative for ChEBI numbers. * * Return 0 on success or -1 if not found. The strand, implicit and canonical * fields are filled out if passed in as non-NULL pointers. */ int bam_mods_query_type(hts_base_mod_state *state, int code, int *strand, int *implicit, char *canonical) { // Find code entry int i; for (i = 0; i < state->nmods; i++) { if (state->type[i] == code) break; } if (i == state->nmods) return -1; // Return data if (strand) *strand = state->strand[i]; if (implicit) *implicit = state->implicit[i]; if (canonical) *canonical = "?AC?G???T??????N"[state->canonical[i]]; return 0; } /* * Returns data about the ith modification type for the alignment record. * * Return 0 on success or -1 if not found. The strand, implicit and canonical * fields are filled out if passed in as non-NULL pointers. */ int bam_mods_queryi(hts_base_mod_state *state, int i, int *strand, int *implicit, char *canonical) { if (i < 0 || i >= state->nmods) return -1; // Return data if (strand) *strand = state->strand[i]; if (implicit) *implicit = state->implicit[i]; if (canonical) *canonical = "?AC?G???T??????N"[state->canonical[i]]; return 0; } pysam-0.23.0/htslib/simd.c000066400000000000000000000210341475062545500153270ustar00rootroot00000000000000/* simd.c -- SIMD optimised versions of various internal functions. Copyright (C) 2024 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include // These must be defined before the first system include to ensure that legacy // BSD types needed by remain defined when _XOPEN_SOURCE is set. #if defined __APPLE__ #define _DARWIN_C_SOURCE #elif defined __NetBSD__ #define _NETBSD_SOURCE #endif #include "htslib/sam.h" #include "sam_internal.h" #if defined __x86_64__ #include #elif defined __ARM_NEON #include #endif #if defined __arm__ || defined __aarch64__ #if defined __linux__ || defined __FreeBSD__ #include #elif defined __APPLE__ #include #include #elif defined __NetBSD__ #include #include #include #ifdef __aarch64__ #include #else #include #endif #elif defined _WIN32 #include #endif static inline int cpu_supports_neon(void) { #if defined __linux__ && defined __arm__ && defined HWCAP_NEON return (getauxval(AT_HWCAP) & HWCAP_NEON) != 0; #elif defined __linux__ && defined __arm__ && defined HWCAP_ARM_NEON return (getauxval(AT_HWCAP) & HWCAP_ARM_NEON) != 0; #elif defined __linux__ && defined __aarch64__ && defined HWCAP_ASIMD return (getauxval(AT_HWCAP) & HWCAP_ASIMD) != 0; #elif defined __APPLE__ && defined __aarch64__ int32_t ctl; size_t ctlsize = sizeof ctl; if (sysctlbyname("hw.optional.AdvSIMD", &ctl, &ctlsize, NULL, 0) != 0) return 0; if (ctlsize != sizeof ctl) return 0; return ctl; #elif defined __FreeBSD__ && defined __arm__ && defined HWCAP_NEON unsigned long cap; if (elf_aux_info(AT_HWCAP, &cap, sizeof cap) != 0) return 0; return (cap & HWCAP_NEON) != 0; #elif defined __FreeBSD__ && defined __aarch64__ && defined HWCAP_ASIMD unsigned long cap; if (elf_aux_info(AT_HWCAP, &cap, sizeof cap) != 0) return 0; return (cap & HWCAP_ASIMD) != 0; #elif defined __NetBSD__ && defined __arm__ && defined ARM_MVFR0_ASIMD_MASK uint32_t buf[16]; size_t buflen = sizeof buf; if (sysctlbyname("machdep.id_mvfr", buf, &buflen, NULL, 0) != 0) return 0; if (buflen < sizeof(uint32_t)) return 0; return (buf[0] & ARM_MVFR0_ASIMD_MASK) == 0x00000002; #elif defined __NetBSD__ && defined __aarch64__ && defined ID_AA64PFR0_EL1_ADVSIMD struct aarch64_sysctl_cpu_id buf; size_t buflen = sizeof buf; if (sysctlbyname("machdep.cpu0.cpu_id", &buf, &buflen, NULL, 0) != 0) return 0; if (buflen < offsetof(struct aarch64_sysctl_cpu_id, ac_aa64pfr0) + sizeof(uint64_t)) return 0; return (buf.ac_aa64pfr0 & ID_AA64PFR0_EL1_ADVSIMD & 0x00e00000) == 0; #elif defined _WIN32 return IsProcessorFeaturePresent(PF_ARM_V8_INSTRUCTIONS_AVAILABLE) != 0; #else return 0; #endif } #endif #ifdef BUILDING_SIMD_NIBBLE2BASE void (*htslib_nibble2base)(uint8_t *nib, char *seq, int len) = nibble2base_default; #if defined __x86_64__ /* * Convert a nibble encoded BAM sequence to a string of bases. * * Using SSSE3 instructions, 16 codepoints that hold 2 bases each can be * unpacked into 32 indexes from 0-15. Using the pshufb instruction these can * be converted to the IUPAC characters. * It falls back on the nibble2base_default function for the remainder. */ __attribute__((target("ssse3"))) static void nibble2base_ssse3(uint8_t *nib, char *seq, int len) { const char *seq_end_ptr = seq + len; char *seq_cursor = seq; uint8_t *nibble_cursor = nib; const char *seq_vec_end_ptr = seq_end_ptr - (2 * sizeof(__m128i) - 1); __m128i nuc_lookup_vec = _mm_lddqu_si128((__m128i *)seq_nt16_str); /* Nucleotides are encoded 4-bits per nucleotide and stored in 8-bit bytes as follows: |AB|CD|EF|GH|. The 4-bit codes (going from 0-15) can be used together with the pshufb instruction as a lookup table. The most efficient way is to use bitwise AND and shift to create two vectors. One with all the upper codes (|A|C|E|G|) and one with the lower codes (|B|D|F|H|). The lookup can then be performed and the resulting vectors can be interleaved again using the unpack instructions. */ while (seq_cursor < seq_vec_end_ptr) { __m128i encoded = _mm_lddqu_si128((__m128i *)nibble_cursor); __m128i encoded_upper = _mm_srli_epi64(encoded, 4); encoded_upper = _mm_and_si128(encoded_upper, _mm_set1_epi8(15)); __m128i encoded_lower = _mm_and_si128(encoded, _mm_set1_epi8(15)); __m128i nucs_upper = _mm_shuffle_epi8(nuc_lookup_vec, encoded_upper); __m128i nucs_lower = _mm_shuffle_epi8(nuc_lookup_vec, encoded_lower); __m128i first_nucleotides = _mm_unpacklo_epi8(nucs_upper, nucs_lower); __m128i second_nucleotides = _mm_unpackhi_epi8(nucs_upper, nucs_lower); _mm_storeu_si128((__m128i *)seq_cursor, first_nucleotides); _mm_storeu_si128((__m128i *)(seq_cursor + sizeof(__m128i)), second_nucleotides); nibble_cursor += sizeof(__m128i); seq_cursor += 2 * sizeof(__m128i); } nibble2base_default(nibble_cursor, seq_cursor, seq_end_ptr - seq_cursor); } __attribute__((constructor)) static void nibble2base_resolve(void) { if (__builtin_cpu_supports("ssse3")) { htslib_nibble2base = nibble2base_ssse3; } } #elif defined __ARM_NEON static void nibble2base_neon(uint8_t *nib, char *seq0, int len) { uint8x16_t low_nibbles_mask = vdupq_n_u8(0x0f); uint8x16_t nuc_lookup_vec = vld1q_u8((const uint8_t *) seq_nt16_str); #ifndef __aarch64__ uint8x8x2_t nuc_lookup_vec2 = {{ vget_low_u8(nuc_lookup_vec), vget_high_u8(nuc_lookup_vec) }}; #endif uint8_t *seq = (uint8_t *) seq0; int blocks; for (blocks = len / 32; blocks > 0; --blocks) { uint8x16_t encoded = vld1q_u8(nib); nib += 16; /* Translate the high and low nibbles to nucleotide letters separately, then interleave them back together via vzipq for writing. */ uint8x16_t high_nibbles = vshrq_n_u8(encoded, 4); uint8x16_t low_nibbles = vandq_u8(encoded, low_nibbles_mask); #ifdef __aarch64__ uint8x16_t high_nucleotides = vqtbl1q_u8(nuc_lookup_vec, high_nibbles); uint8x16_t low_nucleotides = vqtbl1q_u8(nuc_lookup_vec, low_nibbles); #else uint8x8_t high_low = vtbl2_u8(nuc_lookup_vec2, vget_low_u8(high_nibbles)); uint8x8_t high_high = vtbl2_u8(nuc_lookup_vec2, vget_high_u8(high_nibbles)); uint8x16_t high_nucleotides = vcombine_u8(high_low, high_high); uint8x8_t low_low = vtbl2_u8(nuc_lookup_vec2, vget_low_u8(low_nibbles)); uint8x8_t low_high = vtbl2_u8(nuc_lookup_vec2, vget_high_u8(low_nibbles)); uint8x16_t low_nucleotides = vcombine_u8(low_low, low_high); #endif #ifdef __aarch64__ vst1q_u8_x2(seq, vzipq_u8(high_nucleotides, low_nucleotides)); #else // Avoid vst1q_u8_x2 as GCC erroneously omits it on 32-bit ARM uint8x16x2_t nucleotides = {{ high_nucleotides, low_nucleotides }}; vst2q_u8(seq, nucleotides); #endif seq += 32; } if (len % 32 != 0) nibble2base_default(nib, (char *) seq, len % 32); } static __attribute__((constructor)) void nibble2base_resolve(void) { if (cpu_supports_neon()) htslib_nibble2base = nibble2base_neon; } #endif #endif // BUILDING_SIMD_NIBBLE2BASE // Potentially useful diagnostic, and prevents "empty translation unit" errors const char htslib_simd[] = "SIMD functions present:" #ifdef BUILDING_SIMD_NIBBLE2BASE " nibble2base" #endif "."; pysam-0.23.0/htslib/synced_bcf_reader.c000066400000000000000000001376101475062545500200240ustar00rootroot00000000000000/* synced_bcf_reader.c -- stream through multiple VCF files. Copyright (C) 2012-2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #include #include #include #include "htslib/synced_bcf_reader.h" #include "htslib/kseq.h" #include "htslib/khash_str2int.h" #include "htslib/bgzf.h" #include "htslib/thread_pool.h" #include "bcf_sr_sort.h" #define REQUIRE_IDX_ 1 #define ALLOW_NO_IDX_ 2 // Maximum indexable coordinate of .csi, for default min_shift of 14. // This comes out to about 17 Tbp. Limiting factor is the bin number, // which is a uint32_t in CSI. The highest number of levels compatible // with this is 10 (needs 31 bits). #define MAX_CSI_COOR ((1LL << (14 + 30)) - 1) typedef struct { hts_pos_t start, end; // records are marked for skipping have start>end } region1_t; typedef struct bcf_sr_region_t { region1_t *regs; // regions will sorted and merged, redundant records marked for skipping have start>end int nregs, mregs, creg; // creg: the current active region } region_t; #define BCF_SR_AUX(x) ((aux_t*)((x)->aux)) typedef struct { sr_sort_t sort; int regions_overlap, targets_overlap; } aux_t; static bcf_sr_regions_t *bcf_sr_regions_alloc(void); static int _regions_add(bcf_sr_regions_t *reg, const char *chr, hts_pos_t start, hts_pos_t end); static bcf_sr_regions_t *_regions_init_string(const char *str); static int _regions_match_alleles(bcf_sr_regions_t *reg, int als_idx, bcf1_t *rec); static void _regions_sort_and_merge(bcf_sr_regions_t *reg); static int _bcf_sr_regions_overlap(bcf_sr_regions_t *reg, const char *seq, hts_pos_t start, hts_pos_t end, int missed_reg_handler); static void bcf_sr_seek_start(bcf_srs_t *readers); char *bcf_sr_strerror(int errnum) { switch (errnum) { case open_failed: return strerror(errno); case not_bgzf: return "not compressed with bgzip"; case idx_load_failed: return "could not load index"; case file_type_error: return "unknown file type"; case api_usage_error: return "API usage error"; case header_error: return "could not parse header"; case no_eof: return "no BGZF EOF marker; file may be truncated"; case no_memory: return "Out of memory"; case vcf_parse_error: return "VCF parse error"; case bcf_read_error: return "BCF read error"; case noidx_error: return "merge of unindexed files failed"; default: return ""; } } int bcf_sr_set_opt(bcf_srs_t *readers, bcf_sr_opt_t opt, ...) { va_list args; switch (opt) { case BCF_SR_REQUIRE_IDX: readers->require_index = REQUIRE_IDX_; return 0; case BCF_SR_ALLOW_NO_IDX: readers->require_index = ALLOW_NO_IDX_; return 0; case BCF_SR_PAIR_LOGIC: va_start(args, opt); BCF_SR_AUX(readers)->sort.pair = va_arg(args, int); return 0; case BCF_SR_REGIONS_OVERLAP: va_start(args, opt); BCF_SR_AUX(readers)->regions_overlap = va_arg(args, int); if ( readers->regions ) readers->regions->overlap = BCF_SR_AUX(readers)->regions_overlap; return 0; case BCF_SR_TARGETS_OVERLAP: va_start(args, opt); BCF_SR_AUX(readers)->targets_overlap = va_arg(args, int); if ( readers->targets ) readers->targets->overlap = BCF_SR_AUX(readers)->targets_overlap; return 0; default: break; } return 1; } static int *init_filters(bcf_hdr_t *hdr, const char *filters, int *nfilters) { kstring_t str = {0,0,0}; const char *tmp = filters, *prev = filters; int nout = 0, *out = NULL; while ( 1 ) { if ( *tmp==',' || !*tmp ) { int *otmp = (int*) realloc(out, (nout+1)*sizeof(int)); if (!otmp) goto err; out = otmp; if ( tmp-prev==1 && *prev=='.' ) { out[nout] = -1; nout++; } else { str.l = 0; kputsn(prev, tmp-prev, &str); out[nout] = bcf_hdr_id2int(hdr, BCF_DT_ID, str.s); if ( out[nout]>=0 ) nout++; } if ( !*tmp ) break; prev = tmp+1; } tmp++; } if ( str.m ) free(str.s); *nfilters = nout; return out; err: if (str.m) free(str.s); free(out); return NULL; } int bcf_sr_set_regions(bcf_srs_t *readers, const char *regions, int is_file) { if ( readers->nreaders || readers->regions ) { if ( readers->regions ) bcf_sr_regions_destroy(readers->regions); readers->regions = bcf_sr_regions_init(regions,is_file,0,1,-2); bcf_sr_seek_start(readers); return 0; } readers->regions = bcf_sr_regions_init(regions,is_file,0,1,-2); if ( !readers->regions ) return -1; readers->explicit_regs = 1; readers->require_index = REQUIRE_IDX_; readers->regions->overlap = BCF_SR_AUX(readers)->regions_overlap; return 0; } int bcf_sr_set_targets(bcf_srs_t *readers, const char *targets, int is_file, int alleles) { if ( readers->nreaders || readers->targets ) { hts_log_error("Must call bcf_sr_set_targets() before bcf_sr_add_reader()"); return -1; } if ( targets[0]=='^' ) { readers->targets_exclude = 1; targets++; } readers->targets = bcf_sr_regions_init(targets,is_file,0,1,-2); if ( !readers->targets ) return -1; readers->targets_als = alleles; readers->targets->overlap = BCF_SR_AUX(readers)->targets_overlap; return 0; } int bcf_sr_set_threads(bcf_srs_t *files, int n_threads) { if (!(files->n_threads = n_threads)) return 0; files->p = calloc(1, sizeof(*files->p)); if (!files->p) { files->errnum = no_memory; return -1; } if (!(files->p->pool = hts_tpool_init(n_threads))) return -1; return 0; } void bcf_sr_destroy_threads(bcf_srs_t *files) { if (!files->p) return; if (files->p->pool) hts_tpool_destroy(files->p->pool); free(files->p); } int bcf_sr_add_reader(bcf_srs_t *files, const char *fname) { char fmode[5]; strcpy(fmode, "r"); vcf_open_mode(fmode+1, fname, NULL); htsFile* file_ptr = hts_open(fname, fmode); if ( ! file_ptr ) { files->errnum = open_failed; return 0; } files->has_line = (int*) realloc(files->has_line, sizeof(int)*(files->nreaders+1)); files->has_line[files->nreaders] = 0; files->readers = (bcf_sr_t*) realloc(files->readers, sizeof(bcf_sr_t)*(files->nreaders+1)); bcf_sr_t *reader = &files->readers[files->nreaders++]; memset(reader,0,sizeof(bcf_sr_t)); reader->file = file_ptr; files->errnum = 0; if ( reader->file->format.compression==bgzf ) { BGZF *bgzf = hts_get_bgzfp(reader->file); if ( bgzf && bgzf_check_EOF(bgzf) == 0 ) { files->errnum = no_eof; hts_log_warning("No BGZF EOF marker; file '%s' may be truncated", fname); } if (files->p) bgzf_thread_pool(bgzf, files->p->pool, files->p->qsize); } if ( files->require_index==REQUIRE_IDX_ ) { if ( reader->file->format.format==vcf ) { if ( reader->file->format.compression!=bgzf ) { files->errnum = not_bgzf; return 0; } reader->tbx_idx = tbx_index_load(fname); if ( !reader->tbx_idx ) { files->errnum = idx_load_failed; return 0; } reader->header = bcf_hdr_read(reader->file); } else if ( reader->file->format.format==bcf ) { if ( reader->file->format.compression!=bgzf ) { files->errnum = not_bgzf; return 0; } reader->header = bcf_hdr_read(reader->file); reader->bcf_idx = bcf_index_load(fname); if ( !reader->bcf_idx ) { files->errnum = idx_load_failed; return 0; } } else { files->errnum = file_type_error; return 0; } } else { if ( reader->file->format.format==bcf || reader->file->format.format==vcf ) { reader->header = bcf_hdr_read(reader->file); } else { files->errnum = file_type_error; return 0; } files->streaming = 1; } if ( files->streaming && files->nreaders>1 ) { static int no_index_warned = 0; if ( files->require_index==ALLOW_NO_IDX_ && !no_index_warned ) { hts_log_warning("Using multiple unindexed files may produce errors, make sure chromosomes are in the same order!"); no_index_warned = 1; } if ( files->require_index!=ALLOW_NO_IDX_ ) { files->errnum = api_usage_error; hts_log_error("Must set require_index when the number of readers is greater than one"); return 0; } } if ( files->streaming && files->regions ) { files->errnum = api_usage_error; hts_log_error("Cannot tabix-jump in streaming mode"); return 0; } if ( !reader->header ) { files->errnum = header_error; return 0; } reader->fname = strdup(fname); if ( files->apply_filters ) reader->filter_ids = init_filters(reader->header, files->apply_filters, &reader->nfilter_ids); // Update list of chromosomes if ( !files->explicit_regs && !files->streaming ) { int n = 0, i; const char **names; if ( !files->regions ) { files->regions = bcf_sr_regions_alloc(); if ( !files->regions ) { hts_log_error("Cannot allocate regions data structure"); return 0; } } names = reader->tbx_idx ? tbx_seqnames(reader->tbx_idx, &n) : bcf_hdr_seqnames(reader->header, &n); for (i=0; iregions, names[i], -1, -1); } free(names); _regions_sort_and_merge(files->regions); } if ( files->require_index==ALLOW_NO_IDX_ && files->nreaders > 1 ) { bcf_hdr_t *hdr0 = files->readers[0].header; bcf_hdr_t *hdr1 = reader->header; if ( hdr0->n[BCF_DT_CTG]!=hdr1->n[BCF_DT_CTG] ) { files->errnum = noidx_error; hts_log_error("Different number of sequences in the header, refusing to stream multiple unindexed files"); return 0; } int i; for (i=0; in[BCF_DT_CTG]; i++) { if ( strcmp(bcf_hdr_id2name(hdr0,i),bcf_hdr_id2name(hdr1,i)) ) { files->errnum = noidx_error; hts_log_error("Sequences in the header appear in different order, refusing to stream multiple unindexed files"); return 0; } } } return 1; } bcf_srs_t *bcf_sr_init(void) { bcf_srs_t *files = (bcf_srs_t*) calloc(1,sizeof(bcf_srs_t)); files->aux = (aux_t*) calloc(1,sizeof(aux_t)); bcf_sr_sort_init(&BCF_SR_AUX(files)->sort); bcf_sr_set_opt(files,BCF_SR_REGIONS_OVERLAP,1); bcf_sr_set_opt(files,BCF_SR_TARGETS_OVERLAP,0); return files; } static void bcf_sr_destroy1(bcf_sr_t *reader) { free(reader->fname); if ( reader->tbx_idx ) tbx_destroy(reader->tbx_idx); if ( reader->bcf_idx ) hts_idx_destroy(reader->bcf_idx); bcf_hdr_destroy(reader->header); hts_close(reader->file); if ( reader->itr ) tbx_itr_destroy(reader->itr); int j; for (j=0; jmbuffer; j++) bcf_destroy1(reader->buffer[j]); free(reader->buffer); free(reader->samples); free(reader->filter_ids); } void bcf_sr_destroy(bcf_srs_t *files) { int i; for (i=0; inreaders; i++) bcf_sr_destroy1(&files->readers[i]); free(files->has_line); free(files->readers); for (i=0; in_smpl; i++) free(files->samples[i]); free(files->samples); if (files->targets) bcf_sr_regions_destroy(files->targets); if (files->regions) bcf_sr_regions_destroy(files->regions); if (files->tmps.m) free(files->tmps.s); if (files->n_threads) bcf_sr_destroy_threads(files); bcf_sr_sort_destroy(&BCF_SR_AUX(files)->sort); free(files->aux); free(files); } void bcf_sr_remove_reader(bcf_srs_t *files, int i) { assert( !files->samples ); // not ready for this yet bcf_sr_sort_remove_reader(files, &BCF_SR_AUX(files)->sort, i); bcf_sr_destroy1(&files->readers[i]); if ( i+1 < files->nreaders ) { memmove(&files->readers[i], &files->readers[i+1], (files->nreaders-i-1)*sizeof(bcf_sr_t)); memmove(&files->has_line[i], &files->has_line[i+1], (files->nreaders-i-1)*sizeof(int)); } files->nreaders--; } #if DEBUG_SYNCED_READER void debug_buffer(FILE *fp, bcf_sr_t *reader) { int j; for (j=0; j<=reader->nbuffer; j++) { bcf1_t *line = reader->buffer[j]; fprintf(fp,"\t%p\t%s%s\t%s:%"PRIhts_pos"\t%s ", (void*)line,reader->fname,j==0?"*":" ",reader->header->id[BCF_DT_CTG][line->rid].key,line->pos+1,line->n_allele?line->d.allele[0]:""); int k; for (k=1; kn_allele; k++) fprintf(fp," %s", line->d.allele[k]); fprintf(fp,"\n"); } } void debug_buffers(FILE *fp, bcf_srs_t *files) { int i; for (i=0; inreaders; i++) { fprintf(fp, "has_line: %d\t%s\n", bcf_sr_has_line(files,i),files->readers[i].fname); debug_buffer(fp, &files->readers[i]); } fprintf(fp,"\n"); } #endif static inline int has_filter(bcf_sr_t *reader, bcf1_t *line) { int i, j; if ( !line->d.n_flt ) { for (j=0; jnfilter_ids; j++) if ( reader->filter_ids[j]<0 ) return 1; return 0; } for (i=0; id.n_flt; i++) { for (j=0; jnfilter_ids; j++) if ( line->d.flt[i]==reader->filter_ids[j] ) return 1; } return 0; } static int _reader_seek(bcf_sr_t *reader, const char *seq, hts_pos_t start, hts_pos_t end) { if ( end>=MAX_CSI_COOR ) { hts_log_error("The coordinate is out of csi index limit: %"PRIhts_pos, end+1); exit(1); } if ( reader->itr ) { hts_itr_destroy(reader->itr); reader->itr = NULL; } reader->nbuffer = 0; if ( reader->tbx_idx ) { int tid = tbx_name2id(reader->tbx_idx, seq); if ( tid==-1 ) return -1; // the sequence not present in this file reader->itr = tbx_itr_queryi(reader->tbx_idx,tid,start,end+1); } else { int tid = bcf_hdr_name2id(reader->header, seq); if ( tid==-1 ) return -1; // the sequence not present in this file reader->itr = bcf_itr_queryi(reader->bcf_idx,tid,start,end+1); } if (!reader->itr) { hts_log_error("Could not seek: %s:%"PRIhts_pos"-%"PRIhts_pos, seq, start + 1, end + 1); abort(); } return 0; } /* * _readers_next_region() - jumps to next region if necessary * Returns 0 on success or -1 when there are no more regions left */ static int _readers_next_region(bcf_srs_t *files) { // Need to open new chromosome? Check number of lines in all readers' buffers int i, eos = 0; for (i=0; inreaders; i++) if ( !files->readers[i].itr && !files->readers[i].nbuffer ) eos++; if ( eos!=files->nreaders ) { // Some of the readers still has buffered lines return 0; } // No lines in the buffer, need to open new region or quit. int prev_iseq = files->regions->iseq; hts_pos_t prev_end = files->regions->end; if ( bcf_sr_regions_next(files->regions)<0 ) return -1; files->regions->prev_end = prev_iseq==files->regions->iseq ? prev_end : -1; for (i=0; inreaders; i++) _reader_seek(&files->readers[i],files->regions->seq_names[files->regions->iseq],files->regions->start,files->regions->end); return 0; } static void _set_variant_boundaries(bcf1_t *rec, hts_pos_t *beg, hts_pos_t *end) { hts_pos_t off; if ( rec->n_allele ) { off = rec->rlen; bcf_unpack(rec, BCF_UN_STR); int i; for (i=1; in_allele; i++) { // Make symbolic alleles start at POS, although this is not strictly true for // , where POS should be the position BEFORE the deletion/insertion. // However, since arbitrary symbolic alleles can be defined by the user, we // will simplify the interpretation of --targets-overlap and --region-overlap. int j = 0; char *ref = rec->d.allele[0]; char *alt = rec->d.allele[i]; while ( ref[j] && alt[j] && ref[j]==alt[j] ) j++; if ( off > j ) off = j; if ( !off ) break; } } else off = 0; *beg = rec->pos + off; *end = rec->pos + rec->rlen - 1; } /* * _reader_fill_buffer() - buffers all records with the same coordinate */ static int _reader_fill_buffer(bcf_srs_t *files, bcf_sr_t *reader) { // Return if the buffer is full: the coordinate of the last buffered record differs if ( reader->nbuffer && reader->buffer[reader->nbuffer]->pos != reader->buffer[1]->pos ) return 0; // No iterator (sequence not present in this file) and not streaming if ( !reader->itr && !files->streaming ) return 0; // Fill the buffer with records starting at the same position int i, ret = 0; while (1) { if ( reader->nbuffer+1 >= reader->mbuffer ) { // Increase buffer size reader->mbuffer += 8; reader->buffer = (bcf1_t**) realloc(reader->buffer, sizeof(bcf1_t*)*reader->mbuffer); for (i=8; i>0; i--) // initialize { reader->buffer[reader->mbuffer-i] = bcf_init1(); reader->buffer[reader->mbuffer-i]->max_unpack = files->max_unpack; reader->buffer[reader->mbuffer-i]->pos = -1; // for rare cases when VCF starts from 1 } } if ( files->streaming ) { if ( reader->file->format.format==vcf ) { ret = hts_getline(reader->file, KS_SEP_LINE, &files->tmps); if ( ret < -1 ) files->errnum = bcf_read_error; if ( ret < 0 ) break; // no more lines or an error ret = vcf_parse1(&files->tmps, reader->header, reader->buffer[reader->nbuffer+1]); if ( ret<0 ) { files->errnum = vcf_parse_error; break; } } else if ( reader->file->format.format==bcf ) { ret = bcf_read1(reader->file, reader->header, reader->buffer[reader->nbuffer+1]); if ( ret < -1 ) files->errnum = bcf_read_error; if ( ret < 0 ) break; // no more lines or an error } else { hts_log_error("Fixme: not ready for this"); exit(1); } } else if ( reader->tbx_idx ) { ret = tbx_itr_next(reader->file, reader->tbx_idx, reader->itr, &files->tmps); if ( ret < -1 ) files->errnum = bcf_read_error; if ( ret < 0 ) break; // no more lines or an error ret = vcf_parse1(&files->tmps, reader->header, reader->buffer[reader->nbuffer+1]); if ( ret<0 ) { files->errnum = vcf_parse_error; break; } } else { ret = bcf_itr_next(reader->file, reader->itr, reader->buffer[reader->nbuffer+1]); if ( ret < -1 ) files->errnum = bcf_read_error; if ( ret < 0 ) break; // no more lines or an error bcf_subset_format(reader->header,reader->buffer[reader->nbuffer+1]); } // Prevent creation of duplicates from records overlapping multiple regions // and recognize true variant overlaps vs record overlaps (e.g. TA>T vs A>-) if ( files->regions ) { hts_pos_t beg, end; if ( BCF_SR_AUX(files)->regions_overlap==0 ) beg = end = reader->buffer[reader->nbuffer+1]->pos; else if ( BCF_SR_AUX(files)->regions_overlap==1 ) { beg = reader->buffer[reader->nbuffer+1]->pos; end = reader->buffer[reader->nbuffer+1]->pos + reader->buffer[reader->nbuffer+1]->rlen - 1; } else if ( BCF_SR_AUX(files)->regions_overlap==2 ) _set_variant_boundaries(reader->buffer[reader->nbuffer+1], &beg,&end); else { hts_log_error("This should never happen, just to keep clang compiler happy: %d",BCF_SR_AUX(files)->targets_overlap); exit(1); } if ( beg <= files->regions->prev_end || end < files->regions->start || beg > files->regions->end ) continue; } // apply filter if ( !reader->nfilter_ids ) bcf_unpack(reader->buffer[reader->nbuffer+1], BCF_UN_STR); else { bcf_unpack(reader->buffer[reader->nbuffer+1], BCF_UN_STR|BCF_UN_FLT); if ( !has_filter(reader, reader->buffer[reader->nbuffer+1]) ) continue; } reader->nbuffer++; if ( reader->buffer[reader->nbuffer]->rid != reader->buffer[1]->rid ) break; if ( reader->buffer[reader->nbuffer]->pos != reader->buffer[1]->pos ) break; // the buffer is full } if ( ret<0 ) { // done for this region tbx_itr_destroy(reader->itr); reader->itr = NULL; } if ( files->require_index==ALLOW_NO_IDX_ && reader->buffer[reader->nbuffer]->rid < reader->buffer[1]->rid ) { hts_log_error("Sequences out of order, cannot stream multiple unindexed files: %s", reader->fname); exit(1); } return 0; // FIXME: Check for more errs in this function } /* * _readers_shift_buffer() - removes the first line */ static void _reader_shift_buffer(bcf_sr_t *reader) { if ( !reader->nbuffer ) return; int i; bcf1_t *tmp = reader->buffer[1]; for (i=2; i<=reader->nbuffer; i++) reader->buffer[i-1] = reader->buffer[i]; if ( reader->nbuffer > 1 ) reader->buffer[reader->nbuffer] = tmp; reader->nbuffer--; } static int next_line(bcf_srs_t *files) { const char *chr = NULL; hts_pos_t min_pos = HTS_POS_MAX; // Loop until next suitable line is found or all readers have finished while ( 1 ) { // Get all readers ready for the next region. if ( files->regions && _readers_next_region(files)<0 ) break; // Fill buffers and find the minimum chromosome int i, min_rid = INT32_MAX; for (i=0; inreaders; i++) { _reader_fill_buffer(files, &files->readers[i]); if ( files->require_index==ALLOW_NO_IDX_ ) { if ( !files->readers[i].nbuffer ) continue; if ( min_rid > files->readers[i].buffer[1]->rid ) min_rid = files->readers[i].buffer[1]->rid; } } for (i=0; inreaders; i++) { if ( !files->readers[i].nbuffer ) continue; if ( files->require_index==ALLOW_NO_IDX_ && min_rid != files->readers[i].buffer[1]->rid ) continue; // Update the minimum coordinate if ( min_pos > files->readers[i].buffer[1]->pos ) { min_pos = files->readers[i].buffer[1]->pos; chr = bcf_seqname(files->readers[i].header, files->readers[i].buffer[1]); assert(chr); bcf_sr_sort_set_active(&BCF_SR_AUX(files)->sort, i); } else if ( min_pos==files->readers[i].buffer[1]->pos ) bcf_sr_sort_add_active(&BCF_SR_AUX(files)->sort, i); } if ( min_pos==HTS_POS_MAX ) { if ( !files->regions ) break; continue; } // Skip this position if not present in targets if ( files->targets ) { int match = 0; for (i=0; inreaders; i++) { if ( !files->readers[i].nbuffer || files->readers[i].buffer[1]->pos!=min_pos ) continue; hts_pos_t beg, end; if ( BCF_SR_AUX(files)->targets_overlap==0 ) beg = end = min_pos; else if ( BCF_SR_AUX(files)->targets_overlap==1 ) { beg = min_pos; end = min_pos + files->readers[i].buffer[1]->rlen - 1; } else if ( BCF_SR_AUX(files)->targets_overlap==2 ) _set_variant_boundaries(files->readers[i].buffer[1], &beg,&end); else { hts_log_error("This should never happen, just to keep clang compiler happy: %d",BCF_SR_AUX(files)->targets_overlap); exit(1); } int overlap = bcf_sr_regions_overlap(files->targets, chr, beg, end)==0 ? 1 : 0; if ( (!files->targets_exclude && !overlap) || (files->targets_exclude && overlap) ) _reader_shift_buffer(&files->readers[i]); else match = 1; } if ( !match ) { min_pos = HTS_POS_MAX; chr = NULL; continue; } } break; // done: chr and min_pos are set } if ( !chr ) return 0; return bcf_sr_sort_next(files, &BCF_SR_AUX(files)->sort, chr, min_pos); } int bcf_sr_next_line(bcf_srs_t *files) { if ( !files->targets_als ) return next_line(files); while (1) { int i, ret = next_line(files); if ( !ret ) return ret; for (i=0; inreaders; i++) if ( files->has_line[i] ) break; if ( _regions_match_alleles(files->targets, files->targets_als-1, files->readers[i].buffer[0]) ) return ret; // Check if there are more duplicate lines in the buffers. If not, return this line as if it // matched the targets, even if there is a type mismatch for (i=0; inreaders; i++) { if ( !files->has_line[i] ) continue; if ( files->readers[i].nbuffer==0 || files->readers[i].buffer[1]->pos!=files->readers[i].buffer[0]->pos ) continue; break; } if ( i==files->nreaders ) return ret; // no more lines left, output even if target alleles are not of the same type } } static void bcf_sr_seek_start(bcf_srs_t *readers) { bcf_sr_regions_t *reg = readers->regions; int i; for (i=0; inseqs; i++) reg->regs[i].creg = -1; reg->iseq = 0; reg->start = -1; reg->end = -1; reg->prev_seq = -1; reg->prev_start = -1; reg->prev_end = -1; } int bcf_sr_seek(bcf_srs_t *readers, const char *seq, hts_pos_t pos) { if ( !readers->regions ) return 0; bcf_sr_sort_reset(&BCF_SR_AUX(readers)->sort); if ( !seq && !pos ) { // seek to start bcf_sr_seek_start(readers); return 0; } int i, nret = 0; // Need to position both the readers and the regions. The latter is a bit of a mess // because we can have in memory or external regions. The safe way is: // - reset all regions as if they were not read from at all (bcf_sr_seek_start) // - find the requested iseq (stored in the seq_hash) // - position regions to the requested position (bcf_sr_regions_overlap) bcf_sr_seek_start(readers); if ( khash_str2int_get(readers->regions->seq_hash, seq, &i)>=0 ) readers->regions->iseq = i; _bcf_sr_regions_overlap(readers->regions, seq, pos, pos, 0); for (i=0; inreaders; i++) { nret += _reader_seek(&readers->readers[i],seq,pos,MAX_CSI_COOR-1); } return nret; } int bcf_sr_set_samples(bcf_srs_t *files, const char *fname, int is_file) { int i, j, nsmpl, free_smpl = 0; char **smpl = NULL; void *exclude = (fname[0]=='^') ? khash_str2int_init() : NULL; if ( exclude || strcmp("-",fname) ) // "-" stands for all samples { smpl = hts_readlist(fname, is_file, &nsmpl); if ( !smpl ) { hts_log_error("Could not read the file: \"%s\"", fname); return 0; } if ( exclude ) { for (i=0; ireaders[0].header->samples; // intersection of all samples nsmpl = bcf_hdr_nsamples(files->readers[0].header); } files->samples = NULL; files->n_smpl = 0; for (i=0; inreaders; j++) { if ( bcf_hdr_id2int(files->readers[j].header, BCF_DT_SAMPLE, smpl[i])<0 ) break; n_isec++; } if ( n_isec!=files->nreaders ) { hts_log_warning("The sample \"%s\" was not found in %s, skipping", smpl[i], files->readers[n_isec].fname); continue; } files->samples = (char**) realloc(files->samples, (files->n_smpl+1)*sizeof(const char*)); files->samples[files->n_smpl++] = strdup(smpl[i]); } if ( exclude ) khash_str2int_destroy(exclude); if ( free_smpl ) { for (i=0; in_smpl ) { if ( files->nreaders>1 ) hts_log_warning("No samples in common"); return 0; } for (i=0; inreaders; i++) { bcf_sr_t *reader = &files->readers[i]; reader->samples = (int*) malloc(sizeof(int)*files->n_smpl); reader->n_smpl = files->n_smpl; for (j=0; jn_smpl; j++) reader->samples[j] = bcf_hdr_id2int(reader->header, BCF_DT_SAMPLE, files->samples[j]); } return 1; } // Allocate a new region list structure. static bcf_sr_regions_t *bcf_sr_regions_alloc(void) { bcf_sr_regions_t *reg = (bcf_sr_regions_t *) calloc(1, sizeof(bcf_sr_regions_t)); if ( !reg ) return NULL; reg->start = reg->end = -1; reg->prev_start = reg->prev_end = reg->prev_seq = -1; return reg; } // Add a new region into a list. On input the coordinates are 1-based, inclusive, then stored 0-based, // inclusive. Sorting and merging step needed afterwards: qsort(..,cmp_regions) and merge_regions(). static int _regions_add(bcf_sr_regions_t *reg, const char *chr, hts_pos_t start, hts_pos_t end) { if ( start==-1 && end==-1 ) { start = 0; end = MAX_CSI_COOR-1; } else { start--; end--; // store 0-based coordinates } if ( !reg->seq_hash ) reg->seq_hash = khash_str2int_init(); int iseq; if ( khash_str2int_get(reg->seq_hash, chr, &iseq)<0 ) { // the chromosome block does not exist iseq = reg->nseqs++; reg->seq_names = (char**) realloc(reg->seq_names,sizeof(char*)*reg->nseqs); reg->regs = (region_t*) realloc(reg->regs,sizeof(region_t)*reg->nseqs); memset(®->regs[reg->nseqs-1],0,sizeof(region_t)); reg->seq_names[iseq] = strdup(chr); reg->regs[iseq].creg = -1; khash_str2int_set(reg->seq_hash,reg->seq_names[iseq],iseq); } region_t *creg = ®->regs[iseq]; hts_expand(region1_t,creg->nregs+1,creg->mregs,creg->regs); creg->regs[creg->nregs].start = start; creg->regs[creg->nregs].end = end; creg->nregs++; return 0; // FIXME: check for errs in this function } static int regions_cmp(const void *aptr, const void *bptr) { region1_t *a = (region1_t*)aptr; region1_t *b = (region1_t*)bptr; if ( a->start < b->start ) return -1; if ( a->start > b->start ) return 1; if ( a->end < b->end ) return -1; if ( a->end > b->end ) return 1; return 0; } static void regions_merge(region_t *reg) { int i = 0, j; while ( inregs ) { j = i + 1; while ( jnregs && reg->regs[i].end >= reg->regs[j].start ) { if ( reg->regs[i].end < reg->regs[j].end ) reg->regs[i].end = reg->regs[j].end; reg->regs[j].start = 1; reg->regs[j].end = 0; // if beg>end, this region marked for skipping j++; } i = j; } } void _regions_sort_and_merge(bcf_sr_regions_t *reg) { if ( !reg ) return; int i; for (i=0; inseqs; i++) { qsort(reg->regs[i].regs, reg->regs[i].nregs, sizeof(*reg->regs[i].regs), regions_cmp); regions_merge(®->regs[i]); } } // File name or a list of genomic locations. If file name, NULL is returned. // Recognises regions in the form chr, chr:pos, chr:beg-end, chr:beg-, {weird-chr-name}:pos. // Cannot use hts_parse_region() as that requires the header and if header is not present, // wouldn't learn the chromosome name. static bcf_sr_regions_t *_regions_init_string(const char *str) { bcf_sr_regions_t *reg = bcf_sr_regions_alloc(); if ( !reg ) return NULL; kstring_t tmp = {0,0,0}; const char *sp = str, *ep = str; hts_pos_t from, to; while ( 1 ) { tmp.l = 0; if ( *ep=='{' ) { while ( *ep && *ep!='}' ) ep++; if ( !*ep ) { hts_log_error("Could not parse the region, mismatching braces in: \"%s\"", str); goto exit_nicely; } ep++; kputsn(sp+1,ep-sp-2,&tmp); } else { while ( *ep && *ep!=',' && *ep!=':' ) ep++; kputsn(sp,ep-sp,&tmp); } if ( *ep==':' ) { sp = ep+1; from = hts_parse_decimal(sp,(char**)&ep,0); if ( sp==ep ) { hts_log_error("Could not parse the region(s): %s", str); goto exit_nicely; } if ( !*ep || *ep==',' ) { _regions_add(reg, tmp.s, from, from); sp = ep; continue; } if ( *ep!='-' ) { hts_log_error("Could not parse the region(s): %s", str); goto exit_nicely; } ep++; sp = ep; to = hts_parse_decimal(sp,(char**)&ep,0); if ( *ep && *ep!=',' ) { hts_log_error("Could not parse the region(s): %s", str); goto exit_nicely; } if ( sp==ep ) to = MAX_CSI_COOR-1; _regions_add(reg, tmp.s, from, to); if ( !*ep ) break; sp = ep; } else if ( !*ep || *ep==',' ) { if ( tmp.l ) _regions_add(reg, tmp.s, -1, -1); if ( !*ep ) break; sp = ++ep; } else { hts_log_error("Could not parse the region(s): %s", str); goto exit_nicely; } } free(tmp.s); return reg; exit_nicely: bcf_sr_regions_destroy(reg); free(tmp.s); return NULL; } // ichr,ifrom,ito are 0-based; // returns -1 on error, 0 if the line is a comment line, 1 on success static int _regions_parse_line(char *line, int ichr, int ifrom, int ito, char **chr, char **chr_end, hts_pos_t *from, hts_pos_t *to) { if (ifrom < 0 || ito < 0) return -1; *chr_end = NULL; if ( line[0]=='#' ) return 0; int k,l; // index of the start and end column of the tab-delimited file if ( ifrom <= ito ) k = ifrom, l = ito; else l = ifrom, k = ito; int i; char *se = line, *ss = NULL; // start and end char *tmp; for (i=0; i<=k && *se; i++) { ss = i==0 ? se++ : ++se; while (*se && *se!='\t') se++; } if ( i<=k ) return -1; if ( k==l ) { *from = *to = hts_parse_decimal(ss, &tmp, 0); if ( tmp==ss || (*tmp && *tmp!='\t') ) return -1; } else { if ( k==ifrom ) *from = hts_parse_decimal(ss, &tmp, 0); else *to = hts_parse_decimal(ss, &tmp, 0); if ( ss==tmp || (*tmp && *tmp!='\t') ) return -1; for (i=k; i0 ) ss = ++se; while (*se && *se!='\t') se++; } if ( i<=ichr ) return -1; *chr_end = se; *chr = ss; return 1; } bcf_sr_regions_t *bcf_sr_regions_init(const char *regions, int is_file, int ichr, int ifrom, int ito) { bcf_sr_regions_t *reg; if ( !is_file ) { reg = _regions_init_string(regions); _regions_sort_and_merge(reg); return reg; } reg = bcf_sr_regions_alloc(); if ( !reg ) return NULL; reg->file = hts_open(regions, "rb"); if ( !reg->file ) { hts_log_error("Could not open file: %s", regions); free(reg); return NULL; } reg->tbx = tbx_index_load3(regions, NULL, HTS_IDX_SAVE_REMOTE|HTS_IDX_SILENT_FAIL); if ( !reg->tbx ) { size_t iline = 0; int len = strlen(regions); int is_bed = strcasecmp(".bed",regions+len-4) ? 0 : 1; if ( !is_bed && !strcasecmp(".bed.gz",regions+len-7) ) is_bed = 1; if ( reg->file->format.format==vcf ) ito = 1; // read the whole file, tabix index is not present while ( hts_getline(reg->file, KS_SEP_LINE, ®->line) > 0 ) { iline++; char *chr, *chr_end; hts_pos_t from, to; int ret; ret = _regions_parse_line(reg->line.s, ichr,ifrom,abs(ito), &chr,&chr_end,&from,&to); if ( ret < 0 ) { if ( ito<0 ) ret = _regions_parse_line(reg->line.s, ichr,ifrom,ifrom, &chr,&chr_end,&from,&to); if ( ret<0 ) { hts_log_error("Could not parse %zu-th line of file %s, using the columns %d,%d[,%d]", iline, regions,ichr+1,ifrom+1,ito+1); hts_close(reg->file); reg->file = NULL; free(reg); return NULL; } ito = ifrom; } else if ( ito<0 ) ito = abs(ito); if ( !ret ) continue; if ( is_bed ) from++; *chr_end = 0; _regions_add(reg, chr, from, to); *chr_end = '\t'; } hts_close(reg->file); reg->file = NULL; if ( !reg->nseqs ) { free(reg); return NULL; } _regions_sort_and_merge(reg); return reg; } reg->seq_names = (char**) tbx_seqnames(reg->tbx, ®->nseqs); if ( !reg->seq_hash ) reg->seq_hash = khash_str2int_init(); int i; for (i=0; inseqs; i++) { khash_str2int_set(reg->seq_hash,reg->seq_names[i],i); } reg->fname = strdup(regions); reg->is_bin = 1; return reg; } void bcf_sr_regions_destroy(bcf_sr_regions_t *reg) { int i; free(reg->fname); if ( reg->itr ) tbx_itr_destroy(reg->itr); if ( reg->tbx ) tbx_destroy(reg->tbx); if ( reg->file ) hts_close(reg->file); if ( reg->als ) free(reg->als); if ( reg->als_str.s ) free(reg->als_str.s); free(reg->line.s); if ( reg->regs ) { // free only in-memory names, tbx names are const for (i=0; inseqs; i++) { free(reg->seq_names[i]); free(reg->regs[i].regs); } } free(reg->regs); free(reg->seq_names); khash_str2int_destroy(reg->seq_hash); free(reg); } int bcf_sr_regions_seek(bcf_sr_regions_t *reg, const char *seq) { reg->iseq = reg->start = reg->end = -1; if ( khash_str2int_get(reg->seq_hash, seq, ®->iseq) < 0 ) return -1; // sequence seq not in regions // using in-memory regions if ( reg->regs ) { reg->regs[reg->iseq].creg = -1; return 0; } // reading regions from tabix if ( reg->itr ) tbx_itr_destroy(reg->itr); reg->itr = tbx_itr_querys(reg->tbx, seq); if ( reg->itr ) return 0; return -1; } // Returns 0 on success, -1 when done static int advance_creg(region_t *reg) { int i = reg->creg + 1; while ( inregs && reg->regs[i].start > reg->regs[i].end ) i++; // regions with start>end are marked to skip by merge_regions() reg->creg = i; if ( i>=reg->nregs ) return -1; return 0; } int bcf_sr_regions_next(bcf_sr_regions_t *reg) { if ( reg->iseq<0 ) return -1; reg->start = reg->end = -1; reg->nals = 0; // using in-memory regions if ( reg->regs ) { while ( reg->iseq < reg->nseqs ) { if ( advance_creg(®->regs[reg->iseq])==0 ) break; // a valid record was found reg->iseq++; } if ( reg->iseq >= reg->nseqs ) { reg->iseq = -1; return -1; } // no more regions left region1_t *creg = ®->regs[reg->iseq].regs[reg->regs[reg->iseq].creg]; reg->start = creg->start; reg->end = creg->end; return 0; } // reading from tabix char *chr, *chr_end; int ichr = 0, ifrom = 1, ito = 2, is_bed = 0; hts_pos_t from, to; if ( reg->tbx ) { ichr = reg->tbx->conf.sc-1; ifrom = reg->tbx->conf.bc-1; ito = reg->tbx->conf.ec-1; if ( ito<0 ) ito = ifrom; is_bed = reg->tbx->conf.preset==TBX_UCSC ? 1 : 0; } int ret = 0; while ( !ret ) { if ( reg->itr ) { // tabix index present, reading a chromosome block ret = tbx_itr_next(reg->file, reg->tbx, reg->itr, ®->line); if ( ret<0 ) { reg->iseq = -1; return -1; } } else { if ( reg->is_bin ) { // Waited for seek which never came. Reopen in text mode and stream // through the regions, otherwise hts_getline would fail hts_close(reg->file); reg->file = hts_open(reg->fname, "r"); if ( !reg->file ) { hts_log_error("Could not open file: %s", reg->fname); reg->file = NULL; bcf_sr_regions_destroy(reg); return -1; } reg->is_bin = 0; } // tabix index absent, reading the whole file ret = hts_getline(reg->file, KS_SEP_LINE, ®->line); if ( ret<0 ) { reg->iseq = -1; return -1; } } ret = _regions_parse_line(reg->line.s, ichr,ifrom,ito, &chr,&chr_end,&from,&to); if ( ret<0 ) { hts_log_error("Could not parse the file %s, using the columns %d,%d,%d", reg->fname,ichr+1,ifrom+1,ito+1); return -1; } } if ( is_bed ) from++; *chr_end = 0; if ( khash_str2int_get(reg->seq_hash, chr, ®->iseq)<0 ) { hts_log_error("Broken tabix index? The sequence \"%s\" not in dictionary [%s]", chr, reg->line.s); exit(1); } *chr_end = '\t'; reg->start = from - 1; reg->end = to - 1; return 0; } static int _regions_match_alleles(bcf_sr_regions_t *reg, int als_idx, bcf1_t *rec) { if ( reg->regs ) { // payload is not supported for in-memory regions, switch to regidx instead in future hts_log_error("Compressed and indexed targets file is required"); exit(1); } int i = 0, max_len = 0; if ( !reg->nals ) { char *ss = reg->line.s; while ( inals = 1; while ( *se && *se!='\t' ) { if ( *se==',' ) reg->nals++; se++; } ks_resize(®->als_str, se-ss+1+reg->nals); reg->als_str.l = 0; hts_expand(char*,reg->nals,reg->mals,reg->als); reg->nals = 0; se = ss; while ( *(++se) ) { if ( *se=='\t' ) break; if ( *se!=',' ) continue; reg->als[reg->nals] = ®->als_str.s[reg->als_str.l]; kputsn(ss,se-ss,®->als_str); if ( ®->als_str.s[reg->als_str.l] - reg->als[reg->nals] > max_len ) max_len = ®->als_str.s[reg->als_str.l] - reg->als[reg->nals]; reg->als_str.l++; reg->nals++; ss = ++se; } reg->als[reg->nals] = ®->als_str.s[reg->als_str.l]; kputsn(ss,se-ss,®->als_str); if ( ®->als_str.s[reg->als_str.l] - reg->als[reg->nals] > max_len ) max_len = ®->als_str.s[reg->als_str.l] - reg->als[reg->nals]; reg->nals++; reg->als_type = max_len > 1 ? VCF_INDEL : VCF_SNP; // this is a simplified check, see vcf.c:bcf_set_variant_types } int type = bcf_get_variant_types(rec); if ( reg->als_type & VCF_INDEL ) return type & VCF_INDEL ? 1 : 0; return !(type & VCF_INDEL) ? 1 : 0; } int bcf_sr_regions_overlap(bcf_sr_regions_t *reg, const char *seq, hts_pos_t start, hts_pos_t end) { return _bcf_sr_regions_overlap(reg,seq,start,end,1); } static int _bcf_sr_regions_overlap(bcf_sr_regions_t *reg, const char *seq, hts_pos_t start, hts_pos_t end, int missed_reg_handler) { int iseq; if ( khash_str2int_get(reg->seq_hash, seq, &iseq)<0 ) return -1; // no such sequence if ( missed_reg_handler && !reg->missed_reg_handler ) missed_reg_handler = 0; if ( reg->prev_seq==-1 || iseq!=reg->prev_seq || reg->prev_start > start ) // new chromosome or after a seek { // flush regions left on previous chromosome if ( missed_reg_handler && reg->prev_seq!=-1 && reg->iseq!=-1 ) bcf_sr_regions_flush(reg); bcf_sr_regions_seek(reg, seq); reg->start = reg->end = -1; } if ( reg->prev_seq==iseq && reg->iseq!=iseq ) return -2; // no more regions on this chromosome reg->prev_seq = reg->iseq; reg->prev_start = start; while ( iseq==reg->iseq && reg->end < start ) { if ( bcf_sr_regions_next(reg) < 0 ) return -2; // no more regions left if ( reg->iseq != iseq ) return -1; // does not overlap any regions if ( missed_reg_handler && reg->end < start ) reg->missed_reg_handler(reg, reg->missed_reg_data); } if ( reg->start <= end ) return 0; // region overlap return -1; // no overlap } int bcf_sr_regions_flush(bcf_sr_regions_t *reg) { if ( !reg->missed_reg_handler || reg->prev_seq==-1 ) return 0; while ( !bcf_sr_regions_next(reg) ) reg->missed_reg_handler(reg, reg->missed_reg_data); return 0; // FIXME: check for errs in this function } pysam-0.23.0/htslib/tbx.c000066400000000000000000000421701475062545500151740ustar00rootroot00000000000000/* tbx.c -- tabix API functions. Copyright (C) 2009, 2010, 2012-2015, 2017-2020, 2022-2023 Genome Research Ltd. Copyright (C) 2010-2012 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include "htslib/tbx.h" #include "htslib/bgzf.h" #include "htslib/hts_endian.h" #include "hts_internal.h" #include "htslib/khash.h" KHASH_DECLARE(s2i, kh_cstr_t, int64_t) HTSLIB_EXPORT const tbx_conf_t tbx_conf_gff = { 0, 1, 4, 5, '#', 0 }; HTSLIB_EXPORT const tbx_conf_t tbx_conf_bed = { TBX_UCSC, 1, 2, 3, '#', 0 }; HTSLIB_EXPORT const tbx_conf_t tbx_conf_psltbl = { TBX_UCSC, 15, 17, 18, '#', 0 }; HTSLIB_EXPORT const tbx_conf_t tbx_conf_sam = { TBX_SAM, 3, 4, 0, '@', 0 }; HTSLIB_EXPORT const tbx_conf_t tbx_conf_vcf = { TBX_VCF, 1, 2, 0, '#', 0 }; const tbx_conf_t tbx_conf_gaf = { TBX_GAF, 1, 6, 0, '#', 0 }; typedef struct { int64_t beg, end; char *ss, *se; int tid; } tbx_intv_t; static inline int get_tid(tbx_t *tbx, const char *ss, int is_add) { khint_t k; khash_t(s2i) *d; if ((tbx->conf.preset&0xffff) == TBX_GAF) return(0); if (tbx->dict == 0) tbx->dict = kh_init(s2i); if (!tbx->dict) return -1; // Out of memory d = (khash_t(s2i)*)tbx->dict; if (is_add) { int absent; k = kh_put(s2i, d, ss, &absent); if (absent < 0) { return -1; // Out of memory } else if (absent) { char *ss_dup = strdup(ss); if (ss_dup) { kh_key(d, k) = ss_dup; kh_val(d, k) = kh_size(d) - 1; } else { kh_del(s2i, d, k); return -1; // Out of memory } } } else k = kh_get(s2i, d, ss); return k == kh_end(d)? -1 : kh_val(d, k); } int tbx_name2id(tbx_t *tbx, const char *ss) { return get_tid(tbx, ss, 0); } int tbx_parse1(const tbx_conf_t *conf, size_t len, char *line, tbx_intv_t *intv) { size_t i, b = 0; int id = 1; char *s; intv->ss = intv->se = 0; intv->beg = intv->end = -1; for (i = 0; i <= len; ++i) { if (line[i] == '\t' || line[i] == 0) { if (id == conf->sc) { intv->ss = line + b; intv->se = line + i; } else if (id == conf->bc) { // here ->beg is 0-based. if ((conf->preset&0xffff) == TBX_GAF){ // if gaf find the smallest and largest node id char *t; int64_t nodeid = -1; for (s = line + b + 1; s < line + i;) { nodeid = strtoll(s, &t, 0); if(intv->beg == -1){ intv->beg = intv->end = nodeid; } else { if(nodeid < intv->beg){ intv->beg = nodeid; } if(nodeid > intv->end){ intv->end = nodeid; } } s = t + 1; } } else { intv->beg = strtoll(line + b, &s, 0); if (conf->bc <= conf->ec) // don't overwrite an already set end point intv->end = intv->beg; if ( s==line+b ) return -1; // expected int if (!(conf->preset&TBX_UCSC)) --intv->beg; else if (conf->bc <= conf->ec) ++intv->end; if (intv->beg < 0) { hts_log_warning("Coordinate <= 0 detected. " "Did you forget to use the -0 option?"); intv->beg = 0; } if (intv->end < 1) intv->end = 1; } } else { if ((conf->preset&0xffff) == TBX_GENERIC) { if (id == conf->ec) { intv->end = strtoll(line + b, &s, 0); if ( s==line+b ) return -1; // expected int } } else if ((conf->preset&0xffff) == TBX_SAM) { if (id == 6) { // CIGAR int l = 0; char *t; for (s = line + b; s < line + i;) { long x = strtol(s, &t, 10); char op = toupper_c(*t); if (op == 'M' || op == 'D' || op == 'N') l += x; s = t + 1; } if (l == 0) l = 1; intv->end = intv->beg + l; } } else if ((conf->preset&0xffff) == TBX_VCF) { if (id == 4) { if (b < i) intv->end = intv->beg + (i - b); } else if (id == 8) { // look for "END=" int c = line[i]; line[i] = 0; s = strstr(line + b, "END="); if (s == line + b) s += 4; else if (s) { s = strstr(line + b, ";END="); if (s) s += 5; } if (s && *s != '.') { long long end = strtoll(s, &s, 0); if (end <= intv->beg) { static int reported = 0; if (!reported) { int l = intv->ss ? (int) (intv->se - intv->ss) : 0; hts_log_warning("VCF INFO/END=%lld is smaller than POS at %.*s:%"PRIhts_pos"\n" "This tag will be ignored. " "Note: only one invalid END tag will be reported.", end, l >= 0 ? l : 0, intv->ss ? intv->ss : "", intv->beg); reported = 1; } } else { intv->end = end; } } line[i] = c; } } } b = i + 1; ++id; } } if (intv->ss == 0 || intv->se == 0 || intv->beg < 0 || intv->end < 0) return -1; return 0; } static inline int get_intv(tbx_t *tbx, kstring_t *str, tbx_intv_t *intv, int is_add) { if (tbx_parse1(&tbx->conf, str->l, str->s, intv) == 0) { int c = *intv->se; *intv->se = '\0'; if ((tbx->conf.preset&0xffff) == TBX_GAF){ intv->tid = 0; } else { intv->tid = get_tid(tbx, intv->ss, is_add); } *intv->se = c; if (intv->tid < 0) return -2; // get_tid out of memory return (intv->beg >= 0 && intv->end >= 0)? 0 : -1; } else { char *type = NULL; switch (tbx->conf.preset&0xffff) { case TBX_SAM: type = "TBX_SAM"; break; case TBX_VCF: type = "TBX_VCF"; break; case TBX_GAF: type = "TBX_GAF"; break; case TBX_UCSC: type = "TBX_UCSC"; break; default: type = "TBX_GENERIC"; break; } if (hts_is_utf16_text(str)) hts_log_error("Failed to parse %s: offending line appears to be encoded as UTF-16", type); else hts_log_error("Failed to parse %s: was wrong -p [type] used?\nThe offending line was: \"%s\"", type, str->s); return -1; } } /* * Called by tabix iterator to read the next record. * Returns >= 0 on success * -1 on EOF * <= -2 on error */ int tbx_readrec(BGZF *fp, void *tbxv, void *sv, int *tid, hts_pos_t *beg, hts_pos_t *end) { tbx_t *tbx = (tbx_t *) tbxv; kstring_t *s = (kstring_t *) sv; int ret; if ((ret = bgzf_getline(fp, '\n', s)) >= 0) { tbx_intv_t intv; if (get_intv(tbx, s, &intv, 0) < 0) return -2; *tid = intv.tid; *beg = intv.beg; *end = intv.end; } return ret; } static int tbx_set_meta(tbx_t *tbx) { int i, l = 0, l_nm; uint32_t x[7]; char **name; uint8_t *meta; khint_t k; khash_t(s2i) *d = (khash_t(s2i)*)tbx->dict; memcpy(x, &tbx->conf, 24); name = (char**)malloc(sizeof(char*) * kh_size(d)); if (!name) return -1; for (k = kh_begin(d), l = 0; k != kh_end(d); ++k) { if (!kh_exist(d, k)) continue; name[kh_val(d, k)] = (char*)kh_key(d, k); l += strlen(kh_key(d, k)) + 1; // +1 to include '\0' } l_nm = x[6] = l; meta = (uint8_t*)malloc(l_nm + 28); if (!meta) { free(name); return -1; } if (ed_is_big()) for (i = 0; i < 7; ++i) x[i] = ed_swap_4(x[i]); memcpy(meta, x, 28); for (l = 28, i = 0; i < (int)kh_size(d); ++i) { int x = strlen(name[i]) + 1; memcpy(meta + l, name[i], x); l += x; } free(name); hts_idx_set_meta(tbx->idx, l, meta, 0); return 0; } // Minimal effort parser to extract reference length out of VCF header line // This is used only used to adjust the number of levels if necessary, // so not a major problem if it doesn't always work. static void adjust_max_ref_len_vcf(const char *str, int64_t *max_ref_len) { const char *ptr; int64_t len; if (strncmp(str, "##contig", 8) != 0) return; ptr = strstr(str + 8, "length"); if (!ptr) return; for (ptr += 6; *ptr == ' ' || *ptr == '='; ptr++) {} len = strtoll(ptr, NULL, 10); if (*max_ref_len < len) *max_ref_len = len; } // Same for sam files static void adjust_max_ref_len_sam(const char *str, int64_t *max_ref_len) { const char *ptr; int64_t len; if (strncmp(str, "@SQ", 3) != 0) return; ptr = strstr(str + 3, "\tLN:"); if (!ptr) return; ptr += 4; len = strtoll(ptr, NULL, 10); if (*max_ref_len < len) *max_ref_len = len; } // Adjusts number of levels if not big enough. This can happen for // files with very large contigs. static int adjust_n_lvls(int min_shift, int n_lvls, int64_t max_len) { int64_t s = hts_bin_maxpos(min_shift, n_lvls); max_len += 256; for (; max_len > s; ++n_lvls, s <<= 3) {} return n_lvls; } tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf) { tbx_t *tbx; kstring_t str; int ret, first = 0, n_lvls, fmt; int64_t lineno = 0; uint64_t last_off = 0; tbx_intv_t intv; int64_t max_ref_len = 0; str.s = 0; str.l = str.m = 0; tbx = (tbx_t*)calloc(1, sizeof(tbx_t)); if (!tbx) return NULL; tbx->conf = *conf; if (min_shift > 0) n_lvls = (TBX_MAX_SHIFT - min_shift + 2) / 3, fmt = HTS_FMT_CSI; else min_shift = 14, n_lvls = 5, fmt = HTS_FMT_TBI; while ((ret = bgzf_getline(fp, '\n', &str)) >= 0) { ++lineno; if (str.s[0] == tbx->conf.meta_char && fmt == HTS_FMT_CSI) { switch (tbx->conf.preset) { case TBX_SAM: adjust_max_ref_len_sam(str.s, &max_ref_len); break; case TBX_VCF: adjust_max_ref_len_vcf(str.s, &max_ref_len); break; default: break; } } if (lineno <= tbx->conf.line_skip || str.s[0] == tbx->conf.meta_char) { last_off = bgzf_tell(fp); continue; } if (first == 0) { if (fmt == HTS_FMT_CSI) { if (!max_ref_len) max_ref_len = (int64_t)100*1024*1024*1024; // 100G default n_lvls = adjust_n_lvls(min_shift, n_lvls, max_ref_len); } tbx->idx = hts_idx_init(0, fmt, last_off, min_shift, n_lvls); if (!tbx->idx) goto fail; first = 1; } ret = get_intv(tbx, &str, &intv, 1); if (ret < -1) goto fail; // Out of memory if (ret < 0) continue; // Skip unparsable lines if (hts_idx_push(tbx->idx, intv.tid, intv.beg, intv.end, bgzf_tell(fp), 1) < 0) { goto fail; } } if (ret < -1) goto fail; if ( !tbx->idx ) tbx->idx = hts_idx_init(0, fmt, last_off, min_shift, n_lvls); // empty file if (!tbx->idx) goto fail; if ( !tbx->dict ) tbx->dict = kh_init(s2i); if (!tbx->dict) goto fail; if (hts_idx_finish(tbx->idx, bgzf_tell(fp)) != 0) goto fail; if (tbx_set_meta(tbx) != 0) goto fail; free(str.s); return tbx; fail: free(str.s); tbx_destroy(tbx); return NULL; } void tbx_destroy(tbx_t *tbx) { khash_t(s2i) *d = (khash_t(s2i)*)tbx->dict; if (d != NULL) { khint_t k; for (k = kh_begin(d); k != kh_end(d); ++k) if (kh_exist(d, k)) free((char*)kh_key(d, k)); } hts_idx_destroy(tbx->idx); kh_destroy(s2i, d); free(tbx); } int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_conf_t *conf) { tbx_t *tbx; BGZF *fp; int ret; if ((fp = bgzf_open(fn, "r")) == 0) return -1; if ( n_threads ) bgzf_mt(fp, n_threads, 256); if ( bgzf_compression(fp) != bgzf ) { bgzf_close(fp); return -2; } tbx = tbx_index(fp, min_shift, conf); bgzf_close(fp); if ( !tbx ) return -1; ret = hts_idx_save_as(tbx->idx, fn, fnidx, min_shift > 0? HTS_FMT_CSI : HTS_FMT_TBI); tbx_destroy(tbx); return ret; } int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf) { return tbx_index_build3(fn, fnidx, min_shift, 0, conf); } int tbx_index_build(const char *fn, int min_shift, const tbx_conf_t *conf) { return tbx_index_build3(fn, NULL, min_shift, 0, conf); } static tbx_t *index_load(const char *fn, const char *fnidx, int flags) { tbx_t *tbx; uint8_t *meta; char *nm, *p; uint32_t l_meta, l_nm; tbx = (tbx_t*)calloc(1, sizeof(tbx_t)); if (!tbx) return NULL; tbx->idx = hts_idx_load3(fn, fnidx, HTS_FMT_TBI, flags); if ( !tbx->idx ) { free(tbx); return NULL; } meta = hts_idx_get_meta(tbx->idx, &l_meta); if ( !meta || l_meta < 28) goto invalid; tbx->conf.preset = le_to_i32(&meta[0]); tbx->conf.sc = le_to_i32(&meta[4]); tbx->conf.bc = le_to_i32(&meta[8]); tbx->conf.ec = le_to_i32(&meta[12]); tbx->conf.meta_char = le_to_i32(&meta[16]); tbx->conf.line_skip = le_to_i32(&meta[20]); l_nm = le_to_u32(&meta[24]); if (l_nm > l_meta - 28) goto invalid; p = nm = (char*)meta + 28; // This assumes meta is NUL-terminated, so we can merrily strlen away. // hts_idx_load_local() assures this for us by adding a NUL on the end // of whatever it reads. for (; p - nm < l_nm; p += strlen(p) + 1) { if (get_tid(tbx, p, 1) < 0) { hts_log_error("%s", strerror(errno)); goto fail; } } return tbx; invalid: hts_log_error("Invalid index header for %s", fnidx ? fnidx : fn); fail: tbx_destroy(tbx); return NULL; } tbx_t *tbx_index_load3(const char *fn, const char *fnidx, int flags) { return index_load(fn, fnidx, flags); } tbx_t *tbx_index_load2(const char *fn, const char *fnidx) { return index_load(fn, fnidx, 1); } tbx_t *tbx_index_load(const char *fn) { return index_load(fn, NULL, 1); } const char **tbx_seqnames(tbx_t *tbx, int *n) { khash_t(s2i) *d = (khash_t(s2i)*)tbx->dict; if (d == NULL) { *n = 0; return calloc(1, sizeof(char *)); } int tid, m = kh_size(d); const char **names = (const char**) calloc(m,sizeof(const char*)); khint_t k; if (!names) { *n = 0; return NULL; } for (k=kh_begin(d); k Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include "htslib/hfile.h" #include "htslib/kstring.h" #include "htslib/sam.h" // For stringify_argv() declaration #include "hts_internal.h" static int dehex(char c) { if (c >= 'a' && c <= 'f') return c - 'a' + 10; else if (c >= 'A' && c <= 'F') return c - 'A' + 10; else if (c >= '0' && c <= '9') return c - '0'; else return -1; // Hence dehex('\0') = -1 } int hts_decode_percent(char *dest, size_t *destlen, const char *s) { char *d = dest; int hi, lo; while (*s) { if (*s == '%' && (hi = dehex(s[1])) >= 0 && (lo = dehex(s[2])) >= 0) { *d++ = (hi << 4) | lo; s += 3; } else *d++ = *s++; } *d = '\0'; *destlen = d - dest; return 0; } static int debase64(char c) { if (c >= 'a' && c <= 'z') return c - 'a' + 26; else if (c >= 'A' && c <= 'Z') return c - 'A'; else if (c >= '0' && c <= '9') return c - '0' + 52; else if (c == '/') return 63; else if (c == '+') return 62; else return -1; // Hence debase64('\0') = -1 } size_t hts_base64_decoded_length(size_t len) { size_t nquartets = (len + 2) / 4; return 3 * nquartets; } int hts_decode_base64(char *dest, size_t *destlen, const char *s) { char *d = dest; int x0, x1, x2, x3; while (1) { x0 = debase64(*s++); x1 = (x0 >= 0)? debase64(*s++) : -1; x2 = (x1 >= 0)? debase64(*s++) : -1; x3 = (x2 >= 0)? debase64(*s++) : -1; if (x3 < 0) break; *d++ = (x0 << 2) | (x1 >> 4); *d++ = (x1 << 4) | (x2 >> 2); *d++ = (x2 << 6) | x3; } if (x1 >= 0) *d++ = (x0 << 2) | (x1 >> 4); if (x2 >= 0) *d++ = (x1 << 4) | (x2 >> 2); *destlen = d - dest; return 0; } static char *encode_utf8(char *s, unsigned x) { if (x >= 0x10000) { *s++ = 0xF0 | (x >> 18); *s++ = 0x80 | ((x >> 12) & 0x3F); *s++ = 0x80 | ((x >> 6) & 0x3F); *s++ = 0x80 | (x & 0x3F); } else if (x >= 0x800) { *s++ = 0xE0 | (x >> 12); *s++ = 0x80 | ((x >> 6) & 0x3F); *s++ = 0x80 | (x & 0x3F); } else if (x >= 0x80) { *s++ = 0xC0 | (x >> 6); *s++ = 0x80 | (x & 0x3F); } else *s++ = x; return s; } static char *sscan_string(char *s) { char *d = s; int d1, d2, d3, d4; for (;;) switch (*s) { case '\\': switch (s[1]) { case '\0': *d = '\0'; return s+1; case 'b': *d++ = '\b'; s += 2; break; case 'f': *d++ = '\f'; s += 2; break; case 'n': *d++ = '\n'; s += 2; break; case 'r': *d++ = '\r'; s += 2; break; case 't': *d++ = '\t'; s += 2; break; default: *d++ = s[1]; s += 2; break; case 'u': if ((d1 = dehex(s[2])) >= 0 && (d2 = dehex(s[3])) >= 0 && (d3 = dehex(s[4])) >= 0 && (d4 = dehex(s[5])) >= 0) { d = encode_utf8(d, d1 << 12 | d2 << 8 | d3 << 4 | d4); s += 6; } break; } break; case '"': *d = '\0'; return s+1; case '\0': *d = '\0'; return s; default: *d++ = *s++; break; } } static int fscan_string(hFILE *fp, kstring_t *d) { int c, d1, d2, d3, d4; uint32_t e = 0; while ((c = hgetc(fp)) != EOF) switch (c) { case '\\': if ((c = hgetc(fp)) == EOF) return e == 0 ? 0 : -1; switch (c) { case 'b': e |= kputc('\b', d) < 0; break; case 'f': e |= kputc('\f', d) < 0; break; case 'n': e |= kputc('\n', d) < 0; break; case 'r': e |= kputc('\r', d) < 0; break; case 't': e |= kputc('\t', d) < 0; break; default: e |= kputc(c, d) < 0; break; case 'u': if ((c = hgetc(fp)) != EOF && (d1 = dehex(c)) >= 0 && (c = hgetc(fp)) != EOF && (d2 = dehex(c)) >= 0 && (c = hgetc(fp)) != EOF && (d3 = dehex(c)) >= 0 && (c = hgetc(fp)) != EOF && (d4 = dehex(c)) >= 0) { char buf[8]; char *lim = encode_utf8(buf, d1 << 12 | d2 << 8 | d3 << 4 | d4); e |= kputsn(buf, lim - buf, d) < 0; } break; } break; case '"': return e == 0 ? 0 : -1; default: e |= kputc(c, d) < 0; break; } return e == 0 ? 0 : -1; } static char token_type(hts_json_token *token) { const char *s = token->str; switch (*s) { case 'f': return (strcmp(s, "false") == 0)? 'b' : '?'; case 'n': return (strcmp(s, "null") == 0)? '.' : '?'; case 't': return (strcmp(s, "true") == 0)? 'b' : '?'; case '-': case '0': case '1': case '2': case '3': case '4': case '5': case '6': case '7': case '8': case '9': return 'n'; default: return '?'; } } HTSLIB_EXPORT hts_json_token * hts_json_alloc_token(void) { return calloc(1, sizeof(hts_json_token)); } HTSLIB_EXPORT char hts_json_token_type(hts_json_token *token) { return token->type; } HTSLIB_EXPORT void hts_json_free_token(hts_json_token *token) { free(token); } HTSLIB_EXPORT char *hts_json_token_str(hts_json_token *token) { return token->str; } HTSLIB_EXPORT char hts_json_snext(char *str, size_t *state, hts_json_token *token) { char *s = &str[*state >> 2]; int hidden = *state & 3; if (hidden) { *state &= ~3; return token->type = "?}]?"[hidden]; } #define STATE(s,h) (((s) - str) << 2 | (h)) for (;;) switch (*s) { case ' ': case '\t': case '\r': case '\n': case ',': case ':': s++; continue; case '\0': return token->type = '\0'; case '{': case '[': case '}': case ']': *state = STATE(s+1, 0); return token->type = *s; case '"': token->str = s+1; *state = STATE(sscan_string(s+1), 0); return token->type = 's'; default: token->str = s; s += strcspn(s, " \t\r\n,]}"); hidden = (*s == '}')? 1 : (*s == ']')? 2 : 0; if (*s != '\0') *s++ = '\0'; *state = STATE(s, hidden); return token->type = token_type(token); } #undef STATE } HTSLIB_EXPORT char hts_json_fnext(struct hFILE *fp, hts_json_token *token, kstring_t *kstr) { char peek; int c; for (;;) switch (c = hgetc(fp)) { case ' ': case '\t': case '\r': case '\n': case ',': case ':': continue; case EOF: return token->type = '\0'; case '{': case '[': case '}': case ']': return token->type = c; case '"': kstr->l = 0; fscan_string(fp, kstr); if (kstr->l == 0) kputsn("", 0, kstr); token->str = kstr->s; return token->type = 's'; default: kstr->l = 0; kputc(c, kstr); while (hpeek(fp, &peek, 1) == 1 && !strchr(" \t\r\n,]}", peek)) { if ((c = hgetc(fp)) == EOF) break; kputc(c, kstr); } token->str = kstr->s; return token->type = token_type(token); } } typedef char hts_json_nextfn(void *arg1, void *arg2, hts_json_token *token); static char skip_value(char type, hts_json_nextfn *next, void *arg1, void *arg2) { hts_json_token token; int level; switch (type? type : next(arg1, arg2, &token)) { case '\0': return '\0'; case '?': case '}': case ']': return '?'; case '{': case '[': level = 1; break; default: return 'v'; } while (level > 0) switch (next(arg1, arg2, &token)) { case '\0': return '\0'; case '?': return '?'; case '{': case '[': level++; break; case '}': case ']': --level; break; default: break; } return 'v'; } static char snext(void *arg1, void *arg2, hts_json_token *token) { return hts_json_snext(arg1, arg2, token); } HTSLIB_EXPORT char hts_json_sskip_value(char *str, size_t *state, char type) { return skip_value(type, snext, str, state); } static char fnext(void *arg1, void *arg2, hts_json_token *token) { return hts_json_fnext(arg1, token, arg2); } HTSLIB_EXPORT char hts_json_fskip_value(struct hFILE *fp, char type) { kstring_t str = { 0, 0, NULL }; char ret = skip_value(type, fnext, fp, &str); free(str.s); return ret; } /* * A function to help with construction of CL tags in @PG records. * Takes an argc, argv pair and returns a single space-separated string. * This string should be deallocated by the calling function. * * Returns malloced char * on success * NULL on failure */ char *stringify_argv(int argc, char *argv[]) { char *str, *cp; size_t nbytes = 1; int i, j; /* Allocate */ for (i = 0; i < argc; i++) { if (i > 0) nbytes += 1; nbytes += strlen(argv[i]); } if (!(str = malloc(nbytes))) return NULL; /* Copy */ cp = str; for (i = 0; i < argc; i++) { if (i > 0) *cp++ = ' '; j = 0; while (argv[i][j]) { if (argv[i][j] == '\t') *cp++ = ' '; else *cp++ = argv[i][j]; j++; } } *cp++ = 0; return str; } /* Utility function for printing possibly malicious text data */ const char * hts_strprint(char *buf, size_t buflen, char quote, const char *s, size_t len) { const char *slim = (len < SIZE_MAX)? &s[len] : NULL; char *t = buf, *bufend = buf + buflen; size_t qlen = quote? 1 : 0; if (quote) *t++ = quote; for (; slim? (s < slim) : (*s); s++) { char c; size_t clen; switch (*s) { case '\n': c = 'n'; clen = 2; break; case '\r': c = 'r'; clen = 2; break; case '\t': c = 't'; clen = 2; break; case '\0': c = '0'; clen = 2; break; case '\\': c = '\\'; clen = 2; break; default: c = *s; if (c == quote) clen = 2; else clen = isprint_c(c)? 1 : 4; break; } if (t-buf + clen + qlen >= buflen) { while (t-buf + 3 + qlen >= buflen) t--; if (quote) *t++ = quote; strcpy(t, "..."); return buf; } if (clen == 4) { snprintf(t, bufend - t, "\\x%02X", (unsigned char) c); t += clen; } else { if (clen == 2) *t++ = '\\'; *t++ = c; } } if (quote) *t++ = quote; *t = '\0'; return buf; } pysam-0.23.0/htslib/textutils_internal.h000066400000000000000000000364321475062545500203510ustar00rootroot00000000000000/* textutils_internal.h -- non-bioinformatics utility routines for text etc. Copyright (C) 2016,2018-2020, 2024 Genome Research Ltd. Author: John Marshall Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef HTSLIB_TEXTUTILS_INTERNAL_H #define HTSLIB_TEXTUTILS_INTERNAL_H /* N.B. These interfaces may be used by plug-ins */ #include #include #include "htslib/kstring.h" #ifdef __cplusplus extern "C" { #endif /// Decode percent-encoded (URL-encoded) text /** On input, _dest_ should be a buffer at least the same size as _s_, and may be equal to _s_ to decode in place. On output, _dest_ will be NUL-terminated and the number of characters written (not including the NUL) is stored in _destlen_. */ int hts_decode_percent(char *dest, size_t *destlen, const char *s); /// Return decoded data length given length of base64-encoded text /** This gives an upper bound, as it overestimates by a byte or two when the encoded text ends with (possibly omitted) `=` padding characters. */ size_t hts_base64_decoded_length(size_t len); /// Decode base64-encoded data /** On input, _dest_ should be a sufficient buffer (see `hts_base64_length()`), and may be equal to _s_ to decode in place. On output, the number of bytes written is stored in _destlen_. */ int hts_decode_base64(char *dest, size_t *destlen, const char *s); /// Token structure returned by JSON lexing functions /** Structure is defined in hts_internal.h */ typedef struct hts_json_token hts_json_token; /// Allocate an empty JSON token structure, for use with hts_json_* functions /** @return An empty token on success; NULL on failure */ HTSLIB_EXPORT hts_json_token *hts_json_alloc_token(void); /// Free a JSON token HTSLIB_EXPORT void hts_json_free_token(hts_json_token *token); /// Accessor function to get JSON token type /** @param token Pointer to JSON token @return Character indicating the token type Token types correspond to scalar JSON values and selected punctuation as follows: - `s` string - `n` number - `b` boolean literal - `.` null literal - `{`, `}`, `[`, `]` object and array delimiters - `?` lexing error - `!` other errors (e.g. out of memory) - `\0` terminator at end of input */ HTSLIB_EXPORT char hts_json_token_type(hts_json_token *token); /// Accessor function to get JSON token in string form /** @param token Pointer to JSON token @return String representation of the JSON token; NULL if unset If the token was parsed from a string using hts_json_snext(), the return value will point into the string passed as the first parameter to hts_json_snext(). If the token was parsed from a file using hts_json_fnext(), the return value will point at the kstring_t buffer passed as the third parameter to hts_json_fnext(). In that case, the value will only be valid until the next call to hts_json_fnext(). */ HTSLIB_EXPORT char *hts_json_token_str(hts_json_token *token); /// Read one JSON token from a string /** @param str The input C string @param state The input string state @param token On return, filled in with the token read @return The type of the token read On return, `token->str` points into the supplied input string, which is modified by having token-terminating characters overwritten as NULs. The `state` argument records the current position within `str` after each `hts_json_snext()` call, and should be set to 0 before the first call. */ HTSLIB_EXPORT char hts_json_snext(char *str, size_t *state, hts_json_token *token); /// Read and discard a complete JSON value from a string /** @param str The input C string @param state The input string state, as per `hts_json_snext()` @param type If the first token of the value to be discarded has already been read, provide its type; otherwise `'\0'` @return One of `v` (success), `\0` (end of string), and `?` (lexing error) Skips a complete JSON value, which may be a single token or an entire object or array. */ HTSLIB_EXPORT char hts_json_sskip_value(char *str, size_t *state, char type); struct hFILE; /// Read one JSON token from a file /** @param fp The file stream @param token On return, filled in with the token read @param kstr Buffer used to store the token string returned @return The type of the token read The `kstr` buffer is used to store the string value of the token read, so `token->str` is only valid until the next time `hts_json_fnext()` is called with the same `kstr` argument. */ HTSLIB_EXPORT char hts_json_fnext(struct hFILE *fp, hts_json_token *token, kstring_t *kstr); /// Read and discard a complete JSON value from a file /** @param fp The file stream @param type If the first token of the value to be discarded has already been read, provide its type; otherwise `'\0'` @return One of `v` (success), `\0` (EOF), and `?` (lexing error) Skips a complete JSON value, which may be a single token or an entire object or array. */ HTSLIB_EXPORT char hts_json_fskip_value(struct hFILE *fp, char type); // The functions operate on ints such as are returned by fgetc(), // i.e., characters represented as unsigned-char-valued ints, or EOF. // To operate on plain chars (and to avoid warnings on some platforms), // technically one must cast to unsigned char everywhere (see CERT STR37-C) // or less painfully use these *_c() functions that operate on plain chars // (but not EOF, which must be considered separately where it is applicable). // TODO We may eventually wish to implement these functions directly without // using their equivalents, and thus make them immune to locales. static inline int isalnum_c(char c) { return isalnum((unsigned char) c); } static inline int isalpha_c(char c) { return isalpha((unsigned char) c); } static inline int isdigit_c(char c) { return isdigit((unsigned char) c); } static inline int isgraph_c(char c) { return isgraph((unsigned char) c); } static inline int islower_c(char c) { return islower((unsigned char) c); } static inline int isprint_c(char c) { return isprint((unsigned char) c); } static inline int ispunct_c(char c) { return ispunct((unsigned char) c); } static inline int isspace_c(char c) { return isspace((unsigned char) c); } static inline int isupper_c(char c) { return isupper((unsigned char) c); } static inline int isxdigit_c(char c) { return isxdigit((unsigned char) c); } static inline char tolower_c(char c) { return tolower((unsigned char) c); } static inline char toupper_c(char c) { return toupper((unsigned char) c); } /// Copy possibly malicious text data to a buffer /** @param buf Destination buffer @param buflen Size of the destination buffer (>= 4; >= 6 when quotes used) @param quote Quote character (or '\0' for no quoting of the output) @param s String to be copied @param len Length of the input string, or SIZE_MAX to copy until '\0' @return The destination buffer, @a buf. Copies the source text string (escaping any unprintable characters) to the destination buffer. The destination buffer will always be NUL-terminated; the text will be truncated (and "..." appended) if necessary to make it fit. */ const char *hts_strprint(char *buf, size_t buflen, char quote, const char *s, size_t len); // Faster replacements for strtol, for use when parsing lots of numbers. // Note that these only handle base 10 and do not skip leading whitespace /// Convert a string to a signed integer, with overflow detection /** @param[in] in Input string @param[out] end Returned end pointer @param[in] bits Bits available for the converted value @param[out] failed Location of overflow flag @return String value converted to an int64_t Converts a signed decimal string to an int64_t. The string should consist of an optional '+' or '-' sign followed by one or more of the digits 0 to 9. The output value will be limited to fit in the given number of bits (including the sign bit). If the value is too big, the largest possible value will be returned and *failed will be set to 1. The address of the first character following the converted number will be stored in *end. Both end and failed must be non-NULL. */ static inline int64_t hts_str2int(const char *in, char **end, int bits, int *failed) { uint64_t n = 0, limit = (1ULL << (bits - 1)) - 1; uint32_t fast = (bits - 1) * 1000 / 3322 + 1; // log(10)/log(2) ~= 3.322 const unsigned char *v = (const unsigned char *) in; const unsigned int ascii_zero = '0'; // Prevents conversion to signed unsigned int d; int neg; switch(*v) { case '-': limit++; neg=1; v++; // See "dup" comment below while (--fast && *v>='0' && *v<='9') n = n*10 + *v++ - ascii_zero; break; case '+': v++; // fall through default: neg = 0; // dup of above. This is somewhat unstable and mainly for code // size cheats to prevent instruction cache lines spanning 32-byte // blocks in the sam_parse_B_vals calling code. It's been tested // on gcc7, gcc13, clang10 and clang16 with -O2 and -O3. While // not exhaustive, this code duplication gives stable fast results // while a single copy does not. // (NB: system was "seq4d", so quite old) while (--fast && *v>='0' && *v<='9') n = n*10 + *v++ - ascii_zero; break; } // NB gcc7 is slow with (unsigned)(*v - ascii_zero) < 10, // while gcc13 prefers it. if (*v>='0' && !fast) { // rejects ',' and tab uint64_t limit_d_10 = limit / 10; uint64_t limit_m_10 = limit - 10 * limit_d_10; while ((d = *v - ascii_zero) < 10) { if (n < limit_d_10 || (n == limit_d_10 && d <= limit_m_10)) { n = n*10 + d; v++; } else { do { v++; } while (*v - ascii_zero < 10); n = limit; *failed = 1; break; } } } *end = (char *)v; return neg ? (int64_t)-n : (int64_t)n; } /// Convert a string to an unsigned integer, with overflow detection /** @param[in] in Input string @param[out] end Returned end pointer @param[in] bits Bits available for the converted value @param[out] failed Location of overflow flag @return String value converted to a uint64_t Converts an unsigned decimal string to a uint64_t. The string should consist of an optional '+' sign followed by one or more of the digits 0 to 9. The output value will be limited to fit in the given number of bits. If the value is too big, the largest possible value will be returned and *failed will be set to 1. The address of the first character following the converted number will be stored in *end. Both end and failed must be non-NULL. */ static inline uint64_t hts_str2uint(const char *in, char **end, int bits, int *failed) { uint64_t n = 0, limit = (bits < 64 ? (1ULL << bits) : 0) - 1; const unsigned char *v = (const unsigned char *) in; const unsigned int ascii_zero = '0'; // Prevents conversion to signed uint32_t fast = bits * 1000 / 3322 + 1; // log(10)/log(2) ~= 3.322 unsigned int d; if (*v == '+') v++; while (--fast && *v>='0' && *v<='9') n = n*10 + *v++ - ascii_zero; if ((unsigned)(*v - ascii_zero) < 10 && !fast) { uint64_t limit_d_10 = limit / 10; uint64_t limit_m_10 = limit - 10 * limit_d_10; while ((d = *v - ascii_zero) < 10) { if (n < limit_d_10 || (n == limit_d_10 && d <= limit_m_10)) { n = n*10 + d; v++; } else { do { v++; } while (*v - ascii_zero < 10); n = limit; *failed = 1; break; } } } *end = (char *)v; return n; } /// Convert a string to a double, with overflow detection /** @param[in] in Input string @param[out] end Returned end pointer @param[out] failed Location of overflow flag @return String value converted to a double Converts a floating point value string to a double. The string should have the format [+-]?[0-9]*[.]?[0-9]* with at least one and no more than 15 digits. Strings that do not match (inf, nan, values with exponents) will be passed on to strtod() for processing. If the value is too big, the largest possible value will be returned; if it is too small to be represented in a double zero will be returned. In both cases errno will be set to ERANGE. If no characters could be converted, *failed will be set to 1. The address of the first character following the converted number will be stored in *end. Both end and failed must be non-NULL. */ static inline double hts_str2dbl(const char *in, char **end, int *failed) { uint64_t n = 0; int max_len = 15; const unsigned char *v = (const unsigned char *) in; const unsigned int ascii_zero = '0'; // Prevents conversion to signed int neg = 0, point = -1; double d; static double D[] = {1,1, 1e1, 1e2, 1e3, 1e4, 1e5, 1e6, 1e7, 1e8, 1e9, 1e10,1e11,1e12,1e13,1e14,1e15, 1e16,1e17,1e18,1e19,1e20}; while (isspace(*v)) v++; if (*v == '-') { neg = 1; v++; } else if (*v == '+') { v++; } switch(*v) { case '1': case '2': case '3': case '4': case '5': case '6': case '7': case '8': case '9': break; case '0': if (v[1] != 'x' && v[1] != 'X') break; // else fall through - hex number default: // Non numbers, like NaN, Inf d = strtod(in, end); if (*end == in) *failed = 1; return d; } while (*v == '0') ++v; const unsigned char *start = v; while (--max_len && *v>='0' && *v<='9') n = n*10 + *v++ - ascii_zero; if (max_len && *v == '.') { point = v - start; v++; while (--max_len && *v>='0' && *v<='9') n = n*10 + *v++ - ascii_zero; } if (point < 0) point = v - start; // Outside the scope of this quick and dirty parser. if (!max_len || *v == 'e' || *v == 'E') { d = strtod(in, end); if (*end == in) *failed = 1; return d; } *end = (char *)v; d = n / D[v - start - point]; return neg ? -d : d; } #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/thread_pool.c000066400000000000000000001312571475062545500167040ustar00rootroot00000000000000/* thread_pool.c -- A pool of generic worker threads Copyright (c) 2013-2020 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef TEST_MAIN #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #endif #include #include #include #include #include #include #include #include #include #include #include #include "thread_pool_internal.h" #include "htslib/hts_log.h" // Minimum stack size for threads. Required for some rANS codecs // that use over 2Mbytes of stack for encoder / decoder state #define HTS_MIN_THREAD_STACK (3 * 1024 * 1024) static void hts_tpool_process_detach_locked(hts_tpool *p, hts_tpool_process *q); //#define DEBUG #ifdef DEBUG static int worker_id(hts_tpool *p) { int i; pthread_t s = pthread_self(); for (i = 0; i < p->tsize; i++) { if (pthread_equal(s, p->t[i].tid)) return i; } return -1; } void DBG_OUT(FILE *fp, char *fmt, ...) { va_list args; va_start(args, fmt); vfprintf(fp, fmt, args); va_end(args); } #else #define DBG_OUT(...) do{}while(0) #endif /* ---------------------------------------------------------------------------- * A process-queue to hold results from the thread pool. * * Each thread pool may have jobs of multiple types being queued up and * interleaved, so we attach several job process-queues to a single pool. * * The jobs themselves are expected to push their results onto their * appropriate results queue. */ /* * Adds a result to the end of the process result queue. * * Returns 0 on success; * -1 on failure */ static int hts_tpool_add_result(hts_tpool_job *j, void *data) { hts_tpool_process *q = j->q; hts_tpool_result *r; pthread_mutex_lock(&q->p->pool_m); DBG_OUT(stderr, "%d: Adding result to queue %p, serial %"PRId64", %d of %d\n", worker_id(j->p), q, j->serial, q->n_output+1, q->qsize); if (--q->n_processing == 0) pthread_cond_signal(&q->none_processing_c); /* No results queue is fine if we don't want any results back */ if (q->in_only) { pthread_mutex_unlock(&q->p->pool_m); return 0; } if (!(r = malloc(sizeof(*r)))) { pthread_mutex_unlock(&q->p->pool_m); hts_tpool_process_shutdown(q); return -1; } r->next = NULL; r->data = data; r->result_cleanup = j->result_cleanup; r->serial = j->serial; q->n_output++; if (q->output_tail) { q->output_tail->next = r; q->output_tail = r; } else { q->output_head = q->output_tail = r; } assert(r->serial >= q->next_serial // Or it will never be dequeued ... || q->next_serial == INT_MAX); // ... unless flush in progress. if (r->serial == q->next_serial) { DBG_OUT(stderr, "%d: Broadcasting result_avail (id %"PRId64")\n", worker_id(j->p), r->serial); pthread_cond_broadcast(&q->output_avail_c); DBG_OUT(stderr, "%d: Broadcast complete\n", worker_id(j->p)); } pthread_mutex_unlock(&q->p->pool_m); return 0; } static void wake_next_worker(hts_tpool_process *q, int locked); /* Core of hts_tpool_next_result() */ static hts_tpool_result *hts_tpool_next_result_locked(hts_tpool_process *q) { hts_tpool_result *r, *last; if (q->shutdown) return NULL; for (last = NULL, r = q->output_head; r; last = r, r = r->next) { if (r->serial == q->next_serial) break; } if (r) { // Remove r from out linked list if (q->output_head == r) q->output_head = r->next; else last->next = r->next; if (q->output_tail == r) q->output_tail = last; if (!q->output_head) q->output_tail = NULL; q->next_serial++; q->n_output--; if (q->qsize && q->n_output < q->qsize) { // Not technically input full, but can guarantee there is // room for the input to go somewhere so we still signal. // The waiting code will then check the condition again. if (q->n_input < q->qsize) pthread_cond_signal(&q->input_not_full_c); if (!q->shutdown) wake_next_worker(q, 1); } } return r; } /* * Pulls the next item off the process result queue. The caller should free * it (and any internals as appropriate) after use. This doesn't wait for a * result to be present. * * Results will be returned in strict order. * * Returns hts_tpool_result pointer if a result is ready. * NULL if not. */ hts_tpool_result *hts_tpool_next_result(hts_tpool_process *q) { hts_tpool_result *r; DBG_OUT(stderr, "Requesting next result on queue %p\n", q); pthread_mutex_lock(&q->p->pool_m); r = hts_tpool_next_result_locked(q); pthread_mutex_unlock(&q->p->pool_m); DBG_OUT(stderr, "(q=%p) Found %p\n", q, r); return r; } /* * Pulls the next item off the process result queue. The caller should free * it (and any internals as appropriate) after use. This will wait for * a result to be present if none are currently available. * * Results will be returned in strict order. * * Returns hts_tpool_result pointer if a result is ready. * NULL on error or during shutdown. */ hts_tpool_result *hts_tpool_next_result_wait(hts_tpool_process *q) { hts_tpool_result *r; pthread_mutex_lock(&q->p->pool_m); while (!(r = hts_tpool_next_result_locked(q))) { /* Possible race here now avoided via _locked() call, but in case... */ struct timeval now; struct timespec timeout; gettimeofday(&now, NULL); timeout.tv_sec = now.tv_sec + 10; timeout.tv_nsec = now.tv_usec * 1000; q->ref_count++; if (q->shutdown) { int rc = --q->ref_count; pthread_mutex_unlock(&q->p->pool_m); if (rc == 0) hts_tpool_process_destroy(q); return NULL; } pthread_cond_timedwait(&q->output_avail_c, &q->p->pool_m, &timeout); q->ref_count--; } pthread_mutex_unlock(&q->p->pool_m); return r; } /* * Returns true if there are no items in the process results queue and * also none still pending. */ int hts_tpool_process_empty(hts_tpool_process *q) { int empty; pthread_mutex_lock(&q->p->pool_m); empty = q->n_input == 0 && q->n_processing == 0 && q->n_output == 0; pthread_mutex_unlock(&q->p->pool_m); return empty; } void hts_tpool_process_ref_incr(hts_tpool_process *q) { pthread_mutex_lock(&q->p->pool_m); q->ref_count++; pthread_mutex_unlock(&q->p->pool_m); } void hts_tpool_process_ref_decr(hts_tpool_process *q) { pthread_mutex_lock(&q->p->pool_m); if (--q->ref_count <= 0) { pthread_mutex_unlock(&q->p->pool_m); hts_tpool_process_destroy(q); return; } // maybe also call destroy here if needed? pthread_mutex_unlock(&q->p->pool_m); } /* * Returns the number of completed jobs in the process results queue. */ int hts_tpool_process_len(hts_tpool_process *q) { int len; pthread_mutex_lock(&q->p->pool_m); len = q->n_output; pthread_mutex_unlock(&q->p->pool_m); return len; } /* * Returns the number of completed jobs in the process results queue plus the * number running and queued up to run. */ int hts_tpool_process_sz(hts_tpool_process *q) { int len; pthread_mutex_lock(&q->p->pool_m); len = q->n_output + q->n_input + q->n_processing; pthread_mutex_unlock(&q->p->pool_m); return len; } /* * Shutdown a process. * * This sets the shutdown flag and wakes any threads waiting on process * condition variables. */ static void hts_tpool_process_shutdown_locked(hts_tpool_process *q) { q->shutdown = 1; pthread_cond_broadcast(&q->output_avail_c); pthread_cond_broadcast(&q->input_not_full_c); pthread_cond_broadcast(&q->input_empty_c); pthread_cond_broadcast(&q->none_processing_c); } void hts_tpool_process_shutdown(hts_tpool_process *q) { pthread_mutex_lock(&q->p->pool_m); hts_tpool_process_shutdown_locked(q); pthread_mutex_unlock(&q->p->pool_m); } int hts_tpool_process_is_shutdown(hts_tpool_process *q) { pthread_mutex_lock(&q->p->pool_m); int r = q->shutdown; pthread_mutex_unlock(&q->p->pool_m); return r; } /* * Frees a result 'r' and if free_data is true also frees * the internal r->data result too. */ void hts_tpool_delete_result(hts_tpool_result *r, int free_data) { if (!r) return; if (free_data && r->data) free(r->data); free(r); } /* * Returns the data portion of a hts_tpool_result, corresponding * to the actual "result" itself. */ void *hts_tpool_result_data(hts_tpool_result *r) { return r->data; } /* * Initialises a thread process-queue. * * In_only, if true, indicates that the process generates does not need to * hold any output. Otherwise an output queue is used to store the results * of processing each input job. * * Results hts_tpool_process pointer on success; * NULL on failure */ hts_tpool_process *hts_tpool_process_init(hts_tpool *p, int qsize, int in_only) { hts_tpool_process *q = malloc(sizeof(*q)); if (!q) return NULL; pthread_cond_init(&q->output_avail_c, NULL); pthread_cond_init(&q->input_not_full_c, NULL); pthread_cond_init(&q->input_empty_c, NULL); pthread_cond_init(&q->none_processing_c,NULL); q->p = p; q->input_head = NULL; q->input_tail = NULL; q->output_head = NULL; q->output_tail = NULL; q->next_serial = 0; q->curr_serial = 0; q->no_more_input = 0; q->n_input = 0; q->n_output = 0; q->n_processing= 0; q->qsize = qsize; q->in_only = in_only; q->shutdown = 0; q->wake_dispatch = 0; q->ref_count = 1; q->next = NULL; q->prev = NULL; hts_tpool_process_attach(p, q); return q; } /* Deallocates memory for a thread process-queue. * Must be called before the thread pool is destroyed. */ void hts_tpool_process_destroy(hts_tpool_process *q) { DBG_OUT(stderr, "Destroying results queue %p\n", q); if (!q) return; // Prevent dispatch from queuing up any more jobs. // We want to reset (and flush) the queue here, before // we set the shutdown flag, but we need to avoid races // with queue more input during reset. pthread_mutex_lock(&q->p->pool_m); q->no_more_input = 1; pthread_mutex_unlock(&q->p->pool_m); // Ensure it's fully drained before destroying the queue hts_tpool_process_reset(q, 0); pthread_mutex_lock(&q->p->pool_m); hts_tpool_process_detach_locked(q->p, q); hts_tpool_process_shutdown_locked(q); // Maybe a worker is scanning this queue, so delay destruction if (--q->ref_count > 0) { pthread_mutex_unlock(&q->p->pool_m); return; } pthread_cond_destroy(&q->output_avail_c); pthread_cond_destroy(&q->input_not_full_c); pthread_cond_destroy(&q->input_empty_c); pthread_cond_destroy(&q->none_processing_c); pthread_mutex_unlock(&q->p->pool_m); free(q); DBG_OUT(stderr, "Destroyed results queue %p\n", q); } /* * Attach and detach a thread process-queue with / from the thread pool * scheduler. * * We need to do attach after making a thread process, but may also wish * to temporarily detach if we wish to stop running jobs on a specific * process while permitting other process to continue. */ void hts_tpool_process_attach(hts_tpool *p, hts_tpool_process *q) { pthread_mutex_lock(&p->pool_m); if (p->q_head) { q->next = p->q_head; q->prev = p->q_head->prev; p->q_head->prev->next = q; p->q_head->prev = q; } else { q->next = q; q->prev = q; } p->q_head = q; assert(p->q_head && p->q_head->prev && p->q_head->next); pthread_mutex_unlock(&p->pool_m); } static void hts_tpool_process_detach_locked(hts_tpool *p, hts_tpool_process *q) { if (!p->q_head || !q->prev || !q->next) return; hts_tpool_process *curr = p->q_head, *first = curr; do { if (curr == q) { q->next->prev = q->prev; q->prev->next = q->next; p->q_head = q->next; q->next = q->prev = NULL; // Last one if (p->q_head == q) p->q_head = NULL; break; } curr = curr->next; } while (curr != first); } void hts_tpool_process_detach(hts_tpool *p, hts_tpool_process *q) { pthread_mutex_lock(&p->pool_m); hts_tpool_process_detach_locked(p, q); pthread_mutex_unlock(&p->pool_m); } /* ---------------------------------------------------------------------------- * The thread pool. */ #define TDIFF(t2,t1) ((t2.tv_sec-t1.tv_sec)*1000000 + t2.tv_usec-t1.tv_usec) /* * A worker thread. * * Once woken, each thread checks each process-queue in the pool in turn, * looking for input jobs that also have room for the output (if it requires * storing). If found, we execute it and repeat. * * If we checked all input queues and find no such job, then we wait until we * are signalled to check again. */ static void *tpool_worker(void *arg) { hts_tpool_worker *w = (hts_tpool_worker *)arg; hts_tpool *p = w->p; hts_tpool_job *j; pthread_mutex_lock(&p->pool_m); while (!p->shutdown) { // Pop an item off the pool queue assert(p->q_head == 0 || (p->q_head->prev && p->q_head->next)); int work_to_do = 0; hts_tpool_process *first = p->q_head, *q = first; do { // Iterate over queues, finding one with jobs and also // room to put the result. //if (q && q->input_head && !hts_tpool_process_output_full(q)) { if (q && q->input_head && q->qsize - q->n_output > q->n_processing && !q->shutdown) { work_to_do = 1; break; } if (q) q = q->next; } while (q && q != first); if (!work_to_do) { // We scanned all queues and cannot process any, so we wait. p->nwaiting++; // Push this thread to the top of the waiting stack if (p->t_stack_top == -1 || p->t_stack_top > w->idx) p->t_stack_top = w->idx; p->t_stack[w->idx] = 1; // printf("%2d: no work. In=%d Proc=%d Out=%d full=%d\n", // w->idx, p->q_head->n_input, p->q_head->n_processing, p->q_head->n_output, // hts_tpool_process_output_full(p->q_head)); pthread_cond_wait(&w->pending_c, &p->pool_m); p->t_stack[w->idx] = 0; /* Find new t_stack_top */ int i; p->t_stack_top = -1; for (i = 0; i < p->tsize; i++) { if (p->t_stack[i]) { p->t_stack_top = i; break; } } p->nwaiting--; continue; // To outer loop. } // Otherwise work_to_do, so process as many items in this queue as // possible before switching to another queue. This means threads // often end up being dedicated to one type of work. q->ref_count++; while (q->input_head && q->qsize - q->n_output > q->n_processing) { if (p->shutdown) goto shutdown; if (q->shutdown) // Queue shutdown, but there may be other queues break; j = q->input_head; assert(j->p == p); if (!(q->input_head = j->next)) q->input_tail = NULL; // Transitioning from full queue to not-full means we can wake up // any blocked dispatch threads. We broadcast this as it's only // happening once (on the transition) rather than every time we // are below qsize. // (I wish I could remember why io_lib rev 3660 changed this from // == to >=, but keeping it just in case!) q->n_processing++; if (q->n_input-- >= q->qsize) pthread_cond_broadcast(&q->input_not_full_c); if (q->n_input == 0) pthread_cond_signal(&q->input_empty_c); p->njobs--; // Total number of jobs; used to adjust to CPU scaling pthread_mutex_unlock(&p->pool_m); DBG_OUT(stderr, "%d: Processing queue %p, serial %"PRId64"\n", worker_id(j->p), q, j->serial); if (hts_tpool_add_result(j, j->func(j->arg)) < 0) goto err; //memset(j, 0xbb, sizeof(*j)); free(j); pthread_mutex_lock(&p->pool_m); } if (--q->ref_count == 0) { // we were the last user hts_tpool_process_destroy(q); } else { // Out of jobs on this queue, so restart search from next one. // This is equivalent to "work-stealing". if (p->q_head) p->q_head = p->q_head->next; } } shutdown: pthread_mutex_unlock(&p->pool_m); #ifdef DEBUG fprintf(stderr, "%d: Shutting down\n", worker_id(p)); #endif return NULL; err: #ifdef DEBUG fprintf(stderr, "%d: Failed to add result\n", worker_id(p)); #endif // Hard failure, so shutdown all queues pthread_mutex_lock(&p->pool_m); hts_tpool_process *first = p->q_head, *q = first; if (q) { do { hts_tpool_process_shutdown_locked(q); q->shutdown = 2; // signify error. q = q->next; } while (q != first); } pthread_mutex_unlock(&p->pool_m); return NULL; } static void wake_next_worker(hts_tpool_process *q, int locked) { if (!q) return; hts_tpool *p = q->p; if (!locked) pthread_mutex_lock(&p->pool_m); // Update the q_head to be this queue so we'll start processing // the queue we know to have results. assert(q->prev && q->next); // attached p->q_head = q; // Wake up if we have more jobs waiting than CPUs. This partially combats // CPU frequency scaling effects. Starting too many threads and then // running out of jobs can cause each thread to have lots of start/stop // cycles, which then translates often to CPU frequency scaling // adjustments. Instead it is better to only start as many threads as we // need to keep the throughput up, meaning some threads run flat out and // others are idle. // // This isn't perfect as we need to know how many can actually start, // rather than how many are waiting. A limit on output queue size makes // these two figures different. assert(p->njobs >= q->n_input); int running = p->tsize - p->nwaiting; int sig = p->t_stack_top >= 0 && p->njobs > p->tsize - p->nwaiting && (q->n_processing < q->qsize - q->n_output); //#define AVG_USAGE #ifdef AVG_USAGE // Track average number of running threads and try to keep close. // We permit this to change, but slowly. This avoids "boom and bust" cycles // where we read a lot of data, start a lot of jobs, then become idle again. // This way some threads run steadily and others dormant, which is better // for throughput. // // It's 50:50 if this is a good thing. It helps some tasks quite significantly // while slightly hindering other (perhaps more usual) jobs. if (++p->n_count == 256) { p->n_count >>= 1; p->n_running >>= 1; } p->n_running += running; // Built in lag to avoid see-sawing. Is this safe in all cases? if (sig && p->n_count >= 128 && running*p->n_count > p->n_running+1) sig=0; #endif if (0) { printf("%d waiting, %d running, %d output, %d, arun %d => %d\t", p->njobs, running, q->n_output, q->qsize - q->n_output, p->n_running/p->n_count, sig); int i; for (i = 0; i < p->tsize; i++) putchar("x "[p->t_stack[i]]); putchar('\n'); } if (sig) pthread_cond_signal(&p->t[p->t_stack_top].pending_c); if (!locked) pthread_mutex_unlock(&p->pool_m); } /* * Creates a worker pool with n worker threads. * * Returns pool pointer on success; * NULL on failure */ hts_tpool *hts_tpool_init(int n) { int t_idx = 0; size_t stack_size = 0; pthread_attr_t pattr; int pattr_init_done = 0; hts_tpool *p = malloc(sizeof(*p)); if (!p) return NULL; p->tsize = n; p->njobs = 0; p->nwaiting = 0; p->shutdown = 0; p->q_head = NULL; p->t_stack = NULL; p->n_count = 0; p->n_running = 0; p->t = malloc(n * sizeof(p->t[0])); if (!p->t) { free(p); return NULL; } p->t_stack = malloc(n * sizeof(*p->t_stack)); if (!p->t_stack) { free(p->t); free(p); return NULL; } p->t_stack_top = -1; pthread_mutexattr_t attr; pthread_mutexattr_init(&attr); pthread_mutexattr_settype(&attr, PTHREAD_MUTEX_RECURSIVE); pthread_mutex_init(&p->pool_m, &attr); pthread_mutexattr_destroy(&attr); pthread_mutex_lock(&p->pool_m); // Ensure new threads have a reasonably large stack. On some platforms, // for example MacOS which defaults to 512Kb, this is not big enough // for some of the rANS codecs. if (pthread_attr_init(&pattr) < 0) goto cleanup; pattr_init_done = 1; if (pthread_attr_getstacksize(&pattr, &stack_size) < 0) goto cleanup; if (stack_size < HTS_MIN_THREAD_STACK) { if (pthread_attr_setstacksize(&pattr, HTS_MIN_THREAD_STACK) < 0) goto cleanup; } for (t_idx = 0; t_idx < n; t_idx++) { hts_tpool_worker *w = &p->t[t_idx]; p->t_stack[t_idx] = 0; w->p = p; w->idx = t_idx; pthread_cond_init(&w->pending_c, NULL); if (0 != pthread_create(&w->tid, &pattr, tpool_worker, w)) goto cleanup; } pthread_mutex_unlock(&p->pool_m); pthread_attr_destroy(&pattr); return p; cleanup: { // Any threads started will be waiting for p->pool_m, so we can // stop them cleanly by setting p->shutdown, releasing the mutex and // waiting for them to finish. int j; int save_errno = errno; hts_log_error("Couldn't start thread pool worker : %s", strerror(errno)); p->shutdown = 1; pthread_mutex_unlock(&p->pool_m); for (j = 0; j < t_idx; j++) { pthread_join(p->t[j].tid, NULL); pthread_cond_destroy(&p->t[j].pending_c); } pthread_mutex_destroy(&p->pool_m); if (pattr_init_done) pthread_attr_destroy(&pattr); free(p->t_stack); free(p->t); free(p); errno = save_errno; return NULL; } } /* * Returns the number of requested threads for a pool. */ int hts_tpool_size(hts_tpool *p) { return p->tsize; } /* * Adds an item to the work pool. * * Returns 0 on success * -1 on failure */ int hts_tpool_dispatch(hts_tpool *p, hts_tpool_process *q, void *(*func)(void *arg), void *arg) { return hts_tpool_dispatch3(p, q, func, arg, NULL, NULL, 0); } /* * As above but optional non-block flag. * * nonblock 0 => block if input queue is full * nonblock +1 => don't block if input queue is full, but do not add task * nonblock -1 => add task regardless of whether queue is full (over-size) */ int hts_tpool_dispatch2(hts_tpool *p, hts_tpool_process *q, void *(*func)(void *arg), void *arg, int nonblock) { return hts_tpool_dispatch3(p, q, func, arg, NULL, NULL, nonblock); } int hts_tpool_dispatch3(hts_tpool *p, hts_tpool_process *q, void *(*exec_func)(void *arg), void *arg, void (*job_cleanup)(void *arg), void (*result_cleanup)(void *data), int nonblock) { hts_tpool_job *j; pthread_mutex_lock(&p->pool_m); DBG_OUT(stderr, "Dispatching job for queue %p, serial %"PRId64"\n", q, q->curr_serial); if ((q->no_more_input || q->n_input >= q->qsize) && nonblock == 1) { pthread_mutex_unlock(&p->pool_m); errno = EAGAIN; return -1; } if (!(j = malloc(sizeof(*j)))) { pthread_mutex_unlock(&p->pool_m); return -1; } j->func = exec_func; j->arg = arg; j->job_cleanup = job_cleanup; j->result_cleanup = result_cleanup; j->next = NULL; j->p = p; j->q = q; j->serial = q->curr_serial++; if (nonblock == 0) { while ((q->no_more_input || q->n_input >= q->qsize) && !q->shutdown && !q->wake_dispatch) { pthread_cond_wait(&q->input_not_full_c, &q->p->pool_m); } if (q->no_more_input || q->shutdown) { free(j); pthread_mutex_unlock(&p->pool_m); return -1; } if (q->wake_dispatch) { //fprintf(stderr, "Wake => non-block for this operation\n"); q->wake_dispatch = 0; } } p->njobs++; // total across all queues q->n_input++; // queue specific if (q->input_tail) { q->input_tail->next = j; q->input_tail = j; } else { q->input_head = q->input_tail = j; } DBG_OUT(stderr, "Dispatched (serial %"PRId64")\n", j->serial); // Let a worker know we have data. // Keep incoming queue at 1 per running thread, so there is always // something waiting when they end their current task. If we go above // this signal to start more threads (if available). This has the effect // of concentrating jobs to fewer cores when we are I/O bound, which in // turn benefits systems with auto CPU frequency scaling. if (!q->shutdown) wake_next_worker(q, 1); pthread_mutex_unlock(&p->pool_m); return 0; } /* * Wakes up a single thread stuck in dispatch and make it return with * errno EAGAIN. */ void hts_tpool_wake_dispatch(hts_tpool_process *q) { pthread_mutex_lock(&q->p->pool_m); q->wake_dispatch = 1; pthread_cond_signal(&q->input_not_full_c); pthread_mutex_unlock(&q->p->pool_m); } /* * Flushes the process-queue, but doesn't exit. This simply drains the queue * and ensures all worker threads have finished their current tasks * associated with this process. * * NOT: This does not mean the worker threads are not executing jobs in * another process-queue. * * Returns 0 on success; * -1 on failure */ int hts_tpool_process_flush(hts_tpool_process *q) { int i; hts_tpool *p = q->p; DBG_OUT(stderr, "Flushing pool %p\n", p); // Drains the queue pthread_mutex_lock(&p->pool_m); // Wake up everything for the final sprint! for (i = 0; i < p->tsize; i++) if (p->t_stack[i]) pthread_cond_signal(&p->t[i].pending_c); // Ensure there is room for the final sprint. // Ideally we shouldn't get here, but the "q->qsize - q->n_output > // n_processing" check in tpool_worker means we can trigger a // deadlock there. This negates that possibility. if (q->qsize < q->n_output + q->n_input + q->n_processing) q->qsize = q->n_output + q->n_input + q->n_processing; // When shutdown, we won't be launching more, but we can still // wait for any processing jobs complete. if (q->shutdown) { while (q->n_processing) pthread_cond_wait(&q->none_processing_c, &p->pool_m); } // Wait for n_input and n_processing to hit zero. while (!q->shutdown && (q->n_input || q->n_processing)) { struct timeval now; struct timespec timeout; while (q->n_input && !q->shutdown) { gettimeofday(&now, NULL); timeout.tv_sec = now.tv_sec + 1; timeout.tv_nsec = now.tv_usec * 1000; pthread_cond_timedwait(&q->input_empty_c, &p->pool_m, &timeout); } // Note: even if q->shutdown is set, we still have to wait until // q->n_processing is zero as we cannot terminate while things are // running otherwise we free up the data being worked on. while (q->n_processing) { gettimeofday(&now, NULL); timeout.tv_sec = now.tv_sec + 1; timeout.tv_nsec = now.tv_usec * 1000; pthread_cond_timedwait(&q->none_processing_c, &p->pool_m, &timeout); } if (q->shutdown) break; } pthread_mutex_unlock(&p->pool_m); DBG_OUT(stderr, "Flushed complete for pool %p, queue %p\n", p, q); return 0; } /* * Resets a process to the initial state. * * This removes any queued up input jobs, disables any notification of * new results/output, flushes what is left and then discards any * queued output. Anything consumer stuck in a wait on results to * appear should stay stuck and will only wake up when new data is * pushed through the queue. * * Returns 0 on success; * -1 on failure */ int hts_tpool_process_reset(hts_tpool_process *q, int free_results) { hts_tpool_job *j, *jn, *j_head; hts_tpool_result *r, *rn, *r_head; pthread_mutex_lock(&q->p->pool_m); // prevent next_result from returning data during our flush q->next_serial = INT_MAX; // Remove any queued input not yet being acted upon j_head = q->input_head; q->input_head = q->input_tail = NULL; q->n_input = 0; // Remove any queued output, thus ensuring we have room to flush. r_head = q->output_head; q->output_head = q->output_tail = NULL; q->n_output = 0; pthread_mutex_unlock(&q->p->pool_m); // Release memory. This can be done unlocked now the lists have been // removed from the queue for (j = j_head; j; j = jn) { jn = j->next; if (j->job_cleanup) j->job_cleanup(j->arg); free(j); } for (r = r_head; r; r = rn) { rn = r->next; if (r->result_cleanup) { r->result_cleanup(r->data); r->data = NULL; } hts_tpool_delete_result(r, free_results); } // Wait for any jobs being processed to complete. // (TODO: consider how to cancel any currently processing jobs. // Probably this is too hard.) if (hts_tpool_process_flush(q) != 0) return -1; // Remove any new output. pthread_mutex_lock(&q->p->pool_m); r_head = q->output_head; q->output_head = q->output_tail = NULL; q->n_output = 0; // Finally reset the serial back to the starting point. q->next_serial = q->curr_serial = 0; pthread_cond_signal(&q->input_not_full_c); pthread_mutex_unlock(&q->p->pool_m); // Discard unwanted output for (r = r_head; r; r = rn) { //fprintf(stderr, "Discard output %d\n", r->serial); rn = r->next; if (r->result_cleanup) { r->result_cleanup(r->data); r->data = NULL; } hts_tpool_delete_result(r, free_results); } return 0; } /* Returns the process queue size */ int hts_tpool_process_qsize(hts_tpool_process *q) { return q->qsize; } /* * Destroys a thread pool. The threads are joined into the main * thread so they will finish their current work load. */ void hts_tpool_destroy(hts_tpool *p) { int i; DBG_OUT(stderr, "Destroying pool %p\n", p); /* Send shutdown message to worker threads */ pthread_mutex_lock(&p->pool_m); p->shutdown = 1; DBG_OUT(stderr, "Sending shutdown request\n"); for (i = 0; i < p->tsize; i++) pthread_cond_signal(&p->t[i].pending_c); pthread_mutex_unlock(&p->pool_m); DBG_OUT(stderr, "Shutdown complete\n"); for (i = 0; i < p->tsize; i++) pthread_join(p->t[i].tid, NULL); pthread_mutex_destroy(&p->pool_m); for (i = 0; i < p->tsize; i++) pthread_cond_destroy(&p->t[i].pending_c); if (p->t_stack) free(p->t_stack); free(p->t); free(p); DBG_OUT(stderr, "Destroyed pool %p\n", p); } /* * Destroys a thread pool without waiting on jobs to complete. * Use hts_tpool_kill(p) to quickly exit after a fatal error. */ void hts_tpool_kill(hts_tpool *p) { int i; DBG_OUT(stderr, "Destroying pool %p, kill=%d\n", p, kill); for (i = 0; i < p->tsize; i++) pthread_kill(p->t[i].tid, SIGINT); pthread_mutex_destroy(&p->pool_m); for (i = 0; i < p->tsize; i++) pthread_cond_destroy(&p->t[i].pending_c); if (p->t_stack) free(p->t_stack); free(p->t); free(p); DBG_OUT(stderr, "Destroyed pool %p\n", p); } /*============================================================================= * Test app. * * This can be considered both as a basic test and as a worked example for * various usage patterns. *============================================================================= */ #ifdef TEST_MAIN #include #ifndef TASK_SIZE #define TASK_SIZE 1000 #endif /*----------------------------------------------------------------------------- * Unordered x -> x*x test. * Results arrive in order of completion. */ void *doit_square_u(void *arg) { int job = *(int *)arg; usleep(random() % 100000); // to coerce job completion out of order printf("RESULT: %d\n", job*job); free(arg); return NULL; } int test_square_u(int n) { hts_tpool *p = hts_tpool_init(n); hts_tpool_process *q = hts_tpool_process_init(p, n*2, 1); int i; // Dispatch jobs for (i = 0; i < TASK_SIZE; i++) { int *ip = malloc(sizeof(*ip)); *ip = i; hts_tpool_dispatch(p, q, doit_square_u, ip); } hts_tpool_process_flush(q); hts_tpool_process_destroy(q); hts_tpool_destroy(p); return 0; } /*----------------------------------------------------------------------------- * Ordered x -> x*x test. * Results arrive in numerical order. * * This implementation uses a non-blocking dispatch to avoid dead-locks * where one job takes too long to complete. */ void *doit_square(void *arg) { int job = *(int *)arg; int *res; // One excessively slow, to stress test output queue filling and // excessive out of order scenarios. usleep(500000 * ((job&31)==31) + random() % 10000); res = malloc(sizeof(*res)); *res = (job<0) ? -job*job : job*job; free(arg); return res; } int test_square(int n) { hts_tpool *p = hts_tpool_init(n); hts_tpool_process *q = hts_tpool_process_init(p, n*2, 0); int i; hts_tpool_result *r; // Dispatch jobs for (i = 0; i < TASK_SIZE; i++) { int *ip = malloc(sizeof(*ip)); *ip = i; int blk; do { // In the situation where some jobs take much longer than // others, we could end up blocking here as we haven't got // any room in the output queue to place it. (We don't launch a // job if the output queue is full.) // This happens when the next serial number to fetch is, eg, 50 // but jobs 51-100 have all executed really fast and appeared in // the output queue before 50. A dispatch & check-results // alternating loop can fail to find job 50 many times over until // eventually the dispatch blocks before it arrives. // Our solution is to dispatch in non-blocking mode so we are // always to either dispatch or consume a result. blk = hts_tpool_dispatch2(p, q, doit_square, ip, 1); // Check for results. if ((r = hts_tpool_next_result(q))) { printf("RESULT: %d\n", *(int *)hts_tpool_result_data(r)); hts_tpool_delete_result(r, 1); } if (blk == -1) { // The alternative is a separate thread for dispatching and/or // consumption of results. See test_squareB. putchar('.'); fflush(stdout); usleep(10000); } } while (blk == -1); } // Wait for any input-queued up jobs or in-progress jobs to complete. hts_tpool_process_flush(q); while ((r = hts_tpool_next_result(q))) { printf("RESULT: %d\n", *(int *)hts_tpool_result_data(r)); hts_tpool_delete_result(r, 1); } hts_tpool_process_destroy(q); hts_tpool_destroy(p); return 0; } /*----------------------------------------------------------------------------- * Ordered x -> x*x test. * Results arrive in numerical order. * * This implementation uses separate dispatching threads and job consumption * threads (main thread). This means it can use a blocking calls for * simplicity elsewhere. */ struct squareB_opt { hts_tpool *p; hts_tpool_process *q; int n; }; static void *test_squareB_dispatcher(void *arg) { struct squareB_opt *o = (struct squareB_opt *)arg; int i, *ip; for (i = 0; i < o->n; i++) { ip = malloc(sizeof(*ip)); *ip = i; hts_tpool_dispatch(o->p, o->q, doit_square, ip); } // Dispatch an sentinel job to mark the end *(ip = malloc(sizeof(*ip))) = -1; hts_tpool_dispatch(o->p, o->q, doit_square, ip); pthread_exit(NULL); } int test_squareB(int n) { hts_tpool *p = hts_tpool_init(n); hts_tpool_process *q = hts_tpool_process_init(p, n*2, 0); struct squareB_opt o = {p, q, TASK_SIZE}; pthread_t tid; // Launch our job creation thread. pthread_create(&tid, NULL, test_squareB_dispatcher, &o); // Consume all results until we find the end-of-job marker. for(;;) { hts_tpool_result *r = hts_tpool_next_result_wait(q); int x = *(int *)hts_tpool_result_data(r); hts_tpool_delete_result(r, 1); if (x == -1) break; printf("RESULT: %d\n", x); } // Wait for any input-queued up jobs or in-progress jobs to complete. // This should do nothing as we've been executing until the termination // marker of -1. hts_tpool_process_flush(q); assert(hts_tpool_next_result(q) == NULL); hts_tpool_process_destroy(q); hts_tpool_destroy(p); pthread_join(tid, NULL); return 0; } /*----------------------------------------------------------------------------- * A simple pipeline test. * We use a dedicated input thread that does the initial generation of job * and dispatch, several execution steps running in a shared pool, and a * dedicated output thread that prints up the final result. It's key that our * pipeline execution stages can run independently and don't themselves have * any waits. To achieve this we therefore also use some dedicated threads * that take the output from one queue and resubmits the job as the input to * the next queue. * * More generally this could perhaps be a single pipeline thread that * marshalls multiple queues and their interactions, but this is simply a * demonstration of a single pipeline. * * Our process fills out the bottom byte of a 32-bit int and then shifts it * left one byte at a time. Only the final stage needs to be ordered. Each * stage uses its own queue. * * Possible improvement: we only need the last stage to be ordered. By * allocating our own serial numbers for the first job and manually setting * these serials in the last job, perhaps we can permit out of order execution * of all the in-between stages. (I doubt it'll affect speed much though.) */ static void *pipe_input_thread(void *arg); static void *pipe_stage1(void *arg); static void *pipe_stage2(void *arg); static void *pipe_stage3(void *arg); static void *pipe_output_thread(void *arg); typedef struct { hts_tpool *p; hts_tpool_process *q1; hts_tpool_process *q2; hts_tpool_process *q3; int n; } pipe_opt; typedef struct { pipe_opt *o; unsigned int x; int eof; // set with last job. } pipe_job; static void *pipe_input_thread(void *arg) { pipe_opt *o = (pipe_opt *)arg; int i; for (i = 1; i <= o->n; i++) { pipe_job *j = malloc(sizeof(*j)); j->o = o; j->x = i; j->eof = (i == o->n); printf("I %08x\n", j->x); if (hts_tpool_dispatch(o->p, o->q1, pipe_stage1, j) != 0) { free(j); pthread_exit((void *)1); } } pthread_exit(NULL); } static void *pipe_stage1(void *arg) { pipe_job *j = (pipe_job *)arg; j->x <<= 8; usleep(random() % 10000); // fast job printf("1 %08x\n", j->x); return j; } static void *pipe_stage1to2(void *arg) { pipe_opt *o = (pipe_opt *)arg; hts_tpool_result *r; while ((r = hts_tpool_next_result_wait(o->q1))) { pipe_job *j = (pipe_job *)hts_tpool_result_data(r); hts_tpool_delete_result(r, 0); if (hts_tpool_dispatch(j->o->p, j->o->q2, pipe_stage2, j) != 0) pthread_exit((void *)1); if (j->eof) break; } pthread_exit(NULL); } static void *pipe_stage2(void *arg) { pipe_job *j = (pipe_job *)arg; j->x <<= 8; usleep(random() % 100000); // slow job printf("2 %08x\n", j->x); return j; } static void *pipe_stage2to3(void *arg) { pipe_opt *o = (pipe_opt *)arg; hts_tpool_result *r; while ((r = hts_tpool_next_result_wait(o->q2))) { pipe_job *j = (pipe_job *)hts_tpool_result_data(r); hts_tpool_delete_result(r, 0); if (hts_tpool_dispatch(j->o->p, j->o->q3, pipe_stage3, j) != 0) pthread_exit((void *)1); if (j->eof) break; } pthread_exit(NULL); } static void *pipe_stage3(void *arg) { pipe_job *j = (pipe_job *)arg; usleep(random() % 10000); // fast job j->x <<= 8; return j; } static void *pipe_output_thread(void *arg) { pipe_opt *o = (pipe_opt *)arg; hts_tpool_result *r; while ((r = hts_tpool_next_result_wait(o->q3))) { pipe_job *j = (pipe_job *)hts_tpool_result_data(r); int eof = j->eof; printf("O %08x\n", j->x); hts_tpool_delete_result(r, 1); if (eof) break; } pthread_exit(NULL); } int test_pipe(int n) { hts_tpool *p = hts_tpool_init(n); hts_tpool_process *q1 = hts_tpool_process_init(p, n*2, 0); hts_tpool_process *q2 = hts_tpool_process_init(p, n*2, 0); hts_tpool_process *q3 = hts_tpool_process_init(p, n*2, 0); pipe_opt o = {p, q1, q2, q3, TASK_SIZE}; pthread_t tidIto1, tid1to2, tid2to3, tid3toO; void *retv; int ret; // Launch our data source and sink threads. pthread_create(&tidIto1, NULL, pipe_input_thread, &o); pthread_create(&tid1to2, NULL, pipe_stage1to2, &o); pthread_create(&tid2to3, NULL, pipe_stage2to3, &o); pthread_create(&tid3toO, NULL, pipe_output_thread, &o); // Wait for tasks to finish. ret = 0; pthread_join(tidIto1, &retv); ret |= (retv != NULL); pthread_join(tid1to2, &retv); ret |= (retv != NULL); pthread_join(tid2to3, &retv); ret |= (retv != NULL); pthread_join(tid3toO, &retv); ret |= (retv != NULL); printf("Return value %d\n", ret); hts_tpool_process_destroy(q1); hts_tpool_process_destroy(q2); hts_tpool_process_destroy(q3); hts_tpool_destroy(p); return 0; } /*-----------------------------------------------------------------------------*/ int main(int argc, char **argv) { int n; srandom(0); if (argc < 3) { fprintf(stderr, "Usage: %s command n_threads\n", argv[0]); fprintf(stderr, "Where commands are:\n\n"); fprintf(stderr, "unordered # Unordered output\n"); fprintf(stderr, "ordered1 # Main thread with non-block API\n"); fprintf(stderr, "ordered2 # Dispatch thread, blocking API\n"); fprintf(stderr, "pipe # Multi-stage pipeline, several queues\n"); exit(1); } n = atoi(argv[2]); if (strcmp(argv[1], "unordered") == 0) return test_square_u(n); if (strcmp(argv[1], "ordered1") == 0) return test_square(n); if (strcmp(argv[1], "ordered2") == 0) return test_squareB(n); if (strcmp(argv[1], "pipe") == 0) return test_pipe(n); fprintf(stderr, "Unknown sub-command\n"); exit(1); } #endif pysam-0.23.0/htslib/thread_pool_internal.h000066400000000000000000000133351475062545500206010ustar00rootroot00000000000000/* thread_pool_internal.h -- Internal API for the thread pool. Copyright (c) 2013-2016 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* * This file implements a thread pool for multi-threading applications. * It consists of two distinct interfaces: thread pools an thread job queues. * * The pool of threads is given a function pointer and void* data to pass in. * This means the pool can run jobs of multiple types, albeit first come * first served with no job scheduling except to pick tasks from * queues that have room to store the result. * * Upon completion, the return value from the function pointer is * added to back to the queue if the result is required. We may have * multiple queues in use for the one pool. * * To see example usage, please look at the #ifdef TEST_MAIN code in * thread_pool.c. */ #ifndef THREAD_POOL_INTERNAL_H #define THREAD_POOL_INTERNAL_H #include #include #include "htslib/thread_pool.h" #ifdef __cplusplus extern "C" { #endif /* * An input job, before execution. */ typedef struct hts_tpool_job { void *(*func)(void *arg); void *arg; void (*job_cleanup)(void *arg); void (*result_cleanup)(void *data); struct hts_tpool_job *next; struct hts_tpool *p; struct hts_tpool_process *q; uint64_t serial; } hts_tpool_job; /* * An output, after job has executed. */ struct hts_tpool_result { struct hts_tpool_result *next; void (*result_cleanup)(void *data); uint64_t serial; // sequential number for ordering void *data; // result itself }; /* * A per-thread worker struct. */ typedef struct { struct hts_tpool *p; int idx; pthread_t tid; pthread_cond_t pending_c; // when waiting for a job } hts_tpool_worker; /* * An IO queue consists of a queue of jobs to execute * (the "input" side) and a queue of job results post- * execution (the "output" side). * * We have size limits to prevent either queue from * growing too large and serial numbers to ensure * sequential consumption of the output. * * The thread pool may have many hetergeneous tasks, each * using its own io_queue mixed into the same thread pool. */ struct hts_tpool_process { struct hts_tpool *p; // thread pool hts_tpool_job *input_head; // input list hts_tpool_job *input_tail; hts_tpool_result *output_head; // output list hts_tpool_result *output_tail; int qsize; // max size of i/o queues uint64_t next_serial; // next serial for output uint64_t curr_serial; // current serial (next input) int no_more_input; // disable dispatching of more jobs int n_input; // no. items in input queue; was njobs int n_output; // no. items in output queue int n_processing; // no. items being processed (executing) int shutdown; // true if pool is being destroyed int in_only; // if true, don't queue result up. int wake_dispatch; // unblocks waiting dispatchers int ref_count; // used to track safe destruction pthread_cond_t output_avail_c; // Signalled on each new output pthread_cond_t input_not_full_c; // Input queue is no longer full pthread_cond_t input_empty_c; // Input queue has become empty pthread_cond_t none_processing_c;// n_processing has hit zero struct hts_tpool_process *next, *prev;// to form circular linked list. }; /* * The single pool structure itself. * * This knows nothing about the nature of the jobs or where their * output is going, but it maintains a list of queues associated with * this pool from which the jobs are taken. */ struct hts_tpool { int nwaiting; // how many workers waiting for new jobs int njobs; // how many total jobs are waiting in all queues int shutdown; // true if pool is being destroyed // I/O queues to check for jobs in and to put results. // Forms a circular linked list. (q_head may be amended // to point to the most recently updated.) hts_tpool_process *q_head; // threads int tsize; // maximum number of jobs hts_tpool_worker *t; // array of worker IDs free int *t_stack, t_stack_top; // A single mutex used when updating this and any associated structure. pthread_mutex_t pool_m; // Tracking of average number of running jobs. // This can be used to dampen any hysteresis caused by bursty // input availability. int n_count, n_running; // Debugging to check wait time. // FIXME: should we just delete these and cull the associated code? long long total_time, wait_time; }; #ifdef __cplusplus } #endif #endif pysam-0.23.0/htslib/vcf.c000066400000000000000000006125221475062545500151610ustar00rootroot00000000000000/* vcf.c -- VCF/BCF API functions. Copyright (C) 2012, 2013 Broad Institute. Copyright (C) 2012-2024 Genome Research Ltd. Portions copyright (C) 2014 Intel Corporation. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include #include #include #include #include #include #include #include #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION #include "fuzz_settings.h" #endif #include "htslib/vcf.h" #include "htslib/bgzf.h" #include "htslib/tbx.h" #include "htslib/hfile.h" #include "hts_internal.h" #include "htslib/hts_endian.h" #include "htslib/khash_str2int.h" #include "htslib/kstring.h" #include "htslib/sam.h" #include "htslib/khash.h" #if 0 // This helps on Intel a bit, often 6-7% faster VCF parsing. // Conversely sometimes harms AMD Zen4 as ~9% slower. // Possibly related to IPC differences. However for now it's just a // curiousity we ignore and stick with the simpler code. // // Left here as a hint for future explorers. static inline int xstreq(const char *a, const char *b) { while (*a && *a == *b) a++, b++; return *a == *b; } #define KHASH_MAP_INIT_XSTR(name, khval_t) \ KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, xstreq) KHASH_MAP_INIT_XSTR(vdict, bcf_idinfo_t) #else KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t) #endif typedef khash_t(vdict) vdict_t; KHASH_MAP_INIT_STR(hdict, bcf_hrec_t*) typedef khash_t(hdict) hdict_t; #include "htslib/kseq.h" HTSLIB_EXPORT uint32_t bcf_float_missing = 0x7F800001; HTSLIB_EXPORT uint32_t bcf_float_vector_end = 0x7F800002; HTSLIB_EXPORT uint8_t bcf_type_shift[] = { 0, 0, 1, 2, 3, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }; static bcf_idinfo_t bcf_idinfo_def = { .info = { 15, 15, 15 }, .hrec = { NULL, NULL, NULL}, .id = -1 }; /* Partial support for 64-bit POS and Number=1 INFO tags. Notes: - the support for 64-bit values is motivated by POS and INFO/END for large genomes - the use of 64-bit values does not conform to the specification - cannot output 64-bit BCF and if it does, it is not compatible with anything - experimental, use at your risk */ #ifdef VCF_ALLOW_INT64 #define BCF_MAX_BT_INT64 (0x7fffffffffffffff) /* INT64_MAX, for internal use only */ #define BCF_MIN_BT_INT64 -9223372036854775800LL /* INT64_MIN + 8, for internal use only */ #endif #define BCF_IS_64BIT (1<<30) // Opaque structure with auxilary data which allows to extend bcf_hdr_t without breaking ABI. // Note that this preserving API and ABI requires that the first element is vdict_t struct // rather than a pointer, as user programs may (and in some cases do) access the dictionary // directly as (vdict_t*)hdr->dict. typedef struct { vdict_t dict; // bcf_hdr_t.dict[0] vdict_t dictionary which keeps bcf_idinfo_t for BCF_HL_FLT,BCF_HL_INFO,BCF_HL_FMT hdict_t *gen; // hdict_t dictionary which keeps bcf_hrec_t* pointers for generic and structured fields size_t *key_len;// length of h->id[BCF_DT_ID] strings } bcf_hdr_aux_t; static inline bcf_hdr_aux_t *get_hdr_aux(const bcf_hdr_t *hdr) { return (bcf_hdr_aux_t *)hdr->dict[0]; } static char *find_chrom_header_line(char *s) { char *nl; if (strncmp(s, "#CHROM\t", 7) == 0) return s; else if ((nl = strstr(s, "\n#CHROM\t")) != NULL) return nl+1; else return NULL; } /************************* *** VCF header parser *** *************************/ static int bcf_hdr_add_sample_len(bcf_hdr_t *h, const char *s, size_t len) { const char *ss = s; while ( *ss && isspace_c(*ss) && ss - s < len) ss++; if ( !*ss || ss - s == len) { hts_log_error("Empty sample name: trailing spaces/tabs in the header line?"); return -1; } vdict_t *d = (vdict_t*)h->dict[BCF_DT_SAMPLE]; int ret; char *sdup = malloc(len + 1); if (!sdup) return -1; memcpy(sdup, s, len); sdup[len] = 0; // Ensure space is available in h->samples size_t n = kh_size(d); char **new_samples = realloc(h->samples, sizeof(char*) * (n + 1)); if (!new_samples) { free(sdup); return -1; } h->samples = new_samples; int k = kh_put(vdict, d, sdup, &ret); if (ret < 0) { free(sdup); return -1; } if (ret) { // absent kh_val(d, k) = bcf_idinfo_def; kh_val(d, k).id = n; } else { hts_log_error("Duplicated sample name '%s'", sdup); free(sdup); return -1; } h->samples[n] = sdup; h->dirty = 1; return 0; } int bcf_hdr_add_sample(bcf_hdr_t *h, const char *s) { if (!s) { // Allowed for backwards-compatibility, calling with s == NULL // used to trigger bcf_hdr_sync(h); return 0; } return bcf_hdr_add_sample_len(h, s, strlen(s)); } int HTS_RESULT_USED bcf_hdr_parse_sample_line(bcf_hdr_t *hdr, const char *str) { const char *mandatory = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"; if ( strncmp(str,mandatory,strlen(mandatory)) ) { hts_log_error("Could not parse the \"#CHROM..\" line, either the fields are incorrect or spaces are present instead of tabs:\n\t%s",str); return -1; } const char *beg = str + strlen(mandatory), *end; if ( !*beg || *beg=='\n' ) return 0; if ( strncmp(beg,"\tFORMAT\t",8) ) { hts_log_error("Could not parse the \"#CHROM..\" line, either FORMAT is missing or spaces are present instead of tabs:\n\t%s",str); return -1; } beg += 8; int ret = 0; while ( *beg ) { end = beg; while ( *end && *end!='\t' && *end!='\n' ) end++; if ( bcf_hdr_add_sample_len(hdr, beg, end-beg) < 0 ) ret = -1; if ( !*end || *end=='\n' || ret<0 ) break; beg = end + 1; } return ret; } int bcf_hdr_sync(bcf_hdr_t *h) { int i; for (i = 0; i < 3; i++) { vdict_t *d = (vdict_t*)h->dict[i]; khint_t k; if ( h->n[i] < kh_size(d) ) { bcf_idpair_t *new_idpair; // this should be true only for i=2, BCF_DT_SAMPLE new_idpair = (bcf_idpair_t*) realloc(h->id[i], kh_size(d)*sizeof(bcf_idpair_t)); if (!new_idpair) return -1; h->n[i] = kh_size(d); h->id[i] = new_idpair; } for (k=kh_begin(d); kid[i][kh_val(d,k).id].key = kh_key(d,k); h->id[i][kh_val(d,k).id].val = &kh_val(d,k); } } // Invalidate key length cache bcf_hdr_aux_t *aux = get_hdr_aux(h); if (aux && aux->key_len) { free(aux->key_len); aux->key_len = NULL; } h->dirty = 0; return 0; } void bcf_hrec_destroy(bcf_hrec_t *hrec) { if (!hrec) return; free(hrec->key); if ( hrec->value ) free(hrec->value); int i; for (i=0; inkeys; i++) { free(hrec->keys[i]); free(hrec->vals[i]); } free(hrec->keys); free(hrec->vals); free(hrec); } // Copies all fields except IDX. bcf_hrec_t *bcf_hrec_dup(bcf_hrec_t *hrec) { int save_errno; bcf_hrec_t *out = (bcf_hrec_t*) calloc(1,sizeof(bcf_hrec_t)); if (!out) return NULL; out->type = hrec->type; if ( hrec->key ) { out->key = strdup(hrec->key); if (!out->key) goto fail; } if ( hrec->value ) { out->value = strdup(hrec->value); if (!out->value) goto fail; } out->nkeys = hrec->nkeys; out->keys = (char**) malloc(sizeof(char*)*hrec->nkeys); if (!out->keys) goto fail; out->vals = (char**) malloc(sizeof(char*)*hrec->nkeys); if (!out->vals) goto fail; int i, j = 0; for (i=0; inkeys; i++) { if ( hrec->keys[i] && !strcmp("IDX",hrec->keys[i]) ) continue; if ( hrec->keys[i] ) { out->keys[j] = strdup(hrec->keys[i]); if (!out->keys[j]) goto fail; } if ( hrec->vals[i] ) { out->vals[j] = strdup(hrec->vals[i]); if (!out->vals[j]) goto fail; } j++; } if ( i!=j ) out->nkeys -= i-j; // IDX was omitted return out; fail: save_errno = errno; hts_log_error("%s", strerror(errno)); bcf_hrec_destroy(out); errno = save_errno; return NULL; } void bcf_hrec_debug(FILE *fp, bcf_hrec_t *hrec) { fprintf(fp, "key=[%s] value=[%s]", hrec->key, hrec->value?hrec->value:""); int i; for (i=0; inkeys; i++) fprintf(fp, "\t[%s]=[%s]", hrec->keys[i],hrec->vals[i]); fprintf(fp, "\n"); } void bcf_header_debug(bcf_hdr_t *hdr) { int i, j; for (i=0; inhrec; i++) { if ( !hdr->hrec[i]->value ) { fprintf(stderr, "##%s=<", hdr->hrec[i]->key); fprintf(stderr,"%s=%s", hdr->hrec[i]->keys[0], hdr->hrec[i]->vals[0]); for (j=1; jhrec[i]->nkeys; j++) fprintf(stderr,",%s=%s", hdr->hrec[i]->keys[j], hdr->hrec[i]->vals[j]); fprintf(stderr,">\n"); } else fprintf(stderr,"##%s=%s\n", hdr->hrec[i]->key,hdr->hrec[i]->value); } } int bcf_hrec_add_key(bcf_hrec_t *hrec, const char *str, size_t len) { char **tmp; size_t n = hrec->nkeys + 1; assert(len > 0 && len < SIZE_MAX); tmp = realloc(hrec->keys, sizeof(char*)*n); if (!tmp) return -1; hrec->keys = tmp; tmp = realloc(hrec->vals, sizeof(char*)*n); if (!tmp) return -1; hrec->vals = tmp; hrec->keys[hrec->nkeys] = (char*) malloc((len+1)*sizeof(char)); if (!hrec->keys[hrec->nkeys]) return -1; memcpy(hrec->keys[hrec->nkeys],str,len); hrec->keys[hrec->nkeys][len] = 0; hrec->vals[hrec->nkeys] = NULL; hrec->nkeys = n; return 0; } int bcf_hrec_set_val(bcf_hrec_t *hrec, int i, const char *str, size_t len, int is_quoted) { if ( hrec->vals[i] ) { free(hrec->vals[i]); hrec->vals[i] = NULL; } if ( !str ) return 0; if ( is_quoted ) { if (len >= SIZE_MAX - 3) { errno = ENOMEM; return -1; } hrec->vals[i] = (char*) malloc((len+3)*sizeof(char)); if (!hrec->vals[i]) return -1; hrec->vals[i][0] = '"'; memcpy(&hrec->vals[i][1],str,len); hrec->vals[i][len+1] = '"'; hrec->vals[i][len+2] = 0; } else { if (len == SIZE_MAX) { errno = ENOMEM; return -1; } hrec->vals[i] = (char*) malloc((len+1)*sizeof(char)); if (!hrec->vals[i]) return -1; memcpy(hrec->vals[i],str,len); hrec->vals[i][len] = 0; } return 0; } int hrec_add_idx(bcf_hrec_t *hrec, int idx) { int n = hrec->nkeys + 1; char **tmp = (char**) realloc(hrec->keys, sizeof(char*)*n); if (!tmp) return -1; hrec->keys = tmp; tmp = (char**) realloc(hrec->vals, sizeof(char*)*n); if (!tmp) return -1; hrec->vals = tmp; hrec->keys[hrec->nkeys] = strdup("IDX"); if (!hrec->keys[hrec->nkeys]) return -1; kstring_t str = {0,0,0}; if (kputw(idx, &str) < 0) { free(hrec->keys[hrec->nkeys]); return -1; } hrec->vals[hrec->nkeys] = str.s; hrec->nkeys = n; return 0; } int bcf_hrec_find_key(bcf_hrec_t *hrec, const char *key) { int i; for (i=0; inkeys; i++) if ( !strcasecmp(key,hrec->keys[i]) ) return i; return -1; } static void bcf_hrec_set_type(bcf_hrec_t *hrec) { if ( !strcmp(hrec->key, "contig") ) hrec->type = BCF_HL_CTG; else if ( !strcmp(hrec->key, "INFO") ) hrec->type = BCF_HL_INFO; else if ( !strcmp(hrec->key, "FILTER") ) hrec->type = BCF_HL_FLT; else if ( !strcmp(hrec->key, "FORMAT") ) hrec->type = BCF_HL_FMT; else if ( hrec->nkeys>0 ) hrec->type = BCF_HL_STR; else hrec->type = BCF_HL_GEN; } /** The arrays were generated with valid_ctg: perl -le '@v = (split(//,q[!#$%&*+./:;=?@^_|~-]),"a"..."z","A"..."Z","0"..."9"); @a = (0) x 256; foreach $c (@v) { $a[ord($c)] = 1; } print join(", ",@a)' | fold -w 48 valid_tag: perl -le '@v = (split(//,q[_.]),"a"..."z","A"..."Z","0"..."9"); @a = (0) x 256; foreach $c (@v) { $a[ord($c)] = 1; } print join(", ",@a)' | fold -w 48 */ static const uint8_t valid_ctg[256] = { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }; static const uint8_t valid_tag[256] = { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }; /** bcf_hrec_check() - check the validity of structured header lines Returns 0 on success or negative value on error. Currently the return status is not checked by the caller and only a warning is printed on stderr. This should be improved to propagate the error all the way up to the caller and let it decide what to do: throw an error or proceed anyway. */ static int bcf_hrec_check(bcf_hrec_t *hrec) { int i; bcf_hrec_set_type(hrec); if ( hrec->type==BCF_HL_CTG ) { i = bcf_hrec_find_key(hrec,"ID"); if ( i<0 ) goto err_missing_id; char *val = hrec->vals[i]; if ( val[0]=='*' || val[0]=='=' || !valid_ctg[(uint8_t)val[0]] ) goto err_invalid_ctg; while ( *(++val) ) if ( !valid_ctg[(uint8_t)*val] ) goto err_invalid_ctg; return 0; } if ( hrec->type==BCF_HL_INFO ) { i = bcf_hrec_find_key(hrec,"ID"); if ( i<0 ) goto err_missing_id; char *val = hrec->vals[i]; if ( !strcmp(val,"1000G") ) return 0; if ( val[0]=='.' || (val[0]>='0' && val[0]<='9') || !valid_tag[(uint8_t)val[0]] ) goto err_invalid_tag; while ( *(++val) ) if ( !valid_tag[(uint8_t)*val] ) goto err_invalid_tag; return 0; } if ( hrec->type==BCF_HL_FMT ) { i = bcf_hrec_find_key(hrec,"ID"); if ( i<0 ) goto err_missing_id; char *val = hrec->vals[i]; if ( val[0]=='.' || (val[0]>='0' && val[0]<='9') || !valid_tag[(uint8_t)val[0]] ) goto err_invalid_tag; while ( *(++val) ) if ( !valid_tag[(uint8_t)*val] ) goto err_invalid_tag; return 0; } return 0; err_missing_id: hts_log_warning("Missing ID attribute in one or more header lines"); return -1; err_invalid_ctg: hts_log_warning("Invalid contig name: \"%s\"", hrec->vals[i]); return -1; err_invalid_tag: hts_log_warning("Invalid tag name: \"%s\"", hrec->vals[i]); return -1; } static inline int is_escaped(const char *min, const char *str) { int n = 0; while ( --str>=min && *str=='\\' ) n++; return n%2; } bcf_hrec_t *bcf_hdr_parse_line(const bcf_hdr_t *h, const char *line, int *len) { bcf_hrec_t *hrec = NULL; const char *p = line; if (p[0] != '#' || p[1] != '#') { *len = 0; return NULL; } p += 2; const char *q = p; while ( *q && *q!='=' && *q != '\n' ) q++; ptrdiff_t n = q-p; if ( *q!='=' || !n ) // wrong format goto malformed_line; hrec = (bcf_hrec_t*) calloc(1,sizeof(bcf_hrec_t)); if (!hrec) { *len = -1; return NULL; } hrec->key = (char*) malloc(sizeof(char)*(n+1)); if (!hrec->key) goto fail; memcpy(hrec->key,p,n); hrec->key[n] = 0; hrec->type = -1; p = ++q; if ( *p!='<' ) // generic field, e.g. ##samtoolsVersion=0.1.18-r579 { while ( *q && *q!='\n' ) q++; hrec->value = (char*) malloc((q-p+1)*sizeof(char)); if (!hrec->value) goto fail; memcpy(hrec->value, p, q-p); hrec->value[q-p] = 0; *len = q - line + (*q ? 1 : 0); // Skip \n but not \0 return hrec; } // structured line, e.g. // ##INFO= // ##PEDIGREE= int nopen = 1; while ( *q && *q!='\n' && nopen>0 ) { p = ++q; while ( *q && *q==' ' ) { p++; q++; } // ^[A-Za-z_][0-9A-Za-z_.]*$ if (p==q && *q && (isalpha_c(*q) || *q=='_')) { q++; while ( *q && (isalnum_c(*q) || *q=='_' || *q=='.') ) q++; } n = q-p; int m = 0; while ( *q && *q==' ' ) { q++; m++; } if ( *q!='=' || !n ) goto malformed_line; if (bcf_hrec_add_key(hrec, p, q-p-m) < 0) goto fail; p = ++q; while ( *q && *q==' ' ) { p++; q++; } int quoted = 0; char ending = '\0'; switch (*p) { case '"': quoted = 1; ending = '"'; p++; break; case '[': quoted = 1; ending = ']'; break; } if ( quoted ) q++; while ( *q && *q != '\n' ) { if ( quoted ) { if ( *q==ending && !is_escaped(p,q) ) break; } else { if ( *q=='<' ) nopen++; if ( *q=='>' ) nopen--; if ( !nopen ) break; if ( *q==',' && nopen==1 ) break; } q++; } const char *r = q; if (quoted && ending == ']') { if (*q == ending) { r++; q++; quoted = 0; } else { char buffer[320]; hts_log_error("Missing ']' in header line %s", hts_strprint(buffer, sizeof(buffer), '"', line, q-line)); goto fail; } } while ( r > p && r[-1] == ' ' ) r--; if (bcf_hrec_set_val(hrec, hrec->nkeys-1, p, r-p, quoted) < 0) goto fail; if ( quoted && *q==ending ) q++; if ( *q=='>' ) { if (nopen) nopen--; // this can happen with nested angle brackets <> q++; } } if ( nopen ) hts_log_warning("Incomplete header line, trying to proceed anyway:\n\t[%s]\n\t[%d]",line,q[0]); // Skip to end of line int nonspace = 0; p = q; while ( *q && *q!='\n' ) { nonspace |= !isspace_c(*q); q++; } if (nonspace) { char buffer[320]; hts_log_warning("Dropped trailing junk from header line '%s'", hts_strprint(buffer, sizeof(buffer), '"', line, q - line)); } *len = q - line + (*q ? 1 : 0); return hrec; fail: *len = -1; bcf_hrec_destroy(hrec); return NULL; malformed_line: { char buffer[320]; while ( *q && *q!='\n' ) q++; // Ensure *len includes full line hts_log_error("Could not parse the header line: %s", hts_strprint(buffer, sizeof(buffer), '"', line, q - line)); *len = q - line + (*q ? 1 : 0); bcf_hrec_destroy(hrec); return NULL; } } static int bcf_hdr_set_idx(bcf_hdr_t *hdr, int dict_type, const char *tag, bcf_idinfo_t *idinfo) { size_t new_n; // If available, preserve existing IDX if ( idinfo->id==-1 ) idinfo->id = hdr->n[dict_type]; else if ( idinfo->id < hdr->n[dict_type] && hdr->id[dict_type][idinfo->id].key ) { hts_log_error("Conflicting IDX=%d lines in the header dictionary, the new tag is %s", idinfo->id, tag); errno = EINVAL; return -1; } new_n = idinfo->id >= hdr->n[dict_type] ? idinfo->id+1 : hdr->n[dict_type]; #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION // hts_resize() can attempt to allocate up to 2 * requested items if (new_n > FUZZ_ALLOC_LIMIT/(2 * sizeof(bcf_idpair_t))) return -1; #endif if (hts_resize(bcf_idpair_t, new_n, &hdr->m[dict_type], &hdr->id[dict_type], HTS_RESIZE_CLEAR)) { return -1; } hdr->n[dict_type] = new_n; // NB: the next kh_put call can invalidate the idinfo pointer, therefore // we leave it unassigned here. It must be set explicitly in bcf_hdr_sync. hdr->id[dict_type][idinfo->id].key = tag; return 0; } // returns: 1 when hdr needs to be synced, -1 on error, 0 otherwise static int bcf_hdr_register_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec) { // contig int i, ret, replacing = 0; khint_t k; char *str = NULL; bcf_hrec_set_type(hrec); if ( hrec->type==BCF_HL_CTG ) { hts_pos_t len = 0; // Get the contig ID ($str) and length ($j) i = bcf_hrec_find_key(hrec,"length"); if ( i<0 ) len = 0; else { char *end = hrec->vals[i]; len = strtoll(hrec->vals[i], &end, 10); if (end == hrec->vals[i] || len < 0) return 0; } i = bcf_hrec_find_key(hrec,"ID"); if ( i<0 ) return 0; str = strdup(hrec->vals[i]); if (!str) return -1; // Register in the dictionary vdict_t *d = (vdict_t*)hdr->dict[BCF_DT_CTG]; khint_t k = kh_get(vdict, d, str); if ( k != kh_end(d) ) { // already present free(str); str=NULL; if (kh_val(d, k).hrec[0] != NULL) // and not removed return 0; replacing = 1; } else { k = kh_put(vdict, d, str, &ret); if (ret < 0) { free(str); return -1; } } int idx = bcf_hrec_find_key(hrec,"IDX"); if ( idx!=-1 ) { char *tmp = hrec->vals[idx]; idx = strtol(hrec->vals[idx], &tmp, 10); if ( *tmp || idx < 0 || idx >= INT_MAX - 1) { if (!replacing) { kh_del(vdict, d, k); free(str); } hts_log_warning("Error parsing the IDX tag, skipping"); return 0; } } kh_val(d, k) = bcf_idinfo_def; kh_val(d, k).id = idx; kh_val(d, k).info[0] = len; kh_val(d, k).hrec[0] = hrec; if (bcf_hdr_set_idx(hdr, BCF_DT_CTG, kh_key(d,k), &kh_val(d,k)) < 0) { if (!replacing) { kh_del(vdict, d, k); free(str); } return -1; } if ( idx==-1 ) { if (hrec_add_idx(hrec, kh_val(d,k).id) < 0) { return -1; } } return 1; } if ( hrec->type==BCF_HL_STR ) return 1; if ( hrec->type!=BCF_HL_INFO && hrec->type!=BCF_HL_FLT && hrec->type!=BCF_HL_FMT ) return 0; // INFO/FILTER/FORMAT char *id = NULL; uint32_t type = UINT32_MAX, var = UINT32_MAX; int num = -1, idx = -1; for (i=0; inkeys; i++) { if ( !strcmp(hrec->keys[i], "ID") ) id = hrec->vals[i]; else if ( !strcmp(hrec->keys[i], "IDX") ) { char *tmp = hrec->vals[i]; idx = strtol(hrec->vals[i], &tmp, 10); if ( *tmp || idx < 0 || idx >= INT_MAX - 1) { hts_log_warning("Error parsing the IDX tag, skipping"); return 0; } } else if ( !strcmp(hrec->keys[i], "Type") ) { if ( !strcmp(hrec->vals[i], "Integer") ) type = BCF_HT_INT; else if ( !strcmp(hrec->vals[i], "Float") ) type = BCF_HT_REAL; else if ( !strcmp(hrec->vals[i], "String") ) type = BCF_HT_STR; else if ( !strcmp(hrec->vals[i], "Character") ) type = BCF_HT_STR; else if ( !strcmp(hrec->vals[i], "Flag") ) type = BCF_HT_FLAG; else { hts_log_warning("The type \"%s\" is not supported, assuming \"String\"", hrec->vals[i]); type = BCF_HT_STR; } } else if ( !strcmp(hrec->keys[i], "Number") ) { if ( !strcmp(hrec->vals[i],"A") ) var = BCF_VL_A; else if ( !strcmp(hrec->vals[i],"R") ) var = BCF_VL_R; else if ( !strcmp(hrec->vals[i],"G") ) var = BCF_VL_G; else if ( !strcmp(hrec->vals[i],".") ) var = BCF_VL_VAR; else { sscanf(hrec->vals[i],"%d",&num); var = BCF_VL_FIXED; } if (var != BCF_VL_FIXED) num = 0xfffff; } } if (hrec->type == BCF_HL_INFO || hrec->type == BCF_HL_FMT) { if (type == -1) { hts_log_warning("%s %s field has no Type defined. Assuming String", *hrec->key == 'I' ? "An" : "A", hrec->key); type = BCF_HT_STR; } if (var == -1) { hts_log_warning("%s %s field has no Number defined. Assuming '.'", *hrec->key == 'I' ? "An" : "A", hrec->key); var = BCF_VL_VAR; } if ( type==BCF_HT_FLAG && (var!=BCF_VL_FIXED || num!=0) ) { hts_log_warning("The definition of Flag \"%s/%s\" is invalid, forcing Number=0", hrec->key,id); var = BCF_VL_FIXED; num = 0; } } uint32_t info = ((((uint32_t)num) & 0xfffff)<<12 | (var & 0xf) << 8 | (type & 0xf) << 4 | (((uint32_t) hrec->type) & 0xf)); if ( !id ) return 0; str = strdup(id); if (!str) return -1; vdict_t *d = (vdict_t*)hdr->dict[BCF_DT_ID]; k = kh_get(vdict, d, str); if ( k != kh_end(d) ) { // already present free(str); if ( kh_val(d, k).hrec[info&0xf] ) return 0; kh_val(d, k).info[info&0xf] = info; kh_val(d, k).hrec[info&0xf] = hrec; if ( idx==-1 ) { if (hrec_add_idx(hrec, kh_val(d, k).id) < 0) { return -1; } } return 1; } k = kh_put(vdict, d, str, &ret); if (ret < 0) { free(str); return -1; } kh_val(d, k) = bcf_idinfo_def; kh_val(d, k).info[info&0xf] = info; kh_val(d, k).hrec[info&0xf] = hrec; kh_val(d, k).id = idx; if (bcf_hdr_set_idx(hdr, BCF_DT_ID, kh_key(d,k), &kh_val(d,k)) < 0) { kh_del(vdict, d, k); free(str); return -1; } if ( idx==-1 ) { if (hrec_add_idx(hrec, kh_val(d,k).id) < 0) { return -1; } } return 1; } static void bcf_hdr_unregister_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec) { if (hrec->type == BCF_HL_FLT || hrec->type == BCF_HL_INFO || hrec->type == BCF_HL_FMT || hrec->type == BCF_HL_CTG) { int id = bcf_hrec_find_key(hrec, "ID"); if (id < 0 || !hrec->vals[id]) return; vdict_t *dict = (hrec->type == BCF_HL_CTG ? (vdict_t*)hdr->dict[BCF_DT_CTG] : (vdict_t*)hdr->dict[BCF_DT_ID]); khint_t k = kh_get(vdict, dict, hrec->vals[id]); if (k != kh_end(dict)) kh_val(dict, k).hrec[hrec->type==BCF_HL_CTG ? 0 : hrec->type] = NULL; } } static void bcf_hdr_remove_from_hdict(bcf_hdr_t *hdr, bcf_hrec_t *hrec) { kstring_t str = KS_INITIALIZE; bcf_hdr_aux_t *aux = get_hdr_aux(hdr); khint_t k; int id; switch (hrec->type) { case BCF_HL_GEN: if (ksprintf(&str, "##%s=%s", hrec->key,hrec->value) < 0) str.l = 0; break; case BCF_HL_STR: id = bcf_hrec_find_key(hrec, "ID"); if (id < 0) return; if (!hrec->vals[id] || ksprintf(&str, "##%s=", hrec->key, hrec->vals[id]) < 0) str.l = 0; break; default: return; } if (str.l) { k = kh_get(hdict, aux->gen, str.s); } else { // Couldn't get a string for some reason, so try the hard way... for (k = kh_begin(aux->gen); k < kh_end(aux->gen); k++) { if (kh_exist(aux->gen, k) && kh_val(aux->gen, k) == hrec) break; } } if (k != kh_end(aux->gen) && kh_val(aux->gen, k) == hrec) { kh_val(aux->gen, k) = NULL; free((char *) kh_key(aux->gen, k)); kh_key(aux->gen, k) = NULL; kh_del(hdict, aux->gen, k); } free(str.s); } int bcf_hdr_update_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec, const bcf_hrec_t *tmp) { // currently only for bcf_hdr_set_version assert( hrec->type==BCF_HL_GEN ); int ret; khint_t k; bcf_hdr_aux_t *aux = get_hdr_aux(hdr); for (k=kh_begin(aux->gen); kgen); k++) { if ( !kh_exist(aux->gen,k) ) continue; if ( hrec!=(bcf_hrec_t*)kh_val(aux->gen,k) ) continue; break; } assert( kgen) ); // something went wrong, should never happen free((char*)kh_key(aux->gen,k)); kh_del(hdict,aux->gen,k); kstring_t str = {0,0,0}; if ( ksprintf(&str, "##%s=%s", tmp->key,tmp->value) < 0 ) { free(str.s); return -1; } k = kh_put(hdict, aux->gen, str.s, &ret); if ( ret<0 ) { free(str.s); return -1; } free(hrec->value); hrec->value = strdup(tmp->value); if ( !hrec->value ) return -1; return 0; } int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec) { kstring_t str = {0,0,0}; bcf_hdr_aux_t *aux = get_hdr_aux(hdr); int res; if ( !hrec ) return 0; bcf_hrec_check(hrec); // todo: check return status and propagate errors up res = bcf_hdr_register_hrec(hdr,hrec); if (res < 0) return -1; if ( !res ) { // If one of the hashed field, then it is already present if ( hrec->type != BCF_HL_GEN ) { bcf_hrec_destroy(hrec); return 0; } // Is one of the generic fields and already present? if ( ksprintf(&str, "##%s=%s", hrec->key,hrec->value) < 0 ) { free(str.s); return -1; } khint_t k = kh_get(hdict, aux->gen, str.s); if ( k != kh_end(aux->gen) ) { // duplicate record bcf_hrec_destroy(hrec); free(str.s); return 0; } } int i; if ( hrec->type==BCF_HL_STR && (i=bcf_hrec_find_key(hrec,"ID"))>=0 ) { if ( ksprintf(&str, "##%s=", hrec->key,hrec->vals[i]) < 0 ) { free(str.s); return -1; } khint_t k = kh_get(hdict, aux->gen, str.s); if ( k != kh_end(aux->gen) ) { // duplicate record bcf_hrec_destroy(hrec); free(str.s); return 0; } } // New record, needs to be added int n = hdr->nhrec + 1; bcf_hrec_t **new_hrec = realloc(hdr->hrec, n*sizeof(bcf_hrec_t*)); if (!new_hrec) { free(str.s); bcf_hdr_unregister_hrec(hdr, hrec); return -1; } hdr->hrec = new_hrec; if ( str.s ) { khint_t k = kh_put(hdict, aux->gen, str.s, &res); if ( res<0 ) { free(str.s); return -1; } kh_val(aux->gen,k) = hrec; } hdr->hrec[hdr->nhrec] = hrec; hdr->dirty = 1; hdr->nhrec = n; return hrec->type==BCF_HL_GEN ? 0 : 1; } bcf_hrec_t *bcf_hdr_get_hrec(const bcf_hdr_t *hdr, int type, const char *key, const char *value, const char *str_class) { int i; if ( type==BCF_HL_GEN ) { // e.g. ##fileformat=VCFv4.2 // ##source=GenomicsDBImport // ##bcftools_viewVersion=1.16-80-gdfdb0923+htslib-1.16-34-g215d364 if ( value ) { kstring_t str = {0,0,0}; ksprintf(&str, "##%s=%s", key,value); bcf_hdr_aux_t *aux = get_hdr_aux(hdr); khint_t k = kh_get(hdict, aux->gen, str.s); free(str.s); if ( k == kh_end(aux->gen) ) return NULL; return kh_val(aux->gen, k); } for (i=0; inhrec; i++) { if ( hdr->hrec[i]->type!=type ) continue; if ( strcmp(hdr->hrec[i]->key,key) ) continue; return hdr->hrec[i]; } return NULL; } else if ( type==BCF_HL_STR ) { // e.g. ##GATKCommandLine= // ##ALT= if (!str_class) return NULL; if ( !strcmp("ID",key) ) { kstring_t str = {0,0,0}; ksprintf(&str, "##%s=<%s=%s>",str_class,key,value); bcf_hdr_aux_t *aux = get_hdr_aux(hdr); khint_t k = kh_get(hdict, aux->gen, str.s); free(str.s); if ( k == kh_end(aux->gen) ) return NULL; return kh_val(aux->gen, k); } for (i=0; inhrec; i++) { if ( hdr->hrec[i]->type!=type ) continue; if ( strcmp(hdr->hrec[i]->key,str_class) ) continue; int j = bcf_hrec_find_key(hdr->hrec[i],key); if ( j>=0 && !strcmp(hdr->hrec[i]->vals[j],value) ) return hdr->hrec[i]; } return NULL; } vdict_t *d = type==BCF_HL_CTG ? (vdict_t*)hdr->dict[BCF_DT_CTG] : (vdict_t*)hdr->dict[BCF_DT_ID]; khint_t k = kh_get(vdict, d, value); if ( k == kh_end(d) ) return NULL; return kh_val(d, k).hrec[type==BCF_HL_CTG?0:type]; } void bcf_hdr_check_sanity(bcf_hdr_t *hdr) { static int PL_warned = 0, GL_warned = 0; if ( !PL_warned ) { int id = bcf_hdr_id2int(hdr, BCF_DT_ID, "PL"); if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G ) { hts_log_warning("PL should be declared as Number=G"); PL_warned = 1; } } if ( !GL_warned ) { int id = bcf_hdr_id2int(hdr, BCF_DT_ID, "GL"); if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G ) { hts_log_warning("GL should be declared as Number=G"); GL_warned = 1; } } } int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt) { int len, done = 0; char *p = htxt; // Check sanity: "fileformat" string must come as first bcf_hrec_t *hrec = bcf_hdr_parse_line(hdr,p,&len); if ( !hrec || !hrec->key || strcasecmp(hrec->key,"fileformat") ) hts_log_warning("The first line should be ##fileformat; is the VCF/BCF header broken?"); if (bcf_hdr_add_hrec(hdr, hrec) < 0) { bcf_hrec_destroy(hrec); return -1; } // The filter PASS must appear first in the dictionary hrec = bcf_hdr_parse_line(hdr,"##FILTER=",&len); if (!hrec || bcf_hdr_add_hrec(hdr, hrec) < 0) { bcf_hrec_destroy(hrec); return -1; } // Parse the whole header do { while (NULL != (hrec = bcf_hdr_parse_line(hdr, p, &len))) { if (bcf_hdr_add_hrec(hdr, hrec) < 0) { bcf_hrec_destroy(hrec); return -1; } p += len; } assert(hrec == NULL); if (len < 0) { // len < 0 indicates out-of-memory, or similar error hts_log_error("Could not parse header line: %s", strerror(errno)); return -1; } else if (len > 0) { // Bad header line. bcf_hdr_parse_line() will have logged it. // Skip and try again on the next line (p + len will be the start // of the next one). p += len; continue; } // Next should be the sample line. If not, it was a malformed // header, in which case print a warning and skip (many VCF // operations do not really care about a few malformed lines). // In the future we may want to add a strict mode that errors in // this case. if ( strncmp("#CHROM\t",p,7) && strncmp("#CHROM ",p,7) ) { char *eol = strchr(p, '\n'); if (*p != '\0') { char buffer[320]; hts_log_warning("Could not parse header line: %s", hts_strprint(buffer, sizeof(buffer), '"', p, eol ? (eol - p) : SIZE_MAX)); } if (eol) { p = eol + 1; // Try from the next line. } else { done = -1; // No more lines left, give up. } } else { done = 1; // Sample line found } } while (!done); if (done < 0) { // No sample line is fatal. hts_log_error("Could not parse the header, sample line not found"); return -1; } if (bcf_hdr_parse_sample_line(hdr,p) < 0) return -1; if (bcf_hdr_sync(hdr) < 0) return -1; bcf_hdr_check_sanity(hdr); return 0; } int bcf_hdr_append(bcf_hdr_t *hdr, const char *line) { int len; bcf_hrec_t *hrec = bcf_hdr_parse_line(hdr, (char*) line, &len); if ( !hrec ) return -1; if (bcf_hdr_add_hrec(hdr, hrec) < 0) return -1; return 0; } void bcf_hdr_remove(bcf_hdr_t *hdr, int type, const char *key) { int i = 0; bcf_hrec_t *hrec; if ( !key ) { // no key, remove all entries of this type while ( inhrec ) { if ( hdr->hrec[i]->type!=type ) { i++; continue; } hrec = hdr->hrec[i]; bcf_hdr_unregister_hrec(hdr, hrec); bcf_hdr_remove_from_hdict(hdr, hrec); hdr->dirty = 1; hdr->nhrec--; if ( i < hdr->nhrec ) memmove(&hdr->hrec[i],&hdr->hrec[i+1],(hdr->nhrec-i)*sizeof(bcf_hrec_t*)); bcf_hrec_destroy(hrec); } return; } while (1) { if ( type==BCF_HL_FLT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG ) { hrec = bcf_hdr_get_hrec(hdr, type, "ID", key, NULL); if ( !hrec ) return; for (i=0; inhrec; i++) if ( hdr->hrec[i]==hrec ) break; assert( inhrec ); vdict_t *d = type==BCF_HL_CTG ? (vdict_t*)hdr->dict[BCF_DT_CTG] : (vdict_t*)hdr->dict[BCF_DT_ID]; khint_t k = kh_get(vdict, d, key); kh_val(d, k).hrec[type==BCF_HL_CTG?0:type] = NULL; } else { for (i=0; inhrec; i++) { if ( hdr->hrec[i]->type!=type ) continue; if ( type==BCF_HL_GEN ) { if ( !strcmp(hdr->hrec[i]->key,key) ) break; } else { // not all structured lines have ID, we could be more sophisticated as in bcf_hdr_get_hrec() int j = bcf_hrec_find_key(hdr->hrec[i], "ID"); if ( j>=0 && !strcmp(hdr->hrec[i]->vals[j],key) ) break; } } if ( i==hdr->nhrec ) return; hrec = hdr->hrec[i]; bcf_hdr_remove_from_hdict(hdr, hrec); } hdr->nhrec--; if ( i < hdr->nhrec ) memmove(&hdr->hrec[i],&hdr->hrec[i+1],(hdr->nhrec-i)*sizeof(bcf_hrec_t*)); bcf_hrec_destroy(hrec); hdr->dirty = 1; } } int bcf_hdr_printf(bcf_hdr_t *hdr, const char *fmt, ...) { char tmp[256], *line = tmp; va_list ap; va_start(ap, fmt); int n = vsnprintf(line, sizeof(tmp), fmt, ap); va_end(ap); if (n >= sizeof(tmp)) { n++; // For trailing NUL line = (char*)malloc(n); if (!line) return -1; va_start(ap, fmt); vsnprintf(line, n, fmt, ap); va_end(ap); } int ret = bcf_hdr_append(hdr, line); if (line != tmp) free(line); return ret; } /********************** *** BCF header I/O *** **********************/ const char *bcf_hdr_get_version(const bcf_hdr_t *hdr) { bcf_hrec_t *hrec = bcf_hdr_get_hrec(hdr, BCF_HL_GEN, "fileformat", NULL, NULL); if ( !hrec ) { hts_log_warning("No version string found, assuming VCFv4.2"); return "VCFv4.2"; } return hrec->value; } int bcf_hdr_set_version(bcf_hdr_t *hdr, const char *version) { bcf_hrec_t *hrec = bcf_hdr_get_hrec(hdr, BCF_HL_GEN, "fileformat", NULL, NULL); if ( !hrec ) { int len; kstring_t str = {0,0,0}; if ( ksprintf(&str,"##fileformat=%s", version) < 0 ) return -1; hrec = bcf_hdr_parse_line(hdr, str.s, &len); free(str.s); } else { bcf_hrec_t *tmp = bcf_hrec_dup(hrec); if ( !tmp ) return -1; free(tmp->value); tmp->value = strdup(version); if ( !tmp->value ) return -1; bcf_hdr_update_hrec(hdr, hrec, tmp); bcf_hrec_destroy(tmp); } hdr->dirty = 1; return 0; // FIXME: check for errs in this function (return < 0 if so) } bcf_hdr_t *bcf_hdr_init(const char *mode) { int i; bcf_hdr_t *h; h = (bcf_hdr_t*)calloc(1, sizeof(bcf_hdr_t)); if (!h) return NULL; for (i = 0; i < 3; ++i) { if ((h->dict[i] = kh_init(vdict)) == NULL) goto fail; // Supersize the hash to make collisions very unlikely static int dsize[3] = {16384,16384,2048}; // info, contig, format if (kh_resize(vdict, h->dict[i], dsize[i]) < 0) goto fail; } bcf_hdr_aux_t *aux = (bcf_hdr_aux_t*)calloc(1,sizeof(bcf_hdr_aux_t)); if ( !aux ) goto fail; if ( (aux->gen = kh_init(hdict))==NULL ) { free(aux); goto fail; } aux->key_len = NULL; aux->dict = *((vdict_t*)h->dict[0]); free(h->dict[0]); h->dict[0] = aux; if ( strchr(mode,'w') ) { bcf_hdr_append(h, "##fileformat=VCFv4.2"); // The filter PASS must appear first in the dictionary bcf_hdr_append(h, "##FILTER="); } return h; fail: for (i = 0; i < 3; ++i) kh_destroy(vdict, h->dict[i]); free(h); return NULL; } void bcf_hdr_destroy(bcf_hdr_t *h) { int i; khint_t k; if (!h) return; for (i = 0; i < 3; ++i) { vdict_t *d = (vdict_t*)h->dict[i]; if (d == 0) continue; for (k = kh_begin(d); k != kh_end(d); ++k) if (kh_exist(d, k)) free((char*)kh_key(d, k)); if ( i==0 ) { bcf_hdr_aux_t *aux = get_hdr_aux(h); for (k=kh_begin(aux->gen); kgen); k++) if ( kh_exist(aux->gen,k) ) free((char*)kh_key(aux->gen,k)); kh_destroy(hdict, aux->gen); free(aux->key_len); // may exist for dict[0] only } kh_destroy(vdict, d); free(h->id[i]); } for (i=0; inhrec; i++) bcf_hrec_destroy(h->hrec[i]); if (h->nhrec) free(h->hrec); if (h->samples) free(h->samples); free(h->keep_samples); free(h->transl[0]); free(h->transl[1]); free(h->mem.s); free(h); } bcf_hdr_t *bcf_hdr_read(htsFile *hfp) { if (hfp->format.format == vcf) return vcf_hdr_read(hfp); if (hfp->format.format != bcf) { hts_log_error("Input is not detected as bcf or vcf format"); return NULL; } assert(hfp->is_bgzf); BGZF *fp = hfp->fp.bgzf; uint8_t magic[5]; bcf_hdr_t *h; h = bcf_hdr_init("r"); if (!h) { hts_log_error("Failed to allocate bcf header"); return NULL; } if (bgzf_read(fp, magic, 5) != 5) { hts_log_error("Failed to read the header (reading BCF in text mode?)"); bcf_hdr_destroy(h); return NULL; } if (strncmp((char*)magic, "BCF\2\2", 5) != 0) { if (!strncmp((char*)magic, "BCF", 3)) hts_log_error("Invalid BCF2 magic string: only BCFv2.2 is supported"); else hts_log_error("Invalid BCF2 magic string"); bcf_hdr_destroy(h); return NULL; } uint8_t buf[4]; size_t hlen; char *htxt = NULL; if (bgzf_read(fp, buf, 4) != 4) goto fail; hlen = buf[0] | (buf[1] << 8) | (buf[2] << 16) | ((size_t) buf[3] << 24); if (hlen >= SIZE_MAX) { errno = ENOMEM; goto fail; } #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION if (hlen > FUZZ_ALLOC_LIMIT/2) { errno = ENOMEM; goto fail; } #endif htxt = (char*)malloc(hlen + 1); if (!htxt) goto fail; if (bgzf_read(fp, htxt, hlen) != hlen) goto fail; htxt[hlen] = '\0'; // Ensure htxt is terminated if ( bcf_hdr_parse(h, htxt) < 0 ) goto fail; free(htxt); return h; fail: hts_log_error("Failed to read BCF header"); free(htxt); bcf_hdr_destroy(h); return NULL; } int bcf_hdr_write(htsFile *hfp, bcf_hdr_t *h) { if (!h) { errno = EINVAL; return -1; } if ( h->dirty ) { if (bcf_hdr_sync(h) < 0) return -1; } hfp->format.category = variant_data; if (hfp->format.format == vcf || hfp->format.format == text_format) { hfp->format.format = vcf; return vcf_hdr_write(hfp, h); } if (hfp->format.format == binary_format) hfp->format.format = bcf; kstring_t htxt = {0,0,0}; if (bcf_hdr_format(h, 1, &htxt) < 0) { free(htxt.s); return -1; } kputc('\0', &htxt); // include the \0 byte BGZF *fp = hfp->fp.bgzf; if ( bgzf_write(fp, "BCF\2\2", 5) !=5 ) return -1; uint8_t hlen[4]; u32_to_le(htxt.l, hlen); if ( bgzf_write(fp, hlen, 4) !=4 ) return -1; if ( bgzf_write(fp, htxt.s, htxt.l) != htxt.l ) return -1; if ( bgzf_flush(fp) < 0) return -1; free(htxt.s); return 0; } /******************** *** BCF site I/O *** ********************/ bcf1_t *bcf_init(void) { bcf1_t *v; v = (bcf1_t*)calloc(1, sizeof(bcf1_t)); return v; } void bcf_clear(bcf1_t *v) { int i; for (i=0; id.m_info; i++) { if ( v->d.info[i].vptr_free ) { free(v->d.info[i].vptr - v->d.info[i].vptr_off); v->d.info[i].vptr_free = 0; } } for (i=0; id.m_fmt; i++) { if ( v->d.fmt[i].p_free ) { free(v->d.fmt[i].p - v->d.fmt[i].p_off); v->d.fmt[i].p_free = 0; } } v->rid = v->pos = v->rlen = v->unpacked = 0; bcf_float_set_missing(v->qual); v->n_info = v->n_allele = v->n_fmt = v->n_sample = 0; v->shared.l = v->indiv.l = 0; v->d.var_type = -1; v->d.shared_dirty = 0; v->d.indiv_dirty = 0; v->d.n_flt = 0; v->errcode = 0; if (v->d.m_als) v->d.als[0] = 0; if (v->d.m_id) v->d.id[0] = 0; } void bcf_empty(bcf1_t *v) { bcf_clear1(v); free(v->d.id); free(v->d.als); free(v->d.allele); free(v->d.flt); free(v->d.info); free(v->d.fmt); if (v->d.var ) free(v->d.var); free(v->shared.s); free(v->indiv.s); memset(&v->d,0,sizeof(v->d)); memset(&v->shared,0,sizeof(v->shared)); memset(&v->indiv,0,sizeof(v->indiv)); } void bcf_destroy(bcf1_t *v) { if (!v) return; bcf_empty1(v); free(v); } static inline int bcf_read1_core(BGZF *fp, bcf1_t *v) { uint8_t x[32]; ssize_t ret; uint32_t shared_len, indiv_len; if ((ret = bgzf_read(fp, x, 32)) != 32) { if (ret == 0) return -1; return -2; } bcf_clear1(v); shared_len = le_to_u32(x); if (shared_len < 24) return -2; shared_len -= 24; // to exclude six 32-bit integers indiv_len = le_to_u32(x + 4); #ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION // ks_resize() normally allocates 1.5 * requested size to allow for growth if ((uint64_t) shared_len + indiv_len > FUZZ_ALLOC_LIMIT / 3 * 2) return -2; #endif if (ks_resize(&v->shared, shared_len ? shared_len : 1) != 0) return -2; if (ks_resize(&v->indiv, indiv_len ? indiv_len : 1) != 0) return -2; v->rid = le_to_i32(x + 8); v->pos = le_to_u32(x + 12); if ( v->pos==UINT32_MAX ) v->pos = -1; // this is for telomere coordinate, e.g. MT:0 v->rlen = le_to_i32(x + 16); v->qual = le_to_float(x + 20); v->n_info = le_to_u16(x + 24); v->n_allele = le_to_u16(x + 26); v->n_sample = le_to_u32(x + 28) & 0xffffff; v->n_fmt = x[31]; v->shared.l = shared_len; v->indiv.l = indiv_len; // silent fix of broken BCFs produced by earlier versions of bcf_subset, prior to and including bd6ed8b4 if ( (!v->indiv.l || !v->n_sample) && v->n_fmt ) v->n_fmt = 0; if (bgzf_read(fp, v->shared.s, v->shared.l) != v->shared.l) return -2; if (bgzf_read(fp, v->indiv.s, v->indiv.l) != v->indiv.l) return -2; return 0; } #define bit_array_size(n) ((n)/8+1) #define bit_array_set(a,i) ((a)[(i)/8] |= 1 << ((i)%8)) #define bit_array_clear(a,i) ((a)[(i)/8] &= ~(1 << ((i)%8))) #define bit_array_test(a,i) ((a)[(i)/8] & (1 << ((i)%8))) static int bcf_dec_typed_int1_safe(uint8_t *p, uint8_t *end, uint8_t **q, int32_t *val) { uint32_t t; if (end - p < 2) return -1; t = *p++ & 0xf; /* Use if .. else if ... else instead of switch to force order. Assumption is that small integers are more frequent than big ones. */ if (t == BCF_BT_INT8) { *val = *(int8_t *) p++; } else { if (end - p < (1<= end) return -1; *type = *p & 0xf; if (*p>>4 != 15) { *q = p + 1; *num = *p >> 4; return 0; } r = bcf_dec_typed_int1_safe(p + 1, end, q, num); if (r) return r; return *num >= 0 ? 0 : -1; } static const char *get_type_name(int type) { const char *types[9] = { "null", "int (8-bit)", "int (16 bit)", "int (32 bit)", "unknown", "float", "unknown", "char", "unknown" }; int t = (type >= 0 && type < 8) ? type : 8; return types[t]; } static void bcf_record_check_err(const bcf_hdr_t *hdr, bcf1_t *rec, char *type, uint32_t *reports, int i) { if (*reports == 0 || hts_verbose >= HTS_LOG_DEBUG) hts_log_warning("Bad BCF record at %s:%"PRIhts_pos ": Invalid FORMAT %s %d", bcf_seqname_safe(hdr,rec), rec->pos+1, type, i); (*reports)++; } static int bcf_record_check(const bcf_hdr_t *hdr, bcf1_t *rec) { uint8_t *ptr, *end; size_t bytes; uint32_t err = 0; int type = 0; int num = 0; int reflen = 0; uint32_t i, reports; const uint32_t is_integer = ((1 << BCF_BT_INT8) | (1 << BCF_BT_INT16) | #ifdef VCF_ALLOW_INT64 (1 << BCF_BT_INT64) | #endif (1 << BCF_BT_INT32)); const uint32_t is_valid_type = (is_integer | (1 << BCF_BT_NULL) | (1 << BCF_BT_FLOAT) | (1 << BCF_BT_CHAR)); int32_t max_id = hdr ? hdr->n[BCF_DT_ID] : 0; // Check for valid contig ID if (rec->rid < 0 || (hdr && (rec->rid >= hdr->n[BCF_DT_CTG] || hdr->id[BCF_DT_CTG][rec->rid].key == NULL))) { hts_log_warning("Bad BCF record at %"PRIhts_pos": Invalid %s id %d", rec->pos+1, "CONTIG", rec->rid); err |= BCF_ERR_CTG_INVALID; } // Check ID ptr = (uint8_t *) rec->shared.s; end = ptr + rec->shared.l; if (bcf_dec_size_safe(ptr, end, &ptr, &num, &type) != 0) goto bad_shared; if (type != BCF_BT_CHAR) { hts_log_warning("Bad BCF record at %s:%"PRIhts_pos": Invalid %s type %d (%s)", bcf_seqname_safe(hdr,rec), rec->pos+1, "ID", type, get_type_name(type)); err |= BCF_ERR_TAG_INVALID; } bytes = (size_t) num << bcf_type_shift[type]; if (end - ptr < bytes) goto bad_shared; ptr += bytes; // Check REF and ALT if (rec->n_allele < 1) { hts_log_warning("Bad BCF record at %s:%"PRIhts_pos": No REF allele", bcf_seqname_safe(hdr,rec), rec->pos+1); err |= BCF_ERR_TAG_UNDEF; } reports = 0; for (i = 0; i < rec->n_allele; i++) { if (bcf_dec_size_safe(ptr, end, &ptr, &num, &type) != 0) goto bad_shared; if (type != BCF_BT_CHAR) { if (!reports++ || hts_verbose >= HTS_LOG_DEBUG) hts_log_warning("Bad BCF record at %s:%"PRIhts_pos": Invalid %s type %d (%s)", bcf_seqname_safe(hdr,rec), rec->pos+1, "REF/ALT", type, get_type_name(type)); err |= BCF_ERR_CHAR; } if (i == 0) reflen = num; bytes = (size_t) num << bcf_type_shift[type]; if (end - ptr < bytes) goto bad_shared; ptr += bytes; } // Check FILTER reports = 0; if (bcf_dec_size_safe(ptr, end, &ptr, &num, &type) != 0) goto bad_shared; if (num > 0) { bytes = (size_t) num << bcf_type_shift[type]; if (((1 << type) & is_integer) == 0) { hts_log_warning("Bad BCF record at %s:%"PRIhts_pos": Invalid %s type %d (%s)", bcf_seqname_safe(hdr,rec), rec->pos+1, "FILTER", type, get_type_name(type)); err |= BCF_ERR_TAG_INVALID; if (end - ptr < bytes) goto bad_shared; ptr += bytes; } else { if (end - ptr < bytes) goto bad_shared; for (i = 0; i < num; i++) { int32_t key = bcf_dec_int1(ptr, type, &ptr); if (key < 0 || (hdr && (key >= max_id || hdr->id[BCF_DT_ID][key].key == NULL))) { if (!reports++ || hts_verbose >= HTS_LOG_DEBUG) hts_log_warning("Bad BCF record at %s:%"PRIhts_pos": Invalid %s id %d", bcf_seqname_safe(hdr,rec), rec->pos+1, "FILTER", key); err |= BCF_ERR_TAG_UNDEF; } } } } // Check INFO reports = 0; bcf_idpair_t *id_tmp = hdr ? hdr->id[BCF_DT_ID] : NULL; for (i = 0; i < rec->n_info; i++) { int32_t key = -1; if (bcf_dec_typed_int1_safe(ptr, end, &ptr, &key) != 0) goto bad_shared; if (key < 0 || (hdr && (key >= max_id || id_tmp[key].key == NULL))) { if (!reports++ || hts_verbose >= HTS_LOG_DEBUG) hts_log_warning("Bad BCF record at %s:%"PRIhts_pos": Invalid %s id %d", bcf_seqname_safe(hdr,rec), rec->pos+1, "INFO", key); err |= BCF_ERR_TAG_UNDEF; } if (bcf_dec_size_safe(ptr, end, &ptr, &num, &type) != 0) goto bad_shared; if (((1 << type) & is_valid_type) == 0 || (type == BCF_BT_NULL && num > 0)) { if (!reports++ || hts_verbose >= HTS_LOG_DEBUG) hts_log_warning("Bad BCF record at %s:%"PRIhts_pos": Invalid %s type %d (%s)", bcf_seqname_safe(hdr,rec), rec->pos+1, "INFO", type, get_type_name(type)); err |= BCF_ERR_TAG_INVALID; } bytes = (size_t) num << bcf_type_shift[type]; if (end - ptr < bytes) goto bad_shared; ptr += bytes; } // Check FORMAT and individual information ptr = (uint8_t *) rec->indiv.s; end = ptr + rec->indiv.l; reports = 0; for (i = 0; i < rec->n_fmt; i++) { int32_t key = -1; if (bcf_dec_typed_int1_safe(ptr, end, &ptr, &key) != 0) goto bad_indiv; if (key < 0 || (hdr && (key >= max_id || id_tmp[key].key == NULL))) { bcf_record_check_err(hdr, rec, "id", &reports, key); err |= BCF_ERR_TAG_UNDEF; } if (bcf_dec_size_safe(ptr, end, &ptr, &num, &type) != 0) goto bad_indiv; if (((1 << type) & is_valid_type) == 0 || (type == BCF_BT_NULL && num > 0)) { bcf_record_check_err(hdr, rec, "type", &reports, type); err |= BCF_ERR_TAG_INVALID; } bytes = ((size_t) num << bcf_type_shift[type]) * rec->n_sample; if (end - ptr < bytes) goto bad_indiv; ptr += bytes; } if (!err && rec->rlen < 0) { // Treat bad rlen as a warning instead of an error, and try to // fix up by using the length of the stored REF allele. static int warned = 0; if (!warned) { hts_log_warning("BCF record at %s:%"PRIhts_pos" has invalid RLEN (%"PRIhts_pos"). " "Only one invalid RLEN will be reported.", bcf_seqname_safe(hdr,rec), rec->pos+1, rec->rlen); warned = 1; } rec->rlen = reflen >= 0 ? reflen : 0; } rec->errcode |= err; return err ? -2 : 0; // Return -2 so bcf_read() reports an error bad_shared: hts_log_error("Bad BCF record at %s:%"PRIhts_pos" - shared section malformed or too short", bcf_seqname_safe(hdr,rec), rec->pos+1); return -2; bad_indiv: hts_log_error("Bad BCF record at %s:%"PRIhts_pos" - individuals section malformed or too short", bcf_seqname_safe(hdr,rec), rec->pos+1); return -2; } static inline uint8_t *bcf_unpack_fmt_core1(uint8_t *ptr, int n_sample, bcf_fmt_t *fmt); int bcf_subset_format(const bcf_hdr_t *hdr, bcf1_t *rec) { if ( !hdr->keep_samples ) return 0; if ( !bcf_hdr_nsamples(hdr) ) { rec->indiv.l = rec->n_sample = 0; return 0; } int i, j; uint8_t *ptr = (uint8_t*)rec->indiv.s, *dst = NULL, *src; bcf_dec_t *dec = &rec->d; hts_expand(bcf_fmt_t, rec->n_fmt, dec->m_fmt, dec->fmt); for (i=0; im_fmt; ++i) dec->fmt[i].p_free = 0; for (i=0; in_fmt; i++) { ptr = bcf_unpack_fmt_core1(ptr, rec->n_sample, &dec->fmt[i]); src = dec->fmt[i].p - dec->fmt[i].size; if ( dst ) { memmove(dec->fmt[i-1].p + dec->fmt[i-1].p_len, dec->fmt[i].p - dec->fmt[i].p_off, dec->fmt[i].p_off); dec->fmt[i].p = dec->fmt[i-1].p + dec->fmt[i-1].p_len + dec->fmt[i].p_off; } dst = dec->fmt[i].p; for (j=0; jnsamples_ori; j++) { src += dec->fmt[i].size; if ( !bit_array_test(hdr->keep_samples,j) ) continue; memmove(dst, src, dec->fmt[i].size); dst += dec->fmt[i].size; } rec->indiv.l -= dec->fmt[i].p_len - (dst - dec->fmt[i].p); dec->fmt[i].p_len = dst - dec->fmt[i].p; } rec->unpacked |= BCF_UN_FMT; rec->n_sample = bcf_hdr_nsamples(hdr); return 0; } int bcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) { if (fp->format.format == vcf) return vcf_read(fp,h,v); int ret = bcf_read1_core(fp->fp.bgzf, v); if (ret == 0) ret = bcf_record_check(h, v); if ( ret!=0 || !h->keep_samples ) return ret; return bcf_subset_format(h,v); } int bcf_readrec(BGZF *fp, void *null, void *vv, int *tid, hts_pos_t *beg, hts_pos_t *end) { bcf1_t *v = (bcf1_t *) vv; int ret = bcf_read1_core(fp, v); if (ret == 0) ret = bcf_record_check(NULL, v); if (ret >= 0) *tid = v->rid, *beg = v->pos, *end = v->pos + v->rlen; return ret; } static inline int bcf1_sync_id(bcf1_t *line, kstring_t *str) { // single typed string if ( line->d.id && strcmp(line->d.id, ".") ) { return bcf_enc_vchar(str, strlen(line->d.id), line->d.id); } else { return bcf_enc_size(str, 0, BCF_BT_CHAR); } } static inline int bcf1_sync_alleles(bcf1_t *line, kstring_t *str) { // list of typed strings int i; for (i=0; in_allele; i++) { if (bcf_enc_vchar(str, strlen(line->d.allele[i]), line->d.allele[i]) < 0) return -1; } if ( !line->rlen && line->n_allele ) line->rlen = strlen(line->d.allele[0]); return 0; } static inline int bcf1_sync_filter(bcf1_t *line, kstring_t *str) { // typed vector of integers if ( line->d.n_flt ) { return bcf_enc_vint(str, line->d.n_flt, line->d.flt, -1); } else { return bcf_enc_vint(str, 0, 0, -1); } } static inline int bcf1_sync_info(bcf1_t *line, kstring_t *str) { // pairs of typed vectors int i, irm = -1, e = 0; for (i=0; in_info; i++) { bcf_info_t *info = &line->d.info[i]; if ( !info->vptr ) { // marked for removal if ( irm < 0 ) irm = i; continue; } e |= kputsn_(info->vptr - info->vptr_off, info->vptr_len + info->vptr_off, str) < 0; if ( irm >=0 ) { bcf_info_t tmp = line->d.info[irm]; line->d.info[irm] = line->d.info[i]; line->d.info[i] = tmp; while ( irm<=i && line->d.info[irm].vptr ) irm++; } } if ( irm>=0 ) line->n_info = irm; return e == 0 ? 0 : -1; } static int bcf1_sync(bcf1_t *line) { char *shared_ori = line->shared.s; size_t prev_len; kstring_t tmp = {0,0,0}; if ( !line->shared.l ) { // New line created via API, BCF data blocks do not exist. Get it ready for BCF output tmp = line->shared; bcf1_sync_id(line, &tmp); line->unpack_size[0] = tmp.l; prev_len = tmp.l; bcf1_sync_alleles(line, &tmp); line->unpack_size[1] = tmp.l - prev_len; prev_len = tmp.l; bcf1_sync_filter(line, &tmp); line->unpack_size[2] = tmp.l - prev_len; bcf1_sync_info(line, &tmp); line->shared = tmp; } else if ( line->d.shared_dirty ) { // The line was edited, update the BCF data block. if ( !(line->unpacked & BCF_UN_STR) ) bcf_unpack(line,BCF_UN_STR); // ptr_ori points to the original unchanged BCF data. uint8_t *ptr_ori = (uint8_t *) line->shared.s; // ID: single typed string if ( line->d.shared_dirty & BCF1_DIRTY_ID ) bcf1_sync_id(line, &tmp); else kputsn_(ptr_ori, line->unpack_size[0], &tmp); ptr_ori += line->unpack_size[0]; line->unpack_size[0] = tmp.l; prev_len = tmp.l; // REF+ALT: list of typed strings if ( line->d.shared_dirty & BCF1_DIRTY_ALS ) bcf1_sync_alleles(line, &tmp); else { kputsn_(ptr_ori, line->unpack_size[1], &tmp); if ( !line->rlen && line->n_allele ) line->rlen = strlen(line->d.allele[0]); } ptr_ori += line->unpack_size[1]; line->unpack_size[1] = tmp.l - prev_len; prev_len = tmp.l; if ( line->unpacked & BCF_UN_FLT ) { // FILTER: typed vector of integers if ( line->d.shared_dirty & BCF1_DIRTY_FLT ) bcf1_sync_filter(line, &tmp); else if ( line->d.n_flt ) kputsn_(ptr_ori, line->unpack_size[2], &tmp); else bcf_enc_vint(&tmp, 0, 0, -1); ptr_ori += line->unpack_size[2]; line->unpack_size[2] = tmp.l - prev_len; if ( line->unpacked & BCF_UN_INFO ) { // INFO: pairs of typed vectors if ( line->d.shared_dirty & BCF1_DIRTY_INF ) { bcf1_sync_info(line, &tmp); ptr_ori = (uint8_t*)line->shared.s + line->shared.l; } } } int size = line->shared.l - (size_t)ptr_ori + (size_t)line->shared.s; if ( size ) kputsn_(ptr_ori, size, &tmp); free(line->shared.s); line->shared = tmp; } if ( line->shared.s != shared_ori && line->unpacked & BCF_UN_INFO ) { // Reallocated line->shared.s block invalidated line->d.info[].vptr pointers size_t off_new = line->unpack_size[0] + line->unpack_size[1] + line->unpack_size[2]; int i; for (i=0; in_info; i++) { uint8_t *vptr_free = line->d.info[i].vptr_free ? line->d.info[i].vptr - line->d.info[i].vptr_off : NULL; line->d.info[i].vptr = (uint8_t*) line->shared.s + off_new + line->d.info[i].vptr_off; off_new += line->d.info[i].vptr_len + line->d.info[i].vptr_off; if ( vptr_free ) { free(vptr_free); line->d.info[i].vptr_free = 0; } } } if ( line->n_sample && line->n_fmt && (!line->indiv.l || line->d.indiv_dirty) ) { // The genotype fields changed or are not present tmp.l = tmp.m = 0; tmp.s = NULL; int i, irm = -1; for (i=0; in_fmt; i++) { bcf_fmt_t *fmt = &line->d.fmt[i]; if ( !fmt->p ) { // marked for removal if ( irm < 0 ) irm = i; continue; } kputsn_(fmt->p - fmt->p_off, fmt->p_len + fmt->p_off, &tmp); if ( irm >=0 ) { bcf_fmt_t tfmt = line->d.fmt[irm]; line->d.fmt[irm] = line->d.fmt[i]; line->d.fmt[i] = tfmt; while ( irm<=i && line->d.fmt[irm].p ) irm++; } } if ( irm>=0 ) line->n_fmt = irm; free(line->indiv.s); line->indiv = tmp; // Reallocated line->indiv.s block invalidated line->d.fmt[].p pointers size_t off_new = 0; for (i=0; in_fmt; i++) { uint8_t *p_free = line->d.fmt[i].p_free ? line->d.fmt[i].p - line->d.fmt[i].p_off : NULL; line->d.fmt[i].p = (uint8_t*) line->indiv.s + off_new + line->d.fmt[i].p_off; off_new += line->d.fmt[i].p_len + line->d.fmt[i].p_off; if ( p_free ) { free(p_free); line->d.fmt[i].p_free = 0; } } } if ( !line->n_sample ) line->n_fmt = 0; line->d.shared_dirty = line->d.indiv_dirty = 0; return 0; } bcf1_t *bcf_copy(bcf1_t *dst, bcf1_t *src) { bcf1_sync(src); bcf_clear(dst); dst->rid = src->rid; dst->pos = src->pos; dst->rlen = src->rlen; dst->qual = src->qual; dst->n_info = src->n_info; dst->n_allele = src->n_allele; dst->n_fmt = src->n_fmt; dst->n_sample = src->n_sample; if ( dst->shared.m < src->shared.l ) { dst->shared.s = (char*) realloc(dst->shared.s, src->shared.l); dst->shared.m = src->shared.l; } dst->shared.l = src->shared.l; memcpy(dst->shared.s,src->shared.s,dst->shared.l); if ( dst->indiv.m < src->indiv.l ) { dst->indiv.s = (char*) realloc(dst->indiv.s, src->indiv.l); dst->indiv.m = src->indiv.l; } dst->indiv.l = src->indiv.l; memcpy(dst->indiv.s,src->indiv.s,dst->indiv.l); return dst; } bcf1_t *bcf_dup(bcf1_t *src) { bcf1_t *out = bcf_init1(); return bcf_copy(out, src); } int bcf_write(htsFile *hfp, bcf_hdr_t *h, bcf1_t *v) { if ( h->dirty ) { if (bcf_hdr_sync(h) < 0) return -1; } if ( bcf_hdr_nsamples(h)!=v->n_sample ) { hts_log_error("Broken VCF record, the number of columns at %s:%"PRIhts_pos" does not match the number of samples (%d vs %d)", bcf_seqname_safe(h,v), v->pos+1, v->n_sample, bcf_hdr_nsamples(h)); return -1; } if ( hfp->format.format == vcf || hfp->format.format == text_format ) return vcf_write(hfp,h,v); if ( v->errcode & ~BCF_ERR_LIMITS ) // todo: unsure about the other BCF_ERR_LIMITS branches in vcf_parse_format_alloc4() { // vcf_parse1() encountered a new contig or tag, undeclared in the // header. At this point, the header must have been printed, // proceeding would lead to a broken BCF file. Errors must be checked // and cleared by the caller before we can proceed. char errdescription[1024] = ""; hts_log_error("Unchecked error (%d %s) at %s:%"PRIhts_pos, v->errcode, bcf_strerror(v->errcode, errdescription, sizeof(errdescription)), bcf_seqname_safe(h,v), v->pos+1); return -1; } bcf1_sync(v); // check if the BCF record was modified if ( v->unpacked & BCF_IS_64BIT ) { hts_log_error("Data at %s:%"PRIhts_pos" contains 64-bit values not representable in BCF. Please use VCF instead", bcf_seqname_safe(h,v), v->pos+1); return -1; } BGZF *fp = hfp->fp.bgzf; uint8_t x[32]; u32_to_le(v->shared.l + 24, x); // to include six 32-bit integers u32_to_le(v->indiv.l, x + 4); i32_to_le(v->rid, x + 8); u32_to_le(v->pos, x + 12); u32_to_le(v->rlen, x + 16); float_to_le(v->qual, x + 20); u16_to_le(v->n_info, x + 24); u16_to_le(v->n_allele, x + 26); u32_to_le((uint32_t)v->n_fmt<<24 | (v->n_sample & 0xffffff), x + 28); if ( bgzf_write(fp, x, 32) != 32 ) return -1; if ( bgzf_write(fp, v->shared.s, v->shared.l) != v->shared.l ) return -1; if ( bgzf_write(fp, v->indiv.s, v->indiv.l) != v->indiv.l ) return -1; if (hfp->idx) { if (bgzf_idx_push(fp, hfp->idx, v->rid, v->pos, v->pos + v->rlen, bgzf_tell(fp), 1) < 0) return -1; } return 0; } /********************** *** VCF header I/O *** **********************/ static int add_missing_contig_hrec(bcf_hdr_t *h, const char *name) { bcf_hrec_t *hrec = calloc(1, sizeof(bcf_hrec_t)); int save_errno; if (!hrec) goto fail; hrec->key = strdup("contig"); if (!hrec->key) goto fail; if (bcf_hrec_add_key(hrec, "ID", strlen("ID")) < 0) goto fail; if (bcf_hrec_set_val(hrec, hrec->nkeys-1, name, strlen(name), 0) < 0) goto fail; if (bcf_hdr_add_hrec(h, hrec) < 0) goto fail; return 0; fail: save_errno = errno; hts_log_error("%s", strerror(errno)); if (hrec) bcf_hrec_destroy(hrec); errno = save_errno; return -1; } bcf_hdr_t *vcf_hdr_read(htsFile *fp) { kstring_t txt, *s = &fp->line; int ret; bcf_hdr_t *h; tbx_t *idx = NULL; const char **names = NULL; h = bcf_hdr_init("r"); if (!h) { hts_log_error("Failed to allocate bcf header"); return NULL; } txt.l = txt.m = 0; txt.s = 0; while ((ret = hts_getline(fp, KS_SEP_LINE, s)) >= 0) { int e = 0; if (s->l == 0) continue; if (s->s[0] != '#') { hts_log_error("No sample line"); goto error; } if (s->s[1] != '#' && fp->fn_aux) { // insert contigs here kstring_t tmp = { 0, 0, NULL }; hFILE *f = hopen(fp->fn_aux, "r"); if (f == NULL) { hts_log_error("Couldn't open \"%s\"", fp->fn_aux); goto error; } while (tmp.l = 0, kgetline(&tmp, (kgets_func *) hgets, f) >= 0) { char *tab = strchr(tmp.s, '\t'); if (tab == NULL) continue; e |= (kputs("##contig=\n", 2, &txt) < 0); } free(tmp.s); if (hclose(f) != 0) { hts_log_error("Error on closing %s", fp->fn_aux); goto error; } if (e) goto error; } if (kputsn(s->s, s->l, &txt) < 0) goto error; if (kputc('\n', &txt) < 0) goto error; if (s->s[1] != '#') break; } if ( ret < -1 ) goto error; if ( !txt.s ) { hts_log_error("Could not read the header"); goto error; } if ( bcf_hdr_parse(h, txt.s) < 0 ) goto error; // check tabix index, are all contigs listed in the header? add the missing ones idx = tbx_index_load3(fp->fn, NULL, HTS_IDX_SILENT_FAIL); if ( idx ) { int i, n, need_sync = 0; names = tbx_seqnames(idx, &n); if (!names) goto error; for (i=0; ivalue ) { int j, nout = 0; e |= ksprintf(str, "##%s=<", hrec->key) < 0; for (j=0; jnkeys; j++) { // do not output IDX if output is VCF if ( !is_bcf && !strcmp("IDX",hrec->keys[j]) ) continue; if ( nout ) e |= kputc(',',str) < 0; e |= ksprintf(str,"%s=%s", hrec->keys[j], hrec->vals[j]) < 0; nout++; } e |= ksprintf(str,">\n") < 0; } else e |= ksprintf(str,"##%s=%s\n", hrec->key,hrec->value) < 0; return e == 0 ? 0 : -1; } int bcf_hrec_format(const bcf_hrec_t *hrec, kstring_t *str) { return _bcf_hrec_format(hrec,0,str); } int bcf_hdr_format(const bcf_hdr_t *hdr, int is_bcf, kstring_t *str) { int i, r = 0; for (i=0; inhrec; i++) r |= _bcf_hrec_format(hdr->hrec[i], is_bcf, str) < 0; r |= ksprintf(str, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO") < 0; if ( bcf_hdr_nsamples(hdr) ) { r |= ksprintf(str, "\tFORMAT") < 0; for (i=0; isamples[i]) < 0; } r |= ksprintf(str, "\n") < 0; return r ? -1 : 0; } char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) { kstring_t txt = {0,0,0}; if (bcf_hdr_format(hdr, is_bcf, &txt) < 0) return NULL; if ( len ) *len = txt.l; return txt.s; } const char **bcf_hdr_seqnames(const bcf_hdr_t *h, int *n) { vdict_t *d = (vdict_t*)h->dict[BCF_DT_CTG]; int i, tid, m = kh_size(d); const char **names = (const char**) calloc(m,sizeof(const char*)); if ( !names ) { hts_log_error("Failed to allocate memory"); *n = 0; return NULL; } khint_t k; for (k=kh_begin(d); k= m ) { // This can happen after a contig has been removed from BCF header via bcf_hdr_remove() if ( hts_resize(const char*, tid + 1, &m, &names, HTS_RESIZE_CLEAR)<0 ) { hts_log_error("Failed to allocate memory"); *n = 0; free(names); return NULL; } m = tid + 1; } names[tid] = kh_key(d,k); } // ensure there are no gaps for (i=0,tid=0; tidformat.compression!=no_compression ) { ret = bgzf_write(fp->fp.bgzf, htxt.s, htxt.l); if (bgzf_flush(fp->fp.bgzf) != 0) return -1; } else { ret = hwrite(fp->fp.hfile, htxt.s, htxt.l); } free(htxt.s); return ret<0 ? -1 : 0; } /*********************** *** Typed value I/O *** ***********************/ int bcf_enc_vint(kstring_t *s, int n, int32_t *a, int wsize) { int32_t max = INT32_MIN, min = INT32_MAX; int i; if (n <= 0) { return bcf_enc_size(s, 0, BCF_BT_NULL); } else if (n == 1) { return bcf_enc_int1(s, a[0]); } else { if (wsize <= 0) wsize = n; // Equivalent to: // for (i = 0; i < n; ++i) { // if (a[i] == bcf_int32_missing || a[i] == bcf_int32_vector_end ) // continue; // if (max < a[i]) max = a[i]; // if (min > a[i]) min = a[i]; // } int max4[4] = {INT32_MIN, INT32_MIN, INT32_MIN, INT32_MIN}; int min4[4] = {INT32_MAX, INT32_MAX, INT32_MAX, INT32_MAX}; for (i = 0; i < (n&~3); i+=4) { // bcf_int32_missing == INT32_MIN and // bcf_int32_vector_end == INT32_MIN+1. // We skip these, but can mostly avoid explicit checking if (max4[0] < a[i+0]) max4[0] = a[i+0]; if (max4[1] < a[i+1]) max4[1] = a[i+1]; if (max4[2] < a[i+2]) max4[2] = a[i+2]; if (max4[3] < a[i+3]) max4[3] = a[i+3]; if (min4[0] > a[i+0] && a[i+0] > INT32_MIN+1) min4[0] = a[i+0]; if (min4[1] > a[i+1] && a[i+1] > INT32_MIN+1) min4[1] = a[i+1]; if (min4[2] > a[i+2] && a[i+2] > INT32_MIN+1) min4[2] = a[i+2]; if (min4[3] > a[i+3] && a[i+3] > INT32_MIN+1) min4[3] = a[i+3]; } min = min4[0]; if (min > min4[1]) min = min4[1]; if (min > min4[2]) min = min4[2]; if (min > min4[3]) min = min4[3]; max = max4[0]; if (max < max4[1]) max = max4[1]; if (max < max4[2]) max = max4[2]; if (max < max4[3]) max = max4[3]; for (; i < n; ++i) { if (max < a[i]) max = a[i]; if (min > a[i] && a[i] > INT32_MIN+1) min = a[i]; } if (max <= BCF_MAX_BT_INT8 && min >= BCF_MIN_BT_INT8) { if (bcf_enc_size(s, wsize, BCF_BT_INT8) < 0 || ks_resize(s, s->l + n) < 0) return -1; uint8_t *p = (uint8_t *) s->s + s->l; for (i = 0; i < n; ++i, p++) { if ( a[i]==bcf_int32_vector_end ) *p = bcf_int8_vector_end; else if ( a[i]==bcf_int32_missing ) *p = bcf_int8_missing; else *p = a[i]; } s->l += n; } else if (max <= BCF_MAX_BT_INT16 && min >= BCF_MIN_BT_INT16) { uint8_t *p; if (bcf_enc_size(s, wsize, BCF_BT_INT16) < 0 || ks_resize(s, s->l + n * sizeof(int16_t)) < 0) return -1; p = (uint8_t *) s->s + s->l; for (i = 0; i < n; ++i) { int16_t x; if ( a[i]==bcf_int32_vector_end ) x = bcf_int16_vector_end; else if ( a[i]==bcf_int32_missing ) x = bcf_int16_missing; else x = a[i]; i16_to_le(x, p); p += sizeof(int16_t); } s->l += n * sizeof(int16_t); } else { uint8_t *p; if (bcf_enc_size(s, wsize, BCF_BT_INT32) < 0 || ks_resize(s, s->l + n * sizeof(int32_t)) < 0) return -1; p = (uint8_t *) s->s + s->l; for (i = 0; i < n; ++i) { i32_to_le(a[i], p); p += sizeof(int32_t); } s->l += n * sizeof(int32_t); } } return 0; } #ifdef VCF_ALLOW_INT64 static int bcf_enc_long1(kstring_t *s, int64_t x) { uint32_t e = 0; if (x <= BCF_MAX_BT_INT32 && x >= BCF_MIN_BT_INT32) return bcf_enc_int1(s, x); if (x == bcf_int64_vector_end) { e |= bcf_enc_size(s, 1, BCF_BT_INT8); e |= kputc(bcf_int8_vector_end, s) < 0; } else if (x == bcf_int64_missing) { e |= bcf_enc_size(s, 1, BCF_BT_INT8); e |= kputc(bcf_int8_missing, s) < 0; } else { e |= bcf_enc_size(s, 1, BCF_BT_INT64); e |= ks_expand(s, 8); if (e == 0) { u64_to_le(x, (uint8_t *) s->s + s->l); s->l += 8; } } return e == 0 ? 0 : -1; } #endif static inline int serialize_float_array(kstring_t *s, size_t n, const float *a) { uint8_t *p; size_t i; size_t bytes = n * sizeof(float); if (bytes / sizeof(float) != n) return -1; if (ks_resize(s, s->l + bytes) < 0) return -1; p = (uint8_t *) s->s + s->l; for (i = 0; i < n; i++) { float_to_le(a[i], p); p += sizeof(float); } s->l += bytes; return 0; } int bcf_enc_vfloat(kstring_t *s, int n, float *a) { assert(n >= 0); bcf_enc_size(s, n, BCF_BT_FLOAT); serialize_float_array(s, n, a); return 0; // FIXME: check for errs in this function } int bcf_enc_vchar(kstring_t *s, int l, const char *a) { bcf_enc_size(s, l, BCF_BT_CHAR); kputsn(a, l, s); return 0; // FIXME: check for errs in this function } // Special case of n==1 as it also occurs quite often in FORMAT data. // This version is also small enough to get inlined. static inline int bcf_fmt_array1(kstring_t *s, int type, void *data) { uint32_t e = 0; uint8_t *p = (uint8_t *)data; int32_t v; // helps gcc more than clang here. In billions of cycles: // bcf_fmt_array1 bcf_fmt_array // gcc7: 23.2 24.3 // gcc13: 21.6 23.0 // clang13: 27.1 27.8 switch (type) { case BCF_BT_CHAR: e |= kputc_(*p == bcf_str_missing ? '.' : *p, s) < 0; break; case BCF_BT_INT8: if (*(int8_t *)p != bcf_int8_vector_end) { e |= ((*(int8_t *)p == bcf_int8_missing) ? kputc_('.', s) : kputw(*(int8_t *)p, s)) < 0; } break; case BCF_BT_INT16: v = le_to_i16(p); if (v != bcf_int16_vector_end) { e |= (v == bcf_int16_missing ? kputc_('.', s) : kputw(v, s)) < 0; } break; case BCF_BT_INT32: v = le_to_i32(p); if (v != bcf_int32_vector_end) { e |= (v == bcf_int32_missing ? kputc_('.', s) : kputw(v, s)) < 0; } break; case BCF_BT_FLOAT: v = le_to_u32(p); if (v != bcf_float_vector_end) { e |= (v == bcf_float_missing ? kputc_('.', s) : kputd(le_to_float(p), s)) < 0; } break; default: hts_log_error("Unexpected type %d", type); return -1; } return e == 0 ? 0 : -1; } int bcf_fmt_array(kstring_t *s, int n, int type, void *data) { int j = 0; uint32_t e = 0; if (n == 0) { return kputc_('.', s) >= 0 ? 0 : -1; } if (type == BCF_BT_CHAR) { char *p = (char *)data; // Note bcf_str_missing is already accounted for in n==0 above. if (n >= 8) { char *p_end = memchr(p, 0, n); e |= kputsn(p, p_end ? p_end-p : n, s) < 0; } else { for (j = 0; j < n && *p; ++j, ++p) e |= kputc(*p, s) < 0; } } else { #define BRANCH(type_t, convert, is_missing, is_vector_end, kprint) { \ uint8_t *p = (uint8_t *) data; \ for (j=0; jid[BCF_DT_ID][key] vdict int max_m; // number of elements in field array (ie commas) int size; // field size (max_l or max_g*4 if is_gt) int offset; // offset of buf into h->mem uint32_t is_gt:1, // is genotype max_g:31; // maximum number of genotypes uint32_t max_l; // length of field uint32_t y; // h->id[0][fmt[j].key].val->info[BCF_HL_FMT] uint8_t *buf; // Pointer into h->mem } fmt_aux_t; // fmt_aux_t field notes: // max_* are biggest sizes of the various FORMAT fields across all samples. // We use these after pivoting the data to ensure easy random access // of a specific sample. // // max_m is only used for type BCF_HT_REAL or BCF_HT_INT // max_g is only used for is_gt == 1 (will be BCF_HT_STR) // max_l is only used for is_gt == 0 (will be BCF_HT_STR) // // These are computed in vcf_parse_format_max3 and used in // vcf_parse_format_alloc4 to get the size. // // size is computed from max_g, max_l, max_m and is_gt. Once computed // the max values are never accessed again. // // In theory all 4 vars could be coalesced into a single variable, but this // significantly harms speed (even if done via a union). It's about 25-30% // slower. static inline int align_mem(kstring_t *s) { int e = 0; if (s->l&7) { uint64_t zero = 0; e = kputsn((char*)&zero, 8 - (s->l&7), s) < 0; } return e == 0 ? 0 : -1; } #define MAX_N_FMT 255 /* Limited by size of bcf1_t n_fmt field */ // detect FORMAT "." static int vcf_parse_format_empty1(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v, const char *p, const char *q) { const char *end = s->s + s->l; if ( q>=end ) { hts_log_error("FORMAT column with no sample columns starting at %s:%"PRIhts_pos"", bcf_seqname_safe(h,v), v->pos+1); v->errcode |= BCF_ERR_NCOLS; return -1; } v->n_fmt = 0; if ( p[0]=='.' && p[1]==0 ) // FORMAT field is empty "." { v->n_sample = bcf_hdr_nsamples(h); return 1; } return 0; } // get format information from the dictionary static int vcf_parse_format_dict2(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v, const char *p, const char *q, fmt_aux_t *fmt) { const vdict_t *d = (vdict_t*)h->dict[BCF_DT_ID]; char *t; int j; ks_tokaux_t aux1; for (j = 0, t = kstrtok(p, ":", &aux1); t; t = kstrtok(0, 0, &aux1), ++j) { if (j >= MAX_N_FMT) { v->errcode |= BCF_ERR_LIMITS; hts_log_error("FORMAT column at %s:%"PRIhts_pos" lists more identifiers than htslib can handle", bcf_seqname_safe(h,v), v->pos+1); return -1; } *(char*)aux1.p = 0; khint_t k = kh_get(vdict, d, t); if (k == kh_end(d) || kh_val(d, k).info[BCF_HL_FMT] == 15) { if ( t[0]=='.' && t[1]==0 ) { hts_log_error("Invalid FORMAT tag name '.' at %s:%"PRIhts_pos, bcf_seqname_safe(h,v), v->pos+1); v->errcode |= BCF_ERR_TAG_INVALID; return -1; } hts_log_warning("FORMAT '%s' at %s:%"PRIhts_pos" is not defined in the header, assuming Type=String", t, bcf_seqname_safe(h,v), v->pos+1); kstring_t tmp = {0,0,0}; int l; ksprintf(&tmp, "##FORMAT=", t); bcf_hrec_t *hrec = bcf_hdr_parse_line(h,tmp.s,&l); free(tmp.s); int res = hrec ? bcf_hdr_add_hrec((bcf_hdr_t*)h, hrec) : -1; if (res < 0) bcf_hrec_destroy(hrec); if (res > 0) res = bcf_hdr_sync((bcf_hdr_t*)h); k = kh_get(vdict, d, t); v->errcode |= BCF_ERR_TAG_UNDEF; if (res || k == kh_end(d)) { hts_log_error("Could not add dummy header for FORMAT '%s' at %s:%"PRIhts_pos, t, bcf_seqname_safe(h,v), v->pos+1); v->errcode |= BCF_ERR_TAG_INVALID; return -1; } } fmt[j].max_l = fmt[j].max_m = fmt[j].max_g = 0; fmt[j].key = kh_val(d, k).id; fmt[j].is_gt = (t[0] == 'G' && t[1] == 'T' && !t[2]); fmt[j].y = h->id[0][fmt[j].key].val->info[BCF_HL_FMT]; v->n_fmt++; } return 0; } // compute max static int vcf_parse_format_max3(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v, char *p, char *q, fmt_aux_t *fmt) { int n_sample_ori = -1; char *r = q + 1; // r: position in the format string int l = 0, m = 1, g = 1, j; v->n_sample = 0; // m: max vector size, l: max field len, g: max number of alleles const char *end = s->s + s->l; while ( rkeep_samples ) { n_sample_ori++; if ( !bit_array_test(h->keep_samples,n_sample_ori) ) { while ( *r!='\t' && ris_gt) g++; break; case '\t': *r = 0; // fall through default: // valid due to while loop above. case '\0': case ':': l = r - r_start; r_start = r; if (f->max_m < m) f->max_m = m; if (f->max_l < l) f->max_l = l; if (f->is_gt && f->max_g < g) f->max_g = g; l = 0, m = g = 1; if ( *r==':' ) { j++; f++; if ( j>=v->n_fmt ) { hts_log_error("Incorrect number of FORMAT fields at %s:%"PRIhts_pos"", h->id[BCF_DT_CTG][v->rid].key, v->pos+1); v->errcode |= BCF_ERR_NCOLS; return -1; } } else goto end_for; break; } if ( r>=end ) break; r++; } end_for: v->n_sample++; if ( v->n_sample == bcf_hdr_nsamples(h) ) break; r++; } return 0; } // allocate memory for arrays static int vcf_parse_format_alloc4(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v, const char *p, const char *q, fmt_aux_t *fmt) { kstring_t *mem = (kstring_t*)&h->mem; int j; for (j = 0; j < v->n_fmt; ++j) { fmt_aux_t *f = &fmt[j]; if ( !f->max_m ) f->max_m = 1; // omitted trailing format field if ((f->y>>4&0xf) == BCF_HT_STR) { f->size = f->is_gt? f->max_g << 2 : f->max_l; } else if ((f->y>>4&0xf) == BCF_HT_REAL || (f->y>>4&0xf) == BCF_HT_INT) { f->size = f->max_m << 2; } else { hts_log_error("The format type %d at %s:%"PRIhts_pos" is currently not supported", f->y>>4&0xf, bcf_seqname_safe(h,v), v->pos+1); v->errcode |= BCF_ERR_TAG_INVALID; return -1; } if (align_mem(mem) < 0) { hts_log_error("Memory allocation failure at %s:%"PRIhts_pos, bcf_seqname_safe(h,v), v->pos+1); v->errcode |= BCF_ERR_LIMITS; return -1; } // Limit the total memory to ~2Gb per VCF row. This should mean // malformed VCF data is less likely to take excessive memory and/or // time. if ((uint64_t) mem->l + v->n_sample * (uint64_t)f->size > INT_MAX) { static int warned = 0; if ( !warned ) hts_log_warning("Excessive memory required by FORMAT fields at %s:%"PRIhts_pos, bcf_seqname_safe(h,v), v->pos+1); warned = 1; v->errcode |= BCF_ERR_LIMITS; f->size = -1; f->offset = 0; continue; } f->offset = mem->l; if (ks_resize(mem, mem->l + v->n_sample * (size_t)f->size) < 0) { hts_log_error("Memory allocation failure at %s:%"PRIhts_pos, bcf_seqname_safe(h,v), v->pos+1); v->errcode |= BCF_ERR_LIMITS; return -1; } mem->l += v->n_sample * f->size; } { int j; for (j = 0; j < v->n_fmt; ++j) fmt[j].buf = (uint8_t*)mem->s + fmt[j].offset; } // check for duplicate tags int i; for (i=1; in_fmt; i++) { fmt_aux_t *ifmt = &fmt[i]; if ( ifmt->size==-1 ) continue; // already marked for removal for (j=0; jsize==-1 ) continue; // already marked for removal if ( ifmt->key!=jfmt->key ) continue; static int warned = 0; if ( !warned ) hts_log_warning("Duplicate FORMAT tag %s at %s:%"PRIhts_pos, bcf_hdr_int2id(h,BCF_DT_ID,ifmt->key), bcf_seqname_safe(h,v), v->pos+1); warned = 1; v->errcode |= BCF_ERR_TAG_INVALID; ifmt->size = -1; ifmt->offset = 0; break; } } return 0; } // Fill the sample fields static int vcf_parse_format_fill5(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v, const char *p, const char *q, fmt_aux_t *fmt) { static int extreme_val_warned = 0; int n_sample_ori = -1; // At beginning of the loop t points to the first char of a format const char *t = q + 1; int m = 0; // m: sample id const int nsamples = bcf_hdr_nsamples(h); const char *end = s->s + s->l; while ( tkeep_samples ) { n_sample_ori++; if ( !bit_array_test(h->keep_samples,n_sample_ori) ) { while ( *t && ty>>4&0xf; if (!z->buf) { hts_log_error("Memory allocation failure for FORMAT field type %d at %s:%"PRIhts_pos, z->y>>4&0xf, bcf_seqname_safe(h,v), v->pos+1); v->errcode |= BCF_ERR_LIMITS; return -1; } if ( z->size==-1 ) { // this field is to be ignored, it's either too big or a duplicate while ( *t != ':' && *t ) t++; } else if (htype == BCF_HT_STR) { int l; if (z->is_gt) { // Genotypes. // ([|/])+... where is [0-9]+ or ".". int32_t is_phased = 0; uint32_t *x = (uint32_t*)(z->buf + z->size * (size_t)m); uint32_t unreadable = 0; uint32_t max = 0; int overflow = 0; for (l = 0;; ++t) { if (*t == '.') { ++t, x[l++] = is_phased; } else { const char *tt = t; uint32_t val; // Or "v->n_allele < 10", but it doesn't // seem to be any faster and this feels safer. if (*t >= '0' && *t <= '9' && !(t[1] >= '0' && t[1] <= '9')) { val = *t++ - '0'; } else { val = hts_str2uint(t, (char **)&t, sizeof(val) * CHAR_MAX - 2, &overflow); unreadable |= tt == t; } if (max < val) max = val; x[l++] = (val + 1) << 1 | is_phased; } is_phased = (*t == '|'); if (*t != '|' && *t != '/') break; } // Possibly check max against v->n_allele instead? if (overflow || max > (INT32_MAX >> 1) - 1) { hts_log_error("Couldn't read GT data: value too large at %s:%"PRIhts_pos, bcf_seqname_safe(h,v), v->pos+1); return -1; } if (unreadable) { hts_log_error("Couldn't read GT data: value not a number or '.' at %s:%"PRIhts_pos, bcf_seqname_safe(h,v), v->pos+1); return -1; } if ( !l ) x[l++] = 0; // An empty field, insert missing value for (; l < z->size>>2; ++l) x[l] = bcf_int32_vector_end; } else { // Otherwise arbitrary strings char *x = (char*)z->buf + z->size * (size_t)m; for (l = 0; *t != ':' && *t; ++t) x[l++] = *t; if (z->size > l) memset(&x[l], 0, (z->size-l) * sizeof(*x)); } } else if (htype == BCF_HT_INT) { // One or more integers in an array int32_t *x = (int32_t*)(z->buf + z->size * (size_t)m); int l; for (l = 0;; ++t) { if (*t == '.') { x[l++] = bcf_int32_missing, ++t; // ++t to skip "." } else { int overflow = 0; char *te; long int tmp_val = hts_str2int(t, &te, sizeof(tmp_val)*CHAR_BIT, &overflow); if ( te==t || overflow || tmp_valBCF_MAX_BT_INT32 ) { if ( !extreme_val_warned ) { hts_log_warning("Extreme FORMAT/%s value encountered and set to missing at %s:%"PRIhts_pos, h->id[BCF_DT_ID][fmt[j-1].key].key, bcf_seqname_safe(h,v), v->pos+1); extreme_val_warned = 1; } tmp_val = bcf_int32_missing; } x[l++] = tmp_val; t = te; } if (*t != ',') break; } if ( !l ) x[l++] = bcf_int32_missing; for (; l < z->size>>2; ++l) x[l] = bcf_int32_vector_end; } else if (htype == BCF_HT_REAL) { // One of more floating point values in an array float *x = (float*)(z->buf + z->size * (size_t)m); int l; for (l = 0;; ++t) { if (*t == '.' && !isdigit_c(t[1])) { bcf_float_set_missing(x[l++]), ++t; // ++t to skip "." } else { int overflow = 0; char *te; float tmp_val = hts_str2dbl(t, &te, &overflow); if ( (te==t || overflow) && !extreme_val_warned ) { hts_log_warning("Extreme FORMAT/%s value encountered at %s:%"PRIhts_pos, h->id[BCF_DT_ID][fmt[j-1].key].key, bcf_seqname(h,v), v->pos+1); extreme_val_warned = 1; } x[l++] = tmp_val; t = te; } if (*t != ',') break; } if ( !l ) // An empty field, insert missing value bcf_float_set_missing(x[l++]); for (; l < z->size>>2; ++l) bcf_float_set_vector_end(x[l]); } else { hts_log_error("Unknown FORMAT field type %d at %s:%"PRIhts_pos, htype, bcf_seqname_safe(h,v), v->pos+1); v->errcode |= BCF_ERR_TAG_INVALID; return -1; } if (*t == '\0') { break; } else if (*t == ':') { t++; } else { char buffer[8]; hts_log_error("Invalid character %s in '%s' FORMAT field at %s:%"PRIhts_pos"", hts_strprint(buffer, sizeof buffer, '\'', t, 1), h->id[BCF_DT_ID][z->key].key, bcf_seqname_safe(h,v), v->pos+1); v->errcode |= BCF_ERR_CHAR; return -1; } } // fill end-of-vector values for (; j < v->n_fmt; ++j) { fmt_aux_t *z = &fmt[j]; const int htype = z->y>>4&0xf; int l; if (z->size == -1) // this field is to be ignored continue; if (htype == BCF_HT_STR) { if (z->is_gt) { int32_t *x = (int32_t*)(z->buf + z->size * (size_t)m); if (z->size) x[0] = bcf_int32_missing; for (l = 1; l < z->size>>2; ++l) x[l] = bcf_int32_vector_end; } else { char *x = (char*)z->buf + z->size * (size_t)m; if ( z->size ) { x[0] = '.'; memset(&x[1], 0, (z->size-1) * sizeof(*x)); } } } else if (htype == BCF_HT_INT) { int32_t *x = (int32_t*)(z->buf + z->size * (size_t)m); x[0] = bcf_int32_missing; for (l = 1; l < z->size>>2; ++l) x[l] = bcf_int32_vector_end; } else if (htype == BCF_HT_REAL) { float *x = (float*)(z->buf + z->size * (size_t)m); bcf_float_set_missing(x[0]); for (l = 1; l < z->size>>2; ++l) bcf_float_set_vector_end(x[l]); } } m++; t++; } return 0; } // write individual genotype information static int vcf_parse_format_gt6(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v, const char *p, const char *q, fmt_aux_t *fmt) { kstring_t *str = &v->indiv; int i, need_downsize = 0; if (v->n_sample > 0) { for (i = 0; i < v->n_fmt; ++i) { fmt_aux_t *z = &fmt[i]; if ( z->size==-1 ) { need_downsize = 1; continue; } bcf_enc_int1(str, z->key); if ((z->y>>4&0xf) == BCF_HT_STR && !z->is_gt) { bcf_enc_size(str, z->size, BCF_BT_CHAR); kputsn((char*)z->buf, z->size * (size_t)v->n_sample, str); } else if ((z->y>>4&0xf) == BCF_HT_INT || z->is_gt) { bcf_enc_vint(str, (z->size>>2) * v->n_sample, (int32_t*)z->buf, z->size>>2); } else { bcf_enc_size(str, z->size>>2, BCF_BT_FLOAT); if (serialize_float_array(str, (z->size>>2) * (size_t)v->n_sample, (float *) z->buf) != 0) { v->errcode |= BCF_ERR_LIMITS; hts_log_error("Out of memory at %s:%"PRIhts_pos, bcf_seqname_safe(h,v), v->pos+1); return -1; } } } } if ( need_downsize ) { i = 0; while ( i < v->n_fmt ) { if ( fmt[i].size==-1 ) { v->n_fmt--; if ( i < v->n_fmt ) memmove(&fmt[i],&fmt[i+1],sizeof(*fmt)*(v->n_fmt-i)); } else i++; } } return 0; } // validity checking static int vcf_parse_format_check7(const bcf_hdr_t *h, bcf1_t *v) { if ( v->n_sample!=bcf_hdr_nsamples(h) ) { hts_log_error("Number of columns at %s:%"PRIhts_pos" does not match the number of samples (%d vs %d)", bcf_seqname_safe(h,v), v->pos+1, v->n_sample, bcf_hdr_nsamples(h)); v->errcode |= BCF_ERR_NCOLS; return -1; } if ( v->indiv.l > 0xffffffff ) { hts_log_error("The FORMAT at %s:%"PRIhts_pos" is too long", bcf_seqname_safe(h,v), v->pos+1); v->errcode |= BCF_ERR_LIMITS; // Error recovery: return -1 if this is a critical error or 0 if we want to ignore the FORMAT and proceed v->n_fmt = 0; return -1; } return 0; } // p,q is the start and the end of the FORMAT field static int vcf_parse_format(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v, char *p, char *q) { if ( !bcf_hdr_nsamples(h) ) return 0; kstring_t *mem = (kstring_t*)&h->mem; mem->l = 0; fmt_aux_t fmt[MAX_N_FMT]; // detect FORMAT "." int ret; // +ve = ok, -ve = err if ((ret = vcf_parse_format_empty1(s, h, v, p, q))) return ret ? 0 : -1; // get format information from the dictionary if (vcf_parse_format_dict2(s, h, v, p, q, fmt) < 0) return -1; // FORMAT data is per-sample A:B:C A:B:C A:B:C ... but in memory it is // stored as per-type arrays AAA... BBB... CCC... This is basically // a data rotation or pivot. // The size of elements in the array grow to their maximum needed, // permitting fast random access. This means however we have to first // scan the whole FORMAT line to find the maximum of each type, and // then scan it again to find the store the data. // We break this down into compute-max, allocate, fill-out-buffers // TODO: ? // The alternative would be to pivot on the first pass, with fixed // size entries for numerics and concatenated strings otherwise, also // tracking maximum sizes. Then on a second pass we reallocate and // copy the data again to a uniformly sized array. Two passes through // memory, but without doubling string parsing. // compute max if (vcf_parse_format_max3(s, h, v, p, q, fmt) < 0) return -1; // allocate memory for arrays if (vcf_parse_format_alloc4(s, h, v, p, q, fmt) < 0) return -1; // fill the sample fields; at beginning of the loop if (vcf_parse_format_fill5(s, h, v, p, q, fmt) < 0) return -1; // write individual genotype information if (vcf_parse_format_gt6(s, h, v, p, q, fmt) < 0) return -1; // validity checking if (vcf_parse_format_check7(h, v) < 0) return -1; return 0; } static khint_t fix_chromosome(const bcf_hdr_t *h, vdict_t *d, const char *p) { // Simple error recovery for chromosomes not defined in the header. It will not help when VCF header has // been already printed, but will enable tools like vcfcheck to proceed. kstring_t tmp = {0,0,0}; khint_t k; int l; if (ksprintf(&tmp, "##contig=", p) < 0) return kh_end(d); bcf_hrec_t *hrec = bcf_hdr_parse_line(h,tmp.s,&l); free(tmp.s); int res = hrec ? bcf_hdr_add_hrec((bcf_hdr_t*)h, hrec) : -1; if (res < 0) bcf_hrec_destroy(hrec); if (res > 0) res = bcf_hdr_sync((bcf_hdr_t*)h); k = kh_get(vdict, d, p); return k; } static int vcf_parse_filter(kstring_t *str, const bcf_hdr_t *h, bcf1_t *v, char *p, char *q) { int i, n_flt = 1, max_n_flt = 0; char *r, *t; int32_t *a_flt = NULL; ks_tokaux_t aux1; khint_t k; vdict_t *d = (vdict_t*)h->dict[BCF_DT_ID]; // count the number of filters if (*(q-1) == ';') *(q-1) = 0; for (r = p; *r; ++r) if (*r == ';') ++n_flt; if (n_flt > max_n_flt) { a_flt = malloc(n_flt * sizeof(*a_flt)); if (!a_flt) { hts_log_error("Could not allocate memory at %s:%"PRIhts_pos, bcf_seqname_safe(h,v), v->pos+1); v->errcode |= BCF_ERR_LIMITS; // No appropriate code? return -1; } max_n_flt = n_flt; } // add filters for (t = kstrtok(p, ";", &aux1), i = 0; t; t = kstrtok(0, 0, &aux1)) { *(char*)aux1.p = 0; k = kh_get(vdict, d, t); if (k == kh_end(d)) { // Simple error recovery for FILTERs not defined in the header. It will not help when VCF header has // been already printed, but will enable tools like vcfcheck to proceed. hts_log_warning("FILTER '%s' is not defined in the header", t); kstring_t tmp = {0,0,0}; int l; ksprintf(&tmp, "##FILTER=", t); bcf_hrec_t *hrec = bcf_hdr_parse_line(h,tmp.s,&l); free(tmp.s); int res = hrec ? bcf_hdr_add_hrec((bcf_hdr_t*)h, hrec) : -1; if (res < 0) bcf_hrec_destroy(hrec); if (res > 0) res = bcf_hdr_sync((bcf_hdr_t*)h); k = kh_get(vdict, d, t); v->errcode |= BCF_ERR_TAG_UNDEF; if (res || k == kh_end(d)) { hts_log_error("Could not add dummy header for FILTER '%s' at %s:%"PRIhts_pos, t, bcf_seqname_safe(h,v), v->pos+1); v->errcode |= BCF_ERR_TAG_INVALID; free(a_flt); return -1; } } a_flt[i++] = kh_val(d, k).id; } bcf_enc_vint(str, n_flt, a_flt, -1); free(a_flt); return 0; } static int vcf_parse_info(kstring_t *str, const bcf_hdr_t *h, bcf1_t *v, char *p, char *q) { static int extreme_int_warned = 0, negative_rlen_warned = 0; int max_n_val = 0, overflow = 0; char *r, *key; khint_t k; vdict_t *d = (vdict_t*)h->dict[BCF_DT_ID]; int32_t *a_val = NULL; v->n_info = 0; if (*(q-1) == ';') *(q-1) = 0; for (r = key = p;; ++r) { int c; char *val, *end; while (*r > '=' || (*r != ';' && *r != '=' && *r != 0)) r++; if (v->n_info == UINT16_MAX) { hts_log_error("Too many INFO entries at %s:%"PRIhts_pos, bcf_seqname_safe(h,v), v->pos+1); v->errcode |= BCF_ERR_LIMITS; goto fail; } val = end = NULL; c = *r; *r = 0; if (c == '=') { val = r + 1; for (end = val; *end != ';' && *end != 0; ++end); c = *end; *end = 0; } else end = r; if ( !*key ) { if (c==0) break; r = end; key = r + 1; continue; } // faulty VCF, ";;" in the INFO k = kh_get(vdict, d, key); if (k == kh_end(d) || kh_val(d, k).info[BCF_HL_INFO] == 15) { hts_log_warning("INFO '%s' is not defined in the header, assuming Type=String", key); kstring_t tmp = {0,0,0}; int l; ksprintf(&tmp, "##INFO=", key); bcf_hrec_t *hrec = bcf_hdr_parse_line(h,tmp.s,&l); free(tmp.s); int res = hrec ? bcf_hdr_add_hrec((bcf_hdr_t*)h, hrec) : -1; if (res < 0) bcf_hrec_destroy(hrec); if (res > 0) res = bcf_hdr_sync((bcf_hdr_t*)h); k = kh_get(vdict, d, key); v->errcode |= BCF_ERR_TAG_UNDEF; if (res || k == kh_end(d)) { hts_log_error("Could not add dummy header for INFO '%s' at %s:%"PRIhts_pos, key, bcf_seqname_safe(h,v), v->pos+1); v->errcode |= BCF_ERR_TAG_INVALID; goto fail; } } uint32_t y = kh_val(d, k).info[BCF_HL_INFO]; ++v->n_info; bcf_enc_int1(str, kh_val(d, k).id); if (val == 0) { bcf_enc_size(str, 0, BCF_BT_NULL); } else if ((y>>4&0xf) == BCF_HT_FLAG || (y>>4&0xf) == BCF_HT_STR) { // if Flag has a value, treat it as a string bcf_enc_vchar(str, end - val, val); } else { // int/float value/array int i, n_val; char *t, *te; for (t = val, n_val = 1; *t; ++t) // count the number of values if (*t == ',') ++n_val; // Check both int and float size in one step for simplicity if (n_val > max_n_val) { int32_t *a_tmp = (int32_t *)realloc(a_val, n_val * sizeof(*a_val)); if (!a_tmp) { hts_log_error("Could not allocate memory at %s:%"PRIhts_pos, bcf_seqname_safe(h,v), v->pos+1); v->errcode |= BCF_ERR_LIMITS; // No appropriate code? goto fail; } a_val = a_tmp; max_n_val = n_val; } if ((y>>4&0xf) == BCF_HT_INT) { i = 0, t = val; int64_t val1; int is_int64 = 0; #ifdef VCF_ALLOW_INT64 if ( n_val==1 ) { overflow = 0; long long int tmp_val = hts_str2int(val, &te, sizeof(tmp_val)*CHAR_BIT, &overflow); if ( te==val ) tmp_val = bcf_int32_missing; else if ( overflow || tmp_valBCF_MAX_BT_INT64 ) { if ( !extreme_int_warned ) { hts_log_warning("Extreme INFO/%s value encountered and set to missing at %s:%"PRIhts_pos,key,bcf_seqname_safe(h,v), v->pos+1); extreme_int_warned = 1; } tmp_val = bcf_int32_missing; } else is_int64 = 1; val1 = tmp_val; t = te; i = 1; // this is just to avoid adding another nested block... } #endif for (; i < n_val; ++i, ++t) { overflow = 0; long int tmp_val = hts_str2int(t, &te, sizeof(tmp_val)*CHAR_BIT, &overflow); if ( te==t ) tmp_val = bcf_int32_missing; else if ( overflow || tmp_valBCF_MAX_BT_INT32 ) { if ( !extreme_int_warned ) { hts_log_warning("Extreme INFO/%s value encountered and set to missing at %s:%"PRIhts_pos,key,bcf_seqname_safe(h,v), v->pos+1); extreme_int_warned = 1; } tmp_val = bcf_int32_missing; } a_val[i] = tmp_val; for (t = te; *t && *t != ','; t++); } if (n_val == 1) { #ifdef VCF_ALLOW_INT64 if ( is_int64 ) { v->unpacked |= BCF_IS_64BIT; bcf_enc_long1(str, val1); } else bcf_enc_int1(str, (int32_t)val1); #else val1 = a_val[0]; bcf_enc_int1(str, (int32_t)val1); #endif } else { bcf_enc_vint(str, n_val, a_val, -1); } if (n_val==1 && (val1!=bcf_int32_missing || is_int64) && memcmp(key, "END", 4) == 0) { if ( val1 <= v->pos ) { if ( !negative_rlen_warned ) { hts_log_warning("INFO/END=%"PRIhts_pos" is smaller than POS at %s:%"PRIhts_pos,val1,bcf_seqname_safe(h,v),v->pos+1); negative_rlen_warned = 1; } } else v->rlen = val1 - v->pos; } } else if ((y>>4&0xf) == BCF_HT_REAL) { float *val_f = (float *)a_val; for (i = 0, t = val; i < n_val; ++i, ++t) { overflow = 0; val_f[i] = hts_str2dbl(t, &te, &overflow); if ( te==t || overflow ) // conversion failed bcf_float_set_missing(val_f[i]); for (t = te; *t && *t != ','; t++); } bcf_enc_vfloat(str, n_val, val_f); } } if (c == 0) break; r = end; key = r + 1; } free(a_val); return 0; fail: free(a_val); return -1; } int vcf_parse(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v) { int ret = -2, overflow = 0; char *p, *q, *r, *t; kstring_t *str; khint_t k; ks_tokaux_t aux; //#define NOT_DOT(p) strcmp((p), ".") //#define NOT_DOT(p) (!(*p == '.' && !p[1])) //#define NOT_DOT(p) ((*p) != '.' || (p)[1]) //#define NOT_DOT(p) (q-p != 1 || memcmp(p, ".\0", 2)) #define NOT_DOT(p) (memcmp(p, ".\0", 2)) if (!s || !h || !v || !(s->s)) return ret; // Assumed in lots of places, but we may as well spot this early assert(sizeof(float) == sizeof(int32_t)); // Ensure string we parse has space to permit some over-flow when during // parsing. Eg to do memcmp(key, "END", 4) in vcf_parse_info over // the more straight forward looking strcmp, giving a speed advantage. if (ks_resize(s, s->l+4) < 0) return -1; // Force our memory to be initialised so we avoid the technicality of // undefined behaviour in using a 4-byte memcmp. (The reality is this // almost certainly is never detected by the compiler so has no impact, // but equally so this code has minimal (often beneficial) impact on // performance too.) s->s[s->l+0] = 0; s->s[s->l+1] = 0; s->s[s->l+2] = 0; s->s[s->l+3] = 0; bcf_clear1(v); str = &v->shared; memset(&aux, 0, sizeof(ks_tokaux_t)); // CHROM if (!(p = kstrtok(s->s, "\t", &aux))) goto err; *(q = (char*)aux.p) = 0; vdict_t *d = (vdict_t*)h->dict[BCF_DT_CTG]; k = kh_get(vdict, d, p); if (k == kh_end(d)) { hts_log_warning("Contig '%s' is not defined in the header. (Quick workaround: index the file with tabix.)", p); v->errcode = BCF_ERR_CTG_UNDEF; if ((k = fix_chromosome(h, d, p)) == kh_end(d)) { hts_log_error("Could not add dummy header for contig '%s'", p); v->errcode |= BCF_ERR_CTG_INVALID; goto err; } } v->rid = kh_val(d, k).id; // POS if (!(p = kstrtok(0, 0, &aux))) goto err; *(q = (char*)aux.p) = 0; overflow = 0; char *tmp = p; v->pos = hts_str2uint(p, &p, 62, &overflow); if (overflow) { hts_log_error("Position value '%s' is too large", tmp); goto err; } else if ( *p ) { hts_log_error("Could not parse the position '%s'", tmp); goto err; } else { v->pos -= 1; } if (v->pos >= INT32_MAX) v->unpacked |= BCF_IS_64BIT; // ID if (!(p = kstrtok(0, 0, &aux))) goto err; *(q = (char*)aux.p) = 0; if (NOT_DOT(p)) bcf_enc_vchar(str, q - p, p); else bcf_enc_size(str, 0, BCF_BT_CHAR); // REF if (!(p = kstrtok(0, 0, &aux))) goto err; *(q = (char*)aux.p) = 0; bcf_enc_vchar(str, q - p, p); v->n_allele = 1, v->rlen = q - p; // ALT if (!(p = kstrtok(0, 0, &aux))) goto err; *(q = (char*)aux.p) = 0; if (NOT_DOT(p)) { for (r = t = p;; ++r) { if (*r == ',' || *r == 0) { if (v->n_allele == UINT16_MAX) { hts_log_error("Too many ALT alleles at %s:%"PRIhts_pos, bcf_seqname_safe(h,v), v->pos+1); v->errcode |= BCF_ERR_LIMITS; goto err; } bcf_enc_vchar(str, r - t, t); t = r + 1; ++v->n_allele; } if (r == q) break; } } // QUAL if (!(p = kstrtok(0, 0, &aux))) goto err; *(q = (char*)aux.p) = 0; if (NOT_DOT(p)) v->qual = atof(p); else bcf_float_set_missing(v->qual); if ( v->max_unpack && !(v->max_unpack>>1) ) goto end; // BCF_UN_STR // FILTER if (!(p = kstrtok(0, 0, &aux))) goto err; *(q = (char*)aux.p) = 0; if (NOT_DOT(p)) { if (vcf_parse_filter(str, h, v, p, q)) { goto err; } } else bcf_enc_vint(str, 0, 0, -1); if ( v->max_unpack && !(v->max_unpack>>2) ) goto end; // BCF_UN_FLT // INFO if (!(p = kstrtok(0, 0, &aux))) goto err; *(q = (char*)aux.p) = 0; if (NOT_DOT(p)) { if (vcf_parse_info(str, h, v, p, q)) { goto err; } } if ( v->max_unpack && !(v->max_unpack>>3) ) goto end; // FORMAT; optional p = kstrtok(0, 0, &aux); if (p) { *(q = (char*)aux.p) = 0; return vcf_parse_format(s, h, v, p, q) == 0 ? 0 : -2; } else { return 0; } end: ret = 0; err: return ret; } int vcf_open_mode(char *mode, const char *fn, const char *format) { if (format == NULL) { // Try to pick a format based on the filename extension char extension[HTS_MAX_EXT_LEN]; if (find_file_extension(fn, extension) < 0) return -1; return vcf_open_mode(mode, fn, extension); } else if (strcasecmp(format, "bcf") == 0) strcpy(mode, "b"); else if (strcasecmp(format, "vcf") == 0) strcpy(mode, ""); else if (strcasecmp(format, "vcf.gz") == 0 || strcasecmp(format, "vcf.bgz") == 0) strcpy(mode, "z"); else return -1; return 0; } int vcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) { int ret; ret = hts_getline(fp, KS_SEP_LINE, &fp->line); if (ret < 0) return ret; return vcf_parse1(&fp->line, h, v); } static inline uint8_t *bcf_unpack_fmt_core1(uint8_t *ptr, int n_sample, bcf_fmt_t *fmt) { uint8_t *ptr_start = ptr; fmt->id = bcf_dec_typed_int1(ptr, &ptr); fmt->n = bcf_dec_size(ptr, &ptr, &fmt->type); fmt->size = fmt->n << bcf_type_shift[fmt->type]; fmt->p = ptr; fmt->p_off = ptr - ptr_start; fmt->p_free = 0; ptr += n_sample * fmt->size; fmt->p_len = ptr - fmt->p; return ptr; } static inline uint8_t *bcf_unpack_info_core1(uint8_t *ptr, bcf_info_t *info) { uint8_t *ptr_start = ptr; int64_t len = 0; info->key = bcf_dec_typed_int1(ptr, &ptr); len = info->len = bcf_dec_size(ptr, &ptr, &info->type); info->vptr = ptr; info->vptr_off = ptr - ptr_start; info->vptr_free = 0; info->v1.i = 0; if (info->len == 1) { switch(info->type) { case BCF_BT_INT8: case BCF_BT_CHAR: info->v1.i = *(int8_t*)ptr; break; case BCF_BT_INT16: info->v1.i = le_to_i16(ptr); len <<= 1; break; case BCF_BT_INT32: info->v1.i = le_to_i32(ptr); len <<= 2; break; case BCF_BT_FLOAT: info->v1.f = le_to_float(ptr); len <<= 2; break; case BCF_BT_INT64: info->v1.i = le_to_i64(ptr); len <<= 3; break; } } else { len <<= bcf_type_shift[info->type]; } ptr += len; info->vptr_len = ptr - info->vptr; return ptr; } int bcf_unpack(bcf1_t *b, int which) { if ( !b->shared.l ) return 0; // Building a new BCF record from scratch uint8_t *ptr = (uint8_t*)b->shared.s, *ptr_ori; int i; bcf_dec_t *d = &b->d; if (which & BCF_UN_FLT) which |= BCF_UN_STR; if (which & BCF_UN_INFO) which |= BCF_UN_SHR; if ((which&BCF_UN_STR) && !(b->unpacked&BCF_UN_STR)) { kstring_t tmp; // ID tmp.l = 0; tmp.s = d->id; tmp.m = d->m_id; ptr_ori = ptr; ptr = bcf_fmt_sized_array(&tmp, ptr); b->unpack_size[0] = ptr - ptr_ori; kputc_('\0', &tmp); d->id = tmp.s; d->m_id = tmp.m; // REF and ALT are in a single block (d->als) and d->alleles are pointers into this block hts_expand(char*, b->n_allele, d->m_allele, d->allele); // NM: hts_expand() is a macro tmp.l = 0; tmp.s = d->als; tmp.m = d->m_als; ptr_ori = ptr; for (i = 0; i < b->n_allele; ++i) { // Use offset within tmp.s as realloc may change pointer d->allele[i] = (char *)(intptr_t)tmp.l; ptr = bcf_fmt_sized_array(&tmp, ptr); kputc_('\0', &tmp); } b->unpack_size[1] = ptr - ptr_ori; d->als = tmp.s; d->m_als = tmp.m; // Convert our offsets within tmp.s back to pointers again for (i = 0; i < b->n_allele; ++i) d->allele[i] = d->als + (ptrdiff_t)d->allele[i]; b->unpacked |= BCF_UN_STR; } if ((which&BCF_UN_FLT) && !(b->unpacked&BCF_UN_FLT)) { // FILTER ptr = (uint8_t*)b->shared.s + b->unpack_size[0] + b->unpack_size[1]; ptr_ori = ptr; if (*ptr>>4) { int type; d->n_flt = bcf_dec_size(ptr, &ptr, &type); hts_expand(int, d->n_flt, d->m_flt, d->flt); for (i = 0; i < d->n_flt; ++i) d->flt[i] = bcf_dec_int1(ptr, type, &ptr); } else ++ptr, d->n_flt = 0; b->unpack_size[2] = ptr - ptr_ori; b->unpacked |= BCF_UN_FLT; } if ((which&BCF_UN_INFO) && !(b->unpacked&BCF_UN_INFO)) { // INFO ptr = (uint8_t*)b->shared.s + b->unpack_size[0] + b->unpack_size[1] + b->unpack_size[2]; hts_expand(bcf_info_t, b->n_info, d->m_info, d->info); for (i = 0; i < d->m_info; ++i) d->info[i].vptr_free = 0; for (i = 0; i < b->n_info; ++i) ptr = bcf_unpack_info_core1(ptr, &d->info[i]); b->unpacked |= BCF_UN_INFO; } if ((which&BCF_UN_FMT) && b->n_sample && !(b->unpacked&BCF_UN_FMT)) { // FORMAT ptr = (uint8_t*)b->indiv.s; hts_expand(bcf_fmt_t, b->n_fmt, d->m_fmt, d->fmt); for (i = 0; i < d->m_fmt; ++i) d->fmt[i].p_free = 0; for (i = 0; i < b->n_fmt; ++i) ptr = bcf_unpack_fmt_core1(ptr, b->n_sample, &d->fmt[i]); b->unpacked |= BCF_UN_FMT; } return 0; } int vcf_format(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s) { int i; int32_t max_dt_id = h->n[BCF_DT_ID]; const char *chrom = bcf_seqname(h, v); if (!chrom) { hts_log_error("Invalid BCF, CONTIG id=%d not present in the header", v->rid); errno = EINVAL; return -1; } bcf_unpack((bcf1_t*)v, BCF_UN_ALL & ~(BCF_UN_INFO|BCF_UN_FMT)); // Cache of key lengths so we don't keep repeatedly using them. // This assumes we're not modifying the header between successive calls // to vcf_format, but that would lead to many other forms of breakage // so it feels like a valid assumption to make. // // We cannot just do this in bcf_hdr_sync as some code (eg bcftools // annotate) manipulates the headers directly without calling sync to // refresh the data structures. So we must do just-in-time length // calculation during writes instead. bcf_hdr_aux_t *aux = get_hdr_aux(h); if (!aux->key_len) { if (!(aux->key_len = calloc(h->n[BCF_DT_ID]+1, sizeof(*aux->key_len)))) return -1; } size_t *key_len = aux->key_len; kputs(chrom, s); // CHROM kputc_('\t', s); kputll(v->pos + 1, s); // POS kputc_('\t', s); kputs(v->d.id ? v->d.id : ".", s); // ID kputc_('\t', s); // REF if (v->n_allele > 0) kputs(v->d.allele[0], s); else kputc_('.', s); kputc_('\t', s); // ALT if (v->n_allele > 1) { for (i = 1; i < v->n_allele; ++i) { if (i > 1) kputc_(',', s); kputs(v->d.allele[i], s); } } else kputc_('.', s); kputc_('\t', s); // QUAL if ( bcf_float_is_missing(v->qual) ) kputc_('.', s); // QUAL else kputd(v->qual, s); kputc_('\t', s); // FILTER if (v->d.n_flt) { for (i = 0; i < v->d.n_flt; ++i) { int32_t idx = v->d.flt[i]; if (idx < 0 || idx >= max_dt_id || h->id[BCF_DT_ID][idx].key == NULL) { hts_log_error("Invalid BCF, the FILTER tag id=%d at %s:%"PRIhts_pos" not present in the header", idx, bcf_seqname_safe(h, v), v->pos + 1); errno = EINVAL; return -1; } if (i) kputc_(';', s); if (!key_len[idx]) key_len[idx] = strlen(h->id[BCF_DT_ID][idx].key); kputsn(h->id[BCF_DT_ID][idx].key, key_len[idx], s); } } else kputc_('.', s); kputc_('\t', s); // INFO if (v->n_info) { uint8_t *ptr = v->shared.s ? (uint8_t *)v->shared.s + v->unpack_size[0] + v->unpack_size[1] + v->unpack_size[2] : NULL; int first = 1; bcf_info_t *info = v->d.info; // Note if we duplicate this code into custom packed and unpacked // implementations then we gain a bit more speed, particularly with // clang 13 (up to 5%). Not sure why this is, but code duplication // isn't pleasant and it's still faster adding packed support than // not so it's a win, just not as good as it should be. const int info_packed = !(v->unpacked & BCF_UN_INFO) && v->shared.l; for (i = 0; i < v->n_info; ++i) { bcf_info_t in, *z; if (info_packed) { // Use a local bcf_info_t when data is packed z = ∈ z->key = bcf_dec_typed_int1(ptr, &ptr); z->len = bcf_dec_size(ptr, &ptr, &z->type); z->vptr = ptr; ptr += z->len << bcf_type_shift[z->type]; } else { // Else previously unpacked INFO struct z = &info[i]; // Also potentially since deleted if ( !z->vptr ) continue; } bcf_idpair_t *id = z->key >= 0 && z->key < max_dt_id ? &h->id[BCF_DT_ID][z->key] : NULL; if (!id || !id->key) { hts_log_error("Invalid BCF, the INFO tag id=%d is %s at %s:%"PRIhts_pos, z->key, z->key < 0 ? "negative" : (z->key >= max_dt_id ? "too large" : "not present in the header"), bcf_seqname_safe(h, v), v->pos+1); errno = EINVAL; return -1; } // KEY if (!key_len[z->key]) key_len[z->key] = strlen(id->key); size_t id_len = key_len[z->key]; if (ks_resize(s, s->l + 3 + id_len) < 0) return -1; char *sptr = s->s + s->l; if ( !first ) { *sptr++ = ';'; s->l++; } first = 0; memcpy(sptr, id->key, id_len); s->l += id_len; // VALUE if (z->len <= 0) continue; sptr[id_len] = '='; s->l++; if (z->len != 1 || info_packed) { bcf_fmt_array(s, z->len, z->type, z->vptr); } else { // Single length vectors are unpacked into their // own info.v1 union and handled separately. if (z->type == BCF_BT_FLOAT) { if ( bcf_float_is_missing(z->v1.f) ) kputc_('.', s); else kputd(z->v1.f, s); } else if (z->type == BCF_BT_CHAR) { kputc_(z->v1.i, s); } else if (z->type < BCF_BT_INT64) { int64_t missing[] = { 0, // BCF_BT_NULL bcf_int8_missing, bcf_int16_missing, bcf_int32_missing, }; if (z->v1.i == missing[z->type]) kputc_('.', s); else kputw(z->v1.i, s); } else if (z->type == BCF_BT_INT64) { if (z->v1.i == bcf_int64_missing) kputc_('.', s); else kputll(z->v1.i, s); } else { hts_log_error("Unexpected type %d at %s:%"PRIhts_pos, z->type, bcf_seqname_safe(h, v), v->pos+1); errno = EINVAL; return -1; } } } if ( first ) kputc_('.', s); } else kputc_('.', s); // FORMAT and individual information if (v->n_sample) { int i,j; if ( v->n_fmt) { uint8_t *ptr = (uint8_t *)v->indiv.s; int gt_i = -1; bcf_fmt_t *fmt = v->d.fmt; int first = 1; int fmt_packed = !(v->unpacked & BCF_UN_FMT); if (fmt_packed) { // Local fmt as we have an array of num FORMAT keys, // each of which points to N.Sample values. // No real gain to be had in handling unpacked data here, // but it doesn't cost us much in complexity either and // it gives us flexibility. fmt = malloc(v->n_fmt * sizeof(*fmt)); if (!fmt) return -1; } // KEYS for (i = 0; i < (int)v->n_fmt; ++i) { bcf_fmt_t *z; z = &fmt[i]; if (fmt_packed) { z->id = bcf_dec_typed_int1(ptr, &ptr); z->n = bcf_dec_size(ptr, &ptr, &z->type); z->p = ptr; z->size = z->n << bcf_type_shift[z->type]; ptr += v->n_sample * z->size; } if ( !z->p ) continue; kputc_(!first ? ':' : '\t', s); first = 0; bcf_idpair_t *id = z->id >= 0 && z->id < max_dt_id ? &h->id[BCF_DT_ID][z->id] : NULL; if (!id || !id->key) { hts_log_error("Invalid BCF, the FORMAT tag id=%d at %s:%"PRIhts_pos" not present in the header", z->id, bcf_seqname_safe(h, v), v->pos+1); errno = EINVAL; return -1; } if (!key_len[z->id]) key_len[z->id] = strlen(id->key); size_t id_len = key_len[z->id]; kputsn(id->key, id_len, s); if (id_len == 2 && id->key[0] == 'G' && id->key[1] == 'T') gt_i = i; } if ( first ) kputsn("\t.", 2, s); // VALUES per sample for (j = 0; j < v->n_sample; ++j) { kputc_('\t', s); first = 1; bcf_fmt_t *f = fmt; for (i = 0; i < (int)v->n_fmt; i++, f++) { if ( !f->p ) continue; if (!first) kputc_(':', s); first = 0; if (gt_i == i) { bcf_format_gt(f,j,s); break; } else if (f->n == 1) bcf_fmt_array1(s, f->type, f->p + j * (size_t)f->size); else bcf_fmt_array(s, f->n, f->type, f->p + j * (size_t)f->size); } // Simpler loop post GT and at least 1 iteration for (i++, f++; i < (int)v->n_fmt; i++, f++) { if ( !f->p ) continue; kputc_(':', s); if (f->n == 1) bcf_fmt_array1(s, f->type, f->p + j * (size_t)f->size); else bcf_fmt_array(s, f->n, f->type, f->p + j * (size_t)f->size); } if ( first ) kputc_('.', s); } if (fmt_packed) free(fmt); } else for (j=0; j<=v->n_sample; j++) kputsn("\t.", 2, s); } kputc('\n', s); return 0; } int vcf_write_line(htsFile *fp, kstring_t *line) { int ret; if ( line->s[line->l-1]!='\n' ) kputc('\n',line); if ( fp->format.compression!=no_compression ) ret = bgzf_write(fp->fp.bgzf, line->s, line->l); else ret = hwrite(fp->fp.hfile, line->s, line->l); return ret==line->l ? 0 : -1; } int vcf_write(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) { ssize_t ret; fp->line.l = 0; if (vcf_format1(h, v, &fp->line) != 0) return -1; if ( fp->format.compression!=no_compression ) { if (bgzf_flush_try(fp->fp.bgzf, fp->line.l) < 0) return -1; if (fp->idx && !fp->fp.bgzf->mt) hts_idx_amend_last(fp->idx, bgzf_tell(fp->fp.bgzf)); ret = bgzf_write(fp->fp.bgzf, fp->line.s, fp->line.l); } else { ret = hwrite(fp->fp.hfile, fp->line.s, fp->line.l); } if (fp->idx && fp->format.compression == bgzf) { int tid; if ((tid = hts_idx_tbi_name(fp->idx, v->rid, bcf_seqname_safe(h, v))) < 0) return -1; if (bgzf_idx_push(fp->fp.bgzf, fp->idx, tid, v->pos, v->pos + v->rlen, bgzf_tell(fp->fp.bgzf), 1) < 0) return -1; } return ret==fp->line.l ? 0 : -1; } /************************ * Data access routines * ************************/ int bcf_hdr_id2int(const bcf_hdr_t *h, int which, const char *id) { khint_t k; vdict_t *d = (vdict_t*)h->dict[which]; k = kh_get(vdict, d, id); return k == kh_end(d)? -1 : kh_val(d, k).id; } /******************** *** BCF indexing *** ********************/ // Calculate number of index levels given min_shift and the header contig // list. Also returns number of contigs in *nids_out. static int idx_calc_n_lvls_ids(const bcf_hdr_t *h, int min_shift, int starting_n_lvls, int *nids_out) { int n_lvls, i, nids = 0; int64_t max_len = 0, s; for (i = 0; i < h->n[BCF_DT_CTG]; ++i) { if ( !h->id[BCF_DT_CTG][i].val ) continue; if ( max_len < h->id[BCF_DT_CTG][i].val->info[0] ) max_len = h->id[BCF_DT_CTG][i].val->info[0]; nids++; } if ( !max_len ) max_len = (1LL<<31) - 1; // In case contig line is broken. max_len += 256; s = hts_bin_maxpos(min_shift, starting_n_lvls); for (n_lvls = starting_n_lvls; max_len > s; ++n_lvls, s <<= 3); if (nids_out) *nids_out = nids; return n_lvls; } hts_idx_t *bcf_index(htsFile *fp, int min_shift) { int n_lvls; bcf1_t *b = NULL; hts_idx_t *idx = NULL; bcf_hdr_t *h; int r; h = bcf_hdr_read(fp); if ( !h ) return NULL; int nids = 0; n_lvls = idx_calc_n_lvls_ids(h, min_shift, 0, &nids); idx = hts_idx_init(nids, HTS_FMT_CSI, bgzf_tell(fp->fp.bgzf), min_shift, n_lvls); if (!idx) goto fail; b = bcf_init1(); if (!b) goto fail; while ((r = bcf_read1(fp,h, b)) >= 0) { int ret; ret = hts_idx_push(idx, b->rid, b->pos, b->pos + b->rlen, bgzf_tell(fp->fp.bgzf), 1); if (ret < 0) goto fail; } if (r < -1) goto fail; hts_idx_finish(idx, bgzf_tell(fp->fp.bgzf)); bcf_destroy1(b); bcf_hdr_destroy(h); return idx; fail: hts_idx_destroy(idx); bcf_destroy1(b); bcf_hdr_destroy(h); return NULL; } hts_idx_t *bcf_index_load2(const char *fn, const char *fnidx) { return fnidx? hts_idx_load2(fn, fnidx) : bcf_index_load(fn); } hts_idx_t *bcf_index_load3(const char *fn, const char *fnidx, int flags) { return hts_idx_load3(fn, fnidx, HTS_FMT_CSI, flags); } int bcf_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads) { htsFile *fp; hts_idx_t *idx; tbx_t *tbx; int ret; if ((fp = hts_open(fn, "rb")) == 0) return -2; if (n_threads) hts_set_threads(fp, n_threads); if ( fp->format.compression!=bgzf ) { hts_close(fp); return -3; } switch (fp->format.format) { case bcf: if (!min_shift) { hts_log_error("TBI indices for BCF files are not supported"); ret = -1; } else { idx = bcf_index(fp, min_shift); if (idx) { ret = hts_idx_save_as(idx, fn, fnidx, HTS_FMT_CSI); if (ret < 0) ret = -4; hts_idx_destroy(idx); } else ret = -1; } break; case vcf: tbx = tbx_index(hts_get_bgzfp(fp), min_shift, &tbx_conf_vcf); if (tbx) { ret = hts_idx_save_as(tbx->idx, fn, fnidx, min_shift > 0 ? HTS_FMT_CSI : HTS_FMT_TBI); if (ret < 0) ret = -4; tbx_destroy(tbx); } else ret = -1; break; default: ret = -3; break; } hts_close(fp); return ret; } int bcf_index_build2(const char *fn, const char *fnidx, int min_shift) { return bcf_index_build3(fn, fnidx, min_shift, 0); } int bcf_index_build(const char *fn, int min_shift) { return bcf_index_build3(fn, NULL, min_shift, 0); } // Initialise fp->idx for the current format type. // This must be called after the header has been written but no other data. static int vcf_idx_init(htsFile *fp, bcf_hdr_t *h, int min_shift, const char *fnidx) { int n_lvls, fmt; if (min_shift == 0) { min_shift = 14; n_lvls = 5; fmt = HTS_FMT_TBI; } else { // Set initial n_lvls to match tbx_index() int starting_n_lvls = (TBX_MAX_SHIFT - min_shift + 2) / 3; // Increase if necessary n_lvls = idx_calc_n_lvls_ids(h, min_shift, starting_n_lvls, NULL); fmt = HTS_FMT_CSI; } fp->idx = hts_idx_init(0, fmt, bgzf_tell(fp->fp.bgzf), min_shift, n_lvls); if (!fp->idx) return -1; // Tabix meta data, added even in CSI for VCF uint8_t conf[4*7]; u32_to_le(TBX_VCF, conf+0); // fmt u32_to_le(1, conf+4); // name col u32_to_le(2, conf+8); // beg col u32_to_le(0, conf+12); // end col u32_to_le('#', conf+16); // comment u32_to_le(0, conf+20); // n.skip u32_to_le(0, conf+24); // ref name len if (hts_idx_set_meta(fp->idx, sizeof(conf)*sizeof(*conf), (uint8_t *)conf, 1) < 0) { hts_idx_destroy(fp->idx); fp->idx = NULL; return -1; } fp->fnidx = fnidx; return 0; } // Initialise fp->idx for the current format type. // This must be called after the header has been written but no other data. int bcf_idx_init(htsFile *fp, bcf_hdr_t *h, int min_shift, const char *fnidx) { int n_lvls, nids = 0; if (fp->format.compression != bgzf) { hts_log_error("Indexing is only supported on BGZF-compressed files"); return -3; // Matches no-compression return for bcf_index_build3() } if (fp->format.format == vcf) return vcf_idx_init(fp, h, min_shift, fnidx); if (!min_shift) min_shift = 14; n_lvls = idx_calc_n_lvls_ids(h, min_shift, 0, &nids); fp->idx = hts_idx_init(nids, HTS_FMT_CSI, bgzf_tell(fp->fp.bgzf), min_shift, n_lvls); if (!fp->idx) return -1; fp->fnidx = fnidx; return 0; } // Finishes an index. Call after the last record has been written. // Returns 0 on success, <0 on failure. // // NB: same format as SAM/BAM as it uses bgzf. int bcf_idx_save(htsFile *fp) { return sam_idx_save(fp); } /***************** *** Utilities *** *****************/ int bcf_hdr_combine(bcf_hdr_t *dst, const bcf_hdr_t *src) { int i, ndst_ori = dst->nhrec, need_sync = 0, ret = 0, res; for (i=0; inhrec; i++) { if ( src->hrec[i]->type==BCF_HL_GEN && src->hrec[i]->value ) { int j; for (j=0; jhrec[j]->type!=BCF_HL_GEN ) continue; // Checking only the key part of generic lines, otherwise // the VCFs are too verbose. Should we perhaps add a flag // to bcf_hdr_combine() and make this optional? if ( !strcmp(src->hrec[i]->key,dst->hrec[j]->key) ) break; } if ( j>=ndst_ori ) { res = bcf_hdr_add_hrec(dst, bcf_hrec_dup(src->hrec[i])); if (res < 0) return -1; need_sync += res; } } else if ( src->hrec[i]->type==BCF_HL_STR ) { // NB: we are ignoring fields without ID int j = bcf_hrec_find_key(src->hrec[i],"ID"); if ( j>=0 ) { bcf_hrec_t *rec = bcf_hdr_get_hrec(dst, src->hrec[i]->type, "ID", src->hrec[i]->vals[j], src->hrec[i]->key); if ( !rec ) { res = bcf_hdr_add_hrec(dst, bcf_hrec_dup(src->hrec[i])); if (res < 0) return -1; need_sync += res; } } } else { int j = bcf_hrec_find_key(src->hrec[i],"ID"); assert( j>=0 ); // this should always be true for valid VCFs bcf_hrec_t *rec = bcf_hdr_get_hrec(dst, src->hrec[i]->type, "ID", src->hrec[i]->vals[j], NULL); if ( !rec ) { res = bcf_hdr_add_hrec(dst, bcf_hrec_dup(src->hrec[i])); if (res < 0) return -1; need_sync += res; } else if ( src->hrec[i]->type==BCF_HL_INFO || src->hrec[i]->type==BCF_HL_FMT ) { // Check that both records are of the same type. The bcf_hdr_id2length // macro cannot be used here because dst header is not synced yet. vdict_t *d_src = (vdict_t*)src->dict[BCF_DT_ID]; vdict_t *d_dst = (vdict_t*)dst->dict[BCF_DT_ID]; khint_t k_src = kh_get(vdict, d_src, src->hrec[i]->vals[0]); khint_t k_dst = kh_get(vdict, d_dst, src->hrec[i]->vals[0]); if ( (kh_val(d_src,k_src).info[rec->type]>>8 & 0xf) != (kh_val(d_dst,k_dst).info[rec->type]>>8 & 0xf) ) { hts_log_warning("Trying to combine \"%s\" tag definitions of different lengths", src->hrec[i]->vals[0]); ret |= 1; } if ( (kh_val(d_src,k_src).info[rec->type]>>4 & 0xf) != (kh_val(d_dst,k_dst).info[rec->type]>>4 & 0xf) ) { hts_log_warning("Trying to combine \"%s\" tag definitions of different types", src->hrec[i]->vals[0]); ret |= 1; } } } } if ( need_sync ) { if (bcf_hdr_sync(dst) < 0) return -1; } return ret; } bcf_hdr_t *bcf_hdr_merge(bcf_hdr_t *dst, const bcf_hdr_t *src) { if ( !dst ) { // this will effectively strip existing IDX attributes from src to become dst dst = bcf_hdr_init("r"); kstring_t htxt = {0,0,0}; if (bcf_hdr_format(src, 0, &htxt) < 0) { free(htxt.s); return NULL; } if ( bcf_hdr_parse(dst, htxt.s) < 0 ) { bcf_hdr_destroy(dst); dst = NULL; } free(htxt.s); return dst; } int i, ndst_ori = dst->nhrec, need_sync = 0, res; for (i=0; inhrec; i++) { if ( src->hrec[i]->type==BCF_HL_GEN && src->hrec[i]->value ) { int j; for (j=0; jhrec[j]->type!=BCF_HL_GEN ) continue; // Checking only the key part of generic lines, otherwise // the VCFs are too verbose. Should we perhaps add a flag // to bcf_hdr_combine() and make this optional? if ( !strcmp(src->hrec[i]->key,dst->hrec[j]->key) ) break; } if ( j>=ndst_ori ) { res = bcf_hdr_add_hrec(dst, bcf_hrec_dup(src->hrec[i])); if (res < 0) return NULL; need_sync += res; } } else if ( src->hrec[i]->type==BCF_HL_STR ) { // NB: we are ignoring fields without ID int j = bcf_hrec_find_key(src->hrec[i],"ID"); if ( j>=0 ) { bcf_hrec_t *rec = bcf_hdr_get_hrec(dst, src->hrec[i]->type, "ID", src->hrec[i]->vals[j], src->hrec[i]->key); if ( !rec ) { res = bcf_hdr_add_hrec(dst, bcf_hrec_dup(src->hrec[i])); if (res < 0) return NULL; need_sync += res; } } } else { int j = bcf_hrec_find_key(src->hrec[i],"ID"); assert( j>=0 ); // this should always be true for valid VCFs bcf_hrec_t *rec = bcf_hdr_get_hrec(dst, src->hrec[i]->type, "ID", src->hrec[i]->vals[j], NULL); if ( !rec ) { res = bcf_hdr_add_hrec(dst, bcf_hrec_dup(src->hrec[i])); if (res < 0) return NULL; need_sync += res; } else if ( src->hrec[i]->type==BCF_HL_INFO || src->hrec[i]->type==BCF_HL_FMT ) { // Check that both records are of the same type. The bcf_hdr_id2length // macro cannot be used here because dst header is not synced yet. vdict_t *d_src = (vdict_t*)src->dict[BCF_DT_ID]; vdict_t *d_dst = (vdict_t*)dst->dict[BCF_DT_ID]; khint_t k_src = kh_get(vdict, d_src, src->hrec[i]->vals[0]); khint_t k_dst = kh_get(vdict, d_dst, src->hrec[i]->vals[0]); if ( (kh_val(d_src,k_src).info[rec->type]>>8 & 0xf) != (kh_val(d_dst,k_dst).info[rec->type]>>8 & 0xf) ) { hts_log_warning("Trying to combine \"%s\" tag definitions of different lengths", src->hrec[i]->vals[0]); } if ( (kh_val(d_src,k_src).info[rec->type]>>4 & 0xf) != (kh_val(d_dst,k_dst).info[rec->type]>>4 & 0xf) ) { hts_log_warning("Trying to combine \"%s\" tag definitions of different types", src->hrec[i]->vals[0]); } } } } if ( need_sync ) { if (bcf_hdr_sync(dst) < 0) return NULL; } return dst; } int bcf_translate(const bcf_hdr_t *dst_hdr, bcf_hdr_t *src_hdr, bcf1_t *line) { int i; if ( line->errcode ) { char errordescription[1024] = ""; hts_log_error("Unchecked error (%d %s) at %s:%"PRIhts_pos", exiting", line->errcode, bcf_strerror(line->errcode, errordescription, sizeof(errordescription)), bcf_seqname_safe(src_hdr,line), line->pos+1); exit(1); } if ( src_hdr->ntransl==-1 ) return 0; // no need to translate, all tags have the same id if ( !src_hdr->ntransl ) // called for the first time, see what needs translating { int dict; for (dict=0; dict<2; dict++) // BCF_DT_ID and BCF_DT_CTG { src_hdr->transl[dict] = (int*) malloc(src_hdr->n[dict]*sizeof(int)); for (i=0; in[dict]; i++) { if ( !src_hdr->id[dict][i].key ) // gap left after removed BCF header lines { src_hdr->transl[dict][i] = -1; continue; } src_hdr->transl[dict][i] = bcf_hdr_id2int(dst_hdr,dict,src_hdr->id[dict][i].key); if ( src_hdr->transl[dict][i]!=-1 && i!=src_hdr->transl[dict][i] ) src_hdr->ntransl++; } } if ( !src_hdr->ntransl ) { free(src_hdr->transl[0]); src_hdr->transl[0] = NULL; free(src_hdr->transl[1]); src_hdr->transl[1] = NULL; src_hdr->ntransl = -1; } if ( src_hdr->ntransl==-1 ) return 0; } bcf_unpack(line,BCF_UN_ALL); // CHROM if ( src_hdr->transl[BCF_DT_CTG][line->rid] >=0 ) line->rid = src_hdr->transl[BCF_DT_CTG][line->rid]; // FILTER for (i=0; id.n_flt; i++) { int src_id = line->d.flt[i]; if ( src_hdr->transl[BCF_DT_ID][src_id] >=0 ) line->d.flt[i] = src_hdr->transl[BCF_DT_ID][src_id]; line->d.shared_dirty |= BCF1_DIRTY_FLT; } // INFO for (i=0; in_info; i++) { int src_id = line->d.info[i].key; int dst_id = src_hdr->transl[BCF_DT_ID][src_id]; if ( dst_id<0 ) continue; line->d.info[i].key = dst_id; if ( !line->d.info[i].vptr ) continue; // skip deleted int src_size = src_id>>7 ? ( src_id>>15 ? BCF_BT_INT32 : BCF_BT_INT16) : BCF_BT_INT8; int dst_size = dst_id>>7 ? ( dst_id>>15 ? BCF_BT_INT32 : BCF_BT_INT16) : BCF_BT_INT8; if ( src_size==dst_size ) // can overwrite { uint8_t *vptr = line->d.info[i].vptr - line->d.info[i].vptr_off; if ( dst_size==BCF_BT_INT8 ) { vptr[1] = (uint8_t)dst_id; } else if ( dst_size==BCF_BT_INT16 ) { *(uint16_t*)vptr = (uint16_t)dst_id; } else { *(uint32_t*)vptr = (uint32_t)dst_id; } } else // must realloc { bcf_info_t *info = &line->d.info[i]; kstring_t str = {0,0,0}; bcf_enc_int1(&str, dst_id); bcf_enc_size(&str, info->len,info->type); uint32_t vptr_off = str.l; kputsn((char*)info->vptr, info->vptr_len, &str); if( info->vptr_free ) free(info->vptr - info->vptr_off); info->vptr_off = vptr_off; info->vptr = (uint8_t*)str.s + info->vptr_off; info->vptr_free = 1; line->d.shared_dirty |= BCF1_DIRTY_INF; } } // FORMAT for (i=0; in_fmt; i++) { int src_id = line->d.fmt[i].id; int dst_id = src_hdr->transl[BCF_DT_ID][src_id]; if ( dst_id<0 ) continue; line->d.fmt[i].id = dst_id; if( !line->d.fmt[i].p ) continue; // skip deleted int src_size = src_id>>7 ? ( src_id>>15 ? BCF_BT_INT32 : BCF_BT_INT16) : BCF_BT_INT8; int dst_size = dst_id>>7 ? ( dst_id>>15 ? BCF_BT_INT32 : BCF_BT_INT16) : BCF_BT_INT8; if ( src_size==dst_size ) // can overwrite { uint8_t *p = line->d.fmt[i].p - line->d.fmt[i].p_off; // pointer to the vector size (4bits) and BT type (4bits) if ( dst_size==BCF_BT_INT8 ) { p[1] = dst_id; } else if ( dst_size==BCF_BT_INT16 ) { i16_to_le(dst_id, p + 1); } else { i32_to_le(dst_id, p + 1); } } else // must realloc { bcf_fmt_t *fmt = &line->d.fmt[i]; kstring_t str = {0,0,0}; bcf_enc_int1(&str, dst_id); bcf_enc_size(&str, fmt->n, fmt->type); uint32_t p_off = str.l; kputsn((char*)fmt->p, fmt->p_len, &str); if( fmt->p_free ) free(fmt->p - fmt->p_off); fmt->p_off = p_off; fmt->p = (uint8_t*)str.s + fmt->p_off; fmt->p_free = 1; line->d.indiv_dirty = 1; } } return 0; } bcf_hdr_t *bcf_hdr_dup(const bcf_hdr_t *hdr) { bcf_hdr_t *hout = bcf_hdr_init("r"); if (!hout) { hts_log_error("Failed to allocate bcf header"); return NULL; } kstring_t htxt = {0,0,0}; if (bcf_hdr_format(hdr, 1, &htxt) < 0) { free(htxt.s); return NULL; } if ( bcf_hdr_parse(hout, htxt.s) < 0 ) { bcf_hdr_destroy(hout); hout = NULL; } free(htxt.s); return hout; } bcf_hdr_t *bcf_hdr_subset(const bcf_hdr_t *h0, int n, char *const* samples, int *imap) { void *names_hash = khash_str2int_init(); kstring_t htxt = {0,0,0}; kstring_t str = {0,0,0}; bcf_hdr_t *h = bcf_hdr_init("w"); int r = 0; if (!h || !names_hash) { hts_log_error("Failed to allocate bcf header"); goto err; } if (bcf_hdr_format(h0, 1, &htxt) < 0) { hts_log_error("Failed to get header text"); goto err; } bcf_hdr_set_version(h,bcf_hdr_get_version(h0)); int j; for (j=0; j 0) { char *p = find_chrom_header_line(htxt.s); int i = 0, end = n? 8 : 7; while ((p = strchr(p, '\t')) != 0 && i < end) ++i, ++p; if (i != end) { hts_log_error("Wrong number of columns in header #CHROM line"); goto err; } r |= kputsn(htxt.s, p - htxt.s, &str) < 0; for (i = 0; i < n; ++i) { if ( khash_str2int_has_key(names_hash,samples[i]) ) { hts_log_error("Duplicate sample name \"%s\"", samples[i]); goto err; } imap[i] = bcf_hdr_id2int(h0, BCF_DT_SAMPLE, samples[i]); if (imap[i] < 0) continue; r |= kputc('\t', &str) < 0; r |= kputs(samples[i], &str) < 0; r |= khash_str2int_inc(names_hash,samples[i]) < 0; } } else r |= kputsn(htxt.s, htxt.l, &str) < 0; while (str.l && (!str.s[str.l-1] || str.s[str.l-1]=='\n') ) str.l--; // kill trailing zeros and newlines r |= kputc('\n',&str) < 0; if (r) { hts_log_error("%s", strerror(errno)); goto err; } if ( bcf_hdr_parse(h, str.s) < 0 ) { bcf_hdr_destroy(h); h = NULL; } free(str.s); free(htxt.s); khash_str2int_destroy(names_hash); return h; err: ks_free(&str); ks_free(&htxt); khash_str2int_destroy(names_hash); bcf_hdr_destroy(h); return NULL; } int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file) { if ( samples && !strcmp("-",samples) ) return 0; // keep all samples int i, narr = bit_array_size(bcf_hdr_nsamples(hdr)); hdr->keep_samples = (uint8_t*) calloc(narr,1); if (!hdr->keep_samples) return -1; hdr->nsamples_ori = bcf_hdr_nsamples(hdr); if ( !samples ) { // exclude all samples khint_t k; vdict_t *d = (vdict_t*)hdr->dict[BCF_DT_SAMPLE], *new_dict; new_dict = kh_init(vdict); if (!new_dict) return -1; bcf_hdr_nsamples(hdr) = 0; for (k = kh_begin(d); k != kh_end(d); ++k) if (kh_exist(d, k)) free((char*)kh_key(d, k)); kh_destroy(vdict, d); hdr->dict[BCF_DT_SAMPLE] = new_dict; if (bcf_hdr_sync(hdr) < 0) return -1; return 0; } if ( samples[0]=='^' ) for (i=0; ikeep_samples,i); int idx, n, ret = 0; char **smpls = hts_readlist(samples[0]=='^'?samples+1:samples, is_file, &n); if ( !smpls ) return -1; for (i=0; ikeep_samples, idx); else bit_array_set(hdr->keep_samples, idx); } for (i=0; insamples_ori; i++) if ( bit_array_test(hdr->keep_samples,i) ) bcf_hdr_nsamples(hdr)++; if ( !bcf_hdr_nsamples(hdr) ) { free(hdr->keep_samples); hdr->keep_samples=NULL; } else { // Make new list and dictionary with desired samples char **samples = (char**) malloc(sizeof(char*)*bcf_hdr_nsamples(hdr)); vdict_t *new_dict, *d; int k, res; if (!samples) return -1; new_dict = kh_init(vdict); if (!new_dict) { free(samples); return -1; } idx = 0; for (i=0; insamples_ori; i++) { if ( bit_array_test(hdr->keep_samples,i) ) { samples[idx] = hdr->samples[i]; k = kh_put(vdict, new_dict, hdr->samples[i], &res); if (res < 0) { free(samples); kh_destroy(vdict, new_dict); return -1; } kh_val(new_dict, k) = bcf_idinfo_def; kh_val(new_dict, k).id = idx; idx++; } } // Delete desired samples from old dictionary, so we don't free them d = (vdict_t*)hdr->dict[BCF_DT_SAMPLE]; for (i=0; i < idx; i++) { int k = kh_get(vdict, d, samples[i]); if (k < kh_end(d)) kh_del(vdict, d, k); } // Free everything else for (k = kh_begin(d); k != kh_end(d); ++k) if (kh_exist(d, k)) free((char*)kh_key(d, k)); kh_destroy(vdict, d); hdr->dict[BCF_DT_SAMPLE] = new_dict; free(hdr->samples); hdr->samples = samples; if (bcf_hdr_sync(hdr) < 0) return -1; } return ret; } int bcf_subset(const bcf_hdr_t *h, bcf1_t *v, int n, int *imap) { kstring_t ind; ind.s = 0; ind.l = ind.m = 0; if (n) { bcf_fmt_t fmt[MAX_N_FMT]; int i, j; uint8_t *ptr = (uint8_t*)v->indiv.s; for (i = 0; i < v->n_fmt; ++i) ptr = bcf_unpack_fmt_core1(ptr, v->n_sample, &fmt[i]); for (i = 0; i < (int)v->n_fmt; ++i) { bcf_fmt_t *f = &fmt[i]; bcf_enc_int1(&ind, f->id); bcf_enc_size(&ind, f->n, f->type); for (j = 0; j < n; ++j) if (imap[j] >= 0) kputsn((char*)(f->p + imap[j] * f->size), f->size, &ind); } for (i = j = 0; j < n; ++j) if (imap[j] >= 0) ++i; v->n_sample = i; } else v->n_sample = 0; if ( !v->n_sample ) v->n_fmt = 0; free(v->indiv.s); v->indiv = ind; v->unpacked &= ~BCF_UN_FMT; // only BCF is ready for output, VCF will need to unpack again return 0; } int bcf_is_snp(bcf1_t *v) { int i; bcf_unpack(v, BCF_UN_STR); for (i = 0; i < v->n_allele; ++i) { if ( v->d.allele[i][1]==0 && v->d.allele[i][0]!='*' ) continue; // mpileup's allele, see also below. This is not completely satisfactory, // a general library is here narrowly tailored to fit samtools. if ( v->d.allele[i][0]=='<' && v->d.allele[i][1]=='X' && v->d.allele[i][2]=='>' ) continue; if ( v->d.allele[i][0]=='<' && v->d.allele[i][1]=='*' && v->d.allele[i][2]=='>' ) continue; break; } return i == v->n_allele; } static void bcf_set_variant_type(const char *ref, const char *alt, bcf_variant_t *var) { if ( *alt == '*' && !alt[1] ) { var->n = 0; var->type = VCF_OVERLAP; return; } // overlapping variant // The most frequent case if ( !ref[1] && !alt[1] ) { if ( *alt == '.' || *ref==*alt ) { var->n = 0; var->type = VCF_REF; return; } if ( *alt == 'X' ) { var->n = 0; var->type = VCF_REF; return; } // mpileup's X allele shouldn't be treated as variant var->n = 1; var->type = VCF_SNP; return; } if ( alt[0]=='<' ) { if ( alt[1]=='X' && alt[2]=='>' ) { var->n = 0; var->type = VCF_REF; return; } // mpileup's X allele shouldn't be treated as variant if ( alt[1]=='*' && alt[2]=='>' ) { var->n = 0; var->type = VCF_REF; return; } if ( !strcmp("NON_REF>",alt+1) ) { var->n = 0; var->type = VCF_REF; return; } var->type = VCF_OTHER; return; } // Catch "joined before" breakend case if ( alt[0]==']' || alt[0] == '[' ) { var->type = VCF_BND; return; } // Iterate through alt characters that match the reference const char *r = ref, *a = alt; while (*r && *a && toupper_c(*r)==toupper_c(*a) ) { r++; a++; } // unfortunately, matching REF,ALT case is not guaranteed if ( *a && !*r ) { if ( *a==']' || *a=='[' ) { var->type = VCF_BND; return; } // "joined after" breakend while ( *a ) a++; var->n = (a-alt)-(r-ref); var->type = VCF_INDEL | VCF_INS; return; } else if ( *r && !*a ) { while ( *r ) r++; var->n = (a-alt)-(r-ref); var->type = VCF_INDEL | VCF_DEL; return; } else if ( !*r && !*a ) { var->n = 0; var->type = VCF_REF; return; } const char *re = r, *ae = a; while ( re[1] ) re++; while ( ae[1] ) ae++; while ( re>r && ae>a && toupper_c(*re)==toupper_c(*ae) ) { re--; ae--; } if ( ae==a ) { if ( re==r ) { var->n = 1; var->type = VCF_SNP; return; } var->n = -(re-r); if ( toupper_c(*re)==toupper_c(*ae) ) { var->type = VCF_INDEL | VCF_DEL; return; } var->type = VCF_OTHER; return; } else if ( re==r ) { var->n = ae-a; if ( toupper_c(*re)==toupper_c(*ae) ) { var->type = VCF_INDEL | VCF_INS; return; } var->type = VCF_OTHER; return; } var->type = ( re-r == ae-a ) ? VCF_MNP : VCF_OTHER; var->n = ( re-r > ae-a ) ? -(re-r+1) : ae-a+1; // should do also complex events, SVs, etc... } static int bcf_set_variant_types(bcf1_t *b) { if ( !(b->unpacked & BCF_UN_STR) ) bcf_unpack(b, BCF_UN_STR); bcf_dec_t *d = &b->d; if ( d->n_var < b->n_allele ) { bcf_variant_t *new_var = realloc(d->var, sizeof(bcf_variant_t)*b->n_allele); if (!new_var) return -1; d->var = new_var; d->n_var = b->n_allele; } int i; b->d.var_type = 0; d->var[0].type = VCF_REF; d->var[0].n = 0; for (i=1; in_allele; i++) { bcf_set_variant_type(d->allele[0],d->allele[i], &d->var[i]); b->d.var_type |= d->var[i].type; //fprintf(stderr,"[set_variant_type] %d %s %s -> %d %d .. %d\n", b->pos+1,d->allele[0],d->allele[i],d->var[i].type,d->var[i].n, b->d.var_type); } return 0; } // bcf_get_variant_type/bcf_get_variant_types should only return the following, // to be compatible with callers that are not expecting newer values // like VCF_INS, VCF_DEL. The full set is available from the newer // vcf_has_variant_type* interfaces. #define ORIG_VAR_TYPES (VCF_SNP|VCF_MNP|VCF_INDEL|VCF_OTHER|VCF_BND|VCF_OVERLAP) int bcf_get_variant_types(bcf1_t *rec) { if ( rec->d.var_type==-1 ) { if (bcf_set_variant_types(rec) != 0) { hts_log_error("Couldn't get variant types: %s", strerror(errno)); exit(1); // Due to legacy API having no way to report failures } } return rec->d.var_type & ORIG_VAR_TYPES; } int bcf_get_variant_type(bcf1_t *rec, int ith_allele) { if ( rec->d.var_type==-1 ) { if (bcf_set_variant_types(rec) != 0) { hts_log_error("Couldn't get variant types: %s", strerror(errno)); exit(1); // Due to legacy API having no way to report failures } } if (ith_allele < 0 || ith_allele >= rec->n_allele) { hts_log_error("Requested allele outside valid range"); exit(1); } return rec->d.var[ith_allele].type & ORIG_VAR_TYPES; } #undef ORIG_VAR_TYPES int bcf_has_variant_type(bcf1_t *rec, int ith_allele, uint32_t bitmask) { if ( rec->d.var_type==-1 ) { if (bcf_set_variant_types(rec) != 0) return -1; } if (ith_allele < 0 || ith_allele >= rec->n_allele) return -1; if (bitmask == VCF_REF) { // VCF_REF is 0, so handled as a special case return rec->d.var[ith_allele].type == VCF_REF; } return bitmask & rec->d.var[ith_allele].type; } int bcf_variant_length(bcf1_t *rec, int ith_allele) { if ( rec->d.var_type==-1 ) { if (bcf_set_variant_types(rec) != 0) return bcf_int32_missing; } if (ith_allele < 0 || ith_allele >= rec->n_allele) return bcf_int32_missing; return rec->d.var[ith_allele].n; } int bcf_has_variant_types(bcf1_t *rec, uint32_t bitmask, enum bcf_variant_match mode) { if ( rec->d.var_type==-1 ) { if (bcf_set_variant_types(rec) != 0) return -1; } uint32_t type = rec->d.var_type; if ( mode==bcf_match_overlap ) return bitmask & type; // VCF_INDEL is always set with VCF_INS and VCF_DEL by bcf_set_variant_type[s], but the bitmask may // ask for say `VCF_INS` or `VCF_INDEL` only if ( bitmask&(VCF_INS|VCF_DEL) && !(bitmask&VCF_INDEL) ) type &= ~VCF_INDEL; else if ( bitmask&VCF_INDEL && !(bitmask&(VCF_INS|VCF_DEL)) ) type &= ~(VCF_INS|VCF_DEL); if ( mode==bcf_match_subset ) { if ( ~bitmask & type ) return 0; else return bitmask & type; } // mode == bcf_match_exact return type==bitmask ? type : 0; } int bcf_update_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type) { static int negative_rlen_warned = 0; int is_end_tag; // Is the field already present? int i, inf_id = bcf_hdr_id2int(hdr,BCF_DT_ID,key); if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,inf_id) ) return -1; // No such INFO field in the header if ( !(line->unpacked & BCF_UN_INFO) ) bcf_unpack(line, BCF_UN_INFO); is_end_tag = strcmp(key, "END") == 0; for (i=0; in_info; i++) if ( inf_id==line->d.info[i].key ) break; bcf_info_t *inf = i==line->n_info ? NULL : &line->d.info[i]; if ( !n || (type==BCF_HT_STR && !values) ) { if ( n==0 && is_end_tag ) line->rlen = line->n_allele ? strlen(line->d.allele[0]) : 0; if ( inf ) { // Mark the tag for removal, free existing memory if necessary if ( inf->vptr_free ) { free(inf->vptr - inf->vptr_off); inf->vptr_free = 0; } line->d.shared_dirty |= BCF1_DIRTY_INF; inf->vptr = NULL; inf->vptr_off = inf->vptr_len = 0; } return 0; } if (is_end_tag) { if (n != 1) { hts_log_error("END info tag should only have one value at %s:%"PRIhts_pos, bcf_seqname_safe(hdr,line), line->pos+1); line->errcode |= BCF_ERR_TAG_INVALID; return -1; } if (type != BCF_HT_INT && type != BCF_HT_LONG) { hts_log_error("Wrong type (%d) for END info tag at %s:%"PRIhts_pos, type, bcf_seqname_safe(hdr,line), line->pos+1); line->errcode |= BCF_ERR_TAG_INVALID; return -1; } } // Encode the values and determine the size required to accommodate the values kstring_t str = {0,0,0}; bcf_enc_int1(&str, inf_id); if ( type==BCF_HT_INT ) bcf_enc_vint(&str, n, (int32_t*)values, -1); else if ( type==BCF_HT_REAL ) bcf_enc_vfloat(&str, n, (float*)values); else if ( type==BCF_HT_FLAG || type==BCF_HT_STR ) { if ( values==NULL ) bcf_enc_size(&str, 0, BCF_BT_NULL); else bcf_enc_vchar(&str, strlen((char*)values), (char*)values); } #ifdef VCF_ALLOW_INT64 else if ( type==BCF_HT_LONG ) { if (n != 1) { hts_log_error("Only storing a single BCF_HT_LONG value is supported at %s:%"PRIhts_pos, bcf_seqname_safe(hdr,line), line->pos+1); abort(); } bcf_enc_long1(&str, *(int64_t *) values); } #endif else { hts_log_error("The type %d not implemented yet at %s:%"PRIhts_pos, type, bcf_seqname_safe(hdr,line), line->pos+1); abort(); } // Is the INFO tag already present if ( inf ) { // Is it big enough to accommodate new block? if ( inf->vptr && str.l <= inf->vptr_len + inf->vptr_off ) { if ( str.l != inf->vptr_len + inf->vptr_off ) line->d.shared_dirty |= BCF1_DIRTY_INF; uint8_t *ptr = inf->vptr - inf->vptr_off; memcpy(ptr, str.s, str.l); free(str.s); int vptr_free = inf->vptr_free; bcf_unpack_info_core1(ptr, inf); inf->vptr_free = vptr_free; } else { if ( inf->vptr_free ) free(inf->vptr - inf->vptr_off); bcf_unpack_info_core1((uint8_t*)str.s, inf); inf->vptr_free = 1; line->d.shared_dirty |= BCF1_DIRTY_INF; } } else { // The tag is not present, create new one line->n_info++; hts_expand0(bcf_info_t, line->n_info, line->d.m_info , line->d.info); inf = &line->d.info[line->n_info-1]; bcf_unpack_info_core1((uint8_t*)str.s, inf); inf->vptr_free = 1; line->d.shared_dirty |= BCF1_DIRTY_INF; } line->unpacked |= BCF_UN_INFO; if ( n==1 && is_end_tag) { hts_pos_t end = type == BCF_HT_INT ? *(int32_t *) values : *(int64_t *) values; if ( (type == BCF_HT_INT && end!=bcf_int32_missing) || (type == BCF_HT_LONG && end!=bcf_int64_missing) ) { if ( end <= line->pos ) { if ( !negative_rlen_warned ) { hts_log_warning("INFO/END=%"PRIhts_pos" is smaller than POS at %s:%"PRIhts_pos,end,bcf_seqname_safe(hdr,line),line->pos+1); negative_rlen_warned = 1; } line->rlen = line->n_allele ? strlen(line->d.allele[0]) : 0; } else line->rlen = end - line->pos; } } return 0; } int bcf_update_format_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const char **values, int n) { if ( !n ) return bcf_update_format(hdr,line,key,NULL,0,BCF_HT_STR); int i, max_len = 0; for (i=0; i max_len ) max_len = len; } char *out = (char*) malloc(max_len*n); if ( !out ) return -2; for (i=0; iunpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT); for (i=0; in_fmt; i++) if ( line->d.fmt[i].id==fmt_id ) break; bcf_fmt_t *fmt = i==line->n_fmt ? NULL : &line->d.fmt[i]; if ( !n ) { if ( fmt ) { // Mark the tag for removal, free existing memory if necessary if ( fmt->p_free ) { free(fmt->p - fmt->p_off); fmt->p_free = 0; } line->d.indiv_dirty = 1; fmt->p = NULL; } return 0; } line->n_sample = bcf_hdr_nsamples(hdr); int nps = n / line->n_sample; // number of values per sample assert( nps && nps*line->n_sample==n ); // must be divisible by n_sample // Encode the values and determine the size required to accommodate the values kstring_t str = {0,0,0}; bcf_enc_int1(&str, fmt_id); assert(values != NULL); if ( type==BCF_HT_INT ) bcf_enc_vint(&str, n, (int32_t*)values, nps); else if ( type==BCF_HT_REAL ) { bcf_enc_size(&str, nps, BCF_BT_FLOAT); serialize_float_array(&str, nps*line->n_sample, (float *) values); } else if ( type==BCF_HT_STR ) { bcf_enc_size(&str, nps, BCF_BT_CHAR); kputsn((char*)values, nps*line->n_sample, &str); } else { hts_log_error("The type %d not implemented yet at %s:%"PRIhts_pos, type, bcf_seqname_safe(hdr,line), line->pos+1); abort(); } if ( !fmt ) { // Not present, new format field line->n_fmt++; hts_expand0(bcf_fmt_t, line->n_fmt, line->d.m_fmt, line->d.fmt); // Special case: VCF specification requires that GT is always first if ( line->n_fmt > 1 && key[0]=='G' && key[1]=='T' && !key[2] ) { for (i=line->n_fmt-1; i>0; i--) line->d.fmt[i] = line->d.fmt[i-1]; fmt = &line->d.fmt[0]; } else fmt = &line->d.fmt[line->n_fmt-1]; bcf_unpack_fmt_core1((uint8_t*)str.s, line->n_sample, fmt); line->d.indiv_dirty = 1; fmt->p_free = 1; } else { // The tag is already present, check if it is big enough to accommodate the new block if ( fmt->p && str.l <= fmt->p_len + fmt->p_off ) { // good, the block is big enough if ( str.l != fmt->p_len + fmt->p_off ) line->d.indiv_dirty = 1; uint8_t *ptr = fmt->p - fmt->p_off; memcpy(ptr, str.s, str.l); free(str.s); int p_free = fmt->p_free; bcf_unpack_fmt_core1(ptr, line->n_sample, fmt); fmt->p_free = p_free; } else { if ( fmt->p_free ) free(fmt->p - fmt->p_off); bcf_unpack_fmt_core1((uint8_t*)str.s, line->n_sample, fmt); fmt->p_free = 1; line->d.indiv_dirty = 1; } } line->unpacked |= BCF_UN_FMT; return 0; } int bcf_update_filter(const bcf_hdr_t *hdr, bcf1_t *line, int *flt_ids, int n) { if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT); line->d.shared_dirty |= BCF1_DIRTY_FLT; line->d.n_flt = n; if ( !n ) return 0; hts_expand(int, line->d.n_flt, line->d.m_flt, line->d.flt); int i; for (i=0; id.flt[i] = flt_ids[i]; return 0; } int bcf_add_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id) { if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT); int i; for (i=0; id.n_flt; i++) if ( flt_id==line->d.flt[i] ) break; if ( id.n_flt ) return 0; // this filter is already set line->d.shared_dirty |= BCF1_DIRTY_FLT; if ( flt_id==0 ) // set to PASS line->d.n_flt = 1; else if ( line->d.n_flt==1 && line->d.flt[0]==0 ) line->d.n_flt = 1; else line->d.n_flt++; hts_expand(int, line->d.n_flt, line->d.m_flt, line->d.flt); line->d.flt[line->d.n_flt-1] = flt_id; return 1; } int bcf_remove_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id, int pass) { if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT); int i; for (i=0; id.n_flt; i++) if ( flt_id==line->d.flt[i] ) break; if ( i==line->d.n_flt ) return 0; // the filter is not present line->d.shared_dirty |= BCF1_DIRTY_FLT; if ( i!=line->d.n_flt-1 ) memmove(line->d.flt+i,line->d.flt+i+1,(line->d.n_flt-i-1)*sizeof(*line->d.flt)); line->d.n_flt--; if ( !line->d.n_flt && pass ) bcf_add_filter(hdr,line,0); return 0; } int bcf_has_filter(const bcf_hdr_t *hdr, bcf1_t *line, char *filter) { if ( filter[0]=='.' && !filter[1] ) filter = "PASS"; int id = bcf_hdr_id2int(hdr, BCF_DT_ID, filter); if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FLT,id) ) return -1; // not defined in the header if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT); if ( id==0 && !line->d.n_flt) return 1; // PASS int i; for (i=0; id.n_flt; i++) if ( line->d.flt[i]==id ) return 1; return 0; } static inline int _bcf1_sync_alleles(const bcf_hdr_t *hdr, bcf1_t *line, int nals) { line->d.shared_dirty |= BCF1_DIRTY_ALS; line->n_allele = nals; hts_expand(char*, line->n_allele, line->d.m_allele, line->d.allele); char *als = line->d.als; int n = 0; while (nd.allele[n] = als; while ( *als ) als++; als++; n++; } // Update REF length. Note that END is 1-based while line->pos 0-based bcf_info_t *end_info = bcf_get_info(hdr,line,"END"); if ( end_info ) { if ( end_info->type==BCF_HT_INT && end_info->v1.i==bcf_int32_missing ) end_info = NULL; else if ( end_info->type==BCF_HT_LONG && end_info->v1.i==bcf_int64_missing ) end_info = NULL; } if ( end_info && end_info->v1.i > line->pos ) line->rlen = end_info->v1.i - line->pos; else if ( nals > 0 ) line->rlen = strlen(line->d.allele[0]); else line->rlen = 0; return 0; } int bcf_update_alleles(const bcf_hdr_t *hdr, bcf1_t *line, const char **alleles, int nals) { if ( !(line->unpacked & BCF_UN_STR) ) bcf_unpack(line, BCF_UN_STR); char *free_old = NULL; char buffer[256]; size_t used = 0; // The pointers in alleles may point into the existing line->d.als memory, // so care needs to be taken not to clobber them while updating. Usually // they will be short so we can copy through an intermediate buffer. // If they're longer, or won't fit in the existing allocation we // can allocate a new buffer to write into. Note that in either case // pointers to line->d.als memory in alleles may not be valid when we've // finished. int i; size_t avail = line->d.m_als < sizeof(buffer) ? line->d.m_als : sizeof(buffer); for (i=0; id.m_als) // Don't shrink the buffer needed = line->d.m_als; if (needed > INT_MAX) { hts_log_error("REF + alleles too long to fit in a BCF record"); return -1; } new_als = malloc(needed); if (!new_als) return -1; free_old = line->d.als; line->d.als = new_als; line->d.m_als = needed; } // Copy from the temp buffer to the destination if (used) { assert(used <= line->d.m_als); memcpy(line->d.als, buffer, used); } // Add in any remaining entries - if this happens we will always be // writing to a newly-allocated buffer. for (; i < nals; i++) { size_t sz = strlen(alleles[i]) + 1; memcpy(line->d.als + used, alleles[i], sz); used += sz; } if (free_old) free(free_old); return _bcf1_sync_alleles(hdr,line,nals); } int bcf_update_alleles_str(const bcf_hdr_t *hdr, bcf1_t *line, const char *alleles_string) { if ( !(line->unpacked & BCF_UN_STR) ) bcf_unpack(line, BCF_UN_STR); kstring_t tmp; tmp.l = 0; tmp.s = line->d.als; tmp.m = line->d.m_als; kputs(alleles_string, &tmp); line->d.als = tmp.s; line->d.m_als = tmp.m; int nals = 1; char *t = line->d.als; while (*t) { if ( *t==',' ) { *t = 0; nals++; } t++; } return _bcf1_sync_alleles(hdr, line, nals); } int bcf_update_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id) { if ( !(line->unpacked & BCF_UN_STR) ) bcf_unpack(line, BCF_UN_STR); kstring_t tmp; tmp.l = 0; tmp.s = line->d.id; tmp.m = line->d.m_id; if ( id ) kputs(id, &tmp); else kputs(".", &tmp); line->d.id = tmp.s; line->d.m_id = tmp.m; line->d.shared_dirty |= BCF1_DIRTY_ID; return 0; } int bcf_add_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id) { if ( !id ) return 0; if ( !(line->unpacked & BCF_UN_STR) ) bcf_unpack(line, BCF_UN_STR); kstring_t tmp; tmp.l = 0; tmp.s = line->d.id; tmp.m = line->d.m_id; int len = strlen(id); char *dst = line->d.id; while ( *dst && (dst=strstr(dst,id)) ) { if ( dst[len]!=0 && dst[len]!=';' ) dst++; // a prefix, not a match else if ( dst==line->d.id || dst[-1]==';' ) return 0; // already present dst++; // a suffix, not a match } if ( line->d.id && (line->d.id[0]!='.' || line->d.id[1]) ) { tmp.l = strlen(line->d.id); kputc(';',&tmp); } kputs(id,&tmp); line->d.id = tmp.s; line->d.m_id = tmp.m; line->d.shared_dirty |= BCF1_DIRTY_ID; return 0; } bcf_fmt_t *bcf_get_fmt(const bcf_hdr_t *hdr, bcf1_t *line, const char *key) { int id = bcf_hdr_id2int(hdr, BCF_DT_ID, key); if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) ) return NULL; // no such FMT field in the header return bcf_get_fmt_id(line, id); } bcf_info_t *bcf_get_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key) { int id = bcf_hdr_id2int(hdr, BCF_DT_ID, key); if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,id) ) return NULL; // no such INFO field in the header return bcf_get_info_id(line, id); } bcf_fmt_t *bcf_get_fmt_id(bcf1_t *line, const int id) { int i; if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT); for (i=0; in_fmt; i++) { if ( line->d.fmt[i].id==id ) return &line->d.fmt[i]; } return NULL; } bcf_info_t *bcf_get_info_id(bcf1_t *line, const int id) { int i; if ( !(line->unpacked & BCF_UN_INFO) ) bcf_unpack(line, BCF_UN_INFO); for (i=0; in_info; i++) { if ( line->d.info[i].key==id ) return &line->d.info[i]; } return NULL; } int bcf_get_info_values(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, void **dst, int *ndst, int type) { int i, ret = -4, tag_id = bcf_hdr_id2int(hdr, BCF_DT_ID, tag); if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,tag_id) ) return -1; // no such INFO field in the header if ( bcf_hdr_id2type(hdr,BCF_HL_INFO,tag_id)!=(type & 0xff) ) return -2; // expected different type if ( !(line->unpacked & BCF_UN_INFO) ) bcf_unpack(line, BCF_UN_INFO); for (i=0; in_info; i++) if ( line->d.info[i].key==tag_id ) break; if ( i==line->n_info ) return ( type==BCF_HT_FLAG ) ? 0 : -3; // the tag is not present in this record if ( type==BCF_HT_FLAG ) return 1; bcf_info_t *info = &line->d.info[i]; if ( !info->vptr ) return -3; // the tag was marked for removal if ( type==BCF_HT_STR ) { if ( *ndst < info->len+1 ) { *ndst = info->len + 1; *dst = realloc(*dst, *ndst); } memcpy(*dst,info->vptr,info->len); ((uint8_t*)*dst)[info->len] = 0; return info->len; } // Make sure the buffer is big enough int size1; switch (type) { case BCF_HT_INT: size1 = sizeof(int32_t); break; case BCF_HT_LONG: size1 = sizeof(int64_t); break; case BCF_HT_REAL: size1 = sizeof(float); break; default: hts_log_error("Unexpected output type %d at %s:%"PRIhts_pos, type, bcf_seqname_safe(hdr,line), line->pos+1); return -2; } if ( *ndst < info->len ) { *ndst = info->len; *dst = realloc(*dst, *ndst * size1); } #define BRANCH(type_t, convert, is_missing, is_vector_end, set_missing, set_regular, out_type_t) do { \ out_type_t *tmp = (out_type_t *) *dst; \ int j; \ for (j=0; jlen; j++) \ { \ type_t p = convert(info->vptr + j * sizeof(type_t)); \ if ( is_vector_end ) break; \ if ( is_missing ) set_missing; \ else set_regular; \ tmp++; \ } \ ret = j; \ } while (0) switch (info->type) { case BCF_BT_INT8: if (type == BCF_HT_LONG) { BRANCH(int8_t, le_to_i8, p==bcf_int8_missing, p==bcf_int8_vector_end, *tmp=bcf_int64_missing, *tmp=p, int64_t); } else { BRANCH(int8_t, le_to_i8, p==bcf_int8_missing, p==bcf_int8_vector_end, *tmp=bcf_int32_missing, *tmp=p, int32_t); } break; case BCF_BT_INT16: if (type == BCF_HT_LONG) { BRANCH(int16_t, le_to_i16, p==bcf_int16_missing, p==bcf_int16_vector_end, *tmp=bcf_int64_missing, *tmp=p, int64_t); } else { BRANCH(int16_t, le_to_i16, p==bcf_int16_missing, p==bcf_int16_vector_end, *tmp=bcf_int32_missing, *tmp=p, int32_t); } break; case BCF_BT_INT32: if (type == BCF_HT_LONG) { BRANCH(int32_t, le_to_i32, p==bcf_int32_missing, p==bcf_int32_vector_end, *tmp=bcf_int64_missing, *tmp=p, int64_t); break; } else { BRANCH(int32_t, le_to_i32, p==bcf_int32_missing, p==bcf_int32_vector_end, *tmp=bcf_int32_missing, *tmp=p, int32_t); break; } case BCF_BT_FLOAT: BRANCH(uint32_t, le_to_u32, p==bcf_float_missing, p==bcf_float_vector_end, bcf_float_set_missing(*tmp), bcf_float_set(tmp, p), float); break; default: hts_log_error("Unexpected type %d at %s:%"PRIhts_pos, info->type, bcf_seqname_safe(hdr,line), line->pos+1); return -2; } #undef BRANCH return ret; // set by BRANCH } int bcf_get_format_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, char ***dst, int *ndst) { int i,tag_id = bcf_hdr_id2int(hdr, BCF_DT_ID, tag); if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,tag_id) ) return -1; // no such FORMAT field in the header if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=BCF_HT_STR ) return -2; // expected different type if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT); for (i=0; in_fmt; i++) if ( line->d.fmt[i].id==tag_id ) break; if ( i==line->n_fmt ) return -3; // the tag is not present in this record bcf_fmt_t *fmt = &line->d.fmt[i]; if ( !fmt->p ) return -3; // the tag was marked for removal int nsmpl = bcf_hdr_nsamples(hdr); if ( !*dst ) { *dst = (char**) malloc(sizeof(char*)*nsmpl); if ( !*dst ) return -4; // could not alloc (*dst)[0] = NULL; } int n = (fmt->n+1)*nsmpl; if ( *ndst < n ) { (*dst)[0] = realloc((*dst)[0], n); if ( !(*dst)[0] ) return -4; // could not alloc *ndst = n; } for (i=0; ip + i*fmt->n; uint8_t *tmp = (uint8_t*)(*dst)[0] + i*(fmt->n+1); memcpy(tmp,src,fmt->n); tmp[fmt->n] = 0; (*dst)[i] = (char*) tmp; } return n; } int bcf_get_format_values(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, void **dst, int *ndst, int type) { int i,j, tag_id = bcf_hdr_id2int(hdr, BCF_DT_ID, tag); if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,tag_id) ) return -1; // no such FORMAT field in the header if ( tag[0]=='G' && tag[1]=='T' && tag[2]==0 ) { // Ugly: GT field is considered to be a string by the VCF header but BCF represents it as INT. if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=BCF_HT_STR ) return -2; } else if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=type ) return -2; // expected different type if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT); for (i=0; in_fmt; i++) if ( line->d.fmt[i].id==tag_id ) break; if ( i==line->n_fmt ) return -3; // the tag is not present in this record bcf_fmt_t *fmt = &line->d.fmt[i]; if ( !fmt->p ) return -3; // the tag was marked for removal if ( type==BCF_HT_STR ) { int n = fmt->n*bcf_hdr_nsamples(hdr); if ( *ndst < n ) { *dst = realloc(*dst, n); if ( !*dst ) return -4; // could not alloc *ndst = n; } memcpy(*dst,fmt->p,n); return n; } // Make sure the buffer is big enough int nsmpl = bcf_hdr_nsamples(hdr); int size1 = type==BCF_HT_INT ? sizeof(int32_t) : sizeof(float); if ( *ndst < fmt->n*nsmpl ) { *ndst = fmt->n*nsmpl; *dst = realloc(*dst, *ndst*size1); if ( !*dst ) return -4; // could not alloc } #define BRANCH(type_t, convert, is_missing, is_vector_end, set_missing, set_vector_end, set_regular, out_type_t) { \ out_type_t *tmp = (out_type_t *) *dst; \ uint8_t *fmt_p = fmt->p; \ for (i=0; in; j++) \ { \ type_t p = convert(fmt_p + j * sizeof(type_t)); \ if ( is_missing ) set_missing; \ else if ( is_vector_end ) { set_vector_end; break; } \ else set_regular; \ tmp++; \ } \ for (; jn; j++) { set_vector_end; tmp++; } \ fmt_p += fmt->size; \ } \ } switch (fmt->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, p==bcf_int8_missing, p==bcf_int8_vector_end, *tmp=bcf_int32_missing, *tmp=bcf_int32_vector_end, *tmp=p, int32_t); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, p==bcf_int16_missing, p==bcf_int16_vector_end, *tmp=bcf_int32_missing, *tmp=bcf_int32_vector_end, *tmp=p, int32_t); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, p==bcf_int32_missing, p==bcf_int32_vector_end, *tmp=bcf_int32_missing, *tmp=bcf_int32_vector_end, *tmp=p, int32_t); break; case BCF_BT_FLOAT: BRANCH(uint32_t, le_to_u32, p==bcf_float_missing, p==bcf_float_vector_end, bcf_float_set_missing(*tmp), bcf_float_set_vector_end(*tmp), bcf_float_set(tmp, p), float); break; default: hts_log_error("Unexpected type %d at %s:%"PRIhts_pos, fmt->type, bcf_seqname_safe(hdr,line), line->pos+1); exit(1); } #undef BRANCH return nsmpl*fmt->n; } //error description structure definition typedef struct err_desc { int errorcode; const char *description; }err_desc; // error descriptions static const err_desc errdesc_bcf[] = { { BCF_ERR_CTG_UNDEF, "Contig not defined in header"}, { BCF_ERR_TAG_UNDEF, "Tag not defined in header" }, { BCF_ERR_NCOLS, "Incorrect number of columns" }, { BCF_ERR_LIMITS, "Limits reached" }, { BCF_ERR_CHAR, "Invalid character" }, { BCF_ERR_CTG_INVALID, "Invalid contig" }, { BCF_ERR_TAG_INVALID, "Invalid tag" }, }; /// append given description to buffer based on available size and add ... when not enough space /** @param buffer buffer to which description to be appended @param offset offset at which to be appended @param maxbuffer maximum size of the buffer @param description the description to be appended on failure returns -1 - when buffer is not big enough; returns -1 on invalid params and on too small buffer which are improbable due to validation at caller site on success returns 0 */ static int add_desc_to_buffer(char *buffer, size_t *offset, size_t maxbuffer, const char *description) { if (!description || !buffer || !offset || (maxbuffer < 4)) return -1; size_t rembuffer = maxbuffer - *offset; if (rembuffer > (strlen(description) + (rembuffer == maxbuffer ? 0 : 1))) { //add description with optionally required ',' *offset += snprintf(buffer + *offset, rembuffer, "%s%s", (rembuffer == maxbuffer)? "": ",", description); } else { //not enough space for description, put ... size_t tmppos = (rembuffer <= 4) ? maxbuffer - 4 : *offset; snprintf(buffer + tmppos, 4, "..."); //ignore offset update return -1; } return 0; } //get description for given error code. return NULL on error const char *bcf_strerror(int errorcode, char *buffer, size_t maxbuffer) { size_t usedup = 0; int ret = 0; int idx; if (!buffer || maxbuffer < 4) return NULL; //invalid / insufficient buffer if (!errorcode) { buffer[0] = '\0'; //no error, set null return buffer; } for (idx = 0; idx < sizeof(errdesc_bcf) / sizeof(err_desc); ++idx) { if (errorcode & errdesc_bcf[idx].errorcode) { //error is set, add description ret = add_desc_to_buffer(buffer, &usedup, maxbuffer, errdesc_bcf[idx].description); if (ret < 0) break; //not enough space, ... added, no need to continue errorcode &= ~errdesc_bcf[idx].errorcode; //reset the error } } if (errorcode && (ret >= 0)) { //undescribed error is present in error code and had enough buffer, try to add unkonwn error as well§ add_desc_to_buffer(buffer, &usedup, maxbuffer, "Unknown error"); } return buffer; } pysam-0.23.0/htslib/vcf_sweep.c000066400000000000000000000127021475062545500163560ustar00rootroot00000000000000/* vcf_sweep.c -- forward/reverse sweep API. Copyright (C) 2013-2014, 2019 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include "htslib/vcf_sweep.h" #include "htslib/bgzf.h" #define SW_FWD 0 #define SW_BWD 1 struct bcf_sweep_t { htsFile *file; bcf_hdr_t *hdr; BGZF *fp; int direction; // to tell if the direction has changed int block_size; // the size of uncompressed data to hold in memory bcf1_t *rec; // bcf buffer int nrec, mrec; // number of used records; total size of the buffer int lrid, lpos, lnals, lals_len, mlals; // to check uniqueness of a record char *lals; uint64_t *idx; // uncompressed offsets of VCF/BCF records int iidx, nidx, midx; // i: current offset; n: used; m: allocated int idx_done; // the index is built during the first pass }; BGZF *hts_get_bgzfp(htsFile *fp); int hts_useek(htsFile *file, off_t uoffset, int where); off_t hts_utell(htsFile *file); static inline int sw_rec_equal(bcf_sweep_t *sw, bcf1_t *rec) { if ( sw->lrid!=rec->rid ) return 0; if ( sw->lpos!=rec->pos ) return 0; if ( sw->lnals!=rec->n_allele ) return 0; char *t = rec->d.allele[sw->lnals-1]; int len = t - rec->d.allele[0] + 1; while ( *t ) { t++; len++; } if ( sw->lals_len!=len ) return 0; if ( memcmp(sw->lals,rec->d.allele[0],len) ) return 0; return 1; } static int sw_rec_save(bcf_sweep_t *sw, bcf1_t *rec) { sw->lrid = rec->rid; sw->lpos = rec->pos; sw->lnals = rec->n_allele; char *t = rec->d.allele[sw->lnals-1]; int len = t - rec->d.allele[0] + 1; while ( *t ) { t++; len++; } sw->lals_len = len; hts_expand(char, len, sw->mlals, sw->lals); memcpy(sw->lals, rec->d.allele[0], len); return 0; // FIXME: check for errs in this function } static int sw_fill_buffer(bcf_sweep_t *sw) { if ( !sw->iidx ) return 0; sw->iidx--; int ret = hts_useek(sw->file, sw->idx[sw->iidx], 0); assert( ret==0 ); sw->nrec = 0; bcf1_t *rec = &sw->rec[sw->nrec]; while ( (ret=bcf_read1(sw->file, sw->hdr, rec))==0 ) { bcf_unpack(rec, BCF_UN_STR); // if not in the last block, stop at the saved record if ( sw->iidx+1 < sw->nidx && sw_rec_equal(sw,rec) ) break; sw->nrec++; hts_expand0(bcf1_t, sw->nrec+1, sw->mrec, sw->rec); rec = &sw->rec[sw->nrec]; } sw_rec_save(sw, &sw->rec[0]); return 0; // FIXME: check for errs in this function } bcf_sweep_t *bcf_sweep_init(const char *fname) { bcf_sweep_t *sw = (bcf_sweep_t*) calloc(1,sizeof(bcf_sweep_t)); sw->file = hts_open(fname, "r"); sw->fp = hts_get_bgzfp(sw->file); if (sw->fp) bgzf_index_build_init(sw->fp); sw->hdr = bcf_hdr_read(sw->file); sw->mrec = 1; sw->rec = (bcf1_t*) calloc(sw->mrec,(sizeof(bcf1_t))); sw->block_size = 1024*1024*3; sw->direction = SW_FWD; return sw; } void bcf_sweep_destroy(bcf_sweep_t *sw) { int i; for (i=0; imrec; i++) bcf_empty1(&sw->rec[i]); free(sw->idx); free(sw->rec); free(sw->lals); bcf_hdr_destroy(sw->hdr); hts_close(sw->file); free(sw); } static void sw_seek(bcf_sweep_t *sw, int direction) { sw->direction = direction; if ( direction==SW_FWD ) hts_useek(sw->file, sw->idx[0], 0); else { sw->iidx = sw->nidx; sw->nrec = 0; } } bcf1_t *bcf_sweep_fwd(bcf_sweep_t *sw) { if ( sw->direction==SW_BWD ) sw_seek(sw, SW_FWD); off_t pos = hts_utell(sw->file); bcf1_t *rec = &sw->rec[0]; int ret = bcf_read1(sw->file, sw->hdr, rec); if ( ret!=0 ) // last record, get ready for sweeping backwards { sw->idx_done = 1; if (sw->fp) sw->fp->idx_build_otf = 0; sw_seek(sw, SW_BWD); return NULL; } if ( !sw->idx_done ) { if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size ) { sw->nidx++; hts_expand(uint64_t, sw->nidx, sw->midx, sw->idx); sw->idx[sw->nidx-1] = pos; } } return rec; } bcf1_t *bcf_sweep_bwd(bcf_sweep_t *sw) { if ( sw->direction==SW_FWD ) sw_seek(sw, SW_BWD); if ( !sw->nrec ) sw_fill_buffer(sw); if ( !sw->nrec ) return NULL; return &sw->rec[ --sw->nrec ]; } bcf_hdr_t *bcf_sweep_hdr(bcf_sweep_t *sw) { return sw->hdr; } pysam-0.23.0/htslib/vcfutils.c000066400000000000000000001041131475062545500162320ustar00rootroot00000000000000/* vcfutils.c -- allele-related utility functions. Copyright (C) 2012-2018, 2020-2022 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h #include #include #include "htslib/vcfutils.h" #include "htslib/kbitset.h" int bcf_calc_ac(const bcf_hdr_t *header, bcf1_t *line, int *ac, int which) { int i; for (i=0; in_allele; i++) ac[i]=0; // Use INFO/AC,AN field only when asked if ( which&BCF_UN_INFO ) { bcf_unpack(line, BCF_UN_INFO); int an_id = bcf_hdr_id2int(header, BCF_DT_ID, "AN"); int ac_id = bcf_hdr_id2int(header, BCF_DT_ID, "AC"); int i, an=-1, ac_len=0, ac_type=0; uint8_t *ac_ptr=NULL; if ( an_id>=0 && ac_id>=0 ) { for (i=0; in_info; i++) { bcf_info_t *z = &line->d.info[i]; if ( z->key == an_id ) an = z->v1.i; else if ( z->key == ac_id ) { ac_ptr = z->vptr; ac_len = z->len; ac_type = z->type; } } } if ( an>=0 && ac_ptr ) { if ( ac_len != line->n_allele - 1 ) { static int warned = 0; if ( !warned ) { hts_log_warning("Incorrect number of AC fields at %s:%"PRIhts_pos". (This message is printed only once.)\n", header->id[BCF_DT_CTG][line->rid].key, line->pos+1); warned = 1; } return 0; } int nac = 0; #define BRANCH_INT(type_t, convert) { \ for (i=0; iid[BCF_DT_CTG][line->rid].key, line->pos+1); exit(1); break; } #undef BRANCH_INT if ( anid[BCF_DT_CTG][line->rid].key, line->pos+1); exit(1); } ac[0] = an - nac; return 1; } } // Split genotype fields only when asked if ( which&BCF_UN_FMT ) { int i, gt_id = bcf_hdr_id2int(header,BCF_DT_ID,"GT"); if ( gt_id<0 ) return 0; bcf_unpack(line, BCF_UN_FMT); bcf_fmt_t *fmt_gt = NULL; for (i=0; i<(int)line->n_fmt; i++) if ( line->d.fmt[i].id==gt_id ) { fmt_gt = &line->d.fmt[i]; break; } if ( !fmt_gt ) return 0; #define BRANCH_INT(type_t, convert, vector_end) { \ for (i=0; in_sample; i++) \ { \ uint8_t *p = (fmt_gt->p + i*fmt_gt->size); \ int ial; \ for (ial=0; ialn; ial++) \ { \ int32_t val = convert(&p[ial * sizeof(type_t)]); \ if ( val==vector_end ) break; /* smaller ploidy */ \ if ( bcf_gt_is_missing(val) ) continue; /* missing allele */ \ if ( val>>1 > line->n_allele ) \ { \ hts_log_error("Incorrect allele (\"%d\") in %s at %s:%"PRIhts_pos, (val>>1)-1, header->samples[i], header->id[BCF_DT_CTG][line->rid].key, line->pos+1); \ exit(1); \ } \ ac[(val>>1)-1]++; \ } \ } \ } switch (fmt_gt->type) { case BCF_BT_INT8: BRANCH_INT(int8_t, le_to_i8, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH_INT(int16_t, le_to_i16, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH_INT(int32_t, le_to_i32, bcf_int32_vector_end); break; default: hts_log_error("Unexpected type %d at %s:%"PRIhts_pos, fmt_gt->type, header->id[BCF_DT_CTG][line->rid].key, line->pos+1); exit(1); break; } #undef BRANCH_INT return 1; } return 0; } int bcf_gt_type(bcf_fmt_t *fmt_ptr, int isample, int *_ial, int *_jal) { int i, nals = 0, has_ref = 0, has_alt = 0, ial = 0, jal = 0; #define BRANCH_INT(type_t, convert, vector_end) { \ uint8_t *p = fmt_ptr->p + isample*fmt_ptr->size; \ for (i=0; in; i++) \ { \ int32_t val = convert(&p[i * sizeof(type_t)]); \ if ( val == vector_end ) break; /* smaller ploidy */ \ if ( bcf_gt_is_missing(val) ) return GT_UNKN; /* missing allele */ \ int tmp = val>>1; \ if ( tmp>1 ) \ { \ if ( !ial ) { ial = tmp; has_alt = 1; } \ else if ( tmp!=ial ) \ { \ if ( tmptype) { case BCF_BT_INT8: BRANCH_INT(int8_t, le_to_i8, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH_INT(int16_t, le_to_i16, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH_INT(int32_t, le_to_i32, bcf_int32_vector_end); break; default: hts_log_error("Unexpected type %d", fmt_ptr->type); exit(1); break; } #undef BRANCH_INT if ( _ial ) *_ial = ial>0 ? ial-1 : ial; if ( _jal ) *_jal = jal>0 ? jal-1 : jal; if ( !nals ) return GT_UNKN; if ( nals==1 ) return has_ref ? GT_HAPL_R : GT_HAPL_A; if ( !has_ref ) return has_alt==1 ? GT_HOM_AA : GT_HET_AA; if ( !has_alt ) return GT_HOM_RR; return GT_HET_RA; } int bcf_trim_alleles(const bcf_hdr_t *header, bcf1_t *line) { int i, ret = 0, nrm = 0; kbitset_t *rm_set = NULL; bcf_fmt_t *gt = bcf_get_fmt(header, line, "GT"); if ( !gt ) return 0; int *ac = (int*) calloc(line->n_allele,sizeof(int)); // check if all alleles are populated #define BRANCH(type_t, convert, vector_end) { \ for (i=0; in_sample; i++) \ { \ uint8_t *p = gt->p + i*gt->size; \ int ial; \ for (ial=0; ialn; ial++) \ { \ int32_t val = convert(&p[ial * sizeof(type_t)]); \ if ( val==vector_end ) break; /* smaller ploidy */ \ if ( bcf_gt_is_missing(val) ) continue; /* missing allele */ \ if ( (val>>1)-1 >= line->n_allele ) { \ hts_log_error("Allele index is out of bounds at %s:%"PRIhts_pos, header->id[BCF_DT_CTG][line->rid].key, line->pos+1); \ ret = -1; \ goto clean; \ } \ ac[(val>>1)-1]++; \ } \ } \ } switch (gt->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, bcf_int8_vector_end); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, bcf_int16_vector_end); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, bcf_int32_vector_end); break; default: hts_log_error("Unexpected GT %d at %s:%"PRIhts_pos, gt->type, header->id[BCF_DT_CTG][line->rid].key, line->pos + 1); goto clean; } #undef BRANCH rm_set = kbs_init(line->n_allele); for (i=1; in_allele; i++) { if ( !ac[i] ) { kbs_insert(rm_set, i); nrm++; } } if (nrm) { if (bcf_remove_allele_set(header, line, rm_set)) ret = -2; } clean: free(ac); if (rm_set) kbs_destroy(rm_set); return ret ? ret : nrm; } int bcf_remove_alleles(const bcf_hdr_t *header, bcf1_t *line, int rm_mask) { int i; kbitset_t *rm_set = kbs_init(line->n_allele); for (i=1; in_allele; i++) if ( rm_mask & 1<n_allele, sizeof(int)); uint8_t *dat = NULL; bcf_unpack(line, BCF_UN_ALL); // create map of indexes from old to new ALT numbering and modify ALT kstring_t str = {0,0,0}; kputs(line->d.allele[0], &str); int nrm = 0, i,j; // i: ori alleles, j: new alleles for (i=1, j=1; in_allele; i++) { if ( kbs_exists(rm_set, i) ) { // remove this allele line->d.allele[i] = NULL; nrm++; continue; } kputc(',', &str); kputs(line->d.allele[i], &str); map[i] = j; j++; } if ( !nrm ) goto clean; int nR_ori = line->n_allele; int nR_new = line->n_allele-nrm; if ( nR_new<=0 ) // should not be able to remove reference allele { hts_log_error("Cannot remove reference allele at %s:%"PRIhts_pos" [%d]", bcf_seqname_safe(header,line), line->pos+1, nR_new); goto err; } int nA_ori = nR_ori-1; int nA_new = nR_new-1; int nG_ori = nR_ori*(nR_ori + 1)/2; int nG_new = nR_new*(nR_new + 1)/2; bcf_update_alleles_str(header, line, str.s); // remove from Number=G, Number=R and Number=A INFO fields. int mdat = 0, ndat = 0, mdat_bytes = 0, nret; for (i=0; in_info; i++) { bcf_info_t *info = &line->d.info[i]; int vlen = bcf_hdr_id2length(header,BCF_HL_INFO,info->key); if ( vlen!=BCF_VL_A && vlen!=BCF_VL_G && vlen!=BCF_VL_R ) continue; // no need to change int type = bcf_hdr_id2type(header,BCF_HL_INFO,info->key); if ( type==BCF_HT_FLAG ) continue; int size = 1; if ( type==BCF_HT_REAL || type==BCF_HT_INT ) size = 4; mdat = mdat_bytes / size; nret = bcf_get_info_values(header, line, bcf_hdr_int2id(header,BCF_DT_ID,info->key), (void**)&dat, &mdat, type); mdat_bytes = mdat * size; if ( nret<0 ) { hts_log_error("Could not access INFO/%s at %s:%"PRIhts_pos" [%d]", bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname_safe(header,line), line->pos+1, nret); goto err; } if ( nret==0 ) continue; // no data for this tag if ( type==BCF_HT_STR ) { str.l = 0; char *ss = (char*) dat, *se = (char*) dat, s = ss[0]; if ( vlen==BCF_VL_A || vlen==BCF_VL_R ) { int nexp, inc = 0; if ( vlen==BCF_VL_A ) { nexp = nA_ori; inc = 1; } else nexp = nR_ori; for (j=0; jkey), bcf_seqname_safe(header,line), line->pos+1, vlen==BCF_VL_A ? 'A' : 'R', nexp, j); goto err; } } else // Number=G, assuming diploid genotype { int k = 0, n = 0; for (j=0; jkey), bcf_seqname_safe(header,line), line->pos+1, nG_ori, n); goto err; } } nret = bcf_update_info(header, line, bcf_hdr_int2id(header,BCF_DT_ID,info->key), (void*)str.s, str.l, type); if ( nret<0 ) { hts_log_error("Could not update INFO/%s at %s:%"PRIhts_pos" [%d]", bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname_safe(header,line), line->pos+1, nret); goto err; } continue; } if (nret==1) // could be missing - check { int missing = 0; #define BRANCH(type_t, convert, is_missing) { \ type_t val = convert(info->vptr); \ if ( is_missing ) missing = 1; \ } switch (info->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, val==bcf_int8_missing); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, val==bcf_int16_missing); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, val==bcf_int32_missing); break; case BCF_BT_FLOAT: BRANCH(float, le_to_float, bcf_float_is_missing(val)); break; default: hts_log_error("Unexpected type %d", info->type); goto err; } #undef BRANCH if (missing) continue; // could remove this INFO tag? } if ( vlen==BCF_VL_A || vlen==BCF_VL_R ) { int inc = 0, ntop; if ( vlen==BCF_VL_A ) { if ( nret!=nA_ori ) { hts_log_error("Unexpected number of values in INFO/%s at %s:%"PRIhts_pos"; expected Number=A=%d, but found %d", bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname_safe(header,line), line->pos+1, nA_ori, nret); goto err; } ntop = nA_ori; ndat = nA_new; inc = 1; } else { if ( nret!=nR_ori ) { hts_log_error("Unexpected number of values in INFO/%s at %s:%"PRIhts_pos"; expected Number=R=%d, but found %d", bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname_safe(header,line), line->pos+1, nR_ori, nret); goto err; } ntop = nR_ori; ndat = nR_new; } int k = 0; #define BRANCH(type_t,is_vector_end) \ { \ type_t *ptr = (type_t*) dat; \ int size = sizeof(type_t); \ for (j=0; jkey), bcf_seqname_safe(header,line), line->pos+1, nG_ori, nret); goto err; } int k, l_ori = -1, l_new = 0; ndat = nG_new; #define BRANCH(type_t,is_vector_end) \ { \ type_t *ptr = (type_t*) dat; \ int size = sizeof(type_t); \ for (j=0; jkey), (void*)dat, ndat, type); if ( nret<0 ) { hts_log_error("Could not update INFO/%s at %s:%"PRIhts_pos" [%d]", bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname_safe(header,line), line->pos+1, nret); goto err; } } // Update GT fields, the allele indexes might have changed for (i=1; i0 ) { nret /= line->n_sample; int32_t *ptr = (int32_t*) dat; for (i=0; in_sample; i++) { for (j=0; j=0 ) ) { hts_log_error("Problem updating genotypes at %s:%"PRIhts_pos" [ al=0 :: al=%d,nR_ori=%d,map[al]=%d ]", bcf_seqname_safe(header,line), line->pos+1, al, nR_ori, map[al]); goto err; } // if an allele other than the reference is mapped to 0, it has been removed, // so translate it to 'missing', while preserving the phasing bit ptr[j] = ((al>0 && !map[al]) ? bcf_gt_missing : (map[al]+1)<<1) | (ptr[j]&1); } ptr += nret; } nret = bcf_update_genotypes(header, line, (void*)dat, nret*line->n_sample); if ( nret<0 ) { hts_log_error("Could not update FORMAT/GT at %s:%"PRIhts_pos" [%d]", bcf_seqname_safe(header,line), line->pos+1, nret); goto err; } } } // Remove from Number=G, Number=R and Number=A FORMAT fields. // Assuming haploid or diploid GTs for (i=0; in_fmt; i++) { bcf_fmt_t *fmt = &line->d.fmt[i]; int vlen = bcf_hdr_id2length(header,BCF_HL_FMT,fmt->id); if ( vlen!=BCF_VL_A && vlen!=BCF_VL_G && vlen!=BCF_VL_R ) continue; // no need to change int type = bcf_hdr_id2type(header,BCF_HL_FMT,fmt->id); if ( type==BCF_HT_FLAG ) continue; int size = 1; if ( type==BCF_HT_REAL || type==BCF_HT_INT ) size = 4; mdat = mdat_bytes / size; nret = bcf_get_format_values(header, line, bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), (void**)&dat, &mdat, type); mdat_bytes = mdat * size; if ( nret<0 ) { hts_log_error("Could not access FORMAT/%s at %s:%"PRIhts_pos" [%d]", bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname_safe(header,line), line->pos+1, nret); goto err; } if ( nret == 0 ) continue; // no data for this tag if ( type==BCF_HT_STR ) { int size = nret/line->n_sample; // number of bytes per sample str.l = 0; if ( vlen==BCF_VL_A || vlen==BCF_VL_R ) { int nexp, inc = 0; if ( vlen==BCF_VL_A ) { nexp = nA_ori; inc = 1; } else nexp = nR_ori; for (j=0; jn_sample; j++) { char *ss = ((char*)dat) + j*size, *se = ss + size, *ptr = ss, s = ss[0]; int k_src = 0, k_dst = 0, l = str.l; for (k_src=0; k_src=se || !*ptr) break; while ( ptrid), bcf_seqname_safe(header,line), line->pos+1, vlen==BCF_VL_A ? 'A' : 'R', nexp, k_src); goto err; } l = str.l - l; for (; ln_sample; j++) { char *ss = ((char*)dat) + j*size, *se = ss + size, *ptr = ss, s = ss[0]; int k_src = 0, k_dst = 0, l = str.l; int nexp = 0; // diploid or haploid? while ( ptrid), bcf_seqname_safe(header,line), line->pos+1, nG_ori, nR_ori, nexp); goto err; } ptr = ss; if ( nexp==nG_ori ) // diploid { int ia, ib; for (ia=0; ia=se || !*ptr ) break; while ( ptr=se || !*ptr ) break; } } else // haploid { for (k_src=0; k_src=se || !*ptr ) break; while ( ptrid), bcf_seqname_safe(header,line), line->pos+1, nR_ori, k_src); goto err; } l = str.l - l; for (; lid), (void*)str.s, str.l, type); if ( nret<0 ) { hts_log_error("Could not update FORMAT/%s at %s:%"PRIhts_pos" [%d]", bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname_safe(header,line), line->pos+1, nret); goto err; } continue; } int nori = nret / line->n_sample; if ( nori==1 && !(vlen==BCF_VL_A && nori==nA_ori) ) // all values may be missing - check { int all_missing = 1; #define BRANCH(type_t, convert, is_missing) { \ for (j=0; jn_sample; j++) \ { \ type_t val = convert(fmt->p + j*fmt->size); \ if ( !(is_missing)) { all_missing = 0; break; } \ } \ } switch (fmt->type) { case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, val==bcf_int8_missing); break; case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, val==bcf_int16_missing); break; case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, val==bcf_int32_missing); break; case BCF_BT_FLOAT: BRANCH(float, le_to_float, bcf_float_is_missing(val)); break; default: hts_log_error("Unexpected type %d", fmt->type); goto err; } #undef BRANCH if (all_missing) continue; // could remove this FORMAT tag? } if ( vlen==BCF_VL_A || vlen==BCF_VL_R || (vlen==BCF_VL_G && nori==nR_ori) ) // Number=A, R or haploid Number=G { int inc = 0, nnew; if ( vlen==BCF_VL_A ) { if ( nori!=nA_ori ) { hts_log_error("Unexpected number of values in FORMAT/%s at %s:%"PRIhts_pos"; expected Number=A=%d, but found %d", bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname_safe(header,line), line->pos+1, nA_ori, nori); goto err; } ndat = nA_new*line->n_sample; nnew = nA_new; inc = 1; } else { if ( nori!=nR_ori ) { hts_log_error("Unexpected number of values in FORMAT/%s at %s:%"PRIhts_pos"; expected Number=R=%d, but found %d", bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname_safe(header,line), line->pos+1, nR_ori, nori); goto err; } ndat = nR_new*line->n_sample; nnew = nR_new; } #define BRANCH(type_t,is_vector_end,set_missing) \ { \ for (j=0; jn_sample; j++) \ { \ type_t *ptr_src = ((type_t*)dat) + j*nori; \ type_t *ptr_dst = ((type_t*)dat) + j*nnew; \ int size = sizeof(type_t); \ int k_src, k_dst = 0; \ for (k_src=0; k_srcid), bcf_seqname_safe(header,line), line->pos+1, nG_ori, nori); goto err; } ndat = nG_new*line->n_sample; #define BRANCH(type_t,is_vector_end) \ { \ for (j=0; jn_sample; j++) \ { \ type_t *ptr_src = ((type_t*)dat) + j*nori; \ type_t *ptr_dst = ((type_t*)dat) + j*nG_new; \ int size = sizeof(type_t); \ int ia, ib, k_dst = 0, k_src; \ int nset = 0; /* haploid or diploid? */ \ for (k_src=0; k_srcid), (void*)dat, ndat, type); if ( nret<0 ) { hts_log_error("Could not update FORMAT/%s at %s:%"PRIhts_pos" [%d]", bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname_safe(header,line), line->pos+1, nret); goto err; } } clean: free(str.s); free(map); free(dat); return 0; err: free(str.s); free(map); free(dat); return -1; } pysam-0.23.0/htslib/version.sh000077500000000000000000000042561475062545500162620ustar00rootroot00000000000000#!/bin/sh # version.sh -- Script to build the htslib version string # # Author : James Bonfield # # Copyright (C) 2017-2018, 2021 Genome Research Ltd. # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. # Master version, for use in tarballs or non-git source copies VERSION=1.21 # If we have a git clone, then check against the current tag srcdir=${0%/version.sh} if [ -e $srcdir/.git ] then # If we ever get to 10.x this will need to be more liberal v=`cd $srcdir && git describe --always --match '[0-9].[0-9]*' --dirty` case $v in [0-9]*.[0-9]*) VERSION="$v" ;; [0-9a-f][0-9a-f]*) VERSION="$VERSION-1-g$v" ;; esac fi # Numeric version is for use in .dylib or .so libraries # # Follows the same logic from the Makefile commit c2e93911 # as non-numeric versions get bumped to patch level 255 to indicate # an unknown value. if [ "$1" = "numeric" ] then v1=`expr "$VERSION" : '\([0-9]*\)'` v2=`expr "$VERSION" : '[0-9]*.\([0-9]*\)'` v3=`expr "$VERSION" : '[0-9]*.[0-9]*.\([0-9]*\)'` if [ -z "`expr "$VERSION" : '\([0-9.]*\)$'`" ] then VERSION="$v1.$v2.255" else VERSION="$v1.$v2${v3:+.}$v3" fi fi echo $VERSION pysam-0.23.0/import/000077500000000000000000000000001475062545500142545ustar00rootroot00000000000000pysam-0.23.0/import/pysam.c000066400000000000000000000030211475062545500155450ustar00rootroot00000000000000#include #include #include #include #include #include #include "@pysam@.pysam.h" FILE * @pysam@_stderr = NULL; FILE * @pysam@_stdout = NULL; const char * @pysam@_stdout_fn = NULL; FILE * @pysam@_set_stderr(int fd) { if (@pysam@_stderr != NULL) fclose(@pysam@_stderr); @pysam@_stderr = fdopen(fd, "w"); return @pysam@_stderr; } void @pysam@_close_stderr(void) { fclose(@pysam@_stderr); @pysam@_stderr = NULL; } FILE * @pysam@_set_stdout(int fd) { if (@pysam@_stdout != NULL) fclose(@pysam@_stdout); @pysam@_stdout = fdopen(fd, "w"); if (@pysam@_stdout == NULL) { fprintf(@pysam@_stderr, "could not set stdout to fd %i", fd); } return @pysam@_stdout; } void @pysam@_set_stdout_fn(const char *fn) { @pysam@_stdout_fn = fn; } void @pysam@_close_stdout(void) { fclose(@pysam@_stdout); @pysam@_stdout = NULL; } int @pysam@_puts(const char *s) { if (fputs(s, @pysam@_stdout) == EOF) return EOF; return putc('\n', @pysam@_stdout); } static jmp_buf @pysam@_jmpbuf; static int @pysam@_status = 0; int @pysam@_dispatch(int argc, char *argv[]) { /* Reset getopt()/getopt_long() processing. */ #if defined __GLIBC__ optind = 0; #elif defined _OPTRESET || defined _OPTRESET_DECLARED optreset = optind = 1; #else optind = 1; #endif if (setjmp(@pysam@_jmpbuf) == 0) return @pysam@_main(argc, argv); else return @pysam@_status; } void @pysam@_exit(int status) { @pysam@_status = status; longjmp(@pysam@_jmpbuf, 1); } pysam-0.23.0/import/pysam.h000066400000000000000000000035011475062545500155550ustar00rootroot00000000000000#ifndef @pysam@_PYSAM_H #define @pysam@_PYSAM_H #include #ifndef __has_attribute #define __has_attribute(attribute) 0 #endif #ifndef PYSAM_NORETURN #if __has_attribute(__noreturn__) || __GNUC__ >= 3 #define PYSAM_NORETURN __attribute__((__noreturn__)) #else #define PYSAM_NORETURN #endif #endif extern FILE * @pysam@_stderr; extern FILE * @pysam@_stdout; extern const char * @pysam@_stdout_fn; /*! set pysam standard error to point to file descriptor Setting the stderr will close the previous stderr. */ FILE * @pysam@_set_stderr(int fd); /*! set pysam standard output to point to file descriptor Setting the stdout will close the previous stdout. */ FILE * @pysam@_set_stdout(int fd); /*! set pysam standard output to point to filename */ void @pysam@_set_stdout_fn(const char * fn); /*! close pysam standard error and set to NULL */ void @pysam@_close_stderr(void); /*! close pysam standard output and set to NULL */ void @pysam@_close_stdout(void); int @pysam@_puts(const char *s); int @pysam@_dispatch(int argc, char *argv[]); void PYSAM_NORETURN @pysam@_exit(int status); extern int @pysam@_main(int argc, char *argv[]); /* Define these only in samtools/bcftools C source, not Cython code. */ #if !(defined CYTHON_ABI || defined CYTHON_HEX_VERSION) /*! Several non-static function names are used in both samtools and bcftools. Both libcsamtools.so and libcbcftools.so are loaded simultaneously, leading to collisions and wrong functions being called. #define these names so the actual symbol names include distinct prefixes to avoid collisions. */ #define main_consensus @pysam@_main_consensus #define main_reheader @pysam@_main_reheader #define bam_smpl_init @pysam@_bam_smpl_init #define bam_smpl_destroy @pysam@_bam_smpl_destroy #define read_file_list @pysam@_read_file_list #endif #endif pysam-0.23.0/linker_tests/000077500000000000000000000000001475062545500154505ustar00rootroot00000000000000pysam-0.23.0/linker_tests/link_pre_489/000077500000000000000000000000001475062545500176575ustar00rootroot00000000000000pysam-0.23.0/linker_tests/link_pre_489/PysamTestModule_link_pre_489/000077500000000000000000000000001475062545500252455ustar00rootroot00000000000000pysam-0.23.0/linker_tests/link_pre_489/PysamTestModule_link_pre_489/BuildRead.pyx000066400000000000000000000011451475062545500276430ustar00rootroot00000000000000from __future__ import absolute_import from pysam.libchtslib cimport bam1_t, bam_endpos from pysam.libcsamfile cimport aux_type2size from pysam.libcalignedsegment cimport AlignedSegment import pysam cpdef build_read(): cdef AlignedSegment read = pysam.AlignedSegment() read.query_name = "hello" read.query_sequence = "ACGT" read.reference_start = 10 read.cigarstring = "4M" # Test calling htslib function cdef bam1_t *calign = read._delegate print(bam_endpos(calign)) # Test calling pysam htslib_util function print(aux_type2size(12)) return read pysam-0.23.0/linker_tests/link_pre_489/PysamTestModule_link_pre_489/__init__.py000066400000000000000000000001241475062545500273530ustar00rootroot00000000000000from PysamTestModule_link_pre_489.BuildRead import build_read all = ["build_read"] pysam-0.23.0/linker_tests/link_pre_489/cy_build.py000066400000000000000000000056321475062545500220310ustar00rootroot00000000000000import os import re import sys try: from Cython.Distutils import build_ext except ImportError: from setuptools.command.build_ext import build_ext from distutils.extension import Extension from distutils.sysconfig import get_config_var, get_config_vars, get_python_lib, get_python_version from pkg_resources import Distribution if sys.platform == 'darwin': config_vars = get_config_vars() config_vars['LDSHARED'] = config_vars['LDSHARED'].replace('-bundle', '') config_vars['SHLIB_EXT'] = '.so' def is_pip_install(): if "_" in os.environ and os.environ["_"].endswith("pip"): return True if "pip-egg-info" in sys.argv: return True if re.search("/pip-.*-build/", __file__): return True return False class CyExtension(Extension): def __init__(self, *args, **kwargs): self._init_func = kwargs.pop("init_func", None) super().__init__(*args, **kwargs) def extend_includes(self, includes): self.include_dirs.extend(includes) def extend_macros(self, macros): self.define_macros.extend(macros) def extend_extra_objects(self, objs): self.extra_objects.extend(objs) class cy_build_ext(build_ext): def _get_egg_name(self): ei_cmd = self.get_finalized_command("egg_info") return Distribution( None, None, ei_cmd.egg_name, ei_cmd.egg_version, get_python_version(), self.distribution.has_ext_modules() and self.plat_name).egg_name() def build_extension(self, ext): if isinstance(ext, CyExtension) and ext._init_func: ext._init_func(ext) if not self.inplace: ext.library_dirs.append(os.path.join(self.build_lib, "pysam")) if sys.platform == 'darwin': # The idea is to give shared libraries an install name of the form # `@rpath/`, and to set the rpath equal to # @loader_path. This will allow Python packages to find the library # in the expected place, while still giving enough flexibility to # external applications to link against the library. relative_module_path = ext.name.replace(".", os.sep) + get_config_var('EXT_SUFFIX') library_path = os.path.join( "@rpath", os.path.basename(relative_module_path) ) if not ext.extra_link_args: ext.extra_link_args = [] ext.extra_link_args += ['-dynamiclib', '-rpath', '@loader_path', '-Wl,-headerpad_max_install_names', '-Wl,-install_name,%s' % library_path, '-Wl,-x'] else: if not ext.extra_link_args: ext.extra_link_args = [] ext.extra_link_args += ['-Wl,-rpath,$ORIGIN'] super().build_extension(ext) pysam-0.23.0/linker_tests/link_pre_489/setup.py000066400000000000000000000014121475062545500213670ustar00rootroot00000000000000import glob import sys import os from setuptools import setup, find_packages, Extension from cy_build import CyExtension as Extension, cy_build_ext as build_ext import pysam test_module_suffix = os.path.dirname(os.path.abspath(__file__)).split(os.sep)[-1] test_module_name = "PysamTestModule_{}".format(test_module_suffix) TestModule = Extension( "{}.BuildRead".format(test_module_name), ["{}/BuildRead.pyx".format(test_module_name)], include_dirs=pysam.get_include(), extra_link_args=pysam.get_libraries(), define_macros=pysam.get_defines(), ) setup( name=test_module_name, version='0.1', packages=find_packages(), package_dir={test_module_name: test_module_name}, ext_modules=[TestModule], cmdclass={'build_ext': build_ext}, ) pysam-0.23.0/linker_tests/link_pre_489/tests/000077500000000000000000000000001475062545500210215ustar00rootroot00000000000000pysam-0.23.0/linker_tests/link_pre_489/tests/test_module.py000066400000000000000000000005441475062545500237220ustar00rootroot00000000000000import unittest from PysamTestModule_link_pre_489 import build_read class TestModule(unittest.TestCase): def test_pass_if_module_can_be_called(self): read = build_read() self.assertEqual(read.query_name, "hello") self.assertEqual(read.query_sequence, "ACGT") if __name__ == "__main__": unittest.main() pysam-0.23.0/linker_tests/link_with_rpath/000077500000000000000000000000001475062545500206365ustar00rootroot00000000000000pysam-0.23.0/linker_tests/link_with_rpath/PysamTestModule_link_with_rpath/000077500000000000000000000000001475062545500272035ustar00rootroot00000000000000pysam-0.23.0/linker_tests/link_with_rpath/PysamTestModule_link_with_rpath/BuildRead.pyx000066400000000000000000000011451475062545500316010ustar00rootroot00000000000000from __future__ import absolute_import from pysam.libchtslib cimport bam1_t, bam_endpos from pysam.libcsamfile cimport aux_type2size from pysam.libcalignedsegment cimport AlignedSegment import pysam cpdef build_read(): cdef AlignedSegment read = pysam.AlignedSegment() read.query_name = "hello" read.query_sequence = "ACGT" read.reference_start = 10 read.cigarstring = "4M" # Test calling htslib function cdef bam1_t *calign = read._delegate print(bam_endpos(calign)) # Test calling pysam htslib_util function print(aux_type2size(12)) return read pysam-0.23.0/linker_tests/link_with_rpath/PysamTestModule_link_with_rpath/__init__.py000066400000000000000000000001271475062545500313140ustar00rootroot00000000000000from PysamTestModule_link_with_rpath.BuildRead import build_read all = ["build_read"] pysam-0.23.0/linker_tests/link_with_rpath/setup.py000066400000000000000000000017661475062545500223620ustar00rootroot00000000000000import glob import sys import os from setuptools import setup, find_packages, Extension from Cython.Distutils import build_ext import pysam test_module_suffix = os.path.dirname(os.path.abspath(__file__)).split(os.sep)[-1] test_module_name = "PysamTestModule_{}".format(test_module_suffix) pysam_libraries = pysam.get_libraries() pysam_libdirs, pysam_libs = zip(*[os.path.split(x) for x in pysam_libraries]) pysam_libdir = pysam_libdirs[0] # remove lib and .so pysam_libs = [x[3:-3] for x in pysam_libs] TestModule = Extension( "{}.BuildRead".format(test_module_name), ["{}/BuildRead.pyx".format(test_module_name)], include_dirs=pysam.get_include(), library_dirs=[pysam_libdir], libraries=pysam_libs, extra_link_args=['-Wl,-rpath,{}'.format(pysam_libdir)], language="C", ) setup( name=test_module_name, version='0.1', packages=find_packages(), package_dir={test_module_name: test_module_name}, ext_modules=[TestModule], cmdclass={'build_ext': build_ext}, ) pysam-0.23.0/linker_tests/link_with_rpath/tests/000077500000000000000000000000001475062545500220005ustar00rootroot00000000000000pysam-0.23.0/linker_tests/link_with_rpath/tests/test_module.py000066400000000000000000000005471475062545500247040ustar00rootroot00000000000000import unittest from PysamTestModule_link_with_rpath import build_read class TestModule(unittest.TestCase): def test_pass_if_module_can_be_called(self): read = build_read() self.assertEqual(read.query_name, "hello") self.assertEqual(read.query_sequence, "ACGT") if __name__ == "__main__": unittest.main() pysam-0.23.0/linker_tests/link_without_rpath/000077500000000000000000000000001475062545500213665ustar00rootroot00000000000000pysam-0.23.0/linker_tests/link_without_rpath/PysamTestModule_link_without_rpath/000077500000000000000000000000001475062545500304635ustar00rootroot00000000000000pysam-0.23.0/linker_tests/link_without_rpath/PysamTestModule_link_without_rpath/BuildRead.pyx000066400000000000000000000011451475062545500330610ustar00rootroot00000000000000from __future__ import absolute_import from pysam.libchtslib cimport bam1_t, bam_endpos from pysam.libcsamfile cimport aux_type2size from pysam.libcalignedsegment cimport AlignedSegment import pysam cpdef build_read(): cdef AlignedSegment read = pysam.AlignedSegment() read.query_name = "hello" read.query_sequence = "ACGT" read.reference_start = 10 read.cigarstring = "4M" # Test calling htslib function cdef bam1_t *calign = read._delegate print(bam_endpos(calign)) # Test calling pysam htslib_util function print(aux_type2size(12)) return read pysam-0.23.0/linker_tests/link_without_rpath/PysamTestModule_link_without_rpath/__init__.py000066400000000000000000000001321475062545500325700ustar00rootroot00000000000000from PysamTestModule_link_without_rpath.BuildRead import build_read all = ["build_read"] pysam-0.23.0/linker_tests/link_without_rpath/setup.py000066400000000000000000000016721475062545500231060ustar00rootroot00000000000000import glob import sys import os from setuptools import setup, find_packages, Extension from Cython.Distutils import build_ext import pysam test_module_suffix = os.path.dirname(os.path.abspath(__file__)).split(os.sep)[-1] test_module_name = "PysamTestModule_{}".format(test_module_suffix) pysam_libraries = pysam.get_libraries() pysam_libdirs, pysam_libs = zip(*[os.path.split(x) for x in pysam_libraries]) pysam_libdir = pysam_libdirs[0] # remove lib and .so pysam_libs = [x[3:-3] for x in pysam_libs] TestModule = Extension( "{}.BuildRead".format(test_module_name), ["{}/BuildRead.pyx".format(test_module_name)], include_dirs=pysam.get_include(), library_dirs=[pysam_libdir], libraries=pysam_libs, language="C", ) setup( name=test_module_name, version='0.1', packages=find_packages(), package_dir={test_module_name: test_module_name}, ext_modules=[TestModule], cmdclass={'build_ext': build_ext}, ) pysam-0.23.0/linker_tests/link_without_rpath/tests/000077500000000000000000000000001475062545500225305ustar00rootroot00000000000000pysam-0.23.0/linker_tests/link_without_rpath/tests/test_module.py000066400000000000000000000005521475062545500254300ustar00rootroot00000000000000import unittest from PysamTestModule_link_without_rpath import build_read class TestModule(unittest.TestCase): def test_pass_if_module_can_be_called(self): read = build_read() self.assertEqual(read.query_name, "hello") self.assertEqual(read.query_sequence, "ACGT") if __name__ == "__main__": unittest.main() pysam-0.23.0/pyproject.toml000066400000000000000000000017501475062545500156610ustar00rootroot00000000000000[project] name = "pysam" description = "Package for reading, manipulating, and writing genomic data" license = { text = "MIT License" } authors = [ { name = "Andreas Heger", email = "andreas.heger@gmail.com"} ] requires-python = ">=3.6" dynamic = [ "classifiers", "readme", "version", ] [project.urls] "Documentation" = "https://pysam.readthedocs.io/" "Release notes" = "https://pysam.readthedocs.io/en/stable/release.html" [build-system] requires = ["setuptools>=59.0", "Cython>=0.29.12,<4"] build-backend = "setuptools.build_meta:__legacy__" [tool.cibuildwheel] before-all = "{project}/devtools/install-prerequisites.sh" # Necessary until we build libhts.a out-of-tree from within build_temp before-build = "make -C {project}/htslib distclean" test-requires = ["pytest"] test-command = "REF_PATH=: pytest {project}/tests" [tool.tox] legacy_tox_ini = """ [tox] envlist = py36, py311 [testenv] deps = pytest setenv = REF_PATH=: commands = pytest tests """ pysam-0.23.0/pysam/000077500000000000000000000000001475062545500140735ustar00rootroot00000000000000pysam-0.23.0/pysam/Pileup.py000066400000000000000000000213731475062545500157110ustar00rootroot00000000000000'''Tools for working with files in the samtools pileup -c format.''' import collections import pysam PileupSubstitution = collections.namedtuple("PileupSubstitution", ( "chromosome", "pos", "reference_base", "genotype", "consensus_quality", "snp_quality", "mapping_quality", "coverage", "read_bases", "base_qualities")) PileupIndel = collections.namedtuple("PileupIndel", ( "chromosome", "pos", "reference_base", "genotype", "consensus_quality", "snp_quality", "mapping_quality", "coverage", "first_allele", "second_allele", "reads_first", "reads_second", "reads_diff")) def iterate(infile): '''iterate over ``samtools pileup -c`` formatted file. *infile* can be any iterator over a lines. The function yields named tuples of the type :class:`pysam.Pileup.PileupSubstitution` or :class:`pysam.Pileup.PileupIndel`. .. note:: The parser converts to 0-based coordinates ''' conv_subst = (str, lambda x: int(x) - 1, str, str, int, int, int, int, str, str) conv_indel = (str, lambda x: int(x) - 1, str, str, int, int, int, int, str, str, int, int, int) for line in infile: d = line[:-1].split() if d[2] == "*": try: yield PileupIndel(*[x(y) for x, y in zip(conv_indel, d)]) except TypeError: raise pysam.SamtoolsError("parsing error in line: `%s`" % line) else: try: yield PileupSubstitution(*[x(y) for x, y in zip(conv_subst, d)]) except TypeError: raise pysam.SamtoolsError("parsing error in line: `%s`" % line) ENCODE_GENOTYPE = { 'A': 'A', 'C': 'C', 'G': 'G', 'T': 'T', 'AA': 'A', 'CC': 'C', 'GG': 'G', 'TT': 'T', 'UU': 'U', 'AG': 'r', 'GA': 'R', 'CT': 'y', 'TC': 'Y', 'AC': 'm', 'CA': 'M', 'GT': 'k', 'TG': 'K', 'CG': 's', 'GC': 'S', 'AT': 'w', 'TA': 'W', } DECODE_GENOTYPE = { 'A': 'AA', 'C': 'CC', 'G': 'GG', 'T': 'TT', 'r': 'AG', 'R': 'AG', 'y': 'CT', 'Y': 'CT', 'm': 'AC', 'M': 'AC', 'k': 'GT', 'K': 'GT', 's': 'CG', 'S': 'CG', 'w': 'AT', 'W': 'AT', } # ------------------------------------------------------------ def encodeGenotype(code): '''encode genotypes like GG, GA into a one-letter code. The returned code is lower case if code[0] < code[1], otherwise it is uppercase. ''' return ENCODE_GENOTYPE[code.upper()] def decodeGenotype(code): '''decode single letter genotypes like m, M into two letters. This is the reverse operation to :meth:`encodeGenotype`. ''' return DECODE_GENOTYPE[code] def translateIndelGenotypeFromVCF(vcf_genotypes, ref): '''translate indel from vcf to pileup format.''' # indels def getPrefix(s1, s2): '''get common prefix of strings s1 and s2.''' n = min(len(s1), len(s2)) for x in range(n): if s1[x] != s2[x]: return s1[:x] return s1[:n] def getSuffix(s1, s2): '''get common sufix of strings s1 and s2.''' n = min(len(s1), len(s2)) if s1[-1] != s2[-1]: return "" for x in range(-2, -n - 1, -1): if s1[x] != s2[x]: return s1[x + 1:] return s1[-n:] def getGenotype(variant, ref): if variant == ref: return "*", 0 if len(ref) > len(variant): # is a deletion if ref.startswith(variant): return "-%s" % ref[len(variant):], len(variant) - 1 elif ref.endswith(variant): return "-%s" % ref[:-len(variant)], -1 else: prefix = getPrefix(ref, variant) suffix = getSuffix(ref, variant) shared = len(prefix) + len(suffix) - len(variant) # print "-", prefix, suffix, ref, variant, shared, len(prefix), len(suffix), len(ref) if shared < 0: raise ValueError() return "-%s" % ref[len(prefix):-(len(suffix) - shared)], len(prefix) - 1 elif len(ref) < len(variant): # is an insertion if variant.startswith(ref): return "+%s" % variant[len(ref):], len(ref) - 1 elif variant.endswith(ref): return "+%s" % variant[:len(ref)], 0 else: prefix = getPrefix(ref, variant) suffix = getSuffix(ref, variant) shared = len(prefix) + len(suffix) - len(ref) if shared < 0: raise ValueError() return "+%s" % variant[len(prefix):-(len(suffix) - shared)], len(prefix) else: assert 0, "snp?" # in pileup, the position refers to the base # after the coordinate, hence subtract 1 # pos -= 1 genotypes, offsets = [], [] is_error = True for variant in vcf_genotypes: try: g, offset = getGenotype(variant, ref) except ValueError: break genotypes.append(g) if g != "*": offsets.append(offset) else: is_error = False if is_error: raise ValueError() assert len(set(offsets)) == 1, "multiple offsets for indel" offset = offsets[0] genotypes = "/".join(genotypes) return genotypes, offset def vcf2pileup(vcf, sample): '''convert vcf record to pileup record.''' chromosome = vcf.contig pos = vcf.pos reference = vcf.ref allelles = [reference] + vcf.alt data = vcf[sample] # get genotype genotypes = data["GT"] if len(genotypes) > 1: raise ValueError("only single genotype per position, %s" % (str(vcf))) genotypes = genotypes[0] # not a variant if genotypes[0] == ".": return None genotypes = [allelles[int(x)] for x in genotypes if x != "/"] # snp_quality is "genotype quality" snp_quality = consensus_quality = data.get("GQ", [0])[0] mapping_quality = vcf.info.get("MQ", [0])[0] coverage = data.get("DP", 0) if len(reference) > 1 or max([len(x) for x in vcf.alt]) > 1: # indel genotype, offset = translateIndelGenotypeFromVCF(genotypes, reference) return PileupIndel(chromosome, pos + offset, "*", genotype, consensus_quality, snp_quality, mapping_quality, coverage, genotype, "<" * len(genotype), 0, 0, 0) else: genotype = encodeGenotype("".join(genotypes)) read_bases = "" base_qualities = "" return PileupSubstitution(chromosome, pos, reference, genotype, consensus_quality, snp_quality, mapping_quality, coverage, read_bases, base_qualities) def iterate_from_vcf(infile, sample): '''iterate over a vcf-formatted file. *infile* can be any iterator over a lines. The function yields named tuples of the type :class:`pysam.Pileup.PileupSubstitution` or :class:`pysam.Pileup.PileupIndel`. Positions without a snp will be skipped. This method is wasteful and written to support same legacy code that expects samtools pileup output. Better use the vcf parser directly. ''' vcf = pysam.VCF() vcf.connect(infile) if sample not in vcf.getsamples(): raise KeyError("sample %s not vcf file") for row in vcf.fetch(): result = vcf2pileup(row, sample) if result: yield result pysam-0.23.0/pysam/VCF.py.obsolete000066400000000000000000001350261475062545500167050ustar00rootroot00000000000000# # Code to read, write and edit VCF files # # VCF lines are encoded as a dictionary with these keys (note: all lowercase): # 'chrom': string # 'pos': integer # 'id': string # 'ref': string # 'alt': list of strings # 'qual': integer # 'filter': None (missing value), or list of keys (strings); empty list parsed as ["PASS"] # 'info': dictionary of values (see below) # 'format': list of keys (strings) # sample keys: dictionary of values (see below) # # The sample keys are accessible through vcf.getsamples() # # A dictionary of values contains value keys (defined in ##INFO or ##FORMAT lines) which map # to a list, containign integers, floats, strings, or characters. Missing values are replaced # by a particular value, often -1 or . # # Genotypes are not stored as a string, but as a list of 1 or 3 elements (for haploid and diploid samples), # the first (and last) the integer representing an allele, and the second the separation character. # Note that there is just one genotype per sample, but for consistency the single element is stored in a list. # # Header lines other than ##INFO, ##FORMAT and ##FILTER are stored as (key, value) pairs and are accessible # through getheader() # # The VCF class can be instantiated with a 'regions' variable consisting of tuples (chrom,start,end) encoding # 0-based half-open segments. Only variants with a position inside the segment will be parsed. A regions # parser is available under parse_regions. # # When instantiated, a reference can be passed to the VCF class. This may be any class that supports a # fetch(chrom, start, end) method. # # # # NOTE: the position that is returned to Python is 0-based, NOT 1-based as in the VCF file. # # # # TODO: # only v4.0 writing is complete; alleles are not converted to v3.3 format # from collections import namedtuple, defaultdict from operator import itemgetter import sys, re, copy, bisect import pysam gtsRegEx = re.compile("[|/\\\\]") alleleRegEx = re.compile('^[ACGTN]+$') # Utility function. Uses 0-based coordinates def get_sequence(chrom, start, end, fa): # obtain sequence from .fa file, without truncation if end<=start: return "" if not fa: return "N"*(end-start) if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper() sequence = fa.fetch(chrom, start, end).upper() if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence)) return sequence # Utility function. Parses a region string def parse_regions( string ): result = [] for r in string.split(','): elts = r.split(':') chrom, start, end = elts[0], 0, 3000000000 if len(elts)==1: pass elif len(elts)==2: if len(elts[1])>0: ielts = elts[1].split('-') if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r) try: start, end = int(ielts[0])-1, int(ielts[1]) except: raise ValueError("Don't understand region string '%s'" % r) else: raise ValueError("Don't understand region string '%s'" % r) result.append( (chrom,start,end) ) return result FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue') ########################################################################################################### # # New class # ########################################################################################################### class VCFRecord(object): '''vcf record. initialized from data and vcf meta ''' data = None vcf = None def __init__(self, data, vcf): self.data, self.vcf = data, vcf if len(data) != len(self.vcf._samples): self.error(str(data), self.BAD_NUMBER_OF_COLUMNS, "expected %s for %s samples (%s), got %s" % \ (len(self.vcf._samples), len(self.vcf._samples), self.vcf._samples, len(data))) property contig: def __get__( self ): return self.data[0] property pos: def __get__( self ): return self.data.pos property id: def __get__( self ): return self.data[2] property ref: def __get__(self ): # note: gerton substitutes reference if it can be fixed. return self.data[3].upper() property alt: def __get__(self): # convert v3.3 to v4.0 alleles below alt = self.data[4] if alt == ".": alt = [] else: alt = alt.upper().split(',') return alt property qual: def __get__(self): qual = self.data[5] if qual == ".": qual = -1 else: try: qual = float(qual) except: self.error(line,self.QUAL_NOT_NUMERICAL) property filter: def __get__(self): # postpone checking that filters exist. Encode missing filter or no filtering as empty list if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = [] else: filter = cols[6].split(';') return filter property info: def __get__(self): col = self.data[7] # dictionary of keys, and list of values info = {} if col != ".": for blurp in col.split(';'): elts = blurp.split('=') if len(elts) == 1: v = None elif len(elts) == 2: v = elts[1] else: self.error(str(self.data),self.ERROR_INFO_STRING) info[elts[0]] = self.parse_formatdata(elts[0], v, self.vcf._info, line) return info property format: def __get__(self): return self.data[8].split(':') def __getitem__(self, key): # parse sample columns values = self.data[self.vcf._sample2column[key]].split(':') alt = self.alt format = self.format if len(values) > len(format): self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format))) result = {} for idx in range(len(format)): expected = self.vcf.get_expected(format[idx], self.vcf._format, alt) if idx < len(values): value = values[idx] else: if expected == -1: value = "." else: value = ",".join(["."]*expected) result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, line) if expected != -1 and len(result[format[idx]]) != expected: self.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS, "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]])) if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]])) result[format[idx]] = result[format[idx]][:expected] return result def __str__(self): return str(self.data) class VCF: # types NT_UNKNOWN = 0 NT_NUMBER = 1 NT_ALLELES = 2 NT_NR_ALLELES = 3 NT_GENOTYPES = 4 NT_PHASED_GENOTYPES = 5 _errors = { 0:"UNKNOWN_FORMAT_STRING:Unknown file format identifier", 1:"BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string", 2:"BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s", 3:"BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)", 4:"POS_NOT_NUMERICAL:Position column is not numerical", 5:"UNKNOWN_CHAR_IN_REF:Unknown character in reference field", 6:"V33_BAD_REF:Reference should be single-character in v3.3 VCF", 7:"V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF", 8:"POS_NOT_POSITIVE:Position field must be >0", 9:"QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'", 10:"ERROR_INFO_STRING:Error while parsing info field", 11:"ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)", 12:"ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s", 13:"ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string", 14:"FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header", 15:"FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header", 16:"BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)", 17:"BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)", 18:"BAD_GENOTYPE:Cannot parse genotype (%s)", 19:"V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)", 20:"MISSING_REF:Reference allele missing", 21:"V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)", 22:"V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets", 23:"FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes", 24:"V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields", 25:"HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs", 26:"WRONG_REF:Wrong reference %s", 27:"ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data", 28:"BAD_CHR_TAG:Error calculating chr tag for %s", 29:"ZERO_LENGTH_ALLELE:Found zero-length allele", 30:"MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base" } # tag-value pairs; tags are not unique; does not include fileformat, INFO, FILTER or FORMAT fields _header = [] # version number; 33=v3.3; 40=v4.0 _version = 40 # info, filter and format data _info = {} _filter = {} _format = {} # header; and required columns _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"] _samples = [] # control behaviour _ignored_errors = set([11]) # ERROR_UNKNOWN_KEY _warn_errors = set([]) _leftalign = False # reference sequence _reference = None # regions to include; None includes everything _regions = None # statefull stuff _lineno = -1 _line = None _lines = None def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False): # make error identifiers accessible by name for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id if _copy != None: self._leftalign = _copy._leftalign self._header = _copy._header[:] self._version = _copy._version self._info = copy.deepcopy(_copy._info) self._filter = copy.deepcopy(_copy._filter) self._format = copy.deepcopy(_copy._format) self._samples = _copy._samples[:] self._sample2column = copy.deepcopy(_copy._sample2column) self._ignored_errors = copy.deepcopy(_copy._ignored_errors) self._warn_errors = copy.deepcopy(_copy._warn_errors) self._reference = _copy._reference self._regions = _copy._regions if reference: self._reference = reference if regions: self._regions = regions if leftalign: self._leftalign = leftalign self._lines = lines def error(self,line,error,opt=None): if error in self._ignored_errors: return errorlabel, errorstring = self._errors[error].split(':') if opt: errorstring = errorstring % opt errwarn = ["Error","Warning"][error in self._warn_errors] sys.stderr.write("Line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring)) if error in self._warn_errors: return raise ValueError(errorstring) def parse_format(self,line,format,filter=False): if self._version >= 40: if not format.startswith('<'): self.error(line,self.V40_MISSING_ANGLE_BRACKETS) format = "<"+format if not format.endswith('>'): self.error(line,self.V40_MISSING_ANGLE_BRACKETS) format += ">" format = format[1:-1] data = {'id':None,'number':None,'type':None,'descr':None} idx = 0 while len(format.strip())>0: elts = format.strip().split(',') first, rest = elts[0], ','.join(elts[1:]) if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')): if self._version >= 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS) if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) first = ["ID=","Number=","Type=","Description="][idx] + first if first.startswith('ID='): data['id'] = first.split('=')[1] elif first.startswith('Number='): data['number'] = first.split('=')[1] elif first.startswith('Type='): data['type'] = first.split('=')[1] elif first.startswith('Description='): elts = format.split('"') if len(elts)<3: self.error(line,self.FORMAT_MISSING_QUOTES) elts = first.split('=') + [rest] data['descr'] = elts[1] rest = '"'.join(elts[2:]) if rest.startswith(','): rest = rest[1:] else: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) format = rest idx += 1 if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) if not data['descr']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) data['descr'] = '' if not data['type'] and not data['number']: # fine, ##filter format return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.') if not data['type'] in ["Integer","Float","Character","String","Flag"]: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # I would like a missing-value field, but it isn't there if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value else: data['missing'] = '.' if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) try: n = int(data['number']) t = self.NT_NUMBER except ValueError: n = -1 if data['number'] == '.': t = self.NT_UNKNOWN elif data['number'] == '#alleles': t = self.NT_ALLELES elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES elif data['number'] == '#genotypes': t = self.NT_GENOTYPES elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES else: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing']) def format_format( self, fmt, filter=False ): values = [('ID',fmt.id)] if fmt.number != None and not filter: if fmt.numbertype == self.NT_UNKNOWN: nmb = "." elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number) elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles" elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles" elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes" elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes" else: raise ValueError("Unknown number type encountered: %s" % fmt.numbertype) values.append( ('Number',nmb) ) values.append( ('Type', fmt.type) ) values.append( ('Description', '"' + fmt.description + '"') ) if self._version == 33: format = ",".join(v for k,v in values) else: format = "<" + (",".join( "%s=%s" % (k,v) for (k,v) in values )) + ">" return format def get_expected(self, format, formatdict, alt): fmt = formatdict[format] if fmt.numbertype == self.NT_UNKNOWN: return -1 if fmt.numbertype == self.NT_NUMBER: return fmt.number if fmt.numbertype == self.NT_ALLELES: return len(alt)+1 if fmt.numbertype == self.NT_NR_ALLELES: return len(alt) if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2 if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1) return 0 def _add_definition(self, formatdict, key, data, line ): if key in formatdict: return self.error(line,self.ERROR_UNKNOWN_KEY,key) if data == None: formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".") return if data == []: data = [""] # unsure what type -- say string if type(data[0]) == type(0.0): formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None) return if type(data[0]) == type(0): formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None) return formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".") # todo: trim trailing missing values def format_formatdata( self, data, format, key=True, value=True, separator=":" ): output, sdata = [], [] if type(data) == type([]): # for FORMAT field, make data with dummy values d = {} for k in data: d[k] = [] data = d # convert missing values; and silently add definitions if required for k in data: self._add_definition( format, k, data[k], "(output)" ) for idx,v in enumerate(data[k]): if v == format[k].missingvalue: data[k][idx] = "." # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string for k in data: if k != 'GT': sdata.append( (k,data[k]) ) sdata.sort() if 'GT' in data: sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata for k,v in sdata: if v == []: v = None if key and value: if v != None: output.append( k+"="+','.join(map(str,v)) ) else: output.append( k ) elif key: output.append(k) elif value: if v != None: output.append( ','.join(map(str,v)) ) else: output.append( "." ) # should not happen # snip off trailing missing data while len(output) > 1: last = output[-1].replace(',','').replace('.','') if len(last)>0: break output = output[:-1] return separator.join(output) def enter_default_format(self): for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'), FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1), FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1), FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.')]: if f.id not in self._format: self._format[f.id] = f def parse_header( self, line ): assert line.startswith('##') elts = line[2:].split('=') key = elts[0].strip() value = '='.join(elts[1:]).strip() if key == "fileformat": if value == "VCFv3.3": self._version = 33 elif value == "VCFv4.0": self._version = 40 elif value == "VCFv4.1": self._version = 41 else: self.error(line,self.UNKNOWN_FORMAT_STRING) elif key == "INFO": f = self.parse_format(line, value) self._info[ f.id ] = f elif key == "FILTER": f = self.parse_format(line, value, filter=True) self._filter[ f.id ] = f elif key == "FORMAT": f = self.parse_format(line, value) self._format[ f.id ] = f else: # keep other keys in the header field self._header.append( (key,value) ) def write_header( self, stream ): stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10)) for key,value in self._header: stream.write("##%s=%s\n" % (key,value)) for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]: for f in var.itervalues(): stream.write("##%s=%s\n" % (label,self.format_format(f,filter=(label=="FILTER")))) def parse_heading( self, line ): assert line.startswith('#') assert not line.startswith('##') headings = line[1:].split('\t') if len(headings)==1 and len(line[1:].split()) >= 9: self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS) headings = line[1:].split() for i,s in enumerate(self._required): if len(headings)<=i or headings[i] != s: if len(headings) <= i: err = "(%sth entry not found)" % (i+1) else: err = "(found %s, expected %s)" % (headings[i],s) #self.error(line,self.BADLY_FORMATTED_HEADING,err) # allow FORMAT column to be absent if len(headings) == 8: headings.append("FORMAT") else: self.error(line,self.BADLY_FORMATTED_HEADING,err) self._samples = headings[9:] self._sample2column = dict( [(y,x) for x,y in enumerate( self._samples ) ] ) def write_heading( self, stream ): stream.write("#" + "\t".join(self._required + self._samples) + "\n") def convertGT(self, GTstring): if GTstring == ".": return ["."] try: gts = gtsRegEx.split(GTstring) if len(gts) == 1: return [int(gts[0])] if len(gts) != 2: raise ValueError() if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]] return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])] except ValueError: self.error(self._line,self.BAD_GENOTYPE,GTstring) return [".","|","."] def convertGTback(self, GTdata): return ''.join(map(str,GTdata)) def parse_formatdata( self, key, value, formatdict, line ): # To do: check that the right number of values is present f = formatdict.get(key,None) if f == None: self._add_definition(formatdict, key, value, line ) f = formatdict[key] if f.type == "Flag": if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE) return [] values = value.split(',') # deal with trailing data in some early VCF files if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1: self.error(line,self.ERROR_TRAILING_DATA,values[-1]) values[-1] = values[-1].split(';')[0] if f.type == "Integer": for idx,v in enumerate(values): try: if v == ".": values[idx] = f.missingvalue else: values[idx] = int(v) except: self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,values) return [0] * len(values) return values elif f.type == "String": self._line = line if f.id == "GT": values = map( self.convertGT, values ) return values elif f.type == "Character": for v in values: if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR) return values elif f.type == "Float": for idx,v in enumerate(values): if v == ".": values[idx] = f.missingvalue try: return map(float,values) except: self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,values) return [0.0] * len(values) else: # can't happen self.error(line,self.ERROR_INFO_STRING) def inregion(self, chrom, pos): if not self._regions: return True for r in self._regions: if r[0] == chrom and r[1] <= pos < r[2]: return True return False def parse_data( self, line, lineparse=False ): cols = line.split('\t') if len(cols) != len(self._samples)+9: # gracefully deal with absent FORMAT column if len(cols) == 8 and len(self._samples)==0: cols.append("") else: self.error(line, self.BAD_NUMBER_OF_COLUMNS, "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols))) chrom = cols[0] # get 0-based position try: pos = int(cols[1])-1 except: self.error(line,self.POS_NOT_NUMERICAL) if pos < 0: self.error(line,self.POS_NOT_POSITIVE) # implement filtering if not self.inregion(chrom,pos): return None # end of first-pass parse for sortedVCF if lineparse: return chrom, pos, line id = cols[2] ref = cols[3].upper() if ref == ".": self.error(line,self.MISSING_REF) if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference) else: ref = "" else: for c in ref: if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF) if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference) # make sure reference is sane if self._reference: left = max(0,pos-100) faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference) faref = faref_leftflank[pos-left:] if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref)) ref = faref # convert v3.3 to v4.0 alleles below if cols[4] == ".": alt = [] else: alt = cols[4].upper().split(',') if cols[5] == ".": qual = -1 else: try: qual = float(cols[5]) except: self.error(line,self.QUAL_NOT_NUMERICAL) # postpone checking that filters exist. Encode missing filter or no filtering as empty list if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = [] else: filter = cols[6].split(';') # dictionary of keys, and list of values info = {} if cols[7] != ".": for blurp in cols[7].split(';'): elts = blurp.split('=') if len(elts) == 1: v = None elif len(elts) == 2: v = elts[1] else: self.error(line,self.ERROR_INFO_STRING) info[elts[0]] = self.parse_formatdata(elts[0], v, self._info, line) # Gracefully deal with absent FORMAT column if cols[8] == "": format = [] else: format = cols[8].split(':') # check: all filters are defined for f in filter: if f not in self._filter: self.error(line,self.FILTER_NOT_DEFINED, f) # check: format fields are defined for f in format: if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f) # convert v3.3 alleles if self._version == 33: if len(ref) != 1: self.error(line,self.V33_BAD_REF) newalts = [] have_deletions = False for a in alt: if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference elif a.startswith('D'): # allow D and D have_deletions = True try: l = int(a[1:]) # throws ValueError if sequence if len(ref) < l: # add to reference if necessary addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference) ref += addns for i,na in enumerate(newalts): newalts[i] = na+addns a = ref[l:] # new deletion, deleting pos...pos+l except ValueError: s = a[1:] if len(ref) < len(s): # add Ns to reference if necessary addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference) if not s.endswith(addns) and addns != 'N'*len(addns): self.error(line,self.V33_UNMATCHED_DELETION, "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference))) ref += addns for i,na in enumerate(newalts): newalts[i] = na+addns a = ref[len(s):] # new deletion, deleting from pos else: self.error(line,self.V33_BAD_ALLELE) newalts.append(a) alt = newalts # deletion alleles exist, add dummy 1st reference allele, and account for leading base if have_deletions: if pos == 0: # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1 addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference) ref += addn alt = [allele+addn for allele in alt] else: addn = get_sequence(chrom,pos-1,pos,self._reference) ref = addn + ref alt = [addn + allele for allele in alt] pos -= 1 else: # format v4.0 -- just check for nucleotides for allele in alt: if not alleleRegEx.match(allele): self.error(line,self.V40_BAD_ALLELE,allele) # check for leading nucleotide in indel calls for allele in alt: if len(allele) != len(ref): if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE) if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper(): self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE) # trim trailing bases in alleles for i in range(1,min(len(ref),min(map(len,alt)))): if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): break ref, alt = ref[:-1], [allele[:-1] for allele in alt] # left-align alleles, if a reference is available if self._leftalign and self._reference: while left < pos: movable = True for allele in alt: if len(allele) > len(ref): longest, shortest = allele, ref else: longest, shortest = ref, allele if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper(): movable = False if longest[-1].upper() != longest[len(shortest)-1].upper(): movable = False if not movable: break ref = ref[:-1] alt = [allele[:-1] for allele in alt] if min(len(allele) for allele in alt) == 0 or len(ref) == 0: ref = faref_leftflank[pos-left-1] + ref alt = [faref_leftflank[pos-left-1] + allele for allele in alt] pos -= 1 # parse sample columns samples = [] for sample in cols[9:]: dict = {} values = sample.split(':') if len(values) > len(format): self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format))) for idx in range(len(format)): expected = self.get_expected(format[idx], self._format, alt) if idx < len(values): value = values[idx] else: if expected == -1: value = "." else: value = ",".join(["."]*expected) dict[format[idx]] = self.parse_formatdata(format[idx], value, self._format, line) if expected != -1 and len(dict[format[idx]]) != expected: self.error(line,self.BAD_NUMBER_OF_PARAMETERS, "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]])) if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]])) dict[format[idx]] = dict[format[idx]][:expected] samples.append( dict ) # done d = {'chrom':chrom, 'pos':pos, # return 0-based position 'id':id, 'ref':ref, 'alt':alt, 'qual':qual, 'filter':filter, 'info':info, 'format':format} for key,value in zip(self._samples,samples): d[key] = value return d def write_data(self, stream, data): required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples for k in required: if k not in data: raise ValueError("Required key %s not found in data" % str(k)) if data['alt'] == []: alt = "." else: alt = ",".join(data['alt']) if data['filter'] == None: filter = "." elif data['filter'] == []: if self._version == 33: filter = "0" else: filter = "PASS" else: filter = ';'.join(data['filter']) if data['qual'] == -1: qual = "." else: qual = str(data['qual']) output = [data['chrom'], str(data['pos']+1), # change to 1-based position data['id'], data['ref'], alt, qual, filter, self.format_formatdata( data['info'], self._info, separator=";" ), self.format_formatdata( data['format'], self._format, value=False ) ] for s in self._samples: output.append( self.format_formatdata( data[s], self._format, key=False ) ) stream.write( "\t".join(output) + "\n" ) def _parse_header(self, stream): self._lineno = 0 for line in stream: self._lineno += 1 if line.startswith('##'): self.parse_header( line.strip() ) elif line.startswith('#'): self.parse_heading( line.strip() ) self.enter_default_format() else: break return line def _parse(self, line, stream): if len(line.strip()) > 0: d = self.parse_data( line.strip() ) if d: yield d for line in stream: self._lineno += 1 if self._lines and self._lineno > self._lines: raise StopIteration d = self.parse_data( line.strip() ) if d: yield d ###################################################################################################### # # API follows # ###################################################################################################### def getsamples(self): """ List of samples in VCF file """ return self._samples def setsamples(self,samples): """ List of samples in VCF file """ self._samples = samples def getheader(self): """ List of header key-value pairs (strings) """ return self._header def setheader(self,header): """ List of header key-value pairs (strings) """ self._header = header def getinfo(self): """ Dictionary of ##INFO tags, as VCF.FORMAT values """ return self._info def setinfo(self,info): """ Dictionary of ##INFO tags, as VCF.FORMAT values """ self._info = info def getformat(self): """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """ return self._format def setformat(self,format): """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """ self._format = format def getfilter(self): """ Dictionary of ##FILTER tags, as VCF.FORMAT values """ return self._filter def setfilter(self,filter): """ Dictionary of ##FILTER tags, as VCF.FORMAT values """ self._filter = filter def setversion(self, version): if version not in [33,40,41]: raise ValueError("Can only handle v3.3, v4.0 and v4.1 VCF files") self._version = version def setregions(self, regions): self._regions = regions def setreference(self, ref): """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """ self._reference = ref def ignoreerror(self, errorstring): try: self._ignored_errors.add(self.__dict__[errorstring]) except KeyError: raise ValueError("Invalid error string: %s" % errorstring) def warnerror(self, errorstring): try: self._warn_errors.add(self.__dict__[errorstring]) except KeyError: raise ValueError("Invalid error string: %s" % errorstring) def parse(self, stream): """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """ last_line = self._parse_header(stream) # now return a generator that does the actual work. In this way the pre-processing is done # before the first piece of data is yielded return self._parse(last_line, stream) def write(self, stream, datagenerator): """ Writes a VCF file to a stream, using a data generator (or list) """ self.write_header(stream) self.write_heading(stream) for data in datagenerator: self.write_data(stream,data) def writeheader(self, stream): """ Writes a VCF header """ self.write_header(stream) self.write_heading(stream) def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2): """ Utility function: compares two calls for equality """ # a variant should always be assigned to a unique position, one base before # the leftmost position of the alignment gap. If this rule is implemented # correctly, the two positions must be equal for the calls to be identical. if pos1 != pos2: return False # from both calls, trim rightmost bases when identical. Do this safely, i.e. # only when the reference bases are not Ns while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]: ref1 = ref1[:-1] alt1 = alt1[:-1] while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]: ref2 = ref2[:-1] alt2 = alt2[:-1] # now, the alternative alleles must be identical return alt1 == alt2 ########################################################################################################### ########################################################################################################### ## API functions added by Andreas ########################################################################################################### def connect( self, filename ): '''connect to tabix file.''' self.tabixfile = pysam.Tabixfile( filename ) self._parse_header(self.tabixfile.header) def fetch(self, reference = None, start = None, end = None, region = None ): """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """ iter = self.tabixfile.fetch( reference, start, end, region, parser = pysam.asVCF() ) for x in iter: yield VCFRecord( x, self ) def validate( self, record ): '''validate vcf record. returns a validated record. ''' chrom, pos = record.chrom, record.pos # check reference ref = record.ref if ref == ".": self.error(str(record),self.MISSING_REF) if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference) else: ref = "" else: for c in ref: if c not in "ACGTN": self.error(str(record),self.UNKNOWN_CHAR_IN_REF) if "N" in ref: ref = get_sequence(chrom, pos, pos+len(ref), self._reference) # make sure reference is sane if self._reference: left = max(0,self.pos-100) faref_leftflank = get_sequence(chrom,left,self.pos+len(ref),self._reference) faref = faref_leftflank[pos-left:] if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref)) ref = faref # check: format fields are defined for f in record.format: if f not in self._format: self.error(str(record),self.FORMAT_NOT_DEFINED, f) # check: all filters are defined for f in record.filter: if f not in self._filter: self.error(str(record),self.FILTER_NOT_DEFINED, f) # convert v3.3 alleles if self._version == 33: if len(ref) != 1: self.error(line,self.V33_BAD_REF) newalts = [] have_deletions = False for a in alt: if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference elif a.startswith('D'): # allow D and D have_deletions = True try: l = int(a[1:]) # throws ValueError if sequence if len(ref) < l: # add to reference if necessary addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference) ref += addns for i,na in enumerate(newalts): newalts[i] = na+addns a = ref[l:] # new deletion, deleting pos...pos+l except ValueError: s = a[1:] if len(ref) < len(s): # add Ns to reference if necessary addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference) if not s.endswith(addns) and addns != 'N'*len(addns): self.error(line,self.V33_UNMATCHED_DELETION, "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference))) ref += addns for i,na in enumerate(newalts): newalts[i] = na+addns a = ref[len(s):] # new deletion, deleting from pos else: self.error(line,self.V33_BAD_ALLELE) newalts.append(a) alt = newalts # deletion alleles exist, add dummy 1st reference allele, and account for leading base if have_deletions: if pos == 0: # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1 addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference) ref += addn alt = [allele+addn for allele in alt] else: addn = get_sequence(chrom,pos-1,pos,self._reference) ref = addn + ref alt = [addn + allele for allele in alt] pos -= 1 else: # format v4.0 -- just check for nucleotides for allele in alt: if not alleleRegEx.match(allele): self.error(line,self.V40_BAD_ALLELE,allele) # check for leading nucleotide in indel calls for allele in alt: if len(allele) != len(ref): if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE) if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper(): self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE) # trim trailing bases in alleles for i in range(1,min(len(ref),min(map(len,alt)))): if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): break ref, alt = ref[:-1], [allele[:-1] for allele in alt] # left-align alleles, if a reference is available if self._leftalign and self._reference: while left < pos: movable = True for allele in alt: if len(allele) > len(ref): longest, shortest = allele, ref else: longest, shortest = ref, allele if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper(): movable = False if longest[-1].upper() != longest[len(shortest)-1].upper(): movable = False if not movable: break ref = ref[:-1] alt = [allele[:-1] for allele in alt] if min(len(allele) for allele in alt) == 0 or len(ref) == 0: ref = faref_leftflank[pos-left-1] + ref alt = [faref_leftflank[pos-left-1] + allele for allele in alt] pos -= 1 pysam-0.23.0/pysam/__init__.py000066400000000000000000000065471475062545500162200ustar00rootroot00000000000000import os import sysconfig from pysam.libchtslib import * import pysam.libchtslib as libchtslib from pysam.libcsamtools import * from pysam.libcbcftools import * from pysam.libcutils import * import pysam.libcutils as libcutils import pysam.libcfaidx as libcfaidx from pysam.libcfaidx import * import pysam.libctabix as libctabix from pysam.libctabix import * import pysam.libctabixproxies as libctabixproxies from pysam.libctabixproxies import * import pysam.libcsamfile as libcsamfile from pysam.libcsamfile import * import pysam.libcalignmentfile as libcalignmentfile from pysam.libcalignmentfile import * import pysam.libcalignedsegment as libcalignedsegment from pysam.libcalignedsegment import * import pysam.libcvcf as libcvcf from pysam.libcvcf import * import pysam.libcbcf as libcbcf from pysam.libcbcf import * import pysam.libcbgzf as libcbgzf from pysam.libcbgzf import * from pysam.utils import SamtoolsError import pysam.Pileup as Pileup from pysam.samtools import * import pysam.config # export all the symbols from separate modules __all__ = ( libchtslib.__all__ + # type: ignore libcutils.__all__ + # type: ignore libctabix.__all__ + # type: ignore libcvcf.__all__ + # type: ignore libcbcf.__all__ + # type: ignore libcbgzf.__all__ + # type: ignore libcfaidx.__all__ + # type: ignore libctabixproxies.__all__ + # type: ignore libcalignmentfile.__all__ + # type: ignore libcalignedsegment.__all__ + # type: ignore libcsamfile.__all__ + # type: ignore ["SamtoolsError"] + ["Pileup"] ) from pysam.version import __version__, __samtools_version__ def get_include(): '''return a list of include directories.''' dirname = os.path.abspath(os.path.join(os.path.dirname(__file__))) # # Header files may be stored in different relative locations # depending on installation mode (e.g., `python setup.py install`, # `python setup.py develop`. The first entry in each list is # where develop-mode headers can be found. # htslib_possibilities = [os.path.join(dirname, '..', 'htslib'), os.path.join(dirname, 'include', 'htslib')] samtool_possibilities = [os.path.join(dirname, '..', 'samtools'), os.path.join(dirname, 'include', 'samtools')] includes = [dirname] for header_locations in [htslib_possibilities, samtool_possibilities]: for header_location in header_locations: if os.path.exists(header_location): includes.append(os.path.abspath(header_location)) break return includes def get_defines(): '''return a list of defined compilation parameters.''' # ('_FILE_OFFSET_BITS', '64'), # ('_USE_KNETFILE', '')] return [] def get_libraries(): '''return a list of libraries to link against.''' # Note that this list does not include libcsamtools.so as there are # numerous name conflicts with libchtslib.so. dirname = os.path.abspath(os.path.join(os.path.dirname(__file__))) pysam_libs = ['libctabixproxies', 'libcfaidx', 'libcsamfile', 'libcvcf', 'libcbcf', 'libctabix'] if pysam.config.HTSLIB == "builtin": pysam_libs.append('libchtslib') so = sysconfig.get_config_var('EXT_SUFFIX') return [os.path.join(dirname, x + so) for x in pysam_libs] pysam-0.23.0/pysam/alternatives.py.obsolete000066400000000000000000000060271475062545500207660ustar00rootroot00000000000000# This file contains an alternative implementation # to call samtools functions. These are direct calls. # Plus: less overhead # Minus: more trouble in maintaining #in csamtools.pxd # samtools toolkit functions ctypedef int (*pysam_samtools_f)(int argc, char *argv[]) int bam_taf2baf(int argc, char *argv[]) int bam_pileup(int argc, char *argv[]) int bam_merge(int argc, char *argv[]) int bam_index(int argc, char *argv[]) int bam_sort(int argc, char *argv[]) int bam_tview_main(int argc, char *argv[]) int bam_mating(int argc, char *argv[]) int bam_rmdup(int argc, char *argv[]) int bam_rmdupse(int argc, char *argv[]) int bam_flagstat(int argc, char *argv[]) int bam_fillmd(int argc, char *argv[]) int main_samview(int argc, char *argv[]) int main_import(int argc, char *argv[]) int faidx_main(int argc, char *argv[]) int glf3_view_main(int argc, char *argv[]) ## Alternative code in csamtools.pyx cdef class SamtoolsWrapper: '''generic wrapper around samtools functions''' cdef pysam_samtools_f f def __init__(self): self.f = NULL def call(self, *args ): if self.f == NULL: raise NotImplementedError("invalid call to base class" ) cdef char ** cargs cdef int i, n, retval n = len(args) # allocate one more for first (dummy) argument (contains command) cargs = calloc( n+1, sizeof( char *) ) cargs[0] = "method" for i from 0 <= i < n: cargs[i+1] = args[i] for i from 0 <= i < n+1: print cargs[i] retval = self.f(n+1, cargs) free( cargs ) return retval cdef class SamtoolsWrapperImport( SamtoolsWrapper ): def __init__(self): self.f = main_import cdef class SamtoolsWrapperPileup( SamtoolsWrapper ): def __init__(self): self.f = bam_pileup cdef class SamtoolsWrapperMerge( SamtoolsWrapper ): def __init__(self): self.f = bam_merge cdef class SamtoolsWrapperSort( SamtoolsWrapper ): def __init__(self): self.f = bam_sort cdef class SamtoolsWrapperIndex( SamtoolsWrapper ): def __init__(self): self.f = bam_index cdef class SamtoolsWrapperFaidx( SamtoolsWrapper ): def __init__(self): self.f = faidx_main cdef class SamtoolsWrapperFixMate( SamtoolsWrapper ): def __init__(self): self.f = bam_mating cdef class SamtoolsWrapperRmDup( SamtoolsWrapper ): def __init__(self): self.f = bam_rmdup cdef class SamtoolsWrapperRmDupSe( SamtoolsWrapper ): def __init__(self): self.f = bam_rmdupse cdef class SamtoolsWrapperGlf3Viwen( SamtoolsWrapper ): def __init__(self): self.f = glf3_view_main cdef class SamtoolsWrapperFlagStat( SamtoolsWrapper ): def __init__(self): self.f = bam_flagstat cdef class SamtoolsWrapperFillMd( SamtoolsWrapper ): def __init__(self): self.f = bam_fillmd cdef class SamtoolsWrapperCalMd( SamtoolsWrapper ): def __init__(self): self.f = bam_fillmd automatic creation of these functions does not work due to pyrex/cython def sort( *args, **kwargs ): return SamtoolsWrapperSort().call(*args, **kwargs) pysam-0.23.0/pysam/bcftools.py000066400000000000000000000027701475062545500162660ustar00rootroot00000000000000import pysam.utils annotate = pysam.utils.PysamDispatcher('bcftools', 'annotate') call = pysam.utils.PysamDispatcher('bcftools', 'call') cnv = pysam.utils.PysamDispatcher('bcftools', 'cnv') concat = pysam.utils.PysamDispatcher('bcftools', 'concat') consensus = pysam.utils.PysamDispatcher('bcftools', 'consensus') convert = pysam.utils.PysamDispatcher('bcftools', 'convert') csq = pysam.utils.PysamDispatcher('bcftools', 'csq') filter = pysam.utils.PysamDispatcher('bcftools', 'filter') gtcheck = pysam.utils.PysamDispatcher('bcftools', 'gtcheck') head = pysam.utils.PysamDispatcher('bcftools', 'head') index = pysam.utils.PysamDispatcher('bcftools', 'index') isec = pysam.utils.PysamDispatcher('bcftools', 'isec') merge = pysam.utils.PysamDispatcher('bcftools', 'merge') mpileup = pysam.utils.PysamDispatcher('bcftools', 'mpileup') norm = pysam.utils.PysamDispatcher('bcftools', 'norm') plugin = pysam.utils.PysamDispatcher('bcftools', 'plugin') query = pysam.utils.PysamDispatcher('bcftools', 'query') reheader = pysam.utils.PysamDispatcher('bcftools', 'reheader') roh = pysam.utils.PysamDispatcher('bcftools', 'roh') sort = pysam.utils.PysamDispatcher('bcftools', 'sort') stats = pysam.utils.PysamDispatcher('bcftools', 'stats') view = pysam.utils.PysamDispatcher('bcftools', 'view') __all__ = [ 'annotate', 'call', 'cnv', 'concat', 'consensus', 'convert', 'csq', 'filter', 'gtcheck', 'head', 'index', 'isec', 'merge', 'mpileup', 'norm', 'plugin', 'query', 'reheader', 'roh', 'sort', 'stats', 'view', ] pysam-0.23.0/pysam/cbcftools_util.h000066400000000000000000000001461475062545500172600ustar00rootroot00000000000000#ifndef CBCFTOOLS_UTIL_H #define CBCFTOOLS_UTIL_H int bcftools_main(int argc, char *argv[]); #endif pysam-0.23.0/pysam/csamtools_util.h000066400000000000000000000001461475062545500173060ustar00rootroot00000000000000#ifndef CSAMTOOLS_UTIL_H #define CSAMTOOLS_UTIL_H int samtools_main(int argc, char *argv[]); #endif pysam-0.23.0/pysam/htslib_util.c000066400000000000000000000063361475062545500165710ustar00rootroot00000000000000#include #include #include "htslib/khash.h" #include "htslib/ksort.h" #include "htslib/sam.h" #include "htslib/hts.h" #include "htslib/knetfile.h" #include "htslib/kseq.h" #include "htslib_util.h" #include #ifndef inline #define inline __inline #endif // set htslib verbosity level extern int hts_verbose; int hts_set_verbosity(int verbosity) { int old_verbosity = hts_verbose; hts_verbose = verbosity; return old_verbosity; } int hts_get_verbosity(void) { return hts_verbose; } // taken from samtools/bam_import.c static inline uint8_t * alloc_data(bam1_t *b, size_t size) { if (b->m_data < size) { b->m_data = size; kroundup32(b->m_data); b->data = (uint8_t*)realloc(b->data, b->m_data); } return b->data; } // update the variable length data within a bam1_t entry. // Adds *nbytes_new* - *nbytes_old* into the variable length data of *src* at *pos*. // Data within the bam1_t entry is moved so that it is // consistent with the data field lengths. // Return NULL on error (memory allocation) bam1_t * pysam_bam_update(bam1_t * b, const size_t nbytes_old, const size_t nbytes_new, uint8_t * field_start) { int d = nbytes_new - nbytes_old; int new_size; size_t nbytes_before; uint8_t * retval = NULL; // no change if (d == 0) return b; // new size of total data new_size = d + b->l_data; // fields before field in data nbytes_before = field_start - b->data; if (b->l_data != 0) { assert(nbytes_before >= 0); assert(nbytes_before <= b->l_data); } // increase memory if required if (d > 0) { retval = alloc_data(b, new_size); if (retval == NULL) return NULL; field_start = b->data + nbytes_before; } // move data after field to new location memmove(field_start + nbytes_new, field_start + nbytes_old, b->l_data - (nbytes_before + nbytes_old)); // adjust l_data b->l_data = new_size; return b; } // translate a nucleotide character to binary code unsigned char pysam_translate_sequence(const unsigned char s) { return seq_nt16_table[s]; } // Auxiliary functions for B support void bam_aux_appendB(bam1_t *b, const char tag[2], char type, char subtype, int len, uint8_t *data) { int ori_len; int l_data; // check that type is 'B' if('B' != type) return; ori_len = b->l_data; l_data = len * aux_type2size(subtype); // infer the data length from the sub-type b->l_data += 8 + l_data; // htslib: obsolete? // b->l_aux += 8 + l_data; if (b->m_data < b->l_data) { b->m_data = b->l_data; kroundup32(b->m_data); b->data = (uint8_t*)realloc(b->data, b->m_data); } b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1]; // tag b->data[ori_len + 2] = type; // type b->data[ori_len + 3] = subtype; // subtype (*(int32_t*)(b->data + ori_len + 4)) = len; // size memcpy(b->data + ori_len + 8, data, l_data); // data } int aux_type2size(uint8_t type) { switch (type) { case 'A': case 'c': case 'C': return 1; case 's': case 'S': return 2; case 'i': case 'I': case 'f': return 4; case 'd': return 8; case 'Z': case 'H': case 'B': return type; default: return 0; } } pysam-0.23.0/pysam/htslib_util.h000066400000000000000000000050051475062545500165660ustar00rootroot00000000000000#ifndef HTSLIB_UTIL_H #define HTSLIB_UTIL_H #include "htslib/sam.h" #include "htslib/vcf.h" #include "htslib/khash.h" int hts_set_verbosity(int verbosity); int hts_get_verbosity(void); KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t) typedef khash_t(vdict) vdict_t; KHASH_DECLARE(s2i, kh_cstr_t, int64_t) typedef khash_t(s2i) s2i_t; ////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////// // various helper functions // /*! @abstract Update the variable length data within a bam1_t entry Old data is deleted and the data within b are re-arranged to make place for new data. @discussion Return NULL on error, otherwise b is returned. @param b bam1_t data @param nbytes_old size of old data @param nbytes_new size of new data @param pos position of data */ bam1_t * pysam_bam_update(bam1_t * b, const size_t nbytes_old, const size_t nbytes_new, uint8_t * pos); // translate a nucleotide character to binary code unsigned char pysam_translate_sequence(const unsigned char s); // return byte size of type int aux_type2size(uint8_t type); //------------------------------------------------------- // Wrapping accessor macros in sam.h static inline int pysam_bam_is_rev(bam1_t * b) { return bam_is_rev(b);}; static inline int pysam_bam_is_mrev(bam1_t * b) { return bam_is_mrev(b);} static inline char * pysam_bam_get_qname(bam1_t * b) { return bam_get_qname(b);} static inline uint32_t * pysam_bam_get_cigar(bam1_t * b) { return bam_get_cigar(b);} static inline uint8_t * pysam_bam_get_seq(bam1_t * b) { return bam_get_seq(b);} static inline uint8_t * pysam_bam_get_qual(bam1_t * b) { return bam_get_qual(b);} static inline uint8_t * pysam_bam_get_aux(bam1_t * b) { return bam_get_aux(b);} static inline int pysam_bam_get_l_aux(bam1_t * b) { return bam_get_l_aux(b); } static inline char pysam_bam_seqi(uint8_t * s, int i) { return bam_seqi(s,i);} static inline uint8_t pysam_get_qual(bam1_t * b) { return b->core.qual;} static inline uint32_t pysam_get_n_cigar(bam1_t * b) { return b->core.n_cigar;} static inline void pysam_set_qual(bam1_t * b, uint8_t v) { b->core.qual=v;} static inline void pysam_set_n_cigar(bam1_t * b, uint32_t v) { b->core.n_cigar=v;} static inline void pysam_update_flag(bam1_t * b, uint16_t v, uint16_t flag) { if (v) b->core.flag |= flag; else b->core.flag &= ~flag; } #endif pysam-0.23.0/pysam/include/000077500000000000000000000000001475062545500155165ustar00rootroot00000000000000pysam-0.23.0/pysam/include/__init__.py000066400000000000000000000000001475062545500176150ustar00rootroot00000000000000pysam-0.23.0/pysam/libcalignedsegment.pxd000066400000000000000000000055761475062545500204450ustar00rootroot00000000000000# cython: language_level=3 from pysam.libchtslib cimport * cdef extern from "htslib_util.h": # add *nbytes* into the variable length data of *src* at *pos* bam1_t * pysam_bam_update(bam1_t * b, size_t nbytes_old, size_t nbytes_new, uint8_t * pos) # now: static int aux_type2size(int) char * pysam_bam_get_qname(bam1_t * b) uint32_t * pysam_bam_get_cigar(bam1_t * b) uint8_t * pysam_bam_get_seq(bam1_t * b) uint8_t * pysam_bam_get_qual(bam1_t * b) uint8_t * pysam_bam_get_aux(bam1_t * b) int pysam_bam_get_l_aux(bam1_t * b) char pysam_bam_seqi(uint8_t * s, int i) uint8_t pysam_get_qual(bam1_t * b) uint32_t pysam_get_n_cigar(bam1_t * b) void pysam_set_qual(bam1_t * b, uint8_t v) void pysam_set_n_cigar(bam1_t * b, uint32_t v) void pysam_update_flag(bam1_t * b, uint16_t v, uint16_t flag) from pysam.libcalignmentfile cimport AlignmentFile, AlignmentHeader ctypedef AlignmentFile AlignmentFile_t # Note: need to declare all C fields and methods here cdef class AlignedSegment: # object that this AlignedSegment represents cdef bam1_t * _delegate # the header that a read is associated with cdef readonly AlignmentHeader header # caching of array properties for quick access cdef object cache_query_qualities cdef object cache_query_alignment_qualities cdef object cache_query_sequence cdef object cache_query_alignment_sequence # add an alignment tag with value to the AlignedSegment # an existing tag of the same name will be replaced. cpdef set_tag(self, tag, value, value_type=?, replace=?) # get an alignment tag from the AlignedSegment cpdef get_tag(self, tag, with_value_type=?) # return true if tag exists cpdef has_tag(self, tag) # returns a valid sam alignment string cpdef to_string(self) # returns a valid sam alignment string (deprecated) cpdef tostring(self, htsfile=*) cdef class PileupColumn: cdef const bam_pileup1_t ** plp cdef int tid cdef int pos cdef int n_pu cdef AlignmentHeader header cdef uint32_t min_base_quality cdef kstring_t buf cdef char * reference_sequence cdef class PileupRead: cdef int32_t _qpos cdef AlignedSegment _alignment cdef int _indel cdef int _level cdef uint32_t _is_del cdef uint32_t _is_head cdef uint32_t _is_tail cdef uint32_t _is_refskip # factory methods cdef AlignedSegment makeAlignedSegment( bam1_t * src, AlignmentHeader header) cdef PileupColumn makePileupColumn( const bam_pileup1_t ** plp, int tid, int pos, int n_pu, uint32_t min_base_quality, char * reference_sequence, AlignmentHeader header) cdef PileupRead makePileupRead(const bam_pileup1_t * src, AlignmentHeader header) cdef uint32_t get_alignment_length(bam1_t * src) pysam-0.23.0/pysam/libcalignedsegment.pyi000066400000000000000000000150021475062545500204340ustar00rootroot00000000000000import enum import re import sys from array import array from typing import Any, List, Optional, Dict, Tuple, Union, overload if sys.version_info < (3, 8): from typing_extensions import Literal else: from typing import Literal from pysam import AlignmentHeader # type: ignore CMATCH: int CINS: int CDEL: int CREF_SKIP: int CSOFT_CLIP: int CHARD_CLIP: int CPAD: int CEQUAL: int CDIFF: int CBACK: int FPAIRED: int FPROPER_PAIR: int FUNMAP: int FMUNMAP: int FREVERSE: int FMREVERSE: int FREAD1: int FREAD2: int FSECONDARY: int FQCFAIL: int FDUP: int FSUPPLEMENTARY: int CIGAR2CODE: Dict[int, str] CIGAR_REGEX: re.Pattern DATATYPE2FORMAT: Dict[int, Tuple[str, int]] KEY_NAMES: List[str] TagValue = Union[str, int, float, array] class CIGAR_OPS(enum.IntEnum): CBACK = ... CDEL = ... CDIFF = ... CEQUAL = ... CHARD_CLIP = ... CINS = ... CMATCH = ... CPAD = ... CREF_SKIP = ... CSOFT_CLIP = ... class SAM_FLAGS(enum.IntEnum): FDUP = ... FMREVERSE = ... FMUNMAP = ... FPAIRED = ... FPROPER_PAIR = ... FQCFAIL = ... FREAD1 = ... FREAD2 = ... FREVERSE = ... FSECONDARY = ... FSUPPLEMENTARY = ... FUNMAP = ... class AlignedSegment: header: AlignmentHeader query_name: Optional[str] flag: int reference_name: Optional[str] reference_id: int reference_start: int mapping_quality: int cigarstring: Optional[str] next_reference_id: int next_reference_name: Optional[str] next_reference_start: int template_length: int query_sequence: Optional[str] query_qualities: Optional[array] bin: int is_paired: bool is_proper_pair: bool is_unmapped: bool mate_is_unmapped: bool is_mapped: bool mate_is_mapped: bool is_reverse: bool mate_is_reverse: bool is_forward: bool mate_is_forward: bool is_read1: bool is_read2: bool is_secondary: bool is_qcfail: bool is_duplicate: bool is_supplementary: bool cigartuples: Optional[List[Tuple[int, int]]] def __init__(self, header: Optional[AlignmentHeader] = ...) -> None: ... def compare(self, other: Any) -> int: ... def to_string(self) -> str: ... @classmethod def fromstring(cls, sam: str, header: AlignmentHeader) -> AlignedSegment: ... def to_dict(self) -> Dict: ... @classmethod def from_dict(cls, sam_dict: Dict[str, Any], header: AlignmentHeader) -> Any: ... def get_reference_positions(self, full_length: bool = ...) -> List[int]: ... @property def query_length(self) -> int: ... @property def reference_end(self) -> Optional[int]: ... @property def reference_length(self) -> Optional[int]: ... @property def query_alignment_sequence(self) -> Optional[str]: ... @property def query_alignment_qualities(self) -> Optional[array]: ... @property def query_alignment_start(self) -> int: ... @property def query_alignment_end(self) -> int: ... @property def modified_bases(self) -> Optional[Dict[Tuple[str, int, str], List[Tuple[int, int]]]]: ... @property def modified_bases_forward(self) -> Optional[Dict[Tuple[str, int, str], List[Tuple[int, int]]]]: ... @property def query_alignment_length(self) -> int: ... def infer_query_length(self) -> Optional[int]: ... def infer_read_length(self) -> Optional[int]: ... def get_reference_sequence(self) -> str: ... def get_forward_sequence(self) -> Optional[str]: ... def get_forward_qualities(self) -> Optional[array]: ... def get_aligned_pairs( self, matches_only: bool = ..., with_seq: bool = ..., with_cigar: bool = ... ) -> List[Tuple[int, int]]: ... def get_blocks(self) -> List[Tuple[int, int]]: ... def get_overlap(self, start: int, end: int) -> Optional[int]: ... def get_cigar_stats(self) -> Tuple[array, array]: ... def set_tag( self, tag: str, value: Union[int, float, str, bytes, array, List, Tuple, None], value_type: Optional[ Literal["A", "i", "f", "Z", "H", "B", "c", "C", "s", "S", "I"] ] = ..., replace: bool = ..., ) -> None: ... def has_tag(self, tag: str) -> bool: ... @overload def get_tag(self, tag: str, with_value_type: Literal[False] = ...) -> TagValue: ... @overload def get_tag( self, tag: str, with_value_type: Literal[True] ) -> Tuple[TagValue, str]: ... @overload def get_tag( self, tag: str, with_value_type: bool ) -> Union[TagValue, Tuple[TagValue, str]]: ... @overload def get_tags( self, with_value_type: Literal[False] = ... ) -> List[Tuple[str, TagValue]]: ... @overload def get_tags( self, with_value_type: Literal[True] ) -> List[Tuple[str, TagValue, str]]: ... @overload def get_tags( self, with_value_type: bool ) -> Union[List[Tuple[str, TagValue]], List[Tuple[str, TagValue, str]]]: ... @overload def get_tags( self, with_value_type: bool = ... ) -> Union[List[Tuple[str, TagValue, str]], List[Tuple[str, TagValue]]]: ... def set_tags(self, tags: Any) -> None: ... def __eq__(self, other): ... def __ge__(self, other): ... def __gt__(self, other): ... def __le__(self, other): ... def __lt__(self, other): ... def __ne__(self, other): ... class PileupRead: @property def alignment(self) -> AlignedSegment: ... @property def query_position(self) -> Optional[int]: ... @property def query_position_or_next(self) -> int: ... @property def indel(self) -> int: ... @property def level(self) -> int: ... @property def is_del(self) -> int: ... @property def is_head(self) -> int: ... @property def is_tail(self) -> int: ... @property def is_refskip(self) -> int: ... class PileupColumn: nsegments: int def set_min_base_quality(self, min_base_quality: int) -> None: ... def __len__(self) -> int: ... @property def reference_id(self) -> int: ... @property def reference_name(self) -> Optional[str]: ... @property def reference_pos(self) -> int: ... @property def pileups(self) -> List[PileupRead]: ... def get_num_aligned(self) -> int: ... def get_query_sequences( self, mark_matches: bool = ..., mark_ends: bool = ..., add_indels: bool = ..., ) -> List[str]: ... def get_query_qualities(self) -> List[int]: ... def get_mapping_qualities(self) -> List[int]: ... def get_query_positions(self) -> List[int]: ... def get_query_names(self) -> List[str]: ... pysam-0.23.0/pysam/libcalignedsegment.pyx000066400000000000000000003441141475062545500204640ustar00rootroot00000000000000# cython: language_level=3 # cython: embedsignature=True # cython: profile=True ############################################################################### ############################################################################### # Cython wrapper for SAM/BAM/CRAM files based on htslib ############################################################################### # The principal classes defined in this module are: # # class AlignedSegment an aligned segment (read) # # class PileupColumn a collection of segments (PileupRead) aligned to # a particular genomic position. # # class PileupRead an AlignedSegment aligned to a particular genomic # position. Contains additional attributes with respect # to this. # # Additionally this module defines numerous additional classes that are part # of the internal API. These are: # # Various iterator classes to iterate over alignments in sequential (IteratorRow) # or in a stacked fashion (IteratorColumn): # # class IteratorRow # class IteratorRowRegion # class IteratorRowHead # class IteratorRowAll # class IteratorRowAllRefs # class IteratorRowSelection # ############################################################################### # # The MIT License # # Copyright (c) 2015 Andreas Heger # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. # ############################################################################### import re import array import json import string import ctypes import struct cimport cython from cpython cimport array as c_array from cpython cimport PyBytes_FromStringAndSize from libc.string cimport memset, strchr from cpython cimport array as c_array from libc.stdint cimport INT8_MIN, INT16_MIN, INT32_MIN, \ INT8_MAX, INT16_MAX, INT32_MAX, \ UINT8_MAX, UINT16_MAX, UINT32_MAX from pysam.libchtslib cimport HTS_IDX_NOCOOR from pysam.libcutils cimport force_bytes, force_str, \ charptr_to_str, charptr_to_bytes from pysam.libcutils cimport qualities_to_qualitystring, qualitystring_to_array, \ array_to_qualitystring # Constants for binary tag conversion cdef char * htslib_types = 'cCsSiIf' cdef char * parray_types = 'bBhHiIf' # translation tables # cigar code to character and vice versa cdef char* CODE2CIGAR= "MIDNSHP=XB" cdef int NCIGAR_CODES = 10 CIGAR2CODE = dict([y, x] for x, y in enumerate(CODE2CIGAR)) CIGAR_REGEX = re.compile("(\d+)([MIDNSHP=XB])") # names for keys in dictionary representation of an AlignedSegment KEY_NAMES = ["name", "flag", "ref_name", "ref_pos", "map_quality", "cigar", "next_ref_name", "next_ref_pos", "length", "seq", "qual", "tags"] ##################################################################### # C multiplication with wrapping around cdef inline uint32_t c_mul(uint32_t a, uint32_t b): return (a * b) & 0xffffffff cdef inline uint8_t tolower(uint8_t ch): if ch >= 65 and ch <= 90: return ch + 32 else: return ch cdef inline uint8_t toupper(uint8_t ch): if ch >= 97 and ch <= 122: return ch - 32 else: return ch cdef inline uint8_t strand_mark_char(uint8_t ch, bam1_t *b): if ch == b'=': if bam_is_rev(b): return b',' else: return b'.' else: if bam_is_rev(b): return tolower(ch) else: return toupper(ch) cdef inline bint pileup_base_qual_skip(const bam_pileup1_t * p, uint32_t threshold): cdef uint32_t c if p.qpos < p.b.core.l_qseq: c = bam_get_qual(p.b)[p.qpos] else: c = 0 if c < threshold: return True return False cdef inline char map_typecode_htslib_to_python(uint8_t s): """map an htslib typecode to the corresponding python typecode to be used in the struct or array modules.""" # map type from htslib to python array cdef char * f = strchr(htslib_types, s) if f == NULL: return 0 return parray_types[f - htslib_types] cdef inline uint8_t map_typecode_python_to_htslib(char s): """determine value type from type code of array""" cdef char * f = strchr(parray_types, s) if f == NULL: return 0 return htslib_types[f - parray_types] cdef inline void update_bin(bam1_t * src): if src.core.flag & BAM_FUNMAP: # treat alignment as length of 1 for unmapped reads src.core.bin = hts_reg2bin( src.core.pos, src.core.pos + 1, 14, 5) elif pysam_get_n_cigar(src): src.core.bin = hts_reg2bin( src.core.pos, bam_endpos(src), 14, 5) else: src.core.bin = hts_reg2bin( src.core.pos, src.core.pos + 1, 14, 5) # optional tag data manipulation cdef convert_binary_tag(uint8_t * tag): """return bytesize, number of values and array of values in aux_data memory location pointed to by tag.""" cdef uint8_t auxtype cdef uint8_t byte_size cdef int32_t nvalues # get byte size auxtype = tag[0] byte_size = aux_type2size(auxtype) tag += 1 # get number of values in array nvalues = (tag)[0] tag += 4 # define python array cdef c_array.array c_values = array.array( chr(map_typecode_htslib_to_python(auxtype))) c_array.resize(c_values, nvalues) # copy data memcpy(c_values.data.as_voidptr, tag, nvalues * byte_size) # no need to check for endian-ness as bam1_core_t fields # and aux_data are in host endian-ness. See sam.c and calls # to swap_data return byte_size, nvalues, c_values cdef inline uint8_t get_tag_typecode(value, value_type=None): """guess type code for a *value*. If *value_type* is None, the type code will be inferred based on the Python type of *value* """ # 0 is unknown typecode cdef char typecode = 0 if value_type is None: if isinstance(value, int): if value < 0: if value >= INT8_MIN: typecode = b'c' elif value >= INT16_MIN: typecode = b's' elif value >= INT32_MIN: typecode = b'i' # unsigned ints else: if value <= UINT8_MAX: typecode = b'C' elif value <= UINT16_MAX: typecode = b'S' elif value <= UINT32_MAX: typecode = b'I' elif isinstance(value, float): typecode = b'f' elif isinstance(value, str): typecode = b'Z' elif isinstance(value, bytes): typecode = b'Z' elif isinstance(value, array.array) or \ isinstance(value, list) or \ isinstance(value, tuple): typecode = b'B' else: if value_type in 'aAsSIcCZidfH': typecode = force_bytes(value_type)[0] return typecode cdef inline uint8_t get_btag_typecode(value, min_value=None, max_value=None): '''returns the value typecode of a value. If max is specified, the appropriate type is returned for a range where value is the minimum. Note that this method returns types from the extended BAM alphabet of types that includes tags that are not part of the SAM specification. ''' cdef uint8_t typecode t = type(value) if t is float: typecode = b'f' elif t is int: if max_value is None: max_value = value if min_value is None: min_value = value # signed ints if min_value < 0: if min_value >= INT8_MIN and max_value <= INT8_MAX: typecode = b'c' elif min_value >= INT16_MIN and max_value <= INT16_MAX: typecode = b's' elif min_value >= INT32_MIN or max_value <= INT32_MAX: typecode = b'i' else: raise ValueError( "at least one signed integer out of range of " "BAM/SAM specification") # unsigned ints else: if max_value <= UINT8_MAX: typecode = b'C' elif max_value <= UINT16_MAX: typecode = b'S' elif max_value <= UINT32_MAX: typecode = b'I' else: raise ValueError( "at least one integer out of range of BAM/SAM specification") else: # Note: hex strings (H) are not supported yet if t is not bytes: value = value.encode('ascii') if len(value) == 1: typecode = b'A' else: typecode = b'Z' return typecode # mapping python array.array and htslib typecodes to struct typecodes DATATYPE2FORMAT = { ord('c'): ('b', 1), ord('C'): ('B', 1), ord('s'): ('h', 2), ord('S'): ('H', 2), ord('i'): ('i', 4), ord('I'): ('I', 4), ord('f'): ('f', 4), ord('d'): ('d', 8), ord('A'): ('c', 1), ord('a'): ('c', 1)} cdef inline pack_tags(tags): """pack a list of tags. Each tag is a tuple of (tag, tuple). Values are packed into the most space efficient data structure possible unless the tag contains a third field with the typecode. Returns a format string and the associated list of arguments to be used in a call to struct.pack_into. """ fmts, args = ["<"], [] # htslib typecode cdef uint8_t typecode for tag in tags: if len(tag) == 2: pytag, value = tag valuetype = None elif len(tag) == 3: pytag, value, valuetype = tag else: raise ValueError("malformatted tag: %s" % str(tag)) if valuetype is None: typecode = 0 else: # only first character in valuecode matters typecode = force_bytes(valuetype)[0] pytag = force_bytes(pytag) pytype = type(value) if pytype is tuple or pytype is list: # binary tags from tuples or lists if not typecode: # automatically determine value type - first value # determines type. If there is a mix of types, the # result is undefined. typecode = get_btag_typecode(min(value), min_value=min(value), max_value=max(value)) if typecode not in DATATYPE2FORMAT: raise ValueError("invalid value type '{}'".format(chr(typecode))) datafmt = "2sBBI%i%s" % (len(value), DATATYPE2FORMAT[typecode][0]) args.extend([pytag[:2], ord("B"), typecode, len(value)] + list(value)) elif isinstance(value, array.array): # binary tags from arrays if typecode == 0: typecode = map_typecode_python_to_htslib(ord(value.typecode)) if typecode == 0: raise ValueError("unsupported type code '{}'".format(value.typecode)) if typecode not in DATATYPE2FORMAT: raise ValueError("invalid value type '{}'".format(chr(typecode))) # use array.tostring() to retrieve byte representation and # save as bytes datafmt = "2sBBI%is" % (len(value) * DATATYPE2FORMAT[typecode][1]) args.extend([pytag[:2], ord("B"), typecode, len(value), value.tobytes()]) else: if typecode == 0: typecode = get_tag_typecode(value) if typecode == 0: raise ValueError("could not deduce typecode for value {}".format(value)) if typecode == b'a' or typecode == b'A' or typecode == b'Z' or typecode == b'H': value = force_bytes(value) if typecode == b"a": typecode = b'A' if typecode == b'Z' or typecode == b'H': datafmt = "2sB%is" % (len(value)+1) elif typecode in DATATYPE2FORMAT: datafmt = "2sB%s" % DATATYPE2FORMAT[typecode][0] else: raise ValueError("invalid value type '{}'".format(chr(typecode))) args.extend([pytag[:2], typecode, value]) fmts.append(datafmt) return "".join(fmts), args cdef inline int32_t calculateQueryLengthWithoutHardClipping(bam1_t * src): """return query length computed from CIGAR alignment. Length ignores hard-clipped bases. Return 0 if there is no CIGAR alignment. """ cdef uint32_t * cigar_p = pysam_bam_get_cigar(src) if cigar_p == NULL: return 0 cdef uint32_t k, qpos cdef int op qpos = 0 for k from 0 <= k < pysam_get_n_cigar(src): op = cigar_p[k] & BAM_CIGAR_MASK if op == BAM_CMATCH or \ op == BAM_CINS or \ op == BAM_CSOFT_CLIP or \ op == BAM_CEQUAL or \ op == BAM_CDIFF: qpos += cigar_p[k] >> BAM_CIGAR_SHIFT return qpos cdef inline int32_t calculateQueryLengthWithHardClipping(bam1_t * src): """return query length computed from CIGAR alignment. Length includes hard-clipped bases. Return 0 if there is no CIGAR alignment. """ cdef uint32_t * cigar_p = pysam_bam_get_cigar(src) if cigar_p == NULL: return 0 cdef uint32_t k, qpos cdef int op qpos = 0 for k from 0 <= k < pysam_get_n_cigar(src): op = cigar_p[k] & BAM_CIGAR_MASK if op == BAM_CMATCH or \ op == BAM_CINS or \ op == BAM_CSOFT_CLIP or \ op == BAM_CHARD_CLIP or \ op == BAM_CEQUAL or \ op == BAM_CDIFF: qpos += cigar_p[k] >> BAM_CIGAR_SHIFT return qpos cdef inline int32_t getQueryStart(bam1_t *src) except -1: cdef uint32_t * cigar_p cdef uint32_t start_offset = 0 cdef uint32_t k, op cigar_p = pysam_bam_get_cigar(src); for k from 0 <= k < pysam_get_n_cigar(src): op = cigar_p[k] & BAM_CIGAR_MASK if op == BAM_CHARD_CLIP: if start_offset != 0 and start_offset != src.core.l_qseq: raise ValueError('Invalid clipping in CIGAR string') elif op == BAM_CSOFT_CLIP: start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT else: break return start_offset cdef inline int32_t getQueryEnd(bam1_t *src) except -1: cdef uint32_t * cigar_p = pysam_bam_get_cigar(src) cdef uint32_t end_offset = src.core.l_qseq cdef uint32_t k, op # if there is no sequence, compute length from cigar string if end_offset == 0: for k from 0 <= k < pysam_get_n_cigar(src): op = cigar_p[k] & BAM_CIGAR_MASK if op == BAM_CMATCH or \ op == BAM_CINS or \ op == BAM_CEQUAL or \ op == BAM_CDIFF or \ (op == BAM_CSOFT_CLIP and end_offset == 0): end_offset += cigar_p[k] >> BAM_CIGAR_SHIFT else: # walk backwards in cigar string for k from pysam_get_n_cigar(src) > k >= 1: op = cigar_p[k] & BAM_CIGAR_MASK if op == BAM_CHARD_CLIP: if end_offset != src.core.l_qseq: raise ValueError('Invalid clipping in CIGAR string') elif op == BAM_CSOFT_CLIP: end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT else: break return end_offset cdef inline bytes getSequenceInRange(bam1_t *src, uint32_t start, uint32_t end): """return python string of the sequence in a bam1_t object. """ cdef uint8_t * p cdef uint32_t k cdef char * s if not src.core.l_qseq: return None seq = PyBytes_FromStringAndSize(NULL, end - start) s = seq p = pysam_bam_get_seq(src) for k from start <= k < end: # equivalent to seq_nt16_str[bam1_seqi(s, i)] (see bam.c) # note: do not use string literal as it will be a python string s[k-start] = seq_nt16_str[p[k//2] >> 4 * (1 - k%2) & 0xf] return charptr_to_bytes(seq) cdef inline object getQualitiesInRange(bam1_t *src, uint32_t start, uint32_t end): """return python array of quality values from a bam1_t object""" cdef uint8_t * p cdef uint32_t k p = pysam_bam_get_qual(src) if p[0] == 0xff: return None # 'B': unsigned char cdef c_array.array result = array.array('B', [0]) c_array.resize(result, end - start) # copy data memcpy(result.data.as_voidptr, &p[start], end - start) return result ##################################################################### ## factory methods for instantiating extension classes cdef class AlignedSegment cdef AlignedSegment makeAlignedSegment(bam1_t *src, AlignmentHeader header): '''return an AlignedSegment object constructed from `src`''' # note that the following does not call __init__ cdef AlignedSegment dest = AlignedSegment.__new__(AlignedSegment) dest._delegate = bam_dup1(src) dest.header = header return dest cdef class PileupColumn cdef PileupColumn makePileupColumn(const bam_pileup1_t ** plp, int tid, int pos, int n_pu, uint32_t min_base_quality, char * reference_sequence, AlignmentHeader header): '''return a PileupColumn object constructed from pileup in `plp` and setting additional attributes. ''' # note that the following does not call __init__ cdef PileupColumn dest = PileupColumn.__new__(PileupColumn) dest.header = header dest.plp = plp dest.tid = tid dest.pos = pos dest.n_pu = n_pu dest.min_base_quality = min_base_quality dest.reference_sequence = reference_sequence dest.buf.l = dest.buf.m = 0 dest.buf.s = NULL return dest cdef class PileupRead cdef PileupRead makePileupRead(const bam_pileup1_t *src, AlignmentHeader header): '''return a PileupRead object construted from a bam_pileup1_t * object.''' # note that the following does not call __init__ cdef PileupRead dest = PileupRead.__new__(PileupRead) dest._alignment = makeAlignedSegment(src.b, header) dest._qpos = src.qpos dest._indel = src.indel dest._level = src.level dest._is_del = src.is_del dest._is_head = src.is_head dest._is_tail = src.is_tail dest._is_refskip = src.is_refskip return dest cdef inline uint32_t get_alignment_length(bam1_t *src): cdef uint32_t k = 0 cdef uint32_t l = 0 if src == NULL: return 0 cdef uint32_t * cigar_p = bam_get_cigar(src) if cigar_p == NULL: return 0 cdef int op cdef uint32_t n = pysam_get_n_cigar(src) for k from 0 <= k < n: op = cigar_p[k] & BAM_CIGAR_MASK if op == BAM_CSOFT_CLIP or op == BAM_CHARD_CLIP: continue l += cigar_p[k] >> BAM_CIGAR_SHIFT return l cdef inline uint32_t get_md_reference_length(char * md_tag): cdef int l = 0 cdef int md_idx = 0 cdef int nmatches = 0 while md_tag[md_idx] != 0: if md_tag[md_idx] >= 48 and md_tag[md_idx] <= 57: nmatches *= 10 nmatches += md_tag[md_idx] - 48 md_idx += 1 continue else: l += nmatches nmatches = 0 if md_tag[md_idx] == b'^': md_idx += 1 while md_tag[md_idx] >= 65 and md_tag[md_idx] <= 90: md_idx += 1 l += 1 else: md_idx += 1 l += 1 l += nmatches return l # TODO: avoid string copying for getSequenceInRange, reconstituneSequenceFromMD, ... cdef inline bytes build_alignment_sequence(bam1_t * src): """return expanded sequence from MD tag. The sequence includes substitutions and both insertions in the reference as well as deletions to the reference sequence. Combine with the cigar string to reconstitute the query or the reference sequence. Positions corresponding to `N` (skipped region from the reference) or `P` (padding (silent deletion from padded reference)) in the CIGAR string will not appear in the returned sequence. The MD should correspondingly not contain these. Thus proper tags are:: Deletion from the reference: cigar=5M1D5M MD=5^C5 Skipped region from reference: cigar=5M1N5M MD=10 Padded region in the reference: cigar=5M1P5M MD=10 Returns ------- None, if no MD tag is present. """ if src == NULL: return None cdef uint8_t * md_tag_ptr = bam_aux_get(src, "MD") if md_tag_ptr == NULL: return None cdef uint32_t start = getQueryStart(src) cdef uint32_t end = getQueryEnd(src) # get read sequence, taking into account soft-clipping r = getSequenceInRange(src, start, end) cdef char * read_sequence = r cdef uint32_t * cigar_p = pysam_bam_get_cigar(src) if cigar_p == NULL: return None cdef uint32_t r_idx = 0 cdef int op cdef uint32_t k, i, l, x cdef int nmatches = 0 cdef int s_idx = 0 cdef uint32_t max_len = get_alignment_length(src) if max_len == 0: raise ValueError("could not determine alignment length") cdef char * s = calloc(max_len + 1, sizeof(char)) if s == NULL: raise ValueError( "could not allocate sequence of length %i" % max_len) for k from 0 <= k < pysam_get_n_cigar(src): op = cigar_p[k] & BAM_CIGAR_MASK l = cigar_p[k] >> BAM_CIGAR_SHIFT if op == BAM_CMATCH or op == BAM_CEQUAL or op == BAM_CDIFF: for i from 0 <= i < l: s[s_idx] = read_sequence[r_idx] r_idx += 1 s_idx += 1 elif op == BAM_CDEL: for i from 0 <= i < l: s[s_idx] = b'-' s_idx += 1 elif op == BAM_CREF_SKIP: pass elif op == BAM_CINS or op == BAM_CPAD: for i from 0 <= i < l: # encode insertions into reference as lowercase s[s_idx] = read_sequence[r_idx] + 32 r_idx += 1 s_idx += 1 elif op == BAM_CSOFT_CLIP: pass elif op == BAM_CHARD_CLIP: pass # advances neither cdef char md_buffer[2] cdef char *md_tag cdef uint8_t md_typecode = md_tag_ptr[0] if md_typecode == b'Z': md_tag = bam_aux2Z(md_tag_ptr) elif md_typecode == b'A': # Work around HTSeq bug that writes 1-character strings as MD:A:v md_buffer[0] = bam_aux2A(md_tag_ptr) md_buffer[1] = b'\0' md_tag = md_buffer else: raise TypeError('Tagged field MD:{}: does not have expected type MD:Z'.format(chr(md_typecode))) cdef int md_idx = 0 cdef char c s_idx = 0 # Check if MD tag is valid by matching CIGAR length to MD tag defined length # Insertions would be in addition to what is described by MD, so we calculate # the number of insertions separately. cdef int insertions = 0 while s[s_idx] != 0: if s[s_idx] >= b'a': insertions += 1 s_idx += 1 s_idx = 0 cdef uint32_t md_len = get_md_reference_length(md_tag) if md_len + insertions > max_len: free(s) raise AssertionError( "Invalid MD tag: MD length {} mismatch with CIGAR length {} and {} insertions".format( md_len, max_len, insertions)) while md_tag[md_idx] != 0: # c is numerical if md_tag[md_idx] >= 48 and md_tag[md_idx] <= 57: nmatches *= 10 nmatches += md_tag[md_idx] - 48 md_idx += 1 continue else: # save matches up to this point, skipping insertions for x from 0 <= x < nmatches: while s[s_idx] >= b'a': s_idx += 1 s_idx += 1 while s[s_idx] >= b'a': s_idx += 1 r_idx += nmatches nmatches = 0 if md_tag[md_idx] == b'^': md_idx += 1 while md_tag[md_idx] >= 65 and md_tag[md_idx] <= 90: # assert s[s_idx] == '-' s[s_idx] = md_tag[md_idx] s_idx += 1 md_idx += 1 else: # save mismatch # enforce lower case c = md_tag[md_idx] if c <= 90: c += 32 s[s_idx] = c s_idx += 1 r_idx += 1 md_idx += 1 # save matches up to this point, skipping insertions for x from 0 <= x < nmatches: while s[s_idx] >= b'a': s_idx += 1 s_idx += 1 while s[s_idx] >= b'a': s_idx += 1 seq = PyBytes_FromStringAndSize(s, s_idx) free(s) return seq cdef inline bytes build_reference_sequence(bam1_t * src): """return the reference sequence in the region that is covered by the alignment of the read to the reference. This method requires the MD tag to be set. """ cdef uint32_t k, i, l cdef int op cdef int s_idx = 0 ref_seq = build_alignment_sequence(src) if ref_seq is None: raise ValueError("MD tag not present") cdef char * s = calloc(len(ref_seq) + 1, sizeof(char)) if s == NULL: raise ValueError( "could not allocate sequence of length %i" % len(ref_seq)) cdef char * cref_seq = ref_seq cdef uint32_t * cigar_p = pysam_bam_get_cigar(src) cdef uint32_t r_idx = 0 for k from 0 <= k < pysam_get_n_cigar(src): op = cigar_p[k] & BAM_CIGAR_MASK l = cigar_p[k] >> BAM_CIGAR_SHIFT if op == BAM_CMATCH or op == BAM_CEQUAL or op == BAM_CDIFF: for i from 0 <= i < l: s[s_idx] = cref_seq[r_idx] r_idx += 1 s_idx += 1 elif op == BAM_CDEL: for i from 0 <= i < l: s[s_idx] = cref_seq[r_idx] r_idx += 1 s_idx += 1 elif op == BAM_CREF_SKIP: pass elif op == BAM_CINS or op == BAM_CPAD: r_idx += l elif op == BAM_CSOFT_CLIP: pass elif op == BAM_CHARD_CLIP: pass # advances neither seq = PyBytes_FromStringAndSize(s, s_idx) free(s) return seq cdef inline str safe_reference_name(AlignmentHeader header, int tid): if tid == -1: return "*" elif header is not None: return header.get_reference_name(tid) else: return f"#{tid}" # Tuple-building helper functions used by AlignedSegment.get_aligned_pairs() cdef _alignedpairs_positions(qpos, pos, ref_seq, uint32_t r_idx, int op): return (qpos, pos) cdef _alignedpairs_with_seq(qpos, pos, ref_seq, uint32_t r_idx, int op): ref_base = ref_seq[r_idx] if ref_seq is not None else None return (qpos, pos, ref_base) cdef _alignedpairs_with_cigar(qpos, pos, ref_seq, uint32_t r_idx, int op): return (qpos, pos, CIGAR_OPS(op)) cdef _alignedpairs_with_seq_cigar(qpos, pos, ref_seq, uint32_t r_idx, int op): ref_base = ref_seq[r_idx] if ref_seq is not None else None return (qpos, pos, ref_base, CIGAR_OPS(op)) cdef class AlignedSegment: '''Class representing an aligned segment. This class stores a handle to the samtools C-structure representing an aligned read. Member read access is forwarded to the C-structure and converted into python objects. This implementation should be fast, as only the data needed is converted. For write access, the C-structure is updated in-place. This is not the most efficient way to build BAM entries, as the variable length data is concatenated and thus needs to be resized if a field is updated. Furthermore, the BAM entry might be in an inconsistent state. One issue to look out for is that the sequence should always be set *before* the quality scores. Setting the sequence will also erase any quality scores that were set previously. Parameters ---------- header: :class:`~pysam.AlignmentHeader` object to map numerical identifiers to chromosome names. If not given, an empty header is created. ''' # Now only called when instances are created from Python def __init__(self, AlignmentHeader header=None): # see bam_init1 self._delegate = calloc(1, sizeof(bam1_t)) if self._delegate == NULL: raise MemoryError("could not allocated memory of {} bytes".format(sizeof(bam1_t))) # allocate some memory. If size is 0, calloc does not return a # pointer that can be passed to free() so allocate 40 bytes # for a new read self._delegate.m_data = 40 self._delegate.data = calloc( self._delegate.m_data, 1) if self._delegate.data == NULL: raise MemoryError("could not allocate memory of {} bytes".format(self._delegate.m_data)) self._delegate.l_data = 0 # set some data to make read approximately legit. # Note, SAM writing fails with q_name of length 0 self._delegate.core.l_qname = 0 self._delegate.core.tid = -1 self._delegate.core.pos = -1 self._delegate.core.mtid = -1 self._delegate.core.mpos = -1 # caching for selected fields self.cache_query_qualities = None self.cache_query_alignment_qualities = None self.cache_query_sequence = None self.cache_query_alignment_sequence = None self.header = header def __dealloc__(self): bam_destroy1(self._delegate) def __str__(self): """return string representation of alignment. The representation is an approximate :term:`SAM` format, because an aligned read might not be associated with a :term:`AlignmentFile`. Hence when the read does not have an associated :class:`AlignedHeader`, :term:`tid` is shown instead of the reference name. Similarly, the tags field is returned in its parsed state. To get a valid SAM record, use :meth:`to_string`. """ # sam-parsing is done in sam.c/bam_format1_core which # requires a valid header. return "\t".join(map(str, (self.query_name, self.flag, safe_reference_name(self.header, self.reference_id), self.reference_start + 1, self.mapping_quality, self.cigarstring, safe_reference_name(self.header, self.next_reference_id), self.next_reference_start + 1, self.template_length, self.query_sequence, self.query_qualities, self.tags))) def __repr__(self): ref = self.reference_name if self.header is not None else self.reference_id return f'<{type(self).__name__}({self.query_name!r}, flags={self.flag}={self.flag:#x}, ref={ref!r}, zpos={self.reference_start}, mapq={self.mapping_quality}, cigar={self.cigarstring!r}, ...)>' def __copy__(self): return makeAlignedSegment(self._delegate, self.header) def __deepcopy__(self, memo): return makeAlignedSegment(self._delegate, self.header) def compare(self, AlignedSegment other): '''return -1,0,1, if contents in this are binary <,=,> to *other* ''' # avoid segfault when other equals None if other is None: return -1 cdef int retval, x cdef bam1_t *t cdef bam1_t *o t = self._delegate o = other._delegate # uncomment for debugging purposes # cdef unsigned char * oo, * tt # tt = (&t.core) # oo = (&o.core) # for x from 0 <= x < sizeof( bam1_core_t): print x, tt[x], oo[x] # tt = (t.data) # oo = (o.data) # for x from 0 <= x < max(t.l_data, o.l_data): print x, tt[x], oo[x], chr(tt[x]), chr(oo[x]) # Fast-path test for object identity if t == o: return 0 cdef uint8_t *a = &t.core cdef uint8_t *b = &o.core retval = memcmp(&t.core, &o.core, sizeof(bam1_core_t)) if retval: return retval # cmp(t.l_data, o.l_data) retval = (t.l_data > o.l_data) - (t.l_data < o.l_data) if retval: return retval return memcmp(t.data, o.data, t.l_data) def __richcmp__(self, AlignedSegment other, int op): if op == 2: # == operator return self.compare(other) == 0 elif op == 3: # != operator return self.compare(other) != 0 else: return NotImplemented def __hash__(self): cdef bam1_t * src = self._delegate cdef int x # see http://effbot.org/zone/python-hash.htm cdef uint8_t * c = &src.core cdef uint32_t hash_value = c[0] for x from 1 <= x < sizeof(bam1_core_t): hash_value = c_mul(hash_value, 1000003) ^ c[x] c = src.data for x from 0 <= x < src.l_data: hash_value = c_mul(hash_value, 1000003) ^ c[x] return hash_value cpdef to_string(self): """returns a string representation of the aligned segment. The output format is valid SAM format if a header is associated with the AlignedSegment. """ cdef kstring_t line line.l = line.m = 0 line.s = NULL if self.header: if sam_format1(self.header.ptr, self._delegate, &line) < 0: if line.m: free(line.s) raise ValueError('sam_format failed') else: raise NotImplementedError("todo") ret = force_str(line.s[:line.l]) if line.m: free(line.s) return ret @classmethod def fromstring(cls, sam, AlignmentHeader header): """parses a string representation of the aligned segment. The input format should be valid SAM format. Parameters ---------- sam: :term:`SAM` formatted string """ cdef AlignedSegment dest = cls.__new__(cls) dest._delegate = calloc(1, sizeof(bam1_t)) dest.header = header cdef kstring_t line line.l = line.m = len(sam) _sam = force_bytes(sam) line.s = _sam cdef int ret ret = sam_parse1(&line, dest.header.ptr, dest._delegate) if ret < 0: raise ValueError("parsing SAM record string failed (error code {})".format(ret)) return dest cpdef tostring(self, htsfile=None): """deprecated, use :meth:`to_string()` instead. Parameters ---------- htsfile: (deprecated) AlignmentFile object to map numerical identifiers to chromosome names. This parameter is present for backwards compatibility and ignored. """ return self.to_string() def to_dict(self): """returns a json representation of the aligned segment. Field names are abbreviated versions of the class attributes. """ # let htslib do the string conversions, but treat optional field properly as list vals = self.to_string().split("\t") n = len(KEY_NAMES) - 1 return dict(list(zip(KEY_NAMES[:-1], vals[:n])) + [(KEY_NAMES[-1], vals[n:])]) @classmethod def from_dict(cls, sam_dict, AlignmentHeader header): """parses a dictionary representation of the aligned segment. Parameters ---------- sam_dict: dictionary of alignment values, keys corresponding to output from :meth:`todict()`. """ # let htslib do the parsing # the tags field can be missing return cls.fromstring( "\t".join((sam_dict[x] for x in KEY_NAMES[:-1])) + "\t" + "\t".join(sam_dict.get(KEY_NAMES[-1], [])), header) ######################################################## ## Basic attributes in order of appearance in SAM format property query_name: """the query template name (None if not present)""" def __get__(self): cdef bam1_t * src = self._delegate if src.core.l_qname == 0: return None return charptr_to_str(pysam_bam_get_qname(src)) def __set__(self, qname): if qname is None or len(qname) == 0: return if len(qname) > 254: raise ValueError("query length out of range {} > 254".format( len(qname))) qname = force_bytes(qname) cdef bam1_t * src = self._delegate # the qname is \0 terminated cdef uint8_t l = len(qname) + 1 cdef char * p = pysam_bam_get_qname(src) cdef uint8_t l_extranul = 0 if l % 4 != 0: l_extranul = 4 - l % 4 cdef bam1_t * retval = pysam_bam_update(src, src.core.l_qname, l + l_extranul, p) if retval == NULL: raise MemoryError("could not allocate memory") src.core.l_extranul = l_extranul src.core.l_qname = l + l_extranul # re-acquire pointer to location in memory # as it might have moved p = pysam_bam_get_qname(src) strncpy(p, qname, l) # x might be > 255 cdef uint16_t x = 0 for x from l <= x < l + l_extranul: p[x] = b'\0' property flag: """properties flag""" def __get__(self): return self._delegate.core.flag def __set__(self, flag): self._delegate.core.flag = flag property reference_name: """:term:`reference` name""" def __get__(self): if self._delegate.core.tid == -1: return None if self.header: return self.header.get_reference_name(self._delegate.core.tid) else: raise ValueError("reference_name unknown if no header associated with record") def __set__(self, reference): cdef int tid if reference is None or reference == "*": self._delegate.core.tid = -1 elif self.header: tid = self.header.get_tid(reference) if tid < 0: raise ValueError("reference {} does not exist in header".format( reference)) self._delegate.core.tid = tid else: raise ValueError("reference_name can not be set if no header associated with record") property reference_id: """:term:`reference` ID .. note:: This field contains the index of the reference sequence in the sequence dictionary. To obtain the name of the reference sequence, use :meth:`get_reference_name()` """ def __get__(self): return self._delegate.core.tid def __set__(self, tid): if tid != -1 and self.header and not self.header.is_valid_tid(tid): raise ValueError("reference id {} does not exist in header".format( tid)) self._delegate.core.tid = tid property reference_start: """0-based leftmost coordinate""" def __get__(self): return self._delegate.core.pos def __set__(self, pos): ## setting the position requires updating the "bin" attribute cdef bam1_t * src src = self._delegate src.core.pos = pos update_bin(src) property mapping_quality: """mapping quality""" def __get__(self): return pysam_get_qual(self._delegate) def __set__(self, qual): pysam_set_qual(self._delegate, qual) property cigarstring: '''the :term:`cigar` alignment as a string. The cigar string is a string of alternating integers and characters denoting the length and the type of an operation. .. note:: The order length,operation is specified in the SAM format. It is different from the order of the :attr:`cigar` property. Returns None if not present. To unset the cigarstring, assign None or the empty string. ''' def __get__(self): c = self.cigartuples if c is None: return None # reverse order else: return "".join([ "%i%c" % (y,CODE2CIGAR[x]) for x,y in c]) def __set__(self, cigar): if cigar is None or len(cigar) == 0: self.cigartuples = [] else: parts = CIGAR_REGEX.findall(cigar) # reverse order self.cigartuples = [(CIGAR2CODE[ord(y)], int(x)) for x,y in parts] # TODO # property cigar: # """the cigar alignment""" property next_reference_id: """the :term:`reference` id of the mate/next read.""" def __get__(self): return self._delegate.core.mtid def __set__(self, mtid): if mtid != -1 and self.header and not self.header.is_valid_tid(mtid): raise ValueError("reference id {} does not exist in header".format( mtid)) self._delegate.core.mtid = mtid property next_reference_name: """:term:`reference` name of the mate/next read (None if no AlignmentFile is associated)""" def __get__(self): if self._delegate.core.mtid == -1: return None if self.header: return self.header.get_reference_name(self._delegate.core.mtid) else: raise ValueError("next_reference_name unknown if no header associated with record") def __set__(self, reference): cdef int mtid if reference is None or reference == "*": self._delegate.core.mtid = -1 elif reference == "=": self._delegate.core.mtid = self._delegate.core.tid elif self.header: mtid = self.header.get_tid(reference) if mtid < 0: raise ValueError("reference {} does not exist in header".format( reference)) self._delegate.core.mtid = mtid else: raise ValueError("next_reference_name can not be set if no header associated with record") property next_reference_start: """the position of the mate/next read.""" def __get__(self): return self._delegate.core.mpos def __set__(self, mpos): self._delegate.core.mpos = mpos property query_length: """the length of the query/read. This value corresponds to the length of the sequence supplied in the BAM/SAM file. The length of a query is 0 if there is no sequence in the BAM/SAM file. In those cases, the read length can be inferred from the CIGAR alignment, see :meth:`pysam.AlignedSegment.infer_query_length`. The length includes soft-clipped bases and is equal to ``len(query_sequence)``. This property is read-only but is updated when a new query sequence is assigned to this AlignedSegment. Returns 0 if not available. """ def __get__(self): return self._delegate.core.l_qseq property template_length: """the observed query template length""" def __get__(self): return self._delegate.core.isize def __set__(self, isize): self._delegate.core.isize = isize property query_sequence: """read sequence bases, including :term:`soft clipped` bases (None if not present). Assigning to this attribute will invalidate any quality scores. Thus, to in-place edit the sequence and quality scores, copies of the quality scores need to be taken. Consider trimming for example:: q = read.query_qualities read.query_sequence = read.query_sequence[5:10] read.query_qualities = q[5:10] The sequence is returned as it is stored in the BAM file. (This will be the reverse complement of the original read sequence if the mapper has aligned the read to the reverse strand.) """ def __get__(self): if self.cache_query_sequence: return self.cache_query_sequence cdef bam1_t * src cdef char * s src = self._delegate if src.core.l_qseq == 0: return None self.cache_query_sequence = force_str(getSequenceInRange( src, 0, src.core.l_qseq)) return self.cache_query_sequence def __set__(self, seq): # samtools manages sequence and quality length memory together # if no quality information is present, the first byte says 0xff. cdef bam1_t * src cdef uint8_t * p cdef char * s cdef int l, k cdef Py_ssize_t nbytes_new, nbytes_old if seq == None: l = 0 else: l = len(seq) seq = force_bytes(seq) src = self._delegate # as the sequence is stored in half-bytes, the total length (sequence # plus quality scores) is (l+1)/2 + l nbytes_new = (l + 1) // 2 + l nbytes_old = (src.core.l_qseq + 1) // 2 + src.core.l_qseq # acquire pointer to location in memory p = pysam_bam_get_seq(src) src.core.l_qseq = l # change length of data field cdef bam1_t * retval = pysam_bam_update(src, nbytes_old, nbytes_new, p) if retval == NULL: raise MemoryError("could not allocate memory") if l > 0: # re-acquire pointer to location in memory # as it might have moved p = pysam_bam_get_seq(src) for k from 0 <= k < nbytes_new: p[k] = 0 # convert to C string s = seq for k from 0 <= k < l: p[k // 2] |= seq_nt16_table[s[k]] << 4 * (1 - k % 2) # erase qualities p = pysam_bam_get_qual(src) memset(p, 0xff, l) self.cache_query_sequence = force_str(seq) # clear cached values for quality values self.cache_query_qualities = None self.cache_query_alignment_qualities = None property query_qualities: """read sequence base qualities, including :term:`soft clipped` bases (None if not present). Quality scores are returned as a python array of unsigned chars. Note that this is not the ASCII-encoded value typically seen in FASTQ or SAM formatted files. Thus, no offset of 33 needs to be subtracted. Note that to set quality scores the sequence has to be set beforehand as this will determine the expected length of the quality score array. This method raises a ValueError if the length of the quality scores and the sequence are not the same. """ def __get__(self): if self.cache_query_qualities: return self.cache_query_qualities cdef bam1_t * src cdef char * q src = self._delegate if src.core.l_qseq == 0: return None self.cache_query_qualities = getQualitiesInRange(src, 0, src.core.l_qseq) return self.cache_query_qualities def __set__(self, qual): # note that memory is already allocated via setting the sequence # hence length match of sequence and quality needs is checked. cdef bam1_t * src cdef uint8_t * p cdef int l src = self._delegate p = pysam_bam_get_qual(src) if qual is None or len(qual) == 0: # if absent and there is a sequence: set to 0xff memset(p, 0xff, src.core.l_qseq) return # check for length match l = len(qual) if src.core.l_qseq != l: raise ValueError( "quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq)) # create a python array object filling it # with the quality scores # NB: should avoid this copying if qual is # already of the correct type. cdef c_array.array result = c_array.array('B', qual) # copy data memcpy(p, result.data.as_voidptr, l) # save in cache self.cache_query_qualities = qual property bin: """properties bin""" def __get__(self): return self._delegate.core.bin def __set__(self, bin): self._delegate.core.bin = bin ########################################################## # Derived simple attributes. These are simple attributes of # AlignedSegment getting and setting values. ########################################################## # 1. Flags ########################################################## property is_paired: """true if read is paired in sequencing""" def __get__(self): return (self.flag & BAM_FPAIRED) != 0 def __set__(self,val): pysam_update_flag(self._delegate, val, BAM_FPAIRED) property is_proper_pair: """true if read is mapped in a proper pair""" def __get__(self): return (self.flag & BAM_FPROPER_PAIR) != 0 def __set__(self,val): pysam_update_flag(self._delegate, val, BAM_FPROPER_PAIR) property is_unmapped: """true if read itself is unmapped""" def __get__(self): return (self.flag & BAM_FUNMAP) != 0 def __set__(self, val): pysam_update_flag(self._delegate, val, BAM_FUNMAP) # setting the unmapped flag requires recalculation of # bin as alignment length is now implicitly 1 update_bin(self._delegate) property is_mapped: """true if read itself is mapped (implemented in terms of :attr:`is_unmapped`)""" def __get__(self): return (self.flag & BAM_FUNMAP) == 0 def __set__(self, val): pysam_update_flag(self._delegate, not val, BAM_FUNMAP) update_bin(self._delegate) property mate_is_unmapped: """true if the mate is unmapped""" def __get__(self): return (self.flag & BAM_FMUNMAP) != 0 def __set__(self,val): pysam_update_flag(self._delegate, val, BAM_FMUNMAP) property mate_is_mapped: """true if the mate is mapped (implemented in terms of :attr:`mate_is_unmapped`)""" def __get__(self): return (self.flag & BAM_FMUNMAP) == 0 def __set__(self,val): pysam_update_flag(self._delegate, not val, BAM_FMUNMAP) property is_reverse: """true if read is mapped to reverse strand""" def __get__(self): return (self.flag & BAM_FREVERSE) != 0 def __set__(self,val): pysam_update_flag(self._delegate, val, BAM_FREVERSE) property is_forward: """true if read is mapped to forward strand (implemented in terms of :attr:`is_reverse`)""" def __get__(self): return (self.flag & BAM_FREVERSE) == 0 def __set__(self,val): pysam_update_flag(self._delegate, not val, BAM_FREVERSE) property mate_is_reverse: """true if the mate is mapped to reverse strand""" def __get__(self): return (self.flag & BAM_FMREVERSE) != 0 def __set__(self,val): pysam_update_flag(self._delegate, val, BAM_FMREVERSE) property mate_is_forward: """true if the mate is mapped to forward strand (implemented in terms of :attr:`mate_is_reverse`)""" def __get__(self): return (self.flag & BAM_FMREVERSE) == 0 def __set__(self,val): pysam_update_flag(self._delegate, not val, BAM_FMREVERSE) property is_read1: """true if this is read1""" def __get__(self): return (self.flag & BAM_FREAD1) != 0 def __set__(self,val): pysam_update_flag(self._delegate, val, BAM_FREAD1) property is_read2: """true if this is read2""" def __get__(self): return (self.flag & BAM_FREAD2) != 0 def __set__(self, val): pysam_update_flag(self._delegate, val, BAM_FREAD2) property is_secondary: """true if not primary alignment""" def __get__(self): return (self.flag & BAM_FSECONDARY) != 0 def __set__(self, val): pysam_update_flag(self._delegate, val, BAM_FSECONDARY) property is_qcfail: """true if QC failure""" def __get__(self): return (self.flag & BAM_FQCFAIL) != 0 def __set__(self, val): pysam_update_flag(self._delegate, val, BAM_FQCFAIL) property is_duplicate: """true if optical or PCR duplicate""" def __get__(self): return (self.flag & BAM_FDUP) != 0 def __set__(self, val): pysam_update_flag(self._delegate, val, BAM_FDUP) property is_supplementary: """true if this is a supplementary alignment""" def __get__(self): return (self.flag & BAM_FSUPPLEMENTARY) != 0 def __set__(self, val): pysam_update_flag(self._delegate, val, BAM_FSUPPLEMENTARY) # 2. Coordinates and lengths property reference_end: '''aligned reference position of the read on the reference genome. reference_end points to one past the last aligned residue. Returns None if not available (read is unmapped or no cigar alignment present). ''' def __get__(self): cdef bam1_t * src src = self._delegate if (self.flag & BAM_FUNMAP) or pysam_get_n_cigar(src) == 0: return None return bam_endpos(src) property reference_length: '''aligned length of the read on the reference genome. This is equal to `reference_end - reference_start`. Returns None if not available. ''' def __get__(self): cdef bam1_t * src src = self._delegate if (self.flag & BAM_FUNMAP) or pysam_get_n_cigar(src) == 0: return None return bam_endpos(src) - \ self._delegate.core.pos property query_alignment_sequence: """aligned portion of the read. This is a substring of :attr:`query_sequence` that excludes flanking bases that were :term:`soft clipped` (None if not present). It is equal to ``query_sequence[query_alignment_start:query_alignment_end]``. SAM/BAM files may include extra flanking bases that are not part of the alignment. These bases may be the result of the Smith-Waterman or other algorithms, which may not require alignments that begin at the first residue or end at the last. In addition, extra sequencing adapters, multiplex identifiers, and low-quality bases that were not considered for alignment may have been retained. """ def __get__(self): if self.cache_query_alignment_sequence: return self.cache_query_alignment_sequence cdef bam1_t * src cdef uint32_t start, end src = self._delegate if src.core.l_qseq == 0: return None start = getQueryStart(src) end = getQueryEnd(src) self.cache_query_alignment_sequence = force_str( getSequenceInRange(src, start, end)) return self.cache_query_alignment_sequence property query_alignment_qualities: """aligned query sequence quality values (None if not present). These are the quality values that correspond to :attr:`query_alignment_sequence`, that is, they exclude qualities of :term:`soft clipped` bases. This is equal to ``query_qualities[query_alignment_start:query_alignment_end]``. Quality scores are returned as a python array of unsigned chars. Note that this is not the ASCII-encoded value typically seen in FASTQ or SAM formatted files. Thus, no offset of 33 needs to be subtracted. This property is read-only. """ def __get__(self): if self.cache_query_alignment_qualities: return self.cache_query_alignment_qualities cdef bam1_t * src cdef uint32_t start, end src = self._delegate if src.core.l_qseq == 0: return None start = getQueryStart(src) end = getQueryEnd(src) self.cache_query_alignment_qualities = \ getQualitiesInRange(src, start, end) return self.cache_query_alignment_qualities property query_alignment_start: """start index of the aligned query portion of the sequence (0-based, inclusive). This the index of the first base in :attr:`query_sequence` that is not soft-clipped. """ def __get__(self): return getQueryStart(self._delegate) property query_alignment_end: """end index of the aligned query portion of the sequence (0-based, exclusive) This the index just past the last base in :attr:`query_sequence` that is not soft-clipped. """ def __get__(self): return getQueryEnd(self._delegate) property modified_bases: """Modified bases annotations from Ml/Mm tags. The output is Dict[(canonical base, strand, modification)] -> [ (pos,qual), ...] with qual being (256*probability), or -1 if unknown. Strand==0 for forward and 1 for reverse strand modification """ def __get__(self): cdef bam1_t * src cdef hts_base_mod_state *m = hts_base_mod_state_alloc() cdef hts_base_mod mods[5] cdef int pos ret = {} src = self._delegate if bam_parse_basemod(src, m) < 0: return None n = bam_next_basemod(src, m, mods, 5, &pos) while n>0: for i in range(n): mod_code = chr(mods[i].modified_base) if mods[i].modified_base>0 else -mods[i].modified_base mod_strand = mods[i].strand if self.is_reverse: mod_strand = 1 - mod_strand key = (chr(mods[i].canonical_base), mod_strand, mod_code ) ret.setdefault(key,[]).append((pos,mods[i].qual)) n = bam_next_basemod(src, m, mods, 5, &pos) if n<0: return None hts_base_mod_state_free(m) return ret property modified_bases_forward: """Modified bases annotations from Ml/Mm tags. The output is Dict[(canonical base, strand, modification)] -> [ (pos,qual), ...] with qual being (256*probability), or -1 if unknown. Strand==0 for forward and 1 for reverse strand modification. The positions are with respect to the original sequence from get_forward_sequence() """ def __get__(self): pmods = self.modified_bases if pmods and self.is_reverse: rmod = {} # Try to find the length of the original sequence rlen = self.infer_read_length() if rlen is None and self.query_sequence is None: return rmod else: rlen = len(self.query_sequence) for k,mods in pmods.items(): nk = k[0],1 - k[1],k[2] for i in range(len(mods)): mods[i] = (rlen - 1 -mods[i][0], mods[i][1]) rmod[nk] = mods return rmod return pmods property query_alignment_length: """length of the aligned query sequence. This is equal to :attr:`query_alignment_end` - :attr:`query_alignment_start` """ def __get__(self): cdef bam1_t * src src = self._delegate return getQueryEnd(src) - getQueryStart(src) ##################################################### # Computed properties def get_reference_positions(self, full_length=False): """a list of reference positions that this read aligns to. By default, this method returns the (0-based) positions on the reference that are within the read's alignment, leaving gaps corresponding to deletions and other reference skips. When *full_length* is True, the returned list is the same length as the read and additionally includes None values corresponding to insertions or soft-clipping, i.e., to bases of the read that are not aligned to a reference position. (See also :meth:`get_aligned_pairs` which additionally returns the corresponding positions along the read.) """ cdef uint32_t k, i, l, pos cdef int op cdef uint32_t * cigar_p cdef bam1_t * src cdef bint _full = full_length src = self._delegate if pysam_get_n_cigar(src) == 0: return [] result = [] pos = src.core.pos cigar_p = pysam_bam_get_cigar(src) for k from 0 <= k < pysam_get_n_cigar(src): op = cigar_p[k] & BAM_CIGAR_MASK l = cigar_p[k] >> BAM_CIGAR_SHIFT if op == BAM_CSOFT_CLIP or op == BAM_CINS: if _full: for i from 0 <= i < l: result.append(None) elif op == BAM_CMATCH or op == BAM_CEQUAL or op == BAM_CDIFF: for i from pos <= i < pos + l: result.append(i) pos += l elif op == BAM_CDEL or op == BAM_CREF_SKIP: pos += l return result def infer_query_length(self, always=False): """infer query length from CIGAR alignment. This method deduces the query length from the CIGAR alignment but does not include hard-clipped bases. Returns None if CIGAR alignment is not present. If *always* is set to True, `infer_read_length` is used instead. This is deprecated and only present for backward compatibility. """ if always is True: return self.infer_read_length() cdef int32_t l = calculateQueryLengthWithoutHardClipping(self._delegate) if l > 0: return l else: return None def infer_read_length(self): """infer read length from CIGAR alignment. This method deduces the read length from the CIGAR alignment including hard-clipped bases. Returns None if CIGAR alignment is not present. """ cdef int32_t l = calculateQueryLengthWithHardClipping(self._delegate) if l > 0: return l else: return None def get_reference_sequence(self): """return the reference sequence in the region that is covered by the alignment of the read to the reference. This method requires the MD tag to be set. """ return force_str(build_reference_sequence(self._delegate)) def get_forward_sequence(self): """return the original read sequence. Reads mapped to the reverse strand are stored reverse complemented in the BAM file. This method returns such reads reverse complemented back to their original orientation. Returns None if the record has no query sequence. """ if self.query_sequence is None: return None s = force_str(self.query_sequence) if self.is_reverse: s = s.translate(str.maketrans("ACGTacgtNnXx", "TGCAtgcaNnXx"))[::-1] return s def get_forward_qualities(self): """return the original base qualities of the read sequence, in the same format as the :attr:`query_qualities` property. Reads mapped to the reverse strand have their base qualities stored reversed in the BAM file. This method returns such reads' base qualities reversed back to their original orientation. """ if self.is_reverse: return self.query_qualities[::-1] else: return self.query_qualities def get_aligned_pairs(self, matches_only=False, with_seq=False, with_cigar=False): """a list of aligned read (query) and reference positions. Each item in the returned list is a tuple consisting of the 0-based offset from the start of the read sequence followed by the 0-based reference position. For inserts, deletions, skipping either query or reference position may be None. For padding in the reference, the reference position will always be None. Parameters ---------- matches_only : bool If True, only matched bases are returned --- no None on either side. with_seq : bool If True, return a third element in the tuple containing the reference sequence. For CIGAR 'P' (padding in the reference) operations, the third tuple element will be None. Substitutions are lower-case. This option requires an MD tag to be present. with_cigar : bool If True, return an extra element in the tuple containing the CIGAR operator corresponding to this position tuple. Returns ------- aligned_pairs : list of tuples """ cdef uint32_t k, i, pos, qpos, r_idx, l cdef int op cdef uint32_t * cigar_p cdef bam1_t * src = self._delegate cdef bint _matches_only = bool(matches_only) cdef bint _with_seq = bool(with_seq) cdef bint _with_cigar = bool(with_cigar) cdef object (*make_tuple)(object, object, object, uint32_t, int) # TODO: this method performs no checking and assumes that # read sequence, cigar and MD tag are consistent. if _with_seq: # force_str required for py2/py3 compatibility ref_seq = force_str(build_reference_sequence(src)) if ref_seq is None: raise ValueError("MD tag not present") make_tuple = _alignedpairs_with_seq_cigar if _with_cigar else _alignedpairs_with_seq else: ref_seq = None make_tuple = _alignedpairs_with_cigar if _with_cigar else _alignedpairs_positions r_idx = 0 if pysam_get_n_cigar(src) == 0: return [] result = [] pos = src.core.pos qpos = 0 cigar_p = pysam_bam_get_cigar(src) for k from 0 <= k < pysam_get_n_cigar(src): op = cigar_p[k] & BAM_CIGAR_MASK l = cigar_p[k] >> BAM_CIGAR_SHIFT if op == BAM_CMATCH or op == BAM_CEQUAL or op == BAM_CDIFF: for i from pos <= i < pos + l: result.append(make_tuple(qpos, i, ref_seq, r_idx, op)) r_idx += 1 qpos += 1 pos += l elif op == BAM_CINS or op == BAM_CSOFT_CLIP or op == BAM_CPAD: if not _matches_only: for i from pos <= i < pos + l: result.append(make_tuple(qpos, None, None, 0, op)) qpos += 1 else: qpos += l elif op == BAM_CDEL: if not _matches_only: for i from pos <= i < pos + l: result.append(make_tuple(None, i, ref_seq, r_idx, op)) r_idx += 1 else: r_idx += l pos += l elif op == BAM_CHARD_CLIP: pass # advances neither elif op == BAM_CREF_SKIP: if not _matches_only: for i from pos <= i < pos + l: result.append(make_tuple(None, i, None, 0, op)) pos += l return result def get_blocks(self): """ a list of start and end positions of aligned gapless blocks. The start and end positions are in genomic coordinates. Blocks are not normalized, i.e. two blocks might be directly adjacent. This happens if the two blocks are separated by an insertion in the read. """ cdef uint32_t k, pos, l cdef int op cdef uint32_t * cigar_p cdef bam1_t * src src = self._delegate if pysam_get_n_cigar(src) == 0: return [] result = [] pos = src.core.pos cigar_p = pysam_bam_get_cigar(src) l = 0 for k from 0 <= k < pysam_get_n_cigar(src): op = cigar_p[k] & BAM_CIGAR_MASK l = cigar_p[k] >> BAM_CIGAR_SHIFT if op == BAM_CMATCH or op == BAM_CEQUAL or op == BAM_CDIFF: result.append((pos, pos + l)) pos += l elif op == BAM_CDEL or op == BAM_CREF_SKIP: pos += l return result def get_overlap(self, uint32_t start, uint32_t end): """return number of aligned bases of read overlapping the interval *start* and *end* on the reference sequence. Return None if cigar alignment is not available. """ cdef uint32_t k, i, pos, overlap cdef int op, o cdef uint32_t * cigar_p cdef bam1_t * src overlap = 0 src = self._delegate if pysam_get_n_cigar(src) == 0: return None pos = src.core.pos o = 0 cigar_p = pysam_bam_get_cigar(src) for k from 0 <= k < pysam_get_n_cigar(src): op = cigar_p[k] & BAM_CIGAR_MASK l = cigar_p[k] >> BAM_CIGAR_SHIFT if op == BAM_CMATCH or op == BAM_CEQUAL or op == BAM_CDIFF: o = min( pos + l, end) - max( pos, start ) if o > 0: overlap += o if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP or op == BAM_CEQUAL or op == BAM_CDIFF: pos += l return overlap def get_cigar_stats(self): """summary of operations in cigar string. The output order in the array is "MIDNSHP=X" followed by a field for the NM tag. If the NM tag is not present, this field will always be 0. (Accessing this field via index -1 avoids changes if more CIGAR operators are added in future.) +-----+----------------+--------+ |M |pysam.CMATCH |0 | +-----+----------------+--------+ |I |pysam.CINS |1 | +-----+----------------+--------+ |D |pysam.CDEL |2 | +-----+----------------+--------+ |N |pysam.CREF_SKIP |3 | +-----+----------------+--------+ |S |pysam.CSOFT_CLIP|4 | +-----+----------------+--------+ |H |pysam.CHARD_CLIP|5 | +-----+----------------+--------+ |P |pysam.CPAD |6 | +-----+----------------+--------+ |= |pysam.CEQUAL |7 | +-----+----------------+--------+ |X |pysam.CDIFF |8 | +-----+----------------+--------+ |B |pysam.CBACK |9 | +-----+----------------+--------+ |NM |NM tag |10 or -1| +-----+----------------+--------+ If no cigar string is present, empty arrays will be returned. Returns: arrays : two arrays. The first contains the nucleotide counts within each cigar operation, the second contains the number of blocks for each cigar operation. """ cdef int nfields = NCIGAR_CODES + 1 cdef c_array.array base_counts = array.array( "I", [0] * nfields) cdef uint32_t [:] base_view = base_counts cdef c_array.array block_counts = array.array( "I", [0] * nfields) cdef uint32_t [:] block_view = block_counts cdef bam1_t * src = self._delegate cdef int op cdef uint32_t l cdef int32_t k cdef uint32_t * cigar_p = pysam_bam_get_cigar(src) if cigar_p == NULL: return None for k from 0 <= k < pysam_get_n_cigar(src): op = cigar_p[k] & BAM_CIGAR_MASK l = cigar_p[k] >> BAM_CIGAR_SHIFT base_view[op] += l block_view[op] += 1 cdef uint8_t * v = bam_aux_get(src, 'NM') if v != NULL: base_view[nfields - 1] = bam_aux2i(v) return base_counts, block_counts ##################################################### ## Unsorted as yet # TODO: capture in CIGAR object property cigartuples: """the :term:`cigar` alignment. The alignment is returned as a list of tuples of (operation, length). If the alignment is not present, None is returned. The operations are: +-----+----------------+-----+ |M |pysam.CMATCH |0 | +-----+----------------+-----+ |I |pysam.CINS |1 | +-----+----------------+-----+ |D |pysam.CDEL |2 | +-----+----------------+-----+ |N |pysam.CREF_SKIP |3 | +-----+----------------+-----+ |S |pysam.CSOFT_CLIP|4 | +-----+----------------+-----+ |H |pysam.CHARD_CLIP|5 | +-----+----------------+-----+ |P |pysam.CPAD |6 | +-----+----------------+-----+ |= |pysam.CEQUAL |7 | +-----+----------------+-----+ |X |pysam.CDIFF |8 | +-----+----------------+-----+ |B |pysam.CBACK |9 | +-----+----------------+-----+ .. note:: The output is a list of (operation, length) tuples, such as ``[(0, 30)]``. This is different from the SAM specification and the :attr:`cigarstring` property, which uses a (length, operation) order, for example: ``30M``. To unset the cigar property, assign an empty list or None. """ def __get__(self): cdef uint32_t * cigar_p cdef bam1_t * src cdef uint32_t op, l cdef uint32_t k src = self._delegate if pysam_get_n_cigar(src) == 0: return None cigar = [] cigar_p = pysam_bam_get_cigar(src); for k from 0 <= k < pysam_get_n_cigar(src): op = cigar_p[k] & BAM_CIGAR_MASK l = cigar_p[k] >> BAM_CIGAR_SHIFT cigar.append((op, l)) return cigar def __set__(self, values): cdef uint32_t * p cdef bam1_t * src cdef op, l cdef int k k = 0 src = self._delegate # get location of cigar string p = pysam_bam_get_cigar(src) # empty values for cigar string if values is None: values = [] cdef uint32_t ncigar = len(values) cdef bam1_t * retval = pysam_bam_update(src, pysam_get_n_cigar(src) * 4, ncigar * 4, p) if retval == NULL: raise MemoryError("could not allocate memory") # length is number of cigar operations, not bytes pysam_set_n_cigar(src, ncigar) # re-acquire pointer to location in memory # as it might have moved p = pysam_bam_get_cigar(src) # insert cigar operations for op, l in values: p[k] = l << BAM_CIGAR_SHIFT | op k += 1 ## setting the cigar string requires updating the bin update_bin(src) cpdef set_tag(self, tag, value, value_type=None, replace=True): """sets a particular field *tag* to *value* in the optional alignment section. *value_type* describes the type of *value* that is to entered into the alignment record. It can be set explicitly to one of the valid one-letter type codes. If unset, an appropriate type will be chosen automatically based on the python type of *value*. An existing value of the same *tag* will be overwritten unless *replace* is set to False. This is usually not recommended as a tag may only appear once in the optional alignment section. If *value* is `None`, the tag will be deleted. This method accepts valid SAM specification value types, which are:: A: printable char i: signed int f: float Z: printable string H: Byte array in hex format B: Integer or numeric array Additionally, it will accept the integer BAM types ('cCsSI') For htslib compatibility, 'a' is synonymous with 'A' and the method accepts a 'd' type code for a double precision float. When deducing the type code by the python type of *value*, the following mapping is applied:: i: python int f: python float Z: python str or bytes B: python array.array, list or tuple Note that a single character string will be output as 'Z' and not 'A' as the former is the more general type. """ cdef int value_size cdef uint8_t tc cdef uint8_t * value_ptr cdef uint8_t *existing_ptr cdef float float_value cdef double double_value cdef int32_t int32_t_value cdef uint32_t uint32_t_value cdef int16_t int16_t_value cdef uint16_t uint16_t_value cdef int8_t int8_t_value cdef uint8_t uint8_t_value cdef bam1_t * src = self._delegate cdef char * _value_type cdef c_array.array array_value cdef object buffer if len(tag) != 2: raise ValueError('Invalid tag: %s' % tag) tag = force_bytes(tag) if replace: existing_ptr = bam_aux_get(src, tag) if existing_ptr: bam_aux_del(src, existing_ptr) # setting value to None deletes a tag if value is None: return cdef uint8_t typecode = get_tag_typecode(value, value_type) if typecode == 0: raise ValueError("can't guess type or invalid type code specified: {} {}".format( value, value_type)) # sam_format1 for typecasting if typecode == b'Z': value = force_bytes(value) value_ptr = value value_size = len(value)+1 elif typecode == b'H': # Note that hex tags are stored the very same # way as Z string.s value = force_bytes(value) value_ptr = value value_size = len(value)+1 elif typecode == b'A' or typecode == b'a': value = force_bytes(value) value_ptr = value value_size = sizeof(char) typecode = b'A' elif typecode == b'i': int32_t_value = value value_ptr = &int32_t_value value_size = sizeof(int32_t) elif typecode == b'I': uint32_t_value = value value_ptr = &uint32_t_value value_size = sizeof(uint32_t) elif typecode == b's': int16_t_value = value value_ptr = &int16_t_value value_size = sizeof(int16_t) elif typecode == b'S': uint16_t_value = value value_ptr = &uint16_t_value value_size = sizeof(uint16_t) elif typecode == b'c': int8_t_value = value value_ptr = &int8_t_value value_size = sizeof(int8_t) elif typecode == b'C': uint8_t_value = value value_ptr = &uint8_t_value value_size = sizeof(uint8_t) elif typecode == b'd': double_value = value value_ptr = &double_value value_size = sizeof(double) elif typecode == b'f': float_value = value value_ptr = &float_value value_size = sizeof(float) elif typecode == b'B': # the following goes through python, needs to be cleaned up # pack array using struct fmt, args = pack_tags([(tag, value, value_type)]) # remove tag and type code as set by bam_aux_append # first four chars of format (<2sB) fmt = '<' + fmt[4:] # first two values to pack args = args[2:] value_size = struct.calcsize(fmt) # buffer will be freed when object goes out of scope buffer = ctypes.create_string_buffer(value_size) struct.pack_into(fmt, buffer, 0, *args) # bam_aux_append copies data from value_ptr bam_aux_append(src, tag, typecode, value_size, buffer.raw) return else: raise ValueError('unsupported value_type {} in set_option'.format(typecode)) bam_aux_append(src, tag, typecode, value_size, value_ptr) cpdef has_tag(self, tag): """returns true if the optional alignment section contains a given *tag*.""" cdef uint8_t * v cdef int nvalues btag = force_bytes(tag) v = bam_aux_get(self._delegate, btag) return v != NULL cpdef get_tag(self, tag, with_value_type=False): """ retrieves data from the optional alignment section given a two-letter *tag* denoting the field. The returned value is cast into an appropriate python type. This method is the fastest way to access the optional alignment section if only few tags need to be retrieved. Possible value types are "AcCsSiIfZHB" (see BAM format specification) as well as additional value type 'd' as implemented in htslib. Parameters: tag : data tag. with_value_type : Optional[bool] if set to True, the return value is a tuple of (tag value, type code). (default False) Returns: A python object with the value of the `tag`. The type of the object depends on the data type in the data record. Raises: KeyError If `tag` is not present, a KeyError is raised. """ cdef uint8_t * v cdef int nvalues btag = force_bytes(tag) v = bam_aux_get(self._delegate, btag) if v == NULL: raise KeyError("tag '%s' not present" % tag) if chr(v[0]) == "B": auxtype = chr(v[0]) + chr(v[1]) else: auxtype = chr(v[0]) if auxtype in "iIcCsS": value = bam_aux2i(v) elif auxtype == 'f' or auxtype == 'F': value = bam_aux2f(v) elif auxtype == 'd' or auxtype == 'D': value = bam_aux2f(v) elif auxtype == 'A' or auxtype == 'a': # force A to a v[0] = b'A' # there might a more efficient way # to convert a char into a string value = '%c' % bam_aux2A(v) elif auxtype == 'Z' or auxtype == 'H': # Z and H are treated equally as strings in htslib value = charptr_to_str(bam_aux2Z(v)) elif auxtype[0] == 'B': bytesize, nvalues, values = convert_binary_tag(v + 1) value = values else: raise ValueError("unknown auxiliary type '%s'" % auxtype) if with_value_type: return (value, auxtype) else: return value def get_tags(self, with_value_type=False): """the fields in the optional alignment section. Returns a list of all fields in the optional alignment section. Values are converted to appropriate python values. For example: ``[(NM, 2), (RG, "GJP00TM04")]`` If *with_value_type* is set, the value type as encode in the AlignedSegment record will be returned as well: [(NM, 2, "i"), (RG, "GJP00TM04", "Z")] This method will convert all values in the optional alignment section. When getting only one or few tags, please see :meth:`get_tag` for a quicker way to achieve this. """ cdef char * ctag cdef bam1_t * src cdef uint8_t * s cdef char auxtag[3] cdef char auxtype cdef uint8_t byte_size cdef int32_t nvalues src = self._delegate if src.l_data == 0: return [] s = pysam_bam_get_aux(src) result = [] auxtag[2] = 0 while s < (src.data + src.l_data): # get tag auxtag[0] = s[0] auxtag[1] = s[1] s += 2 auxtype = s[0] if auxtype in (b'c', b'C'): value = bam_aux2i(s) s += 1 elif auxtype in (b's', b'S'): value = bam_aux2i(s) s += 2 elif auxtype in (b'i', b'I'): value = bam_aux2i(s) s += 4 elif auxtype == b'f': value = bam_aux2f(s) s += 4 elif auxtype == b'd': value = bam_aux2f(s) s += 8 elif auxtype in (b'A', b'a'): value = "%c" % bam_aux2A(s) s += 1 elif auxtype in (b'Z', b'H'): value = charptr_to_str(bam_aux2Z(s)) # +1 for NULL terminated string s += len(value) + 1 elif auxtype == b'B': s += 1 byte_size, nvalues, value = convert_binary_tag(s) # 5 for 1 char and 1 int s += 5 + (nvalues * byte_size) - 1 else: raise KeyError("unknown type '%s'" % auxtype) s += 1 if with_value_type: result.append((charptr_to_str(auxtag), value, chr(auxtype))) else: result.append((charptr_to_str(auxtag), value)) return result def set_tags(self, tags): """sets the fields in the optional alignment section with a list of (tag, value) tuples. The value type of the values is determined from the python type. Optionally, a type may be given explicitly as a third value in the tuple, For example: x.set_tags([(NM, 2, "i"), (RG, "GJP00TM04", "Z")] This method will not enforce the rule that the same tag may appear only once in the optional alignment section. """ cdef bam1_t * src cdef uint8_t * s cdef char * temp cdef int new_size = 0 cdef int old_size src = self._delegate # convert and pack the data if tags is not None and len(tags) > 0: fmt, args = pack_tags(tags) new_size = struct.calcsize(fmt) buffer = ctypes.create_string_buffer(new_size) struct.pack_into(fmt, buffer, 0, *args) # delete the old data and allocate new space. # If total_size == 0, the aux field will be # empty old_size = pysam_bam_get_l_aux(src) cdef bam1_t * retval = pysam_bam_update(src, old_size, new_size, pysam_bam_get_aux(src)) if retval == NULL: raise MemoryError("could not allocate memory") # copy data only if there is any if new_size > 0: # get location of new data s = pysam_bam_get_aux(src) # check if there is direct path from buffer.raw to tmp p = buffer.raw # create handle to make sure buffer stays alive long # enough for memcpy, see issue 129 temp = p memcpy(s, temp, new_size) ######################################################## # Compatibility Accessors # Functions, properties for compatibility with pysam < 0.8 # # Several options # change the factory functions according to API # * requires code changes throughout, incl passing # handles to factory functions # subclass functions and add attributes at runtime # e.g.: AlignedSegments.qname = AlignedSegments.query_name # * will slow down the default interface # explicit declaration of getters/setters ######################################################## property qname: """deprecated, use :attr:`query_name` instead.""" def __get__(self): return self.query_name def __set__(self, v): self.query_name = v property tid: """deprecated, use :attr:`reference_id` instead.""" def __get__(self): return self.reference_id def __set__(self, v): self.reference_id = v property pos: """deprecated, use :attr:`reference_start` instead.""" def __get__(self): return self.reference_start def __set__(self, v): self.reference_start = v property mapq: """deprecated, use :attr:`mapping_quality` instead.""" def __get__(self): return self.mapping_quality def __set__(self, v): self.mapping_quality = v property rnext: """deprecated, use :attr:`next_reference_id` instead.""" def __get__(self): return self.next_reference_id def __set__(self, v): self.next_reference_id = v property pnext: """deprecated, use :attr:`next_reference_start` instead.""" def __get__(self): return self.next_reference_start def __set__(self, v): self.next_reference_start = v property cigar: """deprecated, use :attr:`cigarstring` or :attr:`cigartuples` instead.""" def __get__(self): r = self.cigartuples if r is None: r = [] return r def __set__(self, v): self.cigartuples = v property tlen: """deprecated, use :attr:`template_length` instead.""" def __get__(self): return self.template_length def __set__(self, v): self.template_length = v property seq: """deprecated, use :attr:`query_sequence` instead.""" def __get__(self): return self.query_sequence def __set__(self, v): self.query_sequence = v property qual: """deprecated, use :attr:`query_qualities` instead.""" def __get__(self): return array_to_qualitystring(self.query_qualities) def __set__(self, v): self.query_qualities = qualitystring_to_array(v) property alen: """deprecated, use :attr:`reference_length` instead.""" def __get__(self): return self.reference_length def __set__(self, v): self.reference_length = v property aend: """deprecated, use :attr:`reference_end` instead.""" def __get__(self): return self.reference_end def __set__(self, v): self.reference_end = v property rlen: """deprecated, use :attr:`query_length` instead.""" def __get__(self): return self.query_length def __set__(self, v): self.query_length = v property query: """deprecated, use :attr:`query_alignment_sequence` instead.""" def __get__(self): return self.query_alignment_sequence def __set__(self, v): self.query_alignment_sequence = v property qqual: """deprecated, use :attr:`query_alignment_qualities` instead.""" def __get__(self): return array_to_qualitystring(self.query_alignment_qualities) def __set__(self, v): self.query_alignment_qualities = qualitystring_to_array(v) property qstart: """deprecated, use :attr:`query_alignment_start` instead.""" def __get__(self): return self.query_alignment_start def __set__(self, v): self.query_alignment_start = v property qend: """deprecated, use :attr:`query_alignment_end` instead.""" def __get__(self): return self.query_alignment_end def __set__(self, v): self.query_alignment_end = v property qlen: """deprecated, use :attr:`query_alignment_length` instead.""" def __get__(self): return self.query_alignment_length def __set__(self, v): self.query_alignment_length = v property mrnm: """deprecated, use :attr:`next_reference_id` instead.""" def __get__(self): return self.next_reference_id def __set__(self, v): self.next_reference_id = v property mpos: """deprecated, use :attr:`next_reference_start` instead.""" def __get__(self): return self.next_reference_start def __set__(self, v): self.next_reference_start = v property rname: """deprecated, use :attr:`reference_id` instead.""" def __get__(self): return self.reference_id def __set__(self, v): self.reference_id = v property isize: """deprecated, use :attr:`template_length` instead.""" def __get__(self): return self.template_length def __set__(self, v): self.template_length = v property blocks: """deprecated, use :meth:`get_blocks()` instead.""" def __get__(self): return self.get_blocks() property aligned_pairs: """deprecated, use :meth:`get_aligned_pairs()` instead.""" def __get__(self): return self.get_aligned_pairs() property inferred_length: """deprecated, use :meth:`infer_query_length()` instead.""" def __get__(self): return self.infer_query_length() property positions: """deprecated, use :meth:`get_reference_positions()` instead.""" def __get__(self): return self.get_reference_positions() property tags: """deprecated, use :meth:`get_tags()` instead.""" def __get__(self): return self.get_tags() def __set__(self, tags): self.set_tags(tags) def overlap(self): """deprecated, use :meth:`get_overlap()` instead.""" return self.get_overlap() def opt(self, tag): """deprecated, use :meth:`get_tag()` instead.""" return self.get_tag(tag) def setTag(self, tag, value, value_type=None, replace=True): """deprecated, use :meth:`set_tag()` instead.""" return self.set_tag(tag, value, value_type, replace) cdef class PileupColumn: '''A pileup of reads at a particular reference sequence position (:term:`column`). A pileup column contains all the reads that map to a certain target base. This class is a proxy for results returned by the samtools pileup engine. If the underlying engine iterator advances, the results of this column will change. ''' def __init__(self): raise TypeError("this class cannot be instantiated from Python") def __str__(self): return "\t".join(map(str, (self.reference_id, self.reference_pos, self.nsegments))) +\ "\n" +\ "\n".join(map(str, self.pileups)) def __dealloc__(self): free(self.buf.s) def set_min_base_quality(self, min_base_quality): """set the minimum base quality for this pileup column. """ self.min_base_quality = min_base_quality def __len__(self): """return number of reads aligned to this column. see :meth:`get_num_aligned` """ return self.get_num_aligned() property reference_id: '''the reference sequence number as defined in the header''' def __get__(self): return self.tid property reference_name: """:term:`reference` name (None if no AlignmentFile is associated)""" def __get__(self): if self.header is not None: return self.header.get_reference_name(self.tid) return None property nsegments: '''number of reads mapping to this column. Note that this number ignores the base quality filter.''' def __get__(self): return self.n_pu def __set__(self, n): self.n_pu = n property reference_pos: '''the position in the reference sequence (0-based).''' def __get__(self): return self.pos property pileups: '''list of reads (:class:`pysam.PileupRead`) aligned to this column''' def __get__(self): if self.plp == NULL or self.plp[0] == NULL: raise ValueError("PileupColumn accessed after iterator finished") cdef int x cdef const bam_pileup1_t * p = NULL pileups = [] # warning: there could be problems if self.n and self.buf are # out of sync. for x from 0 <= x < self.n_pu: p = &(self.plp[0][x]) if p == NULL: raise ValueError( "pileup buffer out of sync - most likely use of iterator " "outside loop") if pileup_base_qual_skip(p, self.min_base_quality): continue pileups.append(makePileupRead(p, self.header)) return pileups ######################################################## # Compatibility Accessors # Functions, properties for compatibility with pysam < 0.8 ######################################################## property pos: """deprecated, use :attr:`reference_pos` instead.""" def __get__(self): return self.reference_pos def __set__(self, v): self.reference_pos = v property tid: """deprecated, use :attr:`reference_id` instead.""" def __get__(self): return self.reference_id def __set__(self, v): self.reference_id = v property n: """deprecated, use :attr:`nsegments` instead.""" def __get__(self): return self.nsegments def __set__(self, v): self.nsegments = v def get_num_aligned(self): """return number of aligned bases at pileup column position. This method applies a base quality filter and the number is equal to the size of :meth:`get_query_sequences`, :meth:`get_mapping_qualities`, etc. """ cdef uint32_t x = 0 cdef uint32_t c = 0 cdef uint32_t cnt = 0 cdef const bam_pileup1_t * p = NULL if self.plp == NULL or self.plp[0] == NULL: raise ValueError("PileupColumn accessed after iterator finished") for x from 0 <= x < self.n_pu: p = &(self.plp[0][x]) if p == NULL: raise ValueError( "pileup buffer out of sync - most likely use of iterator " "outside loop") if pileup_base_qual_skip(p, self.min_base_quality): continue cnt += 1 return cnt def get_query_sequences(self, bint mark_matches=False, bint mark_ends=False, bint add_indels=False): """query bases/sequences at pileup column position. Optionally, the bases/sequences can be annotated according to the samtools mpileup format. This is the format description from the samtools mpileup tool:: Information on match, mismatch, indel, strand, mapping quality and start and end of a read are all encoded at the read base column. At this column, a dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand, a '>' or '<' for a reference skip, `ACGTN' for a mismatch on the forward strand and `acgtn' for a mismatch on the reverse strand. A pattern `\\+[0-9]+[ACGTNacgtn]+' indicates there is an insertion between this reference position and the next reference position. The length of the insertion is given by the integer in the pattern, followed by the inserted sequence. Similarly, a pattern `-[0-9]+[ACGTNacgtn]+' represents a deletion from the reference. The deleted bases will be presented as `*' in the following lines. Also at the read base column, a symbol `^' marks the start of a read. The ASCII of the character following `^' minus 33 gives the mapping quality. A symbol `$' marks the end of a read segment To reproduce samtools mpileup format, set all of mark_matches, mark_ends and add_indels to True. Parameters ---------- mark_matches: bool If True, output bases matching the reference as "." or "," for forward and reverse strand, respectively. This mark requires the reference sequence. If no reference is present, this option is ignored. mark_ends : bool If True, add markers "^" and "$" for read start and end, respectively. add_indels : bool If True, add bases for bases inserted into or skipped from the reference. The latter requires a reference sequence file to have been given, e.g. via `pileup(fastafile = ...)`. If no reference sequence is available, skipped bases are represented as 'N's. Returns ------- a list of bases/sequences per read at pileup column position. : list """ cdef uint32_t x = 0 cdef uint32_t j = 0 cdef uint32_t c = 0 cdef uint8_t cc = 0 cdef uint8_t rb = 0 cdef kstring_t * buf = &self.buf cdef const bam_pileup1_t * p = NULL if self.plp == NULL or self.plp[0] == NULL: raise ValueError("PileupColumn accessed after iterator finished") buf.l = 0 # todo: reference sequence to count matches/mismatches # todo: convert assertions to exceptions for x from 0 <= x < self.n_pu: p = &(self.plp[0][x]) if p == NULL: raise ValueError( "pileup buffer out of sync - most likely use of iterator " "outside loop") if pileup_base_qual_skip(p, self.min_base_quality): continue # see samtools pileup_seq if mark_ends and p.is_head: kputc(b'^', buf) if p.b.core.qual > 93: kputc(126, buf) else: kputc(p.b.core.qual + 33, buf) if not p.is_del: if p.qpos < p.b.core.l_qseq: cc = seq_nt16_str[bam_seqi(bam_get_seq(p.b), p.qpos)] else: cc = b'N' if mark_matches and self.reference_sequence != NULL: rb = self.reference_sequence[self.reference_pos] if seq_nt16_table[cc] == seq_nt16_table[rb]: cc = b'=' kputc(strand_mark_char(cc, p.b), buf) elif add_indels: if p.is_refskip: if bam_is_rev(p.b): kputc(b'<', buf) else: kputc(b'>', buf) else: kputc(b'*', buf) if add_indels: if p.indel > 0: kputc(b'+', buf) kputw(p.indel, buf) for j from 1 <= j <= p.indel: cc = seq_nt16_str[bam_seqi(bam_get_seq(p.b), p.qpos + j)] kputc(strand_mark_char(cc, p.b), buf) elif p.indel < 0: kputc(b'-', buf) kputw(-p.indel, buf) for j from 1 <= j <= -p.indel: # TODO: out-of-range check here? if self.reference_sequence == NULL: cc = b'N' else: cc = self.reference_sequence[self.reference_pos + j] kputc(strand_mark_char(cc, p.b), buf) if mark_ends and p.is_tail: kputc(b'$', buf) kputc(b':', buf) if buf.l == 0: # could be zero if all qualities are too low return "" else: # quicker to ensemble all and split than to encode all separately. # ignore last ":" return force_str(PyBytes_FromStringAndSize(buf.s, buf.l-1)).split(":") def get_query_qualities(self): """query base quality scores at pileup column position. Returns ------- a list of quality scores : list """ cdef uint32_t x = 0 cdef const bam_pileup1_t * p = NULL cdef uint32_t c = 0 result = [] for x from 0 <= x < self.n_pu: p = &(self.plp[0][x]) if p == NULL: raise ValueError( "pileup buffer out of sync - most likely use of iterator " "outside loop") if p.qpos < p.b.core.l_qseq: c = bam_get_qual(p.b)[p.qpos] else: c = 0 if c < self.min_base_quality: continue result.append(c) return result def get_mapping_qualities(self): """query mapping quality scores at pileup column position. Returns ------- a list of quality scores : list """ if self.plp == NULL or self.plp[0] == NULL: raise ValueError("PileupColumn accessed after iterator finished") cdef uint32_t x = 0 cdef const bam_pileup1_t * p = NULL result = [] for x from 0 <= x < self.n_pu: p = &(self.plp[0][x]) if p == NULL: raise ValueError( "pileup buffer out of sync - most likely use of iterator " "outside loop") if pileup_base_qual_skip(p, self.min_base_quality): continue result.append(p.b.core.qual) return result def get_query_positions(self): """positions in read at pileup column position. Returns ------- a list of read positions : list """ if self.plp == NULL or self.plp[0] == NULL: raise ValueError("PileupColumn accessed after iterator finished") cdef uint32_t x = 0 cdef const bam_pileup1_t * p = NULL result = [] for x from 0 <= x < self.n_pu: p = &(self.plp[0][x]) if p == NULL: raise ValueError( "pileup buffer out of sync - most likely use of iterator " "outside loop") if pileup_base_qual_skip(p, self.min_base_quality): continue result.append(p.qpos) return result def get_query_names(self): """query/read names aligned at pileup column position. Returns ------- a list of query names at pileup column position. : list """ if self.plp == NULL or self.plp[0] == NULL: raise ValueError("PileupColumn accessed after iterator finished") cdef uint32_t x = 0 cdef const bam_pileup1_t * p = NULL result = [] for x from 0 <= x < self.n_pu: p = &(self.plp[0][x]) if p == NULL: raise ValueError( "pileup buffer out of sync - most likely use of iterator " "outside loop") if pileup_base_qual_skip(p, self.min_base_quality): continue result.append(charptr_to_str(pysam_bam_get_qname(p.b))) return result cdef class PileupRead: '''Representation of a read aligned to a particular position in the reference sequence. ''' def __init__(self): raise TypeError( "this class cannot be instantiated from Python") def __str__(self): return "\t".join( map(str, (self.alignment, self.query_position, self.indel, self.level, self.is_del, self.is_head, self.is_tail, self.is_refskip))) property alignment: """a :class:`pysam.AlignedSegment` object of the aligned read""" def __get__(self): return self._alignment property query_position: """position of the read base at the pileup site, 0-based. None if :attr:`is_del` or :attr:`is_refskip` is set. """ def __get__(self): if self.is_del or self.is_refskip: return None else: return self._qpos property query_position_or_next: """position of the read base at the pileup site, 0-based. If the current position is a deletion, returns the next aligned base. """ def __get__(self): return self._qpos property indel: """indel length for the position following the current pileup site. This quantity peeks ahead to the next cigar operation in this alignment. If the next operation is an insertion, indel will be positive. If the next operation is a deletion, it will be negation. 0 if the next operation is not an indel. """ def __get__(self): return self._indel property level: """the level of the read in the "viewer" mode. Note that this value is currently not computed.""" def __get__(self): return self._level property is_del: """1 iff the base on the padded read is a deletion""" def __get__(self): return self._is_del property is_head: """1 iff the base on the padded read is the left-most base.""" def __get__(self): return self._is_head property is_tail: """1 iff the base on the padded read is the right-most base.""" def __get__(self): return self._is_tail property is_refskip: """1 iff the base on the padded read is part of CIGAR N op.""" def __get__(self): return self._is_refskip cpdef enum CIGAR_OPS: CMATCH = 0 CINS = 1 CDEL = 2 CREF_SKIP = 3 CSOFT_CLIP = 4 CHARD_CLIP = 5 CPAD = 6 CEQUAL = 7 CDIFF = 8 CBACK = 9 cpdef enum SAM_FLAGS: # the read is paired in sequencing, no matter whether it is mapped in a pair FPAIRED = 1 # the read is mapped in a proper pair FPROPER_PAIR = 2 # the read itself is unmapped; conflictive with FPROPER_PAIR FUNMAP = 4 # the mate is unmapped FMUNMAP = 8 # the read is mapped to the reverse strand FREVERSE = 16 # the mate is mapped to the reverse strand FMREVERSE = 32 # this is read1 FREAD1 = 64 # this is read2 FREAD2 = 128 # not primary alignment FSECONDARY = 256 # QC failure FQCFAIL = 512 # optical or PCR duplicate FDUP = 1024 # supplementary alignment FSUPPLEMENTARY = 2048 __all__ = [ "AlignedSegment", "PileupColumn", "PileupRead", "CMATCH", "CINS", "CDEL", "CREF_SKIP", "CSOFT_CLIP", "CHARD_CLIP", "CPAD", "CEQUAL", "CDIFF", "CBACK", "FPAIRED", "FPROPER_PAIR", "FUNMAP", "FMUNMAP", "FREVERSE", "FMREVERSE", "FREAD1", "FREAD2", "FSECONDARY", "FQCFAIL", "FDUP", "FSUPPLEMENTARY", "KEY_NAMES"] pysam-0.23.0/pysam/libcalignmentfile.pxd000066400000000000000000000067461475062545500202750ustar00rootroot00000000000000# cython: language_level=3 from libc.stdint cimport int8_t, int16_t, int32_t, int64_t from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t from libc.stdlib cimport malloc, calloc, realloc, free from libc.string cimport memcpy, memcmp, strncpy, strlen, strdup from libc.stdio cimport FILE, printf from pysam.libcfaidx cimport faidx_t, FastaFile from pysam.libcalignedsegment cimport AlignedSegment from pysam.libchtslib cimport * from cpython cimport array cimport cython cdef extern from *: ctypedef char* const_char_ptr "const char*" cdef extern from "htslib_util.h": char * pysam_bam_get_qname(bam1_t * b) #################################################################### # Utility types ctypedef struct __iterdata: htsFile * htsfile bam_hdr_t * header hts_itr_t * iter faidx_t * fastafile int tid char * seq int seq_len int min_mapping_quality int flag_require int flag_filter bint compute_baq bint redo_baq bint ignore_orphans int adjust_capq_threshold cdef class AlignmentHeader(object): cdef bam_hdr_t *ptr cdef class AlignmentFile(HTSFile): cdef readonly object reference_filename cdef readonly AlignmentHeader header # pointer to index cdef hts_idx_t *index # current read within iteration cdef bam1_t * b cdef bam1_t * getCurrent(self) cdef int cnext(self) # write an aligned read cpdef int write(self, AlignedSegment read) except -1 cdef class IteratorRow: cdef int retval cdef bam1_t * b cdef AlignmentFile samfile cdef htsFile * htsfile cdef hts_idx_t * index cdef AlignmentHeader header cdef int owns_samfile cdef class IteratorRowRegion(IteratorRow): cdef hts_itr_t * iter cdef bam1_t * getCurrent(self) cdef int cnext(self) cdef class IteratorRowHead(IteratorRow): cdef int max_rows cdef int current_row cdef bam1_t * getCurrent(self) cdef int cnext(self) cdef class IteratorRowAll(IteratorRow): cdef bam1_t * getCurrent(self) cdef int cnext(self) cdef class IteratorRowAllRefs(IteratorRow): cdef int tid cdef IteratorRowRegion rowiter cdef class IteratorRowSelection(IteratorRow): cdef int current_pos cdef positions cdef bam1_t * getCurrent(self) cdef int cnext(self) cdef class IteratorColumn: # result of the last plbuf_push cdef IteratorRowRegion iter cdef int tid cdef int pos cdef int n_plp cdef uint32_t min_base_quality cdef const bam_pileup1_t * plp cdef bam_mplp_t pileup_iter cdef __iterdata iterdata cdef AlignmentFile samfile cdef FastaFile fastafile cdef stepper cdef int max_depth cdef bint ignore_overlaps cdef int cnext(self) cdef char * get_sequence(self) cdef _setup_iterator(self, int tid, int start, int stop, int multiple_iterators=?) cdef _setup_raw_rest_iterator(self) cdef reset(self, tid, start, stop) cdef _free_pileup_iter(self) # backwards compatibility cdef char * getSequence(self) cdef class IteratorColumnRegion(IteratorColumn): cdef int start cdef int stop cdef int truncate cdef class IteratorColumnAllRefs(IteratorColumn): pass cdef class IteratorColumnAll(IteratorColumn): pass cdef class IndexedReads: cdef AlignmentFile samfile cdef htsFile * htsfile cdef object index cdef int owns_samfile cdef AlignmentHeader header pysam-0.23.0/pysam/libcalignmentfile.pyi000066400000000000000000000172401475062545500202720ustar00rootroot00000000000000import array import sys from typing import ( Any, Dict, Type, NamedTuple, Tuple, Optional, Sequence, Union, Callable, List, Iterable, ) if sys.version_info < (3, 8): from typing_extensions import Literal else: from typing import Literal from pysam.libchtslib import HTSFile, _HasFileNo from pysam.libcalignedsegment import AlignedSegment, PileupColumn from pysam.libcfaidx import FastaFile class IndexStats(NamedTuple): contig: str mapped: int unmapped: int total: int VALID_HEADER_TYPES: Dict[str, Type] VALID_HEADERS: Tuple[str] KNOWN_HEADER_FIELDS: Dict[str, Dict[str, Type]] VALID_HEADER_ORDER: Dict[str, Tuple[str]] def build_header_line(fields: Dict[str, str], record: str) -> str: ... class AlignmentHeader: def __init__(self) -> None: ... @classmethod def _from_text_and_lengths( cls, text: Optional[str], reference_names: Optional[Sequence[str]], reference_lengths: Optional[Sequence[int]], ) -> AlignmentHeader: ... @classmethod def from_text(cls, text: str) -> AlignmentHeader: ... @classmethod def from_dict(cls, header_dict: Dict) -> AlignmentHeader: ... @classmethod def from_references( cls, reference_names: Sequence[str], reference_lengths: Sequence[int], text: Optional[str] = ..., add_sq_text: bool = ..., ) -> AlignmentHeader: ... def __bool__(self) -> bool: ... def copy(self) -> AlignmentHeader: ... @property def nreferences(self) -> int: ... @property def references(self) -> Tuple[str]: ... @property def lengths(self) -> Tuple[int]: ... def to_dict(self) -> Dict: ... def get_reference_name(self, tid: int) -> Optional[str]: ... def get_reference_length(self, reference: str) -> int: ... def is_valid_tid(self, tid: int) -> bool: ... def get_tid(self, reference: str) -> int: ... # The iterator produced by AlignmentFile is currently itself, but this may # change in future and code should not make assumptions about this type. AlignmentFileIterator = AlignmentFile class AlignmentFile(HTSFile): def __init__( self, filename: Union[str, bytes, int, _HasFileNo], mode: Optional[ Literal["r", "w", "wh", "rb", "wb", "wbu", "wb0", "rc", "wc"] ] = ..., template: Optional[AlignmentFile] = ..., reference_names: Optional[Sequence[str]] = ..., reference_lengths: Optional[Sequence[int]] = ..., reference_filename: Optional[str] = ..., text: Optional[str] = ..., header: Union[None, Dict, AlignmentHeader] = ..., add_sq_text: bool = ..., add_sam_header: bool = ..., check_sq: bool = ..., index_filename: Optional[str] = ..., filepath_index: Optional[str] = ..., require_index: bool = ..., duplicate_filehandle: bool = ..., ignore_truncation: bool = ..., format_options: Optional[Sequence[str]] = ..., threads: int = ..., ) -> None: ... def has_index(self) -> bool: ... def check_index(self) -> bool: ... def fetch( self, contig: Optional[str] = ..., start: Optional[int] = ..., stop: Optional[int] = ..., region: Optional[str] = ..., tid: Optional[int] = ..., until_eof: bool = ..., multiple_iterators: bool = ..., reference: Optional[str] = ..., end: int = ..., ) -> IteratorRow: ... def head(self, n: int, multiple_iterators: bool = ...) -> IteratorRow: ... def mate(self, read: AlignedSegment) -> AlignedSegment: ... def pileup( self, contig: Optional[str] = ..., start: Optional[int] = ..., stop: Optional[int] = ..., region: Optional[str] = ..., reference: Optional[str] = ..., end: Optional[int] = ..., truncate: bool = ..., max_depth: int = ..., stepper: str = ..., fastafile: Optional[FastaFile] = ..., ignore_overlaps: bool = ..., flag_filter: int = ..., flag_require: int = ..., ignore_orphans: bool = ..., min_base_quality: int = ..., adjust_capq_threshold: int = ..., min_mapping_quality: int = ..., compute_baq: bool = ..., redo_baq: bool = ..., ) -> IteratorColumn: ... def count( self, contig: Optional[str] = ..., start: Optional[int] = ..., stop: Optional[int] = ..., region: Optional[str] = ..., until_eof: bool = ..., read_callback: Union[str, Callable[[AlignedSegment], bool]] = ..., reference: Optional[str] = ..., end: Optional[int] = ..., ) -> int: ... def count_coverage( self, contig: Optional[str] = ..., start: Optional[int] = ..., stop: Optional[int] = ..., region: Optional[str] = ..., quality_threshold: int = ..., read_callback: Union[str, Callable[[AlignedSegment], bool]] = ..., reference: Optional[str] = ..., end: Optional[int] = ..., ) -> Tuple[array.array, array.array, array.array, array.array]: ... def find_introns_slow( self, read_iterator: Iterable[AlignedSegment] ) -> Dict[Tuple[int, int], int]: ... def find_introns( self, read_iterator: Iterable[AlignedSegment] ) -> Dict[Tuple[int, int], int]: ... def close(self) -> None: ... def write(self, read: AlignedSegment) -> int: ... def __enter__(self) -> AlignmentFile: ... def __exit__(self, exc_type, exc_value, traceback): ... @property def mapped(self) -> int: ... @property def unmapped(self) -> int: ... @property def nocoordinate(self) -> int: ... def get_index_statistics(self) -> List[IndexStats]: ... def __iter__(self) -> AlignmentFileIterator: ... def __next__(self) -> AlignedSegment: ... def is_valid_tid(self, tid: int) -> bool: ... def get_tid(self, reference: str) -> int: ... def get_reference_name(self, tid: int) -> str: ... def get_reference_length(self, reference: str) -> int: ... @property def nreferences(self) -> int: ... @property def references(self) -> Tuple[str, ...]: ... @property def lengths(self) -> Tuple[int, ...]: ... @property def reference_filename(self) -> Optional[str]: ... @property def header(self) -> AlignmentHeader: ... class IteratorRow: def __iter__(self) -> IteratorRow: ... def __next__(self) -> AlignedSegment: ... class IteratorRowAll(IteratorRow): ... class IteratorRowAllRefs(IteratorRow): ... class IteratorRowHead(IteratorRow): ... class IteratorRowRegion(IteratorRow): ... class IteratorRowSelection(IteratorRow): ... class IteratorColumn: def __iter__(self) -> IteratorColumn: ... def __next__(self) -> PileupColumn: ... @property def seq_len(self) -> int: ... def add_reference(self, fastafile: FastaFile) -> None: ... def has_reference(self) -> bool: ... class IteratorColumnAll(IteratorColumn): ... class IteratorColumnAllRefs(IteratorColumn): ... class IteratorColumnRegion(IteratorColumn): ... class SNPCall: @property def tid(self) -> int: ... @property def pos(self) -> int: ... @property def reference_base(self) -> str: ... @property def genotype(self) -> str: ... @property def consensus_quality(self) -> int: ... @property def snp_quality(self) -> int: ... @property def mapping_quality(self) -> int: ... @property def coverage(self) -> int: ... class IndexedReads: def __init__( self, samfile: AlignmentFile, multiple_iterators: bool = ... ) -> None: ... def build(self) -> None: ... def find(self, query_name: str) -> IteratorRow: ... pysam-0.23.0/pysam/libcalignmentfile.pyx000066400000000000000000003142631475062545500203160ustar00rootroot00000000000000# cython: embedsignature=True # cython: profile=True ######################################################## ######################################################## # Cython wrapper for SAM/BAM/CRAM files based on htslib ######################################################## # The principal classes defined in this module are: # # class AlignmentFile read/write access to SAM/BAM/CRAM formatted files # # class AlignmentHeader manage SAM/BAM/CRAM header data # # class IndexedReads index a SAM/BAM/CRAM file by query name while keeping # the original sort order intact # # Additionally this module defines numerous additional classes that # are part of the internal API. These are: # # Various iterator classes to iterate over alignments in sequential # (IteratorRow) or in a stacked fashion (IteratorColumn): # # class IteratorRow # class IteratorRowRegion # class IteratorRowHead # class IteratorRowAll # class IteratorRowAllRefs # class IteratorRowSelection # class IteratorColumn # class IteratorColumnRegion # class IteratorColumnAll # class IteratorColumnAllRefs # ######################################################## # # The MIT License # # Copyright (c) 2015 Andreas Heger # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. # ######################################################## import os import collections try: from collections.abc import Sequence, Mapping # noqa except ImportError: from collections import Sequence, Mapping # noqa import re import warnings import array from libc.errno cimport errno, EPIPE from libc.string cimport strcmp, strpbrk, strerror from libc.stdint cimport INT32_MAX from cpython cimport array as c_array from pysam.libcutils cimport force_bytes, force_str, charptr_to_str from pysam.libcutils cimport encode_filename, from_string_and_size from pysam.libcalignedsegment cimport makeAlignedSegment, makePileupColumn from pysam.libchtslib cimport HTSFile, hisremote, sam_index_load2, sam_index_load3, \ HTS_IDX_SAVE_REMOTE, HTS_IDX_SILENT_FAIL from io import StringIO cimport cython __all__ = [ "AlignmentFile", "AlignmentHeader", "IteratorRow", "IteratorColumn", "IndexedReads"] IndexStats = collections.namedtuple("IndexStats", ("contig", "mapped", "unmapped", "total")) ######################################################## ## global variables # maximum genomic coordinace # for some reason, using 'int' causes overflow cdef int MAX_POS = (1 << 31) - 1 # valid types for SAM headers VALID_HEADER_TYPES = {"HD" : Mapping, "SQ" : Sequence, "RG" : Sequence, "PG" : Sequence, "CO" : Sequence} # order of records within SAM headers VALID_HEADERS = ("HD", "SQ", "RG", "PG", "CO") # default type conversions within SAM header records KNOWN_HEADER_FIELDS = {"HD" : {"VN" : str, "SO" : str, "GO" : str, "SS" : str,}, "SQ" : {"SN" : str, "LN" : int, "AS" : str, "M5" : str, "SP" : str, "UR" : str, "AH" : str, "TP" : str, "DS" : str, "AN" : str,}, "RG" : {"ID" : str, "CN" : str, "DS" : str, "DT" : str, "FO" : str, "KS" : str, "LB" : str, "PG" : str, "PI" : str, "PL" : str, "PM" : str, "PU" : str, "SM" : str, "BC" : str,}, "PG" : {"ID" : str, "PN" : str, "CL" : str, "PP" : str, "DS" : str, "VN" : str,},} # output order of fields within records. Ensure that CL is at # the end as parsing a CL will ignore any subsequent records. VALID_HEADER_ORDER = {"HD" : ("VN", "SO", "SS", "GO"), "SQ" : ("SN", "LN", "AS", "M5", "UR", "SP", "AH", "TP", "DS", "AN"), "RG" : ("ID", "CN", "SM", "LB", "PU", "PI", "DT", "DS", "PL", "FO", "KS", "PG", "PM", "BC"), "PG" : ("PN", "ID", "VN", "PP", "DS", "CL"),} def build_header_line(fields, record): '''build a header line from `fields` dictionary for `record`''' # TODO: add checking for field and sort order line = ["@%s" % record] # comment if record == "CO": line.append(fields) # user tags elif record.islower(): for key in sorted(fields): line.append("%s:%s" % (key, str(fields[key]))) # defined tags else: # write fields of the specification for key in VALID_HEADER_ORDER[record]: if key in fields: line.append("%s:%s" % (key, str(fields[key]))) # write user fields for key in fields: if not key.isupper(): line.append("%s:%s" % (key, str(fields[key]))) return "\t".join(line) cdef AlignmentHeader makeAlignmentHeader(bam_hdr_t *hdr): if not hdr: raise ValueError('cannot create AlignmentHeader, received NULL pointer') # check: is AlignmetHeader.__cinit__ called? cdef AlignmentHeader header = AlignmentHeader.__new__(AlignmentHeader) header.ptr = hdr return header def read_failure_reason(code): if code == -2: return 'truncated file' else: return "error {} while reading file".format(code) # the following should be class-method for VariantHeader, but cdef @classmethods # are not implemented in cython. cdef int fill_AlignmentHeader_from_list(bam_hdr_t *dest, reference_names, reference_lengths, add_sq_text=True, text=None) except -1: """build header from list of reference names and lengths. """ cdef class AlignmentHeader(object): """header information for a :class:`AlignmentFile` object Parameters ---------- header_dict : dict build header from a multi-level dictionary. The first level are the four types ('HD', 'SQ', ...). The second level are a list of lines, with each line being a list of tag-value pairs. The header is constructed first from all the defined fields, followed by user tags in alphabetical order. Alternatively, an :class:`~pysam.AlignmentHeader` object can be passed directly. text : string use the string provided as the header reference_names : list see reference_lengths reference_lengths : list build header from list of chromosome names and lengths. By default, 'SQ' and 'LN' tags will be added to the header text. This option can be changed by unsetting the flag `add_sq_text`. add_sq_text : bool do not add 'SQ' and 'LN' tags to header. This option permits construction :term:`SAM` formatted files without a header. """ # See makeVariantHeader for C constructor def __cinit__(self): self.ptr = NULL # Python constructor def __init__(self): self.ptr = bam_hdr_init() if self.ptr is NULL: raise MemoryError("could not create header") @classmethod def _from_text_and_lengths(cls, text, reference_names, reference_lengths): cdef AlignmentHeader self = AlignmentHeader() cdef char *ctext cdef int l_text cdef int n, x if text is not None: btext = force_bytes(text) ctext = btext l_text = len(btext) self.ptr.text = calloc(l_text + 1, sizeof(char)) if self.ptr.text == NULL: raise MemoryError("could not allocate {} bytes".format(l_text + 1), sizeof(char)) self.ptr.l_text = l_text memcpy(self.ptr.text, ctext, l_text + 1) if reference_names and reference_lengths: reference_names = [force_bytes(ref) for ref in reference_names] self.ptr.n_targets = len(reference_names) n = sum([len(reference_names) + 1]) self.ptr.target_name = calloc(n, sizeof(char*)) if self.ptr.target_name == NULL: raise MemoryError("could not allocate {} bytes".format(n, sizeof(char *))) self.ptr.target_len = calloc(n, sizeof(uint32_t)) if self.ptr.target_len == NULL: raise MemoryError("could not allocate {} bytes".format(n, sizeof(uint32_t))) for x from 0 <= x < self.ptr.n_targets: self.ptr.target_len[x] = reference_lengths[x] name = reference_names[x] self.ptr.target_name[x] = calloc(len(name) + 1, sizeof(char)) if self.ptr.target_name[x] == NULL: raise MemoryError("could not allocate {} bytes".format(len(name) + 1, sizeof(char))) strncpy(self.ptr.target_name[x], name, len(name)) return self @classmethod def from_text(cls, text): reference_names, reference_lengths = [], [] for line in text.splitlines(): if line.startswith("@SQ"): fields = dict([x.split(":", 1) for x in line.split("\t")[1:]]) try: reference_names.append(fields["SN"]) reference_lengths.append(int(fields["LN"])) except KeyError: raise KeyError("incomplete sequence information in '%s'" % str(fields)) except ValueError: raise ValueError("wrong sequence information in '%s'" % str(fields)) return cls._from_text_and_lengths(text, reference_names, reference_lengths) @classmethod def from_dict(cls, header_dict): cdef list lines = [] # first: defined tags for record in VALID_HEADERS: if record in header_dict: data = header_dict[record] if not isinstance(data, VALID_HEADER_TYPES[record]): raise ValueError( "invalid type for record %s: %s, expected %s".format( record, type(data), VALID_HEADER_TYPES[record])) if isinstance(data, Mapping): lines.append(build_header_line(data, record)) else: for fields in header_dict[record]: lines.append(build_header_line(fields, record)) # then: user tags (lower case), sorted alphabetically for record, data in sorted(header_dict.items()): if record in VALID_HEADERS: continue if isinstance(data, Mapping): lines.append(build_header_line(data, record)) else: for fields in header_dict[record]: lines.append(build_header_line(fields, record)) text = "\n".join(lines) + "\n" reference_names, reference_lengths = [], [] if "SQ" in header_dict: for fields in header_dict["SQ"]: try: reference_names.append(fields["SN"]) reference_lengths.append(fields["LN"]) except KeyError: raise KeyError("incomplete sequence information in '%s'" % str(fields)) return cls._from_text_and_lengths(text, reference_names, reference_lengths) @classmethod def from_references(cls, reference_names, reference_lengths, text=None, add_sq_text=True): if len(reference_names) != len(reference_lengths): raise ValueError("number of reference names and lengths do not match") # optionally, if there is no text, add a SAM compatible header to output file. if text is None and add_sq_text: text = "".join(["@SQ\tSN:{}\tLN:{}\n".format(x, y) for x, y in zip( reference_names, reference_lengths)]) return cls._from_text_and_lengths(text, reference_names, reference_lengths) def __dealloc__(self): bam_hdr_destroy(self.ptr) self.ptr = NULL def __bool__(self): return self.ptr != NULL def copy(self): return makeAlignmentHeader(bam_hdr_dup(self.ptr)) property nreferences: """int with the number of :term:`reference` sequences in the file. This is a read-only attribute.""" def __get__(self): return self.ptr.n_targets property references: """tuple with the names of :term:`reference` sequences. This is a read-only attribute""" def __get__(self): t = [] cdef int x for x in range(self.ptr.n_targets): t.append(charptr_to_str(self.ptr.target_name[x])) return tuple(t) property lengths: """tuple of the lengths of the :term:`reference` sequences. This is a read-only attribute. The lengths are in the same order as :attr:`pysam.AlignmentFile.references` """ def __get__(self): t = [] cdef int x for x in range(self.ptr.n_targets): t.append(self.ptr.target_len[x]) return tuple(t) def _build_sequence_section(self): """return sequence section of header. The sequence section is built from the list of reference names and lengths stored in the BAM-file and not from any @SQ entries that are part of the header's text section. """ cdef int x text = [] for x in range(self.ptr.n_targets): text.append("@SQ\tSN:{}\tLN:{}\n".format( force_str(self.ptr.target_name[x]), self.ptr.target_len[x])) return "".join(text) def to_dict(self): """return two-level dictionary with header information from the file. The first level contains the record (``HD``, ``SQ``, etc) and the second level contains the fields (``VN``, ``LN``, etc). The parser is validating and will raise an AssertionError if if encounters any record or field tags that are not part of the SAM specification. Use the :attr:`pysam.AlignmentFile.text` attribute to get the unparsed header. The parsing follows the SAM format specification with the exception of the ``CL`` field. This option will consume the rest of a header line irrespective of any additional fields. This behaviour has been added to accommodate command line options that contain characters that are not valid field separators. If no @SQ entries are within the text section of the header, this will be automatically added from the reference names and lengths stored in the binary part of the header. """ result = collections.OrderedDict() # convert to python string t = self.__str__() for line in t.split("\n"): line = line.strip(' \0') if not line: continue assert line.startswith("@"), \ "header line without '@': '%s'" % line fields = line[1:].split("\t") record = fields[0] assert record in VALID_HEADER_TYPES, \ "header line with invalid type '%s': '%s'" % (record, line) # treat comments if record == "CO": if record not in result: result[record] = [] result[record].append("\t".join( fields[1:])) continue # the following is clumsy as generators do not work? x = {} for idx, field in enumerate(fields[1:]): if ":" not in field: raise ValueError("malformatted header: no ':' in field" ) key, value = field.split(":", 1) if key in ("CL",): # special treatment for command line # statements (CL). These might contain # characters that are non-conformant with # the valid field separators in the SAM # header. Thus, in contravention to the # SAM API, consume the rest of the line. key, value = "\t".join(fields[idx+1:]).split(":", 1) x[key] = KNOWN_HEADER_FIELDS[record][key](value) break # interpret type of known header record tags, default to str x[key] = KNOWN_HEADER_FIELDS[record].get(key, str)(value) if VALID_HEADER_TYPES[record] == Mapping: if record in result: raise ValueError( "multiple '%s' lines are not permitted" % record) result[record] = x elif VALID_HEADER_TYPES[record] == Sequence: if record not in result: result[record] = [] result[record].append(x) # if there are no SQ lines in the header, add the # reference names from the information in the bam # file. # # Background: c-samtools keeps the textual part of the # header separate from the list of reference names and # lengths. Thus, if a header contains only SQ lines, # the SQ information is not part of the textual header # and thus are missing from the output. See issue 84. if "SQ" not in result: sq = [] for ref, length in zip(self.references, self.lengths): sq.append({'LN': length, 'SN': ref }) result["SQ"] = sq return result def as_dict(self): """deprecated, use :meth:`to_dict()` instead""" return self.to_dict() def get_reference_name(self, tid): if tid == -1: return None if not 0 <= tid < self.ptr.n_targets: raise ValueError("reference_id %i out of range 0<=tid<%i" % (tid, self.ptr.n_targets)) return charptr_to_str(self.ptr.target_name[tid]) def get_reference_length(self, reference): cdef int tid = self.get_tid(reference) if tid < 0: raise KeyError("unknown reference {}".format(reference)) else: return self.ptr.target_len[tid] def is_valid_tid(self, int tid): """ return True if the numerical :term:`tid` is valid; False otherwise. Note that the unmapped tid code (-1) counts as an invalid. """ return 0 <= tid < self.ptr.n_targets def get_tid(self, reference): """ return the numerical :term:`tid` corresponding to :term:`reference` returns -1 if reference is not known. """ reference = force_bytes(reference) tid = bam_name2id(self.ptr, reference) if tid < -1: raise ValueError('could not parse header') return tid def __str__(self): '''string with the full contents of the :term:`sam file` header as a string. If no @SQ entries are within the text section of the header, this will be automatically added from the reference names and lengths stored in the binary part of the header. See :attr:`pysam.AlignmentFile.header.to_dict()` to get a parsed representation of the header. ''' text = from_string_and_size(self.ptr.text, self.ptr.l_text) if "@SQ" not in text: text += "\n" + self._build_sequence_section() return text # dictionary access methods, for backwards compatibility. def __setitem__(self, key, value): raise TypeError("AlignmentHeader does not support item assignment (use header.to_dict()") def __getitem__(self, key): return self.to_dict().__getitem__(key) def items(self): return self.to_dict().items() # PY2 compatibility def iteritems(self): return self.to_dict().items() def keys(self): return self.to_dict().keys() def values(self): return self.to_dict().values() def get(self, *args): return self.to_dict().get(*args) def __len__(self): return self.to_dict().__len__() def __contains__(self, key): return self.to_dict().__contains__(key) cdef class AlignmentFile(HTSFile): """AlignmentFile(filepath_or_object, mode=None, template=None, reference_names=None, reference_lengths=None, text=NULL, header=None, add_sq_text=False, check_header=True, check_sq=True, reference_filename=None, filename=None, index_filename=None, filepath_index=None, require_index=False, duplicate_filehandle=True, ignore_truncation=False, threads=1) A :term:`SAM`/:term:`BAM`/:term:`CRAM` formatted file. If `filepath_or_object` is a string, the file is automatically opened. If `filepath_or_object` is a python File object, the already opened file will be used. If the file is opened for reading and an index exists (if file is BAM, a .bai file or if CRAM a .crai file), it will be opened automatically. `index_filename` may be specified explicitly. If the index is not named in the standard manner, not located in the same directory as the BAM/CRAM file, or is remote. Without an index, random access via :meth:`~pysam.AlignmentFile.fetch` and :meth:`~pysam.AlignmentFile.pileup` is disabled. For writing, the header of a :term:`SAM` file/:term:`BAM` file can be constituted from several sources (see also the samtools format specification): 1. If `template` is given, the header is copied from another `AlignmentFile` (`template` must be a :class:`~pysam.AlignmentFile`). 2. If `header` is given, the header is built from a multi-level dictionary. 3. If `text` is given, new header text is copied from raw text. 4. The names (`reference_names`) and lengths (`reference_lengths`) are supplied directly as lists. When reading or writing a CRAM file, the filename of a FASTA-formatted reference can be specified with `reference_filename`. By default, if a file is opened in mode 'r', it is checked for a valid header (`check_header` = True) and a definition of chromosome names (`check_sq` = True). Parameters ---------- mode : string `mode` should be ``r`` for reading or ``w`` for writing. The default is text mode (:term:`SAM`). For binary (:term:`BAM`) I/O you should append ``b`` for compressed or ``u`` for uncompressed :term:`BAM` output. Use ``h`` to output header information in text (:term:`TAM`) mode. Use ``c`` for :term:`CRAM` formatted files. If ``b`` is present, it must immediately follow ``r`` or ``w``. Valid modes are ``r``, ``w``, ``wh``, ``rb``, ``wb``, ``wbu``, ``wb0``, ``rc`` and ``wc``. For instance, to open a :term:`BAM` formatted file for reading, type:: f = pysam.AlignmentFile('ex1.bam','rb') If mode is not specified, the method will try to auto-detect in the order 'rb', 'r', thus both the following should work:: f1 = pysam.AlignmentFile('ex1.bam') f2 = pysam.AlignmentFile('ex1.sam') template : AlignmentFile when writing, copy header from file `template`. header : dict or AlignmentHeader when writing, build header from a multi-level dictionary. The first level are the four types ('HD', 'SQ', ...). The second level are a list of lines, with each line being a list of tag-value pairs. The header is constructed first from all the defined fields, followed by user tags in alphabetical order. Alternatively, an :class:`~pysam.AlignmentHeader` object can be passed directly. text : string when writing, use the string provided as the header reference_names : list see reference_lengths reference_lengths : list when writing or opening a SAM file without header build header from list of chromosome names and lengths. By default, 'SQ' and 'LN' tags will be added to the header text. This option can be changed by unsetting the flag `add_sq_text`. add_sq_text : bool do not add 'SQ' and 'LN' tags to header. This option permits construction :term:`SAM` formatted files without a header. add_sam_header : bool when outputting SAM the default is to output a header. This is equivalent to opening the file in 'wh' mode. If this option is set to False, no header will be output. To read such a file, set `check_header=False`. check_header : bool obsolete: when reading a SAM file, check if header is present (default=True) check_sq : bool when reading, check if SQ entries are present in header (default=True) reference_filename : string Path to a FASTA-formatted reference file. Valid only for CRAM files. When reading a CRAM file, this overrides both ``$REF_PATH`` and the URL specified in the header (``UR`` tag), which are normally used to find the reference. index_filename : string Explicit path to the index file. Only needed if the index is not named in the standard manner, not located in the same directory as the BAM/CRAM file, or is remote. An IOError is raised if the index cannot be found or is invalid. filepath_index : string Alias for `index_filename`. require_index : bool When reading, require that an index file is present and is valid or raise an IOError. (default=False) filename : string Alternative to filepath_or_object. Filename of the file to be opened. duplicate_filehandle: bool By default, file handles passed either directly or through File-like objects will be duplicated before passing them to htslib. The duplication prevents issues where the same stream will be closed by htslib and through destruction of the high-level python object. Set to False to turn off duplication. ignore_truncation: bool Issue a warning, instead of raising an error if the current file appears to be truncated due to a missing EOF marker. Only applies to bgzipped formats. (Default=False) format_options: list A list of key=value strings, as accepted by --input-fmt-option and --output-fmt-option in samtools. threads: integer Number of threads to use for compressing/decompressing BAM/CRAM files. Setting threads to > 1 cannot be combined with `ignore_truncation`. (Default=1) """ def __cinit__(self, *args, **kwargs): self.htsfile = NULL self.filename = None self.mode = None self.threads = 1 self.is_stream = False self.is_remote = False self.index = NULL if "filename" in kwargs: args = [kwargs["filename"]] del kwargs["filename"] self._open(*args, **kwargs) # allocate memory for iterator self.b = calloc(1, sizeof(bam1_t)) if self.b == NULL: raise MemoryError("could not allocate memory of size {}".format(sizeof(bam1_t))) def has_index(self): """return true if htsfile has an existing (and opened) index. """ return self.index != NULL def check_index(self): """return True if index is present. Raises ------ AttributeError if htsfile is :term:`SAM` formatted and thus has no index. ValueError if htsfile is closed or index could not be opened. """ if not self.is_open: raise ValueError("I/O operation on closed file") if not self.is_bam and not self.is_cram: raise AttributeError( "AlignmentFile.mapped only available in bam files") if self.index == NULL: raise ValueError( "mapping information not recorded in index " "or index not available") return True def _open(self, filepath_or_object, mode=None, AlignmentFile template=None, reference_names=None, reference_lengths=None, reference_filename=None, text=None, header=None, port=None, add_sq_text=True, add_sam_header=True, check_header=True, check_sq=True, index_filename=None, filepath_index=None, require_index=False, referencenames=None, referencelengths=None, duplicate_filehandle=True, ignore_truncation=False, format_options=None, threads=1): '''open a sam, bam or cram formatted file. If _open is called on an existing file, the current file will be closed and a new file will be opened. ''' cdef char *cfilename = NULL cdef char *creference_filename = NULL cdef char *cindexname = NULL cdef char *cmode = NULL cdef bam_hdr_t * hdr = NULL if threads > 1 and ignore_truncation: # This won't raise errors if reaching a truncated alignment, # because bgzf_mt_reader in htslib does not deal with # bgzf_mt_read_block returning non-zero values, contrary # to bgzf_read (https://github.com/samtools/htslib/blob/1.7/bgzf.c#L888) # Better to avoid this (for now) than to produce seemingly correct results. raise ValueError('Cannot add extra threads when "ignore_truncation" is True') self.threads = threads # for backwards compatibility: if referencenames is not None: reference_names = referencenames if referencelengths is not None: reference_lengths = referencelengths # close a previously opened file if self.is_open: self.close() # autodetection for read if mode is None: mode = "r" if add_sam_header and mode == "w": mode = "wh" assert mode in ("r", "w", "rb", "wb", "wh", "wbu", "rU", "wb0", "rc", "wc"), \ "invalid file opening mode `%s`" % mode self.duplicate_filehandle = duplicate_filehandle # StringIO not supported if isinstance(filepath_or_object, StringIO): raise NotImplementedError( "access from StringIO objects not supported") # reading from a file descriptor elif isinstance(filepath_or_object, int): self.filename = filepath_or_object filename = None self.is_remote = False self.is_stream = True # reading from a File object or other object with fileno elif hasattr(filepath_or_object, "fileno"): if filepath_or_object.closed: raise ValueError('I/O operation on closed file') self.filename = filepath_or_object # .name can be TextIOWrapper try: filename = encode_filename(str(filepath_or_object.name)) cfilename = filename except AttributeError: filename = None self.is_remote = False self.is_stream = True # what remains is a filename else: self.filename = filename = encode_filename(filepath_or_object) cfilename = filename self.is_remote = hisremote(cfilename) self.is_stream = self.filename == b'-' # for htslib, wbu seems to not work if mode == "wbu": mode = "wb0" self.mode = force_bytes(mode) self.reference_filename = reference_filename = encode_filename( reference_filename) if mode[0] == 'w': # open file for writing if not (template or header or text or (reference_names and reference_lengths)): raise ValueError( "either supply options `template`, `header`, `text` or both `reference_names` " "and `reference_lengths` for writing") if template: # header is copied, though at the moment not strictly # necessary as AlignmentHeader is immutable. self.header = template.header.copy() elif isinstance(header, AlignmentHeader): self.header = header.copy() elif isinstance(header, Mapping): self.header = AlignmentHeader.from_dict(header) elif reference_names and reference_lengths: self.header = AlignmentHeader.from_references( reference_names, reference_lengths, add_sq_text=add_sq_text, text=text) elif text: self.header = AlignmentHeader.from_text(text) else: raise ValueError("not enough information to construct header. Please provide template, " "header, text or reference_names/reference_lengths") self.htsfile = self._open_htsfile() if self.htsfile == NULL: if errno: raise IOError(errno, "could not open alignment file `{}`: {}".format( force_str(filename), force_str(strerror(errno)))) else: raise ValueError("could not open alignment file `{}`".format(force_str(filename))) if format_options and len(format_options): self.add_hts_options(format_options) # set filename with reference sequences. If no filename # is given, the CRAM reference arrays will be built from # the @SQ header in the header if "c" in mode and reference_filename: if (hts_set_fai_filename(self.htsfile, self.reference_filename) != 0): raise ValueError("failure when setting reference filename") # write header to htsfile if "b" in mode or "c" in mode or "h" in mode: hdr = self.header.ptr with nogil: sam_hdr_write(self.htsfile, hdr) elif mode[0] == "r": # open file for reading self.htsfile = self._open_htsfile() if self.htsfile == NULL: if errno: raise IOError(errno, "could not open alignment file `{}`: {}".format(force_str(filename), force_str(strerror(errno)))) else: raise ValueError("could not open alignment file `{}`".format(force_str(filename))) if self.htsfile.format.category != sequence_data: raise ValueError("file does not contain alignment data") if format_options and len(format_options): self.add_hts_options(format_options) self.check_truncation(ignore_truncation) # bam/cram files require a valid header if self.is_bam or self.is_cram: with nogil: hdr = sam_hdr_read(self.htsfile) if hdr == NULL: raise ValueError( "file does not have a valid header (mode='%s') " "- is it BAM/CRAM format?" % mode) self.header = makeAlignmentHeader(hdr) else: # in sam files a header is optional. If not given, # user may provide reference names and lengths to built # an on-the-fly header. if reference_names and reference_lengths: # build header from a target names and lengths self.header = AlignmentHeader.from_references( reference_names=reference_names, reference_lengths=reference_lengths, add_sq_text=add_sq_text, text=text) else: with nogil: hdr = sam_hdr_read(self.htsfile) if hdr == NULL: raise ValueError( "SAM? file does not have a valid header (mode='%s'), " "please provide reference_names and reference_lengths") self.header = makeAlignmentHeader(hdr) # set filename with reference sequences if self.is_cram and reference_filename: creference_filename = self.reference_filename hts_set_opt(self.htsfile, CRAM_OPT_REFERENCE, creference_filename) if check_sq and self.header.nreferences == 0: raise ValueError( ("file has no sequences defined (mode='%s') - " "is it SAM/BAM format? Consider opening with " "check_sq=False") % mode) if self.is_bam or self.is_cram: self.index_filename = index_filename or filepath_index if self.index_filename: cindexname = bfile_name = encode_filename(self.index_filename) if cfilename or cindexname: with nogil: self.index = sam_index_load3(self.htsfile, cfilename, cindexname, HTS_IDX_SAVE_REMOTE|HTS_IDX_SILENT_FAIL) if not self.index and (cindexname or require_index): if errno: raise IOError(errno, force_str(strerror(errno))) else: raise IOError('unable to open index file `%s`' % self.index_filename) elif require_index: raise IOError('unable to open index file') # save start of data section if not self.is_stream: self.start_offset = self.tell() def fetch(self, contig=None, start=None, stop=None, region=None, tid=None, until_eof=False, multiple_iterators=False, reference=None, end=None): """fetch reads aligned in a :term:`region`. See :meth:`~pysam.HTSFile.parse_region` for more information on how genomic regions can be specified. :term:`reference` and `end` are also accepted for backward compatibility as synonyms for :term:`contig` and `stop`, respectively. Without a `contig` or `region` all mapped reads in the file will be fetched. The reads will be returned ordered by reference sequence, which will not necessarily be the order within the file. This mode of iteration still requires an index. If there is no index, use `until_eof=True`. If only `contig` is set, all reads aligned to `contig` will be fetched. A :term:`SAM` file does not allow random access. If `region` or `contig` are given, an exception is raised. Parameters ---------- until_eof : bool If `until_eof` is True, all reads from the current file position will be returned in order as they are within the file. Using this option will also fetch unmapped reads. multiple_iterators : bool If `multiple_iterators` is True, multiple iterators on the same file can be used at the same time. The iterator returned will receive its own copy of a filehandle to the file effectively re-opening the file. Re-opening a file creates some overhead, so beware. Returns ------- An iterator over a collection of reads. : IteratorRow Raises ------ ValueError if the genomic coordinates are out of range or invalid or the file does not permit random access to genomic coordinates. """ cdef int rtid, rstart, rstop, has_coord if not self.is_open: raise ValueError( "I/O operation on closed file" ) has_coord, rtid, rstart, rstop = self.parse_region( contig, start, stop, region, tid, end=end, reference=reference) # Turn of re-opening if htsfile is a stream if self.is_stream: multiple_iterators = False if self.is_bam or self.is_cram: if not until_eof and not self.is_remote: if not self.has_index(): raise ValueError( "fetch called on bamfile without index") if has_coord: return IteratorRowRegion( self, rtid, rstart, rstop, multiple_iterators=multiple_iterators) else: if until_eof: return IteratorRowAll( self, multiple_iterators=multiple_iterators) else: # AH: check - reason why no multiple_iterators for # AllRefs? return IteratorRowAllRefs( self, multiple_iterators=multiple_iterators) else: if has_coord: raise ValueError( "fetching by region is not available for SAM files") if multiple_iterators == True: raise ValueError( "multiple iterators not implemented for SAM files") return IteratorRowAll(self, multiple_iterators=multiple_iterators) def head(self, n, multiple_iterators=True): '''return an iterator over the first n alignments. This iterator is is useful for inspecting the bam-file. Parameters ---------- multiple_iterators : bool is set to True by default in order to avoid changing the current file position. Returns ------- an iterator over a collection of reads : IteratorRowHead ''' return IteratorRowHead(self, n, multiple_iterators=multiple_iterators) def mate(self, AlignedSegment read): '''return the mate of :class:`pysam.AlignedSegment` `read`. .. note:: Calling this method will change the file position. This might interfere with any iterators that have not re-opened the file. .. note:: This method is too slow for high-throughput processing. If a read needs to be processed with its mate, work from a read name sorted file or, better, cache reads. Returns ------- the mate : AlignedSegment Raises ------ ValueError if the read is unpaired or the mate is unmapped ''' cdef uint32_t flag = read._delegate.core.flag if flag & BAM_FPAIRED == 0: raise ValueError("read %s: is unpaired" % (read.query_name)) if flag & BAM_FMUNMAP != 0: raise ValueError("mate %s: is unmapped" % (read.query_name)) # xor flags to get the other mate cdef int x = BAM_FREAD1 + BAM_FREAD2 flag = (flag ^ x) & x # Make sure to use a separate file to jump around # to mate as otherwise the original file position # will be lost # The following code is not using the C API and # could thus be made much quicker, for example # by using tell and seek. for mate in self.fetch( read._delegate.core.mpos, read._delegate.core.mpos + 1, tid=read._delegate.core.mtid, multiple_iterators=True): if mate.flag & flag != 0 and \ mate.query_name == read.query_name: break else: raise ValueError("mate not found") return mate def pileup(self, contig=None, start=None, stop=None, region=None, reference=None, end=None, **kwargs): """perform a :term:`pileup` within a :term:`region`. The region is specified by :term:`contig`, `start` and `stop` (using 0-based indexing). :term:`reference` and `end` are also accepted for backward compatibility as synonyms for :term:`contig` and `stop`, respectively. Alternatively, a samtools 'region' string can be supplied. Without 'contig' or 'region' all reads will be used for the pileup. The reads will be returned ordered by :term:`contig` sequence, which will not necessarily be the order within the file. Note that :term:`SAM` formatted files do not allow random access. In these files, if a 'region' or 'contig' are given an exception is raised. .. note:: 'all' reads which overlap the region are returned. The first base returned will be the first base of the first read 'not' necessarily the first base of the region used in the query. Parameters ---------- truncate : bool By default, the samtools pileup engine outputs all reads overlapping a region. If truncate is True and a region is given, only columns in the exact region specified are returned. max_depth : int Maximum read depth permitted. The default limit is '8000'. stepper : string The stepper controls how the iterator advances. Possible options for the stepper are ``all`` skip reads in which any of the following flags are set: BAM_FUNMAP, BAM_FSECONDARY, BAM_FQCFAIL, BAM_FDUP ``nofilter`` uses every single read turning off any filtering. ``samtools`` same filter and read processing as in samtools pileup. For full compatibility, this requires a 'fastafile' to be given. The following options all pertain to filtering of the ``samtools`` stepper. fastafile : :class:`~pysam.FastaFile` object. This is required for some of the steppers. ignore_overlaps: bool If set to True, detect if read pairs overlap and only take the higher quality base. This is the default. flag_filter : int ignore reads where any of the bits in the flag are set. The default is BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP. flag_require : int only use reads where certain flags are set. The default is 0. ignore_orphans: bool ignore orphans (paired reads that are not in a proper pair). The default is to ignore orphans. min_base_quality: int Minimum base quality. Bases below the minimum quality will not be output. The default is 13. adjust_capq_threshold: int adjust mapping quality. The default is 0 for no adjustment. The recommended value for adjustment is 50. min_mapping_quality : int only use reads above a minimum mapping quality. The default is 0. compute_baq: bool re-alignment computing per-Base Alignment Qualities (BAQ). The default is to do re-alignment. Realignment requires a reference sequence. If none is present, no realignment will be performed. redo_baq: bool recompute per-Base Alignment Quality on the fly ignoring existing base qualities. The default is False (use existing base qualities). Returns ------- an iterator over genomic positions. : IteratorColumn """ cdef int rtid, has_coord cdef int32_t rstart, rstop if not self.is_open: raise ValueError("I/O operation on closed file") has_coord, rtid, rstart, rstop = self.parse_region( contig, start, stop, region, reference=reference, end=end) if has_coord: if not self.has_index(): raise ValueError("no index available for pileup") return IteratorColumnRegion(self, tid=rtid, start=rstart, stop=rstop, **kwargs) else: if self.has_index(): return IteratorColumnAllRefs(self, **kwargs) else: return IteratorColumnAll(self, **kwargs) def count(self, contig=None, start=None, stop=None, region=None, until_eof=False, read_callback="nofilter", reference=None, end=None): '''count the number of reads in :term:`region` The region is specified by :term:`contig`, `start` and `stop`. :term:`reference` and `end` are also accepted for backward compatibility as synonyms for :term:`contig` and `stop`, respectively. Alternatively, a `samtools`_ :term:`region` string can be supplied. A :term:`SAM` file does not allow random access and if `region` or `contig` are given, an exception is raised. Parameters ---------- contig : string reference_name of the genomic region (chromosome) start : int start of the genomic region (0-based inclusive) stop : int end of the genomic region (0-based exclusive) region : string a region string in samtools format. until_eof : bool count until the end of the file, possibly including unmapped reads as well. read_callback: string or function select a call-back to ignore reads when counting. It can be either a string with the following values: ``all`` skip reads in which any of the following flags are set: BAM_FUNMAP, BAM_FSECONDARY, BAM_FQCFAIL, BAM_FDUP ``nofilter`` uses every single read Alternatively, `read_callback` can be a function ``check_read(read)`` that should return True only for those reads that shall be included in the counting. reference : string backward compatible synonym for `contig` end : int backward compatible synonym for `stop` Raises ------ ValueError if the genomic coordinates are out of range or invalid. ''' cdef AlignedSegment read cdef long counter = 0 if not self.is_open: raise ValueError("I/O operation on closed file") cdef int filter_method = 0 if read_callback == "all": filter_method = 1 elif read_callback == "nofilter": filter_method = 2 for read in self.fetch(contig=contig, start=start, stop=stop, reference=reference, end=end, region=region, until_eof=until_eof): # apply filter if filter_method == 1: # filter = "all" if (read.flag & (0x4 | 0x100 | 0x200 | 0x400)): continue elif filter_method == 2: # filter = "nofilter" pass else: if not read_callback(read): continue counter += 1 return counter @cython.boundscheck(False) # we do manual bounds checking def count_coverage(self, contig, start=None, stop=None, region=None, quality_threshold=15, read_callback='all', reference=None, end=None): """count the coverage of genomic positions by reads in :term:`region`. The region is specified by :term:`contig`, `start` and `stop`. :term:`reference` and `end` are also accepted for backward compatibility as synonyms for :term:`contig` and `stop`, respectively. Alternatively, a `samtools`_ :term:`region` string can be supplied. The coverage is computed per-base [ACGT]. Parameters ---------- contig : string reference_name of the genomic region (chromosome) start : int start of the genomic region (0-based inclusive). If not given, count from the start of the chromosome. stop : int end of the genomic region (0-based exclusive). If not given, count to the end of the chromosome. region : string a region string. quality_threshold : int quality_threshold is the minimum quality score (in phred) a base has to reach to be counted. read_callback: string or function select a call-back to ignore reads when counting. It can be either a string with the following values: ``all`` skip reads in which any of the following flags are set: BAM_FUNMAP, BAM_FSECONDARY, BAM_FQCFAIL, BAM_FDUP ``nofilter`` uses every single read Alternatively, `read_callback` can be a function ``check_read(read)`` that should return True only for those reads that shall be included in the counting. reference : string backward compatible synonym for `contig` end : int backward compatible synonym for `stop` Raises ------ ValueError if the genomic coordinates are out of range or invalid. Returns ------- four array.arrays of the same length in order A C G T : tuple """ cdef uint32_t contig_length = self.get_reference_length(contig) cdef int _start = start if start is not None else 0 cdef int _stop = stop if stop is not None else contig_length _stop = _stop if _stop < contig_length else contig_length if _stop == _start: raise ValueError("interval of size 0") if _stop < _start: raise ValueError("interval of size less than 0") cdef int length = _stop - _start cdef c_array.array int_array_template = array.array('L', []) cdef c_array.array count_a cdef c_array.array count_c cdef c_array.array count_g cdef c_array.array count_t count_a = c_array.clone(int_array_template, length, zero=True) count_c = c_array.clone(int_array_template, length, zero=True) count_g = c_array.clone(int_array_template, length, zero=True) count_t = c_array.clone(int_array_template, length, zero=True) cdef AlignedSegment read cdef cython.str seq cdef c_array.array quality cdef int qpos cdef int refpos cdef int c = 0 cdef int filter_method = 0 if read_callback == "all": filter_method = 1 elif read_callback == "nofilter": filter_method = 2 cdef int _threshold = quality_threshold or 0 for read in self.fetch(contig=contig, reference=reference, start=start, stop=stop, end=end, region=region): # apply filter if filter_method == 1: # filter = "all" if (read.flag & (0x4 | 0x100 | 0x200 | 0x400)): continue elif filter_method == 2: # filter = "nofilter" pass else: if not read_callback(read): continue # count seq = read.seq if seq is None: continue quality = read.query_qualities for qpos, refpos in read.get_aligned_pairs(True): if qpos is not None and refpos is not None and \ _start <= refpos < _stop: # only check base quality if _threshold > 0 if (_threshold and quality and quality[qpos] >= _threshold) or not _threshold: if seq[qpos] == 'A': count_a.data.as_ulongs[refpos - _start] += 1 if seq[qpos] == 'C': count_c.data.as_ulongs[refpos - _start] += 1 if seq[qpos] == 'G': count_g.data.as_ulongs[refpos - _start] += 1 if seq[qpos] == 'T': count_t.data.as_ulongs[refpos - _start] += 1 return count_a, count_c, count_g, count_t def find_introns_slow(self, read_iterator): """Return a dictionary {(start, stop): count} Listing the intronic sites in the reads (identified by 'N' in the cigar strings), and their support ( = number of reads ). read_iterator can be the result of a .fetch(...) call. Or it can be a generator filtering such reads. Example samfile.find_introns((read for read in samfile.fetch(...) if read.is_reverse) """ res = collections.Counter() for r in read_iterator: if 'N' in r.cigarstring: last_read_pos = False for read_loc, genome_loc in r.get_aligned_pairs(): if read_loc is None and last_read_pos: start = genome_loc elif read_loc and last_read_pos is None: stop = genome_loc # we are right exclusive ,so this is correct res[(start, stop)] += 1 del start del stop last_read_pos = read_loc return res def find_introns(self, read_iterator): """Return a dictionary {(start, stop): count} Listing the intronic sites in the reads (identified by 'N' in the cigar strings), and their support ( = number of reads ). read_iterator can be the result of a .fetch(...) call. Or it can be a generator filtering such reads. Example samfile.find_introns((read for read in samfile.fetch(...) if read.is_reverse) """ cdef: uint32_t base_position, junc_start, nt int op AlignedSegment r int BAM_CREF_SKIP = 3 #BAM_CREF_SKIP res = collections.Counter() match_or_deletion = {0, 2, 7, 8} # only M/=/X (0/7/8) and D (2) are related to genome position for r in read_iterator: base_position = r.pos cigar = r.cigartuples if cigar is None: continue for op, nt in cigar: if op in match_or_deletion: base_position += nt elif op == BAM_CREF_SKIP: junc_start = base_position base_position += nt res[(junc_start, base_position)] += 1 return res def close(self): '''closes the :class:`pysam.AlignmentFile`.''' if self.htsfile == NULL: return if self.index != NULL: hts_idx_destroy(self.index) self.index = NULL cdef int ret = hts_close(self.htsfile) self.htsfile = NULL self.header = None if ret < 0: global errno if errno == EPIPE: errno = 0 else: raise IOError(errno, force_str(strerror(errno))) def __dealloc__(self): cdef int ret = 0 if self.index != NULL: hts_idx_destroy(self.index) self.index = NULL if self.htsfile != NULL: ret = hts_close(self.htsfile) self.htsfile = NULL self.header = None if self.b: bam_destroy1(self.b) self.b = NULL if ret < 0: global errno if errno == EPIPE: errno = 0 else: raise IOError(errno, force_str(strerror(errno))) cpdef int write(self, AlignedSegment read) except -1: ''' write a single :class:`pysam.AlignedSegment` to disk. Raises: ValueError if the writing failed Returns: int : the number of bytes written. If the file is closed, this will be 0. ''' if not self.is_open: return 0 if self.header.ptr.n_targets <= read._delegate.core.tid: raise ValueError( "AlignedSegment refers to reference number {} that " "is larger than the number of references ({}) in the header".format( read._delegate.core.tid, self.header.ptr.n_targets)) cdef int ret with nogil: ret = sam_write1(self.htsfile, self.header.ptr, read._delegate) # kbj: Still need to raise an exception with except -1. Otherwise # when ret == -1 we get a "SystemError: error return without # exception set". if ret < 0: raise IOError( "sam_write1 failed with error code {}".format(ret)) return ret # context manager interface def __enter__(self): return self def __exit__(self, exc_type, exc_value, traceback): self.close() return False ############################################################### ############################################################### ############################################################### ## properties ############################################################### property mapped: """int with total number of mapped alignments according to the statistics recorded in the index. This is a read-only attribute. (This will be 0 for a CRAM file indexed by a .crai index, as that index format does not record these statistics.) """ def __get__(self): self.check_index() cdef int tid cdef uint64_t total = 0 cdef uint64_t mapped, unmapped for tid from 0 <= tid < self.header.nreferences: with nogil: hts_idx_get_stat(self.index, tid, &mapped, &unmapped) total += mapped return total property unmapped: """int with total number of unmapped reads according to the statistics recorded in the index. This number of reads includes the number of reads without coordinates. This is a read-only attribute. (This will be 0 for a CRAM file indexed by a .crai index, as that index format does not record these statistics.) """ def __get__(self): self.check_index() cdef int tid cdef uint64_t total = hts_idx_get_n_no_coor(self.index) cdef uint64_t mapped, unmapped for tid from 0 <= tid < self.header.nreferences: with nogil: hts_idx_get_stat(self.index, tid, &mapped, &unmapped) total += unmapped return total property nocoordinate: """int with total number of reads without coordinates according to the statistics recorded in the index, i.e., the statistic printed for "*" by the ``samtools idxstats`` command. This is a read-only attribute. (This will be 0 for a CRAM file indexed by a .crai index, as that index format does not record these statistics.) """ def __get__(self): self.check_index() cdef uint64_t n with nogil: n = hts_idx_get_n_no_coor(self.index) return n def get_index_statistics(self): """return statistics about mapped/unmapped reads per chromosome as they are stored in the index, similarly to the statistics printed by the ``samtools idxstats`` command. CRAI indexes do not record these statistics, so for a CRAM file with a .crai index the returned statistics will all be 0. Returns: list : a list of records for each chromosome. Each record has the attributes 'contig', 'mapped', 'unmapped' and 'total'. """ self.check_index() cdef int tid cdef uint64_t mapped, unmapped results = [] # TODO: use header for tid from 0 <= tid < self.nreferences: with nogil: hts_idx_get_stat(self.index, tid, &mapped, &unmapped) results.append( IndexStats._make(( self.get_reference_name(tid), mapped, unmapped, mapped + unmapped))) return results ############################################################### ## file-object like iterator access ## note: concurrent access will cause errors (see IteratorRow ## and multiple_iterators) ## Possible solutions: deprecate or open new file handle def __iter__(self): if not self.is_open: raise ValueError("I/O operation on closed file") if not self.is_bam and self.header.nreferences == 0: raise NotImplementedError( "can not iterate over samfile without header") return self cdef bam1_t * getCurrent(self): return self.b cdef int cnext(self): ''' cversion of iterator. Used by :class:`pysam.AlignmentFile.IteratorColumn`. ''' cdef int ret cdef bam_hdr_t * hdr = self.header.ptr with nogil: ret = sam_read1(self.htsfile, hdr, self.b) return ret def __next__(self): cdef int ret = self.cnext() if ret >= 0: return makeAlignedSegment(self.b, self.header) elif ret == -1: raise StopIteration else: raise IOError(read_failure_reason(ret)) ########################################### # methods/properties referencing the header def is_valid_tid(self, int tid): """ return True if the numerical :term:`tid` is valid; False otherwise. Note that the unmapped tid code (-1) counts as an invalid. """ if self.header is None: raise ValueError("header not available in closed files") return self.header.is_valid_tid(tid) def get_tid(self, reference): """ return the numerical :term:`tid` corresponding to :term:`reference` returns -1 if reference is not known. """ if self.header is None: raise ValueError("header not available in closed files") return self.header.get_tid(reference) def get_reference_name(self, tid): """ return :term:`reference` name corresponding to numerical :term:`tid` """ if self.header is None: raise ValueError("header not available in closed files") return self.header.get_reference_name(tid) def get_reference_length(self, reference): """ return :term:`reference` length corresponding to numerical :term:`tid` """ if self.header is None: raise ValueError("header not available in closed files") return self.header.get_reference_length(reference) property nreferences: """int with the number of :term:`reference` sequences in the file. This is a read-only attribute.""" def __get__(self): if self.header: return self.header.nreferences else: raise ValueError("header not available in closed files") property references: """tuple with the names of :term:`reference` sequences. This is a read-only attribute""" def __get__(self): if self.header: return self.header.references else: raise ValueError("header not available in closed files") property lengths: """tuple of the lengths of the :term:`reference` sequences. This is a read-only attribute. The lengths are in the same order as :attr:`pysam.AlignmentFile.references` """ def __get__(self): if self.header: return self.header.lengths else: raise ValueError("header not available in closed files") # Compatibility functions for pysam < 0.14 property text: """deprecated, use :attr:`references` and :attr:`lengths` instead""" def __get__(self): if self.header: return self.header.__str__() else: raise ValueError("header not available in closed files") # Compatibility functions for pysam < 0.8.3 def gettid(self, reference): """deprecated, use :meth:`get_tid` instead""" return self.get_tid(reference) def getrname(self, tid): """deprecated, use :meth:`get_reference_name` instead""" return self.get_reference_name(tid) cdef class IteratorRow: '''abstract base class for iterators over mapped reads. Various iterators implement different behaviours for wrapping around contig boundaries. Examples include: :class:`pysam.IteratorRowRegion` iterate within a single contig and a defined region. :class:`pysam.IteratorRowAll` iterate until EOF. This iterator will also include unmapped reads. :class:`pysam.IteratorRowAllRefs` iterate over all reads in all reference sequences. The method :meth:`AlignmentFile.fetch` returns an IteratorRow. .. note:: It is usually not necessary to create an object of this class explicitly. It is returned as a result of call to a :meth:`AlignmentFile.fetch`. ''' def __init__(self, AlignmentFile samfile, int multiple_iterators=False): cdef char *cfilename cdef char *creference_filename cdef char *cindexname = NULL if not samfile.is_open: raise ValueError("I/O operation on closed file") # makes sure that samfile stays alive as long as the # iterator is alive self.samfile = samfile # reopen the file - note that this makes the iterator # slow and causes pileup to slow down significantly. if multiple_iterators: cfilename = samfile.filename with nogil: self.htsfile = hts_open(cfilename, 'r') assert self.htsfile != NULL if samfile.has_index(): if samfile.index_filename: cindexname = bindex_filename = encode_filename(samfile.index_filename) with nogil: self.index = sam_index_load2(self.htsfile, cfilename, cindexname) else: self.index = NULL # need to advance in newly opened file to position after header # better: use seek/tell? with nogil: hdr = sam_hdr_read(self.htsfile) if hdr is NULL: raise IOError("unable to read header information") self.header = makeAlignmentHeader(hdr) self.owns_samfile = True # options specific to CRAM files if samfile.is_cram and samfile.reference_filename: creference_filename = samfile.reference_filename hts_set_opt(self.htsfile, CRAM_OPT_REFERENCE, creference_filename) else: self.htsfile = samfile.htsfile self.index = samfile.index self.owns_samfile = False self.header = samfile.header self.retval = 0 self.b = bam_init1() def __dealloc__(self): bam_destroy1(self.b) if self.owns_samfile: hts_idx_destroy(self.index) hts_close(self.htsfile) cdef class IteratorRowRegion(IteratorRow): """*(AlignmentFile samfile, int tid, int beg, int stop, int multiple_iterators=False)* iterate over mapped reads in a region. .. note:: It is usually not necessary to create an object of this class explicitly. It is returned as a result of call to a :meth:`AlignmentFile.fetch`. """ def __init__(self, AlignmentFile samfile, int tid, int beg, int stop, int multiple_iterators=False): if not samfile.has_index(): raise ValueError("no index available for iteration") super().__init__(samfile, multiple_iterators=multiple_iterators) with nogil: self.iter = sam_itr_queryi( self.index, tid, beg, stop) def __iter__(self): return self cdef bam1_t * getCurrent(self): return self.b cdef int cnext(self): '''cversion of iterator. Used by IteratorColumn''' with nogil: self.retval = hts_itr_next(hts_get_bgzfp(self.htsfile), self.iter, self.b, self.htsfile) def __next__(self): self.cnext() if self.retval >= 0: return makeAlignedSegment(self.b, self.header) elif self.retval == -1: raise StopIteration elif self.retval == -2: # Note: it is currently not the case that hts_iter_next # returns -2 for a truncated file. # See https://github.com/pysam-developers/pysam/pull/50#issuecomment-64928625 raise IOError('truncated file') else: raise IOError("error while reading file {}: {}".format(self.samfile.filename, self.retval)) def __dealloc__(self): hts_itr_destroy(self.iter) cdef class IteratorRowHead(IteratorRow): """*(AlignmentFile samfile, n, int multiple_iterators=False)* iterate over first n reads in `samfile` .. note:: It is usually not necessary to create an object of this class explicitly. It is returned as a result of call to a :meth:`AlignmentFile.head`. """ def __init__(self, AlignmentFile samfile, int n, int multiple_iterators=False): super().__init__(samfile, multiple_iterators=multiple_iterators) self.max_rows = n self.current_row = 0 def __iter__(self): return self cdef bam1_t * getCurrent(self): return self.b cdef int cnext(self): '''cversion of iterator. Used by IteratorColumn''' cdef int ret cdef bam_hdr_t * hdr = self.header.ptr with nogil: ret = sam_read1(self.htsfile, hdr, self.b) return ret def __next__(self): if self.current_row >= self.max_rows: raise StopIteration cdef int ret = self.cnext() if ret >= 0: self.current_row += 1 return makeAlignedSegment(self.b, self.header) elif ret == -1: raise StopIteration else: raise IOError(read_failure_reason(ret)) cdef class IteratorRowAll(IteratorRow): """*(AlignmentFile samfile, int multiple_iterators=False)* iterate over all reads in `samfile` .. note:: It is usually not necessary to create an object of this class explicitly. It is returned as a result of call to a :meth:`AlignmentFile.fetch`. """ def __init__(self, AlignmentFile samfile, int multiple_iterators=False): super().__init__(samfile, multiple_iterators=multiple_iterators) def __iter__(self): return self cdef bam1_t * getCurrent(self): return self.b cdef int cnext(self): '''cversion of iterator. Used by IteratorColumn''' cdef int ret cdef bam_hdr_t * hdr = self.header.ptr with nogil: ret = sam_read1(self.htsfile, hdr, self.b) return ret def __next__(self): cdef int ret = self.cnext() if ret >= 0: return makeAlignedSegment(self.b, self.header) elif ret == -1: raise StopIteration else: raise IOError(read_failure_reason(ret)) cdef class IteratorRowAllRefs(IteratorRow): """iterates over all mapped reads by chaining iterators over each reference .. note:: It is usually not necessary to create an object of this class explicitly. It is returned as a result of call to a :meth:`AlignmentFile.fetch`. """ def __init__(self, AlignmentFile samfile, multiple_iterators=False): super().__init__(samfile, multiple_iterators=multiple_iterators) if not samfile.has_index(): raise ValueError("no index available for fetch") self.tid = -1 def nextiter(self): # get a new iterator for a chromosome. The file # will not be re-opened. self.rowiter = IteratorRowRegion(self.samfile, self.tid, 0, MAX_POS) # set htsfile and header of the rowiter # to the values in this iterator to reflect multiple_iterators self.rowiter.htsfile = self.htsfile self.rowiter.header = self.header # make sure the iterator understand that IteratorRowAllRefs # has ownership self.rowiter.owns_samfile = False def __iter__(self): return self def __next__(self): # Create an initial iterator if self.tid == -1: if not self.samfile.nreferences: raise StopIteration self.tid = 0 self.nextiter() while 1: self.rowiter.cnext() # If current iterator is not exhausted, return aligned read if self.rowiter.retval > 0: return makeAlignedSegment(self.rowiter.b, self.header) self.tid += 1 # Otherwise, proceed to next reference or stop if self.tid < self.samfile.nreferences: self.nextiter() else: raise StopIteration cdef class IteratorRowSelection(IteratorRow): """*(AlignmentFile samfile)* iterate over reads in `samfile` at a given list of file positions. .. note:: It is usually not necessary to create an object of this class explicitly. It is returned as a result of call to a :meth:`AlignmentFile.fetch`. """ def __init__(self, AlignmentFile samfile, positions, int multiple_iterators=True): super().__init__(samfile, multiple_iterators=multiple_iterators) self.positions = positions self.current_pos = 0 def __iter__(self): return self cdef bam1_t * getCurrent(self): return self.b cdef int cnext(self): '''cversion of iterator''' # end iteration if out of positions if self.current_pos >= len(self.positions): return -1 cdef uint64_t pos = self.positions[self.current_pos] with nogil: bgzf_seek(hts_get_bgzfp(self.htsfile), pos, 0) self.current_pos += 1 cdef int ret cdef bam_hdr_t * hdr = self.header.ptr with nogil: ret = sam_read1(self.htsfile, hdr, self.b) return ret def __next__(self): cdef int ret = self.cnext() if ret >= 0: return makeAlignedSegment(self.b, self.header) elif ret == -1: raise StopIteration else: raise IOError(read_failure_reason(ret)) cdef int __advance_nofilter(void *data, bam1_t *b): '''advance without any read filtering. ''' cdef __iterdata * d = <__iterdata*>data cdef int ret with nogil: ret = sam_itr_next(d.htsfile, d.iter, b) return ret cdef int __advance_raw_nofilter(void *data, bam1_t *b): '''advance (without iterator) without any read filtering. ''' cdef __iterdata * d = <__iterdata*>data cdef int ret with nogil: ret = sam_read1(d.htsfile, d.header, b) return ret cdef int __advance_all(void *data, bam1_t *b): '''only use reads for pileup passing basic filters such as BAM_FUNMAP, BAM_FSECONDARY, BAM_FQCFAIL, BAM_FDUP ''' cdef __iterdata * d = <__iterdata*>data cdef mask = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP cdef int ret while 1: with nogil: ret = sam_itr_next(d.htsfile, d.iter, b) if ret < 0: break if b.core.flag & d.flag_filter: continue break return ret cdef int __advance_raw_all(void *data, bam1_t *b): '''only use reads for pileup passing basic filters such as BAM_FUNMAP, BAM_FSECONDARY, BAM_FQCFAIL, BAM_FDUP ''' cdef __iterdata * d = <__iterdata*>data cdef int ret while 1: with nogil: ret = sam_read1(d.htsfile, d.header, b) if ret < 0: break if b.core.flag & d.flag_filter: continue break return ret cdef int __advance_samtools(void * data, bam1_t * b): '''advance using same filter and read processing as in the samtools pileup. ''' cdef __iterdata * d = <__iterdata*>data cdef int ret cdef int q while 1: with nogil: ret = sam_itr_next(d.htsfile, d.iter, b) if d.iter else sam_read1(d.htsfile, d.header, b) if ret < 0: break if b.core.flag & d.flag_filter: continue if d.flag_require and not (b.core.flag & d.flag_require): continue # reload sequence if d.fastafile != NULL and b.core.tid != d.tid: if d.seq != NULL: free(d.seq) d.tid = b.core.tid with nogil: d.seq = faidx_fetch_seq( d.fastafile, d.header.target_name[d.tid], 0, MAX_POS, &d.seq_len) if d.seq == NULL: raise ValueError( "reference sequence for '{}' (tid={}) not found".format( d.header.target_name[d.tid], d.tid)) # realign read - changes base qualities if d.seq != NULL and d.compute_baq: # 4th option to realign is flag: # apply_baq = flag&1, extend_baq = flag&2, redo_baq = flag&4 if d.redo_baq: sam_prob_realn(b, d.seq, d.seq_len, 7) else: sam_prob_realn(b, d.seq, d.seq_len, 3) if d.seq != NULL and d.adjust_capq_threshold > 10: q = sam_cap_mapq(b, d.seq, d.seq_len, d.adjust_capq_threshold) if q < 0: continue elif b.core.qual > q: b.core.qual = q if b.core.qual < d.min_mapping_quality: continue if d.ignore_orphans and b.core.flag & BAM_FPAIRED and not (b.core.flag & BAM_FPROPER_PAIR): continue break return ret cdef class IteratorColumn: '''abstract base class for iterators over columns. IteratorColumn objects wrap the pileup functionality of samtools. For reasons of efficiency, the iterator points to the current pileup buffer. The pileup buffer is updated at every iteration. This might cause some unexpected behaviour. For example, consider the conversion to a list:: f = AlignmentFile("file.bam", "rb") result = list(f.pileup()) Here, ``result`` will contain ``n`` objects of type :class:`~pysam.PileupColumn` for ``n`` columns, but each object in ``result`` will contain the same information. The desired behaviour can be achieved by list comprehension:: result = [x.pileups() for x in f.pileup()] ``result`` will be a list of ``n`` lists of objects of type :class:`~pysam.PileupRead`. If the iterator is associated with a :class:`~pysam.Fastafile` using the :meth:`add_reference` method, then the iterator will export the current sequence via the methods :meth:`get_sequence` and :meth:`seq_len`. See :class:`~AlignmentFile.pileup` for kwargs to the iterator. ''' def __cinit__( self, AlignmentFile samfile, **kwargs): self.samfile = samfile self.fastafile = kwargs.get("fastafile", None) self.stepper = kwargs.get("stepper", "samtools") self.max_depth = kwargs.get("max_depth", 8000) self.ignore_overlaps = kwargs.get("ignore_overlaps", True) self.min_base_quality = kwargs.get("min_base_quality", 13) self.iterdata.seq = NULL self.iterdata.min_mapping_quality = kwargs.get("min_mapping_quality", 0) self.iterdata.flag_require = kwargs.get("flag_require", 0) self.iterdata.flag_filter = kwargs.get("flag_filter", BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP) self.iterdata.adjust_capq_threshold = kwargs.get("adjust_capq_threshold", 0) self.iterdata.compute_baq = kwargs.get("compute_baq", True) self.iterdata.redo_baq = kwargs.get("redo_baq", False) self.iterdata.ignore_orphans = kwargs.get("ignore_orphans", True) self.tid = 0 self.pos = 0 self.n_plp = 0 self.plp = NULL self.pileup_iter = NULL def __iter__(self): return self cdef int cnext(self): '''perform next iteration. ''' # do not release gil here because of call-backs cdef int ret = bam_mplp_auto(self.pileup_iter, &self.tid, &self.pos, &self.n_plp, &self.plp) return ret cdef char * get_sequence(self): '''return current reference sequence underlying the iterator. ''' return self.iterdata.seq property seq_len: '''current sequence length.''' def __get__(self): return self.iterdata.seq_len def add_reference(self, FastaFile fastafile): ''' add reference sequences in `fastafile` to iterator.''' self.fastafile = fastafile if self.iterdata.seq != NULL: free(self.iterdata.seq) self.iterdata.tid = -1 self.iterdata.fastafile = self.fastafile.fastafile def has_reference(self): ''' return true if iterator is associated with a reference''' return self.fastafile cdef _setup_iterator(self, int tid, int start, int stop, int multiple_iterators=0): '''setup the iterator structure''' self.iter = IteratorRowRegion(self.samfile, tid, start, stop, multiple_iterators) self.iterdata.htsfile = self.samfile.htsfile self.iterdata.iter = self.iter.iter self.iterdata.seq = NULL self.iterdata.tid = -1 self.iterdata.header = self.samfile.header.ptr if self.fastafile is not None: self.iterdata.fastafile = self.fastafile.fastafile else: self.iterdata.fastafile = NULL # Free any previously allocated memory before reassigning # pileup_iter self._free_pileup_iter() cdef void * data[1] data[0] = &self.iterdata if self.stepper is None or self.stepper == "all": with nogil: self.pileup_iter = bam_mplp_init(1, &__advance_all, data) elif self.stepper == "nofilter": with nogil: self.pileup_iter = bam_mplp_init(1, &__advance_nofilter, data) elif self.stepper == "samtools": with nogil: self.pileup_iter = bam_mplp_init(1, &__advance_samtools, data) else: raise ValueError( "unknown stepper option `%s` in IteratorColumn" % self.stepper) if self.max_depth: with nogil: bam_mplp_set_maxcnt(self.pileup_iter, self.max_depth) if self.ignore_overlaps: with nogil: bam_mplp_init_overlaps(self.pileup_iter) cdef _setup_raw_rest_iterator(self): '''set up an "iterator" that just uses sam_read1(), similar to HTS_IDX_REST''' self.iter = None self.iterdata.iter = NULL self.iterdata.htsfile = self.samfile.htsfile self.iterdata.seq = NULL self.iterdata.tid = -1 self.iterdata.header = self.samfile.header.ptr if self.fastafile is not None: self.iterdata.fastafile = self.fastafile.fastafile else: self.iterdata.fastafile = NULL # Free any previously allocated memory before reassigning # pileup_iter self._free_pileup_iter() cdef void * data[1] data[0] = &self.iterdata if self.stepper is None or self.stepper == "all": with nogil: self.pileup_iter = bam_mplp_init(1, &__advance_raw_all, data) elif self.stepper == "nofilter": with nogil: self.pileup_iter = bam_mplp_init(1, &__advance_raw_nofilter, data) elif self.stepper == "samtools": with nogil: self.pileup_iter = bam_mplp_init(1, &__advance_samtools, data) else: raise ValueError( "unknown stepper option `%s` in IteratorColumn" % self.stepper) if self.max_depth: with nogil: bam_mplp_set_maxcnt(self.pileup_iter, self.max_depth) if self.ignore_overlaps: with nogil: bam_mplp_init_overlaps(self.pileup_iter) cdef reset(self, tid, start, stop): '''reset iterator position. This permits using the iterator multiple times without having to incur the full set-up costs. ''' if self.iter is None: raise TypeError("Raw iterator set up without region cannot be reset") self.iter = IteratorRowRegion(self.samfile, tid, start, stop, multiple_iterators=0) self.iterdata.iter = self.iter.iter # invalidate sequence if different tid if self.tid != tid: if self.iterdata.seq != NULL: free(self.iterdata.seq) self.iterdata.seq = NULL self.iterdata.tid = -1 # self.pileup_iter = bam_mplp_init(1 # &__advancepileup, # &self.iterdata) with nogil: bam_mplp_reset(self.pileup_iter) cdef _free_pileup_iter(self): '''free the memory alloc'd by bam_plp_init. This is needed before setup_iterator allocates another pileup_iter, or else memory will be lost. ''' if self.pileup_iter != NULL: with nogil: bam_mplp_reset(self.pileup_iter) bam_mplp_destroy(self.pileup_iter) self.pileup_iter = NULL def __dealloc__(self): # reset in order to avoid memory leak messages for iterators # that have not been fully consumed self._free_pileup_iter() self.plp = NULL if self.iterdata.seq != NULL: free(self.iterdata.seq) self.iterdata.seq = NULL # backwards compatibility def hasReference(self): return self.has_reference() cdef char * getSequence(self): return self.get_sequence() def addReference(self, FastaFile fastafile): return self.add_reference(fastafile) cdef class IteratorColumnRegion(IteratorColumn): '''iterates over a region only. ''' def __cinit__(self, AlignmentFile samfile, int tid = 0, int start = 0, int stop = MAX_POS, int truncate = False, int multiple_iterators = True, **kwargs ): # initialize iterator. Multiple iterators not available # for CRAM. if multiple_iterators and samfile.is_cram: warnings.warn("multiple_iterators not implemented for CRAM") multiple_iterators = False self._setup_iterator(tid, start, stop, multiple_iterators) self.start = start self.stop = stop self.truncate = truncate def __next__(self): cdef int n while 1: n = self.cnext() if n < 0: raise ValueError("error during iteration" ) if n == 0: raise StopIteration if self.truncate: if self.start > self.pos: continue if self.pos >= self.stop: raise StopIteration return makePileupColumn(&self.plp, self.tid, self.pos, self.n_plp, self.min_base_quality, self.iterdata.seq, self.samfile.header) cdef class IteratorColumnAllRefs(IteratorColumn): """iterates over all columns by chaining iterators over each reference """ def __cinit__(self, AlignmentFile samfile, **kwargs): # no iteration over empty files if not samfile.nreferences: raise StopIteration # initialize iterator self._setup_iterator(self.tid, 0, MAX_POS, 1) def __next__(self): cdef int n while 1: n = self.cnext() if n < 0: raise ValueError("error during iteration") # proceed to next reference or stop if n == 0: self.tid += 1 if self.tid < self.samfile.nreferences: self._setup_iterator(self.tid, 0, MAX_POS, 0) else: raise StopIteration continue # return result, if within same reference return makePileupColumn(&self.plp, self.tid, self.pos, self.n_plp, self.min_base_quality, self.iterdata.seq, self.samfile.header) cdef class IteratorColumnAll(IteratorColumn): """iterates over all columns, without using an index """ def __cinit__(self, AlignmentFile samfile, **kwargs): self._setup_raw_rest_iterator() def __next__(self): cdef int n n = self.cnext() if n < 0: raise ValueError("error during iteration") if n == 0: raise StopIteration return makePileupColumn(&self.plp, self.tid, self.pos, self.n_plp, self.min_base_quality, self.iterdata.seq, self.samfile.header) cdef class SNPCall: '''the results of a SNP call.''' cdef int _tid cdef int _pos cdef char _reference_base cdef char _genotype cdef int _consensus_quality cdef int _snp_quality cdef int _rms_mapping_quality cdef int _coverage property tid: '''the chromosome ID as is defined in the header''' def __get__(self): return self._tid property pos: '''nucleotide position of SNP.''' def __get__(self): return self._pos property reference_base: '''reference base at pos. ``N`` if no reference sequence supplied.''' def __get__(self): return from_string_and_size( &self._reference_base, 1 ) property genotype: '''the genotype called.''' def __get__(self): return from_string_and_size( &self._genotype, 1 ) property consensus_quality: '''the genotype quality (Phred-scaled).''' def __get__(self): return self._consensus_quality property snp_quality: '''the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.''' def __get__(self): return self._snp_quality property mapping_quality: '''the root mean square (rms) of the mapping quality of all reads involved in the call.''' def __get__(self): return self._rms_mapping_quality property coverage: '''coverage or read depth - the number of reads involved in the call.''' def __get__(self): return self._coverage def __str__(self): return "\t".join( map(str, ( self.tid, self.pos, self.reference_base, self.genotype, self.consensus_quality, self.snp_quality, self.mapping_quality, self.coverage ) ) ) cdef class IndexedReads: """Index a Sam/BAM-file by query name while keeping the original sort order intact. The index is kept in memory and can be substantial. By default, the file is re-opened to avoid conflicts if multiple operators work on the same file. Set `multiple_iterators` = False to not re-open `samfile`. Parameters ---------- samfile : AlignmentFile File to be indexed. multiple_iterators : bool Flag indicating whether the file should be reopened. Reopening prevents existing iterators being affected by the indexing. """ def __init__(self, AlignmentFile samfile, int multiple_iterators=True): cdef char *cfilename # makes sure that samfile stays alive as long as this # object is alive. self.samfile = samfile cdef bam_hdr_t * hdr = NULL assert samfile.is_bam, "can only apply IndexReads on bam files" # multiple_iterators the file - note that this makes the iterator # slow and causes pileup to slow down significantly. if multiple_iterators: cfilename = samfile.filename with nogil: self.htsfile = hts_open(cfilename, 'r') if self.htsfile == NULL: raise OSError("unable to reopen htsfile") # need to advance in newly opened file to position after header # better: use seek/tell? with nogil: hdr = sam_hdr_read(self.htsfile) if hdr == NULL: raise OSError("unable to read header information") self.header = makeAlignmentHeader(hdr) self.owns_samfile = True else: self.htsfile = self.samfile.htsfile self.header = samfile.header self.owns_samfile = False def build(self): '''build the index.''' self.index = collections.defaultdict(list) # this method will start indexing from the current file position cdef int ret = 1 cdef bam1_t * b = calloc(1, sizeof( bam1_t)) if b == NULL: raise MemoryError("could not allocate {} bytes".format(sizeof(bam1_t))) cdef uint64_t pos cdef bam_hdr_t * hdr = self.header.ptr while ret > 0: with nogil: pos = bgzf_tell(hts_get_bgzfp(self.htsfile)) ret = sam_read1(self.htsfile, hdr, b) if ret > 0: qname = charptr_to_str(pysam_bam_get_qname(b)) self.index[qname].append(pos) bam_destroy1(b) def find(self, query_name): '''find `query_name` in index. Returns ------- IteratorRowSelection Returns an iterator over all reads with query_name. Raises ------ KeyError if the `query_name` is not in the index. ''' if query_name in self.index: return IteratorRowSelection( self.samfile, self.index[query_name], multiple_iterators = False) else: raise KeyError("read %s not found" % query_name) def __dealloc__(self): if self.owns_samfile: hts_close(self.htsfile) pysam-0.23.0/pysam/libcbcf.pxd000066400000000000000000000100241475062545500161710ustar00rootroot00000000000000# cython: language_level=3 ############################################################################### ############################################################################### ## Cython wrapper for htslib VCF/BCF reader/writer ############################################################################### # # The MIT License # # Copyright (c) 2015, 2016 Kevin Jacobs (jacobs@bioinformed.com) # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. # ############################################################################### from libc.stdint cimport int8_t, int16_t, int32_t, int64_t from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t from libc.stdlib cimport malloc, calloc, realloc, free from libc.string cimport memcpy, memcmp, memmove, strncpy, strlen, strdup from pysam.libchtslib cimport * cdef class VariantHeader(object): cdef bcf_hdr_t *ptr cdef _add_sample(self, name) cdef _hdr_sync(self) cdef _subset_samples(self, include_samples) cdef class VariantHeaderRecord(object): cdef readonly VariantHeader header cdef bcf_hrec_t *ptr cdef class VariantHeaderRecords(object): cdef readonly VariantHeader header cdef class VariantHeaderContigs(object): cdef readonly VariantHeader header cdef class VariantHeaderSamples(object): cdef readonly VariantHeader header cdef class VariantContig(object): cdef readonly VariantHeader header cdef int id cdef class VariantMetadata(object): cdef readonly VariantHeader header cdef int type cdef int id cdef class VariantHeaderMetadata(object): cdef readonly VariantHeader header cdef int32_t type cdef class VariantRecord(object): cdef readonly VariantHeader header cdef bcf1_t *ptr cdef class VariantRecordFilter(object): cdef VariantRecord record cdef class VariantRecordFormat(object): cdef VariantRecord record cdef class VariantRecordInfo(object): cdef VariantRecord record cdef class VariantRecordSamples(object): cdef VariantRecord record cdef class VariantRecordSample(object): cdef VariantRecord record cdef readonly int32_t index cdef class BaseIndex(object): cdef tuple refs cdef dict refmap cdef class BCFIndex(BaseIndex): cdef readonly VariantHeader header cdef hts_idx_t *ptr cdef class TabixIndex(BaseIndex): cdef tbx_t *ptr cdef class BaseIterator(object): cdef VariantFile bcf cdef hts_itr_t *iter cdef class BCFIterator(BaseIterator): cdef BCFIndex index cdef class TabixIterator(BaseIterator): cdef TabixIndex index cdef kstring_t line_buffer cdef class VariantFile(HTSFile): cdef readonly VariantHeader header cdef readonly BaseIndex index cdef readonly bint drop_samples # true if sample information is to be ignored # FIXME: Temporary, use htsFormat when it is available cdef readonly bint is_reading # true if file has begun reading records cdef readonly bint header_written # true if header has already been written cpdef int write(self, VariantRecord record) except -1 pysam-0.23.0/pysam/libcbcf.pyi000066400000000000000000000270631475062545500162120ustar00rootroot00000000000000import sys from typing import ( Optional, Union, Any, Sequence, Tuple, Iterator, List, Iterable, Dict, overload, TypeVar, Mapping, Generic, ) if sys.version_info < (3, 8): from typing_extensions import Literal else: from typing import Literal from pysam.libchtslib import HTSFile, _HasFileNo _D = TypeVar("_D") _K = TypeVar("_K", str, Union[int, str]) _V = TypeVar("_V") class _Mapping(Generic[_K, _V]): def __len__(self) -> int: ... def __contains__(self, key: _K) -> bool: ... def __iter__(self) -> Iterator[_K]: ... def iterkeys(self) -> Iterator[_K]: ... def itervalues(self) -> Iterator[_V]: ... def iteritems(self) -> Iterator[Tuple[_K, _V]]: ... def keys(self) -> List[_K]: ... def items(self) -> List[Tuple[_K, _V]]: ... def values(self) -> List[_V]: ... def __bool__(self) -> bool: ... def __getitem__(self, key: _K) -> _V: ... def get(self, key: _K, default: _D = ...) -> Union[_D, _V]: ... class VariantHeaderRecord(_Mapping[str, str]): @property def header(self) -> VariantHeader: ... @property def type(self) -> Optional[str]: ... @property def key(self) -> Optional[str]: ... @property def value(self) -> Optional[str]: ... @property def attrs(self) -> Sequence[Tuple[str, str]]: ... def update(self, items: Union[Iterable, Dict] = ..., **kwargs) -> None: ... def pop(self, key: str, default: str = ...) -> str: ... def remove(self) -> None: ... # crashes class VariantHeaderRecords: @property def header(self) -> VariantHeader: ... def __len__(self) -> int: ... def __bool__(self) -> bool: ... def __getitem__(self, index) -> VariantHeaderRecord: ... def __iter__(self) -> Iterator[VariantHeaderRecord]: ... class VariantMetadata: @property def header(self) -> VariantHeader: ... @property def name(self) -> str: ... # @property # should this be exposed? # def id(self) -> int: ... @property def number(self) -> Optional[str]: ... @property def type(self) -> Optional[str]: ... @property def description(self) -> Optional[str]: ... @property def record(self) -> Optional[VariantHeaderRecord]: ... def remove_header(self) -> None: ... class VariantHeaderMetadata(_Mapping[str, VariantMetadata]): @property def header(self) -> VariantHeader: ... def add( self, id: str, number: Optional[Union[int, str]], type: Optional[str], description: str, **kwargs ) -> None: ... def remove_header(self, key: str) -> None: ... def clear_header(self) -> None: ... class VariantContig: @property def header(self) -> VariantHeader: ... @property def name(self) -> str: ... @property def id(self) -> int: ... @property def length(self) -> Optional[int]: ... @property def header_record(self) -> VariantHeaderRecord: ... def remove_header(self) -> None: ... class VariantHeaderContigs(_Mapping[Union[int, str], VariantContig]): @property def header(self) -> VariantHeader: ... def remove_header(self, key: Union[int, str]) -> None: ... def clear_header(self) -> None: ... def add(self, id: str, length: Optional[int] = ..., **kwargs) -> None: ... class VariantHeaderSamples: @property def header(self) -> VariantHeader: ... def __len__(self) -> int: ... def __bool__(self) -> bool: ... def __getitem__(self, index: int) -> str: ... def __iter__(self) -> Iterator[str]: ... def __contains__(self, key: str) -> bool: ... def add(self, name: str) -> None: ... class VariantHeader: def __init__(self) -> None: ... def __bool__(self) -> bool: ... def copy(self) -> VariantHeader: ... def merge(self, header: VariantHeader) -> None: ... @property def version(self) -> str: ... @property def samples(self) -> VariantHeaderSamples: ... @property def records(self) -> VariantHeaderRecords: ... @property def contigs(self) -> VariantHeaderContigs: ... @property def filters(self) -> VariantHeaderMetadata: ... @property def info(self) -> VariantHeaderMetadata: ... @property def formats(self) -> VariantHeaderMetadata: ... @property def alts(self) -> Dict[str, VariantHeaderRecord]: ... def new_record( self, contig: Optional[str] = ..., start: int = ..., stop: int = ..., alleles: Optional[Tuple[str, ...]] = ..., id: Optional[str] = ..., qual: Optional[float] = ..., filter: Optional[Any] = ..., info: Optional[Mapping[str, _InfoValue]] = ..., samples: Optional[Iterable[Optional[Mapping[str, _FormatValue]]]] = ..., **kwargs ) -> VariantRecord: ... def add_record(self, record: VariantHeaderRecord) -> None: ... def add_line(self, line: str) -> None: ... @overload def add_meta( self, key: str, value: None = ..., items: Iterable[Tuple[str, str]] = ... ) -> None: ... @overload def add_meta(self, key: str, value: str = ..., items: None = ...) -> None: ... def add_sample(self, name: str) -> None: ... def add_samples(self, *args: Union[str, Iterable[str]]) -> None: ... class VariantRecordFilter(_Mapping[Union[int, str], VariantMetadata]): def add(self, key: str) -> None: ... def __delitem__(self, key: Union[int, str]) -> None: ... def clear(self) -> None: ... def __eq__(self, other) -> bool: ... def __ne__(self, other) -> bool: ... class VariantRecordFormat(_Mapping[str, VariantMetadata]): def __delitem__(self, key: str) -> None: ... def clear(self) -> None: ... _InfoValue = Any # TODO see bcf_info_get_value class VariantRecordInfo(_Mapping[str, _InfoValue]): def __setitem__(self, key: str, object: _InfoValue) -> None: ... def __delitem__(self, key: str) -> None: ... def clear(self) -> None: ... def update( self, items: Optional[_Mapping[str, _InfoValue]] = ..., **kwargs ) -> None: ... def pop(self, key: str, default: _D = ...) -> Union[_D, _InfoValue]: ... def __eq__(self, other) -> bool: ... def __ne__(self, other) -> bool: ... class VariantRecordSamples(_Mapping[Union[str, int], "VariantRecordSample"]): def __eq__(self, other) -> bool: ... def __ne__(self, other) -> bool: ... # TODO Do these work? Isn’t the container read only? def update( self, items: Optional[Mapping[Union[str, int], VariantRecordSample]] = ..., **kwargs ) -> None: ... def pop( self, key: Union[str, int], default: _D = ... ) -> Union[_D, VariantRecordSample]: ... class VariantRecord: @property def header(self) -> VariantHeader: ... def copy(self) -> VariantRecord: ... def translate(self, dst_header: VariantHeader) -> None: ... rid: int chrom: str contig: str pos: int start: int stop: int rlen: int qual: Optional[float] id: Optional[str] ref: Optional[str] alleles: Optional[Tuple[str, ...]] alts: Optional[Tuple[str, ...]] @property def filter(self) -> VariantRecordFilter: ... @property def info(self) -> VariantRecordInfo: ... @property def format(self) -> VariantRecordFormat: ... @property def samples(self) -> VariantRecordSamples: ... def __eq__(self, other) -> bool: ... def __ne__(self, other) -> bool: ... _FormatValue = Any # TODO see bcf_format_get_value class VariantRecordSample(_Mapping[str, _FormatValue]): @property def index(self) -> int: ... @property def name(self) -> str: ... allele_indices: Optional[Tuple[Optional[int], ...]] alleles: Optional[Tuple[Optional[str], ...]] phased: bool def __setitem__(self, key: str, value: _FormatValue) -> None: ... def __delitem__(self, key: str) -> None: ... def clear(self) -> None: ... def update( self, items: Optional[Mapping[str, _FormatValue]] = ..., **kwargs ) -> None: ... def pop(self, key: str, default: _D = ...) -> Union[_D, _FormatValue]: ... def __eq__(self, other) -> Any: ... def __ne__(self, other) -> Any: ... class BaseIndex(_Mapping[Union[int, str], str]): refs: Sequence[str] refmap: Dict[str, str] def __init__(self) -> None: ... # TODO Do these work? Isn’t the container read only? def update(self, items: Optional[Mapping[str, str]] = ..., **kwargs) -> None: ... def pop(self, key: str, default: _D = ...) -> Union[_D, str]: ... class BCFIndex(BaseIndex): @property def header(self) -> VariantHeader: ... def __init__(self) -> None: ... def fetch( self, bcf: VariantFile, contig: str, start: Optional[int], stop: Optional[int], reopen: bool, ) -> BCFIterator: ... class TabixIndex(BaseIndex): def __init__(self) -> None: ... def fetch( self, bcf: VariantFile, contig: str, start: Optional[int], stop: Optional[int], reopen: bool, ) -> TabixIterator: ... class BaseIterator: def __init__(self) -> None: ... class BCFIterator(BaseIterator): def __init__( self, bcf: VariantFile, contig: str, start: Optional[int] = ..., stop: Optional[int] = ..., reopen: bool = ..., ) -> None: ... def __iter__(self) -> BCFIterator: ... def __next__(self) -> VariantRecord: ... class TabixIterator(BaseIterator): def __init__( self, bcf: VariantFile, contig: str, start: Optional[int] = ..., stop: Optional[int] = ..., reopen: bool = ..., ) -> None: ... def __iter__(self) -> TabixIterator: ... def __next__(self) -> VariantRecord: ... class VariantFile(HTSFile): @property def header(self) -> VariantHeader: ... @property def index(self) -> BaseIndex: ... @property def drop_samples(self) -> bool: ... @property def is_reading(self) -> bool: ... @property def header_written(self) -> bool: ... def __init__( self, filename: Union[str, bytes, int, _HasFileNo], mode: Optional[Literal["r", "w", "wh", "rb", "wb", "wbu", "wb0"]] = ..., index_filename: Optional[str] = ..., header: Optional[VariantHeader] = ..., drop_samples: bool = ..., duplicate_filehandle: bool = ..., ignore_truncation: bool = ..., threads: int = ..., ) -> None: ... def close(self) -> None: ... def __iter__(self) -> VariantFile: ... def __next__(self) -> VariantRecord: ... def copy(self) -> VariantFile: ... def open( self, filename: Union[str, bytes, int, _HasFileNo], mode: Optional[Literal["r", "w", "wh", "rb", "wb", "wbu", "wb0"]] = ..., index_filename: Optional[str] = ..., header: Optional[VariantHeader] = ..., drop_samples: bool = ..., duplicate_filehandle: bool = ..., ignore_truncation: bool = ..., threads: int = ..., ) -> None: ... def reset(self) -> None: ... def is_valid_tid(self, tid: int) -> bool: ... def get_tid(self, reference: str) -> int: ... def get_reference_name(self, tid: int) -> str: ... def fetch( self, contig: Optional[str] = ..., start: Optional[int] = ..., stop: Optional[int] = ..., region: Optional[str] = ..., reopen: bool = ..., end: Optional[int] = ..., reference: Optional[str] = ..., ) -> Iterator[VariantRecord]: ... def new_record(self, *args, **kwargs) -> Any: ... def write(self, record: VariantRecord) -> int: ... def subset_samples(self, include_samples: Iterable[str]) -> None: ... pysam-0.23.0/pysam/libcbcf.pyx000066400000000000000000004346011475062545500162310ustar00rootroot00000000000000# cython: language_level=3 # cython: embedsignature=True # cython: profile=True ############################################################################### ############################################################################### ## Cython wrapper for htslib VCF/BCF reader/writer ############################################################################### # # NOTICE: This code is incomplete and preliminary. It offers a nearly # complete Pythonic interface to VCF/BCF metadata and data with # reading and writing capability. Documentation and a unit test suite # are in the works. The code is best tested under Python 2, but # should also work with Python 3. Please report any remaining # str/bytes issues on the github site when using Python 3 and I'll # fix them promptly. # # Here is a minimal example of how to use the API: # # $ cat bcfview.py # import sys # from pysam import VariantFile # # bcf_in = VariantFile(sys.argv[1]) # auto-detect input format # bcf_out = VariantFile('-', 'w', header=bcf_in.header) # # for rec in bcf_in: # bcf_out.write(rec) # # Performance is fairly close to that of bcftools view. Here is an example # using some 1k Genomes data: # # $ time python bcfview.py ALL.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.bcf |wc -l # 1103799 # # real 0m56.114s # user 1m4.489s # sys 0m3.102s # # $ time bcftools view ALL.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.bcf |wc -l # 1103800 # bcftools adds an extra header # # real 0m55.126s # user 1m3.502s # sys 0m3.459s # ############################################################################### # # TODO list: # # * more genotype methods # * unit test suite (perhaps py.test based) # * documentation # * pickle support # * left/right locus normalization # * fix reopen to re-use fd # ############################################################################### # # The MIT License # # Copyright (c) 2015,2016 Kevin Jacobs (jacobs@bioinformed.com) # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. # ############################################################################### from __future__ import division, print_function import os import sys from libc.errno cimport errno, EPIPE from libc.string cimport strcmp, strpbrk, strerror from libc.stdint cimport INT8_MAX, INT16_MAX, INT32_MAX cimport cython from cpython.object cimport PyObject from cpython.ref cimport Py_INCREF from cpython.dict cimport PyDict_GetItemString, PyDict_SetItemString from cpython.tuple cimport PyTuple_New, PyTuple_SET_ITEM from cpython.bytes cimport PyBytes_FromStringAndSize from cpython.unicode cimport PyUnicode_DecodeUTF8 from pysam.libchtslib cimport HTSFile, hisremote from pysam.utils import unquoted_str __all__ = ['VariantFile', 'VariantHeader', 'VariantHeaderRecord', 'VariantHeaderRecords', 'VariantMetadata', 'VariantHeaderMetadata', 'VariantContig', 'VariantHeaderContigs', 'VariantHeaderSamples', 'VariantRecordFilter', 'VariantRecordFormat', 'VariantRecordInfo', 'VariantRecordSamples', 'VariantRecord', 'VariantRecordSample', 'BaseIndex', 'BCFIndex', 'TabixIndex', 'BaseIterator', 'BCFIterator', 'TabixIterator', 'VariantRecord'] ######################################################################## ######################################################################## ## Constants ######################################################################## cdef int MAX_POS = (1 << 31) - 1 cdef tuple VALUE_TYPES = ('Flag', 'Integer', 'Float', 'String') cdef tuple METADATA_TYPES = ('FILTER', 'INFO', 'FORMAT', 'CONTIG', 'STRUCTURED', 'GENERIC') cdef tuple METADATA_LENGTHS = ('FIXED', 'VARIABLE', 'A', 'G', 'R') ######################################################################## ######################################################################## ## Python 3 compatibility functions ######################################################################## from pysam.libcutils cimport force_bytes, force_str, charptr_to_str, charptr_to_str_w_len from pysam.libcutils cimport encode_filename, from_string_and_size, decode_bytes ######################################################################## ######################################################################## ## Sentinel object ######################################################################## cdef object _nothing = object() ######################################################################## ######################################################################## ## VCF/BCF string intern system ######################################################################## cdef dict bcf_str_cache = {} cdef inline bcf_str_cache_get_charptr(const char* s): if s == NULL: return None cdef PyObject *pystr = PyDict_GetItemString(bcf_str_cache, s) if pystr: return pystr val = PyUnicode_DecodeUTF8(s, strlen(s), NULL) PyDict_SetItemString(bcf_str_cache, s, val) return val ######################################################################## ######################################################################## ## Genotype math ######################################################################## cdef int comb(int n, int k) except -1: """Return binomial coefficient: n choose k >>> comb(5, 1) 5 >>> comb(5, 2) 10 >>> comb(2, 2) 1 >>> comb(100, 2) 4950 """ if k > n: return 0 elif k == n: return 1 elif k > n // 2: k = n - k cdef d, result d = result = n - k + 1 for i in range(2, k + 1): d += 1 result *= d result //= i return result cdef inline int bcf_geno_combinations(int ploidy, int alleles) except -1: """Return the count of genotypes expected for the given ploidy and number of alleles. >>> bcf_geno_combinations(1, 2) 2 >>> bcf_geno_combinations(2, 2) 3 >>> bcf_geno_combinations(2, 3) 6 >>> bcf_geno_combinations(3, 2) 4 """ return comb(alleles + ploidy - 1, ploidy) ######################################################################## ######################################################################## ## Low level type conversion helpers ######################################################################## cdef inline bint check_header_id(bcf_hdr_t *hdr, int hl_type, int id): return id >= 0 and id < hdr.n[BCF_DT_ID] and bcf_hdr_idinfo_exists(hdr, hl_type, id) cdef inline int is_gt_fmt(bcf_hdr_t *hdr, int fmt_id): return strcmp(bcf_hdr_int2id(hdr, BCF_DT_ID, fmt_id), 'GT') == 0 cdef inline int bcf_genotype_count(bcf_hdr_t *hdr, bcf1_t *rec, int sample) except -1: if sample < 0: raise ValueError('genotype is only valid as a format field') cdef int32_t *gt_arr = NULL cdef int ngt = 0 ngt = bcf_get_genotypes(hdr, rec, >_arr, &ngt) if ngt <= 0 or not gt_arr: return 0 assert ngt % rec.n_sample == 0 cdef int max_ploidy = ngt // rec.n_sample cdef int32_t *gt = gt_arr + sample * max_ploidy cdef int ploidy = 0 while ploidy < max_ploidy and gt[0] != bcf_int32_vector_end: gt += 1 ploidy += 1 free(gt_arr) return bcf_geno_combinations(ploidy, rec.n_allele) cdef tuple char_array_to_tuple(const char **a, ssize_t n, int free_after=0): if not a: return None try: return tuple(charptr_to_str(a[i]) for i in range(n)) finally: if free_after and a: free(a) cdef bcf_array_to_object(void *data, int type, ssize_t n, ssize_t count, int scalar): cdef char *datac cdef int8_t *data8 cdef int16_t *data16 cdef int32_t *data32 cdef float *dataf cdef int i cdef bytes b if not data or n <= 0: return None if type == BCF_BT_CHAR: datac = data if not n: value = () else: # Check if at least one null terminator is present if datac[n-1] == bcf_str_vector_end: # If so, create a string up to the first null terminator b = datac else: # Otherwise, copy the entire block b = datac[:n] value = tuple(decode_bytes(v, 'utf-8') if v and v != bcf_str_missing else None for v in b.split(b',')) else: value = [] if type == BCF_BT_INT8: data8 = data for i in range(n): if data8[i] == bcf_int8_vector_end: break value.append(data8[i] if data8[i] != bcf_int8_missing else None) elif type == BCF_BT_INT16: data16 = data for i in range(n): if data16[i] == bcf_int16_vector_end: break value.append(data16[i] if data16[i] != bcf_int16_missing else None) elif type == BCF_BT_INT32: data32 = data for i in range(n): if data32[i] == bcf_int32_vector_end: break value.append(data32[i] if data32[i] != bcf_int32_missing else None) elif type == BCF_BT_FLOAT: dataf = data for i in range(n): if bcf_float_is_vector_end(dataf[i]): break value.append(dataf[i] if not bcf_float_is_missing(dataf[i]) else None) else: raise TypeError('unsupported info type code') # FIXME: Need to know length? Report errors? Pad with missing values? Not clear what to do. if not value: if scalar: value = None elif count <= 0: value = () else: value = (None,)*count elif scalar and len(value) == 1: value = value[0] else: value = tuple(value) return value cdef bcf_object_to_array(values, void *data, int bt_type, ssize_t n, int vlen): cdef char *datac cdef int8_t *data8 cdef int16_t *data16 cdef int32_t *data32 cdef float *dataf cdef ssize_t i, value_count = len(values) assert value_count <= n if bt_type == BCF_BT_CHAR: if not isinstance(values, (str, bytes)): values = b','.join(force_bytes(v) if v else bcf_str_missing for v in values) value_count = len(values) assert value_count <= n datac = data memcpy(datac, values, value_count) for i in range(value_count, n): datac[i] = 0 elif bt_type == BCF_BT_INT8: datai8 = data for i in range(value_count): val = values[i] datai8[i] = val if val is not None else bcf_int8_missing for i in range(value_count, n): datai8[i] = bcf_int8_vector_end elif bt_type == BCF_BT_INT16: datai16 = data for i in range(value_count): val = values[i] datai16[i] = val if val is not None else bcf_int16_missing for i in range(value_count, n): datai16[i] = bcf_int16_vector_end elif bt_type == BCF_BT_INT32: datai32 = data for i in range(value_count): val = values[i] datai32[i] = val if val is not None else bcf_int32_missing for i in range(value_count, n): datai32[i] = bcf_int32_vector_end elif bt_type == BCF_BT_FLOAT: dataf = data for i in range(value_count): val = values[i] if val is None: bcf_float_set(dataf + i, bcf_float_missing) else: dataf[i] = val for i in range(value_count, n): bcf_float_set(dataf + i, bcf_float_vector_end) else: raise TypeError('unsupported type') cdef bcf_empty_array(int type, ssize_t n, int vlen): cdef char *datac cdef int32_t *data32 cdef float *dataf cdef int i if n <= 0: raise ValueError('Cannot create empty array') if type == BCF_HT_STR: value = PyBytes_FromStringAndSize(NULL, sizeof(char)*n) datac = value for i in range(n): datac[i] = bcf_str_missing if not vlen else bcf_str_vector_end elif type == BCF_HT_INT: value = PyBytes_FromStringAndSize(NULL, sizeof(int32_t)*n) data32 = value for i in range(n): data32[i] = bcf_int32_missing if not vlen else bcf_int32_vector_end elif type == BCF_HT_REAL: value = PyBytes_FromStringAndSize(NULL, sizeof(float)*n) dataf = value for i in range(n): bcf_float_set(dataf + i, bcf_float_missing if not vlen else bcf_float_vector_end) else: raise TypeError('unsupported header type code') return value cdef bcf_copy_expand_array(void *src_data, int src_type, size_t src_values, void *dst_data, int dst_type, size_t dst_values, int vlen): """copy data from src to dest where the size of the elements (src_type/dst_type) differ as well as the number of elements (src_values/dst_values). """ cdef char *src_datac cdef char *dst_datac cdef int8_t *src_datai8 cdef int16_t *src_datai16 cdef int32_t *src_datai32 cdef int32_t *dst_datai cdef float *src_dataf cdef float *dst_dataf cdef ssize_t src_size, dst_size, i, j cdef int val if src_values > dst_values: raise ValueError('Cannot copy arrays with src_values={} > dst_values={}'.format(src_values, dst_values)) if src_type == dst_type == BCF_BT_CHAR: src_datac = src_data dst_datac = dst_data memcpy(dst_datac, src_datac, src_values) for i in range(src_values, dst_values): dst_datac[i] = 0 elif src_type == BCF_BT_INT8 and dst_type == BCF_BT_INT32: src_datai8 = src_data dst_datai = dst_data for i in range(src_values): val = src_datai8[i] if val == bcf_int8_missing: val = bcf_int32_missing elif val == bcf_int8_vector_end: val = bcf_int32_vector_end dst_datai[i] = val for i in range(src_values, dst_values): dst_datai[i] = bcf_int32_missing if not vlen else bcf_int32_vector_end elif src_type == BCF_BT_INT16 and dst_type == BCF_BT_INT32: src_datai16 = src_data dst_datai = dst_data for i in range(src_values): val = src_datai16[i] if val == bcf_int16_missing: val = bcf_int32_missing elif val == bcf_int16_vector_end: val = bcf_int32_vector_end dst_datai[i] = val for i in range(src_values, dst_values): dst_datai[i] = bcf_int32_missing if not vlen else bcf_int32_vector_end elif src_type == BCF_BT_INT32 and dst_type == BCF_BT_INT32: src_datai32 = src_data dst_datai = dst_data for i in range(src_values): dst_datai[i] = src_datai32[i] for i in range(src_values, dst_values): dst_datai[i] = bcf_int32_missing if not vlen else bcf_int32_vector_end elif src_type == BCF_BT_FLOAT and dst_type == BCF_BT_FLOAT: src_dataf = src_data dst_dataf = dst_data for i in range(src_values): dst_dataf[i] = src_dataf[i] for i in range(src_values, dst_values): bcf_float_set(dst_dataf + i, bcf_float_missing if not vlen else bcf_float_vector_end) else: raise TypeError('unsupported types') cdef bcf_get_value_count(VariantRecord record, int hl_type, int id, ssize_t *count, int *scalar, int sample): if record is None: raise ValueError('record must not be None') cdef bcf_hdr_t *hdr = record.header.ptr cdef bcf1_t *r = record.ptr if not check_header_id(hdr, hl_type, id): raise ValueError('Invalid header') cdef int length = bcf_hdr_id2length(hdr, hl_type, id) cdef int number = bcf_hdr_id2number(hdr, hl_type, id) scalar[0] = 0 if hl_type == BCF_HL_FMT and is_gt_fmt(hdr, id): count[0] = number elif length == BCF_VL_FIXED: if number == 1: scalar[0] = 1 count[0] = number elif length == BCF_VL_R: count[0] = r.n_allele elif length == BCF_VL_A: count[0] = r.n_allele - 1 elif length == BCF_VL_G: count[0] = bcf_genotype_count(hdr, r, sample) elif length == BCF_VL_VAR: count[0] = -1 else: raise ValueError('Unknown format length') cdef object bcf_info_get_value(VariantRecord record, const bcf_info_t *z): if record is None: raise ValueError('record must not be None') cdef bcf_hdr_t *hdr = record.header.ptr cdef char *s cdef ssize_t count cdef int scalar bcf_get_value_count(record, BCF_HL_INFO, z.key, &count, &scalar, -1) if z.len == 0: if bcf_hdr_id2type(hdr, BCF_HL_INFO, z.key) == BCF_HT_FLAG: value = True elif scalar: value = None else: value = () elif z.len == 1: if z.type == BCF_BT_INT8: value = z.v1.i if z.v1.i != bcf_int8_missing else None elif z.type == BCF_BT_INT16: value = z.v1.i if z.v1.i != bcf_int16_missing else None elif z.type == BCF_BT_INT32: value = z.v1.i if z.v1.i != bcf_int32_missing else None elif z.type == BCF_BT_FLOAT: value = z.v1.f if not bcf_float_is_missing(z.v1.f) else None elif z.type == BCF_BT_CHAR: value = force_str(chr(z.v1.i)) else: raise TypeError('unsupported info type code') if not scalar and value != (): value = (value,) else: value = bcf_array_to_object(z.vptr, z.type, z.len, count, scalar) return value cdef object bcf_check_values(VariantRecord record, value, int sample, int hl_type, int ht_type, int id, int bt_type, ssize_t bt_len, ssize_t *value_count, int *scalar, int *realloc): if record is None: raise ValueError('record must not be None') bcf_get_value_count(record, hl_type, id, value_count, scalar, sample) # Validate values now that we know the type and size values = (value,) if not isinstance(value, (list, tuple)) else value # Validate values now that we know the type and size if ht_type == BCF_HT_FLAG: value_count[0] = 1 elif hl_type == BCF_HL_FMT and is_gt_fmt(record.header.ptr, id): # KBJ: htslib lies about the cardinality of GT fields-- they're really VLEN (-1) value_count[0] = -1 cdef int given = len(values) if value_count[0] != -1 and value_count[0] != given: if scalar[0]: raise TypeError('value expected to be scalar, given len={}'.format(given)) else: raise TypeError('values expected to be {}-tuple, given len={}'.format(value_count[0], given)) if ht_type == BCF_HT_REAL: for v in values: if not(v is None or isinstance(v, (float, int))): raise TypeError('invalid value for Float format') elif ht_type == BCF_HT_INT: for v in values: if not(v is None or (isinstance(v, (float, int)) and int(v) == v)): raise TypeError('invalid value for Integer format') for v in values: if not(v is None or bcf_int32_missing < v <= INT32_MAX): raise ValueError('Integer value too small/large to store in VCF/BCF') elif ht_type == BCF_HT_STR: values = b','.join(force_bytes(v) if v is not None else b'' for v in values) elif ht_type == BCF_HT_FLAG: if values[0] not in (True, False, None, 1, 0): raise ValueError('Flag values must be: True, False, None, 1, 0') else: raise TypeError('unsupported type') realloc[0] = 0 if len(values) <= 1 and hl_type == BCF_HL_INFO: realloc[0] = 0 elif len(values) > bt_len: realloc[0] = 1 elif bt_type == BCF_BT_INT8: for v in values: if v is not None and not(bcf_int8_missing < v <= INT8_MAX): realloc[0] = 1 break elif bt_type == BCF_BT_INT16: for v in values: if v is not None and not(bcf_int16_missing < v <= INT16_MAX): realloc[0] = 1 break return values cdef bcf_encode_alleles(VariantRecord record, values): if record is None: raise ValueError('record must not be None') cdef bcf1_t *r = record.ptr cdef int32_t nalleles = r.n_allele cdef list gt_values = [] cdef char *s cdef int i if values is None: return () if not isinstance(values, (list, tuple)): values = (values,) for value in values: if value is None: gt_values.append(bcf_gt_missing) elif isinstance(value, (str, bytes)): bvalue = force_bytes(value) s = bvalue for i in range(r.n_allele): if strcmp(r.d.allele[i], s) != 0: gt_values.append(bcf_gt_unphased(i)) break else: raise ValueError('Unknown allele') else: i = value if not (0 <= i < nalleles): raise ValueError('Invalid allele index') gt_values.append(bcf_gt_unphased(i)) return gt_values cdef bcf_info_set_value(VariantRecord record, key, value): if record is None: raise ValueError('record must not be None') cdef bcf_hdr_t *hdr = record.header.ptr cdef bcf1_t *r = record.ptr cdef int info_id, info_type, scalar, dst_type, realloc, vlen = 0 cdef ssize_t i, value_count, alloc_len, alloc_size, dst_size if bcf_unpack(r, BCF_UN_INFO) < 0: raise ValueError('Error unpacking VariantRecord') cdef bytes bkey = force_bytes(key) cdef bcf_info_t *info = bcf_get_info(hdr, r, bkey) if info: info_id = info.key else: info_id = bcf_header_get_info_id(hdr, bkey) if info_id < 0: raise KeyError('unknown INFO: {}'.format(key)) if not check_header_id(hdr, BCF_HL_INFO, info_id): raise ValueError('Invalid header') info_type = bcf_hdr_id2type(hdr, BCF_HL_INFO, info_id) values = bcf_check_values(record, value, -1, BCF_HL_INFO, info_type, info_id, info.type if info else -1, info.len if info else -1, &value_count, &scalar, &realloc) if info_type == BCF_HT_FLAG: if bcf_update_info(hdr, r, bkey, NULL, bool(values[0]), info_type) < 0: raise ValueError('Unable to update INFO values') return vlen = value_count < 0 value_count = len(values) # DISABLED DUE TO ISSUES WITH THE CRAZY POINTERS # If we can, write updated values to existing allocated storage if 0 and info and not realloc: r.d.shared_dirty |= BCF1_DIRTY_INF if value_count == 0: info.len = 0 if not info.vptr: info.vptr = &info.v1.i elif value_count == 1: # FIXME: Check if need to free vptr if info.len > 0? if info.type == BCF_BT_INT8 or info.type == BCF_BT_INT16 or info.type == BCF_BT_INT32: bcf_object_to_array(values, &info.v1.i, BCF_BT_INT32, 1, vlen) elif info.type == BCF_BT_FLOAT: bcf_object_to_array(values, &info.v1.f, BCF_BT_FLOAT, 1, vlen) else: raise TypeError('unsupported info type code') info.len = 1 if not info.vptr: info.vptr = &info.v1.i else: bcf_object_to_array(values, info.vptr, info.type, info.len, vlen) return alloc_len = max(1, value_count) if info and info.len > alloc_len: alloc_len = info.len new_values = bcf_empty_array(info_type, alloc_len, vlen) cdef char *valp = new_values if info_type == BCF_HT_INT: dst_type = BCF_BT_INT32 elif info_type == BCF_HT_REAL: dst_type = BCF_BT_FLOAT elif info_type == BCF_HT_STR: dst_type = BCF_BT_CHAR else: raise ValueError('Unsupported INFO type') bcf_object_to_array(values, valp, dst_type, alloc_len, vlen) if bcf_update_info(hdr, r, bkey, valp, alloc_len, info_type) < 0: raise ValueError('Unable to update INFO values') cdef bcf_info_del_value(VariantRecord record, key): if record is None: raise ValueError('record must not be None') cdef bcf_hdr_t *hdr = record.header.ptr cdef bcf1_t *r = record.ptr cdef ssize_t value_count cdef int scalar if bcf_unpack(r, BCF_UN_INFO) < 0: raise ValueError('Error unpacking VariantRecord') cdef bytes bkey = force_bytes(key) cdef bcf_info_t *info = bcf_get_info(hdr, r, bkey) if not info: raise KeyError(key) bcf_get_value_count(record, BCF_HL_INFO, info.key, &value_count, &scalar, -1) if value_count <= 0: null_value = () elif scalar: null_value = None else: null_value = (None,)*value_count bcf_info_set_value(record, bkey, null_value) cdef bcf_format_get_value(VariantRecordSample sample, key): if sample is None: raise ValueError('sample must not be None') cdef bcf_hdr_t *hdr = sample.record.header.ptr cdef bcf1_t *r = sample.record.ptr cdef ssize_t count cdef int scalar if bcf_unpack(r, BCF_UN_ALL) < 0: raise ValueError('Error unpacking VariantRecord') cdef bytes bkey = force_bytes(key) cdef bcf_fmt_t *fmt = bcf_get_fmt(hdr, r, bkey) if not fmt or not fmt.p: raise KeyError('invalid FORMAT: {}'.format(key)) if is_gt_fmt(hdr, fmt.id): return bcf_format_get_allele_indices(sample) bcf_get_value_count(sample.record, BCF_HL_FMT, fmt.id, &count, &scalar, sample.index) if fmt.p and fmt.n and fmt.size: return bcf_array_to_object(fmt.p + sample.index * fmt.size, fmt.type, fmt.n, count, scalar) elif scalar: return None elif count <= 0: return () else: return (None,)*count cdef bcf_format_set_value(VariantRecordSample sample, key, value): if sample is None: raise ValueError('sample must not be None') if key == 'phased': sample.phased = bool(value) return cdef bcf_hdr_t *hdr = sample.record.header.ptr cdef bcf1_t *r = sample.record.ptr cdef int fmt_id cdef vdict_t *d cdef khiter_t k cdef int fmt_type, scalar, realloc, dst_type, vlen = 0 cdef ssize_t i, nsamples, value_count, alloc_size, alloc_len, dst_size if bcf_unpack(r, BCF_UN_ALL) < 0: raise ValueError('Error unpacking VariantRecord') cdef bytes bkey = force_bytes(key) cdef bcf_fmt_t *fmt = bcf_get_fmt(hdr, r, bkey) if fmt: fmt_id = fmt.id else: d = hdr.dict[BCF_DT_ID] k = kh_get_vdict(d, bkey) if k == kh_end(d) or kh_val_vdict(d, k).info[BCF_HL_FMT] & 0xF == 0xF: raise KeyError('unknown format: {}'.format(key)) fmt_id = kh_val_vdict(d, k).id if not check_header_id(hdr, BCF_HL_FMT, fmt_id): raise ValueError('Invalid header') fmt_type = bcf_hdr_id2type(hdr, BCF_HL_FMT, fmt_id) if fmt_type == BCF_HT_FLAG: raise ValueError('Flag types are not allowed on FORMATs') if is_gt_fmt(hdr, fmt_id): value = bcf_encode_alleles(sample.record, value) # KBJ: GT field is considered to be a string by the VCF header but BCF represents it as INT. fmt_type = BCF_HT_INT values = bcf_check_values(sample.record, value, sample.index, BCF_HL_FMT, fmt_type, fmt_id, fmt.type if fmt else -1, fmt.n if fmt else -1, &value_count, &scalar, &realloc) vlen = value_count < 0 value_count = len(values) # If we can, write updated values to existing allocated storage. if fmt and not realloc: r.d.indiv_dirty = 1 bcf_object_to_array(values, fmt.p + sample.index * fmt.size, fmt.type, fmt.n, vlen) return alloc_len = max(1, value_count) if fmt and fmt.n > alloc_len: alloc_len = fmt.n nsamples = r.n_sample new_values = bcf_empty_array(fmt_type, nsamples * alloc_len, vlen) cdef char *new_values_p = new_values if fmt_type == BCF_HT_INT: dst_type = BCF_BT_INT32 dst_size = sizeof(int32_t) * alloc_len elif fmt_type == BCF_HT_REAL: dst_type = BCF_BT_FLOAT dst_size = sizeof(float) * alloc_len elif fmt_type == BCF_HT_STR: dst_type = BCF_BT_CHAR dst_size = sizeof(char) * alloc_len else: raise ValueError('Unsupported FORMAT type') if fmt and nsamples > 1: for i in range(nsamples): bcf_copy_expand_array(fmt.p + i * fmt.size, fmt.type, fmt.n, new_values_p + i * dst_size, dst_type, alloc_len, vlen) bcf_object_to_array(values, new_values_p + sample.index * dst_size, dst_type, alloc_len, vlen) if bcf_update_format(hdr, r, bkey, new_values_p, (nsamples * alloc_len), fmt_type) < 0: raise ValueError('Unable to update format values') cdef bcf_format_del_value(VariantRecordSample sample, key): if sample is None: raise ValueError('sample must not be None') cdef bcf_hdr_t *hdr = sample.record.header.ptr cdef bcf1_t *r = sample.record.ptr cdef ssize_t value_count cdef int scalar if bcf_unpack(r, BCF_UN_ALL) < 0: raise ValueError('Error unpacking VariantRecord') cdef bytes bkey = force_bytes(key) cdef bcf_fmt_t *fmt = bcf_get_fmt(hdr, r, bkey) if not fmt or not fmt.p: raise KeyError(key) bcf_get_value_count(sample.record, BCF_HL_FMT, fmt.id, &value_count, &scalar, sample.index) if value_count <= 0: null_value = () elif scalar: null_value = None else: null_value = (None,)*value_count bcf_format_set_value(sample, bkey, null_value) cdef bcf_format_get_allele_indices(VariantRecordSample sample): if sample is None: raise ValueError('sample must not be None') cdef bcf_hdr_t *hdr = sample.record.header.ptr cdef bcf1_t *r = sample.record.ptr cdef int32_t n = r.n_sample if bcf_unpack(r, BCF_UN_ALL) < 0: raise ValueError('Error unpacking VariantRecord') if sample.index < 0 or sample.index >= n or not r.n_fmt: return () cdef bcf_fmt_t *fmt0 = r.d.fmt cdef int gt0 = is_gt_fmt(hdr, fmt0.id) if not gt0 or not fmt0.n: return () cdef int8_t *data8 cdef int16_t *data16 cdef int32_t *data32 cdef int32_t a, nalleles = r.n_allele cdef list alleles = [] if fmt0.type == BCF_BT_INT8: data8 = (fmt0.p + sample.index * fmt0.size) for i in range(fmt0.n): if data8[i] == bcf_int8_vector_end: break elif data8[i] == bcf_gt_missing: a = -1 else: a = bcf_gt_allele(data8[i]) alleles.append(a if 0 <= a < nalleles else None) elif fmt0.type == BCF_BT_INT16: data16 = (fmt0.p + sample.index * fmt0.size) for i in range(fmt0.n): if data16[i] == bcf_int16_vector_end: break elif data16[i] == bcf_gt_missing: a = -1 else: a = bcf_gt_allele(data16[i]) alleles.append(a if 0 <= a < nalleles else None) elif fmt0.type == BCF_BT_INT32: data32 = (fmt0.p + sample.index * fmt0.size) for i in range(fmt0.n): if data32[i] == bcf_int32_vector_end: break elif data32[i] == bcf_gt_missing: a = -1 else: a = bcf_gt_allele(data32[i]) alleles.append(a if 0 <= a < nalleles else None) return tuple(alleles) cdef bcf_format_get_alleles(VariantRecordSample sample): if sample is None: raise ValueError('sample must not be None') cdef bcf_hdr_t *hdr = sample.record.header.ptr cdef bcf1_t *r = sample.record.ptr cdef int32_t nsamples = r.n_sample if bcf_unpack(r, BCF_UN_ALL) < 0: raise ValueError('Error unpacking VariantRecord') cdef int32_t nalleles = r.n_allele if sample.index < 0 or sample.index >= nsamples or not r.n_fmt: return () cdef bcf_fmt_t *fmt0 = r.d.fmt cdef int gt0 = is_gt_fmt(hdr, fmt0.id) if not gt0 or not fmt0.n: return () cdef int32_t a cdef int8_t *data8 cdef int16_t *data16 cdef int32_t *data32 alleles = [] if fmt0.type == BCF_BT_INT8: data8 = (fmt0.p + sample.index * fmt0.size) for i in range(fmt0.n): if data8[i] == bcf_int8_vector_end: break a = bcf_gt_allele(data8[i]) alleles.append(charptr_to_str(r.d.allele[a]) if 0 <= a < nalleles else None) elif fmt0.type == BCF_BT_INT16: data16 = (fmt0.p + sample.index * fmt0.size) for i in range(fmt0.n): if data16[i] == bcf_int16_vector_end: break a = bcf_gt_allele(data16[i]) alleles.append(charptr_to_str(r.d.allele[a]) if 0 <= a < nalleles else None) elif fmt0.type == BCF_BT_INT32: data32 = (fmt0.p + sample.index * fmt0.size) for i in range(fmt0.n): if data32[i] == bcf_int32_vector_end: break a = bcf_gt_allele(data32[i]) alleles.append(charptr_to_str(r.d.allele[a]) if 0 <= a < nalleles else None) return tuple(alleles) cdef bint bcf_sample_get_phased(VariantRecordSample sample): if sample is None: raise ValueError('sample must not be None') cdef bcf_hdr_t *hdr = sample.record.header.ptr cdef bcf1_t *r = sample.record.ptr cdef int32_t n = r.n_sample if bcf_unpack(r, BCF_UN_ALL) < 0: raise ValueError('Error unpacking VariantRecord') if sample.index < 0 or sample.index >= n or not r.n_fmt: return False cdef bcf_fmt_t *fmt0 = r.d.fmt cdef int gt0 = is_gt_fmt(hdr, fmt0.id) if not gt0 or not fmt0.n: return False cdef int8_t *data8 cdef int16_t *data16 cdef int32_t *data32 cdef bint phased = False if fmt0.type == BCF_BT_INT8: data8 = (fmt0.p + sample.index * fmt0.size) for i in range(fmt0.n): if data8[i] == bcf_int8_vector_end: break elif data8[i] == bcf_int8_missing: continue elif i and not bcf_gt_is_phased(data8[i]): return False else: phased = True elif fmt0.type == BCF_BT_INT16: data16 = (fmt0.p + sample.index * fmt0.size) for i in range(fmt0.n): if data16[i] == bcf_int16_vector_end: break elif data16[i] == bcf_int16_missing: continue elif i and not bcf_gt_is_phased(data16[i]): return False else: phased = True elif fmt0.type == BCF_BT_INT32: data32 = (fmt0.p + sample.index * fmt0.size) for i in range(fmt0.n): if data32[i] == bcf_int32_vector_end: break elif data32[i] == bcf_int32_missing: continue elif i and not bcf_gt_is_phased(data32[i]): return False else: phased = True return phased cdef bcf_sample_set_phased(VariantRecordSample sample, bint phased): if sample is None: raise ValueError('sample must not be None') cdef bcf_hdr_t *hdr = sample.record.header.ptr cdef bcf1_t *r = sample.record.ptr cdef int32_t n = r.n_sample if bcf_unpack(r, BCF_UN_ALL) < 0: raise ValueError('Error unpacking VariantRecord') if sample.index < 0 or sample.index >= n or not r.n_fmt: return cdef bcf_fmt_t *fmt0 = r.d.fmt cdef int gt0 = is_gt_fmt(hdr, fmt0.id) if not gt0 or not fmt0.n: raise ValueError('Cannot set phased before genotype is set') cdef int8_t *data8 cdef int16_t *data16 cdef int32_t *data32 if fmt0.type == BCF_BT_INT8: data8 = (fmt0.p + sample.index * fmt0.size) for i in range(fmt0.n): if data8[i] == bcf_int8_vector_end: break elif data8[i] == bcf_int8_missing: continue elif i: data8[i] = (data8[i] & 0xFE) | phased elif fmt0.type == BCF_BT_INT16: data16 = (fmt0.p + sample.index * fmt0.size) for i in range(fmt0.n): if data16[i] == bcf_int16_vector_end: break elif data16[i] == bcf_int16_missing: continue elif i: data16[i] = (data16[i] & 0xFFFE) | phased elif fmt0.type == BCF_BT_INT32: data32 = (fmt0.p + sample.index * fmt0.size) for i in range(fmt0.n): if data32[i] == bcf_int32_vector_end: break elif data32[i] == bcf_int32_missing: continue elif i: data32[i] = (data32[i] & 0xFFFFFFFE) | phased cdef inline bcf_sync_end(VariantRecord record): cdef bcf_hdr_t *hdr = record.header.ptr cdef bcf_info_t *info cdef int end_id = bcf_header_get_info_id(record.header.ptr, b'END') cdef int ref_len # allow missing ref when instantiating a new record if record.ref is not None: ref_len = len(record.ref) else: ref_len = 0 # Delete INFO/END if no alleles are present or if rlen is equal to len(ref) # Always keep END for symbolic alleles if not has_symbolic_allele(record) and (not record.ptr.n_allele or record.ptr.rlen == ref_len): # If INFO/END is not defined in the header, it doesn't exist in the record if end_id >= 0: info = bcf_get_info(hdr, record.ptr, b'END') if info and info.vptr: if bcf_update_info(hdr, record.ptr, b'END', NULL, 0, info.type) < 0: raise ValueError('Unable to delete END') else: # Create END header, if not present if end_id < 0: record.header.info.add('END', number=1, type='Integer', description='Stop position of the interval') # Update to reflect stop position bcf_info_set_value(record, b'END', record.ptr.pos + record.ptr.rlen) cdef inline int has_symbolic_allele(VariantRecord record): """Return index of first symbolic allele. 0 if no symbolic alleles.""" for i in range(1, record.ptr.n_allele): alt = record.ptr.d.allele[i] if alt[0] == b'<' and alt[len(alt) - 1] == b'>': return i return 0 ######################################################################## ######################################################################## ## Variant Header objects ######################################################################## cdef bcf_header_remove_hrec(VariantHeader header, int i): if header is None: raise ValueError('header must not be None') cdef bcf_hdr_t *hdr = header.ptr if i < 0 or i >= hdr.nhrec: raise ValueError('Invalid header record index') cdef bcf_hrec_t *hrec = hdr.hrec[i] hdr.nhrec -= 1 if i < hdr.nhrec: memmove(&hdr.hrec[i], &hdr.hrec[i+1], (hdr.nhrec-i)*sizeof(bcf_hrec_t*)) bcf_hrec_destroy(hrec) hdr.hrec[hdr.nhrec] = NULL hdr.dirty = 1 #FIXME: implement a full mapping interface #FIXME: passing bcf_hrec_t* is not safe, since we cannot control the # object lifetime. cdef class VariantHeaderRecord(object): """header record from a :class:`VariantHeader` object""" def __init__(self, *args, **kwargs): raise TypeError('this class cannot be instantiated from Python') @property def type(self): """header type: FILTER, INFO, FORMAT, CONTIG, STRUCTURED, or GENERIC""" cdef bcf_hrec_t *r = self.ptr if not r: return None return METADATA_TYPES[r.type] @property def key(self): """header key (the part before '=', in FILTER/INFO/FORMAT/contig/fileformat etc.)""" cdef bcf_hrec_t *r = self.ptr return bcf_str_cache_get_charptr(r.key) if r and r.key else None @property def value(self): """header value. Set only for generic lines, None for FILTER/INFO, etc.""" cdef bcf_hrec_t *r = self.ptr return charptr_to_str(r.value) if r and r.value else None @property def attrs(self): """sequence of additional header attributes""" cdef bcf_hrec_t *r = self.ptr if not r: return () cdef int i return tuple((bcf_str_cache_get_charptr(r.keys[i]) if r.keys[i] else None, charptr_to_str(r.vals[i]) if r.vals[i] else None) for i in range(r.nkeys)) def __len__(self): cdef bcf_hrec_t *r = self.ptr return r.nkeys if r else 0 def __bool__(self): cdef bcf_hrec_t *r = self.ptr return r != NULL and r.nkeys != 0 def __getitem__(self, key): """get attribute value""" cdef bcf_hrec_t *r = self.ptr cdef int i if r: bkey = force_bytes(key) for i in range(r.nkeys): if r.keys[i] and r.keys[i] == bkey: return charptr_to_str(r.vals[i]) if r.vals[i] else None raise KeyError('cannot find metadata key') def __iter__(self): cdef bcf_hrec_t *r = self.ptr if not r: return cdef int i for i in range(r.nkeys): if r.keys[i]: yield bcf_str_cache_get_charptr(r.keys[i]) def get(self, key, default=None): """D.get(k[,d]) -> D[k] if k in D, else d. d defaults to None.""" try: return self[key] except KeyError: return default def __contains__(self, key): try: self[key] except KeyError: return False else: return True def iterkeys(self): """D.iterkeys() -> an iterator over the keys of D""" return iter(self) def itervalues(self): """D.itervalues() -> an iterator over the values of D""" cdef bcf_hrec_t *r = self.ptr if not r: return cdef int i for i in range(r.nkeys): if r.keys[i]: yield charptr_to_str(r.vals[i]) if r.vals[i] else None def iteritems(self): """D.iteritems() -> an iterator over the (key, value) items of D""" cdef bcf_hrec_t *r = self.ptr if not r: return cdef int i for i in range(r.nkeys): if r.keys[i]: yield (bcf_str_cache_get_charptr(r.keys[i]), charptr_to_str(r.vals[i]) if r.vals[i] else None) def keys(self): """D.keys() -> list of D's keys""" return list(self) def items(self): """D.items() -> list of D's (key, value) pairs, as 2-tuples""" return list(self.iteritems()) def values(self): """D.values() -> list of D's values""" return list(self.itervalues()) def update(self, items=None, **kwargs): """D.update([E, ]**F) -> None. Update D from dict/iterable E and F. """ for k, v in items.items(): self[k] = v if kwargs: for k, v in kwargs.items(): self[k] = v def pop(self, key, default=_nothing): try: value = self[key] del self[key] return value except KeyError: if default is not _nothing: return default raise # Mappings are not hashable by default, but subclasses can change this __hash__ = None #TODO: implement __richcmp__ def __str__(self): cdef bcf_hrec_t *r = self.ptr if not r: raise ValueError('cannot convert deleted record to str') cdef kstring_t hrec_str hrec_str.l = hrec_str.m = 0 hrec_str.s = NULL bcf_hrec_format(r, &hrec_str) ret = charptr_to_str_w_len(hrec_str.s, hrec_str.l) if hrec_str.m: free(hrec_str.s) return ret # FIXME: Not safe -- causes trivial segfaults at the moment def remove(self): cdef bcf_hdr_t *hdr = self.header.ptr cdef bcf_hrec_t *r = self.ptr if not r: return assert r.key cdef char *key = r.key if r.type == BCF_HL_GEN else r.value bcf_hdr_remove(hdr, r.type, key) self.ptr = NULL cdef VariantHeaderRecord makeVariantHeaderRecord(VariantHeader header, bcf_hrec_t *hdr): if not header: raise ValueError('invalid VariantHeader') if not hdr: return None cdef VariantHeaderRecord record = VariantHeaderRecord.__new__(VariantHeaderRecord) record.header = header record.ptr = hdr return record cdef class VariantHeaderRecords(object): """sequence of :class:`VariantHeaderRecord` object from a :class:`VariantHeader` object""" def __init__(self, *args, **kwargs): raise TypeError('this class cannot be instantiated from Python') def __len__(self): return self.header.ptr.nhrec def __bool__(self): return self.header.ptr.nhrec != 0 def __getitem__(self, index): cdef int32_t i = index if i < 0 or i >= self.header.ptr.nhrec: raise IndexError('invalid header record index') return makeVariantHeaderRecord(self.header, self.header.ptr.hrec[i]) def __iter__(self): cdef int32_t i for i in range(self.header.ptr.nhrec): yield makeVariantHeaderRecord(self.header, self.header.ptr.hrec[i]) __hash__ = None cdef VariantHeaderRecords makeVariantHeaderRecords(VariantHeader header): if not header: raise ValueError('invalid VariantHeader') cdef VariantHeaderRecords records = VariantHeaderRecords.__new__(VariantHeaderRecords) records.header = header return records cdef class VariantMetadata(object): """filter, info or format metadata record from a :class:`VariantHeader` object""" def __init__(self, *args, **kwargs): raise TypeError('this class cannot be instantiated from Python') @property def name(self): """metadata name""" cdef bcf_hdr_t *hdr = self.header.ptr return bcf_str_cache_get_charptr(hdr.id[BCF_DT_ID][self.id].key) # Q: Should this be exposed? @property def id(self): """metadata internal header id number""" return self.id @property def number(self): """metadata number (i.e. cardinality)""" cdef bcf_hdr_t *hdr = self.header.ptr if not check_header_id(hdr, self.type, self.id): raise ValueError('Invalid header id') if self.type == BCF_HL_FLT: return None cdef int l = bcf_hdr_id2length(hdr, self.type, self.id) if l == BCF_VL_FIXED: return bcf_hdr_id2number(hdr, self.type, self.id) elif l == BCF_VL_VAR: return '.' else: return METADATA_LENGTHS[l] @property def type(self): """metadata value type""" cdef bcf_hdr_t *hdr = self.header.ptr if not check_header_id(hdr, self.type, self.id): raise ValueError('Invalid header id') if self.type == BCF_HL_FLT: return None return VALUE_TYPES[bcf_hdr_id2type(hdr, self.type, self.id)] @property def description(self): """metadata description (or None if not set)""" descr = self.record.get('Description') if descr: descr = descr.strip('"') return force_str(descr) @property def record(self): """:class:`VariantHeaderRecord` associated with this :class:`VariantMetadata` object""" cdef bcf_hdr_t *hdr = self.header.ptr if not check_header_id(hdr, self.type, self.id): raise ValueError('Invalid header id') cdef bcf_hrec_t *hrec = hdr.id[BCF_DT_ID][self.id].val.hrec[self.type] if not hrec: return None return makeVariantHeaderRecord(self.header, hrec) def remove_header(self): cdef bcf_hdr_t *hdr = self.header.ptr cdef const char *key = hdr.id[BCF_DT_ID][self.id].key bcf_hdr_remove(hdr, self.type, key) cdef VariantMetadata makeVariantMetadata(VariantHeader header, int type, int id): if not header: raise ValueError('invalid VariantHeader') if type != BCF_HL_FLT and type != BCF_HL_INFO and type != BCF_HL_FMT: raise ValueError('invalid metadata type') if id < 0 or id >= header.ptr.n[BCF_DT_ID]: raise ValueError('invalid metadata id') cdef VariantMetadata meta = VariantMetadata.__new__(VariantMetadata) meta.header = header meta.type = type meta.id = id return meta cdef class VariantHeaderMetadata(object): """mapping from filter, info or format name to :class:`VariantMetadata` object""" def __init__(self, *args, **kwargs): raise TypeError('this class cannot be instantiated from Python') def add(self, id, number, type, description, **kwargs): """Add a new filter, info or format record""" if id in self: raise ValueError('Header already exists for id={}'.format(id)) if self.type == BCF_HL_FLT: if number is not None: raise ValueError('Number must be None when adding a filter') if type is not None: raise ValueError('Type must be None when adding a filter') items = [('ID', unquoted_str(id)), ('Description', description)] else: if type not in VALUE_TYPES: raise ValueError('unknown type specified: {}'.format(type)) if number is None: number = '.' items = [('ID', unquoted_str(id)), ('Number', unquoted_str(number)), ('Type', unquoted_str(type)), ('Description', description)] items += kwargs.items() self.header.add_meta(METADATA_TYPES[self.type], items=items) def __len__(self): cdef bcf_hdr_t *hdr = self.header.ptr cdef bcf_idpair_t *idpair cdef int32_t i, n = 0 for i in range(hdr.n[BCF_DT_ID]): idpair = hdr.id[BCF_DT_ID] + i if idpair.key and idpair.val and idpair.val.info[self.type] & 0xF != 0xF: n += 1 return n def __bool__(self): cdef bcf_hdr_t *hdr = self.header.ptr cdef bcf_idpair_t *idpair cdef int32_t i for i in range(hdr.n[BCF_DT_ID]): idpair = hdr.id[BCF_DT_ID] + i if idpair.key and idpair.val and idpair.val.info[self.type] & 0xF != 0xF: return True return False def __getitem__(self, key): cdef bcf_hdr_t *hdr = self.header.ptr cdef vdict_t *d = hdr.dict[BCF_DT_ID] cdef bytes bkey = force_bytes(key) cdef khiter_t k = kh_get_vdict(d, bkey) if k == kh_end(d) or kh_val_vdict(d, k).info[self.type] & 0xF == 0xF: raise KeyError('invalid key: {}'.format(key)) return makeVariantMetadata(self.header, self.type, kh_val_vdict(d, k).id) def remove_header(self, key): cdef bcf_hdr_t *hdr = self.header.ptr cdef vdict_t *d = hdr.dict[BCF_DT_ID] cdef bytes bkey = force_bytes(key) cdef khiter_t k = kh_get_vdict(d, bkey) if k == kh_end(d) or kh_val_vdict(d, k).info[self.type] & 0xF == 0xF: raise KeyError('invalid key: {}'.format(key)) bcf_hdr_remove(hdr, self.type, bkey) #bcf_hdr_sync(hdr) def clear_header(self): cdef bcf_hdr_t *hdr = self.header.ptr bcf_hdr_remove(hdr, self.type, NULL) #bcf_hdr_sync(hdr) def __iter__(self): cdef bcf_hdr_t *hdr = self.header.ptr cdef bcf_idpair_t *idpair cdef int32_t i for i in range(hdr.n[BCF_DT_ID]): idpair = hdr.id[BCF_DT_ID] + i if idpair.key and idpair.val and idpair.val.info[self.type] & 0xF != 0xF: yield bcf_str_cache_get_charptr(idpair.key) def get(self, key, default=None): """D.get(k[,d]) -> D[k] if k in D, else d. d defaults to None.""" try: return self[key] except KeyError: return default def __contains__(self, key): try: self[key] except KeyError: return False else: return True def iterkeys(self): """D.iterkeys() -> an iterator over the keys of D""" return iter(self) def itervalues(self): """D.itervalues() -> an iterator over the values of D""" for key in self: yield self[key] def iteritems(self): """D.iteritems() -> an iterator over the (key, value) items of D""" for key in self: yield (key, self[key]) def keys(self): """D.keys() -> list of D's keys""" return list(self) def items(self): """D.items() -> list of D's (key, value) pairs, as 2-tuples""" return list(self.iteritems()) def values(self): """D.values() -> list of D's values""" return list(self.itervalues()) # Mappings are not hashable by default, but subclasses can change this __hash__ = None #TODO: implement __richcmp__ cdef VariantHeaderMetadata makeVariantHeaderMetadata(VariantHeader header, int32_t type): if not header: raise ValueError('invalid VariantHeader') cdef VariantHeaderMetadata meta = VariantHeaderMetadata.__new__(VariantHeaderMetadata) meta.header = header meta.type = type return meta cdef class VariantContig(object): """contig metadata from a :class:`VariantHeader`""" def __init__(self, *args, **kwargs): raise TypeError('this class cannot be instantiated from Python') @property def name(self): """contig name""" cdef bcf_hdr_t *hdr = self.header.ptr return bcf_str_cache_get_charptr(hdr.id[BCF_DT_CTG][self.id].key) @property def id(self): """contig internal id number""" return self.id @property def length(self): """contig length or None if not available""" cdef bcf_hdr_t *hdr = self.header.ptr cdef uint32_t length = hdr.id[BCF_DT_CTG][self.id].val.info[0] return length if length else None @property def header_record(self): """:class:`VariantHeaderRecord` associated with this :class:`VariantContig` object""" cdef bcf_hdr_t *hdr = self.header.ptr cdef bcf_hrec_t *hrec = hdr.id[BCF_DT_CTG][self.id].val.hrec[0] return makeVariantHeaderRecord(self.header, hrec) def remove_header(self): cdef bcf_hdr_t *hdr = self.header.ptr cdef const char *key = hdr.id[BCF_DT_CTG][self.id].key bcf_hdr_remove(hdr, BCF_HL_CTG, key) cdef VariantContig makeVariantContig(VariantHeader header, int id): if not header: raise ValueError('invalid VariantHeader') if id < 0 or id >= header.ptr.n[BCF_DT_CTG]: raise ValueError('invalid contig id') cdef VariantContig contig = VariantContig.__new__(VariantContig) contig.header = header contig.id = id return contig cdef class VariantHeaderContigs(object): """mapping from contig name or index to :class:`VariantContig` object.""" def __init__(self, *args, **kwargs): raise TypeError('this class cannot be instantiated from Python') def __len__(self): cdef bcf_hdr_t *hdr = self.header.ptr assert kh_size(hdr.dict[BCF_DT_CTG]) == hdr.n[BCF_DT_CTG] return hdr.n[BCF_DT_CTG] def __bool__(self): cdef bcf_hdr_t *hdr = self.header.ptr assert kh_size(hdr.dict[BCF_DT_CTG]) == hdr.n[BCF_DT_CTG] return hdr.n[BCF_DT_CTG] != 0 def __getitem__(self, key): cdef bcf_hdr_t *hdr = self.header.ptr cdef int index if isinstance(key, int): index = key if index < 0 or index >= hdr.n[BCF_DT_CTG]: raise IndexError('invalid contig index') return makeVariantContig(self.header, index) cdef vdict_t *d = hdr.dict[BCF_DT_CTG] cdef bytes bkey = force_bytes(key) cdef khiter_t k = kh_get_vdict(d, bkey) if k == kh_end(d): raise KeyError('invalid contig: {}'.format(key)) cdef int id = kh_val_vdict(d, k).id return makeVariantContig(self.header, id) def remove_header(self, key): cdef bcf_hdr_t *hdr = self.header.ptr cdef int index cdef const char *ckey cdef vdict_t *d cdef khiter_t k if isinstance(key, int): index = key if index < 0 or index >= hdr.n[BCF_DT_CTG]: raise IndexError('invalid contig index') ckey = hdr.id[BCF_DT_CTG][self.id].key else: d = hdr.dict[BCF_DT_CTG] key = force_bytes(key) if kh_get_vdict(d, key) == kh_end(d): raise KeyError('invalid contig: {}'.format(key)) ckey = key bcf_hdr_remove(hdr, BCF_HL_CTG, ckey) def clear_header(self): cdef bcf_hdr_t *hdr = self.header.ptr bcf_hdr_remove(hdr, BCF_HL_CTG, NULL) #bcf_hdr_sync(hdr) def __iter__(self): cdef bcf_hdr_t *hdr = self.header.ptr cdef vdict_t *d = hdr.dict[BCF_DT_CTG] cdef uint32_t n = kh_size(d) assert n == hdr.n[BCF_DT_CTG] for i in range(n): yield bcf_str_cache_get_charptr(bcf_hdr_id2name(hdr, i)) def get(self, key, default=None): """D.get(k[,d]) -> D[k] if k in D, else d. d defaults to None.""" try: return self[key] except KeyError: return default def __contains__(self, key): try: self[key] except KeyError: return False else: return True def iterkeys(self): """D.iterkeys() -> an iterator over the keys of D""" return iter(self) def itervalues(self): """D.itervalues() -> an iterator over the values of D""" for key in self: yield self[key] def iteritems(self): """D.iteritems() -> an iterator over the (key, value) items of D""" for key in self: yield (key, self[key]) def keys(self): """D.keys() -> list of D's keys""" return list(self) def items(self): """D.items() -> list of D's (key, value) pairs, as 2-tuples""" return list(self.iteritems()) def values(self): """D.values() -> list of D's values""" return list(self.itervalues()) # Mappings are not hashable by default, but subclasses can change this __hash__ = None #TODO: implement __richcmp__ def add(self, id, length=None, **kwargs): """Add a new contig record""" if id in self: raise ValueError('Header already exists for contig {}'.format(id)) items = [('ID', unquoted_str(id))] if length is not None: items.append(("length", unquoted_str(length))) items += kwargs.items() self.header.add_meta('contig', items=items) cdef VariantHeaderContigs makeVariantHeaderContigs(VariantHeader header): if not header: raise ValueError('invalid VariantHeader') cdef VariantHeaderContigs contigs = VariantHeaderContigs.__new__(VariantHeaderContigs) contigs.header = header return contigs cdef class VariantHeaderSamples(object): """sequence of sample names from a :class:`VariantHeader` object""" def __init__(self, *args, **kwargs): raise TypeError('this class cannot be instantiated from Python') def __len__(self): return bcf_hdr_nsamples(self.header.ptr) def __bool__(self): return bcf_hdr_nsamples(self.header.ptr) != 0 def __getitem__(self, index): cdef bcf_hdr_t *hdr = self.header.ptr cdef int32_t n = bcf_hdr_nsamples(hdr) cdef int32_t i = index if i < 0 or i >= n: raise IndexError('invalid sample index') return charptr_to_str(hdr.samples[i]) def __iter__(self): cdef bcf_hdr_t *hdr = self.header.ptr cdef int32_t i, n = bcf_hdr_nsamples(hdr) for i in range(n): yield charptr_to_str(hdr.samples[i]) def __contains__(self, key): cdef bcf_hdr_t *hdr = self.header.ptr cdef vdict_t *d = hdr.dict[BCF_DT_SAMPLE] cdef bytes bkey = force_bytes(key) cdef khiter_t k = kh_get_vdict(d, bkey) return k != kh_end(d) # Mappings are not hashable by default, but subclasses can change this __hash__ = None #TODO: implement __richcmp__ def add(self, name): """Add a new sample""" self.header.add_sample(name) cdef VariantHeaderSamples makeVariantHeaderSamples(VariantHeader header): if not header: raise ValueError('invalid VariantHeader') cdef VariantHeaderSamples samples = VariantHeaderSamples.__new__(VariantHeaderSamples) samples.header = header return samples cdef class VariantHeader(object): """header information for a :class:`VariantFile` object""" #FIXME: Add structured proxy #FIXME: Add generic proxy #FIXME: Add mutable methods # See makeVariantHeader for C constructor def __cinit__(self): self.ptr = NULL # Python constructor def __init__(self): self.ptr = bcf_hdr_init(b'w') if not self.ptr: raise ValueError('cannot create VariantHeader') def __dealloc__(self): if self.ptr: bcf_hdr_destroy(self.ptr) self.ptr = NULL def __bool__(self): return self.ptr != NULL def copy(self): return makeVariantHeader(bcf_hdr_dup(self.ptr)) def merge(self, VariantHeader header): if header is None: raise ValueError('header must not be None') bcf_hdr_merge(self.ptr, header.ptr) @property def version(self): """VCF version""" return force_str(bcf_hdr_get_version(self.ptr)) @property def samples(self): """samples (:class:`VariantHeaderSamples`)""" return makeVariantHeaderSamples(self) @property def records(self): """header records (:class:`VariantHeaderRecords`)""" return makeVariantHeaderRecords(self) @property def contigs(self): """contig information (:class:`VariantHeaderContigs`)""" return makeVariantHeaderContigs(self) @property def filters(self): """filter metadata (:class:`VariantHeaderMetadata`)""" return makeVariantHeaderMetadata(self, BCF_HL_FLT) @property def info(self): """info metadata (:class:`VariantHeaderMetadata`)""" return makeVariantHeaderMetadata(self, BCF_HL_INFO) @property def formats(self): """format metadata (:class:`VariantHeaderMetadata`)""" return makeVariantHeaderMetadata(self, BCF_HL_FMT) @property def alts(self): """alt metadata (:class:`dict` ID->record). The data returned just a snapshot of alt records, is created every time the property is requested, and modifications will not be reflected in the header metadata and vice versa. i.e. it is just a dict that reflects the state of alt records at the time it is created. """ return {record['ID']:record for record in self.records if record.key.upper() == 'ALT' } # only safe to do when opening an htsfile cdef _subset_samples(self, include_samples): keep_samples = set(self.samples) include_samples = set(include_samples) missing_samples = include_samples - keep_samples keep_samples &= include_samples if missing_samples: # FIXME: add specialized exception with payload raise ValueError( 'missing {:d} requested samples'.format( len(missing_samples))) keep_samples = force_bytes(','.join(keep_samples)) cdef char *keep = keep_samples if keep_samples else NULL cdef ret = bcf_hdr_set_samples(self.ptr, keep, 0) if ret != 0: raise ValueError( 'bcf_hdr_set_samples failed: ret = {}'.format(ret)) def __str__(self): cdef int hlen cdef kstring_t line line.l = line.m = 0 line.s = NULL if bcf_hdr_format(self.ptr, 0, &line) < 0: if line.m: free(line.s) raise ValueError('bcf_hdr_format failed') ret = charptr_to_str_w_len(line.s, line.l) if line.m: free(line.s) return ret def new_record(self, contig=None, start=0, stop=0, alleles=None, id=None, qual=None, filter=None, info=None, samples=None, **kwargs): """Create a new empty VariantRecord. Arguments are currently experimental. Use with caution and expect changes in upcoming releases. """ rec = makeVariantRecord(self, bcf_init()) if not rec: raise MemoryError('unable to allocate BCF record') rec.ptr.n_sample = bcf_hdr_nsamples(self.ptr) if contig is not None: rec.contig = contig rec.start = start rec.stop = stop rec.id = id rec.qual = qual if alleles is not None: rec.alleles = alleles if filter is not None: if isinstance(filter, (list, tuple, VariantRecordFilter)): for f in filter: rec.filter.add(f) else: rec.filter.add(filter) if info: rec.info.update(info) if kwargs: rec.samples[0].update(kwargs) if samples: for i, sample in enumerate(samples): rec.samples[i].update(sample) return rec def add_record(self, VariantHeaderRecord record): """Add an existing :class:`VariantHeaderRecord` to this header""" if record is None: raise ValueError('record must not be None') cdef bcf_hrec_t *hrec = bcf_hrec_dup(record.ptr) bcf_hdr_add_hrec(self.ptr, hrec) self._hdr_sync() def add_line(self, line): """Add a metadata line to this header""" bline = force_bytes(line) if bcf_hdr_append(self.ptr, bline) < 0: raise ValueError('invalid header line') self._hdr_sync() def add_meta(self, key, value=None, items=None): """Add metadata to this header""" if not ((value is not None) ^ (items is not None)): raise ValueError('either value or items must be specified') cdef bcf_hrec_t *hrec = calloc(1, sizeof(bcf_hrec_t)) cdef int quoted try: key = force_bytes(key) hrec.key = strdup(key) if value is not None: hrec.value = strdup(force_bytes(value)) else: for key, value in items: quoted = not isinstance(value, unquoted_str) and key not in ("ID", "Number", "Type") key = force_bytes(key) bcf_hrec_add_key(hrec, key, len(key)) value = force_bytes(str(value)) bcf_hrec_set_val(hrec, hrec.nkeys-1, value, len(value), quoted) except: bcf_hrec_destroy(hrec) raise bcf_hdr_add_hrec(self.ptr, hrec) self._hdr_sync() cdef _add_sample(self, name): bname = force_bytes(name) if bcf_hdr_add_sample(self.ptr, bname) < 0: raise ValueError('Duplicated sample name: {}'.format(name)) cdef _hdr_sync(self): cdef bcf_hdr_t *hdr = self.ptr if hdr.dirty: if bcf_hdr_sync(hdr) < 0: raise MemoryError('unable to reallocate VariantHeader') def add_sample(self, name): """Add a new sample to this header""" self._add_sample(name) self._hdr_sync() def add_samples(self, *args): """Add several new samples to this header. This function takes multiple arguments, each of which may be either a sample name or an iterable returning sample names (e.g., a list of sample names). """ for arg in args: if isinstance(arg, str): self._add_sample(arg) else: for name in arg: self._add_sample(name) self._hdr_sync() cdef VariantHeader makeVariantHeader(bcf_hdr_t *hdr): if not hdr: raise ValueError('cannot create VariantHeader') cdef VariantHeader header = VariantHeader.__new__(VariantHeader) header.ptr = hdr return header cdef inline int bcf_header_get_info_id(bcf_hdr_t *hdr, key) except? -2: cdef vdict_t *d cdef khiter_t k cdef int info_id if isinstance(key, str): key = force_bytes(key) d = hdr.dict[BCF_DT_ID] k = kh_get_vdict(d, key) if k == kh_end(d) or kh_val_vdict(d, k).info[BCF_HL_INFO] & 0xF == 0xF: return -1 return kh_val_vdict(d, k).id ######################################################################## ######################################################################## ## Variant Record objects ######################################################################## cdef class VariantRecordFilter(object): """Filters set on a :class:`VariantRecord` object, presented as a mapping from filter index or name to :class:`VariantMetadata` object""" def __init__(self, *args, **kwargs): raise TypeError('this class cannot be instantiated from Python') def __len__(self): return self.record.ptr.d.n_flt def __bool__(self): return self.record.ptr.d.n_flt != 0 def __getitem__(self, key): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef int index, id cdef int n = r.d.n_flt if isinstance(key, int): index = key if index < 0 or index >= n: raise IndexError('invalid filter index') id = r.d.flt[index] else: if key == '.': key = 'PASS' bkey = force_bytes(key) id = bcf_hdr_id2int(hdr, BCF_DT_ID, bkey) if not check_header_id(hdr, BCF_HL_FLT, id) or not bcf_has_filter(hdr, r, bkey): raise KeyError('Invalid filter: {}'.format(key)) return makeVariantMetadata(self.record.header, BCF_HL_FLT, id) def add(self, key): """Add a new filter""" cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef int id if key == '.': key = 'PASS' cdef bytes bkey = force_bytes(key) id = bcf_hdr_id2int(hdr, BCF_DT_ID, bkey) if not check_header_id(hdr, BCF_HL_FLT, id): raise KeyError('Invalid filter: {}'.format(key)) bcf_add_filter(hdr, r, id) def __delitem__(self, key): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef int index, id cdef int n = r.d.n_flt if isinstance(key, int): index = key if index < 0 or index >= n: raise IndexError('invalid filter index') id = r.d.flt[index] else: if key == '.': key = 'PASS' bkey = force_bytes(key) id = bcf_hdr_id2int(hdr, BCF_DT_ID, bkey) if not check_header_id(hdr, BCF_HL_FLT, id) or not bcf_has_filter(hdr, r, bkey): raise KeyError('Invalid filter: {}'.format(key)) bcf_remove_filter(hdr, r, id, 0) def clear(self): """Clear all filters""" cdef bcf1_t *r = self.record.ptr r.d.shared_dirty |= BCF1_DIRTY_FLT r.d.n_flt = 0 def __iter__(self): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef int i for i in range(r.d.n_flt): yield bcf_str_cache_get_charptr(bcf_hdr_int2id(hdr, BCF_DT_ID, r.d.flt[i])) def get(self, key, default=None): """D.get(k[,d]) -> D[k] if k in D, else d. d defaults to None.""" try: return self[key] except KeyError: return default def __contains__(self, key): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef bytes bkey = force_bytes(key) return bcf_has_filter(hdr, r, bkey) == 1 def iterkeys(self): """D.iterkeys() -> an iterator over the keys of D""" return iter(self) def itervalues(self): """D.itervalues() -> an iterator over the values of D""" for key in self: yield self[key] def iteritems(self): """D.iteritems() -> an iterator over the (key, value) items of D""" for key in self: yield (key, self[key]) def keys(self): """D.keys() -> list of D's keys""" return list(self) def items(self): """D.items() -> list of D's (key, value) pairs, as 2-tuples""" return list(self.iteritems()) def values(self): """D.values() -> list of D's values""" return list(self.itervalues()) def __richcmp__(VariantRecordFilter self not None, VariantRecordFilter other not None, int op): if op != 2 and op != 3: return NotImplemented cdef bcf1_t *s = self.record.ptr cdef bcf1_t *o = other.record.ptr cdef bint cmp = (s.d.n_flt == o.d.n_flt and list(self) == list(other)) if op == 3: cmp = not cmp return cmp # Mappings are not hashable by default, but subclasses can change this __hash__ = None #TODO: implement __richcmp__ cdef VariantRecordFilter makeVariantRecordFilter(VariantRecord record): if not record: raise ValueError('invalid VariantRecord') cdef VariantRecordFilter filter = VariantRecordFilter.__new__(VariantRecordFilter) filter.record = record return filter cdef class VariantRecordFormat(object): """Format data present for each sample in a :class:`VariantRecord` object, presented as mapping from format name to :class:`VariantMetadata` object.""" def __init__(self, *args, **kwargs): raise TypeError('this class cannot be instantiated from Python') def __len__(self): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef int i, n = 0 for i in range(r.n_fmt): if r.d.fmt[i].p: n += 1 return n def __bool__(self): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef int i for i in range(r.n_fmt): if r.d.fmt[i].p: return True return False def __getitem__(self, key): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef bytes bkey = force_bytes(key) cdef bcf_fmt_t *fmt = bcf_get_fmt(hdr, r, bkey) if not fmt or not fmt.p: raise KeyError('unknown format: {}'.format(key)) return makeVariantMetadata(self.record.header, BCF_HL_FMT, fmt.id) def __delitem__(self, key): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef bytes bkey = force_bytes(key) cdef bcf_fmt_t *fmt = bcf_get_fmt(hdr, r, bkey) if not fmt or not fmt.p: raise KeyError('unknown format: {}'.format(key)) if bcf_update_format(hdr, r, bkey, fmt.p, 0, fmt.type) < 0: raise ValueError('Unable to delete FORMAT') def clear(self): """Clear all formats for all samples within the associated :class:`VariantRecord` instance""" cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef bcf_fmt_t *fmt cdef const char *key cdef int i for i in reversed(range(r.n_fmt)): fmt = &r.d.fmt[i] if fmt.p: key = bcf_hdr_int2id(hdr, BCF_DT_ID, fmt.id) if bcf_update_format(hdr, r, key, fmt.p, 0, fmt.type) < 0: raise ValueError('Unable to delete FORMAT') def __iter__(self): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef bcf_fmt_t *fmt cdef int i for i in range(r.n_fmt): fmt = &r.d.fmt[i] if fmt.p: yield bcf_str_cache_get_charptr(bcf_hdr_int2id(hdr, BCF_DT_ID, fmt.id)) def get(self, key, default=None): """D.get(k[,d]) -> D[k] if k in D, else d. d defaults to None.""" try: return self[key] except KeyError: return default def __contains__(self, key): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef bytes bkey = force_bytes(key) cdef bcf_fmt_t *fmt = bcf_get_fmt(hdr, r, bkey) return fmt != NULL and fmt.p != NULL def iterkeys(self): """D.iterkeys() -> an iterator over the keys of D""" return iter(self) def itervalues(self): """D.itervalues() -> an iterator over the values of D""" for key in self: yield self[key] def iteritems(self): """D.iteritems() -> an iterator over the (key, value) items of D""" for key in self: yield (key, self[key]) def keys(self): """D.keys() -> list of D's keys""" return list(self) def items(self): """D.items() -> list of D's (key, value) pairs, as 2-tuples""" return list(self.iteritems()) def values(self): """D.values() -> list of D's values""" return list(self.itervalues()) # Mappings are not hashable by default, but subclasses can change this __hash__ = None #TODO: implement __richcmp__ cdef VariantRecordFormat makeVariantRecordFormat(VariantRecord record): if not record: raise ValueError('invalid VariantRecord') cdef VariantRecordFormat format = VariantRecordFormat.__new__(VariantRecordFormat) format.record = record return format #TODO: Add a getmeta method to return the corresponding VariantMetadata? cdef class VariantRecordInfo(object): """Info data stored in a :class:`VariantRecord` object, presented as a mapping from info metadata name to value.""" def __init__(self, *args, **kwargs): raise TypeError('this class cannot be instantiated from Python') def __len__(self): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef bcf_info_t *info cdef const char *key cdef int i, count = 0 if bcf_unpack(r, BCF_UN_INFO) < 0: raise ValueError('Error unpacking VariantRecord') for i in range(r.n_info): info = &r.d.info[i] key = bcf_hdr_int2id(hdr, BCF_DT_ID, info.key) if info != NULL and info.vptr != NULL and strcmp(key, b'END') != 0: count += 1 return count def __bool__(self): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef bcf_info_t *info cdef const char *key cdef int i if bcf_unpack(r, BCF_UN_INFO) < 0: raise ValueError('Error unpacking VariantRecord') for i in range(r.n_info): info = &r.d.info[i] key = bcf_hdr_int2id(hdr, BCF_DT_ID, info.key) if info != NULL and info.vptr != NULL and strcmp(key, b'END') != 0: return True return False def __getitem__(self, key): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr if bcf_unpack(r, BCF_UN_INFO) < 0: raise ValueError('Error unpacking VariantRecord') cdef bytes bkey = force_bytes(key) if strcmp(bkey, b'END') == 0: raise KeyError('END is a reserved attribute; access is via record.stop') cdef bcf_info_t *info = bcf_get_info(hdr, r, bkey) # Cannot stop here if info == NULL, since flags must return False cdef int info_id = bcf_header_get_info_id(hdr, bkey) if not info else info.key if info_id < 0: raise KeyError('Unknown INFO field: {}'.format(key)) if not check_header_id(hdr, BCF_HL_INFO, info_id): raise ValueError('Invalid header') # Handle type=Flag values if bcf_hdr_id2type(hdr, BCF_HL_INFO, info_id) == BCF_HT_FLAG: return info != NULL and info.vptr != NULL if not info or not info.vptr: raise KeyError('Invalid INFO field: {}'.format(key)) return bcf_info_get_value(self.record, info) def __setitem__(self, key, value): cdef bytes bkey = force_bytes(key) if strcmp(bkey, b'END') == 0: raise KeyError('END is a reserved attribute; access is via record.stop') if bcf_unpack(self.record.ptr, BCF_UN_INFO) < 0: raise ValueError('Error unpacking VariantRecord') bcf_info_set_value(self.record, key, value) def __delitem__(self, key): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef bytes bkey = force_bytes(key) if strcmp(bkey, b'END') == 0: raise KeyError('END is a reserved attribute; access is via record.stop') if bcf_unpack(r, BCF_UN_INFO) < 0: raise ValueError('Error unpacking VariantRecord') cdef bcf_info_t *info = bcf_get_info(hdr, r, bkey) # Cannot stop here if info == NULL, since flags must return False cdef int info_id = bcf_header_get_info_id(hdr, bkey) if not info else info.key if info_id < 0: raise KeyError('Unknown INFO field: {}'.format(key)) if not check_header_id(hdr, BCF_HL_INFO, info_id): raise ValueError('Invalid header') # Handle flags if bcf_hdr_id2type(hdr, BCF_HL_INFO, info_id) == BCF_HT_FLAG and (not info or not info.vptr): return if not info or not info.vptr: raise KeyError('Unknown INFO field: {}'.format(key)) if bcf_update_info(hdr, r, bkey, NULL, 0, info.type) < 0: raise ValueError('Unable to delete INFO') def clear(self): """Clear all info data""" cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef bcf_info_t *info cdef const char *key cdef int i if bcf_unpack(r, BCF_UN_INFO) < 0: raise ValueError('Error unpacking VariantRecord') for i in range(r.n_info): info = &r.d.info[i] if info and info.vptr: key = bcf_hdr_int2id(hdr, BCF_DT_ID, info.key) if strcmp(key, b'END') == 0: continue if bcf_update_info(hdr, r, key, NULL, 0, info.type) < 0: raise ValueError('Unable to delete INFO') def __iter__(self): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef bcf_info_t *info cdef const char *key cdef int i if bcf_unpack(r, BCF_UN_INFO) < 0: raise ValueError('Error unpacking VariantRecord') for i in range(r.n_info): info = &r.d.info[i] if info and info.vptr: key = bcf_hdr_int2id(hdr, BCF_DT_ID, info.key) if strcmp(key, b'END') != 0: yield bcf_str_cache_get_charptr(key) def get(self, key, default=None): """D.get(k[,d]) -> D[k] if k in D, else d. d defaults to None.""" cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr if bcf_unpack(r, BCF_UN_INFO) < 0: raise ValueError('Error unpacking VariantRecord') cdef bytes bkey = force_bytes(key) if strcmp(bkey, b'END') == 0: return default cdef bcf_info_t *info = bcf_get_info(hdr, r, bkey) # Cannot stop here if info == NULL, since flags must return False cdef int info_id = bcf_header_get_info_id(hdr, bkey) if not info else info.key if not check_header_id(hdr, BCF_HL_INFO, info_id): raise ValueError('Invalid header') # Handle flags if bcf_hdr_id2type(hdr, BCF_HL_INFO, info_id) == BCF_HT_FLAG: return info != NULL and info.vptr != NULL if not info or not info.vptr: return default return bcf_info_get_value(self.record, info) def __contains__(self, key): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr if bcf_unpack(r, BCF_UN_INFO) < 0: raise ValueError('Error unpacking VariantRecord') cdef bytes bkey = force_bytes(key) if strcmp(bkey, b'END') == 0: return False cdef bcf_info_t *info = bcf_get_info(hdr, r, bkey) return info != NULL and info.vptr != NULL def iterkeys(self): """D.iterkeys() -> an iterator over the keys of D""" return iter(self) def itervalues(self): """D.itervalues() -> an iterator over the values of D""" cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef bcf_info_t *info cdef const char *key cdef int i if bcf_unpack(r, BCF_UN_INFO) < 0: raise ValueError('Error unpacking VariantRecord') for i in range(r.n_info): info = &r.d.info[i] if info and info.vptr: key = bcf_hdr_int2id(hdr, BCF_DT_ID, info.key) if strcmp(key, b'END') != 0: yield bcf_info_get_value(self.record, info) def iteritems(self): """D.iteritems() -> an iterator over the (key, value) items of D""" cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef bcf_info_t *info cdef const char *key cdef int i if bcf_unpack(r, BCF_UN_INFO) < 0: raise ValueError('Error unpacking VariantRecord') for i in range(r.n_info): info = &r.d.info[i] if info and info.vptr: key = bcf_hdr_int2id(hdr, BCF_DT_ID, info.key) if strcmp(key, b'END') != 0: value = bcf_info_get_value(self.record, info) yield bcf_str_cache_get_charptr(key), value def keys(self): """D.keys() -> list of D's keys""" return list(self) def items(self): """D.items() -> list of D's (key, value) pairs, as 2-tuples""" return list(self.iteritems()) def values(self): """D.values() -> list of D's values""" return list(self.itervalues()) def update(self, items=None, **kwargs): """D.update([E, ]**F) -> None. Update D from dict/iterable E and F. """ for k, v in items.items(): if k != 'END': self[k] = v if kwargs: kwargs.pop('END', None) for k, v in kwargs.items(): self[k] = v def pop(self, key, default=_nothing): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr if bcf_unpack(r, BCF_UN_INFO) < 0: raise ValueError('Error unpacking VariantRecord') cdef bytes bkey = force_bytes(key) cdef bcf_info_t *info = bcf_get_info(hdr, r, bkey) # Cannot stop here if info == NULL, since flags must return False cdef int info_id = bcf_header_get_info_id(hdr, bkey) if not info else info.key if info_id < 0: if default is _nothing: raise KeyError('Unknown INFO field: {}'.format(key)) return default if not check_header_id(hdr, BCF_HL_INFO, info_id): raise ValueError('Invalid header') # Handle flags if bcf_hdr_id2type(hdr, BCF_HL_INFO, info_id) == BCF_HT_FLAG and (not info or not info.vptr): return if not info or not info.vptr: if default is _nothing: raise KeyError('Unknown INFO field: {}'.format(key)) return default value = bcf_info_get_value(self.record, info) if bcf_update_info(hdr, r, bkey, NULL, 0, info.type) < 0: raise ValueError('Unable to delete INFO') return value def __richcmp__(VariantRecordInfo self not None, VariantRecordInfo other not None, int op): if op != 2 and op != 3: return NotImplemented cdef bcf1_t *s = self.record.ptr cdef bcf1_t *o = other.record.ptr # Cannot use n_info as shortcut logic, since null values may remain cdef bint cmp = dict(self) == dict(other) if op == 3: cmp = not cmp return cmp # Mappings are not hashable by default, but subclasses can change this __hash__ = None cdef VariantRecordInfo makeVariantRecordInfo(VariantRecord record): if not record: raise ValueError('invalid VariantRecord') cdef VariantRecordInfo info = VariantRecordInfo.__new__(VariantRecordInfo) info.record = record return info cdef class VariantRecordSamples(object): """mapping from sample index or name to :class:`VariantRecordSample` object.""" def __init__(self, *args, **kwargs): raise TypeError('this class cannot be instantiated from Python') def __len__(self): return self.record.ptr.n_sample # bcf_hdr_nsamples(self.record.header.ptr) def __bool__(self): return self.record.ptr.n_sample != 0 # bcf_hdr_nsamples(self.record.header.ptr) != 0 def __getitem__(self, key): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef int n = self.record.ptr.n_sample cdef int sample_index cdef vdict_t *d cdef khiter_t k if isinstance(key, int): sample_index = key else: bkey = force_bytes(key) sample_index = bcf_hdr_id2int(hdr, BCF_DT_SAMPLE, bkey) if sample_index < 0: raise KeyError('invalid sample name: {}'.format(key)) if sample_index < 0 or sample_index >= n: raise IndexError('invalid sample index') return makeVariantRecordSample(self.record, sample_index) def __iter__(self): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef int32_t i, n = self.record.ptr.n_sample for i in range(n): yield charptr_to_str(hdr.samples[i]) def get(self, key, default=None): """D.get(k[,d]) -> D[k] if k in D, else d. d defaults to None.""" try: return self[key] except KeyError: return default def __contains__(self, key): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef int n = self.record.ptr.n_sample cdef int sample_index cdef vdict_t *d cdef khiter_t k if isinstance(key, int): sample_index = key else: bkey = force_bytes(key) sample_index = bcf_hdr_id2int(hdr, BCF_DT_SAMPLE, bkey) if sample_index < 0: raise KeyError('invalid sample name: {}'.format(key)) return 0 <= sample_index < n def iterkeys(self): """D.iterkeys() -> an iterator over the keys of D""" return iter(self) def itervalues(self): """D.itervalues() -> an iterator over the values of D""" cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef int32_t i, n = self.record.ptr.n_sample for i in range(n): yield makeVariantRecordSample(self.record, i) def iteritems(self): """D.iteritems() -> an iterator over the (key, value) items of D""" cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef int32_t i, n = self.record.ptr.n_sample for i in range(n): yield (charptr_to_str(hdr.samples[i]), makeVariantRecordSample(self.record, i)) def keys(self): """D.keys() -> list of D's keys""" return list(self) def items(self): """D.items() -> list of D's (key, value) pairs, as 2-tuples""" return list(self.iteritems()) def values(self): """D.values() -> list of D's values""" return list(self.itervalues()) def update(self, items=None, **kwargs): """D.update([E, ]**F) -> None. Update D from dict/iterable E and F. """ for k, v in items.items(): self[k] = v if kwargs: for k, v in kwargs.items(): self[k] = v def pop(self, key, default=_nothing): try: value = self[key] del self[key] return value except KeyError: if default is not _nothing: return default raise def __richcmp__(VariantRecordSamples self not None, VariantRecordSamples other not None, int op): if op != 2 and op != 3: return NotImplemented cdef bcf1_t *s = self.record.ptr cdef bcf1_t *o = other.record.ptr cdef bint cmp = (s.n_sample == o.n_sample and self.values() == other.values()) if op == 3: cmp = not cmp return cmp # Mappings are not hashable by default, but subclasses can change this __hash__ = None cdef VariantRecordSamples makeVariantRecordSamples(VariantRecord record): if not record: raise ValueError('invalid VariantRecord') cdef VariantRecordSamples samples = VariantRecordSamples.__new__( VariantRecordSamples) samples.record = record return samples cdef class VariantRecord(object): """Variant record""" def __init__(self, *args, **kwargs): raise TypeError('this class cannot be instantiated from Python') def __dealloc__(self): if self.ptr: bcf_destroy1(self.ptr) self.ptr = NULL def copy(self): """return a copy of this VariantRecord object""" return makeVariantRecord(self.header, bcf_dup(self.ptr)) def translate(self, VariantHeader dst_header): if dst_header is None: raise ValueError('dst_header must not be None') cdef bcf_hdr_t *src_hdr = self.header.ptr cdef bcf_hdr_t *dst_hdr = dst_header.ptr if src_hdr != dst_hdr: if self.ptr.n_sample != bcf_hdr_nsamples(dst_hdr): msg = 'Cannot translate record. Number of samples does not match header ({} vs {})' raise ValueError(msg.format(self.ptr.n_sample, bcf_hdr_nsamples(dst_hdr))) bcf_translate(dst_hdr, src_hdr, self.ptr) self.header = dst_header @property def rid(self): """internal reference id number""" return self.ptr.rid @rid.setter def rid(self, value): cdef bcf_hdr_t *hdr = self.header.ptr cdef int r = value if r < 0 or r >= hdr.n[BCF_DT_CTG] or not hdr.id[BCF_DT_CTG][r].val: raise ValueError('invalid reference id') self.ptr.rid = r @property def chrom(self): """chromosome/contig name""" cdef bcf_hdr_t *hdr = self.header.ptr cdef int rid = self.ptr.rid if rid < 0 or rid >= hdr.n[BCF_DT_CTG]: raise ValueError('Invalid header') return bcf_str_cache_get_charptr(bcf_hdr_id2name(hdr, rid)) @chrom.setter def chrom(self, value): cdef vdict_t *d = self.header.ptr.dict[BCF_DT_CTG] bchrom = force_bytes(value) cdef khint_t k = kh_get_vdict(d, bchrom) if k == kh_end(d): raise ValueError('Invalid chromosome/contig') self.ptr.rid = kh_val_vdict(d, k).id @property def contig(self): """chromosome/contig name""" cdef bcf_hdr_t *hdr = self.header.ptr cdef int rid = self.ptr.rid if rid < 0 or rid >= hdr.n[BCF_DT_CTG]: raise ValueError('Invalid header') return bcf_str_cache_get_charptr(bcf_hdr_id2name(hdr, rid)) @contig.setter def contig(self, value): cdef vdict_t *d = self.header.ptr.dict[BCF_DT_CTG] bchrom = force_bytes(value) cdef khint_t k = kh_get_vdict(d, bchrom) if k == kh_end(d): raise ValueError('Invalid chromosome/contig') self.ptr.rid = kh_val_vdict(d, k).id @property def pos(self): """record start position on chrom/contig (1-based inclusive)""" return self.ptr.pos + 1 @pos.setter def pos(self, value): cdef int p = value if p < 1: raise ValueError('Position must be positive') self.ptr.pos = p - 1 bcf_sync_end(self) @property def start(self): """record start position on chrom/contig (0-based inclusive)""" return self.ptr.pos @start.setter def start(self, value): cdef int s = value if s < 0: raise ValueError('Start coordinate must be non-negative') self.ptr.pos = s bcf_sync_end(self) @property def stop(self): """record stop position on chrom/contig (0-based exclusive)""" return self.ptr.pos + self.ptr.rlen @stop.setter def stop(self, value): cdef int s = value if s < 0: raise ValueError('Stop coordinate must be non-negative') self.ptr.rlen = s - self.ptr.pos bcf_sync_end(self) @property def rlen(self): """record length on chrom/contig (aka rec.stop - rec.start)""" return self.ptr.rlen @rlen.setter def rlen(self, value): cdef int r = value self.ptr.rlen = r bcf_sync_end(self) @property def qual(self): """phred scaled quality score or None if not available""" return self.ptr.qual if not bcf_float_is_missing(self.ptr.qual) else None @qual.setter def qual(self, value): if value is not None: self.ptr.qual = value else: bcf_float_set(&self.ptr.qual, bcf_float_missing) # @property # def n_allele(self): # return self.ptr.n_allele # @property # def n_sample(self): # return self.ptr.n_sample @property def id(self): """record identifier or None if not available""" cdef bcf1_t *r = self.ptr if bcf_unpack(r, BCF_UN_STR) < 0: raise ValueError('Error unpacking VariantRecord') # causes a memory leak https://github.com/pysam-developers/pysam/issues/773 # return bcf_str_cache_get_charptr(r.d.id) if r.d.id != b'.' else None if (r.d.m_id == 0): raise ValueError('Error extracting ID') return charptr_to_str(r.d.id) if r.d.id != b'.' else None @id.setter def id(self, value): cdef bcf1_t *r = self.ptr if bcf_unpack(r, BCF_UN_STR) < 0: raise ValueError('Error unpacking VariantRecord') cdef char *idstr = NULL if value is not None: bid = force_bytes(value) idstr = bid if bcf_update_id(self.header.ptr, self.ptr, idstr) < 0: raise ValueError('Error updating id') @property def ref(self): """reference allele""" cdef bcf1_t *r = self.ptr if bcf_unpack(r, BCF_UN_STR) < 0: raise ValueError('Error unpacking VariantRecord') return charptr_to_str(r.d.allele[0]) if r.d.allele else None @ref.setter def ref(self, value): cdef bcf1_t *r = self.ptr if bcf_unpack(r, BCF_UN_STR) < 0: raise ValueError('Error unpacking VariantRecord') #FIXME: Set alleles directly -- this is stupid if not value: raise ValueError('ref allele must not be null') value = force_bytes(value) if r.d.allele and r.n_allele: alleles = [r.d.allele[i] for i in range(r.n_allele)] alleles[0] = value else: alleles = [value, ''] self.alleles = alleles bcf_sync_end(self) @property def alleles(self): """tuple of reference allele followed by alt alleles""" cdef bcf1_t *r = self.ptr if bcf_unpack(r, BCF_UN_STR) < 0: raise ValueError('Error unpacking VariantRecord') if not r.d.allele: return None cdef tuple res = PyTuple_New(r.n_allele) for i in range(r.n_allele): a = charptr_to_str(r.d.allele[i]) PyTuple_SET_ITEM(res, i, a) Py_INCREF(a) return res @alleles.setter def alleles(self, values): cdef bcf1_t *r = self.ptr # Cache rlen of symbolic alleles before call to bcf_update_alleles_str cdef int rlen = r.rlen if bcf_unpack(r, BCF_UN_STR) < 0: raise ValueError('Error unpacking VariantRecord') values = [force_bytes(v) for v in values] if len(values) < 2: raise ValueError('must set at least 2 alleles') if b'' in values: raise ValueError('cannot set null allele') value = b','.join(values) if bcf_update_alleles_str(self.header.ptr, r, value) < 0: raise ValueError('Error updating alleles') # Reset rlen if alternate allele isn't symbolic, otherwise used cached if has_symbolic_allele(self): self.ptr.rlen = rlen else: self.ptr.rlen = len(values[0]) r.d.var_type = -1 bcf_sync_end(self) @property def alts(self): """tuple of alt alleles""" cdef bcf1_t *r = self.ptr if bcf_unpack(r, BCF_UN_STR) < 0: raise ValueError('Error unpacking VariantRecord') if r.n_allele < 2 or not r.d.allele: return None cdef tuple res = PyTuple_New(r.n_allele - 1) for i in range(1, r.n_allele): a = charptr_to_str(r.d.allele[i]) PyTuple_SET_ITEM(res, i - 1, a) Py_INCREF(a) return res @alts.setter def alts(self, value): #FIXME: Set alleles directly -- this is stupid cdef bcf1_t *r = self.ptr if bcf_unpack(r, BCF_UN_STR) < 0: raise ValueError('Error unpacking VariantRecord') value = [force_bytes(v) for v in value] if b'' in value: raise ValueError('cannot set null alt allele') ref = [r.d.allele[0] if r.d.allele and r.n_allele else b'.'] self.alleles = ref + value r.d.var_type = -1 @property def filter(self): """filter information (see :class:`VariantRecordFilter`)""" if bcf_unpack(self.ptr, BCF_UN_FLT) < 0: raise ValueError('Error unpacking VariantRecord') return makeVariantRecordFilter(self) @property def info(self): """info data (see :class:`VariantRecordInfo`)""" if bcf_unpack(self.ptr, BCF_UN_INFO) < 0: raise ValueError('Error unpacking VariantRecord') return makeVariantRecordInfo(self) @property def format(self): """sample format metadata (see :class:`VariantRecordFormat`)""" if bcf_unpack(self.ptr, BCF_UN_FMT) < 0: raise ValueError('Error unpacking VariantRecord') return makeVariantRecordFormat(self) @property def samples(self): """sample data (see :class:`VariantRecordSamples`)""" if bcf_unpack(self.ptr, BCF_UN_ALL) < 0: raise ValueError('Error unpacking VariantRecord') return makeVariantRecordSamples(self) property alleles_variant_types: def __get__(self): cdef bcf1_t *r = self.ptr cdef tuple result = PyTuple_New(r.n_allele) for i in range(r.n_allele): tp = bcf_get_variant_type(r, i) if tp == VCF_REF: v_type = "REF" elif tp == VCF_SNP: v_type = "SNP" elif tp == VCF_MNP: v_type = "MNP" elif tp == VCF_INDEL: v_type = "INDEL" elif tp == VCF_BND: v_type = "BND" elif tp == VCF_OVERLAP: v_type = "OVERLAP" else: v_type = "OTHER" PyTuple_SET_ITEM(result, i, v_type) Py_INCREF(v_type) return result def __richcmp__(VariantRecord self not None, VariantRecord other not None, int op): if op != 2 and op != 3: return NotImplemented cdef bcf1_t *s = self.ptr cdef bcf1_t *o = other.ptr cdef bint cmp = self is other or ( s.pos == o.pos and s.rlen == o.rlen and ((bcf_float_is_missing(s.qual) and bcf_float_is_missing(o.qual)) or s.qual == o.qual) and s.n_sample == o.n_sample and s.n_allele == o.n_allele and self.contig == other.contig and self.alleles == other.alleles and self.id == other.id and self.info == other.info and self.filter == other.filter and self.samples == other.samples) if op == 3: cmp = not cmp return cmp def __str__(self): cdef kstring_t line cdef char c line.l = line.m = 0 line.s = NULL if vcf_format(self.header.ptr, self.ptr, &line) < 0: if line.m: free(line.s) raise ValueError('vcf_format failed') # Strip CR/LF? #while line.l: # c = line.s[line.l - 1] # if c != b'\n' and c != b'\r': # break # line.l -= 1 ret = charptr_to_str_w_len(line.s, line.l) if line.m: free(line.s) return ret cdef VariantRecord makeVariantRecord(VariantHeader header, bcf1_t *r): if not header: raise ValueError('invalid VariantHeader') if not r: raise ValueError('cannot create VariantRecord') if r.errcode: msg = [] #if r.errcode & BCF_ERR_CTG_UNDEF: # msg.append('undefined contig') #if r.errcode & BCF_ERR_TAG_UNDEF: # msg.append('undefined tag') if r.errcode & BCF_ERR_NCOLS: msg.append('invalid number of columns') if r.errcode & BCF_ERR_LIMITS: msg.append('limits violated') if r.errcode & BCF_ERR_CHAR: msg.append('invalid character found') if r.errcode & BCF_ERR_CTG_INVALID: msg.append('invalid contig') if r.errcode & BCF_ERR_TAG_INVALID: msg.append('invalid tag') if msg: msg = ', '.join(msg) raise ValueError('Error(s) reading record: {}'.format(msg)) cdef VariantRecord record = VariantRecord.__new__(VariantRecord) record.header = header record.ptr = r return record ######################################################################## ######################################################################## ## Variant Sampletype object ######################################################################## cdef class VariantRecordSample(object): """Data for a single sample from a :class:`VariantRecord` object. Provides data accessors for genotypes and a mapping interface from format name to values. """ def __init__(self, *args, **kwargs): raise TypeError('this class cannot be instantiated from Python') @property def name(self): """sample name""" cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef int32_t n = r.n_sample if self.index < 0 or self.index >= n: raise ValueError('invalid sample index') return charptr_to_str(hdr.samples[self.index]) @property def allele_indices(self): """allele indices for called genotype, if present. Otherwise None""" return bcf_format_get_allele_indices(self) @allele_indices.setter def allele_indices(self, value): self['GT'] = value @allele_indices.deleter def allele_indices(self): self['GT'] = () @property def alleles(self): """alleles for called genotype, if present. Otherwise None""" return bcf_format_get_alleles(self) @alleles.setter def alleles(self, value): # Sets the genotype, supply a tuple of alleles to set. # The supplied alleles need to be defined in the correspoding pysam.libcbcf.VariantRecord # The genotype is reset when an empty tuple, None or (None,) is supplied if value==(None,) or value==tuple() or value is None: self['GT'] = () return if any((type(x) == int for x in value)): raise ValueError('Use .allele_indices to set integer allele indices') # determine and set allele indices: try: self['GT'] = tuple( (self.record.alleles.index(allele) for allele in value) ) except ValueError: raise ValueError("One or more of the supplied sample alleles are not defined as alleles of the corresponding pysam.libcbcf.VariantRecord." "First set the .alleles of this record to define the alleles") @alleles.deleter def alleles(self): self['GT'] = () @property def phased(self): """False if genotype is missing or any allele is unphased. Otherwise True.""" return bcf_sample_get_phased(self) @phased.setter def phased(self, value): bcf_sample_set_phased(self, value) def __len__(self): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef int i, n = 0 if bcf_unpack(r, BCF_UN_FMT) < 0: raise ValueError('Error unpacking VariantRecord') for i in range(r.n_fmt): if r.d.fmt[i].p: n += 1 return n def __bool__(self): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef int i if bcf_unpack(r, BCF_UN_FMT) < 0: raise ValueError('Error unpacking VariantRecord') for i in range(r.n_fmt): if r.d.fmt[i].p: return True return False def __getitem__(self, key): return bcf_format_get_value(self, key) def __setitem__(self, key, value): bcf_format_set_value(self, key, value) def __delitem__(self, key): bcf_format_del_value(self, key) def clear(self): """Clear all format data (including genotype) for this sample""" cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef bcf_fmt_t *fmt cdef int i for i in range(r.n_fmt): fmt = &r.d.fmt[i] if fmt.p: bcf_format_del_value(self, bcf_hdr_int2id(hdr, BCF_DT_ID, fmt.id)) def __iter__(self): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef bcf_fmt_t *fmt cdef int i for i in range(r.n_fmt): fmt = &r.d.fmt[i] if r.d.fmt[i].p: yield bcf_str_cache_get_charptr(bcf_hdr_int2id(hdr, BCF_DT_ID, fmt.id)) def get(self, key, default=None): """D.get(k[,d]) -> D[k] if k in D, else d. d defaults to None.""" try: return self[key] except KeyError: return default def __contains__(self, key): cdef bcf_hdr_t *hdr = self.record.header.ptr cdef bcf1_t *r = self.record.ptr cdef bytes bkey = force_bytes(key) cdef bcf_fmt_t *fmt = bcf_get_fmt(hdr, r, bkey) return fmt != NULL and fmt.p != NULL def iterkeys(self): """D.iterkeys() -> an iterator over the keys of D""" return iter(self) def itervalues(self): """D.itervalues() -> an iterator over the values of D""" for key in self: yield self[key] def iteritems(self): """D.iteritems() -> an iterator over the (key, value) items of D""" for key in self: yield (key, self[key]) def keys(self): """D.keys() -> list of D's keys""" return list(self) def items(self): """D.items() -> list of D's (key, value) pairs, as 2-tuples""" return list(self.iteritems()) def values(self): """D.values() -> list of D's values""" return list(self.itervalues()) def update(self, items=None, **kwargs): """D.update([E, ]**F) -> None. Update D from dict/iterable E and F. """ for k, v in items.items(): self[k] = v if kwargs: for k, v in kwargs.items(): self[k] = v def pop(self, key, default=_nothing): try: value = self[key] del self[key] return value except KeyError: if default is not _nothing: return default raise def __richcmp__(VariantRecordSample self not None, VariantRecordSample other not None, int op): if op != 2 and op != 3: return NotImplemented cdef bint cmp = dict(self) == dict(other) if op == 3: cmp = not cmp return cmp # Mappings are not hashable by default, but subclasses can change this __hash__ = None cdef VariantRecordSample makeVariantRecordSample(VariantRecord record, int32_t sample_index): if not record or sample_index < 0: raise ValueError('cannot create VariantRecordSample') cdef VariantRecordSample sample = VariantRecordSample.__new__(VariantRecordSample) sample.record = record sample.index = sample_index return sample ######################################################################## ######################################################################## ## Index objects ######################################################################## cdef class BaseIndex(object): def __init__(self): self.refs = () self.remap = {} def __len__(self): return len(self.refs) def __bool__(self): return len(self.refs) != 0 def __getitem__(self, key): if isinstance(key, int): return self.refs[key] else: return self.refmap[key] def __iter__(self): return iter(self.refs) def get(self, key, default=None): """D.get(k[,d]) -> D[k] if k in D, else d. d defaults to None.""" try: return self[key] except KeyError: return default def __contains__(self, key): try: self[key] except KeyError: return False else: return True def iterkeys(self): """D.iterkeys() -> an iterator over the keys of D""" return iter(self) def itervalues(self): """D.itervalues() -> an iterator over the values of D""" for key in self: yield self[key] def iteritems(self): """D.iteritems() -> an iterator over the (key, value) items of D""" for key in self: yield (key, self[key]) def keys(self): """D.keys() -> list of D's keys""" return list(self) def items(self): """D.items() -> list of D's (key, value) pairs, as 2-tuples""" return list(self.iteritems()) def values(self): """D.values() -> list of D's values""" return list(self.itervalues()) def update(self, items=None, **kwargs): """D.update([E, ]**F) -> None. Update D from dict/iterable E and F. """ for k, v in items.items(): self[k] = v if kwargs: for k, v in kwargs.items(): self[k] = v def pop(self, key, default=_nothing): try: value = self[key] del self[key] return value except KeyError: if default is not _nothing: return default raise # Mappings are not hashable by default, but subclasses can change this __hash__ = None #TODO: implement __richcmp__ cdef class BCFIndex(object): """CSI index data structure for BCF files""" def __init__(self): self.refs = () self.refmap = {} if not self.ptr: raise ValueError('Invalid index object') cdef int n cdef const char **refs = bcf_index_seqnames(self.ptr, self.header.ptr, &n) self.refs = char_array_to_tuple(refs, n, free_after=1) if refs else () self.refmap = { r:i for i,r in enumerate(self.refs) } def __dealloc__(self): if self.ptr: hts_idx_destroy(self.ptr) self.ptr = NULL def fetch(self, bcf, contig, start, stop, reopen): return BCFIterator(bcf, contig, start, stop, reopen) cdef BCFIndex makeBCFIndex(VariantHeader header, hts_idx_t *idx): if not idx: return None if not header: raise ValueError('invalid VariantHeader') cdef BCFIndex index = BCFIndex.__new__(BCFIndex) index.header = header index.ptr = idx index.__init__() return index cdef class TabixIndex(BaseIndex): """Tabix index data structure for VCF files""" def __init__(self): self.refs = () self.refmap = {} if not self.ptr: raise ValueError('Invalid index object') cdef int n cdef const char **refs = tbx_seqnames(self.ptr, &n) self.refs = char_array_to_tuple(refs, n, free_after=1) if refs else () self.refmap = { r:i for i,r in enumerate(self.refs) } def __dealloc__(self): if self.ptr: tbx_destroy(self.ptr) self.ptr = NULL def fetch(self, bcf, contig, start, stop, reopen): return TabixIterator(bcf, contig, start, stop, reopen) cdef TabixIndex makeTabixIndex(tbx_t *idx): if not idx: return None cdef TabixIndex index = TabixIndex.__new__(TabixIndex) index.ptr = idx index.__init__() return index ######################################################################## ######################################################################## ## Iterators ######################################################################## cdef class BaseIterator(object): pass # Internal function to clean up after iteration stop or failure. # This would be a nested function if it weren't a cdef function. cdef void _stop_BCFIterator(BCFIterator self, bcf1_t *record): bcf_destroy1(record) # destroy iter so future calls to __next__ raise StopIteration bcf_itr_destroy(self.iter) self.iter = NULL cdef class BCFIterator(BaseIterator): def __init__(self, VariantFile bcf, contig=None, start=None, stop=None, reopen=True): if bcf is None: raise ValueError('bcf must not be None') if contig is None: raise ValueError('contig must be specified') if not isinstance(bcf.index, BCFIndex): raise ValueError('bcf index required') cdef BCFIndex index = bcf.index self.bcf = bcf self.index = index cdef int rid, cstart, cstop try: rid = index.refmap[contig] except KeyError: # A query for a non-existent contig yields an empty iterator, does not raise an error self.iter = NULL return if reopen: self.bcf = self.bcf.copy() cstart = start if start is not None else 0 cstop = stop if stop is not None else MAX_POS with nogil: self.iter = bcf_itr_queryi(index.ptr, rid, cstart, cstop) if not self.iter: if errno: raise IOError(errno, strerror(errno)) else: raise IOError('unable to fetch {}:{}-{}'.format(contig, start+1, stop)) def __dealloc__(self): if self.iter: bcf_itr_destroy(self.iter) self.iter = NULL def __iter__(self): return self def __next__(self): if not self.iter: raise StopIteration cdef bcf1_t *record = bcf_init1() if not record: raise MemoryError('unable to allocate BCF record') record.pos = -1 if self.bcf.drop_samples: record.max_unpack = BCF_UN_SHR cdef int ret with nogil: ret = bcf_itr_next(self.bcf.htsfile, self.iter, record) if ret < 0: _stop_BCFIterator(self, record) if ret == -1: raise StopIteration elif ret == -2: raise IOError('truncated file') elif errno: raise IOError(errno, strerror(errno)) else: raise IOError('unable to fetch next record') ret = bcf_subset_format(self.bcf.header.ptr, record) if ret < 0: _stop_BCFIterator(self, record) raise ValueError('error in bcf_subset_format') return makeVariantRecord(self.bcf.header, record) cdef class TabixIterator(BaseIterator): def __cinit__(self, *args, **kwargs): self.line_buffer.l = 0 self.line_buffer.m = 0 self.line_buffer.s = NULL def __init__(self, VariantFile bcf, contig=None, start=None, stop=None, reopen=True): if bcf is None: raise ValueError('bcf must not be None') if not isinstance(bcf.index, TabixIndex): raise ValueError('tabix index required') cdef TabixIndex index = bcf.index self.bcf = bcf self.index = index cdef int rid, cstart, cstop try: rid = index.refmap[contig] except KeyError: # A query for a non-existent contig yields an empty iterator, does not raise an error self.iter = NULL return if reopen: self.bcf = self.bcf.copy() cstart = start if start is not None else 0 cstop = stop if stop is not None else MAX_POS self.iter = tbx_itr_queryi(index.ptr, rid, start, stop) if not self.iter: if errno: raise IOError(errno, strerror(errno)) else: raise IOError('unable to fetch {}:{}-{}'.format(contig, start+1, stop)) def __dealloc__(self): if self.iter: tbx_itr_destroy(self.iter) self.iter = NULL if self.line_buffer.m: free(self.line_buffer.s) self.line_buffer.l = 0 self.line_buffer.m = 0 self.line_buffer.s = NULL def __iter__(self): return self def __next__(self): if not self.iter: raise StopIteration cdef int ret with nogil: ret = tbx_itr_next(self.bcf.htsfile, self.index.ptr, self.iter, &self.line_buffer) if ret < 0: tbx_itr_destroy(self.iter) self.iter = NULL if ret == -1: raise StopIteration elif ret == -2: raise IOError('truncated file') elif errno: raise IOError(errno, strerror(errno)) else: raise IOError('unable to fetch next record') cdef bcf1_t *record = bcf_init1() if not record: raise MemoryError('unable to allocate BCF record') record.pos = -1 if self.bcf.drop_samples: record.max_unpack = BCF_UN_SHR ret = vcf_parse1(&self.line_buffer, self.bcf.header.ptr, record) # FIXME: stop iteration on parse failure? if ret < 0: bcf_destroy1(record) raise ValueError('error in vcf_parse') return makeVariantRecord(self.bcf.header, record) ######################################################################## ######################################################################## ## Variant File ######################################################################## cdef class VariantFile(HTSFile): """*(filename, mode=None, index_filename=None, header=None, drop_samples=False, duplicate_filehandle=True, ignore_truncation=False, threads=1)* A :term:`VCF`/:term:`BCF` formatted file. The file is automatically opened. If an index for a variant file exists (.csi or .tbi), it will be opened automatically. Without an index random access to records via :meth:`fetch` is disabled. For writing, a :class:`VariantHeader` object must be provided, typically obtained from another :term:`VCF` file/:term:`BCF` file. Parameters ---------- mode : string *mode* should be ``r`` for reading or ``w`` for writing. The default is text mode (:term:`VCF`). For binary (:term:`BCF`) I/O you should append ``b`` for compressed or ``u`` for uncompressed :term:`BCF` output. If ``b`` is present, it must immediately follow ``r`` or ``w``. Valid modes are ``r``, ``w``, ``wh``, ``rb``, ``wb``, ``wbu`` and ``wb0``. For instance, to open a :term:`BCF` formatted file for reading, type:: f = pysam.VariantFile('ex1.bcf','r') If mode is not specified, we will try to auto-detect the file type. All of the following should work:: f1 = pysam.VariantFile('ex1.bcf') f2 = pysam.VariantFile('ex1.vcf') f3 = pysam.VariantFile('ex1.vcf.gz') index_filename : string Explicit path to an index file. header : VariantHeader :class:`VariantHeader` object required for writing. drop_samples: bool Ignore sample information when reading. duplicate_filehandle: bool By default, file handles passed either directly or through File-like objects will be duplicated before passing them to htslib. The duplication prevents issues where the same stream will be closed by htslib and through destruction of the high-level python object. Set to False to turn off duplication. ignore_truncation: bool Issue a warning, instead of raising an error if the current file appears to be truncated due to a missing EOF marker. Only applies to bgzipped formats. (Default=False) threads: integer Number of threads to use for compressing/decompressing VCF/BCF files. Setting threads to > 1 cannot be combined with `ignore_truncation`. (Default=1) """ def __cinit__(self, *args, **kwargs): self.htsfile = NULL def __init__(self, *args, **kwargs): self.header = None self.index = None self.filename = None self.mode = None self.threads = 1 self.index_filename = None self.is_stream = False self.is_remote = False self.is_reading = False self.drop_samples = False self.header_written = False self.start_offset = -1 self.open(*args, **kwargs) def __dealloc__(self): if not self.htsfile or not self.header: return # Write header if no records were written if self.htsfile.is_write and not self.header_written: with nogil: bcf_hdr_write(self.htsfile, self.header.ptr) cdef int ret = hts_close(self.htsfile) self.htsfile = NULL self.header = self.index = None if ret < 0: global errno if errno == EPIPE: errno = 0 else: raise IOError(errno, force_str(strerror(errno))) def close(self): """closes the :class:`pysam.VariantFile`.""" if not self.htsfile: return # Write header if no records were written if self.htsfile.is_write and not self.header_written: with nogil: bcf_hdr_write(self.htsfile, self.header.ptr) cdef int ret = hts_close(self.htsfile) self.htsfile = NULL self.header = self.index = None if ret < 0: global errno if errno == EPIPE: errno = 0 else: raise IOError(errno, force_str(strerror(errno))) def __iter__(self): if not self.is_open: raise ValueError('I/O operation on closed file') if self.htsfile.is_write: raise ValueError('cannot iterate over Variantfile opened for writing') self.is_reading = 1 return self def __next__(self): cdef int ret cdef int errcode cdef bcf1_t *record = bcf_init1() if not record: raise MemoryError('unable to allocate BCF record') record.pos = -1 if self.drop_samples: record.max_unpack = BCF_UN_SHR with nogil: ret = bcf_read1(self.htsfile, self.header.ptr, record) if ret < 0: errcode = record.errcode bcf_destroy1(record) if errcode: raise IOError('unable to parse next record') if ret == -1: raise StopIteration elif ret == -2: raise IOError('truncated file') elif errno: raise IOError(errno, strerror(errno)) else: raise IOError('unable to fetch next record') return makeVariantRecord(self.header, record) def copy(self): if not self.is_open: raise ValueError cdef VariantFile vars = VariantFile.__new__(VariantFile) cdef bcf_hdr_t *hdr # FIXME: re-open using fd or else header and index could be invalid vars.htsfile = self._open_htsfile() if not vars.htsfile: raise ValueError('Cannot re-open htsfile') # minimize overhead by re-using header and index. This approach is # currently risky, but see above for how this can be mitigated. vars.header = self.header vars.index = self.index vars.filename = self.filename vars.mode = self.mode vars.threads = self.threads vars.index_filename = self.index_filename vars.drop_samples = self.drop_samples vars.is_stream = self.is_stream vars.is_remote = self.is_remote vars.is_reading = self.is_reading vars.start_offset = self.start_offset vars.header_written = self.header_written if self.htsfile.is_bin: vars.seek(self.tell()) else: with nogil: hdr = bcf_hdr_read(vars.htsfile) makeVariantHeader(hdr) return vars def open(self, filename, mode='r', index_filename=None, VariantHeader header=None, drop_samples=False, duplicate_filehandle=True, ignore_truncation=False, threads=1): """open a vcf/bcf file. If open is called on an existing VariantFile, the current file will be closed and a new file will be opened. """ cdef bcf_hdr_t *hdr cdef BGZF *bgzfp cdef hts_idx_t *idx cdef tbx_t *tidx cdef char *cfilename cdef char *cindex_filename = NULL cdef char *cmode if threads > 1 and ignore_truncation: # This won't raise errors if reaching a truncated alignment, # because bgzf_mt_reader in htslib does not deal with # bgzf_mt_read_block returning non-zero values, contrary # to bgzf_read (https://github.com/samtools/htslib/blob/1.7/bgzf.c#L888) # Better to avoid this (for now) than to produce seemingly correct results. raise ValueError('Cannot add extra threads when "ignore_truncation" is True') self.threads = threads # close a previously opened file if self.is_open: self.close() if not mode or mode[0] not in 'rwa': raise ValueError('mode must begin with r, w or a') self.duplicate_filehandle = duplicate_filehandle format_modes = [m for m in mode[1:] if m in 'bcguz'] if len(format_modes) > 1: raise ValueError('mode contains conflicting format specifiers: {}'.format(''.join(format_modes))) invalid_modes = [m for m in mode[1:] if m not in 'bcguz0123456789ex'] if invalid_modes: raise ValueError('invalid mode options: {}'.format(''.join(invalid_modes))) # Autodetect mode from filename if mode == 'w' and isinstance(filename, str): if filename.endswith('.gz'): mode = 'wz' elif filename.endswith('.bcf'): mode = 'wb' # for htslib, wbu seems to not work if mode == 'wbu': mode = 'wb0' self.mode = mode = force_bytes(mode) try: filename = encode_filename(filename) self.is_remote = hisremote(filename) self.is_stream = filename == b'-' except TypeError: filename = filename self.is_remote = False self.is_stream = True self.filename = filename if index_filename is not None: self.index_filename = index_filename = encode_filename(index_filename) else: self.index_filename = None self.drop_samples = bool(drop_samples) self.header = None self.header_written = False if mode.startswith(b'w'): # open file for writing if index_filename is not None: raise ValueError('Cannot specify an index filename when writing a VCF/BCF file') # header structure (used for writing) if header: self.header = header.copy() else: self.header = VariantHeader() #raise ValueError('a VariantHeader must be specified') # Header is not written until the first write or on close self.htsfile = self._open_htsfile() if not self.htsfile: raise ValueError("could not open file `{}` (mode='{}')".format(filename, mode)) elif mode.startswith(b'r'): # open file for reading self.htsfile = self._open_htsfile() if not self.htsfile: if errno: raise IOError(errno, 'could not open variant file `{}`: {}'.format(filename, force_str(strerror(errno)))) else: raise ValueError('could not open variant file `{}`'.format(filename)) if self.htsfile.format.format not in (bcf, vcf): raise ValueError('invalid file `{}` (mode=`{}`) - is it VCF/BCF format?'.format(filename, mode)) self.check_truncation(ignore_truncation) with nogil: hdr = bcf_hdr_read(self.htsfile) try: self.header = makeVariantHeader(hdr) except ValueError: raise ValueError('file `{}` does not have valid header (mode=`{}`) - is it VCF/BCF format?'.format(filename, mode)) if isinstance(self.filename, bytes): cfilename = self.filename else: cfilename = NULL # check for index and open if present if self.htsfile.format.format == bcf and cfilename: if index_filename is not None: cindex_filename = index_filename with nogil: idx = bcf_index_load2(cfilename, cindex_filename) self.index = makeBCFIndex(self.header, idx) elif self.htsfile.format.compression == bgzf and cfilename: if index_filename is not None: cindex_filename = index_filename with nogil: tidx = tbx_index_load2(cfilename, cindex_filename) self.index = makeTabixIndex(tidx) if not self.is_stream: self.start_offset = self.tell() else: raise ValueError('unknown mode {}'.format(mode)) def reset(self): """reset file position to beginning of file just after the header.""" return self.seek(self.start_offset) def is_valid_tid(self, tid): """ return True if the numerical :term:`tid` is valid; False otherwise. returns -1 if reference is not known. """ if not self.is_open: raise ValueError('I/O operation on closed file') cdef bcf_hdr_t *hdr = self.header.ptr cdef int rid = tid return 0 <= rid < hdr.n[BCF_DT_CTG] def get_tid(self, reference): """ return the numerical :term:`tid` corresponding to :term:`reference` returns -1 if reference is not known. """ if not self.is_open: raise ValueError('I/O operation on closed file') cdef vdict_t *d = self.header.ptr.dict[BCF_DT_CTG] reference = force_bytes(reference) cdef khint_t k = kh_get_vdict(d, reference) return kh_val_vdict(d, k).id if k != kh_end(d) else -1 def get_reference_name(self, tid): """ return :term:`reference` name corresponding to numerical :term:`tid` """ if not self.is_open: raise ValueError('I/O operation on closed file') cdef bcf_hdr_t *hdr = self.header.ptr cdef int rid = tid if rid < 0 or rid >= hdr.n[BCF_DT_CTG]: raise ValueError('Invalid tid') return bcf_str_cache_get_charptr(bcf_hdr_id2name(hdr, rid)) def fetch(self, contig=None, start=None, stop=None, region=None, reopen=False, end=None, reference=None): """fetch records in a :term:`region`, specified either by :term:`contig`, *start*, and *end* (which are 0-based, half-open); or alternatively by a samtools :term:`region` string (which is 1-based inclusive). Without *contig* or *region* all mapped records will be fetched. The records will be returned ordered by contig, which will not necessarily be the order within the file. Set *reopen* to true if you will be using multiple iterators on the same file at the same time. The iterator returned will receive its own copy of a filehandle to the file effectively re-opening the file. Re-opening a file incurrs some overhead, so use with care. If only *contig* is set, all records on *contig* will be fetched. If both *region* and *contig* are given, an exception is raised. Note that a bgzipped :term:`VCF`.gz file without a tabix/CSI index (.tbi/.csi) or a :term:`BCF` file without a CSI index can only be read sequentially. """ if not self.is_open: raise ValueError('I/O operation on closed file') if self.htsfile.is_write: raise ValueError('cannot fetch from Variantfile opened for writing') if contig is None and region is None: self.is_reading = 1 bcf = self.copy() if reopen else self bcf.seek(self.start_offset) return iter(bcf) if self.index is None: raise ValueError('fetch requires an index') _, tid, start, stop = self.parse_region(contig, start, stop, region, None, end=end, reference=reference) if contig is None: contig = self.get_reference_name(tid) self.is_reading = 1 return self.index.fetch(self, contig, start, stop, reopen) def new_record(self, *args, **kwargs): """Create a new empty :class:`VariantRecord`. See :meth:`VariantHeader.new_record` """ return self.header.new_record(*args, **kwargs) cpdef int write(self, VariantRecord record) except -1: """ write a single :class:`pysam.VariantRecord` to disk. returns the number of bytes written. """ if record is None: raise ValueError('record must not be None') if not self.is_open: return ValueError('I/O operation on closed file') if not self.htsfile.is_write: raise ValueError('cannot write to a Variantfile opened for reading') if not self.header_written: self.header_written = True with nogil: bcf_hdr_write(self.htsfile, self.header.ptr) #if record.header is not self.header: # record.translate(self.header) # raise ValueError('Writing records from a different VariantFile is not yet supported') if record.ptr.n_sample != bcf_hdr_nsamples(self.header.ptr): msg = 'Invalid VariantRecord. Number of samples does not match header ({} vs {})' raise ValueError(msg.format(record.ptr.n_sample, bcf_hdr_nsamples(self.header.ptr))) # Sync END annotation before writing bcf_sync_end(record) cdef int ret with nogil: ret = bcf_write1(self.htsfile, self.header.ptr, record.ptr) if ret < 0: raise IOError(errno, strerror(errno)) return ret def subset_samples(self, include_samples): """ Read only a subset of samples to reduce processing time and memory. Must be called prior to retrieving records. """ if not self.is_open: raise ValueError('I/O operation on closed file') if self.htsfile.is_write: raise ValueError('cannot subset samples from Variantfile opened for writing') if self.is_reading: raise ValueError('cannot subset samples after fetching records') self.header._subset_samples(include_samples) # potentially unnecessary optimization that also sets max_unpack if not include_samples: self.drop_samples = True pysam-0.23.0/pysam/libcbcftools.pxd000066400000000000000000000004551475062545500172610ustar00rootroot00000000000000# cython: language_level=3 cdef extern from "bcftools.pysam.h": int bcftools_dispatch(int argc, char *argv[]) void bcftools_set_stderr(int fd) void bcftools_close_stderr() void bcftools_set_stdout(int fd) void bcftools_set_stdout_fn(const char *) void bcftools_close_stdout() pysam-0.23.0/pysam/libcbcftools.pyi000066400000000000000000000000371475062545500172630ustar00rootroot00000000000000def py_bcftools() -> None: ... pysam-0.23.0/pysam/libcbcftools.pyx000066400000000000000000000000341475062545500172770ustar00rootroot00000000000000def py_bcftools(): pass pysam-0.23.0/pysam/libcbgzf.pxd000066400000000000000000000002251475062545500163710ustar00rootroot00000000000000# cython: language_level=3 from pysam.libchtslib cimport BGZF cdef class BGZFile(object): cdef BGZF *bgzf cdef readonly object name, index pysam-0.23.0/pysam/libcbgzf.pyi000066400000000000000000000023161475062545500164020ustar00rootroot00000000000000import sys from typing import Optional, Union, Any, NoReturn if sys.version_info < (3, 8): from typing_extensions import Literal else: from typing import Literal BUFFER_SIZE: int class BGZFile: def __init__( self, filename: str, mode: Optional[Literal["r", "rb", "a", "ab", "w", "wb", "x", "xb"]], index: Optional[str], ) -> None: ... @property def name(self) -> str: ... @property def index(self) -> Optional[str]: ... def write(self, data: Union[bytes, bytearray, memoryview]) -> int: ... def read(self, size: int = ...) -> bytes: ... @property def closed(self) -> bool: ... def close(self) -> None: ... def __enter__(self) -> BGZFile: ... def __exit__(self, type, value, traceback) -> Any: ... def flush(self) -> None: ... def fileno(self) -> NoReturn: ... def rewind(self) -> None: ... def readable(self) -> bool: ... def writable(self) -> bool: ... def seekable(self) -> bool: ... def tell(self) -> int: ... def seek(self, offset: int, whence: int = ...) -> int: ... def readline(self, size: int = ...) -> bytes: ... def __iter__(self) -> BGZFile: ... def __next__(self) -> bytes: ... pysam-0.23.0/pysam/libcbgzf.pyx000066400000000000000000000164151475062545500164260ustar00rootroot00000000000000# cython: language_level=3 """Functions that read and write block gzipped files. The user of the file doesn't have to worry about the compression and random access is allowed if an index file is present.""" # based on Python 3.5's gzip module import io from libc.stdint cimport int8_t, int16_t, int32_t, int64_t from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t from libc.stdio cimport SEEK_SET from libc.stdlib cimport malloc, calloc, realloc, free from cpython.object cimport PyObject from cpython.bytes cimport PyBytes_FromStringAndSize, _PyBytes_Resize from pysam.libcutils cimport force_bytes, encode_filename from pysam.libchtslib cimport bgzf_open, bgzf_index_build_init, bgzf_write, bgzf_read, \ bgzf_flush, bgzf_index_dump, bgzf_close, bgzf_seek, \ bgzf_tell, bgzf_getline, kstring_t, BGZF __all__ = ["BGZFile"] BUFFER_SIZE = io.DEFAULT_BUFFER_SIZE cdef class BGZFile(object): """The BGZFile class simulates most of the methods of a file object with the exception of the truncate() method. This class only supports opening files in binary mode. If you need to open a compressed file in text mode, use the gzip.open() function. """ def __init__(self, filename, mode=None, index=None): """Constructor for the BGZFile class. The mode argument can be any of 'r', 'rb', 'a', 'ab', 'w', 'wb', 'x', or 'xb' depending on whether the file will be read or written. The default is the mode of fileobj if discernible; otherwise, the default is 'rb'. A mode of 'r' is equivalent to one of 'rb', and similarly for 'w' and 'wb', 'a' and 'ab', and 'x' and 'xb'. """ if mode and ('t' in mode or 'U' in mode): raise ValueError("Invalid mode: {!r}".format(mode)) if not mode: mode = 'rb' elif mode and 'b' not in mode: mode += 'b' mode = force_bytes(mode) self.name = encode_filename(filename) self.index = encode_filename(index) if index is not None else None self.bgzf = bgzf_open(self.name, mode) if self.bgzf.is_write and index is not None and bgzf_index_build_init(self.bgzf) < 0: raise IOError('Error building bgzf index') def __dealloc__(self): self.close() def write(self, data): if not self.bgzf: raise ValueError("write() on closed BGZFile object") if not self.bgzf.is_write: import errno raise IOError(errno.EBADF, "write() on read-only BGZFile object") if isinstance(data, bytes): length = len(data) else: # accept any data that supports the buffer protocol data = memoryview(data) length = data.nbytes if length > 0 and bgzf_write(self.bgzf, data, length) < 0: raise IOError('BGZFile write failed') return length def read(self, size=-1): cdef ssize_t read_size if not self.bgzf: raise ValueError("read() on closed BGZFile object") if self.bgzf.is_write: import errno raise IOError(errno.EBADF, "read() on write-only BGZFile object") if size < 0: chunks = [] while 1: chunk = PyBytes_FromStringAndSize(NULL, BUFFER_SIZE) cdata = chunk read_size = bgzf_read(self.bgzf, chunk, BUFFER_SIZE) if read_size < 0: raise IOError('Error reading from BGZFile') elif not read_size: break elif read_size < BUFFER_SIZE: chunk = chunk[:read_size] chunks.append(chunk) return b''.join(chunks) elif size > 0: chunk = PyBytes_FromStringAndSize(NULL, size) read_size = bgzf_read(self.bgzf, chunk, size) if read_size < 0: raise IOError('Error reading from BGZFile') elif read_size < size: chunk = chunk[:read_size] return chunk else: return b'' @property def closed(self): return self.bgzf == NULL def close(self): if not self.bgzf: return if self.bgzf.is_write and bgzf_flush(self.bgzf) < 0: raise IOError('Error flushing BGZFile object') if self.index and bgzf_index_dump(self.bgzf, self.index, NULL) < 0: raise IOError('Cannot write index') cdef ret = bgzf_close(self.bgzf) self.bgzf = NULL if ret < 0: raise IOError('Error closing BGZFile object') def __enter__(self): return self def __exit__(self, type, value, tb): self.close() def flush(self): if not self.bgzf: return if self.bgzf.is_write and bgzf_flush(self.bgzf) < 0: raise IOError('Error flushing BGZFile object') def fileno(self): """Invoke the underlying file object's fileno() method. This will raise AttributeError if the underlying file object doesn't support fileno(). """ raise AttributeError('fileno') def rewind(self): '''Return the uncompressed stream file position indicator to the beginning of the file''' if not self.bgzf: raise ValueError("rewind() on closed BGZFile object") if not self.bgzf.is_write: raise IOError("Can't rewind in write mode") if bgzf_seek(self.bgzf, 0, SEEK_SET) < 0: raise IOError('Error seeking BGZFFile object') def readable(self): if not self.bgzf: raise ValueError("readable() on closed BGZFile object") return self.bgzf != NULL and not self.bgzf.is_write def writable(self): return self.bgzf != NULL and self.bgzf.is_write def seekable(self): return True def tell(self): if not self.bgzf: raise ValueError("seek() on closed BGZFile object") cdef int64_t off = bgzf_tell(self.bgzf) if off < 0: raise IOError('Error in tell on BGZFFile object') return off def seek(self, offset, whence=io.SEEK_SET): if not self.bgzf: raise ValueError("seek() on closed BGZFile object") if whence is not io.SEEK_SET: raise ValueError('Seek from end not supported') cdef int64_t off = bgzf_seek(self.bgzf, offset, SEEK_SET) if off < 0: raise IOError('Error seeking BGZFFile object') return off def readline(self, size=-1): if not self.bgzf: raise ValueError("readline() on closed BGZFile object") cdef kstring_t line cdef char c line.l = line.m = 0 line.s = NULL cdef int ret = bgzf_getline(self.bgzf, b'\n', &line) if ret == -1: s = b'' elif ret == -2: if line.m: free(line.s) raise IOError('Error reading line in BGZFFile object') else: s = line.s[:line.l] if line.m: free(line.s) return s def __iter__(self): return self def __next__(self): line = self.readline() if not line: raise StopIteration() return line pysam-0.23.0/pysam/libcfaidx.pxd000066400000000000000000000042451475062545500165420ustar00rootroot00000000000000# cython: language_level=3 from libc.stdint cimport int8_t, int16_t, int32_t, int64_t from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t from libc.stdlib cimport malloc, calloc, realloc, free from libc.string cimport memcpy, memcmp, strncpy, strlen, strdup from libc.stdio cimport FILE, printf cimport cython from cpython cimport array from pysam.libchtslib cimport faidx_t, kstring_t, BGZF # These functions are put here and not in chtslib.pxd in order # to avoid warnings for unused functions. cdef extern from "pysam_stream.h" nogil: ctypedef struct kstream_t: pass ctypedef struct kseq_t: kstring_t name kstring_t comment kstring_t seq kstring_t qual kseq_t *kseq_init(BGZF *) int kseq_read(kseq_t *) void kseq_destroy(kseq_t *) kstream_t *ks_init(BGZF *) void ks_destroy(kstream_t *) # Retrieve characters from stream until delimiter # is reached placing results in str. int ks_getuntil(kstream_t *, int delimiter, kstring_t * str, int * dret) cdef class FastaFile: cdef bint is_remote cdef object _filename, _references, _lengths, reference2length cdef faidx_t* fastafile cdef char* _fetch(self, char* reference, int start, int end, int* length) except? NULL cdef class FastqProxy: cdef kseq_t * _delegate cdef cython.str to_string(self) cdef cython.str tostring(self) cpdef array.array get_quality_array(self, int offset=*) cdef class FastxRecord: """ Python container for pysam.libcfaidx.FastqProxy with persistence. """ cdef public str comment, quality, sequence, name cdef cython.str to_string(self) cdef cython.str tostring(self) cpdef array.array get_quality_array(self, int offset=*) cdef class FastxFile: cdef object _filename cdef BGZF * fastqfile cdef kseq_t * entry cdef bint persist cdef bint is_remote cdef kseq_t * getCurrent(self) cdef int cnext(self) # Compatibility Layer for pysam 0.8.1 cdef class FastqFile(FastxFile): pass # Compatibility Layer for pysam < 0.8 cdef class Fastafile(FastaFile): pass pysam-0.23.0/pysam/libcfaidx.pyi000066400000000000000000000050241475062545500165440ustar00rootroot00000000000000import array from typing import Optional, Any, Sequence, Iterator class FastaFile: def __init__( self, filename: str, filepath_index: Optional[str] = ..., filepath_index_compressed: Optional[str] = ..., ) -> None: ... def is_open(self) -> bool: ... def __len__(self) -> int: ... def close(self) -> None: ... def __enter__(self) -> FastaFile: ... def __exit__(self, type, value, traceback) -> Any: ... @property def closed(self) -> bool: ... @property def filename(self) -> str: ... @property def references(self) -> Sequence[str]: ... @property def nreferences(self) -> Optional[int]: ... @property def lengths(self) -> Sequence[int]: ... def fetch( self, reference: Optional[str] = ..., start: Optional[int] = ..., end: Optional[int] = ..., region: Optional[str] = ..., ) -> str: ... def get_reference_length(self, reference: str) -> int: ... def __getitem__(self, reference: str) -> str: ... def __contains__(self, reference: str) -> bool: ... class FastqProxy: @property def name(self) -> str: ... @property def sequence(self) -> str: ... @property def comment(self) -> Optional[str]: ... @property def quality(self) -> Optional[str]: ... def to_string(self) -> str: ... def get_quality_array(self, offset: int = ...) -> Optional[array.array]: ... class FastxRecord: comment: Optional[str] = ... quality: Optional[str] = ... sequence: Optional[str] = ... name: Optional[str] = ... def __init__( self, name: Optional[str] = ..., comment: Optional[str] = ..., sequence: Optional[str] = ..., quality: Optional[str] = ..., ) -> None: ... def set_name(self, name: str) -> None: ... def set_comment(self, comment: str) -> None: ... def set_sequence(self, sequence: str, quality: Optional[str] = ...) -> None: ... def get_quality_array(self, offset: int = ...) -> array.array: ... class FastxFile: def __init__(self, filename: str, persist: bool = ...) -> None: ... def is_open(self) -> bool: ... def close(self) -> None: ... def __enter__(self) -> FastxFile: ... def __exit__(self, type, value, traceback) -> Any: ... @property def closed(self) -> bool: ... @property def filename(self) -> str: ... def __iter__(self) -> Iterator[FastxRecord]: ... def __next__(self) -> FastxRecord: ... # deprecated class FastqFile(FastxFile): ... pysam-0.23.0/pysam/libcfaidx.pyx000066400000000000000000000512541475062545500165710ustar00rootroot00000000000000# cython: embedsignature=True # cython: profile=True ############################################################################### ############################################################################### # Cython wrapper for SAM/BAM/CRAM files based on htslib ############################################################################### # The principal classes defined in this module are: # # class FastaFile random read read/write access to faidx indexd files # class FastxFile streamed read/write access to fasta/fastq files # # Additionally this module defines several additional classes that are part # of the internal API. These are: # # class FastqProxy # class FastxRecord # # For backwards compatibility, the following classes are also defined: # # class Fastafile equivalent to FastaFile # class FastqFile equivalent to FastxFile # ############################################################################### # # The MIT License # # Copyright (c) 2015 Andreas Heger # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. # ############################################################################### import sys import os import re from libc.errno cimport errno from libc.string cimport strerror from cpython cimport array from cpython cimport PyErr_SetString, \ PyBytes_Check, \ PyUnicode_Check, \ PyBytes_FromStringAndSize from pysam.libchtslib cimport \ faidx_nseq, fai_load, fai_load3, fai_destroy, fai_fetch, \ faidx_seq_len, faidx_iseq, faidx_seq_len, \ faidx_fetch_seq, hisremote, \ bgzf_open, bgzf_close from pysam.libcutils cimport force_bytes, force_str, charptr_to_str from pysam.libcutils cimport encode_filename, from_string_and_size from pysam.libcutils cimport qualitystring_to_array, parse_region cdef class FastqProxy cdef makeFastqProxy(kseq_t * src): '''enter src into AlignedRead.''' cdef FastqProxy dest = FastqProxy.__new__(FastqProxy) dest._delegate = src return dest ## TODO: ## add automatic indexing. ## add function to get sequence names. cdef class FastaFile: """Random access to fasta formatted files that have been indexed by :term:`faidx`. The file is automatically opened. The index file of file ```` is expected to be called ``.fai``. Parameters ---------- filename : string Filename of fasta file to be opened. filepath_index : string Optional, filename of the index. By default this is the filename + ".fai". filepath_index_compressed : string Optional, filename of the index if fasta file is. By default this is the filename + ".gzi". Raises ------ ValueError if index file is missing IOError if file could not be opened """ def __cinit__(self, *args, **kwargs): self.fastafile = NULL self._filename = None self._references = None self._lengths = None self.reference2length = None self._open(*args, **kwargs) def is_open(self): '''return true if samfile has been opened.''' return self.fastafile != NULL def __len__(self): if self.fastafile == NULL: raise ValueError("calling len() on closed file") return faidx_nseq(self.fastafile) def _open(self, filename, filepath_index=None, filepath_index_compressed=None): '''open an indexed fasta file. This method expects an indexed fasta file. ''' # close a previously opened file if self.fastafile != NULL: self.close() self._filename = encode_filename(filename) cdef char *cfilename = self._filename cdef char *cindexname = NULL cdef char *cindexname_compressed = NULL self.is_remote = hisremote(cfilename) # open file for reading if (self._filename != b"-" and not self.is_remote and not os.path.exists(filename)): raise IOError("file `%s` not found" % filename) # 3 modes to open: # compressed fa: fai_load3 with filename, index_fai and index_gzi # uncompressed fa: fai_load3 with filename and index_fai # uncompressed fa: fai_load with default index name if filepath_index: # when opening, set flags to 0 - do not automatically # build index if it does not exist. if not os.path.exists(filepath_index): raise IOError("filename {} does not exist".format(filepath_index)) cindexname = bindex_filename = encode_filename(filepath_index) if filepath_index_compressed: if not os.path.exists(filepath_index_compressed): raise IOError("filename {} does not exist".format(filepath_index_compressed)) cindexname_compressed = bindex_filename_compressed = encode_filename(filepath_index_compressed) with nogil: self.fastafile = fai_load3(cfilename, cindexname, cindexname_compressed, 0) else: with nogil: self.fastafile = fai_load3(cfilename, cindexname, NULL, 0) else: with nogil: self.fastafile = fai_load(cfilename) if self.fastafile == NULL: raise IOError("error when opening file `%s`" % filename) cdef int nreferences = faidx_nseq(self.fastafile) cdef int x cdef const char * s self._references = [] self._lengths = [] for x from 0 <= x < nreferences: s = faidx_iseq(self.fastafile, x) ss = force_str(s) self._references.append(ss) self._lengths.append(faidx_seq_len(self.fastafile, s)) self.reference2length = dict(zip(self._references, self._lengths)) def close(self): """close the file.""" if self.fastafile != NULL: fai_destroy(self.fastafile) self.fastafile = NULL def __dealloc__(self): if self.fastafile != NULL: fai_destroy(self.fastafile) self.fastafile = NULL # context manager interface def __enter__(self): return self def __exit__(self, exc_type, exc_value, traceback): self.close() return False property closed: """bool indicating the current state of the file object. This is a read-only attribute; the close() method changes the value. """ def __get__(self): return not self.is_open() property filename: """filename associated with this object. This is a read-only attribute.""" def __get__(self): return self._filename property references: '''tuple with the names of :term:`reference` sequences.''' def __get__(self): return self._references property nreferences: """int with the number of :term:`reference` sequences in the file. This is a read-only attribute.""" def __get__(self): return len(self._references) if self.references else None property lengths: """tuple with the lengths of :term:`reference` sequences.""" def __get__(self): return self._lengths def fetch(self, reference=None, start=None, end=None, region=None): """fetch sequences in a :term:`region`. A region can either be specified by :term:`reference`, `start` and `end`. `start` and `end` denote 0-based, half-open intervals. Alternatively, a samtools :term:`region` string can be supplied. If any of the coordinates are missing they will be replaced by the minimum (`start`) or maximum (`end`) coordinate. Note that region strings are 1-based, while `start` and `end` denote an interval in python coordinates. The region is specified by :term:`reference`, `start` and `end`. Returns ------- string : a string with the sequence specified by the region. Raises ------ IndexError if the coordinates are out of range ValueError if the region is invalid """ if not self.is_open(): raise ValueError("I/O operation on closed file" ) cdef int length cdef char *seq cdef char *ref cdef int rstart, rend contig, rstart, rend = parse_region(reference, start, end, region) if contig is None: raise ValueError("no sequence/region supplied.") if rstart == rend: return "" contig_b = force_bytes(contig) ref = contig_b with nogil: length = faidx_seq_len(self.fastafile, ref) if length == -1: raise KeyError("sequence '%s' not present" % contig) if rstart >= length: return "" # fai_fetch adds a '\0' at the end with nogil: seq = faidx_fetch_seq(self.fastafile, ref, rstart, rend-1, &length) if not seq: if errno: raise IOError(errno, strerror(errno)) else: raise ValueError("failure when retrieving sequence on '%s'" % contig) try: return charptr_to_str(seq) finally: free(seq) cdef char *_fetch(self, char *reference, int start, int end, int *length) except? NULL: '''fetch sequence for reference, start and end''' cdef char *seq with nogil: seq = faidx_fetch_seq(self.fastafile, reference, start, end-1, length) if not seq: if errno: raise IOError(errno, strerror(errno)) else: raise ValueError("failure when retrieving sequence on '%s'" % reference) return seq def get_reference_length(self, reference): '''return the length of reference.''' return self.reference2length[reference] def __getitem__(self, reference): return self.fetch(reference) def __contains__(self, reference): '''return true if reference in fasta file.''' return reference in self.reference2length cdef class FastqProxy: """A single entry in a fastq file.""" def __init__(self): raise ValueError("do not instantiate FastqProxy directly") property name: """The name of each entry in the fastq file.""" def __get__(self): return charptr_to_str(self._delegate.name.s) property sequence: """The sequence of each entry in the fastq file.""" def __get__(self): return charptr_to_str(self._delegate.seq.s) property comment: def __get__(self): if self._delegate.comment.l: return charptr_to_str(self._delegate.comment.s) else: return None property quality: """The quality score of each entry in the fastq file, represented as a string.""" def __get__(self): if self._delegate.qual.l: return charptr_to_str(self._delegate.qual.s) else: return None cdef cython.str to_string(self): if self.comment is None: comment = "" else: comment = " %s" % self.comment if self.quality is None: return ">%s%s\n%s" % (self.name, comment, self.sequence) else: return "@%s%s\n%s\n+\n%s" % (self.name, comment, self.sequence, self.quality) cdef cython.str tostring(self): """deprecated : use :meth:`to_string`""" return self.to_string() def __str__(self): return self.to_string() cpdef array.array get_quality_array(self, int offset=33): '''return quality values as integer array after subtracting offset.''' if self.quality is None: return None return qualitystring_to_array(force_bytes(self.quality), offset=offset) cdef class FastxRecord: """A fasta/fastq record. A record must contain a name and a sequence. If either of them are None, a ValueError is raised on writing. """ def __init__(self, name=None, comment=None, sequence=None, quality=None, FastqProxy proxy=None): if proxy is not None: self.comment = proxy.comment self.quality = proxy.quality self.sequence = proxy.sequence self.name = proxy.name else: self.comment = comment self.quality = quality self.sequence = sequence self.name = name def __copy__(self): return FastxRecord(self.name, self.comment, self.sequence, self.quality) def __deepcopy__(self, memo): return FastxRecord(self.name, self.comment, self.sequence, self.quality) cdef cython.str to_string(self): if self.name is None: raise ValueError("can not write record without name") if self.sequence is None: raise ValueError("can not write record without a sequence") if self.comment is None: comment = "" else: comment = " %s" % self.comment if self.quality is None: return ">%s%s\n%s" % (self.name, comment, self.sequence) else: return "@%s%s\n%s\n+\n%s" % (self.name, comment, self.sequence, self.quality) cdef cython.str tostring(self): """deprecated : use :meth:`to_string`""" return self.to_string() def set_name(self, name): if name is None: raise ValueError("FastxRecord must have a name and not None") self.name = name def set_comment(self, comment): self.comment = comment def set_sequence(self, sequence, quality=None): """set sequence of this record. """ self.sequence = sequence if quality is not None: if len(sequence) != len(quality): raise ValueError("sequence and quality length do not match: {} vs {}".format( len(sequence), len(quality))) self.quality = quality else: self.quality = None def __str__(self): return self.to_string() cpdef array.array get_quality_array(self, int offset=33): '''return quality values as array after subtracting offset.''' if self.quality is None: return None return qualitystring_to_array(force_bytes(self.quality), offset=offset) cdef class FastxFile: r"""Stream access to :term:`fasta` or :term:`fastq` formatted files. The file is automatically opened. Entries in the file can be both fastq or fasta formatted or even a mixture of the two. This file object permits iterating over all entries in the file. Random access is not implemented. The iteration returns objects of type :class:`FastqProxy` Parameters ---------- filename : string Filename of fasta/fastq file to be opened. persist : bool If True (default) make a copy of the entry in the file during iteration. If set to False, no copy will be made. This will permit much faster iteration, but an entry will not persist when the iteration continues and an entry is read-only. Notes ----- Prior to version 0.8.2, this class was called FastqFile. Raises ------ IOError if file could not be opened Examples -------- >>> with pysam.FastxFile(filename) as fh: ... for entry in fh: ... print(entry.name) ... print(entry.sequence) ... print(entry.comment) ... print(entry.quality) >>> with pysam.FastxFile(filename) as fin, open(out_filename, mode='w') as fout: ... for entry in fin: ... fout.write(str(entry) + '\n') """ def __cinit__(self, *args, **kwargs): # self.fastqfile = NULL self._filename = None self.entry = NULL self._open(*args, **kwargs) def is_open(self): '''return true if samfile has been opened.''' return self.entry != NULL def _open(self, filename, persist=True): '''open a fastq/fasta file in *filename* Paramentes ---------- persist : bool if True return a copy of the underlying data (default True). The copy will persist even if the iteration on the file continues. ''' if self.fastqfile != NULL: self.close() self._filename = encode_filename(filename) cdef char *cfilename = self._filename self.is_remote = hisremote(cfilename) # open file for reading if (self._filename != b"-" and not self.is_remote and not os.path.exists(filename)): raise IOError("file `%s` not found" % filename) self.persist = persist with nogil: self.fastqfile = bgzf_open(cfilename, "r") self.entry = kseq_init(self.fastqfile) self._filename = filename def close(self): '''close the file.''' if self.fastqfile != NULL: bgzf_close(self.fastqfile) self.fastqfile = NULL if self.entry != NULL: kseq_destroy(self.entry) self.entry = NULL def __dealloc__(self): if self.fastqfile != NULL: bgzf_close(self.fastqfile) if self.entry: kseq_destroy(self.entry) # context manager interface def __enter__(self): return self def __exit__(self, exc_type, exc_value, traceback): self.close() return False property closed: """bool indicating the current state of the file object. This is a read-only attribute; the close() method changes the value. """ def __get__(self): return not self.is_open() property filename: """string with the filename associated with this object.""" def __get__(self): return self._filename def __iter__(self): if not self.is_open(): raise ValueError("I/O operation on closed file") return self cdef kseq_t * getCurrent(self): return self.entry cdef int cnext(self): '''C version of iterator ''' with nogil: return kseq_read(self.entry) def __next__(self): """ python version of next(). """ cdef int l with nogil: l = kseq_read(self.entry) if (l >= 0): if self.persist: return FastxRecord(proxy=makeFastqProxy(self.entry)) return makeFastqProxy(self.entry) elif (l == -1): raise StopIteration elif (l == -2): raise ValueError('truncated quality string in {0}' .format(self._filename)) else: raise ValueError('unknown problem parsing {0}' .format(self._filename)) # Compatibility Layer for pysam 0.8.1 cdef class FastqFile(FastxFile): """FastqFile is deprecated: use FastxFile instead""" pass # Compatibility Layer for pysam < 0.8 cdef class Fastafile(FastaFile): """Fastafile is deprecated: use FastaFile instead""" pass __all__ = ["FastaFile", "FastqFile", "FastxFile", "Fastafile", "FastxRecord", "FastqProxy"] pysam-0.23.0/pysam/libchtslib.pxd000066400000000000000000003255731475062545500167460ustar00rootroot00000000000000# cython: language_level=3 from libc.stdint cimport int8_t, int16_t, int32_t, int64_t from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t from libc.stdlib cimport malloc, calloc, realloc, free from libc.string cimport memcpy, memcmp, strncpy, strlen, strdup from libc.stdio cimport FILE, printf from posix.types cimport off_t cdef extern from "Python.h": FILE* PyFile_AsFile(object) # cython does not wrap stdarg cdef extern from "stdarg.h": ctypedef struct va_list: pass cdef extern from "htslib/kstring.h" nogil: ctypedef struct kstring_t: size_t l, m char *s int kputc(int c, kstring_t *s) int kputw(int c, kstring_t *s) int kputl(long c, kstring_t *s) int ksprintf(kstring_t *s, const char *fmt, ...) cdef extern from "htslib_util.h" nogil: int hts_set_verbosity(int verbosity) int hts_get_verbosity() ctypedef uint32_t khint32_t ctypedef uint32_t khint_t ctypedef khint_t khiter_t # Used to manage BCF Header info ctypedef struct vdict_t: khint_t n_buckets, size, n_occupied, upper_bound khint32_t *flags const char *keys bcf_idinfo_t *vals # Used to manage indexed contigs in Tabix ctypedef struct s2i_t: khint_t n_buckets, size, n_occupied, upper_bound khint32_t *flags const char *keys int64_t *vals # Generic khash methods khint_t kh_size(void *d) khint_t kh_begin(void *d) khint_t kh_end(void *d) int kh_exist(void *d, khiter_t i) # Specialized khash methods for vdict khint_t kh_get_vdict(vdict_t *d, const char *key) const char *kh_key_vdict "kh_key" (vdict_t *d, khint_t i) bcf_idinfo_t kh_val_vdict "kh_val" (vdict_t *d, khint_t i) cdef extern from "htslib/hfile.h" nogil: ctypedef struct hFILE # @abstract Open the named file or URL as a stream # @return An hFILE pointer, or NULL (with errno set) if an error occurred. hFILE *hopen(const char *filename, const char *mode, ...) # @abstract Associate a stream with an existing open file descriptor # @return An hFILE pointer, or NULL (with errno set) if an error occurred. # @notes For socket descriptors (on Windows), mode should contain 's'. hFILE *hdopen(int fd, const char *mode) # @abstract Report whether the file name or URL denotes remote storage # @return 0 if local, 1 if remote. # @notes "Remote" means involving e.g. explicit network access, with the # implication that callers may wish to cache such files' contents locally. int hisremote(const char *filename) # @abstract Flush (for output streams) and close the stream # @return 0 if successful, or EOF (with errno set) if an error occurred. int hclose(hFILE *fp) # @abstract Close the stream, without flushing or propagating errors # @notes For use while cleaning up after an error only. Preserves errno. void hclose_abruptly(hFILE *fp) # @abstract Return the stream's error indicator # @return Non-zero (in fact, an errno value) if an error has occurred. # @notes This would be called herror() and return true/false to parallel # ferror(3), but a networking-related herror(3) function already exists. */ int herrno(hFILE *fp) # @abstract Clear the stream's error indicator void hclearerr(hFILE *fp) # @abstract Reposition the read/write stream offset # @return The resulting offset within the stream (as per lseek(2)), # or negative if an error occurred. off_t hseek(hFILE *fp, off_t offset, int whence) # @abstract Report the current stream offset # @return The offset within the stream, starting from zero. off_t htell(hFILE *fp) # @abstract Read one character from the stream # @return The character read, or EOF on end-of-file or error int hgetc(hFILE *fp) # Read from the stream until the delimiter, up to a maximum length # @param buffer The buffer into which bytes will be written # @param size The size of the buffer # @param delim The delimiter (interpreted as an `unsigned char`) # @param fp The file stream # @return The number of bytes read, or negative on error. # @since 1.4 # # Bytes will be read into the buffer up to and including a delimiter, until # EOF is reached, or _size-1_ bytes have been written, whichever comes first. # The string will then be terminated with a NUL byte (`\0`). ssize_t hgetdelim(char *buffer, size_t size, int delim, hFILE *fp) # Read a line from the stream, up to a maximum length # @param buffer The buffer into which bytes will be written # @param size The size of the buffer # @param fp The file stream # @return The number of bytes read, or negative on error. # @since 1.4 # # Specialization of hgetdelim() for a `\n` delimiter. ssize_t hgetln(char *buffer, size_t size, hFILE *fp) # Read a line from the stream, up to a maximum length # @param buffer The buffer into which bytes will be written # @param size The size of the buffer (must be > 1 to be useful) # @param fp The file stream # @return _buffer_ on success, or `NULL` if an error occurred. # @since 1.4 # # This function can be used as a replacement for `fgets(3)`, or together with # kstring's `kgetline()` to read arbitrarily-long lines into a _kstring_t_. char *hgets(char *buffer, int size, hFILE *fp) # @abstract Peek at characters to be read without removing them from buffers # @param fp The file stream # @param buffer The buffer to which the peeked bytes will be written # @param nbytes The number of bytes to peek at; limited by the size of the # internal buffer, which could be as small as 4K. # @return The number of bytes peeked, which may be less than nbytes if EOF # is encountered; or negative, if there was an I/O error. # @notes The characters peeked at remain in the stream's internal buffer, # and will be returned by later hread() etc calls. ssize_t hpeek(hFILE *fp, void *buffer, size_t nbytes) # @abstract Read a block of characters from the file # @return The number of bytes read, or negative if an error occurred. # @notes The full nbytes requested will be returned, except as limited # by EOF or I/O errors. ssize_t hread(hFILE *fp, void *buffer, size_t nbytes) # @abstract Write a character to the stream # @return The character written, or EOF if an error occurred. int hputc(int c, hFILE *fp) # @abstract Write a string to the stream # @return 0 if successful, or EOF if an error occurred. int hputs(const char *text, hFILE *fp) # @abstract Write a block of characters to the file # @return Either nbytes, or negative if an error occurred. # @notes In the absence of I/O errors, the full nbytes will be written. ssize_t hwrite(hFILE *fp, const void *buffer, size_t nbytes) # @abstract For writing streams, flush buffered output to the underlying stream # @return 0 if successful, or EOF if an error occurred. int hflush(hFILE *fp) cdef extern from "htslib/bgzf.h" nogil: ctypedef struct bgzf_mtaux_t ctypedef struct bgzidx_t ctypedef struct z_stream ctypedef struct BGZF: unsigned errcode unsigned is_write int is_be int compress_level int is_compressed int is_gzip int cache_size int64_t block_address int64_t uncompressed_address void *uncompressed_block void *compressed_block void *cache hFILE *fp bgzf_mtaux_t *mt bgzidx_t *idx int idx_build_otf z_stream *gz_stream #***************** # Basic routines * # *****************/ # Open an existing file descriptor for reading or writing. # # @param fd file descriptor # @param mode mode matching /[rwag][u0-9]+/: 'r' for reading, 'w' for # writing, 'a' for appending, 'g' for gzip rather than BGZF # compression (with 'w' only), and digit specifies the zlib # compression level. # Note that there is a distinction between 'u' and '0': the # first yields plain uncompressed output whereas the latter # outputs uncompressed data wrapped in the zlib format. # @return BGZF file handler; 0 on error BGZF* bgzf_dopen(int fd, const char *mode) BGZF* bgzf_fdopen(int fd, const char *mode) # for backward compatibility # Open the specified file for reading or writing. BGZF* bgzf_open(const char* path, const char *mode) # Open an existing hFILE stream for reading or writing. BGZF* bgzf_hopen(hFILE *fp, const char *mode) # Close the BGZF and free all associated resources. # # @param fp BGZF file handler # @return 0 on success and -1 on error int bgzf_close(BGZF *fp) # Read up to _length_ bytes from the file storing into _data_. # # @param fp BGZF file handler # @param data data array to read into # @param length size of data to read # @return number of bytes actually read; 0 on end-of-file and -1 on error ssize_t bgzf_read(BGZF *fp, void *data, size_t length) # Write _length_ bytes from _data_ to the file. If no I/O errors occur, # the complete _length_ bytes will be written (or queued for writing). # # @param fp BGZF file handler # @param data data array to write # @param length size of data to write # @return number of bytes written (i.e., _length_); negative on error ssize_t bgzf_write(BGZF *fp, const void *data, size_t length) # Read up to _length_ bytes directly from the underlying stream without # decompressing. Bypasses BGZF blocking, so must be used with care in # specialised circumstances only. # # @param fp BGZF file handler # @param data data array to read into # @param length number of raw bytes to read # @return number of bytes actually read; 0 on end-of-file and -1 on error ssize_t bgzf_raw_read(BGZF *fp, void *data, size_t length) # Write _length_ bytes directly to the underlying stream without # compressing. Bypasses BGZF blocking, so must be used with care # in specialised circumstances only. # # @param fp BGZF file handler # @param data data array to write # @param length number of raw bytes to write # @return number of bytes actually written; -1 on error ssize_t bgzf_raw_write(BGZF *fp, const void *data, size_t length) # Write the data in the buffer to the file. int bgzf_flush(BGZF *fp) # Return a virtual file pointer to the current location in the file. # No interpretation of the value should be made, other than a subsequent # call to bgzf_seek can be used to position the file at the same point. # Return value is non-negative on success. int64_t bgzf_tell(BGZF *fp) # Set the file to read from the location specified by _pos_. # # @param fp BGZF file handler # @param pos virtual file offset returned by bgzf_tell() # @param whence must be SEEK_SET (cimported from libc.stdio / posix.unistd) # @return 0 on success and -1 on error # / int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence) # Check if the BGZF end-of-file (EOF) marker is present # # @param fp BGZF file handler opened for reading # @return 1 if the EOF marker is present and correct # 2 if it can't be checked, e.g., because fp isn't seekable # 0 if the EOF marker is absent # -1 (with errno set) on error int bgzf_check_EOF(BGZF *fp) # Check if a file is in the BGZF format # # @param fn file name # @return 1 if _fn_ is BGZF; 0 if not or on I/O error int bgzf_is_bgzf(const char *fn) #********************* # Advanced routines * #********************* # Set the cache size. Only effective when compiled with -DBGZF_CACHE. # # @param fp BGZF file handler # @param size size of cache in bytes; 0 to disable caching (default) void bgzf_set_cache_size(BGZF *fp, int size) # Flush the file if the remaining buffer size is smaller than _size_ # @return 0 if flushing succeeded or was not needed; negative on error int bgzf_flush_try(BGZF *fp, ssize_t size) # Read one byte from a BGZF file. It is faster than bgzf_read() # @param fp BGZF file handler # @return byte read; -1 on end-of-file or error int bgzf_getc(BGZF *fp) # Read one line from a BGZF file. It is faster than bgzf_getc() # # @param fp BGZF file handler # @param delim delimiter # @param str string to write to; must be initialized # @return length of the string; 0 on end-of-file; negative on error int bgzf_getline(BGZF *fp, int delim, kstring_t *str) # Read the next BGZF block. int bgzf_read_block(BGZF *fp) # Enable multi-threading (only effective on writing and when the # library was compiled with -DBGZF_MT) # # @param fp BGZF file handler; must be opened for writing # @param n_threads #threads used for writing # @param n_sub_blks #blocks processed by each thread; a value 64-256 is recommended int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks) # Compress a single BGZF block. # # @param dst output buffer (must have size >= BGZF_MAX_BLOCK_SIZE) # @param dlen size of output buffer; updated on return to the number # of bytes actually written to dst # @param src buffer to be compressed # @param slen size of data to compress (must be <= BGZF_BLOCK_SIZE) # @param level compression level # @return 0 on success and negative on error # int bgzf_compress(void *dst, size_t *dlen, const void *src, size_t slen, int level) #******************* # bgzidx routines * # BGZF at the uncompressed offset # # @param fp BGZF file handler; must be opened for reading # @param uoffset file offset in the uncompressed data # @param where SEEK_SET (cimported from libc.stdio) supported atm # # Returns 0 on success and -1 on error. int bgzf_useek(BGZF *fp, long uoffset, int where) # Position in uncompressed BGZF # # @param fp BGZF file handler; must be opened for reading # # Returns the current offset on success and -1 on error. long bgzf_utell(BGZF *fp) # Tell BGZF to build index while compressing. # # @param fp BGZF file handler; can be opened for reading or writing. # # Returns 0 on success and -1 on error. int bgzf_index_build_init(BGZF *fp) # Load BGZF index # # @param fp BGZF file handler # @param bname base name # @param suffix suffix to add to bname (can be NULL) # # Returns 0 on success and -1 on error. int bgzf_index_load(BGZF *fp, const char *bname, const char *suffix) # Save BGZF index # # @param fp BGZF file handler # @param bname base name # @param suffix suffix to add to bname (can be NULL) # # Returns 0 on success and -1 on error. int bgzf_index_dump(BGZF *fp, const char *bname, const char *suffix) cdef extern from "htslib/hts.h" nogil: uint32_t kroundup32(uint32_t x) ctypedef struct cram_fd union FilePointerUnion: BGZF *bgzf cram_fd *cram hFILE *hfile void *voidp enum htsFormatCategory: unknown_category sequence_data # Sequence data -- SAM, BAM, CRAM, etc variant_data # Variant calling data -- VCF, BCF, etc index_file # Index file associated with some data file region_list # Coordinate intervals or regions -- BED, etc category_maximum enum htsExactFormat: unknown_format binary_format text_format sam, bam, bai, cram, crai, vcf, bcf, csi, gzi, tbi, bed format_maximum enum htsCompression: no_compression, gzip, bgzf, custom compression_maximum cdef enum hts_fmt_option: CRAM_OPT_DECODE_MD, CRAM_OPT_PREFIX, CRAM_OPT_VERBOSITY, CRAM_OPT_SEQS_PER_SLICE, CRAM_OPT_SLICES_PER_CONTAINER, CRAM_OPT_RANGE, CRAM_OPT_VERSION, CRAM_OPT_EMBED_REF, CRAM_OPT_IGNORE_MD5, CRAM_OPT_REFERENCE, CRAM_OPT_MULTI_SEQ_PER_SLICE, CRAM_OPT_NO_REF, CRAM_OPT_USE_BZIP2, CRAM_OPT_SHARED_REF, CRAM_OPT_NTHREADS, CRAM_OPT_THREAD_POOL, CRAM_OPT_USE_LZMA, CRAM_OPT_USE_RANS, CRAM_OPT_REQUIRED_FIELDS, HTS_OPT_COMPRESSION_LEVEL, HTS_OPT_NTHREADS, ctypedef struct htsVersion: short major, minor ctypedef struct htsFormat: htsFormatCategory category htsExactFormat format htsVersion version htsCompression compression short compression_level void *specific ctypedef struct htsFile: uint8_t is_bin uint8_t is_write uint8_t is_be uint8_t is_cram int64_t lineno kstring_t line char *fn char *fn_aux FilePointerUnion fp htsFormat format int hts_verbose cdef union hts_opt_val_union: int i char *s ctypedef struct hts_opt: char *arg hts_fmt_option opt hts_opt_val_union val void *next # @abstract Parses arg and appends it to the option list. # @return 0 on success and -1 on failure int hts_opt_add(hts_opt **opts, const char *c_arg) # @abstract Applies an hts_opt option list to a given htsFile. # @return 0 on success and -1 on failure int hts_opt_apply(htsFile *fp, hts_opt *opts) # @abstract Frees an hts_opt list. void hts_opt_free(hts_opt *opts) # @abstract Table for converting a nucleotide character to 4-bit encoding. # The input character may be either an IUPAC ambiguity code, '=' for 0, or # '0'/'1'/'2'/'3' for a result of 1/2/4/8. The result is encoded as 1/2/4/8 # for A/C/G/T or combinations of these bits for ambiguous bases. const unsigned char *seq_nt16_table # @abstract Table for converting a 4-bit encoded nucleotide to an IUPAC # ambiguity code letter (or '=' when given 0). const char *seq_nt16_str # @abstract Table for converting a 4-bit encoded nucleotide to about 2 bits. # Returns 0/1/2/3 for 1/2/4/8 (i.e., A/C/G/T), or 4 otherwise (0 or ambiguous). const int *seq_nt16_int # @abstract Get the htslib version number # @return For released versions, a string like "N.N[.N]"; or git describe # output if using a library built within a Git repository. const char *hts_version() # @abstract Determine format by peeking at the start of a file # @param fp File opened for reading, positioned at the beginning # @param fmt Format structure that will be filled out on return # @return 0 for success, or negative if an error occurred. int hts_detect_format(hFILE *fp, htsFormat *fmt) # @abstract Get a human-readable description of the file format # @return Description string, to be freed by the caller after use. char *hts_format_description(const htsFormat *format) # @abstract Open a SAM/BAM/CRAM/VCF/BCF/etc file # @param fn The file name or "-" for stdin/stdout # @param mode Mode matching / [rwa][bceguxz0-9]* / # @discussion # With 'r' opens for reading; any further format mode letters are ignored # as the format is detected by checking the first few bytes or BGZF blocks # of the file. With 'w' or 'a' opens for writing or appending, with format # specifier letters: # b binary format (BAM, BCF, etc) rather than text (SAM, VCF, etc) # c CRAM format # g gzip compressed # u uncompressed # z bgzf compressed # [0-9] zlib compression level # and with non-format option letters (for any of 'r'/'w'/'a'): # e close the file on exec(2) (opens with O_CLOEXEC, where supported) # x create the file exclusively (opens with O_EXCL, where supported) # Note that there is a distinction between 'u' and '0': the first yields # plain uncompressed output whereas the latter outputs uncompressed data # wrapped in the zlib format. # @example # [rw]b .. compressed BCF, BAM, FAI # [rw]bu .. uncompressed BCF # [rw]z .. compressed VCF # [rw] .. uncompressed VCF htsFile *hts_open(const char *fn, const char *mode) # @abstract Open a SAM/BAM/CRAM/VCF/BCF/etc file # @param fn The file name or "-" for stdin/stdout # @param mode Open mode, as per hts_open() # @param fmt Optional format specific parameters # @discussion # See hts_open() for description of fn and mode. # // TODO Update documentation for s/opts/fmt/ # Opts contains a format string (sam, bam, cram, vcf, bcf) which will, # if defined, override mode. Opts also contains a linked list of hts_opt # structures to apply to the open file handle. These can contain things # like pointers to the reference or information on compression levels, # block sizes, etc. htsFile *hts_open_format(const char *fn, const char *mode, const htsFormat *fmt) # @abstract Open an existing stream as a SAM/BAM/CRAM/VCF/BCF/etc file # @param fp The already-open file handle # @param fn The file name or "-" for stdin/stdout # @param mode Open mode, as per hts_open() htsFile *hts_hopen(hFILE *fp, const char *fn, const char *mode) # @abstract For output streams, flush any buffered data # @param fp The file handle to be flushed # @return 0 for success, or negative if an error occurred. # @since 1.14 int hts_flush(htsFile *fp) # @abstract Close a file handle, flushing buffered data for output streams # @param fp The file handle to be closed # @return 0 for success, or negative if an error occurred. int hts_close(htsFile *fp) # @abstract Returns the file's format information # @param fp The file handle # @return Read-only pointer to the file's htsFormat. const htsFormat *hts_get_format(htsFile *fp) # @ abstract Returns a string containing the file format extension. # @ param format Format structure containing the file type. # @ return A string ("sam", "bam", etc) or "?" for unknown formats. const char *hts_format_file_extension(const htsFormat *format) # @abstract Sets a specified CRAM option on the open file handle. # @param fp The file handle open the open file. # @param opt The CRAM_OPT_* option. # @param ... Optional arguments, dependent on the option used. # @return 0 for success, or negative if an error occurred. int hts_set_opt(htsFile *fp, hts_fmt_option opt, ...) int hts_getline(htsFile *fp, int delimiter, kstring_t *str) char **hts_readlines(const char *fn, int *_n) # @abstract Parse comma-separated list or read list from a file # @param list File name or comma-separated list # @param is_file # @param _n Size of the output array (number of items read) # @return NULL on failure or pointer to newly allocated array of # strings char **hts_readlist(const char *fn, int is_file, int *_n) # @abstract Create extra threads to aid compress/decompression for this file # @param fp The file handle # @param n The number of worker threads to create # @return 0 for success, or negative if an error occurred. # @notes THIS THREADING API IS LIKELY TO CHANGE IN FUTURE. int hts_set_threads(htsFile *fp, int n) # @abstract Set .fai filename for a file opened for reading # @return 0 for success, negative on failure # @discussion # Called before *_hdr_read(), this provides the name of a .fai file # used to provide a reference list if the htsFile contains no @SQ headers. int hts_set_fai_filename(htsFile *fp, const char *fn_aux) int8_t HTS_IDX_NOCOOR int8_t HTS_IDX_START int8_t HTS_IDX_REST int8_t HTS_IDX_NONE int8_t HTS_FMT_CSI int8_t HTS_FMT_BAI int8_t HTS_FMT_TBI int8_t HTS_FMT_CRAI BGZF *hts_get_bgzfp(htsFile *fp) ctypedef struct hts_idx_t ctypedef struct hts_pair64_t: uint64_t u, v ctypedef int hts_readrec_func(BGZF *fp, void *data, void *r, int *tid, int *beg, int *end) ctypedef struct hts_bins_t: int n, m int *a ctypedef struct hts_itr_t: uint32_t read_rest uint32_t finished int tid, bed, end, n_off, i int curr_tid, curr_beg, curr_end uint64_t curr_off hts_pair64_t *off hts_readrec_func *readfunc hts_bins_t bins hts_idx_t *hts_idx_init(int n, int fmt, uint64_t offset0, int min_shift, int n_lvls) void hts_idx_destroy(hts_idx_t *idx) int hts_idx_push(hts_idx_t *idx, int tid, int beg, int end, uint64_t offset, int is_mapped) void hts_idx_finish(hts_idx_t *idx, uint64_t final_offset) #### Save an index to a file # @param idx Index to be written # @param fn Input BAM/BCF/etc filename, to which .bai/.csi/etc will be added # @param fmt One of the HTS_FMT_* index formats # @return 0 if successful, or negative if an error occurred. int hts_idx_save(const hts_idx_t *idx, const char *fn, int fmt) #### Save an index to a specific file # @param idx Index to be written # @param fn Input BAM/BCF/etc filename # @param fnidx Output filename, or NULL to add .bai/.csi/etc to @a fn # @param fmt One of the HTS_FMT_* index formats # @return 0 if successful, or negative if an error occurred. int hts_idx_save_as(const hts_idx_t *idx, const char *fn, const char *fnidx, int fmt) #### Load an index file # @param fn BAM/BCF/etc filename, to which .bai/.csi/etc will be added or # the extension substituted, to search for an existing index file # @param fmt One of the HTS_FMT_* index formats # @return The index, or NULL if an error occurred. hts_idx_t *hts_idx_load(const char *fn, int fmt) #### Load a specific index file # @param fn Input BAM/BCF/etc filename # @param fnidx The input index filename # @return The index, or NULL if an error occurred. hts_idx_t *hts_idx_load2(const char *fn, const char *fnidx) #### Load a specific index file # @param fn Input BAM/BCF/etc filename # @param fnidx The input index filename # @param fmt One of the HTS_FMT_* index formats # @param flags Flags to alter behaviour (see description) # @return The index, or NULL if an error occurred. hts_idx_t *hts_idx_load3(const char *fn, const char *fnidx, int fmt, int flags) int HTS_IDX_SAVE_REMOTE int HTS_IDX_SILENT_FAIL uint8_t *hts_idx_get_meta(hts_idx_t *idx, uint32_t *l_meta) void hts_idx_set_meta(hts_idx_t *idx, int l_meta, uint8_t *meta, int is_copy) int hts_idx_get_stat(const hts_idx_t* idx, int tid, uint64_t* mapped, uint64_t* unmapped) uint64_t hts_idx_get_n_no_coor(const hts_idx_t* idx) int HTS_PARSE_THOUSANDS_SEP # Ignore ',' separators within numbers # Parse a numeric string # The number may be expressed in scientific notation, and optionally may # contain commas in the integer part (before any decimal point or E notation). # @param str String to be parsed # @param strend If non-NULL, set on return to point to the first character # in @a str after those forming the parsed number # @param flags Or'ed-together combination of HTS_PARSE_* flags # @return Converted value of the parsed number. # # When @a strend is NULL, a warning will be printed (if hts_verbose is 2 # or more) if there are any trailing characters after the number. long long hts_parse_decimal(const char *str, char **strend, int flags) # Parse a "CHR:START-END"-style region string # @param str String to be parsed # @param beg Set on return to the 0-based start of the region # @param end Set on return to the 1-based end of the region # @return Pointer to the colon or '\0' after the reference sequence name, # or NULL if @a str could not be parsed. const char *hts_parse_reg(const char *str, int *beg, int *end) hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec) void hts_itr_destroy(hts_itr_t *iter) ctypedef int (*hts_name2id_f)(void*, const char*) ctypedef const char *(*hts_id2name_f)(void*, int) ctypedef hts_itr_t *hts_itr_query_func( const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec) hts_itr_t *hts_itr_querys( const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec) int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, void *data) const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr) # free only the array, not the values # hts_file_type() - Convenience function to determine file type # @fname: the file name # # Returns one of the FT_* defines. # # DEPRECATED: This function has been replaced by hts_detect_format(). # It and these FT_* macros will be removed in a future HTSlib release. int FT_UNKN int FT_GZ int FT_VCF int FT_VCF_GZ int FT_BCF int FT_BCF_GZ int FT_STDIN int hts_file_type(const char *fname) # /*************************** # * Revised MAQ error model * # ***************************/ ctypedef struct errmod_t errmod_t *errmod_init(double depcorr) void errmod_destroy(errmod_t *em) # /* # n: number of bases # m: maximum base # bases[i]: qual:6, strand:1, base:4 # q[i*m+j]: phred-scaled likelihood of (i,j) # */ int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *Probabilistic) # /***************************************** # * q banded glocal alignment * # *****************************************/ ctypedef struct probaln_par_t: float d, e int bw int probaln_glocal(const uint8_t *ref, int l_ref, const uint8_t *query, int l_query, const uint8_t *iqual, const probaln_par_t *c, int *state, uint8_t *q) # /********************** # * MD5 implementation * # **********************/ ctypedef struct hts_md5_context # /*! @abstract Initialises an MD5 context. # * @discussion # * The expected use is to allocate an hts_md5_context using # * hts_md5_init(). This pointer is then passed into one or more calls # * of hts_md5_update() to compute successive internal portions of the # * MD5 sum, which can then be externalised as a full 16-byte MD5sum # * calculation by calling hts_md5_final(). This can then be turned # * into ASCII via hts_md5_hex(). # * # * To dealloate any resources created by hts_md5_init() call the # * hts_md5_destroy() function. # * # * @return hts_md5_context pointer on success, NULL otherwise. # */ hts_md5_context *hts_md5_init() # /*! @abstract Updates the context with the MD5 of the data. */ void hts_md5_update(hts_md5_context *ctx, const void *data, unsigned long size) # /*! @abstract Computes the final 128-bit MD5 hash from the given context */ void hts_md5_final(unsigned char *digest, hts_md5_context *ctx) # /*! @abstract Resets an md5_context to the initial state, as returned # * by hts_md5_init(). # */ void hts_md5_reset(hts_md5_context *ctx) # /*! @abstract Converts a 128-bit MD5 hash into a 33-byte nul-termninated # * hex string. # */ void hts_md5_hex(char *hex, const unsigned char *digest) # /*! @abstract Deallocates any memory allocated by hts_md5_init. */ void hts_md5_destroy(hts_md5_context *ctx) int hts_reg2bin(int64_t beg, int64_t end, int min_shift, int n_lvls) int hts_bin_bot(int bin, int n_lvls) # * Endianness * int ed_is_big() uint16_t ed_swap_2(uint16_t v) void *ed_swap_2p(void *x) uint32_t ed_swap_4(uint32_t v) void *ed_swap_4p(void *x) uint64_t ed_swap_8(uint64_t v) void *ed_swap_8p(void *x) cdef extern from "htslib/sam.h" nogil: #********************** #*** SAM/BAM header *** #********************** # @abstract Structure for the alignment header. # @field n_targets number of reference sequences # @field l_text length of the plain text in the header # @field target_len lengths of the reference sequences # @field target_name names of the reference sequences # @field text plain text # @field sdict header dictionary ctypedef struct bam_hdr_t: int32_t n_targets, ignore_sam_err uint32_t l_text uint32_t *target_len uint8_t *cigar_tab char **target_name char *text void *sdict #**************************** #*** CIGAR related macros *** #**************************** int BAM_CMATCH int BAM_CINS int BAM_CDEL int BAM_CREF_SKIP int BAM_CSOFT_CLIP int BAM_CHARD_CLIP int BAM_CPAD int BAM_CEQUAL int BAM_CDIFF int BAM_CBACK char *BAM_CIGAR_STR int BAM_CIGAR_SHIFT uint32_t BAM_CIGAR_MASK uint32_t BAM_CIGAR_TYPE char bam_cigar_op(uint32_t c) uint32_t bam_cigar_oplen(uint32_t c) char bam_cigar_opchr(uint32_t) uint32_t bam_cigar_gen(char, uint32_t) int bam_cigar_type(char o) # @abstract the read is paired in sequencing, no matter whether it is mapped in a pair int BAM_FPAIRED # @abstract the read is mapped in a proper pair int BAM_FPROPER_PAIR # @abstract the read itself is unmapped; conflictive with BAM_FPROPER_PAIR int BAM_FUNMAP # @abstract the mate is unmapped int BAM_FMUNMAP # @abstract the read is mapped to the reverse strand int BAM_FREVERSE # @abstract the mate is mapped to the reverse strand int BAM_FMREVERSE # @abstract this is read1 int BAM_FREAD1 # @abstract this is read2 int BAM_FREAD2 # @abstract not primary alignment int BAM_FSECONDARY # @abstract QC failure int BAM_FQCFAIL # @abstract optical or PCR duplicate int BAM_FDUP # @abstract supplementary alignment int BAM_FSUPPLEMENTARY #************************* #*** Alignment records *** #************************* # @abstract Structure for core alignment information. # @field tid chromosome ID, defined by bam_hdr_t # @field pos 0-based leftmost coordinate # @field bin bin calculated by bam_reg2bin() # @field qual mapping quality # @field l_qname length of the query name # @field flag bitwise flag # @field n_cigar number of CIGAR operations # @field l_qseq length of the query sequence (read) # @field mtid chromosome ID of next read in template, defined by bam_hdr_t # @field mpos 0-based leftmost coordinate of next read in template ctypedef struct bam1_core_t: int32_t tid int32_t pos uint16_t bin uint8_t qual uint8_t l_qname uint16_t flag uint8_t unused1 uint8_t l_extranul uint32_t n_cigar int32_t l_qseq int32_t mtid int32_t mpos int32_t isize # @abstract Structure for one alignment. # @field core core information about the alignment # @field l_data current length of bam1_t::data # @field m_data maximum length of bam1_t::data # @field data all variable-length data, concatenated; structure: qname-cigar-seq-qual-aux # # @discussion Notes: # # 1. qname is zero tailing and core.l_qname includes the tailing '\0'. # 2. l_qseq is calculated from the total length of an alignment block # on reading or from CIGAR. # 3. cigar data is encoded 4 bytes per CIGAR operation. # 4. seq is nybble-encoded according to seq_nt16_table. ctypedef struct bam1_t: bam1_core_t core int l_data uint32_t m_data uint8_t *data uint64_t id # @abstract Get whether the query is on the reverse strand # @param b pointer to an alignment # @return boolean true if query is on the reverse strand int bam_is_rev(bam1_t *b) # @abstract Get whether the query's mate is on the reverse strand # @param b pointer to an alignment # @return boolean true if query's mate on the reverse strand int bam_is_mrev(bam1_t *b) # @abstract Get the name of the query # @param b pointer to an alignment # @return pointer to the name string, null terminated char *bam_get_qname(bam1_t *b) # @abstract Get the CIGAR array # @param b pointer to an alignment # @return pointer to the CIGAR array # # @discussion In the CIGAR array, each element is a 32-bit integer. The # lower 4 bits gives a CIGAR operation and the higher 28 bits keep the # length of a CIGAR. uint32_t *bam_get_cigar(bam1_t *b) # @abstract Get query sequence # @param b pointer to an alignment # @return pointer to sequence # # @discussion Each base is encoded in 4 bits: 1 for A, 2 for C, 4 for G, # 8 for T and 15 for N. Two bases are packed in one byte with the base # at the higher 4 bits having smaller coordinate on the read. It is # recommended to use bam_seqi() macro to get the base. char *bam_get_seq(bam1_t *b) # @abstract Get query quality # @param b pointer to an alignment # @return pointer to quality string uint8_t *bam_get_qual(bam1_t *b) # @abstract Get auxiliary data # @param b pointer to an alignment # @return pointer to the concatenated auxiliary data uint8_t *bam_get_aux(bam1_t *b) # @abstract Get length of auxiliary data # @param b pointer to an alignment # @return length of the concatenated auxiliary data int bam_get_l_aux(bam1_t *b) # @abstract Get a base on read # @param s Query sequence returned by bam1_seq() # @param i The i-th position, 0-based # @return 4-bit integer representing the base. char bam_seqi(char *s, int i) #************************** #*** Exported functions *** #************************** #*************** #*** BAM I/O *** #*************** bam_hdr_t *bam_hdr_init() bam_hdr_t *bam_hdr_read(BGZF *fp) int bam_hdr_write(BGZF *fp, const bam_hdr_t *h) void bam_hdr_destroy(bam_hdr_t *h) int bam_name2id(bam_hdr_t *h, const char *ref) bam_hdr_t* bam_hdr_dup(const bam_hdr_t *h0) bam1_t *bam_init1() void bam_destroy1(bam1_t *b) int bam_read1(BGZF *fp, bam1_t *b) int bam_write1(BGZF *fp, const bam1_t *b) bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc) bam1_t *bam_dup1(const bam1_t *bsrc) int bam_cigar2qlen(int n_cigar, const uint32_t *cigar) int bam_cigar2rlen(int n_cigar, const uint32_t *cigar) # @abstract Calculate the rightmost base position of an alignment on the # reference genome. # @param b pointer to an alignment # @return the coordinate of the first base after the alignment, 0-based # @discussion For a mapped read, this is just b->core.pos + bam_cigar2rlen. # For an unmapped read (either according to its flags or if it has no cigar # string), we return b->core.pos + 1 by convention. int32_t bam_endpos(const bam1_t *b) int bam_str2flag(const char *str) # returns negative value on error char *bam_flag2str(int flag) # The string must be freed by the user #************************* #*** BAM/CRAM indexing *** #************************* # These BAM iterator functions work only on BAM files. To work with either # BAM or CRAM files use the sam_index_load() & sam_itr_*() functions. void bam_itr_destroy(hts_itr_t *iter) hts_itr_t *bam_itr_queryi(const hts_idx_t *idx, int tid, int beg, int end) hts_itr_t *bam_itr_querys(const hts_idx_t *idx, bam_hdr_t *hdr, const char *region) int bam_itr_next(htsFile *htsfp, hts_itr_t *itr, void *r) # Load/build .csi or .bai BAM index file. Does not work with CRAM. # It is recommended to use the sam_index_* functions below instead. hts_idx_t *bam_index_load(const char *fn) int bam_index_build(const char *fn, int min_shift) # Load a BAM (.csi or .bai) or CRAM (.crai) index file # @param fp File handle of the data file whose index is being opened # @param fn BAM/CRAM/etc filename to search alongside for the index file # @return The index, or NULL if an error occurred. hts_idx_t *sam_index_load(htsFile *fp, const char *fn) # Load a specific BAM (.csi or .bai) or CRAM (.crai) index file # @param fp File handle of the data file whose index is being opened # @param fn BAM/CRAM/etc data file filename # @param fnidx Index filename, or NULL to search alongside @a fn # @return The index, or NULL if an error occurred. hts_idx_t *sam_index_load2(htsFile *fp, const char *fn, const char *fnidx) # Load or stream a BAM (.csi or .bai) or CRAM (.crai) index file # @param fp File handle of the data file whose index is being opened # @param fn BAM/CRAM/etc data file filename # @param fnidx Index filename, or NULL to search alongside @a fn # @param flags Flags to alter behaviour # @return The index, or NULL if an error occurred. hts_idx_t *sam_index_load3(htsFile *fp, const char *fn, const char *fnidx, int flags) # Generate and save an index file # @param fn Input BAM/etc filename, to which .csi/etc will be added # @param min_shift Positive to generate CSI, or 0 to generate BAI # @return 0 if successful, or negative if an error occurred (usually -1; or # -2: opening fn failed; -3: format not indexable) int sam_index_build(const char *fn, int min_shift) # Generate and save an index to a specific file # @param fn Input BAM/CRAM/etc filename # @param fnidx Output filename, or NULL to add .bai/.csi/etc to @a fn # @param min_shift Positive to generate CSI, or 0 to generate BAI # @return 0 if successful, or negative if an error occurred. int sam_index_build2(const char *fn, const char *fnidx, int min_shift) void sam_itr_destroy(hts_itr_t *iter) hts_itr_t *sam_itr_queryi(const hts_idx_t *idx, int tid, int beg, int end) hts_itr_t *sam_itr_querys(const hts_idx_t *idx, bam_hdr_t *hdr, const char *region) int sam_itr_next(htsFile *htsfp, hts_itr_t *itr, void *r) #*************** #*** SAM I/O *** #*************** htsFile *sam_open(const char *fn, const char *mode) htsFile *sam_open_format(const char *fn, const char *mode, const htsFormat *fmt) int sam_close(htsFile *fp) int sam_open_mode(char *mode, const char *fn, const char *format) # A version of sam_open_mode that can handle ,key=value options. # The format string is allocated and returned, to be freed by the caller. # Prefix should be "r" or "w", char *sam_open_mode_opts(const char *fn, const char *mode, const char *format) bam_hdr_t *sam_hdr_parse(int l_text, const char *text) bam_hdr_t *sam_hdr_read(htsFile *fp) int sam_hdr_write(htsFile *fp, const bam_hdr_t *h) int sam_parse1(kstring_t *s, bam_hdr_t *h, bam1_t *b) int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str) int sam_read1(htsFile *fp, bam_hdr_t *h, bam1_t *b) int sam_write1(htsFile *fp, const bam_hdr_t *h, const bam1_t *b) #************************************* #*** Manipulating auxiliary fields *** #************************************* uint8_t *bam_aux_get(const bam1_t *b, const char *tag) int64_t bam_aux2i(const uint8_t *s) double bam_aux2f(const uint8_t *s) char bam_aux2A(const uint8_t *s) char *bam_aux2Z(const uint8_t *s) void bam_aux_append(bam1_t *b, const char *tag, char type, int len, uint8_t *data) int bam_aux_del(bam1_t *b, uint8_t *s) #************************** #*** Pileup and Mpileup *** #************************** # @abstract Generic pileup 'client data'. # @discussion The pileup iterator allows setting a constructor and # destructor function, which will be called every time a sequence is # fetched and discarded. This permits caching of per-sequence data in # a tidy manner during the pileup process. This union is the cached # data to be manipulated by the "client" (the caller of pileup). # union bam_pileup_cd: void *p int64_t i double f # @abstract Structure for one alignment covering the pileup position. # @field b pointer to the alignment # @field qpos position of the read base at the pileup site, 0-based # @field indel indel length; 0 for no indel, positive for ins and negative for del # @field level the level of the read in the "viewer" mode # @field is_del 1 iff the base on the padded read is a deletion # @field is_head ??? # @field is_tail ??? # @field is_refskip ??? # @field aux ??? # # @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The # difference between the two functions is that the former does not # set bam_pileup1_t::level, while the later does. Level helps the # implementation of alignment viewers, but calculating this has some # overhead. # # is_del, is_head, etc are a bit field, declaring as below should # work as expected, see # https://groups.google.com/forum/#!msg/cython-users/24tD1kwRY7A/pmoPuSmanM0J ctypedef struct bam_pileup1_t: bam1_t *b int32_t qpos int indel, level uint32_t is_del uint32_t is_head uint32_t is_tail uint32_t is_refskip uint32_t aux bam_pileup_cd cd ctypedef int (*bam_plp_auto_f)(void *data, bam1_t *b) ctypedef int (*bam_test_f)() ctypedef struct __bam_plp_t ctypedef __bam_plp_t *bam_plp_t ctypedef struct __bam_mplp_t ctypedef __bam_mplp_t *bam_mplp_t # bam_plp_init() - sets an iterator over multiple # @func: see mplp_func in bam_plcmd.c in samtools for an example. Expected return # status: 0 on success, -1 on end, < -1 on non-recoverable errors # @data: user data to pass to @func bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data) void bam_plp_destroy(bam_plp_t iter) int bam_plp_push(bam_plp_t iter, const bam1_t *b) const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp) const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp) void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt) void bam_plp_reset(bam_plp_t iter) bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data) # bam_mplp_init_overlaps() - if called, mpileup will detect overlapping # read pairs and for each base pair set the base quality of the # lower-quality base to zero, thus effectively discarding it from # calling. If the two bases are identical, the quality of the other base # is increased to the sum of their qualities (capped at 200), otherwise # it is multiplied by 0.8. void bam_mplp_init_overlaps(bam_mplp_t iter) void bam_mplp_destroy(bam_mplp_t iter) void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt) int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp) void bam_mplp_reset(bam_mplp_t iter) void bam_mplp_constructor(bam_mplp_t iter, int (*func)(void *data, const bam1_t *b, bam_pileup_cd *cd)) void bam_mplp_destructor(bam_mplp_t iter, int (*func)(void *data, const bam1_t *b, bam_pileup_cd *cd)) # Added by AH # ctypedef bam_pileup1_t * const_bam_pileup1_t_ptr "const bam_pileup1_t *" # // --------------------------- # // Base modification retrieval # /*! @typedef # @abstract Holds a single base modification. # @field modified_base The short base code (m, h, etc) or -ChEBI (negative) # @field canonical_base The canonical base referred to in the MM tag. # One of A, C, G, T or N. Note this may not be the # explicit base recorded in the SEQ column (esp. if N). # @field strand 0 or 1, indicating + or - strand from MM tag. # @field qual Quality code (256*probability), or -1 if unknown # @discussion # Note this doesn't hold any location data or information on which other # modifications may be possible at this site. ctypedef struct hts_base_mod: int modified_base int canonical_base int strand int qual # /// Allocates an hts_base_mode_state. # /** # * @return An hts_base_mode_state pointer on success, # * NULL on failure. # * # * This just allocates the memory. The initialisation of the contents is # * done using bam_parse_basemod. Successive calls may be made to that # * without the need to free and allocate a new state. # * # * The state be destroyed using the hts_base_mode_state_free function. # */ ctypedef struct hts_base_mod_state hts_base_mod_state *hts_base_mod_state_alloc() # /// Destroys an hts_base_mode_state. # /** # * @param state The base modification state pointer. # * # * The should have previously been created by hts_base_mode_state_alloc. # */ void hts_base_mod_state_free(hts_base_mod_state *state) # /// Parses the Mm and Ml tags out of a bam record. # /** # * @param b BAM alignment record # * @param state The base modification state pointer. # * @return 0 on success, # * -1 on failure. # * # * This fills out the contents of the modification state, resetting the # * iterator location to the first sequence base. # */ int bam_parse_basemod(const bam1_t *b, hts_base_mod_state *state) # /// Finds the next location containing base modifications and returns them # /** # * @param b BAM alignment record # * @param state The base modification state pointer. # * @param mods A supplied array for returning base modifications # * @param n_mods The size of the mods array # * @return The number of modifications found on success, # * 0 if no more modifications are present, # * -1 on failure. # * # * Unlike bam_mods_at_next_pos this skips ahead to the next site # * with modifications. # * # * If more than n_mods modifications are found, the total found is returned. # * Note this means the caller needs to check whether this is higher than # * n_mods. # */ int bam_next_basemod(const bam1_t *b, hts_base_mod_state *state,hts_base_mod *mods, int n_mods, int *pos) # *********************************** # * BAQ calculation and realignment * # ***********************************/ int sam_cap_mapq(bam1_t *b, const char *ref, int ref_len, int thres) int sam_prob_realn(bam1_t *b, const char *ref, int ref_len, int flag) cdef extern from "htslib/faidx.h" nogil: ctypedef struct faidx_t: pass # /// Build index for a FASTA or bgzip-compressed FASTA file. # /** @param fn FASTA file name # @param fnfai Name of .fai file to build. # @param fngzi Name of .gzi file to build (if fn is bgzip-compressed). # @return 0 on success; or -1 on failure # If fnfai is NULL, ".fai" will be appended to fn to make the FAI file name. # If fngzi is NULL, ".gzi" will be appended to fn for the GZI file. The GZI # file will only be built if fn is bgzip-compressed. # */ int fai_build3(const char *fn, const char *fnfai, const char *fngzi) # /// Build index for a FASTA or bgzip-compressed FASTA file. # /** @param fn FASTA file name # @return 0 on success; or -1 on failure # # File "fn.fai" will be generated. This function is equivalent to # fai_build3(fn, NULL, NULL); # */ int fai_build(char *fn) # /// Destroy a faidx_t struct void fai_destroy(faidx_t *fai) # /// Load FASTA indexes. # /** @param fn File name of the FASTA file (can be compressed with bgzip). # @param fnfai File name of the FASTA index. # @param fngzi File name of the bgzip index. # @param flags Option flags to control index file caching and creation. # @return Pointer to a faidx_t struct on success, NULL on failure. # If fnfai is NULL, ".fai" will be appended to fn to make the FAI file name. # If fngzi is NULL, ".gzi" will be appended to fn for the bgzip index name. # The bgzip index is only needed if fn is compressed. # If (flags & FAI_CREATE) is true, the index files will be built using # fai_build3() if they are not already present. # */ faidx_t *fai_load3(const char *fn, const char *fnfai, const char *fngzi, int flags) # /// Load index from "fn.fai". # /** @param fn File name of the FASTA file # @return Pointer to a faidx_t struct on success, NULL on failure. # This function is equivalent to fai_load3(fn, NULL, NULL, FAI_CREATE|FAI_CACHE); # */ faidx_t *fai_load(char *fn) # /// Fetch the sequence in a region # /** @param fai Pointer to the faidx_t struct # @param reg Region in the format "chr2:20,000-30,000" # @param len Length of the region; -2 if seq not present, -1 general error # @return Pointer to the sequence; `NULL` on failure # The returned sequence is allocated by `malloc()` family and should be destroyed # by end users by calling `free()` on it. # */ char *fai_fetch(faidx_t *fai, char *reg, int *len) # /// Fetch the sequence in a region # /** @param fai Pointer to the faidx_t struct # @param c_name Region name # @param p_beg_i Beginning position number (zero-based) # @param p_end_i End position number (zero-based) # @param len Length of the region; -2 if c_name not present, -1 general error # @return Pointer to the sequence; null on failure # The returned sequence is allocated by `malloc()` family and should be destroyed # by end users by calling `free()` on it. # */ char *faidx_fetch_seq(faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len) # /// Query if sequence is present # /** @param fai Pointer to the faidx_t struct # @param seq Sequence name # @return 1 if present or 0 if absent # */ int faidx_has_seq(faidx_t *fai, const char *seq) # /// Fetch the number of sequences # /** @param fai Pointer to the faidx_t struct # @return The number of sequences # */ int faidx_nseq(const faidx_t *fai) # /// Return name of i-th sequence const char *faidx_iseq(const faidx_t *fai, int i) # /// Return sequence length, -1 if not present int faidx_seq_len(faidx_t *fai, const char *seq) # tabix support cdef extern from "htslib/tbx.h" nogil: # tbx.h definitions int8_t TBX_MAX_SHIFT int32_t TBX_GENERIC int32_t TBX_SAM int32_t TBX_VCF int32_t TBX_UCSC ctypedef struct tbx_conf_t: int32_t preset int32_t sc, bc, ec # seq col., beg col. and end col. int32_t meta_char, line_skip ctypedef struct tbx_t: tbx_conf_t conf hts_idx_t *idx void * dict tbx_conf_t tbx_conf_gff tbx_conf_t tbx_conf_bed tbx_conf_t tbx_conf_psltbl tbx_conf_t tbx_conf_sam tbx_conf_t tbx_conf_vcf void tbx_itr_destroy(hts_itr_t * iter) hts_itr_t * tbx_itr_queryi(tbx_t * t, int tid, int bed, int end) hts_itr_t * tbx_itr_querys(tbx_t * t, char * s) int tbx_itr_next(htsFile * fp, tbx_t * t, hts_itr_t * iter, void * data) int tbx_name2id(tbx_t *tbx, char *ss) int tbx_index_build(char *fn, int min_shift, tbx_conf_t *conf) int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf) tbx_t * tbx_index_load(char *fn) tbx_t *tbx_index_load2(const char *fn, const char *fnidx) tbx_t *tbx_index_load3(const char *fn, const char *fnidx, int flags) # free the array but not the values char **tbx_seqnames(tbx_t *tbx, int *n) void tbx_destroy(tbx_t *tbx) # VCF/BCF API cdef extern from "htslib/vcf.h" nogil: # Header struct uint8_t BCF_HL_FLT # header line uint8_t BCF_HL_INFO uint8_t BCF_HL_FMT uint8_t BCF_HL_CTG uint8_t BCF_HL_STR # structured header line TAG= uint8_t BCF_HL_GEN # generic header line uint8_t BCF_HT_FLAG # header type uint8_t BCF_HT_INT uint8_t BCF_HT_REAL uint8_t BCF_HT_STR uint8_t BCF_VL_FIXED # variable length uint8_t BCF_VL_VAR uint8_t BCF_VL_A uint8_t BCF_VL_G uint8_t BCF_VL_R # === Dictionary === # # The header keeps three dictionaries. The first keeps IDs in the # "FILTER/INFO/FORMAT" lines, the second keeps the sequence names and lengths # in the "contig" lines and the last keeps the sample names. bcf_hdr_t::dict[] # is the actual hash table, which is opaque to the end users. In the hash # table, the key is the ID or sample name as a C string and the value is a # bcf_idinfo_t struct. bcf_hdr_t::id[] points to key-value pairs in the hash # table in the order that they appear in the VCF header. bcf_hdr_t::n[] is the # size of the hash table or, equivalently, the length of the id[] arrays. uint8_t BCF_DT_ID # dictionary type uint8_t BCF_DT_CTG uint8_t BCF_DT_SAMPLE # Complete textual representation of a header line ctypedef struct bcf_hrec_t: int type # One of the BCF_HL_* type char *key # The part before '=', i.e. FILTER/INFO/FORMAT/contig/fileformat etc. char *value # Set only for generic lines, NULL for FILTER/INFO, etc. int nkeys # Number of structured fields char **keys # The key=value pairs char **vals ctypedef struct bcf_idinfo_t: uint32_t info[3] # stores Number:20, var:4, Type:4, ColType:4 in info[0..2] bcf_hrec_t *hrec[3] # for BCF_HL_FLT,INFO,FMT and contig length in info[0] for BCF_HL_CTG int id ctypedef struct bcf_idpair_t: const char *key const bcf_idinfo_t *val ctypedef struct bcf_hdr_t: int32_t n[3] # n:the size of the dictionary block in use, (allocated size, m, is below to preserve ABI) bcf_idpair_t *id[3] void *dict[3] # ID dictionary, contig dict and sample dict char **samples bcf_hrec_t **hrec int nhrec, dirty int ntransl int *transl[2] # for bcf_translate() int nsamples_ori # for bcf_hdr_set_samples() uint8_t *keep_samples kstring_t mem int32_t m[3] # m: allocated size of the dictionary block in use (see n above) uint8_t bcf_type_shift[] # * VCF record * uint8_t BCF_BT_NULL uint8_t BCF_BT_INT8 uint8_t BCF_BT_INT16 uint8_t BCF_BT_INT32 uint8_t BCF_BT_FLOAT uint8_t BCF_BT_CHAR uint8_t VCF_REF uint8_t VCF_SNP uint8_t VCF_MNP uint8_t VCF_INDEL uint8_t VCF_OTHER uint8_t VCF_BND uint8_t VCF_OVERLAP ctypedef struct variant_t: int type, n # variant type and the number of bases affected, negative for deletions ctypedef struct bcf_fmt_t: int id # id: numeric tag id, the corresponding string is bcf_hdr_t::id[BCF_DT_ID][$id].key int n, size, type # n: number of values per-sample; size: number of bytes per-sample; type: one of BCF_BT_* types uint8_t *p # same as vptr and vptr_* in bcf_info_t below uint32_t p_len uint32_t p_off uint8_t p_free union bcf_info_union_t: int32_t i # integer value float f # float value ctypedef struct bcf_info_t: int key # key: numeric tag id, the corresponding string is bcf_hdr_t::id[BCF_DT_ID][$key].key int type, len # type: one of BCF_BT_* types; len: vector length, 1 for scalars # v1 union only set if $len==1; for easier access bcf_info_union_t v1 uint8_t *vptr # pointer to data array in bcf1_t->shared.s, excluding the size+type and tag id bytes uint32_t vptr_len # length of the vptr block or, when set, of the vptr_mod block, excluding offset uint32_t vptr_off # vptr offset, i.e., the size of the INFO key plus size+type bytes uint8_t vptr_free # indicates that vptr-vptr_off must be freed; set only when modified and the new # data block is bigger than the original uint8_t BCF1_DIRTY_ID uint8_t BCF1_DIRTY_ALS uint8_t BCF1_DIRTY_FLT uint8_t BCF1_DIRTY_INF ctypedef struct bcf_dec_t: int m_fmt, m_info, m_id, m_als, m_allele, m_flt # allocated size (high-water mark); do not change int n_flt # Number of FILTER fields int *flt # FILTER keys in the dictionary char *id # ID char *als # REF+ALT block (\0-seperated) char **allele # allele[0] is the REF (allele[] pointers to the als block); all null terminated bcf_info_t *info # INFO bcf_fmt_t *fmt # FORMAT and individual sample variant_t *var # $var and $var_type set only when set_variant_types called int n_var, var_type int shared_dirty # if set, shared.s must be recreated on BCF output int indiv_dirty # if set, indiv.s must be recreated on BCF output uint8_t BCF_ERR_CTG_UNDEF uint8_t BCF_ERR_TAG_UNDEF uint8_t BCF_ERR_NCOLS uint8_t BCF_ERR_LIMITS uint8_t BCF_ERR_CHAR uint8_t BCF_ERR_CTG_INVALID uint8_t BCF_ERR_TAG_INVALID # The bcf1_t structure corresponds to one VCF/BCF line. Reading from VCF file # is slower because the string is first to be parsed, packed into BCF line # (done in vcf_parse), then unpacked into internal bcf1_t structure. If it # is known in advance that some of the fields will not be required (notably # the sample columns), parsing of these can be skipped by setting max_unpack # appropriately. # Similarly, it is fast to output a BCF line because the columns (kept in # shared.s, indiv.s, etc.) are written directly by bcf_write, whereas a VCF # line must be formatted in vcf_format. ctypedef struct bcf1_t: int32_t rid # CHROM int32_t pos # POS int32_t rlen # length of REF float qual # QUAL uint32_t n_info, n_allele uint32_t n_fmt, n_sample kstring_t shared, indiv bcf_dec_t d # lazy evaluation: $d is not generated by bcf_read(), but by explicitly calling bcf_unpack() int max_unpack # Set to BCF_UN_STR, BCF_UN_FLT, or BCF_UN_INFO to boost performance of vcf_parse when some of the fields won't be needed int unpacked # remember what has been unpacked to allow calling bcf_unpack() repeatedly without redoing the work int unpack_size[3] # the original block size of ID, REF+ALT and FILTER int errcode # one of BCF_ERR_* codes ####### API ####### # BCF and VCF I/O # # A note about naming conventions: htslib internally represents VCF # records as bcf1_t data structures, therefore most functions are # prefixed with bcf_. There are a few exceptions where the functions must # be aware of both BCF and VCF worlds, such as bcf_parse vs vcf_parse. In # these cases, functions prefixed with bcf_ are more general and work # with both BCF and VCF. # bcf_hdr_init() - create an empty BCF header. # @param mode "r" or "w" # # When opened for writing, the mandatory fileFormat and # FILTER=PASS lines are added automatically. bcf_hdr_t *bcf_hdr_init(const char *mode) # Destroy a BCF header struct void bcf_hdr_destroy(bcf_hdr_t *h) # Initialize a bcf1_t object; equivalent to calloc(1, sizeof(bcf1_t)) bcf1_t *bcf_init() # Deallocate a bcf1_t object void bcf_destroy(bcf1_t *v) # Same as bcf_destroy() but frees only the memory allocated by bcf1_t, # not the bcf1_t object itself. void bcf_empty(bcf1_t *v) # Make the bcf1_t object ready for next read. Intended mostly for # internal use, the user should rarely need to call this function # directly. void bcf_clear(bcf1_t *v) # Reads VCF or BCF header bcf_hdr_t *bcf_hdr_read(htsFile *fp) # bcf_hdr_set_samples() - for more efficient VCF parsing when only one/few samples are needed # @samples: samples to include or exclude from file or as a comma-separated string. # LIST|FILE .. select samples in list/file # ^LIST|FILE .. exclude samples from list/file # - .. include all samples # NULL .. exclude all samples # @is_file: @samples is a file (1) or a comma-separated list (0) # # The bottleneck of VCF reading is parsing of genotype fields. If the # reader knows in advance that only subset of samples is needed (possibly # no samples at all), the performance of bcf_read() can be significantly # improved by calling bcf_hdr_set_samples after bcf_hdr_read(). # The function bcf_read() will subset the VCF/BCF records automatically # with the notable exception when reading records via bcf_itr_next(). # In this case, bcf_subset_format() must be called explicitly, because # bcf_readrec() does not see the header. # # Returns 0 on success, -1 on error or a positive integer if the list # contains samples not present in the VCF header. In such a case, the # return value is the index of the offending sample. # int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file) int bcf_subset_format(const bcf_hdr_t *hdr, bcf1_t *rec) # Writes VCF or BCF header int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h) # Parse VCF line contained in kstring and populate the bcf1_t struct int vcf_parse(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v) # The opposite of vcf_parse. It should rarely be called directly, see vcf_write int vcf_format(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s) # bcf_read() - read next VCF or BCF record # # Returns -1 on critical errors, 0 otherwise. On errors which are not # critical for reading, such as missing header definitions, v->errcode is # set to one of BCF_ERR* code and must be checked before calling # vcf_write(). int bcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) # bcf_unpack() - unpack/decode a BCF record (fills the bcf1_t::d field) # # Note that bcf_unpack() must be called even when reading VCF. It is safe # to call the function repeatedly, it will not unpack the same field # twice. uint8_t BCF_UN_STR # up to ALT inclusive uint8_t BCF_UN_FLT # up to FILTER uint8_t BCF_UN_INFO # up to INFO uint8_t BCF_UN_SHR # all shared information uint8_t BCF_UN_FMT # unpack format and each sample uint8_t BCF_UN_IND # a synonymo of BCF_UN_FMT uint8_t BCF_UN_ALL # everything int bcf_unpack(bcf1_t *b, int which) # bcf_dup() - create a copy of BCF record. # # Note that bcf_unpack() must be called on the returned copy as if it was # obtained from bcf_read(). Also note that bcf_dup() calls bcf_sync1(src) # internally to reflect any changes made by bcf_update_* functions. bcf1_t *bcf_dup(bcf1_t *src) bcf1_t *bcf_copy(bcf1_t *dst, bcf1_t *src) # bcf_write() - write one VCF or BCF record. The type is determined at the open() call. int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v) # The following functions work only with VCFs and should rarely be called # directly. Usually one wants to use their bcf_* alternatives, which work # transparently with both VCFs and BCFs. bcf_hdr_t *vcf_hdr_read(htsFile *fp) int vcf_hdr_write(htsFile *fp, const bcf_hdr_t *h) int vcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) int vcf_write(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) #************************************************************************ # Header querying and manipulation routines #************************************************************************ # Create a new header using the supplied template bcf_hdr_t *bcf_hdr_dup(const bcf_hdr_t *hdr) # Copy header lines from src to dst if not already present in dst. See also bcf_translate(). # Returns 0 on success or sets a bit on error: # 1 .. conflicting definitions of tag length # # todo int bcf_hdr_combine(bcf_hdr_t *dst, const bcf_hdr_t *src) # bcf_hdr_merge() - copy header lines from src to dst, see also bcf_translate() # @param dst: the destination header to be merged into, NULL on the first pass # @param src: the source header # # Notes: # - use as: # bcf_hdr_t *dst = NULL; # for (i=0; i 0 ) # for (i=0; i=0 # # The returned values are: # bcf_hdr_id2length .. whether the number of values is fixed or variable, one of BCF_VL_* # bcf_hdr_id2number .. the number of values, 0xfffff for variable length fields # bcf_hdr_id2type .. the field type, one of BCF_HT_* # bcf_hdr_id2coltype .. the column type, one of BCF_HL_* # # Notes: Prior to using the macros, the presence of the info should be # tested with bcf_hdr_idinfo_exists(). # int bcf_hdr_id2length(const bcf_hdr_t *hdr, int type, int int_id) int bcf_hdr_id2number(const bcf_hdr_t *hdr, int type, int int_id) int bcf_hdr_id2type(const bcf_hdr_t *hdr, int type, int int_id) int bcf_hdr_id2coltype(const bcf_hdr_t *hdr, int type, int int_id) int bcf_hdr_idinfo_exists(const bcf_hdr_t *hdr, int type, int int_id) bcf_hrec_t *bcf_hdr_id2hrec(const bcf_hdr_t *hdr, int type, int col_type, int int_id) void bcf_fmt_array(kstring_t *s, int n, int type, void *data) uint8_t *bcf_fmt_sized_array(kstring_t *s, uint8_t *ptr) void bcf_enc_vchar(kstring_t *s, int l, const char *a) void bcf_enc_vint(kstring_t *s, int n, int32_t *a, int wsize) void bcf_enc_vfloat(kstring_t *s, int n, float *a) #************************************************************************ # BCF index # # Note that these functions work with BCFs only. See synced_bcf_reader.h # which provides (amongst other things) an API to work transparently with # both indexed BCFs and VCFs. #************************************************************************ hts_idx_t *bcf_index_load2(const char *fn, const char *fnidx) hts_idx_t *bcf_index_load3(const char *fn, const char *fnidx, int flags) int bcf_index_build(const char *fn, int min_shift) int bcf_index_build2(const char *fn, const char *fnidx, int min_shift) #******************* # Typed value I/O * #****************** # Note that in contrast with BCFv2.1 specification, HTSlib implementation # allows missing values in vectors. For integer types, the values 0x80, # 0x8000, 0x80000000 are interpreted as missing values and 0x81, 0x8001, # 0x80000001 as end-of-vector indicators. Similarly for floats, the value of # 0x7F800001 is interpreted as a missing value and 0x7F800002 as an # end-of-vector indicator. # Note that the end-of-vector byte is not part of the vector. # This trial BCF version (v2.2) is compatible with the VCF specification and # enables to handle correctly vectors with different ploidy in presence of # missing values. int32_t bcf_int8_vector_end int32_t bcf_int16_vector_end int32_t bcf_int32_vector_end int32_t bcf_str_vector_end int32_t bcf_int8_missing int32_t bcf_int16_missing int32_t bcf_int32_missing int32_t bcf_str_missing uint32_t bcf_float_vector_end uint32_t bcf_float_missing void bcf_float_set(float *ptr, uint32_t value) void bcf_float_set_vector_end(float *x) void bcf_float_set_missing(float *x) int bcf_float_is_missing(float f) int bcf_float_is_vector_end(float f) void bcf_format_gt(bcf_fmt_t *fmt, int isample, kstring_t *str) void bcf_enc_size(kstring_t *s, int size, int type) int bcf_enc_inttype(long x) void bcf_enc_int1(kstring_t *s, int32_t x) int32_t bcf_dec_int1(const uint8_t *p, int type, uint8_t **q) int32_t bcf_dec_typed_int1(const uint8_t *p, uint8_t **q) int32_t bcf_dec_size(const uint8_t *p, uint8_t **q, int *type) # These trivial wrappers are defined only for consistency with other parts of htslib bcf1_t *bcf_init1() int bcf_read1(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) int vcf_read1(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) int bcf_write1(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) int vcf_write1(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) void bcf_destroy1(bcf1_t *v) void bcf_empty1(bcf1_t *v) int vcf_parse1(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v) void bcf_clear1(bcf1_t *v) int vcf_format1(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s) # Other nice wrappers void bcf_itr_destroy(hts_itr_t *iter) hts_itr_t *bcf_itr_queryi(const hts_idx_t *idx, int tid, int beg, int end) hts_itr_t *bcf_itr_querys(const hts_idx_t *idx, const bcf_hdr_t *hdr, char *s) int bcf_itr_next(htsFile *fp, hts_itr_t *iter, void *r) hts_idx_t *bcf_index_load(const char *fn) const char **bcf_index_seqnames(const hts_idx_t *idx, const bcf_hdr_t *hdr, int *nptr) # VCF/BCF utility functions cdef extern from "htslib/vcfutils.h" nogil: struct kbitset_t # bcf_trim_alleles() - remove ALT alleles unused in genotype fields # @header: for access to BCF_DT_ID dictionary # @line: VCF line obtain from vcf_parse1 # # Returns the number of removed alleles on success or negative # on error: # -1 .. some allele index is out of bounds int bcf_trim_alleles(const bcf_hdr_t *header, bcf1_t *line) # bcf_remove_alleles() - remove ALT alleles according to bitmask @mask # @header: for access to BCF_DT_ID dictionary # @line: VCF line obtained from vcf_parse1 # @mask: alleles to remove # # If you have more than 31 alleles, then the integer bit mask will # overflow, so use bcf_remove_allele_set instead void bcf_remove_alleles(const bcf_hdr_t *header, bcf1_t *line, int mask) # bcf_remove_allele_set() - remove ALT alleles according to bitset @rm_set # @header: for access to BCF_DT_ID dictionary # @line: VCF line obtained from vcf_parse1 # @rm_set: pointer to kbitset_t object with bits set for allele # indexes to remove # # Number=A,R,G INFO and FORMAT fields will be updated accordingly. void bcf_remove_allele_set(const bcf_hdr_t *header, bcf1_t *line, kbitset_t *rm_set) # bcf_calc_ac() - calculate the number of REF and ALT alleles # @header: for access to BCF_DT_ID dictionary # @line: VCF line obtained from vcf_parse1 # @ac: array of length line->n_allele # @which: determine if INFO/AN,AC and indv fields be used # # Returns 1 if the call succeeded, or 0 if the value could not # be determined. # # The value of @which determines if existing INFO/AC,AN can be # used (BCF_UN_INFO) and and if indv fields can be split (BCF_UN_FMT). int bcf_calc_ac(const bcf_hdr_t *header, bcf1_t *line, int *ac, int which) # bcf_gt_type() - determines type of the genotype # @fmt_ptr: the GT format field as set for example by set_fmt_ptr # @isample: sample index (starting from 0) # @ial: index of the 1st non-reference allele (starting from 1) # @jal: index of the 2nd non-reference allele (starting from 1) # # Returns the type of the genotype (one of GT_HOM_RR, GT_HET_RA, # GT_HOM_AA, GT_HET_AA, GT_HAPL_R, GT_HAPL_A or GT_UNKN). If $ial # is not NULL and the genotype has one or more non-reference # alleles, $ial will be set. In case of GT_HET_AA, $ial is the # position of the allele which appeared first in ALT. If $jal is # not null and the genotype is GT_HET_AA, $jal will be set and is # the position of the second allele in ALT. uint8_t GT_HOM_RR # note: the actual value of GT_* matters, used in dosage r2 calculation uint8_t GT_HOM_AA uint8_t GT_HET_RA uint8_t GT_HET_AA uint8_t GT_HAPL_R uint8_t GT_HAPL_A uint8_t GT_UNKN int bcf_gt_type(bcf_fmt_t *fmt_ptr, int isample, int *ial, int *jal) int bcf_acgt2int(char c) char bcf_int2acgt(int i) # bcf_ij2G() - common task: allele indexes to Number=G index (diploid) # @i,j: allele indexes, 0-based, i<=j # Returns index to the Number=G diploid array uint32_t bcf_ij2G(uint32_t i, uint32_t j) cdef extern from "htslib/cram.h" nogil: enum cram_block_method: ERROR RAW GZIP BZIP2 LZMA RANS RANS0 RANS1 GZIP_RLE enum cram_content_type: CT_ERROR FILE_HEADER COMPRESSION_HEADER MAPPED_SLICE UNMAPPED_SLICE EXTERNAL CORE # Opaque data types, see cram_structs for the fully fledged versions. ctypedef struct SAM_hdr ctypedef struct cram_file_def ctypedef struct cram_fd ctypedef struct cram_container ctypedef struct cram_block ctypedef struct cram_slice ctypedef struct cram_metrics ctypedef struct cram_block_slice_hdr ctypedef struct cram_block_compression_hdr ctypedef struct refs_t # Accessor functions # #----------------------------------------------------------------------------- # cram_fd # SAM_hdr *cram_fd_get_header(cram_fd *fd) void cram_fd_set_header(cram_fd *fd, SAM_hdr *hdr) int cram_fd_get_version(cram_fd *fd) void cram_fd_set_version(cram_fd *fd, int vers) int cram_major_vers(cram_fd *fd) int cram_minor_vers(cram_fd *fd) hFILE *cram_fd_get_fp(cram_fd *fd) void cram_fd_set_fp(cram_fd *fd, hFILE *fp) # #----------------------------------------------------------------------------- # cram_container # int32_t cram_container_get_length(cram_container *c) void cram_container_set_length(cram_container *c, int32_t length) int32_t cram_container_get_num_blocks(cram_container *c) void cram_container_set_num_blocks(cram_container *c, int32_t num_blocks) int32_t *cram_container_get_landmarks(cram_container *c, int32_t *num_landmarks) void cram_container_set_landmarks(cram_container *c, int32_t num_landmarks, int32_t *landmarks) # Returns true if the container is empty (EOF marker) */ int cram_container_is_empty(cram_fd *fd) # #----------------------------------------------------------------------------- # cram_block # int32_t cram_block_get_content_id(cram_block *b) int32_t cram_block_get_comp_size(cram_block *b) int32_t cram_block_get_uncomp_size(cram_block *b) int32_t cram_block_get_crc32(cram_block *b) void * cram_block_get_data(cram_block *b) cram_content_type cram_block_get_content_type(cram_block *b) void cram_block_set_content_id(cram_block *b, int32_t id) void cram_block_set_comp_size(cram_block *b, int32_t size) void cram_block_set_uncomp_size(cram_block *b, int32_t size) void cram_block_set_crc32(cram_block *b, int32_t crc) void cram_block_set_data(cram_block *b, void *data) int cram_block_append(cram_block *b, void *data, int size) void cram_block_update_size(cram_block *b) # Offset is known as "size" internally, but it can be confusing. size_t cram_block_get_offset(cram_block *b) void cram_block_set_offset(cram_block *b, size_t offset) # # Computes the size of a cram block, including the block # header itself. # uint32_t cram_block_size(cram_block *b) # # Renumbers RG numbers in a cram compression header. # # CRAM stores RG as the Nth number in the header, rather than a # string holding the ID: tag. This is smaller in space, but means # "samtools cat" to join files together that contain single but # different RG lines needs a way of renumbering them. # # The file descriptor is expected to be immediately after the # cram_container structure (ie before the cram compression header). # Due to the nature of the CRAM format, this needs to read and write # the blocks itself. Note that there may be multiple slices within # the container, meaning multiple compression headers to manipulate. # Changing RG may change the size of the compression header and # therefore the length field in the container. Hence we rewrite all # blocks just in case and also emit the adjusted container. # # The current implementation can only cope with renumbering a single # RG (and only then if it is using HUFFMAN or BETA codecs). In # theory it *may* be possible to renumber multiple RGs if they use # HUFFMAN to the CORE block or use an external block unshared by any # other data series. So we have an API that can be upgraded to # support this, but do not implement it for now. An example # implementation of RG as an EXTERNAL block would be to find that # block and rewrite it, returning the number of blocks consumed. # # Returns 0 on success; # -1 if unable to edit; # -2 on other errors (eg I/O). # int cram_transcode_rg(cram_fd *input, cram_fd *output, cram_container *c, int nrg, int *in_rg, int *out_rg) # # Copies the blocks representing the next num_slice slices from a # container from 'in' to 'out'. It is expected that the file pointer # is just after the read of the cram_container and cram compression # header. # # Returns 0 on success # -1 on failure # int cram_copy_slice(cram_fd *input, cram_fd *output, int32_t num_slice) # #----------------------------------------------------------------------------- # SAM_hdr # # Tokenises a SAM header into a hash table. # # Also extracts a few bits on specific data types, such as @RG lines. # # @return # Returns a SAM_hdr struct on success (free with sam_hdr_free()) # NULL on failure # SAM_hdr *sam_hdr_parse_(const char *hdr, int len) # #----------------------------------------------------------------------------- # cram_io basics # # CRAM blocks - the dynamically growable data block. We have code to # create, update, (un)compress and read/write. # # These are derived from the deflate_interlaced.c blocks, but with the # CRAM extension of content types and IDs. # # Allocates a new cram_block structure with a specified content_type and # id. # # @return # Returns block pointer on success; # NULL on failure # cram_block *cram_new_block(cram_content_type content_type, int content_id) # Reads a block from a cram file. # # @return # Returns cram_block pointer on success; # NULL on failure # cram_block *cram_read_block(cram_fd *fd) # Writes a CRAM block. # # @return # Returns 0 on success; # -1 on failure # int cram_write_block(cram_fd *fd, cram_block *b) # Frees a CRAM block, deallocating internal data too. # void cram_free_block(cram_block *b) # Uncompresses a CRAM block, if compressed. # # @return # Returns 0 on success; # -1 on failure # int cram_uncompress_block(cram_block *b) # Compresses a block. # # Compresses a block using one of two different zlib strategies. If we only # want one choice set strat2 to be -1. # # The logic here is that sometimes Z_RLE does a better job than Z_FILTERED # or Z_DEFAULT_STRATEGY on quality data. If so, we'd rather use it as it is # significantly faster. # # @return # Returns 0 on success; # -1 on failure # int cram_compress_block(cram_fd *fd, cram_block *b, cram_metrics *metrics, int method, int level) # Containers # # Creates a new container, specifying the maximum number of slices # and records permitted. # # @return # Returns cram_container ptr on success; # NULL on failure # cram_container *cram_new_container(int nrec, int nslice) void cram_free_container(cram_container *c) # Reads a container header. # # @return # Returns cram_container on success; # NULL on failure or no container left (fd->err == 0). # cram_container *cram_read_container(cram_fd *fd) # Writes a container structure. # # @return # Returns 0 on success; # -1 on failure # int cram_write_container(cram_fd *fd, cram_container *h) # # Stores the container structure in dat and returns *size as the # number of bytes written to dat[]. The input size of dat is also # held in *size and should be initialised to cram_container_size(c). # # Returns 0 on success; # -1 on failure # int cram_store_container(cram_fd *fd, cram_container *c, char *dat, int *size) int cram_container_size(cram_container *c) # The top-level cram opening, closing and option handling # # Opens a CRAM file for read (mode "rb") or write ("wb"). # # The filename may be "-" to indicate stdin or stdout. # # @return # Returns file handle on success; # NULL on failure. # cram_fd *cram_open(const char *filename, const char *mode) # Opens an existing stream for reading or writing. # # @return # Returns file handle on success; # NULL on failure. # cram_fd *cram_dopen(hFILE *fp, const char *filename, const char *mode) # Closes a CRAM file. # # @return # Returns 0 on success; # -1 on failure # int cram_close(cram_fd *fd) # # Seek within a CRAM file. # # Returns 0 on success # -1 on failure # int cram_seek(cram_fd *fd, off_t offset, int whence) # # Flushes a CRAM file. # Useful for when writing to stdout without wishing to close the stream. # # Returns 0 on success # -1 on failure # int cram_flush(cram_fd *fd) # Checks for end of file on a cram_fd stream. # # @return # Returns 0 if not at end of file # 1 if we hit an expected EOF (end of range or EOF block) # 2 for other EOF (end of stream without EOF block) # int cram_eof(cram_fd *fd) # Sets options on the cram_fd. # # See CRAM_OPT_* definitions in hts.h. # Use this immediately after opening. # # @return # Returns 0 on success; # -1 on failure # int cram_set_option(cram_fd *fd, hts_fmt_option opt, ...) # Sets options on the cram_fd. # # See CRAM_OPT_* definitions in hts.h. # Use this immediately after opening. # # @return # Returns 0 on success; # -1 on failure # int cram_set_voption(cram_fd *fd, hts_fmt_option opt, va_list args) # # Attaches a header to a cram_fd. # # This should be used when creating a new cram_fd for writing where # we have an SAM_hdr already constructed (eg from a file we've read # in). # # @return # Returns 0 on success; # -1 on failure # int cram_set_header(cram_fd *fd, SAM_hdr *hdr) # Check if this file has a proper EOF block # # @return # Returns 3 if the file is a version of CRAM that does not contain EOF blocks # 2 if the file is a stream and thus unseekable # 1 if the file contains an EOF block # 0 if the file does not contain an EOF block # -1 if an error occurred whilst reading the file or we could not seek back to where we were # # int cram_check_EOF(cram_fd *fd) # As int32_decoded/encode, but from/to blocks instead of cram_fd */ int int32_put_blk(cram_block *b, int32_t val) # Deallocates all storage used by a SAM_hdr struct. # # This also decrements the header reference count. If after decrementing # it is still non-zero then the header is assumed to be in use by another # caller and the free is not done. # # This is a synonym for sam_hdr_dec_ref(). # void sam_hdr_free(SAM_hdr *hdr) # Returns the current length of the SAM_hdr in text form. # # Call sam_hdr_rebuild() first if editing has taken place. # int sam_hdr_length(SAM_hdr *hdr) # Returns the string form of the SAM_hdr. # # Call sam_hdr_rebuild() first if editing has taken place. # char *sam_hdr_str(SAM_hdr *hdr) # Appends a formatted line to an existing SAM header. # # Line is a full SAM header record, eg "@SQ\tSN:foo\tLN:100", with # optional new-line. If it contains more than 1 line then multiple lines # will be added in order. # # Len is the length of the text data, or 0 if unknown (in which case # it should be null terminated). # # @return # Returns 0 on success; # -1 on failure # # Add an @PG line. # # If we wish complete control over this use sam_hdr_add() directly. This # function uses that, but attempts to do a lot of tedious house work for # you too. # # - It will generate a suitable ID if the supplied one clashes. # - It will generate multiple @PG records if we have multiple PG chains. # # Call it as per sam_hdr_add() with a series of key,value pairs ending # in NULL. # # @return # Returns 0 on success; # -1 on failure # int sam_hdr_add_PG(SAM_hdr *sh, const char *name, ...) # # A function to help with construction of CL tags in @PG records. # Takes an argc, argv pair and returns a single space-separated string. # This string should be deallocated by the calling function. # # @return # Returns malloced char * on success; # NULL on failure # char *stringify_argv(int argc, char *argv[]) # # Returns the refs_t structure used by a cram file handle. # # This may be used in conjunction with option CRAM_OPT_SHARED_REF to # share reference memory between multiple file handles. # # @return # Returns NULL if none exists or the file handle is not a CRAM file. # refs_t *cram_get_refs(htsFile *fd) cdef class HTSFile(object): cdef htsFile *htsfile # pointer to htsFile structure cdef int64_t start_offset # BGZF offset of first record cdef readonly object filename # filename as supplied by user cdef readonly object mode # file opening mode cdef readonly object threads # number of threads to use cdef readonly object index_filename # filename of index, if supplied by user cdef readonly bint is_stream # Is htsfile a non-seekable stream cdef readonly bint is_remote # Is htsfile a remote stream cdef readonly bint duplicate_filehandle # Duplicate filehandle when opening via fh cdef htsFile *_open_htsfile(self) except? NULL pysam-0.23.0/pysam/libchtslib.pyi000066400000000000000000000071641475062545500167450ustar00rootroot00000000000000import sys from typing import List, Union, NoReturn, Iterable, Any, Tuple, Optional, TypeVar if sys.version_info < (3, 8): from typing_extensions import Protocol else: from typing import Protocol class _HasFileNo(Protocol): def fileno(self) -> int: ... def get_verbosity() -> int: ... def set_verbosity(level: int): ... THFile = TypeVar("THFile", bound="HFile") class HFile: def __init__(self, name: Union[int, str], mode: str = ...) -> None: ... def __enter__(self: THFile) -> THFile: ... def __exit__(self, type, value, tb): ... def __iter__(self) -> Any: ... def __next__(self) -> str: ... @property def closed(self) -> bool: ... @property def mode(self) -> str: ... @property def name(self) -> Union[int, str]: ... def close(self) -> None: ... def fileno(self) -> int: ... def flush(self) -> None: ... def isatty(self) -> bool: ... def readable(self) -> bool: ... def read(self, size: int = ...) -> bytes: ... def readall(self) -> bytes: ... def readinto(self, buf: Any) -> bytes: ... def readline(self, size: int = ...) -> bytes: ... def readlines(self) -> List[bytes]: ... def seek(self, offset: int, whence: int = ...) -> int: ... def seekable(self) -> bool: ... def tell(self) -> int: ... def truncate(self, *args) -> NoReturn: ... def writable(self) -> bool: ... def write(self, b: bytes) -> int: ... def writelines(self, lines: Iterable[bytes]) -> None: ... THTSFile = TypeVar("THTSFile", bound="HTSFile") class HTSFile: def __enter__(self: THTSFile) -> THTSFile: ... def __exit__(self, type, value, traceback) -> Any: ... @property def filename(self) -> Any: ... @property def mode(self) -> str: ... @property def threads(self) -> int: ... @property def index_filename(self) -> Optional[str]: ... @property def is_stream(self) -> bool: ... @property def is_remote(self) -> bool: ... @property def duplicate_filehandle(self) -> bool: ... def close(self) -> None: ... def flush(self) -> None: ... def check_truncation(self, ignore_truncation: bool = ...) -> None: ... @property def category(self) -> str: ... @property def format(self) -> str: ... @property def version(self) -> Tuple[int, int]: ... @property def compression(self) -> str: ... @property def description(self) -> str: ... @property def is_open(self) -> bool: ... @property def is_closed(self) -> bool: ... @property def closed(self) -> bool: ... @property def is_write(self) -> bool: ... @property def is_read(self) -> bool: ... @property def is_sam(self) -> bool: ... @property def is_bam(self) -> bool: ... @property def is_cram(self) -> bool: ... @property def is_vcf(self) -> bool: ... @property def is_bcf(self) -> bool: ... def reset(self) -> None: ... def seek(self, offset: int, whence: int = ...) -> int: ... def tell(self) -> int: ... def add_hts_options(self, format_options: Optional[List[str]] = ...) -> None: ... def parse_region( self, contig: Optional[str] = ..., start: Optional[int] = ..., stop: Optional[int] = ..., region: Optional[str] = ..., tid: Optional[int] = ..., reference: Optional[str] = ..., end: Optional[int] = ..., ) -> Tuple[int, int, int, int]: ... def is_valid_tid(self, tid: int) -> bool: ... def is_valid_reference_name(self, contig: str) -> bool: ... def get_tid(self, contig: str) -> int: ... def get_reference_name(self, tid: int) -> Optional[str]: ... pysam-0.23.0/pysam/libchtslib.pyx000066400000000000000000000545001475062545500167600ustar00rootroot00000000000000# cython: language_level=3 # cython: embedsignature=True # cython: profile=True # adds doc-strings for sphinx ######################################################################## ######################################################################## ## Cython cimports ######################################################################## from posix.unistd cimport dup from libc.errno cimport errno from libc.stdint cimport INT32_MAX from cpython cimport PyBytes_FromStringAndSize from pysam.libchtslib cimport * from pysam.libcutils cimport force_bytes, force_str, charptr_to_str, charptr_to_str_w_len from pysam.libcutils cimport encode_filename, from_string_and_size, libc_whence_from_io ######################################################################## ######################################################################## ## Python imports ######################################################################## import os import io import re from warnings import warn ######################################################################## ######################################################################## ## Constants ######################################################################## __all__ = ['get_verbosity', 'set_verbosity', 'HFile', 'HTSFile'] # maximum genomic coordinace cdef int MAX_POS = (1 << 31) - 1 cdef tuple FORMAT_CATEGORIES = ('UNKNOWN', 'ALIGNMENTS', 'VARIANTS', 'INDEX', 'REGIONS') cdef tuple FORMATS = ('UNKNOWN', 'BINARY_FORMAT', 'TEXT_FORMAT', 'SAM', 'BAM', 'BAI', 'CRAM', 'CRAI', 'VCF', 'BCF', 'CSI', 'GZI', 'TBI', 'BED') cdef tuple COMPRESSION = ('NONE', 'GZIP', 'BGZF', 'CUSTOM') ######################################################################## ######################################################################## ## Verbosity functions ######################################################################## cpdef set_verbosity(int verbosity): """Set htslib's hts_verbose global variable to the specified value.""" return hts_set_verbosity(verbosity) cpdef get_verbosity(): """Return the value of htslib's hts_verbose global variable.""" return hts_get_verbosity() ######################################################################## ######################################################################## ## HFile wrapper class ######################################################################## cdef class HFile(object): cdef hFILE *fp cdef readonly object name, mode def __init__(self, name, mode='r', closefd=True): self._open(name, mode, closefd=True) def __dealloc__(self): self.close() @property def closed(self): return self.fp == NULL cdef _open(self, name, mode, closefd=True): self.name = name self.mode = mode mode = force_bytes(mode) if isinstance(name, int): if self.fp != NULL: name = dup(name) self.fp = hdopen(name, mode) else: name = encode_filename(name) self.fp = hopen(name, mode) if not self.fp: raise IOError(errno, 'failed to open HFile', self.name) def close(self): if self.fp == NULL: return cdef hFILE *fp = self.fp self.fp = NULL if hclose(fp) != 0: raise IOError(errno, 'failed to close HFile', self.name) def fileno(self): if self.fp == NULL: raise IOError('operation on closed HFile') if isinstance(self.name, int): return self.name else: raise AttributeError('fileno not available') def __enter__(self): return self def __exit__(self, type, value, tb): self.close() def __iter__(self): return self def __next__(self): line = self.readline() if not line: raise StopIteration() return line def flush(self): if self.fp == NULL: raise IOError('operation on closed HFile') if hflush(self.fp) != 0: raise IOError(herrno(self.fp), 'failed to flush HFile', self.name) def isatty(self): if self.fp == NULL: raise IOError('operation on closed HFile') return False def readable(self): return self.fp != NULL and 'r' in self.mode def read(self, Py_ssize_t size=-1): if self.fp == NULL: raise IOError('operation on closed HFile') if size == 0: return b'' cdef list parts = [] cdef bytes part cdef Py_ssize_t chunk_size, ret, bytes_read = 0 cdef char *cpart while size == -1 or bytes_read < size: chunk_size = 4096 if size != -1: chunk_size = min(chunk_size, size - bytes_read) part = PyBytes_FromStringAndSize(NULL, chunk_size) cpart = part ret = hread(self.fp, cpart, chunk_size) if ret < 0: IOError(herrno(self.fp), 'failed to read HFile', self.name) elif not ret: break bytes_read += ret if ret < chunk_size: part = cpart[:ret] parts.append(part) return b''.join(parts) def readall(self): return self.read() def readinto(self, buf): if self.fp == NULL: raise IOError('operation on closed HFile') size = len(buf) if size == 0: return size mv = memoryview(buf) ret = hread(self.fp, mv, size) if ret < 0: IOError(herrno(self.fp), 'failed to read HFile', self.name) return ret def readline(self, Py_ssize_t size=-1): if self.fp == NULL: raise IOError('operation on closed HFile') if size == 0: return b'' cdef list parts = [] cdef bytes part cdef Py_ssize_t chunk_size, ret, bytes_read = 0 cdef char *cpart while size == -1 or bytes_read < size: chunk_size = 4096 if size != -1: chunk_size = min(chunk_size, size - bytes_read) part = PyBytes_FromStringAndSize(NULL, chunk_size) cpart = part # Python bytes objects allocate an extra byte for a null terminator ret = hgetln(cpart, chunk_size+1, self.fp) if ret < 0: IOError(herrno(self.fp), 'failed to read HFile', self.name) elif not ret: break bytes_read += ret if ret < chunk_size: part = cpart[:ret] cpart = part parts.append(part) if cpart[ret-1] == b'\n': break return b''.join(parts) def readlines(self): return list(self) def seek(self, Py_ssize_t offset, int whence=io.SEEK_SET): if self.fp == NULL: raise IOError('operation on closed HFile') cdef Py_ssize_t off = hseek(self.fp, offset, libc_whence_from_io(whence)) if off < 0: raise IOError(herrno(self.fp), 'seek failed on HFile', self.name) return off def tell(self): if self.fp == NULL: raise IOError('operation on closed HFile') ret = htell(self.fp) if ret < 0: raise IOError(herrno(self.fp), 'tell failed on HFile', self.name) return ret def seekable(self): return self.fp != NULL def truncate(self, size=None): raise NotImplementedError() def writable(self): return self.fp != NULL and 'w' in self.mode def write(self, bytes b): if self.fp == NULL: raise IOError('operation on closed HFile') got = hwrite(self.fp, b, len(b)) if got < 0: raise IOError(herrno(self.fp), 'write failed on HFile', self.name) return got def writelines(self, lines): for line in lines: self.write(line) ######################################################################## ######################################################################## ## Helpers for backward compatibility to hide the difference between ## boolean properties and methods ######################################################################## class CallableValue(object): def __init__(self, value): self.value = value def __call__(self): return self.value def __bool__(self): return self.value def __nonzero__(self): return self.value def __eq__(self, other): return self.value == other def __ne__(self, other): return self.value != other CTrue = CallableValue(True) CFalse = CallableValue(False) ######################################################################## ######################################################################## ## HTSFile wrapper class (base class for AlignmentFile and VariantFile) ######################################################################## cdef class HTSFile(object): """ Base class for HTS file types """ def __cinit__(self, *args, **kwargs): self.htsfile = NULL self.threads = 1 self.duplicate_filehandle = True def close(self): if self.htsfile: hts_close(self.htsfile) self.htsfile = NULL def __dealloc__(self): if self.htsfile: hts_close(self.htsfile) self.htsfile = NULL def flush(self): """Flush any buffered data to the underlying output stream.""" if self.htsfile: if hts_flush(self.htsfile) < 0: raise OSError(errno, f'Flushing {type(self).__name__} failed', force_str(self.filename)) def check_truncation(self, ignore_truncation=False): """Check if file is truncated.""" if not self.htsfile: return if self.htsfile.format.compression != bgzf: return cdef BGZF *bgzfp = hts_get_bgzfp(self.htsfile) if not bgzfp: return cdef int ret = bgzf_check_EOF(bgzfp) if ret < 0: raise IOError(errno, 'error checking for EOF marker') elif ret == 0: msg = 'no BGZF EOF marker; file may be truncated'.format(self.filename) if ignore_truncation: warn(msg) else: raise IOError(msg) def __enter__(self): return self def __exit__(self, exc_type, exc_value, traceback): self.close() return False @property def category(self): """General file format category. One of UNKNOWN, ALIGNMENTS, VARIANTS, INDEX, REGIONS""" if not self.htsfile: raise ValueError('metadata not available on closed file') return FORMAT_CATEGORIES[self.htsfile.format.category] @property def format(self): """File format. One of UNKNOWN, BINARY_FORMAT, TEXT_FORMAT, SAM, BAM, BAI, CRAM, CRAI, VCF, BCF, CSI, GZI, TBI, BED. """ if not self.htsfile: raise ValueError('metadata not available on closed file') return FORMATS[self.htsfile.format.format] @property def version(self): """Tuple of file format version numbers (major, minor)""" if not self.htsfile: raise ValueError('metadata not available on closed file') return self.htsfile.format.version.major, self.htsfile.format.version.minor @property def compression(self): """File compression. One of NONE, GZIP, BGZF, CUSTOM.""" if not self.htsfile: raise ValueError('metadata not available on closed file') return COMPRESSION[self.htsfile.format.compression] @property def description(self): """Vaguely human readable description of the file format""" if not self.htsfile: raise ValueError('metadata not available on closed file') cdef char *desc = hts_format_description(&self.htsfile.format) try: return charptr_to_str(desc) finally: free(desc) @property def is_open(self): """return True if HTSFile is open and in a valid state.""" return CTrue if self.htsfile != NULL else CFalse @property def is_closed(self): """return True if HTSFile is closed.""" return self.htsfile == NULL @property def closed(self): """return True if HTSFile is closed.""" return self.htsfile == NULL @property def is_write(self): """return True if HTSFile is open for writing""" return self.htsfile != NULL and self.htsfile.is_write != 0 @property def is_read(self): """return True if HTSFile is open for reading""" return self.htsfile != NULL and self.htsfile.is_write == 0 @property def is_sam(self): """return True if HTSFile is reading or writing a SAM alignment file""" return self.htsfile != NULL and self.htsfile.format.format == sam @property def is_bam(self): """return True if HTSFile is reading or writing a BAM alignment file""" return self.htsfile != NULL and self.htsfile.format.format == bam @property def is_cram(self): """return True if HTSFile is reading or writing a BAM alignment file""" return self.htsfile != NULL and self.htsfile.format.format == cram @property def is_vcf(self): """return True if HTSFile is reading or writing a VCF variant file""" return self.htsfile != NULL and self.htsfile.format.format == vcf @property def is_bcf(self): """return True if HTSFile is reading or writing a BCF variant file""" return self.htsfile != NULL and self.htsfile.format.format == bcf def reset(self): """reset file position to beginning of file just after the header. Returns ------- The file position after moving the file pointer. : pointer """ return self.seek(self.start_offset) def seek(self, uint64_t offset, int whence=io.SEEK_SET): """move file pointer to position *offset*, see :meth:`pysam.HTSFile.tell`.""" if not self.is_open: raise ValueError('I/O operation on closed file') if self.is_stream: raise IOError('seek not available in streams') whence = libc_whence_from_io(whence) cdef int64_t ret if self.htsfile.format.compression == bgzf: with nogil: ret = bgzf_seek(hts_get_bgzfp(self.htsfile), offset, whence) elif self.htsfile.format.compression == no_compression: ret = 0 if (hseek(self.htsfile.fp.hfile, offset, whence) >= 0) else -1 else: raise NotImplementedError("seek not implemented in files compressed by method {}".format( self.htsfile.format.compression)) return ret def tell(self): """return current file position, see :meth:`pysam.HTSFile.seek`.""" if not self.is_open: raise ValueError('I/O operation on closed file') if self.is_stream: raise IOError('tell not available in streams') cdef int64_t ret if self.htsfile.format.compression == bgzf: with nogil: ret = bgzf_tell(hts_get_bgzfp(self.htsfile)) elif self.htsfile.format.compression == no_compression: ret = htell(self.htsfile.fp.hfile) elif self.htsfile.format.format == cram: with nogil: ret = htell(cram_fd_get_fp(self.htsfile.fp.cram)) else: raise NotImplementedError("seek not implemented in files compressed by method {}".format( self.htsfile.format.compression)) return ret cdef htsFile *_open_htsfile(self) except? NULL: cdef char *cfilename cdef char *cmode = self.mode cdef int fd, dup_fd, threads threads = self.threads - 1 if isinstance(self.filename, bytes): cfilename = self.filename with nogil: htsfile = hts_open(cfilename, cmode) if htsfile != NULL: hts_set_threads(htsfile, threads) return htsfile else: if isinstance(self.filename, int): fd = self.filename else: fd = self.filename.fileno() if self.duplicate_filehandle: dup_fd = dup(fd) else: dup_fd = fd # Replicate mode normalization done in hts_open_format smode = self.mode.replace(b'b', b'').replace(b'c', b'') if b'b' in self.mode: smode += b'b' elif b'c' in self.mode: smode += b'c' cmode = smode hfile = hdopen(dup_fd, cmode) if hfile == NULL: raise IOError('Cannot create hfile') try: # filename.name can be an int filename = str(self.filename.name) except AttributeError: filename = ''.format(fd) filename = encode_filename(filename) cfilename = filename with nogil: htsfile = hts_hopen(hfile, cfilename, cmode) if htsfile != NULL: hts_set_threads(htsfile, threads) return htsfile def add_hts_options(self, format_options=None): """Given a list of key=value format option strings, add them to an open htsFile """ cdef int rval cdef hts_opt *opts = NULL if format_options: for format_option in format_options: rval = hts_opt_add(&opts, format_option) if rval != 0: if opts != NULL: hts_opt_free(opts) raise RuntimeError('Invalid format option ({}) specified'.format(format_option)) if opts != NULL: rval = hts_opt_apply(self.htsfile, opts) if rval != 0: hts_opt_free(opts) raise RuntimeError('An error occurred while applying the requested format options') hts_opt_free(opts) def parse_region(self, contig=None, start=None, stop=None, region=None, tid=None, reference=None, end=None): """parse alternative ways to specify a genomic region. A region can either be specified by :term:`contig`, `start` and `stop`. `start` and `stop` denote 0-based, half-open intervals. :term:`reference` and `end` are also accepted for backward compatibility as synonyms for :term:`contig` and `stop`, respectively. Alternatively, a samtools :term:`region` string can be supplied. If any of the coordinates are missing they will be replaced by the minimum (`start`) or maximum (`stop`) coordinate. Note that region strings are 1-based inclusive, while `start` and `stop` denote an interval in 0-based, half-open coordinates (like BED files and Python slices). If `contig` or `region` or are ``*``, unmapped reads at the end of a BAM file will be returned. Setting either to ``.`` will iterate from the beginning of the file. Returns ------- tuple : a tuple of `flag`, :term:`tid`, `start` and `stop`. The flag indicates whether no coordinates were supplied and the genomic region is the complete genomic space. Raises ------ ValueError for invalid or out of bounds regions. """ cdef int rtid cdef int32_t rstart cdef int32_t rstop if reference is not None: if contig is not None: raise ValueError('contig and reference should not both be specified') contig = reference if end is not None: if stop is not None: raise ValueError('stop and end should not both be specified') stop = end if contig is None and tid is None and region is None: return 0, 0, 0, MAX_POS rtid = -1 rstart = 0 rstop = MAX_POS if start is not None: try: rstart = start except OverflowError: raise ValueError('start out of range (%i)' % start) if stop is not None: try: rstop = stop except OverflowError: raise ValueError('stop out of range (%i)' % stop) if region: region = force_str(region) if ":" in region: contig, coord = region.split(":") parts = coord.split("-") rstart = int(parts[0]) - 1 if len(parts) >= 1: rstop = int(parts[1]) else: contig = region if tid is not None: if not self.is_valid_tid(tid): raise IndexError('invalid tid') rtid = tid else: if contig == "*": rtid = HTS_IDX_NOCOOR elif contig == ".": rtid = HTS_IDX_START else: rtid = self.get_tid(contig) if rtid < 0: raise ValueError('invalid contig `%s`' % contig) if rstart > rstop: raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop)) if not 0 <= rstart < MAX_POS: raise ValueError('start out of range (%i)' % rstart) if not 0 <= rstop <= MAX_POS: raise ValueError('stop out of range (%i)' % rstop) return 1, rtid, rstart, rstop def is_valid_tid(self, tid): """ return True if the numerical :term:`tid` is valid; False otherwise. returns -1 if contig is not known. """ raise NotImplementedError() def is_valid_reference_name(self, contig): """ return True if the contig name :term:`contig` is valid; False otherwise. """ return self.get_tid(contig) != -1 def get_tid(self, contig): """ return the numerical :term:`tid` corresponding to :term:`contig` returns -1 if contig is not known. """ raise NotImplementedError() def get_reference_name(self, tid): """ return :term:`contig` name corresponding to numerical :term:`tid` """ raise NotImplementedError() pysam-0.23.0/pysam/libcsamfile.pxd000066400000000000000000000030021475062545500170550ustar00rootroot00000000000000# cython: language_level=3 from pysam.libcalignmentfile cimport AlignedSegment, AlignmentFile ################################################# # Compatibility Layer for pysam < 0.8 # import all declarations from htslib from pysam.libchtslib cimport * cdef class AlignedRead(AlignedSegment): pass cdef class Samfile(AlignmentFile): pass # import the conversion functions cdef extern from "htslib_util.h": # add *nbytes* into the variable length data of *src* at *pos* bam1_t * pysam_bam_update(bam1_t * b, size_t nbytes_old, size_t nbytes_new, uint8_t * pos) # now: static int aux_type2size(int) char * pysam_bam_get_qname(bam1_t * b) uint32_t * pysam_bam_get_cigar(bam1_t * b) uint8_t * pysam_bam_get_seq(bam1_t * b) uint8_t * pysam_bam_get_qual(bam1_t * b) uint8_t * pysam_bam_get_aux(bam1_t * b) int pysam_bam_get_l_aux(bam1_t * b) char pysam_bam_seqi(uint8_t * s, int i) uint16_t pysam_get_bin(bam1_t * b) uint8_t pysam_get_qual(bam1_t * b) uint8_t pysam_get_l_qname(bam1_t * b) uint16_t pysam_get_flag(bam1_t * b) uint32_t pysam_get_n_cigar(bam1_t * b) void pysam_set_bin(bam1_t * b, uint16_t v) void pysam_set_qual(bam1_t * b, uint8_t v) void pysam_set_l_qname(bam1_t * b, uint8_t v) void pysam_set_flag(bam1_t * b, uint16_t v) void pysam_set_n_cigar(bam1_t * b, uint32_t v) void pysam_update_flag(bam1_t * b, uint16_t v, uint16_t flag) pysam-0.23.0/pysam/libcsamfile.pyi000066400000000000000000000002601475062545500170660ustar00rootroot00000000000000from pysam.libcalignedsegment import AlignedSegment from pysam.libcalignmentfile import AlignmentFile class AlignedRead(AlignedSegment): ... class Samfile(AlignmentFile): ... pysam-0.23.0/pysam/libcsamfile.pyx000066400000000000000000000014661475062545500171160ustar00rootroot00000000000000# cython: embedsignature=True # cython: profile=True # adds doc-strings for sphinx import tempfile import os import sys import types import itertools import struct import ctypes import collections import re import platform import warnings from cpython cimport PyErr_SetString, \ PyBytes_Check, \ PyUnicode_Check, \ PyBytes_FromStringAndSize from pysam.libcalignmentfile cimport AlignmentFile, AlignedSegment cdef class Samfile(AlignmentFile): '''Deprecated alternative for :class:`~pysam.AlignmentFile` Added for backwards compatibility with pysam <= 0.8.0 ''' pass cdef class AlignedRead(AlignedSegment): '''Deprecated alternative for :class:`~pysam.AlignedSegment` Added for backwards compatibility with pysam <= 0.8.0 ''' pass __all__ = ['Samfile', 'AlignedRead'] pysam-0.23.0/pysam/libcsamtools.pxd000066400000000000000000000004551475062545500173070ustar00rootroot00000000000000# cython: language_level=3 cdef extern from "samtools.pysam.h": int samtools_dispatch(int argc, char *argv[]) void samtools_set_stderr(int fd) void samtools_close_stderr() void samtools_set_stdout(int fd) void samtools_set_stdout_fn(const char *) void samtools_close_stdout() pysam-0.23.0/pysam/libcsamtools.pyi000066400000000000000000000000371475062545500173110ustar00rootroot00000000000000def py_samtools() -> None: ... pysam-0.23.0/pysam/libcsamtools.pyx000066400000000000000000000000341475062545500173250ustar00rootroot00000000000000def py_samtools(): pass pysam-0.23.0/pysam/libctabix.pxd000066400000000000000000000051671475062545500165620ustar00rootroot00000000000000# cython: language_level=3 from libc.stdint cimport int8_t, int16_t, int32_t, int64_t from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t from libc.stdlib cimport malloc, calloc, realloc, free from libc.string cimport memcpy, memcmp, strncpy, strlen, strdup from libc.stdio cimport FILE, printf # Note: this replaces python "open"! cdef extern from "fcntl.h": int open(char *pathname, int flags) cdef extern from "unistd.h" nogil: ctypedef int ssize_t ssize_t read(int fd, void *buf, size_t count) int close(int fd) from pysam.libchtslib cimport hts_idx_t, hts_itr_t, htsFile, \ tbx_t, kstring_t, BGZF, HTSFile # These functions are put here and not in chtslib.pxd in order # to avoid warnings for unused functions. cdef extern from "pysam_stream.h" nogil: ctypedef struct kstream_t: pass ctypedef struct kseq_t: kstring_t name kstring_t comment kstring_t seq kstring_t qual kseq_t *kseq_init(BGZF *) int kseq_read(kseq_t *) void kseq_destroy(kseq_t *) kstream_t *ks_init(BGZF *) void ks_destroy(kstream_t *) # Retrieve characters from stream until delimiter # is reached placing results in str. int ks_getuntil(kstream_t *, int delimiter, kstring_t * str, int * dret) cdef class tabix_file_iterator: cdef BGZF * fh cdef kstream_t * kstream cdef kstring_t buffer cdef size_t size cdef Parser parser cdef int fd cdef int duplicated_fd cdef infile cdef __cnext__(self) cdef class TabixFile(HTSFile): # pointer to index structure cdef tbx_t * index cdef readonly object filename_index cdef Parser parser cdef encoding cdef class Parser: cdef encoding cdef parse(self, char * buffer, int len) cdef class asTuple(Parser): cdef parse(self, char * buffer, int len) cdef class asGTF(Parser): pass cdef class asGFF3(Parser): pass cdef class asBed(Parser): pass cdef class asVCF(Parser): pass cdef class TabixIterator: cdef hts_itr_t * iterator cdef TabixFile tabixfile cdef kstring_t buffer cdef encoding cdef int __cnext__(self) cdef class TabixIteratorParsed(TabixIterator): cdef Parser parser cdef class GZIterator: cdef object _filename cdef BGZF * gzipfile cdef kstream_t * kstream cdef kstring_t buffer cdef int __cnext__(self) cdef encoding cdef class GZIteratorHead(GZIterator): pass cdef class GZIteratorParsed(GZIterator): cdef Parser parser # Compatibility Layer for pysam < 0.8 cdef class Tabixfile(TabixFile): pass pysam-0.23.0/pysam/libctabix.pyi000066400000000000000000000061211475062545500165570ustar00rootroot00000000000000import sys from typing import Optional, List, Any if sys.version_info < (3, 8): from typing_extensions import Literal else: from typing import Literal from pysam.libchtslib import HTSFile _ParseResult = Any class Parser: def __init__(self, encoding: str = ...) -> None: ... def get_encoding(self) -> str: ... def set_encoding(self, encoding: str) -> None: ... def __call__(self, buffer: str, length: int) -> _ParseResult: ... class asTuple(Parser): ... class asGFF3(Parser): ... class asGTF(Parser): ... class asBed(Parser): ... class asVCF(Parser): ... class TabixFile(HTSFile): filename_index: bytes = ... @property def header(self) -> List[str]: ... @property def contigs(self) -> List[str]: ... def __init__( self, filename: str, mode: str = ..., parser: Parser = ..., index: Optional[str] = ..., encoding: str = ..., threads: int = ..., *args, **kwargs ) -> None: ... def fetch( self, reference: Optional[str] = ..., start: Optional[int] = ..., end: Optional[int] = ..., region: Optional[str] = ..., parser: Optional[Parser] = ..., multiple_iterators: bool = ..., ) -> Any: ... def close(self) -> None: ... class TabixIterator: def __init__(self, encoding: str = ...) -> None: ... def __iter__(self) -> TabixIterator: ... def __next__(self) -> str: ... class EmptyIterator: def __iter__(self) -> Any: ... def __next__(self) -> Any: ... class TabixIteratorParsed(TabixIterator): def __init__(self, parser: Parser) -> None: ... def __next__(self) -> Any: ... class GZIterator: def __init__( self, filename: str, bufer_size: int = ..., encoding: str = ... ) -> None: ... def __iter__(self) -> GZIterator: ... def __next__(self) -> str: ... class GZIteratorHead(GZIterator): ... class GZIteratorParsed(GZIterator): def __init__(self, parser: Parser) -> None: ... def __next__(self) -> _ParseResult: ... def tabix_compress(filename_in: str, filename_out: str, force: bool = ...) -> None: ... def tabix_index( filename: str, force: bool = ..., seq_col: Optional[int] = ..., start_col: Optional[int] = ..., end_col: Optional[int] = ..., preset: Optional[Literal["gff", "bed", "sam", "vcf", "psltbl", "pileup"]] = ..., meta_char: str = ..., line_skip: int = ..., zerobased: bool = ..., min_shift: int = ..., index: Optional[str] = ..., keep_original: bool = ..., csi: bool = ..., ) -> str: ... class tabix_file_iterator: def __init__(self, infile: str, parser: Parser, buffer_size: int = ...) -> None: ... def __iter__(self) -> tabix_file_iterator: ... def __next__(self) -> _ParseResult: ... class tabix_generic_iterator: def __init__(self, infile: str, parser: Parser) -> None: ... def __iter__(self) -> tabix_generic_iterator: ... def __next__(self) -> _ParseResult: ... def tabix_iterator(infile: str, parser: Optional[Parser]) -> _ParseResult: ... # backwards compatibility class Tabixfile(TabixFile): ... pysam-0.23.0/pysam/libctabix.pyx000066400000000000000000001226701475062545500166060ustar00rootroot00000000000000# cython: language_level=3 # cython: embedsignature=True # cython: profile=True ############################################################################### ############################################################################### # Cython wrapper for access to tabix indexed files in bgzf format ############################################################################### # The principal classes and functions defined in this module are: # # class TabixFile class wrapping tabix indexed files in bgzf format # # class asTuple Parser class for tuples # class asGTF Parser class for GTF formatted rows # class asGFF3 Parser class for GFF3 formatted rows # class asBed Parser class for Bed formatted rows # class asVCF Parser class for VCF formatted rows # # class tabix_generic_iterator Streamed iterator of bgzf formatted files # # Additionally this module defines several additional classes that are part # of the internal API. These are: # # class Parser base class for parsers of tab-separated rows # class tabix_file_iterator # class TabixIterator iterator class over rows in bgzf file # class EmptyIterator # # For backwards compatibility, the following classes are also defined: # # class Tabixfile equivalent to TabixFile # ############################################################################### # # The MIT License # # Copyright (c) 2015 Andreas Heger # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. # ############################################################################### import os import sys from libc.stdio cimport printf, fprintf, stderr from libc.string cimport strerror from libc.errno cimport errno from posix.unistd cimport dup from cpython cimport PyErr_SetString, PyBytes_Check, \ PyUnicode_Check, PyBytes_FromStringAndSize, \ PyObject_AsFileDescriptor cimport pysam.libctabixproxies as ctabixproxies from pysam.libchtslib cimport htsFile, hts_open, hts_close, HTS_IDX_START,\ BGZF, bgzf_open, bgzf_dopen, bgzf_close, bgzf_write, \ tbx_index_build2, tbx_index_load2, tbx_itr_queryi, tbx_itr_querys, \ tbx_conf_t, tbx_seqnames, tbx_itr_next, tbx_itr_destroy, \ tbx_destroy, hisremote, region_list, hts_getline, \ TBX_GENERIC, TBX_SAM, TBX_VCF, TBX_UCSC, hts_get_format, htsFormat, \ no_compression, bcf, bcf_index_build2 from pysam.libcutils cimport force_bytes, force_str, charptr_to_str from pysam.libcutils cimport encode_filename, from_string_and_size cdef class Parser: def __init__(self, encoding="ascii"): self.encoding = encoding def set_encoding(self, encoding): self.encoding = encoding def get_encoding(self): return self.encoding cdef parse(self, char * buffer, int length): raise NotImplementedError( 'parse method of %s not implemented' % str(self)) def __call__(self, char * buffer, int length): return self.parse(buffer, length) cdef class asTuple(Parser): '''converts a :term:`tabix row` into a python tuple. A field in a row is accessed by numeric index. ''' cdef parse(self, char * buffer, int len): cdef ctabixproxies.TupleProxy r r = ctabixproxies.TupleProxy(self.encoding) # need to copy - there were some # persistence issues with "present" r.copy(buffer, len) return r cdef class asGFF3(Parser): '''converts a :term:`tabix row` into a GFF record with the following fields: +----------+----------+-------------------------------+ |*Column* |*Name* |*Content* | +----------+----------+-------------------------------+ |1 |contig |the chromosome name | +----------+----------+-------------------------------+ |2 |feature |The feature type | +----------+----------+-------------------------------+ |3 |source |The feature source | +----------+----------+-------------------------------+ |4 |start |genomic start coordinate | | | |(0-based) | +----------+----------+-------------------------------+ |5 |end |genomic end coordinate | | | |(0-based) | +----------+----------+-------------------------------+ |6 |score |feature score | +----------+----------+-------------------------------+ |7 |strand |strand | +----------+----------+-------------------------------+ |8 |frame |frame | +----------+----------+-------------------------------+ |9 |attributes|the attribute field | +----------+----------+-------------------------------+ ''' cdef parse(self, char * buffer, int len): cdef ctabixproxies.GFF3Proxy r r = ctabixproxies.GFF3Proxy(self.encoding) r.copy(buffer, len) return r cdef class asGTF(Parser): '''converts a :term:`tabix row` into a GTF record with the following fields: +----------+----------+-------------------------------+ |*Column* |*Name* |*Content* | +----------+----------+-------------------------------+ |1 |contig |the chromosome name | +----------+----------+-------------------------------+ |2 |feature |The feature type | +----------+----------+-------------------------------+ |3 |source |The feature source | +----------+----------+-------------------------------+ |4 |start |genomic start coordinate | | | |(0-based) | +----------+----------+-------------------------------+ |5 |end |genomic end coordinate | | | |(0-based) | +----------+----------+-------------------------------+ |6 |score |feature score | +----------+----------+-------------------------------+ |7 |strand |strand | +----------+----------+-------------------------------+ |8 |frame |frame | +----------+----------+-------------------------------+ |9 |attributes|the attribute field | +----------+----------+-------------------------------+ GTF formatted entries also define the following fields that are derived from the attributes field: +--------------------+------------------------------+ |*Name* |*Content* | +--------------------+------------------------------+ |gene_id |the gene identifier | +--------------------+------------------------------+ |transcript_id |the transcript identifier | +--------------------+------------------------------+ ''' cdef parse(self, char * buffer, int len): cdef ctabixproxies.GTFProxy r r = ctabixproxies.GTFProxy(self.encoding) r.copy(buffer, len) return r cdef class asBed(Parser): '''converts a :term:`tabix row` into a bed record with the following fields: +-----------+-----------+------------------------------------------+ |*Column* |*Field* |*Contents* | | | | | +-----------+-----------+------------------------------------------+ |1 |contig |contig | | | | | +-----------+-----------+------------------------------------------+ |2 |start |genomic start coordinate (zero-based) | +-----------+-----------+------------------------------------------+ |3 |end |genomic end coordinate plus one | | | |(zero-based) | +-----------+-----------+------------------------------------------+ |4 |name |name of feature. | +-----------+-----------+------------------------------------------+ |5 |score |score of feature | +-----------+-----------+------------------------------------------+ |6 |strand |strand of feature | +-----------+-----------+------------------------------------------+ |7 |thickStart |thickStart | +-----------+-----------+------------------------------------------+ |8 |thickEnd |thickEnd | +-----------+-----------+------------------------------------------+ |9 |itemRGB |itemRGB | +-----------+-----------+------------------------------------------+ |10 |blockCount |number of bocks | +-----------+-----------+------------------------------------------+ |11 |blockSizes |',' separated string of block sizes | +-----------+-----------+------------------------------------------+ |12 |blockStarts|',' separated string of block genomic | | | |start positions | +-----------+-----------+------------------------------------------+ Only the first three fields are required. Additional fields are optional, but if one is defined, all the preceding need to be defined as well. ''' cdef parse(self, char * buffer, int len): cdef ctabixproxies.BedProxy r r = ctabixproxies.BedProxy(self.encoding) r.copy(buffer, len) return r cdef class asVCF(Parser): '''converts a :term:`tabix row` into a VCF record with the following fields: +----------+---------+------------------------------------+ |*Column* |*Field* |*Contents* | | | | | +----------+---------+------------------------------------+ |1 |contig |chromosome | +----------+---------+------------------------------------+ |2 |pos |chromosomal position, zero-based | +----------+---------+------------------------------------+ |3 |id |id | +----------+---------+------------------------------------+ |4 |ref |reference allele | +----------+---------+------------------------------------+ |5 |alt |alternate alleles | +----------+---------+------------------------------------+ |6 |qual |quality | +----------+---------+------------------------------------+ |7 |filter |filter | +----------+---------+------------------------------------+ |8 |info |info | +----------+---------+------------------------------------+ |9 |format |format specifier. | +----------+---------+------------------------------------+ Access to genotypes is via index:: contig = vcf.contig first_sample_genotype = vcf[0] second_sample_genotype = vcf[1] ''' cdef parse(self, char * buffer, int len): cdef ctabixproxies.VCFProxy r r = ctabixproxies.VCFProxy(self.encoding) r.copy(buffer, len) return r cdef class TabixFile: """Random access to bgzf formatted files that have been indexed by :term:`tabix`. The file is automatically opened. The index file of file ```` is expected to be called ``.tbi`` by default (see parameter `index`). Parameters ---------- filename : string Filename of bgzf file to be opened. index : string The filename of the index. If not set, the default is to assume that the index is called ``filename.tbi`` mode : char The file opening mode. Currently, only ``r`` is permitted. parser : :class:`pysam.Parser` sets the default parser for this tabix file. If `parser` is None, the results are returned as an unparsed string. Otherwise, `parser` is assumed to be a functor that will return parsed data (see for example :class:`~pysam.asTuple` and :class:`~pysam.asGTF`). encoding : string The encoding passed to the parser threads: integer Number of threads to use for decompressing Tabix files. (Default=1) Raises ------ ValueError if index file is missing. IOError if file could not be opened """ def __cinit__(self, filename, mode='r', parser=None, index=None, encoding="ascii", threads=1, *args, **kwargs ): self.htsfile = NULL self.is_remote = False self.is_stream = False self.parser = parser self.threads = threads self._open(filename, mode, index, *args, **kwargs) self.encoding = encoding def _open( self, filename, mode='r', index=None, threads=1, ): '''open a :term:`tabix file` for reading.''' if mode != 'r': raise ValueError("invalid file opening mode `%s`" % mode) if self.htsfile != NULL: self.close() self.htsfile = NULL self.threads=threads filename_index = index or (filename + ".tbi") # encode all the strings to pass to tabix self.filename = encode_filename(filename) self.filename_index = encode_filename(filename_index) self.is_stream = self.filename == b'-' self.is_remote = hisremote(self.filename) if not self.is_remote: if not os.path.exists(filename): raise IOError("file `%s` not found" % filename) if not os.path.exists(filename_index): raise IOError("index `%s` not found" % filename_index) # open file cdef char *cfilename = self.filename cdef char *cfilename_index = self.filename_index with nogil: self.htsfile = hts_open(cfilename, 'r') if self.htsfile == NULL: raise IOError("could not open file `%s`" % filename) #if self.htsfile.format.category != region_list: # raise ValueError("file does not contain region data") with nogil: self.index = tbx_index_load2(cfilename, cfilename_index) if self.index == NULL: raise IOError("could not open index for `%s`" % filename) if not self.is_stream: self.start_offset = self.tell() def _dup(self): '''return a copy of this tabix file. The file is being re-opened. ''' return TabixFile(self.filename, mode="r", threads=self.threads, parser=self.parser, index=self.filename_index, encoding=self.encoding) def fetch(self, reference=None, start=None, end=None, region=None, parser=None, multiple_iterators=False): '''fetch one or more rows in a :term:`region` using 0-based indexing. The region is specified by :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can be supplied. Without *reference* or *region* all entries will be fetched. If only *reference* is set, all reads matching on *reference* will be fetched. If *parser* is None, the default parser will be used for parsing. Set *multiple_iterators* to true if you will be using multiple iterators on the same file at the same time. The iterator returned will receive its own copy of a filehandle to the file effectively re-opening the file. Re-opening a file creates some overhead, so beware. ''' if not self.is_open(): raise ValueError("I/O operation on closed file") # convert coordinates to region string, which is one-based if reference: if end is not None: if end < 0: raise ValueError("end out of range (%i)" % end) if start is None: start = 0 if start < 0: raise ValueError("start out of range (%i)" % end) elif start > end: raise ValueError( 'start (%i) >= end (%i)' % (start, end)) elif start == end: return EmptyIterator() else: region = '%s:%i-%i' % (reference, start + 1, end) elif start is not None: if start < 0: raise ValueError("start out of range (%i)" % end) region = '%s:%i' % (reference, start + 1) else: region = reference # get iterator cdef hts_itr_t * itr cdef char *cstr cdef TabixFile fileobj # reopen the same file if necessary if multiple_iterators: fileobj = self._dup() else: fileobj = self if region is None: # without region or reference - iterate from start with nogil: itr = tbx_itr_queryi(fileobj.index, HTS_IDX_START, 0, 0) else: s = force_bytes(region, encoding=fileobj.encoding) cstr = s with nogil: itr = tbx_itr_querys(fileobj.index, cstr) if itr == NULL: if region is None: if len(self.contigs) > 0: # when accessing a tabix file created prior tabix 1.0 # the full-file iterator is empty. raise ValueError( "could not create iterator, possible " "tabix version mismatch") else: # possible reason is that the file is empty - # return an empty iterator return EmptyIterator() else: raise ValueError( "could not create iterator for region '%s'" % region) # use default parser if no parser is specified if parser is None: parser = fileobj.parser cdef TabixIterator a if parser is None: a = TabixIterator(encoding=fileobj.encoding) else: parser.set_encoding(fileobj.encoding) a = TabixIteratorParsed(parser) a.tabixfile = fileobj a.iterator = itr return a ############################################################### ############################################################### ############################################################### ## properties ############################################################### property header: '''the file header. The file header consists of the lines at the beginning of a file that are prefixed by the comment character ``#``. .. note:: The header is returned as an iterator presenting lines without the newline character. ''' def __get__(self): cdef char *cfilename = self.filename cdef char *cfilename_index = self.filename_index cdef kstring_t buffer buffer.l = buffer.m = 0 buffer.s = NULL cdef htsFile * fp = NULL cdef int KS_SEP_LINE = 2 cdef tbx_t * tbx = NULL lines = [] with nogil: fp = hts_open(cfilename, 'r') if fp == NULL: raise OSError("could not open {} for reading header".format(self.filename)) with nogil: tbx = tbx_index_load2(cfilename, cfilename_index) if tbx == NULL: raise OSError("could not load .tbi/.csi index of {}".format(self.filename)) while hts_getline(fp, KS_SEP_LINE, &buffer) >= 0: if not buffer.l or buffer.s[0] != tbx.conf.meta_char: break lines.append(force_str(buffer.s, self.encoding)) with nogil: hts_close(fp) free(buffer.s) return lines property contigs: '''list of chromosome names''' def __get__(self): cdef const char ** sequences cdef int nsequences with nogil: sequences = tbx_seqnames(self.index, &nsequences) cdef int x result = [] for x from 0 <= x < nsequences: result.append(force_str(sequences[x])) # htslib instructions: # only free container, not the sequences themselves free(sequences) return result def close(self): ''' closes the :class:`pysam.TabixFile`.''' if self.htsfile != NULL: hts_close(self.htsfile) self.htsfile = NULL if self.index != NULL: tbx_destroy(self.index) self.index = NULL def __dealloc__( self ): # remember: dealloc cannot call other python methods # note: no doc string # note: __del__ is not called. if self.htsfile != NULL: hts_close(self.htsfile) self.htsfile = NULL if self.index != NULL: tbx_destroy(self.index) cdef class TabixIterator: """iterates over rows in *tabixfile* in region given by *tid*, *start* and *end*. """ def __init__(self, encoding="ascii"): self.encoding = encoding def __iter__(self): self.buffer.s = NULL self.buffer.l = 0 self.buffer.m = 0 return self cdef int __cnext__(self): '''iterate to next element. Return -5 if file has been closed when this function was called. ''' if self.tabixfile.htsfile == NULL: return -5 cdef int retval while 1: with nogil: retval = tbx_itr_next( self.tabixfile.htsfile, self.tabixfile.index, self.iterator, &self.buffer) if retval < 0: break if self.buffer.s[0] != b'#': break return retval def __next__(self): """python version of next(). pyrex uses this non-standard name instead of next() """ cdef int retval = self.__cnext__() if retval == -5: raise IOError("iteration on closed file") elif retval < 0: raise StopIteration return charptr_to_str(self.buffer.s, self.encoding) def __dealloc__(self): if self.iterator != NULL: tbx_itr_destroy(self.iterator) if self.buffer.s != NULL: free(self.buffer.s) class EmptyIterator: '''empty iterator''' def __iter__(self): return self def __next__(self): raise StopIteration() cdef class TabixIteratorParsed(TabixIterator): """iterates over mapped reads in a region. The *parser* determines the encoding. Returns parsed data. """ def __init__(self, Parser parser): super().__init__() self.parser = parser def __next__(self): """python version of next(). pyrex uses this non-standard name instead of next() """ cdef int retval = self.__cnext__() if retval == -5: raise IOError("iteration on closed file") elif retval < 0: raise StopIteration return self.parser.parse(self.buffer.s, self.buffer.l) cdef class GZIterator: def __init__(self, filename, int buffer_size=65536, encoding="ascii"): '''iterate line-by-line through gzip (or bgzip) compressed file. ''' if not os.path.exists(filename): raise IOError("No such file or directory: %s" % filename) filename = encode_filename(filename) cdef char *cfilename = filename with nogil: self.gzipfile = bgzf_open(cfilename, "r") self._filename = filename self.kstream = ks_init(self.gzipfile) self.encoding = encoding self.buffer.l = 0 self.buffer.m = 0 self.buffer.s = malloc(buffer_size) def __dealloc__(self): '''close file.''' if self.gzipfile != NULL: bgzf_close(self.gzipfile) self.gzipfile = NULL if self.buffer.s != NULL: free(self.buffer.s) if self.kstream != NULL: ks_destroy(self.kstream) def __iter__(self): return self cdef int __cnext__(self): cdef int dret = 0 cdef int retval = 0 while 1: with nogil: retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret) if retval < 0: break return dret return -1 def __next__(self): """python version of next(). """ cdef int retval = self.__cnext__() if retval < 0: raise StopIteration return force_str(self.buffer.s, self.encoding) cdef class GZIteratorHead(GZIterator): '''iterate line-by-line through gzip (or bgzip) compressed file returning comments at top of file. ''' def __next__(self): """python version of next(). """ cdef int retval = self.__cnext__() if retval < 0: raise StopIteration if self.buffer.s[0] == b'#': return self.buffer.s else: raise StopIteration cdef class GZIteratorParsed(GZIterator): '''iterate line-by-line through gzip (or bgzip) compressed file returning comments at top of file. ''' def __init__(self, parser): self.parser = parser def __next__(self): """python version of next(). """ cdef int retval = self.__cnext__() if retval < 0: raise StopIteration return self.parser.parse(self.buffer.s, self.buffer.l) def tabix_compress(filename_in, filename_out, force=False): '''compress *filename_in* writing the output to *filename_out*. Raise an IOError if *filename_out* already exists, unless *force* is set. ''' if not force and os.path.exists(filename_out): raise IOError( "Filename '%s' already exists, use *force* to " "overwrite" % filename_out) cdef int WINDOW_SIZE cdef int c, r cdef void * buffer cdef BGZF * fp cdef int fd_src cdef bint is_empty = True cdef int O_RDONLY O_RDONLY = os.O_RDONLY WINDOW_SIZE = 64 * 1024 fn = encode_filename(filename_out) cdef char *cfn = fn with nogil: fp = bgzf_open(cfn, "w") if fp == NULL: raise IOError("could not open '%s' for writing" % filename_out) fn = encode_filename(filename_in) fd_src = open(fn, O_RDONLY) if fd_src == 0: raise IOError("could not open '%s' for reading" % filename_in) buffer = malloc(WINDOW_SIZE) c = 1 while c > 0: with nogil: c = read(fd_src, buffer, WINDOW_SIZE) if c > 0: is_empty = False r = bgzf_write(fp, buffer, c) if r < 0: free(buffer) raise IOError("writing failed") free(buffer) r = bgzf_close(fp) if r < 0: raise IOError("error %i when writing to file %s" % (r, filename_out)) r = close(fd_src) # an empty file will return with -1, thus ignore this. if r < 0: if not (r == -1 and is_empty): raise IOError("error %i when closing file %s" % (r, filename_in)) def tabix_index(filename, force=False, seq_col=None, start_col=None, end_col=None, preset=None, meta_char="#", int line_skip=0, zerobased=False, int min_shift=-1, index=None, keep_original=False, csi=False, ): '''index tab-separated *filename* using tabix. An existing index will not be overwritten unless *force* is set. The index will be built from coordinates in columns *seq_col*, *start_col* and *end_col*. The contents of *filename* have to be sorted by contig and position - the method does not check if the file is sorted. Column indices are 0-based. Note that this is different from the tabix command line utility where column indices start at 1. Coordinates in the file are assumed to be 1-based unless *zerobased* is set. If *preset* is provided, the column coordinates are taken from a preset. Valid values for preset are "gff", "bed", "sam", "vcf", psltbl", "pileup". Lines beginning with *meta_char* and the first *line_skip* lines will be skipped. If *filename* is not detected as a gzip file it will be automatically compressed. The original file will be removed and only the compressed file will be retained. By default or when *min_shift* is 0, creates a TBI index. If *min_shift* is greater than zero and/or *csi* is True, creates a CSI index with a minimal interval size of 1<<*min_shift* (1<<14 if only *csi* is set). *index* controls the filename which should be used for creating the index. If not set, the default is to append ``.tbi`` to *filename*. When automatically compressing files, if *keep_original* is set the uncompressed file will not be deleted. returns the filename of the compressed data ''' if preset is None and \ (seq_col is None or start_col is None or end_col is None): raise ValueError( "neither preset nor seq_col,start_col and end_col given") fn = encode_filename(filename) cdef char *cfn = fn cdef htsFile *fp = hts_open(cfn, "r") if fp == NULL: raise IOError("Could not open file '%s': %s" % (filename, force_str(strerror(errno)))) cdef htsFormat fmt = hts_get_format(fp)[0] hts_close(fp) if fmt.compression == no_compression: tabix_compress(filename, filename + ".gz", force=force) if not keep_original: os.unlink(filename) filename += ".gz" fn = encode_filename(filename) cfn = fn # columns (1-based): # preset-code, contig, start, end, metachar for # comments, lines to ignore at beginning # 0 is a missing column preset2conf = { 'gff' : (TBX_GENERIC, 1, 4, 5, ord('#'), 0), 'bed' : (TBX_UCSC, 1, 2, 3, ord('#'), 0), 'psltbl' : (TBX_UCSC, 15, 17, 18, ord('#'), 0), 'sam' : (TBX_SAM, 3, 4, 0, ord('@'), 0), 'vcf' : (TBX_VCF, 1, 2, 0, ord('#'), 0), } conf_data = None if preset == "bcf" or fmt.format == bcf: csi = True elif preset: try: conf_data = preset2conf[preset] except KeyError: raise KeyError( "unknown preset '%s', valid presets are '%s'" % (preset, ",".join(preset2conf.keys()))) else: if end_col is None: end_col = -1 preset = 0 # tabix internally works with 0-based coordinates and # open/closed intervals. When using a preset, conversion is # automatically taken care of. Otherwise, the coordinates are # assumed to be 1-based closed intervals and -1 is subtracted # from the start coordinate. To avoid doing this, set the # TI_FLAG_UCSC=0x10000 flag: if zerobased: preset = preset | TBX_UCSC conf_data = (preset, seq_col + 1, start_col + 1, end_col + 1, ord(meta_char), line_skip) cdef tbx_conf_t conf if conf_data: conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data if csi or min_shift > 0: suffix = ".csi" if min_shift <= 0: min_shift = 14 else: suffix = ".tbi" min_shift = 0 index = index or filename + suffix fn_index = encode_filename(index) if not force and os.path.exists(index): raise IOError( "filename '%s' already exists, use *force* to overwrite" % index) cdef char *fnidx = fn_index cdef int retval = 0 if csi and fmt.format == bcf: with nogil: retval = bcf_index_build2(cfn, fnidx, min_shift) else: with nogil: retval = tbx_index_build2(cfn, fnidx, min_shift, &conf) if retval != 0: raise OSError("building of index for {} failed".format(filename)) return filename # ######################################################### # cdef class tabix_file_iterator_old: # '''iterate over ``infile``. # This iterator is not safe. If the :meth:`__next__()` method is called # after ``infile`` is closed, the result is undefined (see ``fclose()``). # The iterator might either raise a StopIteration or segfault. # ''' # def __cinit__(self, # infile, # Parser parser, # int buffer_size = 65536 ): # cdef int fd = PyObject_AsFileDescriptor( infile ) # if fd == -1: raise ValueError( "I/O operation on closed file." ) # self.infile = fdopen( fd, 'r') # if self.infile == NULL: raise ValueError( "I/O operation on closed file." ) # self.buffer = malloc( buffer_size ) # self.size = buffer_size # self.parser = parser # def __iter__(self): # return self # cdef __cnext__(self): # cdef char * b # cdef size_t nbytes # b = self.buffer # while not feof( self.infile ): # nbytes = getline( &b, &self.size, self.infile) # # stop at first error or eof # if (nbytes == -1): break # # skip comments # if (b[0] == '#'): continue # # skip empty lines # if b[0] == '\0' or b[0] == '\n' or b[0] == '\r': continue # # make sure that entry is complete # if b[nbytes-1] != '\n' and b[nbytes-1] != '\r': # result = b # raise ValueError( "incomplete line at %s" % result ) # # make sure that this goes fully through C # # otherwise buffer is copied to/from a # # Python object causing segfaults as # # the wrong memory is freed # return self.parser.parse( b, nbytes ) # raise StopIteration # def __dealloc__(self): # free(self.buffer) # def __next__(self): # return self.__cnext__() ######################################################### ######################################################### ######################################################### ## Iterators for parsing through unindexed files. ######################################################### # cdef buildGzipError(void *gzfp): # cdef int errnum = 0 # cdef char *s = gzerror(gzfp, &errnum) # return "error (%d): %s (%d: %s)" % (errno, strerror(errno), errnum, s) cdef class tabix_file_iterator: '''iterate over a compressed or uncompressed ``infile``. ''' def __cinit__(self, infile, Parser parser, int buffer_size=65536): if infile.closed: raise ValueError("I/O operation on closed file.") self.infile = infile cdef int fd = PyObject_AsFileDescriptor(infile) if fd == -1: raise ValueError("I/O operation on closed file.") self.duplicated_fd = dup(fd) # From the manual: # gzopen can be used to read a file which is not in gzip format; # in this case gzread will directly read from the file without decompression. # When reading, this will be detected automatically by looking # for the magic two-byte gzip header. self.fh = bgzf_dopen(self.duplicated_fd, 'r') if self.fh == NULL: raise IOError('%s' % strerror(errno)) self.kstream = ks_init(self.fh) self.buffer.s = malloc(buffer_size) #if self.buffer == NULL: # raise MemoryError( "tabix_file_iterator: could not allocate %i bytes" % buffer_size) #self.size = buffer_size self.parser = parser def __iter__(self): return self cdef __cnext__(self): cdef char * b cdef int dret = 0 cdef int retval = 0 while 1: with nogil: retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret) if retval < 0: break #raise IOError('gzip error: %s' % buildGzipError( self.fh )) b = self.buffer.s # skip comments if (b[0] == b'#'): continue # skip empty lines if b[0] == b'\0' or b[0] == b'\n' or b[0] == b'\r': continue # gzgets terminates at \n, no need to test # parser creates a copy return self.parser.parse(b, self.buffer.l) raise StopIteration def __dealloc__(self): free(self.buffer.s) ks_destroy(self.kstream) bgzf_close(self.fh) def __next__(self): return self.__cnext__() class tabix_generic_iterator: '''iterate over ``infile``. Permits the use of file-like objects for example from the gzip module. ''' def __init__(self, infile, parser): self.infile = infile if self.infile.closed: raise ValueError("I/O operation on closed file.") self.parser = parser def __iter__(self): return self # cython version - required for python 3 def __next__(self): cdef char * b cdef char * cpy cdef size_t nbytes encoding = self.parser.get_encoding() # note that GzipFile.close() does not close the file # reading is still possible. if self.infile.closed: raise ValueError("I/O operation on closed file.") while 1: line = self.infile.readline() if not line: break s = force_bytes(line, encoding) b = s nbytes = len(line) assert b[nbytes] == b'\0' # skip comments if b[0] == b'#': continue # skip empty lines if b[0] == b'\0' or b[0] == b'\n' or b[0] == b'\r': continue # make sure that entry is complete if b[nbytes-1] != b'\n' and b[nbytes-1] != b'\r': raise ValueError("incomplete line at %s" % line) bytes_cpy = b cpy = bytes_cpy return self.parser(cpy, nbytes) raise StopIteration def tabix_iterator(infile, parser): """return an iterator over all entries in a file. Results are returned parsed as specified by the *parser*. If *parser* is None, the results are returned as an unparsed string. Otherwise, *parser* is assumed to be a functor that will return parsed data (see for example :class:`~pysam.asTuple` and :class:`~pysam.asGTF`). """ return tabix_generic_iterator(infile, parser) cdef class Tabixfile(TabixFile): """Tabixfile is deprecated: use TabixFile instead""" pass __all__ = [ "tabix_index", "tabix_compress", "TabixFile", "Tabixfile", "asTuple", "asGTF", "asGFF3", "asVCF", "asBed", "GZIterator", "GZIteratorHead", "tabix_iterator", "tabix_generic_iterator", "tabix_file_iterator", ] pysam-0.23.0/pysam/libctabixproxies.pxd000066400000000000000000000024521475062545500201660ustar00rootroot00000000000000# cython: language_level=3 from libc.stdint cimport uint8_t, int32_t, uint32_t, int64_t, uint64_t cdef class TupleProxy: cdef: char * data char ** fields int nfields int nbytes int offset bint is_modified cdef encoding cpdef int getMaxFields(self) cpdef int getMinFields(self) # cdef char * _getindex(self, int idx) cdef take(self, char * buffer, size_t nbytes) cdef present(self, char * buffer, size_t nbytes) cdef copy(self, char * buffer, size_t nbytes, bint reset=*) cdef update(self, char * buffer, size_t nbytes) cdef class TupleProxyIterator: cdef TupleProxy proxy cdef int index cdef class NamedTupleProxy(TupleProxy): pass cdef class GTFProxy(NamedTupleProxy): cdef object attribute_dict cpdef int getMaxFields(self) cpdef int getMinFields(self) cdef class GFF3Proxy(GTFProxy): pass cdef class BedProxy(NamedTupleProxy): cdef: char * contig uint32_t start uint32_t end int bedfields cpdef int getMaxFields(self) cpdef int getMinFields(self) cdef update(self, char * buffer, size_t nbytes) cdef class VCFProxy(NamedTupleProxy) : cdef: char * contig uint32_t pos cdef update(self, char * buffer, size_t nbytes) pysam-0.23.0/pysam/libctabixproxies.pyi000066400000000000000000000041171475062545500201740ustar00rootroot00000000000000from typing import ( Optional, overload, List, Dict, OrderedDict, Tuple, Iterable, KeysView, Any, ) class TupleProxyIterator: def __init__(self, proxy: Any): ... def __iter__(self) -> TupleProxyIterator: ... def __next__(self) -> Optional[str]: ... class TupleProxy: def __init__(self, encoding: str = ...) -> None: ... def __copy__(self) -> TupleProxy: ... def compare(self, other: TupleProxy) -> int: ... def getMinFields(self) -> int: ... def getMaxFields(self) -> int: ... def _getindex(self, index: int) -> str: ... @overload def __getitem__(self, key: slice) -> List[str]: ... @overload def __getitem__(self, key: int) -> Any: ... def _setindex(self, index: int, value: Optional[str]) -> None: ... def __setitem__(self, index: int, value: Optional[str]) -> None: ... def __len__(self) -> int: ... def __iter__(self) -> TupleProxyIterator: ... class NamedTupleProxy(TupleProxy): def __setattr__(self, key: str, value: str) -> None: ... def __getattr__(self, key: str) -> str: ... class GTFProxy(NamedTupleProxy): def to_dict(self) -> Dict[str, Any]: ... def from_dict(self, d: Dict[str, Any]) -> None: ... def invert(self, lcontig: int) -> None: ... def keys(self) -> KeysView[str]: ... def setAttribute(self, key: str, value: Any) -> None: ... def attribute_string2dict(self, s: str) -> OrderedDict[str, Any]: ... def dict2attribute_string(self, d: Dict[str, Any]) -> str: ... def attribute_string2iterator(self, s: str) -> Iterable[Tuple[str, Any]]: ... def __getattr__(self, key: str) -> Any: ... def __setattr__(self, key: str, value: Any) -> None: ... # deprecated: # def asDict(self) -> Any: ... # def as_dict(self) -> Any: ... # def fromDict(self, *args, **kwargs) -> Any: ... class GFF3Proxy(GTFProxy): ... class BedProxy(NamedTupleProxy): def __setattr__(self, key: str, value: Any) -> None: ... class VCFProxy(NamedTupleProxy): @property def pos(self) -> int: ... def __setattr__(self, key: str, value: Any) -> None: ... pysam-0.23.0/pysam/libctabixproxies.pyx000066400000000000000000000610141475062545500202120ustar00rootroot00000000000000from cpython cimport PyBytes_FromStringAndSize from libc.stdio cimport printf, feof, fgets from libc.string cimport strcpy, strlen, memcmp, memcpy, memchr, strstr, strchr from libc.stdlib cimport free, malloc, calloc, realloc from libc.stdlib cimport atoi, atol, atof from pysam.libcutils cimport force_bytes, force_str, charptr_to_str from pysam.libcutils cimport encode_filename, from_string_and_size import collections import copy cdef char *StrOrEmpty(char * buffer): if buffer == NULL: return "" else: return buffer cdef int isNew(char * p, char * buffer, size_t nbytes): """return True if `p` is located within `buffer` of size `nbytes` """ if p == NULL: return 0 return not (buffer <= p <= buffer + nbytes) cdef class TupleProxy: '''Proxy class for access to parsed row as a tuple. This class represents a table row for fast read-access. Access to individual fields is via the [] operator. Only read-only access is implemented. ''' def __cinit__(self, encoding="ascii"): self.data = NULL self.fields = NULL self.nbytes = 0 self.is_modified = 0 self.nfields = 0 # start counting at field offset self.offset = 0 self.encoding = encoding def __dealloc__(self): cdef int x if self.is_modified: for x from 0 <= x < self.nfields: if isNew(self.fields[x], self.data, self.nbytes): free(self.fields[x]) self.fields[x] = NULL if self.data != NULL: free(self.data) if self.fields != NULL: free(self.fields) def __copy__(self): if self.is_modified: raise NotImplementedError( "copying modified tuples is not implemented") cdef TupleProxy n = type(self)() n.copy(self.data, self.nbytes, reset=True) return n def compare(self, TupleProxy other): '''return -1,0,1, if contents in this are binary <,=,> to *other* ''' if self.is_modified or other.is_modified: raise NotImplementedError( 'comparison of modified TupleProxies is not implemented') if self.data == other.data: return 0 if self.nbytes < other.nbytes: return -1 elif self.nbytes > other.nbytes: return 1 return memcmp(self.data, other.data, self.nbytes) def __richcmp__(self, TupleProxy other, int op): if op == 2: # == operator return self.compare(other) == 0 elif op == 3: # != operator return self.compare(other) != 0 else: err_msg = "op {0} isn't implemented yet".format(op) raise NotImplementedError(err_msg) cdef take(self, char * buffer, size_t nbytes): '''start presenting buffer. Take ownership of the pointer. ''' self.data = buffer self.nbytes = nbytes self.update(buffer, nbytes) cdef present(self, char * buffer, size_t nbytes): '''start presenting buffer. Do not take ownership of the pointer. ''' self.update(buffer, nbytes) cdef copy(self, char * buffer, size_t nbytes, bint reset=False): '''start presenting buffer of size *nbytes*. Buffer is a '\0'-terminated string without the '\n'. Take a copy of buffer. ''' # +1 for '\0' cdef int s = sizeof(char) * (nbytes + 1) self.data = malloc(s) if self.data == NULL: raise ValueError("out of memory in TupleProxy.copy()") memcpy(self.data, buffer, s) if reset: for x from 0 <= x < nbytes: if self.data[x] == b'\0': self.data[x] = b'\t' self.update(self.data, nbytes) cpdef int getMinFields(self): '''return minimum number of fields.''' # 1 is not a valid tabix entry, but TupleProxy # could be more generic. return 1 cpdef int getMaxFields(self): '''return maximum number of fields. Return 0 for unknown length.''' return 0 cdef update(self, char * buffer, size_t nbytes): '''update internal data. *buffer* is a \0 terminated string. *nbytes* is the number of bytes in buffer (excluding the \0) Update starts work in buffer, thus can be used to collect any number of fields until nbytes is exhausted. If max_fields is set, the number of fields is initialized to max_fields. ''' cdef char * pos cdef char * old_pos cdef int field cdef int max_fields, min_fields, x assert strlen(buffer) == nbytes, \ "length of buffer (%i) != number of bytes (%i)" % ( strlen(buffer), nbytes) if buffer[nbytes] != 0: raise ValueError("incomplete line at %s" % buffer) ################################# # remove line breaks and feeds and update number of bytes x = nbytes - 1 while x > 0 and (buffer[x] == b'\n' or buffer[x] == b'\r'): buffer[x] = b'\0' x -= 1 self.nbytes = x + 1 ################################# # clear data if self.fields != NULL: free(self.fields) for field from 0 <= field < self.nfields: if isNew(self.fields[field], self.data, self.nbytes): free(self.fields[field]) self.is_modified = self.nfields = 0 ################################# # allocate new max_fields = self.getMaxFields() # pre-count fields - better would be # to guess or dynamically grow if max_fields == 0: for x from 0 <= x < nbytes: if buffer[x] == b'\t': max_fields += 1 max_fields += 1 self.fields = calloc(max_fields, sizeof(char *)) if self.fields == NULL: raise ValueError("out of memory in TupleProxy.update()") ################################# # start filling field = 0 self.fields[field] = pos = buffer field += 1 old_pos = pos while 1: pos = memchr(pos, b'\t', nbytes) if pos == NULL: break if field >= max_fields: raise ValueError( "parsing error: more than %i fields in line: %s" % (max_fields, buffer)) pos[0] = b'\0' pos += 1 self.fields[field] = pos field += 1 nbytes -= pos - old_pos if nbytes < 0: break old_pos = pos self.nfields = field if self.nfields < self.getMinFields(): raise ValueError( "parsing error: fewer than %i fields in line: %s" % (self.getMinFields(), buffer)) def _getindex(self, int index): '''return item at idx index''' cdef int i = index if i < 0: i += self.nfields if i < 0: raise IndexError("list index out of range") # apply offset - separating a fixed number # of fields from a variable number such as in VCF i += self.offset if i >= self.nfields: raise IndexError( "list index out of range %i >= %i" % (i, self.nfields)) return force_str(self.fields[i], self.encoding) def __getitem__(self, key): if type(key) == int: return self._getindex(key) # slice object start, end, step = key.indices(self.nfields) result = [] for index in range(start, end, step): result.append(self._getindex(index)) return result def _setindex(self, index, value): '''set item at idx index.''' cdef int idx = index if idx < 0: raise IndexError("list index out of range") if idx >= self.nfields: raise IndexError("list index out of range") if isNew(self.fields[idx], self.data, self.nbytes): free(self.fields[idx]) self.is_modified = 1 if value is None: self.fields[idx] = NULL return # conversion with error checking value = force_bytes(value) cdef char * tmp = value self.fields[idx] = malloc((strlen( tmp ) + 1) * sizeof(char)) if self.fields[idx] == NULL: raise ValueError("out of memory" ) strcpy(self.fields[idx], tmp) def __setitem__(self, index, value): '''set item at *index* to *value*''' cdef int i = index if i < 0: i += self.nfields i += self.offset self._setindex(i, value) def __len__(self): return self.nfields def __iter__(self): return TupleProxyIterator(self) def __str__(self): '''return original data''' # copy and replace \0 bytes with \t characters cdef char * cpy if self.is_modified: # todo: treat NULL values result = [] for x in xrange(0, self.nfields): result.append(StrOrEmpty(self.fields[x]).decode(self.encoding)) return "\t".join(result) else: cpy = calloc(sizeof(char), self.nbytes+1) if cpy == NULL: raise ValueError("out of memory") memcpy(cpy, self.data, self.nbytes+1) for x from 0 <= x < self.nbytes: if cpy[x] == b'\0': cpy[x] = b'\t' result = cpy[:self.nbytes] free(cpy) r = result.decode(self.encoding) return r cdef class TupleProxyIterator: def __init__(self, proxy): self.proxy = proxy self.index = 0 def __iter__(self): return self def __next__(self): if self.index >= self.proxy.nfields: raise StopIteration cdef char *retval = self.proxy.fields[self.index] self.index += 1 return force_str(retval, self.proxy.encoding) if retval != NULL else None def toDot(v): '''convert value to '.' if None''' if v is None: return "." else: return str(v) def quote(v): '''return a quoted attribute.''' if isinstance(v, str): return '"%s"' % v else: return str(v) cdef class NamedTupleProxy(TupleProxy): map_key2field = {} def __setattr__(self, key, value): '''set attribute.''' cdef int idx idx, f = self.map_key2field[key] if idx >= self.nfields: raise KeyError("field %s not set" % key) TupleProxy.__setitem__(self, idx, str(value)) def __getattr__(self, key): cdef int idx idx, f = self.map_key2field[key] if idx >= self.nfields: raise KeyError("field %s not set" % key) if f == str: return force_str(self.fields[idx], self.encoding) return f(self.fields[idx]) cdef dot_or_float(v): if v == "" or v == b".": return None else: try: return int(v) except ValueError: return float(v) cdef dot_or_int(v): if v == "" or v == b".": return None else: return int(v) cdef dot_or_str(v): if v == "" or v == b".": return None else: return force_str(v) cdef int from1based(v): return atoi(v) - 1 cdef str to1based(int v): return str(v + 1) cdef class GTFProxy(NamedTupleProxy): '''Proxy class for access to GTF fields. This class represents a GTF entry for fast read-access. Write-access has been added as well, though some care must be taken. If any of the string fields (contig, source, ...) are set, the new value is tied to the lifetime of the argument that was supplied. The only exception is the attributes field when set from a dictionary - this field will manage its own memory. ''' separator = "; " # first value is field index, the tuple contains conversion # functions for getting (converting internal string representation # to pythonic value) and setting (converting pythonic value to # interval string representation) map_key2field = { 'contig' : (0, (str, str)), 'source' : (1, (dot_or_str, str)), 'feature': (2, (dot_or_str, str)), 'start' : (3, (from1based, to1based)), 'end' : (4, (int, int)), 'score' : (5, (dot_or_float, toDot)), 'strand' : (6, (dot_or_str, str)), 'frame' : (7, (dot_or_int, toDot)), 'attributes': (8, (str, str))} def __cinit__(self): # automatically calls TupleProxy.__cinit__ self.attribute_dict = None cpdef int getMinFields(self): '''return minimum number of fields.''' return 9 cpdef int getMaxFields(self): '''return max number of fields.''' return 9 def to_dict(self): """parse attributes - return as dict The dictionary can be modified to update attributes. """ if not self.attribute_dict: self.attribute_dict = self.attribute_string2dict( self.attributes) self.is_modified = True return self.attribute_dict def as_dict(self): """deprecated: use :meth:`to_dict` """ return self.to_dict() def from_dict(self, d): '''set attributes from a dictionary.''' self.attribute_dict = None attribute_string = force_bytes( self.attribute_dict2string(d), self.encoding) self._setindex(8, attribute_string) def __str__(self): cdef char * cpy cdef int x if self.is_modified: return "\t".join( (self.contig, toDot(self.source), toDot(self.feature), str(self.start + 1), str(self.end), toDot(self.score), toDot(self.strand), toDot(self.frame), self.attributes)) else: return super().__str__() def invert(self, int lcontig): '''invert coordinates to negative strand coordinates This method will only act if the feature is on the negative strand.''' if self.strand[0] == '-': start = min(self.start, self.end) end = max(self.start, self.end) self.start, self.end = lcontig - end, lcontig - start def keys(self): '''return a list of attributes defined in this entry.''' if not self.attribute_dict: self.attribute_dict = self.attribute_string2dict( self.attributes) return self.attribute_dict.keys() def __getitem__(self, key): return self.__getattr__(key) def setAttribute(self, name, value): '''convenience method to set an attribute. ''' if not self.attribute_dict: self.attribute_dict = self.attribute_string2dict( self.attributes) self.attribute_dict[name] = value self.is_modified = True def attribute_string2dict(self, s): return collections.OrderedDict( self.attribute_string2iterator(s)) def __cmp__(self, other): return (self.contig, self.strand, self.start) < \ (other.contig, other.strand, other.start) # python 3 compatibility def __richcmp__(GTFProxy self, GTFProxy other, int op): if op == 0: return (self.contig, self.strand, self.start) < \ (other.contig, other.strand, other.start) elif op == 1: return (self.contig, self.strand, self.start) <= \ (other.contig, other.strand, other.start) elif op == 2: return self.compare(other) == 0 elif op == 3: return self.compare(other) != 0 else: err_msg = "op {0} isn't implemented yet".format(op) raise NotImplementedError(err_msg) def dict2attribute_string(self, d): """convert dictionary to attribute string in GTF format. """ aa = [] for k, v in d.items(): if isinstance(v, str): aa.append('{} "{}"'.format(k, v)) else: aa.append("{} {}".format(k, str(v))) return self.separator.join(aa) + ";" def attribute_string2iterator(self, s): """convert attribute string in GTF format to records and iterate over key, value pairs. """ # remove comments attributes = force_str(s, encoding=self.encoding) # separate into fields # Fields might contain a ";", for example in ENSEMBL GTF file # for mouse, v78: # ...; transcript_name "TXNRD2;-001"; .... # The current heuristic is to split on a semicolon followed by a # space, see also http://mblab.wustl.edu/GTF22.html # Remove white space to prevent a last empty field. fields = [x.strip() for x in attributes.strip().split("; ")] for f in fields: # strip semicolon (GTF files without a space after the last semicolon) if f.endswith(";"): f = f[:-1] # split at most once in order to avoid separating # multi-word values d = [x.strip() for x in f.split(" ", 1)] n, v = d[0], d[1] if len(d) > 2: v = d[1:] if v[0] == '"' and v[-1] == '"': v = v[1:-1] else: ## try to convert to a value try: v = float(v) v = int(v) except ValueError: pass except TypeError: pass yield n, v def __getattr__(self, key): """Generic lookup of attribute from GFF/GTF attributes """ # Only called if there *isn't* an attribute with this name cdef int idx idx, f = self.map_key2field.get(key, (-1, None)) if idx >= 0: # deal with known attributes (fields 0-8) if idx == 8: # flush attributes if requested if self.is_modified and self.attribute_dict is not None: s = self.dict2attribute_string(self.attribute_dict) TupleProxy._setindex(self, idx, s) self.attribute_dict = None return s if f[0] == str: return force_str(self.fields[idx], self.encoding) else: return f[0](self.fields[idx]) else: # deal with generic attributes (gene_id, ...) if self.attribute_dict is None: self.attribute_dict = self.attribute_string2dict( self.attributes) return self.attribute_dict[key] def __setattr__(self, key, value): '''set attribute.''' # Note that __setattr__ is called before properties, so __setattr__ and # properties don't mix well. This is different from __getattr__ which is # called after any properties have been resolved. cdef int idx idx, f = self.map_key2field.get(key, (-1, None)) if idx >= 0: if value is None: s = "." elif f[1] == str: s = force_bytes(value, self.encoding) else: s = str(f[1](value)) TupleProxy._setindex(self, idx, s) else: if self.attribute_dict is None: self.attribute_dict = self.attribute_string2dict( self.attributes) self.attribute_dict[key] = value self.is_modified = True # for backwards compatibility def asDict(self, *args, **kwargs): return self.to_dict(*args, **kwargs) def fromDict(self, *args, **kwargs): return self.from_dict(*args, **kwargs) cdef class GFF3Proxy(GTFProxy): def dict2attribute_string(self, d): """convert dictionary to attribute string.""" return ";".join(["{}={}".format(k, v) for k, v in d.items()]) def attribute_string2iterator(self, s): """convert attribute string in GFF3 format to records and iterate over key, value pairs. """ for f in (x.strip() for x in s.split(";")): if not f: continue key, value = f.split("=", 1) value = value.strip() ## try to convert to a value try: value = float(value) value = int(value) except ValueError: pass except TypeError: pass yield key.strip(), value cdef class BedProxy(NamedTupleProxy): '''Proxy class for access to Bed fields. This class represents a BED entry for fast read-access. ''' map_key2field = { 'contig' : (0, str), 'start' : (1, int), 'end' : (2, int), 'name' : (3, str), 'score' : (4, float), 'strand' : (5, str), 'thickStart' : (6, int), 'thickEnd' : (7, int), 'itemRGB' : (8, str), 'blockCount': (9, int), 'blockSizes': (10, str), 'blockStarts': (11, str), } cpdef int getMinFields(self): '''return minimum number of fields.''' return 3 cpdef int getMaxFields(self): '''return max number of fields.''' return 12 cdef update(self, char * buffer, size_t nbytes): '''update internal data. nbytes does not include the terminal '\0'. ''' NamedTupleProxy.update(self, buffer, nbytes) if self.nfields < 3: raise ValueError( "bed format requires at least three columns") # determines bed format self.bedfields = self.nfields # do automatic conversion self.contig = self.fields[0] self.start = atoi(self.fields[1]) self.end = atoi(self.fields[2]) # __setattr__ in base class seems to take precedence # hence implement setters in __setattr__ #property start: # def __get__( self ): return self.start #property end: # def __get__( self ): return self.end def __str__(self): cdef int save_fields = self.nfields # ensure fields to use correct format self.nfields = self.bedfields retval = super().__str__() self.nfields = save_fields return retval def __setattr__(self, key, value): '''set attribute.''' if key == "start": self.start = value elif key == "end": self.end = value cdef int idx idx, f = self.map_key2field[key] TupleProxy._setindex(self, idx, str(value)) cdef class VCFProxy(NamedTupleProxy): '''Proxy class for access to VCF fields. The genotypes are accessed via a numeric index. Sample headers are not available. ''' map_key2field = { 'contig' : (0, str), 'pos' : (1, int), 'id' : (2, str), 'ref' : (3, str), 'alt' : (4, str), 'qual' : (5, str), 'filter' : (6, str), 'info' : (7, str), 'format' : (8, str) } def __cinit__(self): # automatically calls TupleProxy.__cinit__ # start indexed access at genotypes self.offset = 9 cdef update(self, char * buffer, size_t nbytes): '''update internal data. nbytes does not include the terminal '\0'. ''' NamedTupleProxy.update(self, buffer, nbytes) self.contig = self.fields[0] # vcf counts from 1 - correct here self.pos = atoi(self.fields[1]) - 1 def __len__(self): '''return number of genotype fields.''' return max(0, self.nfields - 9) property pos: '''feature end (in 0-based open/closed coordinates).''' def __get__(self): return self.pos def __setattr__(self, key, value): '''set attribute.''' if key == "pos": self.pos = value value += 1 cdef int idx idx, f = self.map_key2field[key] TupleProxy._setindex(self, idx, str(value)) __all__ = [ "TupleProxy", "NamedTupleProxy", "GTFProxy", "GFF3Proxy", "BedProxy", "VCFProxy"] pysam-0.23.0/pysam/libcutils.pxd000066400000000000000000000030741475062545500166060ustar00rootroot00000000000000# cython: language_level=3 ######################################################################### # Utility functions used across pysam ######################################################################### cimport cython from cpython cimport array as c_array cpdef parse_region(contig=*, start=*, stop=*, region=*, reference=*, end=*) cdef int libc_whence_from_io(int whence) ######################################################################### # Utility functions for quality string conversions cpdef c_array.array qualitystring_to_array(input_str, int offset=*) cpdef array_to_qualitystring(c_array.array arr, int offset=*) cpdef qualities_to_qualitystring(qualities, int offset=*) ######################################################################## ## String encoding configuration facilities ######################################################################## cpdef get_encoding_error_handler() cpdef set_encoding_error_handler(name) ######################################################################## ## Python 3 compatibility functions ######################################################################## cdef charptr_to_str(const char *s, encoding=*, errors=*) cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*) cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*) cdef force_str(object s, encoding=*, errors=*) cdef bytes force_bytes(object s, encoding=*, errors=*) cdef decode_bytes(bytes s, encoding=*, errors=*) cdef bytes encode_filename(object filename) cdef from_string_and_size(const char *s, size_t length) pysam-0.23.0/pysam/libcutils.pyi000066400000000000000000000017151475062545500166140ustar00rootroot00000000000000from array import array from typing import Iterable, Optional, Tuple, Union def get_encoding_error_handler() -> str: ... def set_encoding_error_handler(name: str) -> str: ... def _pysam_dispatch( collection: str, method: str, args: Optional[Iterable[str]], catch_stdout: bool = ..., is_usage: bool = ..., save_stdout: Optional[str] = ..., ) -> Tuple[int, Union[bytes, str], Union[bytes, str]]: ... def parse_region( contig: Optional[str] = ..., start: Optional[int] = ..., stop: Optional[int] = ..., region: Optional[str] = ..., reference: Optional[str] = ..., end: Optional[int] = ..., ) -> Tuple[str, int, int]: ... def qualitystring_to_array( input_str: Optional[str], offset: int = ... ) -> Optional[array]: ... def array_to_qualitystring(qualities: array, offset: int = ...) -> Optional[str]: ... def qualities_to_qualitystring( qualities: Union[array, Iterable[str]], offset: int = ... ) -> Optional[str]: ... pysam-0.23.0/pysam/libcutils.pyx000066400000000000000000000335341475062545500166370ustar00rootroot00000000000000# cython: language_level=3 import types import sys import string import re import tempfile import os import io from contextlib import contextmanager from codecs import register_error from cpython.version cimport PY_MAJOR_VERSION, PY_MINOR_VERSION from cpython cimport PyBytes_Check, PyUnicode_Check from cpython cimport array as c_array from libc.errno cimport errno from libc.stdlib cimport calloc, free from libc.string cimport strncpy from libc.stdint cimport INT32_MAX, int32_t from libc.stdio cimport fprintf, stderr, fflush from libc.stdio cimport stdout as c_stdout from posix.fcntl cimport open as c_open, O_WRONLY, O_CREAT, O_TRUNC from posix.unistd cimport SEEK_SET, SEEK_CUR, SEEK_END from pysam.libcsamtools cimport samtools_dispatch, samtools_set_stdout, samtools_set_stderr, \ samtools_close_stdout, samtools_close_stderr, samtools_set_stdout_fn from pysam.libcbcftools cimport bcftools_dispatch, bcftools_set_stdout, bcftools_set_stderr, \ bcftools_close_stdout, bcftools_close_stderr, bcftools_set_stdout_fn ##################################################################### # hard-coded constants cdef int MAX_POS = (1 << 31) - 1 ################################################################# # Utility functions for quality string conversions cpdef c_array.array qualitystring_to_array(input_str, int offset=33): """convert a qualitystring to an array of quality values.""" if input_str is None: return None qs = force_bytes(input_str) cdef char i return c_array.array('B', [i - offset for i in qs]) cpdef array_to_qualitystring(c_array.array qualities, int offset=33): """convert an array of quality values to a string.""" if qualities is None: return None cdef int x cdef c_array.array result result = c_array.clone(qualities, len(qualities), zero=False) for x from 0 <= x < len(qualities): result[x] = qualities[x] + offset return force_str(result.tobytes()) cpdef qualities_to_qualitystring(qualities, int offset=33): """convert a list or array of quality scores to the string representation used in the SAM format. Parameters ---------- offset : int offset to be added to the quality scores to arrive at the characters of the quality string (default=33). Returns ------- string a quality string """ cdef char x if qualities is None: return None elif isinstance(qualities, c_array.array): return array_to_qualitystring(qualities, offset=offset) else: # tuples and lists return force_str("".join([chr(x + offset) for x in qualities])) ######################################################################## ## String encoding configuration facilities ######################################################################## # Codec error handler that just interprets each bad byte as ISO-8859-1. def latin1_replace(exception): return (chr(exception.object[exception.start]), exception.end) register_error('pysam.latin1replace', latin1_replace) cdef str ERROR_HANDLER = 'strict' cpdef get_encoding_error_handler(): return ERROR_HANDLER cpdef set_encoding_error_handler(name): global ERROR_HANDLER previous = ERROR_HANDLER ERROR_HANDLER = name return previous ######################################################################## ## Python 3 compatibility functions ######################################################################## cdef from_string_and_size(const char* s, size_t length): return s[:length].decode('utf-8', ERROR_HANDLER) # filename encoding (adapted from lxml.etree.pyx) cdef str FILENAME_ENCODING = sys.getfilesystemencoding() or sys.getdefaultencoding() or 'ascii' cdef str TEXT_ENCODING = 'utf-8' cdef bytes encode_filename(object filename): """Make sure a filename is 8-bit encoded (or None).""" if filename is None: return None return os.fsencode(filename) cdef bytes force_bytes(object s, encoding=None, errors=None): """convert string or unicode object to bytes, assuming utf8 encoding. """ if s is None: return None elif PyBytes_Check(s): return s elif PyUnicode_Check(s): return s.encode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER) else: raise TypeError("Argument must be string, bytes or unicode.") cdef charptr_to_str(const char* s, encoding=None, errors=None): if s == NULL: return None return s.decode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER) cdef charptr_to_str_w_len(const char* s, size_t n, encoding=None, errors=None): if s == NULL: return None return s[:n].decode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER) cdef bytes charptr_to_bytes(const char* s, encoding=None, errors=None): if s == NULL: return None else: return s cdef force_str(object s, encoding=None, errors=None): """Return s converted to str type of current Python (bytes in Py2, unicode in Py3)""" if s is None: return None if PyBytes_Check(s): return s.decode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER) # assume unicode return s cdef decode_bytes(bytes s, encoding=None, errors=None): """Return s converted to current Python's str type, always decoding even in Python 2""" if s is None: return None else: return s.decode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER) cpdef parse_region(contig=None, start=None, stop=None, region=None, reference=None, end=None): """parse alternative ways to specify a genomic region. A region can either be specified by :term:`reference`, `start` and `end`. `start` and `end` denote 0-based, half-open intervals. :term:`reference` and `end` are also accepted for backward compatibility as synonyms for :term:`contig` and `stop`, respectively. Alternatively, a samtools :term:`region` string can be supplied. If any of the coordinates are missing they will be replaced by the minimum (`start`) or maximum (`end`) coordinate. Note that region strings are 1-based, while `start` and `end` denote an interval in python coordinates. Returns ------- tuple : a tuple of `reference`, `start` and `end`. Raises ------ ValueError for invalid or out of bounds regions. """ cdef int32_t rstart cdef int32_t rstop if reference is not None: if contig is not None: raise ValueError('contig and reference should not both be specified') contig = reference if contig is not None and region is not None: raise ValueError('contig/reference and region should not both be specified') if end is not None: if stop is not None: raise ValueError('stop and end should not both be specified') stop = end if contig is None and region is None: raise ValueError("neither contig nor region are given") rstart = 0 rstop = MAX_POS if start is not None: try: rstart = start except OverflowError: raise ValueError('start out of range (%i)' % start) if stop is not None: try: rstop = stop except OverflowError: raise ValueError('stop out of range (%i)' % stop) if region: if ":" in region: contig, coord = region.split(":") parts = coord.split("-") rstart = int(parts[0]) - 1 if len(parts) >= 1: rstop = int(parts[1]) else: contig = region if rstart > rstop: raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop)) if not 0 <= rstart < MAX_POS: raise ValueError('start out of range (%i)' % rstart) if not 0 <= rstop <= MAX_POS: raise ValueError('stop out of range (%i)' % rstop) return contig, rstart, rstop cdef int libc_whence_from_io(int whence): # io.SEEK_SET/_CUR/_END are by definition 0/1/2 but C/POSIX's equivalents # have unspecified values. So we must translate, but checking for 0/1/2 # rather than io.SEEK_SET/etc suffices. if whence == 0: return SEEK_SET if whence == 1: return SEEK_CUR if whence == 2: return SEEK_END return whence # Otherwise likely invalid, but let HTSlib or OS report it def _pysam_dispatch(collection, method, args=None, catch_stdout=True, is_usage=False, save_stdout=None): '''call ``method`` in samtools/bcftools providing arguments in args. By default, stdout is redirected to a temporary file using the patched C sources except for a few commands that have an explicit output option (typically: -o). In these commands (such as samtools view), this explicit option is used. If *is_usage* is True, then these explicit output options will not be used. Catching of stdout can be turned off by setting *catch_stdout* to False. ''' if method == "index" and args: # We make sure that at least the first specified input file exists, # and if it doesn't we raise an IOError. ARGUMENTS = ['-m', '--min-shift', '-o', '--output', '--output-file', '-@', '--threads'] skip_next = False for arg in args: if skip_next: skip_next = False continue if arg.startswith('-'): # Skip next argument for e.g. '--min-shift' '12' or '-m' '12' but not '-m12' if arg in ARGUMENTS: skip_next = True continue if not os.path.exists(arg): raise IOError("No such file or directory: '%s'" % arg) else: break if args is None: args = [] else: args = list(args) # redirect stderr to file stderr_h, stderr_f = tempfile.mkstemp() # redirect stdout to file if save_stdout: stdout_f = save_stdout stdout_h = c_open(force_bytes(stdout_f), O_WRONLY|O_CREAT|O_TRUNC, 0666) if stdout_h == -1: raise OSError(errno, "error while opening file for writing", stdout_f) samtools_set_stdout_fn(force_bytes(stdout_f)) bcftools_set_stdout_fn(force_bytes(stdout_f)) elif catch_stdout: stdout_h, stdout_f = tempfile.mkstemp() MAP_STDOUT_OPTIONS = { "samtools": { "view": "-o {}", "mpileup": "-o {}", "depad": "-o {}", "calmd": "", # uses pysam_stdout_fn }, "bcftools": {} } stdout_option = None if collection == "bcftools": # in bcftools, most methods accept -o, the exceptions # are below: if method not in ("head", "index", "roh", "stats"): stdout_option = "-o {}" elif method in MAP_STDOUT_OPTIONS[collection]: # special case - samtools view -c outputs on stdout if not(method == "view" and "-c" in args): stdout_option = MAP_STDOUT_OPTIONS[collection][method] if stdout_option is not None and not is_usage: os.close(stdout_h) samtools_set_stdout_fn(force_bytes(stdout_f)) bcftools_set_stdout_fn(force_bytes(stdout_f)) args.extend(stdout_option.format(stdout_f).split(" ")) stdout_h = c_open(b"/dev/null", O_WRONLY) else: samtools_set_stdout_fn("-") bcftools_set_stdout_fn("-") stdout_h = c_open(b"/dev/null", O_WRONLY) # setup the function call to samtools/bcftools main cdef char ** cargs cdef int i, n, retval, l n = len(args) method = force_bytes(method) collection = force_bytes(collection) args = [force_bytes(a) for a in args] # allocate two more for first (dummy) argument (contains command) cdef int extra_args = 0 if method == b"index": extra_args = 1 # add extra arguments for commands accepting optional arguments # such as 'samtools index x.bam [out.index]' cargs = calloc(n + 2 + extra_args, sizeof(char *)) cargs[0] = collection cargs[1] = method # create copies of strings - getopt for long options permutes # arguments for i from 0 <= i < n: l = len(args[i]) cargs[i + 2] = calloc(l + 1, sizeof(char)) strncpy(cargs[i + 2], args[i], l) # call samtools/bcftools if collection == b"samtools": samtools_set_stdout(stdout_h) samtools_set_stderr(stderr_h) retval = samtools_dispatch(n + 2, cargs) samtools_close_stdout() samtools_close_stderr() elif collection == b"bcftools": bcftools_set_stdout(stdout_h) bcftools_set_stderr(stderr_h) retval = bcftools_dispatch(n + 2, cargs) bcftools_close_stdout() bcftools_close_stderr() else: # unknown -- just return a Unix shell's "command not found" exit status retval = 127 for i from 0 <= i < n: free(cargs[i + 2]) free(cargs) # get error messages def _collect(fn): out = [] try: with open(fn, "r") as inf: out = inf.read() except UnicodeDecodeError: with open(fn, "rb") as inf: # read binary output out = inf.read() finally: os.remove(fn) return out out_stderr = _collect(stderr_f) if save_stdout: out_stdout = None elif catch_stdout: out_stdout = _collect(stdout_f) else: out_stdout = None return retval, out_stderr, out_stdout __all__ = [ "qualitystring_to_array", "array_to_qualitystring", "qualities_to_qualitystring", "get_encoding_error_handler", "set_encoding_error_handler", ] pysam-0.23.0/pysam/libcvcf.pxd000066400000000000000000000000341475062545500162150ustar00rootroot00000000000000# cython: language_level=3 pysam-0.23.0/pysam/libcvcf.pyi000066400000000000000000000000001475062545500162140ustar00rootroot00000000000000pysam-0.23.0/pysam/libcvcf.pyx000066400000000000000000001460021475062545500162500ustar00rootroot00000000000000# cython: embedsignature=True # # Code to read, write and edit VCF files # # VCF lines are encoded as a dictionary with these keys (note: all lowercase): # 'chrom': string # 'pos': integer # 'id': string # 'ref': string # 'alt': list of strings # 'qual': integer # 'filter': None (missing value), or list of keys (strings); empty list parsed as ["PASS"] # 'info': dictionary of values (see below) # 'format': list of keys (strings) # sample keys: dictionary of values (see below) # # The sample keys are accessible through vcf.getsamples() # # A dictionary of values contains value keys (defined in ##INFO or # ##FORMAT lines) which map to a list, containing integers, floats, # strings, or characters. Missing values are replaced by a particular # value, often -1 or . # # Genotypes are not stored as a string, but as a list of 1 or 3 # elements (for haploid and diploid samples), the first (and last) the # integer representing an allele, and the second the separation # character. Note that there is just one genotype per sample, but for # consistency the single element is stored in a list. # # Header lines other than ##INFO, ##FORMAT and ##FILTER are stored as # (key, value) pairs and are accessible through getheader() # # The VCF class can be instantiated with a 'regions' variable # consisting of tuples (chrom,start,end) encoding 0-based half-open # segments. Only variants with a position inside the segment will be # parsed. A regions parser is available under parse_regions. # # When instantiated, a reference can be passed to the VCF class. This # may be any class that supports a fetch(chrom, start, end) method. # # NOTE: the position that is returned to Python is 0-based, NOT # 1-based as in the VCF file. # NOTE: There is also preliminary VCF functionality in the VariantFile class. # # TODO: # only v4.0 writing is complete; alleles are not converted to v3.3 format # from collections import namedtuple, defaultdict from operator import itemgetter import sys, re, copy, bisect from libc.stdlib cimport atoi from libc.stdint cimport int8_t, int16_t, int32_t, int64_t from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t cimport pysam.libctabix as libctabix cimport pysam.libctabixproxies as libctabixproxies from pysam.libcutils cimport force_str import pysam gtsRegEx = re.compile("[|/\\\\]") alleleRegEx = re.compile('^[ACGTN]+$') # Utility function. Uses 0-based coordinates def get_sequence(chrom, start, end, fa): # obtain sequence from .fa file, without truncation if end<=start: return "" if not fa: return "N"*(end-start) if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper() sequence = fa.fetch(chrom, start, end).upper() if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence)) return sequence # Utility function. Parses a region string def parse_regions( string ): result = [] for r in string.split(','): elts = r.split(':') chrom, start, end = elts[0], 0, 3000000000 if len(elts)==1: pass elif len(elts)==2: if len(elts[1])>0: ielts = elts[1].split('-') if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r) try: start, end = int(ielts[0])-1, int(ielts[1]) except: raise ValueError("Don't understand region string '%s'" % r) else: raise ValueError("Don't understand region string '%s'" % r) result.append( (chrom,start,end) ) return result FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue') ########################################################################################################### # # New class # ########################################################################################################### cdef class VCFRecord(libctabixproxies.TupleProxy): '''vcf record. initialized from data and vcf meta ''' cdef vcf cdef char * contig cdef uint32_t pos def __init__(self, vcf): self.vcf = vcf self.encoding = vcf.encoding # if len(data) != len(self.vcf._samples): # self.vcf.error(str(data), # self.BAD_NUMBER_OF_COLUMNS, # "expected %s for %s samples (%s), got %s" % \ # (len(self.vcf._samples), # len(self.vcf._samples), # self.vcf._samples, # len(data))) def __cinit__(self, vcf): # start indexed access at genotypes self.offset = 9 self.vcf = vcf self.encoding = vcf.encoding def error(self, line, error, opt=None): '''raise error.''' # pass to vcf file for error handling return self.vcf.error(line, error, opt) cdef update(self, char * buffer, size_t nbytes): '''update internal data. nbytes does not include the terminal '\0'. ''' libctabixproxies.TupleProxy.update(self, buffer, nbytes) self.contig = self.fields[0] # vcf counts from 1 - correct here self.pos = atoi(self.fields[1]) - 1 def __len__(self): return max(0, self.nfields - 9) property contig: def __get__(self): return self.contig property pos: def __get__(self): return self.pos property id: def __get__(self): return self.fields[2] property ref: def __get__(self): return self.fields[3] property alt: def __get__(self): # convert v3.3 to v4.0 alleles below alt = self.fields[4] if alt == ".": alt = [] else: alt = alt.upper().split(',') return alt property qual: def __get__(self): qual = self.fields[5] if qual == b".": qual = -1 else: try: qual = float(qual) except: self.vcf.error(str(self),self.QUAL_NOT_NUMERICAL) return qual property filter: def __get__(self): f = self.fields[6] # postpone checking that filters exist. Encode missing filter or no filtering as empty list if f == b"." or f == b"PASS" or f == b"0": return [] else: return f.split(';') property info: def __get__(self): col = self.fields[7] # dictionary of keys, and list of values info = {} if col != b".": for blurp in col.split(';'): elts = blurp.split('=') if len(elts) == 1: v = None elif len(elts) == 2: v = elts[1] else: self.vcf.error(str(self),self.ERROR_INFO_STRING) info[elts[0]] = self.vcf.parse_formatdata(elts[0], v, self.vcf._info, str(self.vcf)) return info property format: def __get__(self): return self.fields[8].split(':') property samples: def __get__(self): return self.vcf._samples def __getitem__(self, key): # parse sample columns values = self.fields[self.vcf._sample2column[key]].split(':') alt = self.alt format = self.format if len(values) > len(format): self.vcf.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\ (len(values),key,len(format))) result = {} for idx in range(len(format)): expected = self.vcf.get_expected(format[idx], self.vcf._format, alt) if idx < len(values): value = values[idx] else: if expected == -1: value = "." else: value = ",".join(["."]*expected) result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data)) if expected != -1 and len(result[format[idx]]) != expected: self.vcf.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS, "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]])) if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]])) result[format[idx]] = result[format[idx]][:expected] return result cdef class asVCFRecord(libctabix.Parser): '''converts a :term:`tabix row` into a VCF record.''' cdef vcffile def __init__(self, vcffile): self.vcffile = vcffile cdef parse(self, char * buffer, int len): cdef VCFRecord r r = VCFRecord(self.vcffile) r.copy(buffer, len) return r class VCF(object): # types NT_UNKNOWN = 0 NT_NUMBER = 1 NT_ALLELES = 2 NT_NR_ALLELES = 3 NT_GENOTYPES = 4 NT_PHASED_GENOTYPES = 5 _errors = { 0:"UNKNOWN_FORMAT_STRING:Unknown file format identifier", 1:"BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string", 2:"BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s", 3:"BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)", 4:"POS_NOT_NUMERICAL:Position column is not numerical", 5:"UNKNOWN_CHAR_IN_REF:Unknown character in reference field", 6:"V33_BAD_REF:Reference should be single-character in v3.3 VCF", 7:"V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF", 8:"POS_NOT_POSITIVE:Position field must be >0", 9:"QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'", 10:"ERROR_INFO_STRING:Error while parsing info field", 11:"ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)", 12:"ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s", 13:"ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string", 14:"FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header", 15:"FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header", 16:"BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)", 17:"BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)", 18:"BAD_GENOTYPE:Cannot parse genotype (%s)", 19:"V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)", 20:"MISSING_REF:Reference allele missing", 21:"V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)", 22:"V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets", 23:"FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes", 24:"V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields", 25:"HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs", 26:"WRONG_REF:Wrong reference %s", 27:"ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data", 28:"BAD_CHR_TAG:Error calculating chr tag for %s", 29:"ZERO_LENGTH_ALLELE:Found zero-length allele", 30:"MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base", 31:"ZERO_FOR_NON_FLAG_FIELD: number set to 0, but type is not 'FLAG'", 32:"ERROR_FORMAT_NOT_INTEGER:Expected integer in formatted field; got %s", 33:"ERROR_FLAG_HAS_VALUE:Flag fields should not have a value", } # tag-value pairs; tags are not unique; does not include fileformat, INFO, FILTER or FORMAT fields _header = [] # version number; 33=v3.3; 40=v4.0 _version = 40 # info, filter and format data _info = {} _filter = {} _format = {} # header; and required columns _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"] _samples = [] # control behaviour _ignored_errors = set([11,31]) # ERROR_UNKNOWN_KEY, ERROR_ZERO_FOR_NON_FLAG_FIELD _warn_errors = set([]) _leftalign = False # reference sequence _reference = None # regions to include; None includes everything _regions = None # statefull stuff _lineno = -1 _line = None _lines = None def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False): # make error identifiers accessible by name for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id if _copy != None: self._leftalign = _copy._leftalign self._header = _copy._header[:] self._version = _copy._version self._info = copy.deepcopy(_copy._info) self._filter = copy.deepcopy(_copy._filter) self._format = copy.deepcopy(_copy._format) self._samples = _copy._samples[:] self._sample2column = copy.deepcopy(_copy._sample2column) self._ignored_errors = copy.deepcopy(_copy._ignored_errors) self._warn_errors = copy.deepcopy(_copy._warn_errors) self._reference = _copy._reference self._regions = _copy._regions if reference: self._reference = reference if regions: self._regions = regions if leftalign: self._leftalign = leftalign self._lines = lines self.encoding = "ascii" self.tabixfile = None def error(self,line,error,opt=None): if error in self._ignored_errors: return errorlabel, errorstring = self._errors[error].split(':') if opt: errorstring = errorstring % opt errwarn = ["Error","Warning"][error in self._warn_errors] errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring) if error in self._warn_errors: return raise ValueError(errorstring) def parse_format(self,line,format,filter=False): if self._version == 40: if not format.startswith('<'): self.error(line,self.V40_MISSING_ANGLE_BRACKETS) format = "<"+format if not format.endswith('>'): self.error(line,self.V40_MISSING_ANGLE_BRACKETS) format += ">" format = format[1:-1] data = {'id':None,'number':None,'type':None,'descr':None} idx = 0 while len(format.strip())>0: elts = format.strip().split(',') first, rest = elts[0], ','.join(elts[1:]) if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')): if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS) if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) first = ["ID=","Number=","Type=","Description="][idx] + first if first.startswith('ID='): data['id'] = first.split('=')[1] elif first.startswith('Number='): data['number'] = first.split('=')[1] elif first.startswith('Type='): data['type'] = first.split('=')[1] elif first.startswith('Description='): elts = format.split('"') if len(elts)<3: self.error(line,self.FORMAT_MISSING_QUOTES) elts = first.split('=') + [rest] data['descr'] = elts[1] rest = '"'.join(elts[2:]) if rest.startswith(','): rest = rest[1:] else: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) format = rest idx += 1 if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) if 'descr' not in data: # missing description self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) data['descr'] = "" if not data['type'] and not data['number']: # fine, ##filter format return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.') if not data['type'] in ["Integer","Float","Character","String","Flag"]: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # I would like a missing-value field, but it isn't there if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value else: data['missing'] = '.' if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) try: n = int(data['number']) t = self.NT_NUMBER except ValueError: n = -1 if data['number'] == '.': t = self.NT_UNKNOWN elif data['number'] == '#alleles': t = self.NT_ALLELES elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES elif data['number'] == '#genotypes': t = self.NT_GENOTYPES elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES # abbreviations added in VCF version v4.1 elif data['number'] == 'A': t = self.NT_ALLELES elif data['number'] == 'G': t = self.NT_GENOTYPES else: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # if number is 0 - type must be Flag if n == 0 and data['type'] != 'Flag': self.error( line, self.ZERO_FOR_NON_FLAG_FIELD) # force type 'Flag' if no number data['type'] = 'Flag' return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing']) def format_format( self, fmt, filter=False ): values = [('ID',fmt.id)] if fmt.number != None and not filter: if fmt.numbertype == self.NT_UNKNOWN: nmb = "." elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number) elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles" elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles" elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes" elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes" else: raise ValueError("Unknown number type encountered: %s" % fmt.numbertype) values.append( ('Number',nmb) ) values.append( ('Type', fmt.type) ) values.append( ('Description', '"' + fmt.description + '"') ) if self._version == 33: format = ",".join([v for k,v in values]) else: format = "<" + (",".join( ["%s=%s" % (k,v) for (k,v) in values] )) + ">" return format def get_expected(self, format, formatdict, alt): fmt = formatdict[format] if fmt.numbertype == self.NT_UNKNOWN: return -1 if fmt.numbertype == self.NT_NUMBER: return fmt.number if fmt.numbertype == self.NT_ALLELES: return len(alt)+1 if fmt.numbertype == self.NT_NR_ALLELES: return len(alt) if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2 if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1) return 0 def _add_definition(self, formatdict, key, data, line ): if key in formatdict: return self.error(line,self.ERROR_UNKNOWN_KEY,key) if data == None: formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".") return if data == []: data = [""] # unsure what type -- say string if type(data[0]) == type(0.0): formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None) return if type(data[0]) == type(0): formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None) return formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".") # todo: trim trailing missing values def format_formatdata( self, data, format, key=True, value=True, separator=":" ): output, sdata = [], [] if type(data) == type([]): # for FORMAT field, make data with dummy values d = {} for k in data: d[k] = [] data = d # convert missing values; and silently add definitions if required for k in data: self._add_definition( format, k, data[k], "(output)" ) for idx,v in enumerate(data[k]): if v == format[k].missingvalue: data[k][idx] = "." # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string for k in data: if k != 'GT': sdata.append( (k,data[k]) ) sdata.sort() if 'GT' in data: sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata for k,v in sdata: if v == []: v = None if key and value: if v != None: output.append( k+"="+','.join(map(str,v)) ) else: output.append( k ) elif key: output.append(k) elif value: if v != None: output.append( ','.join(map(str,v)) ) else: output.append( "." ) # should not happen # snip off trailing missing data while len(output) > 1: last = output[-1].replace(',','').replace('.','') if len(last)>0: break output = output[:-1] return separator.join(output) def enter_default_format(self): for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'), FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1), FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'), FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'), FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'), FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1), FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'), FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'), FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'), FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'), FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1), FORMAT('EC',self.NT_ALLELES,1,'Integer','Expected alternate allel counts',-1), FORMAT('MQ',self.NT_NUMBER,1,'Integer','RMS mapping quality',-1), ]: if f.id not in self._format: self._format[f.id] = f def parse_header(self, line): assert line.startswith('##') elts = line[2:].split('=') key = elts[0].strip() value = '='.join(elts[1:]).strip() if key == "fileformat": if value == "VCFv3.3": self._version = 33 elif value == "VCFv4.0": self._version = 40 elif value == "VCFv4.1": # AH - for testing self._version = 40 elif value == "VCFv4.2": # AH - for testing self._version = 40 else: self.error(line,self.UNKNOWN_FORMAT_STRING) elif key == "INFO": f = self.parse_format(line, value) self._info[ f.id ] = f elif key == "FILTER": f = self.parse_format(line, value, filter=True) self._filter[ f.id ] = f elif key == "FORMAT": f = self.parse_format(line, value) self._format[ f.id ] = f else: # keep other keys in the header field self._header.append( (key,value) ) def write_header( self, stream ): stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10)) for key,value in self._header: stream.write("##%s=%s\n" % (key,value)) for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]: for f in var.itervalues(): stream.write("##%s=%s\n" % (label,self.format_format(f,filter=(label=="FILTER")))) def parse_heading( self, line ): assert line.startswith('#') assert not line.startswith('##') headings = line[1:].split('\t') # test for 8, as FORMAT field might be missing if len(headings)==1 and len(line[1:].split()) >= 8: self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS) headings = line[1:].split() for i,s in enumerate(self._required): if len(headings)<=i or headings[i] != s: if len(headings) <= i: err = "(%sth entry not found)" % (i+1) else: err = "(found %s, expected %s)" % (headings[i],s) #self.error(line,self.BADLY_FORMATTED_HEADING,err) # allow FORMAT column to be absent if len(headings) == 8: headings.append("FORMAT") else: self.error(line,self.BADLY_FORMATTED_HEADING,err) self._samples = headings[9:] self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] ) def write_heading( self, stream ): stream.write("#" + "\t".join(self._required + self._samples) + "\n") def convertGT(self, GTstring): if GTstring == ".": return ["."] try: gts = gtsRegEx.split(GTstring) if len(gts) == 1: return [int(gts[0])] if len(gts) != 2: raise ValueError() if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]] return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])] except ValueError: self.error(self._line,self.BAD_GENOTYPE,GTstring) return [".","|","."] def convertGTback(self, GTdata): return ''.join(map(str,GTdata)) def parse_formatdata( self, key, value, formatdict, line ): # To do: check that the right number of values is present f = formatdict.get(key,None) if f == None: self._add_definition(formatdict, key, value, line ) f = formatdict[key] if f.type == "Flag": if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE) return [] values = value.split(',') # deal with trailing data in some early VCF files if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1: self.error(line,self.ERROR_TRAILING_DATA,values[-1]) values[-1] = values[-1].split(';')[0] if f.type == "Integer": for idx,v in enumerate(values): try: if v == ".": values[idx] = f.missingvalue else: values[idx] = int(v) except: self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values))) return [0] * len(values) return values elif f.type == "String": self._line = line if f.id == "GT": values = list(map( self.convertGT, values )) return values elif f.type == "Character": for v in values: if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR) return values elif f.type == "Float": for idx,v in enumerate(values): if v == ".": values[idx] = f.missingvalue try: return list(map(float,values)) except: self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,"%s=%s" % (key, str(values))) return [0.0] * len(values) else: # can't happen self.error(line,self.ERROR_INFO_STRING) def inregion(self, chrom, pos): if not self._regions: return True for r in self._regions: if r[0] == chrom and r[1] <= pos < r[2]: return True return False def parse_data( self, line, lineparse=False ): cols = line.split('\t') if len(cols) != len(self._samples)+9: # gracefully deal with absent FORMAT column # and those missing samples if len(cols) == 8: cols.append("") else: self.error(line, self.BAD_NUMBER_OF_COLUMNS, "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols))) chrom = cols[0] # get 0-based position try: pos = int(cols[1])-1 except: self.error(line,self.POS_NOT_NUMERICAL) if pos < 0: self.error(line,self.POS_NOT_POSITIVE) # implement filtering if not self.inregion(chrom,pos): return None # end of first-pass parse for sortedVCF if lineparse: return chrom, pos, line id = cols[2] ref = cols[3].upper() if ref == ".": self.error(line,self.MISSING_REF) if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference) else: ref = "" else: for c in ref: if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF) if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference) # make sure reference is sane if self._reference: left = max(0,pos-100) faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference) faref = faref_leftflank[pos-left:] if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref)) ref = faref # convert v3.3 to v4.0 alleles below if cols[4] == ".": alt = [] else: alt = cols[4].upper().split(',') if cols[5] == ".": qual = -1 else: try: qual = float(cols[5]) except: self.error(line,self.QUAL_NOT_NUMERICAL) # postpone checking that filters exist. Encode missing filter or no filtering as empty list if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = [] else: filter = cols[6].split(';') # dictionary of keys, and list of values info = {} if cols[7] != ".": for blurp in cols[7].split(';'): elts = blurp.split('=') if len(elts) == 1: v = None elif len(elts) == 2: v = elts[1] else: self.error(line,self.ERROR_INFO_STRING) info[elts[0]] = self.parse_formatdata(elts[0], v, self._info, line) # Gracefully deal with absent FORMAT column if cols[8] == "": format = [] else: format = cols[8].split(':') # check: all filters are defined for f in filter: if f not in self._filter: self.error(line,self.FILTER_NOT_DEFINED, f) # check: format fields are defined if self._format: for f in format: if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f) # convert v3.3 alleles if self._version == 33: if len(ref) != 1: self.error(line,self.V33_BAD_REF) newalts = [] have_deletions = False for a in alt: if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference elif a.startswith('D'): # allow D and D have_deletions = True try: l = int(a[1:]) # throws ValueError if sequence if len(ref) < l: # add to reference if necessary addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference) ref += addns for i,na in enumerate(newalts): newalts[i] = na+addns a = ref[l:] # new deletion, deleting pos...pos+l except ValueError: s = a[1:] if len(ref) < len(s): # add Ns to reference if necessary addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference) if not s.endswith(addns) and addns != 'N'*len(addns): self.error(line,self.V33_UNMATCHED_DELETION, "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference))) ref += addns for i,na in enumerate(newalts): newalts[i] = na+addns a = ref[len(s):] # new deletion, deleting from pos else: self.error(line,self.V33_BAD_ALLELE) newalts.append(a) alt = newalts # deletion alleles exist, add dummy 1st reference allele, and account for leading base if have_deletions: if pos == 0: # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1 addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference) ref += addn alt = [allele+addn for allele in alt] else: addn = get_sequence(chrom,pos-1,pos,self._reference) ref = addn + ref alt = [addn + allele for allele in alt] pos -= 1 else: # format v4.0 -- just check for nucleotides for allele in alt: if not alleleRegEx.match(allele): self.error(line,self.V40_BAD_ALLELE,allele) # check for leading nucleotide in indel calls for allele in alt: if len(allele) != len(ref): if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE) if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper(): self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE) # trim trailing bases in alleles # AH: not certain why trimming this needs to be added # disabled now for unit testing # if alt: # for i in range(1,min(len(ref),min(map(len,alt)))): # if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): # break # ref, alt = ref[:-1], [allele[:-1] for allele in alt] # left-align alleles, if a reference is available if self._leftalign and self._reference: while left < pos: movable = True for allele in alt: if len(allele) > len(ref): longest, shortest = allele, ref else: longest, shortest = ref, allele if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper(): movable = False if longest[-1].upper() != longest[len(shortest)-1].upper(): movable = False if not movable: break ref = ref[:-1] alt = [allele[:-1] for allele in alt] if min([len(allele) for allele in alt]) == 0 or len(ref) == 0: ref = faref_leftflank[pos-left-1] + ref alt = [faref_leftflank[pos-left-1] + allele for allele in alt] pos -= 1 # parse sample columns samples = [] for sample in cols[9:]: dict = {} values = sample.split(':') if len(values) > len(format): self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format))) for idx in range(len(format)): expected = self.get_expected(format[idx], self._format, alt) if idx < len(values): value = values[idx] else: if expected == -1: value = "." else: value = ",".join(["."]*expected) dict[format[idx]] = self.parse_formatdata(format[idx], value, self._format, line) if expected != -1 and len(dict[format[idx]]) != expected: self.error(line,self.BAD_NUMBER_OF_PARAMETERS, "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]])) if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]])) dict[format[idx]] = dict[format[idx]][:expected] samples.append( dict ) # done d = {'chrom':chrom, 'pos':pos, # return 0-based position 'id':id, 'ref':ref, 'alt':alt, 'qual':qual, 'filter':filter, 'info':info, 'format':format} for key,value in zip(self._samples,samples): d[key] = value return d def write_data(self, stream, data): required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples for k in required: if k not in data: raise ValueError("Required key %s not found in data" % str(k)) if data['alt'] == []: alt = "." else: alt = ",".join(data['alt']) if data['filter'] == None: filter = "." elif data['filter'] == []: if self._version == 33: filter = "0" else: filter = "PASS" else: filter = ';'.join(data['filter']) if data['qual'] == -1: qual = "." else: qual = str(data['qual']) output = [data['chrom'], str(data['pos']+1), # change to 1-based position data['id'], data['ref'], alt, qual, filter, self.format_formatdata( data['info'], self._info, separator=";"), self.format_formatdata( data['format'], self._format, value=False)] for s in self._samples: output.append(self.format_formatdata( data[s], self._format, key=False)) stream.write( "\t".join(output) + "\n" ) def _parse_header(self, stream): self._lineno = 0 for line in stream: line = force_str(line, self.encoding) self._lineno += 1 if line.startswith('##'): self.parse_header(line.strip()) elif line.startswith('#'): self.parse_heading(line.strip()) self.enter_default_format() else: break return line def _parse(self, line, stream): # deal with files with header only if line.startswith("##"): return if len(line.strip()) > 0: d = self.parse_data( line.strip() ) if d: yield d for line in stream: self._lineno += 1 if self._lines and self._lineno > self._lines: raise StopIteration d = self.parse_data( line.strip() ) if d: yield d ###################################################################################################### # # API follows # ###################################################################################################### def getsamples(self): """ List of samples in VCF file """ return self._samples def setsamples(self,samples): """ List of samples in VCF file """ self._samples = samples def getheader(self): """ List of header key-value pairs (strings) """ return self._header def setheader(self,header): """ List of header key-value pairs (strings) """ self._header = header def getinfo(self): """ Dictionary of ##INFO tags, as VCF.FORMAT values """ return self._info def setinfo(self,info): """ Dictionary of ##INFO tags, as VCF.FORMAT values """ self._info = info def getformat(self): """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """ return self._format def setformat(self,format): """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """ self._format = format def getfilter(self): """ Dictionary of ##FILTER tags, as VCF.FORMAT values """ return self._filter def setfilter(self,filter): """ Dictionary of ##FILTER tags, as VCF.FORMAT values """ self._filter = filter def setversion(self, version): if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files") self._version = version def setregions(self, regions): self._regions = regions def setreference(self, ref): """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """ self._reference = ref def ignoreerror(self, errorstring): try: self._ignored_errors.add(self.__dict__[errorstring]) except KeyError: raise ValueError("Invalid error string: %s" % errorstring) def warnerror(self, errorstring): try: self._warn_errors.add(self.__dict__[errorstring]) except KeyError: raise ValueError("Invalid error string: %s" % errorstring) def parse(self, stream): """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """ last_line = self._parse_header(stream) # now return a generator that does the actual work. In this way the pre-processing is done # before the first piece of data is yielded return self._parse(last_line, stream) def write(self, stream, datagenerator): """ Writes a VCF file to a stream, using a data generator (or list) """ self.write_header(stream) self.write_heading(stream) for data in datagenerator: self.write_data(stream,data) def writeheader(self, stream): """ Writes a VCF header """ self.write_header(stream) self.write_heading(stream) def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2): """ Utility function: compares two calls for equality """ # a variant should always be assigned to a unique position, one base before # the leftmost position of the alignment gap. If this rule is implemented # correctly, the two positions must be equal for the calls to be identical. if pos1 != pos2: return False # from both calls, trim rightmost bases when identical. Do this safely, i.e. # only when the reference bases are not Ns while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]: ref1 = ref1[:-1] alt1 = alt1[:-1] while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]: ref2 = ref2[:-1] alt2 = alt2[:-1] # now, the alternative alleles must be identical return alt1 == alt2 ########################################################################################################### ########################################################################################################### ## API functions added by Andreas ########################################################################################################### def connect(self, filename, encoding="ascii"): '''connect to tabix file.''' self.encoding=encoding self.tabixfile = pysam.Tabixfile(filename, encoding=encoding) self._parse_header(self.tabixfile.header) def __del__(self): self.close() self.tabixfile = None def close(self): if self.tabixfile: self.tabixfile.close() self.tabixfile = None def fetch(self, reference=None, start=None, end=None, region=None ): """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """ return self.tabixfile.fetch( reference, start, end, region, parser = asVCFRecord(self)) def validate(self, record): '''validate vcf record. returns a validated record. ''' raise NotImplementedError("needs to be checked") chrom, pos = record.chrom, record.pos # check reference ref = record.ref if ref == ".": self.error(str(record),self.MISSING_REF) if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference) else: ref = "" else: for c in ref: if c not in "ACGTN": self.error(str(record),self.UNKNOWN_CHAR_IN_REF) if "N" in ref: ref = get_sequence(chrom, pos, pos+len(ref), self._reference) # make sure reference is sane if self._reference: left = max(0,self.pos-100) faref_leftflank = get_sequence(chrom,left,self.pos+len(ref),self._reference) faref = faref_leftflank[pos-left:] if faref != ref: self.error(str(record),self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref)) ref = faref # check: format fields are defined for f in record.format: if f not in self._format: self.error(str(record),self.FORMAT_NOT_DEFINED, f) # check: all filters are defined for f in record.filter: if f not in self._filter: self.error(str(record),self.FILTER_NOT_DEFINED, f) # convert v3.3 alleles if self._version == 33: if len(ref) != 1: self.error(str(record),self.V33_BAD_REF) newalts = [] have_deletions = False for a in alt: if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference elif a.startswith('D'): # allow D and D have_deletions = True try: l = int(a[1:]) # throws ValueError if sequence if len(ref) < l: # add to reference if necessary addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference) ref += addns for i,na in enumerate(newalts): newalts[i] = na+addns a = ref[l:] # new deletion, deleting pos...pos+l except ValueError: s = a[1:] if len(ref) < len(s): # add Ns to reference if necessary addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference) if not s.endswith(addns) and addns != 'N'*len(addns): self.error(str(record),self.V33_UNMATCHED_DELETION, "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference))) ref += addns for i,na in enumerate(newalts): newalts[i] = na+addns a = ref[len(s):] # new deletion, deleting from pos else: self.error(str(record),self.V33_BAD_ALLELE) newalts.append(a) alt = newalts # deletion alleles exist, add dummy 1st reference allele, and account for leading base if have_deletions: if pos == 0: # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1 addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference) ref += addn alt = [allele+addn for allele in alt] else: addn = get_sequence(chrom,pos-1,pos,self._reference) ref = addn + ref alt = [addn + allele for allele in alt] pos -= 1 else: # format v4.0 -- just check for nucleotides for allele in alt: if not alleleRegEx.match(allele): self.error(str(record),self.V40_BAD_ALLELE,allele) # check for leading nucleotide in indel calls for allele in alt: if len(allele) != len(ref): if len(allele) == 0: self.error(str(record),self.ZERO_LENGTH_ALLELE) if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper(): self.error(str(record),self.MISSING_INDEL_ALLELE_REF_BASE) # trim trailing bases in alleles # AH: not certain why trimming this needs to be added # disabled now for unit testing # for i in range(1,min(len(ref),min(map(len,alt)))): # if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): # break # ref, alt = ref[:-1], [allele[:-1] for allele in alt] # left-align alleles, if a reference is available if self._leftalign and self._reference: while left < pos: movable = True for allele in alt: if len(allele) > len(ref): longest, shortest = allele, ref else: longest, shortest = ref, allele if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper(): movable = False if longest[-1].upper() != longest[len(shortest)-1].upper(): movable = False if not movable: break ref = ref[:-1] alt = [allele[:-1] for allele in alt] if min([len(allele) for allele in alt]) == 0 or len(ref) == 0: ref = faref_leftflank[pos-left-1] + ref alt = [faref_leftflank[pos-left-1] + allele for allele in alt] pos -= 1 __all__ = [ "VCF", "VCFRecord", ] pysam-0.23.0/pysam/py.typed000066400000000000000000000000001475062545500155600ustar00rootroot00000000000000pysam-0.23.0/pysam/pysam_stream.h000066400000000000000000000003771475062545500167570ustar00rootroot00000000000000#ifndef PYSAM_STREAM_H #define PYSAM_STREAM_H #include "htslib/kseq.h" // ####################################################### // fastq parsing // KSEQ_INIT(gzFile, gzread) KSEQ_INIT(BGZF *, bgzf_read) //KSTREAM_INIT( gzFile, gzread, 16384) #endif pysam-0.23.0/pysam/pysam_util.c000066400000000000000000000013001475062545500164170ustar00rootroot00000000000000#include #include #include #include #include #include #include "htslib/khash.h" #include "htslib/ksort.h" #include "htslib/knetfile.h" #if !(_POSIX_C_SOURCE >= 200809L || _XOPEN_SOURCE >= 700) /* * A rudimentary emulation of getline() for systems that dont support it * natively. Since this is used for PPD file reading, it assumes (possibly * falsely) that BUFSIZ is big enough. */ ssize_t getline(char **line, size_t *linelen, FILE *fp) { if (*linelen == 0) { *linelen = BUFSIZ; *line = malloc(*linelen); } memset(*line, 0, *linelen); fgets(*line, *linelen, fp); return (strlen(*line)); } #endif pysam-0.23.0/pysam/pysam_util.h000066400000000000000000000000631475062545500164310ustar00rootroot00000000000000#ifndef PYSAM_UTIL_H #define PYSAM_UTIL_H #endif pysam-0.23.0/pysam/samtools.py000066400000000000000000000061711475062545500163130ustar00rootroot00000000000000import pysam.utils addreplacerg = pysam.utils.PysamDispatcher('samtools', 'addreplacerg') ampliconclip = pysam.utils.PysamDispatcher('samtools', 'ampliconclip') ampliconstats = pysam.utils.PysamDispatcher('samtools', 'ampliconstats') bam2fq = pysam.utils.PysamDispatcher('samtools', 'bam2fq') bamshuf = pysam.utils.PysamDispatcher('samtools', 'bamshuf') bedcov = pysam.utils.PysamDispatcher('samtools', 'bedcov') calmd = pysam.utils.PysamDispatcher('samtools', 'calmd') cat = pysam.utils.PysamDispatcher('samtools', 'cat') collate = pysam.utils.PysamDispatcher('samtools', 'collate') consensus = pysam.utils.PysamDispatcher('samtools', 'consensus') coverage = pysam.utils.PysamDispatcher('samtools', 'coverage') cram_size = pysam.utils.PysamDispatcher('samtools', 'cram-size') depad = pysam.utils.PysamDispatcher('samtools', 'depad') depth = pysam.utils.PysamDispatcher('samtools', 'depth') dict = pysam.utils.PysamDispatcher('samtools', 'dict') faidx = pysam.utils.PysamDispatcher('samtools', 'faidx') fasta = pysam.utils.PysamDispatcher('samtools', 'fasta') fastq = pysam.utils.PysamDispatcher('samtools', 'fastq') fixmate = pysam.utils.PysamDispatcher('samtools', 'fixmate') flags = pysam.utils.PysamDispatcher('samtools', 'flags') flagstat = pysam.utils.PysamDispatcher('samtools', 'flagstat') fqidx = pysam.utils.PysamDispatcher('samtools', 'fqidx') fqimport = pysam.utils.PysamDispatcher('samtools', 'import') head = pysam.utils.PysamDispatcher('samtools', 'head') idxstats = pysam.utils.PysamDispatcher('samtools', 'idxstats') index = pysam.utils.PysamDispatcher('samtools', 'index') markdup = pysam.utils.PysamDispatcher('samtools', 'markdup') merge = pysam.utils.PysamDispatcher('samtools', 'merge') mpileup = pysam.utils.PysamDispatcher('samtools', 'mpileup') pad2unpad = pysam.utils.PysamDispatcher('samtools', 'pad2unpad') phase = pysam.utils.PysamDispatcher('samtools', 'phase') quickcheck = pysam.utils.PysamDispatcher('samtools', 'quickcheck') reference = pysam.utils.PysamDispatcher('samtools', 'reference') reheader = pysam.utils.PysamDispatcher('samtools', 'reheader') reset = pysam.utils.PysamDispatcher('samtools', 'reset') rmdup = pysam.utils.PysamDispatcher('samtools', 'rmdup') samples = pysam.utils.PysamDispatcher('samtools', 'samples') sort = pysam.utils.PysamDispatcher('samtools', 'sort') split = pysam.utils.PysamDispatcher('samtools', 'split') stats = pysam.utils.PysamDispatcher('samtools', 'stats') targetcut = pysam.utils.PysamDispatcher('samtools', 'targetcut') tview = pysam.utils.PysamDispatcher('samtools', 'tview') version = pysam.utils.PysamDispatcher('samtools', 'version') view = pysam.utils.PysamDispatcher('samtools', 'view') __all__ = [ 'addreplacerg', 'ampliconclip', 'ampliconstats', 'bam2fq', 'bamshuf', 'bedcov', 'calmd', 'cat', 'collate', 'consensus', 'coverage', 'cram_size', 'depad', 'depth', 'dict', 'faidx', 'fasta', 'fastq', 'fixmate', 'flags', 'flagstat', 'fqidx', 'fqimport', 'head', 'idxstats', 'index', 'markdup', 'merge', 'mpileup', 'pad2unpad', 'phase', 'quickcheck', 'reference', 'reheader', 'reset', 'rmdup', 'samples', 'sort', 'split', 'stats', 'targetcut', 'tview', 'version', 'view', ] pysam-0.23.0/pysam/utils.py000066400000000000000000000072741475062545500156170ustar00rootroot00000000000000from typing import ( Callable, List, Optional, Tuple, Iterable, Union, ) from pysam.libcutils import _pysam_dispatch class SamtoolsError(Exception): '''exception raised in case of an error incurred in the samtools library.''' def __init__(self, value): self.value = value def __str__(self): return repr(self.value) class PysamDispatcher(object): '''The dispatcher emulates the samtools/bctools command line. Captures stdout and stderr. Raises a :class:`pysam.SamtoolsError` exception in case samtools exits with an error code other than 0. Some command line options are associated with parsers. For example, the samtools command "pileup -c" creates a tab-separated table on standard output. In order to associate parsers with options, an optional list of parsers can be supplied. The list will be processed in order checking for the presence of each option. If no parser is given or no appropriate parser is found, the stdout output of samtools/bcftools commands will be returned. ''' dispatch = None parsers = None collection = None def __init__( self, collection: str, dispatch: str, parsers: Optional[Iterable[Tuple[str, Callable[[Union[str, List[str]]], Union[str, List[str]]]]]] = None, ): self.collection = collection self.dispatch = dispatch self.parsers = parsers self.stderr = [] def __call__(self, *args: str, **kwargs) -> Union[str, List[str]]: ''' execute a samtools command. Keyword arguments: catch_stdout -- redirect stdout from the samtools command and return as variable (default True) save_stdout -- redirect stdout to a filename. raw -- ignore any parsers associated with this samtools command. split_lines -- return stdout (if catch_stdout is True and stderr as a list of strings. ''' retval, stderr, stdout = _pysam_dispatch( self.collection, self.dispatch, args, catch_stdout=kwargs.get("catch_stdout", True), save_stdout=kwargs.get("save_stdout", None)) if kwargs.get("split_lines", False): stdout = stdout.splitlines() if stderr: stderr = stderr.splitlines() if retval: raise SamtoolsError( "%s returned with error %i: " "stdout=%s, stderr=%s" % (self.collection, retval, stdout, stderr)) self.stderr = stderr # call parser for stdout: if not kwargs.get("raw") and stdout and self.parsers: for options, parser in self.parsers: for option in options: if option not in args: break else: return parser(stdout) return stdout def get_messages(self): return self.stderr def usage(self): '''return the samtools usage information for this command''' retval, stderr, stdout = _pysam_dispatch( self.collection, self.dispatch, is_usage=True, catch_stdout=True) # some tools write usage to stderr, such as mpileup if stderr: return stderr else: return stdout class unquoted_str(str): '''Tag a value as an unquoted string. Meta-information in the VCF header takes the form of key=value pairs. By default, pysam will enclose the value in quotation marks. Tagging that value with unquoted_str will prevent this quoting.''' pysam-0.23.0/pysam/version.h000066400000000000000000000003041475062545500157260ustar00rootroot00000000000000// Version information used while compiling samtools, bcftools, and htslib #define SAMTOOLS_VERSION "1.21 (pysam)" #define BCFTOOLS_VERSION "1.21 (pysam)" #define HTS_VERSION_TEXT "1.21 (pysam)" pysam-0.23.0/pysam/version.py000066400000000000000000000002171475062545500161320ustar00rootroot00000000000000# pysam versioning information __version__ = "0.23.0" __samtools_version__ = "1.21" __bcftools_version__ = "1.21" __htslib_version__ = "1.21" pysam-0.23.0/pysam/version.pyi000066400000000000000000000001351475062545500163020ustar00rootroot00000000000000__version__: str __samtools_version__: str __bcftools_version__: str __htslib_version__: str pysam-0.23.0/requirements-dev.txt000066400000000000000000000000231475062545500167750ustar00rootroot00000000000000Cython>=0.29.12,<4 pysam-0.23.0/samtools/000077500000000000000000000000001475062545500146035ustar00rootroot00000000000000pysam-0.23.0/samtools/LICENSE000066400000000000000000000032521475062545500156120ustar00rootroot00000000000000The MIT/Expat License Copyright (C) 2008-2024 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. [The use of a range of years within a copyright notice in this distribution should be interpreted as being equivalent to a list of years including the first and last year specified and all consecutive years between them. For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009, 2011-2012" should be interpreted as being identical to a notice that reads "Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice that reads "Copyright (C) 2005-2012" should be interpreted as being identical to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012".] pysam-0.23.0/samtools/README000066400000000000000000000135471475062545500154750ustar00rootroot00000000000000Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. Building samtools ================= The typical simple case of building Samtools using the HTSlib bundled within this Samtools release tarball is done as follows: cd .../samtools-1.21 # Within the unpacked release directory ./configure make You may wish to copy the resulting samtools executable into somewhere on your $PATH, or run it where it is. Rather than running-in-place like that, the next simplest typical case is to install samtools etc properly into a directory of your choosing. Building for installation using the HTSlib bundled within this Samtools release tarball, and building the various HTSlib utilities such as bgzip is done as follows: cd .../samtools-1.21 # Within the unpacked release directory ./configure --prefix=/path/to/location make all all-htslib make install install-htslib You will likely wish to add /path/to/location/bin to your $PATH. See INSTALL for full building and installation instructions and details. Building with HTSlib plug-in support ==================================== Enabling plug-ins causes some parts of HTSlib to be built as separate modules. There are two advantages to this: * The static library libhts.a has fewer dependencies, which makes linking third-party code against it easier. * It is possible to build extra plug-ins in addition to the ones that are bundled with HTSlib. For example, the hts-plugins repository includes a module that allows direct access to files stored in an iRODS data management repository (see ). To build with plug-ins, you need to use the --enable-plugins configure option as follows: cd .../samtools-1.21 # Within the unpacked release directory ./configure --enable-plugins --prefix=/path/to/location make all all-htslib make install install-htslib There are two other configure options that affect plug-ins. These are: --with-plugin-dir=DIR plug-in installation location --with-plugin-path=PATH default plug-in search path The default for --with-plugin-dir is /libexec/htslib. --with-plugin-path sets the built-in search path used to find the plug-ins. By default this is the directory set by the --with-plugin-dir option. Multiple directories should be separated by colons. Setting --with-plugin-path is useful if you want to run directly from the source distribution instead of installing the package. In that case you can use: cd .../samtools-1.21 # Within the unpacked release directory ./configure --enable-plugins --with-plugin-path=$PWD/htslib-1.21 make all all-htslib It is possible to override the built-in search path using the HTS_PATH environment variable. Directories should be separated by colons. To include the built-in path, add an empty entry to HTS_PATH: export HTS_PATH=:/my/path # Search built-in path first export HTS_PATH=/my/path: # Search built-in path last export HTS_PATH=/my/path1::/my/path2 # Search built-in path between others Using an optimised zlib library =============================== Samtools has been minimally tested against both the Intel-optimised and CloudFlare-optimised zlibs and shown to work. They can be downloaded from: https://github.com/jtkukunas/zlib # Intel https://github.com/cloudflare/zlib # CloudFlare Neither Samtools nor HTSlib needs recompiling to use these optimised libraries, but the LD_LIBRARY_PATH environment variable should be set to a directory containing the libz.so.1 file. Benchmarks comparing the various zlibs are available at: http://www.htslib.org/benchmarks/zlib.html It is recommended that you perform your own rigorous tests for an entire pipeline if you wish to switch to one of the optimised zlib implementations. Citing ====== Please cite this paper when using SAMtools for your publications: Twelve years of SAMtools and BCFtools Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008 @article{10.1093/gigascience/giab008, author = {Danecek, Petr and Bonfield, James K and Liddle, Jennifer and Marshall, John and Ohan, Valeriu and Pollard, Martin O and Whitwham, Andrew and Keane, Thomas and McCarthy, Shane A and Davies, Robert M and Li, Heng}, title = "{Twelve years of SAMtools and BCFtools}", journal = {GigaScience}, volume = {10}, number = {2}, year = {2021}, month = {02}, abstract = "{SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines.Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed \\>1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.}", issn = {2047-217X}, doi = {10.1093/gigascience/giab008}, url = {https://doi.org/10.1093/gigascience/giab008}, note = {giab008}, eprint = {https://academic.oup.com/gigascience/article-pdf/10/2/giab008/36332246/giab008.pdf}, } pysam-0.23.0/samtools/amplicon_stats.c000066400000000000000000001757541475062545500200120ustar00rootroot00000000000000/* stats.c -- This is the former bamcheck integrated into samtools/htslib. Copyright (C) 2020-2021, 2024 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* * This tool is designed to give "samtools stats" style output, but dedicated * to small amplicon sequencing projects. It gathers stats on the * distribution of reads across amplicons. */ /* * TODO: * - Cope with multiple references. What do we do here? Just request one? * - Permit regions rather than consuming whole file (maybe solves above). */ #include #include #include #include #include #include #include #include #include #include #include "samtools.h" #include "sam_opts.h" #include "bam_ampliconclip.h" KHASH_MAP_INIT_INT64(tcoord, int64_t) KHASH_MAP_INIT_STR(qname, int64_t) #ifndef MIN #define MIN(a,b) ((a)<(b)?(a):(b)) #endif #ifndef MAX #define MAX(a,b) ((a)>(b)?(a):(b)) #endif #ifndef ABS #define ABS(a) ((a)>=0?(a):-(a)) #endif #define TCOORD_MIN_COUNT 10 #define MAX_AMP 1000 // Default maximum number of amplicons #define MAX_AMP_LEN 1000 // Default maximum length of any single amplicon #define MAX_PRIMER_PER_AMPLICON 4 // Max primers per LEFT/RIGHT #define MAX_DEPTH 5 // Number of different depths permitted typedef struct { sam_global_args ga; uint32_t flag_require; uint32_t flag_filter; int max_delta; // Used for matching read to amplicon primer loc int min_depth[MAX_DEPTH]; // Used for coverage; must be >= min_depth deep int use_sample_name; int max_amp; // Total number of amplicons int max_amp_len; // Maximum length of an individual amplicon double depth_bin;// aggregate depth within this fraction int tlen_adj; // Adjust tlen by this amount, due to clip but no fixmate FILE *out_fp; char *argv; int tcoord_min_count; int tcoord_bin; int multi_ref; } astats_args_t; typedef struct { int nseq; // total sequence count int nfiltered; // sequence filtered int nfailprimer;// count of sequences not matching the primer locations // Sizes of memory allocated below, to permit reset int max_amp, max_amp_len, max_len; // Summary across all samples, sum(x) plus sum(x^2) for s.d. calc int64_t *nreads, *nreads2; // [max_amp] double *nfull_reads; // [max_amp]; 0.5/read if paired. double *nrperc, *nrperc2; // [max_amp] int64_t *nbases, *nbases2; // [max_amp] int64_t *coverage; // [max_amp][max_amp_len] double (*covered_perc)[MAX_DEPTH]; // [max_amp][MAX_DEPTH] double (*covered_perc2)[MAX_DEPTH];// [max_amp][MAX_DEPTH]; khash_t(tcoord) **tcoord; // [max_amp+1] // 0 is correct pair, 1 is incorrect pair, 2 is unidentified int (*amp_dist)[3]; // [MAX_AMP][3]; int *depth_valid; // [max_len] int *depth_all; // [max_len] khash_t(qname) *qend; // queryname end, for overlap removal } astats_t; // We can have multiple primers for LEFT / RIGHT, so this // permits detection by any compatible combination. // One reference: typedef struct { int64_t left[MAX_PRIMER_PER_AMPLICON]; int nleft; int64_t right[MAX_PRIMER_PER_AMPLICON]; int nright; int64_t max_left, min_right; // inner dimensions int64_t min_left, max_right; // outer dimensions } amplicon_t; // Multiple references, we have an array of amplicons_t - one per used ref. // We have per reference local and global stats here, as some of the stats // are coordinate based. However we report them combined together as a single // list across all references. // "namp" is the number of amplicons in this reference, but they're // numbered first_amp to first_amp+namp-1 inclusively. typedef struct { int tid, namp; int64_t len; bed_entry_list_t *sites; amplicon_t *amp; astats_t *lstats, *gstats; // local (1 file) and global (all file) stats const char *ref; // ref name (pointer to the bed hash table key) int first_amp; // first amplicon number for this ref } amplicons_t; // Reinitialised for each new reference/chromosome. // Counts from 1 to namp, -1 for no match and 0 for ?. static int *pos2start = NULL; static int *pos2end = NULL; static int pos2size = 0; // allocated size of pos2start/end // Lookup table to go from position to amplicon based on // read start / end. static int initialise_amp_pos_lookup(astats_args_t *args, amplicons_t *amps, int ref) { int64_t i, j; amplicon_t *amp = amps[ref].amp; int64_t max_len = amps[ref].len; int namp = amps[ref].namp; if (max_len+1 > pos2size) { if (!(pos2start = realloc(pos2start, (max_len+1)*sizeof(*pos2start)))) return -1; if (!(pos2end = realloc(pos2end, (max_len+1)*sizeof(*pos2end)))) return -1; pos2size = max_len; } for (i = 0; i < max_len; i++) pos2start[i] = pos2end[i] = -1; for (i = 0; i < namp; i++) { for (j = 0; j < amp[i].nleft; j++) { int64_t p; for (p = amp[i].left[j] - args->max_delta; p <= amp[i].left[j] + args->max_delta; p++) { if (p < 1 || p > max_len) continue; pos2start[p-1] = i; } } for (j = 0; j < amp[i].nright; j++) { int64_t p; for (p = amp[i].right[j] - args->max_delta; p <= amp[i].right[j] + args->max_delta; p++) { if (p < 1 || p > max_len) continue; pos2end[p-1] = i; } } } return 0; } // Counts amplicons. // Assumption: input BED file alternates between LEFT and RIGHT primers // per amplicon, thus we can count the number based on the switching // orientation. static int count_amplicon(bed_entry_list_t *sites) { int i, namp, last_rev = 0; for (i = namp = 0; i < sites->length; i++) { if (sites->bp[i].rev == 0 && last_rev) namp++; last_rev = sites->bp[i].rev; } return ++namp; } // We're only interest in the internal part of the amplicon. // Our bed file has LEFT start/end followed by RIGHT start/end, // so collapse these to LEFT end / RIGHT start. // // Returns right most amplicon position on success, // < 0 on error static int64_t bed2amplicon(astats_args_t *args, bed_entry_list_t *sites, amplicon_t *amp, int *namp, int do_title, const char *ref, int first_amp) { int i, j; int64_t max_right = 0; FILE *ofp = args->out_fp; *namp = 0; // Assume all primers for the same amplicon are adjacent in BED // with all + followed by all -. Thus - to + signifies next primer set. int last_rev = 0; amp[0].max_left = 0; amp[0].min_right = INT64_MAX; amp[0].min_left = INT64_MAX; amp[0].max_right = 0; if (do_title) { fprintf(ofp, "# Amplicon locations from BED file.\n"); fprintf(ofp, "# LEFT/RIGHT are - format and " "comma-separated for alt-primers.\n"); if (args->multi_ref) fprintf(ofp, "#\n# AMPLICON\tREF\tNUMBER\tLEFT\tRIGHT\n"); else fprintf(ofp, "#\n# AMPLICON\tNUMBER\tLEFT\tRIGHT\n"); } for (i = j = 0; i < sites->length; i++) { if (i == 0 && sites->bp[i].rev != 0) { fprintf(stderr, "[ampliconstats] error: BED file should start" " with the + strand primer\n"); return -1; } if (sites->bp[i].rev == 0 && last_rev) { j++; if (j >= args->max_amp) { fprintf(stderr, "[ampliconstats] error: too many amplicons" " (%d). Use -a option to raise this.\n", j); return -1; } amp[j].max_left = 0; amp[j].min_right = INT64_MAX; amp[j].min_left = INT64_MAX; amp[j].max_right = 0; } if (sites->bp[i].rev == 0) { if (i == 0 || last_rev) { if (j>0) fprintf(ofp, "\n"); if (args->multi_ref) fprintf(ofp, "AMPLICON\t%s\t%d", ref, j+1 + first_amp); else fprintf(ofp, "AMPLICON\t%d", j+1); } if (amp[j].nleft >= MAX_PRIMER_PER_AMPLICON) { print_error_errno("ampliconstats", "too many primers per amplicon (%d).\n", MAX_PRIMER_PER_AMPLICON); return -1; } amp[j].left[amp[j].nleft++] = sites->bp[i].right; if (amp[j].max_left < sites->bp[i].right+1) amp[j].max_left = sites->bp[i].right+1; if (amp[j].min_left > sites->bp[i].right+1) amp[j].min_left = sites->bp[i].right+1; // BED file, so left+1 as zero based. right(+1-1) as // BED goes one beyond end (and we want inclusive range). fprintf(ofp, "%c%"PRId64"-%"PRId64, "\t,"[amp[j].nleft > 1], sites->bp[i].left+1, sites->bp[i].right); } else { if (amp[j].nright >= MAX_PRIMER_PER_AMPLICON) { print_error_errno("ampliconstats", "too many primers per amplicon (%d)", MAX_PRIMER_PER_AMPLICON); return -1; } amp[j].right[amp[j].nright++] = sites->bp[i].left; if (amp[j].min_right > sites->bp[i].left-1) amp[j].min_right = sites->bp[i].left-1; if (amp[j].max_right < sites->bp[i].left-1) { amp[j].max_right = sites->bp[i].left-1; if (amp[j].max_right - amp[j].min_left + 1 >= args->max_amp_len) { fprintf(stderr, "[ampliconstats] error: amplicon " "longer (%d) than max_amp_len option (%d)\n", (int)(amp[j].max_right - amp[j].min_left + 2), args->max_amp_len); return -1; } if (max_right < amp[j].max_right) max_right = amp[j].max_right; } fprintf(ofp, "%c%"PRId64"-%"PRId64, "\t,"[amp[j].nright > 1], sites->bp[i].left+1, sites->bp[i].right); } last_rev = sites->bp[i].rev; } if (last_rev != 1) { fprintf(ofp, "\n"); // useful if going to stdout fprintf(stderr, "[ampliconstats] error: bed file does not end on" " a reverse strand primer.\n"); return -1; } *namp = ++j; if (j) fprintf(ofp, "\n"); if (j >= args->max_amp) { fprintf(stderr, "[ampliconstats] error: " "too many amplicons (%d). Use -a option to raise this.", j); return -1; } // for (i = 0; i < *namp; i++) { // printf("%d\t%ld", i, amp[i].length); // for (j = 0; j < amp[i].nleft; j++) // printf("%c%ld", "\t,"[j>0], amp[i].left[j]); // for (j = 0; j < amp[i].nright; j++) // printf("%c%ld", "\t,"[j>0], amp[i].right[j]); // printf("\n"); // } return max_right; } void stats_free(astats_t *st) { if (!st) return; free(st->nreads); free(st->nreads2); free(st->nfull_reads); free(st->nrperc); free(st->nrperc2); free(st->nbases); free(st->nbases2); free(st->coverage); free(st->covered_perc); free(st->covered_perc2); free(st->amp_dist); free(st->depth_valid); free(st->depth_all); if (st->tcoord) { int i; for (i = 0; i <= st->max_amp; i++) { if (st->tcoord[i]) kh_destroy(tcoord, st->tcoord[i]); } free(st->tcoord); } khiter_t k; for (k = kh_begin(st->qend); k != kh_end(st->qend); k++) if (kh_exist(st->qend, k)) free((void *)kh_key(st->qend, k)); kh_destroy(qname, st->qend); free(st); } astats_t *stats_alloc(int64_t max_len, int max_amp, int max_amp_len) { astats_t *st = calloc(1, sizeof(*st)); if (!st) return NULL; st->max_amp = max_amp; st->max_amp_len = max_amp_len; st->max_len = max_len; if (!(st->nreads = calloc(max_amp, sizeof(*st->nreads)))) goto err; if (!(st->nreads2 = calloc(max_amp, sizeof(*st->nreads2)))) goto err; if (!(st->nrperc = calloc(max_amp, sizeof(*st->nrperc)))) goto err; if (!(st->nrperc2 = calloc(max_amp, sizeof(*st->nrperc2)))) goto err; if (!(st->nbases = calloc(max_amp, sizeof(*st->nbases)))) goto err; if (!(st->nbases2 = calloc(max_amp, sizeof(*st->nbases2)))) goto err; if (!(st->nfull_reads = calloc(max_amp, sizeof(*st->nfull_reads)))) goto err; if (!(st->coverage = calloc(max_amp*max_amp_len, sizeof(*st->coverage)))) goto err; if (!(st->covered_perc = calloc(max_amp, sizeof(*st->covered_perc)))) goto err; if (!(st->covered_perc2 = calloc(max_amp, sizeof(*st->covered_perc2)))) goto err; if (!(st->tcoord = calloc(max_amp+1, sizeof(*st->tcoord)))) goto err; int i; for (i = 0; i <= st->max_amp; i++) if (!(st->tcoord[i] = kh_init(tcoord))) goto err; if (!(st->qend = kh_init(qname))) goto err; if (!(st->depth_valid = calloc(max_len, sizeof(*st->depth_valid)))) goto err; if (!(st->depth_all = calloc(max_len, sizeof(*st->depth_all)))) goto err; if (!(st->amp_dist = calloc(max_amp, sizeof(*st->amp_dist)))) goto err; return st; err: stats_free(st); return NULL; } static void stats_reset(astats_t *st) { st->nseq = 0; st->nfiltered = 0; st->nfailprimer = 0; memset(st->nreads, 0, st->max_amp * sizeof(*st->nreads)); memset(st->nreads2, 0, st->max_amp * sizeof(*st->nreads2)); memset(st->nfull_reads, 0, st->max_amp * sizeof(*st->nfull_reads)); memset(st->nrperc, 0, st->max_amp * sizeof(*st->nrperc)); memset(st->nrperc2, 0, st->max_amp * sizeof(*st->nrperc2)); memset(st->nbases, 0, st->max_amp * sizeof(*st->nbases)); memset(st->nbases2, 0, st->max_amp * sizeof(*st->nbases2)); memset(st->coverage, 0, st->max_amp * st->max_amp_len * sizeof(*st->coverage)); memset(st->covered_perc, 0, st->max_amp * sizeof(*st->covered_perc)); memset(st->covered_perc2, 0, st->max_amp * sizeof(*st->covered_perc2)); // Keep the allocated entries as it's likely all files will share // the same keys. Instead we reset counters to zero for common ones // and delete rare ones. int i; for (i = 0; i <= st->max_amp; i++) { khiter_t k; for (k = kh_begin(st->tcoord[i]); k != kh_end(st->tcoord[i]); k++) if (kh_exist(st->tcoord[i], k)) { if (kh_value(st->tcoord[i], k) < 5) kh_del(tcoord, st->tcoord[i], k); else kh_value(st->tcoord[i], k) = 0; } } khiter_t k; for (k = kh_begin(st->qend); k != kh_end(st->qend); k++) if (kh_exist(st->qend, k)) free((void *)kh_key(st->qend, k)); kh_clear(qname, st->qend); memset(st->depth_valid, 0, st->max_len * sizeof(*st->depth_valid)); memset(st->depth_all, 0, st->max_len * sizeof(*st->depth_all)); memset(st->amp_dist, 0, st->max_amp * sizeof(*st->amp_dist)); } static void amp_stats_reset(amplicons_t *amps, int nref) { int i; for (i = 0; i < nref; i++) { if (!amps[i].sites) continue; stats_reset(amps[i].lstats); } } static int accumulate_stats(astats_args_t *args, amplicons_t *amps, bam1_t *b) { int ref = b->core.tid; amplicon_t *amp = amps[ref].amp; astats_t *stats = amps[ref].lstats; int len = amps[ref].len; if (!stats) return 0; stats->nseq++; if ((b->core.flag & args->flag_require) != args->flag_require || (b->core.flag & args->flag_filter) != 0) { stats->nfiltered++; return 0; } int64_t start = b->core.pos, mstart = start; // modified start int64_t end = bam_endpos(b), i; // Compute all-template-depth and valid-template-depth. // We track current end location per read name so we can remove overlaps. // Potentially we could use this data for a better amplicon-depth // count too, but for now it's purely for the per-base plots. int ret; khiter_t k; int prev_start = 0, prev_end = 0; if ((b->core.flag & BAM_FPAIRED) && !(b->core.flag & (BAM_FSUPPLEMENTARY | BAM_FSECONDARY))) { k = kh_put(qname, stats->qend, bam_get_qname(b), &ret); if (ret == 0) { prev_start = kh_value(stats->qend, k) & 0xffffffff; prev_end = kh_value(stats->qend, k)>>32; mstart = MAX(mstart, prev_end); // Ideally we'd reuse strings so we don't thrash free/malloc. // However let's see if the official way of doing that (malloc // itself) is fast enough first. free((void *)kh_key(stats->qend, k)); kh_del(qname, stats->qend, k); //fprintf(stderr, "remove overlap %d to %d\n", (int)start, (int)mstart); } else { if (!(kh_key(stats->qend, k) = strdup(bam_get_qname(b)))) return -1; kh_value(stats->qend, k) = start | (end << 32); } } for (i = mstart; i < end && i < len; i++) stats->depth_all[i]++; if (i < end) { print_error("ampliconstats", "record %s overhangs end of reference", bam_get_qname(b)); // But keep going, as it's harmless. } // On single ended runs, eg ONT or PacBio, we just use the start/end // of the template to assign. int anum = (b->core.flag & BAM_FREVERSE) || !(b->core.flag & BAM_FPAIRED) ? (end-1 >= 0 && end-1 < len ? pos2end[end-1] : -1) : (start >= 0 && start < len ? pos2start[start] : -1); // ivar sometimes soft-clips 100% of the bases. // This is essentially unmapped if (end == start && (args->flag_filter & BAM_FUNMAP)) { stats->nfiltered++; return 0; } if (anum == -1) stats->nfailprimer++; if (anum >= 0) { int64_t c = MIN(end,amp[anum].min_right+1) - MAX(start,amp[anum].max_left); if (c > 0) { stats->nreads[anum]++; // NB: ref bases rather than read bases stats->nbases[anum] += c; int64_t i; if (start < 0) start = 0; if (end > len) end = len; int64_t ostart = MAX(start, amp[anum].min_left-1); int64_t oend = MIN(end, amp[anum].max_right); int64_t offset = amp[anum].min_left-1; for (i = ostart; i < oend; i++) stats->coverage[anum*stats->max_amp_len + i-offset]++; } else { stats->nfailprimer++; } } // Template length in terms of amplicon number to amplicon number. // We expect left to right of same amplicon (len 0), but it may go // to next amplicon (len 1) or prev (len -1), etc. int64_t t_end; int oth_anum = -1; if (b->core.flag & BAM_FPAIRED) { t_end = (b->core.flag & BAM_FREVERSE ? end : start) + b->core.isize; // If we've clipped the primers but not followed up with a fixmates // then our start+TLEN will take us to a location which is // length(LEFT_PRIMER) + length(RIGHT_PRIMER) too far away. // // The correct solution is to run samtools fixmate so TLEN is correct. // The hacky solution is to fudge the expected tlen by double the // average primer length (e.g. 50). t_end += b->core.isize > 0 ? -args->tlen_adj : +args->tlen_adj; if (t_end > 0 && t_end < len && b->core.isize != 0) oth_anum = (b->core.flag & BAM_FREVERSE) ? pos2start[t_end] : pos2end[t_end]; } else { // Not paired (see int anum = (REV || !PAIR) ?en :st expr above) oth_anum = pos2start[start]; t_end = end; } // We don't want to count our pairs twice. // If both left/right are known, count it on left only. // If only one is known, we'll only get to this code once // so we can also count it. int astatus = 2; if (anum != -1 && oth_anum != -1) { astatus = oth_anum == anum ? 0 : 1; if (start <= t_end) stats->amp_dist[anum][astatus]++; } else if (anum >= 0) { stats->amp_dist[anum][astatus = 2]++; } if (astatus == 0 && !(b->core.flag & (BAM_FUNMAP | BAM_FMUNMAP))) { if (prev_end && mstart > prev_end) { // 2nd read with gap to 1st; undo previous increment. for (i = prev_start; i < prev_end; i++) stats->depth_valid[i]--; stats->nfull_reads[anum] -= (b->core.flag & BAM_FPAIRED) ? 0.5 : 1; } else { // 1st read, or 2nd read that overlaps 1st for (i = mstart; i < end; i++) stats->depth_valid[i]++; stats->nfull_reads[anum] += (b->core.flag & BAM_FPAIRED) ? 0.5 : 1; } } // Track template start,end frequencies, so we can give stats on // amplicon primer usage. if ((b->core.flag & BAM_FPAIRED) && b->core.isize <= 0) // left to right only, so we don't double count template positions. return 0; start = b->core.pos; t_end = b->core.flag & BAM_FPAIRED ? start + b->core.isize-1 : end; uint64_t tcoord = MIN(start+1, UINT32_MAX) | (MIN(t_end+1, UINT32_MAX)<<32); k = kh_put(tcoord, stats->tcoord[anum+1], tcoord, &ret); if (ret < 0) return -1; if (ret == 0) kh_value(stats->tcoord[anum+1], k)++; else kh_value(stats->tcoord[anum+1], k)=1; kh_value(stats->tcoord[anum+1], k) |= ((int64_t)astatus<<32); return 0; } // Append file local stats to global stats int append_lstats(astats_t *lstats, astats_t *gstats, int namp, int all_nseq) { gstats->nseq += lstats->nseq; gstats->nfiltered += lstats->nfiltered; gstats->nfailprimer += lstats->nfailprimer; int a; for (a = -1; a < namp; a++) { // Add khash local (kl) to khash global (kg) khiter_t kl, kg; for (kl = kh_begin(lstats->tcoord[a+1]); kl != kh_end(lstats->tcoord[a+1]); kl++) { if (!kh_exist(lstats->tcoord[a+1], kl) || kh_value(lstats->tcoord[a+1], kl) == 0) continue; int ret; kg = kh_put(tcoord, gstats->tcoord[a+1], kh_key(lstats->tcoord[a+1], kl), &ret); if (ret < 0) return -1; kh_value(gstats->tcoord[a+1], kg) = (ret == 0 ? (kh_value(gstats->tcoord[a+1], kg) & 0xFFFFFFFF) : 0) + kh_value(lstats->tcoord[a+1], kl); } if (a == -1) continue; gstats->nreads[a] += lstats->nreads[a]; gstats->nreads2[a] += lstats->nreads[a] * lstats->nreads[a]; gstats->nfull_reads[a] += lstats->nfull_reads[a]; // To get mean & sd for amplicon read percentage, we need // to do the divisions here as nseq differs for each sample. double nrperc = all_nseq ? 100.0 * lstats->nreads[a] / all_nseq : 0; gstats->nrperc[a] += nrperc; gstats->nrperc2[a] += nrperc*nrperc; gstats->nbases[a] += lstats->nbases[a]; gstats->nbases2[a] += lstats->nbases[a] * lstats->nbases[a]; int d; for (d = 0; d < MAX_DEPTH; d++) { gstats->covered_perc[a][d] += lstats->covered_perc[a][d]; gstats->covered_perc2[a][d] += lstats->covered_perc[a][d] * lstats->covered_perc[a][d]; } for (d = 0; d < 3; d++) gstats->amp_dist[a][d] += lstats->amp_dist[a][d]; } for (a = 0; a < lstats->max_len; a++) { gstats->depth_valid[a] += lstats->depth_valid[a]; gstats->depth_all[a] += lstats->depth_all[a]; } return 0; } int append_stats(amplicons_t *amps, int nref) { int i, r, all_nseq = 0; for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = amps[r].lstats; all_nseq += stats->nseq - stats->nfiltered - stats->nfailprimer; } for (i = 0; i < nref; i++) { if (!amps[i].sites) continue; if (append_lstats(amps[i].lstats, amps[i].gstats, amps[i].namp, all_nseq) < 0) return -1; } return 0; } typedef struct { int32_t start, end; uint32_t freq; uint32_t status; } tcoord_t; // Sort tcoord by descending frequency and then ascending start and end. static int tcoord_freq_sort(const void *vp1, const void *vp2) { const tcoord_t *t1 = (const tcoord_t *)vp1; const tcoord_t *t2 = (const tcoord_t *)vp2; if (t1->freq != t2->freq) return t2->freq - t1->freq; if (t1->start != t2->start) return t1->start - t2->start; return t1->end - t2->end; } /* * Merges tcoord start,end,freq,status tuples if their coordinates are * close together. We aim to keep the start,end for the most frequent * value and assume that is the correct coordinate and all others are * minor fluctuations due to errors or variants. * * We sort by frequency first and then merge later items in the list into * the earlier more frequent ones. It's O(N^2), but sufficient for now * given current scale of projects. * * If we ever need to resolve that then consider sorting by start * coordinate and scanning the list to find all items within X, find * the most frequent of those, and then cluster that way. (I'd have * done that had I thought of it at the time!) */ static void aggregate_tcoord(astats_args_t *args, tcoord_t *tpos, size_t *np){ size_t n = *np, j, j2, j3, k; // Sort by frequency and cluster infrequent coords into frequent // ones provided they're close by. // This is O(N^2), but we've already binned by tcoord_bin/2 so // the list isn't intended to be vast at this point. qsort(tpos, n, sizeof(*tpos), tcoord_freq_sort); // For frequency ties, find mid start coord, and then find mid end // coord of those matching start. // We make that the first item so we merge into that mid point. for (j = 0; j < n; j++) { for (j2 = j+1; j2 < n; j2++) { if (tpos[j].freq != tpos[j2].freq) break; if (tpos[j2].start - tpos[j].start >= args->tcoord_bin) break; } // j to j2 all within bin of a common start, // m is the mid start. if (j2-1 > j) { size_t m = (j2-1 + j)/2; // Find mid end for this same start while (m > 1 && tpos[m].start == tpos[m-1].start) m--; for (j3 = m+1; j3 < j2; j3++) { if (tpos[m].start != tpos[j3].start) break; if (tpos[m].end - tpos[j3].end >= args->tcoord_bin) break; } if (j3-1 > m) m = (j3-1 + m)/2; // Swap with first item. tcoord_t tmp = tpos[j]; tpos[j] = tpos[m]; tpos[m] = tmp; j = j2-1; } } // Now merge in coordinates. // This bit is O(N^2), so consider binning first to reduce the // size of the list if we have excessive positional variation. for (k = j = 0; j < n; j++) { if (!tpos[j].freq) continue; if (k < j) tpos[k] = tpos[j]; for (j2 = j+1; j2 < n; j2++) { if (ABS(tpos[j].start-tpos[j2].start) < args->tcoord_bin/2 && ABS(tpos[j].end -tpos[j2].end) < args->tcoord_bin/2 && tpos[j].status == tpos[j2].status) { tpos[k].freq += tpos[j2].freq; tpos[j2].freq = 0; } } k++; } *np = k; } int dump_stats(astats_args_t *args, char type, char *name, int nfile, amplicons_t *amps, int nref, int local) { int i, r; FILE *ofp = args->out_fp; tcoord_t *tpos = NULL; size_t ntcoord = 0; // summary stats for this sample (or for all samples) fprintf(ofp, "# Summary stats.\n"); fprintf(ofp, "# Use 'grep ^%cSS | cut -f 2-' to extract this part.\n", type); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; int nmatch = stats->nseq - stats->nfiltered - stats->nfailprimer; char *name_ref = malloc(strlen(name) + strlen(amps[r].ref) + 2); if (!name_ref) return -1; if (args->multi_ref) sprintf(name_ref, "%s\t%s", name, amps[r].ref); else sprintf(name_ref, "%s", name); fprintf(ofp, "%cSS\t%s\traw total sequences:\t%d\n", type, name_ref, stats->nseq); fprintf(ofp, "%cSS\t%s\tfiltered sequences:\t%d\n", type, name_ref, stats->nfiltered); fprintf(ofp, "%cSS\t%s\tfailed primer match:\t%d\n", type, name_ref, stats->nfailprimer); fprintf(ofp, "%cSS\t%s\tmatching sequences:\t%d\n", type, name_ref, nmatch); int d = 0; do { // From first to last amplicon only, so not entire consensus. // If contig length is known, maybe we want to add the missing // count to < DEPTH figures? int64_t start = 0, covered = 0, total = 0; amplicon_t *amp = amps[r].amp; for (i = 0; i < amps[r].namp; i++) { int64_t j, offset = amp[i].min_left-1; if (amp[i].min_right - amp[i].min_left > stats->max_amp_len) { fprintf(stderr, "[ampliconstats] error: " "Maximum amplicon length (%d) exceeded for '%s'\n", stats->max_amp, name); return -1; } for (j = MAX(start, amp[i].max_left-1); j < MAX(start, amp[i].min_right); j++) { if (stats->coverage[i*stats->max_amp_len + j-offset] >= args->min_depth[d]) covered++; total++; } start = MAX(start, amp[i].min_right); } fprintf(ofp, "%cSS\t%s\tconsensus depth count < %d and >= %d:\t%" PRId64"\t%"PRId64"\n", type, name_ref, args->min_depth[d], args->min_depth[d], total-covered, covered); } while (++d < MAX_DEPTH && args->min_depth[d]); free(name_ref); } // Read count fprintf(ofp, "# Absolute matching read counts per amplicon.\n"); fprintf(ofp, "# Use 'grep ^%cREADS | cut -f 2-' to extract this part.\n", type); fprintf(ofp, "%cREADS\t%s", type, name); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { fprintf(ofp, "\t%"PRId64, stats->nreads[i]); } } fprintf(ofp, "\n"); // Valid depth is the number of full length reads (already divided // by the number we expect to cover), so +0.5 per read in pair. // A.k.a "usable depth" in the plots. fprintf(ofp, "%cVDEPTH\t%s", type, name); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) fprintf(ofp, "\t%d", (int)stats->nfull_reads[i]); } fprintf(ofp, "\n"); if (type == 'C') { // For combined we can compute mean & standard deviation too fprintf(ofp, "CREADS\tMEAN"); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { fprintf(ofp, "\t%.1f", stats->nreads[i] / (double)nfile); } } fprintf(ofp, "\n"); fprintf(ofp, "CREADS\tSTDDEV"); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { double n1 = stats->nreads[i]; fprintf(ofp, "\t%.1f", nfile > 1 && stats->nreads2[i] > 0 ? sqrt(stats->nreads2[i]/(double)nfile - (n1/nfile)*(n1/nfile)) : 0); } } fprintf(ofp, "\n"); } fprintf(ofp, "# Read percentage of distribution between amplicons.\n"); fprintf(ofp, "# Use 'grep ^%cRPERC | cut -f 2-' to extract this part.\n", type); fprintf(ofp, "%cRPERC\t%s", type, name); int all_nseq = 0; for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; all_nseq += stats->nseq - stats->nfiltered - stats->nfailprimer; } for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { if (type == 'C') { fprintf(ofp, "\t%.3f", (double)stats->nrperc[i] / nfile); } else { fprintf(ofp, "\t%.3f", all_nseq ? 100.0 * stats->nreads[i] / all_nseq : 0); } } } fprintf(ofp, "\n"); if (type == 'C') { // For combined we compute mean and standard deviation too fprintf(ofp, "CRPERC\tMEAN"); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { fprintf(ofp, "\t%.3f", stats->nrperc[i] / nfile); } } fprintf(ofp, "\n"); fprintf(ofp, "CRPERC\tSTDDEV"); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { // variance = SUM(X^2) - ((SUM(X)^2) / N) double n1 = stats->nrperc[i]; double v = stats->nrperc2[i]/nfile - (n1/nfile)*(n1/nfile); fprintf(ofp, "\t%.3f", v>0?sqrt(v):0); } } fprintf(ofp, "\n"); } // Base depth fprintf(ofp, "# Read depth per amplicon.\n"); fprintf(ofp, "# Use 'grep ^%cDEPTH | cut -f 2-' to extract this part.\n", type); fprintf(ofp, "%cDEPTH\t%s", type, name); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; amplicon_t *amp = amps[r].amp; for (i = 0; i < amps[r].namp; i++) { int nseq = stats->nseq - stats->nfiltered - stats->nfailprimer; int64_t alen = amp[i].min_right - amp[i].max_left+1; fprintf(ofp, "\t%.1f", nseq ? stats->nbases[i] / (double)alen : 0); } } fprintf(ofp, "\n"); if (type == 'C') { // For combined we can compute mean & standard deviation too fprintf(ofp, "CDEPTH\tMEAN"); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; amplicon_t *amp = amps[r].amp; int nseq = stats->nseq - stats->nfiltered - stats->nfailprimer; for (i = 0; i < amps[r].namp; i++) { int64_t alen = amp[i].min_right - amp[i].max_left+1; fprintf(ofp, "\t%.1f", nseq ? stats->nbases[i] / (double)alen / nfile : 0); } } fprintf(ofp, "\n"); fprintf(ofp, "CDEPTH\tSTDDEV"); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; amplicon_t *amp = amps[r].amp; for (i = 0; i < amps[r].namp; i++) { double alen = amp[i].min_right - amp[i].max_left+1; double n1 = stats->nbases[i] / alen; double v = stats->nbases2[i] / (alen*alen) /nfile - (n1/nfile)*(n1/nfile); fprintf(ofp, "\t%.1f", v>0?sqrt(v):0); } } fprintf(ofp, "\n"); } // Percent Coverage if (type == 'F') { fprintf(ofp, "# Percentage coverage per amplicon\n"); fprintf(ofp, "# Use 'grep ^%cPCOV | cut -f 2-' to extract this part.\n", type); int d = 0; do { fprintf(ofp, "%cPCOV-%d\t%s", type, args->min_depth[d], name); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; amplicon_t *amp = amps[r].amp; for (i = 0; i < amps[r].namp; i++) { int covered = 0; if (amp[i].min_right - amp[i].min_left > stats->max_amp_len) { fprintf(stderr, "[ampliconstats] error: " "Maximum amplicon length (%d) exceeded for '%s'\n", stats->max_amp, name); return -1; } int64_t j, offset = amp[i].min_left-1; for (j = amp[i].max_left-1; j < amp[i].min_right; j++) { int apos = i*stats->max_amp_len + j-offset; if (stats->coverage[apos] >= args->min_depth[d]) covered++; } int64_t alen = amp[i].min_right - amp[i].max_left+1; stats->covered_perc[i][d] = 100.0 * covered / alen; fprintf(ofp, "\t%.2f", 100.0 * covered / alen); } } fprintf(ofp, "\n"); } while (++d < MAX_DEPTH && args->min_depth[d]); } else if (type == 'C') { // For combined we can compute mean & standard deviation too int d = 0; do { fprintf(ofp, "CPCOV-%d\tMEAN", args->min_depth[d]); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { fprintf(ofp, "\t%.1f", stats->covered_perc[i][d] / nfile); } } fprintf(ofp, "\n"); fprintf(ofp, "CPCOV-%d\tSTDDEV", args->min_depth[d]); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { double n1 = stats->covered_perc[i][d] / nfile; double v = stats->covered_perc2[i][d] / nfile - n1*n1; fprintf(ofp, "\t%.1f", v>0?sqrt(v):0); } } fprintf(ofp, "\n"); } while (++d < MAX_DEPTH && args->min_depth[d]); } // Plus base depth for all reads, irrespective of amplicon. // This is post overlap removal, if reads in the read-pair overlap. fprintf(ofp, "# Depth per reference base for ALL data.\n"); fprintf(ofp, "# Use 'grep ^%cDP_ALL | cut -f 2-' to extract this part.\n", type); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; if (args->multi_ref) fprintf(ofp, "%cDP_ALL\t%s\t%s", type, name, amps[r].ref); else fprintf(ofp, "%cDP_ALL\t%s", type, name); for (i = 0; i < amps[r].len; i++) { // Basic run-length encoding provided all values are within // +- depth_bin fraction of the mid-point. int dmin = stats->depth_all[i], dmax = stats->depth_all[i], j; double dmid = (dmin + dmax)/2.0; double low = dmid*(1-args->depth_bin); double high = dmid*(1+args->depth_bin); for (j = i+1; j < amps[r].len; j++) { int d = stats->depth_all[j]; if (d < low || d > high) break; if (dmin > d) { dmin = d; dmid = (dmin + dmax)/2.0; low = dmid*(1-args->depth_bin); high = dmid*(1+args->depth_bin); } else if (dmax < d) { dmax = d; dmid = (dmin + dmax)/2.0; low = dmid*(1-args->depth_bin); high = dmid*(1+args->depth_bin); } } fprintf(ofp, "\t%d,%d", (int)dmid, j-i); i = j-1; } fprintf(ofp, "\n"); } // And depth for only reads matching to a single amplicon for full // length. This is post read overlap removal. fprintf(ofp, "# Depth per reference base for full-length valid amplicon data.\n"); fprintf(ofp, "# Use 'grep ^%cDP_VALID | cut -f 2-' to extract this " "part.\n", type); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; if (args->multi_ref) fprintf(ofp, "%cDP_VALID\t%s\t%s", type, name, amps[r].ref); else fprintf(ofp, "%cDP_VALID\t%s", type, name); for (i = 0; i < amps[r].len; i++) { int dmin = stats->depth_valid[i], dmax = stats->depth_valid[i], j; double dmid = (dmin + dmax)/2.0; double low = dmid*(1-args->depth_bin); double high = dmid*(1+args->depth_bin); for (j = i+1; j < amps[r].len; j++) { int d = stats->depth_valid[j]; if (d < low || d > high) break; if (dmin > d) { dmin = d; dmid = (dmin + dmax)/2.0; low = dmid*(1-args->depth_bin); high = dmid*(1+args->depth_bin); } else if (dmax < d) { dmax = d; dmid = (dmin + dmax)/2.0; low = dmid*(1-args->depth_bin); high = dmid*(1+args->depth_bin); } } fprintf(ofp, "\t%d,%d", (int)dmid, j-i); i = j-1; } fprintf(ofp, "\n"); } // TCOORD (start to end) distribution fprintf(ofp, "# Distribution of aligned template coordinates.\n"); fprintf(ofp, "# Use 'grep ^%cTCOORD | cut -f 2-' to extract this part.\n", type); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0 - (nref==1); i < amps[r].namp; i++) { if (ntcoord < kh_size(stats->tcoord[i+1])) { ntcoord = kh_size(stats->tcoord[i+1]); tcoord_t *tmp = realloc(tpos, ntcoord * sizeof(*tmp)); if (!tmp) { free(tpos); return -1; } tpos = tmp; } khiter_t k; size_t n = 0, j; for (k = kh_begin(stats->tcoord[i+1]); k != kh_end(stats->tcoord[i+1]); k++) { if (!kh_exist(stats->tcoord[i+1], k) || (kh_value(stats->tcoord[i+1], k) & 0xFFFFFFFF) == 0) continue; // Key is start,end in 32-bit quantities. // Yes this limits us to 4Gb references, but just how // many primers are we planning on making? Not that many // I hope. tpos[n].start = kh_key(stats->tcoord[i+1], k)&0xffffffff; tpos[n].end = kh_key(stats->tcoord[i+1], k)>>32; // Value is frequency (top 32-bits) and status (bottom 32). tpos[n].freq = kh_value(stats->tcoord[i+1], k)&0xffffffff; tpos[n].status = kh_value(stats->tcoord[i+1], k)>>32; n++; } if (args->tcoord_bin > 1) aggregate_tcoord(args, tpos, &n); fprintf(ofp, "%cTCOORD\t%s\t%d", type, name, i+1+amps[r].first_amp); // per amplicon for (j = 0; j < n; j++) { if (tpos[j].freq < args->tcoord_min_count) continue; fprintf(ofp, "\t%d,%d,%u,%u", tpos[j].start, tpos[j].end, tpos[j].freq, tpos[j].status); } fprintf(ofp, "\n"); } } // AMP length distribution. // 0 = both ends in this amplicon // 1 = ends in different amplicons // 2 = other end matching an unknown amplicon site // (see tcoord for further analysis of where) fprintf(ofp, "# Classification of amplicon status. Columns are\n"); fprintf(ofp, "# number with both primers from this amplicon, number with\n"); fprintf(ofp, "# primers from different amplicon, and number with a position\n"); fprintf(ofp, "# not matching any valid amplicon primer site\n"); fprintf(ofp, "# Use 'grep ^%cAMP | cut -f 2-' to extract this part.\n", type); fprintf(ofp, "%cAMP\t%s\t0", type, name); // all merged int amp_dist[3] = {0}; for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { // accumulate for all amps amp_dist[0] += stats->amp_dist[i][0]; amp_dist[1] += stats->amp_dist[i][1]; amp_dist[2] += stats->amp_dist[i][2]; } } fprintf(ofp, "\t%d\t%d\t%d\n", amp_dist[0], amp_dist[1], amp_dist[2]); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { // per amplicon fprintf(ofp, "%cAMP\t%s\t%d", type, name, i+1+amps[r].first_amp); fprintf(ofp, "\t%d\t%d\t%d\n", stats->amp_dist[i][0], stats->amp_dist[i][1], stats->amp_dist[i][2]); } } free(tpos); return 0; } int dump_lstats(astats_args_t *args, char type, char *name, int nfile, amplicons_t *amps, int nref) { return dump_stats(args, type, name, nfile, amps, nref, 1); } int dump_gstats(astats_args_t *args, char type, char *name, int nfile, amplicons_t *amps, int nref) { return dump_stats(args, type, name, nfile, amps, nref, 0); } char const *get_sample_name(sam_hdr_t *header, char *RG) { kstring_t ks = {0}; sam_hdr_find_tag_id(header, "RG", RG?"ID":NULL, RG, "SM", &ks); return ks.s; } // Return maximum reference length (SQ is NULL) or the length // of the specified reference in SQ. int64_t get_ref_len(sam_hdr_t *header, const char *SQ) { if (SQ) { int tid = SQ ? sam_hdr_name2tid(header, SQ) : 0; return tid >= 0 ? sam_hdr_tid2len(header, tid) : -1; } else { int nref = sam_hdr_nref(header), tid;; int64_t len = 0; for (tid = 0; tid < nref; tid++) { int64_t rl = sam_hdr_tid2len(header, tid); if (len < rl) len = rl; } return len; } } static int amplicon_stats(astats_args_t *args, khash_t(bed_list_hash) *bed_hash, char **filev, int filec) { int i, ref = -1, ref_tid = -1, ret = -1, nref = 0; samFile *fp = NULL; sam_hdr_t *header = NULL; bam1_t *b = bam_init1(); FILE *ofp = args->out_fp; char sname_[8192], *sname = NULL; amplicons_t *amps = NULL; // Report initial SS header. We gather data from the bed_hash entries // as well as from the first SAM header (with the requirement that all // headers should be compatible). if (filec) { if (!(fp = sam_open_format(filev[0], "r", &args->ga.in))) { print_error_errno("ampliconstats", "Cannot open input file \"%s\"", filev[0]); goto err; } if (!(header = sam_hdr_read(fp))) goto err; if (!amps) { amps = calloc(nref=sam_hdr_nref(header), sizeof(*amps)); if (!amps) goto err; fprintf(ofp, "# Summary statistics, used for scaling the plots.\n"); fprintf(ofp, "SS\tSamtools version: %s\n", samtools_version()); fprintf(ofp, "SS\tCommand line: %s\n", args->argv); fprintf(ofp, "SS\tNumber of files:\t%d\n", filec); // Note: order of hash entries will be different to order of // BED file which may also differ to order of SQ headers. // SQ header is canonical ordering (pos sorted file). khiter_t k; int bam_nref = sam_hdr_nref(header); for (i = 0; i < bam_nref; i++) { k = kh_get(bed_list_hash, bed_hash, sam_hdr_tid2name(header, i)); if (!kh_exist(bed_hash, k)) continue; bed_entry_list_t *sites = &kh_value(bed_hash, k); ref = i; amps[ref].ref = kh_key(bed_hash, k); amps[ref].sites = sites; amps[ref].namp = count_amplicon(sites); amps[ref].amp = calloc(sites->length, sizeof(*amps[ref].amp)); if (!amps[ref].amp) goto err; if (args->multi_ref) fprintf(ofp, "SS\tNumber of amplicons:\t%s\t%d\n", kh_key(bed_hash, k), amps[ref].namp); else fprintf(ofp, "SS\tNumber of amplicons:\t%d\n", amps[ref].namp); amps[ref].tid = ref; if (ref_tid == -1) ref_tid = ref; int64_t len = get_ref_len(header, kh_key(bed_hash, k)); amps[ref].len = len; if (args->multi_ref) fprintf(ofp, "SS\tReference length:\t%s\t%"PRId64"\n", kh_key(bed_hash, k), len); else fprintf(ofp, "SS\tReference length:\t%"PRId64"\n", len); amps[ref].lstats = stats_alloc(len, args->max_amp, args->max_amp_len); amps[ref].gstats = stats_alloc(len, args->max_amp, args->max_amp_len); if (!amps[ref].lstats || !amps[ref].gstats) goto err; } } sam_hdr_destroy(header); header = NULL; if (sam_close(fp) < 0) { fp = NULL; goto err; } fp = NULL; } fprintf(ofp, "SS\tEnd of summary\n"); // Extract the bits of amplicon data we need from bed hash and turn // it into a position-to-amplicon lookup table. int offset = 0; for (i = 0; i < nref; i++) { if (!amps[i].sites) continue; amps[i].first_amp = offset; if (bed2amplicon(args, amps[i].sites, amps[i].amp, &s[i].namp, i==0, amps[i].ref, offset) < 0) goto err; offset += amps[i].namp; // cumulative amplicon number across refs } // Now iterate over file contents, one at a time. for (i = 0; i < filec; i++) { char *nstart = filev[i]; fp = sam_open_format(filev[i], "r", &args->ga.in); if (!fp) { print_error_errno("ampliconstats", "Cannot open input file \"%s\"", filev[i]); goto err; } if (args->ga.nthreads > 0) hts_set_threads(fp, args->ga.nthreads); if (!(header = sam_hdr_read(fp))) goto err; if (nref != sam_hdr_nref(header)) { print_error_errno("ampliconstats", "SAM headers are not consistent across input files"); goto err; } int r; for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; if (!amps[r].ref || strcmp(amps[r].ref, sam_hdr_tid2name(header, r)) != 0 || amps[r].len != sam_hdr_tid2len(header, r)) { print_error_errno("ampliconstats", "SAM headers are not consistent across " "input files"); goto err; } } if (args->use_sample_name) sname = (char *)get_sample_name(header, NULL); if (!sname) { sname = sname_; char *nend = filev[i] + strlen(filev[i]), *cp; if ((cp = strrchr(filev[i], '/'))) nstart = cp+1; if ((cp = strrchr(nstart, '.')) && (strcmp(cp, ".bam") == 0 || strcmp(cp, ".sam") == 0 || strcmp(cp, ".cram") == 0)) nend = cp; if (nend - nstart >= 8192) nend = nstart+8191; memcpy(sname, nstart, nend-nstart); sname[nend-nstart] = 0; } // Stats local to this sample only amp_stats_reset(amps, nref); int last_ref = -9; while ((r = sam_read1(fp, header, b)) >= 0) { // Other filter options useful here? if (b->core.tid < 0) continue; if (last_ref != b->core.tid) { last_ref = b->core.tid; if (initialise_amp_pos_lookup(args, amps, last_ref) < 0) goto err; } if (accumulate_stats(args, amps, b) < 0) goto err; } if (r < -1) { print_error_errno("ampliconstats", "Fail reading record"); goto err; } sam_hdr_destroy(header); if (sam_close(fp) < 0) { fp = NULL; goto err; } fp = NULL; header = NULL; if (dump_lstats(args, 'F', sname, filec, amps, nref) < 0) goto err; if (append_stats(amps, nref) < 0) goto err; if (sname && sname != sname_) free(sname); sname = NULL; } if (dump_gstats(args, 'C', "COMBINED", filec, amps, nref) < 0) goto err; ret = 0; err: bam_destroy1(b); if (ret) { if (header) sam_hdr_destroy(header); if (fp) sam_close(fp); } for (i = 0; i < nref; i++) { stats_free(amps[i].lstats); stats_free(amps[i].gstats); free(amps[i].amp); } free(amps); free(pos2start); free(pos2end); if (ret) { if (sname && sname != sname_) free(sname); } return ret; } static int usage(astats_args_t *args, FILE *fp, int exit_status) { fprintf(fp, "\n" "Usage: samtools ampliconstats [options] primers.bed *.bam > astats.txt\n" "\n" "Options:\n"); fprintf(fp, " -f, --required-flag STR|INT\n" " Only include reads with all of the FLAGs present [0x%X]\n",args->flag_require); fprintf(fp, " -F, --filter-flag STR|INT\n" " Only include reads with none of the FLAGs present [0x%X]\n",args->flag_filter & 0xffff); fprintf(fp, " -a, --max-amplicons INT\n" " Change the maximum number of amplicons permitted [%d]\n", MAX_AMP); fprintf(fp, " -l, --max-amplicon-length INT\n" " Change the maximum length of an individual amplicon [%d]\n", MAX_AMP_LEN); fprintf(fp, " -d, --min-depth INT[,INT]...\n" " Minimum base depth(s) to consider position covered [%d]\n", args->min_depth[0]); fprintf(fp, " -m, --pos-margin INT\n" " Margin of error for matching primer positions [%d]\n", args->max_delta); fprintf(fp, " -o, --output FILE\n" " Specify output file [stdout if unset]\n"); fprintf(fp, " -s, --use-sample-name\n" " Use the sample name from the first @RG header line\n"); fprintf(fp, " -t, --tlen-adjust INT\n" " Add/subtract from TLEN; use when clipping but no fixmate step\n"); fprintf(fp, " -b, --tcoord-bin INT\n" " Bin template start,end positions into multiples of INT[1]\n"); fprintf(fp, " -c, --tcoord-min-count INT\n" " Minimum template start,end frequency for recording [%d]\n", TCOORD_MIN_COUNT); fprintf(fp, " -D, --depth-bin FRACTION\n" " Merge FDP values within +/- FRACTION together\n"); fprintf(fp, " -S, --single-ref\n" " Force single-ref (<=1.12) output format\n"); sam_global_opt_help(fp, "I.--.@"); return exit_status; } int main_ampliconstats(int argc, char **argv) { astats_args_t args = { .ga = SAM_GLOBAL_ARGS_INIT, .flag_require = 0, .flag_filter = 0x10B04, //.sites = BED_LIST_INIT, .max_delta = 30, // large enough to cope with alt primers .min_depth = {1}, .use_sample_name = 0, .max_amp = MAX_AMP, .max_amp_len = MAX_AMP_LEN, .tlen_adj = 0, .out_fp = stdout, .tcoord_min_count = TCOORD_MIN_COUNT, .tcoord_bin = 1, .depth_bin = 0.01, .multi_ref = 1 }, oargs = args; static const struct option loptions[] = { SAM_OPT_GLOBAL_OPTIONS('I', 0, '-', '-', 0, '@'), {"help", no_argument, NULL, 'h'}, {"flag-require", required_argument, NULL, 'f'}, {"flag-filter", required_argument, NULL, 'F'}, {"min-depth", required_argument, NULL, 'd'}, {"output", required_argument, NULL, 'o'}, {"pos-margin", required_argument, NULL, 'm'}, {"use-sample-name", no_argument, NULL, 's'}, {"max-amplicons", required_argument, NULL, 'a'}, {"max-amplicon-length", required_argument, NULL, 'l'}, {"tlen-adjust", required_argument, NULL, 't'}, {"tcoord-min-count", required_argument, NULL, 'c'}, {"tcoord-bin", required_argument, NULL, 'b'}, {"depth-bin", required_argument, NULL, 'D'}, {"single-ref", no_argument, NULL, 'S'}, {NULL, 0, NULL, 0} }; int opt, tmp_flag; while ( (opt=getopt_long(argc,argv,"?hf:F:@:p:m:d:sa:l:t:o:c:b:D:S",loptions,NULL))>0 ) { switch (opt) { case 'f': tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("ampliconstats", "Unknown flag '%s'\n", optarg); return 1; } args.flag_require = tmp_flag; break; case 'F': tmp_flag = bam_str2flag(optarg); if (args.flag_filter & 0x10000) args.flag_filter = 0; // strip default on first -F usage if (tmp_flag < 0) { print_error("ampliconstats", "Unknown flag '%s'\n", optarg); return 1; } args.flag_filter |= tmp_flag; break; case 'm': args.max_delta = atoi(optarg); break; // margin case 'D': args.depth_bin = atof(optarg); break; // depth bin fraction case 'd': { int d = 0; char *cp = optarg, *ep; do { long n = strtol(cp, &ep, 10); args.min_depth[d++] = n; if (*ep != ',') break; cp = ep+1; } while (d < MAX_DEPTH); break; } case 'a': args.max_amp = atoi(optarg)+1;break; case 'l': args.max_amp_len = atoi(optarg)+1;break; case 'c': args.tcoord_min_count = atoi(optarg);break; case 'b': args.tcoord_bin = atoi(optarg); if (args.tcoord_bin < 1) args.tcoord_bin = 1; break; case 't': args.tlen_adj = atoi(optarg);break; case 's': args.use_sample_name = 1;break; case 'o': if (!(args.out_fp = fopen(optarg, "w"))) { perror(optarg); return 1; } break; case 'S': args.multi_ref = 0; break; case '?': return usage(&oargs, stderr, EXIT_FAILURE); case 'h': return usage(&oargs, stdout, EXIT_SUCCESS); default: if (parse_sam_global_opt(opt, optarg, loptions, &args.ga) != 0) usage(&oargs,stderr, EXIT_FAILURE); break; } } if (argc <= optind) return usage(&oargs, stdout, EXIT_SUCCESS); if (argc <= optind+1 && isatty(STDIN_FILENO)) return usage(&oargs, stderr, EXIT_FAILURE); khash_t(bed_list_hash) *bed_hash = kh_init(bed_list_hash); if (load_bed_file_multi_ref(argv[optind], 1, 0, bed_hash, NULL, NULL)) { print_error_errno("ampliconstats", "Could not read file \"%s\"", argv[optind]); return 1; } khiter_t k, ref_count = 0; for (k = kh_begin(bed_hash); k != kh_end(bed_hash); k++) { if (!kh_exist(bed_hash, k)) continue; ref_count++; } if (ref_count == 0) return 1; if (ref_count > 1 && args.multi_ref == 0) { print_error("ampliconstats", "Single-ref mode is not permitted for BED files\n" "containing more than one reference."); return 1; } args.argv = stringify_argv(argc, argv); int ret; if (argc == ++optind) { char *av = "-"; ret = amplicon_stats(&args, bed_hash, &av, 1); } else { ret = amplicon_stats(&args, bed_hash, &argv[optind], argc-optind); } free(args.argv); destroy_bed_hash(bed_hash); return ret; } pysam-0.23.0/samtools/amplicon_stats.c.pysam.c000066400000000000000000001763411475062545500213540ustar00rootroot00000000000000#include "samtools.pysam.h" /* stats.c -- This is the former bamcheck integrated into samtools/htslib. Copyright (C) 2020-2021, 2024 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* * This tool is designed to give "samtools stats" style output, but dedicated * to small amplicon sequencing projects. It gathers stats on the * distribution of reads across amplicons. */ /* * TODO: * - Cope with multiple references. What do we do here? Just request one? * - Permit regions rather than consuming whole file (maybe solves above). */ #include #include #include #include #include #include #include #include #include #include #include "samtools.h" #include "sam_opts.h" #include "bam_ampliconclip.h" KHASH_MAP_INIT_INT64(tcoord, int64_t) KHASH_MAP_INIT_STR(qname, int64_t) #ifndef MIN #define MIN(a,b) ((a)<(b)?(a):(b)) #endif #ifndef MAX #define MAX(a,b) ((a)>(b)?(a):(b)) #endif #ifndef ABS #define ABS(a) ((a)>=0?(a):-(a)) #endif #define TCOORD_MIN_COUNT 10 #define MAX_AMP 1000 // Default maximum number of amplicons #define MAX_AMP_LEN 1000 // Default maximum length of any single amplicon #define MAX_PRIMER_PER_AMPLICON 4 // Max primers per LEFT/RIGHT #define MAX_DEPTH 5 // Number of different depths permitted typedef struct { sam_global_args ga; uint32_t flag_require; uint32_t flag_filter; int max_delta; // Used for matching read to amplicon primer loc int min_depth[MAX_DEPTH]; // Used for coverage; must be >= min_depth deep int use_sample_name; int max_amp; // Total number of amplicons int max_amp_len; // Maximum length of an individual amplicon double depth_bin;// aggregate depth within this fraction int tlen_adj; // Adjust tlen by this amount, due to clip but no fixmate FILE *out_fp; char *argv; int tcoord_min_count; int tcoord_bin; int multi_ref; } astats_args_t; typedef struct { int nseq; // total sequence count int nfiltered; // sequence filtered int nfailprimer;// count of sequences not matching the primer locations // Sizes of memory allocated below, to permit reset int max_amp, max_amp_len, max_len; // Summary across all samples, sum(x) plus sum(x^2) for s.d. calc int64_t *nreads, *nreads2; // [max_amp] double *nfull_reads; // [max_amp]; 0.5/read if paired. double *nrperc, *nrperc2; // [max_amp] int64_t *nbases, *nbases2; // [max_amp] int64_t *coverage; // [max_amp][max_amp_len] double (*covered_perc)[MAX_DEPTH]; // [max_amp][MAX_DEPTH] double (*covered_perc2)[MAX_DEPTH];// [max_amp][MAX_DEPTH]; khash_t(tcoord) **tcoord; // [max_amp+1] // 0 is correct pair, 1 is incorrect pair, 2 is unidentified int (*amp_dist)[3]; // [MAX_AMP][3]; int *depth_valid; // [max_len] int *depth_all; // [max_len] khash_t(qname) *qend; // queryname end, for overlap removal } astats_t; // We can have multiple primers for LEFT / RIGHT, so this // permits detection by any compatible combination. // One reference: typedef struct { int64_t left[MAX_PRIMER_PER_AMPLICON]; int nleft; int64_t right[MAX_PRIMER_PER_AMPLICON]; int nright; int64_t max_left, min_right; // inner dimensions int64_t min_left, max_right; // outer dimensions } amplicon_t; // Multiple references, we have an array of amplicons_t - one per used ref. // We have per reference local and global stats here, as some of the stats // are coordinate based. However we report them combined together as a single // list across all references. // "namp" is the number of amplicons in this reference, but they're // numbered first_amp to first_amp+namp-1 inclusively. typedef struct { int tid, namp; int64_t len; bed_entry_list_t *sites; amplicon_t *amp; astats_t *lstats, *gstats; // local (1 file) and global (all file) stats const char *ref; // ref name (pointer to the bed hash table key) int first_amp; // first amplicon number for this ref } amplicons_t; // Reinitialised for each new reference/chromosome. // Counts from 1 to namp, -1 for no match and 0 for ?. static int *pos2start = NULL; static int *pos2end = NULL; static int pos2size = 0; // allocated size of pos2start/end // Lookup table to go from position to amplicon based on // read start / end. static int initialise_amp_pos_lookup(astats_args_t *args, amplicons_t *amps, int ref) { int64_t i, j; amplicon_t *amp = amps[ref].amp; int64_t max_len = amps[ref].len; int namp = amps[ref].namp; if (max_len+1 > pos2size) { if (!(pos2start = realloc(pos2start, (max_len+1)*sizeof(*pos2start)))) return -1; if (!(pos2end = realloc(pos2end, (max_len+1)*sizeof(*pos2end)))) return -1; pos2size = max_len; } for (i = 0; i < max_len; i++) pos2start[i] = pos2end[i] = -1; for (i = 0; i < namp; i++) { for (j = 0; j < amp[i].nleft; j++) { int64_t p; for (p = amp[i].left[j] - args->max_delta; p <= amp[i].left[j] + args->max_delta; p++) { if (p < 1 || p > max_len) continue; pos2start[p-1] = i; } } for (j = 0; j < amp[i].nright; j++) { int64_t p; for (p = amp[i].right[j] - args->max_delta; p <= amp[i].right[j] + args->max_delta; p++) { if (p < 1 || p > max_len) continue; pos2end[p-1] = i; } } } return 0; } // Counts amplicons. // Assumption: input BED file alternates between LEFT and RIGHT primers // per amplicon, thus we can count the number based on the switching // orientation. static int count_amplicon(bed_entry_list_t *sites) { int i, namp, last_rev = 0; for (i = namp = 0; i < sites->length; i++) { if (sites->bp[i].rev == 0 && last_rev) namp++; last_rev = sites->bp[i].rev; } return ++namp; } // We're only interest in the internal part of the amplicon. // Our bed file has LEFT start/end followed by RIGHT start/end, // so collapse these to LEFT end / RIGHT start. // // Returns right most amplicon position on success, // < 0 on error static int64_t bed2amplicon(astats_args_t *args, bed_entry_list_t *sites, amplicon_t *amp, int *namp, int do_title, const char *ref, int first_amp) { int i, j; int64_t max_right = 0; FILE *ofp = args->out_fp; *namp = 0; // Assume all primers for the same amplicon are adjacent in BED // with all + followed by all -. Thus - to + signifies next primer set. int last_rev = 0; amp[0].max_left = 0; amp[0].min_right = INT64_MAX; amp[0].min_left = INT64_MAX; amp[0].max_right = 0; if (do_title) { fprintf(ofp, "# Amplicon locations from BED file.\n"); fprintf(ofp, "# LEFT/RIGHT are - format and " "comma-separated for alt-primers.\n"); if (args->multi_ref) fprintf(ofp, "#\n# AMPLICON\tREF\tNUMBER\tLEFT\tRIGHT\n"); else fprintf(ofp, "#\n# AMPLICON\tNUMBER\tLEFT\tRIGHT\n"); } for (i = j = 0; i < sites->length; i++) { if (i == 0 && sites->bp[i].rev != 0) { fprintf(samtools_stderr, "[ampliconstats] error: BED file should start" " with the + strand primer\n"); return -1; } if (sites->bp[i].rev == 0 && last_rev) { j++; if (j >= args->max_amp) { fprintf(samtools_stderr, "[ampliconstats] error: too many amplicons" " (%d). Use -a option to raise this.\n", j); return -1; } amp[j].max_left = 0; amp[j].min_right = INT64_MAX; amp[j].min_left = INT64_MAX; amp[j].max_right = 0; } if (sites->bp[i].rev == 0) { if (i == 0 || last_rev) { if (j>0) fprintf(ofp, "\n"); if (args->multi_ref) fprintf(ofp, "AMPLICON\t%s\t%d", ref, j+1 + first_amp); else fprintf(ofp, "AMPLICON\t%d", j+1); } if (amp[j].nleft >= MAX_PRIMER_PER_AMPLICON) { print_error_errno("ampliconstats", "too many primers per amplicon (%d).\n", MAX_PRIMER_PER_AMPLICON); return -1; } amp[j].left[amp[j].nleft++] = sites->bp[i].right; if (amp[j].max_left < sites->bp[i].right+1) amp[j].max_left = sites->bp[i].right+1; if (amp[j].min_left > sites->bp[i].right+1) amp[j].min_left = sites->bp[i].right+1; // BED file, so left+1 as zero based. right(+1-1) as // BED goes one beyond end (and we want inclusive range). fprintf(ofp, "%c%"PRId64"-%"PRId64, "\t,"[amp[j].nleft > 1], sites->bp[i].left+1, sites->bp[i].right); } else { if (amp[j].nright >= MAX_PRIMER_PER_AMPLICON) { print_error_errno("ampliconstats", "too many primers per amplicon (%d)", MAX_PRIMER_PER_AMPLICON); return -1; } amp[j].right[amp[j].nright++] = sites->bp[i].left; if (amp[j].min_right > sites->bp[i].left-1) amp[j].min_right = sites->bp[i].left-1; if (amp[j].max_right < sites->bp[i].left-1) { amp[j].max_right = sites->bp[i].left-1; if (amp[j].max_right - amp[j].min_left + 1 >= args->max_amp_len) { fprintf(samtools_stderr, "[ampliconstats] error: amplicon " "longer (%d) than max_amp_len option (%d)\n", (int)(amp[j].max_right - amp[j].min_left + 2), args->max_amp_len); return -1; } if (max_right < amp[j].max_right) max_right = amp[j].max_right; } fprintf(ofp, "%c%"PRId64"-%"PRId64, "\t,"[amp[j].nright > 1], sites->bp[i].left+1, sites->bp[i].right); } last_rev = sites->bp[i].rev; } if (last_rev != 1) { fprintf(ofp, "\n"); // useful if going to samtools_stdout fprintf(samtools_stderr, "[ampliconstats] error: bed file does not end on" " a reverse strand primer.\n"); return -1; } *namp = ++j; if (j) fprintf(ofp, "\n"); if (j >= args->max_amp) { fprintf(samtools_stderr, "[ampliconstats] error: " "too many amplicons (%d). Use -a option to raise this.", j); return -1; } // for (i = 0; i < *namp; i++) { // fprintf(samtools_stdout, "%d\t%ld", i, amp[i].length); // for (j = 0; j < amp[i].nleft; j++) // fprintf(samtools_stdout, "%c%ld", "\t,"[j>0], amp[i].left[j]); // for (j = 0; j < amp[i].nright; j++) // fprintf(samtools_stdout, "%c%ld", "\t,"[j>0], amp[i].right[j]); // fprintf(samtools_stdout, "\n"); // } return max_right; } void stats_free(astats_t *st) { if (!st) return; free(st->nreads); free(st->nreads2); free(st->nfull_reads); free(st->nrperc); free(st->nrperc2); free(st->nbases); free(st->nbases2); free(st->coverage); free(st->covered_perc); free(st->covered_perc2); free(st->amp_dist); free(st->depth_valid); free(st->depth_all); if (st->tcoord) { int i; for (i = 0; i <= st->max_amp; i++) { if (st->tcoord[i]) kh_destroy(tcoord, st->tcoord[i]); } free(st->tcoord); } khiter_t k; for (k = kh_begin(st->qend); k != kh_end(st->qend); k++) if (kh_exist(st->qend, k)) free((void *)kh_key(st->qend, k)); kh_destroy(qname, st->qend); free(st); } astats_t *stats_alloc(int64_t max_len, int max_amp, int max_amp_len) { astats_t *st = calloc(1, sizeof(*st)); if (!st) return NULL; st->max_amp = max_amp; st->max_amp_len = max_amp_len; st->max_len = max_len; if (!(st->nreads = calloc(max_amp, sizeof(*st->nreads)))) goto err; if (!(st->nreads2 = calloc(max_amp, sizeof(*st->nreads2)))) goto err; if (!(st->nrperc = calloc(max_amp, sizeof(*st->nrperc)))) goto err; if (!(st->nrperc2 = calloc(max_amp, sizeof(*st->nrperc2)))) goto err; if (!(st->nbases = calloc(max_amp, sizeof(*st->nbases)))) goto err; if (!(st->nbases2 = calloc(max_amp, sizeof(*st->nbases2)))) goto err; if (!(st->nfull_reads = calloc(max_amp, sizeof(*st->nfull_reads)))) goto err; if (!(st->coverage = calloc(max_amp*max_amp_len, sizeof(*st->coverage)))) goto err; if (!(st->covered_perc = calloc(max_amp, sizeof(*st->covered_perc)))) goto err; if (!(st->covered_perc2 = calloc(max_amp, sizeof(*st->covered_perc2)))) goto err; if (!(st->tcoord = calloc(max_amp+1, sizeof(*st->tcoord)))) goto err; int i; for (i = 0; i <= st->max_amp; i++) if (!(st->tcoord[i] = kh_init(tcoord))) goto err; if (!(st->qend = kh_init(qname))) goto err; if (!(st->depth_valid = calloc(max_len, sizeof(*st->depth_valid)))) goto err; if (!(st->depth_all = calloc(max_len, sizeof(*st->depth_all)))) goto err; if (!(st->amp_dist = calloc(max_amp, sizeof(*st->amp_dist)))) goto err; return st; err: stats_free(st); return NULL; } static void stats_reset(astats_t *st) { st->nseq = 0; st->nfiltered = 0; st->nfailprimer = 0; memset(st->nreads, 0, st->max_amp * sizeof(*st->nreads)); memset(st->nreads2, 0, st->max_amp * sizeof(*st->nreads2)); memset(st->nfull_reads, 0, st->max_amp * sizeof(*st->nfull_reads)); memset(st->nrperc, 0, st->max_amp * sizeof(*st->nrperc)); memset(st->nrperc2, 0, st->max_amp * sizeof(*st->nrperc2)); memset(st->nbases, 0, st->max_amp * sizeof(*st->nbases)); memset(st->nbases2, 0, st->max_amp * sizeof(*st->nbases2)); memset(st->coverage, 0, st->max_amp * st->max_amp_len * sizeof(*st->coverage)); memset(st->covered_perc, 0, st->max_amp * sizeof(*st->covered_perc)); memset(st->covered_perc2, 0, st->max_amp * sizeof(*st->covered_perc2)); // Keep the allocated entries as it's likely all files will share // the same keys. Instead we reset counters to zero for common ones // and delete rare ones. int i; for (i = 0; i <= st->max_amp; i++) { khiter_t k; for (k = kh_begin(st->tcoord[i]); k != kh_end(st->tcoord[i]); k++) if (kh_exist(st->tcoord[i], k)) { if (kh_value(st->tcoord[i], k) < 5) kh_del(tcoord, st->tcoord[i], k); else kh_value(st->tcoord[i], k) = 0; } } khiter_t k; for (k = kh_begin(st->qend); k != kh_end(st->qend); k++) if (kh_exist(st->qend, k)) free((void *)kh_key(st->qend, k)); kh_clear(qname, st->qend); memset(st->depth_valid, 0, st->max_len * sizeof(*st->depth_valid)); memset(st->depth_all, 0, st->max_len * sizeof(*st->depth_all)); memset(st->amp_dist, 0, st->max_amp * sizeof(*st->amp_dist)); } static void amp_stats_reset(amplicons_t *amps, int nref) { int i; for (i = 0; i < nref; i++) { if (!amps[i].sites) continue; stats_reset(amps[i].lstats); } } static int accumulate_stats(astats_args_t *args, amplicons_t *amps, bam1_t *b) { int ref = b->core.tid; amplicon_t *amp = amps[ref].amp; astats_t *stats = amps[ref].lstats; int len = amps[ref].len; if (!stats) return 0; stats->nseq++; if ((b->core.flag & args->flag_require) != args->flag_require || (b->core.flag & args->flag_filter) != 0) { stats->nfiltered++; return 0; } int64_t start = b->core.pos, mstart = start; // modified start int64_t end = bam_endpos(b), i; // Compute all-template-depth and valid-template-depth. // We track current end location per read name so we can remove overlaps. // Potentially we could use this data for a better amplicon-depth // count too, but for now it's purely for the per-base plots. int ret; khiter_t k; int prev_start = 0, prev_end = 0; if ((b->core.flag & BAM_FPAIRED) && !(b->core.flag & (BAM_FSUPPLEMENTARY | BAM_FSECONDARY))) { k = kh_put(qname, stats->qend, bam_get_qname(b), &ret); if (ret == 0) { prev_start = kh_value(stats->qend, k) & 0xffffffff; prev_end = kh_value(stats->qend, k)>>32; mstart = MAX(mstart, prev_end); // Ideally we'd reuse strings so we don't thrash free/malloc. // However let's see if the official way of doing that (malloc // itself) is fast enough first. free((void *)kh_key(stats->qend, k)); kh_del(qname, stats->qend, k); //fprintf(samtools_stderr, "remove overlap %d to %d\n", (int)start, (int)mstart); } else { if (!(kh_key(stats->qend, k) = strdup(bam_get_qname(b)))) return -1; kh_value(stats->qend, k) = start | (end << 32); } } for (i = mstart; i < end && i < len; i++) stats->depth_all[i]++; if (i < end) { print_error("ampliconstats", "record %s overhangs end of reference", bam_get_qname(b)); // But keep going, as it's harmless. } // On single ended runs, eg ONT or PacBio, we just use the start/end // of the template to assign. int anum = (b->core.flag & BAM_FREVERSE) || !(b->core.flag & BAM_FPAIRED) ? (end-1 >= 0 && end-1 < len ? pos2end[end-1] : -1) : (start >= 0 && start < len ? pos2start[start] : -1); // ivar sometimes soft-clips 100% of the bases. // This is essentially unmapped if (end == start && (args->flag_filter & BAM_FUNMAP)) { stats->nfiltered++; return 0; } if (anum == -1) stats->nfailprimer++; if (anum >= 0) { int64_t c = MIN(end,amp[anum].min_right+1) - MAX(start,amp[anum].max_left); if (c > 0) { stats->nreads[anum]++; // NB: ref bases rather than read bases stats->nbases[anum] += c; int64_t i; if (start < 0) start = 0; if (end > len) end = len; int64_t ostart = MAX(start, amp[anum].min_left-1); int64_t oend = MIN(end, amp[anum].max_right); int64_t offset = amp[anum].min_left-1; for (i = ostart; i < oend; i++) stats->coverage[anum*stats->max_amp_len + i-offset]++; } else { stats->nfailprimer++; } } // Template length in terms of amplicon number to amplicon number. // We expect left to right of same amplicon (len 0), but it may go // to next amplicon (len 1) or prev (len -1), etc. int64_t t_end; int oth_anum = -1; if (b->core.flag & BAM_FPAIRED) { t_end = (b->core.flag & BAM_FREVERSE ? end : start) + b->core.isize; // If we've clipped the primers but not followed up with a fixmates // then our start+TLEN will take us to a location which is // length(LEFT_PRIMER) + length(RIGHT_PRIMER) too far away. // // The correct solution is to run samtools fixmate so TLEN is correct. // The hacky solution is to fudge the expected tlen by double the // average primer length (e.g. 50). t_end += b->core.isize > 0 ? -args->tlen_adj : +args->tlen_adj; if (t_end > 0 && t_end < len && b->core.isize != 0) oth_anum = (b->core.flag & BAM_FREVERSE) ? pos2start[t_end] : pos2end[t_end]; } else { // Not paired (see int anum = (REV || !PAIR) ?en :st expr above) oth_anum = pos2start[start]; t_end = end; } // We don't want to count our pairs twice. // If both left/right are known, count it on left only. // If only one is known, we'll only get to this code once // so we can also count it. int astatus = 2; if (anum != -1 && oth_anum != -1) { astatus = oth_anum == anum ? 0 : 1; if (start <= t_end) stats->amp_dist[anum][astatus]++; } else if (anum >= 0) { stats->amp_dist[anum][astatus = 2]++; } if (astatus == 0 && !(b->core.flag & (BAM_FUNMAP | BAM_FMUNMAP))) { if (prev_end && mstart > prev_end) { // 2nd read with gap to 1st; undo previous increment. for (i = prev_start; i < prev_end; i++) stats->depth_valid[i]--; stats->nfull_reads[anum] -= (b->core.flag & BAM_FPAIRED) ? 0.5 : 1; } else { // 1st read, or 2nd read that overlaps 1st for (i = mstart; i < end; i++) stats->depth_valid[i]++; stats->nfull_reads[anum] += (b->core.flag & BAM_FPAIRED) ? 0.5 : 1; } } // Track template start,end frequencies, so we can give stats on // amplicon primer usage. if ((b->core.flag & BAM_FPAIRED) && b->core.isize <= 0) // left to right only, so we don't double count template positions. return 0; start = b->core.pos; t_end = b->core.flag & BAM_FPAIRED ? start + b->core.isize-1 : end; uint64_t tcoord = MIN(start+1, UINT32_MAX) | (MIN(t_end+1, UINT32_MAX)<<32); k = kh_put(tcoord, stats->tcoord[anum+1], tcoord, &ret); if (ret < 0) return -1; if (ret == 0) kh_value(stats->tcoord[anum+1], k)++; else kh_value(stats->tcoord[anum+1], k)=1; kh_value(stats->tcoord[anum+1], k) |= ((int64_t)astatus<<32); return 0; } // Append file local stats to global stats int append_lstats(astats_t *lstats, astats_t *gstats, int namp, int all_nseq) { gstats->nseq += lstats->nseq; gstats->nfiltered += lstats->nfiltered; gstats->nfailprimer += lstats->nfailprimer; int a; for (a = -1; a < namp; a++) { // Add khash local (kl) to khash global (kg) khiter_t kl, kg; for (kl = kh_begin(lstats->tcoord[a+1]); kl != kh_end(lstats->tcoord[a+1]); kl++) { if (!kh_exist(lstats->tcoord[a+1], kl) || kh_value(lstats->tcoord[a+1], kl) == 0) continue; int ret; kg = kh_put(tcoord, gstats->tcoord[a+1], kh_key(lstats->tcoord[a+1], kl), &ret); if (ret < 0) return -1; kh_value(gstats->tcoord[a+1], kg) = (ret == 0 ? (kh_value(gstats->tcoord[a+1], kg) & 0xFFFFFFFF) : 0) + kh_value(lstats->tcoord[a+1], kl); } if (a == -1) continue; gstats->nreads[a] += lstats->nreads[a]; gstats->nreads2[a] += lstats->nreads[a] * lstats->nreads[a]; gstats->nfull_reads[a] += lstats->nfull_reads[a]; // To get mean & sd for amplicon read percentage, we need // to do the divisions here as nseq differs for each sample. double nrperc = all_nseq ? 100.0 * lstats->nreads[a] / all_nseq : 0; gstats->nrperc[a] += nrperc; gstats->nrperc2[a] += nrperc*nrperc; gstats->nbases[a] += lstats->nbases[a]; gstats->nbases2[a] += lstats->nbases[a] * lstats->nbases[a]; int d; for (d = 0; d < MAX_DEPTH; d++) { gstats->covered_perc[a][d] += lstats->covered_perc[a][d]; gstats->covered_perc2[a][d] += lstats->covered_perc[a][d] * lstats->covered_perc[a][d]; } for (d = 0; d < 3; d++) gstats->amp_dist[a][d] += lstats->amp_dist[a][d]; } for (a = 0; a < lstats->max_len; a++) { gstats->depth_valid[a] += lstats->depth_valid[a]; gstats->depth_all[a] += lstats->depth_all[a]; } return 0; } int append_stats(amplicons_t *amps, int nref) { int i, r, all_nseq = 0; for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = amps[r].lstats; all_nseq += stats->nseq - stats->nfiltered - stats->nfailprimer; } for (i = 0; i < nref; i++) { if (!amps[i].sites) continue; if (append_lstats(amps[i].lstats, amps[i].gstats, amps[i].namp, all_nseq) < 0) return -1; } return 0; } typedef struct { int32_t start, end; uint32_t freq; uint32_t status; } tcoord_t; // Sort tcoord by descending frequency and then ascending start and end. static int tcoord_freq_sort(const void *vp1, const void *vp2) { const tcoord_t *t1 = (const tcoord_t *)vp1; const tcoord_t *t2 = (const tcoord_t *)vp2; if (t1->freq != t2->freq) return t2->freq - t1->freq; if (t1->start != t2->start) return t1->start - t2->start; return t1->end - t2->end; } /* * Merges tcoord start,end,freq,status tuples if their coordinates are * close together. We aim to keep the start,end for the most frequent * value and assume that is the correct coordinate and all others are * minor fluctuations due to errors or variants. * * We sort by frequency first and then merge later items in the list into * the earlier more frequent ones. It's O(N^2), but sufficient for now * given current scale of projects. * * If we ever need to resolve that then consider sorting by start * coordinate and scanning the list to find all items within X, find * the most frequent of those, and then cluster that way. (I'd have * done that had I thought of it at the time!) */ static void aggregate_tcoord(astats_args_t *args, tcoord_t *tpos, size_t *np){ size_t n = *np, j, j2, j3, k; // Sort by frequency and cluster infrequent coords into frequent // ones provided they're close by. // This is O(N^2), but we've already binned by tcoord_bin/2 so // the list isn't intended to be vast at this point. qsort(tpos, n, sizeof(*tpos), tcoord_freq_sort); // For frequency ties, find mid start coord, and then find mid end // coord of those matching start. // We make that the first item so we merge into that mid point. for (j = 0; j < n; j++) { for (j2 = j+1; j2 < n; j2++) { if (tpos[j].freq != tpos[j2].freq) break; if (tpos[j2].start - tpos[j].start >= args->tcoord_bin) break; } // j to j2 all within bin of a common start, // m is the mid start. if (j2-1 > j) { size_t m = (j2-1 + j)/2; // Find mid end for this same start while (m > 1 && tpos[m].start == tpos[m-1].start) m--; for (j3 = m+1; j3 < j2; j3++) { if (tpos[m].start != tpos[j3].start) break; if (tpos[m].end - tpos[j3].end >= args->tcoord_bin) break; } if (j3-1 > m) m = (j3-1 + m)/2; // Swap with first item. tcoord_t tmp = tpos[j]; tpos[j] = tpos[m]; tpos[m] = tmp; j = j2-1; } } // Now merge in coordinates. // This bit is O(N^2), so consider binning first to reduce the // size of the list if we have excessive positional variation. for (k = j = 0; j < n; j++) { if (!tpos[j].freq) continue; if (k < j) tpos[k] = tpos[j]; for (j2 = j+1; j2 < n; j2++) { if (ABS(tpos[j].start-tpos[j2].start) < args->tcoord_bin/2 && ABS(tpos[j].end -tpos[j2].end) < args->tcoord_bin/2 && tpos[j].status == tpos[j2].status) { tpos[k].freq += tpos[j2].freq; tpos[j2].freq = 0; } } k++; } *np = k; } int dump_stats(astats_args_t *args, char type, char *name, int nfile, amplicons_t *amps, int nref, int local) { int i, r; FILE *ofp = args->out_fp; tcoord_t *tpos = NULL; size_t ntcoord = 0; // summary stats for this sample (or for all samples) fprintf(ofp, "# Summary stats.\n"); fprintf(ofp, "# Use 'grep ^%cSS | cut -f 2-' to extract this part.\n", type); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; int nmatch = stats->nseq - stats->nfiltered - stats->nfailprimer; char *name_ref = malloc(strlen(name) + strlen(amps[r].ref) + 2); if (!name_ref) return -1; if (args->multi_ref) sprintf(name_ref, "%s\t%s", name, amps[r].ref); else sprintf(name_ref, "%s", name); fprintf(ofp, "%cSS\t%s\traw total sequences:\t%d\n", type, name_ref, stats->nseq); fprintf(ofp, "%cSS\t%s\tfiltered sequences:\t%d\n", type, name_ref, stats->nfiltered); fprintf(ofp, "%cSS\t%s\tfailed primer match:\t%d\n", type, name_ref, stats->nfailprimer); fprintf(ofp, "%cSS\t%s\tmatching sequences:\t%d\n", type, name_ref, nmatch); int d = 0; do { // From first to last amplicon only, so not entire consensus. // If contig length is known, maybe we want to add the missing // count to < DEPTH figures? int64_t start = 0, covered = 0, total = 0; amplicon_t *amp = amps[r].amp; for (i = 0; i < amps[r].namp; i++) { int64_t j, offset = amp[i].min_left-1; if (amp[i].min_right - amp[i].min_left > stats->max_amp_len) { fprintf(samtools_stderr, "[ampliconstats] error: " "Maximum amplicon length (%d) exceeded for '%s'\n", stats->max_amp, name); return -1; } for (j = MAX(start, amp[i].max_left-1); j < MAX(start, amp[i].min_right); j++) { if (stats->coverage[i*stats->max_amp_len + j-offset] >= args->min_depth[d]) covered++; total++; } start = MAX(start, amp[i].min_right); } fprintf(ofp, "%cSS\t%s\tconsensus depth count < %d and >= %d:\t%" PRId64"\t%"PRId64"\n", type, name_ref, args->min_depth[d], args->min_depth[d], total-covered, covered); } while (++d < MAX_DEPTH && args->min_depth[d]); free(name_ref); } // Read count fprintf(ofp, "# Absolute matching read counts per amplicon.\n"); fprintf(ofp, "# Use 'grep ^%cREADS | cut -f 2-' to extract this part.\n", type); fprintf(ofp, "%cREADS\t%s", type, name); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { fprintf(ofp, "\t%"PRId64, stats->nreads[i]); } } fprintf(ofp, "\n"); // Valid depth is the number of full length reads (already divided // by the number we expect to cover), so +0.5 per read in pair. // A.k.a "usable depth" in the plots. fprintf(ofp, "%cVDEPTH\t%s", type, name); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) fprintf(ofp, "\t%d", (int)stats->nfull_reads[i]); } fprintf(ofp, "\n"); if (type == 'C') { // For combined we can compute mean & standard deviation too fprintf(ofp, "CREADS\tMEAN"); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { fprintf(ofp, "\t%.1f", stats->nreads[i] / (double)nfile); } } fprintf(ofp, "\n"); fprintf(ofp, "CREADS\tSTDDEV"); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { double n1 = stats->nreads[i]; fprintf(ofp, "\t%.1f", nfile > 1 && stats->nreads2[i] > 0 ? sqrt(stats->nreads2[i]/(double)nfile - (n1/nfile)*(n1/nfile)) : 0); } } fprintf(ofp, "\n"); } fprintf(ofp, "# Read percentage of distribution between amplicons.\n"); fprintf(ofp, "# Use 'grep ^%cRPERC | cut -f 2-' to extract this part.\n", type); fprintf(ofp, "%cRPERC\t%s", type, name); int all_nseq = 0; for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; all_nseq += stats->nseq - stats->nfiltered - stats->nfailprimer; } for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { if (type == 'C') { fprintf(ofp, "\t%.3f", (double)stats->nrperc[i] / nfile); } else { fprintf(ofp, "\t%.3f", all_nseq ? 100.0 * stats->nreads[i] / all_nseq : 0); } } } fprintf(ofp, "\n"); if (type == 'C') { // For combined we compute mean and standard deviation too fprintf(ofp, "CRPERC\tMEAN"); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { fprintf(ofp, "\t%.3f", stats->nrperc[i] / nfile); } } fprintf(ofp, "\n"); fprintf(ofp, "CRPERC\tSTDDEV"); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { // variance = SUM(X^2) - ((SUM(X)^2) / N) double n1 = stats->nrperc[i]; double v = stats->nrperc2[i]/nfile - (n1/nfile)*(n1/nfile); fprintf(ofp, "\t%.3f", v>0?sqrt(v):0); } } fprintf(ofp, "\n"); } // Base depth fprintf(ofp, "# Read depth per amplicon.\n"); fprintf(ofp, "# Use 'grep ^%cDEPTH | cut -f 2-' to extract this part.\n", type); fprintf(ofp, "%cDEPTH\t%s", type, name); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; amplicon_t *amp = amps[r].amp; for (i = 0; i < amps[r].namp; i++) { int nseq = stats->nseq - stats->nfiltered - stats->nfailprimer; int64_t alen = amp[i].min_right - amp[i].max_left+1; fprintf(ofp, "\t%.1f", nseq ? stats->nbases[i] / (double)alen : 0); } } fprintf(ofp, "\n"); if (type == 'C') { // For combined we can compute mean & standard deviation too fprintf(ofp, "CDEPTH\tMEAN"); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; amplicon_t *amp = amps[r].amp; int nseq = stats->nseq - stats->nfiltered - stats->nfailprimer; for (i = 0; i < amps[r].namp; i++) { int64_t alen = amp[i].min_right - amp[i].max_left+1; fprintf(ofp, "\t%.1f", nseq ? stats->nbases[i] / (double)alen / nfile : 0); } } fprintf(ofp, "\n"); fprintf(ofp, "CDEPTH\tSTDDEV"); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; amplicon_t *amp = amps[r].amp; for (i = 0; i < amps[r].namp; i++) { double alen = amp[i].min_right - amp[i].max_left+1; double n1 = stats->nbases[i] / alen; double v = stats->nbases2[i] / (alen*alen) /nfile - (n1/nfile)*(n1/nfile); fprintf(ofp, "\t%.1f", v>0?sqrt(v):0); } } fprintf(ofp, "\n"); } // Percent Coverage if (type == 'F') { fprintf(ofp, "# Percentage coverage per amplicon\n"); fprintf(ofp, "# Use 'grep ^%cPCOV | cut -f 2-' to extract this part.\n", type); int d = 0; do { fprintf(ofp, "%cPCOV-%d\t%s", type, args->min_depth[d], name); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; amplicon_t *amp = amps[r].amp; for (i = 0; i < amps[r].namp; i++) { int covered = 0; if (amp[i].min_right - amp[i].min_left > stats->max_amp_len) { fprintf(samtools_stderr, "[ampliconstats] error: " "Maximum amplicon length (%d) exceeded for '%s'\n", stats->max_amp, name); return -1; } int64_t j, offset = amp[i].min_left-1; for (j = amp[i].max_left-1; j < amp[i].min_right; j++) { int apos = i*stats->max_amp_len + j-offset; if (stats->coverage[apos] >= args->min_depth[d]) covered++; } int64_t alen = amp[i].min_right - amp[i].max_left+1; stats->covered_perc[i][d] = 100.0 * covered / alen; fprintf(ofp, "\t%.2f", 100.0 * covered / alen); } } fprintf(ofp, "\n"); } while (++d < MAX_DEPTH && args->min_depth[d]); } else if (type == 'C') { // For combined we can compute mean & standard deviation too int d = 0; do { fprintf(ofp, "CPCOV-%d\tMEAN", args->min_depth[d]); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { fprintf(ofp, "\t%.1f", stats->covered_perc[i][d] / nfile); } } fprintf(ofp, "\n"); fprintf(ofp, "CPCOV-%d\tSTDDEV", args->min_depth[d]); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { double n1 = stats->covered_perc[i][d] / nfile; double v = stats->covered_perc2[i][d] / nfile - n1*n1; fprintf(ofp, "\t%.1f", v>0?sqrt(v):0); } } fprintf(ofp, "\n"); } while (++d < MAX_DEPTH && args->min_depth[d]); } // Plus base depth for all reads, irrespective of amplicon. // This is post overlap removal, if reads in the read-pair overlap. fprintf(ofp, "# Depth per reference base for ALL data.\n"); fprintf(ofp, "# Use 'grep ^%cDP_ALL | cut -f 2-' to extract this part.\n", type); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; if (args->multi_ref) fprintf(ofp, "%cDP_ALL\t%s\t%s", type, name, amps[r].ref); else fprintf(ofp, "%cDP_ALL\t%s", type, name); for (i = 0; i < amps[r].len; i++) { // Basic run-length encoding provided all values are within // +- depth_bin fraction of the mid-point. int dmin = stats->depth_all[i], dmax = stats->depth_all[i], j; double dmid = (dmin + dmax)/2.0; double low = dmid*(1-args->depth_bin); double high = dmid*(1+args->depth_bin); for (j = i+1; j < amps[r].len; j++) { int d = stats->depth_all[j]; if (d < low || d > high) break; if (dmin > d) { dmin = d; dmid = (dmin + dmax)/2.0; low = dmid*(1-args->depth_bin); high = dmid*(1+args->depth_bin); } else if (dmax < d) { dmax = d; dmid = (dmin + dmax)/2.0; low = dmid*(1-args->depth_bin); high = dmid*(1+args->depth_bin); } } fprintf(ofp, "\t%d,%d", (int)dmid, j-i); i = j-1; } fprintf(ofp, "\n"); } // And depth for only reads matching to a single amplicon for full // length. This is post read overlap removal. fprintf(ofp, "# Depth per reference base for full-length valid amplicon data.\n"); fprintf(ofp, "# Use 'grep ^%cDP_VALID | cut -f 2-' to extract this " "part.\n", type); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; if (args->multi_ref) fprintf(ofp, "%cDP_VALID\t%s\t%s", type, name, amps[r].ref); else fprintf(ofp, "%cDP_VALID\t%s", type, name); for (i = 0; i < amps[r].len; i++) { int dmin = stats->depth_valid[i], dmax = stats->depth_valid[i], j; double dmid = (dmin + dmax)/2.0; double low = dmid*(1-args->depth_bin); double high = dmid*(1+args->depth_bin); for (j = i+1; j < amps[r].len; j++) { int d = stats->depth_valid[j]; if (d < low || d > high) break; if (dmin > d) { dmin = d; dmid = (dmin + dmax)/2.0; low = dmid*(1-args->depth_bin); high = dmid*(1+args->depth_bin); } else if (dmax < d) { dmax = d; dmid = (dmin + dmax)/2.0; low = dmid*(1-args->depth_bin); high = dmid*(1+args->depth_bin); } } fprintf(ofp, "\t%d,%d", (int)dmid, j-i); i = j-1; } fprintf(ofp, "\n"); } // TCOORD (start to end) distribution fprintf(ofp, "# Distribution of aligned template coordinates.\n"); fprintf(ofp, "# Use 'grep ^%cTCOORD | cut -f 2-' to extract this part.\n", type); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0 - (nref==1); i < amps[r].namp; i++) { if (ntcoord < kh_size(stats->tcoord[i+1])) { ntcoord = kh_size(stats->tcoord[i+1]); tcoord_t *tmp = realloc(tpos, ntcoord * sizeof(*tmp)); if (!tmp) { free(tpos); return -1; } tpos = tmp; } khiter_t k; size_t n = 0, j; for (k = kh_begin(stats->tcoord[i+1]); k != kh_end(stats->tcoord[i+1]); k++) { if (!kh_exist(stats->tcoord[i+1], k) || (kh_value(stats->tcoord[i+1], k) & 0xFFFFFFFF) == 0) continue; // Key is start,end in 32-bit quantities. // Yes this limits us to 4Gb references, but just how // many primers are we planning on making? Not that many // I hope. tpos[n].start = kh_key(stats->tcoord[i+1], k)&0xffffffff; tpos[n].end = kh_key(stats->tcoord[i+1], k)>>32; // Value is frequency (top 32-bits) and status (bottom 32). tpos[n].freq = kh_value(stats->tcoord[i+1], k)&0xffffffff; tpos[n].status = kh_value(stats->tcoord[i+1], k)>>32; n++; } if (args->tcoord_bin > 1) aggregate_tcoord(args, tpos, &n); fprintf(ofp, "%cTCOORD\t%s\t%d", type, name, i+1+amps[r].first_amp); // per amplicon for (j = 0; j < n; j++) { if (tpos[j].freq < args->tcoord_min_count) continue; fprintf(ofp, "\t%d,%d,%u,%u", tpos[j].start, tpos[j].end, tpos[j].freq, tpos[j].status); } fprintf(ofp, "\n"); } } // AMP length distribution. // 0 = both ends in this amplicon // 1 = ends in different amplicons // 2 = other end matching an unknown amplicon site // (see tcoord for further analysis of where) fprintf(ofp, "# Classification of amplicon status. Columns are\n"); fprintf(ofp, "# number with both primers from this amplicon, number with\n"); fprintf(ofp, "# primers from different amplicon, and number with a position\n"); fprintf(ofp, "# not matching any valid amplicon primer site\n"); fprintf(ofp, "# Use 'grep ^%cAMP | cut -f 2-' to extract this part.\n", type); fprintf(ofp, "%cAMP\t%s\t0", type, name); // all merged int amp_dist[3] = {0}; for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { // accumulate for all amps amp_dist[0] += stats->amp_dist[i][0]; amp_dist[1] += stats->amp_dist[i][1]; amp_dist[2] += stats->amp_dist[i][2]; } } fprintf(ofp, "\t%d\t%d\t%d\n", amp_dist[0], amp_dist[1], amp_dist[2]); for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; astats_t *stats = local ? amps[r].lstats : amps[r].gstats; for (i = 0; i < amps[r].namp; i++) { // per amplicon fprintf(ofp, "%cAMP\t%s\t%d", type, name, i+1+amps[r].first_amp); fprintf(ofp, "\t%d\t%d\t%d\n", stats->amp_dist[i][0], stats->amp_dist[i][1], stats->amp_dist[i][2]); } } free(tpos); return 0; } int dump_lstats(astats_args_t *args, char type, char *name, int nfile, amplicons_t *amps, int nref) { return dump_stats(args, type, name, nfile, amps, nref, 1); } int dump_gstats(astats_args_t *args, char type, char *name, int nfile, amplicons_t *amps, int nref) { return dump_stats(args, type, name, nfile, amps, nref, 0); } char const *get_sample_name(sam_hdr_t *header, char *RG) { kstring_t ks = {0}; sam_hdr_find_tag_id(header, "RG", RG?"ID":NULL, RG, "SM", &ks); return ks.s; } // Return maximum reference length (SQ is NULL) or the length // of the specified reference in SQ. int64_t get_ref_len(sam_hdr_t *header, const char *SQ) { if (SQ) { int tid = SQ ? sam_hdr_name2tid(header, SQ) : 0; return tid >= 0 ? sam_hdr_tid2len(header, tid) : -1; } else { int nref = sam_hdr_nref(header), tid;; int64_t len = 0; for (tid = 0; tid < nref; tid++) { int64_t rl = sam_hdr_tid2len(header, tid); if (len < rl) len = rl; } return len; } } static int amplicon_stats(astats_args_t *args, khash_t(bed_list_hash) *bed_hash, char **filev, int filec) { int i, ref = -1, ref_tid = -1, ret = -1, nref = 0; samFile *fp = NULL; sam_hdr_t *header = NULL; bam1_t *b = bam_init1(); FILE *ofp = args->out_fp; char sname_[8192], *sname = NULL; amplicons_t *amps = NULL; // Report initial SS header. We gather data from the bed_hash entries // as well as from the first SAM header (with the requirement that all // headers should be compatible). if (filec) { if (!(fp = sam_open_format(filev[0], "r", &args->ga.in))) { print_error_errno("ampliconstats", "Cannot open input file \"%s\"", filev[0]); goto err; } if (!(header = sam_hdr_read(fp))) goto err; if (!amps) { amps = calloc(nref=sam_hdr_nref(header), sizeof(*amps)); if (!amps) goto err; fprintf(ofp, "# Summary statistics, used for scaling the plots.\n"); fprintf(ofp, "SS\tSamtools version: %s\n", samtools_version()); fprintf(ofp, "SS\tCommand line: %s\n", args->argv); fprintf(ofp, "SS\tNumber of files:\t%d\n", filec); // Note: order of hash entries will be different to order of // BED file which may also differ to order of SQ headers. // SQ header is canonical ordering (pos sorted file). khiter_t k; int bam_nref = sam_hdr_nref(header); for (i = 0; i < bam_nref; i++) { k = kh_get(bed_list_hash, bed_hash, sam_hdr_tid2name(header, i)); if (!kh_exist(bed_hash, k)) continue; bed_entry_list_t *sites = &kh_value(bed_hash, k); ref = i; amps[ref].ref = kh_key(bed_hash, k); amps[ref].sites = sites; amps[ref].namp = count_amplicon(sites); amps[ref].amp = calloc(sites->length, sizeof(*amps[ref].amp)); if (!amps[ref].amp) goto err; if (args->multi_ref) fprintf(ofp, "SS\tNumber of amplicons:\t%s\t%d\n", kh_key(bed_hash, k), amps[ref].namp); else fprintf(ofp, "SS\tNumber of amplicons:\t%d\n", amps[ref].namp); amps[ref].tid = ref; if (ref_tid == -1) ref_tid = ref; int64_t len = get_ref_len(header, kh_key(bed_hash, k)); amps[ref].len = len; if (args->multi_ref) fprintf(ofp, "SS\tReference length:\t%s\t%"PRId64"\n", kh_key(bed_hash, k), len); else fprintf(ofp, "SS\tReference length:\t%"PRId64"\n", len); amps[ref].lstats = stats_alloc(len, args->max_amp, args->max_amp_len); amps[ref].gstats = stats_alloc(len, args->max_amp, args->max_amp_len); if (!amps[ref].lstats || !amps[ref].gstats) goto err; } } sam_hdr_destroy(header); header = NULL; if (sam_close(fp) < 0) { fp = NULL; goto err; } fp = NULL; } fprintf(ofp, "SS\tEnd of summary\n"); // Extract the bits of amplicon data we need from bed hash and turn // it into a position-to-amplicon lookup table. int offset = 0; for (i = 0; i < nref; i++) { if (!amps[i].sites) continue; amps[i].first_amp = offset; if (bed2amplicon(args, amps[i].sites, amps[i].amp, &s[i].namp, i==0, amps[i].ref, offset) < 0) goto err; offset += amps[i].namp; // cumulative amplicon number across refs } // Now iterate over file contents, one at a time. for (i = 0; i < filec; i++) { char *nstart = filev[i]; fp = sam_open_format(filev[i], "r", &args->ga.in); if (!fp) { print_error_errno("ampliconstats", "Cannot open input file \"%s\"", filev[i]); goto err; } if (args->ga.nthreads > 0) hts_set_threads(fp, args->ga.nthreads); if (!(header = sam_hdr_read(fp))) goto err; if (nref != sam_hdr_nref(header)) { print_error_errno("ampliconstats", "SAM headers are not consistent across input files"); goto err; } int r; for (r = 0; r < nref; r++) { if (!amps[r].sites) continue; if (!amps[r].ref || strcmp(amps[r].ref, sam_hdr_tid2name(header, r)) != 0 || amps[r].len != sam_hdr_tid2len(header, r)) { print_error_errno("ampliconstats", "SAM headers are not consistent across " "input files"); goto err; } } if (args->use_sample_name) sname = (char *)get_sample_name(header, NULL); if (!sname) { sname = sname_; char *nend = filev[i] + strlen(filev[i]), *cp; if ((cp = strrchr(filev[i], '/'))) nstart = cp+1; if ((cp = strrchr(nstart, '.')) && (strcmp(cp, ".bam") == 0 || strcmp(cp, ".sam") == 0 || strcmp(cp, ".cram") == 0)) nend = cp; if (nend - nstart >= 8192) nend = nstart+8191; memcpy(sname, nstart, nend-nstart); sname[nend-nstart] = 0; } // Stats local to this sample only amp_stats_reset(amps, nref); int last_ref = -9; while ((r = sam_read1(fp, header, b)) >= 0) { // Other filter options useful here? if (b->core.tid < 0) continue; if (last_ref != b->core.tid) { last_ref = b->core.tid; if (initialise_amp_pos_lookup(args, amps, last_ref) < 0) goto err; } if (accumulate_stats(args, amps, b) < 0) goto err; } if (r < -1) { print_error_errno("ampliconstats", "Fail reading record"); goto err; } sam_hdr_destroy(header); if (sam_close(fp) < 0) { fp = NULL; goto err; } fp = NULL; header = NULL; if (dump_lstats(args, 'F', sname, filec, amps, nref) < 0) goto err; if (append_stats(amps, nref) < 0) goto err; if (sname && sname != sname_) free(sname); sname = NULL; } if (dump_gstats(args, 'C', "COMBINED", filec, amps, nref) < 0) goto err; ret = 0; err: bam_destroy1(b); if (ret) { if (header) sam_hdr_destroy(header); if (fp) sam_close(fp); } for (i = 0; i < nref; i++) { stats_free(amps[i].lstats); stats_free(amps[i].gstats); free(amps[i].amp); } free(amps); free(pos2start); free(pos2end); if (ret) { if (sname && sname != sname_) free(sname); } return ret; } static int usage(astats_args_t *args, FILE *fp, int exit_status) { fprintf(fp, "\n" "Usage: samtools ampliconstats [options] primers.bed *.bam > astats.txt\n" "\n" "Options:\n"); fprintf(fp, " -f, --required-flag STR|INT\n" " Only include reads with all of the FLAGs present [0x%X]\n",args->flag_require); fprintf(fp, " -F, --filter-flag STR|INT\n" " Only include reads with none of the FLAGs present [0x%X]\n",args->flag_filter & 0xffff); fprintf(fp, " -a, --max-amplicons INT\n" " Change the maximum number of amplicons permitted [%d]\n", MAX_AMP); fprintf(fp, " -l, --max-amplicon-length INT\n" " Change the maximum length of an individual amplicon [%d]\n", MAX_AMP_LEN); fprintf(fp, " -d, --min-depth INT[,INT]...\n" " Minimum base depth(s) to consider position covered [%d]\n", args->min_depth[0]); fprintf(fp, " -m, --pos-margin INT\n" " Margin of error for matching primer positions [%d]\n", args->max_delta); fprintf(fp, " -o, --output FILE\n" " Specify output file [samtools_stdout if unset]\n"); fprintf(fp, " -s, --use-sample-name\n" " Use the sample name from the first @RG header line\n"); fprintf(fp, " -t, --tlen-adjust INT\n" " Add/subtract from TLEN; use when clipping but no fixmate step\n"); fprintf(fp, " -b, --tcoord-bin INT\n" " Bin template start,end positions into multiples of INT[1]\n"); fprintf(fp, " -c, --tcoord-min-count INT\n" " Minimum template start,end frequency for recording [%d]\n", TCOORD_MIN_COUNT); fprintf(fp, " -D, --depth-bin FRACTION\n" " Merge FDP values within +/- FRACTION together\n"); fprintf(fp, " -S, --single-ref\n" " Force single-ref (<=1.12) output format\n"); sam_global_opt_help(fp, "I.--.@"); return exit_status; } int main_ampliconstats(int argc, char **argv) { astats_args_t args = { .ga = SAM_GLOBAL_ARGS_INIT, .flag_require = 0, .flag_filter = 0x10B04, //.sites = BED_LIST_INIT, .max_delta = 30, // large enough to cope with alt primers .min_depth = {1}, .use_sample_name = 0, .max_amp = MAX_AMP, .max_amp_len = MAX_AMP_LEN, .tlen_adj = 0, .out_fp = samtools_stdout, .tcoord_min_count = TCOORD_MIN_COUNT, .tcoord_bin = 1, .depth_bin = 0.01, .multi_ref = 1 }, oargs = args; static const struct option loptions[] = { SAM_OPT_GLOBAL_OPTIONS('I', 0, '-', '-', 0, '@'), {"help", no_argument, NULL, 'h'}, {"flag-require", required_argument, NULL, 'f'}, {"flag-filter", required_argument, NULL, 'F'}, {"min-depth", required_argument, NULL, 'd'}, {"output", required_argument, NULL, 'o'}, {"pos-margin", required_argument, NULL, 'm'}, {"use-sample-name", no_argument, NULL, 's'}, {"max-amplicons", required_argument, NULL, 'a'}, {"max-amplicon-length", required_argument, NULL, 'l'}, {"tlen-adjust", required_argument, NULL, 't'}, {"tcoord-min-count", required_argument, NULL, 'c'}, {"tcoord-bin", required_argument, NULL, 'b'}, {"depth-bin", required_argument, NULL, 'D'}, {"single-ref", no_argument, NULL, 'S'}, {NULL, 0, NULL, 0} }; int opt, tmp_flag; while ( (opt=getopt_long(argc,argv,"?hf:F:@:p:m:d:sa:l:t:o:c:b:D:S",loptions,NULL))>0 ) { switch (opt) { case 'f': tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("ampliconstats", "Unknown flag '%s'\n", optarg); return 1; } args.flag_require = tmp_flag; break; case 'F': tmp_flag = bam_str2flag(optarg); if (args.flag_filter & 0x10000) args.flag_filter = 0; // strip default on first -F usage if (tmp_flag < 0) { print_error("ampliconstats", "Unknown flag '%s'\n", optarg); return 1; } args.flag_filter |= tmp_flag; break; case 'm': args.max_delta = atoi(optarg); break; // margin case 'D': args.depth_bin = atof(optarg); break; // depth bin fraction case 'd': { int d = 0; char *cp = optarg, *ep; do { long n = strtol(cp, &ep, 10); args.min_depth[d++] = n; if (*ep != ',') break; cp = ep+1; } while (d < MAX_DEPTH); break; } case 'a': args.max_amp = atoi(optarg)+1;break; case 'l': args.max_amp_len = atoi(optarg)+1;break; case 'c': args.tcoord_min_count = atoi(optarg);break; case 'b': args.tcoord_bin = atoi(optarg); if (args.tcoord_bin < 1) args.tcoord_bin = 1; break; case 't': args.tlen_adj = atoi(optarg);break; case 's': args.use_sample_name = 1;break; case 'o': if (!(args.out_fp = fopen(optarg, "w"))) { perror(optarg); return 1; } break; case 'S': args.multi_ref = 0; break; case '?': return usage(&oargs, samtools_stderr, EXIT_FAILURE); case 'h': return usage(&oargs, samtools_stdout, EXIT_SUCCESS); default: if (parse_sam_global_opt(opt, optarg, loptions, &args.ga) != 0) usage(&oargs,samtools_stderr, EXIT_FAILURE); break; } } if (argc <= optind) return usage(&oargs, samtools_stdout, EXIT_SUCCESS); if (argc <= optind+1 && isatty(STDIN_FILENO)) return usage(&oargs, samtools_stderr, EXIT_FAILURE); khash_t(bed_list_hash) *bed_hash = kh_init(bed_list_hash); if (load_bed_file_multi_ref(argv[optind], 1, 0, bed_hash, NULL, NULL)) { print_error_errno("ampliconstats", "Could not read file \"%s\"", argv[optind]); return 1; } khiter_t k, ref_count = 0; for (k = kh_begin(bed_hash); k != kh_end(bed_hash); k++) { if (!kh_exist(bed_hash, k)) continue; ref_count++; } if (ref_count == 0) return 1; if (ref_count > 1 && args.multi_ref == 0) { print_error("ampliconstats", "Single-ref mode is not permitted for BED files\n" "containing more than one reference."); return 1; } args.argv = stringify_argv(argc, argv); int ret; if (argc == ++optind) { char *av = "-"; ret = amplicon_stats(&args, bed_hash, &av, 1); } else { ret = amplicon_stats(&args, bed_hash, &argv[optind], argc-optind); } free(args.argv); destroy_bed_hash(bed_hash); return ret; } pysam-0.23.0/samtools/bam.c000066400000000000000000000214421475062545500155110ustar00rootroot00000000000000/* bam.c -- miscellaneous BAM functions. Copyright (C) 2008-2013, 2015, 2019-2020, 2022 Genome Research Ltd. Portions copyright (C) 2009-2012 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include "bam.h" #include "htslib/kstring.h" // FIXME: we should also check the LB tag associated with each alignment const char *bam_get_library(sam_hdr_t *h, const bam1_t *b) { const char *rg; kstring_t lib = { 0, 0, NULL }; rg = (char *)bam_aux_get(b, "RG"); if (!rg) return NULL; else rg++; if (sam_hdr_find_tag_id(h, "RG", "ID", rg, "LB", &lib) < 0) return NULL; static char LB_text[1024]; int len = lib.l < sizeof(LB_text) - 1 ? lib.l : sizeof(LB_text) - 1; memcpy(LB_text, lib.s, len); LB_text[len] = 0; free(lib.s); return LB_text; } /************ * Remove B * ************/ #define bam1_seq_seti(s, i, c) ( (s)[(i)>>1] = ((s)[(i)>>1] & 0xf<<(((i)&1)<<2)) | (c)<<((~(i)&1)<<2) ) int bam_remove_B(bam1_t *b) { int i, j, end_j, k, l, no_qual; uint32_t *cigar, *new_cigar; uint8_t *seq, *qual, *p; // test if removal is necessary if (b->core.flag & BAM_FUNMAP) return 0; // unmapped; do nothing cigar = bam_get_cigar(b); for (k = 0; k < b->core.n_cigar; ++k) if (bam_cigar_op(cigar[k]) == BAM_CBACK) break; if (k == b->core.n_cigar) return 0; // no 'B' if (bam_cigar_op(cigar[0]) == BAM_CBACK) goto rmB_err; // cannot be removed // allocate memory for the new CIGAR if (b->l_data + (b->core.n_cigar + 1) * 4 > b->m_data) { // not enough memory b->m_data = b->l_data + b->core.n_cigar * 4; kroundup32(b->m_data); b->data = (uint8_t*)realloc(b->data, b->m_data); cigar = bam_get_cigar(b); // after realloc, cigar may be changed } new_cigar = (uint32_t*)(b->data + (b->m_data - b->core.n_cigar * 4)); // from the end of b->data // the core loop seq = bam_get_seq(b); qual = bam_get_qual(b); no_qual = (qual[0] == 0xff); // test whether base quality is available i = j = 0; end_j = -1; for (k = l = 0; k < b->core.n_cigar; ++k) { int op = bam_cigar_op(cigar[k]); int len = bam_cigar_oplen(cigar[k]); if (op == BAM_CBACK) { // the backward operation int t, u; if (k == b->core.n_cigar - 1) break; // ignore 'B' at the end of CIGAR if (len > j) goto rmB_err; // an excessively long backward for (t = l - 1, u = 0; t >= 0; --t) { // look back int op1 = bam_cigar_op(new_cigar[t]); int len1 = bam_cigar_oplen(new_cigar[t]); if (bam_cigar_type(op1)&1) { // consume the query if (u + len1 >= len) { // stop new_cigar[t] -= (len - u) << BAM_CIGAR_SHIFT; break; } else u += len1; } } if (bam_cigar_oplen(new_cigar[t]) == 0) --t; // squeeze out the zero-length operation l = t + 1; end_j = j; j -= len; } else { // other CIGAR operations new_cigar[l++] = cigar[k]; if (bam_cigar_type(op)&1) { // consume the query if (i != j) { // no need to copy if i == j int u, c, c0; for (u = 0; u < len; ++u) { // construct the consensus c = bam_seqi(seq, i+u); if (j + u < end_j) { // in an overlap c0 = bam_seqi(seq, j+u); if (c != c0) { // a mismatch; choose the better base if (qual[j+u] < qual[i+u]) { // the base in the 2nd segment is better bam1_seq_seti(seq, j+u, c); qual[j+u] = qual[i+u] - qual[j+u]; } else qual[j+u] -= qual[i+u]; // the 1st is better; reduce base quality } else qual[j+u] = qual[j+u] > qual[i+u]? qual[j+u] : qual[i+u]; } else { // not in an overlap; copy over bam1_seq_seti(seq, j+u, c); qual[j+u] = qual[i+u]; } } } i += len, j += len; } } } if (no_qual) qual[0] = 0xff; // in very rare cases, this may be modified // merge adjacent operations if possible for (k = 1; k < l; ++k) if (bam_cigar_op(new_cigar[k]) == bam_cigar_op(new_cigar[k-1])) new_cigar[k] += new_cigar[k-1] >> BAM_CIGAR_SHIFT << BAM_CIGAR_SHIFT, new_cigar[k-1] &= 0xf; // kill zero length operations for (k = i = 0; k < l; ++k) if (new_cigar[k] >> BAM_CIGAR_SHIFT) new_cigar[i++] = new_cigar[k]; l = i; // update b memcpy(cigar, new_cigar, l * 4); // set CIGAR p = b->data + b->core.l_qname + l * 4; memmove(p, seq, (j+1)>>1); p += (j+1)>>1; // set SEQ memmove(p, qual, j); p += j; // set QUAL memmove(p, bam_get_aux(b), bam_get_l_aux(b)); p += bam_get_l_aux(b); // set optional fields b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length b->l_data = p - b->data; // update record length return 0; rmB_err: b->core.flag |= BAM_FUNMAP; return -1; } /* Calculate the current read's start based on the stored cigar string. */ hts_pos_t unclipped_start(bam1_t *b) { uint32_t *cigar = bam_get_cigar(b); int64_t clipped = 0; uint32_t i; for (i = 0; i < b->core.n_cigar; i++) { char c = bam_cigar_opchr(cigar[i]); if (c == 'S' || c == 'H') { // clips clipped += bam_cigar_oplen(cigar[i]); } else { break; } } return b->core.pos - clipped + 1; } /* Calculate the mate's unclipped start based on position and cigar string from MC tag. */ hts_pos_t unclipped_other_start(hts_pos_t op, char *cigar) { char *c = cigar; int64_t clipped = 0; while (*c && *c != '*') { long num = 0; if (isdigit((int)*c)) { num = strtol(c, &c, 10); } else { num = 1; } if (*c == 'S' || *c == 'H') { // clips clipped += num; } else { break; } c++; } return op - clipped + 1; } /* Calculate the current read's end based on the stored cigar string. */ hts_pos_t unclipped_end(bam1_t *b) { uint32_t *cigar = bam_get_cigar(b); hts_pos_t end_pos, clipped = 0; int32_t i; end_pos = bam_endpos(b); // now get the clipped end bases (if any) // if we get to the beginning of the cigar string // without hitting a non-clip then the results are meaningless for (i = b->core.n_cigar - 1; i >= 0; i--) { char c = bam_cigar_opchr(cigar[i]); if (c == 'S' || c == 'H') { // clips clipped += bam_cigar_oplen(cigar[i]); } else { break; } } return end_pos + clipped; } /* Calculate the mate's unclipped end based on start position and cigar string from MC tag.*/ hts_pos_t unclipped_other_end(int64_t op, char *cigar) { char *c = cigar; int64_t refpos = 0; int skip = 1; while (*c && *c != '*') { long num = 0; if (isdigit((int)*c)) { num = strtol(c, &c, 10); } else { num = 1; } switch (*c) { case 'M': case 'D': case 'N': case '=': case 'X': refpos += num; skip = 0; // ignore initial clips break; case 'S': case 'H': if (!skip) { refpos += num; } break; } c++; } return op + refpos; } pysam-0.23.0/samtools/bam.c.pysam.c000066400000000000000000000214771475062545500170720ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam.c -- miscellaneous BAM functions. Copyright (C) 2008-2013, 2015, 2019-2020, 2022 Genome Research Ltd. Portions copyright (C) 2009-2012 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include "bam.h" #include "htslib/kstring.h" // FIXME: we should also check the LB tag associated with each alignment const char *bam_get_library(sam_hdr_t *h, const bam1_t *b) { const char *rg; kstring_t lib = { 0, 0, NULL }; rg = (char *)bam_aux_get(b, "RG"); if (!rg) return NULL; else rg++; if (sam_hdr_find_tag_id(h, "RG", "ID", rg, "LB", &lib) < 0) return NULL; static char LB_text[1024]; int len = lib.l < sizeof(LB_text) - 1 ? lib.l : sizeof(LB_text) - 1; memcpy(LB_text, lib.s, len); LB_text[len] = 0; free(lib.s); return LB_text; } /************ * Remove B * ************/ #define bam1_seq_seti(s, i, c) ( (s)[(i)>>1] = ((s)[(i)>>1] & 0xf<<(((i)&1)<<2)) | (c)<<((~(i)&1)<<2) ) int bam_remove_B(bam1_t *b) { int i, j, end_j, k, l, no_qual; uint32_t *cigar, *new_cigar; uint8_t *seq, *qual, *p; // test if removal is necessary if (b->core.flag & BAM_FUNMAP) return 0; // unmapped; do nothing cigar = bam_get_cigar(b); for (k = 0; k < b->core.n_cigar; ++k) if (bam_cigar_op(cigar[k]) == BAM_CBACK) break; if (k == b->core.n_cigar) return 0; // no 'B' if (bam_cigar_op(cigar[0]) == BAM_CBACK) goto rmB_err; // cannot be removed // allocate memory for the new CIGAR if (b->l_data + (b->core.n_cigar + 1) * 4 > b->m_data) { // not enough memory b->m_data = b->l_data + b->core.n_cigar * 4; kroundup32(b->m_data); b->data = (uint8_t*)realloc(b->data, b->m_data); cigar = bam_get_cigar(b); // after realloc, cigar may be changed } new_cigar = (uint32_t*)(b->data + (b->m_data - b->core.n_cigar * 4)); // from the end of b->data // the core loop seq = bam_get_seq(b); qual = bam_get_qual(b); no_qual = (qual[0] == 0xff); // test whether base quality is available i = j = 0; end_j = -1; for (k = l = 0; k < b->core.n_cigar; ++k) { int op = bam_cigar_op(cigar[k]); int len = bam_cigar_oplen(cigar[k]); if (op == BAM_CBACK) { // the backward operation int t, u; if (k == b->core.n_cigar - 1) break; // ignore 'B' at the end of CIGAR if (len > j) goto rmB_err; // an excessively long backward for (t = l - 1, u = 0; t >= 0; --t) { // look back int op1 = bam_cigar_op(new_cigar[t]); int len1 = bam_cigar_oplen(new_cigar[t]); if (bam_cigar_type(op1)&1) { // consume the query if (u + len1 >= len) { // stop new_cigar[t] -= (len - u) << BAM_CIGAR_SHIFT; break; } else u += len1; } } if (bam_cigar_oplen(new_cigar[t]) == 0) --t; // squeeze out the zero-length operation l = t + 1; end_j = j; j -= len; } else { // other CIGAR operations new_cigar[l++] = cigar[k]; if (bam_cigar_type(op)&1) { // consume the query if (i != j) { // no need to copy if i == j int u, c, c0; for (u = 0; u < len; ++u) { // construct the consensus c = bam_seqi(seq, i+u); if (j + u < end_j) { // in an overlap c0 = bam_seqi(seq, j+u); if (c != c0) { // a mismatch; choose the better base if (qual[j+u] < qual[i+u]) { // the base in the 2nd segment is better bam1_seq_seti(seq, j+u, c); qual[j+u] = qual[i+u] - qual[j+u]; } else qual[j+u] -= qual[i+u]; // the 1st is better; reduce base quality } else qual[j+u] = qual[j+u] > qual[i+u]? qual[j+u] : qual[i+u]; } else { // not in an overlap; copy over bam1_seq_seti(seq, j+u, c); qual[j+u] = qual[i+u]; } } } i += len, j += len; } } } if (no_qual) qual[0] = 0xff; // in very rare cases, this may be modified // merge adjacent operations if possible for (k = 1; k < l; ++k) if (bam_cigar_op(new_cigar[k]) == bam_cigar_op(new_cigar[k-1])) new_cigar[k] += new_cigar[k-1] >> BAM_CIGAR_SHIFT << BAM_CIGAR_SHIFT, new_cigar[k-1] &= 0xf; // kill zero length operations for (k = i = 0; k < l; ++k) if (new_cigar[k] >> BAM_CIGAR_SHIFT) new_cigar[i++] = new_cigar[k]; l = i; // update b memcpy(cigar, new_cigar, l * 4); // set CIGAR p = b->data + b->core.l_qname + l * 4; memmove(p, seq, (j+1)>>1); p += (j+1)>>1; // set SEQ memmove(p, qual, j); p += j; // set QUAL memmove(p, bam_get_aux(b), bam_get_l_aux(b)); p += bam_get_l_aux(b); // set optional fields b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length b->l_data = p - b->data; // update record length return 0; rmB_err: b->core.flag |= BAM_FUNMAP; return -1; } /* Calculate the current read's start based on the stored cigar string. */ hts_pos_t unclipped_start(bam1_t *b) { uint32_t *cigar = bam_get_cigar(b); int64_t clipped = 0; uint32_t i; for (i = 0; i < b->core.n_cigar; i++) { char c = bam_cigar_opchr(cigar[i]); if (c == 'S' || c == 'H') { // clips clipped += bam_cigar_oplen(cigar[i]); } else { break; } } return b->core.pos - clipped + 1; } /* Calculate the mate's unclipped start based on position and cigar string from MC tag. */ hts_pos_t unclipped_other_start(hts_pos_t op, char *cigar) { char *c = cigar; int64_t clipped = 0; while (*c && *c != '*') { long num = 0; if (isdigit((int)*c)) { num = strtol(c, &c, 10); } else { num = 1; } if (*c == 'S' || *c == 'H') { // clips clipped += num; } else { break; } c++; } return op - clipped + 1; } /* Calculate the current read's end based on the stored cigar string. */ hts_pos_t unclipped_end(bam1_t *b) { uint32_t *cigar = bam_get_cigar(b); hts_pos_t end_pos, clipped = 0; int32_t i; end_pos = bam_endpos(b); // now get the clipped end bases (if any) // if we get to the beginning of the cigar string // without hitting a non-clip then the results are meaningless for (i = b->core.n_cigar - 1; i >= 0; i--) { char c = bam_cigar_opchr(cigar[i]); if (c == 'S' || c == 'H') { // clips clipped += bam_cigar_oplen(cigar[i]); } else { break; } } return end_pos + clipped; } /* Calculate the mate's unclipped end based on start position and cigar string from MC tag.*/ hts_pos_t unclipped_other_end(int64_t op, char *cigar) { char *c = cigar; int64_t refpos = 0; int skip = 1; while (*c && *c != '*') { long num = 0; if (isdigit((int)*c)) { num = strtol(c, &c, 10); } else { num = 1; } switch (*c) { case 'M': case 'D': case 'N': case '=': case 'X': refpos += num; skip = 0; // ignore initial clips break; case 'S': case 'H': if (!skip) { refpos += num; } break; } c++; } return op + refpos; } pysam-0.23.0/samtools/bam.h000066400000000000000000000027631475062545500155230ustar00rootroot00000000000000/* bam.h -- miscellaneous BAM functions. Copyright (C) 2008-2014, 2019 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef BAM_BAM_H #define BAM_BAM_H #include "htslib/sam.h" int bam_remove_B(bam1_t *b); const char *bam_get_library(sam_hdr_t *header, const bam1_t *b); hts_pos_t unclipped_start(bam1_t *b); hts_pos_t unclipped_other_start(hts_pos_t op, char *cigar); hts_pos_t unclipped_end(bam1_t *b); hts_pos_t unclipped_other_end(int64_t op, char *cigar); #endif pysam-0.23.0/samtools/bam2depth.c000066400000000000000000001011071475062545500166150ustar00rootroot00000000000000/* bam2depth.c -- depth subcommand. Copyright (C) 2011, 2012 Broad Institute. Copyright (C) 2012-2016, 2018, 2019-2022, 2024 Genome Research Ltd. Author: Heng Li (to 2020) Author: James Bonfield (2021 rewrite) Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* This program demonstrates how to generate pileup from multiple BAMs * simultaneously, to achieve random access and to use the BED interface. * To compile this program separately, you may: * * gcc -g -O2 -Wall -o bam2depth -D_MAIN_BAM2DEPTH bam2depth.c -lhts -lz */ #include #include #include #include #include #include #include "htslib/sam.h" #include "samtools.h" #include "bedidx.h" #include "sam_opts.h" #include "htslib/khash.h" // From bam_plcmd.c int read_file_list(const char *file_list, int *n, char **argv[]); // We accumulate to hist[pos & (size-1)]. This is a ring-buffer. // We track where we last got to in output and what the biggest value // we've written to so far (in absolute unmasked coordinates) in // "last_output" and "end_pos" respectively. // For each new record we just flush anything we haven't written yet // already, between "last_output" and this read's start position, and // initialise any newly seen positions between "end_pos" and this read's // end position. typedef struct { size_t size; int **hist; // hist[nfiles][size] hts_pos_t *end_pos; // end_pos[nfiles] hts_pos_t last_output; int last_ref; int nfiles; const char *ref; kstring_t ks; hts_pos_t beg, end; // limit to region int tid; } depth_hist; typedef struct { int header; int flag; int incl_flag; int require_flag; int min_qual; int min_mqual; int min_len; int skip_del; int all_pos; int remove_overlaps; FILE *out; char *reg; void *bed; } depth_opt; static void zero_region(depth_opt *opt, depth_hist *dh, const char *name, hts_pos_t start, hts_pos_t end) { hts_pos_t i; kstring_t *ks = &dh->ks; kputs(name, ks_clear(ks)); kputc('\t', ks); size_t cur_l = ks->l; if (dh->beg >= 0 && start < dh->beg) start = dh->beg; if (dh->end >= 0 && end > dh->end) end = dh->end; for (i = start; i < end; i++) { // Could be optimised, but needs better API to skip to next // bed region. if (opt->bed && bed_overlap(opt->bed, name, i, i+1) == 0) continue; ks->l = cur_l; kputll(i+1, ks); int n; for (n = 0; n < dh->nfiles; n++) { kputc_('\t', ks); kputc_('0', ks); } kputc('\n', ks); fputs(ks->s, opt->out); } ks->l = cur_l; } // A variation of bam_cigar2qlen which doesn't count soft-clips in to the // equation. Basically it's the number of bases in query that are aligned // in some way to the reference (including insertions, which are considered // to be aligned by dint of being anchored either side). hts_pos_t qlen_used(bam1_t *b) { int n_cigar = b->core.n_cigar; const uint32_t *cigar = bam_get_cigar(b); hts_pos_t l; if (b->core.l_qseq) { // Known SEQ permits of short cut of l_qseq minus CSOFT_CLIPs. // Full scan not needed, which helps on excessively long CIGARs. l = b->core.l_qseq; int kl, kr; for (kl = 0; kl < n_cigar; kl++) if (bam_cigar_op(cigar[kl]) == BAM_CSOFT_CLIP) l -= bam_cigar_oplen(cigar[kl]); else break; for (kr = n_cigar-1; kr > kl; kr--) if (bam_cigar_op(cigar[kr]) == BAM_CSOFT_CLIP) l -= bam_cigar_oplen(cigar[kr]); else break; } else { // Unknown SEQ ("*") needs a full scan through the CIGAR string. static int query[16] = { //M I D N S H P = X B ? ? ? ? ? ? 1,1,0,0, 0,0,0,1, 1,0,0,0, 0,0,0,0 }; int k; for (k = l = 0; k < n_cigar; k++) if (query[bam_cigar_op(cigar[k])]) l += bam_cigar_oplen(cigar[k]); } return l; } // Without HTS_OPT3 gcc11 and earlier don't vectorize this, nor even // unroll it. By adding HTS_OPT3 we can force a better level of optimization. // On an Illumina BAM with gcc11 -O2, with HTS_OPT3 is 9% quicker for the // entire process (ie decompress, iterator, aggregate & report) static inline void HTS_OPT3 incr_hist(int *hist, int oplen) { const int N = 16; int k; for (k = 0; k < (oplen & ~(N-1)); k+=N) { for (int i = 0; i < N; i++) hist[k+i]++; } for (; k < oplen; k++) hist[k]++; } static inline void HTS_OPT3 incr_hist_qual(int *hist, uint8_t *qual, int min_qual, int oplen) { if (!min_qual) { incr_hist(hist, oplen); return; } int k; for (k = 0; k < (oplen & ~31); k+=32) { int pass[32]; // Two separate loops helps clang to vectorize for (int i = 0; i < 32; i++) pass[i]=qual[k+i]>=min_qual; for (int i = 0; i < 32; i++) hist[k+i]+=pass[i]; } for (; k < oplen; k++) hist[k]+=qual[k]>=min_qual; } // Adds the depth for a single read to a depth_hist struct. // For just one file, this is easy. We just have a circular buffer // where we increment values for bits that overlap existing data // and initialise values for coordinates which we're seeing for the first // time. This is tracked by "end_pos" to know where we've got to. // // As the input is sorted, we can flush output from "last_output" to // b->core.pos. // // With multiple files, we must feed data in sorted order as if all files // are merged, but track depth per file. This also means "end_pos" is per // file too, but "last_output" is global as it corresponds to rows printed. static int add_depth(depth_opt *opt, depth_hist *dh, sam_hdr_t *h, bam1_t *b, int overlap_clip, int file) { hts_pos_t i; size_t hmask = dh->size-1; int n; if (!b || b->core.tid != dh->last_ref) { // New ref if (dh->last_ref >= 0) { // do end size_t cur_l = dh->ks.l; int nf = dh->nfiles; i = dh->last_output; for (i = dh->last_output; nf; i++) { nf = 0; for (n = 0; n < dh->nfiles; n++) { if (i < dh->end_pos[n]) nf++; } if (!nf) break; if (opt->bed && bed_overlap(opt->bed, dh->ref, i, i+1) == 0) continue; dh->ks.l = cur_l; kputll(i+1, &dh->ks); for (n = 0; n < dh->nfiles; n++) { kputc_('\t', &dh->ks); int d = i < dh->end_pos[n] ? dh->hist[n][i & hmask] : 0; kputuw(d, &dh->ks); } kputc('\n', &dh->ks); fputs(dh->ks.s, opt->out); } if (opt->all_pos) { // End of last ref zero_region(opt, dh, sam_hdr_tid2name(h, dh->last_ref), i, sam_hdr_tid2len(h, dh->last_ref)); } dh->ks.l = cur_l; } if (opt->all_pos > 1 && !opt->reg) { // Any previous unused refs int lr = dh->last_ref < 0 ? 0 : dh->last_ref+1; int rr = b ? b->core.tid : sam_hdr_nref(h), r; for (r = lr; r < rr; r++) zero_region(opt, dh, sam_hdr_tid2name(h, r), 0, sam_hdr_tid2len(h, r)); } if (!b) { // we're just flushing to end of file if (opt->all_pos && opt->reg && dh->last_ref < 0) // -a or -aa without a single read being output yet zero_region(opt, dh, sam_hdr_tid2name(h, dh->tid), dh->beg, MIN(dh->end, sam_hdr_tid2len(h, dh->tid))); return 0; } for (n = 0; dh->end_pos && n < dh->nfiles; n++) dh->end_pos[n] = 0; dh->last_output = dh->beg >= 0 ? MAX(b->core.pos, dh->beg) : b->core.pos; dh->last_ref = b->core.tid; dh->ref = sam_hdr_tid2name(h, b->core.tid); kputs(dh->ref, ks_clear(&dh->ks)); kputc('\t', &dh->ks); if (opt->all_pos) // Start of ref zero_region(opt, dh, dh->ref, 0, b->core.pos); } else { if (dh->last_output < b->core.pos) { // Flush any depth outputs up to start of new read size_t cur_l = dh->ks.l; int nf = dh->nfiles; for (i = dh->last_output; i < b->core.pos; i++) { nf = 0; for (n = 0; n < dh->nfiles; n++) { if (i < dh->end_pos[n]) nf++; } if (!nf) break; if (opt->bed && bed_overlap(opt->bed, dh->ref, i, i+1) == 0) continue; dh->ks.l = cur_l; kputll(i+1, &dh->ks); for (n = 0; n < dh->nfiles; n++) { kputc_('\t', &dh->ks); int d = i < dh->end_pos[n] ? dh->hist[n][i & hmask] : 0; kputuw(d, &dh->ks); } kputc('\n', &dh->ks); fputs(dh->ks.s, opt->out); } if (opt->all_pos && i < b->core.pos) // Hole in middle of ref zero_region(opt, dh, dh->ref, i, b->core.pos); dh->ks.l = cur_l; dh->last_output = b->core.pos; } } hts_pos_t end_pos = bam_endpos(b); // 0 based, 1 past end. //printf("%d %d\n", (int)b->core.pos+1, (int)end_pos); if (b->core.tid < dh->last_ref || (dh->last_ref == b->core.tid && end_pos < dh->last_output)) { print_error_errno("depth", "Data is not position sorted"); return -1; } // If needed, grow the circular buffer. if (end_pos+1 - b->core.pos >= dh->size) { size_t old_size = dh->size; size_t old_hmask = hmask; while (end_pos+1 - b->core.pos >= dh->size) dh->size = dh->size ? 2*dh->size : 2048; hmask = dh->size-1; if (!dh->hist) { dh->hist = calloc(dh->nfiles, sizeof(*dh->hist)); dh->end_pos = calloc(dh->nfiles, sizeof(*dh->end_pos)); if (!dh->hist || !dh->end_pos) return -1; } for (n = 0; n < dh->nfiles; n++) { int *hist = calloc(dh->size, sizeof(*dh->hist[n])); if (!hist) return -1; // Simple approach for now; copy over old histogram verbatim. for (i = dh->last_output; i < dh->last_output + old_size; i++) hist[i & hmask] = dh->hist[n][i & old_hmask]; free(dh->hist[n]); dh->hist[n] = hist; } } // Accumulate depth, based on CIGAR uint32_t *cig = bam_get_cigar(b); int ncig = b->core.n_cigar, j, k, spos = 0; // Zero new (previously unseen) coordinates so increment works later. hts_pos_t end = MAX(dh->end_pos[file], b->core.pos); if (end_pos > end && (end & hmask) < (end_pos & hmask)) { memset(&dh->hist[file][end & hmask], 0, sizeof(**dh->hist) * (end_pos - end)); } else { for (i = end; i < end_pos; i++) dh->hist[file][i & hmask] = 0; } i = b->core.pos; uint8_t *qual = bam_get_qual(b); int min_qual = opt->min_qual; for (j = 0; j < ncig; j++) { int op = bam_cigar_op(cig[j]); int oplen = bam_cigar_oplen(cig[j]); switch (op) { case BAM_CDEL: case BAM_CREF_SKIP: if (op != BAM_CDEL || opt->skip_del) { // don't increment reference location if (i + oplen >= dh->end_pos[file]) { for (k = 0; k < oplen; k++, i++) { if (i >= dh->end_pos[file]) // redundant due to zero new elements above? dh->hist[file][i & hmask] = 0; } } else { i += oplen; } } else { // op == BAM_CDEL and we count them (-J option), // We don't incr spos here, but we still use qual. // This doesn't make much sense, but it's for compatibility // with the old code. Arguably DEL shouldn't have a min // qual and should always pass (as we've explicitly asked to // include them). int *hist = dh->hist[file]; k = 0; if (overlap_clip) { if (i+oplen < overlap_clip) { i += oplen; break; } else if (i < overlap_clip) { k = overlap_clip - i; i = overlap_clip; } } // Question: should we even check quality values for DEL? // We've explicitly asked to include them, and the quality // is wrong anyway (it's the neighbouring base). We do this // for now for compatibility with the old depth command. if (spos < b->core.l_qseq) for (; k < oplen; k++, i++) hist[i & hmask]+=qual[spos]>=min_qual; else for (; k < oplen; k++, i++) hist[i & hmask]++; } break; case BAM_CMATCH: case BAM_CEQUAL: case BAM_CDIFF: { int *hist = dh->hist[file]; k = 0; if (overlap_clip) { if (i+oplen < overlap_clip) { i += oplen; break; } else if (i < overlap_clip) { oplen -= overlap_clip - i; spos += overlap_clip - i; i = overlap_clip; } } int len = (i & hmask) < ((i+oplen) & hmask) ? oplen // doesn't wrap around : dh->size - (i&hmask); // does wrap around incr_hist_qual(&hist[i & hmask], &qual[spos], min_qual, len); if (oplen > len) incr_hist_qual(hist, &qual[spos+len], min_qual, oplen-len); spos += oplen; i += oplen; break; } case BAM_CINS: case BAM_CSOFT_CLIP: spos += oplen; break; case BAM_CPAD: case BAM_CHARD_CLIP: // ignore break; default: print_error("depth", "Unsupported cigar op '%d'", op); return -1; } } if (dh->end >= 0 && end_pos > dh->end) end_pos = dh->end; if (dh->end_pos[file] < end_pos) dh->end_pos[file] = end_pos; return 0; } // Hash on name -> alignment end pos. This permits a naive overlap removal. // Note it cannot analyse the overlapping sequence and qualities, so the // interaction of basecalls/qualities and the -Q parameter cannot be // applied here (unlike the full mpileup algorithm). KHASH_MAP_INIT_STR(olap_hash, hts_pos_t) typedef khash_t(olap_hash) olap_hash_t; static int fastdepth_core(depth_opt *opt, uint32_t nfiles, char **fn, samFile **fp, hts_itr_t **itr, sam_hdr_t **h) { int ret = -1, err = 1, i; olap_hash_t **overlaps = NULL; depth_hist dh = {0}; // An array of bam structs, one per input file, to hold the next entry bam1_t **b = calloc(nfiles, sizeof(*b)); int *finished = calloc(nfiles, sizeof(*finished)), to_go = nfiles; if (!b || !finished) goto err; for (i = 0; i < nfiles; i++) if (!(b[i] = bam_init1())) goto err; // Do we need one overlap hash per file? Or shared? if (opt->remove_overlaps) { if (!(overlaps = calloc(nfiles, sizeof(*overlaps)))) return -1; for (i = 0; i < nfiles; i++) { if (!(overlaps[i] = kh_init(olap_hash))) return -1; } } // Create the initial histogram dh.nfiles = nfiles; dh.size = 0; dh.hist = NULL; dh.last_ref = -99; dh.end_pos = NULL; dh.last_output = itr && itr[0] ? itr[0]->beg : 0; ks_initialize(&dh.ks); // Clip results to region if specified dh.beg = -1; dh.end = -1; dh.tid = 0; if (itr && itr[0]) { dh.tid = itr[0]->tid; dh.beg = itr[0]->beg; dh.end = itr[0]->end; } if (opt->header) { fprintf(opt->out, "#CHROM\tPOS"); for (i = 0; i < nfiles; i++) fprintf(opt->out, "\t%s", fn[i]); fputc('\n', opt->out); } // Populate first record per file for (i = 0; i < nfiles; i++) { for(;;) { ret = itr && itr[i] ? sam_itr_next(fp[i], itr[i], b[i]) : sam_read1(fp[i], h[i], b[i]); if (ret < -1) goto err; if (ret == -1) { to_go--; finished[i] = 1; break; } if (b[i]->core.tid < 0) continue; if (b[i]->core.flag & opt->flag) continue; // must have none of the flags set if (opt->incl_flag && (b[i]->core.flag & opt->incl_flag) == 0) continue; // must have at least one flag set if ((b[i]->core.flag & opt->require_flag) != opt->require_flag) continue; // must have all lags set if (b[i]->core.qual < opt->min_mqual) continue; // Original samtools depth used the total sequence (l_qseq) // including soft-clips. This doesn't feel like a useful metric // to be filtering on. We now only count sequence bases that // form the used part of the alignment. if (opt->min_len) { if (qlen_used(b[i]) < opt->min_len) continue; } break; } } // Loop through input files, merging in order so we're // always adding the next record in sequence while (to_go) { // Find next record in file list int best_tid = INT_MAX, best_file = 0; hts_pos_t best_pos = HTS_POS_MAX; for (i = 0; i < nfiles; i++) { if (finished[i]) continue; if (best_tid > b[i]->core.tid) { best_tid = b[i]->core.tid; best_pos = b[i]->core.pos; best_file = i; } else if (best_tid == b[i]->core.tid && best_pos > b[i]->core.pos) { best_pos = b[i]->core.pos; best_file = i; } } i = best_file; hts_pos_t clip = 0; if (overlaps && (b[i]->core.flag & BAM_FPAIRED) && !(b[i]->core.flag & BAM_FMUNMAP)) { khiter_t k = kh_get(olap_hash, overlaps[i], bam_get_qname(b[i])); if (k == kh_end(overlaps[i])) { // not seen before hts_pos_t endpos = bam_endpos(b[i]); // Don't add if mate location is known and can't overlap. if (b[i]->core.mpos == -1 || (b[i]->core.tid == b[i]->core.mtid && b[i]->core.mpos <= endpos)) { k = kh_put(olap_hash, overlaps[i], bam_get_qname(b[i]), &ret); if (ret < 0) return -1; kh_key(overlaps[i], k) = strdup(bam_get_qname(b[i])); kh_value(overlaps[i], k) = endpos; } } else { // seen before clip = kh_value(overlaps[i], k); free((char *)kh_key(overlaps[i], k)); kh_del(olap_hash, overlaps[i], k); } } // Add the next merged BAM record to the depth plot if ((ret = add_depth(opt, &dh, h[i], b[i], clip, i)) < 0) { ret = -1; goto err; } // Populate next record from this file for(;!finished[i];) { ret = itr && itr[i] ? sam_itr_next(fp[i], itr[i], b[i]) : sam_read1(fp[i], h[i], b[i]); if (ret < -1) { ret = -1; goto err; } if (ret == -1) { to_go--; finished[i] = 1; break; } if (b[i]->core.tid < 0) continue; if (b[i]->core.flag & opt->flag) continue; // must have none of the flags set if (opt->incl_flag && (b[i]->core.flag & opt->incl_flag) == 0) continue; // must have at least one flag set if ((b[i]->core.flag & opt->require_flag) != opt->require_flag) continue; // must have all lags set if (b[i]->core.qual < opt->min_mqual) continue; if (opt->min_len) { if (qlen_used(b[i]) < opt->min_len) continue; } break; } } // Tidy up end. ret = add_depth(opt, &dh, h[0], NULL, 0, 0); err = 0; err: if (ret == 0 && err) ret = -1; for (i = 0; i < nfiles; i++) { if (b[i]) bam_destroy1(b[i]); if (dh.hist && dh.hist[i]) free(dh.hist[i]); } free(b); free(finished); ks_free(&dh.ks); free(dh.hist); free(dh.end_pos); if (overlaps) { khiter_t k; for (i = 0; i < nfiles; i++) { if (!overlaps[i]) continue; for (k = kh_begin(overlaps[i]); k < kh_end(overlaps[i]); k++) if (kh_exist(overlaps[i], k)) free((char *)kh_key(overlaps[i], k)); kh_destroy(olap_hash, overlaps[i]); } free(overlaps); } return ret; } static void usage_exit(FILE *fp, int exit_status) { fprintf(fp, "Usage: samtools depth [options] in.bam [in.bam ...]\n"); fprintf(fp, "\nOptions:\n"); fprintf(fp, " -a Output all positions (including zero depth)\n"); fprintf(fp, " -a -a, -aa Output absolutely all positions, including unused ref seqs\n"); fprintf(fp, " -r REG Specify a region in chr or chr:from-to syntax\n"); fprintf(fp, " -b FILE Use bed FILE for list of regions\n"); fprintf(fp, " -f FILE Specify list of input BAM/SAM/CRAM filenames\n"); fprintf(fp, " -X Use custom index files (in -X *.bam *.bam.bai order)\n"); fprintf(fp, " -g INT Remove specified flags from default filter-out flag list\n"); fprintf(fp, " -G, --excl-flags FLAGS\n"); fprintf(fp, " Add specified flags to the default filter-out flag list\n"); fprintf(fp, " [UNMAP,SECONDARY,QCFAIL,DUP]\n"); fprintf(fp, " --incl-flags FLAGS\n"); fprintf(fp, " Only include records with at least one the FLAGs present [0]\n"); fprintf(fp, " --require-flags FLAGS\n"); fprintf(fp, " Only include records with all of the FLAGs present [0]\n"); fprintf(fp, " -H Print a file header line\n"); fprintf(fp, " -l INT Minimum read length [0]\n"); fprintf(fp, " -o FILE Write output to FILE [stdout]\n"); fprintf(fp, " -q, --min-BQ INT\n" " Filter bases with base quality smaller than INT [0]\n"); fprintf(fp, " -Q, --min-MQ INT\n" " Filter alignments with mapping quality smaller than INT [0]\n"); fprintf(fp, " -J Include reads with deletions in depth computation\n"); fprintf(fp, " -s Do not count overlapping reads within a template\n"); sam_global_opt_help(fp, "-.--.@-."); exit(exit_status); } int main_depth(int argc, char *argv[]) { int nfiles, i, tmp_flag; samFile **fp; sam_hdr_t **header; int c, has_index_file = 0; char *file_list = NULL, **fn = NULL; char *out_file = NULL; depth_opt opt = { .flag = BAM_FUNMAP | BAM_FSECONDARY | BAM_FDUP | BAM_FQCFAIL, .incl_flag = 0, .require_flag = 0, .min_qual = 0, .min_mqual = 0, .skip_del = 1, .header = 0, .min_len = 0, .out = stdout, .all_pos = 0, .remove_overlaps = 0, .reg = NULL, .bed = NULL, }; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { {"min-MQ", required_argument, NULL, 'Q'}, {"min-mq", required_argument, NULL, 'Q'}, {"min-BQ", required_argument, NULL, 'q'}, {"min-bq", required_argument, NULL, 'q'}, {"excl-flags", required_argument, NULL, 'G'}, {"incl-flags", required_argument, NULL, 1}, {"require-flags", required_argument, NULL, 2}, SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '@'), {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "@:q:Q:JHd:m:l:g:G:o:ar:Xf:b:s", lopts, NULL)) >= 0) { switch (c) { case 'a': opt.all_pos++; break; case 'b': opt.bed = bed_read(optarg); if (!opt.bed) { print_error_errno("depth", "Could not read file \"%s\"", optarg); return 1; } break; case 'f': file_list = optarg; break; case 'd': case 'm': // depth limit - now ignored break; case 'g': tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("depth", "Unknown flag '%s'", optarg); return 1; } opt.flag &= ~tmp_flag; break; case 'G': // reject if any set tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("depth", "Unknown flag '%s'", optarg); return 1; } opt.flag |= tmp_flag; break; case 1: // reject unless at least one set (0 means ignore option) tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("depth", "Unknown flag '%s'", optarg); return 1; } opt.incl_flag |= tmp_flag; break; case 2: // reject unless all set tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("depth", "Unknown flag '%s'", optarg); return 1; } opt.require_flag |= tmp_flag; break; case 'l': opt.min_len = atoi(optarg); break; case 'H': opt.header = 1; break; case 'q': opt.min_qual = atoi(optarg); break; case 'Q': opt.min_mqual = atoi(optarg); break; case 'J': opt.skip_del = 0; break; case 'o': if (opt.out != stdout) break; opt.out = fopen(out_file = optarg, "w"); if (!opt.out) { print_error_errno("depth", "Cannot open \"%s\" for writing.", optarg); return EXIT_FAILURE; } break; case 'r': opt.reg = optarg; break; case 's': opt.remove_overlaps = 1; break; case 'X': has_index_file = 1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage_exit(stderr, EXIT_FAILURE); } } if (argc < optind+1 && !file_list) { if (argc == optind) usage_exit(stdout, EXIT_SUCCESS); else usage_exit(stderr, EXIT_FAILURE); } if (file_list) { if (has_index_file) { print_error("depth", "The -f option cannot be combined with -X"); return 1; } if (read_file_list(file_list, &nfiles, &fn)) return 1; argv = fn; argc = nfiles; optind = 0; } else { nfiles = argc - optind; } if (has_index_file) { if (nfiles%1) { print_error("depth", "-X needs one index specified per bam file"); return 1; } nfiles /= 2; } fp = malloc(nfiles * sizeof(*fp)); header = malloc(nfiles * sizeof(*header)); if (!fp || !header) { print_error_errno("depth", "Out of memory"); return 1; } hts_itr_t **itr = NULL; if (opt.reg) { itr = calloc(nfiles, sizeof(*itr)); if (!itr) return 1; } for (i = 0; i < nfiles; i++, optind++) { fp[i] = sam_open_format(argv[optind], "r", &ga.in); if (fp[i] == NULL) { print_error_errno("depth", "Cannot open input file \"%s\"", argv[optind]); return 1; } if (ga.nthreads > 0) hts_set_threads(fp[i], ga.nthreads); if (hts_set_opt(fp[i], CRAM_OPT_REQUIRED_FIELDS, SAM_FLAG | SAM_RNAME | SAM_POS | SAM_CIGAR | (opt.remove_overlaps ? SAM_QNAME|SAM_RNEXT|SAM_PNEXT : 0) | (opt.min_mqual ? SAM_MAPQ : 0) | (opt.min_len ? SAM_SEQ : 0) | (opt.min_qual ? SAM_QUAL : 0))) { fprintf(stderr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n"); return 1; } if (hts_set_opt(fp[i], CRAM_OPT_DECODE_MD, 0)) { fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n"); return 1; } // FIXME: what if headers differ? header[i] = sam_hdr_read(fp[i]); if (header == NULL) { fprintf(stderr, "Failed to read header for \"%s\"\n", argv[optind]); return 1; } if (opt.reg) { hts_idx_t *idx = has_index_file ? sam_index_load2(fp[i], argv[optind], argv[optind+nfiles]) : sam_index_load(fp[i], argv[optind]); if (!idx) { print_error("depth", "cannot load index for \"%s\"", argv[optind]); return 1; } if (!(itr[i] = sam_itr_querys(idx, header[i], opt.reg))) { print_error("depth", "cannot parse region \"%s\"", opt.reg); return 1; } hts_idx_destroy(idx); } } int ret = fastdepth_core(&opt, nfiles, &argv[argc-nfiles], fp, itr, header) ? 1 : 0; for (i = 0; i < nfiles; i++) { sam_hdr_destroy(header[i]); sam_close(fp[i]); if (itr && itr[i]) hts_itr_destroy(itr[i]); } free(header); free(fp); free(itr); if (file_list) { for (i=0; i (to 2020) Author: James Bonfield (2021 rewrite) Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* This program demonstrates how to generate pileup from multiple BAMs * simultaneously, to achieve random access and to use the BED interface. * To compile this program separately, you may: * * gcc -g -O2 -Wall -o bam2depth -D_MAIN_BAM2DEPTH bam2depth.c -lhts -lz */ #include #include #include #include #include #include #include "htslib/sam.h" #include "samtools.h" #include "bedidx.h" #include "sam_opts.h" #include "htslib/khash.h" // From bam_plcmd.c int read_file_list(const char *file_list, int *n, char **argv[]); // We accumulate to hist[pos & (size-1)]. This is a ring-buffer. // We track where we last got to in output and what the biggest value // we've written to so far (in absolute unmasked coordinates) in // "last_output" and "end_pos" respectively. // For each new record we just flush anything we haven't written yet // already, between "last_output" and this read's start position, and // initialise any newly seen positions between "end_pos" and this read's // end position. typedef struct { size_t size; int **hist; // hist[nfiles][size] hts_pos_t *end_pos; // end_pos[nfiles] hts_pos_t last_output; int last_ref; int nfiles; const char *ref; kstring_t ks; hts_pos_t beg, end; // limit to region int tid; } depth_hist; typedef struct { int header; int flag; int incl_flag; int require_flag; int min_qual; int min_mqual; int min_len; int skip_del; int all_pos; int remove_overlaps; FILE *out; char *reg; void *bed; } depth_opt; static void zero_region(depth_opt *opt, depth_hist *dh, const char *name, hts_pos_t start, hts_pos_t end) { hts_pos_t i; kstring_t *ks = &dh->ks; kputs(name, ks_clear(ks)); kputc('\t', ks); size_t cur_l = ks->l; if (dh->beg >= 0 && start < dh->beg) start = dh->beg; if (dh->end >= 0 && end > dh->end) end = dh->end; for (i = start; i < end; i++) { // Could be optimised, but needs better API to skip to next // bed region. if (opt->bed && bed_overlap(opt->bed, name, i, i+1) == 0) continue; ks->l = cur_l; kputll(i+1, ks); int n; for (n = 0; n < dh->nfiles; n++) { kputc_('\t', ks); kputc_('0', ks); } kputc('\n', ks); fputs(ks->s, opt->out); } ks->l = cur_l; } // A variation of bam_cigar2qlen which doesn't count soft-clips in to the // equation. Basically it's the number of bases in query that are aligned // in some way to the reference (including insertions, which are considered // to be aligned by dint of being anchored either side). hts_pos_t qlen_used(bam1_t *b) { int n_cigar = b->core.n_cigar; const uint32_t *cigar = bam_get_cigar(b); hts_pos_t l; if (b->core.l_qseq) { // Known SEQ permits of short cut of l_qseq minus CSOFT_CLIPs. // Full scan not needed, which helps on excessively long CIGARs. l = b->core.l_qseq; int kl, kr; for (kl = 0; kl < n_cigar; kl++) if (bam_cigar_op(cigar[kl]) == BAM_CSOFT_CLIP) l -= bam_cigar_oplen(cigar[kl]); else break; for (kr = n_cigar-1; kr > kl; kr--) if (bam_cigar_op(cigar[kr]) == BAM_CSOFT_CLIP) l -= bam_cigar_oplen(cigar[kr]); else break; } else { // Unknown SEQ ("*") needs a full scan through the CIGAR string. static int query[16] = { //M I D N S H P = X B ? ? ? ? ? ? 1,1,0,0, 0,0,0,1, 1,0,0,0, 0,0,0,0 }; int k; for (k = l = 0; k < n_cigar; k++) if (query[bam_cigar_op(cigar[k])]) l += bam_cigar_oplen(cigar[k]); } return l; } // Without HTS_OPT3 gcc11 and earlier don't vectorize this, nor even // unroll it. By adding HTS_OPT3 we can force a better level of optimization. // On an Illumina BAM with gcc11 -O2, with HTS_OPT3 is 9% quicker for the // entire process (ie decompress, iterator, aggregate & report) static inline void HTS_OPT3 incr_hist(int *hist, int oplen) { const int N = 16; int k; for (k = 0; k < (oplen & ~(N-1)); k+=N) { for (int i = 0; i < N; i++) hist[k+i]++; } for (; k < oplen; k++) hist[k]++; } static inline void HTS_OPT3 incr_hist_qual(int *hist, uint8_t *qual, int min_qual, int oplen) { if (!min_qual) { incr_hist(hist, oplen); return; } int k; for (k = 0; k < (oplen & ~31); k+=32) { int pass[32]; // Two separate loops helps clang to vectorize for (int i = 0; i < 32; i++) pass[i]=qual[k+i]>=min_qual; for (int i = 0; i < 32; i++) hist[k+i]+=pass[i]; } for (; k < oplen; k++) hist[k]+=qual[k]>=min_qual; } // Adds the depth for a single read to a depth_hist struct. // For just one file, this is easy. We just have a circular buffer // where we increment values for bits that overlap existing data // and initialise values for coordinates which we're seeing for the first // time. This is tracked by "end_pos" to know where we've got to. // // As the input is sorted, we can flush output from "last_output" to // b->core.pos. // // With multiple files, we must feed data in sorted order as if all files // are merged, but track depth per file. This also means "end_pos" is per // file too, but "last_output" is global as it corresponds to rows printed. static int add_depth(depth_opt *opt, depth_hist *dh, sam_hdr_t *h, bam1_t *b, int overlap_clip, int file) { hts_pos_t i; size_t hmask = dh->size-1; int n; if (!b || b->core.tid != dh->last_ref) { // New ref if (dh->last_ref >= 0) { // do end size_t cur_l = dh->ks.l; int nf = dh->nfiles; i = dh->last_output; for (i = dh->last_output; nf; i++) { nf = 0; for (n = 0; n < dh->nfiles; n++) { if (i < dh->end_pos[n]) nf++; } if (!nf) break; if (opt->bed && bed_overlap(opt->bed, dh->ref, i, i+1) == 0) continue; dh->ks.l = cur_l; kputll(i+1, &dh->ks); for (n = 0; n < dh->nfiles; n++) { kputc_('\t', &dh->ks); int d = i < dh->end_pos[n] ? dh->hist[n][i & hmask] : 0; kputuw(d, &dh->ks); } kputc('\n', &dh->ks); fputs(dh->ks.s, opt->out); } if (opt->all_pos) { // End of last ref zero_region(opt, dh, sam_hdr_tid2name(h, dh->last_ref), i, sam_hdr_tid2len(h, dh->last_ref)); } dh->ks.l = cur_l; } if (opt->all_pos > 1 && !opt->reg) { // Any previous unused refs int lr = dh->last_ref < 0 ? 0 : dh->last_ref+1; int rr = b ? b->core.tid : sam_hdr_nref(h), r; for (r = lr; r < rr; r++) zero_region(opt, dh, sam_hdr_tid2name(h, r), 0, sam_hdr_tid2len(h, r)); } if (!b) { // we're just flushing to end of file if (opt->all_pos && opt->reg && dh->last_ref < 0) // -a or -aa without a single read being output yet zero_region(opt, dh, sam_hdr_tid2name(h, dh->tid), dh->beg, MIN(dh->end, sam_hdr_tid2len(h, dh->tid))); return 0; } for (n = 0; dh->end_pos && n < dh->nfiles; n++) dh->end_pos[n] = 0; dh->last_output = dh->beg >= 0 ? MAX(b->core.pos, dh->beg) : b->core.pos; dh->last_ref = b->core.tid; dh->ref = sam_hdr_tid2name(h, b->core.tid); kputs(dh->ref, ks_clear(&dh->ks)); kputc('\t', &dh->ks); if (opt->all_pos) // Start of ref zero_region(opt, dh, dh->ref, 0, b->core.pos); } else { if (dh->last_output < b->core.pos) { // Flush any depth outputs up to start of new read size_t cur_l = dh->ks.l; int nf = dh->nfiles; for (i = dh->last_output; i < b->core.pos; i++) { nf = 0; for (n = 0; n < dh->nfiles; n++) { if (i < dh->end_pos[n]) nf++; } if (!nf) break; if (opt->bed && bed_overlap(opt->bed, dh->ref, i, i+1) == 0) continue; dh->ks.l = cur_l; kputll(i+1, &dh->ks); for (n = 0; n < dh->nfiles; n++) { kputc_('\t', &dh->ks); int d = i < dh->end_pos[n] ? dh->hist[n][i & hmask] : 0; kputuw(d, &dh->ks); } kputc('\n', &dh->ks); fputs(dh->ks.s, opt->out); } if (opt->all_pos && i < b->core.pos) // Hole in middle of ref zero_region(opt, dh, dh->ref, i, b->core.pos); dh->ks.l = cur_l; dh->last_output = b->core.pos; } } hts_pos_t end_pos = bam_endpos(b); // 0 based, 1 past end. //printf("%d %d\n", (int)b->core.pos+1, (int)end_pos); if (b->core.tid < dh->last_ref || (dh->last_ref == b->core.tid && end_pos < dh->last_output)) { print_error_errno("depth", "Data is not position sorted"); return -1; } // If needed, grow the circular buffer. if (end_pos+1 - b->core.pos >= dh->size) { size_t old_size = dh->size; size_t old_hmask = hmask; while (end_pos+1 - b->core.pos >= dh->size) dh->size = dh->size ? 2*dh->size : 2048; hmask = dh->size-1; if (!dh->hist) { dh->hist = calloc(dh->nfiles, sizeof(*dh->hist)); dh->end_pos = calloc(dh->nfiles, sizeof(*dh->end_pos)); if (!dh->hist || !dh->end_pos) return -1; } for (n = 0; n < dh->nfiles; n++) { int *hist = calloc(dh->size, sizeof(*dh->hist[n])); if (!hist) return -1; // Simple approach for now; copy over old histogram verbatim. for (i = dh->last_output; i < dh->last_output + old_size; i++) hist[i & hmask] = dh->hist[n][i & old_hmask]; free(dh->hist[n]); dh->hist[n] = hist; } } // Accumulate depth, based on CIGAR uint32_t *cig = bam_get_cigar(b); int ncig = b->core.n_cigar, j, k, spos = 0; // Zero new (previously unseen) coordinates so increment works later. hts_pos_t end = MAX(dh->end_pos[file], b->core.pos); if (end_pos > end && (end & hmask) < (end_pos & hmask)) { memset(&dh->hist[file][end & hmask], 0, sizeof(**dh->hist) * (end_pos - end)); } else { for (i = end; i < end_pos; i++) dh->hist[file][i & hmask] = 0; } i = b->core.pos; uint8_t *qual = bam_get_qual(b); int min_qual = opt->min_qual; for (j = 0; j < ncig; j++) { int op = bam_cigar_op(cig[j]); int oplen = bam_cigar_oplen(cig[j]); switch (op) { case BAM_CDEL: case BAM_CREF_SKIP: if (op != BAM_CDEL || opt->skip_del) { // don't increment reference location if (i + oplen >= dh->end_pos[file]) { for (k = 0; k < oplen; k++, i++) { if (i >= dh->end_pos[file]) // redundant due to zero new elements above? dh->hist[file][i & hmask] = 0; } } else { i += oplen; } } else { // op == BAM_CDEL and we count them (-J option), // We don't incr spos here, but we still use qual. // This doesn't make much sense, but it's for compatibility // with the old code. Arguably DEL shouldn't have a min // qual and should always pass (as we've explicitly asked to // include them). int *hist = dh->hist[file]; k = 0; if (overlap_clip) { if (i+oplen < overlap_clip) { i += oplen; break; } else if (i < overlap_clip) { k = overlap_clip - i; i = overlap_clip; } } // Question: should we even check quality values for DEL? // We've explicitly asked to include them, and the quality // is wrong anyway (it's the neighbouring base). We do this // for now for compatibility with the old depth command. if (spos < b->core.l_qseq) for (; k < oplen; k++, i++) hist[i & hmask]+=qual[spos]>=min_qual; else for (; k < oplen; k++, i++) hist[i & hmask]++; } break; case BAM_CMATCH: case BAM_CEQUAL: case BAM_CDIFF: { int *hist = dh->hist[file]; k = 0; if (overlap_clip) { if (i+oplen < overlap_clip) { i += oplen; break; } else if (i < overlap_clip) { oplen -= overlap_clip - i; spos += overlap_clip - i; i = overlap_clip; } } int len = (i & hmask) < ((i+oplen) & hmask) ? oplen // doesn't wrap around : dh->size - (i&hmask); // does wrap around incr_hist_qual(&hist[i & hmask], &qual[spos], min_qual, len); if (oplen > len) incr_hist_qual(hist, &qual[spos+len], min_qual, oplen-len); spos += oplen; i += oplen; break; } case BAM_CINS: case BAM_CSOFT_CLIP: spos += oplen; break; case BAM_CPAD: case BAM_CHARD_CLIP: // ignore break; default: print_error("depth", "Unsupported cigar op '%d'", op); return -1; } } if (dh->end >= 0 && end_pos > dh->end) end_pos = dh->end; if (dh->end_pos[file] < end_pos) dh->end_pos[file] = end_pos; return 0; } // Hash on name -> alignment end pos. This permits a naive overlap removal. // Note it cannot analyse the overlapping sequence and qualities, so the // interaction of basecalls/qualities and the -Q parameter cannot be // applied here (unlike the full mpileup algorithm). KHASH_MAP_INIT_STR(olap_hash, hts_pos_t) typedef khash_t(olap_hash) olap_hash_t; static int fastdepth_core(depth_opt *opt, uint32_t nfiles, char **fn, samFile **fp, hts_itr_t **itr, sam_hdr_t **h) { int ret = -1, err = 1, i; olap_hash_t **overlaps = NULL; depth_hist dh = {0}; // An array of bam structs, one per input file, to hold the next entry bam1_t **b = calloc(nfiles, sizeof(*b)); int *finished = calloc(nfiles, sizeof(*finished)), to_go = nfiles; if (!b || !finished) goto err; for (i = 0; i < nfiles; i++) if (!(b[i] = bam_init1())) goto err; // Do we need one overlap hash per file? Or shared? if (opt->remove_overlaps) { if (!(overlaps = calloc(nfiles, sizeof(*overlaps)))) return -1; for (i = 0; i < nfiles; i++) { if (!(overlaps[i] = kh_init(olap_hash))) return -1; } } // Create the initial histogram dh.nfiles = nfiles; dh.size = 0; dh.hist = NULL; dh.last_ref = -99; dh.end_pos = NULL; dh.last_output = itr && itr[0] ? itr[0]->beg : 0; ks_initialize(&dh.ks); // Clip results to region if specified dh.beg = -1; dh.end = -1; dh.tid = 0; if (itr && itr[0]) { dh.tid = itr[0]->tid; dh.beg = itr[0]->beg; dh.end = itr[0]->end; } if (opt->header) { fprintf(opt->out, "#CHROM\tPOS"); for (i = 0; i < nfiles; i++) fprintf(opt->out, "\t%s", fn[i]); fputc('\n', opt->out); } // Populate first record per file for (i = 0; i < nfiles; i++) { for(;;) { ret = itr && itr[i] ? sam_itr_next(fp[i], itr[i], b[i]) : sam_read1(fp[i], h[i], b[i]); if (ret < -1) goto err; if (ret == -1) { to_go--; finished[i] = 1; break; } if (b[i]->core.tid < 0) continue; if (b[i]->core.flag & opt->flag) continue; // must have none of the flags set if (opt->incl_flag && (b[i]->core.flag & opt->incl_flag) == 0) continue; // must have at least one flag set if ((b[i]->core.flag & opt->require_flag) != opt->require_flag) continue; // must have all lags set if (b[i]->core.qual < opt->min_mqual) continue; // Original samtools depth used the total sequence (l_qseq) // including soft-clips. This doesn't feel like a useful metric // to be filtering on. We now only count sequence bases that // form the used part of the alignment. if (opt->min_len) { if (qlen_used(b[i]) < opt->min_len) continue; } break; } } // Loop through input files, merging in order so we're // always adding the next record in sequence while (to_go) { // Find next record in file list int best_tid = INT_MAX, best_file = 0; hts_pos_t best_pos = HTS_POS_MAX; for (i = 0; i < nfiles; i++) { if (finished[i]) continue; if (best_tid > b[i]->core.tid) { best_tid = b[i]->core.tid; best_pos = b[i]->core.pos; best_file = i; } else if (best_tid == b[i]->core.tid && best_pos > b[i]->core.pos) { best_pos = b[i]->core.pos; best_file = i; } } i = best_file; hts_pos_t clip = 0; if (overlaps && (b[i]->core.flag & BAM_FPAIRED) && !(b[i]->core.flag & BAM_FMUNMAP)) { khiter_t k = kh_get(olap_hash, overlaps[i], bam_get_qname(b[i])); if (k == kh_end(overlaps[i])) { // not seen before hts_pos_t endpos = bam_endpos(b[i]); // Don't add if mate location is known and can't overlap. if (b[i]->core.mpos == -1 || (b[i]->core.tid == b[i]->core.mtid && b[i]->core.mpos <= endpos)) { k = kh_put(olap_hash, overlaps[i], bam_get_qname(b[i]), &ret); if (ret < 0) return -1; kh_key(overlaps[i], k) = strdup(bam_get_qname(b[i])); kh_value(overlaps[i], k) = endpos; } } else { // seen before clip = kh_value(overlaps[i], k); free((char *)kh_key(overlaps[i], k)); kh_del(olap_hash, overlaps[i], k); } } // Add the next merged BAM record to the depth plot if ((ret = add_depth(opt, &dh, h[i], b[i], clip, i)) < 0) { ret = -1; goto err; } // Populate next record from this file for(;!finished[i];) { ret = itr && itr[i] ? sam_itr_next(fp[i], itr[i], b[i]) : sam_read1(fp[i], h[i], b[i]); if (ret < -1) { ret = -1; goto err; } if (ret == -1) { to_go--; finished[i] = 1; break; } if (b[i]->core.tid < 0) continue; if (b[i]->core.flag & opt->flag) continue; // must have none of the flags set if (opt->incl_flag && (b[i]->core.flag & opt->incl_flag) == 0) continue; // must have at least one flag set if ((b[i]->core.flag & opt->require_flag) != opt->require_flag) continue; // must have all lags set if (b[i]->core.qual < opt->min_mqual) continue; if (opt->min_len) { if (qlen_used(b[i]) < opt->min_len) continue; } break; } } // Tidy up end. ret = add_depth(opt, &dh, h[0], NULL, 0, 0); err = 0; err: if (ret == 0 && err) ret = -1; for (i = 0; i < nfiles; i++) { if (b[i]) bam_destroy1(b[i]); if (dh.hist && dh.hist[i]) free(dh.hist[i]); } free(b); free(finished); ks_free(&dh.ks); free(dh.hist); free(dh.end_pos); if (overlaps) { khiter_t k; for (i = 0; i < nfiles; i++) { if (!overlaps[i]) continue; for (k = kh_begin(overlaps[i]); k < kh_end(overlaps[i]); k++) if (kh_exist(overlaps[i], k)) free((char *)kh_key(overlaps[i], k)); kh_destroy(olap_hash, overlaps[i]); } free(overlaps); } return ret; } static void usage_exit(FILE *fp, int exit_status) { fprintf(fp, "Usage: samtools depth [options] in.bam [in.bam ...]\n"); fprintf(fp, "\nOptions:\n"); fprintf(fp, " -a Output all positions (including zero depth)\n"); fprintf(fp, " -a -a, -aa Output absolutely all positions, including unused ref seqs\n"); fprintf(fp, " -r REG Specify a region in chr or chr:from-to syntax\n"); fprintf(fp, " -b FILE Use bed FILE for list of regions\n"); fprintf(fp, " -f FILE Specify list of input BAM/SAM/CRAM filenames\n"); fprintf(fp, " -X Use custom index files (in -X *.bam *.bam.bai order)\n"); fprintf(fp, " -g INT Remove specified flags from default filter-out flag list\n"); fprintf(fp, " -G, --excl-flags FLAGS\n"); fprintf(fp, " Add specified flags to the default filter-out flag list\n"); fprintf(fp, " [UNMAP,SECONDARY,QCFAIL,DUP]\n"); fprintf(fp, " --incl-flags FLAGS\n"); fprintf(fp, " Only include records with at least one the FLAGs present [0]\n"); fprintf(fp, " --require-flags FLAGS\n"); fprintf(fp, " Only include records with all of the FLAGs present [0]\n"); fprintf(fp, " -H Print a file header line\n"); fprintf(fp, " -l INT Minimum read length [0]\n"); fprintf(fp, " -o FILE Write output to FILE [samtools_stdout]\n"); fprintf(fp, " -q, --min-BQ INT\n" " Filter bases with base quality smaller than INT [0]\n"); fprintf(fp, " -Q, --min-MQ INT\n" " Filter alignments with mapping quality smaller than INT [0]\n"); fprintf(fp, " -J Include reads with deletions in depth computation\n"); fprintf(fp, " -s Do not count overlapping reads within a template\n"); sam_global_opt_help(fp, "-.--.@-."); samtools_exit(exit_status); } int main_depth(int argc, char *argv[]) { int nfiles, i, tmp_flag; samFile **fp; sam_hdr_t **header; int c, has_index_file = 0; char *file_list = NULL, **fn = NULL; char *out_file = NULL; depth_opt opt = { .flag = BAM_FUNMAP | BAM_FSECONDARY | BAM_FDUP | BAM_FQCFAIL, .incl_flag = 0, .require_flag = 0, .min_qual = 0, .min_mqual = 0, .skip_del = 1, .header = 0, .min_len = 0, .out = samtools_stdout, .all_pos = 0, .remove_overlaps = 0, .reg = NULL, .bed = NULL, }; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { {"min-MQ", required_argument, NULL, 'Q'}, {"min-mq", required_argument, NULL, 'Q'}, {"min-BQ", required_argument, NULL, 'q'}, {"min-bq", required_argument, NULL, 'q'}, {"excl-flags", required_argument, NULL, 'G'}, {"incl-flags", required_argument, NULL, 1}, {"require-flags", required_argument, NULL, 2}, SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '@'), {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "@:q:Q:JHd:m:l:g:G:o:ar:Xf:b:s", lopts, NULL)) >= 0) { switch (c) { case 'a': opt.all_pos++; break; case 'b': opt.bed = bed_read(optarg); if (!opt.bed) { print_error_errno("depth", "Could not read file \"%s\"", optarg); return 1; } break; case 'f': file_list = optarg; break; case 'd': case 'm': // depth limit - now ignored break; case 'g': tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("depth", "Unknown flag '%s'", optarg); return 1; } opt.flag &= ~tmp_flag; break; case 'G': // reject if any set tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("depth", "Unknown flag '%s'", optarg); return 1; } opt.flag |= tmp_flag; break; case 1: // reject unless at least one set (0 means ignore option) tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("depth", "Unknown flag '%s'", optarg); return 1; } opt.incl_flag |= tmp_flag; break; case 2: // reject unless all set tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("depth", "Unknown flag '%s'", optarg); return 1; } opt.require_flag |= tmp_flag; break; case 'l': opt.min_len = atoi(optarg); break; case 'H': opt.header = 1; break; case 'q': opt.min_qual = atoi(optarg); break; case 'Q': opt.min_mqual = atoi(optarg); break; case 'J': opt.skip_del = 0; break; case 'o': if (opt.out != samtools_stdout) break; opt.out = fopen(out_file = optarg, "w"); if (!opt.out) { print_error_errno("depth", "Cannot open \"%s\" for writing.", optarg); return EXIT_FAILURE; } break; case 'r': opt.reg = optarg; break; case 's': opt.remove_overlaps = 1; break; case 'X': has_index_file = 1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage_exit(samtools_stderr, EXIT_FAILURE); } } if (argc < optind+1 && !file_list) { if (argc == optind) usage_exit(samtools_stdout, EXIT_SUCCESS); else usage_exit(samtools_stderr, EXIT_FAILURE); } if (file_list) { if (has_index_file) { print_error("depth", "The -f option cannot be combined with -X"); return 1; } if (read_file_list(file_list, &nfiles, &fn)) return 1; argv = fn; argc = nfiles; optind = 0; } else { nfiles = argc - optind; } if (has_index_file) { if (nfiles%1) { print_error("depth", "-X needs one index specified per bam file"); return 1; } nfiles /= 2; } fp = malloc(nfiles * sizeof(*fp)); header = malloc(nfiles * sizeof(*header)); if (!fp || !header) { print_error_errno("depth", "Out of memory"); return 1; } hts_itr_t **itr = NULL; if (opt.reg) { itr = calloc(nfiles, sizeof(*itr)); if (!itr) return 1; } for (i = 0; i < nfiles; i++, optind++) { fp[i] = sam_open_format(argv[optind], "r", &ga.in); if (fp[i] == NULL) { print_error_errno("depth", "Cannot open input file \"%s\"", argv[optind]); return 1; } if (ga.nthreads > 0) hts_set_threads(fp[i], ga.nthreads); if (hts_set_opt(fp[i], CRAM_OPT_REQUIRED_FIELDS, SAM_FLAG | SAM_RNAME | SAM_POS | SAM_CIGAR | (opt.remove_overlaps ? SAM_QNAME|SAM_RNEXT|SAM_PNEXT : 0) | (opt.min_mqual ? SAM_MAPQ : 0) | (opt.min_len ? SAM_SEQ : 0) | (opt.min_qual ? SAM_QUAL : 0))) { fprintf(samtools_stderr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n"); return 1; } if (hts_set_opt(fp[i], CRAM_OPT_DECODE_MD, 0)) { fprintf(samtools_stderr, "Failed to set CRAM_OPT_DECODE_MD value\n"); return 1; } // FIXME: what if headers differ? header[i] = sam_hdr_read(fp[i]); if (header == NULL) { fprintf(samtools_stderr, "Failed to read header for \"%s\"\n", argv[optind]); return 1; } if (opt.reg) { hts_idx_t *idx = has_index_file ? sam_index_load2(fp[i], argv[optind], argv[optind+nfiles]) : sam_index_load(fp[i], argv[optind]); if (!idx) { print_error("depth", "cannot load index for \"%s\"", argv[optind]); return 1; } if (!(itr[i] = sam_itr_querys(idx, header[i], opt.reg))) { print_error("depth", "cannot parse region \"%s\"", opt.reg); return 1; } hts_idx_destroy(idx); } } int ret = fastdepth_core(&opt, nfiles, &argv[argc-nfiles], fp, itr, header) ? 1 : 0; for (i = 0; i < nfiles; i++) { sam_hdr_destroy(header[i]); sam_close(fp[i]); if (itr && itr[i]) hts_itr_destroy(itr[i]); } free(header); free(fp); free(itr); if (file_list) { for (i=0; i Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include "samtools.h" #include "htslib/thread_pool.h" #include "sam_opts.h" #include #include #include #include #include #include #include typedef enum { overwrite_all, orphan_only, } rg_mode; struct parsed_opts { char* input_name; char* output_name; char* rg_id; char* rg_line; int no_pg; rg_mode mode; sam_global_args ga; htsThreadPool p; int uncompressed; int overwrite_hdr_rg; }; struct state; typedef struct parsed_opts parsed_opts_t; typedef struct state state_t; struct state { samFile* input_file; sam_hdr_t* input_header; samFile* output_file; sam_hdr_t* output_header; char* rg_id; void (*mode_func)(const state_t*, bam1_t*); }; static void cleanup_opts(parsed_opts_t* opts) { if (!opts) return; free(opts->rg_id); free(opts->output_name); free(opts->input_name); free(opts->rg_line); if (opts->p.pool) hts_tpool_destroy(opts->p.pool); sam_global_args_free(&opts->ga); free(opts); } static void cleanup_state(state_t* state) { if (!state) return; free(state->rg_id); if (state->output_file) sam_close(state->output_file); sam_hdr_destroy(state->output_header); if (state->input_file) sam_close(state->input_file); sam_hdr_destroy(state->input_header); free(state); } // Converts \t and \n into real tabs and newlines static char* basic_unescape(const char* in) { assert(in); char *ptr, *out; out = ptr = malloc(strlen(in)+1); size_t size = 0; while (*in) { if (*in == '\\') { ++in; if (*in == '\0') { fprintf(stderr, "[%s] Unterminated escape sequence.\n", __func__); free(out); return NULL; } switch (*in) { case '\\': *ptr = '\\'; break; case 't': *ptr = '\t'; break; case 'n': fprintf(stderr, "[%s] \\n in escape sequence is not supported.\n", __func__); free(out); return NULL; default: fprintf(stderr, "[%s] Unsupported escape sequence.\n", __func__); free(out); return NULL; } } else { *ptr = *in; } ++in; ++ptr; ++size; } *ptr = '\0'; ++size; char* tmp = (char*)realloc(out, size); if (!tmp) { free(out); } return tmp; } // Malloc a string containing [s,slim) or to the end of s if slim is NULL. // If lenp is non-NULL, stores the length of the resulting string there. static char *dup_substring(const char *s, const char *slim, size_t *lenp) { size_t len = slim? (slim - s) : strlen(s); char *ns = malloc(len+1); if (ns == NULL) return NULL; memcpy(ns, s, len); ns[len] = '\0'; if (lenp) *lenp = len; return ns; } // Given a @RG line return the id static char* get_rg_id(const char *line) { const char *id = strstr(line, "\tID:"); if (! id) return NULL; id += 4; return dup_substring(id, strchr(id, '\t'), NULL); } static void usage(FILE *fp) { fprintf(fp, "Usage: samtools addreplacerg [options] [-r <@RG line> | -R ] [-m orphan_only|overwrite_all] [-o ] \n" "\n" "Options:\n" " -m MODE Set the mode of operation from one of overwrite_all, orphan_only [overwrite_all]\n" " -o FILE Where to write output to [stdout]\n" " -r STRING @RG line text\n" " -R STRING ID of @RG line in existing header to use\n" " -u Output uncompressed data\n" " -w Overwrite an existing @RG line\n" " --no-PG Do not add a PG line\n" ); sam_global_opt_help(fp, "..O..@.."); } static bool parse_args(int argc, char** argv, parsed_opts_t** opts) { *opts = NULL; int n; if (argc == 1) { usage(stdout); return true; } parsed_opts_t* retval = calloc(1, sizeof(parsed_opts_t)); if (! retval ) { fprintf(stderr, "[%s] Out of memory allocating parsed_opts_t\n", __func__); return false; } // Set defaults retval->mode = overwrite_all; sam_global_args_init(&retval->ga); static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS(0, 0, 'O', 0, 0, '@'), {"no-PG", no_argument, NULL, 1}, { NULL, 0, NULL, 0 } }; kstring_t rg_line = {0,0,NULL}; while ((n = getopt_long(argc, argv, "r:R:m:o:O:h@:uw", lopts, NULL)) >= 0) { switch (n) { case 'r': // Are we adding to existing rg line? if (ks_len(&rg_line) == 0) { if (strlen(optarg)<3 || (optarg[0] != '@' && optarg[1] != 'R' && optarg[2] != 'G')) { kputs("@RG\t", &rg_line); } } else { kputs("\t", &rg_line); } kputs(optarg, &rg_line); break; case 'R': retval->rg_id = strdup(optarg); break; case 'm': { if (strcmp(optarg, "overwrite_all") == 0) { retval->mode = overwrite_all; } else if (strcmp(optarg, "orphan_only") == 0) { retval->mode = orphan_only; } else { usage(stderr); return false; } break; } case 'o': retval->output_name = strdup(optarg); break; case 'h': usage(stdout); free(retval); return true; case 1: retval->no_pg = 1; break; case 'u': retval->uncompressed = 1; break; case 'w': retval->overwrite_hdr_rg = 1; break; case '?': usage(stderr); free(retval); return false; case 'O': default: if (parse_sam_global_opt(n, optarg, lopts, &retval->ga) == 0) break; usage(stderr); free(retval); return false; } } retval->rg_line = ks_release(&rg_line); if (argc-optind < 1) { fprintf(stderr, "You must specify an input file.\n"); usage(stderr); cleanup_opts(retval); return false; } if (retval->rg_id && retval->rg_line) { fprintf(stderr, "The options -r and -R are mutually exclusive.\n"); cleanup_opts(retval); return false; } if (retval->rg_line) { char* tmp = basic_unescape(retval->rg_line); if ((retval->rg_id = get_rg_id(tmp)) == NULL) { fprintf(stderr, "[%s] The supplied RG line lacks an ID tag.\n", __func__); free(tmp); cleanup_opts(retval); return false; } free(retval->rg_line); retval->rg_line = tmp; } retval->input_name = strdup(argv[optind+0]); if (retval->ga.nthreads > 0) { if (!(retval->p.pool = hts_tpool_init(retval->ga.nthreads))) { fprintf(stderr, "Error creating thread pool\n"); return false; } } *opts = retval; return true; } static void overwrite_all_func(const state_t* state, bam1_t* file_read) { uint8_t* data = (uint8_t*)strdup(state->rg_id); int len = strlen(state->rg_id)+1; // If the old exists delete it uint8_t* old = bam_aux_get(file_read, "RG"); if (old != NULL) { bam_aux_del(file_read, old); } bam_aux_append(file_read, "RG", 'Z', len, data); free(data); } static void orphan_only_func(const state_t* state, bam1_t* file_read) { uint8_t* data = (uint8_t*)strdup(state->rg_id); int len = strlen(state->rg_id)+1; // If the old exists don't do anything uint8_t* old = bam_aux_get(file_read, "RG"); if (old == NULL) { bam_aux_append(file_read, "RG",'Z',len,data); } free(data); } static bool init(const parsed_opts_t* opts, state_t** state_out) { char output_mode[9] = "w"; state_t* retval = (state_t*) calloc(1, sizeof(state_t)); if (retval == NULL) { fprintf(stderr, "[init] Out of memory allocating state struct.\n"); return false; } *state_out = retval; // Open files retval->input_file = sam_open_format(opts->input_name, "r", &opts->ga.in); if (retval->input_file == NULL) { print_error_errno("addreplacerg", "could not open \"%s\"", opts->input_name); return false; } retval->input_header = sam_hdr_read(retval->input_file); retval->output_header = sam_hdr_dup(retval->input_header); if (opts->uncompressed) strcat(output_mode, "0"); if (opts->output_name) // File format auto-detection sam_open_mode(output_mode + strlen(output_mode), opts->output_name, NULL); retval->output_file = sam_open_format(opts->output_name == NULL?"-":opts->output_name, output_mode, &opts->ga.out); if (retval->output_file == NULL) { print_error_errno("addreplacerg", "could not create \"%s\"", opts->output_name); return false; } if (opts->p.pool) { hts_set_opt(retval->input_file, HTS_OPT_THREAD_POOL, &opts->p); hts_set_opt(retval->output_file, HTS_OPT_THREAD_POOL, &opts->p); } if (opts->rg_line) { // Append new RG line to header. // Check does not already exist kstring_t hdr_line = { 0, 0, NULL }; if (sam_hdr_find_line_id(retval->output_header, "RG", "ID", opts->rg_id, &hdr_line) == 0) { if (opts->overwrite_hdr_rg) { if(-1 == sam_hdr_remove_line_id(retval->output_header, "RG", "ID", opts->rg_id)) { fprintf(stderr, "[init] Error removing the RG line with ID:%s from the output header.\n", opts->rg_id); ks_free(&hdr_line); return false; } } else { fprintf(stderr, "[init] RG line with ID:%s already present in the header. Use -w to overwrite.\n", opts->rg_id); ks_free(&hdr_line); return false; } } ks_free(&hdr_line); if (-1 == sam_hdr_add_lines(retval->output_header, opts->rg_line, strlen(opts->rg_line))) { fprintf(stderr, "[init] Error adding RG line with ID:%s to the output header.\n", opts->rg_id); return false; } if (opts->mode == overwrite_all && -1 == sam_hdr_remove_except(retval->output_header, "RG", "ID", opts->rg_id)) { fprintf(stderr, "[init] Error removing the old RG lines from the output header.\n"); return false; } retval->rg_id = strdup(opts->rg_id); } else { if (opts->rg_id) { // Confirm what has been supplied exists kstring_t hdr_line = { 0, 0, NULL }; if (sam_hdr_find_line_id(retval->output_header, "RG", "ID", opts->rg_id, &hdr_line) < 0) { fprintf(stderr, "RG ID supplied does not exist in header. Supply full @RG line with -r instead?\n"); return false; } retval->rg_id = strdup(opts->rg_id); ks_free(&hdr_line); } else { kstring_t rg_id = { 0, 0, NULL }; if (sam_hdr_find_tag_id(retval->output_header, "RG", NULL, NULL, "ID", &rg_id) < 0) { fprintf(stderr, "No RG specified on command line or in existing header.\n"); return false; } retval->rg_id = ks_release(&rg_id); } } switch (opts->mode) { case overwrite_all: retval->mode_func = &overwrite_all_func; break; case orphan_only: retval->mode_func = &orphan_only_func; break; } return true; } static bool readgroupise(parsed_opts_t *opts, state_t* state, char *arg_list) { if (!opts->no_pg && sam_hdr_add_pg(state->output_header, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) return false; if (sam_hdr_write(state->output_file, state->output_header) != 0) { print_error_errno("addreplacerg", "[%s] Could not write header to output file", __func__); return false; } char *idx_fn = NULL; if (opts->ga.write_index) { if (!(idx_fn = auto_index(state->output_file, opts->output_name, state->output_header))) return false; } bam1_t* file_read = bam_init1(); int ret; while ((ret = sam_read1(state->input_file, state->input_header, file_read)) >= 0) { state->mode_func(state, file_read); if (sam_write1(state->output_file, state->output_header, file_read) < 0) { print_error_errno("addreplacerg", "[%s] Could not write read to output file", __func__); bam_destroy1(file_read); free(idx_fn); return false; } } bam_destroy1(file_read); if (ret != -1) { print_error_errno("addreplacerg", "[%s] Error reading from input file", __func__); free(idx_fn); return false; } else { if (opts->ga.write_index) { if (sam_idx_save(state->output_file) < 0) { print_error_errno("addreplacerg", "[%s] Writing index failed", __func__); free(idx_fn); return false; } } free(idx_fn); return true; } } int main_addreplacerg(int argc, char** argv) { parsed_opts_t* opts = NULL; state_t* state = NULL; char *arg_list = stringify_argv(argc+1, argv-1); if (!arg_list) return EXIT_FAILURE; if (!parse_args(argc, argv, &opts)) goto error; if (opts) { // Not an error but user doesn't want us to proceed if (!init(opts, &state) || !readgroupise(opts, state, arg_list)) goto error; } cleanup_state(state); cleanup_opts(opts); free(arg_list); return EXIT_SUCCESS; error: cleanup_state(state); cleanup_opts(opts); free(arg_list); return EXIT_FAILURE; } pysam-0.23.0/samtools/bam_addrprg.c.pysam.c000066400000000000000000000374221475062545500205720ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_addrprg.c -- samtools command to add or replace readgroups. Copyright (c) 2013, 2015-2017, 2019-2021 Genome Research Limited. Author: Martin O. Pollard Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include "samtools.h" #include "htslib/thread_pool.h" #include "sam_opts.h" #include #include #include #include #include #include #include typedef enum { overwrite_all, orphan_only, } rg_mode; struct parsed_opts { char* input_name; char* output_name; char* rg_id; char* rg_line; int no_pg; rg_mode mode; sam_global_args ga; htsThreadPool p; int uncompressed; int overwrite_hdr_rg; }; struct state; typedef struct parsed_opts parsed_opts_t; typedef struct state state_t; struct state { samFile* input_file; sam_hdr_t* input_header; samFile* output_file; sam_hdr_t* output_header; char* rg_id; void (*mode_func)(const state_t*, bam1_t*); }; static void cleanup_opts(parsed_opts_t* opts) { if (!opts) return; free(opts->rg_id); free(opts->output_name); free(opts->input_name); free(opts->rg_line); if (opts->p.pool) hts_tpool_destroy(opts->p.pool); sam_global_args_free(&opts->ga); free(opts); } static void cleanup_state(state_t* state) { if (!state) return; free(state->rg_id); if (state->output_file) sam_close(state->output_file); sam_hdr_destroy(state->output_header); if (state->input_file) sam_close(state->input_file); sam_hdr_destroy(state->input_header); free(state); } // Converts \t and \n into real tabs and newlines static char* basic_unescape(const char* in) { assert(in); char *ptr, *out; out = ptr = malloc(strlen(in)+1); size_t size = 0; while (*in) { if (*in == '\\') { ++in; if (*in == '\0') { fprintf(samtools_stderr, "[%s] Unterminated escape sequence.\n", __func__); free(out); return NULL; } switch (*in) { case '\\': *ptr = '\\'; break; case 't': *ptr = '\t'; break; case 'n': fprintf(samtools_stderr, "[%s] \\n in escape sequence is not supported.\n", __func__); free(out); return NULL; default: fprintf(samtools_stderr, "[%s] Unsupported escape sequence.\n", __func__); free(out); return NULL; } } else { *ptr = *in; } ++in; ++ptr; ++size; } *ptr = '\0'; ++size; char* tmp = (char*)realloc(out, size); if (!tmp) { free(out); } return tmp; } // Malloc a string containing [s,slim) or to the end of s if slim is NULL. // If lenp is non-NULL, stores the length of the resulting string there. static char *dup_substring(const char *s, const char *slim, size_t *lenp) { size_t len = slim? (slim - s) : strlen(s); char *ns = malloc(len+1); if (ns == NULL) return NULL; memcpy(ns, s, len); ns[len] = '\0'; if (lenp) *lenp = len; return ns; } // Given a @RG line return the id static char* get_rg_id(const char *line) { const char *id = strstr(line, "\tID:"); if (! id) return NULL; id += 4; return dup_substring(id, strchr(id, '\t'), NULL); } static void usage(FILE *fp) { fprintf(fp, "Usage: samtools addreplacerg [options] [-r <@RG line> | -R ] [-m orphan_only|overwrite_all] [-o ] \n" "\n" "Options:\n" " -m MODE Set the mode of operation from one of overwrite_all, orphan_only [overwrite_all]\n" " -o FILE Where to write output to [samtools_stdout]\n" " -r STRING @RG line text\n" " -R STRING ID of @RG line in existing header to use\n" " -u Output uncompressed data\n" " -w Overwrite an existing @RG line\n" " --no-PG Do not add a PG line\n" ); sam_global_opt_help(fp, "..O..@.."); } static bool parse_args(int argc, char** argv, parsed_opts_t** opts) { *opts = NULL; int n; if (argc == 1) { usage(samtools_stdout); return true; } parsed_opts_t* retval = calloc(1, sizeof(parsed_opts_t)); if (! retval ) { fprintf(samtools_stderr, "[%s] Out of memory allocating parsed_opts_t\n", __func__); return false; } // Set defaults retval->mode = overwrite_all; sam_global_args_init(&retval->ga); static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS(0, 0, 'O', 0, 0, '@'), {"no-PG", no_argument, NULL, 1}, { NULL, 0, NULL, 0 } }; kstring_t rg_line = {0,0,NULL}; while ((n = getopt_long(argc, argv, "r:R:m:o:O:h@:uw", lopts, NULL)) >= 0) { switch (n) { case 'r': // Are we adding to existing rg line? if (ks_len(&rg_line) == 0) { if (strlen(optarg)<3 || (optarg[0] != '@' && optarg[1] != 'R' && optarg[2] != 'G')) { kputs("@RG\t", &rg_line); } } else { kputs("\t", &rg_line); } kputs(optarg, &rg_line); break; case 'R': retval->rg_id = strdup(optarg); break; case 'm': { if (strcmp(optarg, "overwrite_all") == 0) { retval->mode = overwrite_all; } else if (strcmp(optarg, "orphan_only") == 0) { retval->mode = orphan_only; } else { usage(samtools_stderr); return false; } break; } case 'o': retval->output_name = strdup(optarg); break; case 'h': usage(samtools_stdout); free(retval); return true; case 1: retval->no_pg = 1; break; case 'u': retval->uncompressed = 1; break; case 'w': retval->overwrite_hdr_rg = 1; break; case '?': usage(samtools_stderr); free(retval); return false; case 'O': default: if (parse_sam_global_opt(n, optarg, lopts, &retval->ga) == 0) break; usage(samtools_stderr); free(retval); return false; } } retval->rg_line = ks_release(&rg_line); if (argc-optind < 1) { fprintf(samtools_stderr, "You must specify an input file.\n"); usage(samtools_stderr); cleanup_opts(retval); return false; } if (retval->rg_id && retval->rg_line) { fprintf(samtools_stderr, "The options -r and -R are mutually exclusive.\n"); cleanup_opts(retval); return false; } if (retval->rg_line) { char* tmp = basic_unescape(retval->rg_line); if ((retval->rg_id = get_rg_id(tmp)) == NULL) { fprintf(samtools_stderr, "[%s] The supplied RG line lacks an ID tag.\n", __func__); free(tmp); cleanup_opts(retval); return false; } free(retval->rg_line); retval->rg_line = tmp; } retval->input_name = strdup(argv[optind+0]); if (retval->ga.nthreads > 0) { if (!(retval->p.pool = hts_tpool_init(retval->ga.nthreads))) { fprintf(samtools_stderr, "Error creating thread pool\n"); return false; } } *opts = retval; return true; } static void overwrite_all_func(const state_t* state, bam1_t* file_read) { uint8_t* data = (uint8_t*)strdup(state->rg_id); int len = strlen(state->rg_id)+1; // If the old exists delete it uint8_t* old = bam_aux_get(file_read, "RG"); if (old != NULL) { bam_aux_del(file_read, old); } bam_aux_append(file_read, "RG", 'Z', len, data); free(data); } static void orphan_only_func(const state_t* state, bam1_t* file_read) { uint8_t* data = (uint8_t*)strdup(state->rg_id); int len = strlen(state->rg_id)+1; // If the old exists don't do anything uint8_t* old = bam_aux_get(file_read, "RG"); if (old == NULL) { bam_aux_append(file_read, "RG",'Z',len,data); } free(data); } static bool init(const parsed_opts_t* opts, state_t** state_out) { char output_mode[9] = "w"; state_t* retval = (state_t*) calloc(1, sizeof(state_t)); if (retval == NULL) { fprintf(samtools_stderr, "[init] Out of memory allocating state struct.\n"); return false; } *state_out = retval; // Open files retval->input_file = sam_open_format(opts->input_name, "r", &opts->ga.in); if (retval->input_file == NULL) { print_error_errno("addreplacerg", "could not open \"%s\"", opts->input_name); return false; } retval->input_header = sam_hdr_read(retval->input_file); retval->output_header = sam_hdr_dup(retval->input_header); if (opts->uncompressed) strcat(output_mode, "0"); if (opts->output_name) // File format auto-detection sam_open_mode(output_mode + strlen(output_mode), opts->output_name, NULL); retval->output_file = sam_open_format(opts->output_name == NULL?"-":opts->output_name, output_mode, &opts->ga.out); if (retval->output_file == NULL) { print_error_errno("addreplacerg", "could not create \"%s\"", opts->output_name); return false; } if (opts->p.pool) { hts_set_opt(retval->input_file, HTS_OPT_THREAD_POOL, &opts->p); hts_set_opt(retval->output_file, HTS_OPT_THREAD_POOL, &opts->p); } if (opts->rg_line) { // Append new RG line to header. // Check does not already exist kstring_t hdr_line = { 0, 0, NULL }; if (sam_hdr_find_line_id(retval->output_header, "RG", "ID", opts->rg_id, &hdr_line) == 0) { if (opts->overwrite_hdr_rg) { if(-1 == sam_hdr_remove_line_id(retval->output_header, "RG", "ID", opts->rg_id)) { fprintf(samtools_stderr, "[init] Error removing the RG line with ID:%s from the output header.\n", opts->rg_id); ks_free(&hdr_line); return false; } } else { fprintf(samtools_stderr, "[init] RG line with ID:%s already present in the header. Use -w to overwrite.\n", opts->rg_id); ks_free(&hdr_line); return false; } } ks_free(&hdr_line); if (-1 == sam_hdr_add_lines(retval->output_header, opts->rg_line, strlen(opts->rg_line))) { fprintf(samtools_stderr, "[init] Error adding RG line with ID:%s to the output header.\n", opts->rg_id); return false; } if (opts->mode == overwrite_all && -1 == sam_hdr_remove_except(retval->output_header, "RG", "ID", opts->rg_id)) { fprintf(samtools_stderr, "[init] Error removing the old RG lines from the output header.\n"); return false; } retval->rg_id = strdup(opts->rg_id); } else { if (opts->rg_id) { // Confirm what has been supplied exists kstring_t hdr_line = { 0, 0, NULL }; if (sam_hdr_find_line_id(retval->output_header, "RG", "ID", opts->rg_id, &hdr_line) < 0) { fprintf(samtools_stderr, "RG ID supplied does not exist in header. Supply full @RG line with -r instead?\n"); return false; } retval->rg_id = strdup(opts->rg_id); ks_free(&hdr_line); } else { kstring_t rg_id = { 0, 0, NULL }; if (sam_hdr_find_tag_id(retval->output_header, "RG", NULL, NULL, "ID", &rg_id) < 0) { fprintf(samtools_stderr, "No RG specified on command line or in existing header.\n"); return false; } retval->rg_id = ks_release(&rg_id); } } switch (opts->mode) { case overwrite_all: retval->mode_func = &overwrite_all_func; break; case orphan_only: retval->mode_func = &orphan_only_func; break; } return true; } static bool readgroupise(parsed_opts_t *opts, state_t* state, char *arg_list) { if (!opts->no_pg && sam_hdr_add_pg(state->output_header, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) return false; if (sam_hdr_write(state->output_file, state->output_header) != 0) { print_error_errno("addreplacerg", "[%s] Could not write header to output file", __func__); return false; } char *idx_fn = NULL; if (opts->ga.write_index) { if (!(idx_fn = auto_index(state->output_file, opts->output_name, state->output_header))) return false; } bam1_t* file_read = bam_init1(); int ret; while ((ret = sam_read1(state->input_file, state->input_header, file_read)) >= 0) { state->mode_func(state, file_read); if (sam_write1(state->output_file, state->output_header, file_read) < 0) { print_error_errno("addreplacerg", "[%s] Could not write read to output file", __func__); bam_destroy1(file_read); free(idx_fn); return false; } } bam_destroy1(file_read); if (ret != -1) { print_error_errno("addreplacerg", "[%s] Error reading from input file", __func__); free(idx_fn); return false; } else { if (opts->ga.write_index) { if (sam_idx_save(state->output_file) < 0) { print_error_errno("addreplacerg", "[%s] Writing index failed", __func__); free(idx_fn); return false; } } free(idx_fn); return true; } } int main_addreplacerg(int argc, char** argv) { parsed_opts_t* opts = NULL; state_t* state = NULL; char *arg_list = stringify_argv(argc+1, argv-1); if (!arg_list) return EXIT_FAILURE; if (!parse_args(argc, argv, &opts)) goto error; if (opts) { // Not an error but user doesn't want us to proceed if (!init(opts, &state) || !readgroupise(opts, state, arg_list)) goto error; } cleanup_state(state); cleanup_opts(opts); free(arg_list); return EXIT_SUCCESS; error: cleanup_state(state); cleanup_opts(opts); free(arg_list); return EXIT_FAILURE; } pysam-0.23.0/samtools/bam_ampliconclip.c000066400000000000000000001162061475062545500202460ustar00rootroot00000000000000/* bam_ampliconclip.c -- loads amplicon primers from a BED file and cuts reads from the 5' end. Copyright (C) 2020-2024 Genome Research Ltd. Authors: Andrew Whitwham Rob Davies Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE */ #include #include #include #include #include #include #include #include "htslib/thread_pool.h" #include "sam_opts.h" #include #include "htslib/hfile.h" #include "htslib/kstring.h" #include "htslib/sam.h" #include "samtools.h" #include "bam_ampliconclip.h" typedef enum { soft_clip, hard_clip } clipping_type; typedef struct { int add_pg; int use_strand; int write_clipped; int mark_fail; int both; int fail_len; int filter_len; int unmapped; int oa_tag; int del_tag; int tol; int unmap_len; char *arg_list; char *stats_file; char *primer_counts_file; char *rejects_file; } cl_param_t; static int bed_entry_sort(const void *av, const void *bv) { bed_entry_t *a = (bed_entry_t *) av; bed_entry_t *b = (bed_entry_t *) bv; return a->right < b->right ? -1 : (a->right == b->right ? 0 : 1); } int load_bed_file_multi_ref(char *infile, int get_strand, int sort_by_pos, khash_t(bed_list_hash) *bed_lists, char ***ref_list, size_t *num_refs_out) { hFILE *fp; int line_count = 0, ret; //variables to store the bed file data for each record char ref[1024] = ""; int64_t left, right; char name[1024] = "", score[1024] = ""; char strand; //hash table to store clipping results and bed file data kstring_t line = KS_INITIALIZE; bed_entry_list_t *list; khiter_t bed_itr; //ordered ref names list size_t ref_list_sz = 0; size_t num_refs = 0; if (ref_list) *ref_list = NULL; if (num_refs_out) *num_refs_out = 0; if ((fp = hopen(infile, "r")) == NULL) { print_error_errno("amplicon", "unable to open file %s.", infile); return 1; } while (line.l = 0, kgetline(&line, (kgets_func *)hgets, fp) >= 0) { line_count++; int hret; if (line.l == 0 || *line.s == '#') continue; if (strncmp(line.s, "track ", 6) == 0) continue; if (strncmp(line.s, "browser ", 8) == 0) continue; // A list of the maximal number of columns we may want to parse. // There may be more, but we don't use the ones beyond these. const char *const scanf_str = "%1023s %"SCNd64" %"SCNd64" %1023s %1023s %c"; // Extract the data from the line into the variables. // Variables corresponding to any missing columns will remain // uninitialised. We asked for all columns, but cols_parsed will // return how many we found which can be validated against num_columns. int cols_parsed = sscanf(line.s, scanf_str, ref, &left, &right, name, score, &strand); if (cols_parsed < (get_strand ? 6 : 3)) { fprintf(stderr, "[amplicon] error: invalid bed file format in line %d of %s.\n" "Parsed %d columns, but need at least %d\n" "(N.B. ref/chrom name limited to 1023 characters.)\n", line_count, infile, cols_parsed, get_strand ? 6 : 3); ret = 1; goto error; } bed_itr = kh_get(bed_list_hash, bed_lists, ref); if (bed_itr == kh_end(bed_lists)) { // new ref entry char *ref_name = strdup(ref); // need a copy for the hash key if (!ref_name) { fprintf(stderr, "[amplicon] error: unable to allocate memory for ref name.\n"); ret = 1; goto error; } if (ref_list) { if (hts_resize(char **, num_refs + 1, &ref_list_sz, ref_list, 0) < 0) { fprintf(stderr, "[amplicon] error: unable to allocate memory for ref name list.\n"); ret = 1; goto error; } (*ref_list)[num_refs++] = ref_name; } bed_itr = kh_put(bed_list_hash, bed_lists, ref_name, &hret); if (hret > 0) { list = &kh_val(bed_lists, bed_itr); // initialise the new hash entry list->longest = 0; list->size = 0; list->length = 0; list->bp = NULL; } else { fprintf(stderr, "[amplicon] error: ref hashing failure.\n"); ret = 1; goto error; } } else { // existing ref list = &kh_val(bed_lists, bed_itr); } // add the bed entry to the list, growing the list if necessary if (list->length == list->size) { bed_entry_t *tmp; list->size += list->size / 2 + 256; if ((tmp = realloc(list->bp, list->size * sizeof(bed_entry_t))) == NULL) { fprintf(stderr, "[amplicon] error: unable to allocate more memory for bed data.\n"); ret = 1; goto error; } list->bp = tmp; } list->bp[list->length].left = left; list->bp[list->length].right = right; list->bp[list->length].name = NULL; list->bp[list->length].score = NULL; if (cols_parsed >= 4) { list->bp[list->length].name = strdup(name); if (list->bp[list->length].name == NULL) { fprintf(stderr, "[amplicon] error: unable to allocate memory for name in line %d of %s: %s.\n", line_count, infile, line.s); ret = 1; goto error; } } if (cols_parsed >= 5) { list->bp[list->length].score = strdup(score); if (list->bp[list->length].score == NULL) { fprintf(stderr, "[amplicon] error: unable to allocate memory for score in line %d of %s: %s\n", line_count, infile, line.s); ret = 1; goto error; } } list->bp[list->length].num_reads = 0; if (get_strand) { if (strand == '+') { list->bp[list->length].rev = 0; } else if (strand == '-') { list->bp[list->length].rev = 1; } else { fprintf(stderr, "[amplicon] error: bad strand value in line %d, expecting '+' or '-', found '%c'.\n", line_count, strand); ret = 1; goto error; } } if (right - left > list->longest) list->longest = right - left; list->length++; } if (sort_by_pos) { for (bed_itr = kh_begin(bed_lists); bed_itr != kh_end(bed_lists); ++bed_itr) { if (kh_exist(bed_lists, bed_itr)) { list = &kh_val(bed_lists, bed_itr); qsort(list->bp, list->length, sizeof(list->bp[0]), bed_entry_sort); } } } if (kh_size(bed_lists) > 0) {// any entries ret = 0; } else { ret = 1; } if (num_refs_out) *num_refs_out = num_refs; error: ks_free(&line); if (hclose(fp) != 0) { fprintf(stderr, "[amplicon] warning: failed to close %s", infile); } return ret; } void destroy_bed_hash(khash_t(bed_list_hash) *hash) { khiter_t itr; for (itr = kh_begin(hash); itr != kh_end(hash); ++itr) { if (kh_exist(hash, itr)) { bed_entry_list_t list = kh_val(hash, itr); for (int i = 0; i < list.length; i++) { free(list.bp[i].name); free(list.bp[i].score); } free(list.bp); free((char *)kh_key(hash, itr)); kh_key(hash, itr) = NULL; } } kh_destroy(bed_list_hash, hash); } static int matching_clip_site(bed_entry_list_t *sites, hts_pos_t pos, int is_rev, int use_strand, int64_t longest, cl_param_t *param) { int i, size, used_i; int tol = param->tol; int l = 0, mid = sites->length / 2, r = sites->length; int pos_tol = is_rev ? (pos > tol ? pos - tol : 0) : pos; while (r - l > 1) { if (sites->bp[mid].right <= pos_tol) { l = mid; } else { r = mid; } mid = (l + r) / 2; } size = 0; used_i = -1; for (i = l; i < sites->length; i++) { hts_pos_t mod_left, mod_right; if (use_strand && is_rev != sites->bp[i].rev) continue; if (is_rev) { mod_left = sites->bp[i].left; mod_right = sites->bp[i].right + tol; } else { if (sites->bp[i].left > tol) { mod_left = sites->bp[i].left - tol; } else { mod_left = 0; } mod_right = sites->bp[i].right; } if (pos + longest + tol < mod_right) break; if (pos >= mod_left && pos <= mod_right) { if (is_rev) { if (size < pos - sites->bp[i].left) { size = pos - sites->bp[i].left; used_i = i; } } else { if (size < sites->bp[i].right - pos) { size = sites->bp[i].right - pos; used_i = i; } } } } if (used_i >= 0) { sites->bp[used_i].num_reads++; } return size; } static int bam_trim_left(bam1_t *rec, bam1_t *rec_out, uint32_t bases, clipping_type clipping) { uint32_t *orig_cigar = bam_get_cigar(rec); uint8_t *orig_seq = bam_get_seq(rec); uint8_t *orig_qual = bam_get_qual(rec); uint8_t *orig_aux = bam_get_aux(rec); uint32_t *new_cigar; uint8_t *new_qual; size_t orig_l_aux = bam_get_l_aux(rec); uint32_t i, j; uint32_t ref_remove = bases, qry_removed = 0, hardclip = 0; hts_pos_t new_pos = rec->core.pos; uint32_t cig_type, cig_op; if (rec->l_data + 8 > rec_out->m_data) { uint8_t *new_data = realloc(rec_out->data, rec->l_data + 8); if (!new_data) { fprintf(stderr, "[ampliconclip] error: could not allocate memoy for new bam record\n"); return 1; } rec_out->data = new_data; rec_out->m_data = rec->l_data + 8; } // Copy core data & name memcpy(&rec_out->core, &rec->core, sizeof(rec->core)); memcpy(rec_out->data, rec->data, rec->core.l_qname); // Modify CIGAR new_cigar = bam_get_cigar(rec_out); for (i = 0; i < rec->core.n_cigar; i++) { cig_op = bam_cigar_op(orig_cigar[i]); cig_type = bam_cigar_type(cig_op); if (cig_op == BAM_CHARD_CLIP) { hardclip += bam_cigar_oplen(orig_cigar[i]); } else { if (cig_type & 2) { if (bam_cigar_oplen(orig_cigar[i]) <= ref_remove) { ref_remove -= bam_cigar_oplen(orig_cigar[i]); } else { break; } new_pos += bam_cigar_oplen(orig_cigar[i]); } if (cig_type & 1) { qry_removed += bam_cigar_oplen(orig_cigar[i]); } } } if (i < rec->core.n_cigar) { cig_type = bam_cigar_type(bam_cigar_op(orig_cigar[i])); // account for the last operation if (cig_type & 2) { new_pos += ref_remove; } if (cig_type & 1) { qry_removed += ref_remove; } } else { if (clipping == hard_clip) { rec_out->core.l_qseq = 0; rec_out->core.n_cigar = 0; if (orig_l_aux) memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux); rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux; return 0; } qry_removed = rec->core.l_qseq; } j = 0; if (clipping == hard_clip && hardclip + qry_removed > 0) { new_cigar[j++] = bam_cigar_gen(hardclip + qry_removed, BAM_CHARD_CLIP); } if (clipping == soft_clip) { if (hardclip > 0) { new_cigar[j++] = bam_cigar_gen(hardclip, BAM_CHARD_CLIP); } if (qry_removed > 0) { new_cigar[j++] = bam_cigar_gen(qry_removed, BAM_CSOFT_CLIP); } } if (i < rec->core.n_cigar && bam_cigar_oplen(orig_cigar[i]) > ref_remove) { new_cigar[j++] = bam_cigar_gen(bam_cigar_oplen(orig_cigar[i]) - ref_remove, bam_cigar_op(orig_cigar[i])); // fill in the rest of the cigar i++; for (; i < rec->core.n_cigar; i++) { new_cigar[j++] = orig_cigar[i]; } } rec_out->core.n_cigar = j; if (clipping == soft_clip) { qry_removed = 0; // Copy all the sequence and confidence values } new_qual = bam_get_seq(rec_out) + (rec->core.l_qseq - qry_removed + 1) / 2; // Copy remaining SEQ if ((qry_removed & 1) == 0) { memcpy(bam_get_seq(rec_out), orig_seq + (qry_removed / 2), (rec->core.l_qseq - qry_removed + 1) / 2); // +1 to account for odd numbers } else { uint8_t *in = orig_seq + qry_removed / 2; uint8_t *out = bam_get_seq(rec_out); uint32_t i; for (i = qry_removed; i < rec->core.l_qseq - 1; i += 2) { *out++ = ((in[0] & 0x0f) << 4) | ((in[1] & 0xf0) >> 4); in++; } if (i < rec->core.l_qseq) { *out++ = (in[0] & 0x0f) << 4; } assert(out == new_qual); } // Copy remaining QUAL memmove(new_qual, orig_qual + qry_removed, rec->core.l_qseq - qry_removed); // Set new l_qseq rec_out->core.l_qseq -= qry_removed; // Move AUX if (orig_l_aux) memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux); // Set new l_data rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux; // put in new pos rec_out->core.pos = new_pos; return 0; } static int bam_trim_right(bam1_t *rec, bam1_t *rec_out, uint32_t bases, clipping_type clipping) { uint32_t *orig_cigar = bam_get_cigar(rec); uint8_t *orig_seq = bam_get_seq(rec); uint8_t *orig_qual = bam_get_qual(rec); uint8_t *orig_aux = bam_get_aux(rec); uint32_t *new_cigar; uint32_t new_n_cigar = 0; uint8_t *new_qual; size_t orig_l_aux = bam_get_l_aux(rec); int32_t i; int32_t j; uint32_t ref_remove = bases, qry_removed = 0, hardclip = 0; uint32_t cig_type, cig_op; if (rec->l_data + 8 > rec_out->m_data) { uint8_t *new_data = realloc(rec_out->data, rec->l_data + 8); if (!new_data) { fprintf(stderr, "[ampliconclip] error: could not allocate memoy for new bam record\n"); return 1; } rec_out->data = new_data; rec_out->m_data = rec->l_data + 8; } // Copy core data & name memcpy(&rec_out->core, &rec->core, sizeof(rec->core)); memcpy(rec_out->data, rec->data, rec->core.l_qname); // Modify CIGAR here new_cigar = bam_get_cigar(rec_out); for (i = rec->core.n_cigar - 1; i >= 0; --i) { cig_op = bam_cigar_op(orig_cigar[i]); cig_type = bam_cigar_type(cig_op); if (cig_op == BAM_CHARD_CLIP) { hardclip += bam_cigar_oplen(orig_cigar[i]); } else { if (cig_type & 2) { if (bam_cigar_oplen(orig_cigar[i]) <= ref_remove) { ref_remove -= bam_cigar_oplen(orig_cigar[i]); } else { break; } } if (cig_type & 1) { qry_removed += bam_cigar_oplen(orig_cigar[i]); } } } if (i >= 0) { cig_type = bam_cigar_type(bam_cigar_op(orig_cigar[i])); if (cig_type & 1) { qry_removed += ref_remove; } j = i; if (qry_removed > 0) j++; if (hardclip > 0 && (clipping == soft_clip || qry_removed == 0)) j++; } else { if (clipping == hard_clip) { rec_out->core.l_qseq = 0; rec_out->core.n_cigar = 0; if (orig_l_aux) memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux); rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux; return 0; } qry_removed = rec->core.l_qseq; j = 0; if (hardclip > 0 && clipping == soft_clip) j++; } if (clipping == hard_clip && hardclip + qry_removed > 0) { new_cigar[j] = bam_cigar_gen(hardclip + qry_removed, BAM_CHARD_CLIP); new_n_cigar++; } if (clipping == soft_clip) { if (hardclip > 0) { new_cigar[j] = bam_cigar_gen(hardclip, BAM_CHARD_CLIP); new_n_cigar++; if (qry_removed > 0) --j; } if (qry_removed > 0) { new_cigar[j] = bam_cigar_gen(qry_removed, BAM_CSOFT_CLIP); new_n_cigar++; } } if (j > 0) { new_cigar[--j] = bam_cigar_gen(bam_cigar_oplen(orig_cigar[i]) - ref_remove, bam_cigar_op(orig_cigar[i])); new_n_cigar++; } // fill in the rest of the cigar while (j > 0) { new_cigar[--j] = orig_cigar[--i]; new_n_cigar++; } rec_out->core.n_cigar = new_n_cigar; if (clipping == soft_clip) qry_removed = 0; // Copy all the sequence and confidence values new_qual = bam_get_seq(rec_out) + (rec->core.l_qseq - qry_removed + 1) / 2; // Copy remaining SEQ memcpy(bam_get_seq(rec_out), orig_seq, (rec->core.l_qseq - qry_removed + 1) / 2); // Copy remaining QUAL memcpy(new_qual, orig_qual, rec->core.l_qseq - qry_removed); // Set new l_qseq rec_out->core.l_qseq -= qry_removed; // Copy AUX if (orig_l_aux) memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux); // Set new l_data rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux; return 0; } static hts_pos_t active_query_len(bam1_t *b) { uint32_t *cigar = bam_get_cigar(b); uint32_t cig_type, cig_op; hts_pos_t len = 0; int i; for (i = 0; i < b->core.n_cigar; i++) { cig_op = bam_cigar_op(cigar[i]); cig_type = bam_cigar_type(cig_op); if ((cig_type & 1) && (cig_op != BAM_CSOFT_CLIP)) { len += bam_cigar_oplen(cigar[i]); } } return len; } static inline void swap_bams(bam1_t **a, bam1_t **b) { bam1_t *tmp = *a; *a = *b; *b = tmp; } // Format OA:Z:(RNAME,POS,strand,CIGAR,MAPQ,NM; static inline int tag_original_data(bam1_t *orig, kstring_t *oa_tag) { char strand; uint8_t *nm_tag, *old_oa_tag; uint32_t *cigar; int64_t nm = 0; int i, res = 0; ks_clear(oa_tag); // if there is an existing OA tag the new one gets appended to it if ((old_oa_tag = bam_aux_get(orig, "OA"))) { res |= ksprintf(oa_tag, "%s", bam_aux2Z(old_oa_tag)) < 0; } if (orig->core.flag & BAM_FREVERSE) strand = '-'; else strand = '+'; if ((nm_tag = bam_aux_get(orig, "NM"))) { nm = bam_aux2i(nm_tag); } res |= ksprintf(oa_tag, "%s,%"PRIhts_pos",%c,", bam_get_qname(orig), orig->core.pos + 1, strand) < 0; for (i = 0, cigar = bam_get_cigar(orig); i < orig->core.n_cigar && res == 0; ++i) { res |= kputw(bam_cigar_oplen(cigar[i]), oa_tag) < 0; res |= kputc(bam_cigar_opchr(cigar[i]), oa_tag) < 0; } if (nm_tag) { res |= ksprintf(oa_tag, ",%d,%"PRId64";", orig->core.qual, nm) < 0; } else { res |= ksprintf(oa_tag, "%d,;", orig->core.qual) < 0; } return res; } static int bam_clip(samFile *in, samFile *out, samFile *reject, char *bedfile, clipping_type clipping, cl_param_t *param) { int ret = 1, r, file_open = 0; bam_hdr_t *header = NULL; bam1_t *b = NULL, *b_tmp = NULL; long f_count = 0, r_count = 0, n_count = 0, l_count = 0, l_exclude = 0, b_count = 0; long filtered = 0, written = 0, failed = 0; kstring_t str = KS_INITIALIZE; kstring_t oat = KS_INITIALIZE; kstring_t seq = KS_INITIALIZE; bed_entry_list_t *sites; FILE *stats_fp = stderr; FILE *bed_count_summary_fp = stderr; khash_t(bed_list_hash) *bed_hash = kh_init(bed_list_hash); char **bed_ref_list = NULL; size_t num_bed_refs = 0; if (load_bed_file_multi_ref(bedfile, param->use_strand, 1, bed_hash, &bed_ref_list, &num_bed_refs)) { fprintf(stderr, "[ampliconclip] error: unable to load bed file.\n"); goto fail; } if ((header = sam_hdr_read(in)) == NULL) { fprintf(stderr, "[ampliconclip] error: could not read header\n"); goto fail; } // changing pos can ruin coordinate sort order if (sam_hdr_find_tag_hd(header, "SO", &str) == 0 && str.s && strcmp(str.s, "coordinate") == 0) { const char *new_order = "unknown"; if (sam_hdr_update_hd(header, "SO", new_order) == -1) { fprintf(stderr, "[ampliconclip] error: unable to change sort order to 'SO:%s'\n", new_order); goto fail; } } ks_free(&str); if (param->add_pg && sam_hdr_add_pg(header, "samtools", "VN", samtools_version(), param->arg_list ? "CL" : NULL, param->arg_list ? param->arg_list : NULL, NULL) != 0) { fprintf(stderr, "[ampliconclip] warning: unable to add @PG line to header.\n"); } if (sam_hdr_write(out, header) < 0) { fprintf(stderr, "[ampliconclip] error: could not write header.\n"); goto fail; } if (reject) { if (sam_hdr_write(reject, header) < 0) { fprintf(stderr, "[ampliconclip] error: could not write header to rejects file.\n"); goto fail; } } b = bam_init1(); b_tmp = bam_init1(); if (!b || !b_tmp) { fprintf(stderr, "[ampliconclip] error: out of memory when trying to create record.\n"); goto fail; } int32_t last_tid = -1; int ref_found = 0; while ((r = sam_read1(in, header, b)) >= 0) { hts_pos_t pos; int is_rev; int p_size; int been_clipped = 0, filter = 0; int exclude = (BAM_FUNMAP | BAM_FQCFAIL); khiter_t itr; l_count++; if (b->core.tid != last_tid) { const char *ref_name; ref_found = 0; last_tid = b->core.tid; if ((ref_name = sam_hdr_tid2name(header, b->core.tid)) != NULL) { itr = kh_get(bed_list_hash, bed_hash, ref_name); if (itr != kh_end(bed_hash)) { sites = &kh_val(bed_hash, itr); ref_found = 1; } } } if (!(b->core.flag & exclude) && ref_found) { if (param->oa_tag) if (tag_original_data(b, &oat)) goto fail; if (!param->both) { if (bam_is_rev(b)) { pos = bam_endpos(b); is_rev = 1; } else { pos = b->core.pos; is_rev = 0; } if ((p_size = matching_clip_site(sites, pos, is_rev, param->use_strand, sites->longest, param))) { if (is_rev) { if (bam_trim_right(b, b_tmp, p_size, clipping) != 0) goto fail; swap_bams(&b, &b_tmp); r_count++; } else { if (bam_trim_left(b, b_tmp, p_size, clipping) != 0) goto fail; swap_bams(&b, &b_tmp); f_count++; } if (param->oa_tag) { if (bam_aux_update_str(b, "OA", oat.l + 1, (const char *)oat.s)) goto fail; } if (param->del_tag) { uint8_t *tag; if ((tag = bam_aux_get(b, "NM"))) bam_aux_del(b, tag); if ((tag = bam_aux_get(b, "MD"))) bam_aux_del(b, tag); } been_clipped = 1; } else { if (param->mark_fail) { b->core.flag |= BAM_FQCFAIL; } n_count++; } } else { int left = 0, right = 0; // left first pos = b->core.pos; is_rev = 0; if ((p_size = matching_clip_site(sites, pos, is_rev, param->use_strand, sites->longest, param))) { if (bam_trim_left(b, b_tmp, p_size, clipping) != 0) goto fail; swap_bams(&b, &b_tmp); f_count++; left = 1; been_clipped = 1; } // the right pos = bam_endpos(b); is_rev = 1; if ((p_size = matching_clip_site(sites, pos, is_rev, param->use_strand, sites->longest, param))) { if (bam_trim_right(b, b_tmp, p_size, clipping) != 0) goto fail; swap_bams(&b, &b_tmp); r_count++; right = 1; been_clipped = 1; } if (left || right) { uint8_t *tag; if (param->oa_tag) { if (bam_aux_update_str(b, "OA", oat.l + 1, (const char *)oat.s)) goto fail; } if (param->del_tag) { if ((tag = bam_aux_get(b, "NM"))) bam_aux_del(b, tag); if ((tag = bam_aux_get(b, "MD"))) bam_aux_del(b, tag); } } if (left && right) { b_count++; } else if (!left && !right) { if (param->mark_fail) { b->core.flag |= BAM_FQCFAIL; } n_count++; } } if (param->fail_len >= 0 || param->filter_len >= 0 || param->unmap_len >= 0) { hts_pos_t aql = active_query_len(b); if (param->fail_len >= 0 && aql <= param->fail_len) { b->core.flag |= BAM_FQCFAIL; } if (param->filter_len >= 0 && aql <= param->filter_len) { filter = 1; } if (param->unmap_len >= 0 && aql <= param->unmap_len) { if (ks_resize(&seq, b->core.l_qseq) < 0) { fprintf(stderr, "[ampliconclip] error: allocate memory for sequence %s\n", bam_get_seq(b)); goto fail; } ks_clear(&seq); char *sb = ks_str(&seq); uint8_t *sequence = bam_get_seq(b); int i; for (i = 0; i < b->core.l_qseq ; ++i) { *sb++ = seq_nt16_str[bam_seqi(sequence, i)]; } if (bam_set1(b_tmp, b->core.l_qname - b->core.l_extranul - 1, bam_get_qname(b), (b->core.flag | BAM_FUNMAP), b->core.tid, b->core.pos, 0, 0, NULL, b->core.mtid, b->core.mpos, b->core.isize, b->core.l_qseq, seq.s, (const char *)bam_get_qual(b), bam_get_l_aux(b)) < 0) { fprintf(stderr, "[ampliconclip] error: could not unmap read %s\n", bam_get_seq(b)); goto fail; } memcpy(bam_get_aux(b_tmp), bam_get_aux(b), bam_get_l_aux(b)); b_tmp->l_data += bam_get_l_aux(b); swap_bams(&b, &b_tmp); } } if (b->core.flag & BAM_FQCFAIL) { failed++; } if (param->write_clipped && !been_clipped) { filter = 1; } } else { l_exclude++; if (param->unmapped) { filter = 1; } } if (!filter) { if (sam_write1(out, header, b) < 0) { fprintf(stderr, "[ampliconclip] error: could not write line %ld.\n", l_count); goto fail; } written++; } else { if (reject) { if (sam_write1(reject, header, b) < 0) { fprintf(stderr, "[ampliconclip] error: could not write to reject file %s\n", param->rejects_file); goto fail; } } filtered++; } } if (r < -1) { fprintf(stderr, "[ampliconclip] error: failed to read input.\n"); goto fail; } if (param->stats_file) { if ((stats_fp = fopen(param->stats_file, "w")) == NULL) { fprintf(stderr, "[ampliconclip] warning: cannot write stats to %s.\n", param->stats_file); } else { file_open = 1; } } fprintf(stats_fp, "COMMAND: %s\n" "TOTAL READS: %ld\n" "TOTAL CLIPPED: %ld\n" "FORWARD CLIPPED: %ld\n" "REVERSE CLIPPED: %ld\n" "BOTH CLIPPED: %ld\n" "NOT CLIPPED: %ld\n" "EXCLUDED: %ld\n" "FILTERED: %ld\n" "FAILED: %ld\n" "WRITTEN: %ld\n", param->arg_list, l_count, f_count + r_count, f_count, r_count, b_count, n_count, l_exclude, filtered, failed, written); if (file_open) { fclose(stats_fp); file_open = 0; } if (param->primer_counts_file) { if ((bed_count_summary_fp = fopen(param->primer_counts_file, "w")) == NULL) { fprintf(stderr, "[ampliconclip] warning: cannot write count summary to %s.\n", param->primer_counts_file); } else { file_open = 1; } //print out the number of reads for each bed entry, bedgraph format fprintf(bed_count_summary_fp, "#CHR\tLEFT\tRIGHT\tNAME\tSCORE\tSTRAND\tNUM_CLIPPED\n"); size_t refidx; for (refidx = 0; refidx < num_bed_refs; refidx++) { khiter_t itr = kh_get(bed_list_hash, bed_hash, bed_ref_list[refidx]); if (itr >= kh_end(bed_hash)) { fprintf(stderr, "[ampliconclip] error: %s has gone missing from the hash table\n", bed_ref_list[refidx]); goto fail; } sites = &kh_val(bed_hash, itr); int i; for (i = 0; i < sites->length; i++) { char* strand_out = param->use_strand ? (sites->bp[i].rev ? "-" : "+") : "."; fprintf(bed_count_summary_fp, "%s\t%"PRId64"\t%"PRId64"\t%s\t%s\t%s\t%"PRId64"\n", kh_key(bed_hash, itr), sites->bp[i].left, sites->bp[i].right, sites->bp[i].name, sites->bp[i].score, strand_out, sites->bp[i].num_reads); } } if (file_open) { fclose(bed_count_summary_fp); } } ret = 0; fail: free(bed_ref_list); destroy_bed_hash(bed_hash); ks_free(&oat); ks_free(&seq); sam_hdr_destroy(header); bam_destroy1(b); bam_destroy1(b_tmp); return ret; } static void usage(void) { fprintf(stderr, "Usage: samtools ampliconclip -b BED file -o \n\n"); fprintf(stderr, "Option: \n"); fprintf(stderr, " -b FILE BED file of regions (eg amplicon primers) to be removed.\n"); fprintf(stderr, " -o FILE output file name (default: stdout).\n"); fprintf(stderr, " -f FILE write stats to file name (default: stderr)\n"); fprintf(stderr, " -u Output uncompressed data\n"); fprintf(stderr, " --soft-clip soft clip amplicon primers from reads (default)\n"); fprintf(stderr, " --hard-clip hard clip amplicon primers from reads.\n"); fprintf(stderr, " --both-ends clip on both 5' and 3' ends.\n"); fprintf(stderr, " --strand use strand data from BED file to match read direction.\n"); fprintf(stderr, " --clipped only output clipped reads.\n"); fprintf(stderr, " --fail mark unclipped, mapped reads as QCFAIL.\n"); fprintf(stderr, " --filter-len INT do not output reads INT size or shorter.\n"); fprintf(stderr, " --fail-len INT mark as QCFAIL reads INT size or shorter.\n"); fprintf(stderr, " --unmap-len INT unmap reads INT size or shorter, default 0.\n"); fprintf(stderr, " --no-excluded do not write excluded reads (unmapped or QCFAIL).\n"); fprintf(stderr, " --rejects-file FILE file to write filtered reads.\n"); fprintf(stderr, " --primer-counts FILE file to write read counts per bed entry (bedgraph format).\n"); fprintf(stderr, " --original for clipped entries add an OA tag with original data.\n"); fprintf(stderr, " --keep-tag for clipped entries keep the old NM and MD tags.\n"); fprintf(stderr, " --tolerance match region within this number of bases, default 5.\n"); fprintf(stderr, " --no-PG do not add an @PG line.\n"); sam_global_opt_help(stderr, "-.O..@-."); fprintf(stderr, "\nAbout: Soft clips read alignments where they match BED file defined regions.\n" "Default clipping is only on the 5' end.\n\n"); } int amplicon_clip_main(int argc, char **argv) { int c, ret; char wmode[4] = {'w', 'b', 0, 0}; char *bedfile = NULL, *fnout = "-"; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; htsThreadPool p = {NULL, 0}; samFile *in = NULL, *out = NULL, *reject = NULL; clipping_type clipping = soft_clip; cl_param_t param = {1, 0, 0, 0, 0, -1, -1, 0, 0, 1, 5, 0, NULL, NULL, NULL}; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'), {"no-PG", no_argument, NULL, 1002}, {"soft-clip", no_argument, NULL, 1003}, {"hard-clip", no_argument, NULL, 1004}, {"strand", no_argument, NULL, 1005}, {"clipped", no_argument, NULL, 1006}, {"fail", no_argument, NULL, 1007}, {"both-ends", no_argument, NULL, 1008}, {"filter-len", required_argument, NULL, 1009}, {"fail-len", required_argument, NULL, 1010}, {"no-excluded", no_argument, NULL, 1011}, {"rejects-file", required_argument, NULL, 1012}, {"primer-counts", required_argument, NULL, 1013}, {"original", no_argument, NULL, 1014}, {"keep-tag", no_argument, NULL, 1015}, {"tolerance", required_argument, NULL, 1016}, {"unmap-len", required_argument, NULL, 1017}, {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "b:@:o:O:f:u", lopts, NULL)) >= 0) { switch (c) { case 'b': bedfile = optarg; break; case 'o': fnout = optarg; break; case 'f': param.stats_file = optarg; break; case 'u': wmode[2] = '0'; break; case 1002: param.add_pg = 0; break; case 1003: clipping = soft_clip; break; case 1004: clipping = hard_clip; break; case 1005: param.use_strand = 1; break; case 1006: param.write_clipped = 1; break; case 1007: param.mark_fail = 1; break; case 1008: param.both = 1; break; case 1009: param.filter_len = atoi(optarg); break; case 1010: param.fail_len = atoi(optarg); break; case 1011: param.unmapped = 1; break; case 1012: param.rejects_file = optarg; break; case 1013: param.primer_counts_file = optarg; break; case 1014: param.oa_tag = 1; break; case 1015: param.del_tag = 0; break; case 1016: param.tol = atoi(optarg); break; case 1017: param.unmap_len = atoi(optarg); break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage(); exit(1); } } if (!bedfile) { usage(); return 1; } if (optind + 1 > argc) { usage(); return 1; } if (param.tol < 0) { fprintf(stderr, "[ampliconclip] warning: invalid tolerance of %d," " resetting tolerance to default of 5.\n", param.tol); param.tol = 5; } if ((in = sam_open_format(argv[optind], "rb", &ga.in)) == NULL) { print_error_errno("ampliconclip", "cannot open input file"); return 1; } sam_open_mode(wmode+1, fnout, NULL); if ((out = sam_open_format(fnout, wmode, &ga.out)) == NULL) { print_error_errno("ampliconclip", "cannot open output file"); return 1; } if (param.rejects_file) { sam_open_mode(wmode+1, param.rejects_file, NULL); if ((reject = sam_open_format(param.rejects_file, wmode, &ga.out)) == NULL) { print_error_errno("ampliconclip", "cannot open rejects file"); return 1; } } if (ga.nthreads > 0) { if (!(p.pool = hts_tpool_init(ga.nthreads))) { fprintf(stderr, "[ampliconclip] error: cannot create thread pool.\n"); return 1; } hts_set_opt(in, HTS_OPT_THREAD_POOL, &p); hts_set_opt(out, HTS_OPT_THREAD_POOL, &p); if (reject) { hts_set_opt(reject, HTS_OPT_THREAD_POOL, &p); } } param.arg_list = stringify_argv(argc + 1, argv - 1); ret = bam_clip(in, out, reject, bedfile, clipping, ¶m); // cleanup sam_close(in); if (sam_close(out) < 0) { fprintf(stderr, "[ampliconclip] error: error while closing output file %s.\n", argv[optind+1]); ret = 1; } if (reject) { if (sam_close(reject) < 0) { fprintf(stderr, "[ampliconclip] error: error while closing reject file %s.\n", param.rejects_file); ret = 1; } } if (p.pool) hts_tpool_destroy(p.pool); sam_global_args_free(&ga); free(param.arg_list); return ret; } pysam-0.23.0/samtools/bam_ampliconclip.c.pysam.c000066400000000000000000001172661475062545500216260ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_ampliconclip.c -- loads amplicon primers from a BED file and cuts reads from the 5' end. Copyright (C) 2020-2024 Genome Research Ltd. Authors: Andrew Whitwham Rob Davies Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE */ #include #include #include #include #include #include #include #include "htslib/thread_pool.h" #include "sam_opts.h" #include #include "htslib/hfile.h" #include "htslib/kstring.h" #include "htslib/sam.h" #include "samtools.h" #include "bam_ampliconclip.h" typedef enum { soft_clip, hard_clip } clipping_type; typedef struct { int add_pg; int use_strand; int write_clipped; int mark_fail; int both; int fail_len; int filter_len; int unmapped; int oa_tag; int del_tag; int tol; int unmap_len; char *arg_list; char *stats_file; char *primer_counts_file; char *rejects_file; } cl_param_t; static int bed_entry_sort(const void *av, const void *bv) { bed_entry_t *a = (bed_entry_t *) av; bed_entry_t *b = (bed_entry_t *) bv; return a->right < b->right ? -1 : (a->right == b->right ? 0 : 1); } int load_bed_file_multi_ref(char *infile, int get_strand, int sort_by_pos, khash_t(bed_list_hash) *bed_lists, char ***ref_list, size_t *num_refs_out) { hFILE *fp; int line_count = 0, ret; //variables to store the bed file data for each record char ref[1024] = ""; int64_t left, right; char name[1024] = "", score[1024] = ""; char strand; //hash table to store clipping results and bed file data kstring_t line = KS_INITIALIZE; bed_entry_list_t *list; khiter_t bed_itr; //ordered ref names list size_t ref_list_sz = 0; size_t num_refs = 0; if (ref_list) *ref_list = NULL; if (num_refs_out) *num_refs_out = 0; if ((fp = hopen(infile, "r")) == NULL) { print_error_errno("amplicon", "unable to open file %s.", infile); return 1; } while (line.l = 0, kgetline(&line, (kgets_func *)hgets, fp) >= 0) { line_count++; int hret; if (line.l == 0 || *line.s == '#') continue; if (strncmp(line.s, "track ", 6) == 0) continue; if (strncmp(line.s, "browser ", 8) == 0) continue; // A list of the maximal number of columns we may want to parse. // There may be more, but we don't use the ones beyond these. const char *const scanf_str = "%1023s %"SCNd64" %"SCNd64" %1023s %1023s %c"; // Extract the data from the line into the variables. // Variables corresponding to any missing columns will remain // uninitialised. We asked for all columns, but cols_parsed will // return how many we found which can be validated against num_columns. int cols_parsed = sscanf(line.s, scanf_str, ref, &left, &right, name, score, &strand); if (cols_parsed < (get_strand ? 6 : 3)) { fprintf(samtools_stderr, "[amplicon] error: invalid bed file format in line %d of %s.\n" "Parsed %d columns, but need at least %d\n" "(N.B. ref/chrom name limited to 1023 characters.)\n", line_count, infile, cols_parsed, get_strand ? 6 : 3); ret = 1; goto error; } bed_itr = kh_get(bed_list_hash, bed_lists, ref); if (bed_itr == kh_end(bed_lists)) { // new ref entry char *ref_name = strdup(ref); // need a copy for the hash key if (!ref_name) { fprintf(samtools_stderr, "[amplicon] error: unable to allocate memory for ref name.\n"); ret = 1; goto error; } if (ref_list) { if (hts_resize(char **, num_refs + 1, &ref_list_sz, ref_list, 0) < 0) { fprintf(samtools_stderr, "[amplicon] error: unable to allocate memory for ref name list.\n"); ret = 1; goto error; } (*ref_list)[num_refs++] = ref_name; } bed_itr = kh_put(bed_list_hash, bed_lists, ref_name, &hret); if (hret > 0) { list = &kh_val(bed_lists, bed_itr); // initialise the new hash entry list->longest = 0; list->size = 0; list->length = 0; list->bp = NULL; } else { fprintf(samtools_stderr, "[amplicon] error: ref hashing failure.\n"); ret = 1; goto error; } } else { // existing ref list = &kh_val(bed_lists, bed_itr); } // add the bed entry to the list, growing the list if necessary if (list->length == list->size) { bed_entry_t *tmp; list->size += list->size / 2 + 256; if ((tmp = realloc(list->bp, list->size * sizeof(bed_entry_t))) == NULL) { fprintf(samtools_stderr, "[amplicon] error: unable to allocate more memory for bed data.\n"); ret = 1; goto error; } list->bp = tmp; } list->bp[list->length].left = left; list->bp[list->length].right = right; list->bp[list->length].name = NULL; list->bp[list->length].score = NULL; if (cols_parsed >= 4) { list->bp[list->length].name = strdup(name); if (list->bp[list->length].name == NULL) { fprintf(samtools_stderr, "[amplicon] error: unable to allocate memory for name in line %d of %s: %s.\n", line_count, infile, line.s); ret = 1; goto error; } } if (cols_parsed >= 5) { list->bp[list->length].score = strdup(score); if (list->bp[list->length].score == NULL) { fprintf(samtools_stderr, "[amplicon] error: unable to allocate memory for score in line %d of %s: %s\n", line_count, infile, line.s); ret = 1; goto error; } } list->bp[list->length].num_reads = 0; if (get_strand) { if (strand == '+') { list->bp[list->length].rev = 0; } else if (strand == '-') { list->bp[list->length].rev = 1; } else { fprintf(samtools_stderr, "[amplicon] error: bad strand value in line %d, expecting '+' or '-', found '%c'.\n", line_count, strand); ret = 1; goto error; } } if (right - left > list->longest) list->longest = right - left; list->length++; } if (sort_by_pos) { for (bed_itr = kh_begin(bed_lists); bed_itr != kh_end(bed_lists); ++bed_itr) { if (kh_exist(bed_lists, bed_itr)) { list = &kh_val(bed_lists, bed_itr); qsort(list->bp, list->length, sizeof(list->bp[0]), bed_entry_sort); } } } if (kh_size(bed_lists) > 0) {// any entries ret = 0; } else { ret = 1; } if (num_refs_out) *num_refs_out = num_refs; error: ks_free(&line); if (hclose(fp) != 0) { fprintf(samtools_stderr, "[amplicon] warning: failed to close %s", infile); } return ret; } void destroy_bed_hash(khash_t(bed_list_hash) *hash) { khiter_t itr; for (itr = kh_begin(hash); itr != kh_end(hash); ++itr) { if (kh_exist(hash, itr)) { bed_entry_list_t list = kh_val(hash, itr); for (int i = 0; i < list.length; i++) { free(list.bp[i].name); free(list.bp[i].score); } free(list.bp); free((char *)kh_key(hash, itr)); kh_key(hash, itr) = NULL; } } kh_destroy(bed_list_hash, hash); } static int matching_clip_site(bed_entry_list_t *sites, hts_pos_t pos, int is_rev, int use_strand, int64_t longest, cl_param_t *param) { int i, size, used_i; int tol = param->tol; int l = 0, mid = sites->length / 2, r = sites->length; int pos_tol = is_rev ? (pos > tol ? pos - tol : 0) : pos; while (r - l > 1) { if (sites->bp[mid].right <= pos_tol) { l = mid; } else { r = mid; } mid = (l + r) / 2; } size = 0; used_i = -1; for (i = l; i < sites->length; i++) { hts_pos_t mod_left, mod_right; if (use_strand && is_rev != sites->bp[i].rev) continue; if (is_rev) { mod_left = sites->bp[i].left; mod_right = sites->bp[i].right + tol; } else { if (sites->bp[i].left > tol) { mod_left = sites->bp[i].left - tol; } else { mod_left = 0; } mod_right = sites->bp[i].right; } if (pos + longest + tol < mod_right) break; if (pos >= mod_left && pos <= mod_right) { if (is_rev) { if (size < pos - sites->bp[i].left) { size = pos - sites->bp[i].left; used_i = i; } } else { if (size < sites->bp[i].right - pos) { size = sites->bp[i].right - pos; used_i = i; } } } } if (used_i >= 0) { sites->bp[used_i].num_reads++; } return size; } static int bam_trim_left(bam1_t *rec, bam1_t *rec_out, uint32_t bases, clipping_type clipping) { uint32_t *orig_cigar = bam_get_cigar(rec); uint8_t *orig_seq = bam_get_seq(rec); uint8_t *orig_qual = bam_get_qual(rec); uint8_t *orig_aux = bam_get_aux(rec); uint32_t *new_cigar; uint8_t *new_qual; size_t orig_l_aux = bam_get_l_aux(rec); uint32_t i, j; uint32_t ref_remove = bases, qry_removed = 0, hardclip = 0; hts_pos_t new_pos = rec->core.pos; uint32_t cig_type, cig_op; if (rec->l_data + 8 > rec_out->m_data) { uint8_t *new_data = realloc(rec_out->data, rec->l_data + 8); if (!new_data) { fprintf(samtools_stderr, "[ampliconclip] error: could not allocate memoy for new bam record\n"); return 1; } rec_out->data = new_data; rec_out->m_data = rec->l_data + 8; } // Copy core data & name memcpy(&rec_out->core, &rec->core, sizeof(rec->core)); memcpy(rec_out->data, rec->data, rec->core.l_qname); // Modify CIGAR new_cigar = bam_get_cigar(rec_out); for (i = 0; i < rec->core.n_cigar; i++) { cig_op = bam_cigar_op(orig_cigar[i]); cig_type = bam_cigar_type(cig_op); if (cig_op == BAM_CHARD_CLIP) { hardclip += bam_cigar_oplen(orig_cigar[i]); } else { if (cig_type & 2) { if (bam_cigar_oplen(orig_cigar[i]) <= ref_remove) { ref_remove -= bam_cigar_oplen(orig_cigar[i]); } else { break; } new_pos += bam_cigar_oplen(orig_cigar[i]); } if (cig_type & 1) { qry_removed += bam_cigar_oplen(orig_cigar[i]); } } } if (i < rec->core.n_cigar) { cig_type = bam_cigar_type(bam_cigar_op(orig_cigar[i])); // account for the last operation if (cig_type & 2) { new_pos += ref_remove; } if (cig_type & 1) { qry_removed += ref_remove; } } else { if (clipping == hard_clip) { rec_out->core.l_qseq = 0; rec_out->core.n_cigar = 0; if (orig_l_aux) memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux); rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux; return 0; } qry_removed = rec->core.l_qseq; } j = 0; if (clipping == hard_clip && hardclip + qry_removed > 0) { new_cigar[j++] = bam_cigar_gen(hardclip + qry_removed, BAM_CHARD_CLIP); } if (clipping == soft_clip) { if (hardclip > 0) { new_cigar[j++] = bam_cigar_gen(hardclip, BAM_CHARD_CLIP); } if (qry_removed > 0) { new_cigar[j++] = bam_cigar_gen(qry_removed, BAM_CSOFT_CLIP); } } if (i < rec->core.n_cigar && bam_cigar_oplen(orig_cigar[i]) > ref_remove) { new_cigar[j++] = bam_cigar_gen(bam_cigar_oplen(orig_cigar[i]) - ref_remove, bam_cigar_op(orig_cigar[i])); // fill in the rest of the cigar i++; for (; i < rec->core.n_cigar; i++) { new_cigar[j++] = orig_cigar[i]; } } rec_out->core.n_cigar = j; if (clipping == soft_clip) { qry_removed = 0; // Copy all the sequence and confidence values } new_qual = bam_get_seq(rec_out) + (rec->core.l_qseq - qry_removed + 1) / 2; // Copy remaining SEQ if ((qry_removed & 1) == 0) { memcpy(bam_get_seq(rec_out), orig_seq + (qry_removed / 2), (rec->core.l_qseq - qry_removed + 1) / 2); // +1 to account for odd numbers } else { uint8_t *in = orig_seq + qry_removed / 2; uint8_t *out = bam_get_seq(rec_out); uint32_t i; for (i = qry_removed; i < rec->core.l_qseq - 1; i += 2) { *out++ = ((in[0] & 0x0f) << 4) | ((in[1] & 0xf0) >> 4); in++; } if (i < rec->core.l_qseq) { *out++ = (in[0] & 0x0f) << 4; } assert(out == new_qual); } // Copy remaining QUAL memmove(new_qual, orig_qual + qry_removed, rec->core.l_qseq - qry_removed); // Set new l_qseq rec_out->core.l_qseq -= qry_removed; // Move AUX if (orig_l_aux) memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux); // Set new l_data rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux; // put in new pos rec_out->core.pos = new_pos; return 0; } static int bam_trim_right(bam1_t *rec, bam1_t *rec_out, uint32_t bases, clipping_type clipping) { uint32_t *orig_cigar = bam_get_cigar(rec); uint8_t *orig_seq = bam_get_seq(rec); uint8_t *orig_qual = bam_get_qual(rec); uint8_t *orig_aux = bam_get_aux(rec); uint32_t *new_cigar; uint32_t new_n_cigar = 0; uint8_t *new_qual; size_t orig_l_aux = bam_get_l_aux(rec); int32_t i; int32_t j; uint32_t ref_remove = bases, qry_removed = 0, hardclip = 0; uint32_t cig_type, cig_op; if (rec->l_data + 8 > rec_out->m_data) { uint8_t *new_data = realloc(rec_out->data, rec->l_data + 8); if (!new_data) { fprintf(samtools_stderr, "[ampliconclip] error: could not allocate memoy for new bam record\n"); return 1; } rec_out->data = new_data; rec_out->m_data = rec->l_data + 8; } // Copy core data & name memcpy(&rec_out->core, &rec->core, sizeof(rec->core)); memcpy(rec_out->data, rec->data, rec->core.l_qname); // Modify CIGAR here new_cigar = bam_get_cigar(rec_out); for (i = rec->core.n_cigar - 1; i >= 0; --i) { cig_op = bam_cigar_op(orig_cigar[i]); cig_type = bam_cigar_type(cig_op); if (cig_op == BAM_CHARD_CLIP) { hardclip += bam_cigar_oplen(orig_cigar[i]); } else { if (cig_type & 2) { if (bam_cigar_oplen(orig_cigar[i]) <= ref_remove) { ref_remove -= bam_cigar_oplen(orig_cigar[i]); } else { break; } } if (cig_type & 1) { qry_removed += bam_cigar_oplen(orig_cigar[i]); } } } if (i >= 0) { cig_type = bam_cigar_type(bam_cigar_op(orig_cigar[i])); if (cig_type & 1) { qry_removed += ref_remove; } j = i; if (qry_removed > 0) j++; if (hardclip > 0 && (clipping == soft_clip || qry_removed == 0)) j++; } else { if (clipping == hard_clip) { rec_out->core.l_qseq = 0; rec_out->core.n_cigar = 0; if (orig_l_aux) memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux); rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux; return 0; } qry_removed = rec->core.l_qseq; j = 0; if (hardclip > 0 && clipping == soft_clip) j++; } if (clipping == hard_clip && hardclip + qry_removed > 0) { new_cigar[j] = bam_cigar_gen(hardclip + qry_removed, BAM_CHARD_CLIP); new_n_cigar++; } if (clipping == soft_clip) { if (hardclip > 0) { new_cigar[j] = bam_cigar_gen(hardclip, BAM_CHARD_CLIP); new_n_cigar++; if (qry_removed > 0) --j; } if (qry_removed > 0) { new_cigar[j] = bam_cigar_gen(qry_removed, BAM_CSOFT_CLIP); new_n_cigar++; } } if (j > 0) { new_cigar[--j] = bam_cigar_gen(bam_cigar_oplen(orig_cigar[i]) - ref_remove, bam_cigar_op(orig_cigar[i])); new_n_cigar++; } // fill in the rest of the cigar while (j > 0) { new_cigar[--j] = orig_cigar[--i]; new_n_cigar++; } rec_out->core.n_cigar = new_n_cigar; if (clipping == soft_clip) qry_removed = 0; // Copy all the sequence and confidence values new_qual = bam_get_seq(rec_out) + (rec->core.l_qseq - qry_removed + 1) / 2; // Copy remaining SEQ memcpy(bam_get_seq(rec_out), orig_seq, (rec->core.l_qseq - qry_removed + 1) / 2); // Copy remaining QUAL memcpy(new_qual, orig_qual, rec->core.l_qseq - qry_removed); // Set new l_qseq rec_out->core.l_qseq -= qry_removed; // Copy AUX if (orig_l_aux) memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux); // Set new l_data rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux; return 0; } static hts_pos_t active_query_len(bam1_t *b) { uint32_t *cigar = bam_get_cigar(b); uint32_t cig_type, cig_op; hts_pos_t len = 0; int i; for (i = 0; i < b->core.n_cigar; i++) { cig_op = bam_cigar_op(cigar[i]); cig_type = bam_cigar_type(cig_op); if ((cig_type & 1) && (cig_op != BAM_CSOFT_CLIP)) { len += bam_cigar_oplen(cigar[i]); } } return len; } static inline void swap_bams(bam1_t **a, bam1_t **b) { bam1_t *tmp = *a; *a = *b; *b = tmp; } // Format OA:Z:(RNAME,POS,strand,CIGAR,MAPQ,NM; static inline int tag_original_data(bam1_t *orig, kstring_t *oa_tag) { char strand; uint8_t *nm_tag, *old_oa_tag; uint32_t *cigar; int64_t nm = 0; int i, res = 0; ks_clear(oa_tag); // if there is an existing OA tag the new one gets appended to it if ((old_oa_tag = bam_aux_get(orig, "OA"))) { res |= ksprintf(oa_tag, "%s", bam_aux2Z(old_oa_tag)) < 0; } if (orig->core.flag & BAM_FREVERSE) strand = '-'; else strand = '+'; if ((nm_tag = bam_aux_get(orig, "NM"))) { nm = bam_aux2i(nm_tag); } res |= ksprintf(oa_tag, "%s,%"PRIhts_pos",%c,", bam_get_qname(orig), orig->core.pos + 1, strand) < 0; for (i = 0, cigar = bam_get_cigar(orig); i < orig->core.n_cigar && res == 0; ++i) { res |= kputw(bam_cigar_oplen(cigar[i]), oa_tag) < 0; res |= kputc(bam_cigar_opchr(cigar[i]), oa_tag) < 0; } if (nm_tag) { res |= ksprintf(oa_tag, ",%d,%"PRId64";", orig->core.qual, nm) < 0; } else { res |= ksprintf(oa_tag, "%d,;", orig->core.qual) < 0; } return res; } static int bam_clip(samFile *in, samFile *out, samFile *reject, char *bedfile, clipping_type clipping, cl_param_t *param) { int ret = 1, r, file_open = 0; bam_hdr_t *header = NULL; bam1_t *b = NULL, *b_tmp = NULL; long f_count = 0, r_count = 0, n_count = 0, l_count = 0, l_exclude = 0, b_count = 0; long filtered = 0, written = 0, failed = 0; kstring_t str = KS_INITIALIZE; kstring_t oat = KS_INITIALIZE; kstring_t seq = KS_INITIALIZE; bed_entry_list_t *sites; FILE *stats_fp = samtools_stderr; FILE *bed_count_summary_fp = samtools_stderr; khash_t(bed_list_hash) *bed_hash = kh_init(bed_list_hash); char **bed_ref_list = NULL; size_t num_bed_refs = 0; if (load_bed_file_multi_ref(bedfile, param->use_strand, 1, bed_hash, &bed_ref_list, &num_bed_refs)) { fprintf(samtools_stderr, "[ampliconclip] error: unable to load bed file.\n"); goto fail; } if ((header = sam_hdr_read(in)) == NULL) { fprintf(samtools_stderr, "[ampliconclip] error: could not read header\n"); goto fail; } // changing pos can ruin coordinate sort order if (sam_hdr_find_tag_hd(header, "SO", &str) == 0 && str.s && strcmp(str.s, "coordinate") == 0) { const char *new_order = "unknown"; if (sam_hdr_update_hd(header, "SO", new_order) == -1) { fprintf(samtools_stderr, "[ampliconclip] error: unable to change sort order to 'SO:%s'\n", new_order); goto fail; } } ks_free(&str); if (param->add_pg && sam_hdr_add_pg(header, "samtools", "VN", samtools_version(), param->arg_list ? "CL" : NULL, param->arg_list ? param->arg_list : NULL, NULL) != 0) { fprintf(samtools_stderr, "[ampliconclip] warning: unable to add @PG line to header.\n"); } if (sam_hdr_write(out, header) < 0) { fprintf(samtools_stderr, "[ampliconclip] error: could not write header.\n"); goto fail; } if (reject) { if (sam_hdr_write(reject, header) < 0) { fprintf(samtools_stderr, "[ampliconclip] error: could not write header to rejects file.\n"); goto fail; } } b = bam_init1(); b_tmp = bam_init1(); if (!b || !b_tmp) { fprintf(samtools_stderr, "[ampliconclip] error: out of memory when trying to create record.\n"); goto fail; } int32_t last_tid = -1; int ref_found = 0; while ((r = sam_read1(in, header, b)) >= 0) { hts_pos_t pos; int is_rev; int p_size; int been_clipped = 0, filter = 0; int exclude = (BAM_FUNMAP | BAM_FQCFAIL); khiter_t itr; l_count++; if (b->core.tid != last_tid) { const char *ref_name; ref_found = 0; last_tid = b->core.tid; if ((ref_name = sam_hdr_tid2name(header, b->core.tid)) != NULL) { itr = kh_get(bed_list_hash, bed_hash, ref_name); if (itr != kh_end(bed_hash)) { sites = &kh_val(bed_hash, itr); ref_found = 1; } } } if (!(b->core.flag & exclude) && ref_found) { if (param->oa_tag) if (tag_original_data(b, &oat)) goto fail; if (!param->both) { if (bam_is_rev(b)) { pos = bam_endpos(b); is_rev = 1; } else { pos = b->core.pos; is_rev = 0; } if ((p_size = matching_clip_site(sites, pos, is_rev, param->use_strand, sites->longest, param))) { if (is_rev) { if (bam_trim_right(b, b_tmp, p_size, clipping) != 0) goto fail; swap_bams(&b, &b_tmp); r_count++; } else { if (bam_trim_left(b, b_tmp, p_size, clipping) != 0) goto fail; swap_bams(&b, &b_tmp); f_count++; } if (param->oa_tag) { if (bam_aux_update_str(b, "OA", oat.l + 1, (const char *)oat.s)) goto fail; } if (param->del_tag) { uint8_t *tag; if ((tag = bam_aux_get(b, "NM"))) bam_aux_del(b, tag); if ((tag = bam_aux_get(b, "MD"))) bam_aux_del(b, tag); } been_clipped = 1; } else { if (param->mark_fail) { b->core.flag |= BAM_FQCFAIL; } n_count++; } } else { int left = 0, right = 0; // left first pos = b->core.pos; is_rev = 0; if ((p_size = matching_clip_site(sites, pos, is_rev, param->use_strand, sites->longest, param))) { if (bam_trim_left(b, b_tmp, p_size, clipping) != 0) goto fail; swap_bams(&b, &b_tmp); f_count++; left = 1; been_clipped = 1; } // the right pos = bam_endpos(b); is_rev = 1; if ((p_size = matching_clip_site(sites, pos, is_rev, param->use_strand, sites->longest, param))) { if (bam_trim_right(b, b_tmp, p_size, clipping) != 0) goto fail; swap_bams(&b, &b_tmp); r_count++; right = 1; been_clipped = 1; } if (left || right) { uint8_t *tag; if (param->oa_tag) { if (bam_aux_update_str(b, "OA", oat.l + 1, (const char *)oat.s)) goto fail; } if (param->del_tag) { if ((tag = bam_aux_get(b, "NM"))) bam_aux_del(b, tag); if ((tag = bam_aux_get(b, "MD"))) bam_aux_del(b, tag); } } if (left && right) { b_count++; } else if (!left && !right) { if (param->mark_fail) { b->core.flag |= BAM_FQCFAIL; } n_count++; } } if (param->fail_len >= 0 || param->filter_len >= 0 || param->unmap_len >= 0) { hts_pos_t aql = active_query_len(b); if (param->fail_len >= 0 && aql <= param->fail_len) { b->core.flag |= BAM_FQCFAIL; } if (param->filter_len >= 0 && aql <= param->filter_len) { filter = 1; } if (param->unmap_len >= 0 && aql <= param->unmap_len) { if (ks_resize(&seq, b->core.l_qseq) < 0) { fprintf(samtools_stderr, "[ampliconclip] error: allocate memory for sequence %s\n", bam_get_seq(b)); goto fail; } ks_clear(&seq); char *sb = ks_str(&seq); uint8_t *sequence = bam_get_seq(b); int i; for (i = 0; i < b->core.l_qseq ; ++i) { *sb++ = seq_nt16_str[bam_seqi(sequence, i)]; } if (bam_set1(b_tmp, b->core.l_qname - b->core.l_extranul - 1, bam_get_qname(b), (b->core.flag | BAM_FUNMAP), b->core.tid, b->core.pos, 0, 0, NULL, b->core.mtid, b->core.mpos, b->core.isize, b->core.l_qseq, seq.s, (const char *)bam_get_qual(b), bam_get_l_aux(b)) < 0) { fprintf(samtools_stderr, "[ampliconclip] error: could not unmap read %s\n", bam_get_seq(b)); goto fail; } memcpy(bam_get_aux(b_tmp), bam_get_aux(b), bam_get_l_aux(b)); b_tmp->l_data += bam_get_l_aux(b); swap_bams(&b, &b_tmp); } } if (b->core.flag & BAM_FQCFAIL) { failed++; } if (param->write_clipped && !been_clipped) { filter = 1; } } else { l_exclude++; if (param->unmapped) { filter = 1; } } if (!filter) { if (sam_write1(out, header, b) < 0) { fprintf(samtools_stderr, "[ampliconclip] error: could not write line %ld.\n", l_count); goto fail; } written++; } else { if (reject) { if (sam_write1(reject, header, b) < 0) { fprintf(samtools_stderr, "[ampliconclip] error: could not write to reject file %s\n", param->rejects_file); goto fail; } } filtered++; } } if (r < -1) { fprintf(samtools_stderr, "[ampliconclip] error: failed to read input.\n"); goto fail; } if (param->stats_file) { if ((stats_fp = fopen(param->stats_file, "w")) == NULL) { fprintf(samtools_stderr, "[ampliconclip] warning: cannot write stats to %s.\n", param->stats_file); } else { file_open = 1; } } fprintf(stats_fp, "COMMAND: %s\n" "TOTAL READS: %ld\n" "TOTAL CLIPPED: %ld\n" "FORWARD CLIPPED: %ld\n" "REVERSE CLIPPED: %ld\n" "BOTH CLIPPED: %ld\n" "NOT CLIPPED: %ld\n" "EXCLUDED: %ld\n" "FILTERED: %ld\n" "FAILED: %ld\n" "WRITTEN: %ld\n", param->arg_list, l_count, f_count + r_count, f_count, r_count, b_count, n_count, l_exclude, filtered, failed, written); if (file_open) { fclose(stats_fp); file_open = 0; } if (param->primer_counts_file) { if ((bed_count_summary_fp = fopen(param->primer_counts_file, "w")) == NULL) { fprintf(samtools_stderr, "[ampliconclip] warning: cannot write count summary to %s.\n", param->primer_counts_file); } else { file_open = 1; } //print out the number of reads for each bed entry, bedgraph format fprintf(bed_count_summary_fp, "#CHR\tLEFT\tRIGHT\tNAME\tSCORE\tSTRAND\tNUM_CLIPPED\n"); size_t refidx; for (refidx = 0; refidx < num_bed_refs; refidx++) { khiter_t itr = kh_get(bed_list_hash, bed_hash, bed_ref_list[refidx]); if (itr >= kh_end(bed_hash)) { fprintf(samtools_stderr, "[ampliconclip] error: %s has gone missing from the hash table\n", bed_ref_list[refidx]); goto fail; } sites = &kh_val(bed_hash, itr); int i; for (i = 0; i < sites->length; i++) { char* strand_out = param->use_strand ? (sites->bp[i].rev ? "-" : "+") : "."; fprintf(bed_count_summary_fp, "%s\t%"PRId64"\t%"PRId64"\t%s\t%s\t%s\t%"PRId64"\n", kh_key(bed_hash, itr), sites->bp[i].left, sites->bp[i].right, sites->bp[i].name, sites->bp[i].score, strand_out, sites->bp[i].num_reads); } } if (file_open) { fclose(bed_count_summary_fp); } } ret = 0; fail: free(bed_ref_list); destroy_bed_hash(bed_hash); ks_free(&oat); ks_free(&seq); sam_hdr_destroy(header); bam_destroy1(b); bam_destroy1(b_tmp); return ret; } static void usage(void) { fprintf(samtools_stderr, "Usage: samtools ampliconclip -b BED file -o \n\n"); fprintf(samtools_stderr, "Option: \n"); fprintf(samtools_stderr, " -b FILE BED file of regions (eg amplicon primers) to be removed.\n"); fprintf(samtools_stderr, " -o FILE output file name (default: samtools_stdout).\n"); fprintf(samtools_stderr, " -f FILE write stats to file name (default: samtools_stderr)\n"); fprintf(samtools_stderr, " -u Output uncompressed data\n"); fprintf(samtools_stderr, " --soft-clip soft clip amplicon primers from reads (default)\n"); fprintf(samtools_stderr, " --hard-clip hard clip amplicon primers from reads.\n"); fprintf(samtools_stderr, " --both-ends clip on both 5' and 3' ends.\n"); fprintf(samtools_stderr, " --strand use strand data from BED file to match read direction.\n"); fprintf(samtools_stderr, " --clipped only output clipped reads.\n"); fprintf(samtools_stderr, " --fail mark unclipped, mapped reads as QCFAIL.\n"); fprintf(samtools_stderr, " --filter-len INT do not output reads INT size or shorter.\n"); fprintf(samtools_stderr, " --fail-len INT mark as QCFAIL reads INT size or shorter.\n"); fprintf(samtools_stderr, " --unmap-len INT unmap reads INT size or shorter, default 0.\n"); fprintf(samtools_stderr, " --no-excluded do not write excluded reads (unmapped or QCFAIL).\n"); fprintf(samtools_stderr, " --rejects-file FILE file to write filtered reads.\n"); fprintf(samtools_stderr, " --primer-counts FILE file to write read counts per bed entry (bedgraph format).\n"); fprintf(samtools_stderr, " --original for clipped entries add an OA tag with original data.\n"); fprintf(samtools_stderr, " --keep-tag for clipped entries keep the old NM and MD tags.\n"); fprintf(samtools_stderr, " --tolerance match region within this number of bases, default 5.\n"); fprintf(samtools_stderr, " --no-PG do not add an @PG line.\n"); sam_global_opt_help(samtools_stderr, "-.O..@-."); fprintf(samtools_stderr, "\nAbout: Soft clips read alignments where they match BED file defined regions.\n" "Default clipping is only on the 5' end.\n\n"); } int amplicon_clip_main(int argc, char **argv) { int c, ret; char wmode[4] = {'w', 'b', 0, 0}; char *bedfile = NULL, *fnout = "-"; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; htsThreadPool p = {NULL, 0}; samFile *in = NULL, *out = NULL, *reject = NULL; clipping_type clipping = soft_clip; cl_param_t param = {1, 0, 0, 0, 0, -1, -1, 0, 0, 1, 5, 0, NULL, NULL, NULL}; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'), {"no-PG", no_argument, NULL, 1002}, {"soft-clip", no_argument, NULL, 1003}, {"hard-clip", no_argument, NULL, 1004}, {"strand", no_argument, NULL, 1005}, {"clipped", no_argument, NULL, 1006}, {"fail", no_argument, NULL, 1007}, {"both-ends", no_argument, NULL, 1008}, {"filter-len", required_argument, NULL, 1009}, {"fail-len", required_argument, NULL, 1010}, {"no-excluded", no_argument, NULL, 1011}, {"rejects-file", required_argument, NULL, 1012}, {"primer-counts", required_argument, NULL, 1013}, {"original", no_argument, NULL, 1014}, {"keep-tag", no_argument, NULL, 1015}, {"tolerance", required_argument, NULL, 1016}, {"unmap-len", required_argument, NULL, 1017}, {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "b:@:o:O:f:u", lopts, NULL)) >= 0) { switch (c) { case 'b': bedfile = optarg; break; case 'o': fnout = optarg; break; case 'f': param.stats_file = optarg; break; case 'u': wmode[2] = '0'; break; case 1002: param.add_pg = 0; break; case 1003: clipping = soft_clip; break; case 1004: clipping = hard_clip; break; case 1005: param.use_strand = 1; break; case 1006: param.write_clipped = 1; break; case 1007: param.mark_fail = 1; break; case 1008: param.both = 1; break; case 1009: param.filter_len = atoi(optarg); break; case 1010: param.fail_len = atoi(optarg); break; case 1011: param.unmapped = 1; break; case 1012: param.rejects_file = optarg; break; case 1013: param.primer_counts_file = optarg; break; case 1014: param.oa_tag = 1; break; case 1015: param.del_tag = 0; break; case 1016: param.tol = atoi(optarg); break; case 1017: param.unmap_len = atoi(optarg); break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage(); samtools_exit(1); } } if (!bedfile) { usage(); return 1; } if (optind + 1 > argc) { usage(); return 1; } if (param.tol < 0) { fprintf(samtools_stderr, "[ampliconclip] warning: invalid tolerance of %d," " resetting tolerance to default of 5.\n", param.tol); param.tol = 5; } if ((in = sam_open_format(argv[optind], "rb", &ga.in)) == NULL) { print_error_errno("ampliconclip", "cannot open input file"); return 1; } sam_open_mode(wmode+1, fnout, NULL); if ((out = sam_open_format(fnout, wmode, &ga.out)) == NULL) { print_error_errno("ampliconclip", "cannot open output file"); return 1; } if (param.rejects_file) { sam_open_mode(wmode+1, param.rejects_file, NULL); if ((reject = sam_open_format(param.rejects_file, wmode, &ga.out)) == NULL) { print_error_errno("ampliconclip", "cannot open rejects file"); return 1; } } if (ga.nthreads > 0) { if (!(p.pool = hts_tpool_init(ga.nthreads))) { fprintf(samtools_stderr, "[ampliconclip] error: cannot create thread pool.\n"); return 1; } hts_set_opt(in, HTS_OPT_THREAD_POOL, &p); hts_set_opt(out, HTS_OPT_THREAD_POOL, &p); if (reject) { hts_set_opt(reject, HTS_OPT_THREAD_POOL, &p); } } param.arg_list = stringify_argv(argc + 1, argv - 1); ret = bam_clip(in, out, reject, bedfile, clipping, ¶m); // cleanup sam_close(in); if (sam_close(out) < 0) { fprintf(samtools_stderr, "[ampliconclip] error: error while closing output file %s.\n", argv[optind+1]); ret = 1; } if (reject) { if (sam_close(reject) < 0) { fprintf(samtools_stderr, "[ampliconclip] error: error while closing reject file %s.\n", param.rejects_file); ret = 1; } } if (p.pool) hts_tpool_destroy(p.pool); sam_global_args_free(&ga); free(param.arg_list); return ret; } pysam-0.23.0/samtools/bam_ampliconclip.h000066400000000000000000000035751475062545500202570ustar00rootroot00000000000000/* bam_ampliconclip.h -- shared functions between amplicon clip/stats Copyright (C) 2020-2021 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef BAM_AMPLICONCLIP_H #define BAM_AMPLICONCLIP_H #include "htslib/khash.h" typedef struct { int64_t left; int64_t right; char *name; char *score; int rev; int64_t num_reads; } bed_entry_t; typedef struct { bed_entry_t *bp; int64_t longest; int length; int size; } bed_entry_list_t; KHASH_MAP_INIT_STR(bed_list_hash, bed_entry_list_t) #define BED_LIST_INIT {NULL, 0, 0, 0, {0}} int load_bed_file_multi_ref(char *infile, int get_strand, int sort_by_pos, khash_t(bed_list_hash) *bed_lists, char ***ref_list, size_t *num_refs); void destroy_bed_hash(khash_t(bed_list_hash) *hash); #endif /* BAM_AMPLICONCLIP_H */ pysam-0.23.0/samtools/bam_aux.c000066400000000000000000000041531475062545500163660ustar00rootroot00000000000000/* bam_aux.c -- remaining aux field handling. Copyright (C) 2008-2010, 2013, 2015, 2019 Genome Research Ltd. Portions copyright (C) 2011 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include "htslib/sam.h" static inline int bam_aux_type2size(int x) { if (x == 'C' || x == 'c' || x == 'A') return 1; else if (x == 'S' || x == 's') return 2; else if (x == 'I' || x == 'i' || x == 'f' || x == 'F') return 4; else return 0; } #define __skip_tag(s) do { \ int type = toupper(*(s)); \ ++(s); \ if (type == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \ else if (type == 'B') (s) += 5 + bam_aux_type2size(*(s)) * (*(int32_t*)((s)+1)); \ else (s) += bam_aux_type2size(type); \ } while(0) int bam_aux_drop_other(bam1_t *b, uint8_t *s) { if (s) { uint8_t *p, *aux; aux = bam_get_aux(b); p = s - 2; __skip_tag(s); memmove(aux, p, s - p); b->l_data -= bam_get_l_aux(b) - (s - p); } else { b->l_data -= bam_get_l_aux(b); } return 0; } pysam-0.23.0/samtools/bam_aux.c.pysam.c000066400000000000000000000042101475062545500177310ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_aux.c -- remaining aux field handling. Copyright (C) 2008-2010, 2013, 2015, 2019 Genome Research Ltd. Portions copyright (C) 2011 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include "htslib/sam.h" static inline int bam_aux_type2size(int x) { if (x == 'C' || x == 'c' || x == 'A') return 1; else if (x == 'S' || x == 's') return 2; else if (x == 'I' || x == 'i' || x == 'f' || x == 'F') return 4; else return 0; } #define __skip_tag(s) do { \ int type = toupper(*(s)); \ ++(s); \ if (type == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \ else if (type == 'B') (s) += 5 + bam_aux_type2size(*(s)) * (*(int32_t*)((s)+1)); \ else (s) += bam_aux_type2size(type); \ } while(0) int bam_aux_drop_other(bam1_t *b, uint8_t *s) { if (s) { uint8_t *p, *aux; aux = bam_get_aux(b); p = s - 2; __skip_tag(s); memmove(aux, p, s - p); b->l_data -= bam_get_l_aux(b) - (s - p); } else { b->l_data -= bam_get_l_aux(b); } return 0; } pysam-0.23.0/samtools/bam_cat.c000066400000000000000000001024541475062545500163430ustar00rootroot00000000000000/* bam_cat.c -- efficiently concatenates bam files. Copyright (C) 2008-2009, 2011-2013, 2015-2017, 2019, 2021, 2023-2024 Genome Research Ltd. Modified SAMtools work copyright (C) 2010 Illumina, Inc. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notices and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* bam_cat can be used to concatenate BAM files. Under special circumstances, it can be used as an alternative to 'samtools merge' to concatenate multiple sorted files into a single sorted file. For this to work each file must be sorted, and the sorted files must be given as command line arguments in order such that the final read in file i is less than or equal to the first read in file i+1. This code is derived from the bam_reheader function in samtools 0.1.8 and modified to perform concatenation by Chris Saunders on behalf of Illumina. */ #include #include #include #include #include #include #include "htslib/bgzf.h" #include "htslib/sam.h" #include "htslib/cram.h" #include "htslib/kstring.h" #include "htslib/hfile.h" #include "samtools.h" #include "sam_opts.h" /// cat_check_merge_hdr - check compatibility and merge RG hearders merges RGon both CRAM and BAM. /** @param firstfile - pointer to the 1sr file opened in caller * @param nfn - number of files to be processed, including the firstfile * @param fn - array of file paths to be processed * @param h - sam header pointer which contains explicitly given header * @param vers_maj_p - cram major version set and send out for output creation * @param vers_min_p - cram min version set and send out for output creation * @param out_h - pointer to sam header pointer, outputs the merged header * returns array of opened samFile pointers on success and NULL on failure * This method has the merged header processing for cram and bam. * RG lines are merged for both cram and bam. For cram, version match for each * file and order match of RG lines are compared as well. * Note: it is a simple merge of RG lines alone. */ static samFile** cat_check_merge_hdr(samFile * const firstfile, int nfn, char * const *fn, const sam_hdr_t *h, int *vers_maj_p, int *vers_min_p, sam_hdr_t **out_h) { int i, vers_maj = -1, vers_min = -1; sam_hdr_t *new_h = NULL, *old_h = NULL; samFile *in = NULL; kstring_t ks = KS_INITIALIZE; samFile **files = calloc(nfn, sizeof(samFile *)); if(!files) { fprintf(stderr, "[%s] ERROR: failed to allocate space for file handles.\n", __func__); return NULL; } if (!out_h || !firstfile) { fprintf(stderr, "[%s] ERROR: header check failed.\n", __func__); goto fail; } if (*out_h) { //use header if one is already present new_h = *out_h; } else { if (h) { //use the explicit header given new_h = sam_hdr_dup(h); if (!new_h) { fprintf(stderr, "[%s] ERROR: header duplication failed.\n", __func__); goto fail; } } } for (i = 0; i < nfn; ++i) { int ki; //1st file is already open and passed, rest open locally files[i] = in = i ? sam_open(fn[i], "r") : firstfile; if (in == 0) { print_error_errno("cat", "fail to open file '%s'", fn[i]); goto fail; } if (firstfile->format.format != in->format.format) { print_error("cat", "File %s is of different format!", fn[i]); goto fail; } if (firstfile->format.format == cram) { //version check for cram cram_fd *in_c; in_c = in->fp.cram; int vmaj = cram_major_vers(in_c); int vmin = cram_minor_vers(in_c); if ((vers_maj != -1 && vers_maj != vmaj) || (vers_min != -1 && vers_min != vmin)) { fprintf(stderr, "[%s] ERROR: input files have differing version numbers.\n", __func__); goto fail; } vers_maj = vmaj; vers_min = vmin; } old_h = sam_hdr_read(in); if (!old_h) { fprintf(stderr, "[%s] ERROR: header reading for file '%s' filed.\n", __func__, fn[i]); goto fail; } if (!new_h) { new_h = sam_hdr_dup(old_h); if (!new_h) { fprintf(stderr, "[%s] ERROR: header duplication for file '%s' failed.\n", __func__, fn[i]); goto fail; } sam_hdr_destroy(old_h); old_h = NULL; continue; } //merge RG lines int old_count = sam_hdr_count_lines(old_h, "RG"); for (ki = 0; ki < old_count; ki++) { const char *old_name = sam_hdr_line_name(old_h, "RG", ki); if (old_name) { int new_i = sam_hdr_line_index(new_h, "RG", old_name); if (-1 == new_i) { // line does not exist in the new header if (sam_hdr_find_line_pos(old_h, "RG", ki, &ks) || !ks.s || sam_hdr_add_lines(new_h, ks.s, ks.l)) { fprintf(stderr, "[%s] ERROR: failed to add @RG line 'ID:%s' from file '%s'\n", __func__, old_name, fn[i]); goto fail; } ks_free(&ks); } } else { fprintf(stderr, "[%s] ERROR: failed to read %d @RG line from file '%s'\n", __func__, ki, fn[i]); goto fail; } } if (firstfile->format.format == cram && old_count > 1 && sam_hdr_count_lines(new_h, "RG") == old_count) { //RG order check for cram for (ki = 0; ki < old_count; ki++) { const char *old_name = sam_hdr_line_name(old_h, "RG", ki); const char *new_name = sam_hdr_line_name(new_h, "RG", ki); if (!old_name || !new_name || strcmp(old_name, new_name)) { fprintf(stderr, "[%s] ERROR: Same size @RG lists but differing order / contents\n", __func__); goto fail; } } } sam_hdr_destroy(old_h); old_h = NULL; } ks_free(&ks); if (vers_maj_p) { *vers_maj_p = vers_maj; } if (vers_min_p) { *vers_min_p = vers_min; } *out_h = new_h; return files; fail: ks_free(&ks); if (old_h) sam_hdr_destroy(old_h); if (new_h) sam_hdr_destroy(new_h); *out_h = NULL; for (i = 1; i < nfn; ++i) { //close files other than the firstfile if (files[i]) { sam_close(files[i]); } } free(files); return NULL; } /* ---------------------------------------------------------------------- * CRAM cat */ // Reports the number of CRAM containers spanning a specified region if // specified, or the entire file if not. // This is the implements the "samtools cat -q [-r reg]" functionality. // // Returns 0 on success, <0 on error. static int cram_query_ncont(int nfn, char * const *fn, char *reg) { int i; hts_idx_t *idx = NULL; sam_hdr_t *hdr = NULL; hts_itr_t *iter = NULL; samFile *in = NULL; for (i = 0; i < nfn; i++) { in = sam_open(fn[i], "r"); if (!in) { print_error_errno("cat", "Couldn't open file %s", fn[i]); return -1; } idx = sam_index_load(in, fn[i]); if (!idx) { print_error("cat", "No index found"); goto err; } off_t cstart = 0, cend = 0; if (reg) { sam_hdr_t *hdr = sam_hdr_read(in); hts_itr_t *iter = sam_itr_querys(idx, hdr, reg); if (!hdr) { print_error("cat", "Unable to read header"); goto err; } if (!iter) { print_error("cat", "Unable to parse region"); goto err; } if (cram_index_extents(in->fp.cram, iter->tid, iter->beg, iter->end, &cstart, &cend) < 0) { print_error("cat", "Failed to query index"); goto err; } hts_itr_destroy(iter); sam_hdr_destroy(hdr); } int64_t first, last; int64_t nc = cram_num_containers_between(in->fp.cram, cstart, cend, &first, &last); printf("%s\t%"PRId64"\t%"PRId64"\t%"PRId64"\n", fn[i], nc, first, last); sam_close(in); hts_idx_destroy(idx); } return 0; err: if (idx) hts_idx_destroy(idx); if (hdr) sam_hdr_destroy(hdr); if (iter) hts_itr_destroy(iter); sam_close(in); return -1; } // Container range #:A-B or #:A. // Returns 0 on success, -1 on failure. static int cram_handle_cnum_region(cram_fd *fd, hts_idx_t *idx, char *reg, off_t *cstart, off_t *cend) { int cnum_start, cnum_end; // container versions int n = sscanf(reg, "#:%d-%d", &cnum_start, &cnum_end); if (n == 0) { print_error("cat", "ERROR: Malformed region: %s", reg); return -1; } else if (n == 1) { cnum_end = cnum_start; } int64_t nc = cram_num_containers(fd); if (cnum_end >= nc) { print_error("cat", "Too many containers. " "The end range should be < %"PRId64, nc); return -1; } // Container number to offset *cstart = cram_container_num2offset(fd, cnum_start); *cend = cram_container_num2offset(fd, cnum_end); if (*cstart < 0 || *cend < 0) return -1; // Seek manually return cram_seek(fd, *cstart, SEEK_SET); } // Normal range chr:start-end. // Returns an hts iterator on success, NULL on failure. static hts_itr_t *cram_handle_region(cram_fd *fd, hts_idx_t *idx, sam_hdr_t *h, char *reg, off_t *cstart, off_t *cend) { hts_itr_t *iter; if (!idx) { fprintf(stderr, "[%s] ERROR: No index found.\n", __func__); return NULL; } // This does an implicit seek and modifies the cram_fd. if (!(iter = sam_itr_querys(idx, h, reg))) { print_error("cat", "Unable to parse region %s", reg); return NULL; } if (cram_index_extents(fd, iter->tid, iter->beg, iter->end, cstart, cend) < 0) { print_error("cat", "Failed to query index"); return NULL; } return iter; } // Handle the -p A/B option to subdivide our region or file into portions. // Updates cstart/cend. // returns 0 on success (do something), // 1 on success (but nothing to do), // -1 on failure. static int cram_subdivide_part(cram_fd *fd, hts_idx_t *idx, char *part, off_t *cstart, off_t *cend) { int a, b; // Part N of M if (sscanf(part, "%d/%d", &a, &b) != 2) { print_error("cat", "malformed region %s. Should be e.g. '1/10'", part); return -1; } // Inclusive container numbers for range, 0 to NC-1 // Our part N/M is in container percentages as we can't have // partial containers, so convert to that first. int64_t cnum1, cnum2; if (cstart) { cnum1 = cram_container_offset2num(fd, *cstart); cnum2 = cram_container_offset2num(fd, *cend); } else { cnum1 = 0; cnum2 = cram_num_containers(fd)-1; } // Subdivide cnum1/cnum2 container numbers to new range cnum_start/end int64_t nc = cnum2 - cnum1 + 1; if (b > nc) b = nc; int cnum_start = (a-1)*(double)nc/b; int cnum_end = a*(double)nc/b - 1; if (cnum_start < 0 || cnum_end >= nc) return 1; // Then convert back to file offsets so we can seek and do htell // to detect EOR/EOF. *cstart = cram_container_num2offset(fd, cnum_start + cnum1); *cend = cram_container_num2offset(fd, cnum_end + cnum1); return 0; } // The main cram_cat interface. // Returns 0 on success, < 0 on error. int cram_cat(samFile * const firstfile, int nfn, char * const *fn, const sam_hdr_t *h, const char* outcram, sam_global_args *ga, char *arg_list, int no_pg, char *reg, char *part, int fast_reg) { samFile *out = NULL; cram_fd *out_c; int i, vers_maj, vers_min, ret = -1; sam_hdr_t *new_h = NULL; samFile **files = NULL; hts_idx_t *idx = NULL; hts_itr_t *iter = NULL; sam_hdr_t *old_h = NULL; // Check consistent versioning and compatible headers; // merges RG lines, opens all files and returns them that multiple // non-seekable stream inputs can be handled if (!(files = cat_check_merge_hdr(firstfile, nfn, fn, h, &vers_maj, &vers_min, &new_h))) return -1; if (!new_h) { print_error_errno("cat", "failed to make output header"); goto closefiles; } /* Open the file with cram_vers */ char vers[100]; snprintf(vers, sizeof(vers), "%d.%d", vers_maj, vers_min); // Can override level=1 with e.g. "--output-fmt-option level=9" out = sam_open_format(outcram, "wc1", &ga->out); if (out == 0) { print_error_errno("cat", "fail to open output file '%s'", outcram); goto closefiles; } out_c = out->fp.cram; cram_set_option(out_c, CRAM_OPT_VERSION, vers); if (!no_pg && sam_hdr_add_pg(new_h, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) goto closefiles; if (sam_hdr_write(out, new_h) < 0) { print_error_errno("cat", "Couldn't write header"); goto closefiles; } out_c = out->fp.cram; for (i = 0; i < nfn; ++i) { samFile *in; cram_fd *in_c; cram_container *c; int new_rg = -1; in = files[i]; if (in == 0) { print_error_errno("cat", "fail to open file '%s'", fn[i]); goto closefiles; } in_c = in->fp.cram; old_h = sam_hdr_read(in); if (!old_h) { print_error("cat", "fail to read the header of file '%s'", fn[i]); goto closefiles; } // Compute RG mapping if suitable for changing. if (sam_hdr_count_lines(old_h, "RG") == 1) { const char *old_name = sam_hdr_line_name(old_h, "RG", 0); if (old_name) { new_rg = sam_hdr_line_index(new_h, "RG", old_name); if (new_rg < 0) { print_error("cat", "fail to find @RG line '%s' in the new header", old_name); goto closefiles; } } else { print_error("cat", "fail to find @RG line in file '%s'", fn[i]); goto closefiles; } } else { new_rg = 0; } // We have multiple region syntax. Either the standard chr:start-end // or a cat-specific #:num-num for explicit container numbers. // Both of these seek to a specific file offset and also have the // end offset known so we can use htell to detect when we're done. // Those offsets are in cstart and cend. // // However for the e.g. -p 1/10 syntax we need to know the container // numbers corresponding to the cstart/cend offsets as we can't // start half way through a container when doing fractions. // These are cnum1 and cnum2. (We could short cut this for the // #:num-num, but it's simpler to just treat all regions identically.) off_t cstart = 0, cend = 0; int filter_by_cnum = 0; if (reg || part) { idx = sam_index_load(in, fn[i]); if (!idx) { print_error("cat", "failed to load index"); goto closefiles; } } if (reg) { if (strncmp(reg, "#:", 2) == 0) { // Region as container numbers if (cram_handle_cnum_region(in_c, idx, reg, &cstart,&cend) < 0) goto closefiles; filter_by_cnum = 1; } else { // Normal range chr:start-end if (!(iter = cram_handle_region(in_c, idx, old_h, reg, &cstart, &cend))) goto closefiles; } } // We can also take a range above and subdivide it into parts. // Eg -r chr1 -p 1/10 (... to -p 10/10). Part only implies // portions of the entire file. if (part) { int r = cram_subdivide_part(in_c, idx, part, &cstart, &cend); if (r != 0) { if (r > 0) // Not an error, just nothing to do ret = 0; goto closefiles; } } if (cstart) // reg or part if (0 != cram_seek(in_c, cstart, SEEK_SET)) goto closefiles; // Make refid -2 ("*") come after other chromosomes, for easy sort int itid = iter ? (iter->tid == HTS_IDX_NOCOOR ? INT_MAX : iter->tid) : 0; int last_ref_id = -99; off_t before_hdr = htell(cram_fd_get_fp(in_c)); // Copy contains and blocks within them while ((c = cram_read_container(in_c))) { if (cram_container_is_empty(in_c)) { cram_block *blk; // Container compression header if (!(blk = cram_read_block(in_c))) goto closefiles; cram_free_block(blk); cram_free_container(c); continue; } int filter = 0; // If we have just one RG key and new_rg != 0 then // we need to edit the compression header. IF WE CAN. if (new_rg) { if (reg) { print_error("cat", "Cannot specify a region while " "transcoding RG lines"); goto closefiles; } int zero = 0; //fprintf(stderr, "Transcode RG %d to %d\n", 0, new_rg); cram_transcode_rg(in_c, out_c, c, 1, &zero, &new_rg); } else { int32_t num_slices; if (reg) { if (before_hdr > cend) { cram_free_container(c); break; } } // For chr:start-end regions, do we need to filter or skip? if (iter && reg) { int refid; hts_pos_t start, span, end; cram_container_get_coords(c, &refid, &start, &span); end = start+span; // Make refid -1 ("*") come after other chromosomes if (refid == -1) refid = INT_MAX; if (refid > itid || start > iter->end) { // Beyond the requested range break; } else if (refid == -2) { // Multi-ref containers. We only support this if // the RI data series is in a container by itself. filter = 3; } else if (refid < itid || end < iter->beg) { // Skip, in case of mixed size containers. // Eg: Use "=", skip "-". // ==========|======|= // ---- ==|== ==|== ---- // ----- | ==== ---- filter = 2; } else if (start < iter->beg || end > iter->end) { // Container overlaps region. // Fast mode just copies overlapping containers. // Slow mode does a precise filtering by reading and // filtering each record in turn so it's the same as // a samtools view command. filter = fast_reg ? 0 : 1; } // else we're in an "internal" container, so just copy } if (filter && last_ref_id == -1 && itid == INT_MAX) // Multi-ref containers consisting solely of ref "*" are // common, but if it's sorted then we know it's "*" from // here on so we don't need to filter despite multi-ref. filter = 0; if (filter) { // Filter or skip cram_filter_container(in_c, out_c, c, &last_ref_id); } else { // Copy. Consider adding a cram_copy_container API instead. // Container compression header cram_block *blk; if (!(blk = cram_read_block(in_c))) goto closefiles; // Not switching rg so do the usual read/write loop if (cram_write_container(out_c, c) != 0) goto closefiles; // Contatiner compression header if (cram_write_block(out_c, blk) != 0) { cram_free_block(blk); goto closefiles; } // Container num_blocks can be invalid, due to a bug. // Instead we iterate in slice context instead. (void)cram_container_get_landmarks(c, &num_slices); if (cram_copy_slice(in_c, out_c, num_slices) < 0) { cram_free_block(blk); goto closefiles; } cram_free_block(blk); } } cram_free_container(c); // Location of next container start before_hdr = htell(cram_fd_get_fp(in_c)); if (filter_by_cnum && before_hdr > cend) break; } sam_hdr_destroy(old_h); old_h = NULL; if (idx) { hts_idx_destroy(idx); idx = NULL; } if (iter) { hts_itr_destroy(iter); iter = NULL; } } ret = 0; closefiles: if (old_h) sam_hdr_destroy(old_h); if (idx) hts_idx_destroy(idx); if (iter) hts_itr_destroy(iter); if (out) sam_close(out); if (new_h) sam_hdr_destroy(new_h); for (i = 1; i < nfn; ++i) { //skip firstfile and close rest if (files[i]) { sam_close(files[i]); } } free(files); return ret; } /* ---------------------------------------------------------------------- * BAM cat */ #define BUF_SIZE 0x10000 #define GZIPID1 31 #define GZIPID2 139 #define BGZF_EMPTY_BLOCK_SIZE 28 int bam_cat(samFile * const firstfile, int nfn, char * const *fn, sam_hdr_t *h, const char* outbam, char *arg_list, int no_pg) { BGZF *fp = NULL, *in = NULL; uint8_t *buf = NULL; uint8_t ebuf[BGZF_EMPTY_BLOCK_SIZE]; const int es=BGZF_EMPTY_BLOCK_SIZE; int i; samFile **files = NULL; sam_hdr_t *new_h = NULL; /* merges RG lines, opens all files and returns them that multiple non-seekable stream inputs can be handled */ if (!(files = cat_check_merge_hdr(firstfile, nfn, fn, h, NULL, NULL, &new_h))) return -1; if (!new_h) { print_error_errno("cat", "failed to make output header"); goto fail; } fp = strcmp(outbam, "-")? bgzf_open(outbam, "w") : bgzf_fdopen(fileno(stdout), "w"); if (fp == 0) { print_error_errno("cat", "fail to open output file '%s'", outbam); goto fail; } if (!no_pg && sam_hdr_add_pg(new_h, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) goto fail; if (bam_hdr_write(fp, new_h) < 0) { print_error_errno("cat", "Couldn't write header"); goto fail; } buf = (uint8_t*) malloc(BUF_SIZE); if (!buf) { fprintf(stderr, "[%s] Couldn't allocate buffer\n", __func__); goto fail; } for(i = 0; i < nfn; ++i){ int len,j; in = files[i]->fp.bgzf; if (in == 0) { print_error_errno("cat", "fail to open file '%s'", fn[i]); goto fail; } if (in->is_write) goto fail; if (in->block_offset < in->block_length) { if (bgzf_write(fp, (char *)in->uncompressed_block + in->block_offset, in->block_length - in->block_offset) < 0) goto write_fail; if (bgzf_flush(fp) != 0) goto write_fail; } j=0; while ((len = bgzf_raw_read(in, buf, BUF_SIZE)) > 0) { if(len= 0) { switch (c) { case 'h': { samFile *fph = sam_open(optarg, "r"); if (fph == 0) { fprintf(stderr, "[%s] ERROR: fail to read the header from '%s'.\n", __func__, optarg); ret = 1; goto end; } h = sam_hdr_read(fph); if (h == NULL) { fprintf(stderr, "[%s] ERROR: failed to read the header from '%s'.\n", __func__, optarg); ret = 1; goto end; } sam_close(fph); break; } case 'o': outfn = strdup(optarg); break; case 'b': { // add file names in "optarg" to the list // of files to concatenate int nfns; char **fns_read = hts_readlines(optarg, &nfns); if (fns_read) { infns = realloc(infns, (infns_size + nfns) * sizeof(char*)); if (infns == NULL) { ret = 1; goto end; } memcpy(infns+infns_size, fns_read, nfns * sizeof(char*)); infns_size += nfns; free(fns_read); } else { print_error("cat", "Invalid file list \"%s\"", optarg); ret = 1; } break; } case 1: no_pg = 1; break; case 'r': reg = optarg; break; case 'p': part = optarg; break; case 'f': fast_mode = 1; break; case 'q': query_ncont=1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage=1; break; } } if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) { print_error("cat", "failed to create arg_list"); ret = 1; goto end; } // Append files specified in argv to the list. int nargv_fns = argc - optind; if (nargv_fns > 0) { infns = realloc(infns, (infns_size + nargv_fns) * sizeof(char*)); if (infns == NULL) { ret = 1; goto end; } memcpy(infns + infns_size, argv + optind, nargv_fns * sizeof(char*)); } // Require at least one input file if (infns_size + nargv_fns == 0 || usage) { fprintf(stderr, "Usage: samtools cat [options] [... ]\n"); fprintf(stderr, " samtools cat [options] [... ]\n\n"); fprintf(stderr, "Concatenate BAM or CRAM files, first those in , then those\non the command line.\n\n"); fprintf(stderr, "Options: -b FILE list of input BAM/CRAM file names, one per line\n"); fprintf(stderr, " -h FILE copy the header from FILE [default is 1st input file]\n"); fprintf(stderr, " -o FILE output BAM/CRAM\n"); fprintf(stderr, " --no-PG do not add a PG line\n"); fprintf(stderr, "\nCRAM only options for filtering:\n"); fprintf(stderr, " -r REG filter to region REG.\n"); fprintf(stderr, " REG can also be #:cstart-cend for specific container numbers\n"); fprintf(stderr, " -p N/M Specify part N of M (where N is 1 to M inclusive)\n"); fprintf(stderr, " -f Fast mode: don't filter containers to exactly match region\n"); fprintf(stderr, " -q Query the total number of indexed containers\n"); fprintf(stderr, "\nStandard options:\n"); sam_global_opt_help(stderr, "---.---."); ret = 1; goto end; } in = sam_open(infns[0], "r"); if (!in) { print_error_errno("cat", "failed to open file '%s'", infns[0]); ret = 1; goto end; } switch (hts_get_format(in)->format) { case bam: if (bam_cat(in, infns_size+nargv_fns, infns, h, outfn? outfn : "-", arg_list, no_pg) < 0) ret = 1; break; case cram: if (query_ncont) { if (cram_query_ncont(infns_size+nargv_fns, infns, reg) < 0) ret = 1; } else { if (cram_cat(in, infns_size+nargv_fns, infns, h, outfn? outfn : "-", &ga, arg_list, no_pg, reg, part, fast_mode) < 0) ret = 1; } break; default: fprintf(stderr, "[%s] ERROR: input is not BAM or CRAM\n", __func__); ret = 1; } sam_close(in); end: if (infns_size > 0) { int i; for (i=0; i #include #include #include #include #include #include "htslib/bgzf.h" #include "htslib/sam.h" #include "htslib/cram.h" #include "htslib/kstring.h" #include "htslib/hfile.h" #include "samtools.h" #include "sam_opts.h" /// cat_check_merge_hdr - check compatibility and merge RG hearders merges RGon both CRAM and BAM. /** @param firstfile - pointer to the 1sr file opened in caller * @param nfn - number of files to be processed, including the firstfile * @param fn - array of file paths to be processed * @param h - sam header pointer which contains explicitly given header * @param vers_maj_p - cram major version set and send out for output creation * @param vers_min_p - cram min version set and send out for output creation * @param out_h - pointer to sam header pointer, outputs the merged header * returns array of opened samFile pointers on success and NULL on failure * This method has the merged header processing for cram and bam. * RG lines are merged for both cram and bam. For cram, version match for each * file and order match of RG lines are compared as well. * Note: it is a simple merge of RG lines alone. */ static samFile** cat_check_merge_hdr(samFile * const firstfile, int nfn, char * const *fn, const sam_hdr_t *h, int *vers_maj_p, int *vers_min_p, sam_hdr_t **out_h) { int i, vers_maj = -1, vers_min = -1; sam_hdr_t *new_h = NULL, *old_h = NULL; samFile *in = NULL; kstring_t ks = KS_INITIALIZE; samFile **files = calloc(nfn, sizeof(samFile *)); if(!files) { fprintf(samtools_stderr, "[%s] ERROR: failed to allocate space for file handles.\n", __func__); return NULL; } if (!out_h || !firstfile) { fprintf(samtools_stderr, "[%s] ERROR: header check failed.\n", __func__); goto fail; } if (*out_h) { //use header if one is already present new_h = *out_h; } else { if (h) { //use the explicit header given new_h = sam_hdr_dup(h); if (!new_h) { fprintf(samtools_stderr, "[%s] ERROR: header duplication failed.\n", __func__); goto fail; } } } for (i = 0; i < nfn; ++i) { int ki; //1st file is already open and passed, rest open locally files[i] = in = i ? sam_open(fn[i], "r") : firstfile; if (in == 0) { print_error_errno("cat", "fail to open file '%s'", fn[i]); goto fail; } if (firstfile->format.format != in->format.format) { print_error("cat", "File %s is of different format!", fn[i]); goto fail; } if (firstfile->format.format == cram) { //version check for cram cram_fd *in_c; in_c = in->fp.cram; int vmaj = cram_major_vers(in_c); int vmin = cram_minor_vers(in_c); if ((vers_maj != -1 && vers_maj != vmaj) || (vers_min != -1 && vers_min != vmin)) { fprintf(samtools_stderr, "[%s] ERROR: input files have differing version numbers.\n", __func__); goto fail; } vers_maj = vmaj; vers_min = vmin; } old_h = sam_hdr_read(in); if (!old_h) { fprintf(samtools_stderr, "[%s] ERROR: header reading for file '%s' filed.\n", __func__, fn[i]); goto fail; } if (!new_h) { new_h = sam_hdr_dup(old_h); if (!new_h) { fprintf(samtools_stderr, "[%s] ERROR: header duplication for file '%s' failed.\n", __func__, fn[i]); goto fail; } sam_hdr_destroy(old_h); old_h = NULL; continue; } //merge RG lines int old_count = sam_hdr_count_lines(old_h, "RG"); for (ki = 0; ki < old_count; ki++) { const char *old_name = sam_hdr_line_name(old_h, "RG", ki); if (old_name) { int new_i = sam_hdr_line_index(new_h, "RG", old_name); if (-1 == new_i) { // line does not exist in the new header if (sam_hdr_find_line_pos(old_h, "RG", ki, &ks) || !ks.s || sam_hdr_add_lines(new_h, ks.s, ks.l)) { fprintf(samtools_stderr, "[%s] ERROR: failed to add @RG line 'ID:%s' from file '%s'\n", __func__, old_name, fn[i]); goto fail; } ks_free(&ks); } } else { fprintf(samtools_stderr, "[%s] ERROR: failed to read %d @RG line from file '%s'\n", __func__, ki, fn[i]); goto fail; } } if (firstfile->format.format == cram && old_count > 1 && sam_hdr_count_lines(new_h, "RG") == old_count) { //RG order check for cram for (ki = 0; ki < old_count; ki++) { const char *old_name = sam_hdr_line_name(old_h, "RG", ki); const char *new_name = sam_hdr_line_name(new_h, "RG", ki); if (!old_name || !new_name || strcmp(old_name, new_name)) { fprintf(samtools_stderr, "[%s] ERROR: Same size @RG lists but differing order / contents\n", __func__); goto fail; } } } sam_hdr_destroy(old_h); old_h = NULL; } ks_free(&ks); if (vers_maj_p) { *vers_maj_p = vers_maj; } if (vers_min_p) { *vers_min_p = vers_min; } *out_h = new_h; return files; fail: ks_free(&ks); if (old_h) sam_hdr_destroy(old_h); if (new_h) sam_hdr_destroy(new_h); *out_h = NULL; for (i = 1; i < nfn; ++i) { //close files other than the firstfile if (files[i]) { sam_close(files[i]); } } free(files); return NULL; } /* ---------------------------------------------------------------------- * CRAM cat */ // Reports the number of CRAM containers spanning a specified region if // specified, or the entire file if not. // This is the implements the "samtools cat -q [-r reg]" functionality. // // Returns 0 on success, <0 on error. static int cram_query_ncont(int nfn, char * const *fn, char *reg) { int i; hts_idx_t *idx = NULL; sam_hdr_t *hdr = NULL; hts_itr_t *iter = NULL; samFile *in = NULL; for (i = 0; i < nfn; i++) { in = sam_open(fn[i], "r"); if (!in) { print_error_errno("cat", "Couldn't open file %s", fn[i]); return -1; } idx = sam_index_load(in, fn[i]); if (!idx) { print_error("cat", "No index found"); goto err; } off_t cstart = 0, cend = 0; if (reg) { sam_hdr_t *hdr = sam_hdr_read(in); hts_itr_t *iter = sam_itr_querys(idx, hdr, reg); if (!hdr) { print_error("cat", "Unable to read header"); goto err; } if (!iter) { print_error("cat", "Unable to parse region"); goto err; } if (cram_index_extents(in->fp.cram, iter->tid, iter->beg, iter->end, &cstart, &cend) < 0) { print_error("cat", "Failed to query index"); goto err; } hts_itr_destroy(iter); sam_hdr_destroy(hdr); } int64_t first, last; int64_t nc = cram_num_containers_between(in->fp.cram, cstart, cend, &first, &last); fprintf(samtools_stdout, "%s\t%"PRId64"\t%"PRId64"\t%"PRId64"\n", fn[i], nc, first, last); sam_close(in); hts_idx_destroy(idx); } return 0; err: if (idx) hts_idx_destroy(idx); if (hdr) sam_hdr_destroy(hdr); if (iter) hts_itr_destroy(iter); sam_close(in); return -1; } // Container range #:A-B or #:A. // Returns 0 on success, -1 on failure. static int cram_handle_cnum_region(cram_fd *fd, hts_idx_t *idx, char *reg, off_t *cstart, off_t *cend) { int cnum_start, cnum_end; // container versions int n = sscanf(reg, "#:%d-%d", &cnum_start, &cnum_end); if (n == 0) { print_error("cat", "ERROR: Malformed region: %s", reg); return -1; } else if (n == 1) { cnum_end = cnum_start; } int64_t nc = cram_num_containers(fd); if (cnum_end >= nc) { print_error("cat", "Too many containers. " "The end range should be < %"PRId64, nc); return -1; } // Container number to offset *cstart = cram_container_num2offset(fd, cnum_start); *cend = cram_container_num2offset(fd, cnum_end); if (*cstart < 0 || *cend < 0) return -1; // Seek manually return cram_seek(fd, *cstart, SEEK_SET); } // Normal range chr:start-end. // Returns an hts iterator on success, NULL on failure. static hts_itr_t *cram_handle_region(cram_fd *fd, hts_idx_t *idx, sam_hdr_t *h, char *reg, off_t *cstart, off_t *cend) { hts_itr_t *iter; if (!idx) { fprintf(samtools_stderr, "[%s] ERROR: No index found.\n", __func__); return NULL; } // This does an implicit seek and modifies the cram_fd. if (!(iter = sam_itr_querys(idx, h, reg))) { print_error("cat", "Unable to parse region %s", reg); return NULL; } if (cram_index_extents(fd, iter->tid, iter->beg, iter->end, cstart, cend) < 0) { print_error("cat", "Failed to query index"); return NULL; } return iter; } // Handle the -p A/B option to subdivide our region or file into portions. // Updates cstart/cend. // returns 0 on success (do something), // 1 on success (but nothing to do), // -1 on failure. static int cram_subdivide_part(cram_fd *fd, hts_idx_t *idx, char *part, off_t *cstart, off_t *cend) { int a, b; // Part N of M if (sscanf(part, "%d/%d", &a, &b) != 2) { print_error("cat", "malformed region %s. Should be e.g. '1/10'", part); return -1; } // Inclusive container numbers for range, 0 to NC-1 // Our part N/M is in container percentages as we can't have // partial containers, so convert to that first. int64_t cnum1, cnum2; if (cstart) { cnum1 = cram_container_offset2num(fd, *cstart); cnum2 = cram_container_offset2num(fd, *cend); } else { cnum1 = 0; cnum2 = cram_num_containers(fd)-1; } // Subdivide cnum1/cnum2 container numbers to new range cnum_start/end int64_t nc = cnum2 - cnum1 + 1; if (b > nc) b = nc; int cnum_start = (a-1)*(double)nc/b; int cnum_end = a*(double)nc/b - 1; if (cnum_start < 0 || cnum_end >= nc) return 1; // Then convert back to file offsets so we can seek and do htell // to detect EOR/EOF. *cstart = cram_container_num2offset(fd, cnum_start + cnum1); *cend = cram_container_num2offset(fd, cnum_end + cnum1); return 0; } // The main cram_cat interface. // Returns 0 on success, < 0 on error. int cram_cat(samFile * const firstfile, int nfn, char * const *fn, const sam_hdr_t *h, const char* outcram, sam_global_args *ga, char *arg_list, int no_pg, char *reg, char *part, int fast_reg) { samFile *out = NULL; cram_fd *out_c; int i, vers_maj, vers_min, ret = -1; sam_hdr_t *new_h = NULL; samFile **files = NULL; hts_idx_t *idx = NULL; hts_itr_t *iter = NULL; sam_hdr_t *old_h = NULL; // Check consistent versioning and compatible headers; // merges RG lines, opens all files and returns them that multiple // non-seekable stream inputs can be handled if (!(files = cat_check_merge_hdr(firstfile, nfn, fn, h, &vers_maj, &vers_min, &new_h))) return -1; if (!new_h) { print_error_errno("cat", "failed to make output header"); goto closefiles; } /* Open the file with cram_vers */ char vers[100]; snprintf(vers, sizeof(vers), "%d.%d", vers_maj, vers_min); // Can override level=1 with e.g. "--output-fmt-option level=9" out = sam_open_format(outcram, "wc1", &ga->out); if (out == 0) { print_error_errno("cat", "fail to open output file '%s'", outcram); goto closefiles; } out_c = out->fp.cram; cram_set_option(out_c, CRAM_OPT_VERSION, vers); if (!no_pg && sam_hdr_add_pg(new_h, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) goto closefiles; if (sam_hdr_write(out, new_h) < 0) { print_error_errno("cat", "Couldn't write header"); goto closefiles; } out_c = out->fp.cram; for (i = 0; i < nfn; ++i) { samFile *in; cram_fd *in_c; cram_container *c; int new_rg = -1; in = files[i]; if (in == 0) { print_error_errno("cat", "fail to open file '%s'", fn[i]); goto closefiles; } in_c = in->fp.cram; old_h = sam_hdr_read(in); if (!old_h) { print_error("cat", "fail to read the header of file '%s'", fn[i]); goto closefiles; } // Compute RG mapping if suitable for changing. if (sam_hdr_count_lines(old_h, "RG") == 1) { const char *old_name = sam_hdr_line_name(old_h, "RG", 0); if (old_name) { new_rg = sam_hdr_line_index(new_h, "RG", old_name); if (new_rg < 0) { print_error("cat", "fail to find @RG line '%s' in the new header", old_name); goto closefiles; } } else { print_error("cat", "fail to find @RG line in file '%s'", fn[i]); goto closefiles; } } else { new_rg = 0; } // We have multiple region syntax. Either the standard chr:start-end // or a cat-specific #:num-num for explicit container numbers. // Both of these seek to a specific file offset and also have the // end offset known so we can use htell to detect when we're done. // Those offsets are in cstart and cend. // // However for the e.g. -p 1/10 syntax we need to know the container // numbers corresponding to the cstart/cend offsets as we can't // start half way through a container when doing fractions. // These are cnum1 and cnum2. (We could short cut this for the // #:num-num, but it's simpler to just treat all regions identically.) off_t cstart = 0, cend = 0; int filter_by_cnum = 0; if (reg || part) { idx = sam_index_load(in, fn[i]); if (!idx) { print_error("cat", "failed to load index"); goto closefiles; } } if (reg) { if (strncmp(reg, "#:", 2) == 0) { // Region as container numbers if (cram_handle_cnum_region(in_c, idx, reg, &cstart,&cend) < 0) goto closefiles; filter_by_cnum = 1; } else { // Normal range chr:start-end if (!(iter = cram_handle_region(in_c, idx, old_h, reg, &cstart, &cend))) goto closefiles; } } // We can also take a range above and subdivide it into parts. // Eg -r chr1 -p 1/10 (... to -p 10/10). Part only implies // portions of the entire file. if (part) { int r = cram_subdivide_part(in_c, idx, part, &cstart, &cend); if (r != 0) { if (r > 0) // Not an error, just nothing to do ret = 0; goto closefiles; } } if (cstart) // reg or part if (0 != cram_seek(in_c, cstart, SEEK_SET)) goto closefiles; // Make refid -2 ("*") come after other chromosomes, for easy sort int itid = iter ? (iter->tid == HTS_IDX_NOCOOR ? INT_MAX : iter->tid) : 0; int last_ref_id = -99; off_t before_hdr = htell(cram_fd_get_fp(in_c)); // Copy contains and blocks within them while ((c = cram_read_container(in_c))) { if (cram_container_is_empty(in_c)) { cram_block *blk; // Container compression header if (!(blk = cram_read_block(in_c))) goto closefiles; cram_free_block(blk); cram_free_container(c); continue; } int filter = 0; // If we have just one RG key and new_rg != 0 then // we need to edit the compression header. IF WE CAN. if (new_rg) { if (reg) { print_error("cat", "Cannot specify a region while " "transcoding RG lines"); goto closefiles; } int zero = 0; //fprintf(samtools_stderr, "Transcode RG %d to %d\n", 0, new_rg); cram_transcode_rg(in_c, out_c, c, 1, &zero, &new_rg); } else { int32_t num_slices; if (reg) { if (before_hdr > cend) { cram_free_container(c); break; } } // For chr:start-end regions, do we need to filter or skip? if (iter && reg) { int refid; hts_pos_t start, span, end; cram_container_get_coords(c, &refid, &start, &span); end = start+span; // Make refid -1 ("*") come after other chromosomes if (refid == -1) refid = INT_MAX; if (refid > itid || start > iter->end) { // Beyond the requested range break; } else if (refid == -2) { // Multi-ref containers. We only support this if // the RI data series is in a container by itself. filter = 3; } else if (refid < itid || end < iter->beg) { // Skip, in case of mixed size containers. // Eg: Use "=", skip "-". // ==========|======|= // ---- ==|== ==|== ---- // ----- | ==== ---- filter = 2; } else if (start < iter->beg || end > iter->end) { // Container overlaps region. // Fast mode just copies overlapping containers. // Slow mode does a precise filtering by reading and // filtering each record in turn so it's the same as // a samtools view command. filter = fast_reg ? 0 : 1; } // else we're in an "internal" container, so just copy } if (filter && last_ref_id == -1 && itid == INT_MAX) // Multi-ref containers consisting solely of ref "*" are // common, but if it's sorted then we know it's "*" from // here on so we don't need to filter despite multi-ref. filter = 0; if (filter) { // Filter or skip cram_filter_container(in_c, out_c, c, &last_ref_id); } else { // Copy. Consider adding a cram_copy_container API instead. // Container compression header cram_block *blk; if (!(blk = cram_read_block(in_c))) goto closefiles; // Not switching rg so do the usual read/write loop if (cram_write_container(out_c, c) != 0) goto closefiles; // Contatiner compression header if (cram_write_block(out_c, blk) != 0) { cram_free_block(blk); goto closefiles; } // Container num_blocks can be invalid, due to a bug. // Instead we iterate in slice context instead. (void)cram_container_get_landmarks(c, &num_slices); if (cram_copy_slice(in_c, out_c, num_slices) < 0) { cram_free_block(blk); goto closefiles; } cram_free_block(blk); } } cram_free_container(c); // Location of next container start before_hdr = htell(cram_fd_get_fp(in_c)); if (filter_by_cnum && before_hdr > cend) break; } sam_hdr_destroy(old_h); old_h = NULL; if (idx) { hts_idx_destroy(idx); idx = NULL; } if (iter) { hts_itr_destroy(iter); iter = NULL; } } ret = 0; closefiles: if (old_h) sam_hdr_destroy(old_h); if (idx) hts_idx_destroy(idx); if (iter) hts_itr_destroy(iter); if (out) sam_close(out); if (new_h) sam_hdr_destroy(new_h); for (i = 1; i < nfn; ++i) { //skip firstfile and close rest if (files[i]) { sam_close(files[i]); } } free(files); return ret; } /* ---------------------------------------------------------------------- * BAM cat */ #define BUF_SIZE 0x10000 #define GZIPID1 31 #define GZIPID2 139 #define BGZF_EMPTY_BLOCK_SIZE 28 int bam_cat(samFile * const firstfile, int nfn, char * const *fn, sam_hdr_t *h, const char* outbam, char *arg_list, int no_pg) { BGZF *fp = NULL, *in = NULL; uint8_t *buf = NULL; uint8_t ebuf[BGZF_EMPTY_BLOCK_SIZE]; const int es=BGZF_EMPTY_BLOCK_SIZE; int i; samFile **files = NULL; sam_hdr_t *new_h = NULL; /* merges RG lines, opens all files and returns them that multiple non-seekable stream inputs can be handled */ if (!(files = cat_check_merge_hdr(firstfile, nfn, fn, h, NULL, NULL, &new_h))) return -1; if (!new_h) { print_error_errno("cat", "failed to make output header"); goto fail; } fp = strcmp(outbam, "-")? bgzf_open(outbam, "w") : bgzf_fdopen(fileno(samtools_stdout), "w"); if (fp == 0) { print_error_errno("cat", "fail to open output file '%s'", outbam); goto fail; } if (!no_pg && sam_hdr_add_pg(new_h, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) goto fail; if (bam_hdr_write(fp, new_h) < 0) { print_error_errno("cat", "Couldn't write header"); goto fail; } buf = (uint8_t*) malloc(BUF_SIZE); if (!buf) { fprintf(samtools_stderr, "[%s] Couldn't allocate buffer\n", __func__); goto fail; } for(i = 0; i < nfn; ++i){ int len,j; in = files[i]->fp.bgzf; if (in == 0) { print_error_errno("cat", "fail to open file '%s'", fn[i]); goto fail; } if (in->is_write) goto fail; if (in->block_offset < in->block_length) { if (bgzf_write(fp, (char *)in->uncompressed_block + in->block_offset, in->block_length - in->block_offset) < 0) goto write_fail; if (bgzf_flush(fp) != 0) goto write_fail; } j=0; while ((len = bgzf_raw_read(in, buf, BUF_SIZE)) > 0) { if(len= 0) { switch (c) { case 'h': { samFile *fph = sam_open(optarg, "r"); if (fph == 0) { fprintf(samtools_stderr, "[%s] ERROR: fail to read the header from '%s'.\n", __func__, optarg); ret = 1; goto end; } h = sam_hdr_read(fph); if (h == NULL) { fprintf(samtools_stderr, "[%s] ERROR: failed to read the header from '%s'.\n", __func__, optarg); ret = 1; goto end; } sam_close(fph); break; } case 'o': outfn = strdup(optarg); break; case 'b': { // add file names in "optarg" to the list // of files to concatenate int nfns; char **fns_read = hts_readlines(optarg, &nfns); if (fns_read) { infns = realloc(infns, (infns_size + nfns) * sizeof(char*)); if (infns == NULL) { ret = 1; goto end; } memcpy(infns+infns_size, fns_read, nfns * sizeof(char*)); infns_size += nfns; free(fns_read); } else { print_error("cat", "Invalid file list \"%s\"", optarg); ret = 1; } break; } case 1: no_pg = 1; break; case 'r': reg = optarg; break; case 'p': part = optarg; break; case 'f': fast_mode = 1; break; case 'q': query_ncont=1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage=1; break; } } if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) { print_error("cat", "failed to create arg_list"); ret = 1; goto end; } // Append files specified in argv to the list. int nargv_fns = argc - optind; if (nargv_fns > 0) { infns = realloc(infns, (infns_size + nargv_fns) * sizeof(char*)); if (infns == NULL) { ret = 1; goto end; } memcpy(infns + infns_size, argv + optind, nargv_fns * sizeof(char*)); } // Require at least one input file if (infns_size + nargv_fns == 0 || usage) { fprintf(samtools_stderr, "Usage: samtools cat [options] [... ]\n"); fprintf(samtools_stderr, " samtools cat [options] [... ]\n\n"); fprintf(samtools_stderr, "Concatenate BAM or CRAM files, first those in , then those\non the command line.\n\n"); fprintf(samtools_stderr, "Options: -b FILE list of input BAM/CRAM file names, one per line\n"); fprintf(samtools_stderr, " -h FILE copy the header from FILE [default is 1st input file]\n"); fprintf(samtools_stderr, " -o FILE output BAM/CRAM\n"); fprintf(samtools_stderr, " --no-PG do not add a PG line\n"); fprintf(samtools_stderr, "\nCRAM only options for filtering:\n"); fprintf(samtools_stderr, " -r REG filter to region REG.\n"); fprintf(samtools_stderr, " REG can also be #:cstart-cend for specific container numbers\n"); fprintf(samtools_stderr, " -p N/M Specify part N of M (where N is 1 to M inclusive)\n"); fprintf(samtools_stderr, " -f Fast mode: don't filter containers to exactly match region\n"); fprintf(samtools_stderr, " -q Query the total number of indexed containers\n"); fprintf(samtools_stderr, "\nStandard options:\n"); sam_global_opt_help(samtools_stderr, "---.---."); ret = 1; goto end; } in = sam_open(infns[0], "r"); if (!in) { print_error_errno("cat", "failed to open file '%s'", infns[0]); ret = 1; goto end; } switch (hts_get_format(in)->format) { case bam: if (bam_cat(in, infns_size+nargv_fns, infns, h, outfn? outfn : "-", arg_list, no_pg) < 0) ret = 1; break; case cram: if (query_ncont) { if (cram_query_ncont(infns_size+nargv_fns, infns, reg) < 0) ret = 1; } else { if (cram_cat(in, infns_size+nargv_fns, infns, h, outfn? outfn : "-", &ga, arg_list, no_pg, reg, part, fast_mode) < 0) ret = 1; } break; default: fprintf(samtools_stderr, "[%s] ERROR: input is not BAM or CRAM\n", __func__); ret = 1; } sam_close(in); end: if (infns_size > 0) { int i; for (i=0; i Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include "htslib/sam.h" /*! @abstract Get the color encoding the previous and current base @param b pointer to an alignment @param i The i-th position, 0-based @return color @discussion Returns 0 no color information is found. */ char bam_aux_getCSi(bam1_t *b, int i) { uint8_t *c = bam_aux_get(b, "CS"); char *cs = NULL; // return the base if the tag was not found if(0 == c) return 0; cs = bam_aux2Z(c); // adjust for strandedness and leading adaptor if(bam_is_rev(b)) { i = strlen(cs) - 1 - i; // adjust for leading hard clip uint32_t cigar = bam_get_cigar(b)[0]; if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { i -= cigar >> BAM_CIGAR_SHIFT; } } else { i++; } return cs[i]; } /*! @abstract Get the color quality of the color encoding the previous and current base @param b pointer to an alignment @param i The i-th position, 0-based @return color quality @discussion Returns 0 no color information is found. */ char bam_aux_getCQi(bam1_t *b, int i) { uint8_t *c = bam_aux_get(b, "CQ"); char *cq = NULL; // return the base if the tag was not found if(0 == c) return 0; cq = bam_aux2Z(c); // adjust for strandedness if(bam_is_rev(b)) { i = strlen(cq) - 1 - i; // adjust for leading hard clip uint32_t cigar = bam_get_cigar(b)[0]; if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { i -= (cigar >> BAM_CIGAR_SHIFT); } } return cq[i]; } char bam_aux_nt2int(char a) { switch(toupper(a)) { case 'A': return 0; break; case 'C': return 1; break; case 'G': return 2; break; case 'T': return 3; break; default: return 4; break; } } char bam_aux_ntnt2cs(char a, char b) { a = bam_aux_nt2int(a); b = bam_aux_nt2int(b); if(4 == a || 4 == b) return '4'; return "0123"[(int)(a ^ b)]; } /*! @abstract Get the color error profile at the give position @param b pointer to an alignment @return the original color if the color was an error, '-' (dash) otherwise @discussion Returns 0 no color information is found. */ char bam_aux_getCEi(bam1_t *b, int i) { int cs_i; uint8_t *c = bam_aux_get(b, "CS"); char *cs = NULL; char prev_b, cur_b; char cur_color, cor_color; // return the base if the tag was not found if(0 == c) return 0; cs = bam_aux2Z(c); // adjust for strandedness and leading adaptor if(bam_is_rev(b)) { //reverse strand cs_i = strlen(cs) - 1 - i; // adjust for leading hard clip uint32_t cigar = bam_get_cigar(b)[0]; if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { cs_i -= cigar >> BAM_CIGAR_SHIFT; } // get current color cur_color = cs[cs_i]; // get previous base. Note: must rc adaptor prev_b = (cs_i == 1) ? "TGCAN"[(int)bam_aux_nt2int(cs[0])] : seq_nt16_str[bam_seqi(bam_get_seq(b), i+1)]; // get current base cur_b = seq_nt16_str[bam_seqi(bam_get_seq(b), i)]; } else { cs_i=i+1; // get current color cur_color = cs[cs_i]; // get previous base prev_b = (0 == i) ? cs[0] : seq_nt16_str[bam_seqi(bam_get_seq(b), i-1)]; // get current base cur_b = seq_nt16_str[bam_seqi(bam_get_seq(b), i)]; } // corrected color cor_color = bam_aux_ntnt2cs(prev_b, cur_b); if(cur_color == cor_color) { return '-'; } else { return cur_color; } } pysam-0.23.0/samtools/bam_color.c.pysam.c000066400000000000000000000116061475062545500202610ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_color.c -- color-space support. Copyright (C) 2009, 2012 University of California - Los Angeles. Author: Nils Homer Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include "htslib/sam.h" /*! @abstract Get the color encoding the previous and current base @param b pointer to an alignment @param i The i-th position, 0-based @return color @discussion Returns 0 no color information is found. */ char bam_aux_getCSi(bam1_t *b, int i) { uint8_t *c = bam_aux_get(b, "CS"); char *cs = NULL; // return the base if the tag was not found if(0 == c) return 0; cs = bam_aux2Z(c); // adjust for strandedness and leading adaptor if(bam_is_rev(b)) { i = strlen(cs) - 1 - i; // adjust for leading hard clip uint32_t cigar = bam_get_cigar(b)[0]; if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { i -= cigar >> BAM_CIGAR_SHIFT; } } else { i++; } return cs[i]; } /*! @abstract Get the color quality of the color encoding the previous and current base @param b pointer to an alignment @param i The i-th position, 0-based @return color quality @discussion Returns 0 no color information is found. */ char bam_aux_getCQi(bam1_t *b, int i) { uint8_t *c = bam_aux_get(b, "CQ"); char *cq = NULL; // return the base if the tag was not found if(0 == c) return 0; cq = bam_aux2Z(c); // adjust for strandedness if(bam_is_rev(b)) { i = strlen(cq) - 1 - i; // adjust for leading hard clip uint32_t cigar = bam_get_cigar(b)[0]; if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { i -= (cigar >> BAM_CIGAR_SHIFT); } } return cq[i]; } char bam_aux_nt2int(char a) { switch(toupper(a)) { case 'A': return 0; break; case 'C': return 1; break; case 'G': return 2; break; case 'T': return 3; break; default: return 4; break; } } char bam_aux_ntnt2cs(char a, char b) { a = bam_aux_nt2int(a); b = bam_aux_nt2int(b); if(4 == a || 4 == b) return '4'; return "0123"[(int)(a ^ b)]; } /*! @abstract Get the color error profile at the give position @param b pointer to an alignment @return the original color if the color was an error, '-' (dash) otherwise @discussion Returns 0 no color information is found. */ char bam_aux_getCEi(bam1_t *b, int i) { int cs_i; uint8_t *c = bam_aux_get(b, "CS"); char *cs = NULL; char prev_b, cur_b; char cur_color, cor_color; // return the base if the tag was not found if(0 == c) return 0; cs = bam_aux2Z(c); // adjust for strandedness and leading adaptor if(bam_is_rev(b)) { //reverse strand cs_i = strlen(cs) - 1 - i; // adjust for leading hard clip uint32_t cigar = bam_get_cigar(b)[0]; if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { cs_i -= cigar >> BAM_CIGAR_SHIFT; } // get current color cur_color = cs[cs_i]; // get previous base. Note: must rc adaptor prev_b = (cs_i == 1) ? "TGCAN"[(int)bam_aux_nt2int(cs[0])] : seq_nt16_str[bam_seqi(bam_get_seq(b), i+1)]; // get current base cur_b = seq_nt16_str[bam_seqi(bam_get_seq(b), i)]; } else { cs_i=i+1; // get current color cur_color = cs[cs_i]; // get previous base prev_b = (0 == i) ? cs[0] : seq_nt16_str[bam_seqi(bam_get_seq(b), i-1)]; // get current base cur_b = seq_nt16_str[bam_seqi(bam_get_seq(b), i)]; } // corrected color cor_color = bam_aux_ntnt2cs(prev_b, cur_b); if(cur_color == cor_color) { return '-'; } else { return cur_color; } } pysam-0.23.0/samtools/bam_consensus.c000066400000000000000000003031271475062545500176140ustar00rootroot00000000000000/* bam_consensus.c -- consensus subcommand. Copyright (C) 1998-2001,2003 Medical Research Council (Gap4/5 source) Copyright (C) 2003-2005,2007-2024 Genome Research Ltd. Author: James Bonfield The primary work here is GRL since 2021, under an MIT license. Sections derived from Gap5, which include calculate_consensus_gap5() associated functions, are mostly copyright Genome Research Limited from 2003 onwards. These were originally under a BSD license, but as GRL is copyright holder these portions can be considered to also be under the same MIT license below: Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* * The Gap5 consensus algorithm was in turn derived from the earlier Gap4 * tool, developed by the Medical Research Council as part of the * Staden Package. It is unsure how much of this source code is still * extant, without deep review, but the license used was a compatible * modified BSD license, included below. */ /* Modified BSD license for any legacy components from the Staden Package: Copyright (c) 2003 MEDICAL RESEARCH COUNCIL All rights reserved Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ // FIXME: also use strand to spot possible basecalling errors. // Specifically het calls where mods are predominantly on one // strand. So maybe require + and - calls and check concordance // before calling a het as confident. (Still call, but low qual?) // TODO: call by kmers rather than individual bases? Or use kmers to skew // quality at least. It can identify variants that are low quality due to // neighbouring edits that aren't consistently correlated. // TODO: pileup callback ought to know when it's the last in the region / // chromosome. This means the caller code doesn't have to handle the // termination phase and deduplicates the code. (Changing from // one chr to the next is the same as ending the last.) // // TODO: track which reads contribute to multiple confirmed (HQ) differences // vs which contribute to only one (LQ) difference. Correlated changes // are more likely to be real. Ie consensus more of a path than solely // isolated columns. // // Either that or a dummy "end of data" call is made to signify end to // permit tidying up. Maybe add a "start of data" call too? // Eg 50T 20A seems T/A het, // but 30T+ 20T- 18A+ 2A- seems like a consistent A miscall on one strand // only, while T is spread evenly across both strands. // TODO: Phasing of long reads. // Long reads offer very strong phasing opportunities for SNPs. // From these, we get strong evidence for accuracy of indels. // Specifically whether the distribution of poly-len within a phases // is significantly different to the distribution of poly len between // phases. // TODO end STR trimming. Eg: // REF AAGCTGAAAAGTTAATGTCTTATTTTTTTTTTTTTTTTGAGATGGAGTC // aagctgaaaagttaatgtctta****ttttttttttttgagatggagtc // aagctgaaaagttaatgtcttattttttttt // aagctgaaaagttaatgtctta****ttttttttttttgagatggagtc // Middle seq doesn't validate those initial T alignments. // Qual_train solves this by use of the STR trimmer. // TODO add a weight for proximity to homopolymer. // Maybe length/distance? So 3 away from a 12-mer is similar to 1 away // from a 4-mer? // TODO: Count number of base types between this point and the nearest // indel or end of read. Eg GATCGAGAGAG*TAGC => 2 (A and G). // adj is nbase/4 * score, or (nbase+1)/5? // Perhaps multiplied by length too, to get local complexity score? #include #include #include #include #include #include #include #include #include #include #include "samtools.h" #include "sam_opts.h" #include "bam_plbuf.h" #include "consensus_pileup.h" #ifdef __SSE__ # include #else # define _mm_prefetch(a,b) #endif #ifndef MIN # define MIN(a,b) ((a)<(b)?(a):(b)) #endif #ifndef MAX # define MAX(a,b) ((a)>(b)?(a):(b)) #endif // Defines for experiment code which is currently disabled // Hardy-Weinberg statistics to check heterozygous sites match allelic // frequencies. //#define DO_HDW // Filter bayesian calls by min-depth and min-fract parameters //#define DO_FRACT // Checks uniqueness of surrounding bases to adjust scores //#define K2 2 // Look for strand bias in distribution of homopolymer lengths //#define DO_POLY_DIST // Minimum cutoff for storing mod data; => at least 10% chance #define MOD_CUTOFF 0.46 enum format { FASTQ, FASTA, PILEUP }; typedef unsigned char uc; // Simple recalibration table for substitutions, undercalls and overcalls. // In future, we'll update this to be kmer based too. typedef struct { int smap[101]; // substituion or SNP int umap[101]; // undercall or DEL int omap[101]; // overcall or INS } qcal_t; typedef struct { // User options char *reg; int use_qual; int min_qual; int adj_qual; int use_mqual; double scale_mqual; int nm_adjust; int nm_halo; int sc_cost; int low_mqual; int high_mqual; int min_depth; double call_fract; double het_fract; int mode; // One of MODE_* macros below enum format fmt; int cons_cutoff; int ambig; int line_len; int default_qual; int het_only; int all_bases; int show_del; int show_ins; int mark_ins; int excl_flags; int incl_flags; int min_mqual; double P_het; double P_indel; double het_scale; double homopoly_fix; double homopoly_redux; qcal_t qcal; // Internal state samFile *fp; FILE *fp_out; sam_hdr_t *h; hts_idx_t *idx; hts_itr_t *iter; kstring_t ks_line; kstring_t ks_ins_seq; kstring_t ks_ins_qual; int last_tid; hts_pos_t last_pos; } consensus_opts; /* -------------------------------------------------------------------------- * A bayesian consensus algorithm that analyses the data to work out * which hypothesis of pure A/C/G/T/absent and all combinations of two * such bases meets the observations. * * This has its origins in Gap4 (homozygous) -> Gap5 (heterozygous) * -> Crumble (tidied up to use htslib's pileup) -> here. * */ #define CONS_DISCREP 4 #define CONS_ALL 15 #define CONS_MQUAL 16 typedef struct { /* the most likely base call - we never call N here */ /* A=0, C=1, G=2, T=3, *=4 */ int call; /* The most likely heterozygous base call */ /* Use "ACGT*"[het / 5] vs "ACGT*"[het % 5] for the combination */ int het_call; /* Log-odds for het_call */ int het_logodd; /* Single phred style call */ int phred; /* Sequence depth */ int depth; /* Discrepancy search score */ float discrep; } consensus_t; #define P_HET 1e-3 #define P_INDEL 2e-4 #define P_HOMOPOLY 0.5 #define P_HET_SCALE 1.0 #define LOG10 2.30258509299404568401 #define TENOVERLOG10 4.34294481903251827652 #define TENLOG2OVERLOG10 3.0103 #ifdef __GNUC__ #define ALIGNED(x) __attribute((aligned(x))) #else #define ALIGNED(x) #endif // Initialised once as a global array. This won't work if threaded, // but we'll rewrite if and when that gets added later. static double e_tab_a[1002] ALIGNED(16); static double *e_tab = &e_tab_a[500]; static double e_tab2_a[1002] ALIGNED(16); static double *e_tab2 = &e_tab2_a[500]; static double e_log[501] ALIGNED(16); /* Precomputed matrices for the consensus algorithm */ typedef struct { double prior[25] ALIGNED(16); /* Sum to 1.0 */ double lprior15[15] ALIGNED(16); /* 15 combinations of {ACGT*} */ double pMM[101] ALIGNED(16); double p__[101] ALIGNED(16); double p_M[101] ALIGNED(16); double po_[101] ALIGNED(16); double poM[101] ALIGNED(16); double poo[101] ALIGNED(16); double puu[101] ALIGNED(16); double pum[101] ALIGNED(16); double pmm[101] ALIGNED(16); // Multiplier on homopolymer length before reducing phred qual double poly_mul; } cons_probs; // Two sets of params; recall oriented (gap5) and precision (stf). // We use the former unless MODE_MIXED is set (which is the default // for bayesian consensus mode if P_indel is significant). static cons_probs cons_prob_recall, cons_prob_precise; /* * Lots of confusing matrix terms here, so some definitions will help. * * M = match base * m = match pad * _ = mismatch * o = overcall * u = undercall * * We need to distinguish between homozygous columns and heterozygous columns, * done using a flat prior. This is implemented by treating every observation * as coming from one of two alleles, giving us a 2D matrix of possibilities * (the hypotheses) for each and every call (the observation). * * So pMM[] is the chance that given a call 'x' that it came from the * x/x allele combination. Similarly p_o[] is the chance that call * 'x' came from a mismatch (non-x) / overcall (consensus=*) combination. * * Examples with observation (call) C and * follows * * C | A C G T * * | A C G T * * ----------------- ----------------- * A | __ _M __ __ o_ A | uu uu uu uu um * C | _M MM _M _M oM C | uu uu uu uu um * G | __ _M __ __ o_ G | uu uu uu uu um * T | __ _M __ __ o_ T | uu uu uu uu um * * | o_ oM o_ o_ oo * | um um um um mm * * In calculation terms, the _M is half __ and half MM, similarly o_ and um. * * Relative weights of substitution vs overcall vs undercall are governed on a * per base basis using the P_OVER and P_UNDER scores (subst is * 1-P_OVER-P_UNDER). * * The heterozygosity weight though is a per column calculation as we're * trying to model whether the column is pure or mixed. Hence this is done * once via a prior and has no affect on the individual matrix cells. * * We have a generic indel probability, but it's a catch all for overcall, * undercall, alignment artifacts, homopolymer issues, etc. So we can set * it considerably higher and just let the QUAL skew do the filtering for * us, albeit no longer well calibrated. */ // NB: Should _M be MM? // Ie sample really is A/C het, and we observe C. That should be a match, // not half a match. #define MODE_SIMPLE 0 // freq counting #define MODE_BAYES_116 1 // Samtools 1.16 (no indel param) #define MODE_RECALL 2 // so called as it's the params from Gap5 #define MODE_PRECISE 3 // a more precise set; +FN, --FP #define MODE_MIXED 4 // Combination of GAP5/BAYES #define QCAL_FLAT 0 #define QCAL_HIFI 1 #define QCAL_HISEQ 2 #define QCAL_ONT_R10_4_SUP 3 #define QCAL_ONT_R10_4_DUP 4 #define QCAL_ULTIMA 5 // Calibration tables here don't necessarily reflect the true accuracy. // They have been manually tuned to work in conjunction with other command // line parameters used in the machine profiles. For example reducing one // qual here and increasing sensitivity elsewhere via another parameter. static qcal_t static_qcal[6] = { { // FLAT {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99}, {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99}, {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99} }, { // HiFi {10, 11, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 33, 34, 35, 36, 36, 37, 38, 38, 39, 39, 40, 40, 41, 41, 41, 41, 42, 42, 42, 42, 43, 43, 43, 43, 43, 43, 43, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, }, { 4, 4, 4, 4, 5, 6, 6, 7, 8, 9, 10, 11, 11, 12, 13, 14, 15, 15, 16, 17, 18, 19, 19, 20, 20, 21, 22, 23, 23, 24, 25, 25, 25, 26, 26, 26, 27, 27, 28, 28, 28, 28, 27, 27, 27, 28, 28, 28, 28, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 26, 26, 25, 26, 26, 27, 27, 27, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 28, 29, 28, 28, 28, 27, 27, 27, 27, 27, 27, 28, 28, 30, 30, 30, 30, 30, 30, 30, }, { 8, 8, 8, 8, 9, 10, 11, 12, 13, 14, 15, 15, 16, 17, 18, 19, 19, 20, 20, 21, 21, 22, 22, 23, 23, 23, 24, 24, 24, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 29, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, } }, { // HiSeq { 2, 2, 2, 3, 3, 4, 5, 5, 6, 7, 8, 9, 10, 11, 11, 12, 13, 14, 15, 16, 17, 17, 18, 19, 20, 21, 22, 22, 23, 24, 25, 26, 27, 28, 28, 29, 30, 31, 32, 33, 34, 34, 35, 36, 37, 38, 39, 39, 40, 41, 42, 43, 44, 45, 45, 46, 47, 48, 49, 50, 51, 51, 52, 53, 54, 55, 56, 56, 57, 58, 59, 60, 61, 62, 62, 63, 64, 65, 66, 67, 68, 68, 69, 70, 71, 72, 73, 73, 74, 75, 76, 77, 78, 79, 79, 80, 81, 82, 83, 84, }, { 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 61, 62, 63, 64, 65, 67, 68, 69, 70, 71, 73, 74, 75, 76, 77, 79, 80, 81, 82, 83, 85, 86, 87, 88, 89, 91, 92, 93, 94, 95, 97, 98, 99, 100, 101, 103, 104, 105, 106, 107, 109, 110, 111, 112, 113, 115, 116, 117, 118, 119, }, { 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 61, 62, 63, 64, 65, 67, 68, 69, 70, 71, 73, 74, 75, 76, 77, 79, 80, 81, 82, 83, 85, 86, 87, 88, 89, 91, 92, 93, 94, 95, 97, 98, 99, 100, 101, 103, 104, 105, 106, 107, 109, 110, 111, 112, 113, 115, 116, 117, 118, 119, } }, { // ONT R10.4 super { 0, 2, 2, 2, 3, 4, 4, 5, 6, 7, 7, 8, 9, 12, 13, 14, 15, 15, 16, 17, 18, 19, 20, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 36, 37, 38, 38, 39, 39, 40, 40, 40, 40, 40, 40, 40, 41, 40, 40, 41, 41, 40, 40, 40, 40, 41, 40, 40, 40, 40, 41, 41, 40, 40, 41, 40, 40, 39, 41, 40, 41, 40, 40, 41, 41, 41, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, }, { 0, 2, 2, 2, 3, 4, 5, 6, 7, 8, 8, 9, 9, 10, 10, 10, 11, 12, 12, 13, 13, 13, 14, 14, 15, 16, 16, 17, 18, 18, 19, 19, 20, 21, 22, 23, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, }, { 0, 4, 6, 6, 6, 7, 7, 8, 9, 9, 9, 10, 10, 11, 11, 12, 12, 13, 13, 14, 15, 15, 15, 16, 16, 17, 17, 18, 18, 19, 19, 20, 20, 21, 22, 22, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, } }, { // ONT R10.4 duplex; just a copy of hifi for now {10, 11, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 33, 34, 35, 36, 36, 37, 38, 38, 39, 39, 40, 40, 41, 41, 41, 41, 42, 42, 42, 42, 43, 43, 43, 43, 43, 43, 43, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, }, { 4, 4, 4, 4, 5, 6, 6, 7, 8, 9, 10, 11, 11, 12, 13, 14, 15, 15, 16, 17, 18, 19, 19, 20, 20, 21, 22, 23, 23, 24, 25, 25, 25, 26, 26, 26, 27, 27, 28, 28, 28, 28, 27, 27, 27, 28, 28, 28, 28, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 26, 26, 25, 26, 26, 27, 27, 27, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 28, 29, 28, 28, 28, 27, 27, 27, 27, 27, 27, 28, 28, 30, 30, 30, 30, 30, 30, 30, }, { 8, 8, 8, 8, 9, 10, 11, 12, 13, 14, 15, 15, 16, 17, 18, 19, 19, 20, 20, 21, 21, 22, 22, 23, 23, 23, 24, 24, 24, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 29, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, } }, { // Ultima Genomics { 2, 2, 3, 4, 5, 6, 6, 7, 8, 9, 10, 10, 11, 12, 13, 14, 14, 15, 16, 17, 18, 18, 19, 21, 22, 23, 23, 24, 25, 26, 27, 27, 28, 29, 30, 31, 31, 32, 33, 34, 35, 35, 36, 37, 38, 39, 39, 40, 42, 43, 44, 44, 45, 46, 47, 48, 48, 49, 50, 51, 52, 52, 53, 54, 55, 56, 56, 57, 58, 59, 60, 60, 61, 63, 64, 65, 65, 66, 67, 68, 69, 69, 70, 71, 72, 73, 73, 74, 75, 76, 77, 77, 78, 79, 80, 81, 81, 82, 84, 85, }, { 1, 1, 2, 2, 3, 3, 4, 4, 4, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 10, 10, 10, 11, 12, 13, 13, 13, 14, 15, 16, 16, 16, 17, 18, 18, 19, 19, 20, 20, 21, 21, 22, 22, 22, 22, 23, 23, 24, 24, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, }, { 1, 1, 2, 2, 3, 3, 4, 4, 4, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 10, 10, 10, 11, 12, 13, 13, 13, 14, 15, 16, 16, 16, 17, 18, 18, 19, 19, 20, 20, 21, 21, 22, 22, 22, 22, 23, 23, 24, 24, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, } } }; int set_qcal(qcal_t *q, int id) { if (id < 0 || id >= sizeof(static_qcal)/sizeof(*static_qcal)) return -1; memcpy(q, &static_qcal[id], sizeof(*q)); return 0; } int load_qcal(qcal_t *q, const char *fn) { int i; if (strcmp(fn, ":hifi") == 0) return set_qcal(q, QCAL_HIFI); if (strcmp(fn, ":hiseq") == 0) return set_qcal(q, QCAL_HISEQ); if (strcmp(fn, ":r10.4_sup") == 0) return set_qcal(q, QCAL_ONT_R10_4_SUP); if (strcmp(fn, ":r10.4_dup") == 0) return set_qcal(q, QCAL_ONT_R10_4_DUP); if (strcmp(fn, ":ultima") == 0) return set_qcal(q, QCAL_ULTIMA); // default for (i = 0; i < 101; i++) q->smap[i] = q->umap[i] = q->omap[i] = i; if (strcmp(fn, ":flat") == 0) return 0; hFILE *fp = hopen(fn, "r"); if (!fp) return -1; kstring_t line = KS_INITIALIZE; int max = 0; int last_qual = 0; while (line.l = 0, kgetline(&line, (kgets_func *)hgets, fp) >= 0) { int v, s, u, o; if (*line.s == '#') continue; if (sscanf(line.s, "QUAL %d %d %d %d", &v, &s, &u, &o) != 4) goto err; while (v > last_qual) { q->smap[last_qual+1] = q->smap[last_qual]; q->umap[last_qual+1] = q->umap[last_qual]; q->omap[last_qual+1] = q->omap[last_qual]; last_qual++; } if (v >= 0 && v < 100) { q->smap[v] = s; q->umap[v] = u; q->omap[v] = o; } if (v < max) { fprintf(stderr, "Qual calibration file is not in ascending order\n"); return hclose(fp) ? -2 : -1; } max = v; } for (i = max+1; i < 101; i++) { q->smap[i] = q->smap[max]; q->umap[i] = q->umap[max]; q->omap[i] = q->omap[max]; } ks_free(&line); return hclose(fp) < 0 ? -2 : 0; err: ks_free(&line); return hclose(fp) < 0 ? -2 : -1; } static void consensus_init(double p_het, double p_indel, double het_scale, double poly_mul, qcal_t *qcal, int mode, cons_probs *cp) { int i; // NB: only need to initialise once, but we do here for now for (i = -500; i <= 500; i++) e_tab[i] = exp(i); for (i = -500; i <= 500; i++) e_tab2[i] = exp(i/10.); for (i = 0; i <= 500; i++) e_log[i] = log(i); // EXPERIMENTAL cp->poly_mul = poly_mul; // The priors make very little difference, unless shallow data. // ACGT* by ACGT* // So AA=0, CC=6, GG=12, TT=18, **=24 for (i = 0; i < 25; i++) cp->prior[i] = p_het / 6; // AC AG AT CG CT GT // Flat assumption that it is what we observe, and measure everything else // as relative to this. cp->prior[0]=cp->prior[6]=cp->prior[12]=cp->prior[18]=cp->prior[24] = 1; // heterozygous deletion for (i = 4; i < 24; i+=5) cp->prior[i] = p_indel / 6; // /6 to be scaled vs p_het equivalently // heterozygous insertion for (i = 20; i < 24; i++) cp->prior[i] = p_indel / 6; cp->lprior15[0] = log(cp->prior[0]); cp->lprior15[1] = log(cp->prior[1]); cp->lprior15[2] = log(cp->prior[2]); cp->lprior15[3] = log(cp->prior[3]); cp->lprior15[4] = log(cp->prior[4]); cp->lprior15[5] = log(cp->prior[6]); cp->lprior15[6] = log(cp->prior[7]); cp->lprior15[7] = log(cp->prior[8]); cp->lprior15[8] = log(cp->prior[9]); cp->lprior15[9] = log(cp->prior[12]); cp->lprior15[10] = log(cp->prior[13]); cp->lprior15[11] = log(cp->prior[14]); cp->lprior15[12] = log(cp->prior[18]); cp->lprior15[13] = log(cp->prior[19]); cp->lprior15[14] = log(cp->prior[24]); for (i = 1; i < 101; i++) { double prob = 1 - pow(10, -qcal->smap[i] / 10.0); // Or is it that prob is 1-p(subst)-p(overcall)? cp->pMM[i] = log(prob); //cp->p__[i] = log(1-prob); // Big help to PB-CCS SNPs; unless fudged cp->p__[i] = log((1-prob)/3); // correct? poor on PB-CCS w/o fudge // Mixed alleles; just average two likelihoods cp->p_M[i] = log((exp(cp->pMM[i]) + exp(cp->p__[i]))/2); // What does this really mean? Can we simulate this by priors? // It reduces the likelihood of calling het sites, which is // maybe compensation for alignment artifacts? I'm unsure, // but it works (to differing degrees) on both PacBio HiFi and // Illumina HiSeq. It (obviously) loses true hets, but // potentially this can be compensated for by tweaking P-het // (which is entirely in the priors). // // Low het_scale reduces false positives by making hets less // likely to be called. In high depth data we normally have // enough evidence to call correctly even with low het_scale, // so it's a good +FN vs --FP tradeoff. However on low depth // data, het_scale can filter out too many true variants. // // TODO: So consider adjusting at the end maybe? // Also consider never changing calls, but changing their // confidence, so the data is what produces the call with the // parameters skewing the quality score distribution. cp->p_M[i] += log(het_scale); if (mode == MODE_BAYES_116) { // Compatibility with samtools 1.16 // This had no differention for indel vs substitution error rates, // so o(vercall) and u(undercall) are subst(_). cp->pmm[i] = cp->pMM[i]; cp->poM[i] = cp->p_M[i]; cp->pum[i] = cp->p_M[i]; cp->po_[i] = cp->p__[i]; cp->poo[i] = cp->p__[i]; cp->puu[i] = cp->p__[i]; } else { // When observing A C G T; leads to insertion calls prob = 1 - pow(10, -qcal->omap[i] / 10.0); // /3 for consistency with ACGT rem as relative likelihoods. // Otherwise with flat priors we end up calling all shallow data // as "*", which is illogical. cp->poo[i] = log((1-prob)/3); // Ensure pMM is always more likely. (NB: This shouldn't happen // now with the addition of the /3 step above.) if (cp->poo[i] > cp->pMM[i]-.5) cp->poo[i] = cp->pMM[i]-.5; cp->po_[i] = log((exp(cp->poo[i]) + exp(cp->p__[i]))/2); cp->poM[i] = log((exp(cp->poo[i]) + exp(cp->pMM[i]))/2); // Overcalls should never be twice as likely than mismatches. // Het bases are mix of _M (other) and MM ops (this). // It's fine for _M to be less likely than oM (more likely // to be overcalled than miscalled), but it should never // be stronger when combined with other mixed data. if (cp->poM[i] > cp->p_M[i]+.5) cp->poM[i] = cp->p_M[i]+.5; // Note --low-MQ and --scale-MQ have a big impact on // undercall errs. May need to separate these options per // type, but how? // Multiple-calls, as with mixed mode? This feels like a cheat prob = 1 - pow(10, -qcal->umap[i] / 10.0); cp->pmm[i] = log(prob); cp->puu[i] = log((1-prob)/3); if (cp->puu[i] > cp->pMM[i]-.5) // MM is -ve cp->puu[i] = cp->pMM[i]-.5; cp->pum[i] = log((exp(cp->puu[i]) + exp(cp->pmm[i]))/2); } } cp->pMM[0] = cp->pMM[1]; cp->p__[0] = cp->p__[1]; cp->p_M[0] = cp->p_M[1]; cp->pmm[0] = cp->pmm[1]; cp->poo[0] = cp->poo[1]; cp->po_[0] = cp->po_[1]; cp->poM[0] = cp->poM[1]; cp->puu[0] = cp->puu[1]; cp->pum[0] = cp->pum[1]; } static inline double fast_exp(double y) { if (y >= -50 && y <= 50) return e_tab2[(int)(y*10)]; if (y < -500) y = -500; if (y > 500) y = 500; return e_tab[(int)y]; } /* Taylor (deg 3) implementation of the log */ static inline double fast_log2(double val) { // FP representation is exponent & mantissa, where // value = 2^E * M. // Hence log2(value) = log2(2^E * M) // = log2(2^E)+ log2(M) // = E + log2(M) union { double d; uint64_t x; } u = {val}; const int E = ((u.x >> 52) & 2047) - 1024; // exponent E // Initial log2(M) based on mantissa u.x &= ~(2047LL << 52); u.x += 1023LL << 52; val = ((-1/3.) * u.d + 2) * u.d - 2/3.; return E + val; } #define ph_log(x) (-TENLOG2OVERLOG10*fast_log2((x))) int nins(const bam1_t *b){ int i, indel = 0; uint32_t *cig = bam_get_cigar(b); for (i = 0; i < b->core.n_cigar; i++) { int op = bam_cigar_op(cig[i]); if (op == BAM_CINS || op == BAM_CDEL) indel += bam_cigar_oplen(cig[i]); } return indel; } /* * Some machines, including 454 and PacBio, store the quality values in * homopolymers with the first or last base always being the low quality * state. This can cause problems when reverse-complementing and aligning, * especially when we left-justify indels. * * Other platforms take the approach of having the middle bases high and * the low confidence spread evenly to both start and end. This means * reverse-complementing doesn't introduce any strand bias. * * We redistribute qualities within homopolymers in this style to fix * naive consensus or variant calling algorithms. */ void homopoly_qual_fix(bam1_t *b) { static double ph2err[256] = {0}; int i; if (!ph2err[0]) { for (i = 0; i < 256; i++) ph2err[i] = pow(10, i/-10.0); } uint8_t *seq = bam_get_seq(b); uint8_t *qual = bam_get_qual(b); for (i = 0; i < b->core.l_qseq; i++) { int s = i; // start of homopoly int base = bam_seqi(seq, i); while (i+1 < b->core.l_qseq && bam_seqi(seq, i+1) == base) i++; // s..i inclusive is now homopolymer if (s == i) continue; // Simplest: reverse if end_qual < start_qual // Next: average outer-most two, then next two, etc // Best: fully redistribute so start/end lower qual than centre // Middle route of averaging outer pairs is sufficient? int j, k; for (j = s, k = i; j < k; j++,k--) { double e = ph2err[qual[j]] + ph2err[qual[k]]; qual[j] = qual[k] = -fast_log2(e/2)*3.0104+.49; } } } // Return the local NM figure within halo (+/- HALO) of pos. // This local NM is used as a way to modify MAPQ to get a localised MAPQ // score via an adhoc fashion. double nm_local(const pileup_t *p, const bam1_t *b, hts_pos_t pos) { int *nm = (int *)p->cd; if (!nm) return 0; pos -= b->core.pos; if (pos < 0) return nm[0] & ((1<<24)-1); if (pos >= b->core.l_qseq) return nm[b->core.l_qseq-1] & ((1<<24)-1); return (nm[pos] & ((1<<24)-1)) / 10.0; } int poly_len(const pileup_t *p, const bam1_t *b, hts_pos_t pos) { int *nm = (int *)p->cd; if (!nm) return 0; pos -= b->core.pos; if (pos >= 0 && pos < b->core.l_qseq) return nm[pos] >> 24; else return 0; } /* * Initialise a new sequence appearing in the pileup. We use this to * precompute some metrics that we'll repeatedly use in the consensus * caller; the localised NM score. * * We also directly amend the BAM record (which will be discarded later * anyway) to modify qualities to account for local quality minima. * * Returns 0 (discard) or 1 (keep) on success, -1 on failure. */ int nm_init(void *client_data, samFile *fp, sam_hdr_t *h, pileup_t *p) { consensus_opts *opts = (consensus_opts *)client_data; if (!opts->use_mqual) return 1; const bam1_t *b = &p->b; int qlen = b->core.l_qseq, i; if (qlen <= 0) return 0; int *local_nm = calloc(qlen, sizeof(*local_nm)); if (!local_nm) return -1; p->cd = local_nm; double poly_adj = opts->homopoly_fix ? opts->homopoly_fix : 1; if (opts->adj_qual) { // Set local_nm based on a function of current qual and the local // minimum qual within the surrounding window. // // Basically if we're in a region of low confidence then we downgrade // higher qual outliers as they may not be as trustworthy as they // claim. This may be because the qualities have been assigned to // the wrong or arbitrary base (very common in homopolymers), or the // surrounding quality (hence also error likelihood) have lead to // misalignments and the base may be contributing to the wrong // pileup column. // // The nm_local() function returns these scores and uses it to bias // the mapping quality, which in turn adjusts base quality. uint8_t *qual = bam_get_qual(b); uint8_t *seq = bam_get_seq(b); const int qhalo = 8; // window size for base qual int qmin = qual[0]; // min qual within qhalo const int qhalop = 2;// window size for homopolymer qual int qminp = qual[0]; // min qual within homopolymer halo int base = bam_seqi(seq, 0), polyl = 0, polyr = 0; // pos, not len // Minimum quality of the initial homopolymer for (i = 1; i < qlen; i++) { if (bam_seqi(seq, i) != base) break; if (i < qhalop && qminp > qual[i]) qminp = qual[i]; } // Minimum quality for general bases for (i = 0; i < qlen && i < qhalo; i++) { if (qmin > qual[i]) qmin = qual[i]; } for (;i < qlen-qhalo; i++) { if (opts->homopoly_fix && bam_seqi(seq, i) != base) { polyl = i; base = bam_seqi(seq, i); qminp = qual[i]; int j; for (j = i+1; j < qlen; j++) { if (bam_seqi(seq, j) != base) break; if (i < qhalop && qminp > qual[j]) qminp = qual[j]; } polyr = j-1; } else { // CHECK: do we want to have opts->homopoly_fix above, // so when not in use we don't define pl to non-zero? // Test on SynDip polyr = polyl; } int pl = polyr-polyl; // Useful for SNPS, as we're judging the variation in // length as an indicator for base-misalignment. // Not so useful for indel calling where the longer the indel // the less confident we are on the len variation being real. int t = (opts->mode == MODE_BAYES_116) ? (qual[i] + 5*qmin)/4 : qual[i]/3 + (qminp-pl*2)*poly_adj; local_nm[i] += t < qual[i] ? qual[i]-t : 0; // Brute force qminp in polyl to polyr range. // TODO: optimise this with sliding window qminp = qual[i]; int k; for (k = MAX(polyl,i-qhalop); k <= MIN(polyr,i+qhalop); k++) if (qminp > qual[k]) qminp = qual[k]; if (qmin > qual[i+qhalo]) qmin = qual[i+qhalo]; else if (qmin <= qual[i-qhalo]) { int j; qmin = 99; for (j = i-qhalo+1; j <= i+qhalo; j++) if (qmin > qual[j]) qmin = qual[j]; } } for (; i < qlen; i++) { int t = (opts->mode == MODE_BAYES_116) ? (qual[i] + 5*qmin)/4 : qual[i]/3 + qminp*poly_adj; local_nm[i] += t < qual[i] ? qual[i]-t : 0; } } // Fix e.g. PacBio homopolymer qualities if (opts->homopoly_fix) homopoly_qual_fix((bam1_t *)b); // local_nm[i] & ((1<<24)-1) is for SNP score adjustment. // We also put some more basic poly-X len in local_nm[i] >> 24. uint8_t *seq = bam_get_seq(b); for (i = 0; i < qlen; i++) { int base = bam_seqi(seq, i); int poly = 0, j, k; for (j = i+1; j < qlen; j++) if (bam_seqi(seq, j) != base) break; //printf("%d x %d\n", base, j-i); poly = j-i-1; if (poly > 100) poly = 100; const int HALO=0; for (k = i-HALO; k < j+HALO; k++) if (k >= 0 && k < qlen) local_nm[k] = ((MAX(poly, local_nm[k]>>24))<<24) | (local_nm[k] & ((1<<24)-1)); i = j-1; } // Adjust local_nm array by the number of edits within // a defined region (pos +/- halo). const int halo = opts->nm_halo; const uint8_t *md = bam_aux_get(b, "MD"); if (!md) return 1; md = (const uint8_t *)bam_aux2Z(md); // Handle cost of being near a soft-clip uint32_t *cig = bam_get_cigar(b); int ncig = b->core.n_cigar; if ( (cig[0] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP || ((cig[0] & BAM_CIGAR_MASK) == BAM_CHARD_CLIP && ncig > 1 && (cig[1] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP)) { for (i = 0; i < halo && i < qlen; i++) local_nm[i]+=opts->sc_cost; for (; i < halo*2 && i < qlen; i++) local_nm[i]+=opts->sc_cost>>1; } if ( (cig[ncig-1] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP || ((cig[ncig-1] & BAM_CIGAR_MASK) == BAM_CHARD_CLIP && ncig > 1 && (cig[ncig-2] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP)) { for (i = qlen-1; i >= qlen-halo && i >= 0; i--) local_nm[i]+=opts->sc_cost; for (; i >= qlen-halo*2 && i >= 0; i--) local_nm[i]+=opts->sc_cost>>1; } // Now iterate over MD tag int pos = 0; while (*md) { if (isdigit(*md)) { uint8_t *endptr; long i = strtol((char *)md, (char **)&endptr, 10); md = endptr; pos += i; continue; } // deletion. // Should we bump local_nm here too? Maybe if (*md == '^') { while (*++md && !isdigit(*md)) continue; continue; } // substitution for (i = pos-halo*2 >= 0 ?pos-halo*2 :0; i < pos-halo && i < qlen; i++) local_nm[i]+=5; for (; i < pos+halo && i < qlen; i++) local_nm[i]+=10; for (; i < pos+halo*2 && i < qlen; i++) local_nm[i]+=5; md++; } return 1; } void nm_free(void *client_data, samFile *fp, sam_hdr_t *h, pileup_t *p) { free(p->cd); p->cd = NULL; } #ifdef DO_HDW /* * Stirling's formula with a 1/12n correction applied to improve accuracy. * This seems to hold remarkably true for both low and high numbers too. */ double lnfact(double n) { /* Or Gosper's formula... * return (n*ln(n) - n + ln(2*M_PI*n + M_PI/3) / 2); */ return ((n+0.5)*log(n) - n + log(2*M_PI)/2) + log(1 + 1/(12.0*n)); /* + log(1 + 1/(288.0*n*n)); */ } /* * The binomical coefficient (n,k) for n trials with k successes where * prob(success) = p. * k n-k * P (k|n) = n! / (k! (n-k)!) p (1-p) * p * * The coefficient we are returning here is the n! / (k! (n-k)!) bit. * We compute it using ln(n!) and then exp() the result back to avoid * excessively large numbers. */ double bincoef(int n, double k) { return exp(lnfact(n) - lnfact(k) - lnfact(n-k)); } /* * Given p == 0.5 the binomial expansion simplifies a bit, so we have * a dedicated function for this. */ double binprobhalf(int n, double k) { return bincoef(n, k) * pow(0.5, n); } double lnbinprobhalf(int n, double k) { // ln(binprobhalf) expanded up and simplified return lnfact(n) - lnfact(k) - lnfact(n-k) - 0.69315*n; } #endif static int calculate_consensus_gap5(hts_pos_t pos, int flags, int depth, pileup_t *plp, consensus_opts *opts, consensus_t *cons, int default_qual, cons_probs *cp) { int i, j; static int init_done =0; static double q2p[101], mqual_pow[256]; double min_e_exp = DBL_MIN_EXP * log(2) + 1; double S[15] ALIGNED(16) = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}; double sumsC[6] = {0,0,0,0,0,0}; // A C G T * N // Small hash on seq to check for uniqueness of surrounding bases. // If it's frequent, then it's more likely to be correctly called than // if it's rare. // Helps a bit on deep data, especially with K2=3, but detrimental on // shallow and (currently) quite a slow down. #ifdef K2 int hashN[1<<(K2*4+2)] = {0}; int hash1[1<<2] = {0}; #endif /* Map the 15 possible combinations to 1-base or 2-base encodings */ static int map_sing[15] ALIGNED(16) = {0, 5, 5, 5, 5, 1, 5, 5, 5, 2, 5, 5, 3, 5, 4}; static int map_het[15] ALIGNED(16) = {0, 1, 2, 3, 4, 6, 7, 8, 9, 12, 13, 14, 18, 19, 24}; if (!init_done) { init_done = 1; for (i = 0; i <= 100; i++) { q2p[i] = pow(10, -i/10.0); } for (i = 0; i < 255; i++) { //mqual_pow[i] = 1-pow(10, -(i+.01)/10.0); mqual_pow[i] = 1-pow(10, -(i*.9)/10.0); //mqual_pow[i] = 1-pow(10, -(i/3+.1)/10.0); //mqual_pow[i] = 1-pow(10, -(i/2+.05)/10.0); } // unknown mqual mqual_pow[255] = mqual_pow[10]; } /* Initialise */ int counts[6] = {0}; #ifdef DO_FRACT int counts2[2][6] = {{0}}; #endif /* Accumulate */ #ifdef K2 const pileup_t *ptmp = plp; for (; ptmp; ptmp = ptmp->next) { const pileup_t *p = ptmp; if (p->qual < opts->min_qual) continue; int hb = 0; #define _ 0 static int X[16] = {_,0,1,_,2,_,_,_,3,_,_,_,_,_,_,_}; #undef _ uint8_t *seq = bam_get_seq(&p->b); int i, base1 = X[p->base4]; hash1[base1]++; for (i = p->seq_offset-K2; i <= p->seq_offset+K2; i++) { int base = i >= 0 && i < p->b.core.l_qseq ? X[bam_seqi(seq,i)] : _; hb = (hb<<2)|base; } hashN[hb]++; } #endif int td = depth; // original depth depth = 0; #ifdef DO_POLY_DIST int poly_dist[2][100] = {0}; #endif for (; plp; plp = plp->next) { pileup_t *p = plp; if (p->next) _mm_prefetch(p->next, _MM_HINT_T0); if (p->qual < opts->min_qual) continue; if (p->ref_skip) continue; #ifdef K2 int hb = 0; #define _ 0 static int X[16] = {_,0,1,_,2,_,_,_,3,_,_,_,_,_,_,_}; int i, base1 = X[p->base4]; for (i = p->seq_offset-K2; i <= p->seq_offset+K2; i++) { int base = i >= 0 && i < p->b.core.l_qseq ? X[bam_seqi(seq,i)] : _; hb = (hb<<2)|base; } #undef _ #endif const bam1_t *b = &p->b; uint8_t base = p->base4; uint8_t *qual_arr = bam_get_qual(b); uint8_t qual = p->qual; //qual = qual*qual/40+1; if (qual == 255 || (qual == 0 && *qual_arr == 255)) qual = default_qual; #ifdef K2 //qual = qual * hashN[hb] / hash1[base1]; qual -= -TENOVERLOG10*log(hashN[hb] / (hash1[base1]+.1)); if (qual < 1) qual = 1; #endif // =ACM GRSV TWYH KDBN * static int L[32] = { 5,0,1,5, 2,5,5,5, 3,5,5,5, 5,5,5,5, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, }; // convert from sam base to acgt*n order. base = L[base]; double MM, __, _M, oo, oM, o_, uu, um, mm, qe; // Correction for mapping quality. Maybe speed up via lookups? // Cannot nullify mapping quality completely. Lots of (true) // SNPs means low mapping quality. (Ideally need to know // hamming distance to next best location.) if (flags & CONS_MQUAL) { int mqual = b->core.qual; if (opts->nm_adjust) { //mqual /= (nm_local(p, b, pos)+1); mqual /= (nm_local(p, b, b->core.pos + p->seq_offset+1)+1); mqual *= 1 + 2*(0.5-(td>30?30:td)/60.0); // depth fudge } // higher => call more; +FP, -FN // lower => call less; -FP, +FN mqual *= opts->scale_mqual; // Drop these? They don't seem to ever help. if (mqual < opts->low_mqual) mqual = opts->low_mqual; if (mqual > opts->high_mqual) mqual = opts->high_mqual; double _p = 1-q2p[qual]; double _m = mqual_pow[mqual]; qual = ph_log(1-(_m * _p + (1 - _m)/4)); // CURRENT //qual = ph_log(1-_p*_m); // testing //qual *= 6/sqrt(td); } /* Quality 0 should never be permitted as it breaks the maths */ if (qual < 1) qual = 1; double poly = poly_len(p, b, b->core.pos + p->seq_offset+1); #ifdef DO_POLY_DIST poly_dist[bam_is_rev(b)][MIN(99,(int)poly)]++; #endif // EXPERIMENTAL // Adjust qual based on homopolymer length. // Affects different platforms by differing amounts. // May wish to further separate to qual2 and qual3 for ins and del? int qual2 = MAX(1, qual-(poly-2)*cp->poly_mul); /* MM=match _M=half-match __=mismatch */ __ = cp->p__[qual]; // neither match MM = cp->pMM[qual] - __; // both match _M = cp->p_M[qual] - __; // one allele only (half match) /* observation ACGT, but against hypothesis ** or *base */ oo = cp->poo[qual2] - __; oM = cp->poM[qual2] - __; o_ = cp->po_[qual2] - __; /* observation * */ uu = cp->puu[qual2] - __; um = cp->pum[qual2] - __; mm = cp->pmm[qual2] - __; if (flags & CONS_DISCREP) { qe = q2p[qual]; sumsC[base] += 1 - qe; } counts[base]++; #ifdef DO_FRACT counts2[bam_is_rev(b)][base]++; #endif // oM should never be higher than _M for actual bases! or... //printf("base %d@%d MM %f _M %f oM %f\n", base, qual, MM, _M, oM); switch (base) { case 0: // A S[0] += MM; S[1] += _M; S[2] += _M; S[3] += _M; S[4] += oM; S[8] += o_; S[11] += o_; S[13] += o_; S[14] += oo; break; case 1: // C S[1] += _M; S[5] += MM; S[6] += _M; S[7] += _M; S[8] += oM; S[4] += o_; S[11] += o_; S[13] += o_; S[14] += oo; //fprintf(stderr, "%d %f %f %f\n", qual, MM+__, oo+__, MM-oo); break; case 2: // G S[ 2] += _M; S[ 6] += _M; S[ 9] += MM; S[10] += _M; S[11] += oM; S[4] += o_; S[8] += o_; S[13] += o_; S[14] += oo; break; case 3: // T S[ 3] += _M; // _m S[ 7] += _M; S[10] += _M; S[12] += MM; // mm S[13] += oM; S[4] += o_; S[8] += o_; S[11] += o_; S[14] += oo; // S[14] oo break; case 4: // * // under under under under agree-no-base S[0] += uu; S[1 ]+= uu; S[2 ]+= uu; S[3 ]+= uu; S[4 ]+= um; S[5 ]+= uu; S[6 ]+= uu; S[7 ]+= uu; S[8 ]+= um; S[9 ]+= uu; S[10]+= uu; S[11]+= um; S[12]+= uu; S[13]+= um; S[14]+= mm; break; case 5: /* N => equal weight to all A,C,G,T but not a pad */ S[0] += MM; S[1 ]+= MM; S[2 ]+= MM; S[3 ]+= MM; S[4 ]+= oM; S[5 ]+= MM; S[6 ]+= MM; S[7 ]+= MM; S[8 ]+= oM; S[9 ]+= MM; S[10]+= MM; S[11]+= oM; S[12]+= MM; S[13]+= oM; S[14]+= oo; break; } depth++; } #ifdef DO_POLY_DIST // Or compute mean and s.d per strand. // Then compare likelihood of strands coming from the same distribution? // eg s.d=0.59 vs mean=3.41 sd=0.54... hmm // // Or compare ratio of most frequent to next most frequent, for each // strand. int d1 = 0, d2 = 0; double nd1 = 0, nd2 = 0; int k; for (k = 0; k < 100; k++) { if (!poly_dist[0][k] && !poly_dist[1][k]) continue; // fprintf(stdout, "%ld %d %2d %2d\n", pos, k, poly_dist[0][k], poly_dist[1][k]); d1 += (k+1)*poly_dist[0][k]; d2 += (k+1)*poly_dist[1][k]; nd1 += poly_dist[0][k]; nd2 += poly_dist[1][k]; } // printf("Avg = %f / %f %f / %f / %f\n", // (d1+d2+1)/(nd1+nd2+1.), // (d1+1)/(nd1+1.), (d2+1)/(nd2+1.), // (d2+1)/(nd2+1.) - (d1+1)/(nd1+1.), // ((d2+1)/(nd2+1.) - (d1+1)/(nd1+1.)) / ((d1+d2+1)/(nd1+nd2+1.))); // Find the top two frequent lengths int n1 = 0, n2 = 0, l1 = 0, l2 = 0; for (k = 0; k < 100; k++) { int poly12 = poly_dist[0][k]+poly_dist[1][k]; if (n1 < poly12) { n2 = n1; l2 = l1; n1 = poly12; l1 = k; } else if (n2 < poly12) { n2 = poly12; l2 = k; } } const double N = 5; nd1 += 1; nd2 += 1; // l1 is most common length int pn1p = poly_dist[0][l1]; int pn1m = poly_dist[1][l1]; // l2 2nd most common int pn2p = poly_dist[0][l2]; int pn2m = poly_dist[1][l2]; // ratio if two most common lengths on + double s1 = (pn1p+N) / (pn2p+N); s1 = s1>1?1/s1:s1; // ratio if two most common lengths on - double s2 = (pn1m+N) / (pn2m+N); s2 = s2>1?1/s2:s2; // ratio of s1 and s2 to identify strand bias double sbias = s1 / s2; sbias = sbias>1?1/sbias:sbias; if (pn2p+pn2m > 0 && l1 != l2) { // printf("len %d,%d + %d,%d - %d,%d\tbias = %f %f, %f %f\t%ld\n", // l1, l2, pn1p, pn2p, pn1m, pn2m, // s1, s2, sbias, sqrt(sbias)-1, pos); // adjust score for het indels // sbias is close to 0 for strong strand bias, and 1 for none sbias = 10*log(sbias);//+.5); S[ 4] += sbias; // A* S[ 8] += sbias; // C* S[11] += sbias; // G* S[13] += sbias; // T* } else { sbias = 0; } #endif /* We've accumulated stats, so now we speculate on the consensus call */ double shift, max, max_het, norm[15]; int call = 0, het_call = 0; double tot1 = 0, tot2 = 0; /* * Scale numbers so the maximum score is 0. This shift is essentially * a multiplication in non-log scale to both numerator and denominator, * so it cancels out. We do this to avoid calling exp(-large_num) and * ending up with norm == 0 and hence a 0/0 error. * * Can also generate the base-call here too. */ shift = -DBL_MAX; max = -DBL_MAX; max_het = -DBL_MAX; #ifdef DO_FRACT // Filter by --min-depth and --het-fract. // Also add a slight adjustment for strand bias. for (j = 0; j < 15; j++) { if (j == 0 || j == 5 || j == 9 || j == 12 || j == 14) continue; double c1p = counts2[0][map_het[j]%5]; double c1m = counts2[1][map_het[j]%5]; double c2p = counts2[0][map_het[j]/5]; double c2m = counts2[1][map_het[j]/5]; double c1 = c1p + c1m; double c2 = c2p + c2m; if (c1 && c2) { // Slight decrease in confidence if strong strand bias. const int N = 10; // avoid low sample size problems double b1 = 1 - (N+MIN(c1p,c1m))/(N+MAX(c1p,c1m)); double b2 = 1 - (N+MIN(c2p,c2m))/(N+MAX(c2p,c2m)); if (b1 > 0.5) S[j] -= b1; if (b2 > 0.5) S[j] -= b2; // Fraction based filtering, via --min-depth and --het-fract opts. c1 += 1e-5; c2 += 1e-5; if (c2 > c1) { double tmp = c2; c2 = c1; c1 = tmp; } if (c2 < opts->min_depth) S[j] -= 100; if (c2 / (c1+1e-5) <= opts->het_fract) S[j] -= 100; } } #endif #ifdef DO_HDW /* * Apply Hardy-Weinberg statistics for heterozygous sites. * This helps, but it also loses sensitivity a little. */ for (j = 0; j < 15; j++) { if (j == 0 || j == 5 || j == 9 || j == 12 || j == 14) continue; double c1 = counts[map_het[j]%5]; double c2 = counts[map_het[j]/5]; if (c1 && c2) { c1 += 1e-5; c2 += 1e-5; if (c2 > c1) { double tmp = c2; c2 = c1; c1 = tmp; } // Limit depth for HW as we'll have an allele freq difference, // even if it's just caused by alignment reference bias. double c12 = c1+c2; if (c12 > 20) { c2 *= 20/(c12); c12 = 20; c1 = 20-c2; } // Helps a little, especially reducing FN deletions. c1+=1; c2+=1; c12+=2; S[j] += lnbinprobhalf(c12, c2) + fast_log2(c12)*0.69+.2; } } #endif for (j = 0; j < 15; j++) { S[j] += cp->lprior15[j]; if (shift < S[j]) shift = S[j]; /* Only call pure AA, CC, GG, TT, ** for now */ if (j != 0 && j != 5 && j != 9 && j != 12 && j != 14) { if (max_het < S[j]) { max_het = S[j]; het_call = j; } continue; } if (max < S[j]) { max = S[j]; call = j; } } /* * Shift and normalise. * If call is, say, b we want p = b/(a+b+c+...+n), but then we do * p/(1-p) later on and this has exceptions when p is very close * to 1. * * Hence we compute b/(a+b+c+...+n - b) and * rearrange (p/norm) / (1 - (p/norm)) to be p/norm2. */ for (j = 0; j < 15; j++) { S[j] -= shift; double e = fast_exp(S[j]); S[j] = (S[j] > min_e_exp) ? e : DBL_MIN; norm[j] = 0; } for (j = 0; j < 15; j++) { norm[j] += tot1; norm[14-j] += tot2; tot1 += S[j]; tot2 += S[14-j]; } /* And store result */ if (!depth || depth == counts[5] /* all N */) { cons->call = 4; /* N */ cons->het_call = 0; cons->het_logodd = 0; cons->phred = 0; cons->depth = 0; cons->discrep = 0; return 0; } cons->depth = depth; /* Call */ if (norm[call] == 0) norm[call] = DBL_MIN; // Approximation of phred for when S[call] ~= 1 and norm[call] // is small. Otherwise we need the full calculation. int ph; if (S[call] == 1 && norm[call] < .01) ph = ph_log(norm[call]) + .5; else ph = ph_log(1-S[call]/(norm[call]+S[call])) + .5; cons->call = map_sing[call]; cons->phred = ph < 0 ? 0 : ph; if (norm[het_call] == 0) norm[het_call] = DBL_MIN; ph = TENLOG2OVERLOG10 * (fast_log2(S[het_call]) - fast_log2(norm[het_call])) + .5; cons->het_call = map_het[het_call]; cons->het_logodd = ph; /* Compute discrepancy score */ if (flags & CONS_DISCREP) { double m = sumsC[0]+sumsC[1]+sumsC[2]+sumsC[3]+sumsC[4]; double c; if (cons->het_logodd > 0) c = sumsC[cons->het_call%5] + sumsC[cons->het_call/5]; else c = sumsC[cons->call]; cons->discrep = (m-c)/sqrt(m); } return 0; } // If opts->gap5 is MODE_MIXED then we use two different parameter // sets, favouring cp_p for precision and cp_r for recall. Otherwise it's // always cp_r only. // // When both calls equal, we return the same result. When they differ, // we adjust qual based on accurate vs recall profiles. int calculate_consensus_gap5m(hts_pos_t pos, int flags, int depth, pileup_t *plp, consensus_opts *opts, consensus_t *cons, int default_qual, cons_probs *cp_r, cons_probs *cp_p) { if (opts->mode != MODE_MIXED) return calculate_consensus_gap5(pos, flags, depth, plp, opts, cons, default_qual, opts->mode == MODE_PRECISE ? cp_p : cp_r); // EXPERIMENTAL: mixed mode consensus_t consP, consR; // Favours precision calculate_consensus_gap5(pos, flags, depth, plp, opts, &consP, default_qual, cp_p); // Favours recall calculate_consensus_gap5(pos, flags, depth, plp, opts, &consR, default_qual, cp_r); #define MIN(a,b) ((a)<(b)?(a):(b)) #define MAX(a,b) ((a)>(b)?(a):(b)) // Initial starting point is precise mode memcpy(cons, &consP, sizeof(consP)); if (consP.phred > 0 && consR.phred > 0 && consP.call == consR.call) { // Both strategies match as HOM // Boost qual as both in agreement cons->phred += MIN(20, consR.phred); } else if (consP.het_logodd >= 0 && consR.het_logodd >= 0 && consP.het_call == consR.het_call) { // Both strategies match as HET // Boost qual as both in agreement cons->het_logodd += MIN(20, consR.het_logodd); } else if (consP.het_logodd >= 0) { // Accurate method claims heterozygous, so go with it. // However sensitive method disagrees, so reduce qual a little. int q2 = MAX(consR.phred, consR.het_logodd); cons->het_logodd = MAX(1, (cons->het_logodd - q2/2)); } else if (consR.het_logodd >= 70) { // Accurate is homozygous and consR is het, so we go with it instead // but at a lower quality value. // TODO: may wish to check HET is consistent with HOM? Very unlikely // not to be though. int q1 = consP.phred; int q2 = consR.het_logodd; memcpy(cons, &consR, sizeof(consR)); cons->het_logodd = MIN(15, MAX((q2-q1*2)/2, 1+q2/(q1+1.0))); } else if (consR.het_logodd >= 0) { // As above, but low quality int q1 = consP.phred; int q2 = consR.het_logodd; memcpy(cons, &consR, sizeof(consR)); cons->het_logodd = MAX(1,q2 - 0.3*q1) + 5*(consP.het_call == consR.het_call); cons->phred = 0; } else if (consR.het_logodd < 0) { // Neither are heterozygous, but differing in phred call (V rare). // Pick highest qual, after some scaling? consR.phred = consR.phred / 2; if (consR.phred > consP.phred) memcpy(cons, &consR, sizeof(consR)); cons->phred = MAX(10, cons->phred); } return 0; } /* -------------------------------------------------------------------------- * Main processing logic */ static void dump_fastq(consensus_opts *opts, const char *name, const char *seq, size_t seq_l, const char *qual, size_t qual_l) { enum format fmt = opts->fmt; int line_len = opts->line_len; FILE *fp = opts->fp_out; fprintf(fp, "%c%s\n", ">@"[fmt==FASTQ], name); size_t i; for (i = 0; i < seq_l; i += line_len) fprintf(fp, "%.*s\n", (int)MIN(line_len, seq_l - i), seq+i); if (fmt == FASTQ) { fprintf(fp, "+\n"); for (i = 0; i < seq_l; i += line_len) fprintf(fp, "%.*s\n", (int)MIN(line_len, seq_l - i), qual+i); } } //--------------------------------------------------------------------------- /* * Reads a single alignment record, using either the iterator * or a direct sam_read1 call. */ static int readaln2(void *dat, samFile *fp, sam_hdr_t *h, bam1_t *b) { consensus_opts *opts = (consensus_opts *)dat; for (;;) { int ret = opts->iter ? sam_itr_next(fp, opts->iter, b) : sam_read1(fp, h, b); if (ret < 0) return ret; // Apply hard filters if (opts->incl_flags && !(b->core.flag & opts->incl_flags)) continue; if (opts->excl_flags && (b->core.flag & opts->excl_flags)) continue; if (b->core.qual < opts->min_mqual) continue; return ret; } } /* -------------------------------------------------------------------------- * A simple summing algorithm, either pure base frequency, or by * weighting them according to their quality values. * * This is crude, but easy to understand and fits with several * standard pileup criteria (eg COG-UK / CLIMB Covid-19 seq project). * * * call1 / score1 is the highest scoring allele. * call2 / score2 is the second highest scoring allele. * * Het_fract: score2/score1 * Call_fract: score1 or score1+score2 over total score * Min_depth: minimum total depth of unfiltered bases (above qual/mqual) * Min_score: minimum total score of utilised bases (score1+score2) * * Eg het_fract 0.66, call_fract 0.75 and min_depth 10. * 11A, 2C, 2G (14 total depth) is A. * 9A, 2C, 2G (12 total depth) is N as depth(A) < 10. * 11A, 5C, 5G (21 total depth) is N as 11/21 < 0.75 (call_fract) * * * 6A, 5G, 1C (12 total depth) is AG het as depth(A)+depth(G) >= 10 * and 5/6 >= 0.66 and 11/12 >= 0.75. * * 6A, 5G, 4C (15 total depth) is N as (6+5)/15 < 0.75 (call_fract). * * * Note for the purpose of deletions, a base/del has an ambiguity * code of lower-case base (otherwise it is uppercase). */ static int calculate_consensus_simple(const pileup_t *plp, consensus_opts *opts, int *qual) { int i, min_qual = opts->min_qual; int tot_depth = 0; // Map "seqi" nt16 to A,C,G,T compatibility with weights on pure bases. // where seqi is A | (C<<1) | (G<<2) | (T<<3) // * A C M G R S V T W Y H K D B N static int seqi2A[16] = { 0,8,0,4, 0,4,0,2, 0,4,0,2, 0,2,0,1 }; static int seqi2C[16] = { 0,0,8,4, 0,0,4,2, 0,0,4,2, 0,0,2,1 }; static int seqi2G[16] = { 0,0,0,0, 8,4,4,1, 0,0,0,0, 4,2,2,1 }; static int seqi2T[16] = { 0,0,0,0, 0,0,0,0, 8,4,4,2, 8,2,2,1 }; // Ignore ambiguous bases in seq for now, so we don't treat R, Y, etc // as part of one base and part another. Based on BAM seqi values. // We also use freq[16] as "*" for gap. int freq[17] = {0}; // base frequency, aka depth uint64_t score[17] = {0}; // summation of base qualities // Accumulate for (; plp; plp = plp->next) { const pileup_t *p = plp; if (p->next) _mm_prefetch(p->next, _MM_HINT_T0); int q = p->qual; if (q < min_qual) // Should we still record these in freq[] somewhere so // we can use them in the fracts? // Difference between >= X% of high-qual bases calling Y // and >= X% of all bases are high-quality Y calls. continue; //int b = p->is_del ? 16 : bam_seqi(bam_get_seq(&p->b), p->seq_offset); int b = p->base4; // Map ambiguity codes to one or more component bases. if (b < 16) { int Q = seqi2A[b] * (opts->use_qual ? q : 1); freq[1] += Q?1:0; score[1] += Q?Q:0; Q = seqi2C[b] * (opts->use_qual ? q : 1); freq[2] += Q?1:0; score[2] += Q?Q:0; Q = seqi2G[b] * (opts->use_qual ? q : 1); freq[4] += Q?1:0; score[4] += Q?Q:0; Q = seqi2T[b] * (opts->use_qual ? q : 1); freq[8] += Q?1:0; score[8] += Q?Q:0; } else { /* * */ freq[16] ++; score[16]+=8 * (opts->use_qual ? q : 1); } tot_depth++; } // Total usable depth uint64_t tscore = 0; for (i = 0; i < 5; i++) tscore += score[1<= opts->het_fract * score1 && opts->ambig) { used_base |= call2; used_score += score2; } // N is too shallow, or insufficient proportion of total if (tot_depth < opts->min_depth || used_score < opts->call_fract * tscore) { // But note shallow gaps are still called gaps, not N, as // we're still more confident there is no base than it is // A, C, G or T. used_base = call1 == 16 ? 16 : 0; // * or N } // Our final call. "?" shouldn't be possible to generate const char *het = "NACMGRSVTWYHKDBN" "*ac?g???t???????"; //printf("%c %d\n", het[used_base], tot_depth); if (qual) *qual = used_base ? 100.0 * used_score / tscore : 0; return het[used_base]; } static int empty_pileup2(consensus_opts *opts, sam_hdr_t *h, int tid, hts_pos_t start, hts_pos_t end) { const char *name = sam_hdr_tid2name(h, tid); hts_pos_t i; int err = 0; for (i = start; i < end; i++) err |= fprintf(opts->fp_out, "%s\t%"PRIhts_pos"\t0\t0\tN\t0\t*\t*\n", name, i+1) < 0; return err ? -1 : 0; } /* * Returns 0 on success * -1 on failure */ static int basic_pileup(void *cd, samFile *fp, sam_hdr_t *h, pileup_t *p, int depth, hts_pos_t pos, int nth, int is_insert) { unsigned char *qp, *cp; char *rp; int ref, cb, cq; consensus_opts *opts = (consensus_opts *)cd; int tid = p->b.core.tid; // opts->show_ins=0; // opts->show_del=1; if (!opts->show_ins && nth) return 0; if (opts->iter) { if (opts->iter->beg >= pos || opts->iter->end < pos) return 0; } if (opts->all_bases) { if (tid != opts->last_tid && opts->last_tid >= -1) { if (opts->last_tid >= 0) { // remainder of previous ref hts_pos_t len = sam_hdr_tid2len(opts->h, opts->last_tid); if (opts->iter) len = MIN(opts->iter->end, len); if (empty_pileup2(opts, opts->h, opts->last_tid, opts->last_pos, len) < 0) return -1; } opts->last_pos = opts->iter ? opts->iter->beg : 0; } // Any refs between last_tid and tid if (!opts->iter && tid > opts->last_tid && opts->all_bases > 1) { while (++opts->last_tid < tid) { hts_pos_t len = sam_hdr_tid2len(opts->h, opts->last_tid); if (empty_pileup2(opts, opts->h, opts->last_tid, 0, len) < 0) return -1; } } // Any gaps in this ref (same tid) or at start of this new tid if (opts->last_pos >= 0 && pos > opts->last_pos+1) { if (empty_pileup2(opts, opts->h, p->b.core.tid, opts->last_pos, pos-1) < 0) return -1; } else if (opts->last_pos < 0) { if (empty_pileup2(opts, opts->h, p->b.core.tid, opts->iter ? opts->iter->beg : 0, pos-1) < 0) return -1; } } if (opts->mode != MODE_SIMPLE) { consensus_t cons; calculate_consensus_gap5m(pos, opts->use_mqual ? CONS_MQUAL : 0, depth, p, opts, &cons, opts->default_qual, &cons_prob_recall, &cons_prob_precise); if (cons.depth < opts->min_depth) { cb = 'N'; cq = 0; } else if (cons.het_logodd > 0 && opts->ambig) { cb = "AMRWa" // 5x5 matrix with ACGT* per row / col "MCSYc" "RSGKg" "WYKTt" "acgt*"[cons.het_call]; cq = cons.het_logodd; } else{ cb = "ACGT*"[cons.call]; cq = cons.phred; } if (cq < opts->cons_cutoff && cb != '*') { cb = 'N'; cq = 0; } } else { cb = calculate_consensus_simple(p, opts, &cq); } if (cb < 0) return -1; if (!p) return 0; if (!opts->show_del && cb == '*') return 0; /* Ref, pos, nth, score, seq, qual */ kstring_t *ks = &opts->ks_line; ks->l = 0; ref = p->b.core.tid; rp = (char *)sam_hdr_tid2name(h, ref); int err = 0; err |= kputs(rp, ks) < 0; err |= kputc_('\t', ks) < 0; err |= kputw(pos, ks) < 0; err |= kputc_('\t', ks) < 0; err |= kputw(nth, ks) < 0; err |= kputc_('\t', ks) < 0; err |= kputw(depth, ks) < 0; err |= kputc_('\t', ks) < 0; err |= kputc_(cb, ks) < 0; err |= kputc_('\t', ks) < 0; err |= kputw(cq, ks) < 0; err |= kputc_('\t', ks) < 0; if (err) return -1; /* Seq + qual at predetermined offsets */ if (ks_resize(ks, ks->l + depth*2 + 2) < 0) return -1; cp = (unsigned char *)ks->s + ks->l; ks->l += depth*2 + 2; qp = cp+depth+1; for (; p; p = p->next) { // Too tight a loop to help much, but some benefit still if (p->next && p->next->next) _mm_prefetch(p->next->next, _MM_HINT_T0); if (p->b_is_rev) { *cp++ = p->base == '*' ? '#' : tolower(p->base); } else { *cp++ = p->base; } *qp++ = MIN(p->qual,93) + '!'; } *cp++ = '\t'; *qp++ = '\n'; if (fwrite(ks->s, 1, ks->l, opts->fp_out) != ks->l) return -1; opts->last_pos = pos; opts->last_tid = tid; return 0; } static int basic_fasta(void *cd, samFile *fp, sam_hdr_t *h, pileup_t *p, int depth, hts_pos_t pos, int nth, int is_insert) { int cb, cq; consensus_opts *opts = (consensus_opts *)cd; int tid = p->b.core.tid; kstring_t *seq = &opts->ks_ins_seq; kstring_t *qual = &opts->ks_ins_qual; if (!opts->show_ins && nth) return 0; if (opts->iter) { if (opts->iter->beg >= pos || opts->iter->end < pos) return 0; } next_ref: if (tid != opts->last_tid) { if (opts->last_tid != -1) { if (opts->all_bases) { // Fill in remainder of previous reference int i, N; if (opts->iter) { opts->last_pos = MAX(opts->last_pos, opts->iter->beg-1); N = opts->iter->end; } else { N = INT_MAX; } N = MIN(N, sam_hdr_tid2len(opts->h, opts->last_tid)) - opts->last_pos; if (N > 0) { if (ks_expand(seq, N+1) < 0) return -1; if (ks_expand(qual, N+1) < 0) return -1; for (i = 0; i < N; i++) { seq->s[seq->l++] = 'N'; qual->s[qual->l++] = '!'; } seq->s[seq->l] = 0; qual->s[qual->l] = 0; } } dump_fastq(opts, sam_hdr_tid2name(opts->h, opts->last_tid), seq->s, seq->l, qual->s, qual->l); } seq->l = 0; qual->l = 0; if (!opts->iter && opts->all_bases > 1 && ++opts->last_tid < tid) { opts->last_pos = 0; goto next_ref; } opts->last_tid = tid; if (opts->iter) opts->last_pos = opts->iter->beg; else opts->last_pos = opts->all_bases ? 0 : pos-1; } // share this with basic_pileup if (opts->mode != MODE_SIMPLE) { consensus_t cons; calculate_consensus_gap5m(pos, opts->use_mqual ? CONS_MQUAL : 0, depth, p, opts, &cons, opts->default_qual, &cons_prob_recall, &cons_prob_precise); if (cons.depth < opts->min_depth) { cb = 'N'; cq = 0; } else if (cons.het_logodd > 0 && opts->ambig) { cb = "AMRWa" // 5x5 matrix with ACGT* per row / col "MCSYc" "RSGKg" "WYKTt" "acgt*"[cons.het_call]; cq = cons.het_logodd; } else { cb = "ACGT*"[cons.call]; cq = cons.phred; } if (cq < opts->cons_cutoff && cb != '*' && cons.het_call % 5 != 4 && cons.het_call / 5 != 4) { // het base/* keeps base or * as most likely pure call, else N. // This is because we don't have a traditional way of representing // base or not-base ambiguity. cb = 'N'; cq = 0; } } else { cb = calculate_consensus_simple(p, opts, &cq); } if (cb < 0) return -1; if (!p) return 0; if (!opts->show_del && cb == '*') { opts->last_pos = pos; opts->last_tid = tid; return 0; } if (opts->mark_ins && nth && cb != '*') { kputc('_', seq); kputc('_', qual); } // end of share // Append consensus base/qual to seqs if (pos > opts->last_pos) { if (opts->last_pos >= 0 || opts->all_bases) { // FIXME: don't expand qual if fasta if (ks_expand(seq, pos - opts->last_pos) < 0 || ks_expand(qual, pos - opts->last_pos) < 0) return -1; memset(seq->s + seq->l, 'N', pos - (opts->last_pos+1)); memset(qual->s + qual->l, '!', pos - (opts->last_pos+1)); seq->l += pos - (opts->last_pos+1); qual->l += pos - (opts->last_pos+1); } } if ((nth && opts->show_ins && cb != '*') || cb != '*' || (pos > opts->last_pos && opts->show_del)) { int err = 0; err |= kputc(cb, seq) < 0; err |= kputc(MIN(cq, '~'-'!')+'!', qual) < 0; if (err) return -1; } opts->last_pos = pos; opts->last_tid = tid; return 0; } // END OF NEW PILEUP //--------------------------------------------------------------------------- static void usage_exit(FILE *fp, int exit_status) { fprintf(fp, "Usage: samtools consensus [options] \n"); fprintf(fp, "\nOptions:\n"); fprintf(fp, " -r, --region REG Limit query to REG. Requires an index\n"); fprintf(fp, " -f, --format FMT Output in format FASTA, FASTQ or PILEUP [FASTA]\n"); fprintf(fp, " -l, --line-len INT Wrap FASTA/Q at line length INT [70]\n"); fprintf(fp, " -o, --output FILE Output consensus to FILE\n"); fprintf(fp, " -m, --mode STR Switch consensus mode to \"simple\"/\"bayesian\" [bayesian]\n"); fprintf(fp, " -a Output all bases (start/end of reference)\n"); fprintf(fp, " --rf, --incl-flags STR|INT\n"); fprintf(fp, " Only include reads with any flag bit set [0]\n"); fprintf(fp, " --ff, --excl-flags STR|INT\n"); fprintf(fp, " Exclude reads with any flag bit set\n"); fprintf(fp, " [UNMAP,SECONDARY,QCFAIL,DUP]\n"); fprintf(fp, " --min-MQ INT Exclude reads with mapping quality below INT [0]\n"); fprintf(fp, " --min-BQ INT Exclude reads with base quality below INT [0]\n"); fprintf(fp, " --show-del yes/no Whether to show deletion as \"*\" [no]\n"); fprintf(fp, " --show-ins yes/no Whether to show insertions [yes]\n"); fprintf(fp, " --mark-ins Add '+' before every inserted base/qual [off]\n"); fprintf(fp, " -A, --ambig Enable IUPAC ambiguity codes [off]\n"); fprintf(fp, " -d, --min-depth INT Minimum depth of INT [1]\n"); fprintf(fp, "\nFor simple consensus mode:\n"); fprintf(fp, " -q, --(no-)use-qual Use quality values in calculation [off]\n"); fprintf(fp, " -c, --call-fract INT At least INT portion of bases must agree [0.75]\n"); fprintf(fp, " -H, --het-fract INT Minimum fraction of 2nd-most to most common base [0.15]\n"); fprintf(fp, "\nFor default \"Bayesian\" consensus mode:\n"); fprintf(fp, " -C, --cutoff C Consensus cutoff quality C [10]\n"); fprintf(fp, " --(no-)adj-qual Modify quality with local minima [on]\n"); fprintf(fp, " --(no-)use-MQ Use mapping quality in calculation [on]\n"); fprintf(fp, " --(no-)adj-MQ Modify mapping quality by local NM [on]\n"); fprintf(fp, " --NM-halo INT Size of window for NM count in --adj-MQ [50]\n"); fprintf(fp, " --scale-MQ FLOAT Scale mapping quality by FLOAT [1.00]\n"); fprintf(fp, " --low-MQ INT Cap minimum mapping quality [1]\n"); fprintf(fp, " --high-MQ INT Cap maximum mapping quality [60]\n"); fprintf(fp, " --P-het FLOAT Probability of heterozygous site[%.1e]\n", P_HET); fprintf(fp, " --P-indel FLOAT Probability of indel sites[%.1e]\n", P_INDEL); fprintf(fp, " --het-scale FLOAT Heterozygous SNP probability multiplier[%.1e]\n", P_HET_SCALE); fprintf(fp, " -p, --homopoly-fix Spread low-qual bases to both ends of homopolymers\n"); fprintf(fp, " --homopoly-score FLOAT\n" " Qual fraction adjustment for -p option [%g]\n", P_HOMOPOLY); fprintf(fp, " -t, --qual-calibration FILE / :config (see man page)\n"); fprintf(fp, " Load quality calibration file\n"); fprintf(fp, "\n"); fprintf(fp, " -X, --config STR Use pre-defined configuration set. STR from:\n"); fprintf(fp, " hiseq, hifi, r10.4_sup, r10.4_dup and ultima\n"); fprintf(fp, "\nGlobal options:\n"); sam_global_opt_help(fp, "-.---@-."); exit(exit_status); } int main_consensus(int argc, char **argv) { int c, ret = 1; consensus_opts opts = { // User options .mode = MODE_RECALL, .use_qual = 0, .min_qual = 0, .adj_qual = 1, .use_mqual = 1, .scale_mqual = 1.00, .nm_adjust = 1, .nm_halo = 50, .sc_cost = 60, .low_mqual = 1, .high_mqual = 60, .min_depth = 1, .call_fract = 0.75, .het_fract = 0.5, .het_only = 0, .fmt = FASTA, .cons_cutoff = 10, .ambig = 0, .line_len = 70, .default_qual = 10, .all_bases = 0, .show_del = 0, .show_ins = 1, .mark_ins = 0, .incl_flags = 0, .excl_flags = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP, .min_mqual = 0, .P_het = P_HET, .P_indel = P_INDEL, .het_scale = P_HET_SCALE, .homopoly_fix = 0, .homopoly_redux = 0.01, // Internal state .ks_line = {0,0}, .ks_ins_seq = {0,0}, .ks_ins_qual = {0,0}, .fp = NULL, .fp_out = stdout, .iter = NULL, .idx = NULL, .last_tid = -1, .last_pos = -1, }; set_qcal(&opts.qcal, QCAL_FLAT); sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', '-', '-', '@'), {"use-qual", no_argument, NULL, 'q'}, {"no-use-qual", no_argument, NULL, 'q'+1000}, {"adj-qual", no_argument, NULL, 'q'+100}, {"no-adj-qual", no_argument, NULL, 'q'+101}, {"use-MQ", no_argument, NULL, 'm'+1000}, {"no-use-MQ", no_argument, NULL, 'm'+1001}, {"adj-MQ", no_argument, NULL, 'm'+100}, {"no-adj-MQ", no_argument, NULL, 'm'+101}, {"NM-halo", required_argument, NULL, 'h'+100}, {"SC-cost", required_argument, NULL, 'h'+101}, {"scale-MQ", required_argument, NULL, 14}, {"low-MQ" , required_argument, NULL, 9}, {"high-MQ", required_argument, NULL, 10}, {"min-depth", required_argument, NULL, 'd'}, {"call-fract", required_argument, NULL, 'c'}, {"het-fract", required_argument, NULL, 'H'}, {"region", required_argument, NULL, 'r'}, {"format", required_argument, NULL, 'f'}, {"cutoff", required_argument, NULL, 'C'}, {"ambig", no_argument, NULL, 'A'}, {"line-len", required_argument, NULL, 'l'}, {"default-qual", required_argument, NULL, 1}, {"het-only", no_argument, NULL, 6}, {"show-del", required_argument, NULL, 7}, {"show-ins", required_argument, NULL, 8}, {"mark-ins", no_argument, NULL, 18}, {"output", required_argument, NULL, 'o'}, {"incl-flags", required_argument, NULL, 11}, {"rf", required_argument, NULL, 11}, {"excl-flags", required_argument, NULL, 12}, {"ff", required_argument, NULL, 12}, {"min-MQ", required_argument, NULL, 13}, {"min-BQ", required_argument, NULL, 16}, {"P-het", required_argument, NULL, 15}, {"P-indel", required_argument, NULL, 17}, {"het-scale", required_argument, NULL, 19}, {"mode", required_argument, NULL, 'm'}, {"homopoly-fix", no_argument, NULL, 'p'}, {"homopoly-score", required_argument, NULL, 'p'+100}, {"homopoly-redux", required_argument, NULL, 'p'+200}, {"qual-calibration", required_argument, NULL, 't'}, {"config", required_argument, NULL, 'X'}, {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "@:qd:c:H:r:5f:C:aAl:o:m:pt:X:", lopts, NULL)) >= 0) { switch (c) { case 'a': opts.all_bases++; break; case 'q': opts.use_qual=1; break; case 'q'+1000: opts.use_qual=0; break; case 'm'+1000: opts.use_mqual=1; break; case 'm'+1001: opts.use_mqual=0; break; case 14: opts.scale_mqual = atof(optarg); break; case 9: opts.low_mqual = atoi(optarg); break; case 10: opts.high_mqual = atoi(optarg); break; case 'd': opts.min_depth = atoi(optarg); break; case 'c': opts.call_fract = atof(optarg); break; case 'H': opts.het_fract = atof(optarg); break; case 'r': opts.reg = optarg; break; case 'C': opts.cons_cutoff = atoi(optarg); break; case 'A': opts.ambig = 1; break; case 'p': opts.homopoly_fix = P_HOMOPOLY; break; case 'p'+100: opts.homopoly_fix = atof(optarg); break; case 'p'+200: // EXPERIMENTAL opts.homopoly_redux = atof(optarg); break; case 1: opts.default_qual = atoi(optarg); break; case 6: opts.het_only = 1; break; case 7: opts.show_del = (*optarg == 'y' || *optarg == 'Y'); break; case 8: opts.show_ins = (*optarg == 'y' || *optarg == 'Y'); break; case 18: opts.mark_ins = 1; break; case 13: opts.min_mqual = atoi(optarg); break; case 16: opts.min_qual = atoi(optarg); break; case 15: opts.P_het = atof(optarg); break; case 17: opts.P_indel = atof(optarg); break; case 19: opts.het_scale = atof(optarg); break; case 'q'+100: opts.adj_qual = 1; break; case 'q'+101: opts.adj_qual = 0; break; case 'm'+100: opts.nm_adjust = 1; break; case 'm'+101: opts.nm_adjust = 0; break; case 'h'+100: opts.nm_halo = atoi(optarg); break; case 'h'+101: opts.sc_cost = atoi(optarg); break; case 'm': // mode if (strcasecmp(optarg, "simple") == 0) { opts.mode = MODE_SIMPLE; } else if (strcasecmp(optarg, "bayesian_m") == 0) { // EXPERIMENTAL: // A mixture of modified precise/recall params and a // blending of the two. Sometimes helps a bit. opts.mode = MODE_MIXED; } else if (strcasecmp(optarg, "bayesian_p") == 0) { // EXPERIMENTAL: // favours precision opts.mode = MODE_PRECISE; } else if (strcasecmp(optarg, "bayesian_r") == 0 || strcasecmp(optarg, "bayesian") == 0) { // favours recall; the default opts.mode = MODE_RECALL; } else if (strcasecmp(optarg, "bayesian_116") == 0) { opts.mode = MODE_BAYES_116; } else { fprintf(stderr, "Unknown mode %s\n", optarg); return 1; } break; case 'l': if ((opts.line_len = atoi(optarg)) <= 0) opts.line_len = INT_MAX; break; case 'f': if (strcasecmp(optarg, "fasta") == 0) { opts.fmt = FASTA; } else if (strcasecmp(optarg, "fastq") == 0) { opts.fmt = FASTQ; } else if (strcasecmp(optarg, "pileup") == 0) { opts.fmt = PILEUP; } else { fprintf(stderr, "Unknown format %s\n", optarg); return 1; } break; case 'o': if (!(opts.fp_out = fopen(optarg, "w"))) { perror(optarg); return 1; } break; case 'X': if (strcasecmp(optarg, "hifi") == 0) { set_qcal(&opts.qcal, QCAL_HIFI); opts.mode = MODE_RECALL; opts.homopoly_fix = 0.3; opts.homopoly_redux = 0.01; opts.low_mqual = 5; opts.scale_mqual = 1.5; opts.het_scale = 0.37; } else if (strcasecmp(optarg, "hiseq") == 0) { opts.mode = MODE_RECALL; set_qcal(&opts.qcal, QCAL_HISEQ); opts.homopoly_redux = 0.01; } else if (strcasecmp(optarg, "r10.4_sup") == 0) { // Same as HiFi params, but ONT calibration table. // At higher depth, hifi params work well for ONT // when combined with ONT calibration chart. // // At lower depth we gain a bit from increasing homopoly_redux set_qcal(&opts.qcal, QCAL_ONT_R10_4_SUP); opts.mode = MODE_RECALL; opts.homopoly_fix = 0.3; opts.homopoly_redux = 0.01; opts.low_mqual = 5; opts.scale_mqual = 1.5; opts.het_scale = 0.37; // Also consider, for lower depth: // opts.homopoly_redux = 1; // opts.scale_mqual = 1; // opts.het_scale = 0.45; } else if (strcasecmp(optarg, "r10.4_dup") == 0) { // Just a copy of of HiFi for duplex currently until // we get a good truth set for calibration. set_qcal(&opts.qcal, QCAL_ONT_R10_4_DUP); opts.mode = MODE_RECALL; opts.homopoly_fix = 0.3; opts.homopoly_redux = 0.01; opts.low_mqual = 5; opts.scale_mqual = 1.5; opts.het_scale = 0.37; } else if (strcasecmp(optarg, "ultima") == 0) { // Very similar to HiFi, but with own calibration table opts.mode = MODE_RECALL; set_qcal(&opts.qcal, QCAL_ULTIMA); opts.homopoly_fix = 0.3; opts.homopoly_redux = 0.01; opts.het_scale = 0.37; opts.scale_mqual = 2; opts.low_mqual = 10; } else { // NB consider defaults that are a mixture of all above. // Options are all similar for all bar Illumina. // Unsure what :flat calibration table does to each of // these though. fprintf(stderr, "Unrecognised configuration name: \"%s\"\n", optarg); return 1; } break; case 11: if ((opts.incl_flags = bam_str2flag(optarg)) < 0) { print_error("consensus", "could not parse --rf %s", optarg); return 1; } break; case 12: if ((opts.excl_flags = bam_str2flag(optarg)) < 0) { print_error("consensus", "could not parse --ff %s", optarg); return 1; } break; case 't': // --qual-calibration if (load_qcal(&opts.qcal, optarg) < 0) { print_error("consensus", "failed to load quality calibration '%s'", optarg); return -1; } break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage_exit(stderr, EXIT_FAILURE); } } #if 0 // Dump out the qcal table. Useful for copying into the code above. int i; qcal_t *q = &opts.qcal; fprintf(stderr, "{"); for (i = 0; i < 100; i++) fprintf(stderr, "%2d,%s", q->smap[i],(i+1)%10?" ":"\n"); fprintf(stderr, "},\n{"); for (i = 0; i < 100; i++) fprintf(stderr, "%2d,%s", q->umap[i],(i+1)%10?" ":"\n"); fprintf(stderr, "},\n{"); for (i = 0; i < 100; i++) fprintf(stderr, "%2d,%s", q->omap[i],(i+1)%10?" ":"\n"); fprintf(stderr, "}\n"); #endif if (opts.mode != MODE_SIMPLE) { if (opts.mode == MODE_PRECISE) // More accuracy / precision, but a significant drop // in recall. consensus_init(opts.P_het, opts.P_indel, 0.3 * opts.het_scale, opts.homopoly_redux, &opts.qcal, MODE_PRECISE, &cons_prob_precise); if (opts.mode == MODE_MIXED) // Blend these in when running in mixed mode, so we can // keep sensitivity but have a better joint quality to // reduce the FP rate. consensus_init(pow(opts.P_het, 0.7), pow(opts.P_indel, 0.7), 0.3 * opts.het_scale, opts.homopoly_redux, &opts.qcal, MODE_PRECISE, &cons_prob_precise); // Better recall, at a cost of some accuracy (false positives) consensus_init(opts.P_het, opts.P_indel, opts.het_scale, opts.mode == MODE_RECALL ? opts.homopoly_redux : 0.01, &opts.qcal, MODE_RECALL, &cons_prob_recall); } if (argc != optind+1) { if (argc == optind) usage_exit(stdout, EXIT_SUCCESS); else usage_exit(stderr, EXIT_FAILURE); } opts.fp = sam_open_format(argv[optind], "r", &ga.in); if (opts.fp == NULL) { print_error_errno("consensus", "Cannot open input file \"%s\"", argv[optind]); goto err; } if (ga.nthreads > 0) hts_set_threads(opts.fp, ga.nthreads); if (hts_set_opt(opts.fp, CRAM_OPT_DECODE_MD, 0)) { fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n"); goto err; } if (!(opts.h = sam_hdr_read(opts.fp))) { fprintf(stderr, "Failed to read header for \"%s\"\n", argv[optind]); goto err; } if (opts.reg) { opts.idx = sam_index_load(opts.fp, argv[optind]); if (!opts.idx) { print_error("consensus", "Cannot load index for input file \"%s\"", argv[optind]); goto err; } opts.iter = sam_itr_querys(opts.idx, opts.h, opts.reg); if (!opts.iter) { print_error("consensus", "Failed to parse region \"%s\"", opts.reg); goto err; } } if (opts.fmt == PILEUP) { if (pileup_loop(opts.fp, opts.h, readaln2, opts.mode != MODE_SIMPLE ? nm_init : NULL, basic_pileup, opts.mode != MODE_SIMPLE ? nm_free : NULL, &opts) < 0) goto err; if (opts.all_bases) { int tid = opts.iter ? opts.iter->tid : opts.last_tid; int len = sam_hdr_tid2len(opts.h, tid); int pos = opts.last_pos; if (opts.iter) { len = MIN(opts.iter->end, len); pos = MAX(opts.iter->beg, pos); } if (empty_pileup2(&opts, opts.h, tid, pos, len) < 0) goto err; } while (!opts.iter && opts.all_bases > 1 && ++opts.last_tid < opts.h->n_targets) { int len = sam_hdr_tid2len(opts.h, opts.last_tid); if (empty_pileup2(&opts, opts.h, opts.last_tid, 0, len) < 0) goto err; } } else { if (pileup_loop(opts.fp, opts.h, readaln2, opts.mode != MODE_SIMPLE ? nm_init : NULL, basic_fasta, opts.mode != MODE_SIMPLE ? nm_free : NULL, &opts) < 0) goto err; next_ref_q: if (opts.all_bases) { // fill out terminator int tid = opts.iter ? opts.iter->tid : opts.last_tid; int len = sam_hdr_tid2len(opts.h, tid); int pos = opts.last_pos; if (opts.iter) { len = MIN(opts.iter->end, len); pos = MAX(opts.iter->beg, pos); opts.last_tid = opts.iter->tid; } if (pos < len) { if (ks_expand(&opts.ks_ins_seq, len-pos+1) < 0) goto err; if (ks_expand(&opts.ks_ins_qual, len-pos+1) < 0) goto err; while (pos++ < len) { opts.ks_ins_seq.s [opts.ks_ins_seq.l++] = 'N'; opts.ks_ins_qual.s[opts.ks_ins_qual.l++] = '!'; } opts.ks_ins_seq.s [opts.ks_ins_seq.l] = 0; opts.ks_ins_qual.s[opts.ks_ins_qual.l] = 0; } } if (opts.last_tid >= 0) dump_fastq(&opts, sam_hdr_tid2name(opts.h, opts.last_tid), opts.ks_ins_seq.s, opts.ks_ins_seq.l, opts.ks_ins_qual.s, opts.ks_ins_qual.l); if (!opts.iter && opts.all_bases > 1 && ++opts.last_tid < opts.h->n_targets) { opts.last_pos = 0; opts.ks_ins_seq.l = opts.ks_ins_qual.l = 0; goto next_ref_q; } // if (consensus_loop(&opts) < 0) { // print_error_errno("consensus", "Failed"); // goto err; // } } ret = 0; err: if (opts.iter) hts_itr_destroy(opts.iter); if (opts.idx) hts_idx_destroy(opts.idx); if (opts.fp && sam_close(opts.fp) < 0) { print_error_errno("consensus", "Closing input file \"%s\"", argv[optind]); ret = 1; } if (opts.h) sam_hdr_destroy(opts.h); sam_global_args_free(&ga); if (opts.fp_out && opts.fp_out != stdout) ret |= fclose(opts.fp_out) != 0; else ret |= fflush(stdout) != 0; ks_free(&opts.ks_line); ks_free(&opts.ks_ins_seq); ks_free(&opts.ks_ins_qual); if (ret) print_error("consensus", "failed"); return ret; } pysam-0.23.0/samtools/bam_consensus.c.pysam.c000066400000000000000000003035361475062545500211710ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_consensus.c -- consensus subcommand. Copyright (C) 1998-2001,2003 Medical Research Council (Gap4/5 source) Copyright (C) 2003-2005,2007-2024 Genome Research Ltd. Author: James Bonfield The primary work here is GRL since 2021, under an MIT license. Sections derived from Gap5, which include calculate_consensus_gap5() associated functions, are mostly copyright Genome Research Limited from 2003 onwards. These were originally under a BSD license, but as GRL is copyright holder these portions can be considered to also be under the same MIT license below: Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* * The Gap5 consensus algorithm was in turn derived from the earlier Gap4 * tool, developed by the Medical Research Council as part of the * Staden Package. It is unsure how much of this source code is still * extant, without deep review, but the license used was a compatible * modified BSD license, included below. */ /* Modified BSD license for any legacy components from the Staden Package: Copyright (c) 2003 MEDICAL RESEARCH COUNCIL All rights reserved Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ // FIXME: also use strand to spot possible basecalling errors. // Specifically het calls where mods are predominantly on one // strand. So maybe require + and - calls and check concordance // before calling a het as confident. (Still call, but low qual?) // TODO: call by kmers rather than individual bases? Or use kmers to skew // quality at least. It can identify variants that are low quality due to // neighbouring edits that aren't consistently correlated. // TODO: pileup callback ought to know when it's the last in the region / // chromosome. This means the caller code doesn't have to handle the // termination phase and deduplicates the code. (Changing from // one chr to the next is the same as ending the last.) // // TODO: track which reads contribute to multiple confirmed (HQ) differences // vs which contribute to only one (LQ) difference. Correlated changes // are more likely to be real. Ie consensus more of a path than solely // isolated columns. // // Either that or a dummy "end of data" call is made to signify end to // permit tidying up. Maybe add a "start of data" call too? // Eg 50T 20A seems T/A het, // but 30T+ 20T- 18A+ 2A- seems like a consistent A miscall on one strand // only, while T is spread evenly across both strands. // TODO: Phasing of long reads. // Long reads offer very strong phasing opportunities for SNPs. // From these, we get strong evidence for accuracy of indels. // Specifically whether the distribution of poly-len within a phases // is significantly different to the distribution of poly len between // phases. // TODO end STR trimming. Eg: // REF AAGCTGAAAAGTTAATGTCTTATTTTTTTTTTTTTTTTGAGATGGAGTC // aagctgaaaagttaatgtctta****ttttttttttttgagatggagtc // aagctgaaaagttaatgtcttattttttttt // aagctgaaaagttaatgtctta****ttttttttttttgagatggagtc // Middle seq doesn't validate those initial T alignments. // Qual_train solves this by use of the STR trimmer. // TODO add a weight for proximity to homopolymer. // Maybe length/distance? So 3 away from a 12-mer is similar to 1 away // from a 4-mer? // TODO: Count number of base types between this point and the nearest // indel or end of read. Eg GATCGAGAGAG*TAGC => 2 (A and G). // adj is nbase/4 * score, or (nbase+1)/5? // Perhaps multiplied by length too, to get local complexity score? #include #include #include #include #include #include #include #include #include #include #include "samtools.h" #include "sam_opts.h" #include "bam_plbuf.h" #include "consensus_pileup.h" #ifdef __SSE__ # include #else # define _mm_prefetch(a,b) #endif #ifndef MIN # define MIN(a,b) ((a)<(b)?(a):(b)) #endif #ifndef MAX # define MAX(a,b) ((a)>(b)?(a):(b)) #endif // Defines for experiment code which is currently disabled // Hardy-Weinberg statistics to check heterozygous sites match allelic // frequencies. //#define DO_HDW // Filter bayesian calls by min-depth and min-fract parameters //#define DO_FRACT // Checks uniqueness of surrounding bases to adjust scores //#define K2 2 // Look for strand bias in distribution of homopolymer lengths //#define DO_POLY_DIST // Minimum cutoff for storing mod data; => at least 10% chance #define MOD_CUTOFF 0.46 enum format { FASTQ, FASTA, PILEUP }; typedef unsigned char uc; // Simple recalibration table for substitutions, undercalls and overcalls. // In future, we'll update this to be kmer based too. typedef struct { int smap[101]; // substituion or SNP int umap[101]; // undercall or DEL int omap[101]; // overcall or INS } qcal_t; typedef struct { // User options char *reg; int use_qual; int min_qual; int adj_qual; int use_mqual; double scale_mqual; int nm_adjust; int nm_halo; int sc_cost; int low_mqual; int high_mqual; int min_depth; double call_fract; double het_fract; int mode; // One of MODE_* macros below enum format fmt; int cons_cutoff; int ambig; int line_len; int default_qual; int het_only; int all_bases; int show_del; int show_ins; int mark_ins; int excl_flags; int incl_flags; int min_mqual; double P_het; double P_indel; double het_scale; double homopoly_fix; double homopoly_redux; qcal_t qcal; // Internal state samFile *fp; FILE *fp_out; sam_hdr_t *h; hts_idx_t *idx; hts_itr_t *iter; kstring_t ks_line; kstring_t ks_ins_seq; kstring_t ks_ins_qual; int last_tid; hts_pos_t last_pos; } consensus_opts; /* -------------------------------------------------------------------------- * A bayesian consensus algorithm that analyses the data to work out * which hypothesis of pure A/C/G/T/absent and all combinations of two * such bases meets the observations. * * This has its origins in Gap4 (homozygous) -> Gap5 (heterozygous) * -> Crumble (tidied up to use htslib's pileup) -> here. * */ #define CONS_DISCREP 4 #define CONS_ALL 15 #define CONS_MQUAL 16 typedef struct { /* the most likely base call - we never call N here */ /* A=0, C=1, G=2, T=3, *=4 */ int call; /* The most likely heterozygous base call */ /* Use "ACGT*"[het / 5] vs "ACGT*"[het % 5] for the combination */ int het_call; /* Log-odds for het_call */ int het_logodd; /* Single phred style call */ int phred; /* Sequence depth */ int depth; /* Discrepancy search score */ float discrep; } consensus_t; #define P_HET 1e-3 #define P_INDEL 2e-4 #define P_HOMOPOLY 0.5 #define P_HET_SCALE 1.0 #define LOG10 2.30258509299404568401 #define TENOVERLOG10 4.34294481903251827652 #define TENLOG2OVERLOG10 3.0103 #ifdef __GNUC__ #define ALIGNED(x) __attribute((aligned(x))) #else #define ALIGNED(x) #endif // Initialised once as a global array. This won't work if threaded, // but we'll rewrite if and when that gets added later. static double e_tab_a[1002] ALIGNED(16); static double *e_tab = &e_tab_a[500]; static double e_tab2_a[1002] ALIGNED(16); static double *e_tab2 = &e_tab2_a[500]; static double e_log[501] ALIGNED(16); /* Precomputed matrices for the consensus algorithm */ typedef struct { double prior[25] ALIGNED(16); /* Sum to 1.0 */ double lprior15[15] ALIGNED(16); /* 15 combinations of {ACGT*} */ double pMM[101] ALIGNED(16); double p__[101] ALIGNED(16); double p_M[101] ALIGNED(16); double po_[101] ALIGNED(16); double poM[101] ALIGNED(16); double poo[101] ALIGNED(16); double puu[101] ALIGNED(16); double pum[101] ALIGNED(16); double pmm[101] ALIGNED(16); // Multiplier on homopolymer length before reducing phred qual double poly_mul; } cons_probs; // Two sets of params; recall oriented (gap5) and precision (stf). // We use the former unless MODE_MIXED is set (which is the default // for bayesian consensus mode if P_indel is significant). static cons_probs cons_prob_recall, cons_prob_precise; /* * Lots of confusing matrix terms here, so some definitions will help. * * M = match base * m = match pad * _ = mismatch * o = overcall * u = undercall * * We need to distinguish between homozygous columns and heterozygous columns, * done using a flat prior. This is implemented by treating every observation * as coming from one of two alleles, giving us a 2D matrix of possibilities * (the hypotheses) for each and every call (the observation). * * So pMM[] is the chance that given a call 'x' that it came from the * x/x allele combination. Similarly p_o[] is the chance that call * 'x' came from a mismatch (non-x) / overcall (consensus=*) combination. * * Examples with observation (call) C and * follows * * C | A C G T * * | A C G T * * ----------------- ----------------- * A | __ _M __ __ o_ A | uu uu uu uu um * C | _M MM _M _M oM C | uu uu uu uu um * G | __ _M __ __ o_ G | uu uu uu uu um * T | __ _M __ __ o_ T | uu uu uu uu um * * | o_ oM o_ o_ oo * | um um um um mm * * In calculation terms, the _M is half __ and half MM, similarly o_ and um. * * Relative weights of substitution vs overcall vs undercall are governed on a * per base basis using the P_OVER and P_UNDER scores (subst is * 1-P_OVER-P_UNDER). * * The heterozygosity weight though is a per column calculation as we're * trying to model whether the column is pure or mixed. Hence this is done * once via a prior and has no affect on the individual matrix cells. * * We have a generic indel probability, but it's a catch all for overcall, * undercall, alignment artifacts, homopolymer issues, etc. So we can set * it considerably higher and just let the QUAL skew do the filtering for * us, albeit no longer well calibrated. */ // NB: Should _M be MM? // Ie sample really is A/C het, and we observe C. That should be a match, // not half a match. #define MODE_SIMPLE 0 // freq counting #define MODE_BAYES_116 1 // Samtools 1.16 (no indel param) #define MODE_RECALL 2 // so called as it's the params from Gap5 #define MODE_PRECISE 3 // a more precise set; +FN, --FP #define MODE_MIXED 4 // Combination of GAP5/BAYES #define QCAL_FLAT 0 #define QCAL_HIFI 1 #define QCAL_HISEQ 2 #define QCAL_ONT_R10_4_SUP 3 #define QCAL_ONT_R10_4_DUP 4 #define QCAL_ULTIMA 5 // Calibration tables here don't necessarily reflect the true accuracy. // They have been manually tuned to work in conjunction with other command // line parameters used in the machine profiles. For example reducing one // qual here and increasing sensitivity elsewhere via another parameter. static qcal_t static_qcal[6] = { { // FLAT {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99}, {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99}, {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99} }, { // HiFi {10, 11, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 33, 34, 35, 36, 36, 37, 38, 38, 39, 39, 40, 40, 41, 41, 41, 41, 42, 42, 42, 42, 43, 43, 43, 43, 43, 43, 43, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, }, { 4, 4, 4, 4, 5, 6, 6, 7, 8, 9, 10, 11, 11, 12, 13, 14, 15, 15, 16, 17, 18, 19, 19, 20, 20, 21, 22, 23, 23, 24, 25, 25, 25, 26, 26, 26, 27, 27, 28, 28, 28, 28, 27, 27, 27, 28, 28, 28, 28, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 26, 26, 25, 26, 26, 27, 27, 27, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 28, 29, 28, 28, 28, 27, 27, 27, 27, 27, 27, 28, 28, 30, 30, 30, 30, 30, 30, 30, }, { 8, 8, 8, 8, 9, 10, 11, 12, 13, 14, 15, 15, 16, 17, 18, 19, 19, 20, 20, 21, 21, 22, 22, 23, 23, 23, 24, 24, 24, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 29, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, } }, { // HiSeq { 2, 2, 2, 3, 3, 4, 5, 5, 6, 7, 8, 9, 10, 11, 11, 12, 13, 14, 15, 16, 17, 17, 18, 19, 20, 21, 22, 22, 23, 24, 25, 26, 27, 28, 28, 29, 30, 31, 32, 33, 34, 34, 35, 36, 37, 38, 39, 39, 40, 41, 42, 43, 44, 45, 45, 46, 47, 48, 49, 50, 51, 51, 52, 53, 54, 55, 56, 56, 57, 58, 59, 60, 61, 62, 62, 63, 64, 65, 66, 67, 68, 68, 69, 70, 71, 72, 73, 73, 74, 75, 76, 77, 78, 79, 79, 80, 81, 82, 83, 84, }, { 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 61, 62, 63, 64, 65, 67, 68, 69, 70, 71, 73, 74, 75, 76, 77, 79, 80, 81, 82, 83, 85, 86, 87, 88, 89, 91, 92, 93, 94, 95, 97, 98, 99, 100, 101, 103, 104, 105, 106, 107, 109, 110, 111, 112, 113, 115, 116, 117, 118, 119, }, { 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 61, 62, 63, 64, 65, 67, 68, 69, 70, 71, 73, 74, 75, 76, 77, 79, 80, 81, 82, 83, 85, 86, 87, 88, 89, 91, 92, 93, 94, 95, 97, 98, 99, 100, 101, 103, 104, 105, 106, 107, 109, 110, 111, 112, 113, 115, 116, 117, 118, 119, } }, { // ONT R10.4 super { 0, 2, 2, 2, 3, 4, 4, 5, 6, 7, 7, 8, 9, 12, 13, 14, 15, 15, 16, 17, 18, 19, 20, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 36, 37, 38, 38, 39, 39, 40, 40, 40, 40, 40, 40, 40, 41, 40, 40, 41, 41, 40, 40, 40, 40, 41, 40, 40, 40, 40, 41, 41, 40, 40, 41, 40, 40, 39, 41, 40, 41, 40, 40, 41, 41, 41, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, }, { 0, 2, 2, 2, 3, 4, 5, 6, 7, 8, 8, 9, 9, 10, 10, 10, 11, 12, 12, 13, 13, 13, 14, 14, 15, 16, 16, 17, 18, 18, 19, 19, 20, 21, 22, 23, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, }, { 0, 4, 6, 6, 6, 7, 7, 8, 9, 9, 9, 10, 10, 11, 11, 12, 12, 13, 13, 14, 15, 15, 15, 16, 16, 17, 17, 18, 18, 19, 19, 20, 20, 21, 22, 22, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, } }, { // ONT R10.4 duplex; just a copy of hifi for now {10, 11, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 33, 34, 35, 36, 36, 37, 38, 38, 39, 39, 40, 40, 41, 41, 41, 41, 42, 42, 42, 42, 43, 43, 43, 43, 43, 43, 43, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, }, { 4, 4, 4, 4, 5, 6, 6, 7, 8, 9, 10, 11, 11, 12, 13, 14, 15, 15, 16, 17, 18, 19, 19, 20, 20, 21, 22, 23, 23, 24, 25, 25, 25, 26, 26, 26, 27, 27, 28, 28, 28, 28, 27, 27, 27, 28, 28, 28, 28, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 26, 26, 25, 26, 26, 27, 27, 27, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 28, 29, 28, 28, 28, 27, 27, 27, 27, 27, 27, 28, 28, 30, 30, 30, 30, 30, 30, 30, }, { 8, 8, 8, 8, 9, 10, 11, 12, 13, 14, 15, 15, 16, 17, 18, 19, 19, 20, 20, 21, 21, 22, 22, 23, 23, 23, 24, 24, 24, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 29, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, } }, { // Ultima Genomics { 2, 2, 3, 4, 5, 6, 6, 7, 8, 9, 10, 10, 11, 12, 13, 14, 14, 15, 16, 17, 18, 18, 19, 21, 22, 23, 23, 24, 25, 26, 27, 27, 28, 29, 30, 31, 31, 32, 33, 34, 35, 35, 36, 37, 38, 39, 39, 40, 42, 43, 44, 44, 45, 46, 47, 48, 48, 49, 50, 51, 52, 52, 53, 54, 55, 56, 56, 57, 58, 59, 60, 60, 61, 63, 64, 65, 65, 66, 67, 68, 69, 69, 70, 71, 72, 73, 73, 74, 75, 76, 77, 77, 78, 79, 80, 81, 81, 82, 84, 85, }, { 1, 1, 2, 2, 3, 3, 4, 4, 4, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 10, 10, 10, 11, 12, 13, 13, 13, 14, 15, 16, 16, 16, 17, 18, 18, 19, 19, 20, 20, 21, 21, 22, 22, 22, 22, 23, 23, 24, 24, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, }, { 1, 1, 2, 2, 3, 3, 4, 4, 4, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 10, 10, 10, 11, 12, 13, 13, 13, 14, 15, 16, 16, 16, 17, 18, 18, 19, 19, 20, 20, 21, 21, 22, 22, 22, 22, 23, 23, 24, 24, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, } } }; int set_qcal(qcal_t *q, int id) { if (id < 0 || id >= sizeof(static_qcal)/sizeof(*static_qcal)) return -1; memcpy(q, &static_qcal[id], sizeof(*q)); return 0; } int load_qcal(qcal_t *q, const char *fn) { int i; if (strcmp(fn, ":hifi") == 0) return set_qcal(q, QCAL_HIFI); if (strcmp(fn, ":hiseq") == 0) return set_qcal(q, QCAL_HISEQ); if (strcmp(fn, ":r10.4_sup") == 0) return set_qcal(q, QCAL_ONT_R10_4_SUP); if (strcmp(fn, ":r10.4_dup") == 0) return set_qcal(q, QCAL_ONT_R10_4_DUP); if (strcmp(fn, ":ultima") == 0) return set_qcal(q, QCAL_ULTIMA); // default for (i = 0; i < 101; i++) q->smap[i] = q->umap[i] = q->omap[i] = i; if (strcmp(fn, ":flat") == 0) return 0; hFILE *fp = hopen(fn, "r"); if (!fp) return -1; kstring_t line = KS_INITIALIZE; int max = 0; int last_qual = 0; while (line.l = 0, kgetline(&line, (kgets_func *)hgets, fp) >= 0) { int v, s, u, o; if (*line.s == '#') continue; if (sscanf(line.s, "QUAL %d %d %d %d", &v, &s, &u, &o) != 4) goto err; while (v > last_qual) { q->smap[last_qual+1] = q->smap[last_qual]; q->umap[last_qual+1] = q->umap[last_qual]; q->omap[last_qual+1] = q->omap[last_qual]; last_qual++; } if (v >= 0 && v < 100) { q->smap[v] = s; q->umap[v] = u; q->omap[v] = o; } if (v < max) { fprintf(samtools_stderr, "Qual calibration file is not in ascending order\n"); return hclose(fp) ? -2 : -1; } max = v; } for (i = max+1; i < 101; i++) { q->smap[i] = q->smap[max]; q->umap[i] = q->umap[max]; q->omap[i] = q->omap[max]; } ks_free(&line); return hclose(fp) < 0 ? -2 : 0; err: ks_free(&line); return hclose(fp) < 0 ? -2 : -1; } static void consensus_init(double p_het, double p_indel, double het_scale, double poly_mul, qcal_t *qcal, int mode, cons_probs *cp) { int i; // NB: only need to initialise once, but we do here for now for (i = -500; i <= 500; i++) e_tab[i] = exp(i); for (i = -500; i <= 500; i++) e_tab2[i] = exp(i/10.); for (i = 0; i <= 500; i++) e_log[i] = log(i); // EXPERIMENTAL cp->poly_mul = poly_mul; // The priors make very little difference, unless shallow data. // ACGT* by ACGT* // So AA=0, CC=6, GG=12, TT=18, **=24 for (i = 0; i < 25; i++) cp->prior[i] = p_het / 6; // AC AG AT CG CT GT // Flat assumption that it is what we observe, and measure everything else // as relative to this. cp->prior[0]=cp->prior[6]=cp->prior[12]=cp->prior[18]=cp->prior[24] = 1; // heterozygous deletion for (i = 4; i < 24; i+=5) cp->prior[i] = p_indel / 6; // /6 to be scaled vs p_het equivalently // heterozygous insertion for (i = 20; i < 24; i++) cp->prior[i] = p_indel / 6; cp->lprior15[0] = log(cp->prior[0]); cp->lprior15[1] = log(cp->prior[1]); cp->lprior15[2] = log(cp->prior[2]); cp->lprior15[3] = log(cp->prior[3]); cp->lprior15[4] = log(cp->prior[4]); cp->lprior15[5] = log(cp->prior[6]); cp->lprior15[6] = log(cp->prior[7]); cp->lprior15[7] = log(cp->prior[8]); cp->lprior15[8] = log(cp->prior[9]); cp->lprior15[9] = log(cp->prior[12]); cp->lprior15[10] = log(cp->prior[13]); cp->lprior15[11] = log(cp->prior[14]); cp->lprior15[12] = log(cp->prior[18]); cp->lprior15[13] = log(cp->prior[19]); cp->lprior15[14] = log(cp->prior[24]); for (i = 1; i < 101; i++) { double prob = 1 - pow(10, -qcal->smap[i] / 10.0); // Or is it that prob is 1-p(subst)-p(overcall)? cp->pMM[i] = log(prob); //cp->p__[i] = log(1-prob); // Big help to PB-CCS SNPs; unless fudged cp->p__[i] = log((1-prob)/3); // correct? poor on PB-CCS w/o fudge // Mixed alleles; just average two likelihoods cp->p_M[i] = log((exp(cp->pMM[i]) + exp(cp->p__[i]))/2); // What does this really mean? Can we simulate this by priors? // It reduces the likelihood of calling het sites, which is // maybe compensation for alignment artifacts? I'm unsure, // but it works (to differing degrees) on both PacBio HiFi and // Illumina HiSeq. It (obviously) loses true hets, but // potentially this can be compensated for by tweaking P-het // (which is entirely in the priors). // // Low het_scale reduces false positives by making hets less // likely to be called. In high depth data we normally have // enough evidence to call correctly even with low het_scale, // so it's a good +FN vs --FP tradeoff. However on low depth // data, het_scale can filter out too many true variants. // // TODO: So consider adjusting at the end maybe? // Also consider never changing calls, but changing their // confidence, so the data is what produces the call with the // parameters skewing the quality score distribution. cp->p_M[i] += log(het_scale); if (mode == MODE_BAYES_116) { // Compatibility with samtools 1.16 // This had no differention for indel vs substitution error rates, // so o(vercall) and u(undercall) are subst(_). cp->pmm[i] = cp->pMM[i]; cp->poM[i] = cp->p_M[i]; cp->pum[i] = cp->p_M[i]; cp->po_[i] = cp->p__[i]; cp->poo[i] = cp->p__[i]; cp->puu[i] = cp->p__[i]; } else { // When observing A C G T; leads to insertion calls prob = 1 - pow(10, -qcal->omap[i] / 10.0); // /3 for consistency with ACGT rem as relative likelihoods. // Otherwise with flat priors we end up calling all shallow data // as "*", which is illogical. cp->poo[i] = log((1-prob)/3); // Ensure pMM is always more likely. (NB: This shouldn't happen // now with the addition of the /3 step above.) if (cp->poo[i] > cp->pMM[i]-.5) cp->poo[i] = cp->pMM[i]-.5; cp->po_[i] = log((exp(cp->poo[i]) + exp(cp->p__[i]))/2); cp->poM[i] = log((exp(cp->poo[i]) + exp(cp->pMM[i]))/2); // Overcalls should never be twice as likely than mismatches. // Het bases are mix of _M (other) and MM ops (this). // It's fine for _M to be less likely than oM (more likely // to be overcalled than miscalled), but it should never // be stronger when combined with other mixed data. if (cp->poM[i] > cp->p_M[i]+.5) cp->poM[i] = cp->p_M[i]+.5; // Note --low-MQ and --scale-MQ have a big impact on // undercall errs. May need to separate these options per // type, but how? // Multiple-calls, as with mixed mode? This feels like a cheat prob = 1 - pow(10, -qcal->umap[i] / 10.0); cp->pmm[i] = log(prob); cp->puu[i] = log((1-prob)/3); if (cp->puu[i] > cp->pMM[i]-.5) // MM is -ve cp->puu[i] = cp->pMM[i]-.5; cp->pum[i] = log((exp(cp->puu[i]) + exp(cp->pmm[i]))/2); } } cp->pMM[0] = cp->pMM[1]; cp->p__[0] = cp->p__[1]; cp->p_M[0] = cp->p_M[1]; cp->pmm[0] = cp->pmm[1]; cp->poo[0] = cp->poo[1]; cp->po_[0] = cp->po_[1]; cp->poM[0] = cp->poM[1]; cp->puu[0] = cp->puu[1]; cp->pum[0] = cp->pum[1]; } static inline double fast_exp(double y) { if (y >= -50 && y <= 50) return e_tab2[(int)(y*10)]; if (y < -500) y = -500; if (y > 500) y = 500; return e_tab[(int)y]; } /* Taylor (deg 3) implementation of the log */ static inline double fast_log2(double val) { // FP representation is exponent & mantissa, where // value = 2^E * M. // Hence log2(value) = log2(2^E * M) // = log2(2^E)+ log2(M) // = E + log2(M) union { double d; uint64_t x; } u = {val}; const int E = ((u.x >> 52) & 2047) - 1024; // exponent E // Initial log2(M) based on mantissa u.x &= ~(2047LL << 52); u.x += 1023LL << 52; val = ((-1/3.) * u.d + 2) * u.d - 2/3.; return E + val; } #define ph_log(x) (-TENLOG2OVERLOG10*fast_log2((x))) int nins(const bam1_t *b){ int i, indel = 0; uint32_t *cig = bam_get_cigar(b); for (i = 0; i < b->core.n_cigar; i++) { int op = bam_cigar_op(cig[i]); if (op == BAM_CINS || op == BAM_CDEL) indel += bam_cigar_oplen(cig[i]); } return indel; } /* * Some machines, including 454 and PacBio, store the quality values in * homopolymers with the first or last base always being the low quality * state. This can cause problems when reverse-complementing and aligning, * especially when we left-justify indels. * * Other platforms take the approach of having the middle bases high and * the low confidence spread evenly to both start and end. This means * reverse-complementing doesn't introduce any strand bias. * * We redistribute qualities within homopolymers in this style to fix * naive consensus or variant calling algorithms. */ void homopoly_qual_fix(bam1_t *b) { static double ph2err[256] = {0}; int i; if (!ph2err[0]) { for (i = 0; i < 256; i++) ph2err[i] = pow(10, i/-10.0); } uint8_t *seq = bam_get_seq(b); uint8_t *qual = bam_get_qual(b); for (i = 0; i < b->core.l_qseq; i++) { int s = i; // start of homopoly int base = bam_seqi(seq, i); while (i+1 < b->core.l_qseq && bam_seqi(seq, i+1) == base) i++; // s..i inclusive is now homopolymer if (s == i) continue; // Simplest: reverse if end_qual < start_qual // Next: average outer-most two, then next two, etc // Best: fully redistribute so start/end lower qual than centre // Middle route of averaging outer pairs is sufficient? int j, k; for (j = s, k = i; j < k; j++,k--) { double e = ph2err[qual[j]] + ph2err[qual[k]]; qual[j] = qual[k] = -fast_log2(e/2)*3.0104+.49; } } } // Return the local NM figure within halo (+/- HALO) of pos. // This local NM is used as a way to modify MAPQ to get a localised MAPQ // score via an adhoc fashion. double nm_local(const pileup_t *p, const bam1_t *b, hts_pos_t pos) { int *nm = (int *)p->cd; if (!nm) return 0; pos -= b->core.pos; if (pos < 0) return nm[0] & ((1<<24)-1); if (pos >= b->core.l_qseq) return nm[b->core.l_qseq-1] & ((1<<24)-1); return (nm[pos] & ((1<<24)-1)) / 10.0; } int poly_len(const pileup_t *p, const bam1_t *b, hts_pos_t pos) { int *nm = (int *)p->cd; if (!nm) return 0; pos -= b->core.pos; if (pos >= 0 && pos < b->core.l_qseq) return nm[pos] >> 24; else return 0; } /* * Initialise a new sequence appearing in the pileup. We use this to * precompute some metrics that we'll repeatedly use in the consensus * caller; the localised NM score. * * We also directly amend the BAM record (which will be discarded later * anyway) to modify qualities to account for local quality minima. * * Returns 0 (discard) or 1 (keep) on success, -1 on failure. */ int nm_init(void *client_data, samFile *fp, sam_hdr_t *h, pileup_t *p) { consensus_opts *opts = (consensus_opts *)client_data; if (!opts->use_mqual) return 1; const bam1_t *b = &p->b; int qlen = b->core.l_qseq, i; if (qlen <= 0) return 0; int *local_nm = calloc(qlen, sizeof(*local_nm)); if (!local_nm) return -1; p->cd = local_nm; double poly_adj = opts->homopoly_fix ? opts->homopoly_fix : 1; if (opts->adj_qual) { // Set local_nm based on a function of current qual and the local // minimum qual within the surrounding window. // // Basically if we're in a region of low confidence then we downgrade // higher qual outliers as they may not be as trustworthy as they // claim. This may be because the qualities have been assigned to // the wrong or arbitrary base (very common in homopolymers), or the // surrounding quality (hence also error likelihood) have lead to // misalignments and the base may be contributing to the wrong // pileup column. // // The nm_local() function returns these scores and uses it to bias // the mapping quality, which in turn adjusts base quality. uint8_t *qual = bam_get_qual(b); uint8_t *seq = bam_get_seq(b); const int qhalo = 8; // window size for base qual int qmin = qual[0]; // min qual within qhalo const int qhalop = 2;// window size for homopolymer qual int qminp = qual[0]; // min qual within homopolymer halo int base = bam_seqi(seq, 0), polyl = 0, polyr = 0; // pos, not len // Minimum quality of the initial homopolymer for (i = 1; i < qlen; i++) { if (bam_seqi(seq, i) != base) break; if (i < qhalop && qminp > qual[i]) qminp = qual[i]; } // Minimum quality for general bases for (i = 0; i < qlen && i < qhalo; i++) { if (qmin > qual[i]) qmin = qual[i]; } for (;i < qlen-qhalo; i++) { if (opts->homopoly_fix && bam_seqi(seq, i) != base) { polyl = i; base = bam_seqi(seq, i); qminp = qual[i]; int j; for (j = i+1; j < qlen; j++) { if (bam_seqi(seq, j) != base) break; if (i < qhalop && qminp > qual[j]) qminp = qual[j]; } polyr = j-1; } else { // CHECK: do we want to have opts->homopoly_fix above, // so when not in use we don't define pl to non-zero? // Test on SynDip polyr = polyl; } int pl = polyr-polyl; // Useful for SNPS, as we're judging the variation in // length as an indicator for base-misalignment. // Not so useful for indel calling where the longer the indel // the less confident we are on the len variation being real. int t = (opts->mode == MODE_BAYES_116) ? (qual[i] + 5*qmin)/4 : qual[i]/3 + (qminp-pl*2)*poly_adj; local_nm[i] += t < qual[i] ? qual[i]-t : 0; // Brute force qminp in polyl to polyr range. // TODO: optimise this with sliding window qminp = qual[i]; int k; for (k = MAX(polyl,i-qhalop); k <= MIN(polyr,i+qhalop); k++) if (qminp > qual[k]) qminp = qual[k]; if (qmin > qual[i+qhalo]) qmin = qual[i+qhalo]; else if (qmin <= qual[i-qhalo]) { int j; qmin = 99; for (j = i-qhalo+1; j <= i+qhalo; j++) if (qmin > qual[j]) qmin = qual[j]; } } for (; i < qlen; i++) { int t = (opts->mode == MODE_BAYES_116) ? (qual[i] + 5*qmin)/4 : qual[i]/3 + qminp*poly_adj; local_nm[i] += t < qual[i] ? qual[i]-t : 0; } } // Fix e.g. PacBio homopolymer qualities if (opts->homopoly_fix) homopoly_qual_fix((bam1_t *)b); // local_nm[i] & ((1<<24)-1) is for SNP score adjustment. // We also put some more basic poly-X len in local_nm[i] >> 24. uint8_t *seq = bam_get_seq(b); for (i = 0; i < qlen; i++) { int base = bam_seqi(seq, i); int poly = 0, j, k; for (j = i+1; j < qlen; j++) if (bam_seqi(seq, j) != base) break; //printf("%d x %d\n", base, j-i); poly = j-i-1; if (poly > 100) poly = 100; const int HALO=0; for (k = i-HALO; k < j+HALO; k++) if (k >= 0 && k < qlen) local_nm[k] = ((MAX(poly, local_nm[k]>>24))<<24) | (local_nm[k] & ((1<<24)-1)); i = j-1; } // Adjust local_nm array by the number of edits within // a defined region (pos +/- halo). const int halo = opts->nm_halo; const uint8_t *md = bam_aux_get(b, "MD"); if (!md) return 1; md = (const uint8_t *)bam_aux2Z(md); // Handle cost of being near a soft-clip uint32_t *cig = bam_get_cigar(b); int ncig = b->core.n_cigar; if ( (cig[0] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP || ((cig[0] & BAM_CIGAR_MASK) == BAM_CHARD_CLIP && ncig > 1 && (cig[1] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP)) { for (i = 0; i < halo && i < qlen; i++) local_nm[i]+=opts->sc_cost; for (; i < halo*2 && i < qlen; i++) local_nm[i]+=opts->sc_cost>>1; } if ( (cig[ncig-1] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP || ((cig[ncig-1] & BAM_CIGAR_MASK) == BAM_CHARD_CLIP && ncig > 1 && (cig[ncig-2] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP)) { for (i = qlen-1; i >= qlen-halo && i >= 0; i--) local_nm[i]+=opts->sc_cost; for (; i >= qlen-halo*2 && i >= 0; i--) local_nm[i]+=opts->sc_cost>>1; } // Now iterate over MD tag int pos = 0; while (*md) { if (isdigit(*md)) { uint8_t *endptr; long i = strtol((char *)md, (char **)&endptr, 10); md = endptr; pos += i; continue; } // deletion. // Should we bump local_nm here too? Maybe if (*md == '^') { while (*++md && !isdigit(*md)) continue; continue; } // substitution for (i = pos-halo*2 >= 0 ?pos-halo*2 :0; i < pos-halo && i < qlen; i++) local_nm[i]+=5; for (; i < pos+halo && i < qlen; i++) local_nm[i]+=10; for (; i < pos+halo*2 && i < qlen; i++) local_nm[i]+=5; md++; } return 1; } void nm_free(void *client_data, samFile *fp, sam_hdr_t *h, pileup_t *p) { free(p->cd); p->cd = NULL; } #ifdef DO_HDW /* * Stirling's formula with a 1/12n correction applied to improve accuracy. * This seems to hold remarkably true for both low and high numbers too. */ double lnfact(double n) { /* Or Gosper's formula... * return (n*ln(n) - n + ln(2*M_PI*n + M_PI/3) / 2); */ return ((n+0.5)*log(n) - n + log(2*M_PI)/2) + log(1 + 1/(12.0*n)); /* + log(1 + 1/(288.0*n*n)); */ } /* * The binomical coefficient (n,k) for n trials with k successes where * prob(success) = p. * k n-k * P (k|n) = n! / (k! (n-k)!) p (1-p) * p * * The coefficient we are returning here is the n! / (k! (n-k)!) bit. * We compute it using ln(n!) and then exp() the result back to avoid * excessively large numbers. */ double bincoef(int n, double k) { return exp(lnfact(n) - lnfact(k) - lnfact(n-k)); } /* * Given p == 0.5 the binomial expansion simplifies a bit, so we have * a dedicated function for this. */ double binprobhalf(int n, double k) { return bincoef(n, k) * pow(0.5, n); } double lnbinprobhalf(int n, double k) { // ln(binprobhalf) expanded up and simplified return lnfact(n) - lnfact(k) - lnfact(n-k) - 0.69315*n; } #endif static int calculate_consensus_gap5(hts_pos_t pos, int flags, int depth, pileup_t *plp, consensus_opts *opts, consensus_t *cons, int default_qual, cons_probs *cp) { int i, j; static int init_done =0; static double q2p[101], mqual_pow[256]; double min_e_exp = DBL_MIN_EXP * log(2) + 1; double S[15] ALIGNED(16) = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}; double sumsC[6] = {0,0,0,0,0,0}; // A C G T * N // Small hash on seq to check for uniqueness of surrounding bases. // If it's frequent, then it's more likely to be correctly called than // if it's rare. // Helps a bit on deep data, especially with K2=3, but detrimental on // shallow and (currently) quite a slow down. #ifdef K2 int hashN[1<<(K2*4+2)] = {0}; int hash1[1<<2] = {0}; #endif /* Map the 15 possible combinations to 1-base or 2-base encodings */ static int map_sing[15] ALIGNED(16) = {0, 5, 5, 5, 5, 1, 5, 5, 5, 2, 5, 5, 3, 5, 4}; static int map_het[15] ALIGNED(16) = {0, 1, 2, 3, 4, 6, 7, 8, 9, 12, 13, 14, 18, 19, 24}; if (!init_done) { init_done = 1; for (i = 0; i <= 100; i++) { q2p[i] = pow(10, -i/10.0); } for (i = 0; i < 255; i++) { //mqual_pow[i] = 1-pow(10, -(i+.01)/10.0); mqual_pow[i] = 1-pow(10, -(i*.9)/10.0); //mqual_pow[i] = 1-pow(10, -(i/3+.1)/10.0); //mqual_pow[i] = 1-pow(10, -(i/2+.05)/10.0); } // unknown mqual mqual_pow[255] = mqual_pow[10]; } /* Initialise */ int counts[6] = {0}; #ifdef DO_FRACT int counts2[2][6] = {{0}}; #endif /* Accumulate */ #ifdef K2 const pileup_t *ptmp = plp; for (; ptmp; ptmp = ptmp->next) { const pileup_t *p = ptmp; if (p->qual < opts->min_qual) continue; int hb = 0; #define _ 0 static int X[16] = {_,0,1,_,2,_,_,_,3,_,_,_,_,_,_,_}; #undef _ uint8_t *seq = bam_get_seq(&p->b); int i, base1 = X[p->base4]; hash1[base1]++; for (i = p->seq_offset-K2; i <= p->seq_offset+K2; i++) { int base = i >= 0 && i < p->b.core.l_qseq ? X[bam_seqi(seq,i)] : _; hb = (hb<<2)|base; } hashN[hb]++; } #endif int td = depth; // original depth depth = 0; #ifdef DO_POLY_DIST int poly_dist[2][100] = {0}; #endif for (; plp; plp = plp->next) { pileup_t *p = plp; if (p->next) _mm_prefetch(p->next, _MM_HINT_T0); if (p->qual < opts->min_qual) continue; if (p->ref_skip) continue; #ifdef K2 int hb = 0; #define _ 0 static int X[16] = {_,0,1,_,2,_,_,_,3,_,_,_,_,_,_,_}; int i, base1 = X[p->base4]; for (i = p->seq_offset-K2; i <= p->seq_offset+K2; i++) { int base = i >= 0 && i < p->b.core.l_qseq ? X[bam_seqi(seq,i)] : _; hb = (hb<<2)|base; } #undef _ #endif const bam1_t *b = &p->b; uint8_t base = p->base4; uint8_t *qual_arr = bam_get_qual(b); uint8_t qual = p->qual; //qual = qual*qual/40+1; if (qual == 255 || (qual == 0 && *qual_arr == 255)) qual = default_qual; #ifdef K2 //qual = qual * hashN[hb] / hash1[base1]; qual -= -TENOVERLOG10*log(hashN[hb] / (hash1[base1]+.1)); if (qual < 1) qual = 1; #endif // =ACM GRSV TWYH KDBN * static int L[32] = { 5,0,1,5, 2,5,5,5, 3,5,5,5, 5,5,5,5, 4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4, }; // convert from sam base to acgt*n order. base = L[base]; double MM, __, _M, oo, oM, o_, uu, um, mm, qe; // Correction for mapping quality. Maybe speed up via lookups? // Cannot nullify mapping quality completely. Lots of (true) // SNPs means low mapping quality. (Ideally need to know // hamming distance to next best location.) if (flags & CONS_MQUAL) { int mqual = b->core.qual; if (opts->nm_adjust) { //mqual /= (nm_local(p, b, pos)+1); mqual /= (nm_local(p, b, b->core.pos + p->seq_offset+1)+1); mqual *= 1 + 2*(0.5-(td>30?30:td)/60.0); // depth fudge } // higher => call more; +FP, -FN // lower => call less; -FP, +FN mqual *= opts->scale_mqual; // Drop these? They don't seem to ever help. if (mqual < opts->low_mqual) mqual = opts->low_mqual; if (mqual > opts->high_mqual) mqual = opts->high_mqual; double _p = 1-q2p[qual]; double _m = mqual_pow[mqual]; qual = ph_log(1-(_m * _p + (1 - _m)/4)); // CURRENT //qual = ph_log(1-_p*_m); // testing //qual *= 6/sqrt(td); } /* Quality 0 should never be permitted as it breaks the maths */ if (qual < 1) qual = 1; double poly = poly_len(p, b, b->core.pos + p->seq_offset+1); #ifdef DO_POLY_DIST poly_dist[bam_is_rev(b)][MIN(99,(int)poly)]++; #endif // EXPERIMENTAL // Adjust qual based on homopolymer length. // Affects different platforms by differing amounts. // May wish to further separate to qual2 and qual3 for ins and del? int qual2 = MAX(1, qual-(poly-2)*cp->poly_mul); /* MM=match _M=half-match __=mismatch */ __ = cp->p__[qual]; // neither match MM = cp->pMM[qual] - __; // both match _M = cp->p_M[qual] - __; // one allele only (half match) /* observation ACGT, but against hypothesis ** or *base */ oo = cp->poo[qual2] - __; oM = cp->poM[qual2] - __; o_ = cp->po_[qual2] - __; /* observation * */ uu = cp->puu[qual2] - __; um = cp->pum[qual2] - __; mm = cp->pmm[qual2] - __; if (flags & CONS_DISCREP) { qe = q2p[qual]; sumsC[base] += 1 - qe; } counts[base]++; #ifdef DO_FRACT counts2[bam_is_rev(b)][base]++; #endif // oM should never be higher than _M for actual bases! or... //printf("base %d@%d MM %f _M %f oM %f\n", base, qual, MM, _M, oM); switch (base) { case 0: // A S[0] += MM; S[1] += _M; S[2] += _M; S[3] += _M; S[4] += oM; S[8] += o_; S[11] += o_; S[13] += o_; S[14] += oo; break; case 1: // C S[1] += _M; S[5] += MM; S[6] += _M; S[7] += _M; S[8] += oM; S[4] += o_; S[11] += o_; S[13] += o_; S[14] += oo; //fprintf(samtools_stderr, "%d %f %f %f\n", qual, MM+__, oo+__, MM-oo); break; case 2: // G S[ 2] += _M; S[ 6] += _M; S[ 9] += MM; S[10] += _M; S[11] += oM; S[4] += o_; S[8] += o_; S[13] += o_; S[14] += oo; break; case 3: // T S[ 3] += _M; // _m S[ 7] += _M; S[10] += _M; S[12] += MM; // mm S[13] += oM; S[4] += o_; S[8] += o_; S[11] += o_; S[14] += oo; // S[14] oo break; case 4: // * // under under under under agree-no-base S[0] += uu; S[1 ]+= uu; S[2 ]+= uu; S[3 ]+= uu; S[4 ]+= um; S[5 ]+= uu; S[6 ]+= uu; S[7 ]+= uu; S[8 ]+= um; S[9 ]+= uu; S[10]+= uu; S[11]+= um; S[12]+= uu; S[13]+= um; S[14]+= mm; break; case 5: /* N => equal weight to all A,C,G,T but not a pad */ S[0] += MM; S[1 ]+= MM; S[2 ]+= MM; S[3 ]+= MM; S[4 ]+= oM; S[5 ]+= MM; S[6 ]+= MM; S[7 ]+= MM; S[8 ]+= oM; S[9 ]+= MM; S[10]+= MM; S[11]+= oM; S[12]+= MM; S[13]+= oM; S[14]+= oo; break; } depth++; } #ifdef DO_POLY_DIST // Or compute mean and s.d per strand. // Then compare likelihood of strands coming from the same distribution? // eg s.d=0.59 vs mean=3.41 sd=0.54... hmm // // Or compare ratio of most frequent to next most frequent, for each // strand. int d1 = 0, d2 = 0; double nd1 = 0, nd2 = 0; int k; for (k = 0; k < 100; k++) { if (!poly_dist[0][k] && !poly_dist[1][k]) continue; // fprintf(samtools_stdout, "%ld %d %2d %2d\n", pos, k, poly_dist[0][k], poly_dist[1][k]); d1 += (k+1)*poly_dist[0][k]; d2 += (k+1)*poly_dist[1][k]; nd1 += poly_dist[0][k]; nd2 += poly_dist[1][k]; } // fprintf(samtools_stdout, "Avg = %f / %f %f / %f / %f\n", // (d1+d2+1)/(nd1+nd2+1.), // (d1+1)/(nd1+1.), (d2+1)/(nd2+1.), // (d2+1)/(nd2+1.) - (d1+1)/(nd1+1.), // ((d2+1)/(nd2+1.) - (d1+1)/(nd1+1.)) / ((d1+d2+1)/(nd1+nd2+1.))); // Find the top two frequent lengths int n1 = 0, n2 = 0, l1 = 0, l2 = 0; for (k = 0; k < 100; k++) { int poly12 = poly_dist[0][k]+poly_dist[1][k]; if (n1 < poly12) { n2 = n1; l2 = l1; n1 = poly12; l1 = k; } else if (n2 < poly12) { n2 = poly12; l2 = k; } } const double N = 5; nd1 += 1; nd2 += 1; // l1 is most common length int pn1p = poly_dist[0][l1]; int pn1m = poly_dist[1][l1]; // l2 2nd most common int pn2p = poly_dist[0][l2]; int pn2m = poly_dist[1][l2]; // ratio if two most common lengths on + double s1 = (pn1p+N) / (pn2p+N); s1 = s1>1?1/s1:s1; // ratio if two most common lengths on - double s2 = (pn1m+N) / (pn2m+N); s2 = s2>1?1/s2:s2; // ratio of s1 and s2 to identify strand bias double sbias = s1 / s2; sbias = sbias>1?1/sbias:sbias; if (pn2p+pn2m > 0 && l1 != l2) { // fprintf(samtools_stdout, "len %d,%d + %d,%d - %d,%d\tbias = %f %f, %f %f\t%ld\n", // l1, l2, pn1p, pn2p, pn1m, pn2m, // s1, s2, sbias, sqrt(sbias)-1, pos); // adjust score for het indels // sbias is close to 0 for strong strand bias, and 1 for none sbias = 10*log(sbias);//+.5); S[ 4] += sbias; // A* S[ 8] += sbias; // C* S[11] += sbias; // G* S[13] += sbias; // T* } else { sbias = 0; } #endif /* We've accumulated stats, so now we speculate on the consensus call */ double shift, max, max_het, norm[15]; int call = 0, het_call = 0; double tot1 = 0, tot2 = 0; /* * Scale numbers so the maximum score is 0. This shift is essentially * a multiplication in non-log scale to both numerator and denominator, * so it cancels out. We do this to avoid calling exp(-large_num) and * ending up with norm == 0 and hence a 0/0 error. * * Can also generate the base-call here too. */ shift = -DBL_MAX; max = -DBL_MAX; max_het = -DBL_MAX; #ifdef DO_FRACT // Filter by --min-depth and --het-fract. // Also add a slight adjustment for strand bias. for (j = 0; j < 15; j++) { if (j == 0 || j == 5 || j == 9 || j == 12 || j == 14) continue; double c1p = counts2[0][map_het[j]%5]; double c1m = counts2[1][map_het[j]%5]; double c2p = counts2[0][map_het[j]/5]; double c2m = counts2[1][map_het[j]/5]; double c1 = c1p + c1m; double c2 = c2p + c2m; if (c1 && c2) { // Slight decrease in confidence if strong strand bias. const int N = 10; // avoid low sample size problems double b1 = 1 - (N+MIN(c1p,c1m))/(N+MAX(c1p,c1m)); double b2 = 1 - (N+MIN(c2p,c2m))/(N+MAX(c2p,c2m)); if (b1 > 0.5) S[j] -= b1; if (b2 > 0.5) S[j] -= b2; // Fraction based filtering, via --min-depth and --het-fract opts. c1 += 1e-5; c2 += 1e-5; if (c2 > c1) { double tmp = c2; c2 = c1; c1 = tmp; } if (c2 < opts->min_depth) S[j] -= 100; if (c2 / (c1+1e-5) <= opts->het_fract) S[j] -= 100; } } #endif #ifdef DO_HDW /* * Apply Hardy-Weinberg statistics for heterozygous sites. * This helps, but it also loses sensitivity a little. */ for (j = 0; j < 15; j++) { if (j == 0 || j == 5 || j == 9 || j == 12 || j == 14) continue; double c1 = counts[map_het[j]%5]; double c2 = counts[map_het[j]/5]; if (c1 && c2) { c1 += 1e-5; c2 += 1e-5; if (c2 > c1) { double tmp = c2; c2 = c1; c1 = tmp; } // Limit depth for HW as we'll have an allele freq difference, // even if it's just caused by alignment reference bias. double c12 = c1+c2; if (c12 > 20) { c2 *= 20/(c12); c12 = 20; c1 = 20-c2; } // Helps a little, especially reducing FN deletions. c1+=1; c2+=1; c12+=2; S[j] += lnbinprobhalf(c12, c2) + fast_log2(c12)*0.69+.2; } } #endif for (j = 0; j < 15; j++) { S[j] += cp->lprior15[j]; if (shift < S[j]) shift = S[j]; /* Only call pure AA, CC, GG, TT, ** for now */ if (j != 0 && j != 5 && j != 9 && j != 12 && j != 14) { if (max_het < S[j]) { max_het = S[j]; het_call = j; } continue; } if (max < S[j]) { max = S[j]; call = j; } } /* * Shift and normalise. * If call is, say, b we want p = b/(a+b+c+...+n), but then we do * p/(1-p) later on and this has exceptions when p is very close * to 1. * * Hence we compute b/(a+b+c+...+n - b) and * rearrange (p/norm) / (1 - (p/norm)) to be p/norm2. */ for (j = 0; j < 15; j++) { S[j] -= shift; double e = fast_exp(S[j]); S[j] = (S[j] > min_e_exp) ? e : DBL_MIN; norm[j] = 0; } for (j = 0; j < 15; j++) { norm[j] += tot1; norm[14-j] += tot2; tot1 += S[j]; tot2 += S[14-j]; } /* And store result */ if (!depth || depth == counts[5] /* all N */) { cons->call = 4; /* N */ cons->het_call = 0; cons->het_logodd = 0; cons->phred = 0; cons->depth = 0; cons->discrep = 0; return 0; } cons->depth = depth; /* Call */ if (norm[call] == 0) norm[call] = DBL_MIN; // Approximation of phred for when S[call] ~= 1 and norm[call] // is small. Otherwise we need the full calculation. int ph; if (S[call] == 1 && norm[call] < .01) ph = ph_log(norm[call]) + .5; else ph = ph_log(1-S[call]/(norm[call]+S[call])) + .5; cons->call = map_sing[call]; cons->phred = ph < 0 ? 0 : ph; if (norm[het_call] == 0) norm[het_call] = DBL_MIN; ph = TENLOG2OVERLOG10 * (fast_log2(S[het_call]) - fast_log2(norm[het_call])) + .5; cons->het_call = map_het[het_call]; cons->het_logodd = ph; /* Compute discrepancy score */ if (flags & CONS_DISCREP) { double m = sumsC[0]+sumsC[1]+sumsC[2]+sumsC[3]+sumsC[4]; double c; if (cons->het_logodd > 0) c = sumsC[cons->het_call%5] + sumsC[cons->het_call/5]; else c = sumsC[cons->call]; cons->discrep = (m-c)/sqrt(m); } return 0; } // If opts->gap5 is MODE_MIXED then we use two different parameter // sets, favouring cp_p for precision and cp_r for recall. Otherwise it's // always cp_r only. // // When both calls equal, we return the same result. When they differ, // we adjust qual based on accurate vs recall profiles. int calculate_consensus_gap5m(hts_pos_t pos, int flags, int depth, pileup_t *plp, consensus_opts *opts, consensus_t *cons, int default_qual, cons_probs *cp_r, cons_probs *cp_p) { if (opts->mode != MODE_MIXED) return calculate_consensus_gap5(pos, flags, depth, plp, opts, cons, default_qual, opts->mode == MODE_PRECISE ? cp_p : cp_r); // EXPERIMENTAL: mixed mode consensus_t consP, consR; // Favours precision calculate_consensus_gap5(pos, flags, depth, plp, opts, &consP, default_qual, cp_p); // Favours recall calculate_consensus_gap5(pos, flags, depth, plp, opts, &consR, default_qual, cp_r); #define MIN(a,b) ((a)<(b)?(a):(b)) #define MAX(a,b) ((a)>(b)?(a):(b)) // Initial starting point is precise mode memcpy(cons, &consP, sizeof(consP)); if (consP.phred > 0 && consR.phred > 0 && consP.call == consR.call) { // Both strategies match as HOM // Boost qual as both in agreement cons->phred += MIN(20, consR.phred); } else if (consP.het_logodd >= 0 && consR.het_logodd >= 0 && consP.het_call == consR.het_call) { // Both strategies match as HET // Boost qual as both in agreement cons->het_logodd += MIN(20, consR.het_logodd); } else if (consP.het_logodd >= 0) { // Accurate method claims heterozygous, so go with it. // However sensitive method disagrees, so reduce qual a little. int q2 = MAX(consR.phred, consR.het_logodd); cons->het_logodd = MAX(1, (cons->het_logodd - q2/2)); } else if (consR.het_logodd >= 70) { // Accurate is homozygous and consR is het, so we go with it instead // but at a lower quality value. // TODO: may wish to check HET is consistent with HOM? Very unlikely // not to be though. int q1 = consP.phred; int q2 = consR.het_logodd; memcpy(cons, &consR, sizeof(consR)); cons->het_logodd = MIN(15, MAX((q2-q1*2)/2, 1+q2/(q1+1.0))); } else if (consR.het_logodd >= 0) { // As above, but low quality int q1 = consP.phred; int q2 = consR.het_logodd; memcpy(cons, &consR, sizeof(consR)); cons->het_logodd = MAX(1,q2 - 0.3*q1) + 5*(consP.het_call == consR.het_call); cons->phred = 0; } else if (consR.het_logodd < 0) { // Neither are heterozygous, but differing in phred call (V rare). // Pick highest qual, after some scaling? consR.phred = consR.phred / 2; if (consR.phred > consP.phred) memcpy(cons, &consR, sizeof(consR)); cons->phred = MAX(10, cons->phred); } return 0; } /* -------------------------------------------------------------------------- * Main processing logic */ static void dump_fastq(consensus_opts *opts, const char *name, const char *seq, size_t seq_l, const char *qual, size_t qual_l) { enum format fmt = opts->fmt; int line_len = opts->line_len; FILE *fp = opts->fp_out; fprintf(fp, "%c%s\n", ">@"[fmt==FASTQ], name); size_t i; for (i = 0; i < seq_l; i += line_len) fprintf(fp, "%.*s\n", (int)MIN(line_len, seq_l - i), seq+i); if (fmt == FASTQ) { fprintf(fp, "+\n"); for (i = 0; i < seq_l; i += line_len) fprintf(fp, "%.*s\n", (int)MIN(line_len, seq_l - i), qual+i); } } //--------------------------------------------------------------------------- /* * Reads a single alignment record, using either the iterator * or a direct sam_read1 call. */ static int readaln2(void *dat, samFile *fp, sam_hdr_t *h, bam1_t *b) { consensus_opts *opts = (consensus_opts *)dat; for (;;) { int ret = opts->iter ? sam_itr_next(fp, opts->iter, b) : sam_read1(fp, h, b); if (ret < 0) return ret; // Apply hard filters if (opts->incl_flags && !(b->core.flag & opts->incl_flags)) continue; if (opts->excl_flags && (b->core.flag & opts->excl_flags)) continue; if (b->core.qual < opts->min_mqual) continue; return ret; } } /* -------------------------------------------------------------------------- * A simple summing algorithm, either pure base frequency, or by * weighting them according to their quality values. * * This is crude, but easy to understand and fits with several * standard pileup criteria (eg COG-UK / CLIMB Covid-19 seq project). * * * call1 / score1 is the highest scoring allele. * call2 / score2 is the second highest scoring allele. * * Het_fract: score2/score1 * Call_fract: score1 or score1+score2 over total score * Min_depth: minimum total depth of unfiltered bases (above qual/mqual) * Min_score: minimum total score of utilised bases (score1+score2) * * Eg het_fract 0.66, call_fract 0.75 and min_depth 10. * 11A, 2C, 2G (14 total depth) is A. * 9A, 2C, 2G (12 total depth) is N as depth(A) < 10. * 11A, 5C, 5G (21 total depth) is N as 11/21 < 0.75 (call_fract) * * * 6A, 5G, 1C (12 total depth) is AG het as depth(A)+depth(G) >= 10 * and 5/6 >= 0.66 and 11/12 >= 0.75. * * 6A, 5G, 4C (15 total depth) is N as (6+5)/15 < 0.75 (call_fract). * * * Note for the purpose of deletions, a base/del has an ambiguity * code of lower-case base (otherwise it is uppercase). */ static int calculate_consensus_simple(const pileup_t *plp, consensus_opts *opts, int *qual) { int i, min_qual = opts->min_qual; int tot_depth = 0; // Map "seqi" nt16 to A,C,G,T compatibility with weights on pure bases. // where seqi is A | (C<<1) | (G<<2) | (T<<3) // * A C M G R S V T W Y H K D B N static int seqi2A[16] = { 0,8,0,4, 0,4,0,2, 0,4,0,2, 0,2,0,1 }; static int seqi2C[16] = { 0,0,8,4, 0,0,4,2, 0,0,4,2, 0,0,2,1 }; static int seqi2G[16] = { 0,0,0,0, 8,4,4,1, 0,0,0,0, 4,2,2,1 }; static int seqi2T[16] = { 0,0,0,0, 0,0,0,0, 8,4,4,2, 8,2,2,1 }; // Ignore ambiguous bases in seq for now, so we don't treat R, Y, etc // as part of one base and part another. Based on BAM seqi values. // We also use freq[16] as "*" for gap. int freq[17] = {0}; // base frequency, aka depth uint64_t score[17] = {0}; // summation of base qualities // Accumulate for (; plp; plp = plp->next) { const pileup_t *p = plp; if (p->next) _mm_prefetch(p->next, _MM_HINT_T0); int q = p->qual; if (q < min_qual) // Should we still record these in freq[] somewhere so // we can use them in the fracts? // Difference between >= X% of high-qual bases calling Y // and >= X% of all bases are high-quality Y calls. continue; //int b = p->is_del ? 16 : bam_seqi(bam_get_seq(&p->b), p->seq_offset); int b = p->base4; // Map ambiguity codes to one or more component bases. if (b < 16) { int Q = seqi2A[b] * (opts->use_qual ? q : 1); freq[1] += Q?1:0; score[1] += Q?Q:0; Q = seqi2C[b] * (opts->use_qual ? q : 1); freq[2] += Q?1:0; score[2] += Q?Q:0; Q = seqi2G[b] * (opts->use_qual ? q : 1); freq[4] += Q?1:0; score[4] += Q?Q:0; Q = seqi2T[b] * (opts->use_qual ? q : 1); freq[8] += Q?1:0; score[8] += Q?Q:0; } else { /* * */ freq[16] ++; score[16]+=8 * (opts->use_qual ? q : 1); } tot_depth++; } // Total usable depth uint64_t tscore = 0; for (i = 0; i < 5; i++) tscore += score[1<= opts->het_fract * score1 && opts->ambig) { used_base |= call2; used_score += score2; } // N is too shallow, or insufficient proportion of total if (tot_depth < opts->min_depth || used_score < opts->call_fract * tscore) { // But note shallow gaps are still called gaps, not N, as // we're still more confident there is no base than it is // A, C, G or T. used_base = call1 == 16 ? 16 : 0; // * or N } // Our final call. "?" shouldn't be possible to generate const char *het = "NACMGRSVTWYHKDBN" "*ac?g???t???????"; //printf("%c %d\n", het[used_base], tot_depth); if (qual) *qual = used_base ? 100.0 * used_score / tscore : 0; return het[used_base]; } static int empty_pileup2(consensus_opts *opts, sam_hdr_t *h, int tid, hts_pos_t start, hts_pos_t end) { const char *name = sam_hdr_tid2name(h, tid); hts_pos_t i; int err = 0; for (i = start; i < end; i++) err |= fprintf(opts->fp_out, "%s\t%"PRIhts_pos"\t0\t0\tN\t0\t*\t*\n", name, i+1) < 0; return err ? -1 : 0; } /* * Returns 0 on success * -1 on failure */ static int basic_pileup(void *cd, samFile *fp, sam_hdr_t *h, pileup_t *p, int depth, hts_pos_t pos, int nth, int is_insert) { unsigned char *qp, *cp; char *rp; int ref, cb, cq; consensus_opts *opts = (consensus_opts *)cd; int tid = p->b.core.tid; // opts->show_ins=0; // opts->show_del=1; if (!opts->show_ins && nth) return 0; if (opts->iter) { if (opts->iter->beg >= pos || opts->iter->end < pos) return 0; } if (opts->all_bases) { if (tid != opts->last_tid && opts->last_tid >= -1) { if (opts->last_tid >= 0) { // remainder of previous ref hts_pos_t len = sam_hdr_tid2len(opts->h, opts->last_tid); if (opts->iter) len = MIN(opts->iter->end, len); if (empty_pileup2(opts, opts->h, opts->last_tid, opts->last_pos, len) < 0) return -1; } opts->last_pos = opts->iter ? opts->iter->beg : 0; } // Any refs between last_tid and tid if (!opts->iter && tid > opts->last_tid && opts->all_bases > 1) { while (++opts->last_tid < tid) { hts_pos_t len = sam_hdr_tid2len(opts->h, opts->last_tid); if (empty_pileup2(opts, opts->h, opts->last_tid, 0, len) < 0) return -1; } } // Any gaps in this ref (same tid) or at start of this new tid if (opts->last_pos >= 0 && pos > opts->last_pos+1) { if (empty_pileup2(opts, opts->h, p->b.core.tid, opts->last_pos, pos-1) < 0) return -1; } else if (opts->last_pos < 0) { if (empty_pileup2(opts, opts->h, p->b.core.tid, opts->iter ? opts->iter->beg : 0, pos-1) < 0) return -1; } } if (opts->mode != MODE_SIMPLE) { consensus_t cons; calculate_consensus_gap5m(pos, opts->use_mqual ? CONS_MQUAL : 0, depth, p, opts, &cons, opts->default_qual, &cons_prob_recall, &cons_prob_precise); if (cons.depth < opts->min_depth) { cb = 'N'; cq = 0; } else if (cons.het_logodd > 0 && opts->ambig) { cb = "AMRWa" // 5x5 matrix with ACGT* per row / col "MCSYc" "RSGKg" "WYKTt" "acgt*"[cons.het_call]; cq = cons.het_logodd; } else{ cb = "ACGT*"[cons.call]; cq = cons.phred; } if (cq < opts->cons_cutoff && cb != '*') { cb = 'N'; cq = 0; } } else { cb = calculate_consensus_simple(p, opts, &cq); } if (cb < 0) return -1; if (!p) return 0; if (!opts->show_del && cb == '*') return 0; /* Ref, pos, nth, score, seq, qual */ kstring_t *ks = &opts->ks_line; ks->l = 0; ref = p->b.core.tid; rp = (char *)sam_hdr_tid2name(h, ref); int err = 0; err |= kputs(rp, ks) < 0; err |= kputc_('\t', ks) < 0; err |= kputw(pos, ks) < 0; err |= kputc_('\t', ks) < 0; err |= kputw(nth, ks) < 0; err |= kputc_('\t', ks) < 0; err |= kputw(depth, ks) < 0; err |= kputc_('\t', ks) < 0; err |= kputc_(cb, ks) < 0; err |= kputc_('\t', ks) < 0; err |= kputw(cq, ks) < 0; err |= kputc_('\t', ks) < 0; if (err) return -1; /* Seq + qual at predetermined offsets */ if (ks_resize(ks, ks->l + depth*2 + 2) < 0) return -1; cp = (unsigned char *)ks->s + ks->l; ks->l += depth*2 + 2; qp = cp+depth+1; for (; p; p = p->next) { // Too tight a loop to help much, but some benefit still if (p->next && p->next->next) _mm_prefetch(p->next->next, _MM_HINT_T0); if (p->b_is_rev) { *cp++ = p->base == '*' ? '#' : tolower(p->base); } else { *cp++ = p->base; } *qp++ = MIN(p->qual,93) + '!'; } *cp++ = '\t'; *qp++ = '\n'; if (fwrite(ks->s, 1, ks->l, opts->fp_out) != ks->l) return -1; opts->last_pos = pos; opts->last_tid = tid; return 0; } static int basic_fasta(void *cd, samFile *fp, sam_hdr_t *h, pileup_t *p, int depth, hts_pos_t pos, int nth, int is_insert) { int cb, cq; consensus_opts *opts = (consensus_opts *)cd; int tid = p->b.core.tid; kstring_t *seq = &opts->ks_ins_seq; kstring_t *qual = &opts->ks_ins_qual; if (!opts->show_ins && nth) return 0; if (opts->iter) { if (opts->iter->beg >= pos || opts->iter->end < pos) return 0; } next_ref: if (tid != opts->last_tid) { if (opts->last_tid != -1) { if (opts->all_bases) { // Fill in remainder of previous reference int i, N; if (opts->iter) { opts->last_pos = MAX(opts->last_pos, opts->iter->beg-1); N = opts->iter->end; } else { N = INT_MAX; } N = MIN(N, sam_hdr_tid2len(opts->h, opts->last_tid)) - opts->last_pos; if (N > 0) { if (ks_expand(seq, N+1) < 0) return -1; if (ks_expand(qual, N+1) < 0) return -1; for (i = 0; i < N; i++) { seq->s[seq->l++] = 'N'; qual->s[qual->l++] = '!'; } seq->s[seq->l] = 0; qual->s[qual->l] = 0; } } dump_fastq(opts, sam_hdr_tid2name(opts->h, opts->last_tid), seq->s, seq->l, qual->s, qual->l); } seq->l = 0; qual->l = 0; if (!opts->iter && opts->all_bases > 1 && ++opts->last_tid < tid) { opts->last_pos = 0; goto next_ref; } opts->last_tid = tid; if (opts->iter) opts->last_pos = opts->iter->beg; else opts->last_pos = opts->all_bases ? 0 : pos-1; } // share this with basic_pileup if (opts->mode != MODE_SIMPLE) { consensus_t cons; calculate_consensus_gap5m(pos, opts->use_mqual ? CONS_MQUAL : 0, depth, p, opts, &cons, opts->default_qual, &cons_prob_recall, &cons_prob_precise); if (cons.depth < opts->min_depth) { cb = 'N'; cq = 0; } else if (cons.het_logodd > 0 && opts->ambig) { cb = "AMRWa" // 5x5 matrix with ACGT* per row / col "MCSYc" "RSGKg" "WYKTt" "acgt*"[cons.het_call]; cq = cons.het_logodd; } else { cb = "ACGT*"[cons.call]; cq = cons.phred; } if (cq < opts->cons_cutoff && cb != '*' && cons.het_call % 5 != 4 && cons.het_call / 5 != 4) { // het base/* keeps base or * as most likely pure call, else N. // This is because we don't have a traditional way of representing // base or not-base ambiguity. cb = 'N'; cq = 0; } } else { cb = calculate_consensus_simple(p, opts, &cq); } if (cb < 0) return -1; if (!p) return 0; if (!opts->show_del && cb == '*') { opts->last_pos = pos; opts->last_tid = tid; return 0; } if (opts->mark_ins && nth && cb != '*') { kputc('_', seq); kputc('_', qual); } // end of share // Append consensus base/qual to seqs if (pos > opts->last_pos) { if (opts->last_pos >= 0 || opts->all_bases) { // FIXME: don't expand qual if fasta if (ks_expand(seq, pos - opts->last_pos) < 0 || ks_expand(qual, pos - opts->last_pos) < 0) return -1; memset(seq->s + seq->l, 'N', pos - (opts->last_pos+1)); memset(qual->s + qual->l, '!', pos - (opts->last_pos+1)); seq->l += pos - (opts->last_pos+1); qual->l += pos - (opts->last_pos+1); } } if ((nth && opts->show_ins && cb != '*') || cb != '*' || (pos > opts->last_pos && opts->show_del)) { int err = 0; err |= kputc(cb, seq) < 0; err |= kputc(MIN(cq, '~'-'!')+'!', qual) < 0; if (err) return -1; } opts->last_pos = pos; opts->last_tid = tid; return 0; } // END OF NEW PILEUP //--------------------------------------------------------------------------- static void usage_exit(FILE *fp, int exit_status) { fprintf(fp, "Usage: samtools consensus [options] \n"); fprintf(fp, "\nOptions:\n"); fprintf(fp, " -r, --region REG Limit query to REG. Requires an index\n"); fprintf(fp, " -f, --format FMT Output in format FASTA, FASTQ or PILEUP [FASTA]\n"); fprintf(fp, " -l, --line-len INT Wrap FASTA/Q at line length INT [70]\n"); fprintf(fp, " -o, --output FILE Output consensus to FILE\n"); fprintf(fp, " -m, --mode STR Switch consensus mode to \"simple\"/\"bayesian\" [bayesian]\n"); fprintf(fp, " -a Output all bases (start/end of reference)\n"); fprintf(fp, " --rf, --incl-flags STR|INT\n"); fprintf(fp, " Only include reads with any flag bit set [0]\n"); fprintf(fp, " --ff, --excl-flags STR|INT\n"); fprintf(fp, " Exclude reads with any flag bit set\n"); fprintf(fp, " [UNMAP,SECONDARY,QCFAIL,DUP]\n"); fprintf(fp, " --min-MQ INT Exclude reads with mapping quality below INT [0]\n"); fprintf(fp, " --min-BQ INT Exclude reads with base quality below INT [0]\n"); fprintf(fp, " --show-del yes/no Whether to show deletion as \"*\" [no]\n"); fprintf(fp, " --show-ins yes/no Whether to show insertions [yes]\n"); fprintf(fp, " --mark-ins Add '+' before every inserted base/qual [off]\n"); fprintf(fp, " -A, --ambig Enable IUPAC ambiguity codes [off]\n"); fprintf(fp, " -d, --min-depth INT Minimum depth of INT [1]\n"); fprintf(fp, "\nFor simple consensus mode:\n"); fprintf(fp, " -q, --(no-)use-qual Use quality values in calculation [off]\n"); fprintf(fp, " -c, --call-fract INT At least INT portion of bases must agree [0.75]\n"); fprintf(fp, " -H, --het-fract INT Minimum fraction of 2nd-most to most common base [0.15]\n"); fprintf(fp, "\nFor default \"Bayesian\" consensus mode:\n"); fprintf(fp, " -C, --cutoff C Consensus cutoff quality C [10]\n"); fprintf(fp, " --(no-)adj-qual Modify quality with local minima [on]\n"); fprintf(fp, " --(no-)use-MQ Use mapping quality in calculation [on]\n"); fprintf(fp, " --(no-)adj-MQ Modify mapping quality by local NM [on]\n"); fprintf(fp, " --NM-halo INT Size of window for NM count in --adj-MQ [50]\n"); fprintf(fp, " --scale-MQ FLOAT Scale mapping quality by FLOAT [1.00]\n"); fprintf(fp, " --low-MQ INT Cap minimum mapping quality [1]\n"); fprintf(fp, " --high-MQ INT Cap maximum mapping quality [60]\n"); fprintf(fp, " --P-het FLOAT Probability of heterozygous site[%.1e]\n", P_HET); fprintf(fp, " --P-indel FLOAT Probability of indel sites[%.1e]\n", P_INDEL); fprintf(fp, " --het-scale FLOAT Heterozygous SNP probability multiplier[%.1e]\n", P_HET_SCALE); fprintf(fp, " -p, --homopoly-fix Spread low-qual bases to both ends of homopolymers\n"); fprintf(fp, " --homopoly-score FLOAT\n" " Qual fraction adjustment for -p option [%g]\n", P_HOMOPOLY); fprintf(fp, " -t, --qual-calibration FILE / :config (see man page)\n"); fprintf(fp, " Load quality calibration file\n"); fprintf(fp, "\n"); fprintf(fp, " -X, --config STR Use pre-defined configuration set. STR from:\n"); fprintf(fp, " hiseq, hifi, r10.4_sup, r10.4_dup and ultima\n"); fprintf(fp, "\nGlobal options:\n"); sam_global_opt_help(fp, "-.---@-."); samtools_exit(exit_status); } int main_consensus(int argc, char **argv) { int c, ret = 1; consensus_opts opts = { // User options .mode = MODE_RECALL, .use_qual = 0, .min_qual = 0, .adj_qual = 1, .use_mqual = 1, .scale_mqual = 1.00, .nm_adjust = 1, .nm_halo = 50, .sc_cost = 60, .low_mqual = 1, .high_mqual = 60, .min_depth = 1, .call_fract = 0.75, .het_fract = 0.5, .het_only = 0, .fmt = FASTA, .cons_cutoff = 10, .ambig = 0, .line_len = 70, .default_qual = 10, .all_bases = 0, .show_del = 0, .show_ins = 1, .mark_ins = 0, .incl_flags = 0, .excl_flags = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP, .min_mqual = 0, .P_het = P_HET, .P_indel = P_INDEL, .het_scale = P_HET_SCALE, .homopoly_fix = 0, .homopoly_redux = 0.01, // Internal state .ks_line = {0,0}, .ks_ins_seq = {0,0}, .ks_ins_qual = {0,0}, .fp = NULL, .fp_out = samtools_stdout, .iter = NULL, .idx = NULL, .last_tid = -1, .last_pos = -1, }; set_qcal(&opts.qcal, QCAL_FLAT); sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', '-', '-', '@'), {"use-qual", no_argument, NULL, 'q'}, {"no-use-qual", no_argument, NULL, 'q'+1000}, {"adj-qual", no_argument, NULL, 'q'+100}, {"no-adj-qual", no_argument, NULL, 'q'+101}, {"use-MQ", no_argument, NULL, 'm'+1000}, {"no-use-MQ", no_argument, NULL, 'm'+1001}, {"adj-MQ", no_argument, NULL, 'm'+100}, {"no-adj-MQ", no_argument, NULL, 'm'+101}, {"NM-halo", required_argument, NULL, 'h'+100}, {"SC-cost", required_argument, NULL, 'h'+101}, {"scale-MQ", required_argument, NULL, 14}, {"low-MQ" , required_argument, NULL, 9}, {"high-MQ", required_argument, NULL, 10}, {"min-depth", required_argument, NULL, 'd'}, {"call-fract", required_argument, NULL, 'c'}, {"het-fract", required_argument, NULL, 'H'}, {"region", required_argument, NULL, 'r'}, {"format", required_argument, NULL, 'f'}, {"cutoff", required_argument, NULL, 'C'}, {"ambig", no_argument, NULL, 'A'}, {"line-len", required_argument, NULL, 'l'}, {"default-qual", required_argument, NULL, 1}, {"het-only", no_argument, NULL, 6}, {"show-del", required_argument, NULL, 7}, {"show-ins", required_argument, NULL, 8}, {"mark-ins", no_argument, NULL, 18}, {"output", required_argument, NULL, 'o'}, {"incl-flags", required_argument, NULL, 11}, {"rf", required_argument, NULL, 11}, {"excl-flags", required_argument, NULL, 12}, {"ff", required_argument, NULL, 12}, {"min-MQ", required_argument, NULL, 13}, {"min-BQ", required_argument, NULL, 16}, {"P-het", required_argument, NULL, 15}, {"P-indel", required_argument, NULL, 17}, {"het-scale", required_argument, NULL, 19}, {"mode", required_argument, NULL, 'm'}, {"homopoly-fix", no_argument, NULL, 'p'}, {"homopoly-score", required_argument, NULL, 'p'+100}, {"homopoly-redux", required_argument, NULL, 'p'+200}, {"qual-calibration", required_argument, NULL, 't'}, {"config", required_argument, NULL, 'X'}, {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "@:qd:c:H:r:5f:C:aAl:o:m:pt:X:", lopts, NULL)) >= 0) { switch (c) { case 'a': opts.all_bases++; break; case 'q': opts.use_qual=1; break; case 'q'+1000: opts.use_qual=0; break; case 'm'+1000: opts.use_mqual=1; break; case 'm'+1001: opts.use_mqual=0; break; case 14: opts.scale_mqual = atof(optarg); break; case 9: opts.low_mqual = atoi(optarg); break; case 10: opts.high_mqual = atoi(optarg); break; case 'd': opts.min_depth = atoi(optarg); break; case 'c': opts.call_fract = atof(optarg); break; case 'H': opts.het_fract = atof(optarg); break; case 'r': opts.reg = optarg; break; case 'C': opts.cons_cutoff = atoi(optarg); break; case 'A': opts.ambig = 1; break; case 'p': opts.homopoly_fix = P_HOMOPOLY; break; case 'p'+100: opts.homopoly_fix = atof(optarg); break; case 'p'+200: // EXPERIMENTAL opts.homopoly_redux = atof(optarg); break; case 1: opts.default_qual = atoi(optarg); break; case 6: opts.het_only = 1; break; case 7: opts.show_del = (*optarg == 'y' || *optarg == 'Y'); break; case 8: opts.show_ins = (*optarg == 'y' || *optarg == 'Y'); break; case 18: opts.mark_ins = 1; break; case 13: opts.min_mqual = atoi(optarg); break; case 16: opts.min_qual = atoi(optarg); break; case 15: opts.P_het = atof(optarg); break; case 17: opts.P_indel = atof(optarg); break; case 19: opts.het_scale = atof(optarg); break; case 'q'+100: opts.adj_qual = 1; break; case 'q'+101: opts.adj_qual = 0; break; case 'm'+100: opts.nm_adjust = 1; break; case 'm'+101: opts.nm_adjust = 0; break; case 'h'+100: opts.nm_halo = atoi(optarg); break; case 'h'+101: opts.sc_cost = atoi(optarg); break; case 'm': // mode if (strcasecmp(optarg, "simple") == 0) { opts.mode = MODE_SIMPLE; } else if (strcasecmp(optarg, "bayesian_m") == 0) { // EXPERIMENTAL: // A mixture of modified precise/recall params and a // blending of the two. Sometimes helps a bit. opts.mode = MODE_MIXED; } else if (strcasecmp(optarg, "bayesian_p") == 0) { // EXPERIMENTAL: // favours precision opts.mode = MODE_PRECISE; } else if (strcasecmp(optarg, "bayesian_r") == 0 || strcasecmp(optarg, "bayesian") == 0) { // favours recall; the default opts.mode = MODE_RECALL; } else if (strcasecmp(optarg, "bayesian_116") == 0) { opts.mode = MODE_BAYES_116; } else { fprintf(samtools_stderr, "Unknown mode %s\n", optarg); return 1; } break; case 'l': if ((opts.line_len = atoi(optarg)) <= 0) opts.line_len = INT_MAX; break; case 'f': if (strcasecmp(optarg, "fasta") == 0) { opts.fmt = FASTA; } else if (strcasecmp(optarg, "fastq") == 0) { opts.fmt = FASTQ; } else if (strcasecmp(optarg, "pileup") == 0) { opts.fmt = PILEUP; } else { fprintf(samtools_stderr, "Unknown format %s\n", optarg); return 1; } break; case 'o': if (!(opts.fp_out = fopen(optarg, "w"))) { perror(optarg); return 1; } break; case 'X': if (strcasecmp(optarg, "hifi") == 0) { set_qcal(&opts.qcal, QCAL_HIFI); opts.mode = MODE_RECALL; opts.homopoly_fix = 0.3; opts.homopoly_redux = 0.01; opts.low_mqual = 5; opts.scale_mqual = 1.5; opts.het_scale = 0.37; } else if (strcasecmp(optarg, "hiseq") == 0) { opts.mode = MODE_RECALL; set_qcal(&opts.qcal, QCAL_HISEQ); opts.homopoly_redux = 0.01; } else if (strcasecmp(optarg, "r10.4_sup") == 0) { // Same as HiFi params, but ONT calibration table. // At higher depth, hifi params work well for ONT // when combined with ONT calibration chart. // // At lower depth we gain a bit from increasing homopoly_redux set_qcal(&opts.qcal, QCAL_ONT_R10_4_SUP); opts.mode = MODE_RECALL; opts.homopoly_fix = 0.3; opts.homopoly_redux = 0.01; opts.low_mqual = 5; opts.scale_mqual = 1.5; opts.het_scale = 0.37; // Also consider, for lower depth: // opts.homopoly_redux = 1; // opts.scale_mqual = 1; // opts.het_scale = 0.45; } else if (strcasecmp(optarg, "r10.4_dup") == 0) { // Just a copy of of HiFi for duplex currently until // we get a good truth set for calibration. set_qcal(&opts.qcal, QCAL_ONT_R10_4_DUP); opts.mode = MODE_RECALL; opts.homopoly_fix = 0.3; opts.homopoly_redux = 0.01; opts.low_mqual = 5; opts.scale_mqual = 1.5; opts.het_scale = 0.37; } else if (strcasecmp(optarg, "ultima") == 0) { // Very similar to HiFi, but with own calibration table opts.mode = MODE_RECALL; set_qcal(&opts.qcal, QCAL_ULTIMA); opts.homopoly_fix = 0.3; opts.homopoly_redux = 0.01; opts.het_scale = 0.37; opts.scale_mqual = 2; opts.low_mqual = 10; } else { // NB consider defaults that are a mixture of all above. // Options are all similar for all bar Illumina. // Unsure what :flat calibration table does to each of // these though. fprintf(samtools_stderr, "Unrecognised configuration name: \"%s\"\n", optarg); return 1; } break; case 11: if ((opts.incl_flags = bam_str2flag(optarg)) < 0) { print_error("consensus", "could not parse --rf %s", optarg); return 1; } break; case 12: if ((opts.excl_flags = bam_str2flag(optarg)) < 0) { print_error("consensus", "could not parse --ff %s", optarg); return 1; } break; case 't': // --qual-calibration if (load_qcal(&opts.qcal, optarg) < 0) { print_error("consensus", "failed to load quality calibration '%s'", optarg); return -1; } break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage_exit(samtools_stderr, EXIT_FAILURE); } } #if 0 // Dump out the qcal table. Useful for copying into the code above. int i; qcal_t *q = &opts.qcal; fprintf(samtools_stderr, "{"); for (i = 0; i < 100; i++) fprintf(samtools_stderr, "%2d,%s", q->smap[i],(i+1)%10?" ":"\n"); fprintf(samtools_stderr, "},\n{"); for (i = 0; i < 100; i++) fprintf(samtools_stderr, "%2d,%s", q->umap[i],(i+1)%10?" ":"\n"); fprintf(samtools_stderr, "},\n{"); for (i = 0; i < 100; i++) fprintf(samtools_stderr, "%2d,%s", q->omap[i],(i+1)%10?" ":"\n"); fprintf(samtools_stderr, "}\n"); #endif if (opts.mode != MODE_SIMPLE) { if (opts.mode == MODE_PRECISE) // More accuracy / precision, but a significant drop // in recall. consensus_init(opts.P_het, opts.P_indel, 0.3 * opts.het_scale, opts.homopoly_redux, &opts.qcal, MODE_PRECISE, &cons_prob_precise); if (opts.mode == MODE_MIXED) // Blend these in when running in mixed mode, so we can // keep sensitivity but have a better joint quality to // reduce the FP rate. consensus_init(pow(opts.P_het, 0.7), pow(opts.P_indel, 0.7), 0.3 * opts.het_scale, opts.homopoly_redux, &opts.qcal, MODE_PRECISE, &cons_prob_precise); // Better recall, at a cost of some accuracy (false positives) consensus_init(opts.P_het, opts.P_indel, opts.het_scale, opts.mode == MODE_RECALL ? opts.homopoly_redux : 0.01, &opts.qcal, MODE_RECALL, &cons_prob_recall); } if (argc != optind+1) { if (argc == optind) usage_exit(samtools_stdout, EXIT_SUCCESS); else usage_exit(samtools_stderr, EXIT_FAILURE); } opts.fp = sam_open_format(argv[optind], "r", &ga.in); if (opts.fp == NULL) { print_error_errno("consensus", "Cannot open input file \"%s\"", argv[optind]); goto err; } if (ga.nthreads > 0) hts_set_threads(opts.fp, ga.nthreads); if (hts_set_opt(opts.fp, CRAM_OPT_DECODE_MD, 0)) { fprintf(samtools_stderr, "Failed to set CRAM_OPT_DECODE_MD value\n"); goto err; } if (!(opts.h = sam_hdr_read(opts.fp))) { fprintf(samtools_stderr, "Failed to read header for \"%s\"\n", argv[optind]); goto err; } if (opts.reg) { opts.idx = sam_index_load(opts.fp, argv[optind]); if (!opts.idx) { print_error("consensus", "Cannot load index for input file \"%s\"", argv[optind]); goto err; } opts.iter = sam_itr_querys(opts.idx, opts.h, opts.reg); if (!opts.iter) { print_error("consensus", "Failed to parse region \"%s\"", opts.reg); goto err; } } if (opts.fmt == PILEUP) { if (pileup_loop(opts.fp, opts.h, readaln2, opts.mode != MODE_SIMPLE ? nm_init : NULL, basic_pileup, opts.mode != MODE_SIMPLE ? nm_free : NULL, &opts) < 0) goto err; if (opts.all_bases) { int tid = opts.iter ? opts.iter->tid : opts.last_tid; int len = sam_hdr_tid2len(opts.h, tid); int pos = opts.last_pos; if (opts.iter) { len = MIN(opts.iter->end, len); pos = MAX(opts.iter->beg, pos); } if (empty_pileup2(&opts, opts.h, tid, pos, len) < 0) goto err; } while (!opts.iter && opts.all_bases > 1 && ++opts.last_tid < opts.h->n_targets) { int len = sam_hdr_tid2len(opts.h, opts.last_tid); if (empty_pileup2(&opts, opts.h, opts.last_tid, 0, len) < 0) goto err; } } else { if (pileup_loop(opts.fp, opts.h, readaln2, opts.mode != MODE_SIMPLE ? nm_init : NULL, basic_fasta, opts.mode != MODE_SIMPLE ? nm_free : NULL, &opts) < 0) goto err; next_ref_q: if (opts.all_bases) { // fill out terminator int tid = opts.iter ? opts.iter->tid : opts.last_tid; int len = sam_hdr_tid2len(opts.h, tid); int pos = opts.last_pos; if (opts.iter) { len = MIN(opts.iter->end, len); pos = MAX(opts.iter->beg, pos); opts.last_tid = opts.iter->tid; } if (pos < len) { if (ks_expand(&opts.ks_ins_seq, len-pos+1) < 0) goto err; if (ks_expand(&opts.ks_ins_qual, len-pos+1) < 0) goto err; while (pos++ < len) { opts.ks_ins_seq.s [opts.ks_ins_seq.l++] = 'N'; opts.ks_ins_qual.s[opts.ks_ins_qual.l++] = '!'; } opts.ks_ins_seq.s [opts.ks_ins_seq.l] = 0; opts.ks_ins_qual.s[opts.ks_ins_qual.l] = 0; } } if (opts.last_tid >= 0) dump_fastq(&opts, sam_hdr_tid2name(opts.h, opts.last_tid), opts.ks_ins_seq.s, opts.ks_ins_seq.l, opts.ks_ins_qual.s, opts.ks_ins_qual.l); if (!opts.iter && opts.all_bases > 1 && ++opts.last_tid < opts.h->n_targets) { opts.last_pos = 0; opts.ks_ins_seq.l = opts.ks_ins_qual.l = 0; goto next_ref_q; } // if (consensus_loop(&opts) < 0) { // print_error_errno("consensus", "Failed"); // goto err; // } } ret = 0; err: if (opts.iter) hts_itr_destroy(opts.iter); if (opts.idx) hts_idx_destroy(opts.idx); if (opts.fp && sam_close(opts.fp) < 0) { print_error_errno("consensus", "Closing input file \"%s\"", argv[optind]); ret = 1; } if (opts.h) sam_hdr_destroy(opts.h); sam_global_args_free(&ga); if (opts.fp_out && opts.fp_out != samtools_stdout) ret |= fclose(opts.fp_out) != 0; else ret |= fflush(samtools_stdout) != 0; ks_free(&opts.ks_line); ks_free(&opts.ks_ins_seq); ks_free(&opts.ks_ins_qual); if (ret) print_error("consensus", "failed"); return ret; } pysam-0.23.0/samtools/bam_fastq.c000066400000000000000000001072061475062545500167120ustar00rootroot00000000000000/* bam_fastq.c -- FASTA and FASTQ file generation Copyright (C) 2009-2017, 2019-2020, 2023-2024 Genome Research Ltd. Portions copyright (C) 2009, 2011, 2012 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notices and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include "htslib/sam.h" #include "htslib/klist.h" #include "htslib/kstring.h" #include "htslib/bgzf.h" #include "htslib/thread_pool.h" #include "htslib/khash.h" #include "samtools.h" #include "sam_opts.h" KHASH_SET_INIT_STR(str) typedef khash_t(str) strhash_t; #define DEFAULT_BARCODE_TAG "BC" #define DEFAULT_QUALITY_TAG "QT" #define INDEX_SEPARATOR "+" int8_t seq_comp_table[16] = { 0, 8, 4, 12, 2, 10, 6, 14, 1, 9, 5, 13, 3, 11, 7, 15 }; static void bam2fq_usage(FILE *to, const char *command) { int fq = strcasecmp("fastq", command) == 0 || strcasecmp("bam2fq", command) == 0; fprintf(to, "Usage: samtools %s [options...] \n", command); fprintf(to, "\n" "Description:\n" "Converts a SAM, BAM or CRAM to %s format.\n" "\n" "Options:\n" " -0 FILE write reads designated READ_OTHER to FILE\n" " -1 FILE write reads designated READ1 to FILE\n" " -2 FILE write reads designated READ2 to FILE\n" " -o FILE write reads designated READ1 or READ2 to FILE\n" " note: if a singleton file is specified with -s, only\n" " paired reads will be written to the -1 and -2 files.\n" " -d, --tag TAG[:VAL]\n" " only include reads containing TAG, optionally with value VAL\n" " -D, --tag-file STR:FILE\n" " only include reads containing TAG, with a value listed in FILE\n" " -f, --require-flags INT\n" " only include reads with all of the FLAGs in INT present [0]\n" // F&x == x " -F, --excl[ude]-flags INT\n" " only include reads with none of the FLAGs in INT present [0x900]\n" // F&x == 0 " --rf, --incl[ude]-flags INT\n" " only include reads with any of the FLAGs in INT present [0]\n" // !(F&x == 0) " -G INT only EXCLUDE reads with all of the FLAGs in INT present [0]\n" // !(F&x == x) " -n don't append /1 and /2 to the read name\n" " -N always append /1 and /2 to the read name\n", fq ? "FASTQ" : "FASTA"); if (fq) fprintf(to, " -O output quality in the OQ tag if present\n"); fprintf(to, " -s FILE write singleton reads designated READ1 or READ2 to FILE\n" " -t copy RG, BC and QT tags to the %s header line\n", fq ? "FASTQ" : "FASTA"); fprintf(to, " -T TAGLIST copy arbitrary tags to the %s header line, '*' for all\n", fq ? "FASTQ" : "FASTA"); if (fq) fprintf(to, " -v INT default quality score if not given in file [1]\n" " -i add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)\n" " -c INT compression level [0..9] to use when writing bgzf files [1]\n" " --i1 FILE write first index reads to FILE\n" " --i2 FILE write second index reads to FILE\n" " --barcode-tag TAG\n" " Barcode tag [" DEFAULT_BARCODE_TAG "]\n" " --quality-tag TAG\n" " Quality tag [" DEFAULT_QUALITY_TAG "]\n" " --index-format STR\n" " How to parse barcode and quality tags\n\n"); sam_global_opt_help(to, "-.--.@-."); fprintf(to, "\n" "The files will be automatically compressed if the file names have a .gz\n" "or .bgzf extension. The input to this program must be collated by name.\n" "Run 'samtools collate' or 'samtools sort -n' to achieve this.\n" "\n" "Reads are designated READ1 if FLAG READ1 is set and READ2 is not set.\n" "Reads are designated READ2 if FLAG READ1 is not set and READ2 is set.\n" "Otherwise reads are designated READ_OTHER (both flags set or both flags unset).\n" "Run 'samtools flags' for more information on flag codes and meanings.\n"); fprintf(to, "\n" "The index-format string describes how to parse the barcode and quality tags.\n" "It is made up of 'i' or 'n' followed by a length or '*'. For example:\n" " i14i8 The first 14 characters are index 1, the next 8 are index 2\n" " n8i14 Ignore the first 8 characters, and use the next 14 for index 1\n\n" "If the tag contains a separator, then the numeric part can be replaced with\n" "'*' to mean 'read until the separator or end of tag', for example:\n" " i*i* Break the tag at the separator into index 1 and index 2\n" " n*i* Ignore the left part of the tag until the separator,\n" " then use the second part of the tag as index 1\n"); fprintf(to, "\n" "Examples:\n" "To get just the paired reads in separate files, use:\n" " samtools %s -1 pair1.%s -2 pair2.%s -0 /dev/null -s /dev/null -n in.bam\n" "\nTo get all non-supplementary/secondary reads in a single file, redirect\n" "the output:\n" " samtools %s in.bam > all_reads.%s\n", command, fq ? "fq" : "fa", fq ? "fq" : "fa", command, fq ? "fq" : "fa"); } typedef enum { READ_UNKNOWN = 0, READ_1 = 1, READ_2 = 2 } readpart; typedef enum { FASTA, FASTQ } fastfile; typedef struct bam2fq_opts { char *fnse; char *fnr[3]; char *fn_input; // pointer to input filename in argv do not free bool has12, has12always, use_oq, copy_tags, illumina_tag; int flag_on, flag_off, flag_alloff, flag_anyon; sam_global_args ga; fastfile filetype; int def_qual; char *barcode_tag; char *quality_tag; char *index_file[2]; char *index_format; char *extra_tags; char compression_level; const char *filter_tag; // -d opt strhash_t *filter_tag_vals; } bam2fq_opts_t; typedef struct bam2fq_state { samFile *fp; samFile *fpse; samFile *fpr[3]; samFile *fpi[3]; samFile *hstdout; sam_hdr_t *h; bool has12, use_oq, copy_tags, illumina_tag; int flag_on, flag_off, flag_alloff, flag_anyon; fastfile filetype; int def_qual; char *index_sequence; char compression_level; htsThreadPool p; } bam2fq_state_t; // Adds a single tag value to the filter tag value hash static int add_tag_value(bam2fq_opts_t *opts, char *val) { if (!opts->filter_tag_vals) { if (!(opts->filter_tag_vals = kh_init(str))) return -1; } if (!(val = strdup(val))) return -1; int ret = 0; kh_put(str, opts->filter_tag_vals, val, &ret); if (ret <= 0) free(val); return ret < 0 ? -1 : 0; } // Adds multiple values, listed in a file static int add_tag_file(bam2fq_opts_t *opts, char *fn) { FILE *fp; kstring_t ks = {0,0}; if (!(fp = fopen(fn, "r"))) { print_error_errno("fastq", "failed to open \"%s\" for reading", fn); return -1; } while (ks.l = 0, kgetline(&ks, (kgets_func *)fgets, fp) >= 0) { if (add_tag_value(opts, ks.s) < 0) { ks_free(&ks); return -1; } } ks_free(&ks); return 0; } static readpart which_readpart(const bam1_t *b) { if ((b->core.flag & BAM_FREAD1) && !(b->core.flag & BAM_FREAD2)) { return READ_1; } else if ((b->core.flag & BAM_FREAD2) && !(b->core.flag & BAM_FREAD1)) { return READ_2; } else { return READ_UNKNOWN; } } static void free_opts(bam2fq_opts_t *opts) { if (opts->filter_tag_vals) { khint_t k; for (k = 0; k < kh_end(opts->filter_tag_vals); k++) if (kh_exist(opts->filter_tag_vals, k)) free((char *)kh_key(opts->filter_tag_vals, k)); kh_destroy(str, opts->filter_tag_vals); } free(opts); } // Make mnemonic distinct values for longoption-only options #define LONGOPT(c) ((c) + 128) // return true if valid static bool parse_opts(int argc, char *argv[], bam2fq_opts_t** opts_out) { // Parse args bam2fq_opts_t* opts = calloc(1, sizeof(bam2fq_opts_t)); opts->has12 = true; opts->has12always = false; opts->filetype = FASTQ; opts->def_qual = 1; opts->barcode_tag = NULL; opts->quality_tag = NULL; opts->index_format = NULL; opts->index_file[0] = NULL; opts->index_file[1] = NULL; opts->extra_tags = NULL; opts->compression_level = 1; opts->flag_off = BAM_FSECONDARY|BAM_FSUPPLEMENTARY; int c; sam_global_args_init(&opts->ga); static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '@'), {"require-flags", required_argument, NULL, 'f'}, {"excl-flags", required_argument, NULL, 'F'}, {"exclude-flags", required_argument, NULL, 'F'}, // following the same convention as view: g exists as a longoption_only // argument, accessible from the command line as --rf/--incl[ude]-flags {"rf", required_argument, NULL, LONGOPT('g')}, {"incl-flags", required_argument, NULL, LONGOPT('g')}, {"include-flags", required_argument, NULL, LONGOPT('g')}, {"i1", required_argument, NULL, 1}, {"I1", required_argument, NULL, 1}, {"i2", required_argument, NULL, 2}, {"I2", required_argument, NULL, 2}, {"if", required_argument, NULL, 3}, {"IF", required_argument, NULL, 3}, {"index-format", required_argument, NULL, 3}, {"barcode-tag", required_argument, NULL, 'b'}, {"quality-tag", required_argument, NULL, 'q'}, {"tag", required_argument, NULL, 'd'}, {"tag-file", required_argument, NULL, 'D'}, { NULL, 0, NULL, 0 } }; while ((c = getopt_long(argc, argv, "0:1:2:o:f:F:G:niNOs:c:tT:v:@:d:D:", lopts, NULL)) > 0) { switch (c) { case 'b': opts->barcode_tag = optarg; break; case 'q': opts->quality_tag = optarg; break; case 1 : opts->index_file[0] = optarg; break; case 2 : opts->index_file[1] = optarg; break; case 3 : opts->index_format = optarg; break; case '0': opts->fnr[0] = optarg; break; case '1': opts->fnr[1] = optarg; break; case '2': opts->fnr[2] = optarg; break; case 'o': opts->fnr[1] = optarg; opts->fnr[2] = optarg; break; case 'f': opts->flag_on |= strtol(optarg, 0, 0); break; // note that flag_off does not have |= because it has a default // value of 0x900 which needs to be replaced by the optarg case 'F': opts->flag_off = strtol(optarg, 0, 0); break; case 'G': opts->flag_alloff |= strtol(optarg, 0, 0); break; case LONGOPT('g'): opts->flag_anyon |= strtol(optarg, 0, 0); break; case 'n': opts->has12 = false; break; case 'N': opts->has12always = true; break; case 'O': opts->use_oq = true; break; case 's': opts->fnse = optarg; break; case 't': opts->copy_tags = true; break; case 'i': opts->illumina_tag = true; break; case 'c': opts->compression_level = atoi(optarg); if (opts->compression_level < 0) opts->compression_level = 0; if (opts->compression_level > 9) opts->compression_level = 9; break; case 'T': opts->extra_tags = optarg; break; case 'v': opts->def_qual = atoi(optarg); break; case 'd': if (strlen(optarg) < 2 || (strlen(optarg) > 2 && optarg[2] != ':')) { print_error("fastq", "Invalid \"tag:value\" option: \"%s\"", optarg); free_opts(opts); return false; } if (opts->filter_tag && memcmp(opts->filter_tag, optarg, 2)) { print_error("fastq", "Different tag type specified " "to before"); free_opts(opts); return false; } if (strlen(optarg) >= 3) add_tag_value(opts, optarg+3); opts->filter_tag = optarg; break; case 'D': // Allow ";" as delimiter besides ":" to support MinGW CLI POSIX // path translation as described at: // http://www.mingw.org/wiki/Posix_path_conversion if (strlen(optarg) < 4 || (optarg[2] != ':' && optarg[2] != ';')) { print_error("view", "Invalid \"tag:file\" option: \"%s\"", optarg); free_opts(opts); return false; } if (opts->filter_tag && memcmp(opts->filter_tag, optarg, 2)) { print_error("fastq", "Different tag type specified " "to before"); free_opts(opts); return false; } if (strlen(optarg) >= 3) { if (add_tag_file(opts, optarg+3) < 0) { free_opts(opts); return false; } } opts->filter_tag = optarg; break; case '?': bam2fq_usage(stderr, argv[0]); free_opts(opts); return false; default: if (parse_sam_global_opt(c, optarg, lopts, &opts->ga) != 0) { bam2fq_usage(stderr, argv[0]); free_opts(opts); return false; } break; } } if (opts->fnr[1] || opts->fnr[2]) opts->has12 = false; if (opts->has12always) opts->has12 = true; if (!opts->barcode_tag) opts->barcode_tag = DEFAULT_BARCODE_TAG; if (!opts->quality_tag) opts->quality_tag = DEFAULT_QUALITY_TAG; int nIndex = 0; if (opts->index_format) { char *s; for (s = opts->index_format; *s; s++) { if (*s == 'i') nIndex++; } } if (nIndex>2) { fprintf(stderr,"Invalid index format: more than 2 indexes\n"); bam2fq_usage(stderr, argv[0]); free_opts(opts); return false; } if (opts->index_file[1] && !opts->index_file[0]) { fprintf(stderr, "Index one specified, but index two not given\n"); bam2fq_usage(stderr, argv[0]); free_opts(opts); return false; } if (opts->illumina_tag && !nIndex) { fprintf(stderr, "You must specify an index format (--index-format) with the Illumina Casava (-i) option\n"); bam2fq_usage(stderr, argv[0]); free_opts(opts); return false; } if (nIndex==0 && opts->index_file[0]) { fprintf(stderr, "index_format not specified, but index file given\n"); bam2fq_usage(stderr, argv[0]); free_opts(opts); return false; } if (opts->def_qual < 0 || 93 < opts->def_qual) { fprintf(stderr, "Invalid -v default quality %i, allowed range 0 to 93\n", opts->def_qual); bam2fq_usage(stderr, argv[0]); free_opts(opts); return false; } const char* type_str = argv[0]; if (strcasecmp("fastq", type_str) == 0 || strcasecmp("bam2fq", type_str) == 0) { opts->filetype = FASTQ; } else if (strcasecmp("fasta", type_str) == 0) { opts->filetype = FASTA; } else { print_error("bam2fq", "Unrecognised type call \"%s\", this should be impossible... but you managed it!", type_str); bam2fq_usage(stderr, argv[0]); free_opts(opts); return false; } if (argc == optind && isatty(STDIN_FILENO)) { bam2fq_usage(stdout, argv[0]); free_opts(opts); return true; } if (argc - optind > 1) { fprintf(stderr, "Too many arguments.\n"); bam2fq_usage(stderr, argv[0]); free_opts(opts); return false; } opts->fn_input = argc > optind ? argv[optind] : "-"; *opts_out = opts; return true; } void set_sam_opts(samFile *fp, bam2fq_state_t *state, const bam2fq_opts_t *opts) { if (state->has12) hts_set_opt(fp, FASTQ_OPT_RNUM, 1); if (state->illumina_tag) hts_set_opt(fp, FASTQ_OPT_CASAVA, 1); hts_set_opt(fp, FASTQ_OPT_BARCODE, opts->barcode_tag); if (opts->extra_tags && (*opts->extra_tags == '*' || *opts->extra_tags == '\0')) hts_set_opt(fp, FASTQ_OPT_AUX, NULL); else { kstring_t tag_list = {0,0}; if (state->copy_tags) kputs("RG,BC,QT", &tag_list); if (opts->extra_tags) { if (tag_list.l) kputc(',', &tag_list); kputs(opts->extra_tags, &tag_list); } if (tag_list.l) hts_set_opt(fp, FASTQ_OPT_AUX, tag_list.s); ks_free(&tag_list); } } // Open a file as normal or gzipped based on filename. // Note we always use bgzf and don't bother to attempt non-blocked // gzip streams. This is a departure from the old fastq code. static samFile *sam_open_z(char *fn, char *mode, bam2fq_state_t *state) { char modez[6]; strcpy(modez, mode); size_t l = strlen(fn); if ((l > 3 && strcmp(fn+l-3, ".gz") == 0) || (l > 4 && strcmp(fn+l-4, ".bgz") == 0) || (l > 5 && strcmp(fn+l-5, ".bgzf") == 0)) { char m[3] = {'z', state->compression_level+'0', '\0'}; strcat(modez, m); } samFile *fp = sam_open(fn, modez); if (!fp) return NULL; if (state->p.pool) hts_set_thread_pool(fp, &state->p); return fp; } static bool init_state(const bam2fq_opts_t* opts, bam2fq_state_t** state_out) { char *mode = opts->filetype == FASTA ? "wF" : "wf"; bam2fq_state_t* state = calloc(1, sizeof(bam2fq_state_t)); if (!state) return false; state->flag_on = opts->flag_on; state->flag_off = opts->flag_off; state->flag_alloff = opts->flag_alloff; state->flag_anyon = opts->flag_anyon; state->has12 = opts->has12; state->use_oq = opts->use_oq; state->illumina_tag = opts->illumina_tag; state->copy_tags = opts->copy_tags; state->filetype = opts->filetype; state->def_qual = opts->def_qual; state->index_sequence = NULL; state->hstdout = NULL; state->compression_level = opts->compression_level; state->fp = sam_open_format(opts->fn_input, "r", &opts->ga.in); if (state->fp == NULL) { print_error_errno("bam2fq","Cannot read file \"%s\"", opts->fn_input); free(state); return false; } state->p.pool = NULL; if (opts->ga.nthreads > 0) { if (!(state->p.pool = hts_tpool_init(opts->ga.nthreads))) { fprintf(stderr, "Failed to create thread pool\n"); free(state); return false; } state->p.qsize = opts->ga.nthreads*2; hts_set_thread_pool(state->fp, &state->p); } uint32_t rf = SAM_QNAME | SAM_FLAG | SAM_SEQ | SAM_QUAL; if (opts->use_oq || opts->extra_tags || opts->index_file[0]) rf |= SAM_AUX; if (opts->filter_tag) { if (memcmp(opts->filter_tag, "NM", 2) == 0 || memcmp(opts->filter_tag, "MD", 2) == 0) rf |= SAM_AUX | SAM_SEQ; else if (memcmp(opts->filter_tag, "RG", 2) == 0) rf |= SAM_RGAUX; else rf |= SAM_AUX; } if (hts_set_opt(state->fp, CRAM_OPT_REQUIRED_FIELDS, rf)) { fprintf(stderr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n"); free(state); return false; } if (hts_set_opt(state->fp, CRAM_OPT_DECODE_MD, 0)) { fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n"); free(state); return false; } if (opts->fnse) { if (!(state->fpse = sam_open_z(opts->fnse, mode, state))) { print_error_errno("bam2fq", "Cannot open singleton file \"%s\"", opts->fnse); free(state); return false; } set_sam_opts(state->fpse, state, opts); } if (opts->ga.reference) { if (hts_set_fai_filename(state->fp, opts->ga.reference) != 0) { print_error_errno("bam2fq", "cannot load reference \"%s\"", opts->ga.reference); free(state); return false; } } // single, read1, read2 int i, j; for (i = 0; i < 3; ++i) { if (opts->fnr[i]) { for (j = 0; j < i; j++) if (opts->fnr[j] && strcmp(opts->fnr[j], opts->fnr[i]) == 0) break; if (j == i) { if (!(state->fpr[i] = sam_open_z(opts->fnr[i], mode, state))) { print_error_errno("bam2fq", "Cannot open r%d file \"%s\"", i, opts->fnr[i]); free(state); return false; } set_sam_opts(state->fpr[i], state, opts); } else { state->fpr[i] = state->fpr[j]; } } else { if (!state->hstdout) { if (!(state->hstdout = sam_open_z("-", mode, state))) { print_error_errno("bam2fq", "Cannot open STDOUT"); free(state); return false; } set_sam_opts(state->hstdout, state, opts); autoflush_if_stdout(state->hstdout, "-"); } state->fpr[i] = state->hstdout; } } // index 1, index 2 for (i = 0; i < 2; i++) { state->fpi[i] = NULL; if (opts->index_file[i]) { for (j = 0; j < 3; j++) if (opts->fnr[j] && strcmp(opts->fnr[j], opts->index_file[i]) == 0) break; for (j -= 3; j >= 0 && j < i; j++) if (opts->index_file[j] && strcmp(opts->index_file[j], opts->index_file[i]) == 0) break; if (i == j) { if (!(state->fpi[i] = sam_open_z(opts->index_file[i], mode, state))) { print_error_errno("bam2fq", "Cannot open i%d file \"%s\"", i+1, opts->index_file[i]); free(state); return false; } set_sam_opts(state->fpi[i], state, opts); } else if (j < 0) { state->fpi[i] = state->fpr[j+3]; } else { state->fpi[i] = state->fpi[j]; } } } state->h = sam_hdr_read(state->fp); if (state->h == NULL) { fprintf(stderr, "Failed to read header for \"%s\"\n", opts->fn_input); free(state); return false; } *state_out = state; return true; } static bool destroy_state(const bam2fq_opts_t *opts, bam2fq_state_t *state, int* status) { bool valid = true; sam_hdr_destroy(state->h); check_sam_close("bam2fq", state->fp, opts->fn_input, "file", status); if (state->fpse && sam_close(state->fpse) < 0) { print_error_errno("bam2fq", "Error closing singleton file \"%s\"", opts->fnse); valid = false; } int i, j; for (i = 0; i < 3; ++i) { if (state->fpr[i] != state->hstdout) { for (j = 0; j < i; j++) if (state->fpr[i] == state->fpr[j]) break; if (j == i && sam_close(state->fpr[i])) { print_error_errno("bam2fq", "Error closing r%d file \"%s\"", i, opts->fnr[i]); valid = false; } } } if (state->hstdout) { release_autoflush(state->hstdout); if (sam_close(state->hstdout) < 0) { print_error_errno("bam2fq", "Error closing STDOUT"); valid = false; } } for (i = 0; i < 2; i++) { for (j = 0; j < 3; j++) if (state->fpi[i] == state->fpr[j]) break; for (j -= 3; j >= 0 && j < i; j++) if (state->fpi[i] == state->fpi[j]) break; if (j == i && state->fpi[i] && sam_close(state->fpi[i]) < 0) { print_error_errno("bam2fq", "Error closing i%d file \"%s\"", i+1, opts->index_file[i]); valid = false; } } free(state->index_sequence); if (state->p.pool) hts_tpool_destroy(state->p.pool); free(state); return valid; } static inline bool filter_it_out(const bam1_t *b, const bam2fq_state_t *state, bam2fq_opts_t *opts) { if (opts->filter_tag) { uint8_t *s = bam_aux_get(b, opts->filter_tag); if (!s) return true; if (opts->filter_tag_vals) { char t[32], *val = t; switch (*s) { case 'i': case 'I': case 's': case 'S': case 'c': case 'C': if (snprintf(t, 32, "%"PRId64, bam_aux2i(s)) <= 0) return true; break; case 'f': // Comparing floats is hard. // Eg (double)0.1 - (double)0.1f is -1.5e-9. // Given BAM binary encoding is float however, just keep it. // This means rounding errors will (hopefully) always be the // same and basic equality still works. if (snprintf(t, 32, "%f", (float)bam_aux2f(s)) <= 0) return true; break; case 'A': t[0] = s[1]; t[1] = 0; break; case 'Z': case 'H': val = (char *)s+1; break; default: // Anything unsupported fails the filter match too. return true; } khint_t k = kh_get(str, opts->filter_tag_vals, val); if (k == kh_end(opts->filter_tag_vals)) return 1; // tag value not found } } return ((b->core.flag&(state->flag_on)) != state->flag_on // or reads indicated by filter flags || (b->core.flag&(state->flag_off)) != 0 || (((b->core.flag&(state->flag_anyon)) == 0) && (state->flag_anyon != 0)) || (b->core.flag&(state->flag_alloff) && (b->core.flag&(state->flag_alloff)) == state->flag_alloff)); } int write_index_rec(samFile *fp, bam1_t *b, bam2fq_state_t *state, bam2fq_opts_t* opts, char *seq, int seq_len, char *qual, int qual_len) { if (!fp || !b || !seq_len) return 0; int ret = -1; bam1_t *b2 = bam_init1(); // FIXME: reuse if (!b2) return -1; size_t aux_len = b->data + b->l_data - bam_get_aux(b); if (bam_set1(b2, b->core.l_qname, bam_get_qname(b), (b->core.flag | BAM_FUNMAP) & ~BAM_FREVERSE, -1, -1, 0, // refid, pos, mapq 0, NULL, // cigar -1, -1, 0, // rnext, pnext, tlen seq_len, seq, qual, aux_len) < 0) goto err; uint8_t *q = bam_get_qual(b2); if (qual) { int i; for (i = 0; i < seq_len; i++) q[i] -= '!'; } else { memset(q, opts->def_qual, seq_len); } memcpy(bam_get_aux(b2), bam_get_aux(b), aux_len); b2->l_data += aux_len; if (sam_write1(fp, state->h, b2) < 0) goto err; ret = 0; err: if (b2) bam_destroy1(b2); return ret; } int output_index(bam1_t *b1, bam1_t *b2, bam2fq_state_t *state, bam2fq_opts_t* opts) { bam1_t *b = b1 ? b1 : b2; char *ifmt = opts->index_format; if (!ifmt) ifmt = "i*i*"; // Get seq / qual elements char *bc = NULL, *qt = NULL; if (b1) bc = (char *)bam_aux_get(b1, opts->barcode_tag); if (b2 && !bc) bc = (char *)bam_aux_get(b2, opts->barcode_tag); if (!bc) return 0; else bc++; // skip Z if (b1) qt = (char *)bam_aux_get(b1, opts->quality_tag); if (b2 && !qt) qt = (char *)bam_aux_get(b2, opts->quality_tag); if (qt && strlen(bc) != strlen(qt)-1) qt = NULL; else if (qt) qt++; int inum = 0; while (inum < 2) { char fc = *ifmt++; if (!fc) break; // ran out of index-format long len, rem = 0; if (isdigit(*ifmt)) { rem = len = strtol(ifmt, &ifmt, 10); } else { ifmt++; len = 0; } char *bc_end = bc, *qt_end = qt; if (qt) { while (len ? *bc_end && rem-- : isalpha(*bc_end)) bc_end++, qt_end++; } else { while (len ? *bc_end && rem-- : isalpha(*bc_end)) bc_end++; } switch (fc) { case 'n': // skip bc = bc_end + (len==0); if (qt) qt = qt_end + (len==0); break; case 'i': if (write_index_rec(state->fpi[inum], b, state, opts, bc, bc_end-bc, qt, qt_end-qt) < 0) return -1; bc = bc_end + (len==0); if (qt) qt = qt_end + (len==0); inum++; break; default: fprintf(stderr, "Unknown index-format code\n"); return -1; } } return 0; } static int flush_rec(bam2fq_state_t *state, bam2fq_opts_t* opts, bam1_t *b[4], int score[3], int best[3], int64_t *n_singletons) { // Paired data, with 1 or 2 ends present. if (score[1] > 0 && score[2] > 0) { // If CASAVA tag is required and barcode is only on R1, // copy it to R2 if (state->illumina_tag) { char *tag; if ((tag = (char *)bam_aux_get(b[best[1]], opts->barcode_tag))) if (bam_aux_update_str(b[best[2]], opts->barcode_tag, strlen(tag), tag+1) < 0) goto err; if ((tag = (char *)bam_aux_get(b[best[1]], opts->quality_tag))) if (bam_aux_update_str(b[best[2]], opts->quality_tag, strlen(tag), tag+1) < 0) goto err; } if (sam_write1(state->fpr[1], state->h, b[best[1]]) < 0) goto err; if (sam_write1(state->fpr[2], state->h, b[best[2]]) < 0) goto err; if (output_index(b[best[1]], b[best[2]], state, opts) < 0) goto err; } else if (score[1] > 0 || score[2] > 0) { if (state->fpse) { // print whichever one exists to fpse if (score[1] > 0) { if (sam_write1(state->fpse, state->h, b[best[1]]) < 0) goto err; } else { if (sam_write1(state->fpse, state->h, b[best[2]]) < 0) goto err; } ++(*n_singletons); } else { if (score[1] > 0) { if (sam_write1(state->fpr[1], state->h, b[best[1]]) < 0) goto err; } else { if (sam_write1(state->fpr[2], state->h, b[best[2]]) < 0) goto err; } } if (output_index(score[1] > 0 ? b[best[1]] : NULL, score[2] > 0 ? b[best[2]] : NULL, state, opts) < 0) goto err; } if (score[0]) { // single ended data (neither READ1 nor READ2) if (sam_write1(state->fpr[0], state->h, b[best[0]]) < 0) goto err; if (output_index(b[best[0]], NULL, state, opts) < 0) goto err; } return 0; err: return -1; } static bool bam2fq_mainloop(bam2fq_state_t *state, bam2fq_opts_t* opts) { int n; char *current_qname = NULL; int64_t n_reads = 0, n_singletons = 0; // Statistics int score[3]; int at_eof; bool valid = false; int best[3] = {-1, -1, -1}; // map R0, R1, single to b[] indices; // indexed by [readpart] bam1_t *b[4]; // 3 readparts, plus current record for (n = 0; n < 4; n++) { if (!(b[n] = bam_init1())) { perror("[bam2fq_mainloop] Malloc error for bam record buffer."); return false; } } n = 0; while (true) { int res = sam_read1(state->fp, state->h, b[n]); if (res < -1) { print_error("bam2fq", "Failed to read bam record"); goto err; } at_eof = res < 0; if (!at_eof && filter_it_out(b[n], state, opts)) continue; if (!at_eof) { ++n_reads; // Handle -O option: use OQ for qual uint8_t *oq; if (state->use_oq && (oq = bam_aux_get(b[n],"OQ")) && *oq == 'Z') { int i, l = strlen((char *)++oq); uint8_t *qual = bam_get_qual(b[n]); for (i = 0; i < l && i < b[n]->core.l_qseq; i++) qual[i] = oq[i] - '!'; } } if (at_eof || !current_qname || (strcmp(current_qname, bam_get_qname(b[n])) != 0)) { // New name, so flush best examples of previous name. if (current_qname) if (flush_rec(state, opts, b, score, best, &n_singletons) < 0) goto err; current_qname = bam_get_qname(b[n]); score[0] = score[1] = score[2] = 0; if (at_eof) { break; } } // Prefer a copy of the read that has base qualities int b_score = bam_get_qual(b[n])[0] != 0xff? 2 : 1; readpart rp = which_readpart(b[n]); if (score[rp] < b_score) { score[rp] = b_score; // Record b[n] slot for best copy of readpair and find a new // slot for next bam read best[rp] = n; int used_slot[4] = {0}, i; for (i = 0; i < 3; i++) if (best[i] >= 0) used_slot[best[i]] = 1; for (i = 0; i < 4 && used_slot[i]; i++) ; n = i; } } valid = true; err: if (!valid) print_error_errno("bam2fq", "Error writing to FASTx files."); for (n = 0; n < 4; n++) bam_destroy1(b[n]); fprintf(stderr, "[M::%s] discarded %" PRId64 " singletons\n", __func__, n_singletons); fprintf(stderr, "[M::%s] processed %" PRId64 " reads\n", __func__, n_reads); return valid; } int main_bam2fq(int argc, char *argv[]) { int status = EXIT_FAILURE; bam2fq_opts_t* opts = NULL; bam2fq_state_t* state = NULL; bool valid = parse_opts(argc, argv, &opts); if (!valid || opts == NULL) return valid ? EXIT_SUCCESS : EXIT_FAILURE; if (!init_state(opts, &state)) goto err; if (!bam2fq_mainloop(state,opts)) goto err; if (!destroy_state(opts, state, &status)) goto err; status = EXIT_SUCCESS; err: sam_global_args_free(&opts->ga); free_opts(opts); return status; } pysam-0.23.0/samtools/bam_fastq.c.pysam.c000066400000000000000000001075621475062545500202700ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_fastq.c -- FASTA and FASTQ file generation Copyright (C) 2009-2017, 2019-2020, 2023-2024 Genome Research Ltd. Portions copyright (C) 2009, 2011, 2012 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notices and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include "htslib/sam.h" #include "htslib/klist.h" #include "htslib/kstring.h" #include "htslib/bgzf.h" #include "htslib/thread_pool.h" #include "htslib/khash.h" #include "samtools.h" #include "sam_opts.h" KHASH_SET_INIT_STR(str) typedef khash_t(str) strhash_t; #define DEFAULT_BARCODE_TAG "BC" #define DEFAULT_QUALITY_TAG "QT" #define INDEX_SEPARATOR "+" int8_t seq_comp_table[16] = { 0, 8, 4, 12, 2, 10, 6, 14, 1, 9, 5, 13, 3, 11, 7, 15 }; static void bam2fq_usage(FILE *to, const char *command) { int fq = strcasecmp("fastq", command) == 0 || strcasecmp("bam2fq", command) == 0; fprintf(to, "Usage: samtools %s [options...] \n", command); fprintf(to, "\n" "Description:\n" "Converts a SAM, BAM or CRAM to %s format.\n" "\n" "Options:\n" " -0 FILE write reads designated READ_OTHER to FILE\n" " -1 FILE write reads designated READ1 to FILE\n" " -2 FILE write reads designated READ2 to FILE\n" " -o FILE write reads designated READ1 or READ2 to FILE\n" " note: if a singleton file is specified with -s, only\n" " paired reads will be written to the -1 and -2 files.\n" " -d, --tag TAG[:VAL]\n" " only include reads containing TAG, optionally with value VAL\n" " -D, --tag-file STR:FILE\n" " only include reads containing TAG, with a value listed in FILE\n" " -f, --require-flags INT\n" " only include reads with all of the FLAGs in INT present [0]\n" // F&x == x " -F, --excl[ude]-flags INT\n" " only include reads with none of the FLAGs in INT present [0x900]\n" // F&x == 0 " --rf, --incl[ude]-flags INT\n" " only include reads with any of the FLAGs in INT present [0]\n" // !(F&x == 0) " -G INT only EXCLUDE reads with all of the FLAGs in INT present [0]\n" // !(F&x == x) " -n don't append /1 and /2 to the read name\n" " -N always append /1 and /2 to the read name\n", fq ? "FASTQ" : "FASTA"); if (fq) fprintf(to, " -O output quality in the OQ tag if present\n"); fprintf(to, " -s FILE write singleton reads designated READ1 or READ2 to FILE\n" " -t copy RG, BC and QT tags to the %s header line\n", fq ? "FASTQ" : "FASTA"); fprintf(to, " -T TAGLIST copy arbitrary tags to the %s header line, '*' for all\n", fq ? "FASTQ" : "FASTA"); if (fq) fprintf(to, " -v INT default quality score if not given in file [1]\n" " -i add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)\n" " -c INT compression level [0..9] to use when writing bgzf files [1]\n" " --i1 FILE write first index reads to FILE\n" " --i2 FILE write second index reads to FILE\n" " --barcode-tag TAG\n" " Barcode tag [" DEFAULT_BARCODE_TAG "]\n" " --quality-tag TAG\n" " Quality tag [" DEFAULT_QUALITY_TAG "]\n" " --index-format STR\n" " How to parse barcode and quality tags\n\n"); sam_global_opt_help(to, "-.--.@-."); fprintf(to, "\n" "The files will be automatically compressed if the file names have a .gz\n" "or .bgzf extension. The input to this program must be collated by name.\n" "Run 'samtools collate' or 'samtools sort -n' to achieve this.\n" "\n" "Reads are designated READ1 if FLAG READ1 is set and READ2 is not set.\n" "Reads are designated READ2 if FLAG READ1 is not set and READ2 is set.\n" "Otherwise reads are designated READ_OTHER (both flags set or both flags unset).\n" "Run 'samtools flags' for more information on flag codes and meanings.\n"); fprintf(to, "\n" "The index-format string describes how to parse the barcode and quality tags.\n" "It is made up of 'i' or 'n' followed by a length or '*'. For example:\n" " i14i8 The first 14 characters are index 1, the next 8 are index 2\n" " n8i14 Ignore the first 8 characters, and use the next 14 for index 1\n\n" "If the tag contains a separator, then the numeric part can be replaced with\n" "'*' to mean 'read until the separator or end of tag', for example:\n" " i*i* Break the tag at the separator into index 1 and index 2\n" " n*i* Ignore the left part of the tag until the separator,\n" " then use the second part of the tag as index 1\n"); fprintf(to, "\n" "Examples:\n" "To get just the paired reads in separate files, use:\n" " samtools %s -1 pair1.%s -2 pair2.%s -0 /dev/null -s /dev/null -n in.bam\n" "\nTo get all non-supplementary/secondary reads in a single file, redirect\n" "the output:\n" " samtools %s in.bam > all_reads.%s\n", command, fq ? "fq" : "fa", fq ? "fq" : "fa", command, fq ? "fq" : "fa"); } typedef enum { READ_UNKNOWN = 0, READ_1 = 1, READ_2 = 2 } readpart; typedef enum { FASTA, FASTQ } fastfile; typedef struct bam2fq_opts { char *fnse; char *fnr[3]; char *fn_input; // pointer to input filename in argv do not free bool has12, has12always, use_oq, copy_tags, illumina_tag; int flag_on, flag_off, flag_alloff, flag_anyon; sam_global_args ga; fastfile filetype; int def_qual; char *barcode_tag; char *quality_tag; char *index_file[2]; char *index_format; char *extra_tags; char compression_level; const char *filter_tag; // -d opt strhash_t *filter_tag_vals; } bam2fq_opts_t; typedef struct bam2fq_state { samFile *fp; samFile *fpse; samFile *fpr[3]; samFile *fpi[3]; samFile *hstdout; sam_hdr_t *h; bool has12, use_oq, copy_tags, illumina_tag; int flag_on, flag_off, flag_alloff, flag_anyon; fastfile filetype; int def_qual; char *index_sequence; char compression_level; htsThreadPool p; } bam2fq_state_t; // Adds a single tag value to the filter tag value hash static int add_tag_value(bam2fq_opts_t *opts, char *val) { if (!opts->filter_tag_vals) { if (!(opts->filter_tag_vals = kh_init(str))) return -1; } if (!(val = strdup(val))) return -1; int ret = 0; kh_put(str, opts->filter_tag_vals, val, &ret); if (ret <= 0) free(val); return ret < 0 ? -1 : 0; } // Adds multiple values, listed in a file static int add_tag_file(bam2fq_opts_t *opts, char *fn) { FILE *fp; kstring_t ks = {0,0}; if (!(fp = fopen(fn, "r"))) { print_error_errno("fastq", "failed to open \"%s\" for reading", fn); return -1; } while (ks.l = 0, kgetline(&ks, (kgets_func *)fgets, fp) >= 0) { if (add_tag_value(opts, ks.s) < 0) { ks_free(&ks); return -1; } } ks_free(&ks); return 0; } static readpart which_readpart(const bam1_t *b) { if ((b->core.flag & BAM_FREAD1) && !(b->core.flag & BAM_FREAD2)) { return READ_1; } else if ((b->core.flag & BAM_FREAD2) && !(b->core.flag & BAM_FREAD1)) { return READ_2; } else { return READ_UNKNOWN; } } static void free_opts(bam2fq_opts_t *opts) { if (opts->filter_tag_vals) { khint_t k; for (k = 0; k < kh_end(opts->filter_tag_vals); k++) if (kh_exist(opts->filter_tag_vals, k)) free((char *)kh_key(opts->filter_tag_vals, k)); kh_destroy(str, opts->filter_tag_vals); } free(opts); } // Make mnemonic distinct values for longoption-only options #define LONGOPT(c) ((c) + 128) // return true if valid static bool parse_opts(int argc, char *argv[], bam2fq_opts_t** opts_out) { // Parse args bam2fq_opts_t* opts = calloc(1, sizeof(bam2fq_opts_t)); opts->has12 = true; opts->has12always = false; opts->filetype = FASTQ; opts->def_qual = 1; opts->barcode_tag = NULL; opts->quality_tag = NULL; opts->index_format = NULL; opts->index_file[0] = NULL; opts->index_file[1] = NULL; opts->extra_tags = NULL; opts->compression_level = 1; opts->flag_off = BAM_FSECONDARY|BAM_FSUPPLEMENTARY; int c; sam_global_args_init(&opts->ga); static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '@'), {"require-flags", required_argument, NULL, 'f'}, {"excl-flags", required_argument, NULL, 'F'}, {"exclude-flags", required_argument, NULL, 'F'}, // following the same convention as view: g exists as a longoption_only // argument, accessible from the command line as --rf/--incl[ude]-flags {"rf", required_argument, NULL, LONGOPT('g')}, {"incl-flags", required_argument, NULL, LONGOPT('g')}, {"include-flags", required_argument, NULL, LONGOPT('g')}, {"i1", required_argument, NULL, 1}, {"I1", required_argument, NULL, 1}, {"i2", required_argument, NULL, 2}, {"I2", required_argument, NULL, 2}, {"if", required_argument, NULL, 3}, {"IF", required_argument, NULL, 3}, {"index-format", required_argument, NULL, 3}, {"barcode-tag", required_argument, NULL, 'b'}, {"quality-tag", required_argument, NULL, 'q'}, {"tag", required_argument, NULL, 'd'}, {"tag-file", required_argument, NULL, 'D'}, { NULL, 0, NULL, 0 } }; while ((c = getopt_long(argc, argv, "0:1:2:o:f:F:G:niNOs:c:tT:v:@:d:D:", lopts, NULL)) > 0) { switch (c) { case 'b': opts->barcode_tag = optarg; break; case 'q': opts->quality_tag = optarg; break; case 1 : opts->index_file[0] = optarg; break; case 2 : opts->index_file[1] = optarg; break; case 3 : opts->index_format = optarg; break; case '0': opts->fnr[0] = optarg; break; case '1': opts->fnr[1] = optarg; break; case '2': opts->fnr[2] = optarg; break; case 'o': opts->fnr[1] = optarg; opts->fnr[2] = optarg; break; case 'f': opts->flag_on |= strtol(optarg, 0, 0); break; // note that flag_off does not have |= because it has a default // value of 0x900 which needs to be replaced by the optarg case 'F': opts->flag_off = strtol(optarg, 0, 0); break; case 'G': opts->flag_alloff |= strtol(optarg, 0, 0); break; case LONGOPT('g'): opts->flag_anyon |= strtol(optarg, 0, 0); break; case 'n': opts->has12 = false; break; case 'N': opts->has12always = true; break; case 'O': opts->use_oq = true; break; case 's': opts->fnse = optarg; break; case 't': opts->copy_tags = true; break; case 'i': opts->illumina_tag = true; break; case 'c': opts->compression_level = atoi(optarg); if (opts->compression_level < 0) opts->compression_level = 0; if (opts->compression_level > 9) opts->compression_level = 9; break; case 'T': opts->extra_tags = optarg; break; case 'v': opts->def_qual = atoi(optarg); break; case 'd': if (strlen(optarg) < 2 || (strlen(optarg) > 2 && optarg[2] != ':')) { print_error("fastq", "Invalid \"tag:value\" option: \"%s\"", optarg); free_opts(opts); return false; } if (opts->filter_tag && memcmp(opts->filter_tag, optarg, 2)) { print_error("fastq", "Different tag type specified " "to before"); free_opts(opts); return false; } if (strlen(optarg) >= 3) add_tag_value(opts, optarg+3); opts->filter_tag = optarg; break; case 'D': // Allow ";" as delimiter besides ":" to support MinGW CLI POSIX // path translation as described at: // http://www.mingw.org/wiki/Posix_path_conversion if (strlen(optarg) < 4 || (optarg[2] != ':' && optarg[2] != ';')) { print_error("view", "Invalid \"tag:file\" option: \"%s\"", optarg); free_opts(opts); return false; } if (opts->filter_tag && memcmp(opts->filter_tag, optarg, 2)) { print_error("fastq", "Different tag type specified " "to before"); free_opts(opts); return false; } if (strlen(optarg) >= 3) { if (add_tag_file(opts, optarg+3) < 0) { free_opts(opts); return false; } } opts->filter_tag = optarg; break; case '?': bam2fq_usage(samtools_stderr, argv[0]); free_opts(opts); return false; default: if (parse_sam_global_opt(c, optarg, lopts, &opts->ga) != 0) { bam2fq_usage(samtools_stderr, argv[0]); free_opts(opts); return false; } break; } } if (opts->fnr[1] || opts->fnr[2]) opts->has12 = false; if (opts->has12always) opts->has12 = true; if (!opts->barcode_tag) opts->barcode_tag = DEFAULT_BARCODE_TAG; if (!opts->quality_tag) opts->quality_tag = DEFAULT_QUALITY_TAG; int nIndex = 0; if (opts->index_format) { char *s; for (s = opts->index_format; *s; s++) { if (*s == 'i') nIndex++; } } if (nIndex>2) { fprintf(samtools_stderr,"Invalid index format: more than 2 indexes\n"); bam2fq_usage(samtools_stderr, argv[0]); free_opts(opts); return false; } if (opts->index_file[1] && !opts->index_file[0]) { fprintf(samtools_stderr, "Index one specified, but index two not given\n"); bam2fq_usage(samtools_stderr, argv[0]); free_opts(opts); return false; } if (opts->illumina_tag && !nIndex) { fprintf(samtools_stderr, "You must specify an index format (--index-format) with the Illumina Casava (-i) option\n"); bam2fq_usage(samtools_stderr, argv[0]); free_opts(opts); return false; } if (nIndex==0 && opts->index_file[0]) { fprintf(samtools_stderr, "index_format not specified, but index file given\n"); bam2fq_usage(samtools_stderr, argv[0]); free_opts(opts); return false; } if (opts->def_qual < 0 || 93 < opts->def_qual) { fprintf(samtools_stderr, "Invalid -v default quality %i, allowed range 0 to 93\n", opts->def_qual); bam2fq_usage(samtools_stderr, argv[0]); free_opts(opts); return false; } const char* type_str = argv[0]; if (strcasecmp("fastq", type_str) == 0 || strcasecmp("bam2fq", type_str) == 0) { opts->filetype = FASTQ; } else if (strcasecmp("fasta", type_str) == 0) { opts->filetype = FASTA; } else { print_error("bam2fq", "Unrecognised type call \"%s\", this should be impossible... but you managed it!", type_str); bam2fq_usage(samtools_stderr, argv[0]); free_opts(opts); return false; } if (argc == optind && isatty(STDIN_FILENO)) { bam2fq_usage(samtools_stdout, argv[0]); free_opts(opts); return true; } if (argc - optind > 1) { fprintf(samtools_stderr, "Too many arguments.\n"); bam2fq_usage(samtools_stderr, argv[0]); free_opts(opts); return false; } opts->fn_input = argc > optind ? argv[optind] : "-"; *opts_out = opts; return true; } void set_sam_opts(samFile *fp, bam2fq_state_t *state, const bam2fq_opts_t *opts) { if (state->has12) hts_set_opt(fp, FASTQ_OPT_RNUM, 1); if (state->illumina_tag) hts_set_opt(fp, FASTQ_OPT_CASAVA, 1); hts_set_opt(fp, FASTQ_OPT_BARCODE, opts->barcode_tag); if (opts->extra_tags && (*opts->extra_tags == '*' || *opts->extra_tags == '\0')) hts_set_opt(fp, FASTQ_OPT_AUX, NULL); else { kstring_t tag_list = {0,0}; if (state->copy_tags) kputs("RG,BC,QT", &tag_list); if (opts->extra_tags) { if (tag_list.l) kputc(',', &tag_list); kputs(opts->extra_tags, &tag_list); } if (tag_list.l) hts_set_opt(fp, FASTQ_OPT_AUX, tag_list.s); ks_free(&tag_list); } } // Open a file as normal or gzipped based on filename. // Note we always use bgzf and don't bother to attempt non-blocked // gzip streams. This is a departure from the old fastq code. static samFile *sam_open_z(char *fn, char *mode, bam2fq_state_t *state) { char modez[6]; strcpy(modez, mode); size_t l = strlen(fn); if ((l > 3 && strcmp(fn+l-3, ".gz") == 0) || (l > 4 && strcmp(fn+l-4, ".bgz") == 0) || (l > 5 && strcmp(fn+l-5, ".bgzf") == 0)) { char m[3] = {'z', state->compression_level+'0', '\0'}; strcat(modez, m); } samFile *fp = sam_open(fn, modez); if (!fp) return NULL; if (state->p.pool) hts_set_thread_pool(fp, &state->p); return fp; } static bool init_state(const bam2fq_opts_t* opts, bam2fq_state_t** state_out) { char *mode = opts->filetype == FASTA ? "wF" : "wf"; bam2fq_state_t* state = calloc(1, sizeof(bam2fq_state_t)); if (!state) return false; state->flag_on = opts->flag_on; state->flag_off = opts->flag_off; state->flag_alloff = opts->flag_alloff; state->flag_anyon = opts->flag_anyon; state->has12 = opts->has12; state->use_oq = opts->use_oq; state->illumina_tag = opts->illumina_tag; state->copy_tags = opts->copy_tags; state->filetype = opts->filetype; state->def_qual = opts->def_qual; state->index_sequence = NULL; state->hstdout = NULL; state->compression_level = opts->compression_level; state->fp = sam_open_format(opts->fn_input, "r", &opts->ga.in); if (state->fp == NULL) { print_error_errno("bam2fq","Cannot read file \"%s\"", opts->fn_input); free(state); return false; } state->p.pool = NULL; if (opts->ga.nthreads > 0) { if (!(state->p.pool = hts_tpool_init(opts->ga.nthreads))) { fprintf(samtools_stderr, "Failed to create thread pool\n"); free(state); return false; } state->p.qsize = opts->ga.nthreads*2; hts_set_thread_pool(state->fp, &state->p); } uint32_t rf = SAM_QNAME | SAM_FLAG | SAM_SEQ | SAM_QUAL; if (opts->use_oq || opts->extra_tags || opts->index_file[0]) rf |= SAM_AUX; if (opts->filter_tag) { if (memcmp(opts->filter_tag, "NM", 2) == 0 || memcmp(opts->filter_tag, "MD", 2) == 0) rf |= SAM_AUX | SAM_SEQ; else if (memcmp(opts->filter_tag, "RG", 2) == 0) rf |= SAM_RGAUX; else rf |= SAM_AUX; } if (hts_set_opt(state->fp, CRAM_OPT_REQUIRED_FIELDS, rf)) { fprintf(samtools_stderr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n"); free(state); return false; } if (hts_set_opt(state->fp, CRAM_OPT_DECODE_MD, 0)) { fprintf(samtools_stderr, "Failed to set CRAM_OPT_DECODE_MD value\n"); free(state); return false; } if (opts->fnse) { if (!(state->fpse = sam_open_z(opts->fnse, mode, state))) { print_error_errno("bam2fq", "Cannot open singleton file \"%s\"", opts->fnse); free(state); return false; } set_sam_opts(state->fpse, state, opts); } if (opts->ga.reference) { if (hts_set_fai_filename(state->fp, opts->ga.reference) != 0) { print_error_errno("bam2fq", "cannot load reference \"%s\"", opts->ga.reference); free(state); return false; } } // single, read1, read2 int i, j; for (i = 0; i < 3; ++i) { if (opts->fnr[i]) { for (j = 0; j < i; j++) if (opts->fnr[j] && strcmp(opts->fnr[j], opts->fnr[i]) == 0) break; if (j == i) { if (!(state->fpr[i] = sam_open_z(opts->fnr[i], mode, state))) { print_error_errno("bam2fq", "Cannot open r%d file \"%s\"", i, opts->fnr[i]); free(state); return false; } set_sam_opts(state->fpr[i], state, opts); } else { state->fpr[i] = state->fpr[j]; } } else { if (!state->hstdout) { if (!(state->hstdout = sam_open_z("-", mode, state))) { print_error_errno("bam2fq", "Cannot open STDOUT"); free(state); return false; } set_sam_opts(state->hstdout, state, opts); autoflush_if_stdout(state->hstdout, "-"); } state->fpr[i] = state->hstdout; } } // index 1, index 2 for (i = 0; i < 2; i++) { state->fpi[i] = NULL; if (opts->index_file[i]) { for (j = 0; j < 3; j++) if (opts->fnr[j] && strcmp(opts->fnr[j], opts->index_file[i]) == 0) break; for (j -= 3; j >= 0 && j < i; j++) if (opts->index_file[j] && strcmp(opts->index_file[j], opts->index_file[i]) == 0) break; if (i == j) { if (!(state->fpi[i] = sam_open_z(opts->index_file[i], mode, state))) { print_error_errno("bam2fq", "Cannot open i%d file \"%s\"", i+1, opts->index_file[i]); free(state); return false; } set_sam_opts(state->fpi[i], state, opts); } else if (j < 0) { state->fpi[i] = state->fpr[j+3]; } else { state->fpi[i] = state->fpi[j]; } } } state->h = sam_hdr_read(state->fp); if (state->h == NULL) { fprintf(samtools_stderr, "Failed to read header for \"%s\"\n", opts->fn_input); free(state); return false; } *state_out = state; return true; } static bool destroy_state(const bam2fq_opts_t *opts, bam2fq_state_t *state, int* status) { bool valid = true; sam_hdr_destroy(state->h); check_sam_close("bam2fq", state->fp, opts->fn_input, "file", status); if (state->fpse && sam_close(state->fpse) < 0) { print_error_errno("bam2fq", "Error closing singleton file \"%s\"", opts->fnse); valid = false; } int i, j; for (i = 0; i < 3; ++i) { if (state->fpr[i] != state->hstdout) { for (j = 0; j < i; j++) if (state->fpr[i] == state->fpr[j]) break; if (j == i && sam_close(state->fpr[i])) { print_error_errno("bam2fq", "Error closing r%d file \"%s\"", i, opts->fnr[i]); valid = false; } } } if (state->hstdout) { release_autoflush(state->hstdout); if (sam_close(state->hstdout) < 0) { print_error_errno("bam2fq", "Error closing STDOUT"); valid = false; } } for (i = 0; i < 2; i++) { for (j = 0; j < 3; j++) if (state->fpi[i] == state->fpr[j]) break; for (j -= 3; j >= 0 && j < i; j++) if (state->fpi[i] == state->fpi[j]) break; if (j == i && state->fpi[i] && sam_close(state->fpi[i]) < 0) { print_error_errno("bam2fq", "Error closing i%d file \"%s\"", i+1, opts->index_file[i]); valid = false; } } free(state->index_sequence); if (state->p.pool) hts_tpool_destroy(state->p.pool); free(state); return valid; } static inline bool filter_it_out(const bam1_t *b, const bam2fq_state_t *state, bam2fq_opts_t *opts) { if (opts->filter_tag) { uint8_t *s = bam_aux_get(b, opts->filter_tag); if (!s) return true; if (opts->filter_tag_vals) { char t[32], *val = t; switch (*s) { case 'i': case 'I': case 's': case 'S': case 'c': case 'C': if (snprintf(t, 32, "%"PRId64, bam_aux2i(s)) <= 0) return true; break; case 'f': // Comparing floats is hard. // Eg (double)0.1 - (double)0.1f is -1.5e-9. // Given BAM binary encoding is float however, just keep it. // This means rounding errors will (hopefully) always be the // same and basic equality still works. if (snprintf(t, 32, "%f", (float)bam_aux2f(s)) <= 0) return true; break; case 'A': t[0] = s[1]; t[1] = 0; break; case 'Z': case 'H': val = (char *)s+1; break; default: // Anything unsupported fails the filter match too. return true; } khint_t k = kh_get(str, opts->filter_tag_vals, val); if (k == kh_end(opts->filter_tag_vals)) return 1; // tag value not found } } return ((b->core.flag&(state->flag_on)) != state->flag_on // or reads indicated by filter flags || (b->core.flag&(state->flag_off)) != 0 || (((b->core.flag&(state->flag_anyon)) == 0) && (state->flag_anyon != 0)) || (b->core.flag&(state->flag_alloff) && (b->core.flag&(state->flag_alloff)) == state->flag_alloff)); } int write_index_rec(samFile *fp, bam1_t *b, bam2fq_state_t *state, bam2fq_opts_t* opts, char *seq, int seq_len, char *qual, int qual_len) { if (!fp || !b || !seq_len) return 0; int ret = -1; bam1_t *b2 = bam_init1(); // FIXME: reuse if (!b2) return -1; size_t aux_len = b->data + b->l_data - bam_get_aux(b); if (bam_set1(b2, b->core.l_qname, bam_get_qname(b), (b->core.flag | BAM_FUNMAP) & ~BAM_FREVERSE, -1, -1, 0, // refid, pos, mapq 0, NULL, // cigar -1, -1, 0, // rnext, pnext, tlen seq_len, seq, qual, aux_len) < 0) goto err; uint8_t *q = bam_get_qual(b2); if (qual) { int i; for (i = 0; i < seq_len; i++) q[i] -= '!'; } else { memset(q, opts->def_qual, seq_len); } memcpy(bam_get_aux(b2), bam_get_aux(b), aux_len); b2->l_data += aux_len; if (sam_write1(fp, state->h, b2) < 0) goto err; ret = 0; err: if (b2) bam_destroy1(b2); return ret; } int output_index(bam1_t *b1, bam1_t *b2, bam2fq_state_t *state, bam2fq_opts_t* opts) { bam1_t *b = b1 ? b1 : b2; char *ifmt = opts->index_format; if (!ifmt) ifmt = "i*i*"; // Get seq / qual elements char *bc = NULL, *qt = NULL; if (b1) bc = (char *)bam_aux_get(b1, opts->barcode_tag); if (b2 && !bc) bc = (char *)bam_aux_get(b2, opts->barcode_tag); if (!bc) return 0; else bc++; // skip Z if (b1) qt = (char *)bam_aux_get(b1, opts->quality_tag); if (b2 && !qt) qt = (char *)bam_aux_get(b2, opts->quality_tag); if (qt && strlen(bc) != strlen(qt)-1) qt = NULL; else if (qt) qt++; int inum = 0; while (inum < 2) { char fc = *ifmt++; if (!fc) break; // ran out of index-format long len, rem = 0; if (isdigit(*ifmt)) { rem = len = strtol(ifmt, &ifmt, 10); } else { ifmt++; len = 0; } char *bc_end = bc, *qt_end = qt; if (qt) { while (len ? *bc_end && rem-- : isalpha(*bc_end)) bc_end++, qt_end++; } else { while (len ? *bc_end && rem-- : isalpha(*bc_end)) bc_end++; } switch (fc) { case 'n': // skip bc = bc_end + (len==0); if (qt) qt = qt_end + (len==0); break; case 'i': if (write_index_rec(state->fpi[inum], b, state, opts, bc, bc_end-bc, qt, qt_end-qt) < 0) return -1; bc = bc_end + (len==0); if (qt) qt = qt_end + (len==0); inum++; break; default: fprintf(samtools_stderr, "Unknown index-format code\n"); return -1; } } return 0; } static int flush_rec(bam2fq_state_t *state, bam2fq_opts_t* opts, bam1_t *b[4], int score[3], int best[3], int64_t *n_singletons) { // Paired data, with 1 or 2 ends present. if (score[1] > 0 && score[2] > 0) { // If CASAVA tag is required and barcode is only on R1, // copy it to R2 if (state->illumina_tag) { char *tag; if ((tag = (char *)bam_aux_get(b[best[1]], opts->barcode_tag))) if (bam_aux_update_str(b[best[2]], opts->barcode_tag, strlen(tag), tag+1) < 0) goto err; if ((tag = (char *)bam_aux_get(b[best[1]], opts->quality_tag))) if (bam_aux_update_str(b[best[2]], opts->quality_tag, strlen(tag), tag+1) < 0) goto err; } if (sam_write1(state->fpr[1], state->h, b[best[1]]) < 0) goto err; if (sam_write1(state->fpr[2], state->h, b[best[2]]) < 0) goto err; if (output_index(b[best[1]], b[best[2]], state, opts) < 0) goto err; } else if (score[1] > 0 || score[2] > 0) { if (state->fpse) { // print whichever one exists to fpse if (score[1] > 0) { if (sam_write1(state->fpse, state->h, b[best[1]]) < 0) goto err; } else { if (sam_write1(state->fpse, state->h, b[best[2]]) < 0) goto err; } ++(*n_singletons); } else { if (score[1] > 0) { if (sam_write1(state->fpr[1], state->h, b[best[1]]) < 0) goto err; } else { if (sam_write1(state->fpr[2], state->h, b[best[2]]) < 0) goto err; } } if (output_index(score[1] > 0 ? b[best[1]] : NULL, score[2] > 0 ? b[best[2]] : NULL, state, opts) < 0) goto err; } if (score[0]) { // single ended data (neither READ1 nor READ2) if (sam_write1(state->fpr[0], state->h, b[best[0]]) < 0) goto err; if (output_index(b[best[0]], NULL, state, opts) < 0) goto err; } return 0; err: return -1; } static bool bam2fq_mainloop(bam2fq_state_t *state, bam2fq_opts_t* opts) { int n; char *current_qname = NULL; int64_t n_reads = 0, n_singletons = 0; // Statistics int score[3]; int at_eof; bool valid = false; int best[3] = {-1, -1, -1}; // map R0, R1, single to b[] indices; // indexed by [readpart] bam1_t *b[4]; // 3 readparts, plus current record for (n = 0; n < 4; n++) { if (!(b[n] = bam_init1())) { perror("[bam2fq_mainloop] Malloc error for bam record buffer."); return false; } } n = 0; while (true) { int res = sam_read1(state->fp, state->h, b[n]); if (res < -1) { print_error("bam2fq", "Failed to read bam record"); goto err; } at_eof = res < 0; if (!at_eof && filter_it_out(b[n], state, opts)) continue; if (!at_eof) { ++n_reads; // Handle -O option: use OQ for qual uint8_t *oq; if (state->use_oq && (oq = bam_aux_get(b[n],"OQ")) && *oq == 'Z') { int i, l = strlen((char *)++oq); uint8_t *qual = bam_get_qual(b[n]); for (i = 0; i < l && i < b[n]->core.l_qseq; i++) qual[i] = oq[i] - '!'; } } if (at_eof || !current_qname || (strcmp(current_qname, bam_get_qname(b[n])) != 0)) { // New name, so flush best examples of previous name. if (current_qname) if (flush_rec(state, opts, b, score, best, &n_singletons) < 0) goto err; current_qname = bam_get_qname(b[n]); score[0] = score[1] = score[2] = 0; if (at_eof) { break; } } // Prefer a copy of the read that has base qualities int b_score = bam_get_qual(b[n])[0] != 0xff? 2 : 1; readpart rp = which_readpart(b[n]); if (score[rp] < b_score) { score[rp] = b_score; // Record b[n] slot for best copy of readpair and find a new // slot for next bam read best[rp] = n; int used_slot[4] = {0}, i; for (i = 0; i < 3; i++) if (best[i] >= 0) used_slot[best[i]] = 1; for (i = 0; i < 4 && used_slot[i]; i++) ; n = i; } } valid = true; err: if (!valid) print_error_errno("bam2fq", "Error writing to FASTx files."); for (n = 0; n < 4; n++) bam_destroy1(b[n]); fprintf(samtools_stderr, "[M::%s] discarded %" PRId64 " singletons\n", __func__, n_singletons); fprintf(samtools_stderr, "[M::%s] processed %" PRId64 " reads\n", __func__, n_reads); return valid; } int main_bam2fq(int argc, char *argv[]) { int status = EXIT_FAILURE; bam2fq_opts_t* opts = NULL; bam2fq_state_t* state = NULL; bool valid = parse_opts(argc, argv, &opts); if (!valid || opts == NULL) return valid ? EXIT_SUCCESS : EXIT_FAILURE; if (!init_state(opts, &state)) goto err; if (!bam2fq_mainloop(state,opts)) goto err; if (!destroy_state(opts, state, &status)) goto err; status = EXIT_SUCCESS; err: sam_global_args_free(&opts->ga); free_opts(opts); return status; } pysam-0.23.0/samtools/bam_flags.c000066400000000000000000000062711475062545500166700ustar00rootroot00000000000000/* bam_flags.c -- flags subcommand. Copyright (C) 2013-2014, 2021 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include "samtools.h" static void usage(FILE *fp) { static const struct { int bit; const char *desc; } *fl, flags[] = { { BAM_FPAIRED, "paired-end / multiple-segment sequencing technology" }, { BAM_FPROPER_PAIR, "each segment properly aligned according to aligner" }, { BAM_FUNMAP, "segment unmapped" }, { BAM_FMUNMAP, "next segment in the template unmapped" }, { BAM_FREVERSE, "SEQ is reverse complemented" }, { BAM_FMREVERSE, "SEQ of next segment in template is rev.complemented" }, { BAM_FREAD1, "the first segment in the template" }, { BAM_FREAD2, "the last segment in the template" }, { BAM_FSECONDARY, "secondary alignment" }, { BAM_FQCFAIL, "not passing quality controls or other filters" }, { BAM_FDUP, "PCR or optical duplicate" }, { BAM_FSUPPLEMENTARY, "supplementary alignment" }, { 0, NULL } }; fprintf(fp, "About: Convert between textual and numeric flag representation\n" "Usage: samtools flags FLAGS...\n" "\n" "Each FLAGS argument is either an INT (in decimal/hexadecimal/octal) representing\n" "a combination of the following numeric flag values, or a comma-separated string\n" "NAME,...,NAME representing a combination of the following flag names:\n" "\n"); for (fl = flags; fl->desc; fl++) { char *name = bam_flag2str(fl->bit); fprintf(fp, "%#6x %5d %-15s%s\n", fl->bit, fl->bit, name, fl->desc); free(name); } } int main_flags(int argc, char *argv[]) { if ( argc < 2 ) { usage(stdout); return 0; } int i; for (i = 1; i < argc; i++) { int mask = bam_str2flag(argv[i]); if ( mask<0 ) { print_error("flags", "Could not parse \"%s\"", argv[i]); usage(stderr); return 1; } char *str = bam_flag2str(mask); printf("0x%x\t%d\t%s\n", mask, mask, str); free(str); } return 0; } pysam-0.23.0/samtools/bam_flags.c.pysam.c000066400000000000000000000063721475062545500202430ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_flags.c -- flags subcommand. Copyright (C) 2013-2014, 2021 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include "samtools.h" static void usage(FILE *fp) { static const struct { int bit; const char *desc; } *fl, flags[] = { { BAM_FPAIRED, "paired-end / multiple-segment sequencing technology" }, { BAM_FPROPER_PAIR, "each segment properly aligned according to aligner" }, { BAM_FUNMAP, "segment unmapped" }, { BAM_FMUNMAP, "next segment in the template unmapped" }, { BAM_FREVERSE, "SEQ is reverse complemented" }, { BAM_FMREVERSE, "SEQ of next segment in template is rev.complemented" }, { BAM_FREAD1, "the first segment in the template" }, { BAM_FREAD2, "the last segment in the template" }, { BAM_FSECONDARY, "secondary alignment" }, { BAM_FQCFAIL, "not passing quality controls or other filters" }, { BAM_FDUP, "PCR or optical duplicate" }, { BAM_FSUPPLEMENTARY, "supplementary alignment" }, { 0, NULL } }; fprintf(fp, "About: Convert between textual and numeric flag representation\n" "Usage: samtools flags FLAGS...\n" "\n" "Each FLAGS argument is either an INT (in decimal/hexadecimal/octal) representing\n" "a combination of the following numeric flag values, or a comma-separated string\n" "NAME,...,NAME representing a combination of the following flag names:\n" "\n"); for (fl = flags; fl->desc; fl++) { char *name = bam_flag2str(fl->bit); fprintf(fp, "%#6x %5d %-15s%s\n", fl->bit, fl->bit, name, fl->desc); free(name); } } int main_flags(int argc, char *argv[]) { if ( argc < 2 ) { usage(samtools_stdout); return 0; } int i; for (i = 1; i < argc; i++) { int mask = bam_str2flag(argv[i]); if ( mask<0 ) { print_error("flags", "Could not parse \"%s\"", argv[i]); usage(samtools_stderr); return 1; } char *str = bam_flag2str(mask); fprintf(samtools_stdout, "0x%x\t%d\t%s\n", mask, mask, str); free(str); } return 0; } pysam-0.23.0/samtools/bam_import.c000066400000000000000000000420431475062545500171030ustar00rootroot00000000000000/* bam_import -- Import of FASTQ files. * * samtools import -1 a_1.fq -2 a_2.fq --i1 a_i1.fq --i2 a_i2.fq * samtools import a_1.fq a_2.fq * samtools import a_interleaved.fq * * Copyright (C) 2020-2021, 2023-2024 Genome Research Ltd. * * Author: James Bonfield */ /* Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notices and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ // TODO: Store other non-aux comments; in new sam tag? #include #include #include "htslib/sam.h" #include "htslib/thread_pool.h" #include "samtools.h" #include "sam_opts.h" static int usage(FILE *fp, int exit_status) { fprintf(fp, "Usage: samtools import [options] [file.fastq ...]\n"); fprintf(fp, "\n"); fprintf(fp, "Options:\n"); fprintf(fp, " -s FILE Read paired-ended data from single FILE\n"); fprintf(fp, " -0 FILE Read single-ended data from FILE\n"); fprintf(fp, " -1 FILE Read-1 from FILE\n"); fprintf(fp, " -2 FILE Read-2 from FILE\n"); fprintf(fp, " --i1 FILE Index-1 from FILE\n"); fprintf(fp, " --i2 FILE Index-2 from FILE\n"); fprintf(fp, " -i Parse CASAVA identifier\n"); fprintf(fp, " --barcode-tag TAG\n"); fprintf(fp, " Tag to use with barcode sequences [BC]\n"); fprintf(fp, " --quality-tag TAG\n"); fprintf(fp, " Tag to use with barcode qualities [QT]\n"); fprintf(fp, " -N, --name2 Use 2nd field as read name (SRA format)\n"); fprintf(fp, " -r STRING Build up a complete @RG line\n"); fprintf(fp, " -R STRING Add a simple RG line of \"@RG\\tID:STRING\"\n"); fprintf(fp, " -T TAGLIST Parse tags in SAM format; list of '*' for all\n"); fprintf(fp, " -o FILE Output to FILE instead of stdout\n"); fprintf(fp, " -u Uncompressed output\n"); fprintf(fp, " --order TAG Store Nth record count in TAG\n"); fprintf(fp, "\n"); fprintf(fp, " --no-PG Do not add a PG line\n"); sam_global_opt_help(fp, "-.O.-@--"); fprintf(fp, "\nA single fastq file will be interpreted as -s, -0 or -1 depending on\n"); fprintf(fp, "file contents, and a pair of fastq files as \"-1 FILE1 -2 FILE2\".\n"); return exit_status; } // Order matters here as we want to read index elements before main // sequences so on reading the seqs we can emit a fully annotated record. enum fileno { FQ_I1, FQ_I2, // index seqs for R1 and R2 FQ_R0, // single file and unpaired data (singled-ended tech). FQ_R1, FQ_R2, // separate read1 and read2 files FQ_SINGLE, // single file, but with read1 and/or read2 present. FQ_END }; typedef struct { sam_global_args ga; int no_pg; char *fn[FQ_END], *fn_out; int idx_both; // add index to READ2 too, not just READ1 int casava; char *barcode_seq; char *barcode_qual; char *aux; char *rg; char *rg_line; char *order; int order_str; int compress_level; htsThreadPool p; int name2; } opts_t; // Append a sequence and quality string from a BAM record to a BC:Z and // QT:Z style aux tag string. static int append_index(kstring_t *s, kstring_t *q, bam1_t *b) { char *sp, *qp; if (ks_resize(s, s->l + b->core.l_qseq+1 +1) < 0) return -1; if (ks_resize(q, q->l + b->core.l_qseq+1 +1) < 0) return -1; sp = s->s + s->l - (s->l > 0); qp = q->s + q->l - (q->l > 0); if (s->l) *sp++ = '-'; if (q->l) *qp++ = ' '; int i; uint8_t *seq = bam_get_seq(b); uint8_t *qual = bam_get_qual(b); for (i = 0; i < b->core.l_qseq; i++) { *sp++ = seq_nt16_str[bam_seqi(seq, i)]; *qp++ = qual[i] + '!'; } *sp++ = 0; *qp++ = 0; s->l = sp - s->s; q->l = qp - q->s; return 0; } static int import_fastq(int argc, char **argv, opts_t *opts) { int i, n, ret = 0; samFile *fp_in[FQ_END] = {NULL}; bam1_t *b = bam_init1(); int ids[FQ_END]; samFile *fp_out = NULL; sam_hdr_t *hdr_out = NULL; kstring_t index_str = {0,0}; kstring_t read_str = {0,0}; char *rg = opts->rg; kstring_t rg_line = {0,0}; uint64_t read_num = 0; kstring_t idx_seq = {0}; kstring_t idx_qual = {0}; // Any additional arguments are assumed to be r1 r2, as a // short cut. We support reading index tags out of those too (eg // Illumina CASAVA format), but if we do that we lack the barcode // quality string. // // We also consider a read name ending in /1 or /2 to be a single // file containing interleaved fastq records for both ends. // These will be labeled as fn[FQ_R1] but adjusted during reading. if (argc == 1) opts->fn[FQ_SINGLE] = argv[0]; else for (i = 0; i < 2; i++) if (argc > i) opts->fn[FQ_R1+i] = argv[i]; // Open all files for (i = n = 0; i < FQ_END; i++) { if (!opts->fn[i]) continue; fp_in[i] = sam_open_format(opts->fn[i], "r", &opts->ga.in); if (!fp_in[i]) { perror(opts->fn[i]); ret = -1; goto err; } if (opts->p.pool) hts_set_thread_pool(fp_in[i], &opts->p); ids[n++] = i; if (opts->name2) hts_set_opt(fp_in[i], FASTQ_OPT_NAME2, 1); if (opts->casava) hts_set_opt(fp_in[i], FASTQ_OPT_CASAVA, 1); if (opts->barcode_seq) // for auto-CASAVA parsing hts_set_opt(fp_in[i], FASTQ_OPT_BARCODE, opts->barcode_seq); if (opts->aux) hts_set_opt(fp_in[i], FASTQ_OPT_AUX, *opts->aux == '*' || *opts->aux == '\0' ? NULL : opts->aux); switch (i) { case FQ_I1: kputs("--i1 I1.fastq ", &read_str); kputs("i*", &index_str); break; case FQ_I2: kputs("--i2 I2.fastq ", &read_str); kputs("i*", &index_str); break; case FQ_R0: kputs("-0 unpaired.fastq ", &read_str); break; case FQ_R1: kputs("-1 R1.fastq ", &read_str); break; case FQ_R2: kputs("-2 R2.fastq ", &read_str); break; case FQ_SINGLE: kputs("-N -o paired.fastq ", &read_str); break; default: ks_clear(&read_str); // not reversible kputs("", &read_str); } } if (n == 0) { bam_destroy1(b); return usage(stdout, EXIT_SUCCESS); } char out_mode[10] = {'w', 0, 0}; if (opts->compress_level != -1) out_mode[1] = '0' + opts->compress_level; sam_open_mode(out_mode+strlen(out_mode), opts->fn_out, NULL); fp_out = sam_open_format(opts->fn_out, out_mode, &opts->ga.out); if (!fp_out) { perror(opts->fn_out); goto err; } autoflush_if_stdout(fp_out, opts->fn_out); if (opts->p.pool) hts_set_thread_pool(fp_out, &opts->p); // Create header if (ks_len(&read_str)) { char CO[2100]; if (ks_len(&index_str)) snprintf(CO, sizeof(CO), "@CO\tReverse with: samtools fastq %s " "--index-format=\"%s\"\n", ks_str(&read_str), ks_str(&index_str)); else snprintf(CO, sizeof(CO), "@CO\tReverse with: samtools fastq %s\n", ks_str(&read_str)); hdr_out = sam_hdr_parse(strlen(CO), CO); } else { hdr_out = sam_hdr_init(); } // Add a version line with the sort order to the output header if (sam_hdr_add_line(hdr_out, "HD", "VN", SAM_FORMAT_VERSION, "SO", "unsorted", "GO", "query", NULL) < 0) { fprintf(stderr, "Could not set SO and GO in the header.\n"); goto err; } if (!opts->no_pg) { char *arg_list; if (!(arg_list = stringify_argv(argc+1+optind, argv-1-optind))) { print_error("view", "failed to create arg_list"); goto err; } if (sam_hdr_add_pg(hdr_out, "samtools", "VN", samtools_version(), arg_list ? "CL" : NULL, arg_list ? arg_list : NULL, NULL)) { fprintf(stderr, "Failed to add PG line to the header"); free(arg_list); goto err; } free(arg_list); } // Read group if (opts->rg_line) { if (*opts->rg_line != '@') ksprintf(&rg_line, "@RG\t%s", opts->rg_line); else kputs(opts->rg_line, &rg_line); } else if (opts->rg) { ksprintf(&rg_line, "@RG\tID:%s", opts->rg); } if (ks_len(&rg_line)) { if (sam_hdr_add_lines(hdr_out, ks_str(&rg_line), 0) < 0) goto err; rg = strstr(ks_str(&rg_line), "\tID:"); if (!rg) { fprintf(stderr, "\"-r RG-LINE\" option contained no ID field\n"); goto err; } rg += 4; i = 0; while (rg[i] != '\t' && rg[i] != '\0') i++; rg[i] = 0; } if ((ret = sam_hdr_write(fp_out, hdr_out)) < 0) goto err; // Interleave / combine from n files (ids[0..n-1]). int res = 0; int eof = 0; do { idx_seq.l = idx_qual.l = 0; for (i = 0; i < n; i++) { if ((res = sam_read1(fp_in[ids[i]], NULL, b)) < 0) { if (res == -1) { eof++; continue; } else break; } // index if (ids[i] == FQ_I1 || ids[i] == FQ_I2) { if (append_index(&idx_seq, &idx_qual, b) < 0) { res = -1; break; } continue; } // full read if (idx_seq.l) { if (opts->idx_both || ids[i] == FQ_SINGLE || ids[i] == FQ_R0 || ids[i] == FQ_R1) { if (bam_aux_append(b, opts->barcode_seq, 'Z', idx_seq.l, (uint8_t *)idx_seq.s) || bam_aux_append(b, opts->barcode_qual, 'Z', idx_qual.l, (uint8_t *)idx_qual.s)) { res = -1; break; } } } switch(ids[i]) { case FQ_R0: // unpaired; no flags to declare break; case FQ_SINGLE: // paired (but don't know if R1 or R2) or unpaired. // We rely on the /1 and /2 read suffix parsing in htslib // to distinguish the two cases, or CASAVA tags if // explicitly enabled. break; case FQ_R1: if ((b->core.flag & (BAM_FREAD1 | BAM_FREAD2)) == 0) b->core.flag |= BAM_FREAD1; b->core.flag |= BAM_FPAIRED; if (i+1 < n && ids[i+1] == FQ_R2) b->core.flag |= BAM_FMUNMAP; break; case FQ_R2: b->core.flag |= BAM_FPAIRED | BAM_FREAD2; if (i > 0 && ids[i-1] == FQ_R1) b->core.flag |= BAM_FMUNMAP; break; } if (rg) { if (bam_aux_append(b, "RG", 'Z', strlen(rg)+1, (uint8_t *)rg) < 0) { ret = -1; goto err; } } if (opts->order) { if (opts->order_str) { char buf[25]; snprintf(buf, sizeof(buf), "%0*"PRIu64, opts->order_str, read_num++); if (bam_aux_update_str(b, opts->order, strlen(buf), buf) < 0) { ret = -1; goto err; } } else { if (bam_aux_update_int(b, opts->order, read_num++) < 0) { ret = -1; goto err; } if (read_num == UINT_MAX) fprintf(stderr, "Warning: --order tag has overflowed." " Consider using TAG:LENGTH instead\n"); } } res = sam_write1(fp_out, hdr_out, b); } } while (res >= 0); if (res != -1) { print_error("import", "truncated file. Aborting"); ret = res; goto err; } if (eof != n) { print_error("import", "input files with differing number of records"); ret = -1; goto err; } // Close and return ret = 0; err: bam_destroy1(b); sam_hdr_destroy(hdr_out); ks_free(&rg_line); ks_free(&index_str); ks_free(&read_str); if (fp_out) { release_autoflush(fp_out); if (sam_close(fp_out) < 0) { perror(opts->fn_out); ret |= -1; } } for (i = 0; i < FQ_END; i++) { if (fp_in[i] && sam_close(fp_in[i]) < 0) { perror(opts->fn[i]); ret |= -1; } } ks_free(&idx_seq); ks_free(&idx_qual); return ret; } int main_import(int argc, char *argv[]) { int c; opts_t opts = { .no_pg = 0, .ga = SAM_GLOBAL_ARGS_INIT, .fn = {NULL}, .fn_out = "-", .casava = 0, .barcode_seq = "BC", .barcode_qual = "QT", .aux = NULL, .rg = NULL, .rg_line = NULL, .order = NULL, .order_str = 0, .compress_level = -1, .name2 = 0, }; kstring_t rg = {0}; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, '-', '@'), {"no-PG", no_argument, NULL, 9}, {"i1", required_argument, NULL, 1}, {"i2", required_argument, NULL, 2}, {"r1", required_argument, NULL, '1'}, {"r2", required_argument, NULL, '2'}, {"rg", required_argument, NULL, 'R'}, {"rg-line", required_argument, NULL, 'r'}, {"order", required_argument, NULL, 3}, {"barcode-tag", required_argument, NULL, 4}, {"quality-tag", required_argument, NULL, 5}, {"name2", no_argument, NULL, 'N'}, { NULL, 0, NULL, 0 } }; while ((c = getopt_long(argc, argv, "1:2:s:0:bhiT:r:R:o:O:u@:N", lopts, NULL)) >= 0) { switch (c) { case 'b': opts.idx_both = 1; break; case '0': opts.fn[FQ_R0] = optarg; break; case '1': opts.fn[FQ_R1] = optarg; break; case '2': opts.fn[FQ_R2] = optarg; break; case 1: opts.fn[FQ_I1] = optarg; break; case 2: opts.fn[FQ_I2] = optarg; break; case 's': opts.fn[FQ_SINGLE] = optarg; break; case 'o': opts.fn_out = optarg; break; case 'i': opts.casava = 1; break; case 4: opts.barcode_seq = optarg; break; case 5: opts.barcode_qual = optarg; break; case 'T': opts.aux = optarg; break; case 'u': opts.compress_level = 0; break; case 'R': opts.rg = optarg; break; case 'r': if (*optarg != '@' && ks_len(&rg) == 0) kputs("@RG", &rg); if (ks_len(&rg)) kputc_('\t', &rg); kputs(optarg, &rg); opts.rg_line = rg.s; break; case 'N': opts.name2 = 1; break; case 9: opts.no_pg = 1; break; case 3: opts.order = optarg; if (strlen(optarg) > 3 && optarg[2] == ':') opts.order_str = atoi(optarg+3); break; case 'h': return usage(stdout, EXIT_SUCCESS); case '?': return usage(stderr, EXIT_FAILURE); default: if (parse_sam_global_opt(c, optarg, lopts, &opts.ga) != 0) return usage(stderr, EXIT_FAILURE); break; } } if (opts.ga.nthreads > 0) { if (!(opts.p.pool = hts_tpool_init(opts.ga.nthreads))) { fprintf(stderr, "Failed to create thread pool\n"); if (rg.s) free(rg.s); return -1;; } } int ret = import_fastq(argc-optind, argv+optind, &opts) ? 1 : 0; if (rg.s) free(rg.s); if (opts.p.pool) hts_tpool_destroy(opts.p.pool); return ret; } pysam-0.23.0/samtools/bam_import.c.pysam.c000066400000000000000000000422321475062545500204540ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_import -- Import of FASTQ files. * * samtools import -1 a_1.fq -2 a_2.fq --i1 a_i1.fq --i2 a_i2.fq * samtools import a_1.fq a_2.fq * samtools import a_interleaved.fq * * Copyright (C) 2020-2021, 2023-2024 Genome Research Ltd. * * Author: James Bonfield */ /* Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notices and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ // TODO: Store other non-aux comments; in new sam tag? #include #include #include "htslib/sam.h" #include "htslib/thread_pool.h" #include "samtools.h" #include "sam_opts.h" static int usage(FILE *fp, int exit_status) { fprintf(fp, "Usage: samtools import [options] [file.fastq ...]\n"); fprintf(fp, "\n"); fprintf(fp, "Options:\n"); fprintf(fp, " -s FILE Read paired-ended data from single FILE\n"); fprintf(fp, " -0 FILE Read single-ended data from FILE\n"); fprintf(fp, " -1 FILE Read-1 from FILE\n"); fprintf(fp, " -2 FILE Read-2 from FILE\n"); fprintf(fp, " --i1 FILE Index-1 from FILE\n"); fprintf(fp, " --i2 FILE Index-2 from FILE\n"); fprintf(fp, " -i Parse CASAVA identifier\n"); fprintf(fp, " --barcode-tag TAG\n"); fprintf(fp, " Tag to use with barcode sequences [BC]\n"); fprintf(fp, " --quality-tag TAG\n"); fprintf(fp, " Tag to use with barcode qualities [QT]\n"); fprintf(fp, " -N, --name2 Use 2nd field as read name (SRA format)\n"); fprintf(fp, " -r STRING Build up a complete @RG line\n"); fprintf(fp, " -R STRING Add a simple RG line of \"@RG\\tID:STRING\"\n"); fprintf(fp, " -T TAGLIST Parse tags in SAM format; list of '*' for all\n"); fprintf(fp, " -o FILE Output to FILE instead of samtools_stdout\n"); fprintf(fp, " -u Uncompressed output\n"); fprintf(fp, " --order TAG Store Nth record count in TAG\n"); fprintf(fp, "\n"); fprintf(fp, " --no-PG Do not add a PG line\n"); sam_global_opt_help(fp, "-.O.-@--"); fprintf(fp, "\nA single fastq file will be interpreted as -s, -0 or -1 depending on\n"); fprintf(fp, "file contents, and a pair of fastq files as \"-1 FILE1 -2 FILE2\".\n"); return exit_status; } // Order matters here as we want to read index elements before main // sequences so on reading the seqs we can emit a fully annotated record. enum fileno { FQ_I1, FQ_I2, // index seqs for R1 and R2 FQ_R0, // single file and unpaired data (singled-ended tech). FQ_R1, FQ_R2, // separate read1 and read2 files FQ_SINGLE, // single file, but with read1 and/or read2 present. FQ_END }; typedef struct { sam_global_args ga; int no_pg; char *fn[FQ_END], *fn_out; int idx_both; // add index to READ2 too, not just READ1 int casava; char *barcode_seq; char *barcode_qual; char *aux; char *rg; char *rg_line; char *order; int order_str; int compress_level; htsThreadPool p; int name2; } opts_t; // Append a sequence and quality string from a BAM record to a BC:Z and // QT:Z style aux tag string. static int append_index(kstring_t *s, kstring_t *q, bam1_t *b) { char *sp, *qp; if (ks_resize(s, s->l + b->core.l_qseq+1 +1) < 0) return -1; if (ks_resize(q, q->l + b->core.l_qseq+1 +1) < 0) return -1; sp = s->s + s->l - (s->l > 0); qp = q->s + q->l - (q->l > 0); if (s->l) *sp++ = '-'; if (q->l) *qp++ = ' '; int i; uint8_t *seq = bam_get_seq(b); uint8_t *qual = bam_get_qual(b); for (i = 0; i < b->core.l_qseq; i++) { *sp++ = seq_nt16_str[bam_seqi(seq, i)]; *qp++ = qual[i] + '!'; } *sp++ = 0; *qp++ = 0; s->l = sp - s->s; q->l = qp - q->s; return 0; } static int import_fastq(int argc, char **argv, opts_t *opts) { int i, n, ret = 0; samFile *fp_in[FQ_END] = {NULL}; bam1_t *b = bam_init1(); int ids[FQ_END]; samFile *fp_out = NULL; sam_hdr_t *hdr_out = NULL; kstring_t index_str = {0,0}; kstring_t read_str = {0,0}; char *rg = opts->rg; kstring_t rg_line = {0,0}; uint64_t read_num = 0; kstring_t idx_seq = {0}; kstring_t idx_qual = {0}; // Any additional arguments are assumed to be r1 r2, as a // short cut. We support reading index tags out of those too (eg // Illumina CASAVA format), but if we do that we lack the barcode // quality string. // // We also consider a read name ending in /1 or /2 to be a single // file containing interleaved fastq records for both ends. // These will be labeled as fn[FQ_R1] but adjusted during reading. if (argc == 1) opts->fn[FQ_SINGLE] = argv[0]; else for (i = 0; i < 2; i++) if (argc > i) opts->fn[FQ_R1+i] = argv[i]; // Open all files for (i = n = 0; i < FQ_END; i++) { if (!opts->fn[i]) continue; fp_in[i] = sam_open_format(opts->fn[i], "r", &opts->ga.in); if (!fp_in[i]) { perror(opts->fn[i]); ret = -1; goto err; } if (opts->p.pool) hts_set_thread_pool(fp_in[i], &opts->p); ids[n++] = i; if (opts->name2) hts_set_opt(fp_in[i], FASTQ_OPT_NAME2, 1); if (opts->casava) hts_set_opt(fp_in[i], FASTQ_OPT_CASAVA, 1); if (opts->barcode_seq) // for auto-CASAVA parsing hts_set_opt(fp_in[i], FASTQ_OPT_BARCODE, opts->barcode_seq); if (opts->aux) hts_set_opt(fp_in[i], FASTQ_OPT_AUX, *opts->aux == '*' || *opts->aux == '\0' ? NULL : opts->aux); switch (i) { case FQ_I1: kputs("--i1 I1.fastq ", &read_str); kputs("i*", &index_str); break; case FQ_I2: kputs("--i2 I2.fastq ", &read_str); kputs("i*", &index_str); break; case FQ_R0: kputs("-0 unpaired.fastq ", &read_str); break; case FQ_R1: kputs("-1 R1.fastq ", &read_str); break; case FQ_R2: kputs("-2 R2.fastq ", &read_str); break; case FQ_SINGLE: kputs("-N -o paired.fastq ", &read_str); break; default: ks_clear(&read_str); // not reversible kputs("", &read_str); } } if (n == 0) { bam_destroy1(b); return usage(samtools_stdout, EXIT_SUCCESS); } char out_mode[10] = {'w', 0, 0}; if (opts->compress_level != -1) out_mode[1] = '0' + opts->compress_level; sam_open_mode(out_mode+strlen(out_mode), opts->fn_out, NULL); fp_out = sam_open_format(opts->fn_out, out_mode, &opts->ga.out); if (!fp_out) { perror(opts->fn_out); goto err; } autoflush_if_stdout(fp_out, opts->fn_out); if (opts->p.pool) hts_set_thread_pool(fp_out, &opts->p); // Create header if (ks_len(&read_str)) { char CO[2100]; if (ks_len(&index_str)) snprintf(CO, sizeof(CO), "@CO\tReverse with: samtools fastq %s " "--index-format=\"%s\"\n", ks_str(&read_str), ks_str(&index_str)); else snprintf(CO, sizeof(CO), "@CO\tReverse with: samtools fastq %s\n", ks_str(&read_str)); hdr_out = sam_hdr_parse(strlen(CO), CO); } else { hdr_out = sam_hdr_init(); } // Add a version line with the sort order to the output header if (sam_hdr_add_line(hdr_out, "HD", "VN", SAM_FORMAT_VERSION, "SO", "unsorted", "GO", "query", NULL) < 0) { fprintf(samtools_stderr, "Could not set SO and GO in the header.\n"); goto err; } if (!opts->no_pg) { char *arg_list; if (!(arg_list = stringify_argv(argc+1+optind, argv-1-optind))) { print_error("view", "failed to create arg_list"); goto err; } if (sam_hdr_add_pg(hdr_out, "samtools", "VN", samtools_version(), arg_list ? "CL" : NULL, arg_list ? arg_list : NULL, NULL)) { fprintf(samtools_stderr, "Failed to add PG line to the header"); free(arg_list); goto err; } free(arg_list); } // Read group if (opts->rg_line) { if (*opts->rg_line != '@') ksprintf(&rg_line, "@RG\t%s", opts->rg_line); else kputs(opts->rg_line, &rg_line); } else if (opts->rg) { ksprintf(&rg_line, "@RG\tID:%s", opts->rg); } if (ks_len(&rg_line)) { if (sam_hdr_add_lines(hdr_out, ks_str(&rg_line), 0) < 0) goto err; rg = strstr(ks_str(&rg_line), "\tID:"); if (!rg) { fprintf(samtools_stderr, "\"-r RG-LINE\" option contained no ID field\n"); goto err; } rg += 4; i = 0; while (rg[i] != '\t' && rg[i] != '\0') i++; rg[i] = 0; } if ((ret = sam_hdr_write(fp_out, hdr_out)) < 0) goto err; // Interleave / combine from n files (ids[0..n-1]). int res = 0; int eof = 0; do { idx_seq.l = idx_qual.l = 0; for (i = 0; i < n; i++) { if ((res = sam_read1(fp_in[ids[i]], NULL, b)) < 0) { if (res == -1) { eof++; continue; } else break; } // index if (ids[i] == FQ_I1 || ids[i] == FQ_I2) { if (append_index(&idx_seq, &idx_qual, b) < 0) { res = -1; break; } continue; } // full read if (idx_seq.l) { if (opts->idx_both || ids[i] == FQ_SINGLE || ids[i] == FQ_R0 || ids[i] == FQ_R1) { if (bam_aux_append(b, opts->barcode_seq, 'Z', idx_seq.l, (uint8_t *)idx_seq.s) || bam_aux_append(b, opts->barcode_qual, 'Z', idx_qual.l, (uint8_t *)idx_qual.s)) { res = -1; break; } } } switch(ids[i]) { case FQ_R0: // unpaired; no flags to declare break; case FQ_SINGLE: // paired (but don't know if R1 or R2) or unpaired. // We rely on the /1 and /2 read suffix parsing in htslib // to distinguish the two cases, or CASAVA tags if // explicitly enabled. break; case FQ_R1: if ((b->core.flag & (BAM_FREAD1 | BAM_FREAD2)) == 0) b->core.flag |= BAM_FREAD1; b->core.flag |= BAM_FPAIRED; if (i+1 < n && ids[i+1] == FQ_R2) b->core.flag |= BAM_FMUNMAP; break; case FQ_R2: b->core.flag |= BAM_FPAIRED | BAM_FREAD2; if (i > 0 && ids[i-1] == FQ_R1) b->core.flag |= BAM_FMUNMAP; break; } if (rg) { if (bam_aux_append(b, "RG", 'Z', strlen(rg)+1, (uint8_t *)rg) < 0) { ret = -1; goto err; } } if (opts->order) { if (opts->order_str) { char buf[25]; snprintf(buf, sizeof(buf), "%0*"PRIu64, opts->order_str, read_num++); if (bam_aux_update_str(b, opts->order, strlen(buf), buf) < 0) { ret = -1; goto err; } } else { if (bam_aux_update_int(b, opts->order, read_num++) < 0) { ret = -1; goto err; } if (read_num == UINT_MAX) fprintf(samtools_stderr, "Warning: --order tag has overflowed." " Consider using TAG:LENGTH instead\n"); } } res = sam_write1(fp_out, hdr_out, b); } } while (res >= 0); if (res != -1) { print_error("import", "truncated file. Aborting"); ret = res; goto err; } if (eof != n) { print_error("import", "input files with differing number of records"); ret = -1; goto err; } // Close and return ret = 0; err: bam_destroy1(b); sam_hdr_destroy(hdr_out); ks_free(&rg_line); ks_free(&index_str); ks_free(&read_str); if (fp_out) { release_autoflush(fp_out); if (sam_close(fp_out) < 0) { perror(opts->fn_out); ret |= -1; } } for (i = 0; i < FQ_END; i++) { if (fp_in[i] && sam_close(fp_in[i]) < 0) { perror(opts->fn[i]); ret |= -1; } } ks_free(&idx_seq); ks_free(&idx_qual); return ret; } int main_import(int argc, char *argv[]) { int c; opts_t opts = { .no_pg = 0, .ga = SAM_GLOBAL_ARGS_INIT, .fn = {NULL}, .fn_out = "-", .casava = 0, .barcode_seq = "BC", .barcode_qual = "QT", .aux = NULL, .rg = NULL, .rg_line = NULL, .order = NULL, .order_str = 0, .compress_level = -1, .name2 = 0, }; kstring_t rg = {0}; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, '-', '@'), {"no-PG", no_argument, NULL, 9}, {"i1", required_argument, NULL, 1}, {"i2", required_argument, NULL, 2}, {"r1", required_argument, NULL, '1'}, {"r2", required_argument, NULL, '2'}, {"rg", required_argument, NULL, 'R'}, {"rg-line", required_argument, NULL, 'r'}, {"order", required_argument, NULL, 3}, {"barcode-tag", required_argument, NULL, 4}, {"quality-tag", required_argument, NULL, 5}, {"name2", no_argument, NULL, 'N'}, { NULL, 0, NULL, 0 } }; while ((c = getopt_long(argc, argv, "1:2:s:0:bhiT:r:R:o:O:u@:N", lopts, NULL)) >= 0) { switch (c) { case 'b': opts.idx_both = 1; break; case '0': opts.fn[FQ_R0] = optarg; break; case '1': opts.fn[FQ_R1] = optarg; break; case '2': opts.fn[FQ_R2] = optarg; break; case 1: opts.fn[FQ_I1] = optarg; break; case 2: opts.fn[FQ_I2] = optarg; break; case 's': opts.fn[FQ_SINGLE] = optarg; break; case 'o': opts.fn_out = optarg; break; case 'i': opts.casava = 1; break; case 4: opts.barcode_seq = optarg; break; case 5: opts.barcode_qual = optarg; break; case 'T': opts.aux = optarg; break; case 'u': opts.compress_level = 0; break; case 'R': opts.rg = optarg; break; case 'r': if (*optarg != '@' && ks_len(&rg) == 0) kputs("@RG", &rg); if (ks_len(&rg)) kputc_('\t', &rg); kputs(optarg, &rg); opts.rg_line = rg.s; break; case 'N': opts.name2 = 1; break; case 9: opts.no_pg = 1; break; case 3: opts.order = optarg; if (strlen(optarg) > 3 && optarg[2] == ':') opts.order_str = atoi(optarg+3); break; case 'h': return usage(samtools_stdout, EXIT_SUCCESS); case '?': return usage(samtools_stderr, EXIT_FAILURE); default: if (parse_sam_global_opt(c, optarg, lopts, &opts.ga) != 0) return usage(samtools_stderr, EXIT_FAILURE); break; } } if (opts.ga.nthreads > 0) { if (!(opts.p.pool = hts_tpool_init(opts.ga.nthreads))) { fprintf(samtools_stderr, "Failed to create thread pool\n"); if (rg.s) free(rg.s); return -1;; } } int ret = import_fastq(argc-optind, argv+optind, &opts) ? 1 : 0; if (rg.s) free(rg.s); if (opts.p.pool) hts_tpool_destroy(opts.p.pool); return ret; } pysam-0.23.0/samtools/bam_index.c000066400000000000000000000227541475062545500167070ustar00rootroot00000000000000/* bam_index.c -- index and idxstats subcommands. Copyright (C) 2008-2011, 2013-2016, 2018, 2019, 2023-2024 Genome Research Ltd. Portions copyright (C) 2010 Broad Institute. Portions copyright (C) 2013 Peter Cock, The James Hutton Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notices and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include "samtools.h" #include "sam_opts.h" #define BAM_LIDX_SHIFT 14 static void index_usage(FILE *fp) { fprintf(fp, "Usage: samtools index -M [-bc] [-m INT] ...\n" " or: samtools index [-bc] [-m INT] [out.index]\n" "Options:\n" " -b, --bai Generate BAI-format index for BAM files [default]\n" " -c, --csi Generate CSI-format index for BAM files\n" " -m, --min-shift INT Set minimum interval size for CSI indices to 2^INT [%d]\n" " -M Interpret all filename arguments as files to be indexed\n" " -o, --output FILE Write index to FILE [alternative to in args]\n" " -@, --threads INT Sets the number of threads [none]\n", BAM_LIDX_SHIFT); } // Returns 1 if the file does not exist or can be positively // identified as an index file. static int nonexistent_or_index(const char *fn) { int ret1, ret2; htsFormat fmt; hFILE *fp = hopen(fn, "r"); if (fp == NULL) return 1; ret1 = hts_detect_format2(fp, fn, &fmt); ret2 = hclose(fp); if (ret1 < 0 || ret2 < 0) return 0; return fmt.category == index_file; } int bam_index(int argc, char *argv[]) { int csi = 0; int min_shift = BAM_LIDX_SHIFT; int multiple = 0; int n_threads = 0; int n_files, c, i, ret; const char *fn_idx = NULL; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', '-', '-', '-', '-', '@'), {"output", required_argument, NULL, 'o'}, {"bai", no_argument, NULL, 'b'}, {"csi", no_argument, NULL, 'c'}, {"min-shift", required_argument, NULL, 'm'}, { NULL, 0, NULL, 0 } }; while ((c = getopt_long(argc, argv, "bcm:Mo:@:", lopts, NULL)) >= 0) switch (c) { case 'b': csi = 0; break; case 'c': csi = 1; break; case 'm': csi = 1; min_shift = atoi(optarg); break; case 'M': multiple = 1; break; case 'o': fn_idx = optarg; break; case '@': n_threads = atoi(optarg); break; default: index_usage(stderr); return 1; } n_files = argc - optind; if (n_files == 0) { index_usage(stdout); return 0; } // Handle legacy synopsis if (n_files == 2 && !fn_idx && nonexistent_or_index(argv[optind+1])) { n_files = 1; fn_idx = argv[optind+1]; } if (n_files > 1 && !multiple) { print_error("index", "use -M to enable indexing more than one alignment file"); return EXIT_FAILURE; } if (fn_idx && n_files > 1) { // TODO In future we may allow %* placeholders or similar print_error("index", "can't use -o with multiple input alignment files"); return EXIT_FAILURE; } for (i = optind; i < optind + n_files; i++) { ret = sam_index_build3(argv[i], fn_idx, csi? min_shift : 0, n_threads); if (ret < 0) { if (ret == -2) print_error_errno("index", "failed to open \"%s\"", argv[i]); else if (ret == -3) print_error("index", "\"%s\" is in a format that cannot be usefully indexed", argv[i]); else if (ret == -4 && fn_idx) print_error("index", "failed to create or write index \"%s\"", fn_idx); else if (ret == -4) print_error("index", "failed to create or write index"); else print_error_errno("index", "failed to create index for \"%s\"", argv[i]); return EXIT_FAILURE; } } return EXIT_SUCCESS; } /* * Cram indices do not contain mapped/unmapped record counts, so we have to * decode each record and count. However we can speed this up as much as * possible by using the required fields parameter. * * This prints the stats to stdout in the same manner than the BAM function * does. * * Returns 0 on success, * -1 on failure. */ int slow_idxstats(samFile *fp, sam_hdr_t *header) { int ret, last_tid = -2; bam1_t *b = bam_init1(); if (hts_set_opt(fp, CRAM_OPT_REQUIRED_FIELDS, SAM_RNAME | SAM_FLAG)) return -1; uint64_t (*count0)[2] = calloc(sam_hdr_nref(header)+1, sizeof(*count0)); uint64_t (*counts)[2] = count0+1; if (!count0) return -1; while ((ret = sam_read1(fp, header, b)) >= 0) { if (b->core.tid >= sam_hdr_nref(header) || b->core.tid < -1) { free(count0); return -1; } if (b->core.tid != last_tid) { if (last_tid >= -1) { if (counts[b->core.tid][0] + counts[b->core.tid][1]) { print_error("idxstats", "file is not position sorted"); free(count0); return -1; } } last_tid = b->core.tid; } counts[b->core.tid][(b->core.flag & BAM_FUNMAP) ? 1 : 0]++; } if (ret == -1) { int i; for (i = 0; i < sam_hdr_nref(header); i++) { printf("%s\t%"PRId64"\t%"PRIu64"\t%"PRIu64"\n", sam_hdr_tid2name(header, i), (int64_t) sam_hdr_tid2len(header, i), counts[i][0], counts[i][1]); } printf("*\t0\t%"PRIu64"\t%"PRIu64"\n", counts[-1][0], counts[-1][1]); } free(count0); bam_destroy1(b); return (ret == -1) ? 0 : -1; } static void usage_exit(FILE *fp, int exit_status) { fprintf(fp, "Usage: samtools idxstats [options] \n" " -X Include customized index file\n"); sam_global_opt_help(fp, "-.---@-."); exit(exit_status); } int bam_idxstats(int argc, char *argv[]) { hts_idx_t* idx; sam_hdr_t* header; samFile* fp; int c, has_index_file = 0, file_names = 1; char *index_name = NULL; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', '-', '@'), {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "@:X", lopts, NULL)) >= 0) { switch (c) { case 'X': has_index_file=1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage_exit(stderr, EXIT_FAILURE); } } if (has_index_file) { file_names = 2; index_name = argv[optind + 1]; } if (argc != optind + file_names) { if (argc == optind) usage_exit(stdout, EXIT_SUCCESS); else usage_exit(stderr, EXIT_FAILURE); } fp = sam_open_format(argv[optind], "r", &ga.in); if (fp == NULL) { print_error_errno("idxstats", "failed to open \"%s\"", argv[optind]); return 1; } header = sam_hdr_read(fp); if (header == NULL) { print_error("idxstats", "failed to read header for \"%s\"", argv[optind]); return 1; } if (hts_get_format(fp)->format != bam) { slow_method: if (ga.nthreads) hts_set_threads(fp, ga.nthreads); if (slow_idxstats(fp, header) < 0) { print_error("idxstats", "failed to process \"%s\"", argv[optind]); return 1; } } else { idx = sam_index_load2(fp, argv[optind], index_name); if (idx == NULL) { print_error("idxstats", "fail to load index for \"%s\", " "reverting to slow method", argv[optind]); goto slow_method; } int i; for (i = 0; i < sam_hdr_nref(header); ++i) { // Print out contig name and length printf("%s\t%"PRId64, sam_hdr_tid2name(header, i), (int64_t) sam_hdr_tid2len(header, i)); // Now fetch info about it from the meta bin uint64_t u, v; hts_idx_get_stat(idx, i, &u, &v); printf("\t%" PRIu64 "\t%" PRIu64 "\n", u, v); } // Dump information about unmapped reads printf("*\t0\t0\t%" PRIu64 "\n", hts_idx_get_n_no_coor(idx)); hts_idx_destroy(idx); } sam_hdr_destroy(header); sam_close(fp); return 0; } pysam-0.23.0/samtools/bam_index.c.pysam.c000066400000000000000000000232421475062545500202510ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_index.c -- index and idxstats subcommands. Copyright (C) 2008-2011, 2013-2016, 2018, 2019, 2023-2024 Genome Research Ltd. Portions copyright (C) 2010 Broad Institute. Portions copyright (C) 2013 Peter Cock, The James Hutton Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notices and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include "samtools.h" #include "sam_opts.h" #define BAM_LIDX_SHIFT 14 static void index_usage(FILE *fp) { fprintf(fp, "Usage: samtools index -M [-bc] [-m INT] ...\n" " or: samtools index [-bc] [-m INT] [out.index]\n" "Options:\n" " -b, --bai Generate BAI-format index for BAM files [default]\n" " -c, --csi Generate CSI-format index for BAM files\n" " -m, --min-shift INT Set minimum interval size for CSI indices to 2^INT [%d]\n" " -M Interpret all filename arguments as files to be indexed\n" " -o, --output FILE Write index to FILE [alternative to in args]\n" " -@, --threads INT Sets the number of threads [none]\n", BAM_LIDX_SHIFT); } // Returns 1 if the file does not exist or can be positively // identified as an index file. static int nonexistent_or_index(const char *fn) { int ret1, ret2; htsFormat fmt; hFILE *fp = hopen(fn, "r"); if (fp == NULL) return 1; ret1 = hts_detect_format2(fp, fn, &fmt); ret2 = hclose(fp); if (ret1 < 0 || ret2 < 0) return 0; return fmt.category == index_file; } int bam_index(int argc, char *argv[]) { int csi = 0; int min_shift = BAM_LIDX_SHIFT; int multiple = 0; int n_threads = 0; int n_files, c, i, ret; const char *fn_idx = NULL; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', '-', '-', '-', '-', '@'), {"output", required_argument, NULL, 'o'}, {"bai", no_argument, NULL, 'b'}, {"csi", no_argument, NULL, 'c'}, {"min-shift", required_argument, NULL, 'm'}, { NULL, 0, NULL, 0 } }; while ((c = getopt_long(argc, argv, "bcm:Mo:@:", lopts, NULL)) >= 0) switch (c) { case 'b': csi = 0; break; case 'c': csi = 1; break; case 'm': csi = 1; min_shift = atoi(optarg); break; case 'M': multiple = 1; break; case 'o': fn_idx = optarg; break; case '@': n_threads = atoi(optarg); break; default: index_usage(samtools_stderr); return 1; } n_files = argc - optind; if (n_files == 0) { index_usage(samtools_stdout); return 0; } // Handle legacy synopsis if (n_files == 2 && !fn_idx && nonexistent_or_index(argv[optind+1])) { n_files = 1; fn_idx = argv[optind+1]; } if (n_files > 1 && !multiple) { print_error("index", "use -M to enable indexing more than one alignment file"); return EXIT_FAILURE; } if (fn_idx && n_files > 1) { // TODO In future we may allow %* placeholders or similar print_error("index", "can't use -o with multiple input alignment files"); return EXIT_FAILURE; } for (i = optind; i < optind + n_files; i++) { ret = sam_index_build3(argv[i], fn_idx, csi? min_shift : 0, n_threads); if (ret < 0) { if (ret == -2) print_error_errno("index", "failed to open \"%s\"", argv[i]); else if (ret == -3) print_error("index", "\"%s\" is in a format that cannot be usefully indexed", argv[i]); else if (ret == -4 && fn_idx) print_error("index", "failed to create or write index \"%s\"", fn_idx); else if (ret == -4) print_error("index", "failed to create or write index"); else print_error_errno("index", "failed to create index for \"%s\"", argv[i]); return EXIT_FAILURE; } } return EXIT_SUCCESS; } /* * Cram indices do not contain mapped/unmapped record counts, so we have to * decode each record and count. However we can speed this up as much as * possible by using the required fields parameter. * * This prints the stats to samtools_stdout in the same manner than the BAM function * does. * * Returns 0 on success, * -1 on failure. */ int slow_idxstats(samFile *fp, sam_hdr_t *header) { int ret, last_tid = -2; bam1_t *b = bam_init1(); if (hts_set_opt(fp, CRAM_OPT_REQUIRED_FIELDS, SAM_RNAME | SAM_FLAG)) return -1; uint64_t (*count0)[2] = calloc(sam_hdr_nref(header)+1, sizeof(*count0)); uint64_t (*counts)[2] = count0+1; if (!count0) return -1; while ((ret = sam_read1(fp, header, b)) >= 0) { if (b->core.tid >= sam_hdr_nref(header) || b->core.tid < -1) { free(count0); return -1; } if (b->core.tid != last_tid) { if (last_tid >= -1) { if (counts[b->core.tid][0] + counts[b->core.tid][1]) { print_error("idxstats", "file is not position sorted"); free(count0); return -1; } } last_tid = b->core.tid; } counts[b->core.tid][(b->core.flag & BAM_FUNMAP) ? 1 : 0]++; } if (ret == -1) { int i; for (i = 0; i < sam_hdr_nref(header); i++) { fprintf(samtools_stdout, "%s\t%"PRId64"\t%"PRIu64"\t%"PRIu64"\n", sam_hdr_tid2name(header, i), (int64_t) sam_hdr_tid2len(header, i), counts[i][0], counts[i][1]); } fprintf(samtools_stdout, "*\t0\t%"PRIu64"\t%"PRIu64"\n", counts[-1][0], counts[-1][1]); } free(count0); bam_destroy1(b); return (ret == -1) ? 0 : -1; } static void usage_exit(FILE *fp, int exit_status) { fprintf(fp, "Usage: samtools idxstats [options] \n" " -X Include customized index file\n"); sam_global_opt_help(fp, "-.---@-."); samtools_exit(exit_status); } int bam_idxstats(int argc, char *argv[]) { hts_idx_t* idx; sam_hdr_t* header; samFile* fp; int c, has_index_file = 0, file_names = 1; char *index_name = NULL; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', '-', '@'), {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "@:X", lopts, NULL)) >= 0) { switch (c) { case 'X': has_index_file=1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage_exit(samtools_stderr, EXIT_FAILURE); } } if (has_index_file) { file_names = 2; index_name = argv[optind + 1]; } if (argc != optind + file_names) { if (argc == optind) usage_exit(samtools_stdout, EXIT_SUCCESS); else usage_exit(samtools_stderr, EXIT_FAILURE); } fp = sam_open_format(argv[optind], "r", &ga.in); if (fp == NULL) { print_error_errno("idxstats", "failed to open \"%s\"", argv[optind]); return 1; } header = sam_hdr_read(fp); if (header == NULL) { print_error("idxstats", "failed to read header for \"%s\"", argv[optind]); return 1; } if (hts_get_format(fp)->format != bam) { slow_method: if (ga.nthreads) hts_set_threads(fp, ga.nthreads); if (slow_idxstats(fp, header) < 0) { print_error("idxstats", "failed to process \"%s\"", argv[optind]); return 1; } } else { idx = sam_index_load2(fp, argv[optind], index_name); if (idx == NULL) { print_error("idxstats", "fail to load index for \"%s\", " "reverting to slow method", argv[optind]); goto slow_method; } int i; for (i = 0; i < sam_hdr_nref(header); ++i) { // Print out contig name and length fprintf(samtools_stdout, "%s\t%"PRId64, sam_hdr_tid2name(header, i), (int64_t) sam_hdr_tid2len(header, i)); // Now fetch info about it from the meta bin uint64_t u, v; hts_idx_get_stat(idx, i, &u, &v); fprintf(samtools_stdout, "\t%" PRIu64 "\t%" PRIu64 "\n", u, v); } // Dump information about unmapped reads fprintf(samtools_stdout, "*\t0\t0\t%" PRIu64 "\n", hts_idx_get_n_no_coor(idx)); hts_idx_destroy(idx); } sam_hdr_destroy(header); sam_close(fp); return 0; } pysam-0.23.0/samtools/bam_lpileup.c000066400000000000000000000154451475062545500172510ustar00rootroot00000000000000/* bam_lpileup.c -- lplbuf routines. Copyright (C) 2008, 2009, 2013 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include "bam_plbuf.h" #include "bam_lpileup.h" #include "splaysort.h" #define TV_GAP 2 typedef struct __freenode_t { uint32_t level:28, cnt:4; struct __freenode_t *next; } freenode_t, *freenode_p; #define freenode_lt(a,b) ((a)->cnt < (b)->cnt || ((a)->cnt == (b)->cnt && (a)->level < (b)->level)) SPLAYSORT_INIT(node, freenode_p, freenode_lt) /* Memory pool, similar to the one in bam_pileup.c */ typedef struct { int cnt, n, max; freenode_t **buf; } mempool_t; static mempool_t *mp_init(void) { return (mempool_t*)calloc(1, sizeof(mempool_t)); } static void mp_destroy(mempool_t *mp) { int k; for (k = 0; k < mp->n; ++k) free(mp->buf[k]); free(mp->buf); free(mp); } static inline freenode_t *mp_alloc(mempool_t *mp) { ++mp->cnt; if (mp->n == 0) return (freenode_t*)calloc(1, sizeof(freenode_t)); else return mp->buf[--mp->n]; } static inline void mp_free(mempool_t *mp, freenode_t *p) { --mp->cnt; p->next = 0; p->cnt = TV_GAP; if (mp->n == mp->max) { mp->max = mp->max? mp->max<<1 : 256; mp->buf = (freenode_t**)realloc(mp->buf, sizeof(freenode_t*) * mp->max); } mp->buf[mp->n++] = p; } /* core part */ struct __bam_lplbuf_t { int max, n_cur, n_pre; int max_level, *cur_level, *pre_level; mempool_t *mp; freenode_t **aux, *head, *tail; int n_nodes, m_aux; bam_pileup_f func; void *user_data; bam_plbuf_t *plbuf; }; void bam_lplbuf_reset(bam_lplbuf_t *buf) { freenode_t *p, *q; bam_plbuf_reset(buf->plbuf); for (p = buf->head; p->next;) { q = p->next; mp_free(buf->mp, p); p = q; } buf->head = buf->tail; buf->max_level = 0; buf->n_cur = buf->n_pre = 0; buf->n_nodes = 0; } static int tview_func(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data) { bam_lplbuf_t *tv = (bam_lplbuf_t*)data; freenode_t *p; int i, l, max_level; // allocate memory if necessary if (tv->max < n) { // enlarge tv->max = n; kroundup32(tv->max); tv->cur_level = (int*)realloc(tv->cur_level, sizeof(int) * tv->max); tv->pre_level = (int*)realloc(tv->pre_level, sizeof(int) * tv->max); } tv->n_cur = n; // update cnt for (p = tv->head; p->next; p = p->next) if (p->cnt > 0) --p->cnt; // calculate cur_level[] max_level = 0; for (i = l = 0; i < n; ++i) { const bam_pileup1_t *p = pl + i; if (p->is_head) { if (tv->head->next && tv->head->cnt == 0) { // then take a free slot freenode_t *p = tv->head->next; tv->cur_level[i] = tv->head->level; mp_free(tv->mp, tv->head); tv->head = p; --tv->n_nodes; } else tv->cur_level[i] = ++tv->max_level; } else { tv->cur_level[i] = tv->pre_level[l++]; if (p->is_tail) { // then return a free slot tv->tail->level = tv->cur_level[i]; tv->tail->next = mp_alloc(tv->mp); tv->tail = tv->tail->next; ++tv->n_nodes; } } if (tv->cur_level[i] > max_level) max_level = tv->cur_level[i]; ((bam_pileup1_t*)p)->level = tv->cur_level[i]; } assert(l == tv->n_pre); tv->func(tid, pos, n, pl, tv->user_data); // sort the linked list if (tv->n_nodes) { freenode_t *q; if (tv->n_nodes + 1 > tv->m_aux) { // enlarge tv->m_aux = tv->n_nodes + 1; kroundup32(tv->m_aux); tv->aux = (freenode_t**)realloc(tv->aux, sizeof(freenode_t*) * tv->m_aux); } for (p = tv->head, i = l = 0; p->next;) { if (p->level > max_level) { // then discard this entry q = p->next; mp_free(tv->mp, p); p = q; } else { tv->aux[i++] = p; p = p->next; } } tv->aux[i] = tv->tail; // add a proper tail for the loop below tv->n_nodes = i; if (tv->n_nodes) { splaysort(node, tv->n_nodes, tv->aux); for (i = 0; i < tv->n_nodes; ++i) tv->aux[i]->next = tv->aux[i+1]; tv->head = tv->aux[0]; } else tv->head = tv->tail; } // clean up tv->max_level = max_level; memcpy(tv->pre_level, tv->cur_level, tv->n_cur * 4); // squeeze out terminated levels for (i = l = 0; i < n; ++i) { const bam_pileup1_t *p = pl + i; if (!p->is_tail) tv->pre_level[l++] = tv->pre_level[i]; } tv->n_pre = l; /* fprintf(stderr, "%d\t", pos+1); for (i = 0; i < n; ++i) { const bam_pileup1_t *p = pl + i; if (p->is_head) fprintf(stderr, "^"); if (p->is_tail) fprintf(stderr, "$"); fprintf(stderr, "%d,", p->level); } fprintf(stderr, "\n"); */ return 0; } bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data) { bam_lplbuf_t *tv; tv = (bam_lplbuf_t*)calloc(1, sizeof(bam_lplbuf_t)); tv->mp = mp_init(); tv->head = tv->tail = mp_alloc(tv->mp); tv->func = func; tv->user_data = data; tv->plbuf = bam_plbuf_init(tview_func, tv); return (bam_lplbuf_t*)tv; } void bam_lplbuf_destroy(bam_lplbuf_t *tv) { freenode_t *p, *q; free(tv->cur_level); free(tv->pre_level); bam_plbuf_destroy(tv->plbuf); free(tv->aux); for (p = tv->head; p->next;) { q = p->next; mp_free(tv->mp, p); p = q; } mp_free(tv->mp, p); assert(tv->mp->cnt == 0); mp_destroy(tv->mp); free(tv); } int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *tv) { return bam_plbuf_push(b, tv->plbuf); } pysam-0.23.0/samtools/bam_lpileup.c.pysam.c000066400000000000000000000155571475062545500206260ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_lpileup.c -- lplbuf routines. Copyright (C) 2008, 2009, 2013 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include "bam_plbuf.h" #include "bam_lpileup.h" #include "splaysort.h" #define TV_GAP 2 typedef struct __freenode_t { uint32_t level:28, cnt:4; struct __freenode_t *next; } freenode_t, *freenode_p; #define freenode_lt(a,b) ((a)->cnt < (b)->cnt || ((a)->cnt == (b)->cnt && (a)->level < (b)->level)) SPLAYSORT_INIT(node, freenode_p, freenode_lt) /* Memory pool, similar to the one in bam_pileup.c */ typedef struct { int cnt, n, max; freenode_t **buf; } mempool_t; static mempool_t *mp_init(void) { return (mempool_t*)calloc(1, sizeof(mempool_t)); } static void mp_destroy(mempool_t *mp) { int k; for (k = 0; k < mp->n; ++k) free(mp->buf[k]); free(mp->buf); free(mp); } static inline freenode_t *mp_alloc(mempool_t *mp) { ++mp->cnt; if (mp->n == 0) return (freenode_t*)calloc(1, sizeof(freenode_t)); else return mp->buf[--mp->n]; } static inline void mp_free(mempool_t *mp, freenode_t *p) { --mp->cnt; p->next = 0; p->cnt = TV_GAP; if (mp->n == mp->max) { mp->max = mp->max? mp->max<<1 : 256; mp->buf = (freenode_t**)realloc(mp->buf, sizeof(freenode_t*) * mp->max); } mp->buf[mp->n++] = p; } /* core part */ struct __bam_lplbuf_t { int max, n_cur, n_pre; int max_level, *cur_level, *pre_level; mempool_t *mp; freenode_t **aux, *head, *tail; int n_nodes, m_aux; bam_pileup_f func; void *user_data; bam_plbuf_t *plbuf; }; void bam_lplbuf_reset(bam_lplbuf_t *buf) { freenode_t *p, *q; bam_plbuf_reset(buf->plbuf); for (p = buf->head; p->next;) { q = p->next; mp_free(buf->mp, p); p = q; } buf->head = buf->tail; buf->max_level = 0; buf->n_cur = buf->n_pre = 0; buf->n_nodes = 0; } static int tview_func(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data) { bam_lplbuf_t *tv = (bam_lplbuf_t*)data; freenode_t *p; int i, l, max_level; // allocate memory if necessary if (tv->max < n) { // enlarge tv->max = n; kroundup32(tv->max); tv->cur_level = (int*)realloc(tv->cur_level, sizeof(int) * tv->max); tv->pre_level = (int*)realloc(tv->pre_level, sizeof(int) * tv->max); } tv->n_cur = n; // update cnt for (p = tv->head; p->next; p = p->next) if (p->cnt > 0) --p->cnt; // calculate cur_level[] max_level = 0; for (i = l = 0; i < n; ++i) { const bam_pileup1_t *p = pl + i; if (p->is_head) { if (tv->head->next && tv->head->cnt == 0) { // then take a free slot freenode_t *p = tv->head->next; tv->cur_level[i] = tv->head->level; mp_free(tv->mp, tv->head); tv->head = p; --tv->n_nodes; } else tv->cur_level[i] = ++tv->max_level; } else { tv->cur_level[i] = tv->pre_level[l++]; if (p->is_tail) { // then return a free slot tv->tail->level = tv->cur_level[i]; tv->tail->next = mp_alloc(tv->mp); tv->tail = tv->tail->next; ++tv->n_nodes; } } if (tv->cur_level[i] > max_level) max_level = tv->cur_level[i]; ((bam_pileup1_t*)p)->level = tv->cur_level[i]; } assert(l == tv->n_pre); tv->func(tid, pos, n, pl, tv->user_data); // sort the linked list if (tv->n_nodes) { freenode_t *q; if (tv->n_nodes + 1 > tv->m_aux) { // enlarge tv->m_aux = tv->n_nodes + 1; kroundup32(tv->m_aux); tv->aux = (freenode_t**)realloc(tv->aux, sizeof(freenode_t*) * tv->m_aux); } for (p = tv->head, i = l = 0; p->next;) { if (p->level > max_level) { // then discard this entry q = p->next; mp_free(tv->mp, p); p = q; } else { tv->aux[i++] = p; p = p->next; } } tv->aux[i] = tv->tail; // add a proper tail for the loop below tv->n_nodes = i; if (tv->n_nodes) { splaysort(node, tv->n_nodes, tv->aux); for (i = 0; i < tv->n_nodes; ++i) tv->aux[i]->next = tv->aux[i+1]; tv->head = tv->aux[0]; } else tv->head = tv->tail; } // clean up tv->max_level = max_level; memcpy(tv->pre_level, tv->cur_level, tv->n_cur * 4); // squeeze out terminated levels for (i = l = 0; i < n; ++i) { const bam_pileup1_t *p = pl + i; if (!p->is_tail) tv->pre_level[l++] = tv->pre_level[i]; } tv->n_pre = l; /* fprintf(samtools_stderr, "%d\t", pos+1); for (i = 0; i < n; ++i) { const bam_pileup1_t *p = pl + i; if (p->is_head) fprintf(samtools_stderr, "^"); if (p->is_tail) fprintf(samtools_stderr, "$"); fprintf(samtools_stderr, "%d,", p->level); } fprintf(samtools_stderr, "\n"); */ return 0; } bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data) { bam_lplbuf_t *tv; tv = (bam_lplbuf_t*)calloc(1, sizeof(bam_lplbuf_t)); tv->mp = mp_init(); tv->head = tv->tail = mp_alloc(tv->mp); tv->func = func; tv->user_data = data; tv->plbuf = bam_plbuf_init(tview_func, tv); return (bam_lplbuf_t*)tv; } void bam_lplbuf_destroy(bam_lplbuf_t *tv) { freenode_t *p, *q; free(tv->cur_level); free(tv->pre_level); bam_plbuf_destroy(tv->plbuf); free(tv->aux); for (p = tv->head; p->next;) { q = p->next; mp_free(tv->mp, p); p = q; } mp_free(tv->mp, p); assert(tv->mp->cnt == 0); mp_destroy(tv->mp); free(tv); } int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *tv) { return bam_plbuf_push(b, tv->plbuf); } pysam-0.23.0/samtools/bam_lpileup.h000066400000000000000000000040131475062545500172430ustar00rootroot00000000000000/* bam_lpileup.h -- lplbuf routines (declarations copied from bam.h). Copyright (C) 2008, 2013 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef BAM_LPILEUP_H #define BAM_LPILEUP_H #include struct __bam_lplbuf_t; typedef struct __bam_lplbuf_t bam_lplbuf_t; #ifndef BAM_PILEUP_F_DEFINED #define BAM_PILEUP_F_DEFINED typedef int (*bam_pileup_f)(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data); #endif //BAM_PILEUP_F_DEFINED #ifdef __cplusplus extern "C" { #endif void bam_lplbuf_reset(bam_lplbuf_t *buf); /*! @abstract bam_plbuf_init() equivalent with level calculated. */ bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data); /*! @abstract bam_plbuf_destroy() equivalent with level calculated. */ void bam_lplbuf_destroy(bam_lplbuf_t *tv); /*! @abstract bam_plbuf_push() equivalent with level calculated. */ int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf); #ifdef __cplusplus } #endif #endif // BAM_LPILEUP_H pysam-0.23.0/samtools/bam_markdup.c000066400000000000000000002460351475062545500172430ustar00rootroot00000000000000/* bam_markdup.c -- Mark duplicates from a coord sorted file that has gone through fixmates with the mate scoring option on. Copyright (C) 2017-2023 Genome Research Ltd. Author: Andrew Whitwham Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE Estimate library size derived from Picard DuplicationMetrics.java Copyright (c) 2009,2018 The Broad Institute. MIT license. */ #include #include #include #include #include #include #include #include #include #include #include "htslib/thread_pool.h" #include "htslib/sam.h" #include "sam_opts.h" #include "samtools.h" #include "htslib/khash.h" #include "htslib/klist.h" #include "htslib/kstring.h" #include "tmp_file.h" #include "bam.h" typedef struct { samFile *in; samFile *out; char *prefix; int remove_dups; int32_t max_length; int do_stats; int supp; int tag; int opt_dist; int no_pg; int clear; int mode; int write_index; int include_fails; int check_chain; char *stats_file; char *arg_list; char *out_fn; regex_t *rgx; int rgx_x; int rgx_y; int rgx_t; char *barcode; regex_t *bc_rgx; int read_groups; int json; int dc; } md_param_t; typedef struct { hts_pos_t this_coord; hts_pos_t other_coord; int32_t this_ref; int32_t other_ref; int32_t barcode; int32_t read_group; int8_t single; int8_t leftmost; int8_t orientation; } key_data_t; typedef struct read_queue_s { key_data_t pair_key; key_data_t single_key; bam1_t *b; struct read_queue_s *duplicate; struct read_queue_s *original; int dc; hts_pos_t pos; int dup_checked; int read_group; } read_queue_t; typedef struct { read_queue_t *p; } in_hash_t; typedef struct { char *name; char type; int read_group; } dup_map_t; typedef struct { bam1_t *b; int64_t score; int64_t mate_score; long x; long y; int opt; int beg; int end; int len; } check_t; typedef struct { check_t *c; size_t size; size_t length; } check_list_t; typedef struct { long reading; long writing; long excluded; long duplicate; long single; long pair; long single_dup; long examined; long optical; long single_optical; long np_duplicate; long np_opt_duplicate; } stats_block_t; static khint32_t do_hash(unsigned char *key, khint32_t len); static khint_t hash_key(key_data_t key) { int i = 0; khint_t hash; if (key.single) { unsigned char sig[21]; memcpy(sig + i, &key.this_ref, 4); i += 4; memcpy(sig + i, &key.this_coord, 8); i += 8; memcpy(sig + i, &key.orientation, 1); i += 1; memcpy(sig + i, &key.barcode, 4); i += 4; memcpy(sig + i, &key.read_group, 4); i += 4; hash = do_hash(sig, i); } else { unsigned char sig[34]; memcpy(sig + i, &key.this_ref, 4); i += 4; memcpy(sig + i, &key.this_coord, 8); i += 8; memcpy(sig + i, &key.other_ref, 4); i += 4; memcpy(sig + i, &key.other_coord, 8); i += 8; memcpy(sig + i, &key.leftmost, 1); i += 1; memcpy(sig + i, &key.orientation, 1); i += 1; memcpy(sig + i, &key.barcode, 4); i += 4; memcpy(sig + i, &key.read_group, 4); i += 4; hash = do_hash(sig, i); } return hash; } static int key_equal(key_data_t a, key_data_t b) { int match = 1; if (a.this_coord != b.this_coord) match = 0; else if (a.orientation != b.orientation) match = 0; else if (a.this_ref != b.this_ref) match = 0; else if (a.single != b.single) match = 0; else if (a.barcode != b.barcode) match = 0; else if (a.read_group != b.read_group) match = 0; if (!a.single) { if (a.other_coord != b.other_coord) match = 0; else if (a.leftmost != b.leftmost) match = 0; else if (a.other_ref != b.other_ref) match = 0; } return match; } #define __free_queue_element(p) // Orientations (prime numbers to feed to hashing algorithm) #define O_FF 2 #define O_RR 3 #define O_FR 5 #define O_RF 7 // Left or rightmost #define R_LE 11 #define R_RI 13 #define BMD_WARNING_MAX 10 #define MD_MIN_QUALITY 15 // Duplicate finding mode #define MD_MODE_TEMPLATE 0 #define MD_MODE_SEQUENCE 1 KHASH_INIT(reads, key_data_t, in_hash_t, 1, hash_key, key_equal) // read map hash KLIST_INIT(read_queue, read_queue_t, __free_queue_element) // the reads buffer KHASH_MAP_INIT_STR(duplicates, dup_map_t) // map of duplicates for supplementary dup id KHASH_MAP_INIT_STR(read_groups, int) // read group lookup /* The Bob Jenkins one_at_a_time hash to reduce the key to a 32 bit value. */ static khint32_t do_hash(unsigned char *key, khint32_t len) { khint32_t hash, i; for (hash = 0, i = 0; i < len; ++i) { hash += key[i]; hash += (hash << 10); hash ^= (hash >> 6); } hash += (hash << 3); hash ^= (hash >> 11); hash += (hash << 15); return hash; } /* Get mate score from tag. */ static int64_t get_mate_score(bam1_t *b) { uint8_t *data; int64_t score; if ((data = bam_aux_get(b, "ms"))) { score = bam_aux2i(data); } else { print_error("markdup", "error, no ms score tag. Please run samtools fixmate on file first.\n"); return -1; } return score; } /* Calc current score from quality. */ static int64_t calc_score(bam1_t *b) { int64_t score = 0; uint8_t *qual = bam_get_qual(b); int i; for (i = 0; i < b->core.l_qseq; i++) { if (qual[i] >= MD_MIN_QUALITY) score += qual[i]; } return score; } /* Create a signature hash of the current read and its pair. Uses the unclipped start (or end depending on orientation), the reference id, orientation and whether the current read is leftmost of the pair. */ static int make_pair_key(md_param_t *param, key_data_t *key, bam1_t *bam, int rg_num, long *warnings) { hts_pos_t this_coord, this_end, other_coord, other_end, leftmost; int32_t this_ref, other_ref, barcode = 0; int8_t orientation, left_read; uint8_t *data; char *cig, *bar; long incoming_warnings = *warnings; this_ref = bam->core.tid + 1; // avoid a 0 being put into the hash other_ref = bam->core.mtid + 1; this_coord = unclipped_start(bam); this_end = unclipped_end(bam); if ((data = bam_aux_get(bam, "MC"))) { if (!(cig = bam_aux2Z(data))) { print_error("markdup", "error, MC tag wrong type. Please use the MC tag provided by samtools fixmate.\n"); return 1; } other_end = unclipped_other_end(bam->core.mpos, cig); other_coord = unclipped_other_start(bam->core.mpos, cig); } else { print_error("markdup", "error, no MC tag. Please run samtools fixmate on file first.\n"); return 1; } // work out orientations if (param->mode == MD_MODE_TEMPLATE) { if (this_ref != other_ref) { leftmost = this_ref < other_ref; } else { if (bam_is_rev(bam) == bam_is_mrev(bam)) { if (!bam_is_rev(bam)) { leftmost = this_coord <= other_coord; } else { leftmost = this_end <= other_end; } } else { if (bam_is_rev(bam)) { leftmost = this_end <= other_coord; } else { leftmost = this_coord <= other_end; } } } // pair orientation if (leftmost) { if (bam_is_rev(bam) == bam_is_mrev(bam)) { other_coord = other_end; if (!bam_is_rev(bam)) { if (bam->core.flag & BAM_FREAD1) { orientation = O_FF; } else { orientation = O_RR; } } else { if (bam->core.flag & BAM_FREAD1) { orientation = O_RR; } else { orientation = O_FF; } } } else { if (!bam_is_rev(bam)) { orientation = O_FR; other_coord = other_end; } else { orientation = O_RF; this_coord = this_end; } } } else { if (bam_is_rev(bam) == bam_is_mrev(bam)) { this_coord = this_end; if (!bam_is_rev(bam)) { if (bam->core.flag & BAM_FREAD1) { orientation = O_RR; } else { orientation = O_FF; } } else { if (bam->core.flag & BAM_FREAD1) { orientation = O_FF; } else { orientation = O_RR; } } } else { if (!bam_is_rev(bam)) { orientation = O_RF; other_coord = other_end; } else { orientation = O_FR; this_coord = this_end; } } } } else { // MD_MODE_SEQUENCE if (this_ref != other_ref) { leftmost = this_ref - other_ref; } else { if (bam_is_rev(bam) == bam_is_mrev(bam)) { if (!bam_is_rev(bam)) { leftmost = this_coord - other_coord; } else { leftmost = this_end - other_end; } } else { if (bam_is_rev(bam)) { leftmost = this_end - other_coord; } else { leftmost = this_coord - other_end; } } } if (leftmost < 0) { leftmost = 1; } else if (leftmost > 0) { leftmost = 0; } else { // tie breaks if (bam->core.pos == bam->core.mpos) { if (bam->core.flag & BAM_FREAD1) { leftmost = 1; } else { leftmost = 0; } } else if (bam->core.pos < bam->core.mpos) { leftmost = 1; } else { leftmost = 0; } } // pair orientation if (leftmost) { if (bam_is_rev(bam) == bam_is_mrev(bam)) { if (!bam_is_rev(bam)) { orientation = O_FF; } else { orientation = O_RR; } } else { if (!bam_is_rev(bam)) { orientation = O_FR; } else { orientation = O_RF; } } } else { if (bam_is_rev(bam) == bam_is_mrev(bam)) { if (!bam_is_rev(bam)) { orientation = O_RR; } else { orientation = O_FF; } } else { if (!bam_is_rev(bam)) { orientation = O_RF; } else { orientation = O_FR; } } } if (!bam_is_rev(bam)) { this_coord = unclipped_start(bam); } else { this_coord = unclipped_end(bam); } if (!bam_is_mrev(bam)) { other_coord = unclipped_other_start(bam->core.mpos, cig); } else { other_coord = unclipped_other_end(bam->core.mpos, cig); } } if (!leftmost) left_read = R_RI; else left_read = R_LE; if (param->barcode) { if ((data = bam_aux_get(bam, param->barcode))) { if (!(bar = bam_aux2Z(data))) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, %s tag wrong type. Aux tag needs to be a string type.\n", param->barcode); } } else { barcode = do_hash((unsigned char *)bar, strlen(bar)); } } } else if (param->bc_rgx) { int result; regmatch_t matches[3]; size_t max_matches = 2; char *qname = bam_get_qname(bam); if ((result = regexec(param->bc_rgx, qname, max_matches, matches, 0)) == 0) { int bc_start, bc_end; bc_start = matches[1].rm_so; bc_end = matches[1].rm_eo; if (bc_start != -1) { barcode = do_hash((unsigned char *)qname + bc_start, bc_end - bc_start); } else { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, barcode regex unable to match substring on %s.\n", qname); } } } else { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { char warn_msg[256]; regerror(result, param->bc_rgx, warn_msg, 256); print_error("markdup", "warning, barcode regex match error \"%s\" on %s.\n", warn_msg, qname); } } } if ((*warnings == BMD_WARNING_MAX) && (incoming_warnings != *warnings)) { print_error("markdup", "warning, %ld barcode read warnings. New warnings will not be reported.\n", *warnings); } key->single = 0; key->this_ref = this_ref; key->this_coord = this_coord; key->other_ref = other_ref; key->other_coord = other_coord; key->leftmost = left_read; key->orientation = orientation; key->barcode = barcode; key->read_group = rg_num; return 0; } /* Create a signature hash of single read (or read with an unmatched pair). Uses unclipped start (or end depending on orientation), reference id, and orientation. */ static void make_single_key(md_param_t *param, key_data_t *key, bam1_t *bam, int rg_num, long *warnings) { hts_pos_t this_coord; int32_t this_ref, barcode = 0; int8_t orientation; uint8_t *data; char *bar; long incoming_warnings = *warnings; this_ref = bam->core.tid + 1; // avoid a 0 being put into the hash if (bam_is_rev(bam)) { this_coord = unclipped_end(bam); orientation = O_RR; } else { this_coord = unclipped_start(bam); orientation = O_FF; } if (param->barcode) { if ((data = bam_aux_get(bam, param->barcode))) { if (!(bar = bam_aux2Z(data))) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, %s tag wrong type. Aux tag needs to be a string type.\n", param->barcode); } } else { barcode = do_hash((unsigned char *)bar, strlen(bar)); } } } else if (param->bc_rgx) { int result; regmatch_t matches[3]; size_t max_matches = 2; char *qname = bam_get_qname(bam); if ((result = regexec(param->bc_rgx, qname, max_matches, matches, 0)) == 0) { int bc_start, bc_end; bc_start = matches[1].rm_so; bc_end = matches[1].rm_eo; if (bc_start != -1) { barcode = do_hash((unsigned char *)qname + bc_start, bc_end - bc_start); } else { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, barcode regex unable to match substring on %s.\n", qname); } } } else { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { char warn_msg[256]; regerror(result, param->bc_rgx, warn_msg, 256); print_error("markdup", "warning, barcode regex match error \"%s\" on %s.\n", warn_msg, qname); } } } if ((*warnings == BMD_WARNING_MAX) && (incoming_warnings != *warnings)) { print_error("markdup", "warning, %ld barcode read warnings. New warnings will not be reported.\n", *warnings); } key->single = 1; key->this_ref = this_ref; key->this_coord = this_coord; key->orientation = orientation; key->barcode = barcode; key->read_group = rg_num; } /* Add the duplicate name to a hash if it does not exist. */ static int add_duplicate(khash_t(duplicates) *d_hash, bam1_t *dupe, char *orig_name, char type, int group) { khiter_t d; int ret; d = kh_get(duplicates, d_hash, bam_get_qname(dupe)); if (d == kh_end(d_hash)) { char *name = strdup(bam_get_qname(dupe)); if (name) { d = kh_put(duplicates, d_hash, name, &ret); } else { ret = -1; } if (ret >= 0) { if (orig_name) { if (ret == 0) { // replace old name free(kh_value(d_hash, d).name); free(name); } kh_value(d_hash, d).name = strdup(orig_name); if (kh_value(d_hash, d).name == NULL) { print_error("markdup", "error, unable to allocate memory for duplicate original name.\n"); return 1; } } else { kh_value(d_hash, d).name = NULL; } kh_value(d_hash, d).type = type; kh_value(d_hash, d).read_group = group; } else { print_error("markdup", "error, unable to store supplementary duplicates.\n"); free(name); return 1; } } return 0; } /* Get coordinates from the standard Illumina style read names. Returned values are of the x and y coordinates and a section of the read name to test (t) for string equality e.g. lane and tile part. */ static int get_coordinates_colons(md_param_t *param, const char *qname, int *t_beg, int *t_end, long *x_coord, long *y_coord, long *warnings) { int sep = 0; int pos = 0; int xpos = 0, ypos = 0; char *end; while (qname[pos]) { if (qname[pos] == ':') { sep++; if (sep == 2) { xpos = pos + 1; } else if (sep == 3) { ypos = pos + 1; } else if (sep == 4) { // HiSeq style names xpos = ypos; ypos = pos + 1; } else if (sep == 5) { // Newer Illumina format xpos = pos + 1; } else if (sep == 6) { ypos = pos + 1; } } pos++; } /* The most current Illumina read format at time of writing is: @machine:run:flowcell:lane:tile:x:y:UMI or @machine:run:flowcell:lane:tile:x:y Counting the separating colons gives us a quick format check. Older name formats have fewer elements. */ if (!(sep == 3 || sep == 4 || sep == 6 || sep == 7)) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, cannot decipher read name %s for optical duplicate marking.\n", qname); } return 1; } else { *x_coord = strtol(qname + xpos, &end, 10); if ((qname + xpos) == end) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, cannot decipher x coordinate in %s .\n", qname); } return 1; } *y_coord = strtol(qname + ypos, &end, 10); if ((qname + ypos) == end) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, cannot decipher y coordinate in %s .\n", qname); } return 1; } *t_beg = 0; *t_end = xpos; } return 0; } /* Get the coordinates from the read name. Returned values are of the x and y coordinates and an optional section of the read name to test (t) for string equality e.g. lane and tile part. */ static inline int get_coordinates_regex(md_param_t *param, const char *qname, int *t_beg, int *t_end, long *x_coord, long *y_coord, long *warnings) { regmatch_t matches[5]; size_t max_matches = 5; int xpos, ypos, xend, yend, xlen, ylen; char coord[255]; char *end; if (!param->rgx_t) max_matches = 4; if (regexec(param->rgx, qname, max_matches, matches, 0)) return -1; xpos = matches[param->rgx_x].rm_so; ypos = matches[param->rgx_y].rm_so; if (param->rgx_t) { *t_beg = matches[param->rgx_t].rm_so; *t_end = matches[param->rgx_t].rm_eo; } else { *t_beg = *t_end = 0; } if (xpos == -1 || ypos == -1 || *t_beg == -1) return -1; xend = matches[param->rgx_x].rm_eo; yend = matches[param->rgx_y].rm_eo; if ((xlen = xend - xpos) > 254) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, x coordinate string longer than allowed qname length in %s (%d long).\n", qname, xlen); } return 1; } strncpy(coord, qname + xpos, xlen); coord[xlen] = '\0'; *x_coord = strtol(coord, &end, 10); if (coord == end) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, cannot decipher x coordinate in %s (%s).\n", qname, coord); } return 1; } if ((ylen = yend - ypos) > 254) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, y coordinate string longer than allowed qname length in %s (%d long).\n", qname, ylen); } return 1; } strncpy(coord, qname + ypos, ylen); coord[ylen] = '\0'; *y_coord = strtol(coord, &end, 10); if (coord == end) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, cannot decipher y coordinate in %s (%s).\n", qname, coord); } return 1; } return 0; } static int get_coordinates(md_param_t *param, const char *name, int *t_beg, int *t_end, long *x_coord, long *y_coord, long *warnings) { int ret = 1; if (param->rgx == NULL) { ret = get_coordinates_colons(param, name, t_beg, t_end, x_coord, y_coord, warnings); } else { ret = get_coordinates_regex(param, name, t_beg, t_end, x_coord, y_coord, warnings); } return ret; } /* Using the coordinates from the read name, see whether the duplicated read is close enough (set by max_dist) to the original to be counted as optical.*/ static int is_optical_duplicate(md_param_t *param, bam1_t *ori, bam1_t *dup, long max_dist, long *warnings) { int ret = 0; char *original, *duplicate; long ox, oy, dx, dy; int o_beg = 0, o_end = 0, d_beg = 0, d_end = 0; original = bam_get_qname(ori); duplicate = bam_get_qname(dup); if (get_coordinates(param, original, &o_beg, &o_end, &ox, &oy, warnings)) { return ret; } if (get_coordinates(param, duplicate, &d_beg, &d_end, &dx, &dy, warnings)) { return ret; } int o_len = o_end - o_beg; int d_len = d_end - d_beg; if ((o_len == d_len) && memcmp(original + o_beg, duplicate + d_beg, o_len) == 0) { long xdiff, ydiff; if (ox > dx) { xdiff = ox - dx; } else { xdiff = dx - ox; } if (xdiff <= max_dist) { // still might be optical if (oy > dy) { ydiff = oy - dy; } else { ydiff = dy - oy; } if (ydiff <= max_dist) ret = 1; } } return ret; } /* Using the coordinates from the Illumina read name, see whether the duplicated read is close enough (set by max_dist) to the original to be counted as optical. This function needs the values from the first read to be already calculated. */ static int optical_duplicate_partial(md_param_t *param, const char *name, const int o_beg, const int o_end, const long ox, const long oy, bam1_t *dup, check_t *c, long max_dist, long *warnings) { int ret = 0; char *duplicate; int d_beg = 0, d_end = 0; long dx, dy; duplicate = bam_get_qname(dup); if (get_coordinates(param, duplicate, &d_beg, &d_end, &dx, &dy, warnings)) { return ret; } int o_len = o_end - o_beg; int d_len = d_end - d_beg; if ((o_len == d_len) && memcmp(name + o_beg, duplicate + d_beg, o_len) == 0) { // the initial parts match, look at the numbers long xdiff, ydiff; if (ox > dx) { xdiff = ox - dx; } else { xdiff = dx - ox; } if (xdiff <= max_dist) { // still might be optical if (oy > dy) { ydiff = oy - dy; } else { ydiff = dy - oy; } if (ydiff <= max_dist) ret = 1; } } c->x = dx; c->y = dy; c->beg = d_beg; c->end = d_end; c->len = d_end - d_beg; return ret; } /* Mark the read as a duplicate and update the duplicate hash (if needed) */ static int mark_duplicates(md_param_t *param, khash_t(duplicates) *dup_hash, bam1_t *ori, bam1_t *dup, int read_group, long *optical, long *warn) { char dup_type = 0; long incoming_warnings = *warn; dup->core.flag |= BAM_FDUP; if (param->tag) { if (bam_aux_update_str(dup, "do", strlen(bam_get_qname(ori)) + 1, bam_get_qname(ori))) { print_error("markdup", "error, unable to append 'do' tag.\n"); return -1; } } if (param->opt_dist) { // mark optical duplicates if (is_optical_duplicate(param, ori, dup, param->opt_dist, warn)) { bam_aux_update_str(dup, "dt", 3, "SQ"); dup_type = 'O'; (*optical)++; } else { // not an optical duplicate bam_aux_update_str(dup, "dt", 3, "LB"); } } if ((*warn == BMD_WARNING_MAX) && (incoming_warnings != *warn)) { print_error("markdup", "warning, %ld decipher read name warnings. New warnings will not be reported.\n", *warn); } if (param->supp) { if (bam_aux_get(dup, "SA") || (dup->core.flag & BAM_FMUNMAP) || bam_aux_get(dup, "XA")) { char *original = NULL; if (param->tag) { original = bam_get_qname(ori); } if (add_duplicate(dup_hash, dup, original, dup_type, read_group)) return -1; } } return 0; } /* If the duplicate type has changed to optical then retag and duplicate hash. */ static inline int optical_retag(md_param_t *param, khash_t(duplicates) *dup_hash, bam1_t *b, int paired, stats_block_t *stats) { int ret = 0; if (bam_aux_update_str(b, "dt", 3, "SQ")) { print_error("markdup", "error, unable to update 'dt' tag.\n"); ret = -1; } if (paired) { stats->optical++; } else { stats->single_optical++; } if (param->supp) { // Change the duplicate type if (bam_aux_get(b, "SA") || (b->core.flag & BAM_FMUNMAP) || bam_aux_get(b, "XA")) { khiter_t d; d = kh_get(duplicates, dup_hash, bam_get_qname(b)); if (d == kh_end(dup_hash)) { // error, name should already be in dup hash print_error("markdup", "error, duplicate name %s not found in hash.\n", bam_get_qname(b)); ret = -1; } else { kh_value(dup_hash, d).type = 'O'; } } } return ret; } /* Check all duplicates of the highest quality read (the "original") for consistancy. Also pre-calculate any values for use in check_duplicate_chain later. Returns 0 on success, >0 on coordinate reading error (program can continue) or <0 on an error (program should not continue. */ static int check_chain_against_original(md_param_t *param, khash_t(duplicates) *dup_hash, read_queue_t *ori, check_list_t *list, long *warn, stats_block_t *stats) { int ret = 0, coord_fail = 0; char *ori_name = bam_get_qname(ori->b); read_queue_t *current = ori->duplicate; int t_beg = 0, t_end = 0; long x, y; if (param->opt_dist) { coord_fail = get_coordinates(param, ori_name, &t_beg, &t_end, &x, &y, warn); } list->length = 0; while (current) { check_t *c; if (list->length >= list->size) { check_t *tmp; list->size *= 2; if (!(tmp = realloc(list->c, list->size * sizeof(check_t)))) { print_error("markdup", "error, Unable to expand optical check list.\n"); return -1; } list->c = tmp; } c = &list->c[list->length]; c->b = current->b; c->x = -1; c->y = -1; c->opt = 0; c->score = 0; c->mate_score = 0; current->dup_checked = 1; if (param->tag) { uint8_t *data; // at this stage all duplicates should have a do tag if ((data = bam_aux_get(current->b, "do")) != NULL) { // see if we need to change the tag char *old_name = bam_aux2Z(data); if (old_name) { if (strcmp(old_name, ori_name) != 0) { if (bam_aux_update_str(current->b, "do", strlen(ori_name) + 1, (const char *)ori_name)) { print_error("markdup", "error, unable to update 'do' tag.\n"); ret = -1; break; } } } else { print_error("markdup", "error, 'do' tag has wrong type for read %s.\n", bam_get_qname(current->b)); ret = -1; break; } } } if (param->opt_dist && !coord_fail) { uint8_t *data; char *dup_type; int is_opt = 0; int current_paired = (current->b->core.flag & BAM_FPAIRED) && !(current->b->core.flag & BAM_FMUNMAP); if ((data = bam_aux_get(current->b, "dt"))) { if ((dup_type = bam_aux2Z(data))) { if (strcmp(dup_type, "SQ") == 0) { c->opt = 1; } } } // need to run this to get the duplicates x and y scores is_opt = optical_duplicate_partial(param, ori_name, t_beg, t_end, x, y, current->b, c, param->opt_dist, warn); if (!c->opt && is_opt) { if (optical_retag(param, dup_hash, current->b, current_paired, stats)) { ret = -1; break; } c->opt = 1; } c->score = calc_score(current->b); if (current_paired) { if ((c->mate_score = get_mate_score(current->b)) == -1) { print_error("markdup", "error, no ms score tag. Please run samtools fixmate on file first.\n"); ret = -1; break; } } } current = current->duplicate; list->length++; } if (!ret && coord_fail) ret = coord_fail; ori->dup_checked = 1; return ret; } static int chain_sort(const void *a, const void *b) { check_t *ac = (check_t *) a; check_t *bc = (check_t *) b; int ret; if ((ret = ac->len - bc->len)) return ret; else if ((ret = memcmp(bam_get_qname(ac->b) + ac->beg, bam_get_qname(bc->b) + bc->beg, ac->len))) return ret; return (ac->x - bc->x); } /* Check all the duplicates against each other to see if they are optical duplicates. */ static int check_duplicate_chain(md_param_t *param, khash_t(duplicates) *dup_hash, check_list_t *list, long *warn, stats_block_t *stats) { int ret = 0; size_t curr = 0; qsort(list->c, list->length, sizeof(list->c[0]), chain_sort); while (curr < list->length - 1) { check_t *base = &list->c[curr]; char *base_name = bam_get_qname(base->b); int end_name_match = curr; // find the end of the matching name parts while (++end_name_match < list->length) { check_t *chk = &list->c[end_name_match]; if ((base->len == chk->len) && memcmp(base_name + base->beg, bam_get_qname(chk->b) + chk->beg, base->len) != 0) break; } while (curr < end_name_match) { size_t count = curr; check_t *current = &list->c[curr]; int current_paired = (current->b->core.flag & BAM_FPAIRED) && !(current->b->core.flag & BAM_FMUNMAP); while (++count < end_name_match && (list->c[count].x - current->x <= param->opt_dist)) { // while close enough along the x coordinate check_t *chk = &list->c[count]; if (current->opt && chk->opt) continue; long ydiff; if (current->y > chk->y) { ydiff = current->y - chk->y; } else { ydiff = chk->y - current->y; } if (ydiff > param->opt_dist) continue; // optical duplicates int chk_dup = 0; int chk_paired = (chk->b->core.flag & BAM_FPAIRED) && !(chk->b->core.flag & BAM_FMUNMAP); if (current_paired != chk_paired) { if (!chk_paired) { // chk is single vs pair, this is a dup. chk_dup = 1; } } else { // do it by scores int64_t cur_score, chk_score; if ((current->b->core.flag & BAM_FQCFAIL) != (chk->b->core.flag & BAM_FQCFAIL)) { if (current->b->core.flag & BAM_FQCFAIL) { cur_score = 0; chk_score = 1; } else { cur_score = 1; chk_score = 0; } } else { cur_score = current->score; chk_score = chk->score; if (current_paired) { // they are pairs so add mate scores. chk_score += chk->mate_score; cur_score += current->mate_score; } } if (cur_score == chk_score) { if (strcmp(bam_get_qname(chk->b), bam_get_qname(current->b)) < 0) { chk_score++; } else { chk_score--; } } if (cur_score > chk_score) { chk_dup = 1; } } if (chk_dup) { // the duplicate is the optical duplicate if (!chk->opt) { // only change if not already an optical duplicate if (optical_retag(param, dup_hash, chk->b, chk_paired, stats)) { ret = -1; goto fail; } chk->opt = 1; } } else { if (!current->opt) { if (optical_retag(param, dup_hash, current->b, current_paired, stats)) { ret = -1; goto fail; } current->opt = 1; } } } curr++; } } fail: return ret; } /* Where there is more than one duplicate go down the list and check for optical duplicates and change do tags (where used) to point to original (non-duplicate) read. */ static int find_duplicate_chains(md_param_t *param, read_queue_t *in_read , khash_t(duplicates) *dup_hash, check_list_t *dup_list, long *warn, stats_block_t *stats) { int ret = 0; while (in_read->original) in_read = in_read->original; // check against the original for tagging and optical duplication if ((ret = check_chain_against_original(param, dup_hash, in_read, dup_list, warn, stats + in_read->read_group))) { if (ret < 0) { // real error ret = -1; } else { // coordinate decoding error ret = 0; } } else { // check the rest of the duplicates against each other for optical duplication if (param->opt_dist && check_duplicate_chain(param, dup_hash, dup_list, warn, stats + in_read->read_group)) { ret = -1; } } return ret; } /* Function to use when estimating library size. This is based on an approximate formula for the coverage of a set obtained after sampling it a given number of times with replacement. x = number of items in the set (the number of unique fragments in the library) c = number of unique items (unique read pairs observed) n = number of items samples (total number of read pairs) c and n are known; x is unknown. As n -> infinity, the coverage (c/x) can be given as: c / x = 1 - exp(-n / x) (see https://math.stackexchange.com/questions/32800) This needs to be solved for x, so it is rearranged to put both terms on the left side and estimate_library_size() finds a value of x which gives a result of zero (or as close as it can get). */ static inline double coverage_equation(double x, double c, double n) { return c / x - 1 + exp(-n / x); } /* estimate the library size, based on the Picard code in DuplicationMetrics.java*/ static unsigned long estimate_library_size(unsigned long paired_reads, unsigned long paired_duplicate_reads, unsigned long optical) { unsigned long estimated_size = 0; unsigned long non_optical_pairs = (paired_reads - optical) / 2; unsigned long unique_pairs = (paired_reads - paired_duplicate_reads) / 2; unsigned long duplicate_pairs = (paired_duplicate_reads - optical) / 2; if ((non_optical_pairs && duplicate_pairs && unique_pairs) && (non_optical_pairs > duplicate_pairs)) { double m = 1; double M = 100; int i; if (coverage_equation(m * (double)unique_pairs, (double)unique_pairs, (double)non_optical_pairs) < 0) { print_error("markdup", "warning, unable to calculate estimated library size.\n"); return estimated_size; } while (coverage_equation(M * (double)unique_pairs, (double)unique_pairs, (double)non_optical_pairs) > 0) { M *= 10; } for (i = 0; i < 40; i++) { double r = (m + M) / 2; double u = coverage_equation(r * (double)unique_pairs, (double)unique_pairs, (double)non_optical_pairs); if (u > 0) { m = r; } else if (u < 0) { M = r; } else { break; } } estimated_size = (unsigned long)(unique_pairs * (m + M) / 2); } else { print_error("markdup", "warning, unable to calculate estimated library size." " Read pairs %ld should be greater than duplicate pairs %ld," " which should both be non zero.\n", non_optical_pairs, duplicate_pairs); } return estimated_size; } static void write_stats(FILE *fp, const char *title, const char *title_con, stats_block_t *stats) { unsigned long els; els = estimate_library_size(stats->pair, stats->duplicate, stats->optical); if (title) { fprintf(fp, "%s%s\n", title, title_con); } fprintf(fp, "READ: %ld\n" "WRITTEN: %ld\n" "EXCLUDED: %ld\n" "EXAMINED: %ld\n" "PAIRED: %ld\n" "SINGLE: %ld\n" "DUPLICATE PAIR: %ld\n" "DUPLICATE SINGLE: %ld\n" "DUPLICATE PAIR OPTICAL: %ld\n" "DUPLICATE SINGLE OPTICAL: %ld\n" "DUPLICATE NON PRIMARY: %ld\n" "DUPLICATE NON PRIMARY OPTICAL: %ld\n" "DUPLICATE PRIMARY TOTAL: %ld\n" "DUPLICATE TOTAL: %ld\n" "ESTIMATED_LIBRARY_SIZE: %ld\n", stats->reading, stats->writing, stats->excluded, stats->examined, stats->pair, stats->single, stats->duplicate, stats->single_dup, stats->optical, stats->single_optical, stats->np_duplicate, stats->np_opt_duplicate, stats->single_dup + stats->duplicate, stats->single_dup + stats->duplicate + stats->np_duplicate, els); } static void write_json_stats(FILE *fp, const char *offset, const char *group_name, stats_block_t *stats, const char *end) { unsigned long els; els = estimate_library_size(stats->pair, stats->duplicate, stats->optical); if (group_name) { fprintf(fp, "%s\"READ GROUP\": \"%s\",\n", offset, group_name); } fprintf(fp, "%s\"READ\": %ld,\n", offset, stats->reading); fprintf(fp, "%s\"WRITTEN\": %ld,\n", offset, stats->writing); fprintf(fp, "%s\"EXCLUDED\": %ld,\n", offset, stats->excluded); fprintf(fp, "%s\"EXAMINED\": %ld,\n", offset, stats->examined); fprintf(fp, "%s\"PAIRED\": %ld,\n", offset, stats->pair); fprintf(fp, "%s\"SINGLE\": %ld,\n", offset, stats->single); fprintf(fp, "%s\"DUPLICATE PAIR\": %ld,\n", offset, stats->duplicate); fprintf(fp, "%s\"DUPLICATE SINGLE\": %ld,\n", offset, stats->single_dup); fprintf(fp, "%s\"DUPLICATE PAIR OPTICAL\": %ld,\n", offset, stats->optical); fprintf(fp, "%s\"DUPLICATE SINGLE OPTICAL\": %ld,\n", offset, stats->single_optical); fprintf(fp, "%s\"DUPLICATE NON PRIMARY\": %ld,\n", offset, stats->np_duplicate); fprintf(fp, "%s\"DUPLICATE NON PRIMARY OPTICAL\": %ld,\n", offset, stats->np_opt_duplicate); fprintf(fp, "%s\"DUPLICATE PRIMARY TOTAL\": %ld,\n", offset, stats->single_dup + stats->duplicate); fprintf(fp, "%s\"DUPLICATE TOTAL\": %ld,\n", offset, stats->single_dup + stats->duplicate + stats->np_duplicate); fprintf(fp, "%s\"ESTIMATED_LIBRARY_SIZE\": %ld", offset, els); if (end) { fprintf(fp, "%s", end); } } /* Compare the reads near each other (coordinate sorted) and try to spot the duplicates. Generally the highest quality scoring is chosen as the original and all others the duplicates. The score is based on the sum of the quality values (<= 15) of the read and its mate (if any). While single reads are compared to only one read of a pair, the pair will chosen as the original. The comparison is done on position and orientation, see above for details. Marking the supplementary reads of a duplicate as also duplicates takes an extra file read/write step. This is because the duplicate can occur before the primary read.*/ static int bam_mark_duplicates(md_param_t *param) { bam_hdr_t *header = NULL; khiter_t k; khash_t(reads) *pair_hash = kh_init(reads); khash_t(reads) *single_hash = kh_init(reads); klist_t(read_queue) *read_buffer = kl_init(read_queue); kliter_t(read_queue) *rq; khash_t(duplicates) *dup_hash = kh_init(duplicates); khash_t(read_groups) *rg_hash = kh_init(read_groups); int32_t prev_tid; hts_pos_t prev_coord; read_queue_t *in_read; int ret; stats_block_t *stats, *stat_array = NULL; int num_groups = 0; long opt_warnings = 0, bc_warnings = 0; tmp_file_t temp; char *idx_fn = NULL; int exclude = 0; check_list_t dup_list = {NULL, 0, 0}; if (!pair_hash || !single_hash || !read_buffer || !dup_hash || !rg_hash) { print_error("markdup", "error, unable to allocate memory to initialise structures.\n"); goto fail; } if ((header = sam_hdr_read(param->in)) == NULL) { print_error("markdup", "error reading header\n"); goto fail; } // accept unknown, unsorted or coordinate sort order, but error on queryname sorted. // only really works on coordinate sorted files. kstring_t str = KS_INITIALIZE; if (!sam_hdr_find_tag_hd(header, "SO", &str) && str.s && !strcmp(str.s, "queryname")) { print_error("markdup", "error, queryname sorted, must be sorted by coordinate.\n"); ks_free(&str); goto fail; } ks_free(&str); if (!param->no_pg && sam_hdr_add_pg(header, "samtools", "VN", samtools_version(), param->arg_list ? "CL" : NULL, param->arg_list ? param->arg_list : NULL, NULL) != 0) { print_error("markdup", "warning, unable to add @PG line to header.\n"); } if (sam_hdr_write(param->out, header) < 0) { print_error("markdup", "error writing header.\n"); goto fail; } if (param->write_index) { if (!(idx_fn = auto_index(param->out, param->out_fn, header))) goto fail; } if (param->read_groups) { num_groups = sam_hdr_count_lines(header, "RG"); int g_ret = 0; if (num_groups > 0) { int i; for (i = 0; i < num_groups; i++) { const char *rg_key; khiter_t rg; rg_key = sam_hdr_line_name(header, "RG", i); if (rg_key) { rg = kh_get(read_groups, rg_hash, rg_key); if (rg == kh_end(rg_hash)) { // new entry rg = kh_put(read_groups, rg_hash, rg_key, &g_ret); if (g_ret > 0) { kh_value(rg_hash, rg) = i + 1; } else { print_error("markdup", "error, unable to populate read group ids. " "Read groups will not be used\n"); g_ret = -1; break; } } else { print_error("markdup", "error, duplicate read group ids %s." "Read groups will not be used\n", rg_key); g_ret = -1; break; } } else { print_error("markdup", "error, Unable to retrieve read group at position %d." "Read groups will not be used\n", i); g_ret = -1; break; } } } else { print_error("markdup", "error, no read groups found.\n"); g_ret = -1; } if (g_ret < 0) { print_error("markdup", "error, read groups will not be used.\n"); param->read_groups = 0; num_groups = 0; } } // stat_array[0] will be for ungrouped reads stat_array = calloc(num_groups + 1, sizeof(stats_block_t)); if (stat_array == NULL) { print_error("markdup", "error, unable to allocate memory for stats.\n"); goto fail; } // used for coordinate order checks prev_tid = prev_coord = 0; // get the buffer going in_read = kl_pushp(read_queue, read_buffer); if (!in_read) { print_error("markdup", "error, unable to allocate memory to hold reads.\n"); goto fail; } // handling supplementary reads needs a temporary file if (param->supp) { if (tmp_file_open_write(&temp, param->prefix, 1)) { print_error("markdup", "error, unable to open tmp file %s.\n", param->prefix); goto fail; } } if ((in_read->b = bam_init1()) == NULL) { print_error("markdup", "error, unable to allocate memory for alignment.\n"); goto fail; } if (param->check_chain && !(param->tag || param->opt_dist)) param->check_chain = 0; if (param->check_chain) { dup_list.size = 128; dup_list.c = NULL; if ((dup_list.c = malloc(dup_list.size * sizeof(check_t))) == NULL) { print_error("markdup", "error, unable to allocate memory for dup_list.\n"); goto fail; } } while ((ret = sam_read1(param->in, header, in_read->b)) >= 0) { // do some basic coordinate order checks if (in_read->b->core.tid >= 0) { // -1 for unmapped reads if (in_read->b->core.tid < prev_tid || ((in_read->b->core.tid == prev_tid) && (in_read->b->core.pos < prev_coord))) { print_error("markdup", "error, not in coordinate sorted order.\n"); goto fail; } } prev_coord = in_read->pos = in_read->b->core.pos; prev_tid = in_read->b->core.tid; in_read->pair_key.single = 1; in_read->single_key.single = 0; in_read->duplicate = NULL; in_read->original = NULL; in_read->dup_checked = 0; in_read->read_group = 0; in_read->dc = 1; if (param->read_groups) { uint8_t *data; char *rg; if ((data = bam_aux_get(in_read->b, "RG"))) { if ((rg = bam_aux2Z(data))) { khiter_t r; r = kh_get(read_groups, rg_hash, rg); if (r != kh_end(rg_hash)) { in_read->read_group = kh_value(rg_hash, r); } } } } stats = stat_array + in_read->read_group; stats->reading++; if (param->clear && (in_read->b->core.flag & BAM_FDUP)) { uint8_t *data; in_read->b->core.flag ^= BAM_FDUP; if ((data = bam_aux_get(in_read->b, "dt")) != NULL) { bam_aux_del(in_read->b, data); } if ((data = bam_aux_get(in_read->b, "do")) != NULL) { bam_aux_del(in_read->b, data); } } if (param->include_fails) { exclude |= (BAM_FSECONDARY | BAM_FSUPPLEMENTARY | BAM_FUNMAP); } else { exclude |= (BAM_FSECONDARY | BAM_FSUPPLEMENTARY | BAM_FUNMAP | BAM_FQCFAIL); } // read must not be secondary, supplementary, unmapped or (possibly) failed QC if (!(in_read->b->core.flag & exclude)) { stats->examined++; // look at the pairs first if ((in_read->b->core.flag & BAM_FPAIRED) && !(in_read->b->core.flag & BAM_FMUNMAP)) { int ret, mate_tmp; key_data_t pair_key; key_data_t single_key; in_hash_t *bp; if (make_pair_key(param, &pair_key, in_read->b, in_read->read_group, &bc_warnings)) { print_error("markdup", "error, unable to assign pair hash key.\n"); goto fail; } make_single_key(param, &single_key, in_read->b, in_read->read_group, &bc_warnings); stats->pair++; in_read->pos = single_key.this_coord; // cigar/orientation modified pos // put in singles hash for checking against non paired reads k = kh_put(reads, single_hash, single_key, &ret); if (ret > 0) { // new // add to single duplicate hash bp = &kh_val(single_hash, k); bp->p = in_read; in_read->single_key = single_key; } else if (ret == 0) { // exists // look at singles only for duplication marking bp = &kh_val(single_hash, k); if (!(bp->p->b->core.flag & BAM_FPAIRED) || (bp->p->b->core.flag & BAM_FMUNMAP)) { // singleton will always be marked duplicate even if // scores more than one read of the pair bam1_t *dup = bp->p->b; if (param->check_chain) { in_read->duplicate = bp->p; bp->p->original = in_read; } bp->p = in_read; bp->p->dc += 1; if (mark_duplicates(param, dup_hash, bp->p->b, dup, in_read->read_group, &stats->single_optical, &opt_warnings)) goto fail; stats->single_dup++; } } else { print_error("markdup", "error, single hashing failure for paired read.\n"); goto fail; } // now do the pair k = kh_put(reads, pair_hash, pair_key, &ret); if (ret > 0) { // new // add to the pair hash bp = &kh_val(pair_hash, k); bp->p = in_read; in_read->pair_key = pair_key; } else if (ret == 0) { int64_t old_score, new_score, tie_add = 0; bam1_t *dup = NULL; bp = &kh_val(pair_hash, k); if ((bp->p->b->core.flag & BAM_FQCFAIL) != (in_read->b->core.flag & BAM_FQCFAIL)) { if (bp->p->b->core.flag & BAM_FQCFAIL) { old_score = 0; new_score = 1; } else { old_score = 1; new_score = 0; } } else { if ((mate_tmp = get_mate_score(bp->p->b)) == -1) { print_error("markdup", "error, no ms score tag. Please run samtools fixmate on file first.\n"); goto fail; } else { old_score = calc_score(bp->p->b) + mate_tmp; } if ((mate_tmp = get_mate_score(in_read->b)) == -1) { print_error("markdup", "error, no ms score tag. Please run samtools fixmate on file first.\n"); goto fail; } else { new_score = calc_score(in_read->b) + mate_tmp; } } // choose the highest score as the original // and add it to the pair hash, mark the other as duplicate if (new_score == old_score) { if (strcmp(bam_get_qname(in_read->b), bam_get_qname(bp->p->b)) < 0) { tie_add = 1; } else { tie_add = -1; } } if (new_score + tie_add > old_score) { // swap reads dup = bp->p->b; in_read->dc += bp->p->dc; if (param->check_chain) { if (in_read->duplicate) { read_queue_t *current = in_read->duplicate; while (current->duplicate) { current = current->duplicate; } current->duplicate = bp->p; } else { in_read->duplicate = bp->p; } bp->p->original = in_read; } bp->p = in_read; } else { if (param->check_chain) { if (bp->p->duplicate) { if (in_read->duplicate) { read_queue_t *current = bp->p->duplicate; while (current->duplicate) { current = current->duplicate; } current->duplicate = in_read->duplicate; } in_read->duplicate = bp->p->duplicate; } bp->p->duplicate = in_read; in_read->original = bp->p; } dup = in_read->b; bp->p->dc += 1; } if (mark_duplicates(param, dup_hash, bp->p->b, dup, in_read->read_group, &stats->optical, &opt_warnings)) goto fail; stats->duplicate++; } else { print_error("markdup", "error, pair hashing failure.\n"); goto fail; } } else { // do the single (or effectively single) reads int ret; key_data_t single_key; in_hash_t *bp; make_single_key(param, &single_key, in_read->b, in_read->read_group, &bc_warnings); stats->single++; in_read->pos = single_key.this_coord; // cigar/orientation modified pos k = kh_put(reads, single_hash, single_key, &ret); if (ret > 0) { // new bp = &kh_val(single_hash, k); bp->p = in_read; in_read->single_key = single_key; } else if (ret == 0) { // exists bp = &kh_val(single_hash, k); if ((bp->p->b->core.flag & BAM_FPAIRED) && !(bp->p->b->core.flag & BAM_FMUNMAP)) { // if matched against one of a pair just mark as duplicate if (param->check_chain) { if (bp->p->duplicate) { in_read->duplicate = bp->p->duplicate; } bp->p->duplicate = in_read; in_read->original = bp->p; } bp->p->dc += 1; if (mark_duplicates(param, dup_hash, bp->p->b, in_read->b, in_read->read_group, &stats->single_optical, &opt_warnings)) goto fail; } else { int64_t old_score, new_score; bam1_t *dup = NULL; old_score = calc_score(bp->p->b); new_score = calc_score(in_read->b); // choose the highest score as the original, add it // to the single hash and mark the other as duplicate if (new_score > old_score) { // swap reads dup = bp->p->b; in_read->dc += bp->p->dc; if (param->check_chain) { in_read->duplicate = bp->p; bp->p->original = in_read; } bp->p = in_read; } else { if (param->check_chain) { if (bp->p->duplicate) { in_read->duplicate = bp->p->duplicate; } bp->p->duplicate = in_read; in_read->original = bp->p; } bp->p->dc += 1; dup = in_read->b; } if (mark_duplicates(param, dup_hash, bp->p->b, dup, in_read->read_group, &stats->single_optical, &opt_warnings)) goto fail; } stats->single_dup++; } else { print_error("markdup", "error, single hashing failure for single read.\n"); goto fail; } } } else { stats->excluded++; } // loop through the stored reads and write out those we // no longer need rq = kl_begin(read_buffer); while (rq != kl_end(read_buffer)) { in_read = &kl_val(rq); /* keep a moving window of reads based on coordinates and max read length. Any unaligned reads should just be written as they cannot be matched as duplicates. */ if (in_read->pos + param->max_length > prev_coord && in_read->b->core.tid == prev_tid && (prev_tid != -1 || prev_coord != -1)) { break; } if (param->check_chain && !in_read->dup_checked && (in_read->original || in_read->duplicate)) { if (find_duplicate_chains(param, in_read, dup_hash, &dup_list, &opt_warnings, stat_array)) { print_error("markdup", "error, duplicate checking failed.\n"); goto fail; } } if (!param->remove_dups || !(in_read->b->core.flag & BAM_FDUP)) { if (param->dc && !(in_read->b->core.flag & BAM_FDUP)) { bam_aux_update_int(in_read->b, "dc", in_read->dc); } if (param->supp) { if (tmp_file_write(&temp, in_read->b)) { print_error("markdup", "error, writing temp output failed.\n"); goto fail; } } else { if (sam_write1(param->out, header, in_read->b) < 0) { print_error("markdup", "error, writing output failed.\n"); goto fail; } } stat_array[in_read->read_group].writing++; } // remove from hash if (in_read->pair_key.single == 0) { k = kh_get(reads, pair_hash, in_read->pair_key); kh_del(reads, pair_hash, k); } if (in_read->single_key.single == 1) { k = kh_get(reads, single_hash, in_read->single_key); kh_del(reads, single_hash, k); } kl_shift(read_queue, read_buffer, NULL); bam_destroy1(in_read->b); rq = kl_begin(read_buffer); } // set the next one up for reading in_read = kl_pushp(read_queue, read_buffer); if (!in_read) { print_error("markdup", "error, unable to allocate memory for read in queue.\n"); goto fail; } if ((in_read->b = bam_init1()) == NULL) { print_error("markdup", "error, unable to allocate memory for alignment.\n"); goto fail; } } if (ret < -1) { print_error("markdup", "error, truncated input file.\n"); goto fail; } // write out the end of the list rq = kl_begin(read_buffer); while (rq != kl_end(read_buffer)) { in_read = &kl_val(rq); if (bam_get_qname(in_read->b)) { // last entry will be blank if (param->check_chain && !in_read->dup_checked && (in_read->original || in_read->duplicate)) { if (find_duplicate_chains(param, in_read, dup_hash, &dup_list, &opt_warnings, stat_array)) { print_error("markdup", "error, duplicate checking failed.\n"); goto fail; } } if (!param->remove_dups || !(in_read->b->core.flag & BAM_FDUP)) { if (param->dc && !(in_read->b->core.flag & BAM_FDUP)) { bam_aux_update_int(in_read->b, "dc", in_read->dc); } if (param->supp) { if (tmp_file_write(&temp, in_read->b)) { print_error("markdup", "error, writing temp output failed on final write.\n"); goto fail; } } else { if (param->dc && !(in_read->b->core.flag & BAM_FDUP)) { bam_aux_update_int(in_read->b, "dc", in_read->dc); } if (sam_write1(param->out, header, in_read->b) < 0) { print_error("markdup", "error, writing output failed on final write.\n"); goto fail; } } stat_array[in_read->read_group].writing++; } } kl_shift(read_queue, read_buffer, NULL); bam_destroy1(in_read->b); rq = kl_begin(read_buffer); } if (param->supp) { bam1_t *b; if (tmp_file_end_write(&temp)) { print_error("markdup", "error, unable to end tmp writing.\n"); goto fail; } // read data from temp file and mark duplicate supplementary alignments if (tmp_file_begin_read(&temp)) { goto fail; } b = bam_init1(); while ((ret = tmp_file_read(&temp, b)) > 0) { if ((b->core.flag & BAM_FSUPPLEMENTARY) || (b->core.flag & BAM_FUNMAP) || (b->core.flag & BAM_FSECONDARY)) { k = kh_get(duplicates, dup_hash, bam_get_qname(b)); if (k != kh_end(dup_hash)) { b->core.flag |= BAM_FDUP; stat_array[kh_val(dup_hash, k).read_group].np_duplicate++; if (param->tag && kh_val(dup_hash, k).name) { if (bam_aux_update_str(b, "do", strlen(kh_val(dup_hash, k).name) + 1, (char*)kh_val(dup_hash, k).name)) { print_error("markdup", "error, unable to append supplementary 'do' tag.\n"); goto fail; } } if (param->opt_dist) { if (kh_val(dup_hash, k).type) { bam_aux_update_str(b, "dt", 3, "SQ"); stat_array[kh_val(dup_hash, k).read_group].np_opt_duplicate++; } else { bam_aux_update_str(b, "dt", 3, "LB"); } } } } if (!param->remove_dups || !(b->core.flag & BAM_FDUP)) { if (param->dc && (b->core.flag & BAM_FDUP)) { uint8_t* data = bam_aux_get(b, "dc"); if(data) bam_aux_del(b, data); } if (sam_write1(param->out, header, b) < 0) { print_error("markdup", "error, writing final output failed.\n"); goto fail; } } } if (ret == -1) { print_error("markdup", "error, failed to read tmp file.\n"); goto fail; } for (k = kh_begin(dup_hash); k != kh_end(dup_hash); ++k) { if (kh_exist(dup_hash, k)) { free(kh_val(dup_hash, k).name); free((char *)kh_key(dup_hash, k)); kh_key(dup_hash, k) = NULL; } } tmp_file_destroy(&temp); bam_destroy1(b); } if (opt_warnings) { print_error("markdup", "warning, number of failed attempts to get coordinates from read names = %ld\n", opt_warnings); } if (bc_warnings) { print_error("markdup", "warning, number of failed attempts to get barcodes = %ld\n", bc_warnings); } if (param->do_stats) { FILE *fp; int file_open = 0; stats_block_t total; int i; if (param->stats_file) { if (NULL == (fp = fopen(param->stats_file, "w"))) { print_error("markdup", "warning, cannot write stats to %s.\n", param->stats_file); fp = stderr; } else { file_open = 1; } } else { fp = stderr; } total = stat_array[0]; if (param->read_groups) { for (i = 1; i <= num_groups; i++) { total.reading += stat_array[i].reading; total.writing += stat_array[i].writing; total.excluded += stat_array[i].excluded; total.duplicate += stat_array[i].duplicate; total.single += stat_array[i].single; total.pair += stat_array[i].pair; total.single_dup += stat_array[i].single_dup; total.examined += stat_array[i].examined; total.optical += stat_array[i].optical; total.single_optical += stat_array[i].single_optical; total.np_duplicate += stat_array[i].np_duplicate; total.np_opt_duplicate += stat_array[i].np_opt_duplicate; } } if (!param->json) { write_stats(fp, "COMMAND: ", param->arg_list, &total); fprintf(fp, "\n"); if (param->read_groups) { if (stat_array[0].reading) { write_stats(fp, "READ GROUP: ", "ungrouped", stat_array); fprintf(fp, "\n"); } for (i = 0; i < num_groups; i++) { write_stats(fp, "READ GROUP: ", sam_hdr_line_name(header, "RG", i), stat_array + i + 1); fprintf(fp, "\n"); } } } else { char space4[] = " "; char space8[] = " "; char space12[] = " "; fprintf(fp, "{\n"); fprintf(fp, "%s\"COMMAND\": \"%s\",\n", space4, param->arg_list); write_json_stats(fp, space4, NULL, &total, param->read_groups ? ",\n" : "\n"); if (param->read_groups) { fprintf(fp, "%s\"READ GROUPS\": [\n", space4); if (stat_array[0].reading) { fprintf(fp, "%s{\n", space8); write_json_stats(fp, space12, "ungrouped", stat_array, "\n"); fprintf(fp, "%s},\n", space8); } for (i = 0; i < num_groups; i++) { fprintf(fp, "%s{\n", space8); write_json_stats(fp, space12, sam_hdr_line_name(header, "RG", i), stat_array + i + 1, "\n"); if (i < num_groups -1 ) { fprintf(fp, "%s},\n", space8); } else { fprintf(fp, "%s}\n", space8); } } fprintf(fp, "%s]\n", space4); } fprintf(fp, "}\n"); } if (file_open) { fclose(fp); } } if (param->write_index) { if (sam_idx_save(param->out) < 0) { print_error_errno("markdup", "error, writing index failed"); goto fail; } } if (param->check_chain && (param->tag || param->opt_dist)) free(dup_list.c); free(idx_fn); free(stat_array); kh_destroy(reads, pair_hash); kh_destroy(reads, single_hash); kl_destroy(read_queue, read_buffer); kh_destroy(duplicates, dup_hash); kh_destroy(read_groups, rg_hash); sam_hdr_destroy(header); return 0; fail: for (rq = kl_begin(read_buffer); rq != kl_end(read_buffer); rq = kl_next(rq)) bam_destroy1(kl_val(rq).b); kl_destroy(read_queue, read_buffer); for (k = kh_begin(dup_hash); k != kh_end(dup_hash); ++k) { if (kh_exist(dup_hash, k)) { free((char *)kh_key(dup_hash, k)); } } kh_destroy(duplicates, dup_hash); kh_destroy(read_groups, rg_hash); if (param->check_chain && (param->tag || param->opt_dist)) free(dup_list.c); free(idx_fn); free(stat_array); kh_destroy(reads, pair_hash); kh_destroy(reads, single_hash); sam_hdr_destroy(header); return 1; } static int markdup_usage(void) { fprintf(stderr, "\n"); fprintf(stderr, "Usage: samtools markdup \n\n"); fprintf(stderr, "Option: \n"); fprintf(stderr, " -r Remove duplicate reads\n"); fprintf(stderr, " -l INT Max read length (default 300 bases)\n"); fprintf(stderr, " -S Mark supplementary alignments of duplicates as duplicates (slower).\n"); fprintf(stderr, " -s Report stats.\n"); fprintf(stderr, " -f NAME Write stats to named file. Implies -s.\n"); fprintf(stderr, " --json Output stats in JSON. Also implies -s\n"); fprintf(stderr, " -T PREFIX Write temporary files to PREFIX.samtools.nnnn.nnnn.tmp.\n"); fprintf(stderr, " -d INT Optical distance (if set, marks with dt tag)\n"); fprintf(stderr, " -c Clear previous duplicate settings and tags.\n"); fprintf(stderr, " -m --mode TYPE Duplicate decision method for paired reads.\n" " TYPE = t measure positions based on template start/end (default).\n" " s measure positions based on sequence start.\n"); fprintf(stderr, " -u Output uncompressed data\n"); fprintf(stderr, " --include-fails Include quality check failed reads.\n"); fprintf(stderr, " --no-PG Do not add a PG line\n"); fprintf(stderr, " --no-multi-dup Reduced duplicates of duplicates checking.\n"); fprintf(stderr, " --read-coords STR Regex for coords from read name.\n"); fprintf(stderr, " --coords-order STR Order of regex elements. txy (default). With t being a part of\n" " the read names that must be equal and x/y being coordinates.\n"); fprintf(stderr, " --barcode-tag STR Use barcode a tag that duplicates much match.\n"); fprintf(stderr, " --barcode-name Use the UMI/barcode in the read name (eigth colon delimited part).\n"); fprintf(stderr, " --barcode-rgx STR Regex for barcode in the readname (alternative to --barcode-name).\n"); fprintf(stderr, " --use-read-groups Use the read group tags in duplicate matching.\n"); fprintf(stderr, " -t Mark primary duplicates with the name of the original in a \'do\' tag." " Mainly for information and debugging.\n"); fprintf(stderr, " --duplicate-count Record the original primary read duplication count(include itself) in a \'dc\' tag.\n"); sam_global_opt_help(stderr, "-.O..@.."); fprintf(stderr, "\nThe input file must be coordinate sorted and must have gone" " through fixmates with the mate scoring option on.\n"); return 1; } int bam_markdup(int argc, char **argv) { int c, ret, bc_name = 0; char wmode[4] = {'w', 0, 0, 0}; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; htsThreadPool p = {NULL, 0}; kstring_t tmpprefix = {0, 0, NULL}; struct stat st; unsigned int t; char *regex = NULL, *bc_regex = NULL; char *regex_order = "txy"; md_param_t param = {NULL, NULL, NULL, 0, 300, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, 0, 0}; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'), {"include-fails", no_argument, NULL, 1001}, {"no-PG", no_argument, NULL, 1002}, {"mode", required_argument, NULL, 'm'}, {"no-multi-dup", no_argument, NULL, 1003}, {"read-coords", required_argument, NULL, 1004}, {"coords-order", required_argument, NULL, 1005}, {"barcode-tag", required_argument, NULL, 1006}, {"barcode-name", no_argument, NULL, 1007}, {"barcode-rgx", required_argument, NULL, 1008}, {"use-read-groups", no_argument, NULL, 1009}, {"json", no_argument, NULL, 1010}, {"duplicate-count", no_argument, NULL, 1011}, {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "rsl:StT:O:@:f:d:cm:u", lopts, NULL)) >= 0) { switch (c) { case 'r': param.remove_dups = 1; break; case 'l': param.max_length = atoi(optarg); break; case 's': param.do_stats = 1; break; case 'T': kputs(optarg, &tmpprefix); break; case 'S': param.supp = 1; break; case 't': param.tag = 1; break; case 'f': param.stats_file = optarg; param.do_stats = 1; break; case 'd': param.opt_dist = atoi(optarg); break; case 'c': param.clear = 1; break; case 'm': if (strcmp(optarg, "t") == 0) { param.mode = MD_MODE_TEMPLATE; } else if (strcmp(optarg, "s") == 0) { param.mode = MD_MODE_SEQUENCE; } else { print_error("markdup", "error, unknown mode '%s'.\n", optarg); return markdup_usage(); } break; case 'u': wmode[1] = '0'; break; case 1001: param.include_fails = 1; break; case 1002: param.no_pg = 1; break; case 1003: param.check_chain = 0; break; case 1004: regex = optarg; break; case 1005: regex_order = optarg; break; case 1006: param.barcode = optarg; break; case 1007: bc_name = 1; break; case 1008: bc_name = 1, bc_regex = optarg; break; case 1009: param.read_groups = 1; break; case 1010: param.json = 1; param.do_stats = 1; break; case 1011: param.dc = 1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': return markdup_usage(); } } if (optind + 2 > argc) return markdup_usage(); if (param.barcode && bc_name) { print_error("markdup", "error, cannot specify --barcode-tag and " "--barcode-name (or --barcode-rgx) at same time.\n"); return 1; } if (param.opt_dist < 0) param.opt_dist = 0; if (param.max_length < 0) param.max_length = 300; if (regex) { int result; // set the order the elements of the regex are assigned to. // x and y being coordinates, t being any other important part of the read // e.g. tile and lane // x and y order does not matter as long as it is consistent if ((strncmp(regex_order, "txy", 3) == 0) || (strncmp(regex_order, "tyx", 3) == 0)) { param.rgx_t = 1; param.rgx_x = 2; param.rgx_y = 3; } else if ((strncmp(regex_order, "xyt", 3) == 0) || (strncmp(regex_order, "yxt", 3) == 0)) { param.rgx_x = 1; param.rgx_y = 2; param.rgx_t = 3; } else if ((strncmp(regex_order, "xty", 3) == 0) || (strncmp(regex_order, "ytx", 3) == 0)) { param.rgx_x = 1; param.rgx_t = 2; param.rgx_y = 3; } else if ((strncmp(regex_order, "xy", 2) == 0) || (strncmp(regex_order, "yx", 2) == 0)) { param.rgx_x = 1; param.rgx_y = 2; param.rgx_t = 0; } else { print_error("markdup", "error, could not recognise regex coordinate order \"%s\".\n", regex_order); return 1; } if ((param.rgx = malloc(sizeof(regex_t))) == NULL) { print_error("markdup", "error, could not allocate memory for regex.\n"); return 1; } if ((result = regcomp(param.rgx, regex, REG_EXTENDED))) { char err_msg[256]; regerror(result, param.rgx, err_msg, 256); print_error("markdup", "error, regex fail \"%s\"\n", err_msg); free(param.rgx); return 1; } } if (bc_name) { int result; /* From Illumina UMI documentation: "The UMI sequence is located in the eighth colon-delimited field of the read name (QNAME)". */ char *rgx = "[0-9A-Za-z]+:[0-9A-Za-z]+:[0-9A-Za-z]+:[0-9A-Za-z]+:[0-9A-Za-z]+:[0-9A-Za-z]+:[0-9A-Za-z]+:([!-?A-~]+)"; if ((param.bc_rgx = malloc(sizeof(regex_t))) == NULL) { print_error("markdup", "error, could not allocate memory for barcode regex.\n"); return 1; } if (bc_regex) { rgx = bc_regex; } if ((result = regcomp(param.bc_rgx, rgx, REG_EXTENDED))) { char err_msg[256]; regerror(result, param.bc_rgx, err_msg, 256); print_error("markdup", "error, barcode regex fail \"%s\"\n", err_msg); free(param.bc_rgx); return 1; } } param.in = sam_open_format(argv[optind], "r", &ga.in); if (!param.in) { print_error_errno("markdup", "error, failed to open \"%s\" for input", argv[optind]); return 1; } strcat(wmode, "b"); // default if unknown suffix sam_open_mode(wmode + strlen(wmode)-1, argv[optind + 1], NULL); param.out = sam_open_format(argv[optind + 1], wmode, &ga.out); if (!param.out) { print_error_errno("markdup", "error, failed to open \"%s\" for output", argv[optind + 1]); return 1; } if (ga.nthreads > 0) { if (!(p.pool = hts_tpool_init(ga.nthreads))) { print_error("markdup", "error creating thread pool.\n"); return 1; } hts_set_opt(param.in, HTS_OPT_THREAD_POOL, &p); hts_set_opt(param.out, HTS_OPT_THREAD_POOL, &p); } // actual stuff happens here // we need temp files so fix up the name here if (tmpprefix.l == 0) { if (strcmp(argv[optind + 1], "-") != 0) ksprintf(&tmpprefix, "%s.", argv[optind + 1]); else kputc('.', &tmpprefix); } if (stat(tmpprefix.s, &st) == 0 && S_ISDIR(st.st_mode)) { if (tmpprefix.s[tmpprefix.l-1] != '/') kputc('/', &tmpprefix); } t = ((unsigned) time(NULL)) ^ ((unsigned) clock()); ksprintf(&tmpprefix, "samtools.%d.%u.tmp", (int) getpid(), t % 10000); param.prefix = tmpprefix.s; param.arg_list = stringify_argv(argc + 1, argv - 1); param.write_index = ga.write_index; param.out_fn = argv[optind + 1]; ret = bam_mark_duplicates(¶m); sam_close(param.in); if (sam_close(param.out) < 0) { print_error("markdup", "error closing output file.\n"); ret = 1; } if (p.pool) hts_tpool_destroy(p.pool); if (param.rgx) { regfree(param.rgx); free(param.rgx); } if (param.bc_rgx) { regfree(param.bc_rgx); free(param.bc_rgx); } free(param.arg_list); free(tmpprefix.s); sam_global_args_free(&ga); return ret; } pysam-0.23.0/samtools/bam_markdup.c.pysam.c000066400000000000000000002464771475062545500206260ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_markdup.c -- Mark duplicates from a coord sorted file that has gone through fixmates with the mate scoring option on. Copyright (C) 2017-2023 Genome Research Ltd. Author: Andrew Whitwham Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE Estimate library size derived from Picard DuplicationMetrics.java Copyright (c) 2009,2018 The Broad Institute. MIT license. */ #include #include #include #include #include #include #include #include #include #include #include "htslib/thread_pool.h" #include "htslib/sam.h" #include "sam_opts.h" #include "samtools.h" #include "htslib/khash.h" #include "htslib/klist.h" #include "htslib/kstring.h" #include "tmp_file.h" #include "bam.h" typedef struct { samFile *in; samFile *out; char *prefix; int remove_dups; int32_t max_length; int do_stats; int supp; int tag; int opt_dist; int no_pg; int clear; int mode; int write_index; int include_fails; int check_chain; char *stats_file; char *arg_list; char *out_fn; regex_t *rgx; int rgx_x; int rgx_y; int rgx_t; char *barcode; regex_t *bc_rgx; int read_groups; int json; int dc; } md_param_t; typedef struct { hts_pos_t this_coord; hts_pos_t other_coord; int32_t this_ref; int32_t other_ref; int32_t barcode; int32_t read_group; int8_t single; int8_t leftmost; int8_t orientation; } key_data_t; typedef struct read_queue_s { key_data_t pair_key; key_data_t single_key; bam1_t *b; struct read_queue_s *duplicate; struct read_queue_s *original; int dc; hts_pos_t pos; int dup_checked; int read_group; } read_queue_t; typedef struct { read_queue_t *p; } in_hash_t; typedef struct { char *name; char type; int read_group; } dup_map_t; typedef struct { bam1_t *b; int64_t score; int64_t mate_score; long x; long y; int opt; int beg; int end; int len; } check_t; typedef struct { check_t *c; size_t size; size_t length; } check_list_t; typedef struct { long reading; long writing; long excluded; long duplicate; long single; long pair; long single_dup; long examined; long optical; long single_optical; long np_duplicate; long np_opt_duplicate; } stats_block_t; static khint32_t do_hash(unsigned char *key, khint32_t len); static khint_t hash_key(key_data_t key) { int i = 0; khint_t hash; if (key.single) { unsigned char sig[21]; memcpy(sig + i, &key.this_ref, 4); i += 4; memcpy(sig + i, &key.this_coord, 8); i += 8; memcpy(sig + i, &key.orientation, 1); i += 1; memcpy(sig + i, &key.barcode, 4); i += 4; memcpy(sig + i, &key.read_group, 4); i += 4; hash = do_hash(sig, i); } else { unsigned char sig[34]; memcpy(sig + i, &key.this_ref, 4); i += 4; memcpy(sig + i, &key.this_coord, 8); i += 8; memcpy(sig + i, &key.other_ref, 4); i += 4; memcpy(sig + i, &key.other_coord, 8); i += 8; memcpy(sig + i, &key.leftmost, 1); i += 1; memcpy(sig + i, &key.orientation, 1); i += 1; memcpy(sig + i, &key.barcode, 4); i += 4; memcpy(sig + i, &key.read_group, 4); i += 4; hash = do_hash(sig, i); } return hash; } static int key_equal(key_data_t a, key_data_t b) { int match = 1; if (a.this_coord != b.this_coord) match = 0; else if (a.orientation != b.orientation) match = 0; else if (a.this_ref != b.this_ref) match = 0; else if (a.single != b.single) match = 0; else if (a.barcode != b.barcode) match = 0; else if (a.read_group != b.read_group) match = 0; if (!a.single) { if (a.other_coord != b.other_coord) match = 0; else if (a.leftmost != b.leftmost) match = 0; else if (a.other_ref != b.other_ref) match = 0; } return match; } #define __free_queue_element(p) // Orientations (prime numbers to feed to hashing algorithm) #define O_FF 2 #define O_RR 3 #define O_FR 5 #define O_RF 7 // Left or rightmost #define R_LE 11 #define R_RI 13 #define BMD_WARNING_MAX 10 #define MD_MIN_QUALITY 15 // Duplicate finding mode #define MD_MODE_TEMPLATE 0 #define MD_MODE_SEQUENCE 1 KHASH_INIT(reads, key_data_t, in_hash_t, 1, hash_key, key_equal) // read map hash KLIST_INIT(read_queue, read_queue_t, __free_queue_element) // the reads buffer KHASH_MAP_INIT_STR(duplicates, dup_map_t) // map of duplicates for supplementary dup id KHASH_MAP_INIT_STR(read_groups, int) // read group lookup /* The Bob Jenkins one_at_a_time hash to reduce the key to a 32 bit value. */ static khint32_t do_hash(unsigned char *key, khint32_t len) { khint32_t hash, i; for (hash = 0, i = 0; i < len; ++i) { hash += key[i]; hash += (hash << 10); hash ^= (hash >> 6); } hash += (hash << 3); hash ^= (hash >> 11); hash += (hash << 15); return hash; } /* Get mate score from tag. */ static int64_t get_mate_score(bam1_t *b) { uint8_t *data; int64_t score; if ((data = bam_aux_get(b, "ms"))) { score = bam_aux2i(data); } else { print_error("markdup", "error, no ms score tag. Please run samtools fixmate on file first.\n"); return -1; } return score; } /* Calc current score from quality. */ static int64_t calc_score(bam1_t *b) { int64_t score = 0; uint8_t *qual = bam_get_qual(b); int i; for (i = 0; i < b->core.l_qseq; i++) { if (qual[i] >= MD_MIN_QUALITY) score += qual[i]; } return score; } /* Create a signature hash of the current read and its pair. Uses the unclipped start (or end depending on orientation), the reference id, orientation and whether the current read is leftmost of the pair. */ static int make_pair_key(md_param_t *param, key_data_t *key, bam1_t *bam, int rg_num, long *warnings) { hts_pos_t this_coord, this_end, other_coord, other_end, leftmost; int32_t this_ref, other_ref, barcode = 0; int8_t orientation, left_read; uint8_t *data; char *cig, *bar; long incoming_warnings = *warnings; this_ref = bam->core.tid + 1; // avoid a 0 being put into the hash other_ref = bam->core.mtid + 1; this_coord = unclipped_start(bam); this_end = unclipped_end(bam); if ((data = bam_aux_get(bam, "MC"))) { if (!(cig = bam_aux2Z(data))) { print_error("markdup", "error, MC tag wrong type. Please use the MC tag provided by samtools fixmate.\n"); return 1; } other_end = unclipped_other_end(bam->core.mpos, cig); other_coord = unclipped_other_start(bam->core.mpos, cig); } else { print_error("markdup", "error, no MC tag. Please run samtools fixmate on file first.\n"); return 1; } // work out orientations if (param->mode == MD_MODE_TEMPLATE) { if (this_ref != other_ref) { leftmost = this_ref < other_ref; } else { if (bam_is_rev(bam) == bam_is_mrev(bam)) { if (!bam_is_rev(bam)) { leftmost = this_coord <= other_coord; } else { leftmost = this_end <= other_end; } } else { if (bam_is_rev(bam)) { leftmost = this_end <= other_coord; } else { leftmost = this_coord <= other_end; } } } // pair orientation if (leftmost) { if (bam_is_rev(bam) == bam_is_mrev(bam)) { other_coord = other_end; if (!bam_is_rev(bam)) { if (bam->core.flag & BAM_FREAD1) { orientation = O_FF; } else { orientation = O_RR; } } else { if (bam->core.flag & BAM_FREAD1) { orientation = O_RR; } else { orientation = O_FF; } } } else { if (!bam_is_rev(bam)) { orientation = O_FR; other_coord = other_end; } else { orientation = O_RF; this_coord = this_end; } } } else { if (bam_is_rev(bam) == bam_is_mrev(bam)) { this_coord = this_end; if (!bam_is_rev(bam)) { if (bam->core.flag & BAM_FREAD1) { orientation = O_RR; } else { orientation = O_FF; } } else { if (bam->core.flag & BAM_FREAD1) { orientation = O_FF; } else { orientation = O_RR; } } } else { if (!bam_is_rev(bam)) { orientation = O_RF; other_coord = other_end; } else { orientation = O_FR; this_coord = this_end; } } } } else { // MD_MODE_SEQUENCE if (this_ref != other_ref) { leftmost = this_ref - other_ref; } else { if (bam_is_rev(bam) == bam_is_mrev(bam)) { if (!bam_is_rev(bam)) { leftmost = this_coord - other_coord; } else { leftmost = this_end - other_end; } } else { if (bam_is_rev(bam)) { leftmost = this_end - other_coord; } else { leftmost = this_coord - other_end; } } } if (leftmost < 0) { leftmost = 1; } else if (leftmost > 0) { leftmost = 0; } else { // tie breaks if (bam->core.pos == bam->core.mpos) { if (bam->core.flag & BAM_FREAD1) { leftmost = 1; } else { leftmost = 0; } } else if (bam->core.pos < bam->core.mpos) { leftmost = 1; } else { leftmost = 0; } } // pair orientation if (leftmost) { if (bam_is_rev(bam) == bam_is_mrev(bam)) { if (!bam_is_rev(bam)) { orientation = O_FF; } else { orientation = O_RR; } } else { if (!bam_is_rev(bam)) { orientation = O_FR; } else { orientation = O_RF; } } } else { if (bam_is_rev(bam) == bam_is_mrev(bam)) { if (!bam_is_rev(bam)) { orientation = O_RR; } else { orientation = O_FF; } } else { if (!bam_is_rev(bam)) { orientation = O_RF; } else { orientation = O_FR; } } } if (!bam_is_rev(bam)) { this_coord = unclipped_start(bam); } else { this_coord = unclipped_end(bam); } if (!bam_is_mrev(bam)) { other_coord = unclipped_other_start(bam->core.mpos, cig); } else { other_coord = unclipped_other_end(bam->core.mpos, cig); } } if (!leftmost) left_read = R_RI; else left_read = R_LE; if (param->barcode) { if ((data = bam_aux_get(bam, param->barcode))) { if (!(bar = bam_aux2Z(data))) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, %s tag wrong type. Aux tag needs to be a string type.\n", param->barcode); } } else { barcode = do_hash((unsigned char *)bar, strlen(bar)); } } } else if (param->bc_rgx) { int result; regmatch_t matches[3]; size_t max_matches = 2; char *qname = bam_get_qname(bam); if ((result = regexec(param->bc_rgx, qname, max_matches, matches, 0)) == 0) { int bc_start, bc_end; bc_start = matches[1].rm_so; bc_end = matches[1].rm_eo; if (bc_start != -1) { barcode = do_hash((unsigned char *)qname + bc_start, bc_end - bc_start); } else { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, barcode regex unable to match substring on %s.\n", qname); } } } else { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { char warn_msg[256]; regerror(result, param->bc_rgx, warn_msg, 256); print_error("markdup", "warning, barcode regex match error \"%s\" on %s.\n", warn_msg, qname); } } } if ((*warnings == BMD_WARNING_MAX) && (incoming_warnings != *warnings)) { print_error("markdup", "warning, %ld barcode read warnings. New warnings will not be reported.\n", *warnings); } key->single = 0; key->this_ref = this_ref; key->this_coord = this_coord; key->other_ref = other_ref; key->other_coord = other_coord; key->leftmost = left_read; key->orientation = orientation; key->barcode = barcode; key->read_group = rg_num; return 0; } /* Create a signature hash of single read (or read with an unmatched pair). Uses unclipped start (or end depending on orientation), reference id, and orientation. */ static void make_single_key(md_param_t *param, key_data_t *key, bam1_t *bam, int rg_num, long *warnings) { hts_pos_t this_coord; int32_t this_ref, barcode = 0; int8_t orientation; uint8_t *data; char *bar; long incoming_warnings = *warnings; this_ref = bam->core.tid + 1; // avoid a 0 being put into the hash if (bam_is_rev(bam)) { this_coord = unclipped_end(bam); orientation = O_RR; } else { this_coord = unclipped_start(bam); orientation = O_FF; } if (param->barcode) { if ((data = bam_aux_get(bam, param->barcode))) { if (!(bar = bam_aux2Z(data))) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, %s tag wrong type. Aux tag needs to be a string type.\n", param->barcode); } } else { barcode = do_hash((unsigned char *)bar, strlen(bar)); } } } else if (param->bc_rgx) { int result; regmatch_t matches[3]; size_t max_matches = 2; char *qname = bam_get_qname(bam); if ((result = regexec(param->bc_rgx, qname, max_matches, matches, 0)) == 0) { int bc_start, bc_end; bc_start = matches[1].rm_so; bc_end = matches[1].rm_eo; if (bc_start != -1) { barcode = do_hash((unsigned char *)qname + bc_start, bc_end - bc_start); } else { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, barcode regex unable to match substring on %s.\n", qname); } } } else { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { char warn_msg[256]; regerror(result, param->bc_rgx, warn_msg, 256); print_error("markdup", "warning, barcode regex match error \"%s\" on %s.\n", warn_msg, qname); } } } if ((*warnings == BMD_WARNING_MAX) && (incoming_warnings != *warnings)) { print_error("markdup", "warning, %ld barcode read warnings. New warnings will not be reported.\n", *warnings); } key->single = 1; key->this_ref = this_ref; key->this_coord = this_coord; key->orientation = orientation; key->barcode = barcode; key->read_group = rg_num; } /* Add the duplicate name to a hash if it does not exist. */ static int add_duplicate(khash_t(duplicates) *d_hash, bam1_t *dupe, char *orig_name, char type, int group) { khiter_t d; int ret; d = kh_get(duplicates, d_hash, bam_get_qname(dupe)); if (d == kh_end(d_hash)) { char *name = strdup(bam_get_qname(dupe)); if (name) { d = kh_put(duplicates, d_hash, name, &ret); } else { ret = -1; } if (ret >= 0) { if (orig_name) { if (ret == 0) { // replace old name free(kh_value(d_hash, d).name); free(name); } kh_value(d_hash, d).name = strdup(orig_name); if (kh_value(d_hash, d).name == NULL) { print_error("markdup", "error, unable to allocate memory for duplicate original name.\n"); return 1; } } else { kh_value(d_hash, d).name = NULL; } kh_value(d_hash, d).type = type; kh_value(d_hash, d).read_group = group; } else { print_error("markdup", "error, unable to store supplementary duplicates.\n"); free(name); return 1; } } return 0; } /* Get coordinates from the standard Illumina style read names. Returned values are of the x and y coordinates and a section of the read name to test (t) for string equality e.g. lane and tile part. */ static int get_coordinates_colons(md_param_t *param, const char *qname, int *t_beg, int *t_end, long *x_coord, long *y_coord, long *warnings) { int sep = 0; int pos = 0; int xpos = 0, ypos = 0; char *end; while (qname[pos]) { if (qname[pos] == ':') { sep++; if (sep == 2) { xpos = pos + 1; } else if (sep == 3) { ypos = pos + 1; } else if (sep == 4) { // HiSeq style names xpos = ypos; ypos = pos + 1; } else if (sep == 5) { // Newer Illumina format xpos = pos + 1; } else if (sep == 6) { ypos = pos + 1; } } pos++; } /* The most current Illumina read format at time of writing is: @machine:run:flowcell:lane:tile:x:y:UMI or @machine:run:flowcell:lane:tile:x:y Counting the separating colons gives us a quick format check. Older name formats have fewer elements. */ if (!(sep == 3 || sep == 4 || sep == 6 || sep == 7)) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, cannot decipher read name %s for optical duplicate marking.\n", qname); } return 1; } else { *x_coord = strtol(qname + xpos, &end, 10); if ((qname + xpos) == end) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, cannot decipher x coordinate in %s .\n", qname); } return 1; } *y_coord = strtol(qname + ypos, &end, 10); if ((qname + ypos) == end) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, cannot decipher y coordinate in %s .\n", qname); } return 1; } *t_beg = 0; *t_end = xpos; } return 0; } /* Get the coordinates from the read name. Returned values are of the x and y coordinates and an optional section of the read name to test (t) for string equality e.g. lane and tile part. */ static inline int get_coordinates_regex(md_param_t *param, const char *qname, int *t_beg, int *t_end, long *x_coord, long *y_coord, long *warnings) { regmatch_t matches[5]; size_t max_matches = 5; int xpos, ypos, xend, yend, xlen, ylen; char coord[255]; char *end; if (!param->rgx_t) max_matches = 4; if (regexec(param->rgx, qname, max_matches, matches, 0)) return -1; xpos = matches[param->rgx_x].rm_so; ypos = matches[param->rgx_y].rm_so; if (param->rgx_t) { *t_beg = matches[param->rgx_t].rm_so; *t_end = matches[param->rgx_t].rm_eo; } else { *t_beg = *t_end = 0; } if (xpos == -1 || ypos == -1 || *t_beg == -1) return -1; xend = matches[param->rgx_x].rm_eo; yend = matches[param->rgx_y].rm_eo; if ((xlen = xend - xpos) > 254) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, x coordinate string longer than allowed qname length in %s (%d long).\n", qname, xlen); } return 1; } strncpy(coord, qname + xpos, xlen); coord[xlen] = '\0'; *x_coord = strtol(coord, &end, 10); if (coord == end) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, cannot decipher x coordinate in %s (%s).\n", qname, coord); } return 1; } if ((ylen = yend - ypos) > 254) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, y coordinate string longer than allowed qname length in %s (%d long).\n", qname, ylen); } return 1; } strncpy(coord, qname + ypos, ylen); coord[ylen] = '\0'; *y_coord = strtol(coord, &end, 10); if (coord == end) { (*warnings)++; if (*warnings <= BMD_WARNING_MAX) { print_error("markdup", "warning, cannot decipher y coordinate in %s (%s).\n", qname, coord); } return 1; } return 0; } static int get_coordinates(md_param_t *param, const char *name, int *t_beg, int *t_end, long *x_coord, long *y_coord, long *warnings) { int ret = 1; if (param->rgx == NULL) { ret = get_coordinates_colons(param, name, t_beg, t_end, x_coord, y_coord, warnings); } else { ret = get_coordinates_regex(param, name, t_beg, t_end, x_coord, y_coord, warnings); } return ret; } /* Using the coordinates from the read name, see whether the duplicated read is close enough (set by max_dist) to the original to be counted as optical.*/ static int is_optical_duplicate(md_param_t *param, bam1_t *ori, bam1_t *dup, long max_dist, long *warnings) { int ret = 0; char *original, *duplicate; long ox, oy, dx, dy; int o_beg = 0, o_end = 0, d_beg = 0, d_end = 0; original = bam_get_qname(ori); duplicate = bam_get_qname(dup); if (get_coordinates(param, original, &o_beg, &o_end, &ox, &oy, warnings)) { return ret; } if (get_coordinates(param, duplicate, &d_beg, &d_end, &dx, &dy, warnings)) { return ret; } int o_len = o_end - o_beg; int d_len = d_end - d_beg; if ((o_len == d_len) && memcmp(original + o_beg, duplicate + d_beg, o_len) == 0) { long xdiff, ydiff; if (ox > dx) { xdiff = ox - dx; } else { xdiff = dx - ox; } if (xdiff <= max_dist) { // still might be optical if (oy > dy) { ydiff = oy - dy; } else { ydiff = dy - oy; } if (ydiff <= max_dist) ret = 1; } } return ret; } /* Using the coordinates from the Illumina read name, see whether the duplicated read is close enough (set by max_dist) to the original to be counted as optical. This function needs the values from the first read to be already calculated. */ static int optical_duplicate_partial(md_param_t *param, const char *name, const int o_beg, const int o_end, const long ox, const long oy, bam1_t *dup, check_t *c, long max_dist, long *warnings) { int ret = 0; char *duplicate; int d_beg = 0, d_end = 0; long dx, dy; duplicate = bam_get_qname(dup); if (get_coordinates(param, duplicate, &d_beg, &d_end, &dx, &dy, warnings)) { return ret; } int o_len = o_end - o_beg; int d_len = d_end - d_beg; if ((o_len == d_len) && memcmp(name + o_beg, duplicate + d_beg, o_len) == 0) { // the initial parts match, look at the numbers long xdiff, ydiff; if (ox > dx) { xdiff = ox - dx; } else { xdiff = dx - ox; } if (xdiff <= max_dist) { // still might be optical if (oy > dy) { ydiff = oy - dy; } else { ydiff = dy - oy; } if (ydiff <= max_dist) ret = 1; } } c->x = dx; c->y = dy; c->beg = d_beg; c->end = d_end; c->len = d_end - d_beg; return ret; } /* Mark the read as a duplicate and update the duplicate hash (if needed) */ static int mark_duplicates(md_param_t *param, khash_t(duplicates) *dup_hash, bam1_t *ori, bam1_t *dup, int read_group, long *optical, long *warn) { char dup_type = 0; long incoming_warnings = *warn; dup->core.flag |= BAM_FDUP; if (param->tag) { if (bam_aux_update_str(dup, "do", strlen(bam_get_qname(ori)) + 1, bam_get_qname(ori))) { print_error("markdup", "error, unable to append 'do' tag.\n"); return -1; } } if (param->opt_dist) { // mark optical duplicates if (is_optical_duplicate(param, ori, dup, param->opt_dist, warn)) { bam_aux_update_str(dup, "dt", 3, "SQ"); dup_type = 'O'; (*optical)++; } else { // not an optical duplicate bam_aux_update_str(dup, "dt", 3, "LB"); } } if ((*warn == BMD_WARNING_MAX) && (incoming_warnings != *warn)) { print_error("markdup", "warning, %ld decipher read name warnings. New warnings will not be reported.\n", *warn); } if (param->supp) { if (bam_aux_get(dup, "SA") || (dup->core.flag & BAM_FMUNMAP) || bam_aux_get(dup, "XA")) { char *original = NULL; if (param->tag) { original = bam_get_qname(ori); } if (add_duplicate(dup_hash, dup, original, dup_type, read_group)) return -1; } } return 0; } /* If the duplicate type has changed to optical then retag and duplicate hash. */ static inline int optical_retag(md_param_t *param, khash_t(duplicates) *dup_hash, bam1_t *b, int paired, stats_block_t *stats) { int ret = 0; if (bam_aux_update_str(b, "dt", 3, "SQ")) { print_error("markdup", "error, unable to update 'dt' tag.\n"); ret = -1; } if (paired) { stats->optical++; } else { stats->single_optical++; } if (param->supp) { // Change the duplicate type if (bam_aux_get(b, "SA") || (b->core.flag & BAM_FMUNMAP) || bam_aux_get(b, "XA")) { khiter_t d; d = kh_get(duplicates, dup_hash, bam_get_qname(b)); if (d == kh_end(dup_hash)) { // error, name should already be in dup hash print_error("markdup", "error, duplicate name %s not found in hash.\n", bam_get_qname(b)); ret = -1; } else { kh_value(dup_hash, d).type = 'O'; } } } return ret; } /* Check all duplicates of the highest quality read (the "original") for consistancy. Also pre-calculate any values for use in check_duplicate_chain later. Returns 0 on success, >0 on coordinate reading error (program can continue) or <0 on an error (program should not continue. */ static int check_chain_against_original(md_param_t *param, khash_t(duplicates) *dup_hash, read_queue_t *ori, check_list_t *list, long *warn, stats_block_t *stats) { int ret = 0, coord_fail = 0; char *ori_name = bam_get_qname(ori->b); read_queue_t *current = ori->duplicate; int t_beg = 0, t_end = 0; long x, y; if (param->opt_dist) { coord_fail = get_coordinates(param, ori_name, &t_beg, &t_end, &x, &y, warn); } list->length = 0; while (current) { check_t *c; if (list->length >= list->size) { check_t *tmp; list->size *= 2; if (!(tmp = realloc(list->c, list->size * sizeof(check_t)))) { print_error("markdup", "error, Unable to expand optical check list.\n"); return -1; } list->c = tmp; } c = &list->c[list->length]; c->b = current->b; c->x = -1; c->y = -1; c->opt = 0; c->score = 0; c->mate_score = 0; current->dup_checked = 1; if (param->tag) { uint8_t *data; // at this stage all duplicates should have a do tag if ((data = bam_aux_get(current->b, "do")) != NULL) { // see if we need to change the tag char *old_name = bam_aux2Z(data); if (old_name) { if (strcmp(old_name, ori_name) != 0) { if (bam_aux_update_str(current->b, "do", strlen(ori_name) + 1, (const char *)ori_name)) { print_error("markdup", "error, unable to update 'do' tag.\n"); ret = -1; break; } } } else { print_error("markdup", "error, 'do' tag has wrong type for read %s.\n", bam_get_qname(current->b)); ret = -1; break; } } } if (param->opt_dist && !coord_fail) { uint8_t *data; char *dup_type; int is_opt = 0; int current_paired = (current->b->core.flag & BAM_FPAIRED) && !(current->b->core.flag & BAM_FMUNMAP); if ((data = bam_aux_get(current->b, "dt"))) { if ((dup_type = bam_aux2Z(data))) { if (strcmp(dup_type, "SQ") == 0) { c->opt = 1; } } } // need to run this to get the duplicates x and y scores is_opt = optical_duplicate_partial(param, ori_name, t_beg, t_end, x, y, current->b, c, param->opt_dist, warn); if (!c->opt && is_opt) { if (optical_retag(param, dup_hash, current->b, current_paired, stats)) { ret = -1; break; } c->opt = 1; } c->score = calc_score(current->b); if (current_paired) { if ((c->mate_score = get_mate_score(current->b)) == -1) { print_error("markdup", "error, no ms score tag. Please run samtools fixmate on file first.\n"); ret = -1; break; } } } current = current->duplicate; list->length++; } if (!ret && coord_fail) ret = coord_fail; ori->dup_checked = 1; return ret; } static int chain_sort(const void *a, const void *b) { check_t *ac = (check_t *) a; check_t *bc = (check_t *) b; int ret; if ((ret = ac->len - bc->len)) return ret; else if ((ret = memcmp(bam_get_qname(ac->b) + ac->beg, bam_get_qname(bc->b) + bc->beg, ac->len))) return ret; return (ac->x - bc->x); } /* Check all the duplicates against each other to see if they are optical duplicates. */ static int check_duplicate_chain(md_param_t *param, khash_t(duplicates) *dup_hash, check_list_t *list, long *warn, stats_block_t *stats) { int ret = 0; size_t curr = 0; qsort(list->c, list->length, sizeof(list->c[0]), chain_sort); while (curr < list->length - 1) { check_t *base = &list->c[curr]; char *base_name = bam_get_qname(base->b); int end_name_match = curr; // find the end of the matching name parts while (++end_name_match < list->length) { check_t *chk = &list->c[end_name_match]; if ((base->len == chk->len) && memcmp(base_name + base->beg, bam_get_qname(chk->b) + chk->beg, base->len) != 0) break; } while (curr < end_name_match) { size_t count = curr; check_t *current = &list->c[curr]; int current_paired = (current->b->core.flag & BAM_FPAIRED) && !(current->b->core.flag & BAM_FMUNMAP); while (++count < end_name_match && (list->c[count].x - current->x <= param->opt_dist)) { // while close enough along the x coordinate check_t *chk = &list->c[count]; if (current->opt && chk->opt) continue; long ydiff; if (current->y > chk->y) { ydiff = current->y - chk->y; } else { ydiff = chk->y - current->y; } if (ydiff > param->opt_dist) continue; // optical duplicates int chk_dup = 0; int chk_paired = (chk->b->core.flag & BAM_FPAIRED) && !(chk->b->core.flag & BAM_FMUNMAP); if (current_paired != chk_paired) { if (!chk_paired) { // chk is single vs pair, this is a dup. chk_dup = 1; } } else { // do it by scores int64_t cur_score, chk_score; if ((current->b->core.flag & BAM_FQCFAIL) != (chk->b->core.flag & BAM_FQCFAIL)) { if (current->b->core.flag & BAM_FQCFAIL) { cur_score = 0; chk_score = 1; } else { cur_score = 1; chk_score = 0; } } else { cur_score = current->score; chk_score = chk->score; if (current_paired) { // they are pairs so add mate scores. chk_score += chk->mate_score; cur_score += current->mate_score; } } if (cur_score == chk_score) { if (strcmp(bam_get_qname(chk->b), bam_get_qname(current->b)) < 0) { chk_score++; } else { chk_score--; } } if (cur_score > chk_score) { chk_dup = 1; } } if (chk_dup) { // the duplicate is the optical duplicate if (!chk->opt) { // only change if not already an optical duplicate if (optical_retag(param, dup_hash, chk->b, chk_paired, stats)) { ret = -1; goto fail; } chk->opt = 1; } } else { if (!current->opt) { if (optical_retag(param, dup_hash, current->b, current_paired, stats)) { ret = -1; goto fail; } current->opt = 1; } } } curr++; } } fail: return ret; } /* Where there is more than one duplicate go down the list and check for optical duplicates and change do tags (where used) to point to original (non-duplicate) read. */ static int find_duplicate_chains(md_param_t *param, read_queue_t *in_read , khash_t(duplicates) *dup_hash, check_list_t *dup_list, long *warn, stats_block_t *stats) { int ret = 0; while (in_read->original) in_read = in_read->original; // check against the original for tagging and optical duplication if ((ret = check_chain_against_original(param, dup_hash, in_read, dup_list, warn, stats + in_read->read_group))) { if (ret < 0) { // real error ret = -1; } else { // coordinate decoding error ret = 0; } } else { // check the rest of the duplicates against each other for optical duplication if (param->opt_dist && check_duplicate_chain(param, dup_hash, dup_list, warn, stats + in_read->read_group)) { ret = -1; } } return ret; } /* Function to use when estimating library size. This is based on an approximate formula for the coverage of a set obtained after sampling it a given number of times with replacement. x = number of items in the set (the number of unique fragments in the library) c = number of unique items (unique read pairs observed) n = number of items samples (total number of read pairs) c and n are known; x is unknown. As n -> infinity, the coverage (c/x) can be given as: c / x = 1 - exp(-n / x) (see https://math.stackexchange.com/questions/32800) This needs to be solved for x, so it is rearranged to put both terms on the left side and estimate_library_size() finds a value of x which gives a result of zero (or as close as it can get). */ static inline double coverage_equation(double x, double c, double n) { return c / x - 1 + exp(-n / x); } /* estimate the library size, based on the Picard code in DuplicationMetrics.java*/ static unsigned long estimate_library_size(unsigned long paired_reads, unsigned long paired_duplicate_reads, unsigned long optical) { unsigned long estimated_size = 0; unsigned long non_optical_pairs = (paired_reads - optical) / 2; unsigned long unique_pairs = (paired_reads - paired_duplicate_reads) / 2; unsigned long duplicate_pairs = (paired_duplicate_reads - optical) / 2; if ((non_optical_pairs && duplicate_pairs && unique_pairs) && (non_optical_pairs > duplicate_pairs)) { double m = 1; double M = 100; int i; if (coverage_equation(m * (double)unique_pairs, (double)unique_pairs, (double)non_optical_pairs) < 0) { print_error("markdup", "warning, unable to calculate estimated library size.\n"); return estimated_size; } while (coverage_equation(M * (double)unique_pairs, (double)unique_pairs, (double)non_optical_pairs) > 0) { M *= 10; } for (i = 0; i < 40; i++) { double r = (m + M) / 2; double u = coverage_equation(r * (double)unique_pairs, (double)unique_pairs, (double)non_optical_pairs); if (u > 0) { m = r; } else if (u < 0) { M = r; } else { break; } } estimated_size = (unsigned long)(unique_pairs * (m + M) / 2); } else { print_error("markdup", "warning, unable to calculate estimated library size." " Read pairs %ld should be greater than duplicate pairs %ld," " which should both be non zero.\n", non_optical_pairs, duplicate_pairs); } return estimated_size; } static void write_stats(FILE *fp, const char *title, const char *title_con, stats_block_t *stats) { unsigned long els; els = estimate_library_size(stats->pair, stats->duplicate, stats->optical); if (title) { fprintf(fp, "%s%s\n", title, title_con); } fprintf(fp, "READ: %ld\n" "WRITTEN: %ld\n" "EXCLUDED: %ld\n" "EXAMINED: %ld\n" "PAIRED: %ld\n" "SINGLE: %ld\n" "DUPLICATE PAIR: %ld\n" "DUPLICATE SINGLE: %ld\n" "DUPLICATE PAIR OPTICAL: %ld\n" "DUPLICATE SINGLE OPTICAL: %ld\n" "DUPLICATE NON PRIMARY: %ld\n" "DUPLICATE NON PRIMARY OPTICAL: %ld\n" "DUPLICATE PRIMARY TOTAL: %ld\n" "DUPLICATE TOTAL: %ld\n" "ESTIMATED_LIBRARY_SIZE: %ld\n", stats->reading, stats->writing, stats->excluded, stats->examined, stats->pair, stats->single, stats->duplicate, stats->single_dup, stats->optical, stats->single_optical, stats->np_duplicate, stats->np_opt_duplicate, stats->single_dup + stats->duplicate, stats->single_dup + stats->duplicate + stats->np_duplicate, els); } static void write_json_stats(FILE *fp, const char *offset, const char *group_name, stats_block_t *stats, const char *end) { unsigned long els; els = estimate_library_size(stats->pair, stats->duplicate, stats->optical); if (group_name) { fprintf(fp, "%s\"READ GROUP\": \"%s\",\n", offset, group_name); } fprintf(fp, "%s\"READ\": %ld,\n", offset, stats->reading); fprintf(fp, "%s\"WRITTEN\": %ld,\n", offset, stats->writing); fprintf(fp, "%s\"EXCLUDED\": %ld,\n", offset, stats->excluded); fprintf(fp, "%s\"EXAMINED\": %ld,\n", offset, stats->examined); fprintf(fp, "%s\"PAIRED\": %ld,\n", offset, stats->pair); fprintf(fp, "%s\"SINGLE\": %ld,\n", offset, stats->single); fprintf(fp, "%s\"DUPLICATE PAIR\": %ld,\n", offset, stats->duplicate); fprintf(fp, "%s\"DUPLICATE SINGLE\": %ld,\n", offset, stats->single_dup); fprintf(fp, "%s\"DUPLICATE PAIR OPTICAL\": %ld,\n", offset, stats->optical); fprintf(fp, "%s\"DUPLICATE SINGLE OPTICAL\": %ld,\n", offset, stats->single_optical); fprintf(fp, "%s\"DUPLICATE NON PRIMARY\": %ld,\n", offset, stats->np_duplicate); fprintf(fp, "%s\"DUPLICATE NON PRIMARY OPTICAL\": %ld,\n", offset, stats->np_opt_duplicate); fprintf(fp, "%s\"DUPLICATE PRIMARY TOTAL\": %ld,\n", offset, stats->single_dup + stats->duplicate); fprintf(fp, "%s\"DUPLICATE TOTAL\": %ld,\n", offset, stats->single_dup + stats->duplicate + stats->np_duplicate); fprintf(fp, "%s\"ESTIMATED_LIBRARY_SIZE\": %ld", offset, els); if (end) { fprintf(fp, "%s", end); } } /* Compare the reads near each other (coordinate sorted) and try to spot the duplicates. Generally the highest quality scoring is chosen as the original and all others the duplicates. The score is based on the sum of the quality values (<= 15) of the read and its mate (if any). While single reads are compared to only one read of a pair, the pair will chosen as the original. The comparison is done on position and orientation, see above for details. Marking the supplementary reads of a duplicate as also duplicates takes an extra file read/write step. This is because the duplicate can occur before the primary read.*/ static int bam_mark_duplicates(md_param_t *param) { bam_hdr_t *header = NULL; khiter_t k; khash_t(reads) *pair_hash = kh_init(reads); khash_t(reads) *single_hash = kh_init(reads); klist_t(read_queue) *read_buffer = kl_init(read_queue); kliter_t(read_queue) *rq; khash_t(duplicates) *dup_hash = kh_init(duplicates); khash_t(read_groups) *rg_hash = kh_init(read_groups); int32_t prev_tid; hts_pos_t prev_coord; read_queue_t *in_read; int ret; stats_block_t *stats, *stat_array = NULL; int num_groups = 0; long opt_warnings = 0, bc_warnings = 0; tmp_file_t temp; char *idx_fn = NULL; int exclude = 0; check_list_t dup_list = {NULL, 0, 0}; if (!pair_hash || !single_hash || !read_buffer || !dup_hash || !rg_hash) { print_error("markdup", "error, unable to allocate memory to initialise structures.\n"); goto fail; } if ((header = sam_hdr_read(param->in)) == NULL) { print_error("markdup", "error reading header\n"); goto fail; } // accept unknown, unsorted or coordinate sort order, but error on queryname sorted. // only really works on coordinate sorted files. kstring_t str = KS_INITIALIZE; if (!sam_hdr_find_tag_hd(header, "SO", &str) && str.s && !strcmp(str.s, "queryname")) { print_error("markdup", "error, queryname sorted, must be sorted by coordinate.\n"); ks_free(&str); goto fail; } ks_free(&str); if (!param->no_pg && sam_hdr_add_pg(header, "samtools", "VN", samtools_version(), param->arg_list ? "CL" : NULL, param->arg_list ? param->arg_list : NULL, NULL) != 0) { print_error("markdup", "warning, unable to add @PG line to header.\n"); } if (sam_hdr_write(param->out, header) < 0) { print_error("markdup", "error writing header.\n"); goto fail; } if (param->write_index) { if (!(idx_fn = auto_index(param->out, param->out_fn, header))) goto fail; } if (param->read_groups) { num_groups = sam_hdr_count_lines(header, "RG"); int g_ret = 0; if (num_groups > 0) { int i; for (i = 0; i < num_groups; i++) { const char *rg_key; khiter_t rg; rg_key = sam_hdr_line_name(header, "RG", i); if (rg_key) { rg = kh_get(read_groups, rg_hash, rg_key); if (rg == kh_end(rg_hash)) { // new entry rg = kh_put(read_groups, rg_hash, rg_key, &g_ret); if (g_ret > 0) { kh_value(rg_hash, rg) = i + 1; } else { print_error("markdup", "error, unable to populate read group ids. " "Read groups will not be used\n"); g_ret = -1; break; } } else { print_error("markdup", "error, duplicate read group ids %s." "Read groups will not be used\n", rg_key); g_ret = -1; break; } } else { print_error("markdup", "error, Unable to retrieve read group at position %d." "Read groups will not be used\n", i); g_ret = -1; break; } } } else { print_error("markdup", "error, no read groups found.\n"); g_ret = -1; } if (g_ret < 0) { print_error("markdup", "error, read groups will not be used.\n"); param->read_groups = 0; num_groups = 0; } } // stat_array[0] will be for ungrouped reads stat_array = calloc(num_groups + 1, sizeof(stats_block_t)); if (stat_array == NULL) { print_error("markdup", "error, unable to allocate memory for stats.\n"); goto fail; } // used for coordinate order checks prev_tid = prev_coord = 0; // get the buffer going in_read = kl_pushp(read_queue, read_buffer); if (!in_read) { print_error("markdup", "error, unable to allocate memory to hold reads.\n"); goto fail; } // handling supplementary reads needs a temporary file if (param->supp) { if (tmp_file_open_write(&temp, param->prefix, 1)) { print_error("markdup", "error, unable to open tmp file %s.\n", param->prefix); goto fail; } } if ((in_read->b = bam_init1()) == NULL) { print_error("markdup", "error, unable to allocate memory for alignment.\n"); goto fail; } if (param->check_chain && !(param->tag || param->opt_dist)) param->check_chain = 0; if (param->check_chain) { dup_list.size = 128; dup_list.c = NULL; if ((dup_list.c = malloc(dup_list.size * sizeof(check_t))) == NULL) { print_error("markdup", "error, unable to allocate memory for dup_list.\n"); goto fail; } } while ((ret = sam_read1(param->in, header, in_read->b)) >= 0) { // do some basic coordinate order checks if (in_read->b->core.tid >= 0) { // -1 for unmapped reads if (in_read->b->core.tid < prev_tid || ((in_read->b->core.tid == prev_tid) && (in_read->b->core.pos < prev_coord))) { print_error("markdup", "error, not in coordinate sorted order.\n"); goto fail; } } prev_coord = in_read->pos = in_read->b->core.pos; prev_tid = in_read->b->core.tid; in_read->pair_key.single = 1; in_read->single_key.single = 0; in_read->duplicate = NULL; in_read->original = NULL; in_read->dup_checked = 0; in_read->read_group = 0; in_read->dc = 1; if (param->read_groups) { uint8_t *data; char *rg; if ((data = bam_aux_get(in_read->b, "RG"))) { if ((rg = bam_aux2Z(data))) { khiter_t r; r = kh_get(read_groups, rg_hash, rg); if (r != kh_end(rg_hash)) { in_read->read_group = kh_value(rg_hash, r); } } } } stats = stat_array + in_read->read_group; stats->reading++; if (param->clear && (in_read->b->core.flag & BAM_FDUP)) { uint8_t *data; in_read->b->core.flag ^= BAM_FDUP; if ((data = bam_aux_get(in_read->b, "dt")) != NULL) { bam_aux_del(in_read->b, data); } if ((data = bam_aux_get(in_read->b, "do")) != NULL) { bam_aux_del(in_read->b, data); } } if (param->include_fails) { exclude |= (BAM_FSECONDARY | BAM_FSUPPLEMENTARY | BAM_FUNMAP); } else { exclude |= (BAM_FSECONDARY | BAM_FSUPPLEMENTARY | BAM_FUNMAP | BAM_FQCFAIL); } // read must not be secondary, supplementary, unmapped or (possibly) failed QC if (!(in_read->b->core.flag & exclude)) { stats->examined++; // look at the pairs first if ((in_read->b->core.flag & BAM_FPAIRED) && !(in_read->b->core.flag & BAM_FMUNMAP)) { int ret, mate_tmp; key_data_t pair_key; key_data_t single_key; in_hash_t *bp; if (make_pair_key(param, &pair_key, in_read->b, in_read->read_group, &bc_warnings)) { print_error("markdup", "error, unable to assign pair hash key.\n"); goto fail; } make_single_key(param, &single_key, in_read->b, in_read->read_group, &bc_warnings); stats->pair++; in_read->pos = single_key.this_coord; // cigar/orientation modified pos // put in singles hash for checking against non paired reads k = kh_put(reads, single_hash, single_key, &ret); if (ret > 0) { // new // add to single duplicate hash bp = &kh_val(single_hash, k); bp->p = in_read; in_read->single_key = single_key; } else if (ret == 0) { // exists // look at singles only for duplication marking bp = &kh_val(single_hash, k); if (!(bp->p->b->core.flag & BAM_FPAIRED) || (bp->p->b->core.flag & BAM_FMUNMAP)) { // singleton will always be marked duplicate even if // scores more than one read of the pair bam1_t *dup = bp->p->b; if (param->check_chain) { in_read->duplicate = bp->p; bp->p->original = in_read; } bp->p = in_read; bp->p->dc += 1; if (mark_duplicates(param, dup_hash, bp->p->b, dup, in_read->read_group, &stats->single_optical, &opt_warnings)) goto fail; stats->single_dup++; } } else { print_error("markdup", "error, single hashing failure for paired read.\n"); goto fail; } // now do the pair k = kh_put(reads, pair_hash, pair_key, &ret); if (ret > 0) { // new // add to the pair hash bp = &kh_val(pair_hash, k); bp->p = in_read; in_read->pair_key = pair_key; } else if (ret == 0) { int64_t old_score, new_score, tie_add = 0; bam1_t *dup = NULL; bp = &kh_val(pair_hash, k); if ((bp->p->b->core.flag & BAM_FQCFAIL) != (in_read->b->core.flag & BAM_FQCFAIL)) { if (bp->p->b->core.flag & BAM_FQCFAIL) { old_score = 0; new_score = 1; } else { old_score = 1; new_score = 0; } } else { if ((mate_tmp = get_mate_score(bp->p->b)) == -1) { print_error("markdup", "error, no ms score tag. Please run samtools fixmate on file first.\n"); goto fail; } else { old_score = calc_score(bp->p->b) + mate_tmp; } if ((mate_tmp = get_mate_score(in_read->b)) == -1) { print_error("markdup", "error, no ms score tag. Please run samtools fixmate on file first.\n"); goto fail; } else { new_score = calc_score(in_read->b) + mate_tmp; } } // choose the highest score as the original // and add it to the pair hash, mark the other as duplicate if (new_score == old_score) { if (strcmp(bam_get_qname(in_read->b), bam_get_qname(bp->p->b)) < 0) { tie_add = 1; } else { tie_add = -1; } } if (new_score + tie_add > old_score) { // swap reads dup = bp->p->b; in_read->dc += bp->p->dc; if (param->check_chain) { if (in_read->duplicate) { read_queue_t *current = in_read->duplicate; while (current->duplicate) { current = current->duplicate; } current->duplicate = bp->p; } else { in_read->duplicate = bp->p; } bp->p->original = in_read; } bp->p = in_read; } else { if (param->check_chain) { if (bp->p->duplicate) { if (in_read->duplicate) { read_queue_t *current = bp->p->duplicate; while (current->duplicate) { current = current->duplicate; } current->duplicate = in_read->duplicate; } in_read->duplicate = bp->p->duplicate; } bp->p->duplicate = in_read; in_read->original = bp->p; } dup = in_read->b; bp->p->dc += 1; } if (mark_duplicates(param, dup_hash, bp->p->b, dup, in_read->read_group, &stats->optical, &opt_warnings)) goto fail; stats->duplicate++; } else { print_error("markdup", "error, pair hashing failure.\n"); goto fail; } } else { // do the single (or effectively single) reads int ret; key_data_t single_key; in_hash_t *bp; make_single_key(param, &single_key, in_read->b, in_read->read_group, &bc_warnings); stats->single++; in_read->pos = single_key.this_coord; // cigar/orientation modified pos k = kh_put(reads, single_hash, single_key, &ret); if (ret > 0) { // new bp = &kh_val(single_hash, k); bp->p = in_read; in_read->single_key = single_key; } else if (ret == 0) { // exists bp = &kh_val(single_hash, k); if ((bp->p->b->core.flag & BAM_FPAIRED) && !(bp->p->b->core.flag & BAM_FMUNMAP)) { // if matched against one of a pair just mark as duplicate if (param->check_chain) { if (bp->p->duplicate) { in_read->duplicate = bp->p->duplicate; } bp->p->duplicate = in_read; in_read->original = bp->p; } bp->p->dc += 1; if (mark_duplicates(param, dup_hash, bp->p->b, in_read->b, in_read->read_group, &stats->single_optical, &opt_warnings)) goto fail; } else { int64_t old_score, new_score; bam1_t *dup = NULL; old_score = calc_score(bp->p->b); new_score = calc_score(in_read->b); // choose the highest score as the original, add it // to the single hash and mark the other as duplicate if (new_score > old_score) { // swap reads dup = bp->p->b; in_read->dc += bp->p->dc; if (param->check_chain) { in_read->duplicate = bp->p; bp->p->original = in_read; } bp->p = in_read; } else { if (param->check_chain) { if (bp->p->duplicate) { in_read->duplicate = bp->p->duplicate; } bp->p->duplicate = in_read; in_read->original = bp->p; } bp->p->dc += 1; dup = in_read->b; } if (mark_duplicates(param, dup_hash, bp->p->b, dup, in_read->read_group, &stats->single_optical, &opt_warnings)) goto fail; } stats->single_dup++; } else { print_error("markdup", "error, single hashing failure for single read.\n"); goto fail; } } } else { stats->excluded++; } // loop through the stored reads and write out those we // no longer need rq = kl_begin(read_buffer); while (rq != kl_end(read_buffer)) { in_read = &kl_val(rq); /* keep a moving window of reads based on coordinates and max read length. Any unaligned reads should just be written as they cannot be matched as duplicates. */ if (in_read->pos + param->max_length > prev_coord && in_read->b->core.tid == prev_tid && (prev_tid != -1 || prev_coord != -1)) { break; } if (param->check_chain && !in_read->dup_checked && (in_read->original || in_read->duplicate)) { if (find_duplicate_chains(param, in_read, dup_hash, &dup_list, &opt_warnings, stat_array)) { print_error("markdup", "error, duplicate checking failed.\n"); goto fail; } } if (!param->remove_dups || !(in_read->b->core.flag & BAM_FDUP)) { if (param->dc && !(in_read->b->core.flag & BAM_FDUP)) { bam_aux_update_int(in_read->b, "dc", in_read->dc); } if (param->supp) { if (tmp_file_write(&temp, in_read->b)) { print_error("markdup", "error, writing temp output failed.\n"); goto fail; } } else { if (sam_write1(param->out, header, in_read->b) < 0) { print_error("markdup", "error, writing output failed.\n"); goto fail; } } stat_array[in_read->read_group].writing++; } // remove from hash if (in_read->pair_key.single == 0) { k = kh_get(reads, pair_hash, in_read->pair_key); kh_del(reads, pair_hash, k); } if (in_read->single_key.single == 1) { k = kh_get(reads, single_hash, in_read->single_key); kh_del(reads, single_hash, k); } kl_shift(read_queue, read_buffer, NULL); bam_destroy1(in_read->b); rq = kl_begin(read_buffer); } // set the next one up for reading in_read = kl_pushp(read_queue, read_buffer); if (!in_read) { print_error("markdup", "error, unable to allocate memory for read in queue.\n"); goto fail; } if ((in_read->b = bam_init1()) == NULL) { print_error("markdup", "error, unable to allocate memory for alignment.\n"); goto fail; } } if (ret < -1) { print_error("markdup", "error, truncated input file.\n"); goto fail; } // write out the end of the list rq = kl_begin(read_buffer); while (rq != kl_end(read_buffer)) { in_read = &kl_val(rq); if (bam_get_qname(in_read->b)) { // last entry will be blank if (param->check_chain && !in_read->dup_checked && (in_read->original || in_read->duplicate)) { if (find_duplicate_chains(param, in_read, dup_hash, &dup_list, &opt_warnings, stat_array)) { print_error("markdup", "error, duplicate checking failed.\n"); goto fail; } } if (!param->remove_dups || !(in_read->b->core.flag & BAM_FDUP)) { if (param->dc && !(in_read->b->core.flag & BAM_FDUP)) { bam_aux_update_int(in_read->b, "dc", in_read->dc); } if (param->supp) { if (tmp_file_write(&temp, in_read->b)) { print_error("markdup", "error, writing temp output failed on final write.\n"); goto fail; } } else { if (param->dc && !(in_read->b->core.flag & BAM_FDUP)) { bam_aux_update_int(in_read->b, "dc", in_read->dc); } if (sam_write1(param->out, header, in_read->b) < 0) { print_error("markdup", "error, writing output failed on final write.\n"); goto fail; } } stat_array[in_read->read_group].writing++; } } kl_shift(read_queue, read_buffer, NULL); bam_destroy1(in_read->b); rq = kl_begin(read_buffer); } if (param->supp) { bam1_t *b; if (tmp_file_end_write(&temp)) { print_error("markdup", "error, unable to end tmp writing.\n"); goto fail; } // read data from temp file and mark duplicate supplementary alignments if (tmp_file_begin_read(&temp)) { goto fail; } b = bam_init1(); while ((ret = tmp_file_read(&temp, b)) > 0) { if ((b->core.flag & BAM_FSUPPLEMENTARY) || (b->core.flag & BAM_FUNMAP) || (b->core.flag & BAM_FSECONDARY)) { k = kh_get(duplicates, dup_hash, bam_get_qname(b)); if (k != kh_end(dup_hash)) { b->core.flag |= BAM_FDUP; stat_array[kh_val(dup_hash, k).read_group].np_duplicate++; if (param->tag && kh_val(dup_hash, k).name) { if (bam_aux_update_str(b, "do", strlen(kh_val(dup_hash, k).name) + 1, (char*)kh_val(dup_hash, k).name)) { print_error("markdup", "error, unable to append supplementary 'do' tag.\n"); goto fail; } } if (param->opt_dist) { if (kh_val(dup_hash, k).type) { bam_aux_update_str(b, "dt", 3, "SQ"); stat_array[kh_val(dup_hash, k).read_group].np_opt_duplicate++; } else { bam_aux_update_str(b, "dt", 3, "LB"); } } } } if (!param->remove_dups || !(b->core.flag & BAM_FDUP)) { if (param->dc && (b->core.flag & BAM_FDUP)) { uint8_t* data = bam_aux_get(b, "dc"); if(data) bam_aux_del(b, data); } if (sam_write1(param->out, header, b) < 0) { print_error("markdup", "error, writing final output failed.\n"); goto fail; } } } if (ret == -1) { print_error("markdup", "error, failed to read tmp file.\n"); goto fail; } for (k = kh_begin(dup_hash); k != kh_end(dup_hash); ++k) { if (kh_exist(dup_hash, k)) { free(kh_val(dup_hash, k).name); free((char *)kh_key(dup_hash, k)); kh_key(dup_hash, k) = NULL; } } tmp_file_destroy(&temp); bam_destroy1(b); } if (opt_warnings) { print_error("markdup", "warning, number of failed attempts to get coordinates from read names = %ld\n", opt_warnings); } if (bc_warnings) { print_error("markdup", "warning, number of failed attempts to get barcodes = %ld\n", bc_warnings); } if (param->do_stats) { FILE *fp; int file_open = 0; stats_block_t total; int i; if (param->stats_file) { if (NULL == (fp = fopen(param->stats_file, "w"))) { print_error("markdup", "warning, cannot write stats to %s.\n", param->stats_file); fp = samtools_stderr; } else { file_open = 1; } } else { fp = samtools_stderr; } total = stat_array[0]; if (param->read_groups) { for (i = 1; i <= num_groups; i++) { total.reading += stat_array[i].reading; total.writing += stat_array[i].writing; total.excluded += stat_array[i].excluded; total.duplicate += stat_array[i].duplicate; total.single += stat_array[i].single; total.pair += stat_array[i].pair; total.single_dup += stat_array[i].single_dup; total.examined += stat_array[i].examined; total.optical += stat_array[i].optical; total.single_optical += stat_array[i].single_optical; total.np_duplicate += stat_array[i].np_duplicate; total.np_opt_duplicate += stat_array[i].np_opt_duplicate; } } if (!param->json) { write_stats(fp, "COMMAND: ", param->arg_list, &total); fprintf(fp, "\n"); if (param->read_groups) { if (stat_array[0].reading) { write_stats(fp, "READ GROUP: ", "ungrouped", stat_array); fprintf(fp, "\n"); } for (i = 0; i < num_groups; i++) { write_stats(fp, "READ GROUP: ", sam_hdr_line_name(header, "RG", i), stat_array + i + 1); fprintf(fp, "\n"); } } } else { char space4[] = " "; char space8[] = " "; char space12[] = " "; fprintf(fp, "{\n"); fprintf(fp, "%s\"COMMAND\": \"%s\",\n", space4, param->arg_list); write_json_stats(fp, space4, NULL, &total, param->read_groups ? ",\n" : "\n"); if (param->read_groups) { fprintf(fp, "%s\"READ GROUPS\": [\n", space4); if (stat_array[0].reading) { fprintf(fp, "%s{\n", space8); write_json_stats(fp, space12, "ungrouped", stat_array, "\n"); fprintf(fp, "%s},\n", space8); } for (i = 0; i < num_groups; i++) { fprintf(fp, "%s{\n", space8); write_json_stats(fp, space12, sam_hdr_line_name(header, "RG", i), stat_array + i + 1, "\n"); if (i < num_groups -1 ) { fprintf(fp, "%s},\n", space8); } else { fprintf(fp, "%s}\n", space8); } } fprintf(fp, "%s]\n", space4); } fprintf(fp, "}\n"); } if (file_open) { fclose(fp); } } if (param->write_index) { if (sam_idx_save(param->out) < 0) { print_error_errno("markdup", "error, writing index failed"); goto fail; } } if (param->check_chain && (param->tag || param->opt_dist)) free(dup_list.c); free(idx_fn); free(stat_array); kh_destroy(reads, pair_hash); kh_destroy(reads, single_hash); kl_destroy(read_queue, read_buffer); kh_destroy(duplicates, dup_hash); kh_destroy(read_groups, rg_hash); sam_hdr_destroy(header); return 0; fail: for (rq = kl_begin(read_buffer); rq != kl_end(read_buffer); rq = kl_next(rq)) bam_destroy1(kl_val(rq).b); kl_destroy(read_queue, read_buffer); for (k = kh_begin(dup_hash); k != kh_end(dup_hash); ++k) { if (kh_exist(dup_hash, k)) { free((char *)kh_key(dup_hash, k)); } } kh_destroy(duplicates, dup_hash); kh_destroy(read_groups, rg_hash); if (param->check_chain && (param->tag || param->opt_dist)) free(dup_list.c); free(idx_fn); free(stat_array); kh_destroy(reads, pair_hash); kh_destroy(reads, single_hash); sam_hdr_destroy(header); return 1; } static int markdup_usage(void) { fprintf(samtools_stderr, "\n"); fprintf(samtools_stderr, "Usage: samtools markdup \n\n"); fprintf(samtools_stderr, "Option: \n"); fprintf(samtools_stderr, " -r Remove duplicate reads\n"); fprintf(samtools_stderr, " -l INT Max read length (default 300 bases)\n"); fprintf(samtools_stderr, " -S Mark supplementary alignments of duplicates as duplicates (slower).\n"); fprintf(samtools_stderr, " -s Report stats.\n"); fprintf(samtools_stderr, " -f NAME Write stats to named file. Implies -s.\n"); fprintf(samtools_stderr, " --json Output stats in JSON. Also implies -s\n"); fprintf(samtools_stderr, " -T PREFIX Write temporary files to PREFIX.samtools.nnnn.nnnn.tmp.\n"); fprintf(samtools_stderr, " -d INT Optical distance (if set, marks with dt tag)\n"); fprintf(samtools_stderr, " -c Clear previous duplicate settings and tags.\n"); fprintf(samtools_stderr, " -m --mode TYPE Duplicate decision method for paired reads.\n" " TYPE = t measure positions based on template start/end (default).\n" " s measure positions based on sequence start.\n"); fprintf(samtools_stderr, " -u Output uncompressed data\n"); fprintf(samtools_stderr, " --include-fails Include quality check failed reads.\n"); fprintf(samtools_stderr, " --no-PG Do not add a PG line\n"); fprintf(samtools_stderr, " --no-multi-dup Reduced duplicates of duplicates checking.\n"); fprintf(samtools_stderr, " --read-coords STR Regex for coords from read name.\n"); fprintf(samtools_stderr, " --coords-order STR Order of regex elements. txy (default). With t being a part of\n" " the read names that must be equal and x/y being coordinates.\n"); fprintf(samtools_stderr, " --barcode-tag STR Use barcode a tag that duplicates much match.\n"); fprintf(samtools_stderr, " --barcode-name Use the UMI/barcode in the read name (eigth colon delimited part).\n"); fprintf(samtools_stderr, " --barcode-rgx STR Regex for barcode in the readname (alternative to --barcode-name).\n"); fprintf(samtools_stderr, " --use-read-groups Use the read group tags in duplicate matching.\n"); fprintf(samtools_stderr, " -t Mark primary duplicates with the name of the original in a \'do\' tag." " Mainly for information and debugging.\n"); fprintf(samtools_stderr, " --duplicate-count Record the original primary read duplication count(include itself) in a \'dc\' tag.\n"); sam_global_opt_help(samtools_stderr, "-.O..@.."); fprintf(samtools_stderr, "\nThe input file must be coordinate sorted and must have gone" " through fixmates with the mate scoring option on.\n"); return 1; } int bam_markdup(int argc, char **argv) { int c, ret, bc_name = 0; char wmode[4] = {'w', 0, 0, 0}; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; htsThreadPool p = {NULL, 0}; kstring_t tmpprefix = {0, 0, NULL}; struct stat st; unsigned int t; char *regex = NULL, *bc_regex = NULL; char *regex_order = "txy"; md_param_t param = {NULL, NULL, NULL, 0, 300, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, 0, 0}; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'), {"include-fails", no_argument, NULL, 1001}, {"no-PG", no_argument, NULL, 1002}, {"mode", required_argument, NULL, 'm'}, {"no-multi-dup", no_argument, NULL, 1003}, {"read-coords", required_argument, NULL, 1004}, {"coords-order", required_argument, NULL, 1005}, {"barcode-tag", required_argument, NULL, 1006}, {"barcode-name", no_argument, NULL, 1007}, {"barcode-rgx", required_argument, NULL, 1008}, {"use-read-groups", no_argument, NULL, 1009}, {"json", no_argument, NULL, 1010}, {"duplicate-count", no_argument, NULL, 1011}, {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "rsl:StT:O:@:f:d:cm:u", lopts, NULL)) >= 0) { switch (c) { case 'r': param.remove_dups = 1; break; case 'l': param.max_length = atoi(optarg); break; case 's': param.do_stats = 1; break; case 'T': kputs(optarg, &tmpprefix); break; case 'S': param.supp = 1; break; case 't': param.tag = 1; break; case 'f': param.stats_file = optarg; param.do_stats = 1; break; case 'd': param.opt_dist = atoi(optarg); break; case 'c': param.clear = 1; break; case 'm': if (strcmp(optarg, "t") == 0) { param.mode = MD_MODE_TEMPLATE; } else if (strcmp(optarg, "s") == 0) { param.mode = MD_MODE_SEQUENCE; } else { print_error("markdup", "error, unknown mode '%s'.\n", optarg); return markdup_usage(); } break; case 'u': wmode[1] = '0'; break; case 1001: param.include_fails = 1; break; case 1002: param.no_pg = 1; break; case 1003: param.check_chain = 0; break; case 1004: regex = optarg; break; case 1005: regex_order = optarg; break; case 1006: param.barcode = optarg; break; case 1007: bc_name = 1; break; case 1008: bc_name = 1, bc_regex = optarg; break; case 1009: param.read_groups = 1; break; case 1010: param.json = 1; param.do_stats = 1; break; case 1011: param.dc = 1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': return markdup_usage(); } } if (optind + 2 > argc) return markdup_usage(); if (param.barcode && bc_name) { print_error("markdup", "error, cannot specify --barcode-tag and " "--barcode-name (or --barcode-rgx) at same time.\n"); return 1; } if (param.opt_dist < 0) param.opt_dist = 0; if (param.max_length < 0) param.max_length = 300; if (regex) { int result; // set the order the elements of the regex are assigned to. // x and y being coordinates, t being any other important part of the read // e.g. tile and lane // x and y order does not matter as long as it is consistent if ((strncmp(regex_order, "txy", 3) == 0) || (strncmp(regex_order, "tyx", 3) == 0)) { param.rgx_t = 1; param.rgx_x = 2; param.rgx_y = 3; } else if ((strncmp(regex_order, "xyt", 3) == 0) || (strncmp(regex_order, "yxt", 3) == 0)) { param.rgx_x = 1; param.rgx_y = 2; param.rgx_t = 3; } else if ((strncmp(regex_order, "xty", 3) == 0) || (strncmp(regex_order, "ytx", 3) == 0)) { param.rgx_x = 1; param.rgx_t = 2; param.rgx_y = 3; } else if ((strncmp(regex_order, "xy", 2) == 0) || (strncmp(regex_order, "yx", 2) == 0)) { param.rgx_x = 1; param.rgx_y = 2; param.rgx_t = 0; } else { print_error("markdup", "error, could not recognise regex coordinate order \"%s\".\n", regex_order); return 1; } if ((param.rgx = malloc(sizeof(regex_t))) == NULL) { print_error("markdup", "error, could not allocate memory for regex.\n"); return 1; } if ((result = regcomp(param.rgx, regex, REG_EXTENDED))) { char err_msg[256]; regerror(result, param.rgx, err_msg, 256); print_error("markdup", "error, regex fail \"%s\"\n", err_msg); free(param.rgx); return 1; } } if (bc_name) { int result; /* From Illumina UMI documentation: "The UMI sequence is located in the eighth colon-delimited field of the read name (QNAME)". */ char *rgx = "[0-9A-Za-z]+:[0-9A-Za-z]+:[0-9A-Za-z]+:[0-9A-Za-z]+:[0-9A-Za-z]+:[0-9A-Za-z]+:[0-9A-Za-z]+:([!-?A-~]+)"; if ((param.bc_rgx = malloc(sizeof(regex_t))) == NULL) { print_error("markdup", "error, could not allocate memory for barcode regex.\n"); return 1; } if (bc_regex) { rgx = bc_regex; } if ((result = regcomp(param.bc_rgx, rgx, REG_EXTENDED))) { char err_msg[256]; regerror(result, param.bc_rgx, err_msg, 256); print_error("markdup", "error, barcode regex fail \"%s\"\n", err_msg); free(param.bc_rgx); return 1; } } param.in = sam_open_format(argv[optind], "r", &ga.in); if (!param.in) { print_error_errno("markdup", "error, failed to open \"%s\" for input", argv[optind]); return 1; } strcat(wmode, "b"); // default if unknown suffix sam_open_mode(wmode + strlen(wmode)-1, argv[optind + 1], NULL); param.out = sam_open_format(argv[optind + 1], wmode, &ga.out); if (!param.out) { print_error_errno("markdup", "error, failed to open \"%s\" for output", argv[optind + 1]); return 1; } if (ga.nthreads > 0) { if (!(p.pool = hts_tpool_init(ga.nthreads))) { print_error("markdup", "error creating thread pool.\n"); return 1; } hts_set_opt(param.in, HTS_OPT_THREAD_POOL, &p); hts_set_opt(param.out, HTS_OPT_THREAD_POOL, &p); } // actual stuff happens here // we need temp files so fix up the name here if (tmpprefix.l == 0) { if (strcmp(argv[optind + 1], "-") != 0) ksprintf(&tmpprefix, "%s.", argv[optind + 1]); else kputc('.', &tmpprefix); } if (stat(tmpprefix.s, &st) == 0 && S_ISDIR(st.st_mode)) { if (tmpprefix.s[tmpprefix.l-1] != '/') kputc('/', &tmpprefix); } t = ((unsigned) time(NULL)) ^ ((unsigned) clock()); ksprintf(&tmpprefix, "samtools.%d.%u.tmp", (int) getpid(), t % 10000); param.prefix = tmpprefix.s; param.arg_list = stringify_argv(argc + 1, argv - 1); param.write_index = ga.write_index; param.out_fn = argv[optind + 1]; ret = bam_mark_duplicates(¶m); sam_close(param.in); if (sam_close(param.out) < 0) { print_error("markdup", "error closing output file.\n"); ret = 1; } if (p.pool) hts_tpool_destroy(p.pool); if (param.rgx) { regfree(param.rgx); free(param.rgx); } if (param.bc_rgx) { regfree(param.bc_rgx); free(param.bc_rgx); } free(param.arg_list); free(tmpprefix.s); sam_global_args_free(&ga); return ret; } pysam-0.23.0/samtools/bam_mate.c000066400000000000000000001205201475062545500165140ustar00rootroot00000000000000/* bam_mate.c -- fix mate pairing information and clean up flags. Copyright (C) 2009, 2011-2017, 2019, 2022, 2024 Genome Research Ltd. Portions copyright (C) 2011 Broad Institute. Portions copyright (C) 2012 Peter Cock, The James Hutton Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notices and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "htslib/thread_pool.h" #include "sam_opts.h" #include "htslib/kstring.h" #include "htslib/sam.h" #include "samtools.h" #define MD_MIN_QUALITY 15 /* * This function calculates ct tag for two bams, it assumes they are from the same template and * writes the tag to the first read in position terms. */ static void bam_template_cigar(bam1_t *b1, bam1_t *b2, kstring_t *str) { bam1_t *swap; int i; hts_pos_t end; uint32_t *cigar; str->l = 0; if (b1->core.tid != b2->core.tid || b1->core.tid < 0 || b1->core.pos < 0 || b2->core.pos < 0 || b1->core.flag&BAM_FUNMAP || b2->core.flag&BAM_FUNMAP) return; // coordinateless or not on the same chr; skip if (b1->core.pos > b2->core.pos) swap = b1, b1 = b2, b2 = swap; // make sure b1 has a smaller coordinate kputc((b1->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index kputc((b1->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand for (i = 0, cigar = bam_get_cigar(b1); i < b1->core.n_cigar; ++i) { kputw(bam_cigar_oplen(cigar[i]), str); kputc(bam_cigar_opchr(cigar[i]), str); } end = bam_endpos(b1); kputw(b2->core.pos - end, str); kputc('T', str); kputc((b2->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index kputc((b2->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand for (i = 0, cigar = bam_get_cigar(b2); i < b2->core.n_cigar; ++i) { kputw(bam_cigar_oplen(cigar[i]), str); kputc(bam_cigar_opchr(cigar[i]), str); } uint8_t* data; if ((data = bam_aux_get(b1,"ct")) != NULL) bam_aux_del(b1, data); if ((data = bam_aux_get(b2,"ct")) != NULL) bam_aux_del(b2, data); bam_aux_append(b1, "ct", 'Z', str->l+1, (uint8_t*)str->s); } /* * What This Program is Supposed To Do: * Fill in mate coordinates, ISIZE and mate related flags from a name-sorted * alignment. * * How We Handle Input * * Secondary and supplementary Reads: * -write to output unchanged * All Reads: * -if pos == 0 (1 based), tid == -1 set UNMAPPED flag * single Reads: * -if pos == 0 (1 based), tid == -1, or UNMAPPED then set UNMAPPED, pos = 0, * tid = -1 * -clear bad flags (MREVERSE, PROPER_PAIR) * -set mpos = 0 (1 based), mtid = -1 and isize = 0 * -write to output * Paired Reads: * -if read is unmapped and mate is not, set pos and tid to equal that of mate * -sync mate flags (MREVERSE, MUNMAPPED), mpos, mtid * -recalculate ISIZE if possible, otherwise set it to 0 * -optionally clear PROPER_PAIR flag from reads where mapping or orientation * indicate this is not possible (Illumina orientation only) * -calculate ct and apply to lowest positioned read * -write to output * Limitations * -Does not handle tandem reads * -Should mark supplementary reads the same as primary. * Notes * -CT definition appears to be something else in spec, this was in here before * I started tampering with it, anyone know what is going on here? To work * around this I have demoted the CT this tool generates to ct. */ static void sync_unmapped_pos_inner(bam1_t* src, bam1_t* dest) { if ((dest->core.flag & BAM_FUNMAP) && !(src->core.flag & BAM_FUNMAP)) { // Set unmapped read's RNAME and POS to those of its mapped mate // (recommended best practice, ensures if coord sort will be together) dest->core.tid = src->core.tid; dest->core.pos = src->core.pos; } } static void sync_mate_inner(bam1_t* src, bam1_t* dest) { // sync mate pos information dest->core.mtid = src->core.tid; dest->core.mpos = src->core.pos; // sync flag info if (src->core.flag&BAM_FREVERSE) dest->core.flag |= BAM_FMREVERSE; else dest->core.flag &= ~BAM_FMREVERSE; if (src->core.flag & BAM_FUNMAP) { dest->core.flag |= BAM_FMUNMAP; } } // Is it plausible that these reads are properly paired? // Can't really give definitive answer without checking isize static bool plausibly_properly_paired(bam1_t* a, bam1_t* b) { if ((a->core.flag & BAM_FUNMAP) || (b->core.flag & BAM_FUNMAP)) return false; assert(a->core.tid >= 0); // This should never happen if FUNMAP is set correctly if (a->core.tid != b->core.tid) return false; bam1_t* first = a; bam1_t* second = b; hts_pos_t a_pos = a->core.flag&BAM_FREVERSE ? bam_endpos(a) : a->core.pos; hts_pos_t b_pos = b->core.flag&BAM_FREVERSE ? bam_endpos(b) : b->core.pos; if (a_pos > b_pos) { first = b; second = a; } else { first = a; second = b; } if (!(first->core.flag&BAM_FREVERSE) && (second->core.flag&BAM_FREVERSE)) return true; else return false; } // Returns 0 on success, -1 on failure. static int bam_format_cigar(const bam1_t* b, kstring_t* str) { // An empty cigar is a special case return "*" rather than "" if (b->core.n_cigar == 0) { return (kputc('*', str) == EOF) ? -1 : 0; } const uint32_t *cigar = bam_get_cigar(b); uint32_t i; for (i = 0; i < b->core.n_cigar; ++i) { if (kputw(bam_cigar_oplen(cigar[i]), str) == EOF) return -1; if (kputc(bam_cigar_opchr(cigar[i]), str) == EOF) return -1; } return 0; } // Returns 0 on success, -1 on failure. static int sync_mq_mc(bam1_t* src, bam1_t* dest) { if ( (src->core.flag & BAM_FUNMAP) == 0 ) { // If mapped // Copy Mate Mapping Quality uint32_t mq = src->core.qual; uint8_t* data; if ((data = bam_aux_get(dest,"MQ")) != NULL) { bam_aux_del(dest, data); } bam_aux_append(dest, "MQ", 'i', sizeof(uint32_t), (uint8_t*)&mq); } // Copy mate cigar if either read is mapped if ( (src->core.flag & BAM_FUNMAP) == 0 || (dest->core.flag & BAM_FUNMAP) == 0 ) { uint8_t* data_mc; if ((data_mc = bam_aux_get(dest,"MC")) != NULL) { bam_aux_del(dest, data_mc); } // Convert cigar to string kstring_t mc = { 0, 0, NULL }; if (bam_format_cigar(src, &mc) < 0) return -1; bam_aux_append(dest, "MC", 'Z', ks_len(&mc)+1, (uint8_t*)ks_str(&mc)); free(mc.s); } return 0; } // Copy flags. // Returns 0 on success, -1 on failure. static int sync_mate(bam1_t* a, bam1_t* b) { sync_unmapped_pos_inner(a,b); sync_unmapped_pos_inner(b,a); sync_mate_inner(a,b); sync_mate_inner(b,a); if (sync_mq_mc(a,b) < 0) return -1; if (sync_mq_mc(b,a) < 0) return -1; return 0; } static uint32_t calc_mate_score(bam1_t *b) { uint32_t score = 0; uint8_t *qual = bam_get_qual(b); int i; for (i = 0; i < b->core.l_qseq; i++) { if (qual[i] >= MD_MIN_QUALITY) score += qual[i]; } return score; } static int add_mate_score(bam1_t *src, bam1_t *dest) { uint8_t *data_ms; uint32_t mate_score = calc_mate_score(src); if ((data_ms = bam_aux_get(dest, "ms")) != NULL) { bam_aux_del(dest, data_ms); } if (bam_aux_append(dest, "ms", 'i', sizeof(uint32_t), (uint8_t*)&mate_score) == -1) { return -1; } return 0; } // Completely delete the CIGAR field static void clear_cigar(bam1_t *b) { memmove(bam_get_cigar(b), bam_get_seq(b), b->data + b->l_data - bam_get_seq(b)); b->l_data -= 4*b->core.n_cigar; b->core.n_cigar = 0; } // Trim a CIGAR field to end on reference position "end". Remaining bases // are turned to soft clips. static int bam_trim(bam1_t *b, hts_pos_t end) { hts_pos_t pos = b->core.pos; int n_cigar = b->core.n_cigar, i; uint32_t new_cigar_a[1024]; uint32_t *new_cigar = new_cigar_a; uint32_t *cigar = bam_get_cigar(b); // Find end of alignment or end of ref int op = 0, oplen = 0; for (i = 0; i < n_cigar; i++) { op = bam_cigar_op(cigar[i]); oplen = bam_cigar_oplen(cigar[i]); if (!(bam_cigar_type(op) & 2)) continue; pos += oplen; if (pos > end) break; } if (i == n_cigar) // looks fine already return 0; int old_i = i, j = 0; // At worst we grow by 1 element (eg 100M -> 70M30S) if (n_cigar-i >= 1024-1) { new_cigar = malloc(4*(n_cigar-i+1)); if (!new_cigar) return -1; } // We fill out to new_cigar from here on. if (pos-oplen < end) { // Partial CIGAR op? Split existing tag. cigar[old_i++] = bam_cigar_gen(end - (pos-oplen), op); new_cigar[j++] = bam_cigar_gen(pos-end, BAM_CSOFT_CLIP); } else if (pos > end) { // entirely off the chromosome; this will trigger CIGAR *, MQUAL 0 b->core.flag |= BAM_FUNMAP; b->core.flag &= ~BAM_FPROPER_PAIR; } else { // CIGAR op started on the trim junction new_cigar[j++] = bam_cigar_gen(oplen, BAM_CSOFT_CLIP); } // Replace trailing elements. for (i++; i < n_cigar; i++) { op = bam_cigar_op(cigar[i]); oplen = bam_cigar_oplen(cigar[i]); if (op == BAM_CHARD_CLIP) { new_cigar[j++] = cigar[i]; } else { new_cigar[j-1] = bam_cigar_gen(bam_cigar_oplen(new_cigar[j-1]) + oplen, BAM_CSOFT_CLIP); } } // We now have cigar[0..old_i-1] for existing CIGAR // and new_cigar[0..j-1] for new CIGAR trailing component. if (old_i+j == n_cigar) { // Fits and no data move needed memcpy(&cigar[old_i], new_cigar, j*4); } else { uint8_t *seq_old = bam_get_seq(b); uint8_t *aux_end = b->data + b->l_data; int nshift; if (old_i+j < n_cigar) { // Smaller, and can move data down nshift = -4*(n_cigar - (old_i+j)); } else { // Bigger, so grow BAM and move data up nshift = 4*(old_i+j - n_cigar); // FIXME: make htslib's sam_realloc_bam_data public if (b->l_data + nshift > b->m_data) { uint8_t *new_data = realloc(b->data, b->l_data + nshift); if (!new_data) { if (new_cigar != new_cigar_a) free(new_cigar); return -1; } b->m_data = b->l_data + nshift; if (b->data != new_data) { b->data = new_data; seq_old = bam_get_seq(b); aux_end = b->data + b->l_data; cigar = bam_get_cigar(b); } } } memmove(seq_old+nshift, seq_old, aux_end - seq_old); b->l_data += nshift; memcpy(&cigar[old_i], new_cigar, j*4); b->core.n_cigar = old_i+j; } if (new_cigar != new_cigar_a) free(new_cigar); return 0; } // Parses a comma-separated list of "pos", "mqual", "unmap", "cigar", and "aux" // keywords for the bam sanitizer. int bam_sanitize_options(const char *str) { int opt = 0; while (str && *str) { const char *str_start; while(*str && *str == ',') str++; for (str_start = str; *str && *str != ','; str++); int len = str - str_start; if (strncmp(str_start, "all", 3) == 0 || *str_start == '*') opt = FIX_ALL; else if (strncmp(str_start, "none", 4) == 0 || strncmp(str_start, "off", 3) == 0) opt = 0; else if (strncmp(str_start, "on", 2) == 0) // default for position sorted data opt = FIX_MQUAL | FIX_UNMAP | FIX_CIGAR | FIX_AUX; else if (strncmp(str_start, "pos", 3) == 0) opt |= FIX_POS; else if (strncmp(str_start, "mqual", 5) == 0) opt |= FIX_MQUAL; else if (strncmp(str_start, "unmap", 5) == 0) opt |= FIX_UNMAP; else if (strncmp(str_start, "cigar", 5) == 0) opt |= FIX_CIGAR; else if (strncmp(str_start, "aux", 3) == 0) opt |= FIX_AUX; else { print_error("sanitize", "Unrecognised keyword %.*s\n", len, str_start); return -1; } } return opt; } int bam_sanitize(sam_hdr_t *h, bam1_t *b, int flags) { if ((flags & FIX_POS) && b->core.tid < 0) { // RNAME * => pos 0. NB can break alignment chr/pos sort order b->core.pos = -1; if (flags & FIX_UNMAP) b->core.flag |= BAM_FUNMAP; } if ((flags & FIX_CIGAR) && !(b->core.flag & BAM_FUNMAP)) { // Mapped => unmapped correction if (b->core.pos < 0 && (flags & FIX_UNMAP)) { b->core.flag |= BAM_FUNMAP; } else { hts_pos_t cur_end, rlen = sam_hdr_tid2len(h, b->core.tid); if (b->core.pos >= rlen && (flags & FIX_UNMAP)) { b->core.flag |= BAM_FUNMAP; if (flags & FIX_POS) b->core.tid = b->core.pos = -1; } else if ((cur_end = bam_endpos(b)) > rlen) { if (bam_trim(b, rlen) < 0) return -1; } } } if (b->core.flag & BAM_FUNMAP) { // Unmapped -> cigar/qual correctoins if ((flags & FIX_CIGAR) && b->core.n_cigar > 0) clear_cigar(b); if (flags & FIX_MQUAL) b->core.qual = 0; // Remove NM, MD, CG, SM tags. if (flags & FIX_AUX) { uint8_t *from = bam_aux_first(b); uint8_t *end = b->data + b->l_data; uint8_t *to = from ? from-2 : end; #define XTAG(a) (((a)[0]<<8) + (a)[1]) while (from) { uint8_t *next = bam_aux_next(b, from); if (!next && errno != ENOENT) return -1; // Keep tag unless one of a specific set. // NB "to" always points to an aux tag start, while // "from" is after key. from -= 2; int key = (int)from[0]<<8 | from[1]; if (key != XTAG("NM") && key != XTAG("MD") && key != XTAG("CG") && key != XTAG("SM")) { ptrdiff_t len = (next ? next-2 : end) - from; if (from != to) memmove(to, from, len); to += len; } from = next; } b->l_data = to - b->data; } } return 0; } // Look for 3 tags in one pass, for efficiencies sake. // We also convert the draft tags Mm and Ml to MM and ML here. static inline void find_tags(bam1_t *b, char *t1, uint8_t **t1p, char *t2, uint8_t **t2p, char *t3, uint8_t **t3p) { *t1p = *t2p = *t3p = NULL; uint8_t *aux = bam_aux_first(b); while (aux) { if (aux[-2] == t1[0] && toupper(aux[-1]) == t1[1]) { *t1p = aux; if (islower(aux[-1])) aux[-1] = t1[1]; } else if (aux[-2] == t2[0] && toupper(aux[-1]) == t2[1]) { *t2p = aux; if (islower(aux[-1])) aux[-1] = t2[1]; } else if (aux[-2] == t3[0] && toupper(aux[-1]) == t3[1]) { *t3p = aux; if (islower(aux[-1])) aux[-1] = t3[1]; } aux = bam_aux_next(b, aux); } } // Return 5' and 3' CIGAR hard-clip counts static inline void hard_clips(bam1_t *b, int *end5, int *end3) { uint32_t *cigar = bam_get_cigar(b); int ncigar = b->core.n_cigar; int endL = 0, endR = 0, nh = 0; if (ncigar && bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) endL = bam_cigar_oplen(cigar[0]), nh=1; if (ncigar > nh && bam_cigar_op(cigar[ncigar-1]) == BAM_CHARD_CLIP) endR = bam_cigar_oplen(cigar[ncigar-1]); if (b->core.flag & BAM_FREVERSE) { *end5 = endR; *end3 = endL; } else { *end5 = endL; *end3 = endR; } } // Get MM, ML and MN tags, and 5' and 3' hard-clip lengths. // MNi is integer copy of MN, or -1 if absent/invalid void get_mod_info(bam1_t *b, uint8_t **MM, uint8_t **ML, uint8_t **MN, int *MNi, int *end5, int *end3) { find_tags(b, "MM", MM, "ML", ML, "MN", MN); if (*MN) { int save_errno = errno; errno = 0; *MNi = bam_aux2i(*MN); if (errno == EINVAL) *MNi = -1; errno = save_errno; } else { *MNi = -1; } if (*MM) hard_clips(b, end5, end3); else *end5 = *end3 = 0; // don't need if MM not found } typedef struct MM_state { // tags found on "pre" BAM uint8_t *MM, *ML, *MN; } MM_state; uint8_t *MN_enc(uint8_t *tag, uint32_t n) { if (n > UINT16_MAX) { tag[0] = 'I'; i32_to_le(n, tag+1); tag += 5; } else if (n > UINT8_MAX) { tag[0] = 'S'; i16_to_le(n, tag+1); tag += 3; } else { *tag++ = 'C'; *tag++ = n; } return tag; } // Trim 5'/3' bases off MM and ML tags, using a previous sequence as a guide. int trim_MM(bam1_t *pre, bam1_t *cur, int end5, int end3, uint8_t *MM, uint8_t *ML, uint8_t *MN) { // Count number of bases int counts5[16] = {0}, counts3[16] = {0}; uint8_t *seq = bam_get_seq(pre); int i; for (i = 0; i < end5; i++) counts5[bam_seqi(seq, i)]++; memcpy(counts3, counts5, 16 * sizeof(*counts3)); for (; i < pre->core.l_qseq - end3; i++) counts3[bam_seqi(seq, i)]++; // "p" is position in pre. // "q" is position in cur. // Hence move up "p" to start and copy from there to "q". uint8_t *MMp, *MLp, *MMq = NULL, *MLq = NULL; if (ML && ML[0] == 'B' && ML[1] == 'C') { MLp = ML+6; } else { ML = MLp = NULL; } MMq = MM+1; MLq = MLp; for (MMp = MM+1; *MMp; ) { int fundamental = seq_nt16_table[*MMp]; while (*MMp && *MMp != ',') *MMq++ = *MMp++; if (*MMp) *MMq++ = *MMp++; // Now on comma separated list for MM and BC array for ML. Skip int n = 0; while (*MMp != ';' && n < counts5[fundamental]) { char *endptr; long delta = strtol((char *)MMp, &endptr, 10); if (counts5[fundamental] - n > delta) { // Skip entire delta in MM and ML. // Eg counts[]=10, MM=3,10 ML=<10><20> => MM=10 ML=<20> n += delta+1; if(ML) MLp++; } else if (counts3[fundamental] > counts5[fundamental]) { // Shrink delta, writing MM and ML is unchanged. // Eg counts[]=3, MM=10,4 ML=<10><20> => MM=7,4 ML=<10><20> char num[50]; int l = sprintf(num, "%ld", delta - (counts5[fundamental]-n)); memcpy((char *)MMq, num, l); MMq += l; *MMq++ = *endptr; n += delta+1; if (ML) *MLq++ = *MLp++; } else { // next base mod is on boundary of 3' clip point break; } MMp = (uint8_t *)endptr; if (*MMp != ',') // error? if not ; also? break; MMp++; } // Copy while (*MMp != ';' && n < counts3[fundamental]) { char *endptr; long delta = strtol((char *)MMp, &endptr, 10); if (counts3[fundamental] - n > delta) { // Copy entire delta in MM and ML including [,;] memmove(MMq, MMp, (uint8_t *)endptr - MMp + 1); MMq += (uint8_t *)endptr - MMp + 1; n += delta+1; if (ML) *MLq++ = *MLp++; } else { // Next mod is into 3' cutoff, so can terminate MM/ML now n = counts3[fundamental]; if (ML) MLp++; } MMp = (uint8_t *)endptr; if (*MMp != ',') break; MMp++; } // Skip while (*MMp && *MMp != ';') { while (*MMp && *MMp != ',' && *MMp != ';') MMp++; if (*MMp == ',') MMp++; if (ML) MLp++; } MMq[-1] = ';'; // replaces , with ; if clipping right if (*MMp) MMp++; } MMp++; // skip nul *MMq++ = 0; // Adjust ML B array length if (ML) u32_to_le(MLq-(ML+6), ML+2); // Move MM and ML down to include their MM:Z and ML:B bits if (MM) MM-=2; if (ML) ML-=2; // Now MM/ML are start of tags, MMq/MLq are ends of edited tags, // and MMp/MLp are ends of original tags. Walk through tags taking up // any gaps // // Eg XXXXXXmmmmm--YYYlllll-ZZ (m and l are edited MM and ML tags) // => XXXXXXmmmmmYYYlllllZZ uint8_t *tag = bam_get_aux(cur), *tag_end = cur->data + cur->l_data; uint8_t *to = tag; while (tag && tag < tag_end) { if (tag[0] == 'M' && (tag[1] == 'M' || tag[1] == 'm')) { // Slow but easy memmove(to, MM, MMq-MM); // length of new tag to += MMq-MM; tag = MMp; // size of old tag } else if (tag[0] == 'M' && (tag[1] == 'L' || tag[1] == 'l')) { memmove(to, ML, MLq-ML); to += MLq-ML; tag = MLp; } else if (tag[0] == 'M' && tag[1] == 'N') { tag = bam_aux_next(cur, tag+2); // Skip it as we'll overwrite this later, although this // does change the tag order. Instead we could do: // // *to++ = 'M'; // *to++ = 'N'; // to = MN_enc(to, cur->core.l_qseq); } else { // Want aux_skip, but it's private. // So we use bam_aux_next with work-arounds. :( uint8_t *from = tag; tag = bam_aux_next(cur, tag+2); tag = tag ? tag-2 : tag_end; memmove(to, from, tag-from); to += tag-from; } } cur->l_data = to - cur->data; return 0; } // Removes base modification tags: MM, ML and MN. // This is more efficient than a series of bam_aux_remove and // bam_aux_find calls, as the previous removes shuffle the tags we've // previously found. However it's still not optimal. void delete_mod_tags(bam1_t *b) { uint8_t *tag = bam_aux_first(b), *next; uint8_t *to = tag; while (tag) { next = bam_aux_next(b, tag); if (tag[-2] == 'M' && (tag[-1] == 'M' || tag[-1] == 'm' || tag[-1] == 'L' || tag[-1] == 'l' || tag[-1] == 'N')) { // Skip. Equivalent to bam_aux_remove without multiple passes } else { // Copy. All these +/-2s are an annoyance caused by the // tag iterator pointing to the byte after the 2-letter code uint8_t *end = next ? next : b->data + b->l_data + 2; if (tag != to) memmove(to-2, tag-2, end-tag); to += end-tag; } tag = next; } b->l_data = (to-2) - b->data; } int validate_MM(bam1_t *b, hts_base_mod_state *state) { hts_base_mod mods[10]; int n, pos; while ((n = bam_next_basemod(b, state, mods, 10, &pos)) > 0) { // bam_next_basemod will trigger MM out-of-bound checks } return n; } // Fix base modification tags MM, ML and MN. // For supplementary-style alignments we may have hard-clipped the sequence // and just duplicated the MM/ML tags. Use the primary alignment to get the // clipped sequence so we can trim MM/ML accordingly. // // We call this first on primary reads with pre == NULL. This caches // MM and ML data into MM_state. // // We then call it again on secondary and/or supplementary data with // pre == the primary record and pass in the associated state. This then // validates MM/ML/MN match, and if not adjusts them if they have hard-clips // which yields consistent data. // // TODO: add sanity check on counts of base types and MM tag to ensure it's // possible. We can do this post-trimming, so we sanitize everything. // // Returns 0 on success, // -1 on failure int fix_MM(bam1_t *pre, bam1_t *cur, MM_state *state) { int end5, end3; int MNi = 0; // MN of -1 is used as indicator for no valid mods if (!pre && state) { // First time we've see this name. // Look for base modification tags and sanity check. get_mod_info(cur, &state->MM, &state->ML, &state->MN, &MNi, &end5, &end3); if (!state->MM) { delete_mod_tags(cur); return 0; } if (!end5 && !end3 && MNi <= 0) { // No MN tag, but also no clipping. Assume MM is valid if (cur->core.l_qseq) if (bam_aux_update_int(cur, "MN", cur->core.l_qseq) < 0) return -1; } else if ((end3 || end5) && cur->core.l_qseq != MNi) { // We have hard clips and MN tag, but the MN tag doesn't match // observed sequence length so it appears the hard-clipping // happened after base-mods called without updating. // Fail as this is a primary read. delete_mod_tags(cur); } // Otherwise we assume the base modifications are correct } else if (state) { // A supplementary or secondary alignment with known primary uint8_t *cur_MM = NULL, *cur_ML = NULL, *cur_MN = NULL; MNi = -1; get_mod_info(cur, &cur_MM, &cur_ML, &cur_MN, &MNi, &end5, &end3); if (!cur_MM) { delete_mod_tags(cur); return 0; } // Does MN match seq length? If so, we believe it's already valid if (MNi == cur->core.l_qseq) goto validate; // Length mismatch and/or no known length, so check vs full seq. if (pre->core.l_qseq != cur->core.l_qseq + end3 + end5) { delete_mod_tags(cur); return 0; } else if (end5 || end3) { if (MNi < 0 || MNi == pre->core.l_qseq) trim_MM(pre, cur, end5, end3, cur_MM, cur_ML, cur_MN); } // else no hard clips so MM is already valid // Set MN so we've validated it, provided seq isn't "*". // inefficient, but minimal compared to everything else if (cur->core.l_qseq) if (bam_aux_update_int(cur, "MN", cur->core.l_qseq) < 0) return -1; } validate: ; // Also validate MM length matches sequence length. This mirrors the // logic in htslib/sam_mods.c. // For now we take the inefficient approach of using bam_parse_basemod2. // Inefficient, but robust. hts_base_mod_state *mst = hts_base_mod_state_alloc(); if (!mst) return -1; enum htsLogLevel lvl = hts_get_log_level(); hts_set_log_level(HTS_LOG_OFF); if (bam_parse_basemod(cur, mst) < 0) // Maybe we want hts_log_warning still though? delete_mod_tags(cur); if (validate_MM(cur, mst) < 0) delete_mod_tags(cur); hts_set_log_level(lvl); hts_base_mod_state_free(mst); return 0; } // Ensure the b[] array is at least n. // Returns 0 on success, // -1 on failure static int grow_b_array(bam1_t **b, int *ba, int n) { if (n < *ba) return 0; bam1_t *bnew = realloc(*b, (n+=10) * sizeof(**b)); if (!bnew) return -1; *b = bnew; // bam_init1 equivalent int i; for (i = *ba; i < n; i++) memset(&(*b)[i], 0, sizeof(bam1_t)); *b = bnew; *ba = n; return 0; } // We have b[0]..b[bn-1] entries all from the same template (qname) typedef struct { bam1_t *b; int n, ba; // number used and number allocated int b_next; // b[b_next] for start of next set, -1 if unset int eof; // marker for having seen eof } bam_set; // Fetches a new batch of BAM records all containing the same name. // NB: we cache the last (non-matching) name in b[n], so we can use it to // start the next batch. // Returns the number of records on success, // <0 on failure or EOF (sam_read1 return vals) static int next_template(samFile *in, sam_hdr_t *header, bam_set *bs, int sanitize_flags) { int result; if (bs->eof) return -1; // First time through, prime the template name if (bs->b_next < 0) { if (grow_b_array(&bs->b, &bs->ba, 1) < 0) return -2; result = sam_read1(in, header, &bs->b[0]); if (result < 0) return result; if (bam_sanitize(header, &bs->b[0], sanitize_flags) < 0) return -2; } else { // Otherwise use the previous template name read bam1_t btmp = bs->b[0]; bs->b[0] = bs->b[bs->b_next]; bs->b[bs->b_next] = btmp; // For ->{,l_,m_}data } bs->n = 1; // Now keep reading until we find a read that mismatches or we hit eof. char *name = bam_get_qname(&bs->b[0]); for (;;) { if (grow_b_array(&bs->b, &bs->ba, bs->n+1) < 0) return -2; result = sam_read1(in, header, &bs->b[bs->n]); if (result < -1) return result; if (result < 0) { bs->eof = 1; bs->b_next = -1; break; } else { if (bam_sanitize(header, &bs->b[bs->n], sanitize_flags) < 0) return -2; bs->b_next = bs->n; if (strcmp(name, bam_get_qname(&bs->b[bs->n])) != 0) break; } bs->n++; } return bs->n; } // currently, this function ONLY works if each read has one hit // // Returns 0 on success, // >0 on failure static int bam_mating_core(samFile *in, samFile *out, int remove_reads, int proper_pair_check, int add_ct, int do_mate_scoring, char *arg_list, int no_pg, int sanitize_flags, int base_mods) { sam_hdr_t *header; int result, n; kstring_t str = KS_INITIALIZE; bam_set bs = {NULL, 0, 0, -1, 0}; header = sam_hdr_read(in); if (header == NULL) { fprintf(stderr, "[bam_mating_core] ERROR: Couldn't read header\n"); return 1; } // Accept unknown, unsorted, or queryname sort order, but error on coordinate sorted. if (!sam_hdr_find_tag_hd(header, "SO", &str) && str.s && !strcmp(str.s, "coordinate")) { fprintf(stderr, "[bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.\n"); goto fail; } ks_free(&str); if (!no_pg && sam_hdr_add_pg(header, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) goto fail; if (sam_hdr_write(out, header) < 0) goto write_fail; // Iterate template by template fetching bs->n records at a time while ((result = next_template(in, header, &bs, sanitize_flags)) >= 0) { bam1_t *cur = NULL, *pre = NULL, *rnum[2] = {NULL, NULL}; int prev = -1, curr = -1; hts_pos_t pre_end = 0, cur_end = 0; // Find and fix up primary alignments MM_state state[2]; for (n = 0; n < bs.n; n++) { int is_r2 = (bs.b[n].core.flag & BAM_FREAD2) != 0; if (bs.b[n].core.flag & (BAM_FSECONDARY | BAM_FSUPPLEMENTARY)) continue; if (base_mods) if (fix_MM(NULL, &bs.b[n], &state[is_r2]) < 0) goto fail; if (!pre) { pre = &bs.b[prev = n]; rnum[(pre->core.flag & BAM_FREAD2) != 0] = pre; pre_end = (pre->core.flag & BAM_FUNMAP) == 0 ? bam_endpos(pre) : 0; continue; } // Note, more than 2 primary alignments will use 'curr' as last cur = &bs.b[curr = n]; rnum[(cur->core.flag & BAM_FREAD2) != 0] = cur; cur_end = (cur->core.flag & BAM_FUNMAP) == 0 ? bam_endpos(cur) : 0; pre->core.flag |= BAM_FPAIRED; cur->core.flag |= BAM_FPAIRED; if (sync_mate(pre, cur)) goto fail; // If safe set TLEN/ISIZE if (pre->core.tid == cur->core.tid && !(cur->core.flag & (BAM_FUNMAP | BAM_FMUNMAP)) && !(pre->core.flag & (BAM_FUNMAP | BAM_FMUNMAP))) { hts_pos_t cur5, pre5; cur5 = (cur->core.flag & BAM_FREVERSE) ? cur_end : cur->core.pos; pre5 = (pre->core.flag & BAM_FREVERSE) ? pre_end : pre->core.pos; cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5; } else { cur->core.isize = pre->core.isize = 0; } if (add_ct) bam_template_cigar(pre, cur, &str); // TODO: Add code to properly check if read is in a proper // pair based on ISIZE distribution if (proper_pair_check && !plausibly_properly_paired(pre,cur)) { pre->core.flag &= ~BAM_FPROPER_PAIR; cur->core.flag &= ~BAM_FPROPER_PAIR; } if (do_mate_scoring) { if ((add_mate_score(pre, cur) == -1) || (add_mate_score(cur, pre) == -1)) { fprintf(stderr, "[bam_mating_core] ERROR: " "unable to add mate score.\n"); goto fail; } } // If we have to remove reads make sure we do it in a way that // doesn't create orphans with bad flags if (remove_reads) { if (pre->core.flag&BAM_FUNMAP) cur->core.flag &= ~(BAM_FMREVERSE|BAM_FPROPER_PAIR); if (cur->core.flag&BAM_FUNMAP) pre->core.flag &= ~(BAM_FMREVERSE|BAM_FPROPER_PAIR); } } // Handle unpaired primary data if (!cur && pre) { pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0; pre->core.flag &= ~(BAM_FMREVERSE|BAM_FPROPER_PAIR); } // Now process secondary and supplementary alignments for (n = 0; n < bs.n; n++) { if (!(bs.b[n].core.flag & (BAM_FSECONDARY|BAM_FSUPPLEMENTARY))) { // primary continue; } // Secondary or supplementary int is_r2 = (bs.b[n].core.flag & BAM_FREAD2) != 0; bam1_t *primary = rnum[is_r2]; if (primary) { if (base_mods) fix_MM(primary, &bs.b[n], &state[is_r2]); } else { // Record with base modifications but no known primary //fprintf(stderr, "Unpaired secondary or supplementary\n"); if (base_mods) fix_MM(NULL, &bs.b[n], NULL); } } // Finally having curated everything, write out all records in their // original ordering for (n = 0; n < bs.n; n++) { bam1_t *cur = &bs.b[n]; // We may remove unmapped and secondary alignments if (remove_reads && (cur->core.flag & (BAM_FSECONDARY|BAM_FUNMAP))) continue; if (sam_write1(out, header, cur) < 0) goto write_fail; } } if (result < -1) goto read_fail; sam_hdr_destroy(header); for (n = 0; n < bs.ba; n++) free(bs.b[n].data); free(bs.b); ks_free(&str); return 0; read_fail: print_error("fixmate", "Couldn't read from input file"); goto fail; write_fail: print_error_errno("fixmate", "Couldn't write to output file"); fail: sam_hdr_destroy(header); for (n = 0; n < bs.ba; n++) free(bs.b[n].data); free(bs.b); ks_free(&str); return 1; } void usage(FILE* where) { fprintf(where, "Usage: samtools fixmate \n" "Options:\n" " -r Remove unmapped reads and secondary alignments\n" " -p Disable FR proper pair check\n" " -c Add template cigar ct tag\n" " -m Add mate score tag\n" " -u Uncompressed output\n" " -z, --sanitize FLAG[,FLAG]\n" " Sanitize alignment fields [defaults to all types]\n" " -M Fix base modification tags (MM/ML/MN)\n" " --no-PG do not add a PG line\n"); sam_global_opt_help(where, "-.O..@-."); fprintf(where, "\n" "As elsewhere in samtools, use '-' as the filename for stdin/stdout. The input\n" "file must be grouped by read name (e.g. sorted by name). Coordinated sorted\n" "input is not accepted.\n"); } int bam_mating(int argc, char *argv[]) { htsThreadPool p = {NULL, 0}; samFile *in = NULL, *out = NULL; int c, remove_reads = 0, proper_pair_check = 1, add_ct = 0, res = 1, mate_score = 0, no_pg = 0, sanitize_flags = FIX_ALL, base_mods = 0; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; char wmode[4] = {'w', 'b', 0, 0}; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'), {"no-PG", no_argument, NULL, 1}, { NULL, 0, NULL, 0 } }; char *arg_list = NULL; // parse args if (argc == 1) { usage(stdout); return 0; } while ((c = getopt_long(argc, argv, "rpcmMO:@:uz:", lopts, NULL)) >= 0) { switch (c) { case 'r': remove_reads = 1; break; case 'p': proper_pair_check = 0; break; case 'c': add_ct = 1; break; case 'm': mate_score = 1; break; case 'M': base_mods = 1; break; case 'u': wmode[2] = '0'; break; case 1: no_pg = 1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage(stderr); goto fail; case 'z': if ((sanitize_flags = bam_sanitize_options(optarg)) < 0) exit(1); break; } } if (optind+1 >= argc) { usage(stderr); goto fail; } if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) goto fail; // init if ((in = sam_open_format(argv[optind], "rb", &ga.in)) == NULL) { print_error_errno("fixmate", "cannot open input file"); goto fail; } sam_open_mode(wmode+1, argv[optind+1], NULL); if ((out = sam_open_format(argv[optind+1], wmode, &ga.out)) == NULL) { print_error_errno("fixmate", "cannot open output file"); goto fail; } if (ga.nthreads > 0) { if (!(p.pool = hts_tpool_init(ga.nthreads))) { fprintf(stderr, "Error creating thread pool\n"); goto fail; } hts_set_opt(in, HTS_OPT_THREAD_POOL, &p); hts_set_opt(out, HTS_OPT_THREAD_POOL, &p); } // run res = bam_mating_core(in, out, remove_reads, proper_pair_check, add_ct, mate_score, arg_list, no_pg, sanitize_flags, base_mods); // cleanup sam_close(in); if (sam_close(out) < 0) { fprintf(stderr, "[bam_mating] error while closing output file\n"); res = 1; } if (p.pool) hts_tpool_destroy(p.pool); free(arg_list); sam_global_args_free(&ga); return res; fail: if (in) sam_close(in); if (out) sam_close(out); if (p.pool) hts_tpool_destroy(p.pool); free(arg_list); sam_global_args_free(&ga); return 1; } pysam-0.23.0/samtools/bam_mate.c.pysam.c000066400000000000000000001207201475062545500200670ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_mate.c -- fix mate pairing information and clean up flags. Copyright (C) 2009, 2011-2017, 2019, 2022, 2024 Genome Research Ltd. Portions copyright (C) 2011 Broad Institute. Portions copyright (C) 2012 Peter Cock, The James Hutton Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notices and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "htslib/thread_pool.h" #include "sam_opts.h" #include "htslib/kstring.h" #include "htslib/sam.h" #include "samtools.h" #define MD_MIN_QUALITY 15 /* * This function calculates ct tag for two bams, it assumes they are from the same template and * writes the tag to the first read in position terms. */ static void bam_template_cigar(bam1_t *b1, bam1_t *b2, kstring_t *str) { bam1_t *swap; int i; hts_pos_t end; uint32_t *cigar; str->l = 0; if (b1->core.tid != b2->core.tid || b1->core.tid < 0 || b1->core.pos < 0 || b2->core.pos < 0 || b1->core.flag&BAM_FUNMAP || b2->core.flag&BAM_FUNMAP) return; // coordinateless or not on the same chr; skip if (b1->core.pos > b2->core.pos) swap = b1, b1 = b2, b2 = swap; // make sure b1 has a smaller coordinate kputc((b1->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index kputc((b1->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand for (i = 0, cigar = bam_get_cigar(b1); i < b1->core.n_cigar; ++i) { kputw(bam_cigar_oplen(cigar[i]), str); kputc(bam_cigar_opchr(cigar[i]), str); } end = bam_endpos(b1); kputw(b2->core.pos - end, str); kputc('T', str); kputc((b2->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index kputc((b2->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand for (i = 0, cigar = bam_get_cigar(b2); i < b2->core.n_cigar; ++i) { kputw(bam_cigar_oplen(cigar[i]), str); kputc(bam_cigar_opchr(cigar[i]), str); } uint8_t* data; if ((data = bam_aux_get(b1,"ct")) != NULL) bam_aux_del(b1, data); if ((data = bam_aux_get(b2,"ct")) != NULL) bam_aux_del(b2, data); bam_aux_append(b1, "ct", 'Z', str->l+1, (uint8_t*)str->s); } /* * What This Program is Supposed To Do: * Fill in mate coordinates, ISIZE and mate related flags from a name-sorted * alignment. * * How We Handle Input * * Secondary and supplementary Reads: * -write to output unchanged * All Reads: * -if pos == 0 (1 based), tid == -1 set UNMAPPED flag * single Reads: * -if pos == 0 (1 based), tid == -1, or UNMAPPED then set UNMAPPED, pos = 0, * tid = -1 * -clear bad flags (MREVERSE, PROPER_PAIR) * -set mpos = 0 (1 based), mtid = -1 and isize = 0 * -write to output * Paired Reads: * -if read is unmapped and mate is not, set pos and tid to equal that of mate * -sync mate flags (MREVERSE, MUNMAPPED), mpos, mtid * -recalculate ISIZE if possible, otherwise set it to 0 * -optionally clear PROPER_PAIR flag from reads where mapping or orientation * indicate this is not possible (Illumina orientation only) * -calculate ct and apply to lowest positioned read * -write to output * Limitations * -Does not handle tandem reads * -Should mark supplementary reads the same as primary. * Notes * -CT definition appears to be something else in spec, this was in here before * I started tampering with it, anyone know what is going on here? To work * around this I have demoted the CT this tool generates to ct. */ static void sync_unmapped_pos_inner(bam1_t* src, bam1_t* dest) { if ((dest->core.flag & BAM_FUNMAP) && !(src->core.flag & BAM_FUNMAP)) { // Set unmapped read's RNAME and POS to those of its mapped mate // (recommended best practice, ensures if coord sort will be together) dest->core.tid = src->core.tid; dest->core.pos = src->core.pos; } } static void sync_mate_inner(bam1_t* src, bam1_t* dest) { // sync mate pos information dest->core.mtid = src->core.tid; dest->core.mpos = src->core.pos; // sync flag info if (src->core.flag&BAM_FREVERSE) dest->core.flag |= BAM_FMREVERSE; else dest->core.flag &= ~BAM_FMREVERSE; if (src->core.flag & BAM_FUNMAP) { dest->core.flag |= BAM_FMUNMAP; } } // Is it plausible that these reads are properly paired? // Can't really give definitive answer without checking isize static bool plausibly_properly_paired(bam1_t* a, bam1_t* b) { if ((a->core.flag & BAM_FUNMAP) || (b->core.flag & BAM_FUNMAP)) return false; assert(a->core.tid >= 0); // This should never happen if FUNMAP is set correctly if (a->core.tid != b->core.tid) return false; bam1_t* first = a; bam1_t* second = b; hts_pos_t a_pos = a->core.flag&BAM_FREVERSE ? bam_endpos(a) : a->core.pos; hts_pos_t b_pos = b->core.flag&BAM_FREVERSE ? bam_endpos(b) : b->core.pos; if (a_pos > b_pos) { first = b; second = a; } else { first = a; second = b; } if (!(first->core.flag&BAM_FREVERSE) && (second->core.flag&BAM_FREVERSE)) return true; else return false; } // Returns 0 on success, -1 on failure. static int bam_format_cigar(const bam1_t* b, kstring_t* str) { // An empty cigar is a special case return "*" rather than "" if (b->core.n_cigar == 0) { return (kputc('*', str) == EOF) ? -1 : 0; } const uint32_t *cigar = bam_get_cigar(b); uint32_t i; for (i = 0; i < b->core.n_cigar; ++i) { if (kputw(bam_cigar_oplen(cigar[i]), str) == EOF) return -1; if (kputc(bam_cigar_opchr(cigar[i]), str) == EOF) return -1; } return 0; } // Returns 0 on success, -1 on failure. static int sync_mq_mc(bam1_t* src, bam1_t* dest) { if ( (src->core.flag & BAM_FUNMAP) == 0 ) { // If mapped // Copy Mate Mapping Quality uint32_t mq = src->core.qual; uint8_t* data; if ((data = bam_aux_get(dest,"MQ")) != NULL) { bam_aux_del(dest, data); } bam_aux_append(dest, "MQ", 'i', sizeof(uint32_t), (uint8_t*)&mq); } // Copy mate cigar if either read is mapped if ( (src->core.flag & BAM_FUNMAP) == 0 || (dest->core.flag & BAM_FUNMAP) == 0 ) { uint8_t* data_mc; if ((data_mc = bam_aux_get(dest,"MC")) != NULL) { bam_aux_del(dest, data_mc); } // Convert cigar to string kstring_t mc = { 0, 0, NULL }; if (bam_format_cigar(src, &mc) < 0) return -1; bam_aux_append(dest, "MC", 'Z', ks_len(&mc)+1, (uint8_t*)ks_str(&mc)); free(mc.s); } return 0; } // Copy flags. // Returns 0 on success, -1 on failure. static int sync_mate(bam1_t* a, bam1_t* b) { sync_unmapped_pos_inner(a,b); sync_unmapped_pos_inner(b,a); sync_mate_inner(a,b); sync_mate_inner(b,a); if (sync_mq_mc(a,b) < 0) return -1; if (sync_mq_mc(b,a) < 0) return -1; return 0; } static uint32_t calc_mate_score(bam1_t *b) { uint32_t score = 0; uint8_t *qual = bam_get_qual(b); int i; for (i = 0; i < b->core.l_qseq; i++) { if (qual[i] >= MD_MIN_QUALITY) score += qual[i]; } return score; } static int add_mate_score(bam1_t *src, bam1_t *dest) { uint8_t *data_ms; uint32_t mate_score = calc_mate_score(src); if ((data_ms = bam_aux_get(dest, "ms")) != NULL) { bam_aux_del(dest, data_ms); } if (bam_aux_append(dest, "ms", 'i', sizeof(uint32_t), (uint8_t*)&mate_score) == -1) { return -1; } return 0; } // Completely delete the CIGAR field static void clear_cigar(bam1_t *b) { memmove(bam_get_cigar(b), bam_get_seq(b), b->data + b->l_data - bam_get_seq(b)); b->l_data -= 4*b->core.n_cigar; b->core.n_cigar = 0; } // Trim a CIGAR field to end on reference position "end". Remaining bases // are turned to soft clips. static int bam_trim(bam1_t *b, hts_pos_t end) { hts_pos_t pos = b->core.pos; int n_cigar = b->core.n_cigar, i; uint32_t new_cigar_a[1024]; uint32_t *new_cigar = new_cigar_a; uint32_t *cigar = bam_get_cigar(b); // Find end of alignment or end of ref int op = 0, oplen = 0; for (i = 0; i < n_cigar; i++) { op = bam_cigar_op(cigar[i]); oplen = bam_cigar_oplen(cigar[i]); if (!(bam_cigar_type(op) & 2)) continue; pos += oplen; if (pos > end) break; } if (i == n_cigar) // looks fine already return 0; int old_i = i, j = 0; // At worst we grow by 1 element (eg 100M -> 70M30S) if (n_cigar-i >= 1024-1) { new_cigar = malloc(4*(n_cigar-i+1)); if (!new_cigar) return -1; } // We fill out to new_cigar from here on. if (pos-oplen < end) { // Partial CIGAR op? Split existing tag. cigar[old_i++] = bam_cigar_gen(end - (pos-oplen), op); new_cigar[j++] = bam_cigar_gen(pos-end, BAM_CSOFT_CLIP); } else if (pos > end) { // entirely off the chromosome; this will trigger CIGAR *, MQUAL 0 b->core.flag |= BAM_FUNMAP; b->core.flag &= ~BAM_FPROPER_PAIR; } else { // CIGAR op started on the trim junction new_cigar[j++] = bam_cigar_gen(oplen, BAM_CSOFT_CLIP); } // Replace trailing elements. for (i++; i < n_cigar; i++) { op = bam_cigar_op(cigar[i]); oplen = bam_cigar_oplen(cigar[i]); if (op == BAM_CHARD_CLIP) { new_cigar[j++] = cigar[i]; } else { new_cigar[j-1] = bam_cigar_gen(bam_cigar_oplen(new_cigar[j-1]) + oplen, BAM_CSOFT_CLIP); } } // We now have cigar[0..old_i-1] for existing CIGAR // and new_cigar[0..j-1] for new CIGAR trailing component. if (old_i+j == n_cigar) { // Fits and no data move needed memcpy(&cigar[old_i], new_cigar, j*4); } else { uint8_t *seq_old = bam_get_seq(b); uint8_t *aux_end = b->data + b->l_data; int nshift; if (old_i+j < n_cigar) { // Smaller, and can move data down nshift = -4*(n_cigar - (old_i+j)); } else { // Bigger, so grow BAM and move data up nshift = 4*(old_i+j - n_cigar); // FIXME: make htslib's sam_realloc_bam_data public if (b->l_data + nshift > b->m_data) { uint8_t *new_data = realloc(b->data, b->l_data + nshift); if (!new_data) { if (new_cigar != new_cigar_a) free(new_cigar); return -1; } b->m_data = b->l_data + nshift; if (b->data != new_data) { b->data = new_data; seq_old = bam_get_seq(b); aux_end = b->data + b->l_data; cigar = bam_get_cigar(b); } } } memmove(seq_old+nshift, seq_old, aux_end - seq_old); b->l_data += nshift; memcpy(&cigar[old_i], new_cigar, j*4); b->core.n_cigar = old_i+j; } if (new_cigar != new_cigar_a) free(new_cigar); return 0; } // Parses a comma-separated list of "pos", "mqual", "unmap", "cigar", and "aux" // keywords for the bam sanitizer. int bam_sanitize_options(const char *str) { int opt = 0; while (str && *str) { const char *str_start; while(*str && *str == ',') str++; for (str_start = str; *str && *str != ','; str++); int len = str - str_start; if (strncmp(str_start, "all", 3) == 0 || *str_start == '*') opt = FIX_ALL; else if (strncmp(str_start, "none", 4) == 0 || strncmp(str_start, "off", 3) == 0) opt = 0; else if (strncmp(str_start, "on", 2) == 0) // default for position sorted data opt = FIX_MQUAL | FIX_UNMAP | FIX_CIGAR | FIX_AUX; else if (strncmp(str_start, "pos", 3) == 0) opt |= FIX_POS; else if (strncmp(str_start, "mqual", 5) == 0) opt |= FIX_MQUAL; else if (strncmp(str_start, "unmap", 5) == 0) opt |= FIX_UNMAP; else if (strncmp(str_start, "cigar", 5) == 0) opt |= FIX_CIGAR; else if (strncmp(str_start, "aux", 3) == 0) opt |= FIX_AUX; else { print_error("sanitize", "Unrecognised keyword %.*s\n", len, str_start); return -1; } } return opt; } int bam_sanitize(sam_hdr_t *h, bam1_t *b, int flags) { if ((flags & FIX_POS) && b->core.tid < 0) { // RNAME * => pos 0. NB can break alignment chr/pos sort order b->core.pos = -1; if (flags & FIX_UNMAP) b->core.flag |= BAM_FUNMAP; } if ((flags & FIX_CIGAR) && !(b->core.flag & BAM_FUNMAP)) { // Mapped => unmapped correction if (b->core.pos < 0 && (flags & FIX_UNMAP)) { b->core.flag |= BAM_FUNMAP; } else { hts_pos_t cur_end, rlen = sam_hdr_tid2len(h, b->core.tid); if (b->core.pos >= rlen && (flags & FIX_UNMAP)) { b->core.flag |= BAM_FUNMAP; if (flags & FIX_POS) b->core.tid = b->core.pos = -1; } else if ((cur_end = bam_endpos(b)) > rlen) { if (bam_trim(b, rlen) < 0) return -1; } } } if (b->core.flag & BAM_FUNMAP) { // Unmapped -> cigar/qual correctoins if ((flags & FIX_CIGAR) && b->core.n_cigar > 0) clear_cigar(b); if (flags & FIX_MQUAL) b->core.qual = 0; // Remove NM, MD, CG, SM tags. if (flags & FIX_AUX) { uint8_t *from = bam_aux_first(b); uint8_t *end = b->data + b->l_data; uint8_t *to = from ? from-2 : end; #define XTAG(a) (((a)[0]<<8) + (a)[1]) while (from) { uint8_t *next = bam_aux_next(b, from); if (!next && errno != ENOENT) return -1; // Keep tag unless one of a specific set. // NB "to" always points to an aux tag start, while // "from" is after key. from -= 2; int key = (int)from[0]<<8 | from[1]; if (key != XTAG("NM") && key != XTAG("MD") && key != XTAG("CG") && key != XTAG("SM")) { ptrdiff_t len = (next ? next-2 : end) - from; if (from != to) memmove(to, from, len); to += len; } from = next; } b->l_data = to - b->data; } } return 0; } // Look for 3 tags in one pass, for efficiencies sake. // We also convert the draft tags Mm and Ml to MM and ML here. static inline void find_tags(bam1_t *b, char *t1, uint8_t **t1p, char *t2, uint8_t **t2p, char *t3, uint8_t **t3p) { *t1p = *t2p = *t3p = NULL; uint8_t *aux = bam_aux_first(b); while (aux) { if (aux[-2] == t1[0] && toupper(aux[-1]) == t1[1]) { *t1p = aux; if (islower(aux[-1])) aux[-1] = t1[1]; } else if (aux[-2] == t2[0] && toupper(aux[-1]) == t2[1]) { *t2p = aux; if (islower(aux[-1])) aux[-1] = t2[1]; } else if (aux[-2] == t3[0] && toupper(aux[-1]) == t3[1]) { *t3p = aux; if (islower(aux[-1])) aux[-1] = t3[1]; } aux = bam_aux_next(b, aux); } } // Return 5' and 3' CIGAR hard-clip counts static inline void hard_clips(bam1_t *b, int *end5, int *end3) { uint32_t *cigar = bam_get_cigar(b); int ncigar = b->core.n_cigar; int endL = 0, endR = 0, nh = 0; if (ncigar && bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) endL = bam_cigar_oplen(cigar[0]), nh=1; if (ncigar > nh && bam_cigar_op(cigar[ncigar-1]) == BAM_CHARD_CLIP) endR = bam_cigar_oplen(cigar[ncigar-1]); if (b->core.flag & BAM_FREVERSE) { *end5 = endR; *end3 = endL; } else { *end5 = endL; *end3 = endR; } } // Get MM, ML and MN tags, and 5' and 3' hard-clip lengths. // MNi is integer copy of MN, or -1 if absent/invalid void get_mod_info(bam1_t *b, uint8_t **MM, uint8_t **ML, uint8_t **MN, int *MNi, int *end5, int *end3) { find_tags(b, "MM", MM, "ML", ML, "MN", MN); if (*MN) { int save_errno = errno; errno = 0; *MNi = bam_aux2i(*MN); if (errno == EINVAL) *MNi = -1; errno = save_errno; } else { *MNi = -1; } if (*MM) hard_clips(b, end5, end3); else *end5 = *end3 = 0; // don't need if MM not found } typedef struct MM_state { // tags found on "pre" BAM uint8_t *MM, *ML, *MN; } MM_state; uint8_t *MN_enc(uint8_t *tag, uint32_t n) { if (n > UINT16_MAX) { tag[0] = 'I'; i32_to_le(n, tag+1); tag += 5; } else if (n > UINT8_MAX) { tag[0] = 'S'; i16_to_le(n, tag+1); tag += 3; } else { *tag++ = 'C'; *tag++ = n; } return tag; } // Trim 5'/3' bases off MM and ML tags, using a previous sequence as a guide. int trim_MM(bam1_t *pre, bam1_t *cur, int end5, int end3, uint8_t *MM, uint8_t *ML, uint8_t *MN) { // Count number of bases int counts5[16] = {0}, counts3[16] = {0}; uint8_t *seq = bam_get_seq(pre); int i; for (i = 0; i < end5; i++) counts5[bam_seqi(seq, i)]++; memcpy(counts3, counts5, 16 * sizeof(*counts3)); for (; i < pre->core.l_qseq - end3; i++) counts3[bam_seqi(seq, i)]++; // "p" is position in pre. // "q" is position in cur. // Hence move up "p" to start and copy from there to "q". uint8_t *MMp, *MLp, *MMq = NULL, *MLq = NULL; if (ML && ML[0] == 'B' && ML[1] == 'C') { MLp = ML+6; } else { ML = MLp = NULL; } MMq = MM+1; MLq = MLp; for (MMp = MM+1; *MMp; ) { int fundamental = seq_nt16_table[*MMp]; while (*MMp && *MMp != ',') *MMq++ = *MMp++; if (*MMp) *MMq++ = *MMp++; // Now on comma separated list for MM and BC array for ML. Skip int n = 0; while (*MMp != ';' && n < counts5[fundamental]) { char *endptr; long delta = strtol((char *)MMp, &endptr, 10); if (counts5[fundamental] - n > delta) { // Skip entire delta in MM and ML. // Eg counts[]=10, MM=3,10 ML=<10><20> => MM=10 ML=<20> n += delta+1; if(ML) MLp++; } else if (counts3[fundamental] > counts5[fundamental]) { // Shrink delta, writing MM and ML is unchanged. // Eg counts[]=3, MM=10,4 ML=<10><20> => MM=7,4 ML=<10><20> char num[50]; int l = sprintf(num, "%ld", delta - (counts5[fundamental]-n)); memcpy((char *)MMq, num, l); MMq += l; *MMq++ = *endptr; n += delta+1; if (ML) *MLq++ = *MLp++; } else { // next base mod is on boundary of 3' clip point break; } MMp = (uint8_t *)endptr; if (*MMp != ',') // error? if not ; also? break; MMp++; } // Copy while (*MMp != ';' && n < counts3[fundamental]) { char *endptr; long delta = strtol((char *)MMp, &endptr, 10); if (counts3[fundamental] - n > delta) { // Copy entire delta in MM and ML including [,;] memmove(MMq, MMp, (uint8_t *)endptr - MMp + 1); MMq += (uint8_t *)endptr - MMp + 1; n += delta+1; if (ML) *MLq++ = *MLp++; } else { // Next mod is into 3' cutoff, so can terminate MM/ML now n = counts3[fundamental]; if (ML) MLp++; } MMp = (uint8_t *)endptr; if (*MMp != ',') break; MMp++; } // Skip while (*MMp && *MMp != ';') { while (*MMp && *MMp != ',' && *MMp != ';') MMp++; if (*MMp == ',') MMp++; if (ML) MLp++; } MMq[-1] = ';'; // replaces , with ; if clipping right if (*MMp) MMp++; } MMp++; // skip nul *MMq++ = 0; // Adjust ML B array length if (ML) u32_to_le(MLq-(ML+6), ML+2); // Move MM and ML down to include their MM:Z and ML:B bits if (MM) MM-=2; if (ML) ML-=2; // Now MM/ML are start of tags, MMq/MLq are ends of edited tags, // and MMp/MLp are ends of original tags. Walk through tags taking up // any gaps // // Eg XXXXXXmmmmm--YYYlllll-ZZ (m and l are edited MM and ML tags) // => XXXXXXmmmmmYYYlllllZZ uint8_t *tag = bam_get_aux(cur), *tag_end = cur->data + cur->l_data; uint8_t *to = tag; while (tag && tag < tag_end) { if (tag[0] == 'M' && (tag[1] == 'M' || tag[1] == 'm')) { // Slow but easy memmove(to, MM, MMq-MM); // length of new tag to += MMq-MM; tag = MMp; // size of old tag } else if (tag[0] == 'M' && (tag[1] == 'L' || tag[1] == 'l')) { memmove(to, ML, MLq-ML); to += MLq-ML; tag = MLp; } else if (tag[0] == 'M' && tag[1] == 'N') { tag = bam_aux_next(cur, tag+2); // Skip it as we'll overwrite this later, although this // does change the tag order. Instead we could do: // // *to++ = 'M'; // *to++ = 'N'; // to = MN_enc(to, cur->core.l_qseq); } else { // Want aux_skip, but it's private. // So we use bam_aux_next with work-arounds. :( uint8_t *from = tag; tag = bam_aux_next(cur, tag+2); tag = tag ? tag-2 : tag_end; memmove(to, from, tag-from); to += tag-from; } } cur->l_data = to - cur->data; return 0; } // Removes base modification tags: MM, ML and MN. // This is more efficient than a series of bam_aux_remove and // bam_aux_find calls, as the previous removes shuffle the tags we've // previously found. However it's still not optimal. void delete_mod_tags(bam1_t *b) { uint8_t *tag = bam_aux_first(b), *next; uint8_t *to = tag; while (tag) { next = bam_aux_next(b, tag); if (tag[-2] == 'M' && (tag[-1] == 'M' || tag[-1] == 'm' || tag[-1] == 'L' || tag[-1] == 'l' || tag[-1] == 'N')) { // Skip. Equivalent to bam_aux_remove without multiple passes } else { // Copy. All these +/-2s are an annoyance caused by the // tag iterator pointing to the byte after the 2-letter code uint8_t *end = next ? next : b->data + b->l_data + 2; if (tag != to) memmove(to-2, tag-2, end-tag); to += end-tag; } tag = next; } b->l_data = (to-2) - b->data; } int validate_MM(bam1_t *b, hts_base_mod_state *state) { hts_base_mod mods[10]; int n, pos; while ((n = bam_next_basemod(b, state, mods, 10, &pos)) > 0) { // bam_next_basemod will trigger MM out-of-bound checks } return n; } // Fix base modification tags MM, ML and MN. // For supplementary-style alignments we may have hard-clipped the sequence // and just duplicated the MM/ML tags. Use the primary alignment to get the // clipped sequence so we can trim MM/ML accordingly. // // We call this first on primary reads with pre == NULL. This caches // MM and ML data into MM_state. // // We then call it again on secondary and/or supplementary data with // pre == the primary record and pass in the associated state. This then // validates MM/ML/MN match, and if not adjusts them if they have hard-clips // which yields consistent data. // // TODO: add sanity check on counts of base types and MM tag to ensure it's // possible. We can do this post-trimming, so we sanitize everything. // // Returns 0 on success, // -1 on failure int fix_MM(bam1_t *pre, bam1_t *cur, MM_state *state) { int end5, end3; int MNi = 0; // MN of -1 is used as indicator for no valid mods if (!pre && state) { // First time we've see this name. // Look for base modification tags and sanity check. get_mod_info(cur, &state->MM, &state->ML, &state->MN, &MNi, &end5, &end3); if (!state->MM) { delete_mod_tags(cur); return 0; } if (!end5 && !end3 && MNi <= 0) { // No MN tag, but also no clipping. Assume MM is valid if (cur->core.l_qseq) if (bam_aux_update_int(cur, "MN", cur->core.l_qseq) < 0) return -1; } else if ((end3 || end5) && cur->core.l_qseq != MNi) { // We have hard clips and MN tag, but the MN tag doesn't match // observed sequence length so it appears the hard-clipping // happened after base-mods called without updating. // Fail as this is a primary read. delete_mod_tags(cur); } // Otherwise we assume the base modifications are correct } else if (state) { // A supplementary or secondary alignment with known primary uint8_t *cur_MM = NULL, *cur_ML = NULL, *cur_MN = NULL; MNi = -1; get_mod_info(cur, &cur_MM, &cur_ML, &cur_MN, &MNi, &end5, &end3); if (!cur_MM) { delete_mod_tags(cur); return 0; } // Does MN match seq length? If so, we believe it's already valid if (MNi == cur->core.l_qseq) goto validate; // Length mismatch and/or no known length, so check vs full seq. if (pre->core.l_qseq != cur->core.l_qseq + end3 + end5) { delete_mod_tags(cur); return 0; } else if (end5 || end3) { if (MNi < 0 || MNi == pre->core.l_qseq) trim_MM(pre, cur, end5, end3, cur_MM, cur_ML, cur_MN); } // else no hard clips so MM is already valid // Set MN so we've validated it, provided seq isn't "*". // inefficient, but minimal compared to everything else if (cur->core.l_qseq) if (bam_aux_update_int(cur, "MN", cur->core.l_qseq) < 0) return -1; } validate: ; // Also validate MM length matches sequence length. This mirrors the // logic in htslib/sam_mods.c. // For now we take the inefficient approach of using bam_parse_basemod2. // Inefficient, but robust. hts_base_mod_state *mst = hts_base_mod_state_alloc(); if (!mst) return -1; enum htsLogLevel lvl = hts_get_log_level(); hts_set_log_level(HTS_LOG_OFF); if (bam_parse_basemod(cur, mst) < 0) // Maybe we want hts_log_warning still though? delete_mod_tags(cur); if (validate_MM(cur, mst) < 0) delete_mod_tags(cur); hts_set_log_level(lvl); hts_base_mod_state_free(mst); return 0; } // Ensure the b[] array is at least n. // Returns 0 on success, // -1 on failure static int grow_b_array(bam1_t **b, int *ba, int n) { if (n < *ba) return 0; bam1_t *bnew = realloc(*b, (n+=10) * sizeof(**b)); if (!bnew) return -1; *b = bnew; // bam_init1 equivalent int i; for (i = *ba; i < n; i++) memset(&(*b)[i], 0, sizeof(bam1_t)); *b = bnew; *ba = n; return 0; } // We have b[0]..b[bn-1] entries all from the same template (qname) typedef struct { bam1_t *b; int n, ba; // number used and number allocated int b_next; // b[b_next] for start of next set, -1 if unset int eof; // marker for having seen eof } bam_set; // Fetches a new batch of BAM records all containing the same name. // NB: we cache the last (non-matching) name in b[n], so we can use it to // start the next batch. // Returns the number of records on success, // <0 on failure or EOF (sam_read1 return vals) static int next_template(samFile *in, sam_hdr_t *header, bam_set *bs, int sanitize_flags) { int result; if (bs->eof) return -1; // First time through, prime the template name if (bs->b_next < 0) { if (grow_b_array(&bs->b, &bs->ba, 1) < 0) return -2; result = sam_read1(in, header, &bs->b[0]); if (result < 0) return result; if (bam_sanitize(header, &bs->b[0], sanitize_flags) < 0) return -2; } else { // Otherwise use the previous template name read bam1_t btmp = bs->b[0]; bs->b[0] = bs->b[bs->b_next]; bs->b[bs->b_next] = btmp; // For ->{,l_,m_}data } bs->n = 1; // Now keep reading until we find a read that mismatches or we hit eof. char *name = bam_get_qname(&bs->b[0]); for (;;) { if (grow_b_array(&bs->b, &bs->ba, bs->n+1) < 0) return -2; result = sam_read1(in, header, &bs->b[bs->n]); if (result < -1) return result; if (result < 0) { bs->eof = 1; bs->b_next = -1; break; } else { if (bam_sanitize(header, &bs->b[bs->n], sanitize_flags) < 0) return -2; bs->b_next = bs->n; if (strcmp(name, bam_get_qname(&bs->b[bs->n])) != 0) break; } bs->n++; } return bs->n; } // currently, this function ONLY works if each read has one hit // // Returns 0 on success, // >0 on failure static int bam_mating_core(samFile *in, samFile *out, int remove_reads, int proper_pair_check, int add_ct, int do_mate_scoring, char *arg_list, int no_pg, int sanitize_flags, int base_mods) { sam_hdr_t *header; int result, n; kstring_t str = KS_INITIALIZE; bam_set bs = {NULL, 0, 0, -1, 0}; header = sam_hdr_read(in); if (header == NULL) { fprintf(samtools_stderr, "[bam_mating_core] ERROR: Couldn't read header\n"); return 1; } // Accept unknown, unsorted, or queryname sort order, but error on coordinate sorted. if (!sam_hdr_find_tag_hd(header, "SO", &str) && str.s && !strcmp(str.s, "coordinate")) { fprintf(samtools_stderr, "[bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.\n"); goto fail; } ks_free(&str); if (!no_pg && sam_hdr_add_pg(header, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) goto fail; if (sam_hdr_write(out, header) < 0) goto write_fail; // Iterate template by template fetching bs->n records at a time while ((result = next_template(in, header, &bs, sanitize_flags)) >= 0) { bam1_t *cur = NULL, *pre = NULL, *rnum[2] = {NULL, NULL}; int prev = -1, curr = -1; hts_pos_t pre_end = 0, cur_end = 0; // Find and fix up primary alignments MM_state state[2]; for (n = 0; n < bs.n; n++) { int is_r2 = (bs.b[n].core.flag & BAM_FREAD2) != 0; if (bs.b[n].core.flag & (BAM_FSECONDARY | BAM_FSUPPLEMENTARY)) continue; if (base_mods) if (fix_MM(NULL, &bs.b[n], &state[is_r2]) < 0) goto fail; if (!pre) { pre = &bs.b[prev = n]; rnum[(pre->core.flag & BAM_FREAD2) != 0] = pre; pre_end = (pre->core.flag & BAM_FUNMAP) == 0 ? bam_endpos(pre) : 0; continue; } // Note, more than 2 primary alignments will use 'curr' as last cur = &bs.b[curr = n]; rnum[(cur->core.flag & BAM_FREAD2) != 0] = cur; cur_end = (cur->core.flag & BAM_FUNMAP) == 0 ? bam_endpos(cur) : 0; pre->core.flag |= BAM_FPAIRED; cur->core.flag |= BAM_FPAIRED; if (sync_mate(pre, cur)) goto fail; // If safe set TLEN/ISIZE if (pre->core.tid == cur->core.tid && !(cur->core.flag & (BAM_FUNMAP | BAM_FMUNMAP)) && !(pre->core.flag & (BAM_FUNMAP | BAM_FMUNMAP))) { hts_pos_t cur5, pre5; cur5 = (cur->core.flag & BAM_FREVERSE) ? cur_end : cur->core.pos; pre5 = (pre->core.flag & BAM_FREVERSE) ? pre_end : pre->core.pos; cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5; } else { cur->core.isize = pre->core.isize = 0; } if (add_ct) bam_template_cigar(pre, cur, &str); // TODO: Add code to properly check if read is in a proper // pair based on ISIZE distribution if (proper_pair_check && !plausibly_properly_paired(pre,cur)) { pre->core.flag &= ~BAM_FPROPER_PAIR; cur->core.flag &= ~BAM_FPROPER_PAIR; } if (do_mate_scoring) { if ((add_mate_score(pre, cur) == -1) || (add_mate_score(cur, pre) == -1)) { fprintf(samtools_stderr, "[bam_mating_core] ERROR: " "unable to add mate score.\n"); goto fail; } } // If we have to remove reads make sure we do it in a way that // doesn't create orphans with bad flags if (remove_reads) { if (pre->core.flag&BAM_FUNMAP) cur->core.flag &= ~(BAM_FMREVERSE|BAM_FPROPER_PAIR); if (cur->core.flag&BAM_FUNMAP) pre->core.flag &= ~(BAM_FMREVERSE|BAM_FPROPER_PAIR); } } // Handle unpaired primary data if (!cur && pre) { pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0; pre->core.flag &= ~(BAM_FMREVERSE|BAM_FPROPER_PAIR); } // Now process secondary and supplementary alignments for (n = 0; n < bs.n; n++) { if (!(bs.b[n].core.flag & (BAM_FSECONDARY|BAM_FSUPPLEMENTARY))) { // primary continue; } // Secondary or supplementary int is_r2 = (bs.b[n].core.flag & BAM_FREAD2) != 0; bam1_t *primary = rnum[is_r2]; if (primary) { if (base_mods) fix_MM(primary, &bs.b[n], &state[is_r2]); } else { // Record with base modifications but no known primary //fprintf(samtools_stderr, "Unpaired secondary or supplementary\n"); if (base_mods) fix_MM(NULL, &bs.b[n], NULL); } } // Finally having curated everything, write out all records in their // original ordering for (n = 0; n < bs.n; n++) { bam1_t *cur = &bs.b[n]; // We may remove unmapped and secondary alignments if (remove_reads && (cur->core.flag & (BAM_FSECONDARY|BAM_FUNMAP))) continue; if (sam_write1(out, header, cur) < 0) goto write_fail; } } if (result < -1) goto read_fail; sam_hdr_destroy(header); for (n = 0; n < bs.ba; n++) free(bs.b[n].data); free(bs.b); ks_free(&str); return 0; read_fail: print_error("fixmate", "Couldn't read from input file"); goto fail; write_fail: print_error_errno("fixmate", "Couldn't write to output file"); fail: sam_hdr_destroy(header); for (n = 0; n < bs.ba; n++) free(bs.b[n].data); free(bs.b); ks_free(&str); return 1; } void usage(FILE* where) { fprintf(where, "Usage: samtools fixmate \n" "Options:\n" " -r Remove unmapped reads and secondary alignments\n" " -p Disable FR proper pair check\n" " -c Add template cigar ct tag\n" " -m Add mate score tag\n" " -u Uncompressed output\n" " -z, --sanitize FLAG[,FLAG]\n" " Sanitize alignment fields [defaults to all types]\n" " -M Fix base modification tags (MM/ML/MN)\n" " --no-PG do not add a PG line\n"); sam_global_opt_help(where, "-.O..@-."); fprintf(where, "\n" "As elsewhere in samtools, use '-' as the filename for stdin/samtools_stdout. The input\n" "file must be grouped by read name (e.g. sorted by name). Coordinated sorted\n" "input is not accepted.\n"); } int bam_mating(int argc, char *argv[]) { htsThreadPool p = {NULL, 0}; samFile *in = NULL, *out = NULL; int c, remove_reads = 0, proper_pair_check = 1, add_ct = 0, res = 1, mate_score = 0, no_pg = 0, sanitize_flags = FIX_ALL, base_mods = 0; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; char wmode[4] = {'w', 'b', 0, 0}; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'), {"no-PG", no_argument, NULL, 1}, { NULL, 0, NULL, 0 } }; char *arg_list = NULL; // parse args if (argc == 1) { usage(samtools_stdout); return 0; } while ((c = getopt_long(argc, argv, "rpcmMO:@:uz:", lopts, NULL)) >= 0) { switch (c) { case 'r': remove_reads = 1; break; case 'p': proper_pair_check = 0; break; case 'c': add_ct = 1; break; case 'm': mate_score = 1; break; case 'M': base_mods = 1; break; case 'u': wmode[2] = '0'; break; case 1: no_pg = 1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage(samtools_stderr); goto fail; case 'z': if ((sanitize_flags = bam_sanitize_options(optarg)) < 0) samtools_exit(1); break; } } if (optind+1 >= argc) { usage(samtools_stderr); goto fail; } if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) goto fail; // init if ((in = sam_open_format(argv[optind], "rb", &ga.in)) == NULL) { print_error_errno("fixmate", "cannot open input file"); goto fail; } sam_open_mode(wmode+1, argv[optind+1], NULL); if ((out = sam_open_format(argv[optind+1], wmode, &ga.out)) == NULL) { print_error_errno("fixmate", "cannot open output file"); goto fail; } if (ga.nthreads > 0) { if (!(p.pool = hts_tpool_init(ga.nthreads))) { fprintf(samtools_stderr, "Error creating thread pool\n"); goto fail; } hts_set_opt(in, HTS_OPT_THREAD_POOL, &p); hts_set_opt(out, HTS_OPT_THREAD_POOL, &p); } // run res = bam_mating_core(in, out, remove_reads, proper_pair_check, add_ct, mate_score, arg_list, no_pg, sanitize_flags, base_mods); // cleanup sam_close(in); if (sam_close(out) < 0) { fprintf(samtools_stderr, "[bam_mating] error while closing output file\n"); res = 1; } if (p.pool) hts_tpool_destroy(p.pool); free(arg_list); sam_global_args_free(&ga); return res; fail: if (in) sam_close(in); if (out) sam_close(out); if (p.pool) hts_tpool_destroy(p.pool); free(arg_list); sam_global_args_free(&ga); return 1; } pysam-0.23.0/samtools/bam_md.c000066400000000000000000000443611475062545500161760ustar00rootroot00000000000000/* bam_md.c -- calmd subcommand. Copyright (C) 2009-2011, 2014-2015, 2019-2020, 2022 Genome Research Ltd. Portions copyright (C) 2009-2011 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include "htslib/faidx.h" #include "htslib/sam.h" #include "htslib/kstring.h" #include "htslib/thread_pool.h" #include "sam_opts.h" #include "samtools.h" #define USE_EQUAL 1 #define DROP_TAG 2 #define BIN_QUAL 4 #define UPDATE_NM 8 #define UPDATE_MD 16 #define HASH_QNM 32 typedef struct cached_ref_entry { char *ref; hts_pos_t len; } cached_ref_entry; typedef struct ref_cache { cached_ref_entry *refs; char *last_ref; hts_pos_t last_len; int nref; int last_tid; } ref_cache; int bam_aux_drop_other(bam1_t *b, uint8_t *s); static int bam_fillmd1_core(const char *ref_name, bam1_t *b, char *ref, hts_pos_t ref_len, int flag, int max_nm, int quiet_mode, uint32_t *skipped) { uint8_t *seq = bam_get_seq(b); uint32_t *cigar = bam_get_cigar(b); bam1_core_t *c = &b->core; int i, qpos, matched = 0; hts_pos_t rpos; kstring_t str = KS_INITIALIZE; int32_t old_nm_i = -1, nm = 0; uint32_t err = 0; if (c->l_qseq == 0) { if (!quiet_mode) { if (ref_name) { fprintf(stderr, "[bam_fillmd1] no sequence in alignment " "record for '%s' at %s:%"PRIhts_pos", skipped\n", bam_get_qname(b), ref_name, c->pos + 1); } else { fprintf(stderr, "[bam_fillmd1] no sequence in alignment " "record for '%s', skipped", bam_get_qname(b)); } } if (skipped) (*skipped)++; return 0; } for (i = qpos = 0, rpos = c->pos; i < c->n_cigar; ++i) { int j, oplen = cigar[i]>>4, op = cigar[i]&0xf; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { for (j = 0; j < oplen; ++j) { int c1, c2, z = qpos + j; if (rpos+j >= ref_len || z >= c->l_qseq || ref[rpos+j] == '\0') break; // out of bounds c1 = bam_seqi(seq, z); c2 = seq_nt16_table[(uint8_t)ref[rpos+j]]; if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match if (flag&USE_EQUAL) seq[z/2] &= (z&1)? 0xf0 : 0x0f; ++matched; } else { err |= kputw(matched, &str) < 0; err |= kputc(toupper(ref[rpos+j]), &str) < 0; matched = 0; ++nm; } } if (j < oplen) break; rpos += oplen; qpos += oplen; } else if (op == BAM_CDEL) { err |= kputw(matched, &str) < 0; err |= kputc('^', &str) < 0; for (j = 0; j < oplen; ++j) { if (rpos+j >= ref_len || ref[rpos+j] == '\0') break; err |= kputc(toupper(ref[rpos+j]), &str) < 0; } matched = 0; rpos += j; nm += j; if (j < oplen) break; } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) { qpos += oplen; if (op == BAM_CINS) nm += oplen; } else if (op == BAM_CREF_SKIP) { rpos += oplen; } } err |= kputw(matched, &str) < 0; if (err) { print_error_errno("calmd", "Couldn't build new MD string"); goto fail; } // apply max_nm if (max_nm > 0 && nm >= max_nm) { for (i = qpos = 0, rpos = c->pos; i < c->n_cigar; ++i) { int j, oplen = cigar[i]>>4, op = cigar[i]&0xf; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { for (j = 0; j < oplen; ++j) { int c1, c2, z = qpos + j; if (rpos+j >= ref_len || z >= c->l_qseq || ref[rpos+j] == '\0') break; // out of bounds c1 = bam_seqi(seq, z); c2 = seq_nt16_table[(uint8_t)ref[rpos+j]]; if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match seq[z/2] |= (z&1)? 0x0f : 0xf0; bam_get_qual(b)[z] = 0; } } if (j < oplen) break; rpos += oplen; qpos += oplen; } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) rpos += oplen; else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) qpos += oplen; } } // update NM if ((flag & UPDATE_NM) && !(c->flag & BAM_FUNMAP)) { uint8_t *old_nm = bam_aux_get(b, "NM"); if (old_nm) old_nm_i = bam_aux2i(old_nm); if (!old_nm) { if (bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm) < 0) goto aux_fail; } else if (nm != old_nm_i) { if (!quiet_mode) { fprintf(stderr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam_get_qname(b), old_nm_i, nm); } if (bam_aux_del(b, old_nm) < 0) goto aux_fail; if (bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm) < 0) goto aux_fail; } } // update MD if ((flag & UPDATE_MD) && !(c->flag & BAM_FUNMAP)) { uint8_t *old_md = bam_aux_get(b, "MD"); if (!old_md) { if (bam_aux_append(b, "MD", 'Z', str.l + 1, (uint8_t*)str.s) < 0) goto aux_fail; } else { int is_diff = 0; if (strlen((char*)old_md+1) == str.l) { for (i = 0; i < str.l; ++i) if (toupper(old_md[i+1]) != toupper(str.s[i])) break; if (i < str.l) is_diff = 1; } else is_diff = 1; if (is_diff) { if (!quiet_mode) { fprintf(stderr, "[bam_fillmd1] different MD for read '%s': '%s' -> '%s'\n", bam_get_qname(b), old_md+1, str.s); } if (bam_aux_del(b, old_md) < 0) goto aux_fail; if (bam_aux_append(b, "MD", 'Z', str.l + 1, (uint8_t*)str.s) < 0) goto aux_fail; } } } // drop all tags but RG if (flag&DROP_TAG) { uint8_t *q = bam_aux_get(b, "RG"); bam_aux_drop_other(b, q); } // reduce the resolution of base quality if (flag&BIN_QUAL) { uint8_t *qual = bam_get_qual(b); for (i = 0; i < b->core.l_qseq; ++i) if (qual[i] >= 3) qual[i] = qual[i]/10*10 + 7; } free(str.s); return 0; aux_fail: if (errno == ENOMEM) { print_error("calmd", "Couldn't add aux tag (too long)"); } else if (errno == EINVAL) { print_error("calmd", "Corrupt aux data"); } else { print_error_errno("calmd", "Couldn't add aux tag"); } fail: free(str.s); return -1; } int bam_fillmd1(bam1_t *b, char *ref, int flag, int quiet_mode) { return bam_fillmd1_core(NULL, b, ref, INT_MAX, flag, 0, quiet_mode, NULL); } // Get a new reference sequence. // For position-sorted inputs, the previous reference should never be // needed again and can be discarded to save memory. For other orderings, // references are stored in a cache in case they're required in the future. // The caching mode is turned on if the requested tid is less than the last // one used, indicating the file ordering doesn't match the sequence dictionary. static int get_ref(faidx_t *fai, sam_hdr_t *header, ref_cache *cache, int tid, char **ref_out, const char **ref_name_out, hts_pos_t *len_out) { char *ref = NULL; const char *ref_name; hts_pos_t len = 0; // This should only be called when tid changes assert(tid != cache->last_tid); // Array lookup, should be fast ref_name = sam_hdr_tid2name(header, tid); *ref_name_out = ref_name; // Return a cached entry, if available if (cache->refs && tid >= 0 && tid < cache->nref && cache->refs[tid].ref) { assert(cache->last_ref == NULL); *ref_out = cache->refs[tid].ref; *len_out = cache->refs[tid].len; cache->last_tid = tid; return 0; } // Try to get the reference if (ref_name) ref = fai_fetch64(fai, ref_name, &len); if (!ref) { // Historically, calmd doesn't worry too much about missing refs *ref_out = NULL; *len_out = 0; return 0; } if (!cache->refs && cache->last_tid > tid) { // Going backwards throught the list of tids implies // a non-position-ordered file, so turn on caching mode cache->nref = sam_hdr_nref(header); if (cache->nref < 0) { print_error("calmd", "couldn't get number of refs from header"); return -1; } if (cache->nref > 0) { cache->refs = calloc(cache->nref, sizeof(cache->refs[0])); if (!cache->refs) { print_error_errno("calmd", "couldn't allocate reference cache"); return -1; } // Add the reference we already have as the first entry if (cache->last_tid >= 0 && cache->last_tid < cache->nref) { cache->refs[cache->last_tid].ref = cache->last_ref; cache->refs[cache->last_tid].len = cache->last_len; } else { free(cache->last_ref); } cache->last_ref = NULL; } } if (cache->refs) { assert(cache->last_ref == NULL); // Shouldn't be set when caching // Add the new reference to the cache if (tid >= 0 && tid < cache->nref) { cache->refs[tid].ref = ref; cache->refs[tid].len = len; } } else { // Streaming mode - free the last ref and replace it with this one free(cache->last_ref); cache->last_ref = ref; cache->last_len = len; } *ref_out = ref; *len_out = len; cache->last_tid = tid; return 0; } static void refs_destroy(ref_cache *cache) { if (cache->refs) { int i; assert(cache->last_ref == NULL); for (i = 0; i < cache->nref; i++) free(cache->refs[i].ref); free(cache->refs); } else { free(cache->last_ref); } } int calmd_usage(void) { fprintf(stderr, "Usage: samtools calmd [-eubrAESQ] \n" "Options:\n" " -e change identical bases to '='\n" " -u uncompressed BAM output (for piping)\n" " -b compressed BAM output\n" " -S ignored (input format is auto-detected)\n" " -A modify the quality string\n" " -Q use quiet mode to output less debug info to stdout\n" " -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)\n" " -E extended BAQ for better sensitivity but lower specificity\n" " --no-PG do not add a PG line\n"); sam_global_opt_help(stderr, "-....@-."); return 1; } int bam_fillmd(int argc, char *argv[]) { int c, flt_flag, ret, is_bam_out, is_uncompressed, max_nm, is_realn, capQ, baq_flag, quiet_mode, no_pg = 0; hts_pos_t len = 0; htsThreadPool p = {NULL, 0}; samFile *fp = NULL, *fpout = NULL; sam_hdr_t *header = NULL; faidx_t *fai = NULL; char *ref = NULL, mode_w[8], *ref_file, *arg_list = NULL; ref_cache refs = { NULL, NULL, 0, 0, -2 }; const char *ref_name = NULL; bam1_t *b = NULL; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; uint32_t skipped = 0; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0,'@'), {"no-PG", no_argument, NULL, 1}, { NULL, 0, NULL, 0 } }; flt_flag = UPDATE_NM | UPDATE_MD; is_bam_out = is_uncompressed = is_realn = max_nm = capQ = baq_flag = quiet_mode = 0; strcpy(mode_w, "w"); while ((c = getopt_long(argc, argv, "EqQreuNhbSC:n:Ad@:", lopts, NULL)) >= 0) { switch (c) { case 'r': is_realn = 1; break; case 'e': flt_flag |= USE_EQUAL; break; case 'd': flt_flag |= DROP_TAG; break; case 'q': flt_flag |= BIN_QUAL; break; case 'h': flt_flag |= HASH_QNM; break; case 'N': flt_flag &= ~(UPDATE_MD|UPDATE_NM); break; case 'b': is_bam_out = 1; break; case 'u': is_uncompressed = is_bam_out = 1; break; case 'S': break; case 'n': max_nm = atoi(optarg); break; case 'C': capQ = atoi(optarg); break; case 'A': baq_flag |= 1; break; case 'E': baq_flag |= 2; break; case 'Q': quiet_mode = 1; break; case 1: no_pg = 1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n\n", c); /* else fall-through */ case '?': return calmd_usage(); } } if (is_bam_out) strcat(mode_w, "b"); else strcat(mode_w, "h"); if (is_uncompressed) strcat(mode_w, "0"); if (optind + (ga.reference == NULL) >= argc) return calmd_usage(); fp = sam_open_format(argv[optind], "r", &ga.in); if (fp == NULL) { print_error_errno("calmd", "Failed to open input file '%s'", argv[optind]); return 1; } if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) { print_error("calmd", "failed to create arg_list"); return 1; } header = sam_hdr_read(fp); if (header == NULL || sam_hdr_nref(header) == 0) { // NB: if we have no SQ headers but have aligned data, then this will // be caught during processing with e.g. // "[E::sam_parse1] no SQ lines present in the header" fprintf(stderr, "[bam_fillmd] warning: input SAM does not have " "header, performing a no-op.\n"); } fpout = sam_open_format("-", mode_w, &ga.out); if (fpout == NULL) { print_error_errno("calmd", "Failed to open output"); goto fail; } if (!no_pg && sam_hdr_add_pg(header, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { print_error("calmd", "failed to add PG line to header"); goto fail; } if (sam_hdr_write(fpout, header) < 0) { print_error_errno("calmd", "Failed to write sam header"); goto fail; } if (ga.nthreads > 0) { if (!(p.pool = hts_tpool_init(ga.nthreads))) { fprintf(stderr, "Error creating thread pool\n"); goto fail; } hts_set_opt(fp, HTS_OPT_THREAD_POOL, &p); hts_set_opt(fpout, HTS_OPT_THREAD_POOL, &p); } ref_file = argc > optind + 1 ? argv[optind+1] : ga.reference; fai = fai_load(ref_file); if (!fai) { print_error_errno("calmd", "Failed to open reference file '%s'", ref_file); goto fail; } b = bam_init1(); if (!b) { fprintf(stderr, "[bam_fillmd] Failed to allocate bam struct\n"); goto fail; } while ((ret = sam_read1(fp, header, b)) >= 0) { if (b->core.tid >= 0) { if (refs.last_tid != b->core.tid) { if (get_ref(fai, header, &refs, b->core.tid, &ref, &ref_name, &len) < 0) { goto fail; } if (ref == 0) { // FIXME: Should this always be fatal? fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n", ref_name ? ref_name : "(unknown)"); if (is_realn || capQ > 10) goto fail; // Would otherwise crash } } if (is_realn) { if (sam_prob_realn(b, ref, len, baq_flag) < -3) { print_error_errno("calmd", "BAQ alignment failed"); goto fail; } } if (capQ > 10) { int q = sam_cap_mapq(b, ref, len, capQ); if (b->core.qual > q) b->core.qual = q; } if (ref) { if (bam_fillmd1_core(ref_name, b, ref, len, flt_flag, max_nm, quiet_mode, &skipped) < 0) goto fail; } } if (sam_write1(fpout, header, b) < 0) { print_error_errno("calmd", "failed to write to output file"); goto fail; } } if (ret < -1) { fprintf(stderr, "[bam_fillmd] Error reading input.\n"); goto fail; } if (skipped) { fprintf(stderr, "[calmd] Warning: %"PRIu32" records skipped due " "to no query sequence\n", skipped); } bam_destroy1(b); sam_hdr_destroy(header); free(arg_list); refs_destroy(&refs); fai_destroy(fai); sam_close(fp); if (sam_close(fpout) < 0) { fprintf(stderr, "[bam_fillmd] error when closing output file\n"); return 1; } if (p.pool) hts_tpool_destroy(p.pool); return 0; fail: free(arg_list); refs_destroy(&refs); if (b) bam_destroy1(b); if (header) sam_hdr_destroy(header); if (fai) fai_destroy(fai); if (fp) sam_close(fp); if (fpout) sam_close(fpout); if (p.pool) hts_tpool_destroy(p.pool); return 1; } pysam-0.23.0/samtools/bam_md.c.pysam.c000066400000000000000000000446441475062545500175530ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_md.c -- calmd subcommand. Copyright (C) 2009-2011, 2014-2015, 2019-2020, 2022 Genome Research Ltd. Portions copyright (C) 2009-2011 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include "htslib/faidx.h" #include "htslib/sam.h" #include "htslib/kstring.h" #include "htslib/thread_pool.h" #include "sam_opts.h" #include "samtools.h" #define USE_EQUAL 1 #define DROP_TAG 2 #define BIN_QUAL 4 #define UPDATE_NM 8 #define UPDATE_MD 16 #define HASH_QNM 32 typedef struct cached_ref_entry { char *ref; hts_pos_t len; } cached_ref_entry; typedef struct ref_cache { cached_ref_entry *refs; char *last_ref; hts_pos_t last_len; int nref; int last_tid; } ref_cache; int bam_aux_drop_other(bam1_t *b, uint8_t *s); static int bam_fillmd1_core(const char *ref_name, bam1_t *b, char *ref, hts_pos_t ref_len, int flag, int max_nm, int quiet_mode, uint32_t *skipped) { uint8_t *seq = bam_get_seq(b); uint32_t *cigar = bam_get_cigar(b); bam1_core_t *c = &b->core; int i, qpos, matched = 0; hts_pos_t rpos; kstring_t str = KS_INITIALIZE; int32_t old_nm_i = -1, nm = 0; uint32_t err = 0; if (c->l_qseq == 0) { if (!quiet_mode) { if (ref_name) { fprintf(samtools_stderr, "[bam_fillmd1] no sequence in alignment " "record for '%s' at %s:%"PRIhts_pos", skipped\n", bam_get_qname(b), ref_name, c->pos + 1); } else { fprintf(samtools_stderr, "[bam_fillmd1] no sequence in alignment " "record for '%s', skipped", bam_get_qname(b)); } } if (skipped) (*skipped)++; return 0; } for (i = qpos = 0, rpos = c->pos; i < c->n_cigar; ++i) { int j, oplen = cigar[i]>>4, op = cigar[i]&0xf; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { for (j = 0; j < oplen; ++j) { int c1, c2, z = qpos + j; if (rpos+j >= ref_len || z >= c->l_qseq || ref[rpos+j] == '\0') break; // out of bounds c1 = bam_seqi(seq, z); c2 = seq_nt16_table[(uint8_t)ref[rpos+j]]; if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match if (flag&USE_EQUAL) seq[z/2] &= (z&1)? 0xf0 : 0x0f; ++matched; } else { err |= kputw(matched, &str) < 0; err |= kputc(toupper(ref[rpos+j]), &str) < 0; matched = 0; ++nm; } } if (j < oplen) break; rpos += oplen; qpos += oplen; } else if (op == BAM_CDEL) { err |= kputw(matched, &str) < 0; err |= kputc('^', &str) < 0; for (j = 0; j < oplen; ++j) { if (rpos+j >= ref_len || ref[rpos+j] == '\0') break; err |= kputc(toupper(ref[rpos+j]), &str) < 0; } matched = 0; rpos += j; nm += j; if (j < oplen) break; } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) { qpos += oplen; if (op == BAM_CINS) nm += oplen; } else if (op == BAM_CREF_SKIP) { rpos += oplen; } } err |= kputw(matched, &str) < 0; if (err) { print_error_errno("calmd", "Couldn't build new MD string"); goto fail; } // apply max_nm if (max_nm > 0 && nm >= max_nm) { for (i = qpos = 0, rpos = c->pos; i < c->n_cigar; ++i) { int j, oplen = cigar[i]>>4, op = cigar[i]&0xf; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { for (j = 0; j < oplen; ++j) { int c1, c2, z = qpos + j; if (rpos+j >= ref_len || z >= c->l_qseq || ref[rpos+j] == '\0') break; // out of bounds c1 = bam_seqi(seq, z); c2 = seq_nt16_table[(uint8_t)ref[rpos+j]]; if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match seq[z/2] |= (z&1)? 0x0f : 0xf0; bam_get_qual(b)[z] = 0; } } if (j < oplen) break; rpos += oplen; qpos += oplen; } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) rpos += oplen; else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) qpos += oplen; } } // update NM if ((flag & UPDATE_NM) && !(c->flag & BAM_FUNMAP)) { uint8_t *old_nm = bam_aux_get(b, "NM"); if (old_nm) old_nm_i = bam_aux2i(old_nm); if (!old_nm) { if (bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm) < 0) goto aux_fail; } else if (nm != old_nm_i) { if (!quiet_mode) { fprintf(samtools_stderr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam_get_qname(b), old_nm_i, nm); } if (bam_aux_del(b, old_nm) < 0) goto aux_fail; if (bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm) < 0) goto aux_fail; } } // update MD if ((flag & UPDATE_MD) && !(c->flag & BAM_FUNMAP)) { uint8_t *old_md = bam_aux_get(b, "MD"); if (!old_md) { if (bam_aux_append(b, "MD", 'Z', str.l + 1, (uint8_t*)str.s) < 0) goto aux_fail; } else { int is_diff = 0; if (strlen((char*)old_md+1) == str.l) { for (i = 0; i < str.l; ++i) if (toupper(old_md[i+1]) != toupper(str.s[i])) break; if (i < str.l) is_diff = 1; } else is_diff = 1; if (is_diff) { if (!quiet_mode) { fprintf(samtools_stderr, "[bam_fillmd1] different MD for read '%s': '%s' -> '%s'\n", bam_get_qname(b), old_md+1, str.s); } if (bam_aux_del(b, old_md) < 0) goto aux_fail; if (bam_aux_append(b, "MD", 'Z', str.l + 1, (uint8_t*)str.s) < 0) goto aux_fail; } } } // drop all tags but RG if (flag&DROP_TAG) { uint8_t *q = bam_aux_get(b, "RG"); bam_aux_drop_other(b, q); } // reduce the resolution of base quality if (flag&BIN_QUAL) { uint8_t *qual = bam_get_qual(b); for (i = 0; i < b->core.l_qseq; ++i) if (qual[i] >= 3) qual[i] = qual[i]/10*10 + 7; } free(str.s); return 0; aux_fail: if (errno == ENOMEM) { print_error("calmd", "Couldn't add aux tag (too long)"); } else if (errno == EINVAL) { print_error("calmd", "Corrupt aux data"); } else { print_error_errno("calmd", "Couldn't add aux tag"); } fail: free(str.s); return -1; } int bam_fillmd1(bam1_t *b, char *ref, int flag, int quiet_mode) { return bam_fillmd1_core(NULL, b, ref, INT_MAX, flag, 0, quiet_mode, NULL); } // Get a new reference sequence. // For position-sorted inputs, the previous reference should never be // needed again and can be discarded to save memory. For other orderings, // references are stored in a cache in case they're required in the future. // The caching mode is turned on if the requested tid is less than the last // one used, indicating the file ordering doesn't match the sequence dictionary. static int get_ref(faidx_t *fai, sam_hdr_t *header, ref_cache *cache, int tid, char **ref_out, const char **ref_name_out, hts_pos_t *len_out) { char *ref = NULL; const char *ref_name; hts_pos_t len = 0; // This should only be called when tid changes assert(tid != cache->last_tid); // Array lookup, should be fast ref_name = sam_hdr_tid2name(header, tid); *ref_name_out = ref_name; // Return a cached entry, if available if (cache->refs && tid >= 0 && tid < cache->nref && cache->refs[tid].ref) { assert(cache->last_ref == NULL); *ref_out = cache->refs[tid].ref; *len_out = cache->refs[tid].len; cache->last_tid = tid; return 0; } // Try to get the reference if (ref_name) ref = fai_fetch64(fai, ref_name, &len); if (!ref) { // Historically, calmd doesn't worry too much about missing refs *ref_out = NULL; *len_out = 0; return 0; } if (!cache->refs && cache->last_tid > tid) { // Going backwards throught the list of tids implies // a non-position-ordered file, so turn on caching mode cache->nref = sam_hdr_nref(header); if (cache->nref < 0) { print_error("calmd", "couldn't get number of refs from header"); return -1; } if (cache->nref > 0) { cache->refs = calloc(cache->nref, sizeof(cache->refs[0])); if (!cache->refs) { print_error_errno("calmd", "couldn't allocate reference cache"); return -1; } // Add the reference we already have as the first entry if (cache->last_tid >= 0 && cache->last_tid < cache->nref) { cache->refs[cache->last_tid].ref = cache->last_ref; cache->refs[cache->last_tid].len = cache->last_len; } else { free(cache->last_ref); } cache->last_ref = NULL; } } if (cache->refs) { assert(cache->last_ref == NULL); // Shouldn't be set when caching // Add the new reference to the cache if (tid >= 0 && tid < cache->nref) { cache->refs[tid].ref = ref; cache->refs[tid].len = len; } } else { // Streaming mode - free the last ref and replace it with this one free(cache->last_ref); cache->last_ref = ref; cache->last_len = len; } *ref_out = ref; *len_out = len; cache->last_tid = tid; return 0; } static void refs_destroy(ref_cache *cache) { if (cache->refs) { int i; assert(cache->last_ref == NULL); for (i = 0; i < cache->nref; i++) free(cache->refs[i].ref); free(cache->refs); } else { free(cache->last_ref); } } int calmd_usage(void) { fprintf(samtools_stderr, "Usage: samtools calmd [-eubrAESQ] \n" "Options:\n" " -e change identical bases to '='\n" " -u uncompressed BAM output (for piping)\n" " -b compressed BAM output\n" " -S ignored (input format is auto-detected)\n" " -A modify the quality string\n" " -Q use quiet mode to output less debug info to samtools_stdout\n" " -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)\n" " -E extended BAQ for better sensitivity but lower specificity\n" " --no-PG do not add a PG line\n"); sam_global_opt_help(samtools_stderr, "-....@-."); return 1; } int bam_fillmd(int argc, char *argv[]) { int c, flt_flag, ret, is_bam_out, is_uncompressed, max_nm, is_realn, capQ, baq_flag, quiet_mode, no_pg = 0; hts_pos_t len = 0; htsThreadPool p = {NULL, 0}; samFile *fp = NULL, *fpout = NULL; sam_hdr_t *header = NULL; faidx_t *fai = NULL; char *ref = NULL, mode_w[8], *ref_file, *arg_list = NULL; ref_cache refs = { NULL, NULL, 0, 0, -2 }; const char *ref_name = NULL; bam1_t *b = NULL; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; uint32_t skipped = 0; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0,'@'), {"no-PG", no_argument, NULL, 1}, { NULL, 0, NULL, 0 } }; flt_flag = UPDATE_NM | UPDATE_MD; is_bam_out = is_uncompressed = is_realn = max_nm = capQ = baq_flag = quiet_mode = 0; strcpy(mode_w, "w"); while ((c = getopt_long(argc, argv, "EqQreuNhbSC:n:Ad@:", lopts, NULL)) >= 0) { switch (c) { case 'r': is_realn = 1; break; case 'e': flt_flag |= USE_EQUAL; break; case 'd': flt_flag |= DROP_TAG; break; case 'q': flt_flag |= BIN_QUAL; break; case 'h': flt_flag |= HASH_QNM; break; case 'N': flt_flag &= ~(UPDATE_MD|UPDATE_NM); break; case 'b': is_bam_out = 1; break; case 'u': is_uncompressed = is_bam_out = 1; break; case 'S': break; case 'n': max_nm = atoi(optarg); break; case 'C': capQ = atoi(optarg); break; case 'A': baq_flag |= 1; break; case 'E': baq_flag |= 2; break; case 'Q': quiet_mode = 1; break; case 1: no_pg = 1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; fprintf(samtools_stderr, "[bam_fillmd] unrecognized option '-%c'\n\n", c); /* else fall-through */ case '?': return calmd_usage(); } } if (is_bam_out) strcat(mode_w, "b"); else strcat(mode_w, "h"); if (is_uncompressed) strcat(mode_w, "0"); if (optind + (ga.reference == NULL) >= argc) return calmd_usage(); fp = sam_open_format(argv[optind], "r", &ga.in); if (fp == NULL) { print_error_errno("calmd", "Failed to open input file '%s'", argv[optind]); return 1; } if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) { print_error("calmd", "failed to create arg_list"); return 1; } header = sam_hdr_read(fp); if (header == NULL || sam_hdr_nref(header) == 0) { // NB: if we have no SQ headers but have aligned data, then this will // be caught during processing with e.g. // "[E::sam_parse1] no SQ lines present in the header" fprintf(samtools_stderr, "[bam_fillmd] warning: input SAM does not have " "header, performing a no-op.\n"); } fpout = sam_open_format(samtools_stdout_fn, mode_w, &ga.out); if (fpout == NULL) { print_error_errno("calmd", "Failed to open output"); goto fail; } if (!no_pg && sam_hdr_add_pg(header, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { print_error("calmd", "failed to add PG line to header"); goto fail; } if (sam_hdr_write(fpout, header) < 0) { print_error_errno("calmd", "Failed to write sam header"); goto fail; } if (ga.nthreads > 0) { if (!(p.pool = hts_tpool_init(ga.nthreads))) { fprintf(samtools_stderr, "Error creating thread pool\n"); goto fail; } hts_set_opt(fp, HTS_OPT_THREAD_POOL, &p); hts_set_opt(fpout, HTS_OPT_THREAD_POOL, &p); } ref_file = argc > optind + 1 ? argv[optind+1] : ga.reference; fai = fai_load(ref_file); if (!fai) { print_error_errno("calmd", "Failed to open reference file '%s'", ref_file); goto fail; } b = bam_init1(); if (!b) { fprintf(samtools_stderr, "[bam_fillmd] Failed to allocate bam struct\n"); goto fail; } while ((ret = sam_read1(fp, header, b)) >= 0) { if (b->core.tid >= 0) { if (refs.last_tid != b->core.tid) { if (get_ref(fai, header, &refs, b->core.tid, &ref, &ref_name, &len) < 0) { goto fail; } if (ref == 0) { // FIXME: Should this always be fatal? fprintf(samtools_stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n", ref_name ? ref_name : "(unknown)"); if (is_realn || capQ > 10) goto fail; // Would otherwise crash } } if (is_realn) { if (sam_prob_realn(b, ref, len, baq_flag) < -3) { print_error_errno("calmd", "BAQ alignment failed"); goto fail; } } if (capQ > 10) { int q = sam_cap_mapq(b, ref, len, capQ); if (b->core.qual > q) b->core.qual = q; } if (ref) { if (bam_fillmd1_core(ref_name, b, ref, len, flt_flag, max_nm, quiet_mode, &skipped) < 0) goto fail; } } if (sam_write1(fpout, header, b) < 0) { print_error_errno("calmd", "failed to write to output file"); goto fail; } } if (ret < -1) { fprintf(samtools_stderr, "[bam_fillmd] Error reading input.\n"); goto fail; } if (skipped) { fprintf(samtools_stderr, "[calmd] Warning: %"PRIu32" records skipped due " "to no query sequence\n", skipped); } bam_destroy1(b); sam_hdr_destroy(header); free(arg_list); refs_destroy(&refs); fai_destroy(fai); sam_close(fp); if (sam_close(fpout) < 0) { fprintf(samtools_stderr, "[bam_fillmd] error when closing output file\n"); return 1; } if (p.pool) hts_tpool_destroy(p.pool); return 0; fail: free(arg_list); refs_destroy(&refs); if (b) bam_destroy1(b); if (header) sam_hdr_destroy(header); if (fai) fai_destroy(fai); if (fp) sam_close(fp); if (fpout) sam_close(fpout); if (p.pool) hts_tpool_destroy(p.pool); return 1; } pysam-0.23.0/samtools/bam_plbuf.c000066400000000000000000000041161475062545500167000ustar00rootroot00000000000000/* bam_plbuf.c -- plbuf routines (previously in bam_pileup.c). Copyright (C) 2008-2010, 2013 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "bam_plbuf.h" /***************** * callback APIs * *****************/ void bam_plbuf_reset(bam_plbuf_t *buf) { bam_plp_reset(buf->iter); } bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data) { bam_plbuf_t *buf; buf = calloc(1, sizeof(bam_plbuf_t)); buf->iter = bam_plp_init(0, 0); buf->func = func; buf->data = data; return buf; } void bam_plbuf_destroy(bam_plbuf_t *buf) { bam_plp_destroy(buf->iter); free(buf); } int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf) { int ret, n_plp, tid; hts_pos_t pos; const bam_pileup1_t *plp; ret = bam_plp_push(buf->iter, b); if (ret < 0) return ret; while ((plp = bam_plp64_next(buf->iter, &tid, &pos, &n_plp)) != 0) buf->func(tid, pos, n_plp, plp, buf->data); return 0; } pysam-0.23.0/samtools/bam_plbuf.c.pysam.c000066400000000000000000000041531475062545500202520ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_plbuf.c -- plbuf routines (previously in bam_pileup.c). Copyright (C) 2008-2010, 2013 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "bam_plbuf.h" /***************** * callback APIs * *****************/ void bam_plbuf_reset(bam_plbuf_t *buf) { bam_plp_reset(buf->iter); } bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data) { bam_plbuf_t *buf; buf = calloc(1, sizeof(bam_plbuf_t)); buf->iter = bam_plp_init(0, 0); buf->func = func; buf->data = data; return buf; } void bam_plbuf_destroy(bam_plbuf_t *buf) { bam_plp_destroy(buf->iter); free(buf); } int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf) { int ret, n_plp, tid; hts_pos_t pos; const bam_pileup1_t *plp; ret = bam_plp_push(buf->iter, b); if (ret < 0) return ret; while ((plp = bam_plp64_next(buf->iter, &tid, &pos, &n_plp)) != 0) buf->func(tid, pos, n_plp, plp, buf->data); return 0; } pysam-0.23.0/samtools/bam_plbuf.h000066400000000000000000000035121475062545500167040ustar00rootroot00000000000000/* bam_plbuf.h -- plbuf routines (declarations copied from bam.h). Copyright (C) 2008, 2013, 2021 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef BAM_PLBUF_H #define BAM_PLBUF_H #include #ifndef BAM_PILEUP_F_DEFINED #define BAM_PILEUP_F_DEFINED typedef int (*bam_pileup_f)(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data); #endif //BAM_PILEUP_F_DEFINED typedef struct { bam_plp_t iter; bam_pileup_f func; void *data; } bam_plbuf_t; #ifdef __cplusplus extern "C" { #endif /* Exported from bam_plbuf.c */ void bam_plbuf_reset(bam_plbuf_t *buf); bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data); void bam_plbuf_destroy(bam_plbuf_t *buf); int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf); #ifdef __cplusplus } #endif #endif // BAM_PLBUF_H pysam-0.23.0/samtools/bam_plcmd.c000066400000000000000000001332671475062545500167010ustar00rootroot00000000000000/* bam_plcmd.c -- mpileup subcommand. Copyright (C) 2008-2015, 2019-2021, 2023-2024 Genome Research Ltd. Portions copyright (C) 2009-2012 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "samtools.h" #include "bedidx.h" #include "sam_opts.h" #include "bam_plbuf.h" #define dummy_free(p) KLIST_INIT(auxlist, char *, dummy_free) int pileup_seq(kstring_t *ks_seq, const bam_pileup1_t *p, hts_pos_t pos, hts_pos_t ref_len, const char *ref, kstring_t *ks_mod, int rev_del, int no_ins, int no_ins_mods, int no_del, int no_ends) { no_ins_mods |= no_ins; int j, err = 0; hts_base_mod_state *m = p->cd.p; if (!no_ends && p->is_head) { err |= kputc_('^', ks_seq) < 0; err |= kputc_(p->b->core.qual > 93 ? 126 : p->b->core.qual + 33, ks_seq) < 0; } if (!p->is_del) { // See seq_nt16_str in htslib/hts.c const char seq_nt_str_lc[] = ",acmgrsvtwyhkdbn"; // reverse strand const char seq_nt_str_uc[] = ".ACMGRSVTWYHKDBN"; int c = p->qpos < p->b->core.l_qseq ? bam_seqi(bam_get_seq(p->b), p->qpos) : 15 /*N*/; if (ref) { int rb = pos < ref_len ? seq_nt16_table[(uint8_t)(ref[pos])] : 15/*N*/; if (c == rb) c = 0; // "=", which becomes . or , } c = bam_is_rev(p->b) ? seq_nt_str_lc[c] : seq_nt_str_uc[c]; err |= kputc_(c, ks_seq) < 0; if (m) { int nm; hts_base_mod mod[256]; if ((nm = bam_mods_at_qpos(p->b, p->qpos, m, mod, 256)) > 0) { err |= kputc_('[', ks_seq) < 0; int j; for (j = 0; j < nm && j < 256; j++) { char qual[20]; if (mod[j].qual >= 0) sprintf(qual, "%d", mod[j].qual); else *qual = 0; if (mod[j].modified_base < 0) // ChEBI err |= ksprintf(ks_seq, "%c(%d)%s", "+-"[mod[j].strand], -mod[j].modified_base, qual) < 0; else err |= ksprintf(ks_seq, "%c%c%s", "+-"[mod[j].strand], mod[j].modified_base, qual) < 0; } err |= kputc_(']', ks_seq) < 0; } } } else { err |= kputc_(p->is_refskip ? (bam_is_rev(p->b)? '<' : '>') : ((bam_is_rev(p->b) && rev_del) ? '#' : '*'), ks_seq) < 0; } int del_len = -p->indel; if (p->indel > 0) { int len = bam_plp_insertion_mod(p, m && !no_ins_mods ? m : NULL, ks_mod, &del_len); if (len < 0) { print_error("mpileup", "bam_plp_insertion() failed"); return -1; } if (no_ins < 2) { err |= kputc_('+', ks_seq) < 0; err |= kputuw(len, ks_seq) < 0; } if (!no_ins) { kstring_t *ks = ks_mod; if (bam_is_rev(p->b)) { char pad = rev_del ? '#' : '*'; int in_mod = 0; for (j = 0; j < ks->l; j++) { if (ks->s[j] == '[') in_mod = 1; else if (ks->s[j] == ']') in_mod = 0; err |= kputc_(ks->s[j] != '*' ? (in_mod ? ks->s[j] : tolower(ks->s[j])) : pad, ks_seq) < 0; } } else { int in_mod = 0; for (j = 0; j < ks->l; j++) { if (ks->s[j] == '[') in_mod = 1; if (ks->s[j] == ']') in_mod = 0; err |= kputc_(in_mod ? ks->s[j] : toupper(ks->s[j]), ks_seq) < 0; } } } } if (del_len > 0) { if (no_del < 2) err |= kputw(-del_len, ks_seq) < 0; if (!no_del) { for (j = 1; j <= del_len; ++j) { int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N'; err |= kputc_(bam_is_rev(p->b)? tolower(c) : toupper(c), ks_seq) < 0; } } } if (!no_ends && p->is_tail) err |= kputc_('$', ks_seq) < 0; return -err; } #include "sample.h" #define MPLP_NO_COMP (1<<2) #define MPLP_NO_ORPHAN (1<<3) #define MPLP_REALN (1<<4) #define MPLP_NO_INDEL (1<<5) #define MPLP_REDO_BAQ (1<<6) #define MPLP_ILLUMINA13 (1<<7) #define MPLP_IGNORE_RG (1<<8) #define MPLP_SMART_OVERLAPS (1<<10) #define MPLP_PRINT_MAPQ_CHAR (1<<11) #define MPLP_PRINT_QPOS (1<<12) // Start of struct active_cols elements #define MPLP_PRINT_QNAME (1<<13) #define MPLP_PRINT_FLAG (1<<14) #define MPLP_PRINT_RNAME (1<<15) #define MPLP_PRINT_POS (1<<16) #define MPLP_PRINT_MAPQ (1<<17) #define MPLP_PRINT_CIGAR (1<<18) #define MPLP_PRINT_RNEXT (1<<19) #define MPLP_PRINT_PNEXT (1<<20) #define MPLP_PRINT_TLEN (1<<21) #define MPLP_PRINT_SEQ (1<<22) #define MPLP_PRINT_QUAL (1<<23) #define MPLP_PRINT_RLEN (1<<24) // Must occur after struct active_cols element list #define MPLP_PRINT_MODS (1<<25) #define MPLP_PRINT_QPOS5 (1<<26) #define MPLP_PRINT_LAST (1<<27) // terminator for loop #define MPLP_MAX_DEPTH 8000 #define MPLP_MAX_INDEL_DEPTH 250 typedef struct { int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, all, rev_del; int rflag_require, rflag_filter; char *reg, *pl_list, *fai_fname, *output_fname; faidx_t *fai; void *bed, *rghash, *auxlist; int argc; char **argv; char sep, empty, no_ins, no_ins_mods, no_del, no_ends; sam_global_args ga; } mplp_conf_t; typedef struct { char *ref[2]; int ref_id[2]; hts_pos_t ref_len[2]; } mplp_ref_t; #define MPLP_REF_INIT {{NULL,NULL},{-1,-1},{0,0}} typedef struct { samFile *fp; hts_itr_t *iter; sam_hdr_t *h; mplp_ref_t *ref; const mplp_conf_t *conf; } mplp_aux_t; typedef struct { int n; int *n_plp, *m_plp; bam_pileup1_t **plp; } mplp_pileup_t; static int build_auxlist(mplp_conf_t *conf, char *optstring) { if (!optstring) return 0; void *colhash = khash_str2int_init(); if (!colhash) return 1; struct active_cols { char *name; int supported; }; const struct active_cols colnames[12] = { {"QNAME", 1}, {"FLAG", 1}, {"RNAME", 1}, {"POS", 1}, {"MAPQ", 1}, {"CIGAR", 0}, {"RNEXT", 1}, {"PNEXT", 1}, {"TLEN", 0}, {"SEQ", 0}, {"QUAL", 0}, {"RLEN", 1}, }; int i, f = MPLP_PRINT_QNAME, colno = sizeof(colnames)/sizeof(*colnames); for (i = 0; i < colno; i++, f <<= 1) if (colnames[i].supported) khash_str2int_set(colhash, colnames[i].name, f); conf->auxlist = kl_init(auxlist); if (!conf->auxlist) return 1; char *save_p; char *tag = strtok_r(optstring, ",", &save_p); while (tag) { if (khash_str2int_get(colhash, tag, &f) == 0) { conf->flag |= f; } else { if (strlen(tag) != 2) { fprintf(stderr, "[%s] tag '%s' has more than two characters or not supported\n", __func__, tag); } else { char **tag_p = kl_pushp(auxlist, conf->auxlist); *tag_p = tag; } } tag = strtok_r(NULL, ",", &save_p); } khash_str2int_destroy(colhash); return 0; } static int mplp_get_ref(mplp_aux_t *ma, int tid, char **ref, hts_pos_t *ref_len) { mplp_ref_t *r = ma->ref; //printf("get ref %d {%d/%p, %d/%p}\n", tid, r->ref_id[0], r->ref[0], r->ref_id[1], r->ref[1]); if (!r || !ma->conf->fai) { *ref = NULL; return 0; } // Do we need to reference count this so multiple mplp_aux_t can // track which references are in use? // For now we just cache the last two. Sufficient? if (tid == r->ref_id[0]) { *ref = r->ref[0]; *ref_len = r->ref_len[0]; return 1; } if (tid == r->ref_id[1]) { // Last, swap over int tmp_id; hts_pos_t tmp_len; tmp_id = r->ref_id[0]; r->ref_id[0] = r->ref_id[1]; r->ref_id[1] = tmp_id; tmp_len = r->ref_len[0]; r->ref_len[0] = r->ref_len[1]; r->ref_len[1] = tmp_len; char *tc; tc = r->ref[0]; r->ref[0] = r->ref[1]; r->ref[1] = tc; *ref = r->ref[0]; *ref_len = r->ref_len[0]; return 1; } // New, so migrate to old and load new free(r->ref[1]); r->ref[1] = r->ref[0]; r->ref_id[1] = r->ref_id[0]; r->ref_len[1] = r->ref_len[0]; r->ref_id[0] = tid; r->ref[0] = faidx_fetch_seq64(ma->conf->fai, sam_hdr_tid2name(ma->h, r->ref_id[0]), 0, HTS_POS_MAX, &r->ref_len[0]); if (!r->ref[0]) { r->ref[0] = NULL; r->ref_id[0] = -1; r->ref_len[0] = 0; *ref = NULL; return 0; } *ref = r->ref[0]; *ref_len = r->ref_len[0]; return 1; } // Initialise and destroy the base modifier state data. This is called // as each new read is added or removed from the pileups. static int pileup_cd_create(void *data, const bam1_t *b, bam_pileup_cd *cd) { int ret; hts_base_mod_state *m = hts_base_mod_state_alloc(); ret = bam_parse_basemod(b, m); cd->p = m; return ret; } static int pileup_cd_destroy(void *data, const bam1_t *b, bam_pileup_cd *cd) { hts_base_mod_state_free(cd->p); return 0; } static void print_empty_pileup(FILE *fp, const mplp_conf_t *conf, const char *tname, hts_pos_t pos, int n, const char *ref, hts_pos_t ref_len) { int i; fprintf(fp, "%s\t%"PRIhts_pos"\t%c", tname, pos+1, (ref && pos < ref_len)? ref[pos] : 'N'); for (i = 0; i < n; ++i) { fputs("\t0\t*\t*", fp); int flag_value = MPLP_PRINT_MAPQ_CHAR; while(flag_value < MPLP_PRINT_LAST) { if (flag_value != MPLP_PRINT_MODS && (conf->flag & flag_value)) fputs("\t*", fp); flag_value <<= 1; } if (conf->auxlist) { int t = 0; while(t++ < ((klist_t(auxlist) *)conf->auxlist)->size) fputs("\t*", fp); } } putc('\n', fp); } static int mplp_func(void *data, bam1_t *b) { char *ref; mplp_aux_t *ma = (mplp_aux_t*)data; int ret, skip = 0; hts_pos_t ref_len; do { int has_ref; ret = ma->iter? sam_itr_next(ma->fp, ma->iter, b) : sam_read1(ma->fp, ma->h, b); if (ret < 0) break; // The 'B' cigar operation is not part of the specification, considering as obsolete. // bam_remove_B(b); if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) { // exclude unmapped reads skip = 1; continue; } if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; } if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { skip = 1; continue; } if (ma->conf->bed && ma->conf->all == 0) { // test overlap skip = !bed_overlap(ma->conf->bed, sam_hdr_tid2name(ma->h, b->core.tid), b->core.pos, bam_endpos(b)); if (skip) continue; } if (ma->conf->rghash) { // exclude read groups uint8_t *rg = bam_aux_get(b, "RG"); skip = (rg && khash_str2int_get(ma->conf->rghash, (const char*)(rg+1), NULL)==0); if (skip) continue; } if (ma->conf->flag & MPLP_ILLUMINA13) { int i; uint8_t *qual = bam_get_qual(b); for (i = 0; i < b->core.l_qseq; ++i) qual[i] = qual[i] > 31? qual[i] - 31 : 0; } if (ma->conf->fai && b->core.tid >= 0) { has_ref = mplp_get_ref(ma, b->core.tid, &ref, &ref_len); if (has_ref && ref_len <= b->core.pos) { // exclude reads outside of the reference sequence fprintf(stderr,"[%s] Skipping because %"PRIhts_pos" is outside of %"PRIhts_pos" [ref:%d]\n", __func__, (int64_t) b->core.pos, ref_len, b->core.tid); skip = 1; continue; } } else { has_ref = 0; } skip = 0; if (has_ref && (ma->conf->flag&MPLP_REALN)) sam_prob_realn(b, ref, ref_len, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3); if (has_ref && ma->conf->capQ_thres > 10) { int q = sam_cap_mapq(b, ref, ref_len, ma->conf->capQ_thres); if (q < 0) skip = 1; else if (b->core.qual > q) b->core.qual = q; } if (b->core.qual < ma->conf->min_mq) skip = 1; else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) skip = 1; } while (skip); return ret; } /* * Performs pileup * @param conf configuration for this pileup * @param n number of files specified in fn * @param fn filenames * @param fn_idx index filenames */ static int mpileup(mplp_conf_t *conf, int nfn, char **fn, char **fn_idx) { mplp_aux_t **data; int i, tid, *n_plp, tid0 = 0, max_depth; hts_pos_t pos, beg0 = 0, end0 = HTS_POS_MAX, ref_len; const bam_pileup1_t **plp; mplp_ref_t mp_ref = MPLP_REF_INIT; bam_mplp_t iter; sam_hdr_t *h = NULL; /* header of first file in input list */ char *ref; FILE *pileup_fp = NULL; bam_sample_t *sm = NULL; kstring_t buf; mplp_pileup_t gplp; memset(&gplp, 0, sizeof(mplp_pileup_t)); memset(&buf, 0, sizeof(kstring_t)); data = calloc(nfn, sizeof(mplp_aux_t*)); plp = calloc(nfn, sizeof(bam_pileup1_t*)); n_plp = calloc(nfn, sizeof(int)); sm = bam_smpl_init(); if (nfn == 0) { fprintf(stderr,"[%s] no input file/data given\n", __func__); exit(EXIT_FAILURE); } // read the header of each file in the list and initialize data refs_t *refs = NULL; for (i = 0; i < nfn; ++i) { sam_hdr_t *h_tmp; data[i] = calloc(1, sizeof(mplp_aux_t)); data[i]->fp = sam_open_format(fn[i], "rb", &conf->ga.in); if ( !data[i]->fp ) { fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno)); exit(EXIT_FAILURE); } if (hts_set_opt(data[i]->fp, CRAM_OPT_DECODE_MD, 0)) { fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n"); exit(EXIT_FAILURE); } if (!refs && conf->fai_fname) { if (hts_set_fai_filename(data[i]->fp, conf->fai_fname) != 0) { fprintf(stderr, "[%s] failed to process %s: %s\n", __func__, conf->fai_fname, strerror(errno)); exit(EXIT_FAILURE); } refs = cram_get_refs(data[i]->fp); } else if (conf->fai_fname) { if (hts_set_opt(data[i]->fp, CRAM_OPT_SHARED_REF, refs) != 0) { fprintf(stderr, "[%s] failed to process %s: %s\n", __func__, conf->fai_fname, strerror(errno)); exit(EXIT_FAILURE); } } data[i]->conf = conf; data[i]->ref = &mp_ref; h_tmp = sam_hdr_read(data[i]->fp); if ( !h_tmp ) { fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]); exit(EXIT_FAILURE); } bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : sam_hdr_str(h_tmp)); if (conf->reg) { hts_idx_t *idx = NULL; // If index filename has not been specfied, look in BAM folder if (fn_idx != NULL) { idx = sam_index_load2(data[i]->fp, fn[i], fn_idx[i]); } else { idx = sam_index_load(data[i]->fp, fn[i]); } if (idx == NULL) { fprintf(stderr, "[%s] fail to load index for %s\n", __func__, fn[i]); exit(EXIT_FAILURE); } if ( (data[i]->iter=sam_itr_querys(idx, h_tmp, conf->reg)) == 0) { fprintf(stderr, "[E::%s] fail to parse region '%s' with %s\n", __func__, conf->reg, fn[i]); exit(EXIT_FAILURE); } if (i == 0) beg0 = data[i]->iter->beg, end0 = data[i]->iter->end, tid0 = data[i]->iter->tid; hts_idx_destroy(idx); } else data[i]->iter = NULL; if (i == 0) h = data[i]->h = h_tmp; // save the header of the first file else { // FIXME: check consistency between h and h_tmp sam_hdr_destroy(h_tmp); // we store only the first file's header; it's (alleged to be) // compatible with the i-th file's target_name lookup needs data[i]->h = h; } } fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, nfn); pileup_fp = conf->output_fname? fopen(conf->output_fname, "w") : stdout; if (pileup_fp == NULL) { fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname, strerror(errno)); exit(EXIT_FAILURE); } // init pileup iter = bam_mplp_init(nfn, mplp_func, (void**)data); if (conf->flag & MPLP_PRINT_MODS) { bam_mplp_constructor(iter, pileup_cd_create); bam_mplp_destructor(iter, pileup_cd_destroy); } if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(iter); if ( !conf->max_depth ) { max_depth = INT_MAX; fprintf(stderr, "[%s] Max depth set to maximum value (%d)\n", __func__, INT_MAX); } else { max_depth = conf->max_depth; if ( max_depth * nfn > 1<<20 ) fprintf(stderr, "[%s] Combined max depth is above 1M. Potential memory hog!\n", __func__); } bam_mplp_set_maxcnt(iter, max_depth); int ret; int last_tid = -1; hts_pos_t last_pos = -1; int one_seq = 0; // begin pileup kstring_t ks_seq = KS_INITIALIZE; kstring_t ks_mod = KS_INITIALIZE; kstring_t ks_qual = KS_INITIALIZE; while ( (ret=bam_mplp64_auto(iter, &tid, &pos, n_plp, plp)) > 0) { one_seq = 1; // at least 1 output if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested if (conf->all) { // Deal with missing portions of previous tids while (tid > last_tid) { if (last_tid >= 0 && !conf->reg) { while (++last_pos < sam_hdr_tid2len(h, last_tid)) { if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, last_tid), last_pos, last_pos + 1) == 0) continue; print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, last_tid), last_pos, nfn, ref, ref_len); } } last_tid++; last_pos = -1; if (conf->all < 2) break; if (tid > last_tid) // multiple missing references and -aa used mplp_get_ref(data[0], last_tid, &ref, &ref_len); } } mplp_get_ref(data[0], tid, &ref, &ref_len); if (conf->all) { // Deal with missing portion of current tid while (++last_pos < pos) { if (conf->reg && last_pos < beg0) continue; // out of range; skip if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, tid), last_pos, last_pos + 1) == 0) continue; print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, tid), last_pos, nfn, ref, ref_len); } last_tid = tid; last_pos = pos; } if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, sam_hdr_tid2name(h, tid), pos, pos+1)) continue; fprintf(pileup_fp, "%s\t%"PRIhts_pos"\t%c", sam_hdr_tid2name(h, tid), pos + 1, (ref && pos < ref_len)? ref[pos] : 'N'); for (i = 0; i < nfn; ++i) { int j, cnt, err = 0; ks_clear(&ks_seq); ks_clear(&ks_qual); ks_clear(&ks_mod); for (j = cnt = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; int c = p->qpos < p->b->core.l_qseq ? bam_get_qual(p->b)[p->qpos] : 0; if (c >= conf->min_baseQ) { // Build up seq err |= pileup_seq(&ks_seq, plp[i] + j, pos, ref_len, ref, &ks_mod, conf->rev_del, conf->no_ins, conf->no_ins_mods, conf->no_del, conf->no_ends) < 0; // Build up qual err |= kputc_(c+33 < 126 ? c+33 : 126, &ks_qual) < 0; cnt++; } } if (err) { ret = 1; goto fail; } fprintf(pileup_fp, "\t%d\t", cnt); if (n_plp[i] == 0) { fputs("*\t*", pileup_fp); int flag_value = MPLP_PRINT_MAPQ_CHAR; while(flag_value < MPLP_PRINT_LAST) { if (flag_value != MPLP_PRINT_MODS && (conf->flag & flag_value)) fputs("\t*", pileup_fp); flag_value <<= 1; } if (conf->auxlist) { int t = 0; while(t++ < ((klist_t(auxlist) *)conf->auxlist)->size) fputs("\t*", pileup_fp); } } else { if (ks_seq.l) { fwrite(ks_seq.s, 1, ks_seq.l, pileup_fp); } else { putc('*', pileup_fp); } putc('\t', pileup_fp); if (ks_qual.l) { fwrite(ks_qual.s, 1, ks_qual.l, pileup_fp); } else { putc('*', pileup_fp); } /* Print selected columns */ int flag_value = MPLP_PRINT_MAPQ_CHAR; while(flag_value < MPLP_PRINT_LAST) { if (flag_value != MPLP_PRINT_MODS && (conf->flag & flag_value)) { int n = 0; putc('\t', pileup_fp); for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = &plp[i][j]; int c = p->qpos < p->b->core.l_qseq ? bam_get_qual(p->b)[p->qpos] : 0; if ( c < conf->min_baseQ ) continue; if (n > 0 && flag_value != MPLP_PRINT_MAPQ_CHAR) putc(',', pileup_fp); n++; switch (flag_value) { case MPLP_PRINT_MAPQ_CHAR: c = p->b->core.qual + 33; if (c > 126) c = 126; putc(c, pileup_fp); break; case MPLP_PRINT_QPOS: // query position in current orientation fprintf(pileup_fp, "%d", p->qpos + 1); break; case MPLP_PRINT_QPOS5: { // query position in 5' to 3' orientation int pos5 = bam_is_rev(p->b) ? p->b->core.l_qseq-p->qpos + p->is_del : p->qpos + 1; fprintf(pileup_fp, "%d", pos5); break; } case MPLP_PRINT_QNAME: fputs(bam_get_qname(p->b), pileup_fp); break; case MPLP_PRINT_FLAG: fprintf(pileup_fp, "%d", p->b->core.flag); break; case MPLP_PRINT_RNAME: if (p->b->core.tid >= 0) fputs(sam_hdr_tid2name(h, p->b->core.tid), pileup_fp); else putc('*', pileup_fp); break; case MPLP_PRINT_POS: fprintf(pileup_fp, "%"PRId64, (int64_t) p->b->core.pos + 1); break; case MPLP_PRINT_MAPQ: fprintf(pileup_fp, "%d", p->b->core.qual); break; case MPLP_PRINT_RNEXT: if (p->b->core.mtid >= 0) fputs(sam_hdr_tid2name(h, p->b->core.mtid), pileup_fp); else putc('*', pileup_fp); break; case MPLP_PRINT_PNEXT: fprintf(pileup_fp, "%"PRId64, (int64_t) p->b->core.mpos + 1); break; case MPLP_PRINT_RLEN: fprintf(pileup_fp, "%d", p->b->core.l_qseq); break; } } if (!n) putc('*', pileup_fp); } flag_value <<= 1; } /* Print selected tags */ klist_t(auxlist) *auxlist_p = ((klist_t(auxlist) *)conf->auxlist); if (auxlist_p && auxlist_p->size) { kliter_t(auxlist) *aux; for (aux = kl_begin(auxlist_p); aux != kl_end(auxlist_p); aux = kl_next(aux)) { int n = 0; // NB shadows outer loop putc('\t', pileup_fp); for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = &plp[i][j]; int c = p->qpos < p->b->core.l_qseq ? bam_get_qual(p->b)[p->qpos] : 0; if ( c < conf->min_baseQ ) continue; if (n > 0) putc(conf->sep, pileup_fp); n++; uint8_t* tag_u = bam_aux_get(p->b, kl_val(aux)); if (!tag_u) { putc(conf->empty , pileup_fp); continue; } int tag_supported = 0; /* Tag value is string */ if (*tag_u == 'Z' || *tag_u == 'H') { char *tag_s = bam_aux2Z(tag_u); if (!tag_s) continue; fputs(tag_s, pileup_fp); tag_supported = 1; } /* Tag value is integer */ if (*tag_u == 'I' || *tag_u == 'i' || *tag_u == 'C' || *tag_u == 'c' || *tag_u == 'S' || *tag_u == 's') { int64_t tag_i = bam_aux2i(tag_u); fprintf(pileup_fp, "%" PRId64 "", tag_i); tag_supported = 1; } /* Tag value is float */ if (*tag_u == 'd' || *tag_u == 'f') { double tag_f = bam_aux2f(tag_u); fprintf(pileup_fp, "%lf", tag_f); tag_supported = 1; } /* Tag value is character */ if (*tag_u == 'A') { char tag_c = bam_aux2A(tag_u); putc(tag_c, pileup_fp); tag_supported = 1; } if (!tag_supported) putc('*', pileup_fp); } if (!n) putc('*', pileup_fp); } } } } putc('\n', pileup_fp); } ks_free(&ks_seq); ks_free(&ks_mod); ks_free(&ks_qual); if (ret < 0) { print_error("mpileup", "error reading from input file"); ret = EXIT_FAILURE; goto fail; } if (conf->all) { // Handle terminating region if (last_tid < 0 && conf->reg && conf->all > 1) { last_tid = tid0; last_pos = beg0-1; mplp_get_ref(data[0], tid0, &ref, &ref_len); } else if (last_tid < 0 && !one_seq && conf->all > 1) { last_tid = 0; // --aa on a blank file } while (last_tid >= 0 && last_tid < sam_hdr_nref(h)) { mplp_get_ref(data[0], last_tid, &ref, &ref_len); while (++last_pos < sam_hdr_tid2len(h, last_tid)) { if (last_pos >= end0) break; if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, last_tid), last_pos, last_pos + 1) == 0) continue; print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, last_tid), last_pos, nfn, ref, ref_len); } last_tid++; last_pos = -1; if (conf->all < 2 || conf->reg) break; } } fail: // clean up if (pileup_fp && conf->output_fname) fclose(pileup_fp); bam_smpl_destroy(sm); free(buf.s); for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]); free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp); bam_mplp_destroy(iter); sam_hdr_destroy(h); for (i = 0; i < nfn; ++i) { sam_close(data[i]->fp); if (data[i]->iter) hts_itr_destroy(data[i]->iter); free(data[i]); } free(data); free(plp); free(n_plp); free(mp_ref.ref[0]); free(mp_ref.ref[1]); return ret; } static int is_url(const char *s) { static const char uri_scheme_chars[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+.-"; return s[strspn(s, uri_scheme_chars)] == ':'; } #define MAX_PATH_LEN 1024 int read_file_list(const char *file_list,int *n,char **argv[]) { char buf[MAX_PATH_LEN]; int len, nfiles = 0; char **files = NULL; struct stat sb; *n = 0; *argv = NULL; FILE *fh = fopen(file_list,"r"); if ( !fh ) { fprintf(stderr,"%s: %s\n", file_list,strerror(errno)); return 1; } files = calloc(nfiles,sizeof(char*)); nfiles = 0; while ( fgets(buf,MAX_PATH_LEN,fh) ) { // allow empty lines and trailing spaces len = strlen(buf); while ( len>0 && isspace(buf[len-1]) ) len--; if ( !len ) continue; // check sanity of the file list buf[len] = 0; if (! (is_url(buf) || stat(buf, &sb) == 0)) { // no such file, check if it is safe to print its name int i, safe_to_print = 1; for (i=0; irflag_require); char *tmp_filter = bam_flag2str(mplp->rflag_filter); // Display usage information, formatted for the standard 80 columns. // (The unusual string formatting here aids the readability of this // source code in 80 columns, to the extent that's possible.) fprintf(fp, "\n" "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n" "\n" "Input options:\n" " -6, --illumina1.3+ quality is in the Illumina-1.3+ encoding\n" " -A, --count-orphans do not discard anomalous read pairs\n" " -b, --bam-list FILE list of input BAM filenames, one per line\n" " -B, --no-BAQ disable BAQ (per-Base Alignment Quality)\n" " -C, --adjust-MQ INT adjust mapping quality; recommended:50, disable:0 [0]\n" " -d, --max-depth INT max per-file depth; avoids excessive memory usage [%d]\n", mplp->max_depth); fprintf(fp, " -E, --redo-BAQ recalculate BAQ on the fly, ignore existing BQs\n" " -f, --fasta-ref FILE faidx indexed reference sequence file\n" " -G, --exclude-RG FILE exclude read groups listed in FILE\n" " -l, --positions FILE skip unlisted positions (chr pos) or regions (BED)\n" " -q, --min-MQ INT skip alignments with mapQ smaller than INT [%d]\n", mplp->min_mq); fprintf(fp, " -Q, --min-BQ INT skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ); fprintf(fp, " -r, --region REG region in which pileup is generated\n" " -R, --ignore-RG ignore RG tags (one BAM = one sample)\n" " --rf, --incl-flags STR|INT\n" " required flags: only include reads with any of\n" " the mask bits set [%s]\n", tmp_require); fprintf(fp, " --ff, --excl-flags STR|INT\n" " filter flags: skip reads with any of the mask bits set\n" " [%s]\n", tmp_filter); fprintf(fp, " -x, --ignore-overlaps-removal, --disable-overlap-removal\n" " disable read-pair overlap detection and removal\n" " -X, --customized-index use customized index files\n" // -X flag for index filename "\n" "Output options:\n" " -o, --output FILE write output to FILE [standard output]\n" " -O, --output-BP output base positions on reads, current orientation\n" " --output-BP-5 output base positions on reads, 5' to 3' orientation\n" " -M, --output-mods output base modifications\n" " -s, --output-MQ output mapping quality\n" " --output-QNAME output read names\n" " --output-extra STR output extra read fields and read tag values\n" " --output-sep CHAR set the separator character for tag lists [,]\n" " --output-empty CHAR set the no value character for tag lists [*]\n" " --no-output-ins skip insertion sequence after +NUM\n" " Use twice for complete insertion removal\n" " --no-output-ins-mods don't display base modifications within insertions\n" " --no-output-del skip deletion sequence after -NUM\n" " Use twice for complete deletion removal\n" " --no-output-ends remove ^MQUAL and $ markup in sequence column\n" " --reverse-del use '#' character for deletions on the reverse strand\n" " -a output all positions (including zero depth)\n" " -a -a (or -aa) output absolutely all positions, including unused ref. sequences\n" "\n" "Generic options:\n"); sam_global_opt_help(fp, "-.--.--."); fprintf(fp, "\n" "Note that using \"samtools mpileup\" to generate BCF or VCF files has been\n" "removed. To output these formats, please use \"bcftools mpileup\" instead.\n"); free(tmp_require); free(tmp_filter); } int bam_mpileup(int argc, char *argv[]) { int c; const char *file_list = NULL; char **fn = NULL; int nfiles = 0, use_orphan = 0, has_index_file = 0; mplp_conf_t mplp; memset(&mplp, 0, sizeof(mplp_conf_t)); mplp.min_baseQ = 13; mplp.capQ_thres = 0; mplp.max_depth = MPLP_MAX_DEPTH; mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN | MPLP_SMART_OVERLAPS; mplp.argc = argc; mplp.argv = argv; mplp.rflag_filter = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP; mplp.output_fname = NULL; mplp.all = 0; mplp.rev_del = 0; mplp.sep = ','; mplp.empty = '*'; sam_global_args_init(&mplp.ga); static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '-'), {"rf", required_argument, NULL, 1}, // require flag {"ff", required_argument, NULL, 2}, // filter flag {"incl-flags", required_argument, NULL, 1}, {"excl-flags", required_argument, NULL, 2}, {"output", required_argument, NULL, 3}, {"output-QNAME", no_argument, NULL, 5}, {"output-qname", no_argument, NULL, 5}, {"illumina1.3+", no_argument, NULL, '6'}, {"count-orphans", no_argument, NULL, 'A'}, {"bam-list", required_argument, NULL, 'b'}, {"no-BAQ", no_argument, NULL, 'B'}, {"no-baq", no_argument, NULL, 'B'}, {"adjust-MQ", required_argument, NULL, 'C'}, {"adjust-mq", required_argument, NULL, 'C'}, {"max-depth", required_argument, NULL, 'd'}, {"redo-BAQ", no_argument, NULL, 'E'}, {"redo-baq", no_argument, NULL, 'E'}, {"fasta-ref", required_argument, NULL, 'f'}, {"exclude-RG", required_argument, NULL, 'G'}, {"exclude-rg", required_argument, NULL, 'G'}, {"positions", required_argument, NULL, 'l'}, {"region", required_argument, NULL, 'r'}, {"ignore-RG", no_argument, NULL, 'R'}, {"ignore-rg", no_argument, NULL, 'R'}, {"min-MQ", required_argument, NULL, 'q'}, {"min-mq", required_argument, NULL, 'q'}, {"min-BQ", required_argument, NULL, 'Q'}, {"min-bq", required_argument, NULL, 'Q'}, // NB: old "--ignore-overlaps" auto-completes to this {"ignore-overlaps-removal", no_argument, NULL, 'x'}, {"disable-overlap-removal", no_argument, NULL, 'x'}, {"output-mods", no_argument, NULL, 'M'}, {"output-BP", no_argument, NULL, 'O'}, {"output-bp", no_argument, NULL, 'O'}, {"output-BP-5", no_argument, NULL, 14}, {"output-bp-5", no_argument, NULL, 14}, {"output-MQ", no_argument, NULL, 's'}, {"output-mq", no_argument, NULL, 's'}, {"ext-prob", required_argument, NULL, 'e'}, {"gap-frac", required_argument, NULL, 'F'}, {"tandem-qual", required_argument, NULL, 'h'}, {"skip-indels", no_argument, NULL, 'I'}, {"max-idepth", required_argument, NULL, 'L'}, {"min-ireads ", required_argument, NULL, 'm'}, {"per-sample-mF", no_argument, NULL, 'p'}, {"per-sample-mf", no_argument, NULL, 'p'}, {"platforms", required_argument, NULL, 'P'}, {"customized-index", no_argument, NULL, 'X'}, {"reverse-del", no_argument, NULL, 6}, {"output-extra", required_argument, NULL, 7}, {"output-sep", required_argument, NULL, 8}, {"output-empty", required_argument, NULL, 9}, {"no-output-ins", no_argument, NULL, 10}, {"no-output-ins-mods", no_argument, NULL, 11}, {"no-output-del", no_argument, NULL, 12}, {"no-output-ends", no_argument, NULL, 13}, {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "Af:r:l:q:Q:RC:Bd:b:o:EG:6OsxXaM",lopts,NULL)) >= 0) { switch (c) { case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break; case 1 : mplp.rflag_require = bam_str2flag(optarg); if ( mplp.rflag_require<0 ) { fprintf(stderr,"Could not parse --rf %s\n", optarg); return 1; } break; case 2 : mplp.rflag_filter = bam_str2flag(optarg); if ( mplp.rflag_filter<0 ) { fprintf(stderr,"Could not parse --ff %s\n", optarg); return 1; } break; case 3 : mplp.output_fname = optarg; break; case 5 : mplp.flag |= MPLP_PRINT_QNAME; break; case 6 : mplp.rev_del = 1; break; case 7 : if (build_auxlist(&mplp, optarg) != 0) { fprintf(stderr,"Could not build aux list using '%s'\n", optarg); return 1; } break; case 8: mplp.sep = optarg[0]; break; case 9: mplp.empty = optarg[0]; break; case 10: mplp.no_ins++; break; case 11: mplp.no_ins_mods = 1; break; case 12: mplp.no_del++; break; case 13: mplp.no_ends = 1; break; case 'f': mplp.fai = fai_load(optarg); if (mplp.fai == NULL) return 1; mplp.fai_fname = optarg; break; case 'd': mplp.max_depth = atoi(optarg); break; case 'r': mplp.reg = strdup(optarg); break; case 'l': // In the original version the whole BAM was streamed which is inefficient // with few BED intervals and big BAMs. Todo: devise a heuristic to determine // best strategy, that is streaming or jumping. mplp.bed = bed_read(optarg); if (!mplp.bed) { print_error_errno("mpileup", "Could not read file \"%s\"", optarg); return 1; } break; case 'B': mplp.flag &= ~MPLP_REALN; break; case 'X': has_index_file = 1; break; case 'E': mplp.flag |= MPLP_REDO_BAQ; break; case '6': mplp.flag |= MPLP_ILLUMINA13; break; case 'R': mplp.flag |= MPLP_IGNORE_RG; break; case 's': mplp.flag |= MPLP_PRINT_MAPQ_CHAR; break; case 'O': mplp.flag |= MPLP_PRINT_QPOS; break; case 14: mplp.flag |= MPLP_PRINT_QPOS5; break; case 'M': mplp.flag |= MPLP_PRINT_MODS; break; case 'C': mplp.capQ_thres = atoi(optarg); break; case 'q': mplp.min_mq = atoi(optarg); break; case 'Q': mplp.min_baseQ = atoi(optarg); break; case 'b': file_list = optarg; break; case 'o': mplp.output_fname = optarg; break; case 'A': use_orphan = 1; break; case 'G': { FILE *fp_rg; char buf[1024]; mplp.rghash = khash_str2int_init(); if ((fp_rg = fopen(optarg, "r")) == NULL) fprintf(stderr, "[%s] Fail to open file %s. Continue anyway.\n", __func__, optarg); while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but forgive me... khash_str2int_inc(mplp.rghash, strdup(buf)); fclose(fp_rg); } break; case 'a': mplp.all++; break; default: if (parse_sam_global_opt(c, optarg, lopts, &mplp.ga) == 0) break; /* else fall-through */ case '?': print_usage(stderr, &mplp); return 1; } } if (!mplp.fai && mplp.ga.reference) { mplp.fai_fname = mplp.ga.reference; mplp.fai = fai_load(mplp.fai_fname); if (mplp.fai == NULL) return 1; } if ( !(mplp.flag&MPLP_REALN) && mplp.flag&MPLP_REDO_BAQ ) { fprintf(stderr,"Error: The -B option cannot be combined with -E\n"); return 1; } if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN; if (argc == 1) { print_usage(stderr, &mplp); return 1; } int ret; if (file_list) { if (has_index_file) { fprintf(stderr,"Error: The -b option cannot be combined with -X\n"); // No customize index loc in file list mode return 1; } if ( read_file_list(file_list,&nfiles,&fn) ) return 1; ret = mpileup(&mplp,nfiles,fn,NULL); for (c=0; c Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "samtools.h" #include "bedidx.h" #include "sam_opts.h" #include "bam_plbuf.h" #define dummy_free(p) KLIST_INIT(auxlist, char *, dummy_free) int pileup_seq(kstring_t *ks_seq, const bam_pileup1_t *p, hts_pos_t pos, hts_pos_t ref_len, const char *ref, kstring_t *ks_mod, int rev_del, int no_ins, int no_ins_mods, int no_del, int no_ends) { no_ins_mods |= no_ins; int j, err = 0; hts_base_mod_state *m = p->cd.p; if (!no_ends && p->is_head) { err |= kputc_('^', ks_seq) < 0; err |= kputc_(p->b->core.qual > 93 ? 126 : p->b->core.qual + 33, ks_seq) < 0; } if (!p->is_del) { // See seq_nt16_str in htslib/hts.c const char seq_nt_str_lc[] = ",acmgrsvtwyhkdbn"; // reverse strand const char seq_nt_str_uc[] = ".ACMGRSVTWYHKDBN"; int c = p->qpos < p->b->core.l_qseq ? bam_seqi(bam_get_seq(p->b), p->qpos) : 15 /*N*/; if (ref) { int rb = pos < ref_len ? seq_nt16_table[(uint8_t)(ref[pos])] : 15/*N*/; if (c == rb) c = 0; // "=", which becomes . or , } c = bam_is_rev(p->b) ? seq_nt_str_lc[c] : seq_nt_str_uc[c]; err |= kputc_(c, ks_seq) < 0; if (m) { int nm; hts_base_mod mod[256]; if ((nm = bam_mods_at_qpos(p->b, p->qpos, m, mod, 256)) > 0) { err |= kputc_('[', ks_seq) < 0; int j; for (j = 0; j < nm && j < 256; j++) { char qual[20]; if (mod[j].qual >= 0) sprintf(qual, "%d", mod[j].qual); else *qual = 0; if (mod[j].modified_base < 0) // ChEBI err |= ksprintf(ks_seq, "%c(%d)%s", "+-"[mod[j].strand], -mod[j].modified_base, qual) < 0; else err |= ksprintf(ks_seq, "%c%c%s", "+-"[mod[j].strand], mod[j].modified_base, qual) < 0; } err |= kputc_(']', ks_seq) < 0; } } } else { err |= kputc_(p->is_refskip ? (bam_is_rev(p->b)? '<' : '>') : ((bam_is_rev(p->b) && rev_del) ? '#' : '*'), ks_seq) < 0; } int del_len = -p->indel; if (p->indel > 0) { int len = bam_plp_insertion_mod(p, m && !no_ins_mods ? m : NULL, ks_mod, &del_len); if (len < 0) { print_error("mpileup", "bam_plp_insertion() failed"); return -1; } if (no_ins < 2) { err |= kputc_('+', ks_seq) < 0; err |= kputuw(len, ks_seq) < 0; } if (!no_ins) { kstring_t *ks = ks_mod; if (bam_is_rev(p->b)) { char pad = rev_del ? '#' : '*'; int in_mod = 0; for (j = 0; j < ks->l; j++) { if (ks->s[j] == '[') in_mod = 1; else if (ks->s[j] == ']') in_mod = 0; err |= kputc_(ks->s[j] != '*' ? (in_mod ? ks->s[j] : tolower(ks->s[j])) : pad, ks_seq) < 0; } } else { int in_mod = 0; for (j = 0; j < ks->l; j++) { if (ks->s[j] == '[') in_mod = 1; if (ks->s[j] == ']') in_mod = 0; err |= kputc_(in_mod ? ks->s[j] : toupper(ks->s[j]), ks_seq) < 0; } } } } if (del_len > 0) { if (no_del < 2) err |= kputw(-del_len, ks_seq) < 0; if (!no_del) { for (j = 1; j <= del_len; ++j) { int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N'; err |= kputc_(bam_is_rev(p->b)? tolower(c) : toupper(c), ks_seq) < 0; } } } if (!no_ends && p->is_tail) err |= kputc_('$', ks_seq) < 0; return -err; } #include "sample.h" #define MPLP_NO_COMP (1<<2) #define MPLP_NO_ORPHAN (1<<3) #define MPLP_REALN (1<<4) #define MPLP_NO_INDEL (1<<5) #define MPLP_REDO_BAQ (1<<6) #define MPLP_ILLUMINA13 (1<<7) #define MPLP_IGNORE_RG (1<<8) #define MPLP_SMART_OVERLAPS (1<<10) #define MPLP_PRINT_MAPQ_CHAR (1<<11) #define MPLP_PRINT_QPOS (1<<12) // Start of struct active_cols elements #define MPLP_PRINT_QNAME (1<<13) #define MPLP_PRINT_FLAG (1<<14) #define MPLP_PRINT_RNAME (1<<15) #define MPLP_PRINT_POS (1<<16) #define MPLP_PRINT_MAPQ (1<<17) #define MPLP_PRINT_CIGAR (1<<18) #define MPLP_PRINT_RNEXT (1<<19) #define MPLP_PRINT_PNEXT (1<<20) #define MPLP_PRINT_TLEN (1<<21) #define MPLP_PRINT_SEQ (1<<22) #define MPLP_PRINT_QUAL (1<<23) #define MPLP_PRINT_RLEN (1<<24) // Must occur after struct active_cols element list #define MPLP_PRINT_MODS (1<<25) #define MPLP_PRINT_QPOS5 (1<<26) #define MPLP_PRINT_LAST (1<<27) // terminator for loop #define MPLP_MAX_DEPTH 8000 #define MPLP_MAX_INDEL_DEPTH 250 typedef struct { int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, all, rev_del; int rflag_require, rflag_filter; char *reg, *pl_list, *fai_fname, *output_fname; faidx_t *fai; void *bed, *rghash, *auxlist; int argc; char **argv; char sep, empty, no_ins, no_ins_mods, no_del, no_ends; sam_global_args ga; } mplp_conf_t; typedef struct { char *ref[2]; int ref_id[2]; hts_pos_t ref_len[2]; } mplp_ref_t; #define MPLP_REF_INIT {{NULL,NULL},{-1,-1},{0,0}} typedef struct { samFile *fp; hts_itr_t *iter; sam_hdr_t *h; mplp_ref_t *ref; const mplp_conf_t *conf; } mplp_aux_t; typedef struct { int n; int *n_plp, *m_plp; bam_pileup1_t **plp; } mplp_pileup_t; static int build_auxlist(mplp_conf_t *conf, char *optstring) { if (!optstring) return 0; void *colhash = khash_str2int_init(); if (!colhash) return 1; struct active_cols { char *name; int supported; }; const struct active_cols colnames[12] = { {"QNAME", 1}, {"FLAG", 1}, {"RNAME", 1}, {"POS", 1}, {"MAPQ", 1}, {"CIGAR", 0}, {"RNEXT", 1}, {"PNEXT", 1}, {"TLEN", 0}, {"SEQ", 0}, {"QUAL", 0}, {"RLEN", 1}, }; int i, f = MPLP_PRINT_QNAME, colno = sizeof(colnames)/sizeof(*colnames); for (i = 0; i < colno; i++, f <<= 1) if (colnames[i].supported) khash_str2int_set(colhash, colnames[i].name, f); conf->auxlist = kl_init(auxlist); if (!conf->auxlist) return 1; char *save_p; char *tag = strtok_r(optstring, ",", &save_p); while (tag) { if (khash_str2int_get(colhash, tag, &f) == 0) { conf->flag |= f; } else { if (strlen(tag) != 2) { fprintf(samtools_stderr, "[%s] tag '%s' has more than two characters or not supported\n", __func__, tag); } else { char **tag_p = kl_pushp(auxlist, conf->auxlist); *tag_p = tag; } } tag = strtok_r(NULL, ",", &save_p); } khash_str2int_destroy(colhash); return 0; } static int mplp_get_ref(mplp_aux_t *ma, int tid, char **ref, hts_pos_t *ref_len) { mplp_ref_t *r = ma->ref; //printf("get ref %d {%d/%p, %d/%p}\n", tid, r->ref_id[0], r->ref[0], r->ref_id[1], r->ref[1]); if (!r || !ma->conf->fai) { *ref = NULL; return 0; } // Do we need to reference count this so multiple mplp_aux_t can // track which references are in use? // For now we just cache the last two. Sufficient? if (tid == r->ref_id[0]) { *ref = r->ref[0]; *ref_len = r->ref_len[0]; return 1; } if (tid == r->ref_id[1]) { // Last, swap over int tmp_id; hts_pos_t tmp_len; tmp_id = r->ref_id[0]; r->ref_id[0] = r->ref_id[1]; r->ref_id[1] = tmp_id; tmp_len = r->ref_len[0]; r->ref_len[0] = r->ref_len[1]; r->ref_len[1] = tmp_len; char *tc; tc = r->ref[0]; r->ref[0] = r->ref[1]; r->ref[1] = tc; *ref = r->ref[0]; *ref_len = r->ref_len[0]; return 1; } // New, so migrate to old and load new free(r->ref[1]); r->ref[1] = r->ref[0]; r->ref_id[1] = r->ref_id[0]; r->ref_len[1] = r->ref_len[0]; r->ref_id[0] = tid; r->ref[0] = faidx_fetch_seq64(ma->conf->fai, sam_hdr_tid2name(ma->h, r->ref_id[0]), 0, HTS_POS_MAX, &r->ref_len[0]); if (!r->ref[0]) { r->ref[0] = NULL; r->ref_id[0] = -1; r->ref_len[0] = 0; *ref = NULL; return 0; } *ref = r->ref[0]; *ref_len = r->ref_len[0]; return 1; } // Initialise and destroy the base modifier state data. This is called // as each new read is added or removed from the pileups. static int pileup_cd_create(void *data, const bam1_t *b, bam_pileup_cd *cd) { int ret; hts_base_mod_state *m = hts_base_mod_state_alloc(); ret = bam_parse_basemod(b, m); cd->p = m; return ret; } static int pileup_cd_destroy(void *data, const bam1_t *b, bam_pileup_cd *cd) { hts_base_mod_state_free(cd->p); return 0; } static void print_empty_pileup(FILE *fp, const mplp_conf_t *conf, const char *tname, hts_pos_t pos, int n, const char *ref, hts_pos_t ref_len) { int i; fprintf(fp, "%s\t%"PRIhts_pos"\t%c", tname, pos+1, (ref && pos < ref_len)? ref[pos] : 'N'); for (i = 0; i < n; ++i) { fputs("\t0\t*\t*", fp); int flag_value = MPLP_PRINT_MAPQ_CHAR; while(flag_value < MPLP_PRINT_LAST) { if (flag_value != MPLP_PRINT_MODS && (conf->flag & flag_value)) fputs("\t*", fp); flag_value <<= 1; } if (conf->auxlist) { int t = 0; while(t++ < ((klist_t(auxlist) *)conf->auxlist)->size) fputs("\t*", fp); } } putc('\n', fp); } static int mplp_func(void *data, bam1_t *b) { char *ref; mplp_aux_t *ma = (mplp_aux_t*)data; int ret, skip = 0; hts_pos_t ref_len; do { int has_ref; ret = ma->iter? sam_itr_next(ma->fp, ma->iter, b) : sam_read1(ma->fp, ma->h, b); if (ret < 0) break; // The 'B' cigar operation is not part of the specification, considering as obsolete. // bam_remove_B(b); if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) { // exclude unmapped reads skip = 1; continue; } if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; } if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { skip = 1; continue; } if (ma->conf->bed && ma->conf->all == 0) { // test overlap skip = !bed_overlap(ma->conf->bed, sam_hdr_tid2name(ma->h, b->core.tid), b->core.pos, bam_endpos(b)); if (skip) continue; } if (ma->conf->rghash) { // exclude read groups uint8_t *rg = bam_aux_get(b, "RG"); skip = (rg && khash_str2int_get(ma->conf->rghash, (const char*)(rg+1), NULL)==0); if (skip) continue; } if (ma->conf->flag & MPLP_ILLUMINA13) { int i; uint8_t *qual = bam_get_qual(b); for (i = 0; i < b->core.l_qseq; ++i) qual[i] = qual[i] > 31? qual[i] - 31 : 0; } if (ma->conf->fai && b->core.tid >= 0) { has_ref = mplp_get_ref(ma, b->core.tid, &ref, &ref_len); if (has_ref && ref_len <= b->core.pos) { // exclude reads outside of the reference sequence fprintf(samtools_stderr,"[%s] Skipping because %"PRIhts_pos" is outside of %"PRIhts_pos" [ref:%d]\n", __func__, (int64_t) b->core.pos, ref_len, b->core.tid); skip = 1; continue; } } else { has_ref = 0; } skip = 0; if (has_ref && (ma->conf->flag&MPLP_REALN)) sam_prob_realn(b, ref, ref_len, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3); if (has_ref && ma->conf->capQ_thres > 10) { int q = sam_cap_mapq(b, ref, ref_len, ma->conf->capQ_thres); if (q < 0) skip = 1; else if (b->core.qual > q) b->core.qual = q; } if (b->core.qual < ma->conf->min_mq) skip = 1; else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) skip = 1; } while (skip); return ret; } /* * Performs pileup * @param conf configuration for this pileup * @param n number of files specified in fn * @param fn filenames * @param fn_idx index filenames */ static int mpileup(mplp_conf_t *conf, int nfn, char **fn, char **fn_idx) { mplp_aux_t **data; int i, tid, *n_plp, tid0 = 0, max_depth; hts_pos_t pos, beg0 = 0, end0 = HTS_POS_MAX, ref_len; const bam_pileup1_t **plp; mplp_ref_t mp_ref = MPLP_REF_INIT; bam_mplp_t iter; sam_hdr_t *h = NULL; /* header of first file in input list */ char *ref; FILE *pileup_fp = NULL; bam_sample_t *sm = NULL; kstring_t buf; mplp_pileup_t gplp; memset(&gplp, 0, sizeof(mplp_pileup_t)); memset(&buf, 0, sizeof(kstring_t)); data = calloc(nfn, sizeof(mplp_aux_t*)); plp = calloc(nfn, sizeof(bam_pileup1_t*)); n_plp = calloc(nfn, sizeof(int)); sm = bam_smpl_init(); if (nfn == 0) { fprintf(samtools_stderr,"[%s] no input file/data given\n", __func__); samtools_exit(EXIT_FAILURE); } // read the header of each file in the list and initialize data refs_t *refs = NULL; for (i = 0; i < nfn; ++i) { sam_hdr_t *h_tmp; data[i] = calloc(1, sizeof(mplp_aux_t)); data[i]->fp = sam_open_format(fn[i], "rb", &conf->ga.in); if ( !data[i]->fp ) { fprintf(samtools_stderr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno)); samtools_exit(EXIT_FAILURE); } if (hts_set_opt(data[i]->fp, CRAM_OPT_DECODE_MD, 0)) { fprintf(samtools_stderr, "Failed to set CRAM_OPT_DECODE_MD value\n"); samtools_exit(EXIT_FAILURE); } if (!refs && conf->fai_fname) { if (hts_set_fai_filename(data[i]->fp, conf->fai_fname) != 0) { fprintf(samtools_stderr, "[%s] failed to process %s: %s\n", __func__, conf->fai_fname, strerror(errno)); samtools_exit(EXIT_FAILURE); } refs = cram_get_refs(data[i]->fp); } else if (conf->fai_fname) { if (hts_set_opt(data[i]->fp, CRAM_OPT_SHARED_REF, refs) != 0) { fprintf(samtools_stderr, "[%s] failed to process %s: %s\n", __func__, conf->fai_fname, strerror(errno)); samtools_exit(EXIT_FAILURE); } } data[i]->conf = conf; data[i]->ref = &mp_ref; h_tmp = sam_hdr_read(data[i]->fp); if ( !h_tmp ) { fprintf(samtools_stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]); samtools_exit(EXIT_FAILURE); } bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : sam_hdr_str(h_tmp)); if (conf->reg) { hts_idx_t *idx = NULL; // If index filename has not been specfied, look in BAM folder if (fn_idx != NULL) { idx = sam_index_load2(data[i]->fp, fn[i], fn_idx[i]); } else { idx = sam_index_load(data[i]->fp, fn[i]); } if (idx == NULL) { fprintf(samtools_stderr, "[%s] fail to load index for %s\n", __func__, fn[i]); samtools_exit(EXIT_FAILURE); } if ( (data[i]->iter=sam_itr_querys(idx, h_tmp, conf->reg)) == 0) { fprintf(samtools_stderr, "[E::%s] fail to parse region '%s' with %s\n", __func__, conf->reg, fn[i]); samtools_exit(EXIT_FAILURE); } if (i == 0) beg0 = data[i]->iter->beg, end0 = data[i]->iter->end, tid0 = data[i]->iter->tid; hts_idx_destroy(idx); } else data[i]->iter = NULL; if (i == 0) h = data[i]->h = h_tmp; // save the header of the first file else { // FIXME: check consistency between h and h_tmp sam_hdr_destroy(h_tmp); // we store only the first file's header; it's (alleged to be) // compatible with the i-th file's target_name lookup needs data[i]->h = h; } } fprintf(samtools_stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, nfn); pileup_fp = conf->output_fname? fopen(conf->output_fname, "w") : samtools_stdout; if (pileup_fp == NULL) { fprintf(samtools_stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname, strerror(errno)); samtools_exit(EXIT_FAILURE); } // init pileup iter = bam_mplp_init(nfn, mplp_func, (void**)data); if (conf->flag & MPLP_PRINT_MODS) { bam_mplp_constructor(iter, pileup_cd_create); bam_mplp_destructor(iter, pileup_cd_destroy); } if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(iter); if ( !conf->max_depth ) { max_depth = INT_MAX; fprintf(samtools_stderr, "[%s] Max depth set to maximum value (%d)\n", __func__, INT_MAX); } else { max_depth = conf->max_depth; if ( max_depth * nfn > 1<<20 ) fprintf(samtools_stderr, "[%s] Combined max depth is above 1M. Potential memory hog!\n", __func__); } bam_mplp_set_maxcnt(iter, max_depth); int ret; int last_tid = -1; hts_pos_t last_pos = -1; int one_seq = 0; // begin pileup kstring_t ks_seq = KS_INITIALIZE; kstring_t ks_mod = KS_INITIALIZE; kstring_t ks_qual = KS_INITIALIZE; while ( (ret=bam_mplp64_auto(iter, &tid, &pos, n_plp, plp)) > 0) { one_seq = 1; // at least 1 output if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested if (conf->all) { // Deal with missing portions of previous tids while (tid > last_tid) { if (last_tid >= 0 && !conf->reg) { while (++last_pos < sam_hdr_tid2len(h, last_tid)) { if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, last_tid), last_pos, last_pos + 1) == 0) continue; print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, last_tid), last_pos, nfn, ref, ref_len); } } last_tid++; last_pos = -1; if (conf->all < 2) break; if (tid > last_tid) // multiple missing references and -aa used mplp_get_ref(data[0], last_tid, &ref, &ref_len); } } mplp_get_ref(data[0], tid, &ref, &ref_len); if (conf->all) { // Deal with missing portion of current tid while (++last_pos < pos) { if (conf->reg && last_pos < beg0) continue; // out of range; skip if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, tid), last_pos, last_pos + 1) == 0) continue; print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, tid), last_pos, nfn, ref, ref_len); } last_tid = tid; last_pos = pos; } if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, sam_hdr_tid2name(h, tid), pos, pos+1)) continue; fprintf(pileup_fp, "%s\t%"PRIhts_pos"\t%c", sam_hdr_tid2name(h, tid), pos + 1, (ref && pos < ref_len)? ref[pos] : 'N'); for (i = 0; i < nfn; ++i) { int j, cnt, err = 0; ks_clear(&ks_seq); ks_clear(&ks_qual); ks_clear(&ks_mod); for (j = cnt = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; int c = p->qpos < p->b->core.l_qseq ? bam_get_qual(p->b)[p->qpos] : 0; if (c >= conf->min_baseQ) { // Build up seq err |= pileup_seq(&ks_seq, plp[i] + j, pos, ref_len, ref, &ks_mod, conf->rev_del, conf->no_ins, conf->no_ins_mods, conf->no_del, conf->no_ends) < 0; // Build up qual err |= kputc_(c+33 < 126 ? c+33 : 126, &ks_qual) < 0; cnt++; } } if (err) { ret = 1; goto fail; } fprintf(pileup_fp, "\t%d\t", cnt); if (n_plp[i] == 0) { fputs("*\t*", pileup_fp); int flag_value = MPLP_PRINT_MAPQ_CHAR; while(flag_value < MPLP_PRINT_LAST) { if (flag_value != MPLP_PRINT_MODS && (conf->flag & flag_value)) fputs("\t*", pileup_fp); flag_value <<= 1; } if (conf->auxlist) { int t = 0; while(t++ < ((klist_t(auxlist) *)conf->auxlist)->size) fputs("\t*", pileup_fp); } } else { if (ks_seq.l) { fwrite(ks_seq.s, 1, ks_seq.l, pileup_fp); } else { putc('*', pileup_fp); } putc('\t', pileup_fp); if (ks_qual.l) { fwrite(ks_qual.s, 1, ks_qual.l, pileup_fp); } else { putc('*', pileup_fp); } /* Print selected columns */ int flag_value = MPLP_PRINT_MAPQ_CHAR; while(flag_value < MPLP_PRINT_LAST) { if (flag_value != MPLP_PRINT_MODS && (conf->flag & flag_value)) { int n = 0; putc('\t', pileup_fp); for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = &plp[i][j]; int c = p->qpos < p->b->core.l_qseq ? bam_get_qual(p->b)[p->qpos] : 0; if ( c < conf->min_baseQ ) continue; if (n > 0 && flag_value != MPLP_PRINT_MAPQ_CHAR) putc(',', pileup_fp); n++; switch (flag_value) { case MPLP_PRINT_MAPQ_CHAR: c = p->b->core.qual + 33; if (c > 126) c = 126; putc(c, pileup_fp); break; case MPLP_PRINT_QPOS: // query position in current orientation fprintf(pileup_fp, "%d", p->qpos + 1); break; case MPLP_PRINT_QPOS5: { // query position in 5' to 3' orientation int pos5 = bam_is_rev(p->b) ? p->b->core.l_qseq-p->qpos + p->is_del : p->qpos + 1; fprintf(pileup_fp, "%d", pos5); break; } case MPLP_PRINT_QNAME: fputs(bam_get_qname(p->b), pileup_fp); break; case MPLP_PRINT_FLAG: fprintf(pileup_fp, "%d", p->b->core.flag); break; case MPLP_PRINT_RNAME: if (p->b->core.tid >= 0) fputs(sam_hdr_tid2name(h, p->b->core.tid), pileup_fp); else putc('*', pileup_fp); break; case MPLP_PRINT_POS: fprintf(pileup_fp, "%"PRId64, (int64_t) p->b->core.pos + 1); break; case MPLP_PRINT_MAPQ: fprintf(pileup_fp, "%d", p->b->core.qual); break; case MPLP_PRINT_RNEXT: if (p->b->core.mtid >= 0) fputs(sam_hdr_tid2name(h, p->b->core.mtid), pileup_fp); else putc('*', pileup_fp); break; case MPLP_PRINT_PNEXT: fprintf(pileup_fp, "%"PRId64, (int64_t) p->b->core.mpos + 1); break; case MPLP_PRINT_RLEN: fprintf(pileup_fp, "%d", p->b->core.l_qseq); break; } } if (!n) putc('*', pileup_fp); } flag_value <<= 1; } /* Print selected tags */ klist_t(auxlist) *auxlist_p = ((klist_t(auxlist) *)conf->auxlist); if (auxlist_p && auxlist_p->size) { kliter_t(auxlist) *aux; for (aux = kl_begin(auxlist_p); aux != kl_end(auxlist_p); aux = kl_next(aux)) { int n = 0; // NB shadows outer loop putc('\t', pileup_fp); for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = &plp[i][j]; int c = p->qpos < p->b->core.l_qseq ? bam_get_qual(p->b)[p->qpos] : 0; if ( c < conf->min_baseQ ) continue; if (n > 0) putc(conf->sep, pileup_fp); n++; uint8_t* tag_u = bam_aux_get(p->b, kl_val(aux)); if (!tag_u) { putc(conf->empty , pileup_fp); continue; } int tag_supported = 0; /* Tag value is string */ if (*tag_u == 'Z' || *tag_u == 'H') { char *tag_s = bam_aux2Z(tag_u); if (!tag_s) continue; fputs(tag_s, pileup_fp); tag_supported = 1; } /* Tag value is integer */ if (*tag_u == 'I' || *tag_u == 'i' || *tag_u == 'C' || *tag_u == 'c' || *tag_u == 'S' || *tag_u == 's') { int64_t tag_i = bam_aux2i(tag_u); fprintf(pileup_fp, "%" PRId64 "", tag_i); tag_supported = 1; } /* Tag value is float */ if (*tag_u == 'd' || *tag_u == 'f') { double tag_f = bam_aux2f(tag_u); fprintf(pileup_fp, "%lf", tag_f); tag_supported = 1; } /* Tag value is character */ if (*tag_u == 'A') { char tag_c = bam_aux2A(tag_u); putc(tag_c, pileup_fp); tag_supported = 1; } if (!tag_supported) putc('*', pileup_fp); } if (!n) putc('*', pileup_fp); } } } } putc('\n', pileup_fp); } ks_free(&ks_seq); ks_free(&ks_mod); ks_free(&ks_qual); if (ret < 0) { print_error("mpileup", "error reading from input file"); ret = EXIT_FAILURE; goto fail; } if (conf->all) { // Handle terminating region if (last_tid < 0 && conf->reg && conf->all > 1) { last_tid = tid0; last_pos = beg0-1; mplp_get_ref(data[0], tid0, &ref, &ref_len); } else if (last_tid < 0 && !one_seq && conf->all > 1) { last_tid = 0; // --aa on a blank file } while (last_tid >= 0 && last_tid < sam_hdr_nref(h)) { mplp_get_ref(data[0], last_tid, &ref, &ref_len); while (++last_pos < sam_hdr_tid2len(h, last_tid)) { if (last_pos >= end0) break; if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, last_tid), last_pos, last_pos + 1) == 0) continue; print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, last_tid), last_pos, nfn, ref, ref_len); } last_tid++; last_pos = -1; if (conf->all < 2 || conf->reg) break; } } fail: // clean up if (pileup_fp && conf->output_fname) fclose(pileup_fp); bam_smpl_destroy(sm); free(buf.s); for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]); free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp); bam_mplp_destroy(iter); sam_hdr_destroy(h); for (i = 0; i < nfn; ++i) { sam_close(data[i]->fp); if (data[i]->iter) hts_itr_destroy(data[i]->iter); free(data[i]); } free(data); free(plp); free(n_plp); free(mp_ref.ref[0]); free(mp_ref.ref[1]); return ret; } static int is_url(const char *s) { static const char uri_scheme_chars[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+.-"; return s[strspn(s, uri_scheme_chars)] == ':'; } #define MAX_PATH_LEN 1024 int read_file_list(const char *file_list,int *n,char **argv[]) { char buf[MAX_PATH_LEN]; int len, nfiles = 0; char **files = NULL; struct stat sb; *n = 0; *argv = NULL; FILE *fh = fopen(file_list,"r"); if ( !fh ) { fprintf(samtools_stderr,"%s: %s\n", file_list,strerror(errno)); return 1; } files = calloc(nfiles,sizeof(char*)); nfiles = 0; while ( fgets(buf,MAX_PATH_LEN,fh) ) { // allow empty lines and trailing spaces len = strlen(buf); while ( len>0 && isspace(buf[len-1]) ) len--; if ( !len ) continue; // check sanity of the file list buf[len] = 0; if (! (is_url(buf) || stat(buf, &sb) == 0)) { // no such file, check if it is safe to print its name int i, safe_to_print = 1; for (i=0; irflag_require); char *tmp_filter = bam_flag2str(mplp->rflag_filter); // Display usage information, formatted for the standard 80 columns. // (The unusual string formatting here aids the readability of this // source code in 80 columns, to the extent that's possible.) fprintf(fp, "\n" "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n" "\n" "Input options:\n" " -6, --illumina1.3+ quality is in the Illumina-1.3+ encoding\n" " -A, --count-orphans do not discard anomalous read pairs\n" " -b, --bam-list FILE list of input BAM filenames, one per line\n" " -B, --no-BAQ disable BAQ (per-Base Alignment Quality)\n" " -C, --adjust-MQ INT adjust mapping quality; recommended:50, disable:0 [0]\n" " -d, --max-depth INT max per-file depth; avoids excessive memory usage [%d]\n", mplp->max_depth); fprintf(fp, " -E, --redo-BAQ recalculate BAQ on the fly, ignore existing BQs\n" " -f, --fasta-ref FILE faidx indexed reference sequence file\n" " -G, --exclude-RG FILE exclude read groups listed in FILE\n" " -l, --positions FILE skip unlisted positions (chr pos) or regions (BED)\n" " -q, --min-MQ INT skip alignments with mapQ smaller than INT [%d]\n", mplp->min_mq); fprintf(fp, " -Q, --min-BQ INT skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ); fprintf(fp, " -r, --region REG region in which pileup is generated\n" " -R, --ignore-RG ignore RG tags (one BAM = one sample)\n" " --rf, --incl-flags STR|INT\n" " required flags: only include reads with any of\n" " the mask bits set [%s]\n", tmp_require); fprintf(fp, " --ff, --excl-flags STR|INT\n" " filter flags: skip reads with any of the mask bits set\n" " [%s]\n", tmp_filter); fprintf(fp, " -x, --ignore-overlaps-removal, --disable-overlap-removal\n" " disable read-pair overlap detection and removal\n" " -X, --customized-index use customized index files\n" // -X flag for index filename "\n" "Output options:\n" " -o, --output FILE write output to FILE [standard output]\n" " -O, --output-BP output base positions on reads, current orientation\n" " --output-BP-5 output base positions on reads, 5' to 3' orientation\n" " -M, --output-mods output base modifications\n" " -s, --output-MQ output mapping quality\n" " --output-QNAME output read names\n" " --output-extra STR output extra read fields and read tag values\n" " --output-sep CHAR set the separator character for tag lists [,]\n" " --output-empty CHAR set the no value character for tag lists [*]\n" " --no-output-ins skip insertion sequence after +NUM\n" " Use twice for complete insertion removal\n" " --no-output-ins-mods don't display base modifications within insertions\n" " --no-output-del skip deletion sequence after -NUM\n" " Use twice for complete deletion removal\n" " --no-output-ends remove ^MQUAL and $ markup in sequence column\n" " --reverse-del use '#' character for deletions on the reverse strand\n" " -a output all positions (including zero depth)\n" " -a -a (or -aa) output absolutely all positions, including unused ref. sequences\n" "\n" "Generic options:\n"); sam_global_opt_help(fp, "-.--.--."); fprintf(fp, "\n" "Note that using \"samtools mpileup\" to generate BCF or VCF files has been\n" "removed. To output these formats, please use \"bcftools mpileup\" instead.\n"); free(tmp_require); free(tmp_filter); } int bam_mpileup(int argc, char *argv[]) { int c; const char *file_list = NULL; char **fn = NULL; int nfiles = 0, use_orphan = 0, has_index_file = 0; mplp_conf_t mplp; memset(&mplp, 0, sizeof(mplp_conf_t)); mplp.min_baseQ = 13; mplp.capQ_thres = 0; mplp.max_depth = MPLP_MAX_DEPTH; mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN | MPLP_SMART_OVERLAPS; mplp.argc = argc; mplp.argv = argv; mplp.rflag_filter = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP; mplp.output_fname = NULL; mplp.all = 0; mplp.rev_del = 0; mplp.sep = ','; mplp.empty = '*'; sam_global_args_init(&mplp.ga); static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '-'), {"rf", required_argument, NULL, 1}, // require flag {"ff", required_argument, NULL, 2}, // filter flag {"incl-flags", required_argument, NULL, 1}, {"excl-flags", required_argument, NULL, 2}, {"output", required_argument, NULL, 3}, {"output-QNAME", no_argument, NULL, 5}, {"output-qname", no_argument, NULL, 5}, {"illumina1.3+", no_argument, NULL, '6'}, {"count-orphans", no_argument, NULL, 'A'}, {"bam-list", required_argument, NULL, 'b'}, {"no-BAQ", no_argument, NULL, 'B'}, {"no-baq", no_argument, NULL, 'B'}, {"adjust-MQ", required_argument, NULL, 'C'}, {"adjust-mq", required_argument, NULL, 'C'}, {"max-depth", required_argument, NULL, 'd'}, {"redo-BAQ", no_argument, NULL, 'E'}, {"redo-baq", no_argument, NULL, 'E'}, {"fasta-ref", required_argument, NULL, 'f'}, {"exclude-RG", required_argument, NULL, 'G'}, {"exclude-rg", required_argument, NULL, 'G'}, {"positions", required_argument, NULL, 'l'}, {"region", required_argument, NULL, 'r'}, {"ignore-RG", no_argument, NULL, 'R'}, {"ignore-rg", no_argument, NULL, 'R'}, {"min-MQ", required_argument, NULL, 'q'}, {"min-mq", required_argument, NULL, 'q'}, {"min-BQ", required_argument, NULL, 'Q'}, {"min-bq", required_argument, NULL, 'Q'}, // NB: old "--ignore-overlaps" auto-completes to this {"ignore-overlaps-removal", no_argument, NULL, 'x'}, {"disable-overlap-removal", no_argument, NULL, 'x'}, {"output-mods", no_argument, NULL, 'M'}, {"output-BP", no_argument, NULL, 'O'}, {"output-bp", no_argument, NULL, 'O'}, {"output-BP-5", no_argument, NULL, 14}, {"output-bp-5", no_argument, NULL, 14}, {"output-MQ", no_argument, NULL, 's'}, {"output-mq", no_argument, NULL, 's'}, {"ext-prob", required_argument, NULL, 'e'}, {"gap-frac", required_argument, NULL, 'F'}, {"tandem-qual", required_argument, NULL, 'h'}, {"skip-indels", no_argument, NULL, 'I'}, {"max-idepth", required_argument, NULL, 'L'}, {"min-ireads ", required_argument, NULL, 'm'}, {"per-sample-mF", no_argument, NULL, 'p'}, {"per-sample-mf", no_argument, NULL, 'p'}, {"platforms", required_argument, NULL, 'P'}, {"customized-index", no_argument, NULL, 'X'}, {"reverse-del", no_argument, NULL, 6}, {"output-extra", required_argument, NULL, 7}, {"output-sep", required_argument, NULL, 8}, {"output-empty", required_argument, NULL, 9}, {"no-output-ins", no_argument, NULL, 10}, {"no-output-ins-mods", no_argument, NULL, 11}, {"no-output-del", no_argument, NULL, 12}, {"no-output-ends", no_argument, NULL, 13}, {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "Af:r:l:q:Q:RC:Bd:b:o:EG:6OsxXaM",lopts,NULL)) >= 0) { switch (c) { case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break; case 1 : mplp.rflag_require = bam_str2flag(optarg); if ( mplp.rflag_require<0 ) { fprintf(samtools_stderr,"Could not parse --rf %s\n", optarg); return 1; } break; case 2 : mplp.rflag_filter = bam_str2flag(optarg); if ( mplp.rflag_filter<0 ) { fprintf(samtools_stderr,"Could not parse --ff %s\n", optarg); return 1; } break; case 3 : mplp.output_fname = optarg; break; case 5 : mplp.flag |= MPLP_PRINT_QNAME; break; case 6 : mplp.rev_del = 1; break; case 7 : if (build_auxlist(&mplp, optarg) != 0) { fprintf(samtools_stderr,"Could not build aux list using '%s'\n", optarg); return 1; } break; case 8: mplp.sep = optarg[0]; break; case 9: mplp.empty = optarg[0]; break; case 10: mplp.no_ins++; break; case 11: mplp.no_ins_mods = 1; break; case 12: mplp.no_del++; break; case 13: mplp.no_ends = 1; break; case 'f': mplp.fai = fai_load(optarg); if (mplp.fai == NULL) return 1; mplp.fai_fname = optarg; break; case 'd': mplp.max_depth = atoi(optarg); break; case 'r': mplp.reg = strdup(optarg); break; case 'l': // In the original version the whole BAM was streamed which is inefficient // with few BED intervals and big BAMs. Todo: devise a heuristic to determine // best strategy, that is streaming or jumping. mplp.bed = bed_read(optarg); if (!mplp.bed) { print_error_errno("mpileup", "Could not read file \"%s\"", optarg); return 1; } break; case 'B': mplp.flag &= ~MPLP_REALN; break; case 'X': has_index_file = 1; break; case 'E': mplp.flag |= MPLP_REDO_BAQ; break; case '6': mplp.flag |= MPLP_ILLUMINA13; break; case 'R': mplp.flag |= MPLP_IGNORE_RG; break; case 's': mplp.flag |= MPLP_PRINT_MAPQ_CHAR; break; case 'O': mplp.flag |= MPLP_PRINT_QPOS; break; case 14: mplp.flag |= MPLP_PRINT_QPOS5; break; case 'M': mplp.flag |= MPLP_PRINT_MODS; break; case 'C': mplp.capQ_thres = atoi(optarg); break; case 'q': mplp.min_mq = atoi(optarg); break; case 'Q': mplp.min_baseQ = atoi(optarg); break; case 'b': file_list = optarg; break; case 'o': mplp.output_fname = optarg; break; case 'A': use_orphan = 1; break; case 'G': { FILE *fp_rg; char buf[1024]; mplp.rghash = khash_str2int_init(); if ((fp_rg = fopen(optarg, "r")) == NULL) fprintf(samtools_stderr, "[%s] Fail to open file %s. Continue anyway.\n", __func__, optarg); while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but forgive me... khash_str2int_inc(mplp.rghash, strdup(buf)); fclose(fp_rg); } break; case 'a': mplp.all++; break; default: if (parse_sam_global_opt(c, optarg, lopts, &mplp.ga) == 0) break; /* else fall-through */ case '?': print_usage(samtools_stderr, &mplp); return 1; } } if (!mplp.fai && mplp.ga.reference) { mplp.fai_fname = mplp.ga.reference; mplp.fai = fai_load(mplp.fai_fname); if (mplp.fai == NULL) return 1; } if ( !(mplp.flag&MPLP_REALN) && mplp.flag&MPLP_REDO_BAQ ) { fprintf(samtools_stderr,"Error: The -B option cannot be combined with -E\n"); return 1; } if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN; if (argc == 1) { print_usage(samtools_stderr, &mplp); return 1; } int ret; if (file_list) { if (has_index_file) { fprintf(samtools_stderr,"Error: The -b option cannot be combined with -X\n"); // No customize index loc in file list mode return 1; } if ( read_file_list(file_list,&nfiles,&fn) ) return 1; ret = mpileup(&mplp,nfiles,fn,NULL); for (c=0; c Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include /* File status flags (zero means OK). It's possible for more than one to be * set on a single file. The final exit status is the bitwise-or of the * status of all the files. */ #define QC_FAIL_OPEN 2 #define QC_NOT_SEQUENCE 4 #define QC_BAD_HEADER 8 #define QC_NO_EOF_BLOCK 16 #define QC_FAIL_CLOSE 32 static void usage_quickcheck(FILE *write_to) { fprintf(write_to, "Usage: samtools quickcheck [options] [...]\n" "Options:\n" " -v verbose output (repeat for more verbosity)\n" " -q suppress warning messages\n" " -u unmapped input (do not require targets in header)\n" "\n" "Notes:\n" "\n" "1. By default quickcheck will emit a warning message if and only if a file\n" " fails the checks, in which case the exit status is non-zero. Under normal\n" " behaviour with valid data it will be silent and has a zero exit status.\n" " The warning messages are purely for manual inspection and should not be \n" " parsed by scripts.\n" "\n" "2. In order to use this command programmatically, you should check its exit\n" " status. One way to use quickcheck might be as a check that all BAM files in\n" " a directory are okay:\n" "\n" "\tsamtools quickcheck *.bam && echo 'all ok' \\\n" "\t || echo 'fail!'\n" "\n" " The first level of verbosity lists only files that fail to stdout.\n" " To obtain a parsable list of files that have failed, use this option:\n" "\n" "\tsamtools quickcheck -qv *.bam > bad_bams.fofn \\\n" "\t && echo 'all ok' \\\n" "\t || echo 'some files failed check, see bad_bams.fofn'\n" ); } #define QC_ERR(state, v, msg, arg1) \ file_state |= (state); \ if (!quiet || verbose >= (v)) fprintf(stderr, (msg), (arg1)) int main_quickcheck(int argc, char** argv) { int verbose = 0, quiet = 0, unmapped = 0; hts_verbose = 0; const char* optstring = "vqu"; int opt; while ((opt = getopt(argc, argv, optstring)) != -1) { switch (opt) { case 'u': unmapped = 1; break; case 'v': verbose++; break; case 'q': quiet = 1; break; default: usage_quickcheck(stderr); return 1; } } argc -= optind; argv += optind; if (argc < 1) { usage_quickcheck(stdout); return 1; } if (verbose >= 2) { fprintf(stderr, "verbosity set to %d\n", verbose); } if (verbose >= 4) { hts_verbose = 3; } int ret = 0; int i; for (i = 0; i < argc; i++) { char* fn = argv[i]; int file_state = 0; if (verbose >= 3) fprintf(stderr, "checking %s\n", fn); // attempt to open htsFile *hts_fp = hts_open(fn, "r"); if (hts_fp == NULL) { QC_ERR(QC_FAIL_OPEN, 2, "%s could not be opened for reading.\n", fn); } else { if (verbose >= 3) fprintf(stderr, "opened %s\n", fn); // make sure we have sequence data const htsFormat *fmt = hts_get_format(hts_fp); if (fmt->category != sequence_data ) { QC_ERR(QC_NOT_SEQUENCE, 2, "%s was not identified as sequence data.\n", fn); } else { if (verbose >= 3) fprintf(stderr, "%s is sequence data\n", fn); // check header sam_hdr_t *header = sam_hdr_read(hts_fp); if (header == NULL) { QC_ERR(QC_BAD_HEADER, 2, "%s caused an error whilst reading its header.\n", fn); } else { if (!unmapped && sam_hdr_nref(header) <= 0) { QC_ERR(QC_BAD_HEADER, 2, "%s had no targets in header.\n", fn); } else { if (verbose >= 3) fprintf(stderr, "%s has %d targets in header.\n", fn, sam_hdr_nref(header)); } sam_hdr_destroy(header); } } // check EOF on formats that support this int ret; if ((ret = hts_check_EOF(hts_fp)) < 0) { QC_ERR(QC_NO_EOF_BLOCK, 2, "%s caused an error whilst checking for EOF block.\n", fn); } else { switch (ret) { case 0: QC_ERR(QC_NO_EOF_BLOCK, 2, "%s was missing EOF block when one should be present.\n", fn); break; case 1: if (verbose >= 3) fprintf(stderr, "%s has good EOF block.\n", fn); break; case 2: if (verbose >= 3) fprintf(stderr, "%s cannot be checked for EOF block as it is not seekable.\n", fn); break; case 3: if (verbose >= 3) fprintf(stderr, "%s cannot be checked for EOF block because its filetype does not contain one.\n", fn); break; } } if (hts_close(hts_fp) < 0) { QC_ERR(QC_FAIL_CLOSE, 2, "%s did not close cleanly.\n", fn); } } if (file_state > 0 && verbose >= 1) { fprintf(stdout, "%s\n", fn); } ret |= file_state; } return ret; } pysam-0.23.0/samtools/bam_quickcheck.c.pysam.c000066400000000000000000000153501475062545500212550ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_quickcheck.c -- quickcheck subcommand. Copyright (C) 2015-2017 Genome Research Ltd. Author: Joshua C. Randall Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include /* File status flags (zero means OK). It's possible for more than one to be * set on a single file. The final exit status is the bitwise-or of the * status of all the files. */ #define QC_FAIL_OPEN 2 #define QC_NOT_SEQUENCE 4 #define QC_BAD_HEADER 8 #define QC_NO_EOF_BLOCK 16 #define QC_FAIL_CLOSE 32 static void usage_quickcheck(FILE *write_to) { fprintf(write_to, "Usage: samtools quickcheck [options] [...]\n" "Options:\n" " -v verbose output (repeat for more verbosity)\n" " -q suppress warning messages\n" " -u unmapped input (do not require targets in header)\n" "\n" "Notes:\n" "\n" "1. By default quickcheck will emit a warning message if and only if a file\n" " fails the checks, in which case the exit status is non-zero. Under normal\n" " behaviour with valid data it will be silent and has a zero exit status.\n" " The warning messages are purely for manual inspection and should not be \n" " parsed by scripts.\n" "\n" "2. In order to use this command programmatically, you should check its exit\n" " status. One way to use quickcheck might be as a check that all BAM files in\n" " a directory are okay:\n" "\n" "\tsamtools quickcheck *.bam && echo 'all ok' \\\n" "\t || echo 'fail!'\n" "\n" " The first level of verbosity lists only files that fail to samtools_stdout.\n" " To obtain a parsable list of files that have failed, use this option:\n" "\n" "\tsamtools quickcheck -qv *.bam > bad_bams.fofn \\\n" "\t && echo 'all ok' \\\n" "\t || echo 'some files failed check, see bad_bams.fofn'\n" ); } #define QC_ERR(state, v, msg, arg1) \ file_state |= (state); \ if (!quiet || verbose >= (v)) fprintf(samtools_stderr, (msg), (arg1)) int main_quickcheck(int argc, char** argv) { int verbose = 0, quiet = 0, unmapped = 0; hts_verbose = 0; const char* optstring = "vqu"; int opt; while ((opt = getopt(argc, argv, optstring)) != -1) { switch (opt) { case 'u': unmapped = 1; break; case 'v': verbose++; break; case 'q': quiet = 1; break; default: usage_quickcheck(samtools_stderr); return 1; } } argc -= optind; argv += optind; if (argc < 1) { usage_quickcheck(samtools_stdout); return 1; } if (verbose >= 2) { fprintf(samtools_stderr, "verbosity set to %d\n", verbose); } if (verbose >= 4) { hts_verbose = 3; } int ret = 0; int i; for (i = 0; i < argc; i++) { char* fn = argv[i]; int file_state = 0; if (verbose >= 3) fprintf(samtools_stderr, "checking %s\n", fn); // attempt to open htsFile *hts_fp = hts_open(fn, "r"); if (hts_fp == NULL) { QC_ERR(QC_FAIL_OPEN, 2, "%s could not be opened for reading.\n", fn); } else { if (verbose >= 3) fprintf(samtools_stderr, "opened %s\n", fn); // make sure we have sequence data const htsFormat *fmt = hts_get_format(hts_fp); if (fmt->category != sequence_data ) { QC_ERR(QC_NOT_SEQUENCE, 2, "%s was not identified as sequence data.\n", fn); } else { if (verbose >= 3) fprintf(samtools_stderr, "%s is sequence data\n", fn); // check header sam_hdr_t *header = sam_hdr_read(hts_fp); if (header == NULL) { QC_ERR(QC_BAD_HEADER, 2, "%s caused an error whilst reading its header.\n", fn); } else { if (!unmapped && sam_hdr_nref(header) <= 0) { QC_ERR(QC_BAD_HEADER, 2, "%s had no targets in header.\n", fn); } else { if (verbose >= 3) fprintf(samtools_stderr, "%s has %d targets in header.\n", fn, sam_hdr_nref(header)); } sam_hdr_destroy(header); } } // check EOF on formats that support this int ret; if ((ret = hts_check_EOF(hts_fp)) < 0) { QC_ERR(QC_NO_EOF_BLOCK, 2, "%s caused an error whilst checking for EOF block.\n", fn); } else { switch (ret) { case 0: QC_ERR(QC_NO_EOF_BLOCK, 2, "%s was missing EOF block when one should be present.\n", fn); break; case 1: if (verbose >= 3) fprintf(samtools_stderr, "%s has good EOF block.\n", fn); break; case 2: if (verbose >= 3) fprintf(samtools_stderr, "%s cannot be checked for EOF block as it is not seekable.\n", fn); break; case 3: if (verbose >= 3) fprintf(samtools_stderr, "%s cannot be checked for EOF block because its filetype does not contain one.\n", fn); break; } } if (hts_close(hts_fp) < 0) { QC_ERR(QC_FAIL_CLOSE, 2, "%s did not close cleanly.\n", fn); } } if (file_state > 0 && verbose >= 1) { fprintf(samtools_stdout, "%s\n", fn); } ret |= file_state; } return ret; } pysam-0.23.0/samtools/bam_reheader.c000066400000000000000000000472131475062545500173540ustar00rootroot00000000000000/* bam_reheader.c -- reheader subcommand. Copyright (C) 2010 Broad Institute. Copyright (C) 2012-2019 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "htslib/bgzf.h" #include "htslib/sam.h" #include "htslib/hfile.h" #include "htslib/cram.h" #include "samtools.h" #define BUF_SIZE 0x10000 /* * Reads a file and outputs a new BAM file to fd with 'h' replaced as * the header. No checks are made to the validity. */ int bam_reheader(BGZF *in, sam_hdr_t *h, int fd, const char *arg_list, int no_pg, int skip_header) { BGZF *fp = NULL; ssize_t len; uint8_t *buf = NULL; sam_hdr_t *tmp; if (!h) return -1; if (in->is_write) return -1; buf = malloc(BUF_SIZE); if (!buf) { fprintf(stderr, "Out of memory\n"); return -1; } if (!skip_header) { if ((tmp = bam_hdr_read(in)) == NULL) { fprintf(stderr, "Couldn't read header\n"); goto fail; } sam_hdr_destroy(tmp); } fp = bgzf_fdopen(fd, "w"); if (!fp) { print_error_errno("reheader", "Couldn't open output file"); goto fail; } if (!no_pg && sam_hdr_add_pg(h, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL) != 0) goto fail; if (bam_hdr_write(fp, h) < 0) { print_error_errno("reheader", "Couldn't write header"); goto fail; } if (in->block_offset < in->block_length) { if (bgzf_write(fp, (char *)in->uncompressed_block + in->block_offset, in->block_length - in->block_offset) < 0) goto write_fail; if (bgzf_flush(fp) < 0) goto write_fail; } while ((len = bgzf_raw_read(in, buf, BUF_SIZE)) > 0) { if (bgzf_raw_write(fp, buf, len) < 0) goto write_fail; } if (len < 0) { fprintf(stderr, "[%s] Error reading input file\n", __func__); goto fail; } free(buf); fp->block_offset = in->block_offset = 0; if (bgzf_close(fp) < 0) { fprintf(stderr, "[%s] Error closing output file\n", __func__); return -1; } return 0; write_fail: print_error_errno("reheader", "Error writing to output file"); fail: bgzf_close(fp); free(buf); return -1; } /* * Reads a file and outputs a new CRAM file to stdout with 'h' * replaced as the header. No checks are made to the validity. * * FIXME: error checking */ int cram_reheader(cram_fd *in, sam_hdr_t *h, const char *arg_list, int no_pg) { htsFile *h_out = hts_open("-", "wc"); cram_fd *out = h_out->fp.cram; cram_container *c = NULL; int ret = -1; if (!h) return ret; // Match output version number with input file. char vers[99]; sprintf(vers, "%d.%d", cram_major_vers(in), cram_minor_vers(in)); cram_set_option(out, CRAM_OPT_VERSION, vers); // Attempt to fill out a cram->refs[] array from @SQ headers sam_hdr_t *cram_h = sam_hdr_dup(h); if (!cram_h) return -1; cram_fd_set_header(out, cram_h); if (!no_pg && sam_hdr_add_pg(cram_fd_get_header(out), "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) goto err; if (sam_hdr_write(h_out, cram_h) != 0) goto err; cram_set_option(out, CRAM_OPT_REFERENCE, NULL); while ((c = cram_read_container(in))) { int32_t i, num_blocks = cram_container_get_num_blocks(c); if (cram_write_container(out, c) != 0) goto err; for (i = 0; i < num_blocks; i++) { cram_block *blk = cram_read_block(in); if (!blk || cram_write_block(out, blk) != 0) { if (blk) cram_free_block(blk); goto err; } cram_free_block(blk); } cram_free_container(c); } ret = 0; err: if (hts_close(h_out) != 0) ret = -1; return ret; } /* * Reads a version 2 CRAM file and replaces the header in-place, * provided the header is small enough to fit without growing the * entire file. * * Version 2 format has an uncompressed SAM header with multiple nul * termination bytes to permit inline header editing. * * Returns 0 on success; * -1 on general failure; * -2 on failure due to insufficient size */ int cram_reheader_inplace2(cram_fd *fd, sam_hdr_t *h, const char *arg_list, int no_pg) { cram_container *c = NULL; cram_block *b = NULL; sam_hdr_t *cram_h = NULL; off_t start; int ret = -1; if (!h) goto err; if (cram_major_vers(fd) < 2 || cram_major_vers(fd) > 3) { fprintf(stderr, "[%s] unsupported CRAM version %d\n", __func__, cram_major_vers(fd)); goto err; } cram_h = sam_hdr_dup(h); if (!cram_h) goto err; if (!no_pg && sam_hdr_add_pg(cram_h, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) goto err; int header_len = sam_hdr_length(cram_h); /* Fix M5 strings? Maybe out of scope for this tool */ // Load the existing header if ((start = hseek(cram_fd_get_fp(fd), 26, SEEK_SET)) != 26) goto err; if (!(c = cram_read_container(fd))) goto err; // Version 2.1 has a single uncompressed block which is nul // terminated with many nuls to permit growth. // // So load old block and keep all contents identical bar the // header text itself if (!(b = cram_read_block(fd))) goto err; if (cram_block_get_uncomp_size(b) < header_len+4) { fprintf(stderr, "New header will not fit. Use non-inplace version (%d > %d)\n", header_len+4, cram_block_get_uncomp_size(b)); ret = -2; goto err; } cram_block_set_offset(b, 0); // rewind block int32_put_blk(b, header_len); cram_block_append(b, (void *)sam_hdr_str(cram_h), header_len); // Zero the remaining block memset((char *)cram_block_get_data(b)+cram_block_get_offset(b), 0, cram_block_get_uncomp_size(b) - cram_block_get_offset(b)); // Make sure all sizes and byte-offsets are consistent after memset cram_block_set_offset(b, cram_block_get_uncomp_size(b)); cram_block_set_comp_size(b, cram_block_get_uncomp_size(b)); if (hseek(cram_fd_get_fp(fd), start, SEEK_SET) != start) goto err; if (cram_write_container(fd, c) == -1) goto err; if (cram_write_block(fd, b) == -1) goto err; ret = 0; err: if (c) cram_free_container(c); if (b) cram_free_block(b); if (cram_h) sam_hdr_destroy(cram_h); return ret; } /* * Reads a version 3 CRAM file and replaces the header in-place, * provided the header is small enough to fit without growing the * entire file. * * Version 3 format has a SAM header held as an (optionally) * compressed block within the header container. Additional * uncompressed blocks or simply unallocated space (the difference * between total block sizes and the container size) are used to * provide room for growth or contraction of the compressed header. * * Returns 0 on success; * -1 on general failure; * -2 on failure due to insufficient size */ int cram_reheader_inplace3(cram_fd *fd, sam_hdr_t *h, const char *arg_list, int no_pg) { cram_container *c = NULL; cram_block *b = NULL; sam_hdr_t *cram_h = NULL; off_t start, sz, end; int container_sz, max_container_sz; char *buf = NULL; int ret = -1; if (!h) goto err; if (cram_major_vers(fd) < 2 || cram_major_vers(fd) > 3) { fprintf(stderr, "[%s] unsupported CRAM version %d\n", __func__, cram_major_vers(fd)); goto err; } cram_h = sam_hdr_dup(h); if (!cram_h) goto err; if (!no_pg && sam_hdr_add_pg(cram_h, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) goto err; int header_len = sam_hdr_length(cram_h); /* Fix M5 strings? Maybe out of scope for this tool */ // Find current size of SAM header block if ((start = hseek(cram_fd_get_fp(fd), 26, SEEK_SET)) != 26) goto err; if (!(c = cram_read_container(fd))) goto err; // +5 allows num_landmarks to increase from 0 to 1 (Cramtools) max_container_sz = cram_container_size(c)+5; sz = htell(cram_fd_get_fp(fd)) + cram_container_get_length(c) - start; end = htell(cram_fd_get_fp(fd)) + cram_container_get_length(c); // We force 1 block instead of (optionally) 2. C CRAM // implementations for v3 were writing 1 compressed block followed // by 1 uncompressed block. However this is tricky to deal with // as changing block sizes can mean the block header also changes // size due to itf8 and variable size integers. // // If we had 1 block, this doesn't change anything. // If we had 2 blocks, the new container header will be smaller by // 1+ bytes, requiring the cram_container_get_length(c) to be larger in value. // However this is an int32 instead of itf8 so the container // header structure stays the same size. This means we can always // reduce the number of blocks without running into size problems. cram_container_set_num_blocks(c, 1); int32_t *landmark; int32_t num_landmarks; landmark = cram_container_get_landmarks(c, &num_landmarks); if (num_landmarks && landmark) { num_landmarks = 1; landmark[0] = 0; } else { num_landmarks = 0; } cram_container_set_landmarks(c, num_landmarks, landmark); buf = malloc(max_container_sz); container_sz = max_container_sz; if (cram_store_container(fd, c, buf, &container_sz) != 0) goto err; if (!buf) goto err; // Proposed new length, but changing cram_container_get_length(c) may change the // container_sz and thus the remainder (cram_container_get_length(c) itself). cram_container_set_length(c, sz - container_sz); int old_container_sz = container_sz; container_sz = max_container_sz; if (cram_store_container(fd, c, buf, &container_sz) != 0) goto err; if (old_container_sz != container_sz) { fprintf(stderr, "Quirk of fate makes this troublesome! " "Please use non-inplace version.\n"); goto err; } // Version 3.0 supports compressed header b = cram_new_block(FILE_HEADER, 0); int32_put_blk(b, header_len); cram_block_append(b, (void *)sam_hdr_str(cram_h), header_len); cram_block_update_size(b); cram_compress_block(fd, b, NULL, -1, 9); if (hseek(cram_fd_get_fp(fd), 26, SEEK_SET) != 26) goto err; if (cram_block_size(b) > cram_container_get_length(c)) { fprintf(stderr, "New header will not fit. Use non-inplace version" " (%d > %d)\n", (int)cram_block_size(b), cram_container_get_length(c)); ret = -2; goto err; } if (cram_write_container(fd, c) == -1) goto err; if (cram_write_block(fd, b) == -1) goto err; // Blank out the remainder int rsz = end - htell(cram_fd_get_fp(fd)); assert(rsz >= 0); if (rsz) { char *rem = calloc(1, rsz); ret = hwrite(cram_fd_get_fp(fd), rem, rsz) == rsz ? 0 : -1; free(rem); } err: if (c) cram_free_container(c); if (buf) free(buf); if (b) cram_free_block(b); if (cram_h) sam_hdr_destroy(cram_h); return ret; } int cram_reheader_inplace(cram_fd *fd, sam_hdr_t *h, const char *arg_list, int no_pg) { switch (cram_major_vers(fd)) { case 2: return cram_reheader_inplace2(fd, h, arg_list, no_pg); case 3: return cram_reheader_inplace3(fd, h, arg_list, no_pg); default: fprintf(stderr, "[%s] unsupported CRAM version %d\n", __func__, cram_major_vers(fd)); return -1; } } static void usage(FILE *fp, int ret) { fprintf(fp, "Usage: samtools reheader [-P] in.header.sam in.bam > out.bam\n" " or samtools reheader [-P] -i in.header.sam file.cram\n" " or samtools reheader -c CMD in.bam\n" " or samtools reheader -c CMD in.cram\n" "\n" "Options:\n" " -P, --no-PG Do not generate a @PG header line.\n" " -i, --in-place Modify the CRAM file directly, if possible.\n" " (Defaults to outputting to stdout.)\n" " -c, --command CMD Pass the header in SAM format to external program CMD.\n"); exit(ret); } static sam_hdr_t* external_reheader(samFile* in, const char* external) { char *command = NULL; sam_hdr_t* h = NULL; sam_hdr_t* ih = sam_hdr_read(in); if (ih == NULL) { fprintf(stderr, "[%s] failed to read the header for '%s'.\n", __func__, in->fn); return NULL; } char tmp_fn[] = "reheaderXXXXXX"; int tmp_fd = mkstemp(tmp_fn); if (tmp_fd < 0) { print_error_errno("reheader", "fail to open temp file '%s'", tmp_fn); return NULL; } hFILE* tmp_hf = hdopen(tmp_fd, "w"); if (!tmp_hf) { fprintf(stderr, "[%s] failed to convert to hFILE.\n", __func__); goto cleanup; } samFile* tmp_sf = hts_hopen(tmp_hf, tmp_fn, "w"); if (!tmp_sf) { fprintf(stderr, "[%s] failed to convert to samFile.\n", __func__); goto cleanup; } if (-1 == sam_hdr_write(tmp_sf, ih)) { fprintf(stderr, "[%s] failed to write the header to the temp file.\n", __func__); goto cleanup; } sam_close(tmp_sf); sam_hdr_destroy(ih); int comm_len = strlen(external) + strlen(tmp_fn) + 8; command = calloc(comm_len, 1); if (!command || snprintf(command, comm_len, "( %s ) < %s", external, tmp_fn) != comm_len - 1) { fprintf(stderr, "[%s] failed to create command string.\n", __func__); goto cleanup; } FILE* nh = popen(command, "r"); if (!nh) { print_error_errno("reheader", "[%s] failed to run external command '%s'.\n", __func__, command); goto cleanup; } int nh_fd = dup(fileno(nh)); if (nh_fd < 0) { fprintf(stderr, "[%s] failed to get the file descriptor.\n", __func__); goto cleanup; } hFILE* nh_hf = hdopen(nh_fd, "r"); if (!nh_hf) { fprintf(stderr, "[%s] failed to convert to hFILE.\n", __func__); goto cleanup; } samFile* nh_sf = hts_hopen(nh_hf, tmp_fn, "r"); if (!nh_sf) { fprintf(stderr, "[%s] failed to convert to samFile.\n", __func__); goto cleanup; } h = sam_hdr_read(nh_sf); sam_close(nh_sf); if (h == NULL) { fprintf(stderr, "[%s] failed to read the header from the temp file.\n", __func__); } int res = pclose(nh); if (res != 0) { if (res < 0) { print_error_errno("reheader", "Error on closing pipe from command '%s'.\n", command); } else { print_error("reheader", "Non-zero exit code returned by command '%s'\n", command); } if (h) sam_hdr_destroy(h); h = NULL; } cleanup: free(command); if (unlink(tmp_fn) != 0) { print_error_errno("reheader", "failed to remove the temp file '%s'", tmp_fn); } return h; } int main_reheader(int argc, char *argv[]) { int inplace = 0, r, no_pg = 0, c, skip_header = 0; sam_hdr_t *h; samFile *in; char *arg_list = NULL, *external = NULL; static const struct option lopts[] = { {"help", no_argument, NULL, 'h'}, {"in-place", no_argument, NULL, 'i'}, {"no-PG", no_argument, NULL, 'P'}, {"command", required_argument, NULL, 'c'}, {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "hiPc:", lopts, NULL)) >= 0) { switch (c) { case 'P': no_pg = 1; break; case 'i': inplace = 1; break; case 'c': external = optarg; break; case 'h': usage(stdout, 0); break; default: fprintf(stderr, "Invalid option '%c'\n", c); usage(stderr, 1); } } if ((argc - optind != 2 || external) && (argc - optind != 1 || !external)) usage(stderr, 1); if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) { print_error("reheader", "failed to create arg_list"); return 1; } if (external) { skip_header = 1; in = sam_open(argv[optind], inplace?"r+":"r"); if (in == 0) { print_error_errno("reheader", "fail to open file '%s'", argv[optind]); return 1; } h = external_reheader(in, external); if (h == NULL) { fprintf(stderr, "[%s] failed to read the header from '%s'.\n", __func__, external); sam_close(in); return 1; } } else { // read the header from a separate file samFile *fph = sam_open(argv[optind], "r"); if (fph == 0) { print_error_errno("reheader", "fail to read the header from '%s'", argv[optind]); return 1; } h = sam_hdr_read(fph); sam_close(fph); if (h == NULL) { fprintf(stderr, "[%s] failed to read the header for '%s'.\n", __func__, argv[1]); return 1; } in = sam_open(argv[optind+1], inplace?"r+":"r"); if (in == 0) { print_error_errno("reheader", "fail to open file '%s'", argv[optind+1]); return 1; } } if (hts_get_format(in)->format == bam) { if (inplace) { print_error("reheader", "cannot reheader BAM '%s' in-place", argv[optind+1]); r = -1; } else { r = bam_reheader(in->fp.bgzf, h, fileno(stdout), arg_list, no_pg, skip_header); } } else if (hts_get_format(in)->format == cram) { if (inplace) r = cram_reheader_inplace(in->fp.cram, h, arg_list, no_pg); else r = cram_reheader(in->fp.cram, h, arg_list, no_pg); } else { print_error("reheader", "input file '%s' must be BAM or CRAM", argv[optind+1]); r = -1; } if (sam_close(in) != 0) r = -1; sam_hdr_destroy(h); if (arg_list) free(arg_list); return -r; } pysam-0.23.0/samtools/bam_reheader.c.pysam.c000066400000000000000000000476551475062545500207370ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_reheader.c -- reheader subcommand. Copyright (C) 2010 Broad Institute. Copyright (C) 2012-2019 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "htslib/bgzf.h" #include "htslib/sam.h" #include "htslib/hfile.h" #include "htslib/cram.h" #include "samtools.h" #define BUF_SIZE 0x10000 /* * Reads a file and outputs a new BAM file to fd with 'h' replaced as * the header. No checks are made to the validity. */ int bam_reheader(BGZF *in, sam_hdr_t *h, int fd, const char *arg_list, int no_pg, int skip_header) { BGZF *fp = NULL; ssize_t len; uint8_t *buf = NULL; sam_hdr_t *tmp; if (!h) return -1; if (in->is_write) return -1; buf = malloc(BUF_SIZE); if (!buf) { fprintf(samtools_stderr, "Out of memory\n"); return -1; } if (!skip_header) { if ((tmp = bam_hdr_read(in)) == NULL) { fprintf(samtools_stderr, "Couldn't read header\n"); goto fail; } sam_hdr_destroy(tmp); } fp = bgzf_fdopen(fd, "w"); if (!fp) { print_error_errno("reheader", "Couldn't open output file"); goto fail; } if (!no_pg && sam_hdr_add_pg(h, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL) != 0) goto fail; if (bam_hdr_write(fp, h) < 0) { print_error_errno("reheader", "Couldn't write header"); goto fail; } if (in->block_offset < in->block_length) { if (bgzf_write(fp, (char *)in->uncompressed_block + in->block_offset, in->block_length - in->block_offset) < 0) goto write_fail; if (bgzf_flush(fp) < 0) goto write_fail; } while ((len = bgzf_raw_read(in, buf, BUF_SIZE)) > 0) { if (bgzf_raw_write(fp, buf, len) < 0) goto write_fail; } if (len < 0) { fprintf(samtools_stderr, "[%s] Error reading input file\n", __func__); goto fail; } free(buf); fp->block_offset = in->block_offset = 0; if (bgzf_close(fp) < 0) { fprintf(samtools_stderr, "[%s] Error closing output file\n", __func__); return -1; } return 0; write_fail: print_error_errno("reheader", "Error writing to output file"); fail: bgzf_close(fp); free(buf); return -1; } /* * Reads a file and outputs a new CRAM file to samtools_stdout with 'h' * replaced as the header. No checks are made to the validity. * * FIXME: error checking */ int cram_reheader(cram_fd *in, sam_hdr_t *h, const char *arg_list, int no_pg) { htsFile *h_out = hts_open("-", "wc"); cram_fd *out = h_out->fp.cram; cram_container *c = NULL; int ret = -1; if (!h) return ret; // Match output version number with input file. char vers[99]; sprintf(vers, "%d.%d", cram_major_vers(in), cram_minor_vers(in)); cram_set_option(out, CRAM_OPT_VERSION, vers); // Attempt to fill out a cram->refs[] array from @SQ headers sam_hdr_t *cram_h = sam_hdr_dup(h); if (!cram_h) return -1; cram_fd_set_header(out, cram_h); if (!no_pg && sam_hdr_add_pg(cram_fd_get_header(out), "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) goto err; if (sam_hdr_write(h_out, cram_h) != 0) goto err; cram_set_option(out, CRAM_OPT_REFERENCE, NULL); while ((c = cram_read_container(in))) { int32_t i, num_blocks = cram_container_get_num_blocks(c); if (cram_write_container(out, c) != 0) goto err; for (i = 0; i < num_blocks; i++) { cram_block *blk = cram_read_block(in); if (!blk || cram_write_block(out, blk) != 0) { if (blk) cram_free_block(blk); goto err; } cram_free_block(blk); } cram_free_container(c); } ret = 0; err: if (hts_close(h_out) != 0) ret = -1; return ret; } /* * Reads a version 2 CRAM file and replaces the header in-place, * provided the header is small enough to fit without growing the * entire file. * * Version 2 format has an uncompressed SAM header with multiple nul * termination bytes to permit inline header editing. * * Returns 0 on success; * -1 on general failure; * -2 on failure due to insufficient size */ int cram_reheader_inplace2(cram_fd *fd, sam_hdr_t *h, const char *arg_list, int no_pg) { cram_container *c = NULL; cram_block *b = NULL; sam_hdr_t *cram_h = NULL; off_t start; int ret = -1; if (!h) goto err; if (cram_major_vers(fd) < 2 || cram_major_vers(fd) > 3) { fprintf(samtools_stderr, "[%s] unsupported CRAM version %d\n", __func__, cram_major_vers(fd)); goto err; } cram_h = sam_hdr_dup(h); if (!cram_h) goto err; if (!no_pg && sam_hdr_add_pg(cram_h, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) goto err; int header_len = sam_hdr_length(cram_h); /* Fix M5 strings? Maybe out of scope for this tool */ // Load the existing header if ((start = hseek(cram_fd_get_fp(fd), 26, SEEK_SET)) != 26) goto err; if (!(c = cram_read_container(fd))) goto err; // Version 2.1 has a single uncompressed block which is nul // terminated with many nuls to permit growth. // // So load old block and keep all contents identical bar the // header text itself if (!(b = cram_read_block(fd))) goto err; if (cram_block_get_uncomp_size(b) < header_len+4) { fprintf(samtools_stderr, "New header will not fit. Use non-inplace version (%d > %d)\n", header_len+4, cram_block_get_uncomp_size(b)); ret = -2; goto err; } cram_block_set_offset(b, 0); // rewind block int32_put_blk(b, header_len); cram_block_append(b, (void *)sam_hdr_str(cram_h), header_len); // Zero the remaining block memset((char *)cram_block_get_data(b)+cram_block_get_offset(b), 0, cram_block_get_uncomp_size(b) - cram_block_get_offset(b)); // Make sure all sizes and byte-offsets are consistent after memset cram_block_set_offset(b, cram_block_get_uncomp_size(b)); cram_block_set_comp_size(b, cram_block_get_uncomp_size(b)); if (hseek(cram_fd_get_fp(fd), start, SEEK_SET) != start) goto err; if (cram_write_container(fd, c) == -1) goto err; if (cram_write_block(fd, b) == -1) goto err; ret = 0; err: if (c) cram_free_container(c); if (b) cram_free_block(b); if (cram_h) sam_hdr_destroy(cram_h); return ret; } /* * Reads a version 3 CRAM file and replaces the header in-place, * provided the header is small enough to fit without growing the * entire file. * * Version 3 format has a SAM header held as an (optionally) * compressed block within the header container. Additional * uncompressed blocks or simply unallocated space (the difference * between total block sizes and the container size) are used to * provide room for growth or contraction of the compressed header. * * Returns 0 on success; * -1 on general failure; * -2 on failure due to insufficient size */ int cram_reheader_inplace3(cram_fd *fd, sam_hdr_t *h, const char *arg_list, int no_pg) { cram_container *c = NULL; cram_block *b = NULL; sam_hdr_t *cram_h = NULL; off_t start, sz, end; int container_sz, max_container_sz; char *buf = NULL; int ret = -1; if (!h) goto err; if (cram_major_vers(fd) < 2 || cram_major_vers(fd) > 3) { fprintf(samtools_stderr, "[%s] unsupported CRAM version %d\n", __func__, cram_major_vers(fd)); goto err; } cram_h = sam_hdr_dup(h); if (!cram_h) goto err; if (!no_pg && sam_hdr_add_pg(cram_h, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) goto err; int header_len = sam_hdr_length(cram_h); /* Fix M5 strings? Maybe out of scope for this tool */ // Find current size of SAM header block if ((start = hseek(cram_fd_get_fp(fd), 26, SEEK_SET)) != 26) goto err; if (!(c = cram_read_container(fd))) goto err; // +5 allows num_landmarks to increase from 0 to 1 (Cramtools) max_container_sz = cram_container_size(c)+5; sz = htell(cram_fd_get_fp(fd)) + cram_container_get_length(c) - start; end = htell(cram_fd_get_fp(fd)) + cram_container_get_length(c); // We force 1 block instead of (optionally) 2. C CRAM // implementations for v3 were writing 1 compressed block followed // by 1 uncompressed block. However this is tricky to deal with // as changing block sizes can mean the block header also changes // size due to itf8 and variable size integers. // // If we had 1 block, this doesn't change anything. // If we had 2 blocks, the new container header will be smaller by // 1+ bytes, requiring the cram_container_get_length(c) to be larger in value. // However this is an int32 instead of itf8 so the container // header structure stays the same size. This means we can always // reduce the number of blocks without running into size problems. cram_container_set_num_blocks(c, 1); int32_t *landmark; int32_t num_landmarks; landmark = cram_container_get_landmarks(c, &num_landmarks); if (num_landmarks && landmark) { num_landmarks = 1; landmark[0] = 0; } else { num_landmarks = 0; } cram_container_set_landmarks(c, num_landmarks, landmark); buf = malloc(max_container_sz); container_sz = max_container_sz; if (cram_store_container(fd, c, buf, &container_sz) != 0) goto err; if (!buf) goto err; // Proposed new length, but changing cram_container_get_length(c) may change the // container_sz and thus the remainder (cram_container_get_length(c) itself). cram_container_set_length(c, sz - container_sz); int old_container_sz = container_sz; container_sz = max_container_sz; if (cram_store_container(fd, c, buf, &container_sz) != 0) goto err; if (old_container_sz != container_sz) { fprintf(samtools_stderr, "Quirk of fate makes this troublesome! " "Please use non-inplace version.\n"); goto err; } // Version 3.0 supports compressed header b = cram_new_block(FILE_HEADER, 0); int32_put_blk(b, header_len); cram_block_append(b, (void *)sam_hdr_str(cram_h), header_len); cram_block_update_size(b); cram_compress_block(fd, b, NULL, -1, 9); if (hseek(cram_fd_get_fp(fd), 26, SEEK_SET) != 26) goto err; if (cram_block_size(b) > cram_container_get_length(c)) { fprintf(samtools_stderr, "New header will not fit. Use non-inplace version" " (%d > %d)\n", (int)cram_block_size(b), cram_container_get_length(c)); ret = -2; goto err; } if (cram_write_container(fd, c) == -1) goto err; if (cram_write_block(fd, b) == -1) goto err; // Blank out the remainder int rsz = end - htell(cram_fd_get_fp(fd)); assert(rsz >= 0); if (rsz) { char *rem = calloc(1, rsz); ret = hwrite(cram_fd_get_fp(fd), rem, rsz) == rsz ? 0 : -1; free(rem); } err: if (c) cram_free_container(c); if (buf) free(buf); if (b) cram_free_block(b); if (cram_h) sam_hdr_destroy(cram_h); return ret; } int cram_reheader_inplace(cram_fd *fd, sam_hdr_t *h, const char *arg_list, int no_pg) { switch (cram_major_vers(fd)) { case 2: return cram_reheader_inplace2(fd, h, arg_list, no_pg); case 3: return cram_reheader_inplace3(fd, h, arg_list, no_pg); default: fprintf(samtools_stderr, "[%s] unsupported CRAM version %d\n", __func__, cram_major_vers(fd)); return -1; } } static void usage(FILE *fp, int ret) { fprintf(fp, "Usage: samtools reheader [-P] in.header.sam in.bam > out.bam\n" " or samtools reheader [-P] -i in.header.sam file.cram\n" " or samtools reheader -c CMD in.bam\n" " or samtools reheader -c CMD in.cram\n" "\n" "Options:\n" " -P, --no-PG Do not generate a @PG header line.\n" " -i, --in-place Modify the CRAM file directly, if possible.\n" " (Defaults to outputting to samtools_stdout.)\n" " -c, --command CMD Pass the header in SAM format to external program CMD.\n"); samtools_exit(ret); } static sam_hdr_t* external_reheader(samFile* in, const char* external) { char *command = NULL; sam_hdr_t* h = NULL; sam_hdr_t* ih = sam_hdr_read(in); if (ih == NULL) { fprintf(samtools_stderr, "[%s] failed to read the header for '%s'.\n", __func__, in->fn); return NULL; } char tmp_fn[] = "reheaderXXXXXX"; int tmp_fd = mkstemp(tmp_fn); if (tmp_fd < 0) { print_error_errno("reheader", "fail to open temp file '%s'", tmp_fn); return NULL; } hFILE* tmp_hf = hdopen(tmp_fd, "w"); if (!tmp_hf) { fprintf(samtools_stderr, "[%s] failed to convert to hFILE.\n", __func__); goto cleanup; } samFile* tmp_sf = hts_hopen(tmp_hf, tmp_fn, "w"); if (!tmp_sf) { fprintf(samtools_stderr, "[%s] failed to convert to samFile.\n", __func__); goto cleanup; } if (-1 == sam_hdr_write(tmp_sf, ih)) { fprintf(samtools_stderr, "[%s] failed to write the header to the temp file.\n", __func__); goto cleanup; } sam_close(tmp_sf); sam_hdr_destroy(ih); int comm_len = strlen(external) + strlen(tmp_fn) + 8; command = calloc(comm_len, 1); if (!command || snprintf(command, comm_len, "( %s ) < %s", external, tmp_fn) != comm_len - 1) { fprintf(samtools_stderr, "[%s] failed to create command string.\n", __func__); goto cleanup; } FILE* nh = popen(command, "r"); if (!nh) { print_error_errno("reheader", "[%s] failed to run external command '%s'.\n", __func__, command); goto cleanup; } int nh_fd = dup(fileno(nh)); if (nh_fd < 0) { fprintf(samtools_stderr, "[%s] failed to get the file descriptor.\n", __func__); goto cleanup; } hFILE* nh_hf = hdopen(nh_fd, "r"); if (!nh_hf) { fprintf(samtools_stderr, "[%s] failed to convert to hFILE.\n", __func__); goto cleanup; } samFile* nh_sf = hts_hopen(nh_hf, tmp_fn, "r"); if (!nh_sf) { fprintf(samtools_stderr, "[%s] failed to convert to samFile.\n", __func__); goto cleanup; } h = sam_hdr_read(nh_sf); sam_close(nh_sf); if (h == NULL) { fprintf(samtools_stderr, "[%s] failed to read the header from the temp file.\n", __func__); } int res = pclose(nh); if (res != 0) { if (res < 0) { print_error_errno("reheader", "Error on closing pipe from command '%s'.\n", command); } else { print_error("reheader", "Non-zero exit code returned by command '%s'\n", command); } if (h) sam_hdr_destroy(h); h = NULL; } cleanup: free(command); if (unlink(tmp_fn) != 0) { print_error_errno("reheader", "failed to remove the temp file '%s'", tmp_fn); } return h; } int main_reheader(int argc, char *argv[]) { int inplace = 0, r, no_pg = 0, c, skip_header = 0; sam_hdr_t *h; samFile *in; char *arg_list = NULL, *external = NULL; static const struct option lopts[] = { {"help", no_argument, NULL, 'h'}, {"in-place", no_argument, NULL, 'i'}, {"no-PG", no_argument, NULL, 'P'}, {"command", required_argument, NULL, 'c'}, {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "hiPc:", lopts, NULL)) >= 0) { switch (c) { case 'P': no_pg = 1; break; case 'i': inplace = 1; break; case 'c': external = optarg; break; case 'h': usage(samtools_stdout, 0); break; default: fprintf(samtools_stderr, "Invalid option '%c'\n", c); usage(samtools_stderr, 1); } } if ((argc - optind != 2 || external) && (argc - optind != 1 || !external)) usage(samtools_stderr, 1); if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) { print_error("reheader", "failed to create arg_list"); return 1; } if (external) { skip_header = 1; in = sam_open(argv[optind], inplace?"r+":"r"); if (in == 0) { print_error_errno("reheader", "fail to open file '%s'", argv[optind]); return 1; } h = external_reheader(in, external); if (h == NULL) { fprintf(samtools_stderr, "[%s] failed to read the header from '%s'.\n", __func__, external); sam_close(in); return 1; } } else { // read the header from a separate file samFile *fph = sam_open(argv[optind], "r"); if (fph == 0) { print_error_errno("reheader", "fail to read the header from '%s'", argv[optind]); return 1; } h = sam_hdr_read(fph); sam_close(fph); if (h == NULL) { fprintf(samtools_stderr, "[%s] failed to read the header for '%s'.\n", __func__, argv[1]); return 1; } in = sam_open(argv[optind+1], inplace?"r+":"r"); if (in == 0) { print_error_errno("reheader", "fail to open file '%s'", argv[optind+1]); return 1; } } if (hts_get_format(in)->format == bam) { if (inplace) { print_error("reheader", "cannot reheader BAM '%s' in-place", argv[optind+1]); r = -1; } else { r = bam_reheader(in->fp.bgzf, h, fileno(samtools_stdout), arg_list, no_pg, skip_header); } } else if (hts_get_format(in)->format == cram) { if (inplace) r = cram_reheader_inplace(in->fp.cram, h, arg_list, no_pg); else r = cram_reheader(in->fp.cram, h, arg_list, no_pg); } else { print_error("reheader", "input file '%s' must be BAM or CRAM", argv[optind+1]); r = -1; } if (sam_close(in) != 0) r = -1; sam_hdr_destroy(h); if (arg_list) free(arg_list); return -r; } pysam-0.23.0/samtools/bam_rmdup.c000066400000000000000000000246541475062545500167300ustar00rootroot00000000000000/* bam_rmdup.c -- duplicate read detection. Copyright (C) 2009, 2015, 2016, 2019 Genome Research Ltd. Portions copyright (C) 2009 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "htslib/sam.h" #include "sam_opts.h" #include "samtools.h" #include "bam.h" // for bam_get_library typedef bam1_t *bam1_p; #include "htslib/khash.h" KHASH_SET_INIT_STR(name) KHASH_MAP_INIT_INT64(pos, bam1_p) #define BUFFER_SIZE 0x40000 typedef struct { uint64_t n_checked, n_removed; khash_t(pos) *best_hash; } lib_aux_t; KHASH_MAP_INIT_STR(lib, lib_aux_t) typedef struct { int n, max; bam1_t **a; } tmp_stack_t; static inline void stack_insert(tmp_stack_t *stack, bam1_t *b) { if (stack->n == stack->max) { stack->max = stack->max? stack->max<<1 : 0x10000; stack->a = (bam1_t**)realloc(stack->a, sizeof(bam1_t*) * stack->max); } stack->a[stack->n++] = b; } static inline int dump_best(tmp_stack_t *stack, samFile *out, sam_hdr_t *hdr) { int i; for (i = 0; i != stack->n; ++i) { if (sam_write1(out, hdr, stack->a[i]) < 0) return -1; bam_destroy1(stack->a[i]); stack->a[i] = NULL; } stack->n = 0; return 0; } static inline void clear_stack(tmp_stack_t *stack) { int i; if (!stack->a) return; for (i = 0; i != stack->n; ++i) { bam_destroy1(stack->a[i]); } } static void clear_del_set(khash_t(name) *del_set) { khint_t k; for (k = kh_begin(del_set); k < kh_end(del_set); ++k) if (kh_exist(del_set, k)) free((char*)kh_key(del_set, k)); kh_clear(name, del_set); } static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib) { khint_t k = kh_get(lib, aux, lib); if (k == kh_end(aux)) { int ret; char *p = strdup(lib); lib_aux_t *q; k = kh_put(lib, aux, p, &ret); q = &kh_val(aux, k); q->n_checked = q->n_removed = 0; q->best_hash = kh_init(pos); return q; } else return &kh_val(aux, k); } static void clear_best(khash_t(lib) *aux, int max) { khint_t k; for (k = kh_begin(aux); k != kh_end(aux); ++k) { if (kh_exist(aux, k)) { lib_aux_t *q = &kh_val(aux, k); if (kh_size(q->best_hash) >= max) kh_clear(pos, q->best_hash); } } } static inline int sum_qual(const bam1_t *b) { int i, q; uint8_t *qual = bam_get_qual(b); for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i]; return q; } int bam_rmdup_core(samFile *in, sam_hdr_t *hdr, samFile *out) { bam1_t *b = NULL; int last_tid = -1, last_pos = -1, r; tmp_stack_t stack; khint_t k; khash_t(lib) *aux = NULL; khash_t(name) *del_set = NULL; memset(&stack, 0, sizeof(tmp_stack_t)); aux = kh_init(lib); del_set = kh_init(name); b = bam_init1(); if (!aux || !del_set || !b) { perror(__func__); goto fail; } kh_resize(name, del_set, 4 * BUFFER_SIZE); while ((r = sam_read1(in, hdr, b)) >= 0) { bam1_core_t *c = &b->core; if (c->tid != last_tid || last_pos != c->pos) { if (dump_best(&stack, out, hdr) < 0) goto write_fail; // write the result clear_best(aux, BUFFER_SIZE); if (c->tid != last_tid) { clear_best(aux, 0); if (kh_size(del_set)) { // check fprintf(stderr, "[bam_rmdup_core] %llu unmatched pairs\n", (long long)kh_size(del_set)); clear_del_set(del_set); } if ((int)c->tid == -1) { // append unmapped reads if (sam_write1(out, hdr, b) < 0) goto write_fail; while ((r = sam_read1(in, hdr, b)) >= 0) { if (sam_write1(out, hdr, b) < 0) goto write_fail; } break; } last_tid = c->tid; fprintf(stderr, "[bam_rmdup_core] processing reference %s...\n", sam_hdr_tid2name(hdr, c->tid)); } } if (!(c->flag&BAM_FPAIRED) || (c->flag&(BAM_FUNMAP|BAM_FMUNMAP)) || (c->mtid >= 0 && c->tid != c->mtid)) { if (sam_write1(out, hdr, b) < 0) goto write_fail; } else if (c->isize > 0) { // paired, head uint64_t key = (uint64_t)c->pos<<32 | c->isize; const char *lib; lib_aux_t *q; int ret; lib = bam_get_library(hdr, b); q = lib? get_aux(aux, lib) : get_aux(aux, "\t"); ++q->n_checked; k = kh_put(pos, q->best_hash, key, &ret); if (ret < 0) goto fail; if (ret == 0) { // found in best_hash bam1_t *p = kh_val(q->best_hash, k); ++q->n_removed; if (sum_qual(p) < sum_qual(b)) { // the current alignment is better; this can be accelerated in principle kh_put(name, del_set, strdup(bam_get_qname(p)), &ret); // p will be removed if (ret < 0) goto fail; if (bam_copy1(p, b) == NULL) goto fail; // replaced as b } else kh_put(name, del_set, strdup(bam_get_qname(b)), &ret); // b will be removed if (ret < 0) goto fail; if (ret == 0) fprintf(stderr, "[bam_rmdup_core] inconsistent BAM file for pair '%s'. Continue anyway.\n", bam_get_qname(b)); } else { // not found in best_hash kh_val(q->best_hash, k) = bam_dup1(b); stack_insert(&stack, kh_val(q->best_hash, k)); } } else { // paired, tail k = kh_get(name, del_set, bam_get_qname(b)); if (k != kh_end(del_set)) { free((char*)kh_key(del_set, k)); kh_del(name, del_set, k); } else { if (sam_write1(out, hdr, b) < 0) goto write_fail; } } last_pos = c->pos; } if (r < -1) { fprintf(stderr, "[%s] failed to read input file\n", __func__); goto fail; } for (k = kh_begin(aux); k != kh_end(aux); ++k) { if (kh_exist(aux, k)) { lib_aux_t *q = &kh_val(aux, k); if (dump_best(&stack, out, hdr) < 0) goto write_fail; fprintf(stderr, "[bam_rmdup_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed, (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k)); kh_destroy(pos, q->best_hash); free((char*)kh_key(aux, k)); kh_del(lib, aux, k); } } kh_destroy(lib, aux); clear_del_set(del_set); kh_destroy(name, del_set); free(stack.a); bam_destroy1(b); return 0; write_fail: print_error_errno("rmdup", "failed to write record"); fail: clear_stack(&stack); free(stack.a); if (aux) { for (k = kh_begin(aux); k != kh_end(aux); ++k) { if (kh_exist(aux, k)) { lib_aux_t *q = &kh_val(aux, k); kh_destroy(pos, q->best_hash); free((char*)kh_key(aux, k)); } } kh_destroy(lib, aux); } if (del_set) { clear_del_set(del_set); kh_destroy(name, del_set); } bam_destroy1(b); return 1; } int bam_rmdupse_core(samFile *in, sam_hdr_t *hdr, samFile *out, int force_se); static int rmdup_usage(void) { fprintf(stderr, "\n"); fprintf(stderr, "Usage: samtools rmdup [-sS] \n\n"); fprintf(stderr, "Option: -s rmdup for SE reads\n"); fprintf(stderr, " -S treat PE reads as SE in rmdup (force -s)\n"); sam_global_opt_help(stderr, "-....--."); return 1; } int bam_rmdup(int argc, char *argv[]) { int c, ret, is_se = 0, force_se = 0; samFile *in, *out; sam_hdr_t *header; char wmode[3] = {'w', 'b', 0}; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0, '-'), { NULL, 0, NULL, 0 } }; while ((c = getopt_long(argc, argv, "sS", lopts, NULL)) >= 0) { switch (c) { case 's': is_se = 1; break; case 'S': force_se = is_se = 1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': return rmdup_usage(); } } if (optind + 2 > argc) return rmdup_usage(); in = sam_open_format(argv[optind], "r", &ga.in); if (!in) { print_error_errno("rmdup", "failed to open \"%s\" for input", argv[optind]); return 1; } header = sam_hdr_read(in); if (header == NULL || sam_hdr_nref(header) == 0) { fprintf(stderr, "[bam_rmdup] input SAM does not have header. Abort!\n"); return 1; } sam_open_mode(wmode+1, argv[optind+1], NULL); out = sam_open_format(argv[optind+1], wmode, &ga.out); if (!out) { print_error_errno("rmdup", "failed to open \"%s\" for output", argv[optind+1]); return 1; } if (sam_hdr_write(out, header) < 0) { print_error_errno("rmdup", "failed to write header"); return 1; } if (is_se) ret = bam_rmdupse_core(in, header, out, force_se); else ret = bam_rmdup_core(in, header, out); sam_hdr_destroy(header); sam_close(in); if (sam_close(out) < 0) { fprintf(stderr, "[bam_rmdup] error closing output file\n"); ret = 1; } return ret; } pysam-0.23.0/samtools/bam_rmdup.c.pysam.c000066400000000000000000000250651475062545500202760ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_rmdup.c -- duplicate read detection. Copyright (C) 2009, 2015, 2016, 2019 Genome Research Ltd. Portions copyright (C) 2009 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "htslib/sam.h" #include "sam_opts.h" #include "samtools.h" #include "bam.h" // for bam_get_library typedef bam1_t *bam1_p; #include "htslib/khash.h" KHASH_SET_INIT_STR(name) KHASH_MAP_INIT_INT64(pos, bam1_p) #define BUFFER_SIZE 0x40000 typedef struct { uint64_t n_checked, n_removed; khash_t(pos) *best_hash; } lib_aux_t; KHASH_MAP_INIT_STR(lib, lib_aux_t) typedef struct { int n, max; bam1_t **a; } tmp_stack_t; static inline void stack_insert(tmp_stack_t *stack, bam1_t *b) { if (stack->n == stack->max) { stack->max = stack->max? stack->max<<1 : 0x10000; stack->a = (bam1_t**)realloc(stack->a, sizeof(bam1_t*) * stack->max); } stack->a[stack->n++] = b; } static inline int dump_best(tmp_stack_t *stack, samFile *out, sam_hdr_t *hdr) { int i; for (i = 0; i != stack->n; ++i) { if (sam_write1(out, hdr, stack->a[i]) < 0) return -1; bam_destroy1(stack->a[i]); stack->a[i] = NULL; } stack->n = 0; return 0; } static inline void clear_stack(tmp_stack_t *stack) { int i; if (!stack->a) return; for (i = 0; i != stack->n; ++i) { bam_destroy1(stack->a[i]); } } static void clear_del_set(khash_t(name) *del_set) { khint_t k; for (k = kh_begin(del_set); k < kh_end(del_set); ++k) if (kh_exist(del_set, k)) free((char*)kh_key(del_set, k)); kh_clear(name, del_set); } static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib) { khint_t k = kh_get(lib, aux, lib); if (k == kh_end(aux)) { int ret; char *p = strdup(lib); lib_aux_t *q; k = kh_put(lib, aux, p, &ret); q = &kh_val(aux, k); q->n_checked = q->n_removed = 0; q->best_hash = kh_init(pos); return q; } else return &kh_val(aux, k); } static void clear_best(khash_t(lib) *aux, int max) { khint_t k; for (k = kh_begin(aux); k != kh_end(aux); ++k) { if (kh_exist(aux, k)) { lib_aux_t *q = &kh_val(aux, k); if (kh_size(q->best_hash) >= max) kh_clear(pos, q->best_hash); } } } static inline int sum_qual(const bam1_t *b) { int i, q; uint8_t *qual = bam_get_qual(b); for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i]; return q; } int bam_rmdup_core(samFile *in, sam_hdr_t *hdr, samFile *out) { bam1_t *b = NULL; int last_tid = -1, last_pos = -1, r; tmp_stack_t stack; khint_t k; khash_t(lib) *aux = NULL; khash_t(name) *del_set = NULL; memset(&stack, 0, sizeof(tmp_stack_t)); aux = kh_init(lib); del_set = kh_init(name); b = bam_init1(); if (!aux || !del_set || !b) { perror(__func__); goto fail; } kh_resize(name, del_set, 4 * BUFFER_SIZE); while ((r = sam_read1(in, hdr, b)) >= 0) { bam1_core_t *c = &b->core; if (c->tid != last_tid || last_pos != c->pos) { if (dump_best(&stack, out, hdr) < 0) goto write_fail; // write the result clear_best(aux, BUFFER_SIZE); if (c->tid != last_tid) { clear_best(aux, 0); if (kh_size(del_set)) { // check fprintf(samtools_stderr, "[bam_rmdup_core] %llu unmatched pairs\n", (long long)kh_size(del_set)); clear_del_set(del_set); } if ((int)c->tid == -1) { // append unmapped reads if (sam_write1(out, hdr, b) < 0) goto write_fail; while ((r = sam_read1(in, hdr, b)) >= 0) { if (sam_write1(out, hdr, b) < 0) goto write_fail; } break; } last_tid = c->tid; fprintf(samtools_stderr, "[bam_rmdup_core] processing reference %s...\n", sam_hdr_tid2name(hdr, c->tid)); } } if (!(c->flag&BAM_FPAIRED) || (c->flag&(BAM_FUNMAP|BAM_FMUNMAP)) || (c->mtid >= 0 && c->tid != c->mtid)) { if (sam_write1(out, hdr, b) < 0) goto write_fail; } else if (c->isize > 0) { // paired, head uint64_t key = (uint64_t)c->pos<<32 | c->isize; const char *lib; lib_aux_t *q; int ret; lib = bam_get_library(hdr, b); q = lib? get_aux(aux, lib) : get_aux(aux, "\t"); ++q->n_checked; k = kh_put(pos, q->best_hash, key, &ret); if (ret < 0) goto fail; if (ret == 0) { // found in best_hash bam1_t *p = kh_val(q->best_hash, k); ++q->n_removed; if (sum_qual(p) < sum_qual(b)) { // the current alignment is better; this can be accelerated in principle kh_put(name, del_set, strdup(bam_get_qname(p)), &ret); // p will be removed if (ret < 0) goto fail; if (bam_copy1(p, b) == NULL) goto fail; // replaced as b } else kh_put(name, del_set, strdup(bam_get_qname(b)), &ret); // b will be removed if (ret < 0) goto fail; if (ret == 0) fprintf(samtools_stderr, "[bam_rmdup_core] inconsistent BAM file for pair '%s'. Continue anyway.\n", bam_get_qname(b)); } else { // not found in best_hash kh_val(q->best_hash, k) = bam_dup1(b); stack_insert(&stack, kh_val(q->best_hash, k)); } } else { // paired, tail k = kh_get(name, del_set, bam_get_qname(b)); if (k != kh_end(del_set)) { free((char*)kh_key(del_set, k)); kh_del(name, del_set, k); } else { if (sam_write1(out, hdr, b) < 0) goto write_fail; } } last_pos = c->pos; } if (r < -1) { fprintf(samtools_stderr, "[%s] failed to read input file\n", __func__); goto fail; } for (k = kh_begin(aux); k != kh_end(aux); ++k) { if (kh_exist(aux, k)) { lib_aux_t *q = &kh_val(aux, k); if (dump_best(&stack, out, hdr) < 0) goto write_fail; fprintf(samtools_stderr, "[bam_rmdup_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed, (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k)); kh_destroy(pos, q->best_hash); free((char*)kh_key(aux, k)); kh_del(lib, aux, k); } } kh_destroy(lib, aux); clear_del_set(del_set); kh_destroy(name, del_set); free(stack.a); bam_destroy1(b); return 0; write_fail: print_error_errno("rmdup", "failed to write record"); fail: clear_stack(&stack); free(stack.a); if (aux) { for (k = kh_begin(aux); k != kh_end(aux); ++k) { if (kh_exist(aux, k)) { lib_aux_t *q = &kh_val(aux, k); kh_destroy(pos, q->best_hash); free((char*)kh_key(aux, k)); } } kh_destroy(lib, aux); } if (del_set) { clear_del_set(del_set); kh_destroy(name, del_set); } bam_destroy1(b); return 1; } int bam_rmdupse_core(samFile *in, sam_hdr_t *hdr, samFile *out, int force_se); static int rmdup_usage(void) { fprintf(samtools_stderr, "\n"); fprintf(samtools_stderr, "Usage: samtools rmdup [-sS] \n\n"); fprintf(samtools_stderr, "Option: -s rmdup for SE reads\n"); fprintf(samtools_stderr, " -S treat PE reads as SE in rmdup (force -s)\n"); sam_global_opt_help(samtools_stderr, "-....--."); return 1; } int bam_rmdup(int argc, char *argv[]) { int c, ret, is_se = 0, force_se = 0; samFile *in, *out; sam_hdr_t *header; char wmode[3] = {'w', 'b', 0}; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0, '-'), { NULL, 0, NULL, 0 } }; while ((c = getopt_long(argc, argv, "sS", lopts, NULL)) >= 0) { switch (c) { case 's': is_se = 1; break; case 'S': force_se = is_se = 1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': return rmdup_usage(); } } if (optind + 2 > argc) return rmdup_usage(); in = sam_open_format(argv[optind], "r", &ga.in); if (!in) { print_error_errno("rmdup", "failed to open \"%s\" for input", argv[optind]); return 1; } header = sam_hdr_read(in); if (header == NULL || sam_hdr_nref(header) == 0) { fprintf(samtools_stderr, "[bam_rmdup] input SAM does not have header. Abort!\n"); return 1; } sam_open_mode(wmode+1, argv[optind+1], NULL); out = sam_open_format(argv[optind+1], wmode, &ga.out); if (!out) { print_error_errno("rmdup", "failed to open \"%s\" for output", argv[optind+1]); return 1; } if (sam_hdr_write(out, header) < 0) { print_error_errno("rmdup", "failed to write header"); return 1; } if (is_se) ret = bam_rmdupse_core(in, header, out, force_se); else ret = bam_rmdup_core(in, header, out); sam_hdr_destroy(header); sam_close(in); if (sam_close(out) < 0) { fprintf(samtools_stderr, "[bam_rmdup] error closing output file\n"); ret = 1; } return ret; } pysam-0.23.0/samtools/bam_rmdupse.c000066400000000000000000000165261475062545500172570ustar00rootroot00000000000000/* bam_rmdupse.c -- duplicate read detection for unpaired reads. Copyright (C) 2009, 2015, 2016, 2019 Genome Research Ltd. Portions copyright (C) 2009 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include "bam.h" // for bam_get_library #include "htslib/sam.h" #include "htslib/khash.h" #include "htslib/klist.h" #include "samtools.h" #define QUEUE_CLEAR_SIZE 0x100000 #define MAX_POS 0x7fffffff typedef struct { int endpos; uint32_t score:31, discarded:1; bam1_t *b; } elem_t, *elem_p; #define __free_elem(p) bam_destroy1((p)->data.b) KLIST_INIT(q, elem_t, __free_elem) typedef klist_t(q) queue_t; KHASH_MAP_INIT_INT(best, elem_p) typedef khash_t(best) besthash_t; typedef struct { uint64_t n_checked, n_removed; besthash_t *left, *rght; } lib_aux_t; KHASH_MAP_INIT_STR(lib, lib_aux_t) static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib) { khint_t k = kh_get(lib, aux, lib); if (k == kh_end(aux)) { int ret; char *p = strdup(lib); lib_aux_t *q; k = kh_put(lib, aux, p, &ret); q = &kh_val(aux, k); q->left = kh_init(best); q->rght = kh_init(best); q->n_checked = q->n_removed = 0; return q; } else return &kh_val(aux, k); } static inline int sum_qual(const bam1_t *b) { int i, q; uint8_t *qual = bam_get_qual(b); for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i]; return q; } static inline elem_t *push_queue(queue_t *queue, const bam1_t *b, int endpos, int score) { elem_t *p = kl_pushp(q, queue); p->discarded = 0; p->endpos = endpos; p->score = score; if (p->b == 0) p->b = bam_init1(); if (!p->b) { perror(NULL); exit(EXIT_FAILURE); } if (bam_copy1(p->b, b) == NULL) { perror(NULL); exit(EXIT_FAILURE); } return p; } static void clear_besthash(besthash_t *h, int32_t pos) { khint_t k; for (k = kh_begin(h); k != kh_end(h); ++k) if (kh_exist(h, k) && kh_val(h, k)->endpos <= pos) kh_del(best, h, k); } static int dump_alignment(samFile *out, sam_hdr_t *hdr, queue_t *queue, int32_t pos, khash_t(lib) *h) { if (queue->size > QUEUE_CLEAR_SIZE || pos == MAX_POS) { khint_t k; while (1) { elem_t *q; if (queue->head == queue->tail) break; q = &kl_val(queue->head); if (q->discarded) { q->b->l_data = 0; kl_shift(q, queue, 0); continue; } if ((q->b->core.flag&BAM_FREVERSE) && q->endpos > pos) break; if (sam_write1(out, hdr, q->b) < 0) return -1; q->b->l_data = 0; kl_shift(q, queue, 0); } for (k = kh_begin(h); k != kh_end(h); ++k) { if (kh_exist(h, k)) { clear_besthash(kh_val(h, k).left, pos); clear_besthash(kh_val(h, k).rght, pos); } } } return 0; } int bam_rmdupse_core(samFile *in, sam_hdr_t *hdr, samFile *out, int force_se) { bam1_t *b = NULL; queue_t *queue = NULL; khint_t k; int last_tid = -2, r; khash_t(lib) *aux = NULL; aux = kh_init(lib); b = bam_init1(); queue = kl_init(q); if (!aux || !b || !queue) { perror(__func__); goto fail; } while ((r = sam_read1(in, hdr, b)) >= 0) { bam1_core_t *c = &b->core; int endpos = bam_endpos(b); int score = sum_qual(b); if (last_tid != c->tid) { if (last_tid >= 0) { if (dump_alignment(out, hdr, queue, MAX_POS, aux) < 0) goto write_fail; } last_tid = c->tid; } else { if (dump_alignment(out, hdr, queue, c->pos, aux) < 0) goto write_fail; } if ((c->flag&BAM_FUNMAP) || ((c->flag&BAM_FPAIRED) && !force_se)) { push_queue(queue, b, endpos, score); } else { const char *lib; lib_aux_t *q; besthash_t *h; uint32_t key; int ret; lib = bam_get_library(hdr, b); q = lib? get_aux(aux, lib) : get_aux(aux, "\t"); ++q->n_checked; h = (c->flag&BAM_FREVERSE)? q->rght : q->left; key = (c->flag&BAM_FREVERSE)? endpos : c->pos; k = kh_put(best, h, key, &ret); if (ret == 0) { // in the hash table elem_t *p = kh_val(h, k); ++q->n_removed; if (p->score < score) { if (c->flag&BAM_FREVERSE) { // mark "discarded" and push the queue p->discarded = 1; kh_val(h, k) = push_queue(queue, b, endpos, score); } else { // replace p->score = score; p->endpos = endpos; if (bam_copy1(p->b, b) == NULL) { perror(NULL); exit(EXIT_FAILURE); } } } // otherwise, discard the alignment } else kh_val(h, k) = push_queue(queue, b, endpos, score); } } if (r < -1) { fprintf(stderr, "[%s] error reading input file\n", __func__); goto fail; } if (dump_alignment(out, hdr, queue, MAX_POS, aux) < 0) goto write_fail; for (k = kh_begin(aux); k != kh_end(aux); ++k) { if (kh_exist(aux, k)) { lib_aux_t *q = &kh_val(aux, k); fprintf(stderr, "[bam_rmdupse_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed, (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k)); kh_destroy(best, q->left); kh_destroy(best, q->rght); free((char*)kh_key(aux, k)); kh_del(lib, aux, k); } } kh_destroy(lib, aux); bam_destroy1(b); kl_destroy(q, queue); return 0; write_fail: print_error_errno("rmdup", "failed to write record"); fail: if (aux) { for (k = kh_begin(aux); k != kh_end(aux); ++k) { if (kh_exist(aux, k)) { lib_aux_t *q = &kh_val(aux, k); kh_destroy(best, q->left); kh_destroy(best, q->rght); free((char*)kh_key(aux, k)); } } kh_destroy(lib, aux); } bam_destroy1(b); kl_destroy(q, queue); return 1; } pysam-0.23.0/samtools/bam_rmdupse.c.pysam.c000066400000000000000000000166401475062545500206250ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_rmdupse.c -- duplicate read detection for unpaired reads. Copyright (C) 2009, 2015, 2016, 2019 Genome Research Ltd. Portions copyright (C) 2009 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include "bam.h" // for bam_get_library #include "htslib/sam.h" #include "htslib/khash.h" #include "htslib/klist.h" #include "samtools.h" #define QUEUE_CLEAR_SIZE 0x100000 #define MAX_POS 0x7fffffff typedef struct { int endpos; uint32_t score:31, discarded:1; bam1_t *b; } elem_t, *elem_p; #define __free_elem(p) bam_destroy1((p)->data.b) KLIST_INIT(q, elem_t, __free_elem) typedef klist_t(q) queue_t; KHASH_MAP_INIT_INT(best, elem_p) typedef khash_t(best) besthash_t; typedef struct { uint64_t n_checked, n_removed; besthash_t *left, *rght; } lib_aux_t; KHASH_MAP_INIT_STR(lib, lib_aux_t) static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib) { khint_t k = kh_get(lib, aux, lib); if (k == kh_end(aux)) { int ret; char *p = strdup(lib); lib_aux_t *q; k = kh_put(lib, aux, p, &ret); q = &kh_val(aux, k); q->left = kh_init(best); q->rght = kh_init(best); q->n_checked = q->n_removed = 0; return q; } else return &kh_val(aux, k); } static inline int sum_qual(const bam1_t *b) { int i, q; uint8_t *qual = bam_get_qual(b); for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i]; return q; } static inline elem_t *push_queue(queue_t *queue, const bam1_t *b, int endpos, int score) { elem_t *p = kl_pushp(q, queue); p->discarded = 0; p->endpos = endpos; p->score = score; if (p->b == 0) p->b = bam_init1(); if (!p->b) { perror(NULL); samtools_exit(EXIT_FAILURE); } if (bam_copy1(p->b, b) == NULL) { perror(NULL); samtools_exit(EXIT_FAILURE); } return p; } static void clear_besthash(besthash_t *h, int32_t pos) { khint_t k; for (k = kh_begin(h); k != kh_end(h); ++k) if (kh_exist(h, k) && kh_val(h, k)->endpos <= pos) kh_del(best, h, k); } static int dump_alignment(samFile *out, sam_hdr_t *hdr, queue_t *queue, int32_t pos, khash_t(lib) *h) { if (queue->size > QUEUE_CLEAR_SIZE || pos == MAX_POS) { khint_t k; while (1) { elem_t *q; if (queue->head == queue->tail) break; q = &kl_val(queue->head); if (q->discarded) { q->b->l_data = 0; kl_shift(q, queue, 0); continue; } if ((q->b->core.flag&BAM_FREVERSE) && q->endpos > pos) break; if (sam_write1(out, hdr, q->b) < 0) return -1; q->b->l_data = 0; kl_shift(q, queue, 0); } for (k = kh_begin(h); k != kh_end(h); ++k) { if (kh_exist(h, k)) { clear_besthash(kh_val(h, k).left, pos); clear_besthash(kh_val(h, k).rght, pos); } } } return 0; } int bam_rmdupse_core(samFile *in, sam_hdr_t *hdr, samFile *out, int force_se) { bam1_t *b = NULL; queue_t *queue = NULL; khint_t k; int last_tid = -2, r; khash_t(lib) *aux = NULL; aux = kh_init(lib); b = bam_init1(); queue = kl_init(q); if (!aux || !b || !queue) { perror(__func__); goto fail; } while ((r = sam_read1(in, hdr, b)) >= 0) { bam1_core_t *c = &b->core; int endpos = bam_endpos(b); int score = sum_qual(b); if (last_tid != c->tid) { if (last_tid >= 0) { if (dump_alignment(out, hdr, queue, MAX_POS, aux) < 0) goto write_fail; } last_tid = c->tid; } else { if (dump_alignment(out, hdr, queue, c->pos, aux) < 0) goto write_fail; } if ((c->flag&BAM_FUNMAP) || ((c->flag&BAM_FPAIRED) && !force_se)) { push_queue(queue, b, endpos, score); } else { const char *lib; lib_aux_t *q; besthash_t *h; uint32_t key; int ret; lib = bam_get_library(hdr, b); q = lib? get_aux(aux, lib) : get_aux(aux, "\t"); ++q->n_checked; h = (c->flag&BAM_FREVERSE)? q->rght : q->left; key = (c->flag&BAM_FREVERSE)? endpos : c->pos; k = kh_put(best, h, key, &ret); if (ret == 0) { // in the hash table elem_t *p = kh_val(h, k); ++q->n_removed; if (p->score < score) { if (c->flag&BAM_FREVERSE) { // mark "discarded" and push the queue p->discarded = 1; kh_val(h, k) = push_queue(queue, b, endpos, score); } else { // replace p->score = score; p->endpos = endpos; if (bam_copy1(p->b, b) == NULL) { perror(NULL); samtools_exit(EXIT_FAILURE); } } } // otherwise, discard the alignment } else kh_val(h, k) = push_queue(queue, b, endpos, score); } } if (r < -1) { fprintf(samtools_stderr, "[%s] error reading input file\n", __func__); goto fail; } if (dump_alignment(out, hdr, queue, MAX_POS, aux) < 0) goto write_fail; for (k = kh_begin(aux); k != kh_end(aux); ++k) { if (kh_exist(aux, k)) { lib_aux_t *q = &kh_val(aux, k); fprintf(samtools_stderr, "[bam_rmdupse_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed, (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k)); kh_destroy(best, q->left); kh_destroy(best, q->rght); free((char*)kh_key(aux, k)); kh_del(lib, aux, k); } } kh_destroy(lib, aux); bam_destroy1(b); kl_destroy(q, queue); return 0; write_fail: print_error_errno("rmdup", "failed to write record"); fail: if (aux) { for (k = kh_begin(aux); k != kh_end(aux); ++k) { if (kh_exist(aux, k)) { lib_aux_t *q = &kh_val(aux, k); kh_destroy(best, q->left); kh_destroy(best, q->rght); free((char*)kh_key(aux, k)); } } kh_destroy(lib, aux); } bam_destroy1(b); kl_destroy(q, queue); return 1; } pysam-0.23.0/samtools/bam_samples.c000066400000000000000000000344251475062545500172420ustar00rootroot00000000000000/* bam_samples -- print samples in a set of BAM files Copyright (C) 2021 Pierre Lindenbaum Institut du Thorax. u1087 Nantes. France. @yokofakun Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include KHASH_MAP_INIT_STR(sm, int) /** and chained struct containing the faidx and the fasta filename will be compared with the @SQ lines in the SAM header */ typedef struct FaidxPath { /** path to reference */ char* filename; /** fasta index */ faidx_t* faidx; struct FaidxPath* next; } FaidxPath; /** program parameters */ typedef struct Params { /** output stream */ FILE* out; /** tag in @RG line. default is "SM" */ char tag[3]; /** first faidx/path in chained list */ FaidxPath* faidx; /** show whether the bam is indexed */ int test_index; } Params; /** print usage */ static void usage_samples(FILE *write_to) { fprintf(write_to, "Usage: samtools samples [options] [...]\n" " samtools samples [options] -X f1.bam f2.bam f1.bam.bai f2.bai \n" " find dir1 dir2 -type f \\(-name \"*.bam\" -o -name \"*.cram\" \\) | samtools samples [options]\n" " find dir1 dir2 -type f \\(-name \"*.bam\" -o -name \"*.bai\" \\) | sort | paste - - | samtools samples -X [options]\n" "\n" "Options:\n" " -? print help and exit\n" " -h add the columns header before printing the results\n" " -i test if the file is indexed.\n" " -T provide the sample tag name from the @RG line [SM].\n" " -o output file [stdout].\n" " -f load an indexed fasta file in the collection of references. Can be used multiple times.\n" " -F read a file containing the paths to indexed fasta files. One path per line.\n" " -X use a custom index file.\n" "\n" " Using -f or -F will add a column containing the path to the reference or \".\" if the reference was not found.\n" "\n" ); } /** loads fasta fai file into FaidxPath, add it to params->faidx */ static int load_dictionary(struct Params* params, const char* filename) { FaidxPath* head = params->faidx; FaidxPath* ptr = (FaidxPath*)malloc(sizeof(FaidxPath)); if (ptr == NULL) { print_error_errno("samples", "Out of memory"); return EXIT_FAILURE; } ptr->filename = strdup(filename); if (ptr->filename == NULL) { free(ptr); print_error_errno("samples", "Out of memory"); return EXIT_FAILURE; } ptr->faidx = fai_load(filename); if (ptr->faidx == NULL) { free(ptr->filename); free(ptr); print_error_errno("samples", "Cannot load index from \"%s\"", filename); return EXIT_FAILURE; } /* insert at the beginning of the linked list */ params->faidx = ptr; ptr->next = head; return EXIT_SUCCESS; } /** load a faidx file and append it to params */ static int load_dictionaries(Params* params, const char* filename) { int ret; htsFile* in; int status = EXIT_SUCCESS; in = hts_open(filename, "r"); if (in == NULL) { print_error_errno("samples", "Cannot open \"%s\"", filename); status = EXIT_FAILURE; } else { kstring_t ks = KS_INITIALIZE; while ((ret = hts_getline(in, KS_SEP_LINE, &ks)) >= 0) { if (load_dictionary(params, ks_str(&ks)) != EXIT_SUCCESS) { status = EXIT_FAILURE; break; } } ks_free(&ks); hts_close(in); } return status; } /** print the sample information, search for a reference */ static int print_sample( Params* params, sam_hdr_t *header, int has_index, const char* sample, const char* fname) { fputs(sample, params->out); fputc('\t', params->out); fputs(fname, params->out); if (params->test_index) { fprintf(params->out, "\t%c", has_index ? 'Y' : 'N'); } if (params->faidx != NULL) { FaidxPath* ref = NULL; FaidxPath* curr = params->faidx; while (curr != NULL) { /** check names and length are the same in the same order */ if (faidx_nseq(curr->faidx) == header->n_targets) { int i; for (i = 0; i < faidx_nseq(curr->faidx); i++) { /** check name is the same */ if (strcmp(faidx_iseq(curr->faidx, i), header->target_name[i]) != 0) break; /** check length is the same */ if (faidx_seq_len(curr->faidx, faidx_iseq(curr->faidx, i)) != header->target_len[i]) break; } /* the ref was found */ if (i == faidx_nseq(curr->faidx)) { ref = curr; break; } } curr = curr->next; } fputc('\t', params->out); if (ref == NULL) { fputc('.', params->out); } else { fputs(curr->filename, params->out); } } fputc('\n', params->out); return 0; } /** open a sam file. Search for all samples in the @RG lines */ static int print_samples(Params* params, const char* fname, const char* baifname) { samFile *in = 0; sam_hdr_t *header = NULL; int n_rg; int status = EXIT_SUCCESS; khash_t(sm) *sample_set = NULL; khint_t k; int count_samples = 0; int has_index = 0; if ((sample_set = kh_init(sm)) == NULL) { print_error("samples", "Failed to initialise sample hash"); status = EXIT_FAILURE; goto end_print; } if ((in = sam_open_format(fname, "r", NULL)) == 0) { print_error_errno("samples", "Failed to open \"%s\" for reading", fname); status = EXIT_FAILURE; goto end_print; } if ((header = sam_hdr_read(in)) == 0) { print_error("samples", "Failed to read the header from \"%s\"", fname); status = EXIT_FAILURE; goto end_print; } /* try to load index if required */ if (params->test_index) { hts_idx_t *bam_idx; /* path to bam index was specified */ if (baifname != NULL) { bam_idx = sam_index_load3(in, fname, baifname, HTS_IDX_SILENT_FAIL); } /* get default index */ else { bam_idx = sam_index_load3(in, fname, NULL, HTS_IDX_SILENT_FAIL); } has_index = bam_idx != NULL; if (bam_idx != NULL) hts_idx_destroy(bam_idx); /* and we continue... we have tested the index file but we always test for the samples and the references */ } /* get the RG lines */ n_rg = sam_hdr_count_lines(header, "RG"); if (n_rg > 0) { int i, r, ret; char* sample; kstring_t sm_val = KS_INITIALIZE; for (i = 0; i < n_rg; i++) { r = sam_hdr_find_tag_pos(header, "RG", i, params->tag, &sm_val); if (r < 0) continue; k = kh_get(sm, sample_set, ks_str(&sm_val)); if (k != kh_end(sample_set)) continue; sample = strdup(ks_str(&sm_val)); if (sample == NULL) { print_error_errno("samples", "Out of memory"); status = EXIT_FAILURE; goto end_print; } kh_put(sm, sample_set, sample, &ret); if (ret < 0) { print_error("samples", "Failed to insert key '%s' into sample_set", sample); free(sample); status = EXIT_FAILURE; goto end_print; } ++count_samples; } ks_free(&sm_val); } if (count_samples == 0) { print_sample(params, header, has_index, ".", fname); } else { for (k = kh_begin(sample_set); k != kh_end(sample_set); ++k) { if (kh_exist(sample_set, k)) { char* sample = (char*)kh_key(sample_set, k); print_sample(params, header, has_index, sample, fname); } } } end_print: if (sample_set != NULL) { for (k = kh_begin(sample_set); k != kh_end(sample_set); ++k) { if (kh_exist(sample_set, k)) { char* sample = (char*)kh_key(sample_set, k); free(sample); } } kh_destroy(sm, sample_set); } if (header != NULL) sam_hdr_destroy(header); if (in != NULL) sam_close(in); return status; } int main_samples(int argc, char** argv) { int status = EXIT_SUCCESS; int print_header = 0; int has_index_file = 0; Params params; char* out_filename = NULL; FaidxPath* fai; strcpy(params.tag, "SM"); params.faidx = NULL; params.test_index =0; int opt; while ((opt = getopt_long(argc, argv, "?hiXo:f:F:T:", NULL, NULL)) != -1) { switch (opt) { case 'h': print_header = 1; break; case 'o': out_filename = optarg; break; case 'i': params.test_index = 1; break; case 'f': if (load_dictionary(¶ms, optarg) != EXIT_SUCCESS) { return EXIT_FAILURE; } break; case 'F': if (load_dictionaries(¶ms, optarg) != EXIT_SUCCESS) { return EXIT_FAILURE; } break; case 'T': if (strlen(optarg) != 2) { print_error("samples", "Length of tag \"%s\" is not 2.", optarg); return EXIT_FAILURE; } strcpy(params.tag, optarg); break; case '?': usage_samples(stdout); return EXIT_SUCCESS; case 'X': has_index_file = 1; break; default: usage_samples(stderr); return EXIT_FAILURE; } } /* if no file was provided and input is the terminal, print the usage and exit */ if (argc == optind && isatty(STDIN_FILENO)) { usage_samples(stderr); return EXIT_FAILURE; } if (out_filename != NULL) { params.out = fopen(out_filename, "w"); if (params.out == NULL) { print_error_errno("samples", "Cannot open \"%s\" for writing", out_filename); return EXIT_FAILURE; } } else { params.out = stdout; } if (print_header) { fprintf(params.out, "#%s\tPATH", params.tag); if (params.test_index) fprintf(params.out, "\tINDEX"); if (params.faidx != NULL) fprintf(params.out, "\tREFERENCE"); fprintf(params.out, "\n"); } /* no file was provided, input is stdin, each line contains the path to a bam file */ if (argc == optind) { htsFile* fp = hts_open("-", "r"); if (fp == NULL) { print_error_errno("samples", "Cannot read from stdin"); status = EXIT_FAILURE; } else { kstring_t ks = KS_INITIALIZE; int ret; while ((ret = hts_getline(fp, KS_SEP_LINE, &ks)) >= 0) { char* bai_path = NULL; if (has_index_file) { /* bam path and bam index file are separated by a tab */ char* tab = strchr(ks_str(&ks), '\t'); if (tab == NULL || *(tab+1) == '\0') { print_error_errno("samples", "Expected path-to-bam(tab)path-to-index but got \"%s\"", ks_str(&ks)); status = EXIT_FAILURE; break; } *tab=0; bai_path = (tab + 1); } if (print_samples(¶ms, ks_str(&ks), bai_path) != EXIT_SUCCESS) { status = EXIT_FAILURE; break; } } ks_free(&ks); hts_close(fp); } } /* loop over each file in argc/argv bam index provided */ else if (has_index_file) { /* calculate number of input BAM files */ if ((argc - optind) % 2 != 0) { print_error("samples","Odd number of filenames detected! Each BAM file should have an index file"); status = EXIT_FAILURE; } else { int i; int n = (argc - optind ) / 2; for (i = 0; i < n; i++) { if (print_samples(¶ms, argv[optind+i], argv[optind+i+n]) != EXIT_SUCCESS) { status = EXIT_FAILURE; break; } } } } else { int i; for (i = optind; i < argc; i++) { if (print_samples(¶ms, argv[i], NULL) != EXIT_SUCCESS) { status = EXIT_FAILURE; break; } } } fai = params.faidx; while (fai != NULL) { FaidxPath* next = fai -> next; free(fai->filename); fai_destroy(fai->faidx); free(fai); fai = next; } if (fflush(params.out) != 0) { print_error_errno("samples", "Cannot flush output"); status = EXIT_FAILURE; } if (out_filename != NULL) { fclose(params.out); } return status; } pysam-0.23.0/samtools/bam_samples.c.pysam.c000066400000000000000000000345371475062545500206170ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_samples -- print samples in a set of BAM files Copyright (C) 2021 Pierre Lindenbaum Institut du Thorax. u1087 Nantes. France. @yokofakun Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include KHASH_MAP_INIT_STR(sm, int) /** and chained struct containing the faidx and the fasta filename will be compared with the @SQ lines in the SAM header */ typedef struct FaidxPath { /** path to reference */ char* filename; /** fasta index */ faidx_t* faidx; struct FaidxPath* next; } FaidxPath; /** program parameters */ typedef struct Params { /** output stream */ FILE* out; /** tag in @RG line. default is "SM" */ char tag[3]; /** first faidx/path in chained list */ FaidxPath* faidx; /** show whether the bam is indexed */ int test_index; } Params; /** print usage */ static void usage_samples(FILE *write_to) { fprintf(write_to, "Usage: samtools samples [options] [...]\n" " samtools samples [options] -X f1.bam f2.bam f1.bam.bai f2.bai \n" " find dir1 dir2 -type f \\(-name \"*.bam\" -o -name \"*.cram\" \\) | samtools samples [options]\n" " find dir1 dir2 -type f \\(-name \"*.bam\" -o -name \"*.bai\" \\) | sort | paste - - | samtools samples -X [options]\n" "\n" "Options:\n" " -? print help and exit\n" " -h add the columns header before printing the results\n" " -i test if the file is indexed.\n" " -T provide the sample tag name from the @RG line [SM].\n" " -o output file [samtools_stdout].\n" " -f load an indexed fasta file in the collection of references. Can be used multiple times.\n" " -F read a file containing the paths to indexed fasta files. One path per line.\n" " -X use a custom index file.\n" "\n" " Using -f or -F will add a column containing the path to the reference or \".\" if the reference was not found.\n" "\n" ); } /** loads fasta fai file into FaidxPath, add it to params->faidx */ static int load_dictionary(struct Params* params, const char* filename) { FaidxPath* head = params->faidx; FaidxPath* ptr = (FaidxPath*)malloc(sizeof(FaidxPath)); if (ptr == NULL) { print_error_errno("samples", "Out of memory"); return EXIT_FAILURE; } ptr->filename = strdup(filename); if (ptr->filename == NULL) { free(ptr); print_error_errno("samples", "Out of memory"); return EXIT_FAILURE; } ptr->faidx = fai_load(filename); if (ptr->faidx == NULL) { free(ptr->filename); free(ptr); print_error_errno("samples", "Cannot load index from \"%s\"", filename); return EXIT_FAILURE; } /* insert at the beginning of the linked list */ params->faidx = ptr; ptr->next = head; return EXIT_SUCCESS; } /** load a faidx file and append it to params */ static int load_dictionaries(Params* params, const char* filename) { int ret; htsFile* in; int status = EXIT_SUCCESS; in = hts_open(filename, "r"); if (in == NULL) { print_error_errno("samples", "Cannot open \"%s\"", filename); status = EXIT_FAILURE; } else { kstring_t ks = KS_INITIALIZE; while ((ret = hts_getline(in, KS_SEP_LINE, &ks)) >= 0) { if (load_dictionary(params, ks_str(&ks)) != EXIT_SUCCESS) { status = EXIT_FAILURE; break; } } ks_free(&ks); hts_close(in); } return status; } /** print the sample information, search for a reference */ static int print_sample( Params* params, sam_hdr_t *header, int has_index, const char* sample, const char* fname) { fputs(sample, params->out); fputc('\t', params->out); fputs(fname, params->out); if (params->test_index) { fprintf(params->out, "\t%c", has_index ? 'Y' : 'N'); } if (params->faidx != NULL) { FaidxPath* ref = NULL; FaidxPath* curr = params->faidx; while (curr != NULL) { /** check names and length are the same in the same order */ if (faidx_nseq(curr->faidx) == header->n_targets) { int i; for (i = 0; i < faidx_nseq(curr->faidx); i++) { /** check name is the same */ if (strcmp(faidx_iseq(curr->faidx, i), header->target_name[i]) != 0) break; /** check length is the same */ if (faidx_seq_len(curr->faidx, faidx_iseq(curr->faidx, i)) != header->target_len[i]) break; } /* the ref was found */ if (i == faidx_nseq(curr->faidx)) { ref = curr; break; } } curr = curr->next; } fputc('\t', params->out); if (ref == NULL) { fputc('.', params->out); } else { fputs(curr->filename, params->out); } } fputc('\n', params->out); return 0; } /** open a sam file. Search for all samples in the @RG lines */ static int print_samples(Params* params, const char* fname, const char* baifname) { samFile *in = 0; sam_hdr_t *header = NULL; int n_rg; int status = EXIT_SUCCESS; khash_t(sm) *sample_set = NULL; khint_t k; int count_samples = 0; int has_index = 0; if ((sample_set = kh_init(sm)) == NULL) { print_error("samples", "Failed to initialise sample hash"); status = EXIT_FAILURE; goto end_print; } if ((in = sam_open_format(fname, "r", NULL)) == 0) { print_error_errno("samples", "Failed to open \"%s\" for reading", fname); status = EXIT_FAILURE; goto end_print; } if ((header = sam_hdr_read(in)) == 0) { print_error("samples", "Failed to read the header from \"%s\"", fname); status = EXIT_FAILURE; goto end_print; } /* try to load index if required */ if (params->test_index) { hts_idx_t *bam_idx; /* path to bam index was specified */ if (baifname != NULL) { bam_idx = sam_index_load3(in, fname, baifname, HTS_IDX_SILENT_FAIL); } /* get default index */ else { bam_idx = sam_index_load3(in, fname, NULL, HTS_IDX_SILENT_FAIL); } has_index = bam_idx != NULL; if (bam_idx != NULL) hts_idx_destroy(bam_idx); /* and we continue... we have tested the index file but we always test for the samples and the references */ } /* get the RG lines */ n_rg = sam_hdr_count_lines(header, "RG"); if (n_rg > 0) { int i, r, ret; char* sample; kstring_t sm_val = KS_INITIALIZE; for (i = 0; i < n_rg; i++) { r = sam_hdr_find_tag_pos(header, "RG", i, params->tag, &sm_val); if (r < 0) continue; k = kh_get(sm, sample_set, ks_str(&sm_val)); if (k != kh_end(sample_set)) continue; sample = strdup(ks_str(&sm_val)); if (sample == NULL) { print_error_errno("samples", "Out of memory"); status = EXIT_FAILURE; goto end_print; } kh_put(sm, sample_set, sample, &ret); if (ret < 0) { print_error("samples", "Failed to insert key '%s' into sample_set", sample); free(sample); status = EXIT_FAILURE; goto end_print; } ++count_samples; } ks_free(&sm_val); } if (count_samples == 0) { print_sample(params, header, has_index, ".", fname); } else { for (k = kh_begin(sample_set); k != kh_end(sample_set); ++k) { if (kh_exist(sample_set, k)) { char* sample = (char*)kh_key(sample_set, k); print_sample(params, header, has_index, sample, fname); } } } end_print: if (sample_set != NULL) { for (k = kh_begin(sample_set); k != kh_end(sample_set); ++k) { if (kh_exist(sample_set, k)) { char* sample = (char*)kh_key(sample_set, k); free(sample); } } kh_destroy(sm, sample_set); } if (header != NULL) sam_hdr_destroy(header); if (in != NULL) sam_close(in); return status; } int main_samples(int argc, char** argv) { int status = EXIT_SUCCESS; int print_header = 0; int has_index_file = 0; Params params; char* out_filename = NULL; FaidxPath* fai; strcpy(params.tag, "SM"); params.faidx = NULL; params.test_index =0; int opt; while ((opt = getopt_long(argc, argv, "?hiXo:f:F:T:", NULL, NULL)) != -1) { switch (opt) { case 'h': print_header = 1; break; case 'o': out_filename = optarg; break; case 'i': params.test_index = 1; break; case 'f': if (load_dictionary(¶ms, optarg) != EXIT_SUCCESS) { return EXIT_FAILURE; } break; case 'F': if (load_dictionaries(¶ms, optarg) != EXIT_SUCCESS) { return EXIT_FAILURE; } break; case 'T': if (strlen(optarg) != 2) { print_error("samples", "Length of tag \"%s\" is not 2.", optarg); return EXIT_FAILURE; } strcpy(params.tag, optarg); break; case '?': usage_samples(samtools_stdout); return EXIT_SUCCESS; case 'X': has_index_file = 1; break; default: usage_samples(samtools_stderr); return EXIT_FAILURE; } } /* if no file was provided and input is the terminal, print the usage and exit */ if (argc == optind && isatty(STDIN_FILENO)) { usage_samples(samtools_stderr); return EXIT_FAILURE; } if (out_filename != NULL) { params.out = fopen(out_filename, "w"); if (params.out == NULL) { print_error_errno("samples", "Cannot open \"%s\" for writing", out_filename); return EXIT_FAILURE; } } else { params.out = samtools_stdout; } if (print_header) { fprintf(params.out, "#%s\tPATH", params.tag); if (params.test_index) fprintf(params.out, "\tINDEX"); if (params.faidx != NULL) fprintf(params.out, "\tREFERENCE"); fprintf(params.out, "\n"); } /* no file was provided, input is stdin, each line contains the path to a bam file */ if (argc == optind) { htsFile* fp = hts_open("-", "r"); if (fp == NULL) { print_error_errno("samples", "Cannot read from stdin"); status = EXIT_FAILURE; } else { kstring_t ks = KS_INITIALIZE; int ret; while ((ret = hts_getline(fp, KS_SEP_LINE, &ks)) >= 0) { char* bai_path = NULL; if (has_index_file) { /* bam path and bam index file are separated by a tab */ char* tab = strchr(ks_str(&ks), '\t'); if (tab == NULL || *(tab+1) == '\0') { print_error_errno("samples", "Expected path-to-bam(tab)path-to-index but got \"%s\"", ks_str(&ks)); status = EXIT_FAILURE; break; } *tab=0; bai_path = (tab + 1); } if (print_samples(¶ms, ks_str(&ks), bai_path) != EXIT_SUCCESS) { status = EXIT_FAILURE; break; } } ks_free(&ks); hts_close(fp); } } /* loop over each file in argc/argv bam index provided */ else if (has_index_file) { /* calculate number of input BAM files */ if ((argc - optind) % 2 != 0) { print_error("samples","Odd number of filenames detected! Each BAM file should have an index file"); status = EXIT_FAILURE; } else { int i; int n = (argc - optind ) / 2; for (i = 0; i < n; i++) { if (print_samples(¶ms, argv[optind+i], argv[optind+i+n]) != EXIT_SUCCESS) { status = EXIT_FAILURE; break; } } } } else { int i; for (i = optind; i < argc; i++) { if (print_samples(¶ms, argv[i], NULL) != EXIT_SUCCESS) { status = EXIT_FAILURE; break; } } } fai = params.faidx; while (fai != NULL) { FaidxPath* next = fai -> next; free(fai->filename); fai_destroy(fai->faidx); free(fai); fai = next; } if (fflush(params.out) != 0) { print_error_errno("samples", "Cannot flush output"); status = EXIT_FAILURE; } if (out_filename != NULL) { fclose(params.out); } return status; } pysam-0.23.0/samtools/bam_sort.c000066400000000000000000004066441475062545500165730ustar00rootroot00000000000000/* bam_sort.c -- sorting and merging. Copyright (C) 2008-2024 Genome Research Ltd. Portions copyright (C) 2009-2012 Broad Institute. Author: Heng Li Author: Martin Pollard Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "htslib/ksort.h" #include "htslib/hts_os.h" #include "htslib/khash.h" #include "htslib/klist.h" #include "htslib/kstring.h" #include "htslib/sam.h" #include "htslib/hts_endian.h" #include "htslib/cram.h" #include "htslib/thread_pool.h" #include "sam_opts.h" #include "samtools.h" #include "bedidx.h" #include "bam.h" //#define DEBUG_MINHASH #define BAM_BLOCK_SIZE 2*1024*1024 #define MAX_TMP_FILES 64 // Struct which contains the sorting key for TemplateCoordinate sort. typedef struct { int tid1; int tid2; hts_pos_t pos1; hts_pos_t pos2; bool neg1; bool neg2; const char *library; char *mid; char *name; bool is_upper_of_pair; } template_coordinate_key_t; // Struct to store fixed buffers of template coordinate keys typedef struct { size_t n; // the # of keys stored size_t m; // the # of buffers allocated size_t buffer_size; // # the fixed size of each buffer template_coordinate_key_t **buffers; // the list of buffers } template_coordinate_keys_t; // Gets the idx'th key; does not OOB check static template_coordinate_key_t* template_coordinate_keys_get(template_coordinate_keys_t *keys, size_t idx) { size_t buffer_idx = idx / keys->buffer_size; // the index of the buffer to retrieve in buffer size_t buffer_offset = idx % keys->buffer_size; // the offset into the given buffer to retrieve //assert(buffer_idx < keys->m); //assert(buffer_offset < keys->buffer_size); return &keys->buffers[buffer_idx][buffer_offset]; } // Rellocates the buffers to hold at least max_k entries static int template_coordinate_keys_realloc(template_coordinate_keys_t *keys, int max_k) { size_t cur_m = keys->m; keys->m += 0x100; //assert(keys->m > cur_m); //assert(keys->m * keys->buffer_size >= max_k); if ((keys->buffers = realloc(keys->buffers, keys->m * sizeof(template_coordinate_key_t*))) == NULL) { print_error("sort", "couldn't reallocate memory for template coordinate key buffers"); return -1; } // allocate space for new buffers int j; for (j = cur_m; j < keys->m; ++j) { if ((keys->buffers[j]= malloc(sizeof(template_coordinate_key_t) * keys->buffer_size)) == NULL) { print_error("sort", "couldn't allocate memory for template coordinate key buffer"); return -1; } } return 0; } // Struct which contains the a record, and the pointer to the sort tag (if any) or // a combined ref / position / strand. // Used to speed up sorts (coordinate, by-tag, and template-coordinate). typedef struct bam1_tag { bam1_t *bam_record; union { const uint8_t *tag; uint8_t pos_tid[12]; template_coordinate_key_t *key; } u; } bam1_tag; /* Minimum memory required in megabytes before sort will attempt to run. This is to prevent accidents where failing to use the -m option correctly results in the creation of a temporary file for each read in the input file. Don't forget to update the man page if you change this. */ const size_t SORT_MIN_MEGS_PER_THREAD = 1; /* Default per-thread memory for sort. Must be >= SORT_MIN_MEGS_PER_THREAD. Don't forget to update the man page if you change this. */ const size_t SORT_DEFAULT_MEGS_PER_THREAD = 768; #if !defined(__DARWIN_C_LEVEL) || __DARWIN_C_LEVEL < 900000L #define NEED_MEMSET_PATTERN4 #endif #ifdef NEED_MEMSET_PATTERN4 void memset_pattern4(void *target, const void *pattern, size_t size) { uint32_t* target_iter = target; size_t loops = size/4; size_t i; for (i = 0; i < loops; ++i) { memcpy(target_iter, pattern, 4); ++target_iter; } if (size%4 != 0) memcpy(target_iter, pattern, size%4); } #endif KHASH_INIT(c2c, char*, char*, 1, kh_str_hash_func, kh_str_hash_equal) KHASH_INIT(cset, char*, char, 0, kh_str_hash_func, kh_str_hash_equal) KHASH_MAP_INIT_STR(c2i, int) KHASH_MAP_INIT_STR(const_c2c, char *) #define hdrln_free_char(p) KLIST_INIT(hdrln, char*, hdrln_free_char) static template_coordinate_key_t* template_coordinate_key(bam1_t *b, template_coordinate_key_t *key, sam_hdr_t *hdr, khash_t(const_c2c) *lib_lookup); typedef enum {Coordinate, QueryName, TagCoordinate, TagQueryName, MinHash, TemplateCoordinate} SamOrder; static SamOrder g_sam_order = Coordinate; static int natural_sort = 1; // not ASCII, but alphanumeric: a12b > a7b static char g_sort_tag[2] = {0,0}; #define is_digit(c) ((c)<='9' && (c)>='0') static int strnum_cmp(const char *_a, const char *_b) { if (!natural_sort) return strcmp(_a,_b); const unsigned char *a = (const unsigned char*)_a, *b = (const unsigned char*)_b; const unsigned char *pa = a, *pb = b; while (*pa && *pb) { if (!is_digit(*pa) || !is_digit(*pb)) { if (*pa != *pb) return (int)*pa - (int)*pb; ++pa; ++pb; } else { // skip leading zeros while (*pa == '0') ++pa; while (*pb == '0') ++pb; // skip matching digits while (is_digit(*pa) && *pa == *pb) pa++, pb++; // Now mismatching, so see which ends the number sooner int diff = (int)*pa - (int)*pb; while (is_digit(*pa) && is_digit(*pb)) pa++, pb++; if (is_digit(*pa)) return 1; // pa still going, so larger else if (is_digit(*pb)) return -1; // pb still going, so larger else if (diff) return diff; // same length, so earlier diff } } return *pa? 1 : *pb? -1 : 0; } #define HEAP_EMPTY (UINT64_MAX >> 1) typedef struct { int i; uint32_t tid; uint64_t pos:63, rev:1, idx; bam1_tag entry; } heap1_t; static inline int bam1_cmp_by_tag(const bam1_tag a, const bam1_tag b); static inline int bam1_cmp_by_minhash(const bam1_tag a, const bam1_tag b); static inline int bam1_cmp_template_coordinate(const bam1_tag a, const bam1_tag b); static khash_t(const_c2c) * lookup_libraries(sam_hdr_t *header); static void lib_lookup_destroy(khash_t(const_c2c) *lib_lookup); // Function to compare reads in the heap and determine which one is < the other // Note, unlike the bam1_cmp_by_X functions which return <0, 0, >0 this // is strictly 0 or 1 only. static inline int heap_lt(const heap1_t a, const heap1_t b) { if (!a.entry.bam_record) return 1; if (!b.entry.bam_record) return 0; int t, fa, fb; switch (g_sam_order) { case Coordinate: if (a.tid != b.tid) return a.tid > b.tid; if (a.pos != b.pos) return a.pos > b.pos; if (a.rev != b.rev) return a.rev > b.rev; break; case QueryName: t = strnum_cmp(bam_get_qname(a.entry.bam_record), bam_get_qname(b.entry.bam_record)); if (t != 0) return t > 0; fa = a.entry.bam_record->core.flag; fb = b.entry.bam_record->core.flag; // Sort order is READ1, READ2, (PRIMARY), SUPPLEMENTARY, SECONDARY // Get the bits in this order so sort is a natural a-b fa = ((fa&0xc0)<<8)|((fa&0x100)<<3)|((fa&0x800)>>3); fb = ((fb&0xc0)<<8)|((fb&0x100)<<3)|((fb&0x800)>>3); if (fa != fb) return fa > fb; break; case TagQueryName: case TagCoordinate: t = bam1_cmp_by_tag(a.entry, b.entry); if (t != 0) return t > 0; break; case MinHash: t = bam1_cmp_by_minhash(a.entry, b.entry); if (t != 0) return t > 0; break; case TemplateCoordinate: t = bam1_cmp_template_coordinate(a.entry, b.entry); if (t != 0) return t > 0; break; default: print_error("heap_lt", "unknown sort order: %d", g_sam_order); break; } // This compares by position (i/idx'th read) in the input file(s) if (a.i != b.i) return a.i > b.i; return a.idx > b.idx; } KSORT_INIT(heap, heap1_t, heap_lt) typedef struct merged_header { sam_hdr_t *hdr; kstring_t out_rg; kstring_t out_pg; kstring_t out_co; char **target_name; uint32_t *target_len; size_t n_targets; size_t targets_sz; khash_t(c2i) *sq_tids; khash_t(cset) *rg_ids; khash_t(cset) *pg_ids; bool have_hd; } merged_header_t; typedef struct trans_tbl { int32_t n_targets; int* tid_trans; kh_c2c_t* rg_trans; kh_c2c_t* pg_trans; bool lost_coord_sort; } trans_tbl_t; static void trans_tbl_destroy(trans_tbl_t *tbl) { khiter_t iter; free(tbl->tid_trans); /* * The values for the tbl->rg_trans and tbl->pg_trans hashes are pointers * to keys in the rg_ids and pg_ids sets of the merged_header_t, so * they should not be freed here. * * The keys are unique to each hash entry, so they do have to go. */ for (iter = kh_begin(tbl->rg_trans); iter != kh_end(tbl->rg_trans); ++iter) { if (kh_exist(tbl->rg_trans, iter)) { free(kh_key(tbl->rg_trans, iter)); } } for (iter = kh_begin(tbl->pg_trans); iter != kh_end(tbl->pg_trans); ++iter) { if (kh_exist(tbl->pg_trans, iter)) { free(kh_key(tbl->pg_trans, iter)); } } kh_destroy(c2c,tbl->rg_trans); kh_destroy(c2c,tbl->pg_trans); } /* * Create a merged_header_t struct. */ static merged_header_t * init_merged_header(void) { merged_header_t *merged_hdr; merged_hdr = calloc(1, sizeof(*merged_hdr)); if (merged_hdr == NULL) return NULL; merged_hdr->hdr = sam_hdr_init(); if (!merged_hdr->hdr) goto fail; merged_hdr->targets_sz = 16; merged_hdr->target_name = malloc(merged_hdr->targets_sz * sizeof(*merged_hdr->target_name)); if (NULL == merged_hdr->target_name) goto fail; merged_hdr->target_len = malloc(merged_hdr->targets_sz * sizeof(*merged_hdr->target_len)); if (NULL == merged_hdr->target_len) goto fail; merged_hdr->sq_tids = kh_init(c2i); if (merged_hdr->sq_tids == NULL) goto fail; merged_hdr->rg_ids = kh_init(cset); if (merged_hdr->rg_ids == NULL) goto fail; merged_hdr->pg_ids = kh_init(cset); if (merged_hdr->pg_ids == NULL) goto fail; return merged_hdr; fail: perror("[init_merged_header]"); kh_destroy(cset, merged_hdr->pg_ids); kh_destroy(cset, merged_hdr->rg_ids); kh_destroy(c2i, merged_hdr->sq_tids); free(merged_hdr->target_name); free(merged_hdr->target_len); sam_hdr_destroy(merged_hdr->hdr); free(merged_hdr); return NULL; } /* Some handy kstring manipulating functions */ // Append char range to kstring static inline int range_to_ks(const char *src, int from, int to, kstring_t *dest) { return kputsn(src + from, to - from, dest) != to - from; } // Append a kstring to a kstring static inline int ks_to_ks(kstring_t *src, kstring_t *dest) { return kputsn(ks_str(src), ks_len(src), dest) != ks_len(src); } /* * Generate a unique ID by appending a random suffix to a given prefix. * existing_ids is the set of IDs that are already in use. * If always_add_suffix is true, the suffix will always be included. * If false, prefix will be returned unchanged if it isn't in existing_ids. */ static int gen_unique_id(char *prefix, khash_t(cset) *existing_ids, bool always_add_suffix, kstring_t *dest) { khiter_t iter; if (!always_add_suffix) { // Try prefix on its own first iter = kh_get(cset, existing_ids, prefix); if (iter == kh_end(existing_ids)) { // prefix isn't used yet dest->l = 0; if (kputs(prefix, dest) == EOF) return -1; return 0; } } do { dest->l = 0; ksprintf(dest, "%s-%08lX", prefix, lrand48()); iter = kh_get(cset, existing_ids, ks_str(dest)); } while (iter != kh_end(existing_ids)); return 0; } /* * Add the @HD line to the new header * In practice the @HD line will come from the first input header. */ static int trans_tbl_add_hd(merged_header_t* merged_hdr, sam_hdr_t *translate) { kstring_t hd_line = { 0, 0, NULL }; int res; // TODO: handle case when @HD needs merging. if (merged_hdr->have_hd) return 0; res = sam_hdr_find_hd(translate, &hd_line); if (res < -1) { print_error("merge", "failed to get @HD line from header"); return -1; } if (res < 0) // Not found return 0; if (sam_hdr_add_lines(merged_hdr->hdr, hd_line.s, hd_line.l) < 0) { print_error("merge", "failed to add @HD line to new header"); free(hd_line.s); return -1; } free(hd_line.s); merged_hdr->have_hd = true; return 0; } /* * Add @SQ records to the translation table. * * Go through the target list for the input header. Any new targets found * are added to the output header target list. At the same time, a mapping * from the input to output target ids is stored in tbl. * * If any new targets are found, the header text is scanned to find the * corresponding @SQ records. They are then copied into the * merged_hdr->out_text kstring (which will eventually become the * output header text). * * Returns 0 on success, -1 on failure. */ static int trans_tbl_add_sq(merged_header_t* merged_hdr, sam_hdr_t *translate, trans_tbl_t* tbl) { int32_t i; int min_tid = -1, res; kstring_t sq_line = { 0, 0, NULL }, sq_sn = { 0, 0, NULL }; // Fill in the tid part of the translation table, adding new targets // to the merged header as we go. for (i = 0; i < sam_hdr_nref(translate); ++i) { int trans_tid; sq_sn.l = 0; res = sam_hdr_find_tag_pos(translate, "SQ", i, "SN", &sq_sn); if (res < 0) { print_error("merge", "failed to get @SQ SN #%d from header", i + 1); goto fail; } trans_tid = sam_hdr_name2tid(merged_hdr->hdr, sq_sn.s); if (trans_tid < -1) { print_error("merge", "failed to lookup ref"); goto fail; } if (trans_tid < 0) { // Append missing entries to out_hdr sq_line.l = 0; res = sam_hdr_find_line_id(translate, "SQ", "SN", sq_sn.s, &sq_line); if (res < 0) { print_error("merge", "failed to get @SQ SN:%s from header", sq_sn.s); goto fail; } trans_tid = sam_hdr_nref(merged_hdr->hdr); res = sam_hdr_add_lines(merged_hdr->hdr, sq_line.s, sq_line.l); if (res < 0) { print_error("merge", "failed to add @SQ SN:%s to new header", sq_sn.s); goto fail; } } tbl->tid_trans[i] = trans_tid; if (tbl->tid_trans[i] > min_tid) { min_tid = tbl->tid_trans[i]; } else { tbl->lost_coord_sort = true; } } free(sq_line.s); free(sq_sn.s); return 0; fail: free(sq_line.s); free(sq_sn.s); return -1; } /* * Common code for setting up RG and PG record ID tag translation. * * is_rg is true for RG translation, false for PG. * translate is the input bam header * merge is true if tags with the same ID are to be merged. * known_ids is the set of IDs already in the output header. * id_map is the translation map from input header IDs to output header IDs * If override is set, it will be used to replace the existing ID (RG only) * * known_ids and id_map have entries for the new IDs added to them. * * Return value is a linked list of header lines with the translated IDs, * or NULL if something went wrong (probably out of memory). * */ static klist_t(hdrln) * trans_rg_pg(bool is_rg, sam_hdr_t *translate, bool merge, khash_t(cset)* known_ids, khash_t(c2c)* id_map, char *override) { khiter_t iter; int num_ids, i; const char *rec_type = is_rg ? "RG" : "PG"; klist_t(hdrln) *hdr_lines; hdr_lines = kl_init(hdrln); // Search through translate's header num_ids = sam_hdr_count_lines(translate, rec_type); if (num_ids < 0) goto fail; for (i = 0; i < num_ids; i++) { kstring_t orig_id = { 0, 0, NULL }; // ID in original header kstring_t transformed_id = { 0, 0, NULL }; // ID in output header char *map_value; // Value to store in id_map bool id_changed; // Have we changed the ID? bool not_found_in_output; // ID isn't in the output header (yet) if (sam_hdr_find_tag_pos(translate, rec_type, i, "ID", &orig_id) < 0) goto fail; // is our matched ID in our output ID set already? iter = kh_get(cset, known_ids, ks_str(&orig_id)); not_found_in_output = (iter == kh_end(known_ids)); if (override) { // Override original ID (RG only) #ifdef OVERRIDE_DOES_NOT_MERGE if (gen_unique_id(override, known_ids, false, &transformed_id)) goto memfail; not_found_in_output = true; // As ID now unique #else if (kputs(override, &transformed_id) == EOF) goto memfail; // Know about override already? iter = kh_get(cset, known_ids, ks_str(&transformed_id)); not_found_in_output = (iter == kh_end(known_ids)); #endif id_changed = true; } else { if ( not_found_in_output || merge) { // Not in there or merging so can add it as 1-1 mapping if (ks_to_ks(&orig_id, &transformed_id)) goto memfail; id_changed = false; } else { // It's in there so we need to transform it by appending // a random number to the id if (gen_unique_id(ks_str(&orig_id), known_ids, true, &transformed_id)) goto memfail; id_changed = true; not_found_in_output = true; // As ID now unique } } // Does this line need to go into our output header? if (not_found_in_output) { // Take matched line and replace ID with transformed_id kstring_t new_hdr_line = { 0, 0, NULL }; if (sam_hdr_find_line_id(translate, rec_type, "ID", ks_str(&orig_id), &new_hdr_line) < 0){ goto fail; } if (id_changed) { char *idp = strstr(ks_str(&new_hdr_line), "\tID:"), *id_end; ptrdiff_t id_offset, id_len; if (!idp) { print_error("merge", "failed to find ID in \"%s\"\n", ks_str(&new_hdr_line)); goto fail; } idp += 4; for (id_end = idp; *id_end >= '\n'; id_end++) {} id_offset = idp - new_hdr_line.s; id_len = id_end - idp; if (id_len < transformed_id.l) { if (ks_resize(&new_hdr_line, new_hdr_line.l + transformed_id.l - id_len + 1/*nul*/)) goto fail; } if (id_len != transformed_id.l) { memmove(new_hdr_line.s + id_offset + transformed_id.l, new_hdr_line.s + id_offset + id_len, new_hdr_line.l - id_offset - id_len + 1); } memcpy(new_hdr_line.s + id_offset, transformed_id.s, transformed_id.l); } // append line to output linked list char** ln = kl_pushp(hdrln, hdr_lines); *ln = ks_release(&new_hdr_line); // Give away to linked list // Need to add it to known_ids set int in_there = 0; iter = kh_put(cset, known_ids, ks_str(&transformed_id), &in_there); if (in_there < 0) goto memfail; assert(in_there > 0); // Should not already be in the map map_value = ks_release(&transformed_id); } else { // Use existing string in id_map assert(kh_exist(known_ids, iter)); map_value = kh_key(known_ids, iter); free(ks_release(&transformed_id)); } // Insert it into our translation map int in_there = 0; iter = kh_put(c2c, id_map, ks_release(&orig_id), &in_there); kh_value(id_map, iter) = map_value; } // If there are no RG lines in the file and we are overriding add one if (is_rg && override && hdr_lines->size == 0) { kstring_t new_id = {0, 0, NULL}; kstring_t line = {0, 0, NULL}; kstring_t empty = {0, 0, NULL}; int in_there = 0; char** ln; // Get the new ID if (gen_unique_id(override, known_ids, false, &new_id)) goto memfail; // Make into a header line and add to linked list ksprintf(&line, "@RG\tID:%s", ks_str(&new_id)); ln = kl_pushp(hdrln, hdr_lines); *ln = ks_release(&line); // Put into known_ids set iter = kh_put(cset, known_ids, ks_str(&new_id), &in_there); if (in_there < 0) goto memfail; assert(in_there > 0); // Should be a new entry // Put into translation map (key is empty string) if (kputs("", &empty) == EOF) goto memfail; iter = kh_put(c2c, id_map, ks_release(&empty), &in_there); if (in_there < 0) goto memfail; assert(in_there > 0); // Should be a new entry kh_value(id_map, iter) = ks_release(&new_id); } return hdr_lines; memfail: perror(__func__); fail: if (hdr_lines) kl_destroy(hdrln, hdr_lines); return NULL; } /* * Common code for completing RG and PG record translation. * * Input is a list of header lines, and the mapping from input to * output @PG record IDs. * * RG and PG records can contain tags that cross-reference to other @PG * records. This fixes the tags to contain the new IDs before adding * them to the output header text. */ static int finish_rg_pg(bool is_rg, klist_t(hdrln) *hdr_lines, khash_t(c2c)* pg_map, kstring_t *out_text) { const char *search = is_rg ? "\tPG:" : "\tPP:"; khiter_t idx; char *line = NULL; while ((kl_shift(hdrln, hdr_lines, &line)) == 0) { char *id = strstr(line, search); // Look for tag to fix int pos1 = 0, pos2 = 0; char *new_id = NULL; if (id) { // Found a tag. Look up the value in the translation map // to see what it should be changed to in the output file. char *end, tmp; id += 4; // Point to value end = strchr(id, '\t'); // Find end of tag if (!end) end = id + strlen(id); tmp = *end; *end = '\0'; // Temporarily get the value on its own. // Look-up in translation table idx = kh_get(c2c, pg_map, id); if (idx == kh_end(pg_map)) { // Not found, warn. fprintf(stderr, "[W::%s] Tag %s%s not found in @PG records\n", __func__, search + 1, id); } else { // Remember new id and splice points on original string new_id = kh_value(pg_map, idx); pos1 = id - line; pos2 = end - line; } *end = tmp; // Restore string } // Copy line to output: // line[0..pos1), new_id (if not NULL), line[pos2..end), '\n' if (pos1 && range_to_ks(line, 0, pos1, out_text)) goto memfail; if (new_id && kputs(new_id, out_text) == EOF) goto memfail; if (kputs(line + pos2, out_text) == EOF) goto memfail; if (kputc('\n', out_text) == EOF) goto memfail; free(line); // No longer needed line = NULL; } return 0; memfail: perror(__func__); free(line); // Prevent leakage as no longer on list return -1; } /* * Build the translation table for an input *am file. This stores mappings * which allow IDs to be converted from those used in the input file * to the ones which will be used in the output. The mappings are for: * Reference sequence IDs (for @SQ records) * @RG record ID tags * @PG record ID tags * * At the same time, new header text is built up by copying records * from the input bam file. This will eventually become the header for * the output file. When copied, the ID tags for @RG and @PG records * are replaced with their values. The @PG PP: and @RG PG: tags * are also modified if necessary. * * merged_hdr holds state on the output header (which IDs are present, etc.) * translate is the input header * tbl is the translation table that gets filled in. * merge_rg controls merging of @RG records * merge_pg controls merging of @PG records * If rg_override is not NULL, it will be used to replace the existing @RG ID * * Returns 0 on success, -1 on failure. */ static int trans_tbl_init(merged_header_t* merged_hdr, sam_hdr_t* translate, trans_tbl_t* tbl, bool merge_rg, bool merge_pg, bool copy_co, char* rg_override) { kstring_t lines = { 0, 0, NULL }; klist_t(hdrln) *rg_list = NULL; klist_t(hdrln) *pg_list = NULL; tbl->n_targets = sam_hdr_nref(translate); tbl->rg_trans = tbl->pg_trans = NULL; tbl->tid_trans = (int*)calloc(tbl->n_targets ? tbl->n_targets : 1, sizeof(int)); if (tbl->tid_trans == NULL) goto memfail; tbl->rg_trans = kh_init(c2c); if (tbl->rg_trans == NULL) goto memfail; tbl->pg_trans = kh_init(c2c); if (tbl->pg_trans == NULL) goto memfail; tbl->lost_coord_sort = false; // Get the @HD record (if not there already). if (trans_tbl_add_hd(merged_hdr, translate)) goto fail; // Fill in map and add header lines for @SQ records if (trans_tbl_add_sq(merged_hdr, translate, tbl)) goto fail; // Get translated header lines and fill in map for @RG records rg_list = trans_rg_pg(true, translate, merge_rg, merged_hdr->rg_ids, tbl->rg_trans, rg_override); if (!rg_list) goto fail; // Get translated header lines and fill in map for @PG records pg_list = trans_rg_pg(false, translate, merge_pg, merged_hdr->pg_ids, tbl->pg_trans, NULL); if (!pg_list) goto fail; // Fix-up PG: tags in the new @RG records and add to output if (finish_rg_pg(true, rg_list, tbl->pg_trans, &merged_hdr->out_rg)) goto fail; // Fix-up PP: tags in the new @PG records and add to output lines.l = 0; if (finish_rg_pg(false, pg_list, tbl->pg_trans, &merged_hdr->out_pg)) goto fail; kl_destroy(hdrln, rg_list); rg_list = NULL; kl_destroy(hdrln, pg_list); pg_list = NULL; if (copy_co) { // Just append @CO headers without translation int num_co = sam_hdr_count_lines(translate, "CO"), i; if (num_co < 0) goto fail; for (i = 0; i < num_co; i++) { if (sam_hdr_find_line_pos(translate, "CO", i, &lines) < 0) goto fail; if (ks_to_ks(&lines, &merged_hdr->out_co)) goto fail; if (kputc('\n', &merged_hdr->out_co) < 0) goto fail; } } free(lines.s); return 0; memfail: perror(__func__); fail: trans_tbl_destroy(tbl); if (rg_list) kl_destroy(hdrln, rg_list); if (pg_list) kl_destroy(hdrln, pg_list); free(lines.s); return -1; } static int finish_merged_header(merged_header_t *merged_hdr) { if (sam_hdr_add_lines(merged_hdr->hdr, ks_c_str(&merged_hdr->out_rg), ks_len(&merged_hdr->out_rg)) < 0) return -1; if (sam_hdr_add_lines(merged_hdr->hdr, ks_c_str(&merged_hdr->out_pg), ks_len(&merged_hdr->out_pg)) < 0) return -1; if (sam_hdr_add_lines(merged_hdr->hdr, ks_c_str(&merged_hdr->out_co), ks_len(&merged_hdr->out_co)) < 0) return -1; return 0; } /* * Free a merged_header_t struct and all associated data. * * Note that the keys to the rg_ids and pg_ids sets are also used as * values in the translation tables. This function should therefore not * be called until the translation tables are no longer needed. */ static void free_merged_header(merged_header_t *merged_hdr) { size_t i; khiter_t iter; if (!merged_hdr) return; free(ks_release(&merged_hdr->out_rg)); free(ks_release(&merged_hdr->out_pg)); free(ks_release(&merged_hdr->out_co)); if (merged_hdr->target_name) { for (i = 0; i < merged_hdr->n_targets; i++) { free(merged_hdr->target_name[i]); } free(merged_hdr->target_name); } free(merged_hdr->target_len); kh_destroy(c2i, merged_hdr->sq_tids); if (merged_hdr->rg_ids) { for (iter = kh_begin(merged_hdr->rg_ids); iter != kh_end(merged_hdr->rg_ids); ++iter) { if (kh_exist(merged_hdr->rg_ids, iter)) free(kh_key(merged_hdr->rg_ids, iter)); } kh_destroy(cset, merged_hdr->rg_ids); } if (merged_hdr->pg_ids) { for (iter = kh_begin(merged_hdr->pg_ids); iter != kh_end(merged_hdr->pg_ids); ++iter) { if (kh_exist(merged_hdr->pg_ids, iter)) free(kh_key(merged_hdr->pg_ids, iter)); } kh_destroy(cset, merged_hdr->pg_ids); } free(merged_hdr); } static void bam_translate(bam1_t* b, trans_tbl_t* tbl) { // Update target id if not unmapped tid if ( b->core.tid >= 0 ) { b->core.tid = tbl->tid_trans[b->core.tid]; } if ( b->core.mtid >= 0 ) { b->core.mtid = tbl->tid_trans[b->core.mtid]; } // If we have a RG update it uint8_t *rg = bam_aux_get(b, "RG"); if (rg) { char* decoded_rg = bam_aux2Z(rg); khiter_t k = kh_get(c2c, tbl->rg_trans, decoded_rg); if (k != kh_end(tbl->rg_trans)) { char* translate_rg = kh_value(tbl->rg_trans,k); bam_aux_del(b, rg); if (translate_rg) { bam_aux_append(b, "RG", 'Z', strlen(translate_rg) + 1, (uint8_t*)translate_rg); } } else { char *tmp = strdup(decoded_rg); fprintf(stderr, "[bam_translate] RG tag \"%s\" on read \"%s\" encountered " "with no corresponding entry in header, tag lost. " "Unknown tags are only reported once per input file for " "each tag ID.\n", decoded_rg, bam_get_qname(b)); bam_aux_del(b, rg); // Prevent future whinges if (tmp) { int in_there = 0; k = kh_put(c2c, tbl->rg_trans, tmp, &in_there); if (in_there > 0) kh_value(tbl->rg_trans, k) = NULL; } } } // If we have a PG update it uint8_t *pg = bam_aux_get(b, "PG"); if (pg) { char* decoded_pg = bam_aux2Z(pg); khiter_t k = kh_get(c2c, tbl->pg_trans, decoded_pg); if (k != kh_end(tbl->pg_trans)) { char* translate_pg = kh_value(tbl->pg_trans,k); bam_aux_del(b, pg); if (translate_pg) { bam_aux_append(b, "PG", 'Z', strlen(translate_pg) + 1, (uint8_t*)translate_pg); } } else { char *tmp = strdup(decoded_pg); fprintf(stderr, "[bam_translate] PG tag \"%s\" on read \"%s\" encountered " "with no corresponding entry in header, tag lost. " "Unknown tags are only reported once per input file for " "each tag ID.\n", decoded_pg, bam_get_qname(b)); bam_aux_del(b, pg); // Prevent future whinges if (tmp) { int in_there = 0; k = kh_put(c2c, tbl->pg_trans, tmp, &in_there); if (in_there > 0) kh_value(tbl->pg_trans, k) = NULL; } } } } int* rtrans_build(int n, int n_targets, trans_tbl_t* translation_tbl) { // Create reverse translation table for tids int* rtrans = (int*)malloc(sizeof(int32_t)*n*n_targets); const int32_t NOTID = INT32_MIN; if (!rtrans) return NULL; memset_pattern4((void*)rtrans, &NOTID, sizeof(int32_t)*n*n_targets); int i; for (i = 0; i < n; ++i) { int j; for (j = 0; j < (translation_tbl+i)->n_targets; ++j) { if ((translation_tbl+i)->tid_trans[j] != -1) { rtrans[i*n_targets + (translation_tbl+i)->tid_trans[j]] = j; } } } return rtrans; } #define MERGE_RG 1 // Attach RG tag based on filename #define MERGE_UNCOMP 2 // Generate uncompressed BAM #define MERGE_LEVEL1 4 // Compress the BAM at level 1 (fast) mode #define MERGE_FORCE 8 // Overwrite output BAM if it exists #define MERGE_COMBINE_RG 16 // Combine RG tags frather than redefining them #define MERGE_COMBINE_PG 32 // Combine PG tags frather than redefining them #define MERGE_FIRST_CO 64 // Use only first file's @CO headers (sort cmd only) static hts_reglist_t *duplicate_reglist(const hts_reglist_t *rl, int rn) { if (!rl) return NULL; hts_reglist_t *new_rl = calloc(rn, sizeof(hts_reglist_t)); if (!new_rl) return NULL; int i; for (i=0; i < rn; i++) { new_rl[i].tid = rl[i].tid; new_rl[i].count = rl[i].count; new_rl[i].min_beg = rl[i].min_beg; new_rl[i].max_end = rl[i].max_end; new_rl[i].reg = rl[i].reg; new_rl[i].intervals = malloc(new_rl[i].count * sizeof(hts_pair_pos_t)); if (!new_rl[i].intervals) { hts_reglist_free(new_rl, i); return NULL; } memcpy(new_rl[i].intervals, rl[i].intervals, new_rl[i].count * sizeof(hts_pair_pos_t)); } return new_rl; } /* * How merging is handled * * If a header is defined use we will use that as our output header * otherwise we use the first header from the first input file. * * Now go through each file and create a translation table for that file for: * -RG * -tid * -PG tags * * Then whenever we read a record from a bam we translate that read before * stashing it in the hash. * * In the actual merge, a read is read from each input file, translated and * stashed in the hash. This assumes that all input files are sorted in the * same way. Next we just extract the next position ordered read from the * hash, and replace it if there are still reads left in it's source input * file. Finally we write our chosen read it to the output file. */ /*! @abstract Merge multiple sorted BAM. @param sam_order the order in which the data was sorted @param sort_tag if non-null, the tag that data was sorted by @param out output BAM file name @param mode sam_open() mode to be used to create the final output file (overrides level settings from UNCOMP and LEVEL1 flags) @param headers name of SAM file from which to copy '@' header lines, or NULL to copy them from the first file to be merged @param n number of files to be merged @param fn names of files to be merged @param flag flags that control how the merge is undertaken @param reg region to merge @param n_threads number of threads to use (passed to htslib) @param cmd command name (used in print_error() etc) @param in_fmt format options for input files @param out_fmt output file format and options @param write_index create the index, together with the output file @param arg_list command string for PG line @param no_pg if 1, do not add a new PG line @discussion Padding information may NOT correctly maintained. This function is NOT thread safe. */ int bam_merge_core2(SamOrder sam_order, char* sort_tag, const char *out, const char *mode, const char *headers, int n, char * const *fn, char * const *fn_idx, const char *fn_bed, int flag, const char *reg, int n_threads, const char *cmd, const htsFormat *in_fmt, const htsFormat *out_fmt, int write_index, char *arg_list, int no_pg) { samFile *fpout, **fp = NULL; heap1_t *heap = NULL; sam_hdr_t *hout = NULL; sam_hdr_t *hin = NULL; int i, j, *RG_len = NULL; uint64_t idx = 0; char **RG = NULL; hts_itr_t **iter = NULL; sam_hdr_t **hdr = NULL; trans_tbl_t *translation_tbl = NULL; int *rtrans = NULL; char *out_idx_fn = NULL; void *hreg = NULL; hts_reglist_t *lreg = NULL; merged_header_t *merged_hdr = init_merged_header(); if (!merged_hdr) return -1; refs_t *refs = NULL; template_coordinate_keys_t *keys = NULL; khash_t(const_c2c) *lib_lookup = NULL; // Is there a specified pre-prepared header to use for output? if (headers) { samFile* fpheaders = sam_open(headers, "r"); if (fpheaders == NULL) { print_error_errno(cmd, "cannot open \"%s\"", headers); return -1; } hin = sam_hdr_read(fpheaders); sam_close(fpheaders); if (hin == NULL) { print_error(cmd, "couldn't read headers from \"%s\"", headers); goto mem_fail; } } g_sam_order = sam_order; if (sam_order == TagQueryName || sam_order == TagCoordinate) { g_sort_tag[0] = sort_tag[0]; g_sort_tag[1] = sort_tag[0] ? sort_tag[1] : '\0'; } fp = (samFile**)calloc(n, sizeof(samFile*)); if (!fp) goto mem_fail; heap = (heap1_t*)calloc(n, sizeof(heap1_t)); if (!heap) goto mem_fail; iter = (hts_itr_t**)calloc(n, sizeof(hts_itr_t*)); if (!iter) goto mem_fail; hdr = (sam_hdr_t**)calloc(n, sizeof(sam_hdr_t*)); if (!hdr) goto mem_fail; translation_tbl = (trans_tbl_t*)calloc(n, sizeof(trans_tbl_t)); if (!translation_tbl) goto mem_fail; RG = (char**)calloc(n, sizeof(char*)); if (!RG) goto mem_fail; // prepare RG tag from file names if (flag & MERGE_RG) { RG_len = (int*)calloc(n, sizeof(int)); if (!RG_len) goto mem_fail; for (i = 0; i != n; ++i) { int l = strlen(fn[i]); const char *s = fn[i]; if (l > 4 && (strcmp(s + l - 4, ".bam") == 0 || strcmp(s + l - 4, ".sam") == 0)) l -= 4; if (l > 5 && strcmp(s + l - 5, ".cram") == 0) l -= 5; for (j = l - 1; j >= 0; --j) if (s[j] == '/') break; ++j; l -= j; RG[i] = (char*)calloc(l + 1, 1); if (!RG[i]) goto mem_fail; RG_len[i] = l; strncpy(RG[i], s + j, l); } } if (hin) { // Populate merged_hdr from the pre-prepared header trans_tbl_t dummy; int res; res = trans_tbl_init(merged_hdr, hin, &dummy, flag & MERGE_COMBINE_RG, flag & MERGE_COMBINE_PG, true, NULL); trans_tbl_destroy(&dummy); if (res) return -1; // FIXME: memory leak } // open and read the header from each file for (i = 0; i < n; ++i) { sam_hdr_t *hin; fp[i] = sam_open_format(fn[i], "r", in_fmt); if (fp[i] == NULL) { print_error_errno(cmd, "fail to open \"%s\"", fn[i]); goto fail; } hts_set_opt(fp[i], HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE); hin = sam_hdr_read(fp[i]); if (hin == NULL) { print_error(cmd, "failed to read header from \"%s\"", fn[i]); goto fail; } if (trans_tbl_init(merged_hdr, hin, translation_tbl+i, flag & MERGE_COMBINE_RG, flag & MERGE_COMBINE_PG, (flag & MERGE_FIRST_CO)? (i == 0) : true, RG[i])) goto fail; hdr[i] = hin; int order_ok = 1; if ((translation_tbl+i)->lost_coord_sort && (sam_order == Coordinate || sam_order == MinHash)) { fprintf(stderr, "[bam_merge_core] Order of targets in file %s caused coordinate sort to be lost\n", fn[i]); order_ok = 0; } if (!refs) refs = cram_get_refs(fp[i]); if (order_ok && refs && hts_set_opt(fp[i], CRAM_OPT_SHARED_REF, refs)) goto fail; } // Did we get an @HD line? if (!merged_hdr->have_hd) { fprintf(stderr, "[W::%s] No @HD tag found.\n", __func__); /* FIXME: Should we add an @HD line here, and if so what should we put in it? Ideally we want a way of getting htslib to tell us the SAM version number to assume given no @HD line. Is it also safe to assume that the output is coordinate sorted? SO: is optional so we don't have to have it.*/ /* ksprintf(&merged_hdr->out_hd, "@HD\tVN:1.5\tSO:coordinate\n"); */ } // Transform the header into standard form if (finish_merged_header(merged_hdr) < 0) goto fail; hout = merged_hdr->hdr; if (!hout) goto fail; // If we're only merging a specified region move our iters to start at that point int tid, nreg; hts_pos_t beg, end; if (fn_bed) { hreg = bed_read(fn_bed); if (!hreg) { fprintf(stderr, "[%s] Could not read BED file: \"%s\"\n", __func__, fn_bed); goto fail; } bed_unify(hreg); lreg = bed_reglist(hreg, ALL, &nreg); if (!lreg || !nreg) { fprintf(stderr, "[%s] Null or empty region list\n", __func__); goto fail; } } else if (reg) { rtrans = rtrans_build(n, sam_hdr_nref(hout), translation_tbl); if (!rtrans) goto mem_fail; if (!sam_parse_region(hout, reg, &tid, &beg, &end, 0)) { fprintf(stderr, "[%s] Badly formatted region or unknown reference name: \"%s\"\n", __func__, reg); goto fail; } } if (reg || fn_bed) { hts_idx_t *reg_idx = NULL; for (i = 0; i < n; ++i) { // If index filename has not been specified, look in the BAM folder if (fn_idx != NULL) { reg_idx = sam_index_load2(fp[i], fn[i], fn_idx[i]); } else { reg_idx = sam_index_load(fp[i], fn[i]); } if (reg_idx == NULL) { fprintf(stderr, "[%s] failed to load index for %s. Random alignment retrieval only works for indexed BAM or CRAM files.\n", __func__, fn[i]); free(rtrans); rtrans = NULL; goto fail; } int mapped_tid = INT32_MIN; if (fn_bed) { hts_reglist_t *rl = duplicate_reglist(lreg, nreg); iter[i] = sam_itr_regions(reg_idx, hdr[i], rl, nreg); } else { // (rtrans[i*n+tid]) Look up what hout tid translates to in input tid space mapped_tid = rtrans[i*sam_hdr_nref(hout)+tid]; if (mapped_tid != INT32_MIN) { iter[i] = sam_itr_queryi(reg_idx, mapped_tid, beg, end); } else { iter[i] = sam_itr_queryi(reg_idx, HTS_IDX_NONE, 0, 0); } } if (iter[i] == NULL) { if (fn_bed) { fprintf(stderr, "[%s] failed to get multi-region iterator " "{%s, %s}\n", __func__, fn[i], fn_bed); } else { if (mapped_tid != INT32_MIN) { fprintf(stderr, "[%s] failed to get iterator over " "{%s, %d, %"PRIhts_pos", %"PRIhts_pos"}\n", __func__, fn[i], mapped_tid, beg, end); } else { fprintf(stderr, "[%s] failed to get iterator over " "{%s, HTS_IDX_NONE, 0, 0}\n", __func__, fn[i]); } } hts_idx_destroy(reg_idx); free(rtrans); rtrans = NULL; goto fail; } hts_idx_destroy(reg_idx); } free(rtrans); rtrans = NULL; } // Make sure that there's enough memory for template coordinate keys, one per file to read if (sam_order == TemplateCoordinate) { if ((keys = malloc(sizeof(template_coordinate_keys_t))) == NULL) { print_error(cmd, "could not allocate memory for the top-level keys"); goto mem_fail; } keys->n = 0; keys->m = 0; keys->buffer_size = 0x10000; keys->buffers = NULL; // Make sure that there's enough memory for template coordinate keys, one per file to read if (keys->n + n >= keys->m * keys->buffer_size) { if (template_coordinate_keys_realloc(keys, keys->n + n) < 0) goto mem_fail; } lib_lookup = lookup_libraries(hout); if (!lib_lookup) { goto mem_fail; } } // Load the first read from each file into the heap for (i = 0; i < n; ++i) { heap1_t *h = heap + i; int res; h->i = i; h->entry.bam_record = bam_init1(); h->entry.u.tag = NULL; if (!h->entry.bam_record) goto mem_fail; res = iter[i] ? sam_itr_next(fp[i], iter[i], h->entry.bam_record) : sam_read1(fp[i], hdr[i], h->entry.bam_record); if (res >= 0) { bam_translate(h->entry.bam_record, translation_tbl + i); h->tid = h->entry.bam_record->core.tid; h->pos = (uint64_t)(h->entry.bam_record->core.pos + 1); h->rev = bam_is_rev(h->entry.bam_record); h->idx = idx++; if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) { h->entry.u.tag = bam_aux_get(h->entry.bam_record, g_sort_tag); } else if (g_sam_order == TemplateCoordinate) { template_coordinate_key_t *key = template_coordinate_keys_get(keys, i); // get the next key to use h->entry.u.key = template_coordinate_key(h->entry.bam_record, key, hout, lib_lookup); // update the key if (h->entry.u.key == NULL) goto fail; // key could not be created, error out } else { h->entry.u.tag = NULL; } } else if (res == -1 && (!iter[i] || iter[i]->finished)) { h->pos = HEAP_EMPTY; bam_destroy1(h->entry.bam_record); h->entry.bam_record = NULL; h->entry.u.tag = NULL; h->entry.u.key = NULL; } else { print_error(cmd, "failed to read first record from \"%s\"", fn[i]); goto fail; } } // Open output file and write header if ((fpout = sam_open_format(out, mode, out_fmt)) == 0) { print_error_errno(cmd, "failed to create \"%s\"", out); return -1; } hts_set_opt(fpout, HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE); if (!no_pg && sam_hdr_add_pg(hout, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { print_error(cmd, "failed to add PG line to the header of \"%s\"", out); sam_close(fpout); return -1; } if (sam_hdr_write(fpout, hout) != 0) { print_error_errno(cmd, "failed to write header to \"%s\"", out); sam_close(fpout); return -1; } if (write_index) { if (!(out_idx_fn = auto_index(fpout, out, hout))){ sam_close(fpout); return -1; } } if (!(flag & MERGE_UNCOMP)) hts_set_threads(fpout, n_threads); if (refs && hts_set_opt(fpout, CRAM_OPT_SHARED_REF, refs)) goto fail; // Begin the actual merge ks_heapmake(heap, n, heap); while (heap->pos != HEAP_EMPTY) { bam1_t *b = heap->entry.bam_record; if (flag & MERGE_RG) { uint8_t *rg = bam_aux_get(b, "RG"); if (rg) bam_aux_del(b, rg); bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]); } if (sam_write1(fpout, hout, b) < 0) { print_error_errno(cmd, "failed writing to \"%s\"", out); sam_close(fpout); free(out_idx_fn); return -1; } if ((j = (iter[heap->i]? sam_itr_next(fp[heap->i], iter[heap->i], b) : sam_read1(fp[heap->i], hdr[heap->i], b))) >= 0) { bam_translate(b, translation_tbl + heap->i); heap->tid = b->core.tid; heap->pos = (uint64_t)(b->core.pos + 1); heap->rev = bam_is_rev(b); heap->idx = idx++; if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) { heap->entry.u.tag = bam_aux_get(heap->entry.bam_record, g_sort_tag); } else if (g_sam_order == TemplateCoordinate) { template_coordinate_key_t *key = template_coordinate_keys_get(keys, heap->i); // get the next key to use heap->entry.u.key = template_coordinate_key(heap->entry.bam_record, key, hout, lib_lookup); // update the key if (heap->entry.u.key == NULL) goto fail; // key could not be created, error out } else { heap->entry.u.tag = NULL; } } else if (j == -1 && (!iter[heap->i] || iter[heap->i]->finished)) { heap->pos = HEAP_EMPTY; bam_destroy1(heap->entry.bam_record); heap->entry.bam_record = NULL; heap->entry.u.tag = NULL; } else { print_error(cmd, "\"%s\" is truncated", fn[heap->i]); goto fail; } ks_heapadjust(heap, 0, n, heap); } if (write_index) { if (sam_idx_save(fpout) < 0) { print_error_errno("merge", "writing index failed"); goto fail; } } free(out_idx_fn); // Clean up and close if (flag & MERGE_RG) { for (i = 0; i != n; ++i) free(RG[i]); free(RG_len); } for (i = 0; i < n; ++i) { trans_tbl_destroy(translation_tbl + i); hts_itr_destroy(iter[i]); sam_hdr_destroy(hdr[i]); sam_close(fp[i]); } sam_hdr_destroy(hin); sam_hdr_destroy(hout); free_merged_header(merged_hdr); hts_reglist_free(lreg, nreg); bed_destroy(hreg); free(RG); free(translation_tbl); free(fp); free(heap); free(iter); free(hdr); if (sam_close(fpout) < 0) { print_error_errno(cmd, "error closing output file \"%s\"", out); return -1; } if (keys != NULL) { for (i = 0; i < keys->m; ++i) { free(keys->buffers[i]); } free(keys->buffers); free(keys); } lib_lookup_destroy(lib_lookup); return 0; mem_fail: print_error(cmd, "Out of memory"); fail: if (flag & MERGE_RG) { if (RG) { for (i = 0; i != n; ++i) free(RG[i]); } free(RG_len); } for (i = 0; i < n; ++i) { if (translation_tbl && translation_tbl[i].tid_trans) trans_tbl_destroy(translation_tbl + i); if (iter && iter[i]) hts_itr_destroy(iter[i]); if (hdr && hdr[i]) sam_hdr_destroy(hdr[i]); if (fp && fp[i]) sam_close(fp[i]); if (heap && heap[i].entry.bam_record) bam_destroy1(heap[i].entry.bam_record); } if (hout) sam_hdr_destroy(hout); free(RG); free(translation_tbl); free(hdr); hts_reglist_free(lreg, nreg); bed_destroy(hreg); free(iter); free(heap); free(fp); free(rtrans); free(out_idx_fn); if (keys != NULL) { for (i = 0; i < keys->m; ++i) { free(keys->buffers[i]); } free(keys->buffers); free(keys); } lib_lookup_destroy(lib_lookup); return -1; } // Unused here but may be used by legacy samtools-using third-party code int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg) { char mode[12]; strcpy(mode, "wb"); if (flag & MERGE_UNCOMP) strcat(mode, "0"); else if (flag & MERGE_LEVEL1) strcat(mode, "1"); SamOrder sam_order = by_qname ? QueryName : Coordinate; return bam_merge_core2(sam_order, NULL, out, mode, headers, n, fn, NULL, NULL, flag, reg, 0, "merge", NULL, NULL, 0, NULL, 1); } static void merge_usage(FILE *to) { fprintf(to, "Usage: samtools merge [options] -o [options] ... \n" " or: samtools merge [options] ... \n" "\n" "Options:\n" " -n Input files are sorted by read name (natural)\n" " -N Input files are sorted by read name (ASCII)\n" " -t TAG Input files are sorted by TAG value\n" " -r Attach RG tag (inferred from file names)\n" " -u Uncompressed BAM output\n" " -f Overwrite the output BAM if exist\n" " -o FILE Specify output file via option instead of argument\n" " -1 Compress level 1\n" " -l INT Compression level, from 0 to 9 [-1]\n" " -R STR Merge file in the specified region STR [all]\n" " -h FILE Copy the header in FILE to [in1.bam]\n" " -c Combine @RG headers with colliding IDs [alter IDs to be distinct]\n" " -p Combine @PG headers with colliding IDs [alter IDs to be distinct]\n" " -s VALUE Override random seed\n" " -b FILE List of input BAM filenames, one per line [null]\n" " -X Use customized index files\n" " -L FILE Specify a BED file for multiple region filtering [null]\n" " --no-PG do not add a PG line\n" " --template-coordinate Input files are sorted by template-coordinate\n"); sam_global_opt_help(to, "-.O..@.."); } int bam_merge(int argc, char *argv[]) { int c, flag = 0, ret = 0, level = -1, has_index_file = 0; char *fn_headers = NULL, *reg = NULL, mode[12]; char *sort_tag = NULL, *fnout = NULL, *arg_list = NULL; long random_seed = (long)time(NULL); char** fn = NULL; char** fn_idx = NULL, *fn_bed = NULL; int fn_size = 0, no_pg = 0; SamOrder sam_order = Coordinate; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'), { "threads", required_argument, NULL, '@' }, {"no-PG", no_argument, NULL, 1}, { "template-coordinate", no_argument, NULL, 2}, { NULL, 0, NULL, 0 } }; if (argc == 1) { merge_usage(stdout); return 0; } while ((c = getopt_long(argc, argv, "h:nNru1R:o:f@:l:cps:b:O:t:XL:", lopts, NULL)) >= 0) { switch (c) { case 'r': flag |= MERGE_RG; break; case 'f': flag |= MERGE_FORCE; break; case 'h': fn_headers = optarg; break; case 'N': natural_sort = 0; // fall through case 'n': sam_order = QueryName; break; case 'o': fnout = optarg; break; case 't': sort_tag = optarg; break; case '1': flag |= MERGE_LEVEL1; level = 1; break; case 'u': flag |= MERGE_UNCOMP; level = 0; break; case 'R': reg = strdup(optarg); break; case 'l': level = atoi(optarg); break; case 'c': flag |= MERGE_COMBINE_RG; break; case 'p': flag |= MERGE_COMBINE_PG; break; case 's': random_seed = atol(optarg); break; case 'X': has_index_file = 1; break; // -X flag for index filename case 'L': fn_bed = optarg; break; case 'b': { // load the list of files to read if (has_index_file) { fprintf(stderr,"Error: The -b option cannot be combined with -X\n"); ret = 1; goto end; } int nfiles; char **fn_read = hts_readlines(optarg, &nfiles); if (fn_read) { // Append to end of array fn = realloc(fn, (fn_size+nfiles) * sizeof(char*)); if (fn == NULL) { ret = 1; goto end; } memcpy(fn+fn_size, fn_read, nfiles * sizeof(char*)); fn_size += nfiles; free(fn_read); } else { print_error("merge", "Invalid file list \"%s\"", optarg); ret = 1; } break; } case 1: no_pg = 1; break; case 2: sam_order = TemplateCoordinate; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': merge_usage(stderr); return 1; } } if (sort_tag != NULL) { sam_order = sam_order == QueryName ? TagQueryName : TagCoordinate; } if (fnout == NULL && argc - optind >= 1) { fnout = argv[optind]; optind++; } if (fnout == NULL) { print_error("merge", "You must at least specify the output file"); merge_usage(stderr); return 1; } if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) { print_error("merge", "failed to create arg_list"); return 1; } hts_srand48(random_seed); if (!(flag & MERGE_FORCE) && strcmp(fnout, "-") != 0) { struct stat sbuf; if (stat(fnout, &sbuf) == 0 && S_ISREG(sbuf.st_mode)) { fprintf(stderr, "[%s] File '%s' exists. Please apply '-f' to overwrite. Abort.\n", __func__, fnout); ret = 1; goto end; } } int nargcfiles = 0; if (has_index_file) { // Calculate # of input BAM files if ((argc - optind) % 2 != 0) { fprintf(stderr, "Odd number of filenames detected! Each BAM file should have an index file\n"); ret = 1; goto end; } nargcfiles = (argc - optind) / 2; } else { nargcfiles = argc - optind; } if (nargcfiles > 0) { // Add argc files to end of array fn = realloc(fn, (fn_size+nargcfiles) * sizeof(char*)); if (fn == NULL) { ret = 1; goto end; } memcpy(fn+fn_size, argv + optind, nargcfiles * sizeof(char*)); if(has_index_file) { fn_idx = realloc(fn_idx, nargcfiles * sizeof(char*)); if (fn_idx == NULL) { ret = 1; goto end; } memcpy(fn_idx+fn_size, argv + nargcfiles + optind, nargcfiles * sizeof(char*)); } } if (fn_size+nargcfiles < 1) { print_error("merge", "You must specify at least one (and usually two or more) input files"); merge_usage(stderr); ret = 1; goto end; } if (reg && fn_bed) { print_error("merge", "You must specify either a BED file or a region"); ret = 1; goto end; } strcpy(mode, "wb"); sam_open_mode(mode+1, fnout, NULL); if (level >= 0) sprintf(strchr(mode, '\0'), "%d", level < 9? level : 9); if (bam_merge_core2(sam_order, sort_tag, fnout, mode, fn_headers, fn_size+nargcfiles, fn, fn_idx, fn_bed, flag, reg, ga.nthreads, "merge", &ga.in, &ga.out, ga.write_index, arg_list, no_pg) < 0) ret = 1; end: if (fn_size > 0) { int i; for (i=0; ii, res; if (i < nfiles) { // read from file res = sam_read1(fp[i], hout, heap->entry.bam_record); if (res >= 0 && g_sam_order == TemplateCoordinate) { // file read OK and TemplateCoordinate order // It is assumed that there are nfiles more keys allocated than keys->n; see allocation in bam_merge_simple template_coordinate_key_t *key = template_coordinate_keys_get(keys, keys->n + i); // get the next key to use heap->entry.u.key = template_coordinate_key(heap->entry.bam_record, key, hout, lib_lookup); // update the key if (heap->entry.u.key == NULL) res = -1; // key could not be created, error out } } else { // read from memory if (in_mem[i - nfiles].from < in_mem[i - nfiles].to) { size_t from = in_mem[i - nfiles].from; heap->entry.bam_record = buf[from].bam_record; if (g_sam_order == TemplateCoordinate) heap->entry.u.key = buf[from].u.key; in_mem[i - nfiles].from++; res = 0; } else { res = -1; } } if (res >= 0) { heap->tid = heap->entry.bam_record->core.tid; heap->pos = (uint64_t)(heap->entry.bam_record->core.pos + 1); heap->rev = bam_is_rev(heap->entry.bam_record); heap->idx = (*idx)++; if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) { heap->entry.u.tag = bam_aux_get(heap->entry.bam_record, g_sort_tag); } else if (g_sam_order != TemplateCoordinate) { heap->entry.u.tag = NULL; heap->entry.u.key = NULL; } } else if (res == -1) { heap->pos = HEAP_EMPTY; if (i < nfiles) bam_destroy1(heap->entry.bam_record); heap->entry.bam_record = NULL; heap->entry.u.tag = NULL; heap->entry.u.key = NULL; } else { return -1; } return 0; } static int bam_merge_simple(SamOrder sam_order, char *sort_tag, const char *out, const char *mode, sam_hdr_t *hout, int n, char * const *fn, int num_in_mem, buf_region *in_mem, bam1_tag *buf, template_coordinate_keys_t *keys, khash_t(const_c2c) *lib_lookup, htsThreadPool *htspool, const char *cmd, const htsFormat *in_fmt, const htsFormat *out_fmt, char *arg_list, int no_pg, int write_index, int final_out) { samFile *fpout = NULL, **fp = NULL; heap1_t *heap = NULL; uint64_t idx = 0; int i, heap_size = n + num_in_mem; char *out_idx_fn = NULL; if (sam_order == TagQueryName || sam_order == TagCoordinate) { g_sort_tag[0] = sort_tag[0]; g_sort_tag[1] = sort_tag[0] ? sort_tag[1] : '\0'; } if (n > 0) { fp = (samFile**)calloc(n, sizeof(samFile*)); if (!fp) goto mem_fail; } heap = (heap1_t*)calloc(heap_size, sizeof(heap1_t)); if (!heap) goto mem_fail; // Make sure that there's enough memory for template coordinate keys, one per file to read if (keys && keys->n + n >= keys->m * keys->buffer_size) { if (template_coordinate_keys_realloc(keys, keys->n + n) < 0) goto mem_fail; } // Open each file, read the header and put the first read into the heap for (i = 0; i < heap_size; i++) { sam_hdr_t *hin; heap1_t *h = &heap[i]; if (i < n) { fp[i] = sam_open_format(fn[i], "r", in_fmt); if (fp[i] == NULL) { print_error_errno(cmd, "fail to open \"%s\"", fn[i]); goto fail; } hts_set_opt(fp[i], HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE); if (htspool->pool) hts_set_opt(fp[i], HTS_OPT_THREAD_POOL, htspool); // Read header ... hin = sam_hdr_read(fp[i]); if (hin == NULL) { print_error(cmd, "failed to read header from \"%s\"", fn[i]); goto fail; } // ... and throw it away as we don't really need it sam_hdr_destroy(hin); } // Get a read into the heap h->i = i; h->entry.u.tag = NULL; h->entry.u.key = NULL; if (i < n) { h->entry.bam_record = bam_init1(); if (!h->entry.bam_record) goto mem_fail; } if (heap_add_read(h, n, fp, num_in_mem, in_mem, buf, keys, &idx, hout, lib_lookup) < 0) { assert(i < n); print_error(cmd, "failed to read first record from \"%s\"", fn[i]); goto fail; } } // Open output file and write header if ((fpout = sam_open_format(out, mode, out_fmt)) == 0) { print_error_errno(cmd, "failed to create \"%s\"", out); return -1; } hts_set_opt(fpout, HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE); if (!no_pg && sam_hdr_add_pg(hout, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { print_error(cmd, "failed to add PG line to the header of \"%s\"", out); sam_close(fpout); return -1; } if (htspool->pool) hts_set_opt(fpout, HTS_OPT_THREAD_POOL, htspool); if (sam_hdr_write(fpout, hout) != 0) { print_error_errno(cmd, "failed to write header to \"%s\"", out); sam_close(fpout); return -1; } if (write_index) { if (!(out_idx_fn = auto_index(fpout, out, hout))){ sam_close(fpout); return -1; } } // Now do the merge ks_heapmake(heap, heap_size, heap); while (heap->pos != HEAP_EMPTY) { bam1_t *b = heap->entry.bam_record; if (g_sam_order == MinHash && b->core.tid == -1 && final_out) { // Remove the cached minhash value b->core.pos = -1; b->core.mpos = -1; b->core.isize = 0; } if (sam_write1(fpout, hout, b) < 0) { print_error_errno(cmd, "failed writing to \"%s\"", out); goto fail; } if (heap_add_read(heap, n, fp, num_in_mem, in_mem, buf, keys, &idx, hout, lib_lookup) < 0) { assert(heap->i < n); print_error(cmd, "Error reading \"%s\" : %s", fn[heap->i], strerror(errno)); goto fail; } ks_heapadjust(heap, 0, heap_size, heap); } // Clean up and close for (i = 0; i < n; i++) { if (sam_close(fp[i]) != 0) { print_error(cmd, "Error on closing \"%s\" : %s", fn[i], strerror(errno)); } } free(fp); free(heap); if (write_index) { if (sam_idx_save(fpout) < 0) { print_error_errno("merge", "writing index failed"); goto fail; } free(out_idx_fn); } if (sam_close(fpout) < 0) { print_error_errno(cmd, "error closing output file \"%s\"", out); return -1; } return 0; mem_fail: print_error(cmd, "Out of memory"); fail: for (i = 0; i < n; i++) { if (fp && fp[i]) sam_close(fp[i]); } for (i = 0; i < heap_size; i++) { if (heap && heap[i].i < n && heap[i].entry.bam_record) bam_destroy1(heap[i].entry.bam_record); } free(fp); free(heap); if (fpout) sam_close(fpout); free(out_idx_fn); return -1; } // Function to compare reads and determine which one is < or > the other // Handle sort-by-pos and sort-by-name. Used as the secondary sort in bam1_lt_by_tag, if reads are equivalent by tag. // Returns a value less than, equal to or greater than zero if a is less than, // equal to or greater than b, respectively. static inline int bam1_cmp_core(const bam1_tag a, const bam1_tag b) { uint64_t pa, pb; if (!a.bam_record) return 1; if (!b.bam_record) return 0; if (g_sam_order == QueryName || g_sam_order == TagQueryName) { int t = strnum_cmp(bam_get_qname(a.bam_record), bam_get_qname(b.bam_record)); if (t != 0) return t; int af = a.bam_record->core.flag; int bf = b.bam_record->core.flag; // Sort order is READ1, READ2, (PRIMARY), SUPPLEMENTARY, SECONDARY // Get the bits in this order so sort is a natural a-b af = ((af&0xc0)<<8)|((af&0x100)<<3)|((af&0x800)>>3); bf = ((bf&0xc0)<<8)|((bf&0x100)<<3)|((bf&0x800)>>3); return af - bf; } else { pa = a.bam_record->core.tid; pb = b.bam_record->core.tid; if (pa == pb) { pa = (uint64_t)(a.bam_record->core.pos+1); pb = (uint64_t)(b.bam_record->core.pos+1); } if (pa == pb) { pa = bam_is_rev(a.bam_record); pb = bam_is_rev(b.bam_record); } return pa < pb ? -1 : (pa > pb ? 1 : 0); } } uint8_t normalize_type(const uint8_t* aux) { if (*aux == 'c' || *aux == 'C' || *aux == 's' || *aux == 'S' || *aux == 'i' || *aux == 'I') { return 'c'; } else if (*aux == 'f' || *aux == 'd') { return 'f'; } else if (*aux == 'H' || *aux == 'Z') { return 'H'; } else { return *aux; } } // Sort record by tag, using pos or read name as a secondary key if tags are identical. Reads not carrying the tag sort first. // Tags are first sorted by the type character (in case the types differ), or by the appropriate comparator for that type if they agree. // Returns a value less than, equal to or greater than zero if a is less than, // equal to or greater than b, respectively. static inline int bam1_cmp_by_tag(const bam1_tag a, const bam1_tag b) { const uint8_t* aux_a = a.u.tag; const uint8_t* aux_b = b.u.tag; if (aux_a == NULL && aux_b != NULL) { return -1; } else if (aux_a != NULL && aux_b == NULL) { return 1; } else if (aux_a == NULL && aux_b == NULL) { return bam1_cmp_core(a,b); } // 'Normalize' the letters of the datatypes to a canonical letter, // so that comparison of different types // forms a correct total ordering. uint8_t a_type = normalize_type(aux_a); uint8_t b_type = normalize_type(aux_b); if (a_type != b_type) { // Fix int to float comparisons by using bam_aux2f() to read the int if (a_type == 'c' && b_type == 'f') { a_type = 'f'; } else if (a_type == 'f' && b_type == 'c') { b_type = 'f'; } else { // Unfixable mismatched types return a_type < b_type ? -1 : 1; } } if (a_type == 'c') { int64_t va = bam_aux2i(aux_a); int64_t vb = bam_aux2i(aux_b); if (va != vb) return va < vb ? -1 : 1; return bam1_cmp_core(a, b); } else if (a_type == 'f') { double va = bam_aux2f(aux_a); double vb = bam_aux2f(aux_b); if (va != vb) return va < vb ? -1 : 1; return bam1_cmp_core(a, b); } else if (a_type == 'A') { unsigned char va = bam_aux2A(aux_a); unsigned char vb = bam_aux2A(aux_b); if (va != vb) return va < vb ? -1 : 1; return bam1_cmp_core(a, b); } else if (a_type == 'H') { int t = strcmp(bam_aux2Z(aux_a), bam_aux2Z(aux_b)); if (t) return t; return bam1_cmp_core(a, b); } else { return bam1_cmp_core(a,b); } } // Sort by minimiser (stored in bam1_tag.u.pos). // If equal, sort by position. // // The 64-bit sort key is split over the bam pos and isize fields. // This permits it to survive writing to temporary file and coming back. #ifdef DEBUG_MINHASH static int ntot = 0, nmis = 0, ndup = 0; #endif static inline int bam1_cmp_by_minhash(const bam1_tag a, const bam1_tag b) { const bam1_t *A = a.bam_record; const bam1_t *B = b.bam_record; if (!A) return 1; if (!B) return 0; if (A->core.tid != -1 || B->core.tid != -1) return bam1_cmp_core(a,b); const uint64_t m_a = (((uint64_t)A->core.pos)<<31)|(uint32_t)A->core.mpos; const uint64_t m_b = (((uint64_t)B->core.pos)<<31)|(uint32_t)B->core.mpos; if (m_a < m_b) // by hash return -1; else if (m_a > m_b) return 1; // Bigger pos with size minhash means starts further to left else if (A->core.isize > B->core.isize) // by hash location in seq return -1; else if (A->core.isize < B->core.isize) return 1; else return bam1_cmp_core(a,b); } // compares to molecular identifiers, ignoring any trailing slash and subsequent single-character // * if mid1 is less than mid2, then -1 will be returned // * if mid1 is greater than mid2, then 1 will be returned static inline int template_coordinate_key_compare_mid(const char* mid1, const char* mid2) { size_t i = 0; size_t len1 = strlen(mid1); size_t len2 = strlen(mid2); size_t shortest; // Snip off trailing slash followed by a single character, if present if (len1 >= 2 && mid1[len1-2] == '/') len1 -= 2; if (len2 >= 2 && mid2[len2-2] == '/') len2 -= 2; shortest = len1 < len2 ? len1 : len2; // find first mismatching character while (i < shortest && mid1[i] == mid2[i]) i++; // compare last characters if (i == len1 && i < len2) return -1; // mid1 shorter if (i == len2 && i < len1) return 1; // mid2 shorter if (i == len1 && i == len2) return 0; // all characters match if (mid1[i] < mid2[i]) return -1; // mid1 earlier else return 1; } // Builds a key use to sort in TemplateCoordinate order. Returns NULL if the key could not be created (e.g. MC // tag is missing), otherwise the pointer to the provided key. static template_coordinate_key_t* template_coordinate_key(bam1_t *b, template_coordinate_key_t *key, sam_hdr_t *hdr, khash_t(const_c2c) *lib_lookup) { uint8_t *data; char *rg; khiter_t k; // defaults key->tid1 = key->tid2 = INT32_MAX; key->pos1 = key->pos2 = HTS_POS_MAX; key->neg1 = key->neg2 = false; key->mid = ""; // update values rg = (char *)bam_aux_get(b, "RG"); if (rg && rg[0] == 'Z' &&(k = kh_get(const_c2c, lib_lookup, rg + 1)) < kh_end(lib_lookup)) { key->library = kh_value(lib_lookup, k); } else { key->library = ""; } key->name = bam_get_qname(b); if (!(b->core.flag & BAM_FUNMAP)) { // read is mapped, update coordinates key->tid1 = b->core.tid; key->neg1 = bam_is_rev(b); key->pos1 = (key->neg1) ? unclipped_end(b) : unclipped_start(b); } if (b->core.flag & BAM_FPAIRED && !(b->core.flag & BAM_FMUNMAP)) { // mate is mapped, update coordinates char *cigar; if ((data = bam_aux_get(b, "MC"))) { if (!(cigar = bam_aux2Z(data))) { fprintf(stderr, "[bam_sort] error: MC tag wrong type. Please use the MC tag provided by samtools fixmate.\n"); return NULL; } } else { fprintf(stderr, "[bam_sort] error: no MC tag. Please run samtools fixmate on file first.\n"); return NULL; } key->tid2 = b->core.mtid; key->neg2 = bam_is_mrev(b); key->pos2 = (key->neg2) ? unclipped_other_end(b->core.mpos, cigar) : unclipped_other_start(b->core.mpos, cigar); } if ((data = bam_aux_get(b, "MI"))) { if (!(key->mid=bam_aux2Z(data))) { fprintf(stderr, "[bam_sort] error: MI tag wrong type (not a string).\n"); return NULL; } } // set is_upper_of_pair, and swap if we get the same key regardless of which end // of the pair it is if (key->tid1 < key->tid2 || (key->tid1 == key->tid2 && key->pos1 < key->pos2) || (key->tid1 == key->tid2 && key->pos1 == key->pos2 && !key->neg1)) { key->is_upper_of_pair = false; } else { key->is_upper_of_pair = true; // swap int tmp_tid; hts_pos_t tmp_pos; bool tmp_neg; tmp_tid = key->tid1; key->tid1 = key->tid2; key->tid2 = tmp_tid; tmp_pos = key->pos1; key->pos1 = key->pos2; key->pos2 = tmp_pos; tmp_neg = key->neg1; key->neg1 = key->neg2; key->neg2 = tmp_neg; } return key; } // Function to compare reads and determine which one is < or > the other // Handles template-coordinate, which sorts by: // 1. the earlier unclipped 5' coordinate of the read pair // 2. the higher unclipped 5' coordinate of the read pair // 3. library (from read group) // 4. the molecular identifier (if present) // 5. read name // 6. if unpaired, or if R1 has the lower coordinates of the pair // Returns a value less than, equal to or greater than zero if a is less than, // equal to or greater than b, respectively. static inline int bam1_cmp_template_coordinate(const bam1_tag a, const bam1_tag b) { if (!a.bam_record) return 1; if (!b.bam_record) return 0; const template_coordinate_key_t* key_a = a.u.key; const template_coordinate_key_t* key_b = b.u.key; int retval = 0; if (0 == retval) retval = key_a->tid1 - key_b->tid1; if (0 == retval) retval = key_a->tid2 - key_b->tid2; if (0 == retval) retval = key_a->pos1 < key_b->pos1 ? -1 : (key_a->pos1 > key_b->pos1 ? 1 : 0); if (0 == retval) retval = key_a->pos2 < key_b->pos2 ? -1 : (key_a->pos2 > key_b->pos2 ? 1 : 0); if (0 == retval) retval = key_a->neg1 == key_b->neg1 ? 0 : (key_a->neg1 ? -1 : 1); if (0 == retval) retval = key_a->neg2 == key_b->neg2 ? 0 : (key_a->neg2 ? -1 : 1); if (0 == retval) retval = strcmp(key_a->library, key_b->library); if (0 == retval) retval = template_coordinate_key_compare_mid(key_a->mid, key_b->mid); if (0 == retval) retval = strcmp(key_a->name, key_b->name); if (0 == retval) retval = key_a->is_upper_of_pair == key_b->is_upper_of_pair ? 0 : (key_a->is_upper_of_pair ? 1 : -1); return retval < 0 ? -1 : (retval > 0 ? 1 : 0); } // Function to compare reads and determine which one is < the other // Handle sort-by-pos, sort-by-name, sort-by-tag, or sort-by-template-coordinate. static inline int bam1_lt(const bam1_tag a, const bam1_tag b) { switch (g_sam_order) { case Coordinate: case QueryName: return bam1_cmp_core(a, b) < 0; case TagQueryName: case TagCoordinate: return bam1_cmp_by_tag(a, b) < 0; case MinHash: return bam1_cmp_by_minhash(a, b) < 0; case TemplateCoordinate: return bam1_cmp_template_coordinate(a, b) < 0; default: return bam1_cmp_core(a,b) < 0; } } KSORT_INIT(sort, bam1_tag, bam1_lt) typedef struct { size_t buf_len; bam1_tag *buf; const sam_hdr_t *h; int error; int large_pos; int minimiser_kmer; bool try_rev; bool no_squash; } worker_t; // Returns 0 for success // -1 for failure static int write_buffer(const char *fn, const char *mode, size_t l, bam1_tag *buf, const sam_hdr_t *h, int n_threads, const htsFormat *fmt, int clear_minhash, char *arg_list, int no_pg, int write_index) { size_t i; samFile* fp; char *out_idx_fn = NULL; fp = sam_open_format(fn, mode, fmt); if (fp == NULL) return -1; hts_set_opt(fp, HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE); if (!no_pg && sam_hdr_add_pg((sam_hdr_t *)h, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { goto fail; } if (sam_hdr_write(fp, h) != 0) goto fail; if (write_index) if (!(out_idx_fn = auto_index(fp, fn, (sam_hdr_t *)h))) goto fail; if (n_threads > 1) hts_set_threads(fp, n_threads); for (i = 0; i < l; ++i) { bam1_t *b = buf[i].bam_record; if (clear_minhash && b->core.tid == -1) { // To see the position for debugging // b->core.pos = ((((uint64_t)b->core.pos)<<31)|(uint32_t)b->core.mpos) + b->core.isize; // Remove the cached minhash value b->core.pos = -1; b->core.mpos = -1; b->core.isize = 0; } if (sam_write1(fp, h, b) < 0) goto fail; } if (write_index) { if (sam_idx_save(fp) < 0) { print_error_errno("merge", "writing index failed"); goto fail; } free(out_idx_fn); } if (sam_close(fp) < 0) return -1; return 0; fail: sam_close(fp); free(out_idx_fn); return -1; } #define NUMBASE 256 static int ks_radixsort(size_t n, bam1_tag *buf, const sam_hdr_t *h) { int curr = 0, ret = -1; ssize_t i; bam1_tag *buf_ar2[2], *bam_a, *bam_b; uint64_t max_pos = 1; uint32_t max_tid = 1, tid_bytes = 0, pos_bytes = 0, byte = 0; uint32_t tid_shift_l, tid_shift_r; int nref = sam_hdr_nref(h); // Count number of bytes needed for biggest tid and pos // Notes: Add 1 to core.pos so always positive. // Convert unmapped tid (-1) to number of references so unmapped // sort to the end. for (i = 0; i < n; i++) { bam1_t *b = buf[i].bam_record; uint32_t tid = b->core.tid == -1 ? nref : b->core.tid; uint64_t pos = ((uint64_t)(b->core.pos + 1) << 1) | bam_is_rev(b); if (max_tid < tid) max_tid = tid; if (max_pos < pos) max_pos = pos; } for (; max_pos > 0; max_pos >>= 8) pos_bytes++; for (; max_tid > 0; max_tid >>= 8) tid_bytes++; assert(pos_bytes + tid_bytes < sizeof(buf[0].u.pos_tid)); tid_shift_l = pos_bytes * 8; tid_shift_r = 64 - tid_shift_l; // Write position and tid into bam1_tag::u::pos_tid using minimum number // of bytes required. Values are stored little-endian so that we // get a least-significant digit (byte) radix sort. for (i = 0; i < n; i++) { bam1_t *b = buf[i].bam_record; uint32_t tid = b->core.tid == -1 ? nref : b->core.tid; // 'pos' here includes as many bytes of tid as will fit // in the space remaining above pos_bytes. The rest of tid // is written out separately. uint64_t pos = (bam_is_rev(b) | ((uint64_t)(b->core.pos + 1) << 1) | (tid_shift_l < 64 ? (uint64_t) tid << tid_shift_l : 0)); u64_to_le(pos, buf[i].u.pos_tid); u32_to_le(tid_shift_r < 32 ? tid >> tid_shift_r : 0, &buf[i].u.pos_tid[8]); } buf_ar2[0] = buf; buf_ar2[1] = (bam1_tag *)malloc(sizeof(bam1_tag) * n); if (buf_ar2[1] == NULL) { print_error("sort", "couldn't allocate memory for temporary buf"); goto err; } // Least-significant digit radix sort (where "digits" are bytes) for (byte = 0; byte < pos_bytes + tid_bytes; byte++) { size_t remainders[NUMBASE] = { 0 }; bam_a = buf_ar2[curr]; bam_b = buf_ar2[1-curr]; for (i = 0; i < n; ++i) remainders[bam_a[i].u.pos_tid[byte]]++; for (i = 1; i < NUMBASE; ++i) remainders[i] += remainders[i - 1]; for (i = n - 1; i >= 0; i--) { size_t j = --remainders[bam_a[i].u.pos_tid[byte]]; bam_b[j] = bam_a[i]; } curr = 1 - curr; } if (curr == 1) { bam1_tag *end = buf + n; bam_a = buf_ar2[0]; bam_b = buf_ar2[1]; while (bam_a < end) *bam_a++ = *bam_b++; } ret = 0; err: free(buf_ar2[1]); return ret; } KHASH_MAP_INIT_INT64(kmer, int64_t) static khash_t(kmer) *kmer_h = NULL; // Punt homopolymers somewhere central in the hash space #define XOR 0xdead7878beef7878 /* * Computes the minhash of a sequence using forward strand and if requested * reverse strand. * * This is used as a sort key for unmapped data, to collate like sequences * together and to improve compression ratio. * * The minhash is returned and *pos filled out with location of this hash * key in the sequence if pos != NULL. */ static uint64_t minhash(bam1_t *b, int kmer, int window, int *curr_pos, int *end, int *is_rev, int try_fwd, int try_rev, int no_squash) { uint64_t hashf = 0, minhashf = UINT64_MAX; int minhashpf = *curr_pos, i, j; uint64_t mask = (1L<<(2*kmer))-1; uint8_t *seq = bam_get_seq(b); int len = b->core.l_qseq; uint64_t xor = XOR & mask; if (is_rev) *is_rev = 0; // Lookup tables for bam_seqi to 0123 fwd/rev hashes // =ACM GRSV TWYH KDBN #define X 0 static unsigned char L[16] = { X,0,1,X, 2,X,X,X, 3,X,X,X, X,X,X,X, }; uint64_t R[16] = { X,3,2,X, 1,X,X,X, 0,X,X,X, X,X,X,X, }; for (i = 0; i < 16; i++) R[i] <<= 2*(kmer-1); int i_start = *curr_pos; int i_end = MIN(i_start + window, len); int last_base = -1; if (try_fwd) { // Initialise hash keys for (i = i_start, j = 0; j < kmer-1 && i < i_end; i++) { int base = bam_seqi(seq, i); // collapse homopolymers if (no_squash || last_base != base) { last_base = base; hashf = (hashf<<2) | L[base]; j++; } } // Loop to find minimum if (no_squash) { for (; i < i_end; i++) { int base = bam_seqi(seq, i); hashf = (hashf<<2) | L[base]; uint64_t hashfx = (hashf ^ XOR) & mask; if (minhashf > hashfx) minhashf = hashfx, minhashpf = i; } } else { for (; i < i_end; i++) { int base = bam_seqi(seq, i); if (last_base != base) { last_base = base; hashf = (hashf<<2) | L[base]; uint64_t hashfx = (hashf ^ XOR) & mask; if (minhashf > hashfx) minhashf = hashfx, minhashpf = i; } } } } // Same as above for the reverse strand. // Not used for now, but we may wish to consider indexing in both // strands, recording the strand in value (pos), and comparing in one // strand only. Right now we compare on both against a single-stranded // index. if (try_rev) { uint64_t hashr = 0, minhashr = UINT64_MAX; int minhashpr = *curr_pos; int last_base = -1; for (i = i_start, j = 0; j < kmer-1 && i < len; i++) { int base = bam_seqi(seq, i); if (no_squash || last_base != base) { last_base = base; hashr = (hashr>>2) | R[base]; j++; } } if (no_squash) { for (; i < i_end; i++) { int base = bam_seqi(seq, i); hashr = (hashr>>2) | R[base]; if (minhashr > (hashr^xor)) minhashr = (hashr^xor), minhashpr = len-i+kmer-2; } } else { for (; i < i_end; i++) { int base = bam_seqi(seq, i); if (last_base != base) { last_base = base; hashr = (hashr>>2) | R[base]; if (minhashr > (hashr^xor)) minhashr = (hashr^xor), minhashpr = len-i+kmer-2; } } } if (minhashr < minhashf) { minhashf = minhashr; minhashpf = minhashpr; if (is_rev) *is_rev = 1; } } // "*curr_pos = minhashpf" is faster here, but is sometimes // poorer in compression. Eg 10 million novaseq records with // 75.1MB vs 76.9MB cram BA field. //*curr_pos = minhashpf; *curr_pos = minhashpf - (kmer-1); if (end) *end = (i_end == len); return minhashf; } #define UNIQ_BIT 60 #define UNIQ_TEST(x) (((x) & (1ULL<= 0) { //fprintf(stderr, "LEN\t%d\t%s\n", b->core.l_qseq, bam_get_qname(b)); uint64_t hashf; int pos = 0, end = 0; khiter_t k; int ret; if (b->core.l_qseq < window) continue; // fwd while (!end) { int last_pos = pos; hashf = minhash(b, kmer, window, &pos, &end, NULL, 1, 0, no_squash); k = kh_put(kmer, kmer_h, hashf, &ret); kh_value(kmer_h, k) = tpos+pos + (((uint64_t)!ret)<core.l_qseq; // We could also add reverse keys to the index here. // This would avoid reverse complementing during the matching stage. // We'd need to add a flag (another high bit of kh_value) to indicate // strand. // I'm unsure if this is a good trade-off or not. // // rev // pos = 0; end = 0; // while (!end) { // hashf = minhash(b, kmer, window, &pos, &end, NULL, 0, 1, // no_squash); // k = kh_put(kmer, kmer_h, hashf, &ret); // kh_value(kmer_h, k) = tpos+pos + (((uint64_t)!ret)<core.l_qseq; } if (r < -1) goto err; ret = 0; err: if (b) bam_destroy1(b); if (h) sam_hdr_destroy(h); sam_close(in); return ret; } /* * A variant of minhash that compares against a previously built index. * * We follow the same steps of scanning through this sequence to find the * minimum hash, but we prefer hash keys that have unique placement in the * index, or if not unique, then non-uniquely placed, over ones that * are absent from the index. */ static uint64_t minhash_with_idx(bam1_t *b, int kmer, int *pos, int *rev, bool try_rev) { uint64_t hashf = 0, minhashf = UINT64_MAX, minhashfi = UINT64_MAX; uint64_t minhashfd = UINT64_MAX; int minhashpf = 0, minhashpfi = 0, minhashpfd = 0, i, j; uint64_t mask = (1L<<(2*kmer))-1; unsigned char *seq = bam_get_seq(b); int len = b->core.l_qseq; const uint64_t xor = XOR & mask; // Lookup tables for bam_seqi to 0123 fwd/rev hashes // =ACM GRSV TWYH KDBN #define X 0 unsigned char L[16] = { X,0,1,X, 2,X,X,X, 3,X,X,X, X,X,X,X, }; uint64_t R[16] = { X,3,2,X, 1,X,X,X, 0,X,X,X, X,X,X,X, }; for (i = 0; i < 16; i++) R[i] <<= 2*(kmer-1); // Initialise hash keys for (i = j = 0; j < kmer-1 && i < len; i++, j++) { int base = bam_seqi(seq, i); hashf = (hashf<<2) | L[base]; } // Loop to find minimum int found_f = 0, found_r = 0; for (; i < len; i++) { int base = bam_seqi(seq, i); hashf = ((hashf<<2) | L[base]) & mask; const uint64_t hashfx = hashf^xor; // Priority for sorting // 1. Unique key in index // 2. Dup key in index // 3. Everything else int index = 0; if (minhashfi > hashfx || (found_f < 2 && minhashfd > hashfx)) { khiter_t k = kh_get(kmer, kmer_h, hashfx); if (k != kh_end(kmer_h)) index = UNIQ_TEST(kh_value(kmer_h, k)) ? 2 : 1; } found_f |= index; switch (index) { case 2: minhashfi = hashfx, minhashpfi = i; break; case 1: minhashfd = hashfx, minhashpfd = i; break; default: if (minhashf > hashfx) minhashf = hashfx, minhashpf = i; } } if (minhashfi != UINT64_MAX) minhashf = minhashfi, minhashpf = minhashpfi; else if (minhashfd != UINT64_MAX) minhashf = minhashfd, minhashpf = minhashpfd; // Same as above for the reverse strand int dir = 0; if (try_rev) { uint64_t hashr = 0, minhashr = UINT64_MAX, minhashri = UINT64_MAX; uint64_t minhashrd = UINT64_MAX; int minhashpr = 0, minhashpri = 0, minhashprd = 0; for (i = j = 0; j < kmer-1 && i < len; i++, j++) { int base = bam_seqi(seq, i); hashr = (hashr>>2) | R[base]; } for (; i < len; i++) { int base = bam_seqi(seq, i); hashr = (hashr>>2) | R[base]; const uint64_t hashrx = hashr^xor; int index = 0; if (minhashri > hashrx || (found_r < 2 && minhashrd > hashrx)) { khiter_t k = kh_get(kmer, kmer_h, hashrx); if (k != kh_end(kmer_h)) index = UNIQ_TEST(kh_value(kmer_h, k)) ? 2 : 1; } found_r |= index; switch (index) { case 2: minhashri = hashrx, minhashpri = i; break; case 1: minhashrd = hashrx, minhashprd = i; break; default: if (minhashr > hashrx) minhashr = hashrx, minhashpr = i; } } if (minhashri != UINT64_MAX) minhashr = minhashri, minhashpr = minhashpri; else if (minhashrd != UINT64_MAX) minhashr = minhashrd, minhashpr = minhashprd; // Pick reverse if better mapping if ((minhashf > minhashr) || (!found_f && found_r)) { if (!found_f || found_r) { minhashf = minhashr; minhashpf = b->core.l_qseq - minhashpr + kmer - 2; dir = 1; } } } #ifdef DEBUG_MINHASH ntot++; khiter_t k = kh_get(kmer, kmer_h, minhashf); if (k != kh_end(kmer_h)) { if (!UNIQ_TEST(kh_value(kmer_h, k))) ndup++; minhashf = kh_value(kmer_h, k) & UNIQ_MASK; } else { nmis++; } #else // For indexed kmers, our hash key is the position the kmer // occurs in the concatenated reference rather than the hash itself. khiter_t k = kh_get(kmer, kmer_h, minhashf); if (k != kh_end(kmer_h)) minhashf = kh_value(kmer_h, k) & UNIQ_MASK; #endif if (rev) *rev = dir; if (pos) *pos = minhashpf; return minhashf != UINT64_MAX ? minhashf : 0; } // As per minhash_with_idx but with homopolymer squashing enabled. // This function is duplicated to remove conditionals and speed up the // hashing code. (Minus the ifdef-ed out code, which is kept above mainly // for posterity.) static uint64_t minhash_with_idx_squash(bam1_t *b, int kmer, int *pos, int *rev, bool try_rev) { uint64_t hashf = 0, minhashf = UINT64_MAX, minhashfi = UINT64_MAX; uint64_t minhashfd = UINT64_MAX; int minhashpf = 0, minhashpfi = 0, minhashpfd = 0, i, j; uint64_t mask = (1L<<(2*kmer))-1; unsigned char *seq = bam_get_seq(b); int len = b->core.l_qseq; const uint64_t xor = XOR & mask; // Lookup tables for bam_seqi to 0123 fwd/rev hashes // =ACM GRSV TWYH KDBN #define X 0 unsigned char L[16] = { X,0,1,X, 2,X,X,X, 3,X,X,X, X,X,X,X, }; uint64_t R[16] = { X,3,2,X, 1,X,X,X, 0,X,X,X, X,X,X,X, }; for (i = 0; i < 16; i++) R[i] <<= 2*(kmer-1); // Initialise hash keys int last_base = -1; for (i = j = 0; j < kmer-1 && i < len; i++) { int base = bam_seqi(seq, i); if (base == last_base) continue; last_base = base; j++; hashf = (hashf<<2) | L[base]; } // Loop to find minimum int found_f = 0, found_r = 0; for (; i < len; i++) { int base = bam_seqi(seq, i); if (base == last_base) continue; last_base = base; hashf = ((hashf<<2) | L[base]) & mask; const uint64_t hashfx = hashf^xor; // Priority for sorting // 1. Unique key in index // 2. Dup key in index // 3. Everything else int index = 0; if (minhashfi > hashfx || (found_f < 2 && minhashfd > hashfx)) { khiter_t k = kh_get(kmer, kmer_h, hashfx); if (k != kh_end(kmer_h)) index = UNIQ_TEST(kh_value(kmer_h, k)) ? 2 : 1; } found_f |= index; switch (index) { case 2: minhashfi = hashfx, minhashpfi = i; break; case 1: minhashfd = hashfx, minhashpfd = i; break; default: if (minhashf > hashfx) minhashf = hashfx, minhashpf = i; } } if (minhashfi != UINT64_MAX) minhashf = minhashfi, minhashpf = minhashpfi; else if (minhashfd != UINT64_MAX) minhashf = minhashfd, minhashpf = minhashpfd; // Same as above for the reverse strand int dir = 0; if (try_rev) { uint64_t hashr = 0, minhashr = UINT64_MAX, minhashri = UINT64_MAX; uint64_t minhashrd = UINT64_MAX; int minhashpr = 0, minhashpri = 0, minhashprd = 0; int last_base = -1; for (i = j = 0; j < kmer-1 && i < len; i++) { int base = bam_seqi(seq, i); if (base == last_base) continue; last_base = base; j++; hashr = (hashr>>2) | R[base]; } for (; i < len; i++) { int base = bam_seqi(seq, i); if (base == last_base) continue; last_base = base; hashr = (hashr>>2) | R[base]; const uint64_t hashrx = hashr^xor; int index = 0; if (minhashri > hashrx || (found_r < 2 && minhashrd > hashrx)) { khiter_t k = kh_get(kmer, kmer_h, hashrx); if (k != kh_end(kmer_h)) index = UNIQ_TEST(kh_value(kmer_h, k)) ? 2 : 1; } found_r |= index; switch (index) { case 2: minhashri = hashrx, minhashpri = i; break; case 1: minhashrd = hashrx, minhashprd = i; break; default: if (minhashr > hashrx) minhashr = hashrx, minhashpr = i; } } if (minhashri != UINT64_MAX) minhashr = minhashri, minhashpr = minhashpri; else if (minhashrd != UINT64_MAX) minhashr = minhashrd, minhashpr = minhashprd; // Pick reverse if better mapping if ((minhashf > minhashr) || (!found_f && found_r)) { if (!found_f || found_r) { minhashf = minhashr; minhashpf = b->core.l_qseq - minhashpr + kmer - 2; dir = 1; } } } #ifdef DEBUG_MINHASH ntot++; khiter_t k = kh_get(kmer, kmer_h, minhashf); if (k != kh_end(kmer_h)) { if (!UNIQ_TEST(kh_value(kmer_h, k))) ndup++; minhashf = kh_value(kmer_h, k) & UNIQ_MASK; } else { nmis++; } #else // For indexed kmers, our hash key is the position the kmer // occurs in the concatenated reference rather than the hash itself. khiter_t k = kh_get(kmer, kmer_h, minhashf); if (k != kh_end(kmer_h)) minhashf = kh_value(kmer_h, k) & UNIQ_MASK; #endif if (rev) *rev = dir; if (pos) *pos = minhashpf; return minhashf != UINT64_MAX ? minhashf : 0; } //--- Start of candidates to punt to htslib /*! * @abstract * Extracts the sequence (in current alignment orientation) from * a bam record and places it in buf, which is nul terminated. * * @param b The bam structure * @param buf A buffer at least b->core.l_qseq+1 bytes long */ static void bam_to_seq(bam1_t *b, char *buf) { int i; uint8_t *seq = bam_get_seq(b); for (i = 0; i < b->core.l_qseq; i++) buf[i] = seq_nt16_str[bam_seqi(seq, i)]; buf[i] = 0; } /*! * @abstract * Writes a new sequence, of length b->core.l_qseq, to a BAM record. * * If a sequence of a new length is required the caller must first make * room for it by updating the bam1_t struct. * * @param b The bam structure * @param buf A buffer at least b->core.l_qseq bytes long */ static void seq_to_bam(bam1_t *b, char *buf) { int i; uint8_t *seq = bam_get_seq(b); for (i = 0; i < b->core.l_qseq; i++) bam_set_seqi(seq, i, seq_nt16_table[(unsigned char)buf[i]]); } /*! * @abstract Reverse complements a BAM record. * * It's possible to do this inline, but complex due to the 4-bit sequence * encoding. For now I take the dumb approach. * * @param b Pointer to a BAM alignment * * @return 0 on success, -1 on failure (ENOMEM) */ static int reverse_complement(bam1_t *b) { static char comp[256] = { 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//00 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//10 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//20 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//30 // * * * * E F * * I J * L * * O '@','T','V','G', 'H','E','F','C', 'D','I','H','M', 'L','K','N','O',//40 //P Q * * * * * * X Y Z [ \ ] ^ _ 'P','Q','Y','S', 'A','A','B','W', 'X','Y','Z','[','\\','[','^','_',//50 //` * * * * E F * * I J * L * * O '`','t','v','g', 'h','e','f','c', 'd','i','j','m', 'l','k','n','o',//60 //P Q * * * * * * X Y Z { | } ~ DEL 'p','q','y','s', 'a','a','b','w', 'x','y','z','{', '|','}','~',127,//70 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//80 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//90 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//A0 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//B0 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//C0 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//D0 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//E0 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//F0 }; char seq_[10000], *seq = seq_; uint8_t *qual = bam_get_qual(b); int i, j; if (b->core.l_qseq >= 10000) if (!(seq = malloc(b->core.l_qseq+1))) return -1; bam_to_seq(b, seq); for (i = 0, j = b->core.l_qseq-1; i < j; i++, j--) { unsigned char tmp = seq[i]; seq[i] = comp[(unsigned char)seq[j]]; seq[j] = comp[tmp]; tmp = qual[i]; qual[i] = qual[j]; qual[j] = tmp; } if (i ==j) seq[i] = comp[(unsigned char)seq[i]]; seq_to_bam(b, seq); if (seq != seq_) free(seq); b->core.flag ^= 0x10; return 0; } //--- End of candidates to punt to htslib static inline void worker_minhash(worker_t *w) { int i; for (i = 0; i < w->buf_len; i++) { bam1_t *b = w->buf[i].bam_record; if (b->core.tid != -1) continue; int pos = 0, rev = 0; uint64_t mh = kmer_h ? (w->no_squash ? minhash_with_idx(b, w->minimiser_kmer, &pos, &rev, w->try_rev) : minhash_with_idx_squash(b, w->minimiser_kmer, &pos, &rev, w->try_rev) ) : minhash(b, w->minimiser_kmer, b->core.l_qseq, &pos, NULL, &rev, 1, w->try_rev, w->no_squash); if (rev) reverse_complement(b); if (!kmer_h) { mh += 1LL<<30; pos = 65535-pos >= 0 ? 65535-pos : 0; } else { mh -= pos; pos = 0; } // Store 64-bit hash in unmapped pos and mpos fields. // The position of hash is in isize, which we use for // resolving ties when sorting by hash key. // These are unused for completely unmapped data and // will be reset during final output. b->core.pos = (mh>>31) & 0x7fffffff; b->core.mpos = mh&0x7fffffff; b->core.isize = pos; } } static void *worker(void *data) { worker_t *w = (worker_t*)data; w->error = 0; switch (g_sam_order) { case Coordinate: if (ks_radixsort(w->buf_len, w->buf, w->h) < 0) { w->error = errno; return NULL; } break; case MinHash: worker_minhash(w); // fall-through default: ks_mergesort(sort, w->buf_len, w->buf, 0); } return 0; } static int sort_blocks(size_t k, bam1_tag *buf, const sam_hdr_t *h, int n_threads, buf_region *in_mem, int large_pos, int minimiser_kmer, bool try_rev, bool no_squash) { int i; size_t pos, rest; pthread_t *tid; pthread_attr_t attr; worker_t *w; int n_failed = 0; if (n_threads < 1) n_threads = 1; if (k < n_threads * 64) n_threads = 1; // use a single thread if we only sort a small batch of records pthread_attr_init(&attr); pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE); w = (worker_t*)calloc(n_threads, sizeof(worker_t)); if (!w) return -1; tid = (pthread_t*)calloc(n_threads, sizeof(pthread_t)); if (!tid) { free(w); return -1; } pos = 0; rest = k; for (i = 0; i < n_threads; ++i) { w[i].buf_len = rest / (n_threads - i); w[i].buf = &buf[pos]; w[i].h = h; w[i].large_pos = large_pos; w[i].minimiser_kmer = minimiser_kmer; w[i].try_rev = try_rev; w[i].no_squash = no_squash; in_mem[i].from = pos; in_mem[i].to = pos + w[i].buf_len; pos += w[i].buf_len; rest -= w[i].buf_len; pthread_create(&tid[i], &attr, worker, &w[i]); } for (i = 0; i < n_threads; ++i) { pthread_join(tid[i], 0); if (w[i].error != 0) { errno = w[i].error; print_error_errno("sort", "failed to sort block %d", i); n_failed++; } } free(w); free(tid); return n_failed ? -1 : n_threads; } static void lib_lookup_destroy(khash_t(const_c2c) *lib_lookup) { khiter_t k; if (lib_lookup == NULL) return; for (k = kh_begin(lib_lookup); k < kh_end(lib_lookup); k++) { if (kh_exist(lib_lookup, k)) free(kh_value(lib_lookup, k)); } kh_destroy(const_c2c, lib_lookup); } // Build an RG to LB lookup table, for the template coordinate sort. // Returns a populated hash table (which may be empty) on success; // NULL on failure. static khash_t(const_c2c) * lookup_libraries(sam_hdr_t *header) { khash_t(const_c2c) *lib_lookup = kh_init(const_c2c); kstring_t lib_name = KS_INITIALIZE; int num_rg, i, res; if (!lib_lookup) return NULL; // Iterate through any RG lines and look for library information num_rg = sam_hdr_count_lines(header, "RG"); if (num_rg < 0) goto fail; for (i = 0; i < num_rg; i++) { const char *rg_id = sam_hdr_line_name(header, "RG", i); khiter_t k; if (!rg_id) goto fail; res = sam_hdr_find_tag_pos(header, "RG", i, "LB", &lib_name); if (res < -1) // Error goto fail; if (res < 0 || !lib_name.s) // No LB tag continue; // Add to lookup table k = kh_put(const_c2c, lib_lookup, rg_id, &res); if (res < 0) // Error goto fail; if (res > 0) { // Inserted kh_value(lib_lookup, k) = ks_release(&lib_name); } } free(lib_name.s); return lib_lookup; fail: lib_lookup_destroy(lib_lookup); free(lib_name.s); return NULL; } /*! @abstract Sort an unsorted BAM file based on the provided sort order @param sam_order the order in which the sort should occur @param sort_tag the tag to use if sorting by Tag @param minimiser_kmer the kmer size when sorting by MinHash @param try_rev try reverse strand when sorting by MinHash @param fn name of the file to be sorted @param prefix prefix of the temporary files (prefix.NNNN.bam are written) @param fnout name of the final output file to be written @param modeout sam_open() mode to be used to create the final output file @param max_mem approxiate maximum memory (very inaccurate) @param in_fmt input file format options @param out_fmt output file format and options @param arg_list command string for PG line @param no_pg if 1, do not add a new PG line @paran write_index create index for the output file @return 0 for successful sorting, negative on errors @discussion It may create multiple temporary subalignment files and then merge them by calling bam_merge_simple(). This function is NOT thread safe. */ int bam_sort_core_ext(SamOrder sam_order, char* sort_tag, int minimiser_kmer, bool try_rev, bool no_squash, const char *fn, const char *prefix, const char *fnout, const char *modeout, size_t _max_mem, int n_threads, const htsFormat *in_fmt, const htsFormat *out_fmt, char *arg_list, int no_pg, int write_index) { int ret = -1, res, i, nref, n_files = 0, n_big_files = 0, fn_counter = 0; size_t max_k, k, max_mem, bam_mem_offset; sam_hdr_t *header = NULL; samFile *fp = NULL; bam1_tag *buf = NULL; template_coordinate_keys_t *keys = NULL; bam1_t *b = bam_init1(); uint8_t *bam_mem = NULL; char **fns = NULL; size_t fns_size = 0; const char *new_so = NULL; const char *new_go = NULL; const char *new_ss = NULL; buf_region *in_mem = NULL; khash_t(const_c2c) *lib_lookup = NULL; htsThreadPool htspool = { NULL, 0 }; int num_in_mem = 0; int large_pos = 0; if (!b) { print_error("sort", "couldn't allocate memory for bam record"); return -1; } if (n_threads < 2) n_threads = 1; g_sam_order = sam_order; if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) { g_sort_tag[0] = sort_tag[0]; g_sort_tag[1] = sort_tag[0] ? sort_tag[1] : '\0'; } if (sam_order == TemplateCoordinate) { if ((keys = malloc(sizeof(template_coordinate_keys_t))) == NULL) { print_error("sort", "could not allocate memory for the top-level keys"); goto err; } keys->n = 0; keys->m = 0; keys->buffer_size = 0x10000; keys->buffers = NULL; } max_mem = _max_mem * n_threads; buf = NULL; fp = sam_open_format(fn, "r", in_fmt); if (fp == NULL) { print_error_errno("sort", "can't open \"%s\"", fn); goto err; } hts_set_opt(fp, HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE); header = sam_hdr_read(fp); if (header == NULL) { print_error("sort", "failed to read header from \"%s\"", fn); goto err; } // Inspect the header looking for long chromosomes // If there is one, we need to write temporary files in SAM format nref = sam_hdr_nref(header); for (i = 0; i < nref; i++) { if (sam_hdr_tid2len(header, i) > INT32_MAX) large_pos = 1; } // Also check the output format is large position compatible if (large_pos) { int compatible = (out_fmt->format == sam || (out_fmt->format == cram && out_fmt->version.major >= 4) || (out_fmt->format == unknown_format && modeout[0] == 'w' && (modeout[1] == 'z' || modeout[1] == '\0'))); if (!compatible) { print_error("sort", "output format is not compatible with very large references"); goto err; } } if (g_sam_order == TemplateCoordinate) { lib_lookup = lookup_libraries(header); if (!lib_lookup) goto err; } switch (g_sam_order) { case Coordinate: new_so = "coordinate"; break; case QueryName: new_so = "queryname"; new_ss = natural_sort ? "queryname:natural" : "queryname:lexicographical"; break; case MinHash: new_so = "coordinate"; new_ss = "coordinate:minhash"; break; case TagQueryName: case TagCoordinate: new_so = "unknown"; break; case TemplateCoordinate: new_so = "unsorted"; new_go = "query"; new_ss = "unsorted:template-coordinate"; break; default: new_so = "unknown"; break; } if (new_ss == NULL && new_go == NULL) { // just SO if ((-1 == sam_hdr_update_hd(header, "SO", new_so)) && (-1 == sam_hdr_add_line(header, "HD", "VN", SAM_FORMAT_VERSION, "SO", new_so, NULL)) ) { print_error("sort", "failed to change sort order header to 'SO:%s'\n", new_so); goto err; } } else if (new_ss != NULL && new_go == NULL) { // update SO and SS, but not GO if ((-1 == sam_hdr_update_hd(header, "SO", new_so, "SS", new_ss)) && (-1 == sam_hdr_add_line(header, "HD", "VN", SAM_FORMAT_VERSION, "SO", new_so, "SS", new_ss, NULL)) ) { print_error("sort", "failed to change sort order header to 'SO:%s SS:%s'\n", new_so, new_ss); goto err; } } else if (new_ss == NULL && new_go != NULL) { // update SO and GO, but not SS if ((-1 == sam_hdr_update_hd(header, "SO", new_so, "GO", new_go)) && (-1 == sam_hdr_add_line(header, "HD", "VN", SAM_FORMAT_VERSION, "SO", new_so, "GO", new_go, NULL)) ) { print_error("sort", "failed to change sort order header to 'SO:%s GO:%s'\n", new_so, new_go); goto err; } } else { // update SO, GO, and SS if ((-1 == sam_hdr_update_hd(header, "SO", new_so, "GO", new_go, "SS", new_ss)) && (-1 == sam_hdr_add_line(header, "HD", "VN", SAM_FORMAT_VERSION, "SO", new_so, "GO", new_go, "SS", new_ss, NULL)) ) { print_error("sort", "failed to change sort order header to 'SO:%s GO:%s SS:%s'\n", new_so, new_go, new_ss); goto err; } } if (new_go == NULL) { if (-1 == sam_hdr_remove_tag_hd(header, "GO")) { print_error("sort", "failed to delete group order in header\n"); goto err; } } if (new_ss == NULL) { if (-1 == sam_hdr_remove_tag_hd(header, "SS")) { print_error("sort", "failed to delete sub sort in header\n"); goto err; } } if (n_threads > 1) { htspool.pool = hts_tpool_init(n_threads); if (!htspool.pool) { print_error_errno("sort", "failed to set up thread pool"); goto err; } hts_set_opt(fp, HTS_OPT_THREAD_POOL, &htspool); } if ((bam_mem = malloc(max_mem)) == NULL) { print_error("sort", "couldn't allocate memory for bam_mem"); goto err; } in_mem = calloc(n_threads > 0 ? n_threads : 1, sizeof(in_mem[0])); if (!in_mem) goto err; // write sub files k = max_k = bam_mem_offset = 0; size_t name_len = strlen(prefix) + 30; while ((res = sam_read1(fp, header, b)) >= 0) { int mem_full = 0; if (k == max_k) { bam1_tag *new_buf; max_k = max_k? max_k<<1 : 0x10000; if ((new_buf = realloc(buf, max_k * sizeof(bam1_tag))) == NULL) { print_error("sort", "couldn't allocate memory for buf"); goto err; } buf = new_buf; } if (sam_order == TemplateCoordinate && k >= keys->m * keys->buffer_size) { if (template_coordinate_keys_realloc(keys, k + 1) == -1) { goto err; } } // Check if the BAM record will fit in the memory limit if (bam_mem_offset + sizeof(*b) + b->l_data < max_mem) { // Copy record into the memory block buf[k].bam_record = (bam1_t *)(bam_mem + bam_mem_offset); *buf[k].bam_record = *b; buf[k].bam_record->data = (uint8_t *)((char *)buf[k].bam_record + sizeof(bam1_t)); memcpy(buf[k].bam_record->data, b->data, b->l_data); // store next BAM record in next 8-byte-aligned address after // current one bam_mem_offset = (bam_mem_offset + sizeof(*b) + b->l_data + 8 - 1) & ~((size_t)(8 - 1)); } else { // Add a pointer to the remaining record buf[k].bam_record = b; mem_full = 1; } // Set the tag if sorting by tag, or the key for template cooridinate sorting switch (g_sam_order) { case TagQueryName: case TagCoordinate: buf[k].u.tag = bam_aux_get(buf[k].bam_record, g_sort_tag); break; case TemplateCoordinate: ++keys->n; template_coordinate_key_t *key = template_coordinate_keys_get(keys, k); buf[k].u.key = template_coordinate_key(buf[k].bam_record, key, header, lib_lookup); if (buf[k].u.key == NULL) goto err; break; default: buf[k].u.tag = NULL; buf[k].u.key = NULL; } ++k; if (mem_full) { if (hts_resize(char *, n_files + 1, &fns_size, &fns, 0) < 0) goto err; int sort_res = sort_blocks(k, buf, header, n_threads, in_mem, large_pos, minimiser_kmer, try_rev, no_squash); if (sort_res < 0) goto err; fns[n_files] = calloc(name_len, 1); if (!fns[n_files]) goto err; const int MAX_TRIES = 1000; int tries = 0, merge_res = -1; char *sort_by_tag = (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) ? sort_tag : NULL; int consolidate_from = n_files; if (n_files - n_big_files >= MAX_TMP_FILES/2) consolidate_from = n_big_files; else if (n_files >= MAX_TMP_FILES) consolidate_from = 0; for (;;) { if (tries) { snprintf(fns[n_files], name_len, "%s.%.4d-%.3d.bam", prefix, fn_counter, tries); } else { snprintf(fns[n_files], name_len, "%s.%.4d.bam", prefix, fn_counter); } if (bam_merge_simple(g_sam_order, sort_by_tag, fns[n_files], large_pos ? "wzx1" : "wbx1", header, n_files - consolidate_from, &fns[consolidate_from], n_threads, in_mem, buf, keys, lib_lookup, &htspool, "sort", NULL, NULL, NULL, 1, 0, 0) >= 0) { merge_res = 0; break; } if (errno == EEXIST && tries < MAX_TRIES) { tries++; } else { break; } } fn_counter++; if (merge_res < 0) { if (errno != EEXIST) unlink(fns[n_files]); free(fns[n_files]); goto err; } if (consolidate_from < n_files) { for (i = consolidate_from; i < n_files; i++) { unlink(fns[i]); free(fns[i]); } fns[consolidate_from] = fns[n_files]; n_files = consolidate_from; n_big_files = consolidate_from + 1; } n_files++; k = 0; if (keys != NULL) keys->n = 0; bam_mem_offset = 0; } } if (res != -1) { print_error("sort", "truncated file. Aborting"); goto err; } // Sort last records if (k > 0) { num_in_mem = sort_blocks(k, buf, header, n_threads, in_mem, large_pos, minimiser_kmer, try_rev, no_squash); if (num_in_mem < 0) goto err; } else { num_in_mem = 0; } // write the final output if (n_files == 0 && num_in_mem < 2) { // a single block if (write_buffer(fnout, modeout, k, buf, header, n_threads, out_fmt, minimiser_kmer, arg_list, no_pg, write_index) != 0) { print_error_errno("sort", "failed to create \"%s\"", fnout); goto err; } } else { // then merge fprintf(stderr, "[bam_sort_core] merging from %d files and %d in-memory blocks...\n", n_files, num_in_mem); // Paranoia check - all temporary files should have a name for (i = 0; i < n_files; ++i) { if (!fns[i]) { print_error("sort", "BUG: no name stored for temporary file %d", i); abort(); } } char *sort_by_tag = (sam_order == TagQueryName || sam_order == TagCoordinate) ? sort_tag : NULL; if (bam_merge_simple(sam_order, sort_by_tag, fnout, modeout, header, n_files, fns, num_in_mem, in_mem, buf, keys, lib_lookup, &htspool, "sort", in_fmt, out_fmt, arg_list, no_pg, write_index, 1) < 0) { // Propagate bam_merge_simple() failure; it has already emitted a // message explaining the failure, so no further message is needed. goto err; } } ret = 0; err: // free if (fns) { for (i = 0; i < n_files; ++i) { if (fns[i]) { unlink(fns[i]); free(fns[i]); } } free(fns); } bam_destroy1(b); free(buf); if (keys != NULL) { for (i = 0; i < keys->m; ++i) { free(keys->buffers[i]); } free(keys->buffers); free(keys); } free(bam_mem); free(in_mem); lib_lookup_destroy(lib_lookup); sam_hdr_destroy(header); if (fp) sam_close(fp); if (htspool.pool) hts_tpool_destroy(htspool.pool); return ret; } // Unused here but may be used by legacy samtools-using third-party code int bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem) { int ret; char *fnout = calloc(strlen(prefix) + 4 + 1, 1); if (!fnout) return -1; sprintf(fnout, "%s.bam", prefix); SamOrder sam_order = is_by_qname ? QueryName : Coordinate; g_sam_order = sam_order; ret = bam_sort_core_ext(sam_order, NULL, 0, false, true, fn, prefix, fnout, "wb", max_mem, 0, NULL, NULL, NULL, 1, 0); free(fnout); return ret; } static void sort_usage(FILE *fp) { fprintf(fp, "Usage: samtools sort [options...] [in.bam]\n" "Options:\n" " -l INT Set compression level, from 0 (uncompressed) to 9 (best)\n" " -u Output uncompressed data (equivalent to -l 0)\n" " -m INT Set maximum memory per thread; suffix K/M/G recognized [768M]\n" " -M Use minimiser for clustering unaligned/unplaced reads\n" " -R Do not use reverse strand (only compatible with -M)\n" " -K INT Kmer size to use for minimiser [20]\n" " -I FILE Order minimisers by their position in FILE FASTA\n" " -w INT Window size for minimiser indexing via -I ref.fa [100]\n" " -H Squash homopolymers when computing minimiser\n" " -n Sort by read name (natural): cannot be used with samtools index\n" " -N Sort by read name (ASCII): cannot be used with samtools index\n" " -t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set)\n" " -o FILE Write final output to FILE rather than standard output\n" " -T PREFIX Write temporary files to PREFIX.nnnn.bam\n" " --no-PG\n" " Do not add a PG line\n" " --template-coordinate\n" " Sort by template-coordinate\n"); sam_global_opt_help(fp, "-.O..@.."); } static void complain_about_memory_setting(size_t max_mem) { char *suffix = ""; const size_t nine_k = 9<<10; if (max_mem > nine_k) { max_mem >>= 10; suffix = "K"; } if (max_mem > nine_k) { max_mem >>= 10; suffix = "M"; } fprintf(stderr, "[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n" "Trying to run with -m too small can lead to the creation of a very large number\n" "of temporary files. This may make sort fail due to it exceeding limits on the\n" "number of files it can have open at the same time.\n\n" "Please check your -m parameter. It should be an integer followed by one of the\n" "letters K (for kilobytes), M (megabytes) or G (gigabytes). You should ensure it\n" "is at least the minimum above, and much higher if you are sorting a large file.\n", max_mem, suffix, SORT_MIN_MEGS_PER_THREAD); } int bam_sort(int argc, char *argv[]) { size_t max_mem = SORT_DEFAULT_MEGS_PER_THREAD << 20; int c, nargs, ret, o_seen = 0, level = -1, no_pg = 0; SamOrder sam_order = Coordinate; bool by_tag = false; int minimiser_kmer = 20; bool try_rev = true; char* sort_tag = NULL, *arg_list = NULL; char *fnout = "-", modeout[12]; kstring_t tmpprefix = { 0, 0, NULL }; struct stat st; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; int window = 100; char *minimiser_ref = NULL; int no_squash = 1; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'), { "threads", required_argument, NULL, '@' }, {"no-PG", no_argument, NULL, 1}, { "template-coordinate", no_argument, NULL, 2}, { NULL, 0, NULL, 0 } }; while ((c = getopt_long(argc, argv, "l:m:nNo:O:T:@:t:MI:K:uRw:H", lopts, NULL)) >= 0) { switch (c) { case 'o': fnout = optarg; o_seen = 1; break; case 'N': natural_sort = 0; // fall through case 'n': sam_order = QueryName; break; case 't': by_tag = true; sort_tag = optarg; break; case 'm': { char *q; max_mem = strtol(optarg, &q, 0); if (*q == 'k' || *q == 'K') max_mem <<= 10; else if (*q == 'm' || *q == 'M') max_mem <<= 20; else if (*q == 'g' || *q == 'G') max_mem <<= 30; break; } case 'T': kputs(optarg, &tmpprefix); break; case 'l': level = atoi(optarg); break; case 'u': level = 0; break; case 1: no_pg = 1; break; case 2: sam_order = TemplateCoordinate; break; case 'M': sam_order = MinHash; break; case 'I': sam_order = MinHash; // implicit option minimiser_ref = optarg; break; case 'H': no_squash = 0; break; case 'w': window = atoi(optarg); break; case 'R': try_rev = false; break; case 'K': minimiser_kmer = atoi(optarg); if (minimiser_kmer < 1) minimiser_kmer = 1; else if (minimiser_kmer > 31) minimiser_kmer = 31; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': sort_usage(stderr); ret = EXIT_FAILURE; goto sort_end; } } if (minimiser_ref) { fprintf(stderr, "Building index ... "); fflush(stderr); if (build_minhash_index(minimiser_ref, minimiser_kmer, window, no_squash)) { ret = EXIT_FAILURE; goto sort_end; } fprintf(stderr, "done\n"); } // Change sort order if tag sorting is requested. Must update based on secondary index if (by_tag) { sam_order = sam_order == QueryName ? TagQueryName : TagCoordinate; } nargs = argc - optind; if (nargs == 0 && isatty(STDIN_FILENO)) { sort_usage(stdout); ret = EXIT_SUCCESS; goto sort_end; } else if (nargs >= 2) { // If exactly two, user probably tried to specify legacy if (nargs == 2) fprintf(stderr, "[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files\n"); sort_usage(stderr); ret = EXIT_FAILURE; goto sort_end; } if (ga.write_index && sam_order != Coordinate) { fprintf(stderr, "[W::bam_sort] Ignoring --write-index as it only works for position sorted files.\n"); ga.write_index = 0; } if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) { print_error("sort", "failed to create arg_list"); return 1; } if (max_mem < (SORT_MIN_MEGS_PER_THREAD << 20)) { complain_about_memory_setting(max_mem); ret = EXIT_FAILURE; goto sort_end; } strcpy(modeout, "wb"); sam_open_mode(modeout+1, fnout, NULL); if (level >= 0) sprintf(strchr(modeout, '\0'), "%d", level < 9? level : 9); if (tmpprefix.l == 0) { if (strcmp(fnout, "-") != 0) { char *idx = strstr(fnout, HTS_IDX_DELIM); kputsn(fnout, idx ? idx - fnout : strlen(fnout), &tmpprefix); kputs(".tmp", &tmpprefix); } else { kputc('.', &tmpprefix); } } if (stat(tmpprefix.s, &st) == 0 && S_ISDIR(st.st_mode)) { unsigned t = ((unsigned) time(NULL)) ^ ((unsigned) clock()); if (tmpprefix.s[tmpprefix.l-1] != '/') kputc('/', &tmpprefix); ksprintf(&tmpprefix, "samtools.%d.%u.tmp", (int) getpid(), t % 10000); } ret = bam_sort_core_ext(sam_order, sort_tag, (sam_order == MinHash) ? minimiser_kmer : 0, try_rev, no_squash, (nargs > 0) ? argv[optind] : "-", tmpprefix.s, fnout, modeout, max_mem, ga.nthreads, &ga.in, &ga.out, arg_list, no_pg, ga.write_index); if (ret >= 0) ret = EXIT_SUCCESS; else { char dummy[4]; // If we failed on opening the input file & it has no .bam/.cram/etc // extension, the user probably tried legacy -o if (ret == -2 && o_seen && nargs > 0 && sam_open_mode(dummy, argv[optind], NULL) < 0) fprintf(stderr, "[bam_sort] Note the argument has been replaced by -T/-o options\n"); ret = EXIT_FAILURE; } #ifdef DEBUG_MINHASH fprintf(stderr, "Missed %.1f%%, dup %.1f%%\n", 100.0*nmis/(ntot+.1), 100.0*ndup/(ntot+.1)); #endif sort_end: free(tmpprefix.s); free(arg_list); sam_global_args_free(&ga); return ret; } pysam-0.23.0/samtools/bam_sort.c.pysam.c000066400000000000000000004073741475062545500201450ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_sort.c -- sorting and merging. Copyright (C) 2008-2024 Genome Research Ltd. Portions copyright (C) 2009-2012 Broad Institute. Author: Heng Li Author: Martin Pollard Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "htslib/ksort.h" #include "htslib/hts_os.h" #include "htslib/khash.h" #include "htslib/klist.h" #include "htslib/kstring.h" #include "htslib/sam.h" #include "htslib/hts_endian.h" #include "htslib/cram.h" #include "htslib/thread_pool.h" #include "sam_opts.h" #include "samtools.h" #include "bedidx.h" #include "bam.h" //#define DEBUG_MINHASH #define BAM_BLOCK_SIZE 2*1024*1024 #define MAX_TMP_FILES 64 // Struct which contains the sorting key for TemplateCoordinate sort. typedef struct { int tid1; int tid2; hts_pos_t pos1; hts_pos_t pos2; bool neg1; bool neg2; const char *library; char *mid; char *name; bool is_upper_of_pair; } template_coordinate_key_t; // Struct to store fixed buffers of template coordinate keys typedef struct { size_t n; // the # of keys stored size_t m; // the # of buffers allocated size_t buffer_size; // # the fixed size of each buffer template_coordinate_key_t **buffers; // the list of buffers } template_coordinate_keys_t; // Gets the idx'th key; does not OOB check static template_coordinate_key_t* template_coordinate_keys_get(template_coordinate_keys_t *keys, size_t idx) { size_t buffer_idx = idx / keys->buffer_size; // the index of the buffer to retrieve in buffer size_t buffer_offset = idx % keys->buffer_size; // the offset into the given buffer to retrieve //assert(buffer_idx < keys->m); //assert(buffer_offset < keys->buffer_size); return &keys->buffers[buffer_idx][buffer_offset]; } // Rellocates the buffers to hold at least max_k entries static int template_coordinate_keys_realloc(template_coordinate_keys_t *keys, int max_k) { size_t cur_m = keys->m; keys->m += 0x100; //assert(keys->m > cur_m); //assert(keys->m * keys->buffer_size >= max_k); if ((keys->buffers = realloc(keys->buffers, keys->m * sizeof(template_coordinate_key_t*))) == NULL) { print_error("sort", "couldn't reallocate memory for template coordinate key buffers"); return -1; } // allocate space for new buffers int j; for (j = cur_m; j < keys->m; ++j) { if ((keys->buffers[j]= malloc(sizeof(template_coordinate_key_t) * keys->buffer_size)) == NULL) { print_error("sort", "couldn't allocate memory for template coordinate key buffer"); return -1; } } return 0; } // Struct which contains the a record, and the pointer to the sort tag (if any) or // a combined ref / position / strand. // Used to speed up sorts (coordinate, by-tag, and template-coordinate). typedef struct bam1_tag { bam1_t *bam_record; union { const uint8_t *tag; uint8_t pos_tid[12]; template_coordinate_key_t *key; } u; } bam1_tag; /* Minimum memory required in megabytes before sort will attempt to run. This is to prevent accidents where failing to use the -m option correctly results in the creation of a temporary file for each read in the input file. Don't forget to update the man page if you change this. */ const size_t SORT_MIN_MEGS_PER_THREAD = 1; /* Default per-thread memory for sort. Must be >= SORT_MIN_MEGS_PER_THREAD. Don't forget to update the man page if you change this. */ const size_t SORT_DEFAULT_MEGS_PER_THREAD = 768; #if !defined(__DARWIN_C_LEVEL) || __DARWIN_C_LEVEL < 900000L #define NEED_MEMSET_PATTERN4 #endif #ifdef NEED_MEMSET_PATTERN4 void memset_pattern4(void *target, const void *pattern, size_t size) { uint32_t* target_iter = target; size_t loops = size/4; size_t i; for (i = 0; i < loops; ++i) { memcpy(target_iter, pattern, 4); ++target_iter; } if (size%4 != 0) memcpy(target_iter, pattern, size%4); } #endif KHASH_INIT(c2c, char*, char*, 1, kh_str_hash_func, kh_str_hash_equal) KHASH_INIT(cset, char*, char, 0, kh_str_hash_func, kh_str_hash_equal) KHASH_MAP_INIT_STR(c2i, int) KHASH_MAP_INIT_STR(const_c2c, char *) #define hdrln_free_char(p) KLIST_INIT(hdrln, char*, hdrln_free_char) static template_coordinate_key_t* template_coordinate_key(bam1_t *b, template_coordinate_key_t *key, sam_hdr_t *hdr, khash_t(const_c2c) *lib_lookup); typedef enum {Coordinate, QueryName, TagCoordinate, TagQueryName, MinHash, TemplateCoordinate} SamOrder; static SamOrder g_sam_order = Coordinate; static int natural_sort = 1; // not ASCII, but alphanumeric: a12b > a7b static char g_sort_tag[2] = {0,0}; #define is_digit(c) ((c)<='9' && (c)>='0') static int strnum_cmp(const char *_a, const char *_b) { if (!natural_sort) return strcmp(_a,_b); const unsigned char *a = (const unsigned char*)_a, *b = (const unsigned char*)_b; const unsigned char *pa = a, *pb = b; while (*pa && *pb) { if (!is_digit(*pa) || !is_digit(*pb)) { if (*pa != *pb) return (int)*pa - (int)*pb; ++pa; ++pb; } else { // skip leading zeros while (*pa == '0') ++pa; while (*pb == '0') ++pb; // skip matching digits while (is_digit(*pa) && *pa == *pb) pa++, pb++; // Now mismatching, so see which ends the number sooner int diff = (int)*pa - (int)*pb; while (is_digit(*pa) && is_digit(*pb)) pa++, pb++; if (is_digit(*pa)) return 1; // pa still going, so larger else if (is_digit(*pb)) return -1; // pb still going, so larger else if (diff) return diff; // same length, so earlier diff } } return *pa? 1 : *pb? -1 : 0; } #define HEAP_EMPTY (UINT64_MAX >> 1) typedef struct { int i; uint32_t tid; uint64_t pos:63, rev:1, idx; bam1_tag entry; } heap1_t; static inline int bam1_cmp_by_tag(const bam1_tag a, const bam1_tag b); static inline int bam1_cmp_by_minhash(const bam1_tag a, const bam1_tag b); static inline int bam1_cmp_template_coordinate(const bam1_tag a, const bam1_tag b); static khash_t(const_c2c) * lookup_libraries(sam_hdr_t *header); static void lib_lookup_destroy(khash_t(const_c2c) *lib_lookup); // Function to compare reads in the heap and determine which one is < the other // Note, unlike the bam1_cmp_by_X functions which return <0, 0, >0 this // is strictly 0 or 1 only. static inline int heap_lt(const heap1_t a, const heap1_t b) { if (!a.entry.bam_record) return 1; if (!b.entry.bam_record) return 0; int t, fa, fb; switch (g_sam_order) { case Coordinate: if (a.tid != b.tid) return a.tid > b.tid; if (a.pos != b.pos) return a.pos > b.pos; if (a.rev != b.rev) return a.rev > b.rev; break; case QueryName: t = strnum_cmp(bam_get_qname(a.entry.bam_record), bam_get_qname(b.entry.bam_record)); if (t != 0) return t > 0; fa = a.entry.bam_record->core.flag; fb = b.entry.bam_record->core.flag; // Sort order is READ1, READ2, (PRIMARY), SUPPLEMENTARY, SECONDARY // Get the bits in this order so sort is a natural a-b fa = ((fa&0xc0)<<8)|((fa&0x100)<<3)|((fa&0x800)>>3); fb = ((fb&0xc0)<<8)|((fb&0x100)<<3)|((fb&0x800)>>3); if (fa != fb) return fa > fb; break; case TagQueryName: case TagCoordinate: t = bam1_cmp_by_tag(a.entry, b.entry); if (t != 0) return t > 0; break; case MinHash: t = bam1_cmp_by_minhash(a.entry, b.entry); if (t != 0) return t > 0; break; case TemplateCoordinate: t = bam1_cmp_template_coordinate(a.entry, b.entry); if (t != 0) return t > 0; break; default: print_error("heap_lt", "unknown sort order: %d", g_sam_order); break; } // This compares by position (i/idx'th read) in the input file(s) if (a.i != b.i) return a.i > b.i; return a.idx > b.idx; } KSORT_INIT(heap, heap1_t, heap_lt) typedef struct merged_header { sam_hdr_t *hdr; kstring_t out_rg; kstring_t out_pg; kstring_t out_co; char **target_name; uint32_t *target_len; size_t n_targets; size_t targets_sz; khash_t(c2i) *sq_tids; khash_t(cset) *rg_ids; khash_t(cset) *pg_ids; bool have_hd; } merged_header_t; typedef struct trans_tbl { int32_t n_targets; int* tid_trans; kh_c2c_t* rg_trans; kh_c2c_t* pg_trans; bool lost_coord_sort; } trans_tbl_t; static void trans_tbl_destroy(trans_tbl_t *tbl) { khiter_t iter; free(tbl->tid_trans); /* * The values for the tbl->rg_trans and tbl->pg_trans hashes are pointers * to keys in the rg_ids and pg_ids sets of the merged_header_t, so * they should not be freed here. * * The keys are unique to each hash entry, so they do have to go. */ for (iter = kh_begin(tbl->rg_trans); iter != kh_end(tbl->rg_trans); ++iter) { if (kh_exist(tbl->rg_trans, iter)) { free(kh_key(tbl->rg_trans, iter)); } } for (iter = kh_begin(tbl->pg_trans); iter != kh_end(tbl->pg_trans); ++iter) { if (kh_exist(tbl->pg_trans, iter)) { free(kh_key(tbl->pg_trans, iter)); } } kh_destroy(c2c,tbl->rg_trans); kh_destroy(c2c,tbl->pg_trans); } /* * Create a merged_header_t struct. */ static merged_header_t * init_merged_header(void) { merged_header_t *merged_hdr; merged_hdr = calloc(1, sizeof(*merged_hdr)); if (merged_hdr == NULL) return NULL; merged_hdr->hdr = sam_hdr_init(); if (!merged_hdr->hdr) goto fail; merged_hdr->targets_sz = 16; merged_hdr->target_name = malloc(merged_hdr->targets_sz * sizeof(*merged_hdr->target_name)); if (NULL == merged_hdr->target_name) goto fail; merged_hdr->target_len = malloc(merged_hdr->targets_sz * sizeof(*merged_hdr->target_len)); if (NULL == merged_hdr->target_len) goto fail; merged_hdr->sq_tids = kh_init(c2i); if (merged_hdr->sq_tids == NULL) goto fail; merged_hdr->rg_ids = kh_init(cset); if (merged_hdr->rg_ids == NULL) goto fail; merged_hdr->pg_ids = kh_init(cset); if (merged_hdr->pg_ids == NULL) goto fail; return merged_hdr; fail: perror("[init_merged_header]"); kh_destroy(cset, merged_hdr->pg_ids); kh_destroy(cset, merged_hdr->rg_ids); kh_destroy(c2i, merged_hdr->sq_tids); free(merged_hdr->target_name); free(merged_hdr->target_len); sam_hdr_destroy(merged_hdr->hdr); free(merged_hdr); return NULL; } /* Some handy kstring manipulating functions */ // Append char range to kstring static inline int range_to_ks(const char *src, int from, int to, kstring_t *dest) { return kputsn(src + from, to - from, dest) != to - from; } // Append a kstring to a kstring static inline int ks_to_ks(kstring_t *src, kstring_t *dest) { return kputsn(ks_str(src), ks_len(src), dest) != ks_len(src); } /* * Generate a unique ID by appending a random suffix to a given prefix. * existing_ids is the set of IDs that are already in use. * If always_add_suffix is true, the suffix will always be included. * If false, prefix will be returned unchanged if it isn't in existing_ids. */ static int gen_unique_id(char *prefix, khash_t(cset) *existing_ids, bool always_add_suffix, kstring_t *dest) { khiter_t iter; if (!always_add_suffix) { // Try prefix on its own first iter = kh_get(cset, existing_ids, prefix); if (iter == kh_end(existing_ids)) { // prefix isn't used yet dest->l = 0; if (kputs(prefix, dest) == EOF) return -1; return 0; } } do { dest->l = 0; ksprintf(dest, "%s-%08lX", prefix, lrand48()); iter = kh_get(cset, existing_ids, ks_str(dest)); } while (iter != kh_end(existing_ids)); return 0; } /* * Add the @HD line to the new header * In practice the @HD line will come from the first input header. */ static int trans_tbl_add_hd(merged_header_t* merged_hdr, sam_hdr_t *translate) { kstring_t hd_line = { 0, 0, NULL }; int res; // TODO: handle case when @HD needs merging. if (merged_hdr->have_hd) return 0; res = sam_hdr_find_hd(translate, &hd_line); if (res < -1) { print_error("merge", "failed to get @HD line from header"); return -1; } if (res < 0) // Not found return 0; if (sam_hdr_add_lines(merged_hdr->hdr, hd_line.s, hd_line.l) < 0) { print_error("merge", "failed to add @HD line to new header"); free(hd_line.s); return -1; } free(hd_line.s); merged_hdr->have_hd = true; return 0; } /* * Add @SQ records to the translation table. * * Go through the target list for the input header. Any new targets found * are added to the output header target list. At the same time, a mapping * from the input to output target ids is stored in tbl. * * If any new targets are found, the header text is scanned to find the * corresponding @SQ records. They are then copied into the * merged_hdr->out_text kstring (which will eventually become the * output header text). * * Returns 0 on success, -1 on failure. */ static int trans_tbl_add_sq(merged_header_t* merged_hdr, sam_hdr_t *translate, trans_tbl_t* tbl) { int32_t i; int min_tid = -1, res; kstring_t sq_line = { 0, 0, NULL }, sq_sn = { 0, 0, NULL }; // Fill in the tid part of the translation table, adding new targets // to the merged header as we go. for (i = 0; i < sam_hdr_nref(translate); ++i) { int trans_tid; sq_sn.l = 0; res = sam_hdr_find_tag_pos(translate, "SQ", i, "SN", &sq_sn); if (res < 0) { print_error("merge", "failed to get @SQ SN #%d from header", i + 1); goto fail; } trans_tid = sam_hdr_name2tid(merged_hdr->hdr, sq_sn.s); if (trans_tid < -1) { print_error("merge", "failed to lookup ref"); goto fail; } if (trans_tid < 0) { // Append missing entries to out_hdr sq_line.l = 0; res = sam_hdr_find_line_id(translate, "SQ", "SN", sq_sn.s, &sq_line); if (res < 0) { print_error("merge", "failed to get @SQ SN:%s from header", sq_sn.s); goto fail; } trans_tid = sam_hdr_nref(merged_hdr->hdr); res = sam_hdr_add_lines(merged_hdr->hdr, sq_line.s, sq_line.l); if (res < 0) { print_error("merge", "failed to add @SQ SN:%s to new header", sq_sn.s); goto fail; } } tbl->tid_trans[i] = trans_tid; if (tbl->tid_trans[i] > min_tid) { min_tid = tbl->tid_trans[i]; } else { tbl->lost_coord_sort = true; } } free(sq_line.s); free(sq_sn.s); return 0; fail: free(sq_line.s); free(sq_sn.s); return -1; } /* * Common code for setting up RG and PG record ID tag translation. * * is_rg is true for RG translation, false for PG. * translate is the input bam header * merge is true if tags with the same ID are to be merged. * known_ids is the set of IDs already in the output header. * id_map is the translation map from input header IDs to output header IDs * If override is set, it will be used to replace the existing ID (RG only) * * known_ids and id_map have entries for the new IDs added to them. * * Return value is a linked list of header lines with the translated IDs, * or NULL if something went wrong (probably out of memory). * */ static klist_t(hdrln) * trans_rg_pg(bool is_rg, sam_hdr_t *translate, bool merge, khash_t(cset)* known_ids, khash_t(c2c)* id_map, char *override) { khiter_t iter; int num_ids, i; const char *rec_type = is_rg ? "RG" : "PG"; klist_t(hdrln) *hdr_lines; hdr_lines = kl_init(hdrln); // Search through translate's header num_ids = sam_hdr_count_lines(translate, rec_type); if (num_ids < 0) goto fail; for (i = 0; i < num_ids; i++) { kstring_t orig_id = { 0, 0, NULL }; // ID in original header kstring_t transformed_id = { 0, 0, NULL }; // ID in output header char *map_value; // Value to store in id_map bool id_changed; // Have we changed the ID? bool not_found_in_output; // ID isn't in the output header (yet) if (sam_hdr_find_tag_pos(translate, rec_type, i, "ID", &orig_id) < 0) goto fail; // is our matched ID in our output ID set already? iter = kh_get(cset, known_ids, ks_str(&orig_id)); not_found_in_output = (iter == kh_end(known_ids)); if (override) { // Override original ID (RG only) #ifdef OVERRIDE_DOES_NOT_MERGE if (gen_unique_id(override, known_ids, false, &transformed_id)) goto memfail; not_found_in_output = true; // As ID now unique #else if (kputs(override, &transformed_id) == EOF) goto memfail; // Know about override already? iter = kh_get(cset, known_ids, ks_str(&transformed_id)); not_found_in_output = (iter == kh_end(known_ids)); #endif id_changed = true; } else { if ( not_found_in_output || merge) { // Not in there or merging so can add it as 1-1 mapping if (ks_to_ks(&orig_id, &transformed_id)) goto memfail; id_changed = false; } else { // It's in there so we need to transform it by appending // a random number to the id if (gen_unique_id(ks_str(&orig_id), known_ids, true, &transformed_id)) goto memfail; id_changed = true; not_found_in_output = true; // As ID now unique } } // Does this line need to go into our output header? if (not_found_in_output) { // Take matched line and replace ID with transformed_id kstring_t new_hdr_line = { 0, 0, NULL }; if (sam_hdr_find_line_id(translate, rec_type, "ID", ks_str(&orig_id), &new_hdr_line) < 0){ goto fail; } if (id_changed) { char *idp = strstr(ks_str(&new_hdr_line), "\tID:"), *id_end; ptrdiff_t id_offset, id_len; if (!idp) { print_error("merge", "failed to find ID in \"%s\"\n", ks_str(&new_hdr_line)); goto fail; } idp += 4; for (id_end = idp; *id_end >= '\n'; id_end++) {} id_offset = idp - new_hdr_line.s; id_len = id_end - idp; if (id_len < transformed_id.l) { if (ks_resize(&new_hdr_line, new_hdr_line.l + transformed_id.l - id_len + 1/*nul*/)) goto fail; } if (id_len != transformed_id.l) { memmove(new_hdr_line.s + id_offset + transformed_id.l, new_hdr_line.s + id_offset + id_len, new_hdr_line.l - id_offset - id_len + 1); } memcpy(new_hdr_line.s + id_offset, transformed_id.s, transformed_id.l); } // append line to output linked list char** ln = kl_pushp(hdrln, hdr_lines); *ln = ks_release(&new_hdr_line); // Give away to linked list // Need to add it to known_ids set int in_there = 0; iter = kh_put(cset, known_ids, ks_str(&transformed_id), &in_there); if (in_there < 0) goto memfail; assert(in_there > 0); // Should not already be in the map map_value = ks_release(&transformed_id); } else { // Use existing string in id_map assert(kh_exist(known_ids, iter)); map_value = kh_key(known_ids, iter); free(ks_release(&transformed_id)); } // Insert it into our translation map int in_there = 0; iter = kh_put(c2c, id_map, ks_release(&orig_id), &in_there); kh_value(id_map, iter) = map_value; } // If there are no RG lines in the file and we are overriding add one if (is_rg && override && hdr_lines->size == 0) { kstring_t new_id = {0, 0, NULL}; kstring_t line = {0, 0, NULL}; kstring_t empty = {0, 0, NULL}; int in_there = 0; char** ln; // Get the new ID if (gen_unique_id(override, known_ids, false, &new_id)) goto memfail; // Make into a header line and add to linked list ksprintf(&line, "@RG\tID:%s", ks_str(&new_id)); ln = kl_pushp(hdrln, hdr_lines); *ln = ks_release(&line); // Put into known_ids set iter = kh_put(cset, known_ids, ks_str(&new_id), &in_there); if (in_there < 0) goto memfail; assert(in_there > 0); // Should be a new entry // Put into translation map (key is empty string) if (kputs("", &empty) == EOF) goto memfail; iter = kh_put(c2c, id_map, ks_release(&empty), &in_there); if (in_there < 0) goto memfail; assert(in_there > 0); // Should be a new entry kh_value(id_map, iter) = ks_release(&new_id); } return hdr_lines; memfail: perror(__func__); fail: if (hdr_lines) kl_destroy(hdrln, hdr_lines); return NULL; } /* * Common code for completing RG and PG record translation. * * Input is a list of header lines, and the mapping from input to * output @PG record IDs. * * RG and PG records can contain tags that cross-reference to other @PG * records. This fixes the tags to contain the new IDs before adding * them to the output header text. */ static int finish_rg_pg(bool is_rg, klist_t(hdrln) *hdr_lines, khash_t(c2c)* pg_map, kstring_t *out_text) { const char *search = is_rg ? "\tPG:" : "\tPP:"; khiter_t idx; char *line = NULL; while ((kl_shift(hdrln, hdr_lines, &line)) == 0) { char *id = strstr(line, search); // Look for tag to fix int pos1 = 0, pos2 = 0; char *new_id = NULL; if (id) { // Found a tag. Look up the value in the translation map // to see what it should be changed to in the output file. char *end, tmp; id += 4; // Point to value end = strchr(id, '\t'); // Find end of tag if (!end) end = id + strlen(id); tmp = *end; *end = '\0'; // Temporarily get the value on its own. // Look-up in translation table idx = kh_get(c2c, pg_map, id); if (idx == kh_end(pg_map)) { // Not found, warn. fprintf(samtools_stderr, "[W::%s] Tag %s%s not found in @PG records\n", __func__, search + 1, id); } else { // Remember new id and splice points on original string new_id = kh_value(pg_map, idx); pos1 = id - line; pos2 = end - line; } *end = tmp; // Restore string } // Copy line to output: // line[0..pos1), new_id (if not NULL), line[pos2..end), '\n' if (pos1 && range_to_ks(line, 0, pos1, out_text)) goto memfail; if (new_id && kputs(new_id, out_text) == EOF) goto memfail; if (kputs(line + pos2, out_text) == EOF) goto memfail; if (kputc('\n', out_text) == EOF) goto memfail; free(line); // No longer needed line = NULL; } return 0; memfail: perror(__func__); free(line); // Prevent leakage as no longer on list return -1; } /* * Build the translation table for an input *am file. This stores mappings * which allow IDs to be converted from those used in the input file * to the ones which will be used in the output. The mappings are for: * Reference sequence IDs (for @SQ records) * @RG record ID tags * @PG record ID tags * * At the same time, new header text is built up by copying records * from the input bam file. This will eventually become the header for * the output file. When copied, the ID tags for @RG and @PG records * are replaced with their values. The @PG PP: and @RG PG: tags * are also modified if necessary. * * merged_hdr holds state on the output header (which IDs are present, etc.) * translate is the input header * tbl is the translation table that gets filled in. * merge_rg controls merging of @RG records * merge_pg controls merging of @PG records * If rg_override is not NULL, it will be used to replace the existing @RG ID * * Returns 0 on success, -1 on failure. */ static int trans_tbl_init(merged_header_t* merged_hdr, sam_hdr_t* translate, trans_tbl_t* tbl, bool merge_rg, bool merge_pg, bool copy_co, char* rg_override) { kstring_t lines = { 0, 0, NULL }; klist_t(hdrln) *rg_list = NULL; klist_t(hdrln) *pg_list = NULL; tbl->n_targets = sam_hdr_nref(translate); tbl->rg_trans = tbl->pg_trans = NULL; tbl->tid_trans = (int*)calloc(tbl->n_targets ? tbl->n_targets : 1, sizeof(int)); if (tbl->tid_trans == NULL) goto memfail; tbl->rg_trans = kh_init(c2c); if (tbl->rg_trans == NULL) goto memfail; tbl->pg_trans = kh_init(c2c); if (tbl->pg_trans == NULL) goto memfail; tbl->lost_coord_sort = false; // Get the @HD record (if not there already). if (trans_tbl_add_hd(merged_hdr, translate)) goto fail; // Fill in map and add header lines for @SQ records if (trans_tbl_add_sq(merged_hdr, translate, tbl)) goto fail; // Get translated header lines and fill in map for @RG records rg_list = trans_rg_pg(true, translate, merge_rg, merged_hdr->rg_ids, tbl->rg_trans, rg_override); if (!rg_list) goto fail; // Get translated header lines and fill in map for @PG records pg_list = trans_rg_pg(false, translate, merge_pg, merged_hdr->pg_ids, tbl->pg_trans, NULL); if (!pg_list) goto fail; // Fix-up PG: tags in the new @RG records and add to output if (finish_rg_pg(true, rg_list, tbl->pg_trans, &merged_hdr->out_rg)) goto fail; // Fix-up PP: tags in the new @PG records and add to output lines.l = 0; if (finish_rg_pg(false, pg_list, tbl->pg_trans, &merged_hdr->out_pg)) goto fail; kl_destroy(hdrln, rg_list); rg_list = NULL; kl_destroy(hdrln, pg_list); pg_list = NULL; if (copy_co) { // Just append @CO headers without translation int num_co = sam_hdr_count_lines(translate, "CO"), i; if (num_co < 0) goto fail; for (i = 0; i < num_co; i++) { if (sam_hdr_find_line_pos(translate, "CO", i, &lines) < 0) goto fail; if (ks_to_ks(&lines, &merged_hdr->out_co)) goto fail; if (kputc('\n', &merged_hdr->out_co) < 0) goto fail; } } free(lines.s); return 0; memfail: perror(__func__); fail: trans_tbl_destroy(tbl); if (rg_list) kl_destroy(hdrln, rg_list); if (pg_list) kl_destroy(hdrln, pg_list); free(lines.s); return -1; } static int finish_merged_header(merged_header_t *merged_hdr) { if (sam_hdr_add_lines(merged_hdr->hdr, ks_c_str(&merged_hdr->out_rg), ks_len(&merged_hdr->out_rg)) < 0) return -1; if (sam_hdr_add_lines(merged_hdr->hdr, ks_c_str(&merged_hdr->out_pg), ks_len(&merged_hdr->out_pg)) < 0) return -1; if (sam_hdr_add_lines(merged_hdr->hdr, ks_c_str(&merged_hdr->out_co), ks_len(&merged_hdr->out_co)) < 0) return -1; return 0; } /* * Free a merged_header_t struct and all associated data. * * Note that the keys to the rg_ids and pg_ids sets are also used as * values in the translation tables. This function should therefore not * be called until the translation tables are no longer needed. */ static void free_merged_header(merged_header_t *merged_hdr) { size_t i; khiter_t iter; if (!merged_hdr) return; free(ks_release(&merged_hdr->out_rg)); free(ks_release(&merged_hdr->out_pg)); free(ks_release(&merged_hdr->out_co)); if (merged_hdr->target_name) { for (i = 0; i < merged_hdr->n_targets; i++) { free(merged_hdr->target_name[i]); } free(merged_hdr->target_name); } free(merged_hdr->target_len); kh_destroy(c2i, merged_hdr->sq_tids); if (merged_hdr->rg_ids) { for (iter = kh_begin(merged_hdr->rg_ids); iter != kh_end(merged_hdr->rg_ids); ++iter) { if (kh_exist(merged_hdr->rg_ids, iter)) free(kh_key(merged_hdr->rg_ids, iter)); } kh_destroy(cset, merged_hdr->rg_ids); } if (merged_hdr->pg_ids) { for (iter = kh_begin(merged_hdr->pg_ids); iter != kh_end(merged_hdr->pg_ids); ++iter) { if (kh_exist(merged_hdr->pg_ids, iter)) free(kh_key(merged_hdr->pg_ids, iter)); } kh_destroy(cset, merged_hdr->pg_ids); } free(merged_hdr); } static void bam_translate(bam1_t* b, trans_tbl_t* tbl) { // Update target id if not unmapped tid if ( b->core.tid >= 0 ) { b->core.tid = tbl->tid_trans[b->core.tid]; } if ( b->core.mtid >= 0 ) { b->core.mtid = tbl->tid_trans[b->core.mtid]; } // If we have a RG update it uint8_t *rg = bam_aux_get(b, "RG"); if (rg) { char* decoded_rg = bam_aux2Z(rg); khiter_t k = kh_get(c2c, tbl->rg_trans, decoded_rg); if (k != kh_end(tbl->rg_trans)) { char* translate_rg = kh_value(tbl->rg_trans,k); bam_aux_del(b, rg); if (translate_rg) { bam_aux_append(b, "RG", 'Z', strlen(translate_rg) + 1, (uint8_t*)translate_rg); } } else { char *tmp = strdup(decoded_rg); fprintf(samtools_stderr, "[bam_translate] RG tag \"%s\" on read \"%s\" encountered " "with no corresponding entry in header, tag lost. " "Unknown tags are only reported once per input file for " "each tag ID.\n", decoded_rg, bam_get_qname(b)); bam_aux_del(b, rg); // Prevent future whinges if (tmp) { int in_there = 0; k = kh_put(c2c, tbl->rg_trans, tmp, &in_there); if (in_there > 0) kh_value(tbl->rg_trans, k) = NULL; } } } // If we have a PG update it uint8_t *pg = bam_aux_get(b, "PG"); if (pg) { char* decoded_pg = bam_aux2Z(pg); khiter_t k = kh_get(c2c, tbl->pg_trans, decoded_pg); if (k != kh_end(tbl->pg_trans)) { char* translate_pg = kh_value(tbl->pg_trans,k); bam_aux_del(b, pg); if (translate_pg) { bam_aux_append(b, "PG", 'Z', strlen(translate_pg) + 1, (uint8_t*)translate_pg); } } else { char *tmp = strdup(decoded_pg); fprintf(samtools_stderr, "[bam_translate] PG tag \"%s\" on read \"%s\" encountered " "with no corresponding entry in header, tag lost. " "Unknown tags are only reported once per input file for " "each tag ID.\n", decoded_pg, bam_get_qname(b)); bam_aux_del(b, pg); // Prevent future whinges if (tmp) { int in_there = 0; k = kh_put(c2c, tbl->pg_trans, tmp, &in_there); if (in_there > 0) kh_value(tbl->pg_trans, k) = NULL; } } } } int* rtrans_build(int n, int n_targets, trans_tbl_t* translation_tbl) { // Create reverse translation table for tids int* rtrans = (int*)malloc(sizeof(int32_t)*n*n_targets); const int32_t NOTID = INT32_MIN; if (!rtrans) return NULL; memset_pattern4((void*)rtrans, &NOTID, sizeof(int32_t)*n*n_targets); int i; for (i = 0; i < n; ++i) { int j; for (j = 0; j < (translation_tbl+i)->n_targets; ++j) { if ((translation_tbl+i)->tid_trans[j] != -1) { rtrans[i*n_targets + (translation_tbl+i)->tid_trans[j]] = j; } } } return rtrans; } #define MERGE_RG 1 // Attach RG tag based on filename #define MERGE_UNCOMP 2 // Generate uncompressed BAM #define MERGE_LEVEL1 4 // Compress the BAM at level 1 (fast) mode #define MERGE_FORCE 8 // Overwrite output BAM if it exists #define MERGE_COMBINE_RG 16 // Combine RG tags frather than redefining them #define MERGE_COMBINE_PG 32 // Combine PG tags frather than redefining them #define MERGE_FIRST_CO 64 // Use only first file's @CO headers (sort cmd only) static hts_reglist_t *duplicate_reglist(const hts_reglist_t *rl, int rn) { if (!rl) return NULL; hts_reglist_t *new_rl = calloc(rn, sizeof(hts_reglist_t)); if (!new_rl) return NULL; int i; for (i=0; i < rn; i++) { new_rl[i].tid = rl[i].tid; new_rl[i].count = rl[i].count; new_rl[i].min_beg = rl[i].min_beg; new_rl[i].max_end = rl[i].max_end; new_rl[i].reg = rl[i].reg; new_rl[i].intervals = malloc(new_rl[i].count * sizeof(hts_pair_pos_t)); if (!new_rl[i].intervals) { hts_reglist_free(new_rl, i); return NULL; } memcpy(new_rl[i].intervals, rl[i].intervals, new_rl[i].count * sizeof(hts_pair_pos_t)); } return new_rl; } /* * How merging is handled * * If a header is defined use we will use that as our output header * otherwise we use the first header from the first input file. * * Now go through each file and create a translation table for that file for: * -RG * -tid * -PG tags * * Then whenever we read a record from a bam we translate that read before * stashing it in the hash. * * In the actual merge, a read is read from each input file, translated and * stashed in the hash. This assumes that all input files are sorted in the * same way. Next we just extract the next position ordered read from the * hash, and replace it if there are still reads left in it's source input * file. Finally we write our chosen read it to the output file. */ /*! @abstract Merge multiple sorted BAM. @param sam_order the order in which the data was sorted @param sort_tag if non-null, the tag that data was sorted by @param out output BAM file name @param mode sam_open() mode to be used to create the final output file (overrides level settings from UNCOMP and LEVEL1 flags) @param headers name of SAM file from which to copy '@' header lines, or NULL to copy them from the first file to be merged @param n number of files to be merged @param fn names of files to be merged @param flag flags that control how the merge is undertaken @param reg region to merge @param n_threads number of threads to use (passed to htslib) @param cmd command name (used in print_error() etc) @param in_fmt format options for input files @param out_fmt output file format and options @param write_index create the index, together with the output file @param arg_list command string for PG line @param no_pg if 1, do not add a new PG line @discussion Padding information may NOT correctly maintained. This function is NOT thread safe. */ int bam_merge_core2(SamOrder sam_order, char* sort_tag, const char *out, const char *mode, const char *headers, int n, char * const *fn, char * const *fn_idx, const char *fn_bed, int flag, const char *reg, int n_threads, const char *cmd, const htsFormat *in_fmt, const htsFormat *out_fmt, int write_index, char *arg_list, int no_pg) { samFile *fpout, **fp = NULL; heap1_t *heap = NULL; sam_hdr_t *hout = NULL; sam_hdr_t *hin = NULL; int i, j, *RG_len = NULL; uint64_t idx = 0; char **RG = NULL; hts_itr_t **iter = NULL; sam_hdr_t **hdr = NULL; trans_tbl_t *translation_tbl = NULL; int *rtrans = NULL; char *out_idx_fn = NULL; void *hreg = NULL; hts_reglist_t *lreg = NULL; merged_header_t *merged_hdr = init_merged_header(); if (!merged_hdr) return -1; refs_t *refs = NULL; template_coordinate_keys_t *keys = NULL; khash_t(const_c2c) *lib_lookup = NULL; // Is there a specified pre-prepared header to use for output? if (headers) { samFile* fpheaders = sam_open(headers, "r"); if (fpheaders == NULL) { print_error_errno(cmd, "cannot open \"%s\"", headers); return -1; } hin = sam_hdr_read(fpheaders); sam_close(fpheaders); if (hin == NULL) { print_error(cmd, "couldn't read headers from \"%s\"", headers); goto mem_fail; } } g_sam_order = sam_order; if (sam_order == TagQueryName || sam_order == TagCoordinate) { g_sort_tag[0] = sort_tag[0]; g_sort_tag[1] = sort_tag[0] ? sort_tag[1] : '\0'; } fp = (samFile**)calloc(n, sizeof(samFile*)); if (!fp) goto mem_fail; heap = (heap1_t*)calloc(n, sizeof(heap1_t)); if (!heap) goto mem_fail; iter = (hts_itr_t**)calloc(n, sizeof(hts_itr_t*)); if (!iter) goto mem_fail; hdr = (sam_hdr_t**)calloc(n, sizeof(sam_hdr_t*)); if (!hdr) goto mem_fail; translation_tbl = (trans_tbl_t*)calloc(n, sizeof(trans_tbl_t)); if (!translation_tbl) goto mem_fail; RG = (char**)calloc(n, sizeof(char*)); if (!RG) goto mem_fail; // prepare RG tag from file names if (flag & MERGE_RG) { RG_len = (int*)calloc(n, sizeof(int)); if (!RG_len) goto mem_fail; for (i = 0; i != n; ++i) { int l = strlen(fn[i]); const char *s = fn[i]; if (l > 4 && (strcmp(s + l - 4, ".bam") == 0 || strcmp(s + l - 4, ".sam") == 0)) l -= 4; if (l > 5 && strcmp(s + l - 5, ".cram") == 0) l -= 5; for (j = l - 1; j >= 0; --j) if (s[j] == '/') break; ++j; l -= j; RG[i] = (char*)calloc(l + 1, 1); if (!RG[i]) goto mem_fail; RG_len[i] = l; strncpy(RG[i], s + j, l); } } if (hin) { // Populate merged_hdr from the pre-prepared header trans_tbl_t dummy; int res; res = trans_tbl_init(merged_hdr, hin, &dummy, flag & MERGE_COMBINE_RG, flag & MERGE_COMBINE_PG, true, NULL); trans_tbl_destroy(&dummy); if (res) return -1; // FIXME: memory leak } // open and read the header from each file for (i = 0; i < n; ++i) { sam_hdr_t *hin; fp[i] = sam_open_format(fn[i], "r", in_fmt); if (fp[i] == NULL) { print_error_errno(cmd, "fail to open \"%s\"", fn[i]); goto fail; } hts_set_opt(fp[i], HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE); hin = sam_hdr_read(fp[i]); if (hin == NULL) { print_error(cmd, "failed to read header from \"%s\"", fn[i]); goto fail; } if (trans_tbl_init(merged_hdr, hin, translation_tbl+i, flag & MERGE_COMBINE_RG, flag & MERGE_COMBINE_PG, (flag & MERGE_FIRST_CO)? (i == 0) : true, RG[i])) goto fail; hdr[i] = hin; int order_ok = 1; if ((translation_tbl+i)->lost_coord_sort && (sam_order == Coordinate || sam_order == MinHash)) { fprintf(samtools_stderr, "[bam_merge_core] Order of targets in file %s caused coordinate sort to be lost\n", fn[i]); order_ok = 0; } if (!refs) refs = cram_get_refs(fp[i]); if (order_ok && refs && hts_set_opt(fp[i], CRAM_OPT_SHARED_REF, refs)) goto fail; } // Did we get an @HD line? if (!merged_hdr->have_hd) { fprintf(samtools_stderr, "[W::%s] No @HD tag found.\n", __func__); /* FIXME: Should we add an @HD line here, and if so what should we put in it? Ideally we want a way of getting htslib to tell us the SAM version number to assume given no @HD line. Is it also safe to assume that the output is coordinate sorted? SO: is optional so we don't have to have it.*/ /* ksprintf(&merged_hdr->out_hd, "@HD\tVN:1.5\tSO:coordinate\n"); */ } // Transform the header into standard form if (finish_merged_header(merged_hdr) < 0) goto fail; hout = merged_hdr->hdr; if (!hout) goto fail; // If we're only merging a specified region move our iters to start at that point int tid, nreg; hts_pos_t beg, end; if (fn_bed) { hreg = bed_read(fn_bed); if (!hreg) { fprintf(samtools_stderr, "[%s] Could not read BED file: \"%s\"\n", __func__, fn_bed); goto fail; } bed_unify(hreg); lreg = bed_reglist(hreg, ALL, &nreg); if (!lreg || !nreg) { fprintf(samtools_stderr, "[%s] Null or empty region list\n", __func__); goto fail; } } else if (reg) { rtrans = rtrans_build(n, sam_hdr_nref(hout), translation_tbl); if (!rtrans) goto mem_fail; if (!sam_parse_region(hout, reg, &tid, &beg, &end, 0)) { fprintf(samtools_stderr, "[%s] Badly formatted region or unknown reference name: \"%s\"\n", __func__, reg); goto fail; } } if (reg || fn_bed) { hts_idx_t *reg_idx = NULL; for (i = 0; i < n; ++i) { // If index filename has not been specified, look in the BAM folder if (fn_idx != NULL) { reg_idx = sam_index_load2(fp[i], fn[i], fn_idx[i]); } else { reg_idx = sam_index_load(fp[i], fn[i]); } if (reg_idx == NULL) { fprintf(samtools_stderr, "[%s] failed to load index for %s. Random alignment retrieval only works for indexed BAM or CRAM files.\n", __func__, fn[i]); free(rtrans); rtrans = NULL; goto fail; } int mapped_tid = INT32_MIN; if (fn_bed) { hts_reglist_t *rl = duplicate_reglist(lreg, nreg); iter[i] = sam_itr_regions(reg_idx, hdr[i], rl, nreg); } else { // (rtrans[i*n+tid]) Look up what hout tid translates to in input tid space mapped_tid = rtrans[i*sam_hdr_nref(hout)+tid]; if (mapped_tid != INT32_MIN) { iter[i] = sam_itr_queryi(reg_idx, mapped_tid, beg, end); } else { iter[i] = sam_itr_queryi(reg_idx, HTS_IDX_NONE, 0, 0); } } if (iter[i] == NULL) { if (fn_bed) { fprintf(samtools_stderr, "[%s] failed to get multi-region iterator " "{%s, %s}\n", __func__, fn[i], fn_bed); } else { if (mapped_tid != INT32_MIN) { fprintf(samtools_stderr, "[%s] failed to get iterator over " "{%s, %d, %"PRIhts_pos", %"PRIhts_pos"}\n", __func__, fn[i], mapped_tid, beg, end); } else { fprintf(samtools_stderr, "[%s] failed to get iterator over " "{%s, HTS_IDX_NONE, 0, 0}\n", __func__, fn[i]); } } hts_idx_destroy(reg_idx); free(rtrans); rtrans = NULL; goto fail; } hts_idx_destroy(reg_idx); } free(rtrans); rtrans = NULL; } // Make sure that there's enough memory for template coordinate keys, one per file to read if (sam_order == TemplateCoordinate) { if ((keys = malloc(sizeof(template_coordinate_keys_t))) == NULL) { print_error(cmd, "could not allocate memory for the top-level keys"); goto mem_fail; } keys->n = 0; keys->m = 0; keys->buffer_size = 0x10000; keys->buffers = NULL; // Make sure that there's enough memory for template coordinate keys, one per file to read if (keys->n + n >= keys->m * keys->buffer_size) { if (template_coordinate_keys_realloc(keys, keys->n + n) < 0) goto mem_fail; } lib_lookup = lookup_libraries(hout); if (!lib_lookup) { goto mem_fail; } } // Load the first read from each file into the heap for (i = 0; i < n; ++i) { heap1_t *h = heap + i; int res; h->i = i; h->entry.bam_record = bam_init1(); h->entry.u.tag = NULL; if (!h->entry.bam_record) goto mem_fail; res = iter[i] ? sam_itr_next(fp[i], iter[i], h->entry.bam_record) : sam_read1(fp[i], hdr[i], h->entry.bam_record); if (res >= 0) { bam_translate(h->entry.bam_record, translation_tbl + i); h->tid = h->entry.bam_record->core.tid; h->pos = (uint64_t)(h->entry.bam_record->core.pos + 1); h->rev = bam_is_rev(h->entry.bam_record); h->idx = idx++; if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) { h->entry.u.tag = bam_aux_get(h->entry.bam_record, g_sort_tag); } else if (g_sam_order == TemplateCoordinate) { template_coordinate_key_t *key = template_coordinate_keys_get(keys, i); // get the next key to use h->entry.u.key = template_coordinate_key(h->entry.bam_record, key, hout, lib_lookup); // update the key if (h->entry.u.key == NULL) goto fail; // key could not be created, error out } else { h->entry.u.tag = NULL; } } else if (res == -1 && (!iter[i] || iter[i]->finished)) { h->pos = HEAP_EMPTY; bam_destroy1(h->entry.bam_record); h->entry.bam_record = NULL; h->entry.u.tag = NULL; h->entry.u.key = NULL; } else { print_error(cmd, "failed to read first record from \"%s\"", fn[i]); goto fail; } } // Open output file and write header if ((fpout = sam_open_format(out, mode, out_fmt)) == 0) { print_error_errno(cmd, "failed to create \"%s\"", out); return -1; } hts_set_opt(fpout, HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE); if (!no_pg && sam_hdr_add_pg(hout, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { print_error(cmd, "failed to add PG line to the header of \"%s\"", out); sam_close(fpout); return -1; } if (sam_hdr_write(fpout, hout) != 0) { print_error_errno(cmd, "failed to write header to \"%s\"", out); sam_close(fpout); return -1; } if (write_index) { if (!(out_idx_fn = auto_index(fpout, out, hout))){ sam_close(fpout); return -1; } } if (!(flag & MERGE_UNCOMP)) hts_set_threads(fpout, n_threads); if (refs && hts_set_opt(fpout, CRAM_OPT_SHARED_REF, refs)) goto fail; // Begin the actual merge ks_heapmake(heap, n, heap); while (heap->pos != HEAP_EMPTY) { bam1_t *b = heap->entry.bam_record; if (flag & MERGE_RG) { uint8_t *rg = bam_aux_get(b, "RG"); if (rg) bam_aux_del(b, rg); bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]); } if (sam_write1(fpout, hout, b) < 0) { print_error_errno(cmd, "failed writing to \"%s\"", out); sam_close(fpout); free(out_idx_fn); return -1; } if ((j = (iter[heap->i]? sam_itr_next(fp[heap->i], iter[heap->i], b) : sam_read1(fp[heap->i], hdr[heap->i], b))) >= 0) { bam_translate(b, translation_tbl + heap->i); heap->tid = b->core.tid; heap->pos = (uint64_t)(b->core.pos + 1); heap->rev = bam_is_rev(b); heap->idx = idx++; if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) { heap->entry.u.tag = bam_aux_get(heap->entry.bam_record, g_sort_tag); } else if (g_sam_order == TemplateCoordinate) { template_coordinate_key_t *key = template_coordinate_keys_get(keys, heap->i); // get the next key to use heap->entry.u.key = template_coordinate_key(heap->entry.bam_record, key, hout, lib_lookup); // update the key if (heap->entry.u.key == NULL) goto fail; // key could not be created, error out } else { heap->entry.u.tag = NULL; } } else if (j == -1 && (!iter[heap->i] || iter[heap->i]->finished)) { heap->pos = HEAP_EMPTY; bam_destroy1(heap->entry.bam_record); heap->entry.bam_record = NULL; heap->entry.u.tag = NULL; } else { print_error(cmd, "\"%s\" is truncated", fn[heap->i]); goto fail; } ks_heapadjust(heap, 0, n, heap); } if (write_index) { if (sam_idx_save(fpout) < 0) { print_error_errno("merge", "writing index failed"); goto fail; } } free(out_idx_fn); // Clean up and close if (flag & MERGE_RG) { for (i = 0; i != n; ++i) free(RG[i]); free(RG_len); } for (i = 0; i < n; ++i) { trans_tbl_destroy(translation_tbl + i); hts_itr_destroy(iter[i]); sam_hdr_destroy(hdr[i]); sam_close(fp[i]); } sam_hdr_destroy(hin); sam_hdr_destroy(hout); free_merged_header(merged_hdr); hts_reglist_free(lreg, nreg); bed_destroy(hreg); free(RG); free(translation_tbl); free(fp); free(heap); free(iter); free(hdr); if (sam_close(fpout) < 0) { print_error_errno(cmd, "error closing output file \"%s\"", out); return -1; } if (keys != NULL) { for (i = 0; i < keys->m; ++i) { free(keys->buffers[i]); } free(keys->buffers); free(keys); } lib_lookup_destroy(lib_lookup); return 0; mem_fail: print_error(cmd, "Out of memory"); fail: if (flag & MERGE_RG) { if (RG) { for (i = 0; i != n; ++i) free(RG[i]); } free(RG_len); } for (i = 0; i < n; ++i) { if (translation_tbl && translation_tbl[i].tid_trans) trans_tbl_destroy(translation_tbl + i); if (iter && iter[i]) hts_itr_destroy(iter[i]); if (hdr && hdr[i]) sam_hdr_destroy(hdr[i]); if (fp && fp[i]) sam_close(fp[i]); if (heap && heap[i].entry.bam_record) bam_destroy1(heap[i].entry.bam_record); } if (hout) sam_hdr_destroy(hout); free(RG); free(translation_tbl); free(hdr); hts_reglist_free(lreg, nreg); bed_destroy(hreg); free(iter); free(heap); free(fp); free(rtrans); free(out_idx_fn); if (keys != NULL) { for (i = 0; i < keys->m; ++i) { free(keys->buffers[i]); } free(keys->buffers); free(keys); } lib_lookup_destroy(lib_lookup); return -1; } // Unused here but may be used by legacy samtools-using third-party code int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg) { char mode[12]; strcpy(mode, "wb"); if (flag & MERGE_UNCOMP) strcat(mode, "0"); else if (flag & MERGE_LEVEL1) strcat(mode, "1"); SamOrder sam_order = by_qname ? QueryName : Coordinate; return bam_merge_core2(sam_order, NULL, out, mode, headers, n, fn, NULL, NULL, flag, reg, 0, "merge", NULL, NULL, 0, NULL, 1); } static void merge_usage(FILE *to) { fprintf(to, "Usage: samtools merge [options] -o [options] ... \n" " or: samtools merge [options] ... \n" "\n" "Options:\n" " -n Input files are sorted by read name (natural)\n" " -N Input files are sorted by read name (ASCII)\n" " -t TAG Input files are sorted by TAG value\n" " -r Attach RG tag (inferred from file names)\n" " -u Uncompressed BAM output\n" " -f Overwrite the output BAM if exist\n" " -o FILE Specify output file via option instead of argument\n" " -1 Compress level 1\n" " -l INT Compression level, from 0 to 9 [-1]\n" " -R STR Merge file in the specified region STR [all]\n" " -h FILE Copy the header in FILE to [in1.bam]\n" " -c Combine @RG headers with colliding IDs [alter IDs to be distinct]\n" " -p Combine @PG headers with colliding IDs [alter IDs to be distinct]\n" " -s VALUE Override random seed\n" " -b FILE List of input BAM filenames, one per line [null]\n" " -X Use customized index files\n" " -L FILE Specify a BED file for multiple region filtering [null]\n" " --no-PG do not add a PG line\n" " --template-coordinate Input files are sorted by template-coordinate\n"); sam_global_opt_help(to, "-.O..@.."); } int bam_merge(int argc, char *argv[]) { int c, flag = 0, ret = 0, level = -1, has_index_file = 0; char *fn_headers = NULL, *reg = NULL, mode[12]; char *sort_tag = NULL, *fnout = NULL, *arg_list = NULL; long random_seed = (long)time(NULL); char** fn = NULL; char** fn_idx = NULL, *fn_bed = NULL; int fn_size = 0, no_pg = 0; SamOrder sam_order = Coordinate; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'), { "threads", required_argument, NULL, '@' }, {"no-PG", no_argument, NULL, 1}, { "template-coordinate", no_argument, NULL, 2}, { NULL, 0, NULL, 0 } }; if (argc == 1) { merge_usage(samtools_stdout); return 0; } while ((c = getopt_long(argc, argv, "h:nNru1R:o:f@:l:cps:b:O:t:XL:", lopts, NULL)) >= 0) { switch (c) { case 'r': flag |= MERGE_RG; break; case 'f': flag |= MERGE_FORCE; break; case 'h': fn_headers = optarg; break; case 'N': natural_sort = 0; // fall through case 'n': sam_order = QueryName; break; case 'o': fnout = optarg; break; case 't': sort_tag = optarg; break; case '1': flag |= MERGE_LEVEL1; level = 1; break; case 'u': flag |= MERGE_UNCOMP; level = 0; break; case 'R': reg = strdup(optarg); break; case 'l': level = atoi(optarg); break; case 'c': flag |= MERGE_COMBINE_RG; break; case 'p': flag |= MERGE_COMBINE_PG; break; case 's': random_seed = atol(optarg); break; case 'X': has_index_file = 1; break; // -X flag for index filename case 'L': fn_bed = optarg; break; case 'b': { // load the list of files to read if (has_index_file) { fprintf(samtools_stderr,"Error: The -b option cannot be combined with -X\n"); ret = 1; goto end; } int nfiles; char **fn_read = hts_readlines(optarg, &nfiles); if (fn_read) { // Append to end of array fn = realloc(fn, (fn_size+nfiles) * sizeof(char*)); if (fn == NULL) { ret = 1; goto end; } memcpy(fn+fn_size, fn_read, nfiles * sizeof(char*)); fn_size += nfiles; free(fn_read); } else { print_error("merge", "Invalid file list \"%s\"", optarg); ret = 1; } break; } case 1: no_pg = 1; break; case 2: sam_order = TemplateCoordinate; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': merge_usage(samtools_stderr); return 1; } } if (sort_tag != NULL) { sam_order = sam_order == QueryName ? TagQueryName : TagCoordinate; } if (fnout == NULL && argc - optind >= 1) { fnout = argv[optind]; optind++; } if (fnout == NULL) { print_error("merge", "You must at least specify the output file"); merge_usage(samtools_stderr); return 1; } if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) { print_error("merge", "failed to create arg_list"); return 1; } hts_srand48(random_seed); if (!(flag & MERGE_FORCE) && strcmp(fnout, "-") != 0) { struct stat sbuf; if (stat(fnout, &sbuf) == 0 && S_ISREG(sbuf.st_mode)) { fprintf(samtools_stderr, "[%s] File '%s' exists. Please apply '-f' to overwrite. Abort.\n", __func__, fnout); ret = 1; goto end; } } int nargcfiles = 0; if (has_index_file) { // Calculate # of input BAM files if ((argc - optind) % 2 != 0) { fprintf(samtools_stderr, "Odd number of filenames detected! Each BAM file should have an index file\n"); ret = 1; goto end; } nargcfiles = (argc - optind) / 2; } else { nargcfiles = argc - optind; } if (nargcfiles > 0) { // Add argc files to end of array fn = realloc(fn, (fn_size+nargcfiles) * sizeof(char*)); if (fn == NULL) { ret = 1; goto end; } memcpy(fn+fn_size, argv + optind, nargcfiles * sizeof(char*)); if(has_index_file) { fn_idx = realloc(fn_idx, nargcfiles * sizeof(char*)); if (fn_idx == NULL) { ret = 1; goto end; } memcpy(fn_idx+fn_size, argv + nargcfiles + optind, nargcfiles * sizeof(char*)); } } if (fn_size+nargcfiles < 1) { print_error("merge", "You must specify at least one (and usually two or more) input files"); merge_usage(samtools_stderr); ret = 1; goto end; } if (reg && fn_bed) { print_error("merge", "You must specify either a BED file or a region"); ret = 1; goto end; } strcpy(mode, "wb"); sam_open_mode(mode+1, fnout, NULL); if (level >= 0) sprintf(strchr(mode, '\0'), "%d", level < 9? level : 9); if (bam_merge_core2(sam_order, sort_tag, fnout, mode, fn_headers, fn_size+nargcfiles, fn, fn_idx, fn_bed, flag, reg, ga.nthreads, "merge", &ga.in, &ga.out, ga.write_index, arg_list, no_pg) < 0) ret = 1; end: if (fn_size > 0) { int i; for (i=0; ii, res; if (i < nfiles) { // read from file res = sam_read1(fp[i], hout, heap->entry.bam_record); if (res >= 0 && g_sam_order == TemplateCoordinate) { // file read OK and TemplateCoordinate order // It is assumed that there are nfiles more keys allocated than keys->n; see allocation in bam_merge_simple template_coordinate_key_t *key = template_coordinate_keys_get(keys, keys->n + i); // get the next key to use heap->entry.u.key = template_coordinate_key(heap->entry.bam_record, key, hout, lib_lookup); // update the key if (heap->entry.u.key == NULL) res = -1; // key could not be created, error out } } else { // read from memory if (in_mem[i - nfiles].from < in_mem[i - nfiles].to) { size_t from = in_mem[i - nfiles].from; heap->entry.bam_record = buf[from].bam_record; if (g_sam_order == TemplateCoordinate) heap->entry.u.key = buf[from].u.key; in_mem[i - nfiles].from++; res = 0; } else { res = -1; } } if (res >= 0) { heap->tid = heap->entry.bam_record->core.tid; heap->pos = (uint64_t)(heap->entry.bam_record->core.pos + 1); heap->rev = bam_is_rev(heap->entry.bam_record); heap->idx = (*idx)++; if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) { heap->entry.u.tag = bam_aux_get(heap->entry.bam_record, g_sort_tag); } else if (g_sam_order != TemplateCoordinate) { heap->entry.u.tag = NULL; heap->entry.u.key = NULL; } } else if (res == -1) { heap->pos = HEAP_EMPTY; if (i < nfiles) bam_destroy1(heap->entry.bam_record); heap->entry.bam_record = NULL; heap->entry.u.tag = NULL; heap->entry.u.key = NULL; } else { return -1; } return 0; } static int bam_merge_simple(SamOrder sam_order, char *sort_tag, const char *out, const char *mode, sam_hdr_t *hout, int n, char * const *fn, int num_in_mem, buf_region *in_mem, bam1_tag *buf, template_coordinate_keys_t *keys, khash_t(const_c2c) *lib_lookup, htsThreadPool *htspool, const char *cmd, const htsFormat *in_fmt, const htsFormat *out_fmt, char *arg_list, int no_pg, int write_index, int final_out) { samFile *fpout = NULL, **fp = NULL; heap1_t *heap = NULL; uint64_t idx = 0; int i, heap_size = n + num_in_mem; char *out_idx_fn = NULL; if (sam_order == TagQueryName || sam_order == TagCoordinate) { g_sort_tag[0] = sort_tag[0]; g_sort_tag[1] = sort_tag[0] ? sort_tag[1] : '\0'; } if (n > 0) { fp = (samFile**)calloc(n, sizeof(samFile*)); if (!fp) goto mem_fail; } heap = (heap1_t*)calloc(heap_size, sizeof(heap1_t)); if (!heap) goto mem_fail; // Make sure that there's enough memory for template coordinate keys, one per file to read if (keys && keys->n + n >= keys->m * keys->buffer_size) { if (template_coordinate_keys_realloc(keys, keys->n + n) < 0) goto mem_fail; } // Open each file, read the header and put the first read into the heap for (i = 0; i < heap_size; i++) { sam_hdr_t *hin; heap1_t *h = &heap[i]; if (i < n) { fp[i] = sam_open_format(fn[i], "r", in_fmt); if (fp[i] == NULL) { print_error_errno(cmd, "fail to open \"%s\"", fn[i]); goto fail; } hts_set_opt(fp[i], HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE); if (htspool->pool) hts_set_opt(fp[i], HTS_OPT_THREAD_POOL, htspool); // Read header ... hin = sam_hdr_read(fp[i]); if (hin == NULL) { print_error(cmd, "failed to read header from \"%s\"", fn[i]); goto fail; } // ... and throw it away as we don't really need it sam_hdr_destroy(hin); } // Get a read into the heap h->i = i; h->entry.u.tag = NULL; h->entry.u.key = NULL; if (i < n) { h->entry.bam_record = bam_init1(); if (!h->entry.bam_record) goto mem_fail; } if (heap_add_read(h, n, fp, num_in_mem, in_mem, buf, keys, &idx, hout, lib_lookup) < 0) { assert(i < n); print_error(cmd, "failed to read first record from \"%s\"", fn[i]); goto fail; } } // Open output file and write header if ((fpout = sam_open_format(out, mode, out_fmt)) == 0) { print_error_errno(cmd, "failed to create \"%s\"", out); return -1; } hts_set_opt(fpout, HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE); if (!no_pg && sam_hdr_add_pg(hout, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { print_error(cmd, "failed to add PG line to the header of \"%s\"", out); sam_close(fpout); return -1; } if (htspool->pool) hts_set_opt(fpout, HTS_OPT_THREAD_POOL, htspool); if (sam_hdr_write(fpout, hout) != 0) { print_error_errno(cmd, "failed to write header to \"%s\"", out); sam_close(fpout); return -1; } if (write_index) { if (!(out_idx_fn = auto_index(fpout, out, hout))){ sam_close(fpout); return -1; } } // Now do the merge ks_heapmake(heap, heap_size, heap); while (heap->pos != HEAP_EMPTY) { bam1_t *b = heap->entry.bam_record; if (g_sam_order == MinHash && b->core.tid == -1 && final_out) { // Remove the cached minhash value b->core.pos = -1; b->core.mpos = -1; b->core.isize = 0; } if (sam_write1(fpout, hout, b) < 0) { print_error_errno(cmd, "failed writing to \"%s\"", out); goto fail; } if (heap_add_read(heap, n, fp, num_in_mem, in_mem, buf, keys, &idx, hout, lib_lookup) < 0) { assert(heap->i < n); print_error(cmd, "Error reading \"%s\" : %s", fn[heap->i], strerror(errno)); goto fail; } ks_heapadjust(heap, 0, heap_size, heap); } // Clean up and close for (i = 0; i < n; i++) { if (sam_close(fp[i]) != 0) { print_error(cmd, "Error on closing \"%s\" : %s", fn[i], strerror(errno)); } } free(fp); free(heap); if (write_index) { if (sam_idx_save(fpout) < 0) { print_error_errno("merge", "writing index failed"); goto fail; } free(out_idx_fn); } if (sam_close(fpout) < 0) { print_error_errno(cmd, "error closing output file \"%s\"", out); return -1; } return 0; mem_fail: print_error(cmd, "Out of memory"); fail: for (i = 0; i < n; i++) { if (fp && fp[i]) sam_close(fp[i]); } for (i = 0; i < heap_size; i++) { if (heap && heap[i].i < n && heap[i].entry.bam_record) bam_destroy1(heap[i].entry.bam_record); } free(fp); free(heap); if (fpout) sam_close(fpout); free(out_idx_fn); return -1; } // Function to compare reads and determine which one is < or > the other // Handle sort-by-pos and sort-by-name. Used as the secondary sort in bam1_lt_by_tag, if reads are equivalent by tag. // Returns a value less than, equal to or greater than zero if a is less than, // equal to or greater than b, respectively. static inline int bam1_cmp_core(const bam1_tag a, const bam1_tag b) { uint64_t pa, pb; if (!a.bam_record) return 1; if (!b.bam_record) return 0; if (g_sam_order == QueryName || g_sam_order == TagQueryName) { int t = strnum_cmp(bam_get_qname(a.bam_record), bam_get_qname(b.bam_record)); if (t != 0) return t; int af = a.bam_record->core.flag; int bf = b.bam_record->core.flag; // Sort order is READ1, READ2, (PRIMARY), SUPPLEMENTARY, SECONDARY // Get the bits in this order so sort is a natural a-b af = ((af&0xc0)<<8)|((af&0x100)<<3)|((af&0x800)>>3); bf = ((bf&0xc0)<<8)|((bf&0x100)<<3)|((bf&0x800)>>3); return af - bf; } else { pa = a.bam_record->core.tid; pb = b.bam_record->core.tid; if (pa == pb) { pa = (uint64_t)(a.bam_record->core.pos+1); pb = (uint64_t)(b.bam_record->core.pos+1); } if (pa == pb) { pa = bam_is_rev(a.bam_record); pb = bam_is_rev(b.bam_record); } return pa < pb ? -1 : (pa > pb ? 1 : 0); } } uint8_t normalize_type(const uint8_t* aux) { if (*aux == 'c' || *aux == 'C' || *aux == 's' || *aux == 'S' || *aux == 'i' || *aux == 'I') { return 'c'; } else if (*aux == 'f' || *aux == 'd') { return 'f'; } else if (*aux == 'H' || *aux == 'Z') { return 'H'; } else { return *aux; } } // Sort record by tag, using pos or read name as a secondary key if tags are identical. Reads not carrying the tag sort first. // Tags are first sorted by the type character (in case the types differ), or by the appropriate comparator for that type if they agree. // Returns a value less than, equal to or greater than zero if a is less than, // equal to or greater than b, respectively. static inline int bam1_cmp_by_tag(const bam1_tag a, const bam1_tag b) { const uint8_t* aux_a = a.u.tag; const uint8_t* aux_b = b.u.tag; if (aux_a == NULL && aux_b != NULL) { return -1; } else if (aux_a != NULL && aux_b == NULL) { return 1; } else if (aux_a == NULL && aux_b == NULL) { return bam1_cmp_core(a,b); } // 'Normalize' the letters of the datatypes to a canonical letter, // so that comparison of different types // forms a correct total ordering. uint8_t a_type = normalize_type(aux_a); uint8_t b_type = normalize_type(aux_b); if (a_type != b_type) { // Fix int to float comparisons by using bam_aux2f() to read the int if (a_type == 'c' && b_type == 'f') { a_type = 'f'; } else if (a_type == 'f' && b_type == 'c') { b_type = 'f'; } else { // Unfixable mismatched types return a_type < b_type ? -1 : 1; } } if (a_type == 'c') { int64_t va = bam_aux2i(aux_a); int64_t vb = bam_aux2i(aux_b); if (va != vb) return va < vb ? -1 : 1; return bam1_cmp_core(a, b); } else if (a_type == 'f') { double va = bam_aux2f(aux_a); double vb = bam_aux2f(aux_b); if (va != vb) return va < vb ? -1 : 1; return bam1_cmp_core(a, b); } else if (a_type == 'A') { unsigned char va = bam_aux2A(aux_a); unsigned char vb = bam_aux2A(aux_b); if (va != vb) return va < vb ? -1 : 1; return bam1_cmp_core(a, b); } else if (a_type == 'H') { int t = strcmp(bam_aux2Z(aux_a), bam_aux2Z(aux_b)); if (t) return t; return bam1_cmp_core(a, b); } else { return bam1_cmp_core(a,b); } } // Sort by minimiser (stored in bam1_tag.u.pos). // If equal, sort by position. // // The 64-bit sort key is split over the bam pos and isize fields. // This permits it to survive writing to temporary file and coming back. #ifdef DEBUG_MINHASH static int ntot = 0, nmis = 0, ndup = 0; #endif static inline int bam1_cmp_by_minhash(const bam1_tag a, const bam1_tag b) { const bam1_t *A = a.bam_record; const bam1_t *B = b.bam_record; if (!A) return 1; if (!B) return 0; if (A->core.tid != -1 || B->core.tid != -1) return bam1_cmp_core(a,b); const uint64_t m_a = (((uint64_t)A->core.pos)<<31)|(uint32_t)A->core.mpos; const uint64_t m_b = (((uint64_t)B->core.pos)<<31)|(uint32_t)B->core.mpos; if (m_a < m_b) // by hash return -1; else if (m_a > m_b) return 1; // Bigger pos with size minhash means starts further to left else if (A->core.isize > B->core.isize) // by hash location in seq return -1; else if (A->core.isize < B->core.isize) return 1; else return bam1_cmp_core(a,b); } // compares to molecular identifiers, ignoring any trailing slash and subsequent single-character // * if mid1 is less than mid2, then -1 will be returned // * if mid1 is greater than mid2, then 1 will be returned static inline int template_coordinate_key_compare_mid(const char* mid1, const char* mid2) { size_t i = 0; size_t len1 = strlen(mid1); size_t len2 = strlen(mid2); size_t shortest; // Snip off trailing slash followed by a single character, if present if (len1 >= 2 && mid1[len1-2] == '/') len1 -= 2; if (len2 >= 2 && mid2[len2-2] == '/') len2 -= 2; shortest = len1 < len2 ? len1 : len2; // find first mismatching character while (i < shortest && mid1[i] == mid2[i]) i++; // compare last characters if (i == len1 && i < len2) return -1; // mid1 shorter if (i == len2 && i < len1) return 1; // mid2 shorter if (i == len1 && i == len2) return 0; // all characters match if (mid1[i] < mid2[i]) return -1; // mid1 earlier else return 1; } // Builds a key use to sort in TemplateCoordinate order. Returns NULL if the key could not be created (e.g. MC // tag is missing), otherwise the pointer to the provided key. static template_coordinate_key_t* template_coordinate_key(bam1_t *b, template_coordinate_key_t *key, sam_hdr_t *hdr, khash_t(const_c2c) *lib_lookup) { uint8_t *data; char *rg; khiter_t k; // defaults key->tid1 = key->tid2 = INT32_MAX; key->pos1 = key->pos2 = HTS_POS_MAX; key->neg1 = key->neg2 = false; key->mid = ""; // update values rg = (char *)bam_aux_get(b, "RG"); if (rg && rg[0] == 'Z' &&(k = kh_get(const_c2c, lib_lookup, rg + 1)) < kh_end(lib_lookup)) { key->library = kh_value(lib_lookup, k); } else { key->library = ""; } key->name = bam_get_qname(b); if (!(b->core.flag & BAM_FUNMAP)) { // read is mapped, update coordinates key->tid1 = b->core.tid; key->neg1 = bam_is_rev(b); key->pos1 = (key->neg1) ? unclipped_end(b) : unclipped_start(b); } if (b->core.flag & BAM_FPAIRED && !(b->core.flag & BAM_FMUNMAP)) { // mate is mapped, update coordinates char *cigar; if ((data = bam_aux_get(b, "MC"))) { if (!(cigar = bam_aux2Z(data))) { fprintf(samtools_stderr, "[bam_sort] error: MC tag wrong type. Please use the MC tag provided by samtools fixmate.\n"); return NULL; } } else { fprintf(samtools_stderr, "[bam_sort] error: no MC tag. Please run samtools fixmate on file first.\n"); return NULL; } key->tid2 = b->core.mtid; key->neg2 = bam_is_mrev(b); key->pos2 = (key->neg2) ? unclipped_other_end(b->core.mpos, cigar) : unclipped_other_start(b->core.mpos, cigar); } if ((data = bam_aux_get(b, "MI"))) { if (!(key->mid=bam_aux2Z(data))) { fprintf(samtools_stderr, "[bam_sort] error: MI tag wrong type (not a string).\n"); return NULL; } } // set is_upper_of_pair, and swap if we get the same key regardless of which end // of the pair it is if (key->tid1 < key->tid2 || (key->tid1 == key->tid2 && key->pos1 < key->pos2) || (key->tid1 == key->tid2 && key->pos1 == key->pos2 && !key->neg1)) { key->is_upper_of_pair = false; } else { key->is_upper_of_pair = true; // swap int tmp_tid; hts_pos_t tmp_pos; bool tmp_neg; tmp_tid = key->tid1; key->tid1 = key->tid2; key->tid2 = tmp_tid; tmp_pos = key->pos1; key->pos1 = key->pos2; key->pos2 = tmp_pos; tmp_neg = key->neg1; key->neg1 = key->neg2; key->neg2 = tmp_neg; } return key; } // Function to compare reads and determine which one is < or > the other // Handles template-coordinate, which sorts by: // 1. the earlier unclipped 5' coordinate of the read pair // 2. the higher unclipped 5' coordinate of the read pair // 3. library (from read group) // 4. the molecular identifier (if present) // 5. read name // 6. if unpaired, or if R1 has the lower coordinates of the pair // Returns a value less than, equal to or greater than zero if a is less than, // equal to or greater than b, respectively. static inline int bam1_cmp_template_coordinate(const bam1_tag a, const bam1_tag b) { if (!a.bam_record) return 1; if (!b.bam_record) return 0; const template_coordinate_key_t* key_a = a.u.key; const template_coordinate_key_t* key_b = b.u.key; int retval = 0; if (0 == retval) retval = key_a->tid1 - key_b->tid1; if (0 == retval) retval = key_a->tid2 - key_b->tid2; if (0 == retval) retval = key_a->pos1 < key_b->pos1 ? -1 : (key_a->pos1 > key_b->pos1 ? 1 : 0); if (0 == retval) retval = key_a->pos2 < key_b->pos2 ? -1 : (key_a->pos2 > key_b->pos2 ? 1 : 0); if (0 == retval) retval = key_a->neg1 == key_b->neg1 ? 0 : (key_a->neg1 ? -1 : 1); if (0 == retval) retval = key_a->neg2 == key_b->neg2 ? 0 : (key_a->neg2 ? -1 : 1); if (0 == retval) retval = strcmp(key_a->library, key_b->library); if (0 == retval) retval = template_coordinate_key_compare_mid(key_a->mid, key_b->mid); if (0 == retval) retval = strcmp(key_a->name, key_b->name); if (0 == retval) retval = key_a->is_upper_of_pair == key_b->is_upper_of_pair ? 0 : (key_a->is_upper_of_pair ? 1 : -1); return retval < 0 ? -1 : (retval > 0 ? 1 : 0); } // Function to compare reads and determine which one is < the other // Handle sort-by-pos, sort-by-name, sort-by-tag, or sort-by-template-coordinate. static inline int bam1_lt(const bam1_tag a, const bam1_tag b) { switch (g_sam_order) { case Coordinate: case QueryName: return bam1_cmp_core(a, b) < 0; case TagQueryName: case TagCoordinate: return bam1_cmp_by_tag(a, b) < 0; case MinHash: return bam1_cmp_by_minhash(a, b) < 0; case TemplateCoordinate: return bam1_cmp_template_coordinate(a, b) < 0; default: return bam1_cmp_core(a,b) < 0; } } KSORT_INIT(sort, bam1_tag, bam1_lt) typedef struct { size_t buf_len; bam1_tag *buf; const sam_hdr_t *h; int error; int large_pos; int minimiser_kmer; bool try_rev; bool no_squash; } worker_t; // Returns 0 for success // -1 for failure static int write_buffer(const char *fn, const char *mode, size_t l, bam1_tag *buf, const sam_hdr_t *h, int n_threads, const htsFormat *fmt, int clear_minhash, char *arg_list, int no_pg, int write_index) { size_t i; samFile* fp; char *out_idx_fn = NULL; fp = sam_open_format(fn, mode, fmt); if (fp == NULL) return -1; hts_set_opt(fp, HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE); if (!no_pg && sam_hdr_add_pg((sam_hdr_t *)h, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { goto fail; } if (sam_hdr_write(fp, h) != 0) goto fail; if (write_index) if (!(out_idx_fn = auto_index(fp, fn, (sam_hdr_t *)h))) goto fail; if (n_threads > 1) hts_set_threads(fp, n_threads); for (i = 0; i < l; ++i) { bam1_t *b = buf[i].bam_record; if (clear_minhash && b->core.tid == -1) { // To see the position for debugging // b->core.pos = ((((uint64_t)b->core.pos)<<31)|(uint32_t)b->core.mpos) + b->core.isize; // Remove the cached minhash value b->core.pos = -1; b->core.mpos = -1; b->core.isize = 0; } if (sam_write1(fp, h, b) < 0) goto fail; } if (write_index) { if (sam_idx_save(fp) < 0) { print_error_errno("merge", "writing index failed"); goto fail; } free(out_idx_fn); } if (sam_close(fp) < 0) return -1; return 0; fail: sam_close(fp); free(out_idx_fn); return -1; } #define NUMBASE 256 static int ks_radixsort(size_t n, bam1_tag *buf, const sam_hdr_t *h) { int curr = 0, ret = -1; ssize_t i; bam1_tag *buf_ar2[2], *bam_a, *bam_b; uint64_t max_pos = 1; uint32_t max_tid = 1, tid_bytes = 0, pos_bytes = 0, byte = 0; uint32_t tid_shift_l, tid_shift_r; int nref = sam_hdr_nref(h); // Count number of bytes needed for biggest tid and pos // Notes: Add 1 to core.pos so always positive. // Convert unmapped tid (-1) to number of references so unmapped // sort to the end. for (i = 0; i < n; i++) { bam1_t *b = buf[i].bam_record; uint32_t tid = b->core.tid == -1 ? nref : b->core.tid; uint64_t pos = ((uint64_t)(b->core.pos + 1) << 1) | bam_is_rev(b); if (max_tid < tid) max_tid = tid; if (max_pos < pos) max_pos = pos; } for (; max_pos > 0; max_pos >>= 8) pos_bytes++; for (; max_tid > 0; max_tid >>= 8) tid_bytes++; assert(pos_bytes + tid_bytes < sizeof(buf[0].u.pos_tid)); tid_shift_l = pos_bytes * 8; tid_shift_r = 64 - tid_shift_l; // Write position and tid into bam1_tag::u::pos_tid using minimum number // of bytes required. Values are stored little-endian so that we // get a least-significant digit (byte) radix sort. for (i = 0; i < n; i++) { bam1_t *b = buf[i].bam_record; uint32_t tid = b->core.tid == -1 ? nref : b->core.tid; // 'pos' here includes as many bytes of tid as will fit // in the space remaining above pos_bytes. The rest of tid // is written out separately. uint64_t pos = (bam_is_rev(b) | ((uint64_t)(b->core.pos + 1) << 1) | (tid_shift_l < 64 ? (uint64_t) tid << tid_shift_l : 0)); u64_to_le(pos, buf[i].u.pos_tid); u32_to_le(tid_shift_r < 32 ? tid >> tid_shift_r : 0, &buf[i].u.pos_tid[8]); } buf_ar2[0] = buf; buf_ar2[1] = (bam1_tag *)malloc(sizeof(bam1_tag) * n); if (buf_ar2[1] == NULL) { print_error("sort", "couldn't allocate memory for temporary buf"); goto err; } // Least-significant digit radix sort (where "digits" are bytes) for (byte = 0; byte < pos_bytes + tid_bytes; byte++) { size_t remainders[NUMBASE] = { 0 }; bam_a = buf_ar2[curr]; bam_b = buf_ar2[1-curr]; for (i = 0; i < n; ++i) remainders[bam_a[i].u.pos_tid[byte]]++; for (i = 1; i < NUMBASE; ++i) remainders[i] += remainders[i - 1]; for (i = n - 1; i >= 0; i--) { size_t j = --remainders[bam_a[i].u.pos_tid[byte]]; bam_b[j] = bam_a[i]; } curr = 1 - curr; } if (curr == 1) { bam1_tag *end = buf + n; bam_a = buf_ar2[0]; bam_b = buf_ar2[1]; while (bam_a < end) *bam_a++ = *bam_b++; } ret = 0; err: free(buf_ar2[1]); return ret; } KHASH_MAP_INIT_INT64(kmer, int64_t) static khash_t(kmer) *kmer_h = NULL; // Punt homopolymers somewhere central in the hash space #define XOR 0xdead7878beef7878 /* * Computes the minhash of a sequence using forward strand and if requested * reverse strand. * * This is used as a sort key for unmapped data, to collate like sequences * together and to improve compression ratio. * * The minhash is returned and *pos filled out with location of this hash * key in the sequence if pos != NULL. */ static uint64_t minhash(bam1_t *b, int kmer, int window, int *curr_pos, int *end, int *is_rev, int try_fwd, int try_rev, int no_squash) { uint64_t hashf = 0, minhashf = UINT64_MAX; int minhashpf = *curr_pos, i, j; uint64_t mask = (1L<<(2*kmer))-1; uint8_t *seq = bam_get_seq(b); int len = b->core.l_qseq; uint64_t xor = XOR & mask; if (is_rev) *is_rev = 0; // Lookup tables for bam_seqi to 0123 fwd/rev hashes // =ACM GRSV TWYH KDBN #define X 0 static unsigned char L[16] = { X,0,1,X, 2,X,X,X, 3,X,X,X, X,X,X,X, }; uint64_t R[16] = { X,3,2,X, 1,X,X,X, 0,X,X,X, X,X,X,X, }; for (i = 0; i < 16; i++) R[i] <<= 2*(kmer-1); int i_start = *curr_pos; int i_end = MIN(i_start + window, len); int last_base = -1; if (try_fwd) { // Initialise hash keys for (i = i_start, j = 0; j < kmer-1 && i < i_end; i++) { int base = bam_seqi(seq, i); // collapse homopolymers if (no_squash || last_base != base) { last_base = base; hashf = (hashf<<2) | L[base]; j++; } } // Loop to find minimum if (no_squash) { for (; i < i_end; i++) { int base = bam_seqi(seq, i); hashf = (hashf<<2) | L[base]; uint64_t hashfx = (hashf ^ XOR) & mask; if (minhashf > hashfx) minhashf = hashfx, minhashpf = i; } } else { for (; i < i_end; i++) { int base = bam_seqi(seq, i); if (last_base != base) { last_base = base; hashf = (hashf<<2) | L[base]; uint64_t hashfx = (hashf ^ XOR) & mask; if (minhashf > hashfx) minhashf = hashfx, minhashpf = i; } } } } // Same as above for the reverse strand. // Not used for now, but we may wish to consider indexing in both // strands, recording the strand in value (pos), and comparing in one // strand only. Right now we compare on both against a single-stranded // index. if (try_rev) { uint64_t hashr = 0, minhashr = UINT64_MAX; int minhashpr = *curr_pos; int last_base = -1; for (i = i_start, j = 0; j < kmer-1 && i < len; i++) { int base = bam_seqi(seq, i); if (no_squash || last_base != base) { last_base = base; hashr = (hashr>>2) | R[base]; j++; } } if (no_squash) { for (; i < i_end; i++) { int base = bam_seqi(seq, i); hashr = (hashr>>2) | R[base]; if (minhashr > (hashr^xor)) minhashr = (hashr^xor), minhashpr = len-i+kmer-2; } } else { for (; i < i_end; i++) { int base = bam_seqi(seq, i); if (last_base != base) { last_base = base; hashr = (hashr>>2) | R[base]; if (minhashr > (hashr^xor)) minhashr = (hashr^xor), minhashpr = len-i+kmer-2; } } } if (minhashr < minhashf) { minhashf = minhashr; minhashpf = minhashpr; if (is_rev) *is_rev = 1; } } // "*curr_pos = minhashpf" is faster here, but is sometimes // poorer in compression. Eg 10 million novaseq records with // 75.1MB vs 76.9MB cram BA field. //*curr_pos = minhashpf; *curr_pos = minhashpf - (kmer-1); if (end) *end = (i_end == len); return minhashf; } #define UNIQ_BIT 60 #define UNIQ_TEST(x) (((x) & (1ULL<= 0) { //fprintf(samtools_stderr, "LEN\t%d\t%s\n", b->core.l_qseq, bam_get_qname(b)); uint64_t hashf; int pos = 0, end = 0; khiter_t k; int ret; if (b->core.l_qseq < window) continue; // fwd while (!end) { int last_pos = pos; hashf = minhash(b, kmer, window, &pos, &end, NULL, 1, 0, no_squash); k = kh_put(kmer, kmer_h, hashf, &ret); kh_value(kmer_h, k) = tpos+pos + (((uint64_t)!ret)<core.l_qseq; // We could also add reverse keys to the index here. // This would avoid reverse complementing during the matching stage. // We'd need to add a flag (another high bit of kh_value) to indicate // strand. // I'm unsure if this is a good trade-off or not. // // rev // pos = 0; end = 0; // while (!end) { // hashf = minhash(b, kmer, window, &pos, &end, NULL, 0, 1, // no_squash); // k = kh_put(kmer, kmer_h, hashf, &ret); // kh_value(kmer_h, k) = tpos+pos + (((uint64_t)!ret)<core.l_qseq; } if (r < -1) goto err; ret = 0; err: if (b) bam_destroy1(b); if (h) sam_hdr_destroy(h); sam_close(in); return ret; } /* * A variant of minhash that compares against a previously built index. * * We follow the same steps of scanning through this sequence to find the * minimum hash, but we prefer hash keys that have unique placement in the * index, or if not unique, then non-uniquely placed, over ones that * are absent from the index. */ static uint64_t minhash_with_idx(bam1_t *b, int kmer, int *pos, int *rev, bool try_rev) { uint64_t hashf = 0, minhashf = UINT64_MAX, minhashfi = UINT64_MAX; uint64_t minhashfd = UINT64_MAX; int minhashpf = 0, minhashpfi = 0, minhashpfd = 0, i, j; uint64_t mask = (1L<<(2*kmer))-1; unsigned char *seq = bam_get_seq(b); int len = b->core.l_qseq; const uint64_t xor = XOR & mask; // Lookup tables for bam_seqi to 0123 fwd/rev hashes // =ACM GRSV TWYH KDBN #define X 0 unsigned char L[16] = { X,0,1,X, 2,X,X,X, 3,X,X,X, X,X,X,X, }; uint64_t R[16] = { X,3,2,X, 1,X,X,X, 0,X,X,X, X,X,X,X, }; for (i = 0; i < 16; i++) R[i] <<= 2*(kmer-1); // Initialise hash keys for (i = j = 0; j < kmer-1 && i < len; i++, j++) { int base = bam_seqi(seq, i); hashf = (hashf<<2) | L[base]; } // Loop to find minimum int found_f = 0, found_r = 0; for (; i < len; i++) { int base = bam_seqi(seq, i); hashf = ((hashf<<2) | L[base]) & mask; const uint64_t hashfx = hashf^xor; // Priority for sorting // 1. Unique key in index // 2. Dup key in index // 3. Everything else int index = 0; if (minhashfi > hashfx || (found_f < 2 && minhashfd > hashfx)) { khiter_t k = kh_get(kmer, kmer_h, hashfx); if (k != kh_end(kmer_h)) index = UNIQ_TEST(kh_value(kmer_h, k)) ? 2 : 1; } found_f |= index; switch (index) { case 2: minhashfi = hashfx, minhashpfi = i; break; case 1: minhashfd = hashfx, minhashpfd = i; break; default: if (minhashf > hashfx) minhashf = hashfx, minhashpf = i; } } if (minhashfi != UINT64_MAX) minhashf = minhashfi, minhashpf = minhashpfi; else if (minhashfd != UINT64_MAX) minhashf = minhashfd, minhashpf = minhashpfd; // Same as above for the reverse strand int dir = 0; if (try_rev) { uint64_t hashr = 0, minhashr = UINT64_MAX, minhashri = UINT64_MAX; uint64_t minhashrd = UINT64_MAX; int minhashpr = 0, minhashpri = 0, minhashprd = 0; for (i = j = 0; j < kmer-1 && i < len; i++, j++) { int base = bam_seqi(seq, i); hashr = (hashr>>2) | R[base]; } for (; i < len; i++) { int base = bam_seqi(seq, i); hashr = (hashr>>2) | R[base]; const uint64_t hashrx = hashr^xor; int index = 0; if (minhashri > hashrx || (found_r < 2 && minhashrd > hashrx)) { khiter_t k = kh_get(kmer, kmer_h, hashrx); if (k != kh_end(kmer_h)) index = UNIQ_TEST(kh_value(kmer_h, k)) ? 2 : 1; } found_r |= index; switch (index) { case 2: minhashri = hashrx, minhashpri = i; break; case 1: minhashrd = hashrx, minhashprd = i; break; default: if (minhashr > hashrx) minhashr = hashrx, minhashpr = i; } } if (minhashri != UINT64_MAX) minhashr = minhashri, minhashpr = minhashpri; else if (minhashrd != UINT64_MAX) minhashr = minhashrd, minhashpr = minhashprd; // Pick reverse if better mapping if ((minhashf > minhashr) || (!found_f && found_r)) { if (!found_f || found_r) { minhashf = minhashr; minhashpf = b->core.l_qseq - minhashpr + kmer - 2; dir = 1; } } } #ifdef DEBUG_MINHASH ntot++; khiter_t k = kh_get(kmer, kmer_h, minhashf); if (k != kh_end(kmer_h)) { if (!UNIQ_TEST(kh_value(kmer_h, k))) ndup++; minhashf = kh_value(kmer_h, k) & UNIQ_MASK; } else { nmis++; } #else // For indexed kmers, our hash key is the position the kmer // occurs in the concatenated reference rather than the hash itself. khiter_t k = kh_get(kmer, kmer_h, minhashf); if (k != kh_end(kmer_h)) minhashf = kh_value(kmer_h, k) & UNIQ_MASK; #endif if (rev) *rev = dir; if (pos) *pos = minhashpf; return minhashf != UINT64_MAX ? minhashf : 0; } // As per minhash_with_idx but with homopolymer squashing enabled. // This function is duplicated to remove conditionals and speed up the // hashing code. (Minus the ifdef-ed out code, which is kept above mainly // for posterity.) static uint64_t minhash_with_idx_squash(bam1_t *b, int kmer, int *pos, int *rev, bool try_rev) { uint64_t hashf = 0, minhashf = UINT64_MAX, minhashfi = UINT64_MAX; uint64_t minhashfd = UINT64_MAX; int minhashpf = 0, minhashpfi = 0, minhashpfd = 0, i, j; uint64_t mask = (1L<<(2*kmer))-1; unsigned char *seq = bam_get_seq(b); int len = b->core.l_qseq; const uint64_t xor = XOR & mask; // Lookup tables for bam_seqi to 0123 fwd/rev hashes // =ACM GRSV TWYH KDBN #define X 0 unsigned char L[16] = { X,0,1,X, 2,X,X,X, 3,X,X,X, X,X,X,X, }; uint64_t R[16] = { X,3,2,X, 1,X,X,X, 0,X,X,X, X,X,X,X, }; for (i = 0; i < 16; i++) R[i] <<= 2*(kmer-1); // Initialise hash keys int last_base = -1; for (i = j = 0; j < kmer-1 && i < len; i++) { int base = bam_seqi(seq, i); if (base == last_base) continue; last_base = base; j++; hashf = (hashf<<2) | L[base]; } // Loop to find minimum int found_f = 0, found_r = 0; for (; i < len; i++) { int base = bam_seqi(seq, i); if (base == last_base) continue; last_base = base; hashf = ((hashf<<2) | L[base]) & mask; const uint64_t hashfx = hashf^xor; // Priority for sorting // 1. Unique key in index // 2. Dup key in index // 3. Everything else int index = 0; if (minhashfi > hashfx || (found_f < 2 && minhashfd > hashfx)) { khiter_t k = kh_get(kmer, kmer_h, hashfx); if (k != kh_end(kmer_h)) index = UNIQ_TEST(kh_value(kmer_h, k)) ? 2 : 1; } found_f |= index; switch (index) { case 2: minhashfi = hashfx, minhashpfi = i; break; case 1: minhashfd = hashfx, minhashpfd = i; break; default: if (minhashf > hashfx) minhashf = hashfx, minhashpf = i; } } if (minhashfi != UINT64_MAX) minhashf = minhashfi, minhashpf = minhashpfi; else if (minhashfd != UINT64_MAX) minhashf = minhashfd, minhashpf = minhashpfd; // Same as above for the reverse strand int dir = 0; if (try_rev) { uint64_t hashr = 0, minhashr = UINT64_MAX, minhashri = UINT64_MAX; uint64_t minhashrd = UINT64_MAX; int minhashpr = 0, minhashpri = 0, minhashprd = 0; int last_base = -1; for (i = j = 0; j < kmer-1 && i < len; i++) { int base = bam_seqi(seq, i); if (base == last_base) continue; last_base = base; j++; hashr = (hashr>>2) | R[base]; } for (; i < len; i++) { int base = bam_seqi(seq, i); if (base == last_base) continue; last_base = base; hashr = (hashr>>2) | R[base]; const uint64_t hashrx = hashr^xor; int index = 0; if (minhashri > hashrx || (found_r < 2 && minhashrd > hashrx)) { khiter_t k = kh_get(kmer, kmer_h, hashrx); if (k != kh_end(kmer_h)) index = UNIQ_TEST(kh_value(kmer_h, k)) ? 2 : 1; } found_r |= index; switch (index) { case 2: minhashri = hashrx, minhashpri = i; break; case 1: minhashrd = hashrx, minhashprd = i; break; default: if (minhashr > hashrx) minhashr = hashrx, minhashpr = i; } } if (minhashri != UINT64_MAX) minhashr = minhashri, minhashpr = minhashpri; else if (minhashrd != UINT64_MAX) minhashr = minhashrd, minhashpr = minhashprd; // Pick reverse if better mapping if ((minhashf > minhashr) || (!found_f && found_r)) { if (!found_f || found_r) { minhashf = minhashr; minhashpf = b->core.l_qseq - minhashpr + kmer - 2; dir = 1; } } } #ifdef DEBUG_MINHASH ntot++; khiter_t k = kh_get(kmer, kmer_h, minhashf); if (k != kh_end(kmer_h)) { if (!UNIQ_TEST(kh_value(kmer_h, k))) ndup++; minhashf = kh_value(kmer_h, k) & UNIQ_MASK; } else { nmis++; } #else // For indexed kmers, our hash key is the position the kmer // occurs in the concatenated reference rather than the hash itself. khiter_t k = kh_get(kmer, kmer_h, minhashf); if (k != kh_end(kmer_h)) minhashf = kh_value(kmer_h, k) & UNIQ_MASK; #endif if (rev) *rev = dir; if (pos) *pos = minhashpf; return minhashf != UINT64_MAX ? minhashf : 0; } //--- Start of candidates to punt to htslib /*! * @abstract * Extracts the sequence (in current alignment orientation) from * a bam record and places it in buf, which is nul terminated. * * @param b The bam structure * @param buf A buffer at least b->core.l_qseq+1 bytes long */ static void bam_to_seq(bam1_t *b, char *buf) { int i; uint8_t *seq = bam_get_seq(b); for (i = 0; i < b->core.l_qseq; i++) buf[i] = seq_nt16_str[bam_seqi(seq, i)]; buf[i] = 0; } /*! * @abstract * Writes a new sequence, of length b->core.l_qseq, to a BAM record. * * If a sequence of a new length is required the caller must first make * room for it by updating the bam1_t struct. * * @param b The bam structure * @param buf A buffer at least b->core.l_qseq bytes long */ static void seq_to_bam(bam1_t *b, char *buf) { int i; uint8_t *seq = bam_get_seq(b); for (i = 0; i < b->core.l_qseq; i++) bam_set_seqi(seq, i, seq_nt16_table[(unsigned char)buf[i]]); } /*! * @abstract Reverse complements a BAM record. * * It's possible to do this inline, but complex due to the 4-bit sequence * encoding. For now I take the dumb approach. * * @param b Pointer to a BAM alignment * * @return 0 on success, -1 on failure (ENOMEM) */ static int reverse_complement(bam1_t *b) { static char comp[256] = { 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//00 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//10 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//20 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//30 // * * * * E F * * I J * L * * O '@','T','V','G', 'H','E','F','C', 'D','I','H','M', 'L','K','N','O',//40 //P Q * * * * * * X Y Z [ \ ] ^ _ 'P','Q','Y','S', 'A','A','B','W', 'X','Y','Z','[','\\','[','^','_',//50 //` * * * * E F * * I J * L * * O '`','t','v','g', 'h','e','f','c', 'd','i','j','m', 'l','k','n','o',//60 //P Q * * * * * * X Y Z { | } ~ DEL 'p','q','y','s', 'a','a','b','w', 'x','y','z','{', '|','}','~',127,//70 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//80 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//90 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//A0 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//B0 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//C0 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//D0 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//E0 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//F0 }; char seq_[10000], *seq = seq_; uint8_t *qual = bam_get_qual(b); int i, j; if (b->core.l_qseq >= 10000) if (!(seq = malloc(b->core.l_qseq+1))) return -1; bam_to_seq(b, seq); for (i = 0, j = b->core.l_qseq-1; i < j; i++, j--) { unsigned char tmp = seq[i]; seq[i] = comp[(unsigned char)seq[j]]; seq[j] = comp[tmp]; tmp = qual[i]; qual[i] = qual[j]; qual[j] = tmp; } if (i ==j) seq[i] = comp[(unsigned char)seq[i]]; seq_to_bam(b, seq); if (seq != seq_) free(seq); b->core.flag ^= 0x10; return 0; } //--- End of candidates to punt to htslib static inline void worker_minhash(worker_t *w) { int i; for (i = 0; i < w->buf_len; i++) { bam1_t *b = w->buf[i].bam_record; if (b->core.tid != -1) continue; int pos = 0, rev = 0; uint64_t mh = kmer_h ? (w->no_squash ? minhash_with_idx(b, w->minimiser_kmer, &pos, &rev, w->try_rev) : minhash_with_idx_squash(b, w->minimiser_kmer, &pos, &rev, w->try_rev) ) : minhash(b, w->minimiser_kmer, b->core.l_qseq, &pos, NULL, &rev, 1, w->try_rev, w->no_squash); if (rev) reverse_complement(b); if (!kmer_h) { mh += 1LL<<30; pos = 65535-pos >= 0 ? 65535-pos : 0; } else { mh -= pos; pos = 0; } // Store 64-bit hash in unmapped pos and mpos fields. // The position of hash is in isize, which we use for // resolving ties when sorting by hash key. // These are unused for completely unmapped data and // will be reset during final output. b->core.pos = (mh>>31) & 0x7fffffff; b->core.mpos = mh&0x7fffffff; b->core.isize = pos; } } static void *worker(void *data) { worker_t *w = (worker_t*)data; w->error = 0; switch (g_sam_order) { case Coordinate: if (ks_radixsort(w->buf_len, w->buf, w->h) < 0) { w->error = errno; return NULL; } break; case MinHash: worker_minhash(w); // fall-through default: ks_mergesort(sort, w->buf_len, w->buf, 0); } return 0; } static int sort_blocks(size_t k, bam1_tag *buf, const sam_hdr_t *h, int n_threads, buf_region *in_mem, int large_pos, int minimiser_kmer, bool try_rev, bool no_squash) { int i; size_t pos, rest; pthread_t *tid; pthread_attr_t attr; worker_t *w; int n_failed = 0; if (n_threads < 1) n_threads = 1; if (k < n_threads * 64) n_threads = 1; // use a single thread if we only sort a small batch of records pthread_attr_init(&attr); pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE); w = (worker_t*)calloc(n_threads, sizeof(worker_t)); if (!w) return -1; tid = (pthread_t*)calloc(n_threads, sizeof(pthread_t)); if (!tid) { free(w); return -1; } pos = 0; rest = k; for (i = 0; i < n_threads; ++i) { w[i].buf_len = rest / (n_threads - i); w[i].buf = &buf[pos]; w[i].h = h; w[i].large_pos = large_pos; w[i].minimiser_kmer = minimiser_kmer; w[i].try_rev = try_rev; w[i].no_squash = no_squash; in_mem[i].from = pos; in_mem[i].to = pos + w[i].buf_len; pos += w[i].buf_len; rest -= w[i].buf_len; pthread_create(&tid[i], &attr, worker, &w[i]); } for (i = 0; i < n_threads; ++i) { pthread_join(tid[i], 0); if (w[i].error != 0) { errno = w[i].error; print_error_errno("sort", "failed to sort block %d", i); n_failed++; } } free(w); free(tid); return n_failed ? -1 : n_threads; } static void lib_lookup_destroy(khash_t(const_c2c) *lib_lookup) { khiter_t k; if (lib_lookup == NULL) return; for (k = kh_begin(lib_lookup); k < kh_end(lib_lookup); k++) { if (kh_exist(lib_lookup, k)) free(kh_value(lib_lookup, k)); } kh_destroy(const_c2c, lib_lookup); } // Build an RG to LB lookup table, for the template coordinate sort. // Returns a populated hash table (which may be empty) on success; // NULL on failure. static khash_t(const_c2c) * lookup_libraries(sam_hdr_t *header) { khash_t(const_c2c) *lib_lookup = kh_init(const_c2c); kstring_t lib_name = KS_INITIALIZE; int num_rg, i, res; if (!lib_lookup) return NULL; // Iterate through any RG lines and look for library information num_rg = sam_hdr_count_lines(header, "RG"); if (num_rg < 0) goto fail; for (i = 0; i < num_rg; i++) { const char *rg_id = sam_hdr_line_name(header, "RG", i); khiter_t k; if (!rg_id) goto fail; res = sam_hdr_find_tag_pos(header, "RG", i, "LB", &lib_name); if (res < -1) // Error goto fail; if (res < 0 || !lib_name.s) // No LB tag continue; // Add to lookup table k = kh_put(const_c2c, lib_lookup, rg_id, &res); if (res < 0) // Error goto fail; if (res > 0) { // Inserted kh_value(lib_lookup, k) = ks_release(&lib_name); } } free(lib_name.s); return lib_lookup; fail: lib_lookup_destroy(lib_lookup); free(lib_name.s); return NULL; } /*! @abstract Sort an unsorted BAM file based on the provided sort order @param sam_order the order in which the sort should occur @param sort_tag the tag to use if sorting by Tag @param minimiser_kmer the kmer size when sorting by MinHash @param try_rev try reverse strand when sorting by MinHash @param fn name of the file to be sorted @param prefix prefix of the temporary files (prefix.NNNN.bam are written) @param fnout name of the final output file to be written @param modeout sam_open() mode to be used to create the final output file @param max_mem approxiate maximum memory (very inaccurate) @param in_fmt input file format options @param out_fmt output file format and options @param arg_list command string for PG line @param no_pg if 1, do not add a new PG line @paran write_index create index for the output file @return 0 for successful sorting, negative on errors @discussion It may create multiple temporary subalignment files and then merge them by calling bam_merge_simple(). This function is NOT thread safe. */ int bam_sort_core_ext(SamOrder sam_order, char* sort_tag, int minimiser_kmer, bool try_rev, bool no_squash, const char *fn, const char *prefix, const char *fnout, const char *modeout, size_t _max_mem, int n_threads, const htsFormat *in_fmt, const htsFormat *out_fmt, char *arg_list, int no_pg, int write_index) { int ret = -1, res, i, nref, n_files = 0, n_big_files = 0, fn_counter = 0; size_t max_k, k, max_mem, bam_mem_offset; sam_hdr_t *header = NULL; samFile *fp = NULL; bam1_tag *buf = NULL; template_coordinate_keys_t *keys = NULL; bam1_t *b = bam_init1(); uint8_t *bam_mem = NULL; char **fns = NULL; size_t fns_size = 0; const char *new_so = NULL; const char *new_go = NULL; const char *new_ss = NULL; buf_region *in_mem = NULL; khash_t(const_c2c) *lib_lookup = NULL; htsThreadPool htspool = { NULL, 0 }; int num_in_mem = 0; int large_pos = 0; if (!b) { print_error("sort", "couldn't allocate memory for bam record"); return -1; } if (n_threads < 2) n_threads = 1; g_sam_order = sam_order; if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) { g_sort_tag[0] = sort_tag[0]; g_sort_tag[1] = sort_tag[0] ? sort_tag[1] : '\0'; } if (sam_order == TemplateCoordinate) { if ((keys = malloc(sizeof(template_coordinate_keys_t))) == NULL) { print_error("sort", "could not allocate memory for the top-level keys"); goto err; } keys->n = 0; keys->m = 0; keys->buffer_size = 0x10000; keys->buffers = NULL; } max_mem = _max_mem * n_threads; buf = NULL; fp = sam_open_format(fn, "r", in_fmt); if (fp == NULL) { print_error_errno("sort", "can't open \"%s\"", fn); goto err; } hts_set_opt(fp, HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE); header = sam_hdr_read(fp); if (header == NULL) { print_error("sort", "failed to read header from \"%s\"", fn); goto err; } // Inspect the header looking for long chromosomes // If there is one, we need to write temporary files in SAM format nref = sam_hdr_nref(header); for (i = 0; i < nref; i++) { if (sam_hdr_tid2len(header, i) > INT32_MAX) large_pos = 1; } // Also check the output format is large position compatible if (large_pos) { int compatible = (out_fmt->format == sam || (out_fmt->format == cram && out_fmt->version.major >= 4) || (out_fmt->format == unknown_format && modeout[0] == 'w' && (modeout[1] == 'z' || modeout[1] == '\0'))); if (!compatible) { print_error("sort", "output format is not compatible with very large references"); goto err; } } if (g_sam_order == TemplateCoordinate) { lib_lookup = lookup_libraries(header); if (!lib_lookup) goto err; } switch (g_sam_order) { case Coordinate: new_so = "coordinate"; break; case QueryName: new_so = "queryname"; new_ss = natural_sort ? "queryname:natural" : "queryname:lexicographical"; break; case MinHash: new_so = "coordinate"; new_ss = "coordinate:minhash"; break; case TagQueryName: case TagCoordinate: new_so = "unknown"; break; case TemplateCoordinate: new_so = "unsorted"; new_go = "query"; new_ss = "unsorted:template-coordinate"; break; default: new_so = "unknown"; break; } if (new_ss == NULL && new_go == NULL) { // just SO if ((-1 == sam_hdr_update_hd(header, "SO", new_so)) && (-1 == sam_hdr_add_line(header, "HD", "VN", SAM_FORMAT_VERSION, "SO", new_so, NULL)) ) { print_error("sort", "failed to change sort order header to 'SO:%s'\n", new_so); goto err; } } else if (new_ss != NULL && new_go == NULL) { // update SO and SS, but not GO if ((-1 == sam_hdr_update_hd(header, "SO", new_so, "SS", new_ss)) && (-1 == sam_hdr_add_line(header, "HD", "VN", SAM_FORMAT_VERSION, "SO", new_so, "SS", new_ss, NULL)) ) { print_error("sort", "failed to change sort order header to 'SO:%s SS:%s'\n", new_so, new_ss); goto err; } } else if (new_ss == NULL && new_go != NULL) { // update SO and GO, but not SS if ((-1 == sam_hdr_update_hd(header, "SO", new_so, "GO", new_go)) && (-1 == sam_hdr_add_line(header, "HD", "VN", SAM_FORMAT_VERSION, "SO", new_so, "GO", new_go, NULL)) ) { print_error("sort", "failed to change sort order header to 'SO:%s GO:%s'\n", new_so, new_go); goto err; } } else { // update SO, GO, and SS if ((-1 == sam_hdr_update_hd(header, "SO", new_so, "GO", new_go, "SS", new_ss)) && (-1 == sam_hdr_add_line(header, "HD", "VN", SAM_FORMAT_VERSION, "SO", new_so, "GO", new_go, "SS", new_ss, NULL)) ) { print_error("sort", "failed to change sort order header to 'SO:%s GO:%s SS:%s'\n", new_so, new_go, new_ss); goto err; } } if (new_go == NULL) { if (-1 == sam_hdr_remove_tag_hd(header, "GO")) { print_error("sort", "failed to delete group order in header\n"); goto err; } } if (new_ss == NULL) { if (-1 == sam_hdr_remove_tag_hd(header, "SS")) { print_error("sort", "failed to delete sub sort in header\n"); goto err; } } if (n_threads > 1) { htspool.pool = hts_tpool_init(n_threads); if (!htspool.pool) { print_error_errno("sort", "failed to set up thread pool"); goto err; } hts_set_opt(fp, HTS_OPT_THREAD_POOL, &htspool); } if ((bam_mem = malloc(max_mem)) == NULL) { print_error("sort", "couldn't allocate memory for bam_mem"); goto err; } in_mem = calloc(n_threads > 0 ? n_threads : 1, sizeof(in_mem[0])); if (!in_mem) goto err; // write sub files k = max_k = bam_mem_offset = 0; size_t name_len = strlen(prefix) + 30; while ((res = sam_read1(fp, header, b)) >= 0) { int mem_full = 0; if (k == max_k) { bam1_tag *new_buf; max_k = max_k? max_k<<1 : 0x10000; if ((new_buf = realloc(buf, max_k * sizeof(bam1_tag))) == NULL) { print_error("sort", "couldn't allocate memory for buf"); goto err; } buf = new_buf; } if (sam_order == TemplateCoordinate && k >= keys->m * keys->buffer_size) { if (template_coordinate_keys_realloc(keys, k + 1) == -1) { goto err; } } // Check if the BAM record will fit in the memory limit if (bam_mem_offset + sizeof(*b) + b->l_data < max_mem) { // Copy record into the memory block buf[k].bam_record = (bam1_t *)(bam_mem + bam_mem_offset); *buf[k].bam_record = *b; buf[k].bam_record->data = (uint8_t *)((char *)buf[k].bam_record + sizeof(bam1_t)); memcpy(buf[k].bam_record->data, b->data, b->l_data); // store next BAM record in next 8-byte-aligned address after // current one bam_mem_offset = (bam_mem_offset + sizeof(*b) + b->l_data + 8 - 1) & ~((size_t)(8 - 1)); } else { // Add a pointer to the remaining record buf[k].bam_record = b; mem_full = 1; } // Set the tag if sorting by tag, or the key for template cooridinate sorting switch (g_sam_order) { case TagQueryName: case TagCoordinate: buf[k].u.tag = bam_aux_get(buf[k].bam_record, g_sort_tag); break; case TemplateCoordinate: ++keys->n; template_coordinate_key_t *key = template_coordinate_keys_get(keys, k); buf[k].u.key = template_coordinate_key(buf[k].bam_record, key, header, lib_lookup); if (buf[k].u.key == NULL) goto err; break; default: buf[k].u.tag = NULL; buf[k].u.key = NULL; } ++k; if (mem_full) { if (hts_resize(char *, n_files + 1, &fns_size, &fns, 0) < 0) goto err; int sort_res = sort_blocks(k, buf, header, n_threads, in_mem, large_pos, minimiser_kmer, try_rev, no_squash); if (sort_res < 0) goto err; fns[n_files] = calloc(name_len, 1); if (!fns[n_files]) goto err; const int MAX_TRIES = 1000; int tries = 0, merge_res = -1; char *sort_by_tag = (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) ? sort_tag : NULL; int consolidate_from = n_files; if (n_files - n_big_files >= MAX_TMP_FILES/2) consolidate_from = n_big_files; else if (n_files >= MAX_TMP_FILES) consolidate_from = 0; for (;;) { if (tries) { snprintf(fns[n_files], name_len, "%s.%.4d-%.3d.bam", prefix, fn_counter, tries); } else { snprintf(fns[n_files], name_len, "%s.%.4d.bam", prefix, fn_counter); } if (bam_merge_simple(g_sam_order, sort_by_tag, fns[n_files], large_pos ? "wzx1" : "wbx1", header, n_files - consolidate_from, &fns[consolidate_from], n_threads, in_mem, buf, keys, lib_lookup, &htspool, "sort", NULL, NULL, NULL, 1, 0, 0) >= 0) { merge_res = 0; break; } if (errno == EEXIST && tries < MAX_TRIES) { tries++; } else { break; } } fn_counter++; if (merge_res < 0) { if (errno != EEXIST) unlink(fns[n_files]); free(fns[n_files]); goto err; } if (consolidate_from < n_files) { for (i = consolidate_from; i < n_files; i++) { unlink(fns[i]); free(fns[i]); } fns[consolidate_from] = fns[n_files]; n_files = consolidate_from; n_big_files = consolidate_from + 1; } n_files++; k = 0; if (keys != NULL) keys->n = 0; bam_mem_offset = 0; } } if (res != -1) { print_error("sort", "truncated file. Aborting"); goto err; } // Sort last records if (k > 0) { num_in_mem = sort_blocks(k, buf, header, n_threads, in_mem, large_pos, minimiser_kmer, try_rev, no_squash); if (num_in_mem < 0) goto err; } else { num_in_mem = 0; } // write the final output if (n_files == 0 && num_in_mem < 2) { // a single block if (write_buffer(fnout, modeout, k, buf, header, n_threads, out_fmt, minimiser_kmer, arg_list, no_pg, write_index) != 0) { print_error_errno("sort", "failed to create \"%s\"", fnout); goto err; } } else { // then merge fprintf(samtools_stderr, "[bam_sort_core] merging from %d files and %d in-memory blocks...\n", n_files, num_in_mem); // Paranoia check - all temporary files should have a name for (i = 0; i < n_files; ++i) { if (!fns[i]) { print_error("sort", "BUG: no name stored for temporary file %d", i); abort(); } } char *sort_by_tag = (sam_order == TagQueryName || sam_order == TagCoordinate) ? sort_tag : NULL; if (bam_merge_simple(sam_order, sort_by_tag, fnout, modeout, header, n_files, fns, num_in_mem, in_mem, buf, keys, lib_lookup, &htspool, "sort", in_fmt, out_fmt, arg_list, no_pg, write_index, 1) < 0) { // Propagate bam_merge_simple() failure; it has already emitted a // message explaining the failure, so no further message is needed. goto err; } } ret = 0; err: // free if (fns) { for (i = 0; i < n_files; ++i) { if (fns[i]) { unlink(fns[i]); free(fns[i]); } } free(fns); } bam_destroy1(b); free(buf); if (keys != NULL) { for (i = 0; i < keys->m; ++i) { free(keys->buffers[i]); } free(keys->buffers); free(keys); } free(bam_mem); free(in_mem); lib_lookup_destroy(lib_lookup); sam_hdr_destroy(header); if (fp) sam_close(fp); if (htspool.pool) hts_tpool_destroy(htspool.pool); return ret; } // Unused here but may be used by legacy samtools-using third-party code int bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem) { int ret; char *fnout = calloc(strlen(prefix) + 4 + 1, 1); if (!fnout) return -1; sprintf(fnout, "%s.bam", prefix); SamOrder sam_order = is_by_qname ? QueryName : Coordinate; g_sam_order = sam_order; ret = bam_sort_core_ext(sam_order, NULL, 0, false, true, fn, prefix, fnout, "wb", max_mem, 0, NULL, NULL, NULL, 1, 0); free(fnout); return ret; } static void sort_usage(FILE *fp) { fprintf(fp, "Usage: samtools sort [options...] [in.bam]\n" "Options:\n" " -l INT Set compression level, from 0 (uncompressed) to 9 (best)\n" " -u Output uncompressed data (equivalent to -l 0)\n" " -m INT Set maximum memory per thread; suffix K/M/G recognized [768M]\n" " -M Use minimiser for clustering unaligned/unplaced reads\n" " -R Do not use reverse strand (only compatible with -M)\n" " -K INT Kmer size to use for minimiser [20]\n" " -I FILE Order minimisers by their position in FILE FASTA\n" " -w INT Window size for minimiser indexing via -I ref.fa [100]\n" " -H Squash homopolymers when computing minimiser\n" " -n Sort by read name (natural): cannot be used with samtools index\n" " -N Sort by read name (ASCII): cannot be used with samtools index\n" " -t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set)\n" " -o FILE Write final output to FILE rather than standard output\n" " -T PREFIX Write temporary files to PREFIX.nnnn.bam\n" " --no-PG\n" " Do not add a PG line\n" " --template-coordinate\n" " Sort by template-coordinate\n"); sam_global_opt_help(fp, "-.O..@.."); } static void complain_about_memory_setting(size_t max_mem) { char *suffix = ""; const size_t nine_k = 9<<10; if (max_mem > nine_k) { max_mem >>= 10; suffix = "K"; } if (max_mem > nine_k) { max_mem >>= 10; suffix = "M"; } fprintf(samtools_stderr, "[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n" "Trying to run with -m too small can lead to the creation of a very large number\n" "of temporary files. This may make sort fail due to it exceeding limits on the\n" "number of files it can have open at the same time.\n\n" "Please check your -m parameter. It should be an integer followed by one of the\n" "letters K (for kilobytes), M (megabytes) or G (gigabytes). You should ensure it\n" "is at least the minimum above, and much higher if you are sorting a large file.\n", max_mem, suffix, SORT_MIN_MEGS_PER_THREAD); } int bam_sort(int argc, char *argv[]) { size_t max_mem = SORT_DEFAULT_MEGS_PER_THREAD << 20; int c, nargs, ret, o_seen = 0, level = -1, no_pg = 0; SamOrder sam_order = Coordinate; bool by_tag = false; int minimiser_kmer = 20; bool try_rev = true; char* sort_tag = NULL, *arg_list = NULL; char *fnout = "-", modeout[12]; kstring_t tmpprefix = { 0, 0, NULL }; struct stat st; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; int window = 100; char *minimiser_ref = NULL; int no_squash = 1; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'), { "threads", required_argument, NULL, '@' }, {"no-PG", no_argument, NULL, 1}, { "template-coordinate", no_argument, NULL, 2}, { NULL, 0, NULL, 0 } }; while ((c = getopt_long(argc, argv, "l:m:nNo:O:T:@:t:MI:K:uRw:H", lopts, NULL)) >= 0) { switch (c) { case 'o': fnout = optarg; o_seen = 1; break; case 'N': natural_sort = 0; // fall through case 'n': sam_order = QueryName; break; case 't': by_tag = true; sort_tag = optarg; break; case 'm': { char *q; max_mem = strtol(optarg, &q, 0); if (*q == 'k' || *q == 'K') max_mem <<= 10; else if (*q == 'm' || *q == 'M') max_mem <<= 20; else if (*q == 'g' || *q == 'G') max_mem <<= 30; break; } case 'T': kputs(optarg, &tmpprefix); break; case 'l': level = atoi(optarg); break; case 'u': level = 0; break; case 1: no_pg = 1; break; case 2: sam_order = TemplateCoordinate; break; case 'M': sam_order = MinHash; break; case 'I': sam_order = MinHash; // implicit option minimiser_ref = optarg; break; case 'H': no_squash = 0; break; case 'w': window = atoi(optarg); break; case 'R': try_rev = false; break; case 'K': minimiser_kmer = atoi(optarg); if (minimiser_kmer < 1) minimiser_kmer = 1; else if (minimiser_kmer > 31) minimiser_kmer = 31; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': sort_usage(samtools_stderr); ret = EXIT_FAILURE; goto sort_end; } } if (minimiser_ref) { fprintf(samtools_stderr, "Building index ... "); fflush(samtools_stderr); if (build_minhash_index(minimiser_ref, minimiser_kmer, window, no_squash)) { ret = EXIT_FAILURE; goto sort_end; } fprintf(samtools_stderr, "done\n"); } // Change sort order if tag sorting is requested. Must update based on secondary index if (by_tag) { sam_order = sam_order == QueryName ? TagQueryName : TagCoordinate; } nargs = argc - optind; if (nargs == 0 && isatty(STDIN_FILENO)) { sort_usage(samtools_stdout); ret = EXIT_SUCCESS; goto sort_end; } else if (nargs >= 2) { // If exactly two, user probably tried to specify legacy if (nargs == 2) fprintf(samtools_stderr, "[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files\n"); sort_usage(samtools_stderr); ret = EXIT_FAILURE; goto sort_end; } if (ga.write_index && sam_order != Coordinate) { fprintf(samtools_stderr, "[W::bam_sort] Ignoring --write-index as it only works for position sorted files.\n"); ga.write_index = 0; } if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) { print_error("sort", "failed to create arg_list"); return 1; } if (max_mem < (SORT_MIN_MEGS_PER_THREAD << 20)) { complain_about_memory_setting(max_mem); ret = EXIT_FAILURE; goto sort_end; } strcpy(modeout, "wb"); sam_open_mode(modeout+1, fnout, NULL); if (level >= 0) sprintf(strchr(modeout, '\0'), "%d", level < 9? level : 9); if (tmpprefix.l == 0) { if (strcmp(fnout, "-") != 0) { char *idx = strstr(fnout, HTS_IDX_DELIM); kputsn(fnout, idx ? idx - fnout : strlen(fnout), &tmpprefix); kputs(".tmp", &tmpprefix); } else { kputc('.', &tmpprefix); } } if (stat(tmpprefix.s, &st) == 0 && S_ISDIR(st.st_mode)) { unsigned t = ((unsigned) time(NULL)) ^ ((unsigned) clock()); if (tmpprefix.s[tmpprefix.l-1] != '/') kputc('/', &tmpprefix); ksprintf(&tmpprefix, "samtools.%d.%u.tmp", (int) getpid(), t % 10000); } ret = bam_sort_core_ext(sam_order, sort_tag, (sam_order == MinHash) ? minimiser_kmer : 0, try_rev, no_squash, (nargs > 0) ? argv[optind] : "-", tmpprefix.s, fnout, modeout, max_mem, ga.nthreads, &ga.in, &ga.out, arg_list, no_pg, ga.write_index); if (ret >= 0) ret = EXIT_SUCCESS; else { char dummy[4]; // If we failed on opening the input file & it has no .bam/.cram/etc // extension, the user probably tried legacy -o if (ret == -2 && o_seen && nargs > 0 && sam_open_mode(dummy, argv[optind], NULL) < 0) fprintf(samtools_stderr, "[bam_sort] Note the argument has been replaced by -T/-o options\n"); ret = EXIT_FAILURE; } #ifdef DEBUG_MINHASH fprintf(samtools_stderr, "Missed %.1f%%, dup %.1f%%\n", 100.0*nmis/(ntot+.1), 100.0*ndup/(ntot+.1)); #endif sort_end: free(tmpprefix.s); free(arg_list); sam_global_args_free(&ga); return ret; } pysam-0.23.0/samtools/bam_split.c000066400000000000000000000766601475062545500167400ustar00rootroot00000000000000/* bam_split.c -- split subcommand. Copyright (C) 2013-2016,2018-2019,2023,2024 Genome Research Ltd. Author: Martin Pollard Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include "htslib/thread_pool.h" #include "sam_opts.h" #include "samtools.h" KHASH_MAP_INIT_STR(c2i, int) struct parsed_opts { const char *merged_input_name; const char *unaccounted_header_name; const char *unaccounted_name; const char *output_format_string; const char *tag; long max_split; bool verbose; int no_pg; int zero_pad; sam_global_args ga; }; #define DEFAULT_MAX_SPLIT 100 typedef struct parsed_opts parsed_opts_t; struct state { samFile* merged_input_file; sam_hdr_t* merged_input_header; samFile* unaccounted_file; sam_hdr_t* unaccounted_header; char *unaccounted_idx_fn; size_t output_count; char **tag_vals; char **index_file_name; char **output_file_name; samFile **output_file; sam_hdr_t **output_header; kh_c2i_t* tag_val_hash; htsThreadPool p; int write_index; }; typedef struct state state_t; static int cleanup_state(state_t* status, bool check_close); static void cleanup_opts(parsed_opts_t* opts); static void usage(FILE *write_to) { fprintf(write_to, "Usage: samtools split [-u ] [-h ]\n" " [-f ] [-v] \n" "Options:\n" " -f STRING output filename format string [\"%%*_%%#.%%.\"]\n" " -u FILE1 put left-over reads in FILE1\n" " -h FILE2 ... and override the header with FILE2 (-u file only)\n" " -d TAG split by TAG value. TAG value must be a string.\n" " -p NUMBER zero-pad numbers in filenames to NUMBER digits\n" " -M,--max-split NUM limit number of output files from -d to NUM [%d]\n" " -v verbose output\n" " --no-PG do not add a PG line\n", DEFAULT_MAX_SPLIT); sam_global_opt_help(write_to, "-....@.."); fprintf(write_to, "\n" "Format string expansions:\n" " %%%% %%\n" " %%* basename\n" " %%# index (of @RG in the header, or count of TAG values seen so far)\n" " %%! @RG ID or TAG value\n" " %%. filename extension for output format\n" ); } // Takes the command line options and turns them into something we can understand static parsed_opts_t* parse_args(int argc, char** argv) { if (argc == 1) { usage(stdout); return NULL; } const char *optstring = "vf:h:u:d:M:p:@:"; char *default_format_string = "%*_%#.%."; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0, '@'), {"no-PG", no_argument, NULL, 1}, {"max-split", required_argument, NULL, 'M'}, {"zero-pad", required_argument, NULL, 'p'}, { NULL, 0, NULL, 0 } }; parsed_opts_t* retval = calloc(sizeof(parsed_opts_t), 1); if (! retval ) { perror("cannot allocate option parsing memory"); return NULL; } retval->max_split = DEFAULT_MAX_SPLIT; sam_global_args_init(&retval->ga); int opt; while ((opt = getopt_long(argc, argv, optstring, lopts, NULL)) != -1) { switch (opt) { case 'f': retval->output_format_string = optarg; break; case 'h': retval->unaccounted_header_name = optarg; break; case 'v': retval->verbose = true; break; case 'u': retval->unaccounted_name = optarg; break; case 'd': retval->tag = optarg; default_format_string = "%*_%!.%."; break; case 'M': { char *end = optarg; retval->max_split = strtol(optarg, &end, 10); if (*optarg == '\0' || *end != '\0' || retval->max_split == 0) { print_error("split", "Invalid -M argument: \"%s\"", optarg); free(retval); return NULL; } if (retval->max_split < 0) // No limit requested retval->max_split = LONG_MAX; break; } case 'p': { char *end = optarg; unsigned long val = strtoul(optarg, &end, 10); if (*optarg == '\0' || *end != '\0' || val > 20) { print_error("split", "Invalid -p argument: \"%s\"", optarg); free(retval); return NULL; } retval->zero_pad = (int) val; break; } case 1: retval->no_pg = 1; break; default: if (parse_sam_global_opt(opt, optarg, lopts, &retval->ga) == 0) break; /* else fall-through */ case '?': usage(stdout); free(retval); return NULL; } } if (retval->output_format_string == NULL) retval->output_format_string = default_format_string; argc -= optind; argv += optind; if (argc != 1) { print_error("split", "Invalid number of arguments: %d", argc); usage(stderr); free(retval); return NULL; } retval->merged_input_name = argv[0]; return retval; } // Expands a output filename format string static char* expand_format_string(const char* format_string, const char* basename, const char* tag_val, const int file_idx, const int zero_pad, const htsFormat *format) { kstring_t str = { 0, 0, NULL }; const char* pointer = format_string; const char* next; while ((next = strchr(pointer, '%')) != NULL) { if (kputsn(pointer, next-pointer, &str) < 0) goto memfail; ++next; switch (*next) { case '%': if (kputc('%', &str) < 0) goto memfail; break; case '*': if (kputs(basename, &str) < 0) goto memfail; break; case '#': if (zero_pad == 0) { if (kputl(file_idx, &str) < 0) goto memfail; } else { if (ksprintf(&str, "%0*d", zero_pad, file_idx) < 0) goto memfail; } break; case '!': if (kputs(tag_val, &str) < 0) goto memfail; break; case '.': // Only really need to cope with sam, bam, cram if (format->format != unknown_format) { if (kputs(hts_format_file_extension(format), &str) < 0) goto memfail; } else { if (kputs("bam", &str) < 0) goto memfail; } break; case '\0': print_error("split", "Trailing %% in filename format string"); goto fail; default: // Error is: fprintf(stderr, "bad format string, unknown format specifier\n"); print_error("split", "Unknown specifier %%%c in filename format string", *next); goto fail; } pointer = next + 1; } if (kputs(pointer, &str) < 0) goto memfail; return ks_release(&str); memfail: print_error_errno("split", "Couldn't build output filename"); fail: free(str.s); return NULL; } // Parse the header, count the number of RG tags and return a list of their names static bool count_RG(sam_hdr_t* hdr, size_t* count, char*** output_name) { char **names = NULL; kstring_t id_val = KS_INITIALIZE; int i, n_rg = sam_hdr_count_lines(hdr, "RG"); if (n_rg < 0) { print_error("split", "Failed to get @RG IDs"); *count = 0; *output_name = NULL; return false; } if (n_rg == 0) { *count = 0; *output_name = NULL; return true; } names = calloc(n_rg, sizeof(names[0])); if (!names) goto memfail; for (i = 0; i < n_rg; i++) { if (sam_hdr_find_tag_pos(hdr, "RG", i, "ID", &id_val) < 0) goto memfail; names[i] = ks_release(&id_val); } *count = n_rg; *output_name = names; return true; memfail: print_error_errno("split", "Failed to get @RG IDs"); *count = 0; *output_name = NULL; ks_free(&id_val); free(names); return false; } static int header_compatible(sam_hdr_t *hdr1, sam_hdr_t *hdr2) { size_t n; if (sam_hdr_nref(hdr1) != sam_hdr_nref(hdr2)) { print_error("split", "Unaccounted header contains wrong number of references"); return -1; } for (n = 0; n < sam_hdr_nref(hdr1); n++) { hts_pos_t h1_len = sam_hdr_tid2len(hdr1, n); hts_pos_t h2_len = sam_hdr_tid2len(hdr2, n); if (h1_len != h2_len) { print_error("split", "Unaccounted header reference %zu \"%s\" is not the same length as in the input file", n + 1, sam_hdr_tid2name(hdr2, n)); return -1; } } return 0; } static int grow_output_lists(state_t *state, size_t count) { char **new_list = realloc(state->tag_vals, count * sizeof(char *)); if (!new_list) return -1; state->tag_vals = new_list; new_list = realloc(state->index_file_name, count * sizeof(char *)); if (!new_list) return -1; state->index_file_name = new_list; new_list = realloc(state->output_file_name, count * sizeof(char *)); if (!new_list) return -1; state->output_file_name = new_list; samFile **new_file = realloc(state->output_file, count * sizeof(samFile *)); if (!new_file) return -1; state->output_file = new_file; sam_hdr_t **new_hdr = realloc(state->output_header, count * sizeof(sam_hdr_t *)); if (!new_hdr) return -1; state->output_header = new_hdr; return 0; } static khiter_t prep_sam_file(parsed_opts_t *opts, state_t *state, const char *tag, const char *arg_list, int is_rg) { char *input_base_name = NULL, *new_file_name = NULL, *tag_val = NULL; char *new_idx_fn = NULL; sam_hdr_t *new_hdr = NULL; samFile *new_sam_file = NULL; khiter_t i = kh_get_c2i(state->tag_val_hash, tag); if (i != kh_end(state->tag_val_hash)) { return i; } // create new file if (grow_output_lists(state, state->output_count + 1) != 0) { print_error_errno("split", "Couldn't grow output lists"); return kh_end(state->tag_val_hash); } tag_val = strdup(tag); if (!tag_val) { print_error_errno("split", "Couldn't copy tag value"); return kh_end(state->tag_val_hash); } char *dirsep = strrchr(opts->merged_input_name, '/'); input_base_name = strdup(dirsep? dirsep+1 : opts->merged_input_name); if (!input_base_name) { print_error_errno("split", "Filename parsing failed"); goto fail; } char* extension = strrchr(input_base_name, '.'); if (extension) *extension = '\0'; new_file_name = expand_format_string(opts->output_format_string, input_base_name, tag, kh_size(state->tag_val_hash), opts->zero_pad, &opts->ga.out); if (!new_file_name) { print_error_errno("split", "Filename creation failed"); goto fail; } new_hdr = sam_hdr_dup(state->merged_input_header); if (!new_hdr) { print_error_errno("split", "Duplicating header for file \"%s\" failed", new_file_name); goto fail; } if (!opts->no_pg && sam_hdr_add_pg(new_hdr, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { print_error_errno("split", "Adding PG line to file \"%s\" failed", new_file_name); goto fail; } if (is_rg) { // If here, we've found an RG:Z: tag without a corresponding @RG // line in the header. if (sam_hdr_remove_lines(new_hdr, "RG", "ID", NULL) != 0) { print_error_errno("split", "Failed to remove @RG lines from file \"%s\"", new_file_name); goto fail; } if (sam_hdr_add_line(new_hdr, "RG", "ID", tag_val, NULL) != 0) { print_error_errno("split", "Failed to add @RG line to file \"%s\"", new_file_name); goto fail; } } char outmode[4] = "w"; sam_open_mode(outmode + 1, new_file_name, NULL); new_sam_file = sam_open_format(new_file_name, outmode, &opts->ga.out); if (!new_sam_file) { print_error_errno("split", "Opening filename for writing \"%s\" failed", new_file_name); goto fail; } if (state->p.pool) hts_set_opt(new_sam_file, HTS_OPT_THREAD_POOL, &state->p); if (sam_hdr_write(new_sam_file, new_hdr) != 0) { print_error_errno("split", "Couldn't write header to \"%s\"", new_file_name); goto fail; } if (state->write_index) { new_idx_fn = auto_index(new_sam_file, new_file_name, new_hdr); if (!new_idx_fn) { print_error_errno("split", "Creating index file for file \"%s\" failed", new_file_name); goto fail; } } int ret = -1; i = kh_put_c2i(state->tag_val_hash, tag_val, &ret); if (ret < 0) { print_error_errno("split", "Adding file \"%s\" failed", new_file_name); goto fail; } kh_val(state->tag_val_hash, i) = state->output_count; state->tag_vals[state->output_count] = tag_val; state->index_file_name[state->output_count] = new_idx_fn; state->output_file_name[state->output_count] = new_file_name; state->output_file[state->output_count] = new_sam_file; state->output_header[state->output_count] = new_hdr; state->output_count++; free(input_base_name); return i; fail: free(input_base_name); free(new_file_name); free(tag_val); free(new_idx_fn); if (new_hdr) sam_hdr_destroy(new_hdr); if (new_sam_file) sam_close(new_sam_file); return kh_end(state->tag_val_hash); } // Set the initial state static state_t* init(parsed_opts_t* opts, const char *arg_list) { state_t* retval = calloc(sizeof(state_t), 1); if (!retval) { print_error_errno("split", "Initialisation failed"); return NULL; } if (opts->ga.nthreads > 0) { if (!(retval->p.pool = hts_tpool_init(opts->ga.nthreads))) { fprintf(stderr, "Error creating thread pool\n"); cleanup_state(retval, false); return NULL; } } retval->merged_input_file = sam_open_format(opts->merged_input_name, "r", &opts->ga.in); if (!retval->merged_input_file) { print_error_errno("split", "Could not open \"%s\"", opts->merged_input_name); cleanup_state(retval, false); return NULL; } if (retval->p.pool) hts_set_opt(retval->merged_input_file, HTS_OPT_THREAD_POOL, &retval->p); retval->merged_input_header = sam_hdr_read(retval->merged_input_file); if (retval->merged_input_header == NULL) { print_error("split", "Could not read header from \"%s\"", opts->merged_input_name); cleanup_state(retval, false); return NULL; } retval->write_index = opts->ga.write_index; if (opts->unaccounted_name) { if (opts->unaccounted_header_name) { samFile* hdr_load = sam_open_format(opts->unaccounted_header_name, "r", &opts->ga.in); if (!hdr_load) { print_error_errno("split", "Could not open unaccounted header file \"%s\"", opts->unaccounted_header_name); cleanup_state(retval, false); return NULL; } retval->unaccounted_header = sam_hdr_read(hdr_load); if (retval->unaccounted_header == NULL) { print_error("split", "Could not read header from \"%s\"", opts->unaccounted_header_name); cleanup_state(retval, false); sam_close(hdr_load); return NULL; } sam_close(hdr_load); if (header_compatible(retval->merged_input_header, retval->unaccounted_header) != 0) { cleanup_state(retval, false); return NULL; } } else { retval->unaccounted_header = sam_hdr_dup(retval->merged_input_header); if (!opts->no_pg && sam_hdr_add_pg(retval->unaccounted_header, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { print_error("split", "Could not rewrite header for \"%s\"", opts->unaccounted_name); cleanup_state(retval, false); return NULL; } } char outmode[4] = "w"; sam_open_mode(outmode + 1, opts->unaccounted_name, NULL); retval->unaccounted_file = sam_open_format(opts->unaccounted_name, outmode, &opts->ga.out); if (retval->unaccounted_file == NULL) { print_error_errno("split", "Could not open unaccounted output file \"%s\"", opts->unaccounted_name); cleanup_state(retval, false); return NULL; } if (retval->p.pool) hts_set_opt(retval->unaccounted_file, HTS_OPT_THREAD_POOL, &retval->p); } int is_rg = !opts->tag || strcmp(opts->tag, "RG") == 0; if (is_rg) { if (!count_RG(retval->merged_input_header, &retval->output_count, &retval->tag_vals)) { cleanup_state(retval, false); return NULL; } if (opts->verbose) fprintf(stderr, "@RG's found %zu\n",retval->output_count); } else { retval->output_count = 0; } // Prevent calloc(0, size); size_t num = retval->output_count ? retval->output_count : 1; retval->index_file_name = (char **)calloc(num, sizeof(char *)); retval->output_file_name = (char **)calloc(num, sizeof(char *)); retval->output_file = (samFile**)calloc(num, sizeof(samFile*)); retval->output_header = (sam_hdr_t**)calloc(num, sizeof(sam_hdr_t*)); retval->tag_val_hash = kh_init_c2i(); if (!retval->output_file_name || !retval->output_file || !retval->output_header || !retval->tag_val_hash || !retval->index_file_name) { print_error_errno("split", "Could not initialise output file array"); cleanup_state(retval, false); return NULL; } if (!is_rg) return retval; // Done for this case - outputs will be opened later // Adjust max_split if too small for the read-groups listed in the header if (opts->max_split < retval->output_count) opts->max_split = retval->output_count; // Open output files for RGs char* dirsep = strrchr(opts->merged_input_name, '/'); char* input_base_name = strdup(dirsep? dirsep+1 : opts->merged_input_name); if (!input_base_name) { print_error_errno("split", "Filename manipulation failed"); cleanup_state(retval, false); return NULL; } char* extension = strrchr(input_base_name, '.'); if (extension) *extension = '\0'; size_t i; for (i = 0; i < retval->output_count; i++) { char* output_filename = NULL; char outmode[4] = "w"; output_filename = expand_format_string(opts->output_format_string, input_base_name, retval->tag_vals[i], i, opts->zero_pad, &opts->ga.out); if ( output_filename == NULL ) { cleanup_state(retval, false); free(input_base_name); return NULL; } retval->output_file_name[i] = output_filename; sam_open_mode(outmode + 1, output_filename, NULL); retval->output_file[i] = sam_open_format(output_filename, outmode, &opts->ga.out); if (retval->output_file[i] == NULL) { print_error_errno("split", "Could not open \"%s\"", output_filename); cleanup_state(retval, false); free(input_base_name); return NULL; } if (retval->p.pool) hts_set_opt(retval->output_file[i], HTS_OPT_THREAD_POOL, &retval->p); // Record index in hash int ret; khiter_t iter = kh_put_c2i(retval->tag_val_hash, retval->tag_vals[i], &ret); if (ret < 0) { print_error_errno("split", "Couldn't add @RG ID to look-up table"); cleanup_state(retval, false); free(input_base_name); return NULL; } kh_val(retval->tag_val_hash,iter) = i; // Set and edit header retval->output_header[i] = sam_hdr_dup(retval->merged_input_header); if (sam_hdr_remove_except(retval->output_header[i], "RG", "ID", retval->tag_vals[i]) || (!opts->no_pg && sam_hdr_add_pg(retval->output_header[i], "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL))) { print_error("split", "Could not rewrite header for \"%s\"", output_filename); cleanup_state(retval, false); free(input_base_name); return NULL; } } free(input_base_name); return retval; } static bool split(state_t* state, parsed_opts_t *opts, char *arg_list) { int is_rg = !opts->tag || strcmp(opts->tag, "RG") == 0; if (state->unaccounted_file) { if (sam_hdr_write(state->unaccounted_file, state->unaccounted_header) != 0) { print_error_errno("split", "Could not write output file header"); return false; } if (opts->ga.write_index) { state->unaccounted_idx_fn = auto_index(state->unaccounted_file, opts->unaccounted_name, state->unaccounted_header); if (!state->unaccounted_idx_fn) { print_error_errno("split", "Creating index file for file \"%s\" failed", opts->unaccounted_name); return false; } } } bam1_t* file_read = bam_init1(); // Read the first record int r; if ((r=sam_read1(state->merged_input_file, state->merged_input_header, file_read)) < 0) { // Nothing more to read? Ignore this file bam_destroy1(file_read); file_read = NULL; if (r < -1) { print_error("split", "Could not read first input record"); return false; } } if (is_rg) { size_t i; for (i = 0; i < state->output_count; i++) { if (sam_hdr_write(state->output_file[i], state->output_header[i]) != 0) { print_error_errno("split", "Could not write file header to \"%s\"", state->output_file_name[i]); goto error; } if (state->write_index) { state->index_file_name[i] = auto_index(state->output_file[i], state->output_file_name[i], state->output_header[i]); if (!state->index_file_name[i]) { print_error_errno("split", "Could not create index for file \"%s\"", state->output_file_name[i]); goto error; } } } } while (file_read != NULL) { // Get RG tag from read and look it up in hash to find file to output it to uint8_t* tag = bam_aux_get(file_read, is_rg ? "RG" : opts->tag); char *val = NULL; char number[28]; khiter_t iter; if (tag) { switch (*tag) { case 'Z': case 'H': val = bam_aux2Z(tag); break; case 'c': case 'C': case 's': case 'S': case 'i': case 'I': if (opts->zero_pad == 0) { snprintf(number, sizeof(number), "%"PRId64, bam_aux2i(tag)); } else { int64_t v = bam_aux2i(tag); snprintf(number, sizeof(number), "%0*"PRId64, v < 0 ? opts->zero_pad + 1 : opts->zero_pad, v); } val = number; break; default: break; } } if ( val != NULL ) { iter = kh_get_c2i(state->tag_val_hash, val); } else { iter = kh_end(state->tag_val_hash); } // Check for opts->tag here instead of !is_rg so we open new // files if the user specified '-d RG' and we find a RG:Z: value // that wasn't listed in the header. If the '-d' option is // not used, we don't open a file to preserve existing behaviour. if (opts->tag && val && iter == kh_end(state->tag_val_hash) && state->output_count < opts->max_split) { // Need to open a new output file iter = prep_sam_file(opts, state, val, arg_list, is_rg); if (iter == kh_end(state->tag_val_hash)) { // Open failed print_error("split", "Could not create output file for tag \"%s:%s\"", opts->tag, bam_aux2Z(tag)); goto error; } } // Write the read out to correct file if (iter != kh_end(state->tag_val_hash)) { // if found write to the appropriate untangled bam int i = kh_val(state->tag_val_hash,iter); if (sam_write1(state->output_file[i], state->output_header[i], file_read) < 0) { print_error_errno("split", "Could not write to \"%s\"", state->output_file_name[i]); goto error; } } else { // otherwise write to the unaccounted bam if there is one or fail if (state->unaccounted_file == NULL) { if (tag) { fprintf(stderr, "Read \"%s\" with unaccounted for tag \"%s\".\n", bam_get_qname(file_read), bam_aux2Z(tag)); } else { fprintf(stderr, "Read \"%s\" has no %s tag.\n", bam_get_qname(file_read), is_rg ? "RG" : opts->tag); } goto error; } else { if (sam_write1(state->unaccounted_file, state->unaccounted_header, file_read) < 0) { print_error_errno("split", "Could not write to unaccounted output file"); goto error; } } } // Replace written read with the next one to process if ((r=sam_read1(state->merged_input_file, state->merged_input_header, file_read)) < 0) { // Nothing more to read? Ignore this file in future bam_destroy1(file_read); file_read = NULL; if (r < -1) { print_error("split", "Could not read input record"); return false; } } } if (state->write_index) { size_t i; for (i = 0; i < state->output_count; i++) { if (sam_idx_save(state->output_file[i]) < 0) { print_error_errno("split", "writing index \"%s\" failed", state->index_file_name[i]); return false; } } if (state->unaccounted_file) { if (sam_idx_save(state->unaccounted_file) < 0) { print_error_errno("split", "writing index \"%s\" failed", state->unaccounted_idx_fn); return false; } } } return true; error: bam_destroy1(file_read); return false; } static int cleanup_state(state_t* status, bool check_close) { int ret = 0; if (!status) return 0; if (status->unaccounted_header) sam_hdr_destroy(status->unaccounted_header); if (status->unaccounted_file) { if (sam_close(status->unaccounted_file) < 0 && check_close) { print_error("split", "Error on closing unaccounted file"); ret = -1; } } sam_close(status->merged_input_file); size_t i; for (i = 0; i < status->output_count; i++) { if (status->output_header && status->output_header[i]) sam_hdr_destroy(status->output_header[i]); if (status->output_file && status->output_file[i]) { if (sam_close(status->output_file[i]) < 0 && check_close) { print_error("split", "Error on closing output file \"%s\"", status->output_file_name[i]); ret = -1; } } if (status->tag_vals) free(status->tag_vals[i]); if (status->output_file_name) free(status->output_file_name[i]); if (status->index_file_name[i]) free(status->index_file_name[i]); } if (status->merged_input_header) sam_hdr_destroy(status->merged_input_header); free(status->output_header); free(status->output_file); free(status->output_file_name); free(status->index_file_name); free(status->unaccounted_idx_fn); kh_destroy_c2i(status->tag_val_hash); free(status->tag_vals); if (status->p.pool) hts_tpool_destroy(status->p.pool); free(status); return ret; } static void cleanup_opts(parsed_opts_t* opts) { if (!opts) return; sam_global_args_free(&opts->ga); free(opts); } int main_split(int argc, char** argv) { int ret = 1; char *arg_list = NULL; parsed_opts_t* opts = parse_args(argc, argv); if (!opts) goto cleanup_opts; if (!opts->no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) goto cleanup_opts; state_t* status = init(opts, arg_list); if (!status) goto cleanup_opts; if (!split(status, opts, arg_list)) { cleanup_state(status, false); goto cleanup_opts; } ret = cleanup_state(status, true); cleanup_opts: cleanup_opts(opts); free(arg_list); return ret; } pysam-0.23.0/samtools/bam_split.c.pysam.c000066400000000000000000000770251475062545500203050ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_split.c -- split subcommand. Copyright (C) 2013-2016,2018-2019,2023,2024 Genome Research Ltd. Author: Martin Pollard Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include "htslib/thread_pool.h" #include "sam_opts.h" #include "samtools.h" KHASH_MAP_INIT_STR(c2i, int) struct parsed_opts { const char *merged_input_name; const char *unaccounted_header_name; const char *unaccounted_name; const char *output_format_string; const char *tag; long max_split; bool verbose; int no_pg; int zero_pad; sam_global_args ga; }; #define DEFAULT_MAX_SPLIT 100 typedef struct parsed_opts parsed_opts_t; struct state { samFile* merged_input_file; sam_hdr_t* merged_input_header; samFile* unaccounted_file; sam_hdr_t* unaccounted_header; char *unaccounted_idx_fn; size_t output_count; char **tag_vals; char **index_file_name; char **output_file_name; samFile **output_file; sam_hdr_t **output_header; kh_c2i_t* tag_val_hash; htsThreadPool p; int write_index; }; typedef struct state state_t; static int cleanup_state(state_t* status, bool check_close); static void cleanup_opts(parsed_opts_t* opts); static void usage(FILE *write_to) { fprintf(write_to, "Usage: samtools split [-u ] [-h ]\n" " [-f ] [-v] \n" "Options:\n" " -f STRING output filename format string [\"%%*_%%#.%%.\"]\n" " -u FILE1 put left-over reads in FILE1\n" " -h FILE2 ... and override the header with FILE2 (-u file only)\n" " -d TAG split by TAG value. TAG value must be a string.\n" " -p NUMBER zero-pad numbers in filenames to NUMBER digits\n" " -M,--max-split NUM limit number of output files from -d to NUM [%d]\n" " -v verbose output\n" " --no-PG do not add a PG line\n", DEFAULT_MAX_SPLIT); sam_global_opt_help(write_to, "-....@.."); fprintf(write_to, "\n" "Format string expansions:\n" " %%%% %%\n" " %%* basename\n" " %%# index (of @RG in the header, or count of TAG values seen so far)\n" " %%! @RG ID or TAG value\n" " %%. filename extension for output format\n" ); } // Takes the command line options and turns them into something we can understand static parsed_opts_t* parse_args(int argc, char** argv) { if (argc == 1) { usage(samtools_stdout); return NULL; } const char *optstring = "vf:h:u:d:M:p:@:"; char *default_format_string = "%*_%#.%."; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0, '@'), {"no-PG", no_argument, NULL, 1}, {"max-split", required_argument, NULL, 'M'}, {"zero-pad", required_argument, NULL, 'p'}, { NULL, 0, NULL, 0 } }; parsed_opts_t* retval = calloc(sizeof(parsed_opts_t), 1); if (! retval ) { perror("cannot allocate option parsing memory"); return NULL; } retval->max_split = DEFAULT_MAX_SPLIT; sam_global_args_init(&retval->ga); int opt; while ((opt = getopt_long(argc, argv, optstring, lopts, NULL)) != -1) { switch (opt) { case 'f': retval->output_format_string = optarg; break; case 'h': retval->unaccounted_header_name = optarg; break; case 'v': retval->verbose = true; break; case 'u': retval->unaccounted_name = optarg; break; case 'd': retval->tag = optarg; default_format_string = "%*_%!.%."; break; case 'M': { char *end = optarg; retval->max_split = strtol(optarg, &end, 10); if (*optarg == '\0' || *end != '\0' || retval->max_split == 0) { print_error("split", "Invalid -M argument: \"%s\"", optarg); free(retval); return NULL; } if (retval->max_split < 0) // No limit requested retval->max_split = LONG_MAX; break; } case 'p': { char *end = optarg; unsigned long val = strtoul(optarg, &end, 10); if (*optarg == '\0' || *end != '\0' || val > 20) { print_error("split", "Invalid -p argument: \"%s\"", optarg); free(retval); return NULL; } retval->zero_pad = (int) val; break; } case 1: retval->no_pg = 1; break; default: if (parse_sam_global_opt(opt, optarg, lopts, &retval->ga) == 0) break; /* else fall-through */ case '?': usage(samtools_stdout); free(retval); return NULL; } } if (retval->output_format_string == NULL) retval->output_format_string = default_format_string; argc -= optind; argv += optind; if (argc != 1) { print_error("split", "Invalid number of arguments: %d", argc); usage(samtools_stderr); free(retval); return NULL; } retval->merged_input_name = argv[0]; return retval; } // Expands a output filename format string static char* expand_format_string(const char* format_string, const char* basename, const char* tag_val, const int file_idx, const int zero_pad, const htsFormat *format) { kstring_t str = { 0, 0, NULL }; const char* pointer = format_string; const char* next; while ((next = strchr(pointer, '%')) != NULL) { if (kputsn(pointer, next-pointer, &str) < 0) goto memfail; ++next; switch (*next) { case '%': if (kputc('%', &str) < 0) goto memfail; break; case '*': if (kputs(basename, &str) < 0) goto memfail; break; case '#': if (zero_pad == 0) { if (kputl(file_idx, &str) < 0) goto memfail; } else { if (ksprintf(&str, "%0*d", zero_pad, file_idx) < 0) goto memfail; } break; case '!': if (kputs(tag_val, &str) < 0) goto memfail; break; case '.': // Only really need to cope with sam, bam, cram if (format->format != unknown_format) { if (kputs(hts_format_file_extension(format), &str) < 0) goto memfail; } else { if (kputs("bam", &str) < 0) goto memfail; } break; case '\0': print_error("split", "Trailing %% in filename format string"); goto fail; default: // Error is: fprintf(samtools_stderr, "bad format string, unknown format specifier\n"); print_error("split", "Unknown specifier %%%c in filename format string", *next); goto fail; } pointer = next + 1; } if (kputs(pointer, &str) < 0) goto memfail; return ks_release(&str); memfail: print_error_errno("split", "Couldn't build output filename"); fail: free(str.s); return NULL; } // Parse the header, count the number of RG tags and return a list of their names static bool count_RG(sam_hdr_t* hdr, size_t* count, char*** output_name) { char **names = NULL; kstring_t id_val = KS_INITIALIZE; int i, n_rg = sam_hdr_count_lines(hdr, "RG"); if (n_rg < 0) { print_error("split", "Failed to get @RG IDs"); *count = 0; *output_name = NULL; return false; } if (n_rg == 0) { *count = 0; *output_name = NULL; return true; } names = calloc(n_rg, sizeof(names[0])); if (!names) goto memfail; for (i = 0; i < n_rg; i++) { if (sam_hdr_find_tag_pos(hdr, "RG", i, "ID", &id_val) < 0) goto memfail; names[i] = ks_release(&id_val); } *count = n_rg; *output_name = names; return true; memfail: print_error_errno("split", "Failed to get @RG IDs"); *count = 0; *output_name = NULL; ks_free(&id_val); free(names); return false; } static int header_compatible(sam_hdr_t *hdr1, sam_hdr_t *hdr2) { size_t n; if (sam_hdr_nref(hdr1) != sam_hdr_nref(hdr2)) { print_error("split", "Unaccounted header contains wrong number of references"); return -1; } for (n = 0; n < sam_hdr_nref(hdr1); n++) { hts_pos_t h1_len = sam_hdr_tid2len(hdr1, n); hts_pos_t h2_len = sam_hdr_tid2len(hdr2, n); if (h1_len != h2_len) { print_error("split", "Unaccounted header reference %zu \"%s\" is not the same length as in the input file", n + 1, sam_hdr_tid2name(hdr2, n)); return -1; } } return 0; } static int grow_output_lists(state_t *state, size_t count) { char **new_list = realloc(state->tag_vals, count * sizeof(char *)); if (!new_list) return -1; state->tag_vals = new_list; new_list = realloc(state->index_file_name, count * sizeof(char *)); if (!new_list) return -1; state->index_file_name = new_list; new_list = realloc(state->output_file_name, count * sizeof(char *)); if (!new_list) return -1; state->output_file_name = new_list; samFile **new_file = realloc(state->output_file, count * sizeof(samFile *)); if (!new_file) return -1; state->output_file = new_file; sam_hdr_t **new_hdr = realloc(state->output_header, count * sizeof(sam_hdr_t *)); if (!new_hdr) return -1; state->output_header = new_hdr; return 0; } static khiter_t prep_sam_file(parsed_opts_t *opts, state_t *state, const char *tag, const char *arg_list, int is_rg) { char *input_base_name = NULL, *new_file_name = NULL, *tag_val = NULL; char *new_idx_fn = NULL; sam_hdr_t *new_hdr = NULL; samFile *new_sam_file = NULL; khiter_t i = kh_get_c2i(state->tag_val_hash, tag); if (i != kh_end(state->tag_val_hash)) { return i; } // create new file if (grow_output_lists(state, state->output_count + 1) != 0) { print_error_errno("split", "Couldn't grow output lists"); return kh_end(state->tag_val_hash); } tag_val = strdup(tag); if (!tag_val) { print_error_errno("split", "Couldn't copy tag value"); return kh_end(state->tag_val_hash); } char *dirsep = strrchr(opts->merged_input_name, '/'); input_base_name = strdup(dirsep? dirsep+1 : opts->merged_input_name); if (!input_base_name) { print_error_errno("split", "Filename parsing failed"); goto fail; } char* extension = strrchr(input_base_name, '.'); if (extension) *extension = '\0'; new_file_name = expand_format_string(opts->output_format_string, input_base_name, tag, kh_size(state->tag_val_hash), opts->zero_pad, &opts->ga.out); if (!new_file_name) { print_error_errno("split", "Filename creation failed"); goto fail; } new_hdr = sam_hdr_dup(state->merged_input_header); if (!new_hdr) { print_error_errno("split", "Duplicating header for file \"%s\" failed", new_file_name); goto fail; } if (!opts->no_pg && sam_hdr_add_pg(new_hdr, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { print_error_errno("split", "Adding PG line to file \"%s\" failed", new_file_name); goto fail; } if (is_rg) { // If here, we've found an RG:Z: tag without a corresponding @RG // line in the header. if (sam_hdr_remove_lines(new_hdr, "RG", "ID", NULL) != 0) { print_error_errno("split", "Failed to remove @RG lines from file \"%s\"", new_file_name); goto fail; } if (sam_hdr_add_line(new_hdr, "RG", "ID", tag_val, NULL) != 0) { print_error_errno("split", "Failed to add @RG line to file \"%s\"", new_file_name); goto fail; } } char outmode[4] = "w"; sam_open_mode(outmode + 1, new_file_name, NULL); new_sam_file = sam_open_format(new_file_name, outmode, &opts->ga.out); if (!new_sam_file) { print_error_errno("split", "Opening filename for writing \"%s\" failed", new_file_name); goto fail; } if (state->p.pool) hts_set_opt(new_sam_file, HTS_OPT_THREAD_POOL, &state->p); if (sam_hdr_write(new_sam_file, new_hdr) != 0) { print_error_errno("split", "Couldn't write header to \"%s\"", new_file_name); goto fail; } if (state->write_index) { new_idx_fn = auto_index(new_sam_file, new_file_name, new_hdr); if (!new_idx_fn) { print_error_errno("split", "Creating index file for file \"%s\" failed", new_file_name); goto fail; } } int ret = -1; i = kh_put_c2i(state->tag_val_hash, tag_val, &ret); if (ret < 0) { print_error_errno("split", "Adding file \"%s\" failed", new_file_name); goto fail; } kh_val(state->tag_val_hash, i) = state->output_count; state->tag_vals[state->output_count] = tag_val; state->index_file_name[state->output_count] = new_idx_fn; state->output_file_name[state->output_count] = new_file_name; state->output_file[state->output_count] = new_sam_file; state->output_header[state->output_count] = new_hdr; state->output_count++; free(input_base_name); return i; fail: free(input_base_name); free(new_file_name); free(tag_val); free(new_idx_fn); if (new_hdr) sam_hdr_destroy(new_hdr); if (new_sam_file) sam_close(new_sam_file); return kh_end(state->tag_val_hash); } // Set the initial state static state_t* init(parsed_opts_t* opts, const char *arg_list) { state_t* retval = calloc(sizeof(state_t), 1); if (!retval) { print_error_errno("split", "Initialisation failed"); return NULL; } if (opts->ga.nthreads > 0) { if (!(retval->p.pool = hts_tpool_init(opts->ga.nthreads))) { fprintf(samtools_stderr, "Error creating thread pool\n"); cleanup_state(retval, false); return NULL; } } retval->merged_input_file = sam_open_format(opts->merged_input_name, "r", &opts->ga.in); if (!retval->merged_input_file) { print_error_errno("split", "Could not open \"%s\"", opts->merged_input_name); cleanup_state(retval, false); return NULL; } if (retval->p.pool) hts_set_opt(retval->merged_input_file, HTS_OPT_THREAD_POOL, &retval->p); retval->merged_input_header = sam_hdr_read(retval->merged_input_file); if (retval->merged_input_header == NULL) { print_error("split", "Could not read header from \"%s\"", opts->merged_input_name); cleanup_state(retval, false); return NULL; } retval->write_index = opts->ga.write_index; if (opts->unaccounted_name) { if (opts->unaccounted_header_name) { samFile* hdr_load = sam_open_format(opts->unaccounted_header_name, "r", &opts->ga.in); if (!hdr_load) { print_error_errno("split", "Could not open unaccounted header file \"%s\"", opts->unaccounted_header_name); cleanup_state(retval, false); return NULL; } retval->unaccounted_header = sam_hdr_read(hdr_load); if (retval->unaccounted_header == NULL) { print_error("split", "Could not read header from \"%s\"", opts->unaccounted_header_name); cleanup_state(retval, false); sam_close(hdr_load); return NULL; } sam_close(hdr_load); if (header_compatible(retval->merged_input_header, retval->unaccounted_header) != 0) { cleanup_state(retval, false); return NULL; } } else { retval->unaccounted_header = sam_hdr_dup(retval->merged_input_header); if (!opts->no_pg && sam_hdr_add_pg(retval->unaccounted_header, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { print_error("split", "Could not rewrite header for \"%s\"", opts->unaccounted_name); cleanup_state(retval, false); return NULL; } } char outmode[4] = "w"; sam_open_mode(outmode + 1, opts->unaccounted_name, NULL); retval->unaccounted_file = sam_open_format(opts->unaccounted_name, outmode, &opts->ga.out); if (retval->unaccounted_file == NULL) { print_error_errno("split", "Could not open unaccounted output file \"%s\"", opts->unaccounted_name); cleanup_state(retval, false); return NULL; } if (retval->p.pool) hts_set_opt(retval->unaccounted_file, HTS_OPT_THREAD_POOL, &retval->p); } int is_rg = !opts->tag || strcmp(opts->tag, "RG") == 0; if (is_rg) { if (!count_RG(retval->merged_input_header, &retval->output_count, &retval->tag_vals)) { cleanup_state(retval, false); return NULL; } if (opts->verbose) fprintf(samtools_stderr, "@RG's found %zu\n",retval->output_count); } else { retval->output_count = 0; } // Prevent calloc(0, size); size_t num = retval->output_count ? retval->output_count : 1; retval->index_file_name = (char **)calloc(num, sizeof(char *)); retval->output_file_name = (char **)calloc(num, sizeof(char *)); retval->output_file = (samFile**)calloc(num, sizeof(samFile*)); retval->output_header = (sam_hdr_t**)calloc(num, sizeof(sam_hdr_t*)); retval->tag_val_hash = kh_init_c2i(); if (!retval->output_file_name || !retval->output_file || !retval->output_header || !retval->tag_val_hash || !retval->index_file_name) { print_error_errno("split", "Could not initialise output file array"); cleanup_state(retval, false); return NULL; } if (!is_rg) return retval; // Done for this case - outputs will be opened later // Adjust max_split if too small for the read-groups listed in the header if (opts->max_split < retval->output_count) opts->max_split = retval->output_count; // Open output files for RGs char* dirsep = strrchr(opts->merged_input_name, '/'); char* input_base_name = strdup(dirsep? dirsep+1 : opts->merged_input_name); if (!input_base_name) { print_error_errno("split", "Filename manipulation failed"); cleanup_state(retval, false); return NULL; } char* extension = strrchr(input_base_name, '.'); if (extension) *extension = '\0'; size_t i; for (i = 0; i < retval->output_count; i++) { char* output_filename = NULL; char outmode[4] = "w"; output_filename = expand_format_string(opts->output_format_string, input_base_name, retval->tag_vals[i], i, opts->zero_pad, &opts->ga.out); if ( output_filename == NULL ) { cleanup_state(retval, false); free(input_base_name); return NULL; } retval->output_file_name[i] = output_filename; sam_open_mode(outmode + 1, output_filename, NULL); retval->output_file[i] = sam_open_format(output_filename, outmode, &opts->ga.out); if (retval->output_file[i] == NULL) { print_error_errno("split", "Could not open \"%s\"", output_filename); cleanup_state(retval, false); free(input_base_name); return NULL; } if (retval->p.pool) hts_set_opt(retval->output_file[i], HTS_OPT_THREAD_POOL, &retval->p); // Record index in hash int ret; khiter_t iter = kh_put_c2i(retval->tag_val_hash, retval->tag_vals[i], &ret); if (ret < 0) { print_error_errno("split", "Couldn't add @RG ID to look-up table"); cleanup_state(retval, false); free(input_base_name); return NULL; } kh_val(retval->tag_val_hash,iter) = i; // Set and edit header retval->output_header[i] = sam_hdr_dup(retval->merged_input_header); if (sam_hdr_remove_except(retval->output_header[i], "RG", "ID", retval->tag_vals[i]) || (!opts->no_pg && sam_hdr_add_pg(retval->output_header[i], "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL))) { print_error("split", "Could not rewrite header for \"%s\"", output_filename); cleanup_state(retval, false); free(input_base_name); return NULL; } } free(input_base_name); return retval; } static bool split(state_t* state, parsed_opts_t *opts, char *arg_list) { int is_rg = !opts->tag || strcmp(opts->tag, "RG") == 0; if (state->unaccounted_file) { if (sam_hdr_write(state->unaccounted_file, state->unaccounted_header) != 0) { print_error_errno("split", "Could not write output file header"); return false; } if (opts->ga.write_index) { state->unaccounted_idx_fn = auto_index(state->unaccounted_file, opts->unaccounted_name, state->unaccounted_header); if (!state->unaccounted_idx_fn) { print_error_errno("split", "Creating index file for file \"%s\" failed", opts->unaccounted_name); return false; } } } bam1_t* file_read = bam_init1(); // Read the first record int r; if ((r=sam_read1(state->merged_input_file, state->merged_input_header, file_read)) < 0) { // Nothing more to read? Ignore this file bam_destroy1(file_read); file_read = NULL; if (r < -1) { print_error("split", "Could not read first input record"); return false; } } if (is_rg) { size_t i; for (i = 0; i < state->output_count; i++) { if (sam_hdr_write(state->output_file[i], state->output_header[i]) != 0) { print_error_errno("split", "Could not write file header to \"%s\"", state->output_file_name[i]); goto error; } if (state->write_index) { state->index_file_name[i] = auto_index(state->output_file[i], state->output_file_name[i], state->output_header[i]); if (!state->index_file_name[i]) { print_error_errno("split", "Could not create index for file \"%s\"", state->output_file_name[i]); goto error; } } } } while (file_read != NULL) { // Get RG tag from read and look it up in hash to find file to output it to uint8_t* tag = bam_aux_get(file_read, is_rg ? "RG" : opts->tag); char *val = NULL; char number[28]; khiter_t iter; if (tag) { switch (*tag) { case 'Z': case 'H': val = bam_aux2Z(tag); break; case 'c': case 'C': case 's': case 'S': case 'i': case 'I': if (opts->zero_pad == 0) { snprintf(number, sizeof(number), "%"PRId64, bam_aux2i(tag)); } else { int64_t v = bam_aux2i(tag); snprintf(number, sizeof(number), "%0*"PRId64, v < 0 ? opts->zero_pad + 1 : opts->zero_pad, v); } val = number; break; default: break; } } if ( val != NULL ) { iter = kh_get_c2i(state->tag_val_hash, val); } else { iter = kh_end(state->tag_val_hash); } // Check for opts->tag here instead of !is_rg so we open new // files if the user specified '-d RG' and we find a RG:Z: value // that wasn't listed in the header. If the '-d' option is // not used, we don't open a file to preserve existing behaviour. if (opts->tag && val && iter == kh_end(state->tag_val_hash) && state->output_count < opts->max_split) { // Need to open a new output file iter = prep_sam_file(opts, state, val, arg_list, is_rg); if (iter == kh_end(state->tag_val_hash)) { // Open failed print_error("split", "Could not create output file for tag \"%s:%s\"", opts->tag, bam_aux2Z(tag)); goto error; } } // Write the read out to correct file if (iter != kh_end(state->tag_val_hash)) { // if found write to the appropriate untangled bam int i = kh_val(state->tag_val_hash,iter); if (sam_write1(state->output_file[i], state->output_header[i], file_read) < 0) { print_error_errno("split", "Could not write to \"%s\"", state->output_file_name[i]); goto error; } } else { // otherwise write to the unaccounted bam if there is one or fail if (state->unaccounted_file == NULL) { if (tag) { fprintf(samtools_stderr, "Read \"%s\" with unaccounted for tag \"%s\".\n", bam_get_qname(file_read), bam_aux2Z(tag)); } else { fprintf(samtools_stderr, "Read \"%s\" has no %s tag.\n", bam_get_qname(file_read), is_rg ? "RG" : opts->tag); } goto error; } else { if (sam_write1(state->unaccounted_file, state->unaccounted_header, file_read) < 0) { print_error_errno("split", "Could not write to unaccounted output file"); goto error; } } } // Replace written read with the next one to process if ((r=sam_read1(state->merged_input_file, state->merged_input_header, file_read)) < 0) { // Nothing more to read? Ignore this file in future bam_destroy1(file_read); file_read = NULL; if (r < -1) { print_error("split", "Could not read input record"); return false; } } } if (state->write_index) { size_t i; for (i = 0; i < state->output_count; i++) { if (sam_idx_save(state->output_file[i]) < 0) { print_error_errno("split", "writing index \"%s\" failed", state->index_file_name[i]); return false; } } if (state->unaccounted_file) { if (sam_idx_save(state->unaccounted_file) < 0) { print_error_errno("split", "writing index \"%s\" failed", state->unaccounted_idx_fn); return false; } } } return true; error: bam_destroy1(file_read); return false; } static int cleanup_state(state_t* status, bool check_close) { int ret = 0; if (!status) return 0; if (status->unaccounted_header) sam_hdr_destroy(status->unaccounted_header); if (status->unaccounted_file) { if (sam_close(status->unaccounted_file) < 0 && check_close) { print_error("split", "Error on closing unaccounted file"); ret = -1; } } sam_close(status->merged_input_file); size_t i; for (i = 0; i < status->output_count; i++) { if (status->output_header && status->output_header[i]) sam_hdr_destroy(status->output_header[i]); if (status->output_file && status->output_file[i]) { if (sam_close(status->output_file[i]) < 0 && check_close) { print_error("split", "Error on closing output file \"%s\"", status->output_file_name[i]); ret = -1; } } if (status->tag_vals) free(status->tag_vals[i]); if (status->output_file_name) free(status->output_file_name[i]); if (status->index_file_name[i]) free(status->index_file_name[i]); } if (status->merged_input_header) sam_hdr_destroy(status->merged_input_header); free(status->output_header); free(status->output_file); free(status->output_file_name); free(status->index_file_name); free(status->unaccounted_idx_fn); kh_destroy_c2i(status->tag_val_hash); free(status->tag_vals); if (status->p.pool) hts_tpool_destroy(status->p.pool); free(status); return ret; } static void cleanup_opts(parsed_opts_t* opts) { if (!opts) return; sam_global_args_free(&opts->ga); free(opts); } int main_split(int argc, char** argv) { int ret = 1; char *arg_list = NULL; parsed_opts_t* opts = parse_args(argc, argv); if (!opts) goto cleanup_opts; if (!opts->no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) goto cleanup_opts; state_t* status = init(opts, arg_list); if (!status) goto cleanup_opts; if (!split(status, opts, arg_list)) { cleanup_state(status, false); goto cleanup_opts; } ret = cleanup_state(status, true); cleanup_opts: cleanup_opts(opts); free(arg_list); return ret; } pysam-0.23.0/samtools/bam_stat.c000066400000000000000000000325101475062545500165420ustar00rootroot00000000000000/* bam_stat.c -- flagstat subcommand. Copyright (C) 2009, 2011, 2013-2015, 2019, 2021 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include "htslib/sam.h" #include "samtools.h" #include "sam_opts.h" typedef struct { long long n_reads[2], n_mapped[2], n_pair_all[2], n_pair_map[2], n_pair_good[2]; long long n_sgltn[2], n_read1[2], n_read2[2]; long long n_dup[2]; long long n_diffchr[2], n_diffhigh[2]; long long n_secondary[2], n_supp[2]; long long n_primary[2], n_pmapped[2], n_pdup[2]; } bam_flagstat_t; inline static void flagstat_loop(bam_flagstat_t *s, bam1_core_t *c) { int w = (c->flag & BAM_FQCFAIL)? 1 : 0; ++s->n_reads[w]; if (c->flag & BAM_FSECONDARY ) { ++s->n_secondary[w]; } else if (c->flag & BAM_FSUPPLEMENTARY ) { ++s->n_supp[w]; } else { ++s->n_primary[w]; if (c->flag & BAM_FPAIRED) { ++s->n_pair_all[w]; if ((c->flag & BAM_FPROPER_PAIR) && !(c->flag & BAM_FUNMAP) ) ++s->n_pair_good[w]; if (c->flag & BAM_FREAD1) ++s->n_read1[w]; if (c->flag & BAM_FREAD2) ++s->n_read2[w]; if ((c->flag & BAM_FMUNMAP) && !(c->flag & BAM_FUNMAP)) ++s->n_sgltn[w]; if (!(c->flag & BAM_FUNMAP) && !(c->flag & BAM_FMUNMAP)) { ++s->n_pair_map[w]; if (c->mtid != c->tid) { ++s->n_diffchr[w]; if (c->qual >= 5) ++s->n_diffhigh[w]; } } } if (!(c->flag & BAM_FUNMAP)) ++s->n_pmapped[w]; if (c->flag & BAM_FDUP) ++s->n_pdup[w]; } if (!(c->flag & BAM_FUNMAP)) ++s->n_mapped[w]; if (c->flag & BAM_FDUP) ++s->n_dup[w]; } bam_flagstat_t *bam_flagstat_core(samFile *fp, sam_hdr_t *h) { bam_flagstat_t *s; bam1_t *b; bam1_core_t *c; int ret; s = (bam_flagstat_t*)calloc(1, sizeof(bam_flagstat_t)); b = bam_init1(); c = &b->core; while ((ret = sam_read1(fp, h, b)) >= 0) flagstat_loop(s, c); bam_destroy1(b); if (ret != -1) { free(s); return NULL; } return s; } static const char *percent(char *buffer, long long n, long long total) { if (total != 0) sprintf(buffer, "%.2f%%", (float)n / total * 100.0); else strcpy(buffer, "N/A"); return buffer; } static const char *percent_json(char *buffer, long long n, long long total) { if (total != 0) sprintf(buffer, "%.2f", (float)n / total * 100.0); else strcpy(buffer, "null"); return buffer; } static void usage_exit(FILE *fp, int exit_status) { fprintf(fp, "Usage: samtools flagstat [options] \n"); sam_global_opt_help(fp, "-.---@-."); fprintf(fp, " -O, --"); fprintf(fp, "output-fmt FORMAT[,OPT[=VAL]]...\n" " Specify output format (json, tsv)\n"); exit(exit_status); } static void out_fmt_default(bam_flagstat_t *s) { char b0[16], b1[16]; printf("%lld + %lld in total (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]); printf("%lld + %lld primary\n", s->n_primary[0], s->n_primary[1]); printf("%lld + %lld secondary\n", s->n_secondary[0], s->n_secondary[1]); printf("%lld + %lld supplementary\n", s->n_supp[0], s->n_supp[1]); printf("%lld + %lld duplicates\n", s->n_dup[0], s->n_dup[1]); printf("%lld + %lld primary duplicates\n", s->n_pdup[0], s->n_pdup[1]); printf("%lld + %lld mapped (%s : %s)\n", s->n_mapped[0], s->n_mapped[1], percent(b0, s->n_mapped[0], s->n_reads[0]), percent(b1, s->n_mapped[1], s->n_reads[1])); printf("%lld + %lld primary mapped (%s : %s)\n", s->n_pmapped[0], s->n_pmapped[1], percent(b0, s->n_pmapped[0], s->n_primary[0]), percent(b1, s->n_pmapped[1], s->n_primary[1])); printf("%lld + %lld paired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]); printf("%lld + %lld read1\n", s->n_read1[0], s->n_read1[1]); printf("%lld + %lld read2\n", s->n_read2[0], s->n_read2[1]); printf("%lld + %lld properly paired (%s : %s)\n", s->n_pair_good[0], s->n_pair_good[1], percent(b0, s->n_pair_good[0], s->n_pair_all[0]), percent(b1, s->n_pair_good[1], s->n_pair_all[1])); printf("%lld + %lld with itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]); printf("%lld + %lld singletons (%s : %s)\n", s->n_sgltn[0], s->n_sgltn[1], percent(b0, s->n_sgltn[0], s->n_pair_all[0]), percent(b1, s->n_sgltn[1], s->n_pair_all[1])); printf("%lld + %lld with mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]); printf("%lld + %lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]); } static void out_fmt_json(bam_flagstat_t *s) { char b0[16], b1[16], p0[16], p1[16], pp0[16], pp1[16], s0[16], s1[16]; printf("{\n \"QC-passed reads\": { \n" " \"total\": %lld, \n" " \"primary\": %lld, \n" " \"secondary\": %lld, \n" " \"supplementary\": %lld, \n" " \"duplicates\": %lld, \n" " \"primary duplicates\": %lld, \n" " \"mapped\": %lld, \n" " \"mapped %%\": %s, \n" " \"primary mapped\": %lld, \n" " \"primary mapped %%\": %s, \n" " \"paired in sequencing\": %lld, \n" " \"read1\": %lld, \n" " \"read2\": %lld, \n" " \"properly paired\": %lld, \n" " \"properly paired %%\": %s, \n" " \"with itself and mate mapped\": %lld, \n" " \"singletons\": %lld, \n" " \"singletons %%\": %s, \n" " \"with mate mapped to a different chr\": %lld, \n" " \"with mate mapped to a different chr (mapQ >= 5)\": %lld \n" " }," "\n \"QC-failed reads\": { \n" " \"total\": %lld, \n" " \"primary\": %lld, \n" " \"secondary\": %lld, \n" " \"supplementary\": %lld, \n" " \"duplicates\": %lld, \n" " \"primary duplicates\": %lld, \n" " \"mapped\": %lld, \n" " \"mapped %%\": %s, \n" " \"primary mapped\": %lld, \n" " \"primary mapped %%\": %s, \n" " \"paired in sequencing\": %lld, \n" " \"read1\": %lld, \n" " \"read2\": %lld, \n" " \"properly paired\": %lld, \n" " \"properly paired %%\": %s, \n" " \"with itself and mate mapped\": %lld, \n" " \"singletons\": %lld, \n" " \"singletons %%\": %s, \n" " \"with mate mapped to a different chr\": %lld, \n" " \"with mate mapped to a different chr (mapQ >= 5)\": %lld \n" " }\n" "}\n", s->n_reads[0], s->n_primary[0], s->n_secondary[0], s->n_supp[0], s->n_dup[0], s->n_pdup[0], s->n_mapped[0], percent_json(b0, s->n_mapped[0], s->n_reads[0]), s->n_pmapped[0], percent_json(p0, s->n_pmapped[0], s->n_primary[0]), s->n_pair_all[0], s->n_read1[0], s->n_read2[0], s->n_pair_good[0], percent_json(pp0, s->n_pair_good[0], s->n_pair_all[0]), s->n_pair_map[0], s->n_sgltn[0], percent_json(s0, s->n_sgltn[0], s->n_pair_all[0]), s->n_diffchr[0], s->n_diffhigh[0], s->n_reads[1], s->n_primary[1], s->n_secondary[1], s->n_supp[1], s->n_dup[1], s->n_pdup[1], s->n_mapped[1], percent_json(b1, s->n_mapped[1], s->n_reads[1]), s->n_pmapped[1], percent_json(p1, s->n_pmapped[1], s->n_primary[1]), s->n_pair_all[1], s->n_read1[1], s->n_read2[1], s->n_pair_good[1], percent_json(pp1, s->n_pair_good[1], s->n_pair_all[1]), s->n_pair_map[1], s->n_sgltn[1], percent_json(s1, s->n_sgltn[1], s->n_pair_all[1]), s->n_diffchr[1], s->n_diffhigh[1] ); } static void out_fmt_tsv(bam_flagstat_t *s) { char b0[16], b1[16]; printf("%lld\t%lld\ttotal (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]); printf("%lld\t%lld\tprimary\n", s->n_primary[0], s->n_primary[1]); printf("%lld\t%lld\tsecondary\n", s->n_secondary[0], s->n_secondary[1]); printf("%lld\t%lld\tsupplementary\n", s->n_supp[0], s->n_supp[1]); printf("%lld\t%lld\tduplicates\n", s->n_dup[0], s->n_dup[1]); printf("%lld\t%lld\tprimary duplicates\n", s->n_pdup[0], s->n_pdup[1]); printf("%lld\t%lld\tmapped\n", s->n_mapped[0], s->n_mapped[1]); printf("%s\t%s\tmapped %%\n", percent(b0, s->n_mapped[0], s->n_reads[0]), percent(b1, s->n_mapped[1], s->n_reads[1])); printf("%lld\t%lld\tprimary mapped\n", s->n_pmapped[0], s->n_pmapped[1]); printf("%s\t%s\tprimary mapped %%\n", percent(b0, s->n_pmapped[0], s->n_primary[0]), percent(b1, s->n_pmapped[1], s->n_primary[1])); printf("%lld\t%lld\tpaired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]); printf("%lld\t%lld\tread1\n", s->n_read1[0], s->n_read1[1]); printf("%lld\t%lld\tread2\n", s->n_read2[0], s->n_read2[1]); printf("%lld\t%lld\tproperly paired\n", s->n_pair_good[0], s->n_pair_good[1]); printf("%s\t%s\tproperly paired %%\n", percent(b0, s->n_pair_good[0], s->n_pair_all[0]), percent(b1, s->n_pair_good[1], s->n_pair_all[1])); printf("%lld\t%lld\twith itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]); printf("%lld\t%lld\tsingletons\n", s->n_sgltn[0], s->n_sgltn[1]); printf("%s\t%s\tsingletons %%\n", percent(b0, s->n_sgltn[0], s->n_pair_all[0]), percent(b1, s->n_sgltn[1], s->n_pair_all[1])); printf("%lld\t%lld\twith mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]); printf("%lld\t%lld\twith mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]); } /* * Select flagstats output format to print. */ static void output_fmt(bam_flagstat_t *s, const char *out_fmt) { if (strcmp(out_fmt, "json") == 0 || strcmp(out_fmt, "JSON") == 0) { out_fmt_json(s); } else if (strcmp(out_fmt, "tsv") == 0 || strcmp(out_fmt, "TSV") == 0) { out_fmt_tsv(s); } else { out_fmt_default(s); } } int bam_flagstat(int argc, char *argv[]) { samFile *fp; sam_hdr_t *header; bam_flagstat_t *s; const char *out_fmt = "default"; int c, status = EXIT_SUCCESS; enum { INPUT_FMT_OPTION = CHAR_MAX+1, }; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', '-', '-', '@'), {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "@:O:", lopts, NULL)) >= 0) { switch (c) { case 'O': out_fmt = optarg; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage_exit(stderr, EXIT_FAILURE); } } if (argc != optind+1) { if (argc == optind) usage_exit(stdout, EXIT_SUCCESS); else usage_exit(stderr, EXIT_FAILURE); } fp = sam_open_format(argv[optind], "r", &ga.in); if (fp == NULL) { print_error_errno("flagstat", "Cannot open input file \"%s\"", argv[optind]); return 1; } if (ga.nthreads > 0) hts_set_threads(fp, ga.nthreads); if (hts_set_opt(fp, CRAM_OPT_REQUIRED_FIELDS, SAM_FLAG | SAM_MAPQ | SAM_RNEXT)) { fprintf(stderr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n"); return 1; } if (hts_set_opt(fp, CRAM_OPT_DECODE_MD, 0)) { fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n"); return 1; } header = sam_hdr_read(fp); if (header == NULL) { fprintf(stderr, "Failed to read header for \"%s\"\n", argv[optind]); return 1; } s = bam_flagstat_core(fp, header); if (s) { output_fmt(s, out_fmt); free(s); } else { print_error("flagstat", "error reading from \"%s\"", argv[optind]); status = EXIT_FAILURE; } sam_hdr_destroy(header); sam_close(fp); sam_global_args_free(&ga); return status; } pysam-0.23.0/samtools/bam_stat.c.pysam.c000066400000000000000000000340761475062545500201240ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_stat.c -- flagstat subcommand. Copyright (C) 2009, 2011, 2013-2015, 2019, 2021 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include "htslib/sam.h" #include "samtools.h" #include "sam_opts.h" typedef struct { long long n_reads[2], n_mapped[2], n_pair_all[2], n_pair_map[2], n_pair_good[2]; long long n_sgltn[2], n_read1[2], n_read2[2]; long long n_dup[2]; long long n_diffchr[2], n_diffhigh[2]; long long n_secondary[2], n_supp[2]; long long n_primary[2], n_pmapped[2], n_pdup[2]; } bam_flagstat_t; inline static void flagstat_loop(bam_flagstat_t *s, bam1_core_t *c) { int w = (c->flag & BAM_FQCFAIL)? 1 : 0; ++s->n_reads[w]; if (c->flag & BAM_FSECONDARY ) { ++s->n_secondary[w]; } else if (c->flag & BAM_FSUPPLEMENTARY ) { ++s->n_supp[w]; } else { ++s->n_primary[w]; if (c->flag & BAM_FPAIRED) { ++s->n_pair_all[w]; if ((c->flag & BAM_FPROPER_PAIR) && !(c->flag & BAM_FUNMAP) ) ++s->n_pair_good[w]; if (c->flag & BAM_FREAD1) ++s->n_read1[w]; if (c->flag & BAM_FREAD2) ++s->n_read2[w]; if ((c->flag & BAM_FMUNMAP) && !(c->flag & BAM_FUNMAP)) ++s->n_sgltn[w]; if (!(c->flag & BAM_FUNMAP) && !(c->flag & BAM_FMUNMAP)) { ++s->n_pair_map[w]; if (c->mtid != c->tid) { ++s->n_diffchr[w]; if (c->qual >= 5) ++s->n_diffhigh[w]; } } } if (!(c->flag & BAM_FUNMAP)) ++s->n_pmapped[w]; if (c->flag & BAM_FDUP) ++s->n_pdup[w]; } if (!(c->flag & BAM_FUNMAP)) ++s->n_mapped[w]; if (c->flag & BAM_FDUP) ++s->n_dup[w]; } bam_flagstat_t *bam_flagstat_core(samFile *fp, sam_hdr_t *h) { bam_flagstat_t *s; bam1_t *b; bam1_core_t *c; int ret; s = (bam_flagstat_t*)calloc(1, sizeof(bam_flagstat_t)); b = bam_init1(); c = &b->core; while ((ret = sam_read1(fp, h, b)) >= 0) flagstat_loop(s, c); bam_destroy1(b); if (ret != -1) { free(s); return NULL; } return s; } static const char *percent(char *buffer, long long n, long long total) { if (total != 0) sprintf(buffer, "%.2f%%", (float)n / total * 100.0); else strcpy(buffer, "N/A"); return buffer; } static const char *percent_json(char *buffer, long long n, long long total) { if (total != 0) sprintf(buffer, "%.2f", (float)n / total * 100.0); else strcpy(buffer, "null"); return buffer; } static void usage_exit(FILE *fp, int exit_status) { fprintf(fp, "Usage: samtools flagstat [options] \n"); sam_global_opt_help(fp, "-.---@-."); fprintf(fp, " -O, --"); fprintf(fp, "output-fmt FORMAT[,OPT[=VAL]]...\n" " Specify output format (json, tsv)\n"); samtools_exit(exit_status); } static void out_fmt_default(bam_flagstat_t *s) { char b0[16], b1[16]; fprintf(samtools_stdout, "%lld + %lld in total (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]); fprintf(samtools_stdout, "%lld + %lld primary\n", s->n_primary[0], s->n_primary[1]); fprintf(samtools_stdout, "%lld + %lld secondary\n", s->n_secondary[0], s->n_secondary[1]); fprintf(samtools_stdout, "%lld + %lld supplementary\n", s->n_supp[0], s->n_supp[1]); fprintf(samtools_stdout, "%lld + %lld duplicates\n", s->n_dup[0], s->n_dup[1]); fprintf(samtools_stdout, "%lld + %lld primary duplicates\n", s->n_pdup[0], s->n_pdup[1]); fprintf(samtools_stdout, "%lld + %lld mapped (%s : %s)\n", s->n_mapped[0], s->n_mapped[1], percent(b0, s->n_mapped[0], s->n_reads[0]), percent(b1, s->n_mapped[1], s->n_reads[1])); fprintf(samtools_stdout, "%lld + %lld primary mapped (%s : %s)\n", s->n_pmapped[0], s->n_pmapped[1], percent(b0, s->n_pmapped[0], s->n_primary[0]), percent(b1, s->n_pmapped[1], s->n_primary[1])); fprintf(samtools_stdout, "%lld + %lld paired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]); fprintf(samtools_stdout, "%lld + %lld read1\n", s->n_read1[0], s->n_read1[1]); fprintf(samtools_stdout, "%lld + %lld read2\n", s->n_read2[0], s->n_read2[1]); fprintf(samtools_stdout, "%lld + %lld properly paired (%s : %s)\n", s->n_pair_good[0], s->n_pair_good[1], percent(b0, s->n_pair_good[0], s->n_pair_all[0]), percent(b1, s->n_pair_good[1], s->n_pair_all[1])); fprintf(samtools_stdout, "%lld + %lld with itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]); fprintf(samtools_stdout, "%lld + %lld singletons (%s : %s)\n", s->n_sgltn[0], s->n_sgltn[1], percent(b0, s->n_sgltn[0], s->n_pair_all[0]), percent(b1, s->n_sgltn[1], s->n_pair_all[1])); fprintf(samtools_stdout, "%lld + %lld with mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]); fprintf(samtools_stdout, "%lld + %lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]); } static void out_fmt_json(bam_flagstat_t *s) { char b0[16], b1[16], p0[16], p1[16], pp0[16], pp1[16], s0[16], s1[16]; fprintf(samtools_stdout, "{\n \"QC-passed reads\": { \n" " \"total\": %lld, \n" " \"primary\": %lld, \n" " \"secondary\": %lld, \n" " \"supplementary\": %lld, \n" " \"duplicates\": %lld, \n" " \"primary duplicates\": %lld, \n" " \"mapped\": %lld, \n" " \"mapped %%\": %s, \n" " \"primary mapped\": %lld, \n" " \"primary mapped %%\": %s, \n" " \"paired in sequencing\": %lld, \n" " \"read1\": %lld, \n" " \"read2\": %lld, \n" " \"properly paired\": %lld, \n" " \"properly paired %%\": %s, \n" " \"with itself and mate mapped\": %lld, \n" " \"singletons\": %lld, \n" " \"singletons %%\": %s, \n" " \"with mate mapped to a different chr\": %lld, \n" " \"with mate mapped to a different chr (mapQ >= 5)\": %lld \n" " }," "\n \"QC-failed reads\": { \n" " \"total\": %lld, \n" " \"primary\": %lld, \n" " \"secondary\": %lld, \n" " \"supplementary\": %lld, \n" " \"duplicates\": %lld, \n" " \"primary duplicates\": %lld, \n" " \"mapped\": %lld, \n" " \"mapped %%\": %s, \n" " \"primary mapped\": %lld, \n" " \"primary mapped %%\": %s, \n" " \"paired in sequencing\": %lld, \n" " \"read1\": %lld, \n" " \"read2\": %lld, \n" " \"properly paired\": %lld, \n" " \"properly paired %%\": %s, \n" " \"with itself and mate mapped\": %lld, \n" " \"singletons\": %lld, \n" " \"singletons %%\": %s, \n" " \"with mate mapped to a different chr\": %lld, \n" " \"with mate mapped to a different chr (mapQ >= 5)\": %lld \n" " }\n" "}\n", s->n_reads[0], s->n_primary[0], s->n_secondary[0], s->n_supp[0], s->n_dup[0], s->n_pdup[0], s->n_mapped[0], percent_json(b0, s->n_mapped[0], s->n_reads[0]), s->n_pmapped[0], percent_json(p0, s->n_pmapped[0], s->n_primary[0]), s->n_pair_all[0], s->n_read1[0], s->n_read2[0], s->n_pair_good[0], percent_json(pp0, s->n_pair_good[0], s->n_pair_all[0]), s->n_pair_map[0], s->n_sgltn[0], percent_json(s0, s->n_sgltn[0], s->n_pair_all[0]), s->n_diffchr[0], s->n_diffhigh[0], s->n_reads[1], s->n_primary[1], s->n_secondary[1], s->n_supp[1], s->n_dup[1], s->n_pdup[1], s->n_mapped[1], percent_json(b1, s->n_mapped[1], s->n_reads[1]), s->n_pmapped[1], percent_json(p1, s->n_pmapped[1], s->n_primary[1]), s->n_pair_all[1], s->n_read1[1], s->n_read2[1], s->n_pair_good[1], percent_json(pp1, s->n_pair_good[1], s->n_pair_all[1]), s->n_pair_map[1], s->n_sgltn[1], percent_json(s1, s->n_sgltn[1], s->n_pair_all[1]), s->n_diffchr[1], s->n_diffhigh[1] ); } static void out_fmt_tsv(bam_flagstat_t *s) { char b0[16], b1[16]; fprintf(samtools_stdout, "%lld\t%lld\ttotal (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]); fprintf(samtools_stdout, "%lld\t%lld\tprimary\n", s->n_primary[0], s->n_primary[1]); fprintf(samtools_stdout, "%lld\t%lld\tsecondary\n", s->n_secondary[0], s->n_secondary[1]); fprintf(samtools_stdout, "%lld\t%lld\tsupplementary\n", s->n_supp[0], s->n_supp[1]); fprintf(samtools_stdout, "%lld\t%lld\tduplicates\n", s->n_dup[0], s->n_dup[1]); fprintf(samtools_stdout, "%lld\t%lld\tprimary duplicates\n", s->n_pdup[0], s->n_pdup[1]); fprintf(samtools_stdout, "%lld\t%lld\tmapped\n", s->n_mapped[0], s->n_mapped[1]); fprintf(samtools_stdout, "%s\t%s\tmapped %%\n", percent(b0, s->n_mapped[0], s->n_reads[0]), percent(b1, s->n_mapped[1], s->n_reads[1])); fprintf(samtools_stdout, "%lld\t%lld\tprimary mapped\n", s->n_pmapped[0], s->n_pmapped[1]); fprintf(samtools_stdout, "%s\t%s\tprimary mapped %%\n", percent(b0, s->n_pmapped[0], s->n_primary[0]), percent(b1, s->n_pmapped[1], s->n_primary[1])); fprintf(samtools_stdout, "%lld\t%lld\tpaired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]); fprintf(samtools_stdout, "%lld\t%lld\tread1\n", s->n_read1[0], s->n_read1[1]); fprintf(samtools_stdout, "%lld\t%lld\tread2\n", s->n_read2[0], s->n_read2[1]); fprintf(samtools_stdout, "%lld\t%lld\tproperly paired\n", s->n_pair_good[0], s->n_pair_good[1]); fprintf(samtools_stdout, "%s\t%s\tproperly paired %%\n", percent(b0, s->n_pair_good[0], s->n_pair_all[0]), percent(b1, s->n_pair_good[1], s->n_pair_all[1])); fprintf(samtools_stdout, "%lld\t%lld\twith itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]); fprintf(samtools_stdout, "%lld\t%lld\tsingletons\n", s->n_sgltn[0], s->n_sgltn[1]); fprintf(samtools_stdout, "%s\t%s\tsingletons %%\n", percent(b0, s->n_sgltn[0], s->n_pair_all[0]), percent(b1, s->n_sgltn[1], s->n_pair_all[1])); fprintf(samtools_stdout, "%lld\t%lld\twith mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]); fprintf(samtools_stdout, "%lld\t%lld\twith mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]); } /* * Select flagstats output format to print. */ static void output_fmt(bam_flagstat_t *s, const char *out_fmt) { if (strcmp(out_fmt, "json") == 0 || strcmp(out_fmt, "JSON") == 0) { out_fmt_json(s); } else if (strcmp(out_fmt, "tsv") == 0 || strcmp(out_fmt, "TSV") == 0) { out_fmt_tsv(s); } else { out_fmt_default(s); } } int bam_flagstat(int argc, char *argv[]) { samFile *fp; sam_hdr_t *header; bam_flagstat_t *s; const char *out_fmt = "default"; int c, status = EXIT_SUCCESS; enum { INPUT_FMT_OPTION = CHAR_MAX+1, }; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', '-', '-', '@'), {NULL, 0, NULL, 0} }; while ((c = getopt_long(argc, argv, "@:O:", lopts, NULL)) >= 0) { switch (c) { case 'O': out_fmt = optarg; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage_exit(samtools_stderr, EXIT_FAILURE); } } if (argc != optind+1) { if (argc == optind) usage_exit(samtools_stdout, EXIT_SUCCESS); else usage_exit(samtools_stderr, EXIT_FAILURE); } fp = sam_open_format(argv[optind], "r", &ga.in); if (fp == NULL) { print_error_errno("flagstat", "Cannot open input file \"%s\"", argv[optind]); return 1; } if (ga.nthreads > 0) hts_set_threads(fp, ga.nthreads); if (hts_set_opt(fp, CRAM_OPT_REQUIRED_FIELDS, SAM_FLAG | SAM_MAPQ | SAM_RNEXT)) { fprintf(samtools_stderr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n"); return 1; } if (hts_set_opt(fp, CRAM_OPT_DECODE_MD, 0)) { fprintf(samtools_stderr, "Failed to set CRAM_OPT_DECODE_MD value\n"); return 1; } header = sam_hdr_read(fp); if (header == NULL) { fprintf(samtools_stderr, "Failed to read header for \"%s\"\n", argv[optind]); return 1; } s = bam_flagstat_core(fp, header); if (s) { output_fmt(s, out_fmt); free(s); } else { print_error("flagstat", "error reading from \"%s\"", argv[optind]); status = EXIT_FAILURE; } sam_hdr_destroy(header); sam_close(fp); sam_global_args_free(&ga); return status; } pysam-0.23.0/samtools/bamshuf.c000066400000000000000000000502241475062545500163770ustar00rootroot00000000000000/* bamshuf.c -- collate subcommand. Copyright (C) 2012 Broad Institute. Copyright (C) 2013, 2015-2019,2023 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #ifdef _WIN32 # define WIN32_LEAN_AND_MEAN # include #endif #include "htslib/sam.h" #include "htslib/hts.h" #include "htslib/ksort.h" #include "samtools.h" #include "htslib/thread_pool.h" #include "sam_opts.h" #include "htslib/khash.h" #define DEF_CLEVEL 1 static inline unsigned hash_Wang(unsigned key) { key += ~(key << 15); key ^= (key >> 10); key += (key << 3); key ^= (key >> 6); key += ~(key << 11); key ^= (key >> 16); return key; } static inline unsigned hash_X31_Wang(const char *s) { unsigned h = *s; if (h) { for (++s ; *s; ++s) h = (h << 5) - h + *s; return hash_Wang(h); } else return 0; } typedef struct { unsigned key; bam1_t *b; } elem_t; static inline int elem_lt(elem_t x, elem_t y) { if (x.key < y.key) return 1; if (x.key == y.key) { int t; t = strcmp(bam_get_qname(x.b), bam_get_qname(y.b)); if (t < 0) return 1; return (t == 0 && ((x.b->core.flag>>6&3) < (y.b->core.flag>>6&3))); } else return 0; } KSORT_INIT(bamshuf, elem_t, elem_lt) typedef struct { int written; bam1_t *b; } bam_item_t; typedef struct { bam1_t *bam_pool; bam_item_t *items; size_t size; size_t index; } bam_list_t; typedef struct { bam_item_t *bi; } store_item_t; KHASH_MAP_INIT_STR(bam_store, store_item_t) static bam_item_t *store_bam(bam_list_t *list) { size_t old_index = list->index; list->items[list->index++].written = 0; if (list->index >= list->size) list->index = 0; return &list->items[old_index]; } static int write_bam_needed(bam_list_t *list) { return !list->items[list->index].written; } static void mark_bam_as_written(bam_list_t *list) { list->items[list->index].written = 1; } static int create_bam_list(bam_list_t *list, size_t max_size) { size_t i; list->size = list->index = 0; list->items = NULL; list->bam_pool = NULL; if ((list->items = malloc(max_size * sizeof(bam_item_t))) == NULL) { return 1; } if ((list->bam_pool = calloc(max_size, sizeof(bam1_t))) == NULL) { return 1; } for (i = 0; i < max_size; i++) { list->items[i].b = &list->bam_pool[i]; list->items[i].written = 1; } list->size = max_size; list->index = 0; return 0; } static void destroy_bam_list(bam_list_t *list) { size_t i; for (i = 0; i < list->size; i++) { free(list->bam_pool[i].data); } free(list->bam_pool); free(list->items); } static inline int write_to_bin_file(bam1_t *bam, int64_t *count, samFile **bin_files, char **names, sam_hdr_t *header, int files) { uint32_t x; x = hash_X31_Wang(bam_get_qname(bam)) % files; if (sam_write1(bin_files[x], header, bam) < 0) { print_error_errno("collate", "Couldn't write to intermediate file \"%s\"", names[x]); return 1; } ++count[x]; return 0; } static int bamshuf(const char *fn, int n_files, const char *pre, int clevel, int is_stdout, const char *output_file, int fast, int store_max, sam_global_args *ga, char *arg_list, int no_pg) { samFile *fp, *fpw = NULL, **fpt = NULL; char **fnt = NULL, modew[8]; bam1_t *b = NULL; int i, counter, l, r; sam_hdr_t *h = NULL; int64_t j, max_cnt = 0, *cnt = NULL; elem_t *a = NULL; htsThreadPool p = {NULL, 0}; if (ga->nthreads > 0) { if (!(p.pool = hts_tpool_init(ga->nthreads))) { print_error_errno("collate", "Error creating thread pool\n"); return 1; } } // Read input, distribute reads pseudo-randomly into n_files temporary // files. fp = sam_open_format(fn ? fn : "-", "r", &ga->in); if (fp == NULL) { print_error_errno("collate", "Cannot open input file \"%s\"", fn); return 1; } if (p.pool) hts_set_opt(fp, HTS_OPT_THREAD_POOL, &p); h = sam_hdr_read(fp); if (h == NULL) { fprintf(stderr, "Couldn't read header for '%s'\n", fn); goto fail; } if ((-1 == sam_hdr_update_hd(h, "SO", "unsorted", "GO", "query")) && (-1 == sam_hdr_add_line(h, "HD", "VN", SAM_FORMAT_VERSION, "SO", "unsorted", "GO", "query", NULL)) ) { print_error("collate", "failed to update HD line\n"); goto fail; } // open final output file l = strlen(pre); sprintf(modew, "wb%d", (clevel >= 0 && clevel <= 9)? clevel : DEF_CLEVEL); if (!is_stdout && !output_file) { // output to a file (name based on prefix) char *fnw = (char*)calloc(l + 5, 1); if (!fnw) goto mem_fail; if (ga->out.format == unknown_format) sprintf(fnw, "%s.bam", pre); // "wb" above makes BAM the default else sprintf(fnw, "%s.%s", pre, hts_format_file_extension(&ga->out)); fpw = sam_open_format(fnw, modew, &ga->out); free(fnw); } else if (output_file) { // output to a given file modew[0] = 'w'; modew[1] = '\0'; sam_open_mode(modew + 1, output_file, NULL); j = strlen(modew); snprintf(modew + j, sizeof(modew) - j, "%d", (clevel >= 0 && clevel <= 9)? clevel : DEF_CLEVEL); fpw = sam_open_format(output_file, modew, &ga->out); } else fpw = sam_open_format("-", modew, &ga->out); // output to stdout if (fpw == NULL) { if (is_stdout) print_error_errno("collate", "Cannot open standard output"); else print_error_errno("collate", "Cannot open output file \"%s.bam\"", pre); goto fail; } if (p.pool) hts_set_opt(fpw, HTS_OPT_THREAD_POOL, &p); if (!no_pg && sam_hdr_add_pg(h, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { print_error("collate", "failed to add PG line to header of \"%s\"", output_file); goto fail; } if (sam_hdr_write(fpw, h) < 0) { print_error_errno("collate", "Couldn't write header"); goto fail; } fnt = (char**)calloc(n_files, sizeof(char*)); if (!fnt) goto mem_fail; fpt = (samFile**)calloc(n_files, sizeof(samFile*)); if (!fpt) goto mem_fail; cnt = (int64_t*)calloc(n_files, 8); if (!cnt) goto mem_fail; for (i = counter = 0; i < n_files; ++i) { fnt[i] = (char*)calloc(l + 20, 1); if (!fnt[i]) goto mem_fail; do { sprintf(fnt[i], "%s.%04d.bam", pre, counter++); fpt[i] = sam_open(fnt[i], "wxb1"); } while (!fpt[i] && errno == EEXIST); if (fpt[i] == NULL) { print_error_errno("collate", "Cannot open intermediate file \"%s\"", fnt[i]); goto fail; } if (p.pool) hts_set_opt(fpt[i], HTS_OPT_THREAD_POOL, &p); if (sam_hdr_write(fpt[i], h) < 0) { print_error_errno("collate", "Couldn't write header to intermediate file \"%s\"", fnt[i]); goto fail; } } if (fast) { khash_t(bam_store) *stored = kh_init(bam_store); khiter_t itr; bam_list_t list; int err = 0; if (!stored) goto mem_fail; if (store_max < 2) store_max = 2; if (create_bam_list(&list, store_max)) { fprintf(stderr, "[collate[ ERROR: unable to create bam list.\n"); err = 1; goto fast_fail; } while ((r = sam_read1(fp, h, list.items[list.index].b)) >= 0) { int ret; bam1_t *b = list.items[list.index].b; int readflag = b->core.flag & (BAM_FREAD1 | BAM_FREAD2); // strictly paired reads only if (!(b->core.flag & (BAM_FSECONDARY | BAM_FSUPPLEMENTARY)) && (readflag == BAM_FREAD1 || readflag == BAM_FREAD2)) { itr = kh_get(bam_store, stored, bam_get_qname(b)); if (itr == kh_end(stored)) { // new read itr = kh_put(bam_store, stored, bam_get_qname(b), &ret); if (ret > 0) { // okay to go ahead store it kh_value(stored, itr).bi = store_bam(&list); // see if the next one on the list needs to be written out if (write_bam_needed(&list)) { if (write_to_bin_file(list.items[list.index].b, cnt, fpt, fnt, h, n_files) < 0) { fprintf(stderr, "[collate] ERROR: could not write line.\n"); err = 1; goto fast_fail; } else { mark_bam_as_written(&list); itr = kh_get(bam_store, stored, bam_get_qname(list.items[list.index].b)); if (itr != kh_end(stored)) { kh_del(bam_store, stored, itr); } else { fprintf(stderr, "[collate] ERROR: stored value not in hash.\n"); err = 1; goto fast_fail; } } } } else if (ret == 0) { fprintf(stderr, "[collate] ERROR: value already in hash.\n"); err = 1; goto fast_fail; } else { fprintf(stderr, "[collate] ERROR: unable to store in hash.\n"); err = 1; goto fast_fail; } } else { // we have a match // write out the reads in R1 R2 order bam1_t *r1, *r2; if (b->core.flag & BAM_FREAD1) { r1 = b; r2 = kh_value(stored, itr).bi->b; } else { r1 = kh_value(stored, itr).bi->b; r2 = b; } if (sam_write1(fpw, h, r1) < 0) { fprintf(stderr, "[collate] ERROR: could not write r1 alignment.\n"); err = 1; goto fast_fail; } if (sam_write1(fpw, h, r2) < 0) { fprintf(stderr, "[collate] ERROR: could not write r2 alignment.\n"); err = 1; goto fast_fail; } mark_bam_as_written(&list); // remove stored read kh_value(stored, itr).bi->written = 1; kh_del(bam_store, stored, itr); } } } for (list.index = 0; list.index < list.size; list.index++) { if (write_bam_needed(&list)) { bam1_t *b = list.items[list.index].b; if (write_to_bin_file(b, cnt, fpt, fnt, h, n_files)) { err = 1; goto fast_fail; } else { itr = kh_get(bam_store, stored, bam_get_qname(b)); kh_del(bam_store, stored, itr); } } } fast_fail: if (err) { for (itr = kh_begin(stored); itr != kh_end(stored); ++itr) { if (kh_exist(stored, itr)) { kh_del(bam_store, stored, itr); } } kh_destroy(bam_store, stored); destroy_bam_list(&list); goto fail; } else { kh_destroy(bam_store, stored); destroy_bam_list(&list); } } else { b = bam_init1(); if (!b) goto mem_fail; while ((r = sam_read1(fp, h, b)) >= 0) { if (write_to_bin_file(b, cnt, fpt, fnt, h, n_files)) { bam_destroy1(b); goto fail; } } bam_destroy1(b); } if (r < -1) { fprintf(stderr, "Error reading input file\n"); goto fail; } for (i = 0; i < n_files; ++i) { // Close split output r = sam_close(fpt[i]); fpt[i] = NULL; if (r < 0) { fprintf(stderr, "Error on closing '%s'\n", fnt[i]); return 1; } // Find biggest count if (max_cnt < cnt[i]) max_cnt = cnt[i]; } free(fpt); fpt = NULL; sam_close(fp); fp = NULL; // merge a = malloc(max_cnt * sizeof(elem_t)); if (!a) goto mem_fail; for (j = 0; j < max_cnt; ++j) { a[j].b = bam_init1(); if (!a[j].b) { max_cnt = j; goto mem_fail; } } for (i = 0; i < n_files; ++i) { int64_t c = cnt[i]; fp = sam_open_format(fnt[i], "r", &ga->in); if (NULL == fp) { print_error_errno("collate", "Couldn't open \"%s\"", fnt[i]); goto fail; } if (p.pool) hts_set_opt(fp, HTS_OPT_THREAD_POOL, &p); sam_hdr_destroy(sam_hdr_read(fp)); // Skip over header // Slurp in one of the split files for (j = 0; j < c; ++j) { if (sam_read1(fp, h, a[j].b) < 0) { fprintf(stderr, "Error reading '%s'\n", fnt[i]); goto fail; } a[j].key = hash_X31_Wang(bam_get_qname(a[j].b)); } sam_close(fp); unlink(fnt[i]); free(fnt[i]); fnt[i] = NULL; ks_introsort(bamshuf, c, a); // Shuffle all the reads // Write them out again for (j = 0; j < c; ++j) { if (sam_write1(fpw, h, a[j].b) < 0) { print_error_errno("collate", "Error writing to output"); goto fail; } } } sam_hdr_destroy(h); for (j = 0; j < max_cnt; ++j) bam_destroy1(a[j].b); free(a); free(fnt); free(cnt); sam_global_args_free(ga); if (sam_close(fpw) < 0) { fprintf(stderr, "Error on closing output\n"); return 1; } if (p.pool) hts_tpool_destroy(p.pool); return 0; mem_fail: fprintf(stderr, "Out of memory\n"); fail: if (fp) sam_close(fp); if (fpw) sam_close(fpw); if (h) sam_hdr_destroy(h); for (i = 0; i < n_files; ++i) { if (fnt) free(fnt[i]); if (fpt && fpt[i]) sam_close(fpt[i]); } if (a) { for (j = 0; j < max_cnt; ++j) bam_destroy1(a[j].b); free(a); } free(fnt); free(fpt); free(cnt); if (p.pool) hts_tpool_destroy(p.pool); sam_global_args_free(ga); return 1; } static int usage(FILE *fp, int n_files, int reads_store) { fprintf(fp, "Usage: samtools collate [options...] []\n\n" "Options:\n" " -O Output to stdout\n" " -o Output file name (use prefix if not set)\n" " -u Uncompressed BAM output\n" " -f Fast (only primary alignments)\n" " -r Working reads stored (with -f) [%d]\n" // reads_store " -l INT Compression level [%d]\n" // DEF_CLEVEL " -n INT Number of temporary files [%d]\n" // n_files " -T PREFIX\n" " Write temporary files to PREFIX.nnnn.bam\n" " --no-PG do not add a PG line\n", reads_store, DEF_CLEVEL, n_files); sam_global_opt_help(fp, "-....@-."); fprintf(fp, " is required unless the -o or -O options are used.\n"); return 1; } char *generate_prefix(const char *out_fn) { char *prefix; unsigned int pid = getpid(); if (out_fn && !(*out_fn == '-' && out_fn[1] == '\0')) { // ... size_t plen = strlen(out_fn) + 50; if (!(prefix = malloc(plen))) { perror("collate"); return NULL; } snprintf(prefix, plen, "%s.collate%x", out_fn, pid); return prefix; } #ifdef _WIN32 # define PREFIX_LEN (MAX_PATH + 16) DWORD ret; prefix = calloc(PREFIX_LEN, sizeof(*prefix)); if (!prefix) { perror("collate"); return NULL; } ret = GetTempPathA(MAX_PATH, prefix); if (ret > MAX_PATH || ret == 0) { fprintf(stderr, "[E::collate] Couldn't get path for temporary files.\n"); free(prefix); return NULL; } snprintf(prefix + ret, PREFIX_LEN - ret, "\\%x", pid); return prefix; #else char *tmp_env = getenv("TMPDIR"); if (!tmp_env) tmp_env = "/tmp"; size_t prefix_len = strlen(tmp_env)+20; prefix = malloc(prefix_len); if (!prefix) { perror("collate"); return NULL; } snprintf(prefix, prefix_len, "%s/collate%x", tmp_env, pid); return prefix; #endif } int main_bamshuf(int argc, char *argv[]) { int c, n_files = 64, clevel = DEF_CLEVEL, is_stdout = 0, is_un = 0, fast_coll = 0, reads_store = 10000, ret, pre_mem = 0, no_pg = 0; const char *output_file = NULL; char *prefix = NULL, *arg_list = NULL; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0, '@'), {"no-PG", no_argument, NULL, 1}, { NULL, 0, NULL, 0 } }; while ((c = getopt_long(argc, argv, "n:l:uOo:@:fr:T:", lopts, NULL)) >= 0) { switch (c) { case 'n': n_files = atoi(optarg); break; case 'l': clevel = atoi(optarg); break; case 'u': is_un = 1; break; case 'O': is_stdout = 1; break; case 'o': output_file = optarg; break; case 'f': fast_coll = 1; break; case 'r': reads_store = atoi(optarg); break; case 'T': prefix = optarg; break; case 1: no_pg = 1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': return usage(stderr, n_files, reads_store); } } if (is_un) clevel = 0; if (argc >= optind + 2) prefix = argv[optind+1]; if (argc == optind) { if (argc > 1 || !isatty(STDIN_FILENO)) fprintf(stderr, "collate: no input filename specified.\n"); return usage(argc > 1 || !isatty(STDIN_FILENO) ? stderr : stdout, n_files, reads_store); } if (!(prefix || is_stdout || output_file)) return usage(stderr, n_files, reads_store); if (is_stdout && output_file) { fprintf(stderr, "collate: -o and -O options cannot be used together.\n"); return usage(stderr, n_files, reads_store); } if (!prefix) { prefix = generate_prefix(output_file); pre_mem = 1; } if (!prefix) return EXIT_FAILURE; if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) { print_error("collate", "failed to create arg_list"); return 1; } ret = bamshuf(argv[optind], n_files, prefix, clevel, is_stdout, output_file, fast_coll, reads_store, &ga, arg_list, no_pg); if (pre_mem) free(prefix); free(arg_list); return ret; } pysam-0.23.0/samtools/bamshuf.c.pysam.c000066400000000000000000000506001475062545500177460ustar00rootroot00000000000000#include "samtools.pysam.h" /* bamshuf.c -- collate subcommand. Copyright (C) 2012 Broad Institute. Copyright (C) 2013, 2015-2019,2023 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #ifdef _WIN32 # define WIN32_LEAN_AND_MEAN # include #endif #include "htslib/sam.h" #include "htslib/hts.h" #include "htslib/ksort.h" #include "samtools.h" #include "htslib/thread_pool.h" #include "sam_opts.h" #include "htslib/khash.h" #define DEF_CLEVEL 1 static inline unsigned hash_Wang(unsigned key) { key += ~(key << 15); key ^= (key >> 10); key += (key << 3); key ^= (key >> 6); key += ~(key << 11); key ^= (key >> 16); return key; } static inline unsigned hash_X31_Wang(const char *s) { unsigned h = *s; if (h) { for (++s ; *s; ++s) h = (h << 5) - h + *s; return hash_Wang(h); } else return 0; } typedef struct { unsigned key; bam1_t *b; } elem_t; static inline int elem_lt(elem_t x, elem_t y) { if (x.key < y.key) return 1; if (x.key == y.key) { int t; t = strcmp(bam_get_qname(x.b), bam_get_qname(y.b)); if (t < 0) return 1; return (t == 0 && ((x.b->core.flag>>6&3) < (y.b->core.flag>>6&3))); } else return 0; } KSORT_INIT(bamshuf, elem_t, elem_lt) typedef struct { int written; bam1_t *b; } bam_item_t; typedef struct { bam1_t *bam_pool; bam_item_t *items; size_t size; size_t index; } bam_list_t; typedef struct { bam_item_t *bi; } store_item_t; KHASH_MAP_INIT_STR(bam_store, store_item_t) static bam_item_t *store_bam(bam_list_t *list) { size_t old_index = list->index; list->items[list->index++].written = 0; if (list->index >= list->size) list->index = 0; return &list->items[old_index]; } static int write_bam_needed(bam_list_t *list) { return !list->items[list->index].written; } static void mark_bam_as_written(bam_list_t *list) { list->items[list->index].written = 1; } static int create_bam_list(bam_list_t *list, size_t max_size) { size_t i; list->size = list->index = 0; list->items = NULL; list->bam_pool = NULL; if ((list->items = malloc(max_size * sizeof(bam_item_t))) == NULL) { return 1; } if ((list->bam_pool = calloc(max_size, sizeof(bam1_t))) == NULL) { return 1; } for (i = 0; i < max_size; i++) { list->items[i].b = &list->bam_pool[i]; list->items[i].written = 1; } list->size = max_size; list->index = 0; return 0; } static void destroy_bam_list(bam_list_t *list) { size_t i; for (i = 0; i < list->size; i++) { free(list->bam_pool[i].data); } free(list->bam_pool); free(list->items); } static inline int write_to_bin_file(bam1_t *bam, int64_t *count, samFile **bin_files, char **names, sam_hdr_t *header, int files) { uint32_t x; x = hash_X31_Wang(bam_get_qname(bam)) % files; if (sam_write1(bin_files[x], header, bam) < 0) { print_error_errno("collate", "Couldn't write to intermediate file \"%s\"", names[x]); return 1; } ++count[x]; return 0; } static int bamshuf(const char *fn, int n_files, const char *pre, int clevel, int is_stdout, const char *output_file, int fast, int store_max, sam_global_args *ga, char *arg_list, int no_pg) { samFile *fp, *fpw = NULL, **fpt = NULL; char **fnt = NULL, modew[8]; bam1_t *b = NULL; int i, counter, l, r; sam_hdr_t *h = NULL; int64_t j, max_cnt = 0, *cnt = NULL; elem_t *a = NULL; htsThreadPool p = {NULL, 0}; if (ga->nthreads > 0) { if (!(p.pool = hts_tpool_init(ga->nthreads))) { print_error_errno("collate", "Error creating thread pool\n"); return 1; } } // Read input, distribute reads pseudo-randomly into n_files temporary // files. fp = sam_open_format(fn ? fn : "-", "r", &ga->in); if (fp == NULL) { print_error_errno("collate", "Cannot open input file \"%s\"", fn); return 1; } if (p.pool) hts_set_opt(fp, HTS_OPT_THREAD_POOL, &p); h = sam_hdr_read(fp); if (h == NULL) { fprintf(samtools_stderr, "Couldn't read header for '%s'\n", fn); goto fail; } if ((-1 == sam_hdr_update_hd(h, "SO", "unsorted", "GO", "query")) && (-1 == sam_hdr_add_line(h, "HD", "VN", SAM_FORMAT_VERSION, "SO", "unsorted", "GO", "query", NULL)) ) { print_error("collate", "failed to update HD line\n"); goto fail; } // open final output file l = strlen(pre); sprintf(modew, "wb%d", (clevel >= 0 && clevel <= 9)? clevel : DEF_CLEVEL); if (!is_stdout && !output_file) { // output to a file (name based on prefix) char *fnw = (char*)calloc(l + 5, 1); if (!fnw) goto mem_fail; if (ga->out.format == unknown_format) sprintf(fnw, "%s.bam", pre); // "wb" above makes BAM the default else sprintf(fnw, "%s.%s", pre, hts_format_file_extension(&ga->out)); fpw = sam_open_format(fnw, modew, &ga->out); free(fnw); } else if (output_file) { // output to a given file modew[0] = 'w'; modew[1] = '\0'; sam_open_mode(modew + 1, output_file, NULL); j = strlen(modew); snprintf(modew + j, sizeof(modew) - j, "%d", (clevel >= 0 && clevel <= 9)? clevel : DEF_CLEVEL); fpw = sam_open_format(output_file, modew, &ga->out); } else fpw = sam_open_format("-", modew, &ga->out); // output to samtools_stdout if (fpw == NULL) { if (is_stdout) print_error_errno("collate", "Cannot open standard output"); else print_error_errno("collate", "Cannot open output file \"%s.bam\"", pre); goto fail; } if (p.pool) hts_set_opt(fpw, HTS_OPT_THREAD_POOL, &p); if (!no_pg && sam_hdr_add_pg(h, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { print_error("collate", "failed to add PG line to header of \"%s\"", output_file); goto fail; } if (sam_hdr_write(fpw, h) < 0) { print_error_errno("collate", "Couldn't write header"); goto fail; } fnt = (char**)calloc(n_files, sizeof(char*)); if (!fnt) goto mem_fail; fpt = (samFile**)calloc(n_files, sizeof(samFile*)); if (!fpt) goto mem_fail; cnt = (int64_t*)calloc(n_files, 8); if (!cnt) goto mem_fail; for (i = counter = 0; i < n_files; ++i) { fnt[i] = (char*)calloc(l + 20, 1); if (!fnt[i]) goto mem_fail; do { sprintf(fnt[i], "%s.%04d.bam", pre, counter++); fpt[i] = sam_open(fnt[i], "wxb1"); } while (!fpt[i] && errno == EEXIST); if (fpt[i] == NULL) { print_error_errno("collate", "Cannot open intermediate file \"%s\"", fnt[i]); goto fail; } if (p.pool) hts_set_opt(fpt[i], HTS_OPT_THREAD_POOL, &p); if (sam_hdr_write(fpt[i], h) < 0) { print_error_errno("collate", "Couldn't write header to intermediate file \"%s\"", fnt[i]); goto fail; } } if (fast) { khash_t(bam_store) *stored = kh_init(bam_store); khiter_t itr; bam_list_t list; int err = 0; if (!stored) goto mem_fail; if (store_max < 2) store_max = 2; if (create_bam_list(&list, store_max)) { fprintf(samtools_stderr, "[collate[ ERROR: unable to create bam list.\n"); err = 1; goto fast_fail; } while ((r = sam_read1(fp, h, list.items[list.index].b)) >= 0) { int ret; bam1_t *b = list.items[list.index].b; int readflag = b->core.flag & (BAM_FREAD1 | BAM_FREAD2); // strictly paired reads only if (!(b->core.flag & (BAM_FSECONDARY | BAM_FSUPPLEMENTARY)) && (readflag == BAM_FREAD1 || readflag == BAM_FREAD2)) { itr = kh_get(bam_store, stored, bam_get_qname(b)); if (itr == kh_end(stored)) { // new read itr = kh_put(bam_store, stored, bam_get_qname(b), &ret); if (ret > 0) { // okay to go ahead store it kh_value(stored, itr).bi = store_bam(&list); // see if the next one on the list needs to be written out if (write_bam_needed(&list)) { if (write_to_bin_file(list.items[list.index].b, cnt, fpt, fnt, h, n_files) < 0) { fprintf(samtools_stderr, "[collate] ERROR: could not write line.\n"); err = 1; goto fast_fail; } else { mark_bam_as_written(&list); itr = kh_get(bam_store, stored, bam_get_qname(list.items[list.index].b)); if (itr != kh_end(stored)) { kh_del(bam_store, stored, itr); } else { fprintf(samtools_stderr, "[collate] ERROR: stored value not in hash.\n"); err = 1; goto fast_fail; } } } } else if (ret == 0) { fprintf(samtools_stderr, "[collate] ERROR: value already in hash.\n"); err = 1; goto fast_fail; } else { fprintf(samtools_stderr, "[collate] ERROR: unable to store in hash.\n"); err = 1; goto fast_fail; } } else { // we have a match // write out the reads in R1 R2 order bam1_t *r1, *r2; if (b->core.flag & BAM_FREAD1) { r1 = b; r2 = kh_value(stored, itr).bi->b; } else { r1 = kh_value(stored, itr).bi->b; r2 = b; } if (sam_write1(fpw, h, r1) < 0) { fprintf(samtools_stderr, "[collate] ERROR: could not write r1 alignment.\n"); err = 1; goto fast_fail; } if (sam_write1(fpw, h, r2) < 0) { fprintf(samtools_stderr, "[collate] ERROR: could not write r2 alignment.\n"); err = 1; goto fast_fail; } mark_bam_as_written(&list); // remove stored read kh_value(stored, itr).bi->written = 1; kh_del(bam_store, stored, itr); } } } for (list.index = 0; list.index < list.size; list.index++) { if (write_bam_needed(&list)) { bam1_t *b = list.items[list.index].b; if (write_to_bin_file(b, cnt, fpt, fnt, h, n_files)) { err = 1; goto fast_fail; } else { itr = kh_get(bam_store, stored, bam_get_qname(b)); kh_del(bam_store, stored, itr); } } } fast_fail: if (err) { for (itr = kh_begin(stored); itr != kh_end(stored); ++itr) { if (kh_exist(stored, itr)) { kh_del(bam_store, stored, itr); } } kh_destroy(bam_store, stored); destroy_bam_list(&list); goto fail; } else { kh_destroy(bam_store, stored); destroy_bam_list(&list); } } else { b = bam_init1(); if (!b) goto mem_fail; while ((r = sam_read1(fp, h, b)) >= 0) { if (write_to_bin_file(b, cnt, fpt, fnt, h, n_files)) { bam_destroy1(b); goto fail; } } bam_destroy1(b); } if (r < -1) { fprintf(samtools_stderr, "Error reading input file\n"); goto fail; } for (i = 0; i < n_files; ++i) { // Close split output r = sam_close(fpt[i]); fpt[i] = NULL; if (r < 0) { fprintf(samtools_stderr, "Error on closing '%s'\n", fnt[i]); return 1; } // Find biggest count if (max_cnt < cnt[i]) max_cnt = cnt[i]; } free(fpt); fpt = NULL; sam_close(fp); fp = NULL; // merge a = malloc(max_cnt * sizeof(elem_t)); if (!a) goto mem_fail; for (j = 0; j < max_cnt; ++j) { a[j].b = bam_init1(); if (!a[j].b) { max_cnt = j; goto mem_fail; } } for (i = 0; i < n_files; ++i) { int64_t c = cnt[i]; fp = sam_open_format(fnt[i], "r", &ga->in); if (NULL == fp) { print_error_errno("collate", "Couldn't open \"%s\"", fnt[i]); goto fail; } if (p.pool) hts_set_opt(fp, HTS_OPT_THREAD_POOL, &p); sam_hdr_destroy(sam_hdr_read(fp)); // Skip over header // Slurp in one of the split files for (j = 0; j < c; ++j) { if (sam_read1(fp, h, a[j].b) < 0) { fprintf(samtools_stderr, "Error reading '%s'\n", fnt[i]); goto fail; } a[j].key = hash_X31_Wang(bam_get_qname(a[j].b)); } sam_close(fp); unlink(fnt[i]); free(fnt[i]); fnt[i] = NULL; ks_introsort(bamshuf, c, a); // Shuffle all the reads // Write them out again for (j = 0; j < c; ++j) { if (sam_write1(fpw, h, a[j].b) < 0) { print_error_errno("collate", "Error writing to output"); goto fail; } } } sam_hdr_destroy(h); for (j = 0; j < max_cnt; ++j) bam_destroy1(a[j].b); free(a); free(fnt); free(cnt); sam_global_args_free(ga); if (sam_close(fpw) < 0) { fprintf(samtools_stderr, "Error on closing output\n"); return 1; } if (p.pool) hts_tpool_destroy(p.pool); return 0; mem_fail: fprintf(samtools_stderr, "Out of memory\n"); fail: if (fp) sam_close(fp); if (fpw) sam_close(fpw); if (h) sam_hdr_destroy(h); for (i = 0; i < n_files; ++i) { if (fnt) free(fnt[i]); if (fpt && fpt[i]) sam_close(fpt[i]); } if (a) { for (j = 0; j < max_cnt; ++j) bam_destroy1(a[j].b); free(a); } free(fnt); free(fpt); free(cnt); if (p.pool) hts_tpool_destroy(p.pool); sam_global_args_free(ga); return 1; } static int usage(FILE *fp, int n_files, int reads_store) { fprintf(fp, "Usage: samtools collate [options...] []\n\n" "Options:\n" " -O Output to samtools_stdout\n" " -o Output file name (use prefix if not set)\n" " -u Uncompressed BAM output\n" " -f Fast (only primary alignments)\n" " -r Working reads stored (with -f) [%d]\n" // reads_store " -l INT Compression level [%d]\n" // DEF_CLEVEL " -n INT Number of temporary files [%d]\n" // n_files " -T PREFIX\n" " Write temporary files to PREFIX.nnnn.bam\n" " --no-PG do not add a PG line\n", reads_store, DEF_CLEVEL, n_files); sam_global_opt_help(fp, "-....@-."); fprintf(fp, " is required unless the -o or -O options are used.\n"); return 1; } char *generate_prefix(const char *out_fn) { char *prefix; unsigned int pid = getpid(); if (out_fn && !(*out_fn == '-' && out_fn[1] == '\0')) { // ... size_t plen = strlen(out_fn) + 50; if (!(prefix = malloc(plen))) { perror("collate"); return NULL; } snprintf(prefix, plen, "%s.collate%x", out_fn, pid); return prefix; } #ifdef _WIN32 # define PREFIX_LEN (MAX_PATH + 16) DWORD ret; prefix = calloc(PREFIX_LEN, sizeof(*prefix)); if (!prefix) { perror("collate"); return NULL; } ret = GetTempPathA(MAX_PATH, prefix); if (ret > MAX_PATH || ret == 0) { fprintf(samtools_stderr, "[E::collate] Couldn't get path for temporary files.\n"); free(prefix); return NULL; } snprintf(prefix + ret, PREFIX_LEN - ret, "\\%x", pid); return prefix; #else char *tmp_env = getenv("TMPDIR"); if (!tmp_env) tmp_env = "/tmp"; size_t prefix_len = strlen(tmp_env)+20; prefix = malloc(prefix_len); if (!prefix) { perror("collate"); return NULL; } snprintf(prefix, prefix_len, "%s/collate%x", tmp_env, pid); return prefix; #endif } int main_bamshuf(int argc, char *argv[]) { int c, n_files = 64, clevel = DEF_CLEVEL, is_stdout = 0, is_un = 0, fast_coll = 0, reads_store = 10000, ret, pre_mem = 0, no_pg = 0; const char *output_file = NULL; char *prefix = NULL, *arg_list = NULL; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0, '@'), {"no-PG", no_argument, NULL, 1}, { NULL, 0, NULL, 0 } }; while ((c = getopt_long(argc, argv, "n:l:uOo:@:fr:T:", lopts, NULL)) >= 0) { switch (c) { case 'n': n_files = atoi(optarg); break; case 'l': clevel = atoi(optarg); break; case 'u': is_un = 1; break; case 'O': is_stdout = 1; break; case 'o': output_file = optarg; break; case 'f': fast_coll = 1; break; case 'r': reads_store = atoi(optarg); break; case 'T': prefix = optarg; break; case 1: no_pg = 1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': return usage(samtools_stderr, n_files, reads_store); } } if (is_un) clevel = 0; if (argc >= optind + 2) prefix = argv[optind+1]; if (argc == optind) { if (argc > 1 || !isatty(STDIN_FILENO)) fprintf(samtools_stderr, "collate: no input filename specified.\n"); return usage(argc > 1 || !isatty(STDIN_FILENO) ? samtools_stderr : samtools_stdout, n_files, reads_store); } if (!(prefix || is_stdout || output_file)) return usage(samtools_stderr, n_files, reads_store); if (is_stdout && output_file) { fprintf(samtools_stderr, "collate: -o and -O options cannot be used together.\n"); return usage(samtools_stderr, n_files, reads_store); } if (!prefix) { prefix = generate_prefix(output_file); pre_mem = 1; } if (!prefix) return EXIT_FAILURE; if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) { print_error("collate", "failed to create arg_list"); return 1; } ret = bamshuf(argv[optind], n_files, prefix, clevel, is_stdout, output_file, fast_coll, reads_store, &ga, arg_list, no_pg); if (pre_mem) free(prefix); free(arg_list); return ret; } pysam-0.23.0/samtools/bamtk.c000066400000000000000000000323451475062545500160540ustar00rootroot00000000000000/* bamtk.c -- main samtools command front-end. Copyright (C) 2008-2023 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include "htslib/hts.h" #include "htslib/hfile.h" #include "samtools.h" #include "version.h" int bam_taf2baf(int argc, char *argv[]); int bam_mpileup(int argc, char *argv[]); int bam_merge(int argc, char *argv[]); int bam_index(int argc, char *argv[]); int bam_sort(int argc, char *argv[]); int bam_tview_main(int argc, char *argv[]); int bam_mating(int argc, char *argv[]); int bam_rmdup(int argc, char *argv[]); int bam_flagstat(int argc, char *argv[]); int bam_fillmd(int argc, char *argv[]); int bam_idxstats(int argc, char *argv[]); int bam_markdup(int argc, char *argv[]); int main_samview(int argc, char *argv[]); int main_head(int argc, char *argv[]); int main_reheader(int argc, char *argv[]); int main_cut_target(int argc, char *argv[]); int main_phase(int argc, char *argv[]); int main_cat(int argc, char *argv[]); int main_depth(int argc, char *argv[]); int main_coverage(int argc, char *argv[]); int main_bam2fq(int argc, char *argv[]); int main_pad2unpad(int argc, char *argv[]); int main_bedcov(int argc, char *argv[]); int main_bamshuf(int argc, char *argv[]); int main_stats(int argc, char *argv[]); int main_flags(int argc, char *argv[]); int main_split(int argc, char *argv[]); int main_quickcheck(int argc, char *argv[]); int main_addreplacerg(int argc, char *argv[]); int faidx_main(int argc, char *argv[]); int dict_main(int argc, char *argv[]); int fqidx_main(int argc, char *argv[]); int amplicon_clip_main(int argc, char *argv[]); int main_ampliconstats(int argc, char *argv[]); int main_import(int argc, char *argv[]); int main_samples(int argc, char *argv[]); int main_consensus(int argc, char *argv[]); int main_reference(int argc, char *argv[]); int main_reset(int argc, char *argv[]); int main_cram_size(int argc, char *argv[]); const char *samtools_version(void) { return SAMTOOLS_VERSION; } // These come out of the config.h file built by autoconf or Makefile const char *samtools_feature_string(void) { const char *fmt = #ifdef PACKAGE_URL "build=configure " #else "build=Makefile " #endif #ifdef HAVE_CURSES "curses=yes " #else "curses=no " #endif ; return fmt; } static void long_version(void) { printf("samtools %s\n" "Using htslib %s\n" "Copyright (C) 2024 Genome Research Ltd.\n", samtools_version(), hts_version()); printf("\nSamtools compilation details:\n"); printf(" Features: %s\n", samtools_feature_string()); printf(" CC: %s\n", SAMTOOLS_CC); printf(" CPPFLAGS: %s\n", SAMTOOLS_CPPFLAGS); printf(" CFLAGS: %s\n", SAMTOOLS_CFLAGS); printf(" LDFLAGS: %s\n", SAMTOOLS_LDFLAGS); printf(" HTSDIR: %s\n", SAMTOOLS_HTSDIR); printf(" LIBS: %s\n", SAMTOOLS_LIBS); printf(" CURSES_LIB: %s\n", SAMTOOLS_CURSES_LIB); printf("\nHTSlib compilation details:\n"); printf(" Features: %s\n", hts_feature_string()); printf(" CC: %s\n", hts_test_feature(HTS_FEATURE_CC)); printf(" CPPFLAGS: %s\n", hts_test_feature(HTS_FEATURE_CPPFLAGS)); printf(" CFLAGS: %s\n", hts_test_feature(HTS_FEATURE_CFLAGS)); printf(" LDFLAGS: %s\n", hts_test_feature(HTS_FEATURE_LDFLAGS)); // Plugins and schemes printf("\nHTSlib URL scheme handlers present:\n"); const char *plugins[100]; int np = 100, i, j; if (hfile_list_plugins(plugins, &np) < 0) return; for (i = 0; i < np; i++) { const char *sc_list[100]; int nschemes = 100; if (hfile_list_schemes(plugins[i], sc_list, &nschemes) < 0) return; printf(" %s:\t", plugins[i]); for (j = 0; j < nschemes; j++) printf(" %s%c", sc_list[j], ",\n"[j+1==nschemes]); } } static void usage(FILE *fp) { /* Please improve the grouping */ fprintf(fp, "\n" "Program: samtools (Tools for alignments in the SAM format)\n" "Version: %s (using htslib %s)\n\n", samtools_version(), hts_version()); fprintf(fp, "Usage: samtools [options]\n" "\n" "Commands:\n" " -- Indexing\n" " dict create a sequence dictionary file\n" " faidx index/extract FASTA\n" " fqidx index/extract FASTQ\n" " index index alignment\n" "\n" " -- Editing\n" " calmd recalculate MD/NM tags and '=' bases\n" " fixmate fix mate information\n" " reheader replace BAM header\n" " targetcut cut fosmid regions (for fosmid pool only)\n" " addreplacerg adds or replaces RG tags\n" " markdup mark duplicates\n" " ampliconclip clip oligos from the end of reads\n" "\n" " -- File operations\n" " collate shuffle and group alignments by name\n" " cat concatenate BAMs\n" " consensus produce a consensus Pileup/FASTA/FASTQ\n" " merge merge sorted alignments\n" " mpileup multi-way pileup\n" " sort sort alignment file\n" " split splits a file by read group\n" " quickcheck quickly check if SAM/BAM/CRAM file appears intact\n" " fastq converts a BAM to a FASTQ\n" " fasta converts a BAM to a FASTA\n" " import Converts FASTA or FASTQ files to SAM/BAM/CRAM\n" " reference Generates a reference from aligned data\n" " reset Reverts aligner changes in reads\n" "\n" " -- Statistics\n" " bedcov read depth per BED region\n" " coverage alignment depth and percent coverage\n" " depth compute the depth\n" " flagstat simple stats\n" " idxstats BAM index stats\n" " cram-size list CRAM Content-ID and Data-Series sizes\n" " phase phase heterozygotes\n" " stats generate stats (former bamcheck)\n" " ampliconstats generate amplicon specific stats\n" "\n" " -- Viewing\n" " flags explain BAM flags\n" " head header viewer\n" " tview text alignment viewer\n" " view SAM<->BAM<->CRAM conversion\n" " depad convert padded BAM to unpadded BAM\n" " samples list the samples in a set of SAM/BAM/CRAM files\n" "\n" " -- Misc\n" " help [cmd] display this help message or help for [cmd]\n" " version detailed version information\n" "\n"); } // This is a tricky one, but on Windows the filename wildcard expansion is done by // the application and not by the shell, as traditionally it never had a "shell". // Even now, DOS and Powershell do not do this expansion (but bash does). // // This means that Mingw/Msys implements code before main() that takes e.g. "*" and // expands it up to a list of matching filenames. This in turn breaks things like // specifying "*" as a region (all the unmapped reads). We take a hard line here - // filename expansion is the task of the shell, not our application! #ifdef _WIN32 int _CRT_glob = 0; #endif int main(int argc, char *argv[]) { #ifdef _WIN32 setmode(fileno(stdout), O_BINARY); setmode(fileno(stdin), O_BINARY); #endif if (argc < 2) { usage(stderr); return 1; } if (strcmp(argv[1], "help") == 0 || strcmp(argv[1], "--help") == 0) { if (argc == 2) { usage(stdout); return 0; } // Otherwise change "samtools help COMMAND [...]" to "samtools COMMAND"; // main_xyz() functions by convention display the subcommand's usage // when invoked without any arguments. argv++; argc = 2; } int ret = 0; if (strcmp(argv[1], "view") == 0) ret = main_samview(argc-1, argv+1); else if (strcmp(argv[1], "import") == 0) ret = main_import(argc-1, argv+1); else if (strcmp(argv[1], "mpileup") == 0) ret = bam_mpileup(argc-1, argv+1); else if (strcmp(argv[1], "merge") == 0) ret = bam_merge(argc-1, argv+1); else if (strcmp(argv[1], "sort") == 0) ret = bam_sort(argc-1, argv+1); else if (strcmp(argv[1], "index") == 0) ret = bam_index(argc-1, argv+1); else if (strcmp(argv[1], "idxstat") == 0 || strcmp(argv[1], "idxstats") == 0) ret = bam_idxstats(argc-1, argv+1); else if (strcmp(argv[1], "faidx") == 0) ret = faidx_main(argc-1, argv+1); else if (strcmp(argv[1], "fqidx") == 0) ret = fqidx_main(argc-1, argv+1); else if (strcmp(argv[1], "dict") == 0) ret = dict_main(argc-1, argv+1); else if (strcmp(argv[1], "head") == 0) ret = main_head(argc-1, argv+1); else if (strcmp(argv[1], "fixmate") == 0) ret = bam_mating(argc-1, argv+1); else if (strcmp(argv[1], "rmdup") == 0) ret = bam_rmdup(argc-1, argv+1); else if (strcmp(argv[1], "markdup") == 0) ret = bam_markdup(argc-1, argv+1); else if (strcmp(argv[1], "ampliconclip") == 0) ret = amplicon_clip_main(argc-1, argv+1); else if (strcmp(argv[1], "flagstat") == 0 || strcmp(argv[1], "flagstats") == 0) ret = bam_flagstat(argc-1, argv+1); else if (strcmp(argv[1], "calmd") == 0) ret = bam_fillmd(argc-1, argv+1); else if (strcmp(argv[1], "fillmd") == 0) ret = bam_fillmd(argc-1, argv+1); else if (strcmp(argv[1], "reheader") == 0) ret = main_reheader(argc-1, argv+1); else if (strcmp(argv[1], "cat") == 0) ret = main_cat(argc-1, argv+1); else if (strcmp(argv[1], "targetcut") == 0) ret = main_cut_target(argc-1, argv+1); else if (strcmp(argv[1], "phase") == 0) ret = main_phase(argc-1, argv+1); else if (strcmp(argv[1], "depth") == 0) ret = main_depth(argc-1, argv+1); else if (strcmp(argv[1], "coverage") == 0) ret = main_coverage(argc-1, argv+1); else if (strcmp(argv[1], "bam2fq") == 0 || strcmp(argv[1], "fastq") == 0 || strcmp(argv[1], "fasta") == 0) ret = main_bam2fq(argc-1, argv+1); else if (strcmp(argv[1], "pad2unpad") == 0) ret = main_pad2unpad(argc-1, argv+1); else if (strcmp(argv[1], "depad") == 0) ret = main_pad2unpad(argc-1, argv+1); else if (strcmp(argv[1], "bedcov") == 0) ret = main_bedcov(argc-1, argv+1); else if (strcmp(argv[1], "bamshuf") == 0) ret = main_bamshuf(argc-1, argv+1); else if (strcmp(argv[1], "collate") == 0) ret = main_bamshuf(argc-1, argv+1); else if (strcmp(argv[1], "stat") == 0 || strcmp(argv[1], "stats") == 0) ret = main_stats(argc-1, argv+1); else if (strcmp(argv[1], "flag") == 0 || strcmp(argv[1], "flags") == 0) ret = main_flags(argc-1, argv+1); else if (strcmp(argv[1], "split") == 0) ret = main_split(argc-1, argv+1); else if (strcmp(argv[1], "quickcheck") == 0) ret = main_quickcheck(argc-1, argv+1); else if (strcmp(argv[1], "addreplacerg") == 0) ret = main_addreplacerg(argc-1, argv+1); else if (strcmp(argv[1], "pileup") == 0) { fprintf(stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n"); return 1; } else if (strcmp(argv[1], "tview") == 0) ret = bam_tview_main(argc-1, argv+1); else if (strcmp(argv[1], "ampliconstats") == 0) ret = main_ampliconstats(argc-1, argv+1); else if (strcmp(argv[1], "samples") == 0) ret = main_samples(argc-1, argv+1); else if (strcmp(argv[1], "consensus") == 0) ret = main_consensus(argc-1, argv+1); else if (strcmp(argv[1], "reference") == 0) ret = main_reference(argc-1, argv+1); else if (strcmp(argv[1], "cram-size") == 0) ret = main_cram_size(argc-1, argv+1); else if (strcmp(argv[1], "version") == 0 || \ strcmp(argv[1], "--version") == 0) long_version(); else if (strcmp(argv[1], "--version-only") == 0) { printf("%s+htslib-%s\n", samtools_version(), hts_version()); } else if (strcmp(argv[1], "reset") == 0) ret = main_reset(argc-1, argv+1); else { fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]); return 1; } // For subcommands that may have produced substantial output on stdout, // make a final check for delayed I/O errors. Ignore EBADF as other code // may have already closed stdout. if (fclose(stdout) != 0 && errno != EBADF) { print_error_errno(argv[1], "closing standard output failed"); return 1; } return ret; } pysam-0.23.0/samtools/bamtk.c.pysam.c000066400000000000000000000333521475062545500174240ustar00rootroot00000000000000#include "samtools.pysam.h" /* bamtk.c -- main samtools command front-end. Copyright (C) 2008-2023 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include "htslib/hts.h" #include "htslib/hfile.h" #include "samtools.h" #include "version.h" #include "samtools_config_vars.h" int bam_taf2baf(int argc, char *argv[]); int bam_mpileup(int argc, char *argv[]); int bam_merge(int argc, char *argv[]); int bam_index(int argc, char *argv[]); int bam_sort(int argc, char *argv[]); int bam_tview_main(int argc, char *argv[]); int bam_mating(int argc, char *argv[]); int bam_rmdup(int argc, char *argv[]); int bam_flagstat(int argc, char *argv[]); int bam_fillmd(int argc, char *argv[]); int bam_idxstats(int argc, char *argv[]); int bam_markdup(int argc, char *argv[]); int main_samview(int argc, char *argv[]); int main_head(int argc, char *argv[]); int main_reheader(int argc, char *argv[]); int main_cut_target(int argc, char *argv[]); int main_phase(int argc, char *argv[]); int main_cat(int argc, char *argv[]); int main_depth(int argc, char *argv[]); int main_coverage(int argc, char *argv[]); int main_bam2fq(int argc, char *argv[]); int main_pad2unpad(int argc, char *argv[]); int main_bedcov(int argc, char *argv[]); int main_bamshuf(int argc, char *argv[]); int main_stats(int argc, char *argv[]); int main_flags(int argc, char *argv[]); int main_split(int argc, char *argv[]); int main_quickcheck(int argc, char *argv[]); int main_addreplacerg(int argc, char *argv[]); int faidx_main(int argc, char *argv[]); int dict_main(int argc, char *argv[]); int fqidx_main(int argc, char *argv[]); int amplicon_clip_main(int argc, char *argv[]); int main_ampliconstats(int argc, char *argv[]); int main_import(int argc, char *argv[]); int main_samples(int argc, char *argv[]); int main_consensus(int argc, char *argv[]); int main_reference(int argc, char *argv[]); int main_reset(int argc, char *argv[]); int main_cram_size(int argc, char *argv[]); const char *samtools_version(void) { return SAMTOOLS_VERSION; } // These come out of the config.h file built by autoconf or Makefile const char *samtools_feature_string(void) { const char *fmt = #ifdef PACKAGE_URL "build=configure " #else "build=Makefile " #endif #ifdef HAVE_CURSES "curses=yes " #else "curses=no " #endif ; return fmt; } static void long_version(void) { fprintf(samtools_stdout, "samtools %s\n" "Using htslib %s\n" "Copyright (C) 2024 Genome Research Ltd.\n", samtools_version(), hts_version()); fprintf(samtools_stdout, "\nSamtools compilation details:\n"); fprintf(samtools_stdout, " Features: %s\n", samtools_feature_string()); fprintf(samtools_stdout, " CC: %s\n", SAMTOOLS_CC); fprintf(samtools_stdout, " CPPFLAGS: %s\n", SAMTOOLS_CPPFLAGS); fprintf(samtools_stdout, " CFLAGS: %s\n", SAMTOOLS_CFLAGS); fprintf(samtools_stdout, " LDFLAGS: %s\n", SAMTOOLS_LDFLAGS); fprintf(samtools_stdout, " HTSDIR: %s\n", SAMTOOLS_HTSDIR); fprintf(samtools_stdout, " LIBS: %s\n", SAMTOOLS_LIBS); fprintf(samtools_stdout, " CURSES_LIB: %s\n", SAMTOOLS_CURSES_LIB); fprintf(samtools_stdout, "\nHTSlib compilation details:\n"); fprintf(samtools_stdout, " Features: %s\n", hts_feature_string()); fprintf(samtools_stdout, " CC: %s\n", hts_test_feature(HTS_FEATURE_CC)); fprintf(samtools_stdout, " CPPFLAGS: %s\n", hts_test_feature(HTS_FEATURE_CPPFLAGS)); fprintf(samtools_stdout, " CFLAGS: %s\n", hts_test_feature(HTS_FEATURE_CFLAGS)); fprintf(samtools_stdout, " LDFLAGS: %s\n", hts_test_feature(HTS_FEATURE_LDFLAGS)); // Plugins and schemes fprintf(samtools_stdout, "\nHTSlib URL scheme handlers present:\n"); const char *plugins[100]; int np = 100, i, j; if (hfile_list_plugins(plugins, &np) < 0) return; for (i = 0; i < np; i++) { const char *sc_list[100]; int nschemes = 100; if (hfile_list_schemes(plugins[i], sc_list, &nschemes) < 0) return; fprintf(samtools_stdout, " %s:\t", plugins[i]); for (j = 0; j < nschemes; j++) fprintf(samtools_stdout, " %s%c", sc_list[j], ",\n"[j+1==nschemes]); } } static void usage(FILE *fp) { /* Please improve the grouping */ fprintf(fp, "\n" "Program: samtools (Tools for alignments in the SAM format)\n" "Version: %s (using htslib %s)\n\n", samtools_version(), hts_version()); fprintf(fp, "Usage: samtools [options]\n" "\n" "Commands:\n" " -- Indexing\n" " dict create a sequence dictionary file\n" " faidx index/extract FASTA\n" " fqidx index/extract FASTQ\n" " index index alignment\n" "\n" " -- Editing\n" " calmd recalculate MD/NM tags and '=' bases\n" " fixmate fix mate information\n" " reheader replace BAM header\n" " targetcut cut fosmid regions (for fosmid pool only)\n" " addreplacerg adds or replaces RG tags\n" " markdup mark duplicates\n" " ampliconclip clip oligos from the end of reads\n" "\n" " -- File operations\n" " collate shuffle and group alignments by name\n" " cat concatenate BAMs\n" " consensus produce a consensus Pileup/FASTA/FASTQ\n" " merge merge sorted alignments\n" " mpileup multi-way pileup\n" " sort sort alignment file\n" " split splits a file by read group\n" " quickcheck quickly check if SAM/BAM/CRAM file appears intact\n" " fastq converts a BAM to a FASTQ\n" " fasta converts a BAM to a FASTA\n" " import Converts FASTA or FASTQ files to SAM/BAM/CRAM\n" " reference Generates a reference from aligned data\n" " reset Reverts aligner changes in reads\n" "\n" " -- Statistics\n" " bedcov read depth per BED region\n" " coverage alignment depth and percent coverage\n" " depth compute the depth\n" " flagstat simple stats\n" " idxstats BAM index stats\n" " cram-size list CRAM Content-ID and Data-Series sizes\n" " phase phase heterozygotes\n" " stats generate stats (former bamcheck)\n" " ampliconstats generate amplicon specific stats\n" "\n" " -- Viewing\n" " flags explain BAM flags\n" " head header viewer\n" " tview text alignment viewer\n" " view SAM<->BAM<->CRAM conversion\n" " depad convert padded BAM to unpadded BAM\n" " samples list the samples in a set of SAM/BAM/CRAM files\n" "\n" " -- Misc\n" " help [cmd] display this help message or help for [cmd]\n" " version detailed version information\n" "\n"); } // This is a tricky one, but on Windows the filename wildcard expansion is done by // the application and not by the shell, as traditionally it never had a "shell". // Even now, DOS and Powershell do not do this expansion (but bash does). // // This means that Mingw/Msys implements code before main() that takes e.g. "*" and // expands it up to a list of matching filenames. This in turn breaks things like // specifying "*" as a region (all the unmapped reads). We take a hard line here - // filename expansion is the task of the shell, not our application! #ifdef _WIN32 int _CRT_glob = 0; #endif int samtools_main(int argc, char *argv[]) { #ifdef _WIN32 setmode(fileno(samtools_stdout), O_BINARY); setmode(fileno(stdin), O_BINARY); #endif if (argc < 2) { usage(samtools_stderr); return 1; } if (strcmp(argv[1], "help") == 0 || strcmp(argv[1], "--help") == 0) { if (argc == 2) { usage(samtools_stdout); return 0; } // Otherwise change "samtools help COMMAND [...]" to "samtools COMMAND"; // main_xyz() functions by convention display the subcommand's usage // when invoked without any arguments. argv++; argc = 2; } int ret = 0; if (strcmp(argv[1], "view") == 0) ret = main_samview(argc-1, argv+1); else if (strcmp(argv[1], "import") == 0) ret = main_import(argc-1, argv+1); else if (strcmp(argv[1], "mpileup") == 0) ret = bam_mpileup(argc-1, argv+1); else if (strcmp(argv[1], "merge") == 0) ret = bam_merge(argc-1, argv+1); else if (strcmp(argv[1], "sort") == 0) ret = bam_sort(argc-1, argv+1); else if (strcmp(argv[1], "index") == 0) ret = bam_index(argc-1, argv+1); else if (strcmp(argv[1], "idxstat") == 0 || strcmp(argv[1], "idxstats") == 0) ret = bam_idxstats(argc-1, argv+1); else if (strcmp(argv[1], "faidx") == 0) ret = faidx_main(argc-1, argv+1); else if (strcmp(argv[1], "fqidx") == 0) ret = fqidx_main(argc-1, argv+1); else if (strcmp(argv[1], "dict") == 0) ret = dict_main(argc-1, argv+1); else if (strcmp(argv[1], "head") == 0) ret = main_head(argc-1, argv+1); else if (strcmp(argv[1], "fixmate") == 0) ret = bam_mating(argc-1, argv+1); else if (strcmp(argv[1], "rmdup") == 0) ret = bam_rmdup(argc-1, argv+1); else if (strcmp(argv[1], "markdup") == 0) ret = bam_markdup(argc-1, argv+1); else if (strcmp(argv[1], "ampliconclip") == 0) ret = amplicon_clip_main(argc-1, argv+1); else if (strcmp(argv[1], "flagstat") == 0 || strcmp(argv[1], "flagstats") == 0) ret = bam_flagstat(argc-1, argv+1); else if (strcmp(argv[1], "calmd") == 0) ret = bam_fillmd(argc-1, argv+1); else if (strcmp(argv[1], "fillmd") == 0) ret = bam_fillmd(argc-1, argv+1); else if (strcmp(argv[1], "reheader") == 0) ret = main_reheader(argc-1, argv+1); else if (strcmp(argv[1], "cat") == 0) ret = main_cat(argc-1, argv+1); else if (strcmp(argv[1], "targetcut") == 0) ret = main_cut_target(argc-1, argv+1); else if (strcmp(argv[1], "phase") == 0) ret = main_phase(argc-1, argv+1); else if (strcmp(argv[1], "depth") == 0) ret = main_depth(argc-1, argv+1); else if (strcmp(argv[1], "coverage") == 0) ret = main_coverage(argc-1, argv+1); else if (strcmp(argv[1], "bam2fq") == 0 || strcmp(argv[1], "fastq") == 0 || strcmp(argv[1], "fasta") == 0) ret = main_bam2fq(argc-1, argv+1); else if (strcmp(argv[1], "pad2unpad") == 0) ret = main_pad2unpad(argc-1, argv+1); else if (strcmp(argv[1], "depad") == 0) ret = main_pad2unpad(argc-1, argv+1); else if (strcmp(argv[1], "bedcov") == 0) ret = main_bedcov(argc-1, argv+1); else if (strcmp(argv[1], "bamshuf") == 0) ret = main_bamshuf(argc-1, argv+1); else if (strcmp(argv[1], "collate") == 0) ret = main_bamshuf(argc-1, argv+1); else if (strcmp(argv[1], "stat") == 0 || strcmp(argv[1], "stats") == 0) ret = main_stats(argc-1, argv+1); else if (strcmp(argv[1], "flag") == 0 || strcmp(argv[1], "flags") == 0) ret = main_flags(argc-1, argv+1); else if (strcmp(argv[1], "split") == 0) ret = main_split(argc-1, argv+1); else if (strcmp(argv[1], "quickcheck") == 0) ret = main_quickcheck(argc-1, argv+1); else if (strcmp(argv[1], "addreplacerg") == 0) ret = main_addreplacerg(argc-1, argv+1); else if (strcmp(argv[1], "pileup") == 0) { fprintf(samtools_stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n"); return 1; } //else if (strcmp(argv[1], "tview") == 0) ret = bam_tview_main(argc-1, argv+1); else if (strcmp(argv[1], "ampliconstats") == 0) ret = main_ampliconstats(argc-1, argv+1); else if (strcmp(argv[1], "samples") == 0) ret = main_samples(argc-1, argv+1); else if (strcmp(argv[1], "consensus") == 0) ret = main_consensus(argc-1, argv+1); else if (strcmp(argv[1], "reference") == 0) ret = main_reference(argc-1, argv+1); else if (strcmp(argv[1], "cram-size") == 0) ret = main_cram_size(argc-1, argv+1); else if (strcmp(argv[1], "version") == 0 || \ strcmp(argv[1], "--version") == 0) long_version(); else if (strcmp(argv[1], "--version-only") == 0) { fprintf(samtools_stdout, "%s+htslib-%s\n", samtools_version(), hts_version()); } else if (strcmp(argv[1], "reset") == 0) ret = main_reset(argc-1, argv+1); else { fprintf(samtools_stderr, "[main] unrecognized command '%s'\n", argv[1]); return 1; } // For subcommands that may have produced substantial output on samtools_stdout, // make a final check for delayed I/O errors. Ignore EBADF as other code // may have already closed samtools_stdout. if (0) { //if (fclose(samtools_stdout) != 0 && errno != EBADF) { print_error_errno(argv[1], "closing standard output failed"); return 1; } return ret; } pysam-0.23.0/samtools/bedcov.c000066400000000000000000000265661475062545500162300ustar00rootroot00000000000000/* bedcov.c -- bedcov subcommand. Copyright (C) 2012 Broad Institute. Copyright (C) 2013-2014, 2018-2022, 2024 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "htslib/kstring.h" #include "htslib/sam.h" #include "htslib/thread_pool.h" #include "samtools.h" #include "sam_opts.h" #include "htslib/kseq.h" KSTREAM_INIT(gzFile, gzread, 16384) #define DEFAULT_DEPTH INT_MAX typedef struct { htsFile *fp; sam_hdr_t *header; hts_itr_t *iter; int min_mapQ; uint32_t flags; // read filtering flags int64_t rcnt; } aux_t; static int read_bam(void *data, bam1_t *b) { aux_t *aux = (aux_t*)data; // data in fact is a pointer to an auxiliary structure int ret; while (1) { ret = aux->iter? sam_itr_next(aux->fp, aux->iter, b) : sam_read1(aux->fp, aux->header, b); if ( ret<0 ) break; if ( b->core.flag & aux->flags ) continue; if ( (int)b->core.qual < aux->min_mapQ ) continue; break; } return ret; } static int incr_rcnt(void *data, const bam1_t *b, bam_pileup_cd *cd) { aux_t *aux = (aux_t *)data; aux->rcnt++; return 0; } int main_bedcov(int argc, char *argv[]) { gzFile fp; kstring_t str; kstream_t *ks; hts_idx_t **idx; aux_t **aux; int *n_plp, dret, i, j, m, n, c, ret, status = 0, min_mapQ = 0; int skip_DN = 0, do_rcount = 0; int64_t *cnt, *pcov = NULL; const bam_pileup1_t **plp; int usage = 0, has_index_file = 0; uint32_t flags = (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP); int tflags = 0, min_depth = -1, max_depth = DEFAULT_DEPTH, print_header=0; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { {"min-MQ", required_argument, NULL, 'Q'}, {"min-mq", required_argument, NULL, 'Q'}, {"max-depth", required_argument, NULL, 'd'+1000}, SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '-'), { NULL, 0, NULL, 0 } }; while ((c = getopt_long(argc, argv, "Q:Xg:G:jd:Hc", lopts, NULL)) >= 0) { switch (c) { case 'Q': min_mapQ = atoi(optarg); break; case 'X': has_index_file = 1; break; case 'c': do_rcount = 1; break; case 'H': print_header = 1; break; case 'g': tflags = bam_str2flag(optarg); if (tflags < 0 || tflags > ((BAM_FSUPPLEMENTARY << 1) - 1)) { print_error("bedcov", "Flag value \"%s\" is not supported", optarg); return 1; } flags &= ~tflags; break; case 'G': tflags = bam_str2flag(optarg); if (tflags < 0 || tflags > ((BAM_FSUPPLEMENTARY << 1) - 1)) { print_error("bedcov", "Flag value \"%s\" is not supported", optarg); return 1; } flags |= tflags; break; case 'j': skip_DN = 1; break; case 'd': min_depth = atoi(optarg); break; case 'd'+1000: max_depth = atoi(optarg); break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage = 1; break; } if (usage) break; } if (usage || optind + 2 > argc) { fprintf(stderr, "Usage: samtools bedcov [options] [...]\n\n"); fprintf(stderr, "Options:\n"); fprintf(stderr, " -Q, --min-MQ mapping quality threshold [0]\n"); fprintf(stderr, " -X use customized index files\n"); fprintf(stderr, " -g remove the specified flags from the set used to filter out reads\n"); fprintf(stderr, " -G add the specified flags to the set used to filter out reads\n" " The default set is UNMAP,SECONDARY,QCFAIL,DUP or 0x704\n"); fprintf(stderr, " -j do not include deletions (D) and ref skips (N) in bedcov computation\n"); fprintf(stderr, " --max-depth sets the maximum depth used in the mpileup algorithm\n"); fprintf(stderr, " -d depth threshold. Number of reference bases with coverage above and\n" " including this value will be displayed in a separate column\n"); fprintf(stderr, " -c add an additional column showing read count\n"); fprintf(stderr, " -H print a comment/header line with column information.\n"); sam_global_opt_help(stderr, "-.--.--."); return 1; } if (has_index_file) { if ((argc - optind - 1) % 2 != 0) { // Calculate # of input BAM files fprintf(stderr, "ERROR: odd number of filenames detected! Each BAM file should have an index file\n"); return 1; } n = (argc - optind - 1) / 2; } else { n = argc - optind - 1; } memset(&str, 0, sizeof(kstring_t)); aux = calloc(n, sizeof(aux_t*)); idx = calloc(n, sizeof(hts_idx_t*)); for (i = 0; i < n; ++i) { aux[i] = calloc(1, sizeof(aux_t)); aux[i]->min_mapQ = min_mapQ; aux[i]->fp = sam_open_format(argv[i+optind+1], "r", &ga.in); if (aux[i]->fp) { // If index filename has not been specfied, look in BAM folder if (has_index_file) { idx[i] = sam_index_load2(aux[i]->fp, argv[i+optind+1], argv[i+optind+n+1]); } else { idx[i] = sam_index_load(aux[i]->fp, argv[i+optind+1]); } } if (aux[i]->fp == 0 || idx[i] == 0) { fprintf(stderr, "ERROR: fail to open index BAM file '%s'\n", argv[i+optind+1]); return 2; } // TODO bgzf_set_cache_size(aux[i]->fp, 20); aux[i]->header = sam_hdr_read(aux[i]->fp); if (aux[i]->header == NULL) { fprintf(stderr, "ERROR: failed to read header for '%s'\n", argv[i+optind+1]); return 2; } aux[i]->flags = flags; } cnt = calloc(n, sizeof(*cnt)); if (min_depth >= 0) pcov = calloc(n, sizeof(*pcov)); if (!cnt || (min_depth >= 0 && !pcov)) { print_error_errno("bedcov", "failed to allocate memory"); return 2; } fp = gzopen(argv[optind], "rb"); if (fp == NULL) { print_error_errno("bedcov", "can't open BED file '%s'", argv[optind]); return 2; } if (print_header) { printf("#chrom\tstart\tend"); for (i = 0; i < n; ++i) { printf("\t%s_cov", argv[i+optind+1]); } if (min_depth >= 0) { for (i = 0; i < n; ++i) printf("\t%s_depth", argv[i+optind+1]); } if (do_rcount) { for (i = 0; i < n; ++i) printf("\t%s_count", argv[i+optind+1]); } putchar('\n'); } ks = ks_init(fp); n_plp = calloc(n, sizeof(int)); plp = calloc(n, sizeof(bam_pileup1_t*)); while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) { char *p, *q; int tid, pos, num = 0; int64_t beg = 0, end = 0; bam_mplp_t mplp; if (str.l == 0 || *str.s == '#') continue; /* empty or comment line */ /* Track and browser lines. Also look for a trailing *space* in case someone has badly-chosen a chromosome name (it would be followed by a tab in that case). */ if (strncmp(str.s, "track ", 6) == 0) continue; if (strncmp(str.s, "browser ", 8) == 0) continue; for (p = q = str.s; *p && !isspace(*p); ++p); if (*p == 0) goto bed_error; char c = *p; *p = 0; tid = bam_name2id(aux[0]->header, q); *p = c; if (tid < 0) goto bed_error; num = sscanf(p + 1, "%"SCNd64" %"SCNd64, &beg, &end); if (num < 2 || end < beg) goto bed_error; for (i = 0; i < n; ++i) { if (aux[i]->iter) hts_itr_destroy(aux[i]->iter); aux[i]->iter = sam_itr_queryi(idx[i], tid, beg, end); aux[i]->rcnt = 0; } mplp = bam_mplp_init(n, read_bam, (void**)aux); if (min_depth > max_depth) // NB: never happens given current DEFAULT_DEPTH of INT_MAX bam_mplp_set_maxcnt(mplp, min_depth); else bam_mplp_set_maxcnt(mplp, max_depth); memset(cnt, 0, sizeof(*cnt) * n); if (min_depth >= 0) memset(pcov, 0, sizeof(*pcov) * n); if (do_rcount) bam_mplp_constructor(mplp, incr_rcnt); while ((ret = bam_mplp_auto(mplp, &tid, &pos, n_plp, plp)) > 0) if (pos >= beg && pos < end) { for (i = 0; i < n; ++i) { m = 0; if (skip_DN || min_depth >= 0) { for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *pi = plp[i] + j; if (pi->is_del || pi->is_refskip) ++m; } } int pd = n_plp[i] - m; cnt[i] += pd; if (min_depth >= 0 && pd >= min_depth) pcov[i]++; } } if (ret < 0) { print_error("bedcov", "error reading from input file"); status = 2; bam_mplp_destroy(mplp); break; } for (i = 0; i < n; ++i) { kputc('\t', &str); kputl(cnt[i], &str); } if (min_depth >= 0) { for (i = 0; i < n; ++i) { kputc('\t', &str); kputl(pcov[i], &str); } } if (do_rcount) { for (i = 0; i < n; ++i) { kputc('\t', &str); kputl(aux[i]->rcnt, &str); } } puts(str.s); bam_mplp_destroy(mplp); continue; bed_error: fprintf(stderr, "Errors in BED line '%s'\n", str.s); status = 2; } free(n_plp); free(plp); ks_destroy(ks); gzclose(fp); free(cnt); free(pcov); for (i = 0; i < n; ++i) { if (aux[i]->iter) hts_itr_destroy(aux[i]->iter); hts_idx_destroy(idx[i]); sam_hdr_destroy(aux[i]->header); sam_close(aux[i]->fp); free(aux[i]); } free(aux); free(idx); free(str.s); sam_global_args_free(&ga); return status; } pysam-0.23.0/samtools/bedcov.c.pysam.c000066400000000000000000000272031475062545500175660ustar00rootroot00000000000000#include "samtools.pysam.h" /* bedcov.c -- bedcov subcommand. Copyright (C) 2012 Broad Institute. Copyright (C) 2013-2014, 2018-2022, 2024 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "htslib/kstring.h" #include "htslib/sam.h" #include "htslib/thread_pool.h" #include "samtools.h" #include "sam_opts.h" #include "htslib/kseq.h" KSTREAM_INIT(gzFile, gzread, 16384) #define DEFAULT_DEPTH INT_MAX typedef struct { htsFile *fp; sam_hdr_t *header; hts_itr_t *iter; int min_mapQ; uint32_t flags; // read filtering flags int64_t rcnt; } aux_t; static int read_bam(void *data, bam1_t *b) { aux_t *aux = (aux_t*)data; // data in fact is a pointer to an auxiliary structure int ret; while (1) { ret = aux->iter? sam_itr_next(aux->fp, aux->iter, b) : sam_read1(aux->fp, aux->header, b); if ( ret<0 ) break; if ( b->core.flag & aux->flags ) continue; if ( (int)b->core.qual < aux->min_mapQ ) continue; break; } return ret; } static int incr_rcnt(void *data, const bam1_t *b, bam_pileup_cd *cd) { aux_t *aux = (aux_t *)data; aux->rcnt++; return 0; } int main_bedcov(int argc, char *argv[]) { gzFile fp; kstring_t str; kstream_t *ks; hts_idx_t **idx; aux_t **aux; int *n_plp, dret, i, j, m, n, c, ret, status = 0, min_mapQ = 0; int skip_DN = 0, do_rcount = 0; int64_t *cnt, *pcov = NULL; const bam_pileup1_t **plp; int usage = 0, has_index_file = 0; uint32_t flags = (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP); int tflags = 0, min_depth = -1, max_depth = DEFAULT_DEPTH, print_header=0; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { {"min-MQ", required_argument, NULL, 'Q'}, {"min-mq", required_argument, NULL, 'Q'}, {"max-depth", required_argument, NULL, 'd'+1000}, SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '-'), { NULL, 0, NULL, 0 } }; while ((c = getopt_long(argc, argv, "Q:Xg:G:jd:Hc", lopts, NULL)) >= 0) { switch (c) { case 'Q': min_mapQ = atoi(optarg); break; case 'X': has_index_file = 1; break; case 'c': do_rcount = 1; break; case 'H': print_header = 1; break; case 'g': tflags = bam_str2flag(optarg); if (tflags < 0 || tflags > ((BAM_FSUPPLEMENTARY << 1) - 1)) { print_error("bedcov", "Flag value \"%s\" is not supported", optarg); return 1; } flags &= ~tflags; break; case 'G': tflags = bam_str2flag(optarg); if (tflags < 0 || tflags > ((BAM_FSUPPLEMENTARY << 1) - 1)) { print_error("bedcov", "Flag value \"%s\" is not supported", optarg); return 1; } flags |= tflags; break; case 'j': skip_DN = 1; break; case 'd': min_depth = atoi(optarg); break; case 'd'+1000: max_depth = atoi(optarg); break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage = 1; break; } if (usage) break; } if (usage || optind + 2 > argc) { fprintf(samtools_stderr, "Usage: samtools bedcov [options] [...]\n\n"); fprintf(samtools_stderr, "Options:\n"); fprintf(samtools_stderr, " -Q, --min-MQ mapping quality threshold [0]\n"); fprintf(samtools_stderr, " -X use customized index files\n"); fprintf(samtools_stderr, " -g remove the specified flags from the set used to filter out reads\n"); fprintf(samtools_stderr, " -G add the specified flags to the set used to filter out reads\n" " The default set is UNMAP,SECONDARY,QCFAIL,DUP or 0x704\n"); fprintf(samtools_stderr, " -j do not include deletions (D) and ref skips (N) in bedcov computation\n"); fprintf(samtools_stderr, " --max-depth sets the maximum depth used in the mpileup algorithm\n"); fprintf(samtools_stderr, " -d depth threshold. Number of reference bases with coverage above and\n" " including this value will be displayed in a separate column\n"); fprintf(samtools_stderr, " -c add an additional column showing read count\n"); fprintf(samtools_stderr, " -H print a comment/header line with column information.\n"); sam_global_opt_help(samtools_stderr, "-.--.--."); return 1; } if (has_index_file) { if ((argc - optind - 1) % 2 != 0) { // Calculate # of input BAM files fprintf(samtools_stderr, "ERROR: odd number of filenames detected! Each BAM file should have an index file\n"); return 1; } n = (argc - optind - 1) / 2; } else { n = argc - optind - 1; } memset(&str, 0, sizeof(kstring_t)); aux = calloc(n, sizeof(aux_t*)); idx = calloc(n, sizeof(hts_idx_t*)); for (i = 0; i < n; ++i) { aux[i] = calloc(1, sizeof(aux_t)); aux[i]->min_mapQ = min_mapQ; aux[i]->fp = sam_open_format(argv[i+optind+1], "r", &ga.in); if (aux[i]->fp) { // If index filename has not been specfied, look in BAM folder if (has_index_file) { idx[i] = sam_index_load2(aux[i]->fp, argv[i+optind+1], argv[i+optind+n+1]); } else { idx[i] = sam_index_load(aux[i]->fp, argv[i+optind+1]); } } if (aux[i]->fp == 0 || idx[i] == 0) { fprintf(samtools_stderr, "ERROR: fail to open index BAM file '%s'\n", argv[i+optind+1]); return 2; } // TODO bgzf_set_cache_size(aux[i]->fp, 20); aux[i]->header = sam_hdr_read(aux[i]->fp); if (aux[i]->header == NULL) { fprintf(samtools_stderr, "ERROR: failed to read header for '%s'\n", argv[i+optind+1]); return 2; } aux[i]->flags = flags; } cnt = calloc(n, sizeof(*cnt)); if (min_depth >= 0) pcov = calloc(n, sizeof(*pcov)); if (!cnt || (min_depth >= 0 && !pcov)) { print_error_errno("bedcov", "failed to allocate memory"); return 2; } fp = gzopen(argv[optind], "rb"); if (fp == NULL) { print_error_errno("bedcov", "can't open BED file '%s'", argv[optind]); return 2; } if (print_header) { fprintf(samtools_stdout, "#chrom\tstart\tend"); for (i = 0; i < n; ++i) { fprintf(samtools_stdout, "\t%s_cov", argv[i+optind+1]); } if (min_depth >= 0) { for (i = 0; i < n; ++i) fprintf(samtools_stdout, "\t%s_depth", argv[i+optind+1]); } if (do_rcount) { for (i = 0; i < n; ++i) fprintf(samtools_stdout, "\t%s_count", argv[i+optind+1]); } fputc('\n', samtools_stdout); } ks = ks_init(fp); n_plp = calloc(n, sizeof(int)); plp = calloc(n, sizeof(bam_pileup1_t*)); while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) { char *p, *q; int tid, pos, num = 0; int64_t beg = 0, end = 0; bam_mplp_t mplp; if (str.l == 0 || *str.s == '#') continue; /* empty or comment line */ /* Track and browser lines. Also look for a trailing *space* in case someone has badly-chosen a chromosome name (it would be followed by a tab in that case). */ if (strncmp(str.s, "track ", 6) == 0) continue; if (strncmp(str.s, "browser ", 8) == 0) continue; for (p = q = str.s; *p && !isspace(*p); ++p); if (*p == 0) goto bed_error; char c = *p; *p = 0; tid = bam_name2id(aux[0]->header, q); *p = c; if (tid < 0) goto bed_error; num = sscanf(p + 1, "%"SCNd64" %"SCNd64, &beg, &end); if (num < 2 || end < beg) goto bed_error; for (i = 0; i < n; ++i) { if (aux[i]->iter) hts_itr_destroy(aux[i]->iter); aux[i]->iter = sam_itr_queryi(idx[i], tid, beg, end); aux[i]->rcnt = 0; } mplp = bam_mplp_init(n, read_bam, (void**)aux); if (min_depth > max_depth) // NB: never happens given current DEFAULT_DEPTH of INT_MAX bam_mplp_set_maxcnt(mplp, min_depth); else bam_mplp_set_maxcnt(mplp, max_depth); memset(cnt, 0, sizeof(*cnt) * n); if (min_depth >= 0) memset(pcov, 0, sizeof(*pcov) * n); if (do_rcount) bam_mplp_constructor(mplp, incr_rcnt); while ((ret = bam_mplp_auto(mplp, &tid, &pos, n_plp, plp)) > 0) if (pos >= beg && pos < end) { for (i = 0; i < n; ++i) { m = 0; if (skip_DN || min_depth >= 0) { for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *pi = plp[i] + j; if (pi->is_del || pi->is_refskip) ++m; } } int pd = n_plp[i] - m; cnt[i] += pd; if (min_depth >= 0 && pd >= min_depth) pcov[i]++; } } if (ret < 0) { print_error("bedcov", "error reading from input file"); status = 2; bam_mplp_destroy(mplp); break; } for (i = 0; i < n; ++i) { kputc('\t', &str); kputl(cnt[i], &str); } if (min_depth >= 0) { for (i = 0; i < n; ++i) { kputc('\t', &str); kputl(pcov[i], &str); } } if (do_rcount) { for (i = 0; i < n; ++i) { kputc('\t', &str); kputl(aux[i]->rcnt, &str); } } samtools_puts(str.s); bam_mplp_destroy(mplp); continue; bed_error: fprintf(samtools_stderr, "Errors in BED line '%s'\n", str.s); status = 2; } free(n_plp); free(plp); ks_destroy(ks); gzclose(fp); free(cnt); free(pcov); for (i = 0; i < n; ++i) { if (aux[i]->iter) hts_itr_destroy(aux[i]->iter); hts_idx_destroy(idx[i]); sam_hdr_destroy(aux[i]->header); sam_close(aux[i]->fp); free(aux[i]); } free(aux); free(idx); free(str.s); sam_global_args_free(&ga); return status; } pysam-0.23.0/samtools/bedidx.c000066400000000000000000000471121475062545500162130ustar00rootroot00000000000000/* bedidx.c -- BED file indexing. Copyright (C) 2011 Broad Institute. Copyright (C) 2014, 2017-2019, 2024 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "bedidx.h" #include "htslib/ksort.h" #include "htslib/kseq.h" KSTREAM_INIT(gzFile, gzread, 8192) static inline int lt_pair_pos(hts_pair_pos_t a, hts_pair_pos_t b) { if (a.beg == b.beg) return a.end < b.end; return a.beg < b.beg; } KSORT_INIT_STATIC(hts_pair_pos_t, hts_pair_pos_t, lt_pair_pos) /*! @typedef * @abstract bed_reglist_t - value type of the BED hash table * This structure encodes the list of intervals (ranges) for the regions provided via BED file or * command line arguments. * @field *a pointer to the array of intervals. * @field n actual number of elements contained by a * @field m number of allocated elements to a (n <= m) * @field *idx index array for computing the minimum offset */ typedef struct { int n, m; hts_pair_pos_t *a; int *idx; int filter; hts_pos_t max_idx; } bed_reglist_t; #include "htslib/khash.h" KHASH_MAP_INIT_STR(reg, bed_reglist_t) typedef kh_reg_t reghash_t; #if 0 // Debug function static void bed_print(void *reg_hash) { reghash_t *h = (reghash_t *)reg_hash; bed_reglist_t *p; khint_t k; int i; const char *reg; if (!h) { printf("Hash table is empty!\n"); return; } for (k = kh_begin(h); k < kh_end(h); k++) { if (kh_exist(h,k)) { reg = kh_key(h,k); printf("Region: '%s'\n", reg); if ((p = &kh_val(h,k)) != NULL && p->n > 0) { printf("Filter: %d\n", p->filter); for (i=0; in; i++) { printf("\tinterval[%d]: %"PRIhts_pos"-%"PRIhts_pos"\n", i,p->a[i].beg,p->a[i].end); } } else { printf("Region '%s' has no intervals!\n", reg); } } } } #endif static int bed_index_core(bed_reglist_t *regions) { int i, *idx = NULL; size_t idx_size = 0; hts_pos_t last_end = 0; hts_pair_pos_t *a = regions->a; // Construct a linear index on regions, to allow rapid lookup of // where to start searching for matches for (i = 0; i < regions->n; ++i) { hts_pos_t beg = a[i].beg >= 0 ? a[i].beg >> LIDX_SHIFT : 0; hts_pos_t end = a[i].end >= 0 ? a[i].end >> LIDX_SHIFT : 0; hts_pos_t j; if (end < last_end) continue; // Can happen for a containment if (end + 1 >= SIZE_MAX / sizeof(*idx)) { // Ensure no overflow errno = ENOMEM; free(idx); return -1; } if (hts_resize(int, (size_t) end + 1, &idx_size, &idx, 0) < 0) { free(idx); return -1; } // Fill any gap prior to this region by pointing to the previous one for (j = last_end; j < beg; j++) idx[j] = i > 0 ? i - 1 : 0; // Fill from max(last_end, beg) to `end` (inclusive) with current region for (; j <= end; j++) idx[j] = i; // Remember where finished for the next gap last_end = end + 1; } regions->idx = idx; regions->max_idx = last_end; return 0; } static int bed_index(reghash_t *h) { khint_t k; for (k = 0; k < kh_end(h); ++k) { if (kh_exist(h, k)) { bed_reglist_t *p = &kh_val(h, k); if (p->idx) { free(p->idx); p->idx = NULL; } ks_introsort(hts_pair_pos_t, p->n, p->a); if (bed_index_core(p) != 0) { return -1; } } } return 0; } static int bed_minoff(const bed_reglist_t *p, hts_pos_t beg) { int min_off=0; if (p && p->idx && p->max_idx > 0 && beg >= 0) { min_off = (beg>>LIDX_SHIFT >= p->max_idx)? p->idx[p->max_idx-1] : p->idx[beg>>LIDX_SHIFT]; } return min_off; } static int bed_overlap_core(const bed_reglist_t *p, hts_pos_t beg, hts_pos_t end) { int i, min_off; if (p->n == 0) return 0; min_off = bed_minoff(p, beg); for (i = min_off; i < p->n; ++i) { if (p->a[i].beg >= end) break; // out of range; no need to proceed if (p->a[i].end > beg && p->a[i].beg < end) return 1; // find the overlap; return } return 0; } int bed_overlap(const void *_h, const char *chr, hts_pos_t beg, hts_pos_t end) { const reghash_t *h = (const reghash_t*)_h; khint_t k; if (!h) return 0; k = kh_get(reg, h, chr); if (k == kh_end(h)) return 0; return bed_overlap_core(&kh_val(h, k), beg, end); } /** @brief Trim a sorted interval list, inside a region hash table, * by removing completely contained intervals and merging adjacent or * overlapping intervals. * @param reg_hash the region hash table with interval lists as values */ void bed_unify(void *reg_hash) { int i, j, new_n; reghash_t *h; bed_reglist_t *p; if (!reg_hash) return; h = (reghash_t *)reg_hash; for (i = kh_begin(h); i < kh_end(h); i++) { if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || !(p->n)) continue; for (new_n = 0, j = 1; j < p->n; j++) { if (p->a[new_n].end < p->a[j].beg) { p->a[++new_n] = p->a[j]; } else { if (p->a[new_n].end < p->a[j].end) p->a[new_n].end = p->a[j].end; } } p->n = ++new_n; } } /* "BED" file reader, which actually reads two different formats. BED files contain between three and nine fields per line, of which only the first three (reference, start, end) are of interest to us. BED counts positions from base 0, and the end is the base after the region of interest. While not properly documented in the specification, it is also possible to have 'browser' and 'track' lines in BED files that do not follow the standard format and should be ignored. Examination of the BED file reading code in http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git shows that BED files can also have comment lines starting with '#', leading whitespace is stripped, and that fields are separated by one or more consecutive whitespace characters. The alternative format was originally for reading positions in VCF format. This expects two columns, which indicate the reference and a position. The position corresponds to a single base, and unlike BED counts from 1. Which format is in use is determined based on whether one or two numbers can be decoded on the line. As this choice is made line-by-line in this implementation, it is possible (but probably a bad idea) to mix both formats in the same file. If trying to read a VCF file by this method, it would be important to ensure that the third column (ID) does not contain any entries that start with a digit, to avoid the line erroneously being parsed as a BED file entry. The BED specification is at http://www.genome.ucsc.edu/FAQ/FAQformat.html The VCF specification is at https://github.com/samtools/hts-specs */ void *bed_read(const char *fn) { reghash_t *h = kh_init(reg); gzFile fp; kstream_t *ks = NULL; int dret; unsigned int line = 0, save_errno; kstring_t str = { 0, 0, NULL }; if (NULL == h) return NULL; // read the list fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r"); if (fp == 0) goto fail; ks = ks_init(fp); if (NULL == ks) goto fail; // In case ks_init ever gets error checking... int ks_len; while ((ks_len = ks_getuntil(ks, KS_SEP_LINE, &str, &dret)) >= 0) { // read a line char *ref = str.s, *ref_end; uint64_t beg = 0, end = 0; int num = 0; khint_t k; bed_reglist_t *p; if (ks_len == 0) continue; // skip blank lines line++; while (*ref && isspace(*ref)) ref++; if ('\0' == *ref) continue; // Skip blank lines if ('#' == *ref) continue; // Skip BED file comments ref_end = ref; // look for the end of the reference name while (*ref_end && !isspace(*ref_end)) ref_end++; if ('\0' != *ref_end) { *ref_end = '\0'; // terminate ref and look for start, end num = sscanf(ref_end + 1, "%"SCNu64" %"SCNu64, &beg, &end); } if (1 == num) { // VCF-style format end = beg--; // Counts from 1 instead of 0 for BED files } if (num < 1 || end < beg) { // These two are special lines that can occur in BED files. // Check for them here instead of earlier in case someone really // has called their reference "browser" or "track". if (0 == strcmp(ref, "browser")) continue; if (0 == strcmp(ref, "track")) continue; if (num < 1) { fprintf(stderr, "[bed_read] Parse error reading \"%s\" at line %u\n", fn, line); } else { fprintf(stderr, "[bed_read] Parse error reading \"%s\" at line %u : " "end (%"PRIu64") must not be less " "than start (%"PRIu64")\n", fn, line, end, beg); } errno = 0; // Prevent caller from printing misleading error messages goto fail; } // Put reg in the hash table if not already there k = kh_get(reg, h, ref); if (k == kh_end(h)) { // absent from the hash table int ret; char *s = strdup(ref); if (NULL == s) goto fail; k = kh_put(reg, h, s, &ret); if (-1 == ret) { free(s); goto fail; } memset(&kh_val(h, k), 0, sizeof(bed_reglist_t)); } p = &kh_val(h, k); // Add begin,end to the list if (p->n == p->m) { p->m = p->m ? p->m<<1 : 4; hts_pair_pos_t *new_a = realloc(p->a, p->m * sizeof(p->a[0])); if (NULL == new_a) goto fail; p->a = new_a; } p->a[p->n].beg = beg; p->a[p->n++].end = end; } // FIXME: Need to check for errors in ks_getuntil. At the moment it // doesn't look like it can return one. Possibly use gzgets instead? if (gzclose(fp) != Z_OK) { fp = NULL; goto fail; } if (bed_index(h) != 0) goto fail; ks_destroy(ks); free(str.s); //bed_unify(h); return h; fail: save_errno = errno; if (ks) ks_destroy(ks); if (fp) gzclose(fp); free(str.s); bed_destroy(h); errno = save_errno; return NULL; } void bed_destroy(void *_h) { reghash_t *h; khint_t k; if (!_h) return; h = (reghash_t*)_h; for (k = 0; k < kh_end(h); ++k) { if (kh_exist(h, k)) { free(kh_val(h, k).a); free(kh_val(h, k).idx); free((char*)kh_key(h, k)); } } kh_destroy(reg, h); } static void *bed_insert(void *reg_hash, char *reg, hts_pos_t beg, hts_pos_t end) { reghash_t *h; khint_t k; bed_reglist_t *p; if (!reg_hash) return NULL; h = (reghash_t *)reg_hash; // Put reg in the hash table if not already there k = kh_get(reg, h, reg); //looks strange, but only the second reg is the actual region name. if (k == kh_end(h)) { // absent from the hash table int ret; char *s = strdup(reg); if (NULL == s) goto fail; k = kh_put(reg, h, s, &ret); if (-1 == ret) { free(s); goto fail; } memset(&kh_val(h, k), 0, sizeof(bed_reglist_t)); } p = &kh_val(h, k); // Add beg and end to the list if (p->n == p->m) { p->m = p->m ? p->m<<1 : 4; hts_pair_pos_t *new_a = realloc(p->a, p->m * sizeof(p->a[0])); if (NULL == new_a) goto fail; p->a = new_a; } p->a[p->n].beg = beg; p->a[p->n++].end = end; fail: return h; } /* @brief Filter a region hash table (coming from the BED file) by another * region hash table (coming from CLI), so that only intervals contained in * both hash tables are kept. * @param reg_hash the target region hash table * @param tmp_hash the filter region hash table * @return pointer to the filtered hash table */ static void *bed_filter(void *reg_hash, void *tmp_hash) { reghash_t *h; reghash_t *t; bed_reglist_t *p, *q; khint_t l, k; hts_pair_pos_t *new_a; int i, j, new_n, min_off; const char *reg; hts_pos_t beg, end; h = (reghash_t *)reg_hash; t = (reghash_t *)tmp_hash; if (!h) return NULL; if (!t) return h; for (l = kh_begin(t); l < kh_end(t); l++) { if (!kh_exist(t,l) || !(q = &kh_val(t,l)) || !(q->n)) continue; reg = kh_key(t,l); k = kh_get(reg, h, reg); //looks strange, but only the second reg is a proper argument. if (k == kh_end(h) || !(p = &kh_val(h, k)) || !(p->n)) continue; new_a = calloc(q->n + p->n, sizeof(new_a[0])); if (!new_a) return NULL; new_n = 0; for (i = 0; i < q->n; i++) { beg = q->a[i].beg; end = q->a[i].end; min_off = bed_minoff(p, beg); for (j = min_off; j < p->n; ++j) { if (p->a[j].beg >= end) break; // out of range; no need to proceed if (p->a[j].end > beg && p->a[j].beg < end) { new_a[new_n].beg = MAX(p->a[j].beg, beg); new_a[new_n++].end = MIN(p->a[j].end, end); } } } if (new_n > 0) { free(p->a); p->a = new_a; p->n = new_n; p->m = new_n; p->filter = FILTERED; } else { free(new_a); p->filter = ALL; } } return h; } void *bed_hash_regions(void *reg_hash, char **regs, int first, int last, int *op) { reghash_t *h = (reghash_t *)reg_hash; reghash_t *t = NULL; int i; char reg[1024]; const char *q; int beg, end; if (h) { t = kh_init(reg); if (!t) { fprintf(stderr, "Error when creating the temporary region hash table!\n"); return NULL; } } else { h = kh_init(reg); if (!h) { fprintf(stderr, "Error when creating the region hash table!\n"); return NULL; } *op = 1; } for (i=first; i 1024) { fprintf(stderr, "Region name '%s' is too long (bigger than %d).\n", regs[i], 1024); continue; } strncpy(reg, regs[i], q - regs[i]); reg[q - regs[i]] = 0; } else { // not parsable as a region, but possibly a sequence named "foo:a" if (strlen(regs[i]) + 1 > 1024) { fprintf(stderr, "Region name '%s' is too long (bigger than %d).\n", regs[i], 1024); continue; } strcpy(reg, regs[i]); beg = 0; end = INT_MAX; } //if op==1 insert reg to the bed hash table if (*op && !(bed_insert(h, reg, beg, end))) { fprintf(stderr, "Error when inserting region='%s' in the bed hash table at address=%p!\n", regs[i], (void *)h); } //if op==0, first insert the regions in the temporary hash table, //then filter the bed hash table using it if (!(*op) && !(bed_insert(t, reg, beg, end))) { fprintf(stderr, "Error when inserting region='%s' in the temporary hash table at address=%p!\n", regs[i], (void *)t); } } if (!(*op)) { if (bed_index(t) != 0) goto fail; bed_unify(t); if (bed_filter(h, t) == NULL) goto fail; bed_destroy(t); t = NULL; } if (h) { if (bed_index(h) != 0) goto fail; bed_unify(h); } return h; fail: // Clean up whichever hash we made if (reg_hash) { if (t) bed_destroy(t); } else { if (h) bed_destroy(h); } return NULL; } const char* bed_get(void *reg_hash, int i, int filter) { reghash_t *h; bed_reglist_t *p; if (!reg_hash) return NULL; h = (reghash_t *)reg_hash; if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || (p->filter < filter)) return NULL; return kh_key(h, i); } /** * Create a region list from a the region hash table * @param reg_hash The region hash table * @param filter 0 - allow all regions, 1 - allow only selected regions * @param n_reg Pointer to the returned region number * @return The regions list as a hts_reglist_t */ hts_reglist_t *bed_reglist(void *reg_hash, int filter, int *n_reg) { reghash_t *h; bed_reglist_t *p; khint_t i; hts_reglist_t *reglist = NULL; int count = 0; int j; if (!reg_hash) return NULL; h = (reghash_t *)reg_hash; for (i = kh_begin(h); i < kh_end(h); i++) { if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || (p->filter < filter)) continue; count++; } if (!count) return NULL; reglist = (hts_reglist_t *)calloc(count, sizeof(hts_reglist_t)); if (!reglist) return NULL; *n_reg = count; count = 0; for (i = kh_begin(h); i < kh_end(h) && count < *n_reg; i++) { if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || (p->filter < filter)) continue; reglist[count].reg = kh_key(h,i); reglist[count].intervals = (hts_pair32_t *)calloc(p->n, sizeof(hts_pair32_t)); if(!(reglist[count].intervals)) { hts_reglist_free(reglist, count); return NULL; } reglist[count].count = p->n; reglist[count].max_end = 0; for (j = 0; j < p->n; j++) { reglist[count].intervals[j].beg = p->a[j].beg; reglist[count].intervals[j].end = p->a[j].end; if (reglist[count].intervals[j].end > reglist[count].max_end) reglist[count].max_end = reglist[count].intervals[j].end; } count++; } return reglist; } pysam-0.23.0/samtools/bedidx.c.pysam.c000066400000000000000000000474111475062545500175660ustar00rootroot00000000000000#include "samtools.pysam.h" /* bedidx.c -- BED file indexing. Copyright (C) 2011 Broad Institute. Copyright (C) 2014, 2017-2019, 2024 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "bedidx.h" #include "htslib/ksort.h" #include "htslib/kseq.h" KSTREAM_INIT(gzFile, gzread, 8192) static inline int lt_pair_pos(hts_pair_pos_t a, hts_pair_pos_t b) { if (a.beg == b.beg) return a.end < b.end; return a.beg < b.beg; } KSORT_INIT_STATIC(hts_pair_pos_t, hts_pair_pos_t, lt_pair_pos) /*! @typedef * @abstract bed_reglist_t - value type of the BED hash table * This structure encodes the list of intervals (ranges) for the regions provided via BED file or * command line arguments. * @field *a pointer to the array of intervals. * @field n actual number of elements contained by a * @field m number of allocated elements to a (n <= m) * @field *idx index array for computing the minimum offset */ typedef struct { int n, m; hts_pair_pos_t *a; int *idx; int filter; hts_pos_t max_idx; } bed_reglist_t; #include "htslib/khash.h" KHASH_MAP_INIT_STR(reg, bed_reglist_t) typedef kh_reg_t reghash_t; #if 0 // Debug function static void bed_print(void *reg_hash) { reghash_t *h = (reghash_t *)reg_hash; bed_reglist_t *p; khint_t k; int i; const char *reg; if (!h) { fprintf(samtools_stdout, "Hash table is empty!\n"); return; } for (k = kh_begin(h); k < kh_end(h); k++) { if (kh_exist(h,k)) { reg = kh_key(h,k); fprintf(samtools_stdout, "Region: '%s'\n", reg); if ((p = &kh_val(h,k)) != NULL && p->n > 0) { fprintf(samtools_stdout, "Filter: %d\n", p->filter); for (i=0; in; i++) { fprintf(samtools_stdout, "\tinterval[%d]: %"PRIhts_pos"-%"PRIhts_pos"\n", i,p->a[i].beg,p->a[i].end); } } else { fprintf(samtools_stdout, "Region '%s' has no intervals!\n", reg); } } } } #endif static int bed_index_core(bed_reglist_t *regions) { int i, *idx = NULL; size_t idx_size = 0; hts_pos_t last_end = 0; hts_pair_pos_t *a = regions->a; // Construct a linear index on regions, to allow rapid lookup of // where to start searching for matches for (i = 0; i < regions->n; ++i) { hts_pos_t beg = a[i].beg >= 0 ? a[i].beg >> LIDX_SHIFT : 0; hts_pos_t end = a[i].end >= 0 ? a[i].end >> LIDX_SHIFT : 0; hts_pos_t j; if (end < last_end) continue; // Can happen for a containment if (end + 1 >= SIZE_MAX / sizeof(*idx)) { // Ensure no overflow errno = ENOMEM; free(idx); return -1; } if (hts_resize(int, (size_t) end + 1, &idx_size, &idx, 0) < 0) { free(idx); return -1; } // Fill any gap prior to this region by pointing to the previous one for (j = last_end; j < beg; j++) idx[j] = i > 0 ? i - 1 : 0; // Fill from max(last_end, beg) to `end` (inclusive) with current region for (; j <= end; j++) idx[j] = i; // Remember where finished for the next gap last_end = end + 1; } regions->idx = idx; regions->max_idx = last_end; return 0; } static int bed_index(reghash_t *h) { khint_t k; for (k = 0; k < kh_end(h); ++k) { if (kh_exist(h, k)) { bed_reglist_t *p = &kh_val(h, k); if (p->idx) { free(p->idx); p->idx = NULL; } ks_introsort(hts_pair_pos_t, p->n, p->a); if (bed_index_core(p) != 0) { return -1; } } } return 0; } static int bed_minoff(const bed_reglist_t *p, hts_pos_t beg) { int min_off=0; if (p && p->idx && p->max_idx > 0 && beg >= 0) { min_off = (beg>>LIDX_SHIFT >= p->max_idx)? p->idx[p->max_idx-1] : p->idx[beg>>LIDX_SHIFT]; } return min_off; } static int bed_overlap_core(const bed_reglist_t *p, hts_pos_t beg, hts_pos_t end) { int i, min_off; if (p->n == 0) return 0; min_off = bed_minoff(p, beg); for (i = min_off; i < p->n; ++i) { if (p->a[i].beg >= end) break; // out of range; no need to proceed if (p->a[i].end > beg && p->a[i].beg < end) return 1; // find the overlap; return } return 0; } int bed_overlap(const void *_h, const char *chr, hts_pos_t beg, hts_pos_t end) { const reghash_t *h = (const reghash_t*)_h; khint_t k; if (!h) return 0; k = kh_get(reg, h, chr); if (k == kh_end(h)) return 0; return bed_overlap_core(&kh_val(h, k), beg, end); } /** @brief Trim a sorted interval list, inside a region hash table, * by removing completely contained intervals and merging adjacent or * overlapping intervals. * @param reg_hash the region hash table with interval lists as values */ void bed_unify(void *reg_hash) { int i, j, new_n; reghash_t *h; bed_reglist_t *p; if (!reg_hash) return; h = (reghash_t *)reg_hash; for (i = kh_begin(h); i < kh_end(h); i++) { if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || !(p->n)) continue; for (new_n = 0, j = 1; j < p->n; j++) { if (p->a[new_n].end < p->a[j].beg) { p->a[++new_n] = p->a[j]; } else { if (p->a[new_n].end < p->a[j].end) p->a[new_n].end = p->a[j].end; } } p->n = ++new_n; } } /* "BED" file reader, which actually reads two different formats. BED files contain between three and nine fields per line, of which only the first three (reference, start, end) are of interest to us. BED counts positions from base 0, and the end is the base after the region of interest. While not properly documented in the specification, it is also possible to have 'browser' and 'track' lines in BED files that do not follow the standard format and should be ignored. Examination of the BED file reading code in http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git shows that BED files can also have comment lines starting with '#', leading whitespace is stripped, and that fields are separated by one or more consecutive whitespace characters. The alternative format was originally for reading positions in VCF format. This expects two columns, which indicate the reference and a position. The position corresponds to a single base, and unlike BED counts from 1. Which format is in use is determined based on whether one or two numbers can be decoded on the line. As this choice is made line-by-line in this implementation, it is possible (but probably a bad idea) to mix both formats in the same file. If trying to read a VCF file by this method, it would be important to ensure that the third column (ID) does not contain any entries that start with a digit, to avoid the line erroneously being parsed as a BED file entry. The BED specification is at http://www.genome.ucsc.edu/FAQ/FAQformat.html The VCF specification is at https://github.com/samtools/hts-specs */ void *bed_read(const char *fn) { reghash_t *h = kh_init(reg); gzFile fp; kstream_t *ks = NULL; int dret; unsigned int line = 0, save_errno; kstring_t str = { 0, 0, NULL }; if (NULL == h) return NULL; // read the list fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r"); if (fp == 0) goto fail; ks = ks_init(fp); if (NULL == ks) goto fail; // In case ks_init ever gets error checking... int ks_len; while ((ks_len = ks_getuntil(ks, KS_SEP_LINE, &str, &dret)) >= 0) { // read a line char *ref = str.s, *ref_end; uint64_t beg = 0, end = 0; int num = 0; khint_t k; bed_reglist_t *p; if (ks_len == 0) continue; // skip blank lines line++; while (*ref && isspace(*ref)) ref++; if ('\0' == *ref) continue; // Skip blank lines if ('#' == *ref) continue; // Skip BED file comments ref_end = ref; // look for the end of the reference name while (*ref_end && !isspace(*ref_end)) ref_end++; if ('\0' != *ref_end) { *ref_end = '\0'; // terminate ref and look for start, end num = sscanf(ref_end + 1, "%"SCNu64" %"SCNu64, &beg, &end); } if (1 == num) { // VCF-style format end = beg--; // Counts from 1 instead of 0 for BED files } if (num < 1 || end < beg) { // These two are special lines that can occur in BED files. // Check for them here instead of earlier in case someone really // has called their reference "browser" or "track". if (0 == strcmp(ref, "browser")) continue; if (0 == strcmp(ref, "track")) continue; if (num < 1) { fprintf(samtools_stderr, "[bed_read] Parse error reading \"%s\" at line %u\n", fn, line); } else { fprintf(samtools_stderr, "[bed_read] Parse error reading \"%s\" at line %u : " "end (%"PRIu64") must not be less " "than start (%"PRIu64")\n", fn, line, end, beg); } errno = 0; // Prevent caller from printing misleading error messages goto fail; } // Put reg in the hash table if not already there k = kh_get(reg, h, ref); if (k == kh_end(h)) { // absent from the hash table int ret; char *s = strdup(ref); if (NULL == s) goto fail; k = kh_put(reg, h, s, &ret); if (-1 == ret) { free(s); goto fail; } memset(&kh_val(h, k), 0, sizeof(bed_reglist_t)); } p = &kh_val(h, k); // Add begin,end to the list if (p->n == p->m) { p->m = p->m ? p->m<<1 : 4; hts_pair_pos_t *new_a = realloc(p->a, p->m * sizeof(p->a[0])); if (NULL == new_a) goto fail; p->a = new_a; } p->a[p->n].beg = beg; p->a[p->n++].end = end; } // FIXME: Need to check for errors in ks_getuntil. At the moment it // doesn't look like it can return one. Possibly use gzgets instead? if (gzclose(fp) != Z_OK) { fp = NULL; goto fail; } if (bed_index(h) != 0) goto fail; ks_destroy(ks); free(str.s); //bed_unify(h); return h; fail: save_errno = errno; if (ks) ks_destroy(ks); if (fp) gzclose(fp); free(str.s); bed_destroy(h); errno = save_errno; return NULL; } void bed_destroy(void *_h) { reghash_t *h; khint_t k; if (!_h) return; h = (reghash_t*)_h; for (k = 0; k < kh_end(h); ++k) { if (kh_exist(h, k)) { free(kh_val(h, k).a); free(kh_val(h, k).idx); free((char*)kh_key(h, k)); } } kh_destroy(reg, h); } static void *bed_insert(void *reg_hash, char *reg, hts_pos_t beg, hts_pos_t end) { reghash_t *h; khint_t k; bed_reglist_t *p; if (!reg_hash) return NULL; h = (reghash_t *)reg_hash; // Put reg in the hash table if not already there k = kh_get(reg, h, reg); //looks strange, but only the second reg is the actual region name. if (k == kh_end(h)) { // absent from the hash table int ret; char *s = strdup(reg); if (NULL == s) goto fail; k = kh_put(reg, h, s, &ret); if (-1 == ret) { free(s); goto fail; } memset(&kh_val(h, k), 0, sizeof(bed_reglist_t)); } p = &kh_val(h, k); // Add beg and end to the list if (p->n == p->m) { p->m = p->m ? p->m<<1 : 4; hts_pair_pos_t *new_a = realloc(p->a, p->m * sizeof(p->a[0])); if (NULL == new_a) goto fail; p->a = new_a; } p->a[p->n].beg = beg; p->a[p->n++].end = end; fail: return h; } /* @brief Filter a region hash table (coming from the BED file) by another * region hash table (coming from CLI), so that only intervals contained in * both hash tables are kept. * @param reg_hash the target region hash table * @param tmp_hash the filter region hash table * @return pointer to the filtered hash table */ static void *bed_filter(void *reg_hash, void *tmp_hash) { reghash_t *h; reghash_t *t; bed_reglist_t *p, *q; khint_t l, k; hts_pair_pos_t *new_a; int i, j, new_n, min_off; const char *reg; hts_pos_t beg, end; h = (reghash_t *)reg_hash; t = (reghash_t *)tmp_hash; if (!h) return NULL; if (!t) return h; for (l = kh_begin(t); l < kh_end(t); l++) { if (!kh_exist(t,l) || !(q = &kh_val(t,l)) || !(q->n)) continue; reg = kh_key(t,l); k = kh_get(reg, h, reg); //looks strange, but only the second reg is a proper argument. if (k == kh_end(h) || !(p = &kh_val(h, k)) || !(p->n)) continue; new_a = calloc(q->n + p->n, sizeof(new_a[0])); if (!new_a) return NULL; new_n = 0; for (i = 0; i < q->n; i++) { beg = q->a[i].beg; end = q->a[i].end; min_off = bed_minoff(p, beg); for (j = min_off; j < p->n; ++j) { if (p->a[j].beg >= end) break; // out of range; no need to proceed if (p->a[j].end > beg && p->a[j].beg < end) { new_a[new_n].beg = MAX(p->a[j].beg, beg); new_a[new_n++].end = MIN(p->a[j].end, end); } } } if (new_n > 0) { free(p->a); p->a = new_a; p->n = new_n; p->m = new_n; p->filter = FILTERED; } else { free(new_a); p->filter = ALL; } } return h; } void *bed_hash_regions(void *reg_hash, char **regs, int first, int last, int *op) { reghash_t *h = (reghash_t *)reg_hash; reghash_t *t = NULL; int i; char reg[1024]; const char *q; int beg, end; if (h) { t = kh_init(reg); if (!t) { fprintf(samtools_stderr, "Error when creating the temporary region hash table!\n"); return NULL; } } else { h = kh_init(reg); if (!h) { fprintf(samtools_stderr, "Error when creating the region hash table!\n"); return NULL; } *op = 1; } for (i=first; i 1024) { fprintf(samtools_stderr, "Region name '%s' is too long (bigger than %d).\n", regs[i], 1024); continue; } strncpy(reg, regs[i], q - regs[i]); reg[q - regs[i]] = 0; } else { // not parsable as a region, but possibly a sequence named "foo:a" if (strlen(regs[i]) + 1 > 1024) { fprintf(samtools_stderr, "Region name '%s' is too long (bigger than %d).\n", regs[i], 1024); continue; } strcpy(reg, regs[i]); beg = 0; end = INT_MAX; } //if op==1 insert reg to the bed hash table if (*op && !(bed_insert(h, reg, beg, end))) { fprintf(samtools_stderr, "Error when inserting region='%s' in the bed hash table at address=%p!\n", regs[i], (void *)h); } //if op==0, first insert the regions in the temporary hash table, //then filter the bed hash table using it if (!(*op) && !(bed_insert(t, reg, beg, end))) { fprintf(samtools_stderr, "Error when inserting region='%s' in the temporary hash table at address=%p!\n", regs[i], (void *)t); } } if (!(*op)) { if (bed_index(t) != 0) goto fail; bed_unify(t); if (bed_filter(h, t) == NULL) goto fail; bed_destroy(t); t = NULL; } if (h) { if (bed_index(h) != 0) goto fail; bed_unify(h); } return h; fail: // Clean up whichever hash we made if (reg_hash) { if (t) bed_destroy(t); } else { if (h) bed_destroy(h); } return NULL; } const char* bed_get(void *reg_hash, int i, int filter) { reghash_t *h; bed_reglist_t *p; if (!reg_hash) return NULL; h = (reghash_t *)reg_hash; if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || (p->filter < filter)) return NULL; return kh_key(h, i); } /** * Create a region list from a the region hash table * @param reg_hash The region hash table * @param filter 0 - allow all regions, 1 - allow only selected regions * @param n_reg Pointer to the returned region number * @return The regions list as a hts_reglist_t */ hts_reglist_t *bed_reglist(void *reg_hash, int filter, int *n_reg) { reghash_t *h; bed_reglist_t *p; khint_t i; hts_reglist_t *reglist = NULL; int count = 0; int j; if (!reg_hash) return NULL; h = (reghash_t *)reg_hash; for (i = kh_begin(h); i < kh_end(h); i++) { if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || (p->filter < filter)) continue; count++; } if (!count) return NULL; reglist = (hts_reglist_t *)calloc(count, sizeof(hts_reglist_t)); if (!reglist) return NULL; *n_reg = count; count = 0; for (i = kh_begin(h); i < kh_end(h) && count < *n_reg; i++) { if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || (p->filter < filter)) continue; reglist[count].reg = kh_key(h,i); reglist[count].intervals = (hts_pair32_t *)calloc(p->n, sizeof(hts_pair32_t)); if(!(reglist[count].intervals)) { hts_reglist_free(reglist, count); return NULL; } reglist[count].count = p->n; reglist[count].max_end = 0; for (j = 0; j < p->n; j++) { reglist[count].intervals[j].beg = p->a[j].beg; reglist[count].intervals[j].end = p->a[j].end; if (reglist[count].intervals[j].end > reglist[count].max_end) reglist[count].max_end = reglist[count].intervals[j].end; } count++; } return reglist; } pysam-0.23.0/samtools/bedidx.h000066400000000000000000000033471475062545500162220ustar00rootroot00000000000000/* bedidx.h -- BED file indexing header file. Copyright (C) 2017 Genome Research Ltd. Author: Valeriu Ohan Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef BEDIDX_H #define BEDIDX_H #include "htslib/hts.h" #define LIDX_SHIFT 13 #define ALL 0 #define FILTERED 1 #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) #define MAX(A,B) ( ( (A) > (B) ) ? (A) : (B) ) void *bed_read(const char *fn); void bed_destroy(void *_h); int bed_overlap(const void *_h, const char *chr, hts_pos_t beg, hts_pos_t end); void *bed_hash_regions(void *reg_hash, char **regs, int first, int last, int *op); const char* bed_get(void *reg_hash, int index, int filter); hts_reglist_t *bed_reglist(void *reg_hash, int filter, int *count_regs); void bed_unify(void *_h); #endif pysam-0.23.0/samtools/consensus_pileup.c000066400000000000000000000447721475062545500203630ustar00rootroot00000000000000/* consensus__pileup.h -- Pileup orientated data per consensus column Copyright (C) 2013-2016, 2020-2022 Genome Research Ltd. Author: James Bonfied Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notices and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #ifdef __SSE__ # include #else # define _mm_prefetch(a,b) #endif #include "consensus_pileup.h" #define MIN(a,b) ((a)<(b)?(a):(b)) #define bam_strand(b) (((b)->core.flag & BAM_FREVERSE) != 0) /* * START_WITH_DEL is the mode that Gap5 uses when building this. It prepends * all cigar strings with 1D and decrements the position by one. (And then * has code to reverse this operation in the pileup handler.) * * The reason for this is that it means reads starting with an insertion work. * Otherwise the inserted bases are silently lost. (Try it with "samtools * mpileup" and you can see it has the same issue.) * * However it's probably not want most people expect. */ //#define START_WITH_DEL /* -------------------------------------------------------------------------- * The pileup code itself. * * This consists of the external pileup_loop() function, which takes a * sam/bam samfile_t pointer and a callback function. The callback function * is called once per column of aligned data (so once per base in an * insertion). * * Current known issues. * 1) zero length matches, ie 2S2S cause failures. * 2) Insertions at starts of sequences get included in the soft clip, so * 2S2I2M is treated as if it's 4S2M * 3) From 1 and 2 above, 1S1I2S becomes 2S2S which fails. */ /* * Fetches the next base => the nth base at unpadded position pos. (Nth can * be greater than 0 if we have an insertion in this column). Do not call this * with pos/nth lower than the previous query, although higher is better. * (This allows it to be initialised at base 0.) * * Stores the result in base and also updates is_insert to indicate that * this sequence still has more bases in this position beyond the current * nth parameter. * * Returns 1 if a base was fetched * 0 if not (eg ran off the end of sequence) */ static int get_next_base(pileup_t *p, hts_pos_t pos, int nth, int *is_insert) { bam1_t *b = &p->b; int op = p->cigar_op; p->start -= p->start>0; if (p->first_del && op != BAM_CPAD) p->first_del = 0; *is_insert = 0; /* Find pos first */ while (p->pos < pos) { p->nth = 0; if (p->cigar_len == 0) { if (p->cigar_ind >= b->core.n_cigar) { p->eof = 1; return 0; } op=p->cigar_op = p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK; p->cigar_len = p->b_cigar[p->cigar_ind] >> BAM_CIGAR_SHIFT; p->cigar_ind++; } if ((op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) && p->cigar_len <= pos - p->pos) { p->seq_offset += p->cigar_len; p->pos += p->cigar_len; p->cigar_len = 0; } else { switch (op) { case BAM_CMATCH: case BAM_CEQUAL: case BAM_CDIFF: p->seq_offset++; /* Fall through */ case BAM_CDEL: case BAM_CREF_SKIP: p->pos++; p->cigar_len--; break; case BAM_CINS: case BAM_CSOFT_CLIP: p->seq_offset += p->cigar_len; /* Fall through */ case BAM_CPAD: case BAM_CHARD_CLIP: p->cigar_len = 0; break; default: fprintf(stderr, "Unhandled cigar_op %d\n", op); return -1; } } } /* Now at pos, find nth base */ while (p->nth < nth) { if (p->cigar_len == 0) { if (p->cigar_ind >= b->core.n_cigar) { p->eof = 1; return 0; /* off end of seq */ } op=p->cigar_op = p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK; p->cigar_len = p->b_cigar[p->cigar_ind] >> BAM_CIGAR_SHIFT; p->cigar_ind++; } switch (op) { case BAM_CMATCH: case BAM_CEQUAL: case BAM_CDIFF: case BAM_CSOFT_CLIP: case BAM_CDEL: case BAM_CREF_SKIP: goto at_nth; /* sorry, but it's fast! */ case BAM_CINS: p->seq_offset++; /* Fall through */ case BAM_CPAD: p->cigar_len--; p->nth++; break; case BAM_CHARD_CLIP: p->cigar_len = 0; break; default: fprintf(stderr, "Unhandled cigar_op %d\n", op); return -1; } } at_nth: /* Fill out base & qual fields */ p->ref_skip = 0; if (p->nth < nth && op != BAM_CINS) { //p->base = '-'; p->base = '*'; p->base4 = 16; p->padding = 1; if (p->seq_offset < b->core.l_qseq) p->qual = MIN(p->qual, p->b_qual[p->seq_offset+1]); else p->qual = 0; } else { p->padding = 0; switch(op) { case BAM_CDEL: p->base = '*'; p->base4 = 16; if (p->seq_offset+1 < b->core.l_qseq) p->qual = MIN(p->qual, p->b_qual[p->seq_offset+1]); else p->qual = MIN(p->qual, p->b_qual[p->seq_offset]); break; case BAM_CPAD: //p->base = '+'; p->base = '*'; p->base4 = 16; if (p->seq_offset+1 < b->core.l_qseq) p->qual = MIN(p->qual, p->b_qual[p->seq_offset+1]); else p->qual = MIN(p->qual, p->b_qual[p->seq_offset]); break; case BAM_CREF_SKIP: p->base = '.'; p->base4 = 0; p->qual = 0; /* end of fragment, but not sequence */ p->eof = p->eof ? 2 : 3; p->ref_skip = 1; break; default: if (p->seq_offset < b->core.l_qseq) { p->qual = p->b_qual[p->seq_offset]; p->base4 = p->b_seq[p->seq_offset/2] >> ((~p->seq_offset&1)<<2) & 0xf; p->base = "NACMGRSVTWYHKDBN"[p->base4]; } else { p->base = 'N'; p->base4 = 15; p->qual = 0xff; } break; } } /* Handle moving out of N (skip) into sequence again */ if (p->eof && p->base != '.') { p->start = 1; p->ref_skip = 1; p->eof = 0; } /* Starting with an indel needs a minor fudge */ if (p->start && p->cigar_op == BAM_CDEL) { p->first_del = 1; } /* Check if next op is an insertion of some sort */ if (p->cigar_len == 0) { if (p->cigar_ind < b->core.n_cigar) { op=p->cigar_op = p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK; p->cigar_len = p->b_cigar[p->cigar_ind] >> BAM_CIGAR_SHIFT; p->cigar_ind++; if (op == BAM_CREF_SKIP) { p->eof = 3; p->ref_skip = 1; } } else { p->eof = 1; } } switch (op) { case BAM_CPAD: case BAM_CINS: *is_insert = p->cigar_len; break; case BAM_CSOFT_CLIP: /* Last op 'S' => eof */ p->eof = (p->cigar_ind == b->core.n_cigar || (p->cigar_ind+1 == b->core.n_cigar && (p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK) == BAM_CHARD_CLIP)) ? 1 : 0; break; case BAM_CHARD_CLIP: p->eof = 1; break; default: break; } return 1; } /* * Loops through a set of supplied ranges producing columns of data. * When found, it calls func with clientdata as a callback. Func should * return 0 for success and non-zero for failure. seq_init() is called * on each new entry before we start processing it. It should return 0 or 1 * to indicate reject or accept status (eg to filter unmapped data). * If seq_init() returns -1 we abort the pileup_loop with an error. * seq_init may be NULL. * * Returns 0 on success * -1 on failure */ int pileup_loop(samFile *fp, sam_hdr_t *h, int (*seq_fetch)(void *client_data, samFile *fp, sam_hdr_t *h, bam1_t *b), int (*seq_init)(void *client_data, samFile *fp, sam_hdr_t *h, pileup_t *p), int (*seq_column)(void *client_data, samFile *fp, sam_hdr_t *h, pileup_t *p, int depth, hts_pos_t pos, int nth, int is_insert), void (*seq_free)(void *client_data, samFile *fp, sam_hdr_t *h, pileup_t *p), void *client_data) { int ret = -1; pileup_t *phead = NULL, *p, *pfree = NULL, *last, *next, *ptail = NULL; pileup_t *pnew = NULL; int is_insert, nth = 0, r; hts_pos_t col = 0; int last_ref = -1; /* FIXME: allow for start/stop boundaries rather than consuming all data */ if (NULL == (pnew = calloc(1, sizeof(*p)))) return -1; do { bam1_t *b; hts_pos_t pos; r = seq_fetch(client_data, fp, h, &pnew->b); if (r < -1) { fprintf(stderr, "bam_next_seq() failure.\n"); goto error; } b = &pnew->b; /* Force realloc */ //fp->bs = NULL; //fp->bs_size = 0; //r = samread(fp, pnew->b); if (r >= 0) { if (b->core.flag & BAM_FUNMAP) continue; if (b->core.tid == -1) { /* Another indicator for unmapped */ continue; } else if (b->core.tid == last_ref) { pos = b->core.pos+1; //printf("New seq at pos %d @ %d %s\n", pos, b->core.tid, // bam_name(b)); } else { //printf("New ctg at pos %ld @ %d\n",b->core.pos+1,b->core.tid); pos = HTS_POS_MAX; } } else { pos = HTS_POS_MAX; } if (col > pos) { fprintf(stderr, "BAM/SAM file is not sorted by position. " "Aborting\n"); goto error; } /* Process data between the last column and our latest addition */ while (col < pos && phead) { struct pileup *eof_head = NULL, *eofp = NULL; int v, ins, depth = 0; //printf("Col=%ld pos=%ld nth=%d\n", col, pos, nth); /* Pileup */ is_insert = 0; pileup_t *pnext = phead ? phead->next : NULL; for (p = phead, last = NULL; p; p = pnext) { #if 0 // Simple prefetching pnext = p->next; if (pnext) _mm_prefetch(pnext, _MM_HINT_T0); #else // More complex prefetching => more instructions, but // usually faster. pnext = p->next; if (pnext) { // start memory fetches; a big help on very deep data if (pnext->next) // struct 2 ahead _mm_prefetch(pnext->next, _MM_HINT_T0); // seq/qual 1 ahead _mm_prefetch(pnext->b_qual + pnext->seq_offset, _MM_HINT_T0); _mm_prefetch(pnext->b_seq + pnext->seq_offset/2, _MM_HINT_T0); } #endif if (!get_next_base(p, col, nth, &ins)) p->eof = 1; if (p->eof == 1) { if (eofp) eofp->eofn = p; eofp = p; eofp->eofl = last; if (!eof_head) eof_head = eofp; } else { last = p; } if (is_insert < ins) is_insert = ins; depth++; } if ((ptail = last) == NULL) ptail = phead; /* Call our function on phead linked list */ v = seq_column(client_data, fp, h, phead, depth, #ifdef START_WITH_DEL col-1, #else col, #endif nth, is_insert); /* Remove dead seqs */ for (p = eof_head ; p; p = p->eofn) { if (p->eofl) p->eofl->next = p->next; else phead = p->next; p->next = pfree; pfree = p; if (seq_free) seq_free(client_data, fp, h, p); } if (v == 1) break; /* early abort */ if (v != 0) goto error; /* Next column */ if (is_insert) { nth++; } else { nth = 0; col++; } } /* May happen if we have a hole in the contig */ col = pos; /* New contig */ if (b && b->core.tid != last_ref) { last_ref = b->core.tid; pos = b->core.pos+1; nth = 0; col = pos; } /* * Add this seq. * Note: cigars starting with I or P ops (eg 2P3I10M) mean we have * alignment instructions that take place before the designated * starting location listed in the SAM file. They won't get included * in the callback function until they officially start, which is * already too late. * * So to workaround this, we prefix all CIGAR with 1D, move the * position by 1bp, and then force the callback code to remove * leaving pads (either P or D generated). * * Ie it's a level 10 hack! */ if (r >= 0) { p = pnew; p->next = NULL; p->cd = NULL; p->eofn = NULL; p->eofl = NULL; p->start = 2; p->eof = 0; #ifdef START_WITH_DEL p->pos = pos-1; p->cigar_ind = 0; p->b_cigar = bam_get_cigar(&p->b); if ((p->b_cigar[0] & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { p->cigar_len = p->b_cigar[0] >> BAM_CIGAR_SHIFT; p->cigar_op = BAM_CHARD_CLIP; if ((p->b_cigar[1] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP) { /* xHxS... => xHxS1D... */ p->b_cigar[0] = p->b_cigar[1]; p->b_cigar[1] = (1 << BAM_CIGAR_SHIFT) | BAM_CDEL; } else { /* xH... => xH1D... */ p->b_cigar[0] = (1 << BAM_CIGAR_SHIFT) | BAM_CDEL; } } else { if ((p->b_cigar[0] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP) { /* xS... => xS1D... */ p->cigar_len = p->b_cigar[0] >> BAM_CIGAR_SHIFT; p->cigar_op = BAM_CSOFT_CLIP; p->b_cigar[0] = (1 << BAM_CIGAR_SHIFT) | BAM_CDEL; } else { /* ... => 1D... */ p->cigar_len = 1; /* was 0 */ p->cigar_op = BAM_CDEL; /* was 'X' */ } } p->seq_offset = -1; p->first_del = 1; #else p->pos = pos-1; p->cigar_ind = 0; p->b_cigar = bam_get_cigar(&p->b); p->cigar_len = 0; p->cigar_op = -1; p->seq_offset = -1; p->first_del = 0; #endif p->b_is_rev = bam_is_rev(&p->b); p->b_qual = (uint8_t *)bam_get_qual(&p->b); p->b_seq = (uint8_t *)bam_get_seq(&p->b); if (seq_init) { int v; v = seq_init(client_data, fp, h, p); if (v == -1) goto error; if (v == 1) { /* Keep this seq */ if (phead) { ptail->next = p; } else { phead = p; } ptail = p; } else { /* Push back on free list */ p->next = pfree; pfree = p; } } else { if (phead) ptail->next = p; else phead = p; ptail = p; } /* Allocate the next pileup rec */ if (pfree) { pnew = pfree; pfree = pfree->next; } else { if (NULL == (pnew = calloc(1, sizeof(*pnew)))) goto error; } } } while (r >= 0); ret = 0; error: if (pnew) { free(pnew->b.data); free(pnew); } /* Tidy up */ for (p = pfree; p; p = next) { next = p->next; if (seq_free) seq_free(client_data, fp, h, p); free(p->b.data); free(p); } return ret; } pysam-0.23.0/samtools/consensus_pileup.c.pysam.c000066400000000000000000000450731475062545500217270ustar00rootroot00000000000000#include "samtools.pysam.h" /* consensus__pileup.h -- Pileup orientated data per consensus column Copyright (C) 2013-2016, 2020-2022 Genome Research Ltd. Author: James Bonfied Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notices and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #ifdef __SSE__ # include #else # define _mm_prefetch(a,b) #endif #include "consensus_pileup.h" #define MIN(a,b) ((a)<(b)?(a):(b)) #define bam_strand(b) (((b)->core.flag & BAM_FREVERSE) != 0) /* * START_WITH_DEL is the mode that Gap5 uses when building this. It prepends * all cigar strings with 1D and decrements the position by one. (And then * has code to reverse this operation in the pileup handler.) * * The reason for this is that it means reads starting with an insertion work. * Otherwise the inserted bases are silently lost. (Try it with "samtools * mpileup" and you can see it has the same issue.) * * However it's probably not want most people expect. */ //#define START_WITH_DEL /* -------------------------------------------------------------------------- * The pileup code itself. * * This consists of the external pileup_loop() function, which takes a * sam/bam samfile_t pointer and a callback function. The callback function * is called once per column of aligned data (so once per base in an * insertion). * * Current known issues. * 1) zero length matches, ie 2S2S cause failures. * 2) Insertions at starts of sequences get included in the soft clip, so * 2S2I2M is treated as if it's 4S2M * 3) From 1 and 2 above, 1S1I2S becomes 2S2S which fails. */ /* * Fetches the next base => the nth base at unpadded position pos. (Nth can * be greater than 0 if we have an insertion in this column). Do not call this * with pos/nth lower than the previous query, although higher is better. * (This allows it to be initialised at base 0.) * * Stores the result in base and also updates is_insert to indicate that * this sequence still has more bases in this position beyond the current * nth parameter. * * Returns 1 if a base was fetched * 0 if not (eg ran off the end of sequence) */ static int get_next_base(pileup_t *p, hts_pos_t pos, int nth, int *is_insert) { bam1_t *b = &p->b; int op = p->cigar_op; p->start -= p->start>0; if (p->first_del && op != BAM_CPAD) p->first_del = 0; *is_insert = 0; /* Find pos first */ while (p->pos < pos) { p->nth = 0; if (p->cigar_len == 0) { if (p->cigar_ind >= b->core.n_cigar) { p->eof = 1; return 0; } op=p->cigar_op = p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK; p->cigar_len = p->b_cigar[p->cigar_ind] >> BAM_CIGAR_SHIFT; p->cigar_ind++; } if ((op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) && p->cigar_len <= pos - p->pos) { p->seq_offset += p->cigar_len; p->pos += p->cigar_len; p->cigar_len = 0; } else { switch (op) { case BAM_CMATCH: case BAM_CEQUAL: case BAM_CDIFF: p->seq_offset++; /* Fall through */ case BAM_CDEL: case BAM_CREF_SKIP: p->pos++; p->cigar_len--; break; case BAM_CINS: case BAM_CSOFT_CLIP: p->seq_offset += p->cigar_len; /* Fall through */ case BAM_CPAD: case BAM_CHARD_CLIP: p->cigar_len = 0; break; default: fprintf(samtools_stderr, "Unhandled cigar_op %d\n", op); return -1; } } } /* Now at pos, find nth base */ while (p->nth < nth) { if (p->cigar_len == 0) { if (p->cigar_ind >= b->core.n_cigar) { p->eof = 1; return 0; /* off end of seq */ } op=p->cigar_op = p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK; p->cigar_len = p->b_cigar[p->cigar_ind] >> BAM_CIGAR_SHIFT; p->cigar_ind++; } switch (op) { case BAM_CMATCH: case BAM_CEQUAL: case BAM_CDIFF: case BAM_CSOFT_CLIP: case BAM_CDEL: case BAM_CREF_SKIP: goto at_nth; /* sorry, but it's fast! */ case BAM_CINS: p->seq_offset++; /* Fall through */ case BAM_CPAD: p->cigar_len--; p->nth++; break; case BAM_CHARD_CLIP: p->cigar_len = 0; break; default: fprintf(samtools_stderr, "Unhandled cigar_op %d\n", op); return -1; } } at_nth: /* Fill out base & qual fields */ p->ref_skip = 0; if (p->nth < nth && op != BAM_CINS) { //p->base = '-'; p->base = '*'; p->base4 = 16; p->padding = 1; if (p->seq_offset < b->core.l_qseq) p->qual = MIN(p->qual, p->b_qual[p->seq_offset+1]); else p->qual = 0; } else { p->padding = 0; switch(op) { case BAM_CDEL: p->base = '*'; p->base4 = 16; if (p->seq_offset+1 < b->core.l_qseq) p->qual = MIN(p->qual, p->b_qual[p->seq_offset+1]); else p->qual = MIN(p->qual, p->b_qual[p->seq_offset]); break; case BAM_CPAD: //p->base = '+'; p->base = '*'; p->base4 = 16; if (p->seq_offset+1 < b->core.l_qseq) p->qual = MIN(p->qual, p->b_qual[p->seq_offset+1]); else p->qual = MIN(p->qual, p->b_qual[p->seq_offset]); break; case BAM_CREF_SKIP: p->base = '.'; p->base4 = 0; p->qual = 0; /* end of fragment, but not sequence */ p->eof = p->eof ? 2 : 3; p->ref_skip = 1; break; default: if (p->seq_offset < b->core.l_qseq) { p->qual = p->b_qual[p->seq_offset]; p->base4 = p->b_seq[p->seq_offset/2] >> ((~p->seq_offset&1)<<2) & 0xf; p->base = "NACMGRSVTWYHKDBN"[p->base4]; } else { p->base = 'N'; p->base4 = 15; p->qual = 0xff; } break; } } /* Handle moving out of N (skip) into sequence again */ if (p->eof && p->base != '.') { p->start = 1; p->ref_skip = 1; p->eof = 0; } /* Starting with an indel needs a minor fudge */ if (p->start && p->cigar_op == BAM_CDEL) { p->first_del = 1; } /* Check if next op is an insertion of some sort */ if (p->cigar_len == 0) { if (p->cigar_ind < b->core.n_cigar) { op=p->cigar_op = p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK; p->cigar_len = p->b_cigar[p->cigar_ind] >> BAM_CIGAR_SHIFT; p->cigar_ind++; if (op == BAM_CREF_SKIP) { p->eof = 3; p->ref_skip = 1; } } else { p->eof = 1; } } switch (op) { case BAM_CPAD: case BAM_CINS: *is_insert = p->cigar_len; break; case BAM_CSOFT_CLIP: /* Last op 'S' => eof */ p->eof = (p->cigar_ind == b->core.n_cigar || (p->cigar_ind+1 == b->core.n_cigar && (p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK) == BAM_CHARD_CLIP)) ? 1 : 0; break; case BAM_CHARD_CLIP: p->eof = 1; break; default: break; } return 1; } /* * Loops through a set of supplied ranges producing columns of data. * When found, it calls func with clientdata as a callback. Func should * return 0 for success and non-zero for failure. seq_init() is called * on each new entry before we start processing it. It should return 0 or 1 * to indicate reject or accept status (eg to filter unmapped data). * If seq_init() returns -1 we abort the pileup_loop with an error. * seq_init may be NULL. * * Returns 0 on success * -1 on failure */ int pileup_loop(samFile *fp, sam_hdr_t *h, int (*seq_fetch)(void *client_data, samFile *fp, sam_hdr_t *h, bam1_t *b), int (*seq_init)(void *client_data, samFile *fp, sam_hdr_t *h, pileup_t *p), int (*seq_column)(void *client_data, samFile *fp, sam_hdr_t *h, pileup_t *p, int depth, hts_pos_t pos, int nth, int is_insert), void (*seq_free)(void *client_data, samFile *fp, sam_hdr_t *h, pileup_t *p), void *client_data) { int ret = -1; pileup_t *phead = NULL, *p, *pfree = NULL, *last, *next, *ptail = NULL; pileup_t *pnew = NULL; int is_insert, nth = 0, r; hts_pos_t col = 0; int last_ref = -1; /* FIXME: allow for start/stop boundaries rather than consuming all data */ if (NULL == (pnew = calloc(1, sizeof(*p)))) return -1; do { bam1_t *b; hts_pos_t pos; r = seq_fetch(client_data, fp, h, &pnew->b); if (r < -1) { fprintf(samtools_stderr, "bam_next_seq() failure.\n"); goto error; } b = &pnew->b; /* Force realloc */ //fp->bs = NULL; //fp->bs_size = 0; //r = samread(fp, pnew->b); if (r >= 0) { if (b->core.flag & BAM_FUNMAP) continue; if (b->core.tid == -1) { /* Another indicator for unmapped */ continue; } else if (b->core.tid == last_ref) { pos = b->core.pos+1; //printf("New seq at pos %d @ %d %s\n", pos, b->core.tid, // bam_name(b)); } else { //printf("New ctg at pos %ld @ %d\n",b->core.pos+1,b->core.tid); pos = HTS_POS_MAX; } } else { pos = HTS_POS_MAX; } if (col > pos) { fprintf(samtools_stderr, "BAM/SAM file is not sorted by position. " "Aborting\n"); goto error; } /* Process data between the last column and our latest addition */ while (col < pos && phead) { struct pileup *eof_head = NULL, *eofp = NULL; int v, ins, depth = 0; //printf("Col=%ld pos=%ld nth=%d\n", col, pos, nth); /* Pileup */ is_insert = 0; pileup_t *pnext = phead ? phead->next : NULL; for (p = phead, last = NULL; p; p = pnext) { #if 0 // Simple prefetching pnext = p->next; if (pnext) _mm_prefetch(pnext, _MM_HINT_T0); #else // More complex prefetching => more instructions, but // usually faster. pnext = p->next; if (pnext) { // start memory fetches; a big help on very deep data if (pnext->next) // struct 2 ahead _mm_prefetch(pnext->next, _MM_HINT_T0); // seq/qual 1 ahead _mm_prefetch(pnext->b_qual + pnext->seq_offset, _MM_HINT_T0); _mm_prefetch(pnext->b_seq + pnext->seq_offset/2, _MM_HINT_T0); } #endif if (!get_next_base(p, col, nth, &ins)) p->eof = 1; if (p->eof == 1) { if (eofp) eofp->eofn = p; eofp = p; eofp->eofl = last; if (!eof_head) eof_head = eofp; } else { last = p; } if (is_insert < ins) is_insert = ins; depth++; } if ((ptail = last) == NULL) ptail = phead; /* Call our function on phead linked list */ v = seq_column(client_data, fp, h, phead, depth, #ifdef START_WITH_DEL col-1, #else col, #endif nth, is_insert); /* Remove dead seqs */ for (p = eof_head ; p; p = p->eofn) { if (p->eofl) p->eofl->next = p->next; else phead = p->next; p->next = pfree; pfree = p; if (seq_free) seq_free(client_data, fp, h, p); } if (v == 1) break; /* early abort */ if (v != 0) goto error; /* Next column */ if (is_insert) { nth++; } else { nth = 0; col++; } } /* May happen if we have a hole in the contig */ col = pos; /* New contig */ if (b && b->core.tid != last_ref) { last_ref = b->core.tid; pos = b->core.pos+1; nth = 0; col = pos; } /* * Add this seq. * Note: cigars starting with I or P ops (eg 2P3I10M) mean we have * alignment instructions that take place before the designated * starting location listed in the SAM file. They won't get included * in the callback function until they officially start, which is * already too late. * * So to workaround this, we prefix all CIGAR with 1D, move the * position by 1bp, and then force the callback code to remove * leaving pads (either P or D generated). * * Ie it's a level 10 hack! */ if (r >= 0) { p = pnew; p->next = NULL; p->cd = NULL; p->eofn = NULL; p->eofl = NULL; p->start = 2; p->eof = 0; #ifdef START_WITH_DEL p->pos = pos-1; p->cigar_ind = 0; p->b_cigar = bam_get_cigar(&p->b); if ((p->b_cigar[0] & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { p->cigar_len = p->b_cigar[0] >> BAM_CIGAR_SHIFT; p->cigar_op = BAM_CHARD_CLIP; if ((p->b_cigar[1] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP) { /* xHxS... => xHxS1D... */ p->b_cigar[0] = p->b_cigar[1]; p->b_cigar[1] = (1 << BAM_CIGAR_SHIFT) | BAM_CDEL; } else { /* xH... => xH1D... */ p->b_cigar[0] = (1 << BAM_CIGAR_SHIFT) | BAM_CDEL; } } else { if ((p->b_cigar[0] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP) { /* xS... => xS1D... */ p->cigar_len = p->b_cigar[0] >> BAM_CIGAR_SHIFT; p->cigar_op = BAM_CSOFT_CLIP; p->b_cigar[0] = (1 << BAM_CIGAR_SHIFT) | BAM_CDEL; } else { /* ... => 1D... */ p->cigar_len = 1; /* was 0 */ p->cigar_op = BAM_CDEL; /* was 'X' */ } } p->seq_offset = -1; p->first_del = 1; #else p->pos = pos-1; p->cigar_ind = 0; p->b_cigar = bam_get_cigar(&p->b); p->cigar_len = 0; p->cigar_op = -1; p->seq_offset = -1; p->first_del = 0; #endif p->b_is_rev = bam_is_rev(&p->b); p->b_qual = (uint8_t *)bam_get_qual(&p->b); p->b_seq = (uint8_t *)bam_get_seq(&p->b); if (seq_init) { int v; v = seq_init(client_data, fp, h, p); if (v == -1) goto error; if (v == 1) { /* Keep this seq */ if (phead) { ptail->next = p; } else { phead = p; } ptail = p; } else { /* Push back on free list */ p->next = pfree; pfree = p; } } else { if (phead) ptail->next = p; else phead = p; ptail = p; } /* Allocate the next pileup rec */ if (pfree) { pnew = pfree; pfree = pfree->next; } else { if (NULL == (pnew = calloc(1, sizeof(*pnew)))) goto error; } } } while (r >= 0); ret = 0; error: if (pnew) { free(pnew->b.data); free(pnew); } /* Tidy up */ for (p = pfree; p; p = next) { next = p->next; if (seq_free) seq_free(client_data, fp, h, p); free(p->b.data); free(p); } return ret; } pysam-0.23.0/samtools/consensus_pileup.h000066400000000000000000000110011475062545500203430ustar00rootroot00000000000000/* consensus_pileup.h -- Pileup orientated data per consensus column Copyright (C) 2013-2016, 2020-2022 Genome Research Ltd. Author: James Bonfied Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notices and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include typedef struct pileup { // commonly used things together, to fit in a cache line (64 bytes) struct pileup *next; // A link list, for active seqs void *cd; // General purpose per-seq client-data int eof; // True if this sequence has finished int qual; // Current qual (for active seq only) char start; // True if this is a new sequence char base; // Current base (for active seq only) in ASCII char ref_skip; // True if the cause of eof or start is cigar N char padding; // True if the base was added due to another seq int base4; // Base in 4-bit notation (0-15) hts_pos_t pos; // Current unpadded position in seq int nth; // nth base at unpadded position 'pos' int b_is_rev; // 0 => fwd, 1 => rev int seq_offset; // Current base position in s->seq[] array. unsigned char *b_qual;// cached bam_qual unsigned char *b_seq; // cached bam_seq // --- 64 bytes struct pileup *eofn; // p->eof set, next eof member struct pileup *eofl; // last non-eof that points to p with p->eof uint32_t *b_cigar; // cached bam_cigar int cigar_ind; // Current location in s->alignment cigar str int cigar_op; // Current cigar operation int cigar_len; // Remaining length of this cigar op int first_del; // Used when first base is a deletion bam1_t b; // Bam entry associated with struct } pileup_t; /* * The pileup loop executes and calls callbacks to perform the work. * * seq_fetch returns the next sequence. Return 0 from this indicates no * more data. * * seq_init is called, if non-NULL, when a sequence is added to the pileup, * seq_free likewise, if non-NULL, is called when a sequence is removed * from the pileup. * These two functions are akin to the constructor and destructors added * to mpileup. * * seq_column is the primary work horse which is executed for each * reference position, and for each inserted base per ref pos. * * If we were to invert this from a loop generating callbacks to a polled * style interface like mpileup, then the seq_column bit would be dropped * and replaced by the returned pileup and associated parameters. */ int pileup_loop(samFile *fp, sam_hdr_t *h, int (*seq_fetch)(void *client_data, samFile *fp, sam_hdr_t *h, bam1_t *b), int (*seq_init)(void *client_data, samFile *fp, sam_hdr_t *h, pileup_t *p), int (*seq_column)(void *client_data, samFile *fp, sam_hdr_t *h, pileup_t *p, int depth, hts_pos_t pos, int nth, int is_insert), void (*seq_free)(void *client_data, samFile *fp, sam_hdr_t *h, pileup_t *p), void *client_data); pysam-0.23.0/samtools/coverage.c000066400000000000000000000706451475062545500165560ustar00rootroot00000000000000/* coverage.c -- samtools coverage subcommand Copyright (C) 2018,2019 Florian Breitwieser Portions copyright (C) 2019-2021, 2023-2024 Genome Research Ltd. Author: Florian P Breitwieser Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* This program calculates coverage from multiple BAMs * simultaneously, to achieve random access and to use the BED interface. * To compile this program separately, you may: * * gcc -g -O2 -Wall -o bamcov -D_MAIN_BAMCOV coverage.c -lhts -lz */ // C headers #include #include #include #include #include // variadic functions #include // INT_MAX #include // round #include #include #include #include #ifdef _WIN32 #include #else #include #endif #include "htslib/sam.h" #include "htslib/hts.h" #include "samtools.h" #include "sam_opts.h" typedef struct { // auxiliary data structure to hold stats on coverage unsigned long long n_covered_bases; unsigned long long summed_coverage; unsigned long long summed_baseQ; unsigned long long summed_mapQ; unsigned long long quality_bases; unsigned int n_reads; unsigned int n_selected_reads; bool covered; hts_pos_t beg; hts_pos_t end; int64_t bin_width; } stats_aux_t; typedef struct { // auxiliary data structure to hold a BAM file samFile *fp; // file handle sam_hdr_t *hdr; // file header hts_itr_t *iter; // iterator to a region - NULL for us by default int min_mapQ; // mapQ filter int min_len; // length filter int fail_flags; int required_flags; stats_aux_t *stats; } bam_aux_t; #if __STDC_VERSION__ >= 199901L #define VERTICAL_LINE "\u2502" // BOX DRAWINGS LIGHT VERTICAL // UTF8 specifies block characters in eights going from \u2581 (lower one eight block) to \u2588 (full block) // https://en.wikipedia.org/wiki/Block_Elements // LOWER ONE EIGHTH BLOCK … FULL BLOCK static const char *const BLOCK_CHARS8[8] = {"\u2581", "\u2582", "\u2583", "\u2584", "\u2585", "\u2586", "\u2587", "\u2588"}; // In some terminals / with some fonts not all UTF8 block characters are supported (e.g. Putty). Use only half and full block for those static const char *const BLOCK_CHARS2[2] = {".", ":"}; #else // Fall back to explicit UTF-8 encodings of the same characters #define VERTICAL_LINE "\xE2\x94\x82" static const char *const BLOCK_CHARS8[8] = { "\xE2\x96\x81", "\xE2\x96\x82", "\xE2\x96\x83", "\xE2\x96\x84", "\xE2\x96\x85", "\xE2\x96\x86", "\xE2\x96\x87", "\xE2\x96\x88" }; static const char *const BLOCK_CHARS2[2] = {".", ":"}; #endif // in bam_plcmd.c int read_file_list(const char *file_list, int *n, char **argv[]); static int usage(void) { fprintf(stdout, "Usage: samtools coverage [options] in1.bam [in2.bam [...]]\n\n" "Input options:\n" " -b, --bam-list FILE list of input BAM filenames, one per line\n" " -l, --min-read-len INT ignore reads shorter than INT bp [0]\n" " -q, --min-MQ INT mapping quality threshold [0]\n" " -Q, --min-BQ INT base quality threshold [0]\n" " --rf required flags: skip reads with mask bits unset []\n" " --ff filter flags: skip reads with mask bits set \n" " [UNMAP,SECONDARY,QCFAIL,DUP]\n" " -d, --depth INT maximum allowed coverage depth [1000000].\n" " If 0, depth is set to the maximum integer value,\n" " effectively removing any depth limit.\n" "Output options:\n" " -m, --histogram show histogram instead of tabular output\n" " -D, --plot-depth plot depth instead of tabular output\n" " -A, --ascii show only ASCII characters in histogram\n" " -o, --output FILE write output to FILE [stdout]\n" " -H, --no-header don't print a header in tabular mode\n" " -w, --n-bins INT number of bins in histogram [terminal width - 40]\n" " -r, --region REG show specified region. Format: chr:start-end. \n" " -h, --help help (this page)\n"); fprintf(stdout, "\nGeneric options:\n"); sam_global_opt_help(stdout, "-.--.--."); fprintf(stdout, "\nSee manpage for additional details.\n" " rname Reference name / chromosome\n" " startpos Start position\n" " endpos End position (or sequence length)\n" " numreads Number reads aligned to the region (after filtering)\n" " covbases Number of covered bases with depth >= 1\n" " coverage Percentage of covered bases [0..100]\n" " meandepth Mean depth of coverage\n" " meanbaseq Mean baseQ in covered region\n" " meanmapq Mean mapQ of selected reads\n" ); return EXIT_SUCCESS; } static char* center_text(char *text, char *buf, int width) { int len = strlen(text); assert(len <= width); int padding = (width - len) / 2; int padding_ex = (width - len) % 2; if (padding >= 1) sprintf(buf, " %*s%*s", len+padding, text, padding-1+padding_ex, " "); else sprintf(buf, "%s", text); return buf; } static char* readable_bps(double base_pairs, char *buf) { const char* units[] = {"", "K", "M", "G", "T"}; int i = 0; while (base_pairs >= 1000 && i < (sizeof(units)/sizeof(units[0]) - 1)) { base_pairs /= 1000; i++; } sprintf(buf, "%.*f%s", i, base_pairs, units[i]); return buf; } // read one alignment from one BAM file static int read_bam(void *data, bam1_t *b) { bam_aux_t *aux = (bam_aux_t*)data; // data in fact is a pointer to an auxiliary structure int nref = sam_hdr_nref(aux->hdr); int ret; while (1) { if((ret = aux->iter? sam_itr_next(aux->fp, aux->iter, b) : sam_read1(aux->fp, aux->hdr, b)) < 0) break; if (b->core.tid >= 0 && b->core.tid < nref) aux->stats[b->core.tid].n_reads++; if ( aux->fail_flags && (b->core.flag & aux->fail_flags) ) continue; if ( aux->required_flags && !(b->core.flag & aux->required_flags) ) continue; if ( b->core.qual < aux->min_mapQ ) continue; if ( aux->min_len && bam_cigar2qlen(b->core.n_cigar, bam_get_cigar(b)) < aux->min_len ) continue; if (b->core.tid >= 0 && b->core.tid < nref) { aux->stats[b->core.tid].n_selected_reads++; aux->stats[b->core.tid].summed_mapQ += b->core.qual; } break; } return ret; } void print_tabular_line(FILE *file_out, const sam_hdr_t *h, const stats_aux_t *stats, int tid) { fputs(sam_hdr_tid2name(h, tid), file_out); double region_len = (double) stats[tid].end - stats[tid].beg; fprintf(file_out, "\t%"PRId64"\t%"PRId64"\t%u\t%llu\t%g\t%g\t%.3g\t%.3g\n", stats[tid].beg+1, stats[tid].end, stats[tid].n_selected_reads, stats[tid].n_covered_bases, 100.0 * stats[tid].n_covered_bases / region_len, stats[tid].summed_coverage / region_len, stats[tid].quality_bases > 0? stats[tid].summed_baseQ/(double) stats[tid].quality_bases : 0, stats[tid].n_selected_reads > 0? stats[tid].summed_mapQ/(double) stats[tid].n_selected_reads : 0 ); } void print_hist(FILE *file_out, const sam_hdr_t *h, const stats_aux_t *stats, int tid, const uint32_t *hist, const int hist_size, const bool full_utf, const bool plot_coverage) { int i, col; bool show_percentiles = false; const int n_rows = 10; const char * const * BLOCK_CHARS = full_utf? BLOCK_CHARS8 : BLOCK_CHARS2; const int blockchar_len = full_utf? 8 : 2; double region_len = stats[tid].end - stats[tid].beg; // Calculate histogram that contains percent covered double hist_data[hist_size]; double max_val = 0.0; for (i = 0; i < hist_size; ++i) { hist_data[i] = (plot_coverage?1:100) * hist[i] / (double) stats[tid].bin_width; if (hist_data[i] > max_val) max_val = hist_data[i]; } char buf[30]; fprintf(file_out, "%s (%sbp)\n", sam_hdr_tid2name(h, tid), readable_bps(sam_hdr_tid2len(h, tid), buf)); double row_bin_size = max_val / (double) n_rows; for (i = n_rows-1; i >= 0; --i) { double current_bin = row_bin_size * i; if (plot_coverage) { fprintf(file_out, ">%8.1f ",i*row_bin_size); } else if (show_percentiles) { fprintf(file_out, ">%3i%% ", i*10); } else { fprintf(file_out, ">%7.2f%% ", current_bin); } fprintf(file_out, full_utf ? VERTICAL_LINE : "|"); for (col = 0; col < hist_size; ++col) { // get the difference in eights, or halfs when full UTF8 is not supported int cur_val_diff = round(blockchar_len * (hist_data[col] - current_bin) / row_bin_size) - 1; if (cur_val_diff < 0) { fputc(' ', file_out); } else { if (cur_val_diff >= blockchar_len) cur_val_diff = blockchar_len - 1; fprintf(file_out, "%s", BLOCK_CHARS[cur_val_diff]); } } fprintf(file_out, full_utf ? VERTICAL_LINE : "|"); fputc(' ', file_out); switch (i) { case 9: fprintf(file_out, "Number of reads: %u", stats[tid].n_selected_reads); break; case 8: if (stats[tid].n_reads - stats[tid].n_selected_reads > 0) fprintf(file_out, " (%i filtered)", stats[tid].n_reads - stats[tid].n_selected_reads); break; case 7: fprintf(file_out, "Covered bases: %sbp", readable_bps(stats[tid].n_covered_bases, buf)); break; case 6: fprintf(file_out, "Percent covered: %.4g%%", 100.0 * stats[tid].n_covered_bases / region_len); break; case 5: fprintf(file_out, "Mean coverage: %.3gx", stats[tid].summed_coverage / region_len); break; case 4: fprintf(file_out, "Mean baseQ: %.3g", stats[tid].quality_bases > 0? stats[tid].summed_baseQ/(double) stats[tid].quality_bases : 0); break; case 3: fprintf(file_out, "Mean mapQ: %.3g", stats[tid].summed_mapQ/(double) stats[tid].n_selected_reads); break; case 1: fprintf(file_out, "Histo bin width: %sbp", readable_bps(stats[tid].bin_width, buf)); break; case 0: if (plot_coverage) { fprintf(file_out, "Histo max cov: %.5g", max_val); } else { fprintf(file_out, "Histo max bin: %.5g%%", max_val); } break; }; fputc('\n', file_out); } // print x axis. Could be made pretty for widths that are not divisible // by 10 by variable spacing of the labels, instead of placing a label every 10 characters char buf2[50]; fprintf(file_out, " %s", center_text(readable_bps(stats[tid].beg + 1, buf), buf2, 10)); int rest; for (rest = 10; rest < 10*(hist_size/10); rest += 10) { fprintf(file_out, "%s", center_text(readable_bps(stats[tid].beg + stats[tid].bin_width*rest, buf), buf2, 10)); } int last_padding = hist_size%10; fprintf(file_out, "%*s%s", last_padding, " ", center_text(readable_bps(stats[tid].end, buf), buf2, 10)); fprintf(file_out, "\n"); } int main_coverage(int argc, char *argv[]) { int status = EXIT_SUCCESS; int ret, tid = -1, old_tid = -1, pos, i, j; int max_depth = 1000000; int opt_min_baseQ = 0; int opt_min_mapQ = 0; int opt_min_len = 0; int opt_n_bins = 50; bool opt_full_width = true; char *opt_output_file = NULL; bam_aux_t **data = NULL; bam_mplp_t mplp = NULL; const bam_pileup1_t **plp = NULL; uint32_t *hist = NULL; stats_aux_t *stats = NULL; char *opt_reg = 0; // specified region char *opt_file_list = NULL; int n_bam_files = 0; char **fn = NULL; int fail_flags = (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP); // Default fail flags int required_flags = 0; int print_value_warning = 0; int *n_plp = NULL; sam_hdr_t *h = NULL; // BAM header of the 1st input bool opt_print_header = true; bool opt_print_tabular = true; bool opt_print_histogram = false; bool opt_plot_coverage = false; bool opt_full_utf = true; FILE *file_out = stdout; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '-'), {"rf", required_argument, NULL, 1}, // require flag {"ff", required_argument, NULL, 2}, // filter flag {"incl-flags", required_argument, NULL, 1}, // require flag {"excl-flags", required_argument, NULL, 2}, // filter flag {"bam-list", required_argument, NULL, 'b'}, {"min-read-len", required_argument, NULL, 'l'}, {"min-MQ", required_argument, NULL, 'q'}, {"min-mq", required_argument, NULL, 'q'}, {"min-BQ", required_argument, NULL, 'Q'}, {"min-bq", required_argument, NULL, 'Q'}, {"histogram", no_argument, NULL, 'm'}, {"ascii", no_argument, NULL, 'A'}, {"plot-depth", no_argument, NULL, 'D'}, {"output", required_argument, NULL, 'o'}, {"no-header", no_argument, NULL, 'H'}, {"n-bins", required_argument, NULL, 'w'}, {"region", required_argument, NULL, 'r'}, {"help", no_argument, NULL, 'h'}, {"depth", required_argument, NULL, 'd'}, { NULL, 0, NULL, 0 } }; // parse the command line int c; opterr = 0; while ((c = getopt_long(argc, argv, "Ao:l:q:Q:hHw:r:b:md:D", lopts, NULL)) != -1) { switch (c) { case 1: if ((required_flags = bam_str2flag(optarg)) < 0) { fprintf(stderr,"Could not parse --rf %s\n", optarg); return EXIT_FAILURE; }; break; case 2: if ((fail_flags = bam_str2flag(optarg)) < 0) { fprintf(stderr,"Could not parse --ff %s\n", optarg); return EXIT_FAILURE; }; break; case 'o': opt_output_file = optarg; opt_full_width = false; break; case 'l': opt_min_len = atoi(optarg); break; case 'q': opt_min_mapQ = atoi(optarg); break; case 'Q': opt_min_baseQ = atoi(optarg); break; case 'd': max_depth = atoi(optarg); break; // maximum coverage depth case 'w': opt_n_bins = atoi(optarg); opt_full_width = false; opt_print_histogram = true; opt_print_tabular = false; break; case 'r': opt_reg = optarg; break; // parsing a region requires a BAM header (strdup unnecessary) case 'b': opt_file_list = optarg; break; case 'm': opt_print_histogram = true; opt_print_tabular = false; break; case 'A': opt_full_utf = false; opt_print_histogram = true; opt_print_tabular = false; break; case 'D': opt_print_histogram = true; opt_print_tabular = false; opt_plot_coverage = true; break; case 'H': opt_print_header = false; break; case 'h': return usage(); default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': if (optopt != '?') { // '-?' appeared on command line if (optopt) { // Bad short option print_error("coverage", "invalid option -- '%c'", optopt); } else { // Bad long option // Do our best. There is no good solution to finding // out what the bad option was. // See, e.g. https://stackoverflow.com/questions/2723888/where-does-getopt-long-store-an-unrecognized-option if (optind > 0 && strncmp(argv[optind - 1], "--", 2) == 0) { print_error("coverage", "unrecognised option '%s'", argv[optind - 1]); } } } return usage(); } } if (optind == argc && !opt_file_list) return usage(); // output file provided by user if (opt_output_file != NULL && strcmp(opt_output_file,"-")!=0) { file_out = fopen( opt_output_file, "w" ); if (file_out == NULL) { print_error_errno("coverage", "Cannot open \"%s\" for writing.", opt_output_file); return EXIT_FAILURE; } } if (opt_n_bins <= 0 || opt_full_width) { // get number of columns of terminal const char* env_columns = getenv("COLUMNS"); int columns = 0; if (env_columns == NULL) { #ifdef _WIN32 CONSOLE_SCREEN_BUFFER_INFO csbi; if (GetConsoleScreenBufferInfo(GetStdHandle(STD_OUTPUT_HANDLE), &csbi)) { columns = csbi.srWindow.Right - csbi.srWindow.Left + 1; } #elif defined TIOCGWINSZ struct winsize w; if (ioctl(2, TIOCGWINSZ, &w) == 0) columns = w.ws_col; #endif } else { columns = atoi(env_columns); // atoi(NULL) returns 0 } if (columns > 60) { opt_n_bins = columns - 40; } else { opt_n_bins = 40; } } // setvbuf(file_out, NULL, _IONBF, 0); //turn off buffering // Open all BAM files if (opt_file_list) { // Read file names from opt_file_list into argv, and record the number of files in n_bam_files if (read_file_list(opt_file_list, &n_bam_files, &fn)) { print_error_errno("coverage", "Cannot open file list \"%s\".", opt_file_list); return EXIT_FAILURE; } argv = fn; optind = 0; } else { n_bam_files = argc - optind; // the number of BAMs on the command line } data = (bam_aux_t **)calloc(n_bam_files, sizeof(bam_aux_t*)); // data[i] for the i-th BAM file if (!data) { print_error_errno("coverage", "Failed to allocate memory"); status = EXIT_FAILURE; goto coverage_end; } for (i = 0; i < n_bam_files; ++i) { int rf; data[i] = (bam_aux_t *) calloc(1, sizeof(bam_aux_t)); if (!data[i]) { print_error_errno("coverage", "Failed to allocate memory"); status = EXIT_FAILURE; goto coverage_end; } data[i]->fp = sam_open_format(argv[optind+i], "r", &ga.in); // open BAM if (data[i]->fp == NULL) { print_error_errno("coverage", "Could not open \"%s\"", argv[optind+i]); status = EXIT_FAILURE; goto coverage_end; } rf = SAM_FLAG | SAM_RNAME | SAM_POS | SAM_MAPQ | SAM_CIGAR | SAM_SEQ; if (opt_min_baseQ) rf |= SAM_QUAL; // Set CRAM options on file handle - returns 0 on success if (hts_set_opt(data[i]->fp, CRAM_OPT_REQUIRED_FIELDS, rf)) { print_error("coverage", "Failed to set CRAM_OPT_REQUIRED_FIELDS value"); status = EXIT_FAILURE; goto coverage_end; } if (hts_set_opt(data[i]->fp, CRAM_OPT_DECODE_MD, 0)) { print_error("coverage", "Failed to set CRAM_OPT_DECODE_MD value"); status = EXIT_FAILURE; goto coverage_end; } data[i]->min_mapQ = opt_min_mapQ; // set the mapQ filter data[i]->min_len = opt_min_len; // set the qlen filter data[i]->hdr = sam_hdr_read(data[i]->fp); // read the BAM header data[i]->fail_flags = fail_flags; data[i]->required_flags = required_flags; if (data[i]->hdr == NULL) { print_error_errno("coverage", "Could not read header for \"%s\"", argv[optind+i]); status = EXIT_FAILURE; goto coverage_end; } // Lookup region if specified if (opt_reg) { // if a region is specified hts_idx_t *idx = sam_index_load(data[i]->fp, argv[optind+i]); // load the index if (idx == NULL) { print_error_errno("coverage", "Failed to load index for \"%s\"", argv[optind+i]); status = EXIT_FAILURE; goto coverage_end; } data[i]->iter = sam_itr_querys(idx, data[i]->hdr, opt_reg); // set the iterator hts_idx_destroy(idx); // the index is not needed any more; free the memory if (data[i]->iter == NULL) { print_error("coverage", "Failed to parse region \"%s\". Check the region format or region name presence in the file \"%s\"", opt_reg, argv[optind+i]); status = EXIT_FAILURE; goto coverage_end; } } } if (opt_print_tabular && opt_print_header) fputs("#rname\tstartpos\tendpos\tnumreads\tcovbases\tcoverage\tmeandepth\tmeanbaseq\tmeanmapq\n", file_out); h = data[0]->hdr; // easy access to the header of the 1st BAM int n_targets = sam_hdr_nref(h); stats = calloc(n_targets, sizeof(stats_aux_t)); if (!stats) { print_error_errno("coverage", "Failed to allocate memory"); status = EXIT_FAILURE; goto coverage_end; } int64_t n_bins = opt_n_bins; if (opt_reg) { stats_aux_t *s = stats + data[0]->iter->tid; s->beg = data[0]->iter->beg; // and to the parsed region coordinates s->end = data[0]->iter->end; if (s->end == HTS_POS_MAX) { s->end = sam_hdr_tid2len(h, data[0]->iter->tid); } if (opt_n_bins > s->end - s->beg) { n_bins = s->end - s->beg; } s->bin_width = (s->end-s->beg) / (n_bins > 0 ? n_bins : 1); } for (i=0; istats = stats; int64_t current_bin = 0; // the core multi-pileup loop mplp = bam_mplp_init(n_bam_files, read_bam, (void**)data); // initialization if (max_depth > 0) bam_mplp_set_maxcnt(mplp, max_depth); // set maximum coverage depth else if (!max_depth) bam_mplp_set_maxcnt(mplp, INT_MAX); // Extra info for histogram and coverage counting hist = (uint32_t*) calloc(opt_n_bins, sizeof(uint32_t)); n_plp = (int*) calloc(n_bam_files, sizeof(int*)); // n_plp[i] is the number of covering reads from the i-th BAM plp = (const bam_pileup1_t**) calloc(n_bam_files, sizeof(bam_pileup1_t*)); // plp[i] points to the array of covering reads (internal in mplp) if (!hist || !n_plp || !plp) { print_error_errno("coverage", "Failed to allocate memory"); status = EXIT_FAILURE; goto coverage_end; } while ((ret=bam_mplp_auto(mplp, &tid, &pos, n_plp, plp)) > 0) { // come to the next covered position if (tid != old_tid) { // Next target sequence if (old_tid >= 0) { if (opt_print_histogram) { print_hist(file_out, h, stats, old_tid, hist, n_bins, opt_full_utf, opt_plot_coverage); fputc('\n', file_out); } else if (opt_print_tabular) { print_tabular_line(file_out, h, stats, old_tid); } if (opt_print_histogram) memset(hist, 0, n_bins*sizeof(uint32_t)); } stats[tid].covered = true; if (!opt_reg) stats[tid].end = sam_hdr_tid2len(h, tid); if (opt_print_histogram) { n_bins = opt_n_bins > stats[tid].end-stats[tid].beg? stats[tid].end-stats[tid].beg : opt_n_bins; stats[tid].bin_width = (stats[tid].end-stats[tid].beg) / n_bins; } old_tid = tid; } if (pos < stats[tid].beg || pos >= stats[tid].end) continue; // out of range; skip if (tid >= n_targets) continue; // diff number of @SQ lines per file? if (opt_print_histogram) { current_bin = (pos - stats[tid].beg) / stats[tid].bin_width; } bool count_base = false; for (i = 0; i < n_bam_files; ++i) { // base level filters have to go here int depth_at_pos = n_plp[i]; for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; // DON'T modify plp[][] unless you really know if (p->is_del || p->is_refskip) { --depth_at_pos; // having dels or refskips at tid:pos } else if (p->qpos < p->b->core.l_qseq) { if (bam_get_qual(p->b)[p->qpos] < opt_min_baseQ) { --depth_at_pos; // low base quality } else { stats[tid].summed_baseQ += bam_get_qual(p->b)[p->qpos]; stats[tid].quality_bases++; } } else { print_value_warning = 1; // no quality at position } } if (depth_at_pos > 0) { count_base = true; stats[tid].summed_coverage += depth_at_pos; } if(current_bin < n_bins && opt_plot_coverage) { hist[current_bin] += depth_at_pos; } } if (count_base) { stats[tid].n_covered_bases++; if (opt_print_histogram && current_bin < n_bins && !opt_plot_coverage) ++(hist[current_bin]); // Histogram based on breadth of coverage } } if (tid == -1 && opt_reg && *opt_reg != '*') // Region specified but no data covering it. tid = data[0]->iter->tid; if (tid < n_targets && tid >=0) { if (opt_print_histogram) { print_hist(file_out, h, stats, tid, hist, n_bins, opt_full_utf, opt_plot_coverage); } else if (opt_print_tabular) { print_tabular_line(file_out, h, stats, tid); } } if (!opt_reg && opt_print_tabular) { for (i = 0; i < n_targets; ++i) { if (!stats[i].covered) { stats[i].end = sam_hdr_tid2len(h, i); print_tabular_line(file_out, h, stats, i); } } } if (print_value_warning) { print_error("coverage", "Warning: Missing quality values in alignments. Mean base quality calculated only on available values."); } if (ret < 0) status = EXIT_FAILURE; coverage_end: if (n_plp) free(n_plp); if (plp) free(plp); if (mplp) bam_mplp_destroy(mplp); if (hist) free(hist); if (stats) free(stats); // Close files and free data structures if (!(file_out == stdout || fclose(file_out) == 0)) { if (status == EXIT_SUCCESS) { print_error_errno("coverage", "error on closing \"%s\"", (opt_output_file && strcmp(opt_output_file, "-") != 0? opt_output_file : "stdout")); status = EXIT_FAILURE; } } if (data) { for (i = 0; i < n_bam_files && data[i]; ++i) { sam_hdr_destroy(data[i]->hdr); if (data[i]->fp) sam_close(data[i]->fp); hts_itr_destroy(data[i]->iter); free(data[i]); } free(data); } if (opt_file_list && fn) { for (i = 0; i < n_bam_files; ++i) free(fn[i]); free(fn); } sam_global_args_free(&ga); return status; } #ifdef _MAIN_BAMCOV int main(int argc, char *argv[]) { return main_coverage(argc, argv); } #endif pysam-0.23.0/samtools/coverage.c.pysam.c000066400000000000000000000710561475062545500201240ustar00rootroot00000000000000#include "samtools.pysam.h" /* coverage.c -- samtools coverage subcommand Copyright (C) 2018,2019 Florian Breitwieser Portions copyright (C) 2019-2021, 2023-2024 Genome Research Ltd. Author: Florian P Breitwieser Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* This program calculates coverage from multiple BAMs * simultaneously, to achieve random access and to use the BED interface. * To compile this program separately, you may: * * gcc -g -O2 -Wall -o bamcov -D_MAIN_BAMCOV coverage.c -lhts -lz */ // C headers #include #include #include #include #include // variadic functions #include // INT_MAX #include // round #include #include #include #include #ifdef _WIN32 #include #else #include #endif #include "htslib/sam.h" #include "htslib/hts.h" #include "samtools.h" #include "sam_opts.h" typedef struct { // auxiliary data structure to hold stats on coverage unsigned long long n_covered_bases; unsigned long long summed_coverage; unsigned long long summed_baseQ; unsigned long long summed_mapQ; unsigned long long quality_bases; unsigned int n_reads; unsigned int n_selected_reads; bool covered; hts_pos_t beg; hts_pos_t end; int64_t bin_width; } stats_aux_t; typedef struct { // auxiliary data structure to hold a BAM file samFile *fp; // file handle sam_hdr_t *hdr; // file header hts_itr_t *iter; // iterator to a region - NULL for us by default int min_mapQ; // mapQ filter int min_len; // length filter int fail_flags; int required_flags; stats_aux_t *stats; } bam_aux_t; #if __STDC_VERSION__ >= 199901L #define VERTICAL_LINE "\u2502" // BOX DRAWINGS LIGHT VERTICAL // UTF8 specifies block characters in eights going from \u2581 (lower one eight block) to \u2588 (full block) // https://en.wikipedia.org/wiki/Block_Elements // LOWER ONE EIGHTH BLOCK … FULL BLOCK static const char *const BLOCK_CHARS8[8] = {"\u2581", "\u2582", "\u2583", "\u2584", "\u2585", "\u2586", "\u2587", "\u2588"}; // In some terminals / with some fonts not all UTF8 block characters are supported (e.g. Putty). Use only half and full block for those static const char *const BLOCK_CHARS2[2] = {".", ":"}; #else // Fall back to explicit UTF-8 encodings of the same characters #define VERTICAL_LINE "\xE2\x94\x82" static const char *const BLOCK_CHARS8[8] = { "\xE2\x96\x81", "\xE2\x96\x82", "\xE2\x96\x83", "\xE2\x96\x84", "\xE2\x96\x85", "\xE2\x96\x86", "\xE2\x96\x87", "\xE2\x96\x88" }; static const char *const BLOCK_CHARS2[2] = {".", ":"}; #endif // in bam_plcmd.c int read_file_list(const char *file_list, int *n, char **argv[]); static int usage(void) { fprintf(samtools_stdout, "Usage: samtools coverage [options] in1.bam [in2.bam [...]]\n\n" "Input options:\n" " -b, --bam-list FILE list of input BAM filenames, one per line\n" " -l, --min-read-len INT ignore reads shorter than INT bp [0]\n" " -q, --min-MQ INT mapping quality threshold [0]\n" " -Q, --min-BQ INT base quality threshold [0]\n" " --rf required flags: skip reads with mask bits unset []\n" " --ff filter flags: skip reads with mask bits set \n" " [UNMAP,SECONDARY,QCFAIL,DUP]\n" " -d, --depth INT maximum allowed coverage depth [1000000].\n" " If 0, depth is set to the maximum integer value,\n" " effectively removing any depth limit.\n" "Output options:\n" " -m, --histogram show histogram instead of tabular output\n" " -D, --plot-depth plot depth instead of tabular output\n" " -A, --ascii show only ASCII characters in histogram\n" " -o, --output FILE write output to FILE [samtools_stdout]\n" " -H, --no-header don't print a header in tabular mode\n" " -w, --n-bins INT number of bins in histogram [terminal width - 40]\n" " -r, --region REG show specified region. Format: chr:start-end. \n" " -h, --help help (this page)\n"); fprintf(samtools_stdout, "\nGeneric options:\n"); sam_global_opt_help(samtools_stdout, "-.--.--."); fprintf(samtools_stdout, "\nSee manpage for additional details.\n" " rname Reference name / chromosome\n" " startpos Start position\n" " endpos End position (or sequence length)\n" " numreads Number reads aligned to the region (after filtering)\n" " covbases Number of covered bases with depth >= 1\n" " coverage Percentage of covered bases [0..100]\n" " meandepth Mean depth of coverage\n" " meanbaseq Mean baseQ in covered region\n" " meanmapq Mean mapQ of selected reads\n" ); return EXIT_SUCCESS; } static char* center_text(char *text, char *buf, int width) { int len = strlen(text); assert(len <= width); int padding = (width - len) / 2; int padding_ex = (width - len) % 2; if (padding >= 1) sprintf(buf, " %*s%*s", len+padding, text, padding-1+padding_ex, " "); else sprintf(buf, "%s", text); return buf; } static char* readable_bps(double base_pairs, char *buf) { const char* units[] = {"", "K", "M", "G", "T"}; int i = 0; while (base_pairs >= 1000 && i < (sizeof(units)/sizeof(units[0]) - 1)) { base_pairs /= 1000; i++; } sprintf(buf, "%.*f%s", i, base_pairs, units[i]); return buf; } // read one alignment from one BAM file static int read_bam(void *data, bam1_t *b) { bam_aux_t *aux = (bam_aux_t*)data; // data in fact is a pointer to an auxiliary structure int nref = sam_hdr_nref(aux->hdr); int ret; while (1) { if((ret = aux->iter? sam_itr_next(aux->fp, aux->iter, b) : sam_read1(aux->fp, aux->hdr, b)) < 0) break; if (b->core.tid >= 0 && b->core.tid < nref) aux->stats[b->core.tid].n_reads++; if ( aux->fail_flags && (b->core.flag & aux->fail_flags) ) continue; if ( aux->required_flags && !(b->core.flag & aux->required_flags) ) continue; if ( b->core.qual < aux->min_mapQ ) continue; if ( aux->min_len && bam_cigar2qlen(b->core.n_cigar, bam_get_cigar(b)) < aux->min_len ) continue; if (b->core.tid >= 0 && b->core.tid < nref) { aux->stats[b->core.tid].n_selected_reads++; aux->stats[b->core.tid].summed_mapQ += b->core.qual; } break; } return ret; } void print_tabular_line(FILE *file_out, const sam_hdr_t *h, const stats_aux_t *stats, int tid) { fputs(sam_hdr_tid2name(h, tid), file_out); double region_len = (double) stats[tid].end - stats[tid].beg; fprintf(file_out, "\t%"PRId64"\t%"PRId64"\t%u\t%llu\t%g\t%g\t%.3g\t%.3g\n", stats[tid].beg+1, stats[tid].end, stats[tid].n_selected_reads, stats[tid].n_covered_bases, 100.0 * stats[tid].n_covered_bases / region_len, stats[tid].summed_coverage / region_len, stats[tid].quality_bases > 0? stats[tid].summed_baseQ/(double) stats[tid].quality_bases : 0, stats[tid].n_selected_reads > 0? stats[tid].summed_mapQ/(double) stats[tid].n_selected_reads : 0 ); } void print_hist(FILE *file_out, const sam_hdr_t *h, const stats_aux_t *stats, int tid, const uint32_t *hist, const int hist_size, const bool full_utf, const bool plot_coverage) { int i, col; bool show_percentiles = false; const int n_rows = 10; const char * const * BLOCK_CHARS = full_utf? BLOCK_CHARS8 : BLOCK_CHARS2; const int blockchar_len = full_utf? 8 : 2; double region_len = stats[tid].end - stats[tid].beg; // Calculate histogram that contains percent covered double hist_data[hist_size]; double max_val = 0.0; for (i = 0; i < hist_size; ++i) { hist_data[i] = (plot_coverage?1:100) * hist[i] / (double) stats[tid].bin_width; if (hist_data[i] > max_val) max_val = hist_data[i]; } char buf[30]; fprintf(file_out, "%s (%sbp)\n", sam_hdr_tid2name(h, tid), readable_bps(sam_hdr_tid2len(h, tid), buf)); double row_bin_size = max_val / (double) n_rows; for (i = n_rows-1; i >= 0; --i) { double current_bin = row_bin_size * i; if (plot_coverage) { fprintf(file_out, ">%8.1f ",i*row_bin_size); } else if (show_percentiles) { fprintf(file_out, ">%3i%% ", i*10); } else { fprintf(file_out, ">%7.2f%% ", current_bin); } fprintf(file_out, full_utf ? VERTICAL_LINE : "|"); for (col = 0; col < hist_size; ++col) { // get the difference in eights, or halfs when full UTF8 is not supported int cur_val_diff = round(blockchar_len * (hist_data[col] - current_bin) / row_bin_size) - 1; if (cur_val_diff < 0) { fputc(' ', file_out); } else { if (cur_val_diff >= blockchar_len) cur_val_diff = blockchar_len - 1; fprintf(file_out, "%s", BLOCK_CHARS[cur_val_diff]); } } fprintf(file_out, full_utf ? VERTICAL_LINE : "|"); fputc(' ', file_out); switch (i) { case 9: fprintf(file_out, "Number of reads: %u", stats[tid].n_selected_reads); break; case 8: if (stats[tid].n_reads - stats[tid].n_selected_reads > 0) fprintf(file_out, " (%i filtered)", stats[tid].n_reads - stats[tid].n_selected_reads); break; case 7: fprintf(file_out, "Covered bases: %sbp", readable_bps(stats[tid].n_covered_bases, buf)); break; case 6: fprintf(file_out, "Percent covered: %.4g%%", 100.0 * stats[tid].n_covered_bases / region_len); break; case 5: fprintf(file_out, "Mean coverage: %.3gx", stats[tid].summed_coverage / region_len); break; case 4: fprintf(file_out, "Mean baseQ: %.3g", stats[tid].quality_bases > 0? stats[tid].summed_baseQ/(double) stats[tid].quality_bases : 0); break; case 3: fprintf(file_out, "Mean mapQ: %.3g", stats[tid].summed_mapQ/(double) stats[tid].n_selected_reads); break; case 1: fprintf(file_out, "Histo bin width: %sbp", readable_bps(stats[tid].bin_width, buf)); break; case 0: if (plot_coverage) { fprintf(file_out, "Histo max cov: %.5g", max_val); } else { fprintf(file_out, "Histo max bin: %.5g%%", max_val); } break; }; fputc('\n', file_out); } // print x axis. Could be made pretty for widths that are not divisible // by 10 by variable spacing of the labels, instead of placing a label every 10 characters char buf2[50]; fprintf(file_out, " %s", center_text(readable_bps(stats[tid].beg + 1, buf), buf2, 10)); int rest; for (rest = 10; rest < 10*(hist_size/10); rest += 10) { fprintf(file_out, "%s", center_text(readable_bps(stats[tid].beg + stats[tid].bin_width*rest, buf), buf2, 10)); } int last_padding = hist_size%10; fprintf(file_out, "%*s%s", last_padding, " ", center_text(readable_bps(stats[tid].end, buf), buf2, 10)); fprintf(file_out, "\n"); } int main_coverage(int argc, char *argv[]) { int status = EXIT_SUCCESS; int ret, tid = -1, old_tid = -1, pos, i, j; int max_depth = 1000000; int opt_min_baseQ = 0; int opt_min_mapQ = 0; int opt_min_len = 0; int opt_n_bins = 50; bool opt_full_width = true; char *opt_output_file = NULL; bam_aux_t **data = NULL; bam_mplp_t mplp = NULL; const bam_pileup1_t **plp = NULL; uint32_t *hist = NULL; stats_aux_t *stats = NULL; char *opt_reg = 0; // specified region char *opt_file_list = NULL; int n_bam_files = 0; char **fn = NULL; int fail_flags = (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP); // Default fail flags int required_flags = 0; int print_value_warning = 0; int *n_plp = NULL; sam_hdr_t *h = NULL; // BAM header of the 1st input bool opt_print_header = true; bool opt_print_tabular = true; bool opt_print_histogram = false; bool opt_plot_coverage = false; bool opt_full_utf = true; FILE *file_out = samtools_stdout; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '-'), {"rf", required_argument, NULL, 1}, // require flag {"ff", required_argument, NULL, 2}, // filter flag {"incl-flags", required_argument, NULL, 1}, // require flag {"excl-flags", required_argument, NULL, 2}, // filter flag {"bam-list", required_argument, NULL, 'b'}, {"min-read-len", required_argument, NULL, 'l'}, {"min-MQ", required_argument, NULL, 'q'}, {"min-mq", required_argument, NULL, 'q'}, {"min-BQ", required_argument, NULL, 'Q'}, {"min-bq", required_argument, NULL, 'Q'}, {"histogram", no_argument, NULL, 'm'}, {"ascii", no_argument, NULL, 'A'}, {"plot-depth", no_argument, NULL, 'D'}, {"output", required_argument, NULL, 'o'}, {"no-header", no_argument, NULL, 'H'}, {"n-bins", required_argument, NULL, 'w'}, {"region", required_argument, NULL, 'r'}, {"help", no_argument, NULL, 'h'}, {"depth", required_argument, NULL, 'd'}, { NULL, 0, NULL, 0 } }; // parse the command line int c; opterr = 0; while ((c = getopt_long(argc, argv, "Ao:l:q:Q:hHw:r:b:md:D", lopts, NULL)) != -1) { switch (c) { case 1: if ((required_flags = bam_str2flag(optarg)) < 0) { fprintf(samtools_stderr,"Could not parse --rf %s\n", optarg); return EXIT_FAILURE; }; break; case 2: if ((fail_flags = bam_str2flag(optarg)) < 0) { fprintf(samtools_stderr,"Could not parse --ff %s\n", optarg); return EXIT_FAILURE; }; break; case 'o': opt_output_file = optarg; opt_full_width = false; break; case 'l': opt_min_len = atoi(optarg); break; case 'q': opt_min_mapQ = atoi(optarg); break; case 'Q': opt_min_baseQ = atoi(optarg); break; case 'd': max_depth = atoi(optarg); break; // maximum coverage depth case 'w': opt_n_bins = atoi(optarg); opt_full_width = false; opt_print_histogram = true; opt_print_tabular = false; break; case 'r': opt_reg = optarg; break; // parsing a region requires a BAM header (strdup unnecessary) case 'b': opt_file_list = optarg; break; case 'm': opt_print_histogram = true; opt_print_tabular = false; break; case 'A': opt_full_utf = false; opt_print_histogram = true; opt_print_tabular = false; break; case 'D': opt_print_histogram = true; opt_print_tabular = false; opt_plot_coverage = true; break; case 'H': opt_print_header = false; break; case 'h': return usage(); default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': if (optopt != '?') { // '-?' appeared on command line if (optopt) { // Bad short option print_error("coverage", "invalid option -- '%c'", optopt); } else { // Bad long option // Do our best. There is no good solution to finding // out what the bad option was. // See, e.g. https://stackoverflow.com/questions/2723888/where-does-getopt-long-store-an-unrecognized-option if (optind > 0 && strncmp(argv[optind - 1], "--", 2) == 0) { print_error("coverage", "unrecognised option '%s'", argv[optind - 1]); } } } return usage(); } } if (optind == argc && !opt_file_list) return usage(); // output file provided by user if (opt_output_file != NULL && strcmp(opt_output_file,"-")!=0) { file_out = fopen( opt_output_file, "w" ); if (file_out == NULL) { print_error_errno("coverage", "Cannot open \"%s\" for writing.", opt_output_file); return EXIT_FAILURE; } } if (opt_n_bins <= 0 || opt_full_width) { // get number of columns of terminal const char* env_columns = getenv("COLUMNS"); int columns = 0; if (env_columns == NULL) { #ifdef _WIN32 CONSOLE_SCREEN_BUFFER_INFO csbi; if (GetConsoleScreenBufferInfo(GetStdHandle(STD_OUTPUT_HANDLE), &csbi)) { columns = csbi.srWindow.Right - csbi.srWindow.Left + 1; } #elif defined TIOCGWINSZ struct winsize w; if (ioctl(2, TIOCGWINSZ, &w) == 0) columns = w.ws_col; #endif } else { columns = atoi(env_columns); // atoi(NULL) returns 0 } if (columns > 60) { opt_n_bins = columns - 40; } else { opt_n_bins = 40; } } // setvbuf(file_out, NULL, _IONBF, 0); //turn off buffering // Open all BAM files if (opt_file_list) { // Read file names from opt_file_list into argv, and record the number of files in n_bam_files if (read_file_list(opt_file_list, &n_bam_files, &fn)) { print_error_errno("coverage", "Cannot open file list \"%s\".", opt_file_list); return EXIT_FAILURE; } argv = fn; optind = 0; } else { n_bam_files = argc - optind; // the number of BAMs on the command line } data = (bam_aux_t **)calloc(n_bam_files, sizeof(bam_aux_t*)); // data[i] for the i-th BAM file if (!data) { print_error_errno("coverage", "Failed to allocate memory"); status = EXIT_FAILURE; goto coverage_end; } for (i = 0; i < n_bam_files; ++i) { int rf; data[i] = (bam_aux_t *) calloc(1, sizeof(bam_aux_t)); if (!data[i]) { print_error_errno("coverage", "Failed to allocate memory"); status = EXIT_FAILURE; goto coverage_end; } data[i]->fp = sam_open_format(argv[optind+i], "r", &ga.in); // open BAM if (data[i]->fp == NULL) { print_error_errno("coverage", "Could not open \"%s\"", argv[optind+i]); status = EXIT_FAILURE; goto coverage_end; } rf = SAM_FLAG | SAM_RNAME | SAM_POS | SAM_MAPQ | SAM_CIGAR | SAM_SEQ; if (opt_min_baseQ) rf |= SAM_QUAL; // Set CRAM options on file handle - returns 0 on success if (hts_set_opt(data[i]->fp, CRAM_OPT_REQUIRED_FIELDS, rf)) { print_error("coverage", "Failed to set CRAM_OPT_REQUIRED_FIELDS value"); status = EXIT_FAILURE; goto coverage_end; } if (hts_set_opt(data[i]->fp, CRAM_OPT_DECODE_MD, 0)) { print_error("coverage", "Failed to set CRAM_OPT_DECODE_MD value"); status = EXIT_FAILURE; goto coverage_end; } data[i]->min_mapQ = opt_min_mapQ; // set the mapQ filter data[i]->min_len = opt_min_len; // set the qlen filter data[i]->hdr = sam_hdr_read(data[i]->fp); // read the BAM header data[i]->fail_flags = fail_flags; data[i]->required_flags = required_flags; if (data[i]->hdr == NULL) { print_error_errno("coverage", "Could not read header for \"%s\"", argv[optind+i]); status = EXIT_FAILURE; goto coverage_end; } // Lookup region if specified if (opt_reg) { // if a region is specified hts_idx_t *idx = sam_index_load(data[i]->fp, argv[optind+i]); // load the index if (idx == NULL) { print_error_errno("coverage", "Failed to load index for \"%s\"", argv[optind+i]); status = EXIT_FAILURE; goto coverage_end; } data[i]->iter = sam_itr_querys(idx, data[i]->hdr, opt_reg); // set the iterator hts_idx_destroy(idx); // the index is not needed any more; free the memory if (data[i]->iter == NULL) { print_error("coverage", "Failed to parse region \"%s\". Check the region format or region name presence in the file \"%s\"", opt_reg, argv[optind+i]); status = EXIT_FAILURE; goto coverage_end; } } } if (opt_print_tabular && opt_print_header) fputs("#rname\tstartpos\tendpos\tnumreads\tcovbases\tcoverage\tmeandepth\tmeanbaseq\tmeanmapq\n", file_out); h = data[0]->hdr; // easy access to the header of the 1st BAM int n_targets = sam_hdr_nref(h); stats = calloc(n_targets, sizeof(stats_aux_t)); if (!stats) { print_error_errno("coverage", "Failed to allocate memory"); status = EXIT_FAILURE; goto coverage_end; } int64_t n_bins = opt_n_bins; if (opt_reg) { stats_aux_t *s = stats + data[0]->iter->tid; s->beg = data[0]->iter->beg; // and to the parsed region coordinates s->end = data[0]->iter->end; if (s->end == HTS_POS_MAX) { s->end = sam_hdr_tid2len(h, data[0]->iter->tid); } if (opt_n_bins > s->end - s->beg) { n_bins = s->end - s->beg; } s->bin_width = (s->end-s->beg) / (n_bins > 0 ? n_bins : 1); } for (i=0; istats = stats; int64_t current_bin = 0; // the core multi-pileup loop mplp = bam_mplp_init(n_bam_files, read_bam, (void**)data); // initialization if (max_depth > 0) bam_mplp_set_maxcnt(mplp, max_depth); // set maximum coverage depth else if (!max_depth) bam_mplp_set_maxcnt(mplp, INT_MAX); // Extra info for histogram and coverage counting hist = (uint32_t*) calloc(opt_n_bins, sizeof(uint32_t)); n_plp = (int*) calloc(n_bam_files, sizeof(int*)); // n_plp[i] is the number of covering reads from the i-th BAM plp = (const bam_pileup1_t**) calloc(n_bam_files, sizeof(bam_pileup1_t*)); // plp[i] points to the array of covering reads (internal in mplp) if (!hist || !n_plp || !plp) { print_error_errno("coverage", "Failed to allocate memory"); status = EXIT_FAILURE; goto coverage_end; } while ((ret=bam_mplp_auto(mplp, &tid, &pos, n_plp, plp)) > 0) { // come to the next covered position if (tid != old_tid) { // Next target sequence if (old_tid >= 0) { if (opt_print_histogram) { print_hist(file_out, h, stats, old_tid, hist, n_bins, opt_full_utf, opt_plot_coverage); fputc('\n', file_out); } else if (opt_print_tabular) { print_tabular_line(file_out, h, stats, old_tid); } if (opt_print_histogram) memset(hist, 0, n_bins*sizeof(uint32_t)); } stats[tid].covered = true; if (!opt_reg) stats[tid].end = sam_hdr_tid2len(h, tid); if (opt_print_histogram) { n_bins = opt_n_bins > stats[tid].end-stats[tid].beg? stats[tid].end-stats[tid].beg : opt_n_bins; stats[tid].bin_width = (stats[tid].end-stats[tid].beg) / n_bins; } old_tid = tid; } if (pos < stats[tid].beg || pos >= stats[tid].end) continue; // out of range; skip if (tid >= n_targets) continue; // diff number of @SQ lines per file? if (opt_print_histogram) { current_bin = (pos - stats[tid].beg) / stats[tid].bin_width; } bool count_base = false; for (i = 0; i < n_bam_files; ++i) { // base level filters have to go here int depth_at_pos = n_plp[i]; for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; // DON'T modify plp[][] unless you really know if (p->is_del || p->is_refskip) { --depth_at_pos; // having dels or refskips at tid:pos } else if (p->qpos < p->b->core.l_qseq) { if (bam_get_qual(p->b)[p->qpos] < opt_min_baseQ) { --depth_at_pos; // low base quality } else { stats[tid].summed_baseQ += bam_get_qual(p->b)[p->qpos]; stats[tid].quality_bases++; } } else { print_value_warning = 1; // no quality at position } } if (depth_at_pos > 0) { count_base = true; stats[tid].summed_coverage += depth_at_pos; } if(current_bin < n_bins && opt_plot_coverage) { hist[current_bin] += depth_at_pos; } } if (count_base) { stats[tid].n_covered_bases++; if (opt_print_histogram && current_bin < n_bins && !opt_plot_coverage) ++(hist[current_bin]); // Histogram based on breadth of coverage } } if (tid == -1 && opt_reg && *opt_reg != '*') // Region specified but no data covering it. tid = data[0]->iter->tid; if (tid < n_targets && tid >=0) { if (opt_print_histogram) { print_hist(file_out, h, stats, tid, hist, n_bins, opt_full_utf, opt_plot_coverage); } else if (opt_print_tabular) { print_tabular_line(file_out, h, stats, tid); } } if (!opt_reg && opt_print_tabular) { for (i = 0; i < n_targets; ++i) { if (!stats[i].covered) { stats[i].end = sam_hdr_tid2len(h, i); print_tabular_line(file_out, h, stats, i); } } } if (print_value_warning) { print_error("coverage", "Warning: Missing quality values in alignments. Mean base quality calculated only on available values."); } if (ret < 0) status = EXIT_FAILURE; coverage_end: if (n_plp) free(n_plp); if (plp) free(plp); if (mplp) bam_mplp_destroy(mplp); if (hist) free(hist); if (stats) free(stats); // Close files and free data structures if (!(file_out == samtools_stdout || fclose(file_out) == 0)) { if (status == EXIT_SUCCESS) { print_error_errno("coverage", "error on closing \"%s\"", (opt_output_file && strcmp(opt_output_file, "-") != 0? opt_output_file : "samtools_stdout")); status = EXIT_FAILURE; } } if (data) { for (i = 0; i < n_bam_files && data[i]; ++i) { sam_hdr_destroy(data[i]->hdr); if (data[i]->fp) sam_close(data[i]->fp); hts_itr_destroy(data[i]->iter); free(data[i]); } free(data); } if (opt_file_list && fn) { for (i = 0; i < n_bam_files; ++i) free(fn[i]); free(fn); } sam_global_args_free(&ga); return status; } #ifdef _MAIN_BAMCOV int samtools_coverage_main(int argc, char *argv[]) { return main_coverage(argc, argv); } #endif pysam-0.23.0/samtools/cram_size.c000066400000000000000000000502231475062545500167250ustar00rootroot00000000000000/* cram_size.c -- produces summary of the size of each cram data-series Copyright (C) 2023 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ // TODO: add range query. Eg the ability to look at size for "*" only // (unmapped), or in a specific region such as a centromere. #include #include #include #include #include #include #include "htslib/bgzf.h" #include "htslib/sam.h" #include "htslib/cram.h" #include "htslib/kstring.h" #include "htslib/khash.h" #include "samtools.h" #include "sam_opts.h" #include "htslib/hfile.h" /*---------------------------------------------------------------------- * Compression method handling */ // A numeric version of the cram_method_details struct. // We expand the myriad of struct field combinations into a single // enumerated type so we can index and accumulate statistics for // purposes of reporting. // // These expanded numeric values have no definition within CRAM itself // and never occur within the file format. enum comp_expanded { //---- // Copies from htslib cram_block_method enum COMP_RAW = CRAM_COMP_RAW, COMP_GZIP = CRAM_COMP_GZIP, COMP_BZIP2 = CRAM_COMP_BZIP2, COMP_LZMA = CRAM_COMP_LZMA, COMP_RANS8 = CRAM_COMP_RANS4x8, COMP_RANS16 = CRAM_COMP_RANSNx16, COMP_ARITH = CRAM_COMP_ARITH, COMP_FQZ = CRAM_COMP_FQZ, COMP_TOK3 = CRAM_COMP_TOK3, //---- // Localised variants. // Gzip COMP_GZIP_1, COMP_GZIP_9, // Bzip2 COMP_BZIP2_1, COMP_BZIP2_2, COMP_BZIP2_3, COMP_BZIP2_4, COMP_BZIP2_5, COMP_BZIP2_6, COMP_BZIP2_7, COMP_BZIP2_8, COMP_BZIP2_9, // rans 4x8 COMP_RANS4x8_O0, COMP_RANS4x8_O1, // rans Nx16. Note order here is to enable selection via bit-fields // bit 0: O0/O1 // bit 1: RLE // bit 2: PACK // bit 3: 32x16 COMP_RANS4x16_O0, COMP_RANS4x16_O1, COMP_RANS4x16_O0R, // +RLE COMP_RANS4x16_O1R, COMP_RANS4x16_O0P, // +PACK COMP_RANS4x16_O1P, COMP_RANS4x16_O0PR, // +PACK+RLE COMP_RANS4x16_O1PR, COMP_RANS32x16_O0, // SIMD variants COMP_RANS32x16_O1, COMP_RANS32x16_O0R, // +RLE COMP_RANS32x16_O1R, COMP_RANS32x16_O0P, // +PACK COMP_RANS32x16_O1P, COMP_RANS32x16_O0PR, // +PACK+RLE COMP_RANS32x16_O1PR, COMP_RANSNx16_STRIPE, COMP_RANSNx16_CAT, // Arith COMP_ARITH_O0, COMP_ARITH_O1, COMP_ARITH_O0R, // +RLE COMP_ARITH_O1R, COMP_ARITH_O0P, // +PACK COMP_ARITH_O1P, COMP_ARITH_O0PR, // +PACK+RLE COMP_ARITH_O1PR, COMP_ARITH_STRIPE, COMP_ARITH_CAT, // no entropy encoder COMP_ARITH_EXT, // external entropy encode // Nake tokeniser COMP_TOK3_RANS, COMP_TOK3_ARITH, // To mark maximum size COMP_MAX, }; static enum comp_expanded comp_method2expanded(cram_method_details *cm) { switch (cm->method) { case CRAM_COMP_GZIP: switch (cm->level) { case 1: return COMP_GZIP_1; case 9: return COMP_GZIP_9; default: return COMP_GZIP; } break; case CRAM_COMP_BZIP2: if (cm->level >= 1 && cm->level <= 9) return COMP_BZIP2_1 + cm->level-1; else return COMP_BZIP2; break; case CRAM_COMP_RANS4x8: return cm->order ? COMP_RANS4x8_O1 : COMP_RANS4x8_O0; case CRAM_COMP_RANSNx16: { // 8 4x16, 8 32x16 and 2 stripe/cat if (cm->stripe) return COMP_RANSNx16_STRIPE; if (cm->cat) return COMP_RANSNx16_CAT; int c = COMP_RANS4x16_O0; c += 1*cm->order; c += 2*cm->rle; c += 4*cm->pack; c += 8*(cm->Nway==32); return c; } case CRAM_COMP_ARITH: { // 8 4x16, 8 32x16 and 2 stripe/cat if (cm->stripe) return COMP_ARITH_STRIPE; if (cm->cat) return COMP_ARITH_CAT; if (cm->ext) return COMP_ARITH_EXT; int c = COMP_ARITH_O0; c += 1*cm->order; c += 2*cm->rle; c += 4*cm->pack; return c; } case CRAM_COMP_TOK3: return cm->level < 10 ? COMP_TOK3_RANS : COMP_TOK3_ARITH; default: // Any unspecialised method return (enum comp_expanded)cm->method; } } // Short form of cram_block_method_int type static char comp_method2char[COMP_MAX] = ".gblr0afn" // standard CRAM methods "_G" // gzip "bbbbbbbbB" // bzip2 "rR" // rans4x8 "010101014545454582" // ransNx16 "aAaAaAaAaaa" // arith "nN"; // tok3 // Long form of cram_block_method_int type static char *comp_method2str[COMP_MAX] = { // Standard CRAM methods "raw", "gzip", "bzip2", "lzma", "r4x8", "rNx16", "arith", "fqzcomp", "tok3", // custom gzip "gzip-min", "gzip-max", // custom bzip2 "bzip2-1", "bzip2-2", "bzip2-3", "bzip2-4", "bzip2-5", "bzip2-6", "bzip2-7", "bzip2-8", "bzip2-9", // rANS 4x8 "r4x8-o0", "r4x8-o1", // rANS 4x16 "r4x16-o0", "r4x16-o1", "r4x16-o0R", "r4x16-o1R", "r4x16-o0P", "r4x16-o1P", "r4x16-o0PR", "r4x16-o1PR", "r32x16-o0", "r32x16-o1", "r32x16-o0R", "r32x16-o1R", "r32x16-o0P", "r32x16-o1P", "r32x16-o0PR","r32x16-o1PR", "rNx16-xo0", "rNx16-cat", // Arith "arith-o0", "arith-o1", "arith-o0R", "arith-o1R", "arith-o0P", "arith-o1P", "arith-o0PR", "arith-o1PR", "arith-stripe", "arith-cat", "arith-ext", // Name tokeniser "tok3-rans", "tok3-arith", }; /*---------------------------------------------------------------------- * Manipulation and sorting of Block Content-ID arrays and hashes */ typedef struct { int64_t csize[COMP_MAX]; int64_t usize[COMP_MAX]; } cusize_t; static int64_t total_csize(cusize_t *cu) { int i; int64_t tot = 0; for (i = 0; i < COMP_MAX; i++) tot += cu->csize[i]; return tot; } static int64_t total_usize(cusize_t *cu) { int i; int64_t tot = 0; for (i = 0; i < COMP_MAX; i++) tot += cu->usize[i]; return tot; } // cusize_t array and sorting by compressed size static cusize_t *sort_cusize_global; // avoids a messy extra data type static int sort_cusize_compar(const void *i1, const void *i2) { int64_t n = sort_cusize_global->csize[*(const int *)i2] - sort_cusize_global->csize[*(const int *)i1]; return n > 0 ? 1 : (n < 0 ? -1 : *(const int *)i1 - *(const int *)i2); } // Sort a cusize array by size of used method. // Returns cu->csize[comp] indices in descending size, as static mem static int *sort_cusize(cusize_t *cu) { static int idx[COMP_MAX]; int i; for (i = 0; i < COMP_MAX; i++) idx[i] = i; sort_cusize_global = cu; qsort(idx, COMP_MAX, sizeof(*idx), sort_cusize_compar); return idx; } // Hash table of cusize_t and sorting by key (content-id) KHASH_MAP_INIT_INT(cu, cusize_t) /* Sort by hash key. Global due to rubbish qsort API, but it's simple. */ static khash_t(cu) *global_cu_hash = NULL; static int cu_compar(const void *i1, const void *i2) { return kh_key(global_cu_hash, *(const int *)i1) - kh_key(global_cu_hash, *(const int *)i2); } /*---------------------------------------------------------------------- * Main cram_size reporting and aggregation */ static off_t report_size(FILE *outfp, int verbose, int ref_seq_blk, khash_t(cu) *cu_size, cram_cid2ds_t *cid2ds) { if (!cu_size || !cid2ds) return -1; khiter_t k; off_t tot_size = 0; fprintf(outfp, "# Content_ID Uncomp.size Comp.size Ratio Method%.*s Data_series\n", verbose ? 4 : 0, " "); int *sorted_blocks = malloc(kh_end(cu_size)*sizeof(int)); if (!sorted_blocks) return -1; int nblocks = 0; for (k = kh_begin(cu_size); k != kh_end(cu_size); k++) { if (!kh_exist(cu_size, k)) continue; sorted_blocks[nblocks++] = k; } global_cu_hash = cu_size; qsort(sorted_blocks, nblocks, sizeof(int), cu_compar); int i; for (i = 0; i < nblocks; i++) { k = sorted_blocks[i]; if (verbose) { // FULL output int *comp_idx = sort_cusize(&kh_value(cu_size, k)); int first_line = 1, c, j; for (c = 0; c < COMP_MAX; c++) { int comp = comp_idx[c]; if (!kh_value(cu_size, k).csize[comp] && c) break; if (!first_line) fprintf(outfp, "\n"); first_line = 0; if ((int)kh_key(cu_size, k) < 0) fprintf(outfp, "BLOCK %8s", "CORE"); else fprintf(outfp, "BLOCK %8d", kh_key(cu_size, k)); fprintf(outfp, " %12"PRId64" %12"PRId64, kh_value(cu_size, k).usize[comp], kh_value(cu_size, k).csize[comp]); double f = (100.0*(kh_value(cu_size, k).csize[comp]+.0001)) / (kh_value(cu_size, k).usize[comp]+.0001); if (f > 999) fprintf(outfp, " >999%% %-11s", comp_method2str[comp]); else fprintf(outfp, " %6.2f%% %-11s",f, comp_method2str[comp]); int n, *dsa = cram_cid2ds_query(cid2ds, kh_key(cu_size, k), &n); for (j = 0; j < n; j++) { int d = dsa[j]; if (d > 65535) fprintf(outfp, " %c%c%c", d>>16, (d>>8)&0xff, d&0xff); else fprintf(outfp, " %c%c", (d>>8)&0xff, d&0xff); } } } else { // aggregate by compression type. int64_t csize = total_csize(&kh_value(cu_size, k)); int64_t usize = total_usize(&kh_value(cu_size, k)); int *comp_idx = sort_cusize(&kh_value(cu_size, k)); char cstr[COMP_MAX+1] = {0}; int cidx = 0, c; for (c = 0; c < COMP_MAX; c++) { if (!kh_value(cu_size, k).csize[comp_idx[c]]) break; cstr[cidx++] = comp_method2char[comp_idx[c]]; } if (!*cstr) *cstr = '.'; if ((int)kh_key(cu_size, k) < 0) fprintf(outfp, "BLOCK %8s", "CORE"); else fprintf(outfp, "BLOCK %8d", kh_key(cu_size, k)); fprintf(outfp, " %12"PRId64" %12"PRId64, usize, csize); double f = 100*(csize+.0001)/(usize+.0001); if (f > 999) fprintf(outfp, " >999%% %-7s", cstr); else fprintf(outfp, " %6.2f%% %-7s", f, cstr); int n, j, *dsa = cram_cid2ds_query(cid2ds, kh_key(cu_size, k), &n); for (j = 0; j < n; j++) { int d = dsa[j]; if (d > 65535) fprintf(outfp, " %c%c%c", d>>16, (d>>8)&0xff, d&0xff); else fprintf(outfp, " %c%c", (d>>8)&0xff, d&0xff); } } if ((int)kh_key(cu_size, k) >= 0 && (int)kh_key(cu_size, k) == ref_seq_blk) { fprintf(outfp, " embedded_ref"); } fprintf(outfp, "\n"); tot_size += total_csize(&kh_value(cu_size, k)); } free(sorted_blocks); return tot_size; } /* Main processing loop */ static int cram_size(hFILE *hf_in, samFile *in, sam_hdr_t *h, FILE *outfp, int verbose, int encodings) { cram_fd *in_c; cram_container *c = NULL; cram_block *blk = NULL; cram_block_slice_hdr *shdr = NULL; khiter_t k; int ret; cram_cid2ds_t *cid2ds = NULL; khash_t(cu) *cu_size = kh_init(cu); int ref_seq_blk_used = -1; int64_t nseqs = 0, nbases = 0, ncont = 0, nslice = 0; if (!in->is_cram) { print_error("cram_size", "Input is not a CRAM file"); goto err; } in_c = in->fp.cram; // low level htslib abuse? while ((c = cram_read_container(in_c))) { if (cram_container_is_empty(in_c)) { cram_block *blk; // Container compression header if (!(blk = cram_read_block(in_c))) goto err; cram_free_block(blk); cram_free_container(c); c = NULL; blk = NULL; continue; } nseqs += cram_container_get_num_records(c); nbases += cram_container_get_num_bases(c); // Container compression header int32_t num_slices; if (!(blk = cram_read_block(in_c))) goto err; // Decode compression header... cram_block_compression_hdr *chdr; chdr = cram_decode_compression_header(in_c, blk); if (encodings) { kstring_t ks = KS_INITIALIZE; if (cram_describe_encodings(chdr, &ks) < 0) goto err; fprintf(outfp, "Container encodings\n%s\n", ks_str(&ks)); ks_free(&ks); } cid2ds = cram_update_cid2ds_map(chdr, cid2ds); cram_free_block(blk); blk = NULL; cram_free_compression_header(chdr); // Container num_blocks can be invalid, due to a bug. // Instead we iterate in slice context instead. (void)cram_container_get_landmarks(c, &num_slices); ncont++; nslice += num_slices; int i, j; for (i = 0; i < num_slices; i++) { // Slice header if (!(blk = cram_read_block(in_c))) goto err; if (!(shdr = cram_decode_slice_header(in_c, blk))) goto err; cram_free_block(blk); blk = NULL; int ref_seq_blk = cram_slice_hdr_get_embed_ref_id(shdr); int num_blocks = cram_slice_hdr_get_num_blocks(shdr); // Embedded reference. Check it's consistent (if used this is // an almost guaranteed certainty, so we take the easy route). if (ref_seq_blk >= 0) { if (ref_seq_blk_used == -1) ref_seq_blk_used = ref_seq_blk; else if (ref_seq_blk_used != ref_seq_blk) fprintf(stderr, "Embedded reference is not consistently using the same Content-Id.\n" "Reported figures for reference will be invalid.\n"); } // Slice data blocks for (j = 0; j < num_blocks; j++) { // read and discard, unless it's the ref-ID block if (!(blk = cram_read_block(in_c))) goto err; int32_t csize = cram_block_get_comp_size(blk); int32_t usize = cram_block_get_uncomp_size(blk); int cid = cram_block_get_content_id(blk); enum cram_block_method method = cram_block_get_method(blk); // Expand comp to the internal sub-formats, eg // rANS order-0/1, PACK+RLE, etc. cram_method_details *cm; cm = cram_expand_method(cram_block_get_data(blk), cram_block_get_comp_size(blk), method); if (!cm) goto err; enum comp_expanded comp = comp_method2expanded(cm); free(cm); k = kh_put(cu, cu_size, cid, &ret); if (ret < 0) goto err; if (ret == 0) { kh_value(cu_size, k).csize[comp] += csize; kh_value(cu_size, k).usize[comp] += usize; } else { memset(&kh_value(cu_size, k), 0, sizeof(cusize_t)); kh_value(cu_size, k).csize[comp] = csize; kh_value(cu_size, k).usize[comp] = usize; } cram_free_block(blk); blk = NULL; } cram_free_slice_header(shdr); shdr = NULL; } cram_free_container(c); c = NULL; } off_t tot_size = report_size(outfp, verbose, ref_seq_blk_used, cu_size, cid2ds); if (tot_size < 0) goto err; kh_destroy(cu, cu_size); cram_cid2ds_free(cid2ds); off_t end = htell(hf_in); fprintf(outfp, "\n"); fprintf(outfp, "Number of containers %18"PRId64"\n", ncont); fprintf(outfp, "Number of slices %18"PRId64"\n", nslice); fprintf(outfp, "Number of sequences %18"PRId64"\n", nseqs); fprintf(outfp, "Number of bases %18"PRId64"\n", nbases); fprintf(outfp, "Total file size %18"PRId64"\n", (int64_t) end); fprintf(outfp, "Format overhead size %18"PRId64"\n", (int64_t) (end - tot_size)); return 0; err: // Report anyway so we can get stats on partial files, but be // sure to error too. report_size(outfp, verbose, ref_seq_blk_used, cu_size, cid2ds); print_error("cram_size", "Failed in decoding CRAM file"); if (blk) cram_free_block(blk); if (shdr) cram_free_slice_header(shdr); if (c) cram_free_container(c); if (cid2ds) cram_cid2ds_free(cid2ds); return -1; } /* main() for cram_size */ int main_cram_size(int argc, char *argv[]) { int c, usage = 0, verbose = 0, encodings = 0; sam_hdr_t *h = 0; hFILE *hf_in = NULL; samFile *in = NULL; sam_global_args ga; FILE *outfp = stdout; static const struct option lopts[] = { {"output", required_argument, NULL, 'o'}, {"verbose", no_argument, NULL, 'v'}, {"encodings", no_argument, NULL, 'e'}, SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', '-', '-'), { NULL, 0, NULL, 0 } }; sam_global_args_init(&ga); while ((c = getopt_long(argc, argv, "vo:e", lopts, NULL)) >= 0) { switch (c) { case 'o': if (!(outfp = fopen(optarg, "w"))) { perror(optarg); goto err; } break; case 'v': verbose++; break; case 'e': encodings++; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage=1; break; } } if ((optind == argc && isatty(0)) || usage) { printf("Usage: samtools cram_size [-ve] [-o out.size] [in.cram]\n"); return 0; } char *fn = optind < argc ? argv[optind] : "-"; // We want access to in->fp.cram->fp, but this is an opaque struct so we // can't get that. However we opened with hopen and then reopen as // CRAM with hts_hopen, which will swallow the initial hFILE and take // owenership of it. Hence we now know in->fp.cram->fp. if (!(hf_in = hopen(fn, "r"))) { print_error_errno("cram_size", "failed to open file '%s'", fn); return 1; } if (!(in = hts_hopen(hf_in, fn, "r"))) { print_error_errno("cram_size", "failed to open file '%s'", fn); goto err; } if (!(h = sam_hdr_read(in))) goto err; int ret = cram_size(hf_in, in, h, outfp, verbose, encodings); sam_hdr_destroy(h); sam_close(in); if (outfp != stdout) fclose(outfp); return ret ? 1 : 0; err: if (in) sam_close(in); if (h) sam_hdr_destroy(h); return 1; } pysam-0.23.0/samtools/cram_size.c.pysam.c000066400000000000000000000503351475062545500203020ustar00rootroot00000000000000#include "samtools.pysam.h" /* cram_size.c -- produces summary of the size of each cram data-series Copyright (C) 2023 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ // TODO: add range query. Eg the ability to look at size for "*" only // (unmapped), or in a specific region such as a centromere. #include #include #include #include #include #include #include "htslib/bgzf.h" #include "htslib/sam.h" #include "htslib/cram.h" #include "htslib/kstring.h" #include "htslib/khash.h" #include "samtools.h" #include "sam_opts.h" #include "htslib/hfile.h" /*---------------------------------------------------------------------- * Compression method handling */ // A numeric version of the cram_method_details struct. // We expand the myriad of struct field combinations into a single // enumerated type so we can index and accumulate statistics for // purposes of reporting. // // These expanded numeric values have no definition within CRAM itself // and never occur within the file format. enum comp_expanded { //---- // Copies from htslib cram_block_method enum COMP_RAW = CRAM_COMP_RAW, COMP_GZIP = CRAM_COMP_GZIP, COMP_BZIP2 = CRAM_COMP_BZIP2, COMP_LZMA = CRAM_COMP_LZMA, COMP_RANS8 = CRAM_COMP_RANS4x8, COMP_RANS16 = CRAM_COMP_RANSNx16, COMP_ARITH = CRAM_COMP_ARITH, COMP_FQZ = CRAM_COMP_FQZ, COMP_TOK3 = CRAM_COMP_TOK3, //---- // Localised variants. // Gzip COMP_GZIP_1, COMP_GZIP_9, // Bzip2 COMP_BZIP2_1, COMP_BZIP2_2, COMP_BZIP2_3, COMP_BZIP2_4, COMP_BZIP2_5, COMP_BZIP2_6, COMP_BZIP2_7, COMP_BZIP2_8, COMP_BZIP2_9, // rans 4x8 COMP_RANS4x8_O0, COMP_RANS4x8_O1, // rans Nx16. Note order here is to enable selection via bit-fields // bit 0: O0/O1 // bit 1: RLE // bit 2: PACK // bit 3: 32x16 COMP_RANS4x16_O0, COMP_RANS4x16_O1, COMP_RANS4x16_O0R, // +RLE COMP_RANS4x16_O1R, COMP_RANS4x16_O0P, // +PACK COMP_RANS4x16_O1P, COMP_RANS4x16_O0PR, // +PACK+RLE COMP_RANS4x16_O1PR, COMP_RANS32x16_O0, // SIMD variants COMP_RANS32x16_O1, COMP_RANS32x16_O0R, // +RLE COMP_RANS32x16_O1R, COMP_RANS32x16_O0P, // +PACK COMP_RANS32x16_O1P, COMP_RANS32x16_O0PR, // +PACK+RLE COMP_RANS32x16_O1PR, COMP_RANSNx16_STRIPE, COMP_RANSNx16_CAT, // Arith COMP_ARITH_O0, COMP_ARITH_O1, COMP_ARITH_O0R, // +RLE COMP_ARITH_O1R, COMP_ARITH_O0P, // +PACK COMP_ARITH_O1P, COMP_ARITH_O0PR, // +PACK+RLE COMP_ARITH_O1PR, COMP_ARITH_STRIPE, COMP_ARITH_CAT, // no entropy encoder COMP_ARITH_EXT, // external entropy encode // Nake tokeniser COMP_TOK3_RANS, COMP_TOK3_ARITH, // To mark maximum size COMP_MAX, }; static enum comp_expanded comp_method2expanded(cram_method_details *cm) { switch (cm->method) { case CRAM_COMP_GZIP: switch (cm->level) { case 1: return COMP_GZIP_1; case 9: return COMP_GZIP_9; default: return COMP_GZIP; } break; case CRAM_COMP_BZIP2: if (cm->level >= 1 && cm->level <= 9) return COMP_BZIP2_1 + cm->level-1; else return COMP_BZIP2; break; case CRAM_COMP_RANS4x8: return cm->order ? COMP_RANS4x8_O1 : COMP_RANS4x8_O0; case CRAM_COMP_RANSNx16: { // 8 4x16, 8 32x16 and 2 stripe/cat if (cm->stripe) return COMP_RANSNx16_STRIPE; if (cm->cat) return COMP_RANSNx16_CAT; int c = COMP_RANS4x16_O0; c += 1*cm->order; c += 2*cm->rle; c += 4*cm->pack; c += 8*(cm->Nway==32); return c; } case CRAM_COMP_ARITH: { // 8 4x16, 8 32x16 and 2 stripe/cat if (cm->stripe) return COMP_ARITH_STRIPE; if (cm->cat) return COMP_ARITH_CAT; if (cm->ext) return COMP_ARITH_EXT; int c = COMP_ARITH_O0; c += 1*cm->order; c += 2*cm->rle; c += 4*cm->pack; return c; } case CRAM_COMP_TOK3: return cm->level < 10 ? COMP_TOK3_RANS : COMP_TOK3_ARITH; default: // Any unspecialised method return (enum comp_expanded)cm->method; } } // Short form of cram_block_method_int type static char comp_method2char[COMP_MAX] = ".gblr0afn" // standard CRAM methods "_G" // gzip "bbbbbbbbB" // bzip2 "rR" // rans4x8 "010101014545454582" // ransNx16 "aAaAaAaAaaa" // arith "nN"; // tok3 // Long form of cram_block_method_int type static char *comp_method2str[COMP_MAX] = { // Standard CRAM methods "raw", "gzip", "bzip2", "lzma", "r4x8", "rNx16", "arith", "fqzcomp", "tok3", // custom gzip "gzip-min", "gzip-max", // custom bzip2 "bzip2-1", "bzip2-2", "bzip2-3", "bzip2-4", "bzip2-5", "bzip2-6", "bzip2-7", "bzip2-8", "bzip2-9", // rANS 4x8 "r4x8-o0", "r4x8-o1", // rANS 4x16 "r4x16-o0", "r4x16-o1", "r4x16-o0R", "r4x16-o1R", "r4x16-o0P", "r4x16-o1P", "r4x16-o0PR", "r4x16-o1PR", "r32x16-o0", "r32x16-o1", "r32x16-o0R", "r32x16-o1R", "r32x16-o0P", "r32x16-o1P", "r32x16-o0PR","r32x16-o1PR", "rNx16-xo0", "rNx16-cat", // Arith "arith-o0", "arith-o1", "arith-o0R", "arith-o1R", "arith-o0P", "arith-o1P", "arith-o0PR", "arith-o1PR", "arith-stripe", "arith-cat", "arith-ext", // Name tokeniser "tok3-rans", "tok3-arith", }; /*---------------------------------------------------------------------- * Manipulation and sorting of Block Content-ID arrays and hashes */ typedef struct { int64_t csize[COMP_MAX]; int64_t usize[COMP_MAX]; } cusize_t; static int64_t total_csize(cusize_t *cu) { int i; int64_t tot = 0; for (i = 0; i < COMP_MAX; i++) tot += cu->csize[i]; return tot; } static int64_t total_usize(cusize_t *cu) { int i; int64_t tot = 0; for (i = 0; i < COMP_MAX; i++) tot += cu->usize[i]; return tot; } // cusize_t array and sorting by compressed size static cusize_t *sort_cusize_global; // avoids a messy extra data type static int sort_cusize_compar(const void *i1, const void *i2) { int64_t n = sort_cusize_global->csize[*(const int *)i2] - sort_cusize_global->csize[*(const int *)i1]; return n > 0 ? 1 : (n < 0 ? -1 : *(const int *)i1 - *(const int *)i2); } // Sort a cusize array by size of used method. // Returns cu->csize[comp] indices in descending size, as static mem static int *sort_cusize(cusize_t *cu) { static int idx[COMP_MAX]; int i; for (i = 0; i < COMP_MAX; i++) idx[i] = i; sort_cusize_global = cu; qsort(idx, COMP_MAX, sizeof(*idx), sort_cusize_compar); return idx; } // Hash table of cusize_t and sorting by key (content-id) KHASH_MAP_INIT_INT(cu, cusize_t) /* Sort by hash key. Global due to rubbish qsort API, but it's simple. */ static khash_t(cu) *global_cu_hash = NULL; static int cu_compar(const void *i1, const void *i2) { return kh_key(global_cu_hash, *(const int *)i1) - kh_key(global_cu_hash, *(const int *)i2); } /*---------------------------------------------------------------------- * Main cram_size reporting and aggregation */ static off_t report_size(FILE *outfp, int verbose, int ref_seq_blk, khash_t(cu) *cu_size, cram_cid2ds_t *cid2ds) { if (!cu_size || !cid2ds) return -1; khiter_t k; off_t tot_size = 0; fprintf(outfp, "# Content_ID Uncomp.size Comp.size Ratio Method%.*s Data_series\n", verbose ? 4 : 0, " "); int *sorted_blocks = malloc(kh_end(cu_size)*sizeof(int)); if (!sorted_blocks) return -1; int nblocks = 0; for (k = kh_begin(cu_size); k != kh_end(cu_size); k++) { if (!kh_exist(cu_size, k)) continue; sorted_blocks[nblocks++] = k; } global_cu_hash = cu_size; qsort(sorted_blocks, nblocks, sizeof(int), cu_compar); int i; for (i = 0; i < nblocks; i++) { k = sorted_blocks[i]; if (verbose) { // FULL output int *comp_idx = sort_cusize(&kh_value(cu_size, k)); int first_line = 1, c, j; for (c = 0; c < COMP_MAX; c++) { int comp = comp_idx[c]; if (!kh_value(cu_size, k).csize[comp] && c) break; if (!first_line) fprintf(outfp, "\n"); first_line = 0; if ((int)kh_key(cu_size, k) < 0) fprintf(outfp, "BLOCK %8s", "CORE"); else fprintf(outfp, "BLOCK %8d", kh_key(cu_size, k)); fprintf(outfp, " %12"PRId64" %12"PRId64, kh_value(cu_size, k).usize[comp], kh_value(cu_size, k).csize[comp]); double f = (100.0*(kh_value(cu_size, k).csize[comp]+.0001)) / (kh_value(cu_size, k).usize[comp]+.0001); if (f > 999) fprintf(outfp, " >999%% %-11s", comp_method2str[comp]); else fprintf(outfp, " %6.2f%% %-11s",f, comp_method2str[comp]); int n, *dsa = cram_cid2ds_query(cid2ds, kh_key(cu_size, k), &n); for (j = 0; j < n; j++) { int d = dsa[j]; if (d > 65535) fprintf(outfp, " %c%c%c", d>>16, (d>>8)&0xff, d&0xff); else fprintf(outfp, " %c%c", (d>>8)&0xff, d&0xff); } } } else { // aggregate by compression type. int64_t csize = total_csize(&kh_value(cu_size, k)); int64_t usize = total_usize(&kh_value(cu_size, k)); int *comp_idx = sort_cusize(&kh_value(cu_size, k)); char cstr[COMP_MAX+1] = {0}; int cidx = 0, c; for (c = 0; c < COMP_MAX; c++) { if (!kh_value(cu_size, k).csize[comp_idx[c]]) break; cstr[cidx++] = comp_method2char[comp_idx[c]]; } if (!*cstr) *cstr = '.'; if ((int)kh_key(cu_size, k) < 0) fprintf(outfp, "BLOCK %8s", "CORE"); else fprintf(outfp, "BLOCK %8d", kh_key(cu_size, k)); fprintf(outfp, " %12"PRId64" %12"PRId64, usize, csize); double f = 100*(csize+.0001)/(usize+.0001); if (f > 999) fprintf(outfp, " >999%% %-7s", cstr); else fprintf(outfp, " %6.2f%% %-7s", f, cstr); int n, j, *dsa = cram_cid2ds_query(cid2ds, kh_key(cu_size, k), &n); for (j = 0; j < n; j++) { int d = dsa[j]; if (d > 65535) fprintf(outfp, " %c%c%c", d>>16, (d>>8)&0xff, d&0xff); else fprintf(outfp, " %c%c", (d>>8)&0xff, d&0xff); } } if ((int)kh_key(cu_size, k) >= 0 && (int)kh_key(cu_size, k) == ref_seq_blk) { fprintf(outfp, " embedded_ref"); } fprintf(outfp, "\n"); tot_size += total_csize(&kh_value(cu_size, k)); } free(sorted_blocks); return tot_size; } /* Main processing loop */ static int cram_size(hFILE *hf_in, samFile *in, sam_hdr_t *h, FILE *outfp, int verbose, int encodings) { cram_fd *in_c; cram_container *c = NULL; cram_block *blk = NULL; cram_block_slice_hdr *shdr = NULL; khiter_t k; int ret; cram_cid2ds_t *cid2ds = NULL; khash_t(cu) *cu_size = kh_init(cu); int ref_seq_blk_used = -1; int64_t nseqs = 0, nbases = 0, ncont = 0, nslice = 0; if (!in->is_cram) { print_error("cram_size", "Input is not a CRAM file"); goto err; } in_c = in->fp.cram; // low level htslib abuse? while ((c = cram_read_container(in_c))) { if (cram_container_is_empty(in_c)) { cram_block *blk; // Container compression header if (!(blk = cram_read_block(in_c))) goto err; cram_free_block(blk); cram_free_container(c); c = NULL; blk = NULL; continue; } nseqs += cram_container_get_num_records(c); nbases += cram_container_get_num_bases(c); // Container compression header int32_t num_slices; if (!(blk = cram_read_block(in_c))) goto err; // Decode compression header... cram_block_compression_hdr *chdr; chdr = cram_decode_compression_header(in_c, blk); if (encodings) { kstring_t ks = KS_INITIALIZE; if (cram_describe_encodings(chdr, &ks) < 0) goto err; fprintf(outfp, "Container encodings\n%s\n", ks_str(&ks)); ks_free(&ks); } cid2ds = cram_update_cid2ds_map(chdr, cid2ds); cram_free_block(blk); blk = NULL; cram_free_compression_header(chdr); // Container num_blocks can be invalid, due to a bug. // Instead we iterate in slice context instead. (void)cram_container_get_landmarks(c, &num_slices); ncont++; nslice += num_slices; int i, j; for (i = 0; i < num_slices; i++) { // Slice header if (!(blk = cram_read_block(in_c))) goto err; if (!(shdr = cram_decode_slice_header(in_c, blk))) goto err; cram_free_block(blk); blk = NULL; int ref_seq_blk = cram_slice_hdr_get_embed_ref_id(shdr); int num_blocks = cram_slice_hdr_get_num_blocks(shdr); // Embedded reference. Check it's consistent (if used this is // an almost guaranteed certainty, so we take the easy route). if (ref_seq_blk >= 0) { if (ref_seq_blk_used == -1) ref_seq_blk_used = ref_seq_blk; else if (ref_seq_blk_used != ref_seq_blk) fprintf(samtools_stderr, "Embedded reference is not consistently using the same Content-Id.\n" "Reported figures for reference will be invalid.\n"); } // Slice data blocks for (j = 0; j < num_blocks; j++) { // read and discard, unless it's the ref-ID block if (!(blk = cram_read_block(in_c))) goto err; int32_t csize = cram_block_get_comp_size(blk); int32_t usize = cram_block_get_uncomp_size(blk); int cid = cram_block_get_content_id(blk); enum cram_block_method method = cram_block_get_method(blk); // Expand comp to the internal sub-formats, eg // rANS order-0/1, PACK+RLE, etc. cram_method_details *cm; cm = cram_expand_method(cram_block_get_data(blk), cram_block_get_comp_size(blk), method); if (!cm) goto err; enum comp_expanded comp = comp_method2expanded(cm); free(cm); k = kh_put(cu, cu_size, cid, &ret); if (ret < 0) goto err; if (ret == 0) { kh_value(cu_size, k).csize[comp] += csize; kh_value(cu_size, k).usize[comp] += usize; } else { memset(&kh_value(cu_size, k), 0, sizeof(cusize_t)); kh_value(cu_size, k).csize[comp] = csize; kh_value(cu_size, k).usize[comp] = usize; } cram_free_block(blk); blk = NULL; } cram_free_slice_header(shdr); shdr = NULL; } cram_free_container(c); c = NULL; } off_t tot_size = report_size(outfp, verbose, ref_seq_blk_used, cu_size, cid2ds); if (tot_size < 0) goto err; kh_destroy(cu, cu_size); cram_cid2ds_free(cid2ds); off_t end = htell(hf_in); fprintf(outfp, "\n"); fprintf(outfp, "Number of containers %18"PRId64"\n", ncont); fprintf(outfp, "Number of slices %18"PRId64"\n", nslice); fprintf(outfp, "Number of sequences %18"PRId64"\n", nseqs); fprintf(outfp, "Number of bases %18"PRId64"\n", nbases); fprintf(outfp, "Total file size %18"PRId64"\n", (int64_t) end); fprintf(outfp, "Format overhead size %18"PRId64"\n", (int64_t) (end - tot_size)); return 0; err: // Report anyway so we can get stats on partial files, but be // sure to error too. report_size(outfp, verbose, ref_seq_blk_used, cu_size, cid2ds); print_error("cram_size", "Failed in decoding CRAM file"); if (blk) cram_free_block(blk); if (shdr) cram_free_slice_header(shdr); if (c) cram_free_container(c); if (cid2ds) cram_cid2ds_free(cid2ds); return -1; } /* main() for cram_size */ int main_cram_size(int argc, char *argv[]) { int c, usage = 0, verbose = 0, encodings = 0; sam_hdr_t *h = 0; hFILE *hf_in = NULL; samFile *in = NULL; sam_global_args ga; FILE *outfp = samtools_stdout; static const struct option lopts[] = { {"output", required_argument, NULL, 'o'}, {"verbose", no_argument, NULL, 'v'}, {"encodings", no_argument, NULL, 'e'}, SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', '-', '-'), { NULL, 0, NULL, 0 } }; sam_global_args_init(&ga); while ((c = getopt_long(argc, argv, "vo:e", lopts, NULL)) >= 0) { switch (c) { case 'o': if (!(outfp = fopen(optarg, "w"))) { perror(optarg); goto err; } break; case 'v': verbose++; break; case 'e': encodings++; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage=1; break; } } if ((optind == argc && isatty(0)) || usage) { fprintf(samtools_stdout, "Usage: samtools cram_size [-ve] [-o out.size] [in.cram]\n"); return 0; } char *fn = optind < argc ? argv[optind] : "-"; // We want access to in->fp.cram->fp, but this is an opaque struct so we // can't get that. However we opened with hopen and then reopen as // CRAM with hts_hopen, which will swallow the initial hFILE and take // owenership of it. Hence we now know in->fp.cram->fp. if (!(hf_in = hopen(fn, "r"))) { print_error_errno("cram_size", "failed to open file '%s'", fn); return 1; } if (!(in = hts_hopen(hf_in, fn, "r"))) { print_error_errno("cram_size", "failed to open file '%s'", fn); goto err; } if (!(h = sam_hdr_read(in))) goto err; int ret = cram_size(hf_in, in, h, outfp, verbose, encodings); sam_hdr_destroy(h); sam_close(in); if (outfp != samtools_stdout) fclose(outfp); return ret ? 1 : 0; err: if (in) sam_close(in); if (h) sam_hdr_destroy(h); return 1; } pysam-0.23.0/samtools/cut_target.c000066400000000000000000000213031475062545500171070ustar00rootroot00000000000000/* cut_target.c -- targetcut subcommand. Copyright (C) 2011 Broad Institute. Copyright (C) 2012-2013, 2015, 2016, 2019 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include "htslib/hts.h" #include "htslib/sam.h" #include "htslib/faidx.h" #include "samtools.h" #include "sam_opts.h" #define ERR_DEP 0.83 typedef struct { int e[2][3], p[2][2]; } score_param_t; /* Note that although the two matrics have 10 parameters in total, only 4 * (probably 3) are free. Changing the scoring matrices in a sort of symmetric * way will not change the result. */ static score_param_t g_param = { {{0,0,0},{-4,1,6}}, {{0,-14000}, {0,0}} }; typedef struct { int min_baseQ, tid, max_bases; uint16_t *bases; samFile *fp; sam_hdr_t *h; char *ref; hts_pos_t len; faidx_t *fai; errmod_t *em; } ct_t; static uint16_t gencns(ct_t *g, int n, const bam_pileup1_t *plp) { int i, j, ret, tmp, k, sum[4], qual; float q[16]; if (n > g->max_bases) { // enlarge g->bases g->max_bases = n; kroundup32(g->max_bases); g->bases = realloc(g->bases, (size_t) g->max_bases * 2); } for (i = k = 0; i < n; ++i) { const bam_pileup1_t *p = plp + i; uint8_t *seq; int q, baseQ, b; if (p->is_refskip || p->is_del) continue; baseQ = bam_get_qual(p->b)[p->qpos]; if (baseQ < g->min_baseQ) continue; seq = bam_get_seq(p->b); b = seq_nt16_int[bam_seqi(seq, p->qpos)]; if (b > 3) continue; q = baseQ < p->b->core.qual? baseQ : p->b->core.qual; if (q < 4) q = 4; if (q > 63) q = 63; g->bases[k++] = q<<5 | bam_is_rev(p->b)<<4 | b; } if (k == 0) return 0; errmod_cal(g->em, k, 4, g->bases, q); for (i = 0; i < 4; ++i) sum[i] = (int)(q[i<<2|i] + .499) << 2 | i; for (i = 1; i < 4; ++i) // insertion sort for (j = i; j > 0 && sum[j] < sum[j-1]; --j) tmp = sum[j], sum[j] = sum[j-1], sum[j-1] = tmp; qual = (sum[1]>>2) - (sum[0]>>2); k = k < 256? k : 255; ret = (qual < 63? qual : 63) << 2 | (sum[0]&3); return ret<<8|k; } static void process_cns(sam_hdr_t *h, int tid, hts_pos_t l, uint16_t *cns) { int64_t i, s; int f[2][2], *prev, *curr, *swap_tmp; uint8_t *b; // backtrack array b = calloc(l, 1); f[0][0] = f[0][1] = 0; prev = f[0]; curr = f[1]; // fill the backtrack matrix for (i = 0; i < l; ++i) { int c = (cns[i] == 0)? 0 : (cns[i]>>8 == 0)? 1 : 2; int tmp0, tmp1; // compute f[0] tmp0 = prev[0] + g_param.e[0][c] + g_param.p[0][0]; // (s[i+1],s[i])=(0,0) tmp1 = prev[1] + g_param.e[0][c] + g_param.p[1][0]; // (0,1) if (tmp0 > tmp1) curr[0] = tmp0, b[i] = 0; else curr[0] = tmp1, b[i] = 1; // compute f[1] tmp0 = prev[0] + g_param.e[1][c] + g_param.p[0][1]; // (s[i+1],s[i])=(1,0) tmp1 = prev[1] + g_param.e[1][c] + g_param.p[1][1]; // (1,1) if (tmp0 > tmp1) curr[1] = tmp0, b[i] |= 0<<1; else curr[1] = tmp1, b[i] |= 1<<1; // swap swap_tmp = prev; prev = curr; curr = swap_tmp; } // backtrack s = prev[0] > prev[1]? 0 : 1; for (i = l - 1; i > 0; --i) { b[i] |= s<<2; s = b[i]>>s&1; } // print for (i = 0, s = -1; i < INT64_MAX && i <= l; ++i) { if (i == l || ((b[i]>>2&3) == 0 && s >= 0)) { if (s >= 0) { int64_t j; printf("%s:%"PRId64"-%"PRId64"\t0\t%s\t%"PRId64"\t60\t%"PRId64"M\t*\t0\t0\t", sam_hdr_tid2name(h, tid), s+1, i, sam_hdr_tid2name(h, tid), s+1, i-s); for (j = s; j < i; ++j) { int c = cns[j]>>8; if (c == 0) putchar('N'); else putchar("ACGT"[c&3]); } putchar('\t'); for (j = s; j < i; ++j) putchar(33 + (cns[j]>>8>>2)); putchar('\n'); } //if (s >= 0) printf("%s\t%d\t%d\t%d\n", h->target_name[tid], s, i, i - s); s = -1; } else if ((b[i]>>2&3) && s < 0) s = i; } free(b); } static int read_aln(void *data, bam1_t *b) { ct_t *g = (ct_t*)data; int ret; while (1) { ret = sam_read1(g->fp, g->h, b); if ( ret<0 ) break; if ( b->core.flag & (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP) ) continue; if ( g->fai && b->core.tid >= 0 ) { if (b->core.tid != g->tid) { // then load the sequence free(g->ref); g->ref = fai_fetch64(g->fai, sam_hdr_tid2name(g->h, b->core.tid), &g->len); g->tid = b->core.tid; } sam_prob_realn(b, g->ref, g->len, 1<<1|1); } break; } return ret; } int main_cut_target(int argc, char *argv[]) { int c, tid, pos, n, lasttid = -1, usage = 0, status = EXIT_SUCCESS; hts_pos_t l, max_l; const bam_pileup1_t *p; bam_plp_t plp; uint16_t *cns; ct_t g; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 'f', '-'), { NULL, 0, NULL, 0 } }; memset(&g, 0, sizeof(ct_t)); g.min_baseQ = 13; g.tid = -1; while ((c = getopt_long(argc, argv, "f:Q:i:o:0:1:2:", lopts, NULL)) >= 0) { switch (c) { case 'Q': g.min_baseQ = atoi(optarg); break; // quality cutoff case 'i': g_param.p[0][1] = -atoi(optarg); break; // 0->1 transition (in) PENALTY case '0': g_param.e[1][0] = atoi(optarg); break; // emission SCORE case '1': g_param.e[1][1] = atoi(optarg); break; case '2': g_param.e[1][2] = atoi(optarg); break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage=1; break; } } if (ga.reference) { g.fai = fai_load(ga.reference); if (g.fai == 0) fprintf(stderr, "[%s] fail to load the fasta index.\n", __func__); } if (usage || argc == optind) { fprintf(stderr, "Usage: samtools targetcut [-Q minQ] [-i inPen] [-0 em0] [-1 em1] [-2 em2] \n"); sam_global_opt_help(stderr, "-.--f--."); return 1; } l = max_l = 0; cns = 0; g.fp = sam_open_format(argv[optind], "r", &ga.in); if (g.fp == NULL) { print_error_errno("targetcut", "can't open \"%s\"", argv[optind]); return 1; } g.h = sam_hdr_read(g.fp); if (g.h == NULL) { print_error("targetcut", "couldn't read header for \"%s\"", argv[optind]); sam_close(g.fp); return 1; } g.em = errmod_init(1. - ERR_DEP); plp = bam_plp_init(read_aln, &g); while ((p = bam_plp_auto(plp, &tid, &pos, &n)) != 0) { if (tid < 0) break; if (tid != lasttid) { // change of chromosome if (cns) process_cns(g.h, lasttid, l, cns); if (max_l < sam_hdr_tid2len(g.h, tid)) { max_l = sam_hdr_tid2len(g.h, tid); kroundup32(max_l); cns = realloc(cns, max_l * 2); } l = sam_hdr_tid2len(g.h, tid); memset(cns, 0, max_l * 2); lasttid = tid; } cns[pos] = gencns(&g, n, p); } process_cns(g.h, lasttid, l, cns); if (n < 0) { print_error("targetcut", "error reading from \"%s\"", argv[optind]); status = EXIT_FAILURE; } free(cns); sam_hdr_destroy(g.h); bam_plp_destroy(plp); sam_close(g.fp); if (g.fai) { fai_destroy(g.fai); free(g.ref); } errmod_destroy(g.em); free(g.bases); sam_global_args_free(&ga); return status; } pysam-0.23.0/samtools/cut_target.c.pysam.c000066400000000000000000000215521475062545500204660ustar00rootroot00000000000000#include "samtools.pysam.h" /* cut_target.c -- targetcut subcommand. Copyright (C) 2011 Broad Institute. Copyright (C) 2012-2013, 2015, 2016, 2019 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include "htslib/hts.h" #include "htslib/sam.h" #include "htslib/faidx.h" #include "samtools.h" #include "sam_opts.h" #define ERR_DEP 0.83 typedef struct { int e[2][3], p[2][2]; } score_param_t; /* Note that although the two matrics have 10 parameters in total, only 4 * (probably 3) are free. Changing the scoring matrices in a sort of symmetric * way will not change the result. */ static score_param_t g_param = { {{0,0,0},{-4,1,6}}, {{0,-14000}, {0,0}} }; typedef struct { int min_baseQ, tid, max_bases; uint16_t *bases; samFile *fp; sam_hdr_t *h; char *ref; hts_pos_t len; faidx_t *fai; errmod_t *em; } ct_t; static uint16_t gencns(ct_t *g, int n, const bam_pileup1_t *plp) { int i, j, ret, tmp, k, sum[4], qual; float q[16]; if (n > g->max_bases) { // enlarge g->bases g->max_bases = n; kroundup32(g->max_bases); g->bases = realloc(g->bases, (size_t) g->max_bases * 2); } for (i = k = 0; i < n; ++i) { const bam_pileup1_t *p = plp + i; uint8_t *seq; int q, baseQ, b; if (p->is_refskip || p->is_del) continue; baseQ = bam_get_qual(p->b)[p->qpos]; if (baseQ < g->min_baseQ) continue; seq = bam_get_seq(p->b); b = seq_nt16_int[bam_seqi(seq, p->qpos)]; if (b > 3) continue; q = baseQ < p->b->core.qual? baseQ : p->b->core.qual; if (q < 4) q = 4; if (q > 63) q = 63; g->bases[k++] = q<<5 | bam_is_rev(p->b)<<4 | b; } if (k == 0) return 0; errmod_cal(g->em, k, 4, g->bases, q); for (i = 0; i < 4; ++i) sum[i] = (int)(q[i<<2|i] + .499) << 2 | i; for (i = 1; i < 4; ++i) // insertion sort for (j = i; j > 0 && sum[j] < sum[j-1]; --j) tmp = sum[j], sum[j] = sum[j-1], sum[j-1] = tmp; qual = (sum[1]>>2) - (sum[0]>>2); k = k < 256? k : 255; ret = (qual < 63? qual : 63) << 2 | (sum[0]&3); return ret<<8|k; } static void process_cns(sam_hdr_t *h, int tid, hts_pos_t l, uint16_t *cns) { int64_t i, s; int f[2][2], *prev, *curr, *swap_tmp; uint8_t *b; // backtrack array b = calloc(l, 1); f[0][0] = f[0][1] = 0; prev = f[0]; curr = f[1]; // fill the backtrack matrix for (i = 0; i < l; ++i) { int c = (cns[i] == 0)? 0 : (cns[i]>>8 == 0)? 1 : 2; int tmp0, tmp1; // compute f[0] tmp0 = prev[0] + g_param.e[0][c] + g_param.p[0][0]; // (s[i+1],s[i])=(0,0) tmp1 = prev[1] + g_param.e[0][c] + g_param.p[1][0]; // (0,1) if (tmp0 > tmp1) curr[0] = tmp0, b[i] = 0; else curr[0] = tmp1, b[i] = 1; // compute f[1] tmp0 = prev[0] + g_param.e[1][c] + g_param.p[0][1]; // (s[i+1],s[i])=(1,0) tmp1 = prev[1] + g_param.e[1][c] + g_param.p[1][1]; // (1,1) if (tmp0 > tmp1) curr[1] = tmp0, b[i] |= 0<<1; else curr[1] = tmp1, b[i] |= 1<<1; // swap swap_tmp = prev; prev = curr; curr = swap_tmp; } // backtrack s = prev[0] > prev[1]? 0 : 1; for (i = l - 1; i > 0; --i) { b[i] |= s<<2; s = b[i]>>s&1; } // print for (i = 0, s = -1; i < INT64_MAX && i <= l; ++i) { if (i == l || ((b[i]>>2&3) == 0 && s >= 0)) { if (s >= 0) { int64_t j; fprintf(samtools_stdout, "%s:%"PRId64"-%"PRId64"\t0\t%s\t%"PRId64"\t60\t%"PRId64"M\t*\t0\t0\t", sam_hdr_tid2name(h, tid), s+1, i, sam_hdr_tid2name(h, tid), s+1, i-s); for (j = s; j < i; ++j) { int c = cns[j]>>8; if (c == 0) fputc('N', samtools_stdout); else fputc("ACGT"[c&3], samtools_stdout); } fputc('\t', samtools_stdout); for (j = s; j < i; ++j) fputc(33 + (cns[j]>>8>>2), samtools_stdout); fputc('\n', samtools_stdout); } //if (s >= 0) fprintf(samtools_stdout, "%s\t%d\t%d\t%d\n", h->target_name[tid], s, i, i - s); s = -1; } else if ((b[i]>>2&3) && s < 0) s = i; } free(b); } static int read_aln(void *data, bam1_t *b) { ct_t *g = (ct_t*)data; int ret; while (1) { ret = sam_read1(g->fp, g->h, b); if ( ret<0 ) break; if ( b->core.flag & (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP) ) continue; if ( g->fai && b->core.tid >= 0 ) { if (b->core.tid != g->tid) { // then load the sequence free(g->ref); g->ref = fai_fetch64(g->fai, sam_hdr_tid2name(g->h, b->core.tid), &g->len); g->tid = b->core.tid; } sam_prob_realn(b, g->ref, g->len, 1<<1|1); } break; } return ret; } int main_cut_target(int argc, char *argv[]) { int c, tid, pos, n, lasttid = -1, usage = 0, status = EXIT_SUCCESS; hts_pos_t l, max_l; const bam_pileup1_t *p; bam_plp_t plp; uint16_t *cns; ct_t g; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 'f', '-'), { NULL, 0, NULL, 0 } }; memset(&g, 0, sizeof(ct_t)); g.min_baseQ = 13; g.tid = -1; while ((c = getopt_long(argc, argv, "f:Q:i:o:0:1:2:", lopts, NULL)) >= 0) { switch (c) { case 'Q': g.min_baseQ = atoi(optarg); break; // quality cutoff case 'i': g_param.p[0][1] = -atoi(optarg); break; // 0->1 transition (in) PENALTY case '0': g_param.e[1][0] = atoi(optarg); break; // emission SCORE case '1': g_param.e[1][1] = atoi(optarg); break; case '2': g_param.e[1][2] = atoi(optarg); break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage=1; break; } } if (ga.reference) { g.fai = fai_load(ga.reference); if (g.fai == 0) fprintf(samtools_stderr, "[%s] fail to load the fasta index.\n", __func__); } if (usage || argc == optind) { fprintf(samtools_stderr, "Usage: samtools targetcut [-Q minQ] [-i inPen] [-0 em0] [-1 em1] [-2 em2] \n"); sam_global_opt_help(samtools_stderr, "-.--f--."); return 1; } l = max_l = 0; cns = 0; g.fp = sam_open_format(argv[optind], "r", &ga.in); if (g.fp == NULL) { print_error_errno("targetcut", "can't open \"%s\"", argv[optind]); return 1; } g.h = sam_hdr_read(g.fp); if (g.h == NULL) { print_error("targetcut", "couldn't read header for \"%s\"", argv[optind]); sam_close(g.fp); return 1; } g.em = errmod_init(1. - ERR_DEP); plp = bam_plp_init(read_aln, &g); while ((p = bam_plp_auto(plp, &tid, &pos, &n)) != 0) { if (tid < 0) break; if (tid != lasttid) { // change of chromosome if (cns) process_cns(g.h, lasttid, l, cns); if (max_l < sam_hdr_tid2len(g.h, tid)) { max_l = sam_hdr_tid2len(g.h, tid); kroundup32(max_l); cns = realloc(cns, max_l * 2); } l = sam_hdr_tid2len(g.h, tid); memset(cns, 0, max_l * 2); lasttid = tid; } cns[pos] = gencns(&g, n, p); } process_cns(g.h, lasttid, l, cns); if (n < 0) { print_error("targetcut", "error reading from \"%s\"", argv[optind]); status = EXIT_FAILURE; } free(cns); sam_hdr_destroy(g.h); bam_plp_destroy(plp); sam_close(g.fp); if (g.fai) { fai_destroy(g.fai); free(g.ref); } errmod_destroy(g.em); free(g.bases); sam_global_args_free(&ga); return status; } pysam-0.23.0/samtools/dict.c000066400000000000000000000165461475062545500157060ustar00rootroot00000000000000/* dict.c -- create a sequence dictionary file. Copyright (C) 2015, 2020 Genome Research Ltd. Author: Shane McCarthy Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "htslib/khash.h" #include "htslib/kseq.h" #include "htslib/hts.h" #include "samtools.h" KHASH_SET_INIT_STR(str) KSEQ_INIT(gzFile, gzread) typedef struct _args_t { char *output_fname, *alt_fname; char *assembly, *species, *uri; int alias, header; khash_t(str) *is_alt; } args_t; static void write_dict(const char *fn, args_t *args) { hts_md5_context *md5; int l, i, k; gzFile fp; kseq_t *seq; unsigned char digest[16]; char hex[33]; fp = strcmp(fn, "-") ? gzopen(fn, "r") : gzdopen(fileno(stdin), "r"); if (fp == 0) { print_error_errno("dict", "Cannot open %s", fn); exit(1); } FILE *out = stdout; if (args->output_fname) { out = fopen(args->output_fname, "w"); if (out == NULL) { print_error_errno("dict", "Cannot open %s for writing", args->output_fname); exit(1); } } if (!(md5 = hts_md5_init())) exit(1); seq = kseq_init(fp); if (args->header) fprintf(out, "@HD\tVN:1.0\tSO:unsorted\n"); while ((l = kseq_read(seq)) >= 0) { for (i = k = 0; i < seq->seq.l; ++i) { if (seq->seq.s[i] >= '!' && seq->seq.s[i] <= '~') seq->seq.s[k++] = toupper(seq->seq.s[i]); } hts_md5_reset(md5); hts_md5_update(md5, (unsigned char*)seq->seq.s, k); hts_md5_final(digest, md5); hts_md5_hex(hex, digest); fprintf(out, "@SQ\tSN:%s\tLN:%d\tM5:%s", seq->name.s, k, hex); if (args->is_alt && kh_get(str, args->is_alt, seq->name.s) != kh_end(args->is_alt)) fprintf(out, "\tAH:*"); if (args->alias) { const char *name = seq->name.s; if (strncmp(name, "chr", 3) == 0) { name += 3; fprintf(out, "\tAN:%s", name); } else fprintf(out, "\tAN:chr%s", name); if (strcmp(name, "M") == 0) fprintf(out, ",chrMT,MT"); else if (strcmp(name, "MT") == 0) fprintf(out, ",chrM,M"); } if (args->uri) fprintf(out, "\tUR:%s", args->uri); else if (strcmp(fn, "-") != 0) { #ifdef _WIN32 char *real_path = _fullpath(NULL, fn, PATH_MAX); #else char *real_path = realpath(fn, NULL); #endif fprintf(out, "\tUR:file://%s", real_path); free(real_path); } if (args->assembly) fprintf(out, "\tAS:%s", args->assembly); if (args->species) fprintf(out, "\tSP:%s", args->species); fprintf(out, "\n"); } kseq_destroy(seq); hts_md5_destroy(md5); if (args->output_fname) fclose(out); gzclose(fp); } static void read_alt_file(khash_t(str) *is_alt, const char *fname) { htsFile *fp = hts_open(fname, "r"); if (fp == NULL) { print_error_errno("dict", "Cannot open %s", fname); exit(1); } // .alt files are in a SAM-like format, but we don't use sam_read1() // as these files may not have a complete set of @SQ headers. kstring_t str = KS_INITIALIZE; while (hts_getline(fp, KS_SEP_LINE, &str) >= 0) { if (str.l == 0 || str.s[0] == '@') continue; char *tab = strchr(str.s, '\t'); if (tab) *tab = '\0'; int ret; char *seqname = strdup(str.s); kh_put(str, is_alt, seqname, &ret); if (ret == 0) free(seqname); // Already present } ks_free(&str); hts_close(fp); } static int dict_usage(void) { fprintf(stderr, "\n"); fprintf(stderr, "About: Create a sequence dictionary file from a fasta file\n"); fprintf(stderr, "Usage: samtools dict [options] \n\n"); fprintf(stderr, "Options: -a, --assembly STR assembly\n"); fprintf(stderr, " -A, --alias, --alternative-name\n"); fprintf(stderr, " add AN tag by adding/removing 'chr'\n"); fprintf(stderr, " -H, --no-header do not print @HD line\n"); fprintf(stderr, " -l, --alt FILE add AH:* tag to alternate locus sequences\n"); fprintf(stderr, " -o, --output FILE file to write out dict file [stdout]\n"); fprintf(stderr, " -s, --species STR species\n"); fprintf(stderr, " -u, --uri STR URI [file:///abs/path/to/file.fa]\n"); fprintf(stderr, "\n"); return 1; } int dict_main(int argc, char *argv[]) { args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->header = 1; static const struct option loptions[] = { {"help", no_argument, NULL, 'h'}, {"no-header", no_argument, NULL, 'H'}, {"alias", no_argument, NULL, 'A'}, {"alt", required_argument, NULL, 'l'}, {"alternative-name", no_argument, NULL, 'A'}, {"assembly", required_argument, NULL, 'a'}, {"species", required_argument, NULL, 's'}, {"uri", required_argument, NULL, 'u'}, {"output", required_argument, NULL, 'o'}, {NULL, 0, NULL, 0} }; int c; while ( (c=getopt_long(argc,argv,"?AhHa:l:s:u:o:",loptions,NULL))>0 ) { switch (c) { case 'A': args->alias = 1; break; case 'a': args->assembly = optarg; break; case 'l': args->alt_fname = optarg; break; case 's': args->species = optarg; break; case 'u': args->uri = optarg; break; case 'o': args->output_fname = optarg; break; case 'H': args->header = 0; break; case 'h': return dict_usage(); default: return dict_usage(); } } char *fname = NULL; if ( optind>=argc ) { if ( !isatty(STDIN_FILENO) ) fname = "-"; // reading from stdin else return dict_usage(); } else fname = argv[optind]; if (args->alt_fname) { args->is_alt = kh_init(str); read_alt_file(args->is_alt, args->alt_fname); } write_dict(fname, args); if (args->is_alt) { khint_t k; for (k = 0; k < kh_end(args->is_alt); ++k) if (kh_exist(args->is_alt, k)) free((char *) kh_key(args->is_alt, k)); kh_destroy(str, args->is_alt); } free(args); return 0; } pysam-0.23.0/samtools/dict.c.pysam.c000066400000000000000000000170451475062545500172520ustar00rootroot00000000000000#include "samtools.pysam.h" /* dict.c -- create a sequence dictionary file. Copyright (C) 2015, 2020 Genome Research Ltd. Author: Shane McCarthy Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "htslib/khash.h" #include "htslib/kseq.h" #include "htslib/hts.h" #include "samtools.h" KHASH_SET_INIT_STR(str) KSEQ_INIT(gzFile, gzread) typedef struct _args_t { char *output_fname, *alt_fname; char *assembly, *species, *uri; int alias, header; khash_t(str) *is_alt; } args_t; static void write_dict(const char *fn, args_t *args) { hts_md5_context *md5; int l, i, k; gzFile fp; kseq_t *seq; unsigned char digest[16]; char hex[33]; fp = strcmp(fn, "-") ? gzopen(fn, "r") : gzdopen(fileno(stdin), "r"); if (fp == 0) { print_error_errno("dict", "Cannot open %s", fn); samtools_exit(1); } FILE *out = samtools_stdout; if (args->output_fname) { out = fopen(args->output_fname, "w"); if (out == NULL) { print_error_errno("dict", "Cannot open %s for writing", args->output_fname); samtools_exit(1); } } if (!(md5 = hts_md5_init())) samtools_exit(1); seq = kseq_init(fp); if (args->header) fprintf(out, "@HD\tVN:1.0\tSO:unsorted\n"); while ((l = kseq_read(seq)) >= 0) { for (i = k = 0; i < seq->seq.l; ++i) { if (seq->seq.s[i] >= '!' && seq->seq.s[i] <= '~') seq->seq.s[k++] = toupper(seq->seq.s[i]); } hts_md5_reset(md5); hts_md5_update(md5, (unsigned char*)seq->seq.s, k); hts_md5_final(digest, md5); hts_md5_hex(hex, digest); fprintf(out, "@SQ\tSN:%s\tLN:%d\tM5:%s", seq->name.s, k, hex); if (args->is_alt && kh_get(str, args->is_alt, seq->name.s) != kh_end(args->is_alt)) fprintf(out, "\tAH:*"); if (args->alias) { const char *name = seq->name.s; if (strncmp(name, "chr", 3) == 0) { name += 3; fprintf(out, "\tAN:%s", name); } else fprintf(out, "\tAN:chr%s", name); if (strcmp(name, "M") == 0) fprintf(out, ",chrMT,MT"); else if (strcmp(name, "MT") == 0) fprintf(out, ",chrM,M"); } if (args->uri) fprintf(out, "\tUR:%s", args->uri); else if (strcmp(fn, "-") != 0) { #ifdef _WIN32 char *real_path = _fullpath(NULL, fn, PATH_MAX); #else char *real_path = realpath(fn, NULL); #endif fprintf(out, "\tUR:file://%s", real_path); free(real_path); } if (args->assembly) fprintf(out, "\tAS:%s", args->assembly); if (args->species) fprintf(out, "\tSP:%s", args->species); fprintf(out, "\n"); } kseq_destroy(seq); hts_md5_destroy(md5); if (args->output_fname) fclose(out); gzclose(fp); } static void read_alt_file(khash_t(str) *is_alt, const char *fname) { htsFile *fp = hts_open(fname, "r"); if (fp == NULL) { print_error_errno("dict", "Cannot open %s", fname); samtools_exit(1); } // .alt files are in a SAM-like format, but we don't use sam_read1() // as these files may not have a complete set of @SQ headers. kstring_t str = KS_INITIALIZE; while (hts_getline(fp, KS_SEP_LINE, &str) >= 0) { if (str.l == 0 || str.s[0] == '@') continue; char *tab = strchr(str.s, '\t'); if (tab) *tab = '\0'; int ret; char *seqname = strdup(str.s); kh_put(str, is_alt, seqname, &ret); if (ret == 0) free(seqname); // Already present } ks_free(&str); hts_close(fp); } static int dict_usage(void) { fprintf(samtools_stderr, "\n"); fprintf(samtools_stderr, "About: Create a sequence dictionary file from a fasta file\n"); fprintf(samtools_stderr, "Usage: samtools dict [options] \n\n"); fprintf(samtools_stderr, "Options: -a, --assembly STR assembly\n"); fprintf(samtools_stderr, " -A, --alias, --alternative-name\n"); fprintf(samtools_stderr, " add AN tag by adding/removing 'chr'\n"); fprintf(samtools_stderr, " -H, --no-header do not print @HD line\n"); fprintf(samtools_stderr, " -l, --alt FILE add AH:* tag to alternate locus sequences\n"); fprintf(samtools_stderr, " -o, --output FILE file to write out dict file [samtools_stdout]\n"); fprintf(samtools_stderr, " -s, --species STR species\n"); fprintf(samtools_stderr, " -u, --uri STR URI [file:///abs/path/to/file.fa]\n"); fprintf(samtools_stderr, "\n"); return 1; } int dict_main(int argc, char *argv[]) { args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->header = 1; static const struct option loptions[] = { {"help", no_argument, NULL, 'h'}, {"no-header", no_argument, NULL, 'H'}, {"alias", no_argument, NULL, 'A'}, {"alt", required_argument, NULL, 'l'}, {"alternative-name", no_argument, NULL, 'A'}, {"assembly", required_argument, NULL, 'a'}, {"species", required_argument, NULL, 's'}, {"uri", required_argument, NULL, 'u'}, {"output", required_argument, NULL, 'o'}, {NULL, 0, NULL, 0} }; int c; while ( (c=getopt_long(argc,argv,"?AhHa:l:s:u:o:",loptions,NULL))>0 ) { switch (c) { case 'A': args->alias = 1; break; case 'a': args->assembly = optarg; break; case 'l': args->alt_fname = optarg; break; case 's': args->species = optarg; break; case 'u': args->uri = optarg; break; case 'o': args->output_fname = optarg; break; case 'H': args->header = 0; break; case 'h': return dict_usage(); default: return dict_usage(); } } char *fname = NULL; if ( optind>=argc ) { if ( !isatty(STDIN_FILENO) ) fname = "-"; // reading from stdin else return dict_usage(); } else fname = argv[optind]; if (args->alt_fname) { args->is_alt = kh_init(str); read_alt_file(args->is_alt, args->alt_fname); } write_dict(fname, args); if (args->is_alt) { khint_t k; for (k = 0; k < kh_end(args->is_alt); ++k) if (kh_exist(args->is_alt, k)) free((char *) kh_key(args->is_alt, k)); kh_destroy(str, args->is_alt); } free(args); return 0; } pysam-0.23.0/samtools/faidx.c000066400000000000000000000466321475062545500160550ustar00rootroot00000000000000/* faidx.c -- faidx subcommand. Copyright (C) 2008, 2009, 2013, 2016, 2018-2020, 2022, 2024 Genome Research Ltd. Portions copyright (C) 2011 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. History: * 2016-01-12: Pierre Lindenbaum @yokofakun : added options -o -n */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "sam_opts.h" #include "samtools.h" // Negative indicates the same as input data #define DEFAULT_FASTA_LINE_LEN -60 #ifndef ABS # define ABS(x) ((x)>=0?(x):-(x)) #endif //new params required for output creation typedef struct output { int isbgzip; //is bgzip or uncompressed file FILE *fp; //uncompressed file pointer BGZF *bgzf_fp; //bgzf file pointer sam_global_args *gopt; //options kstring_t buffer; } output; static unsigned char comp_base[256] = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, '!', '"', '#', '$', '%', '&', '\'','(', ')', '*', '+', ',', '-', '.', '/', '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', ':', ';', '<', '=', '>', '?', '@', 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O', 'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z', '[', '\\',']', '^', '_', '`', 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o', 'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', '{', '|', '}', '~', 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, }; static void reverse_complement(char *str, const hts_pos_t len) { char c; hts_pos_t i = 0, j = len - 1; while (i <= j) { c = str[i]; str[i] = comp_base[(unsigned char)str[j]]; str[j] = comp_base[(unsigned char)c]; i++; j--; } } static void reverse(char *str, const hts_pos_t len) { char c; hts_pos_t i = 0, j = len - 1; while (i < j) { c = str[i]; str[i] = str[j]; str[j] = c; i++; j--; } } /// wrappedwrite - wraps the fwrite and bgzf_write /** @param out - pointer to data required to write output * @param buffer - data to write * @param length - data length * returns error or length written on success */ static inline size_t wrappedwrite(output *out, const char *buffer, size_t length) { return out->isbgzip ? bgzf_write(out->bgzf_fp, buffer, length) : fwrite(buffer, 1, length, out->fp); } static int write_line(faidx_t *faid, output *out, const char *line, const char *name, const int ignore, const hts_pos_t length, const hts_pos_t seq_len) { int id; hts_pos_t beg, end; if (seq_len < 0) { fprintf(stderr, "[faidx] Failed to fetch sequence in %s\n", name); if (ignore && seq_len == -2) { return EXIT_SUCCESS; } else { return EXIT_FAILURE; } } else if (seq_len == 0) { fprintf(stderr, "[faidx] Zero length sequence: %s\n", name); } else if (fai_parse_region(faid, name, &id, &beg, &end, 0) && (end < HTS_POS_MAX) && (seq_len != end - beg)) { fprintf(stderr, "[faidx] Truncated sequence: %s\n", name); } hts_pos_t i, seq_sz = seq_len; for (i = 0; i < seq_sz; i += length) { hts_pos_t len = i + length < seq_sz ? length : seq_sz - i; if (wrappedwrite(out, line + i, len) < len || wrappedwrite(out, "\n", 1) < 1) { print_error_errno("faidx", "failed to write output"); return EXIT_FAILURE; } } return EXIT_SUCCESS; } static int write_output(faidx_t *faid, output *out, const char *name, const int ignore, const hts_pos_t length, const int rev, const char *pos_strand_name, const char *neg_strand_name, enum fai_format_options format) { hts_pos_t seq_len, wrap_len = length, len = 0; char *seq = NULL, *qual = NULL; int ret = EXIT_FAILURE; if (wrap_len < 0) wrap_len = fai_line_length(faid, name); if (wrap_len <= 0) wrap_len = HTS_POS_MAX; seq = fai_fetch64(faid, name, &seq_len); if (rev && seq_len > 0) { reverse_complement(seq, seq_len); } //write the name len = ksprintf(&out->buffer, "%c%s%s\n", format == FAI_FASTA ? '>' : '@', name, rev ? neg_strand_name : pos_strand_name); if (wrappedwrite(out, out->buffer.s, out->buffer.l) < len) { fprintf(stderr,"[faidx] Failed to write buffer\n"); goto exit; } ks_clear(&out->buffer); //write bases if ((ret = write_line(faid, out, seq, name, ignore, wrap_len, seq_len) == EXIT_FAILURE)) { goto exit; } if (format == FAI_FASTQ) { //write quality qual = fai_fetchqual64(faid, name, &seq_len); if (rev && seq_len > 0) { reverse(qual, seq_len); } len = ksprintf(&out->buffer, "+\n"); if (wrappedwrite(out, out->buffer.s, out->buffer.l) < len) { fprintf(stderr,"[faidx] Failed to write buffer\n"); goto exit; } ks_clear(&out->buffer); if ((ret = write_line(faid, out, qual, name, ignore, wrap_len, seq_len) == EXIT_FAILURE)) { goto exit; } } ret = EXIT_SUCCESS; exit: if (seq) { free(seq); } if (qual) { free(qual); } return ret; } static int read_regions_from_file(faidx_t *faid, hFILE *in_file, output *out, const int ignore, const hts_pos_t length, const int rev, const char *pos_strand_name, const char *neg_strand_name, enum fai_format_options format) { kstring_t line = {0, 0, NULL}; int ret = EXIT_FAILURE; while (line.l = 0, kgetline(&line, (kgets_func *)hgets, in_file) >= 0) { if ((ret = write_output(faid, out, line.s, ignore, length, rev, pos_strand_name, neg_strand_name, format)) == EXIT_FAILURE) { break; } } free(line.s); return ret; } static int usage(FILE *fp, enum fai_format_options format, int exit_status) { char *tool, *file_type, *index_name; if (format == FAI_FASTA) { tool = "faidx "; file_type = "FASTA"; index_name = "file.fa"; } else { tool = "fqidx "; file_type = "FASTQ"; index_name = "file.fq"; } fprintf(fp, "Usage: samtools %s [ [...]]\n", tool); fprintf(fp, "Option: \n" " -o, --output FILE Write %s to file.\n" " -n, --length INT Length of %s sequence line. [60]\n" " -c, --continue Continue after trying to retrieve missing region.\n" " -r, --region-file FILE File of regions. Format is chr:from-to. One per line.\n" " -i, --reverse-complement Reverse complement sequences.\n" " --mark-strand TYPE Add strand indicator to sequence name\n" " TYPE = rc for /rc on negative strand (default)\n" " no for no strand indicator\n" " sign for (+) / (-)\n" " custom,, for custom indicator\n" " --fai-idx FILE name of the index file (default %s.fai).\n" " --gzi-idx FILE name of compressed file index (default %s.gz.gzi).\n", file_type, file_type, index_name, index_name); if (format == FAI_FASTA) { fprintf(fp, " -f, --fastq File and index in FASTQ format.\n"); } fprintf(fp, " -h, --help This message.\n"); sam_global_opt_help(fp, "---.-@--"); return exit_status; } int faidx_core(int argc, char *argv[], enum fai_format_options format) { int c, ignore_error = 0, rev = 0; hts_pos_t line_len = DEFAULT_FASTA_LINE_LEN ;/* fasta line len */ char* output_file = NULL; /* output file (default is stdout ) */ char *region_file = NULL; // list of regions from file, one per line char *pos_strand_name = ""; // Extension to add to name for +ve strand char *neg_strand_name = "/rc"; // Extension to add to name for -ve strand char *strand_names = NULL; // Used for custom strand annotation char *fai_name = NULL; // specified index name char *gzi_name = NULL; // specified compressed index name sam_global_args ga = SAM_GLOBAL_ARGS_INIT; int exit_status = EXIT_FAILURE, flushed = 0; struct output out = { 0, stdout, NULL, &ga, KS_INITIALIZE}; //data required for output writing faidx_t *fai = NULL; hts_tpool *pool = NULL; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', '-', '-', 0, '-', '@'), //output format opt and thread count - long options { "output", required_argument, NULL, 'o' }, { "help", no_argument, NULL, 'h' }, { "length", required_argument, NULL, 'n' }, { "continue", no_argument, NULL, 'c' }, { "region-file", required_argument, NULL, 'r' }, { "fastq", no_argument, NULL, 'f' }, { "reverse-complement", no_argument, NULL, 'i' }, { "mark-strand", required_argument, NULL, 1000 }, { "fai-idx", required_argument, NULL, 1001 }, { "gzi-idx", required_argument, NULL, 1002 }, { NULL, 0, NULL, 0 } }; while ((c = getopt_long(argc, argv, "ho:n:cr:fi@:", lopts, NULL)) >= 0) { switch (c) { case 'o': { output_file = optarg; char *ext = strrchr(output_file, '.'); if (!ext) { break; } if (!strcmp(ext, ".gz") || !strcmp(ext, ".bgz") || !strcmp(ext, ".bgzf")) { out.isbgzip = 1; //bgzip output } break; } case 'n': line_len = strtol(optarg, NULL, 10); if (line_len < 0) { fprintf(stderr,"[faidx] bad line length '%s', using default:%d\n",optarg,ABS(DEFAULT_FASTA_LINE_LEN)); line_len= ABS(DEFAULT_FASTA_LINE_LEN); } break; case 'c': ignore_error = 1; break; case 'r': region_file = optarg; break; case 'f': format = FAI_FASTQ; break; case 'i': rev = 1; break; case '?': exit_status = usage(stderr, format, EXIT_FAILURE); goto exit2; break; case 'h': exit_status = usage(stdout, format, EXIT_SUCCESS); goto exit2; break; case 1000: if (strcmp(optarg, "no") == 0) { pos_strand_name = neg_strand_name = ""; } else if (strcmp(optarg, "sign") == 0) { pos_strand_name = "(+)"; neg_strand_name = "(-)"; } else if (strcmp(optarg, "rc") == 0) { pos_strand_name = ""; neg_strand_name = "/rc"; } else if (strncmp(optarg, "custom,", 7) == 0) { size_t len = strlen(optarg + 7); size_t comma = strcspn(optarg + 7, ","); free(strand_names); strand_names = pos_strand_name = malloc(len + 2); if (!strand_names) { fprintf(stderr, "[faidx] Out of memory\n"); goto exit2; } neg_strand_name = pos_strand_name + comma + 1; memcpy(pos_strand_name, optarg + 7, comma); pos_strand_name[comma] = '\0'; if (comma < len) memcpy(neg_strand_name, optarg + 7 + comma + 1, len - comma); neg_strand_name[len - comma] = '\0'; } else { fprintf(stderr, "[faidx] Unknown --mark-strand option \"%s\"\n", optarg); exit_status = usage(stderr, format, EXIT_FAILURE); goto exit2; } break; case 1001: fai_name = optarg; break; case 1002: gzi_name = optarg; break; // handle standard samtools options like thread count, compression level... default: if (parse_sam_global_opt(c, optarg, lopts, &ga)) { fprintf(stderr, "[faidx] Invalid option \"%s\"\n", optarg); goto exit2; } break; } } if ( argc==optind ) { exit_status = usage(stdout, format, EXIT_SUCCESS); goto exit2; } if (optind+1 == argc && !region_file) { if (output_file && !fai_name) fai_name = output_file; if (fai_build3(argv[optind], fai_name, gzi_name) != 0) { if (fai_name) fprintf(stderr, "[faidx] Could not build fai index %s", fai_name); else fprintf(stderr, "[faidx] Could not build fai index %s.fai", argv[optind]); if (gzi_name) fprintf(stderr, " or compressed index %s\n", gzi_name); else fprintf(stderr, "\n"); goto exit2; } exit_status = EXIT_SUCCESS; goto exit2; } if (out.gopt->nthreads > 0) { //setup thread pool if (!(pool = hts_tpool_init(out.gopt->nthreads))) { fprintf(stderr, "Failed to setup thread pool\n"); } } fai = fai_load3_format(argv[optind], fai_name, gzi_name, FAI_CREATE, format); if (!fai) { if (fai_name) fprintf(stderr, "[faidx] Could not load fai index %s", fai_name); else fprintf(stderr, "[faidx] Could not load fai index %s.fai", argv[optind]); if (gzi_name) fprintf(stderr, " or compressed index %s\n", gzi_name); else fprintf(stderr, "\n"); goto exit2; } if (pool) { //use thread pool if set if (fai_thread_pool(fai, pool, 0)) { fprintf(stderr, "Failed to set thread pool for reading\n"); } } /** output file provided by user */ if( output_file != NULL ) { if( strcmp( output_file, argv[optind] ) == 0 ) { fprintf(stderr,"[faidx] Same input/output : %s\n", output_file); goto exit2; } if (!out.isbgzip) { out.fp = fopen( output_file, "w" ); } else { hts_opt *opts = (hts_opt *)(out.gopt->out.specific); char mode[13] = "w"; int level = 4; //default compression level while (opts) { if (opts->opt == HTS_OPT_COMPRESSION_LEVEL) { //compression level level = opts->val.i; break; } opts = opts->next; } if (level >= 0) { snprintf(mode, sizeof(mode), "w%d", level); //pass compression with mode } out.bgzf_fp = bgzf_open(output_file, mode); } if( (!out.isbgzip && out.fp == NULL) || (out.isbgzip && out.bgzf_fp == NULL)) { fprintf(stderr,"[faidx] Cannot open \"%s\" for writing :%s.\n", output_file, strerror(errno) ); goto exit2; } if (out.isbgzip && pool) { //use thread pool if set if (bgzf_thread_pool(out.bgzf_fp, pool, 0)) { fprintf(stderr, "Failed to set thread pool for writing\n"); } } } if (region_file) { hFILE *rf; if ((rf = hopen(region_file, "r"))) { exit_status = read_regions_from_file(fai, rf, &out, ignore_error, line_len, rev, pos_strand_name, neg_strand_name, format); if (hclose(rf) != 0) { fprintf(stderr, "[faidx] Warning: failed to close %s", region_file); } if (exit_status == EXIT_FAILURE) { goto exit1; } } else { fprintf(stderr, "[faidx] Failed to open \"%s\" for reading.\n", region_file); goto exit1; } } exit_status = EXIT_SUCCESS; while ( ++optind Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. History: * 2016-01-12: Pierre Lindenbaum @yokofakun : added options -o -n */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "sam_opts.h" #include "samtools.h" // Negative indicates the same as input data #define DEFAULT_FASTA_LINE_LEN -60 #ifndef ABS # define ABS(x) ((x)>=0?(x):-(x)) #endif //new params required for output creation typedef struct output { int isbgzip; //is bgzip or uncompressed file FILE *fp; //uncompressed file pointer BGZF *bgzf_fp; //bgzf file pointer sam_global_args *gopt; //options kstring_t buffer; } output; static unsigned char comp_base[256] = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, '!', '"', '#', '$', '%', '&', '\'','(', ')', '*', '+', ',', '-', '.', '/', '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', ':', ';', '<', '=', '>', '?', '@', 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O', 'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z', '[', '\\',']', '^', '_', '`', 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o', 'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', '{', '|', '}', '~', 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, }; static void reverse_complement(char *str, const hts_pos_t len) { char c; hts_pos_t i = 0, j = len - 1; while (i <= j) { c = str[i]; str[i] = comp_base[(unsigned char)str[j]]; str[j] = comp_base[(unsigned char)c]; i++; j--; } } static void reverse(char *str, const hts_pos_t len) { char c; hts_pos_t i = 0, j = len - 1; while (i < j) { c = str[i]; str[i] = str[j]; str[j] = c; i++; j--; } } /// wrappedwrite - wraps the fwrite and bgzf_write /** @param out - pointer to data required to write output * @param buffer - data to write * @param length - data length * returns error or length written on success */ static inline size_t wrappedwrite(output *out, const char *buffer, size_t length) { return out->isbgzip ? bgzf_write(out->bgzf_fp, buffer, length) : fwrite(buffer, 1, length, out->fp); } static int write_line(faidx_t *faid, output *out, const char *line, const char *name, const int ignore, const hts_pos_t length, const hts_pos_t seq_len) { int id; hts_pos_t beg, end; if (seq_len < 0) { fprintf(samtools_stderr, "[faidx] Failed to fetch sequence in %s\n", name); if (ignore && seq_len == -2) { return EXIT_SUCCESS; } else { return EXIT_FAILURE; } } else if (seq_len == 0) { fprintf(samtools_stderr, "[faidx] Zero length sequence: %s\n", name); } else if (fai_parse_region(faid, name, &id, &beg, &end, 0) && (end < HTS_POS_MAX) && (seq_len != end - beg)) { fprintf(samtools_stderr, "[faidx] Truncated sequence: %s\n", name); } hts_pos_t i, seq_sz = seq_len; for (i = 0; i < seq_sz; i += length) { hts_pos_t len = i + length < seq_sz ? length : seq_sz - i; if (wrappedwrite(out, line + i, len) < len || wrappedwrite(out, "\n", 1) < 1) { print_error_errno("faidx", "failed to write output"); return EXIT_FAILURE; } } return EXIT_SUCCESS; } static int write_output(faidx_t *faid, output *out, const char *name, const int ignore, const hts_pos_t length, const int rev, const char *pos_strand_name, const char *neg_strand_name, enum fai_format_options format) { hts_pos_t seq_len, wrap_len = length, len = 0; char *seq = NULL, *qual = NULL; int ret = EXIT_FAILURE; if (wrap_len < 0) wrap_len = fai_line_length(faid, name); if (wrap_len <= 0) wrap_len = HTS_POS_MAX; seq = fai_fetch64(faid, name, &seq_len); if (rev && seq_len > 0) { reverse_complement(seq, seq_len); } //write the name len = ksprintf(&out->buffer, "%c%s%s\n", format == FAI_FASTA ? '>' : '@', name, rev ? neg_strand_name : pos_strand_name); if (wrappedwrite(out, out->buffer.s, out->buffer.l) < len) { fprintf(samtools_stderr,"[faidx] Failed to write buffer\n"); goto exit; } ks_clear(&out->buffer); //write bases if ((ret = write_line(faid, out, seq, name, ignore, wrap_len, seq_len) == EXIT_FAILURE)) { goto exit; } if (format == FAI_FASTQ) { //write quality qual = fai_fetchqual64(faid, name, &seq_len); if (rev && seq_len > 0) { reverse(qual, seq_len); } len = ksprintf(&out->buffer, "+\n"); if (wrappedwrite(out, out->buffer.s, out->buffer.l) < len) { fprintf(samtools_stderr,"[faidx] Failed to write buffer\n"); goto exit; } ks_clear(&out->buffer); if ((ret = write_line(faid, out, qual, name, ignore, wrap_len, seq_len) == EXIT_FAILURE)) { goto exit; } } ret = EXIT_SUCCESS; exit: if (seq) { free(seq); } if (qual) { free(qual); } return ret; } static int read_regions_from_file(faidx_t *faid, hFILE *in_file, output *out, const int ignore, const hts_pos_t length, const int rev, const char *pos_strand_name, const char *neg_strand_name, enum fai_format_options format) { kstring_t line = {0, 0, NULL}; int ret = EXIT_FAILURE; while (line.l = 0, kgetline(&line, (kgets_func *)hgets, in_file) >= 0) { if ((ret = write_output(faid, out, line.s, ignore, length, rev, pos_strand_name, neg_strand_name, format)) == EXIT_FAILURE) { break; } } free(line.s); return ret; } static int usage(FILE *fp, enum fai_format_options format, int exit_status) { char *tool, *file_type, *index_name; if (format == FAI_FASTA) { tool = "faidx "; file_type = "FASTA"; index_name = "file.fa"; } else { tool = "fqidx "; file_type = "FASTQ"; index_name = "file.fq"; } fprintf(fp, "Usage: samtools %s [ [...]]\n", tool); fprintf(fp, "Option: \n" " -o, --output FILE Write %s to file.\n" " -n, --length INT Length of %s sequence line. [60]\n" " -c, --continue Continue after trying to retrieve missing region.\n" " -r, --region-file FILE File of regions. Format is chr:from-to. One per line.\n" " -i, --reverse-complement Reverse complement sequences.\n" " --mark-strand TYPE Add strand indicator to sequence name\n" " TYPE = rc for /rc on negative strand (default)\n" " no for no strand indicator\n" " sign for (+) / (-)\n" " custom,, for custom indicator\n" " --fai-idx FILE name of the index file (default %s.fai).\n" " --gzi-idx FILE name of compressed file index (default %s.gz.gzi).\n", file_type, file_type, index_name, index_name); if (format == FAI_FASTA) { fprintf(fp, " -f, --fastq File and index in FASTQ format.\n"); } fprintf(fp, " -h, --help This message.\n"); sam_global_opt_help(fp, "---.-@--"); return exit_status; } int faidx_core(int argc, char *argv[], enum fai_format_options format) { int c, ignore_error = 0, rev = 0; hts_pos_t line_len = DEFAULT_FASTA_LINE_LEN ;/* fasta line len */ char* output_file = NULL; /* output file (default is samtools_stdout ) */ char *region_file = NULL; // list of regions from file, one per line char *pos_strand_name = ""; // Extension to add to name for +ve strand char *neg_strand_name = "/rc"; // Extension to add to name for -ve strand char *strand_names = NULL; // Used for custom strand annotation char *fai_name = NULL; // specified index name char *gzi_name = NULL; // specified compressed index name sam_global_args ga = SAM_GLOBAL_ARGS_INIT; int exit_status = EXIT_FAILURE, flushed = 0; struct output out = { 0, samtools_stdout, NULL, &ga, KS_INITIALIZE}; //data required for output writing faidx_t *fai = NULL; hts_tpool *pool = NULL; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', '-', '-', 0, '-', '@'), //output format opt and thread count - long options { "output", required_argument, NULL, 'o' }, { "help", no_argument, NULL, 'h' }, { "length", required_argument, NULL, 'n' }, { "continue", no_argument, NULL, 'c' }, { "region-file", required_argument, NULL, 'r' }, { "fastq", no_argument, NULL, 'f' }, { "reverse-complement", no_argument, NULL, 'i' }, { "mark-strand", required_argument, NULL, 1000 }, { "fai-idx", required_argument, NULL, 1001 }, { "gzi-idx", required_argument, NULL, 1002 }, { NULL, 0, NULL, 0 } }; while ((c = getopt_long(argc, argv, "ho:n:cr:fi@:", lopts, NULL)) >= 0) { switch (c) { case 'o': { output_file = optarg; char *ext = strrchr(output_file, '.'); if (!ext) { break; } if (!strcmp(ext, ".gz") || !strcmp(ext, ".bgz") || !strcmp(ext, ".bgzf")) { out.isbgzip = 1; //bgzip output } break; } case 'n': line_len = strtol(optarg, NULL, 10); if (line_len < 0) { fprintf(samtools_stderr,"[faidx] bad line length '%s', using default:%d\n",optarg,ABS(DEFAULT_FASTA_LINE_LEN)); line_len= ABS(DEFAULT_FASTA_LINE_LEN); } break; case 'c': ignore_error = 1; break; case 'r': region_file = optarg; break; case 'f': format = FAI_FASTQ; break; case 'i': rev = 1; break; case '?': exit_status = usage(samtools_stderr, format, EXIT_FAILURE); goto exit2; break; case 'h': exit_status = usage(samtools_stdout, format, EXIT_SUCCESS); goto exit2; break; case 1000: if (strcmp(optarg, "no") == 0) { pos_strand_name = neg_strand_name = ""; } else if (strcmp(optarg, "sign") == 0) { pos_strand_name = "(+)"; neg_strand_name = "(-)"; } else if (strcmp(optarg, "rc") == 0) { pos_strand_name = ""; neg_strand_name = "/rc"; } else if (strncmp(optarg, "custom,", 7) == 0) { size_t len = strlen(optarg + 7); size_t comma = strcspn(optarg + 7, ","); free(strand_names); strand_names = pos_strand_name = malloc(len + 2); if (!strand_names) { fprintf(samtools_stderr, "[faidx] Out of memory\n"); goto exit2; } neg_strand_name = pos_strand_name + comma + 1; memcpy(pos_strand_name, optarg + 7, comma); pos_strand_name[comma] = '\0'; if (comma < len) memcpy(neg_strand_name, optarg + 7 + comma + 1, len - comma); neg_strand_name[len - comma] = '\0'; } else { fprintf(samtools_stderr, "[faidx] Unknown --mark-strand option \"%s\"\n", optarg); exit_status = usage(samtools_stderr, format, EXIT_FAILURE); goto exit2; } break; case 1001: fai_name = optarg; break; case 1002: gzi_name = optarg; break; // handle standard samtools options like thread count, compression level... default: if (parse_sam_global_opt(c, optarg, lopts, &ga)) { fprintf(samtools_stderr, "[faidx] Invalid option \"%s\"\n", optarg); goto exit2; } break; } } if ( argc==optind ) { exit_status = usage(samtools_stdout, format, EXIT_SUCCESS); goto exit2; } if (optind+1 == argc && !region_file) { if (output_file && !fai_name) fai_name = output_file; if (fai_build3(argv[optind], fai_name, gzi_name) != 0) { if (fai_name) fprintf(samtools_stderr, "[faidx] Could not build fai index %s", fai_name); else fprintf(samtools_stderr, "[faidx] Could not build fai index %s.fai", argv[optind]); if (gzi_name) fprintf(samtools_stderr, " or compressed index %s\n", gzi_name); else fprintf(samtools_stderr, "\n"); goto exit2; } exit_status = EXIT_SUCCESS; goto exit2; } if (out.gopt->nthreads > 0) { //setup thread pool if (!(pool = hts_tpool_init(out.gopt->nthreads))) { fprintf(samtools_stderr, "Failed to setup thread pool\n"); } } fai = fai_load3_format(argv[optind], fai_name, gzi_name, FAI_CREATE, format); if (!fai) { if (fai_name) fprintf(samtools_stderr, "[faidx] Could not load fai index %s", fai_name); else fprintf(samtools_stderr, "[faidx] Could not load fai index %s.fai", argv[optind]); if (gzi_name) fprintf(samtools_stderr, " or compressed index %s\n", gzi_name); else fprintf(samtools_stderr, "\n"); goto exit2; } if (pool) { //use thread pool if set if (fai_thread_pool(fai, pool, 0)) { fprintf(samtools_stderr, "Failed to set thread pool for reading\n"); } } /** output file provided by user */ if( output_file != NULL ) { if( strcmp( output_file, argv[optind] ) == 0 ) { fprintf(samtools_stderr,"[faidx] Same input/output : %s\n", output_file); goto exit2; } if (!out.isbgzip) { out.fp = fopen( output_file, "w" ); } else { hts_opt *opts = (hts_opt *)(out.gopt->out.specific); char mode[13] = "w"; int level = 4; //default compression level while (opts) { if (opts->opt == HTS_OPT_COMPRESSION_LEVEL) { //compression level level = opts->val.i; break; } opts = opts->next; } if (level >= 0) { snprintf(mode, sizeof(mode), "w%d", level); //pass compression with mode } out.bgzf_fp = bgzf_open(output_file, mode); } if( (!out.isbgzip && out.fp == NULL) || (out.isbgzip && out.bgzf_fp == NULL)) { fprintf(samtools_stderr,"[faidx] Cannot open \"%s\" for writing :%s.\n", output_file, strerror(errno) ); goto exit2; } if (out.isbgzip && pool) { //use thread pool if set if (bgzf_thread_pool(out.bgzf_fp, pool, 0)) { fprintf(samtools_stderr, "Failed to set thread pool for writing\n"); } } } if (region_file) { hFILE *rf; if ((rf = hopen(region_file, "r"))) { exit_status = read_regions_from_file(fai, rf, &out, ignore_error, line_len, rev, pos_strand_name, neg_strand_name, format); if (hclose(rf) != 0) { fprintf(samtools_stderr, "[faidx] Warning: failed to close %s", region_file); } if (exit_status == EXIT_FAILURE) { goto exit1; } } else { fprintf(samtools_stderr, "[faidx] Failed to open \"%s\" for reading.\n", region_file); goto exit1; } } exit_status = EXIT_SUCCESS; while ( ++optind 1 > 2) */ #ifndef LZ4_FORCE_MEMORY_ACCESS /* can be defined externally */ # if defined(__GNUC__) && ( defined(__ARM_ARCH_6__) || defined(__ARM_ARCH_6J__) || defined(__ARM_ARCH_6K__) || defined(__ARM_ARCH_6Z__) || defined(__ARM_ARCH_6ZK__) || defined(__ARM_ARCH_6T2__) ) # define LZ4_FORCE_MEMORY_ACCESS 2 # elif defined(__INTEL_COMPILER) || defined(__GNUC__) # define LZ4_FORCE_MEMORY_ACCESS 1 # endif #endif /* * LZ4_FORCE_SW_BITCOUNT * Define this parameter if your target system or compiler does not support hardware bit count */ #if defined(_MSC_VER) && defined(_WIN32_WCE) /* Visual Studio for Windows CE does not support Hardware bit count */ # define LZ4_FORCE_SW_BITCOUNT #endif /*-************************************ * Dependency **************************************/ #include "lz4.h" /* see also "memory routines" below */ /*-************************************ * Compiler Options **************************************/ #ifdef _MSC_VER /* Visual Studio */ # include # pragma warning(disable : 4127) /* disable: C4127: conditional expression is constant */ # pragma warning(disable : 4293) /* disable: C4293: too large shift (32-bits) */ #endif /* _MSC_VER */ #ifndef FORCE_INLINE # ifdef _MSC_VER /* Visual Studio */ # define FORCE_INLINE static __forceinline # else # if defined (__cplusplus) || defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L /* C99 */ # ifdef __GNUC__ # define FORCE_INLINE static inline __attribute__((always_inline)) # else # define FORCE_INLINE static inline # endif # else # define FORCE_INLINE static # endif /* __STDC_VERSION__ */ # endif /* _MSC_VER */ #endif /* FORCE_INLINE */ #if (defined(__GNUC__) && (__GNUC__ >= 3)) || (defined(__INTEL_COMPILER) && (__INTEL_COMPILER >= 800)) || defined(__clang__) # define expect(expr,value) (__builtin_expect ((expr),(value)) ) #else # define expect(expr,value) (expr) #endif #define likely(expr) expect((expr) != 0, 1) #define unlikely(expr) expect((expr) != 0, 0) /*-************************************ * Memory routines **************************************/ #include /* malloc, calloc, free */ #define ALLOCATOR(n,s) calloc(n,s) #define FREEMEM free #include /* memset, memcpy */ #define MEM_INIT memset /*-************************************ * Basic Types **************************************/ #if defined(__cplusplus) || (defined (__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) /* C99 */) # include typedef uint8_t BYTE; typedef uint16_t U16; typedef uint32_t U32; typedef int32_t S32; typedef uint64_t U64; typedef uintptr_t uptrval; #else typedef unsigned char BYTE; typedef unsigned short U16; typedef unsigned int U32; typedef signed int S32; typedef unsigned long long U64; typedef size_t uptrval; /* generally true, except OpenVMS-64 */ #endif #if defined(__x86_64__) typedef U64 reg_t; /* 64-bits in x32 mode */ #else typedef size_t reg_t; /* 32-bits in x32 mode */ #endif /*-************************************ * Reading and writing into memory **************************************/ static unsigned LZ4_isLittleEndian(void) { const union { U32 u; BYTE c[4]; } one = { 1 }; /* don't use static : performance detrimental */ return one.c[0]; } #if defined(LZ4_FORCE_MEMORY_ACCESS) && (LZ4_FORCE_MEMORY_ACCESS==2) /* lie to the compiler about data alignment; use with caution */ static U16 LZ4_read16(const void* memPtr) { return *(const U16*) memPtr; } static U32 LZ4_read32(const void* memPtr) { return *(const U32*) memPtr; } static reg_t LZ4_read_ARCH(const void* memPtr) { return *(const reg_t*) memPtr; } static void LZ4_write16(void* memPtr, U16 value) { *(U16*)memPtr = value; } static void LZ4_write32(void* memPtr, U32 value) { *(U32*)memPtr = value; } #elif defined(LZ4_FORCE_MEMORY_ACCESS) && (LZ4_FORCE_MEMORY_ACCESS==1) /* __pack instructions are safer, but compiler specific, hence potentially problematic for some compilers */ /* currently only defined for gcc and icc */ typedef union { U16 u16; U32 u32; reg_t uArch; } __attribute__((packed)) unalign; static U16 LZ4_read16(const void* ptr) { return ((const unalign*)ptr)->u16; } static U32 LZ4_read32(const void* ptr) { return ((const unalign*)ptr)->u32; } static reg_t LZ4_read_ARCH(const void* ptr) { return ((const unalign*)ptr)->uArch; } static void LZ4_write16(void* memPtr, U16 value) { ((unalign*)memPtr)->u16 = value; } static void LZ4_write32(void* memPtr, U32 value) { ((unalign*)memPtr)->u32 = value; } #else /* safe and portable access through memcpy() */ static U16 LZ4_read16(const void* memPtr) { U16 val; memcpy(&val, memPtr, sizeof(val)); return val; } static U32 LZ4_read32(const void* memPtr) { U32 val; memcpy(&val, memPtr, sizeof(val)); return val; } static reg_t LZ4_read_ARCH(const void* memPtr) { reg_t val; memcpy(&val, memPtr, sizeof(val)); return val; } static void LZ4_write16(void* memPtr, U16 value) { memcpy(memPtr, &value, sizeof(value)); } static void LZ4_write32(void* memPtr, U32 value) { memcpy(memPtr, &value, sizeof(value)); } #endif /* LZ4_FORCE_MEMORY_ACCESS */ static U16 LZ4_readLE16(const void* memPtr) { if (LZ4_isLittleEndian()) { return LZ4_read16(memPtr); } else { const BYTE* p = (const BYTE*)memPtr; return (U16)((U16)p[0] + (p[1]<<8)); } } static void LZ4_writeLE16(void* memPtr, U16 value) { if (LZ4_isLittleEndian()) { LZ4_write16(memPtr, value); } else { BYTE* p = (BYTE*)memPtr; p[0] = (BYTE) value; p[1] = (BYTE)(value>>8); } } static void LZ4_copy8(void* dst, const void* src) { memcpy(dst,src,8); } /* customized variant of memcpy, which can overwrite up to 8 bytes beyond dstEnd */ static void LZ4_wildCopy(void* dstPtr, const void* srcPtr, void* dstEnd) { BYTE* d = (BYTE*)dstPtr; const BYTE* s = (const BYTE*)srcPtr; BYTE* const e = (BYTE*)dstEnd; do { LZ4_copy8(d,s); d+=8; s+=8; } while (d=2) # include # define DEBUGLOG(l, ...) { \ if (l<=LZ4_DEBUG) { \ fprintf(stderr, __FILE__ ": "); \ fprintf(stderr, __VA_ARGS__); \ fprintf(stderr, " \n"); \ } } #else # define DEBUGLOG(l, ...) {} /* disabled */ #endif /*-************************************ * Common functions **************************************/ static unsigned LZ4_NbCommonBytes (register reg_t val) { if (LZ4_isLittleEndian()) { if (sizeof(val)==8) { # if defined(_MSC_VER) && defined(_WIN64) && !defined(LZ4_FORCE_SW_BITCOUNT) unsigned long r = 0; _BitScanForward64( &r, (U64)val ); return (int)(r>>3); # elif (defined(__clang__) || (defined(__GNUC__) && (__GNUC__>=3))) && !defined(LZ4_FORCE_SW_BITCOUNT) return (__builtin_ctzll((U64)val) >> 3); # else static const int DeBruijnBytePos[64] = { 0, 0, 0, 0, 0, 1, 1, 2, 0, 3, 1, 3, 1, 4, 2, 7, 0, 2, 3, 6, 1, 5, 3, 5, 1, 3, 4, 4, 2, 5, 6, 7, 7, 0, 1, 2, 3, 3, 4, 6, 2, 6, 5, 5, 3, 4, 5, 6, 7, 1, 2, 4, 6, 4, 4, 5, 7, 2, 6, 5, 7, 6, 7, 7 }; return DeBruijnBytePos[((U64)((val & -(long long)val) * 0x0218A392CDABBD3FULL)) >> 58]; # endif } else /* 32 bits */ { # if defined(_MSC_VER) && !defined(LZ4_FORCE_SW_BITCOUNT) unsigned long r; _BitScanForward( &r, (U32)val ); return (int)(r>>3); # elif (defined(__clang__) || (defined(__GNUC__) && (__GNUC__>=3))) && !defined(LZ4_FORCE_SW_BITCOUNT) return (__builtin_ctz((U32)val) >> 3); # else static const int DeBruijnBytePos[32] = { 0, 0, 3, 0, 3, 1, 3, 0, 3, 2, 2, 1, 3, 2, 0, 1, 3, 3, 1, 2, 2, 2, 2, 0, 3, 1, 2, 0, 1, 0, 1, 1 }; return DeBruijnBytePos[((U32)((val & -(S32)val) * 0x077CB531U)) >> 27]; # endif } } else /* Big Endian CPU */ { if (sizeof(val)==8) { # if defined(_MSC_VER) && defined(_WIN64) && !defined(LZ4_FORCE_SW_BITCOUNT) unsigned long r = 0; _BitScanReverse64( &r, val ); return (unsigned)(r>>3); # elif (defined(__clang__) || (defined(__GNUC__) && (__GNUC__>=3))) && !defined(LZ4_FORCE_SW_BITCOUNT) return (__builtin_clzll((U64)val) >> 3); # else unsigned r; if (!(val>>32)) { r=4; } else { r=0; val>>=32; } if (!(val>>16)) { r+=2; val>>=8; } else { val>>=24; } r += (!val); return r; # endif } else /* 32 bits */ { # if defined(_MSC_VER) && !defined(LZ4_FORCE_SW_BITCOUNT) unsigned long r = 0; _BitScanReverse( &r, (unsigned long)val ); return (unsigned)(r>>3); # elif (defined(__clang__) || (defined(__GNUC__) && (__GNUC__>=3))) && !defined(LZ4_FORCE_SW_BITCOUNT) return (__builtin_clz((U32)val) >> 3); # else unsigned r; if (!(val>>16)) { r=2; val>>=8; } else { r=0; val>>=24; } r += (!val); return r; # endif } } } #define STEPSIZE sizeof(reg_t) static unsigned LZ4_count(const BYTE* pIn, const BYTE* pMatch, const BYTE* pInLimit) { const BYTE* const pStart = pIn; while (likely(pIn compression run slower on incompressible data */ /*-************************************ * Local Structures and types **************************************/ typedef enum { notLimited = 0, limitedOutput = 1 } limitedOutput_directive; typedef enum { byPtr, byU32, byU16 } tableType_t; typedef enum { noDict = 0, withPrefix64k, usingExtDict } dict_directive; typedef enum { noDictIssue = 0, dictSmall } dictIssue_directive; typedef enum { endOnOutputSize = 0, endOnInputSize = 1 } endCondition_directive; typedef enum { full = 0, partial = 1 } earlyEnd_directive; /*-************************************ * Local Utils **************************************/ int LZ4_versionNumber (void) { return LZ4_VERSION_NUMBER; } const char* LZ4_versionString(void) { return LZ4_VERSION_STRING; } int LZ4_compressBound(int isize) { return LZ4_COMPRESSBOUND(isize); } int LZ4_sizeofState(void) { return LZ4_STREAMSIZE; } /*-****************************** * Compression functions ********************************/ static U32 LZ4_hash4(U32 sequence, tableType_t const tableType) { if (tableType == byU16) return ((sequence * 2654435761U) >> ((MINMATCH*8)-(LZ4_HASHLOG+1))); else return ((sequence * 2654435761U) >> ((MINMATCH*8)-LZ4_HASHLOG)); } static U32 LZ4_hash5(U64 sequence, tableType_t const tableType) { static const U64 prime5bytes = 889523592379ULL; static const U64 prime8bytes = 11400714785074694791ULL; const U32 hashLog = (tableType == byU16) ? LZ4_HASHLOG+1 : LZ4_HASHLOG; if (LZ4_isLittleEndian()) return (U32)(((sequence << 24) * prime5bytes) >> (64 - hashLog)); else return (U32)(((sequence >> 24) * prime8bytes) >> (64 - hashLog)); } FORCE_INLINE U32 LZ4_hashPosition(const void* const p, tableType_t const tableType) { if ((sizeof(reg_t)==8) && (tableType != byU16)) return LZ4_hash5(LZ4_read_ARCH(p), tableType); return LZ4_hash4(LZ4_read32(p), tableType); } static void LZ4_putPositionOnHash(const BYTE* p, U32 h, void* tableBase, tableType_t const tableType, const BYTE* srcBase) { switch (tableType) { case byPtr: { const BYTE** hashTable = (const BYTE**)tableBase; hashTable[h] = p; return; } case byU32: { U32* hashTable = (U32*) tableBase; hashTable[h] = (U32)(p-srcBase); return; } case byU16: { U16* hashTable = (U16*) tableBase; hashTable[h] = (U16)(p-srcBase); return; } } } FORCE_INLINE void LZ4_putPosition(const BYTE* p, void* tableBase, tableType_t tableType, const BYTE* srcBase) { U32 const h = LZ4_hashPosition(p, tableType); LZ4_putPositionOnHash(p, h, tableBase, tableType, srcBase); } static const BYTE* LZ4_getPositionOnHash(U32 h, void* tableBase, tableType_t tableType, const BYTE* srcBase) { if (tableType == byPtr) { const BYTE** hashTable = (const BYTE**) tableBase; return hashTable[h]; } if (tableType == byU32) { const U32* const hashTable = (U32*) tableBase; return hashTable[h] + srcBase; } { const U16* const hashTable = (U16*) tableBase; return hashTable[h] + srcBase; } /* default, to ensure a return */ } FORCE_INLINE const BYTE* LZ4_getPosition(const BYTE* p, void* tableBase, tableType_t tableType, const BYTE* srcBase) { U32 const h = LZ4_hashPosition(p, tableType); return LZ4_getPositionOnHash(h, tableBase, tableType, srcBase); } /** LZ4_compress_generic() : inlined, to ensure branches are decided at compilation time */ FORCE_INLINE int LZ4_compress_generic( LZ4_stream_t_internal* const cctx, const char* const source, char* const dest, const int inputSize, const int maxOutputSize, const limitedOutput_directive outputLimited, const tableType_t tableType, const dict_directive dict, const dictIssue_directive dictIssue, const U32 acceleration) { const BYTE* ip = (const BYTE*) source; const BYTE* base; const BYTE* lowLimit; const BYTE* const lowRefLimit = ip - cctx->dictSize; const BYTE* const dictionary = cctx->dictionary; const BYTE* const dictEnd = dictionary + cctx->dictSize; const ptrdiff_t dictDelta = dictEnd - (const BYTE*)source; const BYTE* anchor = (const BYTE*) source; const BYTE* const iend = ip + inputSize; const BYTE* const mflimit = iend - MFLIMIT; const BYTE* const matchlimit = iend - LASTLITERALS; BYTE* op = (BYTE*) dest; BYTE* const olimit = op + maxOutputSize; U32 forwardH; /* Init conditions */ if ((U32)inputSize > (U32)LZ4_MAX_INPUT_SIZE) return 0; /* Unsupported inputSize, too large (or negative) */ switch(dict) { case noDict: default: base = (const BYTE*)source; lowLimit = (const BYTE*)source; break; case withPrefix64k: base = (const BYTE*)source - cctx->currentOffset; lowLimit = (const BYTE*)source - cctx->dictSize; break; case usingExtDict: base = (const BYTE*)source - cctx->currentOffset; lowLimit = (const BYTE*)source; break; } if ((tableType == byU16) && (inputSize>=LZ4_64Klimit)) return 0; /* Size too large (not within 64K limit) */ if (inputSizehashTable, tableType, base); ip++; forwardH = LZ4_hashPosition(ip, tableType); /* Main Loop */ for ( ; ; ) { ptrdiff_t refDelta = 0; const BYTE* match; BYTE* token; /* Find a match */ { const BYTE* forwardIp = ip; unsigned step = 1; unsigned searchMatchNb = acceleration << LZ4_skipTrigger; do { U32 const h = forwardH; ip = forwardIp; forwardIp += step; step = (searchMatchNb++ >> LZ4_skipTrigger); if (unlikely(forwardIp > mflimit)) goto _last_literals; match = LZ4_getPositionOnHash(h, cctx->hashTable, tableType, base); if (dict==usingExtDict) { if (match < (const BYTE*)source) { refDelta = dictDelta; lowLimit = dictionary; } else { refDelta = 0; lowLimit = (const BYTE*)source; } } forwardH = LZ4_hashPosition(forwardIp, tableType); LZ4_putPositionOnHash(ip, h, cctx->hashTable, tableType, base); } while ( ((dictIssue==dictSmall) ? (match < lowRefLimit) : 0) || ((tableType==byU16) ? 0 : (match + MAX_DISTANCE < ip)) || (LZ4_read32(match+refDelta) != LZ4_read32(ip)) ); } /* Catch up */ while (((ip>anchor) & (match+refDelta > lowLimit)) && (unlikely(ip[-1]==match[refDelta-1]))) { ip--; match--; } /* Encode Literals */ { unsigned const litLength = (unsigned)(ip - anchor); token = op++; if ((outputLimited) && /* Check output buffer overflow */ (unlikely(op + litLength + (2 + 1 + LASTLITERALS) + (litLength/255) > olimit))) return 0; if (litLength >= RUN_MASK) { int len = (int)litLength-RUN_MASK; *token = (RUN_MASK<= 255 ; len-=255) *op++ = 255; *op++ = (BYTE)len; } else *token = (BYTE)(litLength< matchlimit) limit = matchlimit; matchCode = LZ4_count(ip+MINMATCH, match+MINMATCH, limit); ip += MINMATCH + matchCode; if (ip==limit) { unsigned const more = LZ4_count(ip, (const BYTE*)source, matchlimit); matchCode += more; ip += more; } } else { matchCode = LZ4_count(ip+MINMATCH, match+MINMATCH, matchlimit); ip += MINMATCH + matchCode; } if ( outputLimited && /* Check output buffer overflow */ (unlikely(op + (1 + LASTLITERALS) + (matchCode>>8) > olimit)) ) return 0; if (matchCode >= ML_MASK) { *token += ML_MASK; matchCode -= ML_MASK; LZ4_write32(op, 0xFFFFFFFF); while (matchCode >= 4*255) op+=4, LZ4_write32(op, 0xFFFFFFFF), matchCode -= 4*255; op += matchCode / 255; *op++ = (BYTE)(matchCode % 255); } else *token += (BYTE)(matchCode); } anchor = ip; /* Test end of chunk */ if (ip > mflimit) break; /* Fill table */ LZ4_putPosition(ip-2, cctx->hashTable, tableType, base); /* Test next position */ match = LZ4_getPosition(ip, cctx->hashTable, tableType, base); if (dict==usingExtDict) { if (match < (const BYTE*)source) { refDelta = dictDelta; lowLimit = dictionary; } else { refDelta = 0; lowLimit = (const BYTE*)source; } } LZ4_putPosition(ip, cctx->hashTable, tableType, base); if ( ((dictIssue==dictSmall) ? (match>=lowRefLimit) : 1) && (match+MAX_DISTANCE>=ip) && (LZ4_read32(match+refDelta)==LZ4_read32(ip)) ) { token=op++; *token=0; goto _next_match; } /* Prepare next loop */ forwardH = LZ4_hashPosition(++ip, tableType); } _last_literals: /* Encode Last Literals */ { size_t const lastRun = (size_t)(iend - anchor); if ( (outputLimited) && /* Check output buffer overflow */ ((op - (BYTE*)dest) + lastRun + 1 + ((lastRun+255-RUN_MASK)/255) > (U32)maxOutputSize) ) return 0; if (lastRun >= RUN_MASK) { size_t accumulator = lastRun - RUN_MASK; *op++ = RUN_MASK << ML_BITS; for(; accumulator >= 255 ; accumulator-=255) *op++ = 255; *op++ = (BYTE) accumulator; } else { *op++ = (BYTE)(lastRun<internal_donotuse; LZ4_resetStream((LZ4_stream_t*)state); if (acceleration < 1) acceleration = ACCELERATION_DEFAULT; if (maxOutputSize >= LZ4_compressBound(inputSize)) { if (inputSize < LZ4_64Klimit) return LZ4_compress_generic(ctx, source, dest, inputSize, 0, notLimited, byU16, noDict, noDictIssue, acceleration); else return LZ4_compress_generic(ctx, source, dest, inputSize, 0, notLimited, (sizeof(void*)==8) ? byU32 : byPtr, noDict, noDictIssue, acceleration); } else { if (inputSize < LZ4_64Klimit) return LZ4_compress_generic(ctx, source, dest, inputSize, maxOutputSize, limitedOutput, byU16, noDict, noDictIssue, acceleration); else return LZ4_compress_generic(ctx, source, dest, inputSize, maxOutputSize, limitedOutput, (sizeof(void*)==8) ? byU32 : byPtr, noDict, noDictIssue, acceleration); } } int LZ4_compress_fast(const char* source, char* dest, int inputSize, int maxOutputSize, int acceleration) { #if (LZ4_HEAPMODE) void* ctxPtr = ALLOCATOR(1, sizeof(LZ4_stream_t)); /* malloc-calloc always properly aligned */ #else LZ4_stream_t ctx; void* const ctxPtr = &ctx; #endif int const result = LZ4_compress_fast_extState(ctxPtr, source, dest, inputSize, maxOutputSize, acceleration); #if (LZ4_HEAPMODE) FREEMEM(ctxPtr); #endif return result; } int LZ4_compress_default(const char* source, char* dest, int inputSize, int maxOutputSize) { return LZ4_compress_fast(source, dest, inputSize, maxOutputSize, 1); } /* hidden debug function */ /* strangely enough, gcc generates faster code when this function is uncommented, even if unused */ int LZ4_compress_fast_force(const char* source, char* dest, int inputSize, int maxOutputSize, int acceleration) { LZ4_stream_t ctx; LZ4_resetStream(&ctx); if (inputSize < LZ4_64Klimit) return LZ4_compress_generic(&ctx.internal_donotuse, source, dest, inputSize, maxOutputSize, limitedOutput, byU16, noDict, noDictIssue, acceleration); else return LZ4_compress_generic(&ctx.internal_donotuse, source, dest, inputSize, maxOutputSize, limitedOutput, sizeof(void*)==8 ? byU32 : byPtr, noDict, noDictIssue, acceleration); } /*-****************************** * *_destSize() variant ********************************/ static int LZ4_compress_destSize_generic( LZ4_stream_t_internal* const ctx, const char* const src, char* const dst, int* const srcSizePtr, const int targetDstSize, const tableType_t tableType) { const BYTE* ip = (const BYTE*) src; const BYTE* base = (const BYTE*) src; const BYTE* lowLimit = (const BYTE*) src; const BYTE* anchor = ip; const BYTE* const iend = ip + *srcSizePtr; const BYTE* const mflimit = iend - MFLIMIT; const BYTE* const matchlimit = iend - LASTLITERALS; BYTE* op = (BYTE*) dst; BYTE* const oend = op + targetDstSize; BYTE* const oMaxLit = op + targetDstSize - 2 /* offset */ - 8 /* because 8+MINMATCH==MFLIMIT */ - 1 /* token */; BYTE* const oMaxMatch = op + targetDstSize - (LASTLITERALS + 1 /* token */); BYTE* const oMaxSeq = oMaxLit - 1 /* token */; U32 forwardH; /* Init conditions */ if (targetDstSize < 1) return 0; /* Impossible to store anything */ if ((U32)*srcSizePtr > (U32)LZ4_MAX_INPUT_SIZE) return 0; /* Unsupported input size, too large (or negative) */ if ((tableType == byU16) && (*srcSizePtr>=LZ4_64Klimit)) return 0; /* Size too large (not within 64K limit) */ if (*srcSizePtrhashTable, tableType, base); ip++; forwardH = LZ4_hashPosition(ip, tableType); /* Main Loop */ for ( ; ; ) { const BYTE* match; BYTE* token; /* Find a match */ { const BYTE* forwardIp = ip; unsigned step = 1; unsigned searchMatchNb = 1 << LZ4_skipTrigger; do { U32 h = forwardH; ip = forwardIp; forwardIp += step; step = (searchMatchNb++ >> LZ4_skipTrigger); if (unlikely(forwardIp > mflimit)) goto _last_literals; match = LZ4_getPositionOnHash(h, ctx->hashTable, tableType, base); forwardH = LZ4_hashPosition(forwardIp, tableType); LZ4_putPositionOnHash(ip, h, ctx->hashTable, tableType, base); } while ( ((tableType==byU16) ? 0 : (match + MAX_DISTANCE < ip)) || (LZ4_read32(match) != LZ4_read32(ip)) ); } /* Catch up */ while ((ip>anchor) && (match > lowLimit) && (unlikely(ip[-1]==match[-1]))) { ip--; match--; } /* Encode Literal length */ { unsigned litLength = (unsigned)(ip - anchor); token = op++; if (op + ((litLength+240)/255) + litLength > oMaxLit) { /* Not enough space for a last match */ op--; goto _last_literals; } if (litLength>=RUN_MASK) { unsigned len = litLength - RUN_MASK; *token=(RUN_MASK<= 255 ; len-=255) *op++ = 255; *op++ = (BYTE)len; } else *token = (BYTE)(litLength< oMaxMatch) { /* Match description too long : reduce it */ matchLength = (15-1) + (oMaxMatch-op) * 255; } ip += MINMATCH + matchLength; if (matchLength>=ML_MASK) { *token += ML_MASK; matchLength -= ML_MASK; while (matchLength >= 255) { matchLength-=255; *op++ = 255; } *op++ = (BYTE)matchLength; } else *token += (BYTE)(matchLength); } anchor = ip; /* Test end of block */ if (ip > mflimit) break; if (op > oMaxSeq) break; /* Fill table */ LZ4_putPosition(ip-2, ctx->hashTable, tableType, base); /* Test next position */ match = LZ4_getPosition(ip, ctx->hashTable, tableType, base); LZ4_putPosition(ip, ctx->hashTable, tableType, base); if ( (match+MAX_DISTANCE>=ip) && (LZ4_read32(match)==LZ4_read32(ip)) ) { token=op++; *token=0; goto _next_match; } /* Prepare next loop */ forwardH = LZ4_hashPosition(++ip, tableType); } _last_literals: /* Encode Last Literals */ { size_t lastRunSize = (size_t)(iend - anchor); if (op + 1 /* token */ + ((lastRunSize+240)/255) /* litLength */ + lastRunSize /* literals */ > oend) { /* adapt lastRunSize to fill 'dst' */ lastRunSize = (oend-op) - 1; lastRunSize -= (lastRunSize+240)/255; } ip = anchor + lastRunSize; if (lastRunSize >= RUN_MASK) { size_t accumulator = lastRunSize - RUN_MASK; *op++ = RUN_MASK << ML_BITS; for(; accumulator >= 255 ; accumulator-=255) *op++ = 255; *op++ = (BYTE) accumulator; } else { *op++ = (BYTE)(lastRunSize<= LZ4_compressBound(*srcSizePtr)) { /* compression success is guaranteed */ return LZ4_compress_fast_extState(state, src, dst, *srcSizePtr, targetDstSize, 1); } else { if (*srcSizePtr < LZ4_64Klimit) return LZ4_compress_destSize_generic(&state->internal_donotuse, src, dst, srcSizePtr, targetDstSize, byU16); else return LZ4_compress_destSize_generic(&state->internal_donotuse, src, dst, srcSizePtr, targetDstSize, sizeof(void*)==8 ? byU32 : byPtr); } } int LZ4_compress_destSize(const char* src, char* dst, int* srcSizePtr, int targetDstSize) { #if (LZ4_HEAPMODE) LZ4_stream_t* ctx = (LZ4_stream_t*)ALLOCATOR(1, sizeof(LZ4_stream_t)); /* malloc-calloc always properly aligned */ #else LZ4_stream_t ctxBody; LZ4_stream_t* ctx = &ctxBody; #endif int result = LZ4_compress_destSize_extState(ctx, src, dst, srcSizePtr, targetDstSize); #if (LZ4_HEAPMODE) FREEMEM(ctx); #endif return result; } /*-****************************** * Streaming functions ********************************/ LZ4_stream_t* LZ4_createStream(void) { LZ4_stream_t* lz4s = (LZ4_stream_t*)ALLOCATOR(8, LZ4_STREAMSIZE_U64); LZ4_STATIC_ASSERT(LZ4_STREAMSIZE >= sizeof(LZ4_stream_t_internal)); /* A compilation error here means LZ4_STREAMSIZE is not large enough */ LZ4_resetStream(lz4s); return lz4s; } void LZ4_resetStream (LZ4_stream_t* LZ4_stream) { MEM_INIT(LZ4_stream, 0, sizeof(LZ4_stream_t)); } int LZ4_freeStream (LZ4_stream_t* LZ4_stream) { if (!LZ4_stream) return 0; /* support free on NULL */ FREEMEM(LZ4_stream); return (0); } #define HASH_UNIT sizeof(reg_t) int LZ4_loadDict (LZ4_stream_t* LZ4_dict, const char* dictionary, int dictSize) { LZ4_stream_t_internal* dict = &LZ4_dict->internal_donotuse; const BYTE* p = (const BYTE*)dictionary; const BYTE* const dictEnd = p + dictSize; const BYTE* base; if ((dict->initCheck) || (dict->currentOffset > 1 GB)) /* Uninitialized structure, or reuse overflow */ LZ4_resetStream(LZ4_dict); if (dictSize < (int)HASH_UNIT) { dict->dictionary = NULL; dict->dictSize = 0; return 0; } if ((dictEnd - p) > 64 KB) p = dictEnd - 64 KB; dict->currentOffset += 64 KB; base = p - dict->currentOffset; dict->dictionary = p; dict->dictSize = (U32)(dictEnd - p); dict->currentOffset += dict->dictSize; while (p <= dictEnd-HASH_UNIT) { LZ4_putPosition(p, dict->hashTable, byU32, base); p+=3; } return dict->dictSize; } static void LZ4_renormDictT(LZ4_stream_t_internal* LZ4_dict, const BYTE* src) { if ((LZ4_dict->currentOffset > 0x80000000) || ((uptrval)LZ4_dict->currentOffset > (uptrval)src)) { /* address space overflow */ /* rescale hash table */ U32 const delta = LZ4_dict->currentOffset - 64 KB; const BYTE* dictEnd = LZ4_dict->dictionary + LZ4_dict->dictSize; int i; for (i=0; ihashTable[i] < delta) LZ4_dict->hashTable[i]=0; else LZ4_dict->hashTable[i] -= delta; } LZ4_dict->currentOffset = 64 KB; if (LZ4_dict->dictSize > 64 KB) LZ4_dict->dictSize = 64 KB; LZ4_dict->dictionary = dictEnd - LZ4_dict->dictSize; } } int LZ4_compress_fast_continue (LZ4_stream_t* LZ4_stream, const char* source, char* dest, int inputSize, int maxOutputSize, int acceleration) { LZ4_stream_t_internal* streamPtr = &LZ4_stream->internal_donotuse; const BYTE* const dictEnd = streamPtr->dictionary + streamPtr->dictSize; const BYTE* smallest = (const BYTE*) source; if (streamPtr->initCheck) return 0; /* Uninitialized structure detected */ if ((streamPtr->dictSize>0) && (smallest>dictEnd)) smallest = dictEnd; LZ4_renormDictT(streamPtr, smallest); if (acceleration < 1) acceleration = ACCELERATION_DEFAULT; /* Check overlapping input/dictionary space */ { const BYTE* sourceEnd = (const BYTE*) source + inputSize; if ((sourceEnd > streamPtr->dictionary) && (sourceEnd < dictEnd)) { streamPtr->dictSize = (U32)(dictEnd - sourceEnd); if (streamPtr->dictSize > 64 KB) streamPtr->dictSize = 64 KB; if (streamPtr->dictSize < 4) streamPtr->dictSize = 0; streamPtr->dictionary = dictEnd - streamPtr->dictSize; } } /* prefix mode : source data follows dictionary */ if (dictEnd == (const BYTE*)source) { int result; if ((streamPtr->dictSize < 64 KB) && (streamPtr->dictSize < streamPtr->currentOffset)) result = LZ4_compress_generic(streamPtr, source, dest, inputSize, maxOutputSize, limitedOutput, byU32, withPrefix64k, dictSmall, acceleration); else result = LZ4_compress_generic(streamPtr, source, dest, inputSize, maxOutputSize, limitedOutput, byU32, withPrefix64k, noDictIssue, acceleration); streamPtr->dictSize += (U32)inputSize; streamPtr->currentOffset += (U32)inputSize; return result; } /* external dictionary mode */ { int result; if ((streamPtr->dictSize < 64 KB) && (streamPtr->dictSize < streamPtr->currentOffset)) result = LZ4_compress_generic(streamPtr, source, dest, inputSize, maxOutputSize, limitedOutput, byU32, usingExtDict, dictSmall, acceleration); else result = LZ4_compress_generic(streamPtr, source, dest, inputSize, maxOutputSize, limitedOutput, byU32, usingExtDict, noDictIssue, acceleration); streamPtr->dictionary = (const BYTE*)source; streamPtr->dictSize = (U32)inputSize; streamPtr->currentOffset += (U32)inputSize; return result; } } /* Hidden debug function, to force external dictionary mode */ int LZ4_compress_forceExtDict (LZ4_stream_t* LZ4_dict, const char* source, char* dest, int inputSize) { LZ4_stream_t_internal* streamPtr = &LZ4_dict->internal_donotuse; int result; const BYTE* const dictEnd = streamPtr->dictionary + streamPtr->dictSize; const BYTE* smallest = dictEnd; if (smallest > (const BYTE*) source) smallest = (const BYTE*) source; LZ4_renormDictT(streamPtr, smallest); result = LZ4_compress_generic(streamPtr, source, dest, inputSize, 0, notLimited, byU32, usingExtDict, noDictIssue, 1); streamPtr->dictionary = (const BYTE*)source; streamPtr->dictSize = (U32)inputSize; streamPtr->currentOffset += (U32)inputSize; return result; } /*! LZ4_saveDict() : * If previously compressed data block is not guaranteed to remain available at its memory location, * save it into a safer place (char* safeBuffer). * Note : you don't need to call LZ4_loadDict() afterwards, * dictionary is immediately usable, you can therefore call LZ4_compress_fast_continue(). * Return : saved dictionary size in bytes (necessarily <= dictSize), or 0 if error. */ int LZ4_saveDict (LZ4_stream_t* LZ4_dict, char* safeBuffer, int dictSize) { LZ4_stream_t_internal* const dict = &LZ4_dict->internal_donotuse; const BYTE* const previousDictEnd = dict->dictionary + dict->dictSize; if ((U32)dictSize > 64 KB) dictSize = 64 KB; /* useless to define a dictionary > 64 KB */ if ((U32)dictSize > dict->dictSize) dictSize = dict->dictSize; memmove(safeBuffer, previousDictEnd - dictSize, dictSize); dict->dictionary = (const BYTE*)safeBuffer; dict->dictSize = (U32)dictSize; return dictSize; } /*-***************************** * Decompression functions *******************************/ /*! LZ4_decompress_generic() : * This generic decompression function cover all use cases. * It shall be instantiated several times, using different sets of directives * Note that it is important this generic function is really inlined, * in order to remove useless branches during compilation optimization. */ FORCE_INLINE int LZ4_decompress_generic( const char* const source, char* const dest, int inputSize, int outputSize, /* If endOnInput==endOnInputSize, this value is the max size of Output Buffer. */ int endOnInput, /* endOnOutputSize, endOnInputSize */ int partialDecoding, /* full, partial */ int targetOutputSize, /* only used if partialDecoding==partial */ int dict, /* noDict, withPrefix64k, usingExtDict */ const BYTE* const lowPrefix, /* == dest when no prefix */ const BYTE* const dictStart, /* only if dict==usingExtDict */ const size_t dictSize /* note : = 0 if noDict */ ) { /* Local Variables */ const BYTE* ip = (const BYTE*) source; const BYTE* const iend = ip + inputSize; BYTE* op = (BYTE*) dest; BYTE* const oend = op + outputSize; BYTE* cpy; BYTE* oexit = op + targetOutputSize; const BYTE* const lowLimit = lowPrefix - dictSize; const BYTE* const dictEnd = (const BYTE*)dictStart + dictSize; const unsigned dec32table[] = {0, 1, 2, 1, 4, 4, 4, 4}; const int dec64table[] = {0, 0, 0, -1, 0, 1, 2, 3}; const int safeDecode = (endOnInput==endOnInputSize); const int checkOffset = ((safeDecode) && (dictSize < (int)(64 KB))); /* Special cases */ if ((partialDecoding) && (oexit > oend-MFLIMIT)) oexit = oend-MFLIMIT; /* targetOutputSize too high => decode everything */ if ((endOnInput) && (unlikely(outputSize==0))) return ((inputSize==1) && (*ip==0)) ? 0 : -1; /* Empty output buffer */ if ((!endOnInput) && (unlikely(outputSize==0))) return (*ip==0?1:-1); /* Main Loop : decode sequences */ while (1) { size_t length; const BYTE* match; size_t offset; /* get literal length */ unsigned const token = *ip++; if ((length=(token>>ML_BITS)) == RUN_MASK) { unsigned s; do { s = *ip++; length += s; } while ( likely(endOnInput ? ip(partialDecoding?oexit:oend-MFLIMIT)) || (ip+length>iend-(2+1+LASTLITERALS))) ) || ((!endOnInput) && (cpy>oend-WILDCOPYLENGTH)) ) { if (partialDecoding) { if (cpy > oend) goto _output_error; /* Error : write attempt beyond end of output buffer */ if ((endOnInput) && (ip+length > iend)) goto _output_error; /* Error : read attempt beyond end of input buffer */ } else { if ((!endOnInput) && (cpy != oend)) goto _output_error; /* Error : block decoding must stop exactly there */ if ((endOnInput) && ((ip+length != iend) || (cpy > oend))) goto _output_error; /* Error : input must be consumed */ } memcpy(op, ip, length); ip += length; op += length; break; /* Necessarily EOF, due to parsing restrictions */ } LZ4_wildCopy(op, ip, cpy); ip += length; op = cpy; /* get offset */ offset = LZ4_readLE16(ip); ip+=2; match = op - offset; if ((checkOffset) && (unlikely(match < lowLimit))) goto _output_error; /* Error : offset outside buffers */ LZ4_write32(op, (U32)offset); /* costs ~1%; silence an msan warning when offset==0 */ /* get matchlength */ length = token & ML_MASK; if (length == ML_MASK) { unsigned s; do { s = *ip++; if ((endOnInput) && (ip > iend-LASTLITERALS)) goto _output_error; length += s; } while (s==255); if ((safeDecode) && unlikely((uptrval)(op)+length<(uptrval)op)) goto _output_error; /* overflow detection */ } length += MINMATCH; /* check external dictionary */ if ((dict==usingExtDict) && (match < lowPrefix)) { if (unlikely(op+length > oend-LASTLITERALS)) goto _output_error; /* doesn't respect parsing restriction */ if (length <= (size_t)(lowPrefix-match)) { /* match can be copied as a single segment from external dictionary */ memmove(op, dictEnd - (lowPrefix-match), length); op += length; } else { /* match encompass external dictionary and current block */ size_t const copySize = (size_t)(lowPrefix-match); size_t const restSize = length - copySize; memcpy(op, dictEnd - copySize, copySize); op += copySize; if (restSize > (size_t)(op-lowPrefix)) { /* overlap copy */ BYTE* const endOfMatch = op + restSize; const BYTE* copyFrom = lowPrefix; while (op < endOfMatch) *op++ = *copyFrom++; } else { memcpy(op, lowPrefix, restSize); op += restSize; } } continue; } /* copy match within block */ cpy = op + length; if (unlikely(offset<8)) { const int dec64 = dec64table[offset]; op[0] = match[0]; op[1] = match[1]; op[2] = match[2]; op[3] = match[3]; match += dec32table[offset]; memcpy(op+4, match, 4); match -= dec64; } else { LZ4_copy8(op, match); match+=8; } op += 8; if (unlikely(cpy>oend-12)) { BYTE* const oCopyLimit = oend-(WILDCOPYLENGTH-1); if (cpy > oend-LASTLITERALS) goto _output_error; /* Error : last LASTLITERALS bytes must be literals (uncompressed) */ if (op < oCopyLimit) { LZ4_wildCopy(op, match, oCopyLimit); match += oCopyLimit - op; op = oCopyLimit; } while (op16) LZ4_wildCopy(op+8, match+8, cpy); } op=cpy; /* correction */ } /* end of decoding */ if (endOnInput) return (int) (((char*)op)-dest); /* Nb of output bytes decoded */ else return (int) (((const char*)ip)-source); /* Nb of input bytes read */ /* Overflow error detected */ _output_error: return (int) (-(((const char*)ip)-source))-1; } int LZ4_decompress_safe(const char* source, char* dest, int compressedSize, int maxDecompressedSize) { return LZ4_decompress_generic(source, dest, compressedSize, maxDecompressedSize, endOnInputSize, full, 0, noDict, (BYTE*)dest, NULL, 0); } int LZ4_decompress_safe_partial(const char* source, char* dest, int compressedSize, int targetOutputSize, int maxDecompressedSize) { return LZ4_decompress_generic(source, dest, compressedSize, maxDecompressedSize, endOnInputSize, partial, targetOutputSize, noDict, (BYTE*)dest, NULL, 0); } int LZ4_decompress_fast(const char* source, char* dest, int originalSize) { return LZ4_decompress_generic(source, dest, 0, originalSize, endOnOutputSize, full, 0, withPrefix64k, (BYTE*)(dest - 64 KB), NULL, 64 KB); } /*===== streaming decompression functions =====*/ LZ4_streamDecode_t* LZ4_createStreamDecode(void) { LZ4_streamDecode_t* lz4s = (LZ4_streamDecode_t*) ALLOCATOR(1, sizeof(LZ4_streamDecode_t)); return lz4s; } int LZ4_freeStreamDecode (LZ4_streamDecode_t* LZ4_stream) { if (!LZ4_stream) return 0; /* support free on NULL */ FREEMEM(LZ4_stream); return 0; } /*! * LZ4_setStreamDecode() : * Use this function to instruct where to find the dictionary. * This function is not necessary if previous data is still available where it was decoded. * Loading a size of 0 is allowed (same effect as no dictionary). * Return : 1 if OK, 0 if error */ int LZ4_setStreamDecode (LZ4_streamDecode_t* LZ4_streamDecode, const char* dictionary, int dictSize) { LZ4_streamDecode_t_internal* lz4sd = &LZ4_streamDecode->internal_donotuse; lz4sd->prefixSize = (size_t) dictSize; lz4sd->prefixEnd = (const BYTE*) dictionary + dictSize; lz4sd->externalDict = NULL; lz4sd->extDictSize = 0; return 1; } /* *_continue() : These decoding functions allow decompression of multiple blocks in "streaming" mode. Previously decoded blocks must still be available at the memory position where they were decoded. If it's not possible, save the relevant part of decoded data into a safe buffer, and indicate where it stands using LZ4_setStreamDecode() */ int LZ4_decompress_safe_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* source, char* dest, int compressedSize, int maxOutputSize) { LZ4_streamDecode_t_internal* lz4sd = &LZ4_streamDecode->internal_donotuse; int result; if (lz4sd->prefixEnd == (BYTE*)dest) { result = LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, endOnInputSize, full, 0, usingExtDict, lz4sd->prefixEnd - lz4sd->prefixSize, lz4sd->externalDict, lz4sd->extDictSize); if (result <= 0) return result; lz4sd->prefixSize += result; lz4sd->prefixEnd += result; } else { lz4sd->extDictSize = lz4sd->prefixSize; lz4sd->externalDict = lz4sd->prefixEnd - lz4sd->extDictSize; result = LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, endOnInputSize, full, 0, usingExtDict, (BYTE*)dest, lz4sd->externalDict, lz4sd->extDictSize); if (result <= 0) return result; lz4sd->prefixSize = result; lz4sd->prefixEnd = (BYTE*)dest + result; } return result; } int LZ4_decompress_fast_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* source, char* dest, int originalSize) { LZ4_streamDecode_t_internal* lz4sd = &LZ4_streamDecode->internal_donotuse; int result; if (lz4sd->prefixEnd == (BYTE*)dest) { result = LZ4_decompress_generic(source, dest, 0, originalSize, endOnOutputSize, full, 0, usingExtDict, lz4sd->prefixEnd - lz4sd->prefixSize, lz4sd->externalDict, lz4sd->extDictSize); if (result <= 0) return result; lz4sd->prefixSize += originalSize; lz4sd->prefixEnd += originalSize; } else { lz4sd->extDictSize = lz4sd->prefixSize; lz4sd->externalDict = lz4sd->prefixEnd - lz4sd->extDictSize; result = LZ4_decompress_generic(source, dest, 0, originalSize, endOnOutputSize, full, 0, usingExtDict, (BYTE*)dest, lz4sd->externalDict, lz4sd->extDictSize); if (result <= 0) return result; lz4sd->prefixSize = originalSize; lz4sd->prefixEnd = (BYTE*)dest + originalSize; } return result; } /* Advanced decoding functions : *_usingDict() : These decoding functions work the same as "_continue" ones, the dictionary must be explicitly provided within parameters */ FORCE_INLINE int LZ4_decompress_usingDict_generic(const char* source, char* dest, int compressedSize, int maxOutputSize, int safe, const char* dictStart, int dictSize) { if (dictSize==0) return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, noDict, (BYTE*)dest, NULL, 0); if (dictStart+dictSize == dest) { if (dictSize >= (int)(64 KB - 1)) return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, withPrefix64k, (BYTE*)dest-64 KB, NULL, 0); return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, noDict, (BYTE*)dest-dictSize, NULL, 0); } return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, usingExtDict, (BYTE*)dest, (const BYTE*)dictStart, dictSize); } int LZ4_decompress_safe_usingDict(const char* source, char* dest, int compressedSize, int maxOutputSize, const char* dictStart, int dictSize) { return LZ4_decompress_usingDict_generic(source, dest, compressedSize, maxOutputSize, 1, dictStart, dictSize); } int LZ4_decompress_fast_usingDict(const char* source, char* dest, int originalSize, const char* dictStart, int dictSize) { return LZ4_decompress_usingDict_generic(source, dest, 0, originalSize, 0, dictStart, dictSize); } /* debug function */ int LZ4_decompress_safe_forceExtDict(const char* source, char* dest, int compressedSize, int maxOutputSize, const char* dictStart, int dictSize) { return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, endOnInputSize, full, 0, usingExtDict, (BYTE*)dest, (const BYTE*)dictStart, dictSize); } /*=************************************************* * Obsolete Functions ***************************************************/ /* obsolete compression functions */ int LZ4_compress_limitedOutput(const char* source, char* dest, int inputSize, int maxOutputSize) { return LZ4_compress_default(source, dest, inputSize, maxOutputSize); } int LZ4_compress(const char* source, char* dest, int inputSize) { return LZ4_compress_default(source, dest, inputSize, LZ4_compressBound(inputSize)); } int LZ4_compress_limitedOutput_withState (void* state, const char* src, char* dst, int srcSize, int dstSize) { return LZ4_compress_fast_extState(state, src, dst, srcSize, dstSize, 1); } int LZ4_compress_withState (void* state, const char* src, char* dst, int srcSize) { return LZ4_compress_fast_extState(state, src, dst, srcSize, LZ4_compressBound(srcSize), 1); } int LZ4_compress_limitedOutput_continue (LZ4_stream_t* LZ4_stream, const char* src, char* dst, int srcSize, int maxDstSize) { return LZ4_compress_fast_continue(LZ4_stream, src, dst, srcSize, maxDstSize, 1); } int LZ4_compress_continue (LZ4_stream_t* LZ4_stream, const char* source, char* dest, int inputSize) { return LZ4_compress_fast_continue(LZ4_stream, source, dest, inputSize, LZ4_compressBound(inputSize), 1); } /* These function names are deprecated and should no longer be used. They are only provided here for compatibility with older user programs. - LZ4_uncompress is totally equivalent to LZ4_decompress_fast - LZ4_uncompress_unknownOutputSize is totally equivalent to LZ4_decompress_safe */ int LZ4_uncompress (const char* source, char* dest, int outputSize) { return LZ4_decompress_fast(source, dest, outputSize); } int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize) { return LZ4_decompress_safe(source, dest, isize, maxOutputSize); } /* Obsolete Streaming functions */ int LZ4_sizeofStreamState(void) { return LZ4_STREAMSIZE; } static void LZ4_init(LZ4_stream_t* lz4ds, BYTE* base) { MEM_INIT(lz4ds, 0, sizeof(LZ4_stream_t)); lz4ds->internal_donotuse.bufferStart = base; } int LZ4_resetStreamState(void* state, char* inputBuffer) { if ((((uptrval)state) & 3) != 0) return 1; /* Error : pointer is not aligned on 4-bytes boundary */ LZ4_init((LZ4_stream_t*)state, (BYTE*)inputBuffer); return 0; } void* LZ4_create (char* inputBuffer) { LZ4_stream_t* lz4ds = (LZ4_stream_t*)ALLOCATOR(8, sizeof(LZ4_stream_t)); LZ4_init (lz4ds, (BYTE*)inputBuffer); return lz4ds; } char* LZ4_slideInputBuffer (void* LZ4_Data) { LZ4_stream_t_internal* ctx = &((LZ4_stream_t*)LZ4_Data)->internal_donotuse; int dictSize = LZ4_saveDict((LZ4_stream_t*)LZ4_Data, (char*)ctx->bufferStart, 64 KB); return (char*)(ctx->bufferStart + dictSize); } /* Obsolete streaming decompression functions */ int LZ4_decompress_safe_withPrefix64k(const char* source, char* dest, int compressedSize, int maxOutputSize) { return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, endOnInputSize, full, 0, withPrefix64k, (BYTE*)dest - 64 KB, NULL, 64 KB); } int LZ4_decompress_fast_withPrefix64k(const char* source, char* dest, int originalSize) { return LZ4_decompress_generic(source, dest, 0, originalSize, endOnOutputSize, full, 0, withPrefix64k, (BYTE*)dest - 64 KB, NULL, 64 KB); } #endif /* LZ4_COMMONDEFS_ONLY */ pysam-0.23.0/samtools/lz4/lz4.c.pysam.c000066400000000000000000001617071475062545500175560ustar00rootroot00000000000000#include "samtools.pysam.h" /* LZ4 - Fast LZ compression algorithm Copyright (C) 2011-2017, Yann Collet. BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php) Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. You can contact the author at : - LZ4 homepage : http://www.lz4.org - LZ4 source repository : https://github.com/lz4/lz4 */ /*-************************************ * Tuning parameters **************************************/ /* * LZ4_HEAPMODE : * Select how default compression functions will allocate memory for their hash table, * in memory stack (0:default, fastest), or in memory heap (1:requires malloc()). */ #ifndef LZ4_HEAPMODE # define LZ4_HEAPMODE 0 #endif /* * ACCELERATION_DEFAULT : * Select "acceleration" for LZ4_compress_fast() when parameter value <= 0 */ #define ACCELERATION_DEFAULT 1 /*-************************************ * CPU Feature Detection **************************************/ /* LZ4_FORCE_MEMORY_ACCESS * By default, access to unaligned memory is controlled by `memcpy()`, which is safe and portable. * Unfortunately, on some target/compiler combinations, the generated assembly is sub-optimal. * The below switch allow to select different access method for improved performance. * Method 0 (default) : use `memcpy()`. Safe and portable. * Method 1 : `__packed` statement. It depends on compiler extension (ie, not portable). * This method is safe if your compiler supports it, and *generally* as fast or faster than `memcpy`. * Method 2 : direct access. This method is portable but violate C standard. * It can generate buggy code on targets which assembly generation depends on alignment. * But in some circumstances, it's the only known way to get the most performance (ie GCC + ARMv6) * See https://fastcompression.blogspot.fr/2015/08/accessing-unaligned-memory.html for details. * Prefer these methods in priority order (0 > 1 > 2) */ #ifndef LZ4_FORCE_MEMORY_ACCESS /* can be defined externally */ # if defined(__GNUC__) && ( defined(__ARM_ARCH_6__) || defined(__ARM_ARCH_6J__) || defined(__ARM_ARCH_6K__) || defined(__ARM_ARCH_6Z__) || defined(__ARM_ARCH_6ZK__) || defined(__ARM_ARCH_6T2__) ) # define LZ4_FORCE_MEMORY_ACCESS 2 # elif defined(__INTEL_COMPILER) || defined(__GNUC__) # define LZ4_FORCE_MEMORY_ACCESS 1 # endif #endif /* * LZ4_FORCE_SW_BITCOUNT * Define this parameter if your target system or compiler does not support hardware bit count */ #if defined(_MSC_VER) && defined(_WIN32_WCE) /* Visual Studio for Windows CE does not support Hardware bit count */ # define LZ4_FORCE_SW_BITCOUNT #endif /*-************************************ * Dependency **************************************/ #include "lz4.h" /* see also "memory routines" below */ /*-************************************ * Compiler Options **************************************/ #ifdef _MSC_VER /* Visual Studio */ # include # pragma warning(disable : 4127) /* disable: C4127: conditional expression is constant */ # pragma warning(disable : 4293) /* disable: C4293: too large shift (32-bits) */ #endif /* _MSC_VER */ #ifndef FORCE_INLINE # ifdef _MSC_VER /* Visual Studio */ # define FORCE_INLINE static __forceinline # else # if defined (__cplusplus) || defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L /* C99 */ # ifdef __GNUC__ # define FORCE_INLINE static inline __attribute__((always_inline)) # else # define FORCE_INLINE static inline # endif # else # define FORCE_INLINE static # endif /* __STDC_VERSION__ */ # endif /* _MSC_VER */ #endif /* FORCE_INLINE */ #if (defined(__GNUC__) && (__GNUC__ >= 3)) || (defined(__INTEL_COMPILER) && (__INTEL_COMPILER >= 800)) || defined(__clang__) # define expect(expr,value) (__builtin_expect ((expr),(value)) ) #else # define expect(expr,value) (expr) #endif #define likely(expr) expect((expr) != 0, 1) #define unlikely(expr) expect((expr) != 0, 0) /*-************************************ * Memory routines **************************************/ #include /* malloc, calloc, free */ #define ALLOCATOR(n,s) calloc(n,s) #define FREEMEM free #include /* memset, memcpy */ #define MEM_INIT memset /*-************************************ * Basic Types **************************************/ #if defined(__cplusplus) || (defined (__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) /* C99 */) # include typedef uint8_t BYTE; typedef uint16_t U16; typedef uint32_t U32; typedef int32_t S32; typedef uint64_t U64; typedef uintptr_t uptrval; #else typedef unsigned char BYTE; typedef unsigned short U16; typedef unsigned int U32; typedef signed int S32; typedef unsigned long long U64; typedef size_t uptrval; /* generally true, except OpenVMS-64 */ #endif #if defined(__x86_64__) typedef U64 reg_t; /* 64-bits in x32 mode */ #else typedef size_t reg_t; /* 32-bits in x32 mode */ #endif /*-************************************ * Reading and writing into memory **************************************/ static unsigned LZ4_isLittleEndian(void) { const union { U32 u; BYTE c[4]; } one = { 1 }; /* don't use static : performance detrimental */ return one.c[0]; } #if defined(LZ4_FORCE_MEMORY_ACCESS) && (LZ4_FORCE_MEMORY_ACCESS==2) /* lie to the compiler about data alignment; use with caution */ static U16 LZ4_read16(const void* memPtr) { return *(const U16*) memPtr; } static U32 LZ4_read32(const void* memPtr) { return *(const U32*) memPtr; } static reg_t LZ4_read_ARCH(const void* memPtr) { return *(const reg_t*) memPtr; } static void LZ4_write16(void* memPtr, U16 value) { *(U16*)memPtr = value; } static void LZ4_write32(void* memPtr, U32 value) { *(U32*)memPtr = value; } #elif defined(LZ4_FORCE_MEMORY_ACCESS) && (LZ4_FORCE_MEMORY_ACCESS==1) /* __pack instructions are safer, but compiler specific, hence potentially problematic for some compilers */ /* currently only defined for gcc and icc */ typedef union { U16 u16; U32 u32; reg_t uArch; } __attribute__((packed)) unalign; static U16 LZ4_read16(const void* ptr) { return ((const unalign*)ptr)->u16; } static U32 LZ4_read32(const void* ptr) { return ((const unalign*)ptr)->u32; } static reg_t LZ4_read_ARCH(const void* ptr) { return ((const unalign*)ptr)->uArch; } static void LZ4_write16(void* memPtr, U16 value) { ((unalign*)memPtr)->u16 = value; } static void LZ4_write32(void* memPtr, U32 value) { ((unalign*)memPtr)->u32 = value; } #else /* safe and portable access through memcpy() */ static U16 LZ4_read16(const void* memPtr) { U16 val; memcpy(&val, memPtr, sizeof(val)); return val; } static U32 LZ4_read32(const void* memPtr) { U32 val; memcpy(&val, memPtr, sizeof(val)); return val; } static reg_t LZ4_read_ARCH(const void* memPtr) { reg_t val; memcpy(&val, memPtr, sizeof(val)); return val; } static void LZ4_write16(void* memPtr, U16 value) { memcpy(memPtr, &value, sizeof(value)); } static void LZ4_write32(void* memPtr, U32 value) { memcpy(memPtr, &value, sizeof(value)); } #endif /* LZ4_FORCE_MEMORY_ACCESS */ static U16 LZ4_readLE16(const void* memPtr) { if (LZ4_isLittleEndian()) { return LZ4_read16(memPtr); } else { const BYTE* p = (const BYTE*)memPtr; return (U16)((U16)p[0] + (p[1]<<8)); } } static void LZ4_writeLE16(void* memPtr, U16 value) { if (LZ4_isLittleEndian()) { LZ4_write16(memPtr, value); } else { BYTE* p = (BYTE*)memPtr; p[0] = (BYTE) value; p[1] = (BYTE)(value>>8); } } static void LZ4_copy8(void* dst, const void* src) { memcpy(dst,src,8); } /* customized variant of memcpy, which can overwrite up to 8 bytes beyond dstEnd */ static void LZ4_wildCopy(void* dstPtr, const void* srcPtr, void* dstEnd) { BYTE* d = (BYTE*)dstPtr; const BYTE* s = (const BYTE*)srcPtr; BYTE* const e = (BYTE*)dstEnd; do { LZ4_copy8(d,s); d+=8; s+=8; } while (d=2) # include # define DEBUGLOG(l, ...) { \ if (l<=LZ4_DEBUG) { \ fprintf(samtools_stderr, __FILE__ ": "); \ fprintf(samtools_stderr, __VA_ARGS__); \ fprintf(samtools_stderr, " \n"); \ } } #else # define DEBUGLOG(l, ...) {} /* disabled */ #endif /*-************************************ * Common functions **************************************/ static unsigned LZ4_NbCommonBytes (register reg_t val) { if (LZ4_isLittleEndian()) { if (sizeof(val)==8) { # if defined(_MSC_VER) && defined(_WIN64) && !defined(LZ4_FORCE_SW_BITCOUNT) unsigned long r = 0; _BitScanForward64( &r, (U64)val ); return (int)(r>>3); # elif (defined(__clang__) || (defined(__GNUC__) && (__GNUC__>=3))) && !defined(LZ4_FORCE_SW_BITCOUNT) return (__builtin_ctzll((U64)val) >> 3); # else static const int DeBruijnBytePos[64] = { 0, 0, 0, 0, 0, 1, 1, 2, 0, 3, 1, 3, 1, 4, 2, 7, 0, 2, 3, 6, 1, 5, 3, 5, 1, 3, 4, 4, 2, 5, 6, 7, 7, 0, 1, 2, 3, 3, 4, 6, 2, 6, 5, 5, 3, 4, 5, 6, 7, 1, 2, 4, 6, 4, 4, 5, 7, 2, 6, 5, 7, 6, 7, 7 }; return DeBruijnBytePos[((U64)((val & -(long long)val) * 0x0218A392CDABBD3FULL)) >> 58]; # endif } else /* 32 bits */ { # if defined(_MSC_VER) && !defined(LZ4_FORCE_SW_BITCOUNT) unsigned long r; _BitScanForward( &r, (U32)val ); return (int)(r>>3); # elif (defined(__clang__) || (defined(__GNUC__) && (__GNUC__>=3))) && !defined(LZ4_FORCE_SW_BITCOUNT) return (__builtin_ctz((U32)val) >> 3); # else static const int DeBruijnBytePos[32] = { 0, 0, 3, 0, 3, 1, 3, 0, 3, 2, 2, 1, 3, 2, 0, 1, 3, 3, 1, 2, 2, 2, 2, 0, 3, 1, 2, 0, 1, 0, 1, 1 }; return DeBruijnBytePos[((U32)((val & -(S32)val) * 0x077CB531U)) >> 27]; # endif } } else /* Big Endian CPU */ { if (sizeof(val)==8) { # if defined(_MSC_VER) && defined(_WIN64) && !defined(LZ4_FORCE_SW_BITCOUNT) unsigned long r = 0; _BitScanReverse64( &r, val ); return (unsigned)(r>>3); # elif (defined(__clang__) || (defined(__GNUC__) && (__GNUC__>=3))) && !defined(LZ4_FORCE_SW_BITCOUNT) return (__builtin_clzll((U64)val) >> 3); # else unsigned r; if (!(val>>32)) { r=4; } else { r=0; val>>=32; } if (!(val>>16)) { r+=2; val>>=8; } else { val>>=24; } r += (!val); return r; # endif } else /* 32 bits */ { # if defined(_MSC_VER) && !defined(LZ4_FORCE_SW_BITCOUNT) unsigned long r = 0; _BitScanReverse( &r, (unsigned long)val ); return (unsigned)(r>>3); # elif (defined(__clang__) || (defined(__GNUC__) && (__GNUC__>=3))) && !defined(LZ4_FORCE_SW_BITCOUNT) return (__builtin_clz((U32)val) >> 3); # else unsigned r; if (!(val>>16)) { r=2; val>>=8; } else { r=0; val>>=24; } r += (!val); return r; # endif } } } #define STEPSIZE sizeof(reg_t) static unsigned LZ4_count(const BYTE* pIn, const BYTE* pMatch, const BYTE* pInLimit) { const BYTE* const pStart = pIn; while (likely(pIn compression run slower on incompressible data */ /*-************************************ * Local Structures and types **************************************/ typedef enum { notLimited = 0, limitedOutput = 1 } limitedOutput_directive; typedef enum { byPtr, byU32, byU16 } tableType_t; typedef enum { noDict = 0, withPrefix64k, usingExtDict } dict_directive; typedef enum { noDictIssue = 0, dictSmall } dictIssue_directive; typedef enum { endOnOutputSize = 0, endOnInputSize = 1 } endCondition_directive; typedef enum { full = 0, partial = 1 } earlyEnd_directive; /*-************************************ * Local Utils **************************************/ int LZ4_versionNumber (void) { return LZ4_VERSION_NUMBER; } const char* LZ4_versionString(void) { return LZ4_VERSION_STRING; } int LZ4_compressBound(int isize) { return LZ4_COMPRESSBOUND(isize); } int LZ4_sizeofState(void) { return LZ4_STREAMSIZE; } /*-****************************** * Compression functions ********************************/ static U32 LZ4_hash4(U32 sequence, tableType_t const tableType) { if (tableType == byU16) return ((sequence * 2654435761U) >> ((MINMATCH*8)-(LZ4_HASHLOG+1))); else return ((sequence * 2654435761U) >> ((MINMATCH*8)-LZ4_HASHLOG)); } static U32 LZ4_hash5(U64 sequence, tableType_t const tableType) { static const U64 prime5bytes = 889523592379ULL; static const U64 prime8bytes = 11400714785074694791ULL; const U32 hashLog = (tableType == byU16) ? LZ4_HASHLOG+1 : LZ4_HASHLOG; if (LZ4_isLittleEndian()) return (U32)(((sequence << 24) * prime5bytes) >> (64 - hashLog)); else return (U32)(((sequence >> 24) * prime8bytes) >> (64 - hashLog)); } FORCE_INLINE U32 LZ4_hashPosition(const void* const p, tableType_t const tableType) { if ((sizeof(reg_t)==8) && (tableType != byU16)) return LZ4_hash5(LZ4_read_ARCH(p), tableType); return LZ4_hash4(LZ4_read32(p), tableType); } static void LZ4_putPositionOnHash(const BYTE* p, U32 h, void* tableBase, tableType_t const tableType, const BYTE* srcBase) { switch (tableType) { case byPtr: { const BYTE** hashTable = (const BYTE**)tableBase; hashTable[h] = p; return; } case byU32: { U32* hashTable = (U32*) tableBase; hashTable[h] = (U32)(p-srcBase); return; } case byU16: { U16* hashTable = (U16*) tableBase; hashTable[h] = (U16)(p-srcBase); return; } } } FORCE_INLINE void LZ4_putPosition(const BYTE* p, void* tableBase, tableType_t tableType, const BYTE* srcBase) { U32 const h = LZ4_hashPosition(p, tableType); LZ4_putPositionOnHash(p, h, tableBase, tableType, srcBase); } static const BYTE* LZ4_getPositionOnHash(U32 h, void* tableBase, tableType_t tableType, const BYTE* srcBase) { if (tableType == byPtr) { const BYTE** hashTable = (const BYTE**) tableBase; return hashTable[h]; } if (tableType == byU32) { const U32* const hashTable = (U32*) tableBase; return hashTable[h] + srcBase; } { const U16* const hashTable = (U16*) tableBase; return hashTable[h] + srcBase; } /* default, to ensure a return */ } FORCE_INLINE const BYTE* LZ4_getPosition(const BYTE* p, void* tableBase, tableType_t tableType, const BYTE* srcBase) { U32 const h = LZ4_hashPosition(p, tableType); return LZ4_getPositionOnHash(h, tableBase, tableType, srcBase); } /** LZ4_compress_generic() : inlined, to ensure branches are decided at compilation time */ FORCE_INLINE int LZ4_compress_generic( LZ4_stream_t_internal* const cctx, const char* const source, char* const dest, const int inputSize, const int maxOutputSize, const limitedOutput_directive outputLimited, const tableType_t tableType, const dict_directive dict, const dictIssue_directive dictIssue, const U32 acceleration) { const BYTE* ip = (const BYTE*) source; const BYTE* base; const BYTE* lowLimit; const BYTE* const lowRefLimit = ip - cctx->dictSize; const BYTE* const dictionary = cctx->dictionary; const BYTE* const dictEnd = dictionary + cctx->dictSize; const ptrdiff_t dictDelta = dictEnd - (const BYTE*)source; const BYTE* anchor = (const BYTE*) source; const BYTE* const iend = ip + inputSize; const BYTE* const mflimit = iend - MFLIMIT; const BYTE* const matchlimit = iend - LASTLITERALS; BYTE* op = (BYTE*) dest; BYTE* const olimit = op + maxOutputSize; U32 forwardH; /* Init conditions */ if ((U32)inputSize > (U32)LZ4_MAX_INPUT_SIZE) return 0; /* Unsupported inputSize, too large (or negative) */ switch(dict) { case noDict: default: base = (const BYTE*)source; lowLimit = (const BYTE*)source; break; case withPrefix64k: base = (const BYTE*)source - cctx->currentOffset; lowLimit = (const BYTE*)source - cctx->dictSize; break; case usingExtDict: base = (const BYTE*)source - cctx->currentOffset; lowLimit = (const BYTE*)source; break; } if ((tableType == byU16) && (inputSize>=LZ4_64Klimit)) return 0; /* Size too large (not within 64K limit) */ if (inputSizehashTable, tableType, base); ip++; forwardH = LZ4_hashPosition(ip, tableType); /* Main Loop */ for ( ; ; ) { ptrdiff_t refDelta = 0; const BYTE* match; BYTE* token; /* Find a match */ { const BYTE* forwardIp = ip; unsigned step = 1; unsigned searchMatchNb = acceleration << LZ4_skipTrigger; do { U32 const h = forwardH; ip = forwardIp; forwardIp += step; step = (searchMatchNb++ >> LZ4_skipTrigger); if (unlikely(forwardIp > mflimit)) goto _last_literals; match = LZ4_getPositionOnHash(h, cctx->hashTable, tableType, base); if (dict==usingExtDict) { if (match < (const BYTE*)source) { refDelta = dictDelta; lowLimit = dictionary; } else { refDelta = 0; lowLimit = (const BYTE*)source; } } forwardH = LZ4_hashPosition(forwardIp, tableType); LZ4_putPositionOnHash(ip, h, cctx->hashTable, tableType, base); } while ( ((dictIssue==dictSmall) ? (match < lowRefLimit) : 0) || ((tableType==byU16) ? 0 : (match + MAX_DISTANCE < ip)) || (LZ4_read32(match+refDelta) != LZ4_read32(ip)) ); } /* Catch up */ while (((ip>anchor) & (match+refDelta > lowLimit)) && (unlikely(ip[-1]==match[refDelta-1]))) { ip--; match--; } /* Encode Literals */ { unsigned const litLength = (unsigned)(ip - anchor); token = op++; if ((outputLimited) && /* Check output buffer overflow */ (unlikely(op + litLength + (2 + 1 + LASTLITERALS) + (litLength/255) > olimit))) return 0; if (litLength >= RUN_MASK) { int len = (int)litLength-RUN_MASK; *token = (RUN_MASK<= 255 ; len-=255) *op++ = 255; *op++ = (BYTE)len; } else *token = (BYTE)(litLength< matchlimit) limit = matchlimit; matchCode = LZ4_count(ip+MINMATCH, match+MINMATCH, limit); ip += MINMATCH + matchCode; if (ip==limit) { unsigned const more = LZ4_count(ip, (const BYTE*)source, matchlimit); matchCode += more; ip += more; } } else { matchCode = LZ4_count(ip+MINMATCH, match+MINMATCH, matchlimit); ip += MINMATCH + matchCode; } if ( outputLimited && /* Check output buffer overflow */ (unlikely(op + (1 + LASTLITERALS) + (matchCode>>8) > olimit)) ) return 0; if (matchCode >= ML_MASK) { *token += ML_MASK; matchCode -= ML_MASK; LZ4_write32(op, 0xFFFFFFFF); while (matchCode >= 4*255) op+=4, LZ4_write32(op, 0xFFFFFFFF), matchCode -= 4*255; op += matchCode / 255; *op++ = (BYTE)(matchCode % 255); } else *token += (BYTE)(matchCode); } anchor = ip; /* Test end of chunk */ if (ip > mflimit) break; /* Fill table */ LZ4_putPosition(ip-2, cctx->hashTable, tableType, base); /* Test next position */ match = LZ4_getPosition(ip, cctx->hashTable, tableType, base); if (dict==usingExtDict) { if (match < (const BYTE*)source) { refDelta = dictDelta; lowLimit = dictionary; } else { refDelta = 0; lowLimit = (const BYTE*)source; } } LZ4_putPosition(ip, cctx->hashTable, tableType, base); if ( ((dictIssue==dictSmall) ? (match>=lowRefLimit) : 1) && (match+MAX_DISTANCE>=ip) && (LZ4_read32(match+refDelta)==LZ4_read32(ip)) ) { token=op++; *token=0; goto _next_match; } /* Prepare next loop */ forwardH = LZ4_hashPosition(++ip, tableType); } _last_literals: /* Encode Last Literals */ { size_t const lastRun = (size_t)(iend - anchor); if ( (outputLimited) && /* Check output buffer overflow */ ((op - (BYTE*)dest) + lastRun + 1 + ((lastRun+255-RUN_MASK)/255) > (U32)maxOutputSize) ) return 0; if (lastRun >= RUN_MASK) { size_t accumulator = lastRun - RUN_MASK; *op++ = RUN_MASK << ML_BITS; for(; accumulator >= 255 ; accumulator-=255) *op++ = 255; *op++ = (BYTE) accumulator; } else { *op++ = (BYTE)(lastRun<internal_donotuse; LZ4_resetStream((LZ4_stream_t*)state); if (acceleration < 1) acceleration = ACCELERATION_DEFAULT; if (maxOutputSize >= LZ4_compressBound(inputSize)) { if (inputSize < LZ4_64Klimit) return LZ4_compress_generic(ctx, source, dest, inputSize, 0, notLimited, byU16, noDict, noDictIssue, acceleration); else return LZ4_compress_generic(ctx, source, dest, inputSize, 0, notLimited, (sizeof(void*)==8) ? byU32 : byPtr, noDict, noDictIssue, acceleration); } else { if (inputSize < LZ4_64Klimit) return LZ4_compress_generic(ctx, source, dest, inputSize, maxOutputSize, limitedOutput, byU16, noDict, noDictIssue, acceleration); else return LZ4_compress_generic(ctx, source, dest, inputSize, maxOutputSize, limitedOutput, (sizeof(void*)==8) ? byU32 : byPtr, noDict, noDictIssue, acceleration); } } int LZ4_compress_fast(const char* source, char* dest, int inputSize, int maxOutputSize, int acceleration) { #if (LZ4_HEAPMODE) void* ctxPtr = ALLOCATOR(1, sizeof(LZ4_stream_t)); /* malloc-calloc always properly aligned */ #else LZ4_stream_t ctx; void* const ctxPtr = &ctx; #endif int const result = LZ4_compress_fast_extState(ctxPtr, source, dest, inputSize, maxOutputSize, acceleration); #if (LZ4_HEAPMODE) FREEMEM(ctxPtr); #endif return result; } int LZ4_compress_default(const char* source, char* dest, int inputSize, int maxOutputSize) { return LZ4_compress_fast(source, dest, inputSize, maxOutputSize, 1); } /* hidden debug function */ /* strangely enough, gcc generates faster code when this function is uncommented, even if unused */ int LZ4_compress_fast_force(const char* source, char* dest, int inputSize, int maxOutputSize, int acceleration) { LZ4_stream_t ctx; LZ4_resetStream(&ctx); if (inputSize < LZ4_64Klimit) return LZ4_compress_generic(&ctx.internal_donotuse, source, dest, inputSize, maxOutputSize, limitedOutput, byU16, noDict, noDictIssue, acceleration); else return LZ4_compress_generic(&ctx.internal_donotuse, source, dest, inputSize, maxOutputSize, limitedOutput, sizeof(void*)==8 ? byU32 : byPtr, noDict, noDictIssue, acceleration); } /*-****************************** * *_destSize() variant ********************************/ static int LZ4_compress_destSize_generic( LZ4_stream_t_internal* const ctx, const char* const src, char* const dst, int* const srcSizePtr, const int targetDstSize, const tableType_t tableType) { const BYTE* ip = (const BYTE*) src; const BYTE* base = (const BYTE*) src; const BYTE* lowLimit = (const BYTE*) src; const BYTE* anchor = ip; const BYTE* const iend = ip + *srcSizePtr; const BYTE* const mflimit = iend - MFLIMIT; const BYTE* const matchlimit = iend - LASTLITERALS; BYTE* op = (BYTE*) dst; BYTE* const oend = op + targetDstSize; BYTE* const oMaxLit = op + targetDstSize - 2 /* offset */ - 8 /* because 8+MINMATCH==MFLIMIT */ - 1 /* token */; BYTE* const oMaxMatch = op + targetDstSize - (LASTLITERALS + 1 /* token */); BYTE* const oMaxSeq = oMaxLit - 1 /* token */; U32 forwardH; /* Init conditions */ if (targetDstSize < 1) return 0; /* Impossible to store anything */ if ((U32)*srcSizePtr > (U32)LZ4_MAX_INPUT_SIZE) return 0; /* Unsupported input size, too large (or negative) */ if ((tableType == byU16) && (*srcSizePtr>=LZ4_64Klimit)) return 0; /* Size too large (not within 64K limit) */ if (*srcSizePtrhashTable, tableType, base); ip++; forwardH = LZ4_hashPosition(ip, tableType); /* Main Loop */ for ( ; ; ) { const BYTE* match; BYTE* token; /* Find a match */ { const BYTE* forwardIp = ip; unsigned step = 1; unsigned searchMatchNb = 1 << LZ4_skipTrigger; do { U32 h = forwardH; ip = forwardIp; forwardIp += step; step = (searchMatchNb++ >> LZ4_skipTrigger); if (unlikely(forwardIp > mflimit)) goto _last_literals; match = LZ4_getPositionOnHash(h, ctx->hashTable, tableType, base); forwardH = LZ4_hashPosition(forwardIp, tableType); LZ4_putPositionOnHash(ip, h, ctx->hashTable, tableType, base); } while ( ((tableType==byU16) ? 0 : (match + MAX_DISTANCE < ip)) || (LZ4_read32(match) != LZ4_read32(ip)) ); } /* Catch up */ while ((ip>anchor) && (match > lowLimit) && (unlikely(ip[-1]==match[-1]))) { ip--; match--; } /* Encode Literal length */ { unsigned litLength = (unsigned)(ip - anchor); token = op++; if (op + ((litLength+240)/255) + litLength > oMaxLit) { /* Not enough space for a last match */ op--; goto _last_literals; } if (litLength>=RUN_MASK) { unsigned len = litLength - RUN_MASK; *token=(RUN_MASK<= 255 ; len-=255) *op++ = 255; *op++ = (BYTE)len; } else *token = (BYTE)(litLength< oMaxMatch) { /* Match description too long : reduce it */ matchLength = (15-1) + (oMaxMatch-op) * 255; } ip += MINMATCH + matchLength; if (matchLength>=ML_MASK) { *token += ML_MASK; matchLength -= ML_MASK; while (matchLength >= 255) { matchLength-=255; *op++ = 255; } *op++ = (BYTE)matchLength; } else *token += (BYTE)(matchLength); } anchor = ip; /* Test end of block */ if (ip > mflimit) break; if (op > oMaxSeq) break; /* Fill table */ LZ4_putPosition(ip-2, ctx->hashTable, tableType, base); /* Test next position */ match = LZ4_getPosition(ip, ctx->hashTable, tableType, base); LZ4_putPosition(ip, ctx->hashTable, tableType, base); if ( (match+MAX_DISTANCE>=ip) && (LZ4_read32(match)==LZ4_read32(ip)) ) { token=op++; *token=0; goto _next_match; } /* Prepare next loop */ forwardH = LZ4_hashPosition(++ip, tableType); } _last_literals: /* Encode Last Literals */ { size_t lastRunSize = (size_t)(iend - anchor); if (op + 1 /* token */ + ((lastRunSize+240)/255) /* litLength */ + lastRunSize /* literals */ > oend) { /* adapt lastRunSize to fill 'dst' */ lastRunSize = (oend-op) - 1; lastRunSize -= (lastRunSize+240)/255; } ip = anchor + lastRunSize; if (lastRunSize >= RUN_MASK) { size_t accumulator = lastRunSize - RUN_MASK; *op++ = RUN_MASK << ML_BITS; for(; accumulator >= 255 ; accumulator-=255) *op++ = 255; *op++ = (BYTE) accumulator; } else { *op++ = (BYTE)(lastRunSize<= LZ4_compressBound(*srcSizePtr)) { /* compression success is guaranteed */ return LZ4_compress_fast_extState(state, src, dst, *srcSizePtr, targetDstSize, 1); } else { if (*srcSizePtr < LZ4_64Klimit) return LZ4_compress_destSize_generic(&state->internal_donotuse, src, dst, srcSizePtr, targetDstSize, byU16); else return LZ4_compress_destSize_generic(&state->internal_donotuse, src, dst, srcSizePtr, targetDstSize, sizeof(void*)==8 ? byU32 : byPtr); } } int LZ4_compress_destSize(const char* src, char* dst, int* srcSizePtr, int targetDstSize) { #if (LZ4_HEAPMODE) LZ4_stream_t* ctx = (LZ4_stream_t*)ALLOCATOR(1, sizeof(LZ4_stream_t)); /* malloc-calloc always properly aligned */ #else LZ4_stream_t ctxBody; LZ4_stream_t* ctx = &ctxBody; #endif int result = LZ4_compress_destSize_extState(ctx, src, dst, srcSizePtr, targetDstSize); #if (LZ4_HEAPMODE) FREEMEM(ctx); #endif return result; } /*-****************************** * Streaming functions ********************************/ LZ4_stream_t* LZ4_createStream(void) { LZ4_stream_t* lz4s = (LZ4_stream_t*)ALLOCATOR(8, LZ4_STREAMSIZE_U64); LZ4_STATIC_ASSERT(LZ4_STREAMSIZE >= sizeof(LZ4_stream_t_internal)); /* A compilation error here means LZ4_STREAMSIZE is not large enough */ LZ4_resetStream(lz4s); return lz4s; } void LZ4_resetStream (LZ4_stream_t* LZ4_stream) { MEM_INIT(LZ4_stream, 0, sizeof(LZ4_stream_t)); } int LZ4_freeStream (LZ4_stream_t* LZ4_stream) { if (!LZ4_stream) return 0; /* support free on NULL */ FREEMEM(LZ4_stream); return (0); } #define HASH_UNIT sizeof(reg_t) int LZ4_loadDict (LZ4_stream_t* LZ4_dict, const char* dictionary, int dictSize) { LZ4_stream_t_internal* dict = &LZ4_dict->internal_donotuse; const BYTE* p = (const BYTE*)dictionary; const BYTE* const dictEnd = p + dictSize; const BYTE* base; if ((dict->initCheck) || (dict->currentOffset > 1 GB)) /* Uninitialized structure, or reuse overflow */ LZ4_resetStream(LZ4_dict); if (dictSize < (int)HASH_UNIT) { dict->dictionary = NULL; dict->dictSize = 0; return 0; } if ((dictEnd - p) > 64 KB) p = dictEnd - 64 KB; dict->currentOffset += 64 KB; base = p - dict->currentOffset; dict->dictionary = p; dict->dictSize = (U32)(dictEnd - p); dict->currentOffset += dict->dictSize; while (p <= dictEnd-HASH_UNIT) { LZ4_putPosition(p, dict->hashTable, byU32, base); p+=3; } return dict->dictSize; } static void LZ4_renormDictT(LZ4_stream_t_internal* LZ4_dict, const BYTE* src) { if ((LZ4_dict->currentOffset > 0x80000000) || ((uptrval)LZ4_dict->currentOffset > (uptrval)src)) { /* address space overflow */ /* rescale hash table */ U32 const delta = LZ4_dict->currentOffset - 64 KB; const BYTE* dictEnd = LZ4_dict->dictionary + LZ4_dict->dictSize; int i; for (i=0; ihashTable[i] < delta) LZ4_dict->hashTable[i]=0; else LZ4_dict->hashTable[i] -= delta; } LZ4_dict->currentOffset = 64 KB; if (LZ4_dict->dictSize > 64 KB) LZ4_dict->dictSize = 64 KB; LZ4_dict->dictionary = dictEnd - LZ4_dict->dictSize; } } int LZ4_compress_fast_continue (LZ4_stream_t* LZ4_stream, const char* source, char* dest, int inputSize, int maxOutputSize, int acceleration) { LZ4_stream_t_internal* streamPtr = &LZ4_stream->internal_donotuse; const BYTE* const dictEnd = streamPtr->dictionary + streamPtr->dictSize; const BYTE* smallest = (const BYTE*) source; if (streamPtr->initCheck) return 0; /* Uninitialized structure detected */ if ((streamPtr->dictSize>0) && (smallest>dictEnd)) smallest = dictEnd; LZ4_renormDictT(streamPtr, smallest); if (acceleration < 1) acceleration = ACCELERATION_DEFAULT; /* Check overlapping input/dictionary space */ { const BYTE* sourceEnd = (const BYTE*) source + inputSize; if ((sourceEnd > streamPtr->dictionary) && (sourceEnd < dictEnd)) { streamPtr->dictSize = (U32)(dictEnd - sourceEnd); if (streamPtr->dictSize > 64 KB) streamPtr->dictSize = 64 KB; if (streamPtr->dictSize < 4) streamPtr->dictSize = 0; streamPtr->dictionary = dictEnd - streamPtr->dictSize; } } /* prefix mode : source data follows dictionary */ if (dictEnd == (const BYTE*)source) { int result; if ((streamPtr->dictSize < 64 KB) && (streamPtr->dictSize < streamPtr->currentOffset)) result = LZ4_compress_generic(streamPtr, source, dest, inputSize, maxOutputSize, limitedOutput, byU32, withPrefix64k, dictSmall, acceleration); else result = LZ4_compress_generic(streamPtr, source, dest, inputSize, maxOutputSize, limitedOutput, byU32, withPrefix64k, noDictIssue, acceleration); streamPtr->dictSize += (U32)inputSize; streamPtr->currentOffset += (U32)inputSize; return result; } /* external dictionary mode */ { int result; if ((streamPtr->dictSize < 64 KB) && (streamPtr->dictSize < streamPtr->currentOffset)) result = LZ4_compress_generic(streamPtr, source, dest, inputSize, maxOutputSize, limitedOutput, byU32, usingExtDict, dictSmall, acceleration); else result = LZ4_compress_generic(streamPtr, source, dest, inputSize, maxOutputSize, limitedOutput, byU32, usingExtDict, noDictIssue, acceleration); streamPtr->dictionary = (const BYTE*)source; streamPtr->dictSize = (U32)inputSize; streamPtr->currentOffset += (U32)inputSize; return result; } } /* Hidden debug function, to force external dictionary mode */ int LZ4_compress_forceExtDict (LZ4_stream_t* LZ4_dict, const char* source, char* dest, int inputSize) { LZ4_stream_t_internal* streamPtr = &LZ4_dict->internal_donotuse; int result; const BYTE* const dictEnd = streamPtr->dictionary + streamPtr->dictSize; const BYTE* smallest = dictEnd; if (smallest > (const BYTE*) source) smallest = (const BYTE*) source; LZ4_renormDictT(streamPtr, smallest); result = LZ4_compress_generic(streamPtr, source, dest, inputSize, 0, notLimited, byU32, usingExtDict, noDictIssue, 1); streamPtr->dictionary = (const BYTE*)source; streamPtr->dictSize = (U32)inputSize; streamPtr->currentOffset += (U32)inputSize; return result; } /*! LZ4_saveDict() : * If previously compressed data block is not guaranteed to remain available at its memory location, * save it into a safer place (char* safeBuffer). * Note : you don't need to call LZ4_loadDict() afterwards, * dictionary is immediately usable, you can therefore call LZ4_compress_fast_continue(). * Return : saved dictionary size in bytes (necessarily <= dictSize), or 0 if error. */ int LZ4_saveDict (LZ4_stream_t* LZ4_dict, char* safeBuffer, int dictSize) { LZ4_stream_t_internal* const dict = &LZ4_dict->internal_donotuse; const BYTE* const previousDictEnd = dict->dictionary + dict->dictSize; if ((U32)dictSize > 64 KB) dictSize = 64 KB; /* useless to define a dictionary > 64 KB */ if ((U32)dictSize > dict->dictSize) dictSize = dict->dictSize; memmove(safeBuffer, previousDictEnd - dictSize, dictSize); dict->dictionary = (const BYTE*)safeBuffer; dict->dictSize = (U32)dictSize; return dictSize; } /*-***************************** * Decompression functions *******************************/ /*! LZ4_decompress_generic() : * This generic decompression function cover all use cases. * It shall be instantiated several times, using different sets of directives * Note that it is important this generic function is really inlined, * in order to remove useless branches during compilation optimization. */ FORCE_INLINE int LZ4_decompress_generic( const char* const source, char* const dest, int inputSize, int outputSize, /* If endOnInput==endOnInputSize, this value is the max size of Output Buffer. */ int endOnInput, /* endOnOutputSize, endOnInputSize */ int partialDecoding, /* full, partial */ int targetOutputSize, /* only used if partialDecoding==partial */ int dict, /* noDict, withPrefix64k, usingExtDict */ const BYTE* const lowPrefix, /* == dest when no prefix */ const BYTE* const dictStart, /* only if dict==usingExtDict */ const size_t dictSize /* note : = 0 if noDict */ ) { /* Local Variables */ const BYTE* ip = (const BYTE*) source; const BYTE* const iend = ip + inputSize; BYTE* op = (BYTE*) dest; BYTE* const oend = op + outputSize; BYTE* cpy; BYTE* oexit = op + targetOutputSize; const BYTE* const lowLimit = lowPrefix - dictSize; const BYTE* const dictEnd = (const BYTE*)dictStart + dictSize; const unsigned dec32table[] = {0, 1, 2, 1, 4, 4, 4, 4}; const int dec64table[] = {0, 0, 0, -1, 0, 1, 2, 3}; const int safeDecode = (endOnInput==endOnInputSize); const int checkOffset = ((safeDecode) && (dictSize < (int)(64 KB))); /* Special cases */ if ((partialDecoding) && (oexit > oend-MFLIMIT)) oexit = oend-MFLIMIT; /* targetOutputSize too high => decode everything */ if ((endOnInput) && (unlikely(outputSize==0))) return ((inputSize==1) && (*ip==0)) ? 0 : -1; /* Empty output buffer */ if ((!endOnInput) && (unlikely(outputSize==0))) return (*ip==0?1:-1); /* Main Loop : decode sequences */ while (1) { size_t length; const BYTE* match; size_t offset; /* get literal length */ unsigned const token = *ip++; if ((length=(token>>ML_BITS)) == RUN_MASK) { unsigned s; do { s = *ip++; length += s; } while ( likely(endOnInput ? ip(partialDecoding?oexit:oend-MFLIMIT)) || (ip+length>iend-(2+1+LASTLITERALS))) ) || ((!endOnInput) && (cpy>oend-WILDCOPYLENGTH)) ) { if (partialDecoding) { if (cpy > oend) goto _output_error; /* Error : write attempt beyond end of output buffer */ if ((endOnInput) && (ip+length > iend)) goto _output_error; /* Error : read attempt beyond end of input buffer */ } else { if ((!endOnInput) && (cpy != oend)) goto _output_error; /* Error : block decoding must stop exactly there */ if ((endOnInput) && ((ip+length != iend) || (cpy > oend))) goto _output_error; /* Error : input must be consumed */ } memcpy(op, ip, length); ip += length; op += length; break; /* Necessarily EOF, due to parsing restrictions */ } LZ4_wildCopy(op, ip, cpy); ip += length; op = cpy; /* get offset */ offset = LZ4_readLE16(ip); ip+=2; match = op - offset; if ((checkOffset) && (unlikely(match < lowLimit))) goto _output_error; /* Error : offset outside buffers */ LZ4_write32(op, (U32)offset); /* costs ~1%; silence an msan warning when offset==0 */ /* get matchlength */ length = token & ML_MASK; if (length == ML_MASK) { unsigned s; do { s = *ip++; if ((endOnInput) && (ip > iend-LASTLITERALS)) goto _output_error; length += s; } while (s==255); if ((safeDecode) && unlikely((uptrval)(op)+length<(uptrval)op)) goto _output_error; /* overflow detection */ } length += MINMATCH; /* check external dictionary */ if ((dict==usingExtDict) && (match < lowPrefix)) { if (unlikely(op+length > oend-LASTLITERALS)) goto _output_error; /* doesn't respect parsing restriction */ if (length <= (size_t)(lowPrefix-match)) { /* match can be copied as a single segment from external dictionary */ memmove(op, dictEnd - (lowPrefix-match), length); op += length; } else { /* match encompass external dictionary and current block */ size_t const copySize = (size_t)(lowPrefix-match); size_t const restSize = length - copySize; memcpy(op, dictEnd - copySize, copySize); op += copySize; if (restSize > (size_t)(op-lowPrefix)) { /* overlap copy */ BYTE* const endOfMatch = op + restSize; const BYTE* copyFrom = lowPrefix; while (op < endOfMatch) *op++ = *copyFrom++; } else { memcpy(op, lowPrefix, restSize); op += restSize; } } continue; } /* copy match within block */ cpy = op + length; if (unlikely(offset<8)) { const int dec64 = dec64table[offset]; op[0] = match[0]; op[1] = match[1]; op[2] = match[2]; op[3] = match[3]; match += dec32table[offset]; memcpy(op+4, match, 4); match -= dec64; } else { LZ4_copy8(op, match); match+=8; } op += 8; if (unlikely(cpy>oend-12)) { BYTE* const oCopyLimit = oend-(WILDCOPYLENGTH-1); if (cpy > oend-LASTLITERALS) goto _output_error; /* Error : last LASTLITERALS bytes must be literals (uncompressed) */ if (op < oCopyLimit) { LZ4_wildCopy(op, match, oCopyLimit); match += oCopyLimit - op; op = oCopyLimit; } while (op16) LZ4_wildCopy(op+8, match+8, cpy); } op=cpy; /* correction */ } /* end of decoding */ if (endOnInput) return (int) (((char*)op)-dest); /* Nb of output bytes decoded */ else return (int) (((const char*)ip)-source); /* Nb of input bytes read */ /* Overflow error detected */ _output_error: return (int) (-(((const char*)ip)-source))-1; } int LZ4_decompress_safe(const char* source, char* dest, int compressedSize, int maxDecompressedSize) { return LZ4_decompress_generic(source, dest, compressedSize, maxDecompressedSize, endOnInputSize, full, 0, noDict, (BYTE*)dest, NULL, 0); } int LZ4_decompress_safe_partial(const char* source, char* dest, int compressedSize, int targetOutputSize, int maxDecompressedSize) { return LZ4_decompress_generic(source, dest, compressedSize, maxDecompressedSize, endOnInputSize, partial, targetOutputSize, noDict, (BYTE*)dest, NULL, 0); } int LZ4_decompress_fast(const char* source, char* dest, int originalSize) { return LZ4_decompress_generic(source, dest, 0, originalSize, endOnOutputSize, full, 0, withPrefix64k, (BYTE*)(dest - 64 KB), NULL, 64 KB); } /*===== streaming decompression functions =====*/ LZ4_streamDecode_t* LZ4_createStreamDecode(void) { LZ4_streamDecode_t* lz4s = (LZ4_streamDecode_t*) ALLOCATOR(1, sizeof(LZ4_streamDecode_t)); return lz4s; } int LZ4_freeStreamDecode (LZ4_streamDecode_t* LZ4_stream) { if (!LZ4_stream) return 0; /* support free on NULL */ FREEMEM(LZ4_stream); return 0; } /*! * LZ4_setStreamDecode() : * Use this function to instruct where to find the dictionary. * This function is not necessary if previous data is still available where it was decoded. * Loading a size of 0 is allowed (same effect as no dictionary). * Return : 1 if OK, 0 if error */ int LZ4_setStreamDecode (LZ4_streamDecode_t* LZ4_streamDecode, const char* dictionary, int dictSize) { LZ4_streamDecode_t_internal* lz4sd = &LZ4_streamDecode->internal_donotuse; lz4sd->prefixSize = (size_t) dictSize; lz4sd->prefixEnd = (const BYTE*) dictionary + dictSize; lz4sd->externalDict = NULL; lz4sd->extDictSize = 0; return 1; } /* *_continue() : These decoding functions allow decompression of multiple blocks in "streaming" mode. Previously decoded blocks must still be available at the memory position where they were decoded. If it's not possible, save the relevant part of decoded data into a safe buffer, and indicate where it stands using LZ4_setStreamDecode() */ int LZ4_decompress_safe_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* source, char* dest, int compressedSize, int maxOutputSize) { LZ4_streamDecode_t_internal* lz4sd = &LZ4_streamDecode->internal_donotuse; int result; if (lz4sd->prefixEnd == (BYTE*)dest) { result = LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, endOnInputSize, full, 0, usingExtDict, lz4sd->prefixEnd - lz4sd->prefixSize, lz4sd->externalDict, lz4sd->extDictSize); if (result <= 0) return result; lz4sd->prefixSize += result; lz4sd->prefixEnd += result; } else { lz4sd->extDictSize = lz4sd->prefixSize; lz4sd->externalDict = lz4sd->prefixEnd - lz4sd->extDictSize; result = LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, endOnInputSize, full, 0, usingExtDict, (BYTE*)dest, lz4sd->externalDict, lz4sd->extDictSize); if (result <= 0) return result; lz4sd->prefixSize = result; lz4sd->prefixEnd = (BYTE*)dest + result; } return result; } int LZ4_decompress_fast_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* source, char* dest, int originalSize) { LZ4_streamDecode_t_internal* lz4sd = &LZ4_streamDecode->internal_donotuse; int result; if (lz4sd->prefixEnd == (BYTE*)dest) { result = LZ4_decompress_generic(source, dest, 0, originalSize, endOnOutputSize, full, 0, usingExtDict, lz4sd->prefixEnd - lz4sd->prefixSize, lz4sd->externalDict, lz4sd->extDictSize); if (result <= 0) return result; lz4sd->prefixSize += originalSize; lz4sd->prefixEnd += originalSize; } else { lz4sd->extDictSize = lz4sd->prefixSize; lz4sd->externalDict = lz4sd->prefixEnd - lz4sd->extDictSize; result = LZ4_decompress_generic(source, dest, 0, originalSize, endOnOutputSize, full, 0, usingExtDict, (BYTE*)dest, lz4sd->externalDict, lz4sd->extDictSize); if (result <= 0) return result; lz4sd->prefixSize = originalSize; lz4sd->prefixEnd = (BYTE*)dest + originalSize; } return result; } /* Advanced decoding functions : *_usingDict() : These decoding functions work the same as "_continue" ones, the dictionary must be explicitly provided within parameters */ FORCE_INLINE int LZ4_decompress_usingDict_generic(const char* source, char* dest, int compressedSize, int maxOutputSize, int safe, const char* dictStart, int dictSize) { if (dictSize==0) return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, noDict, (BYTE*)dest, NULL, 0); if (dictStart+dictSize == dest) { if (dictSize >= (int)(64 KB - 1)) return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, withPrefix64k, (BYTE*)dest-64 KB, NULL, 0); return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, noDict, (BYTE*)dest-dictSize, NULL, 0); } return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, usingExtDict, (BYTE*)dest, (const BYTE*)dictStart, dictSize); } int LZ4_decompress_safe_usingDict(const char* source, char* dest, int compressedSize, int maxOutputSize, const char* dictStart, int dictSize) { return LZ4_decompress_usingDict_generic(source, dest, compressedSize, maxOutputSize, 1, dictStart, dictSize); } int LZ4_decompress_fast_usingDict(const char* source, char* dest, int originalSize, const char* dictStart, int dictSize) { return LZ4_decompress_usingDict_generic(source, dest, 0, originalSize, 0, dictStart, dictSize); } /* debug function */ int LZ4_decompress_safe_forceExtDict(const char* source, char* dest, int compressedSize, int maxOutputSize, const char* dictStart, int dictSize) { return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, endOnInputSize, full, 0, usingExtDict, (BYTE*)dest, (const BYTE*)dictStart, dictSize); } /*=************************************************* * Obsolete Functions ***************************************************/ /* obsolete compression functions */ int LZ4_compress_limitedOutput(const char* source, char* dest, int inputSize, int maxOutputSize) { return LZ4_compress_default(source, dest, inputSize, maxOutputSize); } int LZ4_compress(const char* source, char* dest, int inputSize) { return LZ4_compress_default(source, dest, inputSize, LZ4_compressBound(inputSize)); } int LZ4_compress_limitedOutput_withState (void* state, const char* src, char* dst, int srcSize, int dstSize) { return LZ4_compress_fast_extState(state, src, dst, srcSize, dstSize, 1); } int LZ4_compress_withState (void* state, const char* src, char* dst, int srcSize) { return LZ4_compress_fast_extState(state, src, dst, srcSize, LZ4_compressBound(srcSize), 1); } int LZ4_compress_limitedOutput_continue (LZ4_stream_t* LZ4_stream, const char* src, char* dst, int srcSize, int maxDstSize) { return LZ4_compress_fast_continue(LZ4_stream, src, dst, srcSize, maxDstSize, 1); } int LZ4_compress_continue (LZ4_stream_t* LZ4_stream, const char* source, char* dest, int inputSize) { return LZ4_compress_fast_continue(LZ4_stream, source, dest, inputSize, LZ4_compressBound(inputSize), 1); } /* These function names are deprecated and should no longer be used. They are only provided here for compatibility with older user programs. - LZ4_uncompress is totally equivalent to LZ4_decompress_fast - LZ4_uncompress_unknownOutputSize is totally equivalent to LZ4_decompress_safe */ int LZ4_uncompress (const char* source, char* dest, int outputSize) { return LZ4_decompress_fast(source, dest, outputSize); } int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize) { return LZ4_decompress_safe(source, dest, isize, maxOutputSize); } /* Obsolete Streaming functions */ int LZ4_sizeofStreamState(void) { return LZ4_STREAMSIZE; } static void LZ4_init(LZ4_stream_t* lz4ds, BYTE* base) { MEM_INIT(lz4ds, 0, sizeof(LZ4_stream_t)); lz4ds->internal_donotuse.bufferStart = base; } int LZ4_resetStreamState(void* state, char* inputBuffer) { if ((((uptrval)state) & 3) != 0) return 1; /* Error : pointer is not aligned on 4-bytes boundary */ LZ4_init((LZ4_stream_t*)state, (BYTE*)inputBuffer); return 0; } void* LZ4_create (char* inputBuffer) { LZ4_stream_t* lz4ds = (LZ4_stream_t*)ALLOCATOR(8, sizeof(LZ4_stream_t)); LZ4_init (lz4ds, (BYTE*)inputBuffer); return lz4ds; } char* LZ4_slideInputBuffer (void* LZ4_Data) { LZ4_stream_t_internal* ctx = &((LZ4_stream_t*)LZ4_Data)->internal_donotuse; int dictSize = LZ4_saveDict((LZ4_stream_t*)LZ4_Data, (char*)ctx->bufferStart, 64 KB); return (char*)(ctx->bufferStart + dictSize); } /* Obsolete streaming decompression functions */ int LZ4_decompress_safe_withPrefix64k(const char* source, char* dest, int compressedSize, int maxOutputSize) { return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, endOnInputSize, full, 0, withPrefix64k, (BYTE*)dest - 64 KB, NULL, 64 KB); } int LZ4_decompress_fast_withPrefix64k(const char* source, char* dest, int originalSize) { return LZ4_decompress_generic(source, dest, 0, originalSize, endOnOutputSize, full, 0, withPrefix64k, (BYTE*)dest - 64 KB, NULL, 64 KB); } #endif /* LZ4_COMMONDEFS_ONLY */ pysam-0.23.0/samtools/lz4/lz4.h000066400000000000000000000560401475062545500162030ustar00rootroot00000000000000/* * LZ4 - Fast LZ compression algorithm * Header File * Copyright (C) 2011-2017, Yann Collet. BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php) Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. You can contact the author at : - LZ4 homepage : http://www.lz4.org - LZ4 source repository : https://github.com/lz4/lz4 */ #if defined (__cplusplus) extern "C" { #endif #ifndef LZ4_H_2983827168210 #define LZ4_H_2983827168210 /* --- Dependency --- */ #include /* size_t */ /** Introduction LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core, scalable with multi-cores CPU. It features an extremely fast decoder, with speed in multiple GB/s per core, typically reaching RAM speed limits on multi-core systems. The LZ4 compression library provides in-memory compression and decompression functions. Compression can be done in: - a single step (described as Simple Functions) - a single step, reusing a context (described in Advanced Functions) - unbounded multiple steps (described as Streaming compression) lz4.h provides block compression functions. It gives full buffer control to user. Decompressing an lz4-compressed block also requires metadata (such as compressed size). Each application is free to encode such metadata in whichever way it wants. An additional format, called LZ4 frame specification (doc/lz4_Frame_format.md), take care of encoding standard metadata alongside LZ4-compressed blocks. If your application requires interoperability, it's recommended to use it. A library is provided to take care of it, see lz4frame.h. */ /*^*************************************************************** * Export parameters *****************************************************************/ /* * LZ4_DLL_EXPORT : * Enable exporting of functions when building a Windows DLL * LZ4LIB_API : * Control library symbols visibility. */ #if defined(LZ4_DLL_EXPORT) && (LZ4_DLL_EXPORT==1) # define LZ4LIB_API __declspec(dllexport) #elif defined(LZ4_DLL_IMPORT) && (LZ4_DLL_IMPORT==1) # define LZ4LIB_API __declspec(dllimport) /* It isn't required but allows to generate better code, saving a function pointer load from the IAT and an indirect jump.*/ #elif defined(__GNUC__) && (__GNUC__ >= 4) # define LZ4LIB_API __attribute__ ((__visibility__ ("default"))) #else # define LZ4LIB_API #endif /*------ Version ------*/ #define LZ4_VERSION_MAJOR 1 /* for breaking interface changes */ #define LZ4_VERSION_MINOR 8 /* for new (non-breaking) interface capabilities */ #define LZ4_VERSION_RELEASE 0 /* for tweaks, bug-fixes, or development */ #define LZ4_VERSION_NUMBER (LZ4_VERSION_MAJOR *100*100 + LZ4_VERSION_MINOR *100 + LZ4_VERSION_RELEASE) #define LZ4_LIB_VERSION LZ4_VERSION_MAJOR.LZ4_VERSION_MINOR.LZ4_VERSION_RELEASE #define LZ4_QUOTE(str) #str #define LZ4_EXPAND_AND_QUOTE(str) LZ4_QUOTE(str) #define LZ4_VERSION_STRING LZ4_EXPAND_AND_QUOTE(LZ4_LIB_VERSION) LZ4LIB_API int LZ4_versionNumber (void); /**< library version number; to be used when checking dll version */ LZ4LIB_API const char* LZ4_versionString (void); /**< library version string; to be used when checking dll version */ /*-************************************ * Tuning parameter **************************************/ /*! * LZ4_MEMORY_USAGE : * Memory usage formula : N->2^N Bytes (examples : 10 -> 1KB; 12 -> 4KB ; 16 -> 64KB; 20 -> 1MB; etc.) * Increasing memory usage improves compression ratio * Reduced memory usage can improve speed, due to cache effect * Default value is 14, for 16KB, which nicely fits into Intel x86 L1 cache */ #ifndef LZ4_MEMORY_USAGE # define LZ4_MEMORY_USAGE 14 #endif /*-************************************ * Simple Functions **************************************/ /*! LZ4_compress_default() : Compresses 'sourceSize' bytes from buffer 'source' into already allocated 'dest' buffer of size 'maxDestSize'. Compression is guaranteed to succeed if 'maxDestSize' >= LZ4_compressBound(sourceSize). It also runs faster, so it's a recommended setting. If the function cannot compress 'source' into a more limited 'dest' budget, compression stops *immediately*, and the function result is zero. As a consequence, 'dest' content is not valid. This function never writes outside 'dest' buffer, nor read outside 'source' buffer. sourceSize : Max supported value is LZ4_MAX_INPUT_VALUE maxDestSize : full or partial size of buffer 'dest' (which must be already allocated) return : the number of bytes written into buffer 'dest' (necessarily <= maxOutputSize) or 0 if compression fails */ LZ4LIB_API int LZ4_compress_default(const char* source, char* dest, int sourceSize, int maxDestSize); /*! LZ4_decompress_safe() : compressedSize : is the precise full size of the compressed block. maxDecompressedSize : is the size of destination buffer, which must be already allocated. return : the number of bytes decompressed into destination buffer (necessarily <= maxDecompressedSize) If destination buffer is not large enough, decoding will stop and output an error code (<0). If the source stream is detected malformed, the function will stop decoding and return a negative result. This function is protected against buffer overflow exploits, including malicious data packets. It never writes outside output buffer, nor reads outside input buffer. */ LZ4LIB_API int LZ4_decompress_safe (const char* source, char* dest, int compressedSize, int maxDecompressedSize); /*-************************************ * Advanced Functions **************************************/ #define LZ4_MAX_INPUT_SIZE 0x7E000000 /* 2 113 929 216 bytes */ #define LZ4_COMPRESSBOUND(isize) ((unsigned)(isize) > (unsigned)LZ4_MAX_INPUT_SIZE ? 0 : (isize) + ((isize)/255) + 16) /*! LZ4_compressBound() : Provides the maximum size that LZ4 compression may output in a "worst case" scenario (input data not compressible) This function is primarily useful for memory allocation purposes (destination buffer size). Macro LZ4_COMPRESSBOUND() is also provided for compilation-time evaluation (stack memory allocation for example). Note that LZ4_compress_default() compress faster when dest buffer size is >= LZ4_compressBound(srcSize) inputSize : max supported value is LZ4_MAX_INPUT_SIZE return : maximum output size in a "worst case" scenario or 0, if input size is too large ( > LZ4_MAX_INPUT_SIZE) */ LZ4LIB_API int LZ4_compressBound(int inputSize); /*! LZ4_compress_fast() : Same as LZ4_compress_default(), but allows to select an "acceleration" factor. The larger the acceleration value, the faster the algorithm, but also the lesser the compression. It's a trade-off. It can be fine tuned, with each successive value providing roughly +~3% to speed. An acceleration value of "1" is the same as regular LZ4_compress_default() Values <= 0 will be replaced by ACCELERATION_DEFAULT (see lz4.c), which is 1. */ LZ4LIB_API int LZ4_compress_fast (const char* source, char* dest, int sourceSize, int maxDestSize, int acceleration); /*! LZ4_compress_fast_extState() : Same compression function, just using an externally allocated memory space to store compression state. Use LZ4_sizeofState() to know how much memory must be allocated, and allocate it on 8-bytes boundaries (using malloc() typically). Then, provide it as 'void* state' to compression function. */ LZ4LIB_API int LZ4_sizeofState(void); LZ4LIB_API int LZ4_compress_fast_extState (void* state, const char* source, char* dest, int inputSize, int maxDestSize, int acceleration); /*! LZ4_compress_destSize() : Reverse the logic, by compressing as much data as possible from 'source' buffer into already allocated buffer 'dest' of size 'targetDestSize'. This function either compresses the entire 'source' content into 'dest' if it's large enough, or fill 'dest' buffer completely with as much data as possible from 'source'. *sourceSizePtr : will be modified to indicate how many bytes where read from 'source' to fill 'dest'. New value is necessarily <= old value. return : Nb bytes written into 'dest' (necessarily <= targetDestSize) or 0 if compression fails */ LZ4LIB_API int LZ4_compress_destSize (const char* source, char* dest, int* sourceSizePtr, int targetDestSize); /*! LZ4_decompress_fast() : originalSize : is the original and therefore uncompressed size return : the number of bytes read from the source buffer (in other words, the compressed size) If the source stream is detected malformed, the function will stop decoding and return a negative result. Destination buffer must be already allocated. Its size must be a minimum of 'originalSize' bytes. note : This function fully respect memory boundaries for properly formed compressed data. It is a bit faster than LZ4_decompress_safe(). However, it does not provide any protection against intentionally modified data stream (malicious input). Use this function in trusted environment only (data to decode comes from a trusted source). */ LZ4LIB_API int LZ4_decompress_fast (const char* source, char* dest, int originalSize); /*! LZ4_decompress_safe_partial() : This function decompress a compressed block of size 'compressedSize' at position 'source' into destination buffer 'dest' of size 'maxDecompressedSize'. The function tries to stop decompressing operation as soon as 'targetOutputSize' has been reached, reducing decompression time. return : the number of bytes decoded in the destination buffer (necessarily <= maxDecompressedSize) Note : this number can be < 'targetOutputSize' should the compressed block to decode be smaller. Always control how many bytes were decoded. If the source stream is detected malformed, the function will stop decoding and return a negative result. This function never writes outside of output buffer, and never reads outside of input buffer. It is therefore protected against malicious data packets */ LZ4LIB_API int LZ4_decompress_safe_partial (const char* source, char* dest, int compressedSize, int targetOutputSize, int maxDecompressedSize); /*-********************************************* * Streaming Compression Functions ***********************************************/ typedef union LZ4_stream_u LZ4_stream_t; /* incomplete type (defined later) */ /*! LZ4_createStream() and LZ4_freeStream() : * LZ4_createStream() will allocate and initialize an `LZ4_stream_t` structure. * LZ4_freeStream() releases its memory. */ LZ4LIB_API LZ4_stream_t* LZ4_createStream(void); LZ4LIB_API int LZ4_freeStream (LZ4_stream_t* streamPtr); /*! LZ4_resetStream() : * An LZ4_stream_t structure can be allocated once and re-used multiple times. * Use this function to init an allocated `LZ4_stream_t` structure and start a new compression. */ LZ4LIB_API void LZ4_resetStream (LZ4_stream_t* streamPtr); /*! LZ4_loadDict() : * Use this function to load a static dictionary into LZ4_stream. * Any previous data will be forgotten, only 'dictionary' will remain in memory. * Loading a size of 0 is allowed. * Return : dictionary size, in bytes (necessarily <= 64 KB) */ LZ4LIB_API int LZ4_loadDict (LZ4_stream_t* streamPtr, const char* dictionary, int dictSize); /*! LZ4_compress_fast_continue() : * Compress buffer content 'src', using data from previously compressed blocks as dictionary to improve compression ratio. * Important : Previous data blocks are assumed to remain present and unmodified ! * 'dst' buffer must be already allocated. * If dstCapacity >= LZ4_compressBound(srcSize), compression is guaranteed to succeed, and runs faster. * If not, and if compressed data cannot fit into 'dst' buffer size, compression stops, and function @return==0. * After an error, the stream status is invalid, it can only be reset or freed. */ LZ4LIB_API int LZ4_compress_fast_continue (LZ4_stream_t* streamPtr, const char* src, char* dst, int srcSize, int dstCapacity, int acceleration); /*! LZ4_saveDict() : * If previously compressed data block is not guaranteed to remain available at its current memory location, * save it into a safer place (char* safeBuffer). * Note : it's not necessary to call LZ4_loadDict() after LZ4_saveDict(), dictionary is immediately usable. * @return : saved dictionary size in bytes (necessarily <= dictSize), or 0 if error. */ LZ4LIB_API int LZ4_saveDict (LZ4_stream_t* streamPtr, char* safeBuffer, int dictSize); /*-********************************************** * Streaming Decompression Functions * Bufferless synchronous API ************************************************/ typedef union LZ4_streamDecode_u LZ4_streamDecode_t; /* incomplete type (defined later) */ /*! LZ4_createStreamDecode() and LZ4_freeStreamDecode() : * creation / destruction of streaming decompression tracking structure */ LZ4LIB_API LZ4_streamDecode_t* LZ4_createStreamDecode(void); LZ4LIB_API int LZ4_freeStreamDecode (LZ4_streamDecode_t* LZ4_stream); /*! LZ4_setStreamDecode() : * Use this function to instruct where to find the dictionary. * Setting a size of 0 is allowed (same effect as reset). * @return : 1 if OK, 0 if error */ LZ4LIB_API int LZ4_setStreamDecode (LZ4_streamDecode_t* LZ4_streamDecode, const char* dictionary, int dictSize); /*! LZ4_decompress_*_continue() : * These decoding functions allow decompression of multiple blocks in "streaming" mode. * Previously decoded blocks *must* remain available at the memory position where they were decoded (up to 64 KB) * In the case of a ring buffers, decoding buffer must be either : * - Exactly same size as encoding buffer, with same update rule (block boundaries at same positions) * In which case, the decoding & encoding ring buffer can have any size, including very small ones ( < 64 KB). * - Larger than encoding buffer, by a minimum of maxBlockSize more bytes. * maxBlockSize is implementation dependent. It's the maximum size you intend to compress into a single block. * In which case, encoding and decoding buffers do not need to be synchronized, * and encoding ring buffer can have any size, including small ones ( < 64 KB). * - _At least_ 64 KB + 8 bytes + maxBlockSize. * In which case, encoding and decoding buffers do not need to be synchronized, * and encoding ring buffer can have any size, including larger than decoding buffer. * Whenever these conditions are not possible, save the last 64KB of decoded data into a safe buffer, * and indicate where it is saved using LZ4_setStreamDecode() */ LZ4LIB_API int LZ4_decompress_safe_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* source, char* dest, int compressedSize, int maxDecompressedSize); LZ4LIB_API int LZ4_decompress_fast_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* source, char* dest, int originalSize); /*! LZ4_decompress_*_usingDict() : * These decoding functions work the same as * a combination of LZ4_setStreamDecode() followed by LZ4_decompress_*_continue() * They are stand-alone, and don't need an LZ4_streamDecode_t structure. */ LZ4LIB_API int LZ4_decompress_safe_usingDict (const char* source, char* dest, int compressedSize, int maxDecompressedSize, const char* dictStart, int dictSize); LZ4LIB_API int LZ4_decompress_fast_usingDict (const char* source, char* dest, int originalSize, const char* dictStart, int dictSize); /*^********************************************** * !!!!!! STATIC LINKING ONLY !!!!!! ***********************************************/ /*-************************************ * Private definitions ************************************** * Do not use these definitions. * They are exposed to allow static allocation of `LZ4_stream_t` and `LZ4_streamDecode_t`. * Using these definitions will expose code to API and/or ABI break in future versions of the library. **************************************/ #define LZ4_HASHLOG (LZ4_MEMORY_USAGE-2) #define LZ4_HASHTABLESIZE (1 << LZ4_MEMORY_USAGE) #define LZ4_HASH_SIZE_U32 (1 << LZ4_HASHLOG) /* required as macro for static allocation */ #if defined(__cplusplus) || (defined (__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) /* C99 */) #include typedef struct { uint32_t hashTable[LZ4_HASH_SIZE_U32]; uint32_t currentOffset; uint32_t initCheck; const uint8_t* dictionary; uint8_t* bufferStart; /* obsolete, used for slideInputBuffer */ uint32_t dictSize; } LZ4_stream_t_internal; typedef struct { const uint8_t* externalDict; size_t extDictSize; const uint8_t* prefixEnd; size_t prefixSize; } LZ4_streamDecode_t_internal; #else typedef struct { unsigned int hashTable[LZ4_HASH_SIZE_U32]; unsigned int currentOffset; unsigned int initCheck; const unsigned char* dictionary; unsigned char* bufferStart; /* obsolete, used for slideInputBuffer */ unsigned int dictSize; } LZ4_stream_t_internal; typedef struct { const unsigned char* externalDict; size_t extDictSize; const unsigned char* prefixEnd; size_t prefixSize; } LZ4_streamDecode_t_internal; #endif /*! * LZ4_stream_t : * information structure to track an LZ4 stream. * init this structure before first use. * note : only use in association with static linking ! * this definition is not API/ABI safe, * it may change in a future version ! */ #define LZ4_STREAMSIZE_U64 ((1 << (LZ4_MEMORY_USAGE-3)) + 4) #define LZ4_STREAMSIZE (LZ4_STREAMSIZE_U64 * sizeof(unsigned long long)) union LZ4_stream_u { unsigned long long table[LZ4_STREAMSIZE_U64]; LZ4_stream_t_internal internal_donotuse; } ; /* previously typedef'd to LZ4_stream_t */ /*! * LZ4_streamDecode_t : * information structure to track an LZ4 stream during decompression. * init this structure using LZ4_setStreamDecode (or memset()) before first use * note : only use in association with static linking ! * this definition is not API/ABI safe, * and may change in a future version ! */ #define LZ4_STREAMDECODESIZE_U64 4 #define LZ4_STREAMDECODESIZE (LZ4_STREAMDECODESIZE_U64 * sizeof(unsigned long long)) union LZ4_streamDecode_u { unsigned long long table[LZ4_STREAMDECODESIZE_U64]; LZ4_streamDecode_t_internal internal_donotuse; } ; /* previously typedef'd to LZ4_streamDecode_t */ /*-************************************ * Obsolete Functions **************************************/ /*! Deprecation warnings Should deprecation warnings be a problem, it is generally possible to disable them, typically with -Wno-deprecated-declarations for gcc or _CRT_SECURE_NO_WARNINGS in Visual. Otherwise, it's also possible to define LZ4_DISABLE_DEPRECATE_WARNINGS */ #ifdef LZ4_DISABLE_DEPRECATE_WARNINGS # define LZ4_DEPRECATED(message) /* disable deprecation warnings */ #else # define LZ4_GCC_VERSION (__GNUC__ * 100 + __GNUC_MINOR__) # if defined (__cplusplus) && (__cplusplus >= 201402) /* C++14 or greater */ # define LZ4_DEPRECATED(message) [[deprecated(message)]] # elif (LZ4_GCC_VERSION >= 405) || defined(__clang__) # define LZ4_DEPRECATED(message) __attribute__((deprecated(message))) # elif (LZ4_GCC_VERSION >= 301) # define LZ4_DEPRECATED(message) __attribute__((deprecated)) # elif defined(_MSC_VER) # define LZ4_DEPRECATED(message) __declspec(deprecated(message)) # else # pragma message("WARNING: You need to implement LZ4_DEPRECATED for this compiler") # define LZ4_DEPRECATED(message) # endif #endif /* LZ4_DISABLE_DEPRECATE_WARNINGS */ /* Obsolete compression functions */ LZ4LIB_API LZ4_DEPRECATED("use LZ4_compress_default() instead") int LZ4_compress (const char* source, char* dest, int sourceSize); LZ4LIB_API LZ4_DEPRECATED("use LZ4_compress_default() instead") int LZ4_compress_limitedOutput (const char* source, char* dest, int sourceSize, int maxOutputSize); LZ4LIB_API LZ4_DEPRECATED("use LZ4_compress_fast_extState() instead") int LZ4_compress_withState (void* state, const char* source, char* dest, int inputSize); LZ4LIB_API LZ4_DEPRECATED("use LZ4_compress_fast_extState() instead") int LZ4_compress_limitedOutput_withState (void* state, const char* source, char* dest, int inputSize, int maxOutputSize); LZ4LIB_API LZ4_DEPRECATED("use LZ4_compress_fast_continue() instead") int LZ4_compress_continue (LZ4_stream_t* LZ4_streamPtr, const char* source, char* dest, int inputSize); LZ4LIB_API LZ4_DEPRECATED("use LZ4_compress_fast_continue() instead") int LZ4_compress_limitedOutput_continue (LZ4_stream_t* LZ4_streamPtr, const char* source, char* dest, int inputSize, int maxOutputSize); /* Obsolete decompression functions */ LZ4LIB_API LZ4_DEPRECATED("use LZ4_decompress_fast() instead") int LZ4_uncompress (const char* source, char* dest, int outputSize); LZ4LIB_API LZ4_DEPRECATED("use LZ4_decompress_safe() instead") int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); /* Obsolete streaming functions; use new streaming interface whenever possible */ LZ4LIB_API LZ4_DEPRECATED("use LZ4_createStream() instead") void* LZ4_create (char* inputBuffer); LZ4LIB_API LZ4_DEPRECATED("use LZ4_createStream() instead") int LZ4_sizeofStreamState(void); LZ4LIB_API LZ4_DEPRECATED("use LZ4_resetStream() instead") int LZ4_resetStreamState(void* state, char* inputBuffer); LZ4LIB_API LZ4_DEPRECATED("use LZ4_saveDict() instead") char* LZ4_slideInputBuffer (void* state); /* Obsolete streaming decoding functions */ LZ4LIB_API LZ4_DEPRECATED("use LZ4_decompress_safe_usingDict() instead") int LZ4_decompress_safe_withPrefix64k (const char* src, char* dst, int compressedSize, int maxDstSize); LZ4LIB_API LZ4_DEPRECATED("use LZ4_decompress_fast_usingDict() instead") int LZ4_decompress_fast_withPrefix64k (const char* src, char* dst, int originalSize); #endif /* LZ4_H_2983827168210 */ #if defined (__cplusplus) } #endif pysam-0.23.0/samtools/padding.c000066400000000000000000000614221475062545500163620ustar00rootroot00000000000000/* padding.c -- depad subcommand. Copyright (C) 2011, 2012 Broad Institute. Copyright (C) 2014-2016, 2019-2020 Genome Research Ltd. Portions copyright (C) 2012, 2013 Peter Cock, The James Hutton Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include "sam_opts.h" #include "samtools.h" #define bam_reg2bin(b,e) hts_reg2bin((b),(e), 14, 5) static int replace_cigar(bam1_t *b, uint32_t n, uint32_t *cigar) { int diff = 0; if (n != b->core.n_cigar) { int o = b->core.l_qname + b->core.n_cigar * 4; if (n > b->core.n_cigar) { diff = (n - b->core.n_cigar) * 4; if ((INT_MAX - b->l_data)/4 < (n - b->core.n_cigar)) { fprintf(stderr, "[depad] ERROR: BAM record too big\n"); return -1; } if (b->l_data + diff > b->m_data) { b->m_data = b->l_data + diff; kroundup32(b->m_data); uint8_t *tmp = (uint8_t*)realloc(b->data, b->m_data); if (!tmp) { fprintf(stderr, "[depad] ERROR: Memory allocation failure.\n"); return -1; } b->data = tmp; } } else { diff = -(int)((b->core.n_cigar - n) * 4); } memmove(b->data + b->core.l_qname + n * 4, b->data + o, b->l_data - o); b->core.n_cigar = n; } memcpy(b->data + b->core.l_qname, cigar, n * 4); b->l_data += diff; return 0; } #define write_cigar(_c, _n, _m, _v) do { \ if (_n == _m) { \ _m = _m? _m<<1 : 4; \ _c = (uint32_t*)realloc(_c, _m * 4); \ if (!(_c)) { \ fprintf(stderr, "[depad] ERROR: Memory allocation failure.\n"); \ return -1; \ } \ } \ _c[_n++] = (_v); \ } while (0) static int unpad_seq(bam1_t *b, kstring_t *s) { // Returns 0 on success, -1 on an error int k, j, i; int length; int cigar_n_warning = 0; /* Make this a global and limit to one CIGAR N warning? */ uint32_t *cigar = bam_get_cigar(b); uint8_t *seq = bam_get_seq(b); // b->core.l_qseq gives length of the SEQ entry (including soft clips, S) // We need the padded length after alignment from the CIGAR (excluding // soft clips S, but including pads from CIGAR D operations) length = bam_cigar2rlen(b->core.n_cigar, cigar); ks_resize(s, length); for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) { int op, ol; op = bam_cigar_op(cigar[k]); ol = bam_cigar_oplen(cigar[k]); if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam_seqi(seq, j); } else if (op == BAM_CSOFT_CLIP) { j += ol; } else if (op == BAM_CHARD_CLIP) { /* do nothing */ } else if (op == BAM_CDEL) { for (i = 0; i < ol; ++i) s->s[s->l++] = 0; } else if (op == BAM_CREF_SKIP) { /* Treat CIGAR N as D (not ideal, but better than ignoring it) */ for (i = 0; i < ol; ++i) s->s[s->l++] = 0; if (0 == cigar_n_warning) { cigar_n_warning = -1; fprintf(stderr, "[depad] WARNING: CIGAR op N treated as op D in read %s\n", bam_get_qname(b)); } } else { fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam_get_qname(b)); return -1; } } return length != s->l; } int load_unpadded_ref(faidx_t *fai, const char *ref_name, hts_pos_t ref_len, kstring_t *seq) { char base; char *fai_ref = 0; hts_pos_t fai_ref_len = 0, k; fai_ref = fai_fetch64(fai, ref_name, &fai_ref_len); if (fai_ref_len != ref_len) { fprintf(stderr, "[depad] ERROR: FASTA sequence %s length %"PRIhts_pos", expected %"PRIhts_pos"\n", ref_name, fai_ref_len, ref_len); free(fai_ref); return -1; } ks_resize(seq, ref_len); seq->l = 0; for (k = 0; k < ref_len; ++k) { base = fai_ref[k]; if (base == '-' || base == '*') { // Map gaps to null to match unpad_seq function seq->s[seq->l++] = 0; } else { int i = seq_nt16_table[(int)base]; if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16 fprintf(stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence %s\n", base, (int)base, ref_name); free(fai_ref); return -1; } seq->s[seq->l++] = i; } } assert(ref_len == seq->l); free(fai_ref); return 0; } hts_pos_t get_unpadded_len(faidx_t *fai, const char *ref_name, hts_pos_t padded_len) { char base; char *fai_ref = 0; hts_pos_t fai_ref_len = 0, k; hts_pos_t bases=0, gaps=0; fai_ref = fai_fetch64(fai, ref_name, &fai_ref_len); if (fai_ref_len != padded_len) { fprintf(stderr, "[depad] ERROR: FASTA sequence '%s' length %"PRIhts_pos", expected %"PRIhts_pos"\n", ref_name, fai_ref_len, padded_len); free(fai_ref); return -1; } for (k = 0; k < padded_len; ++k) { //fprintf(stderr, "[depad] checking base %i of %i or %i\n", k+1, ref_len, strlen(fai_ref)); base = fai_ref[k]; if (base == '-' || base == '*') { gaps += 1; } else { int i = seq_nt16_table[(int)base]; if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16 fprintf(stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence '%s'\n", base, (int)base, ref_name); free(fai_ref); return -1; } bases += 1; } } free(fai_ref); assert (padded_len == bases + gaps); return bases; } static inline int * update_posmap(int *posmap, kstring_t ref) { int i, k; posmap = realloc(posmap, ref.m * sizeof(int)); for (i = k = 0; i < ref.l; ++i) { posmap[i] = k; if (ref.s[i]) ++k; } return posmap; } int bam_pad2unpad(samFile *in, samFile *out, sam_hdr_t *h, faidx_t *fai) { bam1_t *b = 0; kstring_t r, q; int r_tid = -1; uint32_t *cigar2 = 0; int ret = 0, *posmap = 0; uint32_t n2 = 0, m2 = 0; b = bam_init1(); if (!b) { fprintf(stderr, "[depad] Couldn't allocate bam struct\n"); return -1; } r.l = r.m = q.l = q.m = 0; r.s = q.s = 0; int read_ret; while ((read_ret = sam_read1(in, h, b)) >= 0) { // read one alignment from `in' // Cannot depad unmapped CRAM data if (b->core.flag & BAM_FUNMAP) goto next_seq; uint32_t *cigar = bam_get_cigar(b); n2 = 0; if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam_get_qname(b), sam_hdr_tid2name(h, b->core.tid)) == 0) { // fprintf(stderr, "[depad] Found embedded reference '%s'\n", bam_get_qname(b)); r_tid = b->core.tid; if (0!=unpad_seq(b, &r)) { fprintf(stderr, "[depad] ERROR: Problem parsing SEQ and/or CIGAR in reference %s\n", bam_get_qname(b)); return -1; }; if (sam_hdr_tid2len(h, r_tid) != r.l) { fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %"PRId64" in BAM header, but %zu in embedded reference\n", bam_get_qname(b), (int64_t) sam_hdr_tid2len(h, r_tid), r.l); return -1; } if (fai) { // Check the embedded reference matches the FASTA file if (load_unpadded_ref(fai, sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), &q)) { fprintf(stderr, "[depad] ERROR: Failed to load embedded reference '%s' from FASTA\n", sam_hdr_tid2name(h, b->core.tid)); return -1; } assert(r.l == q.l); int i; for (i = 0; i < r.l; ++i) { if (r.s[i] != q.s[i]) { // Show gaps as ASCII 45 fprintf(stderr, "[depad] ERROR: Embedded sequence and reference FASTA don't match for %s base %i, '%c' vs '%c'\n", sam_hdr_tid2name(h, b->core.tid), i+1, r.s[i] ? seq_nt16_str[(int)r.s[i]] : 45, q.s[i] ? seq_nt16_str[(int)q.s[i]] : 45); return -1; } } } write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH)); if (replace_cigar(b, n2, cigar2) < 0) return -1; posmap = update_posmap(posmap, r); } else if (b->core.n_cigar > 0) { int i, k, op; if (b->core.tid < 0) { fprintf(stderr, "[depad] ERROR: Read '%s' has CIGAR but no RNAME\n", bam_get_qname(b)); return -1; } else if (b->core.tid == r_tid) { ; // good case, reference available //fprintf(stderr, "[depad] Have ref '%s' for read '%s'\n", h->target_name[b->core.tid], bam_get_qname(b)); } else if (fai) { if (load_unpadded_ref(fai, sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), &r)) { fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", sam_hdr_tid2name(h, b->core.tid)); return -1; } posmap = update_posmap(posmap, r); r_tid = b->core.tid; // fprintf(stderr, "[depad] Loaded %s from FASTA file\n", h->target_name[b->core.tid]); } else { fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence (and no FASTA file)\n", sam_hdr_tid2name(h, b->core.tid)); return -1; } if (0!=unpad_seq(b, &q)) { fprintf(stderr, "[depad] ERROR: Problem parsing SEQ and/or CIGAR in read %s\n", bam_get_qname(b)); return -1; }; if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) { write_cigar(cigar2, n2, m2, cigar[0]); } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) { write_cigar(cigar2, n2, m2, cigar[0]); if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) { write_cigar(cigar2, n2, m2, cigar[1]); } } /* Determine CIGAR operator for each base in the aligned read */ for (i = 0, k = b->core.pos; i < q.l; ++i, ++k) q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD); /* Include any pads if starts with an insert */ if (q.s[0] == BAM_CINS) { for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k); if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD)); k = 0; } else if (q.s[0] == BAM_CPAD) { // Join 'k' CPAD to our first cigar op CPAD too. for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k); } else { k = 0; } /* Count consecutive CIGAR operators to turn into a CIGAR string */ for (i = 1, k++, op = q.s[0]; i < q.l; ++i) { if (op != q.s[i]) { write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op)); op = q.s[i]; k = 1; } else ++k; } write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op)); if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) { write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]); } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) { if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) { write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]); } write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]); } /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */ int pre_op, post_op; for (i = 2; i < n2; ++i) if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) { pre_op = bam_cigar_op(cigar2[i-2]); post_op = bam_cigar_op(cigar2[i]); /* Note don't need to check for X/= as code above will use M only */ if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) { /* This is a redundant P operator */ cigar2[i-1] = 0; // i.e. 0M /* If had same operator either side, combine them in post_op */ if (pre_op == post_op) { /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/ cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op); cigar2[i-2] = 0; // i.e. 0M } } } /* Remove the zero'd operators (0M) */ for (i = k = 0; i < n2; ++i) if (cigar2[i]) cigar2[k++] = cigar2[i]; n2 = k; if (replace_cigar(b, n2, cigar2) < 0) return -1; } /* Even unmapped reads can have a POS value, e.g. if their mate was mapped */ if (b->core.pos != -1) b->core.pos = posmap[b->core.pos]; if (b->core.mtid < 0 || b->core.mpos < 0) { /* Nice case, no mate to worry about*/ // fprintf(stderr, "[depad] Read '%s' mate not mapped\n", bam_get_qname(b)); /* TODO - Warning if FLAG says mate should be mapped? */ /* Clean up funny input where mate position is given but mate reference is missing: */ b->core.mtid = -1; b->core.mpos = -1; } else if (b->core.mtid == b->core.tid) { /* Nice case, same reference */ // fprintf(stderr, "[depad] Read '%s' mate mapped to same ref\n", bam_get_qname(b)); b->core.mpos = posmap[b->core.mpos]; } else { /* Nasty case, Must load alternative posmap */ // fprintf(stderr, "[depad] Loading reference '%s' temporarily\n", h->target_name[b->core.mtid]); if (!fai) { fprintf(stderr, "[depad] ERROR: Needed reference %s sequence for mate (and no FASTA file)\n", sam_hdr_tid2name(h, b->core.mtid)); return -1; } /* Temporarily load the other reference sequence */ if (load_unpadded_ref(fai, sam_hdr_tid2name(h, b->core.mtid), sam_hdr_tid2len(h, b->core.mtid), &r)) { fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", sam_hdr_tid2name(h, b->core.mtid)); return -1; } posmap = update_posmap(posmap, r); b->core.mpos = posmap[b->core.mpos]; /* Restore the reference and posmap*/ if (load_unpadded_ref(fai, sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), &r)) { fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", sam_hdr_tid2name(h, b->core.tid)); return -1; } posmap = update_posmap(posmap, r); } /* Most reads will have been moved so safest to always recalculate the BIN value */ b->core.bin = bam_reg2bin(b->core.pos, bam_endpos(b)); next_seq: if (sam_write1(out, h, b) < 0) { print_error_errno("depad", "error writing to output"); return -1; } } if (read_ret < -1) { fprintf(stderr, "[depad] truncated file.\n"); ret = 1; } free(r.s); free(q.s); free(posmap); free(cigar2); bam_destroy1(b); return ret; } sam_hdr_t * fix_header(sam_hdr_t *old, faidx_t *fai) { int i = 0, ret = 0; hts_pos_t unpadded_len = 0; sam_hdr_t *header = sam_hdr_dup(old); if (!header) return NULL; int nref = sam_hdr_nref(old); char len_buf[64]; for (i = 0; i < nref; ++i) { unpadded_len = get_unpadded_len(fai, sam_hdr_tid2name(old, i), sam_hdr_tid2len(old, i)); if (unpadded_len < 0) { fprintf(stderr, "[depad] ERROR getting unpadded length of '%s', padded length %"PRIhts_pos"\n", sam_hdr_tid2name(old, i), (hts_pos_t) sam_hdr_tid2len(old, i)); } else if (unpadded_len > sam_hdr_tid2len(old, i)) { fprintf(stderr, "[depad] New unpadded length of '%s' is larger than the padded length (%"PRIhts_pos" > %"PRIhts_pos")\n", sam_hdr_tid2name(old, i), unpadded_len, (hts_pos_t) sam_hdr_tid2len(old, i)); ret = 1; } else { sprintf(len_buf, "%"PRIhts_pos"", unpadded_len); if ((ret |= sam_hdr_update_line(header, "SQ", "SN", sam_hdr_tid2name(header, i), "LN", len_buf, NULL))) fprintf(stderr, "[depad] Error updating length of '%s' from %"PRIhts_pos" to %"PRIhts_pos"\n", sam_hdr_tid2name(header, i), (hts_pos_t) sam_hdr_tid2len(header, i), unpadded_len); //fprintf(stderr, "[depad] Recalculating '%s' length %i -> %i\n", old->target_name[i], old->target_len[i], header->target_len[i]); } } if (ret) { sam_hdr_destroy(header); return NULL; } return header; } static int usage(int is_long_help); int main_pad2unpad(int argc, char *argv[]) { samFile *in = 0, *out = 0; sam_hdr_t *h = 0, *h_fix = 0; faidx_t *fai = 0; int c, compress_level = -1, is_long_help = 0, no_pg = 0; char in_mode[5], out_mode[6], *fn_out = 0, *fn_fai = 0, *fn_out_idx = NULL; int ret=0; char *arg_list = NULL; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 'T', '-'), {"no-PG", no_argument, NULL, 1}, { NULL, 0, NULL, 0 } }; /* parse command-line options */ strcpy(in_mode, "r"); strcpy(out_mode, "w"); while ((c = getopt_long(argc, argv, "SCso:u1T:?", lopts, NULL)) >= 0) { switch (c) { case 'S': break; case 'C': hts_parse_format(&ga.out, "cram"); break; case 's': assert(compress_level == -1); hts_parse_format(&ga.out, "sam"); break; case 'o': fn_out = strdup(optarg); break; case 'u': compress_level = 0; if (ga.out.format == unknown_format) hts_parse_format(&ga.out, "bam"); break; case '1': compress_level = 1; if (ga.out.format == unknown_format) hts_parse_format(&ga.out, "bam"); break; case 1: no_pg = 1; break; case '?': is_long_help = 1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n\n", c); return usage(is_long_help); } } if (argc == optind) return usage(is_long_help); strcat(out_mode, "h"); if (compress_level >= 0) { char tmp[2]; tmp[0] = compress_level + '0'; tmp[1] = '\0'; strcat(out_mode, tmp); } // Load FASTA reference (also needed for SAM -> BAM if missing header) if (ga.reference) { fn_fai = fai_path(ga.reference); fai = fai_load3(ga.reference, fn_fai, NULL, FAI_CREATE); } // open file handlers if ((in = sam_open_format(argv[optind], in_mode, &ga.in)) == 0) { print_error_errno("depad", "failed to open \"%s\" for reading", argv[optind]); ret = 1; goto depad_end; } if (fn_fai && hts_set_fai_filename(in, fn_fai) != 0) { fprintf(stderr, "[depad] failed to load reference file \"%s\".\n", fn_fai); ret = 1; goto depad_end; } if ((h = sam_hdr_read(in)) == 0) { fprintf(stderr, "[depad] failed to read the header from \"%s\".\n", argv[optind]); ret = 1; goto depad_end; } if (fai) { if (!(h_fix = fix_header(h, fai))){ fprintf(stderr, "[depad] failed to fix the header from\n"); ret = 1; goto depad_end; } } else { fprintf(stderr, "[depad] Warning - reference lengths will not be corrected without FASTA reference\n"); h_fix = h; } char wmode[2]; strcat(out_mode, sam_open_mode(wmode, fn_out, NULL)==0 ? wmode : "b"); if ((out = sam_open_format(fn_out? fn_out : "-", out_mode, &ga.out)) == 0) { print_error_errno("depad", "failed to open \"%s\" for writing", fn_out? fn_out : "standard output"); ret = 1; goto depad_end; } // Reference-based CRAM won't work unless we also create a new reference. // We could embed this, but for now we take the easy option. if (ga.out.format == cram) hts_set_opt(out, CRAM_OPT_NO_REF, 1); if (!no_pg) { if(!(arg_list = stringify_argv(argc+1, argv-1))) { fprintf(stderr, "[depad] failed to create arg_list\n"); ret = 1; goto depad_end; } if (sam_hdr_add_pg(h_fix, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { fprintf(stderr, "[depad] failed to add PG line to header\n"); ret = 1; goto depad_end; } } if (sam_hdr_write(out, h_fix) != 0) { fprintf(stderr, "[depad] failed to write header.\n"); ret = 1; goto depad_end; } if (ga.write_index) { if (!(fn_out_idx = auto_index(out, fn_out, h_fix))) { ret = 1; goto depad_end; } } // Do the depad if (bam_pad2unpad(in, out, h, fai) != 0) ret = 1; if (ga.write_index) { if (sam_idx_save(out) < 0) { print_error_errno("depad", "writing index failed"); ret = 1; } } depad_end: // close files, free and return free(arg_list); if (fai) fai_destroy(fai); if (h) sam_hdr_destroy(h); if (h_fix && h_fix != h) sam_hdr_destroy(h_fix); if (in) sam_close(in); if (out && sam_close(out) < 0) { fprintf(stderr, "[depad] error on closing output file.\n"); ret = 1; } free(fn_fai); free(fn_out); if (fn_out_idx) free(fn_out_idx); sam_global_args_free(&ga); return ret; } static int usage(int is_long_help) { fprintf(stderr, "\n"); fprintf(stderr, "Usage: samtools depad \n\n"); fprintf(stderr, "Options:\n"); fprintf(stderr, " -s Output is SAM (default is BAM)\n"); fprintf(stderr, " -S Input is SAM (default is BAM)\n"); fprintf(stderr, " -u Uncompressed BAM output (can't use with -s)\n"); fprintf(stderr, " -1 Fast compression BAM output (can't use with -s)\n"); fprintf(stderr, " -T, --reference FILE\n"); fprintf(stderr, " Padded reference sequence file [null]\n"); fprintf(stderr, " -o FILE Output file name [stdout]\n"); fprintf(stderr, " --no-PG do not add a PG line\n"); fprintf(stderr, " -? Longer help\n"); sam_global_opt_help(stderr, "-...--.."); if (is_long_help) fprintf(stderr, "Notes:\n" "\n" "1. Requires embedded reference sequences (before the reads for that reference),\n" " or ideally a FASTA file of the padded reference sequences (via a -T option).\n" "\n" "2. Input padded alignment reads' CIGAR strings must not use P or I operators.\n" "\n"); return 1; } pysam-0.23.0/samtools/padding.c.pysam.c000066400000000000000000000624601475062545500177360ustar00rootroot00000000000000#include "samtools.pysam.h" /* padding.c -- depad subcommand. Copyright (C) 2011, 2012 Broad Institute. Copyright (C) 2014-2016, 2019-2020 Genome Research Ltd. Portions copyright (C) 2012, 2013 Peter Cock, The James Hutton Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include "sam_opts.h" #include "samtools.h" #define bam_reg2bin(b,e) hts_reg2bin((b),(e), 14, 5) static int replace_cigar(bam1_t *b, uint32_t n, uint32_t *cigar) { int diff = 0; if (n != b->core.n_cigar) { int o = b->core.l_qname + b->core.n_cigar * 4; if (n > b->core.n_cigar) { diff = (n - b->core.n_cigar) * 4; if ((INT_MAX - b->l_data)/4 < (n - b->core.n_cigar)) { fprintf(samtools_stderr, "[depad] ERROR: BAM record too big\n"); return -1; } if (b->l_data + diff > b->m_data) { b->m_data = b->l_data + diff; kroundup32(b->m_data); uint8_t *tmp = (uint8_t*)realloc(b->data, b->m_data); if (!tmp) { fprintf(samtools_stderr, "[depad] ERROR: Memory allocation failure.\n"); return -1; } b->data = tmp; } } else { diff = -(int)((b->core.n_cigar - n) * 4); } memmove(b->data + b->core.l_qname + n * 4, b->data + o, b->l_data - o); b->core.n_cigar = n; } memcpy(b->data + b->core.l_qname, cigar, n * 4); b->l_data += diff; return 0; } #define write_cigar(_c, _n, _m, _v) do { \ if (_n == _m) { \ _m = _m? _m<<1 : 4; \ _c = (uint32_t*)realloc(_c, _m * 4); \ if (!(_c)) { \ fprintf(samtools_stderr, "[depad] ERROR: Memory allocation failure.\n"); \ return -1; \ } \ } \ _c[_n++] = (_v); \ } while (0) static int unpad_seq(bam1_t *b, kstring_t *s) { // Returns 0 on success, -1 on an error int k, j, i; int length; int cigar_n_warning = 0; /* Make this a global and limit to one CIGAR N warning? */ uint32_t *cigar = bam_get_cigar(b); uint8_t *seq = bam_get_seq(b); // b->core.l_qseq gives length of the SEQ entry (including soft clips, S) // We need the padded length after alignment from the CIGAR (excluding // soft clips S, but including pads from CIGAR D operations) length = bam_cigar2rlen(b->core.n_cigar, cigar); ks_resize(s, length); for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) { int op, ol; op = bam_cigar_op(cigar[k]); ol = bam_cigar_oplen(cigar[k]); if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam_seqi(seq, j); } else if (op == BAM_CSOFT_CLIP) { j += ol; } else if (op == BAM_CHARD_CLIP) { /* do nothing */ } else if (op == BAM_CDEL) { for (i = 0; i < ol; ++i) s->s[s->l++] = 0; } else if (op == BAM_CREF_SKIP) { /* Treat CIGAR N as D (not ideal, but better than ignoring it) */ for (i = 0; i < ol; ++i) s->s[s->l++] = 0; if (0 == cigar_n_warning) { cigar_n_warning = -1; fprintf(samtools_stderr, "[depad] WARNING: CIGAR op N treated as op D in read %s\n", bam_get_qname(b)); } } else { fprintf(samtools_stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam_get_qname(b)); return -1; } } return length != s->l; } int load_unpadded_ref(faidx_t *fai, const char *ref_name, hts_pos_t ref_len, kstring_t *seq) { char base; char *fai_ref = 0; hts_pos_t fai_ref_len = 0, k; fai_ref = fai_fetch64(fai, ref_name, &fai_ref_len); if (fai_ref_len != ref_len) { fprintf(samtools_stderr, "[depad] ERROR: FASTA sequence %s length %"PRIhts_pos", expected %"PRIhts_pos"\n", ref_name, fai_ref_len, ref_len); free(fai_ref); return -1; } ks_resize(seq, ref_len); seq->l = 0; for (k = 0; k < ref_len; ++k) { base = fai_ref[k]; if (base == '-' || base == '*') { // Map gaps to null to match unpad_seq function seq->s[seq->l++] = 0; } else { int i = seq_nt16_table[(int)base]; if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16 fprintf(samtools_stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence %s\n", base, (int)base, ref_name); free(fai_ref); return -1; } seq->s[seq->l++] = i; } } assert(ref_len == seq->l); free(fai_ref); return 0; } hts_pos_t get_unpadded_len(faidx_t *fai, const char *ref_name, hts_pos_t padded_len) { char base; char *fai_ref = 0; hts_pos_t fai_ref_len = 0, k; hts_pos_t bases=0, gaps=0; fai_ref = fai_fetch64(fai, ref_name, &fai_ref_len); if (fai_ref_len != padded_len) { fprintf(samtools_stderr, "[depad] ERROR: FASTA sequence '%s' length %"PRIhts_pos", expected %"PRIhts_pos"\n", ref_name, fai_ref_len, padded_len); free(fai_ref); return -1; } for (k = 0; k < padded_len; ++k) { //fprintf(samtools_stderr, "[depad] checking base %i of %i or %i\n", k+1, ref_len, strlen(fai_ref)); base = fai_ref[k]; if (base == '-' || base == '*') { gaps += 1; } else { int i = seq_nt16_table[(int)base]; if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16 fprintf(samtools_stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence '%s'\n", base, (int)base, ref_name); free(fai_ref); return -1; } bases += 1; } } free(fai_ref); assert (padded_len == bases + gaps); return bases; } static inline int * update_posmap(int *posmap, kstring_t ref) { int i, k; posmap = realloc(posmap, ref.m * sizeof(int)); for (i = k = 0; i < ref.l; ++i) { posmap[i] = k; if (ref.s[i]) ++k; } return posmap; } int bam_pad2unpad(samFile *in, samFile *out, sam_hdr_t *h, faidx_t *fai) { bam1_t *b = 0; kstring_t r, q; int r_tid = -1; uint32_t *cigar2 = 0; int ret = 0, *posmap = 0; uint32_t n2 = 0, m2 = 0; b = bam_init1(); if (!b) { fprintf(samtools_stderr, "[depad] Couldn't allocate bam struct\n"); return -1; } r.l = r.m = q.l = q.m = 0; r.s = q.s = 0; int read_ret; while ((read_ret = sam_read1(in, h, b)) >= 0) { // read one alignment from `in' // Cannot depad unmapped CRAM data if (b->core.flag & BAM_FUNMAP) goto next_seq; uint32_t *cigar = bam_get_cigar(b); n2 = 0; if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam_get_qname(b), sam_hdr_tid2name(h, b->core.tid)) == 0) { // fprintf(samtools_stderr, "[depad] Found embedded reference '%s'\n", bam_get_qname(b)); r_tid = b->core.tid; if (0!=unpad_seq(b, &r)) { fprintf(samtools_stderr, "[depad] ERROR: Problem parsing SEQ and/or CIGAR in reference %s\n", bam_get_qname(b)); return -1; }; if (sam_hdr_tid2len(h, r_tid) != r.l) { fprintf(samtools_stderr, "[depad] ERROR: (Padded) length of '%s' is %"PRId64" in BAM header, but %zu in embedded reference\n", bam_get_qname(b), (int64_t) sam_hdr_tid2len(h, r_tid), r.l); return -1; } if (fai) { // Check the embedded reference matches the FASTA file if (load_unpadded_ref(fai, sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), &q)) { fprintf(samtools_stderr, "[depad] ERROR: Failed to load embedded reference '%s' from FASTA\n", sam_hdr_tid2name(h, b->core.tid)); return -1; } assert(r.l == q.l); int i; for (i = 0; i < r.l; ++i) { if (r.s[i] != q.s[i]) { // Show gaps as ASCII 45 fprintf(samtools_stderr, "[depad] ERROR: Embedded sequence and reference FASTA don't match for %s base %i, '%c' vs '%c'\n", sam_hdr_tid2name(h, b->core.tid), i+1, r.s[i] ? seq_nt16_str[(int)r.s[i]] : 45, q.s[i] ? seq_nt16_str[(int)q.s[i]] : 45); return -1; } } } write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH)); if (replace_cigar(b, n2, cigar2) < 0) return -1; posmap = update_posmap(posmap, r); } else if (b->core.n_cigar > 0) { int i, k, op; if (b->core.tid < 0) { fprintf(samtools_stderr, "[depad] ERROR: Read '%s' has CIGAR but no RNAME\n", bam_get_qname(b)); return -1; } else if (b->core.tid == r_tid) { ; // good case, reference available //fprintf(samtools_stderr, "[depad] Have ref '%s' for read '%s'\n", h->target_name[b->core.tid], bam_get_qname(b)); } else if (fai) { if (load_unpadded_ref(fai, sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), &r)) { fprintf(samtools_stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", sam_hdr_tid2name(h, b->core.tid)); return -1; } posmap = update_posmap(posmap, r); r_tid = b->core.tid; // fprintf(samtools_stderr, "[depad] Loaded %s from FASTA file\n", h->target_name[b->core.tid]); } else { fprintf(samtools_stderr, "[depad] ERROR: Missing %s embedded reference sequence (and no FASTA file)\n", sam_hdr_tid2name(h, b->core.tid)); return -1; } if (0!=unpad_seq(b, &q)) { fprintf(samtools_stderr, "[depad] ERROR: Problem parsing SEQ and/or CIGAR in read %s\n", bam_get_qname(b)); return -1; }; if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) { write_cigar(cigar2, n2, m2, cigar[0]); } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) { write_cigar(cigar2, n2, m2, cigar[0]); if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) { write_cigar(cigar2, n2, m2, cigar[1]); } } /* Determine CIGAR operator for each base in the aligned read */ for (i = 0, k = b->core.pos; i < q.l; ++i, ++k) q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD); /* Include any pads if starts with an insert */ if (q.s[0] == BAM_CINS) { for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k); if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD)); k = 0; } else if (q.s[0] == BAM_CPAD) { // Join 'k' CPAD to our first cigar op CPAD too. for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k); } else { k = 0; } /* Count consecutive CIGAR operators to turn into a CIGAR string */ for (i = 1, k++, op = q.s[0]; i < q.l; ++i) { if (op != q.s[i]) { write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op)); op = q.s[i]; k = 1; } else ++k; } write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op)); if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) { write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]); } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) { if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) { write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]); } write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]); } /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */ int pre_op, post_op; for (i = 2; i < n2; ++i) if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) { pre_op = bam_cigar_op(cigar2[i-2]); post_op = bam_cigar_op(cigar2[i]); /* Note don't need to check for X/= as code above will use M only */ if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) { /* This is a redundant P operator */ cigar2[i-1] = 0; // i.e. 0M /* If had same operator either side, combine them in post_op */ if (pre_op == post_op) { /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/ cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op); cigar2[i-2] = 0; // i.e. 0M } } } /* Remove the zero'd operators (0M) */ for (i = k = 0; i < n2; ++i) if (cigar2[i]) cigar2[k++] = cigar2[i]; n2 = k; if (replace_cigar(b, n2, cigar2) < 0) return -1; } /* Even unmapped reads can have a POS value, e.g. if their mate was mapped */ if (b->core.pos != -1) b->core.pos = posmap[b->core.pos]; if (b->core.mtid < 0 || b->core.mpos < 0) { /* Nice case, no mate to worry about*/ // fprintf(samtools_stderr, "[depad] Read '%s' mate not mapped\n", bam_get_qname(b)); /* TODO - Warning if FLAG says mate should be mapped? */ /* Clean up funny input where mate position is given but mate reference is missing: */ b->core.mtid = -1; b->core.mpos = -1; } else if (b->core.mtid == b->core.tid) { /* Nice case, same reference */ // fprintf(samtools_stderr, "[depad] Read '%s' mate mapped to same ref\n", bam_get_qname(b)); b->core.mpos = posmap[b->core.mpos]; } else { /* Nasty case, Must load alternative posmap */ // fprintf(samtools_stderr, "[depad] Loading reference '%s' temporarily\n", h->target_name[b->core.mtid]); if (!fai) { fprintf(samtools_stderr, "[depad] ERROR: Needed reference %s sequence for mate (and no FASTA file)\n", sam_hdr_tid2name(h, b->core.mtid)); return -1; } /* Temporarily load the other reference sequence */ if (load_unpadded_ref(fai, sam_hdr_tid2name(h, b->core.mtid), sam_hdr_tid2len(h, b->core.mtid), &r)) { fprintf(samtools_stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", sam_hdr_tid2name(h, b->core.mtid)); return -1; } posmap = update_posmap(posmap, r); b->core.mpos = posmap[b->core.mpos]; /* Restore the reference and posmap*/ if (load_unpadded_ref(fai, sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), &r)) { fprintf(samtools_stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", sam_hdr_tid2name(h, b->core.tid)); return -1; } posmap = update_posmap(posmap, r); } /* Most reads will have been moved so safest to always recalculate the BIN value */ b->core.bin = bam_reg2bin(b->core.pos, bam_endpos(b)); next_seq: if (sam_write1(out, h, b) < 0) { print_error_errno("depad", "error writing to output"); return -1; } } if (read_ret < -1) { fprintf(samtools_stderr, "[depad] truncated file.\n"); ret = 1; } free(r.s); free(q.s); free(posmap); free(cigar2); bam_destroy1(b); return ret; } sam_hdr_t * fix_header(sam_hdr_t *old, faidx_t *fai) { int i = 0, ret = 0; hts_pos_t unpadded_len = 0; sam_hdr_t *header = sam_hdr_dup(old); if (!header) return NULL; int nref = sam_hdr_nref(old); char len_buf[64]; for (i = 0; i < nref; ++i) { unpadded_len = get_unpadded_len(fai, sam_hdr_tid2name(old, i), sam_hdr_tid2len(old, i)); if (unpadded_len < 0) { fprintf(samtools_stderr, "[depad] ERROR getting unpadded length of '%s', padded length %"PRIhts_pos"\n", sam_hdr_tid2name(old, i), (hts_pos_t) sam_hdr_tid2len(old, i)); } else if (unpadded_len > sam_hdr_tid2len(old, i)) { fprintf(samtools_stderr, "[depad] New unpadded length of '%s' is larger than the padded length (%"PRIhts_pos" > %"PRIhts_pos")\n", sam_hdr_tid2name(old, i), unpadded_len, (hts_pos_t) sam_hdr_tid2len(old, i)); ret = 1; } else { sprintf(len_buf, "%"PRIhts_pos"", unpadded_len); if ((ret |= sam_hdr_update_line(header, "SQ", "SN", sam_hdr_tid2name(header, i), "LN", len_buf, NULL))) fprintf(samtools_stderr, "[depad] Error updating length of '%s' from %"PRIhts_pos" to %"PRIhts_pos"\n", sam_hdr_tid2name(header, i), (hts_pos_t) sam_hdr_tid2len(header, i), unpadded_len); //fprintf(samtools_stderr, "[depad] Recalculating '%s' length %i -> %i\n", old->target_name[i], old->target_len[i], header->target_len[i]); } } if (ret) { sam_hdr_destroy(header); return NULL; } return header; } static int usage(int is_long_help); int main_pad2unpad(int argc, char *argv[]) { samFile *in = 0, *out = 0; sam_hdr_t *h = 0, *h_fix = 0; faidx_t *fai = 0; int c, compress_level = -1, is_long_help = 0, no_pg = 0; char in_mode[5], out_mode[6], *fn_out = 0, *fn_fai = 0, *fn_out_idx = NULL; int ret=0; char *arg_list = NULL; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 'T', '-'), {"no-PG", no_argument, NULL, 1}, { NULL, 0, NULL, 0 } }; /* parse command-line options */ strcpy(in_mode, "r"); strcpy(out_mode, "w"); while ((c = getopt_long(argc, argv, "SCso:u1T:?", lopts, NULL)) >= 0) { switch (c) { case 'S': break; case 'C': hts_parse_format(&ga.out, "cram"); break; case 's': assert(compress_level == -1); hts_parse_format(&ga.out, "sam"); break; case 'o': fn_out = strdup(optarg); break; case 'u': compress_level = 0; if (ga.out.format == unknown_format) hts_parse_format(&ga.out, "bam"); break; case '1': compress_level = 1; if (ga.out.format == unknown_format) hts_parse_format(&ga.out, "bam"); break; case 1: no_pg = 1; break; case '?': is_long_help = 1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; fprintf(samtools_stderr, "[bam_fillmd] unrecognized option '-%c'\n\n", c); return usage(is_long_help); } } if (argc == optind) return usage(is_long_help); strcat(out_mode, "h"); if (compress_level >= 0) { char tmp[2]; tmp[0] = compress_level + '0'; tmp[1] = '\0'; strcat(out_mode, tmp); } // Load FASTA reference (also needed for SAM -> BAM if missing header) if (ga.reference) { fn_fai = fai_path(ga.reference); fai = fai_load3(ga.reference, fn_fai, NULL, FAI_CREATE); } // open file handlers if ((in = sam_open_format(argv[optind], in_mode, &ga.in)) == 0) { print_error_errno("depad", "failed to open \"%s\" for reading", argv[optind]); ret = 1; goto depad_end; } if (fn_fai && hts_set_fai_filename(in, fn_fai) != 0) { fprintf(samtools_stderr, "[depad] failed to load reference file \"%s\".\n", fn_fai); ret = 1; goto depad_end; } if ((h = sam_hdr_read(in)) == 0) { fprintf(samtools_stderr, "[depad] failed to read the header from \"%s\".\n", argv[optind]); ret = 1; goto depad_end; } if (fai) { if (!(h_fix = fix_header(h, fai))){ fprintf(samtools_stderr, "[depad] failed to fix the header from\n"); ret = 1; goto depad_end; } } else { fprintf(samtools_stderr, "[depad] Warning - reference lengths will not be corrected without FASTA reference\n"); h_fix = h; } char wmode[2]; strcat(out_mode, sam_open_mode(wmode, fn_out, NULL)==0 ? wmode : "b"); if ((out = sam_open_format(fn_out? fn_out : "-", out_mode, &ga.out)) == 0) { print_error_errno("depad", "failed to open \"%s\" for writing", fn_out? fn_out : "standard output"); ret = 1; goto depad_end; } // Reference-based CRAM won't work unless we also create a new reference. // We could embed this, but for now we take the easy option. if (ga.out.format == cram) hts_set_opt(out, CRAM_OPT_NO_REF, 1); if (!no_pg) { if(!(arg_list = stringify_argv(argc+1, argv-1))) { fprintf(samtools_stderr, "[depad] failed to create arg_list\n"); ret = 1; goto depad_end; } if (sam_hdr_add_pg(h_fix, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { fprintf(samtools_stderr, "[depad] failed to add PG line to header\n"); ret = 1; goto depad_end; } } if (sam_hdr_write(out, h_fix) != 0) { fprintf(samtools_stderr, "[depad] failed to write header.\n"); ret = 1; goto depad_end; } if (ga.write_index) { if (!(fn_out_idx = auto_index(out, fn_out, h_fix))) { ret = 1; goto depad_end; } } // Do the depad if (bam_pad2unpad(in, out, h, fai) != 0) ret = 1; if (ga.write_index) { if (sam_idx_save(out) < 0) { print_error_errno("depad", "writing index failed"); ret = 1; } } depad_end: // close files, free and return free(arg_list); if (fai) fai_destroy(fai); if (h) sam_hdr_destroy(h); if (h_fix && h_fix != h) sam_hdr_destroy(h_fix); if (in) sam_close(in); if (out && sam_close(out) < 0) { fprintf(samtools_stderr, "[depad] error on closing output file.\n"); ret = 1; } free(fn_fai); free(fn_out); if (fn_out_idx) free(fn_out_idx); sam_global_args_free(&ga); return ret; } static int usage(int is_long_help) { fprintf(samtools_stderr, "\n"); fprintf(samtools_stderr, "Usage: samtools depad \n\n"); fprintf(samtools_stderr, "Options:\n"); fprintf(samtools_stderr, " -s Output is SAM (default is BAM)\n"); fprintf(samtools_stderr, " -S Input is SAM (default is BAM)\n"); fprintf(samtools_stderr, " -u Uncompressed BAM output (can't use with -s)\n"); fprintf(samtools_stderr, " -1 Fast compression BAM output (can't use with -s)\n"); fprintf(samtools_stderr, " -T, --reference FILE\n"); fprintf(samtools_stderr, " Padded reference sequence file [null]\n"); fprintf(samtools_stderr, " -o FILE Output file name [samtools_stdout]\n"); fprintf(samtools_stderr, " --no-PG do not add a PG line\n"); fprintf(samtools_stderr, " -? Longer help\n"); sam_global_opt_help(samtools_stderr, "-...--.."); if (is_long_help) fprintf(samtools_stderr, "Notes:\n" "\n" "1. Requires embedded reference sequences (before the reads for that reference),\n" " or ideally a FASTA file of the padded reference sequences (via a -T option).\n" "\n" "2. Input padded alignment reads' CIGAR strings must not use P or I operators.\n" "\n"); return 1; } pysam-0.23.0/samtools/phase.c000066400000000000000000000725531475062545500160630ustar00rootroot00000000000000/* phase.c -- phase subcommand. Copyright (C) 2011 Broad Institute. Copyright (C) 2013-2016, 2019 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "htslib/hts.h" #include "htslib/sam.h" #include "htslib/kstring.h" #include "sam_opts.h" #include "samtools.h" #include "htslib/hts_os.h" #include "htslib/kseq.h" KSTREAM_INIT(gzFile, gzread, 16384) #define MAX_VARS 256 #define FLIP_PENALTY 2 #define FLIP_THRES 4 #define MASK_THRES 3 #define FLAG_FIX_CHIMERA 0x1 #define FLAG_LIST_EXCL 0x4 #define FLAG_DROP_AMBI 0x8 typedef struct { // configurations, initialized in the main function int flag, k, min_baseQ, min_varLOD, max_depth, no_pg; // other global variables int vpos_shift; samFile* fp; sam_hdr_t* fp_hdr; char *pre, *arg_list; char *out_name[3]; samFile* out[3]; sam_hdr_t* out_hdr[3]; // alignment queue int n, m; bam1_t **b; } phaseg_t; typedef struct { int8_t seq[MAX_VARS]; // TODO: change to dynamic memory allocation! int vpos, beg, end; uint32_t vlen:16, single:1, flip:1, phase:1, phased:1, ambig:1; uint32_t in:16, out:16; // in-phase and out-phase } frag_t, *frag_p; #define rseq_lt(a,b) ((a)->vpos < (b)->vpos) #include "htslib/khash.h" KHASH_SET_INIT_INT64(set64) KHASH_MAP_INIT_INT64(64, frag_t) typedef khash_t(64) nseq_t; #include "htslib/ksort.h" KSORT_INIT(rseq, frag_p, rseq_lt) static inline uint64_t X31_hash_string(const char *s) { uint64_t h = *s; if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s; return h; } static void count1(int l, const uint8_t *seq, int *cnt) { int i, j, n_ambi; uint32_t z, x; if (seq[l-1] == 0) return; // do nothing is the last base is ambiguous for (i = n_ambi = 0; i < l; ++i) // collect ambiguous bases if (seq[i] == 0) ++n_ambi; if (l - n_ambi <= 1) return; // only one SNP for (x = 0; x < 1u<>j&1; ++j; } z = z<<1 | c; } ++cnt[z]; } } static int **count_all(int l, int vpos, nseq_t *hash) { khint_t k; int i, j, **cnt = NULL; uint8_t *seq = NULL; size_t cnt_sz = ((size_t)1) << l; if (cnt_sz > SSIZE_MAX / sizeof(int) / vpos) { errno = ENOMEM; goto fail; } seq = calloc(l, 1); if (!seq) goto fail; cnt = calloc(vpos, sizeof(int*)); if (!cnt) goto fail; for (i = 0; i < vpos; ++i) { cnt[i] = calloc(cnt_sz, sizeof(int)); if (!cnt[i]) goto fail; } for (k = 0; k < kh_end(hash); ++k) { if (kh_exist(hash, k)) { frag_t *f = &kh_val(hash, k); if (f->vpos >= vpos || f->single) continue; // out of region; or singleton if (f->vlen == 1) { // such reads should be flagged as deleted previously if everything is right f->single = 1; continue; } for (j = 1; j < f->vlen; ++j) { for (i = 0; i < l; ++i) seq[i] = j < l - 1 - i? 0 : f->seq[j - (l - 1 - i)]; count1(l, seq, cnt[f->vpos + j]); } } } free(seq); return cnt; fail: free(seq); if (cnt) { for (i = 0; i < vpos; i++) free(cnt[i]); free(cnt); } print_error_errno("phase", "Couldn't allocate memory for counts"); return NULL; } // phasing static int8_t *dynaprog(int l, int vpos, int **w) { int *f[2], *curr, *prev, max, i; int8_t **b, *h = 0; uint32_t x, z = 1u<<(l-1), mask = (1u<>1; y1 = xc>>1; c0 = prev[y0] + wi[x] + wi[xc]; c1 = prev[y1] + wi[x] + wi[xc]; if (c0 > c1) bi[x] = 0, curr[x] = c0; else bi[x] = 1, curr[x] = c1; } tmp = prev; prev = curr; curr = tmp; // swap } { // backtrack uint32_t max_x = 0; int which = 0; h = calloc(vpos, 1); for (x = 0, max = 0, max_x = 0; x < z; ++x) if (prev[x] > max) max = prev[x], max_x = x; for (i = vpos - 1, x = max_x; i >= 0; --i) { h[i] = which? (~x&1) : (x&1); which = b[i][x]? !which : which; x = b[i][x]? (~x&mask)>>1 : x>>1; } } // free for (i = 0; i < vpos; ++i) free(b[i]); free(f[0]); free(f[1]); free(b); return h; } // phase each fragment static uint64_t *fragphase(int vpos, const int8_t *path, nseq_t *hash, int flip) { khint_t k; uint64_t *pcnt; uint32_t *left, *rght, max; left = rght = 0; max = 0; pcnt = calloc(vpos, 8); for (k = 0; k < kh_end(hash); ++k) { if (kh_exist(hash, k)) { int i, c[2]; frag_t *f = &kh_val(hash, k); if (f->vpos >= vpos) continue; // get the phase c[0] = c[1] = 0; for (i = 0; i < f->vlen; ++i) { if (f->seq[i] == 0) continue; ++c[f->seq[i] == path[f->vpos + i] + 1? 0 : 1]; } f->phase = c[0] > c[1]? 0 : 1; f->in = c[f->phase]; f->out = c[1 - f->phase]; f->phased = f->in == f->out? 0 : 1; f->ambig = (f->in && f->out && f->out < 3 && f->in <= f->out + 1)? 1 : 0; // fix chimera f->flip = 0; if (flip && c[0] >= 3 && c[1] >= 3) { int sum[2], m, mi, md; if (f->vlen > max) { // enlarge the array max = f->vlen; kroundup32(max); left = realloc(left, max * 4); rght = realloc(rght, max * 4); } for (i = 0, sum[0] = sum[1] = 0; i < f->vlen; ++i) { // get left counts if (f->seq[i]) { int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1; ++sum[c == path[f->vpos + i]? 0 : 1]; } left[i] = sum[1]<<16 | sum[0]; } for (i = f->vlen - 1, sum[0] = sum[1] = 0; i >= 0; --i) { // get right counts if (f->seq[i]) { int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1; ++sum[c == path[f->vpos + i]? 0 : 1]; } rght[i] = sum[1]<<16 | sum[0]; } // find the best flip point for (i = m = 0, mi = -1, md = -1; i < f->vlen - 1; ++i) { int a[2]; a[0] = (left[i]&0xffff) + (rght[i+1]>>16&0xffff) - (rght[i+1]&0xffff) * FLIP_PENALTY; a[1] = (left[i]>>16&0xffff) + (rght[i+1]&0xffff) - (rght[i+1]>>16&0xffff) * FLIP_PENALTY; if (a[0] > a[1]) { if (a[0] > m) m = a[0], md = 0, mi = i; } else { if (a[1] > m) m = a[1], md = 1, mi = i; } } if (m - c[0] >= FLIP_THRES && m - c[1] >= FLIP_THRES) { // then flip f->flip = 1; if (md == 0) { // flip the tail for (i = mi + 1; i < f->vlen; ++i) if (f->seq[i] == 1) f->seq[i] = 2; else if (f->seq[i] == 2) f->seq[i] = 1; } else { // flip the head for (i = 0; i <= mi; ++i) if (f->seq[i] == 1) f->seq[i] = 2; else if (f->seq[i] == 2) f->seq[i] = 1; } } } // update pcnt[] if (!f->single) { for (i = 0; i < f->vlen; ++i) { int c; if (f->seq[i] == 0) continue; c = f->phase? 2 - f->seq[i] : f->seq[i] - 1; if (c == path[f->vpos + i]) { if (f->phase == 0) ++pcnt[f->vpos + i]; else pcnt[f->vpos + i] += 1ull<<32; } else { if (f->phase == 0) pcnt[f->vpos + i] += 1<<16; else pcnt[f->vpos + i] += 1ull<<48; } } } } } free(left); free(rght); return pcnt; } static uint64_t *genmask(int vpos, const uint64_t *pcnt, int *_n) { int i, max = 0, max_i = -1, m = 0, n = 0, beg = 0, score = 0; uint64_t *list = 0; for (i = 0; i < vpos; ++i) { uint64_t x = pcnt[i]; int c[4], pre = score, s; c[0] = x&0xffff; c[1] = x>>16&0xffff; c[2] = x>>32&0xffff; c[3] = x>>48&0xffff; s = (c[1] + c[3] == 0)? -(c[0] + c[2]) : (c[1] + c[3] - 1); if (c[3] > c[2]) s += c[3] - c[2]; if (c[1] > c[0]) s += c[1] - c[0]; score += s; if (score < 0) score = 0; if (pre == 0 && score > 0) beg = i; // change from zero to non-zero if ((i == vpos - 1 || score == 0) && max >= MASK_THRES) { if (n == m) { m = m? m<<1 : 4; list = realloc(list, m * 8); } list[n++] = (uint64_t)beg<<32 | max_i; i = max_i; // reset i to max_i score = 0; } else if (score > max) max = score, max_i = i; if (score == 0) max = 0; } *_n = n; return list; } // trim heading and tailing ambiguous bases; mark deleted and remove sequence static int clean_seqs(int vpos, nseq_t *hash) { khint_t k; int ret = 0; for (k = 0; k < kh_end(hash); ++k) { if (kh_exist(hash, k)) { frag_t *f = &kh_val(hash, k); int beg, end, i; if (f->vpos >= vpos) { ret = 1; continue; } for (i = 0; i < f->vlen; ++i) if (f->seq[i] != 0) break; beg = i; for (i = f->vlen - 1; i >= 0; --i) if (f->seq[i] != 0) break; end = i + 1; if (end - beg <= 0) kh_del(64, hash, k); else { if (beg != 0) memmove(f->seq, f->seq + beg, end - beg); f->vpos += beg; f->vlen = end - beg; f->single = f->vlen == 1? 1 : 0; } } } return ret; } static int dump_aln(phaseg_t *g, int min_pos, const nseq_t *hash) { int i, is_flip, drop_ambi; drop_ambi = g->flag & FLAG_DROP_AMBI; is_flip = (drand48() < 0.5); for (i = 0; i < g->n; ++i) { int end, which; uint64_t key; khint_t k; bam1_t *b = g->b[i]; key = X31_hash_string(bam_get_qname(b)); end = bam_endpos(b); if (end > min_pos) break; k = kh_get(64, hash, key); if (k == kh_end(hash)) which = 3; else { frag_t *f = &kh_val(hash, k); if (f->ambig) which = drop_ambi? 2 : 3; else if (f->phased && f->flip) which = 2; else if (f->phased == 0) which = 3; else { // phased and not flipped char c = 'Y'; which = f->phase; bam_aux_append(b, "ZP", 'A', 1, (uint8_t*)&c); } if (which < 2 && is_flip) which = 1 - which; // increase the randomness } if (which == 3) which = (drand48() < 0.5); if (sam_write1(g->out[which], g->out_hdr[which], b) < 0) { print_error_errno("phase", "error writing to '%s'", g->out_name[which]); return -1; } bam_destroy1(b); g->b[i] = 0; } memmove(g->b, g->b + i, (g->n - i) * sizeof(void*)); g->n -= i; return 0; } static int phase(phaseg_t *g, const char *chr, int vpos, uint64_t *cns, nseq_t *hash) { int i, j, n_seqs = kh_size(hash), n_masked = 0, min_pos; khint_t k; frag_t **seqs; int8_t *path, *sitemask; uint64_t *pcnt, *regmask; if (vpos == 0) return 0; i = clean_seqs(vpos, hash); // i is true if hash has an element with its vpos >= vpos min_pos = i? cns[vpos]>>32 : 0x7fffffff; if (vpos == 1) { printf("PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1); printf("M0\t%s\t%d\t%d\t%c\t%c\t%d\t0\t0\t0\t0\n//\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1, "ACGTX"[cns[0]&3], "ACGTX"[cns[0]>>16&3], g->vpos_shift + 1); for (k = 0; k < kh_end(hash); ++k) { if (kh_exist(hash, k)) { frag_t *f = &kh_val(hash, k); if (f->vpos) continue; f->flip = 0; if (f->seq[0] == 0) f->phased = 0; else f->phased = 1, f->phase = f->seq[0] - 1; } } if (dump_aln(g, min_pos, hash) < 0) return -1; ++g->vpos_shift; return 1; } { // phase int **cnt; uint64_t *mask; printf("PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[vpos-1]>>32) + 1); sitemask = calloc(vpos, 1); cnt = count_all(g->k, vpos, hash); if (!cnt) return -1; path = dynaprog(g->k, vpos, cnt); for (i = 0; i < vpos; ++i) free(cnt[i]); free(cnt); pcnt = fragphase(vpos, path, hash, 0); // do not fix chimeras when masking mask = genmask(vpos, pcnt, &n_masked); regmask = calloc(n_masked, 8); for (i = 0; i < n_masked; ++i) { regmask[i] = cns[mask[i]>>32]>>32<<32 | cns[(uint32_t)mask[i]]>>32; for (j = mask[i]>>32; j <= (int32_t)mask[i]; ++j) sitemask[j] = 1; } free(mask); if (g->flag & FLAG_FIX_CHIMERA) { free(pcnt); pcnt = fragphase(vpos, path, hash, 1); } } for (i = 0; i < n_masked; ++i) printf("FL\t%s\t%d\t%d\n", chr, (int)(regmask[i]>>32) + 1, (int)regmask[i] + 1); for (i = 0; i < vpos; ++i) { uint64_t x = pcnt[i]; int8_t c[2]; c[0] = (cns[i]&0xffff)>>2 == 0? 4 : (cns[i]&3); c[1] = (cns[i]>>16&0xffff)>>2 == 0? 4 : (cns[i]>>16&3); printf("M%d\t%s\t%d\t%d\t%c\t%c\t%d\t%d\t%d\t%d\t%d\n", sitemask[i]+1, chr, (int)(cns[0]>>32) + 1, (int)(cns[i]>>32) + 1, "ACGTX"[c[path[i]]], "ACGTX"[c[1-path[i]]], i + g->vpos_shift + 1, (int)(x&0xffff), (int)(x>>16&0xffff), (int)(x>>32&0xffff), (int)(x>>48&0xffff)); } free(path); free(pcnt); free(regmask); free(sitemask); seqs = calloc(n_seqs, sizeof(frag_t*)); for (k = 0, i = 0; k < kh_end(hash); ++k) if (kh_exist(hash, k) && kh_val(hash, k).vpos < vpos && !kh_val(hash, k).single) seqs[i++] = &kh_val(hash, k); n_seqs = i; ks_introsort_rseq(n_seqs, seqs); for (i = 0; i < n_seqs; ++i) { frag_t *f = seqs[i]; printf("EV\t0\t%s\t%d\t40\t%dM\t*\t0\t0\t", chr, f->vpos + 1 + g->vpos_shift, f->vlen); for (j = 0; j < f->vlen; ++j) { uint32_t c = cns[f->vpos + j]; if (f->seq[j] == 0) putchar('N'); else putchar("ACGT"[f->seq[j] == 1? (c&3) : (c>>16&3)]); } printf("\t*\tYP:i:%d\tYF:i:%d\tYI:i:%d\tYO:i:%d\tYS:i:%d\n", f->phase, f->flip, f->in, f->out, f->beg+1); } free(seqs); printf("//\n"); fflush(stdout); g->vpos_shift += vpos; if (dump_aln(g, min_pos, hash) < 0) return -1; return vpos; } static void update_vpos(int vpos, nseq_t *hash) { khint_t k; for (k = 0; k < kh_end(hash); ++k) { if (kh_exist(hash, k)) { frag_t *f = &kh_val(hash, k); if (f->vpos < vpos) kh_del(64, hash, k); // TODO: if frag_t::seq is allocated dynamically, free it else f->vpos -= vpos; } } } static nseq_t *shrink_hash(nseq_t *hash) // TODO: to implement { return hash; } static int readaln(void *data, bam1_t *b) { phaseg_t *g = (phaseg_t*)data; int ret; while (1) { ret = sam_read1(g->fp, g->fp_hdr, b); if (ret < 0) break; if ( b->core.flag & (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP) ) continue; if ( g->pre ) { if (g->n == g->m) { g->m = g->m? g->m<<1 : 16; g->b = realloc(g->b, g->m * sizeof(bam1_t*)); } g->b[g->n++] = bam_dup1(b); } break; } return ret; } static khash_t(set64) *loadpos(const char *fn, sam_hdr_t *h) { gzFile fp; kstream_t *ks; int ret, dret; kstring_t *str; khash_t(set64) *hash; fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r"); if (fp == NULL) { print_error_errno("phase", "Couldn't open site file '%s'", fn); return NULL; } hash = kh_init(set64); str = calloc(1, sizeof(kstring_t)); ks = ks_init(fp); while (ks_getuntil(ks, 0, str, &dret) >= 0) { int tid = bam_name2id(h, str->s); if (tid >= 0 && dret != '\n') { if (ks_getuntil(ks, 0, str, &dret) >= 0) { uint64_t x = (uint64_t)tid<<32 | (atoi(str->s) - 1); kh_put(set64, hash, x, &ret); } else break; } if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n'); if (dret < 0) break; } ks_destroy(ks); gzclose(fp); free(str->s); free(str); return hash; } static int gl2cns(float q[16]) { int i, j, min_ij; float min, min2; min = min2 = 1e30; min_ij = -1; for (i = 0; i < 4; ++i) { for (j = i; j < 4; ++j) { if (q[i<<2|j] < min) min_ij = i<<2|j, min2 = min, min = q[i<<2|j]; else if (q[i<<2|j] < min2) min2 = q[i<<2|j]; } } return (min_ij>>2&3) == (min_ij&3)? 0 : 1<<18 | (min_ij>>2&3)<<16 | (min_ij&3) | (int)(min2 - min + .499) << 2; } static int start_output(phaseg_t *g, int c, const char *middle, const htsFormat *fmt) { kstring_t s = { 0, 0, NULL }; ksprintf(&s, "%s.%s.%s", g->pre, middle, hts_format_file_extension(fmt)); g->out_name[c] = ks_release(&s); g->out[c] = sam_open_format(g->out_name[c], "wb", fmt); if (! g->out[c]) { print_error_errno("phase", "Failed to open output file '%s'", g->out_name[c]); return -1; } g->out_hdr[c] = sam_hdr_dup(g->fp_hdr); if (!g->no_pg && sam_hdr_add_pg(g->out_hdr[c], "samtools", "VN", samtools_version(), g->arg_list ? "CL": NULL, g->arg_list ? g->arg_list : NULL, NULL)) { print_error("phase", "failed to add PG line to header"); return -1; } if (sam_hdr_write(g->out[c], g->out_hdr[c]) < 0) { print_error_errno("phase", "Failed to write header for '%s'", g->out_name[c]); return -1; } return 0; } int main_phase(int argc, char *argv[]) { int c, tid, pos, vpos = 0, n, lasttid = -1, max_vpos = 0, usage = 0; int status = EXIT_SUCCESS; const bam_pileup1_t *plp; bam_plp_t iter; nseq_t *seqs; uint64_t *cns = 0; phaseg_t g; char *fn_list = 0; khash_t(set64) *set = 0; errmod_t *em; uint16_t *bases; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0, '-'), {"min-BQ", required_argument, NULL, 'Q'}, {"min-bq", required_argument, NULL, 'Q'}, {"no-PG", no_argument, NULL, 1}, { NULL, 0, NULL, 0 } }; // FIXME Leaks galore in the case of error returns memset(&g, 0, sizeof(phaseg_t)); g.flag = FLAG_FIX_CHIMERA; g.min_varLOD = 37; g.k = 13; g.min_baseQ = 13; g.max_depth = 256; while ((c = getopt_long(argc, argv, "Q:eFq:k:b:l:D:A", lopts, NULL)) >= 0) { switch (c) { case 'D': g.max_depth = atoi(optarg); break; case 'q': g.min_varLOD = atoi(optarg); break; case 'Q': g.min_baseQ = atoi(optarg); break; case 'k': g.k = atoi(optarg); break; case 'F': g.flag &= ~FLAG_FIX_CHIMERA; break; case 'e': g.flag |= FLAG_LIST_EXCL; break; case 'A': g.flag |= FLAG_DROP_AMBI; break; case 'b': g.pre = strdup(optarg); break; case 'l': fn_list = strdup(optarg); break; case 1: g.no_pg = 1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage=1; break; } if (usage) break; } if (usage || argc == optind) { fprintf(stderr, "\n"); fprintf(stderr, "Usage: samtools phase [options] \n\n"); fprintf(stderr, "Options: -k INT block length [%d]\n", g.k); fprintf(stderr, " -b STR prefix of BAMs to output [null]\n"); fprintf(stderr, " -q INT min het phred-LOD [%d]\n", g.min_varLOD); fprintf(stderr, " -Q, --min-BQ INT\n" " min base quality in het calling [%d]\n", g.min_baseQ); fprintf(stderr, " -D INT max read depth [%d]\n", g.max_depth); // fprintf(stderr, " -l FILE list of sites to phase [null]\n"); fprintf(stderr, " -F do not attempt to fix chimeras\n"); fprintf(stderr, " -A drop reads with ambiguous phase\n"); fprintf(stderr, " --no-PG do not add a PG line\n"); // fprintf(stderr, " -e do not discover SNPs (effective with -l)\n"); fprintf(stderr, "\n"); sam_global_opt_help(stderr, "-....--."); return 1; } g.fp = sam_open_format(argv[optind], "r", &ga.in); if (!g.fp) { print_error_errno("phase", "Couldn't open '%s'", argv[optind]); return 1; } g.fp_hdr = sam_hdr_read(g.fp); if (g.fp_hdr == NULL) { fprintf(stderr, "[%s] Failed to read header for '%s'\n", __func__, argv[optind]); return 1; } if (!g.no_pg && !(g.arg_list = stringify_argv(argc+1, argv-1))) { print_error("phase", "failed to create arg_list"); return 1; } if (fn_list) { // read the list of sites to phase set = loadpos(fn_list, g.fp_hdr); if (set == NULL) return 1; free(fn_list); } else g.flag &= ~FLAG_LIST_EXCL; if (g.pre) { // open BAMs to write if (ga.out.format == unknown_format) ga.out.format = bam; // default via "wb". // Open each output file g.out[0..2], dupping and writing the header if (start_output(&g, 0, "0", &ga.out) < 0 || start_output(&g, 1, "1", &ga.out) < 0 || start_output(&g, 2, "chimera", &ga.out) < 0) return 1; } iter = bam_plp_init(readaln, &g); g.vpos_shift = 0; seqs = kh_init(64); em = errmod_init(1. - 0.83); bases = calloc(g.max_depth, 2); printf("CC\n"); printf("CC\tDescriptions:\nCC\n"); printf("CC\t CC comments\n"); printf("CC\t PS start of a phase set\n"); printf("CC\t FL filtered region\n"); printf("CC\t M[012] markers; 0 for singletons, 1 for phased and 2 for filtered\n"); printf("CC\t EV supporting reads; SAM format\n"); printf("CC\t // end of a phase set\nCC\n"); printf("CC\tFormats of PS, FL and M[012] lines (1-based coordinates):\nCC\n"); printf("CC\t PS chr phaseSetStart phaseSetEnd\n"); printf("CC\t FL chr filterStart filterEnd\n"); printf("CC\t M? chr PS pos allele0 allele1 hetIndex #supports0 #errors0 #supp1 #err1\n"); printf("CC\nCC\n"); fflush(stdout); while ((plp = bam_plp_auto(iter, &tid, &pos, &n)) != 0) { int i, k, c, tmp, dophase = 1, in_set = 0; float q[16]; if (tid < 0) break; if (tid != lasttid) { // change of chromosome g.vpos_shift = 0; if (lasttid >= 0) { seqs = shrink_hash(seqs); if (phase(&g, sam_hdr_tid2name(g.fp_hdr, lasttid), vpos, cns, seqs) < 0) { return 1; } update_vpos(0x7fffffff, seqs); } lasttid = tid; vpos = 0; } if (set && kh_get(set64, set, (uint64_t)tid<<32 | pos) != kh_end(set)) in_set = 1; if (n > g.max_depth) continue; // do not proceed if the depth is too high // fill the bases array and check if there is a variant for (i = k = 0; i < n; ++i) { const bam_pileup1_t *p = plp + i; uint8_t *seq; int q, baseQ, b; if (p->is_del || p->is_refskip) continue; baseQ = bam_get_qual(p->b)[p->qpos]; if (baseQ < g.min_baseQ) continue; seq = bam_get_seq(p->b); b = seq_nt16_int[bam_seqi(seq, p->qpos)]; if (b > 3) continue; q = baseQ < p->b->core.qual? baseQ : p->b->core.qual; if (q < 4) q = 4; if (q > 63) q = 63; bases[k++] = q<<5 | (int)bam_is_rev(p->b)<<4 | b; } if (k == 0) continue; errmod_cal(em, k, 4, bases, q); // compute genotype likelihood c = gl2cns(q); // get the consensus // tell if to proceed if (set && (g.flag&FLAG_LIST_EXCL) && !in_set) continue; // not in the list if (!in_set && (c&0xffff)>>2 < g.min_varLOD) continue; // not a variant // add the variant if (vpos == max_vpos) { max_vpos = max_vpos? max_vpos<<1 : 128; cns = realloc(cns, max_vpos * 8); } cns[vpos] = (uint64_t)pos<<32 | c; for (i = 0; i < n; ++i) { const bam_pileup1_t *p = plp + i; uint64_t key; khint_t k; uint8_t *seq = bam_get_seq(p->b); frag_t *f; if (p->is_del || p->is_refskip) continue; if (p->b->core.qual == 0) continue; // get the base code c = seq_nt16_int[bam_seqi(seq, p->qpos)]; if (c == (cns[vpos]&3)) c = 1; else if (c == (cns[vpos]>>16&3)) c = 2; else c = 0; // write to seqs key = X31_hash_string(bam_get_qname(p->b)); k = kh_put(64, seqs, key, &tmp); f = &kh_val(seqs, k); if (tmp == 0) { // present in the hash table if (vpos - f->vpos + 1 < MAX_VARS) { f->vlen = vpos - f->vpos + 1; f->seq[f->vlen-1] = c; f->end = bam_endpos(p->b); } dophase = 0; } else { // absent memset(f->seq, 0, MAX_VARS); f->beg = p->b->core.pos; f->end = bam_endpos(p->b); f->vpos = vpos, f->vlen = 1, f->seq[0] = c, f->single = f->phased = f->flip = f->ambig = 0; } } if (dophase) { seqs = shrink_hash(seqs); if (phase(&g, sam_hdr_tid2name(g.fp_hdr, tid), vpos, cns, seqs) < 0) { return 1; } update_vpos(vpos, seqs); cns[0] = cns[vpos]; vpos = 0; } ++vpos; } if (tid >= 0) { if (phase(&g, sam_hdr_tid2name(g.fp_hdr, tid), vpos, cns, seqs) < 0) { return 1; } } if (n < 0) { print_error("phase", "error reading from '%s'", argv[optind]); status = EXIT_FAILURE; } sam_hdr_destroy(g.fp_hdr); bam_plp_destroy(iter); sam_close(g.fp); kh_destroy(64, seqs); kh_destroy(set64, set); free(cns); errmod_destroy(em); free(bases); if (g.pre) { int res = 0; for (c = 0; c <= 2; ++c) { if (sam_close(g.out[c]) < 0) { fprintf(stderr, "[%s] error on closing '%s'\n", __func__, g.out_name[c]); res = 1; } sam_hdr_destroy(g.out_hdr[c]); free(g.out_name[c]); } free(g.pre); free(g.b); if (res) return 1; } free(g.arg_list); sam_global_args_free(&ga); return status; } pysam-0.23.0/samtools/phase.c.pysam.c000066400000000000000000000737021475062545500174310ustar00rootroot00000000000000#include "samtools.pysam.h" /* phase.c -- phase subcommand. Copyright (C) 2011 Broad Institute. Copyright (C) 2013-2016, 2019 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "htslib/hts.h" #include "htslib/sam.h" #include "htslib/kstring.h" #include "sam_opts.h" #include "samtools.h" #include "htslib/hts_os.h" #include "htslib/kseq.h" KSTREAM_INIT(gzFile, gzread, 16384) #define MAX_VARS 256 #define FLIP_PENALTY 2 #define FLIP_THRES 4 #define MASK_THRES 3 #define FLAG_FIX_CHIMERA 0x1 #define FLAG_LIST_EXCL 0x4 #define FLAG_DROP_AMBI 0x8 typedef struct { // configurations, initialized in the main function int flag, k, min_baseQ, min_varLOD, max_depth, no_pg; // other global variables int vpos_shift; samFile* fp; sam_hdr_t* fp_hdr; char *pre, *arg_list; char *out_name[3]; samFile* out[3]; sam_hdr_t* out_hdr[3]; // alignment queue int n, m; bam1_t **b; } phaseg_t; typedef struct { int8_t seq[MAX_VARS]; // TODO: change to dynamic memory allocation! int vpos, beg, end; uint32_t vlen:16, single:1, flip:1, phase:1, phased:1, ambig:1; uint32_t in:16, out:16; // in-phase and out-phase } frag_t, *frag_p; #define rseq_lt(a,b) ((a)->vpos < (b)->vpos) #include "htslib/khash.h" KHASH_SET_INIT_INT64(set64) KHASH_MAP_INIT_INT64(64, frag_t) typedef khash_t(64) nseq_t; #include "htslib/ksort.h" KSORT_INIT(rseq, frag_p, rseq_lt) static inline uint64_t X31_hash_string(const char *s) { uint64_t h = *s; if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s; return h; } static void count1(int l, const uint8_t *seq, int *cnt) { int i, j, n_ambi; uint32_t z, x; if (seq[l-1] == 0) return; // do nothing is the last base is ambiguous for (i = n_ambi = 0; i < l; ++i) // collect ambiguous bases if (seq[i] == 0) ++n_ambi; if (l - n_ambi <= 1) return; // only one SNP for (x = 0; x < 1u<>j&1; ++j; } z = z<<1 | c; } ++cnt[z]; } } static int **count_all(int l, int vpos, nseq_t *hash) { khint_t k; int i, j, **cnt = NULL; uint8_t *seq = NULL; size_t cnt_sz = ((size_t)1) << l; if (cnt_sz > SSIZE_MAX / sizeof(int) / vpos) { errno = ENOMEM; goto fail; } seq = calloc(l, 1); if (!seq) goto fail; cnt = calloc(vpos, sizeof(int*)); if (!cnt) goto fail; for (i = 0; i < vpos; ++i) { cnt[i] = calloc(cnt_sz, sizeof(int)); if (!cnt[i]) goto fail; } for (k = 0; k < kh_end(hash); ++k) { if (kh_exist(hash, k)) { frag_t *f = &kh_val(hash, k); if (f->vpos >= vpos || f->single) continue; // out of region; or singleton if (f->vlen == 1) { // such reads should be flagged as deleted previously if everything is right f->single = 1; continue; } for (j = 1; j < f->vlen; ++j) { for (i = 0; i < l; ++i) seq[i] = j < l - 1 - i? 0 : f->seq[j - (l - 1 - i)]; count1(l, seq, cnt[f->vpos + j]); } } } free(seq); return cnt; fail: free(seq); if (cnt) { for (i = 0; i < vpos; i++) free(cnt[i]); free(cnt); } print_error_errno("phase", "Couldn't allocate memory for counts"); return NULL; } // phasing static int8_t *dynaprog(int l, int vpos, int **w) { int *f[2], *curr, *prev, max, i; int8_t **b, *h = 0; uint32_t x, z = 1u<<(l-1), mask = (1u<>1; y1 = xc>>1; c0 = prev[y0] + wi[x] + wi[xc]; c1 = prev[y1] + wi[x] + wi[xc]; if (c0 > c1) bi[x] = 0, curr[x] = c0; else bi[x] = 1, curr[x] = c1; } tmp = prev; prev = curr; curr = tmp; // swap } { // backtrack uint32_t max_x = 0; int which = 0; h = calloc(vpos, 1); for (x = 0, max = 0, max_x = 0; x < z; ++x) if (prev[x] > max) max = prev[x], max_x = x; for (i = vpos - 1, x = max_x; i >= 0; --i) { h[i] = which? (~x&1) : (x&1); which = b[i][x]? !which : which; x = b[i][x]? (~x&mask)>>1 : x>>1; } } // free for (i = 0; i < vpos; ++i) free(b[i]); free(f[0]); free(f[1]); free(b); return h; } // phase each fragment static uint64_t *fragphase(int vpos, const int8_t *path, nseq_t *hash, int flip) { khint_t k; uint64_t *pcnt; uint32_t *left, *rght, max; left = rght = 0; max = 0; pcnt = calloc(vpos, 8); for (k = 0; k < kh_end(hash); ++k) { if (kh_exist(hash, k)) { int i, c[2]; frag_t *f = &kh_val(hash, k); if (f->vpos >= vpos) continue; // get the phase c[0] = c[1] = 0; for (i = 0; i < f->vlen; ++i) { if (f->seq[i] == 0) continue; ++c[f->seq[i] == path[f->vpos + i] + 1? 0 : 1]; } f->phase = c[0] > c[1]? 0 : 1; f->in = c[f->phase]; f->out = c[1 - f->phase]; f->phased = f->in == f->out? 0 : 1; f->ambig = (f->in && f->out && f->out < 3 && f->in <= f->out + 1)? 1 : 0; // fix chimera f->flip = 0; if (flip && c[0] >= 3 && c[1] >= 3) { int sum[2], m, mi, md; if (f->vlen > max) { // enlarge the array max = f->vlen; kroundup32(max); left = realloc(left, max * 4); rght = realloc(rght, max * 4); } for (i = 0, sum[0] = sum[1] = 0; i < f->vlen; ++i) { // get left counts if (f->seq[i]) { int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1; ++sum[c == path[f->vpos + i]? 0 : 1]; } left[i] = sum[1]<<16 | sum[0]; } for (i = f->vlen - 1, sum[0] = sum[1] = 0; i >= 0; --i) { // get right counts if (f->seq[i]) { int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1; ++sum[c == path[f->vpos + i]? 0 : 1]; } rght[i] = sum[1]<<16 | sum[0]; } // find the best flip point for (i = m = 0, mi = -1, md = -1; i < f->vlen - 1; ++i) { int a[2]; a[0] = (left[i]&0xffff) + (rght[i+1]>>16&0xffff) - (rght[i+1]&0xffff) * FLIP_PENALTY; a[1] = (left[i]>>16&0xffff) + (rght[i+1]&0xffff) - (rght[i+1]>>16&0xffff) * FLIP_PENALTY; if (a[0] > a[1]) { if (a[0] > m) m = a[0], md = 0, mi = i; } else { if (a[1] > m) m = a[1], md = 1, mi = i; } } if (m - c[0] >= FLIP_THRES && m - c[1] >= FLIP_THRES) { // then flip f->flip = 1; if (md == 0) { // flip the tail for (i = mi + 1; i < f->vlen; ++i) if (f->seq[i] == 1) f->seq[i] = 2; else if (f->seq[i] == 2) f->seq[i] = 1; } else { // flip the head for (i = 0; i <= mi; ++i) if (f->seq[i] == 1) f->seq[i] = 2; else if (f->seq[i] == 2) f->seq[i] = 1; } } } // update pcnt[] if (!f->single) { for (i = 0; i < f->vlen; ++i) { int c; if (f->seq[i] == 0) continue; c = f->phase? 2 - f->seq[i] : f->seq[i] - 1; if (c == path[f->vpos + i]) { if (f->phase == 0) ++pcnt[f->vpos + i]; else pcnt[f->vpos + i] += 1ull<<32; } else { if (f->phase == 0) pcnt[f->vpos + i] += 1<<16; else pcnt[f->vpos + i] += 1ull<<48; } } } } } free(left); free(rght); return pcnt; } static uint64_t *genmask(int vpos, const uint64_t *pcnt, int *_n) { int i, max = 0, max_i = -1, m = 0, n = 0, beg = 0, score = 0; uint64_t *list = 0; for (i = 0; i < vpos; ++i) { uint64_t x = pcnt[i]; int c[4], pre = score, s; c[0] = x&0xffff; c[1] = x>>16&0xffff; c[2] = x>>32&0xffff; c[3] = x>>48&0xffff; s = (c[1] + c[3] == 0)? -(c[0] + c[2]) : (c[1] + c[3] - 1); if (c[3] > c[2]) s += c[3] - c[2]; if (c[1] > c[0]) s += c[1] - c[0]; score += s; if (score < 0) score = 0; if (pre == 0 && score > 0) beg = i; // change from zero to non-zero if ((i == vpos - 1 || score == 0) && max >= MASK_THRES) { if (n == m) { m = m? m<<1 : 4; list = realloc(list, m * 8); } list[n++] = (uint64_t)beg<<32 | max_i; i = max_i; // reset i to max_i score = 0; } else if (score > max) max = score, max_i = i; if (score == 0) max = 0; } *_n = n; return list; } // trim heading and tailing ambiguous bases; mark deleted and remove sequence static int clean_seqs(int vpos, nseq_t *hash) { khint_t k; int ret = 0; for (k = 0; k < kh_end(hash); ++k) { if (kh_exist(hash, k)) { frag_t *f = &kh_val(hash, k); int beg, end, i; if (f->vpos >= vpos) { ret = 1; continue; } for (i = 0; i < f->vlen; ++i) if (f->seq[i] != 0) break; beg = i; for (i = f->vlen - 1; i >= 0; --i) if (f->seq[i] != 0) break; end = i + 1; if (end - beg <= 0) kh_del(64, hash, k); else { if (beg != 0) memmove(f->seq, f->seq + beg, end - beg); f->vpos += beg; f->vlen = end - beg; f->single = f->vlen == 1? 1 : 0; } } } return ret; } static int dump_aln(phaseg_t *g, int min_pos, const nseq_t *hash) { int i, is_flip, drop_ambi; drop_ambi = g->flag & FLAG_DROP_AMBI; is_flip = (drand48() < 0.5); for (i = 0; i < g->n; ++i) { int end, which; uint64_t key; khint_t k; bam1_t *b = g->b[i]; key = X31_hash_string(bam_get_qname(b)); end = bam_endpos(b); if (end > min_pos) break; k = kh_get(64, hash, key); if (k == kh_end(hash)) which = 3; else { frag_t *f = &kh_val(hash, k); if (f->ambig) which = drop_ambi? 2 : 3; else if (f->phased && f->flip) which = 2; else if (f->phased == 0) which = 3; else { // phased and not flipped char c = 'Y'; which = f->phase; bam_aux_append(b, "ZP", 'A', 1, (uint8_t*)&c); } if (which < 2 && is_flip) which = 1 - which; // increase the randomness } if (which == 3) which = (drand48() < 0.5); if (sam_write1(g->out[which], g->out_hdr[which], b) < 0) { print_error_errno("phase", "error writing to '%s'", g->out_name[which]); return -1; } bam_destroy1(b); g->b[i] = 0; } memmove(g->b, g->b + i, (g->n - i) * sizeof(void*)); g->n -= i; return 0; } static int phase(phaseg_t *g, const char *chr, int vpos, uint64_t *cns, nseq_t *hash) { int i, j, n_seqs = kh_size(hash), n_masked = 0, min_pos; khint_t k; frag_t **seqs; int8_t *path, *sitemask; uint64_t *pcnt, *regmask; if (vpos == 0) return 0; i = clean_seqs(vpos, hash); // i is true if hash has an element with its vpos >= vpos min_pos = i? cns[vpos]>>32 : 0x7fffffff; if (vpos == 1) { fprintf(samtools_stdout, "PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1); fprintf(samtools_stdout, "M0\t%s\t%d\t%d\t%c\t%c\t%d\t0\t0\t0\t0\n//\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1, "ACGTX"[cns[0]&3], "ACGTX"[cns[0]>>16&3], g->vpos_shift + 1); for (k = 0; k < kh_end(hash); ++k) { if (kh_exist(hash, k)) { frag_t *f = &kh_val(hash, k); if (f->vpos) continue; f->flip = 0; if (f->seq[0] == 0) f->phased = 0; else f->phased = 1, f->phase = f->seq[0] - 1; } } if (dump_aln(g, min_pos, hash) < 0) return -1; ++g->vpos_shift; return 1; } { // phase int **cnt; uint64_t *mask; fprintf(samtools_stdout, "PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[vpos-1]>>32) + 1); sitemask = calloc(vpos, 1); cnt = count_all(g->k, vpos, hash); if (!cnt) return -1; path = dynaprog(g->k, vpos, cnt); for (i = 0; i < vpos; ++i) free(cnt[i]); free(cnt); pcnt = fragphase(vpos, path, hash, 0); // do not fix chimeras when masking mask = genmask(vpos, pcnt, &n_masked); regmask = calloc(n_masked, 8); for (i = 0; i < n_masked; ++i) { regmask[i] = cns[mask[i]>>32]>>32<<32 | cns[(uint32_t)mask[i]]>>32; for (j = mask[i]>>32; j <= (int32_t)mask[i]; ++j) sitemask[j] = 1; } free(mask); if (g->flag & FLAG_FIX_CHIMERA) { free(pcnt); pcnt = fragphase(vpos, path, hash, 1); } } for (i = 0; i < n_masked; ++i) fprintf(samtools_stdout, "FL\t%s\t%d\t%d\n", chr, (int)(regmask[i]>>32) + 1, (int)regmask[i] + 1); for (i = 0; i < vpos; ++i) { uint64_t x = pcnt[i]; int8_t c[2]; c[0] = (cns[i]&0xffff)>>2 == 0? 4 : (cns[i]&3); c[1] = (cns[i]>>16&0xffff)>>2 == 0? 4 : (cns[i]>>16&3); fprintf(samtools_stdout, "M%d\t%s\t%d\t%d\t%c\t%c\t%d\t%d\t%d\t%d\t%d\n", sitemask[i]+1, chr, (int)(cns[0]>>32) + 1, (int)(cns[i]>>32) + 1, "ACGTX"[c[path[i]]], "ACGTX"[c[1-path[i]]], i + g->vpos_shift + 1, (int)(x&0xffff), (int)(x>>16&0xffff), (int)(x>>32&0xffff), (int)(x>>48&0xffff)); } free(path); free(pcnt); free(regmask); free(sitemask); seqs = calloc(n_seqs, sizeof(frag_t*)); for (k = 0, i = 0; k < kh_end(hash); ++k) if (kh_exist(hash, k) && kh_val(hash, k).vpos < vpos && !kh_val(hash, k).single) seqs[i++] = &kh_val(hash, k); n_seqs = i; ks_introsort_rseq(n_seqs, seqs); for (i = 0; i < n_seqs; ++i) { frag_t *f = seqs[i]; fprintf(samtools_stdout, "EV\t0\t%s\t%d\t40\t%dM\t*\t0\t0\t", chr, f->vpos + 1 + g->vpos_shift, f->vlen); for (j = 0; j < f->vlen; ++j) { uint32_t c = cns[f->vpos + j]; if (f->seq[j] == 0) fputc('N', samtools_stdout); else fputc("ACGT"[f->seq[j] == 1? (c&3) : (c>>16&3)], samtools_stdout); } fprintf(samtools_stdout, "\t*\tYP:i:%d\tYF:i:%d\tYI:i:%d\tYO:i:%d\tYS:i:%d\n", f->phase, f->flip, f->in, f->out, f->beg+1); } free(seqs); fprintf(samtools_stdout, "//\n"); fflush(samtools_stdout); g->vpos_shift += vpos; if (dump_aln(g, min_pos, hash) < 0) return -1; return vpos; } static void update_vpos(int vpos, nseq_t *hash) { khint_t k; for (k = 0; k < kh_end(hash); ++k) { if (kh_exist(hash, k)) { frag_t *f = &kh_val(hash, k); if (f->vpos < vpos) kh_del(64, hash, k); // TODO: if frag_t::seq is allocated dynamically, free it else f->vpos -= vpos; } } } static nseq_t *shrink_hash(nseq_t *hash) // TODO: to implement { return hash; } static int readaln(void *data, bam1_t *b) { phaseg_t *g = (phaseg_t*)data; int ret; while (1) { ret = sam_read1(g->fp, g->fp_hdr, b); if (ret < 0) break; if ( b->core.flag & (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP) ) continue; if ( g->pre ) { if (g->n == g->m) { g->m = g->m? g->m<<1 : 16; g->b = realloc(g->b, g->m * sizeof(bam1_t*)); } g->b[g->n++] = bam_dup1(b); } break; } return ret; } static khash_t(set64) *loadpos(const char *fn, sam_hdr_t *h) { gzFile fp; kstream_t *ks; int ret, dret; kstring_t *str; khash_t(set64) *hash; fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r"); if (fp == NULL) { print_error_errno("phase", "Couldn't open site file '%s'", fn); return NULL; } hash = kh_init(set64); str = calloc(1, sizeof(kstring_t)); ks = ks_init(fp); while (ks_getuntil(ks, 0, str, &dret) >= 0) { int tid = bam_name2id(h, str->s); if (tid >= 0 && dret != '\n') { if (ks_getuntil(ks, 0, str, &dret) >= 0) { uint64_t x = (uint64_t)tid<<32 | (atoi(str->s) - 1); kh_put(set64, hash, x, &ret); } else break; } if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n'); if (dret < 0) break; } ks_destroy(ks); gzclose(fp); free(str->s); free(str); return hash; } static int gl2cns(float q[16]) { int i, j, min_ij; float min, min2; min = min2 = 1e30; min_ij = -1; for (i = 0; i < 4; ++i) { for (j = i; j < 4; ++j) { if (q[i<<2|j] < min) min_ij = i<<2|j, min2 = min, min = q[i<<2|j]; else if (q[i<<2|j] < min2) min2 = q[i<<2|j]; } } return (min_ij>>2&3) == (min_ij&3)? 0 : 1<<18 | (min_ij>>2&3)<<16 | (min_ij&3) | (int)(min2 - min + .499) << 2; } static int start_output(phaseg_t *g, int c, const char *middle, const htsFormat *fmt) { kstring_t s = { 0, 0, NULL }; ksprintf(&s, "%s.%s.%s", g->pre, middle, hts_format_file_extension(fmt)); g->out_name[c] = ks_release(&s); g->out[c] = sam_open_format(g->out_name[c], "wb", fmt); if (! g->out[c]) { print_error_errno("phase", "Failed to open output file '%s'", g->out_name[c]); return -1; } g->out_hdr[c] = sam_hdr_dup(g->fp_hdr); if (!g->no_pg && sam_hdr_add_pg(g->out_hdr[c], "samtools", "VN", samtools_version(), g->arg_list ? "CL": NULL, g->arg_list ? g->arg_list : NULL, NULL)) { print_error("phase", "failed to add PG line to header"); return -1; } if (sam_hdr_write(g->out[c], g->out_hdr[c]) < 0) { print_error_errno("phase", "Failed to write header for '%s'", g->out_name[c]); return -1; } return 0; } int main_phase(int argc, char *argv[]) { int c, tid, pos, vpos = 0, n, lasttid = -1, max_vpos = 0, usage = 0; int status = EXIT_SUCCESS; const bam_pileup1_t *plp; bam_plp_t iter; nseq_t *seqs; uint64_t *cns = 0; phaseg_t g; char *fn_list = 0; khash_t(set64) *set = 0; errmod_t *em; uint16_t *bases; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0, '-'), {"min-BQ", required_argument, NULL, 'Q'}, {"min-bq", required_argument, NULL, 'Q'}, {"no-PG", no_argument, NULL, 1}, { NULL, 0, NULL, 0 } }; // FIXME Leaks galore in the case of error returns memset(&g, 0, sizeof(phaseg_t)); g.flag = FLAG_FIX_CHIMERA; g.min_varLOD = 37; g.k = 13; g.min_baseQ = 13; g.max_depth = 256; while ((c = getopt_long(argc, argv, "Q:eFq:k:b:l:D:A", lopts, NULL)) >= 0) { switch (c) { case 'D': g.max_depth = atoi(optarg); break; case 'q': g.min_varLOD = atoi(optarg); break; case 'Q': g.min_baseQ = atoi(optarg); break; case 'k': g.k = atoi(optarg); break; case 'F': g.flag &= ~FLAG_FIX_CHIMERA; break; case 'e': g.flag |= FLAG_LIST_EXCL; break; case 'A': g.flag |= FLAG_DROP_AMBI; break; case 'b': g.pre = strdup(optarg); break; case 'l': fn_list = strdup(optarg); break; case 1: g.no_pg = 1; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage=1; break; } if (usage) break; } if (usage || argc == optind) { fprintf(samtools_stderr, "\n"); fprintf(samtools_stderr, "Usage: samtools phase [options] \n\n"); fprintf(samtools_stderr, "Options: -k INT block length [%d]\n", g.k); fprintf(samtools_stderr, " -b STR prefix of BAMs to output [null]\n"); fprintf(samtools_stderr, " -q INT min het phred-LOD [%d]\n", g.min_varLOD); fprintf(samtools_stderr, " -Q, --min-BQ INT\n" " min base quality in het calling [%d]\n", g.min_baseQ); fprintf(samtools_stderr, " -D INT max read depth [%d]\n", g.max_depth); // fprintf(samtools_stderr, " -l FILE list of sites to phase [null]\n"); fprintf(samtools_stderr, " -F do not attempt to fix chimeras\n"); fprintf(samtools_stderr, " -A drop reads with ambiguous phase\n"); fprintf(samtools_stderr, " --no-PG do not add a PG line\n"); // fprintf(samtools_stderr, " -e do not discover SNPs (effective with -l)\n"); fprintf(samtools_stderr, "\n"); sam_global_opt_help(samtools_stderr, "-....--."); return 1; } g.fp = sam_open_format(argv[optind], "r", &ga.in); if (!g.fp) { print_error_errno("phase", "Couldn't open '%s'", argv[optind]); return 1; } g.fp_hdr = sam_hdr_read(g.fp); if (g.fp_hdr == NULL) { fprintf(samtools_stderr, "[%s] Failed to read header for '%s'\n", __func__, argv[optind]); return 1; } if (!g.no_pg && !(g.arg_list = stringify_argv(argc+1, argv-1))) { print_error("phase", "failed to create arg_list"); return 1; } if (fn_list) { // read the list of sites to phase set = loadpos(fn_list, g.fp_hdr); if (set == NULL) return 1; free(fn_list); } else g.flag &= ~FLAG_LIST_EXCL; if (g.pre) { // open BAMs to write if (ga.out.format == unknown_format) ga.out.format = bam; // default via "wb". // Open each output file g.out[0..2], dupping and writing the header if (start_output(&g, 0, "0", &ga.out) < 0 || start_output(&g, 1, "1", &ga.out) < 0 || start_output(&g, 2, "chimera", &ga.out) < 0) return 1; } iter = bam_plp_init(readaln, &g); g.vpos_shift = 0; seqs = kh_init(64); em = errmod_init(1. - 0.83); bases = calloc(g.max_depth, 2); fprintf(samtools_stdout, "CC\n"); fprintf(samtools_stdout, "CC\tDescriptions:\nCC\n"); fprintf(samtools_stdout, "CC\t CC comments\n"); fprintf(samtools_stdout, "CC\t PS start of a phase set\n"); fprintf(samtools_stdout, "CC\t FL filtered region\n"); fprintf(samtools_stdout, "CC\t M[012] markers; 0 for singletons, 1 for phased and 2 for filtered\n"); fprintf(samtools_stdout, "CC\t EV supporting reads; SAM format\n"); fprintf(samtools_stdout, "CC\t // end of a phase set\nCC\n"); fprintf(samtools_stdout, "CC\tFormats of PS, FL and M[012] lines (1-based coordinates):\nCC\n"); fprintf(samtools_stdout, "CC\t PS chr phaseSetStart phaseSetEnd\n"); fprintf(samtools_stdout, "CC\t FL chr filterStart filterEnd\n"); fprintf(samtools_stdout, "CC\t M? chr PS pos allele0 allele1 hetIndex #supports0 #errors0 #supp1 #err1\n"); fprintf(samtools_stdout, "CC\nCC\n"); fflush(samtools_stdout); while ((plp = bam_plp_auto(iter, &tid, &pos, &n)) != 0) { int i, k, c, tmp, dophase = 1, in_set = 0; float q[16]; if (tid < 0) break; if (tid != lasttid) { // change of chromosome g.vpos_shift = 0; if (lasttid >= 0) { seqs = shrink_hash(seqs); if (phase(&g, sam_hdr_tid2name(g.fp_hdr, lasttid), vpos, cns, seqs) < 0) { return 1; } update_vpos(0x7fffffff, seqs); } lasttid = tid; vpos = 0; } if (set && kh_get(set64, set, (uint64_t)tid<<32 | pos) != kh_end(set)) in_set = 1; if (n > g.max_depth) continue; // do not proceed if the depth is too high // fill the bases array and check if there is a variant for (i = k = 0; i < n; ++i) { const bam_pileup1_t *p = plp + i; uint8_t *seq; int q, baseQ, b; if (p->is_del || p->is_refskip) continue; baseQ = bam_get_qual(p->b)[p->qpos]; if (baseQ < g.min_baseQ) continue; seq = bam_get_seq(p->b); b = seq_nt16_int[bam_seqi(seq, p->qpos)]; if (b > 3) continue; q = baseQ < p->b->core.qual? baseQ : p->b->core.qual; if (q < 4) q = 4; if (q > 63) q = 63; bases[k++] = q<<5 | (int)bam_is_rev(p->b)<<4 | b; } if (k == 0) continue; errmod_cal(em, k, 4, bases, q); // compute genotype likelihood c = gl2cns(q); // get the consensus // tell if to proceed if (set && (g.flag&FLAG_LIST_EXCL) && !in_set) continue; // not in the list if (!in_set && (c&0xffff)>>2 < g.min_varLOD) continue; // not a variant // add the variant if (vpos == max_vpos) { max_vpos = max_vpos? max_vpos<<1 : 128; cns = realloc(cns, max_vpos * 8); } cns[vpos] = (uint64_t)pos<<32 | c; for (i = 0; i < n; ++i) { const bam_pileup1_t *p = plp + i; uint64_t key; khint_t k; uint8_t *seq = bam_get_seq(p->b); frag_t *f; if (p->is_del || p->is_refskip) continue; if (p->b->core.qual == 0) continue; // get the base code c = seq_nt16_int[bam_seqi(seq, p->qpos)]; if (c == (cns[vpos]&3)) c = 1; else if (c == (cns[vpos]>>16&3)) c = 2; else c = 0; // write to seqs key = X31_hash_string(bam_get_qname(p->b)); k = kh_put(64, seqs, key, &tmp); f = &kh_val(seqs, k); if (tmp == 0) { // present in the hash table if (vpos - f->vpos + 1 < MAX_VARS) { f->vlen = vpos - f->vpos + 1; f->seq[f->vlen-1] = c; f->end = bam_endpos(p->b); } dophase = 0; } else { // absent memset(f->seq, 0, MAX_VARS); f->beg = p->b->core.pos; f->end = bam_endpos(p->b); f->vpos = vpos, f->vlen = 1, f->seq[0] = c, f->single = f->phased = f->flip = f->ambig = 0; } } if (dophase) { seqs = shrink_hash(seqs); if (phase(&g, sam_hdr_tid2name(g.fp_hdr, tid), vpos, cns, seqs) < 0) { return 1; } update_vpos(vpos, seqs); cns[0] = cns[vpos]; vpos = 0; } ++vpos; } if (tid >= 0) { if (phase(&g, sam_hdr_tid2name(g.fp_hdr, tid), vpos, cns, seqs) < 0) { return 1; } } if (n < 0) { print_error("phase", "error reading from '%s'", argv[optind]); status = EXIT_FAILURE; } sam_hdr_destroy(g.fp_hdr); bam_plp_destroy(iter); sam_close(g.fp); kh_destroy(64, seqs); kh_destroy(set64, set); free(cns); errmod_destroy(em); free(bases); if (g.pre) { int res = 0; for (c = 0; c <= 2; ++c) { if (sam_close(g.out[c]) < 0) { fprintf(samtools_stderr, "[%s] error on closing '%s'\n", __func__, g.out_name[c]); res = 1; } sam_hdr_destroy(g.out_hdr[c]); free(g.out_name[c]); } free(g.pre); free(g.b); if (res) return 1; } free(g.arg_list); sam_global_args_free(&ga); return status; } pysam-0.23.0/samtools/reference.c000066400000000000000000000443261475062545500167160ustar00rootroot00000000000000/* bam_reference.c -- extracts an embedded reference from a CRAM file, or creates it from alignments plus MD:Z tags. Copyright (C) 2022 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "htslib/sam.h" #include "htslib/cram.h" #include "samtools.h" #include "sam_opts.h" /* * There are two main modes of operation. * * 1. Extracting the reference from the CRAM file embed_ref blocks. * 2. Generation of reference by analysing consensus plus patches applied * via MD tags. * * The first is very rapid, but only applies to a CRAM files generated with * the specific options (not commonly used and not the default). The second * is a slow operation, but applies to any data type. * * This is also a testing ground for a future CRAM auto-embed-ref option that * permits the use of an embedded reference without having to first extract * the reference. (Note this may require the creation of MD tags during * decode by use of an existing embedded reference, if the records don't * have an MD tag themselves, but that's an issue for htslib when we get * there.) */ /* * --------------------------------------------------------------------------- * Shared utility functions by both methods. */ #define haszero(x) (((x)-0x0101010101010101UL)&~(x)&0x8080808080808080UL) #define MIN(a,b) ((a)<(b)?(a):(b)) static int dump_ref(sam_hdr_t *h, hts_itr_t *iter, int ref_id, char *ref, uint64_t ref_len, FILE *fp, int verbose) { int N = 0; if (iter && iter->end >= HTS_POS_MAX) iter->end = ref_len; if (iter && (iter->beg > 0 || iter->end < ref_len)) { fprintf(fp, ">%s:%"PRIhts_pos"-%"PRIhts_pos"\n", sam_hdr_tid2name(h, ref_id), iter->beg+1, iter->end); ref += iter->beg; ref_len = MIN(ref_len, iter->end) - iter->beg; } else { fprintf(fp, ">%s\n", sam_hdr_tid2name(h, ref_id)); } int i, j; uint64_t rem = ref_len; // Count coverage, purely for information purposes. // About 90% of dump_ref CPU is here, so maybe this isn't useful, // but this is still 3-4x faster than the obvious naive loop. // // Overall though it's only about 5% overhead of the entire process // (was ~20%). if (verbose) { int n4[8] = {0}; for (j = 0; j < ref_len && (((uintptr_t) &ref[j] & 7) != 0); j++) N += ref[j] == 'N'; uint64_t fast_end = ((ref_len - j) & ~7) + j; for (; j < fast_end; j+=8) { uint64_t i64 = *(uint64_t *)&ref[j]; if (!haszero(i64 ^ 0x4e4e4e4e4e4e4e4eUL)) // 'N' <-> 0 continue; n4[0] += ref[j+0] == 'N'; n4[1] += ref[j+1] == 'N'; n4[2] += ref[j+2] == 'N'; n4[3] += ref[j+3] == 'N'; n4[4] += ref[j+4] == 'N'; n4[5] += ref[j+5] == 'N'; n4[6] += ref[j+6] == 'N'; n4[7] += ref[j+7] == 'N'; } for (; j < ref_len; j++) N += ref[j] == 'N'; N += n4[0]+n4[1]+n4[2]+n4[3]+ n4[4]+n4[5]+n4[6]+n4[7]; } // Format reference for (i = 0; i < ref_len; i += 60, rem -= 60) { int len = (int)(rem < 60 ? rem : 60); if (fwrite(ref, 1, len, fp) != len) return -1; putc('\n', fp); ref += 60; } if (verbose) fprintf(stderr, "Dump ref %d len %"PRId64", coverage %.2f%%\n", ref_id, ref_len, 100 - N*100.0 / ref_len); return 0; } /* * --------------------------------------------------------------------------- * CRAM embedded reference method of reference construction */ /* * Extracts an embedded reference from a sorted CRAM file. * Modelled on the CRAM container copy loop from bam_cat.c. */ static int cram2ref(samFile *in, sam_hdr_t *h, hts_idx_t *idx, char *reg, FILE *outfp, int verbose) { cram_fd *in_c; cram_container *c = NULL; cram_block *blk = NULL; cram_block_slice_hdr *shdr = NULL; int curr_ref_id = -99; char *ref = NULL; uint64_t ref_len = 0; // We have no direct public API for seeking in CRAM to a specific // location by genome coordinates. The sam_itr_query API is // designed for fetching records, rather than seeks to specific // file locations. // // TODO: consider exposing cram_range and cram_seek_to_refpos API. // After a sam_index_load which will add the index to infp, these // functions should seek direct to the start of a container. // Or use cram_index *e =cram_index_query(cram, tid, beg, NULL); // // However, fortuitously(?) sam_itr_querys calls cram_seek_to_refpos // so we can do a region query and let that do the initial seek. // We still need to do our own end-range detection though. hts_itr_t *iter = NULL; if (reg) { iter = sam_itr_querys(idx, h, reg); if (!iter) { print_error("reference", "failed to parse region '%s'", reg); goto err; } } in_c = in->fp.cram; // low level htslib abuse? int eor = 0; while (!eor && (c = cram_read_container(in_c))) { if (cram_container_is_empty(in_c)) { cram_block *blk; // Container compression header if (!(blk = cram_read_block(in_c))) goto err; cram_free_block(blk); cram_free_container(c); c = NULL; blk = NULL; continue; } // Container compression header; read and discard int32_t num_slices; if (!(blk = cram_read_block(in_c))) goto err; cram_free_block(blk); blk = NULL; // Container num_blocks can be invalid, due to a bug. // Instead we iterate in slice context instead. (void)cram_container_get_landmarks(c, &num_slices); int i, j; for (i = 0; i < num_slices; i++) { // Slice header if (!(blk = cram_read_block(in_c))) goto err; if (!(shdr = cram_decode_slice_header(in_c, blk))) goto err; cram_free_block(blk); blk = NULL; int num_blocks = cram_slice_hdr_get_num_blocks(shdr); int embed_id = cram_slice_hdr_get_embed_ref_id(shdr); int ref_id; hts_pos_t ref_start, ref_span; cram_slice_hdr_get_coords(shdr, &ref_id, &ref_start, &ref_span); if (iter) { if (iter->tid != ref_id || ref_start > iter->end) { // Beyond end of specified region. cram_free_slice_header(shdr); eor = 1; break; } } if (embed_id < 0 && ref_id != -1) { fprintf(stderr, "CRAM file has slice without embedded " "reference\n"); goto err; } if (ref_id != curr_ref_id) { if (curr_ref_id >= 0) { if (dump_ref(h, iter, curr_ref_id, ref, ref_len, outfp, verbose) < 0) goto err; } ref_len = sam_hdr_tid2len(h, ref_id); if (ref_len) { char *ref2 = realloc(ref, ref_len); if (!ref2) goto err; else ref = ref2; memset(ref, 'N', ref_len); } curr_ref_id = ref_id; } // Slice data blocks for (j = 0; j < num_blocks; j++) { // read and discard, unless it's the ref-ID block if (!(blk = cram_read_block(in_c))) goto err; if (cram_block_get_content_id(blk) == embed_id) { cram_uncompress_block(blk); //printf("%.*s\n", blk->uncomp_size, blk->data); int32_t usize = cram_block_get_uncomp_size(blk); int ref_end = ref_start + usize; if (ref_end > ref_len+1) ref_end = ref_len+1; if (ref_end > ref_start) memcpy(ref + ref_start-1, cram_block_get_data(blk), ref_end - ref_start); } cram_free_block(blk); blk = NULL; } cram_free_slice_header(shdr); shdr = NULL; } cram_free_container(c); c = NULL; } int ret = 0; if (curr_ref_id >= 0) { ret = dump_ref(h, iter, curr_ref_id, ref, ref_len, outfp, verbose); } else if (reg) { // no data present // no data present, but we explicitly asked for the reference so // report it still as Ns. ref_len = MIN(iter->end, sam_hdr_tid2len(h, iter->tid)); ref = malloc(ref_len); memset(ref, 'N', ref_len); if (!ref) goto err; ret = dump_ref(h, iter, iter->tid, ref, ref_len, outfp, verbose); } free(ref); if (iter) hts_itr_destroy(iter); return ret; err: free(ref); if (blk) cram_free_block(blk); if (shdr) cram_free_slice_header(shdr); if (c) cram_free_container(c); if (iter) hts_itr_destroy(iter); return -1; } /* * --------------------------------------------------------------------------- * MD method of reference construction */ // Returns the next cigar op code: one of the BAM_C* codes, // or -1 if no more are present. static inline int next_cigar_op(uint32_t *cigar, int *ncigar, int *skip, int *spos, uint32_t *cig_ind, uint32_t *cig_op, uint32_t *cig_len) { for(;;) { while (*cig_len == 0) { if (*cig_ind < *ncigar) { *cig_op = cigar[*cig_ind] & BAM_CIGAR_MASK; *cig_len = cigar[*cig_ind] >> BAM_CIGAR_SHIFT; (*cig_ind)++; } else { return -1; } } if (skip[*cig_op]) { *spos += (bam_cigar_type(*cig_op)&1) * *cig_len; *cig_len = 0; continue; } (*cig_len)--; break; } return *cig_op; } // Converts a bam object with SEQ, POS/CIGAR and MD:Z to a reference. // Updates ref[] array. // // Returns >0 on success, // 0 on no-MD found, // -1 on failure (eg inconsistent data) static int build_ref(bam1_t *b, char *ref, size_t ref_len) { uint8_t *seq = bam_get_seq(b); uint32_t *cigar = bam_get_cigar(b); int ncigar = b->core.n_cigar; uint32_t cig_op = 0, cig_len = 0, cig_ind = 0; const uint8_t *MD = bam_aux_get(b, "MD"); if (!MD || *MD != 'Z') return 0; MD++; // Walk through MD + seq to generate ref int iseq = 0, iref = b->core.pos, next_op; int cig_skip[16] = {0,1,0,1,1,1,1,0,0,1,1,1,1,1,1,1}; while (iseq < b->core.l_qseq && *MD) { if (isdigit(*MD)) { // match int len = strtol((char *)MD, (char **)&MD, 10); while (iseq < b->core.l_qseq && len) { if ((next_op = next_cigar_op(cigar, &ncigar, cig_skip, &iseq, &cig_ind, &cig_op, &cig_len)) < 0) return -1; if (next_op != BAM_CMATCH && next_op != BAM_CEQUAL) { print_error("MD2ref", "MD:Z and CIGAR are incompatible"); return -1; } if (iref < ref_len) ref[iref] = seq_nt16_str[bam_seqi(seq, iseq)]; iseq++; iref++; len--; } } else if (*MD == '^') { // deletion MD++; while (*MD && isalpha(*MD)) { if ((next_op = next_cigar_op(cigar, &ncigar, cig_skip, &iseq, &cig_ind, &cig_op, &cig_len)) < 0) return -1; if (next_op != BAM_CDEL) { print_error("MD2ref", "MD:Z and CIGAR are incompatible"); return -1; } if (iref < ref_len) ref[iref] = *MD; MD++; iref++; } } else { // substitution if ((next_op = next_cigar_op(cigar, &ncigar, cig_skip, &iseq, &cig_ind, &cig_op, &cig_len)) < 0) return -1; if (next_op != BAM_CMATCH && next_op != BAM_CDIFF) { print_error("MD2ref", "MD:Z and CIGAR are incompatible"); return -1; } if (iref < ref_len) ref[iref] = *MD; MD++; iref++; iseq++; } } return 1; } static int MD2ref(samFile *in, sam_hdr_t *h, hts_idx_t *idx, char *reg, FILE *outfp, int verbose) { bam1_t *b = bam_init1(); int r, last_tid = -99; size_t ref_len = 0; char *ref = NULL; int ret = -1; hts_itr_t *iter = NULL; if (idx && reg) { iter = sam_itr_querys(idx, h, reg); if (!iter) { print_error("reference", "failed to parse region '%s'", reg); goto err; } } while ((r = iter ? sam_itr_next(in, iter, b) : sam_read1(in, h, b)) >= 0) { // check b->core.tid and flush old seq. if (b->core.tid != last_tid) { if (last_tid >= 0) if (dump_ref(h, iter, last_tid, ref, ref_len, outfp, verbose) < 0) goto err; last_tid = b->core.tid; ref_len = sam_hdr_tid2len(h, last_tid); if (ref_len) { char *ref2 = realloc(ref, ref_len); if (!ref2) goto err; else ref = ref2; memset(ref, 'N', ref_len); } } if (build_ref(b, ref, ref_len) < 0) goto err; } if (last_tid >= 0) { if (dump_ref(h, iter, last_tid, ref, ref_len, outfp, verbose) < 0) goto err; } else if (reg) { // no data present, but we explicitly asked for the reference so // report it still as Ns. ref_len = MIN(iter->end, sam_hdr_tid2len(h, iter->tid)); ref = malloc(ref_len); memset(ref, 'N', ref_len); if (!ref) goto err; if (dump_ref(h, iter, iter->tid, ref, ref_len, outfp, verbose) < 0) goto err; } if (r < -1) goto err; ret = 0; err: if (iter) hts_itr_destroy(iter); bam_destroy1(b); free(ref); return ret; } int main_reference(int argc, char *argv[]) { int c, usage = 0, verbose = 1, use_embedded = 0; sam_hdr_t *h = 0; samFile *in = NULL; hts_idx_t *idx = NULL; sam_global_args ga; FILE *outfp = stdout; char *reg = NULL; static const struct option lopts[] = { {"output", required_argument, NULL, 'o'}, {"quiet", no_argument, NULL, 'q'}, {"embedded", no_argument, NULL, 'e'}, {"region", required_argument, NULL, 'r'}, SAM_OPT_GLOBAL_OPTIONS('-', '-', '-', '-', '-', '@'), { NULL, 0, NULL, 0 } }; sam_global_args_init(&ga); while ((c = getopt_long(argc, argv, "@:qo:er:", lopts, NULL)) >= 0) { switch (c) { case 'o': if (!(outfp = fopen(optarg, "w"))) { perror(optarg); goto err; } break; case 'q': verbose = 0; break; case 'e': use_embedded = 1; break; case 'r': reg = optarg; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage=1; break; } } if ((optind == argc && isatty(0)) || usage) { printf("Usage: samtools reference [-@ N] [-r region] [-e] [-q] [-o out.fa] [in.cram]\n"); return 0; } char *fn = optind < argc ? argv[optind] : "-"; if (!(in = sam_open(fn, "r"))) { print_error_errno("reference", "failed to open file '%s'", fn); return 1; } if (ga.nthreads > 0) hts_set_threads(in, ga.nthreads); if (!(h = sam_hdr_read(in))) goto err; if (reg) { idx = sam_index_load(in, fn); if (!idx) { print_error_errno("reference", "Failed to load the index"); goto err; } } int ret = use_embedded ? cram2ref(in, h, idx, reg, outfp, verbose) : MD2ref(in, h, idx, reg, outfp, verbose); sam_hdr_destroy(h); if (outfp != stdout) fclose(outfp); if (idx) hts_idx_destroy(idx); sam_close(in); return ret; err: if (idx) hts_idx_destroy(idx); if (in) sam_close(in); if (h) sam_hdr_destroy(h); return 1; } pysam-0.23.0/samtools/reference.c.pysam.c000066400000000000000000000444511475062545500202660ustar00rootroot00000000000000#include "samtools.pysam.h" /* bam_reference.c -- extracts an embedded reference from a CRAM file, or creates it from alignments plus MD:Z tags. Copyright (C) 2022 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "htslib/sam.h" #include "htslib/cram.h" #include "samtools.h" #include "sam_opts.h" /* * There are two main modes of operation. * * 1. Extracting the reference from the CRAM file embed_ref blocks. * 2. Generation of reference by analysing consensus plus patches applied * via MD tags. * * The first is very rapid, but only applies to a CRAM files generated with * the specific options (not commonly used and not the default). The second * is a slow operation, but applies to any data type. * * This is also a testing ground for a future CRAM auto-embed-ref option that * permits the use of an embedded reference without having to first extract * the reference. (Note this may require the creation of MD tags during * decode by use of an existing embedded reference, if the records don't * have an MD tag themselves, but that's an issue for htslib when we get * there.) */ /* * --------------------------------------------------------------------------- * Shared utility functions by both methods. */ #define haszero(x) (((x)-0x0101010101010101UL)&~(x)&0x8080808080808080UL) #define MIN(a,b) ((a)<(b)?(a):(b)) static int dump_ref(sam_hdr_t *h, hts_itr_t *iter, int ref_id, char *ref, uint64_t ref_len, FILE *fp, int verbose) { int N = 0; if (iter && iter->end >= HTS_POS_MAX) iter->end = ref_len; if (iter && (iter->beg > 0 || iter->end < ref_len)) { fprintf(fp, ">%s:%"PRIhts_pos"-%"PRIhts_pos"\n", sam_hdr_tid2name(h, ref_id), iter->beg+1, iter->end); ref += iter->beg; ref_len = MIN(ref_len, iter->end) - iter->beg; } else { fprintf(fp, ">%s\n", sam_hdr_tid2name(h, ref_id)); } int i, j; uint64_t rem = ref_len; // Count coverage, purely for information purposes. // About 90% of dump_ref CPU is here, so maybe this isn't useful, // but this is still 3-4x faster than the obvious naive loop. // // Overall though it's only about 5% overhead of the entire process // (was ~20%). if (verbose) { int n4[8] = {0}; for (j = 0; j < ref_len && (((uintptr_t) &ref[j] & 7) != 0); j++) N += ref[j] == 'N'; uint64_t fast_end = ((ref_len - j) & ~7) + j; for (; j < fast_end; j+=8) { uint64_t i64 = *(uint64_t *)&ref[j]; if (!haszero(i64 ^ 0x4e4e4e4e4e4e4e4eUL)) // 'N' <-> 0 continue; n4[0] += ref[j+0] == 'N'; n4[1] += ref[j+1] == 'N'; n4[2] += ref[j+2] == 'N'; n4[3] += ref[j+3] == 'N'; n4[4] += ref[j+4] == 'N'; n4[5] += ref[j+5] == 'N'; n4[6] += ref[j+6] == 'N'; n4[7] += ref[j+7] == 'N'; } for (; j < ref_len; j++) N += ref[j] == 'N'; N += n4[0]+n4[1]+n4[2]+n4[3]+ n4[4]+n4[5]+n4[6]+n4[7]; } // Format reference for (i = 0; i < ref_len; i += 60, rem -= 60) { int len = (int)(rem < 60 ? rem : 60); if (fwrite(ref, 1, len, fp) != len) return -1; putc('\n', fp); ref += 60; } if (verbose) fprintf(samtools_stderr, "Dump ref %d len %"PRId64", coverage %.2f%%\n", ref_id, ref_len, 100 - N*100.0 / ref_len); return 0; } /* * --------------------------------------------------------------------------- * CRAM embedded reference method of reference construction */ /* * Extracts an embedded reference from a sorted CRAM file. * Modelled on the CRAM container copy loop from bam_cat.c. */ static int cram2ref(samFile *in, sam_hdr_t *h, hts_idx_t *idx, char *reg, FILE *outfp, int verbose) { cram_fd *in_c; cram_container *c = NULL; cram_block *blk = NULL; cram_block_slice_hdr *shdr = NULL; int curr_ref_id = -99; char *ref = NULL; uint64_t ref_len = 0; // We have no direct public API for seeking in CRAM to a specific // location by genome coordinates. The sam_itr_query API is // designed for fetching records, rather than seeks to specific // file locations. // // TODO: consider exposing cram_range and cram_seek_to_refpos API. // After a sam_index_load which will add the index to infp, these // functions should seek direct to the start of a container. // Or use cram_index *e =cram_index_query(cram, tid, beg, NULL); // // However, fortuitously(?) sam_itr_querys calls cram_seek_to_refpos // so we can do a region query and let that do the initial seek. // We still need to do our own end-range detection though. hts_itr_t *iter = NULL; if (reg) { iter = sam_itr_querys(idx, h, reg); if (!iter) { print_error("reference", "failed to parse region '%s'", reg); goto err; } } in_c = in->fp.cram; // low level htslib abuse? int eor = 0; while (!eor && (c = cram_read_container(in_c))) { if (cram_container_is_empty(in_c)) { cram_block *blk; // Container compression header if (!(blk = cram_read_block(in_c))) goto err; cram_free_block(blk); cram_free_container(c); c = NULL; blk = NULL; continue; } // Container compression header; read and discard int32_t num_slices; if (!(blk = cram_read_block(in_c))) goto err; cram_free_block(blk); blk = NULL; // Container num_blocks can be invalid, due to a bug. // Instead we iterate in slice context instead. (void)cram_container_get_landmarks(c, &num_slices); int i, j; for (i = 0; i < num_slices; i++) { // Slice header if (!(blk = cram_read_block(in_c))) goto err; if (!(shdr = cram_decode_slice_header(in_c, blk))) goto err; cram_free_block(blk); blk = NULL; int num_blocks = cram_slice_hdr_get_num_blocks(shdr); int embed_id = cram_slice_hdr_get_embed_ref_id(shdr); int ref_id; hts_pos_t ref_start, ref_span; cram_slice_hdr_get_coords(shdr, &ref_id, &ref_start, &ref_span); if (iter) { if (iter->tid != ref_id || ref_start > iter->end) { // Beyond end of specified region. cram_free_slice_header(shdr); eor = 1; break; } } if (embed_id < 0 && ref_id != -1) { fprintf(samtools_stderr, "CRAM file has slice without embedded " "reference\n"); goto err; } if (ref_id != curr_ref_id) { if (curr_ref_id >= 0) { if (dump_ref(h, iter, curr_ref_id, ref, ref_len, outfp, verbose) < 0) goto err; } ref_len = sam_hdr_tid2len(h, ref_id); if (ref_len) { char *ref2 = realloc(ref, ref_len); if (!ref2) goto err; else ref = ref2; memset(ref, 'N', ref_len); } curr_ref_id = ref_id; } // Slice data blocks for (j = 0; j < num_blocks; j++) { // read and discard, unless it's the ref-ID block if (!(blk = cram_read_block(in_c))) goto err; if (cram_block_get_content_id(blk) == embed_id) { cram_uncompress_block(blk); //printf("%.*s\n", blk->uncomp_size, blk->data); int32_t usize = cram_block_get_uncomp_size(blk); int ref_end = ref_start + usize; if (ref_end > ref_len+1) ref_end = ref_len+1; if (ref_end > ref_start) memcpy(ref + ref_start-1, cram_block_get_data(blk), ref_end - ref_start); } cram_free_block(blk); blk = NULL; } cram_free_slice_header(shdr); shdr = NULL; } cram_free_container(c); c = NULL; } int ret = 0; if (curr_ref_id >= 0) { ret = dump_ref(h, iter, curr_ref_id, ref, ref_len, outfp, verbose); } else if (reg) { // no data present // no data present, but we explicitly asked for the reference so // report it still as Ns. ref_len = MIN(iter->end, sam_hdr_tid2len(h, iter->tid)); ref = malloc(ref_len); memset(ref, 'N', ref_len); if (!ref) goto err; ret = dump_ref(h, iter, iter->tid, ref, ref_len, outfp, verbose); } free(ref); if (iter) hts_itr_destroy(iter); return ret; err: free(ref); if (blk) cram_free_block(blk); if (shdr) cram_free_slice_header(shdr); if (c) cram_free_container(c); if (iter) hts_itr_destroy(iter); return -1; } /* * --------------------------------------------------------------------------- * MD method of reference construction */ // Returns the next cigar op code: one of the BAM_C* codes, // or -1 if no more are present. static inline int next_cigar_op(uint32_t *cigar, int *ncigar, int *skip, int *spos, uint32_t *cig_ind, uint32_t *cig_op, uint32_t *cig_len) { for(;;) { while (*cig_len == 0) { if (*cig_ind < *ncigar) { *cig_op = cigar[*cig_ind] & BAM_CIGAR_MASK; *cig_len = cigar[*cig_ind] >> BAM_CIGAR_SHIFT; (*cig_ind)++; } else { return -1; } } if (skip[*cig_op]) { *spos += (bam_cigar_type(*cig_op)&1) * *cig_len; *cig_len = 0; continue; } (*cig_len)--; break; } return *cig_op; } // Converts a bam object with SEQ, POS/CIGAR and MD:Z to a reference. // Updates ref[] array. // // Returns >0 on success, // 0 on no-MD found, // -1 on failure (eg inconsistent data) static int build_ref(bam1_t *b, char *ref, size_t ref_len) { uint8_t *seq = bam_get_seq(b); uint32_t *cigar = bam_get_cigar(b); int ncigar = b->core.n_cigar; uint32_t cig_op = 0, cig_len = 0, cig_ind = 0; const uint8_t *MD = bam_aux_get(b, "MD"); if (!MD || *MD != 'Z') return 0; MD++; // Walk through MD + seq to generate ref int iseq = 0, iref = b->core.pos, next_op; int cig_skip[16] = {0,1,0,1,1,1,1,0,0,1,1,1,1,1,1,1}; while (iseq < b->core.l_qseq && *MD) { if (isdigit(*MD)) { // match int len = strtol((char *)MD, (char **)&MD, 10); while (iseq < b->core.l_qseq && len) { if ((next_op = next_cigar_op(cigar, &ncigar, cig_skip, &iseq, &cig_ind, &cig_op, &cig_len)) < 0) return -1; if (next_op != BAM_CMATCH && next_op != BAM_CEQUAL) { print_error("MD2ref", "MD:Z and CIGAR are incompatible"); return -1; } if (iref < ref_len) ref[iref] = seq_nt16_str[bam_seqi(seq, iseq)]; iseq++; iref++; len--; } } else if (*MD == '^') { // deletion MD++; while (*MD && isalpha(*MD)) { if ((next_op = next_cigar_op(cigar, &ncigar, cig_skip, &iseq, &cig_ind, &cig_op, &cig_len)) < 0) return -1; if (next_op != BAM_CDEL) { print_error("MD2ref", "MD:Z and CIGAR are incompatible"); return -1; } if (iref < ref_len) ref[iref] = *MD; MD++; iref++; } } else { // substitution if ((next_op = next_cigar_op(cigar, &ncigar, cig_skip, &iseq, &cig_ind, &cig_op, &cig_len)) < 0) return -1; if (next_op != BAM_CMATCH && next_op != BAM_CDIFF) { print_error("MD2ref", "MD:Z and CIGAR are incompatible"); return -1; } if (iref < ref_len) ref[iref] = *MD; MD++; iref++; iseq++; } } return 1; } static int MD2ref(samFile *in, sam_hdr_t *h, hts_idx_t *idx, char *reg, FILE *outfp, int verbose) { bam1_t *b = bam_init1(); int r, last_tid = -99; size_t ref_len = 0; char *ref = NULL; int ret = -1; hts_itr_t *iter = NULL; if (idx && reg) { iter = sam_itr_querys(idx, h, reg); if (!iter) { print_error("reference", "failed to parse region '%s'", reg); goto err; } } while ((r = iter ? sam_itr_next(in, iter, b) : sam_read1(in, h, b)) >= 0) { // check b->core.tid and flush old seq. if (b->core.tid != last_tid) { if (last_tid >= 0) if (dump_ref(h, iter, last_tid, ref, ref_len, outfp, verbose) < 0) goto err; last_tid = b->core.tid; ref_len = sam_hdr_tid2len(h, last_tid); if (ref_len) { char *ref2 = realloc(ref, ref_len); if (!ref2) goto err; else ref = ref2; memset(ref, 'N', ref_len); } } if (build_ref(b, ref, ref_len) < 0) goto err; } if (last_tid >= 0) { if (dump_ref(h, iter, last_tid, ref, ref_len, outfp, verbose) < 0) goto err; } else if (reg) { // no data present, but we explicitly asked for the reference so // report it still as Ns. ref_len = MIN(iter->end, sam_hdr_tid2len(h, iter->tid)); ref = malloc(ref_len); memset(ref, 'N', ref_len); if (!ref) goto err; if (dump_ref(h, iter, iter->tid, ref, ref_len, outfp, verbose) < 0) goto err; } if (r < -1) goto err; ret = 0; err: if (iter) hts_itr_destroy(iter); bam_destroy1(b); free(ref); return ret; } int main_reference(int argc, char *argv[]) { int c, usage = 0, verbose = 1, use_embedded = 0; sam_hdr_t *h = 0; samFile *in = NULL; hts_idx_t *idx = NULL; sam_global_args ga; FILE *outfp = samtools_stdout; char *reg = NULL; static const struct option lopts[] = { {"output", required_argument, NULL, 'o'}, {"quiet", no_argument, NULL, 'q'}, {"embedded", no_argument, NULL, 'e'}, {"region", required_argument, NULL, 'r'}, SAM_OPT_GLOBAL_OPTIONS('-', '-', '-', '-', '-', '@'), { NULL, 0, NULL, 0 } }; sam_global_args_init(&ga); while ((c = getopt_long(argc, argv, "@:qo:er:", lopts, NULL)) >= 0) { switch (c) { case 'o': if (!(outfp = fopen(optarg, "w"))) { perror(optarg); goto err; } break; case 'q': verbose = 0; break; case 'e': use_embedded = 1; break; case 'r': reg = optarg; break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': usage=1; break; } } if ((optind == argc && isatty(0)) || usage) { fprintf(samtools_stdout, "Usage: samtools reference [-@ N] [-r region] [-e] [-q] [-o out.fa] [in.cram]\n"); return 0; } char *fn = optind < argc ? argv[optind] : "-"; if (!(in = sam_open(fn, "r"))) { print_error_errno("reference", "failed to open file '%s'", fn); return 1; } if (ga.nthreads > 0) hts_set_threads(in, ga.nthreads); if (!(h = sam_hdr_read(in))) goto err; if (reg) { idx = sam_index_load(in, fn); if (!idx) { print_error_errno("reference", "Failed to load the index"); goto err; } } int ret = use_embedded ? cram2ref(in, h, idx, reg, outfp, verbose) : MD2ref(in, h, idx, reg, outfp, verbose); sam_hdr_destroy(h); if (outfp != samtools_stdout) fclose(outfp); if (idx) hts_idx_destroy(idx); sam_close(in); return ret; err: if (idx) hts_idx_destroy(idx); if (in) sam_close(in); if (h) sam_hdr_destroy(h); return 1; } pysam-0.23.0/samtools/reset.c000066400000000000000000000533441475062545500161020ustar00rootroot00000000000000/* reset.c -- removes aligner updates and reference data from input sam / bam / cram file and makes read data raw for new processing Copyright (C) 2022 - 2024 Genome Research Ltd. Author: Vasudeva Sarma Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE */ #include #include "samtools.h" #include "htslib/sam.h" #include "sam_opts.h" #include "htslib/thread_pool.h" #include "htslib/khash.h" #include "sam_utils.h" #include #define TAGNUM(X) (((X)[0] << 8) | (X)[1]) //to create key for aux tags, like type key in htslib #define LONG_OPT(X) (128 + (X)) //to handle long and short options with same char #define RESET_KEEPDUPFLAG 1 //keep dup flag as such, as in initial implementation typedef struct conf_data { int keepRGs; //RG line handling int noPGentry; //PG line for reset op or not int ctrlFlags; //control flags auxhash_t aux_keep; //SET that holds the aux tags to be retained auxhash_t aux_remove; //SET that holds the aux tags to be removed char *pgid; //PG id onwards which to be removed } conf_data; /// usage - print the usage /** @param fp pointer to the file / terminal to which usage to be dumped returns nothing */ static void usage(FILE *fp) { fprintf(fp, "Usage: samtools reset [options]\n\ -o FILE Output file\n\ -x, --remove-tag STR\n\ Aux tags to be removed\n\ --keep-tag STR\n\ Aux tags to be retained. Equivalent to -x ^STR\n\ --reject-PG ID\n\ Removes PG line with ID matching to input and succeeding PG lines\n\ --no-RG To have RG lines or not\n\ --no-PG To have PG entry or not for reset operation\n\ --dupflag\n\ Keeps the duplicate flag as it is\n"); sam_global_opt_help(fp, "--O--@--"); return; } /// update_aux_conf - update the user given aux tag configuration with defaults /** @param config - pointer to conf_data returns nothing */ void update_aux_conf(conf_data *config) { const char rg[] = "RG"; const char *default_tags[] = {"AS", "CC", "CG", "CP", "H1", "H2", "HI", "H0", "IH", "MC", "MD", "MQ", "NM", "SA", "TS"}; khint_t iter = 0; int ret = 0, i = 0; if (!config) return; if (!config->aux_keep && !config->aux_remove) { //none of aux tag filter in use, create remove filter config->aux_remove = kh_init(aux_exists); } if (config->aux_keep) { //keep set in use, remove RG if present if (!config->keepRGs) { iter = kh_get(aux_exists, config->aux_keep, TAGNUM(rg)); if (iter != kh_end(config->aux_keep)) { kh_del(aux_exists, config->aux_keep, iter); } } } if (config->aux_remove) { if (!config->keepRGs) { //remove set in use, add RG if not present iter = kh_get(aux_exists, config->aux_remove, TAGNUM(rg)); if (iter == kh_end(config->aux_remove)) { kh_put(aux_exists, config->aux_remove, TAGNUM(rg), &ret); } } //add the default tags if not present in remove set //note, keep has priority and this may not be honoured for (i = 0; i < sizeof(default_tags) / sizeof(default_tags[0]); ++i) { iter = kh_get(aux_exists, config->aux_remove, TAGNUM(default_tags[i])); if (iter == kh_end(config->aux_remove)) { kh_put(aux_exists, config->aux_remove, TAGNUM(default_tags[i]), &ret); } } } } /// removeauxtags - remove aux tags in bam data which are not present in acceptable tag set /** @param bamdata - pointer to the bamdata from which needs the filtering * @param config - pointer to conf_data returns nothing */ void removeauxtags(bam1_t *bamdata, conf_data *config) { uint8_t *auxdata = NULL; const char *tag = NULL; khint_t iter = 0; if (!bamdata || !config) return; for (auxdata = bam_aux_first(bamdata); auxdata; ) { tag = bam_aux_tag(auxdata); if (config->aux_keep) { //keep option or remove option with ^ in use iter = kh_get(aux_exists, config->aux_keep, TAGNUM(tag)); if (iter == kh_end(config->aux_keep)) { //not present in keep, remove auxdata = bam_aux_remove(bamdata, auxdata); } else { //present, keep auxdata = bam_aux_next(bamdata, auxdata); } } else if (config->aux_remove) { //remove option in use iter = kh_get(aux_exists, config->aux_remove, TAGNUM(tag)); if (iter != kh_end(config->aux_remove)) { //present in remove, remove auxdata = bam_aux_remove(bamdata, auxdata); } else { //not present, keep auxdata = bam_aux_next(bamdata, auxdata); } } //else impossible } } /// getRGlines - add RG lines from input header to output header /** @param in_samhdr - pointer to input sam header data * @param out_samhdr - pointer to output sam header data returns 1 on failure 0 on success */ int getRGlines(sam_hdr_t *in_samhdr, sam_hdr_t *out_samhdr) { kstring_t line = KS_INITIALIZE; int i = 0, ret = 0, count = 0; const char rg[] = "RG"; if (!in_samhdr || !out_samhdr) { fprintf(stderr, "Invalid parameters in getRGlines!\n"); return 1; } if (-1 == (count = sam_hdr_count_lines(in_samhdr, rg))) { fprintf(stderr, "Failed to get RG count!\n"); return 1; } for (i = 0; i < count; ++i) { ks_clear(&line); if (sam_hdr_find_line_pos(in_samhdr, rg, i, &line)) { fprintf(stderr, "Failed to get RG data!\n"); ret = 1; break; } if (sam_hdr_add_lines(out_samhdr, line.s, line.l)) { fprintf(stderr, "Failed to add RG data!\n"); ret = 1; break; } } ks_free(&line); return ret; } /// getPGlines - add PG lines from input header to output header based on user option /** @param in_samhdr - pointer to input sam header data * @param out_samhdr - pointer to output sam header data * @param config - pointer to internal configuration data * @param argdump - string containing dump of command line invocation returns 1 on failure 0 on success */ int getPGlines(sam_hdr_t *in_samhdr, sam_hdr_t *out_samhdr, conf_data *config, const char *argdump) { kstring_t line = KS_INITIALIZE, id = KS_INITIALIZE; int i = 0, ret = 0, count = 0; const char pg[] = "PG"; if (!in_samhdr || !out_samhdr || !config) { fprintf(stderr, "Invalid parameters in getPGlines!\n"); return 1; } if (-1 == (count = sam_hdr_count_lines(in_samhdr, pg))) { fprintf(stderr, "Failed to get PG count!\n"); return 1; } if (config->pgid && config->pgid[0]) { //when reject-PG is given, and is not empty, remove given pg onwards for (i = 0; i < count; ++i) { if (sam_hdr_find_tag_pos(in_samhdr, pg, i, "ID", &id)) { fprintf(stderr, "Failed to get PG entry fields for line %d!\n", i + 1); break; } if (!strcmp(id.s, config->pgid)) break; //either current PG is prior to rejected one or all PGs are in, get PG line and add ks_clear(&line); if (sam_hdr_find_line_pos(in_samhdr, "PG", i, &line)) { fprintf(stderr, "Failed to get PG data at %d!\n", i + 1); ret = 1; break; } //add to output if (sam_hdr_add_lines(out_samhdr, line.s, line.l)) { fprintf(stderr, "Failed to add PG data!\n"); ret = 1; break; } } } else { //keep all for (i = 0; i < count; ++i) { if (sam_hdr_find_line_pos(in_samhdr, "PG", i, &line)) { fprintf(stderr, "Failed to get PG data at %d!\n", i + 1); ret = 1; break; } //line has the required PG data if (sam_hdr_add_lines(out_samhdr, line.s, line.l)) { fprintf(stderr, "Failed to add PG data!\n"); ret = 1; break; } } } if (!ret && !config->noPGentry) { //add PG entry with reset command if (-1 == (ret = sam_hdr_add_pg(out_samhdr, "samtools", "CL", argdump, NULL))) { fprintf(stderr, "Failed to set PG entry!\n"); } } ks_free(&line); ks_free(&id); return ret; } /// reset - do the reset of data and create output; create output header with required rg/pg data, add bamdata with flags set to unmapped, pair info and orientation reset, // reerse and complement alignment if required /** @param infile - input samfile pointer * @param outfile - output sam file pointer * @param config - pointer to internal configuration data * @param args - string containing dump of command line invocation returns 1 on failure 0 on success */ int reset(samFile *infile, samFile *outfile, conf_data *config, char *args) { sam_hdr_t *in_samhdr = NULL, *out_samhdr = NULL; int ret = EXIT_FAILURE, ret_r = 0, ret_w = 0, i = 0; bam1_t *bamdata = NULL, *outdata = NULL; kstring_t querydata = KS_INITIALIZE, qualdata = KS_INITIALIZE; char *sp = NULL, *qp = NULL; uint8_t *bamquery = NULL, *bamqual = NULL; if (!infile || !outfile) { fprintf(stderr, "Invalid parameters in reset!\n"); goto error; } //read input header in_samhdr = sam_hdr_read(infile); if (!in_samhdr) { fprintf(stderr, "Failed to read header from file!\n"); goto error; } //create output header if (!(out_samhdr = sam_hdr_init())) { fprintf(stderr, "Failed to create output header!\n"); goto error; } //add version to output header if (-1 == sam_hdr_add_line(out_samhdr,"HD", "VN", SAM_FORMAT_VERSION, NULL)) { fprintf(stderr, "Failed to set header data!\n"); goto error; } //add RG / PG lines if configured if ((config->keepRGs && getRGlines(in_samhdr, out_samhdr)) || getPGlines(in_samhdr, out_samhdr, config, args)) { goto error; } //write output header if (sam_hdr_write(outfile, out_samhdr)) { print_error_errno("reset", "Output header write failed (%d)!\n", errno); goto error; } bamdata = bam_init1(); //input bam outdata = bam_init1(); //output bam if (!bamdata || !outdata) { fprintf(stderr, "Failed to allocate data memory!\n"); goto error; } errno = 0; i = 0; sp = NULL; qp = NULL; bamquery = NULL; bamqual = NULL; //get bam data, make updates and dump to output while (0 <= (ret_r = sam_read1(infile, in_samhdr, bamdata))) { sp = NULL; qp = NULL; bamquery = NULL; bamqual = NULL; // read data if (bamdata->core.flag & BAM_FSECONDARY || bamdata->core.flag & BAM_FSUPPLEMENTARY) { continue; } //update flags uint16_t flags = bamdata->core.flag & ~BAM_FPROPER_PAIR; //reset pair info flags |= BAM_FUNMAP; //mark as unmapped if (bamdata->core.flag & BAM_FPAIRED) { flags |= BAM_FMUNMAP; //mark mate as unmapped, if it was a pair } flags &= ~BAM_FMREVERSE; //reset mate orientation if (!(config->ctrlFlags & RESET_KEEPDUPFLAG)) { flags &= ~BAM_FDUP; //reset dup flag from alignment } if (0 > ks_resize(&querydata, bamdata->core.l_qseq) || 0 > ks_resize(&qualdata, bamdata->core.l_qseq)) { fprintf(stderr, "Failed to get allocate memory!\n"); ret_r = -4; break; } ks_clear(&querydata); ks_clear(&qualdata); sp = ks_str(&querydata); qp = ks_str(&qualdata); bamquery = bam_get_seq(bamdata); bamqual = bam_get_qual(bamdata); if (bamdata->core.flag & BAM_FREVERSE) { //sequence data ordered as reverse complemented, reorder/complement sequence and quality data as read and clear the flag for (i = bamdata->core.l_qseq - 1; i >= 0; --i) { *sp++ = "=TGKCYSBAWRDMHVN"[bam_seqi(bamquery, i)]; *qp++ = bamqual[i]; } flags &= ~BAM_FREVERSE; //reset flag as well } else { //data in read order itself for (i = 0; i < bamdata->core.l_qseq ; ++i) { *sp++ = seq_nt16_str[bam_seqi(bamquery, i)]; } memcpy(qp, bam_get_qual(bamdata), bamdata->core.l_qseq); } removeauxtags(bamdata, config); if (0 > (ret_w = bam_set1(outdata, bamdata->core.l_qname - bamdata->core.l_extranul - 1, bam_get_qname(bamdata), flags, -1, -1, 0, 0, NULL, -1, -1, 0, bamdata->core.l_qseq, querydata.s, qualdata.s, bam_get_l_aux(bamdata)))) { print_error_errno("reset", "Failed to set output data (%d)!\n", errno); break; } memcpy(bam_get_aux(outdata), bam_get_aux(bamdata), bam_get_l_aux(bamdata)); outdata->l_data += bam_get_l_aux(bamdata); errno = 0; //write bam data to output if (0 > (ret_w = sam_write1(outfile, out_samhdr, outdata))) { print_error_errno("reset", "Failed to write output data (%d)!\n", errno); break; } // wrote the data, continue read/write cycle errno = 0; } if (-1 > ret_r || 0 > ret_w) { //some error fprintf(stderr, "Error during %s!\n", (-1 > ret_r)? "read" : "write"); } else { // no error! ret = EXIT_SUCCESS; } error: // clean up and return result if (in_samhdr) sam_hdr_destroy(in_samhdr); if (out_samhdr) sam_hdr_destroy(out_samhdr); if (bamdata) bam_destroy1(bamdata); if (outdata) bam_destroy1(outdata); if (qualdata.s) ks_free(&qualdata); if (querydata.s) ks_free(&querydata); return ret; } /// cleanup - free up allocations made /** @param config - pointer to internal configuration data returns nothing */ void cleanup(conf_data *config) { if (config->aux_keep) { kh_destroy(aux_exists, config->aux_keep); config->aux_keep = NULL; } if (config->aux_remove) { kh_destroy(aux_exists, config->aux_remove); config->aux_remove = NULL; } } /// main_reset - starts the reset of data /** @param argc - count of arguments * @param argv - pointer to array of arguments returns 1 on failure 0 on success */ int main_reset(int argc, char *argv[]) { static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', '-', 'O', '-', '-', '@'), //let output format and thread count be given by user - long options {"keep-tag", required_argument, NULL, LONG_OPT('x')}, //aux tags to be retained, supports ^ STR {"remove-tag", required_argument, NULL, 'x'}, //aux tags to be removed {"no-RG", no_argument, NULL, 1}, //no RG lines in output, default is to keep them //reject PG lines from input, default is to keep them (i.e. option not given); without optional filename, all PGs removed and those given in file are filtered when optional filename is given {"reject-PG", required_argument, NULL, 'p'}, //reject entries from this PG onwards {"no-PG", no_argument, NULL, 2}, //do not add PG entry for reset operation, default is to add it {"dupflag", no_argument, NULL, 3}, //keep the dup flag as it is - as in initial reset implementation {NULL, 0, NULL, 0} }; samFile *infile = NULL, *outfile = NULL; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; htsThreadPool tpool = {NULL, 0}; const char *inname = NULL, *outname = NULL; int c = 0, ret = EXIT_FAILURE; char outmode[4] = "w", *args = NULL; conf_data resetconf = {1, 0, 0, NULL, NULL, NULL}; //keep RGs and PGs by default, ctrlflags = 0 //samtools reset -o outfile -x/--remove-tag ... --keep-tag ... --threads=n --output-fmt=fmt --no-RG --reject-PG pgid --no-PG [] while ((c = getopt_long(argc, argv, "o:@:x:O:", lopts, NULL)) >= 0) { switch (c) { case 1: //--no-RG if (!resetconf.keepRGs) { usage(stderr); //already given! goto exit; } resetconf.keepRGs = 0; break; case 2: //--no-PG if (resetconf.noPGentry) { usage(stderr); //already given! goto exit; } resetconf.noPGentry = 1; break; case 3: //keep dup flag as it is / no reset resetconf.ctrlFlags |= RESET_KEEPDUPFLAG; break; case 'p': //--reject-PG= if (resetconf.pgid) { usage(stderr); //already given! goto exit; } resetconf.pgid = optarg; break; case 'o': //output file name if (outname) { //already given! usage(stderr); goto exit; } outname = optarg; break; case 'x': //remove aux tag if (*optarg == '^') { //remove all except given ones! if (parse_aux_list(&resetconf.aux_keep, optarg+1, "main_reset")) { usage(stderr); goto exit; } } else { //remove given ones if (parse_aux_list(&resetconf.aux_remove, optarg, "main_reset")) { usage(stderr); goto exit; } } break; case LONG_OPT('x'): //keep aux tags if (parse_aux_list(&resetconf.aux_keep, optarg, "main_reset")) { usage(stderr); goto exit; } break; // handle standard samtool options like thread count, verbosity... default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; // else fall-through // couldn't parse or unknown options, show usage! case '?': //unknown options found! usage(stderr); goto exit; break; } } if (argc == 1 && isatty(STDIN_FILENO)) { //no args and input is stdin -- it is the usage check usage(stdout); ret = EXIT_SUCCESS; goto exit; } //else have other args or input from redirection/pipe/other device -- validate and work if (!outname) outname = "-"; //check and fail if unnecessary parameters are given c = argc - optind; if (c > 1) { usage(stderr); goto exit; } if (c == 1) { inname = argv[optind]; } else { inname = "-"; } //update aux tag configuration update_aux_conf(&resetconf); //set output file format based on name sam_open_mode(outmode + 1, outname, NULL); //open input and output files infile = sam_open(inname, "r"); outfile = sam_open_format(outname, outmode, &ga.out); if (!infile || !outfile) { fprintf(stderr, "Could not open %s%s%s\n", !infile ? inname : "", (!infile && !outfile)? ", " : "", !outfile ? outname : ""); goto exit; } // set the thread count if given as argument if (ga.nthreads > 0) { if (!(tpool.pool = hts_tpool_init(ga.nthreads))) { fprintf(stderr, "\nFailed to setup thread pool\n"); goto exit; } hts_set_opt(infile, HTS_OPT_THREAD_POOL, &tpool); hts_set_opt(outfile, HTS_OPT_THREAD_POOL, &tpool); } args = stringify_argv(argc + 1, argv - 1); //to dump invocation in PG line //do the reset! ret = reset(infile, outfile, &resetconf, args); exit: if (args) free(args); if (infile) sam_close(infile); if (outfile) sam_close(outfile); if (tpool.pool) hts_tpool_destroy(tpool.pool); cleanup(&resetconf); sam_global_args_free(&ga); return ret; } pysam-0.23.0/samtools/reset.c.pysam.c000066400000000000000000000540301475062545500174440ustar00rootroot00000000000000#include "samtools.pysam.h" /* reset.c -- removes aligner updates and reference data from input sam / bam / cram file and makes read data raw for new processing Copyright (C) 2022 - 2024 Genome Research Ltd. Author: Vasudeva Sarma Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE */ #include #include "samtools.h" #include "htslib/sam.h" #include "sam_opts.h" #include "htslib/thread_pool.h" #include "htslib/khash.h" #include "sam_utils.h" #include #define TAGNUM(X) (((X)[0] << 8) | (X)[1]) //to create key for aux tags, like type key in htslib #define LONG_OPT(X) (128 + (X)) //to handle long and short options with same char #define RESET_KEEPDUPFLAG 1 //keep dup flag as such, as in initial implementation typedef struct conf_data { int keepRGs; //RG line handling int noPGentry; //PG line for reset op or not int ctrlFlags; //control flags auxhash_t aux_keep; //SET that holds the aux tags to be retained auxhash_t aux_remove; //SET that holds the aux tags to be removed char *pgid; //PG id onwards which to be removed } conf_data; /// usage - print the usage /** @param fp pointer to the file / terminal to which usage to be dumped returns nothing */ static void usage(FILE *fp) { fprintf(fp, "Usage: samtools reset [options]\n\ -o FILE Output file\n\ -x, --remove-tag STR\n\ Aux tags to be removed\n\ --keep-tag STR\n\ Aux tags to be retained. Equivalent to -x ^STR\n\ --reject-PG ID\n\ Removes PG line with ID matching to input and succeeding PG lines\n\ --no-RG To have RG lines or not\n\ --no-PG To have PG entry or not for reset operation\n\ --dupflag\n\ Keeps the duplicate flag as it is\n"); sam_global_opt_help(fp, "--O--@--"); return; } /// update_aux_conf - update the user given aux tag configuration with defaults /** @param config - pointer to conf_data returns nothing */ void update_aux_conf(conf_data *config) { const char rg[] = "RG"; const char *default_tags[] = {"AS", "CC", "CG", "CP", "H1", "H2", "HI", "H0", "IH", "MC", "MD", "MQ", "NM", "SA", "TS"}; khint_t iter = 0; int ret = 0, i = 0; if (!config) return; if (!config->aux_keep && !config->aux_remove) { //none of aux tag filter in use, create remove filter config->aux_remove = kh_init(aux_exists); } if (config->aux_keep) { //keep set in use, remove RG if present if (!config->keepRGs) { iter = kh_get(aux_exists, config->aux_keep, TAGNUM(rg)); if (iter != kh_end(config->aux_keep)) { kh_del(aux_exists, config->aux_keep, iter); } } } if (config->aux_remove) { if (!config->keepRGs) { //remove set in use, add RG if not present iter = kh_get(aux_exists, config->aux_remove, TAGNUM(rg)); if (iter == kh_end(config->aux_remove)) { kh_put(aux_exists, config->aux_remove, TAGNUM(rg), &ret); } } //add the default tags if not present in remove set //note, keep has priority and this may not be honoured for (i = 0; i < sizeof(default_tags) / sizeof(default_tags[0]); ++i) { iter = kh_get(aux_exists, config->aux_remove, TAGNUM(default_tags[i])); if (iter == kh_end(config->aux_remove)) { kh_put(aux_exists, config->aux_remove, TAGNUM(default_tags[i]), &ret); } } } } /// removeauxtags - remove aux tags in bam data which are not present in acceptable tag set /** @param bamdata - pointer to the bamdata from which needs the filtering * @param config - pointer to conf_data returns nothing */ void removeauxtags(bam1_t *bamdata, conf_data *config) { uint8_t *auxdata = NULL; const char *tag = NULL; khint_t iter = 0; if (!bamdata || !config) return; for (auxdata = bam_aux_first(bamdata); auxdata; ) { tag = bam_aux_tag(auxdata); if (config->aux_keep) { //keep option or remove option with ^ in use iter = kh_get(aux_exists, config->aux_keep, TAGNUM(tag)); if (iter == kh_end(config->aux_keep)) { //not present in keep, remove auxdata = bam_aux_remove(bamdata, auxdata); } else { //present, keep auxdata = bam_aux_next(bamdata, auxdata); } } else if (config->aux_remove) { //remove option in use iter = kh_get(aux_exists, config->aux_remove, TAGNUM(tag)); if (iter != kh_end(config->aux_remove)) { //present in remove, remove auxdata = bam_aux_remove(bamdata, auxdata); } else { //not present, keep auxdata = bam_aux_next(bamdata, auxdata); } } //else impossible } } /// getRGlines - add RG lines from input header to output header /** @param in_samhdr - pointer to input sam header data * @param out_samhdr - pointer to output sam header data returns 1 on failure 0 on success */ int getRGlines(sam_hdr_t *in_samhdr, sam_hdr_t *out_samhdr) { kstring_t line = KS_INITIALIZE; int i = 0, ret = 0, count = 0; const char rg[] = "RG"; if (!in_samhdr || !out_samhdr) { fprintf(samtools_stderr, "Invalid parameters in getRGlines!\n"); return 1; } if (-1 == (count = sam_hdr_count_lines(in_samhdr, rg))) { fprintf(samtools_stderr, "Failed to get RG count!\n"); return 1; } for (i = 0; i < count; ++i) { ks_clear(&line); if (sam_hdr_find_line_pos(in_samhdr, rg, i, &line)) { fprintf(samtools_stderr, "Failed to get RG data!\n"); ret = 1; break; } if (sam_hdr_add_lines(out_samhdr, line.s, line.l)) { fprintf(samtools_stderr, "Failed to add RG data!\n"); ret = 1; break; } } ks_free(&line); return ret; } /// getPGlines - add PG lines from input header to output header based on user option /** @param in_samhdr - pointer to input sam header data * @param out_samhdr - pointer to output sam header data * @param config - pointer to internal configuration data * @param argdump - string containing dump of command line invocation returns 1 on failure 0 on success */ int getPGlines(sam_hdr_t *in_samhdr, sam_hdr_t *out_samhdr, conf_data *config, const char *argdump) { kstring_t line = KS_INITIALIZE, id = KS_INITIALIZE; int i = 0, ret = 0, count = 0; const char pg[] = "PG"; if (!in_samhdr || !out_samhdr || !config) { fprintf(samtools_stderr, "Invalid parameters in getPGlines!\n"); return 1; } if (-1 == (count = sam_hdr_count_lines(in_samhdr, pg))) { fprintf(samtools_stderr, "Failed to get PG count!\n"); return 1; } if (config->pgid && config->pgid[0]) { //when reject-PG is given, and is not empty, remove given pg onwards for (i = 0; i < count; ++i) { if (sam_hdr_find_tag_pos(in_samhdr, pg, i, "ID", &id)) { fprintf(samtools_stderr, "Failed to get PG entry fields for line %d!\n", i + 1); break; } if (!strcmp(id.s, config->pgid)) break; //either current PG is prior to rejected one or all PGs are in, get PG line and add ks_clear(&line); if (sam_hdr_find_line_pos(in_samhdr, "PG", i, &line)) { fprintf(samtools_stderr, "Failed to get PG data at %d!\n", i + 1); ret = 1; break; } //add to output if (sam_hdr_add_lines(out_samhdr, line.s, line.l)) { fprintf(samtools_stderr, "Failed to add PG data!\n"); ret = 1; break; } } } else { //keep all for (i = 0; i < count; ++i) { if (sam_hdr_find_line_pos(in_samhdr, "PG", i, &line)) { fprintf(samtools_stderr, "Failed to get PG data at %d!\n", i + 1); ret = 1; break; } //line has the required PG data if (sam_hdr_add_lines(out_samhdr, line.s, line.l)) { fprintf(samtools_stderr, "Failed to add PG data!\n"); ret = 1; break; } } } if (!ret && !config->noPGentry) { //add PG entry with reset command if (-1 == (ret = sam_hdr_add_pg(out_samhdr, "samtools", "CL", argdump, NULL))) { fprintf(samtools_stderr, "Failed to set PG entry!\n"); } } ks_free(&line); ks_free(&id); return ret; } /// reset - do the reset of data and create output; create output header with required rg/pg data, add bamdata with flags set to unmapped, pair info and orientation reset, // reerse and complement alignment if required /** @param infile - input samfile pointer * @param outfile - output sam file pointer * @param config - pointer to internal configuration data * @param args - string containing dump of command line invocation returns 1 on failure 0 on success */ int reset(samFile *infile, samFile *outfile, conf_data *config, char *args) { sam_hdr_t *in_samhdr = NULL, *out_samhdr = NULL; int ret = EXIT_FAILURE, ret_r = 0, ret_w = 0, i = 0; bam1_t *bamdata = NULL, *outdata = NULL; kstring_t querydata = KS_INITIALIZE, qualdata = KS_INITIALIZE; char *sp = NULL, *qp = NULL; uint8_t *bamquery = NULL, *bamqual = NULL; if (!infile || !outfile) { fprintf(samtools_stderr, "Invalid parameters in reset!\n"); goto error; } //read input header in_samhdr = sam_hdr_read(infile); if (!in_samhdr) { fprintf(samtools_stderr, "Failed to read header from file!\n"); goto error; } //create output header if (!(out_samhdr = sam_hdr_init())) { fprintf(samtools_stderr, "Failed to create output header!\n"); goto error; } //add version to output header if (-1 == sam_hdr_add_line(out_samhdr,"HD", "VN", SAM_FORMAT_VERSION, NULL)) { fprintf(samtools_stderr, "Failed to set header data!\n"); goto error; } //add RG / PG lines if configured if ((config->keepRGs && getRGlines(in_samhdr, out_samhdr)) || getPGlines(in_samhdr, out_samhdr, config, args)) { goto error; } //write output header if (sam_hdr_write(outfile, out_samhdr)) { print_error_errno("reset", "Output header write failed (%d)!\n", errno); goto error; } bamdata = bam_init1(); //input bam outdata = bam_init1(); //output bam if (!bamdata || !outdata) { fprintf(samtools_stderr, "Failed to allocate data memory!\n"); goto error; } errno = 0; i = 0; sp = NULL; qp = NULL; bamquery = NULL; bamqual = NULL; //get bam data, make updates and dump to output while (0 <= (ret_r = sam_read1(infile, in_samhdr, bamdata))) { sp = NULL; qp = NULL; bamquery = NULL; bamqual = NULL; // read data if (bamdata->core.flag & BAM_FSECONDARY || bamdata->core.flag & BAM_FSUPPLEMENTARY) { continue; } //update flags uint16_t flags = bamdata->core.flag & ~BAM_FPROPER_PAIR; //reset pair info flags |= BAM_FUNMAP; //mark as unmapped if (bamdata->core.flag & BAM_FPAIRED) { flags |= BAM_FMUNMAP; //mark mate as unmapped, if it was a pair } flags &= ~BAM_FMREVERSE; //reset mate orientation if (!(config->ctrlFlags & RESET_KEEPDUPFLAG)) { flags &= ~BAM_FDUP; //reset dup flag from alignment } if (0 > ks_resize(&querydata, bamdata->core.l_qseq) || 0 > ks_resize(&qualdata, bamdata->core.l_qseq)) { fprintf(samtools_stderr, "Failed to get allocate memory!\n"); ret_r = -4; break; } ks_clear(&querydata); ks_clear(&qualdata); sp = ks_str(&querydata); qp = ks_str(&qualdata); bamquery = bam_get_seq(bamdata); bamqual = bam_get_qual(bamdata); if (bamdata->core.flag & BAM_FREVERSE) { //sequence data ordered as reverse complemented, reorder/complement sequence and quality data as read and clear the flag for (i = bamdata->core.l_qseq - 1; i >= 0; --i) { *sp++ = "=TGKCYSBAWRDMHVN"[bam_seqi(bamquery, i)]; *qp++ = bamqual[i]; } flags &= ~BAM_FREVERSE; //reset flag as well } else { //data in read order itself for (i = 0; i < bamdata->core.l_qseq ; ++i) { *sp++ = seq_nt16_str[bam_seqi(bamquery, i)]; } memcpy(qp, bam_get_qual(bamdata), bamdata->core.l_qseq); } removeauxtags(bamdata, config); if (0 > (ret_w = bam_set1(outdata, bamdata->core.l_qname - bamdata->core.l_extranul - 1, bam_get_qname(bamdata), flags, -1, -1, 0, 0, NULL, -1, -1, 0, bamdata->core.l_qseq, querydata.s, qualdata.s, bam_get_l_aux(bamdata)))) { print_error_errno("reset", "Failed to set output data (%d)!\n", errno); break; } memcpy(bam_get_aux(outdata), bam_get_aux(bamdata), bam_get_l_aux(bamdata)); outdata->l_data += bam_get_l_aux(bamdata); errno = 0; //write bam data to output if (0 > (ret_w = sam_write1(outfile, out_samhdr, outdata))) { print_error_errno("reset", "Failed to write output data (%d)!\n", errno); break; } // wrote the data, continue read/write cycle errno = 0; } if (-1 > ret_r || 0 > ret_w) { //some error fprintf(samtools_stderr, "Error during %s!\n", (-1 > ret_r)? "read" : "write"); } else { // no error! ret = EXIT_SUCCESS; } error: // clean up and return result if (in_samhdr) sam_hdr_destroy(in_samhdr); if (out_samhdr) sam_hdr_destroy(out_samhdr); if (bamdata) bam_destroy1(bamdata); if (outdata) bam_destroy1(outdata); if (qualdata.s) ks_free(&qualdata); if (querydata.s) ks_free(&querydata); return ret; } /// cleanup - free up allocations made /** @param config - pointer to internal configuration data returns nothing */ void cleanup(conf_data *config) { if (config->aux_keep) { kh_destroy(aux_exists, config->aux_keep); config->aux_keep = NULL; } if (config->aux_remove) { kh_destroy(aux_exists, config->aux_remove); config->aux_remove = NULL; } } /// main_reset - starts the reset of data /** @param argc - count of arguments * @param argv - pointer to array of arguments returns 1 on failure 0 on success */ int main_reset(int argc, char *argv[]) { static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', '-', 'O', '-', '-', '@'), //let output format and thread count be given by user - long options {"keep-tag", required_argument, NULL, LONG_OPT('x')}, //aux tags to be retained, supports ^ STR {"remove-tag", required_argument, NULL, 'x'}, //aux tags to be removed {"no-RG", no_argument, NULL, 1}, //no RG lines in output, default is to keep them //reject PG lines from input, default is to keep them (i.e. option not given); without optional filename, all PGs removed and those given in file are filtered when optional filename is given {"reject-PG", required_argument, NULL, 'p'}, //reject entries from this PG onwards {"no-PG", no_argument, NULL, 2}, //do not add PG entry for reset operation, default is to add it {"dupflag", no_argument, NULL, 3}, //keep the dup flag as it is - as in initial reset implementation {NULL, 0, NULL, 0} }; samFile *infile = NULL, *outfile = NULL; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; htsThreadPool tpool = {NULL, 0}; const char *inname = NULL, *outname = NULL; int c = 0, ret = EXIT_FAILURE; char outmode[4] = "w", *args = NULL; conf_data resetconf = {1, 0, 0, NULL, NULL, NULL}; //keep RGs and PGs by default, ctrlflags = 0 //samtools reset -o outfile -x/--remove-tag ... --keep-tag ... --threads=n --output-fmt=fmt --no-RG --reject-PG pgid --no-PG [] while ((c = getopt_long(argc, argv, "o:@:x:O:", lopts, NULL)) >= 0) { switch (c) { case 1: //--no-RG if (!resetconf.keepRGs) { usage(samtools_stderr); //already given! goto exit; } resetconf.keepRGs = 0; break; case 2: //--no-PG if (resetconf.noPGentry) { usage(samtools_stderr); //already given! goto exit; } resetconf.noPGentry = 1; break; case 3: //keep dup flag as it is / no reset resetconf.ctrlFlags |= RESET_KEEPDUPFLAG; break; case 'p': //--reject-PG= if (resetconf.pgid) { usage(samtools_stderr); //already given! goto exit; } resetconf.pgid = optarg; break; case 'o': //output file name if (outname) { //already given! usage(samtools_stderr); goto exit; } outname = optarg; break; case 'x': //remove aux tag if (*optarg == '^') { //remove all except given ones! if (parse_aux_list(&resetconf.aux_keep, optarg+1, "main_reset")) { usage(samtools_stderr); goto exit; } } else { //remove given ones if (parse_aux_list(&resetconf.aux_remove, optarg, "main_reset")) { usage(samtools_stderr); goto exit; } } break; case LONG_OPT('x'): //keep aux tags if (parse_aux_list(&resetconf.aux_keep, optarg, "main_reset")) { usage(samtools_stderr); goto exit; } break; // handle standard samtool options like thread count, verbosity... default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; // else fall-through // couldn't parse or unknown options, show usage! case '?': //unknown options found! usage(samtools_stderr); goto exit; break; } } if (argc == 1 && isatty(STDIN_FILENO)) { //no args and input is stdin -- it is the usage check usage(samtools_stdout); ret = EXIT_SUCCESS; goto exit; } //else have other args or input from redirection/pipe/other device -- validate and work if (!outname) outname = "-"; //check and fail if unnecessary parameters are given c = argc - optind; if (c > 1) { usage(samtools_stderr); goto exit; } if (c == 1) { inname = argv[optind]; } else { inname = "-"; } //update aux tag configuration update_aux_conf(&resetconf); //set output file format based on name sam_open_mode(outmode + 1, outname, NULL); //open input and output files infile = sam_open(inname, "r"); outfile = sam_open_format(outname, outmode, &ga.out); if (!infile || !outfile) { fprintf(samtools_stderr, "Could not open %s%s%s\n", !infile ? inname : "", (!infile && !outfile)? ", " : "", !outfile ? outname : ""); goto exit; } // set the thread count if given as argument if (ga.nthreads > 0) { if (!(tpool.pool = hts_tpool_init(ga.nthreads))) { fprintf(samtools_stderr, "\nFailed to setup thread pool\n"); goto exit; } hts_set_opt(infile, HTS_OPT_THREAD_POOL, &tpool); hts_set_opt(outfile, HTS_OPT_THREAD_POOL, &tpool); } args = stringify_argv(argc + 1, argv - 1); //to dump invocation in PG line //do the reset! ret = reset(infile, outfile, &resetconf, args); exit: if (args) free(args); if (infile) sam_close(infile); if (outfile) sam_close(outfile); if (tpool.pool) hts_tpool_destroy(tpool.pool); cleanup(&resetconf); sam_global_args_free(&ga); return ret; } pysam-0.23.0/samtools/sam_opts.c000066400000000000000000000155411475062545500166020ustar00rootroot00000000000000/* sam_opts.c -- utilities to aid parsing common command line options. Copyright (C) 2015, 2019 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include "sam_opts.h" /* * Processes a standard "global" samtools long option. * * The 'c' value is the return value from a getopt_long() call. It is checked * against the lopt[] array to find the corresponding value as this may have * been reassigned by the individual subcommand. * * Having found the entry, the corresponding long form is used to apply the * option, storing the setting in sam_global_args *ga. * * Returns 0 on success, * -1 on failure. */ int parse_sam_global_opt(int c, const char *optarg, const struct option *lopt, sam_global_args *ga) { int r = 0; while (lopt->name) { if (c != lopt->val) { lopt++; continue; } if (strcmp(lopt->name, "input-fmt") == 0) { r = hts_parse_format(&ga->in, optarg); break; } else if (strcmp(lopt->name, "input-fmt-option") == 0) { r = hts_opt_add((hts_opt **)&ga->in.specific, optarg); break; } else if (strcmp(lopt->name, "output-fmt") == 0) { r = hts_parse_format(&ga->out, optarg); break; } else if (strcmp(lopt->name, "output-fmt-option") == 0) { r = hts_opt_add((hts_opt **)&ga->out.specific, optarg); break; } else if (strcmp(lopt->name, "reference") == 0) { char *ref = malloc(10 + strlen(optarg) + 1); if (!ref) { fprintf(stderr, "Unable to allocate memory in " "parse_sam_global_opt.\n"); return -1; } sprintf(ref, "reference=%s", optarg); if (!(ga->reference = strdup(optarg))) { fprintf(stderr, "Unable to allocate memory in " "parse_sam_global_opt.\n"); return -1; } r = hts_opt_add((hts_opt **)&ga->in.specific, ref); r |= hts_opt_add((hts_opt **)&ga->out.specific, ref); free(ref); break; } else if (strcmp(lopt->name, "threads") == 0) { ga->nthreads = atoi(optarg); break; } else if (strcmp(lopt->name, "write-index") == 0) { ga->write_index = 1; break; } else if (strcmp(lopt->name, "verbosity") == 0) { hts_verbose = atoi(optarg); break; } } if (!lopt->name) { fprintf(stderr, "Unexpected global option.\n"); return -1; } /* * SAM format with compression enabled implies SAM.bgzf */ if (ga->out.format == sam) { hts_opt *opts = (hts_opt *)ga->out.specific; while (opts) { if (opts->opt == HTS_OPT_COMPRESSION_LEVEL) ga->out.compression = bgzf; opts = opts->next; } } return r; } /* * Report the usage for global options. * * This accepts a string with one character per SAM_OPT_GLOBAL_OPTIONS option * to determine which options need to be printed and how. * Each character should be one of: * '.' No short option has been assigned. Use --long-opt only. * '-' The long (and short) option has been disabled. * Otherwise the short option is character . */ void sam_global_opt_help(FILE *fp, const char *shortopts) { int i = 0; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS(0,0,0,0,0,0), { NULL, 0, NULL, 0 } }; for (i = 0; shortopts && shortopts[i] && lopts[i].name; i++) { if (shortopts[i] == '-') continue; if (shortopts[i] == '.') fprintf(fp, " --"); else fprintf(fp, " -%c, --", shortopts[i]); if (strcmp(lopts[i].name, "input-fmt") == 0) fprintf(fp,"input-fmt FORMAT[,OPT[=VAL]]...\n" " Specify input format (SAM, BAM, CRAM)\n"); else if (strcmp(lopts[i].name, "input-fmt-option") == 0) fprintf(fp,"input-fmt-option OPT[=VAL]\n" " Specify a single input file format option in the form\n" " of OPTION or OPTION=VALUE\n"); else if (strcmp(lopts[i].name, "output-fmt") == 0) fprintf(fp,"output-fmt FORMAT[,OPT[=VAL]]...\n" " Specify output format (SAM, BAM, CRAM)\n"); else if (strcmp(lopts[i].name, "output-fmt-option") == 0) fprintf(fp,"output-fmt-option OPT[=VAL]\n" " Specify a single output file format option in the form\n" " of OPTION or OPTION=VALUE\n"); else if (strcmp(lopts[i].name, "reference") == 0) fprintf(fp,"reference FILE\n" " Reference sequence FASTA FILE [null]\n"); else if (strcmp(lopts[i].name, "threads") == 0) fprintf(fp,"threads INT\n" " Number of additional threads to use [0]\n"); else if (strcmp(lopts[i].name, "write-index") == 0) fprintf(fp,"write-index\n" " Automatically index the output files [off]\n"); else if (strcmp(lopts[i].name, "verbosity") == 0) fprintf(fp,"verbosity INT\n" " Set level of verbosity\n"); } } void sam_global_args_init(sam_global_args *ga) { if (!ga) return; memset(ga, 0, sizeof(*ga)); } void sam_global_args_free(sam_global_args *ga) { if (ga->in.specific) hts_opt_free(ga->in.specific); if (ga->out.specific) hts_opt_free(ga->out.specific); if (ga->reference) free(ga->reference); } pysam-0.23.0/samtools/sam_opts.c.pysam.c000066400000000000000000000156311475062545500201530ustar00rootroot00000000000000#include "samtools.pysam.h" /* sam_opts.c -- utilities to aid parsing common command line options. Copyright (C) 2015, 2019 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include "sam_opts.h" /* * Processes a standard "global" samtools long option. * * The 'c' value is the return value from a getopt_long() call. It is checked * against the lopt[] array to find the corresponding value as this may have * been reassigned by the individual subcommand. * * Having found the entry, the corresponding long form is used to apply the * option, storing the setting in sam_global_args *ga. * * Returns 0 on success, * -1 on failure. */ int parse_sam_global_opt(int c, const char *optarg, const struct option *lopt, sam_global_args *ga) { int r = 0; while (lopt->name) { if (c != lopt->val) { lopt++; continue; } if (strcmp(lopt->name, "input-fmt") == 0) { r = hts_parse_format(&ga->in, optarg); break; } else if (strcmp(lopt->name, "input-fmt-option") == 0) { r = hts_opt_add((hts_opt **)&ga->in.specific, optarg); break; } else if (strcmp(lopt->name, "output-fmt") == 0) { r = hts_parse_format(&ga->out, optarg); break; } else if (strcmp(lopt->name, "output-fmt-option") == 0) { r = hts_opt_add((hts_opt **)&ga->out.specific, optarg); break; } else if (strcmp(lopt->name, "reference") == 0) { char *ref = malloc(10 + strlen(optarg) + 1); if (!ref) { fprintf(samtools_stderr, "Unable to allocate memory in " "parse_sam_global_opt.\n"); return -1; } sprintf(ref, "reference=%s", optarg); if (!(ga->reference = strdup(optarg))) { fprintf(samtools_stderr, "Unable to allocate memory in " "parse_sam_global_opt.\n"); return -1; } r = hts_opt_add((hts_opt **)&ga->in.specific, ref); r |= hts_opt_add((hts_opt **)&ga->out.specific, ref); free(ref); break; } else if (strcmp(lopt->name, "threads") == 0) { ga->nthreads = atoi(optarg); break; } else if (strcmp(lopt->name, "write-index") == 0) { ga->write_index = 1; break; } else if (strcmp(lopt->name, "verbosity") == 0) { hts_verbose = atoi(optarg); break; } } if (!lopt->name) { fprintf(samtools_stderr, "Unexpected global option.\n"); return -1; } /* * SAM format with compression enabled implies SAM.bgzf */ if (ga->out.format == sam) { hts_opt *opts = (hts_opt *)ga->out.specific; while (opts) { if (opts->opt == HTS_OPT_COMPRESSION_LEVEL) ga->out.compression = bgzf; opts = opts->next; } } return r; } /* * Report the usage for global options. * * This accepts a string with one character per SAM_OPT_GLOBAL_OPTIONS option * to determine which options need to be printed and how. * Each character should be one of: * '.' No short option has been assigned. Use --long-opt only. * '-' The long (and short) option has been disabled. * Otherwise the short option is character . */ void sam_global_opt_help(FILE *fp, const char *shortopts) { int i = 0; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS(0,0,0,0,0,0), { NULL, 0, NULL, 0 } }; for (i = 0; shortopts && shortopts[i] && lopts[i].name; i++) { if (shortopts[i] == '-') continue; if (shortopts[i] == '.') fprintf(fp, " --"); else fprintf(fp, " -%c, --", shortopts[i]); if (strcmp(lopts[i].name, "input-fmt") == 0) fprintf(fp,"input-fmt FORMAT[,OPT[=VAL]]...\n" " Specify input format (SAM, BAM, CRAM)\n"); else if (strcmp(lopts[i].name, "input-fmt-option") == 0) fprintf(fp,"input-fmt-option OPT[=VAL]\n" " Specify a single input file format option in the form\n" " of OPTION or OPTION=VALUE\n"); else if (strcmp(lopts[i].name, "output-fmt") == 0) fprintf(fp,"output-fmt FORMAT[,OPT[=VAL]]...\n" " Specify output format (SAM, BAM, CRAM)\n"); else if (strcmp(lopts[i].name, "output-fmt-option") == 0) fprintf(fp,"output-fmt-option OPT[=VAL]\n" " Specify a single output file format option in the form\n" " of OPTION or OPTION=VALUE\n"); else if (strcmp(lopts[i].name, "reference") == 0) fprintf(fp,"reference FILE\n" " Reference sequence FASTA FILE [null]\n"); else if (strcmp(lopts[i].name, "threads") == 0) fprintf(fp,"threads INT\n" " Number of additional threads to use [0]\n"); else if (strcmp(lopts[i].name, "write-index") == 0) fprintf(fp,"write-index\n" " Automatically index the output files [off]\n"); else if (strcmp(lopts[i].name, "verbosity") == 0) fprintf(fp,"verbosity INT\n" " Set level of verbosity\n"); } } void sam_global_args_init(sam_global_args *ga) { if (!ga) return; memset(ga, 0, sizeof(*ga)); } void sam_global_args_free(sam_global_args *ga) { if (ga->in.specific) hts_opt_free(ga->in.specific); if (ga->out.specific) hts_opt_free(ga->out.specific); if (ga->reference) free(ga->reference); } pysam-0.23.0/samtools/sam_opts.h000066400000000000000000000100321475062545500165750ustar00rootroot00000000000000/* sam_opts.h -- utilities to aid parsing common command line options. Copyright (C) 2015, 2019 Genome Research Ltd. Author: James Bonfield Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef SAM_OPTS_H #define SAM_OPTS_H #include #include #include #include typedef struct sam_global_args { htsFormat in; htsFormat out; char *reference; int nthreads; int write_index; } sam_global_args; #define SAM_GLOBAL_ARGS_INIT {{0},{0}} enum { SAM_OPT_INPUT_FMT = CHAR_MAX+1, SAM_OPT_INPUT_FMT_OPTION, SAM_OPT_OUTPUT_FMT, SAM_OPT_OUTPUT_FMT_OPTION, SAM_OPT_REFERENCE, SAM_OPT_NTHREADS, SAM_OPT_WRITE_INDEX, SAM_OPT_VERBOSITY, }; #define SAM_OPT_VAL(val, defval) ((val) == '-')? '?' : (val)? (val) : (defval) // Use this within struct option lopts[] = {...} to add the standard global // options. The arguments determine whether the corresponding option is // enabled and, if so, whether it has a short option equivalent: // 0 No short option has been assigned. Use --long-opt only. // '-' Both long and short options are disabled. // Otherwise the equivalent short option is character . #define SAM_OPT_GLOBAL_OPTIONS(o1, o2, o3, o4, o5, o6) \ {"input-fmt", required_argument, NULL, SAM_OPT_VAL(o1, SAM_OPT_INPUT_FMT)}, \ {"input-fmt-option", required_argument, NULL, SAM_OPT_VAL(o2, SAM_OPT_INPUT_FMT_OPTION)}, \ {"output-fmt", required_argument, NULL, SAM_OPT_VAL(o3, SAM_OPT_OUTPUT_FMT)}, \ {"output-fmt-option", required_argument, NULL, SAM_OPT_VAL(o4, SAM_OPT_OUTPUT_FMT_OPTION)}, \ {"reference", required_argument, NULL, SAM_OPT_VAL(o5, SAM_OPT_REFERENCE)}, \ {"threads", required_argument, NULL, SAM_OPT_VAL(o6, SAM_OPT_NTHREADS)}, \ {"write-index", no_argument, NULL, SAM_OPT_WRITE_INDEX}, \ {"verbosity", required_argument, NULL, SAM_OPT_VERBOSITY} /* * Processes a standard "global" samtools long option. * * The 'c' value is the return value from a getopt_long() call. It is checked * against the lopt[] array to find the corresponding value as this may have * been reassigned by the individual subcommand. * * Having found the entry, the corresponding long form is used to apply the * option, storing the setting in sam_global_args *ga. * * Returns 0 on success, * -1 on failure. */ int parse_sam_global_opt(int c, const char *optarg, const struct option *lopt, sam_global_args *ga); /* * Report the usage for global options. * * This accepts a string with one character per SAM_OPT_GLOBAL_OPTIONS option * to determine which options need to be printed and how. * Each character should be one of: * '.' No short option has been assigned. Use --long-opt only. * '-' The long (and short) option has been disabled. * Otherwise the short option is character . */ void sam_global_opt_help(FILE *fp, const char *shortopts); void sam_global_args_init(sam_global_args *ga); void sam_global_args_free(sam_global_args *ga); #endif pysam-0.23.0/samtools/sam_utils.c000066400000000000000000000133361475062545500167550ustar00rootroot00000000000000/* sam_utils.c -- various utilities internal to samtools. Copyright (C) 2014-2016, 2018, 2019, 2023 Genome Research Ltd. Author: John Marshall Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "sam_utils.h" static htsFile *samtools_stdout = NULL; void autoflush_if_stdout(htsFile *fp, const char *fname) { if (fname == NULL || strcmp(fname, "-") == 0) samtools_stdout = fp; } void release_autoflush(htsFile *fp) { if (samtools_stdout == fp) samtools_stdout = NULL; } static void HTS_FORMAT(HTS_PRINTF_FMT, 2, 0) vprint_error_core(const char *subcommand, const char *format, va_list args, const char *extra) { fflush(stdout); if (samtools_stdout) hts_flush(samtools_stdout); if (subcommand && *subcommand) fprintf(stderr, "samtools %s: ", subcommand); else fprintf(stderr, "samtools: "); vfprintf(stderr, format, args); if (extra) fprintf(stderr, ": %s\n", extra); else fprintf(stderr, "\n"); fflush(stderr); } void print_error(const char *subcommand, const char *format, ...) { va_list args; va_start(args, format); vprint_error_core(subcommand, format, args, NULL); va_end(args); } void print_error_errno(const char *subcommand, const char *format, ...) { int err = errno; va_list args; va_start(args, format); vprint_error_core(subcommand, format, args, err? strerror(err) : NULL); va_end(args); } void check_sam_close(const char *subcmd, samFile *fp, const char *fname, const char *null_fname, int *retp) { release_autoflush(fp); int r = sam_close(fp); if (r >= 0) return; // TODO Need error infrastructure so we can print a message instead of r if (fname) print_error(subcmd, "error closing \"%s\": %d", fname, r); else print_error(subcmd, "error closing %s: %d", null_fname, r); *retp = EXIT_FAILURE; } /* Pick an index suffix based on the output file descriptor type. */ static char *idx_suffix(htsFile *fp) { switch (fp->format.format) { case sam: case bam: // Tough cheese if you wanted bai! // New feature => mandatory new index too, for simplicity of CLI. return "csi"; case cram: return "crai"; default: return NULL; } } /* * Utility function to add an index to a file we've opened for write. * NB: Call this after writing the header and before writing sequences. * * The returned index filename should be freed by the caller, but only * after sam_idx_save has been called. * * Returns index filename on success, * NULL on failure. */ char *auto_index(htsFile *fp, const char *fn, bam_hdr_t *header) { char *fn_idx; int min_shift = 14; /* CSI */ if (!fn || !*fn || strcmp(fn, "-") == 0) return NULL; char *delim = strstr(fn, HTS_IDX_DELIM); if (delim != NULL) { delim += strlen(HTS_IDX_DELIM); fn_idx = strdup(delim); if (!fn_idx) return NULL; size_t l = strlen(fn_idx); if (l >= 4 && strcmp(fn_idx + l - 4, ".bai") == 0) min_shift = 0; } else { char *suffix = idx_suffix(fp); if (!suffix) return NULL; fn_idx = malloc(strlen(fn)+6); if (!fn_idx) return NULL; sprintf(fn_idx, "%s.%s", fn, suffix); } if (sam_idx_init(fp, header, min_shift, fn_idx) < 0) { print_error_errno("auto_index", "failed to open index \"%s\" for writing", fn_idx); free(fn_idx); return NULL; } return fn_idx; } /// parse_aux_list - parses given string for aux tags which are ',' separated /** @param h - pointer to a SET holding aux tags * @param optarg - string having the ',' separated aux tags * @param msgheader - string to be used during error output as a header returns -1 on failure and 0 on success moved from sam_view.c to here for common usage at different source files */ int parse_aux_list(auxhash_t *h, char *optarg, const char *msgheader) { if (!*h) *h = kh_init(aux_exists); while (strlen(optarg) >= 2) { int x = optarg[0]<<8 | optarg[1]; int ret = 0; kh_put(aux_exists, *h, x, &ret); if (ret < 0) { kh_destroy(aux_exists, *h); *h = NULL; return -1; } optarg += 2; if (*optarg == ',') // allow white-space too for easy `cat file`? optarg++; else if (*optarg != 0) break; } if (strlen(optarg) != 0) { fprintf(stderr, "%s: Error parsing option, " "auxiliary tags should be exactly two characters long.\n", msgheader ? msgheader : ""); kh_destroy(aux_exists, *h); *h = NULL; return -1; } return 0; } pysam-0.23.0/samtools/sam_utils.c.pysam.c000066400000000000000000000135711475062545500203270ustar00rootroot00000000000000#include "samtools.pysam.h" /* sam_utils.c -- various utilities internal to samtools. Copyright (C) 2014-2016, 2018, 2019, 2023 Genome Research Ltd. Author: John Marshall Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "sam_utils.h" static htsFile *samtools_stdout_internal = NULL; void autoflush_if_stdout(htsFile *fp, const char *fname) { if (fname == NULL || strcmp(fname, "-") == 0) samtools_stdout_internal = fp; } void release_autoflush(htsFile *fp) { if (samtools_stdout_internal == fp) samtools_stdout_internal = NULL; } static void HTS_FORMAT(HTS_PRINTF_FMT, 2, 0) vprint_error_core(const char *subcommand, const char *format, va_list args, const char *extra) { fflush(samtools_stdout); if (samtools_stdout_internal) hts_flush(samtools_stdout_internal); if (subcommand && *subcommand) fprintf(samtools_stderr, "samtools %s: ", subcommand); else fprintf(samtools_stderr, "samtools: "); vfprintf(samtools_stderr, format, args); if (extra) fprintf(samtools_stderr, ": %s\n", extra); else fprintf(samtools_stderr, "\n"); fflush(samtools_stderr); } void print_error(const char *subcommand, const char *format, ...) { va_list args; va_start(args, format); vprint_error_core(subcommand, format, args, NULL); va_end(args); } void print_error_errno(const char *subcommand, const char *format, ...) { int err = errno; va_list args; va_start(args, format); vprint_error_core(subcommand, format, args, err? strerror(err) : NULL); va_end(args); } void check_sam_close(const char *subcmd, samFile *fp, const char *fname, const char *null_fname, int *retp) { release_autoflush(fp); int r = sam_close(fp); if (r >= 0) return; // TODO Need error infrastructure so we can print a message instead of r if (fname) print_error(subcmd, "error closing \"%s\": %d", fname, r); else print_error(subcmd, "error closing %s: %d", null_fname, r); *retp = EXIT_FAILURE; } /* Pick an index suffix based on the output file descriptor type. */ static char *idx_suffix(htsFile *fp) { switch (fp->format.format) { case sam: case bam: // Tough cheese if you wanted bai! // New feature => mandatory new index too, for simplicity of CLI. return "csi"; case cram: return "crai"; default: return NULL; } } /* * Utility function to add an index to a file we've opened for write. * NB: Call this after writing the header and before writing sequences. * * The returned index filename should be freed by the caller, but only * after sam_idx_save has been called. * * Returns index filename on success, * NULL on failure. */ char *auto_index(htsFile *fp, const char *fn, bam_hdr_t *header) { char *fn_idx; int min_shift = 14; /* CSI */ if (!fn || !*fn || strcmp(fn, "-") == 0) return NULL; char *delim = strstr(fn, HTS_IDX_DELIM); if (delim != NULL) { delim += strlen(HTS_IDX_DELIM); fn_idx = strdup(delim); if (!fn_idx) return NULL; size_t l = strlen(fn_idx); if (l >= 4 && strcmp(fn_idx + l - 4, ".bai") == 0) min_shift = 0; } else { char *suffix = idx_suffix(fp); if (!suffix) return NULL; fn_idx = malloc(strlen(fn)+6); if (!fn_idx) return NULL; sprintf(fn_idx, "%s.%s", fn, suffix); } if (sam_idx_init(fp, header, min_shift, fn_idx) < 0) { print_error_errno("auto_index", "failed to open index \"%s\" for writing", fn_idx); free(fn_idx); return NULL; } return fn_idx; } /// parse_aux_list - parses given string for aux tags which are ',' separated /** @param h - pointer to a SET holding aux tags * @param optarg - string having the ',' separated aux tags * @param msgheader - string to be used during error output as a header returns -1 on failure and 0 on success moved from sam_view.c to here for common usage at different source files */ int parse_aux_list(auxhash_t *h, char *optarg, const char *msgheader) { if (!*h) *h = kh_init(aux_exists); while (strlen(optarg) >= 2) { int x = optarg[0]<<8 | optarg[1]; int ret = 0; kh_put(aux_exists, *h, x, &ret); if (ret < 0) { kh_destroy(aux_exists, *h); *h = NULL; return -1; } optarg += 2; if (*optarg == ',') // allow white-space too for easy `cat file`? optarg++; else if (*optarg != 0) break; } if (strlen(optarg) != 0) { fprintf(samtools_stderr, "%s: Error parsing option, " "auxiliary tags should be exactly two characters long.\n", msgheader ? msgheader : ""); kh_destroy(aux_exists, *h); *h = NULL; return -1; } return 0; } pysam-0.23.0/samtools/sam_utils.h000066400000000000000000000064261475062545500167640ustar00rootroot00000000000000/* sam_utils.c -- to hold utility functions and types Copyright (C) 2023 Genome Research Ltd. Author: Vasudeva Sarma Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef SAM_UTIL_H #define SAM_UTIL_H #include "htslib/khash.h" #include "htslib/sam.h" //this file may contain any utility functions and data types to be shared across /*below parse_aux_list and aux_exists are moved from sam_view.c to here for common *usage at different source files */ KHASH_SET_INIT_INT(aux_exists) //SET data type to hold aux tags typedef khash_t(aux_exists) *auxhash_t; /// parse_aux_list - parses given string for aux tags which are ',' separated /** @param h - pointer to a SET holding aux tags * @param optarg - string having the ',' separated aux tags * @param msgheader - string to be used during error output as a header returns -1 on failure and 0 on success moved from sam_view.c to here for common usage at different source files */ int parse_aux_list(auxhash_t *h, char *optarg, const char *msgheader); // below utility function declarations moved from samtools.h to here and this header is included in samtools.h #define CHECK_PRINTF(fmt,args) HTS_FORMAT(HTS_PRINTF_FMT, (fmt), (args)) void print_error(const char *subcommand, const char *format, ...) CHECK_PRINTF(2, 3); void print_error_errno(const char *subcommand, const char *format, ...) CHECK_PRINTF(2, 3); void check_sam_close(const char *subcmd, samFile *fp, const char *fname, const char *null_fname, int *retp); /* Utility functions to register an output htsFile/samFile/vcfFile that * might be stdout. If FNAME is "-" or NULL, records FP so that print_error() * et al can automatically flush it before printing an error message. */ void autoflush_if_stdout(htsFile *fp, const char *fname); /* Call this before closing FP; check_sam_close() does this automatically. */ void release_autoflush(htsFile *fp); /* * Utility function to add an index to a file we've opened for write. * NB: Call this after writing the header and before writing sequences. * * The returned index filename should be freed by the caller, but only * after sam_idx_save has been called. * * Returns index filename on success, * NULL on failure. */ char *auto_index(htsFile *fp, const char *fn, bam_hdr_t *header); #endif //SAM_UTIL_H pysam-0.23.0/samtools/sam_view.c000066400000000000000000001731431475062545500165720ustar00rootroot00000000000000/* sam_view.c -- SAM<->BAM<->CRAM conversion. Copyright (C) 2009-2024 Genome Research Ltd. Portions copyright (C) 2009, 2011, 2012 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notices and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include "htslib/sam.h" #include "htslib/faidx.h" #include "htslib/khash.h" #include "htslib/kstring.h" #include "htslib/thread_pool.h" #include "htslib/hts_expr.h" #include "samtools.h" #include "sam_opts.h" #include "bam.h" // for bam_get_library and bam_remove_B #include "bedidx.h" #include "sam_utils.h" KHASH_SET_INIT_STR(str) typedef khash_t(str) *strhash_t; // This structure contains the settings for a samview run typedef struct samview_settings { strhash_t rghash; strhash_t rnhash; strhash_t tvhash; int min_mapQ; int rghash_discard; // 0 keep, 1 discard int rnhash_discard; // 0 keep, 1 discard // Described here in the same terms as the usage statement. // The code however always negates to "reject if" keep if: int flag_on; // keep if (FLAG & N) == N (all on) int flag_off; // keep if (FLAG & N) == 0 (all off) int flag_anyon; // keep if (FLAG & N) != 0 (any on) int flag_alloff; // reject if (FLAG & N) == N (any off) int min_qlen; int remove_B; uint32_t subsam_seed; double subsam_frac; char* library; void* bed; size_t remove_aux_len; char** remove_aux; int multi_region; char* tag; hts_filter_t *filter; int remove_flag; int add_flag; int unmap; auxhash_t remove_tag; auxhash_t keep_tag; hts_idx_t *hts_idx; sam_hdr_t *header; samFile *in, *out, *un_out; int64_t count; int is_count; char *fn_in, *fn_idx_in, *fn_out, *fn_fai, *fn_un_out, *fn_out_idx, *fn_un_out_idx; int fetch_pairs, nreglist; hts_reglist_t *reglist; int sanitize; int count_rf; // CRAM_OPT_REQUIRED_FIELDS for view -c } samview_settings_t; // Copied from htslib/sam.c. // TODO: we need a proper interface to find the length of an aux tag, // or at the very make exportable versions of these in htslib. static inline int aux_type2size(uint8_t type) { switch (type) { case 'A': case 'c': case 'C': return 1; case 's': case 'S': return 2; case 'i': case 'I': case 'f': return 4; case 'd': return 8; case 'Z': case 'H': case 'B': return type; default: return 0; } } // Copied from htslib/sam.c. static inline uint8_t *skip_aux(uint8_t *s, uint8_t *end) { int size; uint32_t n; if (s >= end) return end; size = aux_type2size(*s); ++s; // skip type switch (size) { case 'Z': case 'H': while (s < end && *s) ++s; return s < end ? s + 1 : end; case 'B': if (end - s < 5) return NULL; size = aux_type2size(*s); ++s; n = le_to_u32(s); s += 4; if (size == 0 || end - s < size * n) return NULL; return s + size * n; case 0: return NULL; default: if (end - s < size) return NULL; return s + size; } } // Returns 0 to indicate read should be output 1 otherwise, // and -1 on error. static int process_aln(const sam_hdr_t *h, bam1_t *b, samview_settings_t* settings) { if (settings->filter) { int r = sam_passes_filter(h, b, settings->filter); if (r < 0) // err return -1; if (r == 0) // filter-out return 1; } if (settings->remove_B) bam_remove_B(b); if (settings->min_qlen > 0) { int k, qlen = 0; uint32_t *cigar = bam_get_cigar(b); for (k = 0; k < b->core.n_cigar; ++k) if ((bam_cigar_type(bam_cigar_op(cigar[k]))&1) || bam_cigar_op(cigar[k]) == BAM_CHARD_CLIP) qlen += bam_cigar_oplen(cigar[k]); if (qlen < settings->min_qlen) return 1; } if (b->core.qual < settings->min_mapQ || ((b->core.flag & settings->flag_on) != settings->flag_on) || (b->core.flag & settings->flag_off)) return 1; if (settings->flag_alloff && ((b->core.flag & settings->flag_alloff) == settings->flag_alloff)) return 1; if (settings->flag_anyon && ((b->core.flag & settings->flag_anyon) == 0)) return 1; if (!settings->multi_region && settings->bed && (b->core.tid < 0 || !bed_overlap(settings->bed, sam_hdr_tid2name(h, b->core.tid), b->core.pos, bam_endpos(b)))) return 1; if (settings->subsam_frac > 0.) { uint32_t k = __ac_Wang_hash(__ac_X31_hash_string(bam_get_qname(b)) ^ settings->subsam_seed); if ((double)(k&0xffffff) / 0x1000000 >= settings->subsam_frac) return 1; } if (settings->rghash) { uint8_t *s = bam_aux_get(b, "RG"); if (s) { khint_t k = kh_get(str, settings->rghash, (char*)(s + 1)); if ((k == kh_end(settings->rghash)) != settings->rghash_discard) return 1; } } if (settings->tag) { uint8_t *s = bam_aux_get(b, settings->tag); if (s) { if (settings->tvhash) { char t[32], *val; if (*s == 'i' || *s == 'I' || *s == 's' || *s == 'S' || *s == 'c' || *s == 'C') { int ret = snprintf(t, 32, "%"PRId64, bam_aux2i(s)); if (ret > 0) val = t; else return 1; } else if (*s == 'A') { t[0] = *(s+1); t[1] = 0; val = t; } else { val = (char *)(s+1); } khint_t k = kh_get(str, settings->tvhash, val); if (k == kh_end(settings->tvhash)) return 1; } } else { return 1; } } if (settings->rnhash) { const char* rn = bam_get_qname(b); strhash_t h = settings->rnhash; if (!rn && !settings->rnhash_discard) return 1; if ((kh_get(str, h, rn) == kh_end(h)) != settings->rnhash_discard) return 1; } if (settings->library) { const char *p = bam_get_library((sam_hdr_t*)h, b); if (!p || strcmp(p, settings->library) != 0) return 1; } return 0; } static int adjust_tags(const sam_hdr_t *h, bam1_t *b, samview_settings_t* settings) { if (settings->keep_tag) { uint8_t *s_from, *s_to, *end = b->data + b->l_data; auxhash_t h = settings->keep_tag; s_from = s_to = bam_get_aux(b); while (s_from < end) { int x = (int)s_from[0]<<8 | s_from[1]; uint8_t *s = skip_aux(s_from+2, end); if (s == NULL) { print_error("view", "malformed aux data for record \"%s\"", bam_get_qname(b)); return -1; } if (kh_get(aux_exists, h, x) != kh_end(h) ) { if (s_to != s_from) memmove(s_to, s_from, s - s_from); s_to += s - s_from; } s_from = s; } b->l_data = s_to - b->data; } else if (settings->remove_tag) { uint8_t *s_from, *s_to, *end = b->data + b->l_data; auxhash_t h = settings->remove_tag; s_from = s_to = bam_get_aux(b); while (s_from < end) { int x = (int)s_from[0]<<8 | s_from[1]; uint8_t *s = skip_aux(s_from+2, end); if (s == NULL) { print_error("view", "malformed aux data for record \"%s\"", bam_get_qname(b)); return -1; } if (kh_get(aux_exists, h, x) == kh_end(h) ) { if (s_to != s_from) memmove(s_to, s_from, s - s_from); s_to += s - s_from; } s_from = s; } b->l_data = s_to - b->data; } return 0; } static int usage(FILE *fp, int exit_status, int is_long_help); static int populate_lookup_from_file(const char *subcmd, strhash_t lookup, char *fn) { FILE *fp; char buf[1024]; int ret = 0; fp = fopen(fn, "r"); if (fp == NULL) { print_error_errno(subcmd, "failed to open \"%s\" for reading", fn); return -1; } while (ret != -1 && !feof(fp) && fscanf(fp, "%1023s", buf) > 0) { char *d = strdup(buf); if (d != NULL) { kh_put(str, lookup, d, &ret); if (ret == 0) free(d); /* Duplicate */ } else { ret = -1; } } if (ferror(fp)) ret = -1; if (ret == -1) { print_error_errno(subcmd, "failed to read \"%s\"", fn); } fclose(fp); return (ret != -1) ? 0 : -1; } static int add_read_group_single(const char *subcmd, samview_settings_t *settings, char *name) { char *d = strdup(name); int ret = 0; if (d == NULL) goto err; if (settings->rghash == NULL) { settings->rghash = kh_init(str); if (settings->rghash == NULL) goto err; } else if (settings->rghash_discard == 1) { print_error("view", "cannot mix include and exclude read-group files in the same command line"); free(d); return -1; } settings->rghash_discard = 0; kh_put(str, settings->rghash, d, &ret); if (ret == -1) goto err; if (ret == 0) free(d); /* Duplicate */ return 0; err: print_error(subcmd, "Couldn't add \"%s\" to read group list: memory exhausted?", name); free(d); return -1; } static int add_read_names_file(const char *subcmd, samview_settings_t *settings, char *fn) { if (settings->rnhash == NULL) { settings->rnhash = kh_init(str); if (settings->rnhash == NULL) { perror(NULL); return -1; } } else if ((settings->rnhash_discard == 0 && *fn == '^') || (settings->rnhash_discard == 1 && *fn != '^')) { print_error("view", "cannot mix include and exclude read-name files in the same command line"); return -1; } settings->rnhash_discard = (*fn == '^'); return populate_lookup_from_file(subcmd, settings->rnhash, fn + (*fn == '^')); } static int add_read_groups_file(const char *subcmd, samview_settings_t *settings, char *fn) { if (settings->rghash == NULL) { settings->rghash = kh_init(str); if (settings->rghash == NULL) { perror(NULL); return -1; } } else if ((settings->rghash_discard == 0 && *fn == '^') || (settings->rghash_discard == 1 && *fn != '^')) { print_error("view", "cannot mix include and exclude read-group files in the same command line"); return -1; } settings->rghash_discard = (*fn == '^'); return populate_lookup_from_file(subcmd, settings->rghash, fn + (*fn == '^')); } static int add_tag_value_single(const char *subcmd, samview_settings_t *settings, char *name) { char *d = strdup(name); int ret = 0; if (d == NULL) goto err; if (settings->tvhash == NULL) { settings->tvhash = kh_init(str); if (settings->tvhash == NULL) goto err; } kh_put(str, settings->tvhash, d, &ret); if (ret == -1) goto err; if (ret == 0) free(d); /* Duplicate */ return 0; err: print_error(subcmd, "Couldn't add \"%s\" to tag values list: memory exhausted?", name); free(d); return -1; } static int add_tag_values_file(const char *subcmd, samview_settings_t *settings, char *fn) { if (settings->tvhash == NULL) { settings->tvhash = kh_init(str); if (settings->tvhash == NULL) { perror(NULL); return -1; } } return populate_lookup_from_file(subcmd, settings->tvhash, fn); } static inline int check_sam_write1(samFile *fp, const sam_hdr_t *h, const bam1_t *b, const char *fname, int *retp) { int r = sam_write1(fp, h, b); if (r >= 0) return r; if (fname) print_error_errno("view", "writing to \"%s\" failed", fname); else print_error_errno("view", "writing to standard output failed"); *retp = EXIT_FAILURE; return r; } static inline void change_flag(bam1_t *b, samview_settings_t *settings) { if (settings->add_flag) b->core.flag |= settings->add_flag; if (settings->remove_flag) b->core.flag &= ~settings->remove_flag; } static int cmp_reglist_intervals(const void *aptr, const void *bptr) { hts_pair_pos_t *a = (hts_pair_pos_t*)aptr; hts_pair_pos_t *b = (hts_pair_pos_t*)bptr; if ( a->beg < b->beg ) return -1; if ( a->beg > b->beg ) return 1; if ( a->end < b->end ) return -1; if ( a->end > b->end ) return 1; return 0; } static int cmp_reglist_tids(const void *aptr, const void *bptr) { hts_reglist_t *a = (hts_reglist_t*)aptr; hts_reglist_t *b = (hts_reglist_t*)bptr; if ( b->tid==HTS_IDX_NOCOOR || a->tid < b->tid ) return -1; if ( a->tid==HTS_IDX_NOCOOR || a->tid > b->tid ) return 1; return 0; } static hts_reglist_t *_reglist_dup(sam_hdr_t *hdr, hts_reglist_t *src, int nsrc) { int i,j; hts_reglist_t *dst = (hts_reglist_t*)calloc(nsrc,sizeof(hts_reglist_t)); if ( !dst ) { print_error_errno("view", "[%s:%d] could not allocate region list" ,__FILE__ ,__LINE__); return NULL; } for (i=0; i tid ) imax = i - 1; else break; } if ( i<0 || reg[i].tid < tid ) i++; // not found, i will be the index of the inserted element return i; } static int _reglist_push(hts_reglist_t **_reg, int *_nreg, int tid, hts_pos_t beg, hts_pos_t end) { hts_reglist_t *reg = *_reg; int nreg = *_nreg; int i = _reglist_find_tid(reg,nreg,tid); if ( i>=nreg || reg[i].tid!=tid ) { nreg++; reg = (hts_reglist_t*)realloc(reg,sizeof(hts_reglist_t)*nreg); if ( !reg ) { print_error_errno("view", "[%s:%d] could not extend region list", __FILE__, __LINE__); return -1; } if ( i+1 < nreg ) memmove(reg + i + 1, reg + i, sizeof(hts_reglist_t)*(nreg - i - 1)); reg[i].reg = NULL; reg[i].tid = tid; reg[i].min_beg = beg; reg[i].max_end = end; reg[i].intervals = NULL; reg[i].count = 0; } *_reg = reg; *_nreg = nreg; if ( reg[i].count > 0 && reg[i].intervals[reg[i].count - 1].beg==beg && reg[i].intervals[reg[i].count - 1].end==end ) { return 0; } hts_pair_pos_t *new_intervals = realloc(reg[i].intervals, sizeof(hts_pair_pos_t)*(reg[i].count + 1)); if (!new_intervals) { print_error_errno("view", "[%s:%d] could not extend region list", __FILE__, __LINE__); return -1; } reg[i].intervals = new_intervals; reg[i].intervals[reg[i].count].beg = beg; reg[i].intervals[reg[i].count].end = end; reg[i].count++; return 0; } static void _reglist_merge(hts_reglist_t *reg, int nreg) { int i,j; for (i=0; ibed, regs, 0, nregs, &filter_op); // insert(1) or filter out(0) the regions from the command line in the same hash table as the bed file if (!bed) { print_error_errno("view", "Couldn't %s region list", filter_op ? "build" : "filter"); return NULL; } conf->bed = bed; if ( !filter_op ) filter_state = FILTERED; } else bed_unify(conf->bed); // This check is probably redundant, but left just in case if ( !conf->bed) { // index is unavailable or no regions have been specified print_error("view", "No regions or BED file have been provided. Aborting."); return NULL; } int regcount = 0; hts_reglist_t *reglist = bed_reglist(conf->bed, filter_state, ®count); if (!reglist) { print_error("view", "Region list is empty or could not be created. Aborting."); return NULL; } if ( conf->fetch_pairs ) { conf->reglist = _reglist_dup(conf->header,reglist,regcount); if (!conf->reglist) return NULL; conf->nreglist = regcount; } iter = sam_itr_regions(conf->hts_idx, conf->header, reglist, regcount); if ( !iter ) { print_error("view", "Iterator could not be created. Aborting."); return NULL; } return iter; } KHASH_SET_INIT_STR(names) static int fetch_pairs_collect_mates(samview_settings_t *conf, hts_itr_multi_t *iter) { khint_t k; int nunmap = 0, r = 0, nmates = 0, write_error = 0, retval = EXIT_FAILURE; kh_names_t *mate_names = kh_init(names); bam1_t *rec = bam_init1(); if (!mate_names) { print_error_errno("view", "could not allocate mate names table"); goto out; } if (!rec) { print_error_errno("view", "could not allocate bam record"); goto out; } while ((r =sam_itr_multi_next(conf->in, iter, rec))>=0) { if ( (rec->core.flag & BAM_FPAIRED) == 0 ) continue; if ( rec->core.mtid>=0 && bed_overlap(conf->bed, sam_hdr_tid2name(conf->header,rec->core.mtid), rec->core.mpos, rec->core.mpos) ) continue; int p = process_aln(conf->header, rec, conf); if (p < 0) goto out; if (p == 1) continue; nmates++; k = kh_get(names,mate_names,bam_get_qname(rec)); if ( k == kh_end(mate_names) ) { int ret = 0; char *name_copy = strdup(bam_get_qname(rec)); if (!name_copy) { print_error_errno("view", "[%s:%d] could not store sample name, %d elements", __FILE__,__LINE__,nmates); goto out; } kh_put(names, mate_names, name_copy, &ret); if ( ret<0 ) { print_error_errno("view", "[%s:%d] could not store sample name, %d elements",__FILE__,__LINE__,nmates); free(name_copy); goto out; } } if ( rec->core.mtid < 0 ) { nunmap = 1; } else { if (_reglist_push(&conf->reglist, &conf->nreglist, rec->core.mtid, rec->core.mpos,rec->core.mpos+1) != 0) goto out; } } if (r < -1) { print_error_errno("view", "error reading file \"%s\"", conf->fn_in); goto out; } _reglist_merge(conf->reglist, conf->nreglist); if ( nunmap ) { if (_reglist_push(&conf->reglist,&conf->nreglist,HTS_IDX_NOCOOR,0,HTS_POS_MAX) != 0) goto out; } hts_itr_multi_destroy(iter); iter = sam_itr_regions(conf->hts_idx, conf->header, conf->reglist, conf->nreglist); if ( !iter ) { print_error_errno("view", "[%s:%d] iterator could not be created",__FILE__,__LINE__); goto out; } while ((r = sam_itr_multi_next(conf->in, iter, rec))>=0) { int drop = 1; if (rec->core.tid >=0 && bed_overlap(conf->bed, sam_hdr_tid2name(conf->header,rec->core.tid), rec->core.pos, bam_endpos(rec))) drop = 0; if ( drop ) { k = kh_get(names,mate_names,bam_get_qname(rec)); if ( k != kh_end(mate_names) ) drop = 0; } int p = 0; if (!drop && (p=process_aln(conf->header, rec, conf))== 0) { if (adjust_tags(conf->header, rec, conf) != 0) goto out; if (check_sam_write1(conf->out, conf->header, rec, conf->fn_out, &write_error) < 0) goto out; } if (p < 0) goto out; } if (r < -1) { print_error_errno("view", "error reading file \"%s\"", conf->fn_in); goto out; } retval = EXIT_SUCCESS; out: hts_itr_multi_destroy(iter); hts_idx_destroy(conf->hts_idx); // destroy the BAM index conf->hts_idx = NULL; if (mate_names) { // free khash keys for (k = 0; k < kh_end(mate_names); ++k) if ( kh_exist(mate_names,k) ) free((char*)kh_key(mate_names, k)); kh_destroy(names,mate_names); } bam_destroy1(rec); return retval; } // Common code for processing and writing a record static inline int process_one_record(samview_settings_t *conf, bam1_t *b, int *write_error) { if (conf->sanitize) if (bam_sanitize(conf->header, b, conf->sanitize) < 0) return -1; int p; if ((p = process_aln(conf->header, b, conf)) < 0) { // error return -1; } else if (p == 0) { // emit read if (!conf->is_count) { change_flag(b, conf); if (adjust_tags(conf->header, b, conf) != 0) return -1; if (check_sam_write1(conf->out, conf->header, b, conf->fn_out, write_error) < 0) { return -1; } } conf->count++; } else if (conf->unmap) { b->core.flag |= BAM_FUNMAP; b->core.qual = 0; b->core.isize = 0; // remove CIGAR if (b->core.n_cigar) { memmove(bam_get_cigar(b), bam_get_seq(b), b->data + b->l_data - bam_get_seq(b)); b->l_data -= 4*b->core.n_cigar; b->core.n_cigar = 0; } if (check_sam_write1(conf->out, conf->header, b, conf->fn_out, write_error) < 0) { return -1; } } else { if (conf->un_out) { if (check_sam_write1(conf->un_out, conf->header, b, conf->fn_un_out, write_error) < 0) { return -1; } } } return 0; } static int stream_view(samview_settings_t *conf) { bam1_t *b = bam_init1(); int write_error = 0, r, p = 0; if (!b) { print_error_errno("view", "could not allocate bam record"); return 1; } errno = 0; // prevent false error messages. while ((r = sam_read1(conf->in, conf->header, b)) >= 0) { if ((p = process_one_record(conf, b, &write_error)) < 0) break; } bam_destroy1(b); if (r < -1 || p < 0) { print_error_errno("view", "error reading file \"%s\"", conf->fn_in); return 1; } return write_error; } static int multi_region_view(samview_settings_t *conf, hts_itr_multi_t *iter) { bam1_t *b = bam_init1(); int write_error = 0, result; if (!b) { print_error_errno("view", "could not allocate bam record"); return 1; } // fetch alignments while ((result = sam_itr_multi_next(conf->in, iter, b)) >= 0) { if (process_one_record(conf, b, &write_error) < 0) break; } bam_destroy1(b); if (result < -1) { print_error("view", "retrieval of region #%d failed", iter->curr_tid); write_error = 1; } hts_itr_multi_destroy(iter); return write_error; } // Make mnemonic distinct values for longoption-only options #define LONGOPT(c) ((c) + 128) // Check for ".sam" filenames as sam_open_mode cannot distinguish between // foo.sam and foo.unknown, both getting mode "". static int is_sam(const char *fn) { if (!fn) return 0; size_t l = strlen(fn); return (l >= 4 && strcasecmp(fn + l-4, ".sam") == 0); } static void aux_list_free(samview_settings_t *settings) { if (settings->keep_tag) kh_destroy(aux_exists, settings->keep_tag); if (settings->remove_tag) kh_destroy(aux_exists, settings->remove_tag); } int main_samview(int argc, char *argv[]) { samview_settings_t settings; int c, is_header = 0, is_header_only = 0, ret = 0, compress_level = -1, has_index_file = 0, no_pg = 0; FILE *fp_out = NULL; char out_mode[6] = {0}, out_un_mode[6] = {0}; char *out_format = ""; char *arg_list = NULL; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; htsThreadPool p = {NULL, 0}; memset(&settings,0,sizeof(settings)); settings.subsam_frac = -1.0; settings.count_rf = SAM_FLAG; // don't want 0, and this is quick static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 'T', '@'), {"add-flags", required_argument, NULL, LONGOPT('a')}, {"bam", no_argument, NULL, 'b'}, {"count", no_argument, NULL, 'c'}, {"cram", no_argument, NULL, 'C'}, {"customised-index", no_argument, NULL, 'X'}, {"customized-index", no_argument, NULL, 'X'}, {"excl-flags", required_argument, NULL, 'F'}, {"exclude-flags", required_argument, NULL, 'F'}, {"expr", required_argument, NULL, 'e'}, {"expression", required_argument, NULL, 'e'}, {"fai-reference", required_argument, NULL, 't'}, {"fast", no_argument, NULL, '1'}, {"fetch-pairs", no_argument, NULL, 'P'}, {"header-only", no_argument, NULL, 'H'}, {"help", no_argument, NULL, LONGOPT('?')}, {"incl-flags", required_argument, NULL, LONGOPT('g')}, {"include-flags", required_argument, NULL, LONGOPT('g')}, {"rf", required_argument, NULL, LONGOPT('g')}, // aka incl-flags {"keep-tag", required_argument, NULL, LONGOPT('x') }, {"library", required_argument, NULL, 'l'}, {"min-mapq", required_argument, NULL, 'q'}, {"min-MQ", required_argument, NULL, 'q'}, {"min-mq", required_argument, NULL, 'q'}, {"min-qlen", required_argument, NULL, 'm'}, {"no-header", no_argument, NULL, LONGOPT('H')}, {"no-PG", no_argument, NULL, LONGOPT('P')}, {"output", required_argument, NULL, 'o'}, {"output-unselected", required_argument, NULL, 'U'}, {"QNAME-file", required_argument, NULL, 'N'}, {"qname-file", required_argument, NULL, 'N'}, {"read-group", required_argument, NULL, 'r'}, {"read-group-file", required_argument, NULL, 'R'}, {"readgroup", required_argument, NULL, 'r'}, {"readgroup-file", required_argument, NULL, 'R'}, {"region-file", required_argument, NULL, LONGOPT('L')}, {"regions-file", required_argument, NULL, LONGOPT('L')}, {"remove-B", no_argument, NULL, 'B'}, {"remove-flags", required_argument, NULL, LONGOPT('r')}, {"remove-tag", required_argument, NULL, 'x'}, {"require-flags", required_argument, NULL, 'f'}, {"subsample", required_argument, NULL, LONGOPT('s')}, {"subsample-seed", required_argument, NULL, LONGOPT('S')}, {"tag", required_argument, NULL, 'd'}, {"tag-file", required_argument, NULL, 'D'}, {"target-file", required_argument, NULL, 'L'}, {"targets-file", required_argument, NULL, 'L'}, {"uncompressed", no_argument, NULL, 'u'}, {"unmap", no_argument, NULL, 'p'}, {"unoutput", required_argument, NULL, 'U'}, {"use-index", no_argument, NULL, 'M'}, {"with-header", no_argument, NULL, 'h'}, {"sanitize", required_argument, NULL, 'z'}, {NULL, 0, NULL, 0} }; /* parse command-line options */ strcpy(out_mode, "w"); strcpy(out_un_mode, "w"); if (argc == 1 && isatty(STDIN_FILENO)) return usage(stdout, EXIT_SUCCESS, 0); // Suppress complaints about '?' being an unrecognised option. Without // this we have to put '?' in the options list, which makes it hard to // tell a bad long option from the use of '-?' (both return '?' and // set optopt to '\0'). opterr = 0; char *tmp; int tmp_flag; while ((c = getopt_long(argc, argv, "SbBcCt:h1Ho:O:q:f:F:G:ul:r:T:R:N:d:D:L:s:@:m:x:U:MXe:pPz:", lopts, NULL)) >= 0) { switch (c) { case 's': settings.subsam_seed = strtol(optarg, &tmp, 10); if (tmp && *tmp == '.') { settings.subsam_frac = strtod(tmp, &tmp); if (*tmp) ret = 1; } else { ret = 1; } if (ret == 1) { print_error("view", "Incorrect sampling argument \"%s\"", optarg); goto view_end; } settings.count_rf |= SAM_QNAME; break; case LONGOPT('s'): settings.subsam_frac = strtod(optarg, &tmp); if (*tmp || settings.subsam_frac < 0.0 || settings.subsam_frac > 1.0) { print_error("view", "Incorrect sampling argument \"%s\"", optarg); goto view_end; } settings.count_rf |= SAM_QNAME; break; case LONGOPT('S'): settings.subsam_seed = atoi(optarg); break; case 'm': settings.min_qlen = atoi(optarg); settings.count_rf |= SAM_SEQ; break; case 'c': settings.is_count = 1; break; case 'S': break; case 'b': out_format = "b"; break; case 'C': out_format = "c"; break; case 't': settings.fn_fai = strdup(optarg); break; case 'h': is_header = 1; break; case 'H': is_header_only = 1; break; case LONGOPT('H'): is_header = is_header_only = 0; break; case 'o': settings.fn_out = strdup(optarg); break; case 'U': settings.fn_un_out = strdup(optarg); break; case 'X': has_index_file = 1; break; case 'f': tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("view", "Unknown flag '%s'", optarg); return 1; } settings.flag_on |= tmp_flag; settings.count_rf |= SAM_FLAG | SAM_RNEXT; break; case 'F': tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("view", "Unknown flag '%s'", optarg); return 1; } settings.flag_off |= tmp_flag; settings.count_rf |= SAM_FLAG | SAM_RNEXT; break; case LONGOPT('g'): tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("view", "Unknown flag '%s'", optarg); return 1; } settings.flag_anyon |= tmp_flag; settings.count_rf |= SAM_FLAG | SAM_RNEXT; break; case 'G': tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("view", "Unknown flag '%s'", optarg); return 1; } settings.flag_alloff |= tmp_flag; settings.count_rf |= SAM_FLAG | SAM_RNEXT; break; case 'q': settings.min_mapQ = atoi(optarg); settings.count_rf |= SAM_MAPQ; break; case 'u': compress_level = 0; break; case '1': compress_level = 1; break; case 'l': settings.library = strdup(optarg); settings.count_rf |= SAM_RGAUX; break; case 'p': settings.unmap = 1; break; case 'P': settings.fetch_pairs = 1; settings.multi_region = 1; break; case 'z': if ((settings.sanitize = bam_sanitize_options(optarg)) < 0) { ret = 1; goto view_end; } break; case LONGOPT('L'): settings.multi_region = 1; // fall through case 'L': if ((settings.bed = bed_read(optarg)) == NULL) { print_error_errno("view", "Could not read file \"%s\"", optarg); ret = 1; goto view_end; } settings.count_rf |= SAM_POS | SAM_RNAME | SAM_CIGAR; break; case 'r': if (add_read_group_single("view", &settings, optarg) != 0) { ret = 1; goto view_end; } settings.count_rf |= SAM_RGAUX; break; case 'R': if (add_read_groups_file("view", &settings, optarg) != 0) { ret = 1; goto view_end; } settings.count_rf |= SAM_RGAUX; break; case 'N': if (add_read_names_file("view", &settings, optarg) != 0) { ret = 1; goto view_end; } settings.count_rf |= SAM_QNAME; break; case 'd': if (strlen(optarg) < 2 || (strlen(optarg) > 2 && optarg[2] != ':')) { print_error("view", "Invalid \"tag:value\" option: \"%s\"", optarg); ret = 1; goto view_end; } if (settings.tag) { if (settings.tag[0] != optarg[0] || settings.tag[1] != optarg[1]) { print_error("view", "Different tag \"%s\" was specified before: \"%s\"", settings.tag, optarg); ret = 1; goto view_end; } } else { if (!(settings.tag = calloc(3, 1))) { print_error("view", "Could not allocate memory for tag: \"%s\"", optarg); ret = 1; goto view_end; } memcpy(settings.tag, optarg, 2); } if (strlen(optarg) > 3 && add_tag_value_single("view", &settings, optarg+3) != 0) { print_error("view", "Could not add tag:value \"%s\"", optarg); ret = 1; goto view_end; } // Some tag filtering affects other fields if (memcmp(settings.tag, "NM", 2) == 0 || memcmp(settings.tag, "MD", 2) == 0) settings.count_rf |= SAM_AUX | SAM_SEQ; else if (memcmp(settings.tag, "RG", 2) == 0) settings.count_rf |= SAM_RGAUX; else settings.count_rf |= SAM_AUX; break; case 'D': // Allow ";" as delimiter besides ":" to support MinGW CLI POSIX // path translation as described at: // http://www.mingw.org/wiki/Posix_path_conversion if (strlen(optarg) < 4 || (optarg[2] != ':' && optarg[2] != ';')) { print_error("view", "Invalid \"tag:file\" option: \"%s\"", optarg); ret = 1; goto view_end; } if (settings.tag) { if (settings.tag[0] != optarg[0] || settings.tag[1] != optarg[1]) { print_error("view", "Different tag \"%s\" was specified before: \"%s\"", settings.tag, optarg); ret = 1; goto view_end; } } else { if (!(settings.tag = calloc(3, 1))) { print_error("view", "Could not allocate memory for tag: \"%s\"", optarg); ret = 1; goto view_end; } memcpy(settings.tag, optarg, 2); } if (add_tag_values_file("view", &settings, optarg+3) != 0) { ret = 1; goto view_end; } // Some tag filtering affects other fields if (memcmp(settings.tag, "NM", 2) == 0 || memcmp(settings.tag, "MD", 2) == 0) settings.count_rf |= SAM_AUX | SAM_SEQ; else if (memcmp(settings.tag, "RG", 2) == 0) settings.count_rf |= SAM_RGAUX; else settings.count_rf |= SAM_AUX; break; case LONGOPT('?'): return usage(stdout, EXIT_SUCCESS, 1); case '?': if (optopt == '?') { // '-?' appeared on command line return usage(stdout, EXIT_SUCCESS, 1); } else { if (optopt) { // Bad short option print_error("view", "invalid option -- '%c'", optopt); } else { // Bad long option // Do our best. There is no good solution to finding // out what the bad option was. // See, e.g. https://stackoverflow.com/questions/2723888/where-does-getopt-long-store-an-unrecognized-option if (optind > 0 && strncmp(argv[optind - 1], "--", 2) == 0) { print_error("view", "unrecognised option '%s'", argv[optind - 1]); } } return usage(stderr, EXIT_FAILURE, 0); } case 'B': settings.remove_B = 1; break; case 'M': settings.multi_region = 1; break; case LONGOPT('P'): no_pg = 1; break; case 'e': if (!(settings.filter = hts_filter_init(optarg))) { print_error("main_samview", "Couldn't initialise filter"); return 1; } settings.count_rf = INT_MAX; // no way to know what we need break; case LONGOPT('r'): tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("view", "Unknown flag '%s'", optarg); return 1; } settings.remove_flag |= tmp_flag; break; case LONGOPT('a'): tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("view", "Unknown flag '%s'", optarg); return 1; } settings.add_flag |= tmp_flag; break; case 'x': if (*optarg == '^') { if (parse_aux_list(&settings.keep_tag, optarg+1, "main_samview")) { aux_list_free(&settings); return usage(stderr, EXIT_FAILURE, 0); } } else { if (parse_aux_list(&settings.remove_tag, optarg, "main_samview")) { aux_list_free(&settings); return usage(stderr, EXIT_FAILURE, 0); } } break; case LONGOPT('x'): if (parse_aux_list(&settings.keep_tag, optarg, "main_samview")) { aux_list_free(&settings); return usage(stderr, EXIT_FAILURE, 0); } break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) != 0) return usage(stderr, EXIT_FAILURE, 0); break; } } if (settings.is_count && settings.fetch_pairs) { print_error("view","The options -P and -c cannot be combined\n"); return 1; } if (settings.fn_fai == 0 && ga.reference) settings.fn_fai = fai_path(ga.reference); if (is_header_only) is_header = 1; // File format auto-detection first if (settings.fn_out) sam_open_mode(out_mode+1, settings.fn_out, NULL); if (settings.fn_un_out) sam_open_mode(out_un_mode+1, settings.fn_un_out, NULL); // -1 or -u without an explicit format (-b, -C) => check fn extensions if (!*out_format && compress_level >= 0) { if (compress_level == 0 && (out_mode[strlen(out_mode)-1] == 'z' || out_un_mode[strlen(out_un_mode)-1] == 'z')) // z, fz, Fz sanity check fprintf(stderr, "[view] Warning option -u ignored due to" " filename suffix\n"); // If known extension, use it, otherwise BAM if (!(out_mode[1] || is_sam(settings.fn_out))) out_mode[1] = 'b'; if (!(out_un_mode[1] || is_sam(settings.fn_un_out))) out_un_mode[1] = 'b'; } else if (*out_format) { out_mode[1] = out_un_mode[1] = *out_format; } if (compress_level >= 0) { char tmp[2]; tmp[0] = compress_level + '0'; tmp[1] = '\0'; strcat(out_mode, tmp); strcat(out_un_mode, tmp); } if (argc == optind && isatty(STDIN_FILENO)) { print_error("view", "No input provided or missing option argument."); return usage(stderr, EXIT_FAILURE, 0); // potential memory leak... } if (settings.unmap && settings.fn_un_out) { print_error("view", "Options --unoutput and --unmap are mutually exclusive."); ret = 1; goto view_end; } if (settings.subsam_seed != 0) { // Convert likely user input 1,2,... to pseudo-random // values with more entropy and more bits set srand(settings.subsam_seed); settings.subsam_seed = rand(); } settings.fn_in = (optind < argc)? argv[optind] : "-"; if ((settings.in = sam_open_format(settings.fn_in, "r", &ga.in)) == 0) { print_error_errno("view", "failed to open \"%s\" for reading", settings.fn_in); ret = 1; goto view_end; } if (settings.fn_fai) { if (hts_set_fai_filename(settings.in, settings.fn_fai) != 0) { fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", settings.fn_fai); ret = 1; goto view_end; } } if ((settings.header = sam_hdr_read(settings.in)) == 0) { fprintf(stderr, "[main_samview] fail to read the header from \"%s\".\n", settings.fn_in); ret = 1; goto view_end; } if (settings.rghash) { sam_hdr_remove_lines(settings.header, "RG", "ID", settings.rghash); } if (!settings.is_count) { if ((settings.out = sam_open_format(settings.fn_out? settings.fn_out : "-", out_mode, &ga.out)) == 0) { print_error_errno("view", "failed to open \"%s\" for writing", settings.fn_out? settings.fn_out : "standard output"); ret = 1; goto view_end; } if (settings.fn_fai) { if (hts_set_fai_filename(settings.out, settings.fn_fai) != 0) { fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", settings.fn_fai); ret = 1; goto view_end; } } autoflush_if_stdout(settings.out, settings.fn_out); if (!no_pg) { if (!(arg_list = stringify_argv(argc+1, argv-1))) { print_error("view", "failed to create arg_list"); ret = 1; goto view_end; } if (sam_hdr_add_pg(settings.header, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { print_error("view", "failed to add PG line to the header"); ret = 1; goto view_end; } } if (ga.write_index || is_header || out_mode[1] == 'b' || out_mode[1] == 'c' || (ga.out.format != sam && ga.out.format != unknown_format)) { if (sam_hdr_write(settings.out, settings.header) != 0) { fprintf(stderr, "[main_samview] failed to write the SAM header\n"); ret = 1; goto view_end; } } if (ga.write_index) { if (!(settings.fn_out_idx = auto_index(settings.out, settings.fn_out, settings.header))) { ret = 1; goto view_end; } } if (settings.fn_un_out) { if ((settings.un_out = sam_open_format(settings.fn_un_out, out_un_mode, &ga.out)) == 0) { print_error_errno("view", "failed to open \"%s\" for writing", settings.fn_un_out); ret = 1; goto view_end; } if (settings.fn_fai) { if (hts_set_fai_filename(settings.un_out, settings.fn_fai) != 0) { fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", settings.fn_fai); ret = 1; goto view_end; } } autoflush_if_stdout(settings.un_out, settings.fn_un_out); if (ga.write_index || is_header || out_un_mode[1] == 'b' || out_un_mode[1] == 'c' || (ga.out.format != sam && ga.out.format != unknown_format)) { if (sam_hdr_write(settings.un_out, settings.header) != 0) { fprintf(stderr, "[main_samview] failed to write the SAM header\n"); ret = 1; goto view_end; } } if (ga.write_index) { if (!(settings.fn_un_out_idx = auto_index(settings.un_out, settings.fn_un_out, settings.header))) { ret = 1; goto view_end; } } } } else { if (settings.fn_out) { fp_out = fopen(settings.fn_out, "w"); if (fp_out == NULL) { print_error_errno("view", "can't create \"%s\"", settings.fn_out); ret = EXIT_FAILURE; goto view_end; } } settings.unmap = 0; // Not valid in counting mode } if (ga.nthreads > 0) { if (!(p.pool = hts_tpool_init(ga.nthreads))) { fprintf(stderr, "Error creating thread pool\n"); ret = 1; goto view_end; } hts_set_opt(settings.in, HTS_OPT_THREAD_POOL, &p); if (settings.out) hts_set_opt(settings.out, HTS_OPT_THREAD_POOL, &p); } if (is_header_only) goto view_end; // no need to print alignments // Initialize BAM/CRAM index char **regs = NULL; int nregs = 0; if ( has_index_file && optind <= argc - 2 ) { regs = optind < argc-2 ? &argv[optind+2] : NULL; nregs = argc - optind - 2; settings.fn_idx_in = argv[optind+1]; } else if (!has_index_file && optind < argc - 1 ) { regs = &argv[optind+1]; nregs = argc - optind - 1; } else if ( has_index_file && argc-optind < 2) { print_error("view", "Incorrect number of arguments for -X option. Aborting."); return 1; } if (regs) settings.count_rf |= SAM_POS | SAM_RNAME | SAM_CIGAR; if ( settings.fn_idx_in || nregs || settings.multi_region ) { settings.hts_idx = settings.fn_idx_in ? sam_index_load2(settings.in, settings.fn_in, settings.fn_idx_in) : sam_index_load(settings.in, settings.fn_in); if ( !settings.hts_idx ) { print_error("view", "Random alignment retrieval only works for indexed SAM.gz, BAM or CRAM files."); return 1; } } if (settings.is_count) // Won't fail, but also wouldn't matter if it did hts_set_opt(settings.in, CRAM_OPT_REQUIRED_FIELDS, settings.count_rf); if ( settings.fetch_pairs ) { hts_itr_multi_t *iter = multi_region_init(&settings, regs, nregs); ret = iter ? fetch_pairs_collect_mates(&settings, iter) : 1; if (ret) goto view_end; } else if ( settings.multi_region ) { hts_itr_multi_t *iter = multi_region_init(&settings, regs, nregs); ret = iter ? multi_region_view(&settings, iter) : 1; if (ret) goto view_end; } else if ( !settings.hts_idx || optind+1 >= argc-has_index_file ) { // stream through the entire file ret = stream_view(&settings); if (ret) goto view_end; } else { // retrieve alignments in specified regions int i; for (i = (has_index_file)? optind+2 : optind+1; i < argc; ++i) { hts_itr_t *iter = sam_itr_querys(settings.hts_idx, settings.header, argv[i]); // parse a region in the format like `chr2:100-200' if (iter == NULL) { // region invalid or reference name not found fprintf(stderr, "[main_samview] region \"%s\" specifies an invalid region or unknown reference. Continue anyway.\n", argv[i]); continue; } // fetch alignments ret = multi_region_view(&settings, iter); if (ret) goto view_end; } } if (ga.write_index) { if (sam_idx_save(settings.out) < 0) { print_error_errno("view", "writing index failed"); ret = 1; } if (settings.un_out && sam_idx_save(settings.un_out) < 0) { print_error_errno("view", "writing index failed"); ret = 1; } } view_end: if ( settings.hts_idx ) hts_idx_destroy(settings.hts_idx); if (settings.is_count && ret == 0) { if (fprintf(settings.fn_out? fp_out : stdout, "%" PRId64 "\n", settings.count) < 0) { if (settings.fn_out) print_error_errno("view", "writing to \"%s\" failed", settings.fn_out); else print_error_errno("view", "writing to standard output failed"); ret = EXIT_FAILURE; } } // close files, free and return if (settings.in) check_sam_close("view", settings.in, settings.fn_in, "standard input", &ret); if (settings.out) check_sam_close("view", settings.out, settings.fn_out, "standard output", &ret); if (settings.un_out) check_sam_close("view", settings.un_out, settings.fn_un_out, "file", &ret); if (fp_out) fclose(fp_out); free(settings.fn_fai); free(settings.fn_out); free(settings.library); free(settings.fn_un_out); sam_global_args_free(&ga); if ( settings.header ) sam_hdr_destroy(settings.header); if (settings.bed) bed_destroy(settings.bed); if (settings.rghash) { khint_t k; for (k = 0; k < kh_end(settings.rghash); ++k) if (kh_exist(settings.rghash, k)) free((char*)kh_key(settings.rghash, k)); kh_destroy(str, settings.rghash); } if (settings.rnhash) { khint_t k; for (k = 0; k < kh_end(settings.rnhash); ++k) if (kh_exist(settings.rnhash, k)) free((char*)kh_key(settings.rnhash, k)); kh_destroy(str, settings.rnhash); } if (settings.tvhash) { khint_t k; for (k = 0; k < kh_end(settings.tvhash); ++k) if (kh_exist(settings.tvhash, k)) free((char*)kh_key(settings.tvhash, k)); kh_destroy(str, settings.tvhash); } if (settings.remove_aux_len) { free(settings.remove_aux); } if (settings.tag) { free(settings.tag); } if (settings.filter) hts_filter_free(settings.filter); if (p.pool) hts_tpool_destroy(p.pool); if (settings.fn_out_idx) free(settings.fn_out_idx); if (settings.fn_un_out_idx) free(settings.fn_un_out_idx); free(arg_list); aux_list_free(&settings); return ret; } static int usage(FILE *fp, int exit_status, int is_long_help) { fprintf(fp, "\n" "Usage: samtools view [options] || [region ...]\n" "\n" "Output options:\n" " -b, --bam Output BAM\n" " -C, --cram Output CRAM (requires -T)\n" " -1, --fast Use fast BAM compression (and default to --bam)\n" " -u, --uncompressed Uncompressed BAM output (and default to --bam)\n" " -h, --with-header Include header in SAM output\n" " -H, --header-only Print SAM header only (no alignments)\n" " --no-header Print SAM alignment records only [default]\n" " -c, --count Print only the count of matching records\n" " -o, --output FILE Write output to FILE [standard output]\n" " -U, --unoutput FILE, --output-unselected FILE\n" " Output reads not selected by filters to FILE\n" " -p, --unmap Set flag to UNMAP on reads not selected\n" " then write to output file.\n" " -P, --fetch-pairs Retrieve complete pairs even when outside of region\n" "Input options:\n" " -t, --fai-reference FILE FILE listing reference names and lengths\n" " -M, --use-index Use index and multi-region iterator for regions\n" " --region[s]-file FILE Use index to include only reads overlapping FILE\n" " -X, --customized-index Expect extra index file argument after \n" "\n" "Filtering options (Only include in output reads that...):\n" " -L, --target[s]-file FILE ...overlap (BED) regions in FILE\n" " -N, --qname-file [^]FILE ...whose read name is listed in FILE (\"^\" negates)\n" " -r, --read-group STR ...are in read group STR\n" " -R, --read-group-file [^]FILE\n" " ...are in a read group listed in FILE\n" " -d, --tag STR1[:STR2] ...have a tag STR1 (with associated value STR2)\n" " -D, --tag-file STR:FILE ...have a tag STR whose value is listed in FILE\n" " -q, --min-MQ INT ...have mapping quality >= INT\n" " -l, --library STR ...are in library STR\n" " -m, --min-qlen INT ...cover >= INT query bases (as measured via CIGAR)\n" " -e, --expr STR ...match the filter expression STR\n" " -f, --require-flags FLAG ...have all of the FLAGs present\n" // F&x == x " -F, --excl[ude]-flags FLAG ...have none of the FLAGs present\n" // F&x == 0 " --rf, --incl-flags, --include-flags FLAG\n" " ...have some of the FLAGs present\n" " -G FLAG EXCLUDE reads with all of the FLAGs present\n" // !(F&x == x) TODO long option " --subsample FLOAT Keep only FLOAT fraction of templates/read pairs\n" " --subsample-seed INT Influence WHICH reads are kept in subsampling [0]\n" " -s INT.FRAC Same as --subsample 0.FRAC --subsample-seed INT\n" "\n" "Processing options:\n" " --add-flags FLAG Add FLAGs to reads\n" " --remove-flags FLAG Remove FLAGs from reads\n" " -x, --remove-tag STR\n" " Comma-separated read tags to strip (repeatable) [null]\n" " --keep-tag STR\n" " Comma-separated read tags to preserve (repeatable) [null].\n" " Equivalent to \"-x ^STR\"\n" " -B, --remove-B Collapse the backward CIGAR operation\n" " -z, --sanitize FLAGS Perform sanitity checking and fixing on records.\n" " FLAGS is comma separated (see manual). [off]\n" "\n" "General options:\n" " -?, --help Print long help, including note about region specification\n" " -S Ignored (input format is auto-detected)\n" " --no-PG Do not add a PG line\n"); sam_global_opt_help(fp, "-.O.T@.."); fprintf(fp, "\n"); if (is_long_help) fprintf(fp, "Notes:\n" "\n" "1. This command now auto-detects the input format (BAM/CRAM/SAM).\n" " Further control over the CRAM format can be specified by using the\n" " --output-fmt-option, e.g. to specify the number of sequences per slice\n" " and to use avoid reference based compression:\n" "\n" "\tsamtools view -C --output-fmt-option seqs_per_slice=5000 \\\n" "\t --output-fmt-option no_ref -o out.cram in.bam\n" "\n" " Options can also be specified as a comma separated list within the\n" " --output-fmt value too. For example this is equivalent to the above\n" "\n" "\tsamtools view --output-fmt cram,seqs_per_slice=5000,no_ref \\\n" "\t -o out.cram in.bam\n" "\n" "2. The file supplied with `-t' is SPACE/TAB delimited with the first\n" " two fields of each line consisting of the reference name and the\n" " corresponding sequence length. The `.fai' file generated by \n" " `samtools faidx' is suitable for use as this file. This may be an\n" " empty file if reads are unaligned.\n" "\n" "3. SAM->BAM conversion: samtools view -bT ref.fa in.sam.gz\n" "\n" "4. BAM->SAM conversion: samtools view -h in.bam\n" "\n" "5. A region should be presented in one of the following formats:\n" " `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n" " specified, the input alignment file must be a sorted and indexed\n" " alignment (BAM/CRAM) file.\n" "\n" "6. Option `-u' is preferred over `-b' when the output is piped to\n" " another samtools command.\n" "\n" "7. Option `-M`/`--use-index` causes overlaps with `-L` BED file regions and\n" " command-line region arguments to be computed using the multi-region iterator\n" " and an index. This increases speed, omits duplicates, and outputs the reads\n" " as they are ordered in the input SAM/BAM/CRAM file.\n" "\n" "8. Options `-L`/`--target[s]-file` and `--region[s]-file` may not be used\n" " together. `--region[s]-file FILE` is simply equivalent to `-M -L FILE`,\n" " so using both causes one of the specified BED files to be ignored.\n" "\n"); return exit_status; } static int head_usage(FILE *fp, int exit_status) { fprintf(fp, "Usage: samtools head [OPTION]... [FILE]\n" "Options:\n" " -h, --headers INT Display INT header lines [all]\n" " -n, --records INT Display INT alignment record lines [none]\n" ); sam_global_opt_help(fp, "-.--T@-."); return exit_status; } int main_head(int argc, char *argv[]) { static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 'T', '@'), { "headers", required_argument, NULL, 'h' }, { "records", required_argument, NULL, 'n' }, { NULL, 0, NULL, 0 } }; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; int all_headers = 1; uint64_t nheaders = 0; uint64_t nrecords = 0; int c, nargs; while ((c = getopt_long(argc, argv, "h:n:T:@:", lopts, NULL)) >= 0) switch (c) { case 'h': all_headers = 0; nheaders = strtoull(optarg, NULL, 0); break; case 'n': nrecords = strtoull(optarg, NULL, 0); break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': return head_usage(stderr, EXIT_FAILURE); } nargs = argc - optind; if (nargs == 0 && isatty(STDIN_FILENO)) return head_usage(stdout, EXIT_SUCCESS); else if (nargs > 1) return head_usage(stderr, EXIT_FAILURE); samFile *fp = NULL; sam_hdr_t *hdr = NULL; kstring_t str = KS_INITIALIZE; bam1_t *b = NULL; const char *fname = (nargs == 1)? argv[optind] : "-"; fp = sam_open_format(fname, "r", &ga.in); if (fp == NULL) { if (strcmp(fname, "-") != 0) print_error_errno("head", "failed to open \"%s\" for reading", fname); else print_error_errno("head", "failed to open standard input for reading"); goto err; } if (ga.nthreads > 0) hts_set_threads(fp, ga.nthreads); hdr = sam_hdr_read(fp); if (hdr == NULL) { if (strcmp(fname, "-") != 0) print_error("head", "failed to read the header from \"%s\"", fname); else print_error("head", "failed to read the header"); goto err; } if (all_headers) { fputs(sam_hdr_str(hdr), stdout); } else if (nheaders > 0) { const char *text = sam_hdr_str(hdr); const char *lim = text; uint64_t n; for (n = 0; n < nheaders; n++) { lim = strchr(lim, '\n'); if (lim) lim++; else break; } if (lim) fwrite(text, lim - text, 1, stdout); else fputs(text, stdout); } if (nrecords > 0) { b = bam_init1(); uint64_t n; int r = 0; for (n = 0; n < nrecords && (r = sam_read1(fp, hdr, b)) >= 0; n++) { if (sam_format1(hdr, b, &str) < 0) { print_error_errno("head", "couldn't format record"); goto err; } puts(ks_str(&str)); } if (r < -1) { print_error("head", "\"%s\" is truncated", fname); goto err; } bam_destroy1(b); ks_free(&str); } sam_hdr_destroy(hdr); sam_close(fp); sam_global_args_free(&ga); return EXIT_SUCCESS; err: if (fp) sam_close(fp); sam_hdr_destroy(hdr); bam_destroy1(b); ks_free(&str); sam_global_args_free(&ga); return EXIT_FAILURE; } pysam-0.23.0/samtools/sam_view.c.pysam.c000066400000000000000000001735521475062545500201470ustar00rootroot00000000000000#include "samtools.pysam.h" /* sam_view.c -- SAM<->BAM<->CRAM conversion. Copyright (C) 2009-2024 Genome Research Ltd. Portions copyright (C) 2009, 2011, 2012 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notices and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include "htslib/sam.h" #include "htslib/faidx.h" #include "htslib/khash.h" #include "htslib/kstring.h" #include "htslib/thread_pool.h" #include "htslib/hts_expr.h" #include "samtools.h" #include "sam_opts.h" #include "bam.h" // for bam_get_library and bam_remove_B #include "bedidx.h" #include "sam_utils.h" KHASH_SET_INIT_STR(str) typedef khash_t(str) *strhash_t; // This structure contains the settings for a samview run typedef struct samview_settings { strhash_t rghash; strhash_t rnhash; strhash_t tvhash; int min_mapQ; int rghash_discard; // 0 keep, 1 discard int rnhash_discard; // 0 keep, 1 discard // Described here in the same terms as the usage statement. // The code however always negates to "reject if" keep if: int flag_on; // keep if (FLAG & N) == N (all on) int flag_off; // keep if (FLAG & N) == 0 (all off) int flag_anyon; // keep if (FLAG & N) != 0 (any on) int flag_alloff; // reject if (FLAG & N) == N (any off) int min_qlen; int remove_B; uint32_t subsam_seed; double subsam_frac; char* library; void* bed; size_t remove_aux_len; char** remove_aux; int multi_region; char* tag; hts_filter_t *filter; int remove_flag; int add_flag; int unmap; auxhash_t remove_tag; auxhash_t keep_tag; hts_idx_t *hts_idx; sam_hdr_t *header; samFile *in, *out, *un_out; int64_t count; int is_count; char *fn_in, *fn_idx_in, *fn_out, *fn_fai, *fn_un_out, *fn_out_idx, *fn_un_out_idx; int fetch_pairs, nreglist; hts_reglist_t *reglist; int sanitize; int count_rf; // CRAM_OPT_REQUIRED_FIELDS for view -c } samview_settings_t; // Copied from htslib/sam.c. // TODO: we need a proper interface to find the length of an aux tag, // or at the very make exportable versions of these in htslib. static inline int aux_type2size(uint8_t type) { switch (type) { case 'A': case 'c': case 'C': return 1; case 's': case 'S': return 2; case 'i': case 'I': case 'f': return 4; case 'd': return 8; case 'Z': case 'H': case 'B': return type; default: return 0; } } // Copied from htslib/sam.c. static inline uint8_t *skip_aux(uint8_t *s, uint8_t *end) { int size; uint32_t n; if (s >= end) return end; size = aux_type2size(*s); ++s; // skip type switch (size) { case 'Z': case 'H': while (s < end && *s) ++s; return s < end ? s + 1 : end; case 'B': if (end - s < 5) return NULL; size = aux_type2size(*s); ++s; n = le_to_u32(s); s += 4; if (size == 0 || end - s < size * n) return NULL; return s + size * n; case 0: return NULL; default: if (end - s < size) return NULL; return s + size; } } // Returns 0 to indicate read should be output 1 otherwise, // and -1 on error. static int process_aln(const sam_hdr_t *h, bam1_t *b, samview_settings_t* settings) { if (settings->filter) { int r = sam_passes_filter(h, b, settings->filter); if (r < 0) // err return -1; if (r == 0) // filter-out return 1; } if (settings->remove_B) bam_remove_B(b); if (settings->min_qlen > 0) { int k, qlen = 0; uint32_t *cigar = bam_get_cigar(b); for (k = 0; k < b->core.n_cigar; ++k) if ((bam_cigar_type(bam_cigar_op(cigar[k]))&1) || bam_cigar_op(cigar[k]) == BAM_CHARD_CLIP) qlen += bam_cigar_oplen(cigar[k]); if (qlen < settings->min_qlen) return 1; } if (b->core.qual < settings->min_mapQ || ((b->core.flag & settings->flag_on) != settings->flag_on) || (b->core.flag & settings->flag_off)) return 1; if (settings->flag_alloff && ((b->core.flag & settings->flag_alloff) == settings->flag_alloff)) return 1; if (settings->flag_anyon && ((b->core.flag & settings->flag_anyon) == 0)) return 1; if (!settings->multi_region && settings->bed && (b->core.tid < 0 || !bed_overlap(settings->bed, sam_hdr_tid2name(h, b->core.tid), b->core.pos, bam_endpos(b)))) return 1; if (settings->subsam_frac > 0.) { uint32_t k = __ac_Wang_hash(__ac_X31_hash_string(bam_get_qname(b)) ^ settings->subsam_seed); if ((double)(k&0xffffff) / 0x1000000 >= settings->subsam_frac) return 1; } if (settings->rghash) { uint8_t *s = bam_aux_get(b, "RG"); if (s) { khint_t k = kh_get(str, settings->rghash, (char*)(s + 1)); if ((k == kh_end(settings->rghash)) != settings->rghash_discard) return 1; } } if (settings->tag) { uint8_t *s = bam_aux_get(b, settings->tag); if (s) { if (settings->tvhash) { char t[32], *val; if (*s == 'i' || *s == 'I' || *s == 's' || *s == 'S' || *s == 'c' || *s == 'C') { int ret = snprintf(t, 32, "%"PRId64, bam_aux2i(s)); if (ret > 0) val = t; else return 1; } else if (*s == 'A') { t[0] = *(s+1); t[1] = 0; val = t; } else { val = (char *)(s+1); } khint_t k = kh_get(str, settings->tvhash, val); if (k == kh_end(settings->tvhash)) return 1; } } else { return 1; } } if (settings->rnhash) { const char* rn = bam_get_qname(b); strhash_t h = settings->rnhash; if (!rn && !settings->rnhash_discard) return 1; if ((kh_get(str, h, rn) == kh_end(h)) != settings->rnhash_discard) return 1; } if (settings->library) { const char *p = bam_get_library((sam_hdr_t*)h, b); if (!p || strcmp(p, settings->library) != 0) return 1; } return 0; } static int adjust_tags(const sam_hdr_t *h, bam1_t *b, samview_settings_t* settings) { if (settings->keep_tag) { uint8_t *s_from, *s_to, *end = b->data + b->l_data; auxhash_t h = settings->keep_tag; s_from = s_to = bam_get_aux(b); while (s_from < end) { int x = (int)s_from[0]<<8 | s_from[1]; uint8_t *s = skip_aux(s_from+2, end); if (s == NULL) { print_error("view", "malformed aux data for record \"%s\"", bam_get_qname(b)); return -1; } if (kh_get(aux_exists, h, x) != kh_end(h) ) { if (s_to != s_from) memmove(s_to, s_from, s - s_from); s_to += s - s_from; } s_from = s; } b->l_data = s_to - b->data; } else if (settings->remove_tag) { uint8_t *s_from, *s_to, *end = b->data + b->l_data; auxhash_t h = settings->remove_tag; s_from = s_to = bam_get_aux(b); while (s_from < end) { int x = (int)s_from[0]<<8 | s_from[1]; uint8_t *s = skip_aux(s_from+2, end); if (s == NULL) { print_error("view", "malformed aux data for record \"%s\"", bam_get_qname(b)); return -1; } if (kh_get(aux_exists, h, x) == kh_end(h) ) { if (s_to != s_from) memmove(s_to, s_from, s - s_from); s_to += s - s_from; } s_from = s; } b->l_data = s_to - b->data; } return 0; } static int usage(FILE *fp, int exit_status, int is_long_help); static int populate_lookup_from_file(const char *subcmd, strhash_t lookup, char *fn) { FILE *fp; char buf[1024]; int ret = 0; fp = fopen(fn, "r"); if (fp == NULL) { print_error_errno(subcmd, "failed to open \"%s\" for reading", fn); return -1; } while (ret != -1 && !feof(fp) && fscanf(fp, "%1023s", buf) > 0) { char *d = strdup(buf); if (d != NULL) { kh_put(str, lookup, d, &ret); if (ret == 0) free(d); /* Duplicate */ } else { ret = -1; } } if (ferror(fp)) ret = -1; if (ret == -1) { print_error_errno(subcmd, "failed to read \"%s\"", fn); } fclose(fp); return (ret != -1) ? 0 : -1; } static int add_read_group_single(const char *subcmd, samview_settings_t *settings, char *name) { char *d = strdup(name); int ret = 0; if (d == NULL) goto err; if (settings->rghash == NULL) { settings->rghash = kh_init(str); if (settings->rghash == NULL) goto err; } else if (settings->rghash_discard == 1) { print_error("view", "cannot mix include and exclude read-group files in the same command line"); free(d); return -1; } settings->rghash_discard = 0; kh_put(str, settings->rghash, d, &ret); if (ret == -1) goto err; if (ret == 0) free(d); /* Duplicate */ return 0; err: print_error(subcmd, "Couldn't add \"%s\" to read group list: memory exhausted?", name); free(d); return -1; } static int add_read_names_file(const char *subcmd, samview_settings_t *settings, char *fn) { if (settings->rnhash == NULL) { settings->rnhash = kh_init(str); if (settings->rnhash == NULL) { perror(NULL); return -1; } } else if ((settings->rnhash_discard == 0 && *fn == '^') || (settings->rnhash_discard == 1 && *fn != '^')) { print_error("view", "cannot mix include and exclude read-name files in the same command line"); return -1; } settings->rnhash_discard = (*fn == '^'); return populate_lookup_from_file(subcmd, settings->rnhash, fn + (*fn == '^')); } static int add_read_groups_file(const char *subcmd, samview_settings_t *settings, char *fn) { if (settings->rghash == NULL) { settings->rghash = kh_init(str); if (settings->rghash == NULL) { perror(NULL); return -1; } } else if ((settings->rghash_discard == 0 && *fn == '^') || (settings->rghash_discard == 1 && *fn != '^')) { print_error("view", "cannot mix include and exclude read-group files in the same command line"); return -1; } settings->rghash_discard = (*fn == '^'); return populate_lookup_from_file(subcmd, settings->rghash, fn + (*fn == '^')); } static int add_tag_value_single(const char *subcmd, samview_settings_t *settings, char *name) { char *d = strdup(name); int ret = 0; if (d == NULL) goto err; if (settings->tvhash == NULL) { settings->tvhash = kh_init(str); if (settings->tvhash == NULL) goto err; } kh_put(str, settings->tvhash, d, &ret); if (ret == -1) goto err; if (ret == 0) free(d); /* Duplicate */ return 0; err: print_error(subcmd, "Couldn't add \"%s\" to tag values list: memory exhausted?", name); free(d); return -1; } static int add_tag_values_file(const char *subcmd, samview_settings_t *settings, char *fn) { if (settings->tvhash == NULL) { settings->tvhash = kh_init(str); if (settings->tvhash == NULL) { perror(NULL); return -1; } } return populate_lookup_from_file(subcmd, settings->tvhash, fn); } static inline int check_sam_write1(samFile *fp, const sam_hdr_t *h, const bam1_t *b, const char *fname, int *retp) { int r = sam_write1(fp, h, b); if (r >= 0) return r; if (fname) print_error_errno("view", "writing to \"%s\" failed", fname); else print_error_errno("view", "writing to standard output failed"); *retp = EXIT_FAILURE; return r; } static inline void change_flag(bam1_t *b, samview_settings_t *settings) { if (settings->add_flag) b->core.flag |= settings->add_flag; if (settings->remove_flag) b->core.flag &= ~settings->remove_flag; } static int cmp_reglist_intervals(const void *aptr, const void *bptr) { hts_pair_pos_t *a = (hts_pair_pos_t*)aptr; hts_pair_pos_t *b = (hts_pair_pos_t*)bptr; if ( a->beg < b->beg ) return -1; if ( a->beg > b->beg ) return 1; if ( a->end < b->end ) return -1; if ( a->end > b->end ) return 1; return 0; } static int cmp_reglist_tids(const void *aptr, const void *bptr) { hts_reglist_t *a = (hts_reglist_t*)aptr; hts_reglist_t *b = (hts_reglist_t*)bptr; if ( b->tid==HTS_IDX_NOCOOR || a->tid < b->tid ) return -1; if ( a->tid==HTS_IDX_NOCOOR || a->tid > b->tid ) return 1; return 0; } static hts_reglist_t *_reglist_dup(sam_hdr_t *hdr, hts_reglist_t *src, int nsrc) { int i,j; hts_reglist_t *dst = (hts_reglist_t*)calloc(nsrc,sizeof(hts_reglist_t)); if ( !dst ) { print_error_errno("view", "[%s:%d] could not allocate region list" ,__FILE__ ,__LINE__); return NULL; } for (i=0; i tid ) imax = i - 1; else break; } if ( i<0 || reg[i].tid < tid ) i++; // not found, i will be the index of the inserted element return i; } static int _reglist_push(hts_reglist_t **_reg, int *_nreg, int tid, hts_pos_t beg, hts_pos_t end) { hts_reglist_t *reg = *_reg; int nreg = *_nreg; int i = _reglist_find_tid(reg,nreg,tid); if ( i>=nreg || reg[i].tid!=tid ) { nreg++; reg = (hts_reglist_t*)realloc(reg,sizeof(hts_reglist_t)*nreg); if ( !reg ) { print_error_errno("view", "[%s:%d] could not extend region list", __FILE__, __LINE__); return -1; } if ( i+1 < nreg ) memmove(reg + i + 1, reg + i, sizeof(hts_reglist_t)*(nreg - i - 1)); reg[i].reg = NULL; reg[i].tid = tid; reg[i].min_beg = beg; reg[i].max_end = end; reg[i].intervals = NULL; reg[i].count = 0; } *_reg = reg; *_nreg = nreg; if ( reg[i].count > 0 && reg[i].intervals[reg[i].count - 1].beg==beg && reg[i].intervals[reg[i].count - 1].end==end ) { return 0; } hts_pair_pos_t *new_intervals = realloc(reg[i].intervals, sizeof(hts_pair_pos_t)*(reg[i].count + 1)); if (!new_intervals) { print_error_errno("view", "[%s:%d] could not extend region list", __FILE__, __LINE__); return -1; } reg[i].intervals = new_intervals; reg[i].intervals[reg[i].count].beg = beg; reg[i].intervals[reg[i].count].end = end; reg[i].count++; return 0; } static void _reglist_merge(hts_reglist_t *reg, int nreg) { int i,j; for (i=0; ibed, regs, 0, nregs, &filter_op); // insert(1) or filter out(0) the regions from the command line in the same hash table as the bed file if (!bed) { print_error_errno("view", "Couldn't %s region list", filter_op ? "build" : "filter"); return NULL; } conf->bed = bed; if ( !filter_op ) filter_state = FILTERED; } else bed_unify(conf->bed); // This check is probably redundant, but left just in case if ( !conf->bed) { // index is unavailable or no regions have been specified print_error("view", "No regions or BED file have been provided. Aborting."); return NULL; } int regcount = 0; hts_reglist_t *reglist = bed_reglist(conf->bed, filter_state, ®count); if (!reglist) { print_error("view", "Region list is empty or could not be created. Aborting."); return NULL; } if ( conf->fetch_pairs ) { conf->reglist = _reglist_dup(conf->header,reglist,regcount); if (!conf->reglist) return NULL; conf->nreglist = regcount; } iter = sam_itr_regions(conf->hts_idx, conf->header, reglist, regcount); if ( !iter ) { print_error("view", "Iterator could not be created. Aborting."); return NULL; } return iter; } KHASH_SET_INIT_STR(names) static int fetch_pairs_collect_mates(samview_settings_t *conf, hts_itr_multi_t *iter) { khint_t k; int nunmap = 0, r = 0, nmates = 0, write_error = 0, retval = EXIT_FAILURE; kh_names_t *mate_names = kh_init(names); bam1_t *rec = bam_init1(); if (!mate_names) { print_error_errno("view", "could not allocate mate names table"); goto out; } if (!rec) { print_error_errno("view", "could not allocate bam record"); goto out; } while ((r =sam_itr_multi_next(conf->in, iter, rec))>=0) { if ( (rec->core.flag & BAM_FPAIRED) == 0 ) continue; if ( rec->core.mtid>=0 && bed_overlap(conf->bed, sam_hdr_tid2name(conf->header,rec->core.mtid), rec->core.mpos, rec->core.mpos) ) continue; int p = process_aln(conf->header, rec, conf); if (p < 0) goto out; if (p == 1) continue; nmates++; k = kh_get(names,mate_names,bam_get_qname(rec)); if ( k == kh_end(mate_names) ) { int ret = 0; char *name_copy = strdup(bam_get_qname(rec)); if (!name_copy) { print_error_errno("view", "[%s:%d] could not store sample name, %d elements", __FILE__,__LINE__,nmates); goto out; } kh_put(names, mate_names, name_copy, &ret); if ( ret<0 ) { print_error_errno("view", "[%s:%d] could not store sample name, %d elements",__FILE__,__LINE__,nmates); free(name_copy); goto out; } } if ( rec->core.mtid < 0 ) { nunmap = 1; } else { if (_reglist_push(&conf->reglist, &conf->nreglist, rec->core.mtid, rec->core.mpos,rec->core.mpos+1) != 0) goto out; } } if (r < -1) { print_error_errno("view", "error reading file \"%s\"", conf->fn_in); goto out; } _reglist_merge(conf->reglist, conf->nreglist); if ( nunmap ) { if (_reglist_push(&conf->reglist,&conf->nreglist,HTS_IDX_NOCOOR,0,HTS_POS_MAX) != 0) goto out; } hts_itr_multi_destroy(iter); iter = sam_itr_regions(conf->hts_idx, conf->header, conf->reglist, conf->nreglist); if ( !iter ) { print_error_errno("view", "[%s:%d] iterator could not be created",__FILE__,__LINE__); goto out; } while ((r = sam_itr_multi_next(conf->in, iter, rec))>=0) { int drop = 1; if (rec->core.tid >=0 && bed_overlap(conf->bed, sam_hdr_tid2name(conf->header,rec->core.tid), rec->core.pos, bam_endpos(rec))) drop = 0; if ( drop ) { k = kh_get(names,mate_names,bam_get_qname(rec)); if ( k != kh_end(mate_names) ) drop = 0; } int p = 0; if (!drop && (p=process_aln(conf->header, rec, conf))== 0) { if (adjust_tags(conf->header, rec, conf) != 0) goto out; if (check_sam_write1(conf->out, conf->header, rec, conf->fn_out, &write_error) < 0) goto out; } if (p < 0) goto out; } if (r < -1) { print_error_errno("view", "error reading file \"%s\"", conf->fn_in); goto out; } retval = EXIT_SUCCESS; out: hts_itr_multi_destroy(iter); hts_idx_destroy(conf->hts_idx); // destroy the BAM index conf->hts_idx = NULL; if (mate_names) { // free khash keys for (k = 0; k < kh_end(mate_names); ++k) if ( kh_exist(mate_names,k) ) free((char*)kh_key(mate_names, k)); kh_destroy(names,mate_names); } bam_destroy1(rec); return retval; } // Common code for processing and writing a record static inline int process_one_record(samview_settings_t *conf, bam1_t *b, int *write_error) { if (conf->sanitize) if (bam_sanitize(conf->header, b, conf->sanitize) < 0) return -1; int p; if ((p = process_aln(conf->header, b, conf)) < 0) { // error return -1; } else if (p == 0) { // emit read if (!conf->is_count) { change_flag(b, conf); if (adjust_tags(conf->header, b, conf) != 0) return -1; if (check_sam_write1(conf->out, conf->header, b, conf->fn_out, write_error) < 0) { return -1; } } conf->count++; } else if (conf->unmap) { b->core.flag |= BAM_FUNMAP; b->core.qual = 0; b->core.isize = 0; // remove CIGAR if (b->core.n_cigar) { memmove(bam_get_cigar(b), bam_get_seq(b), b->data + b->l_data - bam_get_seq(b)); b->l_data -= 4*b->core.n_cigar; b->core.n_cigar = 0; } if (check_sam_write1(conf->out, conf->header, b, conf->fn_out, write_error) < 0) { return -1; } } else { if (conf->un_out) { if (check_sam_write1(conf->un_out, conf->header, b, conf->fn_un_out, write_error) < 0) { return -1; } } } return 0; } static int stream_view(samview_settings_t *conf) { bam1_t *b = bam_init1(); int write_error = 0, r, p = 0; if (!b) { print_error_errno("view", "could not allocate bam record"); return 1; } errno = 0; // prevent false error messages. while ((r = sam_read1(conf->in, conf->header, b)) >= 0) { if ((p = process_one_record(conf, b, &write_error)) < 0) break; } bam_destroy1(b); if (r < -1 || p < 0) { print_error_errno("view", "error reading file \"%s\"", conf->fn_in); return 1; } return write_error; } static int multi_region_view(samview_settings_t *conf, hts_itr_multi_t *iter) { bam1_t *b = bam_init1(); int write_error = 0, result; if (!b) { print_error_errno("view", "could not allocate bam record"); return 1; } // fetch alignments while ((result = sam_itr_multi_next(conf->in, iter, b)) >= 0) { if (process_one_record(conf, b, &write_error) < 0) break; } bam_destroy1(b); if (result < -1) { print_error("view", "retrieval of region #%d failed", iter->curr_tid); write_error = 1; } hts_itr_multi_destroy(iter); return write_error; } // Make mnemonic distinct values for longoption-only options #define LONGOPT(c) ((c) + 128) // Check for ".sam" filenames as sam_open_mode cannot distinguish between // foo.sam and foo.unknown, both getting mode "". static int is_sam(const char *fn) { if (!fn) return 0; size_t l = strlen(fn); return (l >= 4 && strcasecmp(fn + l-4, ".sam") == 0); } static void aux_list_free(samview_settings_t *settings) { if (settings->keep_tag) kh_destroy(aux_exists, settings->keep_tag); if (settings->remove_tag) kh_destroy(aux_exists, settings->remove_tag); } int main_samview(int argc, char *argv[]) { samview_settings_t settings; int c, is_header = 0, is_header_only = 0, ret = 0, compress_level = -1, has_index_file = 0, no_pg = 0; FILE *fp_out = NULL; char out_mode[6] = {0}, out_un_mode[6] = {0}; char *out_format = ""; char *arg_list = NULL; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; htsThreadPool p = {NULL, 0}; memset(&settings,0,sizeof(settings)); settings.subsam_frac = -1.0; settings.count_rf = SAM_FLAG; // don't want 0, and this is quick static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 'T', '@'), {"add-flags", required_argument, NULL, LONGOPT('a')}, {"bam", no_argument, NULL, 'b'}, {"count", no_argument, NULL, 'c'}, {"cram", no_argument, NULL, 'C'}, {"customised-index", no_argument, NULL, 'X'}, {"customized-index", no_argument, NULL, 'X'}, {"excl-flags", required_argument, NULL, 'F'}, {"exclude-flags", required_argument, NULL, 'F'}, {"expr", required_argument, NULL, 'e'}, {"expression", required_argument, NULL, 'e'}, {"fai-reference", required_argument, NULL, 't'}, {"fast", no_argument, NULL, '1'}, {"fetch-pairs", no_argument, NULL, 'P'}, {"header-only", no_argument, NULL, 'H'}, {"help", no_argument, NULL, LONGOPT('?')}, {"incl-flags", required_argument, NULL, LONGOPT('g')}, {"include-flags", required_argument, NULL, LONGOPT('g')}, {"rf", required_argument, NULL, LONGOPT('g')}, // aka incl-flags {"keep-tag", required_argument, NULL, LONGOPT('x') }, {"library", required_argument, NULL, 'l'}, {"min-mapq", required_argument, NULL, 'q'}, {"min-MQ", required_argument, NULL, 'q'}, {"min-mq", required_argument, NULL, 'q'}, {"min-qlen", required_argument, NULL, 'm'}, {"no-header", no_argument, NULL, LONGOPT('H')}, {"no-PG", no_argument, NULL, LONGOPT('P')}, {"output", required_argument, NULL, 'o'}, {"output-unselected", required_argument, NULL, 'U'}, {"QNAME-file", required_argument, NULL, 'N'}, {"qname-file", required_argument, NULL, 'N'}, {"read-group", required_argument, NULL, 'r'}, {"read-group-file", required_argument, NULL, 'R'}, {"readgroup", required_argument, NULL, 'r'}, {"readgroup-file", required_argument, NULL, 'R'}, {"region-file", required_argument, NULL, LONGOPT('L')}, {"regions-file", required_argument, NULL, LONGOPT('L')}, {"remove-B", no_argument, NULL, 'B'}, {"remove-flags", required_argument, NULL, LONGOPT('r')}, {"remove-tag", required_argument, NULL, 'x'}, {"require-flags", required_argument, NULL, 'f'}, {"subsample", required_argument, NULL, LONGOPT('s')}, {"subsample-seed", required_argument, NULL, LONGOPT('S')}, {"tag", required_argument, NULL, 'd'}, {"tag-file", required_argument, NULL, 'D'}, {"target-file", required_argument, NULL, 'L'}, {"targets-file", required_argument, NULL, 'L'}, {"uncompressed", no_argument, NULL, 'u'}, {"unmap", no_argument, NULL, 'p'}, {"unoutput", required_argument, NULL, 'U'}, {"use-index", no_argument, NULL, 'M'}, {"with-header", no_argument, NULL, 'h'}, {"sanitize", required_argument, NULL, 'z'}, {NULL, 0, NULL, 0} }; /* parse command-line options */ strcpy(out_mode, "w"); strcpy(out_un_mode, "w"); if (argc == 1 && isatty(STDIN_FILENO)) return usage(samtools_stdout, EXIT_SUCCESS, 0); // Suppress complaints about '?' being an unrecognised option. Without // this we have to put '?' in the options list, which makes it hard to // tell a bad long option from the use of '-?' (both return '?' and // set optopt to '\0'). opterr = 0; char *tmp; int tmp_flag; while ((c = getopt_long(argc, argv, "SbBcCt:h1Ho:O:q:f:F:G:ul:r:T:R:N:d:D:L:s:@:m:x:U:MXe:pPz:", lopts, NULL)) >= 0) { switch (c) { case 's': settings.subsam_seed = strtol(optarg, &tmp, 10); if (tmp && *tmp == '.') { settings.subsam_frac = strtod(tmp, &tmp); if (*tmp) ret = 1; } else { ret = 1; } if (ret == 1) { print_error("view", "Incorrect sampling argument \"%s\"", optarg); goto view_end; } settings.count_rf |= SAM_QNAME; break; case LONGOPT('s'): settings.subsam_frac = strtod(optarg, &tmp); if (*tmp || settings.subsam_frac < 0.0 || settings.subsam_frac > 1.0) { print_error("view", "Incorrect sampling argument \"%s\"", optarg); goto view_end; } settings.count_rf |= SAM_QNAME; break; case LONGOPT('S'): settings.subsam_seed = atoi(optarg); break; case 'm': settings.min_qlen = atoi(optarg); settings.count_rf |= SAM_SEQ; break; case 'c': settings.is_count = 1; break; case 'S': break; case 'b': out_format = "b"; break; case 'C': out_format = "c"; break; case 't': settings.fn_fai = strdup(optarg); break; case 'h': is_header = 1; break; case 'H': is_header_only = 1; break; case LONGOPT('H'): is_header = is_header_only = 0; break; case 'o': settings.fn_out = strdup(optarg); break; case 'U': settings.fn_un_out = strdup(optarg); break; case 'X': has_index_file = 1; break; case 'f': tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("view", "Unknown flag '%s'", optarg); return 1; } settings.flag_on |= tmp_flag; settings.count_rf |= SAM_FLAG | SAM_RNEXT; break; case 'F': tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("view", "Unknown flag '%s'", optarg); return 1; } settings.flag_off |= tmp_flag; settings.count_rf |= SAM_FLAG | SAM_RNEXT; break; case LONGOPT('g'): tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("view", "Unknown flag '%s'", optarg); return 1; } settings.flag_anyon |= tmp_flag; settings.count_rf |= SAM_FLAG | SAM_RNEXT; break; case 'G': tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("view", "Unknown flag '%s'", optarg); return 1; } settings.flag_alloff |= tmp_flag; settings.count_rf |= SAM_FLAG | SAM_RNEXT; break; case 'q': settings.min_mapQ = atoi(optarg); settings.count_rf |= SAM_MAPQ; break; case 'u': compress_level = 0; break; case '1': compress_level = 1; break; case 'l': settings.library = strdup(optarg); settings.count_rf |= SAM_RGAUX; break; case 'p': settings.unmap = 1; break; case 'P': settings.fetch_pairs = 1; settings.multi_region = 1; break; case 'z': if ((settings.sanitize = bam_sanitize_options(optarg)) < 0) { ret = 1; goto view_end; } break; case LONGOPT('L'): settings.multi_region = 1; // fall through case 'L': if ((settings.bed = bed_read(optarg)) == NULL) { print_error_errno("view", "Could not read file \"%s\"", optarg); ret = 1; goto view_end; } settings.count_rf |= SAM_POS | SAM_RNAME | SAM_CIGAR; break; case 'r': if (add_read_group_single("view", &settings, optarg) != 0) { ret = 1; goto view_end; } settings.count_rf |= SAM_RGAUX; break; case 'R': if (add_read_groups_file("view", &settings, optarg) != 0) { ret = 1; goto view_end; } settings.count_rf |= SAM_RGAUX; break; case 'N': if (add_read_names_file("view", &settings, optarg) != 0) { ret = 1; goto view_end; } settings.count_rf |= SAM_QNAME; break; case 'd': if (strlen(optarg) < 2 || (strlen(optarg) > 2 && optarg[2] != ':')) { print_error("view", "Invalid \"tag:value\" option: \"%s\"", optarg); ret = 1; goto view_end; } if (settings.tag) { if (settings.tag[0] != optarg[0] || settings.tag[1] != optarg[1]) { print_error("view", "Different tag \"%s\" was specified before: \"%s\"", settings.tag, optarg); ret = 1; goto view_end; } } else { if (!(settings.tag = calloc(3, 1))) { print_error("view", "Could not allocate memory for tag: \"%s\"", optarg); ret = 1; goto view_end; } memcpy(settings.tag, optarg, 2); } if (strlen(optarg) > 3 && add_tag_value_single("view", &settings, optarg+3) != 0) { print_error("view", "Could not add tag:value \"%s\"", optarg); ret = 1; goto view_end; } // Some tag filtering affects other fields if (memcmp(settings.tag, "NM", 2) == 0 || memcmp(settings.tag, "MD", 2) == 0) settings.count_rf |= SAM_AUX | SAM_SEQ; else if (memcmp(settings.tag, "RG", 2) == 0) settings.count_rf |= SAM_RGAUX; else settings.count_rf |= SAM_AUX; break; case 'D': // Allow ";" as delimiter besides ":" to support MinGW CLI POSIX // path translation as described at: // http://www.mingw.org/wiki/Posix_path_conversion if (strlen(optarg) < 4 || (optarg[2] != ':' && optarg[2] != ';')) { print_error("view", "Invalid \"tag:file\" option: \"%s\"", optarg); ret = 1; goto view_end; } if (settings.tag) { if (settings.tag[0] != optarg[0] || settings.tag[1] != optarg[1]) { print_error("view", "Different tag \"%s\" was specified before: \"%s\"", settings.tag, optarg); ret = 1; goto view_end; } } else { if (!(settings.tag = calloc(3, 1))) { print_error("view", "Could not allocate memory for tag: \"%s\"", optarg); ret = 1; goto view_end; } memcpy(settings.tag, optarg, 2); } if (add_tag_values_file("view", &settings, optarg+3) != 0) { ret = 1; goto view_end; } // Some tag filtering affects other fields if (memcmp(settings.tag, "NM", 2) == 0 || memcmp(settings.tag, "MD", 2) == 0) settings.count_rf |= SAM_AUX | SAM_SEQ; else if (memcmp(settings.tag, "RG", 2) == 0) settings.count_rf |= SAM_RGAUX; else settings.count_rf |= SAM_AUX; break; case LONGOPT('?'): return usage(samtools_stdout, EXIT_SUCCESS, 1); case '?': if (optopt == '?') { // '-?' appeared on command line return usage(samtools_stdout, EXIT_SUCCESS, 1); } else { if (optopt) { // Bad short option print_error("view", "invalid option -- '%c'", optopt); } else { // Bad long option // Do our best. There is no good solution to finding // out what the bad option was. // See, e.g. https://stackoverflow.com/questions/2723888/where-does-getopt-long-store-an-unrecognized-option if (optind > 0 && strncmp(argv[optind - 1], "--", 2) == 0) { print_error("view", "unrecognised option '%s'", argv[optind - 1]); } } return usage(samtools_stderr, EXIT_FAILURE, 0); } case 'B': settings.remove_B = 1; break; case 'M': settings.multi_region = 1; break; case LONGOPT('P'): no_pg = 1; break; case 'e': if (!(settings.filter = hts_filter_init(optarg))) { print_error("main_samview", "Couldn't initialise filter"); return 1; } settings.count_rf = INT_MAX; // no way to know what we need break; case LONGOPT('r'): tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("view", "Unknown flag '%s'", optarg); return 1; } settings.remove_flag |= tmp_flag; break; case LONGOPT('a'): tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("view", "Unknown flag '%s'", optarg); return 1; } settings.add_flag |= tmp_flag; break; case 'x': if (*optarg == '^') { if (parse_aux_list(&settings.keep_tag, optarg+1, "main_samview")) { aux_list_free(&settings); return usage(samtools_stderr, EXIT_FAILURE, 0); } } else { if (parse_aux_list(&settings.remove_tag, optarg, "main_samview")) { aux_list_free(&settings); return usage(samtools_stderr, EXIT_FAILURE, 0); } } break; case LONGOPT('x'): if (parse_aux_list(&settings.keep_tag, optarg, "main_samview")) { aux_list_free(&settings); return usage(samtools_stderr, EXIT_FAILURE, 0); } break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) != 0) return usage(samtools_stderr, EXIT_FAILURE, 0); break; } } if (settings.is_count && settings.fetch_pairs) { print_error("view","The options -P and -c cannot be combined\n"); return 1; } if (settings.fn_fai == 0 && ga.reference) settings.fn_fai = fai_path(ga.reference); if (is_header_only) is_header = 1; // File format auto-detection first if (settings.fn_out) sam_open_mode(out_mode+1, settings.fn_out, NULL); if (settings.fn_un_out) sam_open_mode(out_un_mode+1, settings.fn_un_out, NULL); // -1 or -u without an explicit format (-b, -C) => check fn extensions if (!*out_format && compress_level >= 0) { if (compress_level == 0 && (out_mode[strlen(out_mode)-1] == 'z' || out_un_mode[strlen(out_un_mode)-1] == 'z')) // z, fz, Fz sanity check fprintf(samtools_stderr, "[view] Warning option -u ignored due to" " filename suffix\n"); // If known extension, use it, otherwise BAM if (!(out_mode[1] || is_sam(settings.fn_out))) out_mode[1] = 'b'; if (!(out_un_mode[1] || is_sam(settings.fn_un_out))) out_un_mode[1] = 'b'; } else if (*out_format) { out_mode[1] = out_un_mode[1] = *out_format; } if (compress_level >= 0) { char tmp[2]; tmp[0] = compress_level + '0'; tmp[1] = '\0'; strcat(out_mode, tmp); strcat(out_un_mode, tmp); } if (argc == optind && isatty(STDIN_FILENO)) { print_error("view", "No input provided or missing option argument."); return usage(samtools_stderr, EXIT_FAILURE, 0); // potential memory leak... } if (settings.unmap && settings.fn_un_out) { print_error("view", "Options --unoutput and --unmap are mutually exclusive."); ret = 1; goto view_end; } if (settings.subsam_seed != 0) { // Convert likely user input 1,2,... to pseudo-random // values with more entropy and more bits set srand(settings.subsam_seed); settings.subsam_seed = rand(); } settings.fn_in = (optind < argc)? argv[optind] : "-"; if ((settings.in = sam_open_format(settings.fn_in, "r", &ga.in)) == 0) { print_error_errno("view", "failed to open \"%s\" for reading", settings.fn_in); ret = 1; goto view_end; } if (settings.fn_fai) { if (hts_set_fai_filename(settings.in, settings.fn_fai) != 0) { fprintf(samtools_stderr, "[main_samview] failed to use reference \"%s\".\n", settings.fn_fai); ret = 1; goto view_end; } } if ((settings.header = sam_hdr_read(settings.in)) == 0) { fprintf(samtools_stderr, "[main_samview] fail to read the header from \"%s\".\n", settings.fn_in); ret = 1; goto view_end; } if (settings.rghash) { sam_hdr_remove_lines(settings.header, "RG", "ID", settings.rghash); } if (!settings.is_count) { if ((settings.out = sam_open_format(settings.fn_out? settings.fn_out : "-", out_mode, &ga.out)) == 0) { print_error_errno("view", "failed to open \"%s\" for writing", settings.fn_out? settings.fn_out : "standard output"); ret = 1; goto view_end; } if (settings.fn_fai) { if (hts_set_fai_filename(settings.out, settings.fn_fai) != 0) { fprintf(samtools_stderr, "[main_samview] failed to use reference \"%s\".\n", settings.fn_fai); ret = 1; goto view_end; } } autoflush_if_stdout(settings.out, settings.fn_out); if (!no_pg) { if (!(arg_list = stringify_argv(argc+1, argv-1))) { print_error("view", "failed to create arg_list"); ret = 1; goto view_end; } if (sam_hdr_add_pg(settings.header, "samtools", "VN", samtools_version(), arg_list ? "CL": NULL, arg_list ? arg_list : NULL, NULL)) { print_error("view", "failed to add PG line to the header"); ret = 1; goto view_end; } } if (ga.write_index || is_header || out_mode[1] == 'b' || out_mode[1] == 'c' || (ga.out.format != sam && ga.out.format != unknown_format)) { if (sam_hdr_write(settings.out, settings.header) != 0) { fprintf(samtools_stderr, "[main_samview] failed to write the SAM header\n"); ret = 1; goto view_end; } } if (ga.write_index) { if (!(settings.fn_out_idx = auto_index(settings.out, settings.fn_out, settings.header))) { ret = 1; goto view_end; } } if (settings.fn_un_out) { if ((settings.un_out = sam_open_format(settings.fn_un_out, out_un_mode, &ga.out)) == 0) { print_error_errno("view", "failed to open \"%s\" for writing", settings.fn_un_out); ret = 1; goto view_end; } if (settings.fn_fai) { if (hts_set_fai_filename(settings.un_out, settings.fn_fai) != 0) { fprintf(samtools_stderr, "[main_samview] failed to use reference \"%s\".\n", settings.fn_fai); ret = 1; goto view_end; } } autoflush_if_stdout(settings.un_out, settings.fn_un_out); if (ga.write_index || is_header || out_un_mode[1] == 'b' || out_un_mode[1] == 'c' || (ga.out.format != sam && ga.out.format != unknown_format)) { if (sam_hdr_write(settings.un_out, settings.header) != 0) { fprintf(samtools_stderr, "[main_samview] failed to write the SAM header\n"); ret = 1; goto view_end; } } if (ga.write_index) { if (!(settings.fn_un_out_idx = auto_index(settings.un_out, settings.fn_un_out, settings.header))) { ret = 1; goto view_end; } } } } else { if (settings.fn_out) { fp_out = fopen(settings.fn_out, "w"); if (fp_out == NULL) { print_error_errno("view", "can't create \"%s\"", settings.fn_out); ret = EXIT_FAILURE; goto view_end; } } settings.unmap = 0; // Not valid in counting mode } if (ga.nthreads > 0) { if (!(p.pool = hts_tpool_init(ga.nthreads))) { fprintf(samtools_stderr, "Error creating thread pool\n"); ret = 1; goto view_end; } hts_set_opt(settings.in, HTS_OPT_THREAD_POOL, &p); if (settings.out) hts_set_opt(settings.out, HTS_OPT_THREAD_POOL, &p); } if (is_header_only) goto view_end; // no need to print alignments // Initialize BAM/CRAM index char **regs = NULL; int nregs = 0; if ( has_index_file && optind <= argc - 2 ) { regs = optind < argc-2 ? &argv[optind+2] : NULL; nregs = argc - optind - 2; settings.fn_idx_in = argv[optind+1]; } else if (!has_index_file && optind < argc - 1 ) { regs = &argv[optind+1]; nregs = argc - optind - 1; } else if ( has_index_file && argc-optind < 2) { print_error("view", "Incorrect number of arguments for -X option. Aborting."); return 1; } if (regs) settings.count_rf |= SAM_POS | SAM_RNAME | SAM_CIGAR; if ( settings.fn_idx_in || nregs || settings.multi_region ) { settings.hts_idx = settings.fn_idx_in ? sam_index_load2(settings.in, settings.fn_in, settings.fn_idx_in) : sam_index_load(settings.in, settings.fn_in); if ( !settings.hts_idx ) { print_error("view", "Random alignment retrieval only works for indexed SAM.gz, BAM or CRAM files."); return 1; } } if (settings.is_count) // Won't fail, but also wouldn't matter if it did hts_set_opt(settings.in, CRAM_OPT_REQUIRED_FIELDS, settings.count_rf); if ( settings.fetch_pairs ) { hts_itr_multi_t *iter = multi_region_init(&settings, regs, nregs); ret = iter ? fetch_pairs_collect_mates(&settings, iter) : 1; if (ret) goto view_end; } else if ( settings.multi_region ) { hts_itr_multi_t *iter = multi_region_init(&settings, regs, nregs); ret = iter ? multi_region_view(&settings, iter) : 1; if (ret) goto view_end; } else if ( !settings.hts_idx || optind+1 >= argc-has_index_file ) { // stream through the entire file ret = stream_view(&settings); if (ret) goto view_end; } else { // retrieve alignments in specified regions int i; for (i = (has_index_file)? optind+2 : optind+1; i < argc; ++i) { hts_itr_t *iter = sam_itr_querys(settings.hts_idx, settings.header, argv[i]); // parse a region in the format like `chr2:100-200' if (iter == NULL) { // region invalid or reference name not found fprintf(samtools_stderr, "[main_samview] region \"%s\" specifies an invalid region or unknown reference. Continue anyway.\n", argv[i]); continue; } // fetch alignments ret = multi_region_view(&settings, iter); if (ret) goto view_end; } } if (ga.write_index) { if (sam_idx_save(settings.out) < 0) { print_error_errno("view", "writing index failed"); ret = 1; } if (settings.un_out && sam_idx_save(settings.un_out) < 0) { print_error_errno("view", "writing index failed"); ret = 1; } } view_end: if ( settings.hts_idx ) hts_idx_destroy(settings.hts_idx); if (settings.is_count && ret == 0) { if (fprintf(settings.fn_out? fp_out : samtools_stdout, "%" PRId64 "\n", settings.count) < 0) { if (settings.fn_out) print_error_errno("view", "writing to \"%s\" failed", settings.fn_out); else print_error_errno("view", "writing to standard output failed"); ret = EXIT_FAILURE; } } // close files, free and return if (settings.in) check_sam_close("view", settings.in, settings.fn_in, "standard input", &ret); if (settings.out) check_sam_close("view", settings.out, settings.fn_out, "standard output", &ret); if (settings.un_out) check_sam_close("view", settings.un_out, settings.fn_un_out, "file", &ret); if (fp_out) fclose(fp_out); free(settings.fn_fai); free(settings.fn_out); free(settings.library); free(settings.fn_un_out); sam_global_args_free(&ga); if ( settings.header ) sam_hdr_destroy(settings.header); if (settings.bed) bed_destroy(settings.bed); if (settings.rghash) { khint_t k; for (k = 0; k < kh_end(settings.rghash); ++k) if (kh_exist(settings.rghash, k)) free((char*)kh_key(settings.rghash, k)); kh_destroy(str, settings.rghash); } if (settings.rnhash) { khint_t k; for (k = 0; k < kh_end(settings.rnhash); ++k) if (kh_exist(settings.rnhash, k)) free((char*)kh_key(settings.rnhash, k)); kh_destroy(str, settings.rnhash); } if (settings.tvhash) { khint_t k; for (k = 0; k < kh_end(settings.tvhash); ++k) if (kh_exist(settings.tvhash, k)) free((char*)kh_key(settings.tvhash, k)); kh_destroy(str, settings.tvhash); } if (settings.remove_aux_len) { free(settings.remove_aux); } if (settings.tag) { free(settings.tag); } if (settings.filter) hts_filter_free(settings.filter); if (p.pool) hts_tpool_destroy(p.pool); if (settings.fn_out_idx) free(settings.fn_out_idx); if (settings.fn_un_out_idx) free(settings.fn_un_out_idx); free(arg_list); aux_list_free(&settings); return ret; } static int usage(FILE *fp, int exit_status, int is_long_help) { fprintf(fp, "\n" "Usage: samtools view [options] || [region ...]\n" "\n" "Output options:\n" " -b, --bam Output BAM\n" " -C, --cram Output CRAM (requires -T)\n" " -1, --fast Use fast BAM compression (and default to --bam)\n" " -u, --uncompressed Uncompressed BAM output (and default to --bam)\n" " -h, --with-header Include header in SAM output\n" " -H, --header-only Print SAM header only (no alignments)\n" " --no-header Print SAM alignment records only [default]\n" " -c, --count Print only the count of matching records\n" " -o, --output FILE Write output to FILE [standard output]\n" " -U, --unoutput FILE, --output-unselected FILE\n" " Output reads not selected by filters to FILE\n" " -p, --unmap Set flag to UNMAP on reads not selected\n" " then write to output file.\n" " -P, --fetch-pairs Retrieve complete pairs even when outside of region\n" "Input options:\n" " -t, --fai-reference FILE FILE listing reference names and lengths\n" " -M, --use-index Use index and multi-region iterator for regions\n" " --region[s]-file FILE Use index to include only reads overlapping FILE\n" " -X, --customized-index Expect extra index file argument after \n" "\n" "Filtering options (Only include in output reads that...):\n" " -L, --target[s]-file FILE ...overlap (BED) regions in FILE\n" " -N, --qname-file [^]FILE ...whose read name is listed in FILE (\"^\" negates)\n" " -r, --read-group STR ...are in read group STR\n" " -R, --read-group-file [^]FILE\n" " ...are in a read group listed in FILE\n" " -d, --tag STR1[:STR2] ...have a tag STR1 (with associated value STR2)\n" " -D, --tag-file STR:FILE ...have a tag STR whose value is listed in FILE\n" " -q, --min-MQ INT ...have mapping quality >= INT\n" " -l, --library STR ...are in library STR\n" " -m, --min-qlen INT ...cover >= INT query bases (as measured via CIGAR)\n" " -e, --expr STR ...match the filter expression STR\n" " -f, --require-flags FLAG ...have all of the FLAGs present\n" // F&x == x " -F, --excl[ude]-flags FLAG ...have none of the FLAGs present\n" // F&x == 0 " --rf, --incl-flags, --include-flags FLAG\n" " ...have some of the FLAGs present\n" " -G FLAG EXCLUDE reads with all of the FLAGs present\n" // !(F&x == x) TODO long option " --subsample FLOAT Keep only FLOAT fraction of templates/read pairs\n" " --subsample-seed INT Influence WHICH reads are kept in subsampling [0]\n" " -s INT.FRAC Same as --subsample 0.FRAC --subsample-seed INT\n" "\n" "Processing options:\n" " --add-flags FLAG Add FLAGs to reads\n" " --remove-flags FLAG Remove FLAGs from reads\n" " -x, --remove-tag STR\n" " Comma-separated read tags to strip (repeatable) [null]\n" " --keep-tag STR\n" " Comma-separated read tags to preserve (repeatable) [null].\n" " Equivalent to \"-x ^STR\"\n" " -B, --remove-B Collapse the backward CIGAR operation\n" " -z, --sanitize FLAGS Perform sanitity checking and fixing on records.\n" " FLAGS is comma separated (see manual). [off]\n" "\n" "General options:\n" " -?, --help Print long help, including note about region specification\n" " -S Ignored (input format is auto-detected)\n" " --no-PG Do not add a PG line\n"); sam_global_opt_help(fp, "-.O.T@.."); fprintf(fp, "\n"); if (is_long_help) fprintf(fp, "Notes:\n" "\n" "1. This command now auto-detects the input format (BAM/CRAM/SAM).\n" " Further control over the CRAM format can be specified by using the\n" " --output-fmt-option, e.g. to specify the number of sequences per slice\n" " and to use avoid reference based compression:\n" "\n" "\tsamtools view -C --output-fmt-option seqs_per_slice=5000 \\\n" "\t --output-fmt-option no_ref -o out.cram in.bam\n" "\n" " Options can also be specified as a comma separated list within the\n" " --output-fmt value too. For example this is equivalent to the above\n" "\n" "\tsamtools view --output-fmt cram,seqs_per_slice=5000,no_ref \\\n" "\t -o out.cram in.bam\n" "\n" "2. The file supplied with `-t' is SPACE/TAB delimited with the first\n" " two fields of each line consisting of the reference name and the\n" " corresponding sequence length. The `.fai' file generated by \n" " `samtools faidx' is suitable for use as this file. This may be an\n" " empty file if reads are unaligned.\n" "\n" "3. SAM->BAM conversion: samtools view -bT ref.fa in.sam.gz\n" "\n" "4. BAM->SAM conversion: samtools view -h in.bam\n" "\n" "5. A region should be presented in one of the following formats:\n" " `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n" " specified, the input alignment file must be a sorted and indexed\n" " alignment (BAM/CRAM) file.\n" "\n" "6. Option `-u' is preferred over `-b' when the output is piped to\n" " another samtools command.\n" "\n" "7. Option `-M`/`--use-index` causes overlaps with `-L` BED file regions and\n" " command-line region arguments to be computed using the multi-region iterator\n" " and an index. This increases speed, omits duplicates, and outputs the reads\n" " as they are ordered in the input SAM/BAM/CRAM file.\n" "\n" "8. Options `-L`/`--target[s]-file` and `--region[s]-file` may not be used\n" " together. `--region[s]-file FILE` is simply equivalent to `-M -L FILE`,\n" " so using both causes one of the specified BED files to be ignored.\n" "\n"); return exit_status; } static int head_usage(FILE *fp, int exit_status) { fprintf(fp, "Usage: samtools head [OPTION]... [FILE]\n" "Options:\n" " -h, --headers INT Display INT header lines [all]\n" " -n, --records INT Display INT alignment record lines [none]\n" ); sam_global_opt_help(fp, "-.--T@-."); return exit_status; } int main_head(int argc, char *argv[]) { static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 'T', '@'), { "headers", required_argument, NULL, 'h' }, { "records", required_argument, NULL, 'n' }, { NULL, 0, NULL, 0 } }; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; int all_headers = 1; uint64_t nheaders = 0; uint64_t nrecords = 0; int c, nargs; while ((c = getopt_long(argc, argv, "h:n:T:@:", lopts, NULL)) >= 0) switch (c) { case 'h': all_headers = 0; nheaders = strtoull(optarg, NULL, 0); break; case 'n': nrecords = strtoull(optarg, NULL, 0); break; default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': return head_usage(samtools_stderr, EXIT_FAILURE); } nargs = argc - optind; if (nargs == 0 && isatty(STDIN_FILENO)) return head_usage(samtools_stdout, EXIT_SUCCESS); else if (nargs > 1) return head_usage(samtools_stderr, EXIT_FAILURE); samFile *fp = NULL; sam_hdr_t *hdr = NULL; kstring_t str = KS_INITIALIZE; bam1_t *b = NULL; const char *fname = (nargs == 1)? argv[optind] : "-"; fp = sam_open_format(fname, "r", &ga.in); if (fp == NULL) { if (strcmp(fname, "-") != 0) print_error_errno("head", "failed to open \"%s\" for reading", fname); else print_error_errno("head", "failed to open standard input for reading"); goto err; } if (ga.nthreads > 0) hts_set_threads(fp, ga.nthreads); hdr = sam_hdr_read(fp); if (hdr == NULL) { if (strcmp(fname, "-") != 0) print_error("head", "failed to read the header from \"%s\"", fname); else print_error("head", "failed to read the header"); goto err; } if (all_headers) { fputs(sam_hdr_str(hdr), samtools_stdout); } else if (nheaders > 0) { const char *text = sam_hdr_str(hdr); const char *lim = text; uint64_t n; for (n = 0; n < nheaders; n++) { lim = strchr(lim, '\n'); if (lim) lim++; else break; } if (lim) fwrite(text, lim - text, 1, samtools_stdout); else fputs(text, samtools_stdout); } if (nrecords > 0) { b = bam_init1(); uint64_t n; int r = 0; for (n = 0; n < nrecords && (r = sam_read1(fp, hdr, b)) >= 0; n++) { if (sam_format1(hdr, b, &str) < 0) { print_error_errno("head", "couldn't format record"); goto err; } samtools_puts(ks_str(&str)); } if (r < -1) { print_error("head", "\"%s\" is truncated", fname); goto err; } bam_destroy1(b); ks_free(&str); } sam_hdr_destroy(hdr); sam_close(fp); sam_global_args_free(&ga); return EXIT_SUCCESS; err: if (fp) sam_close(fp); sam_hdr_destroy(hdr); bam_destroy1(b); ks_free(&str); sam_global_args_free(&ga); return EXIT_FAILURE; } pysam-0.23.0/samtools/sample.c000066400000000000000000000106741475062545500162400ustar00rootroot00000000000000/* sample.c -- group data by sample. Copyright (C) 2010, 2011 Broad Institute. Copyright (C) 2013 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include "sample.h" #include "htslib/khash.h" KHASH_MAP_INIT_STR(sm, int) bam_sample_t *bam_smpl_init(void) { bam_sample_t *s; s = calloc(1, sizeof(bam_sample_t)); s->rg2smid = kh_init(sm); s->sm2id = kh_init(sm); return s; } void bam_smpl_destroy(bam_sample_t *sm) { int i; khint_t k; khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid; if (sm == 0) return; for (i = 0; i < sm->n; ++i) free(sm->smpl[i]); free(sm->smpl); for (k = kh_begin(rg2smid); k != kh_end(rg2smid); ++k) if (kh_exist(rg2smid, k)) free((char*)kh_key(rg2smid, k)); kh_destroy(sm, sm->rg2smid); kh_destroy(sm, sm->sm2id); free(sm); } static void add_pair(bam_sample_t *sm, khash_t(sm) *sm2id, const char *key, const char *val) { khint_t k_rg, k_sm; int ret; khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid; k_rg = kh_get(sm, rg2smid, key); if (k_rg != kh_end(rg2smid)) return; // duplicated @RG-ID k_rg = kh_put(sm, rg2smid, strdup(key), &ret); k_sm = kh_get(sm, sm2id, val); if (k_sm == kh_end(sm2id)) { // absent if (sm->n == sm->m) { sm->m = sm->m? sm->m<<1 : 1; sm->smpl = realloc(sm->smpl, sizeof(char*) * sm->m); } sm->smpl[sm->n] = strdup(val); k_sm = kh_put(sm, sm2id, sm->smpl[sm->n], &ret); kh_val(sm2id, k_sm) = sm->n++; } kh_val(rg2smid, k_rg) = kh_val(sm2id, k_sm); } int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt) { const char *p = txt, *q, *r; kstring_t buf, first_sm; int n = 0; khash_t(sm) *sm2id = (khash_t(sm)*)sm->sm2id; if (txt == 0) { add_pair(sm, sm2id, fn, fn); return 0; } memset(&buf, 0, sizeof(kstring_t)); memset(&first_sm, 0, sizeof(kstring_t)); while ((q = strstr(p, "@RG")) != 0) { p = q + 3; r = q = 0; if ((q = strstr(p, "\tID:")) != 0) q += 4; if ((r = strstr(p, "\tSM:")) != 0) r += 4; if (r && q) { char *u, *v; int oq, or; for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u); for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v); oq = *u; or = *v; *u = *v = '\0'; buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf); add_pair(sm, sm2id, buf.s, r); if ( !first_sm.s ) kputs(r,&first_sm); *u = oq; *v = or; } else break; p = q > r? q : r; ++n; } if (n == 0) add_pair(sm, sm2id, fn, fn); // If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but // use the tag instead. else if ( n==1 && first_sm.s ) add_pair(sm,sm2id,fn,first_sm.s); if ( first_sm.s ) free(first_sm.s); // add_pair(sm, sm2id, fn, fn); free(buf.s); return 0; } int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str) { khint_t k; khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid; if (rg) { str->l = 0; kputs(fn, str); kputc('/', str); kputs(rg, str); k = kh_get(sm, rg2smid, str->s); } else k = kh_get(sm, rg2smid, fn); return k == kh_end(rg2smid)? -1 : kh_val(rg2smid, k); } pysam-0.23.0/samtools/sample.c.pysam.c000066400000000000000000000107311475062545500176030ustar00rootroot00000000000000#include "samtools.pysam.h" /* sample.c -- group data by sample. Copyright (C) 2010, 2011 Broad Institute. Copyright (C) 2013 Genome Research Ltd. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include "sample.h" #include "htslib/khash.h" KHASH_MAP_INIT_STR(sm, int) bam_sample_t *bam_smpl_init(void) { bam_sample_t *s; s = calloc(1, sizeof(bam_sample_t)); s->rg2smid = kh_init(sm); s->sm2id = kh_init(sm); return s; } void bam_smpl_destroy(bam_sample_t *sm) { int i; khint_t k; khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid; if (sm == 0) return; for (i = 0; i < sm->n; ++i) free(sm->smpl[i]); free(sm->smpl); for (k = kh_begin(rg2smid); k != kh_end(rg2smid); ++k) if (kh_exist(rg2smid, k)) free((char*)kh_key(rg2smid, k)); kh_destroy(sm, sm->rg2smid); kh_destroy(sm, sm->sm2id); free(sm); } static void add_pair(bam_sample_t *sm, khash_t(sm) *sm2id, const char *key, const char *val) { khint_t k_rg, k_sm; int ret; khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid; k_rg = kh_get(sm, rg2smid, key); if (k_rg != kh_end(rg2smid)) return; // duplicated @RG-ID k_rg = kh_put(sm, rg2smid, strdup(key), &ret); k_sm = kh_get(sm, sm2id, val); if (k_sm == kh_end(sm2id)) { // absent if (sm->n == sm->m) { sm->m = sm->m? sm->m<<1 : 1; sm->smpl = realloc(sm->smpl, sizeof(char*) * sm->m); } sm->smpl[sm->n] = strdup(val); k_sm = kh_put(sm, sm2id, sm->smpl[sm->n], &ret); kh_val(sm2id, k_sm) = sm->n++; } kh_val(rg2smid, k_rg) = kh_val(sm2id, k_sm); } int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt) { const char *p = txt, *q, *r; kstring_t buf, first_sm; int n = 0; khash_t(sm) *sm2id = (khash_t(sm)*)sm->sm2id; if (txt == 0) { add_pair(sm, sm2id, fn, fn); return 0; } memset(&buf, 0, sizeof(kstring_t)); memset(&first_sm, 0, sizeof(kstring_t)); while ((q = strstr(p, "@RG")) != 0) { p = q + 3; r = q = 0; if ((q = strstr(p, "\tID:")) != 0) q += 4; if ((r = strstr(p, "\tSM:")) != 0) r += 4; if (r && q) { char *u, *v; int oq, or; for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u); for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v); oq = *u; or = *v; *u = *v = '\0'; buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf); add_pair(sm, sm2id, buf.s, r); if ( !first_sm.s ) kputs(r,&first_sm); *u = oq; *v = or; } else break; p = q > r? q : r; ++n; } if (n == 0) add_pair(sm, sm2id, fn, fn); // If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but // use the tag instead. else if ( n==1 && first_sm.s ) add_pair(sm,sm2id,fn,first_sm.s); if ( first_sm.s ) free(first_sm.s); // add_pair(sm, sm2id, fn, fn); free(buf.s); return 0; } int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str) { khint_t k; khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid; if (rg) { str->l = 0; kputs(fn, str); kputc('/', str); kputs(rg, str); k = kh_get(sm, rg2smid, str->s); } else k = kh_get(sm, rg2smid, fn); return k == kh_end(rg2smid)? -1 : kh_val(rg2smid, k); } pysam-0.23.0/samtools/sample.h000066400000000000000000000030301475062545500162310ustar00rootroot00000000000000/* sample.h -- group data by sample. Copyright (C) 2010 Broad Institute. Author: Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef BAM_SAMPLE_H #define BAM_SAMPLE_H #include "htslib/kstring.h" typedef struct { int n, m; char **smpl; void *rg2smid, *sm2id; } bam_sample_t; bam_sample_t *bam_smpl_init(void); int bam_smpl_add(bam_sample_t *sm, const char *abs, const char *txt); int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str); void bam_smpl_destroy(bam_sample_t *sm); #endif pysam-0.23.0/samtools/samtools.h000066400000000000000000000035611475062545500166220ustar00rootroot00000000000000/* samtools.h -- utility routines. Copyright (C) 2013-2015, 2019, 2023 Genome Research Ltd. Author: Petr Danecek Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef SAMTOOLS_H #define SAMTOOLS_H #include "htslib/hts_defs.h" #include "htslib/sam.h" #include "sam_utils.h" const char *samtools_version(void); /* BAM sanitizer options */ #define FIX_POS 2 #define FIX_MQUAL 4 #define FIX_UNMAP 8 #define FIX_CIGAR 16 #define FIX_AUX 32 // default for position sorted data #define FIX_ON (FIX_MQUAL|FIX_UNMAP|FIX_CIGAR|FIX_AUX) #define FIX_ALL 255 // Parses a comma-separated list of "pos", "mqual", "unmap", "cigar", and "aux" // keywords for the bam sanitizer. int bam_sanitize_options(const char *str); // Sanitize a BAM record, using FIX_* bit flags as defined above. // Returns 0 on success, // <0 on failure. int bam_sanitize(sam_hdr_t *h, bam1_t *b, int flags); #endif pysam-0.23.0/samtools/samtools.pysam.c000066400000000000000000000030651475062545500177440ustar00rootroot00000000000000#include #include #include #include #include #include #include "samtools.pysam.h" FILE * samtools_stderr = NULL; FILE * samtools_stdout = NULL; const char * samtools_stdout_fn = NULL; FILE * samtools_set_stderr(int fd) { if (samtools_stderr != NULL) fclose(samtools_stderr); samtools_stderr = fdopen(fd, "w"); return samtools_stderr; } void samtools_close_stderr(void) { fclose(samtools_stderr); samtools_stderr = NULL; } FILE * samtools_set_stdout(int fd) { if (samtools_stdout != NULL) fclose(samtools_stdout); samtools_stdout = fdopen(fd, "w"); if (samtools_stdout == NULL) { fprintf(samtools_stderr, "could not set stdout to fd %i", fd); } return samtools_stdout; } void samtools_set_stdout_fn(const char *fn) { samtools_stdout_fn = fn; } void samtools_close_stdout(void) { fclose(samtools_stdout); samtools_stdout = NULL; } int samtools_puts(const char *s) { if (fputs(s, samtools_stdout) == EOF) return EOF; return putc('\n', samtools_stdout); } static jmp_buf samtools_jmpbuf; static int samtools_status = 0; int samtools_dispatch(int argc, char *argv[]) { /* Reset getopt()/getopt_long() processing. */ #if defined __GLIBC__ optind = 0; #elif defined _OPTRESET || defined _OPTRESET_DECLARED optreset = optind = 1; #else optind = 1; #endif if (setjmp(samtools_jmpbuf) == 0) return samtools_main(argc, argv); else return samtools_status; } void samtools_exit(int status) { samtools_status = status; longjmp(samtools_jmpbuf, 1); } pysam-0.23.0/samtools/samtools.pysam.h000066400000000000000000000035241475062545500177510ustar00rootroot00000000000000#ifndef samtools_PYSAM_H #define samtools_PYSAM_H #include #ifndef __has_attribute #define __has_attribute(attribute) 0 #endif #ifndef PYSAM_NORETURN #if __has_attribute(__noreturn__) || __GNUC__ >= 3 #define PYSAM_NORETURN __attribute__((__noreturn__)) #else #define PYSAM_NORETURN #endif #endif extern FILE * samtools_stderr; extern FILE * samtools_stdout; extern const char * samtools_stdout_fn; /*! set pysam standard error to point to file descriptor Setting the stderr will close the previous stderr. */ FILE * samtools_set_stderr(int fd); /*! set pysam standard output to point to file descriptor Setting the stdout will close the previous stdout. */ FILE * samtools_set_stdout(int fd); /*! set pysam standard output to point to filename */ void samtools_set_stdout_fn(const char * fn); /*! close pysam standard error and set to NULL */ void samtools_close_stderr(void); /*! close pysam standard output and set to NULL */ void samtools_close_stdout(void); int samtools_puts(const char *s); int samtools_dispatch(int argc, char *argv[]); void PYSAM_NORETURN samtools_exit(int status); extern int samtools_main(int argc, char *argv[]); /* Define these only in samtools/bcftools C source, not Cython code. */ #if !(defined CYTHON_ABI || defined CYTHON_HEX_VERSION) /*! Several non-static function names are used in both samtools and bcftools. Both libcsamtools.so and libcbcftools.so are loaded simultaneously, leading to collisions and wrong functions being called. #define these names so the actual symbol names include distinct prefixes to avoid collisions. */ #define main_consensus samtools_main_consensus #define main_reheader samtools_main_reheader #define bam_smpl_init samtools_bam_smpl_init #define bam_smpl_destroy samtools_bam_smpl_destroy #define read_file_list samtools_read_file_list #endif #endif pysam-0.23.0/samtools/splaysort.h000066400000000000000000000344351475062545500170250ustar00rootroot00000000000000/* The MIT License Copyright (c) 2021 Genome Research Ltd (GRL). Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef SPLAYSORT_H #define SPLAYSORT_H #define SPLAYSORT_INIT(name, type_t, __sort_lt) \ typedef struct splaynode_##name { \ type_t value; \ struct splaynode_##name *left; \ struct splaynode_##name *right; \ struct splaynode_##name *parent; \ } splaynode_##name; \ \ void rotate_left_##name(splaynode_##name *node); \ void rotate_right_##name(splaynode_##name *node); \ int splay_sort_##name(size_t n, type_t array[] ); \ int splay_flatten_##name(splaynode_##name *node, type_t dest[], size_t n);\ splaynode_##name *splay_tree_##name(splaynode_##name *node); \ splaynode_##name *splay_insert_##name(splaynode_##name *node, \ type_t value, \ splaynode_##name *node_ptr); \ \ void rotate_left_##name(splaynode_##name *node) { \ splaynode_##name *parent = node->parent; \ splaynode_##name *grandparent = parent->parent; \ parent->right = node->left; \ if (node->left != NULL) { \ node->left->parent = parent; \ } \ node->left = parent; \ parent->parent = node; \ node->parent = grandparent; \ \ if (grandparent != NULL) { \ if (grandparent->left == parent) { \ grandparent->left = node; \ } else { \ grandparent->right = node; \ } \ } \ } \ \ void rotate_right_##name(splaynode_##name *node) { \ splaynode_##name *parent = node->parent; \ splaynode_##name *grandparent = parent->parent; \ parent->left = node->right; \ \ if (node->right != NULL) { \ node->right->parent = parent; \ } \ node->right = parent; \ parent->parent = node; \ node->parent = grandparent; \ \ if (grandparent != NULL) { \ if (grandparent->left == parent) { \ grandparent->left = node; \ } else { \ grandparent->right = node; \ } \ } \ } \ int splay_sort_##name(size_t n, type_t array[] ) { \ if (n < 1) { \ return 0; \ } \ int i; \ splaynode_##name *node_pool = malloc(sizeof(splaynode_##name) * n); \ if (node_pool == NULL) return -1; \ splaynode_##name *head = node_pool; \ head->value = array[0]; \ head->left = NULL; head->right = NULL; head->parent = NULL; \ for (i = 1; i < n; i++) { \ head = splay_insert_##name(head, array[i], node_pool + i ); \ } \ \ if (splay_flatten_##name(head, array, n) == -1) { \ free(node_pool); \ return -1; \ } \ free(node_pool); \ return 0; \ } \ \ int splay_flatten_##name(splaynode_##name *head, type_t *dest, size_t n) {\ int sp = 0, i = 0; \ splaynode_##name *current = head; \ splaynode_##name **stack = malloc(sizeof(current)*n); \ if (stack == NULL) return -1; \ \ do { \ while (current != NULL && sp < n) { \ stack[sp++] = current; \ current = current->left; \ } \ if (sp != 0) { \ sp--; \ dest[i++] = stack[sp]->value; \ current = stack[sp]->right; \ } \ } while (!(current == NULL && sp == 0)); \ \ free(stack); \ return 0; \ } \ splaynode_##name *splay_insert_##name(splaynode_##name *head, \ type_t value, \ splaynode_##name *node_ptr) { \ splaynode_##name *parent = NULL; \ while (head != NULL) { \ parent = head; \ if (__sort_lt(value, head->value)) { \ head = head->left; \ } else { \ head = head->right; \ } \ } \ splaynode_##name *new_node = node_ptr; \ new_node->value = value; \ new_node->left = NULL; \ new_node->right = NULL; \ new_node->parent = parent; \ if (parent) { \ if (__sort_lt(value, parent->value)) { \ parent->left = new_node; \ } else { \ parent->right = new_node; \ } \ } \ new_node = splay_tree_##name(new_node); \ return new_node; \ } \ \ splaynode_##name *splay_tree_##name(splaynode_##name *node) { \ splaynode_##name *parent = node->parent; \ \ if (node->parent == NULL) { \ return node; \ } \ if (node == parent->left) { \ if (parent->parent == NULL) { \ /* zig */ \ rotate_right_##name(node); \ } else if (parent->parent->left == parent) { \ /* left zig zig */ \ rotate_right_##name(node); \ rotate_right_##name(node); \ } else { \ /* right left zig zag */ \ rotate_right_##name(node); \ rotate_left_##name(node); \ } \ } else { \ if (parent->parent == NULL) { \ /* zig */ \ rotate_left_##name(node); \ } else if (parent->parent->right == parent) { \ /* right zig zig */ \ rotate_left_##name(node); \ rotate_left_##name(node); \ } else { \ /* left right zig zag */ \ rotate_left_##name(node); \ rotate_right_##name(node); \ } \ } \ \ if (node->parent != NULL) { \ return splay_tree_##name(node); \ } \ return node; \ } \ #define splaysort(name, n, array) splay_sort_##name(n, array) #endif pysam-0.23.0/samtools/stats.c000066400000000000000000003256251475062545500161220ustar00rootroot00000000000000/* stats.c -- This is the former bamcheck integrated into samtools/htslib. Copyright (C) 2012-2024 Genome Research Ltd. Author: Petr Danecek Author: Sam Nicholls Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Assumptions, approximations and other issues: - GC-depth graph does not split reads, the starting position determines which bin is incremented. There are small overlaps between bins (max readlen-1). However, the bins are big (20k). - coverage distribution ignores softclips and deletions - some stats require sorted BAMs - GC content graph can have an untidy, step-like pattern when BAM contains multiple read lengths. - 'bases mapped' (stats->nbases_mapped) is calculated from read lengths given by BAM (core.l_qseq) - With the -t option, the whole reads are used. Except for the number of mapped bases (cigar) counts, no splicing is done, no indels or soft clips are considered, even small overlap is good enough to include the read in the stats. - GC content of reads not calculated for "=" sequences */ #include #include // for isatty() #include #include #include #include #include #include #include #include #include #include #include // for crc32 #include #include #include #include #include "samtools.h" #include #include #include "stats_isize.h" #include "sam_opts.h" #include "bedidx.h" #define BWA_MIN_RDLEN 35 #define DEFAULT_CHUNK_NO 8 #define DEFAULT_PAIR_MAX 10000 #define ERROR_LIMIT 200 // From the spec // If 0x4 is set, no assumptions can be made about RNAME, POS, CIGAR, MAPQ, bits 0x2, 0x10, 0x100 and 0x800, and the bit 0x20 of the previous read in the template. #define IS_PAIRED(bam) ((bam)->core.flag&BAM_FPAIRED) #define IS_PAIRED_AND_MAPPED(bam) (((bam)->core.flag&BAM_FPAIRED) && !((bam)->core.flag&BAM_FUNMAP) && !((bam)->core.flag&BAM_FMUNMAP)) #define IS_PROPERLYPAIRED(bam) (((bam)->core.flag&(BAM_FPAIRED|BAM_FPROPER_PAIR)) == (BAM_FPAIRED|BAM_FPROPER_PAIR) && !((bam)->core.flag&BAM_FUNMAP)) #define IS_UNMAPPED(bam) ((bam)->core.flag&BAM_FUNMAP) #define IS_REVERSE(bam) ((bam)->core.flag&BAM_FREVERSE) #define IS_MATE_REVERSE(bam) ((bam)->core.flag&BAM_FMREVERSE) #define IS_READ1(bam) ((bam)->core.flag&BAM_FREAD1) #define IS_READ2(bam) ((bam)->core.flag&BAM_FREAD2) #define IS_DUP(bam) ((bam)->core.flag&BAM_FDUP) #define IS_ORIGINAL(bam) (((bam)->core.flag&(BAM_FSECONDARY|BAM_FSUPPLEMENTARY)) == 0) #define READ_ORDER_NONE 0 #define READ_ORDER_FIRST 1 #define READ_ORDER_LAST 2 #define READ_ORDER_MIDDLE 3 #define REG_INC 100 #define POS_INC 1000 // The GC-depth graph works as follows: split the reference sequence into // segments and calculate GC content and depth in each bin. Then sort // these segments by their GC and plot the depth distribution by means // of 10th, 25th, etc. depth percentiles. typedef struct { float gc; uint32_t depth; } gc_depth_t; // For coverage distribution, a simple pileup typedef struct { hts_pos_t pos; int size, start; int *buffer; } round_buffer_t; typedef struct { int npos, mpos, cpos; hts_pair_pos_t *pos; } regions_t; typedef struct { uint64_t a; uint64_t c; uint64_t g; uint64_t t; uint64_t n; uint64_t other; } acgtno_count_t; typedef struct { char tag_name[3]; char qual_name[3]; uint32_t nbases; int32_t tag_sep; // Index of the separator (if present) int32_t max_qual; uint32_t offset; // Where the tag stats info is located in the allocated memory } barcode_info_t; typedef struct { // Auxiliary data int flag_require, flag_filter; faidx_t *fai; // Reference sequence for GC-depth graph int argc; // Command line arguments to be printed on the output char **argv; int gcd_bin_size; // The size of GC-depth bin int nisize; // The maximum insert size that the allocated array can hold - 0 indicates no limit int trim_qual; // bwa trim quality float isize_main_bulk; // There are always some unrealistically big insert sizes, report only the main part int cov_min,cov_max,cov_step; // Minimum, maximum coverage and size of the coverage bins samFile* sam; sam_hdr_t* sam_header; // Filters int filter_readlen; // Misc char *split_tag; // Tag on which to perform stats splitting char *split_prefix; // Path or string prefix for filenames created when splitting int remove_overlaps; int cov_threshold; } stats_info_t; typedef struct { // Dimensions of the quality histogram holder (quals_1st,quals_2nd), GC content holder (gc_1st,gc_2nd), // insert size histogram holder int nquals; // The number of quality bins int nbases; // The maximum sequence length the allocated array can hold int ngc; // The size of gc_1st and gc_2nd int nindels; // The maximum indel length for indel distribution // Arrays for the histogram data uint64_t *quals_1st, *quals_2nd; uint64_t *gc_1st, *gc_2nd; acgtno_count_t *acgtno_cycles_1st, *acgtno_cycles_2nd; acgtno_count_t *acgtno_revcomp; uint64_t *read_lengths, *read_lengths_1st, *read_lengths_2nd; uint64_t *insertions, *deletions; uint64_t *ins_cycles_1st, *ins_cycles_2nd, *del_cycles_1st, *del_cycles_2nd; isize_t *isize; uint64_t* mapping_qualities; // The extremes encountered int max_len; // Maximum read length int max_len_1st; // Maximum read length for forward reads int max_len_2nd; // Maximum read length for reverse reads int max_qual; // Maximum quality int is_sorted; // Summary numbers uint64_t total_len; uint64_t total_len_1st; uint64_t total_len_2nd; uint64_t total_len_dup; uint64_t nreads_1st; uint64_t nreads_2nd; uint64_t nreads_other; uint64_t nreads_filtered; uint64_t nreads_dup; uint64_t nreads_unmapped; uint64_t nreads_single_mapped; uint64_t nreads_paired_and_mapped; uint64_t nreads_properly_paired; uint64_t nreads_paired_tech; uint64_t nreads_anomalous; uint64_t nreads_mq0; uint64_t nbases_mapped; uint64_t nbases_mapped_cigar; uint64_t nbases_trimmed; // bwa trimmed bases uint64_t nmismatches; uint64_t nreads_QCfailed, nreads_secondary, nreads_supplementary; struct { uint32_t names, reads, quals; } checksum; // GC-depth related data uint32_t ngcd, igcd; // The maximum number of GC depth bins and index of the current bin gc_depth_t *gcd; // The GC-depth bins holder int32_t tid; // Position of the current bin hts_pos_t gcd_pos, pos; // Position of the last read // Coverage distribution related data int ncov; // The number of coverage bins uint64_t *cov; // The coverage frequencies round_buffer_t cov_rbuf; // Pileup round buffer // Mismatches by read cycle uint8_t *rseq_buf; // A buffer for reference sequence to check the mismatches against int mrseq_buf; // The size of the buffer hts_pos_t rseq_pos; // The coordinate of the first base in the buffer int64_t nrseq_buf; // The used part of the buffer uint64_t *mpc_buf; // Mismatches per cycle // Target regions int nregions; hts_pos_t reg_from, reg_to; regions_t *regions; // Auxiliary data double sum_qual; // For calculating average quality value void *rg_hash; // Read groups to include, the array is null-terminated // Split char* split_name; stats_info_t* info; // Pointer to options and settings struct hts_pair_pos_t *chunks; uint32_t nchunks; uint32_t pair_count; // Number of active pairs in the pairing hash table uint64_t target_count; // Number of bases covered by the target file uint32_t last_pair_tid; uint32_t last_read_flush; // Barcode statistics acgtno_count_t *acgtno_barcode; uint64_t *quals_barcode; barcode_info_t *tags_barcode; uint32_t ntags; uint32_t error_number; } stats_t; KHASH_MAP_INIT_STR(c2stats, stats_t*) typedef struct { uint32_t first; // 1 - first read, 2 - second read uint32_t n, m; // number of chunks, allocated chunks hts_pair_pos_t *chunks; // chunk array of size m } pair_t; KHASH_MAP_INIT_STR(qn2pair, pair_t*) KHASH_SET_INIT_STR(rg) static void HTS_NORETURN error(const char *format, ...); int is_in_regions(bam1_t *bam_line, stats_t *stats); void realloc_buffers(stats_t *stats, int seq_len); static int regions_lt(const void *r1, const void *r2) { int64_t from_diff = ((hts_pair_pos_t *)r1)->beg - ((hts_pair_pos_t *)r2)->beg; int64_t to_diff = ((hts_pair_pos_t *)r1)->end - ((hts_pair_pos_t *)r2)->end; return from_diff > 0 ? 1 : from_diff < 0 ? -1 : to_diff > 0 ? 1 : to_diff < 0 ? -1 : 0; } // Coverage distribution methods static inline int coverage_idx(int min, int max, int n, int step, int depth) { if ( depth < min ) return 0; if ( depth > max ) return n-1; return 1 + (depth - min) / step; } static inline int round_buffer_lidx2ridx(int offset, int size, hts_pos_t refpos, hts_pos_t pos) { return (offset + (pos-refpos) % size) % size; } void round_buffer_flush(stats_t *stats, hts_pos_t pos) { int ibuf,idp; if ( pos==stats->cov_rbuf.pos ) return; hts_pos_t new_pos = pos; if ( pos==-1 || pos - stats->cov_rbuf.pos >= stats->cov_rbuf.size ) { // Flush the whole buffer, but in sequential order, pos = stats->cov_rbuf.pos + stats->cov_rbuf.size - 1; } if ( pos < stats->cov_rbuf.pos ) error("Expected coordinates in ascending order, got %"PRIhts_pos" after %"PRIhts_pos"\n", pos, stats->cov_rbuf.pos); int ifrom = stats->cov_rbuf.start; int ito = round_buffer_lidx2ridx(stats->cov_rbuf.start, stats->cov_rbuf.size, stats->cov_rbuf.pos, pos-1); if ( ifrom>ito ) { for (ibuf=ifrom; ibufcov_rbuf.size; ibuf++) { if ( !stats->cov_rbuf.buffer[ibuf] ) continue; idp = coverage_idx(stats->info->cov_min,stats->info->cov_max,stats->ncov,stats->info->cov_step,stats->cov_rbuf.buffer[ibuf]); stats->cov[idp]++; stats->cov_rbuf.buffer[ibuf] = 0; } ifrom = 0; } for (ibuf=ifrom; ibuf<=ito; ibuf++) { if ( !stats->cov_rbuf.buffer[ibuf] ) continue; idp = coverage_idx(stats->info->cov_min,stats->info->cov_max,stats->ncov,stats->info->cov_step,stats->cov_rbuf.buffer[ibuf]); stats->cov[idp]++; stats->cov_rbuf.buffer[ibuf] = 0; } stats->cov_rbuf.start = (new_pos==-1) ? 0 : round_buffer_lidx2ridx(stats->cov_rbuf.start, stats->cov_rbuf.size, stats->cov_rbuf.pos, pos); stats->cov_rbuf.pos = new_pos; } /** * [from, to) - 0 based half-open */ static void round_buffer_insert_read(round_buffer_t *rbuf, hts_pos_t from, hts_pos_t to) { if ( to-from > rbuf->size ) error("The read length too big (%"PRIhts_pos"), please increase the buffer length (currently %d)\n", to-from, rbuf->size); if ( from < rbuf->pos ) error("The reads are not sorted (%"PRIhts_pos" comes after %"PRIhts_pos").\n", from, rbuf->pos); int ifrom, ito, ibuf; ifrom = round_buffer_lidx2ridx(rbuf->start, rbuf->size, rbuf->pos, from); ito = round_buffer_lidx2ridx(rbuf->start, rbuf->size, rbuf->pos, to); if ( ifrom>ito ) { for (ibuf=ifrom; ibufsize; ibuf++) rbuf->buffer[ibuf]++; ifrom = 0; } for (ibuf=ifrom; ibufbuffer[ibuf]++; } // Calculate the number of bases in the read trimmed by BWA int bwa_trim_read(int trim_qual, uint8_t *quals, int len, int reverse) { if ( lenmax_sum ) { max_sum = sum; // This is the correct way, but bwa clips from some reason one base less // max_l = l+1; max_l = l; } } return max_l; } void count_indels(stats_t *stats,bam1_t *bam_line) { int is_fwd = IS_REVERSE(bam_line) ? 0 : 1; uint32_t order = IS_PAIRED(bam_line) ? (IS_READ1(bam_line) ? READ_ORDER_FIRST : 0) + (IS_READ2(bam_line) ? READ_ORDER_LAST : 0) : READ_ORDER_FIRST; int icig; int icycle = 0; int read_len = bam_line->core.l_qseq; for (icig=0; icigcore.n_cigar; icig++) { int cig = bam_cigar_op(bam_get_cigar(bam_line)[icig]); int ncig = bam_cigar_oplen(bam_get_cigar(bam_line)[icig]); if ( !ncig ) continue; // curiously, this can happen: 0D if ( cig==BAM_CINS ) { int idx = is_fwd ? icycle : read_len-icycle-ncig; if ( idx<0 ) error("FIXME: read_len=%d vs icycle=%d\n", read_len,icycle); if ( idx >= stats->nbases || idx<0 ) error("FIXME: %d vs %d, %s:%"PRIhts_pos" %s\n", idx, stats->nbases, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line)); if ( order == READ_ORDER_FIRST ) stats->ins_cycles_1st[idx]++; if ( order == READ_ORDER_LAST ) stats->ins_cycles_2nd[idx]++; icycle += ncig; if ( ncig<=stats->nindels ) stats->insertions[ncig-1]++; continue; } if ( cig==BAM_CDEL ) { int idx = is_fwd ? icycle-1 : read_len-icycle-1; if ( idx<0 ) continue; // discard meaningless deletions if ( idx >= stats->nbases ) error("FIXME: %d vs %d\n", idx,stats->nbases); if ( order == READ_ORDER_FIRST ) stats->del_cycles_1st[idx]++; if ( order == READ_ORDER_LAST ) stats->del_cycles_2nd[idx]++; if ( ncig<=stats->nindels ) stats->deletions[ncig-1]++; continue; } if ( cig!=BAM_CREF_SKIP && cig!=BAM_CHARD_CLIP && cig!=BAM_CPAD ) icycle += ncig; } } int unclipped_length(bam1_t *bam_line) { int icig, read_len = bam_line->core.l_qseq; for (icig=0; icigcore.n_cigar; icig++) { int cig = bam_cigar_op(bam_get_cigar(bam_line)[icig]); if ( cig==BAM_CHARD_CLIP ) read_len += bam_cigar_oplen(bam_get_cigar(bam_line)[icig]); } return read_len; } void count_mismatches_per_cycle(stats_t *stats, bam1_t *bam_line, int read_len) { int is_fwd = IS_REVERSE(bam_line) ? 0 : 1; int icig, iread=0, icycle=0; hts_pos_t iref = bam_line->core.pos - stats->rseq_pos; uint8_t *read = bam_get_seq(bam_line); uint8_t *quals = bam_get_qual(bam_line); uint64_t *mpc_buf = stats->mpc_buf; for (icig=0; icigcore.n_cigar; icig++) { int cig = bam_cigar_op(bam_get_cigar(bam_line)[icig]); int ncig = bam_cigar_oplen(bam_get_cigar(bam_line)[icig]); if ( cig==BAM_CINS ) { iread += ncig; icycle += ncig; continue; } if ( cig==BAM_CDEL ) { iref += ncig; continue; } if ( cig==BAM_CSOFT_CLIP ) { icycle += ncig; // Soft-clips are present in the sequence, but the position of the read marks a start of the sequence after clipping // iref += ncig; iread += ncig; continue; } if ( cig==BAM_CHARD_CLIP ) { icycle += ncig; continue; } // Ignore H and N CIGARs. The letter are inserted e.g. by TopHat and often require very large // chunk of refseq in memory. Not very frequent and not noticeable in the stats. if ( cig==BAM_CREF_SKIP || cig==BAM_CHARD_CLIP || cig==BAM_CPAD ) continue; if ( cig!=BAM_CMATCH && cig!=BAM_CEQUAL && cig!=BAM_CDIFF ) // not relying on precalculated diffs error("TODO: cigar %d, %s:%"PRIhts_pos" %s\n", cig, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line)); if ( ncig+iref > stats->nrseq_buf ) error("FIXME: %d+%"PRIhts_pos" > %"PRId64", %s, %s:%"PRIhts_pos"\n", ncig, iref, stats->nrseq_buf, bam_get_qname(bam_line), sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1); int im; for (im=0; imrseq_buf[iref]; // ---------------15 // =ACMGRSVTWYHKDBN if ( cread==15 ) { int idx = is_fwd ? icycle : read_len-icycle-1; if ( idx>stats->max_len ) error("mpc: %d>%d\n",idx,stats->max_len); idx = idx*stats->nquals; if ( idx>=stats->nquals*stats->nbases ) error("FIXME: mpc_buf overflow\n"); mpc_buf[idx]++; } else if ( cref && cread && cref!=cread ) { uint8_t qual = quals[iread] + 1; if ( qual>=stats->nquals ) error("TODO: quality too high %d>=%d (%s %"PRIhts_pos" %s)\n", qual, stats->nquals, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line)); int idx = is_fwd ? icycle : read_len-icycle-1; if ( idx>stats->max_len ) error("mpc: %d>%d (%s %"PRIhts_pos" %s)\n", idx, stats->max_len, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line)); idx = idx*stats->nquals + qual; if ( idx>=stats->nquals*stats->nbases ) error("FIXME: mpc_buf overflow\n"); mpc_buf[idx]++; } iref++; iread++; icycle++; } } } void read_ref_seq(stats_t *stats, int32_t tid, hts_pos_t pos, hts_pos_t end) { int i; hts_pos_t fai_ref_len; char *fai_ref; if (end < pos+stats->mrseq_buf-1) end = pos+stats->mrseq_buf-1; else if (stats->mrseq_buf < end - pos) { size_t sz = end - pos; uint8_t *new_rseq = realloc(stats->rseq_buf, sz); if (!new_rseq) error("Couldn't expand the reference sequence buffer\n"); stats->rseq_buf = new_rseq; stats->mrseq_buf = sz; } fai_ref = faidx_fetch_seq64(stats->info->fai, sam_hdr_tid2name(stats->info->sam_header, tid), pos, pos+stats->mrseq_buf-1, &fai_ref_len); if ( fai_ref_len < 0 ) error("Failed to fetch the sequence \"%s\"\n", sam_hdr_tid2name(stats->info->sam_header, tid)); uint8_t *ptr = stats->rseq_buf; for (i=0; imrseq_buf ) memset(ptr,0, stats->mrseq_buf - fai_ref_len); stats->nrseq_buf = fai_ref_len; stats->rseq_pos = pos; stats->tid = tid; } float fai_gc_content(stats_t *stats, hts_pos_t pos, int len) { uint32_t gc,count,c; hts_pos_t i = pos - stats->rseq_pos, ito = i + len; assert( i>=0 ); if ( ito > stats->nrseq_buf ) ito = stats->nrseq_buf; // Count GC content gc = count = 0; for (; irseq_buf[i]; if ( c==2 || c==4 ) { gc++; count++; } else if ( c==1 || c==8 ) count++; } return count ? (float)gc/count : 0; } void realloc_rseq_buffer(stats_t *stats) { int n = stats->nbases*10; if ( stats->info->gcd_bin_size > n ) n = stats->info->gcd_bin_size; if ( stats->mrseq_bufrseq_buf = realloc(stats->rseq_buf,sizeof(uint8_t)*n); if (!stats->rseq_buf) { error("Could not reallocate reference sequence buffer"); } stats->mrseq_buf = n; } } void realloc_gcd_buffer(stats_t *stats, int seq_len) { hts_expand0(gc_depth_t,stats->igcd+1,stats->ngcd,stats->gcd); realloc_rseq_buffer(stats); } void realloc_buffers(stats_t *stats, int seq_len) { int n = 2*(1 + seq_len - stats->nbases) + stats->nbases; stats->quals_1st = realloc(stats->quals_1st, n*stats->nquals*sizeof(uint64_t)); if ( !stats->quals_1st ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*stats->nquals*sizeof(uint64_t)); memset(stats->quals_1st + stats->nbases*stats->nquals, 0, (n-stats->nbases)*stats->nquals*sizeof(uint64_t)); stats->quals_2nd = realloc(stats->quals_2nd, n*stats->nquals*sizeof(uint64_t)); if ( !stats->quals_2nd ) error("Could not realloc buffers, the sequence too long: %d (2x%ld)\n", seq_len,n*stats->nquals*sizeof(uint64_t)); memset(stats->quals_2nd + stats->nbases*stats->nquals, 0, (n-stats->nbases)*stats->nquals*sizeof(uint64_t)); if ( stats->mpc_buf ) { stats->mpc_buf = realloc(stats->mpc_buf, n*stats->nquals*sizeof(uint64_t)); if ( !stats->mpc_buf ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*stats->nquals*sizeof(uint64_t)); memset(stats->mpc_buf + stats->nbases*stats->nquals, 0, (n-stats->nbases)*stats->nquals*sizeof(uint64_t)); } stats->acgtno_cycles_1st = realloc(stats->acgtno_cycles_1st, n*sizeof(acgtno_count_t)); if ( !stats->acgtno_cycles_1st ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len, n*sizeof(acgtno_count_t)); memset(stats->acgtno_cycles_1st + stats->nbases, 0, (n-stats->nbases)*sizeof(acgtno_count_t)); stats->acgtno_cycles_2nd = realloc(stats->acgtno_cycles_2nd, n*sizeof(acgtno_count_t)); if ( !stats->acgtno_cycles_2nd ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len, n*sizeof(acgtno_count_t)); memset(stats->acgtno_cycles_2nd + stats->nbases, 0, (n-stats->nbases)*sizeof(acgtno_count_t)); stats->acgtno_revcomp = realloc(stats->acgtno_revcomp, n*sizeof(acgtno_count_t)); if ( !stats->acgtno_revcomp ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len, n*sizeof(acgtno_count_t)); memset(stats->acgtno_revcomp + stats->nbases, 0, (n-stats->nbases)*sizeof(acgtno_count_t)); stats->read_lengths = realloc(stats->read_lengths, n*sizeof(uint64_t)); if ( !stats->read_lengths ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t)); memset(stats->read_lengths + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->read_lengths_1st = realloc(stats->read_lengths_1st, n*sizeof(uint64_t)); if ( !stats->read_lengths_1st ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t)); memset(stats->read_lengths_1st + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->read_lengths_2nd = realloc(stats->read_lengths_2nd, n*sizeof(uint64_t)); if ( !stats->read_lengths_2nd ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t)); memset(stats->read_lengths_2nd + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->insertions = realloc(stats->insertions, n*sizeof(uint64_t)); if ( !stats->insertions ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t)); memset(stats->insertions + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->deletions = realloc(stats->deletions, n*sizeof(uint64_t)); if ( !stats->deletions ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t)); memset(stats->deletions + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->ins_cycles_1st = realloc(stats->ins_cycles_1st, (n+1)*sizeof(uint64_t)); if ( !stats->ins_cycles_1st ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t)); memset(stats->ins_cycles_1st + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->ins_cycles_2nd = realloc(stats->ins_cycles_2nd, (n+1)*sizeof(uint64_t)); if ( !stats->ins_cycles_2nd ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t)); memset(stats->ins_cycles_2nd + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->del_cycles_1st = realloc(stats->del_cycles_1st, (n+1)*sizeof(uint64_t)); if ( !stats->del_cycles_1st ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t)); memset(stats->del_cycles_1st + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->del_cycles_2nd = realloc(stats->del_cycles_2nd, (n+1)*sizeof(uint64_t)); if ( !stats->del_cycles_2nd ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t)); memset(stats->del_cycles_2nd + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->nbases = n; // Realloc the coverage distribution buffer int *rbuffer = calloc(sizeof(int),seq_len*5); if (!rbuffer) { error("Could not allocate coverage distribution buffer"); } n = stats->cov_rbuf.size-stats->cov_rbuf.start; memcpy(rbuffer,stats->cov_rbuf.buffer+stats->cov_rbuf.start,n); if ( stats->cov_rbuf.start>1 ) memcpy(rbuffer+n,stats->cov_rbuf.buffer,stats->cov_rbuf.start); stats->cov_rbuf.start = 0; free(stats->cov_rbuf.buffer); stats->cov_rbuf.buffer = rbuffer; stats->cov_rbuf.size = seq_len*5; realloc_rseq_buffer(stats); } void update_checksum(bam1_t *bam_line, stats_t *stats) { uint8_t *name = (uint8_t*) bam_get_qname(bam_line); int len = 0; while ( name[len] ) len++; stats->checksum.names += crc32(0L, name, len); int seq_len = bam_line->core.l_qseq; if ( !seq_len ) return; uint8_t *seq = bam_get_seq(bam_line); stats->checksum.reads += crc32(0L, seq, (seq_len+1)/2); uint8_t *qual = bam_get_qual(bam_line); stats->checksum.quals += crc32(0L, qual, (seq_len+1)/2); } // Collect statistics about the barcode tags specified by init_barcode_tags method static void collect_barcode_stats(bam1_t* bam_line, stats_t* stats) { uint32_t nbases, tag, i; acgtno_count_t *acgtno; uint64_t *quals; int32_t *separator, *maxqual; for (tag = 0; tag < stats->ntags; tag++) { const char *barcode_tag = stats->tags_barcode[tag].tag_name, *qual_tag = stats->tags_barcode[tag].qual_name; uint8_t* bc = bam_aux_get(bam_line, barcode_tag); if (!bc) continue; char* barcode = bam_aux2Z(bc); if (!barcode) continue; uint32_t barcode_len = strlen(barcode); if (!barcode_len) { continue; //consider 0 size barcode same as no barcode - avoids issues with realloc below } if (!stats->tags_barcode[tag].nbases) { // tag seen for the first time uint32_t offset = 0; for (i = 0; i < stats->ntags; i++) offset += stats->tags_barcode[i].nbases; stats->tags_barcode[tag].offset = offset; stats->tags_barcode[tag].nbases = barcode_len; stats->acgtno_barcode = realloc(stats->acgtno_barcode, (offset + barcode_len) * sizeof(acgtno_count_t)); stats->quals_barcode = realloc(stats->quals_barcode, (offset + barcode_len) * stats->nquals * sizeof(uint64_t)); if (!stats->acgtno_barcode || !stats->quals_barcode) error("Error allocating memory. Aborting!\n"); memset(stats->acgtno_barcode + offset, 0, barcode_len*sizeof(acgtno_count_t)); memset(stats->quals_barcode + offset*stats->nquals, 0, barcode_len*stats->nquals*sizeof(uint64_t)); } nbases = stats->tags_barcode[tag].nbases; if (barcode_len > nbases) { fprintf(stderr, "Barcodes with tag %s differ in length at sequence '%s'\n", barcode_tag, bam_get_qname(bam_line)); continue; } acgtno = stats->acgtno_barcode + stats->tags_barcode[tag].offset; quals = stats->quals_barcode + stats->tags_barcode[tag].offset*stats->nquals; maxqual = &stats->tags_barcode[tag].max_qual; separator = &stats->tags_barcode[tag].tag_sep; int error_flag = 0; for (i = 0; i < barcode_len; i++) { switch (barcode[i]) { case 'A': acgtno[i].a++; break; case 'C': acgtno[i].c++; break; case 'G': acgtno[i].g++; break; case 'T': acgtno[i].t++; break; case 'N': acgtno[i].n++; break; default: if (*separator >= 0) { if (*separator != i) { if (stats->error_number < ERROR_LIMIT) { fprintf(stderr, "Barcode separator for tag %s is in a different position or wrong barcode content('%s') at sequence '%s'\n", barcode_tag, barcode, bam_get_qname(bam_line)); stats->error_number++; } error_flag = 1; } } else { *separator = i; } } /* don't process the rest of the tag bases */ if (error_flag) break; } /* skip to the next tag */ if (error_flag) continue; uint8_t* qt = bam_aux_get(bam_line, qual_tag); if (!qt) continue; char* barqual = bam_aux2Z(qt); if (!barqual) continue; uint32_t barqual_len = strlen(barqual); if (barqual_len == barcode_len) { for (i = 0; i < barcode_len; i++) { int32_t qual = (int32_t)barqual[i] - '!'; // Phred + 33 if (qual >= 0 && qual < stats->nquals) { quals[i * stats->nquals + qual]++; if (qual > *maxqual) *maxqual = qual; } } } else { if (stats->error_number++ < ERROR_LIMIT) { fprintf(stderr, "%s length and %s length don't match for sequence '%s'\n", barcode_tag, qual_tag, bam_get_qname(bam_line)); } } } } // These stats should only be calculated for the original reads ignoring // supplementary artificial reads otherwise we'll accidentally double count void collect_orig_read_stats(bam1_t *bam_line, stats_t *stats, int* gc_count_out) { int seq_len = bam_line->core.l_qseq; stats->total_len += seq_len; // This ignores clipping so only count primary if ( bam_line->core.flag & BAM_FQCFAIL ) stats->nreads_QCfailed++; if ( bam_line->core.flag & BAM_FPAIRED ) stats->nreads_paired_tech++; uint32_t order = IS_PAIRED(bam_line) ? (IS_READ1(bam_line) ? READ_ORDER_FIRST : 0) + (IS_READ2(bam_line) ? READ_ORDER_LAST : 0) : READ_ORDER_FIRST; // Count GC and ACGT per cycle. Note that cycle is approximate, clipping is ignored uint8_t *seq = bam_get_seq(bam_line); int i, read_cycle, gc_count = 0, reverse = IS_REVERSE(bam_line); acgtno_count_t *acgtno_cycles = (order == READ_ORDER_FIRST) ? stats->acgtno_cycles_1st : (order == READ_ORDER_LAST) ? stats->acgtno_cycles_2nd : NULL ; if (acgtno_cycles) { for (i=0; iacgtno_revcomp[ read_cycle ].t++ : stats->acgtno_revcomp[ read_cycle ].a++; break; case 2: acgtno_cycles[ read_cycle ].c++; reverse ? stats->acgtno_revcomp[ read_cycle ].g++ : stats->acgtno_revcomp[ read_cycle ].c++; gc_count++; break; case 4: acgtno_cycles[ read_cycle ].g++; reverse ? stats->acgtno_revcomp[ read_cycle ].c++ : stats->acgtno_revcomp[ read_cycle ].g++; gc_count++; break; case 8: reverse ? stats->acgtno_revcomp[ read_cycle ].a++ : stats->acgtno_revcomp[ read_cycle ].t++; acgtno_cycles[ read_cycle ].t++; break; case 15: acgtno_cycles[ read_cycle ].n++; break; default: /* * count "=" sequences in "other" along * with MRSVWYHKDB ambiguity codes */ acgtno_cycles[ read_cycle ].other++; break; } } } int gc_idx_min = gc_count*(stats->ngc-1)/seq_len; int gc_idx_max = (gc_count+1)*(stats->ngc-1)/seq_len; if ( gc_idx_max >= stats->ngc ) gc_idx_max = stats->ngc - 1; // Determine which array (1st or 2nd read) will these stats go to, // trim low quality bases from end the same way BWA does, // fill GC histogram uint64_t *quals = NULL; uint8_t *bam_quals = bam_get_qual(bam_line); switch (order) { case READ_ORDER_FIRST: quals = stats->quals_1st; stats->nreads_1st++; stats->total_len_1st += seq_len; for (i=gc_idx_min; igc_1st[i]++; break; case READ_ORDER_LAST: quals = stats->quals_2nd; stats->nreads_2nd++; stats->total_len_2nd += seq_len; for (i=gc_idx_min; igc_2nd[i]++; break; default: stats->nreads_other++; } if ( stats->info->trim_qual>0 ) stats->nbases_trimmed += bwa_trim_read(stats->info->trim_qual, bam_quals, seq_len, reverse); // Quality histogram and average quality. Clipping is neglected. if (quals) { for (i=0; i=stats->nquals ) error("TODO: quality too high %d>=%d (%s %"PRIhts_pos" %s)\n", qual, stats->nquals, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line)); if ( qual>stats->max_qual ) stats->max_qual = qual; quals[ i*stats->nquals+qual ]++; stats->sum_qual += qual; } } // Barcode statistics if (order == READ_ORDER_FIRST) { collect_barcode_stats(bam_line, stats); } // Look at the flags and increment appropriate counters (mapped, paired, etc) if ( IS_UNMAPPED(bam_line) ) { stats->nreads_unmapped++; } else { stats->nbases_mapped += seq_len; // This ignores clipping so only count primary if ( !bam_line->core.qual ) stats->nreads_mq0++; if ( !IS_PAIRED_AND_MAPPED(bam_line) ) stats->nreads_single_mapped++; else { stats->nreads_paired_and_mapped++; if (IS_PROPERLYPAIRED(bam_line)) stats->nreads_properly_paired++; if ( bam_line->core.tid!=bam_line->core.mtid ) stats->nreads_anomalous++; } } *gc_count_out = gc_count; } static int cleanup_overlaps(khash_t(qn2pair) *read_pairs, hts_pos_t max) { if ( !read_pairs ) return 0; int count = 0; khint_t k; for (k = kh_begin(read_pairs); k < kh_end(read_pairs); k++) { if ( kh_exist(read_pairs, k) ) { char *key = (char *)kh_key(read_pairs, k); pair_t *val = kh_val(read_pairs, k); if ( val && val->chunks ) { if ( val->chunks[val->n-1].end < max ) { free(val->chunks); free(val); free(key); kh_del(qn2pair, read_pairs, k); count++; } } else { free(key); kh_del(qn2pair, read_pairs, k); count++; } } } if ( max == INT64_MAX ) kh_destroy(qn2pair, read_pairs); return count; } /** * [pmin, pmax) - 0 based half-open */ static void remove_overlaps(bam1_t *bam_line, khash_t(qn2pair) *read_pairs, stats_t *stats, hts_pos_t pmin, hts_pos_t pmax) { if ( !bam_line || !read_pairs || !stats ) return; uint32_t order = (IS_READ1(bam_line) ? READ_ORDER_FIRST : 0) + (IS_READ2(bam_line) ? READ_ORDER_LAST : 0); if ( !(bam_line->core.flag & BAM_FPAIRED) || (bam_line->core.flag & BAM_FMUNMAP) || (llabs(bam_line->core.isize) >= 2*bam_line->core.l_qseq) || (order != READ_ORDER_FIRST && order != READ_ORDER_LAST) ) { if ( pmin >= 0 ) round_buffer_insert_read(&(stats->cov_rbuf), pmin, pmax); return; } char *qname = bam_get_qname(bam_line); if ( !qname ) { fprintf(stderr, "Error retrieving qname for line starting at pos %"PRIhts_pos"\n", bam_line->core.pos); return; } khint_t k = kh_get(qn2pair, read_pairs, qname); if ( k == kh_end(read_pairs) ) { //first chunk from this template if ( pmin == -1 ) return; int ret; char *s = strdup(qname); if ( !s ) { fprintf(stderr, "Error allocating memory\n"); return; } k = kh_put(qn2pair, read_pairs, s, &ret); if ( -1 == ret ) { error("Error inserting read '%s' in pair hash table\n", qname); } pair_t *pc = calloc(1, sizeof(pair_t)); if ( !pc ) { fprintf(stderr, "Error allocating memory\n"); return; } pc->m = DEFAULT_CHUNK_NO; pc->chunks = calloc(pc->m, sizeof(hts_pair_pos_t)); if ( !pc->chunks ) { fprintf(stderr, "Error allocating memory\n"); free(pc); return; } pc->chunks[0].beg = pmin; pc->chunks[0].end = pmax; pc->n = 1; pc->first = order; kh_val(read_pairs, k) = pc; stats->pair_count++; } else { //template already present pair_t *pc = kh_val(read_pairs, k); if ( !pc ) { fprintf(stderr, "Invalid hash table entry\n"); return; } if ( order == pc->first ) { //chunk from an existing line if ( pmin == -1 ) return; if ( pc->n == pc->m ) { hts_pair_pos_t *tmp = realloc(pc->chunks, (pc->m<<1)*sizeof(hts_pair_pos_t)); if ( !tmp ) { fprintf(stderr, "Error allocating memory\n"); return; } pc->chunks = tmp; pc->m<<=1; } pc->chunks[pc->n].beg = pmin; pc->chunks[pc->n].end = pmax; pc->n++; } else { //the other line, check for overlapping if ( pmin == -1 && kh_exist(read_pairs, k) ) { //job done, delete entry char *key = (char *)kh_key(read_pairs, k); pair_t *val = kh_val(read_pairs, k); if ( val) { free(val->chunks); free(val); } free(key); kh_del(qn2pair, read_pairs, k); stats->pair_count--; return; } int i; for (i=0; in; i++) { if ( pmin >= pc->chunks[i].end ) continue; if ( pmax <= pc->chunks[i].beg ) //no overlap break; if ( pmin < pc->chunks[i].beg ) { //overlap at the beginning round_buffer_insert_read(&(stats->cov_rbuf), pmin, pc->chunks[i].beg); pmin = pc->chunks[i].beg; } if ( pmax <= pc->chunks[i].end ) { //completely contained stats->nbases_mapped_cigar -= (pmax - pmin); return; } else { //overlap at the end stats->nbases_mapped_cigar -= (pc->chunks[i].end - pmin); pmin = pc->chunks[i].end; } } } } round_buffer_insert_read(&(stats->cov_rbuf), pmin, pmax); } void collect_stats(bam1_t *bam_line, stats_t *stats, khash_t(qn2pair) *read_pairs) { if ( !is_in_regions(bam_line,stats) ) return; if ( stats->rg_hash ) { const uint8_t *rg = bam_aux_get(bam_line, "RG"); if ( !rg ) return; // certain read groups were requested but this record has none khint_t k = kh_get(rg, stats->rg_hash, (const char*)(rg + 1)); if ( k == kh_end((kh_rg_t *)stats->rg_hash) ) return; } if ( stats->info->flag_require && (bam_line->core.flag & stats->info->flag_require)!=stats->info->flag_require ) { stats->nreads_filtered++; return; } if ( stats->info->flag_filter && (bam_line->core.flag & stats->info->flag_filter) ) { stats->nreads_filtered++; return; } if ( stats->info->filter_readlen!=-1 && bam_line->core.l_qseq!=stats->info->filter_readlen ) return; update_checksum(bam_line, stats); // Secondary reads don't count for most stats purposes if ( bam_line->core.flag & BAM_FSECONDARY ) { stats->nreads_secondary++; return; } if ( bam_line->core.flag & BAM_FSUPPLEMENTARY ) { stats->nreads_supplementary++; } // If line has no sequence cannot continue int seq_len = bam_line->core.l_qseq; if ( !seq_len ) return; if ( IS_DUP(bam_line) ) { stats->total_len_dup += seq_len; stats->nreads_dup++; } uint32_t order = IS_PAIRED(bam_line) ? (IS_READ1(bam_line) ? READ_ORDER_FIRST : 0) + (IS_READ2(bam_line) ? READ_ORDER_LAST : 0) : READ_ORDER_FIRST; int read_len = unclipped_length(bam_line); if ( read_len >= stats->nbases ) realloc_buffers(stats,read_len); // Update max_len observed if ( stats->max_lenmax_len = read_len; if ( order == READ_ORDER_FIRST && stats->max_len_1st < read_len ) stats->max_len_1st = read_len; if ( order == READ_ORDER_LAST && stats->max_len_2nd < read_len ) stats->max_len_2nd = read_len; if ( ( bam_line->core.flag & (BAM_FUNMAP|BAM_FSECONDARY|BAM_FSUPPLEMENTARY|BAM_FQCFAIL|BAM_FDUP) ) == 0 ) stats->mapping_qualities[bam_line->core.qual]++; int i; int gc_count = 0; // These stats should only be calculated for the original reads ignoring supplementary artificial reads // otherwise we'll accidentally double count if ( IS_ORIGINAL(bam_line) ) { stats->read_lengths[read_len]++; if ( order == READ_ORDER_FIRST ) stats->read_lengths_1st[read_len]++; if ( order == READ_ORDER_LAST ) stats->read_lengths_2nd[read_len]++; collect_orig_read_stats(bam_line, stats, &gc_count); } // Look at the flags and increment appropriate counters (mapped, paired, etc) if ( IS_UNMAPPED(bam_line) ) return; count_indels(stats, bam_line); if ( IS_PAIRED_AND_MAPPED(bam_line) && IS_ORIGINAL(bam_line) ) { // The insert size is tricky, because for long inserts the libraries are // prepared differently and the pairs point in other direction. BWA does // not set the paired flag for them. Similar thing is true also for 454 // reads. Mates mapped to different chromosomes have isize==0. int32_t isize = bam_line->core.isize; if ( isize<0 ) isize = -isize; if ( stats->info->nisize > 0 && isize > stats->info->nisize ) isize = stats->info->nisize; if ( isize>0 || bam_line->core.tid==bam_line->core.mtid ) { hts_pos_t pos_fst = bam_line->core.mpos - bam_line->core.pos; int is_fst = IS_READ1(bam_line) ? 1 : -1; int is_fwd = IS_REVERSE(bam_line) ? -1 : 1; int is_mfwd = IS_MATE_REVERSE(bam_line) ? -1 : 1; if ( is_fwd*is_mfwd>0 ) stats->isize->inc_other(stats->isize->data, isize); else if ( is_fst*pos_fst>=0 ) { if ( is_fst*is_fwd>0 ) stats->isize->inc_inward(stats->isize->data, isize); else stats->isize->inc_outward(stats->isize->data, isize); } else if ( is_fst*pos_fst<0 ) { if ( is_fst*is_fwd>0 ) stats->isize->inc_outward(stats->isize->data, isize); else stats->isize->inc_inward(stats->isize->data, isize); } } } // Number of mismatches uint8_t *nm = bam_aux_get(bam_line,"NM"); if (nm) stats->nmismatches += bam_aux2i(nm); // Number of mapped bases from cigar if ( bam_line->core.n_cigar == 0) error("FIXME: mapped read with no cigar?\n"); int readlen=seq_len; if ( stats->regions ) { // Count only on-target bases hts_pos_t iref = bam_line->core.pos + 1; for (i=0; icore.n_cigar; i++) { int cig = bam_cigar_op(bam_get_cigar(bam_line)[i]); int ncig = bam_cigar_oplen(bam_get_cigar(bam_line)[i]); if ( !ncig ) continue; // curiously, this can happen: 0D if ( cig==BAM_CDEL ) readlen += ncig; else if ( cig==BAM_CMATCH || cig==BAM_CEQUAL || cig==BAM_CDIFF ) { if ( iref < stats->reg_from ) ncig -= stats->reg_from-iref; else if ( iref+ncig-1 > stats->reg_to ) ncig -= iref+ncig-1 - stats->reg_to; if ( ncig<0 ) ncig = 0; stats->nbases_mapped_cigar += ncig; iref += bam_cigar_oplen(bam_get_cigar(bam_line)[i]); } else if ( cig==BAM_CINS ) { iref += ncig; if ( iref>=stats->reg_from && iref<=stats->reg_to ) stats->nbases_mapped_cigar += ncig; } } } else { // Count the whole read for (i=0; icore.n_cigar; i++) { int cig = bam_cigar_op(bam_get_cigar(bam_line)[i]); if ( cig==BAM_CMATCH || cig==BAM_CINS || cig==BAM_CEQUAL || cig==BAM_CDIFF ) stats->nbases_mapped_cigar += bam_cigar_oplen(bam_get_cigar(bam_line)[i]); if ( cig==BAM_CDEL ) readlen += bam_cigar_oplen(bam_get_cigar(bam_line)[i]); } } if ( stats->tid==bam_line->core.tid && bam_line->core.pospos ) stats->is_sorted = 0; stats->pos = bam_line->core.pos; if ( stats->is_sorted ) { if ( stats->tid==-1 || stats->tid!=bam_line->core.tid ) { round_buffer_flush(stats, -1); } //cleanup the pair hash table to free memory stats->last_read_flush++; if ( stats->pair_count > DEFAULT_PAIR_MAX && stats->last_read_flush > DEFAULT_PAIR_MAX) { stats->pair_count -= cleanup_overlaps(read_pairs, bam_line->core.pos); stats->last_read_flush = 0; } if ( stats->last_pair_tid != bam_line->core.tid) { stats->pair_count -= cleanup_overlaps(read_pairs, INT64_MAX-1); stats->last_pair_tid = bam_line->core.tid; stats->last_read_flush = 0; } // Mismatches per cycle and GC-depth graph. For simplicity, reads overlapping GCD bins // are not splitted which results in up to seq_len-1 overlaps. The default bin size is // 20kbp, so the effect is negligible. if ( stats->info->fai ) { hts_pos_t inc_ref = 0; int inc_gcd = 0; // First pass or new chromosome, or read goes beyond the rseq buffer if ( stats->rseq_pos==-1 || stats->tid != bam_line->core.tid || stats->rseq_pos+stats->nrseq_buf < bam_line->core.pos+readlen) { inc_ref=bam_line->core.pos+readlen; inc_gcd=1; } // Read overlaps the next gcd bin else if ( stats->gcd_pos+stats->info->gcd_bin_size < bam_line->core.pos+readlen ) { inc_gcd = 1; if ( stats->rseq_pos+stats->nrseq_buf < bam_line->core.pos+stats->info->gcd_bin_size ) inc_ref = bam_line->core.pos+stats->info->gcd_bin_size; } if ( inc_gcd ) { stats->igcd++; if ( stats->igcd >= stats->ngcd ) realloc_gcd_buffer(stats, readlen); if ( inc_ref ) read_ref_seq(stats, bam_line->core.tid, bam_line->core.pos, inc_ref); stats->gcd_pos = bam_line->core.pos; stats->gcd[ stats->igcd ].gc = fai_gc_content(stats, stats->gcd_pos, stats->info->gcd_bin_size); } count_mismatches_per_cycle(stats,bam_line,read_len); } // No reference and first pass, new chromosome or sequence going beyond the end of the gcd bin else if ( stats->gcd_pos==-1 || stats->tid != bam_line->core.tid || bam_line->core.pos - stats->gcd_pos > stats->info->gcd_bin_size ) { // First pass or a new chromosome stats->tid = bam_line->core.tid; stats->gcd_pos = bam_line->core.pos; stats->igcd++; if ( stats->igcd >= stats->ngcd ) realloc_gcd_buffer(stats, readlen); } stats->gcd[ stats->igcd ].depth++; // When no reference sequence is given, approximate the GC from the read (much shorter window, but otherwise OK) if ( !stats->info->fai ) stats->gcd[ stats->igcd ].gc += (float) gc_count / seq_len; // Coverage distribution graph round_buffer_flush(stats,bam_line->core.pos); if ( stats->regions ) { hts_pos_t p = bam_line->core.pos, pnew, pmin = 0, pmax = 0; uint32_t j = 0; i = 0; while ( j < bam_line->core.n_cigar && i < stats->nchunks ) { int op = bam_cigar_op(bam_get_cigar(bam_line)[j]); int oplen = bam_cigar_oplen(bam_get_cigar(bam_line)[j]); switch(op) { case BAM_CMATCH: case BAM_CEQUAL: case BAM_CDIFF: pmin = MAX(p, stats->chunks[i].beg-1); // 0 based pmax = MIN(p+oplen, stats->chunks[i].end); // 1 based if ( pmax > pmin ) { if ( stats->info->remove_overlaps ) remove_overlaps(bam_line, read_pairs, stats, pmin, pmax); else round_buffer_insert_read(&(stats->cov_rbuf), pmin, pmax); } break; case BAM_CDEL: break; } pnew = p + (bam_cigar_type(op)&2 ? oplen : 0); // consumes reference if ( pnew >= stats->chunks[i].end ) { // go to the next chunk i++; } else { // go to the next CIGAR op j++; p = pnew; } } } else { hts_pos_t p = bam_line->core.pos; uint32_t j; for (j = 0; j < bam_line->core.n_cigar; j++) { int op = bam_cigar_op(bam_get_cigar(bam_line)[j]); int oplen = bam_cigar_oplen(bam_get_cigar(bam_line)[j]); switch(op) { case BAM_CMATCH: case BAM_CEQUAL: case BAM_CDIFF: if ( stats->info->remove_overlaps ) remove_overlaps(bam_line, read_pairs, stats, p, p+oplen); else round_buffer_insert_read(&(stats->cov_rbuf), p, p+oplen); break; case BAM_CDEL: break; } p += bam_cigar_type(op)&2 ? oplen : 0; // consumes reference } } if ( stats->info->remove_overlaps ) remove_overlaps(bam_line, read_pairs, stats, -1LL, -1LL); //remove the line from the hash table } } // Sort by GC and depth #define GCD_t(x) ((gc_depth_t *)x) static int gcd_cmp(const void *a, const void *b) { if ( GCD_t(a)->gc < GCD_t(b)->gc ) return -1; if ( GCD_t(a)->gc > GCD_t(b)->gc ) return 1; if ( GCD_t(a)->depth < GCD_t(b)->depth ) return -1; if ( GCD_t(a)->depth > GCD_t(b)->depth ) return 1; return 0; } #undef GCD_t float gcd_percentile(gc_depth_t *gcd, int N, int p) { float n,d; int k; n = (float)p*(N+1)/100; k = n; if ( k<=0 ) return gcd[0].depth; if ( k>=N ) return gcd[N-1].depth; d = n - k; return gcd[k-1].depth + d*(gcd[k].depth - gcd[k-1].depth); } void output_stats(FILE *to, stats_t *stats, int sparse) { // Calculate average insert size and standard deviation (from the main bulk data only) int isize, ibulk=0, icov, imapq=0; uint64_t nisize=0, nisize_inward=0, nisize_outward=0, nisize_other=0, cov_sum=0; double bulk=0, avg_isize=0, sd_isize=0; for (isize=0; isizeisize->nitems(stats->isize->data); isize++) { // Each pair was counted twice stats->isize->set_inward(stats->isize->data, isize, stats->isize->inward(stats->isize->data, isize) * 0.5); stats->isize->set_outward(stats->isize->data, isize, stats->isize->outward(stats->isize->data, isize) * 0.5); stats->isize->set_other(stats->isize->data, isize, stats->isize->other(stats->isize->data, isize) * 0.5); nisize_inward += stats->isize->inward(stats->isize->data, isize); nisize_outward += stats->isize->outward(stats->isize->data, isize); nisize_other += stats->isize->other(stats->isize->data, isize); nisize += stats->isize->inward(stats->isize->data, isize) + stats->isize->outward(stats->isize->data, isize) + stats->isize->other(stats->isize->data, isize); } for (isize=0; isizeisize->nitems(stats->isize->data); isize++) { uint64_t num = stats->isize->inward(stats->isize->data, isize) + stats->isize->outward(stats->isize->data, isize) + stats->isize->other(stats->isize->data, isize); if (num > 0) ibulk = isize + 1; bulk += num; avg_isize += isize * (stats->isize->inward(stats->isize->data, isize) + stats->isize->outward(stats->isize->data, isize) + stats->isize->other(stats->isize->data, isize)); if ( bulk/nisize > stats->info->isize_main_bulk ) { ibulk = isize+1; nisize = bulk; break; } } avg_isize /= nisize ? nisize : 1; for (isize=1; isizeisize->inward(stats->isize->data, isize) + stats->isize->outward(stats->isize->data, isize) +stats->isize->other(stats->isize->data, isize)) * (isize-avg_isize)*(isize-avg_isize) / (nisize ? nisize : 1); sd_isize = sqrt(sd_isize); fprintf(to, "# This file was produced by samtools stats (%s+htslib-%s) and can be plotted using plot-bamstats\n", samtools_version(), hts_version()); if( stats->split_name != NULL ){ fprintf(to, "# This file contains statistics only for reads with tag: %s=%s\n", stats->info->split_tag, stats->split_name); } else{ fprintf(to, "# This file contains statistics for all reads.\n"); } fprintf(to, "# The command line was: %s",stats->info->argv[0]); int i; for (i=1; iinfo->argc; i++) fprintf(to, " %s", stats->info->argv[i]); fprintf(to, "\n"); fprintf(to, "# CHK, Checksum\t[2]Read Names\t[3]Sequences\t[4]Qualities\n"); fprintf(to, "# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)\n"); fprintf(to, "CHK\t%08x\t%08x\t%08x\n", stats->checksum.names,stats->checksum.reads,stats->checksum.quals); fprintf(to, "# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.\n"); fprintf(to, "SN\traw total sequences:\t%ld\t# excluding supplementary and secondary reads\n", (long)(stats->nreads_filtered+stats->nreads_1st+stats->nreads_2nd+stats->nreads_other)); // not counting excluded seqs (and none of the below) fprintf(to, "SN\tfiltered sequences:\t%ld\n", (long)stats->nreads_filtered); fprintf(to, "SN\tsequences:\t%ld\n", (long)(stats->nreads_1st+stats->nreads_2nd+stats->nreads_other)); fprintf(to, "SN\tis sorted:\t%d\n", stats->is_sorted ? 1 : 0); fprintf(to, "SN\t1st fragments:\t%ld\n", (long)stats->nreads_1st); fprintf(to, "SN\tlast fragments:\t%ld\n", (long)stats->nreads_2nd); fprintf(to, "SN\treads mapped:\t%ld\n", (long)(stats->nreads_paired_and_mapped+stats->nreads_single_mapped)); fprintf(to, "SN\treads mapped and paired:\t%ld\t# paired-end technology bit set + both mates mapped\n", (long)stats->nreads_paired_and_mapped); fprintf(to, "SN\treads unmapped:\t%ld\n", (long)stats->nreads_unmapped); fprintf(to, "SN\treads properly paired:\t%ld\t# proper-pair bit set\n", (long)stats->nreads_properly_paired); fprintf(to, "SN\treads paired:\t%ld\t# paired-end technology bit set\n", (long)stats->nreads_paired_tech); fprintf(to, "SN\treads duplicated:\t%ld\t# PCR or optical duplicate bit set\n", (long)stats->nreads_dup); fprintf(to, "SN\treads MQ0:\t%ld\t# mapped and MQ=0\n", (long)stats->nreads_mq0); fprintf(to, "SN\treads QC failed:\t%ld\n", (long)stats->nreads_QCfailed); fprintf(to, "SN\tnon-primary alignments:\t%ld\n", (long)stats->nreads_secondary); fprintf(to, "SN\tsupplementary alignments:\t%ld\n", (long)stats->nreads_supplementary); fprintf(to, "SN\ttotal length:\t%ld\t# ignores clipping\n", (long)stats->total_len); fprintf(to, "SN\ttotal first fragment length:\t%ld\t# ignores clipping\n", (long)stats->total_len_1st); fprintf(to, "SN\ttotal last fragment length:\t%ld\t# ignores clipping\n", (long)stats->total_len_2nd); fprintf(to, "SN\tbases mapped:\t%ld\t# ignores clipping\n", (long)stats->nbases_mapped); // the length of the whole read goes here, including soft-clips etc. fprintf(to, "SN\tbases mapped (cigar):\t%ld\t# more accurate\n", (long)stats->nbases_mapped_cigar); // only matched and inserted bases are counted here fprintf(to, "SN\tbases trimmed:\t%ld\n", (long)stats->nbases_trimmed); fprintf(to, "SN\tbases duplicated:\t%ld\n", (long)stats->total_len_dup); fprintf(to, "SN\tmismatches:\t%ld\t# from NM fields\n", (long)stats->nmismatches); fprintf(to, "SN\terror rate:\t%e\t# mismatches / bases mapped (cigar)\n", stats->nbases_mapped_cigar ? (float)stats->nmismatches/stats->nbases_mapped_cigar : 0); float avg_read_length = (stats->nreads_1st + stats->nreads_2nd + stats->nreads_other) ? (float)stats->total_len / (stats->nreads_1st + stats->nreads_2nd + stats->nreads_other) : 0; fprintf(to, "SN\taverage length:\t%.0f\n", avg_read_length); fprintf(to, "SN\taverage first fragment length:\t%.0f\n", stats->nreads_1st? (float)stats->total_len_1st/stats->nreads_1st:0); fprintf(to, "SN\taverage last fragment length:\t%.0f\n", stats->nreads_2nd? (float)stats->total_len_2nd/stats->nreads_2nd:0); fprintf(to, "SN\tmaximum length:\t%d\n", stats->max_len); fprintf(to, "SN\tmaximum first fragment length:\t%d\n", stats->max_len_1st); fprintf(to, "SN\tmaximum last fragment length:\t%d\n", stats->max_len_2nd); fprintf(to, "SN\taverage quality:\t%.1f\n", stats->total_len?stats->sum_qual/stats->total_len:0); fprintf(to, "SN\tinsert size average:\t%.1f\n", avg_isize); fprintf(to, "SN\tinsert size standard deviation:\t%.1f\n", sd_isize); fprintf(to, "SN\tinward oriented pairs:\t%ld\n", (long)nisize_inward); fprintf(to, "SN\toutward oriented pairs:\t%ld\n", (long)nisize_outward); fprintf(to, "SN\tpairs with other orientation:\t%ld\n", (long)nisize_other); fprintf(to, "SN\tpairs on different chromosomes:\t%ld\n", (long)stats->nreads_anomalous/2); fprintf(to, "SN\tpercentage of properly paired reads (%%):\t%.1f\n", (stats->nreads_1st+stats->nreads_2nd+stats->nreads_other)? (float)(100*stats->nreads_properly_paired)/(stats->nreads_1st+stats->nreads_2nd+stats->nreads_other):0); if ( stats->target_count ) { fprintf(to, "SN\tbases inside the target:\t%" PRIu64 "\n", stats->target_count); for (icov=stats->info->cov_threshold+1; icovncov; icov++) cov_sum += stats->cov[icov]; fprintf(to, "SN\tpercentage of target genome with coverage > %d (%%):\t%.2f\n", stats->info->cov_threshold, (float)(100*cov_sum)/stats->target_count); } int ibase,iqual; if ( stats->max_lennbases ) stats->max_len++; if ( stats->max_qual+1nquals ) stats->max_qual++; fprintf(to, "# First Fragment Qualities. Use `grep ^FFQ | cut -f 2-` to extract this part.\n"); fprintf(to, "# Columns correspond to qualities and rows to cycles. First column is the cycle number.\n"); for (ibase=0; ibasemax_len_1st; ibase++) { fprintf(to, "FFQ\t%d",ibase+1); for (iqual=0; iqual<=stats->max_qual; iqual++) { fprintf(to, "\t%ld", (long)stats->quals_1st[ibase*stats->nquals+iqual]); } fprintf(to, "\n"); } fprintf(to, "# Last Fragment Qualities. Use `grep ^LFQ | cut -f 2-` to extract this part.\n"); fprintf(to, "# Columns correspond to qualities and rows to cycles. First column is the cycle number.\n"); for (ibase=0; ibasemax_len_2nd; ibase++) { fprintf(to, "LFQ\t%d",ibase+1); for (iqual=0; iqual<=stats->max_qual; iqual++) { fprintf(to, "\t%ld", (long)stats->quals_2nd[ibase*stats->nquals+iqual]); } fprintf(to, "\n"); } if ( stats->mpc_buf ) { fprintf(to, "# Mismatches per cycle and quality. Use `grep ^MPC | cut -f 2-` to extract this part.\n"); fprintf(to, "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second\n"); fprintf(to, "# is the number of N's and the rest is the number of mismatches\n"); for (ibase=0; ibasemax_len; ibase++) { fprintf(to, "MPC\t%d",ibase+1); for (iqual=0; iqual<=stats->max_qual; iqual++) { fprintf(to, "\t%ld", (long)stats->mpc_buf[ibase*stats->nquals+iqual]); } fprintf(to, "\n"); } } fprintf(to, "# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part.\n"); int ibase_prev = 0; for (ibase=0; ibasengc; ibase++) { if ( stats->gc_1st[ibase]==stats->gc_1st[ibase_prev] ) continue; fprintf(to, "GCF\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1), (long)stats->gc_1st[ibase_prev]); ibase_prev = ibase; } fprintf(to, "# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part.\n"); ibase_prev = 0; for (ibase=0; ibasengc; ibase++) { if ( stats->gc_2nd[ibase]==stats->gc_2nd[ibase_prev] ) continue; fprintf(to, "GCL\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1), (long)stats->gc_2nd[ibase_prev]); ibase_prev = ibase; } fprintf(to, "# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]; and N and O counts as a percentage of all A/C/G/T bases [%%]\n"); for (ibase=0; ibasemax_len; ibase++) { acgtno_count_t *acgtno_count_1st = &(stats->acgtno_cycles_1st[ibase]); acgtno_count_t *acgtno_count_2nd = &(stats->acgtno_cycles_2nd[ibase]); uint64_t acgt_sum = acgtno_count_1st->a + acgtno_count_1st->c + acgtno_count_1st->g + acgtno_count_1st->t + acgtno_count_2nd->a + acgtno_count_2nd->c + acgtno_count_2nd->g + acgtno_count_2nd->t; if ( ! acgt_sum ) continue; fprintf(to, "GCC\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase+1, 100.*(acgtno_count_1st->a + acgtno_count_2nd->a)/acgt_sum, 100.*(acgtno_count_1st->c + acgtno_count_2nd->c)/acgt_sum, 100.*(acgtno_count_1st->g + acgtno_count_2nd->g)/acgt_sum, 100.*(acgtno_count_1st->t + acgtno_count_2nd->t)/acgt_sum, 100.*(acgtno_count_1st->n + acgtno_count_2nd->n)/acgt_sum, 100.*(acgtno_count_1st->other + acgtno_count_2nd->other)/acgt_sum); } fprintf(to, "# ACGT content per cycle, read oriented. Use `grep ^GCT | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]\n"); for (ibase=0; ibasemax_len; ibase++) { acgtno_count_t *acgtno_count = &(stats->acgtno_revcomp[ibase]); uint64_t acgt_sum = acgtno_count->a + acgtno_count->c + acgtno_count->g + acgtno_count->t; if ( ! acgt_sum ) continue; fprintf(to, "GCT\t%d\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase+1, 100.*(acgtno_count->a)/acgt_sum, 100.*(acgtno_count->c)/acgt_sum, 100.*(acgtno_count->g)/acgt_sum, 100.*(acgtno_count->t)/acgt_sum); } uint64_t tA=0, tC=0, tG=0, tT=0, tN=0; fprintf(to, "# ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]; and N and O counts as a percentage of all A/C/G/T bases [%%]\n"); for (ibase=0; ibasemax_len; ibase++) { acgtno_count_t *acgtno_count_1st = &(stats->acgtno_cycles_1st[ibase]); uint64_t acgt_sum_1st = acgtno_count_1st->a + acgtno_count_1st->c + acgtno_count_1st->g + acgtno_count_1st->t; tA += acgtno_count_1st->a; tC += acgtno_count_1st->c; tG += acgtno_count_1st->g; tT += acgtno_count_1st->t; tN += acgtno_count_1st->n; if ( acgt_sum_1st ) fprintf(to, "FBC\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase+1, 100.*acgtno_count_1st->a/acgt_sum_1st, 100.*acgtno_count_1st->c/acgt_sum_1st, 100.*acgtno_count_1st->g/acgt_sum_1st, 100.*acgtno_count_1st->t/acgt_sum_1st, 100.*acgtno_count_1st->n/acgt_sum_1st, 100.*acgtno_count_1st->other/acgt_sum_1st); } fprintf(to, "# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters\n"); fprintf(to, "FTC\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\n", tA, tC, tG, tT, tN); tA=0, tC=0, tG=0, tT=0, tN=0; fprintf(to, "# ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]; and N and O counts as a percentage of all A/C/G/T bases [%%]\n"); for (ibase=0; ibasemax_len; ibase++) { acgtno_count_t *acgtno_count_2nd = &(stats->acgtno_cycles_2nd[ibase]); uint64_t acgt_sum_2nd = acgtno_count_2nd->a + acgtno_count_2nd->c + acgtno_count_2nd->g + acgtno_count_2nd->t; tA += acgtno_count_2nd->a; tC += acgtno_count_2nd->c; tG += acgtno_count_2nd->g; tT += acgtno_count_2nd->t; tN += acgtno_count_2nd->n; if ( acgt_sum_2nd ) fprintf(to, "LBC\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase+1, 100.*acgtno_count_2nd->a/acgt_sum_2nd, 100.*acgtno_count_2nd->c/acgt_sum_2nd, 100.*acgtno_count_2nd->g/acgt_sum_2nd, 100.*acgtno_count_2nd->t/acgt_sum_2nd, 100.*acgtno_count_2nd->n/acgt_sum_2nd, 100.*acgtno_count_2nd->other/acgt_sum_2nd); } fprintf(to, "# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters\n"); fprintf(to, "LTC\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\n", tA, tC, tG, tT, tN); int tag; for (tag=0; tagntags; tag++) { if (stats->tags_barcode[tag].nbases) { fprintf(to, "# ACGT content per cycle for barcodes. Use `grep ^%sC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]; and N counts as a percentage of all A/C/G/T bases [%%]\n", stats->tags_barcode[tag].tag_name); for (ibase=0; ibasetags_barcode[tag].nbases; ibase++) { if (ibase == stats->tags_barcode[tag].tag_sep) continue; acgtno_count_t *acgtno_count = stats->acgtno_barcode + stats->tags_barcode[tag].offset + ibase; uint64_t acgt_sum = acgtno_count->a + acgtno_count->c + acgtno_count->g + acgtno_count->t; if ( acgt_sum ) fprintf(to, "%sC%d\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", stats->tags_barcode[tag].tag_name, stats->tags_barcode[tag].tag_sep < 0 || ibase < stats->tags_barcode[tag].tag_sep ? 1 : 2, stats->tags_barcode[tag].tag_sep < 0 || ibase < stats->tags_barcode[tag].tag_sep ? ibase+1 : ibase-stats->tags_barcode[tag].tag_sep, 100.*acgtno_count->a/acgt_sum, 100.*acgtno_count->c/acgt_sum, 100.*acgtno_count->g/acgt_sum, 100.*acgtno_count->t/acgt_sum, 100.*acgtno_count->n/acgt_sum); } fprintf(to, "# Barcode Qualities. Use `grep ^%sQ | cut -f 2-` to extract this part.\n", stats->tags_barcode[tag].qual_name); fprintf(to, "# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number.\n"); for (ibase=0; ibasetags_barcode[tag].nbases; ibase++) { if (ibase == stats->tags_barcode[tag].tag_sep) continue; fprintf(to, "%sQ%d\t%d", stats->tags_barcode[tag].qual_name, stats->tags_barcode[tag].tag_sep < 0 || ibase < stats->tags_barcode[tag].tag_sep ? 1 : 2, stats->tags_barcode[tag].tag_sep < 0 || ibase < stats->tags_barcode[tag].tag_sep ? ibase+1 : ibase-stats->tags_barcode[tag].tag_sep); for (iqual=0; iqual<=stats->tags_barcode[tag].max_qual; iqual++) { fprintf(to, "\t%ld", (long)stats->quals_barcode[(stats->tags_barcode[tag].offset + ibase)*stats->nquals+iqual]); } fprintf(to, "\n"); } } } fprintf(to, "# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs\n"); for (isize=0; isizeisize->inward(stats->isize->data, isize)); long out = (long)(stats->isize->outward(stats->isize->data, isize)); long other = (long)(stats->isize->other(stats->isize->data, isize)); if (!sparse || in + out + other > 0) { fprintf(to, "IS\t%d\t%ld\t%ld\t%ld\t%ld\n", isize, in+out+other, in , out, other); } } fprintf(to, "# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count\n"); int ilen; for (ilen=0; ilenmax_len; ilen++) { if ( stats->read_lengths[ilen+1]>0 ) fprintf(to, "RL\t%d\t%ld\n", ilen+1, (long)stats->read_lengths[ilen+1]); } fprintf(to, "# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count\n"); for (ilen=0; ilenmax_len_1st; ilen++) { if ( stats->read_lengths_1st[ilen+1]>0 ) fprintf(to, "FRL\t%d\t%ld\n", ilen+1, (long)stats->read_lengths_1st[ilen+1]); } fprintf(to, "# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count\n"); for (ilen=0; ilenmax_len_2nd; ilen++) { if ( stats->read_lengths_2nd[ilen+1]>0 ) fprintf(to, "LRL\t%d\t%ld\n", ilen+1, (long)stats->read_lengths_2nd[ilen+1]); } fprintf(to, "# Mapping qualities for reads !(UNMAP|SECOND|SUPPL|QCFAIL|DUP). Use `grep ^MAPQ | cut -f 2-` to extract this part. The columns are: mapq, count\n"); for (imapq=0; imapq < 256; imapq++) { if ( stats->mapping_qualities[imapq]>0 ) fprintf(to, "MAPQ\t%d\t%ld\n", imapq, (long)stats->mapping_qualities[imapq]); } fprintf(to, "# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions\n"); for (ilen=0; ilennindels; ilen++) { if ( stats->insertions[ilen]>0 || stats->deletions[ilen]>0 ) fprintf(to, "ID\t%d\t%ld\t%ld\n", ilen+1, (long)stats->insertions[ilen], (long)stats->deletions[ilen]); } fprintf(to, "# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)\n"); for (ilen=0; ilen<=stats->nbases; ilen++) { // For deletions we print the index of the cycle before the deleted base (1-based) and for insertions // the index of the cycle of the first inserted base (also 1-based) if ( stats->ins_cycles_1st[ilen]>0 || stats->ins_cycles_2nd[ilen]>0 || stats->del_cycles_1st[ilen]>0 || stats->del_cycles_2nd[ilen]>0 ) fprintf(to, "IC\t%d\t%ld\t%ld\t%ld\t%ld\n", ilen+1, (long)stats->ins_cycles_1st[ilen], (long)stats->ins_cycles_2nd[ilen], (long)stats->del_cycles_1st[ilen], (long)stats->del_cycles_2nd[ilen]); } fprintf(to, "# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.\n"); if ( stats->cov[0] ) fprintf(to, "COV\t[<%d]\t%d\t%ld\n",stats->info->cov_min,stats->info->cov_min-1, (long)stats->cov[0]); for (icov=1; icovncov-1; icov++) if ( stats->cov[icov] ) fprintf(to, "COV\t[%d-%d]\t%d\t%ld\n",stats->info->cov_min + (icov-1)*stats->info->cov_step, stats->info->cov_min + icov*stats->info->cov_step-1,stats->info->cov_min + icov*stats->info->cov_step-1, (long)stats->cov[icov]); if ( stats->cov[stats->ncov-1] ) fprintf(to, "COV\t[%d<]\t%d\t%ld\n",stats->info->cov_min + (stats->ncov-2)*stats->info->cov_step-1,stats->info->cov_min + (stats->ncov-2)*stats->info->cov_step-1, (long)stats->cov[stats->ncov-1]); // Calculate average GC content, then sort by GC and depth fprintf(to, "# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile\n"); uint32_t igcd; for (igcd=0; igcdigcd; igcd++) { if ( stats->info->fai ) stats->gcd[igcd].gc = rint(100. * stats->gcd[igcd].gc); else if ( stats->gcd[igcd].depth ) stats->gcd[igcd].gc = rint(100. * stats->gcd[igcd].gc / stats->gcd[igcd].depth); } if ( stats->ngcd ) qsort(stats->gcd, stats->igcd+1, sizeof(gc_depth_t), gcd_cmp); igcd = 0; while ( igcd < stats->igcd ) { // Calculate percentiles (10,25,50,75,90th) for the current GC content and print uint32_t nbins=0, itmp=igcd; float gc = stats->gcd[igcd].gc; while ( itmpigcd && fabs(stats->gcd[itmp].gc-gc)<0.1 ) { nbins++; itmp++; } fprintf(to, "GCD\t%.1f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\n", gc, (igcd+nbins+1)*100./(stats->igcd+1), gcd_percentile(&(stats->gcd[igcd]),nbins,10) *avg_read_length/stats->info->gcd_bin_size, gcd_percentile(&(stats->gcd[igcd]),nbins,25) *avg_read_length/stats->info->gcd_bin_size, gcd_percentile(&(stats->gcd[igcd]),nbins,50) *avg_read_length/stats->info->gcd_bin_size, gcd_percentile(&(stats->gcd[igcd]),nbins,75) *avg_read_length/stats->info->gcd_bin_size, gcd_percentile(&(stats->gcd[igcd]),nbins,90) *avg_read_length/stats->info->gcd_bin_size ); igcd += nbins; } } static void init_regions(stats_t *stats, const char *file, stats_info_t* info) { FILE *fp = fopen(file,"r"); if ( !fp ) error("%s: %s\n",file,strerror(errno)); kstring_t line = { 0, 0, NULL }; int warned = 0, r, p, new_p; int prev_tid=-1; hts_pos_t prev_pos=-1LL; while (line.l = 0, kgetline(&line, (kgets_func *)fgets, fp) >= 0) { if ( line.s[0] == '#' ) continue; int i = 0; while ( i=line.l ) error("Could not parse the file: %s [%s]\n", file, line.s); line.s[i] = '\0'; int tid = bam_name2id(stats->info->sam_header, line.s); if ( tid < 0 ) { if ( !warned ) fprintf(stderr,"Warning: Some sequences not present in the BAM, e.g. \"%s\". This message is printed only once.\n", line.s); warned = 1; continue; } if ( tid >= stats->nregions ) { if(!(stats->regions = realloc(stats->regions,sizeof(regions_t)*(tid+REG_INC)))) error("Could not allocate memory for region.\n"); int j; for (j=stats->nregions; jregions[j].npos = stats->regions[j].mpos = stats->regions[j].cpos = 0; stats->regions[j].pos = NULL; } stats->nregions = tid+REG_INC; } int npos = stats->regions[tid].npos; if ( npos >= stats->regions[tid].mpos ) { stats->regions[tid].mpos = npos+POS_INC; if (!(stats->regions[tid].pos = realloc(stats->regions[tid].pos, sizeof(hts_pair_pos_t)*stats->regions[tid].mpos))) error("Could not allocate memory for interval.\n"); } if ( (sscanf(&line.s[i+1],"%"SCNd64" %"SCNd64, &stats->regions[tid].pos[npos].beg, &stats->regions[tid].pos[npos].end))!=2 ) error("Could not parse the region [%s]\n", &line.s[i+1]); if ( prev_tid==-1 || prev_tid!=tid ) { prev_tid = tid; prev_pos = stats->regions[tid].pos[npos].beg; } if ( prev_pos>stats->regions[tid].pos[npos].beg ) error("The positions are not in chromosomal order (%s:%"PRIhts_pos" comes after %"PRIhts_pos")\n", line.s, stats->regions[tid].pos[npos].beg, prev_pos); stats->regions[tid].npos++; if ( stats->regions[tid].npos > stats->nchunks ) stats->nchunks = stats->regions[tid].npos; } free(line.s); if ( !stats->regions ) error("Unable to map the -t sequences to the BAM sequences.\n"); fclose(fp); // sort region intervals and remove duplicates for (r = 0; r < stats->nregions; r++) { regions_t *reg = &stats->regions[r]; if ( reg->npos > 1 ) { qsort(reg->pos, reg->npos, sizeof(hts_pair_pos_t), regions_lt); for (new_p = 0, p = 1; p < reg->npos; p++) { if ( reg->pos[new_p].end < reg->pos[p].beg ) reg->pos[++new_p] = reg->pos[p]; else if ( reg->pos[new_p].end < reg->pos[p].end ) reg->pos[new_p].end = reg->pos[p].end; } reg->npos = ++new_p; } for (p = 0; p < reg->npos; p++) { if (reg->pos[p].end < HTS_POS_MAX) { stats->target_count += (reg->pos[p].end - reg->pos[p].beg + 1); } else { uint64_t hdr_end = sam_hdr_tid2len(info->sam_header, r); if (hdr_end) stats->target_count += (hdr_end - reg->pos[p].beg + 1); } } } if (!(stats->chunks = calloc(stats->nchunks, sizeof(hts_pair_pos_t)))) error("Could not allocate memory for chunk.\n"); } void destroy_regions(stats_t *stats) { int i; for (i=0; inregions; i++) { if ( !stats->regions[i].mpos ) continue; free(stats->regions[i].pos); } if ( stats->regions ) free(stats->regions); if ( stats->chunks ) free(stats->chunks); } void reset_regions(stats_t *stats) { int i; for (i=0; inregions; i++) stats->regions[i].cpos = 0; } int is_in_regions(bam1_t *bam_line, stats_t *stats) { if ( !stats->regions ) return 1; if ( bam_line->core.tid >= stats->nregions || bam_line->core.tid<0 ) return 0; if ( !stats->is_sorted ) error("The BAM must be sorted in order for -t to work.\n"); regions_t *reg = &stats->regions[bam_line->core.tid]; if ( reg->cpos==reg->npos ) return 0; // done for this chr // Find a matching interval or skip this read. No splicing of reads is done, no indels or soft clips considered, // even small overlap is enough to include the read in the stats. int i = reg->cpos; while ( inpos && reg->pos[i].end<=bam_line->core.pos ) i++; if ( i>=reg->npos ) { reg->cpos = reg->npos; return 0; } int64_t endpos = bam_endpos(bam_line); if ( endpos < reg->pos[i].beg ) return 0; //found a read overlapping a region reg->cpos = i; stats->reg_from = reg->pos[i].beg; stats->reg_to = reg->pos[i].end; //now find all the overlapping chunks stats->nchunks = 0; while (i < reg->npos) { if (bam_line->core.pos < reg->pos[i].end && endpos >= reg->pos[i].beg) { stats->chunks[stats->nchunks].beg = MAX(bam_line->core.pos+1, reg->pos[i].beg); stats->chunks[stats->nchunks].end = MIN(endpos, reg->pos[i].end); stats->nchunks++; } i++; } return 1; } int replicate_regions(stats_t *stats, hts_itr_multi_t *iter, stats_info_t *info) { if ( !stats || !iter) return 1; int i, j, tid; stats->nregions = iter->n_reg; stats->regions = calloc(stats->nregions, sizeof(regions_t)); stats->chunks = calloc(stats->nchunks, sizeof(hts_pair_pos_t)); if ( !stats->regions || !stats->chunks ) return 1; for (i = 0; i < iter->n_reg; i++) { tid = iter->reg_list[i].tid; if ( tid < 0 ) continue; if ( tid >= stats->nregions ) { regions_t *tmp = realloc(stats->regions, (tid+10) * sizeof(regions_t)); if ( !tmp ) return 1; stats->regions = tmp; memset(stats->regions + stats->nregions, 0, (tid+10-stats->nregions) * sizeof(regions_t)); stats->nregions = tid+10; } stats->regions[tid].mpos = stats->regions[tid].npos = iter->reg_list[i].count; stats->regions[tid].pos = calloc(stats->regions[tid].mpos, sizeof(hts_pair_pos_t)); if ( !stats->regions[tid].pos ) return 1; for (j = 0; j < stats->regions[tid].npos; j++) { stats->regions[tid].pos[j].beg = iter->reg_list[i].intervals[j].beg+1; stats->regions[tid].pos[j].end = iter->reg_list[i].intervals[j].end; if (stats->regions[tid].pos[j].end < HTS_POS_MAX) { stats->target_count += (stats->regions[tid].pos[j].end - stats->regions[tid].pos[j].beg + 1); } else { uint64_t hdr_end = sam_hdr_tid2len(info->sam_header, tid); if (hdr_end) stats->target_count += (hdr_end - stats->regions[tid].pos[j].beg + 1); } } } return 0; } static void init_group_id(stats_t *stats, stats_info_t *info, const char *id) { stats->rg_hash = kh_init(rg); if (!stats->rg_hash) error("Could not initialise RG set\n"); sam_hdr_t *hdr = info->sam_header; const char *key; kstring_t sm = KS_INITIALIZE; int i, ret, nrg = sam_hdr_count_lines(hdr, "RG"); if (nrg < 0) error("Could not parse header\n"); for (i=0; irg_hash, key, &ret); if (ret == -1) { ks_free(&sm); error("Could not add key \"%s\" to RG set\n", key); } } else { /* Check for SM name, as per manual */ if (!sam_hdr_find_tag_pos(hdr, "RG", i, "SM", &sm)) { if (!strcmp(ks_c_str(&sm), id)) { kh_put(rg, stats->rg_hash, key, &ret); if (ret == -1) { ks_free(&sm); error("Could not add key \"%s\" to RG set\n", key); } } } } } ks_free(&sm); } static void HTS_FORMAT(HTS_PRINTF_FMT, 1, 2) HTS_NORETURN error(const char *format, ...) { if ( !format ) { printf("About: The program collects statistics from BAM files. The output can be visualized using plot-bamstats.\n"); printf("Usage: samtools stats [OPTIONS] file.bam\n"); printf(" samtools stats [OPTIONS] file.bam chr:from-to\n"); printf("Options:\n"); printf(" -c, --coverage ,, Coverage distribution min,max,step [1,1000,1]\n"); printf(" -d, --remove-dups Exclude from statistics reads marked as duplicates\n"); printf(" -X, --customized-index-file Use a customized index file\n"); printf(" -f, --required-flag Required flag, 0 for unset. See also `samtools flags` [0]\n"); printf(" -F, --filtering-flag Filtering flag, 0 for unset. See also `samtools flags` [0]\n"); printf(" --GC-depth the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4]\n"); printf(" -h, --help This help message\n"); printf(" -i, --insert-size Maximum insert size [8000]\n"); printf(" -I, --id Include only listed read group or sample name\n"); printf(" -l, --read-length Include in the statistics only reads with the given read length [-1]\n"); printf(" -m, --most-inserts Report only the main part of inserts [0.99]\n"); printf(" -P, --split-prefix Path or string prefix for filepaths output by -S (default is input filename)\n"); printf(" -q, --trim-quality The BWA trimming parameter [0]\n"); printf(" -r, --ref-seq Reference sequence (required for GC-depth and mismatches-per-cycle calculation).\n"); printf(" -s, --sam Ignored (input format is auto-detected).\n"); printf(" -S, --split Also write statistics to separate files split by tagged field.\n"); printf(" -t, --target-regions Do stats in these regions only. Tab-delimited file chr,from,to, 1-based, inclusive.\n"); printf(" -x, --sparse Suppress outputting IS rows where there are no insertions.\n"); printf(" -p, --remove-overlaps Remove overlaps of paired-end reads from coverage and base count computations.\n"); printf(" -g, --cov-threshold Only bases with coverage above this value will be included in the target percentage computation [0]\n"); sam_global_opt_help(stdout, "-.--.@-."); printf("\n"); } else { va_list ap; va_start(ap, format); vfprintf(stderr, format, ap); va_end(ap); } exit(1); } void cleanup_stats_info(stats_info_t* info){ if (info->fai) fai_destroy(info->fai); if (info->sam) sam_close(info->sam); free(info); } void cleanup_stats(stats_t* stats) { free(stats->cov_rbuf.buffer); free(stats->cov); free(stats->quals_1st); free(stats->quals_2nd); free(stats->gc_1st); free(stats->gc_2nd); stats->isize->isize_free(stats->isize->data); free(stats->isize); free(stats->gcd); free(stats->rseq_buf); free(stats->mpc_buf); free(stats->acgtno_cycles_1st); free(stats->acgtno_cycles_2nd); free(stats->acgtno_revcomp); free(stats->read_lengths); free(stats->read_lengths_1st); free(stats->read_lengths_2nd); free(stats->insertions); free(stats->deletions); free(stats->ins_cycles_1st); free(stats->ins_cycles_2nd); free(stats->del_cycles_1st); free(stats->del_cycles_2nd); if (stats->acgtno_barcode) free(stats->acgtno_barcode); if (stats->quals_barcode) free(stats->quals_barcode); free(stats->tags_barcode); destroy_regions(stats); if ( stats->rg_hash ) kh_destroy(rg, stats->rg_hash); free(stats->split_name); free(stats->mapping_qualities); free(stats); } void output_split_stats(khash_t(c2stats) *split_hash, char* bam_fname, int sparse) { int i = 0; kstring_t output_filename = { 0, 0, NULL }; stats_t *curr_stats = NULL; for(i = kh_begin(split_hash); i != kh_end(split_hash); ++i){ if(!kh_exist(split_hash, i)) continue; curr_stats = kh_value(split_hash, i); round_buffer_flush(curr_stats, -1); output_filename.l = 0; if (curr_stats->info->split_prefix) kputs(curr_stats->info->split_prefix, &output_filename); else kputs(bam_fname, &output_filename); kputc('_', &output_filename); kputs(curr_stats->split_name, &output_filename); kputs(".bamstat", &output_filename); FILE *to = fopen(output_filename.s, "w"); if(to == NULL){ error("Could not open '%s' for writing.\n", output_filename.s); } output_stats(to, curr_stats, sparse); fclose(to); } free(output_filename.s); } void destroy_split_stats(khash_t(c2stats) *split_hash) { if (!split_hash) return; int i = 0; stats_t *curr_stats = NULL; for(i = kh_begin(split_hash); i != kh_end(split_hash); ++i){ if(!kh_exist(split_hash, i)) continue; curr_stats = kh_value(split_hash, i); cleanup_stats(curr_stats); } kh_destroy(c2stats, split_hash); } stats_info_t* stats_info_init(int argc, char *argv[]) { stats_info_t* info = calloc(1, sizeof(stats_info_t)); if (!info) { return NULL; } info->nisize = 8000; info->isize_main_bulk = 0.99; // There are always outliers at the far end info->gcd_bin_size = 20e3; info->cov_min = 1; info->cov_max = 1000; info->cov_step = 1; info->filter_readlen = -1; info->argc = argc; info->argv = argv; info->remove_overlaps = 0; info->cov_threshold = 0; return info; } int init_stat_info_fname(stats_info_t* info, const char* bam_fname, const htsFormat* in_fmt) { // .. bam samFile* sam; if ((sam = sam_open_format(bam_fname, "r", in_fmt)) == 0) { print_error_errno("stats", "failed to open \"%s\"", bam_fname); return 1; } info->sam = sam; info->sam_header = sam_hdr_read(sam); if (info->sam_header == NULL) { print_error("stats", "failed to read header for \"%s\"", bam_fname); return 1; } return 0; } stats_t* stats_init(void) { stats_t *stats = calloc(1,sizeof(stats_t)); if (!stats) return NULL; stats->ngc = 200; stats->nquals = 256; stats->nbases = 300; stats->rseq_pos = -1; stats->tid = -1; stats->gcd_pos = -1LL; stats->igcd = 0; stats->is_sorted = 1; stats->nindels = stats->nbases; stats->split_name = NULL; stats->nchunks = 0; stats->pair_count = 0; stats->last_pair_tid = -2; stats->last_read_flush = 0; stats->target_count = 0; return stats; } static int init_barcode_tags(stats_t* stats) { stats->ntags = 4; stats->tags_barcode = calloc(stats->ntags, sizeof(barcode_info_t)); if (!stats->tags_barcode) return -1; stats->tags_barcode[0] = (barcode_info_t){"BC", "QT", 0, -1, -1, 0}; stats->tags_barcode[1] = (barcode_info_t){"CR", "CY", 0, -1, -1, 0}; stats->tags_barcode[2] = (barcode_info_t){"OX", "BZ", 0, -1, -1, 0}; stats->tags_barcode[3] = (barcode_info_t){"RX", "QX", 0, -1, -1, 0}; return 0; } static void init_stat_structs(stats_t* stats, stats_info_t* info, const char* group_id, const char* targets) { // Give stats_t a pointer to the info struct // This saves us having to pass the stats_info_t to every function stats->info = info; // Init structures // .. coverage bins and round buffer if ( info->cov_step > info->cov_max - info->cov_min + 1 ) { info->cov_step = info->cov_max - info->cov_min; if ( info->cov_step <= 0 ) info->cov_step = 1; } stats->ncov = 3 + (info->cov_max-info->cov_min) / info->cov_step; info->cov_max = info->cov_min + ((info->cov_max-info->cov_min)/info->cov_step +1)*info->cov_step - 1; stats->cov = calloc(sizeof(uint64_t),stats->ncov); if (!stats->cov) goto nomem; stats->cov_rbuf.size = stats->nbases*5; stats->cov_rbuf.buffer = calloc(sizeof(int32_t),stats->cov_rbuf.size); if (!stats->cov_rbuf.buffer) goto nomem; if ( group_id ) init_group_id(stats, info, group_id); // .. arrays stats->quals_1st = calloc(stats->nquals*stats->nbases,sizeof(uint64_t)); if (!stats->quals_1st) goto nomem; stats->quals_2nd = calloc(stats->nquals*stats->nbases,sizeof(uint64_t)); if (!stats->quals_2nd) goto nomem; stats->gc_1st = calloc(stats->ngc,sizeof(uint64_t)); if (!stats->gc_1st) goto nomem; stats->gc_2nd = calloc(stats->ngc,sizeof(uint64_t)); if (!stats->gc_2nd) goto nomem; stats->isize = init_isize_t(info->nisize ?info->nisize+1 :0); if (!stats->isize) goto nomem; stats->gcd = calloc(stats->ngcd,sizeof(gc_depth_t)); if (!stats->gcd) goto nomem; if (info->fai) { stats->mpc_buf = calloc(stats->nquals*stats->nbases,sizeof(uint64_t)); if (!stats->mpc_buf) goto nomem; } else { stats->mpc_buf = NULL; } stats->acgtno_cycles_1st = calloc(stats->nbases,sizeof(acgtno_count_t)); if (!stats->acgtno_cycles_1st) goto nomem; stats->acgtno_cycles_2nd = calloc(stats->nbases,sizeof(acgtno_count_t)); if (!stats->acgtno_cycles_2nd) goto nomem; stats->acgtno_revcomp = calloc(stats->nbases,sizeof(acgtno_count_t)); if (!stats->acgtno_revcomp) goto nomem; stats->read_lengths = calloc(stats->nbases,sizeof(uint64_t)); if (!stats->read_lengths) goto nomem; stats->read_lengths_1st = calloc(stats->nbases,sizeof(uint64_t)); if (!stats->read_lengths_1st) goto nomem; stats->read_lengths_2nd = calloc(stats->nbases,sizeof(uint64_t)); if (!stats->read_lengths_2nd) goto nomem; stats->insertions = calloc(stats->nbases,sizeof(uint64_t)); if (!stats->insertions) goto nomem; stats->deletions = calloc(stats->nbases,sizeof(uint64_t)); if (!stats->deletions) goto nomem; stats->ins_cycles_1st = calloc(stats->nbases+1,sizeof(uint64_t)); if (!stats->ins_cycles_1st) goto nomem; stats->ins_cycles_2nd = calloc(stats->nbases+1,sizeof(uint64_t)); if (!stats->ins_cycles_2nd) goto nomem; stats->del_cycles_1st = calloc(stats->nbases+1,sizeof(uint64_t)); if (!stats->del_cycles_1st) goto nomem; stats->del_cycles_2nd = calloc(stats->nbases+1,sizeof(uint64_t)); if (!stats->del_cycles_2nd) goto nomem; stats->mapping_qualities = calloc(256,sizeof(uint64_t)); if(!stats->mapping_qualities) goto nomem; if (init_barcode_tags(stats) < 0) goto nomem; realloc_rseq_buffer(stats); if ( targets ) init_regions(stats, targets, info); return; nomem: error("Out of memory"); } static stats_t* get_curr_split_stats(bam1_t* bam_line, khash_t(c2stats)* split_hash, stats_info_t* info, char* targets) { stats_t *curr_stats = NULL; const uint8_t *tag_val = bam_aux_get(bam_line, info->split_tag); if(tag_val == 0){ error("Tag '%s' not found in bam_line.\n", info->split_tag); } char* split_name = strdup(bam_aux2Z(tag_val)); // New stats object, under split khiter_t k = kh_get(c2stats, split_hash, split_name); if(k == kh_end(split_hash)){ curr_stats = stats_init(); // mallocs new instance if (!curr_stats) { error("Couldn't allocate split stats"); } init_stat_structs(curr_stats, info, NULL, targets); curr_stats->split_name = split_name; // Record index in hash int ret = 0; khiter_t iter = kh_put(c2stats, split_hash, split_name, &ret); if( ret < 0 ){ error("Failed to insert key '%s' into split_hash", split_name); } kh_val(split_hash, iter) = curr_stats; // store pointer to stats } else{ curr_stats = kh_value(split_hash, k); free(split_name); // don't need to hold on to this if it wasn't new } return curr_stats; } int main_stats(int argc, char *argv[]) { char *targets = NULL; char *bam_fname = NULL; char *bam_idx_fname = NULL; char *group_id = NULL; int sparse = 0, has_index_file = 0, ret = 1; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; stats_info_t *info = stats_info_init(argc, argv); if (!info) { fprintf(stderr, "Could not allocate memory for info.\n"); return 1; } static const struct option loptions[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '@'), {"help", no_argument, NULL, 'h'}, {"remove-dups", no_argument, NULL, 'd'}, {"sam", no_argument, NULL, 's'}, {"customized-index-file", required_argument, NULL, 'X'}, {"ref-seq", required_argument, NULL, 'r'}, {"coverage", required_argument, NULL, 'c'}, {"read-length", required_argument, NULL, 'l'}, {"insert-size", required_argument, NULL, 'i'}, {"most-inserts", required_argument, NULL, 'm'}, {"trim-quality", required_argument, NULL, 'q'}, {"target-regions", required_argument, NULL, 't'}, {"required-flag", required_argument, NULL, 'f'}, {"filtering-flag", required_argument, NULL, 'F'}, {"id", required_argument, NULL, 'I'}, {"GC-depth", required_argument, NULL, 1}, {"sparse", no_argument, NULL, 'x'}, {"split", required_argument, NULL, 'S'}, {"split-prefix", required_argument, NULL, 'P'}, {"remove-overlaps", no_argument, NULL, 'p'}, {"cov-threshold", required_argument, NULL, 'g'}, {NULL, 0, NULL, 0} }; int opt, tmp_flag; while ( (opt=getopt_long(argc,argv,"?hdsXxpr:c:l:i:t:m:q:f:F:g:I:S:P:@:",loptions,NULL))>0 ) { switch (opt) { case 'f': tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("stats", "Unknown flag '%s'", optarg); return 1; } info->flag_require = tmp_flag; break; case 'F': tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("stats", "Unknown flag '%s'", optarg); return 1; } info->flag_filter |= tmp_flag; break; case 'd': info->flag_filter |= BAM_FDUP; break; case 'X': has_index_file = 1; break; case 's': break; case 'r': info->fai = fai_load(optarg); if (info->fai==NULL) error("Could not load faidx: %s\n", optarg); break; case 1 : info->gcd_bin_size = atof(optarg); break; case 'c': if ( sscanf(optarg,"%d,%d,%d",&info->cov_min,&info->cov_max,&info->cov_step)!= 3 ) error("Unable to parse -c %s\n", optarg); break; case 'l': info->filter_readlen = atoi(optarg); break; case 'i': info->nisize = atoi(optarg); break; case 'm': info->isize_main_bulk = atof(optarg); break; case 'q': info->trim_qual = atoi(optarg); break; case 't': targets = optarg; break; case 'I': group_id = optarg; break; case 'x': sparse = 1; break; case 'S': info->split_tag = optarg; break; case 'P': info->split_prefix = optarg; break; case 'p': info->remove_overlaps = 1; break; case 'g': info->cov_threshold = atoi(optarg); if ( info->cov_threshold < 0 || info->cov_threshold == INT_MAX ) error("Unsupported value for coverage threshold %d\n", info->cov_threshold); break; case '?': case 'h': error(NULL); /* no break */ default: if (parse_sam_global_opt(opt, optarg, loptions, &ga) != 0) error("Unknown argument: %s\n", optarg); break; } } bam_fname = argv[optind++]; if ( !bam_fname ) { if ( isatty(STDIN_FILENO) ) error(NULL); bam_fname = "-"; } if (init_stat_info_fname(info, bam_fname, &ga.in)) { cleanup_stats_info(info); return 1; } if (has_index_file && !(bam_idx_fname = argv[optind++])) { fprintf(stderr, "No index file provided\n"); cleanup_stats_info(info); return 1; } if (ga.nthreads > 0) hts_set_threads(info->sam, ga.nthreads); stats_t *all_stats = stats_init(); if (!all_stats) { fprintf(stderr, "Could not allocate memory for stats.\n"); cleanup_stats_info(info); return 1; } stats_t *curr_stats = NULL; init_stat_structs(all_stats, info, group_id, targets); // Init // .. hash khash_t(c2stats)* split_hash = kh_init(c2stats); if (!split_hash) goto cleanup_all_stats; khash_t(qn2pair)* read_pairs = kh_init(qn2pair); if (!read_pairs) goto cleanup_split_hash; // Collect statistics bam1_t *bam_line = bam_init1(); if (!bam_line) goto cleanup_read_pairs; if (optind < argc) { // Region:interval arguments in the command line hts_idx_t *bam_idx = NULL; if (has_index_file) { bam_idx = sam_index_load2(info->sam, bam_fname, bam_idx_fname); } else { // If an index filename has not been specified, look alongside the alignment file bam_idx = sam_index_load(info->sam, bam_fname); } if (bam_idx) { hts_itr_multi_t *iter = sam_itr_regarray(bam_idx, info->sam_header, &argv[optind], argc - optind); if (iter) { if (!targets) { all_stats->nchunks = argc-optind; if (replicate_regions(all_stats, iter, info)) fprintf(stderr, "Replications of the regions failed\n"); } if ( all_stats->nregions && all_stats->regions ) { while ((ret = sam_itr_next(info->sam, iter, bam_line)) >= 0) { if (info->split_tag) { curr_stats = get_curr_split_stats(bam_line, split_hash, info, targets); collect_stats(bam_line, curr_stats, read_pairs); } collect_stats(bam_line, all_stats, read_pairs); } if (ret < -1) { fprintf(stderr, "Failure while running the iterator\n"); hts_itr_multi_destroy(iter); hts_idx_destroy(bam_idx); goto cleanup; } } hts_itr_multi_destroy(iter); } else { fprintf(stderr, "Multi-region iterator could not be created\n"); hts_idx_destroy(bam_idx); goto cleanup; } hts_idx_destroy(bam_idx); } else { if (has_index_file) fprintf(stderr, "Invalid index file '%s'\n", bam_idx_fname); fprintf(stderr, "Random alignment retrieval only works for indexed files\n"); goto cleanup; } } else { if ( info->cov_threshold > 0 && !targets ) { fprintf(stderr, "Coverage percentage calculation requires a list of target regions\n"); goto cleanup; } // Stream through the entire BAM ignoring off-target regions if -t is given while ((ret = sam_read1(info->sam, info->sam_header, bam_line)) >= 0) { if (info->split_tag) { curr_stats = get_curr_split_stats(bam_line, split_hash, info, targets); collect_stats(bam_line, curr_stats, read_pairs); } collect_stats(bam_line, all_stats, read_pairs); } if (ret < -1) { fprintf(stderr, "Failure while decoding file\n"); goto cleanup; } } round_buffer_flush(all_stats, -1); output_stats(stdout, all_stats, sparse); if (info->split_tag) output_split_stats(split_hash, bam_fname, sparse); ret = 0; cleanup: bam_destroy1(bam_line); sam_hdr_destroy(info->sam_header); sam_global_args_free(&ga); cleanup_read_pairs: cleanup_overlaps(read_pairs, INT64_MAX); cleanup_split_hash: destroy_split_stats(split_hash); cleanup_all_stats: cleanup_stats(all_stats); cleanup_stats_info(info); return ret; } pysam-0.23.0/samtools/stats.c.pysam.c000066400000000000000000003271141475062545500174660ustar00rootroot00000000000000#include "samtools.pysam.h" /* stats.c -- This is the former bamcheck integrated into samtools/htslib. Copyright (C) 2012-2024 Genome Research Ltd. Author: Petr Danecek Author: Sam Nicholls Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Assumptions, approximations and other issues: - GC-depth graph does not split reads, the starting position determines which bin is incremented. There are small overlaps between bins (max readlen-1). However, the bins are big (20k). - coverage distribution ignores softclips and deletions - some stats require sorted BAMs - GC content graph can have an untidy, step-like pattern when BAM contains multiple read lengths. - 'bases mapped' (stats->nbases_mapped) is calculated from read lengths given by BAM (core.l_qseq) - With the -t option, the whole reads are used. Except for the number of mapped bases (cigar) counts, no splicing is done, no indels or soft clips are considered, even small overlap is good enough to include the read in the stats. - GC content of reads not calculated for "=" sequences */ #include #include // for isatty() #include #include #include #include #include #include #include #include #include #include #include // for crc32 #include #include #include #include #include "samtools.h" #include #include #include "stats_isize.h" #include "sam_opts.h" #include "bedidx.h" #define BWA_MIN_RDLEN 35 #define DEFAULT_CHUNK_NO 8 #define DEFAULT_PAIR_MAX 10000 #define ERROR_LIMIT 200 // From the spec // If 0x4 is set, no assumptions can be made about RNAME, POS, CIGAR, MAPQ, bits 0x2, 0x10, 0x100 and 0x800, and the bit 0x20 of the previous read in the template. #define IS_PAIRED(bam) ((bam)->core.flag&BAM_FPAIRED) #define IS_PAIRED_AND_MAPPED(bam) (((bam)->core.flag&BAM_FPAIRED) && !((bam)->core.flag&BAM_FUNMAP) && !((bam)->core.flag&BAM_FMUNMAP)) #define IS_PROPERLYPAIRED(bam) (((bam)->core.flag&(BAM_FPAIRED|BAM_FPROPER_PAIR)) == (BAM_FPAIRED|BAM_FPROPER_PAIR) && !((bam)->core.flag&BAM_FUNMAP)) #define IS_UNMAPPED(bam) ((bam)->core.flag&BAM_FUNMAP) #define IS_REVERSE(bam) ((bam)->core.flag&BAM_FREVERSE) #define IS_MATE_REVERSE(bam) ((bam)->core.flag&BAM_FMREVERSE) #define IS_READ1(bam) ((bam)->core.flag&BAM_FREAD1) #define IS_READ2(bam) ((bam)->core.flag&BAM_FREAD2) #define IS_DUP(bam) ((bam)->core.flag&BAM_FDUP) #define IS_ORIGINAL(bam) (((bam)->core.flag&(BAM_FSECONDARY|BAM_FSUPPLEMENTARY)) == 0) #define READ_ORDER_NONE 0 #define READ_ORDER_FIRST 1 #define READ_ORDER_LAST 2 #define READ_ORDER_MIDDLE 3 #define REG_INC 100 #define POS_INC 1000 // The GC-depth graph works as follows: split the reference sequence into // segments and calculate GC content and depth in each bin. Then sort // these segments by their GC and plot the depth distribution by means // of 10th, 25th, etc. depth percentiles. typedef struct { float gc; uint32_t depth; } gc_depth_t; // For coverage distribution, a simple pileup typedef struct { hts_pos_t pos; int size, start; int *buffer; } round_buffer_t; typedef struct { int npos, mpos, cpos; hts_pair_pos_t *pos; } regions_t; typedef struct { uint64_t a; uint64_t c; uint64_t g; uint64_t t; uint64_t n; uint64_t other; } acgtno_count_t; typedef struct { char tag_name[3]; char qual_name[3]; uint32_t nbases; int32_t tag_sep; // Index of the separator (if present) int32_t max_qual; uint32_t offset; // Where the tag stats info is located in the allocated memory } barcode_info_t; typedef struct { // Auxiliary data int flag_require, flag_filter; faidx_t *fai; // Reference sequence for GC-depth graph int argc; // Command line arguments to be printed on the output char **argv; int gcd_bin_size; // The size of GC-depth bin int nisize; // The maximum insert size that the allocated array can hold - 0 indicates no limit int trim_qual; // bwa trim quality float isize_main_bulk; // There are always some unrealistically big insert sizes, report only the main part int cov_min,cov_max,cov_step; // Minimum, maximum coverage and size of the coverage bins samFile* sam; sam_hdr_t* sam_header; // Filters int filter_readlen; // Misc char *split_tag; // Tag on which to perform stats splitting char *split_prefix; // Path or string prefix for filenames created when splitting int remove_overlaps; int cov_threshold; } stats_info_t; typedef struct { // Dimensions of the quality histogram holder (quals_1st,quals_2nd), GC content holder (gc_1st,gc_2nd), // insert size histogram holder int nquals; // The number of quality bins int nbases; // The maximum sequence length the allocated array can hold int ngc; // The size of gc_1st and gc_2nd int nindels; // The maximum indel length for indel distribution // Arrays for the histogram data uint64_t *quals_1st, *quals_2nd; uint64_t *gc_1st, *gc_2nd; acgtno_count_t *acgtno_cycles_1st, *acgtno_cycles_2nd; acgtno_count_t *acgtno_revcomp; uint64_t *read_lengths, *read_lengths_1st, *read_lengths_2nd; uint64_t *insertions, *deletions; uint64_t *ins_cycles_1st, *ins_cycles_2nd, *del_cycles_1st, *del_cycles_2nd; isize_t *isize; uint64_t* mapping_qualities; // The extremes encountered int max_len; // Maximum read length int max_len_1st; // Maximum read length for forward reads int max_len_2nd; // Maximum read length for reverse reads int max_qual; // Maximum quality int is_sorted; // Summary numbers uint64_t total_len; uint64_t total_len_1st; uint64_t total_len_2nd; uint64_t total_len_dup; uint64_t nreads_1st; uint64_t nreads_2nd; uint64_t nreads_other; uint64_t nreads_filtered; uint64_t nreads_dup; uint64_t nreads_unmapped; uint64_t nreads_single_mapped; uint64_t nreads_paired_and_mapped; uint64_t nreads_properly_paired; uint64_t nreads_paired_tech; uint64_t nreads_anomalous; uint64_t nreads_mq0; uint64_t nbases_mapped; uint64_t nbases_mapped_cigar; uint64_t nbases_trimmed; // bwa trimmed bases uint64_t nmismatches; uint64_t nreads_QCfailed, nreads_secondary, nreads_supplementary; struct { uint32_t names, reads, quals; } checksum; // GC-depth related data uint32_t ngcd, igcd; // The maximum number of GC depth bins and index of the current bin gc_depth_t *gcd; // The GC-depth bins holder int32_t tid; // Position of the current bin hts_pos_t gcd_pos, pos; // Position of the last read // Coverage distribution related data int ncov; // The number of coverage bins uint64_t *cov; // The coverage frequencies round_buffer_t cov_rbuf; // Pileup round buffer // Mismatches by read cycle uint8_t *rseq_buf; // A buffer for reference sequence to check the mismatches against int mrseq_buf; // The size of the buffer hts_pos_t rseq_pos; // The coordinate of the first base in the buffer int64_t nrseq_buf; // The used part of the buffer uint64_t *mpc_buf; // Mismatches per cycle // Target regions int nregions; hts_pos_t reg_from, reg_to; regions_t *regions; // Auxiliary data double sum_qual; // For calculating average quality value void *rg_hash; // Read groups to include, the array is null-terminated // Split char* split_name; stats_info_t* info; // Pointer to options and settings struct hts_pair_pos_t *chunks; uint32_t nchunks; uint32_t pair_count; // Number of active pairs in the pairing hash table uint64_t target_count; // Number of bases covered by the target file uint32_t last_pair_tid; uint32_t last_read_flush; // Barcode statistics acgtno_count_t *acgtno_barcode; uint64_t *quals_barcode; barcode_info_t *tags_barcode; uint32_t ntags; uint32_t error_number; } stats_t; KHASH_MAP_INIT_STR(c2stats, stats_t*) typedef struct { uint32_t first; // 1 - first read, 2 - second read uint32_t n, m; // number of chunks, allocated chunks hts_pair_pos_t *chunks; // chunk array of size m } pair_t; KHASH_MAP_INIT_STR(qn2pair, pair_t*) KHASH_SET_INIT_STR(rg) static void HTS_NORETURN error(const char *format, ...); int is_in_regions(bam1_t *bam_line, stats_t *stats); void realloc_buffers(stats_t *stats, int seq_len); static int regions_lt(const void *r1, const void *r2) { int64_t from_diff = ((hts_pair_pos_t *)r1)->beg - ((hts_pair_pos_t *)r2)->beg; int64_t to_diff = ((hts_pair_pos_t *)r1)->end - ((hts_pair_pos_t *)r2)->end; return from_diff > 0 ? 1 : from_diff < 0 ? -1 : to_diff > 0 ? 1 : to_diff < 0 ? -1 : 0; } // Coverage distribution methods static inline int coverage_idx(int min, int max, int n, int step, int depth) { if ( depth < min ) return 0; if ( depth > max ) return n-1; return 1 + (depth - min) / step; } static inline int round_buffer_lidx2ridx(int offset, int size, hts_pos_t refpos, hts_pos_t pos) { return (offset + (pos-refpos) % size) % size; } void round_buffer_flush(stats_t *stats, hts_pos_t pos) { int ibuf,idp; if ( pos==stats->cov_rbuf.pos ) return; hts_pos_t new_pos = pos; if ( pos==-1 || pos - stats->cov_rbuf.pos >= stats->cov_rbuf.size ) { // Flush the whole buffer, but in sequential order, pos = stats->cov_rbuf.pos + stats->cov_rbuf.size - 1; } if ( pos < stats->cov_rbuf.pos ) error("Expected coordinates in ascending order, got %"PRIhts_pos" after %"PRIhts_pos"\n", pos, stats->cov_rbuf.pos); int ifrom = stats->cov_rbuf.start; int ito = round_buffer_lidx2ridx(stats->cov_rbuf.start, stats->cov_rbuf.size, stats->cov_rbuf.pos, pos-1); if ( ifrom>ito ) { for (ibuf=ifrom; ibufcov_rbuf.size; ibuf++) { if ( !stats->cov_rbuf.buffer[ibuf] ) continue; idp = coverage_idx(stats->info->cov_min,stats->info->cov_max,stats->ncov,stats->info->cov_step,stats->cov_rbuf.buffer[ibuf]); stats->cov[idp]++; stats->cov_rbuf.buffer[ibuf] = 0; } ifrom = 0; } for (ibuf=ifrom; ibuf<=ito; ibuf++) { if ( !stats->cov_rbuf.buffer[ibuf] ) continue; idp = coverage_idx(stats->info->cov_min,stats->info->cov_max,stats->ncov,stats->info->cov_step,stats->cov_rbuf.buffer[ibuf]); stats->cov[idp]++; stats->cov_rbuf.buffer[ibuf] = 0; } stats->cov_rbuf.start = (new_pos==-1) ? 0 : round_buffer_lidx2ridx(stats->cov_rbuf.start, stats->cov_rbuf.size, stats->cov_rbuf.pos, pos); stats->cov_rbuf.pos = new_pos; } /** * [from, to) - 0 based half-open */ static void round_buffer_insert_read(round_buffer_t *rbuf, hts_pos_t from, hts_pos_t to) { if ( to-from > rbuf->size ) error("The read length too big (%"PRIhts_pos"), please increase the buffer length (currently %d)\n", to-from, rbuf->size); if ( from < rbuf->pos ) error("The reads are not sorted (%"PRIhts_pos" comes after %"PRIhts_pos").\n", from, rbuf->pos); int ifrom, ito, ibuf; ifrom = round_buffer_lidx2ridx(rbuf->start, rbuf->size, rbuf->pos, from); ito = round_buffer_lidx2ridx(rbuf->start, rbuf->size, rbuf->pos, to); if ( ifrom>ito ) { for (ibuf=ifrom; ibufsize; ibuf++) rbuf->buffer[ibuf]++; ifrom = 0; } for (ibuf=ifrom; ibufbuffer[ibuf]++; } // Calculate the number of bases in the read trimmed by BWA int bwa_trim_read(int trim_qual, uint8_t *quals, int len, int reverse) { if ( lenmax_sum ) { max_sum = sum; // This is the correct way, but bwa clips from some reason one base less // max_l = l+1; max_l = l; } } return max_l; } void count_indels(stats_t *stats,bam1_t *bam_line) { int is_fwd = IS_REVERSE(bam_line) ? 0 : 1; uint32_t order = IS_PAIRED(bam_line) ? (IS_READ1(bam_line) ? READ_ORDER_FIRST : 0) + (IS_READ2(bam_line) ? READ_ORDER_LAST : 0) : READ_ORDER_FIRST; int icig; int icycle = 0; int read_len = bam_line->core.l_qseq; for (icig=0; icigcore.n_cigar; icig++) { int cig = bam_cigar_op(bam_get_cigar(bam_line)[icig]); int ncig = bam_cigar_oplen(bam_get_cigar(bam_line)[icig]); if ( !ncig ) continue; // curiously, this can happen: 0D if ( cig==BAM_CINS ) { int idx = is_fwd ? icycle : read_len-icycle-ncig; if ( idx<0 ) error("FIXME: read_len=%d vs icycle=%d\n", read_len,icycle); if ( idx >= stats->nbases || idx<0 ) error("FIXME: %d vs %d, %s:%"PRIhts_pos" %s\n", idx, stats->nbases, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line)); if ( order == READ_ORDER_FIRST ) stats->ins_cycles_1st[idx]++; if ( order == READ_ORDER_LAST ) stats->ins_cycles_2nd[idx]++; icycle += ncig; if ( ncig<=stats->nindels ) stats->insertions[ncig-1]++; continue; } if ( cig==BAM_CDEL ) { int idx = is_fwd ? icycle-1 : read_len-icycle-1; if ( idx<0 ) continue; // discard meaningless deletions if ( idx >= stats->nbases ) error("FIXME: %d vs %d\n", idx,stats->nbases); if ( order == READ_ORDER_FIRST ) stats->del_cycles_1st[idx]++; if ( order == READ_ORDER_LAST ) stats->del_cycles_2nd[idx]++; if ( ncig<=stats->nindels ) stats->deletions[ncig-1]++; continue; } if ( cig!=BAM_CREF_SKIP && cig!=BAM_CHARD_CLIP && cig!=BAM_CPAD ) icycle += ncig; } } int unclipped_length(bam1_t *bam_line) { int icig, read_len = bam_line->core.l_qseq; for (icig=0; icigcore.n_cigar; icig++) { int cig = bam_cigar_op(bam_get_cigar(bam_line)[icig]); if ( cig==BAM_CHARD_CLIP ) read_len += bam_cigar_oplen(bam_get_cigar(bam_line)[icig]); } return read_len; } void count_mismatches_per_cycle(stats_t *stats, bam1_t *bam_line, int read_len) { int is_fwd = IS_REVERSE(bam_line) ? 0 : 1; int icig, iread=0, icycle=0; hts_pos_t iref = bam_line->core.pos - stats->rseq_pos; uint8_t *read = bam_get_seq(bam_line); uint8_t *quals = bam_get_qual(bam_line); uint64_t *mpc_buf = stats->mpc_buf; for (icig=0; icigcore.n_cigar; icig++) { int cig = bam_cigar_op(bam_get_cigar(bam_line)[icig]); int ncig = bam_cigar_oplen(bam_get_cigar(bam_line)[icig]); if ( cig==BAM_CINS ) { iread += ncig; icycle += ncig; continue; } if ( cig==BAM_CDEL ) { iref += ncig; continue; } if ( cig==BAM_CSOFT_CLIP ) { icycle += ncig; // Soft-clips are present in the sequence, but the position of the read marks a start of the sequence after clipping // iref += ncig; iread += ncig; continue; } if ( cig==BAM_CHARD_CLIP ) { icycle += ncig; continue; } // Ignore H and N CIGARs. The letter are inserted e.g. by TopHat and often require very large // chunk of refseq in memory. Not very frequent and not noticeable in the stats. if ( cig==BAM_CREF_SKIP || cig==BAM_CHARD_CLIP || cig==BAM_CPAD ) continue; if ( cig!=BAM_CMATCH && cig!=BAM_CEQUAL && cig!=BAM_CDIFF ) // not relying on precalculated diffs error("TODO: cigar %d, %s:%"PRIhts_pos" %s\n", cig, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line)); if ( ncig+iref > stats->nrseq_buf ) error("FIXME: %d+%"PRIhts_pos" > %"PRId64", %s, %s:%"PRIhts_pos"\n", ncig, iref, stats->nrseq_buf, bam_get_qname(bam_line), sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1); int im; for (im=0; imrseq_buf[iref]; // ---------------15 // =ACMGRSVTWYHKDBN if ( cread==15 ) { int idx = is_fwd ? icycle : read_len-icycle-1; if ( idx>stats->max_len ) error("mpc: %d>%d\n",idx,stats->max_len); idx = idx*stats->nquals; if ( idx>=stats->nquals*stats->nbases ) error("FIXME: mpc_buf overflow\n"); mpc_buf[idx]++; } else if ( cref && cread && cref!=cread ) { uint8_t qual = quals[iread] + 1; if ( qual>=stats->nquals ) error("TODO: quality too high %d>=%d (%s %"PRIhts_pos" %s)\n", qual, stats->nquals, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line)); int idx = is_fwd ? icycle : read_len-icycle-1; if ( idx>stats->max_len ) error("mpc: %d>%d (%s %"PRIhts_pos" %s)\n", idx, stats->max_len, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line)); idx = idx*stats->nquals + qual; if ( idx>=stats->nquals*stats->nbases ) error("FIXME: mpc_buf overflow\n"); mpc_buf[idx]++; } iref++; iread++; icycle++; } } } void read_ref_seq(stats_t *stats, int32_t tid, hts_pos_t pos, hts_pos_t end) { int i; hts_pos_t fai_ref_len; char *fai_ref; if (end < pos+stats->mrseq_buf-1) end = pos+stats->mrseq_buf-1; else if (stats->mrseq_buf < end - pos) { size_t sz = end - pos; uint8_t *new_rseq = realloc(stats->rseq_buf, sz); if (!new_rseq) error("Couldn't expand the reference sequence buffer\n"); stats->rseq_buf = new_rseq; stats->mrseq_buf = sz; } fai_ref = faidx_fetch_seq64(stats->info->fai, sam_hdr_tid2name(stats->info->sam_header, tid), pos, pos+stats->mrseq_buf-1, &fai_ref_len); if ( fai_ref_len < 0 ) error("Failed to fetch the sequence \"%s\"\n", sam_hdr_tid2name(stats->info->sam_header, tid)); uint8_t *ptr = stats->rseq_buf; for (i=0; imrseq_buf ) memset(ptr,0, stats->mrseq_buf - fai_ref_len); stats->nrseq_buf = fai_ref_len; stats->rseq_pos = pos; stats->tid = tid; } float fai_gc_content(stats_t *stats, hts_pos_t pos, int len) { uint32_t gc,count,c; hts_pos_t i = pos - stats->rseq_pos, ito = i + len; assert( i>=0 ); if ( ito > stats->nrseq_buf ) ito = stats->nrseq_buf; // Count GC content gc = count = 0; for (; irseq_buf[i]; if ( c==2 || c==4 ) { gc++; count++; } else if ( c==1 || c==8 ) count++; } return count ? (float)gc/count : 0; } void realloc_rseq_buffer(stats_t *stats) { int n = stats->nbases*10; if ( stats->info->gcd_bin_size > n ) n = stats->info->gcd_bin_size; if ( stats->mrseq_bufrseq_buf = realloc(stats->rseq_buf,sizeof(uint8_t)*n); if (!stats->rseq_buf) { error("Could not reallocate reference sequence buffer"); } stats->mrseq_buf = n; } } void realloc_gcd_buffer(stats_t *stats, int seq_len) { hts_expand0(gc_depth_t,stats->igcd+1,stats->ngcd,stats->gcd); realloc_rseq_buffer(stats); } void realloc_buffers(stats_t *stats, int seq_len) { int n = 2*(1 + seq_len - stats->nbases) + stats->nbases; stats->quals_1st = realloc(stats->quals_1st, n*stats->nquals*sizeof(uint64_t)); if ( !stats->quals_1st ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*stats->nquals*sizeof(uint64_t)); memset(stats->quals_1st + stats->nbases*stats->nquals, 0, (n-stats->nbases)*stats->nquals*sizeof(uint64_t)); stats->quals_2nd = realloc(stats->quals_2nd, n*stats->nquals*sizeof(uint64_t)); if ( !stats->quals_2nd ) error("Could not realloc buffers, the sequence too long: %d (2x%ld)\n", seq_len,n*stats->nquals*sizeof(uint64_t)); memset(stats->quals_2nd + stats->nbases*stats->nquals, 0, (n-stats->nbases)*stats->nquals*sizeof(uint64_t)); if ( stats->mpc_buf ) { stats->mpc_buf = realloc(stats->mpc_buf, n*stats->nquals*sizeof(uint64_t)); if ( !stats->mpc_buf ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*stats->nquals*sizeof(uint64_t)); memset(stats->mpc_buf + stats->nbases*stats->nquals, 0, (n-stats->nbases)*stats->nquals*sizeof(uint64_t)); } stats->acgtno_cycles_1st = realloc(stats->acgtno_cycles_1st, n*sizeof(acgtno_count_t)); if ( !stats->acgtno_cycles_1st ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len, n*sizeof(acgtno_count_t)); memset(stats->acgtno_cycles_1st + stats->nbases, 0, (n-stats->nbases)*sizeof(acgtno_count_t)); stats->acgtno_cycles_2nd = realloc(stats->acgtno_cycles_2nd, n*sizeof(acgtno_count_t)); if ( !stats->acgtno_cycles_2nd ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len, n*sizeof(acgtno_count_t)); memset(stats->acgtno_cycles_2nd + stats->nbases, 0, (n-stats->nbases)*sizeof(acgtno_count_t)); stats->acgtno_revcomp = realloc(stats->acgtno_revcomp, n*sizeof(acgtno_count_t)); if ( !stats->acgtno_revcomp ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len, n*sizeof(acgtno_count_t)); memset(stats->acgtno_revcomp + stats->nbases, 0, (n-stats->nbases)*sizeof(acgtno_count_t)); stats->read_lengths = realloc(stats->read_lengths, n*sizeof(uint64_t)); if ( !stats->read_lengths ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t)); memset(stats->read_lengths + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->read_lengths_1st = realloc(stats->read_lengths_1st, n*sizeof(uint64_t)); if ( !stats->read_lengths_1st ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t)); memset(stats->read_lengths_1st + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->read_lengths_2nd = realloc(stats->read_lengths_2nd, n*sizeof(uint64_t)); if ( !stats->read_lengths_2nd ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t)); memset(stats->read_lengths_2nd + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->insertions = realloc(stats->insertions, n*sizeof(uint64_t)); if ( !stats->insertions ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t)); memset(stats->insertions + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->deletions = realloc(stats->deletions, n*sizeof(uint64_t)); if ( !stats->deletions ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t)); memset(stats->deletions + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->ins_cycles_1st = realloc(stats->ins_cycles_1st, (n+1)*sizeof(uint64_t)); if ( !stats->ins_cycles_1st ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t)); memset(stats->ins_cycles_1st + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->ins_cycles_2nd = realloc(stats->ins_cycles_2nd, (n+1)*sizeof(uint64_t)); if ( !stats->ins_cycles_2nd ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t)); memset(stats->ins_cycles_2nd + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->del_cycles_1st = realloc(stats->del_cycles_1st, (n+1)*sizeof(uint64_t)); if ( !stats->del_cycles_1st ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t)); memset(stats->del_cycles_1st + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->del_cycles_2nd = realloc(stats->del_cycles_2nd, (n+1)*sizeof(uint64_t)); if ( !stats->del_cycles_2nd ) error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t)); memset(stats->del_cycles_2nd + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->nbases = n; // Realloc the coverage distribution buffer int *rbuffer = calloc(sizeof(int),seq_len*5); if (!rbuffer) { error("Could not allocate coverage distribution buffer"); } n = stats->cov_rbuf.size-stats->cov_rbuf.start; memcpy(rbuffer,stats->cov_rbuf.buffer+stats->cov_rbuf.start,n); if ( stats->cov_rbuf.start>1 ) memcpy(rbuffer+n,stats->cov_rbuf.buffer,stats->cov_rbuf.start); stats->cov_rbuf.start = 0; free(stats->cov_rbuf.buffer); stats->cov_rbuf.buffer = rbuffer; stats->cov_rbuf.size = seq_len*5; realloc_rseq_buffer(stats); } void update_checksum(bam1_t *bam_line, stats_t *stats) { uint8_t *name = (uint8_t*) bam_get_qname(bam_line); int len = 0; while ( name[len] ) len++; stats->checksum.names += crc32(0L, name, len); int seq_len = bam_line->core.l_qseq; if ( !seq_len ) return; uint8_t *seq = bam_get_seq(bam_line); stats->checksum.reads += crc32(0L, seq, (seq_len+1)/2); uint8_t *qual = bam_get_qual(bam_line); stats->checksum.quals += crc32(0L, qual, (seq_len+1)/2); } // Collect statistics about the barcode tags specified by init_barcode_tags method static void collect_barcode_stats(bam1_t* bam_line, stats_t* stats) { uint32_t nbases, tag, i; acgtno_count_t *acgtno; uint64_t *quals; int32_t *separator, *maxqual; for (tag = 0; tag < stats->ntags; tag++) { const char *barcode_tag = stats->tags_barcode[tag].tag_name, *qual_tag = stats->tags_barcode[tag].qual_name; uint8_t* bc = bam_aux_get(bam_line, barcode_tag); if (!bc) continue; char* barcode = bam_aux2Z(bc); if (!barcode) continue; uint32_t barcode_len = strlen(barcode); if (!barcode_len) { continue; //consider 0 size barcode same as no barcode - avoids issues with realloc below } if (!stats->tags_barcode[tag].nbases) { // tag seen for the first time uint32_t offset = 0; for (i = 0; i < stats->ntags; i++) offset += stats->tags_barcode[i].nbases; stats->tags_barcode[tag].offset = offset; stats->tags_barcode[tag].nbases = barcode_len; stats->acgtno_barcode = realloc(stats->acgtno_barcode, (offset + barcode_len) * sizeof(acgtno_count_t)); stats->quals_barcode = realloc(stats->quals_barcode, (offset + barcode_len) * stats->nquals * sizeof(uint64_t)); if (!stats->acgtno_barcode || !stats->quals_barcode) error("Error allocating memory. Aborting!\n"); memset(stats->acgtno_barcode + offset, 0, barcode_len*sizeof(acgtno_count_t)); memset(stats->quals_barcode + offset*stats->nquals, 0, barcode_len*stats->nquals*sizeof(uint64_t)); } nbases = stats->tags_barcode[tag].nbases; if (barcode_len > nbases) { fprintf(samtools_stderr, "Barcodes with tag %s differ in length at sequence '%s'\n", barcode_tag, bam_get_qname(bam_line)); continue; } acgtno = stats->acgtno_barcode + stats->tags_barcode[tag].offset; quals = stats->quals_barcode + stats->tags_barcode[tag].offset*stats->nquals; maxqual = &stats->tags_barcode[tag].max_qual; separator = &stats->tags_barcode[tag].tag_sep; int error_flag = 0; for (i = 0; i < barcode_len; i++) { switch (barcode[i]) { case 'A': acgtno[i].a++; break; case 'C': acgtno[i].c++; break; case 'G': acgtno[i].g++; break; case 'T': acgtno[i].t++; break; case 'N': acgtno[i].n++; break; default: if (*separator >= 0) { if (*separator != i) { if (stats->error_number < ERROR_LIMIT) { fprintf(samtools_stderr, "Barcode separator for tag %s is in a different position or wrong barcode content('%s') at sequence '%s'\n", barcode_tag, barcode, bam_get_qname(bam_line)); stats->error_number++; } error_flag = 1; } } else { *separator = i; } } /* don't process the rest of the tag bases */ if (error_flag) break; } /* skip to the next tag */ if (error_flag) continue; uint8_t* qt = bam_aux_get(bam_line, qual_tag); if (!qt) continue; char* barqual = bam_aux2Z(qt); if (!barqual) continue; uint32_t barqual_len = strlen(barqual); if (barqual_len == barcode_len) { for (i = 0; i < barcode_len; i++) { int32_t qual = (int32_t)barqual[i] - '!'; // Phred + 33 if (qual >= 0 && qual < stats->nquals) { quals[i * stats->nquals + qual]++; if (qual > *maxqual) *maxqual = qual; } } } else { if (stats->error_number++ < ERROR_LIMIT) { fprintf(samtools_stderr, "%s length and %s length don't match for sequence '%s'\n", barcode_tag, qual_tag, bam_get_qname(bam_line)); } } } } // These stats should only be calculated for the original reads ignoring // supplementary artificial reads otherwise we'll accidentally double count void collect_orig_read_stats(bam1_t *bam_line, stats_t *stats, int* gc_count_out) { int seq_len = bam_line->core.l_qseq; stats->total_len += seq_len; // This ignores clipping so only count primary if ( bam_line->core.flag & BAM_FQCFAIL ) stats->nreads_QCfailed++; if ( bam_line->core.flag & BAM_FPAIRED ) stats->nreads_paired_tech++; uint32_t order = IS_PAIRED(bam_line) ? (IS_READ1(bam_line) ? READ_ORDER_FIRST : 0) + (IS_READ2(bam_line) ? READ_ORDER_LAST : 0) : READ_ORDER_FIRST; // Count GC and ACGT per cycle. Note that cycle is approximate, clipping is ignored uint8_t *seq = bam_get_seq(bam_line); int i, read_cycle, gc_count = 0, reverse = IS_REVERSE(bam_line); acgtno_count_t *acgtno_cycles = (order == READ_ORDER_FIRST) ? stats->acgtno_cycles_1st : (order == READ_ORDER_LAST) ? stats->acgtno_cycles_2nd : NULL ; if (acgtno_cycles) { for (i=0; iacgtno_revcomp[ read_cycle ].t++ : stats->acgtno_revcomp[ read_cycle ].a++; break; case 2: acgtno_cycles[ read_cycle ].c++; reverse ? stats->acgtno_revcomp[ read_cycle ].g++ : stats->acgtno_revcomp[ read_cycle ].c++; gc_count++; break; case 4: acgtno_cycles[ read_cycle ].g++; reverse ? stats->acgtno_revcomp[ read_cycle ].c++ : stats->acgtno_revcomp[ read_cycle ].g++; gc_count++; break; case 8: reverse ? stats->acgtno_revcomp[ read_cycle ].a++ : stats->acgtno_revcomp[ read_cycle ].t++; acgtno_cycles[ read_cycle ].t++; break; case 15: acgtno_cycles[ read_cycle ].n++; break; default: /* * count "=" sequences in "other" along * with MRSVWYHKDB ambiguity codes */ acgtno_cycles[ read_cycle ].other++; break; } } } int gc_idx_min = gc_count*(stats->ngc-1)/seq_len; int gc_idx_max = (gc_count+1)*(stats->ngc-1)/seq_len; if ( gc_idx_max >= stats->ngc ) gc_idx_max = stats->ngc - 1; // Determine which array (1st or 2nd read) will these stats go to, // trim low quality bases from end the same way BWA does, // fill GC histogram uint64_t *quals = NULL; uint8_t *bam_quals = bam_get_qual(bam_line); switch (order) { case READ_ORDER_FIRST: quals = stats->quals_1st; stats->nreads_1st++; stats->total_len_1st += seq_len; for (i=gc_idx_min; igc_1st[i]++; break; case READ_ORDER_LAST: quals = stats->quals_2nd; stats->nreads_2nd++; stats->total_len_2nd += seq_len; for (i=gc_idx_min; igc_2nd[i]++; break; default: stats->nreads_other++; } if ( stats->info->trim_qual>0 ) stats->nbases_trimmed += bwa_trim_read(stats->info->trim_qual, bam_quals, seq_len, reverse); // Quality histogram and average quality. Clipping is neglected. if (quals) { for (i=0; i=stats->nquals ) error("TODO: quality too high %d>=%d (%s %"PRIhts_pos" %s)\n", qual, stats->nquals, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line)); if ( qual>stats->max_qual ) stats->max_qual = qual; quals[ i*stats->nquals+qual ]++; stats->sum_qual += qual; } } // Barcode statistics if (order == READ_ORDER_FIRST) { collect_barcode_stats(bam_line, stats); } // Look at the flags and increment appropriate counters (mapped, paired, etc) if ( IS_UNMAPPED(bam_line) ) { stats->nreads_unmapped++; } else { stats->nbases_mapped += seq_len; // This ignores clipping so only count primary if ( !bam_line->core.qual ) stats->nreads_mq0++; if ( !IS_PAIRED_AND_MAPPED(bam_line) ) stats->nreads_single_mapped++; else { stats->nreads_paired_and_mapped++; if (IS_PROPERLYPAIRED(bam_line)) stats->nreads_properly_paired++; if ( bam_line->core.tid!=bam_line->core.mtid ) stats->nreads_anomalous++; } } *gc_count_out = gc_count; } static int cleanup_overlaps(khash_t(qn2pair) *read_pairs, hts_pos_t max) { if ( !read_pairs ) return 0; int count = 0; khint_t k; for (k = kh_begin(read_pairs); k < kh_end(read_pairs); k++) { if ( kh_exist(read_pairs, k) ) { char *key = (char *)kh_key(read_pairs, k); pair_t *val = kh_val(read_pairs, k); if ( val && val->chunks ) { if ( val->chunks[val->n-1].end < max ) { free(val->chunks); free(val); free(key); kh_del(qn2pair, read_pairs, k); count++; } } else { free(key); kh_del(qn2pair, read_pairs, k); count++; } } } if ( max == INT64_MAX ) kh_destroy(qn2pair, read_pairs); return count; } /** * [pmin, pmax) - 0 based half-open */ static void remove_overlaps(bam1_t *bam_line, khash_t(qn2pair) *read_pairs, stats_t *stats, hts_pos_t pmin, hts_pos_t pmax) { if ( !bam_line || !read_pairs || !stats ) return; uint32_t order = (IS_READ1(bam_line) ? READ_ORDER_FIRST : 0) + (IS_READ2(bam_line) ? READ_ORDER_LAST : 0); if ( !(bam_line->core.flag & BAM_FPAIRED) || (bam_line->core.flag & BAM_FMUNMAP) || (llabs(bam_line->core.isize) >= 2*bam_line->core.l_qseq) || (order != READ_ORDER_FIRST && order != READ_ORDER_LAST) ) { if ( pmin >= 0 ) round_buffer_insert_read(&(stats->cov_rbuf), pmin, pmax); return; } char *qname = bam_get_qname(bam_line); if ( !qname ) { fprintf(samtools_stderr, "Error retrieving qname for line starting at pos %"PRIhts_pos"\n", bam_line->core.pos); return; } khint_t k = kh_get(qn2pair, read_pairs, qname); if ( k == kh_end(read_pairs) ) { //first chunk from this template if ( pmin == -1 ) return; int ret; char *s = strdup(qname); if ( !s ) { fprintf(samtools_stderr, "Error allocating memory\n"); return; } k = kh_put(qn2pair, read_pairs, s, &ret); if ( -1 == ret ) { error("Error inserting read '%s' in pair hash table\n", qname); } pair_t *pc = calloc(1, sizeof(pair_t)); if ( !pc ) { fprintf(samtools_stderr, "Error allocating memory\n"); return; } pc->m = DEFAULT_CHUNK_NO; pc->chunks = calloc(pc->m, sizeof(hts_pair_pos_t)); if ( !pc->chunks ) { fprintf(samtools_stderr, "Error allocating memory\n"); free(pc); return; } pc->chunks[0].beg = pmin; pc->chunks[0].end = pmax; pc->n = 1; pc->first = order; kh_val(read_pairs, k) = pc; stats->pair_count++; } else { //template already present pair_t *pc = kh_val(read_pairs, k); if ( !pc ) { fprintf(samtools_stderr, "Invalid hash table entry\n"); return; } if ( order == pc->first ) { //chunk from an existing line if ( pmin == -1 ) return; if ( pc->n == pc->m ) { hts_pair_pos_t *tmp = realloc(pc->chunks, (pc->m<<1)*sizeof(hts_pair_pos_t)); if ( !tmp ) { fprintf(samtools_stderr, "Error allocating memory\n"); return; } pc->chunks = tmp; pc->m<<=1; } pc->chunks[pc->n].beg = pmin; pc->chunks[pc->n].end = pmax; pc->n++; } else { //the other line, check for overlapping if ( pmin == -1 && kh_exist(read_pairs, k) ) { //job done, delete entry char *key = (char *)kh_key(read_pairs, k); pair_t *val = kh_val(read_pairs, k); if ( val) { free(val->chunks); free(val); } free(key); kh_del(qn2pair, read_pairs, k); stats->pair_count--; return; } int i; for (i=0; in; i++) { if ( pmin >= pc->chunks[i].end ) continue; if ( pmax <= pc->chunks[i].beg ) //no overlap break; if ( pmin < pc->chunks[i].beg ) { //overlap at the beginning round_buffer_insert_read(&(stats->cov_rbuf), pmin, pc->chunks[i].beg); pmin = pc->chunks[i].beg; } if ( pmax <= pc->chunks[i].end ) { //completely contained stats->nbases_mapped_cigar -= (pmax - pmin); return; } else { //overlap at the end stats->nbases_mapped_cigar -= (pc->chunks[i].end - pmin); pmin = pc->chunks[i].end; } } } } round_buffer_insert_read(&(stats->cov_rbuf), pmin, pmax); } void collect_stats(bam1_t *bam_line, stats_t *stats, khash_t(qn2pair) *read_pairs) { if ( !is_in_regions(bam_line,stats) ) return; if ( stats->rg_hash ) { const uint8_t *rg = bam_aux_get(bam_line, "RG"); if ( !rg ) return; // certain read groups were requested but this record has none khint_t k = kh_get(rg, stats->rg_hash, (const char*)(rg + 1)); if ( k == kh_end((kh_rg_t *)stats->rg_hash) ) return; } if ( stats->info->flag_require && (bam_line->core.flag & stats->info->flag_require)!=stats->info->flag_require ) { stats->nreads_filtered++; return; } if ( stats->info->flag_filter && (bam_line->core.flag & stats->info->flag_filter) ) { stats->nreads_filtered++; return; } if ( stats->info->filter_readlen!=-1 && bam_line->core.l_qseq!=stats->info->filter_readlen ) return; update_checksum(bam_line, stats); // Secondary reads don't count for most stats purposes if ( bam_line->core.flag & BAM_FSECONDARY ) { stats->nreads_secondary++; return; } if ( bam_line->core.flag & BAM_FSUPPLEMENTARY ) { stats->nreads_supplementary++; } // If line has no sequence cannot continue int seq_len = bam_line->core.l_qseq; if ( !seq_len ) return; if ( IS_DUP(bam_line) ) { stats->total_len_dup += seq_len; stats->nreads_dup++; } uint32_t order = IS_PAIRED(bam_line) ? (IS_READ1(bam_line) ? READ_ORDER_FIRST : 0) + (IS_READ2(bam_line) ? READ_ORDER_LAST : 0) : READ_ORDER_FIRST; int read_len = unclipped_length(bam_line); if ( read_len >= stats->nbases ) realloc_buffers(stats,read_len); // Update max_len observed if ( stats->max_lenmax_len = read_len; if ( order == READ_ORDER_FIRST && stats->max_len_1st < read_len ) stats->max_len_1st = read_len; if ( order == READ_ORDER_LAST && stats->max_len_2nd < read_len ) stats->max_len_2nd = read_len; if ( ( bam_line->core.flag & (BAM_FUNMAP|BAM_FSECONDARY|BAM_FSUPPLEMENTARY|BAM_FQCFAIL|BAM_FDUP) ) == 0 ) stats->mapping_qualities[bam_line->core.qual]++; int i; int gc_count = 0; // These stats should only be calculated for the original reads ignoring supplementary artificial reads // otherwise we'll accidentally double count if ( IS_ORIGINAL(bam_line) ) { stats->read_lengths[read_len]++; if ( order == READ_ORDER_FIRST ) stats->read_lengths_1st[read_len]++; if ( order == READ_ORDER_LAST ) stats->read_lengths_2nd[read_len]++; collect_orig_read_stats(bam_line, stats, &gc_count); } // Look at the flags and increment appropriate counters (mapped, paired, etc) if ( IS_UNMAPPED(bam_line) ) return; count_indels(stats, bam_line); if ( IS_PAIRED_AND_MAPPED(bam_line) && IS_ORIGINAL(bam_line) ) { // The insert size is tricky, because for long inserts the libraries are // prepared differently and the pairs point in other direction. BWA does // not set the paired flag for them. Similar thing is true also for 454 // reads. Mates mapped to different chromosomes have isize==0. int32_t isize = bam_line->core.isize; if ( isize<0 ) isize = -isize; if ( stats->info->nisize > 0 && isize > stats->info->nisize ) isize = stats->info->nisize; if ( isize>0 || bam_line->core.tid==bam_line->core.mtid ) { hts_pos_t pos_fst = bam_line->core.mpos - bam_line->core.pos; int is_fst = IS_READ1(bam_line) ? 1 : -1; int is_fwd = IS_REVERSE(bam_line) ? -1 : 1; int is_mfwd = IS_MATE_REVERSE(bam_line) ? -1 : 1; if ( is_fwd*is_mfwd>0 ) stats->isize->inc_other(stats->isize->data, isize); else if ( is_fst*pos_fst>=0 ) { if ( is_fst*is_fwd>0 ) stats->isize->inc_inward(stats->isize->data, isize); else stats->isize->inc_outward(stats->isize->data, isize); } else if ( is_fst*pos_fst<0 ) { if ( is_fst*is_fwd>0 ) stats->isize->inc_outward(stats->isize->data, isize); else stats->isize->inc_inward(stats->isize->data, isize); } } } // Number of mismatches uint8_t *nm = bam_aux_get(bam_line,"NM"); if (nm) stats->nmismatches += bam_aux2i(nm); // Number of mapped bases from cigar if ( bam_line->core.n_cigar == 0) error("FIXME: mapped read with no cigar?\n"); int readlen=seq_len; if ( stats->regions ) { // Count only on-target bases hts_pos_t iref = bam_line->core.pos + 1; for (i=0; icore.n_cigar; i++) { int cig = bam_cigar_op(bam_get_cigar(bam_line)[i]); int ncig = bam_cigar_oplen(bam_get_cigar(bam_line)[i]); if ( !ncig ) continue; // curiously, this can happen: 0D if ( cig==BAM_CDEL ) readlen += ncig; else if ( cig==BAM_CMATCH || cig==BAM_CEQUAL || cig==BAM_CDIFF ) { if ( iref < stats->reg_from ) ncig -= stats->reg_from-iref; else if ( iref+ncig-1 > stats->reg_to ) ncig -= iref+ncig-1 - stats->reg_to; if ( ncig<0 ) ncig = 0; stats->nbases_mapped_cigar += ncig; iref += bam_cigar_oplen(bam_get_cigar(bam_line)[i]); } else if ( cig==BAM_CINS ) { iref += ncig; if ( iref>=stats->reg_from && iref<=stats->reg_to ) stats->nbases_mapped_cigar += ncig; } } } else { // Count the whole read for (i=0; icore.n_cigar; i++) { int cig = bam_cigar_op(bam_get_cigar(bam_line)[i]); if ( cig==BAM_CMATCH || cig==BAM_CINS || cig==BAM_CEQUAL || cig==BAM_CDIFF ) stats->nbases_mapped_cigar += bam_cigar_oplen(bam_get_cigar(bam_line)[i]); if ( cig==BAM_CDEL ) readlen += bam_cigar_oplen(bam_get_cigar(bam_line)[i]); } } if ( stats->tid==bam_line->core.tid && bam_line->core.pospos ) stats->is_sorted = 0; stats->pos = bam_line->core.pos; if ( stats->is_sorted ) { if ( stats->tid==-1 || stats->tid!=bam_line->core.tid ) { round_buffer_flush(stats, -1); } //cleanup the pair hash table to free memory stats->last_read_flush++; if ( stats->pair_count > DEFAULT_PAIR_MAX && stats->last_read_flush > DEFAULT_PAIR_MAX) { stats->pair_count -= cleanup_overlaps(read_pairs, bam_line->core.pos); stats->last_read_flush = 0; } if ( stats->last_pair_tid != bam_line->core.tid) { stats->pair_count -= cleanup_overlaps(read_pairs, INT64_MAX-1); stats->last_pair_tid = bam_line->core.tid; stats->last_read_flush = 0; } // Mismatches per cycle and GC-depth graph. For simplicity, reads overlapping GCD bins // are not splitted which results in up to seq_len-1 overlaps. The default bin size is // 20kbp, so the effect is negligible. if ( stats->info->fai ) { hts_pos_t inc_ref = 0; int inc_gcd = 0; // First pass or new chromosome, or read goes beyond the rseq buffer if ( stats->rseq_pos==-1 || stats->tid != bam_line->core.tid || stats->rseq_pos+stats->nrseq_buf < bam_line->core.pos+readlen) { inc_ref=bam_line->core.pos+readlen; inc_gcd=1; } // Read overlaps the next gcd bin else if ( stats->gcd_pos+stats->info->gcd_bin_size < bam_line->core.pos+readlen ) { inc_gcd = 1; if ( stats->rseq_pos+stats->nrseq_buf < bam_line->core.pos+stats->info->gcd_bin_size ) inc_ref = bam_line->core.pos+stats->info->gcd_bin_size; } if ( inc_gcd ) { stats->igcd++; if ( stats->igcd >= stats->ngcd ) realloc_gcd_buffer(stats, readlen); if ( inc_ref ) read_ref_seq(stats, bam_line->core.tid, bam_line->core.pos, inc_ref); stats->gcd_pos = bam_line->core.pos; stats->gcd[ stats->igcd ].gc = fai_gc_content(stats, stats->gcd_pos, stats->info->gcd_bin_size); } count_mismatches_per_cycle(stats,bam_line,read_len); } // No reference and first pass, new chromosome or sequence going beyond the end of the gcd bin else if ( stats->gcd_pos==-1 || stats->tid != bam_line->core.tid || bam_line->core.pos - stats->gcd_pos > stats->info->gcd_bin_size ) { // First pass or a new chromosome stats->tid = bam_line->core.tid; stats->gcd_pos = bam_line->core.pos; stats->igcd++; if ( stats->igcd >= stats->ngcd ) realloc_gcd_buffer(stats, readlen); } stats->gcd[ stats->igcd ].depth++; // When no reference sequence is given, approximate the GC from the read (much shorter window, but otherwise OK) if ( !stats->info->fai ) stats->gcd[ stats->igcd ].gc += (float) gc_count / seq_len; // Coverage distribution graph round_buffer_flush(stats,bam_line->core.pos); if ( stats->regions ) { hts_pos_t p = bam_line->core.pos, pnew, pmin = 0, pmax = 0; uint32_t j = 0; i = 0; while ( j < bam_line->core.n_cigar && i < stats->nchunks ) { int op = bam_cigar_op(bam_get_cigar(bam_line)[j]); int oplen = bam_cigar_oplen(bam_get_cigar(bam_line)[j]); switch(op) { case BAM_CMATCH: case BAM_CEQUAL: case BAM_CDIFF: pmin = MAX(p, stats->chunks[i].beg-1); // 0 based pmax = MIN(p+oplen, stats->chunks[i].end); // 1 based if ( pmax > pmin ) { if ( stats->info->remove_overlaps ) remove_overlaps(bam_line, read_pairs, stats, pmin, pmax); else round_buffer_insert_read(&(stats->cov_rbuf), pmin, pmax); } break; case BAM_CDEL: break; } pnew = p + (bam_cigar_type(op)&2 ? oplen : 0); // consumes reference if ( pnew >= stats->chunks[i].end ) { // go to the next chunk i++; } else { // go to the next CIGAR op j++; p = pnew; } } } else { hts_pos_t p = bam_line->core.pos; uint32_t j; for (j = 0; j < bam_line->core.n_cigar; j++) { int op = bam_cigar_op(bam_get_cigar(bam_line)[j]); int oplen = bam_cigar_oplen(bam_get_cigar(bam_line)[j]); switch(op) { case BAM_CMATCH: case BAM_CEQUAL: case BAM_CDIFF: if ( stats->info->remove_overlaps ) remove_overlaps(bam_line, read_pairs, stats, p, p+oplen); else round_buffer_insert_read(&(stats->cov_rbuf), p, p+oplen); break; case BAM_CDEL: break; } p += bam_cigar_type(op)&2 ? oplen : 0; // consumes reference } } if ( stats->info->remove_overlaps ) remove_overlaps(bam_line, read_pairs, stats, -1LL, -1LL); //remove the line from the hash table } } // Sort by GC and depth #define GCD_t(x) ((gc_depth_t *)x) static int gcd_cmp(const void *a, const void *b) { if ( GCD_t(a)->gc < GCD_t(b)->gc ) return -1; if ( GCD_t(a)->gc > GCD_t(b)->gc ) return 1; if ( GCD_t(a)->depth < GCD_t(b)->depth ) return -1; if ( GCD_t(a)->depth > GCD_t(b)->depth ) return 1; return 0; } #undef GCD_t float gcd_percentile(gc_depth_t *gcd, int N, int p) { float n,d; int k; n = (float)p*(N+1)/100; k = n; if ( k<=0 ) return gcd[0].depth; if ( k>=N ) return gcd[N-1].depth; d = n - k; return gcd[k-1].depth + d*(gcd[k].depth - gcd[k-1].depth); } void output_stats(FILE *to, stats_t *stats, int sparse) { // Calculate average insert size and standard deviation (from the main bulk data only) int isize, ibulk=0, icov, imapq=0; uint64_t nisize=0, nisize_inward=0, nisize_outward=0, nisize_other=0, cov_sum=0; double bulk=0, avg_isize=0, sd_isize=0; for (isize=0; isizeisize->nitems(stats->isize->data); isize++) { // Each pair was counted twice stats->isize->set_inward(stats->isize->data, isize, stats->isize->inward(stats->isize->data, isize) * 0.5); stats->isize->set_outward(stats->isize->data, isize, stats->isize->outward(stats->isize->data, isize) * 0.5); stats->isize->set_other(stats->isize->data, isize, stats->isize->other(stats->isize->data, isize) * 0.5); nisize_inward += stats->isize->inward(stats->isize->data, isize); nisize_outward += stats->isize->outward(stats->isize->data, isize); nisize_other += stats->isize->other(stats->isize->data, isize); nisize += stats->isize->inward(stats->isize->data, isize) + stats->isize->outward(stats->isize->data, isize) + stats->isize->other(stats->isize->data, isize); } for (isize=0; isizeisize->nitems(stats->isize->data); isize++) { uint64_t num = stats->isize->inward(stats->isize->data, isize) + stats->isize->outward(stats->isize->data, isize) + stats->isize->other(stats->isize->data, isize); if (num > 0) ibulk = isize + 1; bulk += num; avg_isize += isize * (stats->isize->inward(stats->isize->data, isize) + stats->isize->outward(stats->isize->data, isize) + stats->isize->other(stats->isize->data, isize)); if ( bulk/nisize > stats->info->isize_main_bulk ) { ibulk = isize+1; nisize = bulk; break; } } avg_isize /= nisize ? nisize : 1; for (isize=1; isizeisize->inward(stats->isize->data, isize) + stats->isize->outward(stats->isize->data, isize) +stats->isize->other(stats->isize->data, isize)) * (isize-avg_isize)*(isize-avg_isize) / (nisize ? nisize : 1); sd_isize = sqrt(sd_isize); fprintf(to, "# This file was produced by samtools stats (%s+htslib-%s) and can be plotted using plot-bamstats\n", samtools_version(), hts_version()); if( stats->split_name != NULL ){ fprintf(to, "# This file contains statistics only for reads with tag: %s=%s\n", stats->info->split_tag, stats->split_name); } else{ fprintf(to, "# This file contains statistics for all reads.\n"); } fprintf(to, "# The command line was: %s",stats->info->argv[0]); int i; for (i=1; iinfo->argc; i++) fprintf(to, " %s", stats->info->argv[i]); fprintf(to, "\n"); fprintf(to, "# CHK, Checksum\t[2]Read Names\t[3]Sequences\t[4]Qualities\n"); fprintf(to, "# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)\n"); fprintf(to, "CHK\t%08x\t%08x\t%08x\n", stats->checksum.names,stats->checksum.reads,stats->checksum.quals); fprintf(to, "# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.\n"); fprintf(to, "SN\traw total sequences:\t%ld\t# excluding supplementary and secondary reads\n", (long)(stats->nreads_filtered+stats->nreads_1st+stats->nreads_2nd+stats->nreads_other)); // not counting excluded seqs (and none of the below) fprintf(to, "SN\tfiltered sequences:\t%ld\n", (long)stats->nreads_filtered); fprintf(to, "SN\tsequences:\t%ld\n", (long)(stats->nreads_1st+stats->nreads_2nd+stats->nreads_other)); fprintf(to, "SN\tis sorted:\t%d\n", stats->is_sorted ? 1 : 0); fprintf(to, "SN\t1st fragments:\t%ld\n", (long)stats->nreads_1st); fprintf(to, "SN\tlast fragments:\t%ld\n", (long)stats->nreads_2nd); fprintf(to, "SN\treads mapped:\t%ld\n", (long)(stats->nreads_paired_and_mapped+stats->nreads_single_mapped)); fprintf(to, "SN\treads mapped and paired:\t%ld\t# paired-end technology bit set + both mates mapped\n", (long)stats->nreads_paired_and_mapped); fprintf(to, "SN\treads unmapped:\t%ld\n", (long)stats->nreads_unmapped); fprintf(to, "SN\treads properly paired:\t%ld\t# proper-pair bit set\n", (long)stats->nreads_properly_paired); fprintf(to, "SN\treads paired:\t%ld\t# paired-end technology bit set\n", (long)stats->nreads_paired_tech); fprintf(to, "SN\treads duplicated:\t%ld\t# PCR or optical duplicate bit set\n", (long)stats->nreads_dup); fprintf(to, "SN\treads MQ0:\t%ld\t# mapped and MQ=0\n", (long)stats->nreads_mq0); fprintf(to, "SN\treads QC failed:\t%ld\n", (long)stats->nreads_QCfailed); fprintf(to, "SN\tnon-primary alignments:\t%ld\n", (long)stats->nreads_secondary); fprintf(to, "SN\tsupplementary alignments:\t%ld\n", (long)stats->nreads_supplementary); fprintf(to, "SN\ttotal length:\t%ld\t# ignores clipping\n", (long)stats->total_len); fprintf(to, "SN\ttotal first fragment length:\t%ld\t# ignores clipping\n", (long)stats->total_len_1st); fprintf(to, "SN\ttotal last fragment length:\t%ld\t# ignores clipping\n", (long)stats->total_len_2nd); fprintf(to, "SN\tbases mapped:\t%ld\t# ignores clipping\n", (long)stats->nbases_mapped); // the length of the whole read goes here, including soft-clips etc. fprintf(to, "SN\tbases mapped (cigar):\t%ld\t# more accurate\n", (long)stats->nbases_mapped_cigar); // only matched and inserted bases are counted here fprintf(to, "SN\tbases trimmed:\t%ld\n", (long)stats->nbases_trimmed); fprintf(to, "SN\tbases duplicated:\t%ld\n", (long)stats->total_len_dup); fprintf(to, "SN\tmismatches:\t%ld\t# from NM fields\n", (long)stats->nmismatches); fprintf(to, "SN\terror rate:\t%e\t# mismatches / bases mapped (cigar)\n", stats->nbases_mapped_cigar ? (float)stats->nmismatches/stats->nbases_mapped_cigar : 0); float avg_read_length = (stats->nreads_1st + stats->nreads_2nd + stats->nreads_other) ? (float)stats->total_len / (stats->nreads_1st + stats->nreads_2nd + stats->nreads_other) : 0; fprintf(to, "SN\taverage length:\t%.0f\n", avg_read_length); fprintf(to, "SN\taverage first fragment length:\t%.0f\n", stats->nreads_1st? (float)stats->total_len_1st/stats->nreads_1st:0); fprintf(to, "SN\taverage last fragment length:\t%.0f\n", stats->nreads_2nd? (float)stats->total_len_2nd/stats->nreads_2nd:0); fprintf(to, "SN\tmaximum length:\t%d\n", stats->max_len); fprintf(to, "SN\tmaximum first fragment length:\t%d\n", stats->max_len_1st); fprintf(to, "SN\tmaximum last fragment length:\t%d\n", stats->max_len_2nd); fprintf(to, "SN\taverage quality:\t%.1f\n", stats->total_len?stats->sum_qual/stats->total_len:0); fprintf(to, "SN\tinsert size average:\t%.1f\n", avg_isize); fprintf(to, "SN\tinsert size standard deviation:\t%.1f\n", sd_isize); fprintf(to, "SN\tinward oriented pairs:\t%ld\n", (long)nisize_inward); fprintf(to, "SN\toutward oriented pairs:\t%ld\n", (long)nisize_outward); fprintf(to, "SN\tpairs with other orientation:\t%ld\n", (long)nisize_other); fprintf(to, "SN\tpairs on different chromosomes:\t%ld\n", (long)stats->nreads_anomalous/2); fprintf(to, "SN\tpercentage of properly paired reads (%%):\t%.1f\n", (stats->nreads_1st+stats->nreads_2nd+stats->nreads_other)? (float)(100*stats->nreads_properly_paired)/(stats->nreads_1st+stats->nreads_2nd+stats->nreads_other):0); if ( stats->target_count ) { fprintf(to, "SN\tbases inside the target:\t%" PRIu64 "\n", stats->target_count); for (icov=stats->info->cov_threshold+1; icovncov; icov++) cov_sum += stats->cov[icov]; fprintf(to, "SN\tpercentage of target genome with coverage > %d (%%):\t%.2f\n", stats->info->cov_threshold, (float)(100*cov_sum)/stats->target_count); } int ibase,iqual; if ( stats->max_lennbases ) stats->max_len++; if ( stats->max_qual+1nquals ) stats->max_qual++; fprintf(to, "# First Fragment Qualities. Use `grep ^FFQ | cut -f 2-` to extract this part.\n"); fprintf(to, "# Columns correspond to qualities and rows to cycles. First column is the cycle number.\n"); for (ibase=0; ibasemax_len_1st; ibase++) { fprintf(to, "FFQ\t%d",ibase+1); for (iqual=0; iqual<=stats->max_qual; iqual++) { fprintf(to, "\t%ld", (long)stats->quals_1st[ibase*stats->nquals+iqual]); } fprintf(to, "\n"); } fprintf(to, "# Last Fragment Qualities. Use `grep ^LFQ | cut -f 2-` to extract this part.\n"); fprintf(to, "# Columns correspond to qualities and rows to cycles. First column is the cycle number.\n"); for (ibase=0; ibasemax_len_2nd; ibase++) { fprintf(to, "LFQ\t%d",ibase+1); for (iqual=0; iqual<=stats->max_qual; iqual++) { fprintf(to, "\t%ld", (long)stats->quals_2nd[ibase*stats->nquals+iqual]); } fprintf(to, "\n"); } if ( stats->mpc_buf ) { fprintf(to, "# Mismatches per cycle and quality. Use `grep ^MPC | cut -f 2-` to extract this part.\n"); fprintf(to, "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second\n"); fprintf(to, "# is the number of N's and the rest is the number of mismatches\n"); for (ibase=0; ibasemax_len; ibase++) { fprintf(to, "MPC\t%d",ibase+1); for (iqual=0; iqual<=stats->max_qual; iqual++) { fprintf(to, "\t%ld", (long)stats->mpc_buf[ibase*stats->nquals+iqual]); } fprintf(to, "\n"); } } fprintf(to, "# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part.\n"); int ibase_prev = 0; for (ibase=0; ibasengc; ibase++) { if ( stats->gc_1st[ibase]==stats->gc_1st[ibase_prev] ) continue; fprintf(to, "GCF\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1), (long)stats->gc_1st[ibase_prev]); ibase_prev = ibase; } fprintf(to, "# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part.\n"); ibase_prev = 0; for (ibase=0; ibasengc; ibase++) { if ( stats->gc_2nd[ibase]==stats->gc_2nd[ibase_prev] ) continue; fprintf(to, "GCL\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1), (long)stats->gc_2nd[ibase_prev]); ibase_prev = ibase; } fprintf(to, "# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]; and N and O counts as a percentage of all A/C/G/T bases [%%]\n"); for (ibase=0; ibasemax_len; ibase++) { acgtno_count_t *acgtno_count_1st = &(stats->acgtno_cycles_1st[ibase]); acgtno_count_t *acgtno_count_2nd = &(stats->acgtno_cycles_2nd[ibase]); uint64_t acgt_sum = acgtno_count_1st->a + acgtno_count_1st->c + acgtno_count_1st->g + acgtno_count_1st->t + acgtno_count_2nd->a + acgtno_count_2nd->c + acgtno_count_2nd->g + acgtno_count_2nd->t; if ( ! acgt_sum ) continue; fprintf(to, "GCC\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase+1, 100.*(acgtno_count_1st->a + acgtno_count_2nd->a)/acgt_sum, 100.*(acgtno_count_1st->c + acgtno_count_2nd->c)/acgt_sum, 100.*(acgtno_count_1st->g + acgtno_count_2nd->g)/acgt_sum, 100.*(acgtno_count_1st->t + acgtno_count_2nd->t)/acgt_sum, 100.*(acgtno_count_1st->n + acgtno_count_2nd->n)/acgt_sum, 100.*(acgtno_count_1st->other + acgtno_count_2nd->other)/acgt_sum); } fprintf(to, "# ACGT content per cycle, read oriented. Use `grep ^GCT | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]\n"); for (ibase=0; ibasemax_len; ibase++) { acgtno_count_t *acgtno_count = &(stats->acgtno_revcomp[ibase]); uint64_t acgt_sum = acgtno_count->a + acgtno_count->c + acgtno_count->g + acgtno_count->t; if ( ! acgt_sum ) continue; fprintf(to, "GCT\t%d\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase+1, 100.*(acgtno_count->a)/acgt_sum, 100.*(acgtno_count->c)/acgt_sum, 100.*(acgtno_count->g)/acgt_sum, 100.*(acgtno_count->t)/acgt_sum); } uint64_t tA=0, tC=0, tG=0, tT=0, tN=0; fprintf(to, "# ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]; and N and O counts as a percentage of all A/C/G/T bases [%%]\n"); for (ibase=0; ibasemax_len; ibase++) { acgtno_count_t *acgtno_count_1st = &(stats->acgtno_cycles_1st[ibase]); uint64_t acgt_sum_1st = acgtno_count_1st->a + acgtno_count_1st->c + acgtno_count_1st->g + acgtno_count_1st->t; tA += acgtno_count_1st->a; tC += acgtno_count_1st->c; tG += acgtno_count_1st->g; tT += acgtno_count_1st->t; tN += acgtno_count_1st->n; if ( acgt_sum_1st ) fprintf(to, "FBC\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase+1, 100.*acgtno_count_1st->a/acgt_sum_1st, 100.*acgtno_count_1st->c/acgt_sum_1st, 100.*acgtno_count_1st->g/acgt_sum_1st, 100.*acgtno_count_1st->t/acgt_sum_1st, 100.*acgtno_count_1st->n/acgt_sum_1st, 100.*acgtno_count_1st->other/acgt_sum_1st); } fprintf(to, "# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters\n"); fprintf(to, "FTC\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\n", tA, tC, tG, tT, tN); tA=0, tC=0, tG=0, tT=0, tN=0; fprintf(to, "# ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]; and N and O counts as a percentage of all A/C/G/T bases [%%]\n"); for (ibase=0; ibasemax_len; ibase++) { acgtno_count_t *acgtno_count_2nd = &(stats->acgtno_cycles_2nd[ibase]); uint64_t acgt_sum_2nd = acgtno_count_2nd->a + acgtno_count_2nd->c + acgtno_count_2nd->g + acgtno_count_2nd->t; tA += acgtno_count_2nd->a; tC += acgtno_count_2nd->c; tG += acgtno_count_2nd->g; tT += acgtno_count_2nd->t; tN += acgtno_count_2nd->n; if ( acgt_sum_2nd ) fprintf(to, "LBC\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase+1, 100.*acgtno_count_2nd->a/acgt_sum_2nd, 100.*acgtno_count_2nd->c/acgt_sum_2nd, 100.*acgtno_count_2nd->g/acgt_sum_2nd, 100.*acgtno_count_2nd->t/acgt_sum_2nd, 100.*acgtno_count_2nd->n/acgt_sum_2nd, 100.*acgtno_count_2nd->other/acgt_sum_2nd); } fprintf(to, "# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters\n"); fprintf(to, "LTC\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\n", tA, tC, tG, tT, tN); int tag; for (tag=0; tagntags; tag++) { if (stats->tags_barcode[tag].nbases) { fprintf(to, "# ACGT content per cycle for barcodes. Use `grep ^%sC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]; and N counts as a percentage of all A/C/G/T bases [%%]\n", stats->tags_barcode[tag].tag_name); for (ibase=0; ibasetags_barcode[tag].nbases; ibase++) { if (ibase == stats->tags_barcode[tag].tag_sep) continue; acgtno_count_t *acgtno_count = stats->acgtno_barcode + stats->tags_barcode[tag].offset + ibase; uint64_t acgt_sum = acgtno_count->a + acgtno_count->c + acgtno_count->g + acgtno_count->t; if ( acgt_sum ) fprintf(to, "%sC%d\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", stats->tags_barcode[tag].tag_name, stats->tags_barcode[tag].tag_sep < 0 || ibase < stats->tags_barcode[tag].tag_sep ? 1 : 2, stats->tags_barcode[tag].tag_sep < 0 || ibase < stats->tags_barcode[tag].tag_sep ? ibase+1 : ibase-stats->tags_barcode[tag].tag_sep, 100.*acgtno_count->a/acgt_sum, 100.*acgtno_count->c/acgt_sum, 100.*acgtno_count->g/acgt_sum, 100.*acgtno_count->t/acgt_sum, 100.*acgtno_count->n/acgt_sum); } fprintf(to, "# Barcode Qualities. Use `grep ^%sQ | cut -f 2-` to extract this part.\n", stats->tags_barcode[tag].qual_name); fprintf(to, "# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number.\n"); for (ibase=0; ibasetags_barcode[tag].nbases; ibase++) { if (ibase == stats->tags_barcode[tag].tag_sep) continue; fprintf(to, "%sQ%d\t%d", stats->tags_barcode[tag].qual_name, stats->tags_barcode[tag].tag_sep < 0 || ibase < stats->tags_barcode[tag].tag_sep ? 1 : 2, stats->tags_barcode[tag].tag_sep < 0 || ibase < stats->tags_barcode[tag].tag_sep ? ibase+1 : ibase-stats->tags_barcode[tag].tag_sep); for (iqual=0; iqual<=stats->tags_barcode[tag].max_qual; iqual++) { fprintf(to, "\t%ld", (long)stats->quals_barcode[(stats->tags_barcode[tag].offset + ibase)*stats->nquals+iqual]); } fprintf(to, "\n"); } } } fprintf(to, "# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs\n"); for (isize=0; isizeisize->inward(stats->isize->data, isize)); long out = (long)(stats->isize->outward(stats->isize->data, isize)); long other = (long)(stats->isize->other(stats->isize->data, isize)); if (!sparse || in + out + other > 0) { fprintf(to, "IS\t%d\t%ld\t%ld\t%ld\t%ld\n", isize, in+out+other, in , out, other); } } fprintf(to, "# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count\n"); int ilen; for (ilen=0; ilenmax_len; ilen++) { if ( stats->read_lengths[ilen+1]>0 ) fprintf(to, "RL\t%d\t%ld\n", ilen+1, (long)stats->read_lengths[ilen+1]); } fprintf(to, "# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count\n"); for (ilen=0; ilenmax_len_1st; ilen++) { if ( stats->read_lengths_1st[ilen+1]>0 ) fprintf(to, "FRL\t%d\t%ld\n", ilen+1, (long)stats->read_lengths_1st[ilen+1]); } fprintf(to, "# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count\n"); for (ilen=0; ilenmax_len_2nd; ilen++) { if ( stats->read_lengths_2nd[ilen+1]>0 ) fprintf(to, "LRL\t%d\t%ld\n", ilen+1, (long)stats->read_lengths_2nd[ilen+1]); } fprintf(to, "# Mapping qualities for reads !(UNMAP|SECOND|SUPPL|QCFAIL|DUP). Use `grep ^MAPQ | cut -f 2-` to extract this part. The columns are: mapq, count\n"); for (imapq=0; imapq < 256; imapq++) { if ( stats->mapping_qualities[imapq]>0 ) fprintf(to, "MAPQ\t%d\t%ld\n", imapq, (long)stats->mapping_qualities[imapq]); } fprintf(to, "# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions\n"); for (ilen=0; ilennindels; ilen++) { if ( stats->insertions[ilen]>0 || stats->deletions[ilen]>0 ) fprintf(to, "ID\t%d\t%ld\t%ld\n", ilen+1, (long)stats->insertions[ilen], (long)stats->deletions[ilen]); } fprintf(to, "# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)\n"); for (ilen=0; ilen<=stats->nbases; ilen++) { // For deletions we print the index of the cycle before the deleted base (1-based) and for insertions // the index of the cycle of the first inserted base (also 1-based) if ( stats->ins_cycles_1st[ilen]>0 || stats->ins_cycles_2nd[ilen]>0 || stats->del_cycles_1st[ilen]>0 || stats->del_cycles_2nd[ilen]>0 ) fprintf(to, "IC\t%d\t%ld\t%ld\t%ld\t%ld\n", ilen+1, (long)stats->ins_cycles_1st[ilen], (long)stats->ins_cycles_2nd[ilen], (long)stats->del_cycles_1st[ilen], (long)stats->del_cycles_2nd[ilen]); } fprintf(to, "# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.\n"); if ( stats->cov[0] ) fprintf(to, "COV\t[<%d]\t%d\t%ld\n",stats->info->cov_min,stats->info->cov_min-1, (long)stats->cov[0]); for (icov=1; icovncov-1; icov++) if ( stats->cov[icov] ) fprintf(to, "COV\t[%d-%d]\t%d\t%ld\n",stats->info->cov_min + (icov-1)*stats->info->cov_step, stats->info->cov_min + icov*stats->info->cov_step-1,stats->info->cov_min + icov*stats->info->cov_step-1, (long)stats->cov[icov]); if ( stats->cov[stats->ncov-1] ) fprintf(to, "COV\t[%d<]\t%d\t%ld\n",stats->info->cov_min + (stats->ncov-2)*stats->info->cov_step-1,stats->info->cov_min + (stats->ncov-2)*stats->info->cov_step-1, (long)stats->cov[stats->ncov-1]); // Calculate average GC content, then sort by GC and depth fprintf(to, "# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile\n"); uint32_t igcd; for (igcd=0; igcdigcd; igcd++) { if ( stats->info->fai ) stats->gcd[igcd].gc = rint(100. * stats->gcd[igcd].gc); else if ( stats->gcd[igcd].depth ) stats->gcd[igcd].gc = rint(100. * stats->gcd[igcd].gc / stats->gcd[igcd].depth); } if ( stats->ngcd ) qsort(stats->gcd, stats->igcd+1, sizeof(gc_depth_t), gcd_cmp); igcd = 0; while ( igcd < stats->igcd ) { // Calculate percentiles (10,25,50,75,90th) for the current GC content and print uint32_t nbins=0, itmp=igcd; float gc = stats->gcd[igcd].gc; while ( itmpigcd && fabs(stats->gcd[itmp].gc-gc)<0.1 ) { nbins++; itmp++; } fprintf(to, "GCD\t%.1f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\n", gc, (igcd+nbins+1)*100./(stats->igcd+1), gcd_percentile(&(stats->gcd[igcd]),nbins,10) *avg_read_length/stats->info->gcd_bin_size, gcd_percentile(&(stats->gcd[igcd]),nbins,25) *avg_read_length/stats->info->gcd_bin_size, gcd_percentile(&(stats->gcd[igcd]),nbins,50) *avg_read_length/stats->info->gcd_bin_size, gcd_percentile(&(stats->gcd[igcd]),nbins,75) *avg_read_length/stats->info->gcd_bin_size, gcd_percentile(&(stats->gcd[igcd]),nbins,90) *avg_read_length/stats->info->gcd_bin_size ); igcd += nbins; } } static void init_regions(stats_t *stats, const char *file, stats_info_t* info) { FILE *fp = fopen(file,"r"); if ( !fp ) error("%s: %s\n",file,strerror(errno)); kstring_t line = { 0, 0, NULL }; int warned = 0, r, p, new_p; int prev_tid=-1; hts_pos_t prev_pos=-1LL; while (line.l = 0, kgetline(&line, (kgets_func *)fgets, fp) >= 0) { if ( line.s[0] == '#' ) continue; int i = 0; while ( i=line.l ) error("Could not parse the file: %s [%s]\n", file, line.s); line.s[i] = '\0'; int tid = bam_name2id(stats->info->sam_header, line.s); if ( tid < 0 ) { if ( !warned ) fprintf(samtools_stderr,"Warning: Some sequences not present in the BAM, e.g. \"%s\". This message is printed only once.\n", line.s); warned = 1; continue; } if ( tid >= stats->nregions ) { if(!(stats->regions = realloc(stats->regions,sizeof(regions_t)*(tid+REG_INC)))) error("Could not allocate memory for region.\n"); int j; for (j=stats->nregions; jregions[j].npos = stats->regions[j].mpos = stats->regions[j].cpos = 0; stats->regions[j].pos = NULL; } stats->nregions = tid+REG_INC; } int npos = stats->regions[tid].npos; if ( npos >= stats->regions[tid].mpos ) { stats->regions[tid].mpos = npos+POS_INC; if (!(stats->regions[tid].pos = realloc(stats->regions[tid].pos, sizeof(hts_pair_pos_t)*stats->regions[tid].mpos))) error("Could not allocate memory for interval.\n"); } if ( (sscanf(&line.s[i+1],"%"SCNd64" %"SCNd64, &stats->regions[tid].pos[npos].beg, &stats->regions[tid].pos[npos].end))!=2 ) error("Could not parse the region [%s]\n", &line.s[i+1]); if ( prev_tid==-1 || prev_tid!=tid ) { prev_tid = tid; prev_pos = stats->regions[tid].pos[npos].beg; } if ( prev_pos>stats->regions[tid].pos[npos].beg ) error("The positions are not in chromosomal order (%s:%"PRIhts_pos" comes after %"PRIhts_pos")\n", line.s, stats->regions[tid].pos[npos].beg, prev_pos); stats->regions[tid].npos++; if ( stats->regions[tid].npos > stats->nchunks ) stats->nchunks = stats->regions[tid].npos; } free(line.s); if ( !stats->regions ) error("Unable to map the -t sequences to the BAM sequences.\n"); fclose(fp); // sort region intervals and remove duplicates for (r = 0; r < stats->nregions; r++) { regions_t *reg = &stats->regions[r]; if ( reg->npos > 1 ) { qsort(reg->pos, reg->npos, sizeof(hts_pair_pos_t), regions_lt); for (new_p = 0, p = 1; p < reg->npos; p++) { if ( reg->pos[new_p].end < reg->pos[p].beg ) reg->pos[++new_p] = reg->pos[p]; else if ( reg->pos[new_p].end < reg->pos[p].end ) reg->pos[new_p].end = reg->pos[p].end; } reg->npos = ++new_p; } for (p = 0; p < reg->npos; p++) { if (reg->pos[p].end < HTS_POS_MAX) { stats->target_count += (reg->pos[p].end - reg->pos[p].beg + 1); } else { uint64_t hdr_end = sam_hdr_tid2len(info->sam_header, r); if (hdr_end) stats->target_count += (hdr_end - reg->pos[p].beg + 1); } } } if (!(stats->chunks = calloc(stats->nchunks, sizeof(hts_pair_pos_t)))) error("Could not allocate memory for chunk.\n"); } void destroy_regions(stats_t *stats) { int i; for (i=0; inregions; i++) { if ( !stats->regions[i].mpos ) continue; free(stats->regions[i].pos); } if ( stats->regions ) free(stats->regions); if ( stats->chunks ) free(stats->chunks); } void reset_regions(stats_t *stats) { int i; for (i=0; inregions; i++) stats->regions[i].cpos = 0; } int is_in_regions(bam1_t *bam_line, stats_t *stats) { if ( !stats->regions ) return 1; if ( bam_line->core.tid >= stats->nregions || bam_line->core.tid<0 ) return 0; if ( !stats->is_sorted ) error("The BAM must be sorted in order for -t to work.\n"); regions_t *reg = &stats->regions[bam_line->core.tid]; if ( reg->cpos==reg->npos ) return 0; // done for this chr // Find a matching interval or skip this read. No splicing of reads is done, no indels or soft clips considered, // even small overlap is enough to include the read in the stats. int i = reg->cpos; while ( inpos && reg->pos[i].end<=bam_line->core.pos ) i++; if ( i>=reg->npos ) { reg->cpos = reg->npos; return 0; } int64_t endpos = bam_endpos(bam_line); if ( endpos < reg->pos[i].beg ) return 0; //found a read overlapping a region reg->cpos = i; stats->reg_from = reg->pos[i].beg; stats->reg_to = reg->pos[i].end; //now find all the overlapping chunks stats->nchunks = 0; while (i < reg->npos) { if (bam_line->core.pos < reg->pos[i].end && endpos >= reg->pos[i].beg) { stats->chunks[stats->nchunks].beg = MAX(bam_line->core.pos+1, reg->pos[i].beg); stats->chunks[stats->nchunks].end = MIN(endpos, reg->pos[i].end); stats->nchunks++; } i++; } return 1; } int replicate_regions(stats_t *stats, hts_itr_multi_t *iter, stats_info_t *info) { if ( !stats || !iter) return 1; int i, j, tid; stats->nregions = iter->n_reg; stats->regions = calloc(stats->nregions, sizeof(regions_t)); stats->chunks = calloc(stats->nchunks, sizeof(hts_pair_pos_t)); if ( !stats->regions || !stats->chunks ) return 1; for (i = 0; i < iter->n_reg; i++) { tid = iter->reg_list[i].tid; if ( tid < 0 ) continue; if ( tid >= stats->nregions ) { regions_t *tmp = realloc(stats->regions, (tid+10) * sizeof(regions_t)); if ( !tmp ) return 1; stats->regions = tmp; memset(stats->regions + stats->nregions, 0, (tid+10-stats->nregions) * sizeof(regions_t)); stats->nregions = tid+10; } stats->regions[tid].mpos = stats->regions[tid].npos = iter->reg_list[i].count; stats->regions[tid].pos = calloc(stats->regions[tid].mpos, sizeof(hts_pair_pos_t)); if ( !stats->regions[tid].pos ) return 1; for (j = 0; j < stats->regions[tid].npos; j++) { stats->regions[tid].pos[j].beg = iter->reg_list[i].intervals[j].beg+1; stats->regions[tid].pos[j].end = iter->reg_list[i].intervals[j].end; if (stats->regions[tid].pos[j].end < HTS_POS_MAX) { stats->target_count += (stats->regions[tid].pos[j].end - stats->regions[tid].pos[j].beg + 1); } else { uint64_t hdr_end = sam_hdr_tid2len(info->sam_header, tid); if (hdr_end) stats->target_count += (hdr_end - stats->regions[tid].pos[j].beg + 1); } } } return 0; } static void init_group_id(stats_t *stats, stats_info_t *info, const char *id) { stats->rg_hash = kh_init(rg); if (!stats->rg_hash) error("Could not initialise RG set\n"); sam_hdr_t *hdr = info->sam_header; const char *key; kstring_t sm = KS_INITIALIZE; int i, ret, nrg = sam_hdr_count_lines(hdr, "RG"); if (nrg < 0) error("Could not parse header\n"); for (i=0; irg_hash, key, &ret); if (ret == -1) { ks_free(&sm); error("Could not add key \"%s\" to RG set\n", key); } } else { /* Check for SM name, as per manual */ if (!sam_hdr_find_tag_pos(hdr, "RG", i, "SM", &sm)) { if (!strcmp(ks_c_str(&sm), id)) { kh_put(rg, stats->rg_hash, key, &ret); if (ret == -1) { ks_free(&sm); error("Could not add key \"%s\" to RG set\n", key); } } } } } ks_free(&sm); } static void HTS_FORMAT(HTS_PRINTF_FMT, 1, 2) HTS_NORETURN error(const char *format, ...) { if ( !format ) { fprintf(samtools_stdout, "About: The program collects statistics from BAM files. The output can be visualized using plot-bamstats.\n"); fprintf(samtools_stdout, "Usage: samtools stats [OPTIONS] file.bam\n"); fprintf(samtools_stdout, " samtools stats [OPTIONS] file.bam chr:from-to\n"); fprintf(samtools_stdout, "Options:\n"); fprintf(samtools_stdout, " -c, --coverage ,, Coverage distribution min,max,step [1,1000,1]\n"); fprintf(samtools_stdout, " -d, --remove-dups Exclude from statistics reads marked as duplicates\n"); fprintf(samtools_stdout, " -X, --customized-index-file Use a customized index file\n"); fprintf(samtools_stdout, " -f, --required-flag Required flag, 0 for unset. See also `samtools flags` [0]\n"); fprintf(samtools_stdout, " -F, --filtering-flag Filtering flag, 0 for unset. See also `samtools flags` [0]\n"); fprintf(samtools_stdout, " --GC-depth the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4]\n"); fprintf(samtools_stdout, " -h, --help This help message\n"); fprintf(samtools_stdout, " -i, --insert-size Maximum insert size [8000]\n"); fprintf(samtools_stdout, " -I, --id Include only listed read group or sample name\n"); fprintf(samtools_stdout, " -l, --read-length Include in the statistics only reads with the given read length [-1]\n"); fprintf(samtools_stdout, " -m, --most-inserts Report only the main part of inserts [0.99]\n"); fprintf(samtools_stdout, " -P, --split-prefix Path or string prefix for filepaths output by -S (default is input filename)\n"); fprintf(samtools_stdout, " -q, --trim-quality The BWA trimming parameter [0]\n"); fprintf(samtools_stdout, " -r, --ref-seq Reference sequence (required for GC-depth and mismatches-per-cycle calculation).\n"); fprintf(samtools_stdout, " -s, --sam Ignored (input format is auto-detected).\n"); fprintf(samtools_stdout, " -S, --split Also write statistics to separate files split by tagged field.\n"); fprintf(samtools_stdout, " -t, --target-regions Do stats in these regions only. Tab-delimited file chr,from,to, 1-based, inclusive.\n"); fprintf(samtools_stdout, " -x, --sparse Suppress outputting IS rows where there are no insertions.\n"); fprintf(samtools_stdout, " -p, --remove-overlaps Remove overlaps of paired-end reads from coverage and base count computations.\n"); fprintf(samtools_stdout, " -g, --cov-threshold Only bases with coverage above this value will be included in the target percentage computation [0]\n"); sam_global_opt_help(samtools_stdout, "-.--.@-."); fprintf(samtools_stdout, "\n"); } else { va_list ap; va_start(ap, format); vfprintf(samtools_stderr, format, ap); va_end(ap); } samtools_exit(1); } void cleanup_stats_info(stats_info_t* info){ if (info->fai) fai_destroy(info->fai); if (info->sam) sam_close(info->sam); free(info); } void cleanup_stats(stats_t* stats) { free(stats->cov_rbuf.buffer); free(stats->cov); free(stats->quals_1st); free(stats->quals_2nd); free(stats->gc_1st); free(stats->gc_2nd); stats->isize->isize_free(stats->isize->data); free(stats->isize); free(stats->gcd); free(stats->rseq_buf); free(stats->mpc_buf); free(stats->acgtno_cycles_1st); free(stats->acgtno_cycles_2nd); free(stats->acgtno_revcomp); free(stats->read_lengths); free(stats->read_lengths_1st); free(stats->read_lengths_2nd); free(stats->insertions); free(stats->deletions); free(stats->ins_cycles_1st); free(stats->ins_cycles_2nd); free(stats->del_cycles_1st); free(stats->del_cycles_2nd); if (stats->acgtno_barcode) free(stats->acgtno_barcode); if (stats->quals_barcode) free(stats->quals_barcode); free(stats->tags_barcode); destroy_regions(stats); if ( stats->rg_hash ) kh_destroy(rg, stats->rg_hash); free(stats->split_name); free(stats->mapping_qualities); free(stats); } void output_split_stats(khash_t(c2stats) *split_hash, char* bam_fname, int sparse) { int i = 0; kstring_t output_filename = { 0, 0, NULL }; stats_t *curr_stats = NULL; for(i = kh_begin(split_hash); i != kh_end(split_hash); ++i){ if(!kh_exist(split_hash, i)) continue; curr_stats = kh_value(split_hash, i); round_buffer_flush(curr_stats, -1); output_filename.l = 0; if (curr_stats->info->split_prefix) kputs(curr_stats->info->split_prefix, &output_filename); else kputs(bam_fname, &output_filename); kputc('_', &output_filename); kputs(curr_stats->split_name, &output_filename); kputs(".bamstat", &output_filename); FILE *to = fopen(output_filename.s, "w"); if(to == NULL){ error("Could not open '%s' for writing.\n", output_filename.s); } output_stats(to, curr_stats, sparse); fclose(to); } free(output_filename.s); } void destroy_split_stats(khash_t(c2stats) *split_hash) { if (!split_hash) return; int i = 0; stats_t *curr_stats = NULL; for(i = kh_begin(split_hash); i != kh_end(split_hash); ++i){ if(!kh_exist(split_hash, i)) continue; curr_stats = kh_value(split_hash, i); cleanup_stats(curr_stats); } kh_destroy(c2stats, split_hash); } stats_info_t* stats_info_init(int argc, char *argv[]) { stats_info_t* info = calloc(1, sizeof(stats_info_t)); if (!info) { return NULL; } info->nisize = 8000; info->isize_main_bulk = 0.99; // There are always outliers at the far end info->gcd_bin_size = 20e3; info->cov_min = 1; info->cov_max = 1000; info->cov_step = 1; info->filter_readlen = -1; info->argc = argc; info->argv = argv; info->remove_overlaps = 0; info->cov_threshold = 0; return info; } int init_stat_info_fname(stats_info_t* info, const char* bam_fname, const htsFormat* in_fmt) { // .. bam samFile* sam; if ((sam = sam_open_format(bam_fname, "r", in_fmt)) == 0) { print_error_errno("stats", "failed to open \"%s\"", bam_fname); return 1; } info->sam = sam; info->sam_header = sam_hdr_read(sam); if (info->sam_header == NULL) { print_error("stats", "failed to read header for \"%s\"", bam_fname); return 1; } return 0; } stats_t* stats_init(void) { stats_t *stats = calloc(1,sizeof(stats_t)); if (!stats) return NULL; stats->ngc = 200; stats->nquals = 256; stats->nbases = 300; stats->rseq_pos = -1; stats->tid = -1; stats->gcd_pos = -1LL; stats->igcd = 0; stats->is_sorted = 1; stats->nindels = stats->nbases; stats->split_name = NULL; stats->nchunks = 0; stats->pair_count = 0; stats->last_pair_tid = -2; stats->last_read_flush = 0; stats->target_count = 0; return stats; } static int init_barcode_tags(stats_t* stats) { stats->ntags = 4; stats->tags_barcode = calloc(stats->ntags, sizeof(barcode_info_t)); if (!stats->tags_barcode) return -1; stats->tags_barcode[0] = (barcode_info_t){"BC", "QT", 0, -1, -1, 0}; stats->tags_barcode[1] = (barcode_info_t){"CR", "CY", 0, -1, -1, 0}; stats->tags_barcode[2] = (barcode_info_t){"OX", "BZ", 0, -1, -1, 0}; stats->tags_barcode[3] = (barcode_info_t){"RX", "QX", 0, -1, -1, 0}; return 0; } static void init_stat_structs(stats_t* stats, stats_info_t* info, const char* group_id, const char* targets) { // Give stats_t a pointer to the info struct // This saves us having to pass the stats_info_t to every function stats->info = info; // Init structures // .. coverage bins and round buffer if ( info->cov_step > info->cov_max - info->cov_min + 1 ) { info->cov_step = info->cov_max - info->cov_min; if ( info->cov_step <= 0 ) info->cov_step = 1; } stats->ncov = 3 + (info->cov_max-info->cov_min) / info->cov_step; info->cov_max = info->cov_min + ((info->cov_max-info->cov_min)/info->cov_step +1)*info->cov_step - 1; stats->cov = calloc(sizeof(uint64_t),stats->ncov); if (!stats->cov) goto nomem; stats->cov_rbuf.size = stats->nbases*5; stats->cov_rbuf.buffer = calloc(sizeof(int32_t),stats->cov_rbuf.size); if (!stats->cov_rbuf.buffer) goto nomem; if ( group_id ) init_group_id(stats, info, group_id); // .. arrays stats->quals_1st = calloc(stats->nquals*stats->nbases,sizeof(uint64_t)); if (!stats->quals_1st) goto nomem; stats->quals_2nd = calloc(stats->nquals*stats->nbases,sizeof(uint64_t)); if (!stats->quals_2nd) goto nomem; stats->gc_1st = calloc(stats->ngc,sizeof(uint64_t)); if (!stats->gc_1st) goto nomem; stats->gc_2nd = calloc(stats->ngc,sizeof(uint64_t)); if (!stats->gc_2nd) goto nomem; stats->isize = init_isize_t(info->nisize ?info->nisize+1 :0); if (!stats->isize) goto nomem; stats->gcd = calloc(stats->ngcd,sizeof(gc_depth_t)); if (!stats->gcd) goto nomem; if (info->fai) { stats->mpc_buf = calloc(stats->nquals*stats->nbases,sizeof(uint64_t)); if (!stats->mpc_buf) goto nomem; } else { stats->mpc_buf = NULL; } stats->acgtno_cycles_1st = calloc(stats->nbases,sizeof(acgtno_count_t)); if (!stats->acgtno_cycles_1st) goto nomem; stats->acgtno_cycles_2nd = calloc(stats->nbases,sizeof(acgtno_count_t)); if (!stats->acgtno_cycles_2nd) goto nomem; stats->acgtno_revcomp = calloc(stats->nbases,sizeof(acgtno_count_t)); if (!stats->acgtno_revcomp) goto nomem; stats->read_lengths = calloc(stats->nbases,sizeof(uint64_t)); if (!stats->read_lengths) goto nomem; stats->read_lengths_1st = calloc(stats->nbases,sizeof(uint64_t)); if (!stats->read_lengths_1st) goto nomem; stats->read_lengths_2nd = calloc(stats->nbases,sizeof(uint64_t)); if (!stats->read_lengths_2nd) goto nomem; stats->insertions = calloc(stats->nbases,sizeof(uint64_t)); if (!stats->insertions) goto nomem; stats->deletions = calloc(stats->nbases,sizeof(uint64_t)); if (!stats->deletions) goto nomem; stats->ins_cycles_1st = calloc(stats->nbases+1,sizeof(uint64_t)); if (!stats->ins_cycles_1st) goto nomem; stats->ins_cycles_2nd = calloc(stats->nbases+1,sizeof(uint64_t)); if (!stats->ins_cycles_2nd) goto nomem; stats->del_cycles_1st = calloc(stats->nbases+1,sizeof(uint64_t)); if (!stats->del_cycles_1st) goto nomem; stats->del_cycles_2nd = calloc(stats->nbases+1,sizeof(uint64_t)); if (!stats->del_cycles_2nd) goto nomem; stats->mapping_qualities = calloc(256,sizeof(uint64_t)); if(!stats->mapping_qualities) goto nomem; if (init_barcode_tags(stats) < 0) goto nomem; realloc_rseq_buffer(stats); if ( targets ) init_regions(stats, targets, info); return; nomem: error("Out of memory"); } static stats_t* get_curr_split_stats(bam1_t* bam_line, khash_t(c2stats)* split_hash, stats_info_t* info, char* targets) { stats_t *curr_stats = NULL; const uint8_t *tag_val = bam_aux_get(bam_line, info->split_tag); if(tag_val == 0){ error("Tag '%s' not found in bam_line.\n", info->split_tag); } char* split_name = strdup(bam_aux2Z(tag_val)); // New stats object, under split khiter_t k = kh_get(c2stats, split_hash, split_name); if(k == kh_end(split_hash)){ curr_stats = stats_init(); // mallocs new instance if (!curr_stats) { error("Couldn't allocate split stats"); } init_stat_structs(curr_stats, info, NULL, targets); curr_stats->split_name = split_name; // Record index in hash int ret = 0; khiter_t iter = kh_put(c2stats, split_hash, split_name, &ret); if( ret < 0 ){ error("Failed to insert key '%s' into split_hash", split_name); } kh_val(split_hash, iter) = curr_stats; // store pointer to stats } else{ curr_stats = kh_value(split_hash, k); free(split_name); // don't need to hold on to this if it wasn't new } return curr_stats; } int main_stats(int argc, char *argv[]) { char *targets = NULL; char *bam_fname = NULL; char *bam_idx_fname = NULL; char *group_id = NULL; int sparse = 0, has_index_file = 0, ret = 1; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; stats_info_t *info = stats_info_init(argc, argv); if (!info) { fprintf(samtools_stderr, "Could not allocate memory for info.\n"); return 1; } static const struct option loptions[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '@'), {"help", no_argument, NULL, 'h'}, {"remove-dups", no_argument, NULL, 'd'}, {"sam", no_argument, NULL, 's'}, {"customized-index-file", required_argument, NULL, 'X'}, {"ref-seq", required_argument, NULL, 'r'}, {"coverage", required_argument, NULL, 'c'}, {"read-length", required_argument, NULL, 'l'}, {"insert-size", required_argument, NULL, 'i'}, {"most-inserts", required_argument, NULL, 'm'}, {"trim-quality", required_argument, NULL, 'q'}, {"target-regions", required_argument, NULL, 't'}, {"required-flag", required_argument, NULL, 'f'}, {"filtering-flag", required_argument, NULL, 'F'}, {"id", required_argument, NULL, 'I'}, {"GC-depth", required_argument, NULL, 1}, {"sparse", no_argument, NULL, 'x'}, {"split", required_argument, NULL, 'S'}, {"split-prefix", required_argument, NULL, 'P'}, {"remove-overlaps", no_argument, NULL, 'p'}, {"cov-threshold", required_argument, NULL, 'g'}, {NULL, 0, NULL, 0} }; int opt, tmp_flag; while ( (opt=getopt_long(argc,argv,"?hdsXxpr:c:l:i:t:m:q:f:F:g:I:S:P:@:",loptions,NULL))>0 ) { switch (opt) { case 'f': tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("stats", "Unknown flag '%s'", optarg); return 1; } info->flag_require = tmp_flag; break; case 'F': tmp_flag = bam_str2flag(optarg); if (tmp_flag < 0) { print_error("stats", "Unknown flag '%s'", optarg); return 1; } info->flag_filter |= tmp_flag; break; case 'd': info->flag_filter |= BAM_FDUP; break; case 'X': has_index_file = 1; break; case 's': break; case 'r': info->fai = fai_load(optarg); if (info->fai==NULL) error("Could not load faidx: %s\n", optarg); break; case 1 : info->gcd_bin_size = atof(optarg); break; case 'c': if ( sscanf(optarg,"%d,%d,%d",&info->cov_min,&info->cov_max,&info->cov_step)!= 3 ) error("Unable to parse -c %s\n", optarg); break; case 'l': info->filter_readlen = atoi(optarg); break; case 'i': info->nisize = atoi(optarg); break; case 'm': info->isize_main_bulk = atof(optarg); break; case 'q': info->trim_qual = atoi(optarg); break; case 't': targets = optarg; break; case 'I': group_id = optarg; break; case 'x': sparse = 1; break; case 'S': info->split_tag = optarg; break; case 'P': info->split_prefix = optarg; break; case 'p': info->remove_overlaps = 1; break; case 'g': info->cov_threshold = atoi(optarg); if ( info->cov_threshold < 0 || info->cov_threshold == INT_MAX ) error("Unsupported value for coverage threshold %d\n", info->cov_threshold); break; case '?': case 'h': error(NULL); /* no break */ default: if (parse_sam_global_opt(opt, optarg, loptions, &ga) != 0) error("Unknown argument: %s\n", optarg); break; } } bam_fname = argv[optind++]; if ( !bam_fname ) { if ( isatty(STDIN_FILENO) ) error(NULL); bam_fname = "-"; } if (init_stat_info_fname(info, bam_fname, &ga.in)) { cleanup_stats_info(info); return 1; } if (has_index_file && !(bam_idx_fname = argv[optind++])) { fprintf(samtools_stderr, "No index file provided\n"); cleanup_stats_info(info); return 1; } if (ga.nthreads > 0) hts_set_threads(info->sam, ga.nthreads); stats_t *all_stats = stats_init(); if (!all_stats) { fprintf(samtools_stderr, "Could not allocate memory for stats.\n"); cleanup_stats_info(info); return 1; } stats_t *curr_stats = NULL; init_stat_structs(all_stats, info, group_id, targets); // Init // .. hash khash_t(c2stats)* split_hash = kh_init(c2stats); if (!split_hash) goto cleanup_all_stats; khash_t(qn2pair)* read_pairs = kh_init(qn2pair); if (!read_pairs) goto cleanup_split_hash; // Collect statistics bam1_t *bam_line = bam_init1(); if (!bam_line) goto cleanup_read_pairs; if (optind < argc) { // Region:interval arguments in the command line hts_idx_t *bam_idx = NULL; if (has_index_file) { bam_idx = sam_index_load2(info->sam, bam_fname, bam_idx_fname); } else { // If an index filename has not been specified, look alongside the alignment file bam_idx = sam_index_load(info->sam, bam_fname); } if (bam_idx) { hts_itr_multi_t *iter = sam_itr_regarray(bam_idx, info->sam_header, &argv[optind], argc - optind); if (iter) { if (!targets) { all_stats->nchunks = argc-optind; if (replicate_regions(all_stats, iter, info)) fprintf(samtools_stderr, "Replications of the regions failed\n"); } if ( all_stats->nregions && all_stats->regions ) { while ((ret = sam_itr_next(info->sam, iter, bam_line)) >= 0) { if (info->split_tag) { curr_stats = get_curr_split_stats(bam_line, split_hash, info, targets); collect_stats(bam_line, curr_stats, read_pairs); } collect_stats(bam_line, all_stats, read_pairs); } if (ret < -1) { fprintf(samtools_stderr, "Failure while running the iterator\n"); hts_itr_multi_destroy(iter); hts_idx_destroy(bam_idx); goto cleanup; } } hts_itr_multi_destroy(iter); } else { fprintf(samtools_stderr, "Multi-region iterator could not be created\n"); hts_idx_destroy(bam_idx); goto cleanup; } hts_idx_destroy(bam_idx); } else { if (has_index_file) fprintf(samtools_stderr, "Invalid index file '%s'\n", bam_idx_fname); fprintf(samtools_stderr, "Random alignment retrieval only works for indexed files\n"); goto cleanup; } } else { if ( info->cov_threshold > 0 && !targets ) { fprintf(samtools_stderr, "Coverage percentage calculation requires a list of target regions\n"); goto cleanup; } // Stream through the entire BAM ignoring off-target regions if -t is given while ((ret = sam_read1(info->sam, info->sam_header, bam_line)) >= 0) { if (info->split_tag) { curr_stats = get_curr_split_stats(bam_line, split_hash, info, targets); collect_stats(bam_line, curr_stats, read_pairs); } collect_stats(bam_line, all_stats, read_pairs); } if (ret < -1) { fprintf(samtools_stderr, "Failure while decoding file\n"); goto cleanup; } } round_buffer_flush(all_stats, -1); output_stats(samtools_stdout, all_stats, sparse); if (info->split_tag) output_split_stats(split_hash, bam_fname, sparse); ret = 0; cleanup: bam_destroy1(bam_line); sam_hdr_destroy(info->sam_header); sam_global_args_free(&ga); cleanup_read_pairs: cleanup_overlaps(read_pairs, INT64_MAX); cleanup_split_hash: destroy_split_stats(split_hash); cleanup_all_stats: cleanup_stats(all_stats); cleanup_stats_info(info); return ret; } pysam-0.23.0/samtools/stats_isize.c000066400000000000000000000176131475062545500173200ustar00rootroot00000000000000/* stats_isize.c -- generalised insert size calculation for samtools stats. Copyright (C) 2014, 2018 Genome Research Ltd. Author: Nicholas Clarke Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include "stats_isize.h" #include typedef enum {IN,OUT,OTHER} isize_insert_t; static int max(int a, int b) { if (a < b) { return b; } else { return a; } } static isize_sparse_record_t * sparse_get_f(isize_data_t data, int at) { isize_sparse_data_t *a = data.sparse; khash_t(m32) *h = a->array; khint_t k = kh_get(m32, h, at); if (k != kh_end(h)) { return kh_value(h, k); } else { return NULL; } } static uint64_t sparse_in_f(isize_data_t data, int at) { isize_sparse_record_t* a = sparse_get_f(data, at); if (a != NULL) { return a->isize_inward; } else { return 0; } } static uint64_t sparse_out_f(isize_data_t data, int at) { isize_sparse_record_t* a = sparse_get_f(data, at); if (a != NULL) { return a->isize_outward; } else { return 0; } } static uint64_t sparse_other_f(isize_data_t data, int at) { isize_sparse_record_t* a = sparse_get_f(data, at); if (a != NULL) { return a->isize_other; } else { return 0; } } static void sparse_set_f(isize_data_t data, int at, isize_insert_t field, uint64_t value) { isize_sparse_data_t *a = data.sparse; khash_t(m32) *h = a->array; khint_t k = kh_get(m32, h, at); isize_sparse_record_t *rec; if (k != kh_end(h)) { rec = kh_value(h, k); } else if (value != 0) { rec = malloc(sizeof(isize_sparse_record_t)); if (rec != NULL) { rec->isize_inward = 0; rec->isize_outward = 0; rec->isize_other = 0; int stupid = 0; khint_t it = kh_put(m32, h, at, & stupid); kh_value(h, it) = rec; a->max = max(at, a->max); } else { fprintf(stderr, "%s\n", "Failed to allocate memory for isize_sparse_record_t"); exit(11); } } else { return; } if (field == IN) { rec->isize_inward = value; } else if (field == OUT) { rec->isize_outward = value; } else { rec->isize_other = value; } } static void sparse_set_in_f(isize_data_t data, int at, uint64_t value) { sparse_set_f(data, at, IN, value); } static void sparse_set_out_f(isize_data_t data, int at, uint64_t value) { sparse_set_f(data, at, OUT, value); } static void sparse_set_other_f(isize_data_t data, int at, uint64_t value) { sparse_set_f(data, at, OTHER, value); } static void sparse_inc_in_f(isize_data_t data, int at) { sparse_set_in_f(data, at, sparse_in_f(data, at) + 1); } static void sparse_inc_out_f(isize_data_t data, int at) { sparse_set_out_f(data, at, sparse_out_f(data, at) + 1); } static void sparse_inc_other_f(isize_data_t data, int at) { sparse_set_other_f(data, at, sparse_other_f(data, at) + 1); } static void sparse_isize_free(isize_data_t data) { isize_sparse_data_t *a = data.sparse; khint_t k; for (k = 0; k < kh_end(a->array); ++k) if (kh_exist(a->array, k)) free(kh_val(a->array, k)); kh_destroy(m32, a->array); free(a); } static int sparse_nitems(isize_data_t data) { isize_sparse_data_t *a = data.sparse; return a->max + 1; } static uint64_t dense_in_f(isize_data_t data, int at) { return data.dense->isize_inward[at]; } static uint64_t dense_out_f(isize_data_t data, int at) { return data.dense->isize_outward[at]; } static uint64_t dense_other_f(isize_data_t data, int at) { return data.dense->isize_other[at]; } static void dense_set_in_f(isize_data_t data, int at, uint64_t value) { data.dense->isize_inward[at] = value; } static void dense_set_out_f(isize_data_t data, int at, uint64_t value) { data.dense->isize_outward[at] = value; } static void dense_set_other_f(isize_data_t data, int at, uint64_t value) { data.dense->isize_other[at] = value; } static void dense_inc_in_f(isize_data_t data, int at) { data.dense->isize_inward[at] += 1; } static void dense_inc_out_f(isize_data_t data, int at) { data.dense->isize_outward[at] += 1; } static void dense_inc_other_f(isize_data_t data, int at) { data.dense->isize_other[at] += 1; } static void dense_isize_free(isize_data_t data) { isize_dense_data_t *a = data.dense; free(a->isize_inward); free(a->isize_outward); free(a->isize_other); free(a); } static int dense_nitems(isize_data_t data) { isize_dense_data_t *a = data.dense; return a->total; } // Construct a relevant isize_t given the bound. isize_t *init_isize_t(int bound) { if (bound <= 0) { // Use sparse data structure. isize_sparse_data_t *data = (isize_sparse_data_t *) malloc(sizeof(isize_sparse_data_t)); if (!data) return NULL; // Initialise data->max = 0; data->array = kh_init(m32); if (!data->array) { free(data); return NULL; } isize_t *isize = (isize_t *)malloc(sizeof(isize_t)); if (!isize) { kh_destroy(m32, data->array); free(data); return NULL; } isize->data.sparse = data; isize->nitems = & sparse_nitems; isize->inward = & sparse_in_f; isize->outward = & sparse_out_f; isize->other = & sparse_other_f; isize->set_inward = & sparse_set_in_f; isize->set_outward = & sparse_set_out_f; isize->set_other = & sparse_set_other_f; isize->inc_inward = & sparse_inc_in_f; isize->inc_outward = & sparse_inc_out_f; isize->inc_other = & sparse_inc_other_f; isize->isize_free = & sparse_isize_free; return isize; } else { uint64_t* in = calloc(bound,sizeof(uint64_t)); uint64_t* out = calloc(bound,sizeof(uint64_t)); uint64_t* other = calloc(bound,sizeof(uint64_t)); isize_dense_data_t *rec = (isize_dense_data_t *)malloc(sizeof(isize_dense_data_t)); isize_t *isize = (isize_t *)malloc(sizeof(isize_t)); if (!in || !out || !other || !rec || !isize) { free(in); free(out); free(other); free(rec); free(isize); return NULL; } rec->isize_inward = in; rec->isize_outward = out; rec->isize_other = other; rec->total=bound; isize->data.dense = rec; isize->nitems = & dense_nitems; isize->inward = & dense_in_f; isize->outward = & dense_out_f; isize->other = & dense_other_f; isize->set_inward = & dense_set_in_f; isize->set_outward = & dense_set_out_f; isize->set_other = & dense_set_other_f; isize->inc_inward = & dense_inc_in_f; isize->inc_outward = & dense_inc_out_f; isize->inc_other = & dense_inc_other_f; isize->isize_free = & dense_isize_free; return isize; } } pysam-0.23.0/samtools/stats_isize.c.pysam.c000066400000000000000000000176721475062545500206760ustar00rootroot00000000000000#include "samtools.pysam.h" /* stats_isize.c -- generalised insert size calculation for samtools stats. Copyright (C) 2014, 2018 Genome Research Ltd. Author: Nicholas Clarke Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include "stats_isize.h" #include typedef enum {IN,OUT,OTHER} isize_insert_t; static int max(int a, int b) { if (a < b) { return b; } else { return a; } } static isize_sparse_record_t * sparse_get_f(isize_data_t data, int at) { isize_sparse_data_t *a = data.sparse; khash_t(m32) *h = a->array; khint_t k = kh_get(m32, h, at); if (k != kh_end(h)) { return kh_value(h, k); } else { return NULL; } } static uint64_t sparse_in_f(isize_data_t data, int at) { isize_sparse_record_t* a = sparse_get_f(data, at); if (a != NULL) { return a->isize_inward; } else { return 0; } } static uint64_t sparse_out_f(isize_data_t data, int at) { isize_sparse_record_t* a = sparse_get_f(data, at); if (a != NULL) { return a->isize_outward; } else { return 0; } } static uint64_t sparse_other_f(isize_data_t data, int at) { isize_sparse_record_t* a = sparse_get_f(data, at); if (a != NULL) { return a->isize_other; } else { return 0; } } static void sparse_set_f(isize_data_t data, int at, isize_insert_t field, uint64_t value) { isize_sparse_data_t *a = data.sparse; khash_t(m32) *h = a->array; khint_t k = kh_get(m32, h, at); isize_sparse_record_t *rec; if (k != kh_end(h)) { rec = kh_value(h, k); } else if (value != 0) { rec = malloc(sizeof(isize_sparse_record_t)); if (rec != NULL) { rec->isize_inward = 0; rec->isize_outward = 0; rec->isize_other = 0; int stupid = 0; khint_t it = kh_put(m32, h, at, & stupid); kh_value(h, it) = rec; a->max = max(at, a->max); } else { fprintf(samtools_stderr, "%s\n", "Failed to allocate memory for isize_sparse_record_t"); samtools_exit(11); } } else { return; } if (field == IN) { rec->isize_inward = value; } else if (field == OUT) { rec->isize_outward = value; } else { rec->isize_other = value; } } static void sparse_set_in_f(isize_data_t data, int at, uint64_t value) { sparse_set_f(data, at, IN, value); } static void sparse_set_out_f(isize_data_t data, int at, uint64_t value) { sparse_set_f(data, at, OUT, value); } static void sparse_set_other_f(isize_data_t data, int at, uint64_t value) { sparse_set_f(data, at, OTHER, value); } static void sparse_inc_in_f(isize_data_t data, int at) { sparse_set_in_f(data, at, sparse_in_f(data, at) + 1); } static void sparse_inc_out_f(isize_data_t data, int at) { sparse_set_out_f(data, at, sparse_out_f(data, at) + 1); } static void sparse_inc_other_f(isize_data_t data, int at) { sparse_set_other_f(data, at, sparse_other_f(data, at) + 1); } static void sparse_isize_free(isize_data_t data) { isize_sparse_data_t *a = data.sparse; khint_t k; for (k = 0; k < kh_end(a->array); ++k) if (kh_exist(a->array, k)) free(kh_val(a->array, k)); kh_destroy(m32, a->array); free(a); } static int sparse_nitems(isize_data_t data) { isize_sparse_data_t *a = data.sparse; return a->max + 1; } static uint64_t dense_in_f(isize_data_t data, int at) { return data.dense->isize_inward[at]; } static uint64_t dense_out_f(isize_data_t data, int at) { return data.dense->isize_outward[at]; } static uint64_t dense_other_f(isize_data_t data, int at) { return data.dense->isize_other[at]; } static void dense_set_in_f(isize_data_t data, int at, uint64_t value) { data.dense->isize_inward[at] = value; } static void dense_set_out_f(isize_data_t data, int at, uint64_t value) { data.dense->isize_outward[at] = value; } static void dense_set_other_f(isize_data_t data, int at, uint64_t value) { data.dense->isize_other[at] = value; } static void dense_inc_in_f(isize_data_t data, int at) { data.dense->isize_inward[at] += 1; } static void dense_inc_out_f(isize_data_t data, int at) { data.dense->isize_outward[at] += 1; } static void dense_inc_other_f(isize_data_t data, int at) { data.dense->isize_other[at] += 1; } static void dense_isize_free(isize_data_t data) { isize_dense_data_t *a = data.dense; free(a->isize_inward); free(a->isize_outward); free(a->isize_other); free(a); } static int dense_nitems(isize_data_t data) { isize_dense_data_t *a = data.dense; return a->total; } // Construct a relevant isize_t given the bound. isize_t *init_isize_t(int bound) { if (bound <= 0) { // Use sparse data structure. isize_sparse_data_t *data = (isize_sparse_data_t *) malloc(sizeof(isize_sparse_data_t)); if (!data) return NULL; // Initialise data->max = 0; data->array = kh_init(m32); if (!data->array) { free(data); return NULL; } isize_t *isize = (isize_t *)malloc(sizeof(isize_t)); if (!isize) { kh_destroy(m32, data->array); free(data); return NULL; } isize->data.sparse = data; isize->nitems = & sparse_nitems; isize->inward = & sparse_in_f; isize->outward = & sparse_out_f; isize->other = & sparse_other_f; isize->set_inward = & sparse_set_in_f; isize->set_outward = & sparse_set_out_f; isize->set_other = & sparse_set_other_f; isize->inc_inward = & sparse_inc_in_f; isize->inc_outward = & sparse_inc_out_f; isize->inc_other = & sparse_inc_other_f; isize->isize_free = & sparse_isize_free; return isize; } else { uint64_t* in = calloc(bound,sizeof(uint64_t)); uint64_t* out = calloc(bound,sizeof(uint64_t)); uint64_t* other = calloc(bound,sizeof(uint64_t)); isize_dense_data_t *rec = (isize_dense_data_t *)malloc(sizeof(isize_dense_data_t)); isize_t *isize = (isize_t *)malloc(sizeof(isize_t)); if (!in || !out || !other || !rec || !isize) { free(in); free(out); free(other); free(rec); free(isize); return NULL; } rec->isize_inward = in; rec->isize_outward = out; rec->isize_other = other; rec->total=bound; isize->data.dense = rec; isize->nitems = & dense_nitems; isize->inward = & dense_in_f; isize->outward = & dense_out_f; isize->other = & dense_other_f; isize->set_inward = & dense_set_in_f; isize->set_outward = & dense_set_out_f; isize->set_other = & dense_set_other_f; isize->inc_inward = & dense_inc_in_f; isize->inc_outward = & dense_inc_out_f; isize->inc_other = & dense_inc_other_f; isize->isize_free = & dense_isize_free; return isize; } } pysam-0.23.0/samtools/stats_isize.h000066400000000000000000000046641475062545500173270ustar00rootroot00000000000000/* stats_isize.h -- generalised insert size calculation for samtools stats. Copyright (C) 2014 Genome Research Ltd. Author: Nicholas Clarke Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include typedef struct { int total; uint64_t *isize_inward, *isize_outward, *isize_other; } isize_dense_data_t; typedef struct { uint64_t isize_inward, isize_outward, isize_other; } isize_sparse_record_t; KHASH_MAP_INIT_INT(m32, isize_sparse_record_t *) typedef struct { int max; khash_t(m32) *array; } isize_sparse_data_t; typedef union { isize_sparse_data_t *sparse; isize_dense_data_t *dense; } isize_data_t; // Insert size structure typedef struct { isize_data_t data; // Maximum int (*nitems)(isize_data_t); // Fetch the number of inserts of a given size uint64_t (*inward)(isize_data_t, int); uint64_t (*outward)(isize_data_t, int); uint64_t (*other)(isize_data_t, int); // Set the number of inserts of a given size void (*set_inward)(isize_data_t, int, uint64_t); void (*set_outward)(isize_data_t, int, uint64_t); void (*set_other)(isize_data_t, int, uint64_t); // Increment the number of inserts of a given size void (*inc_inward)(isize_data_t, int); void (*inc_outward)(isize_data_t, int); void (*inc_other)(isize_data_t, int); // Free this structure void (*isize_free)(isize_data_t); } isize_t; isize_t *init_isize_t(int bound); pysam-0.23.0/samtools/tmp_file.c000066400000000000000000000327271475062545500165610ustar00rootroot00000000000000/* tmp_file.c - write to and read from a temporary binary file for fast storage plus added compression. Copyright (C) 2017, 2018 Genome Research Ltd. Author: Andrew Whitwham Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE */ #include #include #include #include #include #include #include #include #ifdef _WIN32 #include #endif /* _WIN32 */ #include "tmp_file.h" #include "htslib/sam.h" static void HTS_FORMAT(HTS_PRINTF_FMT, 2, 3) tmp_print_error(tmp_file_t *tmp, const char *fmt, ...) { va_list argp; if (tmp->verbose) { va_start(argp, fmt); vfprintf(stderr, fmt, argp); va_end(argp); } } static int tmp_file_init(tmp_file_t *tmp, int verbose) { tmp->stream = LZ4_createStream(); tmp->data_size = 0; tmp->group_size = TMP_SAM_GROUP_SIZE; tmp->input_size = 0; tmp->read_size = 0; tmp->output_size = 0; tmp->entry_number = 0; tmp->offset = 0; tmp->max_data_size = TMP_SAM_MAX_DATA + sizeof(bam1_t); // arbitrary but growable tmp->ring_buffer_size = TMP_SAM_RING_SIZE; // arbitrary (min 64K) but growable tmp->comp_buffer_size = LZ4_COMPRESSBOUND(tmp->max_data_size * tmp->group_size); tmp->ring_buffer = malloc(sizeof(uint8_t) * tmp->ring_buffer_size); tmp->ring_index = tmp->ring_buffer; tmp->comp_buffer = malloc(tmp->comp_buffer_size); tmp->verbose = verbose; tmp->dict = NULL; tmp->groups_written = 0; if (!tmp->ring_buffer || !tmp->comp_buffer || !tmp->stream) { tmp_print_error(tmp, "[tmp_file] Error: unable to allocate compression buffers.\n"); return TMP_SAM_MEM_ERROR; } return TMP_SAM_OK; } /* * Opens the temp file and initialises memory. * Verbose mode prints out error messages to stderr. * Returns 0 on success, a negative number on failure. */ int tmp_file_open_write(tmp_file_t *tmp, char *tmp_name, int verbose) { int ret; unsigned int count = 1; const unsigned int max_count = 100000; // more tries than this then something else is wrong int fd; if ((ret = tmp_file_init(tmp, verbose))) { return ret; } // make space to write extended file name if ((tmp->name = malloc(strlen(tmp_name) + 7)) == NULL) { tmp_print_error(tmp, "[tmp_file] Error: unable to allocate memory for %s.\n", tmp_name); return TMP_SAM_MEM_ERROR; } // make sure temp file has a unique name while (count < max_count) { sprintf(tmp->name, "%s.%d", tmp_name, count); #ifdef _WIN32 if ((fd = _open(tmp->name, O_RDWR|O_CREAT|O_EXCL|O_BINARY|O_TEMPORARY, 0600)) == -1) { #else if ((fd = open(tmp->name, O_RDWR|O_CREAT|O_EXCL, 0600)) == -1) { #endif /* _WIN32 */ if (errno != EEXIST) { tmp_print_error(tmp, "[tmp_file] Error: unable to create tmp file %s.\n", tmp->name); return TMP_SAM_FILE_ERROR; } count++; continue; } break; } if (count >= max_count) { tmp_print_error(tmp, "[tmp_file] Error: unable to create unique temp file.\n"); return TMP_SAM_FILE_ERROR; } if ((tmp->fp = fdopen(fd, "w+b")) == NULL) { tmp_print_error(tmp, "[tmp_file] Error: unable to open write file %s.\n", tmp->name); return TMP_SAM_FILE_ERROR; } #ifndef _WIN32 unlink(tmp->name); // should auto delete when closed on linux #endif return TMP_SAM_OK; } /* * The ring buffer stores precompressionn/post decompression data. LZ4 requires that * previous data (64K worth) be available for efficient compression. This function grows * the ring buffer when needed. * Returns 0 on success, a negative number on failure. */ static int tmp_file_grow_ring_buffer(tmp_file_t *tmp, size_t new_size) { // save the dictionary so lz4 can continue to function int dict_size = 64 * 1024; // 64K max size if (tmp->groups_written) { // if compression has been done then there is a dictionary to save if (tmp->dict == NULL) { if ((tmp->dict = malloc(sizeof(char) * dict_size)) == NULL) { tmp_print_error(tmp, "[tmp_file] Error: unable to allocate memory for compression dictionary.\n"); return TMP_SAM_MEM_ERROR; } } if (LZ4_saveDict(tmp->stream, tmp->dict, dict_size) == 0) { tmp_print_error(tmp, "[tmp_file] Error: unable to save compression dictionary.\n"); return TMP_SAM_LZ4_ERROR; } } if ((tmp->ring_buffer = realloc(tmp->ring_buffer, sizeof(char) * new_size)) == NULL) { tmp_print_error(tmp, "[tmp_file] Error: unable to reallocate ring buffer.\n"); return TMP_SAM_MEM_ERROR; } tmp->ring_buffer_size = new_size; return TMP_SAM_OK; } /* * This does the actual compression and writing to a file. The file format consists of a * single size_t for the size of the compressed data followed by the data itself. * Returns 0 on success, a negative number on failure. */ static int tmp_file_write_to_file(tmp_file_t *tmp) { size_t comp_size; if (tmp->input_size > tmp->max_data_size) { tmp->max_data_size += tmp->input_size + sizeof(bam1_t); tmp->comp_buffer_size = LZ4_COMPRESSBOUND(tmp->max_data_size); if ((tmp->comp_buffer = realloc(tmp->comp_buffer, sizeof(char) * tmp->comp_buffer_size)) == NULL) { tmp_print_error(tmp, "[tmp_file] Error: unable to reallocate compression buffer.\n"); return TMP_SAM_MEM_ERROR; } // make sure the ring buffer is big enough to accommodate the new max_data_size if (tmp->ring_buffer_size < tmp->max_data_size * 5) { int ret; if ((ret = tmp_file_grow_ring_buffer(tmp, tmp->max_data_size * 5))) { return ret; } } } tmp->ring_index = tmp->ring_buffer + tmp->offset; comp_size = LZ4_compress_fast_continue(tmp->stream, (const char *)tmp->ring_index, tmp->comp_buffer, tmp->input_size, tmp->comp_buffer_size, 1); if (comp_size == 0) { tmp_print_error(tmp, "[tmp_file] Error: compression failed.\n"); return TMP_SAM_LZ4_ERROR; } if (fwrite(&comp_size, sizeof(size_t), 1, tmp->fp) < 1) { tmp_print_error(tmp, "[tmp_file] Error: tmp file write size failed.\n"); return TMP_SAM_FILE_ERROR; } if (fwrite(tmp->comp_buffer, sizeof(char), comp_size, tmp->fp) < comp_size) { tmp_print_error(tmp, "[tmp_file] Error: tmp file write data failed.\n"); return TMP_SAM_FILE_ERROR; } tmp->offset += tmp->input_size; if (tmp->offset >= tmp->ring_buffer_size - tmp->max_data_size) tmp->offset = 0; tmp->input_size = 0; tmp->entry_number = 0; tmp->groups_written++; return TMP_SAM_OK; } /* * Stores an in memory bam structure for writing and if enough are gathered together writes * it to a file. Multiple alignments compress better that single ones though after a certain number * there is a law of diminishing returns. * Returns 0 on success, a negative number on failure. */ int tmp_file_write(tmp_file_t *tmp, bam1_t *inbam) { if ((tmp->offset + tmp->input_size + sizeof(bam1_t) + inbam->l_data) >= tmp->ring_buffer_size) { int ret; if ((ret = tmp_file_grow_ring_buffer(tmp, (tmp->offset + tmp->input_size + sizeof(bam1_t) + inbam->l_data) * 2))) { tmp_print_error(tmp, "[tmp_file] Error: input line too big. (%zu).\n", (tmp->input_size + inbam->l_data)); return ret; } } tmp->ring_index = tmp->ring_buffer + tmp->offset + tmp->input_size; // copy data into the ring buffer memcpy(tmp->ring_index, inbam, sizeof(bam1_t)); memcpy(tmp->ring_index + sizeof(bam1_t) , inbam->data, inbam->l_data); tmp->input_size += sizeof(bam1_t) + inbam->l_data; tmp->entry_number++; if (tmp->entry_number == tmp->group_size) { // actually write out the data int ret; if ((ret = tmp_file_write_to_file(tmp))) { return ret; } } return TMP_SAM_OK; } /* * Marks the end of file writing. Adds a size_t 0 to mark the end of * the file. Companion function to tmp_file_begin_read below. * Returns 0 on success, a negative number on failure. */ int tmp_file_end_write(tmp_file_t *tmp) { size_t terminator = 0; if (tmp->entry_number) { int ret; if ((ret = tmp_file_write_to_file(tmp))) { return ret; } } if (fwrite(&terminator, sizeof(size_t), 1, tmp->fp) < 1) { tmp_print_error(tmp, "[tmp_file] Error: tmp file write terminator failed.\n"); return TMP_SAM_FILE_ERROR; } fflush(tmp->fp); LZ4_freeStream(tmp->stream); return TMP_SAM_OK; } /* * Prepares the file for reading. * Companion function to tmp_file_end_write above. * Returns 0 on success, a negative number on failure. */ int tmp_file_begin_read(tmp_file_t *tmp) { rewind(tmp->fp); tmp->dstream = LZ4_createStreamDecode(); tmp->offset = 0; tmp->entry_number = tmp->group_size; if (!tmp->dstream) { tmp_print_error(tmp, "[tmp_file] Error: unable to allocate compression stream.\n"); return TMP_SAM_MEM_ERROR; } return TMP_SAM_OK; } /* * Read the next alignment, either from memory or from a file. * Returns size of entry on success, 0 on end of file or a negative on error. */ int tmp_file_read(tmp_file_t *tmp, bam1_t *inbam) { int entry_size; uint8_t *data = inbam->data; /* while tmp_file_read assumes that the same bam1_t variable is being used in each call, this may not be the case. So default to the lowest memory size for safety. */ if (tmp->data_size > inbam->m_data) { tmp->data_size = inbam->m_data; } if (tmp->entry_number == tmp->group_size) { // read more data size_t comp_size; if (fread(&comp_size, sizeof(size_t), 1, tmp->fp) == 0 || comp_size == 0) { return TMP_SAM_OK; } if (tmp->offset >= tmp->ring_buffer_size - tmp->max_data_size) tmp->offset = 0; tmp->ring_index = tmp->ring_buffer + tmp->offset; if (fread(tmp->comp_buffer, sizeof(char), comp_size, tmp->fp) > comp_size) { tmp_print_error(tmp, "[tmp_file] Error: error reading compressed data.\n"); return TMP_SAM_FILE_ERROR; } tmp->output_size = LZ4_decompress_safe_continue(tmp->dstream, tmp->comp_buffer, (char *)tmp->ring_index, comp_size, tmp->max_data_size); if (tmp->output_size == 0) { tmp_print_error(tmp, "[tmp_file] Error: decompression failed.\n"); return TMP_SAM_LZ4_ERROR; } tmp->entry_number = 0; tmp->read_size = 0; } tmp->ring_index = tmp->ring_buffer + tmp->offset; memcpy(inbam, tmp->ring_index, sizeof(bam1_t)); inbam->data = data; // put the pointer to real bam data back if ((unsigned int)inbam->l_data > tmp->data_size) { uint8_t *tmp_data; tmp->data_size = inbam->l_data; kroundup32(tmp->data_size); if ((tmp_data = realloc(inbam->data, sizeof(uint8_t) * tmp->data_size)) == NULL) { tmp_print_error(tmp, "[tmp_file] Error: unable to allocate tmp bam data memory.\n"); return TMP_SAM_MEM_ERROR; } inbam->data = tmp_data; } inbam->m_data = tmp->data_size; // set to the actual data size entry_size = sizeof(bam1_t); memcpy(inbam->data, tmp->ring_index + entry_size, inbam->l_data); entry_size += inbam->l_data; tmp->offset += entry_size; tmp->read_size += entry_size; tmp->entry_number++; if (tmp->read_size > tmp->output_size) { tmp_print_error(tmp, "[tmp_file] Error: wrong size of data returned RS:%zu OS:%zu EN:%zu GS:%zu.\n", tmp->read_size, tmp->output_size, tmp->entry_number, tmp->group_size); return TMP_SAM_LZ4_ERROR; } if (tmp->read_size == tmp->output_size && tmp->entry_number != tmp->group_size) { // hopefully the last entries in the read file tmp->entry_number = tmp->group_size; } return entry_size; } /* * Frees up memory, closes the file and deletes it. * Returns 0 on success or EOF on failure. */ int tmp_file_destroy(tmp_file_t *tmp) { int ret = 0; ret = fclose(tmp->fp); LZ4_freeStreamDecode(tmp->dstream); free(tmp->ring_buffer); free(tmp->comp_buffer); free(tmp->name); free(tmp->dict); return ret; } pysam-0.23.0/samtools/tmp_file.c.pysam.c000066400000000000000000000330061475062545500201210ustar00rootroot00000000000000#include "samtools.pysam.h" /* tmp_file.c - write to and read from a temporary binary file for fast storage plus added compression. Copyright (C) 2017, 2018 Genome Research Ltd. Author: Andrew Whitwham Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE */ #include #include #include #include #include #include #include #include #ifdef _WIN32 #include #endif /* _WIN32 */ #include "tmp_file.h" #include "htslib/sam.h" static void HTS_FORMAT(HTS_PRINTF_FMT, 2, 3) tmp_print_error(tmp_file_t *tmp, const char *fmt, ...) { va_list argp; if (tmp->verbose) { va_start(argp, fmt); vfprintf(samtools_stderr, fmt, argp); va_end(argp); } } static int tmp_file_init(tmp_file_t *tmp, int verbose) { tmp->stream = LZ4_createStream(); tmp->data_size = 0; tmp->group_size = TMP_SAM_GROUP_SIZE; tmp->input_size = 0; tmp->read_size = 0; tmp->output_size = 0; tmp->entry_number = 0; tmp->offset = 0; tmp->max_data_size = TMP_SAM_MAX_DATA + sizeof(bam1_t); // arbitrary but growable tmp->ring_buffer_size = TMP_SAM_RING_SIZE; // arbitrary (min 64K) but growable tmp->comp_buffer_size = LZ4_COMPRESSBOUND(tmp->max_data_size * tmp->group_size); tmp->ring_buffer = malloc(sizeof(uint8_t) * tmp->ring_buffer_size); tmp->ring_index = tmp->ring_buffer; tmp->comp_buffer = malloc(tmp->comp_buffer_size); tmp->verbose = verbose; tmp->dict = NULL; tmp->groups_written = 0; if (!tmp->ring_buffer || !tmp->comp_buffer || !tmp->stream) { tmp_print_error(tmp, "[tmp_file] Error: unable to allocate compression buffers.\n"); return TMP_SAM_MEM_ERROR; } return TMP_SAM_OK; } /* * Opens the temp file and initialises memory. * Verbose mode prints out error messages to samtools_stderr. * Returns 0 on success, a negative number on failure. */ int tmp_file_open_write(tmp_file_t *tmp, char *tmp_name, int verbose) { int ret; unsigned int count = 1; const unsigned int max_count = 100000; // more tries than this then something else is wrong int fd; if ((ret = tmp_file_init(tmp, verbose))) { return ret; } // make space to write extended file name if ((tmp->name = malloc(strlen(tmp_name) + 7)) == NULL) { tmp_print_error(tmp, "[tmp_file] Error: unable to allocate memory for %s.\n", tmp_name); return TMP_SAM_MEM_ERROR; } // make sure temp file has a unique name while (count < max_count) { sprintf(tmp->name, "%s.%d", tmp_name, count); #ifdef _WIN32 if ((fd = _open(tmp->name, O_RDWR|O_CREAT|O_EXCL|O_BINARY|O_TEMPORARY, 0600)) == -1) { #else if ((fd = open(tmp->name, O_RDWR|O_CREAT|O_EXCL, 0600)) == -1) { #endif /* _WIN32 */ if (errno != EEXIST) { tmp_print_error(tmp, "[tmp_file] Error: unable to create tmp file %s.\n", tmp->name); return TMP_SAM_FILE_ERROR; } count++; continue; } break; } if (count >= max_count) { tmp_print_error(tmp, "[tmp_file] Error: unable to create unique temp file.\n"); return TMP_SAM_FILE_ERROR; } if ((tmp->fp = fdopen(fd, "w+b")) == NULL) { tmp_print_error(tmp, "[tmp_file] Error: unable to open write file %s.\n", tmp->name); return TMP_SAM_FILE_ERROR; } #ifndef _WIN32 unlink(tmp->name); // should auto delete when closed on linux #endif return TMP_SAM_OK; } /* * The ring buffer stores precompressionn/post decompression data. LZ4 requires that * previous data (64K worth) be available for efficient compression. This function grows * the ring buffer when needed. * Returns 0 on success, a negative number on failure. */ static int tmp_file_grow_ring_buffer(tmp_file_t *tmp, size_t new_size) { // save the dictionary so lz4 can continue to function int dict_size = 64 * 1024; // 64K max size if (tmp->groups_written) { // if compression has been done then there is a dictionary to save if (tmp->dict == NULL) { if ((tmp->dict = malloc(sizeof(char) * dict_size)) == NULL) { tmp_print_error(tmp, "[tmp_file] Error: unable to allocate memory for compression dictionary.\n"); return TMP_SAM_MEM_ERROR; } } if (LZ4_saveDict(tmp->stream, tmp->dict, dict_size) == 0) { tmp_print_error(tmp, "[tmp_file] Error: unable to save compression dictionary.\n"); return TMP_SAM_LZ4_ERROR; } } if ((tmp->ring_buffer = realloc(tmp->ring_buffer, sizeof(char) * new_size)) == NULL) { tmp_print_error(tmp, "[tmp_file] Error: unable to reallocate ring buffer.\n"); return TMP_SAM_MEM_ERROR; } tmp->ring_buffer_size = new_size; return TMP_SAM_OK; } /* * This does the actual compression and writing to a file. The file format consists of a * single size_t for the size of the compressed data followed by the data itself. * Returns 0 on success, a negative number on failure. */ static int tmp_file_write_to_file(tmp_file_t *tmp) { size_t comp_size; if (tmp->input_size > tmp->max_data_size) { tmp->max_data_size += tmp->input_size + sizeof(bam1_t); tmp->comp_buffer_size = LZ4_COMPRESSBOUND(tmp->max_data_size); if ((tmp->comp_buffer = realloc(tmp->comp_buffer, sizeof(char) * tmp->comp_buffer_size)) == NULL) { tmp_print_error(tmp, "[tmp_file] Error: unable to reallocate compression buffer.\n"); return TMP_SAM_MEM_ERROR; } // make sure the ring buffer is big enough to accommodate the new max_data_size if (tmp->ring_buffer_size < tmp->max_data_size * 5) { int ret; if ((ret = tmp_file_grow_ring_buffer(tmp, tmp->max_data_size * 5))) { return ret; } } } tmp->ring_index = tmp->ring_buffer + tmp->offset; comp_size = LZ4_compress_fast_continue(tmp->stream, (const char *)tmp->ring_index, tmp->comp_buffer, tmp->input_size, tmp->comp_buffer_size, 1); if (comp_size == 0) { tmp_print_error(tmp, "[tmp_file] Error: compression failed.\n"); return TMP_SAM_LZ4_ERROR; } if (fwrite(&comp_size, sizeof(size_t), 1, tmp->fp) < 1) { tmp_print_error(tmp, "[tmp_file] Error: tmp file write size failed.\n"); return TMP_SAM_FILE_ERROR; } if (fwrite(tmp->comp_buffer, sizeof(char), comp_size, tmp->fp) < comp_size) { tmp_print_error(tmp, "[tmp_file] Error: tmp file write data failed.\n"); return TMP_SAM_FILE_ERROR; } tmp->offset += tmp->input_size; if (tmp->offset >= tmp->ring_buffer_size - tmp->max_data_size) tmp->offset = 0; tmp->input_size = 0; tmp->entry_number = 0; tmp->groups_written++; return TMP_SAM_OK; } /* * Stores an in memory bam structure for writing and if enough are gathered together writes * it to a file. Multiple alignments compress better that single ones though after a certain number * there is a law of diminishing returns. * Returns 0 on success, a negative number on failure. */ int tmp_file_write(tmp_file_t *tmp, bam1_t *inbam) { if ((tmp->offset + tmp->input_size + sizeof(bam1_t) + inbam->l_data) >= tmp->ring_buffer_size) { int ret; if ((ret = tmp_file_grow_ring_buffer(tmp, (tmp->offset + tmp->input_size + sizeof(bam1_t) + inbam->l_data) * 2))) { tmp_print_error(tmp, "[tmp_file] Error: input line too big. (%zu).\n", (tmp->input_size + inbam->l_data)); return ret; } } tmp->ring_index = tmp->ring_buffer + tmp->offset + tmp->input_size; // copy data into the ring buffer memcpy(tmp->ring_index, inbam, sizeof(bam1_t)); memcpy(tmp->ring_index + sizeof(bam1_t) , inbam->data, inbam->l_data); tmp->input_size += sizeof(bam1_t) + inbam->l_data; tmp->entry_number++; if (tmp->entry_number == tmp->group_size) { // actually write out the data int ret; if ((ret = tmp_file_write_to_file(tmp))) { return ret; } } return TMP_SAM_OK; } /* * Marks the end of file writing. Adds a size_t 0 to mark the end of * the file. Companion function to tmp_file_begin_read below. * Returns 0 on success, a negative number on failure. */ int tmp_file_end_write(tmp_file_t *tmp) { size_t terminator = 0; if (tmp->entry_number) { int ret; if ((ret = tmp_file_write_to_file(tmp))) { return ret; } } if (fwrite(&terminator, sizeof(size_t), 1, tmp->fp) < 1) { tmp_print_error(tmp, "[tmp_file] Error: tmp file write terminator failed.\n"); return TMP_SAM_FILE_ERROR; } fflush(tmp->fp); LZ4_freeStream(tmp->stream); return TMP_SAM_OK; } /* * Prepares the file for reading. * Companion function to tmp_file_end_write above. * Returns 0 on success, a negative number on failure. */ int tmp_file_begin_read(tmp_file_t *tmp) { rewind(tmp->fp); tmp->dstream = LZ4_createStreamDecode(); tmp->offset = 0; tmp->entry_number = tmp->group_size; if (!tmp->dstream) { tmp_print_error(tmp, "[tmp_file] Error: unable to allocate compression stream.\n"); return TMP_SAM_MEM_ERROR; } return TMP_SAM_OK; } /* * Read the next alignment, either from memory or from a file. * Returns size of entry on success, 0 on end of file or a negative on error. */ int tmp_file_read(tmp_file_t *tmp, bam1_t *inbam) { int entry_size; uint8_t *data = inbam->data; /* while tmp_file_read assumes that the same bam1_t variable is being used in each call, this may not be the case. So default to the lowest memory size for safety. */ if (tmp->data_size > inbam->m_data) { tmp->data_size = inbam->m_data; } if (tmp->entry_number == tmp->group_size) { // read more data size_t comp_size; if (fread(&comp_size, sizeof(size_t), 1, tmp->fp) == 0 || comp_size == 0) { return TMP_SAM_OK; } if (tmp->offset >= tmp->ring_buffer_size - tmp->max_data_size) tmp->offset = 0; tmp->ring_index = tmp->ring_buffer + tmp->offset; if (fread(tmp->comp_buffer, sizeof(char), comp_size, tmp->fp) > comp_size) { tmp_print_error(tmp, "[tmp_file] Error: error reading compressed data.\n"); return TMP_SAM_FILE_ERROR; } tmp->output_size = LZ4_decompress_safe_continue(tmp->dstream, tmp->comp_buffer, (char *)tmp->ring_index, comp_size, tmp->max_data_size); if (tmp->output_size == 0) { tmp_print_error(tmp, "[tmp_file] Error: decompression failed.\n"); return TMP_SAM_LZ4_ERROR; } tmp->entry_number = 0; tmp->read_size = 0; } tmp->ring_index = tmp->ring_buffer + tmp->offset; memcpy(inbam, tmp->ring_index, sizeof(bam1_t)); inbam->data = data; // put the pointer to real bam data back if ((unsigned int)inbam->l_data > tmp->data_size) { uint8_t *tmp_data; tmp->data_size = inbam->l_data; kroundup32(tmp->data_size); if ((tmp_data = realloc(inbam->data, sizeof(uint8_t) * tmp->data_size)) == NULL) { tmp_print_error(tmp, "[tmp_file] Error: unable to allocate tmp bam data memory.\n"); return TMP_SAM_MEM_ERROR; } inbam->data = tmp_data; } inbam->m_data = tmp->data_size; // set to the actual data size entry_size = sizeof(bam1_t); memcpy(inbam->data, tmp->ring_index + entry_size, inbam->l_data); entry_size += inbam->l_data; tmp->offset += entry_size; tmp->read_size += entry_size; tmp->entry_number++; if (tmp->read_size > tmp->output_size) { tmp_print_error(tmp, "[tmp_file] Error: wrong size of data returned RS:%zu OS:%zu EN:%zu GS:%zu.\n", tmp->read_size, tmp->output_size, tmp->entry_number, tmp->group_size); return TMP_SAM_LZ4_ERROR; } if (tmp->read_size == tmp->output_size && tmp->entry_number != tmp->group_size) { // hopefully the last entries in the read file tmp->entry_number = tmp->group_size; } return entry_size; } /* * Frees up memory, closes the file and deletes it. * Returns 0 on success or EOF on failure. */ int tmp_file_destroy(tmp_file_t *tmp) { int ret = 0; ret = fclose(tmp->fp); LZ4_freeStreamDecode(tmp->dstream); free(tmp->ring_buffer); free(tmp->comp_buffer); free(tmp->name); free(tmp->dict); return ret; } pysam-0.23.0/samtools/tmp_file.h000066400000000000000000000070731475062545500165620ustar00rootroot00000000000000/* tmp_file.h - write to and read from a temporary binary file for fast storage plus added compression. Copyright (C) 2017, 2018 Genome Research Ltd. Author: Andrew Whitwham Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE */ #ifndef _TMP_SAM_FILE_H_ #define _TMP_SAM_FILE_H_ #include #include "htslib/sam.h" #ifdef __cplusplus extern "C" { #endif // Group size that seems to give reasonable compression. #define TMP_SAM_GROUP_SIZE 100 // Arbitrary initial size values but growable. #define TMP_SAM_MAX_DATA 1024 #define TMP_SAM_RING_SIZE 1048576 // Error numbers. #define TMP_SAM_OK 0 #define TMP_SAM_MEM_ERROR -1 #define TMP_SAM_FILE_ERROR -2 #define TMP_SAM_LZ4_ERROR -3 #define TMP_SAM_INPUT_ERROR -4 typedef struct { FILE *fp; LZ4_stream_t *stream; LZ4_streamDecode_t *dstream; size_t data_size; size_t max_data_size; size_t ring_buffer_size; size_t comp_buffer_size; size_t offset; uint8_t *ring_buffer; uint8_t *ring_index; char *comp_buffer; char *name; size_t group_size; size_t input_size; size_t read_size; size_t output_size; size_t entry_number; int verbose; char *dict; size_t groups_written; } tmp_file_t; /* * Opens the temp file and initialises memory. * Verbose mode prints out error messages to stderr. * Returns 0 on success, a negative number on failure. */ int tmp_file_open_write(tmp_file_t *tmp, char *tmp_name, int verbose); /* * Stores an in memory bam structure for writing and if enough are gathered together writes * it to a file. Multiple alignments compress better that single ones though after a certain number * there is a law of diminishing returns. * Returns 0 on success, a negative number on failure. */ int tmp_file_write(tmp_file_t *tmp, bam1_t *inbam); /* * Marks the end of file writing. Adds a size_t 0 to mark the end of * the file. Companion function to tmp_file_begin_read below. * Returns 0 on success, a negative number on failure. */ int tmp_file_end_write(tmp_file_t *tmp); /* * Prepares the file for reading. * Companion function to tmp_file_end_write above. * Returns 0 on success, a negative number on failure. */ int tmp_file_begin_read(tmp_file_t *tmp); /* * Read the next alignment, either from memory or from a file. * Returns size of entry on success, 0 on end of file or a negative on error. */ int tmp_file_read(tmp_file_t *tmp, bam1_t *inbam); /* * Frees up memory, closes the file and deletes it. * Returns 0 on success or EOF on failure. */ int tmp_file_destroy(tmp_file_t *tmp); #ifdef __cplusplus } #endif #endif /* _TMP_SAM_FILE_H_ */ pysam-0.23.0/samtools/version.sh000077500000000000000000000030011475062545500166210ustar00rootroot00000000000000#!/bin/sh # version.sh -- Script to build the htslib version string # # Author : James Bonfield # # Copyright (C) 2017, 2019 Genome Research Ltd. # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. # Master version, for use in tarballs or non-git source copies VERSION=1.21 # If we have a git clone, then check against the current tag if [ -e .git ] then # If we ever get to 10.x this will need to be more liberal VERSION=`git describe --match '[0-9].[0-9]*' --dirty --always` fi echo $VERSION pysam-0.23.0/setup.cfg000066400000000000000000000031021475062545500145570ustar00rootroot00000000000000[bdist_wheel] universal = 0 [tool:pytest] # -s: do not capture stdout, conflicts with pysam.dispatch # -v: verbose output addopts = -s -v testpaths = pysam tests [flake8] max-line-length = 100 max-complexity = 23 extend-ignore = E117, E124, E125, E201, E202, E211, E225, E231, E265, E266, E302, E303, E305, E402, E501, E701, E713, E722, E741, F403, F405, F811, F821, F841, W291, W293, W391, W605 per-file-ignores = __init__.py:F401 # E117 over-indented # E124 closing bracket does not match visual indentation # E125 continuation line with same indent as next logical line # E201 whitespace after '{' # E202 whitespace before '}' # E211 whitespace before '(' # E225 missing whitespace around operator # E231 missing whitespace after ':' # E265 block comment should start with '# ' # E266 too many leading '#' for block comment # E302 expected 2 blank lines, found 1 # E303 too many blank lines # E305 expected 2 blank lines after class or function definition, found 1 # E402 module level import not at top of file # E501 line too long # E701 multiple statements on one line (colon) # E713 test for membership should be 'not in' # E722 do not use bare 'except' # E741 ambiguous variable name '...' # F403 'from ... import *' used; unable to detect undefined names # F405 '...' may be undefined, or defined from star imports: ... # F811 redefinition of unused '...' from line ... # F821 undefined name '...' # F841 local variable '...' is assigned to but never used # W291 trailing whitespace # W293 blank line contains whitespace # W391 blank line at end of file # W605 invalid escape sequence '...' pysam-0.23.0/setup.py000066400000000000000000000620571475062545500144660ustar00rootroot00000000000000#! /usr/bin/python '''pysam --- a Python package for reading, manipulating, and writing genomic data sets. pysam is a lightweight wrapper of the HTSlib API and provides facilities to read and write SAM/BAM/CRAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command-line functionality of samtools and bcftools. The module supports compression and random access through indexing. This module provides a low-level wrapper around HTSlib's C API using Cython and a high-level API for convenient access to the data within standard genomic file formats. ''' import collections import glob import logging import os import platform import re import subprocess import sys import sysconfig from contextlib import contextmanager from setuptools import setup, Command from setuptools.command.sdist import sdist from setuptools.extension import Extension try: from setuptools.errors import LinkError except ImportError: from distutils.errors import LinkError try: from Cython.Distutils import build_ext except ImportError: from setuptools.command.build_ext import build_ext try: import cython # noqa HAVE_CYTHON = True except ImportError: HAVE_CYTHON = False IS_DARWIN = platform.system() == 'Darwin' log = logging.getLogger('pysam') @contextmanager def changedir(path): save_dir = os.getcwd() os.chdir(path) try: yield finally: os.chdir(save_dir) def run_configure(option): sys.stdout.flush() try: retcode = subprocess.call( " ".join(("./configure", option)), shell=True) if retcode != 0: return False else: return True except OSError as e: return False def run_make(targets): sys.stdout.flush() subprocess.check_call([os.environ.get("MAKE", "make")] + targets) def run_make_print_config(): stdout = subprocess.check_output(["make", "-s", "print-config"], encoding="ascii") make_print_config = {} for line in stdout.splitlines(): if "=" in line: row = line.split("=") if len(row) == 2: make_print_config.update( {row[0].strip(): row[1].strip()}) return make_print_config def run_nm_defined_symbols(objfile): stdout = subprocess.check_output(["nm", "-g", "-P", objfile], encoding="ascii") symbols = set() for line in stdout.splitlines(): (sym, symtype) = line.split()[:2] if symtype not in "UFNWw": if IS_DARWIN: # On macOS, all symbols have a leading underscore symbols.add(sym.lstrip('_')) else: # Ignore symbols such as _edata (present in all shared objects) if sym[0] not in "_$.@": symbols.add(sym) return symbols # This function emulates the way distutils combines settings from sysconfig, # environment variables, and the extension being built. It returns a dictionary # representing the usual set of variables, suitable for writing to a generated # file or for running configure (provided the returned LIBS is ignored). def build_config_dict(ext): def env(var): return [os.environ[var]] if var in os.environ else [] def sc(var): value = sysconfig.get_config_var(var) return [value] if value is not None else [] def optionise(option, valuelist): def quote(s): return "'"+s+"'" if " " in s else s return list(quote(option+v) for v in valuelist) def kvtuples(pairlist): def appendoptvalue(t): return t[0] if t[1] is None else t[0]+"="+t[1] return map(appendoptvalue, pairlist) # For CC, select the first of these that is set cc = (env('CC') + sc('CC') + ['gcc'])[0] # distutils ignores sysconfig for CPPFLAGS cppflags = " ".join(env('CPPFLAGS') + optionise('-I', ext.include_dirs) + optionise('-D', kvtuples(ext.define_macros)) + optionise('-U', ext.undef_macros)) cflags = " ".join(sc('CFLAGS') + env('CFLAGS') + sc('CCSHARED') + ext.extra_compile_args) # distutils actually includes $CPPFLAGS here too, but that's weird and # unnecessary for us as we know the output LDFLAGS will be used correctly ldflags = " ".join(sc('LDFLAGS') + env('LDFLAGS') + env('CFLAGS') + optionise('-L', ext.library_dirs) + ext.extra_link_args) # ext.libraries is computed (incorporating $LIBS etc) during configure libs = " ".join(optionise('-l', ext.libraries)) return { 'CC': cc, 'CPPFLAGS': cppflags, 'CFLAGS': cflags, 'LDFLAGS': ldflags, 'LIBS': libs } def write_configvars_header(filename, ext, prefix): config = build_config_dict(ext) if prefix != 'HTS': config['HTSDIR'] = '(unused)' config['CURSES_LIB'] = '(unused)' log.info("creating %s for '%s' extension", filename, ext.name) with open(filename, "w") as outf: for var, value in config.items(): outf.write('#define {}_{} "{}"\n'.format(prefix, var, value)) @contextmanager def set_compiler_envvars(): tmp_vars = [] for var in ['CC', 'CFLAGS', 'LDFLAGS']: if var in os.environ: if var == 'CFLAGS' and 'CCSHARED' in sysconfig.get_config_vars(): os.environ[var] += ' ' + sysconfig.get_config_var('CCSHARED') print("# pysam: (env) {}={}".format(var, os.environ[var])) elif var in sysconfig.get_config_vars(): value = sysconfig.get_config_var(var) if var == 'CFLAGS' and 'CCSHARED' in sysconfig.get_config_vars(): value += ' ' + sysconfig.get_config_var('CCSHARED') print("# pysam: (sysconfig) {}={}".format(var, value)) os.environ[var] = value tmp_vars += [var] try: yield finally: for var in tmp_vars: del os.environ[var] def format_macro_option(name, value): return f"-D{name}={value}" if value is not None else f"-D{name}" def configure_library(library_dir, env_options=None, options=[]): configure_script = os.path.join(library_dir, "configure") on_rtd = os.environ.get("READTHEDOCS") == "True" # RTD has no bzip2 development libraries installed: if on_rtd: env_options = "--disable-bz2" if not os.path.exists(configure_script): raise ValueError( "configure script {} does not exist".format(configure_script)) with changedir(library_dir), set_compiler_envvars(): if env_options is not None: if run_configure(env_options): return env_options for option in options: if run_configure(option): return option return None def get_pysam_version(): sys.path.insert(0, "pysam") import version return version.__version__ # Override sdist command to ensure Cythonized *.c files are included. class cythonize_sdist(sdist): # Remove when setuptools (as installed on GH runners) has these options if not any(opt[0] == 'owner=' for opt in sdist.user_options): sdist.user_options.append(('owner=', 'u', 'Specify owner inside tar')) if not any(opt[0] == 'group=' for opt in sdist.user_options): sdist.user_options.append(('group=', 'g', 'Specify group inside tar')) def run(self): from Cython.Build import cythonize cythonize(self.distribution.ext_modules) super().run() # Override Cythonised build_ext command to customise macOS shared libraries. class CyExtension(Extension): def __init__(self, *args, **kwargs): self._init_func = kwargs.pop("init_func", None) self._prebuild_func = kwargs.pop("prebuild_func", None) super().__init__(*args, **kwargs) def extend_includes(self, includes): self.include_dirs.extend(includes) def extend_macros(self, macros): self.define_macros.extend(macros) def extend_extra_objects(self, objs): self.extra_objects.extend(objs) class cy_build_ext(build_ext): def check_ext_symbol_conflicts(self): """Checks for symbols defined in multiple extension modules, which can lead to crashes due to incorrect functions being invoked. Avoid by adding an appropriate #define to import/pysam.h or in unusual cases adding another rewrite rule to devtools/import.py. """ symbols = dict() for ext in self.distribution.ext_modules: for sym in run_nm_defined_symbols(self.get_ext_fullpath(ext.name)): symbols.setdefault(sym, []).append(ext.name.lstrip('pysam.')) errors = 0 for (sym, objs) in symbols.items(): if (len(objs) > 1): log.error("conflicting symbol (%s): %s", " ".join(objs), sym) errors += 1 if errors > 0: raise LinkError("symbols defined in multiple extensions") def run(self): if sys.platform == 'darwin': ldshared = os.environ.get('LDSHARED', sysconfig.get_config_var('LDSHARED')) os.environ['LDSHARED'] = ldshared.replace('-bundle', '') super().run() try: if HTSLIB_MODE != 'separate': self.check_ext_symbol_conflicts() except OSError as e: log.warning("skipping symbol collision check (invoking nm failed: %s)", e) except subprocess.CalledProcessError: log.warning("skipping symbol collision check (invoking nm failed)") def build_extension(self, ext): if isinstance(ext, CyExtension) and ext._init_func: ext._init_func(ext) if not self.inplace: ext.library_dirs.append(os.path.join(self.build_lib, "pysam")) if sys.platform == 'darwin': # The idea is to give shared libraries an install name of the form # `@rpath/`, and to set the rpath equal to # @loader_path. This will allow Python packages to find the library # in the expected place, while still giving enough flexibility to # external applications to link against the library. relative_module_path = ext.name.replace(".", os.sep) + sysconfig.get_config_var('EXT_SUFFIX') library_path = os.path.join( "@rpath", os.path.basename(relative_module_path) ) if not ext.extra_link_args: ext.extra_link_args = [] ext.extra_link_args += ['-dynamiclib', '-rpath', '@loader_path', '-Wl,-headerpad_max_install_names', '-Wl,-install_name,%s' % library_path, '-Wl,-x'] else: if not ext.extra_link_args: ext.extra_link_args = [] ext.extra_link_args += ['-Wl,-rpath,$ORIGIN'] if isinstance(ext, CyExtension) and ext._prebuild_func: ext._prebuild_func(ext, self.force) super().build_extension(ext) class clean_ext(Command): description = "clean up Cython temporary files" user_options = [] def initialize_options(self): pass def finalize_options(self): pass def run(self): objs = glob.glob(os.path.join("pysam", "libc*.c")) if objs: log.info("removing 'pysam/libc*.c' (%s Cython objects)", len(objs)) for obj in objs: os.remove(obj) headers = (glob.glob(os.path.join("htslib", "*config*.h")) + glob.glob(os.path.join("samtools", "*config*.h")) + glob.glob(os.path.join("bcftools", "*config*.h"))) if headers: log.info("removing '*/*config*.h' (%s generated headers)", len(headers)) for header in headers: os.remove(header) objects = (glob.glob(os.path.join("htslib", "*.[oa]")) + glob.glob(os.path.join("htslib", "cram", "*.o")) + glob.glob(os.path.join("htslib", "htscodecs", "htscodecs", "*.o"))) if objects: log.info("removing 'htslib/**/*.o' and libhts.a (%s objects)", len(objects)) for obj in objects: os.remove(obj) # How to link against HTSLIB # shared: build shared chtslib from builtin htslib code. # external: use shared libhts.so compiled outside of # pysam # separate: use included htslib and include in each extension # module. No dependencies between modules and works with # setup.py install, but wasteful in terms of memory and # compilation time. Fallback if shared module compilation # fails. HTSLIB_MODE = os.environ.get("HTSLIB_MODE", "shared") HTSLIB_LIBRARY_DIR = os.environ.get("HTSLIB_LIBRARY_DIR", None) HTSLIB_INCLUDE_DIR = os.environ.get("HTSLIB_INCLUDE_DIR", None) HTSLIB_CONFIGURE_OPTIONS = os.environ.get("HTSLIB_CONFIGURE_OPTIONS", None) HTSLIB_SOURCE = None package_list = ['pysam', 'pysam.include', 'pysam.include.samtools', 'pysam.include.bcftools'] package_dirs = {'pysam': 'pysam', 'pysam.include.samtools': 'samtools', 'pysam.include.bcftools': 'bcftools'} # list of config files that will be automatically generated should # they not already exist or be created by configure scripts in the # subpackages. config_headers = ["samtools/config.h", "bcftools/config.h"] # If cython is available, the pysam will be built using cython from # the .pyx files. If no cython is available, the C-files included in the # distribution will be used. if HAVE_CYTHON: print("# pysam: cython is available - using cythonize if necessary") source_pattern = "pysam/libc%s.pyx" else: print("# pysam: no cython available - using pre-compiled C") source_pattern = "pysam/libc%s.c" # Exit if there are no pre-compiled files and no cython available fn = source_pattern % "htslib" if not os.path.exists(fn): raise ValueError( "no cython installed, but can not find {}." "Make sure that cython is installed when building " "from the repository" .format(fn)) print("# pysam: htslib mode is {}".format(HTSLIB_MODE)) print("# pysam: HTSLIB_CONFIGURE_OPTIONS={}".format( HTSLIB_CONFIGURE_OPTIONS)) htslib_configure_options = None if HTSLIB_MODE in ['shared', 'separate']: package_list += ['pysam.include.htslib', 'pysam.include.htslib.htslib'] package_dirs.update({'pysam.include.htslib':'htslib'}) htslib_configure_options = configure_library( "htslib", HTSLIB_CONFIGURE_OPTIONS, ["--enable-libcurl", "--disable-libcurl"]) HTSLIB_SOURCE = "builtin" print("# pysam: htslib configure options: {}".format( str(htslib_configure_options))) config_headers += ["htslib/config.h"] if htslib_configure_options is None: # create empty config.h file with open("htslib/config.h", "w") as outf: outf.write( "/* empty config.h created by pysam */\n") outf.write( "/* conservative compilation options */\n") with changedir("htslib"): htslib_make_options = run_make_print_config() for key, value in htslib_make_options.items(): print("# pysam: htslib_config {}={}".format(key, value)) external_htslib_libraries = ['z'] if "LIBS" in htslib_make_options: external_htslib_libraries.extend( [re.sub("^-l", "", x) for x in htslib_make_options["LIBS"].split(" ") if x.strip()]) if HTSLIB_LIBRARY_DIR: # linking against a shared, externally installed htslib version, # no sources or built libhts.a required for htslib htslib_objects = [] separate_htslib_objects = [] chtslib_sources = [] htslib_library_dirs = [HTSLIB_LIBRARY_DIR] htslib_include_dirs = [HTSLIB_INCLUDE_DIR] external_htslib_libraries = ['z', 'hts'] elif HTSLIB_MODE == 'separate': # add to each pysam component a separately compiled # htslib htslib_objects = ['htslib/libhts.a'] separate_htslib_objects = ['htslib/libhts.a'] htslib_library_dirs = [] htslib_include_dirs = ['htslib'] elif HTSLIB_MODE == 'shared': # link each pysam component against the same # htslib built from sources included in the pysam # package. # Link with the object files rather than the final htslib/libhts.a, to ensure that # all object files are pulled into the link, even those not used by htslib itself. htslib_objects = [os.path.join("htslib", x) for x in htslib_make_options["LIBHTS_OBJS"].split(" ")] separate_htslib_objects = [] htslib_library_dirs = ["."] # when using setup.py develop? htslib_include_dirs = ['htslib'] else: raise ValueError("unknown HTSLIB value '%s'" % HTSLIB_MODE) # build config.py with open(os.path.join("pysam", "config.py"), "w") as outf: outf.write('HTSLIB = "{}"\n'.format(HTSLIB_SOURCE)) config_values = collections.defaultdict(int) if HTSLIB_SOURCE == "builtin": with open(os.path.join("htslib", "config.h")) as inf: for line in inf: if line.startswith("#define"): key, value = re.match( r"#define (\S+)\s+(\S+)", line).groups() config_values[key] = value for key in ["ENABLE_GCS", "ENABLE_PLUGINS", "ENABLE_S3", "HAVE_COMMONCRYPTO", "HAVE_HMAC", "HAVE_LIBBZ2", "HAVE_LIBCURL", "HAVE_LIBDEFLATE", "HAVE_LIBLZMA", "HAVE_MMAP"]: outf.write("{} = {}\n".format(key, config_values[key])) print("# pysam: config_option: {}={}".format(key, config_values[key])) # create empty config.h files if they have not been created automatically # or created by the user: for fn in config_headers: if not os.path.exists(fn): with open(fn, "w") as outf: outf.write( "/* empty config.h created by pysam */\n") outf.write( "/* conservative compilation options */\n") ####################################################### # Windows compatibility - untested if platform.system() == 'Windows': include_os = ['win32'] os_c_files = ['win32/getopt.c'] extra_compile_args = [] else: include_os = [] os_c_files = [] # for python 3.4, see for example # http://stackoverflow.com/questions/25587039/ # error-compiling-rpy2-on-python3-4-due-to-werror- # declaration-after-statement extra_compile_args = [ "-Wno-unused", "-Wno-strict-prototypes", "-Wno-sign-compare", "-Wno-error=declaration-after-statement"] define_macros = [] if os.environ.get("CIBUILDWHEEL", "0") == "1": define_macros.append(("BUILDING_WHEEL", None)) suffix = sysconfig.get_config_var('EXT_SUFFIX') internal_htslib_libraries = [ os.path.splitext("chtslib{}".format(suffix))[0]] internal_samtools_libraries = [ os.path.splitext("csamtools{}".format(suffix))[0], os.path.splitext("cbcftools{}".format(suffix))[0], ] internal_pysamutil_libraries = [ os.path.splitext("cutils{}".format(suffix))[0]] libraries_for_pysam_module = external_htslib_libraries + internal_htslib_libraries + internal_pysamutil_libraries # Order of modules matters in order to make sure that dependencies are resolved. # The structures of dependencies is as follows: # libchtslib: htslib utility functions and htslib itself if builtin is set. # libcsamtools: samtools code (builtin) # libcbcftools: bcftools code (builtin) # libcutils: General utility functions, depends on all of the above # libcXXX (pysam module): depends on libchtslib and libcutils # The list below uses the union of include_dirs and library_dirs for # reasons of simplicity. def prebuild_libchtslib(ext, force): if HTSLIB_MODE not in ['shared', 'separate']: return write_configvars_header("htslib/config_vars.h", ext, "HTS") if force or not os.path.exists("htslib/libhts.a"): log.info("building 'libhts.a'") with changedir("htslib"): # TODO Eventually by running configure here, we can set these # extra flags for configure instead of hacking on ALL_CPPFLAGS. args = " ".join(ext.extra_compile_args) defines = " ".join([format_macro_option(*pair) for pair in ext.define_macros]) run_make(["ALL_CPPFLAGS=-I. " + args + " " + defines + " $(CPPFLAGS)", "lib-static"]) else: log.warning("skipping 'libhts.a' (already built)") def prebuild_libcsamtools(ext, force): write_configvars_header("samtools/samtools_config_vars.h", ext, "SAMTOOLS") modules = [ dict(name="pysam.libchtslib", prebuild_func=prebuild_libchtslib, sources=[source_pattern % "htslib", "pysam/htslib_util.c"] + os_c_files, extra_objects=htslib_objects, libraries=external_htslib_libraries), dict(name="pysam.libcsamtools", prebuild_func=prebuild_libcsamtools, sources=[source_pattern % "samtools"] + glob.glob(os.path.join("samtools", "*.pysam.c")) + [os.path.join("samtools", "lz4", "lz4.c")] + os_c_files, extra_objects=separate_htslib_objects, libraries=external_htslib_libraries + internal_htslib_libraries), dict(name="pysam.libcbcftools", sources=[source_pattern % "bcftools"] + glob.glob(os.path.join("bcftools", "*.pysam.c")) + os_c_files, extra_objects=separate_htslib_objects, libraries=external_htslib_libraries + internal_htslib_libraries), dict(name="pysam.libcutils", sources=[source_pattern % "utils", "pysam/pysam_util.c"] + os_c_files, extra_objects=separate_htslib_objects, libraries=external_htslib_libraries + internal_htslib_libraries + internal_samtools_libraries), dict(name="pysam.libcalignmentfile", sources=[source_pattern % "alignmentfile"] + os_c_files, extra_objects=separate_htslib_objects, libraries=libraries_for_pysam_module), dict(name="pysam.libcsamfile", sources=[source_pattern % "samfile"] + os_c_files, extra_objects=separate_htslib_objects, libraries=libraries_for_pysam_module), dict(name="pysam.libcalignedsegment", sources=[source_pattern % "alignedsegment"] + os_c_files, extra_objects=separate_htslib_objects, libraries=libraries_for_pysam_module), dict(name="pysam.libctabix", sources=[source_pattern % "tabix"] + os_c_files, extra_objects=separate_htslib_objects, libraries=libraries_for_pysam_module), dict(name="pysam.libcfaidx", sources=[source_pattern % "faidx"] + os_c_files, extra_objects=separate_htslib_objects, libraries=libraries_for_pysam_module), dict(name="pysam.libcbcf", sources=[source_pattern % "bcf"] + os_c_files, extra_objects=separate_htslib_objects, libraries=libraries_for_pysam_module), dict(name="pysam.libcbgzf", sources=[source_pattern % "bgzf"] + os_c_files, extra_objects=separate_htslib_objects, libraries=libraries_for_pysam_module), dict(name="pysam.libctabixproxies", sources=[source_pattern % "tabixproxies"] + os_c_files, extra_objects=separate_htslib_objects, libraries=libraries_for_pysam_module), dict(name="pysam.libcvcf", sources=[source_pattern % "vcf"] + os_c_files, extra_objects=separate_htslib_objects, libraries=libraries_for_pysam_module), ] common_options = dict( language="c", extra_compile_args=extra_compile_args, define_macros=define_macros, # for out-of-tree compilation, use absolute paths library_dirs=[os.path.abspath(x) for x in ["pysam"] + htslib_library_dirs], include_dirs=[os.path.abspath(x) for x in ["pysam"] + htslib_include_dirs + \ ["samtools", "samtools/lz4", "bcftools", "."] + include_os]) # add common options (in python >3.5, could use n = {**a, **b} for module in modules: module.update(**common_options) classifiers = """ Development Status :: 4 - Beta Intended Audience :: Science/Research Intended Audience :: Developers License :: OSI Approved Programming Language :: Python Topic :: Software Development Topic :: Scientific/Engineering Operating System :: POSIX Operating System :: Unix Operating System :: MacOS """ metadata = { 'name': "pysam", 'version': get_pysam_version(), 'description': "Package for reading, manipulating, and writing genomic data", 'long_description': __doc__, 'long_description_content_type': "text/x-rst", 'author': "Andreas Heger", 'author_email': "andreas.heger@gmail.com", 'license': "MIT", 'platforms': ["POSIX", "UNIX", "MacOS"], 'classifiers': [_f for _f in classifiers.split("\n") if _f], 'url': "https://github.com/pysam-developers/pysam", 'packages': package_list, 'ext_modules': [CyExtension(**opts) for opts in modules], 'cmdclass': {'build_ext': cy_build_ext, 'clean_ext': clean_ext, 'sdist': cythonize_sdist}, 'package_dir': package_dirs, 'package_data': {'': ['*.pxd', '*.h', 'py.typed', '*.pyi'], }, # do not pack in order to permit linking to csamtools.so 'zip_safe': False, } if __name__ == '__main__': dist = setup(**metadata) pysam-0.23.0/tests/000077500000000000000000000000001475062545500141045ustar00rootroot00000000000000pysam-0.23.0/tests/00README.txt000066400000000000000000000012461475062545500157450ustar00rootroot00000000000000File ex1.fa contains two sequences cut from the human genome build36. They were extracted with command: samtools faidx human_b36.fa 2:2043966-2045540 20:67967-69550 Sequence names were changed manually for simplicity. File ex1.sam.gz contains MAQ alignments extracted with: (samtools view NA18507_maq.bam 2:2044001-2045500; samtools view NA18507_maq.bam 20:68001-69500) and processed with `samtools fixmate' to make it self-consistent as a standalone alignment. In order for the script pysam_test.py to work, you will need pysam in your PYTHONPATH. In order for the script example.py to work, you will need pysam in your PYTHONPATH and run make all beforehand. pysam-0.23.0/tests/AlignedSegment_bench.py000066400000000000000000000012451475062545500205050ustar00rootroot00000000000000"""Benchmarking module for AlignedSegment functionality""" import os import array import pysam from TestUtils import BAM_DATADIR def set_binary_tag(): read = pysam.AlignedSegment() read.set_tag('FZ', array.array('H', range(1000))) return len(read.get_tag('FZ')) def read_binary_tag(fn): with pysam.AlignmentFile(fn) as inf: read = next(inf.fetch()) return len(read.get_tag('FZ')) def test_set_binary_tag(benchmark): result = benchmark(set_binary_tag) assert result == 1000 def test_read_binary_tag(benchmark): result = benchmark(read_binary_tag, os.path.join( BAM_DATADIR, "example_btag.bam")) assert result == 260 pysam-0.23.0/tests/AlignedSegment_test.py000066400000000000000000001677471475062545500204310ustar00rootroot00000000000000import os import pysam import unittest import json import collections import struct import copy import array from pysam import CDEL, CDIFF, CEQUAL, CINS, CMATCH, CPAD, CREF_SKIP, CSOFT_CLIP from TestUtils import ( checkFieldEqual, make_data_files, BAM_DATADIR, get_temp_filename, get_temp_context, ) def setUpModule(): make_data_files(BAM_DATADIR) class ReadTest(unittest.TestCase): def build_read(self): """build an example read.""" header = pysam.AlignmentHeader.from_references( ["chr1", "chr2"], [10000000, 10000000] ) a = pysam.AlignedSegment(header) a.query_name = "read_12345" a.query_sequence = "ATGC" * 10 a.flag = 0 a.reference_id = 0 a.reference_start = 20 a.mapping_quality = 20 a.cigartuples = ((0, 10), (2, 1), (0, 9), (1, 1), (0, 20)) a.next_reference_id = 0 a.next_reference_start = 200 a.template_length = 167 a.query_qualities = pysam.qualitystring_to_array("1234") * 10 return a class TestAlignedSegment(ReadTest): """tests to check if aligned read can be constructed and manipulated. """ def check_get_aligned_pairs_combos(self, a, exp): def positions(exp): return [(ppos, rpos) for ppos, rpos, base, cigar in exp] def with_seq(exp): return [(ppos, rpos, base) for ppos, rpos, base, cigar in exp] def with_cigar(exp): return [(ppos, rpos, cigar) for ppos, rpos, base, cigar in exp] self.assertEqual(a.get_aligned_pairs(), positions(exp)) self.assertEqual(a.get_aligned_pairs(with_seq=True), with_seq(exp)) self.assertEqual(a.get_aligned_pairs(with_cigar=True), with_cigar(exp)) self.assertEqual(a.get_aligned_pairs(with_seq=True, with_cigar=True), exp) exp = [(ppos, rpos, base, cigar) for ppos, rpos, base, cigar in exp if ppos is not None and rpos is not None] self.assertEqual(a.get_aligned_pairs(matches_only=True), positions(exp)) self.assertEqual(a.get_aligned_pairs(matches_only=True, with_seq=True), with_seq(exp)) self.assertEqual(a.get_aligned_pairs(matches_only=True, with_cigar=True), with_cigar(exp)) self.assertEqual(a.get_aligned_pairs(matches_only=True, with_seq=True, with_cigar=True), exp) def check_get_aligned_pairs_combos_without_MD(self, a, exp): def positions(exp): return [(ppos, rpos) for ppos, rpos, cigar in exp] self.assertEqual(a.get_aligned_pairs(), positions(exp)) with self.assertRaises(ValueError): a.get_aligned_pairs(with_seq=True) self.assertEqual(a.get_aligned_pairs(with_cigar=True), exp) with self.assertRaises(ValueError): a.get_aligned_pairs(with_seq=True, with_cigar=True) exp = [(ppos, rpos, cigar) for ppos, rpos, cigar in exp if ppos is not None and rpos is not None] self.assertEqual(a.get_aligned_pairs(matches_only=True), positions(exp)) with self.assertRaises(ValueError): a.get_aligned_pairs(matches_only=True, with_seq=True) self.assertEqual(a.get_aligned_pairs(matches_only=True, with_cigar=True), exp) with self.assertRaises(ValueError): a.get_aligned_pairs(matches_only=True, with_seq=True, with_cigar=True) def testEmpty(self): a = pysam.AlignedSegment() self.assertEqual(a.query_name, None) self.assertEqual(a.query_sequence, None) self.assertEqual(pysam.qualities_to_qualitystring(a.query_qualities), None) self.assertEqual(a.flag, 0) self.assertEqual(a.reference_id, -1) self.assertEqual(a.mapping_quality, 0) self.assertEqual(a.cigartuples, None) self.assertEqual(a.get_tags(), []) self.assertEqual(a.next_reference_id, -1) self.assertEqual(a.next_reference_start, -1) self.assertEqual(a.template_length, 0) def testStrOfEmptyRead(self): a = pysam.AlignedSegment() s = str(a) self.assertEqual("None\t0\t*\t0\t0\tNone\t*\t0\t0\tNone\tNone\t[]", s) def testSettingTagInEmptyRead(self): """see issue 62""" a = pysam.AlignedSegment() a.tags = (("NM", 1),) a.query_qualities = None self.assertEqual(a.tags, [("NM", 1),]) def testCompare(self): """check comparison functions.""" a = self.build_read() b = None self.assertFalse(a is b) self.assertFalse(a == b) self.assertEqual(-1, a.compare(b)) b = self.build_read() self.assertEqual(0, a.compare(b)) self.assertEqual(0, b.compare(a)) self.assertTrue(a == b) self.assertTrue(b == a) self.assertFalse(a != b) self.assertFalse(b != a) b.tid = 1 self.assertFalse(a == b) self.assertFalse(b == a) self.assertTrue(a != b) self.assertTrue(b != a) def testHashing(self): a = self.build_read() b = self.build_read() self.assertEqual(hash(a), hash(b)) b.tid = 1 self.assertNotEqual(hash(a), hash(b)) def testUpdate(self): """check if updating fields affects other variable length data """ a = self.build_read() b = self.build_read() # check qname b.query_name = "read_123" checkFieldEqual(self, a, b, "query_name") b.query_name = "read_12345678" checkFieldEqual(self, a, b, "query_name") b.query_name = "read_12345" checkFieldEqual(self, a, b) # check cigar b.cigartuples = ((0, 10),) checkFieldEqual(self, a, b, "cigartuples") b.cigartuples = ((0, 10), (2, 1), (0, 10)) checkFieldEqual(self, a, b, "cigartuples") b.cigartuples = ((0, 10), (2, 1), (0, 9), (1, 1), (0, 20)) checkFieldEqual(self, a, b) # check seq b.query_sequence = "ATGC" checkFieldEqual( self, a, b, ("query_sequence", "query_qualities", "query_length") ) b.query_sequence = "ATGC" * 3 checkFieldEqual( self, a, b, ("query_sequence", "query_qualities", "query_length") ) b.query_sequence = "ATGC" * 10 checkFieldEqual(self, a, b, ("query_qualities",)) # reset qual b = self.build_read() def dual(name): if name.endswith('is_unmapped'): return name.replace('unmapped', 'mapped') elif name.endswith('is_mapped'): return name.replace('mapped', 'unmapped') elif name.endswith('is_reverse'): return name.replace('reverse', 'forward') elif name.endswith('is_forward'): return name.replace('forward', 'reverse') else: return name # check flags: for x in ( "is_paired", "is_proper_pair", "is_unmapped", "mate_is_unmapped", "is_reverse", "mate_is_reverse", "is_read1", "is_read2", "is_secondary", "is_qcfail", "is_duplicate", "is_supplementary", ): setattr(b, x, True) self.assertEqual(getattr(b, x), True) checkFieldEqual(self, a, b, ("flag", x, dual(x),)) setattr(b, x, False) self.assertEqual(getattr(b, x), False) checkFieldEqual(self, a, b) for x in ( "is_mapped", "mate_is_mapped", "is_forward", "mate_is_forward", ): setattr(b, x, False) self.assertEqual(getattr(b, x), False) checkFieldEqual(self, a, b, ("flag", x, dual(x),)) setattr(b, x, True) self.assertEqual(getattr(b, x), True) checkFieldEqual(self, a, b) def testUpdate2(self): """issue 135: inplace update of sequence and quality score. This does not work as setting the sequence will erase the quality scores. """ a = self.build_read() a.query_sequence = a.query_sequence[5:10] self.assertEqual(pysam.qualities_to_qualitystring(a.query_qualities), None) a = self.build_read() s = pysam.qualities_to_qualitystring(a.query_qualities) a.query_sequence = a.query_sequence[5:10] a.query_qualities = pysam.qualitystring_to_array(s[5:10]) self.assertEqual(pysam.qualities_to_qualitystring(a.query_qualities), s[5:10]) def testUpdateQual(self): """Ensure SEQ and QUAL updates leading to absent QUAL set all bytes to 0xff""" a = self.build_read() with get_temp_context("absent_qual.bam") as fname: with pysam.AlignmentFile(fname, "wb", header=a.header) as outf: a.query_sequence = "ATGC" outf.write(a) a.query_sequence = "ATGCATGCATGC" outf.write(a) a.query_sequence = "ATGCATGC" a.query_qualities = pysam.qualitystring_to_array("<<<<<<<<") a.query_qualities = None outf.write(a) with pysam.BGZFile(fname) as f: # Skip BAM header (l_text,) = struct.unpack("<4xL", f.read(8)) f.read(l_text) (n_ref,) = struct.unpack(" /dev/null | wc -l".format(fn)).read() return int(retval.strip()) def build_fetch_with_samtoolspipe(fn): FNULL = open(os.devnull, 'w') with subprocess.Popen(["samtools", "view", fn], stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=FNULL) as proc: return len(proc.stdout.readlines()) def build_fetch_with_pysam(*args, **kwargs): with pysam.AlignmentFile(*args, **kwargs) as inf: return len(list(inf.fetch())) def build_query_sequences_with_samtoolsshell(fn): retval = os.popen("samtools view {} 2> /dev/null | cut -f 11".format(fn)).read() return force_str(retval).splitlines() def build_query_sequences_with_samtoolspipe(fn): FNULL = open(os.devnull, 'w') with subprocess.Popen(["samtools", "view", fn], stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=FNULL) as proc: data = [force_str(x).split()[10] for x in proc.stdout.readlines()] return data def build_query_sequences_with_pysam(*args, **kwargs): with pysam.AlignmentFile(*args, **kwargs) as inf: data = [x.query_sequence for x in inf] return data def build_query_qualities_with_pysam(*args, **kwargs): with pysam.AlignmentFile(*args, **kwargs) as inf: data = [x.query_qualities for x in inf] return data def build_query_sequences_flagfilter_with_samtoolsshell(fn): retval = os.popen("samtools view -f 2 {} 2> /dev/null | cut -f 11".format(fn)).read() return force_str(retval).splitlines() def build_query_sequences_flagfilter_with_samtoolspipe(fn): FNULL = open(os.devnull, 'w') with subprocess.Popen(["samtools", "view", "-f", "2", fn], stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=FNULL) as proc: data = [force_str(x).split()[10] for x in proc.stdout.readlines()] return data def build_query_sequences_flagfilter_with_pysam(*args, **kwargs): with pysam.AlignmentFile(*args, **kwargs) as inf: data = [x.query_sequence for x in inf if x.is_proper_pair] return data def build_query_sequences_directflagfilter_with_pysam(*args, **kwargs): with pysam.AlignmentFile(*args, **kwargs) as inf: data = [x.query_sequence for x in inf if x.flag & 2] return data def build_aligned_pairs_with_pysam(*args, **kwargs): matches_only = kwargs.pop("matches_only", False) with_seq = kwargs.pop("with_seq", False) with pysam.AlignmentFile(*args, **kwargs) as inf: data = [x.get_aligned_pairs(matches_only=matches_only, with_seq=with_seq) for x in inf if x.is_mapped] return data pysam-0.23.0/tests/AlignmentFileFetch_bench.py000066400000000000000000000065431475062545500213150ustar00rootroot00000000000000"""Benchmarking module for AlignmentFile functionality""" import pytest from TestUtils import BAM_DATADIR from AlignmentFileFetchTestUtils import * def test_build_fetch_from_bam_with_samtoolsshell(benchmark): result = benchmark(build_fetch_with_samtoolsshell, os.path.join(BAM_DATADIR, "ex2.bam")) assert result == 3270 def test_build_fetch_from_bam_with_samtoolspipe(benchmark): result = benchmark(build_fetch_with_samtoolspipe, os.path.join(BAM_DATADIR, "ex2.bam")) assert result == 3270 def test_build_fetch_from_bam_with_pysam(benchmark): result = benchmark(build_fetch_with_pysam, os.path.join(BAM_DATADIR, "ex2.bam")) assert result == 3270 def test_build_query_sequences_from_bam_with_samtoolsshell(benchmark): result = benchmark(build_query_sequences_with_samtoolsshell, os.path.join(BAM_DATADIR, "ex2.bam")) assert len(result) == 3270 def test_build_query_sequences_from_bam_with_samtoolspipe(benchmark): result = benchmark(build_query_sequences_with_samtoolspipe, os.path.join(BAM_DATADIR, "ex2.bam")) assert len(result) == 3270 def test_build_query_sequences_from_bam_with_pysam(benchmark): result = benchmark(build_query_sequences_with_pysam, os.path.join(BAM_DATADIR, "ex2.bam")) assert len(result) == 3270 def test_build_query_qualities_from_bam_with_pysam(benchmark): result = benchmark(build_query_qualities_with_pysam, os.path.join(BAM_DATADIR, "ex2.bam")) assert len(result) == 3270 def test_build_query_sequences_from_bam_flagfilter_with_samtoolsshell(benchmark): result = benchmark(build_query_sequences_flagfilter_with_samtoolsshell, os.path.join(BAM_DATADIR, "ex2.bam")) assert len(result) == 3124 def test_build_query_sequences_from_bam_flagfilter_with_samtoolspipe(benchmark): result = benchmark(build_query_sequences_flagfilter_with_samtoolspipe, os.path.join(BAM_DATADIR, "ex2.bam")) assert len(result) == 3124 def test_build_query_sequences_from_bam_flagfilter_with_pysam(benchmark): result = benchmark(build_query_sequences_flagfilter_with_pysam, os.path.join(BAM_DATADIR, "ex2.bam")) assert len(result) == 3124 def test_build_query_sequences_from_bam_directflagfilter_with_pysam(benchmark): result = benchmark(build_query_sequences_flagfilter_with_pysam, os.path.join(BAM_DATADIR, "ex2.bam")) assert len(result) == 3124 @pytest.mark.aligned_pairs def test_build_aligned_pairs_default_with_pysam(benchmark): result = benchmark(build_aligned_pairs_with_pysam, os.path.join(BAM_DATADIR, "with_md.bam")) assert len(result) == 3235 @pytest.mark.aligned_pairs def test_build_aligned_pairs_matchesonly_with_pysam(benchmark): result = benchmark(build_aligned_pairs_with_pysam, os.path.join(BAM_DATADIR, "with_md.bam"), matches_only=True) assert len(result) == 3235 @pytest.mark.aligned_pairs def test_build_aligned_pairs_withseq_with_pysam(benchmark): result = benchmark(build_aligned_pairs_with_pysam, os.path.join(BAM_DATADIR, "with_md.bam"), with_seq=True) assert len(result) == 3235 pysam-0.23.0/tests/AlignmentFileHeader_test.py000066400000000000000000000300101475062545500213360ustar00rootroot00000000000000#!/usr/bin/env python '''unit testing code for pysam. Execute in the :file:`tests` directory as it requires the Makefile and data files located there. ''' import unittest import os import re import copy from collections import OrderedDict as odict import pysam import pysam.samtools from TestUtils import get_temp_filename, make_data_files, BAM_DATADIR def setUpModule(): make_data_files(BAM_DATADIR) class TestHeaderConstruction(unittest.TestCase): """testing header construction.""" header_dict = odict( [('SQ', [odict([('LN', 1575), ('SN', 'chr1'), ('AH', 'chr1:5000000-5010000')]), odict([('LN', 1584), ('SN', 'chr2'), ('AH', '*'), ('TP', 'linear')])]), ('RG', [odict([('LB', 'SC_1'), ('ID', 'L1'), ('SM', 'NA12891'), ('PU', 'SC_1_10'), ("CN", "name:with:colon")]), odict([('LB', 'SC_2'), ('ID', 'L2'), ('SM', 'NA12891'), ('PU', 'SC_2_12'), ("CN", "name:with:colon")])]), ('PG', [odict([('ID', 'P1'), ('VN', '1.0')]), odict([('ID', 'P2'), ('VN', '1.1')])]), ('HD', odict([('VN', '1.0')])), ('CO', ['this is a comment', 'this is another comment']), ]) header_text = ("@HD\tVN:1.0\n" "@SQ\tSN:chr1\tLN:1575\tAH:chr1:5000000-5010000\n" "@SQ\tSN:chr2\tLN:1584\tAH:*\tTP:linear\n" "@RG\tID:L1\tPU:SC_1_10\tLB:SC_1\tSM:NA12891\tCN:name:with:colon\n" "@RG\tID:L2\tPU:SC_2_12\tLB:SC_2\tSM:NA12891\tCN:name:with:colon\n" "@PG\tID:P1\tVN:1.0\n" "@PG\tID:P2\tVN:1.1\n" "@CO\tthis is a comment\n" "@CO\tthis is another comment\n") header_from_references = odict( [('SQ', [odict([('LN', 1575), ('SN', 'chr1')]), odict([('LN', 1584), ('SN', 'chr2')])]), ('RG', [odict([('LB', 'SC_1'), ('ID', 'L1'), ('SM', 'NA12891'), ('PU', 'SC_1_10'), ("CN", "name:with:colon")]), odict([('LB', 'SC_2'), ('ID', 'L2'), ('SM', 'NA12891'), ('PU', 'SC_2_12'), ("CN", "name:with:colon")])]), ('PG', [odict([('ID', 'P1'), ('VN', '1.0')]), odict([('ID', 'P2'), ('VN', '1.1')])]), ('HD', odict([('VN', '1.0')])), ('CO', ['this is a comment', 'this is another comment']), ]) header_without_text = odict( [('SQ', [odict([('LN', 1575), ('SN', 'chr1')]), odict([('LN', 1584), ('SN', 'chr2')])]), ]) def compare_headers(self, test_header, ref_header=None): '''compare two headers a and b.''' test_header_dict = test_header.as_dict() if ref_header is None: ref_header = self.header_dict for ak, av in test_header_dict.items(): self.assertTrue(ak in self.header_dict, "key '%s' not in '%s' " % (ak, ref_header)) self.assertEqual(av, ref_header[ak]) for ak, av in ref_header.items(): self.assertTrue(ak in test_header_dict, "key '%s' not in '%s' " % (ak, test_header_dict)) self.assertEqual(av, test_header_dict[ak]) def check_name_mapping(self, test_header): for x, y in enumerate(("chr1", "chr2")): tid = test_header.get_tid(y) ref = test_header.get_reference_name(x) self.assertEqual(tid, x) self.assertEqual(ref, y) self.assertEqual(test_header.get_tid("chr?"), -1) self.assertRaises(ValueError, test_header.get_reference_name, 2) def test_header_constructed_from_dict(self): header = pysam.AlignmentHeader.from_dict(self.header_dict) self.compare_headers(header) self.check_name_mapping(header) def test_header_constructed_from_text(self): header = pysam.AlignmentHeader.from_text(self.header_text) self.compare_headers(header) self.check_name_mapping(header) def test_header_constructed_from_header(self): header = pysam.AlignmentHeader.from_text(self.header_text) self.compare_headers(header.copy()) self.check_name_mapping(header) def test_header_constructed_from_references(self): text = re.sub("@SQ[^\n]+\n", "", self.header_text) assert "@SQ" not in text header = pysam.AlignmentHeader.from_references( reference_names=["chr1", "chr2"], reference_lengths=[1575, 1584], text=text) self.compare_headers(header, self.header_from_references) self.check_name_mapping(header) def test_header_constructed_from_references_without_text(self): header = pysam.AlignmentHeader.from_references( reference_names=["chr1", "chr2"], reference_lengths=[1575, 1584]) self.compare_headers(header, self.header_without_text) self.check_name_mapping(header) class TestHeaderSAM(unittest.TestCase): """testing header manipulation""" header = {'SQ': [{'LN': 1575, 'SN': 'chr1', 'AH': 'chr1:5000000-5010000'}, {'LN': 1584, 'SN': 'chr2', 'AH': '*'}], 'RG': [{'LB': 'SC_1', 'ID': 'L1', 'SM': 'NA12891', 'PU': 'SC_1_10', "CN": "name:with:colon"}, {'LB': 'SC_2', 'ID': 'L2', 'SM': 'NA12891', 'PU': 'SC_2_12', "CN": "name:with:colon"}], 'PG': [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}], 'HD': {'VN': '1.0'}, 'CO': ['this is a comment', 'this is another comment'], } def compare_headers(self, a, b): '''compare two headers a and b.''' for ak, av in a.items(): self.assertTrue(ak in b, "key '%s' not in '%s' " % (ak, b)) self.assertEqual(av, b[ak]) def setUp(self): self.samfile = pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex3.sam"), "r") def test_header_content_is_as_expected(self): self.compare_headers(self.header, self.samfile.header.to_dict()) self.compare_headers(self.samfile.header.to_dict(), self.header) def test_text_access_works(self): self.assertEqual(self.samfile.text, self.samfile.header.__str__()) def test_name_mapping(self): for x, y in enumerate(("chr1", "chr2")): tid = self.samfile.gettid(y) ref = self.samfile.getrname(x) self.assertEqual(tid, x) self.assertEqual(ref, y) self.assertEqual(self.samfile.gettid("chr?"), -1) self.assertRaises(ValueError, self.samfile.getrname, 2) def test_dictionary_access_works(self): for key in self.header.keys(): self.compare_headers({key: self.header[key]}, {key: self.samfile.header[key]}) def test_dictionary_setting_raises_error(self): self.assertRaises(TypeError, self.samfile.header.__setitem__, "CO", ["This is a final comment"]) def test_dictionary_len_works(self): self.assertEqual(len(self.header), len(self.samfile.header)) def test_dictionary_keys_works(self): # sort for py2.7 self.assertEqual(sorted(self.header.keys()), sorted(self.samfile.header.keys())) def test_dictionary_values_works(self): self.assertEqual(len(self.header.values()), len(self.samfile.header.values())) def test_dictionary_get_works(self): self.assertEqual(self.header.get("HD"), {'VN': '1.0'}) self.assertEqual(self.header.get("UK", "xyz"), "xyz") self.assertEqual(self.header.get("UK"), None) def test_dictionary_contains_works(self): self.assertTrue("HD" in self.header) self.assertFalse("UK" in self.header) def tearDown(self): self.samfile.close() class TestHeaderBAM(TestHeaderSAM): def setUp(self): self.samfile = pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex3.bam"), "rb") class TestHeaderCRAM(TestHeaderSAM): def setUp(self): self.samfile = pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex3.cram"), "rc") def compare_headers(self, a, b): '''compare two headers a and b.''' def _strip(dd): for x in dd: for y in ("M5", "UR"): if y in x: del x[y] for ak, av in a.items(): _strip(av) self.assertTrue(ak in b, "key '%s' not in '%s' " % (ak, b)) _strip(b[ak]) self.assertEqual(av, b[ak]) class TestHeaderFromRefs(unittest.TestCase): '''see issue 144 reference names need to be converted to string for python 3 ''' # def testHeader( self ): # refs = ['chr1', 'chr2'] # tmpfile = "tmp_%i" % id(self) # s = pysam.AlignmentFile(tmpfile, 'wb', # referencenames=refs, # referencelengths=[100]*len(refs)) # s.close() # self.assertTrue( checkBinaryEqual( 'issue144.bam', tmpfile ), # 'bam files differ') # os.unlink( tmpfile ) class TestHeaderWriteRead(unittest.TestCase): header = {'SQ': [{'LN': 1575, 'SN': 'chr1'}, {'LN': 1584, 'SN': 'chr2'}], 'RG': [{'LB': 'SC_1', 'ID': 'L1', 'SM': 'NA12891', 'PU': 'SC_1_10', "CN": "name:with:colon"}, {'LB': 'SC_2', 'ID': 'L2', 'SM': 'NA12891', 'PU': 'SC_2_12', "CN": "name:with:colon"}], 'PG': [{'ID': 'P1', 'VN': '1.0', 'CL': 'tool'}, {'ID': 'P2', 'VN': '1.1', 'CL': 'tool with in option -R a\tb', 'PP': 'P1'}], 'HD': {'VN': '1.0'}, 'CO': ['this is a comment', 'this is another comment'], } def compare_headers(self, a, header_b): '''compare two headers a and b. Ignore M5 and UR field as they are set application specific. ''' b = header_b.to_dict() for ak, av in a.items(): self.assertTrue(ak in b, "key '%s' not in '%s' " % (ak, b)) self.assertEqual( len(av), len(b[ak]), "unequal number of entries for key {}: {} vs {}" .format(ak, av, b[ak])) for row_a, row_b in zip(av, b[ak]): if isinstance(row_b, dict): for x in ["M5", "UR"]: try: del row_b[x] except KeyError: pass self.assertEqual(row_a, row_b) def check_read_write(self, flag_write, header): fn = get_temp_filename() with pysam.AlignmentFile( fn, flag_write, header=header, reference_filename=os.path.join(BAM_DATADIR, "ex1.fa")) as outf: a = pysam.AlignedSegment() a.query_name = "abc" a.flag = pysam.FUNMAP outf.write(a) with pysam.AlignmentFile(fn) as inf: read_header = inf.header os.unlink(fn) self.compare_headers(header, read_header) expected_lengths = dict([(x["SN"], x["LN"]) for x in header["SQ"]]) self.assertEqual(expected_lengths, dict(zip(read_header.references, read_header.lengths))) def test_SAM(self): self.check_read_write("wh", self.header) def test_BAM(self): self.check_read_write("wb", self.header) def test_CRAM(self): header = copy.copy(self.header) if "PG" in header: # for CRAM, \t needs to be quoted: header['PG'][1]['CL'] = re.sub(r"\t", r"\\\\t", header['PG'][1]['CL']) self.check_read_write("wc", header) class TestHeaderLargeContigs(TestHeaderWriteRead): """see issue 741""" header = {'SQ': [{'LN': 2147483647, 'SN': 'chr1'}, {'LN': 1584, 'SN': 'chr2'}], 'HD': {'VN': '1.0'}} pysam-0.23.0/tests/AlignmentFilePileup_bench.py000066400000000000000000000132731475062545500215200ustar00rootroot00000000000000"""Benchmarking module for AlignmentFile functionality""" from TestUtils import BAM_DATADIR, flatten_nested_list from PileupTestUtils import * def test_build_pileup_from_bam_with_samtoolsshell(benchmark): result = benchmark(build_pileup_with_samtoolsshell, os.path.join(BAM_DATADIR, "ex2.bam")) assert result == 2998 def test_build_pileup_from_bam_with_samtoolspipe(benchmark): result = benchmark(build_pileup_with_samtoolspipe, os.path.join(BAM_DATADIR, "ex2.bam")) assert result == 2998 def test_build_pileup_from_bam_with_pysam(benchmark): result = benchmark(build_pileup_with_pysam, os.path.join(BAM_DATADIR, "ex2.bam")) assert result == 2998 def test_build_depth_from_bam_with_samtoolsshell(benchmark): result = benchmark(build_depth_with_samtoolsshell, os.path.join(BAM_DATADIR, "ex2.bam")) assert result == 107241 def test_build_depth_from_bam_with_samtoolspipe(benchmark): result = benchmark(build_depth_with_samtoolspipe, os.path.join(BAM_DATADIR, "ex2.bam")) assert sum(result) == 107241 def test_build_depth_from_bam_with_pysam(benchmark): result = benchmark(build_depth_with_pysam, os.path.join(BAM_DATADIR, "ex2.bam")) # different value, as samtools filters with a minimum # base quality of 13 assert sum(result) == 110015 def test_build_depth_with_filter_from_bam_with_pysam(benchmark): result = benchmark(build_depth_with_filter_with_pysam, os.path.join(BAM_DATADIR, "ex2.bam")) assert sum(result) == 107241 def test_build_query_bases_from_bam_with_samtoolsshell(benchmark): result = benchmark(build_query_bases_with_samtoolsshell, os.path.join(BAM_DATADIR, "ex2.bam")) assert result == 116308 def test_build_query_bases_from_bam_with_samtoolspysam(benchmark): result = benchmark(build_query_bases_with_samtoolspysam, os.path.join(BAM_DATADIR, "ex2.bam")) assert len("".join(flatten_nested_list(result))) == 116308 def test_build_query_bases_from_bam_with_samtoolspipe(benchmark): result = benchmark(build_query_bases_with_samtoolspipe, os.path.join(BAM_DATADIR, "ex2.bam")) assert len("".join(flatten_nested_list(result))) == 116308 def test_build_query_bases_from_bam_with_pysam_pileups(benchmark): # note that there is no overlap detection here result = benchmark(build_query_bases_with_pysam_pileups, os.path.join(BAM_DATADIR, "ex2.bam")) assert len("".join(flatten_nested_list(result))) == 107241 def test_build_query_bases_from_bam_with_pysam(benchmark): result = benchmark(build_query_bases_with_pysam, os.path.join(BAM_DATADIR, "ex2.bam")) assert len("".join(flatten_nested_list(result))) == 116308 # note that pileups with/without reference sequence will differ due to # realignment. def test_build_query_bases_with_reference_from_bam_with_samtoolspipe(benchmark): result = benchmark(build_query_bases_with_samtoolspipe, os.path.join(BAM_DATADIR, "ex2.bam"), "-f", os.path.join(BAM_DATADIR, "ex1.fa")) assert len("".join(flatten_nested_list(result))) == 115924 def test_build_query_bases_with_reference_from_bam_with_pysam(benchmark): with pysam.FastaFile(os.path.join(BAM_DATADIR, "ex1.fa")) as fasta: result = benchmark(build_query_bases_with_pysam, os.path.join(BAM_DATADIR, "ex2.bam"), fastafile=fasta) assert len("".join(flatten_nested_list(result))) == 115924 def test_build_query_bases_with_reference_from_bam_with_samtoolspysam(benchmark): result = benchmark(build_query_bases_with_samtoolspysam, os.path.join(BAM_DATADIR, "ex2.bam"), "-f", os.path.join(BAM_DATADIR, "ex1.fa")) assert len("".join(flatten_nested_list(result))) == 115924 def test_build_query_qualities_from_bam_with_samtoolspipe(benchmark): result = benchmark(build_query_qualities_with_samtoolspipe, os.path.join(BAM_DATADIR, "ex2.bam")) assert len("".join(result)) == 107241 def test_build_query_qualities_from_bam_with_pysam(benchmark): result = benchmark(build_query_qualities_with_pysam, os.path.join(BAM_DATADIR, "ex2.bam")) assert sum([len(x) for x in result]) == 107241 def test_build_query_names_from_bam_with_pysam(benchmark): result = benchmark(build_query_names_with_pysam, os.path.join(BAM_DATADIR, "ex2.bam")) assert len("".join([x for column in result for x in column])) == 2307343 def test_build_mapping_qualities_from_bam_with_samtoolspipe(benchmark): result = benchmark(build_mapping_qualities_with_samtoolspipe, os.path.join(BAM_DATADIR, "ex2.bam")) assert len("".join(result)) == 107241 def test_build_mapping_qualities_from_bam_with_pysam(benchmark): result = benchmark(build_mapping_qualities_with_pysam, os.path.join(BAM_DATADIR, "ex2.bam")) assert sum([len(x) for x in result]) == 107241 def test_build_query_positions_from_bam_with_samtoolspipe(benchmark): result = benchmark(build_query_positions_with_samtoolspipe, os.path.join(BAM_DATADIR, "ex2.bam")) # positions output by samtools are 1-based assert sum([sum(x) - len(x) for x in result]) == 1841699 def test_build_query_positions_from_bam_with_pysam(benchmark): result = benchmark(build_query_positions_with_pysam, os.path.join(BAM_DATADIR, "ex2.bam")) assert sum([sum(x) for x in result]) == 1841699 pysam-0.23.0/tests/AlignmentFilePileup_test.py000066400000000000000000000372201475062545500214160ustar00rootroot00000000000000"""Benchmarking module for AlignmentFile functionality""" import os import pysam import sys import unittest from TestUtils import make_data_files, BAM_DATADIR, force_str, flatten_nested_list import PileupTestUtils def setUpModule(): make_data_files(BAM_DATADIR) class TestPileupReadSelection(unittest.TestCase): '''test pileup functionality.''' samfilename = os.path.join(BAM_DATADIR, "ex1.bam") fastafilename = os.path.join(BAM_DATADIR, "ex1.fa") def setUp(self): self.samfile = pysam.AlignmentFile(self.samfilename) self.fastafile = pysam.FastaFile(self.fastafilename) def tearDown(self): self.samfile.close() self.fastafile.close() def check_equal(self, references, iterator): for x, column in enumerate(iterator): v = references[x][:-1].split("\t") self.assertEqual( len(v), 6, "expected 6 values, got {}".format(v)) (contig, pos, reference_base, read_bases, read_qualities, alignment_mapping_qualities) \ = v self.assertEqual(int(pos) - 1, column.reference_pos) def test_samtools_stepper(self): refs = force_str( pysam.samtools.mpileup( "-f", self.fastafilename, self.samfilename)).splitlines(True) iterator = self.samfile.pileup( stepper="samtools", fastafile=self.fastafile) self.check_equal(refs, iterator) def test_all_stepper(self): refs = force_str( pysam.samtools.mpileup( "-f", self.fastafilename, "-A", "-B", self.samfilename)).splitlines(True) iterator = self.samfile.pileup( stepper="all", fastafile=self.fastafile) self.check_equal(refs, iterator) def test_ignore_overlaps(self): refs = force_str( pysam.samtools.mpileup( "-f", self.fastafilename, "-A", "-B", "-x", self.samfilename)).splitlines(True) iterator = self.samfile.pileup( stepper="all", fastafile=self.fastafile, ignore_overlaps=False) self.check_equal(refs, iterator) def test_samtools_stepper_mapping_quality_threshold(self): refs = force_str( pysam.samtools.mpileup( "-f", self.fastafilename, "--min-MQ", "15", self.samfilename)).splitlines(True) iterator = self.samfile.pileup( stepper="samtools", fastafile=self.fastafile, min_mapping_quality=15) self.check_equal(refs, iterator) def test_samtools_stepper_base_quality_threshold(self): refs = force_str( pysam.samtools.mpileup( "-f", self.fastafilename, "--min-BQ", "20", self.samfilename)).splitlines(True) iterator = self.samfile.pileup( stepper="samtools", fastafile=self.fastafile, min_base_quality=20) self.check_equal(refs, iterator) def test_samtools_stepper_ignore_orphans(self): refs = force_str( pysam.samtools.mpileup( "-f", self.fastafilename, "--count-orphans", self.samfilename)).splitlines(True) iterator = self.samfile.pileup( stepper="samtools", fastafile=self.fastafile, ignore_orphans=False) self.check_equal(refs, iterator) def test_samtools_stepper_redo_baq(self): refs = force_str( pysam.samtools.mpileup( "-f", self.fastafilename, "--redo-BAQ", self.samfilename)).splitlines(True) iterator = self.samfile.pileup( stepper="samtools", fastafile=self.fastafile, redo_baq=True) self.check_equal(refs, iterator) class TestPileupReadSelectionFastafile(TestPileupReadSelection): '''test pileup functionality - backwards compatibility''' samfilename = os.path.join(BAM_DATADIR, "ex1.bam") fastafilename = os.path.join(BAM_DATADIR, "ex1.fa") def setUp(self): self.samfile = pysam.AlignmentFile(self.samfilename) self.fastafile = pysam.Fastafile(self.fastafilename) class TestPileupQueryPosition(unittest.TestCase): filename = "test_query_position.bam" def testPileup(self): last = {} with pysam.AlignmentFile(os.path.join(BAM_DATADIR, self.filename)) as inf: for col in inf.pileup(): for r in col.pileups: # print r.alignment.query_name # print r.query_position, r.query_position_or_next, r.is_del if r.is_del: self.assertEqual(r.query_position, None) self.assertEqual(r.query_position_or_next, last[r.alignment.query_name] + 1) else: self.assertNotEqual(r.query_position, None) last[r.alignment.query_name] = r.query_position class TestPileupObjects(unittest.TestCase): def setUp(self): self.samfile = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"), "rb") def testPileupColumn(self): for pcolumn1 in self.samfile.pileup(region="chr1:105-106"): if pcolumn1.reference_pos == 104: self.assertEqual( pcolumn1.reference_id, 0, "chromosome/target id mismatch in position 1: %s != %s" % (pcolumn1.reference_id, 0)) self.assertEqual( pcolumn1.reference_name, "chr1", "chromosome mismatch in position 1: %s != %s" % (pcolumn1.reference_name, "chr1")) self.assertEqual( pcolumn1.reference_pos, 105 - 1, "position mismatch in position 1: %s != %s" % (pcolumn1.reference_pos, 105 - 1)) self.assertEqual( pcolumn1.nsegments, 1, "# reads mismatch in position 1: %s != %s" % (pcolumn1.nsegments, 1)) self.assertEqual( len(pcolumn1.pileups), 1, "# reads aligned to column mismatch in position 1" ": %s != %s" % (len(pcolumn1.pileups), 1)) for pcolumn2 in self.samfile.pileup(region="chr2:1480-1481"): if pcolumn2.reference_pos == 1479: self.assertEqual( pcolumn2.reference_id, 1, "chromosome/target id mismatch in position 1: %s != %s" % (pcolumn2.reference_id, 1)) self.assertEqual( pcolumn2.reference_name, "chr2", "chromosome mismatch in position 1: %s != %s" % (pcolumn2.reference_name, "chr2")) self.assertEqual( pcolumn2.reference_pos, 1480 - 1, "position mismatch in position 1: %s != %s" % (pcolumn2.reference_pos, 1480 - 1)) self.assertEqual( pcolumn2.nsegments, 12, "# reads mismatch in position 1: %s != %s" % (pcolumn2.nsegments, 12)) def tearDown(self): self.samfile.close() @unittest.skipIf(sys.version_info >= (3, 11), "exercises invalid accesses, which crashes with Python 3.11") def testIteratorOutOfScope(self): '''test if exception is raised if pileup col is accessed after iterator is exhausted.''' max_n = 0 for pileupcol in self.samfile.pileup(): if max_n < pileupcol.n: max_col = pileupcol max_n = pileupcol.n self.assertRaises(ValueError, getattr, max_col, "pileups") self.assertRaises(ValueError, max_col.get_query_sequences) self.assertRaises(ValueError, max_col.get_num_aligned) self.assertRaises(ValueError, max_col.get_query_qualities) self.assertRaises(ValueError, max_col.get_mapping_qualities) self.assertRaises(ValueError, max_col.get_query_positions) self.assertRaises(ValueError, max_col.get_query_names) class TestIteratorColumnBAM(unittest.TestCase): '''test iterator column against contents of ex4.bam.''' # note that samfile contains 1-based coordinates # 1D means deletion with respect to reference sequence # mCoverages = {'chr1': [0] * 20 + [1] * 36 + [0] * (100 - 20 - 35), 'chr2': [0] * 20 + [1] * 35 + [0] * (100 - 20 - 35), } def setUp(self): self.samfile = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex4.bam"), "rb") def checkRange(self, contig, start=None, end=None, truncate=False): '''compare results from iterator with those from samtools.''' # check if the same reads are returned and in the same order for column in self.samfile.pileup( contig, start, end, truncate=truncate, min_base_quality=0): if truncate: self.assertGreaterEqual(column.reference_pos, start) self.assertLess(column.reference_pos, end) thiscov = len(column.pileups) refcov = self.mCoverages[ self.samfile.getrname(column.reference_id)][column.reference_pos] self.assertEqual(thiscov, refcov, "wrong coverage at pos %s:%i %i should be %i" % ( self.samfile.getrname(column.reference_id), column.reference_pos, thiscov, refcov)) def testIterateAll(self): '''check random access per contig''' self.checkRange(None) def testIteratePerContig(self): '''check random access per contig''' for contig in self.samfile.references: self.checkRange(contig) def testIterateRanges(self): '''check random access per range''' for contig, length in zip( self.samfile.references, self.samfile.lengths): for start in range(1, length, 90): # this includes empty ranges self.checkRange(contig, start, start + 90) def testInverse(self): '''test the inverse, is point-wise pileup accurate.''' for contig, refseq in list(self.mCoverages.items()): refcolumns = sum(refseq) for pos, refcov in enumerate(refseq): columns = list(self.samfile.pileup(contig, pos, pos + 1)) if refcov == 0: # if no read, no coverage self.assertEqual( len(columns), refcov, "wrong number of pileup columns returned for position %s:%i, %i should be %i" % ( contig, pos, len(columns), refcov)) elif refcov == 1: # one read, all columns of the read are returned self.assertEqual( len(columns), refcolumns, "pileup incomplete at position %i: got %i, expected %i " % (pos, len(columns), refcolumns)) def testIterateTruncate(self): '''check random access per range''' for contig, length in zip(self.samfile.references, self.samfile.lengths): for start in range(1, length, 90): # this includes empty ranges self.checkRange(contig, start, start + 90, truncate=True) def tearDown(self): self.samfile.close() class TestIteratorColumn2(unittest.TestCase): '''test iterator column against contents of ex1.bam.''' def setUp(self): self.samfile = pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex1.bam"), "rb") def testStart(self): # print self.samfile.fetch().next().reference_start # print self.samfile.pileup().next().reference_start pass def testTruncate(self): '''see issue 107.''' # note that ranges in regions start from 1 p = self.samfile.pileup(region='chr1:170-172', truncate=True) columns = [x.reference_pos for x in p] self.assertEqual(len(columns), 3) self.assertEqual(columns, [169, 170, 171]) p = self.samfile.pileup('chr1', 169, 172, truncate=True) columns = [x.reference_pos for x in p] self.assertEqual(len(columns), 3) self.assertEqual(columns, [169, 170, 171]) def testAccessOnClosedIterator(self): '''see issue 131 Accessing pileup data after iterator has closed. ''' pcolumn = self.samfile.pileup('chr1', 170, 180).__next__() self.assertRaises(ValueError, getattr, pcolumn, "pileups") def testStr(self): '''test if PileupRead can be printed.''' iter = self.samfile.pileup('chr1', 170, 180) pcolumn = iter.__next__() s = str(pcolumn) self.assertEqual(len(s.split("\n")), 2) class PileUpColumnTests(unittest.TestCase): fn = os.path.join(BAM_DATADIR, "ex2.bam") fn_fasta = os.path.join(BAM_DATADIR, "ex1.fa") def test_pileup_depths_are_equal(self): samtools_result = PileupTestUtils.build_depth_with_samtoolspipe(self.fn) pysam_result = PileupTestUtils.build_depth_with_filter_with_pysam(self.fn) self.assertEqual(pysam_result, samtools_result) def test_pileup_query_bases_without_reference_are_equal(self): samtools_result = PileupTestUtils.build_query_bases_with_samtoolspipe(self.fn) pysam_result = PileupTestUtils.build_query_bases_with_pysam(self.fn) self.assertEqual(["".join(x) for x in pysam_result], samtools_result) def test_pileup_query_bases_with_reference_are_equal(self): samtools_result = PileupTestUtils.build_query_bases_with_samtoolspipe(self.fn, "-f", self.fn_fasta) with pysam.FastaFile(self.fn_fasta) as fasta: pysam_result = PileupTestUtils.build_query_bases_with_pysam(self.fn, fastafile=fasta, stepper="samtools") self.assertEqual(["".join(x) for x in pysam_result], samtools_result) def test_pileup_query_qualities_are_equal(self): samtools_result = PileupTestUtils.build_query_qualities_with_samtoolspipe(self.fn) pysam_result = PileupTestUtils.build_query_qualities_with_pysam(self.fn) pysam_result = [ [chr(min(126, x + 33)) for x in l] for l in pysam_result] self.assertEqual("".join(flatten_nested_list(pysam_result)), "".join(flatten_nested_list(samtools_result))) def test_pileup_mapping_qualities_are_equal(self): samtools_result = PileupTestUtils.build_mapping_qualities_with_samtoolspipe(self.fn) pysam_result = PileupTestUtils.build_mapping_qualities_with_pysam(self.fn) # convert to chars pysam_result = [ [chr(min(126, x + 33)) for x in l] for l in pysam_result] self.assertEqual("".join(flatten_nested_list(pysam_result)), "".join(flatten_nested_list(samtools_result))) def test_pileup_query_qualities_from_pileups_are_equal(self): samtools_result = PileupTestUtils.build_query_qualities_with_samtoolspipe(self.fn) pysam_result = PileupTestUtils.build_query_qualities_with_pysam_pileups(self.fn) pysam_result = [ "".join([chr(min(126, x + 33)) for x in l]) for l in pysam_result] self.assertEqual(pysam_result, samtools_result) if __name__ == "__main__": unittest.main() pysam-0.23.0/tests/AlignmentFile_bench.py000066400000000000000000000036011475062545500203330ustar00rootroot00000000000000"""Benchmarking module for AlignmentFile functionality""" import os import subprocess import pysam from TestUtils import BAM_DATADIR def count_number_lines_with_samtools(fn): os.system("samtools view {} | wc -l > /dev/null".format(fn)) return 3270 def count_number_lines_with_samtoolspipe(fn): with subprocess.Popen(["samtools", "view", fn], stdin=subprocess.PIPE, stdout=subprocess.PIPE) as proc: return len(proc.stdout.readlines()) def count_number_lines_with_pysam(*args, **kwargs): with pysam.AlignmentFile(*args, **kwargs) as inf: return len(list(inf.fetch())) def test_count_number_lines_from_sam_with_samtools(benchmark): result = benchmark(count_number_lines_with_samtools, os.path.join(BAM_DATADIR, "ex2.sam")) assert result == 3270 def test_count_number_lines_from_sam_with_samtoolspipe(benchmark): result = benchmark(count_number_lines_with_samtoolspipe, os.path.join(BAM_DATADIR, "ex2.sam")) assert result == 3270 def test_count_number_lines_from_sam_with_pysam(benchmark): result = benchmark(count_number_lines_with_pysam, os.path.join(BAM_DATADIR, "ex2.sam"), "r") assert result == 3270 def test_count_number_lines_from_bam_with_samtools(benchmark): result = benchmark(count_number_lines_with_samtools, os.path.join(BAM_DATADIR, "ex2.bam")) assert result == 3270 def test_count_number_lines_from_bam_with_samtoolspipe(benchmark): result = benchmark(count_number_lines_with_samtoolspipe, os.path.join(BAM_DATADIR, "ex2.bam")) assert result == 3270 def test_count_number_lines_from_bam_with_pysam(benchmark): result = benchmark(count_number_lines_with_pysam, os.path.join(BAM_DATADIR, "ex2.bam")) assert result == 3270 pysam-0.23.0/tests/AlignmentFile_test.py000066400000000000000000002544111475062545500202420ustar00rootroot00000000000000#!/usr/bin/env python '''unit testing code for pysam. Execute in the :file:`tests` directory as it requires the Makefile and data files located there. ''' import unittest import pytest import os import shutil import collections import subprocess import logging import array from io import StringIO from functools import partial import pysam import pysam.samtools from TestUtils import checkBinaryEqual, checkGZBinaryEqual, check_url, \ check_samtools_view_equal, checkFieldEqual, force_str, \ get_temp_filename, make_data_files, BAM_DATADIR def setUpModule(): make_data_files(BAM_DATADIR) ################################################## # # Detailed test of file contents # # Data are read either through file based iterator # access (BasicTestBAMFromFile) or by calling fetch # without coordinates (BasicTestBAMFromFetch) ################################################## class BasicTestBAMFromFetch(unittest.TestCase): '''basic first test - detailed testing if information in file is consistent with information in AlignedSegment object.''' def setUp(self): self.samfile = pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex3.bam"), "rb") self.reads = list(self.samfile.fetch()) def tearDown(self): self.samfile.close() def testARqname(self): self.assertEqual(self.reads[0].query_name, "read_28833_29006_6945") self.assertEqual(self.reads[1].query_name, "read_28701_28881_323b") def testARflag(self): self.assertEqual(self.reads[0].flag, 99) self.assertEqual(self.reads[1].flag, 147) def testARrname(self): self.assertEqual(self.reads[0].reference_id, 0) self.assertEqual(self.reads[1].reference_id, 1) def testARpos(self): self.assertEqual(self.reads[0].reference_start, 33 - 1) self.assertEqual(self.reads[1].reference_start, 88 - 1) def testARmapq(self): self.assertEqual(self.reads[0].mapping_quality, 20) self.assertEqual(self.reads[1].mapping_quality, 30) def testARcigar(self): self.assertEqual(self.reads[0].cigartuples, [(0, 10), (2, 1), (0, 25)]) self.assertEqual(self.reads[1].cigartuples, [(0, 35)]) def testARcigarstring(self): self.assertEqual(self.reads[0].cigarstring, '10M1D25M') self.assertEqual(self.reads[1].cigarstring, '35M') def testARmrnm(self): self.assertEqual(self.reads[0].next_reference_id, 0) self.assertEqual(self.reads[1].next_reference_id, 1) self.assertEqual(self.reads[0].next_reference_id, 0) self.assertEqual(self.reads[1].next_reference_id, 1) def testARmpos(self): self.assertEqual(self.reads[0].next_reference_start, 200 - 1) self.assertEqual(self.reads[1].next_reference_start, 500 - 1) self.assertEqual(self.reads[0].next_reference_start, 200 - 1) self.assertEqual(self.reads[1].next_reference_start, 500 - 1) def testARQueryLength(self): self.assertEqual( self.reads[0].query_length, 35, "insert size mismatch in read 1: %s != %s" % (self.reads[0].query_length, 35)) self.assertEqual( self.reads[1].query_length, 35, "insert size mismatch in read 2: %s != %s" % (self.reads[1].query_length, 35)) self.assertEqual( self.reads[0].query_length, 35, "insert size mismatch in read 1: %s != %s" % (self.reads[0].query_length, 35)) self.assertEqual( self.reads[1].query_length, 35, "insert size mismatch in read 2: %s != %s" % (self.reads[1].query_length, 35)) def testARseq(self): self.assertEqual( self.reads[0].query_sequence, "AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG") self.assertEqual( self.reads[1].query_sequence, "ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA") self.assertEqual( self.reads[3].query_sequence, "AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG") def testARqual(self): self.assertEqual( pysam.qualities_to_qualitystring(self.reads[0].query_qualities), "<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<") self.assertEqual( pysam.qualities_to_qualitystring(self.reads[1].query_qualities), "<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<") self.assertEqual( pysam.qualities_to_qualitystring(self.reads[3].query_qualities), "<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<") def testARquery(self): self.assertEqual( self.reads[0].query_alignment_sequence, "AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG", "query mismatch in read 1: %s != %s" % (self.reads[0].query_alignment_sequence, "AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG")) self.assertEqual( self.reads[1].query_alignment_sequence, "ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA", "query size mismatch in read 2: %s != %s" % (self.reads[1].query_alignment_sequence, "ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA")) self.assertEqual( self.reads[3].query_alignment_sequence, "TAGCTAGCTACCTATATCTTGGTCTT", "query mismatch in read 4: %s != %s" % (self.reads[3].query_alignment_sequence, "TAGCTAGCTACCTATATCTTGGTCTT")) def testARqqual(self): self.assertEqual( pysam.qualities_to_qualitystring( self.reads[0].query_alignment_qualities), "<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<", "qquality string mismatch in read 1: %s != %s" % (pysam.qualities_to_qualitystring(self.reads[0].query_alignment_qualities), "<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<")) self.assertEqual( pysam.qualities_to_qualitystring( self.reads[1].query_alignment_qualities), "<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<", "qquality string mismatch in read 2: %s != %s" % (pysam.qualities_to_qualitystring(self.reads[1].query_alignment_qualities), "<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<")) self.assertEqual( pysam.qualities_to_qualitystring( self.reads[3].query_alignment_qualities), "<<<<<<<<<<<<<<<<<:<9/,&,22", "qquality string mismatch in read 3: %s != %s" % (pysam.qualities_to_qualitystring(self.reads[3].query_alignment_qualities), "<<<<<<<<<<<<<<<<<:<9/,&,22")) def testPresentOptionalFields(self): self.assertEqual( self.reads[0].opt('NM'), 22, "optional field mismatch in read 1, NM: %s != %s" % (self.reads[0].opt('NM'), 22)) self.assertEqual( self.reads[0].opt('RG'), 'L1', "optional field mismatch in read 1, RG: %s != %s" % (self.reads[0].opt('RG'), 'L1')) self.assertEqual( self.reads[1].opt('RG'), 'L2', "optional field mismatch in read 2, RG: %s != %s" % (self.reads[1].opt('RG'), 'L2')) self.assertEqual( self.reads[1].opt('MF'), 18, "optional field mismatch in read 2, MF: %s != %s" % (self.reads[1].opt('MF'), 18)) def testPairedBools(self): self.assertEqual(self.reads[0].is_paired, True, "is paired mismatch in read 1: %s != %s" % ( self.reads[0].is_paired, True)) self.assertEqual(self.reads[1].is_paired, True, "is paired mismatch in read 2: %s != %s" % ( self.reads[1].is_paired, True)) self.assertEqual(self.reads[0].is_proper_pair, True, "is proper pair mismatch in read 1: %s != %s" % ( self.reads[0].is_proper_pair, True)) self.assertEqual(self.reads[1].is_proper_pair, True, "is proper pair mismatch in read 2: %s != %s" % ( self.reads[1].is_proper_pair, True)) def testTags(self): self.assertEqual(self.reads[0].tags, [('NM', 22), ('RG', 'L1'), ('PG', 'P1'), ('XT', 'U')]) self.assertEqual(self.reads[1].tags, [('MF', 18), ('RG', 'L2'), ('PG', 'P2'), ('XT', 'R')]) def testOpt(self): self.assertEqual(self.reads[0].opt("XT"), "U") self.assertEqual(self.reads[1].opt("XT"), "R") class BasicTestSAMFromFetch(BasicTestBAMFromFetch): def setUp(self): self.samfile = pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex3.sam"), "r") self.reads = list(self.samfile.fetch()) class BasicTestCRAMFromFetch(BasicTestBAMFromFetch): def setUp(self): self.samfile = pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex3.cram"), "rc") self.reads = list(self.samfile.fetch()) def testTags(self): self.assertEqual( sorted(self.reads[0].tags), sorted([('RG', 'L1'), ('NM', 22), ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), ('PG', 'P1'), ('XT', 'U'), ])) self.assertEqual( sorted(self.reads[1].tags), sorted([('RG', 'L2'), ('NM', 26), ('MD', '1G0A0A1G1G0G2C0A0G0A0A0C0T0T0G0A0A0G0A0C0A0A1T2C0T0T1'), ('MF', 18), ('PG', 'P2'), ('XT', 'R')])) def testPresentOptionalFields(self): self.assertEqual( self.reads[0].opt('NM'), 22, "optional field mismatch in read 1, NM: %s != %s" % (self.reads[0].opt('NM'), 22)) self.assertEqual( self.reads[0].opt('RG'), 'L1', "optional field mismatch in read 1, RG: %s != %s" % (self.reads[0].opt('RG'), 'L1')) self.assertEqual( self.reads[1].opt('RG'), 'L2', "optional field mismatch in read 2, RG: %s != %s" % (self.reads[1].opt('RG'), 'L2')) self.assertEqual( self.reads[1].opt('MF'), 18, "optional field mismatch in read 2, MF: %s != %s" % (self.reads[1].opt('MF'), 18)) class BasicTestSAMFromFilename(BasicTestBAMFromFetch): def setUp(self): self.samfile = pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex3.sam"), "r") self.reads = [r for r in self.samfile] class BasicTestCRAMFromFilename(BasicTestCRAMFromFetch): def setUp(self): self.samfile = pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex3.cram"), "rc") self.reads = [r for r in self.samfile] class BasicTestBAMFromFilename(BasicTestBAMFromFetch): def setUp(self): self.samfile = pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex3.bam"), "rb") self.reads = [r for r in self.samfile] class BasicTestBAMFromFile(BasicTestBAMFromFetch): def setUp(self): with open(os.path.join(BAM_DATADIR, "ex3.bam")) as f: self.samfile = pysam.AlignmentFile( f, "rb") self.reads = [r for r in self.samfile] class BasicTestBAMFromFileNo(BasicTestBAMFromFetch): def setUp(self): with open(os.path.join(BAM_DATADIR, "ex3.bam")) as f: self.samfile = pysam.AlignmentFile( f.fileno(), "rb") self.reads = [r for r in self.samfile] class BasicTestSAMFromFile(BasicTestBAMFromFetch): def setUp(self): with open(os.path.join(BAM_DATADIR, "ex3.sam")) as f: self.samfile = pysam.AlignmentFile( f, "r") self.reads = [r for r in self.samfile] class BasicTestSAMFromFileNo(BasicTestBAMFromFetch): def setUp(self): with open(os.path.join(BAM_DATADIR, "ex3.sam")) as f: self.samfile = pysam.AlignmentFile( f.fileno(), "r") self.reads = [r for r in self.samfile] class BasicTestCRAMFromFile(BasicTestCRAMFromFetch): def setUp(self): with open(os.path.join(BAM_DATADIR, "ex3.cram")) as f: self.samfile = pysam.AlignmentFile(f, "rc") self.reads = [r for r in self.samfile] class BasicTestCRAMFromFileNo(BasicTestCRAMFromFetch): def setUp(self): with open(os.path.join(BAM_DATADIR, "ex3.cram")) as f: self.samfile = pysam.AlignmentFile( f.fileno(), "rc") self.reads = [r for r in self.samfile] class BasicTestSAMFromStringIO(BasicTestBAMFromFetch): def testRaises(self): statement = "samtools view -h {}".format( os.path.join(BAM_DATADIR, "ex3.bam")) stdout = subprocess.check_output(statement.split(" "), encoding="ascii") bam = StringIO() bam.write(stdout) bam.seek(0) self.assertRaises(NotImplementedError, pysam.AlignmentFile, bam) # self.reads = [r for r in samfile] ################################################## # # Test of basic File I/O # # * format conversions # * reading with/without index # * reading from closed files # ################################################## class TestIO(unittest.TestCase): '''check if reading samfile and writing a samfile are consistent.''' def checkEcho(self, input_filename, reference_filename, output_filename, input_mode, output_mode, sequence_filename=None, use_template=True, checkf=checkBinaryEqual, **kwargs): '''iterate through *input_filename* writing to *output_filename* and comparing the output to *reference_filename*. The files are opened according to the *input_mode* and *output_mode*. If *use_template* is set, the header is copied from infile using the template mechanism, otherwise target names and lengths are passed explicitly. The *checkf* is used to determine if the files are equal. ''' with pysam.AlignmentFile( os.path.join(BAM_DATADIR, input_filename), input_mode) as infile: if "b" in input_mode: self.assertTrue(infile.is_bam) self.assertFalse(infile.is_cram) elif "c" in input_mode: self.assertFalse(infile.is_bam) self.assertTrue(infile.is_cram) else: self.assertFalse(infile.is_cram) self.assertFalse(infile.is_bam) if use_template: outfile = pysam.AlignmentFile( output_filename, output_mode, reference_filename=sequence_filename, template=infile, **kwargs) else: outfile = pysam.AlignmentFile( output_filename, output_mode, reference_names=infile.references, reference_lengths=infile.lengths, reference_filename=sequence_filename, add_sq_text=False, **kwargs) iter = infile.fetch() for x in iter: outfile.write(x) outfile.close() self.assertTrue(checkf( os.path.join(BAM_DATADIR, reference_filename), output_filename), "files %s and %s are not the same" % (reference_filename, output_filename)) os.unlink(output_filename) def testSAM2SAM(self): self.checkEcho("ex2.sam", "ex2.sam", "tmp_ex2.sam", "r", "wh") def testSAM2SAMWithoutHeader(self): self.checkEcho("ex2.sam", "ex1.sam", "tmp_ex2.sam", "r", "w", add_sam_header=False) def testBAM2BAM(self): self.checkEcho("ex2.bam", "ex2.bam", "tmp_ex2.bam", "rb", "wb", checkf=checkGZBinaryEqual) def testCRAM2CRAM(self): # in some systems different reference sequence paths might be # embedded in the CRAM files which will result in different headers # see #542 self.checkEcho("ex2.cram", "ex2.cram", "tmp_ex2.cram", "rc", "wc", sequence_filename=os.path.join(BAM_DATADIR, "ex1.fa"), checkf=partial( check_samtools_view_equal, without_header=True)) def testSAM2BAM(self): self.checkEcho("ex2.sam", "ex2.bam", "tmp_ex2.bam", "r", "wb", checkf=checkGZBinaryEqual) def testBAM2SAM(self): self.checkEcho("ex2.bam", "ex2.sam", "tmp_ex2.sam", "rb", "wh") def testBAM2CRAM(self): # ignore header (md5 sum) self.checkEcho("ex2.bam", "ex2.cram", "tmp_ex2.cram", "rb", "wc", sequence_filename=os.path.join(BAM_DATADIR, "ex1.fa"), checkf=partial( check_samtools_view_equal, without_header=True)) def testCRAM2BAM(self): # ignore header (md5 sum) self.checkEcho("ex2.cram", "ex2.bam", "tmp_ex2.bam", "rc", "wb", sequence_filename=os.path.join(BAM_DATADIR, "ex1.fa"), checkf=partial( check_samtools_view_equal, without_header=True)) def testSAM2CRAM(self): self.checkEcho("ex2.sam", "ex2.cram", "tmp_ex2.cram", "r", "wc", sequence_filename=os.path.join(BAM_DATADIR, "ex1.fa"), checkf=partial( check_samtools_view_equal, without_header=True)) def testCRAM2SAM(self): self.checkEcho("ex2.cram", "ex2.sam", "tmp_ex2.sam", "rc", "wh", sequence_filename=os.path.join(BAM_DATADIR, "ex1.fa"), checkf=partial( check_samtools_view_equal, without_header=True)) # Disabled - should work, files are not binary equal, but are # non-binary equal: # diff <(samtools view pysam_ex1.bam) <(samtools view pysam_data/ex1.bam) # def testReadWriteBamWithTargetNames(self): # input_filename = "ex1.bam" # output_filename = "pysam_ex1.bam" # reference_filename = "ex1.bam" # self.checkEcho(input_filename, reference_filename, output_filename, # "rb", "wb", use_template=False) def testReadSamWithoutTargetNames(self): '''see issue 104.''' input_filename = os.path.join( BAM_DATADIR, "example_unmapped_reads_no_sq.sam") # raise exception in default mode self.assertRaises(ValueError, pysam.AlignmentFile, input_filename, "r") # raise exception if no SQ files self.assertRaises(ValueError, pysam.AlignmentFile, input_filename, "r", check_header=True) with pysam.AlignmentFile( input_filename, check_header=False, check_sq=False) as infile: result = list(infile.fetch(until_eof=True)) self.assertEqual(2, len(result)) def testReadBamWithoutTargetNames(self): '''see issue 104.''' input_filename = os.path.join( BAM_DATADIR, "example_unmapped_reads_no_sq.bam") # raise exception in default mode self.assertRaises(ValueError, pysam.AlignmentFile, input_filename, "r") # raise exception if no SQ files self.assertRaises(ValueError, pysam.AlignmentFile, input_filename, "r", check_header=True) with pysam.AlignmentFile( input_filename, check_sq=False) as infile: result = list(infile.fetch(until_eof=True)) def test_fail_read_sam_without_header(self): input_filename = os.path.join(BAM_DATADIR, "ex1.sam") self.assertRaises(ValueError, pysam.AlignmentFile, input_filename, "r") def test_pass_read_sam_without_header_with_refs(self): with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.sam"), "r", reference_names=["chr1", "chr2"], reference_lengths=[1575, 1584]) as samfile: self.assertEqual(len(list(samfile.fetch(until_eof=True))), 3270) def test_pass_read_sam_with_header_without_header_check(self): with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex2.sam"), "r", check_header=False) as samfile: self.assertEqual(len(list(samfile.fetch(until_eof=True))), 3270) def test_fail_when_reading_unformatted_files(self): '''test reading from a file that is not bam/sam formatted''' input_filename = os.path.join(BAM_DATADIR, 'Makefile') self.assertRaises(ValueError, pysam.AlignmentFile, input_filename, "rb") self.assertRaises(ValueError, pysam.AlignmentFile, input_filename, "r") def testBAMWithoutAlignedSegments(self): '''see issue 117''' input_filename = os.path.join(BAM_DATADIR, "test_unaligned.bam") samfile = pysam.AlignmentFile(input_filename, "rb", check_sq=False) samfile.fetch(until_eof=True) def testBAMWithShortBAI(self): '''see issue 116''' input_filename = os.path.join(BAM_DATADIR, "example_bai.bam") samfile = pysam.AlignmentFile(input_filename, "rb", check_sq=False) samfile.fetch('chr2') def testFetchFromClosedFile(self): samfile = pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex1.bam"), "rb") samfile.close() self.assertRaises(ValueError, samfile.fetch, 'chr1', 100, 120) def testFetchFromClosedFileObject(self): f = open(os.path.join(BAM_DATADIR, "ex1.bam")) samfile = pysam.AlignmentFile(f, "rb") f.close() self.assertTrue(f.closed) # access to Samfile still works self.checkEcho("ex1.bam", "ex1.bam", "tmp_ex1.bam", "rb", "wb", checkf=checkGZBinaryEqual) f = open(os.path.join(BAM_DATADIR, "ex1.bam")) samfile = pysam.AlignmentFile(f, "rb") self.assertFalse(f.closed) samfile.close() # python file needs to be closed separately self.assertFalse(f.closed) def test_accessing_attributes_in_closed_file_raises_errors(self): '''test that access to a closed samfile raises ValueError.''' samfile = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"), "rb") samfile.close() self.assertRaises(ValueError, samfile.fetch, 'chr1', 100, 120) self.assertRaises(ValueError, samfile.pileup, 'chr1', 100, 120) self.assertRaises(ValueError, samfile.getrname, 0) # TODO self.assertRaises(ValueError, samfile.tell) self.assertRaises(ValueError, samfile.seek, 0) self.assertRaises(ValueError, getattr, samfile, "nreferences") self.assertRaises(ValueError, getattr, samfile, "references") self.assertRaises(ValueError, getattr, samfile, "lengths") self.assertEqual(samfile.header, None) # write on closed file self.assertEqual(0, samfile.write(None)) def test_header_available_after_closing_file(self): def load_bam(): with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"), "rb") as inf: header = inf.header return header header = load_bam() self.assertTrue(header) self.assertEqual(header.nreferences, 2) self.assertEqual(header.references, ("chr1", "chr2")) def test_reference_name_available_after_closing_file(self): """read tids can be mapped to references after AlignmentFile has been closed. see issue #517""" def load_bam(): with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"), "rb") as inf: read = next(inf) return read read = load_bam() self.assertEqual(read.reference_name, "chr1") # TODO # def testReadingFromSamFileWithoutHeader(self): # '''read from samfile without header. # ''' # samfile = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex7.sam"), # check_header=False, # check_sq=False) # self.assertRaises(NotImplementedError, samfile.__iter__) def testReadingFromFileWithoutIndex(self): '''read from bam file without index.''' dest = get_temp_filename("tmp_ex2.bam") shutil.copyfile(os.path.join(BAM_DATADIR, "ex2.bam"), dest) samfile = pysam.AlignmentFile(dest, "rb") self.assertRaises(ValueError, samfile.fetch) self.assertEqual( len(list(samfile.fetch(until_eof=True))), 3270) os.unlink(dest) # def testReadingUniversalFileMode(self): # '''read from samfile without header. # ''' # input_filename = "ex2.sam" # output_filename = "pysam_ex2.sam" # reference_filename = "ex1.sam" # self.checkEcho(input_filename, # reference_filename, # output_filename, # "rU", "w") def testHead(self): '''test IteratorRowHead''' samfile = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"), "rb") l10 = list(samfile.head(10)) l100 = list(samfile.head(100)) self.assertEqual(len(l10), 10) self.assertEqual(len(l100), 100) self.assertEqual(list(map(str, l10)), list(map(str, l100[:10]))) def testWriteUncompressedBAMFile(self): '''read from uncompressed BAM file, see issue #43''' input_filename = "ex2.sam" output_filename = "pysam_uncompressed.bam" reference_filename = "uncompressed.bam" self.checkEcho(input_filename, reference_filename, output_filename, "r", "wb0") self.checkEcho(input_filename, reference_filename, output_filename, "r", "wbu") def testEmptyBAM(self): samfile = pysam.Samfile(os.path.join(BAM_DATADIR, "empty.bam"), "rb") self.assertEqual(samfile.mapped, 0) self.assertEqual(samfile.unmapped, 0) self.assertEqual(samfile.nocoordinate, 0) def testEmptyWithHeaderBAM(self): self.assertRaises( ValueError, pysam.Samfile, os.path.join(BAM_DATADIR, "example_empty_with_header.bam"), "rb") samfile = pysam.Samfile( os.path.join(BAM_DATADIR, "example_empty_with_header.bam"), "rb", check_sq=False) self.assertEqual(samfile.mapped, 0) self.assertEqual(samfile.unmapped, 0) self.assertEqual(samfile.nocoordinate, 0) self.assertEqual([], list(samfile.fetch())) def testOpenFromFilename(self): samfile = pysam.AlignmentFile( filename=os.path.join(BAM_DATADIR, "ex1.bam"), mode="rb") self.assertEqual(len(list(samfile.fetch())), 3270) def testBAMWithCSIIndex(self): '''see issue 116''' input_filename = os.path.join(BAM_DATADIR, "ex1_csi.bam") samfile = pysam.AlignmentFile(input_filename, "rb", check_sq=False) samfile.fetch('chr2') def test_fetch_by_tid(self): with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"), "rb") as samfile: self.assertEqual(len(list(samfile.fetch('chr1'))), len(list(samfile.fetch(tid=0)))) self.assertEqual(len(list(samfile.fetch('chr2'))), len(list(samfile.fetch(tid=1)))) self.assertRaises( IndexError, samfile.fetch, tid=2) self.assertRaises( IndexError, samfile.fetch, tid=-1) self.assertEqual(len(list(samfile.fetch('chr1', start=1000, end=2000))), len(list(samfile.fetch(tid=0, start=1000, end=2000)))) def test_write_bam_to_unknown_path_fails(self): '''see issue 116''' input_filename = os.path.join(BAM_DATADIR, "ex1.bam") with pysam.AlignmentFile(input_filename) as inf: self.assertRaises(IOError, pysam.AlignmentFile, "missing_directory/new_file.bam", "wb", template=inf) class TestAutoDetect(unittest.TestCase): def testSAM(self): """test SAM autodetection.""" with pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex3.sam")) as inf: self.assertFalse(inf.is_bam) self.assertFalse(inf.is_cram) self.assertRaises(ValueError, inf.fetch, 'chr1') def testBAM(self): """test BAM autodetection.""" with pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex3.bam")) as inf: self.assertTrue(inf.is_bam) self.assertFalse(inf.is_cram) self.assertEqual(len(list(inf.fetch('chr1'))), 1) self.assertEqual(len(list(inf.fetch('chr2'))), 3) def testCRAM(self): """test CRAM autodetection.""" with pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex3.cram")) as inf: self.assertFalse(inf.is_bam) self.assertTrue(inf.is_cram) self.assertEqual(len(list(inf.fetch('chr1'))), 1) self.assertEqual(len(list(inf.fetch('chr2'))), 3) ################################################## # # Random access iterator tests # ################################################## class TestIteratorRowBAM(unittest.TestCase): filename = os.path.join(BAM_DATADIR, "ex2.bam") mode = "rb" reference_filename = None def setUp(self): self.samfile = pysam.AlignmentFile( self.filename, self.mode, reference_filename=self.reference_filename, ) def tearDown(self): self.samfile.close() def checkRange(self, rnge): '''compare results from iterator with those from samtools.''' ps = list(self.samfile.fetch(region=rnge)) sa = force_str( pysam.samtools.view( self.filename, rnge, raw=True)).splitlines(True) self.assertEqual( len(ps), len(sa), "unequal number of results for range %s: %i != %i" % (rnge, len(ps), len(sa))) # check if the same reads are returned and in the same order for line, (a, b) in enumerate(list(zip(ps, sa))): d = b.split("\t") self.assertEqual( a.query_name, d[0], "line %i: read id mismatch: %s != %s" % (line, a.reference_id, d[0])) self.assertEqual( a.reference_start, int(d[3]) - 1, "line %i: read position mismatch: %s != %s, \n%s\n%s\n" % (line, a.reference_start, int(d[3]) - 1, str(a), str(d))) qual = d[10] self.assertEqual( pysam.qualities_to_qualitystring(a.query_qualities), qual, "line %i: quality mismatch: %s != %s, \n%s\n%s\n" % (line, pysam.qualities_to_qualitystring(a.query_qualities), qual, str(a), str(d))) def testIteratePerContig(self): '''check random access per contig''' for contig in self.samfile.references: self.checkRange(contig) def testIterateRanges(self): '''check random access per range''' for contig, length in zip(self.samfile.references, self.samfile.lengths): for start in range(1, length, 90): # this includes empty ranges self.checkRange("%s:%i-%i" % (contig, start, start + 90)) class TestIteratorRowAllBAM(unittest.TestCase): filename = os.path.join(BAM_DATADIR, "ex2.bam") mode = "rb" def setUp(self): self.samfile = pysam.AlignmentFile( self.filename, self.mode) def testIterate(self): '''compare results from iterator with those from samtools.''' ps = list(self.samfile.fetch()) sa = pysam.samtools.view(self.filename, raw=True).splitlines() self.assertEqual( len(ps), len(sa), "unequal number of results: %i != %i" % (len(ps), len(sa))) # check if the same reads are returned for line, pair in enumerate(list(zip(ps, sa))): data = force_str(pair[1]).split("\t") self.assertEqual( pair[0].query_name, data[0], "read id mismatch in line %i: %s != %s" % (line, pair[0].reference_id, data[0])) def tearDown(self): self.samfile.close() class TestIteratorRowCRAM(TestIteratorRowBAM): filename = os.path.join(BAM_DATADIR, "ex2.cram") mode = "rc" class TestIteratorRowCRAMWithReferenceFilename(TestIteratorRowCRAM): reference_filename = os.path.join(BAM_DATADIR, "ex1.fa") # needs to be implemented # class TestAlignedSegmentFromSamWithoutHeader(TestAlignedSegmentFromBam): # # def setUp(self): # self.samfile=pysam.AlignmentFile( "ex7.sam","r" ) # self.reads=list(self.samfile.fetch()) class TestFloatTagBug(unittest.TestCase): '''see issue 71''' def testFloatTagBug(self): '''a float tag before another exposed a parsing bug in bam_aux_get. Fixed in 0.1.19 ''' samfile = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "tag_bug.bam")) read = next(samfile.fetch(until_eof=True)) self.assertTrue(('XC', 1) in read.tags) self.assertEqual(read.opt('XC'), 1) class TestLargeFieldBug(unittest.TestCase): '''see issue 100''' def testLargeFileBug(self): '''when creating a read with a large entry in the tag field causes an error: NotImplementedError: tags field too large ''' samfile = pysam.AlignmentFile( os.path.join(BAM_DATADIR, "issue100.bam")) read = next(samfile.fetch(until_eof=True)) new_read = pysam.AlignedSegment() new_read.tags = read.tags self.assertEqual(new_read.tags, read.tags) class TestClipping(unittest.TestCase): def testClipping(self): self.samfile = pysam.AlignmentFile( os.path.join(BAM_DATADIR, "softclip.bam"), "rb") for read in self.samfile: if read.query_name == "r001": self.assertEqual(read.query_sequence, 'AAAAGATAAGGATA') self.assertEqual(read.query_alignment_sequence, 'AGATAAGGATA') self.assertEqual(pysam.qualities_to_qualitystring(read.query_qualities), None) self.assertEqual( pysam.qualities_to_qualitystring( read.query_alignment_qualities), None) elif read.query_name == "r002": self.assertEqual(read.query_sequence, 'GCCTAAGCTAA') self.assertEqual(read.query_alignment_sequence, 'AGCTAA') self.assertEqual( pysam.qualities_to_qualitystring(read.query_qualities), '01234567890') self.assertEqual( pysam.qualities_to_qualitystring( read.query_alignment_qualities), '567890') elif read.query_name == "r003": self.assertEqual(read.query_sequence, 'GCCTAAGCTAA') self.assertEqual(read.query_alignment_sequence, 'GCCTAA') self.assertEqual( pysam.qualities_to_qualitystring(read.query_qualities), '01234567890') self.assertEqual( pysam.qualities_to_qualitystring( read.query_alignment_qualities), '012345') elif read.query_name == "r004": self.assertEqual(read.query_sequence, 'TAGGC') self.assertEqual(read.query_alignment_sequence, 'TAGGC') self.assertEqual( pysam.qualities_to_qualitystring(read.query_qualities), '01234') self.assertEqual( pysam.qualities_to_qualitystring( read.query_alignment_qualities), '01234') class TestUnmappedReadsRetrieval(unittest.TestCase): def test_fetch_from_sam_with_until_eof_reads_unmapped_reads(self): with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex5.sam"), "rb") as samfile: self.assertEqual(len(list(samfile.fetch(until_eof=True))), 2) def test_fetch_from_bam_with_until_eof_reads_unmapped_reads(self): with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex5.bam"), "rb") as samfile: self.assertEqual(len(list(samfile.fetch(until_eof=True))), 2) def test_fetch_with_asterisk_only_returns_unmapped_reads(self): with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "test_mapped_unmapped.bam"), "rb") as samfile: self.assertEqual(len(list(samfile.fetch(region="*"))), 4) def test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig(self): with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "test_mapped_unmapped.bam"), "rb") as samfile: self.assertEqual(len(list(samfile.fetch(contig="*"))), 4) class TestContextManager(unittest.TestCase): def testManager(self): with pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'ex1.bam'), 'rb') as samfile: samfile.fetch() self.assertEqual(samfile.closed, True) class TestMultiThread(unittest.TestCase): def testSingleThreadEqualsMultithread(self): input_bam = os.path.join(BAM_DATADIR, 'ex1.bam') single_thread_out = get_temp_filename("tmp_single.bam") multi_thread_out = get_temp_filename("tmp_multi.bam") with pysam.AlignmentFile(input_bam, 'rb') as samfile: reads = [r for r in samfile] with pysam.AlignmentFile(single_thread_out, mode='wb', template=samfile, threads=1) as single_out: [single_out.write(r) for r in reads] with pysam.AlignmentFile(multi_thread_out, mode='wb', template=samfile, threads=2) as multi_out: [single_out.write(r) for r in reads] with pysam.AlignmentFile(input_bam) as inp, \ pysam.AlignmentFile(single_thread_out) as single, \ pysam.AlignmentFile(multi_thread_out) as multi: for r1, r2, r3 in zip(inp, single, multi): assert r1.to_string == r2.to_string == r3.to_string def TestNoMultiThreadingWithIgnoreTruncation(self): self.assertRaises( ValueError, pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'ex1.bam'), threads=2, ignore_truncation=True) ) class TestExceptions(unittest.TestCase): def setUp(self): self.samfile = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"), "rb") def testMissingFile(self): self.assertRaises( IOError, pysam.AlignmentFile, "exdoesntexist.bam", "rb") self.assertRaises( IOError, pysam.AlignmentFile, "exdoesntexist.sam", "r") self.assertRaises( IOError, pysam.AlignmentFile, "exdoesntexist.bam", "r") self.assertRaises( IOError, pysam.AlignmentFile, "exdoesntexist.sam", "rb") def testBadContig(self): self.assertRaises(ValueError, self.samfile.fetch, "chr88") def testMeaninglessCrap(self): self.assertRaises(ValueError, self.samfile.fetch, "skljf") def testBackwardsOrderNewFormat(self): self.assertRaises(ValueError, self.samfile.fetch, 'chr1', 100, 10) def testBackwardsOrderOldFormat(self): self.assertRaises(ValueError, self.samfile.fetch, region="chr1:100-10") def testOutOfRangeNegativeNewFormat(self): self.assertRaises(ValueError, self.samfile.fetch, "chr1", 5, -10) self.assertRaises(ValueError, self.samfile.fetch, "chr1", 5, 0) self.assertRaises(ValueError, self.samfile.fetch, "chr1", -5, -10) self.assertRaises(ValueError, self.samfile.count, "chr1", 5, -10) self.assertRaises(ValueError, self.samfile.count, "chr1", 5, 0) self.assertRaises(ValueError, self.samfile.count, "chr1", -5, -10) def testOutOfRangeNegativeOldFormat(self): self.assertRaises(ValueError, self.samfile.fetch, region="chr1:-5-10") self.assertRaises(ValueError, self.samfile.fetch, region="chr1:-5-0") self.assertRaises(ValueError, self.samfile.fetch, region="chr1:-5--10") self.assertRaises(ValueError, self.samfile.count, region="chr1:-5-10") self.assertRaises(ValueError, self.samfile.count, region="chr1:-5-0") self.assertRaises(ValueError, self.samfile.count, region="chr1:-5--10") def testOutOfRangNewFormat(self): self.assertRaises( ValueError, self.samfile.fetch, "chr1", 9999999999, 99999999999) self.assertRaises( ValueError, self.samfile.count, "chr1", 9999999999, 99999999999) def testOutOfRangeLargeNewFormat(self): self.assertRaises(ValueError, self.samfile.fetch, "chr1", 9999999999999999999999999999999, 9999999999999999999999999999999999999999) self.assertRaises(ValueError, self.samfile.count, "chr1", 9999999999999999999999999999999, 9999999999999999999999999999999999999999) def testOutOfRangeLargeOldFormat(self): self.assertRaises( ValueError, self.samfile.fetch, "chr1:99999999999999999-999999999999999999") self.assertRaises( ValueError, self.samfile.count, "chr1:99999999999999999-999999999999999999") def testZeroToZero(self): '''see issue 44''' self.assertEqual(len(list(self.samfile.fetch('chr1', 0, 0))), 0) def tearDown(self): self.samfile.close() class TestWrongFormat(unittest.TestCase): '''test cases for opening files not in bam/sam format.''' def testOpenSamAsBam(self): self.assertRaises(ValueError, pysam.AlignmentFile, os.path.join(BAM_DATADIR, 'ex1.sam'), 'rb') def testOpenBamAsSam(self): # test fails, needs to be implemented. # sam.fetch() fails on reading, not on opening # self.assertRaises(ValueError, pysam.AlignmentFile, # os.path.join(BAM_DATADIR, 'ex1.bam'), # 'r') pass def testOpenFastaAsSam(self): # test fails, needs to be implemented. # sam.fetch() fails on reading, not on opening # self.assertRaises( ValueError, pysam.AlignmentFile, 'ex1.fa', 'r' ) pass def testOpenFastaAsBam(self): self.assertRaises(ValueError, pysam.AlignmentFile, os.path.join(BAM_DATADIR, 'ex1.fa'), 'rb') class TestRegionParsing(unittest.TestCase): def test_dash_in_chr(self): with pysam.AlignmentFile( os.path.join(BAM_DATADIR, "example_dash_in_chr.bam")) as inf: self.assertEqual(len(list(inf.fetch(contig="chr-1"))), 1) self.assertEqual(len(list(inf.fetch(contig="chr2"))), 1) self.assertEqual(len(list(inf.fetch(region="chr-1"))), 1) self.assertEqual(len(list(inf.fetch(region="chr2"))), 1) class TestDeNovoConstruction(unittest.TestCase): '''check BAM/SAM file construction using ex6.sam (note these are +1 coordinates): read_28833_29006_6945 99 chr1 33 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 RG:Z:L1 read_28701_28881_323b 147 chr2 88 30 35M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 RG:Z:L2 ''' # noqa header = {'HD': {'VN': '1.0'}, 'SQ': [{'LN': 1575, 'SN': 'chr1'}, {'LN': 1584, 'SN': 'chr2'}], } bamfile = os.path.join(BAM_DATADIR, "ex6.bam") samfile = os.path.join(BAM_DATADIR, "ex6.sam") def setUp(self): header = pysam.AlignmentHeader.from_dict(self.header) a = pysam.AlignedSegment(header) a.query_name = "read_28833_29006_6945" a.query_sequence = "AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG" a.flag = 99 a.reference_id = 0 a.reference_start = 32 a.mapping_quality = 20 a.cigartuples = ((0, 10), (2, 1), (0, 25)) a.next_reference_id = 0 a.next_reference_start = 199 a.template_length = 167 a.query_qualities = pysam.qualitystring_to_array( "<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<") a.tags = (("NM", 1), ("RG", "L1")) b = pysam.AlignedSegment(header) b.query_name = "read_28701_28881_323b" b.query_sequence = "ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA" b.flag = 147 b.reference_id = 1 b.reference_start = 87 b.mapping_quality = 30 b.cigartuples = ((0, 35), ) b.next_reference_id = 1 b.next_reference_start = 499 b.template_length = 412 b.query_qualities = pysam.qualitystring_to_array( "<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<") b.tags = (("MF", 18), ("RG", "L2")) self.reads = (a, b) # TODO # def testSAMWholeFile(self): # tmpfilename = "tmp_%i.sam" % id(self) # outfile = pysam.AlignmentFile(tmpfilename, # "wh", # header=self.header) # for x in self.reads: # outfile.write(x) # outfile.close() # self.assertTrue(checkBinaryEqual(tmpfilename, self.samfile), # "mismatch when construction SAM file, see %s %s" % (tmpfilename, self.samfile)) # os.unlink(tmpfilename) def test_pass_if_reads_binary_equal(self): '''check if individual reads are binary equal.''' infile = pysam.AlignmentFile(self.bamfile, "rb") references = list(infile) for denovo, reference in zip(references, self.reads): checkFieldEqual(self, reference, denovo) self.assertEqual(reference.compare(denovo), 0) # TODO # def testSAMPerRead(self): # '''check if individual reads are binary equal.''' # infile = pysam.AlignmentFile(self.samfile, "r") # others = list(infile) # for denovo, other in zip(others, self.reads): # checkFieldEqual(self, other, denovo) # self.assertEqual(other.compare(denovo), 0) def testBAMWholeFile(self): tmpfilename = "tmp_%i.bam" % id(self) outfile = pysam.AlignmentFile(tmpfilename, "wb", header=self.header) for x in self.reads: outfile.write(x) outfile.close() self.assertTrue( checkGZBinaryEqual(tmpfilename, self.bamfile), "mismatch when construction BAM file, see %s %s" % (tmpfilename, self.bamfile)) os.unlink(tmpfilename) class TestEmptyHeader(unittest.TestCase): '''see issue 84.''' def testEmptyHeader(self): s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'example_empty_header.bam')) self.assertEqual(s.header.to_dict(), {'SQ': [{'LN': 1000, 'SN': 'chr1'}]}) def test_bam_without_seq_in_header(self): s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "0example_no_seq_in_header.bam")) self.assertTrue("SQ" in s.header.to_dict()) self.assertTrue("@SQ" in str(s.header)) def test_bam_without_seq_with_null_bytes_in_header(self): s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "0example_no_seq_in_header_null_bytes.bam")) self.assertTrue("SQ" in s.header.to_dict()) self.assertTrue("@SQ" in str(s.header)) class TestMismatchingHeader(unittest.TestCase): '''see issue 716.''' def testMismatchingHeader(self): # Note: no chr2 header = { 'SQ': [{'SN': 'chr1', 'LN': 1575}], 'PG': [{'ID': 'bwa', 'PN': 'bwa', 'VN': '0.7.15', 'CL': 'bwa mem xx -'}], } dest = get_temp_filename("tmp_ex3.bam") with pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'ex3.bam')) as inf: with pysam.AlignmentFile(dest, mode="wb", header=header) as outf: for read in inf: if read.reference_name == "chr1": outf.write(read) else: self.assertRaises(ValueError, outf.write, read) os.unlink(dest) class TestHeaderWithProgramOptions(unittest.TestCase): '''see issue 39.''' def testHeader(self): s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'rg_with_tab.bam')) self.assertEqual( s.header.to_dict(), {'SQ': [{'LN': 1575, 'SN': 'chr1'}, {'LN': 1584, 'SN': 'chr2'}], 'PG': [{'PN': 'bwa', 'ID': 'bwa', 'VN': '0.7.9a-r786', 'CL': 'bwa mem -p -t 8 -M -R ' '@RG ID:None SM:None /mnt/data/hg19.fa ' '/mnt/analysis/default-0.fastq'}]}) class TestTruncatedBAM(unittest.TestCase): '''see pull request 50.''' def testTruncatedBam2(self): self.assertRaises(IOError, pysam.AlignmentFile, os.path.join(BAM_DATADIR, 'ex2_truncated.bam')) @pytest.mark.filterwarnings('ignore:no BGZF EOF marker') def testTruncatedBamIterator(self): s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'ex2_truncated.bam'), ignore_truncation=True) def iterall(x): return len([a for a in x]) self.assertRaises(IOError, iterall, s) # Ignore closing errors, as s is now in an error state try: s.close() except IOError: pass class TestCorruptBAM(unittest.TestCase): """See pull request 1035.""" def testCorruptBamIterator(self): s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex2_corrupt.bam")) def iterall(x): return len([a for a in x]) self.assertRaises(IOError, iterall, s) COMPARE_BTAG = [100, 1, 91, 0, 7, 101, 0, 201, 96, 204, 0, 0, 87, 109, 0, 7, 97, 112, 1, 12, 78, 197, 0, 7, 100, 95, 101, 202, 0, 6, 0, 1, 186, 0, 84, 0, 244, 0, 0, 324, 0, 107, 195, 101, 113, 0, 102, 0, 104, 3, 0, 101, 1, 0, 212, 6, 0, 0, 1, 0, 74, 1, 11, 0, 196, 2, 197, 103, 0, 108, 98, 2, 7, 0, 1, 2, 194, 0, 180, 0, 108, 0, 203, 104, 16, 5, 205, 0, 0, 0, 1, 1, 100, 98, 0, 0, 204, 6, 0, 79, 0, 0, 101, 7, 109, 90, 265, 1, 27, 10, 109, 102, 9, 0, 292, 0, 110, 0, 0, 102, 112, 0, 0, 84, 100, 103, 2, 81, 126, 0, 2, 90, 0, 15, 96, 15, 1, 0, 2, 0, 107, 92, 0, 0, 101, 3, 98, 15, 102, 13, 116, 116, 90, 93, 198, 0, 0, 0, 199, 92, 26, 495, 100, 5, 0, 100, 5, 209, 0, 92, 107, 90, 0, 0, 0, 0, 109, 194, 7, 94, 200, 0, 40, 197, 0, 11, 0, 0, 112, 110, 6, 4, 200, 28, 0, 196, 0, 203, 1, 129, 0, 0, 1, 0, 94, 0, 1, 0, 107, 5, 201, 3, 3, 100, 0, 121, 0, 7, 0, 1, 105, 306, 3, 86, 8, 183, 0, 12, 163, 17, 83, 22, 0, 0, 1, 8, 109, 103, 0, 0, 295, 0, 200, 16, 172, 3, 16, 182, 3, 11, 0, 0, 223, 111, 103, 0, 5, 225, 0, 95] class TestBTagSam(unittest.TestCase): '''see issue 81.''' compare = [COMPARE_BTAG, [-100, 200, -300, -400], [-100, 12], [12, 15], [-1.0, 5.0, 2.5]] filename = os.path.join(BAM_DATADIR, 'example_btag.sam') read0 = [('RG', 'QW85I'), ('PG', 'tmap'), ('MD', '140'), ('NM', 0), ('AS', 140), ('FZ', array.array('H', COMPARE_BTAG)), ('XA', 'map2-1'), ('XS', 53), ('XT', 38), ('XF', 1), ('XE', 0)] def testReadTags(self): s = pysam.AlignmentFile(self.filename) for x, read in enumerate(s): tags = read.tags if x == 0: self.assertEqual(tags, self.read0) fz = list(dict(tags)["FZ"]) self.assertEqual(fz, self.compare[x]) self.assertEqual(list(read.opt("FZ")), self.compare[x]) self.assertEqual(tags, read.get_tags()) for tag, value in tags: self.assertEqual(value, read.get_tag(tag)) def testReadWriteTags(self): s = pysam.AlignmentFile(self.filename) for read in s: before = read.tags read.tags = before self.assertEqual(read.tags, before) read.set_tags(before) self.assertEqual(read.tags, before) for tag, value in before: read.set_tag(tag, value) self.assertEqual(value, read.get_tag(tag)) class TestBTagBam(TestBTagSam): filename = os.path.join(BAM_DATADIR, 'example_btag.bam') class TestDoubleFetchBAM(unittest.TestCase): '''check if two iterators on the same bamfile are independent.''' filename = os.path.join(BAM_DATADIR, 'ex1.bam') mode = "rb" def testDoubleFetch(self): with pysam.AlignmentFile(self.filename, self.mode) as samfile1: for a, b in zip(samfile1.fetch(multiple_iterators=True), samfile1.fetch(multiple_iterators=True)): self.assertEqual(a.compare(b), 0) def testDoubleFetchWithRegionTrueTrue(self): with pysam.AlignmentFile(self.filename, self.mode) as samfile1: contig, start, stop = 'chr2', 200, 3000000 # just making sure the test has something to catch self.assertTrue(len(list(samfile1.fetch(contig, start, stop))) > 0) for a, b in zip(samfile1.fetch(contig, start, stop, multiple_iterators=True), samfile1.fetch(contig, start, stop, multiple_iterators=True)): self.assertEqual(a.compare(b), 0) def testDoubleFetchWithRegionFalseTrue(self): with pysam.AlignmentFile(self.filename, self.mode) as samfile1: contig, start, stop = 'chr2', 200, 3000000 # just making sure the test has something to catch self.assertTrue(len(list(samfile1.fetch(contig, start, stop))) > 0) for a, b in zip(samfile1.fetch(contig, start, stop, multiple_iterators=False), samfile1.fetch(contig, start, stop, multiple_iterators=True)): self.assertEqual(a.compare(b), 0) def testDoubleFetchWithRegionTrueFalse(self): with pysam.AlignmentFile(self.filename, self.mode) as samfile1: contig, start, stop = 'chr2', 200, 3000000 # just making sure the test has something to catch self.assertTrue(len(list(samfile1.fetch(contig, start, stop))) > 0) for a, b in zip(samfile1.fetch(contig, start, stop, multiple_iterators=True), samfile1.fetch(contig, start, stop, multiple_iterators=False)): self.assertEqual(a.compare(b), 0) def testDoubleFetchUntilEOF(self): with pysam.AlignmentFile(self.filename, self.mode) as samfile1: for a, b in zip(samfile1.fetch(until_eof=True), samfile1.fetch(until_eof=True, multiple_iterators=True)): self.assertEqual(a.compare(b), 0) class TestDoubleFetchCRAM(TestDoubleFetchBAM): filename = os.path.join(BAM_DATADIR, 'ex2.cram') mode = "rc" class TestDoubleFetchCRAMWithReference(TestDoubleFetchBAM): filename = os.path.join(BAM_DATADIR, 'ex2.cram') mode = "rc" reference_filename = os.path.join(BAM_DATADIR, 'ex1.fa') class TestRemoteFileFTP(unittest.TestCase): '''test remote access. ''' # Need to find an ftp server without password on standard # port. url = "ftp://ftp.sanger.ac.uk/pub/rd/humanSequences/CV.bam" region = "1:1-1000" def testFTPView(self): return if not check_url(self.url): return result = pysam.samtools.view(self.url, self.region) self.assertEqual(len(result), 36) def testFTPFetch(self): return if not check_url(self.url): return samfile = pysam.AlignmentFile(self.url, "rb") result = list(samfile.fetch(region=self.region)) self.assertEqual(len(result), 36) class TestRemoteFileHTTP(unittest.TestCase): url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/ex1.bam" region = "chr1:1-1000" local = os.path.join(BAM_DATADIR, "ex1.bam") def testView(self): if not check_url(self.url): return samfile_local = pysam.AlignmentFile(self.local, "rb") ref = list(samfile_local.fetch(region=self.region)) result = pysam.samtools.view(self.url, self.region) self.assertEqual(len(result.splitlines()), len(ref)) def testFetch(self): if not check_url(self.url): return with pysam.AlignmentFile(self.url, "rb") as samfile: result = list(samfile.fetch(region=self.region)) with pysam.AlignmentFile(self.local, "rb") as samfile_local: ref = list(samfile_local.fetch(region=self.region)) self.assertEqual(len(ref), len(result)) for x, y in zip(result, ref): self.assertEqual(x.compare(y), 0) def testFetchAll(self): if not check_url(self.url): return with pysam.AlignmentFile(self.url, "rb") as samfile: result = list(samfile.fetch()) with pysam.AlignmentFile(self.local, "rb") as samfile_local: ref = list(samfile_local.fetch()) self.assertEqual(len(ref), len(result)) for x, y in zip(result, ref): self.assertEqual(x.compare(y), 0) class TestLargeOptValues(unittest.TestCase): ints = (65536, 214748, 2147484, 2147483647) floats = (65536.0, 214748.0, 2147484.0) def check(self, samfile): i = samfile.fetch() for exp in self.ints: rr = next(i) obs = rr.opt("ZP") self.assertEqual(exp, obs, "expected %s, got %s\n%s" % (str(exp), str(obs), str(rr))) for exp in [-x for x in self.ints]: rr = next(i) obs = rr.opt("ZP") self.assertEqual(exp, obs, "expected %s, got %s\n%s" % (str(exp), str(obs), str(rr))) for exp in self.floats: rr = next(i) obs = rr.opt("ZP") self.assertEqual(exp, obs, "expected %s, got %s\n%s" % (str(exp), str(obs), str(rr))) for exp in [-x for x in self.floats]: rr = next(i) obs = rr.opt("ZP") self.assertEqual(exp, obs, "expected %s, got %s\n%s" % (str(exp), str(obs), str(rr))) def testSAM(self): samfile = pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex10.sam"), "r") self.check(samfile) def testBAM(self): samfile = pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex10.bam"), "rb") self.check(samfile) class TestCountCoverage(unittest.TestCase): samfilename = os.path.join(BAM_DATADIR, "ex1.bam") fastafilename = os.path.join(BAM_DATADIR, "ex1.fa") def setUp(self): self.fastafile = pysam.Fastafile(self.fastafilename) self.tmpfilename = get_temp_filename(".bam") with pysam.AlignmentFile(self.samfilename) as inf: with pysam.AlignmentFile( self.tmpfilename, 'wb', template=inf) as outf: for ii, read in enumerate(inf.fetch()): # if ii % 2 == 0: # setting BFUNMAP makes no sense... #read.flag = read.flag | 0x4 if ii % 3 == 0: read.flag = read.flag | 0x100 if ii % 5 == 0: read.flag = read.flag | 0x200 if ii % 7 == 0: read.flag = read.flag | 0x400 outf.write(read) pysam.samtools.index(self.tmpfilename) def tearDown(self): self.fastafile.close() os.unlink(self.tmpfilename) os.unlink(self.tmpfilename + ".bai") def count_coverage_python(self, bam, chrom, start, stop, read_callback, quality_threshold=15): stop = min(stop, bam.get_reference_length(chrom)) l = stop - start count_a = array.array('L', [0] * l) count_c = array.array('L', [0] * l) count_g = array.array('L', [0] * l) count_t = array.array('L', [0] * l) for p in bam.pileup(chrom, start, stop, truncate=True, stepper='nofilter', min_base_quality=quality_threshold, ignore_overlaps=False): rpos = p.reference_pos - start for read in p.pileups: if not read.is_del and not read.is_refskip and \ read_callback(read.alignment): try: if read.alignment.query_qualities[read.query_position] \ >= quality_threshold: letter = read.alignment.query[read.query_position] if letter == 'A': count_a[rpos] += 1 elif letter == 'C': count_c[rpos] += 1 elif letter == 'G': count_g[rpos] += 1 elif letter == 'T': count_t[rpos] += 1 except IndexError: pass return count_a, count_c, count_g, count_t def test_count_coverage_with_coordinates_works(self): with pysam.AlignmentFile(self.samfilename) as inf: c = inf.count_coverage("chr1") self.assertEqual(len(c[0]), inf.get_reference_length("chr1")) self.assertEqual(len(c[0]), 1575) c = inf.count_coverage("chr1", 100) self.assertEqual(len(c[0]), inf.get_reference_length("chr1") - 100) c = inf.count_coverage("chr1", 100, 200) self.assertEqual(len(c[0]), 200 - 100) c = inf.count_coverage("chr1", None, 200) self.assertEqual(len(c[0]), 200) c = inf.count_coverage("chr1", None, inf.get_reference_length("chr1") + 10000) self.assertEqual(len(c[0]), inf.get_reference_length("chr1")) def test_count_coverage_without_coordinates_fails(self): with pysam.AlignmentFile(self.samfilename) as inf: self.assertRaises(TypeError, inf.count_coverage) def test_count_coverage_wrong_coordinates_fails(self): with pysam.AlignmentFile(self.samfilename) as inf: self.assertRaises(ValueError, inf.count_coverage, "chr1", 200, 100) self.assertRaises(KeyError, inf.count_coverage, "chrUnknown", 100, 200) def test_counting_the_same_region_works(self): with pysam.AlignmentFile(self.samfilename) as inf: c1 = inf.count_coverage("chr1") c2 = inf.count_coverage("chr1") self.assertEqual(c1, c2) def test_count_coverage_counts_as_expected(self): chrom = 'chr1' start = 0 stop = 1000 with pysam.AlignmentFile(self.samfilename) as inf: manual_counts = self.count_coverage_python( inf, chrom, start, stop, lambda read: True, quality_threshold=0) fast_counts = inf.count_coverage( chrom, start, stop, read_callback=lambda read: True, quality_threshold=0) self.assertEqual(list(fast_counts[0]), list(manual_counts[0])) self.assertEqual(list(fast_counts[1]), list(manual_counts[1])) self.assertEqual(list(fast_counts[2]), list(manual_counts[2])) self.assertEqual(list(fast_counts[3]), list(manual_counts[3])) def test_count_coverage_quality_filter(self): chrom = 'chr1' start = 0 stop = 1000 with pysam.AlignmentFile(self.samfilename) as inf: manual_counts = self.count_coverage_python( inf, chrom, start, stop, lambda read: True, quality_threshold=0) fast_counts = inf.count_coverage( chrom, start, stop, read_callback=lambda read: True, quality_threshold=15) # we filtered harder, should be less for i in range(4): for r in range(start, stop): self.assertTrue(fast_counts[i][r] <= manual_counts[i][r]) def test_count_coverage_read_callback(self): chrom = 'chr1' start = 0 stop = 1000 with pysam.AlignmentFile(self.samfilename) as inf: manual_counts = self.count_coverage_python( inf, chrom, start, stop, lambda read: read.flag & 0x10, quality_threshold=0) fast_counts = inf.count_coverage( chrom, start, stop, read_callback=lambda read: True, quality_threshold=0) for i in range(4): for r in range(start, stop): self.assertTrue(fast_counts[i][r] >= manual_counts[i][r]) fast_counts = inf.count_coverage( chrom, start, stop, read_callback=lambda read: read.flag & 0x10, quality_threshold=0) self.assertEqual(fast_counts[0], manual_counts[0]) self.assertEqual(fast_counts[1], manual_counts[1]) self.assertEqual(fast_counts[2], manual_counts[2]) self.assertEqual(fast_counts[3], manual_counts[3]) def test_count_coverage_read_all(self): chrom = 'chr1' start = 0 stop = 1000 def filter(read): return not (read.flag & (0x4 | 0x100 | 0x200 | 0x400)) with pysam.AlignmentFile(self.tmpfilename) as samfile: fast_counts = samfile.count_coverage( chrom, start, stop, read_callback='all', # read_callback = lambda read: ~(read.flag & (0x4 | 0x100 | 0x200 | 0x400)), quality_threshold=0) manual_counts = samfile.count_coverage( chrom, start, stop, read_callback=lambda read: not( read.flag & (0x4 | 0x100 | 0x200 | 0x400)), quality_threshold=0) self.assertEqual(fast_counts[0], manual_counts[0]) self.assertEqual(fast_counts[1], manual_counts[1]) self.assertEqual(fast_counts[2], manual_counts[2]) self.assertEqual(fast_counts[3], manual_counts[3]) def test_count_coverage_nofilter(self): with pysam.AlignmentFile(self.samfilename) as inf: with pysam.AlignmentFile( self.tmpfilename, 'wb', template=inf) as outf: for ii, read in enumerate(inf.fetch()): # if ii % 2 == 0: # setting BFUNMAP makes no sense... # read.flag = read.flag | 0x4 if ii % 3 == 0: read.flag = read.flag | 0x100 if ii % 5 == 0: read.flag = read.flag | 0x200 if ii % 7 == 0: read.flag = read.flag | 0x400 outf.write(read) pysam.samtools.index(self.tmpfilename) chr = 'chr1' start = 0 stop = 1000 with pysam.AlignmentFile(self.tmpfilename) as inf: fast_counts = inf.count_coverage(chr, start, stop, read_callback='nofilter', quality_threshold=0) manual_counts = self.count_coverage_python(inf, chr, start, stop, read_callback=lambda x: True, quality_threshold=0) self.assertEqual(fast_counts[0], manual_counts[0]) self.assertEqual(fast_counts[1], manual_counts[1]) self.assertEqual(fast_counts[2], manual_counts[2]) self.assertEqual(fast_counts[3], manual_counts[3]) class TestFindIntrons(unittest.TestCase): samfilename = os.path.join(BAM_DATADIR, "ex_spliced.bam") def setUp(self): self.samfile = pysam.AlignmentFile(self.samfilename) def tearDown(self): self.samfile.close() def test_total(self): all_read_counts = self.samfile.count() splice_sites = self.samfile.find_introns(self.samfile.fetch()) # there is a single unspliced read and a single unmapped read in there self.assertEqual(sum(splice_sites.values()), all_read_counts - 2) def test_first(self): reads = list(self.samfile.fetch())[:10] splice_sites = self.samfile.find_introns(reads) starts = [14792 + 38 - 1] stops = [14792 + 38 + 140 - 1] self.assertEqual(len(splice_sites), 1) self.assertTrue((starts[0], stops[0]) in splice_sites) # first one is the unspliced read self.assertEqual(splice_sites[(starts[0], stops[0])], 9) def test_all(self): reads = list(self.samfile.fetch()) splice_sites = self.samfile.find_introns(reads) should = collections.Counter({ (14829, 14969): 33, (15038, 15795): 24, (15947, 16606): 3, (16765, 16857): 9, (16765, 16875): 1, (17055, 17232): 19, (17055, 17605): 3, (17055, 17914): 1, (17368, 17605): 7, }) self.assertEqual(should, splice_sites) class TestLogging(unittest.TestCase): '''test around bug issue 42, failed in versions < 0.4 ''' def check(self, bamfile, log): if log: logger = logging.getLogger('franklin') logger.setLevel(logging.INFO) formatter = logging.Formatter( '%(asctime)s %(levelname)s %(message)s') log_hand = logging.FileHandler('log.txt') log_hand.setFormatter(formatter) logger.addHandler(log_hand) with pysam.AlignmentFile(bamfile, 'rb') as bam: cols = bam.pileup() self.assertTrue(True) def tearDown(self): if os.path.exists('log.txt'): os.unlink('log.txt') def testFail1(self): self.check(os.path.join(BAM_DATADIR, "ex9_fail.bam"), False) self.check(os.path.join(BAM_DATADIR, "ex9_fail.bam"), True) def testNoFail1(self): self.check(os.path.join(BAM_DATADIR, "ex9_nofail.bam"), False) self.check(os.path.join(BAM_DATADIR, "ex9_nofail.bam"), True) def testNoFail2(self): self.check(os.path.join(BAM_DATADIR, "ex9_nofail.bam"), True) self.check(os.path.join(BAM_DATADIR, "ex9_nofail.bam"), True) # TODOS # 1. finish testing all properties within pileup objects # 2. check exceptions and bad input problems (missing files, optional fields that aren't present, etc...) # 3. check: presence of sequence class TestAlignmentFileUtilityFunctions(unittest.TestCase): def testCount(self): with pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex1.bam"), "rb") as samfile: for contig in ("chr1", "chr2"): for start in range(0, 2000, 100): end = start + 1 self.assertEqual( len(list(samfile.fetch(contig, start, end))), samfile.count(contig, start, end), 'number mismatch for %s:%i-%i %i != %i' % ( contig, start, end, len(list(samfile.fetch(contig, start, end))), samfile.count(contig, start, end))) # test empty intervals self.assertEqual( len(list(samfile.fetch(contig, start, start))), samfile.count(contig, start, start), 'number mismatch for %s:%i-%i %i != %i' % ( contig, start, start, len(list(samfile.fetch(contig, start, start))), samfile.count(contig, start, start))) # test half empty intervals self.assertEqual(len(list(samfile.fetch(contig, start))), samfile.count(contig, start)) self.assertEqual( len(list(samfile.fetch(contig, start))), samfile.count(contig, start), 'number mismatch for %s:%i %i != %i' % ( contig, start, len(list(samfile.fetch(contig, start))), samfile.count(contig, start))) def testMate(self): '''test mate access.''' with open(os.path.join(BAM_DATADIR, "ex1.sam"), "rb") as inf: readnames = [x.decode("ascii").split("\t")[0] for x in inf.readlines()] counts = collections.defaultdict(int) for x in readnames: counts[x] += 1 with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"), "rb") as samfile: for read in samfile.fetch(): if not read.is_paired: self.assertRaises(ValueError, samfile.mate, read) elif read.mate_is_unmapped: self.assertRaises(ValueError, samfile.mate, read) else: if counts[read.query_name] == 1: self.assertRaises(ValueError, samfile.mate, read) else: mate = samfile.mate(read) self.assertEqual(read.query_name, mate.query_name) self.assertEqual(read.is_read1, mate.is_read2) self.assertEqual(read.is_read2, mate.is_read1) self.assertEqual( read.reference_start, mate.next_reference_start) self.assertEqual( read.next_reference_start, mate.reference_start) def testIndexStats(self): '''test if total number of mapped/unmapped reads is correct.''' with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"), "rb") as samfile: self.assertEqual(samfile.mapped, 3235) self.assertEqual(samfile.unmapped, 35) self.assertEqual(samfile.nocoordinate, 0) class TestMappedUnmapped(unittest.TestCase): filename = "test_mapped_unmapped.bam" def test_counts_of_mapped_and_unmapped_are_correct(self): with pysam.AlignmentFile(os.path.join(BAM_DATADIR, self.filename)) as inf: unmapped_flag = 0 unmapped_nopos = 0 mapped_flag = 0 for x in inf.fetch(until_eof=True): if x.is_unmapped: if x.reference_id < 0: unmapped_nopos += 1 else: unmapped_flag += 1 else: mapped_flag += 1 self.assertEqual(inf.mapped, mapped_flag) self.assertEqual(inf.unmapped, unmapped_flag + unmapped_nopos) inf.reset() self.assertEqual(inf.count(), inf.mapped + unmapped_flag) inf.reset() self.assertEqual(inf.count(until_eof=True), inf.mapped + unmapped_flag + unmapped_nopos) inf.reset() self.assertEqual(inf.count(read_callback="all"), inf.mapped) inf.reset() self.assertEqual(inf.count(until_eof=True, read_callback="all"), inf.mapped) def test_counts_of_mapped_and_unmapped_are_correct_per_chromosome(self): with pysam.AlignmentFile(os.path.join(BAM_DATADIR, self.filename)) as inf: counts = inf.get_index_statistics() counts_contigs = [x.contig for x in counts] self.assertEqual(sorted(counts_contigs), sorted(inf.references)) for contig in inf.references: unmapped_flag = 0 unmapped_nopos = 0 mapped_flag = 0 for x in inf.fetch(contig=contig): if x.is_unmapped: unmapped_flag += 1 else: mapped_flag += 1 cc = [c for c in counts if c.contig == contig][0] self.assertEqual(cc.mapped, mapped_flag) self.assertEqual(cc.unmapped, unmapped_flag) self.assertEqual(cc.total, mapped_flag + unmapped_flag) class TestSamtoolsProxy(unittest.TestCase): '''tests for sanity checking access to samtools functions.''' def testIndex(self): self.assertRaises(IOError, pysam.samtools.index, "missing_file") def testView(self): # note that view still echos "open: No such file or directory" self.assertRaises(pysam.SamtoolsError, pysam.samtools.view, "missing_file") def testSort(self): self.assertRaises(pysam.SamtoolsError, pysam.samtools.sort, "missing_file") class TestAlignmentFileIndex(unittest.TestCase): def testIndex(self): samfile = pysam.AlignmentFile( os.path.join(BAM_DATADIR, "ex1.bam"), "rb") index = pysam.IndexedReads(samfile) index.build() reads = collections.defaultdict(int) for read in samfile: reads[read.query_name] += 1 for qname, counts in reads.items(): found = list(index.find(qname)) self.assertEqual(len(found), counts) for x in found: self.assertEqual(x.query_name, qname) class TestExplicitIndex(unittest.TestCase): def testExplicitIndexBAM(self): with pysam.AlignmentFile( os.path.join(BAM_DATADIR, "explicit_index.bam"), "rb", filepath_index=os.path.join(BAM_DATADIR, 'ex1.bam.bai')) as samfile: samfile.fetch("chr1") def testExplicitIndexCRAM(self): with pysam.AlignmentFile( os.path.join(BAM_DATADIR, "explicit_index.cram"), "rc", filepath_index=os.path.join(BAM_DATADIR, 'ex1.cram.crai')) as samfile: samfile.fetch("chr1") def testRemoteExplicitIndexBAM(self): if not check_url( "http://genserv.anat.ox.ac.uk/downloads/pysam/test/noindex.bam"): return with pysam.AlignmentFile( "http://genserv.anat.ox.ac.uk/downloads/pysam/test/noindex.bam", "rb", filepath_index=os.path.join(BAM_DATADIR, 'ex1.bam.bai')) as samfile: samfile.fetch("chr1") class TestVerbosity(unittest.TestCase): '''test if setting/getting of verbosity works.''' def testVerbosity(self): self.assertEqual(pysam.get_verbosity(), 3) old = pysam.set_verbosity(0) self.assertEqual(pysam.get_verbosity(), 0) new = pysam.set_verbosity(old) self.assertEqual(new, 0) self.assertEqual(pysam.get_verbosity(), 3) class TestSanityCheckingBAM(unittest.TestCase): mode = "wb" def check_write(self, read): fn = "tmp_test_sanity_check.bam" names = ["chr1"] lengths = [10000] with pysam.AlignmentFile( fn, self.mode, reference_names=names, reference_lengths=lengths) as outf: outf.write(read) if os.path.exists(fn): os.unlink(fn) def test_empty_read_gives_value_error(self): read = pysam.AlignedSegment() self.check_write(read) class TestLargeCigar(unittest.TestCase): def setUp(self): self.read_length = 70000 self.header = pysam.AlignmentHeader.from_references( ["chr1", "chr2"], [self.read_length * 2, self.read_length * 2]) def build_read(self): '''build an example read.''' a = pysam.AlignedSegment(self.header) l = self.read_length a.query_name = "read_12345" a.query_sequence = "A" * (l + 1) a.flag = 0 a.reference_id = 0 a.reference_start = 20 a.mapping_quality = 20 a.cigarstring = "1M1D" * l + "1M" self.assertEqual(len(a.cigartuples), 2 * l + 1) a.next_reference_id = 0 a.next_reference_start = 0 a.template_length = l a.query_qualities = pysam.qualitystring_to_array("1") * (l + 1) return a def check_read(self, read, mode="bam"): fn = get_temp_filename("tmp_largecigar.{}".format(mode)) fn_reference = get_temp_filename("tmp_largecigar.fa") nrows = int(self.read_length * 2 / 80) s = "\n".join(["A" * 80 for x in range(nrows)]) with open(fn_reference, "w") as outf: outf.write(">chr1\n{seq}\n>chr2\n{seq}\n".format( seq=s)) if mode == "bam": write_mode = "wb" elif mode == "sam": write_mode = "w" elif mode == "cram": write_mode = "wc" with pysam.AlignmentFile(fn, write_mode, header=self.header, reference_filename=fn_reference) as outf: outf.write(read) with pysam.AlignmentFile(fn) as inf: ref_read = next(inf) if mode == "cram": # in CRAM, the tag field is kept, while it is emptied by the BAM/SAM reader self.assertEqual(read.cigarstring, ref_read.cigarstring) else: self.assertEqual(read, ref_read) os.unlink(fn) os.unlink(fn_reference) def test_reading_writing_sam(self): read = self.build_read() self.check_read(read, mode="sam") def test_reading_writing_bam(self): read = self.build_read() self.check_read(read, mode="bam") @unittest.skip("fails on linux - https issue?") def test_reading_writing_cram(self): # The following test fails with htslib 1.9, but worked with previous versions. # Error is: # [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/ac9fac7c3e9c476f74f1d0e47abc8be2": Input/output error # Error can be reproduced using samtools 1.9 command line. # Could be a conda configuration issue, see # https://github.com/bioconda/bioconda-recipes/issues/9056 return read = self.build_read() self.check_read(read, mode="cram") # SAM writing fails, as query length is 0 # class TestSanityCheckingSAM(TestSanityCheckingSAM): # mode = "w" if __name__ == "__main__": print("starting tests") unittest.main() print("completed tests") pysam-0.23.0/tests/PileupTestUtils.py000066400000000000000000000132251475062545500176000ustar00rootroot00000000000000import os import subprocess import pysam from TestUtils import force_str def build_pileup_with_samtoolsshell(fn): os.system("samtools mpileup {} 2> /dev/null | wc -l > /dev/null".format(fn)) return 2998 def build_pileup_with_samtoolspipe(fn): FNULL = open(os.devnull, 'w') with subprocess.Popen(["samtools", "mpileup", fn], stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=FNULL) as proc: return len(proc.stdout.readlines()) def build_pileup_with_pysam(*args, **kwargs): with pysam.AlignmentFile(*args, **kwargs) as inf: return len(list(inf.pileup(stepper="samtools"))) def build_depth_with_samtoolsshell(fn): os.system( "samtools mpileup {} 2> /dev/null | awk '{{a += $4}} END {{print a}}' > /dev/null".format(fn)) return 107241 def build_depth_with_samtoolspipe(fn): FNULL = open(os.devnull, 'w') with subprocess.Popen(["samtools", "mpileup", fn], stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=FNULL) as proc: data = [x.split() for x in proc.stdout.readlines()] return [int(x[3]) for x in data] def build_depth_with_filter_with_pysam(*args, **kwargs): with pysam.AlignmentFile(*args, **kwargs) as inf: return [x.get_num_aligned() for x in inf.pileup(stepper="samtools")] def build_depth_with_pysam(*args, **kwargs): with pysam.AlignmentFile(*args, **kwargs) as inf: return [x.nsegments for x in inf.pileup(stepper="samtools")] def build_query_bases_with_samtoolsshell(fn): os.system("samtools mpileup {} 2> /dev/null | awk '{{a = a $5}} END {{print a}}' | wc -c > /dev/null".format(fn)) return 116308 def build_query_bases_with_samtoolspipe(fn, *args, **kwargs): FNULL = open(os.devnull, 'w') with subprocess.Popen(["samtools", "mpileup", fn] + list(args), stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=FNULL) as proc: stdout = proc.stdout.read().decode() return [x.split()[4] for x in stdout.splitlines()] def build_query_bases_with_samtoolspysam(fn, *args): return [x.split()[4] for x in pysam.samtools.mpileup(fn, *args).splitlines()] def build_query_bases_with_pysam_pileups(*args, **kwargs): total_pileup = [] with pysam.AlignmentFile(*args, **kwargs) as inf: total_pileup = [ [r.alignment.query_sequence[r.query_position_or_next] for r in column.pileups if r.query_position_or_next is not None] for column in inf.pileup(stepper="samtools")] return total_pileup def build_query_qualities_with_pysam_pileups(*args, **kwargs): total_pileup = [] with pysam.AlignmentFile(*args, **kwargs) as inf: total_pileup = [ [r.alignment.query_qualities[r.query_position_or_next] for r in column.pileups if r.query_position_or_next is not None] for column in inf.pileup(stepper="samtools")] return total_pileup def build_query_bases_with_pysam(fn, *args, **kwargs): total_pileup = [] with pysam.AlignmentFile(fn) as inf: total_pileup = [column.get_query_sequences( mark_ends=True, add_indels=True, mark_matches=True) for column in inf.pileup(*args, **kwargs)] return total_pileup def build_query_names_with_pysam(*args, **kwargs): total_pileup = [] with pysam.AlignmentFile(*args, **kwargs) as inf: total_pileup = [column.get_query_names() for column in inf.pileup(stepper="samtools")] return total_pileup def build_query_qualities_with_samtoolspipe(fn): FNULL = open(os.devnull, 'w') with subprocess.Popen(["samtools", "mpileup", fn], stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=FNULL) as proc: data = [force_str(x).split()[5] for x in proc.stdout.readlines()] return data def build_query_qualities_with_pysam(*args, **kwargs): total_pileup = [] with pysam.AlignmentFile(*args, **kwargs) as inf: total_pileup = [column.get_query_qualities() for column in inf.pileup(stepper="samtools")] return total_pileup def build_mapping_qualities_with_samtoolspipe(fn): FNULL = open(os.devnull, 'w') with subprocess.Popen(["samtools", "mpileup", "-s", fn], stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=FNULL) as proc: data = [force_str(x).split()[6] for x in proc.stdout.readlines()] return data def build_mapping_qualities_with_pysam(*args, **kwargs): total_pileup = [] with pysam.AlignmentFile(*args, **kwargs) as inf: total_pileup = [column.get_mapping_qualities() for column in inf.pileup(stepper="samtools")] return total_pileup def build_query_positions_with_samtoolspipe(fn): FNULL = open(os.devnull, 'w') with subprocess.Popen(["samtools", "mpileup", "-O", fn], stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=FNULL) as proc: data = [list(map(int, force_str(x).split()[6].split(","))) for x in proc.stdout.readlines()] return data def build_query_positions_with_pysam(*args, **kwargs): total_pileup = [] with pysam.AlignmentFile(*args, **kwargs) as inf: total_pileup = [column.get_query_positions() for column in inf.pileup(stepper="samtools")] return total_pileup pysam-0.23.0/tests/StreamFiledescriptors_test.py000066400000000000000000000056471475062545500220460ustar00rootroot00000000000000import os import subprocess import threading import errno import unittest from pysam import AlignmentFile from TestUtils import make_data_files, BAM_DATADIR def setUpModule(): make_data_files(BAM_DATADIR) def alignmentfile_writer_thread(infile, outfile): def _writer_thread(infile, outfile): """read from infile and write to outfile""" try: i = 0 for record in infile: outfile.write(record) i += 1 except IOError as e: if e.errno != errno.EPIPE: pass finally: outfile.close() writer = threading.Thread(target=_writer_thread, args=(infile, outfile)) writer.daemon = True writer.start() return writer class StreamTest(unittest.TestCase): def stream_process(self, proc, in_stream, out_stream, writer): with AlignmentFile(proc.stdout) as infile: read = 0 for record in infile: read += 1 return 0, read def test_text_processing(self): with subprocess.Popen('head -n200', stdin=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) as proc: in_stream = AlignmentFile(os.path.join(BAM_DATADIR, 'ex1.bam')) out_stream = AlignmentFile( proc.stdin, 'wh', header=in_stream.header) writer = alignmentfile_writer_thread(in_stream, out_stream) written, read = self.stream_process(proc, in_stream, out_stream, writer) self.assertEqual(read, 198) @unittest.skip("test contains bug") def test_samtools_processing(self): # The following test causes the suite to hang # as the stream_processor raises: # ValueError: file has no sequences defined (mode='r') - is it SAM/BAM format? # The whole setup then hangs during exception handling. with subprocess.Popen('samtools view -b -f 4', stdin=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) as proc: in_stream = AlignmentFile(os.path.join(BAM_DATADIR, 'ex1.bam')) out_stream = AlignmentFile( proc.stdin, 'wb', header=in_stream.header) writer = alignmentfile_writer_thread(in_stream, out_stream) written, read = self.stream_process(proc, in_stream, out_stream, writer) self.assertEqual(read, 35) if __name__ == "__main__": unittest.main() pysam-0.23.0/tests/TestUtils.py000066400000000000000000000174371475062545500164320ustar00rootroot00000000000000import os import glob import gzip import contextlib import inspect import subprocess import tempfile import time import pysam WORKDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), "pysam_test_work")) BAM_DATADIR = os.path.abspath(os.path.join(os.path.dirname(__file__), "pysam_data")) TABIX_DATADIR = os.path.abspath(os.path.join(os.path.dirname(__file__), "tabix_data")) CBCF_DATADIR = os.path.abspath(os.path.join(os.path.dirname(__file__), "cbcf_data")) LINKDIR = os.path.abspath(os.path.join( os.path.dirname(__file__), "..", "linker_tests")) TESTS_TEMPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), "tmp")) from itertools import zip_longest from urllib.request import urlopen def force_str(s): try: return s.decode('ascii') except AttributeError: return s def force_bytes(s): try: return s.encode('ascii') except AttributeError: return s def openfile(fn): if fn.endswith(".gz"): try: return gzip.open(fn, "rt", encoding="utf-8") except TypeError: return gzip.open(fn, "r") else: return open(fn) def checkBinaryEqual(filename1, filename2): '''return true if the two files are binary equal. ''' if os.path.getsize(filename1) != os.path.getsize(filename2): return False infile1 = open(filename1, "rb") infile2 = open(filename2, "rb") def chariter(infile): while 1: c = infile.read(1) if c == b"": break yield c found = False for c1, c2 in zip_longest(chariter(infile1), chariter(infile2)): if c1 != c2: break else: found = True infile1.close() infile2.close() return found def checkGZBinaryEqual(filename1, filename2): '''return true if the decompressed contents of the two files are binary equal. ''' with gzip.open(filename1, "rb") as infile1: d1 = infile1.read() with gzip.open(filename2, "rb") as infile2: d2 = infile2.read() if d1 == d2: return True return False def check_samtools_view_equal( filename1, filename2, without_header=False): '''return true if the two files are equal in their content through samtools view. ''' # strip MD and NM tags, as not preserved in CRAM files args = ["-x", "MD", "-x", "NM"] if not without_header: args.append("-h") lines1 = pysam.samtools.view(*(args + [filename1])) lines2 = pysam.samtools.view(*(args + [filename2])) if len(lines1) != len(lines2): return False if lines1 != lines2: # line by line comparison # sort each line, as tags get rearranged between # BAM/CRAM for n, pair in enumerate(zip(lines1, lines2)): l1, l2 = pair l1 = sorted(l1[:-1].split("\t")) l2 = sorted(l2[:-1].split("\t")) if l1 != l2: print("mismatch in line %i" % n) print(l1) print(l2) return False else: return False return True def check_url(url): '''return True if URL is available. A URL might not be available if it is the wrong URL or there is no connection to the URL. ''' try: urlopen(url, timeout=1) return True except: return False def checkFieldEqual(cls, read1, read2, exclude=[]): '''check if two reads are equal by comparing each field.''' # add the . for refactoring purposes. for x in (".query_name", ".query_sequence", ".flag", ".reference_id", ".reference_start", ".mapping_quality", ".cigartuples", ".next_reference_id", ".next_reference_start", ".template_length", ".query_length", ".query_qualities", ".bin", ".is_paired", ".is_proper_pair", ".is_unmapped", ".is_mapped", ".mate_is_unmapped", ".mate_is_mapped", ".is_reverse", ".is_forward", ".mate_is_reverse", ".mate_is_forward", ".is_read1", ".is_read2", ".is_secondary", ".is_qcfail", ".is_duplicate"): n = x[1:] if n in exclude: continue cls.assertEqual(getattr(read1, n), getattr(read2, n), "attribute mismatch for %s: %s != %s" % (n, getattr(read1, n), getattr(read2, n))) def check_lines_equal(cls, a, b, sort=False, filter_f=None, msg=None): """check if contents of two files are equal comparing line-wise. sort: bool sort contents of both files before comparing. filter_f: remover lines in both a and b where expression is True """ with openfile(a) as inf: aa = inf.readlines() with openfile(b) as inf: bb = inf.readlines() if filter_f is not None: aa = [x for x in aa if not filter_f(x)] bb = [x for x in bb if not filter_f(x)] if sort: cls.assertEqual(sorted(aa), sorted(bb), msg) else: cls.assertEqual(aa, bb, msg) def get_temp_filename(suffix=""): caller_name = inspect.getouterframes(inspect.currentframe(), 2)[1][3] try: os.makedirs(TESTS_TEMPDIR) except OSError: pass f = tempfile.NamedTemporaryFile( prefix="pysamtests_tmp_{}_".format(caller_name), suffix=suffix, delete=False, dir=TESTS_TEMPDIR) f.close() return f.name @contextlib.contextmanager def get_temp_context(suffix="", keep=False): caller_name = inspect.getouterframes(inspect.currentframe(), 3)[1][3] try: os.makedirs(TESTS_TEMPDIR) except OSError: pass f = tempfile.NamedTemporaryFile( prefix="pysamtests_tmp_{}_".format(caller_name), suffix=suffix, delete=False, dir=TESTS_TEMPDIR) f.close() yield f.name if not keep: # clear up any indices as well for f in glob.glob(f.name + "*"): os.unlink(f) def make_data_files(directory): if os.path.exists(os.path.join(directory, 'all.stamp')): return make = os.environ.get('MAKE', 'make') for attempt in range(1, 6): try: os.mkdir(os.path.join(directory, 'all.lock'), 0o700) break except FileExistsError: time.sleep(attempt) continue else: raise RuntimeError(f'Directory {directory!r} already locked: try `{make} clean` there') try: subprocess.check_output([make, '-C', directory], stderr=subprocess.STDOUT, encoding='ascii') except subprocess.CalledProcessError as e: raise RuntimeError(f'Making test data in {directory!r} failed:\n{e.output}') from None finally: os.rmdir(os.path.join(directory, 'all.lock')) def load_and_convert(filename, encode=True): '''load data from filename and convert all fields to string. Filename can be either plain or compressed (ending in .gz). ''' data = [] if filename.endswith(".gz"): with gzip.open(filename) as inf: for line in inf: line = line.decode("ascii") if line.startswith("#"): continue d = line.strip().split("\t") data.append(d) else: with open(filename) as f: for line in f: if line.startswith("#"): continue d = line.strip().split("\t") data.append(d) return data def flatten_nested_list(l): return [i for ll in l for i in ll] pysam-0.23.0/tests/VariantFileFetchTestUtils.py000066400000000000000000000034741475062545500215250ustar00rootroot00000000000000import os import subprocess import pysam try: import cyvcf2 except ImportError: pass def build_filter_from_vcf_with_samtoolsshell(fn): retval = os.popen( "bcftools filter -e \"N_ALT != 1 || QUAL < 20 || maf[0]>0.05\" {} | grep -cv ^# ".format(fn)).read() return int(retval.strip()) def build_filter_from_vcf_with_bcftoolspipe(fn): FNULL = open(os.devnull, 'w') with subprocess.Popen([ "bcftools", "filter", "-e", "N_ALT != 1 || QUAL < 20 || maf[0]>0.05", fn], stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=FNULL) as proc: data = [line for line in proc.stdout.readlines() if not line.startswith(b"#")] return len(data) def build_filter_from_vcf_with_cyvcf2(fn): n = 0 try: for v in cyvcf2.VCF(fn): if len(v.ALT) > 1: continue if v.QUAL < 20: continue if v.aaf > 0.05: continue n += 1 except NameError: n = 9120 return n def build_filter_from_vcf_with_pysam(fn): n = 0 with pysam.VariantFile(fn) as vcf: for v in vcf: # the two commands below take >1s out of 19s total if len(v.alts) > 1: continue if v.qual < 20: continue # this takes 12s out of 19s total gts = [s['GT'] for s in v.samples.values()] # the lines below take 6s out of 19s total an = sum(len(gt) for gt in gts) ac = sum(sum(gt) for gt in gts) aaf = (float(ac) / float(an)) if aaf > 0.05: continue n += 1 return n pysam-0.23.0/tests/VariantFile_bench.py000066400000000000000000000033231475062545500200220ustar00rootroot00000000000000"""Benchmarking module for AlignmentFile functionality""" import pytest from VariantFileFetchTestUtils import * GENOMES_URL = "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr{chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" CHROM = 22 @pytest.fixture def genomes_data(): url = GENOMES_URL.format(chrom=CHROM) fn = os.path.basename(url) print(fn) if not os.path.exists(fn): os.system("wget {}".format(url)) if not os.path.exists(fn + ".tbi"): os.system("wget {}".format(url + ".tbi")) fn_small = "small.vcf.gz" if not os.path.exists(fn_small): os.system("bcftools view {} | head -n 10000 | bgzip > {}".format(fn, fn_small)) os.system("tabix -f -p vcf {}".format(fn_small)) return fn_small @pytest.mark.benchmark(min_rounds=1) def test_build_filter_from_vcf_with_bcftoolsshell(benchmark, genomes_data): result = benchmark(build_filter_from_vcf_with_samtoolsshell, genomes_data) assert result == 9120 @pytest.mark.benchmark(min_rounds=1) def test_build_filter_from_vcf_with_bcftoolpipe(benchmark, genomes_data): result = benchmark(build_filter_from_vcf_with_bcftoolspipe, genomes_data) assert result == 9120 @pytest.mark.benchmark(min_rounds=1) def test_build_filter_from_vcf_with_cyvcf2(benchmark, genomes_data): result = benchmark(build_filter_from_vcf_with_cyvcf2, genomes_data) # note: inconsistent with bcftools assert result == 9114 @pytest.mark.benchmark(min_rounds=1) def test_build_filter_from_vcf_with_pysam(benchmark, genomes_data): result = benchmark(build_filter_from_vcf_with_pysam, genomes_data) # note: inconsistent with bcftools assert result == 9114 pysam-0.23.0/tests/VariantFile_test.py000066400000000000000000000620211475062545500177220ustar00rootroot00000000000000# -*- coding: utf-8 -*- import os import glob import unittest import pysam import shutil import gzip from pathlib import Path from TestUtils import get_temp_filename, check_lines_equal, load_and_convert, make_data_files, CBCF_DATADIR, get_temp_context def setUpModule(): make_data_files(CBCF_DATADIR) def read_header(filename): data = [] if filename.endswith(".gz"): for line in gzip.open(filename): line = line.decode("ascii") if line.startswith("#"): data.append(line) else: with open(filename) as f: for line in f: if line.startswith("#"): data.append(line) return data def read_index_header(filename): with gzip.open(filename) as infile: magic = infile.read(4) return magic class TestMissingGenotypes(unittest.TestCase): filename = "missing_genotypes.vcf" def setUp(self): self.compare = load_and_convert( os.path.join(CBCF_DATADIR, self.filename), encode=False) def check(self, filename): """see issue 203 - check for segmentation fault""" fn = os.path.join(CBCF_DATADIR, filename) self.assertEqual(True, os.path.exists(fn)) v = pysam.VariantFile(fn) for site in v: for ss, rec in site.samples.items(): a, b = ss, rec v = pysam.VariantFile(fn) for x, site in enumerate(v): for ss, rec in site.samples.items(): a, b = ss, rec.alleles a, b = ss, rec.allele_indices def testVCF(self): self.check(self.filename) def testVCFGZ(self): self.check(self.filename + ".gz") class TestMissingSamples(unittest.TestCase): filename = "gnomad.vcf" def setUp(self): self.compare = load_and_convert( os.path.join(CBCF_DATADIR, self.filename), encode=False) def check(self, filename): """see issue #593""" fn = os.path.join(CBCF_DATADIR, filename) self.assertEqual(True, os.path.exists(fn)) expect_fail = not "fixed" in self.filename with pysam.VariantFile(fn) as inf: rec = next(inf.fetch()) if expect_fail: self.assertRaises(ValueError, rec.info.__getitem__, "GC") else: self.assertEqual(rec.info["GC"], (27, 35, 16)) def testVCF(self): self.check(self.filename) def testVCFGZ(self): self.check(self.filename + ".gz") class TestMissingSamplesFixed(TestMissingSamples): # workaround for NUMBER=G in INFO records: # perl 's/Number=G/Number=./ if (/INFO/)' filename = "gnomad_fixed.vcf" class TestOpening(unittest.TestCase): def testMissingFile(self): self.assertRaises(IOError, pysam.VariantFile, "missing_file.vcf") def testMissingFileVCFGZ(self): self.assertRaises(IOError, pysam.VariantFile, "missing_file.vcf.gz") def testEmptyFileVCF(self): with get_temp_context("tmp_testEmptyFile.vcf") as fn: with open(fn, "w"): pass self.assertRaises(ValueError, pysam.VariantFile, fn) def testEmptyFileVCFFromPath(self): with get_temp_context("tmp_testEmptyFile.vcf") as fn: with open(fn, "w"): pass self.assertRaises(ValueError, pysam.VariantFile, Path(fn)) def testEmptyFileVCFGZWithIndex(self): with get_temp_context("tmp_testEmptyFile.vcf") as fn: with open(fn, "w"): pass # tabix_index will automatically compress pysam.tabix_index(fn, preset="vcf", force=True) self.assertRaises(ValueError, pysam.VariantFile, fn + ".gz") def testEmptyFileVCFGZWithoutIndex(self): with get_temp_context("tmp_testEmptyFileWithoutIndex.vcf") as fn: with open(fn, "w"): pass pysam.tabix_compress(fn, fn + ".gz", force=True) self.assertRaises(ValueError, pysam.VariantFile, fn + ".gz") def testEmptyFileVCFOnlyHeader(self): with pysam.VariantFile(os.path.join( CBCF_DATADIR, "example_vcf42_only_header.vcf")) as inf: self.assertEqual(len(list(inf.fetch())), 0) def testEmptyFileVCFGZOnlyHeader(self): with pysam.VariantFile(os.path.join( CBCF_DATADIR, "example_vcf42_only_header.vcf")) as inf: self.assertEqual(len(list(inf.fetch())), 0) def testDetectVCF(self): with pysam.VariantFile(os.path.join(CBCF_DATADIR, "example_vcf40.vcf")) as inf: self.assertEqual(inf.category, 'VARIANTS') self.assertEqual(inf.format, 'VCF') self.assertEqual(inf.compression, 'NONE') self.assertFalse(inf.is_remote) self.assertFalse(inf.is_stream) self.assertEqual(len(list(inf.fetch())), 5) def testDetectVCFGZ(self): with pysam.VariantFile(os.path.join(CBCF_DATADIR, "example_vcf40.vcf.gz")) as inf: self.assertEqual(inf.category, 'VARIANTS') self.assertEqual(inf.format, 'VCF') self.assertEqual(inf.compression, 'BGZF') self.assertFalse(inf.is_remote) self.assertFalse(inf.is_stream) self.assertEqual(len(list(inf.fetch())), 5) def testDetectBCF(self): with pysam.VariantFile(os.path.join( CBCF_DATADIR, "example_vcf40.bcf")) as inf: self.assertEqual(inf.category, 'VARIANTS') self.assertEqual(inf.format, 'BCF') self.assertEqual(inf.compression, 'BGZF') self.assertFalse(inf.is_remote) self.assertFalse(inf.is_stream) self.assertEqual(len(list(inf.fetch())), 5) class TestIndexFormatsVCF(unittest.TestCase): vcf_filename = os.path.join(CBCF_DATADIR, "example_vcf40.vcf") bcf_filename = os.path.join(CBCF_DATADIR, "example_vcf40.bcf") def test_vcf_with_tbi_index(self): with get_temp_context("tmp_fn.vcf") as fn: shutil.copyfile(self.vcf_filename, fn) pysam.tabix_index(fn, preset="vcf", force=True) self.assertTrue(os.path.exists(fn + ".gz" + ".tbi")) self.assertEqual(read_index_header(fn + ".gz.tbi"), b"TBI\1") self.assertFalse(os.path.exists(fn + ".gz" + ".csi")) with pysam.VariantFile(fn + ".gz") as inf: self.assertEqual(len(list(inf.fetch("20"))), 3) def test_vcf_with_csi_index(self): with get_temp_context("tmp_fn.vcf") as fn: shutil.copyfile(self.vcf_filename, fn) pysam.tabix_index(fn, preset="vcf", force=True, csi=True) self.assertTrue(os.path.exists(fn + ".gz" + ".csi")) self.assertEqual(read_index_header(fn + ".gz.csi"), b"CSI\1") self.assertFalse(os.path.exists(fn + ".gz" + ".tbi")) with pysam.VariantFile(fn + ".gz") as inf: self.assertEqual(len(list(inf.fetch("20"))), 3) def test_bcf_with_prebuilt_csi(self): with get_temp_context("tmp_fn.bcf") as fn: shutil.copyfile(self.bcf_filename, fn) shutil.copyfile(self.bcf_filename + ".csi", fn + ".csi") self.assertTrue(os.path.exists(fn + ".csi")) self.assertEqual(read_index_header(fn + ".csi"), b"CSI\1") self.assertFalse(os.path.exists(fn + ".tbi")) with pysam.VariantFile(fn) as inf: self.assertEqual(len(list(inf.fetch("20"))), 3) def test_bcf_with_tbi_index_will_produce_csi(self): with get_temp_context("tmp_fn.bcf") as fn: shutil.copyfile(self.bcf_filename, fn) pysam.tabix_index(fn, preset="bcf", force=True, csi=False) self.assertTrue(os.path.exists(fn + ".csi")) self.assertEqual(read_index_header(fn + ".csi"), b"CSI\1") self.assertFalse(os.path.exists(fn + ".tbi")) with pysam.VariantFile(fn) as inf: self.assertEqual(len(list(inf.fetch("20"))), 3) def test_bcf_with_csi_index(self): with get_temp_context("tmp_fn.bcf") as fn: shutil.copyfile(self.bcf_filename, fn) pysam.tabix_index(fn, preset="vcf", force=True, csi=True) self.assertTrue(os.path.exists(fn + ".csi")) self.assertEqual(read_index_header(fn + ".csi"), b"CSI\1") self.assertFalse(os.path.exists(fn + ".tbi")) with pysam.VariantFile(fn) as inf: self.assertEqual(len(list(inf.fetch("20"))), 3) class TestHeader(unittest.TestCase): filename = "example_vcf40.vcf" def testStr(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) ref = read_header(fn) comp = str(v.header).splitlines(True) self.assertEqual(sorted(ref), sorted(comp)) def testIterator(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) ref = read_header(fn) # remove last header line starting with #CHROM ref.pop() ref = sorted(ref) comp = sorted(str(x) for x in v.header.records) self.assertEqual(len(ref), len(comp)) for x, y in zip(ref, comp): self.assertEqual(x, y) # These tests need to be separate and start from newly opened files. This # is because htslib's parser is lazy and the pysam API needs to trigger # appropriate parsing when accessing each time of data. Failure to do so # will result in crashes or return of incorrect data. Thus this test suite # is testing both the triggering of the lazy parser and the results of the # parser. class TestParsing(unittest.TestCase): filename = "example_vcf40.vcf.gz" def testChrom(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) chrom = [rec.chrom for rec in v] self.assertEqual(chrom, ['M', '17', '20', '20', '20']) def testChromFromPath(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(Path(fn)) chrom = [rec.chrom for rec in v] self.assertEqual(chrom, ['M', '17', '20', '20', '20']) def testPos(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) pos = [rec.pos for rec in v] self.assertEqual(pos, [1230237, 14370, 17330, 1110696, 1234567]) def testStart(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) start = [rec.start for rec in v] self.assertEqual(start, [1230236, 14369, 17329, 1110695, 1234566]) def testStop(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) stop = [rec.stop for rec in v] self.assertEqual(stop, [1230237, 14370, 17330, 1110696, 1234570]) def testId(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) ids = [rec.id for rec in v] self.assertEqual( ids, [None, 'rs6054257', None, 'rs6040355', 'microsat1']) def testRef(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) ref = [rec.ref for rec in v] self.assertEqual(ref, ['T', 'G', 'T', 'A', 'GTCT']) def testAlt(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) alts = [rec.alts for rec in v] self.assertEqual(alts, [None, ('A',), ('A',), ('G', 'T'), ('G', 'GTACT')]) def testAlleles(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) alleles = [rec.alleles for rec in v] self.assertEqual(alleles, [ ('T',), ('G', 'A'), ('T', 'A'), ('A', 'G', 'T'), ('GTCT', 'G', 'GTACT')]) def testAllelesVariantTypes(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) rec = next(v) self.assertEqual(rec.alleles, ('T',)) self.assertEqual(rec.alleles_variant_types, ("REF",)) rec.alleles = ("T", "C") self.assertEqual(rec.alleles_variant_types, ("REF", "SNP")) rec.alts = ("TC",) self.assertEqual(rec.alleles_variant_types, ("REF", "INDEL")) rec.ref = "AG" self.assertEqual(rec.alleles_variant_types, ("REF", "MNP")) def testQual(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) qual = [rec.qual for rec in v] self.assertEqual(qual, [47.0, 29.0, 3.0, 67.0, 50.0]) def testFilter(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) filter = [rec.filter.keys() for rec in v] self.assertEqual(filter, [['PASS'], ['PASS'], ['q10'], ['PASS'], ['PASS']]) def testInfo(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) info = [rec.info.items() for rec in v] self.assertEqual(info, [[('NS', 3), ('DP', 13), ('AA', 'T')], [('NS', 3), ('DP', 14), ('AF', (0.5,)), ('DB', True), ('H2', True)], [('NS', 3), ('DP', 11), ('AF', (0.017000000923871994,))], [('NS', 2), ('DP', 10), ('AF', (0.3330000042915344, 0.6669999957084656)), ('AA', 'T'), ('DB', True)], [('NS', 3), ('DP', 9), ('AA', 'G')]]) def testFormat(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) format = [rec.format.keys() for rec in v] self.assertEqual(format, [['GT', 'GQ', 'DP', 'HQ'], ['GT', 'GQ', 'DP', 'HQ'], ['GT', 'GQ', 'DP', 'HQ'], ['GT', 'GQ', 'DP', 'HQ'], ['GT', 'GQ', 'DP']]) def testSampleAlleles(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) alleles = [s.alleles for rec in v for s in rec.samples.values()] self.assertEqual(alleles, [('T', 'T'), ('T', 'T'), ('T', 'T'), ('G', 'G'), ('A', 'G'), ('A', 'A'), ('T', 'T'), ('T', 'A'), ('T', 'T'), ('G', 'T'), ('T', 'G'), ('T', 'T'), ('GTCT', 'G'), ('GTCT', 'GTACT'), ('G', 'G')]) def testSampleFormats(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) format = [s.items() for rec in v for s in rec.samples.values()] self.assertEqual(format, [[('GT', (0, 0)), ('GQ', 54), ('DP', 7), ('HQ', (56, 60))], [('GT', (0, 0)), ('GQ', 48), ('DP', 4), ('HQ', (51, 51))], [('GT', (0, 0)), ('GQ', 61), ('DP', 2), ('HQ', (None,))], [('GT', (0, 0)), ('GQ', 48), ('DP', 1), ('HQ', (51, 51))], [('GT', (1, 0)), ('GQ', 48), ('DP', 8), ('HQ', (51, 51))], [('GT', (1, 1)), ('GQ', 43), ('DP', 5), ('HQ', (None, None))], [('GT', (0, 0)), ('GQ', 49), ('DP', 3), ('HQ', (58, 50))], [('GT', (0, 1)), ('GQ', 3), ('DP', 5), ('HQ', (65, 3))], [('GT', (0, 0)), ('GQ', 41), ('DP', 3), ('HQ', (None,))], [('GT', (1, 2)), ('GQ', 21), ('DP', 6), ('HQ', (23, 27))], [('GT', (2, 1)), ('GQ', 2), ('DP', 0), ('HQ', (18, 2))], [('GT', (2, 2)), ('GQ', 35), ('DP', 4), ('HQ', (None,))], [('GT', (0, 1)), ('GQ', 35), ('DP', 4)], [('GT', (0, 2)), ('GQ', 17), ('DP', 2)], [('GT', (1, 1)), ('GQ', 40), ('DP', 3)]]) def testSampleAlleleIndices(self): fn = os.path.join(CBCF_DATADIR, self.filename) v = pysam.VariantFile(fn) indices = [s.allele_indices for rec in v for s in rec.samples.values()] self.assertEqual(indices, [(0, 0), (0, 0), (0, 0), (0, 0), (1, 0), (1, 1), (0, 0), (0, 1), (0, 0), (1, 2), (2, 1), (2, 2), (0, 1), (0, 2), (1, 1)]) class TestIndexFilename(unittest.TestCase): filenames = [('example_vcf40.vcf.gz', 'example_vcf40.vcf.gz.tbi'), ('example_vcf40.vcf.gz', 'example_vcf40.vcf.gz.csi'), ('example_vcf40.bcf', 'example_vcf40.bcf.csi')] def testOpen(self): for fn, idx_fn in self.filenames: fn = os.path.join(CBCF_DATADIR, fn) idx_fn = os.path.join(CBCF_DATADIR, idx_fn) with pysam.VariantFile(fn, index_filename=idx_fn) as inf: self.assertEqual(len(list(inf.fetch('20'))), 3) class TestConstructionVCFWithContigs(unittest.TestCase): """construct VariantFile from scratch.""" filename = "example_vcf42_withcontigs.vcf" compression = 'NONE' description = 'VCF version 4.2 variant calling text' def testBase(self): with pysam.VariantFile(os.path.join(CBCF_DATADIR, self.filename)) as inf: self.assertEqual(inf.category, 'VARIANTS') self.assertEqual(inf.format, 'VCF') self.assertEqual(inf.version, (4, 2)) self.assertEqual(inf.compression, self.compression) self.assertEqual(inf.description, self.description) self.assertTrue(inf.is_open) self.assertEqual(inf.is_read, True) self.assertEqual(inf.is_write, False) def complete_check(self, fn_in, fn_out): self.maxDiff = None check_lines_equal( self, fn_in, fn_out, sort=True, filter_f=lambda x: x.startswith("##contig")) os.unlink(fn_out) def testConstructionWithRecords(self): fn_in = os.path.join(CBCF_DATADIR, self.filename) fn_out = get_temp_filename(suffix=".vcf") vcf_in = pysam.VariantFile(fn_in) header = pysam.VariantHeader() for record in vcf_in.header.records: header.add_record(record) for sample in vcf_in.header.samples: header.add_sample(sample) vcf_out = pysam.VariantFile(fn_out, "w", header=header) for record in vcf_in: record.translate(header) vcf_out.write(record) vcf_in.close() vcf_out.close() self.complete_check(fn_in, fn_out) def testConstructionFromCopy(self): fn_in = os.path.join(CBCF_DATADIR, self.filename) fn_out = get_temp_filename(suffix=".vcf") vcf_in = pysam.VariantFile(fn_in) vcf_out = pysam.VariantFile(fn_out, "w", header=vcf_in.header) for record in vcf_in: vcf_out.write(record) vcf_in.close() vcf_out.close() self.complete_check(fn_in, fn_out) def testConstructionWithLines(self): fn_in = os.path.join(CBCF_DATADIR, self.filename) fn_out = get_temp_filename(suffix=".vcf") vcf_in = pysam.VariantFile(fn_in) header = pysam.VariantHeader() header.add_samples(vcf_in.header.samples) for hr in vcf_in.header.records: header.add_line(str(hr)) vcf_out = pysam.VariantFile(fn_out, "w", header=header) for record in vcf_in: vcf_out.write(record) vcf_out.close() vcf_in.close() self.complete_check(fn_in, fn_out) # class TestConstructionVCFWithoutContigs(TestConstructionVCFWithContigs): # """construct VariantFile from scratch.""" # filename = "example_vcf40.vcf" class TestConstructionVCFGZWithContigs(TestConstructionVCFWithContigs): """construct VariantFile from scratch.""" filename = "example_vcf42_withcontigs.vcf.gz" compression = 'BGZF' description = 'VCF version 4.2 BGZF-compressed variant calling data' class TestConstructionVCFGZWithoutContigs(TestConstructionVCFWithContigs): """construct VariantFile from scratch.""" filename = "example_vcf42.vcf.gz" compression = 'BGZF' description = 'VCF version 4.2 BGZF-compressed variant calling data' class TestSettingRecordValues(unittest.TestCase): filename = "example_vcf40.vcf" def testBase(self): with pysam.VariantFile(os.path.join(CBCF_DATADIR, self.filename)) as inf: self.assertEqual(inf.category, 'VARIANTS') self.assertEqual(inf.format, 'VCF') self.assertEqual(inf.version, (4, 0)) self.assertEqual(inf.compression, 'NONE') self.assertEqual( inf.description, 'VCF version 4.0 variant calling text') self.assertTrue(inf.is_open) self.assertEqual(inf.is_read, True) self.assertEqual(inf.is_write, False) def testSetQual(self): with pysam.VariantFile(os.path.join(CBCF_DATADIR, self.filename)) as inf: record = next(inf) self.assertEqual(record.qual, 47) record.qual = record.qual self.assertEqual(record.qual, 47) record.qual = 10 self.assertEqual(record.qual, 10) self.assertEqual(str(record).split("\t")[5], "10") def testGenotype(self): with pysam.VariantFile(os.path.join(CBCF_DATADIR, self.filename)) as inf: record = next(inf) sample = record.samples["NA00001"] print(sample["GT"]) self.assertEqual(sample["GT"], (0, 0)) sample["GT"] = sample["GT"] class TestMultiThreading(unittest.TestCase): filename = os.path.join(CBCF_DATADIR, "example_vcf42.vcf.gz") def testSingleThreadEqualsMultithreadResult(self): with pysam.VariantFile(self.filename) as inf: header = inf.header single = [r for r in inf] with pysam.VariantFile(self.filename, threads=2) as inf: multi = [r for r in inf] for r1, r2 in zip(single, multi): assert str(r1) == str(r2) bcf_out = get_temp_filename(suffix=".bcf") with pysam.VariantFile(bcf_out, mode='wb', header=header, threads=2) as out: for r in single: out.write(r) with pysam.VariantFile(bcf_out) as inf: multi_out = [r for r in inf] for r1, r2 in zip(single, multi_out): assert str(r1) == str(r2) def testNoMultiThreadingWithIgnoreTruncation(self): with self.assertRaises(ValueError): pysam.VariantFile(self.filename, threads=2, ignore_truncation=True) class TestSubsetting(unittest.TestCase): filename = "example_vcf42.vcf.gz" def testSubsetting(self): with pysam.VariantFile(os.path.join(CBCF_DATADIR, self.filename)) as inf: inf.subset_samples(["NA00001"]) class TestVCFVersions(unittest.TestCase): def setUp(self): self.files_to_test = (glob.glob(os.path.join(CBCF_DATADIR, "example_v*.vcf.gz")) + glob.glob(os.path.join(CBCF_DATADIR, "example_v*.vcf")) + glob.glob(os.path.join(CBCF_DATADIR, "example_v*.bcf"))) def test_all_records_can_be_fetched(self): for fn in self.files_to_test: with pysam.VariantFile(fn) as inf: records = list(inf.fetch()) class TestUnicode(unittest.TestCase): filename = "example_vcf43_with_utf8.vcf.gz" def test_record_with_unicode(self): with pysam.VariantFile(os.path.join(CBCF_DATADIR, self.filename)) as inf: records = list(inf.fetch("20", 2345677, 2345678)) self.assertEqual(len(records), 1) record = records.pop() self.assertEqual( record.info["CLNVI"], ('Institute_of_Human_Genetics', u'Friedrich-Alexander-Universität_Erlangen-Nürnberg')) self.assertEqual(record.samples[0]["AN"], "alpha") self.assertEqual(record.samples[1]["AN"], u"ä") self.assertEqual(record.samples[2]["AN"], u"ü") if __name__ == "__main__": print("starting tests") unittest.main() print("completed tests") pysam-0.23.0/tests/VariantRecord_test.py000066400000000000000000000073201475062545500202620ustar00rootroot00000000000000import pysam import pytest from TestUtils import make_data_files, CBCF_DATADIR def setUpModule(): make_data_files(CBCF_DATADIR) @pytest.fixture def vcf_header(): vcf_header = pysam.VariantHeader() vcf_header.add_samples("sample1", "sample2") vcf_header.contigs.add("1") return vcf_header ## segfault without coordinates def test_ascii_annotation_can_be_added(vcf_header): vcf_header.formats.add("AN", 1, "String", "An annotation") record = vcf_header.new_record( contig="1", start=12, stop=13, samples=[ {"AN": "anno1"}, {"AN": "anno2"}]) assert str(record)[:-1].split("\t")[-2:] == ["anno1", "anno2"] def test_ascii_annotation_with_variable_length_can_be_added(vcf_header): vcf_header.formats.add("AN", 1, "String", "An annotation") record = vcf_header.new_record( contig="1", start=12, stop=13, samples=[ {"AN": "anno1b"}, {"AN": "anno1"}]) assert str(record)[:-1].split("\t")[-2:] == ["anno1b", "anno1"] record = vcf_header.new_record( contig="1", start=12, stop=13, samples=[ {"AN": "anno2"}, {"AN": "anno2b"}]) assert str(record)[:-1].split("\t")[-2:] == ["anno2", "anno2b"] def test_unicode_annotation_can_be_added(vcf_header): vcf_header.formats.add("AN", 1, "String", "An annotation") record = vcf_header.new_record( contig="1", start=12, stop=13, samples=[ {"AN": "anno1"}, {"AN": "Friedrich-Alexander-Universit\u00E4t_Erlangen-N\u00FCrnberg"}]) assert str(record)[:-1].split("\t")[-2:] == [ "anno1", "Friedrich-Alexander-Universit\u00E4t_Erlangen-N\u00FCrnberg"] def test_set_sample_alleles(vcf_header): vcf_header.formats.add('GT',1,'String',"Genotype") # id, number, type, description record = vcf_header.new_record( contig="1", start=20, stop=21, alleles=('A','T') ) record.samples['sample1'].alleles = ('T', 'A') assert record.samples['sample1'].alleles == ('T','A') # Empty record: record.samples['sample1'].alleles = (None, ) assert record.samples['sample1'].alleles == tuple() record.samples['sample1'].alleles = None assert record.samples['sample1'].alleles == tuple() record.samples['sample1'].alleles = tuple() assert record.samples['sample1'].alleles == tuple() # check error conditions: with pytest.raises(ValueError, match='One or more of the supplied sample alleles are not defined'): record.samples['sample1'].alleles = ('C', 'A') with pytest.raises(ValueError, match='Use .allele_indices to set integer allele indices'): record.samples['sample1'].alleles = (1, 0) def test_repeated_new_record(vcf_header): vcf_header.formats.add('GT', 1, 'String', "Genotype") vcf_header.formats.add("AA", 1, "String", "An annotation") vcf_header.formats.add("BB", 1, "String", "Another annotation") data = {'id': 'INS_1', 'contig': '1', 'start': 10, 'stop': 15, 'alleles': ['A', 'TCGA'], 'samples': [{'AA': ('one'), 'GT': (0, 1), 'BB': ('two')}, {'GT': (1, 0), 'BB': ('three')}]} record1 = vcf_header.new_record(**data) assert '\tGT:' in str(record1) # Verify that GT is output first assert record1.samples['sample1'].alleles == ('A', 'TCGA') assert record1.samples['sample2'].alleles == ('TCGA', 'A') record2 = vcf_header.new_record(**data) assert '\tGT:' in str(record2) # Verify that GT is actually emitted and is output first assert record2.samples['sample1'].alleles == ('A', 'TCGA') assert record2.samples['sample2'].alleles == ('TCGA', 'A') pysam-0.23.0/tests/_compile_test.pyx000066400000000000000000000012071475062545500174740ustar00rootroot00000000000000# cython: language_level=3 from pysam.libcalignmentfile cimport AlignmentFile, AlignedSegment from pysam.libctabix cimport Tabixfile cdef AlignmentFile samfile cdef Tabixfile tabixfile def testCountBAM(AlignmentFile samfile): '''test reading from a BAM file accessing the flag field directly.''' cdef AlignedSegment read cdef int n = 0 for read in samfile.fetch(): flag = read._delegate.core.flag n += 1 return n def testCountGTF(Tabixfile tabixfile): '''test reading from a tabixfile.''' cdef int n = 0 for entry in tabixfile.fetch(): n += 1 return n pysam-0.23.0/tests/_compile_test.pyxbld000066400000000000000000000004771475062545500201660ustar00rootroot00000000000000# link against pysam def make_ext(modname, pyxfilename): from distutils.extension import Extension import pysam return Extension(name = modname, sources = [pyxfilename], include_dirs = pysam.get_include(), define_macros = pysam.get_defines()) pysam-0.23.0/tests/_cython_flagstat.pyx000066400000000000000000000010651475062545500202000ustar00rootroot00000000000000# cython: language_level=3 from pysam.libcalignmentfile cimport AlignmentFile, AlignedSegment from pysam.libcalignmentfile cimport BAM_FPROPER_PAIR, BAM_FPAIRED from pysam.libcalignedsegment cimport pysam_get_flag def count(AlignmentFile samfile): cdef int is_proper = 0 cdef int is_paired = 0 cdef AlignedSegment read cdef int f for read in samfile: f = pysam_get_flag(read._delegate) if f & BAM_FPAIRED: is_paired += 1 if f & BAM_FPROPER_PAIR: is_proper += 1 return is_paired, is_proper pysam-0.23.0/tests/_cython_flagstat.pyxbld000066400000000000000000000005351475062545500206630ustar00rootroot00000000000000def make_ext(modname, pyxfilename): from distutils.extension import Extension import pysam return Extension(name=modname, sources=[pyxfilename], extra_link_args=pysam.get_libraries(), include_dirs=pysam.get_include(), define_macros=pysam.get_defines()) pysam-0.23.0/tests/cbcf_data/000077500000000000000000000000001475062545500157725ustar00rootroot00000000000000pysam-0.23.0/tests/cbcf_data/Makefile000066400000000000000000000007331475062545500174350ustar00rootroot00000000000000ALL_VCF=$(wildcard *.vcf) VCF=$(filter-out example_empty.vcf,$(ALL_VCF)) VCFGZ=$(VCF:%.vcf=%.vcf.gz) BCF=$(VCF:%.vcf=%.bcf) all: all.stamp all.stamp: $(VCFGZ) $(BCF) touch $@ %.vcf.gz: %.vcf bgzip < $< > $@ tabix -f -p vcf $@ # create tbi index bcftools index -f $@ # create csi index %.bcf: %.vcf.gz bcftools view -O b $< -o $@ bcftools index -f $@ example_empty.bcf: example_empty.vcf.gz touch $@ clean: -rm -rf all.lock all.stamp *.gz *.tbi *.csi *.bcf pysam-0.23.0/tests/cbcf_data/example_empty.vcf000066400000000000000000000000001475062545500213310ustar00rootroot00000000000000pysam-0.23.0/tests/cbcf_data/example_vcf40.vcf000066400000000000000000000030201475062545500211220ustar00rootroot00000000000000##fileformat=VCFv4.0 ##fileDate=20090805 ##source=myImputationProgramV3.1 ##reference=1000GenomesPilot-NCBI36 ##phasing=partial ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 M 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 17 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 20 1234567 microsat1 GTCT G,GTACT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 pysam-0.23.0/tests/cbcf_data/example_vcf42.vcf000066400000000000000000000030261475062545500211320ustar00rootroot00000000000000##fileformat=VCFv4.2 ##fileDate=20090805 ##source=myImputationProgramV3.1 ##reference=1000GenomesPilot-NCBI36 ##phasing=partial ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 M 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2:. 17 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:. 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:. 20 1234567 microsat1 GTCT G,GTACT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 pysam-0.23.0/tests/cbcf_data/example_vcf42_only_header.vcf000066400000000000000000000020321475062545500234770ustar00rootroot00000000000000##fileformat=VCFv4.2 ##fileDate=20090805 ##source=myImputationProgramV3.1 ##reference=1000GenomesPilot-NCBI36 ##phasing=partial ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 pysam-0.23.0/tests/cbcf_data/example_vcf42_withcontigs.vcf000066400000000000000000000031101475062545500235460ustar00rootroot00000000000000##fileformat=VCFv4.2 ##fileDate=20090805 ##source=myImputationProgramV3.1 ##reference=1000GenomesPilot-NCBI36 ##phasing=partial ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##contig= ##contig= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 M 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2:. 17 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:. 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:. 20 1234567 microsat1 GTCT G,GTACT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 pysam-0.23.0/tests/cbcf_data/example_vcf43.vcf000066400000000000000000000031551475062545500211360ustar00rootroot00000000000000##fileformat=VCFv4.3 ##fileDate=20090805 ##source=myImputationProgramV3.1 ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta ##contig= ##phasing=partial ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 pysam-0.23.0/tests/cbcf_data/example_vcf43_with_utf8.vcf000066400000000000000000000040251475062545500231340ustar00rootroot00000000000000##fileformat=VCFv4.3 ##fileDate=20090805 ##source=myImputationProgramV3.1 ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta ##contig= ##phasing=partial ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 20 2345678 rs123 G A 29 PASS NS=3;DP=14;AF=0.5;CLNVI=Institute_of_Human_Genetics,Friedrich-Alexander-Universität_Erlangen-Nürnberg;DB;H2 GT:GQ:DP:HQ:AN 0|0:48:1:51,51:alpha 1|0:48:8:51,51:ä 1/1:43:5:.,.:ü pysam-0.23.0/tests/cbcf_data/gnomad.vcf000066400000000000000000000766661475062545500177640ustar00rootroot00000000000000##fileformat=VCFv4.2 ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FILTER= ##FILTER== 20, DP >= 10, AB => 0.2 for het calls))"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta #CHROM POS ID REF ALT QUAL FILTER INFO 22 16050036 rs374742143 A C 442156.34 RF AC=67;AF=4.29487e-01;AN=156;BaseQRankSum=7.36000e-01;ClippingRankSum=2.96000e-01;DB;DP=50165;FS=7.05600e+00;InbreedingCoeff=3.82000e-01;MQ=2.71500e+01;MQRankSum=-1.02600e+00;QD=2.47500e+01;ReadPosRankSum=-2.11000e-01;SOR=1.26750e+01;VQSLOD=-9.58600e+02;VQSR_culprit=MQ;GQ_HIST_ALT=16|1279|299|254|155|24|16|28|50|135|78|4|6|11|32|43|6|4|3|35;DP_HIST_ALT=1769|653|51|5|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|2|5|24|36|11|89|2|125|31|61|85|24|60|34|8|3|7;GQ_HIST_ALL=2359|2810|730|651|296|51|34|33|53|135|78|4|6|11|32|43|6|4|3|35;DP_HIST_ALL=5518|1756|94|6|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|2|5|24|36|11|89|2|125|31|61|85|24|60|34|8|3|7;AC_AFR=3;AC_AMR=7;AC_ASJ=0;AC_EAS=0;AC_FIN=50;AC_NFE=3;AC_OTH=4;AC_Male=32;AC_Female=35;AN_AFR=14;AN_AMR=10;AN_ASJ=0;AN_EAS=0;AN_FIN=84;AN_NFE=42;AN_OTH=6;AN_Male=80;AN_Female=76;AF_AFR=2.14286e-01;AF_AMR=7.00000e-01;AF_ASJ=.;AF_EAS=.;AF_FIN=5.95238e-01;AF_NFE=7.14286e-02;AF_OTH=6.66667e-01;AF_Male=4.00000e-01;AF_Female=4.60526e-01;GC_AFR=4,3,0;GC_AMR=0,3,2;GC_ASJ=0,0,0;GC_EAS=0,0,0;GC_FIN=4,26,12;GC_NFE=18,3,0;GC_OTH=1,0,2;GC_Male=16,16,8;GC_Female=11,19,8;AC_raw=4349;AN_raw=14748;AF_raw=2.94887e-01;GC_raw=4896,607,1871;GC=27,35,16;Hom_AFR=0;Hom_AMR=2;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=12;Hom_NFE=0;Hom_OTH=2;Hom_Male=8;Hom_Female=8;Hom_raw=1871;Hom=16;POPMAX=AMR;AC_POPMAX=7;AN_POPMAX=10;AF_POPMAX=7.00000e-01;DP_MEDIAN=3;DREF_MEDIAN=5.60406e-10;GQ_MEDIAN=12;AB_MEDIAN=5.55556e-01;AS_RF=4.71609e-02;AS_FilterStatus=RF;CSQ=C|intergenic_variant|MODIFIER|||||||||||||||rs374742143|1||||SNV|1|||||||||||||||||||||||||||||||||||||||||||| 22 16050068 . A G 82.46 RF;AC0 AC=0;AF=0.00000e+00;AN=2708;DP=111486;FS=0.00000e+00;InbreedingCoeff=-3.63000e-02;MQ=3.20200e+01;QD=1.64900e+01;SOR=3.61100e+00;VQSLOD=-9.28900e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;DP_HIST_ALT=0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST_ALL=1227|4189|2184|3537|2071|618|693|346|97|92|61|9|18|0|7|4|4|0|0|0;DP_HIST_ALL=7502|6289|1163|169|26|8|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=0;AC_OTH=0;AC_Male=0;AC_Female=0;AN_AFR=280;AN_AMR=162;AN_ASJ=34;AN_EAS=74;AN_FIN=748;AN_NFE=1300;AN_OTH=110;AN_Male=1584;AN_Female=1124;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=0.00000e+00;AF_OTH=0.00000e+00;AF_Male=0.00000e+00;AF_Female=0.00000e+00;GC_AFR=140,0,0;GC_AMR=81,0,0;GC_ASJ=17,0,0;GC_EAS=37,0,0;GC_FIN=374,0,0;GC_NFE=650,0,0;GC_OTH=55,0,0;GC_Male=792,0,0;GC_Female=562,0,0;AC_raw=2;AN_raw=30314;AF_raw=6.59761e-05;GC_raw=15156,0,1;GC=1354,0,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=1;Hom=0;POPMAX=.;AC_POPMAX=.;AN_POPMAX=.;AF_POPMAX=.;DP_MEDIAN=5;DREF_MEDIAN=1.22034e-16;GQ_MEDIAN=15;AB_MEDIAN=5.00000e-01;AS_RF=5.87186e-02;AS_FilterStatus=RF|AC0;CSQ=G|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1|||||||||||||||||||||||||||||||||||||||||||| 22 16050069 . C T 43.44 RF;AC0 AC=0;AF=0.00000e+00;AN=2802;BaseQRankSum=7.20000e-01;ClippingRankSum=-1.38000e+00;DP=112972;FS=0.00000e+00;InbreedingCoeff=-3.70000e-02;MQ=3.67700e+01;MQRankSum=7.20000e-01;QD=7.24000e+00;ReadPosRankSum=1.38000e+00;SOR=1.32900e+00;VQSLOD=-3.27400e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0;DP_HIST_ALT=0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0;GQ_HIST_ALL=1200|4098|2219|3540|2117|622|710|352|104|101|64|10|20|1|8|3|4|0|0|0;DP_HIST_ALL=7405|6348|1203|181|28|8|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=0;AC_OTH=0;AC_Male=0;AC_Female=0;AN_AFR=296;AN_AMR=164;AN_ASJ=36;AN_EAS=70;AN_FIN=766;AN_NFE=1354;AN_OTH=116;AN_Male=1638;AN_Female=1164;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=0.00000e+00;AF_OTH=0.00000e+00;AF_Male=0.00000e+00;AF_Female=0.00000e+00;GC_AFR=148,0,0;GC_AMR=82,0,0;GC_ASJ=18,0,0;GC_EAS=35,0,0;GC_FIN=383,0,0;GC_NFE=677,0,0;GC_OTH=58,0,0;GC_Male=819,0,0;GC_Female=582,0,0;AC_raw=1;AN_raw=30346;AF_raw=3.29533e-05;GC_raw=15172,1,0;GC=1401,0,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=0;Hom=0;POPMAX=.;AC_POPMAX=.;AN_POPMAX=.;AF_POPMAX=.;DP_MEDIAN=6;DREF_MEDIAN=3.16178e-11;GQ_MEDIAN=38;AB_MEDIAN=6.66667e-01;AS_RF=9.22976e-02;AS_FilterStatus=RF|AC0;CSQ=T|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1|||||||||||||||||||||||||||||||||||||||||||| 22 16050098 . G A 242.82 RF AC=2;AF=2.40964e-04;AN=8300;BaseQRankSum=2.45000e+00;ClippingRankSum=1.03000e-01;DP=167171;FS=0.00000e+00;InbreedingCoeff=-1.46000e-02;MQ=3.06100e+01;MQRankSum=-9.35000e-01;QD=1.05600e+01;ReadPosRankSum=6.60000e-01;SOR=3.84000e-01;VQSLOD=-4.11500e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2;DP_HIST_ALT=0|0|2|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|1|1|0|0|0|0|0|0|0|0|0;GQ_HIST_ALL=350|1697|1483|3462|3106|1262|1746|994|348|436|237|88|141|14|39|5|22|4|8|7;DP_HIST_ALL=3368|7876|3165|776|212|33|16|3|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|1|1|0|0|0|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=2;AC_OTH=0;AC_Male=2;AC_Female=0;AN_AFR=1298;AN_AMR=334;AN_ASJ=84;AN_EAS=380;AN_FIN=1460;AN_NFE=4412;AN_OTH=332;AN_Male=4748;AN_Female=3552;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=4.53309e-04;AF_OTH=0.00000e+00;AF_Male=4.21230e-04;AF_Female=0.00000e+00;GC_AFR=649,0,0;GC_AMR=167,0,0;GC_ASJ=42,0,0;GC_EAS=190,0,0;GC_FIN=730,0,0;GC_NFE=2204,2,0;GC_OTH=166,0,0;GC_Male=2372,2,0;GC_Female=1776,0,0;AC_raw=2;AN_raw=30898;AF_raw=6.47291e-05;GC_raw=15447,2,0;GC=4148,2,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=0;Hom=0;POPMAX=NFE;AC_POPMAX=2;AN_POPMAX=4412;AF_POPMAX=4.53309e-04;DP_MEDIAN=11;DREF_MEDIAN=6.29479e-16;GQ_MEDIAN=99;AB_MEDIAN=4.80769e-01;AS_RF=3.30908e-01;AS_FilterStatus=RF;CSQ=A|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1|||||||||||||||||||||||||||||||||||||||||||| 22 16050115 rs587755077 G A 10684.53 RF AC=31;AF=2.54057e-03;AN=12202;BaseQRankSum=1.59000e+00;ClippingRankSum=6.70000e-02;DP=196906;FS=0.00000e+00;InbreedingCoeff=1.40000e-02;MQ=3.37700e+01;MQRankSum=4.06000e-01;QD=8.23000e+00;ReadPosRankSum=3.22000e-01;SOR=4.23100e+00;VQSLOD=-1.16300e+02;VQSR_culprit=MQ;GQ_HIST_ALT=3|6|10|5|3|3|6|13|17|16|2|3|9|12|8|11|5|3|3|14;DP_HIST_ALT=22|95|32|3|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|4|6|16|20|8|21|1|28|5|7|7|7|7|8|0|0|0;GQ_HIST_ALL=237|959|984|2740|3098|1328|2215|1483|527|685|442|163|289|52|79|25|61|6|27|39;DP_HIST_ALL=1972|7287|4327|1314|407|79|44|9|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|4|6|16|20|8|21|1|28|5|7|7|7|7|8|0|0|0;AC_AFR=30;AC_AMR=1;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=0;AC_OTH=0;AC_Male=16;AC_Female=15;AN_AFR=2236;AN_AMR=436;AN_ASJ=144;AN_EAS=640;AN_FIN=1862;AN_NFE=6410;AN_OTH=474;AN_Male=6874;AN_Female=5328;AF_AFR=1.34168e-02;AF_AMR=2.29358e-03;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=0.00000e+00;AF_OTH=0.00000e+00;AF_Male=2.32761e-03;AF_Female=2.81532e-03;GC_AFR=1088,30,0;GC_AMR=217,1,0;GC_ASJ=72,0,0;GC_EAS=320,0,0;GC_FIN=931,0,0;GC_NFE=3205,0,0;GC_OTH=237,0,0;GC_Male=3421,16,0;GC_Female=2649,15,0;AC_raw=159;AN_raw=30878;AF_raw=5.14930e-03;GC_raw=15287,145,7;GC=6070,31,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=7;Hom=0;POPMAX=AFR;AC_POPMAX=30;AN_POPMAX=2236;AF_POPMAX=1.34168e-02;DP_MEDIAN=7;DREF_MEDIAN=1.74246e-08;GQ_MEDIAN=48;AB_MEDIAN=4.44444e-01;AS_RF=5.02621e-02;AS_FilterStatus=RF;CSQ=A|intergenic_variant|MODIFIER|||||||||||||||rs587755077|1||||SNV|1||||||||||||||||A:0.0064|||||||||||||||||||||||||||| 22 16050116 . G C 28395.88 RF AC=246;AF=2.51431e-02;AN=9784;BaseQRankSum=2.48000e-01;ClippingRankSum=0.00000e+00;DP=201089;FS=0.00000e+00;InbreedingCoeff=-7.09000e-02;MQ=3.23400e+01;MQRankSum=-1.23100e+00;QD=3.27000e+00;ReadPosRankSum=2.48000e-01;SOR=7.16400e+00;VQSLOD=-3.11400e+02;VQSR_culprit=MQ;GQ_HIST_ALT=0|3|6|9|32|41|110|119|73|75|49|48|27|32|38|16|4|9|19|27;DP_HIST_ALT=21|356|285|60|12|3|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|11|105|184|174|98|40|64|2|30|5|11|8|2|2|0|0|0|0;GQ_HIST_ALL=2616|992|935|2244|2407|1109|1723|1219|458|593|382|175|259|62|105|27|46|11|38|55;DP_HIST_ALL=1838|7215|4403|1404|443|92|50|11|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|11|105|184|174|98|40|64|2|30|5|11|8|2|2|0|0|0|0;AC_AFR=18;AC_AMR=5;AC_ASJ=4;AC_EAS=3;AC_FIN=5;AC_NFE=202;AC_OTH=9;AC_Male=141;AC_Female=105;AN_AFR=2166;AN_AMR=402;AN_ASJ=88;AN_EAS=650;AN_FIN=1722;AN_NFE=4390;AN_OTH=366;AN_Male=5450;AN_Female=4334;AF_AFR=8.31025e-03;AF_AMR=1.24378e-02;AF_ASJ=4.54545e-02;AF_EAS=4.61538e-03;AF_FIN=2.90360e-03;AF_NFE=4.60137e-02;AF_OTH=2.45902e-02;AF_Male=2.58716e-02;AF_Female=2.42270e-02;GC_AFR=1065,18,0;GC_AMR=196,5,0;GC_ASJ=40,4,0;GC_EAS=322,3,0;GC_FIN=856,5,0;GC_NFE=1993,202,0;GC_OTH=174,9,0;GC_Male=2584,141,0;GC_Female=2062,105,0;AC_raw=738;AN_raw=30912;AF_raw=2.38742e-02;GC_raw=14719,736,1;GC=4646,246,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=1;Hom=0;POPMAX=NFE;AC_POPMAX=202;AN_POPMAX=4390;AF_POPMAX=4.60137e-02;DP_MEDIAN=9;DREF_MEDIAN=6.30918e-05;GQ_MEDIAN=42;AB_MEDIAN=2.50000e-01;AS_RF=8.65786e-03;AS_FilterStatus=RF;CSQ=C|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1|||||||||||||||||||||||||||||||||||||||||||| 22 16050129 . G GACA,C 1164.92 PASS AC=3,0;AF=1.81378e-04,0.00000e+00;AN=16540;BaseQRankSum=-2.24000e-01;ClippingRankSum=-2.63000e-01;DP=230703;FS=8.86700e+00;InbreedingCoeff=5.80000e-03;MQ=3.46800e+01;MQRankSum=1.43000e-01;QD=1.01300e+01;ReadPosRankSum=-2.13000e-01;SOR=3.30000e-02;VQSLOD=-1.37800e+00;VQSR_culprit=SOR;VQSR_NEGATIVE_TRAIN_SITE;GQ_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|1|0|0|4,0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0;DP_HIST_ALT=0|3|2|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0,0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|2|0|1|1|1|0|0|0|0|1|0|0|0|0,0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0;GQ_HIST_ALL=104|464|608|1985|2741|1441|2526|1859|721|1069|690|260|538|62|159|47|92|8|46|68;DP_HIST_ALL=1018|6123|5177|2097|791|161|97|24|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|2|0|1|1|1|0|1|0|0|1|0|0|0|0;AC_AFR=0,0;AC_AMR=0,0;AC_ASJ=0,0;AC_EAS=0,0;AC_FIN=0,0;AC_NFE=3,0;AC_OTH=0,0;AC_Male=3,0;AC_Female=0,0;AN_AFR=3614;AN_AMR=528;AN_ASJ=180;AN_EAS=892;AN_FIN=2256;AN_NFE=8466;AN_OTH=604;AN_Male=9308;AN_Female=7232;AF_AFR=0.00000e+00,0.00000e+00;AF_AMR=0.00000e+00,0.00000e+00;AF_ASJ=0.00000e+00,0.00000e+00;AF_EAS=0.00000e+00,0.00000e+00;AF_FIN=0.00000e+00,0.00000e+00;AF_NFE=3.54359e-04,0.00000e+00;AF_OTH=0.00000e+00,0.00000e+00;AF_Male=3.22303e-04,0.00000e+00;AF_Female=0.00000e+00,0.00000e+00;GC_AFR=1807,0,0,0,0,0;GC_AMR=264,0,0,0,0,0;GC_ASJ=90,0,0,0,0,0;GC_EAS=446,0,0,0,0,0;GC_FIN=1128,0,0,0,0,0;GC_NFE=4230,3,0,0,0,0;GC_OTH=302,0,0,0,0,0;GC_Male=4651,3,0,0,0,0;GC_Female=3616,0,0,0,0,0;AC_raw=6,1;AN_raw=30976;AF_raw=1.93698e-04,3.22831e-05;GC_raw=15481,6,0,1,0,0;GC=8267,3,0,0,0,0;Hom_AFR=0,0;Hom_AMR=0,0;Hom_ASJ=0,0;Hom_EAS=0,0;Hom_FIN=0,0;Hom_NFE=0,0;Hom_OTH=0,0;Hom_Male=0,0;Hom_Female=0,0;Hom_raw=0,0;Hom=0,0;POPMAX=NFE,.;AC_POPMAX=3,.;AN_POPMAX=8466,.;AF_POPMAX=3.54359e-04,.;DP_MEDIAN=10,8;DREF_MEDIAN=3.15558e-20,2.51189e-13;GQ_MEDIAN=99,72;AB_MEDIAN=4.41558e-01,6.25000e-01;AS_RF=5.16800e-01,3.29197e-01;AS_FilterStatus=PASS,RF|AC0;CSQ=C|intergenic_variant|MODIFIER||||||||||||||||2||||insertion|1|||||||||||||||||||||||||||||||||||||||||||| 22 16050141 . C A 108.57 PASS AC=1;AF=5.09632e-05;AN=19622;BaseQRankSum=-7.51000e-01;ClippingRankSum=-1.43000e-01;DP=255559;FS=0.00000e+00;InbreedingCoeff=-4.70000e-03;MQ=3.40100e+01;MQRankSum=-3.32000e-01;QD=9.87000e+00;ReadPosRankSum=6.60000e-02;SOR=9.90000e-02;VQSLOD=-3.45100e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;DP_HIST_ALT=0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0;GQ_HIST_ALL=90|295|443|1443|2398|1347|2546|2110|845|1318|842|356|727|79|237|59|159|7|90|99;DP_HIST_ALL=626|4935|5582|2741|1103|289|169|45|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=1;AC_OTH=0;AC_Male=1;AC_Female=0;AN_AFR=4696;AN_AMR=588;AN_ASJ=206;AN_EAS=1092;AN_FIN=2392;AN_NFE=9986;AN_OTH=662;AN_Male=10956;AN_Female=8666;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=1.00140e-04;AF_OTH=0.00000e+00;AF_Male=9.12742e-05;AF_Female=0.00000e+00;GC_AFR=2348,0,0;GC_AMR=294,0,0;GC_ASJ=103,0,0;GC_EAS=546,0,0;GC_FIN=1196,0,0;GC_NFE=4992,1,0;GC_OTH=331,0,0;GC_Male=5477,1,0;GC_Female=4333,0,0;AC_raw=1;AN_raw=30980;AF_raw=3.22789e-05;GC_raw=15489,1,0;GC=9810,1,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=0;Hom=0;POPMAX=NFE;AC_POPMAX=1;AN_POPMAX=9986;AF_POPMAX=1.00140e-04;DP_MEDIAN=11;DREF_MEDIAN=7.94328e-18;GQ_MEDIAN=99;AB_MEDIAN=5.45455e-01;AS_RF=4.14273e-01;AS_FilterStatus=PASS;CSQ=A|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1|||||||||||||||||||||||||||||||||||||||||||| 22 16050146 . A T 48.32 RF;AC0 AC=0;AF=0.00000e+00;AN=20636;BaseQRankSum=-3.54000e-01;ClippingRankSum=5.50000e-01;DP=264413;FS=2.76200e+00;InbreedingCoeff=-4.10000e-03;MQ=3.73000e+01;MQRankSum=2.00000e+00;QD=6.90000e+00;ReadPosRankSum=2.00000e+00;SOR=1.53600e+00;VQSLOD=-3.42700e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0;DP_HIST_ALT=0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0;GQ_HIST_ALL=84|258|359|1323|2262|1285|2499|2192|869|1402|937|374|819|84|270|69|176|10|92|126;DP_HIST_ALL=524|4533|5628|2926|1267|363|187|58|4|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=0;AC_OTH=0;AC_Male=0;AC_Female=0;AN_AFR=5074;AN_AMR=602;AN_ASJ=216;AN_EAS=1154;AN_FIN=2448;AN_NFE=10458;AN_OTH=684;AN_Male=11480;AN_Female=9156;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=0.00000e+00;AF_OTH=0.00000e+00;AF_Male=0.00000e+00;AF_Female=0.00000e+00;GC_AFR=2537,0,0;GC_AMR=301,0,0;GC_ASJ=108,0,0;GC_EAS=577,0,0;GC_FIN=1224,0,0;GC_NFE=5229,0,0;GC_OTH=342,0,0;GC_Male=5740,0,0;GC_Female=4578,0,0;AC_raw=1;AN_raw=30980;AF_raw=3.22789e-05;GC_raw=15489,1,0;GC=10318,0,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=0;Hom=0;POPMAX=.;AC_POPMAX=.;AN_POPMAX=.;AF_POPMAX=.;DP_MEDIAN=7;DREF_MEDIAN=1.00000e-11;GQ_MEDIAN=78;AB_MEDIAN=5.71429e-01;AS_RF=2.11047e-01;AS_FilterStatus=RF|AC0;CSQ=T|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1|||||||||||||||||||||||||||||||||||||||||||| pysam-0.23.0/tests/cbcf_data/gnomad_fixed.vcf000066400000000000000000000766661475062545500211430ustar00rootroot00000000000000##fileformat=VCFv4.2 ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FILTER= ##FILTER== 20, DP >= 10, AB => 0.2 for het calls))"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta #CHROM POS ID REF ALT QUAL FILTER INFO 22 16050036 rs374742143 A C 442156.34 RF AC=67;AF=4.29487e-01;AN=156;BaseQRankSum=7.36000e-01;ClippingRankSum=2.96000e-01;DB;DP=50165;FS=7.05600e+00;InbreedingCoeff=3.82000e-01;MQ=2.71500e+01;MQRankSum=-1.02600e+00;QD=2.47500e+01;ReadPosRankSum=-2.11000e-01;SOR=1.26750e+01;VQSLOD=-9.58600e+02;VQSR_culprit=MQ;GQ_HIST_ALT=16|1279|299|254|155|24|16|28|50|135|78|4|6|11|32|43|6|4|3|35;DP_HIST_ALT=1769|653|51|5|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|2|5|24|36|11|89|2|125|31|61|85|24|60|34|8|3|7;GQ_HIST_ALL=2359|2810|730|651|296|51|34|33|53|135|78|4|6|11|32|43|6|4|3|35;DP_HIST_ALL=5518|1756|94|6|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|2|5|24|36|11|89|2|125|31|61|85|24|60|34|8|3|7;AC_AFR=3;AC_AMR=7;AC_ASJ=0;AC_EAS=0;AC_FIN=50;AC_NFE=3;AC_OTH=4;AC_Male=32;AC_Female=35;AN_AFR=14;AN_AMR=10;AN_ASJ=0;AN_EAS=0;AN_FIN=84;AN_NFE=42;AN_OTH=6;AN_Male=80;AN_Female=76;AF_AFR=2.14286e-01;AF_AMR=7.00000e-01;AF_ASJ=.;AF_EAS=.;AF_FIN=5.95238e-01;AF_NFE=7.14286e-02;AF_OTH=6.66667e-01;AF_Male=4.00000e-01;AF_Female=4.60526e-01;GC_AFR=4,3,0;GC_AMR=0,3,2;GC_ASJ=0,0,0;GC_EAS=0,0,0;GC_FIN=4,26,12;GC_NFE=18,3,0;GC_OTH=1,0,2;GC_Male=16,16,8;GC_Female=11,19,8;AC_raw=4349;AN_raw=14748;AF_raw=2.94887e-01;GC_raw=4896,607,1871;GC=27,35,16;Hom_AFR=0;Hom_AMR=2;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=12;Hom_NFE=0;Hom_OTH=2;Hom_Male=8;Hom_Female=8;Hom_raw=1871;Hom=16;POPMAX=AMR;AC_POPMAX=7;AN_POPMAX=10;AF_POPMAX=7.00000e-01;DP_MEDIAN=3;DREF_MEDIAN=5.60406e-10;GQ_MEDIAN=12;AB_MEDIAN=5.55556e-01;AS_RF=4.71609e-02;AS_FilterStatus=RF;CSQ=C|intergenic_variant|MODIFIER|||||||||||||||rs374742143|1||||SNV|1|||||||||||||||||||||||||||||||||||||||||||| 22 16050068 . A G 82.46 RF;AC0 AC=0;AF=0.00000e+00;AN=2708;DP=111486;FS=0.00000e+00;InbreedingCoeff=-3.63000e-02;MQ=3.20200e+01;QD=1.64900e+01;SOR=3.61100e+00;VQSLOD=-9.28900e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;DP_HIST_ALT=0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST_ALL=1227|4189|2184|3537|2071|618|693|346|97|92|61|9|18|0|7|4|4|0|0|0;DP_HIST_ALL=7502|6289|1163|169|26|8|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=0;AC_OTH=0;AC_Male=0;AC_Female=0;AN_AFR=280;AN_AMR=162;AN_ASJ=34;AN_EAS=74;AN_FIN=748;AN_NFE=1300;AN_OTH=110;AN_Male=1584;AN_Female=1124;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=0.00000e+00;AF_OTH=0.00000e+00;AF_Male=0.00000e+00;AF_Female=0.00000e+00;GC_AFR=140,0,0;GC_AMR=81,0,0;GC_ASJ=17,0,0;GC_EAS=37,0,0;GC_FIN=374,0,0;GC_NFE=650,0,0;GC_OTH=55,0,0;GC_Male=792,0,0;GC_Female=562,0,0;AC_raw=2;AN_raw=30314;AF_raw=6.59761e-05;GC_raw=15156,0,1;GC=1354,0,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=1;Hom=0;POPMAX=.;AC_POPMAX=.;AN_POPMAX=.;AF_POPMAX=.;DP_MEDIAN=5;DREF_MEDIAN=1.22034e-16;GQ_MEDIAN=15;AB_MEDIAN=5.00000e-01;AS_RF=5.87186e-02;AS_FilterStatus=RF|AC0;CSQ=G|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1|||||||||||||||||||||||||||||||||||||||||||| 22 16050069 . C T 43.44 RF;AC0 AC=0;AF=0.00000e+00;AN=2802;BaseQRankSum=7.20000e-01;ClippingRankSum=-1.38000e+00;DP=112972;FS=0.00000e+00;InbreedingCoeff=-3.70000e-02;MQ=3.67700e+01;MQRankSum=7.20000e-01;QD=7.24000e+00;ReadPosRankSum=1.38000e+00;SOR=1.32900e+00;VQSLOD=-3.27400e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0;DP_HIST_ALT=0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0;GQ_HIST_ALL=1200|4098|2219|3540|2117|622|710|352|104|101|64|10|20|1|8|3|4|0|0|0;DP_HIST_ALL=7405|6348|1203|181|28|8|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=0;AC_OTH=0;AC_Male=0;AC_Female=0;AN_AFR=296;AN_AMR=164;AN_ASJ=36;AN_EAS=70;AN_FIN=766;AN_NFE=1354;AN_OTH=116;AN_Male=1638;AN_Female=1164;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=0.00000e+00;AF_OTH=0.00000e+00;AF_Male=0.00000e+00;AF_Female=0.00000e+00;GC_AFR=148,0,0;GC_AMR=82,0,0;GC_ASJ=18,0,0;GC_EAS=35,0,0;GC_FIN=383,0,0;GC_NFE=677,0,0;GC_OTH=58,0,0;GC_Male=819,0,0;GC_Female=582,0,0;AC_raw=1;AN_raw=30346;AF_raw=3.29533e-05;GC_raw=15172,1,0;GC=1401,0,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=0;Hom=0;POPMAX=.;AC_POPMAX=.;AN_POPMAX=.;AF_POPMAX=.;DP_MEDIAN=6;DREF_MEDIAN=3.16178e-11;GQ_MEDIAN=38;AB_MEDIAN=6.66667e-01;AS_RF=9.22976e-02;AS_FilterStatus=RF|AC0;CSQ=T|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1|||||||||||||||||||||||||||||||||||||||||||| 22 16050098 . G A 242.82 RF AC=2;AF=2.40964e-04;AN=8300;BaseQRankSum=2.45000e+00;ClippingRankSum=1.03000e-01;DP=167171;FS=0.00000e+00;InbreedingCoeff=-1.46000e-02;MQ=3.06100e+01;MQRankSum=-9.35000e-01;QD=1.05600e+01;ReadPosRankSum=6.60000e-01;SOR=3.84000e-01;VQSLOD=-4.11500e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2;DP_HIST_ALT=0|0|2|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|1|1|0|0|0|0|0|0|0|0|0;GQ_HIST_ALL=350|1697|1483|3462|3106|1262|1746|994|348|436|237|88|141|14|39|5|22|4|8|7;DP_HIST_ALL=3368|7876|3165|776|212|33|16|3|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|1|1|0|0|0|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=2;AC_OTH=0;AC_Male=2;AC_Female=0;AN_AFR=1298;AN_AMR=334;AN_ASJ=84;AN_EAS=380;AN_FIN=1460;AN_NFE=4412;AN_OTH=332;AN_Male=4748;AN_Female=3552;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=4.53309e-04;AF_OTH=0.00000e+00;AF_Male=4.21230e-04;AF_Female=0.00000e+00;GC_AFR=649,0,0;GC_AMR=167,0,0;GC_ASJ=42,0,0;GC_EAS=190,0,0;GC_FIN=730,0,0;GC_NFE=2204,2,0;GC_OTH=166,0,0;GC_Male=2372,2,0;GC_Female=1776,0,0;AC_raw=2;AN_raw=30898;AF_raw=6.47291e-05;GC_raw=15447,2,0;GC=4148,2,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=0;Hom=0;POPMAX=NFE;AC_POPMAX=2;AN_POPMAX=4412;AF_POPMAX=4.53309e-04;DP_MEDIAN=11;DREF_MEDIAN=6.29479e-16;GQ_MEDIAN=99;AB_MEDIAN=4.80769e-01;AS_RF=3.30908e-01;AS_FilterStatus=RF;CSQ=A|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1|||||||||||||||||||||||||||||||||||||||||||| 22 16050115 rs587755077 G A 10684.53 RF AC=31;AF=2.54057e-03;AN=12202;BaseQRankSum=1.59000e+00;ClippingRankSum=6.70000e-02;DP=196906;FS=0.00000e+00;InbreedingCoeff=1.40000e-02;MQ=3.37700e+01;MQRankSum=4.06000e-01;QD=8.23000e+00;ReadPosRankSum=3.22000e-01;SOR=4.23100e+00;VQSLOD=-1.16300e+02;VQSR_culprit=MQ;GQ_HIST_ALT=3|6|10|5|3|3|6|13|17|16|2|3|9|12|8|11|5|3|3|14;DP_HIST_ALT=22|95|32|3|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|4|6|16|20|8|21|1|28|5|7|7|7|7|8|0|0|0;GQ_HIST_ALL=237|959|984|2740|3098|1328|2215|1483|527|685|442|163|289|52|79|25|61|6|27|39;DP_HIST_ALL=1972|7287|4327|1314|407|79|44|9|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|4|6|16|20|8|21|1|28|5|7|7|7|7|8|0|0|0;AC_AFR=30;AC_AMR=1;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=0;AC_OTH=0;AC_Male=16;AC_Female=15;AN_AFR=2236;AN_AMR=436;AN_ASJ=144;AN_EAS=640;AN_FIN=1862;AN_NFE=6410;AN_OTH=474;AN_Male=6874;AN_Female=5328;AF_AFR=1.34168e-02;AF_AMR=2.29358e-03;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=0.00000e+00;AF_OTH=0.00000e+00;AF_Male=2.32761e-03;AF_Female=2.81532e-03;GC_AFR=1088,30,0;GC_AMR=217,1,0;GC_ASJ=72,0,0;GC_EAS=320,0,0;GC_FIN=931,0,0;GC_NFE=3205,0,0;GC_OTH=237,0,0;GC_Male=3421,16,0;GC_Female=2649,15,0;AC_raw=159;AN_raw=30878;AF_raw=5.14930e-03;GC_raw=15287,145,7;GC=6070,31,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=7;Hom=0;POPMAX=AFR;AC_POPMAX=30;AN_POPMAX=2236;AF_POPMAX=1.34168e-02;DP_MEDIAN=7;DREF_MEDIAN=1.74246e-08;GQ_MEDIAN=48;AB_MEDIAN=4.44444e-01;AS_RF=5.02621e-02;AS_FilterStatus=RF;CSQ=A|intergenic_variant|MODIFIER|||||||||||||||rs587755077|1||||SNV|1||||||||||||||||A:0.0064|||||||||||||||||||||||||||| 22 16050116 . G C 28395.88 RF AC=246;AF=2.51431e-02;AN=9784;BaseQRankSum=2.48000e-01;ClippingRankSum=0.00000e+00;DP=201089;FS=0.00000e+00;InbreedingCoeff=-7.09000e-02;MQ=3.23400e+01;MQRankSum=-1.23100e+00;QD=3.27000e+00;ReadPosRankSum=2.48000e-01;SOR=7.16400e+00;VQSLOD=-3.11400e+02;VQSR_culprit=MQ;GQ_HIST_ALT=0|3|6|9|32|41|110|119|73|75|49|48|27|32|38|16|4|9|19|27;DP_HIST_ALT=21|356|285|60|12|3|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|11|105|184|174|98|40|64|2|30|5|11|8|2|2|0|0|0|0;GQ_HIST_ALL=2616|992|935|2244|2407|1109|1723|1219|458|593|382|175|259|62|105|27|46|11|38|55;DP_HIST_ALL=1838|7215|4403|1404|443|92|50|11|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|11|105|184|174|98|40|64|2|30|5|11|8|2|2|0|0|0|0;AC_AFR=18;AC_AMR=5;AC_ASJ=4;AC_EAS=3;AC_FIN=5;AC_NFE=202;AC_OTH=9;AC_Male=141;AC_Female=105;AN_AFR=2166;AN_AMR=402;AN_ASJ=88;AN_EAS=650;AN_FIN=1722;AN_NFE=4390;AN_OTH=366;AN_Male=5450;AN_Female=4334;AF_AFR=8.31025e-03;AF_AMR=1.24378e-02;AF_ASJ=4.54545e-02;AF_EAS=4.61538e-03;AF_FIN=2.90360e-03;AF_NFE=4.60137e-02;AF_OTH=2.45902e-02;AF_Male=2.58716e-02;AF_Female=2.42270e-02;GC_AFR=1065,18,0;GC_AMR=196,5,0;GC_ASJ=40,4,0;GC_EAS=322,3,0;GC_FIN=856,5,0;GC_NFE=1993,202,0;GC_OTH=174,9,0;GC_Male=2584,141,0;GC_Female=2062,105,0;AC_raw=738;AN_raw=30912;AF_raw=2.38742e-02;GC_raw=14719,736,1;GC=4646,246,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=1;Hom=0;POPMAX=NFE;AC_POPMAX=202;AN_POPMAX=4390;AF_POPMAX=4.60137e-02;DP_MEDIAN=9;DREF_MEDIAN=6.30918e-05;GQ_MEDIAN=42;AB_MEDIAN=2.50000e-01;AS_RF=8.65786e-03;AS_FilterStatus=RF;CSQ=C|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1|||||||||||||||||||||||||||||||||||||||||||| 22 16050129 . G GACA,C 1164.92 PASS AC=3,0;AF=1.81378e-04,0.00000e+00;AN=16540;BaseQRankSum=-2.24000e-01;ClippingRankSum=-2.63000e-01;DP=230703;FS=8.86700e+00;InbreedingCoeff=5.80000e-03;MQ=3.46800e+01;MQRankSum=1.43000e-01;QD=1.01300e+01;ReadPosRankSum=-2.13000e-01;SOR=3.30000e-02;VQSLOD=-1.37800e+00;VQSR_culprit=SOR;VQSR_NEGATIVE_TRAIN_SITE;GQ_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|1|0|0|4,0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0;DP_HIST_ALT=0|3|2|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0,0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|2|0|1|1|1|0|0|0|0|1|0|0|0|0,0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0;GQ_HIST_ALL=104|464|608|1985|2741|1441|2526|1859|721|1069|690|260|538|62|159|47|92|8|46|68;DP_HIST_ALL=1018|6123|5177|2097|791|161|97|24|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|2|0|1|1|1|0|1|0|0|1|0|0|0|0;AC_AFR=0,0;AC_AMR=0,0;AC_ASJ=0,0;AC_EAS=0,0;AC_FIN=0,0;AC_NFE=3,0;AC_OTH=0,0;AC_Male=3,0;AC_Female=0,0;AN_AFR=3614;AN_AMR=528;AN_ASJ=180;AN_EAS=892;AN_FIN=2256;AN_NFE=8466;AN_OTH=604;AN_Male=9308;AN_Female=7232;AF_AFR=0.00000e+00,0.00000e+00;AF_AMR=0.00000e+00,0.00000e+00;AF_ASJ=0.00000e+00,0.00000e+00;AF_EAS=0.00000e+00,0.00000e+00;AF_FIN=0.00000e+00,0.00000e+00;AF_NFE=3.54359e-04,0.00000e+00;AF_OTH=0.00000e+00,0.00000e+00;AF_Male=3.22303e-04,0.00000e+00;AF_Female=0.00000e+00,0.00000e+00;GC_AFR=1807,0,0,0,0,0;GC_AMR=264,0,0,0,0,0;GC_ASJ=90,0,0,0,0,0;GC_EAS=446,0,0,0,0,0;GC_FIN=1128,0,0,0,0,0;GC_NFE=4230,3,0,0,0,0;GC_OTH=302,0,0,0,0,0;GC_Male=4651,3,0,0,0,0;GC_Female=3616,0,0,0,0,0;AC_raw=6,1;AN_raw=30976;AF_raw=1.93698e-04,3.22831e-05;GC_raw=15481,6,0,1,0,0;GC=8267,3,0,0,0,0;Hom_AFR=0,0;Hom_AMR=0,0;Hom_ASJ=0,0;Hom_EAS=0,0;Hom_FIN=0,0;Hom_NFE=0,0;Hom_OTH=0,0;Hom_Male=0,0;Hom_Female=0,0;Hom_raw=0,0;Hom=0,0;POPMAX=NFE,.;AC_POPMAX=3,.;AN_POPMAX=8466,.;AF_POPMAX=3.54359e-04,.;DP_MEDIAN=10,8;DREF_MEDIAN=3.15558e-20,2.51189e-13;GQ_MEDIAN=99,72;AB_MEDIAN=4.41558e-01,6.25000e-01;AS_RF=5.16800e-01,3.29197e-01;AS_FilterStatus=PASS,RF|AC0;CSQ=C|intergenic_variant|MODIFIER||||||||||||||||2||||insertion|1|||||||||||||||||||||||||||||||||||||||||||| 22 16050141 . C A 108.57 PASS AC=1;AF=5.09632e-05;AN=19622;BaseQRankSum=-7.51000e-01;ClippingRankSum=-1.43000e-01;DP=255559;FS=0.00000e+00;InbreedingCoeff=-4.70000e-03;MQ=3.40100e+01;MQRankSum=-3.32000e-01;QD=9.87000e+00;ReadPosRankSum=6.60000e-02;SOR=9.90000e-02;VQSLOD=-3.45100e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;DP_HIST_ALT=0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0;GQ_HIST_ALL=90|295|443|1443|2398|1347|2546|2110|845|1318|842|356|727|79|237|59|159|7|90|99;DP_HIST_ALL=626|4935|5582|2741|1103|289|169|45|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=1;AC_OTH=0;AC_Male=1;AC_Female=0;AN_AFR=4696;AN_AMR=588;AN_ASJ=206;AN_EAS=1092;AN_FIN=2392;AN_NFE=9986;AN_OTH=662;AN_Male=10956;AN_Female=8666;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=1.00140e-04;AF_OTH=0.00000e+00;AF_Male=9.12742e-05;AF_Female=0.00000e+00;GC_AFR=2348,0,0;GC_AMR=294,0,0;GC_ASJ=103,0,0;GC_EAS=546,0,0;GC_FIN=1196,0,0;GC_NFE=4992,1,0;GC_OTH=331,0,0;GC_Male=5477,1,0;GC_Female=4333,0,0;AC_raw=1;AN_raw=30980;AF_raw=3.22789e-05;GC_raw=15489,1,0;GC=9810,1,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=0;Hom=0;POPMAX=NFE;AC_POPMAX=1;AN_POPMAX=9986;AF_POPMAX=1.00140e-04;DP_MEDIAN=11;DREF_MEDIAN=7.94328e-18;GQ_MEDIAN=99;AB_MEDIAN=5.45455e-01;AS_RF=4.14273e-01;AS_FilterStatus=PASS;CSQ=A|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1|||||||||||||||||||||||||||||||||||||||||||| 22 16050146 . A T 48.32 RF;AC0 AC=0;AF=0.00000e+00;AN=20636;BaseQRankSum=-3.54000e-01;ClippingRankSum=5.50000e-01;DP=264413;FS=2.76200e+00;InbreedingCoeff=-4.10000e-03;MQ=3.73000e+01;MQRankSum=2.00000e+00;QD=6.90000e+00;ReadPosRankSum=2.00000e+00;SOR=1.53600e+00;VQSLOD=-3.42700e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0;DP_HIST_ALT=0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0;GQ_HIST_ALL=84|258|359|1323|2262|1285|2499|2192|869|1402|937|374|819|84|270|69|176|10|92|126;DP_HIST_ALL=524|4533|5628|2926|1267|363|187|58|4|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=0;AC_OTH=0;AC_Male=0;AC_Female=0;AN_AFR=5074;AN_AMR=602;AN_ASJ=216;AN_EAS=1154;AN_FIN=2448;AN_NFE=10458;AN_OTH=684;AN_Male=11480;AN_Female=9156;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=0.00000e+00;AF_OTH=0.00000e+00;AF_Male=0.00000e+00;AF_Female=0.00000e+00;GC_AFR=2537,0,0;GC_AMR=301,0,0;GC_ASJ=108,0,0;GC_EAS=577,0,0;GC_FIN=1224,0,0;GC_NFE=5229,0,0;GC_OTH=342,0,0;GC_Male=5740,0,0;GC_Female=4578,0,0;AC_raw=1;AN_raw=30980;AF_raw=3.22789e-05;GC_raw=15489,1,0;GC=10318,0,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=0;Hom=0;POPMAX=.;AC_POPMAX=.;AN_POPMAX=.;AF_POPMAX=.;DP_MEDIAN=7;DREF_MEDIAN=1.00000e-11;GQ_MEDIAN=78;AB_MEDIAN=5.71429e-01;AS_RF=2.11047e-01;AS_FilterStatus=RF|AC0;CSQ=T|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1|||||||||||||||||||||||||||||||||||||||||||| pysam-0.23.0/tests/cbcf_data/missing_genotypes.vcf000066400000000000000000000003571475062545500222450ustar00rootroot00000000000000##fileformat=VCFv4.1 ##contig= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 chr1 1 . A G 999 . . GT 0/0 1/1 chr1 50 . T C 999 . . GT ./. 0/1 pysam-0.23.0/tests/compile_test.py000066400000000000000000000022261475062545500171470ustar00rootroot00000000000000''' compile_test.py - check pyximport functionality with pysam ========================================================== test script for checking if compilation against pysam and tabix works. ''' # clean up previous compilation import os import pytest import pysam from TestUtils import make_data_files, BAM_DATADIR, TABIX_DATADIR def setUpModule(): make_data_files(BAM_DATADIR) make_data_files(TABIX_DATADIR) try: os.unlink('tests/_compile_test.c') os.unlink('tests/_compile_test.pyxbldc') except OSError: pass NO_PYXIMPORT = False try: import pyximport pyximport.install(build_in_temp=False) import _compile_test except: NO_PYXIMPORT = True @pytest.mark.skipif(NO_PYXIMPORT, reason="no pyximport") def test_bam(): input_filename = os.path.join(BAM_DATADIR, "ex1.bam") nread = _compile_test.testCountBAM( pysam.Samfile(input_filename)) assert nread == 3270 @pytest.mark.skipif(NO_PYXIMPORT, reason="no pyximport") def test_gtf(): input_filename = os.path.join(TABIX_DATADIR, "example.gtf.gz") nread = _compile_test.testCountGTF( pysam.Tabixfile(input_filename)) assert nread == 237 pysam-0.23.0/tests/faidx_bench.py000066400000000000000000000040441475062545500167120ustar00rootroot00000000000000"""Benchmarking the cfaidx module. Usage:: pytest benchmark/faidx_bench.py """ import os import pysam from TestUtils import BAM_DATADIR def iterate_over_fastx(fn, persist=True): return len(list(pysam.FastxFile(fn, persist=persist))) def iterate_over_fastx_as_file(fn): with open(fn) as inf: return len(inf.read()) def test_fasta_iteration_short_sequences(benchmark): result = benchmark(iterate_over_fastx, os.path.join( BAM_DATADIR, "faidx_ex1.fa")) assert result == 3270 def test_fasta_iteration_long_sequences(benchmark): result = benchmark(iterate_over_fastx, os.path.join(BAM_DATADIR, "ex1.fa")) assert result == 2 def test_fasta_iteration_short_sequences_without_persistence(benchmark): result = benchmark(iterate_over_fastx, os.path.join( BAM_DATADIR, "faidx_ex1.fa"), persist=False) assert result == 3270 def test_fasta_iteration_long_sequences_without_persistence(benchmark): result = benchmark(iterate_over_fastx, os.path.join( BAM_DATADIR, "ex1.fa"), persist=False) assert result == 2 def test_fasta_iteration_short_sequences_as_file(benchmark): result = benchmark(iterate_over_fastx_as_file, os.path.join(BAM_DATADIR, "faidx_ex1.fa")) assert result == 195399 def test_fasta_iteration_long_sequences_as_file(benchmark): result = benchmark(iterate_over_fastx_as_file, os.path.join(BAM_DATADIR, "ex1.fa")) assert result == 3225 def test_fastq_iteration_short_sequences(benchmark): result = benchmark(iterate_over_fastx, os.path.join( BAM_DATADIR, "faidx_ex1.fq")) assert result == 3270 def test_fastq_iteration_short_sequences_without_persistence(benchmark): result = benchmark(iterate_over_fastx, os.path.join( BAM_DATADIR, "faidx_ex1.fq"), persist=False) assert result == 3270 def test_fastq_iteration_short_sequences_as_file(benchmark): result = benchmark(iterate_over_fastx_as_file, os.path.join(BAM_DATADIR, "faidx_ex1.fq")) assert result == 320458 pysam-0.23.0/tests/faidx_test.py000066400000000000000000000347771475062545500166320ustar00rootroot00000000000000import pysam import unittest import os import gzip import copy import shutil from TestUtils import check_url, make_data_files, BAM_DATADIR, get_temp_filename def setUpModule(): make_data_files(BAM_DATADIR) class TestFastaFile(unittest.TestCase): sequences = { 'chr1': "CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTGGCTGAGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAATGAAAACTATATTTATGCTATTCAGTTCTAAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGTTACCAAATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCAATGGACCTGTGATATCTGGATTCTGGGAAATTCTTCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAGCCATCACAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCAACCTCATACACACACATGGTTTAGGGGTATAATACCTCTACATGGCTGATTATGAAAACAATGTTCCCCAGATACCATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCCTACACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTTTCCCATCATGAAGCACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATACATGAGATTATTAGGAAATGCTTTACTGTCATAACTATGAAGAGACTATTGCCAGATGAACCACACATTAATACTATGTTTCTTATCTGCACATTACTACCCTGCAATTAATATAATTGTGTCCATGTACACACGCTGTCCTATGTACTTATCATGACTCTATCCCAAATTCCCAATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACATAATCCCACGCTTCCTATGGAAAGGTTGTTGGGAGATTTTTAATGATTCCTCAATGTTAAAATGTCTATTTTTGTCTTGACACCCAACTAATATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCGTCTTCTTA", # noqa 'chr2': "TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAAGAAATTACAAAATATAGTTGAAAGCTCTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGAATTAACCCAGTCAGACAAAAATAAAGAAAAAAATTTTAAAAATGAACAGAGCTTTCAAGAAGTATGAGATTATGTAAAGTAACTGAACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGGAAATCCCATCAGAATAACAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAAGAGATTGGATCTAATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGTTATGCCCTGCTAAACTAAGCATCATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATAATTCATCATCACTAAACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAATACACACAAAAGTACAAAACTCACAGGTTTTATAAAACAATTGAGACTACAGAGCAACTAGGTAAAAAATTAACATTACAACAGGAACAAAACCTCATATATCAATATTAACTTTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAGATATAGATTGGCAGAACAGATTTAAAAACATGAACTAACTATATGCTGTTTACAAGAAACTCATTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAAACCAAATGAGAGAAGGAGTAGCTATACTTATATCAGATAAAGCACACTTTAAATCAACAACAGTAAAATAAAACAAAGGAGGTCATCATACAATGATAAAAAGATCAATTCAGCAAGAAGATATAACCATCCTACTAAATACATATGCACCTAACACAAGACTACCCAGATTCATAAAACAAATACTACTAGACCTAAGAGGGATGAGAAATTACCTAATTGGTACAATGTACAATATTCTGATGATGGTTACACTAAAAGCCCATACTTTACTGCTACTCAATATATCCATGTAACAAATCTGCGCTTGTACTTCTAAATCTATAAAAAAATTAAAATTTAACAAAAGTAAATAAAACACATAGCTAAAACTAAAAAAGCAAAAACAAAAACTATGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAGTATAAATTGTTTTCCACTTTGGAAAACAATTTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTTGCATGCCAGAAAAAAATATTTACAGTAACT", # noqa } def setUp(self): self.file = pysam.FastaFile(os.path.join(BAM_DATADIR, "ex1.fa")) def testFetch(self): for id, seq in list(self.sequences.items()): self.assertEqual(seq, self.file.fetch(id)) for x in range(0, len(seq), 10): self.assertEqual(seq[x:x + 10], self.file.fetch(id, x, x + 10)) # test x:end self.assertEqual(seq[x:], self.file.fetch(id, x)) # test 0:x self.assertEqual(seq[:x], self.file.fetch(id, None, x)) # unknown sequence raises IndexError self.assertRaises(KeyError, self.file.fetch, "chr12") def testOutOfRangeAccess(self): '''test out of range access.''' # out of range access returns an empty string for contig, s in self.sequences.items(): self.assertEqual(self.file.fetch(contig, len(s), len(s) + 1), "") def testFetchErrors(self): self.assertRaises(ValueError, self.file.fetch) self.assertRaises(ValueError, self.file.fetch, "chr1", -1, 10) self.assertRaises(ValueError, self.file.fetch, "chr1", 20, 10) self.assertRaises(KeyError, self.file.fetch, "chr3", 0, 100) def test_fetch_with_region_and_contig_raises_exception(self): self.assertRaises(ValueError, self.file.fetch, "chr1", 10, 20, "chr1:11-20") def test_fetch_with_region_is_equivalent(self): self.assertEqual(self.file.fetch("chr1", 10, 20), self.file.fetch(region="chr1:11-20")) def testLength(self): self.assertEqual(len(self.file), 2) def testSequenceLengths(self): self.assertEqual(1575, self.file.get_reference_length("chr1")) self.assertEqual(1584, self.file.get_reference_length("chr2")) def tearDown(self): self.file.close() class TestFastaFilePathIndex(unittest.TestCase): filename = os.path.join(BAM_DATADIR, "ex1.fa") data_suffix = ".fa" def test_raise_exception_if_index_is_missing(self): self.assertRaises(IOError, pysam.FastaFile, self.filename, filepath_index="garbage" + self.data_suffix + ".fai") def test_open_file_without_index_succeeds(self): with pysam.FastaFile(self.filename) as inf: self.assertEqual(len(inf), 2) def test_open_file_with_explicit_index_succeeds(self): with pysam.FastaFile(self.filename, filepath_index=self.filename + ".fai") as inf: self.assertEqual(len(inf), 2) def test_open_file_with_explicit_abritrarily_named_index_succeeds(self): tmpfilename = get_temp_filename(self.data_suffix) shutil.copyfile(self.filename, tmpfilename) filepath_index = self.filename + ".fai" filepath_index_compressed = self.filename + ".gzi" if not os.path.exists(filepath_index_compressed): filepath_index_compressed = None with pysam.FastaFile(tmpfilename, filepath_index=filepath_index, filepath_index_compressed=filepath_index_compressed) as inf: self.assertEqual(len(inf), 2) # index should not be auto-generated self.assertFalse(os.path.exists(tmpfilename + ".fai")) os.unlink(tmpfilename) class TestFastaFilePathIndexCompressed(TestFastaFilePathIndex): filename = os.path.join(BAM_DATADIR, "ex1.fa.gz") data_suffix = ".fa.gz" class TestFastxFileFastq(unittest.TestCase): filetype = pysam.FastxFile filename = "faidx_ex1.fq" persist = True def setUp(self): self.file = self.filetype(os.path.join(BAM_DATADIR, self.filename), persist=self.persist) self.has_quality = self.filename.endswith('.fq') def tearDown(self): self.file.close() def checkFirst(self, s): # test first entry self.assertEqual(s.sequence, "GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC") self.assertEqual(s.name, "B7_589:1:101:825:28") if self.has_quality: self.assertEqual(s.quality, "<<86<<;<78<<<)<;4<67<;<;<74-7;,;8,;") self.assertEqual(list(s.get_quality_array()), [ord(x) - 33 for x in s.quality]) self.assertEqual(str(s), "@B7_589:1:101:825:28\n" "GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC\n" "+\n" "<<86<<;<78<<<)<;4<67<;<;<74-7;,;8,;") else: self.assertEqual(s.quality, None) self.assertEqual(s.get_quality_array(), None) self.assertEqual(str(s), ">B7_589:1:101:825:28\n" "GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC") def checkLast(self, s): self.assertEqual(s.sequence, "TAATTGAAAAATTCATTTAAGAAATTACAAAATAT") self.assertEqual(s.name, "EAS56_65:8:64:507:478") if self.has_quality: self.assertEqual(s.quality, "<<<<<;<<<<<<<<<<<<<<<;;;<<<;<<8;<;<") self.assertEqual(list(s.get_quality_array()), [ord(x) - 33 for x in s.quality]) else: self.assertEqual(s.quality, None) self.assertEqual(s.get_quality_array(), None) def testCounts(self): self.assertEqual(len([x for x in self.file]), 3270) def testMissingFile(self): self.assertRaises(IOError, self.filetype, "nothere.fq") def testSequence(self): first = self.file.__next__() self.checkFirst(first) for last in self.file: pass self.checkLast(last) # test for persistence if self.persist: self.checkFirst(first) else: self.checkLast(first) def testManager(self): with self.filetype(os.path.join(BAM_DATADIR, self.filename), persist=self.persist) as inf: first = inf.__next__() self.checkFirst(first) for last in inf: pass self.checkLast(last) self.assertEqual(inf.closed, True) # Test for backwards compatibility class TestFastqFileFastq(TestFastxFileFastq): filetype = pysam.FastqFile # Test for backwards compatibility class TestFastxFileFasta(TestFastxFileFastq): filetype = pysam.FastqFile filename = "faidx_ex1.fa" class TestFastxFileFastqStream(TestFastxFileFastq): persist = False class TestFastxFileWithEmptySequence(unittest.TestCase): """see issue 204: iteration over fastq file with empty sequence stops prematurely """ filetype = pysam.FastxFile filename = "faidx_empty_seq.fq.gz" def testIteration(self): fn = os.path.join(BAM_DATADIR, self.filename) with gzip.open(fn) as inf: ref_num = len(list(inf)) / 4 with self.filetype(fn) as f: l = len(list(f)) self.assertEqual(ref_num, l) class TestRemoteFileFTP(unittest.TestCase): '''test remote access. ''' url = ("ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/" "GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa") def testFTPView(self): if not check_url(self.url): return try: with pysam.Fastafile(self.url) as f: self.assertEqual( len(f.fetch("chr1", 0, 1000)), 1000) except (OSError, IOError): pass def test_sequence_lengths_are_available(self): if not check_url(self.url): return try: with pysam.Fastafile(self.url) as f: self.assertEqual(len(f.references), 3366) self.assertTrue("chr1" in f.references) self.assertEqual(f.lengths[0], 248956422) self.assertEqual(f.get_reference_length("chr1"), 248956422) except (OSError, IOError): pass class TestFastqRecord(unittest.TestCase): filetype = pysam.FastxFile filename = "faidx_ex1.fq" def setUp(self): with self.filetype(os.path.join(BAM_DATADIR, self.filename), persist=True) as inf: self.record = next(inf) def test_fastx_record_sequence_can_be_modified(self): old_sequence = self.record.sequence new_record = copy.copy(self.record) new_sequence = "AAAC" new_record.set_sequence(new_sequence) self.assertEqual(str(new_record), ">{}\n{}".format( self.record.name, new_sequence)) self.assertEqual(self.record.sequence, old_sequence) self.assertEqual(new_record.sequence, new_sequence) def test_fastx_record_name_can_be_modified(self): old_name = self.record.name new_name = "new_name" new_record = copy.copy(self.record) new_record.set_name(new_name) self.assertEqual(new_record.name, new_name) self.assertEqual(self.record.name, old_name) def test_fastx_record_fail_if_name_is_None(self): self.assertRaises(ValueError, self.record.set_name, None) def test_fastx_record_comment_can_be_modified(self): old_comment = self.record.comment new_comment = "this is a new comment" new_record = copy.copy(self.record) new_record.set_comment(new_comment) self.assertEqual(new_record.comment, new_comment) self.assertEqual(self.record.comment, old_comment) def test_fastx_record_comment_can_be_None(self): old_comment = self.record.comment new_comment = None new_record = copy.copy(self.record) new_record.set_comment(new_comment) self.assertEqual(new_record.comment, new_comment) self.assertEqual(self.record.comment, old_comment) def test_fastx_record_quality_can_be_modified(self): old_quality = self.record.quality new_quality = "A" * len(old_quality) new_record = copy.copy(self.record) new_record.set_sequence(self.record.sequence, new_quality) self.assertEqual(new_record.quality, new_quality) self.assertEqual(self.record.quality, old_quality) def test_fastx_record_fail_if_quality_is_wrong_length(self): self.assertRaises(ValueError, self.record.set_sequence, self.record.sequence, self.record.quality * 2) def test_fastx_record_can_be_created_from_scratch(self): fastx_record = pysam.FastxRecord() self.assertRaises(ValueError, str, fastx_record) fastx_record.set_name("name") self.assertRaises(ValueError, str, fastx_record) fastx_record.set_sequence("sequence") self.assertEqual(str(fastx_record), ">name\nsequence") class TestFastqProxy(unittest.TestCase): def test_fastq_proxy_instantiation_raises_error(self): self.assertRaises(ValueError, pysam.FastqProxy) if __name__ == "__main__": unittest.main() pysam-0.23.0/tests/linking_test.py000066400000000000000000000052351475062545500171550ustar00rootroot00000000000000"""test linking against pysam. """ import unittest import os import subprocess import pysam from TestUtils import LINKDIR def check_import(statement): try: output = subprocess.check_output( statement, stderr=subprocess.STDOUT, shell=True) except subprocess.CalledProcessError as exc: if b"ImportError" in exc.output: raise ImportError( "module could not be imported: {}".format(str(exc.output))) else: raise def check_pass(statement): try: output = subprocess.check_output( statement, stderr=subprocess.STDOUT, shell=True) except subprocess.CalledProcessError as exc: raise ValueError("{}: {}".format(exc, exc.output)) if b"FAILED" in output: raise ValueError("module tests failed") return True @unittest.skipUnless( os.environ.get("PYSAM_LINKING_TESTS", None), "enable linking tests by setting PYSAM_LINKING_TESTS environment variable") class TestLinking(unittest.TestCase): package_name = "link_with_rpath" def setUp(self): self.workdir = os.path.join(LINKDIR, self.package_name) def test_package_can_be_installed(self): subprocess.check_output( "cd {} && rm -rf build && python setup.py install".format( self.workdir), shell=True) @unittest.skipUnless( os.environ.get("PYSAM_LINKING_TESTS", None), "enable linking tests by setting PYSAM_LINKING_TESTS environment variable") class TestLinkWithRpath(TestLinking): package_name = "link_with_rpath" def test_package_tests_pass(self): self.assertTrue(check_pass( "cd {} && python test_module.py".format(os.path.join(self.workdir, "tests")))) @unittest.skipUnless( os.environ.get("PYSAM_LINKING_TESTS", None), "enable linking tests by setting PYSAM_LINKING_TESTS environment variable") class TestLinkWithoutRpath(TestLinking): package_name = "link_without_rpath" def test_package_tests_fail_on_import(self): self.assertRaises( ImportError, check_import, "cd {} && python test_module.py".format(os.path.join(self.workdir, "tests"))) def test_package_tests_pass_if_ld_library_path_set(self): pysam_libraries = pysam.get_libraries() pysam_libdirs, pysam_libs = zip( *[os.path.split(x) for x in pysam_libraries]) pysam_libdir = pysam_libdirs[0] self.assertTrue(check_pass( "export LD_LIBRARY_PATH={}:$PATH && cd {} && python test_module.py".format( pysam_libdir, os.path.join(self.workdir, "tests")))) if __name__ == "__main__": unittest.main() pysam-0.23.0/tests/pysam_data/000077500000000000000000000000001475062545500162265ustar00rootroot00000000000000pysam-0.23.0/tests/pysam_data/0example_no_seq_in_header.bam000066400000000000000000000016711475062545500237710ustar00rootroot00000000000000BCe;HPᣥ%ࠠIV->g}+"FZh6IAGquP(uwvQ\t:8\Mg@ D{cĠ">ftH pSƌljϼ(1]42Tkmd-,tre*~.W삩tN%^V#β!q)=L&pI=~Ť)aʍ%®V (MjySFN.z2!"7>8q<5 CIkSN0<9󺲊-q! hz n#U@Fl9| fjzMC|& Av0{(7讘A1gOo6/i=|̥?26BCOk@I`ֲ[NLwf2 x1 Az,~uݣ_CA<ߣn&(>C~<&' |!#B<]d|w3 &P uҼdN(B2"a^N' _<"ί7 tm\D)n MU^ϟ"d]aEuIL/wIV"22%f6-^5(ι4Zfu}xރ>u)(aIZV(5hl@B&Yo.3k KONϿc'UJozXq-~pjfIyx:PZϬR#еRJX5c4^U)%{8(Uɍ3+fDڜt0z'J\:|j^>rAf?#^t}V4,kFZݏ_?OНBCpysam-0.23.0/tests/pysam_data/0example_no_seq_in_header_null_bytes.bam000066400000000000000000000016721475062545500262320ustar00rootroot00000000000000BCe;HPᣥpP$Mb[-UoE$H mRࠈ:X(>uwvQ\pup'߹h "}1fbPy/3:Xik)Od)cFOg^EH9MXZ/hmӪ-,dtred5U}rAZ,g 9MxXdq )mMBT^ ʫbмwC.SZySSF]0 : Cq?۫SJH %AgX!x,:uS]CGn끀vXyHd`!^t %h#$J2v^,'?U$LRMCu\| ~DCBBRqEj?S>;L0`.CCPBCOk@I`ֲ[NLwf2 x1 Az,~uݣ_CA<ߣn&(>C~<&' |!#B<]d|w3 &P uҼdN(B2"a^N' _<"ί7 tm\D)n MU^ϟ"d]aEuIL/wIV"22%f6-^5(ι4Zfu}xރ>u)(aIZV(5hl@B&Yo.3k KONϿc'UJozXq-~pjfIyx:PZϬR#еRJX5c4^U)%{8(Uɍ3+fDڜt0z'J\:|j^>rAf?#^t}V4,kFZݏ_?OНBCpysam-0.23.0/tests/pysam_data/MM-chebi.sam000066400000000000000000000002541475062545500203120ustar00rootroot00000000000000@CO Separate m, h and N modifications * 0 * 0 0 * * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA * Mm:Z:C+m,2,2,1,4,1;C+76792,6,7;N+n,15; Ml:B:C,102,128,153,179,204,161,33,212 pysam-0.23.0/tests/pysam_data/MM-double.sam000066400000000000000000000003761475062545500205170ustar00rootroot00000000000000@CO Modifications called on both strands of the same record, @CO including potentially at the same location simultaneously. * 0 * 0 0 * * 0 0 AGGATCTCTAGCGGATCGGCGGGGGATATGCCATAT * Mm:Z:C+m,1,3,0;G-m,0,2,0,4;G+o,4; Ml:B:C,128,153,179,115,141,166,192,102 pysam-0.23.0/tests/pysam_data/MM-explicit.sam000066400000000000000000000020731475062545500210620ustar00rootroot00000000000000@CO Testing explicit vs implicit base modifications. @CO This covers the case where a lack of a signal could be either @CO implicitly assumed to be no-mod (default) or assumed to be @CO unchecked and require an explicit statement to indicate it was @CO looked at and no base modification was observed. @CO @CO ATCATCATTCCTACCGCTATAGCCT r1; implicit @CO - - .. -. - -- @CO Mm M @CO - - .. -. - -- @CO hH h @CO @CO ATCATCATTCCTACCGCTATAGCCT r2; explicit to a small region @CO - - ?? ?? ? -- @CO Mm mM m @CO - - ?? ?? ? -- @CO hH hh h @CO @CO ATCATCATTCCTACCGCTATAGCCT r3; mixture @CO - - . -. - -- @CO M M @CO - - ?? ?? ? -- @CO hH hh h -- @CO r1 0 * 0 0 * * 0 0 ATCATCATTCCTACCGCTATAGCCT * Mm:Z:C+mh,2,0,1; Ml:B:C,200,10,50,170,160,20 r2 0 * 0 0 * * 0 0 ATCATCATTCCTACCGCTATAGCCT * Mm:Z:C+mh?,2,0,0,0,0; Ml:B:C,200,10,50,170,10,5,160,20,10,5 r3 0 * 0 0 * * 0 0 ATCATCATTCCTACCGCTATAGCCT * Mm:Z:C+m.,2,2;C+h?,2,0,0,0,0; Ml:B:C,200,160,10,170,5,20,5 pysam-0.23.0/tests/pysam_data/MM-multi.sam000066400000000000000000000010311475062545500203640ustar00rootroot00000000000000@CO Testing multiple m, h and N modifications on the same read. @CO r1 has them separated out. @CO r2 has them combined together, for example as produced by @CO a joint basecaller which assigns probabilities to all @CO trained events simultaneously. r1 0 * 0 0 * * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA * Mm:Z:C+m,2,2,1,4,1;C+h,6,7;N+n,15,2; Ml:B:C,128,153,179,204,230,159,6,215,240 MN:i:36 r2 0 * 0 0 * * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA * Mm:Z:C+mh,2,2,0,0,4,1;N+n,15; Ml:B:C,77,159,103,133,128,108,154,82,179,57,204,31,240 pysam-0.23.0/tests/pysam_data/MM-orient.sam000066400000000000000000000007761475062545500205510ustar00rootroot00000000000000@CO Testing mods on top and bottom strand, but also in @CO original vs reverse-complemented orientation top-fwd 0 * 0 0 * * 0 0 AGGATCTCTAGCGGATCGGCGGGGGATATGCCATAT * Mm:Z:C+m,1,3,0; Ml:B:C,128,153,179 top-rev 16 * 0 0 * * 0 0 ATATGGCATATCCCCCGCCGATCCGCTAGAGATCCT * Mm:Z:C+m,1,3,0; Ml:B:C,128,153,179 bot-fwd 0 * 0 0 * * 0 0 AGGATCTCTAGCGGATCGGCGGGGGATATGCCATAT * Mm:Z:G-m,0,0,4,3; Ml:B:C,115,141,166,192 bot-rev 16 * 0 0 * * 0 0 ATATGGCATATCCCCCGCCGATCCGCTAGAGATCCT * Mm:Z:G-m,0,0,4,3; Ml:B:C,115,141,166,192 pysam-0.23.0/tests/pysam_data/Makefile000066400000000000000000000050251475062545500176700ustar00rootroot00000000000000SAM=$(wildcard *.sam) BAM=$(SAM:%.sam=%.bam) BAI=$(BAM:%.bam=%.bam.bai) CRAM=ex1.cram ex2.cram ex3.cram CRAI=$(CRAM:%.cram=%.cram.crai) NO_PG:=$(findstring --no-PG,$(shell samtools view '-?')) # ex2.bam - bam file without index all: all.stamp all.stamp: ex1.pileup.gz \ ex1.sam ex1.bam \ ex2.sam.gz ex2.sam ex2.bam ex2.bam.bai \ with_md.sam.gz with_md.bam with_md.bam.bai \ uncompressed.bam \ $(BAM) $(BAI) \ $(CRAM) $(CRAI) \ example_bai.bam \ rg_with_tab.bam \ ex2_truncated.bam \ ex2_corrupt.bam \ empty.bam empty.bam.bai \ explicit_index.bam explicit_index.cram \ faidx_empty_seq.fq.gz \ ex1.fa.gz ex1.fa.gz.fai ex1.fa.gz.gzi \ ex1_csi.bam \ example_reverse_complement.bam \ example_dash_in_chr.bam touch $@ # ex2.sam - as ex1.sam, but with header ex2.sam.gz: ex1.bam ex1.bam.bai samtools view $(NO_PG) -h ex1.bam | gzip > ex2.sam.gz with_md.sam.gz: ex2.bam ex1.fa samtools calmd $(NO_PG) --output-fmt BAM $^ > $@ #%.bam: %.sam ex1.fa.fai # samtools view $(NO_PG) -bo $@ -t ex1.fa.fai $< uncompressed.bam: ex2.sam samtools view $(NO_PG) -bu -o $@ $< %.bam: %.sam samtools view $(NO_PG) -bo $@ $< %.cram: %.sam samtools view $(NO_PG) -Co $@ -T ex1.fa $< %.cram.crai: %.cram samtools index $< %.sam: %.sam.gz gunzip < $< > $@ %.fa.fai: %.fa samtools faidx $< %.fa.gz.fai %.fa.gz.gzi: %.fa.gz samtools faidx $< ex1.bam:ex1.sam.gz ex1.fa.fai samtools view $(NO_PG) -bo ex1.bam -t ex1.fa.fai ex1.sam.gz %.bam.bai:%.bam samtools index $< ex1.pileup.gz:ex1.bam ex1.fa samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz ex2_truncated.bam: ex2.bam dd if=ex2.bam of=ex2_truncated.bam bs=$$((`wc -c < ex2.bam`-512)) count=1 # Append a corrupt read with block_size < sizeof(bam_core_t fields) ex2_corrupt.bam: ex2.bam (bgzip -d < $<; printf '\37\0\0\0\1\0\0\0') | bgzip > $@ ex1_csi.bam: ex1.bam cp ex1.bam ex1_csi.bam samtools index -c ex1_csi.bam empty.bam: ex2.sam grep "^@" $< | samtools view $(NO_PG) -bo $@ - example_unmapped_reads_no_sq.bam: example_unmapped_reads_no_sq.sam touch tmp.list samtools view $(NO_PG) -bo $@ -t tmp.list $< rm -f tmp.list example_bai.bam: ex1.bam cp ex1.bam $@ samtools index $@ mv $@.bai example_bai.bai explicit_index.bam: ex1.bam cp ex1.bam $@ explicit_index.cram: ex1.cram cp ex1.cram $@ clean: rm -fr [A-Za-z]*.bam *.bai *.csi *.fai *.gzi *.pileup* [A-Za-z]*.cram *.crai \ all.lock all.stamp *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ *.fq.gz %.fq.gz: %.fq gzip < $< > $@ %.fa.gz: %.fa bgzip < $< > $@ pysam-0.23.0/tests/pysam_data/ex1.bed000066400000000000000000000000321475062545500173720ustar00rootroot00000000000000chr1 10 100 chr1 100 1000 pysam-0.23.0/tests/pysam_data/ex1.fa000066400000000000000000000062311475062545500172350ustar00rootroot00000000000000>chr1 CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGCT GTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTGGCTGAGGGGTGCAGAGCCGAGTCAC GGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAG TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAATGAAAACTATATTTATGCTATTC AGTTCTAAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAA CAACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGTTACC AAATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCT CTTCTTCCAAAGATGAAACGCGTAACTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA ATGGACCTGTGATATCTGGATTCTGGGAAATTCTTCATCCTGGACCCTGAGAGATTCTGC AGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAGCCATCACAATGAAC AACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCAACCTCATACACACAC ATGGTTTAGGGGTATAATACCTCTACATGGCTGATTATGAAAACAATGTTCCCCAGATAC CATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCT TTTGGCATTTGCCTTCAGACCCTACACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTT TCCCATCATGAAGCACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAGGTGCACTAAT GCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAAT ACATGAGATTATTAGGAAATGCTTTACTGTCATAACTATGAAGAGACTATTGCCAGATGA ACCACACATTAATACTATGTTTCTTATCTGCACATTACTACCCTGCAATTAATATAATTG TGTCCATGTACACACGCTGTCCTATGTACTTATCATGACTCTATCCCAAATTCCCAATTA CGTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAG TCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGC TTGGGCTGTAATGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTC TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTCTG TTTCTTTGTTTGATTTGGTGGAAGACATAATCCCACGCTTCCTATGGAAAGGTTGTTGGG AGATTTTTAATGATTCCTCAATGTTAAAATGTCTATTTTTGTCTTGACACCCAACTAATA TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTC TCCCTCGTCTTCTTA >chr2 TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAAGAAATTACAAAATATAGTTGAAAG CTCTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCT TATGAATTAACCCAGTCAGACAAAAATAAAGAAAAAAATTTTAAAAATGAACAGAGCTTT CAAGAAGTATGAGATTATGTAAAGTAACTGAACCTATGAGTCACAGGTATTCCTGAGGAA AAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT AGTCTTGCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATAC ATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAG GAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGGAAATCCCAT CAGAATAACAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAAGAGATTGGATCTAATT TTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGTTATGCCCTGCTAAACTA AGCATCATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATA ATTCATCATCACTAAACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAAT TAAAGTTCAATACTCACCATCATAAATACACACAAAAGTACAAAACTCACAGGTTTTATA AAACAATTGAGACTACAGAGCAACTAGGTAAAAAATTAACATTACAACAGGAACAAAACC TCATATATCAATATTAACTTTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAGATATA GATTGGCAGAACAGATTTAAAAACATGAACTAACTATATGCTGTTTACAAGAAACTCATT AATAAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAAACCA AATGAGAGAAGGAGTAGCTATACTTATATCAGATAAAGCACACTTTAAATCAACAACAGT AAAATAAAACAAAGGAGGTCATCATACAATGATAAAAAGATCAATTCAGCAAGAAGATAT AACCATCCTACTAAATACATATGCACCTAACACAAGACTACCCAGATTCATAAAACAAAT ACTACTAGACCTAAGAGGGATGAGAAATTACCTAATTGGTACAATGTACAATATTCTGAT GATGGTTACACTAAAAGCCCATACTTTACTGCTACTCAATATATCCATGTAACAAATCTG CGCTTGTACTTCTAAATCTATAAAAAAATTAAAATTTAACAAAAGTAAATAAAACACATA GCTAAAACTAAAAAAGCAAAAACAAAAACTATGCTAAGTATTGGTAAAGATGTGGGGAAA AAAGTAAACTCTCAAATATTGCTAGTGGGAGTATAAATTGTTTTCCACTTTGGAAAACAA TTTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTTGCATGC CAGAAAAAAATATTTACAGTAACT pysam-0.23.0/tests/pysam_data/ex1.sam.gz000066400000000000000000003262021475062545500200510ustar00rootroot000000000000009_ex1.sam}ɒȲkvL2QZk&Sj m {`p@>7o㢍"QuF? _?y>qПŸOUC_RSM!%uK ?YB1u#|;AHw (Sj\ |E[tQվ +IZU`YAi݂y`+ $[":zg8 \|>~~bAU_g.nӆN)P0VU{X]]Wv*$D%h9$d]_F%vV_W՝?JG\|> +ߜ~9Pn0RP^vKc?i-Oo\Q(uP1H(kvta\ZܰFvBЭ"X]j_Hӎ V`BB+fђ]3ٱBK>9]K7$QD) ,FHn*YxƨOn,9x ]`JDkv7ޤqPM`9:|p}G,"mn[>%5zf DqZk>Koc уÌH!?tpn,ѡov;x[fk5Q[gh+ܻctm|u{e^-.WKd5w-LGx?9ox@ciqܠj~zL]ޚWDdz*KKdGgLnG Ig,cI[ " q؊й  <'??RҰtguEJ f~nugέҳpގNK+I q+ , uue/GnϠ+΃0PܼzZlXN0O1k8NImMo|r*2h`ZnWEpQ5MyA]x$69QV_Dy(/w̔MM Iڤd&z ߁KT=l7ICy[KLFl}}qot@; 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Uܢ'1C֕MCzbj灀h=*NR^@m Lb!zjl] @ Д^_HV:R b˜N6ӘeAa 8EF-(bK|J9|R btK{6gF7 -ش'Ñ8~~҉!㷊 -킔$]>$v htׇzrBf=UdIk^NocRǑ%6"]|K$,CMR-ȝSKNYF*hXf/_7N|ەT*cvofWUzHmYSIܫG\TQ}JSHJ,], O^16E&JB'm.'6\ܘYV8] {7T"Sg۶!T%Po poMzAp(@[[ϮI*H#J mQ §fٝב`(lsXYXOZ?;U+ hU aXVTăw$uHnV)4XeRJP"Ih;=I4hrK@r|mlT2ڶ*)U;=|pF|31!߮\1ODEK9`n0@,Br:V̙lb"+ō W^ NJ,?~\*= 9cWyW{ {ƆSzSNGRP26$-N"k[6B:wp@ɋDA~>.p""$I$ID2Bޞ'zk$Iy~4H$I$I$I̎&I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$IdN;|&I%$["v.$Gk;\!I$I$I$I$I$I^[jBC1NaБBJ숄֎QJo<&PbCA<ыXӹqvB8yyogV!I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$O65"Ӹk^h>of4nګ{9Wjy=yJo2xn^u?zێ3]_7:H<#I$I$I$I$I$I$I$I$y/BC5;JAQXF*,sxa b <[X> ?$Iun$Ir~ $I$Irzw'-$I$I$I$I$I$I$I$I_I$I$I$I$I$I$I${7}-b8ۓe%a/ϥ̟rOV3:y՝Nﺗ^E6>g>~է[K$I$Izs%I$I$I$I$9:/&9]$I$I$I$i]ݺVBC] ACAف|,B)qg4V4ogv0a܇$Iو$I$I$I1I$I$I$I$I$I$I$I$IiھA/qslSU',yZ#ON[:nK?3/I$I$I$I$I$I$I$I$I$g;$I$I$I$I$I$I$I$I$Ig BC ݽiP3M60 Ft Gs!;+ m p""8$I$I$I$I$IC$I$I$Iޏnz0sQ|zgw?]2_u^or[?=տ~է晿_$I$I$I$I$Gv;k$I$I$I$I$I$I$I$I$I$IXm$I$I$I$I$I$I$I_<:BC;K]AJ-B@"&B:!W$Gcc#i,ۥ_Hi*`aa#XXX[$I$I$$I$I$ICd~) {EgA3$|) zZJkFϿP9>lH$IN>I$I#I$I̳cCsy>0Ϗ(mf$I$I$Ir":qm]{eNDnd~W%F{ u. #/|޶őy*g:oΗs?/Kk{_ב>8|&I$I$Il?so$$I$I$I$I$I$I$g~;g~{$I$IYӀ$լBߙ5f5Q( m|Ոg_ ?l|ӯYgSZۖ1@]ٰkmgFj(|_^ ?|ޮx%\Gp9KwsKΗ/oBsBCŻ 04We,  Rv$K>m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۞{_m۶k|mm۶m۶rm۶m۶m۶m۶m۶m۶ksOv_CBC =jaY0`aeH Rx k &J,񱫶x^fFDfq$I$I$I$I$I$I$IigA$I$I$I$I$I$I$I$I$I$u#&I$I$I$I93.ҚXWec棏H$3#:~i|yM'wy{?0r_O߲_mwH$I$I$I$I$I$I$I|ϿBC;ϻJCAR} m iM)"j[t!o`cgelm<8HZ ->foDq|윐$I$I$I$I$I+wNI$I$I$I$I$I$I$I$I$I$I$I$I$II$I$I$I$IrtI$I$I$I$IwӅk-G4n]fo*mgxG?mdarWrt5bk]׼waﳮwKޫVޒco{'I$I$ 6BC=DPvC^o-^DUO4}cc۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m۶m?鼰}՟ҶmPٶm۶m۶m۶m۶mSm۶m۶m۶7?4iU3ݷ"$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I$I8NCBCpysam-0.23.0/tests/pysam_data/ex10.sam000066400000000000000000000033701475062545500175100ustar00rootroot00000000000000@HD VN:1.0 @SQ SN:1 LN:249250621 read1 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:i:65536 ZL:i:25 read2 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:i:214748 ZL:i:25 read3 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:i:2147484 ZL:i:25 read4 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:i:2147483647 ZL:i:25 read5 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:i:-65536 ZL:i:25 read6 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:i:-214748 ZL:i:25 read7 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:i:-2147484 ZL:i:25 read8 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:i:-2147483647 ZL:i:25 read1 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:f:65536 ZL:i:25 read2 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:f:214748 ZL:i:25 read3 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:f:2147484 ZL:i:25 read5 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:f:-65536 ZL:i:25 read6 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:f:-214748 ZL:i:25 read7 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:f:-2147484 ZL:i:25 pysam-0.23.0/tests/pysam_data/ex3.sam000066400000000000000000000015471475062545500174360ustar00rootroot00000000000000@HD VN:1.0 @SQ SN:chr1 LN:1575 AH:chr1:5000000-5010000 @SQ SN:chr2 LN:1584 AH:* @RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 CN:name:with:colon @RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 CN:name:with:colon @PG ID:P1 VN:1.0 @PG ID:P2 VN:1.1 @CO this is a comment @CO this is another comment read_28833_29006_6945 99 chr1 33 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:22 RG:Z:L1 PG:Z:P1 XT:A:U read_28701_28881_323b 147 chr2 88 30 35M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 RG:Z:L2 PG:Z:P2 XT:A:R read_28701_28881_323c 147 chr2 88 30 35M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< test_clipped1 99 chr2 997 20 4S6M1D20M5S = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:21 RG:Z:L1 PG:Z:P1 XT:A:U pysam-0.23.0/tests/pysam_data/ex4.sam000066400000000000000000000007141475062545500174320ustar00rootroot00000000000000@HD VN:1.0 @SQ SN:chr1 LN:100 @SQ SN:chr2 LN:100 @RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 @RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 @CO this is a comment @CO this is another comment read_28833_29006_6945 99 chr1 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 RG:Z:L1 read_28701_28881_323b 147 chr2 21 30 35M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 RG:Z:L2 pysam-0.23.0/tests/pysam_data/ex5.sam000066400000000000000000000004251475062545500174320ustar00rootroot00000000000000@HD VN:1.0 @SQ SN:chr1 LN:100 @SQ SN:chr2 LN:100 read_28833_29006_6945 0 * 0 0 * * 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< read_28701_28881_323b 0 * 0 0 * * 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< pysam-0.23.0/tests/pysam_data/ex6.sam000066400000000000000000000005141475062545500174320ustar00rootroot00000000000000@HD VN:1.0 @SQ SN:chr1 LN:1575 @SQ SN:chr2 LN:1584 read_28833_29006_6945 99 chr1 33 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 RG:Z:L1 read_28701_28881_323b 147 chr2 88 30 35M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 RG:Z:L2 pysam-0.23.0/tests/pysam_data/ex7.sam.donottest000066400000000000000000000004671475062545500214640ustar00rootroot00000000000000read_28833_29006_6945 99 chr1 33 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 RG:Z:L1 PG:Z:P1 XT:A:U read_28701_28881_323b 147 chr2 88 30 35M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 RG:Z:L2 PG:Z:P2 XT:A:R pysam-0.23.0/tests/pysam_data/ex8.sam000066400000000000000000000010041475062545500174270ustar00rootroot00000000000000@HD VN:1.0 @SQ SN:2 LN:48297693 GJP00TM04CAQ5W 0 2 38297693 60 45H51M1D13M1D12M1D9M2D5M1D7M4D2M1I6M1D28M1D5M1D2M1D18M55H * 0 0 CATGAAGAACCGCTGGGTATGGAGCACACCTCACCTGATGGACAGTTGATTATGCTCACCTTAACGCTAATTGAGAGCAGCACAAGAGGACTGGAAACTAGAATTTACTCCTCATCTCCGAAGATGTGAATATTCTAAATTCAGCTTGCCTCTTGCTTC IID7757111/=;?///:D>777;EEGAAAEEIHHIIIIIIIIIIIIIIBBBIIIIH==<<<<>>D?1112544556::03---//25.22=;DD?;;;>BDDDEEEGGGA<8889>?999<0////8888>=??@DDDDFFFF???:;;;;AAA???DDDDFFFAAAAFFD8AAFFFC???CFFFFFFFFFFFFFFFFAAAAFFFFCCCF<<<=424226622....666=?==4466444@?4444==?;;;9688<0...:::9<:7988989????984444A@?AABBA=?==; AS:i:260 XS:i:239 XF:i:2 XE:i:3 XN:i:1 RG:Z:mu16_454_mu16 pysam-0.23.0/tests/pysam_data/ex9_nofail.sam000066400000000000000000000637511475062545500210010ustar00rootroot00000000000000@HD VN:1.0 GO:none SO:coordinate @SQ SN:CUTC000001 LN:810 @SQ SN:CUTC000002 LN:1213 @SQ SN:CUTC000003 LN:525 @SQ SN:CUTC000004 LN:620 @SQ SN:CUTC000005 LN:550 @SQ SN:CUTC000006 LN:723 @SQ SN:CUTC000007 LN:773 @SQ SN:CUTC000008 LN:667 @SQ SN:CUTC000009 LN:593 @SQ SN:CUTC000010 LN:556 @SQ SN:CUTC000011 LN:519 @SQ SN:CUTC000012 LN:537 @SQ SN:CUTC000013 LN:930 @SQ SN:CUTC000014 LN:944 @SQ SN:CUTC000015 LN:829 @SQ SN:CUTC000016 LN:1109 @SQ SN:CUTC000017 LN:513 @SQ SN:CUTC000018 LN:1043 @SQ SN:CUTC000019 LN:884 @SQ SN:CUTC000020 LN:567 @SQ SN:CUTC000021 LN:1001 @SQ SN:CUTC000022 LN:754 @SQ SN:CUTC000023 LN:1045 @SQ SN:CUTC000024 LN:1091 @SQ SN:CUTC000025 LN:606 @SQ SN:CUTC000026 LN:635 @SQ SN:CUTC000027 LN:563 @SQ SN:CUTC000028 LN:830 @SQ SN:CUTC000029 LN:1456 @SQ SN:CUTC000030 LN:872 @SQ SN:CUTC000031 LN:742 @SQ SN:CUTC000032 LN:553 @SQ SN:CUTC000033 LN:624 @SQ SN:CUTC000034 LN:641 @SQ SN:CUTC000035 LN:695 @SQ SN:CUTC000036 LN:1519 @SQ SN:CUTC000037 LN:536 @SQ SN:CUTC000038 LN:619 @SQ SN:CUTC000039 LN:643 @SQ SN:CUTC000040 LN:650 @SQ SN:CUTC000041 LN:571 @SQ SN:CUTC000042 LN:1457 @SQ SN:CUTC000043 LN:618 @SQ SN:CUTC000044 LN:1261 @SQ SN:CUTC000045 LN:544 @SQ SN:CUTC000046 LN:1234 @SQ SN:CUTC000047 LN:867 @SQ SN:CUTC000048 LN:792 @SQ SN:CUTC000049 LN:1076 @SQ SN:CUTC000050 LN:479 @SQ SN:CUTC000051 LN:584 @SQ SN:CUTC000052 LN:841 @SQ SN:CUTC000053 LN:518 @SQ SN:CUTC000054 LN:1052 @SQ SN:CUTC000055 LN:626 @SQ SN:CUTC000056 LN:773 @SQ SN:CUTC000057 LN:542 @SQ SN:CUTC000058 LN:566 @SQ SN:CUTC000059 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SN:CUTC001002 LN:1005 @SQ SN:CUTC001003 LN:1411 @SQ SN:CUTC001004 LN:853 @SQ SN:CUTC001005 LN:621 @SQ SN:CUTC001006 LN:1374 @SQ SN:CUTC001007 LN:1122 @SQ SN:CUTC001008 LN:1098 @SQ SN:CUTC001009 LN:819 @SQ SN:CUTC001010 LN:939 @SQ SN:CUTC001011 LN:591 @SQ SN:CUTC001012 LN:580 @SQ SN:CUTC001013 LN:1057 @SQ SN:CUTC001014 LN:1551 @SQ SN:CUTC001015 LN:701 @SQ SN:CUTC001016 LN:885 @SQ SN:CUTC001017 LN:1209 @RG ID:mu16_454_mu16 PL:454 LB:mu16 SM:mu16 @RG ID:upv196_454_upv196 PL:454 LB:upv196 SM:upv196 CUESOXRA74 0 CUTC000001 1 10 77M1I222M * 0 0 GCCTTTTATAATTATTATAAATTTCGGTTGACCCGACCCCATTAGACAGAGTCTATTAAAGCCCCGTGAAAGCCCGGCAAAACCCAGTAGCGCAGAGATCGGCGAGGGCGAATTTTCGATTGCATTTTCGTTCGTTTCTCTTCTGAATTTCTGTAATCTGTAACGATGTCTCAGACTACTGTCCTCAAGGTTGCTATGTCATGTCAGGGCTGTGTTGGAGCCGCCAAAAGGGTCTTGGGGAAACTGGAAGGTGTTGAAACATTTGACATCGACATAGATGCACAAAAGGTGACTGTGAAA 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@SQ SN:GL000009.2 LN:201709 @SQ SN:GL000194.1 LN:191469 @SQ SN:GL000195.1 LN:182896 @SQ SN:GL000205.2 LN:185591 @SQ SN:GL000208.1 LN:92689 @SQ SN:GL000213.1 LN:164239 @SQ SN:GL000214.1 LN:137718 @SQ SN:GL000216.2 LN:176608 @SQ SN:GL000218.1 LN:161147 @SQ SN:GL000219.1 LN:179198 @SQ SN:GL000220.1 LN:161802 @SQ SN:GL000221.1 LN:155397 @SQ SN:GL000224.1 LN:179693 @SQ SN:GL000225.1 LN:211173 @SQ SN:GL000226.1 LN:15008 @SQ SN:KI270302.1 LN:2274 @SQ SN:KI270303.1 LN:1942 @SQ SN:KI270304.1 LN:2165 @SQ SN:KI270305.1 LN:1472 @SQ SN:KI270310.1 LN:1201 @SQ SN:KI270311.1 LN:12399 @SQ SN:KI270312.1 LN:998 @SQ SN:KI270315.1 LN:2276 @SQ SN:KI270316.1 LN:1444 @SQ SN:KI270317.1 LN:37690 @SQ SN:KI270320.1 LN:4416 @SQ SN:KI270322.1 LN:21476 @SQ SN:KI270329.1 LN:1040 @SQ SN:KI270330.1 LN:1652 @SQ SN:KI270333.1 LN:2699 @SQ SN:KI270334.1 LN:1368 @SQ SN:KI270335.1 LN:1048 @SQ SN:KI270336.1 LN:1026 @SQ SN:KI270337.1 LN:1121 @SQ SN:KI270338.1 LN:1428 @SQ SN:KI270340.1 LN:1428 @SQ SN:KI270362.1 LN:3530 @SQ SN:KI270363.1 LN:1803 @SQ SN:KI270364.1 LN:2855 @SQ SN:KI270366.1 LN:8320 @SQ SN:KI270371.1 LN:2805 @SQ SN:KI270372.1 LN:1650 @SQ SN:KI270373.1 LN:1451 @SQ SN:KI270374.1 LN:2656 @SQ SN:KI270375.1 LN:2378 @SQ SN:KI270376.1 LN:1136 @SQ SN:KI270378.1 LN:1048 @SQ SN:KI270379.1 LN:1045 @SQ SN:KI270381.1 LN:1930 @SQ SN:KI270382.1 LN:4215 @SQ SN:KI270383.1 LN:1750 @SQ SN:KI270384.1 LN:1658 @SQ SN:KI270385.1 LN:990 @SQ SN:KI270386.1 LN:1788 @SQ SN:KI270387.1 LN:1537 @SQ SN:KI270388.1 LN:1216 @SQ SN:KI270389.1 LN:1298 @SQ SN:KI270390.1 LN:2387 @SQ SN:KI270391.1 LN:1484 @SQ SN:KI270392.1 LN:971 @SQ SN:KI270393.1 LN:1308 @SQ SN:KI270394.1 LN:970 @SQ SN:KI270395.1 LN:1143 @SQ SN:KI270396.1 LN:1880 @SQ SN:KI270411.1 LN:2646 @SQ SN:KI270412.1 LN:1179 @SQ SN:KI270414.1 LN:2489 @SQ SN:KI270417.1 LN:2043 @SQ SN:KI270418.1 LN:2145 @SQ SN:KI270419.1 LN:1029 @SQ SN:KI270420.1 LN:2321 @SQ SN:KI270422.1 LN:1445 @SQ SN:KI270423.1 LN:981 @SQ SN:KI270424.1 LN:2140 @SQ SN:KI270425.1 LN:1884 @SQ SN:KI270429.1 LN:1361 @SQ SN:KI270435.1 LN:92983 @SQ SN:KI270438.1 LN:112505 @SQ SN:KI270442.1 LN:392061 @SQ SN:KI270448.1 LN:7992 @SQ SN:KI270465.1 LN:1774 @SQ SN:KI270466.1 LN:1233 @SQ SN:KI270467.1 LN:3920 @SQ SN:KI270468.1 LN:4055 @SQ SN:KI270507.1 LN:5353 @SQ SN:KI270508.1 LN:1951 @SQ SN:KI270509.1 LN:2318 @SQ SN:KI270510.1 LN:2415 @SQ SN:KI270511.1 LN:8127 @SQ SN:KI270512.1 LN:22689 @SQ SN:KI270515.1 LN:6361 @SQ SN:KI270516.1 LN:1300 @SQ SN:KI270517.1 LN:3253 @SQ SN:KI270518.1 LN:2186 @SQ SN:KI270519.1 LN:138126 @SQ SN:KI270521.1 LN:7642 @SQ SN:KI270522.1 LN:5674 @SQ SN:KI270528.1 LN:2983 @SQ SN:KI270529.1 LN:1899 @SQ SN:KI270530.1 LN:2168 @SQ SN:KI270538.1 LN:91309 @SQ SN:KI270539.1 LN:993 @SQ SN:KI270544.1 LN:1202 @SQ SN:KI270548.1 LN:1599 @SQ SN:KI270579.1 LN:31033 @SQ SN:KI270580.1 LN:1553 @SQ SN:KI270581.1 LN:7046 @SQ SN:KI270582.1 LN:6504 @SQ SN:KI270583.1 LN:1400 @SQ SN:KI270584.1 LN:4513 @SQ SN:KI270587.1 LN:2969 @SQ SN:KI270588.1 LN:6158 @SQ SN:KI270589.1 LN:44474 @SQ SN:KI270590.1 LN:4685 @SQ SN:KI270591.1 LN:5796 @SQ SN:KI270593.1 LN:3041 @SQ SN:KI270706.1 LN:175055 @SQ SN:KI270707.1 LN:32032 @SQ SN:KI270708.1 LN:127682 @SQ SN:KI270709.1 LN:66860 @SQ SN:KI270710.1 LN:40176 @SQ SN:KI270711.1 LN:42210 @SQ SN:KI270712.1 LN:176043 @SQ SN:KI270713.1 LN:40745 @SQ SN:KI270714.1 LN:41717 @SQ SN:KI270715.1 LN:161471 @SQ SN:KI270716.1 LN:153799 @SQ SN:KI270717.1 LN:40062 @SQ SN:KI270718.1 LN:38054 @SQ SN:KI270719.1 LN:176845 @SQ SN:KI270720.1 LN:39050 @SQ SN:KI270721.1 LN:100316 @SQ SN:KI270722.1 LN:194050 @SQ SN:KI270723.1 LN:38115 @SQ SN:KI270724.1 LN:39555 @SQ SN:KI270725.1 LN:172810 @SQ SN:KI270726.1 LN:43739 @SQ SN:KI270727.1 LN:448248 @SQ SN:KI270728.1 LN:1872759 @SQ SN:KI270729.1 LN:280839 @SQ SN:KI270730.1 LN:112551 @SQ SN:KI270731.1 LN:150754 @SQ SN:KI270732.1 LN:41543 @SQ SN:KI270733.1 LN:179772 @SQ SN:KI270734.1 LN:165050 @SQ SN:KI270735.1 LN:42811 @SQ SN:KI270736.1 LN:181920 @SQ SN:KI270737.1 LN:103838 @SQ SN:KI270738.1 LN:99375 @SQ SN:KI270739.1 LN:73985 @SQ SN:KI270740.1 LN:37240 @SQ SN:KI270741.1 LN:157432 @SQ SN:KI270742.1 LN:186739 @SQ SN:KI270743.1 LN:210658 @SQ SN:KI270744.1 LN:168472 @SQ SN:KI270745.1 LN:41891 @SQ SN:KI270746.1 LN:66486 @SQ SN:KI270747.1 LN:198735 @SQ SN:KI270748.1 LN:93321 @SQ SN:KI270749.1 LN:158759 @SQ SN:KI270750.1 LN:148850 @SQ SN:KI270751.1 LN:150742 @SQ SN:KI270752.1 LN:27745 @SQ SN:KI270753.1 LN:62944 @SQ SN:KI270754.1 LN:40191 @SQ SN:KI270755.1 LN:36723 @SQ SN:KI270756.1 LN:79590 @SQ SN:KI270757.1 LN:71251 @PG ID:STAR PN:STAR VN:STAR_2.4.1a HWI-C00113:131:HMHYWADXX:1:2202:17748:47494 272 1 14792 0 51M * 0 0 GGGCCTCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCAT CCCFFFFFHHHHHFHIIJJIJAFHJJJJJGJIIHGIJGGIJJIIJIIJJJG NH:i:6 HI:i:3 AS:i:47 nM:i:1 HWI-C00113:131:HMHYWADXX:1:2202:17748:47494 272 1 14792 0 38M140N13M * 0 0 GGGCCTCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCAT CCCFFFFFHHHHHFHIIJJIJAFHJJJJJGJIIHGIJGGIJJIIJIIJJJG NH:i:6 HI:i:3 AS:i:47 nM:i:1 HWI-C00113:131:HMHYWADXX:2:1214:7658:35836 272 1 14792 0 38M140N13M * 0 0 GGGCCCCTCACCAGCCCCAGGTCTTTTCCCAGAGATGCCCTTGCGCCTCAT CCCFFFFFHHHHHJJJJJJJJCGHIJJIJJJJJJIJJGIJJIJIJIJJJJI NH:i:6 HI:i:3 AS:i:47 nM:i:1 HWI-C00113:131:HMHYWADXX:1:2114:4116:44566 272 1 14794 0 36M140N15M * 0 0 GCCCCTCACCAGCCCCAGGTCTTTTCCCAGAGATGCCCTTGCGCCTCATGA <@@DDDDDDFHCFHEFGBE+2AFH@GIEGF=GGHII9FB?BFFDEE??BD?D@DADDDDBDDD@FGHFHFHIHGI@?DGC@CF NH:i:7 HI:i:4 AS:i:47 nM:i:1 HWI-C00113:131:HMHYWADXX:1:1105:1515:82248 272 1 14802 0 28M140N23M * 0 0 CCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTG ??:ADBDDDDD:A<+C?AFDB@E?F4<*?:?1:??):??0009??9?(8BC NH:i:7 HI:i:4 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:1:1110:16355:5537 272 1 14802 0 28M140N23M * 0 0 CCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTG @CCFFFFFHH?ADHGIJIJJJJJIIEHIJJJJJIJIGIIJJIJJIIJIJJJ NH:i:7 HI:i:4 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:1102:17802:20689 272 1 14805 0 25M140N26M * 0 0 GCTCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTG CCCFFFFFHHHHHJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJI NH:i:7 HI:i:4 AS:i:47 nM:i:1 HWI-C00113:131:HMHYWADXX:2:1104:7670:95815 272 1 14805 0 25M140N26M * 0 0 GCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTG @@@DBDDDHHBFDBFGEBBGHG@HIBHIDHBGGGEFBDDDFDGBBBGCHHI NH:i:7 HI:i:4 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:1110:11368:101298 272 1 14805 0 25M140N26M * 0 0 GCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTG BCCFFFFFCFHHHJJJJJIJJJJJJJJJJJJJGJJJJJJJJJJJJJJJIJJ NH:i:7 HI:i:4 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:1115:2363:85646 272 1 14805 0 25M140N26M * 0 0 GCTCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTG @C@FFFB?CFDFHDHGIIIIEGIIIIEDGIIIIIIIIIGGIIGIIGCGHIH NH:i:7 HI:i:4 AS:i:47 nM:i:1 HWI-C00113:131:HMHYWADXX:2:2213:6044:80821 272 1 14805 0 25M140N26M * 0 0 GCTCCGGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTG @@@FFFFFFFBFDGIIJIJGGFHIIIJIIJGIIEHICHIGEGFG?FGHGA>9B8BF@ NH:i:7 HI:i:4 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:1215:4185:31561 272 1 14815 0 15M140N36M * 0 0 CTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCG CCCFFFFFHHHHGJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJH NH:i:7 HI:i:4 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:1:2108:1506:70629 272 1 14816 0 14M140N37M * 0 0 TTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGA ?@@;BDDD=DFFDDDFGGFCA?)1@F?F+AAEEEBFFIIF@DE4= NH:i:8 HI:i:2 AS:i:47 nM:i:1 HWI-C00113:131:HMHYWADXX:1:1108:6828:32713 272 1 15003 0 36M757N15M * 0 0 CCGGCATCAAGTCCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT ?@@ADDDDD?CDD:CFB@:@G@ABGFGFGFBFEAFEEEFCFCF@F=)8=@> NH:i:8 HI:i:2 AS:i:45 nM:i:2 HWI-C00113:131:HMHYWADXX:1:1111:7491:39504 272 1 15003 0 36M757N15M * 0 0 CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT CCCFFDFFFHHHFIGEGHIGIGGDGIJFHEHGGIJJJIJIJJJJJIIIIGI NH:i:8 HI:i:2 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:1:1212:16079:85811 272 1 15003 0 36M757N15M * 0 0 CCGGCATCAAGTCCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT @CCFFFFFHGHHHJJJJJJJIIJJJJJIJIJJHIIJJJJIJJJJJJJIJJJ NH:i:8 HI:i:2 AS:i:45 nM:i:2 HWI-C00113:131:HMHYWADXX:1:2101:7167:50357 272 1 15003 0 36M757N15M * 0 0 CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT @@@DD?DDFHHHD@?CG?FHGIIIIG@??BGHIE;8@BFEG NH:i:8 HI:i:2 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:1211:4828:84953 272 1 15003 0 36M757N15M * 0 0 CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT @BB?DFFFHHHHHIJIJJJJJJJJJJJHIJJIIJJJJJJIIIJJJJJJIJI NH:i:8 HI:i:2 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:2107:20905:80208 272 1 15003 0 36M757N15M * 0 0 CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT @CCFFFFFHHHFBHIIEIIDIHGGGGG@GGHCFGHIIJIGGGGIJIGIGGH NH:i:8 HI:i:2 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:2112:6263:84991 272 1 15003 0 36M757N15M * 0 0 CCGACATCAAGTCCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT @@@?DDDDFBH?FHIGIGIIGG;GHBGCD?DCGIIGHEGBBFHGGIHBFIG NH:i:8 HI:i:2 AS:i:47 nM:i:1 HWI-C00113:131:HMHYWADXX:2:2202:10314:26844 272 1 15003 0 36M757N15M * 0 0 CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT CCCFFFFFHHHHHJJJJJJJJJJJJJJIJJJJIIJJJJJJJJJJJJJJJJJ NH:i:8 HI:i:2 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:2213:21028:90280 272 1 15003 0 36M757N15M * 0 0 CCGACATCAAGTCCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT @@@BDDDAD?FDF9GIBB@@FFG3CFF:DD)?BD*9D@@F4BDEEEFFF8= NH:i:8 HI:i:2 AS:i:47 nM:i:1 HWI-C00113:131:HMHYWADXX:1:1216:14847:22529 272 1 15004 0 35M757N16M * 0 0 CGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCTT @@@FFFFDHHBDHIIIJJJJIIIIIIJJIJJGIJIFIJJIDHHGBEHIJJJ NH:i:8 HI:i:2 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:2111:14281:81135 272 1 15007 0 32M757N19M * 0 0 CATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCTTCTG @@@DDDBD42=:ACFFIE?FFGAFF@FFFDGEAG>D@DBB9BC3D@EDFFA NH:i:8 HI:i:2 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:1:2203:4824:93169 272 1 15008 0 31M757N20M * 0 0 ATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCTTCTGC CCCFFFFFHHHHHJJJJIJJJJHIJIJJJJJJJJGIJJJJI?DFGFHIHJF NH:i:8 HI:i:2 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:1:1112:17298:87937 272 1 15925 1 23M659N28M * 0 0 CACTTCCCTGGGAGCTCCCTGGACTGAAGGAGACGCGCTGCTGCTGCTGTC ?@;;BA;3ABC?C?6EGDGIIBA+AACACD>>:9:??2< NH:i:6 HI:i:2 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:2109:14386:93817 272 1 16728 0 38M92N13M * 0 0 GGGCGGTGGGGGTGGTGTTAGTACCCCATCTTGTAGGTCTTGAGAGGCTCG @CCFFFDDHHHHDHIFHIJJJGHHIIJHHHHHHFFFFEFEEEECDDDDDDB NH:i:6 HI:i:2 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:1:2203:14322:7218 272 1 16741 0 25M110N26M * 0 0 GGTGTTAGTACCCCATCTTGTAGGTCTCAGTGTGGAAGGTGGGCAGTTCTG ?@?DDD?BFFHHFB7EFGGGEFHIHADB8D>822BDG?FHBGEH?FHGG3 NH:i:6 HI:i:1 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:1:2116:7403:96086 272 1 17020 0 36M177N15M * 0 0 GCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTG :?=DDD=AAAC:+BDIIIIIIA? NH:i:7 HI:i:5 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:1209:11002:81132 272 1 17020 0 36M177N15M * 0 0 GCCCGGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTG @@@DD@A<@DDDF;BCGF<4CHCEG?EG@FGF9)?BB:?B?DBF>D?**9B NH:i:7 HI:i:4 AS:i:47 nM:i:1 HWI-C00113:131:HMHYWADXX:2:1115:8064:78307 272 1 17021 0 35M177N16M * 0 0 CCCTGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGC 11844BBDD=FDFEFFFDFI?HEHAFBEHEEEFC?E:FDGDDDH9CBEHHHEEFB?F>GD@3?FB?BB@ NH:i:7 HI:i:6 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:1101:15891:42282 272 1 17028 0 28M177N23M * 0 0 CTGGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCT CCCFFFFFHHHHHJHHIIJJJJJJJJJJIIJJJJIJJJIJJJJJJJJJJJJ NH:i:7 HI:i:6 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:1:1107:10929:6659 272 1 17030 0 26M177N25M * 0 0 GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG CCCFFFFFHHHHDHIHHJJGJJJJJJJIJJIJGIJJJIJJJIJJJJJIJJG NH:i:7 HI:i:6 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:1:1114:7098:71178 272 1 17030 0 26M177N25M * 0 0 GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG =?@BDEEFHBDHFBGIEGIHEHIGDHGEIIJIIIEHIHIIGHDGHIGIIH@ NH:i:7 HI:i:6 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:1:1209:3383:100724 272 1 17030 0 26M177N25M * 0 0 GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG ?@@ADDDDDHDH?EEFHEHIGIIGHGHIFII>BFIH? NH:i:7 HI:i:6 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:1:2111:3771:31345 272 1 17030 0 26M177N25M * 0 0 GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG @@@DFFFFGHDHHHJGIHJJJJGIJJIJIJIIJJIIJJIGHIJJJIJJIJ< NH:i:7 HI:i:6 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:1:2205:14794:36455 272 1 17030 0 26M177N25M * 0 0 GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG CCCFFFFFHHHHHIJJJJJJJJJJJJJJJJJJIJJJJIJJIJJJJJJJJJJ NH:i:7 HI:i:6 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:1107:19701:64552 272 1 17030 0 26M177N25M * 0 0 GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG CCCFFDFFHHHHDGIIJIJJJIIJDGHGJJJJJJIJJJJJJJGIJJJJJJF NH:i:7 HI:i:6 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:1210:18711:88303 272 1 17030 0 26M177N25M * 0 0 GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG CCCFFFFFHHHHHJJJJJJJJIJFIJJJEIIHIIJJIIJJGJJJIJJJJJE NH:i:7 HI:i:6 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:2212:19113:15559 272 1 17030 0 26M177N25M * 0 0 GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG @@@7B>DDC=@BFBGBAFCGBFDB@DHIHIDD>@@GHID NH:i:7 HI:i:6 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:1212:15591:47491 272 1 17031 0 25M177N26M * 0 0 GCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTGC @@C+ADDDDHFFDEGEGIIIDFHIFHIIIIIGEHIIBH>FGGGHGHFGGII NH:i:7 HI:i:6 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:2215:10125:81395 272 1 17031 0 25M859N26M * 0 0 GCACATAGAAGTAGTTCTCTGGGACCTGCAGGGCCCGCTCGTCCAGGGGGC CCCFFFFFGHHHHJJJJJJJJJHJJJJJJIJIIJJJHIJJJJJJJJJIJHE NH:i:6 HI:i:1 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:PLACED:UNMAPPED 4 1 17032 0 * * 0 0 ATGC HIJK HWI-C00113:131:HMHYWADXX:1:2102:9065:90529 16 1 17033 0 2S23M550N26M * 0 0 GTACATAGAAGTAGTTCTCTGGGACAGGTTCTCGGTGGTGTTGAAGAGCAG C@CFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJFHIFHIJIJJJJJJJJ NH:i:5 HI:i:2 AS:i:47 nM:i:0 HWI-C00113:131:HMHYWADXX:1:2204:7767:77376 16 1 17033 0 2S23M550N26M * 0 0 GTACATAGAAGTAGTTCTCTGGGACAGGTTCTCGGTGGTGTTGAAGAGCAG @@@FDFDDBFHADEHEIGIGIJIGHIHG?EDGHGGCFH:B?BD@FGFHGIH NH:i:5 HI:i:2 AS:i:47 nM:i:0 HWI-C00113:131:HMHYWADXX:2:1212:6793:42000 16 1 17033 0 2S23M550N26M * 0 0 GTACATAGAAGTAGTTCTCTGGGACAGGTTCTCGGTGGTGTTGAAGAGCAG @@?DADBD8CFADGFHIIIIE3A9?DH?FHGHH@EHGIEHGGIIIGGHIGHGFDEHGH=FHGIIH NH:i:3 HI:i:1 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:2207:3786:78354 16 1 17340 1 29M237N22M * 0 0 GGGGGTCCAGGAAGACATACTTCTTCTACAGGTTCTCGGTGGTGTTGAAGA CCCFFFFFHHHHHJJJJJIIJJJJJJJJJJJJHHIJIHHBFIHIIJJJJJI NH:i:3 HI:i:1 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:1:1115:8438:81914 16 1 17341 1 28M237N23M * 0 0 GGGGTCCAGGAAGACATACTTCTTCTACAGGTTCTCGGTGGTGTTGAAGAG @@CFFFFDHH?HDGGHIIGIGHIGHGIDIIIFGIIGHHDG:?DFHEHIIII NH:i:3 HI:i:1 AS:i:49 nM:i:0 HWI-C00113:131:HMHYWADXX:2:1114:13486:49038 16 1 17341 1 28M237N23M * 0 0 GGGGTCCAGGAAGACATACTTCTTCTACAGGTTCTCGGTGGTGTTGAAGAG ?@@:D@DDFHAFFHGGFHFHH@CCHIIIII@:CFGFGGC?D)?8DHHGCGI NH:i:3 HI:i:1 AS:i:49 nM:i:0 pysam-0.23.0/tests/pysam_data/example_aligned_pairs.sam000066400000000000000000000571021475062545500232510ustar00rootroot00000000000000@HD VN:1.0 GO:none SO:coordinate @SQ SN:chrM LN:16571 @SQ SN:chr1 LN:249250621 @SQ SN:chr2 LN:243199373 @SQ SN:chr3 LN:198022430 @SQ SN:chr4 LN:191154276 @SQ SN:chr5 LN:180915260 @SQ SN:chr6 LN:171115067 @SQ SN:chr7 LN:159138663 @SQ SN:chr8 LN:146364022 @SQ SN:chr9 LN:141213431 @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 @SQ SN:chr12 LN:133851895 @SQ SN:chr13 LN:115169878 @SQ SN:chr14 LN:107349540 @SQ SN:chr15 LN:102531392 @SQ SN:chr16 LN:90354753 @SQ SN:chr17 LN:81195210 @SQ SN:chr18 LN:78077248 @SQ SN:chr19 LN:59128983 @SQ SN:chr20 LN:63025520 @SQ SN:chr21 LN:48129895 @SQ SN:chr22 LN:51304566 @SQ SN:chrX LN:155270560 @SQ SN:chrY LN:59373566 @RG ID:FC1_NA12892_03 PL:ILLUMINA SM:FC1_NA12892_03 @PG ID:bwa PN:bwa VN:0.7.7-isis-1.0.0 @PG ID:GATK IndelRealigner VN:1.6-23-gf0210b3 CL:knownAlleles=[] targetIntervals=/data/scratch/workspace/RunFolder/Data/Intensities/BaseCalls/Alignment/FC1-NA12892-03_S1_chrM.intervals LODThresholdForCleaning=5.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=150000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=20000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null D0004:230:H08B1ADXX:1:1204:18619:71946 163 chr22 16084109 27 149M = 16084228 268 GTGCAGGCATGGAGATTCTGGGGTGAATCTGCTGAGTTTAAAAGCTTCCTTTGGAGATGCCCCTGGCCCCCTCCACCTGTCAAGAAGAGGCCATCCTATCTGCCTGTCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGC BBBFFBFFFFFFFFFIFIFIFFI0BBFIFIIIIIFFFFIFIIIFFBIFIIIIFI>>>>>>====>=>>;:8,,((1*0536;;=<>;:;>>>>>>>>>>>>>>>>>>>><9=556.2<<<8===<<<9;9=>=>>>>>>>>>>>>>>>>.>>>===>>>>>>>4=>>==;<<896=>===<>>588-1.19<= RG:Z:QW85I PG:Z:tmap MD:Z:140 NM:i:0 AS:i:140 FZ:B:S,100,1,91,0,7,101,0,201,96,204,0,0,87,109,0,7,97,112,1,12,78,197,0,7,100,95,101,202,0,6,0,1,186,0,84,0,244,0,0,324,0,107,195,101,113,0,102,0,104,3,0,101,1,0,212,6,0,0,1,0,74,1,11,0,196,2,197,103,0,108,98,2,7,0,1,2,194,0,180,0,108,0,203,104,16,5,205,0,0,0,1,1,100,98,0,0,204,6,0,79,0,0,101,7,109,90,265,1,27,10,109,102,9,0,292,0,110,0,0,102,112,0,0,84,100,103,2,81,126,0,2,90,0,15,96,15,1,0,2,0,107,92,0,0,101,3,98,15,102,13,116,116,90,93,198,0,0,0,199,92,26,495,100,5,0,100,5,209,0,92,107,90,0,0,0,0,109,194,7,94,200,0,40,197,0,11,0,0,112,110,6,4,200,28,0,196,0,203,1,129,0,0,1,0,94,0,1,0,107,5,201,3,3,100,0,121,0,7,0,1,105,306,3,86,8,183,0,12,163,17,83,22,0,0,1,8,109,103,0,0,295,0,200,16,172,3,16,182,3,11,0,0,223,111,103,0,5,225,0,95 XA:Z:map2-1 XS:i:53 XT:i:38 XF:i:1 XE:i:0 QW85I:468:729 0 chr1 156268499 63 140M15H * 0 0 GTCCAGTCTCCTGTAATTCTTGGGCTTGACTAGGCTTCCGACAACCTGGAGGCATTGCTCTTTCAGGGTATACACTGCAGTGTGATGTTGGCAAAAACAGGCTGTCCATTAACATTGGAAGATGGCACAAACAATTCAGT >>>>>>>====>=>>;:8,,((1*0536;;=<>;:;>>>>>>>>>>>>>>>>>>>><9=556.2<<<8===<<<9;9=>=>>>>>>>>>>>>>>>>.>>>===>>>>>>>4=>>==;<<896=>===<>>588-1.19<= RG:Z:QW85I PG:Z:tmap MD:Z:140 NM:i:0 AS:i:140 FZ:B:s,-100,200,-300,-400 XA:Z:map2-1 XS:i:53 XT:i:38 XF:i:1 XE:i:0 QW85I:468:729 0 chr1 156268499 63 140M15H * 0 0 GTCCAGTCTCCTGTAATTCTTGGGCTTGACTAGGCTTCCGACAACCTGGAGGCATTGCTCTTTCAGGGTATACACTGCAGTGTGATGTTGGCAAAAACAGGCTGTCCATTAACATTGGAAGATGGCACAAACAATTCAGT >>>>>>>====>=>>;:8,,((1*0536;;=<>;:;>>>>>>>>>>>>>>>>>>>><9=556.2<<<8===<<<9;9=>=>>>>>>>>>>>>>>>>.>>>===>>>>>>>4=>>==;<<896=>===<>>588-1.19<= RG:Z:QW85I PG:Z:tmap MD:Z:140 NM:i:0 AS:i:140 FZ:B:c,-100,12 XA:Z:map2-1 XS:i:53 XT:i:38 XF:i:1 XE:i:0 QW85I:468:729 0 chr1 156268499 63 140M15H * 0 0 GTCCAGTCTCCTGTAATTCTTGGGCTTGACTAGGCTTCCGACAACCTGGAGGCATTGCTCTTTCAGGGTATACACTGCAGTGTGATGTTGGCAAAAACAGGCTGTCCATTAACATTGGAAGATGGCACAAACAATTCAGT >>>>>>>====>=>>;:8,,((1*0536;;=<>;:;>>>>>>>>>>>>>>>>>>>><9=556.2<<<8===<<<9;9=>=>>>>>>>>>>>>>>>>.>>>===>>>>>>>4=>>==;<<896=>===<>>588-1.19<= RG:Z:QW85I PG:Z:tmap MD:Z:140 NM:i:0 AS:i:140 FZ:B:C,12,15 XA:Z:map2-1 XS:i:53 XT:i:38 XF:i:1 XE:i:0 QW85I:468:729 0 chr1 156268499 63 140M15H * 0 0 GTCCAGTCTCCTGTAATTCTTGGGCTTGACTAGGCTTCCGACAACCTGGAGGCATTGCTCTTTCAGGGTATACACTGCAGTGTGATGTTGGCAAAAACAGGCTGTCCATTAACATTGGAAGATGGCACAAACAATTCAGT >>>>>>>====>=>>;:8,,((1*0536;;=<>;:;>>>>>>>>>>>>>>>>>>>><9=556.2<<<8===<<<9;9=>=>>>>>>>>>>>>>>>>.>>>===>>>>>>>4=>>==;<<896=>===<>>588-1.19<= RG:Z:QW85I PG:Z:tmap MD:Z:140 NM:i:0 AS:i:140 FZ:B:f,-1.0,5.0,2.5 XA:Z:map2-1 XS:i:53 XT:i:38 XF:i:1 XE:i:0 pysam-0.23.0/tests/pysam_data/example_dash_in_chr.sam000066400000000000000000000006361475062545500227110ustar00rootroot00000000000000@HD VN:1.0 @SQ SN:chr-1 LN:1575 @SQ SN:chr2 LN:1584 @CO this is a comment @CO this is another comment read_28833_29006_6945 99 chr-1 33 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 RG:Z:L1 PG:Z:P1 XT:A:U read_28701_28881_323b 147 chr2 88 30 35M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 RG:Z:L2 PG:Z:P2 XT:A:R pysam-0.23.0/tests/pysam_data/example_empty_header.sam000066400000000000000000002614751475062545500231300ustar00rootroot00000000000000@SQ SN:chr1 LN:1000 XXX0000 0 chr1 100 170 171M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTC * AS:i:170 MS:i:50 XXX0001 0 chr1 100 255 284M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGT * AS:i:283 MS:i:50 XXX0002 0 chr1 100 205 206M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGA * AS:i:205 MS:i:50 XXX0003 0 chr1 100 212 213M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCC * AS:i:212 MS:i:50 XXX0004 0 chr1 100 208 209M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGG * AS:i:208 MS:i:50 XXX0005 0 chr1 100 245 245M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGG * AS:i:245 MS:i:50 XXX0006 0 chr1 100 251 251M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATC * AS:i:251 MS:i:50 XXX0007 0 chr1 100 255 257M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAA * AS:i:257 MS:i:50 XXX0008 0 chr1 100 255 285M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTT * AS:i:284 MS:i:50 XXX0009 0 chr1 100 255 261M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTA * AS:i:261 MS:i:50 XXX0010 0 chr1 100 255 289M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCG * AS:i:288 MS:i:50 XXX0011 0 chr1 100 173 174M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCG * AS:i:173 MS:i:50 XXX0012 0 chr1 100 255 265M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCC * AS:i:265 MS:i:50 XXX0013 0 chr1 100 255 293M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATC * AS:i:292 MS:i:50 XXX0014 0 chr1 100 166 167M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGA * AS:i:166 MS:i:50 XXX0015 0 chr1 100 247 247M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAA * AS:i:247 MS:i:50 XXX0016 0 chr1 100 255 295M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCA * AS:i:294 MS:i:50 XXX0017 0 chr1 100 210 211M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTC * AS:i:210 MS:i:50 XXX0018 0 chr1 100 235 236M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTG * AS:i:235 MS:i:50 XXX0019 0 chr1 100 195 196M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCC * AS:i:195 MS:i:50 XXX0020 0 chr1 100 178 179M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGG * AS:i:178 MS:i:50 XXX0021 0 chr1 100 255 259M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGG * AS:i:259 MS:i:50 XXX0022 0 chr1 100 238 239M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACT * AS:i:238 MS:i:50 XXX0023 0 chr1 100 255 272M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCAC * AS:i:272 MS:i:50 XXX0024 0 chr1 100 255 257M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAA * AS:i:257 MS:i:50 XXX0025 0 chr1 100 255 268M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCA * AS:i:268 MS:i:50 XXX0026 0 chr1 100 201 202M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGG * AS:i:201 MS:i:50 XXX0027 0 chr1 100 180 181M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGT * AS:i:180 MS:i:50 XXX0028 0 chr1 100 153 154M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCG * AS:i:153 MS:i:50 XXX0029 0 chr1 100 255 280M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGA * AS:i:279 MS:i:50 XXX0030 0 chr1 100 255 275M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCC * AS:i:274 MS:i:50 XXX0031 0 chr1 100 255 259M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGG * AS:i:259 MS:i:50 XXX0032 0 chr1 100 229 230M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCC * AS:i:229 MS:i:50 XXX0033 0 chr1 100 229 230M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCC * AS:i:229 MS:i:50 XXX0034 0 chr1 100 172 173M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGC * AS:i:172 MS:i:50 XXX0035 0 chr1 100 246 246M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGA * AS:i:246 MS:i:50 XXX0036 0 chr1 100 187 188M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACT * AS:i:187 MS:i:50 XXX0037 0 chr1 100 189 190M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTG * AS:i:189 MS:i:50 XXX0038 0 chr1 100 192 193M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTC * AS:i:192 MS:i:50 XXX0039 0 chr1 100 221 222M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAA * AS:i:221 MS:i:50 XXX0040 0 chr1 100 186 187M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCAC * AS:i:186 MS:i:50 XXX0041 0 chr1 100 185 186M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCA * AS:i:185 MS:i:50 XXX0042 0 chr1 100 255 299M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACT * AS:i:298 MS:i:50 XXX0043 0 chr1 100 156 157M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTT * AS:i:156 MS:i:50 XXX0044 0 chr1 100 255 270M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACC * AS:i:270 MS:i:50 XXX0045 0 chr1 100 206 207M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGAC * AS:i:206 MS:i:50 XXX0046 0 chr1 100 255 262M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAA * AS:i:262 MS:i:50 XXX0047 0 chr1 100 249 249M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGA * AS:i:249 MS:i:50 XXX0048 0 chr1 100 226 226M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGT * AS:i:226 MS:i:50 XXX0049 0 chr1 100 233 234M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACG * AS:i:233 MS:i:50 XXX0050 0 chr1 100 162 163M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGT * AS:i:162 MS:i:50 XXX0051 0 chr1 100 242 242M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATA * AS:i:242 MS:i:50 XXX0052 0 chr1 100 255 288M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCC * AS:i:287 MS:i:50 XXX0053 0 chr1 100 255 267M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCC * AS:i:267 MS:i:50 XXX0054 0 chr1 100 196 197M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCA * AS:i:196 MS:i:50 XXX0055 0 chr1 100 236 237M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGA * AS:i:236 MS:i:50 XXX0056 0 chr1 100 223 223M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAA * AS:i:223 MS:i:50 XXX0057 0 chr1 100 171 172M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCG * AS:i:171 MS:i:50 XXX0058 0 chr1 100 178 179M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGG * AS:i:178 MS:i:50 XXX0059 0 chr1 100 255 269M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCAC * AS:i:269 MS:i:50 XXX0060 0 chr1 100 195 196M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCC * AS:i:195 MS:i:50 XXX0061 0 chr1 100 212 213M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCC * AS:i:212 MS:i:50 XXX0062 0 chr1 100 255 258M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAG * AS:i:258 MS:i:50 XXX0063 0 chr1 100 157 158M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTC * AS:i:157 MS:i:50 XXX0064 0 chr1 100 173 174M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCG * AS:i:173 MS:i:50 XXX0065 0 chr1 100 178 179M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGG * AS:i:178 MS:i:50 XXX0066 0 chr1 100 186 187M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCAC * AS:i:186 MS:i:50 XXX0067 0 chr1 100 255 290M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGG * AS:i:289 MS:i:50 XXX0068 0 chr1 100 238 239M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACT * AS:i:238 MS:i:50 XXX0069 0 chr1 100 176 177M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAG * AS:i:176 MS:i:50 XXX0070 0 chr1 100 255 288M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCC * AS:i:287 MS:i:50 XXX0071 0 chr1 100 206 207M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGAC * AS:i:206 MS:i:50 XXX0072 0 chr1 100 224 224M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAA * AS:i:224 MS:i:50 XXX0073 0 chr1 100 218 219M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTA * AS:i:218 MS:i:50 XXX0074 0 chr1 100 237 238M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGAC * AS:i:237 MS:i:50 XXX0075 0 chr1 100 250 250M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGAT * AS:i:250 MS:i:50 XXX0076 0 chr1 100 255 265M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCC * AS:i:265 MS:i:50 XXX0077 0 chr1 100 255 264M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGC * AS:i:264 MS:i:50 XXX0078 0 chr1 100 242 242M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATA * AS:i:242 MS:i:50 XXX0079 0 chr1 100 159 160M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTT * AS:i:159 MS:i:50 XXX0080 0 chr1 100 248 248M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAG * AS:i:248 MS:i:50 XXX0081 0 chr1 100 253 253M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCA * AS:i:253 MS:i:50 XXX0082 0 chr1 100 199 200M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAA * AS:i:199 MS:i:50 XXX0083 0 chr1 100 168 169M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATT * AS:i:168 MS:i:50 XXX0084 0 chr1 100 249 249M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGA * AS:i:249 MS:i:50 XXX0085 0 chr1 100 255 268M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCA * AS:i:268 MS:i:50 XXX0086 0 chr1 100 255 298M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACAC * AS:i:297 MS:i:50 XXX0087 0 chr1 100 229 230M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCC * AS:i:229 MS:i:50 XXX0088 0 chr1 100 255 278M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCA * AS:i:277 MS:i:50 XXX0089 0 chr1 100 198 199M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAA * AS:i:198 MS:i:50 XXX0090 0 chr1 100 255 273M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACC * AS:i:272 MS:i:50 XXX0091 0 chr1 100 182 183M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGA * AS:i:182 MS:i:50 XXX0092 0 chr1 100 211 212M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCC * AS:i:211 MS:i:50 XXX0093 0 chr1 100 207 208M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACG * AS:i:207 MS:i:50 XXX0094 0 chr1 100 221 222M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAA * AS:i:221 MS:i:50 XXX0095 0 chr1 100 177 178M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGG * AS:i:177 MS:i:50 XXX0096 0 chr1 100 255 289M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCG * AS:i:288 MS:i:50 XXX0097 0 chr1 100 255 276M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCT * AS:i:275 MS:i:50 XXX0098 0 chr1 100 237 238M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGAC * AS:i:237 MS:i:50 XXX0099 0 chr1 100 255 273M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACC * AS:i:272 MS:i:50 XXX0100 0 chr1 100 255 264M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGC * AS:i:264 MS:i:50 XXX0101 0 chr1 100 255 285M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTT * AS:i:284 MS:i:50 XXX0102 0 chr1 100 233 234M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACG * AS:i:233 MS:i:50 XXX0103 0 chr1 100 237 238M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGAC * AS:i:237 MS:i:50 XXX0104 0 chr1 100 214 215M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCAT * AS:i:214 MS:i:50 XXX0105 0 chr1 100 154 155M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGT * AS:i:154 MS:i:50 XXX0106 0 chr1 100 181 182M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTG * AS:i:181 MS:i:50 XXX0107 0 chr1 100 255 265M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCC * AS:i:265 MS:i:50 XXX0108 0 chr1 100 255 259M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGG * AS:i:259 MS:i:50 XXX0109 0 chr1 100 186 187M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCAC * AS:i:186 MS:i:50 XXX0110 0 chr1 100 172 173M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGC * AS:i:172 MS:i:50 XXX0111 0 chr1 100 155 156M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTT * AS:i:155 MS:i:50 XXX0112 0 chr1 100 209 210M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGT * AS:i:209 MS:i:50 XXX0113 0 chr1 100 255 257M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAA * AS:i:257 MS:i:50 XXX0114 0 chr1 100 255 260M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGT * AS:i:260 MS:i:50 XXX0115 0 chr1 100 195 196M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCC * AS:i:195 MS:i:50 XXX0116 0 chr1 100 200 201M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAG * AS:i:200 MS:i:50 XXX0117 0 chr1 100 255 271M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCA * AS:i:271 MS:i:50 XXX0118 0 chr1 100 255 297M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACA * AS:i:296 MS:i:50 XXX0119 0 chr1 100 163 164M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTA * AS:i:163 MS:i:50 XXX0120 0 chr1 100 255 256M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGA * AS:i:256 MS:i:50 XXX0121 0 chr1 100 255 284M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGT * AS:i:283 MS:i:50 XXX0122 0 chr1 100 176 177M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAG * AS:i:176 MS:i:50 XXX0123 0 chr1 100 251 251M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATC * AS:i:251 MS:i:50 XXX0124 0 chr1 100 255 260M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGT * AS:i:260 MS:i:50 XXX0125 0 chr1 100 255 285M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTT * AS:i:284 MS:i:50 XXX0126 0 chr1 100 201 202M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGG * AS:i:201 MS:i:50 XXX0127 0 chr1 100 165 166M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACG * AS:i:165 MS:i:50 XXX0128 0 chr1 100 255 279M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAG * AS:i:278 MS:i:50 XXX0129 0 chr1 100 165 166M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACG * AS:i:165 MS:i:50 XXX0130 0 chr1 100 204 205M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGG * AS:i:204 MS:i:50 XXX0131 0 chr1 100 199 200M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAA * AS:i:199 MS:i:50 XXX0132 0 chr1 100 208 209M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGG * AS:i:208 MS:i:50 XXX0133 0 chr1 100 209 210M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGT * AS:i:209 MS:i:50 XXX0134 0 chr1 100 183 184M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGAT * AS:i:183 MS:i:50 XXX0135 0 chr1 100 255 266M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCC * AS:i:266 MS:i:50 XXX0136 0 chr1 100 255 293M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATC * AS:i:292 MS:i:50 XXX0137 0 chr1 100 255 285M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTT * AS:i:284 MS:i:50 XXX0138 0 chr1 100 219 220M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAG * AS:i:219 MS:i:50 XXX0139 0 chr1 100 247 247M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAA * AS:i:247 MS:i:50 XXX0140 0 chr1 100 192 193M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTC * AS:i:192 MS:i:50 XXX0141 0 chr1 100 255 261M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTA * AS:i:261 MS:i:50 XXX0142 0 chr1 100 212 213M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCC * AS:i:212 MS:i:50 XXX0143 0 chr1 100 255 276M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCT * AS:i:275 MS:i:50 XXX0144 0 chr1 100 177 178M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGG * AS:i:177 MS:i:50 XXX0145 0 chr1 100 179 180M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGG * AS:i:179 MS:i:50 XXX0146 0 chr1 100 255 263M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAG * AS:i:263 MS:i:50 XXX0147 0 chr1 100 255 272M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCAC * AS:i:272 MS:i:50 XXX0148 0 chr1 100 255 299M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACT * AS:i:298 MS:i:50 XXX0149 0 chr1 100 255 274M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCC * AS:i:273 MS:i:50 XXX0150 0 chr1 100 255 300M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTC * AS:i:299 MS:i:50 XXX0151 0 chr1 100 157 158M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTC * AS:i:157 MS:i:50 XXX0152 0 chr1 100 161 162M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTG * AS:i:161 MS:i:50 XXX0153 0 chr1 100 202 203M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGC * AS:i:202 MS:i:50 XXX0154 0 chr1 100 171 172M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCG * AS:i:171 MS:i:50 XXX0155 0 chr1 100 183 184M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGAT * AS:i:183 MS:i:50 XXX0156 0 chr1 100 255 286M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTG * AS:i:285 MS:i:50 XXX0157 0 chr1 100 255 257M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAA * AS:i:257 MS:i:50 XXX0158 0 chr1 100 255 275M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCC * AS:i:274 MS:i:50 XXX0159 0 chr1 100 255 276M * 0 0 CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCT * AS:i:275 MS:i:50 XXX0174 16 chr1 201 255 300M * 0 0 CCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:298 MS:i:50 XXX0238 16 chr1 202 255 299M * 0 0 CTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:297 MS:i:50 XXX0286 16 chr1 203 255 298M * 0 0 TGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:296 MS:i:50 XXX0249 16 chr1 204 255 297M * 0 0 GAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:295 MS:i:50 XXX0201 16 chr1 205 255 296M * 0 0 AGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:294 MS:i:50 XXX0225 16 chr1 205 255 296M * 0 0 AGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:294 MS:i:50 XXX0265 16 chr1 206 255 295M * 0 0 GACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:293 MS:i:50 XXX0182 16 chr1 207 255 294M * 0 0 ACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:292 MS:i:50 XXX0275 16 chr1 207 255 294M * 0 0 ACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:292 MS:i:50 XXX0168 16 chr1 209 255 292M * 0 0 ACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:290 MS:i:50 XXX0208 16 chr1 209 255 292M * 0 0 ACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:290 MS:i:50 XXX0264 16 chr1 209 255 292M * 0 0 ACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:290 MS:i:50 XXX0258 16 chr1 210 255 291M * 0 0 CGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:289 MS:i:50 XXX0226 16 chr1 211 255 290M * 0 0 GGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:288 MS:i:50 XXX0228 16 chr1 211 255 290M * 0 0 GGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:288 MS:i:50 XXX0263 16 chr1 211 255 290M * 0 0 GGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:288 MS:i:50 XXX0205 16 chr1 212 255 289M * 0 0 GGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:287 MS:i:50 XXX0276 16 chr1 212 255 289M * 0 0 GGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:287 MS:i:50 XXX0192 16 chr1 213 255 288M * 0 0 GATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:286 MS:i:50 XXX0298 16 chr1 213 255 288M * 0 0 GATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:286 MS:i:50 XXX0196 16 chr1 214 255 287M * 0 0 ATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:285 MS:i:50 XXX0291 16 chr1 215 255 286M * 0 0 TCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:284 MS:i:50 XXX0245 16 chr1 216 255 285M * 0 0 CTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:283 MS:i:50 XXX0284 16 chr1 220 255 281M * 0 0 ATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:278 MS:i:50 XXX0227 16 chr1 221 255 280M * 0 0 TCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:277 MS:i:50 XXX0166 16 chr1 222 255 279M * 0 0 CGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:276 MS:i:50 XXX0294 16 chr1 222 255 279M * 0 0 CGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:276 MS:i:50 XXX0300 16 chr1 224 255 277M * 0 0 CCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:274 MS:i:50 XXX0212 16 chr1 228 255 273M * 0 0 TGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:271 MS:i:50 XXX0313 16 chr1 228 255 273M * 0 0 TGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:271 MS:i:50 XXX0318 16 chr1 229 255 272M * 0 0 GAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:270 MS:i:50 XXX0193 16 chr1 230 255 271M * 0 0 AGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:268 MS:i:50 XXX0315 16 chr1 230 255 271M * 0 0 AGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:268 MS:i:50 XXX0211 16 chr1 231 255 270M * 0 0 GACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:267 MS:i:50 XXX0295 16 chr1 231 255 270M * 0 0 GACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:267 MS:i:50 XXX0235 16 chr1 232 255 269M * 0 0 ACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:266 MS:i:50 XXX0170 16 chr1 233 255 268M * 0 0 CCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:265 MS:i:50 XXX0310 16 chr1 233 255 268M * 0 0 CCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:265 MS:i:50 XXX0252 16 chr1 234 255 267M * 0 0 CCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:265 MS:i:50 XXX0206 16 chr1 235 255 266M * 0 0 CACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:264 MS:i:50 XXX0223 16 chr1 236 255 265M * 0 0 ACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:263 MS:i:50 XXX0229 16 chr1 236 255 265M * 0 0 ACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:263 MS:i:50 XXX0268 16 chr1 236 255 265M * 0 0 ACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:263 MS:i:50 XXX0189 16 chr1 237 255 264M * 0 0 CACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:262 MS:i:50 XXX0299 16 chr1 237 255 264M * 0 0 CACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:262 MS:i:50 XXX0316 16 chr1 238 255 263M * 0 0 ACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:261 MS:i:50 XXX0224 16 chr1 239 255 262M * 0 0 CACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:260 MS:i:50 XXX0255 16 chr1 240 255 261M * 0 0 ACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:259 MS:i:50 XXX0278 16 chr1 241 255 260M * 0 0 CCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:258 MS:i:50 XXX0314 16 chr1 243 255 258M * 0 0 ACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:257 MS:i:50 XXX0282 16 chr1 244 255 257M * 0 0 CGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:256 MS:i:50 XXX0311 16 chr1 244 255 257M * 0 0 CGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:256 MS:i:50 XXX0176 16 chr1 245 255 256M * 0 0 GCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:255 MS:i:50 XXX0188 16 chr1 246 254 255M * 0 0 CTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:254 MS:i:50 XXX0290 16 chr1 246 254 255M * 0 0 CTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:254 MS:i:50 XXX0187 16 chr1 248 252 253M * 0 0 TTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:252 MS:i:50 XXX0259 16 chr1 248 252 253M * 0 0 TTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:252 MS:i:50 XXX0292 16 chr1 248 252 253M * 0 0 TTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:252 MS:i:50 XXX0222 16 chr1 250 249 251M * 0 0 CCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:249 MS:i:50 XXX0256 16 chr1 250 249 251M * 0 0 CCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:249 MS:i:50 XXX0296 16 chr1 250 249 251M * 0 0 CCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:249 MS:i:50 XXX0281 16 chr1 252 248 249M * 0 0 CGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:248 MS:i:50 XXX0289 16 chr1 252 248 249M * 0 0 CGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:248 MS:i:50 XXX0171 16 chr1 253 247 248M * 0 0 GTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:247 MS:i:50 XXX0181 16 chr1 253 247 248M * 0 0 GTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:247 MS:i:50 XXX0266 16 chr1 253 247 248M * 0 0 GTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:247 MS:i:50 XXX0319 16 chr1 253 247 248M * 0 0 GTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:247 MS:i:50 XXX0172 16 chr1 255 245 246M * 0 0 TTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:245 MS:i:50 XXX0317 16 chr1 255 245 246M * 0 0 TTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:245 MS:i:50 XXX0207 16 chr1 257 242 244M * 0 0 CTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:242 MS:i:50 XXX0240 16 chr1 258 242 243M * 0 0 TTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:242 MS:i:50 XXX0246 16 chr1 258 242 243M * 0 0 TTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:242 MS:i:50 XXX0203 16 chr1 259 240 242M * 0 0 TTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:240 MS:i:50 XXX0217 16 chr1 259 240 242M * 0 0 TTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:240 MS:i:50 XXX0216 16 chr1 262 237 239M * 0 0 TACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:237 MS:i:50 XXX0230 16 chr1 262 237 239M * 0 0 TACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:237 MS:i:50 XXX0277 16 chr1 263 236 238M * 0 0 ACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:236 MS:i:50 XXX0308 16 chr1 263 236 238M * 0 0 ACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:236 MS:i:50 XXX0288 16 chr1 264 235 237M * 0 0 CGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:235 MS:i:50 XXX0305 16 chr1 264 235 237M * 0 0 CGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:235 MS:i:50 XXX0210 16 chr1 265 234 236M * 0 0 GATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:234 MS:i:50 XXX0164 16 chr1 266 233 235M * 0 0 ATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:233 MS:i:50 XXX0221 16 chr1 267 232 234M * 0 0 TTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:232 MS:i:50 XXX0163 16 chr1 268 231 233M * 0 0 TTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:231 MS:i:50 XXX0244 16 chr1 270 228 231M * 0 0 CGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:228 MS:i:50 XXX0237 16 chr1 272 226 229M * 0 0 CGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:226 MS:i:50 XXX0178 16 chr1 273 226 228M * 0 0 GCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:226 MS:i:50 XXX0202 16 chr1 273 226 228M * 0 0 GCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:226 MS:i:50 XXX0236 16 chr1 273 226 228M * 0 0 GCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:226 MS:i:50 XXX0304 16 chr1 273 226 228M * 0 0 GCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:226 MS:i:50 XXX0270 16 chr1 274 225 227M * 0 0 CAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:225 MS:i:50 XXX0161 16 chr1 276 223 225M * 0 0 GGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:223 MS:i:50 XXX0287 16 chr1 277 222 224M * 0 0 GGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:222 MS:i:50 XXX0306 16 chr1 277 222 224M * 0 0 GGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:222 MS:i:50 XXX0173 16 chr1 279 220 222M * 0 0 GTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:220 MS:i:50 XXX0269 16 chr1 280 219 221M * 0 0 TGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:219 MS:i:50 XXX0303 16 chr1 282 216 219M * 0 0 ATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:216 MS:i:50 XXX0220 16 chr1 283 215 218M * 0 0 TCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:215 MS:i:50 XXX0219 16 chr1 284 214 217M * 0 0 CACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:214 MS:i:50 XXX0177 16 chr1 286 212 215M * 0 0 CTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:212 MS:i:50 XXX0257 16 chr1 287 211 214M * 0 0 TTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:211 MS:i:50 XXX0241 16 chr1 288 210 213M * 0 0 TGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:210 MS:i:50 XXX0167 16 chr1 289 209 212M * 0 0 GGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:209 MS:i:50 XXX0261 16 chr1 290 208 211M * 0 0 GTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:208 MS:i:50 XXX0312 16 chr1 293 205 208M * 0 0 TCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:205 MS:i:50 XXX0272 16 chr1 294 204 207M * 0 0 CCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:204 MS:i:50 XXX0253 16 chr1 295 203 206M * 0 0 CAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:203 MS:i:50 XXX0254 16 chr1 296 202 205M * 0 0 AAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:202 MS:i:50 XXX0307 16 chr1 297 201 204M * 0 0 AAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:201 MS:i:50 XXX0169 16 chr1 298 200 203M * 0 0 AAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:200 MS:i:50 XXX0232 16 chr1 299 199 202M * 0 0 AGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:199 MS:i:50 XXX0195 16 chr1 300 198 201M * 0 0 GGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:198 MS:i:50 XXX0179 16 chr1 302 196 199M * 0 0 CGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:196 MS:i:50 XXX0160 16 chr1 305 193 196M * 0 0 ACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:193 MS:i:50 XXX0271 16 chr1 305 193 196M * 0 0 ACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:193 MS:i:50 XXX0180 16 chr1 306 192 195M * 0 0 CGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:192 MS:i:50 XXX0185 16 chr1 306 192 195M * 0 0 CGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:192 MS:i:50 XXX0199 16 chr1 306 192 195M * 0 0 CGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:192 MS:i:50 XXX0191 16 chr1 310 188 191M * 0 0 CCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:188 MS:i:50 XXX0250 16 chr1 311 187 190M * 0 0 CCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:187 MS:i:50 XXX0273 16 chr1 312 186 189M * 0 0 CATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:186 MS:i:50 XXX0239 16 chr1 314 184 187M * 0 0 TGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:184 MS:i:50 XXX0301 16 chr1 314 184 187M * 0 0 TGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:184 MS:i:50 XXX0197 16 chr1 316 182 185M * 0 0 TTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:182 MS:i:50 XXX0260 16 chr1 317 181 184M * 0 0 TAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:181 MS:i:50 XXX0190 16 chr1 319 179 182M * 0 0 GAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:179 MS:i:50 XXX0309 16 chr1 319 179 182M * 0 0 GAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:179 MS:i:50 XXX0285 16 chr1 320 178 181M * 0 0 AAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:178 MS:i:50 XXX0214 16 chr1 322 176 179M * 0 0 AAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:176 MS:i:50 XXX0279 16 chr1 322 176 179M * 0 0 AAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:176 MS:i:50 XXX0280 16 chr1 322 176 179M * 0 0 AAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:176 MS:i:50 XXX0242 16 chr1 323 175 178M * 0 0 AGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:175 MS:i:50 XXX0213 16 chr1 325 173 176M * 0 0 TTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:173 MS:i:50 XXX0233 16 chr1 325 173 176M * 0 0 TTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:173 MS:i:50 XXX0297 16 chr1 325 173 176M * 0 0 TTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:173 MS:i:50 XXX0183 16 chr1 326 172 175M * 0 0 TCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:172 MS:i:50 XXX0194 16 chr1 326 172 175M * 0 0 TCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:172 MS:i:50 XXX0283 16 chr1 326 172 175M * 0 0 TCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:172 MS:i:50 XXX0215 16 chr1 328 170 173M * 0 0 CCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:170 MS:i:50 XXX0162 16 chr1 332 166 169M * 0 0 CGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:166 MS:i:50 XXX0262 16 chr1 333 165 168M * 0 0 GTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:165 MS:i:50 XXX0200 16 chr1 335 163 166M * 0 0 GACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:163 MS:i:50 XXX0234 16 chr1 336 161 165M * 0 0 ACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:161 MS:i:50 XXX0186 16 chr1 337 161 164M * 0 0 CTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:161 MS:i:50 XXX0218 16 chr1 337 161 164M * 0 0 CTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:161 MS:i:50 XXX0248 16 chr1 338 160 163M * 0 0 TATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:160 MS:i:50 XXX0267 16 chr1 338 160 163M * 0 0 TATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:160 MS:i:50 XXX0247 16 chr1 339 158 162M * 0 0 ATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:158 MS:i:50 XXX0274 16 chr1 339 158 162M * 0 0 ATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:158 MS:i:50 XXX0198 16 chr1 340 158 161M * 0 0 TATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:158 MS:i:50 XXX0251 16 chr1 340 158 161M * 0 0 TATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:158 MS:i:50 XXX0204 16 chr1 341 156 160M * 0 0 ATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:156 MS:i:50 XXX0175 16 chr1 342 155 159M * 0 0 TGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:155 MS:i:50 XXX0209 16 chr1 342 155 159M * 0 0 TGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:155 MS:i:50 XXX0243 16 chr1 343 154 158M * 0 0 GGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:154 MS:i:50 XXX0165 16 chr1 345 152 156M * 0 0 AAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:152 MS:i:50 XXX0231 16 chr1 346 151 155M * 0 0 AGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:151 MS:i:50 XXX0293 16 chr1 349 148 152M * 0 0 TCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:148 MS:i:50 XXX0302 16 chr1 349 148 152M * 0 0 TCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:148 MS:i:50 XXX0184 16 chr1 351 146 150M * 0 0 CAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA * AS:i:146 MS:i:50 pysam-0.23.0/tests/pysam_data/example_empty_with_header.sam000066400000000000000000000000311475062545500241360ustar00rootroot00000000000000@HD VN:1.3 SO:coordinate pysam-0.23.0/tests/pysam_data/example_reverse_complement.sam000066400000000000000000000055261475062545500243510ustar00rootroot00000000000000@SQ SN:chr1 LN:249250621 @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 @SQ SN:chr12 LN:133851895 @SQ SN:chr13 LN:115169878 @SQ SN:chr14 LN:107349540 @SQ SN:chr15 LN:102531392 @SQ SN:chr16 LN:90354753 @SQ SN:chr17 LN:81195210 @SQ SN:chr18 LN:78077248 @SQ SN:chr19 LN:59128983 @SQ SN:chr2 LN:243199373 @SQ SN:chr20 LN:63025520 @SQ SN:chr21 LN:48129895 @SQ SN:chr22 LN:51304566 @SQ SN:chr3 LN:198022430 @SQ SN:chr4 LN:191154276 @SQ SN:chr5 LN:180915260 @SQ SN:chr6 LN:171115067 @SQ SN:chr7 LN:159138663 @SQ SN:chr8 LN:146364022 @SQ SN:chr9 LN:141213431 @SQ SN:chrM LN:16571 @SQ SN:chrX LN:155270560 @SQ SN:chrY LN:59373566 @PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa mem /ifs/mirror/genomes/bwa-0.7.5a/hg19 both.fq chr22:25000000-25000500 0 chr22 25000000 60 501M * 0 0 GCTCTGTGCCGCAAGGGTGGAAACTGTGAGAGACAGATTCCAACTCCACGTCTGGGTAGTAAGCATCCAGTCCAGGGCTGTAGGCAGTCCTGGGGAAGACGCCAGAGATCTGTGCATTCTCATATCGAGGGATAGCGACTCCAGGCTGGGGGCTGGCAGGGTAAGGGGTGGGTGGGTCCTGGGCTTACCCGCAGGTCTGCAGACTTCCTGGGGCCAGCTGACCTCGTAAAATCCCTTTTGTCTAAGCTTCAGTTTCCTGCCTGTGAATGGGGTTGGGGCTGTGCTCTGGTTTCACCCTTGTGGCTCTGGGGTTGTGGTGACAAAGCCATCAAGCTGGGTTGAAGGATTAACCAGGAAACTTCAGACTGGCTGCCGTGTCTACCTCTTCCTCATACTCCTCTCTCTGCTGCATCCTGGGAAGCTGCTCTGCTCAGCCTAAATGAGGCTCAGTTGTGTGTGTGCGCACGTGCTTGCACGTGTGTTGGAAGTGGGTGATACTGA GCTCTGTGCCGCAAGGGTGGAAACTGTGAGAGACAGATTCCAACTCCACGTCTGGGTAGTAAGCATCCAGTCCAGGGCTGTAGGCAGTCCTGGGGAAGACGCCAGAGATCTGTGCATTCTCATATCGAGGGATAGCGACTCCAGGCTGGGGGCTGGCAGGGTAAGGGGTGGGTGGGTCCTGGGCTTACCCGCAGGTCTGCAGACTTCCTGGGGCCAGCTGACCTCGTAAAATCCCTTTTGTCTAAGCTTCAGTTTCCTGCCTGTGAATGGGGTTGGGGCTGTGCTCTGGTTTCACCCTTGTGGCTCTGGGGTTGTGGTGACAAAGCCATCAAGCTGGGTTGAAGGATTAACCAGGAAACTTCAGACTGGCTGCCGTGTCTACCTCTTCCTCATACTCCTCTCTCTGCTGCATCCTGGGAAGCTGCTCTGCTCAGCCTAAATGAGGCTCAGTTGTGTGTGTGCGCACGTGCTTGCACGTGTGTTGGAAGTGGGTGATACTGA NM:i:0 MD:Z:501 AS:i:501 XS:i:343 chr22:25000000-25000500 16 chr22 25000000 60 501M * 0 0 GCTCTGTGCCGCAAGGGTGGAAACTGTGAGAGACAGATTCCAACTCCACGTCTGGGTAGTAAGCATCCAGTCCAGGGCTGTAGGCAGTCCTGGGGAAGACGCCAGAGATCTGTGCATTCTCATATCGAGGGATAGCGACTCCAGGCTGGGGGCTGGCAGGGTAAGGGGTGGGTGGGTCCTGGGCTTACCCGCAGGTCTGCAGACTTCCTGGGGCCAGCTGACCTCGTAAAATCCCTTTTGTCTAAGCTTCAGTTTCCTGCCTGTGAATGGGGTTGGGGCTGTGCTCTGGTTTCACCCTTGTGGCTCTGGGGTTGTGGTGACAAAGCCATCAAGCTGGGTTGAAGGATTAACCAGGAAACTTCAGACTGGCTGCCGTGTCTACCTCTTCCTCATACTCCTCTCTCTGCTGCATCCTGGGAAGCTGCTCTGCTCAGCCTAAATGAGGCTCAGTTGTGTGTGTGCGCACGTGCTTGCACGTGTGTTGGAAGTGGGTGATACTGA CGAGACACGGCGTTCCCACCTTTGACACTCTCTGTCTAAGGTTGAGGTGCAGACCCATCATTCGTAGGTCAGGTCCCGACATCCGTCAGGACCCCTTCTGCGGTCTCTAGACACGTAAGAGTATAGCTCCCTATCGCTGAGGTCCGACCCCCGACCGTCCCATTCCCCACCCACCCAGGACCCGAATGGGCGTCCAGACGTCTGAAGGACCCCGGTCGACTGGAGCATTTTAGGGAAAACAGATTCGAAGTCAAAGGACGGACACTTACCCCAACCCCGACACGAGACCAAAGTGGGAACACCGAGACCCCAACACCACTGTTTCGGTAGTTCGACCCAACTTCCTAATTGGTCCTTTGAAGTCTGACCGACGGCACAGATGGAGAAGGAGTATGAGGAGAGAGACGACGTAGGACCCTTCGACGAGACGAGTCGGATTTACTCCGAGTCAACACACACACGCGTGCACGAACGTGCACACAACCTTCACCCACTATGACT NM:i:0 MD:Z:501 AS:i:501 XS:i:343 pysam-0.23.0/tests/pysam_data/example_unmapped_reads_no_sq.sam000066400000000000000000000003571475062545500246360ustar00rootroot00000000000000@HD VN:1.0 read_28833_29006_6945 0 * 0 0 * * 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< read_28701_28881_323b 0 * 0 0 * * 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< pysam-0.23.0/tests/pysam_data/faidx_empty_seq.fq000066400000000000000000000021001475062545500217300ustar00rootroot00000000000000@HISEQ2500-10:332:HCWLKBCXX:1:1101:6834:72051:TCGCTGTG TACCTCTAAAGGGGAGCGCTTTGGA + IBBBBBEEEEEEEEEEEEBBBBBII @HISEQ2500-10:332:HCWLKBCXX:1:1101:6822:72067:TCGCTGTG TGCTCTAGAATTACCACAGTTATGA + @A<;BB<<0BA0B?A?B7_589:1:101:825:28 GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC >B7_589:1:101:825:28 TGTGTCCATGTACACACGCTGTCCTATGTACTTAT >B7_589:1:110:543:934 AAGAATTGTAAAAGTCAAAATTAAAGTTCAATACT >B7_589:1:110:543:934 ACAAGCCAGAAGAGATTGGATCTAATTTTTGGACT >B7_589:1:122:337:968 ACAGGGGGCTGCGCGGTTTCCCATCATGAAGCACT >B7_589:1:122:337:968 GCTTTACTGTCTAAACTATGAAGAGACTATTGCCA >B7_589:1:122:77:789 ACTATATTTATGCTATTCAGTTCTAAATATAGAAA >B7_589:1:122:77:789 GGACGCTGAAGAACTTTGATGCCCTCTTCTTCCAA >B7_589:1:168:69:249 ATATGCTGTTTACAAGAAACTCATTAATAAAGACA >B7_589:1:168:69:249 TTCAGCAAGAAGATATAACCATCCTACTAAATACA >B7_589:1:29:529:379 CAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAAT >B7_589:1:29:529:379 GACTCTATCCCAAATTCCCAATTACGTCCTATCTT >B7_589:2:30:644:942 TACCTAATTGGTACAATGTACAATATTCTGATGAT >B7_589:2:30:644:942 TATATCAGATAAAGCACACTTTAAATCAACAACAG >B7_589:2:73:730:487 AGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTT >B7_589:2:73:730:487 TAGCCATTTCTTTTGGCATTTGCCTTCAGACCCTA >B7_589:2:9:49:661 TACACACAAAAGTACAAAACTCACAGGTTTTATAA >B7_589:2:9:49:661 TGCTAAACTAAGCATCATAAATGAAGCGGAAATAA >B7_589:3:71:478:175 ACAGAGCTTTCAAGAAGTATGAGATTATGTAAAGT >B7_589:3:71:478:175 TAGACATCTAAATGAAAGAGGCTCAAAGAATGCCA >B7_589:3:82:13:897 ATACAGTCATCTATAAAGGAAATCCCAGCAGAATA >B7_589:3:82:13:897 CATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCT >B7_589:4:54:989:654 ACTTATCATGACTCTATCCCAAATTCCCAATTACG >B7_589:4:54:989:654 TCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTT >B7_589:5:147:405:738 AGGGATTAAATTCCCCCACTTAAGAGATATAGATT >B7_589:5:147:405:738 ATCAGATAAAGCACACTTTAAATCAACAACAGTAA >B7_589:5:198:564:731 ACAAAGGAGGTCATCATACAATGATAAAAAGATCA >B7_589:5:198:564:731 ATAGATTGGCAGAACAGATTTAAAAACATGAACTA >B7_589:5:50:950:562 CTATTTTTGTCTTGACACCCTACTAATATTTGTCT >B7_589:5:50:950:562 GCCCCATCTCTTGTAATCTCTCTCCTTTTTGCTGC >B7_589:5:68:440:424 ACACTTTAAATCAACAACAGTAAAATAAAACAAAG >B7_589:5:68:440:424 TGGTACAATGTACAATATTCTGATGATGGTTACAC >B7_589:6:108:958:42 AAAGTACAAAACTCACAGGTTTTATAAAACAATTA >B7_589:6:108:958:42 TATGCCCTGCTAAACTAAGCATCATAAATGAAGGG >B7_589:6:114:714:317 AACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGC >B7_589:6:114:714:317 TGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCA >B7_589:6:120:14:944 CAAAAGGTGATGTGTGTTCTCATCAACCTCATACA >B7_589:6:120:14:944 CAAAGATGAAACGCGTAACTGCGCTCTCATTCACT >B7_589:6:33:356:636 TTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTT >B7_589:7:112:203:90 CCTGTCACCCAATGGACCTGTGATATCTGGATTCT >B7_589:7:112:203:90 CTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGA >B7_589:7:154:26:712 ATTGAGACTACAGAGCAACTAGGTAAAAAATTAAC >B7_589:7:154:26:712 TTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAA >B7_589:7:72:916:763 CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGT >B7_589:7:72:916:763 GTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGT >B7_589:7:76:306:561 GGTGGAAAAAGATGTTCTACGCAAACAGAAACCAA >B7_589:7:76:306:561 TACAGAGCAACTAGGTAAAAAATTAACATTACAAC >B7_589:7:93:634:323 CTTAAAGAAAAAAAAACCTGTCAAACACGAATGTT >B7_589:7:93:634:323 TAAAGTTCAATACTCACCATCATAAATACACACAA >B7_589:8:113:968:19 GAAAACTATATTTATGCTATTCAGTTCTAAATATA >B7_589:8:118:829:36 AGTATTGGTAAAGATGTGGGGAAAAAAGTAAACTC >B7_589:8:118:829:36 TAATTGGTACAATGTACAATATTCTGATGATGGTT >B7_589:8:139:727:808 AAGTAAATAAAACACATAGCTAAAACTAAAAAAGC >B7_589:8:139:727:808 ACAAATACTACTAGACCTAAGAGGGATGAGAAATT >B7_589:8:157:935:374 CAGTTACCAAATGTGTTTATTACCAGAGGGATGGA >B7_589:8:157:935:374 TCTTCATCCTGGACCCTGAGAGATTCTGCAGCCCA >B7_589:8:2:434:715 AGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCT >B7_589:8:2:434:715 CTTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTT >B7_589:8:74:674:124 CACTGAACTTCCACGTCTCATCTAGGGGAACAGGG >B7_589:8:74:674:124 TTCTTATCTGCACATTACTACCCTGCAATTAATAT >B7_591:1:191:462:705 CAGATCCAGATTGCTTGTGGTCTGACAGGCTGCAAC >B7_591:1:191:462:705 CATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAG >B7_591:1:60:837:923 CATCAACCGCATACACTCACATGGTTTAGGGGTATA >B7_591:1:60:837:923 TTCACGCCAGCTCCCTGTCACCCAATGGACCTCTGA >B7_591:2:123:924:645 TATATCAGATAAAGCACACTTTAAATCAACAACAGT >B7_591:2:123:924:645 TGAATAAAAAGGGATTAAATTCCCCCACTTAAGAGA >B7_591:2:134:868:252 AAGAACTTTGATGCCCTCTTCTTCCAAAGATGAAAC >B7_591:2:134:868:252 ATGAACAACAGGAAGAAAAGGTCTTTCAAAAGGTGA >B7_591:2:13:100:876 ACAGGGATTCCTGAGGAAAAAGAAAAAGTGAGAAGT >B7_591:2:13:100:876 AGAATATATAAAGTCAACATGAAGGAAAAAAATTCT >B7_591:2:223:583:968 AATATAGTTGAAAGCTCTAACAATAGACTAAACCAA >B7_591:2:223:583:968 TATGAGGCACAGGTATTCCTGAGGAAAAAGAAAAAG >B7_591:2:240:603:890 GCTCCCAAGAGGGAAAGCTTTCAACGCTTCTAGCCA >B7_591:2:240:603:890 TCACAATGAACAACAGGAAGAAAAGGTCTTTCAAAA >B7_591:2:279:124:41 GAATTAACCCAGTCAGACAAAAANNAAGAAAAAAGA >B7_591:2:279:124:41 GCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAA >B7_591:2:27:280:592 AATAACAATGGGCTTCTCAGCGGAAACCTTACAAGC >B7_591:2:27:280:592 AGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGA >B7_591:2:309:798:997 TTTTTTTTTTTTTTTTTTCTCTTTTTTTTTTTTTTT >B7_591:2:323:639:311 AAGCCGTTCTATTTGTAATGAAAACTATATTTAGGC >B7_591:2:323:639:311 TACCAAATGTGTTTATTACCAGAGGGATGGAGGGAA >B7_591:2:46:220:58 CAAATCTGCGCTTGTACTTCTAAATCTATAAAAAAA >B7_591:2:46:220:58 TTCCACTTTGGAAAACAATTTGGTAATTTCGTTTTT >B7_591:3:168:69:605 TACCCGAGGGATGGAGGGTAGAGGGACGCTGAAGTG >B7_591:3:168:69:605 TCTGACAGGCGGCAACTGTGAGCCATCACAATGAAC >B7_591:3:179:496:161 AAAAACATGAACTAACTATATGCTGTTTACAAGAAA >B7_591:3:179:496:161 AAGTACAAAACTCACAGGTTTTATAAAACAATTAAT >B7_591:3:277:458:330 AATGTCAGGGAAGGAGCCTTTTGTCAGTTACCAAAT >B7_591:3:277:458:330 TGATATCTGGATTCTGGGAAATTCTTCATCCTGGAC >B7_591:3:291:404:199 TATAAAACAATTAATTGAGACTACAGAGCAACTAGG >B7_591:3:291:404:199 TGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGC >B7_591:3:305:565:952 GTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGT >B7_591:3:305:565:952 TAATACTATGTTTCTTATCTGCACATTACTACCCTG >B7_591:3:45:294:380 ATAATTGTGTCCATGTACACACGATGTCATATGTAC >B7_591:3:45:294:380 CCTCGTCCACACTGGTTCGCTTGAAAGCTTGGGCTG >B7_591:4:103:111:720 CAGTTACCAAATGTGTTTATTACCAGAGGGATGGAG >B7_591:4:103:111:720 TCTTCATCCTGGACCCTGAGAGATTCTGCAGCCCAG >B7_591:4:159:508:571 CAAAACCTCATATATCAATATTAACTTTGAATAAAA >B7_591:4:159:508:571 TGGAAAAAGATGTTCTACGCAAACAGAAACCAAATG >B7_591:4:216:650:516 GAACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAA >B7_591:4:216:650:516 TTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT >B7_591:4:329:339:408 CAATCCAGAAGAGATTGGATCTAATTTTTGGACTTC >B7_591:4:329:339:408 TAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATAC >B7_591:4:92:411:955 GGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAG >B7_591:4:92:411:955 TACTAAATACATATGCACCTAACACAAGACTACCCA >B7_591:5:124:978:501 AATTTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTC >B7_591:5:124:978:501 ATGTAACAAATCTGCGCTTGTACTTCTAAATCTATA >B7_591:5:134:751:831 AGCTCCCTGTCACCCAATGGACCTGTGATATCTGGA >B7_591:5:134:751:831 ATACACACACATGGTTTAGGGGTATAATACCTCTAC >B7_591:5:243:557:560 AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA >B7_591:5:243:557:560 CTAAGCAGAAACCTTACAAGCCAGAAGAGATTGGAT >B7_591:5:254:542:848 CCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAA >B7_591:5:254:542:848 CTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAAC >B7_591:5:289:132:526 CACCCGGTCCCTGCCCCATCTCTTGTAATCTCTCTC >B7_591:5:289:132:526 TCTATTTTTGTCTTGACACCCAACTAATATTTGTCT >B7_591:5:42:540:501 CTATATTTATGCTATTCAGTTCTAAATATAGAAATT >B7_591:5:90:828:633 CTGCAGCCCAGATCCAGATTGCTTGTGGTCTGACAG >B7_591:5:90:828:633 GGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATG >B7_591:6:11:646:628 GTACTTATCATGACTCTATCCCAAATTCCCAATTAC >B7_591:6:11:646:628 TTCTGCCCCCAGCATGGTTGTACTGGGCAATACATG >B7_591:6:155:12:674 CTATATTTATGCTATTCAGTTCTAAATATAGAAATT >B7_591:6:181:191:418 AAACTATATTTATGCTATTCAGTTCTAAATATAGAA >B7_591:6:181:191:418 AGGGAAGAGGGACGCTGAAGAACTTTGATGCCCTCT >B7_591:6:190:42:671 TATTGCCAGATGAACCACACATTAATACTATGTTTC >B7_591:6:190:42:671 TGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCA >B7_591:6:29:575:453 TACTACCCTGCAATTAATATAATTGTGTCCATTTAC >B7_591:6:29:575:453 TCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCTTG >B7_591:7:116:814:89 ACTATGCTAAGTATTGGTAAAGATGTGGGGAAAAAA >B7_591:7:116:814:89 CCTAATTGGTACAATGTACAATATTCTGATGATGGT >B7_591:7:129:956:115 AGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATAC >B7_591:7:129:956:115 GCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCA >B7_591:7:157:447:758 AAAGATGTTCTACGCAAACAGAAACCAAATGAGAGA >B7_591:7:157:447:758 ACAAAACCTCATATATCAATATTAACTTTGAATAAA >B7_591:7:200:192:373 AGTGCCTTTGTTCACATAGACCCCCTTGCAACAACC >B7_591:7:200:192:373 CTCTCATTCACTCCAGCTCCCTGTCACCCAATGGAC >B7_591:7:22:632:176 AAAGGAGGTCATCATACAATGATAAAAAGATCAATT >B7_591:7:22:632:176 AGATATAGATTGGCAGAACAGATTTAAAAACATGAA >B7_591:7:68:242:834 AAATAAAAAAGCAAAAACAAAAACTATGCTAAGTAT >B7_591:7:68:242:834 TACTACTAGACCTAAGAGGGATGAGAAATTACCTAA >B7_591:7:89:67:709 TTTTTTTTTTTGTCTTCTCTTTTTTTTTTTTTTTTT >B7_591:8:4:841:340 TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAA >B7_593:1:12:158:458 CTGGGAAATTCTTCATCCTGGACCCTGAGAGATTCT >B7_593:1:12:158:458 TAATAATGCTACATGGATGATTATGAAATCAATGTT >B7_593:1:189:876:833 CAAGACTACCCAGATTCATAAAACAAATACTACTAG >B7_593:1:189:876:833 TTAAAATTTAACAAAAGTAAATAAAACACATAGCTA >B7_593:1:19:695:59 AACAGGAACAAAACCTCATATATCAATATTAACTTT >B7_593:1:19:695:59 GTGGAAAAAGATGTTCTACGCAAACAGAAACCAAAT >B7_593:1:200:559:765 GGAAGGAGCATTTTGTCAGTTACCAAATGTGTTTAT >B7_593:1:200:559:765 TGGACCCTGAGAGATTCTGCAGCCCAGATCCAGATT >B7_593:1:215:861:605 GAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTC >B7_593:1:215:861:605 NAAGACAAGTCTCTTATGAATTAACCCAGTCAGACA >B7_593:1:36:485:632 AAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCA >B7_593:1:36:485:632 GGCATTTGCCTTCAGACCCTACACGAATGCGTCTCT >B7_593:1:85:361:418 AGCCAGAAGAGATTGGATCTAATTTTTGGACTTCTT >B7_593:1:85:361:418 GAAGATACATTGCAAGACAGACTTCATCAAGATATG >B7_593:2:104:744:280 CATATGGAAAGGTTGTTGGGATTTTTTTAATGATTC >B7_593:2:104:744:280 TGGGCTGTAATGATGCCCCTTGTCCATCACCCGGTC >B7_593:2:125:875:553 AACAGTAAAATAAAACAAAGGAGGTCATCATACAAT >B7_593:2:125:875:553 TAATTGGTACAATGTACAATATTCTGATGATGGTTA >B7_593:2:128:555:941 AACCAAAAGAGAGAAGGAGTAGTTATACACATATCA >B7_593:2:133:460:542 CCTATAAGCCGTTCTATTTGTAATGAAAACTATATT >B7_593:2:133:460:542 TTACCAAATGTGTTTATTACCAGAGGGATGGAGGGA >B7_593:2:259:467:737 CTATGTACTTATCATGACTCTATCCCAAATTCCCAA >B7_593:2:259:467:737 TCACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCA >B7_593:2:270:430:269 AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA >B7_593:2:270:430:269 CCAGAAGAGATTGGATCTAATTTTTGGACTTCTTAA >B7_593:2:273:348:37 AGAAATGCGCAAAAGAATTGTAAAAGTCAAAATTAA >B7_593:2:273:348:37 GAATAACAATGGGCTTCTCAGCAGAAACCTTACACG >B7_593:2:313:531:169 GAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATG >B7_593:2:313:531:169 GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATT >B7_593:2:43:239:977 TGAACTTCTGTAATTGAAAAATTCATTTAAGAAATT >B7_593:2:68:140:542 AAAAACAAAAACTATGCTAAGTATTGGTAAAGATGT >B7_593:2:68:140:542 GGGATGAGAAATTACCTAATTGGTACAATGTACAAT >B7_593:2:68:692:347 TATCAATTTGGTGTTCTGTGTAAAGTCTCATGGAGC >B7_593:2:68:692:347 TGTCTTGATTTACTTGTTGTTGGTTTTCTGTTTCTT >B7_593:2:81:435:410 AGACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGT >B7_593:2:81:435:410 ATTAATTGAGACTACAGAGCAACTAGGTAAAAAATT >B7_593:3:102:856:670 AAACCTCATATATCAATATTAACTTTGAATAAAAAG >B7_593:3:102:856:670 AGAGAAGGAGTAGCTATACTTATATCAGATAAAGCA >B7_593:3:115:649:259 ATTAATTGAGAATACAGAGCAACTAGGTAAAAAATT >B7_593:3:115:649:259 GGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATG >B7_593:3:148:437:481 CGCTTCTAGCCATTTCTTTTGGCATTTGCCTTCAGA >B7_593:3:148:437:481 GTACTGGGCAATACATGAGATTATTAGGAAATGCTT >B7_593:3:180:89:582 ATGCTAAGATAATTCATCATCACTAAACCAGTCCTA >B7_593:3:180:89:582 TAAAAAATTAACATTACAACAGGAACAAAACCTCAT >B7_593:3:194:168:684 AAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGT >B7_593:3:194:168:684 CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGTT >B7_593:3:196:11:27 AAGACCCAGTTAGCCGTCCGTGTCCTCCCATCTGGC >B7_593:3:196:11:27 CTATGTTTCTTATCTGCNCATTACTACCCTGCAATT >B7_593:3:303:131:673 ACAAGAAACTCATTAATAAAGACATGAGTTCAGGTA >B7_593:3:303:131:673 ATAAAAAGATCAATTCAGCAAGAAGATATAACCATC >B7_593:3:310:193:629 CATACAATGATAAAAAGATCAATTCAGCAAGAAGAT >B7_593:3:310:193:629 TACACTAAAAGCCCATACTTTACTGCTACTCAATAT >B7_593:4:104:153:698 CCAGATACCATCCCTGTCTTACTTCCAGCTCCCCAG >B7_593:4:104:153:698 CTAATGCGCTCCACGCCCAAGCCCTTCTCACAGTTT >B7_593:4:106:316:452 CTATATTTATGCTATTCAGTTCTAAATATAGAAATT >B7_593:4:142:63:937 GAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATC >B7_593:4:142:63:937 TTCTTTTGGCATTTGCCTTCAGACCCTACACGAATG >B7_593:4:28:781:723 AATACCTCTACATGGCTGATTATGAAAACAATGTTC >B7_593:4:28:781:723 ACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAG >B7_593:4:29:794:282 CACATTAATACTATGTTTCTTATCTGCACATTACTA >B7_593:4:29:794:282 TAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATCTG >B7_593:4:30:117:411 TCTTGACACCCAACTAATATTTGTCTGAGCAAAACA >B7_593:4:30:117:411 TCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTC >B7_593:4:30:812:345 TATGTTTCTTATCTGCACATTACTACCCTGCAATTA >B7_593:4:30:812:345 TCATCTAGGGGAACAGGGAGGTGCACTAATGCGCTC >B7_593:4:315:201:673 AAGATATGTAGTCATCAGACTATCTAAAGTCAACAT >B7_593:4:315:201:673 TTGGACTTATTAAAGAAAAAAAAACCTGTCAAACAC >B7_593:5:171:343:758 ACTAATATTTGTCTGAGCAAAACAGTCTAGATGAGA >B7_593:5:171:343:758 GCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTG >B7_593:5:267:71:603 TTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAA >B7_593:5:267:71:603 TTTAATGATTCCTCAATGTTAAAATGTCTATTTTTG >B7_593:5:299:743:762 AAAATTAAAATTTAACAAAAGTAAATAAAACACATA >B7_593:5:299:743:762 CAAGACTACCCAGATTCATAAAACAAATACTACTAG >B7_593:5:30:599:589 CTACGCAAACAGAAACCAAATGAGAGAAGGAGCAGC >B7_593:5:30:599:589 TCATAAAACAAATACTACTAGACCTAAGAGGGATGA >B7_593:6:118:121:760 GAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAA >B7_593:6:119:428:415 GCTATACTTATATCAGATAAAGCACACTTTAAATCA >B7_593:6:119:428:415 TAAATTCCCCCACTTAAGAGATATAGATTGGCAGAA >B7_593:6:185:96:948 CTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATA >B7_593:6:185:96:948 TTTAAAAATGAACAGAGCTTTCAAGAAGTATGAGAT >B7_593:6:38:332:54 CCATCATAAATACACACAAAAGTACAAAACTCACAG >B7_593:6:38:332:54 TGGCAGAACAGATTTAAAAACATGAACTAACTATAT >B7_593:6:61:628:681 CAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCTT >B7_593:6:61:628:681 GCCATCACAATGAACAACAGGAAGAAAAGGTCTTTC >B7_593:7:15:244:876 AAAAGTAAACTCTCAAATATTGCTAGTGTGAGTATA >B7_593:7:15:244:876 GTACAATATTCTGATGATGGTTACACTAAAAGCCCA >B7_593:7:189:530:40 AAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATAC >B7_593:7:189:530:40 CCCCACTTAAGAGATATAGATTGGCAGAACAGATTT >B7_593:7:256:354:173 CATTAATAAAGACATGAGTTCAGGTAAAGGGGTGGA >B7_593:7:256:354:173 TCAATTCAGCAAGAAGATATAACCATCCTACTAAAT >B7_593:7:283:186:707 AATACATATGCACCTAACACAAGACTACCCAGATTC >B7_593:7:283:186:707 CGCTTGTACTTCTAAATCTATAACAAAATTAAAATT >B7_593:7:307:481:625 AAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAG >B7_593:7:307:481:625 TCAACATGAAGGAAAAAAATTCTAAAATCAGCAAGA >B7_593:7:67:302:762 GTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCC >B7_593:7:67:302:762 TTACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTA >B7_593:7:6:585:132 GCCCCTTGACCACCACCCAGTCCCTGCCCCATCTCT >B7_593:7:6:585:132 TGTACTTATCATGTTTCTTTCCTAATTTTTCAATTA >B7_593:7:87:89:696 TGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCCCC >B7_593:7:87:89:696 TTCCTATGGAAAGGTTGTTGGGAGATTTTTAATGAT >B7_595:1:209:345:87 AAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGT >B7_595:1:209:345:87 TTACTTGTTGTTGGTTTTCTGTTTCTTTTTTTGAT >B7_595:1:209:653:400 AGGAGCATTTTGTCAGTTACCAAATGTGTTTATTA >B7_595:1:209:653:400 CTAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTCT >B7_595:1:252:19:955 AGCCAGTTCTTTTGGCATTTGCCTTCAGACCCTCC >B7_595:1:252:19:955 TGAACAAAAGGAAGAAAAGGTCTTTCAAAAGGTGA >B7_595:1:81:1000:375 ACCCTGAGAGATTCTGCAGCCCAGCTCCAGATTGC >B7_595:1:81:1000:375 NATGTCAGGGAAGGAGCATTTTGTCAGTTACCAAA >B7_595:2:178:77:424 CTACCCTGCAATTAATATAATTGTGTCCATGTACA >B7_595:2:178:77:424 TGCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTG >B7_595:2:251:121:479 GGCTGCAACTGTGAGCCATCACAATGAACAACAGG >B7_595:2:251:121:479 GGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTG >B7_595:2:29:729:70 AAACAGAAACCAAATGAGAGAAGGAGTAGCTATAC >B7_595:2:29:729:70 ANTATTANCTTTGANNAAAAAGGGATTAAATTCCC >B7_595:3:229:543:583 ATAACCATCCTACTAAATACATATGCACCTAACAC >B7_595:3:229:543:583 TCAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAA >B7_595:3:297:637:86 CAATGTTCCCCAGATACCATCCCTGTCTTACTTCC >B7_595:3:297:637:86 TCTCAGCTAGGGGAACAGGGAGGTGCACTAATGCG >B7_595:3:57:735:151 CTATCCCAAATTCCCAATTACGTCCTATCTTCTTC >B7_595:3:57:735:151 TAAACTCTCACCTTATTGCTGCATCCCTGTCTTCC >B7_595:3:85:964:950 AACAGATTTAAAAACATGAACTAACTATATGCTGT >B7_595:3:85:964:950 GAGGTCATCATACAATGATAAAAAGATCAATTCAG >B7_595:4:12:402:843 AGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCC >B7_595:4:12:402:843 ATATAATTGTGTCCATGTACACACGCTGTCCTATG >B7_595:4:319:250:718 AAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTG >B7_595:4:319:250:718 AGTTGAAAGCTCTAACAATAGACTAAACCAAGCAG >B7_595:4:58:703:72 GTACACACGCTGTCCTATGTACTTATCATGACTCT >B7_595:4:58:703:72 TCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCC >B7_595:4:84:802:737 CATAGACCCCCTTGCAACAACCTTGAGAACCCCAG >B7_595:4:84:802:737 CTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAG >B7_595:5:184:912:258 ATTCTAAAATCAGCAAGAGAAAAGCATACAGTCAT >B7_595:5:184:912:258 GTTATGCCCTGCTAAACTAAGCATCATAAATGAAG >B7_595:5:36:649:554 AAGAGATTGGATCTAATTTTTGGACTTCTTAAAGA >B7_595:5:36:649:554 CAGGAAGATACATTGCAAGACAGACTTCATCAAGA >B7_595:5:84:91:614 GAACCACACATTAATACTATGTTTCTTATCTGCAC >B7_595:5:84:91:614 TTTCCCATCATGAAGCACTGATCTTCCACGTCTCA >B7_595:6:119:730:190 AGTCTCTTATGAATTAACCCAGTCAGACAAAAATA >B7_595:6:119:730:190 AGTCTTGCTAGAGATTTAGACATCTAAATGAAAGA >B7_595:6:137:811:130 AAAATTTAACAAAAGTAAATAAAACACATAGCTAA >B7_595:6:137:811:130 AGACTACCCAGATTCATAAAACAAATACTACTAGA >B7_595:6:290:270:557 ACATTACTACCCTGCAATTAATATAATTGTGTCCA >B7_595:6:290:270:557 GGAACAGGGAGGTGCACTAATGCGCTCCACGCCCA >B7_595:6:47:720:789 CCCTTGGCCATCACCCGGTCCCGGCCCCTTCTCTT >B7_595:6:47:720:789 TCCTCAATGTTAAAATGTCTATTTTTGTCTTGACA >B7_595:6:52:751:360 AAAAACTATTTGAGGAAGTAATTGGGGAAAACCTC >B7_595:6:52:751:360 AGAGAAAAGCATACAGTCATCTATAAAGGAAATCC >B7_595:6:99:557:427 AACAAAATTAAAATTTAACAAAAGTAAATAAAACA >B7_595:6:99:557:427 ATTCATAAAACAAATACTACTAGACCTAAGAGGGA >B7_595:7:123:610:472 GTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTC >B7_595:7:123:610:472 TGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGT >B7_595:7:149:123:265 AAGAGGGATGAGAAATTACCTAATTGGTACAATGT >B7_595:7:149:123:265 AGCAAAAACAAAAACTATGCTAAGTATTGGTAAAG >B7_595:7:166:203:416 AATTACGTCCTATCTTCTTCTTAGGGAAGAACAGC >B7_595:7:166:203:416 ATGAGATTATTAGGAAATGCTTTACTGTCATAACT >B7_595:7:188:802:71 ATGCTATTCAGTTCTAAATATAGAAATTGAAACAG >B7_595:7:188:802:71 TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGC >B7_595:7:190:481:295 GAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTG >B7_595:7:190:481:295 TCATAACTATGAAGAGACTATTGCCAGATGAACCA >B7_595:7:242:4:593 ATATACACACGCTGTCCTATGTACTTATCATGACT >B7_595:7:242:4:593 TCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCC >B7_595:8:26:242:35 ATAAAACAAAGGAGGTCATCATACAATGATAAAAA >B7_595:8:26:242:35 ATATTTTGATGATGGTTACACTAAAAGCCCATACT >B7_597:2:100:563:301 GAACTTCTGTAATTGAAAAATTCATTTAAGAAATT >B7_597:2:132:493:921 ACGGGGTTGCCAGCACAGGGGCTTAACCTCTGGTG >B7_597:2:132:493:921 GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC >B7_597:2:165:431:857 GAACTTTGATGCCCTCTTCTTCCAAAGATGAAACG >B7_597:2:165:431:857 TTGGGGTCTGACAGGCTGCAACTGTGAGCCATCAC >B7_597:2:168:829:88 ACAGACTTCATCAAGATATGTAGTCATCAGACTAT >B7_597:2:168:829:88 TAACTGAACCTATGAGTCACAGGTATTCCTGAGGA >B7_597:2:42:28:552 AAGAAGATATAACCATCCTACTAAATACATATGCA >B7_597:2:42:28:552 ACTCAATATATCCATGTAACAAATCTGCGCTTGTA >B7_597:3:10:394:392 TCATCAAGATATGTAGTCATCAGACTATCTAAATT >B7_597:3:10:394:392 TTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACA >B7_597:3:115:646:430 CACAGGTTTTATAAAACAATTAATTGAGACTACAG >B7_597:3:115:646:430 GTTATGCCCTGCTAAACTTAGCATCATAAATGAAG >B7_597:3:133:707:886 ACCTAATAAATACATATGCACCTAACACAAGACTA >B7_597:3:133:707:886 AGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAAC >B7_597:3:157:361:309 CCTGCTAAACTAAGCATCATAAATGAAGGGGAAAT >B7_597:3:157:361:309 TACACACAAAAGTACAAAACTCACAGGTTTTATAA >B7_597:3:39:966:551 ACATTAATACTATGTTTCTTATCTGCACATTACTA >B7_597:3:39:966:551 AGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTC >B7_597:3:46:981:766 TCTTTTGGCATTTGCCTTCAGACCCTACACGAATG >B7_597:3:46:981:766 TGCCCCCAGCATGGTTGTACTGGGCAATACATGAG >B7_597:3:53:616:842 CTTATCATGACTCTATCCCAAATTCCCACTTACGT >B7_597:3:53:616:842 TCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTC >B7_597:3:67:620:344 AGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATT >B7_597:3:67:620:344 CCCCCGCCCAAGCCCTTCTCACAGTTTCTGCCCCC >B7_597:3:73:273:488 AAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGG >B7_597:3:73:273:488 CTCTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTG >B7_597:4:138:211:582 CATTAATAAAGACATGAGTTCAGGTAAAGGGGTGG >B7_597:4:138:211:582 TGAGACTACAGAGCAAATAGGTAAAAAATTAACAT >B7_597:4:144:492:61 AAATACTCACCATCATAAATACACACAAAAGTACA >B7_597:4:144:492:61 AACCTGTCAAACACGAATGTTATGCCCTGCTAAAC >B7_597:4:146:961:63 TACTTATATCAGATAAAGCACACTTTAAATCAACA >B7_597:4:146:961:63 TGAATAAAAAGGGCTTAAATTCCCCCACTTAAGGG >B7_597:4:38:999:463 GCGGAAACCTTACAAGCCAGAAGAGATTGGATCTA >B7_597:4:38:999:463 TAGACATCTAAATGAAAGNNGCNNNAAGAATGCCA >B7_597:5:125:957:753 TTTTTTTTTTTTCTCTCCTCTTTTTTTTTTTTTTT >B7_597:5:160:434:853 ATATAATTGTGTCCATGTACACACGCTGTCCTATG >B7_597:5:160:434:853 GCTTGGGCTGTAATGATGCCCCTTGGCCATCACCC >B7_597:5:58:684:520 AGACAGACTTCATCAAGATATGTAGTCATCAGACT >B7_597:5:58:684:520 ATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCA >B7_597:5:6:882:784 CATGGCTGATTATGAAAACAATGTTCCCCAGATAC >B7_597:5:6:882:784 CTGGATTCTGGGAAATTCTTCATCCTGGACCCTGA >B7_597:5:98:995:929 GTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGT >B7_597:5:98:995:929 TATAACAATATTAACTTTGAATAAAAAGGGATTAA >B7_597:6:106:595:322 GAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTGC >B7_597:6:106:595:322 GCAAGAGAAAAGCATACAGTCATCTATAAAGGAAA >B7_597:6:193:661:771 AAACTCATTAATAAAGACATGAGTTCAGGTAAAGG >B7_597:6:193:661:771 GCAAGAAGATATAACCATCCTACTAAATACATATG >B7_597:6:20:592:496 CTCAAAGAATGCCAGGAAGATACATTGCAAGACAG >B7_597:6:20:592:496 TCTCAGCGGAAACCTTACAAGCCAGAAGAGATTGG >B7_597:6:29:249:878 ATTGTGTCCATGTACACACGCTGTCCTATGTACTT >B7_597:6:29:249:878 TCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGG >B7_597:6:73:420:812 CTAAGTATTGGTAAAGATGTGGGGAAAAAAGTAAA >B7_597:6:73:420:812 CTAATTGGTACAATGTACAATATTCTGATGATGGT >B7_597:7:103:731:697 AATTAACCCAGTCAGACAAAAATAAAGAAAAAAGA >B7_597:7:103:731:697 CTTGCTAGAGATTTAGACATCTAAATGAAAGAGGC >B7_597:7:113:408:211 AAACTCATTAATAAAGACATGAGTTCAGGTAAAGG >B7_597:7:113:408:211 GAGACTACAGAGCAACTAGGTAAAAAATTAACATT >B7_597:7:31:948:254 CCTCTACATGGCTGATTATGAAAACAATGTTCCCC >B7_597:7:31:948:254 TGAAGCACTGAACTTCCACGTCTCATCTAGGGGAA >B7_597:7:41:34:211 CACCTAACACAAGACTACCCAGATTCATAAAACAA >B7_597:7:41:34:211 GTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAG >B7_597:7:5:753:806 AAAATATAGTTGAAAGCTCTAACAATAGACTAAAC >B7_597:7:5:753:806 ATGTAAAGTAACTGAACCTATGAGTCACAGGTATT >B7_597:7:94:273:165 AGAAAGAAGATATAACCATCCTACTAAATACATAT >B7_597:7:94:273:165 TTACAAGAAACTCATTAATAAAGACATGAGTTCAG >B7_597:8:147:360:141 TGCGCTTGTACTTCTAAATCTATAACAAAATTAAA >B7_597:8:147:360:141 TTTGGTAATTTAGTTTTTTTTTTTTCTTTTCTCTT >B7_597:8:186:850:838 GGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTT >B7_597:8:186:850:838 GTTCTATTTGTAATGAAAACTATATTTATGCTATT >B7_597:8:35:118:589 TCATAAAACAAATACTACTAGACCTAAGAGGGATG >B7_597:8:35:118:589 TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA >B7_597:8:48:805:860 AAACCTGTCAAACACGAATGTTATGCCCTGCTAAA >B7_597:8:48:805:860 AAAGTACAAAACTCACAGGTTTTATAAAACAATTA >B7_610:1:12:88:200 ACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTT >B7_610:1:12:88:200 GAAGATATAACCATCCTACTAAATACATATGCACC >B7_610:1:139:152:856 AGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTT >B7_610:1:139:152:856 CTAAGCCGTTCTATTTGTAATGAAAACTATATTTA >B7_610:1:37:652:403 CCCCTCTAAGCCGTTCTATTTGTAATGAAAACTAT >B7_610:1:37:652:403 TTTTGTCAGTTACCAAATGTGTTTATTACCAGAGG >B7_610:2:189:831:878 AGAAAAAAAAACCTGTCAAACACGAATGTTATGCC >B7_610:2:189:831:878 AGGAAGATACATTGCAAGACAGACTTCATCAAGAT >B7_610:2:194:688:289 TCAGACCCTACACGAATGCGTCTCTACCACAGGGG >B7_610:2:194:688:289 TGTGTGTTCTCATCAACCTCATACACACACATGGT >B7_610:2:6:529:366 CATACAATGATAAAAAGATCAATTCAGCAAGAAGA >B7_610:2:6:529:366 GCTACTCAATATATCCATGTAACAAATCTGCGCTT >B7_610:2:75:887:149 TACAACAGGAACAAAACCTCATATATCAATATTAA >B7_610:2:75:887:149 TACGCAAACAGAAACCAAATGAGAGAAGGAGTAGC >B7_610:3:102:825:507 TGCTGCATCCCTGTCTTCCTCTGTCTTGATTTACT >B7_610:3:102:825:507 TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAAC >B7_610:3:120:63:653 AACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATG >B7_610:3:120:63:653 TCTTCTTCCAAAGATGAAACGCGTAACTGCGCTCT >B7_610:3:137:895:681 CTTCCTATGGAAAGGTTGTTGGGAGATTTTTAATG >B7_610:3:137:895:681 GCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGC >B7_610:3:148:340:479 TCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTC >B7_610:3:148:340:479 TTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGG >B7_610:3:182:23:585 AGAACAGCTTAGGTATCAATTTGGTGTTCTGTGTA >B7_610:3:182:23:585 ATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGT >B7_610:3:5:863:302 ACGTCTCATCTAGGGGAACAGGGAGGTGCACTAAT >B7_610:3:5:863:302 TGAAAACAATGTTCCCCAGATACCATCCCTGTCTT >B7_610:3:82:998:566 ATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCT >B7_610:3:82:998:566 GCACATTACTACCCTGCAATTAATATAATTGTGTC >B7_610:3:84:101:328 AATGGACCTGTGATATCTGGATTCTGGGAAATTCT >B7_610:3:84:101:328 TATAATACCTCTACATGGCTGATTATGAAAACAAT >B7_610:3:85:219:371 GACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGT >B7_610:3:85:219:371 TAACATTACAACAGGAACAAAACCTCATATATCAA >B7_610:4:139:989:144 ACTAAAAAAGCAAAAACAAAAACTATGCTAAGTAT >B7_610:4:139:989:144 ACTACTAGACCTAAGAGGGATGAGAAATTACCTAA >B7_610:4:15:805:420 ATGAAGAGACTATTCACATGTGAACCACACATTTA >B7_610:4:15:805:420 GAACAGTTTAGGTATCAATTTGGTGTTCTTTGTAA >B7_610:4:198:59:675 AATCTGCGCTTGTACTTCTAAATCTATAACAAAAT >B7_610:4:198:59:675 ACTAAATACATATGCACCTAACACAAGACTATCCT >B7_610:4:67:317:249 CTACATGGCTGATTATGAAATCTATGTTCCCCATA >B7_610:4:67:317:249 TTCCCATCATGACGCACCGAACTTCCACGTCTCAT >B7_610:5:102:915:87 AACAATAGACTAAACCAAGCAGAAGAAAGAGGTTC >B7_610:5:102:915:87 CACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAA >B7_610:5:120:596:847 AACCTATGAGTCACAGGTATTCCTGAGGAAAAAGA >B7_610:5:120:596:847 TCAACATGAAGGAAAAAAATTCTAAAATCAGCAAG >B7_610:5:136:260:254 AAATTAACATTACAACAGGAACAAAACCTCATATA >B7_610:5:136:260:254 GTGGAAAAAGATGTTCTACGCAAACAGAAACCAAA >B7_610:5:147:68:353 AACAACCTTGAGAACCCCAGGGAATTTGTCAATGT >B7_610:5:147:68:353 CCTTTGATATCTGGATTCTGGGAAATTCTTCATCC >B7_610:5:51:904:391 ACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAA >B7_610:5:51:904:391 TATCTAAAGTCAACATGAAGGAAAAAAATTCTAAA >B7_610:5:7:761:623 CCGGCATGGTTGTACTGGGCAATACATGAGATTAT >B7_610:5:7:761:623 CTTTCAACGCTTCTAGCCATTTCTTTTGGCATTTG >B7_610:6:107:252:533 AGAGAAGGAGTAGCTATACTTATATCAGATAAAGC >B7_610:6:107:252:533 CAAGACTACCCAGATTCATAAAACAAATACTACTA >B7_610:6:111:379:700 ACACTAAAAGCCCATACTTTACTGCTACTCAATAT >B7_610:6:111:379:700 CGCACTGGCAATATTTGTGTGTTTACTTTTTTGCA >B7_610:6:143:620:158 ACTTTACTGCTACTCAATATATCCATGTAACAAAT >B7_610:6:143:620:158 CAATGATAAAAAGATCAATTCAGCAAGAAGATATA >B7_610:6:148:776:486 AACTGTGAGCCATCACAATGAACAACAGGAAGAAA >B7_610:6:148:776:486 AGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATT >B7_610:7:116:157:612 GTAAAAGTCAAAATTAAAGTTCAATACTCACCATC >B7_610:7:116:157:612 TTAAGAGATATAGATTGGCAGTACAGATTTAAAAA >B7_610:7:117:857:942 AGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCT >B7_610:7:117:857:942 GGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGAC >B7_610:7:158:943:467 AAAGCTCTAACAATAGACTAAACCAAGCAGAAGAA >B7_610:7:158:943:467 AGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTT >B7_610:7:15:696:693 TCAAACACGAATGTTAATCCCTGCTAAACTAATCA >B7_610:7:15:696:693 TCTAAAGTCAACATGAAGGAAAAAAATTCTAAAAT >B7_610:7:177:469:800 AAAATCAGCAAGAGAAAAGCATACAGTCATCTATA >B7_610:7:177:469:800 TTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAA >B7_610:7:26:749:174 CAGATTCATAAAACAAATACTACTAGACCTAAGAG >B7_610:7:26:749:174 TAACAAAAGTAAATAAAACACATAGCTAAAACTAA >B7_610:7:34:144:868 AATTACCTAATTGGTACAATGTACAATATTCTGAT >B7_610:7:34:144:868 AGCTAAGGAATGGGAAAGGTGTGGGGAAAAAAGTA >B7_610:7:35:378:681 GCGTCTCTACCACAGGGGGCTGCGCGGTTTCCCAT >B7_610:7:35:378:681 GTGTGTTCTCATCAACCTCATACACACACATGGTT >B7_610:8:163:757:432 CCAGATGAACCACACATTAATACTATGTTTCTCAT >B7_610:8:163:757:432 GGTTTCCCATCATGAAGCACTGAACTTCCACGTCT >B7_610:8:68:570:705 AACAGATTTAAAAACATGAACTAACTATATGCTGT >B7_610:8:68:570:705 CATCATACAATGATAAAAAGATCAATTCAGCAAGA >B7_610:8:95:426:791 CCAAATGTGTTTATTACCAGAGGGATGGAGGGAAG >B7_610:8:95:426:791 GNTCCAGATTGCTTGTGGTCTGACAGGCTGCAACT >EAS112_32:7:113:809:364 GATGCCCTCTTCTTCCAAAGATGAAACGCGTAACT >EAS112_32:7:113:809:364 TATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTG >EAS112_32:7:135:401:735 AATTGTAAAAGTCAAAATTAAAGTTCAATACTCAC >EAS112_32:7:135:401:735 CCTTACAAGCCAGAAGAGATTGGATCTAATTTTTG >EAS112_32:7:168:117:441 TCATAACTATGAAGAGACTATTGCCAGATGAACCA >EAS112_32:7:168:117:441 TCTTCTTAGGGAAGAACAGCTTAGGTATCAATTTG >EAS112_32:7:272:328:400 CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA >EAS112_32:7:272:328:400 CTAAATACATATGCACCTAACACAAGACTACCCAG >EAS112_32:7:322:391:742 ATCAATATTAACTTTGAATAAAAAGGGATTAAATT >EAS112_32:7:322:391:742 CATCACTAAACCAGTCCTATAAGAAATGCTCAAAA >EAS112_32:7:42:804:114 ATACTTTACTGCTACTCAATATATCCATGTAACAA >EAS112_32:7:42:804:114 TCAAATATTGCTAGTGGGAGTATAAATTGTTTTCC >EAS112_32:8:88:90:59 ATAATACCTCTACATGTCTGATTATGAAAACAATG >EAS112_32:8:88:90:59 TGCACCTCCCTGTTCACCTAGATGCTAGGAGGACA >EAS112_32:8:89:254:332 AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT >EAS112_32:8:89:254:332 GAATTAACCCAGTCAGACAAAAATAAAGAAAAAAG >EAS112_34:4:12:273:89 AGTCTTTCCTGACAAGCAAATGCTAAGATAATTCA >EAS112_34:4:12:273:89 CCATCAGAATAACAATGGGCTTCTCAGCGGAAACC >EAS112_34:4:17:989:186 TTAGTCTTGCTAGAGATTTAGACATCTAAATGAAA >EAS112_34:4:17:989:186 TTATGAATTAACCCAGTCAGACAAAAATAAAGAAA >EAS112_34:4:22:206:150 AAAAAAGAGCAACTAGGTAAAAAATTAACATTACA >EAS112_34:4:22:206:150 GAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGC >EAS112_34:4:74:570:695 CACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGA >EAS112_34:4:74:570:695 TTGGGAGATTTTTAATGATTCCTCAATGTTAAAAT >EAS112_34:4:92:412:435 AGATTCATAAAACAAATACTACTAGACCTAAGAGG >EAS112_34:4:92:412:435 CTACGCAAACAGAAACCAANTGAGAGAAGGAGTAG >EAS112_34:6:127:153:861 CTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTC >EAS112_34:6:127:153:861 TTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACAT >EAS112_34:6:130:865:838 AAAGCATACAGTCATCTATAAAGGAAATCCCATCA >EAS112_34:6:130:865:838 AATGCTAAGATAATTCATCATCACTAAACCAGTCC >EAS112_34:6:145:144:263 TTTCGTTTTTTTTTTTTTTTTTTCCCCTTTCTTTT >EAS112_34:6:43:47:279 AAAACTATGCTAAGTATTGGTAAAGATGTGGGGAA >EAS112_34:6:43:47:279 TAGACCTAAGAGGGATGAGAAGTTACCTAATTGGT >EAS112_34:6:71:85:629 CCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGA >EAS112_34:6:71:85:629 TTGACACCCAACTAATATTTGTCTGAGCAAAACAG >EAS112_34:6:75:615:555 AAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGG >EAS112_34:6:75:615:555 TGAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAA >EAS112_34:7:118:523:591 GAGGGACGCTGAAGAACTTTGATGCCCTCTTCTTC >EAS112_34:7:118:523:591 GGTCTGACAGGCTGCAACTGTGAGCCATCACAATG >EAS112_34:7:141:80:875 AGCCGAGTCACGGGGTTGCCAGCACAGGGGCTTAA >EAS112_34:7:141:80:875 AGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCA >EAS112_34:7:142:457:584 GGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGT >EAS112_34:7:142:457:584 TGAAGAGACTATTTCCAGATGAACCACACATTAAT >EAS112_34:7:71:62:254 AAAAAAGTAAACTCTCAAATATTGCTAGTGGGAGT >EAS112_34:7:71:62:254 GGTTACACTAAAAGCCCATACTTTCCTGCTACTCA >EAS112_34:7:86:498:373 CACTAATGCGCTCCACGCCCAAGCCCTTCTCACAG >EAS112_34:7:86:498:373 GATACCATCCCTGTCTTACTTCCAGCTCACCAGAG >EAS112_34:7:96:489:453 AAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT >EAS112_34:7:96:489:453 AGAAAAGCATACAGTCATCTATAAAGGAAATCCCA >EAS112_34:8:103:812:255 ATGTTAAAATGTCTATTTTTGTCTTGACACCCAAC >EAS112_34:8:103:812:255 TGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCC >EAS112_34:8:174:557:872 GGTAAAGATGTGGGGAAAAAAGTAAACTCTCAAAT >EAS112_34:8:174:557:872 TGGTACAATGTACAATATTCTGATGATGGTTACAC >EAS112_34:8:179:13:782 GACAGTCTACAACTGTGAGCCATCACAATGAACAA >EAS112_34:8:179:13:782 TGATGCCCTCTTCTTCCAAAGATGAAACGCGTAAC >EAS112_34:8:30:816:90 ACTACCCTGCAATTAATATAATTGTGTCCATGTAC >EAS112_34:8:30:816:90 AGGGAGGTGCACTAATGCGCTCCACGCCCCAGCCC >EAS112_34:8:45:800:733 ACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGA >EAS112_34:8:45:800:733 ATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTG >EAS112_34:8:4:841:339 ACCTCATACACACACATGGTTTAGGGGTATAATAC >EAS112_34:8:4:841:339 CTTCAGACCCTACACGAATGCGTCTCTACCACAGG >EAS114_26:1:113:367:659 AGTCATCAGACTATCTAAAGTCAACATGAAGGAAA >EAS114_26:1:113:367:659 CACAGGTATTCCTGAGGAAAAAGAAAAAGCGAGAA >EAS114_26:1:155:807:19 AAAAGGGATTAAATTCCCCCACTTAAGAGATATAG >EAS114_26:1:155:807:19 CAACAGTAAAATAAAACAAAGGAGGTCATCATACA >EAS114_26:1:171:527:247 AACAAATGCTACTAGACCTAAGAGGGATGAGAAAT >EAS114_26:1:171:527:247 AGAAGGAGTAGCTAGACTTATATCAGATAAAGCAC >EAS114_26:1:324:238:736 AGACAGACTTCATCAAGATATGTAGTCATCAGACT >EAS114_26:1:324:238:736 TCAAGAAGTATGAGATTATGTAAAGTAACTGAACC >EAS114_26:1:35:522:294 GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA >EAS114_26:1:35:522:294 TTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTT >EAS114_26:1:99:212:522 ACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTT >EAS114_26:1:99:212:522 AGAGACTATTGCCAGATGAACCACACATTAATACT >EAS114_26:2:130:609:467 AAATTCCCCCACTTAAGAGATATAGATTGGCAGAA >EAS114_26:2:130:609:467 CAATACTCACCATCATAAATACACACAAAAGTACA >EAS114_26:2:214:950:32 ACAAGAAACTCATTAATAAAGACATGAGTTCAGGT >EAS114_26:2:214:950:32 AGAAGATATAACCATCCTACTAAATACATATGCAC >EAS114_26:2:237:497:165 GAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGC >EAS114_26:2:237:497:165 TACAGTCATCTATAAAGGAAATCCCATCAGAATAA >EAS114_26:2:315:219:7 GAAAGAGGCTCAAAGAATGCCAGGAAGATACATTG >EAS114_26:2:329:458:365 GTGTTCTGTGTAAAGTCTCAGGGAGCCGTCCGTGT >EAS114_26:2:329:458:365 TTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGG >EAS114_26:2:73:513:102 GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC >EAS114_26:2:73:513:102 TGAAAACAATGTTCCCCAGATACCATCCCTGTCTT >EAS114_26:3:117:284:589 ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA >EAS114_26:3:117:284:589 GAACCTATGAGTCACAGGTATTCCTGAGGAAAAAG >EAS114_26:3:284:261:124 ACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTG >EAS114_26:3:287:665:495 GAATTGTAAAAGTCAAAATTAAAGTTCAATACTCA >EAS114_26:3:287:665:495 TGGATCTAATTTTTGGACTTCTTAAAGAAAAAAAA >EAS114_26:4:100:238:596 ATGAGAAATTACCTAATTGGTACAATGTACAATAT >EAS114_26:4:100:238:596 CAAAAACTATTCTAAGTATTGGTAAAGATGTGGGG >EAS114_26:4:110:840:431 CTGTCAAACACGAATGTTATGCCCTGCTAAACTAA >EAS114_26:4:110:840:431 GTAGTCATCAGACTATCTAAAGTCAACATGAAGGA >EAS114_26:4:123:1001:580 AGGTTTTATAAAACAATTAATTGAGACTACAGAGC >EAS114_26:4:123:1001:580 GGGAANTAAAGTCAAGTCTTTCCTGACAAGCAAAT >EAS114_26:4:253:285:104 CTCTCATTCACTCCAGCTCCCTGTCACCCAATGGA >EAS114_26:4:253:285:104 GTGATGTGTGTTCTCATCAACCTCATACACACACA >EAS114_26:4:306:388:342 CCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACT >EAS114_26:4:306:388:342 GGGGAAGACATAATCCCACGCTTCCTATGGAAAGG >EAS114_26:4:40:352:151 ATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCT >EAS114_26:4:40:352:151 TTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT >EAS114_26:5:139:331:63 GACACCCAACTAATATTTGTCTGAGCAAAACAGTC >EAS114_26:5:139:331:63 TTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT >EAS114_26:5:228:189:826 AAGCCCTTCTCACAGTTTCTGCCCCCCGCATGGTT >EAS114_26:5:228:189:826 ATCATGACTCTATCCCAAATTCCCAATTACGTCCT >EAS114_26:5:238:31:968 ACACCATCCCTGTCTTACTTCCAGCTCCCCAGAGG >EAS114_26:5:238:31:968 ATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCTG >EAS114_26:5:43:114:617 AATCATAAATACACACAAAAGTACAAAACTCACAG >EAS114_26:5:43:114:617 AATGTTATGCCCTGCTAAACTAAGCATCATAAATG >EAS114_26:6:129:694:359 CCCTGAGAGATTCTGCAGCCCAGATCCAGATTGCT >EAS114_26:6:129:694:359 TGTCAGTTACCAAATGTGTTTATTACCCGAGGGAT >EAS114_26:6:140:253:322 AATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTC >EAS114_26:6:140:253:322 GAAATGCTCAAAAGAATTGTAAAAGTCAAAATTAA >EAS114_26:6:183:697:555 AAAGAATGCCAGGAAGATACATTGCCAGACAGACT >EAS114_26:6:183:697:555 AGAAATCTTAGAAGCCAGAAGAGATTGGATCTAAT >EAS114_26:6:46:13:880 AAAACCTCTTTAGTCTTGCTAGAGATTTAGACATC >EAS114_26:6:46:13:880 AGAAAAGCATACAGTCATCTATAAAGGAAATCCCA >EAS114_26:7:13:172:720 AATTCATTTAAGAAATTACAAAATATAGTTGAAAG >EAS114_26:7:157:876:302 AAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGA >EAS114_26:7:157:876:302 CAACTAGGTAAAAAATTAACATTACAACACGAACA >EAS114_26:7:218:858:445 AAAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTT >EAS114_26:7:218:858:445 GAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATA >EAS114_26:7:245:323:744 ACCTCTACATGGCTGATTATGAAAACAATGTTCCC >EAS114_26:7:245:323:744 GATTCTGGGAAATTCTTCATCCTGGACCCTGAGAG >EAS114_26:7:37:79:581 TTAAAATTTAAAAAAAGTAAATAAAACACATAGCT >EAS114_26:7:37:79:581 TTTTTTTTTTTTTTTTTTTTTTTCATGCCAGAAAA >EAS114_26:7:86:308:648 GAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTG >EAS114_26:7:86:308:648 TATTAGGAAATGCTTTACTGTCATAACTATGAAGA >EAS114_28:1:144:242:602 ATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGG >EAS114_28:1:144:242:602 ATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAG >EAS114_28:1:168:389:889 GAAATTACAAAATATAGTTGAAAGCTCTAACAATAG >EAS114_28:1:168:389:889 TAACTGAACCTATGAGTCACAGGTATTCCTGAGGAA >EAS114_28:1:168:609:646 GGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG >EAS114_28:1:168:609:646 GGTTACACTAAAAGCCCATACTTTACTGCTACTCAA >EAS114_28:1:220:801:282 AACCTCATATATCAATATTAACTTTGAATAAAAAGG >EAS114_28:1:220:801:282 AATTCATCATCACTAAACCAGTCCTATAAGAAATGC >EAS114_28:1:232:351:909 ACATGGCTGATTATGAAATCAATGTTCCCCAGATGC >EAS114_28:1:232:351:909 CCATCATGAAGCGCTGAACTTCCACGTCTCATCTAG >EAS114_28:1:28:708:463 CCCAATGGACCTGTGATATCTGGATTCTGGGAAATT >EAS114_28:1:28:708:463 GTATAATACCTCTACATGGCTGATTATGAAAACAAT >EAS114_28:2:114:938:216 CTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT >EAS114_28:2:114:938:216 GAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGA >EAS114_28:2:141:7:963 CACTTTAAATCAACAACAGTAAAATAAAACAAAGGA >EAS114_28:2:141:7:963 TACAATGTACAATATTCTGATGATGGTTACACTAAA >EAS114_28:2:149:650:44 CGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCC >EAS114_28:2:149:650:44 CTGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTC >EAS114_28:2:167:905:852 AGAAAAGCATACAGTCATCTATAAAGAAAATCCCAT >EAS114_28:2:167:905:852 CAAATGCTAAGATAATTCATCATCACTAAACCAGTC >EAS114_28:2:251:819:772 TCCCCCACTTAAGAGATATAGATTGGCAGAACAGAT >EAS114_28:2:251:819:772 TTCAATACTCACCATCATAAATACACACAAAAGTAC >EAS114_28:2:28:474:566 ACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAG >EAS114_28:2:28:474:566 TGAACCACACATTAATACTATGTTTCTTATCTGCAC >EAS114_28:2:329:437:643 AAGATACATTGCAAGACAGACTTCATCAAGATATGT >EAS114_28:2:329:437:643 TTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAAC >EAS114_28:2:55:562:403 CAACAGGAACAAAACCTCATATATCAATATTAACTT >EAS114_28:2:55:562:403 CAAGCAAATGCTAAGATAATTCATCATCACTAAACC >EAS114_28:3:110:984:98 AAGGAGGTCATCATACAATGATAAAAAGATCAATTC >EAS114_28:3:110:984:98 ACTAAAACCCCATACTTTACTGCTACTCAATATATC >EAS114_28:3:173:627:465 GTAAACTCTCAAATATTGCTAGTGGGAGTATAAATT >EAS114_28:3:173:627:465 TGATGGTTACACTAAAAGCCCATACTTTACTGCTAC >EAS114_28:3:176:402:458 AAATAGCTAAAACTAAAAAAGCAAAAACAAAAACTA >EAS114_28:3:176:402:458 CCTAAGAGGGATGAGAAATTACCTAATTGGTACAAT >EAS114_28:3:202:275:776 CAAATACTACTAGACCTAAGAGGGATGAGAAATTAC >EAS114_28:3:202:275:776 TCTACGCAAACAGAAACCAAATGAGAGAAGGAGTAG >EAS114_28:3:250:628:423 CAATGGGCTTCTCAGCGGAAACCTTACAAGCCAGAA >EAS114_28:3:250:628:423 CTCTTTAGTCTTGCTAGAGATTTAGACATCTAAATG >EAS114_28:3:279:763:945 CTGCACATTACTACCCTGCAATTAATATAATTGTGT >EAS114_28:3:279:763:945 GCCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACT >EAS114_28:3:308:509:948 AATATATCCATGTAACAAATCTGCGCTTGTACTTCT >EAS114_28:3:308:509:948 AATTCAGCAAGAAGATATAACCATCCTACTAAATAC >EAS114_28:3:32:492:907 CAAACACGAATGTTATGCCCTGCTAAACTAAGCATC >EAS114_28:3:32:492:907 TGTAGTCATCAGACTATCTAAAGTCAACATGAAGGA >EAS114_28:3:78:773:660 ATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCTGA >EAS114_28:3:78:773:660 CCCCAGATACCATCCCTGTCTTACTTCCAGCTCCCC >EAS114_28:4:13:701:55 AAACCAAATGAGAGAAGGAGTAGCTATACTTATATC >EAS114_28:4:13:701:55 TTCATAAAACAAATACTACTAGACCTAAGAGGGATG >EAS114_28:4:149:572:877 ATGTAAAGTAACTGAACCTATGAGTCACAGGTATTC >EAS114_28:4:149:572:877 GAGGCTCAAAGAATGCCAGGAAGATACATTGCAAGA >EAS114_28:4:215:246:640 AAAAGCATACAGTCATCTATAAAGGAAATCCCATCA >EAS114_28:4:215:246:640 AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT >EAS114_28:4:305:707:258 AAAAAGATGTTCTACGCAAGCAGAAACCAAATGAGA >EAS114_28:4:305:707:258 GAACAAAACCTCATATATCAATATTAACTTTGAATA >EAS114_28:4:322:631:245 CCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC >EAS114_28:4:322:631:245 TATTTTTGTCTTGACACCCAACTAATATTTGTCTGA >EAS114_28:4:9:55:730 ATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGC >EAS114_28:4:9:55:730 CAGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCT >EAS114_28:5:104:350:749 AAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTT >EAS114_28:5:104:350:749 TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGCG >EAS114_28:5:11:868:62 TCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGT >EAS114_28:5:11:868:62 TTTACTGTCATAACTATGAAGAGACTATTGCCAGAT >EAS114_28:5:163:832:715 TAAAAACATGAACTAACTATATGCTGTTTACAAGAA >EAS114_28:5:163:832:715 TAAAACAAAGGAGGTCATCATACAATGATAAAAAGA >EAS114_28:5:206:671:49 ACCATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAA >EAS114_28:5:206:671:49 GCTTGTGGTCTGACAGGCTGCAACTGTGAGCCATCA >EAS114_28:5:209:778:588 AACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCT >EAS114_28:5:209:778:588 TTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT >EAS114_28:5:23:944:377 AATGTTATGCCCTGCTAAACTAAGCATCATAAATGA >EAS114_28:5:23:944:377 AGTACAAAACTCACAGGTTTTATAAAACAATTAATT >EAS114_28:6:11:151:750 GTTTTTATTTTTTTCCTCTCTCTTTTTTTTTTTTTT >EAS114_28:6:155:68:326 CCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAA >EAS114_28:6:155:68:326 GTCAGGGAAGGAGCATTTTGTCAGTTACCAAATGTG >EAS114_28:6:175:705:982 CATGGTTTAGGGGTATAATACCTCTACATGGCTGAT >EAS114_28:6:175:705:982 CTGGATTCTGGGAAATTCTTCATCCTGGACCCTGAG >EAS114_28:6:185:87:475 AAGAAACTCATTAATAAAGACATGAGTTCAGGTAAA >EAS114_28:6:185:87:475 ATTGAGACTACAGAGCAACTAGGTAAAAAATTAACA >EAS114_28:6:187:996:432 TGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTTC >EAS114_28:6:187:996:432 TTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAG >EAS114_28:6:51:506:878 TAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCCT >EAS114_28:6:51:506:878 TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACT >EAS114_28:6:54:263:585 TGAAAGCTTGGGCTGTAATGATGCCCCTTGGCCATC >EAS114_28:6:54:263:585 TGTCCATGTACACACGCTGTCCTATGTACTTATCAT >EAS114_28:7:133:514:754 AGCTATACTTATATCAGATAAAGCACACTTTAAATC >EAS114_28:7:133:514:754 TAAATTTGAATAAAAAGGGATTAAATTCCCCCACTT >EAS114_28:7:157:786:424 GCTTTACTGTCATAACTATGAAGAGACTATTGCCAG >EAS114_28:7:157:786:424 TTAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAG >EAS114_28:7:178:276:693 GTTCAGAACTTGAAGACAAGTCTCTTATGAATTAAC >EAS114_28:7:178:276:693 TTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAAC >EAS114_28:7:215:863:521 ACTCACCATCATAAATACACACAAAAGTACAAAACT >EAS114_28:7:215:863:521 TAAGAGATATAGATTGGCAGAACAGATTTAAAAACA >EAS114_28:7:242:354:637 AACTATATTTATGCTATTCAGTTCTAAATATAGAAA >EAS114_28:7:242:354:637 CCCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCT >EAS114_28:7:287:492:169 CGCTCTCATTCACTCCAGCTCCCTGTCACCCAATGG >EAS114_28:7:287:492:169 GTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAAC >EAS114_28:7:57:324:546 GTCATCTATAAAGGAAATCCCATCAGAATAACAATG >EAS114_28:7:57:324:546 TAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATT >EAS114_30:1:134:379:893 AGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATA >EAS114_30:1:134:379:893 CGCTGTCCTATGTACTTATCATGACTCTATCCCAA >EAS114_30:1:154:818:165 GAACAGGGAGGTGCACTAATGCGCTCCACGCCCAA >EAS114_30:1:154:818:165 TTCTTATCTGCACATTACTACCCTGCAATTAATAT >EAS114_30:1:176:168:513 ATTTGTAATGAAAACTATATTTATGCTATTCAGTT >EAS114_30:1:176:168:513 TTTGATGCCCTCTTCTTCCAAAGATGAAACGCGTA >EAS114_30:1:188:863:790 CATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTC >EAS114_30:1:188:863:790 TTAATTGAGACTACAGAGCAACTAGGTAAAAAATT >EAS114_30:1:243:10:911 TATTCAGTTCTAAATATAGAAATTGAAACAGCTGT >EAS114_30:1:64:526:339 ACATTACAACAGGAACAAAACCTCATATATCAATA >EAS114_30:1:64:526:339 CAAATGAGAGAAGGAGTATCTATACTTATATCAGA >EAS114_30:2:111:142:21 ATCAGAATAACAATGGGCTTCACAGCGGAAACCTT >EAS114_30:2:111:142:21 CTTGCTAGAGATTTAGACATCTAAATGAAAGAGGC >EAS114_30:2:226:885:729 AAAAGGGATTAAATTCCCCCACTTAAGAGATATAG >EAS114_30:2:226:885:729 GCTGAACTTACATCAGATAAAGCACACTTTAAATC >EAS114_30:2:272:750:698 GTGTTTATTACCAGAGGGATGGAGGGATGACGGAC >EAS114_30:2:272:750:698 TGCAGCCCAGATCCAGATTGCTTGTGGTCTGACAG >EAS114_30:2:297:949:26 ACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAA >EAS114_30:2:297:949:26 CATATATCAATATTAACTTTGAATAAAAAGGGATT >EAS114_30:2:303:428:326 AAAATTAAAATTTAACAAAAGTAAATAAAACACAT >EAS114_30:2:303:428:326 TTTTTTTTTTTTTTTTTCTCTTTTTTTTTTTTTTT >EAS114_30:2:30:887:404 CAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTG >EAS114_30:2:30:887:404 TTGCCTTCAGACCCTGCACGAATGCGTCTCTACCA >EAS114_30:2:315:412:921 GTAAAGATGTGGGGAAAAAAGTAAACTCTCAAATA >EAS114_30:2:315:412:921 TTCTGATGATGGTTACACTACAAGCCCATACTGTA >EAS114_30:2:82:963:128 ATTAAAGTTCAATACTCACCATCATAAATACACAC >EAS114_30:2:82:963:128 GGCAGAACAGATTTAAAAACATGAACTAACTATAT >EAS114_30:3:139:117:262 AGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTG >EAS114_30:3:139:117:262 GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC >EAS114_30:3:14:697:541 TAAAAGCAGCAAGAGAAAAGCATACAGTCATCTAT >EAS114_30:3:14:697:541 TTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAA >EAS114_30:3:161:366:544 CTTCTGTAATTGAAAAATTCATTTAAGAAATTACA >EAS114_30:3:181:582:435 CAAGTCTTTCCTGACAAGCAAATGCTAAGATAATT >EAS114_30:3:181:582:435 GAAATCCCATCAGAATAACAATGGGCTTCTCAGCA >EAS114_30:3:187:294:947 ACAGGGGGCTGCGCGGTTTCCCATCATGAAGCACT >EAS114_30:3:187:294:947 AGAGACTATTGCCAGATGAACCACACATTAATACT >EAS114_30:3:215:840:760 AAGTATTGGTAAAGATGTGGGGAAAAAAGTAAACT >EAS114_30:3:215:840:760 CTGATGATGGTTACACTAAAAGCCCATACTTTCCT >EAS114_30:3:24:195:604 TCACAGTTTCTGCCCCCAGCATGGTTGTACTGTGC >EAS114_30:3:24:195:604 TGTCCTATGTACTTATCATGACTCTATCCCAAATT >EAS114_30:3:302:288:657 AGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAGG >EAS114_30:3:302:288:657 CCAGATGAACCACACATTAATACTATGTTTCTTAT >EAS114_30:3:35:361:546 TGCACTAATGCGCTCCACGCCCAAGCCCTTCTCAC >EAS114_30:3:35:361:546 TTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACG >EAS114_30:3:39:348:594 AAGCATCATAAATGAAGGGGAAATAAAGTCAAGTC >EAS114_30:3:39:348:594 CTAAAATCAGCAAGAGAAAAGCATACAGTCATCTA >EAS114_30:4:183:852:253 ACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGT >EAS114_30:4:183:852:253 CCATTTCTTTTGGCATTTGCCTTCAGACCCTACAC >EAS114_30:4:317:378:535 AGCTTGGGCTGTAATGATGCCCCTTGGCCATCACC >EAS114_30:4:317:378:535 GCTGTCCTATGTACTTATCATGACTCTATCCCAAA >EAS114_30:4:327:795:103 AACCTTGAGAACCCCAGGGAATTTGTCAATGTCAG >EAS114_30:4:327:795:103 ACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGC >EAS114_30:4:328:537:640 AAGTATGAGATTATGTAAAGTAACTGAACCTATGA >EAS114_30:4:328:537:640 GGAAGATACATTGCAAGACAGACTTCATCAAGATA >EAS114_30:5:327:991:508 ACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCA >EAS114_30:5:327:991:508 TCTGGATTCTGGGAAATTCTTCATCCTGGACCCTG >EAS114_30:5:32:461:154 ACAGGTTTTATAAAACAATTAATTGAGACTACAGA >EAS114_30:5:32:461:154 TTACAAGAAACTCATTAATAAAGACATGAGTTCAG >EAS114_30:6:137:741:866 ACACTAAAAGCCCATACTTTACTGCTACTCAATAT >EAS114_30:6:137:741:866 GATGAGGGGAAAAAAGTAAACTCTCAAATATTGCT >EAS114_30:6:157:42:763 TCTGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCG >EAS114_30:6:157:42:763 TTTCTTATCTGCACATTACTACCCTGCAATTATTA >EAS114_30:6:163:312:891 CCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTGC >EAS114_30:6:163:312:891 TTCCCCAGATACCGTCCCTGTCTTACTTCCAGCTC >EAS114_30:6:214:565:337 AAATGAAAGAGGCTCAAAGAATGCCAGGAAGATAC >EAS114_30:6:214:565:337 CAGAATAACAATGGGCTTCTCAGCAGAAACCTTAC >EAS114_30:6:220:809:850 GGGGGGAAAAAGATGTGCTACACAAAAAGATTCCA >EAS114_30:6:220:809:850 TTCATAAAACAAATACTACTAGACCTAAGAGGGAT >EAS114_30:6:238:803:383 ACAATTAATTGAGACTACAGAGCAACTAGGTAAAA >EAS114_30:6:238:803:383 ACTCATTAATAAAGACATGAGTTCAGGTAAAGGGG >EAS114_30:6:243:209:110 AAAACATGAACTAACTATATGCTGTTTACAAGAAA >EAS114_30:6:243:209:110 CACAGGTTTTATAAAACAATTAATTGAGACTACAG >EAS114_30:6:277:397:932 TTTCTTTTCACTTTTTTTTTTTTTTTTTTTTACTT >EAS114_30:6:290:146:36 CTTTCCCATCCCCCGGTCCCTGCCCCATCTCTTGT >EAS114_30:6:290:146:36 TTATCATGACTCTATCCCAAATTCCCAATTACGTC >EAS114_30:6:326:309:149 CAACCTTGAGAACCCCAGGGAATTTGTCAATGTCA >EAS114_30:6:326:309:149 CTCCCTGTCACCCAATGGACCTGTGATATCTGGAT >EAS114_30:6:41:461:436 TAAAGTAACTGAACCTATGAGTCACAGGTATTCCT >EAS114_30:6:41:461:436 TAGTCATCAGACTATCTAAAGTCAACATGAAGGAA >EAS114_30:6:49:656:507 AAGGAAATCCCATCAGAATAACAATGGGCTTCTCA >EAS114_30:6:49:656:507 TCCTGACAAGCAAATGCTAAGATAATTCATCATCA >EAS114_30:6:4:665:771 GAATAAAAAGGGATTAAATTCCCCCACTTAAGAGA >EAS114_30:6:4:665:771 GTGCTTTATCTGATATCAATGCCGATAAACTGCCT >EAS114_30:6:62:386:959 AAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGGC >EAS114_30:6:62:386:959 AATGAACAACAGGAAGAAAAGGTCTTTCAAAAGGT >EAS114_30:7:269:944:220 ATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAA >EAS114_30:7:269:944:220 TGGGCAATACATGAGATTATTAGGAAATGCTTTAC >EAS114_30:7:283:799:560 ACATAGACCCCCTTGCAACAACCTTGAGAACCCCA >EAS114_30:7:283:799:560 GGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGAC >EAS114_30:7:310:155:312 CAGCAAGAGAAAAGCATACAGTCATCTATAAAGGA >EAS114_30:7:310:155:312 CATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCT >EAS114_30:7:319:11:255 TACCCAGATTCATAAAACAAATACTACTAGACCTA >EAS114_30:7:319:11:255 TCTATAAAAAAATTAAAATTTAACAAAAGTAAATA >EAS114_30:7:59:871:351 GTAAAAAATTAACATTACAACAGGAACAAAACCTC >EAS114_30:7:59:871:351 TAAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAG >EAS114_30:7:71:311:202 TATGAGATTATGTAAAGTAACTGAACCTATGAGTC >EAS114_30:7:71:311:202 TCAAGATATGTAGTCATCAGACTATCTAAAGTCAA >EAS114_32:1:199:760:42 ACCCAATTAATATTTTTCTTAGCAAAACAGTCTAG >EAS114_32:1:199:760:42 CTCTCTAATTTTTGCTGCTTCCATGTCTTACTCTG >EAS114_32:1:208:971:600 AAAAAAACCTGTCAAACACGAATGTTATGCCCTGC >EAS114_32:1:208:971:600 AGATATGTAGTCATCAGACTATCTAAAGTCAACAT >EAS114_32:2:163:618:570 AGGCTGCAACTGTGAGCCATCACAATGAACAACAG >EAS114_32:2:163:618:570 GGAAAGCTGTCAACGCTTCTAGCCATTTCTTTTGG >EAS114_32:2:197:170:559 CTCATTCACTCCAGCTCCCTGTCACCCAATGGACC >EAS114_32:2:197:170:559 TTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAACA >EAS114_32:2:247:900:123 AAAACATGAACTAACTATATGCTGTTTACAAGAAA >EAS114_32:2:247:900:123 AATTCAGCAAGAAGATATAACCATCCTACTAAATA >EAS114_32:2:283:577:398 ACAATGGGCTTCTCAGCGGAAACCTTACAAGCCAG >EAS114_32:2:283:577:398 CTAGAGATTTAGACATCTAAATGAAAGAGGCTCAA >EAS114_32:2:306:119:56 CTTCTCACAGTTTCTGCCCCCAGCATGGTTGTACT >EAS114_32:2:306:119:56 TCCATGTACACACGCTGTCCTATGTACTTATCATG >EAS114_32:3:236:475:254 AGATAAAGCACACTTTAAATCAACAACAGTAAAAT >EAS114_32:3:236:475:254 TTCCCCCACTTAAGAGATATAGATTGGCAGAACAG >EAS114_32:3:307:113:346 AATTCAGCAAGAAGATATAACCATCCTACTAAATA >EAS114_32:3:307:113:346 ATGCTGTTTACAAGAAACTCATTAATAAAGACATG >EAS114_32:4:156:21:69 AAAAATGAACAGAGCTTTCAAGAAGTATGAGATTA >EAS114_32:4:156:21:69 TTGCAAGACAGACTTCATCAAGATATGTAGTCATC >EAS114_32:4:20:41:138 CATTTCTTTTGGCATTTGCCTTCAGACCCTACACG >EAS114_32:4:20:41:138 GTCTTTCAAAAGGTGATGTGTGTTCTCATCAACCT >EAS114_32:4:228:587:504 GCACATTACGACCCGGCAAGGTGTATAATTGTGTC >EAS114_32:4:228:587:504 GTGCACTAATGCGCTCCACGCCCAAGCCCTTCTCA >EAS114_32:4:246:647:765 GATCAATTCAGCAAGAAGATATAACCATCCTACTA >EAS114_32:4:246:647:765 TATGCTGTTTACAAGAAACTCATTAATAAAGACAT >EAS114_32:4:42:923:169 ACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAA >EAS114_32:4:42:923:169 TTCCTATGTACTTATCATGAATCTATCCCAAATTC >EAS114_32:4:5:396:292 ATACATATGCACCTAACACAAGACTACCCAGATTC >EAS114_32:4:5:396:292 TAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGA >EAS114_32:4:7:282:424 CAAAAACAAAAACTATGCTAAGTATTGTTAAAGAT >EAS114_32:4:7:282:424 TAATTGGTACAATGTACAATATTCTGATGATGGTT >EAS114_32:5:109:199:592 ACGAATATTATGCCCTGCTAAACTAAGCATCATAA >EAS114_32:5:109:199:592 AGTCATCAGACTATCTAAAGTCAACATGAAGGAAA >EAS114_32:5:182:313:319 AATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGT >EAS114_32:5:182:313:319 GATGAACCACACATTAATACTATGTTTCTTATCTG >EAS114_32:5:267:170:250 CATAAAACAAATACTACTAGACCTAAGAGGGATGA >EAS114_32:5:267:170:250 CATAGCTAAAACTAAAAAAGCAAAAACAAAAACTA >EAS114_32:5:78:583:499 TTTACGCTATTCAGTACTAAATATAGAAATTGAAA >EAS114_32:6:122:342:296 AAAGCTTGGGCTGTAATGATGCCCCTTGGCCATCA >EAS114_32:6:122:342:296 TCCTATGTACTTATCATGACTCTATCCCAAATTCC >EAS114_32:6:178:342:866 AACAAATCTGCGCTTGTACTTCTAAATCTATAAAA >EAS114_32:6:178:342:866 ATACATATGCACCTAACACAAGACTACCCAGATTC >EAS114_32:6:179:735:569 ATGTTAAAATGTCTATTTTTGTCTTGACACCCAAC >EAS114_32:6:179:735:569 CATCACCCGGTCCCTGCCCCATCTCTTGTAATCTC >EAS114_32:6:199:818:124 AACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT >EAS114_32:6:199:818:124 ACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTG >EAS114_32:6:78:909:394 ATTGCTTGGTGTCTGACAGGCTGCAACTGTGAGCC >EAS114_32:6:78:909:394 TACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGA >EAS114_32:6:88:162:587 GGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGAC >EAS114_32:6:88:162:587 TTCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCT >EAS114_32:7:174:597:66 TCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCT >EAS114_32:7:174:597:66 TCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAAT >EAS114_32:7:201:959:19 CTCTACATGGCTGATTATTAAAACAATGTTCCCCA >EAS114_32:7:201:959:19 TATCTGGATTCTGGGAAATTCTTCATCCTGGACCC >EAS114_32:7:256:407:470 AACGCTTCTAGCCATTTCTTTTGGCATTTGCCTTC >EAS114_32:7:256:407:470 CAGCATGGTTGTACTGGGCAATACATGAGATTATT >EAS114_39:1:12:884:219 GAGCCATCACAATGAACAACAGGAAGAAAAGGTCT >EAS114_39:1:12:884:219 GCTTTCAACGCTTCTAGCCATTTCTTTTGGCATTT >EAS114_39:1:28:350:895 ATATAGTTGAAAGCTCTAACAATAGACTAAACCAA >EAS114_39:1:28:350:895 TATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAA >EAS114_39:1:43:1120:878 ACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGT >EAS114_39:1:43:1120:878 TAATTGTGTCCATGTACACACGCTGTCCTATGTAC >EAS114_39:1:70:147:84 ATAGACCCCCTTGCAACAACCTTGAGAACCCCAGG >EAS114_39:1:70:147:84 CCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGA >EAS114_39:1:71:636:533 GCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGC >EAS114_39:1:71:636:533 GTGGAAGACATAATCCCACGCTTCCTATGGAAAGG >EAS114_39:1:73:302:1574 AAGGTTGTTGGGAGATTTTTAATGATTCCTCAATG >EAS114_39:1:73:302:1574 CCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGCT >EAS114_39:1:98:641:1040 CAGAACAGATTTAAAAACATGAACTAACTATATGC >EAS114_39:1:98:641:1040 TAAAACAAAGGAGGTCATCATACAATGATAAAAAG >EAS114_39:2:18:967:582 AAGCCGTTCTATTTGTAATGAAAACTATATTTATG >EAS114_39:2:18:967:582 ACGCTGAAGAACTTTGATGCCCTCTTCTTCCAAAG >EAS114_39:2:38:670:564 CAGGTTTTATAAAACAATTAATTGAGACTACAGAG >EAS114_39:2:38:670:564 CTAACTATATGCTGTTTACAAGAAACTCATTAATA >EAS114_39:2:41:576:1016 CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC >EAS114_39:2:41:576:1016 TGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTT >EAS114_39:2:57:1064:925 TGACAAGCAAATGCTAAGATAATTCATCATCACTA >EAS114_39:2:5:1219:137 AAAACTAAAAAAGCAAAAACAAAAACTATGCTAAG >EAS114_39:2:5:1219:137 ACCTAAGAGGGATGAGAAATTACATAATTGGTACA >EAS114_39:3:11:1238:1728 AGAGATTTAGACATCTAAATGAAAGAGGCTCAAAG >EAS114_39:3:11:1238:1728 TCCCATCAGAATAACAATGGGCTTCTCAGCGGAAA >EAS114_39:3:55:464:146 AAAAAGATCAATTCAGCAAGAAGATATAACCATCC >EAS114_39:3:55:464:146 CTCAATATATCCATGTAACAAATCTGCGCTTGTAC >EAS114_39:3:6:1064:1805 TAAAATTTAACAAAAGTAAATAAAACACATAGCTA >EAS114_39:3:6:1064:1805 TTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTCTT >EAS114_39:3:88:84:1558 AGTAACTGAACCTATGAGTCACAGGTATTCCTGTG >EAS114_39:3:88:84:1558 ATCAGACTATCTAAAGTCAACATGAAGGAAAAAAA >EAS114_39:4:10:1312:1558 AACTAACTATATGCTGTTTACAAGAAACTCATTAA >EAS114_39:4:10:1312:1558 AGGTTTTATAAAACAATTAATTGAGACTACAGAGC >EAS114_39:4:30:432:228 ATCCTACTAAATACATATGCACCTAACACAAGACT >EAS114_39:4:30:432:228 GACATGAGTTCAGGGAAAGGGGTGGAAAAAGATGT >EAS114_39:4:30:570:902 AAAAACCTGTCAAACACGAATGTTATGCCCTGCTA >EAS114_39:4:30:570:902 ATACTCACCATCATAAATACGCACAAAAGTACAAA >EAS114_39:4:43:1047:1626 GATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGT >EAS114_39:4:43:1047:1626 GTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAA >EAS114_39:4:58:271:612 AGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTA >EAS114_39:4:58:271:612 ATGAAGGAAAAAAATTCTAAAATCAGCAAGAGCAA >EAS114_39:4:93:77:1338 GCTGCTTACAAGAAGCGCATTAATAAAGACATGAG >EAS114_39:4:93:77:1338 GTCATCATACAATGAAAAAAAGATCAATTCAGCAA >EAS114_39:5:17:1222:783 AAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCGT >EAS114_39:5:17:1222:783 TGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATT >EAS114_39:5:42:1223:1087 CAGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTT >EAS114_39:5:42:1223:1087 TTGTCTTGACACCCAACTAATATTTGTCTGAGCAA >EAS114_39:5:50:972:1286 AGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTT >EAS114_39:5:50:972:1286 TTGTGGTCTGACAGGCTGCAACTGTGAGCCATCAC >EAS114_39:5:61:1000:1534 CTTGAAGACAAGTCTCTTATGAATTAACCCAGTCA >EAS114_39:5:61:1000:1534 GGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGA >EAS114_39:5:93:312:331 AACTCATTAATAAAGACATGAGTTCAGGTAAAGGG >EAS114_39:5:93:312:331 ATCCTACTAAATACATATGCACCTAACACAAGACT >EAS114_39:6:13:1034:1144 AAAGATGAAACGCGTAACTGCGCTCTCATTCACTC >EAS114_39:6:13:1034:1144 AATTGAAACAGCTGTGTTTAGTGCCTTTGTTCACA >EAS114_39:6:34:380:815 AAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGA >EAS114_39:6:34:380:815 ATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTT >EAS114_39:6:71:644:1792 AAAAGTACAAAACTCACAGGTTTTATAAAACAATT >EAS114_39:6:71:644:1792 CCTGCTAAACTAAGCATCATAAATGAAGGGGAAAT >EAS114_39:6:76:282:1668 AACAAAAACTATGCTAAGTATTGGTAAAGATGTGG >EAS114_39:6:76:282:1668 TACAATGTACAATATTCTGATGATGGTTACACTAA >EAS114_39:6:7:492:1088 ACAGGTTTTATAAAACAATTAATTGAGACTACAGA >EAS114_39:6:7:492:1088 TGAACTAACTATATGCTGTTTACAAGAAACTCATT >EAS114_39:6:85:1224:625 GAACTCCCCTGGAGGTCTGATGGCGTTTCTCCCTC >EAS114_39:6:85:1224:625 GCTGCATCCCTGTCTTCCTCTGTCTTGATTTCCTT >EAS114_39:6:94:1273:1462 AAGATGTTCTACGCAAACAGAAACCAAATGAGAGA >EAS114_39:6:94:1273:1462 CCTAACACAAGACTACCCAGATTCATAAAACAAAT >EAS114_39:7:100:708:1984 AGATGAACCACACATTAATACTATGTTTCTTATCT >EAS114_39:7:100:708:1984 TACCACAGGGGGCTGCGCGGTTTCCCATCATGAAG >EAS114_39:7:23:1126:1886 ACACTAAAAGCCCATACTTTACTGCTACTCAATAT >EAS114_39:7:23:1126:1886 GGAGGTCATCATACAATGATAAAAAGATCAATTCA >EAS114_39:7:32:562:1695 GATGATGGTTACACTAAAAGCCCATACTTTACTGC >EAS114_39:7:32:562:1695 TAAAACAAAGGAGGTCATCATACAATGATAAAAAG >EAS114_39:7:57:1114:2032 TAACTATATGCTGTTTACAAGAAACTCATTAATAA >EAS114_39:7:57:1114:2032 TATTACAATGATAAAAAGATCAATTCAGCAAGAAG >EAS114_39:7:90:406:631 CATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTG >EAS114_39:7:90:406:631 TGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTT >EAS114_45:1:100:979:1863 ATTACAAAACTCACAGGTTTTATAAAACAATTAAT >EAS114_45:1:100:979:1863 TTATGCCCTGCTAAACTAAGCATCATAAATGAAGG >EAS114_45:1:12:1296:358 CTTGAAAGCTTGGTCTGTAATGATGCCCCTTGGCC >EAS114_45:1:12:1296:358 GTCCATGTACACACGCTGTCCTATGTACTTATCAT >EAS114_45:1:2:1422:1820 CACCTAACACAAGACTACCCAGATTCATAAAACAA >EAS114_45:1:2:1422:1820 TACGCAAACAGAAACCAAATGAGAGAAGGAGTAGC >EAS114_45:1:30:1882:1210 ATCATCACTAAACCAGTCCTATAAGAAATGCTCAA >EAS114_45:1:30:1882:1210 GCAGAAACCTTACAAGCCAGAAGAGATTGGATCTA >EAS114_45:1:33:1407:94 TAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAG >EAS114_45:1:33:1407:94 TTACTTGTTGTTGGTTTTCTGTTTCTTTGTTTGAT >EAS114_45:1:77:1000:1780 AGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAG >EAS114_45:1:77:1000:1780 TGAATTAACCCAGTCAGACAAAAATAAAGAAAAAA >EAS114_45:1:84:275:1572 AGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCC >EAS114_45:1:84:275:1572 TTATGCTATTCAGTTCTAAATATAGAAATTGAAAC >EAS114_45:1:95:1530:28 AAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA >EAS114_45:1:95:1530:28 AATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAA >EAS114_45:1:9:1289:215 AGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCC >EAS114_45:1:9:1289:215 TATGCTATTCAGTTCTAAATATAGAAATTGAAACA >EAS114_45:2:13:1507:1146 AAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGA >EAS114_45:2:13:1507:1146 CAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCT >EAS114_45:2:15:1497:1530 AATTACGTCCTATCTTCTTCTTAGGGAAGAACAGC >EAS114_45:2:15:1497:1530 TAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCC >EAS114_45:2:1:1140:1206 TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGT >EAS114_45:2:1:1140:1206 TTTATTACCAGAGGGATGGAGGGAAGAGGGACGCT >EAS114_45:2:20:413:1334 CCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTT >EAS114_45:2:20:413:1334 TTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAG >EAS114_45:2:23:1754:796 CTTCTAAATCTATAAAAAAATTAAAATTTAACAAA >EAS114_45:2:23:1754:796 CTTTGGAAAACAATTTGGTAATTTCGTTTTTTTTT >EAS114_45:2:33:1445:1357 TATGAATTAACCCAGTCAGACAAAAATAAAGAAAA >EAS114_45:2:33:1445:1357 TTAGTCTTGCTAGAGATTTAGACATCTAAATGAAA >EAS114_45:2:41:199:388 AGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGG >EAS114_45:2:41:199:388 TCTAAAGTCAACATGAAGGAAAAAAATTCTAAAAT >EAS114_45:2:49:163:904 GCTCTCATTCACTCCAGCTCCCTGTCACCCAATGG >EAS114_45:2:49:163:904 TCTTTCAAAAGGTGATGTGTGTTCTCATCAACCTC >EAS114_45:2:54:1886:719 CTGTTTACAAGAAACTCATTAATAAAGACATGAGT >EAS114_45:2:54:1886:719 TTCAGCAAGAAGATATAACCATCCTACTAAATACA >EAS114_45:2:59:396:359 GGGTATAATACCTCTACATGGCTGATTATGAAAAC >EAS114_45:2:59:396:359 TCACCCAATGGACCTGTGATATCTGGATTCTGGGA >EAS114_45:2:76:1765:700 AAAAAGGGATTAAATTCCCCCACTTAAGAGATATA >EAS114_45:2:76:1765:700 GTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGT >EAS114_45:2:79:554:354 AAATAAAACAAAGGAGGTCATCATACAATGATAAA >EAS114_45:2:79:554:354 CAATGTACAATATTCTGATGATGGTTACACTAAAA >EAS114_45:3:26:1867:162 ATATAACCATCCTACTAAATACATATGCACCTAAC >EAS114_45:3:26:1867:162 ATATATCCATGTAACAAATCTGCGCTTGTACTTCT >EAS114_45:3:27:1881:486 AAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTC >EAS114_45:3:27:1881:486 CCAAAGATGAAACGCGTAACTGCGCTCTCATTCAC >EAS114_45:3:2:1200:1076 CATTTGCCTTCAGACCCTACACGAATGCGTCTCTA >EAS114_45:3:2:1200:1076 GATGTGTGTTCTCATCAACCTCATACACACACATG >EAS114_45:3:32:1379:738 TTAAGAAATTACAAAATATAGTTGAAAGCTCTAAC >EAS114_45:3:35:896:1588 CTAGACCTAAGAGGGATGAGAAATTACCTAATTGG >EAS114_45:3:35:896:1588 GAGTAGCTATACTTATATCAGATAAAGCACACTTT >EAS114_45:3:39:208:644 ATTGTAAAAGTCAAAATTAAAGTTCAATACTCACC >EAS114_45:3:39:208:644 TTTGAATAAAAAGGGATTAAATTCCCCCACTTAAG >EAS114_45:3:3:1377:1663 CTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA >EAS114_45:3:3:1377:1663 GGTGATGTGTGTTCTCATCAACCTCATACACACAC >EAS114_45:3:3:864:1888 AATGTTATGCCCTGCTAAACTAAGCATCATAAATG >EAS114_45:3:3:864:1888 CAACATGAAGGAAAAAAATTCTAAAATCAGCAAGA >EAS114_45:3:41:653:1568 AACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT >EAS114_45:3:41:653:1568 GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA >EAS114_45:3:44:1578:1674 CCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCT >EAS114_45:3:44:1578:1674 GCTGCAACTGTGAGCCATCACAATGAACAACAGGA >EAS114_45:3:75:217:337 GACAGGCTGCAACTGTGAGCCATCACAATGAACAA >EAS114_45:3:75:217:337 GAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCT >EAS114_45:3:90:1403:1635 TGTCTTGACACCCAACTAATATTTGTCTGAGCAAA >EAS114_45:3:90:1403:1635 TTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTCT >EAS114_45:4:48:310:473 TGAATTAACCCAGTCAGACAAAAATAAAGAAAAAA >EAS114_45:4:48:310:473 TTTAGTCTTGCTAGAGATTTAGACATCTAAATGAA >EAS114_45:4:73:1208:495 AGATGAAACGCGTAACTGCGCTCTCATTCACTCCA >EAS114_45:4:73:1208:495 TAAATATAGAAATTGAAACAGCTGTGTTTAGTGCC >EAS114_45:4:7:1347:375 CTAAAAGCCCATACTTTACTGCTACTCAATATATC >EAS114_45:4:7:1347:375 GGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGA >EAS114_45:4:87:323:895 ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT >EAS114_45:4:87:323:895 GGTATAATACCTCTACATGGCTGATTATGAAAACA >EAS114_45:4:88:55:1187 GTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAG >EAS114_45:4:88:55:1187 GTCATCAGACTATCTAAAGTCAACATGAAGGAAAA >EAS114_45:5:56:1757:1319 CATTAATAAAGACATGAGTTCAGGTAAAGGGGTGG >EAS114_45:5:56:1757:1319 TTTATAAAACAATTAATTGAGACTACAGAGCAACT >EAS114_45:5:62:841:1994 ATATCCATGTAACAAATCTGCGCTTGTACTTCTAA >EAS114_45:5:62:841:1994 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT >EAS114_45:5:66:959:1311 CAGAGCTGCTGGCAAGCTAGAGGCCCATCTGGAGC >EAS114_45:5:66:959:1311 GGGAAGGAGCATTTTGTCAGTTACCAAATGTGTTT >EAS114_45:5:82:843:1838 CTAGGTAAAAAATTAACATTACAACAGGAACAAAA >EAS114_45:5:82:843:1838 TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA >EAS114_45:5:85:401:1190 TACACACACATGGTTTAGGGGTATAATACCTCTAC >EAS114_45:5:85:401:1190 TCACTCCAGCTCCCTGTCACCCAATGGACCTGTGA >EAS114_45:5:91:89:666 GAAAACCTCTTTAGTCTTGCTAGAGATTTAGACAT >EAS114_45:6:14:1211:1332 AGGAAGATACATTGCAAGACAGACTTCATCAAGAT >EAS114_45:6:14:1211:1332 TTTCAAGAAGTATGAGATTATGTAAAGTAACTGAA >EAS114_45:6:37:156:134 AGAGAAAAGCATACAGTCATCTATAAAGGAAATCC >EAS114_45:6:37:156:134 GGAAAAACTATTTGAGGAAGTAATTGGGGAAAACC >EAS114_45:6:39:956:676 TAAAACAAATACTACTAGACCTAAGAGGGATGAGA >EAS114_45:6:39:956:676 TGAGAGAAGGAGTAGCTATACTTATATCAGATAAA >EAS114_45:6:44:77:1255 CTCATTAATAAAGACATGAGTTCAGGTAAAGGGGT >EAS114_45:6:44:77:1255 TAAAAAGATCAATTCAGCAAGAAGATATAACCATC >EAS114_45:6:45:1769:1130 ACCCAATGGACCTGTGATATCTGGATTCTGGGAAA >EAS114_45:6:45:1769:1130 TGTTCTCATCAACCTCATACACACACATGGTTTAG >EAS114_45:6:47:1791:444 AAGAGGGATGAGAAATTACCTAATTGGTACAATGT >EAS114_45:6:47:1791:444 TACTTATATCAGATAAAGCACACTTTAAATCAACA >EAS114_45:6:59:1548:1096 CCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTG >EAS114_45:6:59:1548:1096 GTCCTATGTACTTATCATGACTCTATCCCAAATTC >EAS114_45:6:5:730:1436 GAAGAACTTTGATGCCCTCTTCTTCCAAAGATGAA >EAS114_45:6:5:730:1436 TATTCAGTTCTAAATATAGAAATTGAAACAGCTGT >EAS114_45:6:86:693:234 AAGTAACTGAACCTATGAGTCACAGGTATTCCTGA >EAS114_45:6:86:693:234 GTAGTCATCAGACTATCTAAAGTCAACATGAAGGA >EAS114_45:6:86:859:1779 TTTTTTTCATTTCTCTTTTTTTTTTTTTTTTTTTT >EAS114_45:6:90:561:850 ACAGGAACAAAACCTCATATATCAATATTAACTTT >EAS114_45:6:90:561:850 TACGCAAACAGAAACCAAATGAGAGAAGGAGTAGC >EAS114_45:6:93:1475:542 TGAAAGCTTGGGCTGTAATGATGCCCCTTGGCCAT >EAS114_45:6:93:1475:542 TTATCATGACTCTATCCCAAATTCCCAATTACGTC >EAS114_45:7:14:1256:204 AAATGTCTATTTTTGTCTTGACACCCAACTAATAT >EAS114_45:7:14:1256:204 TCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTC >EAS114_45:7:14:978:1296 ATACAATGATAAAAAGATCAATTCAGCAAGAAGAT >EAS114_45:7:14:978:1296 CAATATTCTGATGATGGTTACACTAAAAGCCCATA >EAS114_45:7:24:1374:211 AGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTG >EAS114_45:7:24:1374:211 TGCAATTAATATAATTGTGTCCATGTACACACGCT >EAS114_45:7:2:168:1878 AAAAAACCTGGCAAACACGAATGTTATGACATGTN >EAS114_45:7:2:168:1878 TAAATACACACAAAAGTAGAAAACGCACCAGTTTT >EAS114_45:7:33:1566:588 ACAGCTTAGGCATCAATTTGGTGTTCTGTGTAAAG >EAS114_45:7:33:1566:588 TACTGTCATAACTATGAAGAGCCTATTGCCAGATG >EAS114_45:7:35:538:1882 TATGCACCTAACACAAGACTACCCAGATTCATAAA >EAS114_45:7:35:538:1882 TCTATAACAAAATTAAAATTTAACAAAAGTAAATA >EAS114_45:7:37:763:1437 AAAGATGTTCTACGCAAACAGAAACCAAATGAGAG >EAS114_45:7:37:763:1437 TAAAACAAATACTACTAGACCTAAGAGGGATGAGA >EAS114_45:7:45:1339:1807 GACATCTAAATGAAAGAGGCTCAAAGAATGCCAGG >EAS114_45:7:69:1130:832 ATAGTTGAAAGCTCTAACAATAGACTAAACCAAGC >EAS114_45:7:69:1130:832 TCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAA >EAS114_45:7:6:758:988 AAACAAAGGAGGTCATCATACAATGATAAAAAGAT >EAS114_45:7:6:758:988 ATTCTGATGATGGTTACACTAAAAGCCCATACTTT >EAS114_45:7:88:451:1773 ATAAATACACACAAAAGTACAAAACTCACAGGTTT >EAS114_45:7:88:451:1773 ATTGGCAGAACAGATTTAAAAACATGAACTAACTA >EAS114_45:7:97:1584:777 CCAGATGAACCACACATTAATACTATGTTTCTTAT >EAS114_45:7:97:1584:777 GTCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCC >EAS114_45:7:9:512:826 AACTTCCACGTCTCATCTAGGGGAACAGGGAGGTG >EAS114_45:7:9:512:826 ACCACACATTAATACTATGTTTCTTATCTGCACAT >EAS139_11:1:35:631:594 ATCATGACTCTATCCCAAATTCCCAATTACGTCCT >EAS139_11:1:35:631:594 ATGATGCCCCTTGGCCATCACCCGGTCCCTGCCCC >EAS139_11:1:59:742:549 ACAAGCAAATGCTAAGATAATTCATCATCACTAAA >EAS139_11:1:59:742:549 TTAACATTACAACAGGAACAAAACCTCATATATCA >EAS139_11:1:81:1019:558 ACAAAACTCACAGGTTTTATAAAACAATTAATTGA >EAS139_11:1:81:1019:558 TGAACTAACTATATGCTGTTTACAAGAAACTCATT >EAS139_11:1:84:92:1246 GAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG >EAS139_11:1:84:92:1246 GTTACACTAAAAGCCCATACTTTACTGCTACTCAA >EAS139_11:2:31:628:1820 AACCAGTCCTATAAGAAATGCTCAAAAGAATTGTA >EAS139_11:2:31:628:1820 CAGGAACAAAACCTCATATATCAATATTAACTTTG >EAS139_11:2:42:333:516 AGACAAGTCTCTTATGAATTAACCCAGTCAGACAA >EAS139_11:2:42:333:516 TCTTTAGTCTTGCTAGAGATTTAGACATCTAAATG >EAS139_11:2:55:296:1457 CACTTTAAATCAACAACAGTAAAATAAAACAAAGG >EAS139_11:2:55:296:1457 CCCACTTAAGAGATATAGATTGGCAGAACAGATTT >EAS139_11:2:63:816:921 AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT >EAS139_11:2:63:816:921 TGAAGACAAGTCTCTTATGAATTAACCCAGTCAGA >EAS139_11:2:6:251:1557 AAAACAATGTTCCCCAGATACCATCCCTGTCTTAC >EAS139_11:2:6:251:1557 CCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTT >EAS139_11:2:71:83:58 AAAGAAAAAAGAATTTTAAAAATGAACAGAGCTTT >EAS139_11:2:71:83:58 CCAGGAAGATACATTGCAAGACAGACTTCATCAAG >EAS139_11:3:34:970:1374 ATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGG >EAS139_11:3:34:970:1374 CTGGACCCTGAGAGATTCTGCAGCCCAGATCCAGA >EAS139_11:3:43:1229:1855 ATGTACAATATTCTGATGATGGTTACACTAAAAGC >EAS139_11:3:43:1229:1855 CAACAGTAAAATAAAACAAAGGAGGTCATCATACA >EAS139_11:3:65:556:1505 CAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGG >EAS139_11:3:65:556:1505 TGCCTTCAGACCCTACACGAATGCGTCTCTACCAC >EAS139_11:3:81:12:1231 AAAAAGCAAAAACAAAAACTATGCTAAGTATTGGT >EAS139_11:3:81:12:1231 TTACCTAATTGGTACAATGTACAATATTCTGATGA >EAS139_11:4:26:137:1382 AATGTTATGCCCTGCTAAACTAAGCATCATAAATG >EAS139_11:4:26:137:1382 AGACTATCTAAAGTCAACATGAAGGAAAAAAATTC >EAS139_11:4:36:1184:994 GCCAGAAGAGATTGGATCTAATTTTTGGACTTCTT >EAS139_11:4:36:1184:994 TACATTGCAAGACAGACTTCATCAAGATATGTAGT >EAS139_11:4:36:1231:1381 AAGAGATATAGATTGGCAGAACAGATTTAAAAACA >EAS139_11:4:36:1231:1381 TAAAAGTCAAAATTAAAGTTCAATACTCACCATCA >EAS139_11:4:38:557:1441 GATAAAAATAAAAAAGCAAAAACAAAAACTATGCT >EAS139_11:4:38:557:1441 TAAGAGGGATGAGAAATTACCTAATTGGTACAATG >EAS139_11:4:50:30:15 AGATTATGTAAAGTAACTTAACCTATGAGTCCAAG >EAS139_11:4:50:30:15 TACATTGCAAGACAGTCGTCAGCAAGATATGTAGT >EAS139_11:4:63:527:1923 GCTTTACTGTCATAACCATGAAGAGACTATTGCCA >EAS139_11:4:63:527:1923 TACACGAATGCGTCTCTACCACAGGGGGCTGCGCG >EAS139_11:5:32:686:735 AAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGG >EAS139_11:5:32:686:735 CAGAAGAAAGAGGTTCANANNNTGANGACAAGTCT >EAS139_11:5:41:314:1173 AAGAAAAAAAAACCTGTCAAACACGAATGTTATGC >EAS139_11:5:41:314:1173 AATTAAAGTTCAATACTCACCATCATAAATACACA >EAS139_11:5:52:1278:1478 GCTTGTACTTCTAAATCTATAACAAAATTAAAATT >EAS139_11:5:52:1278:1478 GTTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTT >EAS139_11:5:61:38:1182 AGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTC >EAS139_11:5:61:38:1182 GTTTGATTTGGTGGAAGACATAATCCCACGCTTCC >EAS139_11:5:64:199:1288 GTAAAATAAAACAAAGGAGGTCATCATACAATGAT >EAS139_11:5:64:199:1288 TACAATGTACAATATTCTGATGATGGTTACACTAA >EAS139_11:5:78:775:555 AATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAG >EAS139_11:5:78:775:555 TTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAA >EAS139_11:6:11:285:1567 ACATGGCTGATTATGAAAACAATGTTCCCCAGATA >EAS139_11:6:11:285:1567 CCCTGAGAGATTCTGCAGCCCAGATCCAGATTGCT >EAS139_11:6:11:360:1577 GAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCT >EAS139_11:6:11:360:1577 TTTGGCATTTGCCTTCAGACCCTACACGAATGCGT >EAS139_11:6:13:682:680 AGAATAACAATGGGCTTCTCAGCGGAAACCTTACA >EAS139_11:6:13:682:680 ATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAA >EAS139_11:6:17:1179:393 CTAATTGGTACAATGTACAATATTCTGATGATGGT >EAS139_11:6:17:1179:393 TGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTA >EAS139_11:6:19:306:982 ATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCA >EAS139_11:6:19:306:982 GACAGACTTCATCAAGATATGTAGTCATCAGACTA >EAS139_11:6:75:946:1035 AACCCCCTTGCAACAACCTTGAGAACCCCAGGGAA >EAS139_11:6:75:946:1035 AATGGACCTGTGATATCTGGATTCTGGGAAATTCT >EAS139_11:6:82:164:1924 GAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTT >EAS139_11:6:82:164:1924 GCCCAGCACCAGATTGCTTGTGGTCTGACAGGCTG >EAS139_11:6:89:1151:1878 CCATCACAATGAACAACAGGAAGAAAAGGTCTTTC >EAS139_11:6:89:1151:1878 CTTTCAACGATTCTAGCCATTTCTTTTGGCATTTG >EAS139_11:7:24:1345:1627 AGATTGGCAGAACAGATTTAAAAACATGAACTAAC >EAS139_11:7:24:1345:1627 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN >EAS139_11:7:42:1091:1726 CAGGGAAGGAGCATTTTGTCAGTTACCAAATGTGT >EAS139_11:7:42:1091:1726 TCTGGGAAATTCTTCATCCTGGACCCTGAGAGATT >EAS139_11:7:46:695:738 CAAAGATGAAACGCGTAACTGCGCTCTCATTCACT >EAS139_11:7:46:695:738 TGAAACAGCTGAGTTTAGCGCCTGTGTTCACATAG >EAS139_11:7:50:1229:1313 ACATAGCTAAAACTAAAAAAGCAAAAACAAAAACT >EAS139_11:7:50:1229:1313 TTTTTTCTTTTTTTTTTTTTTTTTTTTGCATGCCA >EAS139_11:7:53:458:581 CTCAATTAATTGTTTTATAAAACCTGTGAGTTTTG >EAS139_11:7:53:458:581 TTATGCCCTGCTAAACTAAGCATCATAAATGAAGG >EAS139_11:7:60:163:1612 AGCAAGAGAAAAGCATACAGTCATCTATAAAGGAA >EAS139_11:7:60:163:1612 GGGAACTAAAGTCAAGTCTTTCCTGACAAGCAAAT >EAS139_11:7:74:213:877 AGATGTTCTACGCAAACAGAAACCAAATGAGAGAA >EAS139_11:7:74:213:877 TTAACATTACAACAGGAACAAAACCTCATATATCA >EAS139_11:7:92:367:1495 ACCACAGGGGGCTGCGCGGTTTCCCATCATGAAGC >EAS139_11:7:92:367:1495 CTGTCATAACTATGAAGAGACTATTGCCAGATGAA >EAS139_11:8:17:437:1378 ACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAA >EAS139_11:8:17:437:1378 ATCAATATTAACTTTGAATAAAAAGGGATTAAATT >EAS139_11:8:26:1221:222 AAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCT >EAS139_11:8:26:1221:222 CTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA >EAS139_11:8:38:842:395 GTAACTGCGCTCTCATTCACTCCAGCTCCCTGTCA >EAS139_11:8:76:205:587 GAATAACAATGGGCTTCTCAGCGGAAACCTTACGA >EAS139_11:8:76:205:587 TGCTAGAGATTTAGACATCTAAATGAAAGAGGCTC >EAS139_11:8:82:566:1096 CAAAAGGTGATGTGTGTTCTCATCAACCTCATACA >EAS139_11:8:82:566:1096 CTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA >EAS139_11:8:96:1314:1448 CCTATGAGTCACAGGTATTCCTGAGGAAAAATAAA >EAS139_11:8:96:1314:1448 GTAGTCATCAGACTATCTAAAGTCAACATGAAGGA >EAS139_19:1:14:420:712 TGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTCCC >EAS139_19:1:14:420:712 TGTTGGTTTTCTGTTTCTTTGTTTGATTTTTTTGAAGACA >EAS139_19:1:1:1598:843 TCAGCGGAAACCTTACAAGCCAGAAGAGATTGGATCTAAT >EAS139_19:1:1:1598:843 TGCCAGGAAGATACATTGCAAGACAGACTTCATCAAGATA >EAS139_19:1:36:481:1079 GTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAA >EAS139_19:1:36:481:1079 TCCCCCACTTAAGAGATATAGATTGGCAGAACAGATTTAA >EAS139_19:1:40:1596:1433 CCATCACAATGAACAACAGGAAGAAAAGGTCTTTCAAAAG >EAS139_19:1:40:1596:1433 GCTTTCAACGCTTCTAGCCATTTCTTTTGGCATTTGCCTT >EAS139_19:1:47:352:1492 AGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGCCCACTA >EAS139_19:1:47:352:1492 TTTGTTTTGTATGGTGGAAGACATAATCCCACGCTTCCTA >EAS139_19:1:53:463:1132 ATGATAAAAAGATCAATTCAGCAAGAAGATATAACCATCC >EAS139_19:1:53:463:1132 ATTTAAAAACATGAACTAACTATATGCTGTTTACANGAAA >EAS139_19:1:58:726:1746 AGATTGGCAGAACAGATTTAAAAACATGAACTAACTATAT >EAS139_19:1:58:726:1746 CAATTTAAATCAACAACAGTAAAATAAAACAAAGGAGGTC >EAS139_19:1:82:946:392 CAATATATCCATGTAACAAATCTGCGCTTGTACTTCAAAA >EAS139_19:1:82:946:392 GAAAACAATTTGGTAATTTCGTTTTTTTTTTTTTCTTTTC >EAS139_19:1:85:1521:58 AAATTAACATTACAACAGGAACAAAACCTCATATATCAAT >EAS139_19:1:85:1521:58 CTGACAAGCAAATGCTAAGATAATTCATCATCACTAAACC >EAS139_19:1:87:1222:878 TATAGGGCCTTTGTTCAAACCCCTTGCAACAACCTTGAGA >EAS139_19:1:87:1222:878 TCAGCGCGTCACTCCGCTCTCATTCACCCCAGCTCCCTGT >EAS139_19:1:99:1632:76 AAAGAAAAAAAACCCTGTCAAACACGAATGTTATGCCCTG >EAS139_19:1:99:1632:76 TTGTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATA >EAS139_19:2:12:1335:1372 GAAGAACAGATTTAAAAACATGAACTAACTATATGCTGTT >EAS139_19:2:12:1335:1372 TAAAGTTCAATACTCACCATCATAAATACACACAAAAGTA >EAS139_19:2:29:1822:1881 AGAAAAAAGAATTTTAAAAATGAACAGAGCTTTCAAGAAG >EAS139_19:2:29:1822:1881 ATGAAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCAA >EAS139_19:2:2:1217:398 CAATTAATTGAGACTACAGAGCAACTAGGTAAAAAATTAA >EAS139_19:2:2:1217:398 TAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGC >EAS139_19:2:33:1193:664 GCCCCATCTCTTGTAATCTCTCTCCTTTTTTCTGCATCCC >EAS139_19:2:33:1193:664 TATTTTTGTCTTGACACCCAACTAATATTTGTCTGAGCAA >EAS139_19:2:57:1672:1890 CCCCCCCCCCCCCCCCCAGCCACTGCGGCCCCCCCAGCCA >EAS139_19:2:57:1672:1890 TATTCAGTTCTAAATATAGAAATTGAAACAGCTGTGTTTA >EAS139_19:2:82:154:1333 TTAAAATTTAACAAAAGTAAATAAAACACACAGCTAAAAC >EAS139_19:2:82:154:1333 TTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTT >EAS139_19:3:10:349:1147 GCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAA >EAS139_19:3:24:1135:563 CTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCAATGGA >EAS139_19:3:24:1135:563 GCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAACC >EAS139_19:3:4:1502:1911 CTACACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTTT >EAS139_19:3:4:1502:1911 TACACACACATGGTTTAGGGGTATAATACCTCTACATGGC >EAS139_19:3:58:923:1915 GCAAACAGAAACCAAATGAGAGAAGGAGTAGCTATACTTA >EAS139_19:3:58:923:1915 TATCAATATTAACTTTGAATAAAAAGGGATTAAATTCCCC >EAS139_19:3:5:538:401 AAGGTGATGTGTGTTCTCATCAACCTCATACACACACATG >EAS139_19:3:5:538:401 TTTGCCTTCACACCCTACACGAATGCGTCTCTGCCACAGG >EAS139_19:3:66:718:481 AACAACAGTAAAATAAAACAAAGGAGGTCATCATACAATG >EAS139_19:3:66:718:481 AAGAGATATAGATTGGCAGAACAGATTTAAAAACATGAAC >EAS139_19:3:73:1158:535 AATAAAGATATGTAGTCATCAGACTATCTAAAGTCAACAT >EAS139_19:3:73:1158:535 CCTATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTG >EAS139_19:3:73:936:1509 CTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTTATTT >EAS139_19:3:73:936:1509 TTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCT >EAS139_19:3:75:732:442 CGGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC >EAS139_19:3:75:732:442 CTATCCCAAATTCCCAATTACGTCCTATCTTCTTCTTAGG >EAS139_19:3:87:133:930 CAGTCTCAGGGCGCCGTCCGTTTCCTCCCATCTGGCCTCG >EAS139_19:3:87:133:930 TTATCTGCACATTACTACCCTGCAATTAATATAATTGTGT >EAS139_19:3:88:1656:896 AGGGAAGAGGGATGCTGAAGAACTTTGATGCCCTCTTCTT >EAS139_19:3:88:1656:896 TGCAGCCCAGATCCAGATTGCTTGTGGTCTGACAGGCTGC >EAS139_19:4:13:1155:631 ACCCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTTGTG >EAS139_19:4:13:1155:631 AGGGGTATAATACCTCTACATGGCTGATTATGAAAACAAT >EAS139_19:4:18:1335:1514 ATTGGTACAATGTACAATATTCTGATGATGGTTACACTAA >EAS139_19:4:18:1335:1514 CTTTAAATCAACAACAGTAAAATAAAACAAAGGAGGTCAT >EAS139_19:4:1:156:196 AAAAGGGATTAAATTCCCCCACTTAAGAGATATAGATTGG >EAS139_19:4:1:156:196 ACTTATATCAGATAAAGCACACTTTAAATCAACAACAGTA >EAS139_19:4:26:1312:1400 ACTGAACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAA >EAS139_19:4:26:1312:1400 TATGTAGTCATCAGACTATCTAAAGTCAACATGAAGGAAA >EAS139_19:4:26:274:1078 AATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGAC >EAS139_19:4:26:274:1078 GTCATCTATAAAGGAAATCCCATCAGAATAACAATGGGCT >EAS139_19:4:68:1122:79 ATGGCTGATTATGAAAACAATGTTCCCCAGATACCATCCC >EAS139_19:4:68:1122:79 TGAGAGATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCT >EAS139_19:4:69:1593:819 ATTGAGACTACAGAGCAACTAGGTAAAAAATTAACATTAC >EAS139_19:4:69:1593:819 CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAA >EAS139_19:4:77:1780:693 GGAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGAT >EAS139_19:4:77:1780:693 TGAAGACAAGTCTCTTATGAATTAACCCAGTCAGACAAAA >EAS139_19:4:78:806:800 AAATTAAAGTTCAATACTCACCATCATAAATACACACAAA >EAS139_19:4:78:806:800 AACCTGTCAAACACGAATGTTATGCCCTGCTAAACTAAGC >EAS139_19:5:29:411:1208 AAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATACTCAC >EAS139_19:5:29:411:1208 CCCCCACTTAAGAGATATAGATTGGCAGAACAGATTTAAA >EAS139_19:5:40:758:116 GTCTCTACCACAGGGGGCTGCGCGGTTTCCCATCATGAAG >EAS139_19:5:40:758:116 GTGTGTTCTCATCAACCTCATACACACACATGGTTTAGGG >EAS139_19:5:4:939:2021 AAATACTACTAGACCTAAGAGGGATGAGAAATTACCTAAT >EAS139_19:5:4:939:2021 GGAGTAGCTATACTTATATCAGATAAAGCACACTTTAAAT >EAS139_19:5:57:366:844 AAATTCCCCCACTTAAGAGATATAGATTGGCAGAACAGAT >EAS139_19:5:57:366:844 TAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAAT >EAS139_19:5:61:1885:163 AGCAAGAAGATATAACCATCCTACTAAATACATATGCACC >EAS139_19:5:61:1885:163 ATACTTTACTGCTACTCAATATATCCATGTAACAAATCTG >EAS139_19:5:66:1381:181 GGACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGT >EAS139_19:5:66:1381:181 TTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACT >EAS139_19:5:68:306:409 AACTTTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAG >EAS139_19:5:68:306:409 CCTATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATT >EAS139_19:5:70:318:1631 TAAGAAATTACAAAATATAGTTGAAAGCTCTAACAATAGA >EAS139_19:5:74:668:424 GACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGTT >EAS139_19:5:74:668:424 GTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAA >EAS139_19:5:89:525:113 GACGCTGAAGAACTTTGATTCCCTCTTCTTCCAAAGATGA >EAS139_19:5:89:525:113 TATTTATGCTATTCAGTTATAAATATAGAAATTGAAACAG >EAS139_19:5:95:944:247 GGTACAATGTACAATATTCTGATGATGGTTACACTAAAAG >EAS139_19:5:95:944:247 GTAAAGATGTGGGGAAAAAAGTAAACTCTCAAATATTGCT >EAS139_19:6:21:1601:1666 GAAAGCTCTAACAATAGACTAAACCAAGCAGAAGAAAGAG >EAS139_19:6:21:1601:1666 TATTACTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAA >EAS139_19:6:52:1455:1212 CCATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTGT >EAS139_19:6:52:1455:1212 TTCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTCT >EAS139_19:6:72:308:839 AGTTACCAAATGTGTTTATTACCAGAGGGATGGAGGGAAG >EAS139_19:6:72:308:839 ATCGTGGACCCTGAGAGATTCTGCAGCCCAGATCCAGATT >EAS139_19:6:75:1503:1399 CAAGAAGATATAACCATCCTACTAAATACATATGCACCTA >EAS139_19:6:75:1503:1399 CATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGC >EAS139_19:6:78:1029:512 AGATAATTCATCATCACTAAACCAGTCCTATAAGAAATGC >EAS139_19:6:78:1029:512 TCAGCAGAAACCTTACAAGCCAGAAGAGATTGGATCTAAT >EAS139_19:6:82:1051:921 GCAAATAGGTAAAAAATTAACATTACAACAGGAACAAAAC >EAS139_19:6:82:1051:921 GGGGAAATAAAGTCAAGGCTTTCCTGACAAGCAAATGCTA >EAS139_19:6:84:438:1505 ATTAATATAATTGTGTCCATGTACACACTCTGTCCTATGT >EAS139_19:6:84:438:1505 GCACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGTTTC >EAS139_19:7:44:1807:833 ATATCCATGTAACAAATCTGCGCTTGTACTTCTAAATCTA >EAS139_19:7:44:1807:833 CTCTCAAATATTGCTAGTGGGAGTATAAATTGTTTTCCAC >EAS139_19:7:85:262:751 CCATGTAACAAATCTGCGCTTGTACTTCTAAATCTATAAC >EAS139_19:7:85:262:751 TACAATGATAAAAAGATCAATTCAGCAAGAAGATATAACC >EAS139_19:7:92:288:1354 TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATT >EAS139_19:7:92:288:1354 TGTCTTGACACCCAACTAATATTTGTCTGAGCAAAACAGT >EAS188_4:5:103:870:105 AAACTAAGCATCATAAATGAAGGGGAAATAAAGTC >EAS188_4:5:103:870:105 ATAAAACAATTAATTGAGACTACAGAGCAACTAGG >EAS188_4:5:166:776:590 CTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGCC >EAS188_4:5:166:776:590 TAATTGTGTCCATGTACACACGCTGTCCTATGTAC >EAS188_4:5:202:326:680 ACTTATCATGACTCTATCCCAAATTCTCAATTACG >EAS188_4:5:202:326:680 GTAATGATGCCCCTTGGCCATCACCCGGTCCCTGC >EAS188_4:5:295:547:216 ATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCT >EAS188_4:5:295:547:216 TAAAAAATTAACATTACAACAGGAACAAAACCTCA >EAS188_4:5:302:997:951 ATGAACTTCTGTAATTGAAAAATTCATTTAAGAAA >EAS188_4:5:308:552:77 TTTTCTTTTTTTTCTTTTCTCTTTTTTTTTTTTTT >EAS188_4:5:8:377:655 CTATTTTTGTCTTGACACCCAACTAATATTTGTCT >EAS188_4:5:8:377:655 CTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGCT >EAS188_4:7:282:567:481 GGAACAGGGAGGCGCACTAATGCGCTCCACGCCCA >EAS188_4:7:282:567:481 TGCAATTAATATAATTGTGTCCACGTACACACGCT >EAS188_4:7:296:401:60 AATGAAAGAGGCTCAAAGAATGCCAGGAAGATACA >EAS188_4:7:35:408:348 AAGAAACGCGTAACTGCGCTCTCATACACTCCAGC >EAS188_4:7:35:408:348 GGTTCTCAAGGTTGTTGCAATGGGGTCTATGTGAA >EAS188_4:7:78:583:670 CAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTT >EAS188_4:7:78:583:670 TAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCT >EAS188_4:7:96:899:106 TCTATAAAGGAAATCCCATCAGAATAACAATGGGC >EAS188_4:7:96:899:106 TTCCTGACAAGCAAATGCTAAGATAATTCATCATC >EAS188_7:1:115:683:296 AACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTC >EAS188_7:1:115:683:296 CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC >EAS188_7:1:177:522:118 TAAACTAAGCATCATAAATGAAGGGGAAATAAAGT >EAS188_7:1:177:522:118 TCTCAATTAATTGTTTTATAAAACCTGTGAGTTTT >EAS188_7:1:290:286:763 TTAAAATTTAACAAAAGTAAATAAAACACATAGCT >EAS188_7:1:290:286:763 TTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTTT >EAS188_7:1:316:949:122 TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCT >EAS188_7:1:316:949:122 TTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTT >EAS188_7:1:77:251:446 CAGCATGGTTGTACTGGGCAATACATGAGATTATT >EAS188_7:1:77:251:446 TTATCATGACTCTATCCCAAATGCCCAATTACGTC >EAS188_7:2:152:765:744 ACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCGT >EAS188_7:2:152:765:744 TTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACAT >EAS188_7:2:172:622:707 ACATGGCTGATTATGAAAACAATGTTCCCCAGATA >EAS188_7:2:172:622:707 TTCTTCATCCTGGACCCTGAGAGATTCTGCAGCCC >EAS188_7:2:187:227:818 CAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAG >EAS188_7:2:187:227:818 CCCCCTTGCAACAACCTTGAGAACCCCAGGGAATT >EAS188_7:2:19:736:559 AAGACTTCATCAAGATATGTAGTCATCAGACTATC >EAS188_7:2:19:736:559 TGAACCTATGAGTCACAGGTATTCCTGAGGAAAAA >EAS188_7:2:218:877:489 TATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTG >EAS188_7:2:259:219:114 GAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCA >EAS188_7:2:259:219:114 TTGATGCCCTCTTCTTCCAAAGATGAAACGCGTAA >EAS188_7:3:100:735:530 GCACACTTTAAATCAACAACAGTAAAATAAAACAA >EAS188_7:3:100:735:530 TGATGATGGTTACACTAAAAGCCCATACTTTACTG >EAS188_7:3:101:572:491 CAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTG >EAS188_7:3:101:572:491 TTCCAAAGATGAAACGCGTAACTGCGCTCTCATTC >EAS188_7:3:13:122:187 AGCATTTTGTCAGTTACCAAATGTGTTTATTACCA >EAS188_7:3:13:122:187 GACTGCCAGAGCTGCTGGCAAGCTAGAGTCCCCTT >EAS188_7:3:15:568:42 TTTTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT >EAS188_7:3:15:568:42 TTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTATA >EAS188_7:3:182:104:921 ATCAAGATATGTAGTCATCAGACTATCTAAAGTCA >EAS188_7:3:182:104:921 CACGAATGTTATGCCCTGCTAAACTAAGCATCATA >EAS188_7:3:200:712:439 CGTCACCCGGTCCCTGCCCCATCTCTTGTAATCTC >EAS188_7:3:200:712:439 GTTGGGAGATTTTTAATGATTCCTCAATGTTAAAA >EAS188_7:3:296:224:724 ATAGTTGAAAGCTCTAACAATAGACTAAACCAAGC >EAS188_7:3:296:224:724 TGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAAC >EAS188_7:3:76:333:905 AATTGTGTCCATGTACACACGCTGTCCTATGTACT >EAS188_7:3:76:333:905 TTTCTGCCCCCAGCATGGTTGTACTGGGCAATACA >EAS188_7:4:164:719:947 AAATTAACATTACAACAGGAACAAAACCTCATATA >EAS188_7:4:164:719:947 ACGCAAACAGAAACCAAATGAGAGAAGGAGTAGCT >EAS188_7:4:171:104:398 AGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCC >EAS188_7:4:171:104:398 CAATTAATATAATTGTGTCCATGTACACACGCTGT >EAS188_7:4:21:443:404 AGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTCC >EAS188_7:4:21:443:404 TTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTCT >EAS188_7:4:238:441:727 GTAATTGAAAAATTCATTTAAGAAATTACAAAATA >EAS188_7:4:259:869:641 GTTGGGAGATTTTTAATGATTCCTCAATGTTAAAA >EAS188_7:4:259:869:641 TGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCA >EAS188_7:4:92:693:228 AAGGTTTTATAAAAAAATTAATTGAGACTACAGAG >EAS188_7:4:92:693:228 AGCATCATAAATGAAGGGGAAATAAAGTCAAGTCT >EAS188_7:5:112:51:128 AGACCCCCTTGCAACAACCTTGAGAACCCCAGGGA >EAS188_7:5:112:51:128 CCCAATGGACCTGTGATATCTGGATTCTGGGAAAT >EAS188_7:5:115:249:673 TAAAGAAAAAAAAACCTGTCAAACACGAATGTTAT >EAS188_7:5:115:249:673 TAAATACACACAAAAGTACAAAACTCACAGGTTTT >EAS188_7:5:163:982:695 CTCAGCAGAAACCTTACAAGCCAGAAGAGATTGGA >EAS188_7:5:163:982:695 TCAAAGAATGCCAGGAAGATACATTGCAAGACAGA >EAS188_7:5:308:354:124 GCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTT >EAS188_7:5:308:354:124 TGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCT >EAS188_7:5:74:329:459 ACAGAGCAACTAGGTAAAAAATTAACATTACAACA >EAS188_7:5:74:329:459 TAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAG >EAS188_7:6:107:447:488 TAATTGGTACAATGTACAATATTCTGATGATGGTT >EAS188_7:6:107:447:488 TGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTA >EAS188_7:6:107:636:642 AAGTCTTTCCTGACAAGCAAATGCTAAGATAATTC >EAS188_7:6:107:636:642 GTCATCTATAAAGGAAATCCCATCAGAATAACAAT >EAS188_7:6:11:994:584 GAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAAG >EAS188_7:6:11:994:584 GGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTT >EAS188_7:6:191:540:493 AAAAGCCCATACTTTACTGCTACTCAATATATCCA >EAS188_7:6:191:540:493 GTGGGGAAAAAAGTAAACTCTCAAATATTGCTAGT >EAS188_7:6:194:998:663 ACCTAACACAAGACTACCCAGATTCATAAAACAAA >EAS188_7:6:194:998:663 TCTACGCAAACAGAAACCAAATGAGAGAAGGAGTA >EAS188_7:6:205:873:464 AGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAG >EAS188_7:6:205:873:464 CCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATT >EAS188_7:6:46:122:479 AAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTT >EAS188_7:6:46:122:479 AAGTGAGAAGTTTGGAAGAACTATTTGAGGAAGTA >EAS188_7:7:19:886:279 CCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTA >EAS188_7:7:19:886:279 GAAAGGAGCATTTTGTCAGTTACCAAATGTGTTTA >EAS188_7:7:213:309:373 TAGACATCTAAATGAAAGAGGCTCAAAGAATGCCA >EAS188_7:7:213:309:373 TTAAAAATGAACAGAGCTTTCAAGAAGTATGAGAT >EAS188_7:7:243:876:758 AGCCCAGATCCAGATTGCTTGTGGTCTGACAGGCT >EAS188_7:7:243:876:758 CCCAGATACCATCCCTGTCTTACTTCCAGCTCCCC >EAS188_7:7:67:719:786 GGATGAGAAATTACCTAATTGGTACACTGTACAAT >EAS188_7:7:67:719:786 TAAAAAAAAAAAAGCAAAAACAAAAACTATGCTAA >EAS188_7:8:60:182:718 GTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTT >EAS188_7:8:60:182:718 TGACACCCAACTAATATTTGTCTGAGCAAAACAGT >EAS188_7:8:64:350:174 CCTAACACAAGACTACCCAGATTCATAAAACAAAT >EAS188_7:8:64:350:174 GTTCTACGCAAACAGAAACCAAATGAGAGAAGGAG >EAS192_3:1:114:19:769 AAACACGAATGTTATGCCCTGCTAAACTAAGCATC >EAS192_3:1:114:19:769 TAAAGTCAACATGAAGGAAAAAAATTCTAAAATCA >EAS192_3:1:225:195:543 AACAACCTTGAGAACCCCAGGGAATTTGTCAATGT >EAS192_3:1:225:195:543 GGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTG >EAS192_3:3:194:378:230 AATACTACTAGACCTAAGAGGGATGAGAAATTACC >EAS192_3:3:194:378:230 ATGAGAGAAGGAGTAGCTATACTTATATCAGATAA >EAS192_3:3:221:881:916 TAACACAAGACTACCCAGATTCATAAAACAAATAC >EAS192_3:3:221:881:916 TAATTCTAAATCTAGAACAAAATTAAAATTTAACA >EAS192_3:3:257:611:440 ACCCTGAGAGATTCTGCAGCCCAGATCCAGATTGC >EAS192_3:3:257:611:440 GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAC >EAS192_3:3:27:973:518 CTGATTATGAAAACAATGTTCCCCAGATACCATCC >EAS192_3:3:27:973:518 TCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGT >EAS192_3:3:285:349:797 ATCATAAATGAAGGGGAAATAAAGTCAAGTCTTTC >EAS192_3:3:285:349:797 GTTTTAAAAAACCAATAATTGAGACTACAGAGCAA >EAS192_3:3:309:187:267 ATTGAGACTACAGAGCAACTAGGTAAAAAATTAAC >EAS192_3:3:309:187:267 GGGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAA >EAS192_3:3:88:866:774 ATGTAACAAATCTGCTCTTGTACTTCTAAATCTAT >EAS192_3:3:88:866:774 TTGTTTTCCACTTTGGAAAACAATTTGGTAATTTC >EAS192_3:4:184:237:476 ATCATACAATGATAAAAAGATCAATTCAGCAAGAA >EAS192_3:4:184:237:476 ATGAACTAACTATATGCTGTTTACAAGAAACTCAT >EAS192_3:4:255:549:422 AAGTCATCTATAAAGGAAATCCCATCAGAATAACA >EAS192_3:4:255:549:422 CTCTTTAGTCTTGCTAGAGATTTAGACATCTAAAT >EAS192_3:4:293:168:240 ATGAACAGAGCTTTCAAGAAGTATGAGATTATGTA >EAS192_3:4:293:168:240 CAAAGAATGCCAGGAAGATACATTGCAAGACAGAC >EAS192_3:4:312:915:751 AATAAAGTCAAGTCTTTCCTGACAAGCAAAAGCTA >EAS192_3:4:312:915:751 ATCTATAAAGGAAATCCCATCAGAATAACAATGGG >EAS192_3:4:63:5:870 AAAGAAAAAAGAATTTTAAAAATGAACAGAGCTTT >EAS192_3:4:63:5:870 GAAAGAGGCTCAAAGAATGCCAGGAAGATACATTG >EAS192_3:5:197:914:256 ACTAGACCTAAGAGGGATGAGAAATTACCTAATTG >EAS192_3:5:197:914:256 TCAGATAAAGCACACTTTAAATCAACAACAGTAAA >EAS192_3:5:223:142:410 CTATTCAGTTCTAAATATAGAAATTGAAACAGCTG >EAS192_3:5:27:577:849 AGTCTCTTATGAATTAACCCAGTCAGACAAAAATA >EAS192_3:5:27:577:849 TTAGACATCTAAATGAAAGAGGCTCAAAGAATGCC >EAS192_3:5:287:334:110 GATGAATACTAAGATTGATGTAGCAGCTTTTGCAA >EAS192_3:5:287:334:110 TATGTAAAGTAACTGAACCTATGAGTCACAGGTAT >EAS192_3:6:116:464:261 CAATGATAAAAAGATCAATTCAGCAAGAAGATATA >EAS192_3:6:116:464:261 CTATATGCTGTTTACAAGAAACTCATTAATAAAGA >EAS192_3:6:170:169:57 GGCTTGACCTCTGGTGACTGCCAGAGCTGCTGGCC >EAS192_3:6:170:169:57 TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA >EAS192_3:6:175:437:950 CCAAATTCCCAATTACGTCCTATCTTCTTCTTAGG >EAS192_3:6:175:437:950 CCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC >EAS192_3:6:185:868:496 CCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTT >EAS192_3:6:185:868:496 GATTTTTAATGATTCCTCAATGTTAAAATGTCTAT >EAS192_3:6:201:195:757 CCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC >EAS192_3:6:201:195:757 TATGTACTTATCATGACTCTATCCCAAATTCCCAA >EAS192_3:6:216:292:528 GGGAGATTTTTAATGATTCCTCAATGTTAAAATGT >EAS192_3:6:216:292:528 TAATGATGCCCCTTGGCCATCACCCAGTCCCTGCC >EAS192_3:6:235:505:553 GGTGGAAAAAGATGTTCTACGCAAACAGAAACCAA >EAS192_3:6:235:505:553 GTAAAAAATTAACATTACAACAGGAACAAAACCTC >EAS192_3:6:326:887:180 CTAAACCAGTCCTATAAGAAATGCTCAAAAGAATT >EAS192_3:6:326:887:180 TGGGCTTCTCAGCAGAAACCTTACAAGCCAGAAGC >EAS192_3:6:45:183:25 CAGCGGAAACCTTACAAGCCAGAAGAGATTGGATC >EAS192_3:6:45:183:25 CTAAACCAGTCCTATAAGAAATGCTCAAAAGAATT >EAS192_3:7:149:354:667 CTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCTT >EAS192_3:7:149:354:667 GAGGTGCACTAATGCGCTCCACGCCCAAGCCCTTC >EAS192_3:7:298:644:697 CTATGTTTCTTATCTGCACATTACTACCCTGCAAT >EAS192_3:7:298:644:697 TCCACGTCTCATCTAGGGGAACAGGGAGGTGCACT >EAS192_3:7:66:891:294 AGCACACTTTAAATCAACAACAGTAAAATAAAACA >EAS192_3:7:66:891:294 TAATTGGTACAATGTACAATATTCTGATGATGGTT >EAS192_3:7:78:692:671 AATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACA >EAS192_3:7:78:692:671 CAGCAAGAGAAAAGCATACAGTCATCTATAAAGGA >EAS192_3:7:93:945:176 CCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTC >EAS192_3:7:93:945:176 GTGAGCCATCACAATGAACAACAGGAAGAAAAGGT >EAS192_3:8:6:104:118 AAGAATTTTAAAAATGAACAGAGCTTTCAAGAAGT >EAS192_3:8:6:104:118 TCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGA >EAS192_3:8:6:237:885 AAAATCAGCAAGAGAAAAGCATACAGTCATCTATA >EAS192_3:8:6:237:885 TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT >EAS1_103:1:151:159:43 AACCTCATACACACACATGGTTTAGGGGTATAATA >EAS1_103:1:151:159:43 TCTCATTCACTCCAGCTCCCTGTCACCCAATGGAC >EAS1_103:1:228:736:747 AAGATATGTAGTCATCAGACTATCTAAAGTCAACA >EAS1_103:1:228:736:747 TTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACA >EAS1_103:1:274:176:479 CCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTAT >EAS1_103:1:274:176:479 GAAATGCTTTACTGTCATAACTATGAAGAGACTAT >EAS1_103:1:2:831:692 GTGTTCTCATCAACCTCATACACACACATGGTTTA >EAS1_103:1:2:831:692 TCCAGCTCCCTGTCACCCAATGGACCTGTGATATC >EAS1_103:2:184:980:396 AAGGAGGTCATCATACAATGATAAAAAGATCAATT >EAS1_103:2:184:980:396 ACATGAACTAACTATATGCTGTTTACAAGAAACTC >EAS1_103:2:226:302:758 GGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGG >EAS1_103:2:226:302:758 TGCTTGTGGTCTGACAGGCTGCAACTTTGAGCGNT >EAS1_103:2:234:167:381 AAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT >EAS1_103:2:234:167:381 AGAGAAAAGCATACAGTCATCTATAAAGGAAATCC >EAS1_103:2:235:805:373 TATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCA >EAS1_103:2:235:805:373 TTTACTGTCATAACTATGAAGAGACTATTTCCAGA >EAS1_103:2:307:252:632 ACCATCCTGCTAAATACATATGCACCTAACACAAG >EAS1_103:2:307:252:632 ATGTTCTACGCAAACAGAAACCAAATGAGAGAAGG >EAS1_103:3:253:175:31 CAAACAGAAACCAAATGAGAGAAGGAGTAGCTATA >EAS1_103:3:253:175:31 TTCATAAAACAAATACTACTAGACCTAAGAGGGAT >EAS1_103:3:277:921:474 AAAATATAGTTGAAAGCTCTAACAATAGACTAAAC >EAS1_103:3:277:921:474 AAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGA >EAS1_103:3:320:505:814 ACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCT >EAS1_103:3:320:505:814 CTGTCTTGATTTACTTGTTGTTGGTTTTCTTTTTC >EAS1_103:3:323:196:855 ACAAGCAAATGCTAAGATAATTCATCATCACTAAA >EAS1_103:3:323:196:855 TAAAAAATTAACATTACAACAGGAACAAAACCTCA >EAS1_103:3:41:474:283 TGAACCACACATTAATACTATGTTTCTTATCTGCA >EAS1_103:3:41:474:283 TTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGTCC >EAS1_103:4:143:560:194 GTTGTACTGGGCAATACATGAGATTATTAGGAAAT >EAS1_103:4:143:560:194 TCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCC >EAS1_103:4:164:79:134 ACAATGGGCTTCTCAGCGGAAACCTTACAAGCCAG >EAS1_103:4:164:79:134 AGATAATTCATCATCACTAAACCAGTCCTATAAGA >EAS1_103:4:231:815:626 GATCAATACAGCAAGAAGATATAACCATCCTACTA >EAS1_103:4:231:815:626 GCTGTTTACAAGAAACTCATTAATAAAGACATGAG >EAS1_103:4:235:899:847 AGAAACTCATTAATAAAGACATGAGTTCAGGTAAA >EAS1_103:4:235:899:847 ATAAAAAGATCAATTCAGCAAGAAGATATAACCAT >EAS1_103:4:294:525:849 AGGAGCATTTTGTCAGTTACCAAATGTGTTTATTA >EAS1_103:4:294:525:849 CTGGCAAGCTAGAGTCCCATTTGGAGCCCCTCTAA >EAS1_103:4:61:433:385 ACTGTGAGCCATCACAATGAACAACAGGAAGAAAA >EAS1_103:4:61:433:385 GGATGGAGGGAAGAGGGACGCTGAAGCACTTTGAT >EAS1_103:5:141:711:813 TATTACCAGAGGGATGGAGGGAAGAGGGACGCTGA >EAS1_103:5:141:711:813 TATTTGTAATGAAAACTATATTTATGCTATTCAGT >EAS1_103:5:188:20:592 CTACTAGACCTAAGAGGGATGAGAAATTACCTAAT >EAS1_103:5:188:20:592 GAGTAGCTATACTTATATCAGATAAAGCACACTTT >EAS1_103:5:285:241:560 GAAATTACAAAATATAGTTGAAAGCTCTAACAATA >EAS1_103:5:285:241:560 TAAAGTAACTGAACCTATGAGTCACAGGTATTCCT >EAS1_103:5:319:165:698 ATCACCCAGTCCCTGCCCCATATCTTGTAATCTCT >EAS1_103:5:319:165:698 TGACACCCAACTAATATTTGTCTGAGCAAAACAGT >EAS1_103:6:7:858:437 CAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGG >EAS1_103:6:7:858:437 CCATTTCTTTTGGCATTTGCCTTCAGACCCTACAC >EAS1_103:7:112:578:782 AAAATAAAACACATAGCTAAAACTAAAAAAGCAAA >EAS1_103:7:112:578:782 CAGATTCATAAAACAAATACTACTAGACCTAAGAG >EAS1_103:7:139:578:951 AAAAACATGAACTAACTATATGCTGTTTACAAGAA >EAS1_103:7:139:578:951 GAGGTCATCATACAATGATAAAAAGATCAATTCAG >EAS1_103:7:166:84:766 ATAACACAAGACTACCCAGATTCATAAAACAAATA >EAS1_103:7:166:84:766 GGAAAAAGATGTTCTACGCAAACAGAAACCAAATG >EAS1_103:7:311:100:539 AAATTCTTCATCCTGGACCCTGAGAGATTCTGCAG >EAS1_103:7:311:100:539 CAGTTACCAAATGTGTTTATTACCAGAGGGATGGA >EAS1_103:7:313:83:546 TCATTCACTCCAGCTCCCTGTCACCCAATGGACCT >EAS1_103:7:313:83:546 TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA >EAS1_103:7:53:783:78 AAAAACCTGTCAAACACGAATGTTATGCCCTGCTA >EAS1_103:7:53:783:78 TGCAAGACAGACTTCATCAAGATATGTAGTCATCA >EAS1_105:1:115:226:443 AAATCTGCGCTTGTACTTCTAAATCTATAAAAAAA >EAS1_105:1:115:226:443 ATATAACCATCCTACTAAATACATATGCACCTAAC >EAS1_105:1:141:415:738 AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGA >EAS1_105:1:141:415:738 TTACCTAGTTGCTCTGTAGTCTCAATTAATTGTTT >EAS1_105:1:234:185:359 AAGGAGTAGCTATACTTATATCAGATAAAGCACAC >EAS1_105:1:234:185:359 CAGATTCATAAAACAAATACTACTAGACCTAAGAG >EAS1_105:1:28:745:352 ATATGCACCTAACACAAGACTACCCAGATTCATAA >EAS1_105:1:28:745:352 CTTCTAAATCTATAACAAAATTAAAATTTAACAAA >EAS1_105:1:297:283:948 CCAGATTGCTTGTGGTCTGACAGGCTGCAACTGTG >EAS1_105:1:297:283:948 TGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTC >EAS1_105:1:329:407:872 TTCGTTTTTTTTTTTTTTTTTTCCCTTTTTTTTTT >EAS1_105:1:3:903:957 AAGCCAGAAGAGATTGGATCTAATTTTTGGACTTC >EAS1_105:1:3:903:957 ATTCATCATCACTAAACCAGTCCTATAAGAAATGC >EAS1_105:1:45:239:851 CTAAGAGGGATGAGAAATTACCTAATTGGTACAAT >EAS1_105:1:45:239:851 TGAGAGAAGGAGTAGCTATACTTATATCAGATAAA >EAS1_105:1:87:430:995 GAAAAGAGTTAAAAACATGAACTAACTATATGCTG >EAS1_105:1:87:430:995 TACTCACCATCATAAATACACACAAAATTACAAAA >EAS1_105:2:110:584:649 CCATGTACACACGCTGTCCTATGTACTTATCATGA >EAS1_105:2:110:584:649 CTGTAATGATGCCCCTTGGCCATCACCCGGTCCCT >EAS1_105:2:146:374:692 AAATGCTCAAAAGAATTGTAAAAGTCAAAATTAAA >EAS1_105:2:146:374:692 ATTAAATTCCCCCACTTAAGAGATATAGATTGGCA >EAS1_105:2:179:532:82 CCATCACCCGGTCCCTGCCCCATCTCTTGTAATCT >EAS1_105:2:179:532:82 TGTACTTATCATGACTCTATCCCAAATTCCCAATT >EAS1_105:2:280:662:939 AAGAGAAAAGCATACAGTCATCTATAAAGGAAATC >EAS1_105:2:280:662:939 CCTCTTTAGTCTTGCTAGAGATTTAGACATCTAAA >EAS1_105:2:299:360:220 ATTCAGTTCTAAATATAGAAATTGAAACAGCTGTG >EAS1_105:2:299:360:220 GAAGAACTTAGATGCCCTCTTCTTCCAAAGATGAA >EAS1_105:2:301:161:195 ACAGTAAAATAAAACAAAGGAGGTCATCATACAAT >EAS1_105:2:301:161:195 GTACAATGTACAATATTCTGATGATGGTTACACTA >EAS1_105:3:176:431:647 ATCATGACTCTATCCCAAATTCCCAATTACGTCCT >EAS1_105:3:176:431:647 CCATCACCCAGTCCCTGCCCCATCTCTTGTAATCT >EAS1_105:3:182:404:693 ACCTCATACACACACATGGTTTAGGGGTATAATAC >EAS1_105:3:182:404:693 GCGTCTCTACCACAGGGGGCTGCGCGGTTTCCCAT >EAS1_105:3:232:364:583 CAATTAATTGAGACTACAGAGCAACTAGGTAAAAA >EAS1_105:3:232:364:583 TCATTAATAAAGACATGAGTTCAGGTAAAGGGGTG >EAS1_105:3:308:66:538 CGCTTGTACTTCTAAATCTATAACAAAATTAAAAT >EAS1_105:3:308:66:538 TATAACCATCCTACTAAATACATATGCACCTAACA >EAS1_105:3:329:177:267 CATGAGATTATTAGGAAATGCTTTACTGTCATAAC >EAS1_105:3:329:177:267 TACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTA >EAS1_105:3:7:35:528 TTTTTTTTTTGTTCTTTACTCTTTTTTTTTTTTTT >EAS1_105:3:86:823:683 ACTTTGATGCCCTCTTCTTCCAAAGATGAAACGCG >EAS1_105:3:86:823:683 CAGTTCTAAATATAGAAATTGAAACAGCTGTGTTT >EAS1_105:6:134:853:558 AATATAATTGTGTCCATGTACACACGCTGTCCTAT >EAS1_105:6:134:853:558 GGAACAGGGAGGTGCACTAATGCGCTCCACGCCCA >EAS1_105:6:162:594:858 CTACCACAGGGGGCTGCGCGGTTTCCCATCATGAA >EAS1_105:6:162:594:858 GTGTTCTCATCAACCTCATACACACACATGGTTTA >EAS1_105:6:172:827:592 AATTGTAAAAGTCAAAATTAAAGTTCAATACTCAC >EAS1_105:6:172:827:592 TAGATTGGCAGAACAGATTTAAAAACATGAACTAA >EAS1_105:6:23:885:274 ACAAAGGAGGTCATCATACAATGATAAAAAGATCA >EAS1_105:6:23:885:274 CTACTACTCAATATATCCATGTAACAAATCTGCGC >EAS1_105:6:267:953:459 ACCTTACAAGCCAGAAGAGATTGGATCTAATTTTT >EAS1_105:6:267:953:459 CATCACTAAACCAGTCCTATAAGAAATGCTCAAAA >EAS1_105:7:110:355:323 ACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGG >EAS1_105:7:110:355:323 CCCAATGGACCTGTGATATCTGGATTCTGGGAAAT >EAS1_105:7:168:247:414 AAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATA >EAS1_105:7:168:247:414 TAAATTCCCCCACTTAAGAGATATAGATTGGCAGA >EAS1_105:7:289:472:86 ATGAACTTCTGTAATTGAAAAATTCATTTAAGAAA >EAS1_105:7:45:462:455 TCCCTGTCTTACTTCCAGCTCCCCAGACGGAACGC >EAS1_105:7:45:462:455 TCTAGGGGAACAGGGAGGTGCACTAATGCGCTCCA >EAS1_105:7:57:722:347 ACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGT >EAS1_105:7:57:722:347 CGCGTAACTGCGCTCTCATTCACTCCAGCTCCCTG >EAS1_105:8:160:130:351 CAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAAT >EAS1_105:8:160:130:351 TGGATCTAATTTTTGGACTTCTTAAAGAAAAAAAA >EAS1_105:8:179:119:876 ATAAAAAGATCAATTCAGCAAGAAGATATAACCAT >EAS1_105:8:179:119:876 TTAAAAACATGAACTAACTATATGCTGTTTACCAG >EAS1_105:8:24:718:322 AACTCATTAATAATGTCATGAGTTCAGGTAAAGGG >EAS1_105:8:24:718:322 ACAATTAATTGAGACTACAGACCAATTATGTAAAA >EAS1_105:8:254:617:73 AACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT >EAS1_105:8:254:617:73 GCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTC >EAS1_105:8:256:404:584 ACTGTCCTATGTACTTATCATGACTCTATCCCAAA >EAS1_105:8:256:404:584 GTTTCTGCCCCCAGCATGGTTGTACTGGGCAATAC >EAS1_105:8:96:720:940 AAAGGAAATCCCATCAGAATAACAATGGGCTTCTC >EAS1_105:8:96:720:940 TAAGATAATTCATCATCACTAAACCAGTCCTATAA >EAS1_108:1:111:796:737 ATCATGACTCTATCCCAAATTCCCAATTACGTCCT >EAS1_108:1:111:796:737 CCCCAGCATGGTTGTACTGGGCAATACATGTGATT >EAS1_108:1:131:518:588 AAAATCAGCAAGAGAAAAGCATACAGTCATCTATA >EAS1_108:1:131:518:588 ATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTG >EAS1_108:1:148:286:316 AGAACTTCCCTGGAGGTCTGATGGCGTTTCTCCCT >EAS1_108:1:148:286:316 CCTCTGTCTTGATTTACTTGTTGTTGGTTTTCTGT >EAS1_108:1:155:809:543 AAATTTAACAAAAGTAAATAAAACACATAGCTAAA >EAS1_108:1:155:809:543 TACATATGCACCTAACACAAGACTACCCAGATTCA >EAS1_108:1:16:438:245 TTGAATAAAAAGGGATTAAATTCCCCCACTTAAGA >EAS1_108:1:189:863:213 CTACTAGACCTAAGAGGGATGAGAAATTACCTAAT >EAS1_108:1:189:863:213 TATACTTATATCAGATAAAGCACACTTTAAATCAA >EAS1_108:1:242:419:512 AATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAA >EAS1_108:1:242:419:512 CTAAACCAGTCCTATAAGAAATGCTCAAAAGAATT >EAS1_108:1:277:194:143 TGGGCTGTAATGATGCCCCTTGGCCATCACCCGGT >EAS1_108:1:277:194:143 TTTTTAATGATTCCTCAATGTTAAAATGTCTATTT >EAS1_108:1:328:614:638 AAAGGTTGTTGGGAGATTTTTAATGATTCCTCAAT >EAS1_108:1:328:614:638 ACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGC >EAS1_108:1:33:779:821 AATGTTATGCCCTGCTAAACTAAGCATCATAAATG >EAS1_108:1:33:779:821 TGAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAA >EAS1_108:1:49:911:980 ACAATGTACAATATTCTGATGATGGTTACACTAAA >EAS1_108:1:49:911:980 GGGGAAAAAAGTAAACTCTCAAATATTGCTAGTGG >EAS1_108:1:65:787:74 TGTAATGAAAACTATATTTATGCTATTCAGTTCTA >EAS1_108:2:102:543:160 CAACAGGAACAAAACCTCATATATCAATATTAACT >EAS1_108:2:102:543:160 CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA >EAS1_108:2:116:966:193 ATTAACATTACAACAGGAACAAAACCTCATATATC >EAS1_108:2:116:966:193 GACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGT >EAS1_108:2:170:326:433 CTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCGTC >EAS1_108:2:170:326:433 TTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGG >EAS1_108:2:176:653:957 AAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAA >EAS1_108:2:176:653:957 ACATTACAACAGGAACAAAACCTCATATATCAATA >EAS1_108:2:204:737:61 AAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGT >EAS1_108:2:204:737:61 TCAGCAAGAGAAAAGCATACAGTCATCTATAAAGG >EAS1_108:2:240:593:842 ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT >EAS1_108:2:240:593:842 CATGGTTTAGGGGTATAATACCTCTACATGGCTGA >EAS1_108:2:266:994:429 ACAGGTTTTATAAAACAATTAATTGAGACTACAGA >EAS1_108:2:266:994:429 TGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAG >EAS1_108:2:316:176:543 ATGTCTATTTTTGTCTTGACACCCAACTAATATTT >EAS1_108:2:316:176:543 CATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCC >EAS1_108:2:49:271:588 CACATGGTTTAGGGGTATAATACCTCTACATGGCT >EAS1_108:2:49:271:588 GCTGCGCGGTTTCCCATCATGAAGCACTGAACTTC >EAS1_108:2:62:879:264 AATGAAAACTATATTTATGCTATTCAGTTCTAAAT >EAS1_108:2:62:879:264 GGACGCTGAAGAACTTTGATGCCCTCTTCTTCCAA >EAS1_108:2:82:879:246 AAGAGGGACGCTGAAGAATTTTGATGCCCTCTTCT >EAS1_108:2:82:879:246 ACAACTGTGAGCCATCACAATGAACAACAGGAAGA >EAS1_108:2:85:580:481 AAAAAAGTAAATAAAACACATAGCTAAAACTAAAA >EAS1_108:2:85:580:481 CTAACACAAGACTACCCAGATTCATAAAACAAATA >EAS1_108:3:216:988:883 AAGCCAACACAATGAACAACAGGAAGAAAAGGTCT >EAS1_108:3:216:988:883 AGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTT >EAS1_108:3:24:319:429 GTTATGCCCTGCTAAACTAAGCATCATAAATGAAG >EAS1_108:3:24:319:429 TAATAAATACACACAAAAGTACAAAACTCACAGGT >EAS1_108:3:75:934:439 AAGAGACTATTGCCAGATGAACCACACATTAATAC >EAS1_108:3:75:934:439 CCCATCATGAAGCACTGAACTTCCACGTCTCATCT >EAS1_108:3:82:356:253 AGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATA >EAS1_108:3:82:356:253 GAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGGC >EAS1_108:4:163:611:211 TAAAGTCAACATGAAGGAAAAAAATTCTAAAATCA >EAS1_108:4:163:611:211 TGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAAC >EAS1_108:4:248:753:731 TATGCTATTCAGTTCTAAATATAGAAATTGAAACA >EAS1_108:4:248:753:731 TGAAGAACTTTGATGCCCTCTTCTTCCAAAGATGA >EAS1_108:4:31:622:216 ATTTAACAAAAGTAAATAAAACACATAGCTAAAAC >EAS1_108:4:37:604:389 ATGTTCTACGCAAACAGAAACCAAATGAGAGAAGG >EAS1_108:4:37:604:389 TCATAAAACAAATACTACTAGACCTAAGAGGGATG >EAS1_108:4:75:166:463 GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAAT >EAS1_108:4:75:166:463 TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT >EAS1_108:4:91:521:517 CCACACTGGTTCTCTTGAAAGCTTGGGCTGTAATG >EAS1_108:4:91:521:517 CCCTGCAATTAATATAATTGTGTCCATGTACACAC >EAS1_108:5:115:193:231 GAAGAGATTGGATCTAATTTTTGGACTTCTTAAAG >EAS1_108:5:115:193:231 TATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAA >EAS1_108:5:11:555:330 CGCTTGTACTTCTAAATCTATAAAAAAATTAAAAT >EAS1_108:5:11:555:330 GGAAAACAATTTGGTAATTTCGTTTTTTTTTTTTT >EAS1_108:5:175:149:296 AAAAATTAACATTACAACAGGAACAAAACCTCATA >EAS1_108:5:175:149:296 AAGGGGAAATAAAGTCAAGCCTTTCCTGACAAGCA >EAS1_108:5:180:905:36 CCTCCGTGTCCTCCCATCTGGCCTCGTCCACACTG >EAS1_108:5:180:905:36 TACTATGTTTCTTATCTGCACATTACTACCCTGCA >EAS1_108:5:229:717:121 ACTATGAAGAGACTATTGCCAGATGAACCACACAC >EAS1_108:5:229:717:121 TTCTTCTGAGGGAAGAACAGCTTAGGTATCAATTT >EAS1_108:5:321:712:224 AGATAAAGCACACTTTAAATCAACAACAGAAAAAT >EAS1_108:5:321:712:224 ATGAGAAATTACCTAATTGGTACAATGTACAATAT >EAS1_108:5:89:942:84 AAAACCTGTCAAACACGAATGTTATGCCCTGCTAA >EAS1_108:5:89:942:84 TACAAAACTCACAGGTTTTATAAAACAATTAATTG >EAS1_108:6:159:493:275 ACAAAACTCACAGGTTTTATAAAACAATTAATTGA >EAS1_108:6:159:493:275 TGCTGTTTACAAGAAACTCATTAATAAAGACATGA >EAS1_108:6:165:464:123 CATACACACACATGGTTTAGGGGTATAATACCTCT >EAS1_108:6:165:464:123 GTCTCTACCACAGGGGGCTGCGCGGTTTCCCATCA >EAS1_108:6:222:579:961 AGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAG >EAS1_108:6:222:579:961 CAGAAACCTTACAAGCCAGAAGAGATTGGATCTAA >EAS1_108:6:71:187:824 AGACAGACTTCATCAAGATATGTAGTCATCAGACT >EAS1_108:6:71:187:824 TCTAATTTTTGGACTTCTTAAAGAAAAAAAAACCT >EAS1_108:6:73:735:329 AAAGGGATTAAATTCCCCCACTTAAGAGATATAGA >EAS1_108:6:73:735:329 TAGCTATACTTATATCAGATAAAGCACACTTTAAA >EAS1_108:6:77:48:860 CTCTGTCTTGATTTACTTGTTGTTTGTTTTCTGTT >EAS1_108:6:77:48:860 TAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGC >EAS1_108:6:94:294:387 ACCATCATAAATACACACAAAAGTACAAAACTCAC >EAS1_108:6:94:294:387 GAATGTTATGCCCTGCTAAACTAAGCATCATAAAT >EAS1_108:6:95:235:746 CTAAGCATCATAAATGAAGGGGAAATAAAGTCAAG >EAS1_108:6:95:235:746 TCTAAAATCAGCAAGAGAAAAGCATACAGACATCT >EAS1_108:7:108:440:208 CCCATCCTACTAAATACATATGCACCTAACACAAG >EAS1_108:7:108:440:208 TTCAGGTAAAGGGGAGGAAAAAGATGTTCTACGCA >EAS1_108:7:222:538:267 ATAATTGTGTCCATGTACACACGCTGTCCTATTTA >EAS1_108:7:222:538:267 TCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCTT >EAS1_108:7:266:556:252 CCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAA >EAS1_108:7:266:556:252 GATTTGGTGGAAGACATAATCCCACGCTTCCTATG >EAS1_108:7:82:926:112 CAATGTCAGGGAAGGAGCATTTTGTCAGTTGCCAA >EAS1_108:7:82:926:112 CTGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCTC >EAS1_108:8:118:440:850 AATTGAAAAATTCATTTAAGAAATTACAAAATATA >EAS1_108:8:129:477:427 ATGGACCTGTGATATCTGGATTCTGGGAAATTCTT >EAS1_108:8:129:477:427 TACACACACATGGTTTAGGGGTATAATACCTCTAC >EAS1_108:8:19:929:765 AAAAACATGAACTAACTATATGCTGTTTACAAGAA >EAS1_108:8:19:929:765 ATCAACAACAGTAAAATAAAACAAAGGAGGTCATC >EAS1_93:1:131:946:353 TCTCTTGAAAGCTTGGGCTGTAATGATGCCCCTTG >EAS1_93:1:131:946:353 TGTACACACGCTGTCCTATGTACTTATCATGACTC >EAS1_93:1:179:629:513 GTCAACATGAAGGAAAAAAATTCTAAAATCAGCAA >EAS1_93:1:179:629:513 GTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAG >EAS1_93:1:20:635:509 CAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGT >EAS1_93:1:20:635:509 TGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGT >EAS1_93:1:214:784:690 AAATCCCATCAGAATAACAATGGGCTTCTCAGCGG >EAS1_93:1:214:784:690 GATAATTCATCATCACTAAACCAGTCCTATAAGAA >EAS1_93:1:216:381:608 TAATTGTGTCCATGTACACTCGCTGTCCTATGTAC >EAS1_93:1:216:381:608 TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG >EAS1_93:1:253:59:242 CCCCATCTCTTGTAATCTCTCTCCTTTTTGCTGCA >EAS1_93:1:253:59:242 TTTGTCTTGACACCCAACTAATATTTGTCTGAGCA >EAS1_93:1:264:988:663 CGAGGGGAACAGGGAGGTGCACTAATGCGCTCCAC >EAS1_93:1:264:988:663 TGGCTGATTATGAAAACAATGTTCCCCAGATACCA >EAS1_93:1:92:213:217 ACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCT >EAS1_93:1:92:213:217 TGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGT >EAS1_93:2:173:995:93 GCTGGAGGGAAGAGGGACGCTGAAGAACTTTGATG >EAS1_93:2:173:995:93 TAATGAAAACTATATTTATGCTATTCAGTTCTAAA >EAS1_93:2:286:923:549 TCAAATGAACTTCTGTAATTGAAAAATTCATTTAA >EAS1_93:2:30:466:652 AAAAATGAACAGAGCTTTCAAGAAGTATGAGATTA >EAS1_93:2:30:466:652 AAGAGGCTAAAAGAATGCCAGGAAGATACATTGCA >EAS1_93:2:313:711:530 ACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTT >EAS1_93:2:313:711:530 TAATTGAGACTACAGAGCAACTAGGTAAAAAATTA >EAS1_93:3:181:93:694 ACTCATTAATAAAGACATGAGTTCAGGTAAAGGGG >EAS1_93:3:181:93:694 TTAATTGAGACTACAGAGCAACTAGGTAAAAAATT >EAS1_93:3:79:879:15 AGACTACAGAGCAACTAGGTAAAAAATTAACATTA >EAS1_93:3:79:879:15 AGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATA >EAS1_93:4:160:896:275 AAAACTATATTTATGCTATTCAGTTCTAAATATAG >EAS1_93:4:160:896:275 AGGGAAGAGGGACGCTGAAGAACTTTGATGCCCTC >EAS1_93:4:321:271:138 GTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCA >EAS1_93:4:321:271:138 TTTGGTGGAAGACATAATCCCACGCTTCCTATGGA >EAS1_93:4:325:352:67 ATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAA >EAS1_93:4:325:352:67 TACAGAGCAACTAGGTAAAAAATTAACATTACAAC >EAS1_93:5:197:52:58 AAATGAACAGAGCTTTCAAGAAGTATGAGATTATG >EAS1_93:5:197:52:58 TCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGA >EAS1_93:5:246:177:525 CATCATAAATACACACAAAAGTAAAAAACTCACAG >EAS1_93:5:246:177:525 TCTTAAAGAAAAAAAAACCTGTCAAACACGAATGT >EAS1_93:5:256:444:399 CTGCTACTCAATATATCCATGTAACAAATCTGCGC >EAS1_93:5:256:444:399 GAAGATATAACCATCCTACTAAATACATATGCACC >EAS1_93:5:292:122:666 GGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTG >EAS1_93:5:292:122:666 TACTGTCATAACTATGAAGAGACTATTGTCAGATG >EAS1_93:5:62:969:12 TATAAAGGAAATCCCATCAGAATAACAATGGGCTT >EAS1_93:5:62:969:12 TCTTGCTAGAGATTTAGACATCTAAATGAAAGAGG >EAS1_93:5:66:372:343 ATTACAAAATATAGTTGAAAGATCTAACAATAGAC >EAS1_93:5:66:372:343 TATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGG >EAS1_93:6:132:717:233 AGAGAACTTCCCTGGAGGTCTGATGGAGTTTCTCC >EAS1_93:6:132:717:233 TGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGA >EAS1_93:6:159:273:253 TTAGTCTTGCTAGAGATTTAGACATCTAAATGAAA >EAS1_93:6:191:948:257 AACTAATATTTGTCTGAGCAAAACAGTCTAGATGA >EAS1_93:6:191:948:257 CTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGAT >EAS1_93:6:216:47:302 AAAAAAAAACCTGTCAAACACGAATGTTATGCCCT >EAS1_93:6:216:47:302 AATACTCACCATCATAAATACACACAAAAGTACAA >EAS1_93:6:218:144:794 GGGTGCATTGCTATGTTGCGGTCGCTTTGCCTCCT >EAS1_93:6:218:144:794 TTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTT >EAS1_93:6:238:514:194 AAACTATTTGAGGAAGTAATTGGGGAAAACCTCTT >EAS1_93:6:238:514:194 AATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGA >EAS1_93:6:255:441:47 AACAACAGTAAAATAAAACAAAGGAGGTCATCATA >EAS1_93:6:255:441:47 TGGTACAATGTACAATATTCTGATGATGGTTACAC >EAS1_93:6:271:244:568 ATGGACCTGTGATATCTGGATTCTGGGAAATTCTT >EAS1_93:6:271:244:568 CTTGCAACAACCTTGAGAACCCCAGGGAATTTGTC >EAS1_93:6:45:601:439 AATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAG >EAS1_93:6:45:601:439 ATAAAAAGGGATTAAATTCCCCCACTTAAGAGATA >EAS1_93:7:14:426:613 AGGGAGGGAGGGAAGAGGGACGCTGAAGAACTTTG >EAS1_93:7:14:426:613 GTAATGAAAACTATATTTATGCTATTCAGTTCTAA >EAS1_93:7:252:171:323 GCTATTCAGTTCTAAATATAGAAATTGAAACAGCT >EAS1_93:7:270:995:918 AAAATTCATTTAAGAAATTACAAAATATAGTTGAA >EAS1_93:7:319:280:57 AAAGGAAATCCCATCAGAATAACAATGGGCTTCTC >EAS1_93:7:319:280:57 TGCTAGAGATTTAGACATCTAAATGAAAGAGGCTC >EAS1_93:8:13:325:483 AAAAACATGAACTAACTATATGCTGTTTACAAGAA >EAS1_93:8:13:325:483 ATCATACAATGATAAAAAGATCAATTCAGCAAGAA >EAS1_93:8:14:601:624 AAAAGGTGATGTGTGTTCTCATCAACCTCATACAC >EAS1_93:8:14:601:624 CTGCGCTCTCATTCACTCCAGCTCCCTGTCAACCC >EAS1_95:1:16:823:343 AGACATAACCCCACGCTTCCTATGGAAAGGTTGTT >EAS1_95:1:16:823:343 TCCCATCTGGCCTCGTCCACACTGGTTCTCTTGAA >EAS1_95:1:196:533:921 AAATGTGTTTATTACCAGAGGGATGGAGGGAAGAG >EAS1_95:1:196:533:921 CCTGAGAGATTCTGCAGCCCAGATCCAGATTGCTT >EAS1_95:1:202:341:984 GGAGGTCATCATACAATGATAAAAAGATCAATTCA >EAS1_95:1:202:341:984 TGAACTAACTATATGCTGTTTACAAGAAACTCATT >EAS1_95:1:249:986:224 CTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGAT >EAS1_95:1:249:986:224 TATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGA >EAS1_95:1:261:504:780 TCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGTT >EAS1_95:1:261:504:780 TTTGTCTGAGAAAAACAGTCTAGATGAGAGAGAAC >EAS1_95:1:301:54:240 AACAGGGAGGTGCACTAATGCGCTCCACGCCCAAG >EAS1_95:1:301:54:240 CCCTGCAATTAATATAATTGTGTCCATGTACACAC >EAS1_95:1:77:589:741 AGTAAAATAAAACAAAGGAGGTCATCATACAATGA >EAS1_95:1:77:589:741 TGGTTACACTAAAAGCCCATACTTTACTGCTACTC >EAS1_95:2:142:353:398 CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA >EAS1_95:2:142:353:398 GGTAAAAAATTAACATTACAACAGGAACAAAACCT >EAS1_95:2:162:503:769 AGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTT >EAS1_95:2:162:503:769 AGGCTGCAACTGTGAGCCATCACAATGAACAACAG >EAS1_95:2:198:691:595 ACACACATGGTTTAGGGGTATAATACCTCTACATG >EAS1_95:2:198:691:595 CATGAAGCACTGAACTTCCACGTCTCATCTAGGGG >EAS1_95:2:211:954:174 AAAGAAAAAACAAAAACTATGCTAAGTATTGGTAA >EAS1_95:2:211:954:174 AGACCTAAGAGGGATGAGAAATTACCTAATTGGTA >EAS1_95:2:228:915:631 AAGATATGTAGTCATCAGACTATCTAAAGTCAACA >EAS1_95:2:228:915:631 ATTATTAAAGAAAAAAAAACCTGTCAAACACGAAT >EAS1_95:2:278:918:892 AGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCT >EAS1_95:2:278:918:892 CCATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAA >EAS1_95:2:40:918:950 AATATAATTGTGTCCATGTACACACGCTTTCCTTT >EAS1_95:2:40:918:950 GTTCTCTTGAAAGCTTGGGCTGTAATGATGCCCCT >EAS1_95:3:268:523:511 ACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGAT >EAS1_95:3:268:523:511 TGTCCATGTACACACGCTGTCCTATGTACTTATCA >EAS1_95:3:303:970:243 AACCTGTCAAACACGAATGTTATGCCCTGCTAAAC >EAS1_95:3:303:970:243 CAGACTTCATCAAGATATGTAGTCATCAGACTATC >EAS1_95:3:308:956:873 ATAAAAATAAGTGTGTCCATGTACACACGCTGTCC >EAS1_95:3:308:956:873 CTCATCTAGGGGAACAGGGAGGTGCACTAATGCGC >EAS1_95:4:174:157:573 CAGAAACCAAATGAGAGAAGGAGTAGCTATACTTA >EAS1_95:4:174:157:573 TAAAACAAATACTACTAGACCTAAGAGGGATGAGA >EAS1_95:4:176:971:874 TAAAATCAGAAGAGAAAAGCATACAGTCATCTATA >EAS1_95:4:176:971:874 TGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTG >EAS1_95:4:184:17:636 TACACACACATGGTTTAGGGGTATAATACCTCTAC >EAS1_95:4:184:17:636 TTTTTTTTTTTTTTTTTTTTTTTTTTTTCACAGGT >EAS1_95:4:224:592:744 GATATGTAGTCATCAGACTATCTAAAGTCAACATG >EAS1_95:4:224:592:744 TATGAGATTATGTAAAGTAACTGAACCTATGAGTC >EAS1_95:4:238:124:196 TTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTT >EAS1_95:4:61:631:567 AAGAAGATATAACCATCCTACTAAATACATATGCA >EAS1_95:4:61:631:567 CATTAATAAAGACATGAGTTCAGGTAAAGGGGTGG >EAS1_95:4:66:179:118 CCATGTACACACGCTGTCCTATGTACTTATCATGA >EAS1_95:4:66:179:118 TGGGCTGTAATGATGCCCCTTGGCCATCACCCAGT >EAS1_95:4:71:517:742 AACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT >EAS1_95:4:71:517:742 AAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAG >EAS1_95:5:257:654:116 TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT >EAS1_95:5:257:654:116 TCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAA >EAS1_95:5:263:511:936 CAAATAGGTAAAAAATTAACATTACAACAGGAACA >EAS1_95:5:263:511:936 CAAGTCTTTCCTGACAAGCAAATGCTAAGATAATT >EAS1_95:5:284:212:932 CTTTAAATCAACAACAATAAAAAAAAACAAAGGAG >EAS1_95:5:284:212:932 TGATGATGGTTACGCTAAAAGTCCATGCTTTACTG >EAS1_95:6:174:650:125 AAGCATCATAAATGAAGGGGAAATAAAGTCAAGTC >EAS1_95:6:174:650:125 CAGGTTTTATAAAACAATTAATTGAGACTACAGAG >EAS1_95:6:185:312:167 CTGAAGAACTTTGATGCCCTCTTCTTCCAAAGATG >EAS1_95:6:185:312:167 TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT >EAS1_95:6:194:696:490 ACATTAATACTATGTTTCTTATCTGCACATTACTA >EAS1_95:6:194:696:490 TTCCACGTCTCATCTAGGGGAACAGGGAGGTGCAC >EAS1_95:6:53:156:845 ACACCCAACTAATATTTGTCTGAGCAAAACAGTCT >EAS1_95:6:53:156:845 TTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTCT >EAS1_95:6:87:734:888 ATACCATCCCTGTCTTACTTCCAGCTCCCCAGAGG >EAS1_95:6:87:734:888 TGCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTG >EAS1_95:7:155:530:532 AGCAAGAAGATATAACCATCCTACTAAATACATAT >EAS1_95:7:155:530:532 TGCGCTTGTACTTCTAAATCTATAACAAAATTAAA >EAS1_95:7:280:607:113 ATCCATGTAACAAATCTGCGCTTGTACTTCTAAAT >EAS1_95:7:280:607:113 GGAGTATAAATTGTTTTCCACTTTGGAAAACAATT >EAS1_95:7:282:817:710 TGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCC >EAS1_95:7:282:817:710 TTTGTAATGAAAACTATATTTATGCTATTCAGTTC >EAS1_95:7:310:800:761 AAAGCACACTTTAAATCAACAACAGTAAAATAAAA >EAS1_95:7:310:800:761 CAATATTCTGATGATGGTTACACTAAAAGCCCATA >EAS1_95:7:46:522:426 AAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGA >EAS1_95:7:46:522:426 GGTAAAAAATTAACATTACAACAGGAACAAAACCT >EAS1_95:7:55:506:125 CTTTACTGTCATAACTATGAAGAGACTACTGCCAG >EAS1_95:7:55:506:125 TCTACCACAGGGGGCTGCGCGGTTTCCCATCATGA >EAS1_95:7:61:702:720 ATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAA >EAS1_95:7:61:702:720 CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC >EAS1_95:7:74:866:49 CATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTC >EAS1_95:7:74:866:49 CCAACCTACTAAATACATATGCACCTAACACAAGA >EAS1_97:2:128:629:484 AAAAAAGTAAATAAAACACATAGCTAAAACTAAAA >EAS1_97:2:128:629:484 GATTCATAAAACAAATACTACTAGACCTAAGAGGG >EAS1_97:2:193:420:78 ATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTG >EAS1_97:2:193:420:78 TTGAGACTACAGAGCAACTAGGTAAAAAATTAACA >EAS1_97:2:59:882:980 AATATAATTGTGTCCATGTACACACGCTGTCCTAT >EAS1_97:2:59:882:980 GGGCTGTAATGATGCCCCTTGGCCATCACCCGGTC >EAS1_97:2:96:419:327 TACTAAATACATATGCACCTAACACAAGACTACCC >EAS1_97:2:96:419:327 TCTAAATCTATAACAAAATTAAAATTTAACAAAAG >EAS1_97:2:9:203:653 CACCCAACTAATATTTGTCTGAGCAAAACAGTCTA >EAS1_97:2:9:203:653 TCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTT >EAS1_97:3:147:423:584 GAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAG >EAS1_97:3:147:423:584 GCATACAGTCATCTATAAAGGAAATCCCATCAGAA >EAS1_97:3:160:173:889 TATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAA >EAS1_97:3:160:173:889 TCAAGATATGTAGTCATCAGACTATCTAAAGTCAA >EAS1_97:3:277:144:848 TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT >EAS1_97:3:277:144:848 TATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGG >EAS1_97:3:73:292:429 GAAAGCTTTCAACGCTTCTAGCCATTTCTTTTTGC >EAS1_97:3:73:292:429 TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG >EAS1_97:4:261:267:597 GGGTAATAAAGTCAAGTCTTTCCTGACAAGCAAAT >EAS1_97:4:261:267:597 TTGAGAATAAAGAGCAACTAGGTAAAAAATTAACA >EAS1_97:4:274:287:423 CTAAATCTATAAAAAAATTAAAATTTAACAAAAGT >EAS1_97:4:274:287:423 TTTTTTTTTTTTTTTTTCTCTTTTTTTTTTTTTTT >EAS1_97:4:290:121:79 ATTGGTAAAGATGTGGGGAAAAAAGTAAACTCTCA >EAS1_97:4:290:121:79 TGATGATGGTTACACTAAAAGCCCATACTTTACTG >EAS1_97:4:77:29:126 ACAGGGAATTTGTCAATGTCAGGGAAGGAGCATTT >EAS1_97:4:77:29:126 GCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCT >EAS1_97:4:83:731:540 CTAGGTAAAAAATTAACATTACAACAGGAACAAAA >EAS1_97:4:83:731:540 TAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAG >EAS1_97:5:154:952:558 AAAGACTACCCAGATTCATAAAACAAATACTACTA >EAS1_97:5:154:952:558 GCAAACAGAAACCAAATGAGAGAAGGAGTAGCTAT >EAS1_97:5:219:174:684 AAAAAAACTGTCAAACACGAATGTTATGCCCTGCT >EAS1_97:5:219:174:684 AGTCATCAGACTATCTAAAGTCAACATGAAGGAAA >EAS1_97:5:28:538:148 AAAAAAAAACCTGTCAAACACGAATGTTATGCCCT >EAS1_97:5:28:538:148 TCATCAAGATATGTAGTCATCAGACTATCTAAAGT >EAS1_97:5:318:177:383 TACTACCCTGCAATTAATATAATTGTGTCCATGTA >EAS1_97:5:318:177:383 TCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGC >EAS1_97:5:84:927:843 CCAGCATGGTTGTACTGGGCAATACATGAGATTAT >EAS1_97:5:84:927:843 TTACGTCCTATCTTCTTCTTAGGGAAGAACAGCTT >EAS1_97:6:222:305:337 TTTTTTTTTTTTTTTTTTCCCTTTTTTTTTTTTTT >EAS1_97:6:308:667:658 AAAGATCACTTCAGCAATAAGATATAACCATCCTA >EAS1_97:6:308:667:658 TAAAAACATGAACTAACTATATCCTTCTTACAATA >EAS1_97:6:93:334:858 CTGCCCCCAGCATGGTTGTACTTGGCAATACATGA >EAS1_97:6:93:334:858 GTACTTATCATGACTCTATCCCAAATTCCCAATTA >EAS1_97:7:20:979:96 GAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCA >EAS1_97:7:264:642:506 AAATATAGAAATTGAAACAGCTGTGTTTATTGTAT >EAS1_97:7:264:642:506 ACTTCATCCAAAGATGAAACGCGTAACTGCGCTCT >EAS1_97:7:28:979:519 AAAAAGTAAACTCTCAAATATTGCTAGTGGGAGTA >EAS1_97:7:28:979:519 CCCATACTTTACTGCTACTCAATATATCCATGTAA >EAS1_97:7:63:727:203 AAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGA >EAS1_97:7:63:727:203 AGTCTCTTATGAATTAACCCAGTCAGACAAAAATA >EAS1_97:7:9:648:712 AAGAAGTATGAGATTATGTAAAGTAACTGAACCTA >EAS1_97:7:9:648:712 TACATTGCAAGACAGACTTCATCAAGATATGTAGT >EAS1_97:8:36:927:478 AAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATC >EAS1_97:8:36:927:478 GACCCTACACGAATGCGTCTCTACCACAGGGGGCT >EAS1_99:1:17:595:863 AAGCTACTCAATATATCCATGTAACAAATCTGCGC >EAS1_99:1:17:595:863 ATAACCATCCTACTAAATACACATGCACCTAACTC >EAS1_99:1:187:715:521 AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT >EAS1_99:1:187:715:521 GCATACAGTCATCTATAAAGGAAATCCCATCAGAA >EAS1_99:1:34:649:318 AAGAATAACAATGGGCTTCACAGCGGAACCCTTAC >EAS1_99:1:34:649:318 ATGAAAGAGGCTCAAAGAATGCCAGGAAGATACAT >EAS1_99:1:86:871:319 GGCTTCTCAGCGGAAACCTTACAAGCCAGAAGAGA >EAS1_99:1:86:871:319 TGCTAAGATAATTCATCATCACTAAACCAGTCCTA >EAS1_99:2:152:355:962 CAGTCATCTATAAAGGAAATCCCATCAGAATAACA >EAS1_99:2:152:355:962 TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT >EAS1_99:2:162:257:203 AAAAAGATCAATTCAGCAAGAAGATATAACCATCC >EAS1_99:2:162:257:203 ATATCCATGTAACAAATCTGCGCTTGTACTTCTAA >EAS1_99:2:188:782:483 CTAAAATCAGCAAGAGAAAAGCATACAGTCATCTA >EAS1_99:2:188:782:483 GAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAG >EAS1_99:3:118:851:285 CCCAATTACGTCCTATCTTCTTCTTAGGGAAGAAC >EAS1_99:3:118:851:285 TGGGCAATACATGAGATTATTAGGAAATGCTTTAC >EAS1_99:3:135:543:760 ATTTGCCTTCAGACCCTACACGAATGCGTCTCTAC >EAS1_99:3:135:543:760 TTCAAAAGGTGATGTGTGTTCTCATCAACCTCATA >EAS1_99:3:187:791:153 AATACATGAGATTATTAGGAAATGCTTTACTGTCA >EAS1_99:3:187:791:153 TACACGAATGCGTCTCTACCACAGGGGGCTGCGCG >EAS1_99:3:21:423:169 ACTAAAAGCCCATACTTTACTGCTACTCAATATAT >EAS1_99:3:21:423:169 GGAGTATAAATTGTTTTCCACTTTGGAAAACAATT >EAS1_99:3:61:183:767 GTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATC >EAS1_99:3:61:183:767 TTGCCAGATGAACCACACCTTAATACTATGTTTCT >EAS1_99:5:147:479:41 CTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTT >EAS1_99:5:147:479:41 TACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTA >EAS1_99:5:191:885:623 TGCAAGACAGACTTCATCAAGATATGTAGTCATCA >EAS1_99:5:191:885:623 TTAAAGAAAAAAAAACCTGTCAAACACGAATGTTA >EAS1_99:6:135:354:66 GATACATTGCAAGACAGACTTCATCAAGATATGTA >EAS1_99:6:135:354:66 TATGAGATTATGTAAAGTAACTGAACCTATGAGTC >EAS1_99:6:177:562:806 ACAGTGTAGATGAGAGAGACCTTCCCTGGAGGTCT >EAS1_99:6:177:562:806 TGATTTACTTGTTGTTGGTTTTCTGTTTCTTTTTT >EAS1_99:6:181:392:500 GGAAATCCCATCAGAATAACAATGGGCTTCTCAGC >EAS1_99:6:181:392:500 TTAGTCTTGCTAGAGATTTAGACATCTAAATGAAA >EAS1_99:6:63:48:631 CAATACATGAGATTATTAGGAAATGCTTTACTGTC >EAS1_99:6:63:48:631 TCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTA >EAS1_99:7:126:361:250 AAAAAATTAACATTACAACAGGAACAAAACCTCAT >EAS1_99:7:126:361:250 TCTACGCAAACAGAAACCAAATGAGAGAAGGAGTA >EAS1_99:7:171:196:287 ATAACAATGGGCTTCTCAGCAGAAACCTTACAAGC >EAS1_99:7:171:196:287 ATAATTCATCATCACTAAACCAGTCCTATAAGAAA >EAS1_99:7:183:645:699 GTGGCCCTCCCCCATTCCCTGCCCCATCTCTTGTA >EAS1_99:7:183:645:699 TATCCCAAATTCCCAATTACGTCCTATCTTCTTCT >EAS1_99:7:37:400:627 ACATGAGATTATTAGGAAATGCTTTACTGTCATAA >EAS1_99:7:37:400:627 TCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTG >EAS1_99:8:117:578:853 AATGAACTTCTGTAATTGAAAAATTCATTTAAGAA >EAS1_99:8:152:778:228 ATCATAAATACACACAAAAGTACAAAACTCACAGG >EAS1_99:8:152:778:228 ATTTAAAAACATGAACTAACTATATGCTGTTTACA >EAS1_99:8:187:199:369 TGAAAGAGGCTCAAAGAATGCCAGGAAGATACATT >EAS1_99:8:27:228:31 AAATAAAACAAAGGAGGTCATCATACAATGATAAA >EAS1_99:8:27:228:31 GGTTACACTAAAAGCCCATACTTTACTGCTACTCA >EAS1_99:8:99:756:130 GAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCT >EAS1_99:8:99:756:130 GACCCTACACGAATGCGTCTCTACCACAGGGGGCT >EAS218_1:2:10:686:1024 ACAAGAAACTCATTAATAAAGACATGAGTTCAGGT >EAS218_1:2:10:686:1024 CATACAATGATAAAAAGATCAATTCAGCAAGAAGA >EAS218_1:2:15:1763:1143 AAACAAATACTACTAGACCTAAGAGGGATGAGAAA >EAS218_1:2:15:1763:1143 TGAGAGAAGGAGTAGCTATACTTATATCAGATAAA >EAS218_1:2:18:1498:1475 CTTGGGCTGTAATGATGCCCCTTGGCCATCACCCG >EAS218_1:2:18:1498:1475 GAAAGGTTGTTGGGAGATTTTTAATGATTCCTCAA >EAS218_1:2:19:752:816 CGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTG >EAS218_1:2:19:752:816 TTTGGTGGAAGACATAATCCCACGCTTCCTATGGA >EAS218_1:2:26:211:481 ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA >EAS218_1:2:26:211:481 CACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAA >EAS218_1:2:40:1291:1045 CTAACACAAGACTACCCAGATTCATAAAACAAATA >EAS218_1:2:40:1291:1045 GTAAAGGGGTGGAAAAAGATGTTCTACGCAACAAG >EAS218_1:2:64:1318:1711 GGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTT >EAS218_1:2:64:1318:1711 TGAAAACTATATTTATGCTATTCAGTTCTAAATAT >EAS218_1:4:14:1872:1521 TCAAAGAATGCCAGGAAGATACATTGCAAGTCAGA >EAS218_1:4:14:1872:1521 TCATCAAAAACCTTACAAGCCAGAAGAGATTGGAT >EAS218_1:4:15:856:340 CACGCTGTCCTATGTACTTATCATGACTCTATCCC >EAS218_1:4:15:856:340 CCCCAGCATGGTTGCACTGGGCAATACATGAGATT >EAS218_1:4:28:315:310 AAACTGTTCTCTTGAAAGCTTGGGCTGTAATGATG >EAS218_1:4:28:315:310 CATGTACACACGCTGTCCTATGTACTTATCATGAC >EAS218_1:4:37:1626:862 ACCCAACTAATATTTGTCTGAGCAAAACAGTCTAG >EAS218_1:4:37:1626:862 TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCT >EAS218_1:4:61:1369:440 AAAGACATGATTTCAGGTAAAGGGGTGGAAAAAGA >EAS218_1:4:61:1369:440 CAGGTTTTATAAAACAATTAATTGAGACTACAGAG >EAS218_1:4:62:561:531 AGCTATACTTATATCAGATAAAGCACACTTTAAAT >EAS218_1:4:62:561:531 TACTAGACCTAAGAGGGATGAGAAATTACCTAATT >EAS218_1:4:71:832:743 ACCCAGTCCCTGCCCCATCTCTTGTAATCTCTCTC >EAS218_1:4:71:832:743 CTATGTACTTATCATGACTCTATCCCAAATTCCCA >EAS218_1:4:73:42:1038 AAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGT >EAS218_1:4:73:42:1038 TCTGTCTTGATTTACTTGTTGTTGGTTTTCTGTTT >EAS218_1:4:75:555:1591 TGAACTTCTGTAATTGAAAAATTCATTTAAGAAAT >EAS218_1:6:49:905:27 CCACAGGGGGCTGCGCGGTTTCCCATCCTGAAGCA >EAS218_1:6:49:905:27 GAAGAGACTATTGCCAGTTGAACCACACATTAATA >EAS218_1:6:66:1282:1215 GTGATGTGTGTTCTCATCAACCTCATACACACACA >EAS218_1:6:66:1282:1215 TTCAGACCCTACACGAATGCGTCTCTACCACAGGG >EAS218_1:6:77:1529:522 AAAACCTGTCAAACACGAATGTTATGCCCTGCTAA >EAS218_1:6:77:1529:522 AAAGTTCAATACTCACCATCATAAATACACACAAA >EAS218_1:6:88:1413:14 AATGAAAGAGGCTCAAAGAATGCCAGGAAGATACA >EAS218_1:8:13:1729:1844 ATGAACTTCTGTAATTGAAAAATTCATTTAAGAAA >EAS218_1:8:16:1081:1894 AAGGTGATGTGTGTTCTCATCAACCTCATACACAC >EAS218_1:8:16:1081:1894 AGATGAAACGCGTAACTGGGCTCTCATTCACTCCA >EAS218_1:8:26:785:882 CAGTTTCTGCCCCAAGCATGGTTGTACTGGGCAAT >EAS218_1:8:26:785:882 TACTTATCATGACTCTATCCCAAATTCCCAATTAC >EAS218_1:8:61:1797:113 CAGATAGCTTGTGGTCTGACAGGCTGCAACTGTGA >EAS218_1:8:61:1797:113 GGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGA >EAS218_1:8:70:445:1289 CTAATTTTTGGACTTCTTAAAGAAAAAAAAACCTG >EAS218_1:8:70:445:1289 GAATTGTAAAAGTCAAAATTAAAGTTCAATACTCA >EAS218_1:8:82:1540:77 ATTGAGACTACAGAGCAACTAGGTAAAAAATTAAC >EAS218_1:8:82:1540:77 GAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGC >EAS218_1:8:90:706:1276 AATTAACATTACAACAGGAACAAAACCTCATATAT >EAS218_1:8:90:706:1276 GTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAG >EAS218_4:1:34:1614:558 CAACATGAAGGAAAAAAATTCTAAAATCAGCAAGA >EAS218_4:1:34:1614:558 GTCAAACACGAATGTTATGCCCTGCTAAACTAAGC >EAS218_4:1:48:9:409 CAGCTCCCTGTCACCCAATGGACCTGTGATATCTG >EAS218_4:1:48:9:409 GTTTAGTGCCTTTGTTCACATAGACCCCCTTGCAA >EAS218_4:1:84:1505:1037 GTCAACATGAAGGAAAAAAATTCTAAAATCAGCAA >EAS218_4:1:84:1505:1037 TGCCCTGCTAAACTAAGCATCATAAATGAAGGGGA >EAS218_4:1:9:206:901 AGTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGA >EAS218_4:1:9:206:901 CTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTC >EAS218_4:3:12:630:707 ATTTAAAAACATGAACTAACTATATGCTGTTTACA >EAS218_4:3:12:630:707 CACAAAAGTACAAAACTCACAGGTTTTATAAAACA >EAS218_4:3:39:1671:1928 AGCCCATACTTTACTGCTACTCAATATATCCATGT >EAS218_4:3:39:1671:1928 CAAATATTGCTAGTGGGAGTATAAATTGTTTTCCA >EAS218_4:3:41:1281:1785 ACTATCTAAAGTCAACATGAAGGAAAAAAATTCTA >EAS218_4:3:41:1281:1785 GGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTAT >EAS218_4:3:65:85:1547 AAATCAGCAAGAGAAAAGCATACAGTCATCTATAA >EAS218_4:3:65:85:1547 GTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAA >EAS218_4:5:41:118:1246 ACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAA >EAS218_4:5:41:118:1246 CTCCAGATTGCTTGTGGTCTGACAGGCTGCAACTG >EAS218_4:5:63:875:1339 CCCCAGATACCATCCCTGTCTTACTTCCAGCTCCC >EAS218_4:5:63:875:1339 GGGAACAGGGAGGTGCACTAATGCGCTCCACGCCC >EAS218_4:7:71:31:1973 AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGC >EAS218_4:7:72:1288:1211 ATTGGTACAATGTACAATATTCTGATGATGGTTAC >EAS218_4:7:72:1288:1211 GATAAAGCACACTTTAAATCAACAACAGTAAAATA >EAS218_4:7:85:923:726 ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA >EAS218_4:7:85:923:726 GTAAAGTAACTGAACCTATGAGTCACAGGTATTCC >EAS218_4:7:87:964:826 CACAGGGGGCTGCGCGGTTTCCCATCATGAAGCAC >EAS218_4:7:87:964:826 TGAAGAGACTATTGCCAGATGAACCACACATTAAT >EAS218_4:7:89:1487:520 CACGAATGCGTCTCTACCACAGGGGGCTGCGCGGT >EAS218_4:7:89:1487:520 TATGAAGAGACTATTGCCAGATGAACCACACATTA >EAS218_4:7:90:1873:89 GAGATTCTGCAGCCCAGATCCAGATTGCTTGTGGT >EAS218_4:7:90:1873:89 GCATTTTGTCAGTTACCAAATGTGTTTATTACCAG >EAS219_1:1:22:490:2011 ATAACAATGGGCTTCTCAGCGGAAACCTTACAAGC >EAS219_1:1:22:490:2011 GCTAGAGATTTAGACATCTAAATGAAAGAGGCTCA >EAS219_1:1:37:1004:1136 CCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTT >EAS219_1:1:37:1004:1136 GTCACCCAATGGACCTGTGATATCTGGATTCTGGG >EAS219_1:1:44:1466:425 GTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGG >EAS219_1:1:44:1466:425 TTATCTGCACATTACTACCCTGCAATTAATATAAT >EAS219_1:1:50:257:341 AAATTAACATTACAACAGGAACAAAACCTCATATA >EAS219_1:1:50:257:341 TGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTA >EAS219_1:1:5:497:687 AAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTC >EAS219_1:1:5:497:687 TTGCCTTCAGACCCTACACGAATGCGTCTCTACCA >EAS219_1:1:60:1420:660 AATGCTAAGATAATTCATCATCACTAAACCAGTCC >EAS219_1:1:60:1420:660 GTAAAAAATTAACATTACAACAGGAACAAAACCTC >EAS219_1:1:63:28:1549 AAAAAGTAAACTCTCAAATATTGCTAGTGGGAGTA >EAS219_1:1:63:28:1549 TACAATATTCTGATGATGGTTACACTAAAAGCCCA >EAS219_1:1:67:191:668 ACTATGAAGAGACTATTGCCAGATGAACCACACCT >EAS219_1:1:67:191:668 CCAATTACGTCCTATCTTCTTCTTAGGGAAGAACA >EAS219_1:3:11:706:1030 ATCTCTTGTAATCTCTCTCATCTTTGCTGCATCCC >EAS219_1:3:11:706:1030 ATGTCTATTTTTGTCTTGACACCCAACTAATATTT >EAS219_1:3:33:1168:1762 AGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAG >EAS219_1:3:33:1168:1762 GTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCA >EAS219_1:3:4:1620:413 CATCACAATGAACAACAGGAAGAAAAGGTCTTTCA >EAS219_1:3:4:1620:413 TCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCC >EAS219_1:3:62:603:1552 AATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGT >EAS219_1:3:62:603:1552 GAACCACACATTAATACTATGTTTCTTATCTGCAC >EAS219_1:3:88:465:1877 AAAGCACACTTTAAATCAACAACAGTAAAATAAAA >EAS219_1:3:88:465:1877 TAAGAGGGATGAGAAATTACCTAATTGGTACAATG >EAS219_1:3:90:219:528 ACGAATGTTATGCCCTGCTAAACTAAGCATCATAA >EAS219_1:3:90:219:528 GTACAAAACTCACAGGTTTTATAAAACAATTAATT >EAS219_1:5:5:259:250 GTCTCTTATGAATTAACCCAGTCAGACAAAAATAA >EAS219_1:5:5:259:250 TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT >EAS219_1:5:6:1067:91 CTTGACACCCAACTAATATTTGTCTGAGCAAAACA >EAS219_1:5:6:1067:91 CTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGAT >EAS219_1:7:16:1343:1621 AAATTCTAAAATCAGCAAGAGAAAAGCATACAGTC >EAS219_1:7:16:1343:1621 AAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTA >EAS219_1:7:18:571:1110 GAGGTGCACTAATGCGCTCCACGCCCAAGCCCTTC >EAS219_1:7:18:571:1110 TAATATAATTGTGTCCATGTACACACGCTGTCCTA >EAS219_1:7:20:1444:328 AAAAGATGTTCTACGCAAACAGAAACCAAATGAGA >EAS219_1:7:20:1444:328 TACTAAATACATATGCACCTAACACAAGACTACCC >EAS219_1:7:35:392:2042 ATAAATCTATAAAAAAATTAAAATTTAACAAAAGT >EAS219_1:7:35:392:2042 TAACACAAGACTACCCAGATTCATAAAACNAATAC >EAS219_1:7:50:1339:1154 CATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCC >EAS219_1:7:50:1339:1154 GTCTTGACACCCAACTAATATTTGTCTGAGCAAAA >EAS219_1:7:62:1076:540 CCCCCACTTAAGAGATATAGATTGGCAGAACAGAT >EAS219_1:7:62:1076:540 TAAATCAACAACAGTAAAATAAAACAAAGGAGGTC >EAS219_1:7:94:1655:1921 AAAAGCATACAGTCATCTATAAAGGAAATCCCATC >EAS219_1:7:94:1655:1921 TTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAA >EAS219_FC30151:1:18:1418:237 CCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGG >EAS219_FC30151:1:18:1418:237 CTGGGAAATTCTTCATCCTGGACCCTGAGAGATTC >EAS219_FC30151:1:53:140:421 AACCAAATGAGAGAAGGAGTAGCTATACTTATATC >EAS219_FC30151:1:53:140:421 GATTCATAAAACAAATACTACTAGACCTAAGAGGG >EAS219_FC30151:1:54:436:1452 AAGACAAGTCTCTTATGAATTAACCCAGTCAGACA >EAS219_FC30151:1:54:436:1452 AGGAAGTAATTGGGGAAAACCTCTTTAGTCTTGCT >EAS219_FC30151:1:55:8:1412 ATATAATTGTGTCCATGTACACACGCTGTCCTATG >EAS219_FC30151:1:55:8:1412 GCCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCAT >EAS219_FC30151:1:76:34:691 ATATATCAATATTAACTTTGAATAAAAAGGGATTA >EAS219_FC30151:1:88:1454:418 CCAGGAAGATACATTGCAAGACAGACTTCATCAAG >EAS219_FC30151:1:88:1454:418 GAAGAGATTGGATCTAATTTTTGGACTTCTTAAAG >EAS219_FC30151:3:13:674:1717 AGAAAAGCATGCAGTCATCTATAAAGGAAATCCCA >EAS219_FC30151:3:13:674:1717 TAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAG >EAS219_FC30151:3:40:1128:1940 CCCCTTACAACAACCTTGAGAACCCCAGGGAATTT >EAS219_FC30151:3:40:1128:1940 CCGAGTCACGGGGTTGCCAGCACAGGGGCTTAACC >EAS219_FC30151:3:55:74:1040 CTACCACAGGGGGCTGCGCGGTTTCCCATCATGAA >EAS219_FC30151:3:55:74:1040 GGAAATGCTTTACTGTCATAACTATGAAGAGACTA >EAS219_FC30151:3:73:1458:1337 AAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGAC >EAS219_FC30151:3:73:1458:1337 AGGTAAAAAATTAACATTACAACAGGAACAAAACC >EAS219_FC30151:3:81:1723:1820 ATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTT >EAS219_FC30151:3:81:1723:1820 CATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTG >EAS219_FC30151:3:90:1906:1528 CACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAA >EAS219_FC30151:3:90:1906:1528 TTACAAAATATAGTTGAAAGCTCTAACAATAGACT >EAS219_FC30151:3:9:1595:1826 ACTAATATTTGTCTGAGCAAAACAGTCTAGATGAG >EAS219_FC30151:3:9:1595:1826 ATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCCTC >EAS219_FC30151:5:29:817:854 AGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTG >EAS219_FC30151:5:29:817:854 GTTCTCAAGGTTGTTGCAAGGGGGTTTATGTGAAC >EAS219_FC30151:5:54:1351:910 ACTAAAAGCCCATACTTTACTGCTACTCAATATAT >EAS219_FC30151:5:54:1351:910 ACTCTCAAATATTGCTAGTGGGAGTATAAATTGTT >EAS219_FC30151:5:63:424:1643 GACCCTACACGAATGCGTCTCTACCACAGGGGGCT >EAS219_FC30151:5:63:424:1643 GGTCTTTCAAAAGGTGATGTGTGTTCTCATCAACC >EAS219_FC30151:5:6:1243:981 ATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAA >EAS219_FC30151:5:6:1243:981 TTACCTAGTTGCTCTGTAGTCTCAATTAATTGTTT >EAS219_FC30151:5:70:348:972 GAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTC >EAS219_FC30151:5:70:348:972 TCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTT >EAS219_FC30151:5:72:1426:1883 ACATAATCCCACGCTTCCTATGGAAAGGTTGTTGG >EAS219_FC30151:5:72:1426:1883 CATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGC >EAS219_FC30151:7:11:1261:1200 AAAAAAAACCTGTCAAACACGAATGTTATGCCCTG >EAS219_FC30151:7:11:1261:1200 TTGCAAGACAGACTTCATCAAGTTATGTAGTCATC >EAS219_FC30151:7:51:1429:1043 TATTTGTAATGAAAACTATATTTATGCTATTCAGT >EAS219_FC30151:7:87:1289:83 ACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGA >EAS219_FC30151:7:87:1289:83 ATGCCCTGCTAAACTAAGCATCATAAATGAAGGGG >EAS219_FC30151:7:94:1440:2016 AACCTGTCAAACACGAATGTTATGCCCTGCTAAAC >EAS219_FC30151:7:94:1440:2016 CACAAAAGTACAAAACTCACAGGTTTTATAAAACA >EAS220_1:2:11:1274:1230 TGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCT >EAS220_1:2:11:1274:1230 TTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT >EAS220_1:2:43:656:1866 TGAACTTCTGTAATTGAAAAATTCATTTAAGAAAT >EAS220_1:2:47:591:698 CAAATCTGCGCTTGTACTTCTAAATCTATAACAAA >EAS220_1:2:47:591:698 TCCTACTAAATACATATGCACCTAACACAAGACTA >EAS220_1:2:50:513:882 AAAACAAATACTACTAGACCTAAGAGGGATGAGAA >EAS220_1:2:50:513:882 GGAGTAGCTATACTTATATCAGATAAAGCACACTT >EAS220_1:2:52:1779:1664 CCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTG >EAS220_1:2:52:1779:1664 TGTTAAAATGTCTATTTTTGTCTTGACACCCAACT >EAS220_1:2:54:91:1232 AAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAG >EAS220_1:2:54:91:1232 AAAGCTCTAACAATAGACTAAACCAAGCAGAAGAA >EAS220_1:2:62:1109:804 TAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTCTA >EAS220_1:2:62:1109:804 TGTCAGTTACCAAATGTGTTTATTACCAGAGGGAT >EAS220_1:2:63:267:545 ATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTT >EAS220_1:2:63:267:545 CTTGATTTACTTGTTGTTGGTTTTCTGTTTCTTTG >EAS220_1:2:72:1809:1398 AATACATGAGATTATTAGGAAATGCTTTACTGTCA >EAS220_1:2:72:1809:1398 CTATCTTCTTCTTAGGGAAGAACAGCTTAGGTATC >EAS220_1:4:100:20:1199 AAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCA >EAS220_1:4:100:20:1199 CAGTCATCTATAAAGGAAATCCCATCAGAATAACA >EAS220_1:4:14:1665:1772 GGGCTGTAATGATGCCCCTTGGCCATCACCCGGTC >EAS220_1:4:14:1665:1772 TATAATGGTGTCCATGTACACACGCTGTCCTATGT >EAS220_1:4:46:1566:668 CTACTAAATACATATGCACCTAACACAAGACTACC >EAS220_1:4:46:1566:668 TTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAA >EAS220_1:4:69:88:1154 ATAACTATGAAGAGACTATTGCCAGATGAACCACA >EAS220_1:4:69:88:1154 CACGAATGCGTCTCTACCACAGGCGGCTGCGCGGT >EAS220_1:4:6:1178:1105 GATAATTCATCATCACTAAACCAGTCCTATAAGAA >EAS220_1:4:6:1178:1105 GGAACAAAACCTCATATATCAATATTAACTTTGAA >EAS220_1:4:70:766:2016 AAAAAAATTCTAAAATCAGCAAGAGAAAAGCATAC >EAS220_1:4:70:766:2016 ATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTG >EAS220_1:6:24:105:1046 AGATTCATAAAACAAATACTACTAGACCTAAGAGG >EAS220_1:6:24:105:1046 CATAGCTAAAACTAAAAAAGCAAAAACAAAAACTA >EAS220_1:6:7:1547:1933 AATATTTGACTGAGCAAAACAGTCTAGATGAGAGA >EAS220_1:6:7:1547:1933 CTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTG >EAS220_1:8:18:1757:95 ATGAGTCGCAGGTATTCCTGAGGAAAAAGAAAAAG >EAS220_1:8:18:1757:95 CTTCATCAAGATATGTAGTCATCAGACTATCTAAA >EAS220_1:8:33:672:473 ATGTCAGGGAAGGAGCATTTTGTCAGTTACCAAAT >EAS220_1:8:33:672:473 TCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCT >EAS220_1:8:38:1576:1923 CACAGGGGGCTGCGCGGTTTCCCATCATGAAGCAC >EAS220_1:8:38:1576:1923 CTGTCATAACTATGAAGAGACTATTGCCAGATGAA >EAS220_1:8:45:178:1321 AGGTTTTATAAAACAATTAATTGAGACTACAGAGC >EAS220_1:8:45:178:1321 CATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCT >EAS220_1:8:46:1528:799 ATGATAAAAAGATCAATTCAGCAAGAAGATATAAC >EAS220_1:8:46:1528:799 CATGTAACAAATCTGCGCTTGTACTTCTAAATCTA >EAS220_1:8:46:485:482 AGAGATTCTGCAGCCCAGATCCAGATTGCTTGTGG >EAS220_1:8:46:485:482 ATTACCAGAGGGATGAAGGGAAGAGGGACGCTGAA >EAS220_1:8:5:996:2000 AGTCAACATGAAGGAAAAAAATTCTAAAATCAGCA >EAS220_1:8:5:996:2000 CACGAATGTTATGCCCTGCTAAACTAAGCATCATA >EAS220_1:8:66:1046:167 ACAATGTACAATATTCTGATGATGGTTACACTAAA >EAS220_1:8:66:1046:167 ACACTTTAAATCAACAACAGTAAAATAAAACAAAG >EAS220_1:8:83:1456:1854 AAGATCAATTCAGCAAGAAGATATAACCATCCTAC >EAS220_1:8:83:1456:1854 AAGCCCATACTTTACTGCTACTCAATATATCCATG >EAS221_1:2:23:127:880 CGGAAACCTTACAAGCCAGAAGAGATTGGATCTAA >EAS221_1:2:23:127:880 TAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAAT >EAS221_1:2:24:1037:84 TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGC >EAS221_1:2:24:1037:84 TTCAGTTCTAAATATAGAAATTGAAACAGCTGTGT >EAS221_1:2:29:1486:672 AATTGAAACAGCTGTGTTTAGTGCCTTTGTTCACA >EAS221_1:2:3:542:428 AAGACATGAGTTCAGGTACAGGGGTGGAAAAAGAT >EAS221_1:2:3:542:428 AGAGCAACTAGGTAAAAAATTAACATTACAACAGG >EAS221_1:2:3:945:2005 AACCAAGCAGAAGAAAGAGGCTCAGAACTTGAAGA >EAS221_1:2:3:945:2005 GAAAAACTATTTGAGGAAGTAATTGGGGAAAACCT >EAS221_1:2:52:1144:509 AAAAGGGATTAAATTCCCCCACTTAAGAGATATAG >EAS221_1:2:52:1144:509 TGTAAAAGTCAAAATTAAAGTTCAATACTCACCAT >EAS221_1:2:73:955:728 AATTCATCATCACTAAACCAGTCCTATAAGAAATG >EAS221_1:2:73:955:728 TACAACAGGAACAAAACCTCATATATCAATATTAA >EAS221_1:2:8:327:522 AACAGGAACAAAACCTCATATATCAATATTAACTT >EAS221_1:2:8:327:522 TTCTACGCAAACAGAAACCAAATGAGAGAAGGAGT >EAS221_1:2:90:986:1224 CTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAAC >EAS221_1:2:91:856:504 CTAGATGAGAGAGAACTTCCCTGGAGGTCTGATGG >EAS221_1:2:91:856:504 GTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTT >EAS221_1:4:36:1402:1709 AGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTC >EAS221_1:4:36:1402:1709 TTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATT >EAS221_1:4:3:248:1491 TTAAAATTTAACAAAAGTAAATAAAACACATAGCT >EAS221_1:4:41:519:609 AACAAAAACTATGCTAAGTATTGGTAAAGATGTGG >EAS221_1:4:41:519:609 TACCTAATTGGTACAATGGACAATATTCTGATGAT >EAS221_1:4:4:1732:88 GCTGTAATGATGCCCCTTGGCCATCACCCGGTCCC >EAS221_1:4:4:1732:88 TGTACACACGCTGTCCTATGTACTTATCATGACTC >EAS221_1:4:68:64:783 AAGACATAATCCCACGCTTCCTATGGAAAGGTTGT >EAS221_1:4:68:64:783 TCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGT >EAS221_1:4:87:1375:1303 AGGAGCATTTTGTCAGTTACCAAATGTGTTTATTA >EAS221_1:4:87:1375:1303 GAGAGATTCTGCAGCCCAGATCCAGATTGCTTGTG >EAS221_1:6:38:1071:155 ATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATC >EAS221_1:6:38:1071:155 TAAAATGTCTATTTTTGTCTTGACACCCAACTAAT >EAS221_1:6:4:1131:104 ACTTTGGAAAACAATTTGGTAATTTCGTTTTTTTT >EAS221_1:6:4:1131:104 ATGTAACAAATCTGCGCTTGTACTTCTAAATCTAT >EAS221_1:6:57:1342:1166 AAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGA >EAS221_1:6:57:1342:1166 CAGAGCAACTAGGTAAAAAATTAACATTACAACAG >EAS221_1:6:60:1037:1146 AAAAGCATACAGTCATCTATAAAGGAAATCCCATC >EAS221_1:6:60:1037:1146 GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAAT >EAS221_1:6:69:735:1915 AATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAG >EAS221_1:6:69:735:1915 ACTGCCAGAGCTGCTGGCAAGCTAGAGTCCCATTT >EAS221_1:6:89:1164:573 AAAAAACCTGTCAAACACGAATGTTATGCCCTGCT >EAS221_1:6:89:1164:573 AGACTTCATCAAGAGATGTAGTCATCAGACTATCT >EAS221_1:6:92:1807:1185 AGCATGGTTGTACTGGGCAATACATGAGATTATTA >EAS221_1:6:92:1807:1185 CTCTATCCCAAATTCCCAATTACGTCCTATCTTCT >EAS221_1:6:96:491:1891 AGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGG >EAS221_1:6:96:491:1891 GTCAACATGAAGGAAAAAAATTCTAAAATCAGCAA >EAS221_1:8:15:881:1932 CACTTAAGAGATATAGATTGGCAGAACAGATTTAA >EAS221_1:8:15:881:1932 CACTTTAAATCAACAACAGTAAAATAAAACAAAGG >EAS221_1:8:4:679:110 AATGTTCCCCAGATACCATCCCTGTCTTACTTCCA >EAS221_1:8:4:679:110 TCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGT >EAS221_1:8:58:369:244 CTGTAATGATGCCCCTTGGCCATCACCCAGTCCCT >EAS221_1:8:58:369:244 TTGGGAGATTTTTAATGATTCCTCAATGTTAAAAT >EAS221_1:8:60:1020:1259 CTATGAAGAGACTATTGCCAGATGAACCACACATT >EAS221_1:8:60:1020:1259 TAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTC >EAS221_1:8:65:1928:1125 CATCACAATGAACAACAGGAAGAAAAGGTCTTTCA >EAS221_1:8:65:1928:1125 GGCATTTGCCTTCAGACCCTACACGAATACGTCTC >EAS221_1:8:67:1797:1931 GGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTG >EAS221_1:8:67:1797:1931 TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT >EAS221_1:8:70:1349:1788 ATTATATCAGATAAAGCACACTTTAAATCAACAAC >EAS221_1:8:70:1349:1788 TACTAGACCTAAGAGGGATGAGAAATTACCTAATT >EAS221_1:8:73:108:1621 GAACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTC >EAS221_1:8:73:108:1621 GTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACA >EAS221_1:8:77:781:676 TCATGAAGCACTGAACTTCCACGTATCATCTAGGG >EAS221_1:8:77:781:676 TTGCCAGATGAACCACACATTAATACTATGTTTCT >EAS221_1:8:78:1478:1446 GGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTT >EAS221_1:8:78:1478:1446 TGTGGTCTGACAGGCTGCAACTGTGAGCCATCACA >EAS221_1:8:84:1013:1074 GCAAGGGGGTCTATGTGAACAAAGGCACTAAACAC >EAS221_1:8:84:1013:1074 TTGATGCCCTCTTCTTCCAAAGATGAAACGCGTAA >EAS221_1:8:8:1351:1986 CCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATG >EAS221_1:8:8:1351:1986 TCTTACTTCCAGATCCCCAGAGGGAAAGCTTTCAA >EAS221_3:2:100:1147:124 AAAAAAGAATTTTAAAAATGAACAGAGCTTTCAAG >EAS221_3:2:100:1147:124 AATGCCAGGAAGATACATTGCAAGACAGACTTCAT >EAS221_3:2:22:1623:709 GAAGACAAGTCTCTTATGAATTAACCCAGTCAGAC >EAS221_3:2:22:1623:709 GGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGAC >EAS221_3:2:2:491:1886 CTCTTTAGTCTTGCTAGAGATTTAGACATCTAAAT >EAS221_3:2:59:1576:946 AACTGTGAGCCATCACAATGAACAACAGGAAGAAA >EAS221_3:2:59:1576:946 CAACGCTTCTAGCCATTTCTTTTGGCATTTGCCTT >EAS221_3:2:60:590:1760 AAAGTAACTGAACCTATGAGTCACAGGTATTCCTG >EAS221_3:2:60:590:1760 TCATCAAGATATGTAGTCATCAGACTATCTAAAGT >EAS221_3:2:67:1467:1447 AAAGTTCAATACTCACCATCATAAATACACACAAA >EAS221_3:2:67:1467:1447 ATAGATTGGCAGAACAGATTTAAAAACATGAACTA >EAS221_3:2:67:1864:477 AATGATGCCCCTTGGCCATCACCCAGTCCCTGCCC >EAS221_3:2:67:1864:477 TAAAATGTCTATTTTTGTCTTGACACCCAACTAAT >EAS221_3:2:76:1729:813 TAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTT >EAS221_3:2:76:1729:813 TCTGCGCTTGTACTTCTAAATCTATAAAAAAATTA >EAS221_3:4:12:276:1797 ACTATTGCCAGATGAACCACACATTAATACTATGT >EAS221_3:4:12:276:1797 TCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTC >EAS221_3:4:21:132:1423 GCCAGATGAACCACACATTAATACTATGTTTCTTA >EAS221_3:4:21:132:1423 TCAATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCC >EAS221_3:4:29:1061:574 ATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGG >EAS221_3:4:29:1061:574 GGTCTGACAGGCTGCAACTGTGAGCCATCACAATG >EAS221_3:4:30:1452:1563 ATGAATTAACCAAGTCAGACAAAAATAAAGAAAAA >EAS221_3:4:30:1452:1563 GATTTAGACATCTAAATGAAAGAGGCTCAAAGAAT >EAS221_3:4:41:1308:619 CATTGCAAGACAGACTTCATCAAGATATGTAGTCA >EAS221_3:4:41:1308:619 GAAGTATGAGATTATGTAAAGTAACTGAACCTATG >EAS221_3:4:57:1675:720 TATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAA >EAS221_3:4:57:1675:720 TCATATATCAATATTAACTTTGAATAAAAAGGGAT >EAS221_3:4:66:584:407 GCATTTGCCTTCAGACCCTACACGAATGCGTCTCT >EAS221_3:4:66:584:407 GGGCAATACATGAGATTATTAGGAAATGCTTTACT >EAS221_3:4:78:1314:1275 AGGAAATCCCATCAGAATAACAATGGGCTTCTCAG >EAS221_3:4:78:1314:1275 GAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAG >EAS221_3:4:81:687:1379 CCTAAGAGGGATGAGAAATTACCTAATTGGTACAA >EAS221_3:4:81:687:1379 TAAATAAAACACATAGCTAAAACTAAAAAAGCAAA >EAS221_3:4:90:247:212 ACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCT >EAS221_3:4:90:247:212 TGACAGGCTGCAACTGTGAGCCATCACAATGAACA >EAS221_3:6:20:492:850 AGTATGAAAACAATGTTCCCCAGATGCCGTCCCGG >EAS221_3:6:20:492:850 CCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTT >EAS221_3:6:26:227:1053 ATTCTTCATCCTGGACCCTGAGAGATTCTGCAGCC >EAS221_3:6:26:227:1053 GGTTTAGGGGTATAATACCTCTACATGGCTGATTA >EAS221_3:6:51:1486:1131 ATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAA >EAS221_3:6:51:1486:1131 TCAGCAGAAACCTTACAAGCCAGAAGAGATTGGAT >EAS221_3:6:70:843:706 AATGATTCCTCAATGTTAAAATGTCTATTTTTGTC >EAS221_3:6:70:843:706 ATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCC >EAS221_3:8:33:1240:846 ACCTTACAAGCCAGAAGAGATTGGATCTAATTTTT >EAS221_3:8:33:1240:846 ATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAA >EAS221_3:8:34:956:1309 AACTATGAAGAGACTATTGCCAGATGAACCACACA >EAS221_3:8:34:956:1309 AGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTC >EAS221_3:8:50:1203:1094 AAATATAGTTGAAAGCTCTAACAATAGACTAAACC >EAS221_3:8:50:1203:1094 ACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAG >EAS221_3:8:55:932:613 TAGTCATCAGACTATCTAAAGTCAACATGAAGGAA >EAS221_3:8:55:932:613 TGTCAAACACGAATGTTATGCCCTGCTAAACTAAG >EAS221_3:8:63:1265:820 CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC >EAS221_3:8:63:1265:820 TGTCTTGACACCCAACTAATATTTGTCTGAGCAAA >EAS221_3:8:65:463:703 GAAACCTTACAAGCCAGAAGAGATTGGATCTAATT >EAS221_3:8:65:463:703 TGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTT >EAS221_3:8:74:770:1712 ACATTACTACCCTGCAATTAATATAATTGTGTCCA >EAS221_3:8:74:770:1712 GAGCCGTCCGTGTCCTCCCATCTGGCCTCGTCCAC >EAS221_3:8:7:1864:1569 AAAAACCTGTCAAACACGAATGTTATGCCCTGCTA >EAS221_3:8:7:1864:1569 AGATATGTAGTCATCAGACTATCTAAAGTCAACAT >EAS51_62:1:38:250:647 AATAATAAAATGATAAAAAGATCAATTCAGCAAGA >EAS51_62:1:38:250:647 ACTATATGCTGTTTACAAGAAACTCATTAATAAAT >EAS51_62:2:133:8:379 ATAAGATAATTCATCATCACTAAACCAGTCCTATA >EAS51_62:2:133:8:379 GGAAATCCCATCAGAATAACAATGGGCTTCTCAGC >EAS51_62:2:258:266:101 ACGCTGTCCTATGTACTTATCATGACTCTATCCCA >EAS51_62:2:258:266:101 CCATCACCCAGTCCCTGCCCCATCTCTTGTAATCT >EAS51_62:2:260:147:818 AAAATTTGGTAATTTAGTTTTTTTTTTTTTCTTTT >EAS51_62:2:260:147:818 ATCCATGTAACAAATCTGCGCTTTTACTTCTAAAT >EAS51_62:3:103:443:166 ACCTGTCAAACACGAATGTTATGCCCTGCTAAACT >EAS51_62:3:103:443:166 TACACACAAAAGTACAAAACTCACAGGTTTTATAA >EAS51_62:3:169:292:652 ATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCC >EAS51_62:3:169:292:652 GCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGA >EAS51_62:3:200:263:280 AGTAAAATAAAACAAAGGAGGTCATCATACAATGA >EAS51_62:3:200:263:280 TTGGTACAATGTACAATATTCTGATGATGGTTACA >EAS51_62:3:263:74:407 AAGCTTTCAACGCTTCTAGCCATTTCTTTTGGCAT >EAS51_62:3:263:74:407 CTGCAACTGTGAGCCATCACAATGAACAACAGGAA >EAS51_62:3:314:386:190 AGACCCCCTTGCAACAACCTTGAGAACCCCAGGGA >EAS51_62:3:314:386:190 CACTCCAGCTCCCTGTCACCCAATGGACCTGTGAT >EAS51_62:3:50:312:219 ACTGCTACTCAATATATCCATGTAACAAATCTGCG >EAS51_62:3:50:312:219 TCCTACTAAATACATATGCACCTAACACAAGACTA >EAS51_62:3:55:340:837 TCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAAT >EAS51_62:3:55:340:837 TTAATATAATTGTGTCCATGTACACACGCTGTCCT >EAS51_62:3:68:996:104 AGAGGGATGAGAAATTACCTAATTGGTACAATGTA >EAS51_62:3:68:996:104 TACTTATATCAGATAAAGCACACTTTAAATCAACA >EAS51_62:4:156:857:494 CTCATACACACACATGGTTTAGGGGTATAATACCT >EAS51_62:4:156:857:494 GTTTCCCATCATGAAGCACTGAACTTCCACGTCTC >EAS51_62:4:187:907:145 TTTCTTCTCTCTCTTTTTTTTTTTTTTTATTGCAT >EAS51_62:4:282:962:46 GAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG >EAS51_62:4:282:962:46 TACTTTACTGCTACTCAATATATCCATGTAACAAA >EAS51_62:4:308:614:911 AAAAACAATTTGGTAATTTAGTTTTTTTTTTTTTC >EAS51_62:4:308:614:911 TGCGCTTGTACTTCTAAATCTATAACAAAATTAAA >EAS51_62:5:119:38:945 ATTCTAAAATCAGCAAGAGAAAAGCATACAGTCAT >EAS51_62:5:119:38:945 TCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGA >EAS51_62:5:131:779:345 GTCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAA >EAS51_62:5:131:779:345 TGGAAGACATAATCCCACGCTTCCTATGGAAAGGT >EAS51_62:5:154:669:853 GTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCA >EAS51_62:5:154:669:853 TGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGA >EAS51_62:5:192:716:235 ATACACACACATGGTTTAGGGGTATAATACCTCTA >EAS51_62:5:192:716:235 GACCCTACACGAATGCGTCTCTACCACAGGGGGCT >EAS51_62:5:236:498:526 ACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGT >EAS51_62:5:236:498:526 CAGCACATTACTACCCTGCAATTAATATAATTGTG >EAS51_62:5:290:319:736 CGAGTCACGGGGTTGCCAGCACAGGGGCTTAACCT >EAS51_62:5:290:319:736 GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC >EAS51_62:5:295:882:282 AATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAG >EAS51_62:5:295:882:282 CAGAAGAGATTGGATCTAATTTTTGGACTTCTTAA >EAS51_62:5:86:697:941 AAAAAAATCCCGGAAGATACATTGCAAGACAGACT >EAS51_62:5:86:697:941 GTATGAGATTATGTAAAGTAACTGAACCTATGAGT >EAS51_62:6:12:484:836 AAACACATAGCTAAAACTAAAAAAGCAAAAACAAA >EAS51_62:6:12:484:836 AAATACTACTAGACCTAAGAGGGATGAGAAATTAC >EAS51_62:6:148:170:895 AAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGT >EAS51_62:6:148:170:895 AAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGA >EAS51_62:6:50:542:881 CCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGA >EAS51_62:6:50:542:881 TCCCAATTACGTCCTATCTTCTTCTTAGGTAAGAA >EAS51_62:7:144:28:475 AGGAAATGCTTTACTGTCATAACTATGAAGAGACT >EAS51_62:7:144:28:475 CAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGT >EAS51_62:7:157:784:936 GCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTCT >EAS51_62:7:157:784:936 TGATTTACTTGTTGTTGGTTTTCTGTTTCTTTGTT >EAS51_62:7:162:195:761 AACATGAACTAACTATATGCTGTTTACAAGAAACT >EAS51_62:7:162:195:761 TCACAGGTTTTATAAAACAATTAATTGAGACTACA >EAS51_62:7:178:286:414 CACGCCCAAGCCCTTCTCACAGTTTCTGCCCCCAG >EAS51_62:7:178:286:414 TTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACG >EAS51_62:7:196:511:896 ATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTT >EAS51_62:7:196:511:896 GAAAAGCATACAGTCATCTATAAAGGAAATCCCAT >EAS51_62:7:248:17:435 ATAACCATCCTACTAAATACATATGCACCTAACAC >EAS51_62:7:248:17:435 CATGAGTTCAGGAAAAGGGGTGGAAAAAGATGTTC >EAS51_62:7:312:236:655 GAGAAATTACCTAATTGGTACAATGTACAATATTC >EAS51_62:7:312:236:655 TGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTA >EAS51_62:7:96:836:737 ATCAACCTCATACACACACATGGTTTAGGGGTATA >EAS51_62:7:96:836:737 TCCCATCATGAAGCACTGAACTTCCACGTCTCATC >EAS51_62:8:52:967:804 AACTAAGCATCATAAATGAAGGGGAAATAAAGTCA >EAS51_62:8:52:967:804 TTACCTAGTTGCTCTGTAGTCTCAATTAATTGTTT >EAS51_64:2:326:153:231 ATTGTTTTCAACTTTGGAAAACAATTTGGTAATTT >EAS51_64:2:326:153:231 TGCTACTCAATATATCCATGTAACAAATCTGCGCT >EAS51_64:3:143:310:958 CTGCACATTACTACCCTGCAATTAATATAATTGTG >EAS51_64:3:143:310:958 GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC >EAS51_64:3:190:727:308 ACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTG >EAS51_64:3:190:727:308 GGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGG >EAS51_64:3:255:45:399 AAAAACTATGCTAAGTATTGGTAAAGATGTGGGGA >EAS51_64:3:255:45:399 GGTACAATGTACAATATTCTGATGATGGTTACACT >EAS51_64:3:285:417:147 AGTCAAAATTAAAGTTCAATACTCACCATCATAAA >EAS51_64:3:285:417:147 TTGGATCTAATTTTTGGACTTCTTAAAGAAAAAAA >EAS51_64:3:309:303:278 CTATGAAGAGACTATTGCCAGATGAACCACACATT >EAS51_64:3:309:303:278 TCAATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCC >EAS51_64:3:67:782:132 ATATTTGTCTGAGCAAAACAGTCTAGATGAGAGAG >EAS51_64:3:67:782:132 TCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTT >EAS51_64:3:7:268:263 TCGTACAGAAGTTTAATGGAGCCTTGGGACCTTAC >EAS51_64:3:7:268:263 TTGCGTTATTTGAGTTGGTGGAAGACATAATCCCA >EAS51_64:3:80:885:513 GAAATTCTTCATCCTGGACCCTGAGAGATTCTGCA >EAS51_64:3:80:885:513 GCATTTTGTCAGTTACCAAATGTGTTTATTACCAG >EAS51_64:3:90:435:691 GGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGT >EAS51_64:3:90:435:691 TCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAGT >EAS51_64:4:102:467:897 AGCATGGTTGTACAGGGCAATACATGAGATTATTA >EAS51_64:4:102:467:897 GCTTTCAACGCTTCTAGCCATTTCTTTTGTCTTTT >EAS51_64:4:116:738:142 AAAGTTCAATACTCACCATCATAAATACACACAAA >EAS51_64:4:116:738:142 TGTCAAACACGAATGTTATGCCCTGCTAAACTAAG >EAS51_64:4:163:31:455 CTTACTTCCAGCTCCCCAGAGGGACAGCTNNCAAC >EAS51_64:4:163:31:455 GGGAGGTGCACTAATGCGCTCCACGCCCAAGCCCT >EAS51_64:4:179:389:585 TGGCCACTTTTTATCGCATTTCCCTTTAGAACCTA >EAS51_64:4:179:389:585 TGTGAAATGAATGAGATTATTAGGAAATGCTTTAC >EAS51_64:4:181:476:394 AACAATATTAACTTTGAATAAAAAGGGATTAAATT >EAS51_64:4:181:476:394 TCATCACTAAACCAGTCCTATAAGAAATGCTCAAA >EAS51_64:4:189:467:475 CTACATGGCTGATTATGAAAACAATGTTCCCCAGA >EAS51_64:4:189:467:475 TATCTGGATTCTGGGAAATTCTTCATCCTGGACCC >EAS51_64:4:189:571:366 AACAAATACTACTAGACCTAAGAGGGATGAGAAAT >EAS51_64:4:189:571:366 TCTACGCAAACAGAAACCAAATGAGAGAAGGAGTA >EAS51_64:4:318:345:156 GGACCCTGAGAGATTCTGCAGCCCAGATCCAGATT >EAS51_64:4:318:345:156 TTATGAAAACAATGTTCCCCAGATACCATCCCTGT >EAS51_64:4:57:786:414 CTCATTCACTCCAGCTCCCTGTCACCCAATGGACC >EAS51_64:4:57:786:414 TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA >EAS51_64:5:177:24:389 AGCTTTCAAGAAGTATGAGATTATGTAAAGTAACT >EAS51_64:5:177:24:389 CAAGACAGACTTCATCAAGATATGTAGTCATCAGA >EAS51_64:5:202:39:380 CAGGGAAGGAGCATTTTGTCAGTTACCAAATGTGT >EAS51_64:5:202:39:380 CTTCATCCTGGACCCTGAGAGATTCTGCAGCCCAG >EAS51_64:5:290:247:509 AGCCCATACTTTACTGCTACTCAATATATCCATGT >EAS51_64:5:290:247:509 TCTCAAATATTGCTAGTGGGAGTATAAATTGTTTT >EAS51_64:6:118:41:489 ACAATTAATTGAGACTACAGAGCAACTAGGTAAAA >EAS51_64:6:118:41:489 CCCTGCTAAACTAAGCATCATAAATGAAGGGGAAA >EAS51_64:6:124:128:489 CTCTGTCTTGATTTACTTGTTGTTGGTTTTCTGTT >EAS51_64:6:124:128:489 GTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGT >EAS51_64:6:143:763:480 AAACGCGTAACTGCGCTCTCATTCACTCCAGCTCC >EAS51_64:6:143:763:480 CTGAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA >EAS51_64:6:195:348:703 CAGTTACCAAATGTGTTTATTACCAGAGGGATGGA >EAS51_64:6:195:348:703 TAATGAAAACTATATTTATGCTATTCAGTTCTAAA >EAS51_64:6:206:994:556 ATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTC >EAS51_64:6:206:994:556 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN >EAS51_64:6:210:809:735 AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT >EAS51_64:6:210:809:735 GAGGTTCAGAACTTGAAGACAAGTCTCTTATGAAT >EAS51_64:6:213:54:878 CTCTGTCTTGATTTACTTGTTGTTGGTTTTTTGTT >EAS51_64:6:300:622:86 GGTTACACTAAAAGCCCATACTTTACTGCTACTCA >EAS51_64:6:300:622:86 TCATACAATGATAAAAAGATCAATTCAGCAAGAAG >EAS51_64:6:54:695:952 ACAGTAAAATAAAACAAAGGAGGTCATCATACAAT >EAS51_64:6:54:695:952 GGTTACACTAAAAGCCCATACTTTACTGCTACTCA >EAS51_64:7:104:965:517 AGAGGCTCAAAGAATGCCAGGAAGATACATTGCAA >EAS51_64:7:104:965:517 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN >EAS51_64:7:140:752:822 CATCACTAAACCAGTCCTATAAGAAATGCTCAAAA >EAS51_64:7:140:752:822 GCTTCTCAGCGGAAACCTTACAAGCCAGAAGAGAT >EAS51_64:7:152:918:824 TACTATGTTTCTTATCTGCACATTACTACCCTGCA >EAS51_64:7:152:918:824 TTTCCCATCATGAAGCACTGAACTTCCACGTCTCA >EAS51_64:7:92:493:891 AAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTG >EAS51_64:7:92:493:891 AGTCAACATGAAGGAAAAAAATTCTAAAATCAGCA >EAS51_66:1:282:274:50 ATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAA >EAS51_66:1:282:274:50 CCCCTCTAAGCCGTTCTATTTGTAATGAAAACTAT >EAS51_66:1:289:207:323 CCATACTTTACTGCTACTCAATATATCCATGTAAC >EAS51_66:1:289:207:323 CTAGTGGGAGTATAAATTGATTTCCACTTTGGAAA >EAS51_66:1:64:182:741 AAAAAAACAAATTAAACTCTAACAAAAGTAAATAA >EAS51_66:3:102:511:946 ATGTAAAAGTGACTGTTATTGTCTTGACACCCAAC >EAS51_66:3:102:511:946 CCCAGTCCCTGCCCCATCTCGGGTAATCTCTCTCC >EAS51_66:3:155:375:623 AAGGAGTAGCTATACTTATATCAGATAAAGCACAC >EAS51_66:3:155:375:623 CAATATTAACTTTGAATAAAAAGGGATTAAATTCC >EAS51_66:3:166:532:438 AACAAATACTACTAGACCTAAGAGGGATGAGAAAT >EAS51_66:3:166:532:438 AACTAAAAAAGCAAAAACAAAAACTATGCTAAGTA >EAS51_66:3:233:191:520 TGAACTTCTGTAATTGAAAAATTCATTTAAGAAAT >EAS51_66:3:246:711:981 AAAAAAACCTGTCAAACACGAATGTTATGCCCTGC >EAS51_66:3:246:711:981 AGACTTCATCAAGATATGTAGTCATCAGACTATCT >EAS51_66:3:263:689:572 AAAGAAAAAAAAACCTGTCAAACACGAATGTTATG >EAS51_66:3:263:689:572 AAGATATGTAGTCATCAGACTATCTAAAGTCAACA >EAS51_66:3:29:381:169 ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT >EAS51_66:3:29:381:169 CATCAACCTCATACACACACATGGTTTAGGGGTAT >EAS51_66:3:39:59:738 GAGATTATTAGGAAATGCTTTACTGTCATAATTAT >EAS51_66:3:39:59:738 GTCCTATGTTCTTCTTAGGGAAGAACAGCTTAGGT >EAS51_66:4:188:460:1000 GTGTCCATGTACACACGCTGTCCTATGTACTTATC >EAS51_66:4:188:460:1000 TCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGC >EAS51_66:4:191:40:536 ATAAAAAAAGACTACCCAGATTCATAAAACAAATA >EAS51_66:4:191:40:536 CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA >EAS51_66:4:209:92:210 GAGATTATTAGGAAATGCTTTACTGTCATAACTAT >EAS51_66:4:209:92:210 TTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTT >EAS51_66:4:240:264:231 CAACAGATCAAGAAGGAGGGGCAATGGACGAGTTA >EAS51_66:4:240:264:231 TGTAATGAAAACTATATTTATGCTATTCAGTTCTA >EAS51_66:4:277:482:316 CACTAATGCGCTCCACGCCCAAGCCCTTCTCACAG >EAS51_66:4:277:482:316 TGTCCTATGTACTTATCATGACTCTATCCCAAATT >EAS51_66:4:310:287:420 AAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGAT >EAS51_66:4:310:287:420 TACAGAGCAACTAGGTAAAAAATTAACATTACAAC >EAS51_66:4:322:350:374 ACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAA >EAS51_66:4:322:350:374 CATTGCAAGACAGACTTCATCAAGATATGTAGTCA >EAS51_66:5:210:674:911 TCATAAATACACACAAAAGTACAAAACTCACAGGT >EAS51_66:5:210:674:911 TGGCAGAACAGATTTAAAAACATGAACTAACTATA >EAS51_66:5:269:280:716 TGATATCTGGATTCTGGGAAATTCTTCATCCTGGA >EAS51_66:5:269:280:716 TTTGTCAATGTCAGGGAAGGAGCATTTTTTCAGTT >EAS51_66:5:273:545:1001 AACAAAGGAGGTCATCATACAATGATAAAAAGATC >EAS51_66:5:273:545:1001 AGATTTAAAAACATGAACTAACTATATGCTGTTTA >EAS51_66:5:285:395:450 GTCATCTATAAAGGAAATCCCATCAGAATAACAAT >EAS51_66:5:285:395:450 TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT >EAS51_66:5:308:400:602 ATAGACCCCCTTGCAACAACCTTGAGAACCCCAGG >EAS51_66:5:308:400:602 CCTGTCACCCAATGGACCTGTGATATCTGGATTCT >EAS51_66:6:284:442:747 AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGC >EAS51_66:6:310:747:415 TGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGT >EAS51_66:6:310:747:415 TGTAGTCATCAGACTATCTAAAGTCAACATGAAGG >EAS51_66:7:174:987:334 ACACCCAAGCCCTTCTCACAGTTTCTGCCCCCAGC >EAS51_66:7:174:987:334 GTCCATGTACACACGCTGTCCTATGTACTTATCAT >EAS51_66:7:4:234:610 AAAAAACCTGTCAAACACGAATGTTATGCCCTCCT >EAS51_66:7:4:234:610 AAAAATCAACATCACAAATACACACAAAAGTACAA >EAS51_66:7:84:411:336 GCTTGTACTTCTAAATCTATAAAAAAATTAAAATT >EAS51_66:8:36:688:722 ATGTCTATTTTTGTCTTGACACCCAACTAATATTT >EAS51_66:8:36:688:722 GTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTT >EAS51_66:8:43:972:506 AGAAACCTTACAAGCCAGAAGAGATTGGATCTAAT >EAS51_66:8:43:972:506 TAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAAT >EAS51_66:8:66:655:769 TCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCT >EAS51_66:8:66:655:769 TTTGTCAGTTACCAAATGTGTTTATTACCAGAGGG >EAS51_66:8:9:80:353 AATTAATATAATTGTGTCCATGTACACACGCTGTC >EAS51_66:8:9:80:353 CCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGCT >EAS51_78:7:113:43:634 ATTTGTCTGAGAAAAACAGTCTAGATGAGAGAGAA >EAS51_78:7:113:43:634 CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTTTT >EAS51_78:7:147:64:416 AAACAATGTCCCCCAGATACCATCCCTGTCTTACT >EAS51_78:7:147:64:416 CTCATCTAGGGGAACAGGGAGGTGCACTAATGCGC >EAS51_78:7:164:727:977 GAAATGCTCAAAAGAATTGTAAAAGTCAAAATTAA >EAS51_78:7:164:727:977 TACAAGCCAGAAGAGATTGGATCTAATTTTTCGAC >EAS51_78:7:186:199:927 CTACGCGAATGCGTCTCTACCACAGGGGGCTGCGC >EAS51_78:7:186:199:927 TGGCATTTGCCTTCAGACCCTACACGAATGCGTCT >EAS51_78:7:215:516:299 AAGCTATGCTAAGTATTGGTAAAGATGTGGGGAAA >EAS51_78:7:215:516:299 AATTACCTAATTGGTACAATGTACAATATTCTGAT >EAS51_78:7:270:448:491 GTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTC >EAS51_78:7:270:448:491 TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAAC >EAS51_78:7:303:402:142 AGCATTTTGTCAGTTACCAAATGTGTTTATTACCA >EAS51_78:7:303:402:142 TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGT >EAS51_78:7:316:961:576 TGTGATATCTGGATTCTGGGAAATTCTTCATCCCG >EAS51_78:7:316:961:576 TTACGGGTGTAATCTCTCTACATGGCTAATTATGA >EAS54_61:1:115:868:887 CATACACACACATGGTTTAGGGGTATAATACCTCT >EAS54_61:1:115:868:887 TCTCATTCACTCCAGCTCCCTGTCACCCAATGGAC >EAS54_61:2:168:61:867 GATGTTCTACGCAAACAGAAACCAAATGAGAGAAG >EAS54_61:2:168:61:867 TCATAAAACAAATACTACTAGACCTAAGAGGGATG >EAS54_61:2:66:757:918 CCATCCTACTAAATACATATGCACCTAACACAAGA >EAS54_61:2:66:757:918 GGGGTGGAAAAAGATGTTCTACGCAAACAGAAACC >EAS54_61:3:150:933:810 AGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATT >EAS54_61:3:150:933:810 CAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGG >EAS54_61:3:155:758:710 ATCAGATAAAGCACACTTTAAATCAACAACAGTAA >EAS54_61:3:155:758:710 TTTGAATAAAAAGGGATTAAATTCCCCCACTTAAG >EAS54_61:3:20:762:748 CACAATGAACAACAGGAAGAAAAGGTCTTTCAAAA >EAS54_61:3:20:762:748 TTCTTTTGGCATTTGCCTTCAGACCCTACACGAAT >EAS54_61:4:143:69:578 ATTGGGAGCCCCTCTAAGCCGTTCTATTTGTAATG >EAS54_61:4:83:452:970 AATGAAAACTATATTTATGCTATTCAGTTCTAAAT >EAS54_61:4:83:452:970 AGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTG >EAS54_61:4:86:660:932 AATACATATGCACCTAACACAAGACTACCCAGATT >EAS54_61:4:86:660:932 ATATAAAAAAATTAAAATTTAACAAAAGTAAATAA >EAS54_61:6:126:541:194 AGTACGACCAGCTCCCCAGAGGGAAAGCTTTCAAC >EAS54_61:6:126:541:194 CAGCCCAGATCCAGATTGCTTGTGGTCTGACAGGC >EAS54_61:6:25:949:33 AAAGTAACTGAACCTATGAGTCACAGGTATTCCTG >EAS54_61:6:25:949:33 GATATGTAGTCATCAGACTATCTAAAGTCAACATG >EAS54_61:7:114:506:971 ACTAAATACATATGCACCTAACACAAGACTACCCA >EAS54_61:7:114:506:971 GGGTGGAAAAAGATGTTCTACGCAAACAGAAACCA >EAS54_61:7:64:37:257 CCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTT >EAS54_61:7:64:37:257 TTTGATTTGGTGGAAGACATAATCCCACGCTTCCT >EAS54_61:8:165:441:708 CCATCATAAATACACACAAAAGTACAAAACTCACA >EAS54_61:8:165:441:708 CTTAAAGAAAAAAAAACCTGTCAAACACGAATGTT >EAS54_61:8:4:173:814 CTGCTACTCAATATATCCATGTAACAAATCTGCGC >EAS54_61:8:4:173:814 GATAAAAAGATCAATTCAGCAAGAAGATATAACCA >EAS54_65:2:127:288:655 ACTAGGTAAAAAATTAACATTACAACAGGAACAAA >EAS54_65:2:127:288:655 TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA >EAS54_65:2:182:924:833 TTTTTTTTTTTTTATTTGCGCTTTTTTTTTTTTTT >EAS54_65:2:264:157:150 GGAAAAATGGACAAGATTCTGATGAGGGTTACACT >EAS54_65:2:264:157:150 TAAAGCACACTTTAAATCAACAACAGTAAAATAAA >EAS54_65:2:94:356:809 AAATCTATAACAAAATTAAAATTTAACAAAAGTAA >EAS54_65:2:94:356:809 CTAAATACATATGCACCTAACACAAGACTACCCAG >EAS54_65:3:102:884:63 GTCTTGACACCCAACTAATATTTGTCTGAGCAAAA >EAS54_65:3:102:884:63 TGTCTTCCTCTGTCTTGATTTCCTTGTTGTTGGTT >EAS54_65:3:155:541:234 CTAAATACATATGCACCTAACACAAGACTACCCAG >EAS54_65:3:155:541:234 TGCGCTTGTACTTCTAAATCTATAAAAAAATTAAA >EAS54_65:3:214:946:229 AAATGAACAGAGCTTTCAAGAAGTATGATATTATG >EAS54_65:3:214:946:229 ACAAAGAATGCCAGGAAGATACATTGCAAGACAGA >EAS54_65:3:273:901:459 CCAGCATGGTTGTACTGGGCAATACATGAGATTAT >EAS54_65:3:273:901:459 TGTCCTATGTACTTATCATGACTCTATCCCAAATT >EAS54_65:3:290:558:349 ACCATCCCTGTCTTACTTCCAGCTCCCCAGCGGGA >EAS54_65:3:290:558:349 TCTCAGCTAGGGGAACAGGGAGGTGCACTAATGCG >EAS54_65:3:320:20:250 AAATAAAACACATAGCTAAAACTAAAAAAGCAAAA >EAS54_65:3:320:20:250 TTTTTTTTTTTTTTTTTTTTTTTGCATGCCAGAAA >EAS54_65:3:321:311:983 ATTTATGCTATTCAGTTCTAAATATAGAAATTGAA >EAS54_65:3:326:652:890 TTCTGTAATTGAAAAATTCATTTAAGAAATTACAA >EAS54_65:4:137:319:642 CTTGTTGTTGGTTTTCTGTTTCTTTTTTTGATTTT >EAS54_65:4:174:753:617 ATATATCCATGTAACAAATCTGCGCTTGTACTTCT >EAS54_65:4:174:753:617 GATATAACCATCCTACTAAATACATATGCACCTAA >EAS54_65:4:192:714:341 AAATTAAAATTTAACAAAAGTAAATAAAACACATA >EAS54_65:4:192:714:341 ACACAAGACTACCCAGATTCATAAAACAAATACTA >EAS54_65:4:193:38:987 AGGGAAGAACAGCTTAGGTATCAATTTTGTGTTCT >EAS54_65:4:193:38:987 TGAGATTATTAGGAAATGCTTTACTGTCATAACTA >EAS54_65:4:246:313:499 ACAATGAACAACAGGAAGAAAAGGTCTTTCAAAAG >EAS54_65:4:246:313:499 CTTTAAACGCTTCTAGCCATTTCTTTTGGCATTTG >EAS54_65:4:325:795:213 AGACTACAGAGCAACTAGGTAAAAAATTAACATTA >EAS54_65:4:325:795:213 GGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATG >EAS54_65:4:61:346:384 CAACTAAGAAGAAACCTTACAAGCCAGAAGAGATT >EAS54_65:4:61:346:384 CTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGAT >EAS54_65:4:91:267:655 CAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGT >EAS54_65:4:91:267:655 TGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGT >EAS54_65:6:115:538:276 CAAATGTGTTTATTACCAGAGGGATGGAGGGAAGA >EAS54_65:6:115:538:276 TATTTGTAATGAAAACTATATTTATGCTATTCAGT >EAS54_65:6:164:797:930 AGCTAGAGACCCATTTGGAGCCCCTCTAAGCCGTT >EAS54_65:6:164:797:930 GTCAGGGAAGGAGCATTTTGTCAGTTACCAAATGT >EAS54_65:6:18:376:416 GCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGA >EAS54_65:6:18:376:416 TTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGTTT >EAS54_65:6:277:590:364 CTCTACATGGCTGATTATGAAAACAATGTTCCCCA >EAS54_65:6:277:590:364 CTGGGAAATTCTTCATCCTGGACCCTGAGAGATTC >EAS54_65:6:326:71:741 TCTCGTTTTTTTTTCTTTCTTTTCTCTTTTTTTTT >EAS54_65:6:49:183:435 CCATCATGAAGCACTGAACTTCCACGTCTCATCTA >EAS54_65:6:49:183:435 GACTATTGCCAGATGAACCACACATTAATACTATG >EAS54_65:6:67:56:806 TATAAAGGAAATCCCATCAGAATAACAATGGGCTT >EAS54_65:6:67:56:806 TCCTGACAAGCAAATGCTAAGATAATTCATCATCA >EAS54_65:7:117:452:744 AATATTAACTTTGAATAAAAAGGGATTAAATTCCC >EAS54_65:7:117:452:744 ACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAA >EAS54_65:7:155:629:357 AGAAGAGATTGGATCTAATTTTTGGACTTCTTAAA >EAS54_65:7:155:629:357 AGAGGCTCAAAGAATGCCAGGAAGATACATTGCAA >EAS54_65:7:159:253:353 ATAAAACAATTAATTGAGACTACAGAGCAACTAGG >EAS54_65:7:159:253:353 GAAGGGGAAATAAAGTCAAGTCTTTCCTGACAGGC >EAS54_65:7:56:57:985 TTCTGTCTTCTCTCCTGTCTTCTTTTCTCTTCTTT >EAS54_65:7:56:57:985 TTTTTTCTCTTTTCTCTTTTTTTTTTTTTTTTTTT >EAS54_65:7:68:825:405 AAAACCTCATATATCAATATTAACTTTGAATAAAA >EAS54_65:7:68:825:405 AAACCAAATGAGAGAAGGAGTAGCTATACTTATAT >EAS54_65:8:10:975:766 AATAACACAAGACTACCCAGATTCATAAAACAAAT >EAS54_65:8:10:975:766 TTAATAAAGACATGAGTTCAGGTAAAGGGGTGAAA >EAS54_65:8:140:924:923 GAACAACAGGAAGAAAAGGTCTTTCAAAAGGTGAT >EAS54_65:8:140:924:923 TTTTAGCCATTTCTTTTGGCATTTGCCTTCAGACC >EAS54_65:8:147:687:428 ATATGCACCTAACACAAGACTACCCAGATTCATAA >EAS54_65:8:147:687:428 ATGTTCTACGCAAACAGAAACCAAATGAGAGAAGG >EAS54_65:8:178:187:610 AAATACACACAAAAGTACAAAACTCACAGGTTTTA >EAS54_65:8:178:187:610 TTGGCAGAACAGATTTAAAAACATGAACTAACTAT >EAS54_65:8:240:719:799 AGATTGGCAGAACAGATTTAAAAACATGAACTAAC >EAS54_65:8:240:719:799 TTAAAGTTCAATACTCACCATCATAAATACACACA >EAS54_65:8:305:819:245 AAATTCATTTAAGAAATTACAAAATATAGTTGAAA >EAS54_65:8:76:493:708 TTTATGCTATTCAGTTCTAAATATAGAAATTGAAA >EAS54_67:1:138:186:274 GGCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGG >EAS54_67:1:138:186:274 TAATTGTGTCCATGTACACACGCTGTCCTATGTAC >EAS54_67:1:159:222:274 GAACCACACATTAATACTATGTTTCTTATCTGCAC >EAS54_67:1:159:222:274 GTCTGGGGAAAGTCTCAGGGAGCCGTCCGTGTCCT >EAS54_67:1:15:381:715 GACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTT >EAS54_67:1:15:381:715 GGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTAT >EAS54_67:1:88:54:900 ATCAACAACAGAAAAATAAAACAAAGGAGGTCATC >EAS54_67:1:88:54:900 TGATGATGGTTACACTAAAAGCCCATACTTCACTG >EAS54_67:2:22:471:500 GTAAATAAAACACATAGCTAAAACTAAAAAAGCAA >EAS54_67:2:22:471:500 TACTACTAGACCTAAGAGGGATGAGAAATTACCTA >EAS54_67:3:114:736:433 AACAAAACCTCATATATCAATATTAACTTTGAATA >EAS54_67:3:114:736:433 ATGTTCTACGCAAACAGAAACCAAGTGAGAGAAGG >EAS54_67:3:172:196:746 AAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCT >EAS54_67:3:172:196:746 GCATACAGTCATCTATAAAGGAAATCCCATCAGAA >EAS54_67:3:175:730:949 TTATGCTATTCAGTTCTAAATATAGAAATTGAAAC >EAS54_67:3:197:261:624 GACTATCTAAAGTCAACATGAAGGAAAAAAATTCT >EAS54_67:3:197:261:624 GCCCTGCTAAACTAAGCATCATAAATGAAGGGGAA >EAS54_67:3:47:471:858 ACACCCAACTAATATTTGTCTGAGCAAAACAGTCT >EAS54_67:3:47:471:858 CATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTG >EAS54_67:4:142:943:582 TTCAAATGAACTTCTGTAATTGAAAAATTCATTTA >EAS54_67:4:145:607:216 AACGCGTAACTGCGCTCTCATTCACTCCAGCTCCC >EAS54_67:4:145:607:216 TGAAAAACAGGAAGAAAAGGTCTTTCAAAAGGTGA >EAS54_67:4:7:526:343 TCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCT >EAS54_67:4:7:526:343 TGAAAACAGTGTTCCCCAGATACCATCCCTGTCTT >EAS54_67:5:117:33:262 AATTAACATTACAACAGGAACAAAACCTCATATAT >EAS54_67:5:117:33:262 ACAAGCAAATGCTAAGATAATTCATCATCACTAAA >EAS54_67:5:124:241:608 CTGAACTTCCACGTCTCATCTAGGGGAACAGGGAG >EAS54_67:5:124:241:608 GGGTATAATACCTCTACATGGCTGATTATGAAAAC >EAS54_67:5:127:828:697 ATGCCAGGAAGATACATTGCAAGACAGACTTCATC >EAS54_67:5:127:828:697 TAAAGAAAAAAAAACCTGTCAAACACGAATGTTAT >EAS54_67:5:149:639:910 CAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGA >EAS54_67:5:149:639:910 TCACTAAACCAGTCCTATAAGAAATGCTCAAAAGA >EAS54_67:5:71:408:741 AGTCATCTATAAAGGAAATCCCATCAGAATAACAA >EAS54_67:5:71:408:741 TCCTGACAAGCAAATGCTAAGATAATTCATCATCA >EAS54_67:6:107:395:312 CAAAATATAGTTGAAAGCTCTAACAATAGACTAAA >EAS54_67:6:107:395:312 CAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGT >EAS54_67:6:109:953:668 CAATATATCCATGTAACAAATCTGCGCTTGTACTT >EAS54_67:6:109:953:668 CCACTTTGGAAAACAATTTGGTAATTTCGTTTTTT >EAS54_67:6:198:503:669 CAATGATAAAAAGATCAATTCAGCAAGAAGATATA >EAS54_67:6:198:503:669 CAGATTTAAAAACATGAACTAACTATATGCTGTTT >EAS54_67:6:43:859:229 TTCAAATGAACTTCTGTAATTGAAAAATTCATTTA >EAS54_67:6:46:285:790 AACGCGTAACTGCGCTCTCATTCACTCCAGCTCCC >EAS54_67:6:46:285:790 TCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAAG >EAS54_67:7:101:752:996 AACCTTACAAGCCAGAAGAGATTGGATCTAATTTT >EAS54_67:7:101:752:996 AAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATT >EAS54_67:7:197:399:319 CAAAAAACAAATACTACTAGACCTAAGAGGGATGA >EAS54_67:7:197:399:319 TAGAAACCAAATGAGAGAAGGAGTAGCTATACTTA >EAS54_67:8:19:855:491 TGGCATTTGCCTTCAGACCCTACACGAATGCGTCT >EAS54_67:8:19:855:491 TGTGTGTTCTCATCAACCTCATACACACACATGGT >EAS54_67:8:46:900:610 GATATCTGGATTCTGGGAAATTCTTCATCCTGGAC >EAS54_67:8:46:900:610 TACATGGCTGATTATGAAAACAATGTTCCCCAGAT >EAS54_71:2:125:628:79 GCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGA >EAS54_71:2:125:628:79 TTTATGCTATTCAGTTCTAAATATAGAAATTGAAA >EAS54_71:2:204:264:413 CAATGAACAACAGAAAGAAAAGTTCTTTCAAAAGG >EAS54_71:2:204:264:413 TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTG >EAS54_71:2:85:686:696 AATCAGCAAGAGAAAAGCATACAGTCATCTATAAA >EAS54_71:2:85:686:696 TAAACTAAGCATCATAAATGAAGTGGAAATAAAG >EAS54_71:3:186:989:869 ACACACATGGTTTAGGGGTATAATACCTCTACATG >EAS54_71:3:186:989:869 GGGAAATTCTTCATCCTGGACCCTGAGAGATTCT >EAS54_71:3:254:32:275 GATGGAGGGAAGAGGGACGCTGAAGAACTTTGAT >EAS54_71:3:254:32:275 TGCAACTGTGAGCCATCACAATGAACAACAGGAAG >EAS54_71:3:257:288:731 AAGAAGATATAACCATCCTACTAAATACATATGCA >EAS54_71:3:257:288:731 TGCTGTTTACAAGAAACTCATTAATAAAGACATG >EAS54_71:3:267:821:860 GCATACAGTCATCTATAAAGGAAATCCCATCAGA >EAS54_71:3:267:821:860 TCTTTAGTCTTGCTAGAGATTTAGACATCTAAATG >EAS54_71:3:78:855:352 AAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTT >EAS54_71:3:78:855:352 AACAATAGACTAAACCAAGCAGAAGAAAGAGGTTC >EAS54_71:4:127:725:381 AATTACAAAATATAGTTGAAAGCTCTAACAATAGA >EAS54_71:4:127:725:381 TGAACCTATGAGTCACAGGTATTCCTGAGGAAAA >EAS54_71:4:13:981:659 CGGGACAATGGACGAGGTAAACCGCACATTGACAA >EAS54_71:4:13:981:659 TGTAGCCCCTCTAAGGCGTTCTATTTGTAATGAA >EAS54_71:4:14:88:306 AAAGAATGCCAGGAAGATACATTGCAAGACAGAC >EAS54_71:4:14:88:306 AGAAGAGATTAGATCTAATTTTTGGACTTCTTAAA >EAS54_71:4:165:397:25 GCAACTGTGAGCCATCACAATGAACAACAGGAAGA >EAS54_71:4:165:397:25 TTCAACGCTTCTAGCCATTTCTTTTGGCATTTGC >EAS54_71:4:169:256:888 AGGTTCAGAACTTGAAGACAAGTCTCTTATGAATT >EAS54_71:4:169:256:888 ATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT >EAS54_71:4:169:862:829 AAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCA >EAS54_71:4:169:862:829 GCCATTTCTTTTGGCATTTGCCTTCAGACCCTAC >EAS54_71:4:206:741:810 ACTAACTATATGCTGTTTACAAGAAACTCATTAA >EAS54_71:4:206:741:810 CAAAAGTACAAAACTCACAGGTTTTATAAAACAAT >EAS54_71:4:209:159:130 CTTATCATGACTCTATCCCAAATTCCCAATTACGT >EAS54_71:4:209:159:130 GCCCCCAGCATGGTTGTACTGGGCAATACATGAG >EAS54_71:4:233:97:262 ACCACACATTAATACTATGTTTCTTATCTGCCCA >EAS54_71:4:233:97:262 GTATCAATTTGGTGTTCTGTGTAAAGTCTCAGGGA >EAS54_71:4:252:428:683 TGTCTTGATTTACTTGTTGTTGGTTTTCTGTTTCT >EAS54_71:4:284:269:882 TTTCTTTTCTCTTTTTTTTTTTTTTGTTTTTGCA >EAS54_71:4:328:669:662 GGAAGGAGCATTTTGTCAGTTACCAAATGTGTTT >EAS54_71:4:328:669:662 TCTTCATCCTGTACCCTGAGAGATTCTGCAGCCCA >EAS54_71:4:72:63:435 CCTTGCAACAACCTTGAGAACCCCAGGGAATTTG >EAS54_71:4:72:63:435 TGATATCTGGATTCTGGGAAATTCTTCATCCTGGA >EAS54_71:4:73:182:444 AACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCG >EAS54_71:4:73:182:444 CTTGATTTACTTGTTGTTGGTTTTCTGTTTCTTT >EAS54_71:5:153:543:671 GCCCCATCTCTTGTAATCTCTCTCCTTTTTGCTG >EAS54_71:5:153:543:671 TAAAATGTCTATTTTTGTCTTGACACCCAACTAAT >EAS54_71:5:16:434:204 AGATGAGAGAGAACTTCCCTGGAGGTCTGATGGC >EAS54_71:5:16:434:204 CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGT >EAS54_71:5:81:685:141 ACTGAACCTATGAGTCACAGGTATTCCTGAGGAA >EAS54_71:5:81:685:141 AGATATGTAGTCATCAGACTATCTAAAGTCAACAT >EAS54_71:6:172:896:83 AGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGT >EAS54_71:6:172:896:83 CATTTGCCTTCAGACCCTACACGAATGCGTCTCTA >EAS54_71:6:215:133:909 TGTGTGTTCTCATCAACCTCATACACACACATGG >EAS54_71:6:215:133:909 TTGCCTTCAGACCCTACACGAATGCGTCTCTACCA >EAS54_71:6:224:932:942 CTCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGG >EAS54_71:6:224:932:942 GTCCATGTACACACGCTGTCCTATGTACTTATCA >EAS54_71:6:228:354:203 AATGGACCTGTGATATCTGGATTCTGGGAAATTC >EAS54_71:6:228:354:203 TCAACCTCATACACACACATGGTTTAGGGGTATAA >EAS54_71:6:264:705:89 AAACATATGCACCTAACACAAGACTACCCAGATTC >EAS54_71:6:264:705:89 AAGGGGTGGAAAAAGATGTTCTACGCAAACAGAA >EAS54_71:6:324:515:230 AAAACAGTCTAGATGAGAGAGAACTTCCCTGGAG >EAS54_71:6:324:515:230 CCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGG >EAS54_71:6:82:932:400 GACACCCAACTAATATTTGTCTGAGCAAAACAGTC >EAS54_71:6:82:932:400 GTAATCTCTCTCCTCTTCGCTGCATCCCTGTCTT >EAS54_71:7:130:260:553 AGCAAGAGAAAAGCATACAGTCATCTATAAAGGAA >EAS54_71:7:130:260:553 GTGAGAAGTTTGGAAAAACTATTTGAGGAAGCAC >EAS54_71:7:194:867:616 ATCCATGTAACAAATCTGCGCTTGTACTTCTATT >EAS54_71:7:194:867:616 TTTTCCACTTTGGAAAACAATTTGGTAATTTCGTT >EAS54_71:7:212:329:348 AACCACACATTAATACTATGTTTCTTATCTGCAC >EAS54_71:7:212:329:348 CCCATCATGAAGCACTGAACTTCCACGTCTCATCT >EAS54_71:7:250:698:842 AAAAAGTACAAAACTCACAGGTTTTATAAAACAA >EAS54_71:7:250:698:842 AAGAAAAAAAAACCTGTCAAACACGAATGTTATGC >EAS54_71:7:80:760:490 CATGGCTGATTATGAAAACAATGTTCCCCAGATAC >EAS54_71:7:80:760:490 CTGGACCCTGAGAGATTCTGCAGCCCAGCTCCAG >EAS54_71:7:97:743:602 AAGCAAATGCTAAGATAATTCATCATCACTAAACC >EAS54_71:7:97:743:602 ATTACAACAGGAACAAAACCTCATATATCAATAT >EAS54_71:8:105:854:975 ATTTAACAAAAGTAAATAAAACACATAGCTAAAAC >EAS54_71:8:105:854:975 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG >EAS54_71:8:113:856:319 AAATCAACAACAGTAAAATAAAACAAAGGAGGT >EAS54_71:8:113:856:319 CCCACTTAAGAGATATAGATTGGCAGAACAGATTT >EAS54_71:8:215:830:609 AAGACATCTAAATGAAAGAGGCTCAAAGAATGC >EAS54_71:8:234:21:950 TTTTTTTTTTTTCTCCTCTCTTTTTTTTTTTTT >EAS54_71:8:321:642:388 TACCAAATGTGTTTATTACCAGAGGGATGGAGG >EAS54_71:8:321:642:388 TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGT >EAS54_71:8:38:856:336 AATGGACCTGTGATATCTGGATTCTGGGAAATT >EAS54_71:8:38:856:336 CACACATGGTTTAGGGGTATAATACCTCTACATGG >EAS54_73:3:203:419:243 GGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTAT >EAS54_73:3:203:419:243 TTGAAAGCTCTAACAATAGACTAAACCAAGCAGAA >EAS54_73:3:239:796:221 ATAACTATGAAGAGACTATTGCCAGCTGACCCCCC >EAS54_73:3:239:796:221 GGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGT >EAS54_73:3:23:502:103 AGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTT >EAS54_73:3:23:502:103 GACACCCAACTAATATTTGTCTGAGCAAAACAGTC >EAS54_73:3:29:833:612 AAGCTCTAACAATAGACTAAACCAAGCAGAAGAAA >EAS54_73:3:29:833:612 CAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGT >EAS54_73:3:313:827:992 AAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATCTG >EAS54_73:3:313:827:992 TGTTTCTTTGTTTGATTTGGTGGAAGACATAATCC >EAS54_73:3:37:761:635 CCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCT >EAS54_73:3:37:761:635 TGTGAGCCATCACAATGAACAACAGGAAGAAAAGG >EAS54_73:3:4:854:140 CCTGACAAGCAAATGCTAAGATAATTCATCATCAC >EAS54_73:3:4:854:140 GTCATCTATAAAGGAAATCCCATCAGAATAACAAT >EAS54_73:3:88:24:744 GTCCTGTGATATCTGGATTCTGGGAAATTCTTCAT >EAS54_73:3:88:24:744 TGTCAATGTCAGGGAAGGAGCATTTTTGAAGTTTA >EAS54_73:5:145:635:390 TAAACCAGTCCTATAAGAAATGCTCAAAAGAATTG >EAS54_73:5:145:635:390 TTGAATAAAAAGGGATTAAATTCCCCCACTTAAGA >EAS54_73:5:169:714:644 CCTAATTGGTACAATGTACAATATTCTGATGATGG >EAS54_73:5:169:714:644 GAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG >EAS54_73:5:220:733:736 CCATCCTACTAAATACATATGCACCTAACACAAGA >EAS54_73:5:220:733:736 TTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAA >EAS54_73:5:231:339:551 CTGAGAGATTCTGCAGCCCAGATCCAGATTGCTTG >EAS54_73:5:231:339:551 TGTCAGTTACCAAATGTGTTTATTACCAGAGGGAT >EAS54_73:5:255:796:239 AAGGGATTAAATTCCCCCACTTAAGAGATAGAGAT >EAS54_73:5:255:796:239 ATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGT >EAS54_73:5:263:557:988 AATGATAAAAAGATCAATTCAGCAAGAAGATATAA >EAS54_73:5:263:557:988 CTGCTACTCAATATATCCATGTAACAAATCTGCGC >EAS54_73:5:271:874:367 AAAAAACCTGTCAAACACGAATGTTATGCCCTGCT >EAS54_73:5:271:874:367 ATATGTAGTCATCAGACTATCTAAAGTCAACATTA >EAS54_73:5:3:233:911 GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC >EAS54_73:5:3:233:911 TGGCTGATTATGAAAACAATGTTCCCCAGATACCA >EAS54_73:5:44:498:945 ATAGGGATGGAGGGAAGAGGGCCGCTGAAGAACTT >EAS54_73:5:44:498:945 CCTATAAGCCGTTCTATTTGTAATGAAAACTATAT >EAS54_73:5:53:61:31 AAGAAACTCATTAATAAAGACATGAGTTCAGATAA >EAS54_73:5:53:61:31 CAATTCAGCAAGAAGATATAACCATCCTACTAAAT >EAS54_73:7:134:243:630 ACATTACTACCCTGCAATTAATATAATTGTGTCCA >EAS54_73:7:134:243:630 TCATCTAGGGGAACAGGGAGGCGCACTAATGAGCT >EAS54_73:7:200:65:291 CAATACTCACCATCATAAATACACACAAAAGTACA >EAS54_73:7:200:65:291 CTAACTATATGCTGTTTACAAGAAACTCATTAATA >EAS54_73:7:223:440:667 AATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATT >EAS54_73:7:223:440:667 TTCAGAACTTGAAGACAAGTCTCTTATGAATTAAC >EAS54_73:7:254:572:431 AAGAGATATAGATTGGCAGAACAGATTTAAAAACA >EAS54_73:7:254:572:431 ATCAGATAAAGCACACTTTAAATCAACAACAGTAA >EAS54_73:7:63:854:610 AATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGT >EAS54_73:7:63:854:610 GACTATTGCCAGATGAACCACACATTAATACTATG >EAS54_73:7:97:892:419 AATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTA >EAS54_73:7:97:892:419 GCAACTAGGTAAAAAATTAACATTACAACAGGAAC >EAS54_81:2:128:394:455 GTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTC >EAS54_81:2:128:394:455 TTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTT >EAS54_81:2:27:856:401 ACCTCTACATGGCTGATTATGAAAACAATGTTCCC >EAS54_81:2:27:856:401 TCATCTAGGGGAACAGGGAGGTGCACTAATGCGCT >EAS54_81:2:280:512:316 GGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTG >EAS54_81:2:280:512:316 TTACTGTCATAACTATGAAGAGACTATTGCCAGCT >EAS54_81:2:285:367:932 ATAGACCCCCTTGCAACAACCTTGAGAACCCCAGG >EAS54_81:2:285:367:932 GCGTAACTGCGCTCTCATTCACTCCAGCTCCCTGT >EAS54_81:2:317:72:221 AAAAAAATTCTAAAATCAGCAAGAGAAAAGCATAC >EAS54_81:2:317:72:221 ATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTC >EAS54_81:2:31:98:804 CACGAATGCGTCTCTACCACAGGGGGCTGCGCGGC >EAS54_81:2:31:98:804 CTTTACTGTCATAACTATGAAGAGACTATTGCCAG >EAS54_81:2:49:330:699 AAAGTTCAATACTCACCATCATAAATACACACAAA >EAS54_81:2:49:330:699 TTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAA >EAS54_81:2:5:491:391 CCCTGCTCACAGTTTCTGCCCCCAGCATGGTTGTA >EAS54_81:2:5:491:391 TTGGCATTTGCCTTCAGACCCTACACGAATGCGTC >EAS54_81:6:11:801:386 AAAGGGATTAAATTCCCCCACTTAAGAGATATAGA >EAS54_81:6:11:801:386 CACTATAAATCAACAACAGTAAAATAAAACAAAGG >EAS54_81:6:122:589:134 AAAACCTGTCAAACACGAATGTTATGCCCTGCTAA >EAS54_81:6:122:589:134 ACAGACTTCATCAAGATATGTAGTCATCAGACTAT >EAS54_81:6:199:511:426 AATTCTTCATCCTGGACCCTGAGAGATTCTGCAGC >EAS54_81:6:199:511:426 GGGGTATAATACCTCTACATGGCTGATTATGAAAA >EAS54_81:6:204:779:181 AACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATG >EAS54_81:6:204:779:181 CTTTTGGCATTTGCCTTCAGACCCTACACGAATGC >EAS54_81:6:265:251:147 AAAAGTACAAAACTCACAGGTTTTATAAAACAATT >EAS54_81:6:265:251:147 TGTTATGCCCTGCTAAACTAAGCATCATAAATGAA >EAS54_81:6:273:424:207 AAGAGATATAGATTGGCAGAACAGATTTAAAAACA >EAS54_81:6:273:424:207 TAAATCAACAACAGTAAAATAAAACAAAGGAGGTC >EAS54_81:6:35:186:412 ATAACCATCCTACTAAATACATATGCACCTAACAC >EAS54_81:6:35:186:412 CATGTAACAAATCTGCGCTTGTACTTCTAAATCTA >EAS54_81:6:75:917:886 ACTGGGCAATACATGAGATTATTAGGAAATGCTTT >EAS54_81:6:75:917:886 TTATCATGACTCTATCCCAAATTCCCAATTACGTC >EAS54_81:7:124:253:889 CTAAGCATCATAAATGAAGGGGAAATAAAGTCAAG >EAS54_81:7:124:253:889 TCAGCAAGAGAAAAGCATACAGTCATCTATAAAGG >EAS54_81:7:166:979:531 ATCCCACGCTTCCTATGGAAAGGTTGTTGGGAGAT >EAS54_81:7:166:979:531 TGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCCC >EAS54_81:7:226:869:36 ATATATAAAGGAAATCCCATCAGAATAACAATGGG >EAS54_81:7:226:869:36 TGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTG >EAS54_81:7:246:205:734 CTCCAGGGAAGTTATCTCTCATCTAGANNNNNTTG >EAS54_81:7:246:205:734 CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGT >EAS54_81:7:293:355:321 GCTAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTC >EAS54_81:7:293:355:321 TTACCAAATGTGTTTATTACCAGAGGGATGGAGGG >EAS54_81:7:324:472:791 AAAGCCAATACTTTACTGCTACTCAATATATCCAT >EAS54_81:7:324:472:791 TGATAAAAAGATCAATTCAGCAAGAAGATATAACC >EAS54_81:7:325:150:465 AACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATG >EAS54_81:7:325:150:465 TGATGCCCTCTTCTTCCAAAGATGAAACGCGTAAC >EAS54_81:7:74:596:137 CTCTATCCCAAATTCCCAATTACGTCCTATCTTCT >EAS54_81:7:74:596:137 GGTCCCTGCCCCATCGCTTGTAATCTCTCGCCTTT >EAS54_81:8:130:912:658 TACACACACATGGTTTAGGGGTATAATACCTCTAC >EAS54_81:8:130:912:658 TCCCATCATGAAGCACTGAACTTCCACGTCTCATC >EAS54_81:8:142:858:903 ATGGTTGTACTGGGCAATACATGAGATTATTAGGA >EAS54_81:8:142:858:903 CTATCCCAAATTCCCAATTACGTCCTATCTTCTTC >EAS54_81:8:14:360:580 ACCCTACACGAATGCGTCTCTACCACAGGGGGCGG >EAS54_81:8:14:360:580 ATGAGATTATTAGGAAATGCTTTACTGTCATAACT >EAS54_81:8:159:71:155 AAAGGTTGTTGGGAGATTTTTAATGATTCCTCGAT >EAS54_81:8:159:71:155 GTCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAA >EAS54_81:8:177:800:714 CTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGAT >EAS54_81:8:177:800:714 TTCTCAGCAGAAACCTTACAAGCCAGAAGAGATTG >EAS54_81:8:271:180:509 AATACTCACCATCATAAATACACACAAAAGTACAA >EAS54_81:8:271:180:509 ATATAGATTGGCAGAACAGATTTAAAAACATGAAC >EAS54_81:8:40:925:442 GAGGTTCAGAACTTGAAGACAAGTCTCTTATGAAT >EAS54_81:8:40:925:442 TTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCT >EAS54_81:8:41:530:663 AGAACAGATTTAAAAACATGAACTAACTATATGCT >EAS54_81:8:41:530:663 ATACTCACCATCATAAATACACACAAAATTACAAA >EAS54_81:8:63:930:152 ACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATTC >EAS54_81:8:63:930:152 ATCCCACGCTTCCTATGGAAAGGTTGTTGGGAGAT >EAS54_81:8:78:735:536 TTTTTTTTTTTTTCATTTCTCTTTTTTTTTTTTTT >EAS56_53:1:124:243:35 GCATATCCAGATTGCTGGTGGTCTGACAGGCAGCA >EAS56_53:1:124:243:35 TGTGTTTATTACCAGAGGGATGGAGGGAAGAGCGA >EAS56_53:1:154:118:488 AAAAGCATACAGTCATCTATAAAGGAAATCCCATC >EAS56_53:1:154:118:488 AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGA >EAS56_53:1:23:403:981 TACTGTCATAACTATGAAGAGACTATTGCCAGATG >EAS56_53:1:23:403:981 TCTTCATAGGGAAGAACAGCTTAGGTATCAATTTG >EAS56_53:1:47:303:887 ACATTACTACCCTGCCATTAATATACTTGTGTCCA >EAS56_53:1:47:303:887 CACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGA >EAS56_53:1:92:875:345 AAATGCTCAAAAGAATTGTAAAAGTCAAAATTAAA >EAS56_53:1:92:875:345 CGGAAACCTTACAAGCCAGAAGAGATTGGATCTAA >EAS56_53:2:170:265:818 GAGGGGAAGCTTTCAACGCTTCTAGCACTTTCTTT >EAS56_53:2:170:265:818 TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG >EAS56_53:2:59:286:290 AAAGGAAATCCCATCAGAATAACAATGGGCTTCTC >EAS56_53:2:59:286:290 TCAAGTCTTTCCTGACAAGCAAATGCTAAGATAAT >EAS56_53:3:101:809:776 GTACTTCTAAATCTATAAAAAAATTAAAATTTAAC >EAS56_53:3:101:809:776 TATGCACCTAACACAAGACTACCCAGATTCATAAA >EAS56_53:3:107:738:484 GGTCATCATACAATGATAAAAAGATCAATTCAGCA >EAS56_53:3:107:738:484 TGAACTAACTATATGCTGTTTACAAGAAACTCATT >EAS56_53:3:126:558:408 TTCTATTTGTAATGAAAACTATATTTATGCTATTC >EAS56_53:3:126:558:408 TTTATTACCAGAGGGATGGAGGGAAGAGGGACGCT >EAS56_53:3:134:126:465 AAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAA >EAS56_53:3:134:126:465 AAATCAGCAAGAGAAAAGCATACAGTCATCTATAA >EAS56_53:4:130:568:978 TAAATATAGAAATTGAAACAGCTGTGTTTAGTGAC >EAS56_53:4:130:568:978 TGAAACGCGAAACTGCACTCTCATTCACTCCAGCT >EAS56_53:4:153:977:200 TCATCAACCTCATACACACACATGGTTTAGGGGTA >EAS56_53:4:153:977:200 TGTCACCCAATGGACCTGTGATATCTGGATTCTGG >EAS56_53:4:154:762:630 AGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTT >EAS56_53:4:154:762:630 CCTTCAGACCCTACACGAATGCGTCTCTACCACAG >EAS56_53:4:168:528:288 CAGGCTGCAACTGTGAGCCATCACAATGAACAACA >EAS56_53:4:168:528:288 GCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCC >EAS56_53:4:45:707:147 AAAAATTCTAAAATCAGCAAGAGAAAAGCATACAG >EAS56_53:4:45:707:147 ATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAG >EAS56_53:6:180:695:621 ATACAGTCATCTATAAAGGAAATCCCATCAGAATA >EAS56_53:6:180:695:621 TACTGAAAAGCAAATGCTAAGATAATTCATCATCA >EAS56_53:7:22:22:934 ATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAA >EAS56_53:7:22:22:934 CTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTG >EAS56_53:8:122:430:882 CCTACTAAATACATATGCACCTAACACAAGACTAC >EAS56_53:8:122:430:882 CTATAAAAAAATTAAAATTTAACAAAAGTAAATAA >EAS56_53:8:179:549:753 TACTACCCTGCAATTAATATAATTGTGTCCATGTA >EAS56_53:8:179:549:753 TGTCCTCCCATCTGGCCTCGTCCACACTGGTTCTC >EAS56_53:8:28:701:724 TGGACCCTGAGAGATTCTGCAGCCCAGCTCCAGAT >EAS56_53:8:28:701:724 TTTTGTCAGTTACCAAATGTGTTTATTACCAGAGG >EAS56_57:1:122:38:103 ATAAAACAATTAATTGAGACTACAGAGCAACTAGG >EAS56_57:1:122:38:103 GAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTAC >EAS56_57:1:125:884:276 TTGCAAGACAGACTTCATCAAGATATGTAGTCATC >EAS56_57:1:125:884:276 TTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAAC >EAS56_57:1:189:130:136 ATTTAGACATCTAAATGAAAGAGGCTCAAAGAATG >EAS56_57:1:189:130:136 GGCTTCTCAGCAGAAACCTTACAAGCCAGAAGAGA >EAS56_57:1:189:503:110 ATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGA >EAS56_57:1:189:503:110 CTAACAATAGACTAAACCAAGCAGAAGAAAGAGTT >EAS56_57:1:228:182:717 GGTCTGACAGGCTGCAACTGTGAGCCATCCCCATG >EAS56_57:1:228:182:717 TCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAA >EAS56_57:1:278:440:902 AAGCACTGAACTTCCACGTCTCATCTAGGGGAACA >EAS56_57:1:278:440:902 ATACTATGTTTCTTATCTGCACATTACTACCCTGC >EAS56_57:1:288:384:444 TAACTTTGAATAAAAAGGGATTAAATTCCCCCACT >EAS56_57:1:288:384:444 TCAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAA >EAS56_57:2:158:909:321 ATACAGTCATCTATAAAGGAAATCCCATCAGAATA >EAS56_57:2:158:909:321 TTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCT >EAS56_57:2:178:192:499 GTGAGCCATCACAATGAACAACAGGAAGAAAAGGT >EAS56_57:2:178:192:499 TCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCC >EAS56_57:2:206:873:186 ACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCA >EAS56_57:2:206:873:186 GTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTG >EAS56_57:2:236:841:20 AAAGGAAATCCCATCAGAATAACAATGGGCTTCTC >EAS56_57:2:236:841:20 GCTAAGATAATTCATCATCACTAAACCAGTCCTAT >EAS56_57:2:237:855:581 CTAAACGCCCATACTTTACTGCTACTCAATATATC >EAS56_57:2:237:855:581 TACAATGATAAAAAGATCAATTCAGCAAGAAGATA >EAS56_57:2:23:268:529 TGAAAGAGGCTCAAAGAATGCCAGGAAGATACATT >EAS56_57:2:259:42:969 GCTGTAATGATGCCCCTTGGCCATCACCCGGTCCC >EAS56_57:2:259:42:969 GGAAAGGTTGTTGGGAGATTTTTAATGATTCCTCA >EAS56_57:2:262:297:601 TGGACCTGTGATATCTGGATTCTGGGAAATTCTTC >EAS56_57:2:262:297:601 TGTTCTCATCAACCTCATACACACACATGGTTTAG >EAS56_57:2:284:597:682 AAAAAAAAACCTGTCAAACACGAATGTTATGCCCT >EAS56_57:2:284:597:682 TTCATCAAGATATGTAGTCATCAGACTATCTAAAG >EAS56_57:2:44:153:969 AAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAA >EAS56_57:2:44:153:969 AAAAGCATACAGTCATCTATAAAGGAAATCCCATC >EAS56_57:3:112:729:591 ATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTT >EAS56_57:3:112:729:591 GAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCT >EAS56_57:3:119:761:239 CGTCTCTACCACAGGGGGCTGCGCGGTTTCCCATC >EAS56_57:3:119:761:239 TGAAGAGACTATTGCCAGATGAACCACACATTAAT >EAS56_57:3:285:489:327 AATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGA >EAS56_57:3:285:489:327 CTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAA >EAS56_57:3:319:174:811 CACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATG >EAS56_57:3:319:174:811 TTATCTGCACATTTCTACCCTGCAATTAATATAAT >EAS56_57:3:41:739:907 CAGAAGAGATTGGATCTAATTTTTGGACTTCTTAA >EAS56_57:3:41:739:907 GAATGCCAGGAAGATACATTGCAAGACAGACTTCA >EAS56_57:3:81:786:340 TACTATGTTTCTTATCTGCACATTACTACCCTGCA >EAS56_57:3:81:786:340 TCCACGTCTCATCTAGGGGAACAGAGAGGTGCACT >EAS56_57:4:233:478:792 GCCTTCAGACCCTACACGAATGCGTCTCTACCACA >EAS56_57:4:233:478:792 GTGTTCTCATCAACCTCATACACACACATGGTTTA >EAS56_57:4:262:965:756 AGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCC >EAS56_57:4:262:965:756 TTAATATAATTGTGTCCATGTACACACGCTGTCCT >EAS56_57:4:71:707:568 CTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTG >EAS56_57:4:71:707:568 GTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGAT >EAS56_57:4:98:862:154 AAAGATCAATTCAGCAAGAAGATATAACCATCCTA >EAS56_57:4:98:862:154 TGCTACTCAATATATCCATGTAACAAATCTGCGCT >EAS56_57:5:105:521:563 TATGTACTTATCATGACTCTATCCCAAATTCCCAA >EAS56_57:5:105:521:563 TGTAATGCTGCCCCTTGGCCATCCCCCGGTCCCTG >EAS56_57:5:136:389:320 TCCTATGTACTTATCATGACTCTATCCCAAATTCC >EAS56_57:5:136:389:320 TTCTGCCCCCAGCATGGTTGTACTGGGCAATACAT >EAS56_57:5:145:383:182 AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT >EAS56_57:5:145:383:182 TTGAAGACAAGTCTCTTATGAATTAACCCAGTCAG >EAS56_57:5:207:926:427 GGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTG >EAS56_57:5:207:926:427 TAGGAAATGCTTTACTGTCATAACTATGAAGAGAC >EAS56_57:5:214:644:390 AAAAACATGAACTAACTATATGCTGTTTACAAGAA >EAS56_57:5:214:644:390 AAATAAAACAAAGGAGGTCATGATACAATGATAAA >EAS56_57:5:24:284:360 AGTCATCAGACTATCTAAAGTCAACATGAAGGAAA >EAS56_57:5:24:284:360 CTGTCAAACACGAATGTTATGCCCTGCTAAACTAA >EAS56_57:5:266:133:789 AAAAAATTAACATTACAACAGGAACAAAACCTCAT >EAS56_57:5:266:133:789 GTGGAAAAAGATGTTCTACGCAAACAGAAACCAAA >EAS56_57:5:303:542:924 AATAAAACAAAGGAGGTCATCATACAATGATAAAA >EAS56_57:5:303:542:924 CAATGTACAATATTCTGATGATGGTTACACTAAAA >EAS56_57:5:309:109:987 AACAAATACTACTAGACCTAAGAGGGATGAGAAAT >EAS56_57:5:309:109:987 GAGAGAAGGAGTAGCTATACTTATATCAGATAAAG >EAS56_57:5:30:788:376 ACGTCTCATCTAGGGGAACAGGGAGGTGCACTAAT >EAS56_57:5:30:788:376 TGTTTCTTATCTGCACATTACTACCCTGCAATTAA >EAS56_57:5:324:728:956 ATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGT >EAS56_57:5:324:728:956 TGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCTCT >EAS56_57:5:53:544:889 AGGCTCAAAGAATGCCAGGAAGATACATTGCAAGA >EAS56_57:5:53:544:889 GCTTCTCAGCGGAAACCTTACAAGCCAGAAGAGAT >EAS56_57:5:71:994:576 AAGATAATTCATCATCACTAAACCAGTCCTATAAG >EAS56_57:5:71:994:576 TAGGTAAAAAATTAACATTACAACAGGAACAAAAC >EAS56_57:6:145:144:796 ATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGTC >EAS56_57:6:145:144:796 GGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGAC >EAS56_57:6:157:643:175 GGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGA >EAS56_57:6:157:643:175 TTCTATTTGTAATGAAAACTATATTTATGCTATTC >EAS56_57:6:175:289:351 CATCCTACTAAATACATATGCACCTAACACAAGAC >EAS56_57:6:175:289:351 TGCGCTTGTACTTCTAAATCTATAAAAAAATTAAA >EAS56_57:6:190:289:82 AGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCAC >EAS56_57:6:190:289:82 CTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA >EAS56_57:6:21:553:57 AAATACTACTAGACCTAAGAGGGATGAGAAATTAC >EAS56_57:6:21:553:57 AACAAAAGTAAATAAAACACATAGCTAAAACTAAA >EAS56_57:6:234:787:12 AAGCTTGGGCTGTAATGATGCCCCTTGGCCATCAC >EAS56_57:6:234:787:12 ACACGCTGGCCTATGTACTTATAATGACTCTATCC >EAS56_57:6:325:759:288 GCTGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCT >EAS56_57:6:325:759:288 GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAC >EAS56_57:6:44:280:641 AACCCCCTTGCAACAACCTTGAGAACCCCAGGGAA >EAS56_57:6:44:280:641 TCATTCACTCCAGCTCCCTGTCACCCAATGGACCT >EAS56_57:6:4:223:776 AGTAACTGAACCTATGAGTCACAGGTATTCCTGAG >EAS56_57:6:4:223:776 TGTAGTCATCAGACTATCTAAAGTCAACATGAAGG >EAS56_57:7:159:125:297 GCAAGCTAGAGTCCCATTTGGAGCCACTCTAAGAC >EAS56_57:7:159:125:297 GGAAGGAGCATTTTGTCAGTTACCAAATGTGTTTA >EAS56_57:7:247:522:670 CTATCCCAAATTCCCAATTACGTCCTATCTTCTTC >EAS56_57:7:247:522:670 TACATGAGATTATTAGGAAATGCTTTACTGTCATA >EAS56_57:7:273:562:954 AAAGTTCAATACTCACCATCATAAATACACACAAA >EAS56_57:7:273:562:954 TTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAA >EAS56_57:7:287:258:321 TAATACTATGTTTCTTATCTGCACATTACTACCCT >EAS56_57:7:287:258:321 TGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCAT >EAS56_57:7:33:954:724 CCTAAGAGGGATGAGAAATTACCTAATTGGTACAA >EAS56_57:7:33:954:724 TCAGATAAAGCACACTTTAAATCAACAACAGTAAA >EAS56_57:7:57:826:977 ATTGGATCTAATTTTTGGACTTCTTAAAGAAAAAA >EAS56_57:7:57:826:977 TGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTT >EAS56_57:7:76:786:458 GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAC >EAS56_57:7:76:786:458 TCTGGGAAATTCTTCATCCTGGACCCTGAGAGATT >EAS56_57:8:72:44:435 AAAAGCAAAAACAAAAACTATGCTAAGTATTGGTA >EAS56_57:8:72:44:435 ATTGGTACAATGTACAATATTCTGATGATGGTTAA >EAS56_59:1:126:526:276 GAACTTCTGTAATTGAAAAATTCATTTAAGAAATT >EAS56_59:1:128:584:952 ATCATACAATGATAAAAAGATCAATTCAGCAAGAA >EAS56_59:1:128:584:952 GCCCATACTTTACTGCTACTCAATATATCCATGTA >EAS56_59:1:219:294:861 CTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCC >EAS56_59:1:219:294:861 TATAATTGTGTCCATGTACACACGCTGTCCTCTGT >EAS56_59:1:248:122:558 AATGTACAATATTCTGATGATGGTTACACTAAAAG >EAS56_59:1:248:122:558 GGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGA >EAS56_59:1:278:906:933 AATATAATTGTGTCCATGTACACACGCTGTCCTAT >EAS56_59:1:278:906:933 TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG >EAS56_59:1:82:670:302 AGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACG >EAS56_59:1:82:670:302 TCCTACTAAATACATATGCACCTAACACAAGACTA >EAS56_59:1:93:490:901 AGAAAAGCATACAGTCATCTATAAAGGAAATCCCA >EAS56_59:1:93:490:901 GTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGA >EAS56_59:2:104:402:732 AAATCAGCAAGAGAAAAGCATACAGTCATCTATAA >EAS56_59:2:104:402:732 AATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACA >EAS56_59:2:162:272:415 ACATGAACTAACTATATGCTGTTTACAAGAAACTC >EAS56_59:2:162:272:415 ATAAAAAGATCAATTCAGCAAGAAGATATAACCAT >EAS56_59:2:177:266:842 ACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGT >EAS56_59:2:177:266:842 GGCATTTGCCTTCAGACCCTACACGAATGCGTCTC >EAS56_59:2:177:552:234 ACGCTGTCCTATGTACTTATCATGACTCTATCCCA >EAS56_59:2:177:552:234 GCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCC >EAS56_59:2:201:768:529 AGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTT >EAS56_59:2:201:768:529 CAGACTATCTAAAGTCAACATGAAGGAAAAAAATT >EAS56_59:2:239:1001:406 AGCATACAGTCATCTATAAAGGAAATCCCATCAGA >EAS56_59:2:239:1001:406 CTTTCCTGACAAGCAAATGCTAAGATAATTCATCA >EAS56_59:2:60:677:921 CATCAGACTATCTAAAGTCAACATGAAGGAAAAAA >EAS56_59:2:60:677:921 GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAAT >EAS56_59:3:149:953:349 AGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTG >EAS56_59:3:149:953:349 TTCTTTTGGCATTTGCCTTCAGACCCTACACGAAT >EAS56_59:3:166:626:836 AGTACAAAACTCACAGGTTTTATAAAACAATTAAT >EAS56_59:3:166:626:836 CTGTCAAACACGAATGTTATGCCCTGCTAAACTAA >EAS56_59:3:182:1002:639 AAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAG >EAS56_59:3:182:1002:639 AACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGA >EAS56_59:3:316:25:230 GATGCCCCTTGGCCATCACCCGGTCCCTGCCCCAT >EAS56_59:3:316:25:230 TGTCCTATGTACTTATCATGACTCTATCCCAAATT >EAS56_59:4:119:651:88 GATTGGATCTAATTTTTGGACTTCTTAAAGAAAAA >EAS56_59:4:119:651:88 GCTCAAAGAATGCCAGGAAGATACATTGCAAGACA >EAS56_59:4:262:928:237 TGAGTTCAGGTAAAGGTGTGGAAAAAGATGTTCTA >EAS56_59:4:262:928:237 TTGAGACTACAGAGCAACTAGGTAAAAAATTAACA >EAS56_59:4:267:394:437 AAACATCATAAATACACACAAAAGTACAAAACTCA >EAS56_59:4:267:394:437 GGACTTCTTAAAGAAAAAAAAACCTGTCAAACACG >EAS56_59:4:278:524:521 CACATTAATACTATGTTTCTTATCTGCACATTACT >EAS56_59:4:278:524:521 CCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAA >EAS56_59:4:329:577:757 AACGCGTAACTGCGCTCTCATTCACTCCAGCTCCC >EAS56_59:4:329:577:757 TCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAAG >EAS56_59:5:113:694:725 CTGTAATGATGCCCCTTGGCCATCACCCGGTCCCT >EAS56_59:5:113:694:725 GTACACACGCTGTCCTATGTACTTATCATGACTCT >EAS56_59:5:125:137:58 AACTATATGCTGTTTACAAGAAACTCATTAATAAA >EAS56_59:5:125:137:58 GGTTTTATAAAACAATTAATTGAGACTACAGAGCA >EAS56_59:5:181:713:140 AGGGGAAATAAAGTCAAGTATTTCCTGACAAGCAA >EAS56_59:5:181:713:140 CTACAGAGCAACAAGGTAAAAAATTAACATTACAA >EAS56_59:5:198:929:684 AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGA >EAS56_59:5:198:929:684 GAAATCCCATCAGAATAACAATGGGCTTCTCAGCA >EAS56_59:5:232:336:46 ATTTTTTTTTTTTCTTTTCTCTTGTTTCTTTTTTT >EAS56_59:5:325:544:349 AAAATTAAAGTTCAATACTCACCATCATAAATACA >EAS56_59:5:325:544:349 CAAGCCAGAAGAGATTGGATCTAATTTTTGGACTT >EAS56_59:5:90:629:652 AGCCCATACTTTACTGCTACTCAATATATCCATGT >EAS56_59:5:90:629:652 ATATTGCTAGTGGGAGTATAAATTGTTTTCCACTT >EAS56_59:6:187:925:547 GGCTGATTATGAAAACAATGTTCCCAAGATACCAT >EAS56_59:6:187:925:547 TGAACTTCCACGTCTCATCTAGGGGAACAGGGAGG >EAS56_59:6:199:327:965 ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT >EAS56_59:6:199:327:965 NCAACAACCTTGAGAACCCCAGGGAATTTGTCAAT >EAS56_59:6:227:657:95 GTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGA >EAS56_59:6:227:657:95 GTCATCTATAAAGGAAATCCCATCAGAATAACAAT >EAS56_59:6:286:753:854 TCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTC >EAS56_59:6:286:753:854 TTATCATGACTCTATCCCAAATTCCCAATTACGTC >EAS56_59:6:312:837:406 AGGTGCACTAATGCGCTCCACGCCCAAGCCCTTCT >EAS56_59:6:312:837:406 CTGCACATTACTACCCTGCAATTAATATAATTGTG >EAS56_59:6:3:186:68 AAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATT >EAS56_59:6:3:186:68 TTACAAGCCAGAAGAGATTGGATCTAATTTTTGTA >EAS56_59:6:89:457:591 ATGCCCTGCTAAACTAAGCATCATAAATGAAGGGG >EAS56_59:6:89:457:591 CAGGTTTTATAAAACAATTAATTGAGACTACATAG >EAS56_59:7:260:985:520 TCCCTGTCACCCAATGGACCTGTGATATCTGGATT >EAS56_59:7:260:985:520 TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA >EAS56_59:7:318:679:883 GATTTAGACATCTAAATGAAAGAGGCTCAAAGAAT >EAS56_59:7:319:246:304 CTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGA >EAS56_59:7:319:246:304 TGTCACCCAATGGACCTGTGATATCTGGATTCTGG >EAS56_59:7:82:902:868 CTGTCACCCAATGGACCTGTGATATCTGGATTCTG >EAS56_59:7:82:902:868 TTGCAACAACCTTGAGAACCCCAGGGAATTTGTCA >EAS56_59:8:49:182:192 ACACAAAAGTACAAAACTCACAGGTTTTATAAAAC >EAS56_59:8:49:182:192 GTTATGCCCTGCTAAACTGAGCATCATAAATGAAG >EAS56_59:8:80:542:549 AGTAAACTCTCAAATATTGCTAGTGGGAGTATAAA >EAS56_59:8:80:542:549 CTAAAAGCCCATACTTTACTGCTACTCAATATATC >EAS56_61:1:119:880:781 ACAAATCTGCGCTTGTACTTCTAAATCTATAACAA >EAS56_61:1:119:880:781 ACATATGCACCTAACACAAGACTACCCAGATTCAT >EAS56_61:1:210:880:606 GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAT >EAS56_61:1:210:880:606 TCCTGGACCCTGAGAGATTCTGCAGCCCAGCTCCA >EAS56_61:1:303:184:14 CAACCTTGAGAACCCCAGGGAATTTGTCAATGTCA >EAS56_61:1:303:184:14 CAATGGACCTGTGATATCTGGATTCTGGGAAATTC >EAS56_61:2:152:860:286 AGACTATTGCCAGATGAACCACACATTAATACTAT >EAS56_61:2:152:860:286 TTAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCA >EAS56_61:3:140:522:212 CGCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGA >EAS56_61:3:140:522:212 GACAGGCTGCAACTGTGAGCCATCACAATGAACAA >EAS56_61:3:165:665:220 ACAATTAATTGAGACTACAGAGCAACTAGGTAAAA >EAS56_61:3:165:665:220 GGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATG >EAS56_61:3:208:118:673 AAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA >EAS56_61:3:208:118:673 GAACAGAGCTTTCAAGAAGTATGAGATTATGTAAA >EAS56_61:3:260:827:289 AAACCTCATATATCAATATTAACTTTGAATAAAAA >EAS56_61:3:260:827:289 TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA >EAS56_61:3:45:758:616 ATAAATTGTTTTCCACTTTGGAAAACAATTTGGTA >EAS56_61:3:45:758:616 CATACTTTACTGCTACTCAATATATCCATGTAACA >EAS56_61:3:5:45:441 TTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTT >EAS56_61:4:262:456:74 TACCAAATGTGTTTATTACCAGAGGGATGGAGGGA >EAS56_61:4:262:456:74 TGGGAAATTCTTCATCCTGGACCCTGAGAGATTCT >EAS56_61:5:194:470:416 AAACTATTTGAGGAAGTAATTGGGGAAAACCTCTT >EAS56_61:5:194:470:416 TCAGAACTTGAAGACAAGTCTCTTATGAATTAACC >EAS56_61:5:209:824:866 ATCATCACTAAACCAGTCCTATAAGAAATGCTCAA >EAS56_61:5:209:824:866 CAGCAACAAAACCTCATATATCAATATTAACTTTG >EAS56_61:5:263:314:696 AACTCATTAATAAAGACATGAGTTCAGGTAAAGGG >EAS56_61:5:263:314:696 AAGATCAATTCAGCAAGAAGATATAACCATCCTAC >EAS56_61:5:272:240:950 CAGCAGAGCTTGGATCTAATTTTTGGACTTCTTCA >EAS56_61:5:272:240:950 TCAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAA >EAS56_61:6:10:106:737 ACAAGAAACTCATTAATAAAGACATGAGTTCAGGT >EAS56_61:6:10:106:737 ACAATGATAAAAAGATCAATTCAGCAAGAAGATAT >EAS56_61:6:160:272:398 AATGTTCCCCAGATACCATCCCTGTCTTACTTCCA >EAS56_61:6:160:272:398 GTGCACTAATGCGCTCCACGCCCAAGCCCTTCTCA >EAS56_61:6:226:370:91 AGAATAACAATGGGCTTCTCAGCGGAAACCTTACA >EAS56_61:6:226:370:91 AGGCTCAAAGAATGCCAGGAAGATACATTGCAAGA >EAS56_61:6:227:259:597 AATATAGAAATTGAAACAGCTGTGTTTAGTGCCTT >EAS56_61:6:256:67:461 TCATGTTTGTGTCTTTCTATGCATTTTTTTTTTTT >EAS56_61:6:256:67:461 TTGTTTTTTCTTCTTTTCTCTTTTTTTTTTTTTTT >EAS56_61:6:283:963:234 AAAAAGATGTTCTACGCAAACAGAAACCAAATGAG >EAS56_61:6:283:963:234 ACATATGCACCTAACACAAGACTACCCAGATTCAT >EAS56_61:6:307:208:477 AAAGTCAAAATTAAAGTTCAATACTCACCATCATA >EAS56_61:6:307:208:477 ACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAA >EAS56_61:7:280:133:495 AGATGAACCACACATTAATACTATGTTTCTTATCT >EAS56_61:7:280:133:495 CCATCATGAAGCACTGAACTTCCACGTCTCATCTA >EAS56_61:7:41:745:603 CATTGCAAGACAGACTTCATCAAGATATGTAGTCA >EAS56_61:7:41:745:603 TAATTTTTGGACTTCTTAAAGAAAAAAAAACCTGT >EAS56_61:7:7:682:201 CATACAGTCATCTATAAAGGAAATCCCATCAGAAT >EAS56_61:7:7:682:201 GGAAAACCTCTTTAGTCTTGCTAGAGATTTAGACA >EAS56_61:8:60:358:494 GGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACA >EAS56_61:8:60:358:494 TACCCAGATTCATAAAACAAATACTACTAGACCTA >EAS56_61:8:7:171:402 GTGATATCTGGATTCTGGGAAATTCTTCATCCTGG >EAS56_61:8:7:171:402 TCTACATGGCTGATTATGAAAACAATGTTCCCCAG >EAS56_63:1:119:446:185 TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT >EAS56_63:1:119:446:185 TTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAG >EAS56_63:1:145:71:26 CTAGGGGAACAGGGAGGTGCACTAATGCGCTCCAC >EAS56_63:1:145:71:26 TTTCTTATCTGCACATTACTACCCTGCAATTAATA >EAS56_63:2:119:161:322 ATCAGAATAACAATGGGCTTCTCAGCAGAAACCTT >EAS56_63:2:119:161:322 CTTTAGTCTTGCTAGAGATTTAGACATCTAAATGA >EAS56_63:2:33:357:858 AAAATTAAAGTTCAATACTCACCATCATAAATACA >EAS56_63:2:33:357:858 AGGGATTAAATTCCCCCACTTAAGAGATATAGATT >EAS56_63:2:74:656:272 AACAAAGGAGGTCATCATACAATGATAAAAAGATC >EAS56_63:2:74:656:272 TGTACAATATTCTGATGATGGTTACACTAAAAGCC >EAS56_63:3:40:594:752 ATACACACACATGGTTTAGGGGTATAATACCTCTA >EAS56_63:3:40:594:752 CTGCGCGGTTTCCCATCATGAAGCACTGAACTTCC >EAS56_63:3:41:468:459 AAATTTAACAAAAGTAAATAAAACACATAGCTAAA >EAS56_63:3:41:468:459 TTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTT >EAS56_63:3:93:1002:845 AATTCCCAATTACGTCCTATCTTCTTCTTAGGGAA >EAS56_63:3:93:1002:845 GGGCAATACATGAGATTATTAGGAAATGCTTTACT >EAS56_63:4:141:9:811 TTTCTTTTCTCCTTTTTTTTTTTTTTTTTCTACAT >EAS56_63:4:184:659:377 AAAAAGATGTTCTACGCAAACAGAAACCAAATGAG >EAS56_63:4:184:659:377 CAAAACTACCCAGATTCATAAAACAAATACTACTA >EAS56_63:4:38:28:122 AAATATAGTTGAAAGCTCTAACAATAGACTAAACC >EAS56_63:4:38:28:122 GTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTG >EAS56_63:5:117:570:971 ACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAG >EAS56_63:5:117:570:971 ACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGA >EAS56_63:5:123:998:248 ATCACAATGAACAACAGGAAGAAAAGGTCTTTCAA >EAS56_63:5:123:998:248 TTTCTTTTGGCATTTGCCTTCAGACCCTACACGAA >EAS56_63:5:36:678:316 ATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAA >EAS56_63:5:36:678:316 TTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTTA >EAS56_63:5:96:788:614 TAGGGGTATAATACCTCTACATGGCTGATTATGAA >EAS56_63:5:96:788:614 TTCCACGTCTCATCTAGGGGAACAGGGAGGTGCAC >EAS56_63:6:102:816:260 AAATTACCTAATTGGTACAATGTACAATATTCTGA >EAS56_63:6:102:816:260 TCAGATAAAGCACACTTTAAATCAACAACAGTAAA >EAS56_63:6:42:920:522 AATTAATATAATTGTGTCCATGTACACACGCTGTT >EAS56_63:6:42:920:522 CTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCC >EAS56_63:6:91:360:585 AAGATGAAACGCGTAACTGCGCTCTCATTCACTCC >EAS56_63:6:91:360:585 GACATCACAATGAACAACAGGAAGAAAAGGTCTTT >EAS56_63:7:109:22:383 ATGTACAATATTCTGATGATGGTTACACTAAAAGC >EAS56_63:7:109:22:383 CAACAACAGTAAAATAAAACAAAGGAGGTCATCAT >EAS56_63:7:137:139:248 GTCAAACACGAATGTTATGCCCTGCTAAACTAAGC >EAS56_63:7:137:139:248 TATCTAAAGTCAACATGAAGGAAAAAAATTCTAAA >EAS56_63:7:166:42:147 AATGCGCTCCACGCCCAAGCCCTTCTAACAGTTTC >EAS56_63:7:166:42:147 CTGCACATTACTACCCTGCAATTAATATAATTGTG >EAS56_63:7:185:213:330 CAATGTCAGGGAAGGAGCATTTTGTCAGTTACCAA >EAS56_63:7:185:213:330 TCTGGGAAATTCTTCATCCTGGACCCTGAGAGATT >EAS56_63:7:190:95:706 TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG >EAS56_63:7:190:95:706 TTGTGTCCATGTACACACGCTGTCCTATGTACTTA >EAS56_63:7:34:334:825 CATTTAAGAAATTACAAAATATAGTTGAAAGCTCT >EAS56_63:8:138:186:459 CATTGCAAGACAGACTTCATCAAGATATGTAGTCA >EAS56_63:8:138:186:459 GCCAGAAGAGATTGGAGCTAATTTTTGGACTTCTT >EAS56_63:8:150:508:757 ATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGT >EAS56_63:8:150:508:757 CTTGACACCCAACTAATATTTGTCTGAGCAAAACA >EAS56_63:8:4:571:820 AAGAGATATAGATTGGCAGAACAGATTTAAAAACA >EAS56_63:8:4:571:820 CAACAACAGTAAAATAAAACAAAGGAGGTCATCAT >EAS56_63:8:62:125:888 CGGAAACCTTACAAGCCAGAAGAGATTGGATCTAA >EAS56_63:8:62:125:888 TGCCAGGAAGATACATTGCAAGACAGACTTCATCA >EAS56_65:1:163:846:223 CCAGCTCCCTGTCACCCAATGGACCTGTGATATCT >EAS56_65:1:163:846:223 GCCTTTGTTCACATAGACCCCCTTGCAACAACCTT >EAS56_65:1:178:305:843 ATGTTTCTTATCTGCACATTACTACCCTGCAATTA >EAS56_65:1:178:305:843 CCACGTCTCATCTAGGGGAACAGGGAGGTGCACTA >EAS56_65:1:23:536:229 AAAGCATACAGTCATCTATAAAGGAAATCCCATCA >EAS56_65:1:23:536:229 AAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCA >EAS56_65:1:53:272:944 CAACCCCCTTGCAACAACCTTGCGAACCCCAGGGA >EAS56_65:1:53:272:944 TGCGCTCTCATTCACTCCAGCTCCCTGTCACCCAA >EAS56_65:2:224:579:433 ATAACAATGGGCTTCTCAGCAGAAACCTTACAAGC >EAS56_65:2:224:579:433 TTCATCATCACTAAACCAGTCCTATAAGAAATGCT >EAS56_65:2:56:155:49 ATCCTACTAAATACATATGCACCTAACACAAGACT >EAS56_65:2:56:155:49 ATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCT >EAS56_65:3:168:741:680 AGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCC >EAS56_65:3:168:741:680 TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT >EAS56_65:3:47:64:359 TTTTTTTTTTTCTCTCCTCTTTTTTTTTTTTTTTT >EAS56_65:4:124:367:72 AGACTACCCAGATTCATAAAACAAATACTACTAGA >EAS56_65:4:124:367:72 CATAGCTAAAACTAAAAAAGCAAAAACAAAAACTA >EAS56_65:4:126:966:514 AGAAGAAGTAGCTATACTTATATCAGATAAAGCAC >EAS56_65:4:126:966:514 TAAAAAGGGATTAAATTCCCCCACTTAAGAGATAT >EAS56_65:4:150:94:843 AAAGGGATTAAATTCCCCCACTTAAGAGATATAGA >EAS56_65:4:150:94:843 CAGATACATCCCACTTTAAATCAACCACAGTAAAA >EAS56_65:4:296:78:421 TCTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTT >EAS56_65:4:296:78:421 TGTTGGTGTTCGTTTTTTCTCCTGTTTCTTTTTCT >EAS56_65:5:121:380:656 AATGTGTTTATTACCAGAGGGATGGAGGGAAGAGG >EAS56_65:5:121:380:656 GCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTG >EAS56_65:5:131:742:561 TCAAAAGGTGATGTGTGTTCTCATCAACCTCATAC >EAS56_65:5:131:742:561 TGCCTTCAGACCCTACACGAATGCGTCTCTACCAC >EAS56_65:5:211:84:84 CTATTTGAGGAAGTAATTGGGGAAAACCTCTTTAG >EAS56_65:5:211:84:84 GCAAGAGAAAAGCATACAGTCATCTATAAAGGAAA >EAS56_65:5:262:53:888 AAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGAT >EAS56_65:5:262:53:888 TTGAGACTACAGAGCAACTAGGTAAAAAATTAACA >EAS56_65:5:278:848:765 GTACACACGCTGTCCTATGTACTTATCATGACTCT >EAS56_65:5:278:848:765 TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG >EAS56_65:5:299:336:613 ATCCTACTAAATACATATGCACCTAACACAAGACT >EAS56_65:5:299:336:613 TACTCAATATATCCATGTAACAAATCTGCGCTTGT >EAS56_65:5:30:92:753 TATAATACCTCTACATGGCTGATTATGAAAACAAT >EAS56_65:5:30:92:753 TGGATTCTGGGAAATTCTTCATCCTGGACCCTGAG >EAS56_65:5:312:985:871 ATAAAACACATAGCTAAAACTAAAAAAGCAAAAAC >EAS56_65:5:312:985:871 TAAGAGGGATGAGAAATTACCTAATTGGTACAATG >EAS56_65:5:37:611:267 AATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACA >EAS56_65:5:37:611:267 TATAAAGGAAATCCCATAAGAATAACAATGGGCTT >EAS56_65:5:75:637:650 CTGATTATGAAAACAATGTTCCCCAGATACCATCC >EAS56_65:5:75:637:650 GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC >EAS56_65:6:197:759:975 AAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATA >EAS56_65:6:197:759:975 AATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTC >EAS56_65:6:37:610:260 CAAGCCCTTCTCACAGTTTCTGCCCCCAGCATGGT >EAS56_65:6:37:610:260 CCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTC >EAS56_65:6:46:173:214 AACAATGGGCTTCTCAGCAGAAACCTTACAAGCCA >EAS56_65:6:46:173:214 CTAGAGATTTAGACATCTAAATGAAAGAGGCTCAA >EAS56_65:6:66:257:524 ATACATGAGATTATTAGGAAATGCTTTACTGTCAT >EAS56_65:6:66:257:524 GCCTTCAGACCCTACACGAATGCGTCTCTACCACC >EAS56_65:6:67:800:450 TCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGA >EAS56_65:6:67:800:450 TTACAAAATATAGTTGAAAGCTCTAACAATAGACT >EAS56_65:6:82:822:767 AACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAA >EAS56_65:6:82:822:767 TTAGGAAATGCTTTACTGTCATAACTATGAAGAGA >EAS56_65:7:118:775:467 AACAGTAAAATAAAACAAAGGAGGTCATCATACAA >EAS56_65:7:118:775:467 TGTACAATATTCTGATGATGGTTACACTAAAAGCC >EAS56_65:7:122:398:994 GGGATTAAATTCCCCCACTTAAGAGATATAGATTG >EAS56_65:7:122:398:994 TAAAAGTCAAAATTAAAGTTCAATACTCACCATCA >EAS56_65:7:219:40:833 CCCATACTTTACTGCTACTCAATATATCCATGTAA >EAS56_65:7:219:40:833 GGAGGTCATCATACAATGATAAAAAGATCAATTCA >EAS56_65:7:288:552:440 AGAGGGAACGCTTTCAACTCTTCTAGCCATTTCTT >EAS56_65:7:288:552:440 TGTGGTCTGACAGGCTGCAACTGTGAGCCTTCCAT >EAS56_65:7:67:692:110 ATTGCCAGATGAACCACACATTAATACTATGTTTC >EAS56_65:7:67:692:110 GTATCAATTTGGTGTTCTGTGTAAAGTCTCAGGGA >EAS56_65:8:117:156:84 GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA >EAS56_65:8:117:156:84 TGGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAG >EAS56_65:8:206:563:262 ATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCT >EAS56_65:8:206:563:262 ATTAGGAAATGCTTTACTGTCATAACTATGAAGAG >EAS56_65:8:218:173:667 CCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC >EAS56_65:8:218:173:667 TAATGATTCCTCAATGTTAAAATGTCTATTTTTGT >EAS56_65:8:24:415:944 GTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGC >EAS56_65:8:24:415:944 TAGGTAAAAAATTAACATTACAACAGGAACAAAAC >EAS56_65:8:275:851:240 CCCCAGAGGGAAAGCTTTCAACGTTTCTAGCCATT >EAS56_65:8:275:851:240 GTGGTCTGACAGGCTGCAACTGTGAGCCATCACAA >EAS56_65:8:317:83:500 TTTTTTTTTTTTCTTTTCTCCTTTTTTTTTTGTTT >EAS56_65:8:64:507:478 TAATTGAAAAATTCATTTAAGAAATTACAAAATAT pysam-0.23.0/tests/pysam_data/faidx_ex1.fq000066400000000000000000011617121475062545500204370ustar00rootroot00000000000000@B7_589:1:101:825:28 GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC + <<86<<;<78<<<)<;4<67<;<;<74-7;,;8,; @B7_589:1:101:825:28 TGTGTCCATGTACACACGCTGTCCTATGTACTTAT + 0;0'0;<<<<<<8<;<<<<;;3<<;;<<<8<<<<< @B7_589:1:110:543:934 AAGAATTGTAAAAGTCAAAATTAAAGTTCAATACT + <<<<<5<<;<<<<<<;<<<<<<<<<<<;<<<<<<< @B7_589:1:110:543:934 ACAAGCCAGAAGAGATTGGATCTAATTTTTGGACT + <<<<<<<<<<<<;<<<<<;;<<<;;<<<<<,,;<< @B7_589:1:122:337:968 ACAGGGGGCTGCGCGGTTTCCCATCATGAAGCACT + <<<<<;<<<<<<<<<<<<<<<<<<<;<<;;<;;;; @B7_589:1:122:337:968 GCTTTACTGTCTAAACTATGAAGAGACTATTGCCA + %454<75!7<+!990<9<6<<<<6<<<< @B7_597:6:29:249:878 TCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGG + <<<<<<<<<<<<<<<<<<<<<<:<:<<=<<:<<6& @B7_597:6:73:420:812 CTAAGTATTGGTAAAGATGTGGGGAAAAAAGTAAA + 5'<<<,<&,<<,<<<<<7<<<<<<<<<<<<<<<<< @B7_597:6:73:420:812 CTAATTGGTACAATGTACAATATTCTGATGATGGT + <<<<<1<<<<::1<7<:<96<9<:<<:4<70:11< @B7_597:7:103:731:697 AATTAACCCAGTCAGACAAAAATAAAGAAAAAAGA + <<<<<<<<<<<<<<<<<<:<:<<6<<<<<<<:<;: @B7_597:7:103:731:697 CTTGCTAGAGATTTAGACATCTAAATGAAAGAGGC + :::;3:<<<<<<<:<<<<<<:<<<<<<<<<<<<<< @B7_597:7:113:408:211 AAACTCATTAATAAAGACATGAGTTCAGGTAAAGG + <:;:;:<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @B7_597:7:113:408:211 GAGACTACAGAGCAACTAGGTAAAAAATTAACATT + <<<<<<<<<<<<<<<:&<<<&:<<<<<<<<<<;:/ @B7_597:7:31:948:254 CCTCTACATGGCTGATTATGAAAACAATGTTCCCC + <<<<<<<<<<<<<<<<<<<;<<<<<:<<8<;;;;< @B7_597:7:31:948:254 TGAAGCACTGAACTTCCACGTCTCATCTAGGGGAA + 7;;;98<<7<<<<<<<<<<<<<<<<<<8<<<<<<< @B7_597:7:41:34:211 CACCTAACACAAGACTACCCAGATTCATAAAACAA + 7<<<<<<<<<<<<<<<< @B7_610:5:136:260:254 GTGGAAAAAGATGTTCTACGCAAACAGAAACCAAA + ;:;;<<<<<<<<<<<<<<;<;<<<<<<<<<<<<<< @B7_610:5:147:68:353 AACAACCTTGAGAACCCCAGGGAATTTGTCAATGT + <;<;<<7<<<<<<<7<<;;<7<4<8<<<8.;4;;; @B7_610:5:147:68:353 CCTTTGATATCTGGATTCTGGGAAATTCTTCATCC + <<;;<<<<<<<<+;<<;<<0;<<<<;<<<<<<<<< @B7_610:5:51:904:391 ACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAA + <<<<<<<<<<<<<<<<<;<<<<<;:;<2<6;;;;; @B7_610:5:51:904:391 TATCTAAAGTCAACATGAAGGAAAAAAATTCTAAA + ;<96<<<<<<7<<7<<<<<<<<<<<<<<;<<<<<< @B7_610:5:7:761:623 CCGGCATGGTTGTACTGGGCAATACATGAGATTAT + ::';-8);<<<<;<1<<<<:<<<<<<<<<<<<<<< @B7_610:5:7:761:623 CTTTCAACGCTTCTAGCCATTTCTTTTGGCATTTG + <<<<<<<<<<<<<8<<<<;;<0<<<<<;;<;<;;& @B7_610:6:107:252:533 AGAGAAGGAGTAGCTATACTTATATCAGATAAAGC + <<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;<<;9 @B7_610:6:107:252:533 CAAGACTACCCAGATTCATAAAACAAATACTACTA + 3<<<<+<<96<<<<<<;<<<<<<;<<<<<<<<<<< @B7_610:6:111:379:700 ACACTAAAAGCCCATACTTTACTGCTACTCAATAT + 7<<:<<<<02<<6&<==>=>=>=>>>==>>>=>>> @EAS114_26:2:130:609:467 CAATACTCACCATCATAAATACACACAAAAGTACA + ==8=====;==8==;=4=;;8=====;6=177.== @EAS114_26:2:214:950:32 ACAAGAAACTCATTAATAAAGACATGAGTTCAGGT + >>=>>>>==>=>>>==>=>=:=====;=:=6:::6 @EAS114_26:2:214:950:32 AGAAGATATAACCATCCTACTAAATACATATGCAC + =&==4======:;==6<==:=============== @EAS114_26:2:237:497:165 GAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGC + 9=:=======2=27======<>&<=,==4>4=>>= @EAS114_26:2:237:497:165 TACAGTCATCTATAAAGGAAATCCCATCAGAATAA + 8===<8===========37=<===7=;7=8===== @EAS114_26:2:315:219:7 GAAAGAGGCTCAAAGAATGCCAGGAAGATACATTG + 7==::<2=8<<<=====>888<=2=>==>,>,>>8 @EAS114_26:2:329:458:365 GTGTTCTGTGTAAAGTCTCAGGGAGCCGTCCGTGT + ==========================9======== @EAS114_26:2:329:458:365 TTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGG + ====:==9========>==7>==9>=7=>=>>=>> @EAS114_26:2:73:513:102 GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC + ==::===8=>=====>=>=>>>=>>==>=>>>>>> @EAS114_26:2:73:513:102 TGAAAACAATGTTCCCCAGATACCATCCCTGTCTT + ===========================;======= @EAS114_26:3:117:284:589 ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA + ==================================0 @EAS114_26:3:117:284:589 GAACCTATGAGTCACAGGTATTCCTGAGGAAAAAG + ==8==;==================;========== @EAS114_26:3:284:261:124 ACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTG + ===27===.====&===========;;======== @EAS114_26:3:287:665:495 GAATTGTAAAAGTCAAAATTAAAGTTCAATACTCA + ===,9=;;====7=====5===;==1========= @EAS114_26:3:287:665:495 TGGATCTAATTTTTGGACTTCTTAAAGAAAAAAAA + ==========================98====8=8 @EAS114_26:4:100:238:596 ATGAGAAATTACCTAATTGGTACAATGTACAATAT + ======9=====;=======5===;====/=;=== @EAS114_26:4:100:238:596 CAAAAACTATTCTAAGTATTGGTAAAGATGTGGGG + 4<<<<;<3<3&<3<1<5<31<<3<<<<<<2<<;<, @EAS114_26:4:110:840:431 CTGTCAAACACGAATGTTATGCCCTGCTAAACTAA + 77<;7<<<<<<<<<4<<<<<<<:<<<<<<<<<<<< @EAS114_26:4:110:840:431 GTAGTCATCAGACTATCTAAAGTCAACATGAAGGA + =====================5:======54=+3+ @EAS114_26:4:123:1001:580 AGGTTTTATAAAACAATTAATTGAGACTACAGAGC + <.00..3<6<<<<<<<3;<<08<<<<<6<<<<<<< @EAS114_26:4:123:1001:580 GGGAANTAAAGTCAAGTCTTTCCTGACAAGCAAAT + =====!=====================1.8131*= @EAS114_26:4:253:285:104 CTCTCATTCACTCCAGCTCCCTGTCACCCAATGGA + ======================:========7==; @EAS114_26:4:253:285:104 GTGATGTGTGTTCTCATCAACCTCATACACACACA + 2<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS114_26:4:306:388:342 CCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACT + ================5====:=====;==1=4== @EAS114_26:4:306:388:342 GGGGAAGACATAATCCCACGCTTCCTATGGAAAGG + 9/<9;<<<;<;<<7<<<7<<<<<<<<<<<<<<<<< @EAS114_26:4:40:352:151 ATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCT + <<<<<<<<<<<<<<<;<<9<<<<:<<<<;<99<3< @EAS114_26:4:40:352:151 TTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT + ;=;;5=:-=9=====;;================== @EAS114_26:5:139:331:63 GACACCCAACTAATATTTGTCTGAGCAAAACAGTC + 7===================:=:============ @EAS114_26:5:139:331:63 TTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT + ====================<<============= @EAS114_26:5:228:189:826 AAGCCCTTCTCACAGTTTCTGCCCCCCGCATGGTT + ;9=========;=1======9=====1;=<3=:6; @EAS114_26:5:228:189:826 ATCATGACTCTATCCCAAATTCCCAATTACGTCCT + :74=:.==1========================== @EAS114_26:5:238:31:968 ACACCATCCCTGTCTTACTTCCAGCTCCCCAGAGG + =(.7=5%===9:7==+==77=============== @EAS114_26:5:238:31:968 ATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCTG + 9======8====*=====,=1=======<=7:::, @EAS114_26:5:43:114:617 AATCATAAATACACACAAAAGTACAAAACTCACAG + +=22=6=================9=========== @EAS114_26:5:43:114:617 AATGTTATGCCCTGCTAAACTAAGCATCATAAATG + =============;=========;=========== @EAS114_26:6:129:694:359 CCCTGAGAGATTCTGCAGCCCAGATCCAGATTGCT + 7777<7<7;77+<3<<;<<;<<<<;<<<<<<<<<< @EAS114_26:6:129:694:359 TGTCAGTTACCAAATGTGTTTATTACCCGAGGGAT + ============+7=======:==;;;'=;==7;= @EAS114_26:6:140:253:322 AATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTC + <<<<<<<<<<<<<;<<<<<<<<<<<<<<<;;;<<; @EAS114_26:6:140:253:322 GAAATGCTCAAAAGAATTGTAAAAGTCAAAATTAA + =;===;54:====================>>===> @EAS114_26:6:183:697:555 AAAGAATGCCAGGAAGATACATTGCCAGACAGACT + =====================:===&==:;==5;; @EAS114_26:6:183:697:555 AGAAATCTTAGAAGCCAGAAGAGATTGGATCTAAT + <<<;&,.;);&96<84<<81<<&<<<9<<8<8<<1 @EAS114_26:6:46:13:880 AAAACCTCTTTAGTCTTGCTAGAGATTTAGACATC + <<<<<<<<<<<<<<<<<<<<;<7<3<<<9<+;;<9 @EAS114_26:6:46:13:880 AGAAAAGCATACAGTCATCTATAAAGGAAATCCCA + =&====8==========0================= @EAS114_26:7:13:172:720 AATTCATTTAAGAAATTACAAAATATAGTTGAAAG + ============:3<==:====<=9=3===;==83 @EAS114_26:7:157:876:302 AAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGA + ===:=8=;==:892=,28==88==28====8=;;8 @EAS114_26:7:157:876:302 CAACTAGGTAAAAAATTAACATTACAACACGAACA + 2<<;<<<22<<<<<<77<<<<22<7<<<<%-<<1< @EAS114_26:7:218:858:445 AAAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTT + ;===5=;=======;==3======9;,79==;=== @EAS114_26:7:218:858:445 GAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATA + ;<<<<<<<8;:<<<<<<;<<:<<<<<<<<<<<<;< @EAS114_26:7:245:323:744 ACCTCTACATGGCTGATTATGAAAACAATGTTCCC + /.848299;&;9;9;=2.=7========;;===== @EAS114_26:7:245:323:744 GATTCTGGGAAATTCTTCATCCTGGACCCTGAGAG + <;<<<<<<<<<<<<<<<<<<<<<;<+<<<<<<<4< @EAS114_26:7:37:79:581 TTAAAATTTAAAAAAAGTAAATAAAACACATAGCT + <>4<>>>>;>>&>->9>9;4>->>>>,4>9>,<1> @EAS114_26:7:37:79:581 TTTTTTTTTTTTTTTTTTTTTTTCATGCCAGAAAA + 3,,,===6===<===<;=====-============ @EAS114_26:7:86:308:648 GAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTG + <7<<<;<<<<+;<<<2<5<<<77;<<2<;;<<<<< @EAS114_26:7:86:308:648 TATTAGGAAATGCTTTACTGTCATAACTATGAAGA + =8=====;=8======;=======35==;=;.;25 @EAS114_28:1:144:242:602 ATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGG + ========================;=====<;;<<; @EAS114_28:1:144:242:602 ATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAG + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS114_28:1:168:389:889 GAAATTACAAAATATAGTTGAAAGCTCTAACAATAG + <<<<<<<<<<<<<<<<<<<<;<<<<<<<;9;;<<<< @EAS114_28:1:168:389:889 TAACTGAACCTATGAGTCACAGGTATTCCTGAGGAA + ;<<;;56;==================8========8 @EAS114_28:1:168:609:646 GGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG + ;;<<<<=======;;:;======;==<========= @EAS114_28:1:168:609:646 GGTTACACTAAAAGCCCATACTTTACTGCTACTCAA + <<<<<<<<<<<;<<<<<:<8<<<<;<<<<<4<<<9< @EAS114_28:1:220:801:282 AACCTCATATATCAATATTAACTTTGAATAAAAAGG + ;7;87;===;==;====:===<==7=========== @EAS114_28:1:220:801:282 AATTCATCATCACTAAACCAGTCCTATAAGAAATGC + <<<<<<<<<<<<<<<<<<<<<;<+<;<<<<<::<<: @EAS114_28:1:232:351:909 ACATGGCTGATTATGAAATCAATGTTCCCCAGATGC + <<<<<99<<<<<<99<7<'<9<<<6<<+<;7;<<&; @EAS114_28:1:232:351:909 CCATCATGAAGCGCTGAACTTCCACGTCTCATCTAG + :8%3<8====130=8==+===;=3=8===48==;3* @EAS114_28:1:28:708:463 CCCAATGGACCTGTGATATCTGGATTCTGGGAAATT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<;<9;<:<< @EAS114_28:1:28:708:463 GTATAATACCTCTACATGGCTGATTATGAAAACAAT + ;;<;<<====3=====5=================== @EAS114_28:2:114:938:216 CTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4; @EAS114_28:2:114:938:216 GAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGA + <<<<7<6<<<<<<<6<<<<<<<<<<<<<<<<<<<<< @EAS114_28:2:141:7:963 CACTTTAAATCAACAACAGTAAAATAAAACAAAGGA + <<<<<<<<<<<<;<:<<<<<<1<<&<;<;<<;,<;5 @EAS114_28:2:141:7:963 TACAATGTACAATATTCTGATGATGGTTACACTAAA + 95+<<9<<5<;;<<;<<;'<<<<<;<<<7<9<<<<< @EAS114_28:2:149:650:44 CGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCC + ;8<<7><>;>+>>/;>>=>=>=:>><>=<<==;)<=8; @EAS114_28:4:149:572:877 GAGGCTCAAAGAATGCCAGGAAGATACATTGCAAGA + 6<94693<;<<<<;;<<<<<<<<<<;9<<<<<<<<< @EAS114_28:4:215:246:640 AAAAGCATACAGTCATCTATAAAGGAAATCCCATCA + <<<<<<<<<<9<;<<<<<<<<<<9;<<<<<<3;<;3 @EAS114_28:4:215:246:640 AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT + ;<<,<<<96<<:<:<9<6<97<<<<<9<<<<9<<9< @EAS114_28:4:305:707:258 AAAAAGATGTTCTACGCAAGCAGAAACCAAATGAGA + 3<<7<,;<<<<0<66<6+<%<<<.<<<<<<<<<9<< @EAS114_28:4:305:707:258 GAACAAAACCTCATATATCAATATTAACTTTGAATA + 9<<<<<<<<<<<<;<<-<<;;<;<<9<<;<<+99;7 @EAS114_28:4:322:631:245 CCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC + <<<<<<<<<<<<<<<<<0<<<<<<<<<<<<<<<<5; @EAS114_28:4:322:631:245 TATTTTTGTCTTGACACCCAACTAATATTTGTCTGA + <<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<< @EAS114_28:4:9:55:730 ATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGC + <:<;;<6<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS114_28:4:9:55:730 CAGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCT + >>=>>+==>>==<==<=8=><:;8/;7<<<<<<<<<<<<<< @EAS114_45:6:37:156:134 GGAAAAACTATTTGAGGAAGTAATTGGGGAAAACC + ;;;;;;;;;;9;;;;;;;;;;;;;;;9;;;77679 @EAS114_45:6:39:956:676 TAAAACAAATACTACTAGACCTAAGAGGGATGAGA + 899985;;<;:9;;:9<;:9:5;<;;;<;<;<<<< @EAS114_45:6:39:956:676 TGAGAGAAGGAGTAGCTATACTTATATCAGATAAA + ;;;;;;;;;;;;9;;;;;;;;;;;;;;;9957777 @EAS114_45:6:44:77:1255 CTCATTAATAAAGACATGAGTTCAGGTAAAGGGGT + ;;;;;;;8;;;7;8;;;;;;;;;;886;;;76777 @EAS114_45:6:44:77:1255 TAAAAAGATCAATTCAGCAAGAAGATATAACCATC + 79998;;;9:;<696<;.<;;<<;<;<;<;;;<8; @EAS114_45:6:45:1769:1130 ACCCAATGGACCTGTGATATCTGGATTCTGGGAAA + ;;;;;;;;;;;;9;;;;;;19;;;9;;;;176777 @EAS114_45:6:45:1769:1130 TGTTCTCATCAACCTCATACACACACATGGTTTAG + 88989;<;97;9<<;<;;;;9<98<<<<<<<;<<< @EAS114_45:6:47:1791:444 AAGAGGGATGAGAAATTACCTAATTGGTACAATGT + 978879;:;;<:;;<<;:<9<<<<;6;;;;<<<<; @EAS114_45:6:47:1791:444 TACTTATATCAGATAAAGCACACTTTAAATCAACA + ;3;;;;;;;;;;;;;;;;;;;;;;;;;;;877977 @EAS114_45:6:59:1548:1096 CCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTG + 88888;;88;;;;8;;9;;;<<<<<<<<<<<<<<; @EAS114_45:6:59:1548:1096 GTCCTATGTACTTATCATGACTCTATCCCAAATTC + ;.;;;;;;;;6;;;;;;;;;;;;;;;73;;77777 @EAS114_45:6:5:730:1436 GAAGAACTTTGATGCCCTCTTCTTCCAAAGATGAA + 7977979;;;;;;;;;7;3<;2<;26;<;<<;;<< @EAS114_45:6:5:730:1436 TATTCAGTTCTAAATATAGAAATTGAAACAGCTGT + ;;;;;;;;;;;;;;;;;;8;;;;;8;;;;;67777 @EAS114_45:6:86:693:234 AAGTAACTGAACCTATGAGTCACAGGTATTCCTGA + ;;;;;;;;;;;;;;;;9;;;;;;;;99;;&70777 @EAS114_45:6:86:693:234 GTAGTCATCAGACTATCTAAAGTCAACATGAAGGA + 83997;<;;;;98;;3*6<<;<:8;;;;;<;;<<< @EAS114_45:6:86:859:1779 TTTTTTTCATTTCTCTTTTTTTTTTTTTTTTTTTT + ;;;;;;;;;;;;;;;;;;;;;;;;;;;8;;)7699 @EAS114_45:6:90:561:850 ACAGGAACAAAACCTCATATATCAATATTAACTTT + ;;;;;;;;;;;;;;;;;;;;;;;;9;9;6;77777 @EAS114_45:6:90:561:850 TACGCAAACAGAAACCAAATGAGAGAAGGAGTAGC + 78376<;;9<;<<;:9<<<6;<;<;;8;;<;/;;; @EAS114_45:6:93:1475:542 TGAAAGCTTGGGCTGTAATGATGCCCCTTGGCCAT + 98987:9:<:;:;;;;;<<;<;<;;;;<<<;;;<< @EAS114_45:6:93:1475:542 TTATCATGACTCTATCCCAAATTCCCAATTACGTC + ;;;;;;;;;;;;;;;;;;;;;;9;;;9;;;77777 @EAS114_45:7:14:1256:204 AAATGTCTATTTTTGTCTTGACACCCAACTAATAT + 66777:;;37;;:;;0;:;;;;):;;:7;;;;;;; @EAS114_45:7:14:1256:204 TCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTC + <<<<<;;;;;;<;;;;;;;<;<;;;;<:-;79697 @EAS114_45:7:14:978:1296 ATACAATGATAAAAAGATCAATTCAGCAAGAAGAT + ;6;;;;;;;;;;;:;;;;;;;6;;;;;;;;77777 @EAS114_45:7:14:978:1296 CAATATTCTGATGATGGTTACACTAAAAGCCCATA + 77177;9;2:;;:;;(;;9;<;;;;:;;;:7;<<; @EAS114_45:7:24:1374:211 AGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTG + ;;:<<;<;:;;;;;;;;;;<::;;;6;;2+74917 @EAS114_45:7:24:1374:211 TGCAATTAATATAATTGTGTCCATGTACACACGCT + 77661;;;5;;:;;:;:;;;;;;8:;;;:;;;;;: @EAS114_45:7:2:168:1878 AAAAAACCTGGCAAACACGAATGTTATGACATGTN + ;<:;;<:<;<;<;;;;:;<;:::&9:&:68&6&*! @EAS114_45:7:2:168:1878 TAAATACACACAAAAGTAGAAAACGCACCAGTTTT + *3/6)9.;;;;;;;;5;;);;;3;(;;;+(;7.)3 @EAS114_45:7:33:1566:588 ACAGCTTAGGCATCAATTTGGTGTTCTGTGTAAAG + -6246;;97;77;;97;;;;;;9;7;79;)&;37; @EAS114_45:7:33:1566:588 TACTGTCATAACTATGAAGAGCCTATTGCCAGATG + <;.;;;;6;;;;6;;29;;;<+9;;;.3;;73797 @EAS114_45:7:35:538:1882 TATGCACCTAACACAAGACTACCCAGATTCATAAA + ;);43.50;3;93;;4;3;;;9-7.;*;;966*75 @EAS114_45:7:35:538:1882 TCTATAACAAAATTAAAATTTAACAAAAGTAAATA + 73797;;3<;;<6;;<<<;8:;:;<;:<:;<<;;; @EAS114_45:7:37:763:1437 AAAGATGTTCTACGCAAACAGAAACCAAATGAGAG + ;;;;;6;;;;;;;;;:;6;5;5;;;;;76;767/7 @EAS114_45:7:37:763:1437 TAAAACAAATACTACTAGACCTAAGAGGGATGAGA + 79979;<;<;;;<;;;;;;6:;<:;<:8;<<<<;< @EAS114_45:7:45:1339:1807 GACATCTAAATGAAAGAGGCTCAAAGAATGCCAGG + 77797;;:;::&:;;0:;8;;4;;:;;6;;;;;;; @EAS114_45:7:69:1130:832 ATAGTTGAAAGCTCTAACAATAGACTAAACCAAGC + ;;2<;<;;<;9;<;;;;;;;7;8;;7;;;;77437 @EAS114_45:7:69:1130:832 TCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAA + 6)377;3;;;;;;;;;1;;;;;;;;;;;;;;;;;; @EAS114_45:7:6:758:988 AAACAAAGGAGGTCATCATACAATGATAAAAAGAT + 3+;0;0;;;0;;;;;;5;;;9;;;;90;;;57560 @EAS114_45:7:6:758:988 ATTCTGATGATGGTTACACTAAAAGCCCATACTTT + 3-7*73;;399:9;9;7<-(<;;<;;:;9::;;7; @EAS114_45:7:88:451:1773 ATAAATACACACAAAAGTACAAAACTCACAGGTTT + ;;:::<:;:<<;:6::;:;;:::;;<;;;367177 @EAS114_45:7:88:451:1773 ATTGGCAGAACAGATTTAAAAACATGAACTAACTA + 973776;;;;;;;;;::;;;;;;;;;;;;;;3;;; @EAS114_45:7:97:1584:777 CCAGATGAACCACACATTAATACTATGTTTCTTAT + <<;<;;;;<;<;<<;;;;;;;;;;;;;;:;79979 @EAS114_45:7:97:1584:777 GTCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCC + 66746,9::9;;;;:;;;;;;;;;;;;;;;:;;;; @EAS114_45:7:9:512:826 AACTTCCACGTCTCATCTAGGGGAACAGGGAGGTG + 67<<<;;;<;;<<;;<;<:;9;;;9;;;;<59777 @EAS114_45:7:9:512:826 ACCACACATTAATACTATGTTTCTTATCTGCACAT + 76777:;;;;;;;;;;;;;;;;;;;;;;;;;:;;; @EAS139_11:1:35:631:594 ATCATGACTCTATCCCAAATTCCCAATTACGTCCT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS139_11:1:35:631:594 ATGATGCCCCTTGGCCATCACCCGGTCCCTGCCCC + <<<<4<<<<<.<<<<<<<<<<<<<<<<<<<<<<<< @EAS139_11:1:59:742:549 ACAAGCAAATGCTAAGATAATTCATCATCACTAAA + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<8< @EAS139_11:1:59:742:549 TTAACATTACAACAGGAACAAAACCTCATATATCA + -<<<3<<<<6<<6<<<<<6<<<<6<<<<<<<<<<< @EAS139_11:1:81:1019:558 ACAAAACTCACAGGTTTTATAAAACAATTAATTGA + <<<<<<<<<<<6<<<<<<<<<<<<<<<<<<<<<7< @EAS139_11:1:81:1019:558 TGAACTAACTATATGCTGTTTACAAGAAACTCATT + <<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS139_11:1:84:92:1246 GAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG + <<<<<<<<<<<<<<<8<<<<<<5<<<<<<<<<<<< @EAS139_11:1:84:92:1246 GTTACACTAAAAGCCCATACTTTACTGCTACTCAA + <<<<<<<<<<<<<<<<5<:<<5<<<<<<<<<<<<< @EAS139_11:2:31:628:1820 AACCAGTCCTATAAGAAATGCTCAAAAGAATTGTA + <<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<<<<< @EAS139_11:2:31:628:1820 CAGGAACAAAACCTCATATATCAATATTAACTTTG + <<<<<<:<<<<:6<<<<<<<<<<<<<<<<<<<<<< @EAS139_11:2:42:333:516 AGACAAGTCTCTTATGAATTAACCCAGTCAGACAA + <<<<<5<*<2<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<:<<<< @EAS192_3:7:149:354:667 GAGGTGCACTAATGCGCTCCACGCCCAAGCCCTTC + ;<;;;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<< @EAS192_3:7:298:644:697 CTATGTTTCTTATCTGCACATTACTACCCTGCAAT + 8:<8;<;:7;<<;4;:+<7<<<<;<<<<<<<<<<< @EAS192_3:7:298:644:697 TCCACGTCTCATCTAGGGGAACAGGGAGGTGCACT + <<<<<<<<<<<<<<<::;;;6<8:;;9;98;668; @EAS192_3:7:66:891:294 AGCACACTTTAAATCAACAACAGTAAAATAAAACA + <<<<<<<<<<<<<<<<<<<<<<<9<<<<<<;<<<< @EAS192_3:7:66:891:294 TAATTGGTACAATGTACAATATTCTGATGATGGTT + :<<5;;<<<4<<<<<<<<<<<<<<<<<<<<<<<<< @EAS192_3:7:78:692:671 AATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACA + <<);<<;;<<<<<;<<<<<<<<<<<<<6<<<<<<< @EAS192_3:7:78:692:671 CAGCAAGAGAAAAGCATACAGTCATCTATAAAGGA + <<<<<<<<<<<<<;<<<<<<<:<<:<<<:8<<0;; @EAS192_3:7:93:945:176 CCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTC + 6;;;8<<3<<8.<;6)<<<<<9<<<<<<<<<<<<< @EAS192_3:7:93:945:176 GTGAGCCATCACAATGAACAACAGGAAGAAAAGGT + <<<<<<<<<<<<<<<<<<<<<;<<<<;;<;:7;<3 @EAS192_3:8:6:104:118 AAGAATTTTAAAAATGAACAGAGCTTTCAAGAAGT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<=<<<<<< @EAS192_3:8:6:104:118 TCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGA + ;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS192_3:8:6:237:885 AAAATCAGCAAGAGAAAAGCATACAGTCATCTATA + <<<<1:<;:<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS192_3:8:6:237:885 TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT + <<<<<<<<9<<<<<<<<<<<<<<<<<<<<<;;;<; @EAS1_103:1:151:159:43 AACCTCATACACACACATGGTTTAGGGGTATAATA + ;;4;6<<;<<<<7<77<6;<6<<<<<;;<<<<<<< @EAS1_103:1:151:159:43 TCTCATTCACTCCAGCTCCCTGTCACCCAATGGAC + <<<<<<<;<<<8<<<;<;8<<<<7<77;;79<09+ @EAS1_103:1:228:736:747 AAGATATGTAGTCATCAGACTATCTAAAGTCAACA + <<<<<<<<<;<<<<<<<;;<<;<<<<;::<;;7;7 @EAS1_103:1:228:736:747 TTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACA + <07<<&<;+<<<<<<<<<<<<<<<<;<<<<<<<<< @EAS1_103:1:274:176:479 CCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTAT + 7)<<7<626<<7<<<<<<<<<<<<<<<<<<<3<<< @EAS1_103:1:274:176:479 GAAATGCTTTACTGTCATAACTATGAAGAGACTAT + <<<<<<<<<<<<<;<<<<<<<<<<;<<9<59<<<< @EAS1_103:1:2:831:692 GTGTTCTCATCAACCTCATACACACACATGGTTTA + 2749'979<9<<<6;<<<0<;<<<<<3<<<<<<<< @EAS1_103:1:2:831:692 TCCAGCTCCCTGTCACCCAATGGACCTGTGATATC + <<<<<<<<;<<<<<<<<<<9<<:9<<<;;96<796 @EAS1_103:2:184:980:396 AAGGAGGTCATCATACAATGATAAAAAGATCAATT + <<;;<77;;<<;<<<<<<<<<<<<<<<<<<<<<<< @EAS1_103:2:184:980:396 ACATGAACTAACTATATGCTGTTTACAAGAAACTC + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<< @EAS1_103:2:226:302:758 GGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGG + ;<<<<9;<<<<<<<<<<7<<<<<<<<<<<<<<<<< @EAS1_103:2:226:302:758 TGCTTGTGGTCTGACAGGCTGCAACTTTGAGCGNT + <<<<<<<;;;,<;<92;66<;))42<&2&(/1!!! @EAS1_103:2:234:167:381 AAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT + <<;<;<<<<;<<<<7<<<<<<<<<<<<<<<<<<<< @EAS1_103:2:234:167:381 AGAGAAAAGCATACAGTCATCTATAAAGGAAATCC + <<<<<<<<<<<<<<<<<<<<<<<<<;<<<;;7<;; @EAS1_103:2:235:805:373 TATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCA + <<;<<<<<<9<9<<<<<<<<<<<<<<<<<<<<<<< @EAS1_103:2:235:805:373 TTTACTGTCATAACTATGAAGAGACTATTTCCAGA + <<<<<<<<<<<<<<<<<<<<;<;<<<<<<;;<99; @EAS1_103:2:307:252:632 ACCATCCTGCTAAATACATATGCACCTAACACAAG + <77<;,5<,9<<<<<<;<<<<<7<;<<<<<<<<<< @EAS1_103:2:307:252:632 ATGTTCTACGCAAACAGAAACCAAATGAGAGAAGG + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;;<;; @EAS1_103:3:253:175:31 CAAACAGAAACCAAATGAGAGAAGGAGTAGCTATA + <<<<<<<<<<<<<<<<<<<<<<:<<<<<<<:<;;; @EAS1_103:3:253:175:31 TTCATAAAACAAATACTACTAGACCTAAGAGGGAT + ;+;<;<<<<<<<<9<<9<<<<<;<<<<<<<<<<<< @EAS1_103:3:277:921:474 AAAATATAGTTGAAAGCTCTAACAATAGACTAAAC + <<<<<<<<<<<<<<<:<<<<<<<<<<<5<<;;;;; @EAS1_103:3:277:921:474 AAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGA + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS1_103:3:320:505:814 ACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCT + <2<;;5<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS1_103:3:320:505:814 CTGTCTTGATTTACTTGTTGTTGGTTTTCTTTTTC + <<<<<<<<<<<<<<<<;<<8<<76<<<<;<&<<<7 @EAS1_103:3:323:196:855 ACAAGCAAATGCTAAGATAATTCATCATCACTAAA + <<<<<<<7<<<<<<:<<<<<<<<<<<<<<<<<;7: @EAS1_103:3:323:196:855 TAAAAAATTAACATTACAACAGGAACAAAACCTCA + &<<<<<<09<<7<7;<;<<0<<<<<;<<<<<<<<< @EAS1_103:3:41:474:283 TGAACCACACATTAATACTATGTTTCTTATCTGCA + <<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<+<< @EAS1_103:3:41:474:283 TTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGTCC + 6/;;;88;;<:;48<<<<<;<;<<<<<<<<<<;<< @EAS1_103:4:143:560:194 GTTGTACTGGGCAATACATGAGATTATTAGGAAAT + 9:<;7<:::<:<;<<<<<<<<<<:<<<<<<<<<<< @EAS1_103:4:143:560:194 TCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCC + <<<<;;<<<<<<<<<<<6<;<<<<;;<<;9<999< @EAS1_103:4:164:79:134 ACAATGGGCTTCTCAGCGGAAACCTTACAAGCCAG + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7< @EAS1_103:4:164:79:134 AGATAATTCATCATCACTAAACCAGTCCTATAAGA + <;<;<<<;<<;<<<<<<<<<<<<<<<<<<<<<<<< @EAS1_103:4:231:815:626 GATCAATACAGCAAGAAGATATAACCATCCTACTA + '<4%<<<22<<,<<;<<4;<<<<<<<<<<<<<<7< @EAS1_103:4:231:815:626 GCTGTTTACAAGAAACTCATTAATAAAGACATGAG + <;<<<<9<<<<<<<<<<<<<<<<<;<<;5<<<;:; @EAS1_103:4:235:899:847 AGAAACTCATTAATAAAGACATGAGTTCAGGTAAA + <<3<;<<<<<<<<<;;<<<<<<<+<<<+6<8<3/< @EAS1_103:4:235:899:847 ATAAAAAGATCAATTCAGCAAGAAGATATAACCAT + <7<<<<<<<<:<<<<:<<<<<1>><<<< @EAS1_108:2:102:543:160 CAACAGGAACAAAACCTCATATATCAATATTAACT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<:< @EAS1_108:2:102:543:160 CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA + 9==9=====;=====================<=== @EAS1_108:2:116:966:193 ATTAACATTACAACAGGAACAAAACCTCATATATC + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<< @EAS1_108:2:116:966:193 GACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGT + =================================== @EAS1_108:2:170:326:433 CTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCGTC + :44<<<<<<<<<<:6<<<<<<<:<<<<<<<<<<<< @EAS1_108:2:170:326:433 TTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGG + =====<=9===:=<:==2=======2:===9==/5 @EAS1_108:2:176:653:957 AAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAA + ===::=============<==<====<======== @EAS1_108:2:176:653:957 ACATTACAACAGGAACAAAACCTCATATATCAATA + ????????????<=>>>==>>===>==> @EAS1_108:6:159:493:275 ACAAAACTCACAGGTTTTATAAAACAATTAATTGA + =====3============================= @EAS1_108:6:159:493:275 TGCTGTTTACAAGAAACTCATTAATAAAGACATGA + 4949;<<<<<<<<<<<6<;<<<<;<<<<<*<<<<< @EAS1_108:6:165:464:123 CATACACACACATGGTTTAGGGGTATAATACCTCT + ===============7==============8==== @EAS1_108:6:165:464:123 GTCTCTACCACAGGGGGCTGCGCGGTTTCCCATCA + 9;<)<<%<<9<<<<<<<<<<<<<<<<<<<<<<<<< @EAS1_108:6:222:579:961 AGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAG + =58====;==8=======;================ @EAS1_108:6:222:579:961 CAGAAACCTTACAAGCCAGAAGAGATTGGATCTAA + <<<<<<<<<<<<<<<<<<<<<<<<<7<<:7;;;68 @EAS1_108:6:71:187:824 AGACAGACTTCATCAAGATATGTAGTCATCAGACT + ;===;======3==;==========4=;=7;;3;6 @EAS1_108:6:71:187:824 TCTAATTTTTGGACTTCTTAAAGAAAAAAAAACCT + 0040;<7<<<<0<7<<<;<7*<<<<<7<<771<<< @EAS1_108:6:73:735:329 AAAGGGATTAAATTCCCCCACTTAAGAGATATAGA + ================;==;====;=;=======; @EAS1_108:6:73:735:329 TAGCTATACTTATATCAGATAAAGCACACTTTAAA + ;;;9;<<7<<<<<<<<<<<<<<<<<<<2<<<<<<< @EAS1_108:6:77:48:860 CTCTGTCTTGATTTACTTGTTGTTTGTTTTCTGTT + =========;===========9==*;5=;=;=,7= @EAS1_108:6:77:48:860 TAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGC + ;8;8;<9<9<<<<<<<<<4<<<<<<<<<<<<<<<< @EAS1_108:6:94:294:387 ACCATCATAAATACACACAAAAGTACAAAACTCAC + 779=53=9===;=:=;=========;========= @EAS1_108:6:94:294:387 GAATGTTATGCCCTGCTAAACTAAGCATCATAAAT + <<<<<<<;<<<<<<<<<:<<<<<<<<<<<<;)7;; @EAS1_108:6:95:235:746 CTAAGCATCATAAATGAAGGGGAAATAAAGTCAAG + ==&=;===7=3===8======;=;8===8=====; @EAS1_108:6:95:235:746 TCTAAAATCAGCAAGAGAAAAGCATACAGACATCT + <<<<;<<<<<<<<79<<<<<<<<<<<<<<*;;;<9 @EAS1_108:7:108:440:208 CCCATCCTACTAAATACATATGCACCTAACACAAG + +35:486<<4<<<<<<<<<<<-<<<<<7<<)<<<- @EAS1_108:7:108:440:208 TTCAGGTAAAGGGGAGGAAAAAGATGTTCTACGCA + <<<;<<<<<<<<<<<8<<<<<><<<<<><<<<<<<<<<<<<<< @EAS1_95:7:280:607:113 ATCCATGTAACAAATCTGCGCTTGTACTTCTAAAT + ===================;===;=====<=7=9: @EAS1_95:7:280:607:113 GGAGTATAAATTGTTTTCCACTTTGGAAAACAATT + 18<-<<<<<<<<<<<<<8<<<<<<<<<<<<<<<<< @EAS1_95:7:282:817:710 TGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCC + 366=6;======8====:========;======== @EAS1_95:7:282:817:710 TTTGTAATGAAAACTATATTTATGCTATTCAGTTC + <<<<<<<<<<<<<<<<<<<<<<<;:<<<<:8,<<8 @EAS1_95:7:310:800:761 AAAGCACACTTTAAATCAACAACAGTAAAATAAAA + ===========================+======= @EAS1_95:7:310:800:761 CAATATTCTGATGATGGTTACACTAAAAGCCCATA + 1<<:<:<:<<<<:<<<<<<<<<;<<<<<<<<<<<< @EAS1_95:7:46:522:426 AAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGA + <<<<<:<<<<<<1/<<<<<<<<<<<<<<<<<<<<< @EAS1_95:7:46:522:426 GGTAAAAAATTAACATTACAACAGGAACAAAACCT + =======================:==;<===78== @EAS1_95:7:55:506:125 CTTTACTGTCATAACTATGAAGAGACTACTGCCAG + 118%67;1;8,4:187<4>::1:818;;&::<>.; @EAS1_95:7:55:506:125 TCTACCACAGGGGGCTGCGCGGTTTCCCATCATGA + <<<<<<<<<;<9<;<<;558<<<<5(5*<<<<<51 @EAS1_95:7:61:702:720 ATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAA + <<<4<4+0;<<:<<<<<<<<-<<<<<<<<<<<<<< @EAS1_95:7:61:702:720 CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC + ==============;=======&=========3:= @EAS1_95:7:74:866:49 CATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTC + ====================9==91==<=6==;:= @EAS1_95:7:74:866:49 CCAACCTACTAAATACATATGCACCTAACACAAGA + :8<&<<<<7<<<<:<<<<<<8<5<<<<<<<<<<<< @EAS1_97:2:128:629:484 AAAAAAGTAAATAAAACACATAGCTAAAACTAAAA + :(::<<<<<<<<<7<<<<<<<<=<<<<<<<<<<<<<< @EAS1_99:8:27:228:31 AAATAAAACAAAGGAGGTCATCATACAATGATAAA + <<<<<<<<<<<<<<<<<;9<:;<<<<<<75<<<<< @EAS1_99:8:27:228:31 GGTTACACTAAAAGCCCATACTTTACTGCTACTCA + 99;;;<<<<<<:<<;<;<<;<<<<;<<;<<<<<<< @EAS1_99:8:99:756:130 GAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCT + ;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<<;< @EAS1_99:8:99:756:130 GACCCTACACGAATGCGTCTCTACCACAGGGGGCT + ;;<<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS218_1:2:10:686:1024 ACAAGAAACTCATTAATAAAGACATGAGTTCAGGT + <:<<<<:<<<<<<<<<<:<:<<<<<<<<<<<5<<< @EAS218_1:2:10:686:1024 CATACAATGATAAAAAGATCAATTCAGCAAGAAGA + &<<<3<<<<<<<<<<<<<<7<<<<<<<<<<7<<<< @EAS218_1:2:15:1763:1143 AAACAAATACTACTAGACCTAAGAGGGATGAGAAA + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS218_1:2:15:1763:1143 TGAGAGAAGGAGTAGCTATACTTATATCAGATAAA + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS218_1:2:18:1498:1475 CTTGGGCTGTAATGATGCCCCTTGGCCATCACCCG + <<<<<7<<<<<<+<<-3<<3<:<2<1<<:<<<<<+ @EAS218_1:2:18:1498:1475 GAAAGGTTGTTGGGAGATTTTTAATGATTCCTCAA + :<4<*7<<<<<<<:<<:<<<<<<<<<<<<<<<<<< @EAS218_1:2:19:752:816 CGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTG + <<<<<<<<<<<<<<<<<<<8<7;<;<<767277;6 @EAS218_1:2:19:752:816 TTTGGTGGAAGACATAATCCCACGCTTCCTATGGA + +<<+<--/<<<<4<2<<<<45<<<:<<<<<<+<<< @EAS218_1:2:26:211:481 ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA + <<<<<<<<<<<<<<<<<<<<<<<7<<<<<:<7<<< @EAS218_1:2:26:211:481 CACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAA + :<:<<<<<<9:5<<<<<<<<<<<<<<:<:<<<<<< @EAS218_1:2:40:1291:1045 CTAACACAAGACTACCCAGATTCATAAAACAAATA + *<<<9<<<<<<:0<9<<<<<<<;<<<<<<<<<<<< @EAS218_1:2:40:1291:1045 GTAAAGGGGTGGAAAAAGATGTTCTACGCAACAAG + <<<<<<<<<5<<5<<<<7<<<<<<<<<5<9<&%73 @EAS218_1:2:64:1318:1711 GGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS218_1:2:64:1318:1711 TGAAAACTATATTTATGCTATTCAGTTCTAAATAT + <<<<<<<<<<<<<<<<7<<<<<<<:<<<<<2<<<< @EAS218_1:4:14:1872:1521 TCAAAGAATGCCAGGAAGATACATTGCAAGTCAGA + 7<<<<77<<<3<3<7.'<<<<<7<67<+.0%4*<4 @EAS218_1:4:14:1872:1521 TCATCAAAAACCTTACAAGCCAGAAGAGATTGGAT + /1<%73&7<1<3577,<<<7/733<<<<<<<<1<< @EAS218_1:4:15:856:340 CACGCTGTCCTATGTACTTATCATGACTCTATCCC + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS218_1:4:15:856:340 CCCCAGCATGGTTGCACTGGGCAATACATGAGATT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<77<< @EAS218_1:4:28:315:310 AAACTGTTCTCTTGAAAGCTTGGGCTGTAATGATG + +%,768<<:<:<2<<<<<<<<<<<<<<<<<<<<<< @EAS218_1:4:28:315:310 CATGTACACACGCTGTCCTATGTACTTATCATGAC + <<<<<<<<<<<<<<<<<<<<<:<+.<<.<+7<*17 @EAS218_1:4:37:1626:862 ACCCAACTAATATTTGTCTGAGCAAAACAGTCTAG + :663<<3<<<<<<<<<<:<<<<7<<<<<<<<<<<< @EAS218_1:4:37:1626:862 TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS218_1:4:61:1369:440 AAAGACATGATTTCAGGTAAAGGGGTGGAAAAAGA + <<<<<<<<<<8<<<<<<<<<<<<<<<<<<<<<<<< @EAS218_1:4:61:1369:440 CAGGTTTTATAAAACAATTAATTGAGACTACAGAG + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<8 @EAS218_1:4:62:561:531 AGCTATACTTATATCAGATAAAGCACACTTTAAAT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS218_1:4:62:561:531 TACTAGACCTAAGAGGGATGAGAAATTACCTAATT + <<7<<<<:<8<<<<<<<<<<<<<<<<<<<<<<<<< @EAS218_1:4:71:832:743 ACCCAGTCCCTGCCCCATCTCTTGTAATCTCTCTC + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS218_1:4:71:832:743 CTATGTACTTATCATGACTCTATCCCAAATTCCCA + <<<<<<<<<<<<<<<<<<<<<<<<<<<*<<<<<<< @EAS218_1:4:73:42:1038 AAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS218_1:4:73:42:1038 TCTGTCTTGATTTACTTGTTGTTGGTTTTCTGTTT + <<<<<<<<<<<<<<<<<<<<<<<:<<<<<.<<<<< @EAS218_1:4:75:555:1591 TGAACTTCTGTAATTGAAAAATTCATTTAAGAAAT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<<<< @EAS218_1:6:49:905:27 CCACAGGGGGCTGCGCGGTTTCCCATCCTGAAGCA + <<;<.89<9.<2<9<:91+447.9,04&000(,+( @EAS218_1:6:49:905:27 GAAGAGACTATTGCCAGTTGAACCACACATTAATA + 99515<<&<<6595-56%;86&<;<<<6<<<<6;< @EAS218_1:6:66:1282:1215 GTGATGTGTGTTCTCATCAACCTCATACACACACA + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;;; @EAS218_1:6:66:1282:1215 TTCAGACCCTACACGAATGCGTCTCTACCACAGGG + ::;<;<<<<:<<<<<<<<<<<<<<<<<<<<<<<<< @EAS218_1:6:77:1529:522 AAAACCTGTCAAACACGAATGTTATGCCCTGCTAA + <<;<<<<<<<<<<<4<<4<;;:;2:7<<<2*<;;8 @EAS218_1:6:77:1529:522 AAAGTTCAATACTCACCATCATAAATACACACAAA + <<<;7;,<<<<<<.<,6<<6<<<<<<<;<<<<<<< @EAS218_1:6:88:1413:14 AATGAAAGAGGCTCAAAGAATGCCAGGAAGATACA + <<<<<<<<<<<;;;<<<<<<;<;;<<<<<<<<<<< @EAS218_1:8:13:1729:1844 ATGAACTTCTGTAATTGAAAAATTCATTTAAGAAA + <<<;;<;7<<<<4<<<<762;6<<<<<<<;6;618 @EAS218_1:8:16:1081:1894 AAGGTGATGTGTGTTCTCATCAACCTCATACACAC + ;5;;&<;<<<<<<<<;<;<<;<<<;<<<<<<<<<< @EAS218_1:8:16:1081:1894 AGATGAAACGCGTAACTGGGCTCTCATTCACTCCA + <<<<<<<<<<<<<<<<<<8<<<<;<<;<<<<<<<+ @EAS218_1:8:26:785:882 CAGTTTCTGCCCCAAGCATGGTTGTACTGGGCAAT + <<<0<<<<<<<<<6,<<)<<<<<<<&<<0<<,<'< @EAS218_1:8:26:785:882 TACTTATCATGACTCTATCCCAAATTCCCAATTAC + <<&5&<<<<5.;5<'<<;.76<<<<<7<7<<<<<< @EAS218_1:8:61:1797:113 CAGATAGCTTGTGGTCTGACAGGCTGCAACTGTGA + <<0<<&<<<<;<<4;;3<;<:<<<<<<<<<<<<<< @EAS218_1:8:61:1797:113 GGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGA + <<<<<<;<<<<;:<3<<<<;;<<<8<<;:<<;3<. @EAS218_1:8:70:445:1289 CTAATTTTTGGACTTCTTAAAGAAAAAAAAACCTG + <<<<<<<<<<2<<<<<<<<<<:<<<<<<<;;;;<: @EAS218_1:8:70:445:1289 GAATTGTAAAAGTCAAAATTAAAGTTCAATACTCA + <<<:<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<< @EAS218_1:8:82:1540:77 ATTGAGACTACAGAGCAACTAGGTAAAAAATTAAC + <48;<;<<<<< @EAS221_1:6:96:491:1891 AGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGG + <:<<<<<::<<<<<<<<<<<<<<<<:<<::7<<:7 @EAS221_1:6:96:491:1891 GTCAACATGAAGGAAAAAAATTCTAAAATCAGCAA + :;5<<7<;:<<;<<<<<<<<<<;<<<<<<<<<<<< @EAS221_1:8:15:881:1932 CACTTAAGAGATATAGATTGGCAGAACAGATTTAA + <<<<<<<<<<<<<<<;<<<<:<<<2<26<8<<;;. @EAS221_1:8:15:881:1932 CACTTTAAATCAACAACAGTAAAATAAAACAAAGG + )<4<<<<<<<4<<4<<4<<<<<<<<<<<<<<<<<< @EAS221_1:8:4:679:110 AATGTTCCCCAGATACCATCCCTGTCTTACTTCCA + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS221_1:8:4:679:110 TCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGT + <<<<<<<<<<<<<<<<<<<;<<<<<<<<::<;;:7 @EAS221_1:8:58:369:244 CTGTAATGATGCCCCTTGGCCATCACCCAGTCCCT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS221_1:8:58:369:244 TTGGGAGATTTTTAATGATTCCTCAATGTTAAAAT + <<<<<<<<<<<<<<<<<<<<;<<;<<<<<<<<<<< @EAS221_1:8:60:1020:1259 CTATGAAGAGACTATTGCCAGATGAACCACACATT + <;<<<<;<<<<<<<<<;<<<<<<<8<<<<<:<:<< @EAS221_1:8:60:1020:1259 TAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTC + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS221_1:8:65:1928:1125 CATCACAATGAACAACAGGAAGAAAAGGTCTTTCA + <<;<<<7<<7<;<7<<<<<<<7<<<<;<.-;<+88 @EAS221_1:8:65:1928:1125 GGCATTTGCCTTCAGACCCTACACGAATACGTCTC + <+<<<2<4<<<0<<4<<<<<6<<<6<<<'<<<<0< @EAS221_1:8:67:1797:1931 GGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTG + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS221_1:8:67:1797:1931 TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT + <<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<< @EAS221_1:8:70:1349:1788 ATTATATCAGATAAAGCACACTTTAAATCAACAAC + &<8<<<85:580;<:0-><;>588>9<>7:<0<9; @EAS221_1:8:70:1349:1788 TACTAGACCTAAGAGGGATGAGAAATTACCTAATT + <7;<<8<74;;<1<<71<;7<;;<;<7<<<<<<<< @EAS221_1:8:73:108:1621 GAACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTC + <<8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS221_1:8:73:108:1621 GTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACA + <<<<<<<<71<<<<<<<<<+<<<<70:0<9<<61< @EAS221_1:8:77:781:676 TCATGAAGCACTGAACTTCCACGTATCATCTAGGG + <<<<<<<5<<5<<<<<<<<<<<<13<<2<<<<<,< @EAS221_1:8:77:781:676 TTGCCAGATGAACCACACATTAATACTATGTTTCT + :<;<2<<<<<<26<<<<6<;<<<<<<<<<<<<<<< @EAS221_1:8:78:1478:1446 GGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTT + <<<<<<<<<<<<<<<<<<<<;<<<<<<<<<:<<<; @EAS221_1:8:78:1478:1446 TGTGGTCTGACAGGCTGCAACTGTGAGCCATCACA + <8,8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS221_1:8:84:1013:1074 GCAAGGGGGTCTATGTGAACAAAGGCACTAAACAC + <7<<<<<<<<9<<<<<<<<<<<<<<<<<<<<<<<< @EAS221_1:8:84:1013:1074 TTGATGCCCTCTTCTTCCAAAGATGAAACGCGTAA + 8;;<;8744<7<<4<<47<<<<<<7<<<<<<<<<< @EAS221_1:8:8:1351:1986 CCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATG + <8;<<<<<<<<<<<;<<;<<<<<<<<<<<<<<<<< @EAS221_1:8:8:1351:1986 TCTTACTTCCAGATCCCCAGAGGGAAAGCTTTCAA + <<<<<<<<<<<<-<<<<<<<<<<<<<<<<<<<<<< @EAS221_3:2:100:1147:124 AAAAAAGAATTTTAAAAATGAACAGAGCTTTCAAG + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<< @EAS221_3:2:100:1147:124 AATGCCAGGAAGATACATTGCAAGACAGACTTCAT + <<<<96<<<<<<<<<<<<<<<<<<<<<<:<<<<<< @EAS221_3:2:22:1623:709 GAAGACAAGTCTCTTATGAATTAACCCAGTCAGAC + <<<<<<<<<7<<<<<<<:<<<<<<<<:85:<:2<< @EAS221_3:2:22:1623:709 GGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGAC + <'<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS221_3:2:2:491:1886 CTCTTTAGTCTTGCTAGAGATTTAGACATCTAAAT + <<:<8:<<<:<<<<<<<<<<<9<<<<<<<<<<<<: @EAS221_3:2:59:1576:946 AACTGTGAGCCATCACAATGAACAACAGGAAGAAA + <:<<<<<<<<<<<<:<:<<<<<<<8<<::1<<<<< @EAS221_3:2:59:1576:946 CAACGCTTCTAGCCATTTCTTTTGGCATTTGCCTT + 9<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS221_3:2:60:590:1760 AAAGTAACTGAACCTATGAGTCACAGGTATTCCTG + <:<<<<<2<<<<:<::<<<::<<<<<6<<<<<<<6 @EAS221_3:2:60:590:1760 TCATCAAGATATGTAGTCATCAGACTATCTAAAGT + <8<-<<<<<<<82<<<4<<<<<<<<<<<<<8<<<< @EAS221_3:2:67:1467:1447 AAAGTTCAATACTCACCATCATAAATACACACAAA + <<<<<<<<<<<<<<<<<<<<<<7<<<<<<<<<<<< @EAS221_3:2:67:1467:1447 ATAGATTGGCAGAACAGATTTAAAAACATGAACTA + <<<<<::<<:<<<<:<<<<<<<<<<<<<<<<<<<< @EAS221_3:2:67:1864:477 AATGATGCCCCTTGGCCATCACCCAGTCCCTGCCC + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS221_3:2:67:1864:477 TAAAATGTCTATTTTTGTCTTGACACCCAACTAAT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS221_3:2:76:1729:813 TAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTT + <+6<<<&1<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS221_3:2:76:1729:813 TCTGCGCTTGTACTTCTAAATCTATAAAAAAATTA + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS221_3:4:12:276:1797 ACTATTGCCAGATGAACCACACATTAATACTATGT + <<<<<<<<<<<<:>>>>>>>>>>>>>;<>>>>><<>>>;<+<<<+<<<<:<<<<2<;<<<;<<<<<<<<<<< @EAS54_67:3:172:196:746 GCATACAGTCATCTATAAAGGAAATCCCATCAGAA + <<<<<<<<9<<<<9<<<<<<<<<;<<<<6<<<<;< @EAS54_67:3:175:730:949 TTATGCTATTCAGTTCTAAATATAGAAATTGAAAC + <<<<;+<<<<7<;<<;<<<<<<<<<<<<<<<<<<< @EAS54_67:3:197:261:624 GACTATCTAAAGTCAACATGAAGGAAAAAAATTCT + <<<<<<<<<<<;<<<<<<<;<<;<<<<<<;<<<9< @EAS54_67:3:197:261:624 GCCCTGCTAAACTAAGCATCATAAATGAAGGGGAA + 866;2:/;<<<;:<<<;<;;<<<<<<<<<<<<<<< @EAS54_67:3:47:471:858 ACACCCAACTAATATTTGTCTGAGCAAAACAGTCT + /;9<<63<<<<3<;<<<<<<<<<<<<<<<<<<<9< @EAS54_67:3:47:471:858 CATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTG + <<;<<<<<<<<9<<<4;;<<<<;<<<<<.<<4;<4 @EAS54_67:4:142:943:582 TTCAAATGAACTTCTGTAATTGAAAAATTCATTTA + <<<<<<;<<<<<<:<<;<<<<;<<<;<<<:;<<<5 @EAS54_67:4:145:607:216 AACGCGTAACTGCGCTCTCATTCACTCCAGCTCCC + <<<<<<<<8<<<<<<<<<<4<<<7<:<<1<<;;99 @EAS54_67:4:145:607:216 TGAAAAACAGGAAGAAAAGGTCTTTCAAAAGGTGA + /;<<&<<8<<<<<<<<<<<<<;872<<<<<<<<<< @EAS54_67:4:7:526:343 TCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCT + <<<<<<<<<<<<<<<:<<<5<<<<<<5;<<<+8<; @EAS54_67:4:7:526:343 TGAAAACAGTGTTCCCCAGATACCATCCCTGTCTT + (7:;;;<<;;;<1<1<<<<<<<<<<<<<<<<<<<< @EAS54_67:5:117:33:262 AATTAACATTACAACAGGAACAAAACCTCATATAT + <<;;<<;<:8<7<<;<<<<<<<<<<<<<<<<<<<< @EAS54_67:5:117:33:262 ACAAGCAAATGCTAAGATAATTCATCATCACTAAA + <<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<; @EAS54_67:5:124:241:608 CTGAACTTCCACGTCTCATCTAGGGGAACAGGGAG + 9;;<<;<<<;<<<;<:<<<<;<<<<<<<<<<<<<< @EAS54_67:5:124:241:608 GGGTATAATACCTCTACATGGCTGATTATGAAAAC + <<<<<<<<<;<<<<<<<<<;;<<<;<<<<;;8;;: @EAS54_67:5:127:828:697 ATGCCAGGAAGATACATTGCAAGACAGACTTCATC + <<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;;<; @EAS54_67:5:127:828:697 TAAAGAAAAAAAAACCTGTCAAACACGAATGTTAT + ;<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS54_67:5:149:639:910 CAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGA + <<<<<<<<<<<<<<<<<<<<<<<<7<;;<<;<<;< @EAS54_67:5:149:639:910 TCACTAAACCAGTCCTATAAGAAATGCTCAAAAGA + <;49;<<;;<<<<8;<<<<<<<<<<<<<<<<<<;< @EAS54_67:5:71:408:741 AGTCATCTATAAAGGAAATCCCATCAGAATAACAA + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;< @EAS54_67:5:71:408:741 TCCTGACAAGCAAATGCTAAGATAATTCATCATCA + ;7;<;<0<<<<<<<<:;<<<<<<<<<<<<<<<<<< @EAS54_67:6:107:395:312 CAAAATATAGTTGAAAGCTCTAACAATAGACTAAA + <<<<<<<<<<<<<<<<<<<<<<<<<;<;;<:<<<< @EAS54_67:6:107:395:312 CAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGT + ;<;;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS54_67:6:109:953:668 CAATATATCCATGTAACAAATCTGCGCTTGTACTT + ;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<8<;<< @EAS54_67:6:109:953:668 CCACTTTGGAAAACAATTTGGTAATTTCGTTTTTT + <:)9<<<<<<<<8:<<<<<<<<<<<<<<<<<<<<< @EAS54_67:6:198:503:669 CAATGATAAAAAGATCAATTCAGCAAGAAGATATA + 5<<:<<;<<<<<<<;;<<9<<<<<<<<;<<<<;<< @EAS54_67:6:198:503:669 CAGATTTAAAAACATGAACTAACTATATGCTGTTT + <<<<<<<<<<;8<<<<<;<<<<<<;<;<8<<8<<< @EAS54_67:6:43:859:229 TTCAAATGAACTTCTGTAATTGAAAAATTCATTTA + +37<=<.;<<7.;77<5<<0<<<;<<<27<<<<<< @EAS54_67:6:46:285:790 AACGCGTAACTGCGCTCTCATTCACTCCAGCTCCC + ;;<8<;<<<<88<8<<;;<;<<;<<<<<<<<;<<< @EAS54_67:6:46:285:790 TCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAAG + !!<<3<<<;;<<<<<<<<<;<;7<<7<<<<<<;<< @EAS54_67:7:101:752:996 AACCTTACAAGCCAGAAGAGATTGGATCTAATTTT + <<<<<<<<<<<<<<<;<<<<<9<<<<<<;<<;;;; @EAS54_67:7:101:752:996 AAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATT + <<<<<<<<7<7<<<<<<<<<<<<<<<<<;<<<<<< @EAS54_67:7:197:399:319 CAAAAAACAAATACTACTAGACCTAAGAGGGATGA + &<+==<<5<<<8<89;;<<<<<<8<<<<<<<<<<< @EAS54_67:7:197:399:319 TAGAAACCAAATGAGAGAAGGAGTAGCTATACTTA + +<<<<<<<<<<<<<<<<<;<<<<<<<<<<<;;<<; @EAS54_67:8:19:855:491 TGGCATTTGCCTTCAGACCCTACACGAATGCGTCT + 8<<<<;:<<<<:<<<<<:<;;<<<<<<<;<<<;<; @EAS54_67:8:19:855:491 TGTGTGTTCTCATCAACCTCATACACACACATGGT + <<<<<<<<<<<;<<.:<<<<;;;<4<:<:<7<;;; @EAS54_67:8:46:900:610 GATATCTGGATTCTGGGAAATTCTTCATCCTGGAC + <<<<<<<<<<<<;<<<<<<<<<<<<<<<<<;;4;< @EAS54_67:8:46:900:610 TACATGGCTGATTATGAAAACAATGTTCCCCAGAT + <;5<;<<<;<<<<<<;<<<<<<<<<<8<<<<<8<< @EAS54_71:2:125:628:79 GCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGA + 95&<<<<<<<63<<<6<<<<8<;<<8<<<<<<<< @EAS54_71:2:125:628:79 TTTATGCTATTCAGTTCTAAATATAGAAATTGAAA + ==================<6<====<<:<==7;:: @EAS54_71:2:204:264:413 CAATGAACAACAGAAAGAAAAGTTCTTTCAAAAGG + 1==(4=::;/7::&===;====/=;===;;===== @EAS54_71:2:204:264:413 TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTG + <<<<<<<<<<<<<;:59<+<<:<<<9<<;:62<) @EAS54_71:2:85:686:696 AATCAGCAAGAGAAAAGCATACAGTCATCTATAAA + ==================<=====:==<=<;=:== @EAS54_71:2:85:686:696 TAAACTAAGCATCATAAATGAAGTGGAAATAAAG + :<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS54_71:3:186:989:869 ACACACATGGTTTAGGGGTATAATACCTCTACATG + ;<<;:<<<7:<<<<<<:<<<<<<<<<<<<<<<<<< @EAS54_71:3:186:989:869 GGGAAATTCTTCATCCTGGACCCTGAGAGATTCT + <<<<<<<<<<<<<<<<<<<<7;:<<<<<<<<<$< @EAS54_71:3:254:32:275 GATGGAGGGAAGAGGGACGCTGAAGAACTTTGAT + <<<<<<<<<<<<<<<<<<<<<<;;<:<::<:2*< @EAS54_71:3:254:32:275 TGCAACTGTGAGCCATCACAATGAACAACAGGAAG + (6+<;+6:9<<:7:<95<<<<<<<<<<<<<<<<<< @EAS54_71:3:257:288:731 AAGAAGATATAACCATCCTACTAAATACATATGCA + <<:<<7<<<<<;<5<<<<<<<<<<<<<<<<<<<<< @EAS54_71:3:257:288:731 TGCTGTTTACAAGAAACTCATTAATAAAGACATG + <<<<<<<<8<8<<;<;<<<;<<<5<;;88.8<6< @EAS54_71:3:267:821:860 GCATACAGTCATCTATAAAGGAAATCCCATCAGA + $&<<<.<:;6<<;<<<<<<<<<<<<<<<<<<<<< @EAS54_71:3:267:821:860 TCTTTAGTCTTGCTAGAGATTTAGACATCTAAATG + ;<<<<<8<<<<<8<<;<8<<<<<5<;<<<<<2;<5 @EAS54_71:3:78:855:352 AAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTT + 2<<<<<<<9<<4<<<<<<<<<<<<<<<<<<<<<< @EAS54_71:3:78:855:352 AACAATAGACTAAACCAAGCAGAAGAAAGAGGTTC + <<<<<<<<;<<<<<<<<<;<<<<<<<<;<;<<:<: @EAS54_71:4:127:725:381 AATTACAAAATATAGTTGAAAGCTCTAACAATAGA + <<<<<<<<<<<<<<<<<<<<<;<<<<;;;;;<<8: @EAS54_71:4:127:725:381 TGAACCTATGAGTCACAGGTATTCCTGAGGAAAA + +<<.<<;<;<<<3;<;<<<<<<6<8;<<<<<<<1 @EAS54_71:4:13:981:659 CGGGACAATGGACGAGGTAAACCGCACATTGACAA + +)---3&&3&--+0)&+3:7777).333:<06<<< @EAS54_71:4:13:981:659 TGTAGCCCCTCTAAGGCGTTCTATTTGTAATGAA + ()&)06636;;<664*6;<<<<<<<<<<<<<<<1 @EAS54_71:4:14:88:306 AAAGAATGCCAGGAAGATACATTGCAAGACAGAC + <<<<<<8<<<<<<;<<<3<<<8<<;<;;<15<:6 @EAS54_71:4:14:88:306 AGAAGAGATTAGATCTAATTTTTGGACTTCTTAAA + <1;<;<;<4<&<<<:<<<:<<<<;<<<<<<<<<<< @EAS54_71:4:165:397:25 GCAACTGTGAGCCATCACAATGAACAACAGGAAGA + <<7<<<<<<)97<6<:3:60:3+37-37+<:33:3 @EAS54_71:4:165:397:25 TTCAACGCTTCTAGCCATTTCTTTTGGCATTTGC + &(33'60;-'+'<7;<<*3-<;;183<<<;<;<< @EAS54_71:4:169:256:888 AGGTTCAGAACTTGAAGACAAGTCTCTTATGAATT + <<<<<<<<<<<<<<<<<<<<<<;;<;<<;<<:;;< @EAS54_71:4:169:256:888 ATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT + &<<:<;<<;;<8<;<<<<<<<<<<<<<<<<<<<< @EAS54_71:4:169:862:829 AAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCA + <<<<<<<<<<<<<<<<<;<<<;<;<<<<:<;;<78 @EAS54_71:4:169:862:829 GCCATTTCTTTTGGCATTTGCCTTCAGACCCTAC + ,1<6<<<<<7<<<<<<<<<<<<<<<<<7<<<<<< @EAS54_71:4:206:741:810 ACTAACTATATGCTGTTTACAAGAAACTCATTAA + <3<<;5<<<<<;:<<<<<<<<<<<<<<<<<<<<< @EAS54_71:4:206:741:810 CAAAAGTACAAAACTCACAGGTTTTATAAAACAAT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<;:-;<< @EAS54_71:4:209:159:130 CTTATCATGACTCTATCCCAAATTCCCAATTACGT + ;:6<:<8::;<<<;<-<<<<<<<<<<<<<<<<<<< @EAS54_71:4:209:159:130 GCCCCCAGCATGGTTGTACTGGGCAATACATGAG + <<<<<<8<<<<<<&<<+7<<4<<<22<;<<<<3< @EAS54_71:4:233:97:262 ACCACACATTAATACTATGTTTCTTATCTGCCCA + <<<<<<<<<<<;<;<<:<<<<<<<<<<<<.<&77 @EAS54_71:4:233:97:262 GTATCAATTTGGTGTTCTGTGTAAAGTCTCAGGGA + --;;7<;<;;:;<;<<<<<<<<<<<<<<<<<<<<< @EAS54_71:4:252:428:683 TGTCTTGATTTACTTGTTGTTGGTTTTCTGTTTCT + <<<<<<;<<<<<<<<7<<7<<&+<<<<:<&<<<4< @EAS54_71:4:284:269:882 TTTCTTTTCTCTTTTTTTTTTTTTTGTTTTTGCA + <;<<<<<8<7<8;<<<;<7<<<<<;272;73&&) @EAS54_71:4:328:669:662 GGAAGGAGCATTTTGTCAGTTACCAAATGTGTTT + <<<<<<<<<<<<<<<<<<<<<<<<+9;<;;.<<< @EAS54_71:4:328:669:662 TCTTCATCCTGTACCCTGAGAGATTCTGCAGCCCA + 4<<;<<8<.<88.<<;4<<<<<<<4<.<<<<7<<< @EAS54_71:4:72:63:435 CCTTGCAACAACCTTGAGAACCCCAGGGAATTTG + <<<<<<<<<<<<<<<<<<<<;<<<;<;;39:7:7 @EAS54_71:4:72:63:435 TGATATCTGGATTCTGGGAAATTCTTCATCCTGGA + ::<;<<<<;;;<<<<<<<<<<<<<<<<<<<<<<<< @EAS54_71:4:73:182:444 AACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCG + :1<4;;::<<;<<<<;<<<<<<<<<<<;<<<<<<< @EAS54_71:4:73:182:444 CTTGATTTACTTGTTGTTGGTTTTCTGTTTCTTT + <<<<;;<<<<<<<<<<<<;<;<<<<<:<<<<<7< @EAS54_71:5:153:543:671 GCCCCATCTCTTGTAATCTCTCTCCTTTTTGCTG + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<2<<7 @EAS54_71:5:153:543:671 TAAAATGTCTATTTTTGTCTTGACACCCAACTAAT + ;;;;;=;==================;========= @EAS54_71:5:16:434:204 AGATGAGAGAGAACTTCCCTGGAGGTCTGATGGC + <:7:<<<<<<<<<<<9<<<+<<<<<<<<<<<<<< @EAS54_71:5:16:434:204 CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGT + =================;)===8===:==7;<+%; @EAS54_71:5:81:685:141 ACTGAACCTATGAGTCACAGGTATTCCTGAGGAA + <<<<<<<<<<<<<<<<<<<<<;;<<;<<<',7,7 @EAS54_71:5:81:685:141 AGATATGTAGTCATCAGACTATCTAAAGTCAACAT + ;+;(;)..=3.1=.7=;=8;==<4====;====== @EAS54_71:6:172:896:83 AGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGT + <<<<<<<<<<<<<<<<<:;;+;<<<<<<<<9;;; @EAS54_71:6:172:896:83 CATTTGCCTTCAGACCCTACACGAATGCGTCTCTA + ;<.5.;;<+;<<<<<<<4<<<<<<<;<<<<<;<<< @EAS54_71:6:215:133:909 TGTGTGTTCTCATCAACCTCATACACACACATGG + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<996( @EAS54_71:6:215:133:909 TTGCCTTCAGACCCTACACGAATGCGTCTCTACCA + 7758;<;<;8<<<<;<;<<<<<:;<<<<<<<<<<< @EAS54_71:6:224:932:942 CTCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGG + <;<<;;<<<;<<<<<<<<<<<<<<<<<<<<<<<<< @EAS54_71:6:224:932:942 GTCCATGTACACACGCTGTCCTATGTACTTATCA + <<<<<<<<<<<<<<<<<<<<<<;<<<<7<<(;3, @EAS54_71:6:228:354:203 AATGGACCTGTGATATCTGGATTCTGGGAAATTC + 88<<<8<<<<<<<<<8<<<<<<<<<4<<<4/9/; @EAS54_71:6:228:354:203 TCAACCTCATACACACACATGGTTTAGGGGTATAA + %1<851<5<<<982<<<<<<<<::<<<<7<<<<3< @EAS54_71:6:264:705:89 AAACATATGCACCTAACACAAGACTACCCAGATTC + <(<2<&<)<<<7<8<<<<<<<<<<.<<<<<<<<<< @EAS54_71:6:264:705:89 AAGGGGTGGAAAAAGATGTTCTACGCAAACAGAA + <<<<<<<<<<;8<<<<<<<<<<<<<<<&<<,;;( @EAS54_71:6:324:515:230 AAAACAGTCTAGATGAGAGAGAACTTCCCTGGAG + 7<<1<<<7<+<<<;<<<<<<<<<<<<<<<<<<<< @EAS54_71:6:324:515:230 CCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGG + <<;<<<<<<<<<<<<<<<:<<<<8<<<4<<4<<34 @EAS54_71:6:82:932:400 GACACCCAACTAATATTTGTCTGAGCAAAACAGTC + <<;<<72<<7<<<<<<<<<<;<<<+7<<<<<<<<< @EAS54_71:6:82:932:400 GTAATCTCTCTCCTCTTCGCTGCATCCCTGTCTT + <<<<<<8<1<<<<8+<<&<<<8<<<<<<<+(,/8 @EAS54_71:7:130:260:553 AGCAAGAGAAAAGCATACAGTCATCTATAAAGGAA + <*;<<7<);<<;9;<5<*<9<;<<;;<7<<<<<1< @EAS54_71:7:130:260:553 GTGAGAAGTTTGGAAAAACTATTTGAGGAAGCAC + <<<<<1<<<<<<<<<<6<<81============= @EAS56_59:2:60:677:921 GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAAT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS56_59:3:149:953:349 AGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTG + 2;<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS56_59:3:149:953:349 TTCTTTTGGCATTTGCCTTCAGACCCTACACGAAT + <<<<<<<<;<<<<<<<<<<<;7:<:<<:<:;;::; @EAS56_59:3:166:626:836 AGTACAAAACTCACAGGTTTTATAAAACAATTAAT + <;;7<<<<<<;<7;<<<<<<<<<<<<7<<<<<<<+ @EAS56_59:3:166:626:836 CTGTCAAACACGAATGTTATGCCCTGCTAAACTAA + <<<<<<<<<<<<<<<<<<<<9<<<<<<<<;<;;;9 @EAS56_59:3:182:1002:639 AAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAG + <<;;9;9<<<<<<;<7;<;<<<<;;<<<;<<7;<< @EAS56_59:3:182:1002:639 AACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGA + <<<<<<<<<<<<<<<<<<<<<9-<<<<4<;<;;<; @EAS56_59:3:316:25:230 GATGCCCCTTGGCCATCACCCGGTCCCTGCCCCAT + 8;8;<<;<;;<<<<<;<<<<<<<<<<<<<<<<<<< @EAS56_59:3:316:25:230 TGTCCTATGTACTTATCATGACTCTATCCCAAATT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<);2;; @EAS56_59:4:119:651:88 GATTGGATCTAATTTTTGGACTTCTTAAAGAAAAA + <<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS56_59:4:119:651:88 GCTCAAAGAATGCCAGGAAGATACATTGCAAGACA + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9;< @EAS56_59:4:262:928:237 TGAGTTCAGGTAAAGGTGTGGAAAAAGATGTTCTA + ;<<<<<;<<<<<<<<<;<<<<<<<<<<<<<<<<<< @EAS56_59:4:262:928:237 TTGAGACTACAGAGCAACTAGGTAAAAAATTAACA + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7<< @EAS56_59:4:267:394:437 AAACATCATAAATACACACAAAAGTACAAAACTCA + &<&,<8.<;<<<;<8<8<7<<<<<<<<<<<<<<<< @EAS56_59:4:267:394:437 GGACTTCTTAAAGAAAAAAAAACCTGTCAAACACG + <<<<<<<<<<;<;<<<<<;;<<<<<;<<:;8<;<8 @EAS56_59:4:278:524:521 CACATTAATACTATGTTTCTTATCTGCACATTACT + <<<;<<;<<<<<<<;<<<<<<<<<<7;5;<<<;;< @EAS56_59:4:278:524:521 CCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAA + 7777,<;<<7<<<<;;<<;;<<<<<<<<<<<<<<< @EAS56_59:4:329:577:757 AACGCGTAACTGCGCTCTCATTCACTCCAGCTCCC + ;;;888;<<<<<<6<<<2;<<<<<<;<<<<<<<<< @EAS56_59:4:329:577:757 TCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAAG + !!<<<<9;<:<<;<<<<<<<<;<<<<<<<<<<<<< @EAS56_59:5:113:694:725 CTGTAATGATGCCCCTTGGCCATCACCCGGTCCCT + ;::<<:<:<<<<<<<<<<:<:<<<<<<;<<<<<<< @EAS56_59:5:113:694:725 GTACACACGCTGTCCTATGTACTTATCATGACTCT + <<<<<<<<<<<<9<<<<<:<<<<<<<<<<:;;<;; @EAS56_59:5:125:137:58 AACTATATGCTGTTTACAAGAAACTCATTAATAAA + <<9;<<<<<;<;<<<<;<<<<<<;<<<<<<<<<<< @EAS56_59:5:125:137:58 GGTTTTATAAAACAATTAATTGAGACTACAGAGCA + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<9;< @EAS56_59:5:181:713:140 AGGGGAAATAAAGTCAAGTATTTCCTGACAAGCAA + <7<<<<<<<<<<<<7<7<6+<<<5;<;<2<;;+;; @EAS56_59:5:181:713:140 CTACAGAGCAACAAGGTAAAAAATTAACATTACAA + 78<+<7<-7;;;&<5<7<<<<7<<<<<<<<<<<7< @EAS56_59:5:198:929:684 AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGA + <<;<<<<<:<<<<<<<<<<<<<<<<<;<<<<<<<< @EAS56_59:5:198:929:684 GAAATCCCATCAGAATAACAATGGGCTTCTCAGCA + <7<<<<;<<<<<<<<<<<<;<<<<<:<<<<::<:7 @EAS56_59:5:232:336:46 ATTTTTTTTTTTTCTTTTCTCTTGTTTCTTTTTTT + +<<<<<<<<<<<<6<<<<;<6<<&&<,3<<<<3,, @EAS56_59:5:325:544:349 AAAATTAAAGTTCAATACTCACCATCATAAATACA + <<<<57<<<7<;6<<<<;<7<7;<<7<<<<<<<<< @EAS56_59:5:325:544:349 CAAGCCAGAAGAGATTGGATCTAATTTTTGGACTT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<6;;;<< @EAS56_59:5:90:629:652 AGCCCATACTTTACTGCTACTCAATATATCCATGT + <<<<<<<<<<<<<<<<<<<<<<<:<;<<<<<<<<< @EAS56_59:5:90:629:652 ATATTGCTAGTGGGAGTATAAATTGTTTTCCACTT + <:<7::<:<<<<<8<<<<<<<<<<<<<<<<<<<7< @EAS56_59:6:187:925:547 GGCTGATTATGAAAACAATGTTCCCAAGATACCAT + 43<<<:9<;;;:7<<<<6<:<8<-4-/,81<(48: @EAS56_59:6:187:925:547 TGAACTTCCACGTCTCATCTAGGGGAACAGGGAGG + ((988+&8<<;<09<;<<9<<4<<-<99<<;<9<; @EAS56_59:6:199:327:965 ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT + <5<:<<<58<:<<<<<<8<<<<<<<<<;<<<<<<< @EAS56_59:6:199:327:965 NCAACAACCTTGAGAACCCCAGGGAATTTGTCAAT + !,+*+++++++++++*+++++++**)+*+**+(** @EAS56_59:6:227:657:95 GTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGA + <<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<8<85 @EAS56_59:6:227:657:95 GTCATCTATAAAGGAAATCCCATCAGAATAACAAT + ;3;<);<<<<<<<<<<<<18<<<<<<<<<<<<<<< @EAS56_59:6:286:753:854 TCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTC + ;<2<<<,57:<<9<<<<<<<<<<<<<<<<<<<<<< @EAS56_59:6:286:753:854 TTATCATGACTCTATCCCAAATTCCCAATTACGTC + <<<<<<<<<<<<<<<<<<3<<<<<<9999<;<<9; @EAS56_59:6:312:837:406 AGGTGCACTAATGCGCTCCACGCCCAAGCCCTTCT + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS56_59:6:312:837:406 CTGCACATTACTACCCTGCAATTAATATAATTGTG + ;<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS56_59:6:3:186:68 AAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATT + <<;<<<<<&:,<<<<<<<<<<<<<<<<<<<<<<<< @EAS56_59:6:3:186:68 TTACAAGCCAGAAGAGATTGGATCTAATTTTTGTA + <<<<<<<<<<<<;<<<<<<<<<<<<;;<<<<<&%8 @EAS56_59:6:89:457:591 ATGCCCTGCTAAACTAAGCATCATAAATGAAGGGG + <<<<<<<<<<<4<<<<<<<<<<<<8<7/4<<<<4+ @EAS56_59:6:89:457:591 CAGGTTTTATAAAACAATTAATTGAGACTACATAG + 797<<9<<<<<<<3<7<<<<<<<<<<)<<<<<07< @EAS56_59:7:260:985:520 TCCCTGTCACCCAATGGACCTGTGATATCTGGATT + ;9;7<<<<<<<<<<<<<<<<<:<<<<<<<<<<<<< @EAS56_59:7:260:985:520 TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA + <<<<<<<<<<<<<<<<<;:;<<;<:<<<,:1;)<; @EAS56_59:7:318:679:883 GATTTAGACATCTAAATGAAAGAGGCTCAAAGAAT + <<;4<<;<:<<7<<<<<<<<<<<<<<<<<<<<<<< @EAS56_59:7:319:246:304 CTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGA + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;: @EAS56_59:7:319:246:304 TGTCACCCAATGGACCTGTGATATCTGGATTCTGG + ;;<;;;<<<<8;<<<<;<<<<<<<<<<<<<<<;<< @EAS56_59:7:82:902:868 CTGTCACCCAATGGACCTGTGATATCTGGATTCTG + <<;;<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<< @EAS56_59:7:82:902:868 TTGCAACAACCTTGAGAACCCCAGGGAATTTGTCA + <<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS56_59:8:49:182:192 ACACAAAAGTACAAAACTCACAGGTTTTATAAAAC + <5<;<<<<<<<<<<<:<<<<<<<<<<<<<<<<<<< @EAS56_59:8:49:182:192 GTTATGCCCTGCTAAACTGAGCATCATAAATGAAG + =====================;============< @EAS56_59:8:80:542:549 AGTAAACTCTCAAATATTGCTAGTGGGAGTATAAA + =9====7=;=======;;==;========<===== @EAS56_59:8:80:542:549 CTAAAAGCCCATACTTTACTGCTACTCAATATATC + <<<<<<<<;<<<<<<<<:<<<<-<;;<;7<;3;9; @EAS56_61:1:119:880:781 ACAAATCTGCGCTTGTACTTCTAAATCTATAACAA + ;8<<;<<<<:<84<<<<:<<<<<<<<<<<<<5<<< @EAS56_61:1:119:880:781 ACATATGCACCTAACACAAGACTACCCAGATTCAT + <<<<<<<<<<<<<<<<<<<<<<<<+<<<<7<<<<< @EAS56_61:1:210:880:606 GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAT + <<<<<<<<<<<<<<<<<<;<<<<<<:<<<<3<<8& @EAS56_61:1:210:880:606 TCCTGGACCCTGAGAGATTCTGCAGCCCAGCTCCA + .<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS56_61:1:303:184:14 CAACCTTGAGAACCCCAGGGAATTTGTCAATGTCA + <<<<<<8<0<<<<-<-98<<--<<<6;076;75+& @EAS56_61:1:303:184:14 CAATGGACCTGTGATATCTGGATTCTGGGAAATTC + :<<.<;;7<:<<<<<<7<<<<<<<<<<<<<<<<<< @EAS56_61:2:152:860:286 AGACTATTGCCAGATGAACCACACATTAATACTAT + <;<<<;<<0:<3<:<<2<<<<<7+<7+47<9(999 @EAS56_61:2:152:860:286 TTAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCA + 2;5;8<<;5<<<;<2<8<<<<<<;8<;<<<<;<<< @EAS56_61:3:140:522:212 CGCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGA + <<<<<<<<<<<<<<<<<;<<<<<<<<<<<;<;95; @EAS56_61:3:140:522:212 GACAGGCTGCAACTGTGAGCCATCACAATGAACAA + :;8;:::<<:<<<<<<<<<7<<<<<<<<<<<<<<< @EAS56_61:3:165:665:220 ACAATTAATTGAGACTACAGAGCAACTAGGTAAAA + <:<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @EAS56_61:3:165:665:220 GGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATG + <<<<<<<<<<<<<<<<<<<<<;<;;<<<;;<;<<; @EAS56_61:3:208:118:673 AAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA + <<<<<;;<;<<<<<<<<<:<<<<<<<<<<<<<<<< @EAS56_61:3:208:118:673 GAACAGAGCTTTCAAGAAGTATGAGATTATGTAAA + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;; @EAS56_61:3:260:827:289 AAACCTCATATATCAATATTAACTTTGAATAAAAA + <<<<2<<<<;<<<<;<<<<<<:<<<&-<8<<88<3 @EAS56_61:3:260:827:289 TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA + 6;99+<<<<<<<<<<<<<<6<<<<<7<<<<<<<<< @EAS56_61:3:45:758:616 ATAAATTGTTTTCCACTTTGGAAAACAATTTGGTA + <<;<:<<<<<<<<<;<<<<<<<<<<<<<<<<<<<< @EAS56_61:3:45:758:616 CATACTTTACTGCTACTCAATATATCCATGTAACA + <<<<<<<<<<<<<<<<<<<<<<<<<6<<<<<<;;< @EAS56_61:3:5:45:441 TTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTT + ;;58:<:<(:<<11<&<1<<;<<<<><<<<<<<<< @EAS56_61:4:262:456:74 TACCAAATGTGTTTATTACCAGAGGGATGGAGGGA + <<<<<<<<<<<<<<<<<<<<:;;:;7:<::7<7:3 @EAS56_61:4:262:456:74 TGGGAAATTCTTCATCCTGGACCCTGAGAGATTCT + 862;<<<:;<;<<<;;;<<<<;;<<<<<<<<<<<< @EAS56_61:5:194:470:416 AAACTATTTGAGGAAGTAATTGGGGAAAACCTCTT + <<<7<<;<<<<<<<<<:<<<<<<<<<<<<<<<<<< @EAS56_61:5:194:470:416 TCAGAACTTGAAGACAAGTCTCTTATGAATTAACC + <<<<<<<<<<<<<<<<<<<<<<<<;<;<<<<<<<< @EAS56_61:5:209:824:866 ATCATCACTAAACCAGTCCTATAAGAAATGCTCAA + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<; @EAS56_61:5:209:824:866 CAGCAACAAAACCTCATATATCAATATTAACTTTG + ;<:&<<:<<<<;<<;<<<<<<<<<<<<<<<<<<<< @EAS56_61:5:263:314:696 AACTCATTAATAAAGACATGAGTTCAGGTAAAGGG + <<<<<<<<<<<<<<;<<<<<<<<<<<<:<<;<775 @EAS56_61:5:263:314:696 AAGATCAATTCAGCAAGAAGATATAACCATCCTAC + <<;<;:<<<<7<<:<<<<<<<<<<<<<<<<<<<<< @EAS56_61:5:272:240:950 CAGCAGAGCTTGGATCTAATTTTTGGACTTCTTCA + 6<<&:<<<&<::;&7<<<3<;<<;<:;:<8:<<(< @EAS56_61:5:272:240:950 TCAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAA + 37<<<<<<<<<<<<<<<<<<<<<<;;<;<<<<<<; @EAS56_61:6:10:106:737 ACAAGAAACTCATTAATAAAGACATGAGTTCAGGT + <<<;<1<;<<<<<<9<<<<;;<<<<<99<<94008 @EAS56_61:6:10:106:737 ACAATGATAAAAAGATCAATTCAGCAAGAAGATAT + <-<<;<<<<<<<<<<<;<<<<;<<;<<<<<<<<<< @EAS56_61:6:160:272:398 AATGTTCCCCAGATACCATCCCTGTCTTACTTCCA + 9<<<3<<<<<<<<<<<9<<;8<<<<;<+.;;89.. @EAS56_61:6:160:272:398 GTGCACTAATGCGCTCCACGCCCAAGCCCTTCTCA + 3:,<,;;<<;<<1<<<<<<<;<;<<<<<<<<<<<< @EAS56_61:6:226:370:91 AGAATAACAATGGGCTTCTCAGCGGAAACCTTACA + <':<6<;<<<;2<;<-7;;;<<<<<<<;;;<<7;< @EAS56_61:6:226:370:91 AGGCTCAAAGAATGCCAGGAAGATACATTGCAAGA + 8<<<;<8<8<;<<<8<<;7<7;8784<<,;864<& @EAS56_61:6:227:259:597 AATATAGAAATTGAAACAGCTGTGTTTAGTGCCTT + <8<;2;9;<;;-92<;;;<;<<<<<<<<<<<<<<< @EAS56_61:6:256:67:461 TCATGTTTGTGTCTTTCTATGCATTTTTTTTTTTT + !!7181!63:6-:!-163(-1%-18<<4<<<<<<< @EAS56_61:6:256:67:461 TTGTTTTTTCTTCTTTTCTCTTTTTTTTTTTTTTT + *.%53.:)1+9;3397;1795507+335;.&51)5 @EAS56_61:6:283:963:234 AAAAAGATGTTCTACGCAAACAGAAACCAAATGAG + <<<<<<<<<<<<<<<;<<<<<<<<<<<;<<;<<;< @EAS56_61:6:283:963:234 ACATATGCACCTAACACAAGACTACCCAGATTCAT + <5<;<;97;;:;<<7<;<<<<<<<<<<<<<<<<<< @EAS56_61:6:307:208:477 AAAGTCAAAATTAAAGTTCAATACTCACCATCATA + <<<<<.<<<<<<<<<<<<;<;<<<<<<<<<<<<<< @EAS56_61:6:307:208:477 ACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAA + <<<<<<<;<<;<<<<<<<<<<<<<<<<;:<<<88; @EAS56_61:7:280:133:495 AGATGAACCACACATTAATACTATGTTTCTTATCT + <:<9:<<7:<6<<<<<<<<<<<<<<<<<<<<<<<< @EAS56_61:7:280:133:495 CCATCATGAAGCACTGAACTTCCACGTCTCATCTA + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<; @EAS56_61:7:41:745:603 CATTGCAAGACAGACTTCATCAAGATATGTAGTCA + <<<<<<<<<<<<:<<<<<<<<<<<<<<<6<:8<<: @EAS56_61:7:41:745:603 TAATTTTTGGACTTCTTAAAGAAAAAAAAACCTGT + ;<<;;<;<8<<<<<<<<<<<;<<;<<<<<<<<<;< @EAS56_61:7:7:682:201 CATACAGTCATCTATAAAGGAAATCCCATCAGAAT + 0:8;5<8<1:78<<<<<<<<<<<<:8<<2<<<<:< @EAS56_61:7:7:682:201 GGAAAACCTCTTTAGTCTTGCTAGAGATTTAGACA + <<<<<<<7<<7<<<<77&;-9<97<76<;<<993< @EAS56_61:8:60:358:494 GGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACA + <<<<<<<<<<<<<<<<<<<<<<<<<<:<:<<;;4; @EAS56_61:8:60:358:494 TACCCAGATTCATAAAACAAATACTACTAGACCTA + 7<77;<<<<<;<<<<<<<<<<<<<<<<<<<<<<<< @EAS56_61:8:7:171:402 GTGATATCTGGATTCTGGGAAATTCTTCATCCTGG + <<<<<<<<<<<<<<<;/<<<<;<<<<<;<<1<<<4 @EAS56_61:8:7:171:402 TCTACATGGCTGATTATGAAAACAATGTTCCCCAG + :086::::847:<7<<7<<<<<<;7<<;<<<<7<< @EAS56_63:1:119:446:185 TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT + +70730;<0<77;;<<<<<9<<<<<<9<<<<<<<< @EAS56_63:1:119:446:185 TTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAG + <<<<<<<7<<<4<<<<9<<54<:<7<5:<::7-5; @EAS56_63:1:145:71:26 CTAGGGGAACAGGGAGGTGCACTAATGCGCTCCAC + <<<<<<<<<<<<<<<<<;<;;<<;<;<9<9;;99; @EAS56_63:1:145:71:26 TTTCTTATCTGCACATTACTACCCTGCAATTAATA + 882;8;<;;887<<<;;<<<<;<<<<<<<<<<<<< @EAS56_63:2:119:161:322 ATCAGAATAACAATGGGCTTCTCAGCAGAAACCTT + <83<;<<;<;<<<<<<<<<<<<<<<<<<<<<<<<< @EAS56_63:2:119:161:322 CTTTAGTCTTGCTAGAGATTTAGACATCTAAATGA + <<<<<<<<<<<<<<;<<<<<<<;<<<<<<<<<<<<<1>><<<< MF:i:18 Aq:i:21 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_66:4:240:264:231 121 chr1 213 66 35M = 213 0 TGTAATGAAAACTATATTTATGCTATTCAGTTCTA 9;,;;62<9<)29<<<;96<<<;<<7<<<<<<;<< MF:i:64 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_66:4:240:264:231 181 chr1 213 0 * = 213 0 CAACAGATCAAGAAGGAGGGGCAATGGACGAGTTA %15+5022))0&<<)0)+7:4+&<0<<:0<<<7<< MF:i:192 EAS1_93:7:14:426:613 99 chr1 214 99 35M = 379 200 GTAATGAAAACTATATTTATGCTATTCAGTTCTAA ======;=;==========;;==3=;==-=<;<;< MF:i:18 Aq:i:71 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_93:2:173:995:93 163 chr1 215 99 35M = 382 202 TAATGAAAACTATATTTATGCTATTCAGTTCTAAA <<<<<<<<<<<<<<<<<<<7:<<<<;:<:<<<<:7 MF:i:18 Aq:i:73 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_64:6:195:348:703 163 chr1 215 99 35M = 353 173 TAATGAAAACTATATTTATGCTATTCAGTTCTAAA <<<<<<<;<<<<<;:<<<<<<<<<<<<:<1:<:7< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_108:2:62:879:264 163 chr1 216 99 35M = 396 215 AATGAAAACTATATTTATGCTATTCAGTTCTAAAT <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<2<< MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_61:4:83:452:970 99 chr1 216 99 35M = 379 198 AATGAAAACTATATTTATGCTATTCAGTTCTAAAT ==========================;======== MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS218_1:2:64:1318:1711 99 chr1 218 99 35M = 389 206 TGAAAACTATATTTATGCTATTCAGTTCTAAATAT <<<<<<<<<<<<<<<<7<<<<<<<:<<<<<2<<<< MF:i:18 Aq:i:77 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_589:8:113:968:19 83 chr1 219 99 35M = 50 -204 GAAAACTATATTTATGCTATTCAGTTCTAAATATA 8;<;8;9<<<<<<<9<:<<<<<<<<<;<<<<<<<< MF:i:18 Aq:i:63 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_93:4:160:896:275 163 chr1 220 99 35M = 387 202 AAAACTATATTTATGCTATTCAGTTCTAAATATAG ============<====<==<====<==<==;=:6 MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_591:6:181:191:418 163 chr1 221 99 36M = 387 202 AAACTATATTTATGCTATTCAGTTCTAAATATAGAA <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<988 MF:i:18 Aq:i:77 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_28:7:242:354:637 99 chr1 222 99 36M = 417 231 AACTATATTTATGCTATTCAGTTCTAAATATAGAAA <<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<6<;; MF:i:18 Aq:i:75 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_589:1:122:77:789 163 chr1 223 99 35M = 396 208 ACTATATTTATGCTATTCAGTTCTAAATATAGAAA <<<:<4<<9<:7<<<:<<<7<<<<<<<<<<9<9<< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_591:5:42:540:501 147 chr1 224 99 36M = 60 -200 CTATATTTATGCTATTCAGTTCTAAATATAGAAATT ;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:69 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_591:6:155:12:674 83 chr1 224 99 36M = 52 -208 CTATATTTATGCTATTCAGTTCTAAATATAGAAATT ;<<<<<<<<<<;<<<<;<<<<8<<<<<<<<<<<<<< MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_593:4:106:316:452 147 chr1 224 99 36M = 49 -211 CTATATTTATGCTATTCAGTTCTAAATATAGAAATT :<<<<<;<<<<:<<:<<<<<<7<<<<<<<<<<<<<< MF:i:18 Aq:i:71 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_19:5:89:525:113 163 chr1 227 78 40M = 397 210 TATTTATGCTATTCAGTTATAAATATAGAAATTGAAACAG <1<7<6;+0;7;7'<70;-<7<:<:<<5<<:9<5:7:%:7 MF:i:18 Aq:i:39 NM:i:1 UQ:i:12 H0:i:0 H1:i:1 EAS54_65:3:321:311:983 147 chr1 228 99 35M = 51 -212 ATTTATGCTATTCAGTTCTAAATATAGAAATTGAA ;;4;;<7<<<<<<77<<<<<<<<<<17<<<<<<<< MF:i:18 Aq:i:62 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_65:8:76:493:708 147 chr1 229 44 35M = 73 -191 TTTATGCTATTCAGTTCTAAATATAGAAATTGAAA 5/)63.&1517(544(055(0454&7706566679 MF:i:18 Aq:i:44 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_71:2:125:628:79 163 chr1 229 99 35M = 400 205 TTTATGCTATTCAGTTCTAAATATAGAAATTGAAA ==================<6<====<<:<==7;:: MF:i:18 Aq:i:69 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_32:5:78:583:499 83 chr1 229 74 35M = 37 -227 TTTACGCTATTCAGTACTAAATATAGAAATTGAAA &6&9774&<;67<44&-4<;<9<7<<<<<;<<<<< MF:i:18 Aq:i:37 NM:i:2 UQ:i:27 H0:i:0 H1:i:1 EAS54_67:3:175:730:949 83 chr1 230 99 35M = 70 -195 TTATGCTATTCAGTTCTAAATATAGAAATTGAAAC <<<<;+<<<<7<;<<;<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:65 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_45:1:84:275:1572 163 chr1 230 99 35M = 394 199 TTATGCTATTCAGTTCTAAATATAGAAATTGAAAC /6;;;4;;;;;;;;7;;4;.4;;;;;6;;;77077 MF:i:18 Aq:i:62 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_108:4:248:753:731 99 chr1 231 99 35M = 402 206 TATGCTATTCAGTTCTAAATATAGAAATTGAAACA <<<<<<<<<<<8<<<<<<<<<<<<:<<<<&<:<.: MF:i:18 Aq:i:70 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_45:1:9:1289:215 99 chr1 231 99 35M = 394 198 TATGCTATTCAGTTCTAAATATAGAAATTGAAACA ;;;;;;9;;;67;;;;;99;9;;;;;;;;977747 MF:i:18 Aq:i:59 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_595:7:188:802:71 163 chr1 232 99 35M = 415 218 ATGCTATTCAGTTCTAAATATAGAAATTGAAACAG <<<<<<<<<;<<<<<9<<<:<<<:<<<<<<:<<<; MF:i:18 Aq:i:75 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_93:7:252:171:323 83 chr1 234 99 35M = 43 -226 GCTATTCAGTTCTAAATATAGAAATTGAAACAGCT ;8<;<=3=6==:====;;======;========== MF:i:18 Aq:i:62 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS192_3:5:223:142:410 147 chr1 235 99 35M = 60 -210 CTATTCAGTTCTAAATATAGAAATTGAAACAGCTG 8;<<<;<<<<;<<<<<<;<;<<<<<<<<<<<<;<< MF:i:18 Aq:i:39 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_30:1:243:10:911 83 chr1 236 99 35M = 63 -208 TATTCAGTTCTAAATATAGAAATTGAAACAGCTGT ;<;;;<4;9:<<<;<<;<<<<<;;<<<<<<<<<<< MF:i:18 Aq:i:64 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_45:6:5:730:1436 163 chr1 236 99 35M = 403 202 TATTCAGTTCTAAATATAGAAATTGAAACAGCTGT ;;;;;;;;;;;;;;;;;;8;;;;;8;;;;;67777 MF:i:18 Aq:i:67 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_19:2:57:1672:1890 121 chr1 236 75 40M = 236 0 TATTCAGTTCTAAATATAGAAATTGAAACAGCTGTGTTTA :;;;9<8;;*<<<<<<:<<<<<<<<1:<<<<<<<<<<<7< MF:i:64 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_19:2:57:1672:1890 181 chr1 236 0 * = 236 0 CCCCCCCCCCCCCCCCCAGCCACTGCGGCCCCCCCAGCCA -+)%)'-'+,,<066,))090+:&486083:5&&:<<5<0 MF:i:192 EAS1_105:2:299:360:220 99 chr1 237 99 35M = 403 201 ATTCAGTTCTAAATATAGAAATTGAAACAGCTGTG <<<<<<<9<9<<<<<<<<<<<<<<<<<5<;<0<<< MF:i:18 Aq:i:43 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS221_1:2:24:1037:84 163 chr1 238 99 35M = 415 212 TTCAGTTCTAAATATAGAAATTGAAACAGCTGTGT <<<<<<<<<<<<<<<<<<<<<<;<<<<<<;:<57< MF:i:18 Aq:i:73 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_105:3:86:823:683 163 chr1 240 99 35M = 408 203 CAGTTCTAAATATAGAAATTGAAACAGCTGTGTTT <<<<<<<<;<<<<<<<<<<<<<<<<<<<<;;9<<< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_53:4:130:568:978 99 chr1 246 88 35M = 434 223 TAAATATAGAAATTGAAACAGCTGTGTTTAGTGAC 7<<;<<;<7<:;<7<<<<<<<<);4;+<7+3+%;< MF:i:18 Aq:i:24 NM:i:1 UQ:i:26 H0:i:1 H1:i:0 EAS114_45:4:73:1208:495 163 chr1 246 99 35M = 431 220 TAAATATAGAAATTGAAACAGCTGTGTTTAGTGCC ;;;;;;;;;;;;;;;;;;;;;;;;5;;;;;37377 MF:i:18 Aq:i:67 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_97:7:264:642:506 99 chr1 247 99 35M = 420 208 AAATATAGAAATTGAAACAGCTGTGTTTATTGTAT <<;<<<<<<;<<<;:;;:;;<<;<<<<;*+;*&.4 MF:i:18 Aq:i:56 NM:i:3 UQ:i:28 H0:i:1 H1:i:0 EAS114_28:5:104:350:749 163 chr1 247 99 36M = 415 204 AAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTT <<8<<<<<<<<<<<;<<<<<<<<0;<<<9;<85;;; MF:i:18 Aq:i:73 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_61:6:227:259:597 147 chr1 248 99 35M = 61 -222 AATATAGAAATTGAAACAGCTGTGTTTAGTGCCTT <8<;2;9;<;;-92<;;;<;<<<<<<<<<<<<<<< MF:i:18 Aq:i:61 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS112_32:7:113:809:364 99 chr1 250 99 35M = 413 198 TATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTG <<<<<<<<<<<<<<<<<<<<<<<<<<7<;<;<<<4 MF:i:18 Aq:i:77 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS188_7:2:218:877:489 83 chr1 250 86 35M = 80 -205 TATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTG 9<<<8<<<;<9<<<<<<<<<<;<<<<<<<<<<<<< MF:i:18 Aq:i:10 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_97:7:20:979:96 83 chr1 254 99 35M = 79 -210 GAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCA '9996;(:;-<;1<<<<=<<<<=<<<<<<<<<<<< MF:i:18 Aq:i:37 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS188_7:2:259:219:114 99 chr1 254 99 35M = 411 192 GAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCA <<<<<<<<<<<<<<<;<<<<<<7<7<<<<<0<<9< MF:i:18 Aq:i:69 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_39:6:13:1034:1144 99 chr1 256 99 35M = 429 208 AATTGAAACAGCTGTGTTTAGTGCCTTTGTTCACA <<<<<<<<<<<<<<<<<<<<<<<<3<<<;<<;<++ MF:i:18 Aq:i:69 NM:i:2 UQ:i:48 H0:i:1 H1:i:0 EAS221_1:2:29:1486:672 147 chr1 256 99 35M = 79 -212 AATTGAAACAGCTGTGTTTAGTGCCTTTGTTCACA <<:<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<++ MF:i:18 Aq:i:29 NM:i:2 UQ:i:54 H0:i:0 H1:i:0 EAS139_11:7:46:695:738 163 chr1 259 74 35M = 428 204 TGAAACAGCTGAGTTTAGCGCCTGTGTTCACATAG <;<<<<;<<),&4<3<<7&7<0;)).3;79;7<;0 MF:i:130 Aq:i:74 NM:i:3 UQ:i:18 H0:i:0 H1:i:0 EAS139_11:8:26:1221:222 163 chr1 261 99 35M = 446 220 AAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCT <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:78 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_64:3:190:727:308 147 chr1 263 99 35M = 103 -195 ACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTG ;;<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:73 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_26:3:284:261:124 83 chr1 263 99 35M = 79 -219 ACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTG ===27===.====&===========;;======== MF:i:18 Aq:i:39 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS112_34:7:141:80:875 147 chr1 265 99 35M = 110 -190 AGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCA 6/<;84<;<;<<<<<<5<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:69 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_19:3:24:1135:563 163 chr1 266 99 40M = 446 220 GCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAACC <<<<:<<<<:1:<<<<<<.<<<<<<<<;<;;;43+:30:: MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS221_1:2:90:986:1224 83 chr1 267 99 35M = 67 -235 CTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAAC <7*37;;;;;;;9<<;<7<<<<<<<<<<<;;<<<< MF:i:18 Aq:i:41 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_28:7:287:492:169 99 chr1 269 99 36M = 449 216 GTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAAC <<<7<<<<<<<<<<<<<<<<<<<<<<<8;;<;6<<; MF:i:18 Aq:i:69 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS218_4:1:48:9:409 99 chr1 271 75 18M5I12M = 464 228 GTTTAGTGCCTTTGTTCACATAGACCCCCTTGCAA <<<<<<<<<<<<<:<<<<<<<<<<<<<<<<<<<<< MF:i:130 Aq:i:75 NM:i:0 UQ:i:0 H0:i:0 H1:i:0 EAS139_19:1:87:1222:878 163 chr1 272 10 40M = 435 203 TATAGGGCCTTTGTTCAAACCCCTTGCAACAACCTTGAGA &+6<6&<:<<9<1112<<;)9227>>>>>>>>>>>>>;<>>>>><<>>>;<+<>=>>+==>>==<==<=8=><:;8/;7<<<<<<<<;<:<<<< MF:i:18 Aq:i:77 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_591:2:240:603:890 83 chr1 740 99 36M = 590 -186 GCTCCCAAGAGGGAAAGCTTTCAACGCTTCTAGCCA ;+&+//&<<<<<<<<<<9<<<8<<<<9<<<<<<<<< MF:i:18 Aq:i:66 NM:i:1 UQ:i:5 H0:i:1 H1:i:0 B7_591:7:129:956:115 163 chr1 740 99 36M = 927 223 GCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCA <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;877- MF:i:18 Aq:i:75 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_53:4:168:528:288 83 chr1 740 99 35M = 570 -205 GCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCC 8<%<31;<<;<;<<<<<<<;<<<<<<<<<<;<<<< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_65:8:275:851:240 147 chr1 743 99 35M = 561 -217 CCCCAGAGGGAAAGCTTTCAACGTTTCTAGCCATT 66614/&3616630666&66666&66666868666 MF:i:18 Aq:i:31 NM:i:1 UQ:i:5 H0:i:0 H1:i:1 EAS188_7:6:205:873:464 147 chr1 743 99 35M = 552 -226 CCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATT <-((+:+;289<--;<;-;<:;;<<<;;<<<<<<< MF:i:18 Aq:i:63 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_65:6:37:610:260 163 chr1 745 99 35M = 913 203 CCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTC <<<;<;<<7<<<<<<<<<<<<<<;6<963;;;3;1 MF:i:18 Aq:i:68 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS192_3:7:93:945:176 147 chr1 745 99 35M = 582 -198 CCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTC 6;;;8<<3<<8.<;6)<<<<<9<<<<<<<<<<<<< MF:i:18 Aq:i:70 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_593:6:61:628:681 83 chr1 746 99 36M = 586 -196 CAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCTT 95<<<<<<<<;<<<<;<<<:<<;;<<<<<<<<<<<< MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_65:7:288:552:440 83 chr1 747 87 35M = 560 -222 AGAGGGAACGCTTTCAACTCTTCTAGCCATTTCTT 9<<%'%<<.2<<<<<<<<5:<<<<<<<<<<<<<<< MF:i:18 Aq:i:26 NM:i:2 UQ:i:33 H0:i:0 H1:i:0 EAS56_53:2:170:265:818 163 chr1 748 10 35M = 920 207 GAGGGGAAGCTTTCAACGCTTCTAGCACTTTCTTT <<<<<(5/959<8.<9<8<<<2<&59&&:22:8+( MF:i:18 Aq:i:10 NM:i:3 UQ:i:17 H0:i:0 H1:i:0 B7_595:2:251:121:479 83 chr1 750 99 35M = 572 -213 GGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTG <<<<<6'..663;&<<;<<9<<<9<<<<<<<<<<< MF:i:18 Aq:i:65 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS221_1:8:67:1797:1931 147 chr1 750 99 35M = 562 -223 GGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTG <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:77 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_103:2:226:302:758 83 chr1 751 99 35M = 556 -230 GGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGG ;<<<<9;<<<<<<<<<<7<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:33 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_32:2:163:618:570 83 chr1 751 99 35M = 571 -215 GGAAAGCTGTCAACGCTTCTAGCCATTTCTTTTGG <9774<88&:8<:8<8:8<8<<<<<;88<88<<<< MF:i:18 Aq:i:41 NM:i:1 UQ:i:5 H0:i:0 H1:i:1 EAS1_97:3:73:292:429 99 chr1 752 99 35M = 920 203 GAAAGCTTTCAACGCTTCTAGCCATTTCTTTTTGC <<<<<<<<<<7<<;<<<<<<<2<<<5<<<<<:%)< MF:i:18 Aq:i:69 NM:i:1 UQ:i:4 H0:i:1 H1:i:0 EAS1_108:3:82:356:253 99 chr1 752 99 35M = 927 210 GAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGGC ===================<========;===39= MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_30:6:62:386:959 147 chr1 752 99 35M = 594 -193 AAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGGC %;71131((<<6<92(+<1<<;<-3<8<<;<;;<< MF:i:18 Aq:i:57 NM:i:1 UQ:i:4 H0:i:1 H1:i:0 EAS51_62:3:263:74:407 83 chr1 754 99 35M = 574 -215 AAGCTTTCAACGCTTCTAGCCATTTCTTTTGGCAT ;;88<::+;<)<5<<:<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:68 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_597:3:67:620:344 99 chr1 755 99 35M = 905 185 AGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATT <<<<2<:2<<<<<<7<<<<:<<*<<<<<<***3<< MF:i:18 Aq:i:33 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_610:6:148:776:486 83 chr1 755 99 35M = 578 -212 AGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATT ;:<<<;<<;<<<<<;<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_61:3:150:933:810 83 chr1 755 99 35M = 593 -197 AGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATT :89===:=:=;;==;==================== MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_64:4:102:467:897 99 chr1 756 97 35M = 940 219 GCTTTCAACGCTTCTAGCCATTTCTTTTGTCTTTT <<<<9<<<<9<2<<<&,/=====>=>=>>>=>>==>=>>>>>> MF:i:18 Aq:i:77 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_595:3:297:637:86 83 chr1 869 99 35M = 704 -200 TCTCAGCTAGGGGAACAGGGAGGTGCACTAATGCG <:75<;<;;<<<<<<;;<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:68 NM:i:1 UQ:i:26 H0:i:1 H1:i:0 EAS54_65:3:290:558:349 147 chr1 869 99 35M = 719 -185 TCTCAGCTAGGGGAACAGGGAGGTGCACTAATGCG 2;2;;'5&;<<5<<;5/<<<<<7<<;+;<<+1<8< MF:i:18 Aq:i:59 NM:i:1 UQ:i:6 H0:i:1 H1:i:0 EAS1_95:3:308:956:873 99 chr1 870 99 35M = 1068 233 CTCATCTAGGGGAACAGGGAGGTGCACTAATGCGC <<<<<<<<<<<<<;<;<;1<<<<<.<9<;<<<<+; MF:i:18 Aq:i:31 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_78:7:147:64:416 147 chr1 870 99 35M = 701 -204 CTCATCTAGGGGAACAGGGAGGTGCACTAATGCGC /;49;:6<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:47 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_593:4:30:812:345 163 chr1 871 99 36M = 1036 201 TCATCTAGGGGAACAGGGAGGTGCACTAATGCGCTC <<<<<<<7<;<<7<;77;3<&0-;<5<;6<1'13<: MF:i:18 Aq:i:64 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_73:7:134:243:630 163 chr1 871 99 35M = 1052 216 TCATCTAGGGGAACAGGGAGGCGCACTAATGAGCT <<<:<<<<::1:818;;&::<>.; MF:i:18 Aq:i:35 NM:i:1 UQ:i:5 H0:i:0 H1:i:1 EAS54_81:2:31:98:804 147 chr1 982 99 35M = 805 -212 CTTTACTGTCATAACTATGAAGAGACTATTGCCAG ====;========7===================== MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_103:2:235:805:373 163 chr1 983 99 35M = 1146 198 TTTACTGTCATAACTATGAAGAGACTATTTCCAGA <<<<<<<<<<<<<<<<<<<<;<;<<<<<<;;<99; MF:i:18 Aq:i:74 NM:i:1 UQ:i:26 H0:i:1 H1:i:0 EAS114_28:5:11:868:62 99 chr1 983 99 36M = 1154 207 TTTACTGTCATAACTATGAAGAGACTATTGCCAGAT <<<<<<<<<<<<<<<<<<<<:<<<;<<<<(7:7039 MF:i:18 Aq:i:69 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_81:2:280:512:316 163 chr1 984 99 35M = 1159 210 TTACTGTCATAACTATGAAGAGACTATTGCCAGCT ==<========6==4==6;;==:===;=2/:+8%6 MF:i:18 Aq:i:68 NM:i:1 UQ:i:4 H0:i:1 H1:i:0 EAS1_93:5:292:122:666 99 chr1 985 99 35M = 1159 209 TACTGTCATAACTATGAAGAGACTATTGTCAGATG <<<<<<6<<<<<<<<8;<<<<<<<<<<3&9+;;(; MF:i:18 Aq:i:68 NM:i:1 UQ:i:5 H0:i:1 H1:i:0 EAS56_53:1:23:403:981 99 chr1 985 99 35M = 1151 201 TACTGTCATAACTATGAAGAGACTATTGCCAGATG <8<<<;<<<<<<;<<<<<<8;<<<9<9,3;,6(91 MF:i:18 Aq:i:65 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_45:7:33:1566:588 99 chr1 985 76 35M = 1166 216 TACTGTCATAACTATGAAGAGCCTATTGCCAGATG <;.;;;;6;;;;6;;29;;;<+9;;;.3;;73797 MF:i:18 Aq:i:37 NM:i:1 UQ:i:10 H0:i:0 H1:i:1 EAS139_11:7:92:367:1495 83 chr1 987 99 35M = 820 -202 CTGTCATAACTATGAAGAGACTATTGCCAGATGAA <8<88<<<<7<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:78 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS220_1:8:38:1576:1923 83 chr1 987 99 35M = 822 -200 CTGTCATAACTATGAAGAGACTATTGCCAGATGAA 8;<98<<<<<<<;<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:77 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_595:7:190:481:295 163 chr1 990 99 35M = 1161 206 TCATAACTATGAAGAGACTATTGCCAGATGAACCA <<<<<<<<<<<<<<<<<<<<<<9<<<<<9<7<2:: MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS112_32:7:168:117:441 99 chr1 990 99 35M = 1151 196 TCATAACTATGAAGAGACTATTGCCAGATGAACCA <<3<<<<<<<<<<<<<<<<<<<+<<17;<;:<995 MF:i:18 Aq:i:71 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_73:3:239:796:221 163 chr1 992 99 35M = 1160 203 ATAACTATGAAGAGACTATTGCCAGCTGACCCCCC <<<7<<7<<7<<7<;<<<<<,;;,+'<+/+99%:' MF:i:18 Aq:i:37 NM:i:4 UQ:i:26 H0:i:0 H1:i:1 EAS220_1:4:69:88:1154 147 chr1 992 99 35M = 805 -222 ATAACTATGAAGAGACTATTGCCAGATGAACCACA <<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:47 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS221_3:8:34:956:1309 99 chr1 994 99 35M = 1168 209 AACTATGAAGAGACTATTGCCAGATGAACCACACA <<<<<<7<<<<<<<<<<<6<<<<<<<<<<<:<8<8 MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_108:5:229:717:121 99 chr1 995 99 35M = 1150 190 ACTATGAAGAGACTATTGCCAGATGAACCACACAC =================<)=<4<0=.<<<71;41& MF:i:18 Aq:i:43 NM:i:1 UQ:i:5 H0:i:1 H1:i:0 EAS219_1:1:67:191:668 99 chr1 995 99 35M = 1134 174 ACTATGAAGAGACTATTGCCAGATGAACCACACCT <<<<<<<<<<<<<<<<<6<<;<;<;<<<<<<6;%2 MF:i:18 Aq:i:74 NM:i:1 UQ:i:4 H0:i:1 H1:i:0 EAS51_64:3:309:303:278 163 chr1 996 99 35M = 1178 217 CTATGAAGAGACTATTGCCAGATGAACCACACATT <<<<<<<<<<<<<<<<+<<+<<7<<<<<5<<<;;; MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS221_1:8:60:1020:1259 99 chr1 996 99 35M = 1157 196 CTATGAAGAGACTATTGCCAGATGAACCACACATT <;<<<<;<<<<<<<<<;<<<<<<<8<<<<<:<:<< MF:i:18 Aq:i:77 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS218_4:7:89:1487:520 83 chr1 997 99 35M = 805 -227 TATGAAGAGACTATTGCCAGATGAACCACACATTA 4;;/<<<<<:<;<;<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:70 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_610:4:15:805:420 163 chr1 998 35 35M = 1164 201 ATGAAGAGACTATTCACATGTGAACCACACATTTA ;73;;;;67.;1<<+*.;*&<4947<&474&*9*( MF:i:130 Aq:i:35 NM:i:4 UQ:i:33 H0:i:0 H1:i:0 EAS56_57:3:119:761:239 147 chr1 999 99 35M = 813 -221 TGAAGAGACTATTGCCAGATGAACCACACATTAAT ;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS112_34:7:142:457:584 99 chr1 999 99 35M = 1160 196 TGAAGAGACTATTTCCAGATGAACCACACATTAAT <<<<<<<<<<<<<<< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_63:7:190:95:706 147 chr1 1078 99 35M = 920 -193 TTGTGTCCATGTACACACGCTGTCCTATGTACTTA 9;97437;<;;<<;<;<<<<<<;<<<<<<<<<<<< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_589:1:101:825:28 83 chr1 1079 99 35M = 879 -235 TGTGTCCATGTACACACGCTGTCCTATGTACTTAT 0;0'0;<<<<<<8<;<<<<;;3<<;;<<<8<<<<< MF:i:18 Aq:i:39 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_66:4:188:460:1000 99 chr1 1080 99 35M = 1251 206 GTGTCCATGTACACACGCTGTCCTATGTACTTATC <<<<<<<<<<<<<<<<7<<;:4;44<;;:8;;9;; MF:i:18 Aq:i:70 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_95:3:268:523:511 99 chr1 1081 99 35M = 1241 195 TGTCCATGTACACACGCTGTCCTATGTACTTATCA <<<<<<<<<<<<<<<<<<<<;<<<<6<:9<<3<44 MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_28:6:54:263:585 99 chr1 1081 99 36M = 1254 209 TGTCCATGTACACACGCTGTCCTATGTACTTATCAT <<<<<<<<<<<<<<<<<<<:;<<;<:;::<<;;:;4 MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_66:7:174:987:334 83 chr1 1082 99 35M = 908 -209 GTCCATGTACACACGCTGTCCTATGTACTTATCAT ,;<;;<<<&<<<1<<<<<<<<<<<<<;<<<<<<<< MF:i:18 Aq:i:41 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_71:6:224:932:942 99 chr1 1082 99 34M = 1250 203 GTCCATGTACACACGCTGTCCTATGTACTTATCA <<<<<<<<<<<<<<<<<<<<<<;<<<<7<<(;3, MF:i:18 Aq:i:69 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_45:1:12:1296:358 99 chr1 1082 96 35M = 1252 205 GTCCATGTACACACGCTGTCCTATGTACTTATCAT ;;;6;7;7;;;;;7;9;;-*1;9;699/99/7477 MF:i:18 Aq:i:37 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_32:2:306:119:56 147 chr1 1083 99 35M = 919 -199 TCCATGTACACACGCTGTCCTATGTACTTATCATG ;;;;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_95:4:66:179:118 163 chr1 1084 99 35M = 1262 213 CCATGTACACACGCTGTCCTATGTACTTATCATGA <<<<<<<<<<<<<<<<<<<<<<<<<<:<<;<<6<< MF:i:18 Aq:i:75 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_105:2:110:584:649 99 chr1 1084 99 35M = 1266 217 CCATGTACACACGCTGTCCTATGTACTTATCATGA <<<<<<<<<<<<<<<<<<<<<<<<;<<<<<::<38 MF:i:18 Aq:i:43 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS218_1:4:28:315:310 163 chr1 1085 99 35M = 1242 192 CATGTACACACGCTGTCCTATGTACTTATCATGAC <<<<<<<<<<<<<<<<<<<<<:<+.<<.<+7<*17 MF:i:18 Aq:i:68 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_595:7:242:4:593 147 chr1 1086 99 35M = 905 -216 ATATACACACGCTGTCCTATGTACTTATCATGACT 1.%55877+8+88808887+7;7;18:8;;;.&;8 MF:i:18 Aq:i:53 NM:i:1 UQ:i:4 H0:i:1 H1:i:0 EAS1_93:1:131:946:353 163 chr1 1087 99 35M = 1249 197 TGTACACACGCTGTCCTATGTACTTATCATGACTC <<<<<<<<<<<<<;<<<<;;<<<<<<<;<:52;<2 MF:i:18 Aq:i:73 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS221_1:4:4:1732:88 99 chr1 1087 99 35M = 1265 213 TGTACACACGCTGTCCTATGTACTTATCATGACTC <<<<<<<<<<<<<<<<<2<8;8<;<8;<2;2:<:< MF:i:18 Aq:i:45 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_595:4:58:703:72 83 chr1 1088 99 35M = 905 -218 GTACACACGCTGTCCTATGTACTTATCATGACTCT 5&<<7;+95;7'6<<<<<.<<<<<;<<9<7<<<<< MF:i:18 Aq:i:65 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_59:5:113:694:725 163 chr1 1088 99 35M = 1266 213 GTACACACGCTGTCCTATGTACTTATCATGACTCT <<<<<<<<<<<<9<<<<<:<<<<<<<<<<:;;<;; MF:i:18 Aq:i:47 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_65:5:278:848:765 147 chr1 1088 99 35M = 920 -203 GTACACACGCTGTCCTATGTACTTATCATGACTCT 7;;<;5<55<<;;<;<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_57:6:234:787:12 163 chr1 1092 97 35M = 1257 200 ACACGCTGGCCTATGTACTTATAATGACTCTATCC <;<<<9<<&+9;3;<993;<9<+94;9&41;08%9 MF:i:18 Aq:i:24 NM:i:2 UQ:i:15 H0:i:0 H1:i:0 EAS218_1:4:15:856:340 147 chr1 1093 99 35M = 936 -192 CACGCTGTCCTATGTACTTATCATGACTCTATCCC <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:47 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_62:2:258:266:101 163 chr1 1094 99 35M = 1285 226 ACGCTGTCCTATGTACTTATCATGACTCTATCCCA <<<<<<<<<<<<<<<<<<5<;,<-2<<<<;68<<6 MF:i:18 Aq:i:68 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_59:2:177:552:234 147 chr1 1094 99 35M = 903 -226 ACGCTGTCCTATGTACTTATCATGACTCTATCCCA ::;:=;=99=====;;====;==========<=== MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_30:1:134:379:893 147 chr1 1095 99 35M = 927 -203 CGCTGTCCTATGTACTTATCATGACTCTATCCCAA 7137::;<<<<<<<;<<<<<<<<<<;<<<<<<<<< MF:i:18 Aq:i:71 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_105:8:256:404:584 147 chr1 1096 99 35M = 928 -203 ACTGTCCTATGTACTTATCATGACTCTATCCCAAA &&326+23<3<<<+:<<<<<< MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_595:3:57:735:151 99 chr1 1121 94 35M = 1314 228 CTATCCCAAATTCCCAATTACGTCCTATCTTCTTC <<<<<<<<8<<8<:<<*<:<<<4<<<;,<<<<:<: MF:i:18 Aq:i:26 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_81:8:142:858:903 147 chr1 1121 99 35M = 943 -213 CTATCCCAAATTCCCAATTACGTCCTATCTTCTTC <<<<<;<<<<9<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_57:7:247:522:670 83 chr1 1121 99 35M = 960 -196 CTATCCCAAATTCCCAATTACGTCCTATCTTCTTC ;;;9;:<<<<<;<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:75 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_19:3:75:732:442 99 chr1 1121 99 40M = 1293 212 CTATCCCAAATTCCCAATTACGTCCTATCTTCTTCTTAGG <<<<<;<<<<<9<<<;<<;<<<5<<;8<<<<<<<<;:9%% MF:i:18 Aq:i:60 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_99:7:183:645:699 99 chr1 1122 86 35M = 1281 194 TATCCCAAATTCCCAATTACGTCCTATCTTCTTCT <<9<9<<<<<<<<<;<<;<<*175;173<;;;<-/ MF:i:18 Aq:i:21 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS192_3:6:175:437:950 163 chr1 1126 99 35M = 1298 207 CCAAATTCCCAATTACGTCCTATCTTCTTCTTAGG <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:59 MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_63:3:93:1002:845 83 chr1 1129 99 35M = 954 -210 AATTCCCAATTACGTCCTATCTTCTTCTTAGGGAA <<::;;;<<<<<<<<<<<<<<<<;<<<<<<<<<<< MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_62:6:50:542:881 163 chr1 1132 99 35M = 1324 227 TCCCAATTACGTCCTATCTTCTTCTTAGGTAAGAA <<<<<4<09<<9<<2<<<<<<<<<<<2/.&2<%<7 MF:i:18 Aq:i:63 NM:i:1 UQ:i:5 H0:i:1 H1:i:0 EAS1_99:3:118:851:285 83 chr1 1133 99 35M = 953 -215 CCCAATTACGTCCTATCTTCTTCTTAGGGAAGAAC 3+7<<<;<;<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS219_1:1:67:191:668 147 chr1 1134 99 35M = 995 -174 CCAATTACGTCCTATCTTCTTCTTAGGGAAGAACA <<<<<7<<7<<<<<<<;<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_595:7:166:203:416 83 chr1 1136 99 35M = 963 -208 AATTACGTCCTATCTTCTTCTTAGGGAAGAACAGC <<<<<<<<::<<<<<<<<<;<<<<<<<<<<<<<<< MF:i:18 Aq:i:75 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_45:2:15:1497:1530 99 chr1 1136 99 35M = 1314 213 AATTACGTCCTATCTTCTTCTTAGGGAAGAACAGC 0<;;;9;;86<;;;<<&<<.<<;)3;7;654-471 MF:i:18 Aq:i:57 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_65:8:206:563:262 83 chr1 1137 99 35M = 971 -201 ATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCT <<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7 MF:i:18 Aq:i:75 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_26:4:40:352:151 99 chr1 1137 99 35M = 1327 225 ATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCT <<<<<<<<<<<<<<<;<<9<<<<:<<<<;<99<3< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_593:7:67:302:762 99 chr1 1138 99 36M = 1313 211 TTACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTA <<<<<<<<<<<<<<<<<<<<;;65;<-<;<:8<<<3 MF:i:18 Aq:i:73 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_97:5:84:927:843 147 chr1 1138 99 35M = 938 -235 TTACGTCCTATCTTCTTCTTAGGGAAGAACAGCTT 588;<:<<<<<<<6<<<<;<<<:/<<3<:;<*<<< MF:i:18 Aq:i:69 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_99:5:147:479:41 163 chr1 1139 99 35M = 1322 218 TACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTA <<<<<<<<<<<<<<<<<<<<::6<<;<<<;;9;;6 MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_105:3:329:177:267 83 chr1 1139 99 35M = 962 -212 TACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTA <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:75 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_589:7:72:916:763 163 chr1 1142 99 35M = 1340 233 GTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGT ==7>==9>=7=>=>>=>> MF:i:18 Aq:i:78 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_65:4:91:267:655 147 chr1 1365 99 35M = 1204 -196 TGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGT ;,:;5:<6:<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:71 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS221_1:2:91:856:504 99 chr1 1366 99 35M = 1520 189 GTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTT <<<<<<<<<<<<<<7<<<<<<<7<<<&;<<<&&<& MF:i:18 Aq:i:68 NM:i:1 UQ:i:5 H0:i:1 H1:i:0 EAS1_108:2:170:326:433 99 chr1 1367 99 35M = 1535 203 TTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGG =====<=9===:=<:==2=======2:===9==/5 MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_93:6:132:717:233 99 chr1 1368 99 35M = 1529 196 TGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGA <<<<<<<<<<<<;<<<<<<<<<<<7<<<<&-<4<1 MF:i:18 Aq:i:47 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_19:1:14:420:712 99 chr1 1368 99 40M = 1525 197 TGTTGGTTTTCTGTTTCTTTGTTTGATTTTTTTGAAGACA <<<<<<<<<<<<;<<<<<<<;<<<-;<<<&,<&*8111:6 MF:i:18 Aq:i:66 NM:i:3 UQ:i:21 H0:i:1 H1:i:0 EAS114_39:4:43:1047:1626 163 chr1 1369 99 35M = 1523 189 GTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAA <<<<<<<<<<<<<<<<<<<:<<<:<<<<:+;-4:( MF:i:18 Aq:i:70 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_45:2:20:413:1334 147 chr1 1370 99 35M = 1215 -190 TTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAG 88878777;:;:1:;9;;;6;;;6;9;;;;;296; MF:i:18 Aq:i:60 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_62:5:154:669:853 83 chr1 1371 99 35M = 1193 -213 TGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGA <::<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:77 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_610:7:117:857:942 99 chr1 1372 99 35M = 1527 190 GGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGAC <<<<<<<<<<<<<<<<<<<<<<<<<:6<;;7;9<; MF:i:18 Aq:i:73 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_57:6:145:144:796 147 chr1 1372 99 35M = 1181 -226 GGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGAC ;<<<;<<<<<<<<<;<<<;<<<<<<<<<<<<<<<< MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_32:6:88:162:587 147 chr1 1372 99 35M = 1189 -218 GGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGAC 386;;388-<8;<;68<<;;<;<6<<<8<<<<<<< MF:i:18 Aq:i:63 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS221_1:8:73:108:1621 99 chr1 1373 99 35M = 1532 194 GTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACA <<<<<<<<71<<<<<<<<<+<<<<70:0<9<<61< MF:i:18 Aq:i:71 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS112_34:6:127:153:861 147 chr1 1374 99 35M = 1202 -207 TTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACAT :;:6;9<<1;<<95<<<9<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS188_7:2:152:765:744 163 chr1 1374 99 35M = 1534 195 TTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACAT <<<<<<<<<<<<<<<<<<:<<<<<<<<&<7293<< MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_73:3:313:827:992 147 chr1 1379 99 35M = 1197 -217 TGTTTCTTTGTTTGATTTGGTGGAAGACATAATCC '187:1'<75<.*<<:5<..<<*<<917<<7<<17 MF:i:18 Aq:i:57 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_64:3:7:268:263 121 chr1 1381 22 35M = 1381 0 TTGCGTTATTTGAGTTGGTGGAAGACATAATCCCA ',)*&2<$7+<<<'<-<7<<<<<<<7<<7><>;>+>>/;>>=>=>=:>><>=<<==;)<=8; MF:i:18 Aq:i:73 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS218_4:7:85:923:726 147 chr2 199 99 35M = 43 -191 GTAAAGTAACTGAACCTATGAGTCACAGGTATTCC <:<<<%3<<1<<86<<-<<<<<<<<<<<<6<<1<< MF:i:18 Aq:i:44 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_103:5:285:241:560 83 chr2 200 99 35M = 37 -198 TAAAGTAACTGAACCTATGAGTCACAGGTATTCCT :<<<<;<<,<<<<5<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_30:6:41:461:436 163 chr2 200 74 35M = 389 224 TAAAGTAACTGAACCTATGAGTCACAGGTATTCCT <<<<<<<<<<<<<<<<<<<:<<<<<<<<;<;;;:; MF:i:18 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_61:6:25:949:33 99 chr2 201 99 35M = 383 217 AAAGTAACTGAACCTATGAGTCACAGGTATTCCTG =;===/8========*==&;6=&=&:=6&:=::67 MF:i:18 Aq:i:63 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS221_3:2:60:590:1760 99 chr2 201 99 35M = 376 210 AAAGTAACTGAACCTATGAGTCACAGGTATTCCTG <:<<<<<2<<<<:<::<<<::<<<<<6<<<<<<<6 MF:i:18 Aq:i:51 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_45:6:86:693:234 163 chr2 202 82 35M = 388 221 AAGTAACTGAACCTATGAGTCACAGGTATTCCTGA ;;;;;;;;;;;;;;;;9;;;;;;;;99;;&70777 MF:i:18 Aq:i:18 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_57:6:4:223:776 163 chr2 203 93 35M = 387 219 AGTAACTGAACCTATGAGTCACAGGTATTCCTGAG <<<<<<<<<<<<<<<<<<<<<<<<<9<<<:;<;2< MF:i:18 Aq:i:19 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_39:3:88:84:1558 99 chr2 203 95 35M = 394 226 AGTAACTGAACCTATGAGTCACAGGTATTCCTGTG <<;<<<<<<<<<<<<;;<<<<<<<::<<<<<<7&< MF:i:18 Aq:i:22 NM:i:1 UQ:i:5 H0:i:1 H1:i:0 B7_597:2:168:829:88 163 chr2 205 99 35M = 369 199 TAACTGAACCTATGAGTCACAGGTATTCCTGAGGA <<<<<<<<<<<<<<<<<<<<<<<6<<<<<<9;4;2 MF:i:18 Aq:i:68 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_28:1:168:389:889 147 chr2 205 99 36M = 37 -204 TAACTGAACCTATGAGTCACAGGTATTCCTGAGGAA ;<<;;56;==================8========8 MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_71:5:81:685:141 99 chr2 207 85 34M = 382 210 ACTGAACCTATGAGTCACAGGTATTCCTGAGGAA <<<<<<<<<<<<<<<<<<<<<;;<<;<<<',7,7 MF:i:18 Aq:i:17 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_19:4:26:1312:1400 99 chr2 207 99 40M = 385 218 ACTGAACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAA <<<<;<<<:<<:<;<:<<<;:;<<<<<<:<8<1;;:::88 MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_71:4:127:725:381 83 chr2 209 99 34M = 39 -204 TGAACCTATGAGTCACAGGTATTCCTGAGGAAAA +<<.<<;<;<<<3;<;<<<<<<6<8;<<<<<<<1 MF:i:18 Aq:i:54 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS188_7:2:19:736:559 99 chr2 209 99 35M = 370 196 TGAACCTATGAGTCACAGGTATTCCTGAGGAAAAA <<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<< MF:i:18 Aq:i:70 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_26:3:117:284:589 83 chr2 210 99 35M = 43 -202 GAACCTATGAGTCACAGGTATTCCTGAGGAAAAAG ==8==;==================;========== MF:i:18 Aq:i:56 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_610:5:120:596:847 163 chr2 211 83 35M = 410 234 AACCTATGAGTCACAGGTATTCCTGAGGAAAAAGA <<<<<<<<<<<<<;<<<9<<<<<<<;:<62;58;2 MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:1 B7_610:5:51:904:391 163 chr2 212 97 35M = 401 224 ACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAA <<<<<<<<<<<<<<<<<;<<<<<;:;<2<6;;;;; MF:i:18 Aq:i:24 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_11:8:96:1314:1448 163 chr2 213 93 35M = 388 210 CCTATGAGTCACAGGTATTCCTGAGGAAAAATAAA <<<<<<<<<<<<<<<<<<<<<<<<5<4<<<<-<<< MF:i:18 Aq:i:18 NM:i:1 UQ:i:12 H0:i:1 H1:i:0 EAS139_19:3:73:1158:535 163 chr2 213 99 40M = 377 204 CCTATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTG <<<<<<<<<<<<<<<<<<<<<<8<;;<<<<<9<<9::8:8 MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_591:2:223:583:968 147 chr2 215 88 36M = 47 -204 TATGAGGCACAGGTATTCCTGAGGAAAAAGAAAAAG 1<';<<&%-:<<<<<:66%<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:30 NM:i:1 UQ:i:5 H0:i:1 H1:i:0 EAS1_97:3:160:173:889 163 chr2 215 99 35M = 379 199 TATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAA <<<<<<<<<<<<<<<<<<<<;0<7<<;<<<;7<09 MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_39:1:28:350:895 83 chr2 215 95 35M = 48 -202 TATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAA :<;<<<:;<-<<<<<4;77<<<<<<<<<<<<<<<< MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_53:4:45:707:147 163 chr2 216 99 35M = 424 243 ATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAG <<<<<<<<<<<<&<<<<:<<9<<<9<<<<75;;;< MF:i:18 Aq:i:51 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS220_1:8:18:1757:95 99 chr2 216 45 35M = 374 193 ATGAGTCGCAGGTATTCCTGAGGAAAAAGAAAAAG <<<<<<<<<<<<<<<<<<<1<:<<<<<<:<<<;:< MF:i:18 Aq:i:0 NM:i:1 UQ:i:27 H0:i:0 H1:i:1 EAS51_66:6:310:747:415 163 chr2 217 99 35M = 387 205 TGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGT <<<<<<<<<<<<<<<<<<:<<<<<;<<<<<;<;<; MF:i:18 Aq:i:24 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_28:2:114:938:216 147 chr2 218 99 36M = 63 -191 GAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGA <<<<7<6<<<<<<<6<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_93:1:179:629:513 163 chr2 220 99 35M = 409 224 GTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAG <<<<<<<<<<<<<<<;<;<<<<<<<<<<<<<;<<< MF:i:18 Aq:i:49 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_45:4:88:55:1187 99 chr2 220 66 35M = 391 206 GTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAG ;;<;;;<<99<<;;<;;;;;:;49;:;;;;87898 MF:i:18 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_62:5:119:38:945 99 chr2 221 99 35M = 428 242 TCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGA <<<<<<<<<<<<<<<8<<<<<8<<<8<;<<7<:<< MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_65:6:67:800:450 147 chr2 221 99 35M = 41 -215 TCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGA 9-<9<;<<<<9;5<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:49 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_610:5:102:915:87 147 chr2 222 99 35M = 65 -192 CACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAA ;<8<;;<<<<7;<<<;<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_26:1:113:367:659 163 chr2 222 72 35M = 390 203 CACAGGTATTCCTGAGGAAAAAGAAAAAGCGAGAA =9====8==========:=:=====9=:=&====5 MF:i:18 Aq:i:0 NM:i:1 UQ:i:5 H0:i:1 H1:i:0 EAS218_1:2:26:211:481 147 chr2 222 99 35M = 43 -214 CACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAA :<:<<<<<<9:5<<<<<<<<<<<<<<:<:<<<<<< MF:i:18 Aq:i:54 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS219_FC30151:3:90:1906:1528 83 chr2 222 99 35M = 41 -216 CACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAA :<<<<<<<<<3:<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:49 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_591:2:13:100:876 163 chr2 223 73 36M = 397 210 ACAGGGATTCCTGAGGAAAAAGAAAAAGTGAGAAGT <8<<<*<2<7<<<6<<<<<<6<<8<<<<5<<<<4<9 MF:i:18 Aq:i:30 NM:i:1 UQ:i:9 H0:i:0 H1:i:1 EAS56_63:5:117:570:971 163 chr2 223 99 35M = 413 225 ACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAG <<<<<<<<<<<<<;;;<<<<6<7;9;<:;<;<;;< MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS221_3:8:50:1203:1094 83 chr2 223 99 35M = 46 -212 ACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAG <7<<<<<5:+63<<<<<<<<<<<<<<<<2<<<<<< MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_67:6:107:395:312 83 chr2 224 99 35M = 44 -215 CAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGT ;<;;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:27 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_73:3:29:833:612 83 chr2 224 99 35M = 58 -201 CAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGT <<;<<<;<::<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:27 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_610:7:158:943:467 83 chr2 225 99 35M = 57 -203 AGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTT <:<<;;<:5<<<<<<<<<<<<<<<<<<;<<<;<<< MF:i:18 Aq:i:46 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_59:2:201:768:529 163 chr2 225 99 35M = 396 206 AGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTT ==========================1=======; MF:i:18 Aq:i:54 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS188_7:6:11:994:584 99 chr2 226 97 35M = 417 226 GGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTT <<<<<<<<<<<7<<<<<<<<<<<<<6<<<<<<3<6 MF:i:18 Aq:i:24 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_57:2:206:873:186 83 chr2 227 99 35M = 66 -196 GTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTG ;<<;--7<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_63:4:38:28:122 83 chr2 227 99 35M = 46 -216 GTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTG ;9;9;-1<<<<<<<<<<<<<<<<<;<<<<<<<<<< MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_93:5:66:372:343 83 chr2 228 99 35M = 40 -223 TATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGG ;<1;89<<<<<;<9<<<<9<<<;8<9<;<<<<<;8 MF:i:18 Aq:i:43 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_97:3:277:144:848 83 chr2 228 99 35M = 64 -199 TATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGG <<<)63<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_19:6:21:1601:1666 83 chr2 228 99 40M = 56 -212 TATTACTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAA -;;3&1<<<<<<<<<<<<1<<<<<<<<<<<7<<<<<<<<=<<<<<<<<<<<<<< MF:i:32 Aq:i:19 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_57:2:23:268:529 153 chr2 329 71 35M * 0 0 TGAAAGAGGCTCAAAGAATGCCAGGAAGATACATT 7;<<<<<<57;-<<<<<<:<77<<<<<<<;<;<<< MF:i:32 Aq:i:28 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_26:2:315:219:7 153 chr2 330 69 35M * 0 0 GAAAGAGGCTCAAAGAATGCCAGGAAGATACATTG 7==::<2=8<<<=====>888<=2=>==>,>,>>8 MF:i:32 Aq:i:19 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS192_3:4:63:5:870 83 chr2 330 75 35M = 148 -217 GAAAGAGGCTCAAAGAATGCCAGGAAGATACATTG :<;<;<<<4:;<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:75 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_591:5:243:557:560 163 chr2 331 75 36M = 499 204 AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA <<<<<<<9<<<<<<<<<<<<<<<<<<;<<89<<9<; MF:i:18 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_593:2:270:430:269 163 chr2 331 99 36M = 519 224 AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;7;: MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_66:6:284:442:747 89 chr2 331 75 35M * 0 0 AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGC <;<<<<<:<;<<<<<<<<;<<<<<<<<<<<<<<<< MF:i:32 Aq:i:29 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS218_4:7:71:31:1973 89 chr2 331 76 35M * 0 0 AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGC <<<<<7<:<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:32 Aq:i:29 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_93:2:30:466:652 147 chr2 332 98 35M = 163 -204 AAGAGGCTAAAAGAATGCCAGGAAGATACATTGCA <<<<<;3;&<<<<<<<============= MF:i:18 Aq:i:22 NM:i:0 UQ:i:0 H0:i:4 H1:i:13 EAS114_39:3:88:84:1558 147 chr2 394 95 35M = 203 -226 ATCAGACTATCTAAAGTCAACATGAAGGAAAAAAA ;;<<;<<;<<5<<<<<<;<<:<<<;<<<<<<;<<< MF:i:18 Aq:i:22 NM:i:0 UQ:i:0 H0:i:2 H1:i:3 EAS56_59:2:201:768:529 83 chr2 396 99 35M = 225 -206 CAGACTATCTAAAGTCAACATGAAGGAAAAAAATT 3<:<9<<;<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:54 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_591:2:13:100:876 83 chr2 397 73 36M = 223 -210 AGAATATATAAAGTCAACATGAAGGAAAAAAATTCT ;9<$<<<$<<<<<<<<75<<<<<<<9<9<<<<<<<< MF:i:18 Aq:i:30 NM:i:2 UQ:i:6 H0:i:1 H1:i:1 EAS139_11:4:26:137:1382 99 chr2 397 99 35M = 579 217 AGACTATCTAAAGTCAACATGAAGGAAAAAAATTC <<<<<<7<<<77<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:49 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_59:1:93:490:901 83 chr2 445 99 35M = 280 -200 AGAAAAGCATACAGTCATCTATAAAGGAAATCCCA <<<<<<<;<<<;<<<;<<;<<;<<<<<<<<<<<<< MF:i:18 Aq:i:53 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS112_34:7:96:489:453 99 chr2 445 99 35M = 625 215 AGAAAAGCATACAGTCATCTATAAAGGAAATCCCA <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;;: MF:i:18 Aq:i:54 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_26:6:46:13:880 147 chr2 445 99 35M = 290 -190 AGAAAAGCATACAGTCATCTATAAAGGAAATCCCA =&====8==========0================= MF:i:18 Aq:i:43 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_28:2:167:905:852 163 chr2 445 99 36M = 647 238 AGAAAAGCATACAGTCATCTATAAAGAAAATCCCAT <<<7<<<<<<<<<<<<<<:<:<<:::&.<:<66:3< MF:i:18 Aq:i:43 NM:i:1 UQ:i:5 H0:i:0 H1:i:1 EAS219_FC30151:3:13:674:1717 163 chr2 445 99 35M = 623 213 AGAAAAGCATGCAGTCATCTATAAAGGAAATCCCA <<<<<<<<<<%<<<<<<<<<<<<<<<<<<<;:;;; MF:i:18 Aq:i:45 NM:i:1 UQ:i:4 H0:i:0 H1:i:1 EAS51_62:7:196:511:896 83 chr2 446 99 35M = 283 -198 GAAAAGCATACAGTCATCTATAAAGGAAATCCCAT 8<<<<<;<<<:<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:52 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_53:1:154:118:488 163 chr2 447 99 35M = 624 212 AAAAGCATACAGTCATCTATAAAGGAAATCCCATC <<<<<<<<<<<<<<<<<<<<<<:7<<<<7<:;;:: MF:i:18 Aq:i:54 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_57:2:44:153:969 83 chr2 447 95 35M = 245 -237 AAAAGCATACAGTCATCTATAAAGGAAATCCCATC <<5<:7<72<51<7<*79<<<<<5<<<<<<<<<2< MF:i:18 Aq:i:36 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_28:4:215:246:640 99 chr2 447 99 36M = 624 213 AAAAGCATACAGTCATCTATAAAGGAAATCCCATCA <<<<<<<<<<9<;<<<<<<<<<<9;<<<<<<3;<;3 MF:i:18 Aq:i:54 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS219_1:7:94:1655:1921 147 chr2 447 85 35M = 258 -224 AAAAGCATACAGTCATCTATAAAGGAAATCCCATC <<<<;:===<==;<==<;================; MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS221_1:6:60:1037:1146 147 chr2 447 99 35M = 250 -232 AAAAGCATACAGTCATCTATAAAGGAAATCCCATC <<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:53 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_65:1:23:536:229 99 chr2 448 99 35M = 614 201 AAAGCATACAGTCATCTATAAAGGAAATCCCATCA <<<<<<<<<<<<<<<<<:<8<:<<;<<<<<<7<<< MF:i:18 Aq:i:54 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS112_34:6:130:865:838 163 chr2 448 99 35M = 649 236 AAAGCATACAGTCATCTATAAAGGAAATCCCATCA <<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;:<;3 MF:i:18 Aq:i:54 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_59:2:239:1001:406 99 chr2 450 99 35M = 634 219 AGCATACAGTCATCTATAAAGGAAATCCCATCAGA <<<<<<7<<<<<<<<8<;<<<7<<<<36<<3<:33 MF:i:18 Aq:i:49 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_97:3:147:423:584 147 chr2 451 99 35M = 277 -209 GCATACAGTCATCTATAAAGGAAATCCCATCAGAA 27<;<3<<<+<<;<<<;;-4<<<<<;<<<<<<<<< MF:i:18 Aq:i:69 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_99:1:187:715:521 83 chr2 451 99 35M = 291 -195 GCATACAGTCATCTATAAAGGAAATCCCATCAGAA <7<:<9<<<<<<<<<;<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_67:3:172:196:746 99 chr2 451 99 35M = 620 204 GCATACAGTCATCTATAAAGGAAATCCCATCAGAA <<<<<<<<9<<<<9<<<<<<<<<;<<<<6<<<<;< MF:i:18 Aq:i:71 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_71:3:267:821:860 83 chr2 451 99 34M = 296 -189 GCATACAGTCATCTATAAAGGAAATCCCATCAGA $&<<<.<:;6<<;<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:3 EAS56_61:7:7:682:201 83 chr2 452 99 35M = 288 -199 CATACAGTCATCTATAAAGGAAATCCCATCAGAAT 0:8;5<8<1:78<<<<<<<<<<<<:8<<2<<<<:< MF:i:18 Aq:i:66 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_589:3:82:13:897 163 chr2 453 99 35M = 606 188 ATACAGTCATCTATAAAGGAAATCCCAGCAGAATA <<<<;<<<<<<;<;<;5<51;<1<<<<%<<<<,58 MF:i:18 Aq:i:41 NM:i:1 UQ:i:4 H0:i:0 H1:i:1 EAS56_53:6:180:695:621 99 chr2 453 99 35M = 637 219 ATACAGTCATCTATAAAGGAAATCCCATCAGAATA <<<<<<<<<<<<<<<<<<<<<<<<<<<<<;::<<< MF:i:18 Aq:i:68 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_57:2:158:909:321 83 chr2 453 99 35M = 271 -217 ATACAGTCATCTATAAAGGAAATCCCATCAGAATA <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_26:2:237:497:165 99 chr2 454 99 35M = 619 200 TACAGTCATCTATAAAGGAAATCCCATCAGAATAA 8===<8===========37=<===7=;7=8===== MF:i:18 Aq:i:68 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_99:2:152:355:962 83 chr2 456 99 35M = 269 -222 CAGTCATCTATAAAGGAAATCCCATCAGAATAACA &<.9.<;+;<;<<<<<<<<<<::<<:<<<<<<<<< MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:2 EAS192_3:4:255:549:422 83 chr2 456 99 35M = 295 -196 AAGTCATCTATAAAGGAAATCCCATCAGAATAACA &<;;+<;4;<<<<<<<<<<<;<;<<;<<<<<<<<< MF:i:18 Aq:i:30 NM:i:1 UQ:i:5 H0:i:1 H1:i:2 EAS220_1:4:100:20:1199 163 chr2 456 99 35M = 614 193 CAGTCATCTATAAAGGAAATCCCATCAGAATAACA 7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4<< MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_67:5:71:408:741 163 chr2 457 99 35M = 637 215 AGTCATCTATAAAGGAAATCCCATCAGAATAACAA <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_66:5:285:395:450 147 chr2 458 99 35M = 269 -224 GTCATCTATAAAGGAAATCCCATCAGAATAACAAT 8)3<8+;<)<<<<<<<<97:7<<<<<<<<<<<<<< MF:i:18 Aq:i:65 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_73:3:4:854:140 99 chr2 458 72 35M = 638 215 GTCATCTATAAAGGAAATCCCATCAGAATAACAAT <<<6<<<:<6<<<:36:<<<<3<<8:.6<38::4< MF:i:18 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_59:6:227:657:95 147 chr2 458 99 35M = 280 -213 GTCATCTATAAAGGAAATCCCATCAGAATAACAAT ;3;<);<<<<<<<<<<<<18<<<<<<<<<<<<<<< MF:i:18 Aq:i:59 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_28:7:57:324:546 83 chr2 458 99 36M = 281 -213 GTCATCTATAAAGGAAATCCCATCAGAATAACAATG ;;5<;,<<<;;<<<<<<<97<<<<<<<<<<9<<<<< MF:i:18 Aq:i:73 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_19:4:26:274:1078 83 chr2 458 99 40M = 282 -216 GTCATCTATAAAGGAAATCCCATCAGAATAACAATGGGCT 9:*:64<<;<<<<<<<<<;8;<<:<<<<<<<<<<<<<<<< MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS188_7:6:107:636:642 163 chr2 458 99 35M = 630 207 GTCATCTATAAAGGAAATCCCATCAGAATAACAAT <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:77 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_81:7:226:869:36 147 chr2 461 99 35M = 273 -223 ATATATAAAGGAAATCCCATCAGAATAACAATGGG <0/)&<=,==4>4=>>= MF:i:18 Aq:i:68 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS218_1:8:82:1540:77 163 chr2 619 99 35M = 786 202 GAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGC <<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<<:8 MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_67:3:172:196:746 147 chr2 620 99 35M = 451 -204 AAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCT <<<;><<+<<<<:<<<<2<;<<<;<<<<<<<<<<< MF:i:18 Aq:i:71 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_73:7:97:892:419 163 chr2 621 99 35M = 800 214 AATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTA <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS192_3:4:312:915:751 147 chr2 621 99 35M = 461 -195 AATAAAGTCAAGTCTTTCCTGACAAGCAAAAGCTA <:-<<<99:::);:7<4;8<<<<<<<;<2<+8<;< MF:i:18 Aq:i:41 NM:i:1 UQ:i:10 H0:i:0 H1:i:1 EAS1_93:4:325:352:67 163 chr2 622 99 35M = 794 207 ATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAA ==================<========<=<;-=== MF:i:18 Aq:i:75 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_97:4:83:731:540 99 chr2 623 99 35M = 804 216 TAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAG <<<<<<<<<;<<<<<<<<<<<<<:<7<*;&;<;;9 MF:i:18 Aq:i:69 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS188_7:5:74:329:459 163 chr2 623 99 35M = 795 207 TAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAG <<<<<<<<<<<<<<<<<<<<<<<;<<;<<;9;599 MF:i:18 Aq:i:73 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS219_FC30151:3:13:674:1717 83 chr2 623 99 35M = 445 -213 TAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAG <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:45 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_105:1:141:415:738 69 chr2 624 0 * = 624 0 TTACCTAGTTGCTCTGTAGTCTCAATTAATTGTTT <<<<<<<<<<<<<<<<<<<<<<<;<<<<<;<8<<< MF:i:192 EAS1_105:1:141:415:738 137 chr2 624 76 35M = 624 0 AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGA <<<<<<<<<<<<<<<<<<<<<<:<<;<<;<<<<6: MF:i:64 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_53:1:154:118:488 83 chr2 624 99 35M = 447 -212 AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGA <<<;58<<95:<<;<;<<<;<<<;;<<<<<<<<<< MF:i:18 Aq:i:54 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_59:5:198:929:684 83 chr2 624 99 35M = 471 -188 AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGA <<;<<<<<:<<<<<<<<<<<<<<<<<;<<<<<<<< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_28:4:215:246:640 147 chr2 624 99 36M = 447 -213 AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT ;<<,<<<96<<:<:<9<6<97<<<<<9<<<<9<<9< MF:i:18 Aq:i:54 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_103:2:234:167:381 83 chr2 625 99 35M = 443 -217 AAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT <<;<;<<<<;<<<<7<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:49 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS112_34:7:96:489:453 147 chr2 625 99 35M = 445 -215 AAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT ;<;;;<<<<5:<<:<<<<:<<<<<<<<<<<<<<<< MF:i:18 Aq:i:54 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_93:3:79:879:15 99 chr2 626 99 35M = 790 199 AGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATA <<<<<<<<<<<<<<<<<<<<<<<<<<<<2<;<<1< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_53:2:59:286:290 147 chr2 628 99 35M = 467 -196 TCAAGTCTTTCCTGACAAGCAAATGCTAAGATAAT 77<<<<7<<<97<<,7<<<;<<<;<9<<<<<<<<< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_95:5:263:511:936 99 chr2 629 99 35M = 801 207 CAAGTCTTTCCTGACAAGCAAATGCTAAGATAATT <<<<<<<<<<<<<<<<<;<<<<<;<<:<:<<<<<< MF:i:18 Aq:i:71 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_30:3:181:582:435 147 chr2 629 99 35M = 471 -193 CAAGTCTTTCCTGACAAGCAAATGCTAAGATAATT <<<<<<<<;<<<<<;<<4<<<<<<;<<<<<<<<<< MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS188_7:6:107:636:642 83 chr2 630 99 35M = 458 -207 AAGTCTTTCCTGACAAGCAAATGCTAAGATAATTC <<<<<<<;<<<<<;<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:77 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS112_34:4:12:273:89 83 chr2 631 99 35M = 477 -189 AGTCTTTCCTGACAAGCAAATGCTAAGATAATTCA <:737<288<<<7<<<<<<<<<:9<<<<<<<<<<< MF:i:18 Aq:i:71 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_59:2:239:1001:406 147 chr2 634 99 35M = 450 -219 CTTTCCTGACAAGCAAATGCTAAGATAATTCATCA 0':.71;;:9==9=;====;=;============= MF:i:18 Aq:i:49 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS188_4:7:96:899:106 147 chr2 636 99 35M = 462 -209 TTCCTGACAAGCAAATGCTAAGATAATTCATCATC ;;;;<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:75 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_65:6:67:56:806 147 chr2 637 99 35M = 464 -208 TCCTGACAAGCAAATGCTAAGATAATTCATCATCA 844:8;7<88;8<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:70 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_67:5:71:408:741 83 chr2 637 99 35M = 457 -215 TCCTGACAAGCAAATGCTAAGATAATTCATCATCA ;7;<;<0<<<<<<<<:;<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_53:6:180:695:621 147 chr2 637 99 35M = 453 -219 TACTGAAAAGCAAATGCTAAGATAATTCATCATCA ;&377<&<<;7<<<<<7<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:68 NM:i:2 UQ:i:10 H0:i:1 H1:i:0 EAS114_30:6:49:656:507 147 chr2 637 99 35M = 468 -204 TCCTGACAAGCAAATGCTAAGATAATTCATCATCA %44;;<:<<;<;<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_73:3:4:854:140 147 chr2 638 72 35M = 458 -215 CCTGACAAGCAAATGCTAAGATAATTCATCATCAC :9':<;<<<;<<<;<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_19:1:85:1521:58 99 chr2 639 99 40M = 813 214 CTGACAAGCAAATGCTAAGATAATTCATCATCACTAAACC <<<<<<<<9<<<<<<<<<<<<<7<<<<<<<<<<<<;;:7: MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_39:2:57:1064:925 137 chr2 640 76 35M * 0 0 TGACAAGCAAATGCTAAGATAATTCATCATCACTA <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<< MF:i:32 Aq:i:29 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_103:3:323:196:855 163 chr2 642 99 35M = 809 202 ACAAGCAAATGCTAAGATAATTCATCATCACTAAA <<<<<<<7<<<<<<:<<<<<<<<<<<<<<<<<;7: MF:i:18 Aq:i:69 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_67:5:117:33:262 163 chr2 642 99 35M = 814 207 ACAAGCAAATGCTAAGATAATTCATCATCACTAAA <<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<; MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_11:1:59:742:549 99 chr2 642 99 35M = 816 209 ACAAGCAAATGCTAAGATAATTCATCATCACTAAA <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<8< MF:i:18 Aq:i:48 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_28:2:55:562:403 163 chr2 643 99 36M = 825 218 CAAGCAAATGCTAAGATAATTCATCATCACTAAACC <<<<<<<<<<<<<<<<<<<<<;<<;<<<<<<<;<;: MF:i:18 Aq:i:51 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_71:7:97:743:602 163 chr2 644 99 35M = 821 211 AAGCAAATGCTAAGATAATTCATCATCACTAAACC <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<: MF:i:18 Aq:i:26 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_28:2:167:905:852 83 chr2 647 99 36M = 445 -238 CAAATGCTAAGATAATTCATCATCACTAAACCAGTC +<<<9;7;<<+<<<<<39<;9<;9<<7<<<<<<<<< MF:i:18 Aq:i:43 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS112_34:6:130:865:838 83 chr2 649 99 35M = 448 -236 AATGCTAAGATAATTCATCATCACTAAACCAGTCC ;<:84<<<4<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:54 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS219_1:1:60:1420:660 163 chr2 649 99 35M = 808 194 AATGCTAAGATAATTCATCATCACTAAACCAGTCC <<<<<<<<<<<<<<<<<<<<<<<<<<;<<<8<<<< MF:i:18 Aq:i:77 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_593:3:180:89:582 99 chr2 650 99 36M = 809 195 ATGCTAAGATAATTCATCATCACTAAACCAGTCCTA <<<<<<<<<7<<<<<<<<<7<<<:<<<:<<::77:< MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_99:1:86:871:319 147 chr2 651 71 35M = 494 -192 TGCTAAGATAATTCATCATCACTAAACCAGTCCTA 7;+1;<:<<<<<<<<;<<;<<9<<<<<<<<<<<<< MF:i:18 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_57:2:236:841:20 83 chr2 652 99 35M = 467 -220 GCTAAGATAATTCATCATCACTAAACCAGTCCTAT 7;<<<;<<<<;;<<<<<<<<<<<<<<<<<<<<;<< MF:i:18 Aq:i:75 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_62:2:133:8:379 83 chr2 653 99 35M = 470 -218 ATAAGATAATTCATCATCACTAAACCAGTCCTATA &=========='==7==0=2====28===00==== MF:i:18 Aq:i:70 NM:i:1 UQ:i:5 H0:i:1 H1:i:0 EAS1_105:8:96:720:940 83 chr2 654 99 35M = 467 -222 TAAGATAATTCATCATCACTAAACCAGTCCTATAA *<<<<;<<<9<<;,<;0<;<<<<<<<<<<<<<<<< MF:i:18 Aq:i:69 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_57:5:71:994:576 99 chr2 655 99 35M = 805 185 AAGATAATTCATCATCACTAAACCAGTCCTATAAG <<<<<<<<<<<<<<<<<<<<<<<;<<5<<<<<<<< MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_103:4:164:79:134 147 chr2 656 99 35M = 488 -203 AGATAATTCATCATCACTAAACCAGTCCTATAAGA <;<;<<<;<<;<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:47 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_19:6:78:1029:512 83 chr2 656 99 40M = 500 -196 AGATAATTCATCATCACTAAACCAGTCCTATAAGAAATGC ;;;;;<;;<<<.<<6;<<;<;8<<<<::<<<<<<<<;<<< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_93:1:214:784:690 147 chr2 657 99 35M = 472 -220 GATAATTCATCATCACTAAACCAGTCCTATAAGAA -<7<<7<:<<2<<<<;<<<<<;<<<<3<<<<<<<< MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:1 EAS220_1:4:6:1178:1105 99 chr2 657 93 35M = 830 208 GATAATTCATCATCACTAAACCAGTCCTATAAGAA <<<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:17 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_99:7:171:196:287 83 chr2 658 99 35M = 485 -208 ATAATTCATCATCACTAAACCAGTCCTATAAGAAA <;;;98;<;&<;;<<<<<<<;<<<<<<<<<<<<<< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_28:1:220:801:282 99 chr2 660 99 36M = 837 213 AATTCATCATCACTAAACCAGTCCTATAAGAAATGC <<<<<<<<<<<<<<<<<<<<<;<+<;<<<<<::<<: MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:2 EAS221_1:2:73:955:728 163 chr2 660 44 35M = 823 198 AATTCATCATCACTAAACCAGTCCTATAAGAAATG <<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<< MF:i:18 Aq:i:14 NM:i:0 UQ:i:0 H0:i:1 H1:i:2 EAS1_105:1:3:903:957 147 chr2 661 99 35M = 516 -180 ATTCATCATCACTAAACCAGTCCTATAAGAAATGC <%12<&<<<;<:<<<<<<<<<7<<<<<<<<<<<<< MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:1 EAS56_65:2:224:579:433 83 chr2 662 99 35M = 485 -212 TTCATCATCACTAAACCAGTCCTATAAGAAATGCT '<08/8<+<>===> MF:i:18 Aq:i:75 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_105:2:146:374:692 99 chr2 690 99 35M = 874 219 AAATGCTCAAAAGAATTGTAAAAGTCAAAATTAAA <<<<<<<<<<<<<<<=>>>==>>===>==> MF:i:130 Aq:i:74 NM:i:0 UQ:i:0 H0:i:0 H1:i:0 EAS1_108:6:159:493:275 99 chr2 760 72 35M = 939 214 ACAAAACTCACAGGTTTTATAAAACAATTAATTGA =====3============================= MF:i:130 Aq:i:72 NM:i:0 UQ:i:0 H0:i:0 H1:i:0 EAS139_11:1:81:1019:558 163 chr2 760 77 35M = 926 201 ACAAAACTCACAGGTTTTATAAAACAATTAATTGA <<<<<<<<<<<6<<<<<<<<<<<<<<<<<<<<<7< MF:i:130 Aq:i:77 NM:i:0 UQ:i:0 H0:i:0 H1:i:0 EAS51_62:7:162:195:761 163 chr2 767 30 18M4I13M = 922 190 TCACAGGTTTTATAAAACAATTAATTGAGACTACA <<<<<<<<<<<<<<<<<<<<<<<<<<;<:<<<<;; MF:i:130 Aq:i:30 NM:i:0 UQ:i:0 H0:i:0 H1:i:0 B7_597:3:115:646:430 147 chr2 768 45 17M4I14M = 582 -217 CACAGGTTTTATAAAACAATTAATTGAGACTACAG 5;5<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:130 Aq:i:45 NM:i:0 UQ:i:0 H0:i:0 H1:i:0 EAS114_30:6:243:209:110 163 chr2 768 48 17M4I14M = 920 187 CACAGGTTTTATAAAACAATTAATTGAGACTACAG <<<<<;<;<<<;<<<<<<<<<<<;<:;<<:;;+85 MF:i:130 Aq:i:48 NM:i:0 UQ:i:0 H0:i:0 H1:i:0 EAS1_108:2:266:994:429 147 chr2 769 76 16M4I15M = 612 -188 ACAGGTTTTATAAAACAATTAATTGAGACTACAGA <<<<<<<<<<<<<<<< MF:i:18 Aq:i:54 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_19:1:85:1521:58 147 chr2 813 99 40M = 639 -214 AAATTAACATTACAACAGGAACAAAACCTCATATATCAAT :::86<<:<<8<<<<;<<8<<<<<<<<<<<<<<<;<<<<< MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS188_7:4:164:719:947 99 chr2 813 99 35M = 1005 227 AAATTAACATTACAACAGGAACAAAACCTCATATA <<<<<<<<<<<<<<<<<<<;<<<<<<<<<;<<<<< MF:i:18 Aq:i:64 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS219_1:1:50:257:341 163 chr2 813 99 35M = 971 193 AAATTAACATTACAACAGGAACAAAACCTCATATA <<<<<<<<<<<<<<<<<<<<<<<<<<<<7<6<<<< MF:i:18 Aq:i:77 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_67:5:117:33:262 83 chr2 814 99 35M = 642 -207 AATTAACATTACAACAGGAACAAAACCTCATATAT <<;;<<;<:8<7<<;<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS218_1:8:90:706:1276 163 chr2 814 99 35M = 980 201 AATTAACATTACAACAGGAACAAAACCTCATATAT <<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<:<:< MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_108:2:116:966:193 163 chr2 815 99 35M = 967 187 ATTAACATTACAACAGGAACAAAACCTCATATATC <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<< MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_11:1:59:742:549 147 chr2 816 99 35M = 642 -209 TTAACATTACAACAGGAACAAAACCTCATATATCA -<<<3<<<<6<<6<<<<<6<<<<6<<<<<<<<<<< MF:i:18 Aq:i:48 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_11:7:74:213:877 99 chr2 816 99 35M = 996 215 TTAACATTACAACAGGAACAAAACCTCATATATCA <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:2 B7_610:3:85:219:371 163 chr2 817 99 35M = 967 185 TAACATTACAACAGGAACAAAACCTCATATATCAA <<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<<;<; MF:i:18 Aq:i:54 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_108:2:176:653:957 163 chr2 819 82 35M = 982 198 ACATTACAACAGGAACAAAACCTCATATATCAATA ????????????<==>=>=>=>>>==>>>=>>> MF:i:18 Aq:i:71 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_19:5:57:366:844 83 chr2 877 99 40M = 708 -209 AAATTCCCCCACTTAAGAGATATAGATTGGCAGAACAGAT ;;;7:8&555<,;<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:73 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_32:3:236:475:254 163 chr2 880 99 35M = 1051 206 TTCCCCCACTTAAGAGATATAGATTGGCAGAACAG <<<<<<<<<<<<<<<<<<<<<<<<<:::<:;>=>>>>==>=>>>==>=>=:=====;=:=6:::6 MF:i:18 Aq:i:74 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS218_1:2:10:686:1024 163 chr2 947 99 35M = 1103 191 ACAAGAAACTCATTAATAAAGACATGAGTTCAGGT <:<<<<:<<<<<<<<<<:<:<<<<<<<<<<<5<<< MF:i:18 Aq:i:30 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_73:5:53:61:31 163 chr2 949 99 35M = 1122 208 AAGAAACTCATTAATAAAGACATGAGTTCAGATAA <<<7;<7<<<;7<;;<7<7<7<;5<73<<<;>588>9<>7:<0<9; MF:i:18 Aq:i:30 NM:i:1 UQ:i:5 H0:i:0 H1:i:1 B7_589:2:30:644:942 99 chr2 1045 83 35M = 1229 219 TATATCAGATAAAGCACACTTTAAATCAACAACAG <<<<<<<<<<<<<<<<<<<<<<<9<<<<<<9;<9< MF:i:18 Aq:i:22 NM:i:0 UQ:i:0 H0:i:1 H1:i:3 B7_591:2:123:924:645 83 chr2 1045 84 36M = 861 -220 TATATCAGATAAAGCACACTTTAAATCAACAACAGT ;<<<<*<<<<<<<<8<<<<<><<<<<><<<<<<<<<<<<<<< MF:i:18 Aq:i:47 NM:i:1 UQ:i:27 H0:i:0 H1:i:1 EAS51_62:4:308:614:911 99 chr2 1319 90 35M = 1493 209 TGCGCTTGTACTTCTAAATCTATAACAAAATTAAA <<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<<8< MF:i:18 Aq:i:43 NM:i:1 UQ:i:27 H0:i:0 H1:i:1 EAS54_65:3:155:541:234 83 chr2 1319 99 35M = 1151 -203 TGCGCTTGTACTTCTAAATCTATAAAAAAATTAAA 78;<7<<<<<<<<<<<<<<;<<<<<<<<<<;<<<< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_57:6:175:289:351 147 chr2 1319 99 35M = 1144 -210 TGCGCTTGTACTTCTAAATCTATAAAAAAATTAAA 9;;:+<<<<<;<<:<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:73 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_593:7:283:186:707 83 chr2 1321 99 36M = 1154 -203 CGCTTGTACTTCTAAATCTATAACAAAATTAAAATT 889;<7;<7<<7<<<<<7<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:45 NM:i:1 UQ:i:27 H0:i:0 H1:i:1 EAS1_105:3:308:66:538 147 chr2 1321 99 35M = 1138 -218 CGCTTGTACTTCTAAATCTATAACAAAATTAAAAT 996999;<9;<:<<<<<:<<7<<<<<<<<<<<<<< MF:i:18 Aq:i:45 NM:i:1 UQ:i:27 H0:i:0 H1:i:1 EAS1_108:5:11:555:330 163 chr2 1321 99 35M = 1492 206 CGCTTGTACTTCTAAATCTATAAAAAAATTAAAAT <<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<4<;< MF:i:18 Aq:i:56 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS51_66:7:84:411:336 73 chr2 1322 75 35M * 0 0 GCTTGTACTTCTAAATCTATAAAAAAATTAAAATT <<<;<<<;<<<<<<<<<<<<:<<;<<<<<<;8<;< MF:i:32 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS139_11:5:52:1278:1478 163 chr2 1322 47 35M = 1513 226 GCTTGTACTTCTAAATCTATAACAAAATTAAAATT <<<<<<<<<<<<<<9<<<<<<<<<<<<<<<<9<<< MF:i:18 Aq:i:0 NM:i:1 UQ:i:27 H0:i:0 H1:i:1 EAS56_53:3:101:809:776 147 chr2 1326 99 35M = 1160 -201 GTACTTCTAAATCTATAAAAAAATTAAAATTTAAC <<<-<;7;<<<<:;<<<7<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS192_3:3:221:881:916 147 chr2 1327 96 35M = 1168 -194 TAATTCTAAATCTAGAACAAAATTAAAATTTAACA 44%-4(5<;9/,:<68:1<:8<:<<84;<<<<<;< MF:i:18 Aq:i:24 NM:i:3 UQ:i:41 H0:i:0 H1:i:0 EAS1_105:1:28:745:352 147 chr2 1329 99 35M = 1159 -205 CTTCTAAATCTATAACAAAATTAAAATTTAACAAA 4;;*;<<<;;<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:45 NM:i:1 UQ:i:27 H0:i:0 H1:i:1 EAS114_45:2:23:1754:796 99 chr2 1329 99 35M = 1488 194 CTTCTAAATCTATAAAAAAATTAAAATTTAACAAA ;<<;<;<;<;<;<<;;;;;<<<<;;<<<<<97999 MF:i:18 Aq:i:69 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_97:2:96:419:327 147 chr2 1331 99 35M = 1149 -217 TCTAAATCTATAACAAAATTAAAATTTAACAAAAG ;1<<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:47 NM:i:1 UQ:i:27 H0:i:0 H1:i:1 EAS1_97:4:274:287:423 163 chr2 1332 75 35M = 1515 218 CTAAATCTATAAAAAAATTAAAATTTAACAAAAGT <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<< MF:i:18 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS219_1:7:35:392:2042 83 chr2 1332 99 35M = 1168 -199 ATAAATCTATAAAAAAATTAAAATTTAACAAAAGT +<<<<4<>>>>;>>&>->9>9;4>->>>>,4>9>,<1> MF:i:18 Aq:i:27 NM:i:1 UQ:i:5 H0:i:0 H1:i:1 EAS139_19:2:82:154:1333 99 chr2 1349 77 40M = 1511 202 TTAAAATTTAACAAAAGTAAATAAAACACACAGCTAAAAC <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;;:;: MF:i:18 Aq:i:0 NM:i:1 UQ:i:27 H0:i:1 H1:i:0 EAS188_7:1:290:286:763 99 chr2 1349 75 35M = 1515 201 TTAAAATTTAACAAAAGTAAATAAAACACATAGCT <<<<<<<<<<<<<<<<7<<<<<<<<<<<<<<<8<< MF:i:18 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS221_1:4:3:248:1491 73 chr2 1349 99 35M * 0 0 TTAAAATTTAACAAAAGTAAATAAAACACATAGCT <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:8:< MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS114_39:3:6:1064:1805 99 chr2 1350 99 35M = 1502 187 TAAAATTTAACAAAAGTAAATAAAACACATAGCTA <<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<< MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_595:6:137:811:130 83 chr2 1351 99 35M = 1175 -211 AAAATTTAACAAAAGTAAATAAAACACATAGCTAA <<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:47 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_108:1:155:809:543 83 chr2 1352 99 35M = 1156 -231 AAATTTAACAAAAGTAAATAAAACACATAGCTAAA <<<+0<<<9<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:73 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_63:3:41:468:459 99 chr2 1352 75 35M = 1513 196 AAATTTAACAAAAGTAAATAAAACACATAGCTAAA <<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<;;7 MF:i:18 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_108:4:31:622:216 73 chr2 1354 99 35M * 0 0 ATTTAACAAAAGTAAATAAAACACATAGCTAAAAC <<<<<<<<<<<<<<<<<<<<<<<<<<<<8<<96<7 MF:i:18 Aq:i:70 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS54_71:8:105:854:975 163 chr2 1354 71 35M = 1523 202 ATTTAACAAAAGTAAATAAAACACATAGCTAAAAC <<<<<<<<<<<<<<<<<<<<<<<<<<<7:<;;;;5 MF:i:18 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 B7_610:7:26:749:174 147 chr2 1357 78 35M = 1183 -209 TAACAAAAGTAAATAAAACACATAGCTAAAACTAA (<<)<<<<6<<<<<<<<<<&:<3<<<6<<<)<:<< MF:i:18 Aq:i:11 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS56_57:6:21:553:57 147 chr2 1358 99 35M = 1197 -196 AACAAAAGTAAATAAAACACATAGCTAAAACTAAA <<+<<<<<<<<<;<<<<8<<<<<<8<<<<<;<<<< MF:i:18 Aq:i:71 NM:i:0 UQ:i:0 H0:i:1 H1:i:0 EAS1_97:2:128:629:484 83 chr2 1359 96 35M = 1185 -209 AAAAAAGTAAATAAAACACATAGCTAAAACTAAAA :(::<<<<<<<<<< MF:i:32 Aq:i:0 NM:i:0 UQ:i:0 H0:i:82 H1:i:85 B7_589:6:33:356:636 73 chr2 1520 0 35M * 0 0 TTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTT <<<<<<<8;<<<<<<<<<<<<<7<<<<<<<;;3&3 MF:i:32 Aq:i:0 NM:i:0 UQ:i:0 H0:i:14 H1:i:85 EAS114_45:6:86:859:1779 137 chr2 1520 0 35M * 0 0 TTTTTTTCATTTCTCTTTTTTTTTTTTTTTTTTTT ;;;;;;;;;;;;;;;;;;;;;;;;;;;8;;)7699 MF:i:32 Aq:i:0 NM:i:1 UQ:i:26 H0:i:0 H1:i:15 EAS54_71:8:105:854:975 83 chr2 1523 71 33M = 1354 -202 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG <<<<;<:<<;<&<;<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:0 NM:i:0 UQ:i:0 H0:i:85 H1:i:85 EAS51_62:4:187:907:145 153 chr2 1524 28 35M * 0 0 TTTCTTCTCTCTCTTTTTTTTTTTTTTTATTGCAT <<<+;;,6<<<<6<<<<<<<<<<<<<<<<<<<<<< MF:i:32 Aq:i:28 NM:i:3 UQ:i:59 H0:i:0 H1:i:0 EAS54_71:4:284:269:882 73 chr2 1524 0 34M * 0 0 TTTCTTTTCTCTTTTTTTTTTTTTTGTTTTTGCA <;<<<<<8<7<8;<<<;<7<<<<<;272;73&&) MF:i:32 Aq:i:0 NM:i:1 UQ:i:17 H0:i:0 H1:i:85 EAS56_63:4:141:9:811 137 chr2 1524 10 35M * 0 0 TTTCTTTTCTCCTTTTTTTTTTTTTTTTTCTACAT <<<;<<<<<<<;<;<:<<<;<<<<<<<<..));;. MF:i:32 Aq:i:0 NM:i:3 UQ:i:47 H0:i:2 H1:i:27 EAS114_30:6:277:397:932 73 chr2 1524 0 35M * 0 0 TTTCTTTTCACTTTTTTTTTTTTTTTTTTTTACTT <<<<<<<<<<<<<<<<<<<<<<<<<<<<:8(,0%( MF:i:32 Aq:i:0 NM:i:3 UQ:i:42 H0:i:2 H1:i:85 EAS139_11:7:50:1229:1313 83 chr2 1528 77 35M = 1376 -187 TTTTTTCTTTTTTTTTTTTTTTTTTTTGCATGCCA <<<<,<&<7<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:18 Aq:i:0 NM:i:1 UQ:i:11 H0:i:3 H1:i:7 EAS54_65:3:320:20:250 147 chr2 1532 77 35M = 1367 -200 TTTTTTTTTTTTTTTTTTTTTTTGCATGCCAGAAA +'''/<<<<7:;+<;::<<<;;<<<<<<<<<<<<< MF:i:18 Aq:i:6 NM:i:2 UQ:i:24 H0:i:1 H1:i:2 EAS114_26:7:37:79:581 83 chr2 1533 68 35M = 1349 -219 TTTTTTTTTTTTTTTTTTTTTTTCATGCCAGAAAA 3,,,===6===<===<;=====-============ MF:i:18 Aq:i:27 NM:i:2 UQ:i:23 H0:i:0 H1:i:1 pysam-0.23.0/tests/pysam_data/softclip.sam000066400000000000000000000003551475062545500205560ustar00rootroot00000000000000@HD VN:1.5 SO:coordinate @SQ SN:ref LN:45 r001 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA * r002 0 ref 9 30 5S6M * 0 0 GCCTAAGCTAA 01234567890 r003 0 ref 9 30 6M5S * 0 0 GCCTAAGCTAA 01234567890 r004 2064 ref 29 17 6H5M * 0 0 TAGGC 01234 pysam-0.23.0/tests/pysam_data/tag_bug.sam000066400000000000000000000010341475062545500203360ustar00rootroot00000000000000@SQ SN:2L LN:23011544 @SQ SN:2LHet LN:368872 @SQ SN:2R LN:21146708 @SQ SN:2RHet LN:3288761 @SQ SN:3L LN:24543557 @SQ SN:3LHet LN:2555491 @SQ SN:3R LN:27905053 @SQ SN:3RHet LN:2517507 @SQ SN:4 LN:1351857 @SQ SN:U LN:10049037 @SQ SN:Uextra LN:29004656 @SQ SN:X LN:22422827 @SQ SN:XHet LN:204112 @SQ SN:YHet LN:347038 @SQ SN:dmel_mitochondrion_genome LN:19517 HWI-EAS241:138:4:17:7389-21153#0 256 2L 8878 3 36M * 0 0 CGCTGGACTCGCAAAGTGGACTTGTTCAGCAAGGAC FEAAEDBEEFEDGDGGG@88GBEED:BBggw!һk)B]m^צ5UmX1^$_L)@ZkqN;,H%r'LG)H]dRGTP54<36Uϵeۻv?ڹ:! X}B ҭ 6Czpysam-0.23.0/tests/pysam_data/test_mapped_unmapped.sam000066400000000000000000000060471475062545500231350ustar00rootroot00000000000000@HD VN:1.0 @SQ SN:chr1 LN:100 @SQ SN:chr2 LN:100 @CO Test counting of mapped/unmapped reads read1_mapped 0 chr1 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 read2_unmapped 4 chr1 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 read3_unmapped 20 chr1 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 pair1a_mapped 67 chr1 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 pair1b_mapped 131 chr1 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 pair2a_unmapped 71 chr1 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 pair2b_mapped 139 chr1 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 pair3a_unmapped 77 chr1 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 pair3b_unmapped 141 chr1 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 noseq2b_mapped 139 chr1 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 bread1_mapped 0 chr2 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 bread2_unmapped 4 chr2 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 bread3_unmapped 20 chr2 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 bpair1a_mapped 67 chr2 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 bpair1b_mapped 131 chr2 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 bpair2a_unmapped 71 chr2 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 bpair2b_mapped 139 chr2 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 bpair3a_unmapped 77 chr2 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 bpair3b_unmapped 141 chr2 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 bnoseq2b_mapped 139 chr2 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 noseq1_unmapped 4 * 0 20 * = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 noseq2a_unmapped 71 * 0 20 * = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 pair3a_unmapped 77 * 0 20 * = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 pair3b_unmapped 141 * 0 20 * = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 pysam-0.23.0/tests/pysam_data/test_query_position.sam000066400000000000000000000010571475062545500230630ustar00rootroot00000000000000@HD VN:1.0 @SQ SN:chr1 LN:100 @SQ SN:chr2 LN:100 @SQ SN:chr3 LN:100 @SQ SN:chr4 LN:100 read1 0 chr1 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 read2 0 chr2 21 30 10M2D25M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 read1 16 chr3 21 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 read2 16 chr4 21 30 10M2D25M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 pysam-0.23.0/tests/pysam_data/test_unaligned.sam000066400000000000000000000017651475062545500217460ustar00rootroot00000000000000@HD VN:1.0 SO:queryname @RG ID:myid PL:illumina PU:P123456 LB:L123456 DT:2013-03-20T21:00:00-0700 SM:S123456 CN:MYCN B123456:6:1101:10000:137074 77 * 0 0 * * 0 0 CATGTGTATCACCCAGTACAATGCCTGACACACAGCAGTCACTTAAAGAGTGCTATTGCTATTATACAGTCATACT HHHHHHHHHHHHHHHHFHHHHHHHHHHGHHHHHHHBHHEFFHHHHHHHHHDHHHFHFHHHHHFHHEHFB@CDCCDE RG:Z:myid AM:i:0 SM:i:0 B123456:6:1101:10000:137074 141 * 0 0 * * 0 0 CAAGGAACTTTACAGTTCAGGGGAGTTTTCCAGTGGCAGAAAGTGGGAAGATGATGCTCCCAAGGAAGAAGTAGAT HHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHFHGHFHDFEF?EFEDEFFHHHFHDFHHHFHHHEFBBHD@D=C# RG:Z:myid AM:i:0 SM:i:0 B123456:6:1101:10000:171579 589 * 0 0 * * 0 0 GAAGCATAGGACATGTCAATGATGGCCAGGTGTGTGAGGAAGAAGTACATGGGGGTGTGAAGCTTAGAGTCCAGGC ############################################################################ RG:Z:myid AM:i:0 SM:i:0 B123456:6:1101:10000:171579 653 * 0 0 * * 0 0 ACCCTGCTGGGGAATGGGGTCATCTTTGGGATTATCTGCCTGGACTCTAAGCTTCACACACCCATGTACTTCTTCC 8BBBB>6><937964@?:@@B;A@8>=<>CB=CD########################## RG:Z:myid AM:i:0 SM:i:23 pysam-0.23.0/tests/refactoring.pl000066400000000000000000000034361475062545500167520ustar00rootroot00000000000000while () { # Samfile refactoring s/Samfile/AlignmentFile/g; # AlignedRead refactoring s/AlignedRead/AlignedSegment/g; # Do these patterns first as they match # the new names s/\.query/\.query_alignment_sequence/g; s/\.positions/\.getReferencePositions()/g; # Tabixfile, etc s/Tabixfile/TabixFile/g; s/Fastafile/FastaFile/g; s/Fastqfile/FastqFile/g; # basic attributes s/\.qname/\.query_name/g; s/\.tid/\.reference_id/g; s/\.pos/\.reference_start/g; s/\.mapq/\.mapping_quality/g; s/\.rnext/\.next_reference_id/g; s/\.pnext/\.next_reference_start/g; s/\.tlen/\.query_length/g; s/\.seq/\.query_sequence/g; if (/\.qual =/) { s/([[\].0-9a-zA-Z]*)\.qual = (\S*)/$1.query_qualities = pysam.fromQualityString($2)/g; } else { s/([[\].0-9a-zA-Z]*)\.qual/pysam.toQualityString($1\.query_qualities)/g; } s/\.alen/\.reference_length/g; s/\.aend/\.reference_end/g; s/\.rlen/\.query_alignment_length/g; s/([[\].0-9a-zA-Z]*)\.qqual/pysam.toQualityString($1\.query_alignment_qualities)/g; s/\.qstart/\.query_alignment_start/g; s/\.qend/\.query_alignment_end/g; s/\.qlen/\.query_alignment_length/g; s/\.mrnm/\.next_reference_id/g; s/\.rnext/\.next_reference_id/g; s/\.mpos/\.next_reference_start/g; s/\.rname/\.reference_id/g; s/\.isize/\.query_length/g; s/\.cigar/\.cigartuples/g unless (/\.cigarstring/); s/\.blocks/\.getBlocks()/g; s/\.aligned_pairs/\.getAlignedPairs()/g; s/\.inferred_length/\.getInferredQueryLength()/g; s/\.overlap()/\.getOverlap()/g; # PileupProxy s/\.n([^a-zA-Z])/\.nsegments$1/g; # if (/\.mrnm/ || /\.rnext/ || /\.mpos/ || /\.rname/) # { # warn "Deprecated tag $& at line $.\n"; # } print; } pysam-0.23.0/tests/refactoring.txt000066400000000000000000000167231475062545500171610ustar00rootroot00000000000000;; This buffer is for notes you don't want to save, and for Lisp evaluation. ;; If you want to create a file, visit that file with C-x C-f, ;; then enter the text in that file's own buffer. Samfile -> AlignmentFile AlignedRead -> AlignedSegment Tabixfile -> TabixFile Fastafile -> FastaFile Fastqfile -> FastqFile Changes to the AlignedSegment.API: Basic attributes ================ qname -> query_name tid -> reference_id pos -> reference_start mapq -> mapping_quality rnext -> next_reference_id pnext -> next_reference_start cigar = alignment (now returns CigarAlignment object) cigarstring = cigarstring tlen -> query_length seq -> query_sequence qual -> query_qualities, now returns array tags = tags (now returns Tags object) Derived simple attributes ========================= alen -> reference_length, reference is always "alignment", so removed aend -> reference_end rlen -> query_length query -> query_alignment_sequence qqual -> query_alignment_qualities, now returns array qstart -> query_alignment_start qend -> query_alignment_end qlen -> query_alignment_length, kept, because can be computed without fetching the sequence mrnm -> next_reference_id mpos -> next_reference_start rname -> reference_id isize -> query_length Complex attributes - functions =============================== blocks -> getBlocks() aligned_pairs -> getAlignedPairs() inferred_length -> inferQueryLength() positions -> getReferencePositions() overlap() -> getOverlap() Backwards incompatible changes: ================================ 1. Empty cigarstring now returns None (instead of '') 2. Empty cigar now returns None (instead of []) 3. When using the extension classes in cython modules, AlignedRead needs to be substituted with AlignedSegment. Automatic casting of the base class to the derived class seems not to work? 4. fancy_str() has been removed ===================================================== Kevin's suggestions: * smarter file opener * CRAM support * CSI index support (create and use) * better attribute and property names * remove deprecated names * add object oriented CIGAR and tag handling * fetch query that recruits mate pairs that overlap query region * other commonly re-invented functionality qname -> template_name pos -> reference_start aend -> reference_stop alen -> reference_length tid -> ref_id qname -> template_name (not a high priority, but would be clearer) qstart -> query_start (really segment_align_start) qend -> query_stop (really segment_align_stop) qlen -> query_length (really segment_align_length) qqual -> query_qual (really segment_align_qual) rlen -> drop in favor of len(align.seq) inferred_length -> inferred_query_length is_* -> replace with flag object that is a subclass of int cigarstring -> str(align.cigar) tags -> opts object with a mapping-like interface Non-backward compatible: rname, mrnm, mpos, isize -> remove cigar -> CigarSequence object (or something similar) All coordinate and length queries return None when a value is not available (currently some return None, some 0) Store qualities as an array or bytes type Marcel's suggestions: I recently sent in a pull request (which was merged) that improves the pysam doc a bit. While preparing that, I also wrote down some ways in which the API itself could be improved. I think the API is ok, but for someone like me who uses pysam not every day, some of the details are hard to remember and every time I do very basic things I end up looking them up again in the docs. I can recommend this article, written for C++, but many points still apply: http://qt-project.org/wiki/API_Design_Principles . Originally, I wanted to convert at least some of these suggestions to pull requests, but I'm not sure I have the time for that in the near future. So before I forget about this completely, I thought it's best to at least send this to the list. I'm concentrating on issues I found in Samfile and AlignedRead here. - The terminology is inconsistent - often two words are used to describe the same thing: opt vs. tag, query vs. read, reference vs. target. My suggestion is to consistently use the same terms as in the SAM spec: tag, query, reference. This applies both to documentation and function/property names. - In line with the document linked to above (see the section "The Art of Naming"): Do not abbreviate function and property names. For example, tlen -> template_length, pos -> position, mapq -> mapping_quality etc. - Be consistent with multiword function and variable names. I suggest to use the PEP8 convention. This isn't so visible to the user in Samfile and AlignedRead, it seems, but there are things like convertBinaryTagToList which could be renamed to convert_binary_tag_to_list. - Don't make functions that are not setters or getters a property. This applies to AlignedRead.positions/.inferred_length/.aligned_pairs/.blocks and currently also Samfile.references, for example. Making these a property implies to the user that access requires constant time. This is important in code like this: for i in range(n): do_something_with(read.positions[i]) This looks inconspicuous, but is possibly inefficient since .positions actually builds up the result it returns each time it's accessed. - Update the examples in the docs to use context manager syntax. Particular to Samfile: - Deprecate Samfile.nreferences: propose to use len(samfile.references) instead. Cache Samfile.references so it's not re-created every time. - Move Samfile.mapped/.unmapped/.nocoordinate into a .stats attribute (Samfile.stats.mapped/.unmapped/.noocordinate). Particular to AlignedRead: - When read is an AlignedRead, print(read) should print out a properly formatted SAM line. - Force assignment to .qual/.seq to go through a function that sets both at the same time. This avoids the problem that they must be set in a particular order, which is easy to forget and only 'enforced' through documentation. - Deprecate rlen, use len(read.seq) instead. - Handling of tags is a little awkward. Would be cool if this worked: read.tags['XK'] = 'hello' # add a new tag if it doesn't exist read.tags['AS'] += 17 # update the value of a tag del read.tags['AS'] if 'AS' in read.tags: ... - Add a property AlignedRead.qualities that behaves like a Py3-bytes object in both Py2 and Py3. That is, accessing read.qualities[0] gives you an int value that represents the quality. The fact that qualities are encoded as ASCII(q+33) is an implementation detail that can be hidden. Done - And finally: Add a Cigar class. I guess this is already what 'improved CIGAR string handling' refers to in the roadmap. AlignedRead.cigar would then return a Cigar object that can be printed, compared and concatenated to others, whose length can be measured etc. The .unclipped and .inferred length properties can also be moved here. Or perhaps: Make this an Alignment class that even knows about the two strings it is aligning. One could then also iterate over all columns of the alignment. But I guess this goes too far since that's what the AlignedRead itself should be. Regards, Marcel pysam-0.23.0/tests/samtools_test.py000066400000000000000000000332621475062545500173640ustar00rootroot00000000000000#!/usr/bin/env python '''unit testing code for pysam. Execute in the :file:`tests` directory as it requires the Makefile and data files located there. ''' import warnings import unittest import os import re import glob import sys import subprocess import shutil import pysam import pysam.samtools import pysam.bcftools from TestUtils import checkBinaryEqual, check_lines_equal, \ check_samtools_view_equal, get_temp_filename, force_bytes, WORKDIR, \ make_data_files, BAM_DATADIR def setUpModule(): make_data_files(BAM_DATADIR) def run_command(cmd): '''run a samtools command''' try: retcode = subprocess.call(cmd, shell=True, stderr=subprocess.PIPE) if retcode < 0: print("Child was terminated by signal", -retcode) except OSError as e: print("Execution failed:", e) def get_version(executable): '''return samtools/bcftools version''' with subprocess.Popen(executable, shell=True, stderr=subprocess.PIPE).stderr as pipe: lines = b"".join(pipe.readlines()).decode("ascii") try: x = re.search(r"Version:\s+(\S+)", lines).groups()[0] except AttributeError: raise ValueError("could not get version from %s" % lines) return x class SamtoolsTest(unittest.TestCase): '''test samtools command line commands and compare against pysam commands. Tests fail, if the output is not binary identical. ''' requisites = [ "ex1.fa", "ex1.fa.fai", "ex1.sam.gz", "ex1.bam", "ex1.bam.bai", "ex1.sam", "ex1.sam", "ex2.bam", "ex2.sam", "ex1.bed"] # a list of statements to test # should contain at least one %(out)s component indicating # an output file. statements = [ "view ex1.bam > %(out)s_ex1.view", "view -c ex1.bam > %(out)s_ex1.count", # ("view -bT ex1.fa -o %(out)s_ex1.view2 ex1.sam", "sort ex1.bam -o %(out)s_ex1.sort.bam", "mpileup ex1.bam > %(out)s_ex1.pileup", "depth ex1.bam > %(out)s_ex1.depth", # TODO: issues with file naming # "faidx ex1.fa; %(out)s_ex1.fa.fai", "index ex1.bam %(out)s_ex1.bam.fai", "index -@2 ex1.bam %(out)s_ex1.bam.fai", "idxstats ex1.bam > %(out)s_ex1.idxstats", # TODO: fixmate behaviour changed in 1.21 #"fixmate ex1.bam %(out)s_ex1.fixmate.bam", "flagstat ex1.bam > %(out)s_ex1.flagstat", "calmd ex1.bam ex1.fa > %(out)s_ex1.calmd.bam", # use -s option, otherwise the following error in samtools 1.2: # Samtools-htslib-API: bam_get_library() not yet implemented # causes downstream problems # TODO: The following cause subsequent commands to fail # unknown option # "rmdup -s ex1.bam %(out)s_ex1.rmdup.bam", # "merge -f %(out)s_ex1.merge.bam ex1.bam ex1.bam", "reheader ex2.sam ex1.bam > %(out)s_ex1.reheader.bam", "cat -o %(out)s_ex1.cat.bam ex1.bam ex1.bam", "targetcut ex1.bam > %(out)s_ex1.targetcut", "phase ex1.bam > %(out)s_ex1.phase", "view -bt ex1.fa.fai ex1.sam.gz > %(out)s_ex1.bam", "bam2fq ex1.bam > %(out)s_ex1.bam2fq", # TODO: not the same # "pad2unpad -T ex1.fa ex2.bam > %(out)s_ex2.unpad", # TODO: command line option problem # "bamshuf ex1.bam -O --output-fmt SAM > %(out)s_ex1.bamshuf.sam", # "collate ex1.bam %(out)s_ex1.collate", "bedcov ex1.bed ex1.bam > %(out)s_ex1.bedcov", "stats ex1.bam > %(out)s_ex1.stats", "dict ex1.bam > %(out)s_ex1.dict", # TODO: not the same # ("addreplacerg -r 'RG\tID:ga\tSM:hs' ex1.bam > %(out)s_ex1.addreplacerg", ] map_command = { } executable = "samtools" module = pysam.samtools def check_version(self): samtools_version = get_version(self.executable) def _r(s): # patch - remove any of the alpha/beta suffixes, i.e., 0.1.12a -> # 0.1.12 if s.count('-') > 0: s = s[0:s.find('-')] return re.sub("[^0-9.]", "", s) if _r(samtools_version) != _r(pysam.__samtools_version__): warnings.warn( "versions of pysam.%s and %s differ: %s != %s" % (self.executable, self.executable, pysam.__samtools_version__, samtools_version)) def setUp(self): '''setup tests. For setup, all commands will be run before the first test is executed. Individual tests will then just compare the output files. ''' self.check_version() self.workdir = os.path.join(WORKDIR, "samtools_test") if not os.path.exists(self.workdir): os.makedirs(self.workdir) for f in self.requisites: shutil.copy(os.path.join(BAM_DATADIR, f), os.path.join(self.workdir, f)) self.savedir = os.getcwd() os.chdir(self.workdir) return def get_command(self, statement, map_to_internal=True): """return samtools command from statement""" parts = statement.split(" ") command = parts[0] if map_to_internal: return self.map_command.get(command, command) else: return command def check_statement(self, statement): parts = statement.split(" ") r_samtools = {"out": self.executable} r_pysam = {"out": "pysam"} command = self.get_command(statement) targets = [x for x in parts if "%(out)s" in x] samtools_targets = [x % r_samtools for x in targets] pysam_targets = [x % r_pysam for x in targets] pysam_method = getattr(self.module, command) # run samtools full_statement = re.sub(r"%\(out\)s", self.executable, statement) run_command(" ".join((self.executable, full_statement))) # sys.stdout.write("%s %s ok" % (command, self.executable)) # run pysam if ">" in statement: assert parts[-2] == ">" parts = parts[:-2] # avoid interpolation to preserve string quoting, tab chars, etc. pysam_parts = [re.sub(r"%\(out\)s", "pysam", x) for x in parts[1:]] output = pysam_method(*pysam_parts, raw=True, catch_stdout=True) # sys.stdout.write(" pysam ok\n") if ">" in statement: with open(pysam_targets[-1], "wb") as outfile: if output is not None: outfile.write(force_bytes(output)) for samtools_target, pysam_target in zip(samtools_targets, pysam_targets): if os.path.isdir(samtools_target): samtools_files = glob.glob(os.path.join( samtools_target, "*")) pysam_files = glob.glob(os.path.join(pysam_target, "*")) self.assertEqual(len(samtools_files), len(pysam_files)) # need to be able to exclude files like README, etc. continue else: samtools_files = [samtools_target] pysam_files = [pysam_target] for s, p in zip(samtools_files, pysam_files): binary_equal = checkBinaryEqual(s, p) error_msg = "%s failed: files %s and %s are not the same" % ( command, s, p) if binary_equal: continue elif s.endswith(".bam"): self.assertTrue( check_samtools_view_equal( s, p, without_header=True), error_msg) else: check_lines_equal( self, s, p, filter_f=lambda x: x.startswith("#"), msg=error_msg) def testStatements(self): for statement in self.statements: command = self.get_command(statement, map_to_internal=False) # bam2fq differs between version 1.5 and 1.6 - re-enable if # bioconda samtools will be available. # flagstat differs between version <=1.12 and >=1.13 if command in ("bedcov", "stats", "dict", "bam2fq", "flagstat"): continue self.check_statement(statement) @unittest.skipUnless(sys.stdin.isatty(), "skipping usage tests, stdin is not a tty") def testUsage(self): if self.executable == "bcftools": # bcftools usage messages end with exit(1) return for statement in self.statements: command = self.get_command(statement, map_to_internal=False) # ignore commands that exit or cause other failures # TODO: check - if reheader or phase is run in testStatements, sort fails # here if command in ("view", "sort", "bam2fq", "flagstat", "reheader", "stats", "idxstats"): continue mapped_command = self.get_command(statement, map_to_internal=True) pysam_method = getattr(self.module, mapped_command) usage_msg = pysam_method.usage() expected = r"Usage:\s+{} {}".format(self.executable, command) self.assertTrue(re.search(expected, usage_msg) is not None) def tearDown(self): if os.path.exists(self.workdir): shutil.rmtree(self.workdir) os.chdir(self.savedir) class EmptyIndexTest(unittest.TestCase): def testEmptyIndex(self): self.assertRaises(IOError, pysam.samtools.index, "exdoesntexist.bam") def testEmptyIndexWithExtraFlag(self): self.assertRaises(IOError, pysam.samtools.index, "-c", "exdoesntexist.bam") def testEmptyIndexWithExtraArg(self): self.assertRaises(IOError, pysam.samtools.index, "-c", "-m", "14", "exdoesntexist.bam") if sys.platform != "darwin": # fails with segfault with htslib 1.5 on Osx, an issue with flockfile # issue seems to be with repeated calls to interface class TestReturnType(unittest.TestCase): def testReturnValueString(self): retval = pysam.idxstats(os.path.join(BAM_DATADIR, "ex1.bam")) self.assertFalse(isinstance(retval, bytes)) self.assertTrue(isinstance(retval, str)) def testReturnValueData(self): args = "-O BAM {}".format(os.path.join(BAM_DATADIR, "ex1.bam")).split(" ") retval = pysam.view(*args) self.assertTrue(isinstance(retval, bytes)) self.assertFalse(isinstance(retval, str)) class StdoutTest(unittest.TestCase): '''test if stdout can be redirected.''' def testWithRedirectedStdout(self): r = pysam.samtools.flagstat( os.path.join(BAM_DATADIR, "ex1.bam")) self.assertTrue(len(r) > 0) def testWithoutRedirectedStdout(self): r = pysam.samtools.flagstat( os.path.join(BAM_DATADIR, "ex1.bam"), catch_stdout=False) self.assertEqual(r, None) def testDoubleCalling(self): # The following would fail if there is an # issue with stdout being improperly caught. retvals = pysam.idxstats( os.path.join(BAM_DATADIR, "ex1.bam")) retvals = pysam.idxstats( os.path.join(BAM_DATADIR, "ex1.bam")) def testSaveStdout(self): outfile = get_temp_filename(suffix=".tsv") r = pysam.samtools.flagstat( os.path.join(BAM_DATADIR, "ex1.bam"), save_stdout=outfile) self.assertEqual(r, None) with open(outfile) as inf: r = inf.read() self.assertTrue(len(r) > 0) class PysamTest(SamtoolsTest): """check access to samtools command in the pysam main package. This is for backwards capability. """ module = pysam # class BcftoolsTest(SamtoolsTest): # requisites = [ # "ex1.fa", # "ex1.vcf.gz", # "ex1.vcf.gz.tbi", # ] # # a list of statements to test # # should contain at least one %(out)s component indicating # # an output file. # statements = [ # # "index -n ex1.vcf.gz > %(out)s_ex1.index", # "annotate -x ID ex1.vcf.gz > %(out)s_ex1.annotate", # "concat -a ex1.vcf.gz ex1.vcf.gz > %(out)s_ex1.concat", # "isec -p %(out)s_ex1.isec ex1.vcf.gz ex1.vcf.gz", # "merge --force-samples ex1.vcf.gz ex1.vcf.gz > %(out)s_ex1.norm", # "norm -m +both ex1.vcf.gz > %(out)s_ex1.norm", # # "plugin", # # "query -f '%CHROM\n' ex1.vcf.gz > %(out)s_ex1.query", # # "reheader -s A > %(out)s_ex1.reheader", # # "view ex1.vcf.gz > %(out)s_ex1.view", # # "call -m ex1.vcf.gz > %(out)s_ex1.call", # # bad file descriptor # # "consensus -f ex1.fa ex1.vcf.gz > %(out)s_ex1.consensus" # # need appropriate VCF file # # "cnv", # # segfault # # "filter -s A ex1.vcf.gz > %(out)s_ex1.filter", # # exit # # "gtcheck -s A ex1.vcf.gz > %(out)s_ex1.gtcheck", # # segfault, used to work with bcftools 1.3 # # "roh -s A ex1.vcf.gz > %(out)s_ex1.roh", # "stats ex1.vcf.gz > %(out)s_ex1.stats", # ] # map_command = { # } # executable = "bcftools" # module = pysam.bcftools if __name__ == "__main__": print("starting tests") unittest.main() print("completed tests") pysam-0.23.0/tests/tabix_bench.py000066400000000000000000000121631475062545500167270ustar00rootroot00000000000000import gzip import os import pysam from TestUtils import TABIX_DATADIR FN_COMPRESSED = "example.bed.gz" FN_UNCOMPRESSED = "example.bed" FN_LARGE_COMPRESSED = "example_large.bed.gz" FN_LARGE_UNCOMPRESSED = "example_large.bed" def read_python_compressed(fn): '''iterate through with python.''' with gzip.open(fn, mode="r") as f: return len([x.split(b"\t") for x in f]) def read_python_uncompressed(fn): with open(fn) as f: return len([x.split("\t") for x in f]) def fetch_plain(fn): with pysam.Tabixfile(fn) as f: return len(list(f.fetch())) def fetch_parsed(fn): with pysam.Tabixfile(fn) as f: return len(list(f.fetch(parser=pysam.asBed()))) def iterate_generic_compressed(fn): with gzip.open(fn) as f: return len(list(pysam.tabix_generic_iterator(f, parser=pysam.asBed()))) def iterate_generic_uncompressed(fn): with open(fn) as f: return len(list(pysam.tabix_generic_iterator(f, parser=pysam.asBed()))) def iterate_parsed_compressed(fn): with gzip.open(fn) as f: return len(list(pysam.tabix_iterator(f, parser=pysam.asBed()))) def iterate_parsed_uncompressed(fn): with open(fn) as f: return len(list(pysam.tabix_iterator(f, parser=pysam.asBed()))) def iterate_file_compressed(fn): with gzip.open(fn) as f: return len(list(pysam.tabix_file_iterator(f, parser=pysam.asBed()))) def iterate_file_uncompressed(fn): with open(fn) as f: return len(list(pysam.tabix_file_iterator(f, parser=pysam.asBed()))) def test_read_python_compressed(benchmark): result = benchmark(read_python_compressed, os.path.join(TABIX_DATADIR, FN_COMPRESSED)) assert result == 164 def test_read_python_uncompressed(benchmark): result = benchmark(read_python_uncompressed, os.path.join(TABIX_DATADIR, FN_UNCOMPRESSED)) assert result == 164 def test_fetch_plain(benchmark): result = benchmark(fetch_plain, os.path.join(TABIX_DATADIR, FN_COMPRESSED)) assert result == 164 def test_fetch_parsed(benchmark): result = benchmark(fetch_parsed, os.path.join( TABIX_DATADIR, FN_COMPRESSED)) assert result == 164 def test_iterate_generic_compressed(benchmark): result = benchmark(iterate_generic_compressed, os.path.join(TABIX_DATADIR, FN_COMPRESSED)) assert result == 164 def test_iterate_generic_uncompressed(benchmark): result = benchmark(iterate_generic_uncompressed, os.path.join(TABIX_DATADIR, FN_UNCOMPRESSED)) assert result == 164 def test_iterate_parsed_compressed(benchmark): result = benchmark(iterate_parsed_compressed, os.path.join(TABIX_DATADIR, FN_COMPRESSED)) assert result == 164 def test_iterate_parsed_uncompressed(benchmark): result = benchmark(iterate_parsed_uncompressed, os.path.join(TABIX_DATADIR, FN_UNCOMPRESSED)) assert result == 164 def test_iterate_file_compressed(benchmark): result = benchmark(iterate_file_compressed, os.path.join(TABIX_DATADIR, FN_COMPRESSED)) assert result == 164 def test_iterate_file_uncompressed(benchmark): result = benchmark(iterate_file_uncompressed, os.path.join(TABIX_DATADIR, FN_UNCOMPRESSED)) assert result == 164 def test_read_python_large_compressed(benchmark): result = benchmark(read_python_compressed, os.path.join( TABIX_DATADIR, FN_LARGE_COMPRESSED)) assert result == 100000 def test_read_python_large_uncompressed(benchmark): result = benchmark(read_python_uncompressed, os.path.join( TABIX_DATADIR, FN_LARGE_UNCOMPRESSED)) assert result == 100000 def test_fetch_plain(benchmark): result = benchmark(fetch_plain, os.path.join( TABIX_DATADIR, FN_LARGE_COMPRESSED)) assert result == 100000 def test_fetch_parsed(benchmark): result = benchmark(fetch_parsed, os.path.join( TABIX_DATADIR, FN_LARGE_COMPRESSED)) assert result == 100000 def test_iterate_generic_large_compressed(benchmark): result = benchmark(iterate_generic_compressed, os.path.join( TABIX_DATADIR, FN_LARGE_COMPRESSED)) assert result == 100000 def test_iterate_generic_large_uncompressed(benchmark): result = benchmark(iterate_generic_uncompressed, os.path.join( TABIX_DATADIR, FN_LARGE_UNCOMPRESSED)) assert result == 100000 def test_iterate_parsed_large_compressed(benchmark): result = benchmark(iterate_parsed_compressed, os.path.join( TABIX_DATADIR, FN_LARGE_COMPRESSED)) assert result == 100000 def test_iterate_parsed_large_uncompressed(benchmark): result = benchmark(iterate_parsed_uncompressed, os.path.join( TABIX_DATADIR, FN_LARGE_UNCOMPRESSED)) assert result == 100000 def test_iterate_file_large_compressed(benchmark): result = benchmark(iterate_file_compressed, os.path.join( TABIX_DATADIR, FN_LARGE_COMPRESSED)) assert result == 100000 def test_iterate_file_large_uncompressed(benchmark): result = benchmark(iterate_file_uncompressed, os.path.join( TABIX_DATADIR, FN_LARGE_UNCOMPRESSED)) assert result == 100000 pysam-0.23.0/tests/tabix_data/000077500000000000000000000000001475062545500162045ustar00rootroot00000000000000pysam-0.23.0/tests/tabix_data/Makefile000066400000000000000000000014701475062545500176460ustar00rootroot00000000000000all: all.stamp DERIVED_FILES = \ empty.bed.gz.tbi \ example.bed.gz example.bed.gz.tbi \ example.gff2.gz.tbi \ example.gff3.gz.tbi \ example.sam.gz.tbi \ example.vcf.gz.tbi \ example_badcomments.bed.gz.tbi \ example_badcomments.gtf.gz.tbi \ example_badcomments.sam.gz.tbi \ example_badcomments.vcf.gz.tbi \ example_comments.bed.gz.tbi \ example_comments.gtf.gz.tbi \ example_comments.sam.gz.tbi \ example_comments.vcf.gz.tbi \ example_large.bed.gz.tbi \ fivecolumns.bed.gz fivecolumns.bed.gz.tbi all.stamp: $(DERIVED_FILES) touch $@ %.gz: % bgzip -c $< > $@ %.gff2.gz.tbi: %.gff2.gz tabix -f -p gff $< %.gff3.gz.tbi: %.gff3.gz tabix -f -p gff $< %.gtf.gz.tbi: 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T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 17 14370 Reneé G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 20 1110696 Grün A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 20 1234567 Señor GTCT G,GTACT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 pysam-0.23.0/tests/tabix_data/fivecolumns.bed000066400000000000000000000001421475062545500212070ustar00rootroot00000000000000chr1 100 200 one apple chr1 300 400 two banana chr2 100 600 three carrot chr2 700 800 four durian pysam-0.23.0/tests/tabix_data/gtf_toofew_fields.gtf.gz000066400000000000000000000006201475062545500230140ustar00rootroot00000000000000BCsKk@bؗBH i"$B[kÆ e w{7]\[9Fp)-܏#$4C":Pd,Nj&%9堥YRXab"(wඛ"x :e+LGY:A{~{c@~uЖ7,1%zvD(in1bJݗ;o|/"C}5i[CNjODqf_%C<ӜQR%ڛ0s-i#1b3&Djjvn{WAR' FN)3bJwգtӪ BCpysam-0.23.0/tests/tabix_data/gtf_toomany_fields.gtf.gz000066400000000000000000000006201475062545500231770ustar00rootroot00000000000000BCsKk@ӟ9hcBjڣ.#Z!.xfvpp]aM׷ր-jA\g4 PE1Y 0Ӣ`I-:xN9hi<~Dض2]>ezN ~';Dl'NPuv!_]7rL^]g)J@iouXR~N gP_M{쐓QdW)dɐ94eTɿ#4\KtyG،I.2-]'ޕzjP{'GJ@2~fi(fjz}+9 BCpysam-0.23.0/tests/tabix_data/gtf_wrong_fields.gtf.gz000066400000000000000000000006201475062545500226450ustar00rootroot00000000000000BCsKk@ӟ9hcBjڣ.#Z!.xfvpp]aM׷ր-jA\g4 PE1Y 0Ӣ`I-:xN9hi<~Dض2]>ezN ~';Dl'NPuv!_]7rL^]g)J@iouXR~N gP_M{쐓QdW)dɐ94eTɿ#4\KtyG،I.2-]'ޕzjP{'GJ@2~fi(fjz}+9 BCpysam-0.23.0/tests/tabix_data/vcf/000077500000000000000000000000001475062545500167625ustar00rootroot00000000000000pysam-0.23.0/tests/tabix_data/vcf/10.vcf000066400000000000000000003236411475062545500177130ustar00rootroot00000000000000##fileformat=VCFv4.0 ##FILTER= ##FILTER= ##FILTER= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##ValidationMetrics_HardyWeinbergViolations="25 (8%)" ##ValidationMetrics_HomVarViolations="0 (0%)" ##ValidationMetrics_NoCallViolations="13 (4%)" ##ValidationMetrics_PolymorphicPassingRecords="195 (75%)" ##ValidationMetrics_RecordsPassingFilters="258 (87%)" ##ValidationMetrics_RecordsProcessed=296 ##ValidationMetrics_SamplesAssayed=383 ##VariantValidationAssessor="analysis_type=VariantValidationAssessor input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[rawData/plink.renamed.sorted.fixed.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub maxHardy=20.0 maxNoCall=0.05 maxHomVar=1.1" ##source=PLINK #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00127 HG00128 HG00136 HG00137 HG00138 HG00139 HG00152 HG00156 HG00234 HG00235 HG00237 HG00242 HG00244 HG00262 HG01055 HG01079 NA19138 NA18974 NA18523 NA12717 NA19209 NA18577 NA18973 NA18943 NA12873 NA18623 NA18622 NA18948 NA19171 NA19204 NA06994 NA18563 NA18547 NA18861 NA18608 NA18995 NA10851 NA18976 NA18603 NA19200 HG01204 HG01191 HG01101 HG00146 HG00306 NA18985 HG00160 HG00635 HG00372 HG00357 HG00634 NA18541 NA18950 NA19759 HG00351 HG00257 HG00118 HG00336 HG00448 HG01354 NA18609 HG00428 HG00326 NA11894 NA18956 HG00173 HG00117 NA11893 HG01251 HG01441 HG01437 HG00182 HG00330 HG01060 HG00329 NA18960 NA18856 NA07346 NA18871 NA19057 NA18868 NA18636 NA12830 NA19007 NA18910 NA18874 NA19056 NA19064 NA19066 NA18487 NA18642 NA19236 NA07056 NA18637 NA19235 NA19309 NA19311 NA19334 NA19346 NA19347 NA19372 NA19376 NA19383 NA19384 NA19394 NA19428 NA19430 NA19451 NA19466 NA19313 NA19321 NA19324 NA19332 NA19390 NA19436 NA19439 NA19440 NA19463 NA19470 NA19471 NA19472 NA19676 NA19660 NA19661 NA19663 NA19722 NA19725 NA19728 NA19729 NA19731 NA19749 NA19755 NA19756 NA19758 NA19770 NA19773 NA19777 NA19780 NA19783 NA20525 NA20589 NA20765 NA20802 NA20804 NA18544 NA18602 NA18546 NA18610 NA18957 NA18615 NA18616 NA19010 NA18638 NA18639 NA18627 NA19072 NA18630 NA19074 NA19080 NA19081 NA19083 NA19085 NA19088 NA20287 NA19835 NA20276 NA19818 NA20278 NA20282 NA20342 NA20296 NA20314 NA20346 NA19712 NA19198 NA19108 NA18934 NA18916 NA18907 NA18917 NA06989 NA12058 NA12341 NA12546 NA12489 HG01197 NA18983 NA11843 NA11892 NA12749 NA12282 NA12751 NA18959 NA19331 NA19453 NA20537 NA12046 NA20515 NA20516 NA20521 NA20524 NA20528 NA20759 NA20768 NA20769 NA20774 NA20775 NA20783 NA20787 NA20790 NA20800 NA20819 NA20812 NA20505 NA20530 NA20540 NA20538 NA20581 NA20815 NA20544 NA20810 NA20807 NA20816 NA20504 NA20753 NA20502 NA12342 NA19150 NA19468 NA20336 NA19395 NA19257 NA19360 NA19700 NA18867 NA20317 NA18968 NA19107 HG00111 HG00108 NA19077 NA19684 NA18511 NA12044 NA19382 NA19457 NA18933 NA18923 NA18965 HG00141 NA20341 NA18740 HG00537 HG00346 HG01173 HG00702 HG00313 HG00150 NA18612 HG00339 NA12273 HG00250 NA18593 NA18621 HG00478 HG00251 HG01070 NA19160 HG00479 HG00608 NA18573 HG00375 NA19248 NA19093 HG01170 HG00534 HG01171 HG01522 NA18624 HG00683 HG01521 NA19005 NA20412 NA18971 HG00446 NA12748 HG00530 HG00690 HG01356 HG01516 NA20532 HG00344 HG00328 NA18542 HG00254 HG00321 HG00577 HG00656 HG00342 HG00524 HG00650 HG00557 HG00319 HG00457 HG00125 HG00578 HG00543 HG00638 HG00171 HG00699 HG00595 HG00187 HG00704 HG00533 HG00596 HG00268 HG01083 HG00651 HG01133 HG00671 HG00327 HG01148 HG00246 HG00672 HG00556 HG00436 HG00554 NA18633 NA20344 NA11993 NA07037 NA11930 HG01366 HG01389 HG00620 NA19740 HG00190 HG00419 NA18535 HG01495 NA18592 HG01497 HG00174 HG01140 NA12287 HG00689 HG01550 HG00334 HG01375 HG00637 NA18507 HG01113 NA18550 NA19129 HG01551 HG01462 HG00331 NA12413 HG01456 HG01360 HG00708 HG01350 HG00684 NA19099 HG00284 NA12399 NA12286 NA12777 HG00277 HG00266 NA19985 HG00353 HG01102 NA07347 NA07051 NA19900 NA18984 NA07048 HG00640 HG01066 NA12812 HG01174 HG01188 20 676148 . A AC . PASS AC=0;AN=758;HW=0.00;HetPct=0.0;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=1.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1342549 . A AAGAT . PASS AC=0;AN=760;HW=0.00;HetPct=0.0;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1366475 . CT C . 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A AG . 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T TC . 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AT A . 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T TC . 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A AT . 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ATC A . 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A AGT . 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C CA . 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T TG . 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TGAG T . 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C CA . 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T TG . 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A AG . 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A AC . 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AG A . 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0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 pysam-0.23.0/tests/tabix_data/vcf/11.vcf000066400000000000000000011706571475062545500177240ustar00rootroot00000000000000##fileformat=VCFv4.0 ##FILTER= ##FILTER= ##FILTER= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##ValidationMetrics_HardyWeinbergViolations="25 (8%)" ##ValidationMetrics_HomVarViolations="0 (0%)" ##ValidationMetrics_NoCallViolations="13 (4%)" ##ValidationMetrics_PolymorphicPassingRecords="195 (75%)" ##ValidationMetrics_RecordsPassingFilters="258 (87%)" ##ValidationMetrics_RecordsProcessed=296 ##ValidationMetrics_SamplesAssayed=383 ##VariantValidationAssessor="analysis_type=VariantValidationAssessor input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[rawData/plink.renamed.sorted.fixed.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub maxHardy=20.0 maxNoCall=0.05 maxHomVar=1.1" ##source=PLINK #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00127 HG00128 HG00136 HG00137 HG00138 HG00139 HG00152 HG00156 HG00234 HG00235 HG00237 HG00242 HG00244 HG00262 HG01055 HG01079 NA19138 NA18974 NA18523 NA12717 NA19209 NA18577 NA18973 NA18943 NA12873 NA18623 NA18622 NA18948 NA19171 NA19204 NA06994 NA18563 NA18547 NA18861 NA18608 NA18995 NA10851 NA18976 NA18603 NA19200 HG01204 HG01191 HG01101 HG00146 HG00306 NA18985 HG00160 HG00635 HG00372 HG00357 HG00634 NA18541 NA18950 NA19759 HG00351 HG00257 HG00118 HG00336 HG00448 HG01354 NA18609 HG00428 HG00326 NA11894 NA18956 HG00173 HG00117 NA11893 HG01251 HG01441 HG01437 HG00182 HG00330 HG01060 HG00329 NA18960 NA18856 NA07346 NA18871 NA19057 NA18868 NA18636 NA12830 NA19007 NA18910 NA18874 NA19056 NA19064 NA19066 NA18487 NA18642 NA19236 NA07056 NA18637 NA19235 NA19309 NA19311 NA19334 NA19346 NA19347 NA19372 NA19376 NA19383 NA19384 NA19394 NA19428 NA19430 NA19451 NA19466 NA19313 NA19321 NA19324 NA19332 NA19390 NA19436 NA19439 NA19440 NA19463 NA19470 NA19471 NA19472 NA19676 NA19660 NA19661 NA19663 NA19722 NA19725 NA19728 NA19729 NA19731 NA19749 NA19755 NA19756 NA19758 NA19770 NA19773 NA19777 NA19780 NA19783 NA20525 NA20589 NA20765 NA20802 NA20804 NA18544 NA18602 NA18546 NA18610 NA18957 NA18615 NA18616 NA19010 NA18638 NA18639 NA18627 NA19072 NA18630 NA19074 NA19080 NA19081 NA19083 NA19085 NA19088 NA20287 NA19835 NA20276 NA19818 NA20278 NA20282 NA20342 NA20296 NA20314 NA20346 NA19712 NA19198 NA19108 NA18934 NA18916 NA18907 NA18917 NA06989 NA12058 NA12341 NA12546 NA12489 HG01197 NA18983 NA11843 NA11892 NA12749 NA12282 NA12751 NA18959 NA19331 NA19453 NA20537 NA12046 NA20515 NA20516 NA20521 NA20524 NA20528 NA20759 NA20768 NA20769 NA20774 NA20775 NA20783 NA20787 NA20790 NA20800 NA20819 NA20812 NA20505 NA20530 NA20540 NA20538 NA20581 NA20815 NA20544 NA20810 NA20807 NA20816 NA20504 NA20753 NA20502 NA12342 NA19150 NA19468 NA20336 NA19395 NA19257 NA19360 NA19700 NA18867 NA20317 NA18968 NA19107 HG00111 HG00108 NA19077 NA19684 NA18511 NA12044 NA19382 NA19457 NA18933 NA18923 NA18965 HG00141 NA20341 NA18740 HG00537 HG00346 HG01173 HG00702 HG00313 HG00150 NA18612 HG00339 NA12273 HG00250 NA18593 NA18621 HG00478 HG00251 HG01070 NA19160 HG00479 HG00608 NA18573 HG00375 NA19248 NA19093 HG01170 HG00534 HG01171 HG01522 NA18624 HG00683 HG01521 NA19005 NA20412 NA18971 HG00446 NA12748 HG00530 HG00690 HG01356 HG01516 NA20532 HG00344 HG00328 NA18542 HG00254 HG00321 HG00577 HG00656 HG00342 HG00524 HG00650 HG00557 HG00319 HG00457 HG00125 HG00578 HG00543 HG00638 HG00171 HG00699 HG00595 HG00187 HG00704 HG00533 HG00596 HG00268 HG01083 HG00651 HG01133 HG00671 HG00327 HG01148 HG00246 HG00672 HG00556 HG00436 HG00554 NA18633 NA20344 NA11993 NA07037 NA11930 HG01366 HG01389 HG00620 NA19740 HG00190 HG00419 NA18535 HG01495 NA18592 HG01497 HG00174 HG01140 NA12287 HG00689 HG01550 HG00334 HG01375 HG00637 NA18507 HG01113 NA18550 NA19129 HG01551 HG01462 HG00331 NA12413 HG01456 HG01360 HG00708 HG01350 HG00684 NA19099 HG00284 NA12399 NA12286 NA12777 HG00277 HG00266 NA19985 HG00353 HG01102 NA07347 NA07051 NA19900 NA18984 NA07048 HG00640 HG01066 NA12812 HG01174 HG01188 20 669442 . TG T . PASS AC=54;AN=766;HW=6.74;HetPct=12.0;HomRefPct=86.9;HomVarPct=1.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 719486 . C CT . PASS AC=1;AN=760;HW=0.00;HetPct=0.3;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 890696 . C CAT . PASS AC=6;AN=766;HW=0.00;HetPct=1.6;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1102516 . CT C . PASS AC=3;AN=760;HW=0.00;HetPct=0.8;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1149576 . CT C . PASS AC=2;AN=764;HW=0.00;HetPct=0.5;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1195706 . AAG A . PASS AC=334;AN=764;HW=9.47;HetPct=44.9;HomRefPct=33.7;HomVarPct=21.1;NoCallPct=0.3 GT 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 . 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 1/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 1/1 20 1655540 . AT A . PASS AC=4;AN=764;HW=0.00;HetPct=1.0;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 2889034 . AAAAT A . PASS AC=6;AN=762;HW=0.00;HetPct=1.6;HomRefPct=97.9;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 3203741 . CT C . 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TC T . 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G GA . 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CATT C . 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CAAAT C . 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CCTTGA C . 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C CATTTTAGG . 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GA G . 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CA C . PASS AC=2;AN=752;HW=0.00;HetPct=0.5;HomRefPct=97.7;HomVarPct=0.0;NoCallPct=1.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 5432262 . AGT A . PASS AC=4;AN=752;HW=0.00;HetPct=1.0;HomRefPct=97.1;HomVarPct=0.0;NoCallPct=1.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 6877907 . CA C . 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CAAAGAAT C . 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T TA . 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AG A . 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C CT . 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C CT . 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TACTC T . 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TAG T . 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AAAGT A . 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T TG . 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T TA . 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AC A . 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ATTAG A . 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A AG . 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CTT C . 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CTA C . 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GACA G . 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TTATC T . 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GGGA G . 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CT C . 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CAT C . PASS AC=134;AN=760;HW=0.21;HetPct=29.2;HomRefPct=67.1;HomVarPct=2.9;NoCallPct=0.8 GT 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 1/1 0/1 0/1 . 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/1 . 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 . 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 20 13566260 . AAATTG A . PASS AC=374;AN=764;HW=3.95;HetPct=47.5;HomRefPct=27.2;HomVarPct=25.1;NoCallPct=0.3 GT 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 0/0 0/1 . 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 1/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 0/1 0/0 0/1 1/1 1/1 20 13685184 . AT A . PASS AC=2;AN=764;HW=0.00;HetPct=0.5;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 13716193 . GAGAA G . 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TC T . 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T TA . 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TA T . 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G GA . 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TTC T . 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GA G . 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TG T . 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TGA T . 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AG A . 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TG T . 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TG T . 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AG A . 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TA T . PASS AC=186;AN=764;HW=15.27;HetPct=32.4;HomRefPct=59.3;HomVarPct=8.1;NoCallPct=0.3 GT 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 20 16312599 . CTA C . PASS AC=2;AN=764;HW=0.00;HetPct=0.5;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16723642 . GGTT G . PASS AC=6;AN=760;HW=0.00;HetPct=1.6;HomRefPct=97.7;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16747221 . CA C . 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C CA . 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TA T . 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TGC T . 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A AGT . 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AC A . 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AAG A . 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TAA T . 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C CT . 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CCTT C . 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CT C . PASS AC=362;AN=766;HW=6.74;HetPct=46.5;HomRefPct=29.5;HomVarPct=24.0;NoCallPct=0.0 GT 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/1 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 20 20286529 . A AC . 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ATTACAGACT A . 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CA C . 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TG T . 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T TC . 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ACTT A . 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AG A . PASS AC=1;AN=766;HW=0.00;HetPct=0.3;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 21852048 . CA C . 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AC A . PASS AC=7;AN=762;HW=12.61;HetPct=1.3;HomRefPct=97.9;HomVarPct=0.3;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 22434333 . C CA . PASS AC=8;AN=766;HW=0.00;HetPct=2.1;HomRefPct=97.9;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 20 22637424 . C CAGCCA . 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TATC T . PASS AC=6;AN=766;HW=0.00;HetPct=1.6;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23200197 . ATT A . PASS AC=1;AN=766;HW=0.00;HetPct=0.3;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23293728 . CA C . 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CT C . 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CT C . 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GA G . 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CT C . 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CATA C . 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TATATC T . 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TTATACTA T . 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CT C . 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CT C . 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CAG C . 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A AG . 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GGCGTCTGA G . 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A AAG . 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C CA . 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TAA T . 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CT C . 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GA G . 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CTT C . 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TG T . 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TC T . 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TAAAG T . 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ATAC A . 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CAG C . 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TG T . 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CAT C . 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C CTGG . PASS AC=7;AN=762;HW=0.00;HetPct=1.8;HomRefPct=97.7;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37712193 . AAG A . 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AAAT A . 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T TAA . 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TA T . 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T TA . 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GAAGA G . 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CCTT C . 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T TG . 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AG A . 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TG T . 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T TG . 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T TATCA . 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A AAG . 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CTAAGGAGGGAAAAAGATATAAT C . 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TA T . 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GC G . 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C CATTT . 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CACTT C . 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T TA . 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CT C . 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T TGGGTC . PASS AC=3;AN=764;HW=0.00;HetPct=0.8;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 42918721 . AG A . 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AG A . 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T TAG . 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CA C . 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C CT . 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T TC . 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AACAG A . 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T TA . 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GA G . 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G GC . 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GT G . 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T TTC . 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T TAAGC . 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TC T . PASS AC=2;AN=760;HW=0.00;HetPct=0.5;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 46569465 . CTG C . PASS AC=10;AN=762;HW=0.00;HetPct=2.6;HomRefPct=96.9;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 46720983 . ATACTTGG A . PASS AC=3;AN=764;HW=0.00;HetPct=0.8;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 47032179 . GC G . PASS AC=2;AN=760;HW=0.00;HetPct=0.5;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 47136092 . A AGTC . 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GC G . 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CA C . 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CCTA C . 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G GT . 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AG A . 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TTTTC T . 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A AT . 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G GAA . 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G GT . 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AC A . 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GA G . PASS AC=4;AN=756;HW=17.99;HetPct=0.5;HomRefPct=97.9;HomVarPct=0.3;NoCallPct=1.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 51961394 . ATTTG A . PASS AC=8;AN=760;HW=0.00;HetPct=2.1;HomRefPct=97.1;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 53081927 . CATGA C . 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T TA . 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T TC . 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CAG C . 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AC A . 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CAT C . 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TGAGC T . 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GT G . 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AG A . PASS AC=232;AN=762;HW=15.89;HetPct=37.1;HomRefPct=50.7;HomVarPct=11.7;NoCallPct=0.5 GT 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 1/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 . 0/0 . 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 20 55608811 . CT C . PASS AC=35;AN=762;HW=19.90;HetPct=7.0;HomRefPct=91.4;HomVarPct=1.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 20 55611547 . CAA C . 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CA C . 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T TGAGG . 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GT G . 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T TG . 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TG T . 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CCTTT C . 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TC T . 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CTG C . 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CCT C . 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TG T . 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C CT . 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AC A . 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GC G . 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TCTGC T . 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PASS AC=1;AN=756;HW=0.00;HetPct=0.3;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=1.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 62871860 . C CCCGCA . PASS AC=27;AN=764;HW=17.87;HetPct=5.5;HomRefPct=93.5;HomVarPct=0.8;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 pysam-0.23.0/tests/tabix_data/vcf/12.vcf000066400000000000000000002723361475062545500177210ustar00rootroot00000000000000##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT DNA_pool_A chr1 1281168 . A G 14 . DP=37;AF1=0.6243;CI95=0.5,1;DP4=4,0,6,0;MQ=15;PV4=1,0.027,1,1 PL:GT:GQ 43,0,4:0/1:6 chr1 1281205 . T C 26 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 58,9,0:1/1:63 chr1 1281206 . G C 25 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 57,9,0:1/1:63 chr1 1922737 . G C 13.2 . DP=21;AF1=1;CI95=1,1;DP4=0,0,0,21;MQ=22 PL:GT:GQ 46,63,0:1/1:99 chr1 21197513 . A G 55.1 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=41 PL:GT:GQ 88,21,0:1/1:84 chr1 21343209 . T C 5.45 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=14 PL:GT:GQ 37,51,0:1/1:99 chr1 22097362 . T C 4.75 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 35,9,0:1/1:63 chr1 22254012 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 22650927 . G A 48.1 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=24 PL:GT:GQ 81,21,0:1/1:84 chr1 23535401 . C T 40.4 . DP=25;AF1=1;CI95=0.5,1;DP4=0,16,0,5;MQ=19;PV4=1,0.2,1,1 PL:GT:GQ 73,13,0:1/1:65 chr1 23543855 . T C 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44 PL:GT:GQ 82,18,0:1/1:90 chr1 24245107 . C G 32 . DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,1,1 PL:GT:GQ 62,0,35:0/1:38 chr1 24274412 . G C 39.5 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=32 PL:GT:GQ 72,12,0:1/1:72 chr1 36529832 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr1 37788090 . A G 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr1 43120440 . C T 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=49;PV4=1,1,1,1 PL:GT:GQ 64,0,31:0/1:34 chr1 43980466 . C T 43 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=19 PL:GT:GQ 76,45,0:1/1:99 chr1 46047795 . T C 29.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=31 PL:GT:GQ 62,18,0:1/1:90 chr1 48860309 . C T 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=46 PL:GT:GQ 141,18,0:1/1:90 chr1 49415599 . T C 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 34,6,0:1/1:49 chr1 51601816 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 51955459 . G C 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr1 68479569 . T G 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 43,6,0:1/1:49 chr1 69032455 . A G 15.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 47,9,0:1/1:63 chr1 71888225 . G T 9.31 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr1 72381528 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr1 82004013 . A G 37.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 70,12,0:1/1:72 chr1 86289622 . C T 18 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 50,9,0:1/1:63 chr1 90267663 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45 PL:GT:GQ 54,9,0:1/1:63 chr1 92699542 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr1 94867317 . G A 26.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 58,6,0:1/1:49 chr1 96428713 . C G 3.98 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=27 PL:GT:GQ 33,6,0:1/1:49 chr1 100466329 . G C 4.85 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=22 PL:GT:GQ 36,18,0:1/1:90 chr1 101909281 . G A 70 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=46;PV4=1,1,0.096,1 PL:GT:GQ 100,0,88:0/1:91 chr1 106216572 . T A 22 . DP=18;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=21 PL:GT:GQ 55,48,0:1/1:99 chr1 107901770 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 40,6,0:1/1:49 chr1 108431179 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=41 PL:GT:GQ 155,24,0:1/1:96 chr1 112005344 . C T 99 . DP=52;AF1=1;CI95=1,1;DP4=7,0,27,0;MQ=44;PV4=1,1,1,1 PL:GT:GQ 196,25,0:1/1:99 chr1 116625452 . C T 36 . DP=44;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,20;MQ=49;PV4=1,2.3e-69,0.42,1 PL:GT:GQ 66,0,179:0/1:69 chr1 118060710 . G T 6.98 . DP=8;AF1=0.4999;CI95=0.5,0.5;DP4=4,0,3,0;MQ=47;PV4=1,0.0071,1,1 PL:GT:GQ 36,0,73:0/1:39 chr1 118198177 . A G 15.9 . DP=23;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 47,6,0:1/1:49 chr1 118586346 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr1 120809555 . G A 20 . DP=8;AF1=0.5;CI95=0.5,0.5;DP4=6,0,2,0;MQ=46;PV4=1,1,1,1 PL:GT:GQ 50,0,106:0/1:53 chr1 130723110 . C A 20.7 . DP=8;AF1=0.5939;CI95=0.5,1;DP4=0,6,0,2;MQ=26;PV4=1,1,1,1 PL:GT:GQ 50,0,5:0/1:7 chr1 133979895 . T C 14.9 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 46,6,0:1/1:49 chr1 134977940 . C T 30 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,1,0.26,1 PL:GT:GQ 60,0,31:0/1:34 chr1 141768589 . G A 18.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=4,0,4,0;MQ=51;PV4=1,2.7e-05,1,1 PL:GT:GQ 48,0,100:0/1:51 chr1 141768590 . G A 22 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=2,0,4,0;MQ=50;PV4=1,0.0033,1,1 PL:GT:GQ 52,0,40:0/1:43 chr1 146506051 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43 PL:GT:GQ 76,9,0:1/1:63 chr1 150997009 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr1 162915612 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 168455400 . A G 4.12 . DP=28;AF1=1;CI95=1,1;DP4=0,0,0,27;MQ=10 PL:GT:GQ 35,81,0:1/1:99 chr1 172784744 . T C 17.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 49,6,0:1/1:49 chr1 183627307 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 185789457 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr1 187081827 . T C 4.77 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=17 PL:GT:GQ 36,30,0:1/1:99 chr1 188468339 . C T 33 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=24 PL:GT:GQ 66,39,0:1/1:99 chr1 188595435 . C T 41.8 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr1 188670561 . G C 3.55 . DP=22;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=18 PL:GT:GQ 34,27,0:1/1:99 chr1 188924877 . G A 6.2 . DP=10;AF1=0.9999;CI95=0.5,1;DP4=2,0,3,0;MQ=21;PV4=1,1,1,0.3 PL:GT:GQ 35,3,0:1/1:41 chr1 190536295 . G A 68 . DP=38;AF1=1;CI95=1,1;DP4=0,0,36,0;MQ=18 PL:GT:GQ 101,108,0:1/1:99 chr1 191129408 . T A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr1 195937816 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr1 198857619 . T C 89 . DP=61;AF1=0.5;CI95=0.5,0.5;DP4=0,38,0,17;MQ=30;PV4=1,0.032,1,1 PL:GT:GQ 119,0,139:0/1:99 chr1 199057483 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 44,6,0:1/1:49 chr1 200133619 . G C 5.83 . DP=49;AF1=1;CI95=0.5,1;DP4=2,0,8,0;MQ=17;PV4=1,0.059,1,0.2 PL:GT:GQ 37,12,0:1/1:72 chr1 200729661 . A T 36 . DP=15;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=27 PL:GT:GQ 69,42,0:1/1:99 chr1 201374519 . T C 69.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39 PL:GT:GQ 102,12,0:1/1:72 chr1 202811668 . G A 20.2 . DP=4;AF1=0.5163;CI95=0.5,1;DP4=0,1,0,3;MQ=24;PV4=1,1,1,1 PL:GT:GQ 50,0,12:0/1:15 chr1 202960650 . C T 16.6 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27 PL:GT:GQ 49,12,0:1/1:72 chr1 205686638 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr1 205949857 . A G 3.14 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=21 PL:GT:GQ 33,15,0:1/1:75 chr1 209806643 . A G 13.2 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=21 PL:GT:GQ 46,24,0:1/1:96 chr1 209871501 . C T 25 . DP=12;AF1=0.5;CI95=0.5,0.5;DP4=5,0,4,0;MQ=41;PV4=1,7.7e-06,1,1 PL:GT:GQ 55,0,84:0/1:58 chr1 211051323 . G A 99 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=49 PL:GT:GQ 176,24,0:1/1:96 chr1 211389716 . C T 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 43,6,0:1/1:49 chr1 211868415 . G A 3.54 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=14 PL:GT:GQ 34,33,0:1/1:99 chr1 211914531 . C T 84.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=46;PV4=1,1,1,1 PL:GT:GQ 116,7,0:1/1:57 chr1 214691313 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr1 215184650 . C T 40.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 72,6,0:1/1:49 chr1 215995258 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr1 217031394 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 217986960 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 76,9,0:1/1:63 chr1 218086681 . A G 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34 PL:GT:GQ 142,27,0:1/1:99 chr1 218546019 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 218632417 . G T 17.1 . DP=19;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=26 PL:GT:GQ 50,21,0:1/1:84 chr1 218833355 . C G 23 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=5,0,2,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 53,0,63:0/1:56 chr1 219303186 . T C 7.79 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=12 PL:GT:GQ 40,75,0:1/1:99 chr1 219517634 . G A 26.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42 PL:GT:GQ 59,12,0:1/1:72 chr1 219590158 . T C 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 33,12,0:1/1:72 chr1 219709853 . A T 99 . DP=124;AF1=0.5;CI95=0.5,0.5;DP4=80,0,41,0;MQ=44;PV4=1,0.26,1,1 PL:GT:GQ 143,0,156:0/1:99 chr1 222457988 . A G 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23 PL:GT:GQ 42,6,0:1/1:49 chr1 222477914 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr1 223010233 . A G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr1 223796360 . G A 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=21 PL:GT:GQ 37,6,0:1/1:49 chr1 224273784 . A T 14.2 . DP=18;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=15 PL:GT:GQ 47,30,0:1/1:99 chr1 224454685 . C T 46.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32 PL:GT:GQ 79,15,0:1/1:75 chr1 224514706 . G C 21 . DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=19 PL:GT:GQ 54,114,0:1/1:99 chr1 224515793 . C T 99 . DP=26;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=45 PL:GT:GQ 211,78,0:1/1:99 chr1 224692969 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 40,6,0:1/1:49 chr1 225607249 . A G 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,1,0,1 PL:GT:GQ 64,0,31:0/1:34 chr1 226923918 . C A 29.1 . DP=52;AF1=1;CI95=0.5,1;DP4=0,2,0,10;MQ=27;PV4=1,1,1,1 PL:GT:GQ 62,18,0:1/1:90 chr1 227125189 . T C 56.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=41 PL:GT:GQ 89,12,0:1/1:72 chr1 227133712 . A T 20.1 . DP=26;AF1=0.5;CI95=0.5,0.5;DP4=11,0,10,0;MQ=23;PV4=1,1,0.48,1 PL:GT:GQ 50,0,39:0/1:42 chr1 227943954 . G C 47 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37 PL:GT:GQ 79,9,0:1/1:63 chr1 227943974 . G A 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34 PL:GT:GQ 66,12,0:1/1:72 chr1 228067480 . A G 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45 PL:GT:GQ 75,15,0:1/1:75 chr1 228067510 . A G 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45 PL:GT:GQ 140,15,0:1/1:75 chr1 228088778 . C T 6.79 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23 PL:GT:GQ 37,6,0:1/1:49 chr1 228117888 . A C 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 45,6,0:1/1:49 chr1 228139641 . T C 44.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 77,12,0:1/1:72 chr1 228577146 . T C 26 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,14;MQ=22;PV4=1,1,1,0.027 PL:GT:GQ 56,0,77:0/1:59 chr1 229001369 . C A 45 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 77,9,0:1/1:63 chr1 229001386 . C T 8.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 39,6,0:1/1:49 chr1 229348080 . T C 18.1 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=40;PV4=1,0.33,0.17,0.33 PL:GT:GQ 48,0,31:0/1:34 chr1 229439710 . C T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=32 PL:GT:GQ 66,12,0:1/1:72 chr1 229655149 . T C 30 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=30 PL:GT:GQ 63,24,0:1/1:96 chr1 229660873 . C G 81 . DP=28;AF1=0.5;CI95=0.5,0.5;DP4=0,20,0,7;MQ=36;PV4=1,1,1,1 PL:GT:GQ 111,0,120:0/1:99 chr2a 3661005 . C G 24 . DP=13;AF1=0.5001;CI95=0.5,0.5;DP4=7,0,4,0;MQ=27;PV4=1,1.1e-05,1,1 PL:GT:GQ 54,0,34:0/1:37 chr2a 4140063 . G A 81 . DP=26;AF1=0.6671;CI95=0.5,1;DP4=18,0,8,0;MQ=24;PV4=1,8.3e-09,1,1 PL:GT:GQ 110,0,3:0/1:5 chr2a 4248440 . T C 20 . DP=28;AF1=0.5;CI95=0.5,0.5;DP4=11,0,7,0;MQ=25;PV4=1,1,0.47,1 PL:GT:GQ 50,0,92:0/1:53 chr2a 4707656 . A G 63 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 95,9,0:1/1:63 chr2a 5194801 . G A 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=24 PL:GT:GQ 38,6,0:1/1:49 chr2a 14111103 . A G 7.84 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=20 PL:GT:GQ 40,21,0:1/1:84 chr2a 17799746 . A G 11.3 . DP=5;AF1=0.5001;CI95=0.5,0.5;DP4=0,3,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 41,0,35:0/1:37 chr2a 24728910 . G A 45.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28 PL:GT:GQ 78,15,0:1/1:75 chr2a 29627939 . G T 5.44 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=27 PL:GT:GQ 36,9,0:1/1:63 chr2a 31373164 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr2a 33935228 . T C 41.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr2a 36311856 . G A 99 . DP=30;AF1=1;CI95=1,1;DP4=0,0,0,29;MQ=44 PL:GT:GQ 213,87,0:1/1:99 chr2a 39281204 . T C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr2a 41087565 . C T 74.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=38 PL:GT:GQ 107,12,0:1/1:72 chr2a 45574768 . C A 11.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=18 PL:GT:GQ 43,9,0:1/1:63 chr2a 55464464 . T C 26.1 . DP=7;AF1=0.9966;CI95=0.5,1;DP4=5,0,2,0;MQ=26;PV4=1,1,1,1 PL:GT:GQ 55,1,0:1/1:23 chr2a 63107673 . T A 70.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34 PL:GT:GQ 103,12,0:1/1:72 chr2a 63141732 . A T 22.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 54,6,0:1/1:49 chr2a 63141910 . G A 3.41 . DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr2a 63141911 . C T 9.55 . DP=16;AF1=0.5031;CI95=0.5,0.5;DP4=0,2,0,3;MQ=33;PV4=1,0.43,1,1 PL:GT:GQ 39,0,19:0/1:22 chr2a 63143543 . C T 28 . DP=18;AF1=1;CI95=1,1;DP4=0,1,0,17;MQ=16;PV4=1,1,1,1 PL:GT:GQ 61,42,0:1/1:99 chr2a 66419805 . G A 3.69 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 34,15,0:1/1:75 chr2a 66563922 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr2a 67719136 . C T 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 71,6,0:1/1:49 chr2a 72781453 . A C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr2a 76733211 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr2a 78190502 . A C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr2a 85021209 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr2a 88554861 . A T 39 . DP=74;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=46;PV4=1,1,1,1 PL:GT:GQ 69,0,92:0/1:72 chr2a 88554877 . A G 92 . DP=90;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,13;MQ=41;PV4=1,0.3,1,1 PL:GT:GQ 122,0,128:0/1:99 chr2a 88824857 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr2a 93546675 . C T 26 . DP=6;AF1=0.5;CI95=0.5,0.5;DP4=4,0,2,0;MQ=46;PV4=1,1,1,1 PL:GT:GQ 56,0,87:0/1:59 chr2a 94788853 . A G 34.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 67,15,0:1/1:75 chr2a 96738146 . T C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr2a 102737384 . A G 12.3 . DP=18;AF1=1;CI95=1,1;DP4=0,0,18,0;MQ=11 PL:GT:GQ 45,54,0:1/1:99 chr2a 103407172 . A G 35 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=19 PL:GT:GQ 68,24,0:1/1:96 chr2a 105774580 . T G 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=30 PL:GT:GQ 135,39,0:1/1:99 chr2a 106376301 . C G 24.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19 PL:GT:GQ 57,18,0:1/1:90 chr2a 106376315 . C T 8.75 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19 PL:GT:GQ 41,18,0:1/1:90 chr2a 112422267 . C T 30 . DP=20;AF1=0.5;CI95=0.5,0.5;DP4=14,0,5,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 60,0,131:0/1:63 chr2b 3049384 . A C 14.9 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 3049385 . G C 14.9 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 3049406 . C G 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=36 PL:GT:GQ 135,18,0:1/1:90 chr2b 4213802 . T C 89.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr2b 5022895 . G A 66 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=49 PL:GT:GQ 99,30,0:1/1:99 chr2b 6037666 . G T 56 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=17 PL:GT:GQ 89,39,0:1/1:99 chr2b 13656952 . G A 19.2 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=21 PL:GT:GQ 52,18,0:1/1:90 chr2b 15026944 . A G 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 37,6,0:1/1:49 chr2b 23362613 . A G 5.64 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 37,15,0:1/1:75 chr2b 45947861 . C G 68 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=50 PL:GT:GQ 101,33,0:1/1:99 chr2b 46597824 . T C 65.6 . DP=39;AF1=0.5939;CI95=0.5,1;DP4=23,0,10,0;MQ=22;PV4=1,0.014,1,1 PL:GT:GQ 95,0,5:0/1:7 chr2b 49665191 . G T 34.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37 PL:GT:GQ 67,21,0:1/1:84 chr2b 61001546 . A G 48 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=26 PL:GT:GQ 81,24,0:1/1:96 chr2b 88502851 . T C 4.77 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=37;PV4=1,1,0.46,1 PL:GT:GQ 33,0,34:0/1:33 chr2b 91675431 . C T 30 . DP=14;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=27 PL:GT:GQ 63,24,0:1/1:96 chr2b 91870148 . T G 67 . DP=14;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=47;PV4=1,1,1,1 PL:GT:GQ 100,31,0:1/1:99 chr2b 97066826 . G A 20.1 . DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=0,6,0,2;MQ=31;PV4=1,1,1,1 PL:GT:GQ 50,0,35:0/1:38 chr2b 97670822 . G A 4.85 . DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=18 PL:GT:GQ 36,18,0:1/1:90 chr2b 102773175 . A G 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 49,9,0:1/1:63 chr2b 109805532 . T C 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=45 PL:GT:GQ 176,24,0:1/1:96 chr2b 110841448 . A G 11.1 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 42,6,0:1/1:49 chr2b 123217025 . T C 31.5 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=37 PL:GT:GQ 64,12,0:1/1:72 chr2b 123263214 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 43,9,0:1/1:63 chr2b 127747292 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=52 PL:GT:GQ 100,9,0:1/1:63 chr2b 130121958 . A G 89.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 122,15,0:1/1:75 chr2b 130253633 . A G 14.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 130692761 . C T 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=51 PL:GT:GQ 82,18,0:1/1:90 chr2b 130743365 . A G 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42 PL:GT:GQ 140,15,0:1/1:75 chr2b 131553874 . A C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37 PL:GT:GQ 43,9,0:1/1:63 chr2b 131716894 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40 PL:GT:GQ 137,24,0:1/1:96 chr2b 131716936 . G A 99 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=36 PL:GT:GQ 173,36,0:1/1:99 chr2b 131716952 . A G 99 . DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,14;MQ=36;PV4=1,1,1,1 PL:GT:GQ 152,0,43:0/1:46 chr2b 133360184 . C T 99 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,20;MQ=32 PL:GT:GQ 163,60,0:1/1:99 chr2b 133644741 . T A 16.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=27 PL:GT:GQ 49,15,0:1/1:75 chr2b 133720595 . T C 41 . DP=15;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=29 PL:GT:GQ 74,36,0:1/1:99 chr2b 133727192 . C T 19.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 52,15,0:1/1:75 chr2b 133727260 . G A 3.56 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18 PL:GT:GQ 34,24,0:1/1:95 chr2b 133800294 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=23 PL:GT:GQ 40,6,0:1/1:49 chr2b 134582754 . A C 56.1 . DP=37;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=36 PL:GT:GQ 89,21,0:1/1:84 chr2b 134582763 . G C 78 . DP=37;AF1=1;CI95=1,1;DP4=0,0,0,36;MQ=34 PL:GT:GQ 111,108,0:1/1:99 chr2b 134809668 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr3 527814 . C G 46 . DP=9;AF1=0.5;CI95=0.5,0.5;DP4=6,0,3,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 76,0,106:0/1:79 chr3 559510 . G A 38 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=10,0,17,0;MQ=28;PV4=1,1,0.014,1 PL:GT:GQ 68,0,111:0/1:71 chr3 879433 . T G 32 . DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 62,0,34:0/1:37 chr3 1809645 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr3 3235812 . C T 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 38,6,0:1/1:49 chr3 3250176 . A G 83 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=32 PL:GT:GQ 116,24,0:1/1:96 chr3 5049073 . T A 99 . DP=25;AF1=0.5;CI95=0.5,0.5;DP4=16,0,9,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 136,0,129:0/1:99 chr3 5142874 . G A 99 . DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=28 PL:GT:GQ 179,114,0:1/1:99 chr3 5554864 . T C 3.54 . DP=7;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,3;MQ=27;PV4=1,1,1,1 PL:GT:GQ 31,0,35:0/1:33 chr3 5749648 . G A 21.2 . DP=26;AF1=0.7303;CI95=0.5,1;DP4=0,7,0,7;MQ=26;PV4=1,0.16,1,0.17 PL:GT:GQ 50,0,2:0/1:3 chr3 16451708 . A T 71.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38 PL:GT:GQ 104,15,0:1/1:75 chr3 23410276 . G A 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 140,15,0:1/1:75 chr3 51368824 . A G 28 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 60,9,0:1/1:63 chr3 53000453 . A G 54 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19 PL:GT:GQ 87,30,0:1/1:99 chr3 53000463 . A G 54 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19 PL:GT:GQ 87,30,0:1/1:99 chr3 59077423 . C T 77.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=33 PL:GT:GQ 110,15,0:1/1:75 chr3 60040501 . T C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 43,9,0:1/1:63 chr3 64203481 . A G 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 66,12,0:1/1:72 chr3 67947441 . C T 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr3 76372631 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 76,9,0:1/1:63 chr3 80611316 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr3 81554381 . G T 17.6 . DP=24;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26 PL:GT:GQ 50,12,0:1/1:72 chr3 87614647 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr3 93900455 . A T 11.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=13 PL:GT:GQ 44,15,0:1/1:75 chr3 96174457 . A G 4.11 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=24 PL:GT:GQ 34,9,0:1/1:63 chr3 96215569 . A C 3.41 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr3 96587998 . A C 7.08 . DP=9;AF1=1;CI95=1,1;DP4=0,0,6,0;MQ=17 PL:GT:GQ 39,18,0:1/1:90 chr3 99711220 . A C 12.8 . DP=11;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 42,2,0:1/1:37 chr3 99789741 . C G 99 . DP=18;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=47 PL:GT:GQ 210,51,0:1/1:99 chr3 103667651 . A C 3.98 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 33,6,0:1/1:49 chr3 104604896 . G C 55 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 87,9,0:1/1:63 chr3 104997217 . G A 33.1 . DP=18;AF1=1;CI95=1,1;DP4=1,0,16,0;MQ=34;PV4=1,3e-10,0.17,0.36 PL:GT:GQ 66,19,0:1/1:76 chr3 106097816 . A G 28 . DP=15;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=26 PL:GT:GQ 61,45,0:1/1:99 chr3 106822259 . G C 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=50 PL:GT:GQ 140,15,0:1/1:75 chr3 109946413 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 44,6,0:1/1:49 chr3 121238963 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr3 126248567 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 45,6,0:1/1:49 chr3 129733836 . A G 6.2 . DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.02,0.31,1 PL:GT:GQ 35,0,28:0/1:30 chr3 131372785 . C T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=34 PL:GT:GQ 76,9,0:1/1:63 chr3 132290987 . C T 22 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=45 PL:GT:GQ 54,9,0:1/1:63 chr3 136054421 . C T 73 . DP=82;AF1=1;CI95=1,1;DP4=0,0,78,0;MQ=28 PL:GT:GQ 106,235,0:1/1:99 chr3 141075246 . G A 30.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41 PL:GT:GQ 62,6,0:1/1:49 chr3 141075262 . T G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41 PL:GT:GQ 73,6,0:1/1:49 chr3 141430649 . G T 81.8 . DP=6;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=41;PV4=1,0.34,1,0.25 PL:GT:GQ 113,6,0:1/1:49 chr3 143617747 . G T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 54,9,0:1/1:63 chr3 163576128 . C T 5.6 . DP=4;AF1=0.7302;CI95=0.5,1;DP4=2,0,2,0;MQ=23;PV4=1,1,1,1 PL:GT:GQ 33,0,2:0/1:3 chr3 163839828 . A G 4.45 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26 PL:GT:GQ 35,12,0:1/1:72 chr3 175839340 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr3 190193258 . G T 3.98 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 33,6,0:1/1:49 chr3 190777007 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr3 190970350 . A G 61 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=37 PL:GT:GQ 94,30,0:1/1:99 chr3 198686408 . G A 36.6 . DP=17;AF1=1;CI95=0.5,1;DP4=0,1,0,16;MQ=25;PV4=1,1,0.026,1 PL:GT:GQ 69,11,0:1/1:66 chr3 199277478 . T C 3.61 . DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=21 PL:GT:GQ 34,18,0:1/1:90 chr3 199780181 . G T 77 . DP=45;AF1=0.5;CI95=0.5,0.5;DP4=0,35,0,10;MQ=33;PV4=1,1,1,1 PL:GT:GQ 107,0,114:0/1:99 chr3 199889335 . A C 9.54 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18 PL:GT:GQ 42,24,0:1/1:96 chr3 200018161 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr4 195475 . A G 13 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 44,6,0:1/1:49 chr4 639141 . C A 14.9 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr4 639152 . C T 15.2 . DP=17;AF1=0.5016;CI95=0.5,0.5;DP4=0,2,0,2;MQ=33;PV4=1,1,1,1 PL:GT:GQ 45,0,22:0/1:25 chr4 986497 . G T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=33 PL:GT:GQ 163,30,0:1/1:99 chr4 986516 . C T 55.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37 PL:GT:GQ 88,21,0:1/1:84 chr4 1207485 . A C 14.9 . DP=22;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 46,6,0:1/1:49 chr4 1323502 . G A 13.2 . DP=13;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=22 PL:GT:GQ 46,33,0:1/1:99 chr4 1613521 . G A 89 . DP=16;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=32 PL:GT:GQ 122,48,0:1/1:99 chr4 1748790 . C T 38 . DP=21;AF1=0.5005;CI95=0.5,0.5;DP4=6,0,8,0;MQ=40;PV4=1,0.09,1,1 PL:GT:GQ 68,0,27:0/1:30 chr4 2255732 . T C 99 . DP=29;AF1=1;CI95=1,1;DP4=0,0,28,0;MQ=31 PL:GT:GQ 186,84,0:1/1:99 chr4 3010159 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr4 3545023 . A G 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=38 PL:GT:GQ 145,27,0:1/1:99 chr4 3586344 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr4 3879337 . A G 16.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 49,12,0:1/1:72 chr4 3940733 . A G 47.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 80,15,0:1/1:75 chr4 4410338 . T C 13.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31 PL:GT:GQ 46,15,0:1/1:75 chr4 4796408 . T C 41 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=17 PL:GT:GQ 74,48,0:1/1:99 chr4 4796414 . A G 11.3 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=17 PL:GT:GQ 44,45,0:1/1:99 chr4 6436959 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr4 9494256 . T C 3.41 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37 PL:GT:GQ 32,6,0:1/1:49 chr4 24881479 . G A 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 46,9,0:1/1:63 chr4 26128644 . A G 23 . DP=18;AF1=0.5006;CI95=0.5,0.5;DP4=8,0,10,0;MQ=22;PV4=1,1,1,1 PL:GT:GQ 53,0,26:0/1:29 chr4 42109100 . G A 17.1 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 49,9,0:1/1:63 chr4 42309652 . C T 68 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr4 46913966 . C T 9.08 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=16 PL:GT:GQ 41,12,0:1/1:72 chr4 50335142 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr4 51658550 . C A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr4 58258023 . T C 26 . DP=5;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,2;MQ=34;PV4=1,1,1,0.05 PL:GT:GQ 56,0,32:0/1:35 chr4 59219112 . C A 42.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50 PL:GT:GQ 75,12,0:1/1:72 chr4 62746067 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr4 67404338 . G T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39 PL:GT:GQ 66,12,0:1/1:72 chr4 73353380 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr4 73946294 . G C 4.77 . DP=51;AF1=0.4999;CI95=0.5,0.5;DP4=0,5,0,3;MQ=40;PV4=1,0.19,0.37,0.11 PL:GT:GQ 33,0,64:0/1:36 chr4 79607484 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr4 82337365 . G C 90 . DP=54;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=28 PL:GT:GQ 123,48,0:1/1:99 chr4 82653801 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 34,9,0:1/1:63 chr4 87130164 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 43,9,0:1/1:63 chr4 87130176 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 43,9,0:1/1:63 chr4 91459729 . C A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr4 96130778 . G C 99 . DP=19;AF1=1;CI95=1,1;DP4=0,0,0,19;MQ=45 PL:GT:GQ 211,57,0:1/1:99 chr4 100709417 . A G 45.1 . DP=16;AF1=0.505;CI95=0.5,0.5;DP4=12,0,4,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 75,0,17:0/1:20 chr4 107276770 . C T 70 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=31;PV4=1,1,1,1 PL:GT:GQ 100,0,97:0/1:98 chr4 115327550 . G C 42 . DP=67;AF1=1;CI95=1,1;DP4=0,1,0,66;MQ=35;PV4=1,3.2e-24,0.13,1 PL:GT:GQ 75,162,0:1/1:99 chr4 136558502 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr4 159572459 . G A 15.1 . DP=126;AF1=0.5;CI95=0.5,0.5;DP4=0,69,0,57;MQ=39;PV4=1,4.1e-96,0.077,1 PL:GT:GQ 45,0,175:0/1:48 chr4 174968484 . G C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 40,6,0:1/1:49 chr4 175030633 . T C 14.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=29 PL:GT:GQ 47,18,0:1/1:90 chr4 183410027 . G T 6.2 . DP=31;AF1=0.5003;CI95=0.5,0.5;DP4=2,0,2,0;MQ=45;PV4=1,0.035,1,0.21 PL:GT:GQ 35,0,28:0/1:30 chr4 190907368 . T C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50 PL:GT:GQ 66,12,0:1/1:72 chr4 192175690 . A G 76.8 . DP=7;AF1=0.95;CI95=0.5,1;DP4=0,3,0,4;MQ=35;PV4=1,1,1,1 PL:GT:GQ 105,0,0:1/1:10 chr4 192673268 . G A 14.2 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=22 PL:GT:GQ 47,27,0:1/1:99 chr4 192943966 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr4 195460104 . C G 23.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=19 PL:GT:GQ 56,24,0:1/1:96 chr4 198277830 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr5 170098 . A G 13 . DP=12;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 44,6,0:1/1:49 chr5 395814 . T C 4.77 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,0.48,1 PL:GT:GQ 33,0,33:0/1:33 chr5 414024 . T A 10.4 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=20 PL:GT:GQ 42,9,0:1/1:63 chr5 496767 . T C 13.9 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr5 805676 . C G 45 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=32 PL:GT:GQ 78,51,0:1/1:99 chr5 1252896 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr5 1418370 . G A 3.65 . DP=8;AF1=0.7301;CI95=0.5,1;DP4=4,0,4,0;MQ=13;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr5 1494911 . G C 62 . DP=9;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=46 PL:GT:GQ 95,24,0:1/1:96 chr5 1494932 . C T 6.98 . DP=8;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=46;PV4=1,0.1,0.077,1 PL:GT:GQ 36,0,31:0/1:33 chr5 1506037 . T C 24.1 . DP=24;AF1=1;CI95=0.5,1;DP4=11,0,13,0;MQ=16;PV4=1,1,1,1 PL:GT:GQ 55,5,0:1/1:46 chr5 1509406 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 73,6,0:1/1:49 chr5 1733649 . A G 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=47 PL:GT:GQ 212,75,0:1/1:99 chr5 1747304 . A G 12.3 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19 PL:GT:GQ 45,36,0:1/1:99 chr5 1747308 . C A 44 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19 PL:GT:GQ 77,36,0:1/1:99 chr5 3519783 . C T 21.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18 PL:GT:GQ 54,24,0:1/1:96 chr5 4101593 . A G 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43 PL:GT:GQ 102,12,0:1/1:72 chr5 7204332 . T A 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=24 PL:GT:GQ 34,6,0:1/1:49 chr5 11510398 . A C 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=51;PV4=1,1,0,1 PL:GT:GQ 64,0,31:0/1:34 chr5 15406720 . T C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 36,6,0:1/1:49 chr5 25152417 . C A 10.9 . DP=28;AF1=0.5718;CI95=0.5,1;DP4=0,2,0,6;MQ=25;PV4=1,1,0.21,1 PL:GT:GQ 40,0,6:0/1:8 chr5 39072637 . A G 35.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=50 PL:GT:GQ 68,15,0:1/1:75 chr5 46022699 . G A 44 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 76,9,0:1/1:63 chr5 55664181 . C G 10.4 . DP=8;AF1=0.9999;CI95=0.5,1;DP4=3,0,5,0;MQ=18;PV4=1,1,1,1 PL:GT:GQ 40,3,0:1/1:41 chr5 56253386 . T C 50.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=36 PL:GT:GQ 83,21,0:1/1:84 chr5 56253447 . C T 42.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=45 PL:GT:GQ 75,12,0:1/1:72 chr5 71950166 . G T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr5 72703090 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 40,6,0:1/1:49 chr5 73570280 . G T 5.45 . DP=41;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=15 PL:GT:GQ 37,123,0:1/1:99 chr5 73701762 . G T 40.8 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 72,6,0:1/1:49 chr5 76956867 . T C 10.2 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 41,6,0:1/1:49 chr5 79097961 . C G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 54,9,0:1/1:63 chr5 87026167 . T C 22 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr5 97680525 . T C 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23 PL:GT:GQ 33,12,0:1/1:72 chr5 100674737 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr5 105389966 . T C 3.52 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=15 PL:GT:GQ 33,9,0:1/1:63 chr5 109998341 . A C 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr5 120629105 . C T 6.79 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 37,6,0:1/1:49 chr5 128383954 . C T 23 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,3.3e-07,1,1 PL:GT:GQ 53,0,98:0/1:56 chr5 133925142 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr5 135375404 . T C 11.8 . DP=6;AF1=1;CI95=0.5,1;DP4=1,0,3,0;MQ=31;PV4=1,0.03,1,1 PL:GT:GQ 42,4,0:1/1:45 chr5 136498281 . T G 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr5 136717285 . A G 82.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 115,12,0:1/1:72 chr5 136910734 . G A 62 . DP=19;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=23;PV4=1,1,1,1 PL:GT:GQ 95,31,0:1/1:99 chr5 141208149 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr5 148056348 . C A 37.1 . DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=38;PV4=1,1,1,1 PL:GT:GQ 66,1,0:1/1:23 chr5 151941534 . G T 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34 PL:GT:GQ 79,12,0:1/1:72 chr5 159967229 . G C 22.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 55,12,0:1/1:72 chr5 174024541 . T G 29.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 59,2,0:1/1:37 chr5 175525290 . A G 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=20 PL:GT:GQ 33,12,0:1/1:72 chr5 175988954 . A C 14.2 . DP=23;AF1=0.5;CI95=0.5,0.5;DP4=0,6,0,4;MQ=47;PV4=1,1,0.2,1 PL:GT:GQ 44,0,76:0/1:47 chr5 176782226 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr5 179132834 . C G 99 . DP=28;AF1=1;CI95=1,1;DP4=0,0,0,28;MQ=41 PL:GT:GQ 207,84,0:1/1:99 chr5 180155809 . G C 3.01 . DP=36;AF1=0.4997;CI95=0.5,0.5;DP4=25,0,9,0;MQ=35;PV4=1,1e-15,1,1 PL:GT:GQ 30,0,121:0/1:33 chr5 181282819 . T G 38.3 . DP=11;AF1=1;CI95=0.5,1;DP4=0,2,0,9;MQ=23;PV4=1,1,1,1 PL:GT:GQ 71,14,0:1/1:70 chr5 182426125 . G C 29 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26 PL:GT:GQ 61,9,0:1/1:63 chr5 182443682 . G A 3.69 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=21 PL:GT:GQ 34,15,0:1/1:75 chr5 183008993 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr5 183312016 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr6_cox_hap1 519146 . G A 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30 PL:GT:GQ 49,9,0:1/1:63 chr6_cox_hap1 687497 . A G 33 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,0.0016,1,1 PL:GT:GQ 63,3,0:1/1:41 chr6_qbl_hap2 120066 . T C 99 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 139,27,0:1/1:99 chr6 277954 . C T 53 . DP=41;AF1=1;CI95=1,1;DP4=4,0,37,0;MQ=19;PV4=1,1,0.3,1 PL:GT:GQ 86,49,0:1/1:99 chr6 593158 . A G 4.61 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 34,6,0:1/1:49 chr6 2865562 . T G 25 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=23 PL:GT:GQ 58,27,0:1/1:99 chr6 3751403 . G A 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32 PL:GT:GQ 75,15,0:1/1:75 chr6 3884989 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr6 4127278 . A T 13.9 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr6 5887783 . C G 99 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34 PL:GT:GQ 142,21,0:1/1:84 chr6 5887811 . C T 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34 PL:GT:GQ 88,21,0:1/1:84 chr6 6937170 . G C 99 . DP=47;AF1=1;CI95=1,1;DP4=0,0,0,47;MQ=28 PL:GT:GQ 157,141,0:1/1:99 chr6 7262317 . C T 13.2 . DP=50;AF1=0.5;CI95=0.5,0.5;DP4=21,0,9,0;MQ=36;PV4=1,4e-05,0.17,0.26 PL:GT:GQ 43,0,158:0/1:46 chr6 7533214 . A G 10.4 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 42,9,0:1/1:63 chr6 20979907 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=38 PL:GT:GQ 76,9,0:1/1:63 chr6 22321632 . A G 41 . DP=5;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=46;PV4=1,0.24,0.19,0.33 PL:GT:GQ 71,0,28:0/1:31 chr6 25352296 . G A 7.8 . DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=0,1,0,3;MQ=38;PV4=1,1,0.16,1 PL:GT:GQ 37,0,28:0/1:30 chr6 26298040 . T A 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=48;PV4=1,1,0.21,0.33 PL:GT:GQ 64,0,31:0/1:34 chr6 33428755 . G A 70 . DP=14;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=32 PL:GT:GQ 103,27,0:1/1:99 chr6 39512099 . G A 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=50 PL:GT:GQ 88,21,0:1/1:84 chr6 39961094 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr6 40452120 . A G 40.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 72,6,0:1/1:49 chr6 43204766 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=51 PL:GT:GQ 176,24,0:1/1:96 chr6 52696512 . C T 70 . DP=76;AF1=0.5;CI95=0.5,0.5;DP4=0,34,0,42;MQ=18;PV4=1,0.11,1,1 PL:GT:GQ 100,0,51:0/1:54 chr6 53785550 . A G 99 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=46 PL:GT:GQ 190,30,0:1/1:99 chr6 53897484 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr6 57038290 . C T 10.2 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 41,6,0:1/1:49 chr6 62925087 . G C 35 . DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,4,0;MQ=36;PV4=1,1,0.2,1 PL:GT:GQ 65,0,25:0/1:28 chr6 62925094 . T C 25.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36 PL:GT:GQ 58,15,0:1/1:75 chr6 70834405 . G A 72.1 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=29 PL:GT:GQ 105,21,0:1/1:84 chr6 71026058 . C T 48.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=42 PL:GT:GQ 81,18,0:1/1:90 chr6 74420752 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 76,9,0:1/1:63 chr6 77498624 . T C 16.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 48,6,0:1/1:49 chr6 80416836 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr6 113611590 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46 PL:GT:GQ 100,9,0:1/1:63 chr6 119308431 . T C 38.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40 PL:GT:GQ 71,12,0:1/1:72 chr6 151758592 . T C 3.07 . DP=17;AF1=0.9966;CI95=0.5,1;DP4=0,8,0,9;MQ=13;PV4=1,1,1,1 PL:GT:GQ 29,1,0:1/1:23 chr6 151759358 . A G 99 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=12,0,15,0;MQ=44;PV4=1,1,1,0.19 PL:GT:GQ 171,0,128:0/1:99 chr6 154741755 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr6 161061053 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52 PL:GT:GQ 40,6,0:1/1:49 chr6 161474189 . C T 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 36,6,0:1/1:49 chr6 164304657 . C T 10.4 . DP=63;AF1=0.5;CI95=0.5,0.5;DP4=0,29,0,19;MQ=22;PV4=1,7.7e-11,1,0.049 PL:GT:GQ 40,0,37:0/1:38 chr6 164703105 . T C 99 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=40 PL:GT:GQ 165,30,0:1/1:99 chr6 167518328 . A G 78 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=27,0,14,0;MQ=33;PV4=1,0.026,0.43,0.056 PL:GT:GQ 108,0,149:0/1:99 chr6 169906323 . G A 41.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr6 171893912 . G A 69.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33 PL:GT:GQ 102,15,0:1/1:75 chr6 173631604 . A G 6.98 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=4,0,3,0;MQ=37;PV4=1,0.069,1,1 PL:GT:GQ 36,0,34:0/1:35 chr7 835856 . C T 27.5 . DP=13;AF1=0.9998;CI95=0.5,1;DP4=4,0,6,0;MQ=23;PV4=1,0.46,1,1 PL:GT:GQ 57,2,0:1/1:37 chr7 1046005 . C T 11.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 43,9,0:1/1:63 chr7 1564339 . C T 71 . DP=66;AF1=0.5;CI95=0.5,0.5;DP4=36,0,24,0;MQ=29;PV4=1,1,0.35,1 PL:GT:GQ 101,0,134:0/1:99 chr7 1806266 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr7 1936013 . G T 7.77 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=17 PL:GT:GQ 39,9,0:1/1:63 chr7 2319532 . C A 4.11 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=14 PL:GT:GQ 34,9,0:1/1:63 chr7 2682121 . C T 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr7 3248116 . T C 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=37;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr7 3624766 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 40,6,0:1/1:49 chr7 5291140 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr7 5314457 . C A 3.56 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18 PL:GT:GQ 34,24,0:1/1:95 chr7 5595072 . T A 79 . DP=13;AF1=0.5;CI95=0.5,0.5;DP4=8,0,5,0;MQ=31;PV4=1,1,1,1 PL:GT:GQ 109,0,57:0/1:60 chr7 5646060 . G C 7.79 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=10 PL:GT:GQ 40,30,0:1/1:99 chr7 6056816 . C G 7.08 . DP=6;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=23;PV4=1,1,1,1 PL:GT:GQ 35,1,0:1/1:23 chr7 6412641 . C T 40 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33 PL:GT:GQ 73,33,0:1/1:99 chr7 6766874 . A G 34.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=43 PL:GT:GQ 67,15,0:1/1:75 chr7 8482729 . C T 5.08 . DP=16;AF1=0.8276;CI95=0.5,1;DP4=3,0,3,0;MQ=22;PV4=1,1,1,0.19 PL:GT:GQ 32,0,1:1/1:5 chr7 9238362 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr7 9687781 . G A 33 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,12;MQ=48;PV4=1,6.5e-38,1,1 PL:GT:GQ 63,0,170:0/1:66 chr7 9752803 . A T 14.2 . DP=17;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18 PL:GT:GQ 47,27,0:1/1:99 chr7 10240910 . T C 45.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 78,12,0:1/1:72 chr7 11046187 . C T 86.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=47 PL:GT:GQ 119,12,0:1/1:72 chr7 11548207 . C G 14.6 . DP=13;AF1=1;CI95=0.5,1;DP4=6,1,0,5;MQ=18;PV4=0.015,1,1,1 PL:GT:GQ 46,7,0:1/1:57 chr7 11580317 . C T 42 . DP=12;AF1=1;CI95=1,1;DP4=0,1,0,10;MQ=22;PV4=1,1,1,1 PL:GT:GQ 75,23,0:1/1:92 chr7 11585384 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr7 13498356 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 73,6,0:1/1:49 chr7 13500887 . G A 15.1 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=22 PL:GT:GQ 48,30,0:1/1:99 chr7 13827079 . C T 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 36,6,0:1/1:49 chr7 14403976 . T G 59 . DP=30;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39 PL:GT:GQ 92,24,0:1/1:96 chr7 14756588 . A G 44 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,5.3e-18,1,1 PL:GT:GQ 74,0,70:0/1:72 chr7 14756619 . T G 44 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,6.4e-10,1,1 PL:GT:GQ 74,0,70:0/1:72 chr7 36734598 . A C 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 42,6,0:1/1:49 chr7 36734599 . A T 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 42,6,0:1/1:49 chr7 36734603 . G C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 40,6,0:1/1:49 chr7 40634921 . A C 55 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=39 PL:GT:GQ 88,39,0:1/1:99 chr7 48271285 . A T 73 . DP=15;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=25 PL:GT:GQ 106,30,0:1/1:99 chr7 56264700 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr7 62326003 . C A 26.1 . DP=35;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28 PL:GT:GQ 59,18,0:1/1:90 chr7 109468934 . T G 5.13 . DP=10;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=39;PV4=1,0.031,1,1 PL:GT:GQ 33,2,0:1/1:37 chr7 110208327 . C G 16.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 48,6,0:1/1:49 chr7 125654934 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=27 PL:GT:GQ 34,9,0:1/1:63 chr7 125770209 . A C 32 . DP=31;AF1=0.5;CI95=0.5,0.5;DP4=11,0,13,0;MQ=34;PV4=1,0.00017,0.16,0.22 PL:GT:GQ 62,0,105:0/1:65 chr7 125770265 . G C 36 . DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,0.0047,0.016,0.035 PL:GT:GQ 66,0,110:0/1:69 chr7 126687042 . A G 21.1 . DP=36;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=22 PL:GT:GQ 54,21,0:1/1:84 chr7 132292897 . G T 99 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=43 PL:GT:GQ 167,21,0:1/1:84 chr7 132334562 . A C 23 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=23 PL:GT:GQ 56,30,0:1/1:99 chr7 132431838 . C T 13.3 . DP=5;AF1=1;CI95=0.5,1;DP4=1,0,4,0;MQ=23;PV4=1,1,1,1 PL:GT:GQ 44,5,0:1/1:46 chr7 136324945 . T C 13.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 46,12,0:1/1:72 chr7 136957634 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr7 141746871 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 40,6,0:1/1:49 chr7 146831870 . C T 4.77 . DP=14;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=37;PV4=1,0.0029,0.28,1 PL:GT:GQ 33,0,28:0/1:30 chr7 147142770 . T C 45 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=31 PL:GT:GQ 77,9,0:1/1:63 chr7 147713906 . C T 4.77 . DP=8;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,4,0;MQ=35;PV4=1,8.9e-06,0.48,0.27 PL:GT:GQ 33,0,29:0/1:31 chr7 148742642 . G A 68 . DP=14;AF1=0.5032;CI95=0.5,0.5;DP4=4,0,10,0;MQ=28;PV4=1,1,1,1 PL:GT:GQ 98,0,19:0/1:22 chr7 148879148 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr7 149484407 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr7 152444478 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 44,6,0:1/1:49 chr7 154106613 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=51 PL:GT:GQ 100,9,0:1/1:63 chr7 154776891 . G T 14.4 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 47,15,0:1/1:75 chr7 155882061 . A C 29 . DP=24;AF1=0.502;CI95=0.5,0.5;DP4=0,1,0,4;MQ=46;PV4=1,0.018,0.15,0.29 PL:GT:GQ 59,0,21:0/1:24 chr7 155956844 . G C 23 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=38;PV4=1,1,0.38,1 PL:GT:GQ 53,0,103:0/1:56 chr7 156277694 . G A 62 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=46 PL:GT:GQ 95,24,0:1/1:96 chr7 156720588 . T C 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr7 156807649 . T C 3.01 . DP=30;AF1=0.4997;CI95=0.5,0.5;DP4=0,4,0,3;MQ=43;PV4=1,0.16,0.15,1 PL:GT:GQ 30,0,72:0/1:33 chr7 157331292 . G T 43.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=34 PL:GT:GQ 76,21,0:1/1:84 chr7 157382957 . T C 33.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 66,12,0:1/1:72 chr8 556382 . A G 37.1 . DP=5;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=31;PV4=1,1,1,1 PL:GT:GQ 66,1,0:1/1:23 chr8 1661673 . T C 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr8 7379751 . C A 6.24 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19 PL:GT:GQ 38,21,0:1/1:84 chr8 8160505 . A T 68.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 101,12,0:1/1:72 chr8 8160508 . C T 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 57,12,0:1/1:72 chr8 16781011 . A G 55.5 . DP=9;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34 PL:GT:GQ 88,12,0:1/1:72 chr8 18716499 . A T 20 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,4,0,2;MQ=29;PV4=1,1,1,1 PL:GT:GQ 50,0,52:0/1:51 chr8 23326483 . A G 60 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47 PL:GT:GQ 92,9,0:1/1:63 chr8 25842819 . T A 12 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 43,6,0:1/1:49 chr8 26300279 . T C 34 . DP=44;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=21 PL:GT:GQ 67,123,0:1/1:99 chr8 29673470 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 73,6,0:1/1:49 chr8 29673473 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 40,6,0:1/1:49 chr8 31685466 . C T 34 . DP=17;AF1=0.5;CI95=0.5,0.5;DP4=10,0,5,0;MQ=28;PV4=1,0.072,1,0.36 PL:GT:GQ 64,0,50:0/1:53 chr8 37378739 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr8 51325952 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr8 59221963 . G A 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr8 62764995 . T G 20 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=32 PL:GT:GQ 52,9,0:1/1:63 chr8 63157426 . C G 41.6 . DP=22;AF1=1;CI95=0.5,1;DP4=0,7,0,15;MQ=19;PV4=1,1,1,0.25 PL:GT:GQ 74,11,0:1/1:66 chr8 68710444 . G A 30 . DP=5;AF1=0.6671;CI95=0.5,1;DP4=3,0,2,0;MQ=32;PV4=1,1,1,1 PL:GT:GQ 59,0,3:0/1:5 chr8 76416560 . G A 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=46 PL:GT:GQ 122,12,0:1/1:72 chr8 81425275 . T G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr8 89842286 . G C 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30 PL:GT:GQ 34,6,0:1/1:49 chr8 100926281 . G A 38 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 70,9,0:1/1:63 chr8 102746002 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr8 107850176 . C T 43.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=45 PL:GT:GQ 76,18,0:1/1:90 chr8 109966441 . T C 27.3 . DP=9;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38 PL:GT:GQ 60,15,0:1/1:75 chr8 118811716 . G T 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=50 PL:GT:GQ 155,18,0:1/1:90 chr8 119440254 . A T 58.5 . DP=5;AF1=0.8277;CI95=0.5,1;DP4=2,0,3,0;MQ=34;PV4=1,1,1,0.14 PL:GT:GQ 87,0,1:1/1:5 chr8 121236024 . G A 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 71,6,0:1/1:49 chr8 125489079 . C T 13 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr8 128502549 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr8 128502551 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr8 130951113 . G A 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=19 PL:GT:GQ 34,6,0:1/1:49 chr8 135307123 . G A 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 36,6,0:1/1:49 chr8 138814155 . C T 57.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 90,18,0:1/1:90 chr8 140566111 . A G 18.1 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=15 PL:GT:GQ 51,36,0:1/1:99 chr8 141586480 . T G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr8 143376712 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr8 150662729 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr8 150741294 . A G 25.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=34 PL:GT:GQ 58,18,0:1/1:90 chr8 150975618 . A G 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr8 151580103 . T C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=20 PL:GT:GQ 36,6,0:1/1:49 chr8 151634410 . G T 48 . DP=17;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,5;MQ=39;PV4=1,0.072,1,1 PL:GT:GQ 78,0,125:0/1:81 chr8 151709267 . G A 91.1 . DP=8;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=40;PV4=1,1,0.28,0.37 PL:GT:GQ 121,0,16:0/1:19 chr8 152636420 . G A 8.75 . DP=3;AF1=0.9966;CI95=0.5,1;DP4=0,1,0,2;MQ=30;PV4=1,1,1,1 PL:GT:GQ 37,1,0:1/1:23 chr8 152706967 . G A 3.01 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=16 PL:GT:GQ 33,30,0:1/1:99 chr8 152786522 . T C 80.1 . DP=16;AF1=0.5102;CI95=0.5,0.5;DP4=0,4,0,12;MQ=31;PV4=1,0.25,1,1 PL:GT:GQ 110,0,14:0/1:17 chr8 152863132 . T G 5.44 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30 PL:GT:GQ 36,9,0:1/1:63 chr9 23235268 . C T 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 43,6,0:1/1:49 chr9 26391176 . T C 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 47,6,0:1/1:49 chr9 26868232 . C G 63 . DP=20;AF1=0.5025;CI95=0.5,0.5;DP4=7,0,13,0;MQ=22;PV4=1,0.2,1,0.44 PL:GT:GQ 93,0,20:0/1:23 chr9 34223668 . C T 22 . DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,7;MQ=27;PV4=1,0.14,0.34,1 PL:GT:GQ 52,0,79:0/1:55 chr9 39696645 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr9 40654130 . T G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr9 41145321 . T G 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 79,12,0:1/1:72 chr9 42273483 . G A 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr9 55633192 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 58705807 . T C 70 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=24 PL:GT:GQ 103,30,0:1/1:99 chr9 61697149 . C G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 63152790 . A C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr9 63703913 . C G 90.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=38 PL:GT:GQ 123,21,0:1/1:84 chr9 65116068 . T C 70 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=49 PL:GT:GQ 103,39,0:1/1:99 chr9 71266598 . C A 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 33,6,0:1/1:49 chr9 73188677 . G T 52 . DP=294;AF1=1;CI95=1,1;DP4=44,0,245,0;MQ=33;PV4=1,0.28,0.0092,1 PL:GT:GQ 85,147,0:1/1:99 chr9 78854179 . G T 22 . DP=97;AF1=0.5;CI95=0.5,0.5;DP4=21,0,12,0;MQ=44;PV4=1,0.02,0.032,0.0033 PL:GT:GQ 52,0,158:0/1:55 chr9 82964679 . A C 13.2 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=36 PL:GT:GQ 45,9,0:1/1:63 chr9 84124545 . G T 57 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=2,0,3,0;MQ=49;PV4=1,1,0.024,1 PL:GT:GQ 87,0,59:0/1:62 chr9 86552862 . C T 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=26 PL:GT:GQ 47,15,0:1/1:75 chr9 87548941 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr9 89021101 . G A 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr9 90447825 . G A 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 40,6,0:1/1:49 chr9 92462035 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 40,6,0:1/1:49 chr9 93077294 . T G 5.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31 PL:GT:GQ 36,9,0:1/1:63 chr9 93998137 . G A 68 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46 PL:GT:GQ 100,9,0:1/1:63 chr9 93998148 . C T 21.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36 PL:GT:GQ 54,15,0:1/1:75 chr9 95028964 . C A 99 . DP=83;AF1=0.5;CI95=0.5,0.5;DP4=0,57,0,26;MQ=32;PV4=1,9.3e-08,1,0.092 PL:GT:GQ 134,0,120:0/1:99 chr9 103829155 . A G 33 . DP=96;AF1=1;CI95=1,1;DP4=0,0,96,0;MQ=16 PL:GT:GQ 66,255,0:1/1:99 chr9 104981331 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 73,6,0:1/1:49 chr9 111070656 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 117395657 . T C 16.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 49,15,0:1/1:75 chr9 117718907 . A G 46.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=29 PL:GT:GQ 79,18,0:1/1:90 chr9 119149161 . T C 3.14 . DP=65;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 33,15,0:1/1:75 chr9 124528802 . G A 78 . DP=23;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=25 PL:GT:GQ 111,39,0:1/1:99 chr9 126707903 . G A 26 . DP=37;AF1=0.5;CI95=0.5,0.5;DP4=0,21,0,8;MQ=46;PV4=1,2.6e-07,0.21,0.42 PL:GT:GQ 56,0,175:0/1:59 chr9 128700686 . C G 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 66,12,0:1/1:72 chr9 129084077 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr9 129116900 . A T 20 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 52,9,0:1/1:63 chr9 130290720 . C G 21.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 53,6,0:1/1:49 chr9 130306057 . C G 71 . DP=14;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=28 PL:GT:GQ 104,42,0:1/1:99 chr9 130528990 . G A 99 . DP=31;AF1=1;CI95=1,1;DP4=0,0,31,0;MQ=27 PL:GT:GQ 174,93,0:1/1:99 chr9 130529002 . A T 7.79 . DP=30;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=15 PL:GT:GQ 40,33,0:1/1:99 chr9 130639996 . A G 8.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 39,6,0:1/1:49 chr9 130704890 . A G 3.27 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=26 PL:GT:GQ 33,12,0:1/1:72 chr9 130708345 . G A 13.3 . DP=11;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=38;PV4=1,0.096,1,1 PL:GT:GQ 42,1,0:1/1:23 chr9 131001601 . T A 3.98 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 33,6,0:1/1:49 chr9 131058539 . T A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 44,6,0:1/1:49 chr9 131808965 . C T 42 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 75,27,0:1/1:99 chr9 132551867 . C T 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 49,9,0:1/1:63 chr9 132685120 . A G 4.75 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 35,9,0:1/1:63 chr9 133175050 . A G 18.1 . DP=30;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=20 PL:GT:GQ 51,51,0:1/1:99 chr9 133584978 . A G 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=45 PL:GT:GQ 212,75,0:1/1:99 chr9 133661895 . A G 99 . DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31 PL:GT:GQ 138,42,0:1/1:99 chr9 133670376 . T C 68 . DP=19;AF1=1;CI95=1,1;DP4=0,1,0,16;MQ=39;PV4=1,1.4e-20,1,1 PL:GT:GQ 101,39,0:1/1:99 chr9 133843777 . T C 99 . DP=9;AF1=0.5129;CI95=0.5,0.5;DP4=1,0,8,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 154,0,13:0/1:16 chr9 134017265 . G C 3.27 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=13 PL:GT:GQ 33,12,0:1/1:72 chr9 134105563 . T C 34.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=39 PL:GT:GQ 67,18,0:1/1:90 chr9 134608906 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr9 134861929 . T A 9.49 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 41,9,0:1/1:63 chr10 796662 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 54,9,0:1/1:63 chr10 1216716 . T A 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr10 1220781 . G A 21 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18 PL:GT:GQ 54,27,0:1/1:99 chr10 1225208 . T C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47 PL:GT:GQ 100,9,0:1/1:63 chr10 1727946 . T C 14.2 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27 PL:GT:GQ 47,21,0:1/1:84 chr10 5986542 . T C 83 . DP=93;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39 PL:GT:GQ 116,30,0:1/1:99 chr10 6436277 . G A 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 36,6,0:1/1:49 chr10 7704114 . C A 35 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=0,2,0,4;MQ=29;PV4=1,0.27,1,0.27 PL:GT:GQ 65,3,0:1/1:41 chr10 10881734 . A G 9.52 . DP=9;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=42;PV4=1,0.0026,0.14,1 PL:GT:GQ 39,0,91:0/1:42 chr10 13099383 . G A 27.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 60,12,0:1/1:72 chr10 15764077 . G C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr10 18091502 . T C 47 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 79,9,0:1/1:63 chr10 19645913 . A T 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 47,6,0:1/1:49 chr10 22845062 . C T 18.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=18 PL:GT:GQ 51,21,0:1/1:84 chr10 28282802 . T C 69 . DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=42 PL:GT:GQ 102,36,0:1/1:99 chr10 28496872 . T G 8.44 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 39,6,0:1/1:49 chr10 32746793 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr10 41437604 . T G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr10 43051239 . C T 6.98 . DP=3;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=40;PV4=1,0.33,0.33,1 PL:GT:GQ 36,0,31:0/1:33 chr10 44455192 . C T 4.41 . DP=6;AF1=0.8276;CI95=0.5,1;DP4=0,3,0,3;MQ=21;PV4=1,1,1,1 PL:GT:GQ 31,0,1:1/1:5 chr10 48387336 . A G 13 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr10 51561705 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr10 51561712 . C G 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 71,6,0:1/1:49 chr10 55617954 . G A 8.44 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 39,6,0:1/1:49 chr10 55718281 . T A 3.41 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr10 55888771 . T C 23.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 56,12,0:1/1:72 chr10 56025569 . C G 34.1 . DP=3;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,2;MQ=39;PV4=1,1,1,1 PL:GT:GQ 64,0,16:0/1:19 chr10 57384943 . G T 84 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=16,0,13,0;MQ=26;PV4=1,0.015,1,1 PL:GT:GQ 114,0,110:0/1:99 chr10 59873077 . T G 49 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=42 PL:GT:GQ 82,24,0:1/1:96 chr10 61329572 . C T 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 47,6,0:1/1:49 chr10 63790636 . T G 32.1 . DP=19;AF1=1;CI95=1,1;DP4=1,0,10,0;MQ=28;PV4=1,0.14,1,1 PL:GT:GQ 65,22,0:1/1:88 chr10 64466048 . C G 18.2 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28 PL:GT:GQ 51,18,0:1/1:90 chr10 65053440 . G T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39 PL:GT:GQ 153,30,0:1/1:99 chr10 65407358 . C G 84.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 117,15,0:1/1:75 chr10 65605291 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr10 66104447 . T C 99 . DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,21;MQ=34;PV4=1,1,0.15,1 PL:GT:GQ 136,0,162:0/1:99 chr10 82160859 . G C 99 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=36 PL:GT:GQ 153,39,0:1/1:99 chr10 82198579 . C T 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr10 87086290 . A G 4.13 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=17 PL:GT:GQ 35,27,0:1/1:99 chr10 89550621 . T G 74 . DP=47;AF1=1;CI95=1,1;DP4=0,0,0,45;MQ=45 PL:GT:GQ 107,135,0:1/1:99 chr10 92325046 . G A 42.3 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 75,15,0:1/1:75 chr10 94488050 . A G 5.46 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,0.16,1,1 PL:GT:GQ 34,0,34:0/1:34 chr10 95024815 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr10 95466306 . G A 53 . DP=7;AF1=0.6671;CI95=0.5,1;DP4=0,4,0,3;MQ=33;PV4=1,1,1,1 PL:GT:GQ 82,0,3:0/1:5 chr10 100256777 . T G 3.83 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23 PL:GT:GQ 34,12,0:1/1:72 chr10 101510485 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr10 101530760 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr10 101879744 . T C 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=44 PL:GT:GQ 54,9,0:1/1:63 chr10 102147276 . G C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33 PL:GT:GQ 43,9,0:1/1:63 chr10 102642248 . T G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr10 107666616 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr10 108319945 . C G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 43,9,0:1/1:63 chr10 109734371 . G A 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr10 112870604 . C T 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=36 PL:GT:GQ 79,12,0:1/1:72 chr10 115304673 . T C 11.3 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr10 119380588 . G A 14.2 . DP=4;AF1=0.502;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.18,0.32,1 PL:GT:GQ 44,0,21:0/1:24 chr10 123063756 . C T 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=23 PL:GT:GQ 46,9,0:1/1:63 chr10 128424770 . T G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 45,6,0:1/1:49 chr10 131229204 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr10 132420570 . G C 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr10 132528066 . C T 99 . DP=19;AF1=1;CI95=1,1;DP4=0,0,19,0;MQ=42 PL:GT:GQ 213,57,0:1/1:99 chr10 132644619 . G A 19.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23 PL:GT:GQ 52,15,0:1/1:75 chr10 132707581 . G C 9.11 . DP=51;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=25;PV4=1,1,1,1 PL:GT:GQ 38,2,0:1/1:37 chr10 133026892 . T C 55.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44 PL:GT:GQ 88,18,0:1/1:90 chr11 768033 . T C 33.5 . DP=4;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 62,0,1:1/1:5 chr11 768042 . T C 33.5 . DP=6;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 62,0,1:1/1:5 chr11 874568 . G C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 66,12,0:1/1:72 chr11 1009210 . T C 4 . DP=70;AF1=0.6241;CI95=0.5,1;DP4=0,3,0,8;MQ=24;PV4=1,1,0.5,1 PL:GT:GQ 31,0,4:0/1:6 chr11 1016692 . C T 27 . DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=22 PL:GT:GQ 60,114,0:1/1:99 chr11 1034477 . A G 66 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 98,9,0:1/1:63 chr11 1074037 . G A 4.13 . DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,5,0;MQ=24;PV4=1,1,0.43,1 PL:GT:GQ 32,0,30:0/1:31 chr11 1556298 . G A 11.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 44,12,0:1/1:72 chr11 1824777 . T C 27 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=28 PL:GT:GQ 60,30,0:1/1:99 chr11 3395801 . C T 22 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr11 3411901 . G A 4.75 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 35,9,0:1/1:63 chr11 3731606 . A C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr11 3783855 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr11 3967636 . A G 4.29 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24 PL:GT:GQ 35,15,0:1/1:75 chr11 4385618 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr11 4424365 . T A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr11 5295586 . C T 3.01 . DP=52;AF1=0.4997;CI95=0.5,0.5;DP4=33,0,10,0;MQ=29;PV4=1,0.0045,0.3,0.17 PL:GT:GQ 30,0,131:0/1:33 chr11 6157144 . C G 45.1 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=35 PL:GT:GQ 78,21,0:1/1:84 chr11 6352044 . C T 18 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31 PL:GT:GQ 50,9,0:1/1:63 chr11 6767356 . T C 9.63 . DP=3;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=29;PV4=1,1,1,1 PL:GT:GQ 38,1,0:1/1:23 chr11 6999404 . G C 21 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37 PL:GT:GQ 53,9,0:1/1:63 chr11 9120930 . C G 17.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr11 9373125 . T C 19.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 51,6,0:1/1:49 chr11 9585101 . C T 67 . DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=45 PL:GT:GQ 100,42,0:1/1:99 chr11 10266192 . A C 14.3 . DP=22;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=27 PL:GT:GQ 47,18,0:1/1:90 chr11 10303263 . T C 8.64 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=18 PL:GT:GQ 41,51,0:1/1:99 chr11 10420170 . T C 35 . DP=17;AF1=1;CI95=1,1;DP4=0,1,0,15;MQ=28;PV4=1,0.12,1,0.4 PL:GT:GQ 68,36,0:1/1:99 chr11 10912169 . G A 99 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=49 PL:GT:GQ 155,18,0:1/1:90 chr11 11315826 . T G 6.29 . DP=27;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=19 PL:GT:GQ 38,18,0:1/1:90 chr11 11603859 . A C 22 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=34;PV4=1,9.5e-13,0.22,1 PL:GT:GQ 52,0,115:0/1:55 chr11 11700034 . C T 33 . DP=11;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=30 PL:GT:GQ 66,27,0:1/1:99 chr11 11822758 . G A 15.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,3;MQ=38;PV4=1,0.18,1,1 PL:GT:GQ 45,0,88:0/1:48 chr11 11976636 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=24 PL:GT:GQ 54,9,0:1/1:63 chr11 14380517 . C G 16.1 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=5,0,5,0;MQ=48;PV4=1,2.1e-05,0.13,1 PL:GT:GQ 46,0,113:0/1:49 chr11 14419212 . A G 91.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38 PL:GT:GQ 124,18,0:1/1:90 chr11 14846792 . A G 55 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=19 PL:GT:GQ 88,33,0:1/1:99 chr11 15494556 . C T 99 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=22,0,14,0;MQ=34;PV4=1,0.0071,1,1 PL:GT:GQ 146,0,159:0/1:99 chr11 16262879 . A C 16.1 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=43;PV4=1,0.061,0.24,0.33 PL:GT:GQ 46,0,28:0/1:31 chr11 21514947 . T C 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=41 PL:GT:GQ 57,12,0:1/1:72 chr11 22532576 . C G 28 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=17 PL:GT:GQ 61,51,0:1/1:99 chr11 23529238 . G T 4.29 . DP=13;AF1=0.5334;CI95=0.5,1;DP4=1,0,3,0;MQ=37;PV4=1,1,0.34,0.21 PL:GT:GQ 32,0,9:0/1:12 chr11 24249554 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr11 24853167 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr11 33353903 . T C 24.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=36 PL:GT:GQ 57,15,0:1/1:75 chr11 35126569 . T C 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 57,12,0:1/1:72 chr11 35132248 . C T 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr11 35155482 . T C 68 . DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=46 PL:GT:GQ 101,66,0:1/1:99 chr11 52494088 . T C 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 140,27,0:1/1:99 chr11 57899943 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr11 62261460 . G T 19.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,5;MQ=27;PV4=1,1.1e-06,1,1 PL:GT:GQ 49,0,58:0/1:51 chr11 67456049 . C T 39.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=19 PL:GT:GQ 72,18,0:1/1:90 chr11 68509708 . C G 3.65 . DP=9;AF1=0.7301;CI95=0.5,1;DP4=0,5,0,4;MQ=17;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr11 70115115 . T A 99 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=49 PL:GT:GQ 140,15,0:1/1:75 chr11 72643951 . T C 70 . DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=39 PL:GT:GQ 103,66,0:1/1:99 chr11 72647930 . G A 36 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=41;PV4=1,1,0.3,1 PL:GT:GQ 66,0,28:0/1:31 chr11 73330148 . C T 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr11 81720893 . A G 5.83 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=19 PL:GT:GQ 37,12,0:1/1:72 chr11 83813797 . A G 23.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 56,12,0:1/1:72 chr11 85949488 . C A 54 . DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=37 PL:GT:GQ 87,42,0:1/1:99 chr11 87634829 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr11 90913093 . A T 35.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 67,6,0:1/1:49 chr11 93793348 . G A 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=31 PL:GT:GQ 139,24,0:1/1:96 chr11 100802294 . T C 16.6 . DP=21;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 49,12,0:1/1:72 chr11 107455449 . C T 8.44 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=26 PL:GT:GQ 39,6,0:1/1:49 chr11 111344355 . A G 69.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43 PL:GT:GQ 102,12,0:1/1:72 chr11 111611115 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr11 113050466 . G C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 36,6,0:1/1:49 chr11 114332544 . T C 3.54 . DP=17;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,5;MQ=37;PV4=1,0.32,0.13,1 PL:GT:GQ 31,0,37:0/1:33 chr11 114332549 . G A 3.54 . DP=17;AF1=0.4998;CI95=0.5,0.5;DP4=0,9,0,8;MQ=36;PV4=1,3.1e-10,0.088,1 PL:GT:GQ 31,0,127:0/1:34 chr11 114843578 . G C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr11 115580279 . A G 99 . DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=48 PL:GT:GQ 190,45,0:1/1:99 chr11 116434328 . G A 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr11 125914161 . A G 20.8 . DP=7;AF1=0.95;CI95=0.5,1;DP4=3,0,4,0;MQ=38;PV4=1,0.074,1,1 PL:GT:GQ 49,0,0:1/1:10 chr11 125917089 . C T 12.3 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,28,0,12;MQ=44;PV4=1,4.7e-25,1,1 PL:GT:GQ 42,0,167:0/1:45 chr11 127194100 . A G 60 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=49 PL:GT:GQ 93,24,0:1/1:96 chr12 70856 . G A 27.5 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 60,12,0:1/1:72 chr12 153693 . T C 52.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=38 PL:GT:GQ 85,15,0:1/1:75 chr12 924547 . C G 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 69,6,0:1/1:49 chr12 1555916 . G A 7.18 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 39,15,0:1/1:75 chr12 1919860 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr12 2283756 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr12 2805983 . G C 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr12 6088203 . T C 72.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=37 PL:GT:GQ 105,15,0:1/1:75 chr12 7099460 . G C 10.8 . DP=6;AF1=0.8277;CI95=0.5,1;DP4=3,0,3,0;MQ=26;PV4=1,0.027,1,1 PL:GT:GQ 39,0,1:1/1:5 chr12 7099464 . G A 13.3 . DP=6;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=28;PV4=1,0.16,1,1 PL:GT:GQ 42,1,0:1/1:23 chr12 7198516 . T G 4.61 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 34,6,0:1/1:49 chr12 23331895 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr12 28209020 . T G 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 47,15,0:1/1:75 chr12 30074073 . C T 32.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 64,6,0:1/1:49 chr12 30563452 . T C 25 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 57,9,0:1/1:63 chr12 30563453 . A G 25 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 57,9,0:1/1:63 chr12 30563464 . C A 78.8 . DP=8;AF1=1;CI95=0.5,1;DP4=0,2,0,5;MQ=34;PV4=1,0.29,1,1 PL:GT:GQ 110,6,0:1/1:49 chr12 31505085 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr12 34041336 . G A 5.46 . DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=36;PV4=1,1,0.48,0.21 PL:GT:GQ 34,0,34:0/1:34 chr12 49003648 . C G 42 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=39 PL:GT:GQ 75,24,0:1/1:96 chr12 51280690 . G A 69 . DP=98;AF1=0.5;CI95=0.5,0.5;DP4=13,0,18,0;MQ=45;PV4=1,1,0.051,1 PL:GT:GQ 99,0,84:0/1:87 chr12 69206633 . T C 17.1 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=17 PL:GT:GQ 50,33,0:1/1:99 chr12 80417253 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr12 86633033 . C T 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=43;PV4=1,1,0.33,1 PL:GT:GQ 64,0,31:0/1:34 chr12 98097274 . C T 47.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31 PL:GT:GQ 80,15,0:1/1:75 chr12 105269319 . C T 19 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26 PL:GT:GQ 51,9,0:1/1:63 chr12 109053425 . G A 9.53 . DP=8;AF1=0.5012;CI95=0.5,0.5;DP4=2,0,6,0;MQ=25;PV4=1,1,0.19,1 PL:GT:GQ 39,0,23:0/1:26 chr12 111904540 . A G 3.41 . DP=65;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 32,6,0:1/1:49 chr12 115038686 . T C 15.2 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27 PL:GT:GQ 48,21,0:1/1:84 chr12 115039419 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 34,9,0:1/1:63 chr12 115103890 . G A 66 . DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=49 PL:GT:GQ 99,114,0:1/1:99 chr12 115833830 . G A 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr12 116361873 . T G 6.34 . DP=5;AF1=0.7302;CI95=0.5,1;DP4=0,2,0,2;MQ=23;PV4=1,1,1,1 PL:GT:GQ 34,0,2:0/1:3 chr12 123583527 . G A 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 46,9,0:1/1:63 chr12 124115330 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 76,9,0:1/1:63 chr12 125062296 . G A 41.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr12 126718106 . A G 8.76 . DP=50;AF1=0.5163;CI95=0.5,1;DP4=2,0,6,0;MQ=26;PV4=1,0.33,0.37,1 PL:GT:GQ 38,0,12:0/1:15 chr12 133348311 . G A 24 . DP=18;AF1=0.5;CI95=0.5,0.5;DP4=14,0,3,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 54,0,118:0/1:57 chr12 134494475 . C T 28 . DP=18;AF1=0.6671;CI95=0.5,1;DP4=8,0,10,0;MQ=18;PV4=1,1,1,1 PL:GT:GQ 57,0,3:0/1:5 chr12 134831761 . C T 41.3 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=27 PL:GT:GQ 74,15,0:1/1:75 chr12 134992770 . A C,T 84 . DP=47;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=29 PL:GT:GQ 117,72,114,0,44,114:1/1:99 chr12 135261117 . G A 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 82,18,0:1/1:90 chr12 135261144 . A G 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 155,18,0:1/1:90 chr12 135460302 . G A 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=40 PL:GT:GQ 198,69,0:1/1:99 chr12 135463758 . A G 83 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=26 PL:GT:GQ 116,48,0:1/1:99 chr12 135523325 . G A 99 . DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=26 PL:GT:GQ 136,66,0:1/1:99 chr12 135782401 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr12 135795472 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr13 18040027 . G C 42 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33 PL:GT:GQ 74,9,0:1/1:63 chr13 19494625 . G T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr13 20121126 . A G 15.1 . DP=36;AF1=0.5;CI95=0.5,0.5;DP4=25,0,9,0;MQ=36;PV4=1,1,0.13,1 PL:GT:GQ 45,0,153:0/1:48 chr13 21536703 . A G 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr13 23160035 . G T 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 33,6,0:1/1:49 chr13 23476554 . C A 6.79 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52 PL:GT:GQ 37,6,0:1/1:49 chr13 26632967 . C G 32 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34 PL:GT:GQ 65,27,0:1/1:99 chr13 26790010 . T C 89.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35 PL:GT:GQ 122,15,0:1/1:75 chr13 36083571 . T C 43 . DP=84;AF1=1;CI95=1,1;DP4=1,0,37,0;MQ=16;PV4=1,1,1,0.3 PL:GT:GQ 76,99,0:1/1:99 chr13 44432419 . C T 3.58 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19 PL:GT:GQ 34,21,0:1/1:84 chr13 46592359 . T C 16.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 48,6,0:1/1:49 chr13 52764657 . A T 3.14 . DP=32;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 33,15,0:1/1:75 chr13 53084193 . C T 9.11 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=29;PV4=1,1,1,1 PL:GT:GQ 38,2,0:1/1:37 chr13 57763228 . C T 45 . DP=555;AF1=1;CI95=1,1;DP4=2,0,21,0;MQ=23;PV4=1,0.00021,1,0.3 PL:GT:GQ 78,45,0:1/1:99 chr13 73857921 . G C 31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 63,9,0:1/1:63 chr13 76718001 . G A 59 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=45;PV4=1,1,0.12,1 PL:GT:GQ 89,0,28:0/1:31 chr13 100912695 . A T 23 . DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,6;MQ=31;PV4=1,0.029,1,0.35 PL:GT:GQ 53,0,103:0/1:56 chr13 101332001 . G C 21 . DP=23;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=21 PL:GT:GQ 54,69,0:1/1:99 chr13 102637334 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr13 102895627 . C T 63 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=48 PL:GT:GQ 96,27,0:1/1:99 chr13 103830322 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr13 112842448 . G A 39 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=27 PL:GT:GQ 72,27,0:1/1:99 chr13 113310291 . C T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 66,12,0:1/1:72 chr13 114775162 . A G 80 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=21 PL:GT:GQ 113,51,0:1/1:99 chr13 115267482 . A G 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr13 116068676 . C T 3.83 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27 PL:GT:GQ 34,12,0:1/1:72 chr13 116455918 . A G 33 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=13,0,15,0;MQ=42;PV4=1,1.8e-20,0.3,1 PL:GT:GQ 63,0,146:0/1:66 chr13 116765012 . G A 30.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 62,6,0:1/1:49 chr13 116779773 . C T 17.1 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=27,0,11,0;MQ=24;PV4=1,4.5e-35,1,1 PL:GT:GQ 47,0,106:0/1:50 chr13 116779791 . C T 57 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=24,0,14,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 87,0,103:0/1:90 chr14 20159250 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr14 23510676 . T C 52 . DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=32 PL:GT:GQ 85,66,0:1/1:99 chr14 24735256 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr14 29525577 . G A 21 . DP=10;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=16 PL:GT:GQ 54,27,0:1/1:99 chr14 36186389 . C T 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20 PL:GT:GQ 37,6,0:1/1:49 chr14 36186394 . A G 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20 PL:GT:GQ 37,6,0:1/1:49 chr14 37440609 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr14 40432807 . A G 18.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=23 PL:GT:GQ 51,12,0:1/1:72 chr14 59466268 . T C 15.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25 PL:GT:GQ 47,9,0:1/1:63 chr14 61368162 . G T 7.18 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=17 PL:GT:GQ 39,15,0:1/1:75 chr14 65152922 . G A 92 . DP=33;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,15;MQ=36;PV4=1,0.059,0.35,1 PL:GT:GQ 122,0,144:0/1:99 chr14 69749148 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25 PL:GT:GQ 40,6,0:1/1:49 chr14 74877658 . C T 45 . DP=48;AF1=1;CI95=1,1;DP4=0,1,0,12;MQ=36;PV4=1,0.02,1,0.39 PL:GT:GQ 78,28,0:1/1:99 chr14 75546678 . C T 19.2 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=17 PL:GT:GQ 52,18,0:1/1:90 chr14 76439185 . T C 67.1 . DP=7;AF1=0.505;CI95=0.5,0.5;DP4=0,1,0,6;MQ=33;PV4=1,1,0.056,0.29 PL:GT:GQ 97,0,17:0/1:20 chr14 77313295 . T A 99 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=48 PL:GT:GQ 191,30,0:1/1:99 chr14 77673422 . G A 11.5 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=24 PL:GT:GQ 44,18,0:1/1:90 chr14 78646125 . T C 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40 PL:GT:GQ 153,24,0:1/1:96 chr14 91702449 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr14 91769842 . G A 63 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47 PL:GT:GQ 95,9,0:1/1:63 chr14 91775899 . C G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr14 91775924 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr14 93482918 . A C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr14 93665819 . C T 75 . DP=7;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,4;MQ=42;PV4=1,1,1,1 PL:GT:GQ 105,0,31:0/1:34 chr14 95422276 . A G 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=45 PL:GT:GQ 88,21,0:1/1:84 chr14 95731986 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr14 96045464 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr14 97172020 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=51 PL:GT:GQ 100,9,0:1/1:63 chr14 100515480 . A G 6.98 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,0.14,0.085,0.33 PL:GT:GQ 36,0,30:0/1:32 chr14 100770214 . A T 8.69 . DP=20;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16 PL:GT:GQ 41,21,0:1/1:84 chr14 101258303 . G A 82 . DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=26 PL:GT:GQ 115,45,0:1/1:99 chr14 101701492 . C G 66 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=49 PL:GT:GQ 99,30,0:1/1:99 chr14 102113772 . T C 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30 PL:GT:GQ 33,6,0:1/1:49 chr14 102751431 . A C 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr14 103708033 . A G 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=27 PL:GT:GQ 141,36,0:1/1:99 chr14 104744582 . G A 3.52 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 33,9,0:1/1:63 chr14 105989100 . C T 3.14 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 33,15,0:1/1:75 chr14 105989162 . C T 3.65 . DP=12;AF1=0.7301;CI95=0.5,1;DP4=0,6,0,6;MQ=15;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr14 106234810 . G A 25.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=39 PL:GT:GQ 58,15,0:1/1:75 chr14 106995572 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr14 107283057 . T C 5.5 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=20 PL:GT:GQ 37,21,0:1/1:84 chr14 107285319 . T C 33 . DP=36;AF1=1;CI95=1,1;DP4=0,0,0,35;MQ=22 PL:GT:GQ 66,105,0:1/1:99 chr14 107640449 . A G 11.8 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36 PL:GT:GQ 44,12,0:1/1:72 chr15 20082092 . T G 18.3 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24 PL:GT:GQ 51,15,0:1/1:75 chr15 22955884 . T C 67 . DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=48 PL:GT:GQ 100,36,0:1/1:99 chr15 22971987 . A G 5.29 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=22 PL:GT:GQ 35,6,0:1/1:49 chr15 23233324 . C A 47 . DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31 PL:GT:GQ 80,42,0:1/1:99 chr15 25175286 . C T 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=42;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr15 25385709 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr15 27372396 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr15 35998093 . C T 9.53 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=17 PL:GT:GQ 42,27,0:1/1:99 chr15 36716538 . C G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr15 36793360 . G T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 76,9,0:1/1:63 chr15 53783097 . A G 10.5 . DP=31;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16 PL:GT:GQ 43,21,0:1/1:84 chr15 54180175 . C T 10.4 . DP=7;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,3,0;MQ=27;PV4=1,1.2e-05,1,1 PL:GT:GQ 40,0,32:0/1:34 chr15 54939306 . C T 99 . DP=34;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,16;MQ=49;PV4=1,1,0.18,1 PL:GT:GQ 172,0,181:0/1:99 chr15 59377916 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr15 59685961 . G C 68 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=36 PL:GT:GQ 101,33,0:1/1:99 chr15 60306384 . A G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr15 60345642 . G C 14.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 46,6,0:1/1:49 chr15 60367387 . G A 13.2 . DP=6;AF1=0.5001;CI95=0.5,0.5;DP4=3,0,3,0;MQ=34;PV4=1,0.098,0.24,1 PL:GT:GQ 43,0,35:0/1:37 chr15 60367446 . C T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr15 61763755 . G A 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45 PL:GT:GQ 100,9,0:1/1:63 chr15 61831362 . C G 11.3 . DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,3;MQ=30;PV4=1,0.00077,0.47,1 PL:GT:GQ 41,0,42:0/1:41 chr15 63978880 . G C 60 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 90,3,0:1/1:41 chr15 64342445 . A G 12.2 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=18 PL:GT:GQ 44,9,0:1/1:63 chr15 65424859 . T C 11.3 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=21 PL:GT:GQ 44,30,0:1/1:99 chr15 65603698 . C T 60 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 92,9,0:1/1:63 chr15 67005078 . G A 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr15 71133512 . G C 22.3 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25 PL:GT:GQ 55,15,0:1/1:75 chr15 72619009 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr15 73272688 . C T 70.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=39 PL:GT:GQ 103,15,0:1/1:75 chr15 73699335 . T A 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=45 PL:GT:GQ 175,27,0:1/1:99 chr15 74513352 . C T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=37 PL:GT:GQ 139,30,0:1/1:99 chr15 75540536 . G A 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr15 75822537 . C A 17.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23 PL:GT:GQ 50,15,0:1/1:75 chr15 78554005 . T C 12 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 43,6,0:1/1:49 chr15 80089369 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=28 PL:GT:GQ 40,6,0:1/1:49 chr15 83089149 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 40,6,0:1/1:49 chr15 86839307 . T C 90.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 123,15,0:1/1:75 chr15 89836258 . T C 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39 PL:GT:GQ 141,24,0:1/1:96 chr15 89837706 . G A 4.13 . DP=8;AF1=0.4998;CI95=0.5,0.5;DP4=0,4,0,4;MQ=30;PV4=1,1,0.25,1 PL:GT:GQ 32,0,59:0/1:35 chr15 89857648 . T C 99 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=8,0,8,0;MQ=40;PV4=1,1,0.3,1 PL:GT:GQ 133,0,130:0/1:99 chr15 89864228 . A C 32 . DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,2,0;MQ=42;PV4=1,1,1,1 PL:GT:GQ 62,0,31:0/1:34 chr15 91261235 . G A 7.8 . DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=44;PV4=1,1,0.32,1 PL:GT:GQ 37,0,30:0/1:32 chr16 256990 . A C 10.4 . DP=16;AF1=0.5008;CI95=0.5,0.5;DP4=4,0,3,0;MQ=23;PV4=1,0.34,1,1 PL:GT:GQ 40,0,25:0/1:28 chr16 260794 . T C 3.01 . DP=19;AF1=0.4999;CI95=0.5,0.5;DP4=13,0,2,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 30,0,32:0/1:31 chr16 419905 . A G 7.9 . DP=5;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=22;PV4=1,1,1,1 PL:GT:GQ 36,1,0:1/1:23 chr16 824086 . T C 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr16 1085063 . C T 52 . DP=12;AF1=0.5;CI95=0.5,0.5;DP4=6,0,6,0;MQ=42;PV4=1,1,0.014,1 PL:GT:GQ 82,0,128:0/1:85 chr16 1221305 . T C 54 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=0,3,0,3;MQ=40;PV4=1,1,1,1 PL:GT:GQ 84,0,60:0/1:63 chr16 1411728 . A G 32.3 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35 PL:GT:GQ 65,15,0:1/1:75 chr16 1443197 . C G 64 . DP=26;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=36 PL:GT:GQ 97,75,0:1/1:99 chr16 1478746 . A T 32 . DP=20;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=28 PL:GT:GQ 65,24,0:1/1:96 chr16 1514438 . A C 45 . DP=49;AF1=1;CI95=1,1;DP4=0,0,48,0;MQ=26 PL:GT:GQ 78,144,0:1/1:99 chr16 1601989 . T C 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=29 PL:GT:GQ 133,39,0:1/1:99 chr16 2043883 . C T 30 . DP=33;AF1=1;CI95=1,1;DP4=0,0,0,33;MQ=14 PL:GT:GQ 63,99,0:1/1:99 chr16 2137470 . A C 39 . DP=38;AF1=0.5016;CI95=0.5,0.5;DP4=4,0,6,0;MQ=34;PV4=1,0.02,1,1 PL:GT:GQ 69,0,22:0/1:25 chr16 2537260 . A G 99 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=40 PL:GT:GQ 177,33,0:1/1:99 chr16 2564737 . T C 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,22;MQ=41 PL:GT:GQ 199,66,0:1/1:99 chr16 2612605 . A T 62.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28 PL:GT:GQ 95,15,0:1/1:75 chr16 2704518 . G A 41 . DP=48;AF1=0.5;CI95=0.5,0.5;DP4=0,17,0,12;MQ=48;PV4=1,1.9e-23,0.24,0.034 PL:GT:GQ 71,0,175:0/1:74 chr16 3274307 . G T 68 . DP=39;AF1=0.5;CI95=0.5,0.5;DP4=0,30,0,8;MQ=37;PV4=1,1,1,1 PL:GT:GQ 98,0,138:0/1:99 chr16 5467292 . G C 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 69,6,0:1/1:49 chr16 10079145 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr16 11483702 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr16 12038227 . A T 23 . DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,22,0,23;MQ=32;PV4=1,4.4e-66,0.47,0.028 PL:GT:GQ 53,0,135:0/1:56 chr16 21336880 . G C 55 . DP=35;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,19;MQ=47;PV4=1,5.6e-21,1,1 PL:GT:GQ 85,0,121:0/1:88 chr16 21980241 . C T 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr16 23275383 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 44,6,0:1/1:49 chr16 27546495 . G T 25 . DP=35;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43 PL:GT:GQ 57,9,0:1/1:63 chr16 27700399 . A T 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=17 PL:GT:GQ 50,12,0:1/1:72 chr16 28021935 . A G 18.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 51,15,0:1/1:75 chr16 29070016 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr16 29478618 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr16 29718140 . C T 46.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 79,15,0:1/1:75 chr16 30700759 . T C 17.1 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=14 PL:GT:GQ 50,42,0:1/1:99 chr16 35139103 . A G 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37 PL:GT:GQ 79,12,0:1/1:72 chr16 35473348 . G A 3.83 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 34,12,0:1/1:72 chr16 36213667 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr16 36705528 . G A 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=32 PL:GT:GQ 47,15,0:1/1:75 chr16 43831353 . C T 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42 PL:GT:GQ 102,12,0:1/1:72 chr16 44715166 . A C 25 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=32 PL:GT:GQ 58,24,0:1/1:96 chr16 44957661 . T C 7.03 . DP=23;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=18 PL:GT:GQ 39,21,0:1/1:84 chr16 44958698 . C T 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=49 PL:GT:GQ 75,15,0:1/1:75 chr16 44959163 . T C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 66,12,0:1/1:72 chr16 45167959 . C T 4.45 . DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=24 PL:GT:GQ 35,12,0:1/1:72 chr16 50254956 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr16 52383122 . A C 46.5 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=42 PL:GT:GQ 79,12,0:1/1:72 chr16 55978159 . C T 10.7 . DP=20;AF1=0.5336;CI95=0.5,1;DP4=2,0,5,0;MQ=35;PV4=1,0.038,1,0.059 PL:GT:GQ 40,0,9:0/1:12 chr16 61358878 . T A 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 47,6,0:1/1:49 chr16 61392487 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 44,6,0:1/1:49 chr16 61621603 . G T 6.59 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=22 PL:GT:GQ 38,12,0:1/1:72 chr16 69120890 . G C 51.3 . DP=36;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42 PL:GT:GQ 84,15,0:1/1:75 chr16 70778219 . A G 21.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=39 PL:GT:GQ 53,6,0:1/1:49 chr16 71899519 . T C 40 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33 PL:GT:GQ 73,33,0:1/1:99 chr16 72079251 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr16 72093003 . G C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr16 72672428 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr16 72864515 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr16 72890560 . G A 47.1 . DP=10;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=49;PV4=1,0.0019,0.0033,1 PL:GT:GQ 77,0,16:0/1:19 chr16 73048929 . A G 6.29 . DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=27;PV4=1,1,1,0.33 PL:GT:GQ 34,1,0:1/1:23 chr16 73177179 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr16 73191468 . C T 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40 PL:GT:GQ 102,12,0:1/1:72 chr16 73367439 . A C 7.41 . DP=36;AF1=1;CI95=0.5,1;DP4=0,2,0,13;MQ=26;PV4=1,1,0.027,1 PL:GT:GQ 37,4,0:1/1:45 chr16 74259316 . C T 89.5 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr16 75271450 . C G 6.99 . DP=15;AF1=0.5015;CI95=0.5,0.5;DP4=0,1,0,3;MQ=44;PV4=1,0.065,0.31,1 PL:GT:GQ 36,0,22:0/1:25 chr16 76199870 . G A 26 . DP=14;AF1=0.5;CI95=0.5,0.5;DP4=8,0,6,0;MQ=47;PV4=1,1.2e-06,0.32,1 PL:GT:GQ 56,0,141:0/1:59 chr16 77723692 . A G 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 122,12,0:1/1:72 chr17 165875 . G A 40.8 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 72,6,0:1/1:49 chr17 1443809 . C G 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr17 1618253 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=39 PL:GT:GQ 54,9,0:1/1:63 chr17 2815309 . T G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr17 3537486 . T G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr17 3734367 . C A 23.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36 PL:GT:GQ 56,12,0:1/1:72 chr17 5634764 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr17 6408090 . C G 3.54 . DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=3,0,2,0;MQ=40;PV4=1,1,0.36,1 PL:GT:GQ 31,0,66:0/1:34 chr17 7089723 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr17 8731503 . G C 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 42,6,0:1/1:49 chr17 9282935 . T C,G 24.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=40 PL:GT:GQ 57,12,61,0,3,61:1/1:72 chr17 17284831 . T C 29 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 61,9,0:1/1:63 chr17 18439515 . G A 4.11 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25 PL:GT:GQ 34,9,0:1/1:63 chr17 18602146 . C T 4.76 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=16 PL:GT:GQ 36,33,0:1/1:99 chr17 19427888 . C T 57 . DP=104;AF1=0.5;CI95=0.5,0.5;DP4=45,0,29,0;MQ=39;PV4=1,2.2e-12,1,1 PL:GT:GQ 87,0,131:0/1:90 chr17 19604159 . T C 9.31 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr17 19610366 . C T 13 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr17 20484706 . C G 51 . DP=35;AF1=0.5001;CI95=0.5,0.5;DP4=0,11,0,21;MQ=21;PV4=1,0.39,0.49,1 PL:GT:GQ 81,0,36:0/1:39 chr17 20555720 . A G 26.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=28 PL:GT:GQ 59,15,0:1/1:75 chr17 24328984 . A C 15.4 . DP=34;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25 PL:GT:GQ 48,15,0:1/1:75 chr17 26237090 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr17 28394766 . C A 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr17 31218277 . A G 3.62 . DP=38;AF1=0.5161;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,0.26,1,1 PL:GT:GQ 31,0,12:0/1:15 chr17 31254021 . C T 15.1 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35 PL:GT:GQ 47,9,0:1/1:63 chr17 32516798 . G A 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 69,6,0:1/1:49 chr17 32600253 . A G 16.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 49,12,0:1/1:72 chr17 34255214 . G C 19.2 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=21 PL:GT:GQ 52,18,0:1/1:90 chr17 34365900 . T C 93.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38 PL:GT:GQ 126,18,0:1/1:90 chr17 35380386 . A T 6.79 . DP=44;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 37,6,0:1/1:49 chr17 41993344 . C T 64 . DP=41;AF1=1;CI95=1,1;DP4=0,0,0,41;MQ=16 PL:GT:GQ 97,123,0:1/1:99 chr17 42128201 . A G 4.13 . DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=0,2,0,2;MQ=52;PV4=1,0.0041,1,1 PL:GT:GQ 32,0,62:0/1:35 chr17 42984490 . C A 56 . DP=33;AF1=0.5001;CI95=0.5,0.5;DP4=6,0,12,0;MQ=42;PV4=1,0.004,1,1 PL:GT:GQ 86,0,34:0/1:37 chr17 43419457 . G A 99 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=45 PL:GT:GQ 185,42,0:1/1:99 chr17 43421225 . A G 65.1 . DP=31;AF1=1;CI95=0.5,1;DP4=0,6,0,17;MQ=43;PV4=1,0.004,1,1 PL:GT:GQ 98,18,0:1/1:90 chr17 45206897 . G A 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47 PL:GT:GQ 54,9,0:1/1:63 chr17 45381302 . T C 18.6 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr17 45530812 . C A 3.54 . DP=6;AF1=0.4998;CI95=0.5,0.5;DP4=0,3,0,2;MQ=40;PV4=1,1,0.37,1 PL:GT:GQ 31,0,58:0/1:34 chr17 50242633 . G A 44 . DP=42;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,13;MQ=32;PV4=1,0.084,0.14,1 PL:GT:GQ 74,0,154:0/1:77 chr17 51275317 . G A 14.9 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 46,6,0:1/1:49 chr17 52325530 . C T 29 . DP=19;AF1=1;CI95=1,1;DP4=0,0,0,18;MQ=24 PL:GT:GQ 62,54,0:1/1:99 chr17 52411748 . T G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr17 53190746 . C G 62.1 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=40 PL:GT:GQ 95,18,0:1/1:90 chr17 58289916 . T C 18.2 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=22 PL:GT:GQ 51,18,0:1/1:90 chr17 59796875 . C T 42 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35 PL:GT:GQ 74,9,0:1/1:63 pysam-0.23.0/tests/tabix_data/vcf/13.vcf000066400000000000000000001506611475062545500177160ustar00rootroot00000000000000##fileformat=VCFv4.0 ##fileDate=2011-10-11 ##source=Platypus_Version_0.1.5 ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT WTCHG_27173_05.bam WTCHG_27173_04.bam chr1 1451489 . T C 103 PASS ABPV=1.00e+00;FPV=7.56e-01;FR=0.2501;HP=7;MMLQ=30;NF=2;NR=18;PP=103;RMP=57.54;RPV=1.00e-00;SC=CCGGTGTGGGTGGGGAGGCCG;TC=42;TCF=7;TCR=35;TR=20;func=intronic;gene=ATAD3A;segdup=0.91;1000g=0.36;dbsnp=rs76717221 GT:GL:GQ:NR 0/0:-43.28,-51.0,-125.34:35:18 1/0:-135.58,-103.29,-138.87:100:24 chr1 1451490 . G A 73 PASS ABPV=1.00e+00;FPV=9.29e-01;FR=0.2501;HP=3;MMLQ=30;NF=3;NR=16;PP=73;RMP=58.79;RPV=9.98e-01;SC=CGGTGTGGGTGGGGAGGCCGG;TC=42;TCF=7;TCR=35;TR=19;func=intronic;gene=ATAD3A;segdup=0.91;1000g=0.33;dbsnp=rs9439460 GT:GL:GQ:NR 0/0:-43.28,-50.99,-127.79:35:18 0/1:-135.58,-110.35,-146.87:100:24 chr1 12939904 . A C 109 PASS ABPV=1.00e+00;FPV=7.66e-01;FR=0.2500;HP=1;MMLQ=37;NF=22;NR=1;PP=109;RMP=45.66;RPV=4.46e-06;SC=ATTGTGAGGAACTTTAACGAG;TC=132;TCF=79;TCR=53;TR=23 GT:GL:GQ:NR 0/0:-40.31,-50.48,-301.89:45:53 0/1:-121.0,-87.39,-396.61:100:79 chr1 16902943 . T C 50 PASS ABPV=1.00e+00;FPV=2.90e-01;FR=0.2506;HP=2;MMLQ=34;NF=30;NR=18;PP=50;RMP=46.42;RPV=8.84e-01;SC=GGGTCAGCTCTCGTTCCTGAG;TC=191;TCF=133;TCR=58;TR=48 GT:GL:GQ:NR 0/0:-337.26,-342.92,-618.53:26:93 0/1:-428.71,-408.75,-668.15:84:98 chr1 16902982 . G T 41 PASS ABPV=1.00e+00;FPV=5.26e-02;FR=0.2500;HP=1;MMLQ=36;NF=29;NR=10;PP=41;RMP=55.68;RPV=1.90e-02;SC=ATTGCCTAAGGTGAGACGGTA;TC=223;TCF=152;TCR=71;TR=39 GT:GL:GQ:NR 0/0:-282.16,-293.75,-760.18:52:108 0/1:-308.83,-290.99,-786.16:75:115 chr1 16918180 . C T 200 PASS ABPV=1.00e+00;FPV=7.60e-05;FR=0.2500;HP=1;MMLQ=37;NF=8;NR=11;PP=200;RMP=57.84;RPV=6.15e-01;SC=TACTTTGGTACCTCTGTCTTC;TC=134;TCF=91;TCR=43;TR=19 GT:GL:GQ:NR 0/0:-48.3,-68.7,-289.28:90:47 0/1:-194.28,-132.13,-452.09:100:87 chr1 17083652 . C T 200 PASS ABPV=3.06e-02;FPV=6.38e-13;FR=0.2500;HP=2;MMLQ=36;NF=29;NR=3;PP=200;RMP=38.16;RPV=2.05e-02;SC=AAATCTCAACCTTGAGTACAA;TC=350;TCF=317;TCR=33;TR=32;func=ncRNA;gene=MST1P9;cons46=632 Name=lod=492;segdup=0.99;1000g=0.37;dbsnp=rs113710576 GT:GL:GQ:NR 0/0:-547.14,-559.85,-1017.76:56:159 0/1:-723.35,-656.42,-1167.76:100:191 chr1 17083776 . C A 79 PASS ABPV=1.08e-01;FPV=7.38e-01;FR=0.2500;HP=1;MMLQ=35;NF=1;NR=22;PP=79;RMP=76.99;RPV=1.13e-09;SC=CACAGAGACACGCGTGAAGAC;TC=238;TCF=4;TCR=234;TR=23;func=ncRNA;gene=MST1P9;cons46=632 Name=lod=492;segdup=0.99;1000g=0.20;dbsnp=rs56318124 GT:GL:GQ:NR 0/0:-442.45,-455.85,-790.66:59:121 0/1:-451.84,-425.21,-717.41:100:117 chr1 17575714 . G A 59 PASS ABPV=2.52e-01;FPV=3.10e-02;FR=0.2500;HP=1;MMLQ=31;NF=1;NR=4;PP=59;RMP=43.35;RPV=1.94e-02;SC=GACCCTCGTGGACATTTATGG;TC=58;TCF=19;TCR=39;TR=5 GT:GL:GQ:NR 0/0:-14.49,-33.87,-234.95:85:32 0/1:-39.36,-17.32,-168.9:93:26 chr1 21751228 . T TCGCGCCCGGC 66 PASS ABPV=3.86e-06;FPV=8.03e-37;FR=0.2500;HP=4;NF=1;NR=1;PP=66;RMP=15.56;RPV=1.98e-06;SC=CTCAAATGAGTAAAAGGCACT;TC=133;TCF=77;TCR=56;TR=2 GT:GL:GQ:NR 0/0:-178.34,-190.57,-398.5:54:72 0/1:-308.3,-271.14,-540.05:100:98 chr1 21755539 . C A 27 PASS ABPV=1.00e+00;FPV=9.84e-01;FR=0.2503;HP=1;MMLQ=31;NF=2;NR=1;PP=27;RMP=65.83;RPV=4.98e-02;SC=GGCCAACAACCGCCAGGTGCG;TC=20;TCF=3;TCR=17;TR=3;func=intergenic;gene=ECE1(dist=83505) NBPF3(dist=11092);cons46=807 Name=lod=2532;segdup=0.99;1000g=0.80;dbsnp=rs3855556 GT:GL:GQ:NR 0/0:0.0,-6.22,-62.68:28:10 1/0:-21.51,-6.92,-52.98:61:10 chr1 40798730 . A AT 59 PASS ABPV=1.00e+00;FPV=6.06e-01;FR=0.2504;HP=10;NF=7;NR=1;PP=59;RMP=50.29;RPV=7.38e-01;SC=GAAGTCTTCTATTTTTTTTTA;TC=28;TCF=24;TCR=4;TR=8;func=intergenic;gene=COL9A2(dist=15791) SMAP2(dist=40648);dbsnp=rs34372767 GT:GL:GQ:NR 0/0:0.0,-6.13,-39.37:28:12 0/1:-35.97,-10.49,-31.53:98:16 chr1 142803580 . TA T 145 PASS ABPV=1.00e+00;FPV=6.35e-02;FR=0.2500;HP=6;NF=1;NR=11;PP=145;RMP=65.89;RPV=8.29e-02;SC=TTCATAGATTTAAAAAATTAT;TC=81;TCF=16;TCR=65;TR=12 GT:GL:GQ:NR 0/0:-39.18,-49.93,-242.54:48:33 1/0:-80.12,-35.74,-249.72:100:48 chr1 144854799 . C T 50 PASS ABPV=1.00e+00;FPV=9.37e-01;FR=0.2504;HP=1;MMLQ=34;NF=1;NR=19;PP=50;RMP=60.89;RPV=9.86e-01;SC=GCCTCGGATACCTCCAGCTGA;TC=52;TCF=2;TCR=50;TR=20;func=intronic;gene=PDE4DIP;segdup=0.96;dbsnp=rs5004097 GT:GL:GQ:NR 0/0:-89.24,-95.22,-205.12:27:25 0/1:-177.25,-157.18,-246.67:85:27 chr1 145116027 . T C 127 PASS ABPV=1.00e+00;FPV=1.00e+00;FR=0.2501;HP=2;MMLQ=34;NF=0;NR=7;PP=127;RMP=54.07;RPV=5.14e-01;SC=AAAAGAGATGTCCTGAAAATG;TC=30;TCF=0;TCR=30;TR=7;func=UTR3;gene=SEC22B;cons46=340 Name=lod=32;1000g=0.45;dbsnp=rs7550440 GT:GL:GQ:NR 0/0:0.0,-7.61,-92.94:34:11 0/1:-56.84,-19.14,-106.99:100:19 chr1 146554532 . C T 57 PASS ABPV=1.00e+00;FPV=5.18e-01;FR=0.2501;HP=12;MMLQ=31;NF=4;NR=5;PP=57;RMP=66.19;RPV=4.68e-01;SC=CTTCTTCTTTCTTTTTTTTTA;TC=41;TCF=18;TCR=23;TR=9;func=intergenic;gene=LOC728989(dist=39933) PRKAB2(dist=72153);segdup=0.93;dbsnp=rs9662613 GT:GL:GQ:NR 0/0:-13.82,-21.42,-95.53:34:13 0/1:-131.76,-110.18,-223.87:91:28 chr1 148344564 . T C 34 PASS ABPV=3.69e-01;FPV=1.16e-03;FR=0.2500;HP=2;MMLQ=36;NF=24;NR=1;PP=34;RMP=22.65;RPV=1.98e-06;SC=TTCGTTCTTATTTCTCCCCGC;TC=218;TCF=162;TCR=56;TR=25 GT:GL:GQ:NR 0/0:-210.1,-224.84,-651.44:65:104 0/1:-232.74,-216.41,-586.14:69:114 chr1 148853862 . G T 37 PASS ABPV=3.79e-01;FPV=1.94e-02;FR=0.2500;HP=3;MMLQ=31;NF=6;NR=2;PP=37;RMP=50.34;RPV=2.58e-02;SC=CGCTCCTGGAGCCCAGCCCGG;TC=76;TCF=50;TCR=26;TR=8 GT:GL:GQ:NR 0/0:-247.75,-257.0,-317.61:41:35 1/0:-179.5,-162.62,-280.47:71:41 chr1 148854004 . C T 32 PASS ABPV=1.83e-01;FPV=3.17e-02;FR=0.2500;HP=1;MMLQ=34;NF=0;NR=3;PP=32;RMP=93.74;RPV=2.52e-02;SC=GCCCGCACTGCTGCAGCGCCC;TC=44;TCF=12;TCR=32;TR=3 GT:GL:GQ:NR 0/0:-75.02,-87.66,-197.34:56:26 1/0:-55.07,-39.25,-94.0:66:18 chr1 152187606 . G A 200 PASS ABPV=3.64e-01;FPV=4.08e-07;FR=0.2500;HP=2;MMLQ=32;NF=7;NR=16;PP=200;RMP=30.4;RPV=4.89e-02;SC=GAAGACTGACGGGAGCCAGAC;TC=202;TCF=109;TCR=93;TR=23;func=exonic;gene=HRNR;exon_func=nonsynonymous SNV;AAchange=NM_001009931:c.C6499T:p.R2167C;segdup=0.98;1000g=0.05;sift=0.2;pp2=0.269490;phylop=0.009549;mutT=0.062064;LRT=0.589002 GT:GL:GQ:NR 0/0:-190.82,-206.2,-650.62:68:98 0/1:-306.73,-239.37,-605.74:100:104 chr1 152281007 . A G 38 PASS ABPV=1.00e+00;FPV=2.01e-01;FR=0.2500;HP=1;MMLQ=31;NF=37;NR=62;PP=38;RMP=56.83;RPV=9.75e-01;SC=GCCTGATCATAATGGGATCCT;TC=370;TCF=169;TCR=201;TR=99 GT:GL:GQ:NR 0/0:-830.31,-842.03,-1695.93:52:178 0/1:-1104.87,-1087.65,-1851.72:72:192 chr1 152281008 . A G 56 PASS ABPV=1.00e+00;FPV=2.26e-01;FR=0.2500;HP=1;MMLQ=31;NF=37;NR=62;PP=56;RMP=57.69;RPV=9.75e-01;SC=CCTGATCATAATGGGATCCTT;TC=368;TCF=167;TCR=201;TR=99 GT:GL:GQ:NR 0/0:-836.29,-850.28,-1704.3:62:178 1/0:-1097.96,-1076.67,-1811.19:90:190 chr1 152281466 . C T 200 PASS ABPV=1.00e+00;FPV=3.99e-04;FR=0.2500;HP=2;MMLQ=33;NF=26;NR=66;PP=200;RMP=66.62;RPV=7.23e-01;SC=TGCCCGTGACCGGCTCTGTCT;TC=430;TCF=180;TCR=250;TR=92 GT:GL:GQ:NR 0/0:-912.94,-966.99,-1954.85:100:223 1/0:-939.3,-872.22,-1720.42:100:207 chr1 168549565 . T C 28 PASS ABPV=1.00e+00;FPV=1.00e+00;FR=0.2504;HP=2;MMLQ=37;NF=0;NR=8;PP=28;RMP=72.28;RPV=1.34e-01;SC=TCCTTATCAATCATGTCTTTC;TC=47;TCF=0;TCR=47;TR=8 GT:GL:GQ:NR 0/0:-27.57,-33.72,-167.32:28:21 1/0:-34.62,-19.62,-182.0:63:26 chr1 236647542 . G T 46 PASS ABPV=1.00e+00;FPV=9.99e-01;FR=0.2500;HP=3;MMLQ=34;NF=16;NR=40;PP=46;RMP=62.31;RPV=1.00e-00;SC=GTGCAAGCTGGCCCAGGCCAA;TC=104;TCF=32;TCR=72;TR=56 GT:GL:GQ:NR 0/0:-318.17,-328.23,-521.3:45:54 1/0:-498.22,-479.17,-572.27:80:50 chr1 236647562 . T C 73 PASS ABPV=1.00e+00;FPV=9.95e-01;FR=0.2503;HP=2;MMLQ=37;NF=11;NR=36;PP=73;RMP=64.25;RPV=1.00e-00;SC=ATGGTTGGTGTGTCATGGTGC;TC=85;TCF=23;TCR=62;TR=47 GT:GL:GQ:NR 0/0:-240.39,-246.81,-405.51:29:42 0/1:-421.95,-396.59,-483.66:100:43 chr1 236700807 . T A 130 PASS ABPV=1.00e+00;FPV=5.12e-01;FR=0.2502;HP=2;MMLQ=33;NF=8;NR=7;PP=130;RMP=47.87;RPV=8.70e-01;SC=GTAATCCCGTTTGTTGGCACC;TC=55;TCF=34;TCR=21;TR=15;func=exonic;gene=LGALS8;exon_func=nonsynonymous SNV;AAchange=NM_201544:c.T56A:p.F19Y;cons46=463 Name=lod=102;1000g=0.62;dbsnp=rs2737713;pp2=0.0;phylop=0.983932;mutT=4.6E-5;LRT=0.999982 GT:GL:GQ:NR 0/0:-41.35,-48.14,-183.02:31:21 0/1:-204.57,-166.19,-295.14:100:34 chr1 236700823 . T C 200 PASS ABPV=1.00e+00;FPV=6.24e-01;FR=0.2504;HP=2;MMLQ=32;NF=9;NR=8;PP=200;RMP=58.62;RPV=8.49e-01;SC=GCACCATTCCTGATCAGCTGG;TC=60;TCF=35;TCR=25;TR=17;func=exonic;gene=LGALS8;exon_func=synonymous SNV;AAchange=NM_201544:c.T72C:p.P24P;cons46=463 Name=lod=102;1000g=0.61;dbsnp=rs1041934 GT:GL:GQ:NR 0/0:-41.35,-47.43,-173.43:28:22 1/0:-232.08,-183.12,-325.41:100:38 chr1 241663902 . TGA T 37 PASS ABPV=2.57e-03;FPV=3.07e-05;FR=0.2507;HP=2;NF=0;NR=3;PP=37;RMP=44.45;RPV=2.39e-06;SC=TTTGAGTGAGTGAGAGAGAGA;TC=90;TCF=18;TCR=72;TR=3;func=intronic;gene=FH GT:GL:GQ:NR 0/0:-115.58,-120.99,-206.17:25:29 1/0:-208.1,-188.38,-347.52:83:62 chr10 52420020 . G A 135 PASS ABPV=1.00e+00;FPV=2.24e-01;FR=0.2502;HP=2;MMLQ=35;NF=3;NR=3;PP=135;RMP=58.04;RPV=7.75e-01;SC=GAGAACTTCCGGCTGCAGTAC;TC=30;TCF=20;TCR=10;TR=6 GT:GL:GQ:NR 0/0:-65.01,-71.52,-138.01:30:16 0/1:-83.86,-44.38,-74.93:100:14 chr10 118380701 . G A 77 PASS ABPV=1.00e+00;FPV=5.15e-01;FR=0.2503;HP=3;MMLQ=32;NF=5;NR=0;PP=77;RMP=22.32;RPV=5.62e-01;SC=CCGGGTTGCGGGGCGTCTGTT;TC=24;TCF=22;TCR=2;TR=5 GT:GL:GQ:NR 0/0:-4.14,-10.38,-77.71:28:10 0/1:-51.41,-25.11,-83.53:100:14 chr11 1651169 . T C 84 PASS ABPV=1.00e+00;FPV=9.98e-01;FR=0.2502;HP=2;MMLQ=33;NF=8;NR=26;PP=84;RMP=71.99;RPV=1.00e-00;SC=GCTGTGGCTCTGGCTGTGGGG;TC=71;TCF=14;TCR=57;TR=34;func=exonic;gene=KRTAP5-5;exon_func=synonymous SNV;AAchange=NM_001001480:c.T99C:p.S33S;1000g=0.29;dbsnp=rs71454095 GT:GL:GQ:NR 0/0:-199.38,-206.33,-365.55:31:38 0/1:-226.68,-198.86,-282.14:100:33 chr11 3431576 . G A 33 PASS ABPV=4.46e-01;FPV=4.99e-05;FR=0.2500;HP=1;MMLQ=30;NF=13;NR=10;PP=33;RMP=62.67;RPV=1.90e-02;SC=TCGTGTGTGAGTCCTACAGTG;TC=194;TCF=123;TCR=71;TR=23 GT:GL:GQ:NR 0/0:-71.93,-106.62,-693.75:100:102 1/0:-110.6,-94.58,-543.82:67:92 chr11 43918703 . C CTTTTCATATTAT 36 PASS ABPV=4.61e-02;FPV=1.12e-04;FR=0.2500;HP=3;NF=2;NR=0;PP=36;RMP=5.0;RPV=1.00e+00;SC=CTGACAGTGGCTTTATATATA;TC=49;TCF=49;TCR=0;TR=2 GT:GL:GQ:NR 0/0:-14.5,-34.6,-394.96:89:42 1/0:-47.66,-15.24,-223.69:100:36 chr11 48366812 . A C 48 PASS ABPV=1.00e+00;FPV=9.80e-01;FR=0.2502;HP=1;MMLQ=35;NF=16;NR=2;PP=48;RMP=45.69;RPV=1.00e+00;SC=AGATAATTGAATGTCCCAAGT;TC=44;TCF=42;TCR=2;TR=18 GT:GL:GQ:NR 0/0:-92.79,-99.69,-183.18:31:18 0/1:-133.87,-114.4,-228.26:82:26 chr11 48387506 . A G 48 PASS ABPV=1.00e+00;FPV=6.15e-01;FR=0.2500;HP=3;MMLQ=34;NF=28;NR=52;PP=48;RMP=59.69;RPV=1.00e-00;SC=AAATCCCCCGACCCATGCCAT;TC=227;TCF=109;TCR=118;TR=80;func=intergenic;gene=OR4C45(dist=13507) OR4A47(dist=122839);dbsnp=rs72898882;sift=0.42 GT:GL:GQ:NR 0/0:-665.75,-691.04,-1124.95:100:117 0/1:-697.01,-677.56,-1037.3:82:110 chr11 56143357 . G A 91 PASS ABPV=1.00e+00;FPV=9.70e-04;FR=0.2500;HP=3;MMLQ=36;NF=7;NR=60;PP=91;RMP=66.63;RPV=1.00e-00;SC=GGAATTTCTTGTACAAACAAA;TC=221;TCF=72;TCR=149;TR=67;func=exonic;gene=OR8U1 OR8U8;exon_func=synonymous SNV;AAchange=NM_001005204:c.G258A:p.L86L;dbsnp=rs76949582 GT:GL:GQ:NR 0/0:-538.52,-560.54,-1080.28:97:104 1/0:-924.01,-894.57,-1497.61:100:131 chr11 56468493 . A G 86 PASS ABPV=1.00e+00;FPV=1.31e-03;FR=0.2500;HP=1;MMLQ=30;NF=23;NR=16;PP=86;RMP=49.16;RPV=3.74e-01;SC=TCTGCCCCGCAGTGCTCATCC;TC=227;TCF=156;TCR=71;TR=39 GT:GL:GQ:NR 0/0:-212.22,-234.78,-819.52:99:105 0/1:-472.13,-443.86,-1063.46:100:122 chr11 92592540 . T G 22 PASS ABPV=9.72e-03;FPV=5.62e-02;FR=0.2501;HP=3;MMLQ=35;NF=0;NR=3;PP=22;RMP=99.66;RPV=8.62e-06;SC=GTTAGTGTTTTGGCTCTTGGA;TC=77;TCF=10;TCR=67;TR=3 GT:GL:GQ:NR 0/0:-302.47,-309.64,-322.1:32:36 0/1:-338.7,-325.07,-335.6:52:41 chr11 123504959 . C G 200 PASS ABPV=1.00e+00;FPV=4.20e-01;FR=0.2508;HP=2;MMLQ=40;NF=0;NR=7;PP=200;RMP=63.62;RPV=9.72e-01;SC=CAGTGCCCAGCGTGGGAACAC;TC=19;TCF=3;TCR=16;TR=7;func=intronic;gene=SCN3B;1000g=0.72;dbsnp=rs1148110 GT:GL:GQ:NR 0/0:-1.61,-6.93,-61.43:24:8 1/0:-66.0,-7.62,-36.11:100:11 chr12 92675 . C T 152 PASS ABPV=1.00e+00;FPV=7.38e-01;FR=0.2500;HP=1;MMLQ=37;NF=1;NR=7;PP=152;RMP=66.0;RPV=3.57e-01;SC=GGACTGTTTCCTGCTTGTAGC;TC=38;TCF=4;TCR=34;TR=8 GT:GL:GQ:NR 0/0:-41.61,-49.75,-120.62:37:14 1/0:-68.65,-25.34,-113.9:100:24 chr12 11183642 . A G 154 PASS ABPV=1.00e+00;FPV=8.37e-01;FR=0.2500;HP=1;MMLQ=34;NF=47;NR=62;PP=154;RMP=57.25;RPV=1.00e-00;SC=GCTAGTAGCAAGCCAGTTGCT;TC=311;TCF=168;TCR=143;TR=109;func=exonic;gene=TAS2R31;exon_func=nonsynonymous SNV;AAchange=NM_176885:c.T293C:p.L98P;segdup=0.93;dbsnp=rs73049067 GT:GL:GQ:NR 0/0:-561.52,-579.71,-1246.3:80:152 0/1:-826.02,-782.04,-1401.37:100:159 chr12 29908580 . A ATTGTT 200 PASS ABPV=1.00e+00;FPV=9.78e-01;FR=0.2507;HP=3;NF=10;NR=0;PP=200;RMP=36.19;RPV=1.00e+00;SC=TTTGGAAACTATTAAGTAATT;TC=24;TCF=24;TCR=0;TR=10;func=intronic;gene=TMTC1;dbsnp=rs3830194 GT:GL:GQ:NR 0/0:0.0,-5.55,-96.69:25:9 1/0:-151.5,-15.23,-76.28:100:17 chr12 31282765 . A T 21 PASS ABPV=1.00e+00;FPV=8.68e-01;FR=0.2502;HP=2;MMLQ=35;NF=12;NR=5;PP=21;RMP=46.72;RPV=8.51e-01;SC=AATGAATACAAATTTTTTCAT;TC=53;TCF=38;TCR=15;TR=17 GT:GL:GQ:NR 0/0:-83.08,-89.72,-221.87:30:27 1/0:-63.64,-50.39,-170.59:55:26 chr12 52843779 . T C 52 PASS ABPV=1.00e+00;FPV=1.21e-05;FR=0.2500;HP=4;MMLQ=20;NF=8;NR=16;PP=52;RMP=64.54;RPV=6.52e-01;SC=TTTGAACCCCTGGCTTCATCT;TC=161;TCF=100;TCR=61;TR=24;func=intronic;gene=KRT6B;segdup=0.93;dbsnp=rs380379 GT:GL:GQ:NR 0/0:-109.82,-139.81,-567.08:100:82 0/1:-186.27,-165.75,-481.84:87:79 chr12 65471467 . A G 200 PASS ABPV=1.00e+00;FPV=6.42e-01;FR=0.2501;HP=2;MMLQ=36;NF=7;NR=0;PP=200;RMP=38.97;RPV=4.22e-01;SC=TGCATCTTAAATATTCTTATC;TC=30;TCF=27;TCR=3;TR=7;func=intronic;gene=WIF1;1000g=0.27;dbsnp=rs2289936 GT:GL:GQ:NR 0/0:0.0,-7.62,-98.02:34:12 1/0:-69.82,-23.48,-105.09:100:18 chr12 99175091 . AAC A 86 PASS ABPV=3.61e-01;FPV=7.09e-04;FR=0.2503;HP=1;NF=4;NR=0;PP=86;RMP=34.87;RPV=9.95e-03;SC=AAACAACAACAACACACACAC;TC=43;TCF=27;TCR=16;TR=4;func=intronic;gene=ANKS1B GT:GL:GQ:NR 0/0:-4.37,-10.61,-100.0:28:17 0/1:-72.08,-41.09,-136.47:100:27 chr12 104378526 . G GACACAGAAACT 200 PASS ABPV=2.37e-01;FPV=8.53e-03;FR=0.2500;HP=1;NF=5;NR=0;PP=200;RMP=8.25;RPV=5.63e-02;SC=TGTGATTCTAGCTCTGCTATG;TC=59;TCF=49;TCR=10;TR=5 GT:GL:GQ:NR 0/0:0.0,-15.25,-297.25:67:32 1/0:-137.95,-64.82,-429.82:100:44 chr13 25169091 . A G 41 PASS ABPV=1.00e+00;FPV=1.23e-02;FR=0.2501;HP=3;MMLQ=35;NF=18;NR=1;PP=41;RMP=17.52;RPV=3.10e-02;SC=AATAACCAAAACAGTTTTTTA;TC=133;TCF=114;TCR=19;TR=19 GT:GL:GQ:NR 0/0:-140.13,-147.81,-405.22:35:57 0/1:-204.4,-186.51,-512.07:75:76 chr13 37795039 . G T 20 PASS ABPV=5.69e-01;FPV=5.25e-01;FR=0.2502;HP=1;MMLQ=40;NF=2;NR=0;PP=20;RMP=33.0;RPV=7.49e-02;SC=TCCTTGGCCTGAGCTTCTTTG;TC=19;TCF=10;TCR=9;TR=2 GT:GL:GQ:NR 0/0:0.0,-6.93,-89.94:31:11 1/0:-22.03,-9.0,-57.23:54:8 chr13 100517209 . G A 21 PASS ABPV=2.00e-01;FPV=2.14e-03;FR=0.2500;HP=2;MMLQ=35;NF=6;NR=7;PP=21;RMP=94.07;RPV=9.71e-04;SC=GTGTGTGTGTGTATATGTGTG;TC=134;TCF=62;TCR=72;TR=13 GT:GL:GQ:NR 0/0:-265.23,-279.13,-623.6:62:70 1/0:-308.0,-294.6,-524.58:56:64 chr13 114540947 . C CTCTGCTCTT 45 PASS ABPV=1.42e-01;FPV=3.34e-03;FR=0.2500;HP=2;NF=2;NR=0;PP=45;RMP=1.0;RPV=5.62e-01;SC=CCACAGGAACCCAGCCAGCAG;TC=37;TCF=35;TCR=2;TR=2 GT:GL:GQ:NR 0/0:0.0,-11.09,-214.96:49:19 1/0:-74.37,-43.34,-288.0:100:27 chr14 19118192 . A G 200 PASS ABPV=1.00e+00;FPV=1.32e-05;FR=0.2507;HP=2;MMLQ=32;NF=68;NR=76;PP=200;RMP=53.85;RPV=5.74e-02;SC=TGCTTGCCATATGTCATGGAT;TC=771;TCF=415;TCR=356;TR=144;func=intergenic;gene=NONE(dist=NONE) OR11H12(dist=259402);segdup=0.96;dbsnp=rs77434589 GT:GL:GQ:NR 0/0:-730.61,-736.03,-2441.78:25:349 1/0:-997.51,-891.65,-2847.93:100:422 chr14 19500081 . A G 22 PASS ABPV=1.00e+00;FPV=1.61e-01;FR=0.2505;HP=3;MMLQ=22;NF=3;NR=0;PP=22;RMP=47.77;RPV=1.00e+00;SC=GGTGCACACCACTGTGGACGT;TC=22;TCF=22;TCR=0;TR=3 GT:GL:GQ:NR 0/0:-15.46,-21.36,-64.18:27:10 0/1:-27.84,-14.25,-57.82:57:12 chr14 20137380 . C T 33 PASS ABPV=1.24e-02;FPV=1.12e-09;FR=0.2500;HP=1;MMLQ=31;NF=8;NR=17;PP=33;RMP=61.98;RPV=3.46e-06;SC=TCACTGCCCTCGCCGCATGCA;TC=303;TCF=142;TCR=161;TR=25 GT:GL:GQ:NR 0/0:-373.48,-389.86,-1035.03:72:144 0/1:-475.48,-459.41,-1121.57:68:159 chr14 64496872 . G C 96 PASS ABPV=1.00e+00;FPV=1.00e+00;FR=0.2503;HP=1;MMLQ=37;NF=0;NR=4;PP=96;RMP=55.12;RPV=5.17e-01;SC=AGAAATTCCAGTGGTATTCAG;TC=18;TCF=0;TCR=18;TR=4;func=intronic;gene=SYNE2;1000g=0.90;dbsnp=rs3866737 GT:GL:GQ:NR 0/0:0.0,-6.24,-83.73:28:9 0/1:-36.8,-6.24,-45.77:100:9 chr14 106881425 . A G 71 PASS ABPV=1.00e+00;FPV=1.15e-01;FR=0.2500;HP=1;MMLQ=32;NF=4;NR=10;PP=71;RMP=49.71;RPV=2.88e-01;SC=CCATCCACTCAAGCCCTTGTC;TC=78;TCF=29;TCR=49;TR=14 GT:GL:GQ:NR 0/0:-39.35,-48.57,-258.02:41:30 1/0:-231.62,-206.72,-399.17:100:48 chr14 106881452 . T C 66 PASS ABPV=1.00e+00;FPV=3.03e-01;FR=0.2509;HP=1;MMLQ=27;NF=3;NR=10;PP=66;RMP=65.33;RPV=1.89e-01;SC=CTGGTCACACTGAATTCATAC;TC=71;TCF=18;TCR=53;TR=13 GT:GL:GQ:NR 0/0:-57.13,-62.37,-258.3:24:30 0/1:-168.08,-144.38,-338.93:100:41 chr14 107034967 . T C 105 PASS ABPV=1.00e+00;FPV=6.54e-01;FR=0.2500;HP=1;MMLQ=34;NF=6;NR=9;PP=105;RMP=58.51;RPV=6.64e-01;SC=ACAGGAGATCTTCAGAGACTC;TC=57;TCF=23;TCR=34;TR=15 GT:GL:GQ:NR 0/0:-163.23,-172.19,-255.57:40:20 1/0:-379.46,-346.84,-445.34:100:39 chr15 20083754 . G A 54 PASS ABPV=1.00e+00;FPV=5.67e-01;FR=0.2500;HP=2;MMLQ=36;NF=33;NR=5;PP=54;RMP=47.07;RPV=4.22e-01;SC=AAATCATTATGTGCTTTGAGA;TC=155;TCF=131;TCR=24;TR=38 GT:GL:GQ:NR 0/0:-122.79,-137.29,-483.11:64:64 1/0:-176.25,-155.43,-655.46:88:91 chr15 20446256 . G C 57 PASS ABPV=1.00e+00;FPV=1.00e+00;FR=0.2500;HP=2;MMLQ=34;NF=1;NR=7;PP=57;RMP=71.88;RPV=4.32e-01;SC=CATGCAAGAAGCTGGAAAGCC;TC=33;TCF=1;TCR=32;TR=8;func=intergenic;gene=NONE(dist=NONE) LOC646096(dist=41741);segdup=0.97;dbsnp=rs3907011 GT:GL:GQ:NR 0/0:-13.82,-23.14,-131.81:42:16 0/1:-45.04,-23.56,-104.26:91:17 chr15 20875055 . C G 154 PASS ABPV=1.00e+00;FPV=7.50e-01;FR=0.2504;HP=3;MMLQ=37;NF=0;NR=12;PP=154;RMP=60.19;RPV=1.71e-01;SC=AATTTAAACGCAAATTAGTAA;TC=64;TCF=1;TCR=63;TR=12;func=ncRNA;gene=NBEAP1;segdup=0.93;1000g=0.26;dbsnp=rs7496378 GT:GL:GQ:NR 0/0:-9.2,-15.25,-188.16:27:22 0/1:-137.96,-94.13,-342.43:100:42 chr15 20875100 . A G 21 PASS ABPV=1.00e+00;FPV=7.50e-01;FR=0.2502;HP=4;MMLQ=35;NF=0;NR=6;PP=21;RMP=81.39;RPV=2.77e-01;SC=AGAGGTTAAAAATAACTTTCT;TC=33;TCF=1;TCR=32;TR=6;func=ncRNA;gene=NBEAP1;cons46=243 Name=lod=13;segdup=0.93;1000g=0.28;dbsnp=rs7497715 GT:GL:GQ:NR 0/0:-7.83,-14.75,-92.12:31:10 1/0:-92.65,-79.35,-211.07:56:23 chr15 21140945 . C T 26 PASS ABPV=1.00e+00;FPV=1.00e-01;FR=0.2506;HP=2;MMLQ=33;NF=1;NR=3;PP=26;RMP=65.04;RPV=7.12e-01;SC=ACATGTACAGCGCCACACTTC;TC=25;TCF=14;TCR=11;TR=4;func=intergenic;gene=NF1P2(dist=6320) LOC348120(dist=4822);cons46=679 Name=lod=765;segdup=1.00;1000g=0.24;dbsnp=rs12324229 GT:GL:GQ:NR 0/0:-16.95,-22.6,-60.18:26:13 0/1:-36.66,-22.19,-44.85:61:12 chr15 28900400 . G T 133 PASS ABPV=1.00e+00;FPV=6.31e-01;FR=0.2502;HP=3;MMLQ=34;NF=14;NR=0;PP=133;RMP=36.99;RPV=4.21e-01;SC=GCTTGTCATTGTAAATTTTCT;TC=57;TCF=54;TCR=3;TR=14 GT:GL:GQ:NR 0/0:-26.38,-32.94,-192.24:30:27 1/0:-71.34,-32.36,-180.89:100:30 chr15 75656200 . G A 75 PASS ABPV=1.00e+00;FPV=6.28e-01;FR=0.2507;HP=6;MMLQ=37;NF=4;NR=0;PP=75;RMP=47.43;RPV=1.00e+00;SC=CCAGCCCCCCGGCCCCGTTTT;TC=16;TCF=16;TCR=0;TR=4 GT:GL:GQ:NR 0/0:-7.14,-12.68,-76.44:25:8 0/1:-34.75,-8.99,-31.71:100:8 chr15 76075732 . A C 29 PASS ABPV=1.00e+00;FPV=9.97e-01;FR=0.2501;HP=2;MMLQ=34;NF=11;NR=15;PP=29;RMP=61.41;RPV=9.58e-01;SC=ATCCCTATCTATCCAGGCCTT;TC=64;TCF=22;TCR=42;TR=26 GT:GL:GQ:NR 0/0:-89.15,-96.33,-237.9:32:31 1/0:-134.14,-119.09,-238.26:63:33 chr15 100340178 . C G 52 PASS ABPV=1.00e+00;FPV=1.76e-01;FR=0.2500;HP=1;MMLQ=31;NF=5;NR=5;PP=52;RMP=87.78;RPV=1.32e-01;SC=AGTGTCTTCTCGTTCCCACGC;TC=64;TCF=31;TCR=33;TR=10;func=ncRNA;gene=DNM1P46;cons46=699 Name=lod=923;segdup=0.97;sift=0.27 GT:GL:GQ:NR 0/0:-139.12,-149.96,-310.47:37:36 1/0:-206.67,-186.19,-317.68:87:38 chr15 102303399 . C T 65 PASS ABPV=1.00e+00;FPV=4.32e-02;FR=0.2500;HP=2;MMLQ=34;NF=5;NR=30;PP=65;RMP=65.58;RPV=1.00e-00;SC=AGAGCTGCTGCCCAACCTGCA;TC=90;TCF=40;TCR=50;TR=35;func=intergenic;gene=TARSL2(dist=38754) OR4F6(dist=42524);cons46=920 Name=lod=7327;segdup=0.98;1000g=0.50;dbsnp=rs71416239 GT:GL:GQ:NR 0/0:-129.26,-138.34,-250.21:41:46 0/1:-118.78,-95.27,-224.48:100:44 chr15 102506389 . C T 50 PASS ABPV=6.29e-01;FPV=1.27e-01;FR=0.2500;HP=1;MMLQ=34;NF=1;NR=3;PP=50;RMP=67.19;RPV=2.63e-01;SC=GGATGCCCTGCAGTACCTGCA;TC=32;TCF=13;TCR=19;TR=4 GT:GL:GQ:NR 0/0:-3.9,-15.65,-133.88:52:17 0/1:-31.25,-11.29,-72.06:84:15 chr16 9250260 . T G 22 PASS ABPV=1.00e+00;FPV=1.00e-02;FR=0.2500;HP=2;MMLQ=29;NF=0;NR=4;PP=22;RMP=37.36;RPV=8.85e-01;SC=CACCTATTATTCCATGAATTC;TC=27;TCF=16;TCR=11;TR=4;func=intergenic;gene=C16orf72(dist=36705) MIR548X(dist=78514);cons46=749 Name=lod=1471;1000g=0.73;dbsnp=rs12929693 GT:GL:GQ:NR 0/0:-1.84,-10.83,-100.69:40:14 0/1:-25.85,-12.37,-70.66:56:13 chr16 21747662 . G A 36 PASS ABPV=1.00e+00;FPV=2.01e-01;FR=0.2500;HP=1;MMLQ=34;NF=16;NR=6;PP=36;RMP=40.34;RPV=5.40e-05;SC=CTGTCTTTCAGTCTGTTCGGA;TC=159;TCF=79;TCR=80;TR=22 GT:GL:GQ:NR 0/0:-69.29,-88.69,-470.14:85:75 1/0:-171.53,-154.82,-534.35:70:84 chr16 28618446 . T C 36 PASS ABPV=1.00e+00;FPV=8.61e-01;FR=0.2500;HP=3;MMLQ=32;NF=6;NR=14;PP=36;RMP=63.74;RPV=5.40e-01;SC=ACACAGCCTGTCCCAGGCCAG;TC=75;TCF=18;TCR=57;TR=20 GT:GL:GQ:NR 0/0:-33.24,-41.67,-205.86:38:27 0/1:-113.92,-97.17,-312.83:70:48 chr16 33390329 . G C 24 PASS ABPV=6.16e-01;FPV=4.32e-02;FR=0.2500;HP=2;MMLQ=34;NF=5;NR=0;PP=24;RMP=54.47;RPV=1.00e+00;SC=TTAGAAACAGGTTCACAATTG;TC=40;TCF=40;TCR=0;TR=5;func=intergenic;gene=LOC390705(dist=91627) LINC00273(dist=570723);segdup=0.97;1000g=0.32;dbsnp=rs12232434 GT:GL:GQ:NR 0/0:-6.09,-14.55,-170.95:38:21 0/1:-47.14,-33.16,-147.34:58:19 chr16 33401967 . G A 116 PASS ABPV=1.00e+00;FPV=1.64e-02;FR=0.2500;HP=2;MMLQ=34;NF=16;NR=15;PP=116;RMP=51.2;RPV=2.96e-01;SC=GAGGTCTGCCGACAGCTGCAC;TC=172;TCF=102;TCR=70;TR=31;func=intergenic;gene=LOC390705(dist=103265) LINC00273(dist=559085);cons46=611 Name=lod=406;segdup=0.97;dbsnp=rs8047578 GT:GL:GQ:NR 0/0:-133.55,-144.14,-490.22:47:76 1/0:-209.17,-173.99,-648.51:100:96 chr16 33407954 . C G 34 PASS ABPV=1.00e+00;FPV=4.21e-01;FR=0.2507;HP=3;MMLQ=34;NF=0;NR=3;PP=34;RMP=61.08;RPV=5.19e-01;SC=GAAATTGTCTCGGGCCTGAAG;TC=17;TCF=3;TCR=14;TR=3 GT:GL:GQ:NR 0/0:-10.82,-16.36,-77.44:25:9 1/0:-63.55,-47.37,-59.15:58:8 chr16 46405120 . C G 37 PASS ABPV=3.94e-02;FPV=4.07e-03;FR=0.2510;HP=2;MMLQ=40;NF=2;NR=1;PP=37;RMP=51.27;RPV=3.18e-03;SC=CGATTCCATTCGATAATGATT;TC=62;TCF=34;TCR=28;TR=3 GT:GL:GQ:NR 0/0:-129.24,-134.38,-161.33:24:28 0/1:-205.7,-188.69,-196.8:42:34 chr16 58148083 . C CACACGCAGGTACA 31 PASS ABPV=1.69e-01;FPV=1.00e+00;FR=0.2500;HP=2;NF=0;NR=2;PP=31;RMP=88.0;RPV=3.34e-03;SC=CAGGGAAGCACCCACCCTTGT;TC=35;TCF=0;TCR=35;TR=2 GT:GL:GQ:NR 0/0:-11.28,-21.68,-223.8:46:16 0/1:-62.86,-30.44,-243.59:100:20 chr17 5036281 . G C 48 PASS ABPV=1.00e+00;FPV=8.00e-01;FR=0.2500;HP=1;MMLQ=32;NF=14;NR=49;PP=48;RMP=47.67;RPV=9.22e-01;SC=AAGCACAGTAGCAAAGTAATG;TC=214;TCF=48;TCR=166;TR=63 GT:GL:GQ:NR 0/0:-506.02,-514.23,-1090.2:37:117 0/1:-460.03,-440.62,-871.14:82:97 chr17 6328747 . T G 200 PASS ABPV=1.00e+00;FPV=8.77e-01;FR=0.2507;HP=4;MMLQ=32;NF=8;NR=5;PP=200;RMP=59.22;RPV=9.45e-01;SC=GGCCACTTGCTCCCTGCCTGG;TC=36;TCF=24;TCR=12;TR=13 GT:GL:GQ:NR 0/0:-4.84,-10.37,-69.24:25:8 0/1:-116.1,-23.7,-86.84:100:28 chr17 14140191 . G A 125 PASS ABPV=1.00e+00;FPV=3.98e-02;FR=0.2500;HP=1;MMLQ=34;NF=2;NR=11;PP=125;RMP=71.76;RPV=3.84e-02;SC=AGCTGTTTACGGCGCTGACTC;TC=95;TCF=24;TCR=71;TR=13;func=upstream;gene=CDRT15;segdup=0.99;1000g=0.17;dbsnp=rs28533558 GT:GL:GQ:NR 0/0:-146.51,-156.3,-338.05:44:40 0/1:-162.79,-125.58,-384.62:100:55 chr17 21904955 . G A 29 PASS ABPV=1.46e-01;FPV=3.00e-01;FR=0.2500;HP=2;MMLQ=33;NF=1;NR=7;PP=29;RMP=77.08;RPV=5.90e-05;SC=GTGGCACGGCGCTGTATCCTG;TC=95;TCF=9;TCR=86;TR=8 GT:GL:GQ:NR 0/0:-95.23,-110.26,-302.39:67:42 0/1:-104.15,-88.94,-334.7:64:53 chr17_gl000205_random 114392 . G GC 200 PASS ABPV=1.00e+00;FPV=1.00e+00;FR=0.2503;HP=1;NF=1;NR=9;PP=200;RMP=62.13;RPV=8.86e-01;SC=GAGCTTCTATGAGGCGTGGGG;TC=28;TCF=1;TCR=27;TR=10;func=intergenic;gene=NONE(dist=NONE) MGC70870(dist=2231) GT:GL:GQ:NR 0/0:0.0,-6.24,-93.01:28:9 0/1:-137.06,-63.68,-124.76:100:19 chr17_gl000205_random 118186 . TCGC T 157 PASS ABPV=1.00e+00;FPV=4.85e-02;FR=0.2506;HP=1;NF=4;NR=5;PP=157;RMP=51.77;RPV=1.51e-01;SC=CCATCATAAGTCGCATCCCGG;TC=55;TCF=23;TCR=32;TR=9;func=ncRNA;gene=MGC70870;cons46=824 Name=lod=2972;segdup=0.90 GT:GL:GQ:NR 0/0:-80.93,-86.51,-246.22:26:23 0/1:-151.92,-104.34,-309.99:100:34 chr17_gl000205_random 118289 . G A 30 PASS ABPV=1.00e+00;FPV=2.43e-02;FR=0.2500;HP=1;MMLQ=38;NF=1;NR=4;PP=30;RMP=51.3;RPV=5.18e-01;SC=TGAGCTCAGTGGTGCTACCTA;TC=38;TCF=20;TCR=18;TR=5 GT:GL:GQ:NR 0/0:-92.27,-100.53,-170.2:37:15 0/1:-193.59,-178.31,-262.43:64:23 chr17_gl000205_random 122791 . T C 124 PASS ABPV=1.00e+00;FPV=6.72e-01;FR=0.2504;HP=1;MMLQ=34;NF=8;NR=0;PP=124;RMP=54.5;RPV=1.00e+00;SC=GATATAAACTTCTAAAATTCA;TC=30;TCF=30;TCR=0;TR=8;func=intergenic;gene=MGC70870(dist=3059) NONE(dist=NONE) GT:GL:GQ:NR 0/0:-33.82,-39.98,-100.64:28:10 1/0:-177.82,-140.79,-190.46:100:20 chr18 14183747 . T C 115 PASS ABPV=1.00e+00;FPV=9.72e-01;FR=0.2500;HP=5;MMLQ=36;NF=49;NR=88;PP=115;RMP=54.47;RPV=9.86e-01;SC=ACAAAGAAAATAGAACGCCTT;TC=444;TCF=156;TCR=288;TR=137 GT:GL:GQ:NR 0/0:-919.95,-948.86,-1765.89:100:211 0/1:-1189.4,-1154.37,-1918.79:100:233 chr19 3611146 . A G 30 PASS ABPV=1.00e+00;FPV=5.15e-01;FR=0.2501;HP=1;MMLQ=24;NF=6;NR=1;PP=30;RMP=42.3;RPV=2.44e-01;SC=CCCTGTGCTCAGAGGTGGGGG;TC=36;TCF=26;TCR=10;TR=7;func=ncRNA;gene=C19orf29-AS1;1000g=0.56;dbsnp=rs2074786 GT:GL:GQ:NR 0/0:-27.63,-35.13,-121.04:34:15 0/1:-69.97,-54.53,-137.67:65:21 chr19 12543121 . C G 200 PASS ABPV=1.00e+00;FPV=7.14e-01;FR=0.2502;HP=7;MMLQ=40;NF=11;NR=0;PP=200;RMP=33.87;RPV=7.50e-01;SC=TTCTTTGCTTCTTTTTAAATT;TC=41;TCF=40;TCR=1;TR=11;func=intronic;gene=ZNF443;segdup=0.96;dbsnp=rs74181652 GT:GL:GQ:NR 0/0:-8.47,-15.46,-153.74:32:20 0/1:-71.21,-15.46,-97.4:100:21 chr19 15014189 . T C 90 PASS ABPV=1.00e+00;FPV=1.97e-01;FR=0.2500;HP=4;MMLQ=100;NF=2;NR=5;PP=90;RMP=90.56;RPV=4.68e-01;SC=GAGTGAGTTGTGGGTTGCAGC;TC=39;TCF=16;TCR=23;TR=7 GT:GL:GQ:NR 0/0:-190.71,-200.49,-255.11:44:24 1/0:-174.95,-145.84,-178.61:100:15 chr19 41515263 . A G 88 PASS ABPV=3.76e-01;FPV=1.82e-01;FR=0.2500;HP=2;MMLQ=33;NF=7;NR=3;PP=88;RMP=64.16;RPV=2.48e-04;SC=AGCGCCCCCAAGGACCTCATC;TC=93;TCF=40;TCR=53;TR=10;func=exonic;gene=CYP2B6;exon_func=nonsynonymous SNV;AAchange=NM_000767:c.A785G:p.K262R;segdup=0.92;1000g=0.20;dbsnp=rs2279343;pp2=0.0;phylop=0.086093;mutT=1.0E-6;LRT=0.999974 GT:GL:GQ:NR 0/0:-4.81,-28.32,-273.38:100:41 0/1:-65.82,-37.11,-263.4:100:52 chr19 42188037 . C T 114 PASS ABPV=1.00e+00;FPV=6.06e-02;FR=0.2500;HP=4;MMLQ=34;NF=2;NR=8;PP=114;RMP=98.9;RPV=1.54e-02;SC=GTGTGGCCCCCTTGGTTCCCC;TC=73;TCF=11;TCR=62;TR=10 GT:GL:GQ:NR 0/0:-205.49,-214.25,-251.15:29:29 0/1:-379.34,-343.91,-357.8:15:44 chr19 50474708 . T G 61 PASS ABPV=1.00e+00;FPV=7.17e-01;FR=0.2501;HP=2;MMLQ=30;NF=5;NR=1;PP=61;RMP=67.96;RPV=3.09e-02;SC=CTGGGCTCAGTGTCCCAGAGC;TC=37;TCF=18;TCR=19;TR=6 GT:GL:GQ:NR 0/0:-86.34,-93.74,-137.77:33:15 0/1:-129.81,-107.4,-147.05:95:22 chr19 52977823 . A G 102 PASS ABPV=1.00e+00;FPV=3.15e-01;FR=0.2507;HP=2;MMLQ=35;NF=0;NR=4;PP=102;RMP=41.58;RPV=8.84e-01;SC=GTTTCTCTCCAGTATGAATTC;TC=15;TCF=4;TCR=11;TR=4;func=intronic;gene=ZNF578;cons46=395 Name=lod=54;1000g=0.94;dbsnp=rs1673901 GT:GL:GQ:NR 0/0:0.0,-5.54,-65.87:25:9 1/0:-36.12,-4.16,-18.86:71:6 chr19 54726711 . G T 43 PASS ABPV=1.00e+00;FPV=1.00e-00;FR=0.2504;HP=3;MMLQ=31;NF=22;NR=2;PP=43;RMP=52.84;RPV=6.78e-01;SC=GTCCCCGCCCGGGTGCCTCCT;TC=53;TCF=45;TCR=8;TR=24 GT:GL:GQ:NR 0/0:-47.88,-54.03,-95.64:28:18 1/0:-164.89,-146.64,-206.88:77:35 chr2 905553 . G C 76 PASS ABPV=1.62e-02;FPV=5.75e-08;FR=0.2500;HP=2;MMLQ=31;NF=1;NR=7;PP=76;RMP=95.73;RPV=1.04e-02;SC=GCCTGCACTGGGTCTGGTGTT;TC=128;TCF=69;TCR=59;TR=8 GT:GL:GQ:NR 0/0:-314.19,-325.21,-450.94:49:57 0/1:-390.34,-364.48,-513.78:100:71 chr2 905595 . G C 24 PASS ABPV=1.21e-01;FPV=1.79e-02;FR=0.2500;HP=2;MMLQ=35;NF=5;NR=1;PP=24;RMP=13.0;RPV=6.96e-04;SC=GCCTGCACTGGGTCTGGTGTT;TC=79;TCF=45;TCR=34;TR=6 GT:GL:GQ:NR 0/0:-210.22,-219.58,-290.19:42:42 1/0:-197.49,-183.47,-250.46:59:38 chr2 91885842 . G A 37 PASS ABPV=1.00e+00;FPV=2.46e-01;FR=0.2502;HP=1;MMLQ=36;NF=4;NR=0;PP=37;RMP=71.85;RPV=4.22e-01;SC=CCAACATTACGGAATTTGGAT;TC=27;TCF=24;TCR=3;TR=4 GT:GL:GQ:NR 0/0:-11.45,-18.39,-83.47:31:11 0/1:-59.01,-41.99,-86.53:72:16 chr2 96525556 . C T 37 PASS ABPV=1.00e+00;FPV=1.00e-00;FR=0.2503;HP=1;MMLQ=37;NF=60;NR=2;PP=37;RMP=45.25;RPV=9.49e-01;SC=TCTCCTTATACGTCTTTAATA;TC=91;TCF=87;TCR=4;TR=62 GT:GL:GQ:NR 0/0:-304.4,-310.82,-406.42:29:43 0/1:-411.62,-394.62,-459.09:72:48 chr2 107042620 . C T 45 PASS ABPV=1.00e+00;FPV=7.50e-01;FR=0.2500;HP=4;MMLQ=33;NF=0;NR=10;PP=45;RMP=77.64;RPV=2.94e-02;SC=GCAAGAGCTACAAATACAAAA;TC=69;TCF=1;TCR=68;TR=10;func=intronic;gene=RGPD3;cons46=333 Name=lod=30;segdup=0.99;dbsnp=rs2433787 GT:GL:GQ:NR 0/0:-9.17,-23.45,-154.19:63:21 1/0:-107.84,-88.96,-294.09:80:48 chr2 132860931 . G A 113 PASS ABPV=1.00e+00;FPV=5.61e-01;FR=0.2507;HP=1;MMLQ=38;NF=0;NR=8;PP=113;RMP=69.43;RPV=9.58e-01;SC=GAAGAATGTGGTAAAGCCTTT;TC=22;TCF=2;TCR=20;TR=8 GT:GL:GQ:NR 0/0:-12.66,-18.1,-56.72:25:9 1/0:-57.64,-23.24,-50.67:100:13 chr2 133020074 . G A 33 PASS ABPV=1.00e+00;FPV=9.94e-01;FR=0.2501;HP=2;MMLQ=36;NF=45;NR=12;PP=33;RMP=47.59;RPV=9.08e-01;SC=ATTTCAGAAGGGAAAATATCC;TC=167;TCF=131;TCR=36;TR=57;func=intergenic;gene=ANKRD30BL(dist=4532) GPR39(dist=154073);cons46=762 Name=lod=1662;segdup=0.91;dbsnp=rs111959326 GT:GL:GQ:NR 0/0:-698.84,-706.52,-798.38:35:80 1/0:-786.87,-770.7,-903.5:68:87 chr2 133020186 . T C 66 PASS ABPV=1.00e+00;FPV=1.55e-01;FR=0.2500;HP=1;MMLQ=34;NF=52;NR=51;PP=66;RMP=46.69;RPV=9.65e-01;SC=TAGCTTTGTGTTCATACCACT;TC=402;TCF=237;TCR=165;TR=103;func=intergenic;gene=ANKRD30BL(dist=4644) GPR39(dist=153961);cons46=762 Name=lod=1662;segdup=0.91;dbsnp=rs112259198 GT:GL:GQ:NR 0/0:-1712.52,-1737.48,-1975.72:100:192 1/0:-1974.59,-1950.96,-2276.74:100:211 chr2 133020542 . G A 50 PASS ABPV=1.00e+00;FPV=1.14e-01;FR=0.2503;HP=1;MMLQ=32;NF=3;NR=6;PP=50;RMP=53.94;RPV=7.08e-02;SC=CTATCCAAGTGGATCCAAATT;TC=66;TCF=24;TCR=42;TR=9;func=intergenic;gene=ANKRD30BL(dist=5000) GPR39(dist=153605);cons46=762 Name=lod=1662;segdup=0.93;dbsnp=rs2257591 GT:GL:GQ:NR 0/0:-181.04,-187.42,-271.44:29:29 1/0:-243.98,-224.07,-313.1:84:37 chr2 166801924 . C G 78 PASS ABPV=1.00e+00;FPV=5.71e-01;FR=0.2507;HP=3;MMLQ=34;NF=4;NR=0;PP=78;RMP=67.75;RPV=7.49e-01;SC=TATTTACAAACTGGCAATAGA;TC=18;TCF=17;TCR=1;TR=4;func=ncRNA;gene=LOC100506134;1000g=0.64;dbsnp=rs6432853 GT:GL:GQ:NR 0/0:-34.05,-39.57,-91.24:25:8 1/0:-42.79,-16.34,-58.89:100:10 chr2 204055943 . T C 59 PASS ABPV=2.58e-01;FPV=8.29e-02;FR=0.2500;HP=2;MMLQ=33;NF=11;NR=2;PP=59;RMP=61.13;RPV=3.22e-06;SC=ATGGCCGCCATCCTCATGACA;TC=128;TCF=65;TCR=63;TR=13;func=intronic;gene=NBEAL1;cons46=702 Name=lod=950;dbsnp=rs4561645 GT:GL:GQ:NR 0/0:-41.52,-53.03,-440.53:51:70 1/0:-89.56,-67.55,-350.54:93:58 chr2 210594540 . A G 200 PASS ABPV=1.00e+00;FPV=9.70e-01;FR=0.2507;HP=1;MMLQ=30;NF=10;NR=1;PP=200;RMP=52.61;RPV=9.37e-01;SC=CGAATGCAAGATATAGTTAAA;TC=27;TCF=25;TCR=2;TR=11;func=intronic;gene=MAP2;1000g=0.88;dbsnp=rs4673486 GT:GL:GQ:NR 0/0:0.0,-5.54,-62.54:25:8 0/1:-93.19,-14.77,-63.29:100:19 chr2 211444533 . GGT G 32 PASS ABPV=1.78e-01;FPV=1.96e-01;FR=0.2503;HP=2;NF=1;NR=3;PP=32;RMP=50.82;RPV=2.40e-03;SC=TGTTTCTTCGGGTGTGTGTGT;TC=54;TCF=11;TCR=43;TR=4 GT:GL:GQ:NR 0/0:-4.14,-10.38,-103.02:28:17 1/0:-41.6,-23.06,-172.26:78:37 chr2 227659818 . T TCAAGTGAGGA 93 PASS ABPV=3.68e-02;FPV=2.37e-01;FR=0.2500;HP=1;NF=0;NR=3;PP=93;RMP=91.0;RPV=7.64e-05;SC=CTCTCACCGCTGCCCAGGGGT;TC=63;TCF=5;TCR=58;TR=3 GT:GL:GQ:NR 0/0:-17.96,-35.28,-330.9:77:30 0/1:-94.07,-50.73,-458.79:100:41 chr2 227954599 . G A 200 PASS ABPV=1.00e+00;FPV=9.19e-01;FR=0.2507;HP=2;MMLQ=31;NF=6;NR=4;PP=200;RMP=46.35;RPV=9.51e-01;SC=TCTCCTTTTGGGCCTCTTCCT;TC=25;TCF=16;TCR=9;TR=10;func=exonic;gene=COL4A4;exon_func=nonsynonymous SNV;AAchange=NM_000092:c.C1444T:p.P482S;1000g=0.55;dbsnp=rs2229814;sift=0.44;pp2=0.0;phylop=0.897442;mutT=9.0E-5;LRT=0.824593 GT:GL:GQ:NR 0/0:0.0,-5.54,-68.56:25:9 0/1:-80.77,-11.53,-34.97:100:16 chr2 233273018 . G A 32 PASS ABPV=1.00e+00;FPV=3.62e-01;FR=0.2500;HP=3;MMLQ=34;NF=13;NR=4;PP=32;RMP=56.47;RPV=8.89e-03;SC=TTCCCATGGGGACCCCAGACC;TC=102;TCF=59;TCR=43;TR=17 GT:GL:GQ:NR 0/0:-50.24,-59.48,-309.03:41:45 0/1:-159.89,-144.07,-409.74:66:57 chr20 29633938 . A G 28 PASS ABPV=1.00e+00;FPV=1.27e-01;FR=0.2500;HP=2;MMLQ=34;NF=16;NR=24;PP=28;RMP=56.91;RPV=2.94e-01;SC=AAATGACTGGAATTTTTGTTT;TC=192;TCF=84;TCR=108;TR=40;func=ncRNA;gene=FRG1B;cons46=514 Name=lod=163;segdup=0.96;dbsnp=rs4006818 GT:GL:GQ:NR 0/0:-963.63,-978.07,-1139.59:64:101 1/0:-1046.34,-1031.41,-1112.07:63:91 chr20 33356511 . C T 44 PASS ABPV=1.00e+00;FPV=7.49e-01;FR=0.2507;HP=1;MMLQ=37;NF=0;NR=4;PP=44;RMP=57.46;RPV=6.28e-01;SC=AGTTTACCACCAGAAAAATGG;TC=17;TCF=1;TCR=16;TR=4;func=intronic;gene=NCOA6;cons46=243 Name=lod=13;1000g=0.36;dbsnp=rs2295353 GT:GL:GQ:NR 0/0:0.0,-5.54,-70.65:25:8 0/1:-49.75,-31.07,-63.51:79:9 chr21 14424170 . C G 200 PASS ABPV=1.00e+00;FPV=7.37e-05;FR=0.2502;HP=1;MMLQ=31;NF=51;NR=68;PP=200;RMP=55.06;RPV=7.01e-02;SC=GGAAAGAACACCTGACACGGC;TC=637;TCF=318;TCR=319;TR=119 GT:GL:GQ:NR 0/0:-1068.97,-1075.78,-2090.04:31:272 1/0:-1608.82,-1559.51,-2814.14:100:365 chr22 16256578 . G T 200 PASS ABPV=2.18e-01;FPV=6.87e-08;FR=0.2502;HP=4;MMLQ=34;NF=19;NR=8;PP=200;RMP=40.16;RPV=2.46e-02;SC=TGGCTCTGATGTTTCATTATG;TC=253;TCF=194;TCR=59;TR=27 GT:GL:GQ:NR 0/0:-139.12,-145.98,-745.94:31:118 0/1:-324.53,-220.54,-788.14:100:135 chr22 24640438 . TCA T 58 PASS ABPV=5.57e-01;FPV=3.19e-02;FR=0.2503;HP=2;NF=2;NR=1;PP=58;RMP=48.68;RPV=9.37e-01;SC=ATACATTCACTCACACACACA;TC=27;TCF=25;TCR=2;TR=3 GT:GL:GQ:NR 0/0:-4.37,-10.61,-107.94:28:12 0/1:-47.48,-22.82,-120.6:100:15 chr22 42524924 . A G 32 PASS ABPV=1.00e+00;FPV=1.78e-02;FR=0.2500;HP=2;MMLQ=35;NF=0;NR=4;PP=32;RMP=71.83;RPV=5.74e-01;SC=TGTCCAAGAGACCGTTGGGGC;TC=31;TCF=14;TCR=17;TR=4 GT:GL:GQ:NR 0/0:-1.84,-12.87,-112.28:49:17 1/0:-35.2,-19.47,-73.62:66:14 chr3 6522043 . G A 62 PASS ABPV=1.00e+00;FPV=5.16e-01;FR=0.2507;HP=3;MMLQ=37;NF=4;NR=0;PP=62;RMP=44.82;RPV=7.49e-01;SC=TAACTGCAAAGTAGGAACACG;TC=19;TCF=18;TCR=1;TR=4 GT:GL:GQ:NR 0/0:0.0,-5.54,-65.36:25:9 1/0:-46.21,-23.49,-68.33:96:10 chr3 135742089 . GAAAATA G 56 PASS ABPV=2.53e-02;FPV=5.62e-01;FR=0.2500;HP=4;NF=0;NR=2;PP=56;RMP=97.0;RPV=4.10e-05;SC=GTTTTGTTTTGAAAATATTTT;TC=55;TCF=2;TCR=53;TR=2 GT:GL:GQ:NR 0/0:-171.19,-180.69,-401.53:43:27 1/0:-163.7,-138.73,-368.83:100:28 chr3 195453014 . G A 73 PASS ABPV=1.00e+00;FPV=9.99e-01;FR=0.2500;HP=3;MMLQ=31;NF=44;NR=44;PP=73;RMP=52.04;RPV=1.00e-00;SC=GACAGCACCCGGGGCCACGAC;TC=210;TCF=115;TCR=95;TR=88 GT:GL:GQ:NR 0/0:-596.82,-608.68,-929.74:53:99 0/1:-825.59,-800.41,-1040.36:100:111 chr3 195453412 . C T 21 PASS ABPV=1.00e+00;FPV=1.25e-02;FR=0.2502;HP=2;MMLQ=25;NF=13;NR=52;PP=21;RMP=62.2;RPV=1.00e-00;SC=CCACGACTGCCCGGACGAGGC;TC=219;TCF=89;TCR=130;TR=65 GT:GL:GQ:NR 0/0:-275.62,-282.43,-681.47:31:103 0/1:-362.65,-349.41,-719.87:55:117 chr3 195506775 . G A 87 PASS ABPV=1.00e+00;FPV=8.81e-01;FR=0.2500;HP=1;MMLQ=34;NF=11;NR=4;PP=87;RMP=30.23;RPV=4.10e-02;SC=AGGAAGTGTCGGTGACAGGAA;TC=69;TCF=34;TCR=35;TR=15;func=exonic;gene=MUC4;exon_func=synonymous SNV;AAchange=NM_018406:c.C11676T:p.H3892H;cons46=381 Name=lod=47;segdup=0.92;1000g=0.48;dbsnp=rs79609066 GT:GL:GQ:NR 0/0:-215.78,-225.62,-329.97:44:31 0/1:-253.55,-225.09,-324.19:100:38 chr3 195507372 . C A 72 PASS ABPV=1.00e+00;FPV=9.50e-01;FR=0.2510;HP=1;MMLQ=31;NF=12;NR=10;PP=72;RMP=82.02;RPV=4.71e-01;SC=GAGGGGTGGCCTGACCTGTGG;TC=76;TCF=33;TCR=43;TR=22 GT:GL:GQ:NR 0/0:-85.59,-90.71,-175.03:23:27 0/1:-302.0,-277.02,-435.24:100:49 chr3 195509974 . A G 107 PASS ABPV=1.00e+00;FPV=4.52e-02;FR=0.2501;HP=1;MMLQ=33;NF=7;NR=15;PP=107;RMP=66.83;RPV=1.62e-01;SC=ATGACCTGTGAACACTGAGGA;TC=127;TCF=50;TCR=77;TR=22 GT:GL:GQ:NR 0/0:-281.04,-289.1,-469.31:36:51 0/1:-474.46,-441.44,-679.46:100:76 chr4 3589510 . G A 82 PASS ABPV=1.00e+00;FPV=1.00e-00;FR=0.2500;HP=1;MMLQ=35;NF=28;NR=15;PP=82;RMP=39.79;RPV=1.00e-00;SC=ACTTCCAGATGAGACTTCCTG;TC=89;TCF=62;TCR=27;TR=43;func=ncRNA;gene=FLJ35424 GT:GL:GQ:NR 0/0:-202.17,-216.0,-372.38:61:36 0/1:-618.94,-591.66,-690.1:100:53 chr4 5747131 . C A 40 PASS ABPV=1.00e+00;FPV=6.32e-01;FR=0.2502;HP=2;MMLQ=33;NF=1;NR=19;PP=40;RMP=63.27;RPV=9.99e-01;SC=AAATTGGCTACATTAGAGAGA;TC=45;TCF=5;TCR=40;TR=20 GT:GL:GQ:NR 0/0:-175.23,-182.17,-227.63:31:19 1/0:-264.71,-246.95,-301.81:75:26 chr4 70261725 . G A 25 PASS ABPV=1.00e+00;FPV=8.43e-01;FR=0.2503;HP=3;MMLQ=36;NF=1;NR=5;PP=25;RMP=77.58;RPV=8.09e-01;SC=TGTGGCCCTGGGGTAGTTACT;TC=19;TCF=3;TCR=16;TR=6 GT:GL:GQ:NR 0/0:-25.09,-31.31,-100.1:28:11 1/0:-62.48,-48.33,-68.8:59:8 chr5 837488 . C A 84 PASS ABPV=3.03e-01;FPV=2.26e-02;FR=0.2502;HP=2;MMLQ=35;NF=22;NR=3;PP=84;RMP=67.65;RPV=4.45e-09;SC=ACCTGGAGAACTCCTTTGTCC;TC=225;TCF=128;TCR=97;TR=25 GT:GL:GQ:NR 0/0:-71.02,-77.56,-596.34:30:92 0/1:-157.13,-129.33,-794.35:100:133 chr5 34192944 . A G 136 PASS ABPV=3.53e-01;FPV=1.29e-04;FR=0.2500;HP=1;MMLQ=31;NF=17;NR=13;PP=136;RMP=51.73;RPV=7.15e-05;SC=GCAGTGGATGAAGGCCCCTCA;TC=261;TCF=140;TCR=121;TR=30 GT:GL:GQ:NR 0/0:-120.41,-138.2,-806.35:79:120 0/1:-199.6,-159.91,-913.41:100:141 chr5 36200413 . G A 33 PASS ABPV=1.25e-02;FPV=1.03e-02;FR=0.2511;HP=3;MMLQ=34;NF=2;NR=4;PP=33;RMP=98.68;RPV=2.69e-06;SC=GAAAATGTATGTTATAAATAT;TC=109;TCF=30;TCR=79;TR=6 GT:GL:GQ:NR 0/0:-295.77,-300.82,-490.03:23:53 1/0:-290.08,-274.08,-469.93:67:56 chr5 41909830 . C T 27 PASS ABPV=5.28e-01;FPV=2.35e-03;FR=0.2504;HP=18;MMLQ=0;NF=0;NR=3;PP=27;RMP=14.14;RPV=9.29e-01;SC=AGATATCTTTCTTTTTTTTTT;TC=28;TCF=21;TCR=7;TR=3 GT:GL:GQ:NR 0/0:-4.61,-10.58,-40.73:26:11 0/1:-41.44,-26.72,-53.62:62:17 chr5 54329850 . C CTGCTTTACTTA 68 PASS ABPV=5.01e-01;FPV=1.00e+00;FR=0.2503;HP=1;NF=0;NR=2;PP=68;RMP=90.0;RPV=7.41e-02;SC=CATATGGGGTCCATTTTTGCA;TC=21;TCF=0;TCR=21;TR=2 GT:GL:GQ:NR 0/0:0.0,-6.24,-122.94:28:9 1/0:-45.59,-6.93,-110.5:100:12 chr5 58121059 . G A 112 PASS ABPV=1.00e+00;FPV=4.22e-01;FR=0.2501;HP=2;MMLQ=35;NF=0;NR=5;PP=112;RMP=75.51;RPV=4.68e-01;SC=TACAGAGTCCGAGCTAATTGT;TC=26;TCF=3;TCR=23;TR=5 GT:GL:GQ:NR 0/0:-31.77,-39.38,-124.25:34:12 0/1:-43.94,-9.7,-79.61:100:15 chr5 169535734 . C A 20 PASS ABPV=1.00e+00;FPV=1.00e+00;FR=0.2507;HP=1;MMLQ=34;NF=0;NR=2;PP=20;RMP=68.72;RPV=3.31e-01;SC=CAGGAGCCTCCGAGGAATCCA;TC=13;TCF=0;TCR=13;TR=2;func=UTR3;gene=FOXI1;1000g=0.35;dbsnp=rs6873124 GT:GL:GQ:NR 0/0:-5.3,-10.84,-76.27:25:8 1/0:-15.88,-2.77,-16.56:54:5 chr5 175467765 . A C 34 PASS ABPV=1.00e+00;FPV=6.86e-01;FR=0.2503;HP=3;MMLQ=37;NF=4;NR=7;PP=34;RMP=58.23;RPV=9.60e-01;SC=AGGAAAGCAGATTTGTACATC;TC=32;TCF=15;TCR=17;TR=11 GT:GL:GQ:NR 0/0:-48.25,-54.62,-116.89:29:16 0/1:-64.43,-48.26,-102.15:68:18 chr5 180047739 . CGT C 40 PASS ABPV=3.01e-01;FPV=4.20e-02;FR=0.2503;HP=3;NF=0;NR=2;PP=40;RMP=66.37;RPV=1.63e-01;SC=AAGGGGCCGGCGTGTGTGTGT;TC=28;TCF=11;TCR=17;TR=2 GT:GL:GQ:NR 0/0:-15.43,-21.66,-115.16:28:17 0/1:-35.79,-15.44,-86.67:86:11 chr6 26370657 . A G 26 PASS ABPV=1.00e+00;FPV=9.98e-01;FR=0.2500;HP=1;MMLQ=34;NF=25;NR=18;PP=26;RMP=46.67;RPV=9.65e-01;SC=ACAGTGGAGCAACGCCAAGGG;TC=112;TCF=61;TCR=51;TR=43 GT:GL:GQ:NR 0/0:-408.78,-416.97,-671.27:37:70 1/0:-270.25,-255.76,-422.39:61:42 chr6 26370659 . C T 32 PASS ABPV=1.00e+00;FPV=9.98e-01;FR=0.2500;HP=2;MMLQ=34;NF=25;NR=17;PP=32;RMP=48.69;RPV=9.08e-01;SC=AGTGGAGCAACGCCAAGGGAG;TC=114;TCF=61;TCR=53;TR=42 GT:GL:GQ:NR 0/0:-408.78,-419.23,-664.68:47:70 1/0:-278.07,-262.18,-440.62:67:44 chr6 35838820 . A ATTCTTACTTGG 44 PASS ABPV=1.42e-01;FPV=7.50e-01;FR=0.2500;HP=1;NF=0;NR=2;PP=44;RMP=90.0;RPV=2.64e-03;SC=CTCTACCAGAATGAAAAGTCT;TC=37;TCF=1;TCR=36;TR=2 GT:GL:GQ:NR 0/0:-22.8,-33.89,-243.84:49:19 1/0:-50.19,-17.08,-221.97:100:21 chr6 58777098 . A T 42 PASS ABPV=1.00e+00;FPV=2.57e-03;FR=0.2500;HP=2;MMLQ=34;NF=14;NR=25;PP=42;RMP=50.5;RPV=1.85e-01;SC=GTAACTCTAGATTGAAGAATT;TC=224;TCF=105;TCR=119;TR=39;func=intergenic;gene=GUSBP4(dist=489374) NONE(dist=NONE);dbsnp=rs4330557 GT:GL:GQ:NR 0/0:-1161.42,-1180.18,-1411.53:83:106 0/1:-1283.78,-1265.72,-1460.11:76:119 chr6 116774635 . C G 38 PASS ABPV=1.00e+00;FPV=3.66e-01;FR=0.2504;HP=1;MMLQ=36;NF=4;NR=12;PP=38;RMP=76.7;RPV=4.76e-01;SC=CTTTTTCCACCACAAATTCTT;TC=72;TCF=21;TCR=51;TR=16 GT:GL:GQ:NR 0/0:-45.72,-51.81,-228.46:28:30 0/1:-179.58,-162.43,-353.98:72:42 chr6 136599000 . T TCATCTGTGA 73 PASS ABPV=2.21e-05;FPV=2.55e-09;FR=0.2505;HP=4;NF=2;NR=0;PP=73;RMP=1.41;RPV=3.11e-04;SC=TTTTAGTTTTTACCTTTTTAA;TC=118;TCF=90;TCR=28;TR=2;func=intronic;gene=BCLAF1;cons46=573 Name=lod=284;segdup=0.97 GT:GL:GQ:NR 0/0:-44.16,-49.89,-603.4:26:61 1/0:-105.25,-67.59,-750.95:100:79 chr6 155757781 . T A 106 PASS ABPV=1.00e+00;FPV=3.16e-01;FR=0.2504;HP=2;MMLQ=36;NF=0;NR=5;PP=106;RMP=66.42;RPV=6.16e-01;SC=TACAGTGAGCTCTGAAATATC;TC=24;TCF=4;TCR=20;TR=5;func=intronic;gene=NOX3;1000g=0.22;dbsnp=rs231961 GT:GL:GQ:NR 0/0:0.0,-6.09,-69.03:28:9 0/1:-48.54,-15.69,-84.63:100:15 chr7 65159983 . A G 128 PASS ABPV=1.00e+00;FPV=5.13e-01;FR=0.2500;HP=2;MMLQ=33;NF=9;NR=0;PP=128;RMP=42.05;RPV=1.33e-01;SC=TTGCTTAGTTACCAGGTAGAA;TC=45;TCF=38;TCR=7;TR=9;func=ncRNA;gene=INTS4L2 LOC441242;cons46=439 Name=lod=81;segdup=0.99;1000g=0.26;dbsnp=rs2949280 GT:GL:GQ:NR 0/0:0.0,-9.67,-99.87:43:16 0/1:-63.32,-25.43,-98.84:100:29 chr7 100552044 . T G 46 PASS ABPV=1.00e+00;FPV=1.00e-00;FR=0.2500;HP=1;MMLQ=33;NF=133;NR=185;PP=46;RMP=54.24;RPV=1.00e-00;SC=CTGTTCCTTCTTCACCATACA;TC=776;TCF=387;TCR=389;TR=318 GT:GL:GQ:NR 0/0:-2768.08,-2799.9,-3980.82:100:373 0/1:-3148.55,-3129.5,-4372.1:80:403 chr7 102319079 . G A 34 PASS ABPV=4.40e-01;FPV=1.00e+00;FR=0.2500;HP=1;MMLQ=38;NF=0;NR=6;PP=34;RMP=53.53;RPV=6.65e-03;SC=TGTGAGATGCGTGTGAAAATG;TC=56;TCF=0;TCR=56;TR=6;func=intergenic;gene=POLR2J2(dist=6903) FAM185A(dist=70320);segdup=1.00;1000g=0.17;dbsnp=rs62458736 GT:GL:GQ:NR 0/0:-9.39,-20.95,-166.2:51:26 0/1:-46.26,-30.07,-176.58:68:30 chr7 106272259 . C T 200 PASS ABPV=1.00e+00;FPV=1.51e-04;FR=0.2501;HP=2;MMLQ=31;NF=27;NR=25;PP=200;RMP=18.87;RPV=1.08e-05;SC=CTCATTCCAACCTCTGCTTCC;TC=391;TCF=192;TCR=199;TR=52 GT:GL:GQ:NR 0/0:-1599.11,-1606.25,-1841.06:32:195 0/1:-1703.84,-1621.18,-1787.33:100:196 chr7 128492558 . G A 32 PASS ABPV=1.00e+00;FPV=9.80e-01;FR=0.2501;HP=6;MMLQ=35;NF=15;NR=1;PP=32;RMP=45.11;RPV=5.34e-01;SC=TGAGTCCAGGGGGGGCTGCTC;TC=45;TCF=39;TCR=6;TR=16 GT:GL:GQ:NR 0/0:-82.82,-89.89,-214.44:32:24 0/1:-137.27,-121.35,-194.99:67:21 chr7 142223942 . A G 200 PASS ABPV=1.00e+00;FPV=1.00e-00;FR=0.2500;HP=1;MMLQ=33;NF=86;NR=42;PP=200;RMP=48.5;RPV=9.93e-01;SC=ACTGTGAATCATCTACTACAC;TC=282;TCF=160;TCR=122;TR=128 GT:GL:GQ:NR 0/0:-840.21,-856.54,-1228.56:72:124 1/0:-1069.18,-1023.08,-1489.98:100:158 chr7 142498735 . A C 51 PASS ABPV=1.00e+00;FPV=9.39e-01;FR=0.2500;HP=4;MMLQ=34;NF=23;NR=20;PP=51;RMP=54.1;RPV=9.74e-01;SC=AGGACCTGAAAAACGTGTTCC;TC=127;TCF=71;TCR=56;TR=43;func=intergenic;gene=TRY6(dist=16336) EPHB6(dist=54057);sift=0.35 GT:GL:GQ:NR 0/0:-407.53,-415.97,-666.18:38:67 0/1:-407.94,-387.73,-626.55:86:62 chr7 143295456 . A C 200 PASS ABPV=1.00e+00;FPV=7.75e-01;FR=0.2500;HP=1;MMLQ=26;NF=24;NR=7;PP=200;RMP=70.65;RPV=6.11e-02;SC=GCCTCCTCGCAGTGGGGGGCA;TC=135;TCF=87;TCR=48;TR=31 GT:GL:GQ:NR 0/0:-28.78,-39.63,-253.37:48:66 0/1:-158.76,-57.73,-187.94:100:69 chr7 143453710 . T A 66 PASS ABPV=1.00e+00;FPV=5.62e-01;FR=0.2501;HP=3;MMLQ=36;NF=0;NR=15;PP=66;RMP=54.55;RPV=5.68e-01;SC=TCTTCCTTTGTTTTGTCCACT;TC=62;TCF=2;TCR=60;TR=15 GT:GL:GQ:NR 0/0:-65.41,-73.41,-216.2:36:31 0/1:-102.8,-79.18,-187.97:100:31 chr7 143956461 . T C 37 PASS ABPV=1.00e+00;FPV=8.34e-02;FR=0.2500;HP=2;MMLQ=31;NF=5;NR=0;PP=37;RMP=48.38;RPV=1.00e+00;SC=TGGGCTTGGCTGGATGCAGGA;TC=36;TCF=36;TCR=0;TR=5 GT:GL:GQ:NR 0/0:-6.63,-15.42,-125.53:39:20 1/0:-33.93,-16.96,-77.4:71:16 chr7 157367205 . TGA T 52 PASS ABPV=3.26e-01;FPV=5.62e-01;FR=0.2503;HP=2;NF=0;NR=2;PP=52;RMP=55.44;RPV=3.19e-02;SC=AGAGTAATAATGAGAGAGAGA;TC=27;TCF=2;TCR=25;TR=2;func=intronic;gene=PTPRN2 GT:GL:GQ:NR 0/0:-10.36,-16.59,-113.87:28:16 1/0:-39.42,-16.12,-59.64:99:12 chr8 8095880 . C T 131 PASS ABPV=1.00e+00;FPV=2.37e-01;FR=0.2500;HP=3;MMLQ=37;NF=0;NR=10;PP=131;RMP=64.63;RPV=8.71e-01;SC=GCCACATGGCCCCAGGCCCAA;TC=36;TCF=5;TCR=31;TR=10;func=ncRNA;gene=FLJ10661;segdup=0.98 GT:GL:GQ:NR 0/0:-78.8,-87.2,-171.27:38:18 0/1:-81.81,-43.3,-81.08:100:18 chr8 12236123 . T G 111 PASS ABPV=1.00e+00;FPV=1.38e-39;FR=0.2500;HP=2;MMLQ=30;NF=16;NR=9;PP=111;RMP=18.14;RPV=9.45e-01;SC=GTATTTGTGTTTGTGTGTGTG;TC=103;TCF=79;TCR=24;TR=25 GT:GL:GQ:NR 0/0:-265.16,-270.76,-457.35:100:49 1/0:-317.4,-305.02,-585.97:25:76 chr8 12428634 . C T 69 PASS ABPV=1.00e+00;FPV=7.50e-01;FR=0.2500;HP=1;MMLQ=36;NF=0;NR=5;PP=69;RMP=63.98;RPV=2.03e-01;SC=TCTTAACAACCGCCATGGTGC;TC=31;TCF=1;TCR=30;TR=5 GT:GL:GQ:NR 0/0:-10.77,-21.63,-134.62:48:17 1/0:-41.03,-16.59,-80.89:100:14 chr8 35608374 . T C 24 PASS ABPV=1.00e+00;FPV=6.32e-01;FR=0.2502;HP=2;MMLQ=34;NF=1;NR=34;PP=24;RMP=69.53;RPV=1.00e-00;SC=TGAAAGTGTGTGTTTTCCAAA;TC=62;TCF=5;TCR=57;TR=35 GT:GL:GQ:NR 0/0:-248.65,-255.21,-376.27:30:35 1/0:-265.91,-251.92,-307.04:58:27 chr8 121500323 . A AGTGGGATTGC 40 PASS ABPV=2.19e-01;FPV=8.43e-03;FR=0.2500;HP=2;NF=2;NR=0;PP=40;RMP=1.0;RPV=7.50e-01;SC=ATTATATCCTATGGATCAAAT;TC=32;TCF=31;TCR=1;TR=2 GT:GL:GQ:NR 0/0:-2.07,-11.08,-162.96:40:13 1/0:-47.66,-16.63,-264.67:100:25 chr9 14510 . CTGT C 200 PASS ABPV=2.20e-01;FPV=4.66e-14;FR=0.2500;HP=1;NF=12;NR=0;PP=200;RMP=43.31;RPV=1.00e-02;SC=TAAAAGCACACTGTTGGTTTC;TC=123;TCF=107;TCR=16;TR=12 GT:GL:GQ:NR 0/0:-22.04,-38.67,-350.71:73:53 0/1:-133.83,-67.48,-425.73:100:75 chr9 34724786 . G A 54 PASS ABPV=1.00e+00;FPV=5.46e-01;FR=0.2503;HP=2;MMLQ=31;NF=10;NR=18;PP=54;RMP=64.11;RPV=9.71e-01;SC=GGATTTCCACGGGACTAGGCT;TC=91;TCF=41;TCR=50;TR=28 GT:GL:GQ:NR 0/0:-77.92,-84.2,-224.15:29:46 1/0:-101.32,-80.48,-207.58:88:45 chr9 44118498 . G C 200 PASS ABPV=1.00e+00;FPV=9.49e-01;FR=0.2503;HP=2;MMLQ=34;NF=2;NR=7;PP=200;RMP=65.44;RPV=6.41e-01;SC=GAGGGCAGCTGCCTGTCACCT;TC=31;TCF=4;TCR=27;TR=9;func=intergenic;gene=CNTNAP3B(dist=196025) FAM27C(dist=871738);segdup=0.98;1000g=0.77;dbsnp=rs28610048 GT:GL:GQ:NR 0/0:-11.97,-18.32,-91.33:29:13 0/1:-73.63,-27.61,-81.59:100:18 chr9 67281836 . T G 200 PASS ABPV=1.00e+00;FPV=3.12e-01;FR=0.2500;HP=2;MMLQ=34;NF=6;NR=21;PP=200;RMP=63.02;RPV=5.58e-01;SC=GTGGACCTGATACAGTGGCCC;TC=115;TCF=31;TCR=84;TR=27;func=ncRNA;gene=AQP7P1;segdup=0.99;1000g=0.26;dbsnp=rs75812522 GT:GL:GQ:NR 0/0:-227.43,-240.42,-365.47:58:50 0/1:-353.09,-303.78,-464.7:100:65 chr9 67293649 . T G 200 PASS ABPV=1.00e+00;FPV=2.40e-02;FR=0.2509;HP=2;MMLQ=32;NF=8;NR=20;PP=200;RMP=65.85;RPV=6.29e-01;SC=GTGTGCCAAGTGACTTCATCT;TC=136;TCF=59;TCR=77;TR=28 GT:GL:GQ:NR 0/0:-52.46,-57.7,-399.51:24:62 0/1:-141.44,-82.05,-400.07:100:74 chr9 68358140 . T C 101 PASS ABPV=1.00e+00;FPV=4.09e-01;FR=0.2501;HP=2;MMLQ=31;NF=10;NR=13;PP=101;RMP=52.55;RPV=9.14e-01;SC=CCGCTTCAGATAGTGAAGAAG;TC=84;TCF=45;TCR=39;TR=23;func=intergenic;gene=ANKRD20A3(dist=387847) LOC642236(dist=69643);cons46=780 Name=lod=1967;segdup=0.98;dbsnp=rs62544188 GT:GL:GQ:NR 0/0:-99.49,-107.4,-306.63:36:46 0/1:-122.69,-91.06,-221.21:100:38 chr9 92995102 . C T 25 PASS ABPV=1.74e-02;FPV=2.34e-06;FR=0.2500;HP=3;MMLQ=33;NF=11;NR=10;PP=25;RMP=36.17;RPV=2.75e-07;SC=ATAAAATTGTCCCCTCCATTC;TC=258;TCF=127;TCR=131;TR=21;func=intergenic;gene=LOC286370(dist=191321) LOC340515(dist=229612);segdup=0.96 GT:GL:GQ:NR 0/0:-127.8,-170.89,-839.43:100:127 1/0:-164.37,-150.07,-829.28:60:131 chr9 139572068 . C G 44 PASS ABPV=1.00e+00;FPV=4.21e-01;FR=0.2507;HP=2;MMLQ=29;NF=0;NR=3;PP=44;RMP=57.58;RPV=7.11e-01;SC=GGCTGGGGCGCGAAGGCCTGG;TC=14;TCF=3;TCR=11;TR=3;func=intronic;gene=AGPAT2;1000g=0.57;dbsnp=rs2236514 GT:GL:GQ:NR 0/0:0.0,-5.54,-62.14:25:9 1/0:-29.67,-11.06,-23.48:61:5 chr9 140777194 . A AGAGCGGCT 200 PASS ABPV=7.76e-05;FPV=4.77e-24;FR=0.2500;HP=2;NF=2;NR=1;PP=200;RMP=4.36;RPV=2.92e-05;SC=CGCTTCTCCTAGGACGACACG;TC=123;TCF=77;TCR=46;TR=3;func=splicing;gene=CACNA1B(NM_000718:c.390-2->CATGTCCGAGCGGCT NM_001243812:c.390-2->CATGTCCGAGCGGCT);cons46=573 Name=lod=285 GT:GL:GQ:NR 0/0:-260.4,-275.23,-819.04:71:85 0/1:-510.15,-408.95,-886.86:3:93 chrUn_gl000214 53458 . T A 82 PASS ABPV=4.34e-01;FPV=7.36e-06;FR=0.2500;HP=4;MMLQ=34;NF=22;NR=0;PP=82;RMP=47.4;RPV=5.62e-01;SC=AAACACTATATAAATATAATT;TC=187;TCF=185;TCR=2;TR=22;func=intergenic;gene=NONE(dist=NONE) NONE(dist=NONE);segdup=0.98 GT:GL:GQ:NR 0/0:-154.3,-180.61,-694.01:100:88 1/0:-304.62,-277.18,-752.95:100:99 chrUn_gl000214 61035 . A G 25 PASS ABPV=2.68e-01;FPV=1.27e-06;FR=0.2500;HP=2;MMLQ=34;NF=20;NR=0;PP=25;RMP=60.63;RPV=4.22e-01;SC=ATGTTTACCTATATAACAAAC;TC=187;TCF=184;TCR=3;TR=20 GT:GL:GQ:NR 0/0:-517.15,-538.58,-910.78:94:80 0/1:-812.82,-798.54,-1242.08:60:107 chrUn_gl000214 74804 . T C 45 PASS ABPV=5.69e-01;FPV=4.33e-02;FR=0.2500;HP=2;MMLQ=35;NF=5;NR=0;PP=45;RMP=36.66;RPV=5.62e-01;SC=ATCACTTGAATGCAGTAGGCA;TC=42;TCF=40;TCR=2;TR=5 GT:GL:GQ:NR 0/0:-65.35,-75.06,-177.61:43:16 0/1:-180.67,-161.94,-279.38:79:26 chrUn_gl000220 121703 . T C 75 PASS ABPV=9.31e-02;FPV=1.94e-05;FR=0.2500;HP=2;MMLQ=31;NF=5;NR=8;PP=75;RMP=52.13;RPV=2.81e-03;SC=GTGGGCACGGTACGCTCTGGT;TC=150;TCF=78;TCR=72;TR=13 GT:GL:GQ:NR 0/0:-64.92,-78.18,-505.13:59:80 1/0:-102.59,-76.78,-453.86:100:70 chrUn_gl000220 128026 . C T 73 PASS ABPV=1.00e+00;FPV=1.39e-05;FR=0.2500;HP=1;MMLQ=37;NF=12;NR=5;PP=73;RMP=48.23;RPV=2.65e-03;SC=TCTCTGTCTCCGTCTCTGTCT;TC=117;TCF=62;TCR=55;TR=17 GT:GL:GQ:NR 0/0:-175.58,-193.94,-521.81:81:62 1/0:-151.61,-126.36,-397.61:100:57 chrUn_gl000220 132074 . G A 200 PASS ABPV=1.00e+00;FPV=2.39e-03;FR=0.2500;HP=2;MMLQ=34;NF=10;NR=11;PP=200;RMP=61.51;RPV=6.72e-03;SC=CTCTCTGTCCGTCTCTGTCTT;TC=167;TCF=84;TCR=83;TR=21;func=intergenic;gene=LOC100507412(dist=5378) RN5-8S1(dist=23923);segdup=0.95 GT:GL:GQ:NR 0/0:-248.2,-257.69,-615.12:42:77 0/1:-290.71,-234.79,-658.31:100:90 chrUn_gl000220 145002 . C T 28 PASS ABPV=3.17e-02;FPV=7.56e-08;FR=0.2500;HP=4;MMLQ=31;NF=1;NR=3;PP=28;RMP=65.86;RPV=4.70e-03;SC=ACTAGCCGGGCGCGGTGGCAC;TC=76;TCF=36;TCR=40;TR=4 GT:GL:GQ:NR 0/0:-17.73,-43.17,-320.69:100:46 1/0:-67.96,-52.99,-236.43:63:37 chrUn_gl000220 145368 . T C 30 PASS ABPV=1.09e-01;FPV=1.31e-02;FR=0.2500;HP=1;MMLQ=29;NF=8;NR=2;PP=30;RMP=72.81;RPV=1.92e-05;SC=AGCCGGGCGCTGTGCTGTGCT;TC=119;TCF=63;TCR=56;TR=10;func=intergenic;gene=LOC100507412(dist=18672) RN5-8S1(dist=10629);dbsnp=rs3878955 GT:GL:GQ:NR 0/0:-48.56,-59.69,-409.13:50:53 0/1:-66.74,-51.46,-448.03:64:66 chrUn_gl000225 30398 . C T 29 PASS ABPV=1.13e-01;FPV=3.15e-04;FR=0.2502;HP=1;MMLQ=33;NF=1;NR=5;PP=29;RMP=58.12;RPV=2.55e-02;SC=CCTGCTCCTCCGAGCCTTTGA;TC=80;TCF=37;TCR=43;TR=6 GT:GL:GQ:NR 0/0:-195.73,-202.53,-342.72:31:35 1/0:-230.45,-215.31,-371.74:63:45 chrUn_gl000225 43193 . C T 46 PASS ABPV=1.00e+00;FPV=7.84e-02;FR=0.2507;HP=3;MMLQ=31;NF=8;NR=12;PP=46;RMP=44.42;RPV=4.19e-02;SC=GCCAGAGAGACGGGCCTCCCG;TC=126;TCF=51;TCR=75;TR=20 GT:GL:GQ:NR 0/0:-577.5,-583.01,-743.98:25:63 1/0:-604.31,-585.16,-703.98:81:63 chrX 106390898 . G A 65 PASS ABPV=4.78e-01;FPV=1.49e-02;FR=0.2500;HP=1;MMLQ=39;NF=5;NR=0;PP=65;RMP=43.16;RPV=1.00e+00;SC=GTTTGGTCATGGAGCATACAA;TC=46;TCF=46;TCR=0;TR=5 GT:GL:GQ:NR 0/0:0.0,-11.78,-148.84:52:17 1/0:-49.23,-25.85,-211.17:99:29 pysam-0.23.0/tests/tabix_data/vcf/15.vcf000066400000000000000000016654451475062545500177340ustar00rootroot00000000000000##fileformat=VCFv4.0 ##FILTER= ##FILTER= ##FILTER= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##ValidationMetrics_HardyWeinbergViolations="25 (8%)" ##ValidationMetrics_HomVarViolations="0 (0%)" ##ValidationMetrics_NoCallViolations="13 (4%)" ##ValidationMetrics_PolymorphicPassingRecords="195 (75%)" ##ValidationMetrics_RecordsPassingFilters="258 (87%)" ##ValidationMetrics_RecordsProcessed=296 ##ValidationMetrics_SamplesAssayed=383 ##VariantValidationAssessor="analysis_type=VariantValidationAssessor input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[rawData/plink.renamed.sorted.fixed.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub maxHardy=20.0 maxNoCall=0.05 maxHomVar=1.1" ##source=PLINK #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00127 HG00128 HG00136 HG00137 HG00138 HG00139 HG00152 HG00156 HG00234 HG00235 HG00237 HG00242 HG00244 HG00262 HG01055 HG01079 NA19138 NA18974 NA18523 NA12717 NA19209 NA18577 NA18973 NA18943 NA12873 NA18623 NA18622 NA18948 NA19171 NA19204 NA06994 NA18563 NA18547 NA18861 NA18608 NA18995 NA10851 NA18976 NA18603 NA19200 HG01204 HG01191 HG01101 HG00146 HG00306 NA18985 HG00160 HG00635 HG00372 HG00357 HG00634 NA18541 NA18950 NA19759 HG00351 HG00257 HG00118 HG00336 HG00448 HG01354 NA18609 HG00428 HG00326 NA11894 NA18956 HG00173 HG00117 NA11893 HG01251 HG01441 HG01437 HG00182 HG00330 HG01060 HG00329 NA18960 NA18856 NA07346 NA18871 NA19057 NA18868 NA18636 NA12830 NA19007 NA18910 NA18874 NA19056 NA19064 NA19066 NA18487 NA18642 NA19236 NA07056 NA18637 NA19235 NA19309 NA19311 NA19334 NA19346 NA19347 NA19372 NA19376 NA19383 NA19384 NA19394 NA19428 NA19430 NA19451 NA19466 NA19313 NA19321 NA19324 NA19332 NA19390 NA19436 NA19439 NA19440 NA19463 NA19470 NA19471 NA19472 NA19676 NA19660 NA19661 NA19663 NA19722 NA19725 NA19728 NA19729 NA19731 NA19749 NA19755 NA19756 NA19758 NA19770 NA19773 NA19777 NA19780 NA19783 NA20525 NA20589 NA20765 NA20802 NA20804 NA18544 NA18602 NA18546 NA18610 NA18957 NA18615 NA18616 NA19010 NA18638 NA18639 NA18627 NA19072 NA18630 NA19074 NA19080 NA19081 NA19083 NA19085 NA19088 NA20287 NA19835 NA20276 NA19818 NA20278 NA20282 NA20342 NA20296 NA20314 NA20346 NA19712 NA19198 NA19108 NA18934 NA18916 NA18907 NA18917 NA06989 NA12058 NA12341 NA12546 NA12489 HG01197 NA18983 NA11843 NA11892 NA12749 NA12282 NA12751 NA18959 NA19331 NA19453 NA20537 NA12046 NA20515 NA20516 NA20521 NA20524 NA20528 NA20759 NA20768 NA20769 NA20774 NA20775 NA20783 NA20787 NA20790 NA20800 NA20819 NA20812 NA20505 NA20530 NA20540 NA20538 NA20581 NA20815 NA20544 NA20810 NA20807 NA20816 NA20504 NA20753 NA20502 NA12342 NA19150 NA19468 NA20336 NA19395 NA19257 NA19360 NA19700 NA18867 NA20317 NA18968 NA19107 HG00111 HG00108 NA19077 NA19684 NA18511 NA12044 NA19382 NA19457 NA18933 NA18923 NA18965 HG00141 NA20341 NA18740 HG00537 HG00346 HG01173 HG00702 HG00313 HG00150 NA18612 HG00339 NA12273 HG00250 NA18593 NA18621 HG00478 HG00251 HG01070 NA19160 HG00479 HG00608 NA18573 HG00375 NA19248 NA19093 HG01170 HG00534 HG01171 HG01522 NA18624 HG00683 HG01521 NA19005 NA20412 NA18971 HG00446 NA12748 HG00530 HG00690 HG01356 HG01516 NA20532 HG00344 HG00328 NA18542 HG00254 HG00321 HG00577 HG00656 HG00342 HG00524 HG00650 HG00557 HG00319 HG00457 HG00125 HG00578 HG00543 HG00638 HG00171 HG00699 HG00595 HG00187 HG00704 HG00533 HG00596 HG00268 HG01083 HG00651 HG01133 HG00671 HG00327 HG01148 HG00246 HG00672 HG00556 HG00436 HG00554 NA18633 NA20344 NA11993 NA07037 NA11930 HG01366 HG01389 HG00620 NA19740 HG00190 HG00419 NA18535 HG01495 NA18592 HG01497 HG00174 HG01140 NA12287 HG00689 HG01550 HG00334 HG01375 HG00637 NA18507 HG01113 NA18550 NA19129 HG01551 HG01462 HG00331 NA12413 HG01456 HG01360 HG00708 HG01350 HG00684 NA19099 HG00284 NA12399 NA12286 NA12777 HG00277 HG00266 NA19985 HG00353 HG01102 NA07347 NA07051 NA19900 NA18984 NA07048 HG00640 HG01066 NA12812 HG01174 HG01188 20 439104 . AG A . 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TG T . 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A AC . 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C CT . 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C CAT . PASS AC=6;AN=766;HW=0.00;HetPct=1.6;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1102516 . CT C . PASS AC=3;AN=760;HW=0.00;HetPct=0.8;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1149576 . CT C . PASS AC=2;AN=764;HW=0.00;HetPct=0.5;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1195706 . AAG A . PASS AC=334;AN=764;HW=9.47;HetPct=44.9;HomRefPct=33.7;HomVarPct=21.1;NoCallPct=0.3 GT 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 . 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 1/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 1/1 20 1342549 . A AAGAT . PASS AC=0;AN=760;HW=0.00;HetPct=0.0;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1366475 . CT C . PASS AC=0;AN=764;HW=0.00;HetPct=0.0;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1390810 . T TTC . HighNoCallRate AC=0;AN=566;HW=0.00;HetPct=0.0;HomRefPct=73.9;HomVarPct=0.0;NoCallPct=26.1 GT 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 . 0/0 . 0/0 . . . . . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 . . 0/0 . 0/0 0/0 0/0 . 0/0 . 0/0 . . 0/0 0/0 . 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 . . . 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 0/0 . . 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . . . 0/0 . 0/0 0/0 . 0/0 0/0 0/0 . . . 0/0 0/0 . 0/0 . . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 . . 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . . . . 0/0 . 0/0 . 0/0 0/0 0/0 . 0/0 . . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 . 0/0 0/0 . 0/0 . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 20 1550416 . C CT . PASS AC=0;AN=760;HW=0.00;HetPct=0.0;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1655540 . AT A . PASS AC=4;AN=764;HW=0.00;HetPct=1.0;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 2133769 . GA G . HardyWeinbergViolation AC=379;AN=766;HW=85.69;HetPct=34.7;HomRefPct=33.2;HomVarPct=32.1;NoCallPct=0.0 GT 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 1/1 0/0 1/1 0/0 0/1 0/0 1/1 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 1/1 0/0 1/1 1/1 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 1/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 20 2217137 . CT C . HighNoCallRate AC=0;AN=704;HW=0.00;HetPct=0.0;HomRefPct=91.9;HomVarPct=0.0;NoCallPct=8.1 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 20 2263095 . TG T . HardyWeinbergViolation AC=358;AN=766;HW=812.29;HetPct=93.5;HomRefPct=6.5;HomVarPct=0.0;NoCallPct=0.0 GT 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 20 2426886 . G GAATT . HighNoCallRate AC=11;AN=680;HW=0.00;HetPct=2.9;HomRefPct=85.9;HomVarPct=0.0;NoCallPct=11.2 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . . . 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/1 . 0/1 . 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 . . . 0/0 0/0 . 0/0 0/0 0/0 0/0 . . . 0/1 . . 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 20 2889034 . AAAAT A . PASS AC=6;AN=762;HW=0.00;HetPct=1.6;HomRefPct=97.9;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 3203741 . CT C . PASS AC=4;AN=762;HW=0.00;HetPct=1.0;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 3327993 . CAA C . HardyWeinbergViolation AC=3;AN=766;HW=21.06;HetPct=0.3;HomRefPct=99.5;HomVarPct=0.3;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 3700705 . CTTTGGG C . PASS AC=0;AN=762;HW=0.00;HetPct=0.0;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 4037626 . TC T . 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G GA . 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CATT C . 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CAAAT C . 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CCTTGA C . 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C CATTTTAGG . 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GA G . PASS AC=377;AN=764;HW=5.70;HetPct=53.0;HomRefPct=24.0;HomVarPct=22.7;NoCallPct=0.3 GT 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 0/0 1/1 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 . 0/0 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/0 0/1 0/0 20 5416109 . CA C . PASS AC=2;AN=752;HW=0.00;HetPct=0.5;HomRefPct=97.7;HomVarPct=0.0;NoCallPct=1.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 5432262 . AGT A . PASS AC=4;AN=752;HW=0.00;HetPct=1.0;HomRefPct=97.1;HomVarPct=0.0;NoCallPct=1.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 5724449 . T TC . PASS AC=0;AN=764;HW=0.00;HetPct=0.0;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 5928403 . T TA . HardyWeinbergViolation AC=196;AN=762;HW=47.13;HetPct=29.2;HomRefPct=59.3;HomVarPct=11.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 1/1 0/1 1/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 . 0/0 . 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 1/1 0/0 1/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 20 6877907 . CA C . PASS AC=2;AN=766;HW=0.00;HetPct=0.5;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 6969412 . CAAAGAAT C . PASS AC=2;AN=762;HW=0.00;HetPct=0.5;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 7035110 . CT C . HardyWeinbergViolation AC=340;AN=758;HW=1038.45;HetPct=1.0;HomRefPct=54.0;HomVarPct=43.9;NoCallPct=1.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 1/1 1/1 0/0 0/0 1/1 0/0 1/1 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 1/1 0/0 1/1 1/1 1/1 0/0 0/0 1/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 1/1 1/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 1/1 0/0 0/0 1/1 1/1 1/1 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/1 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 1/1 1/1 1/1 1/1 0/0 1/1 1/1 0/0 1/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/0 1/1 1/1 0/0 0/0 1/1 0/0 1/1 1/1 0/0 0/0 0/0 1/1 0/0 0/0 1/1 1/1 0/0 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 0/0 0/0 1/1 1/1 1/1 1/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 1/1 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 1/1 . 0/0 . 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/0 1/1 1/1 0/0 1/1 1/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 1/1 1/1 0/0 0/0 0/0 1/1 1/1 0/0 1/1 0/0 0/0 1/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 1/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/0 0/0 1/1 . 1/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 1/1 0/0 1/1 0/0 0/0 1/1 1/1 1/1 0/0 0/1 1/1 0/0 0/0 0/0 1/1 0/0 1/1 0/0 1/1 1/1 1/1 0/0 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 1/1 0/0 1/1 20 7229260 . T TA . PASS AC=2;AN=764;HW=0.00;HetPct=0.5;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 7239075 . AG A . PASS AC=5;AN=766;HW=0.00;HetPct=1.3;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 7942727 . A AC . PASS AC=0;AN=766;HW=0.00;HetPct=0.0;HomRefPct=100.0;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 7950562 . C CT . PASS AC=4;AN=760;HW=18.01;HetPct=0.5;HomRefPct=98.4;HomVarPct=0.3;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 8195466 . C CT . PASS AC=1;AN=762;HW=0.00;HetPct=0.3;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 8233352 . TACTC T . PASS AC=56;AN=764;HW=1.84;HetPct=13.1;HomRefPct=85.9;HomVarPct=0.8;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 20 8504000 . TAG T . PASS AC=5;AN=762;HW=0.00;HetPct=1.3;HomRefPct=98.2;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 8779672 . TG T . HighNoCallRate AC=0;AN=86;HW=0.00;HetPct=0.0;HomRefPct=11.2;HomVarPct=0.0;NoCallPct=88.8 GT . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . 0/0 . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0/0 0/0 . . . 0/0 . 0/0 . . . 0/0 . . . . . . . 0/0 . 0/0 0/0 . 0/0 . 0/0 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . 0/0 0/0 0/0 0/0 . . . 0/0 . . . . . 0/0 0/0 . . . . 0/0 . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . 0/0 . . . . 0/0 . . . . . . . . . 0/0 . 0/0 . 0/0 0/0 . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . 0/0 . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . 0/0 0/0 . . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . 0/0 0/0 . 0/0 . . 0/0 . . . 0/0 . . . . . . . . . . . 0/0 . . . . . . . . . . . 20 8794142 . AG A . HardyWeinbergViolation AC=52;AN=756;HW=57.86;HetPct=8.4;HomRefPct=87.7;HomVarPct=2.6;NoCallPct=1.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 . 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 20 9231138 . AT A . PASS AC=0;AN=764;HW=0.00;HetPct=0.0;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 9900218 . C CT . HardyWeinbergViolation AC=3;AN=766;HW=21.06;HetPct=0.3;HomRefPct=99.5;HomVarPct=0.3;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 9921724 . AAAGT A . PASS AC=11;AN=758;HW=0.00;HetPct=2.9;HomRefPct=96.1;HomVarPct=0.0;NoCallPct=1.0 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 9925738 . T TG . PASS AC=1;AN=760;HW=0.00;HetPct=0.3;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 10090376 . T TG . PASS AC=0;AN=764;HW=0.00;HetPct=0.0;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 10377174 . ATAAAAC A . HighNoCallRate AC=107;AN=514;HW=4.54;HetPct=20.6;HomRefPct=42.8;HomVarPct=3.7;NoCallPct=32.9 GT . . 0/0 0/0 . 0/0 . 0/1 . 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 . . . . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 . 0/1 0/0 . . 0/0 . 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/0 . . 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 . . . . . . 0/0 . 1/1 . 0/0 . 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 . . . . 0/1 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 . . 0/0 . . . . . 0/0 0/0 1/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . . 0/0 0/0 . . . . 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/1 . . . . . 0/0 . 0/1 0/1 . . 0/0 0/0 0/0 . 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 . 0/0 . 0/1 0/1 0/1 . 0/1 0/1 0/0 . 0/1 0/0 . . 0/0 . . . . . 0/0 0/1 0/1 0/0 0/1 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 . . . 0/0 0/0 0/0 0/1 . . 0/1 . . . 0/0 0/0 0/1 0/0 0/0 0/0 0/0 . . 0/1 . . . . . . . . . . . 0/1 0/0 . 0/0 . 0/1 0/1 . . . . . . . . . . 0/0 0/1 . . 0/0 . 0/0 . . . 0/1 . . . 0/1 . . 0/1 . . . . 0/0 . 0/1 0/0 . 0/1 . 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 . . . 1/1 0/1 . . 0/0 . 0/0 0/0 0/0 0/0 0/1 . 0/1 0/1 . . 0/0 0/0 0/0 0/0 0/1 0/0 20 11229169 . T TA . PASS AC=3;AN=756;HW=0.00;HetPct=0.8;HomRefPct=97.9;HomVarPct=0.0;NoCallPct=1.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 11511920 . AC A . PASS AC=2;AN=766;HW=0.00;HetPct=0.5;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 11893900 . ATTAG A . 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A AG . 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TTATC T . 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GGGA G . PASS AC=3;AN=762;HW=0.00;HetPct=0.8;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 13128894 . CT C . PASS AC=10;AN=764;HW=0.00;HetPct=2.6;HomRefPct=97.1;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 20 13287841 . CAT C . PASS AC=134;AN=760;HW=0.21;HetPct=29.2;HomRefPct=67.1;HomVarPct=2.9;NoCallPct=0.8 GT 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 1/1 0/1 0/1 . 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/1 . 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 . 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 20 13365589 . T TG . PASS AC=0;AN=762;HW=0.00;HetPct=0.0;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 13566260 . AAATTG A . 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AT A . 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GAGAA G . 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TA T . 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TC T . 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T TA . 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AGT A . 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TTC T . 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AGCC A . 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T TC . 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GA G . 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TG T . 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TGA T . PASS AC=29;AN=764;HW=0.00;HetPct=7.6;HomRefPct=92.2;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 15543319 . AG A . 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TG T . 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TG T . PASS AC=87;AN=750;HW=3.63;HetPct=19.1;HomRefPct=77.0;HomVarPct=1.8;NoCallPct=2.1 GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 . 0/0 0/0 0/1 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/1 0/0 0/1 0/0 . 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 . 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 15871330 . AG A . 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TA T . PASS AC=186;AN=764;HW=15.27;HetPct=32.4;HomRefPct=59.3;HomVarPct=8.1;NoCallPct=0.3 GT 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 20 16172883 . G GTAGC . HardyWeinbergViolation AC=79;AN=762;HW=42.59;HetPct=13.8;HomRefPct=82.2;HomVarPct=3.4;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 . 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16192114 . AT A . PASS AC=0;AN=760;HW=0.00;HetPct=0.0;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16259934 . C CAA . PASS AC=0;AN=758;HW=0.00;HetPct=0.0;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=1.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16312599 . CTA C . 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GGTT G . PASS AC=6;AN=760;HW=0.00;HetPct=1.6;HomRefPct=97.7;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16747221 . CA C . PASS AC=291;AN=764;HW=3.13;HetPct=45.2;HomRefPct=39.2;HomVarPct=15.4;NoCallPct=0.3 GT 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 . 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 20 16769262 . TTTC T . HighNoCallRate AC=8;AN=600;HW=0.00;HetPct=2.1;HomRefPct=76.2;HomVarPct=0.0;NoCallPct=21.7 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 . 0/0 . . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . . 0/1 . . 0/0 0/0 0/0 0/0 0/0 0/0 . . . . 0/0 0/1 . 0/1 . . 0/1 0/0 0/0 . . . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . . . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/1 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/1 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . . 0/1 . . 0/0 0/0 . 0/0 0/0 . 0/0 . . . . . 0/0 . . . 0/0 0/0 0/0 . . 0/0 . . . 0/0 . 0/0 0/0 . 0/0 . 0/0 0/0 . . 0/0 . . 0/0 0/0 0/0 0/0 . 0/0 . . . 0/0 0/0 . 0/0 0/0 0/0 0/0 . . . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16813850 . C CA . 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T TC . 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TA T . 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TGC T . 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A AGT . 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C CA . 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AAG A . 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A ATT . 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TAA T . 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C CT . 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T TC . 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T TC . 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GGCCTGGGATGTAAA G . 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CCTT C . 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A AC . 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ATTACAGACT A . 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TA T . 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CA C . 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TG T . 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T TC . 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TC T . 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ACTT A . 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AG A . 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CA C . PASS AC=330;AN=762;HW=4.15;HetPct=46.5;HomRefPct=33.2;HomVarPct=19.8;NoCallPct=0.5 GT 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 . 0/1 1/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/0 . 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 1/1 0/0 1/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 20 21968507 . AC A . PASS AC=7;AN=762;HW=12.61;HetPct=1.3;HomRefPct=97.9;HomVarPct=0.3;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 22411326 . CA C . HardyWeinbergViolation AC=321;AN=762;HW=136.49;HetPct=29.5;HomRefPct=42.8;HomVarPct=27.2;NoCallPct=0.5 GT 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 . 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/0 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 1/1 0/1 0/1 1/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 1/1 0/0 0/0 1/1 1/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 1/1 1/1 0/0 0/0 0/1 0/0 0/1 20 22434333 . C CA . PASS AC=8;AN=766;HW=0.00;HetPct=2.1;HomRefPct=97.9;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 20 22637424 . C CAGCCA . PASS AC=3;AN=760;HW=0.00;HetPct=0.8;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 22655862 . TATC T . PASS AC=6;AN=766;HW=0.00;HetPct=1.6;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23169038 . TGTC T . HardyWeinbergViolation AC=380;AN=766;HW=1034.24;HetPct=98.7;HomRefPct=1.0;HomVarPct=0.3;NoCallPct=0.0 GT 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 20 23200197 . ATT A . PASS AC=1;AN=766;HW=0.00;HetPct=0.3;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23293728 . CA C . PASS AC=8;AN=754;HW=11.33;HetPct=1.6;HomRefPct=96.6;HomVarPct=0.3;NoCallPct=1.6 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23319459 . CAT C . HardyWeinbergViolation AC=10;AN=766;HW=26.72;HetPct=1.6;HomRefPct=97.9;HomVarPct=0.5;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23813095 . CT C . PASS AC=26;AN=762;HW=1.46;HetPct=6.3;HomRefPct=93.0;HomVarPct=0.3;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 20 23815381 . CT C . PASS AC=1;AN=762;HW=0.00;HetPct=0.3;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23889003 . GA G . PASS AC=2;AN=766;HW=0.00;HetPct=0.5;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 24541328 . TA T . HighNoCallRate AC=0;AN=430;HW=0.00;HetPct=0.0;HomRefPct=56.1;HomVarPct=0.0;NoCallPct=43.9 GT . 0/0 0/0 0/0 0/0 0/0 . . . . . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 . . . . 0/0 0/0 . . . 0/0 . . . . 0/0 0/0 . . . . 0/0 0/0 0/0 . . . 0/0 . . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . . . . 0/0 . . . 0/0 0/0 . . 0/0 0/0 . 0/0 . . 0/0 . 0/0 0/0 . 0/0 . . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . . 0/0 . 0/0 . 0/0 . . . . . . 0/0 0/0 . 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . 0/0 0/0 . . . . . . 0/0 . 0/0 0/0 0/0 0/0 . . . 0/0 . . . . . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . . . 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 . . . . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . . . 0/0 . . . 0/0 0/0 0/0 0/0 0/0 . . . 0/0 0/0 0/0 . . 0/0 . . 0/0 . 0/0 . 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 . 0/0 . 0/0 0/0 . 0/0 . . 0/0 . . . . . . 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 . . . 0/0 . . 0/0 0/0 . . 0/0 . . . 0/0 . 0/0 0/0 0/0 0/0 . . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . . 0/0 . 0/0 0/0 0/0 . . . 0/0 0/0 0/0 . 0/0 . 0/0 . 0/0 0/0 . 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 . 0/0 . 0/0 0/0 . 0/0 20 24710482 . GT G . PASS AC=0;AN=764;HW=0.00;HetPct=0.0;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 24855121 . CT C . PASS AC=6;AN=760;HW=0.00;HetPct=1.6;HomRefPct=97.7;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 25283938 . A AG . HardyWeinbergViolation AC=326;AN=762;HW=30.59;HetPct=40.2;HomRefPct=36.8;HomVarPct=22.5;NoCallPct=0.5 GT 0/0 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 1/1 1/1 1/1 . 0/1 . 0/0 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 1/1 20 25503211 . CATA C . 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GT G . 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CCTT C . 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C CCACAAGAAG . 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TATATC T . 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CG C . PASS AC=0;AN=764;HW=0.00;HetPct=0.0;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 31881479 . AG A . HardyWeinbergViolation AC=40;AN=764;HW=34.05;HetPct=7.3;HomRefPct=90.9;HomVarPct=1.6;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 32015223 . CT C . PASS AC=5;AN=764;HW=0.00;HetPct=1.3;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 32158330 . CAG C . PASS AC=4;AN=760;HW=0.00;HetPct=1.0;HomRefPct=98.2;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 32456076 . GT G . 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CA C . 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A AG . 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GGCGTCTGA G . 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GTC G . 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A AAG . 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C CA . 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A AT . 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TAA T . 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CT C . 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ATC A . 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GA G . PASS AC=5;AN=764;HW=0.00;HetPct=1.3;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 35847597 . CTT C . PASS AC=1;AN=764;HW=0.00;HetPct=0.3;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 36250348 . CG C . HighNoCallRate AC=0;AN=414;HW=0.00;HetPct=0.0;HomRefPct=54.0;HomVarPct=0.0;NoCallPct=46.0 GT 0/0 . 0/0 . . 0/0 0/0 . 0/0 0/0 . . 0/0 . 0/0 . 0/0 . 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 . 0/0 . 0/0 . . 0/0 . . 0/0 . 0/0 . . . 0/0 . 0/0 . . . 0/0 0/0 0/0 . . 0/0 . . 0/0 . . . 0/0 0/0 . . . 0/0 0/0 . . 0/0 . . . 0/0 . 0/0 . 0/0 . 0/0 . 0/0 0/0 . 0/0 . 0/0 . 0/0 0/0 . 0/0 0/0 . 0/0 0/0 . 0/0 0/0 . . . . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . . . 0/0 0/0 . . . . . 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 0/0 . 0/0 . . . 0/0 0/0 . . 0/0 . . 0/0 0/0 . 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 0/0 0/0 0/0 . . 0/0 . 0/0 . 0/0 0/0 . . . 0/0 . 0/0 . 0/0 . 0/0 . 0/0 . . . 0/0 0/0 . 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . . . 0/0 . 0/0 0/0 . . 0/0 0/0 . 0/0 . . . . 0/0 0/0 0/0 0/0 0/0 . . . . . 0/0 0/0 0/0 . 0/0 0/0 0/0 . . 0/0 0/0 0/0 . 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . . 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . . . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . . 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 . . . 0/0 0/0 0/0 0/0 0/0 . 0/0 . . . . 0/0 . . 0/0 . 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 . 0/0 . . . . 0/0 0/0 0/0 . 0/0 . . 0/0 0/0 . . . 0/0 . 0/0 . 0/0 . . 0/0 . . . . 20 36658020 . TG T . 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TC T . 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TAAAG T . 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ATAC A . 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CAG C . 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CAG C . 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TG T . 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CAT C . PASS AC=7;AN=762;HW=0.00;HetPct=1.8;HomRefPct=97.7;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37678954 . C CTGG . PASS AC=7;AN=762;HW=0.00;HetPct=1.8;HomRefPct=97.7;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37712193 . AAG A . PASS AC=29;AN=762;HW=0.00;HetPct=7.6;HomRefPct=91.9;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37836124 . AAAT A . PASS AC=3;AN=760;HW=0.00;HetPct=0.8;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37954797 . A AGT . PASS AC=0;AN=762;HW=0.00;HetPct=0.0;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37962643 . T TAA . 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TA T . 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T TA . 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GAAGA G . 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CCTT C . 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T TG . 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AG A . 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T TG . 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TGAG T . 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A AG . 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TG T . 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CTAAGGAGGGAAAAAGATATAAT C . 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TATC T . 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TG T . 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GC G . 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CACTT C . 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T TA . 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CT C . 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T TGGGTC . 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AG A . 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A AG . 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AG A . 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AG A . 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T TC . 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GC G . 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CA C . 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C CT . 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T TC . 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AACAG A . 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T TA . 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GAGTGTCGT G . 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GA G . 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T TTC . 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CTG C . PASS AC=86;AN=762;HW=16.06;HetPct=17.2;HomRefPct=79.6;HomVarPct=2.6;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 20 46011017 . GAT G . HighNoCallRate AC=4;AN=706;HW=0.00;HetPct=1.0;HomRefPct=91.1;HomVarPct=0.0;NoCallPct=7.8 GT . . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 46051811 . T TAAGC . PASS AC=2;AN=762;HW=0.00;HetPct=0.5;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 46353646 . A AG . PASS AC=0;AN=764;HW=0.00;HetPct=0.0;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 46413551 . TC T . PASS AC=2;AN=760;HW=0.00;HetPct=0.5;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 46569465 . CTG C . PASS AC=10;AN=762;HW=0.00;HetPct=2.6;HomRefPct=96.9;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 46720983 . ATACTTGG A . 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GC G . PASS AC=2;AN=760;HW=0.00;HetPct=0.5;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 47136092 . A AGTC . PASS AC=1;AN=760;HW=0.00;HetPct=0.3;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 47239432 . T TA . HardyWeinbergViolation AC=3;AN=762;HW=21.03;HetPct=0.3;HomRefPct=99.0;HomVarPct=0.3;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 47335386 . GC G . 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C CA . 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CA C . 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CCTA C . 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G GT . 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T TG . PASS AC=0;AN=766;HW=0.00;HetPct=0.0;HomRefPct=100.0;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 49537420 . AG A . 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A AG . 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A AC . 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ACTTTT A . 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TTTTC T . 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A AT . 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T TC . 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G GAA . 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G GT . 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AC A . PASS AC=1;AN=762;HW=0.00;HetPct=0.3;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 51758677 . A ATT . HardyWeinbergViolation AC=87;AN=762;HW=72.50;HetPct=13.3;HomRefPct=81.5;HomVarPct=4.7;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 1/1 1/1 1/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 20 51838824 . GA G . PASS AC=4;AN=756;HW=17.99;HetPct=0.5;HomRefPct=97.9;HomVarPct=0.3;NoCallPct=1.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 51961394 . ATTTG A . PASS AC=8;AN=760;HW=0.00;HetPct=2.1;HomRefPct=97.1;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 53081927 . CATGA C . 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T TG . 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T TA . 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T TC . 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CAG C . 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AC A . 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CAT C . 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A AC . 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TGAGC T . 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GT G . 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AG A . 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AAAC A . HardyWeinbergViolation AC=10;AN=764;HW=26.69;HetPct=1.6;HomRefPct=97.7;HomVarPct=0.5;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 55608811 . CT C . PASS AC=35;AN=762;HW=19.90;HetPct=7.0;HomRefPct=91.4;HomVarPct=1.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 20 55611547 . CAA C . 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GT G . 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CA C . 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T TGAGG . 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TG T . 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HardyWeinbergViolation AC=137;AN=764;HW=48.09;HetPct=22.2;HomRefPct=70.8;HomVarPct=6.8;NoCallPct=0.3 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 1/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 1/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 20 57676578 . CCTTT C . PASS AC=7;AN=764;HW=0.00;HetPct=1.8;HomRefPct=97.9;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 . 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 57693627 . AG A . HighNoCallRate AC=12;AN=292;HW=71.95;HetPct=0.5;HomRefPct=36.3;HomVarPct=1.3;NoCallPct=61.9 GT . . 0/0 . . . 0/0 . . . . 0/0 . 1/1 . . 0/0 . 0/0 . 0/0 . . . . . . . 0/0 0/0 . . . 0/0 . . . . . 0/0 . 0/0 . . 0/0 0/0 . . . . . . . . 0/0 . . . . 0/0 . . . 0/0 . 0/0 0/0 0/0 . . 0/0 . . 0/0 0/0 . 0/0 . . . 0/0 . . . . . . . . 0/0 . 0/0 . . 0/0 0/0 0/0 . . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 1/1 . . . . . . . 0/0 . . . 0/0 . . . . . . 0/0 1/1 . . . 0/0 . . . . . . . . 0/0 . 0/0 . . . 0/0 . . . . 0/0 0/0 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . . . . 0/0 . 0/0 . . . . 0/0 . . 0/0 . . 1/1 . 0/0 0/0 . 0/0 0/0 0/1 . . 0/0 . 0/0 1/1 . . . . . . . 0/0 0/0 . . . . . . . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . . . . 0/0 0/0 0/0 0/0 . 0/0 0/0 . . . 0/0 . 0/0 . 0/0 0/0 . . . . . 0/0 . 0/0 . 0/0 . 0/0 0/0 0/0 0/0 . . . . . . . 0/0 . . 0/0 . . 0/0 . 0/0 0/0 . . 0/0 . . . 0/0 0/0 . . . . 0/0 . . . 0/0 . . . 0/0 . . . 0/0 . . 0/0 . 0/0 . . . . . . 0/0 . . . . . . . 0/0 . . 0/1 0/0 . . . . . 0/0 0/0 0/0 0/0 0/0 . . 0/0 . . 0/0 . . 0/0 . . . . 0/0 . . . . . 0/0 . 0/0 . . 0/0 . 0/0 . . . 0/0 20 57781799 . TGGG T . HardyWeinbergViolation AC=43;AN=764;HW=30.12;HetPct=8.1;HomRefPct=90.1;HomVarPct=1.6;NoCallPct=0.3 GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 20 58288793 . TC T . PASS AC=44;AN=766;HW=12.53;HetPct=9.4;HomRefPct=89.6;HomVarPct=1.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 58790761 . TG T . HardyWeinbergViolation AC=232;AN=762;HW=35.81;HetPct=33.9;HomRefPct=52.2;HomVarPct=13.3;NoCallPct=0.5 GT 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/1 1/1 . 0/1 . 1/1 0/0 0/1 1/1 0/1 0/0 1/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 20 59072457 . AAGG A . HardyWeinbergViolation AC=12;AN=756;HW=41.94;HetPct=1.6;HomRefPct=96.3;HomVarPct=0.8;NoCallPct=1.3 GT . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 59153061 . CTG C . 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TATTA T . 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CCT C . 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TG T . 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C CT . 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TG T . HighNoCallRate AC=0;AN=712;HW=0.00;HetPct=0.0;HomRefPct=93.0;HomVarPct=0.0;NoCallPct=7.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 . 0/0 0/0 . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 60337932 . AC A . PASS AC=3;AN=764;HW=0.00;HetPct=0.8;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 60925525 . GC G . PASS AC=2;AN=762;HW=0.00;HetPct=0.5;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 60961768 . GA G . HardyWeinbergViolation AC=365;AN=766;HW=84.86;HetPct=34.7;HomRefPct=35.0;HomVarPct=30.3;NoCallPct=0.0 GT 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 1/1 1/1 1/1 0/1 0/0 1/1 1/1 0/0 0/0 1/1 1/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 1/1 1/1 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 20 61000018 . GC G . PASS AC=203;AN=762;HW=0.38;HetPct=39.4;HomRefPct=53.3;HomVarPct=6.8;NoCallPct=0.5 GT 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 . 0/1 . 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 20 61531765 . AG A . PASS AC=0;AN=766;HW=0.00;HetPct=0.0;HomRefPct=100.0;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 61983510 . TCTGC T . PASS AC=75;AN=766;HW=0.03;HetPct=18.0;HomRefPct=81.2;HomVarPct=0.8;NoCallPct=0.0 GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 20 62154368 . G GA . PASS AC=2;AN=760;HW=0.00;HetPct=0.5;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 62310426 . CTT C . PASS AC=1;AN=756;HW=0.00;HetPct=0.3;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=1.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 62871860 . C CCCGCA . PASS AC=27;AN=764;HW=17.87;HetPct=5.5;HomRefPct=93.5;HomVarPct=0.8;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 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rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/combined.phase1.chr20.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false recal_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.recal tranches_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub ts_filter_level=93.0 ignore_filter=null mode=INDEL" ##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR/AFR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN/ASN.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR/AMR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR/EUR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR.admix/AFR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN.admix/ASN.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR.admix/AMR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR.admix/EUR.admix.phase1.chr20.42.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=AFR.admix,AMR.admix,EUR.admix,ASN.admix,AFR,AMR,EUR,ASN printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 masterMerge=false mergeInfoWithMaxAC=true" ##FILTER= ##FILTER== 4 && (MQ0 / (1.0 * DP)) > 0.1"> ##FILTER=10)"> ##FILTER=20.0"> ##FILTER= 7500"> ##FILTER==15"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER==-1.0"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##LeftAlignVariants="analysis_type=LeftAlignVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/ebanks/ALL.chr20.Oxford.20110407.indels.genotypes.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub" ##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/dindel/20110208.chr20.dindel2.ALL.sites.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null select_expressions=[] excludeNonVariants=false excludeFiltered=false discordance= concordance= family_structure= mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_number=0 select_random_fraction=0.0 selectSNPs=false selectIndels=true" ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/broad/shptmp/delangel/calls/chr20/CHB.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CHS.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CLM.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/JPT.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/MXL.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/PUR.phase1.chr20.42.cleaned.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.combined.chr20.vcf, /humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=50 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=8 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=INDEL p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=GENOTYPE_GIVEN_ALLELES output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=4.0 standard_min_confidence_threshold_for_emitting=4.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=true output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[MappingQualityZeroFraction]" ##VariantFiltration="analysis_type=VariantFiltration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/humgen/1kg/processing/pipeline_test_bams/chr22_chunked.hg19.intervals] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/broad/shptmp/rpoplin/ALL.phase1.chr22.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub filterExpression=[MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1, QUAL<30.0, SB>=-1.0, QD<1.0, HRun>=15, HaplotypeScore>20.0] filterName=[HARD_TO_VALIDATE, LowQual, StrandBias, QualByDepth, HomopolymerRun, HaplotypeScore] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false" ##commandline="/share/software/freebayes/bin/freebayes --stdin --min-alternate-count 2 --genotype-combo-step-max 20 --genotype-variant-threshold 4 --no-marginals --pvar 0.0001 --indels --mnps --no-filters --binomial-obs-priors --allele-balance-priors --region 20:0..100000 --vcf /d1/data/1000G/20101123/populations/finalised.phase1/integrated/including454/wg/ALL/Pipeline/none//freebayes/freebayes.20:0-100000.baq.20110328.vcf --fasta-reference /d2/data/references/build_37/human_reference_v37.fa" ##fileDate=2011-03-28 ##filedate=2011-02-08 ##filter="( SNP | MNP ) & ( MQM > 65 | QUAL > 1 ) & ABP < 30 & AB < 0.9 | ( INS | DEL ) & QUAL > 500" ##phasing=none ##platypusOptions={'bamFiles': ['/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06984', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06985', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06986', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06989', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06994', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07000', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07037', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07048', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07051', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07056', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07346', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07347', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07357', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA10847', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA10851', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11829', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11830', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11831', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11832', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11843', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11881', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11892', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11893', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11894', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11918', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11919', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11920', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11930', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11931', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11932', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11933', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11992', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11993', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11994', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11995', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12003', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12004', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12005', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12006', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12043', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12044', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12045', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12046', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12058', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12144', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12154', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12155', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12156', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12234', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12249', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12272', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12273', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12275', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12282', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12283', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12286', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12287', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12340', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12341', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12342', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12347', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12348', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12383', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12399', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12400', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12413', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12414', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12489', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12546', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12716', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12717', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12718', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12748', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12749', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12750', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12751', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12761', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12763', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12775', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12776', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12777', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12778', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12813', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12827', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12828', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12829', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12830', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12842', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12843', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12889', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12890', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18486', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18487', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18488', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18489', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18498', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18499', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18501', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18502', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18504', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18505', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18507', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18508', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18510', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18511', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18516', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18517', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18519', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18520', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18522', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18523', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18526', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18530', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18532', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18533', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18534', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18535', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18536', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18537', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18538', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18539', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18541', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18542', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18543', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18544', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18545', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18546', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18547', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18548', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18549', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18550', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18552', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18553', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18555', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18557', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18558', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18559', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18560', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18561', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18562', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18563', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18564', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18565', 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G GA 4567.01 PASS AA=20;AB=0.61111;ABA=14;ABP=6.8707;ABR=22;AC=38;AF=0.0544;AN=698;BL=374;BR=1129;BVAR;BaseQRankSum=13.364;DP=15979;DP4=1882,2188,45,37;Dels=0.00;EL=5;EPP=13.868;ER=15;FR;FS=6.503;HETAR=11;HOMA=2;HOMR=985;HP=1;HPLen=2;HR=2;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0157;LEN=1;LRB=0.50233;LRBP=826.56;MQ=66.16;MQ0Fraction=0.0110;MQM=70.5;MQRankSum=-3.158;NF;NR;NS=998;PP;PV4=0.15,1,0.42,0.15;RA=3173;RL=1;RPP=38.188;RR=19;RUN=1;ReadPosRankSum=-2.346;SAB=0.7;SAF=14;SAP=9.959;SAR=6;SC=GGGCGTGGTGGTGCATGTAAT;SRB=0.50047;SRF=1588;SRP=3.0165;SRR=1585;TC;TR=9;TU=GGT;VQSLOD=10.0079;set=Intersection;sumGLbyD=23.94 20 539571 . TG T 18546 PASS AA=71;AB=0.92482;ABA=63;ABP=1316.6;ABR=775;AC=42;AF=0.03512;AN=1196;BL=3915;BR=252;BVAR;BaseQRankSum=0.556;DEL;DP=10073;Dels=0.01;EL=47;EPP=19.189;ER=24;FS=2.124;HETAR=290;HOMA=156;HOMR=570;HRun=1;InbreedingCoeff=0.0620;LEN=1;LRB=0.87905;LRBP=6995.1;MQ0=0;MQ0Fraction=0.0000;MQM=127.99;MQRankSum=0.410;NS=1016;RA=3090;RL=71;RPP=157.18;RR=0;RUN=1;ReadPosRankSum=-11.038;SAB=0.66197;SAF=47;SAP=19.189;SAR=24;SRB=0.55016;SRF=1700;SRP=70.544;SRR=1390;VQSLOD=2.6772;set=filterInVQSR-2of5;sumGLbyD=4.71 20 573764 . TA T 591.51 PASS AC=91;AF=0.1987;AN=458;BaseQRankSum=0.137;DP=519;FS=3.153;HRun=1;HaplotypeScore=14.0744;InbreedingCoeff=0.1460;MQ=48.16;MQ0=26;MQ0Fraction=0.0501;MQRankSum=-1.636;QD=3.63;ReadPosRankSum=-4.140;SB=-408.14;VQSLOD=5.2458;set=VQSR 20 766143 . C A,CATCTGGTA 5521.70 PASS AA=24;AB=0.5;ABA=18;ABP=3.0103;ABR=18;AC=14;AF=0.0289;AF1=0.02038;AN=484;BL=655;BR=1542;BVAR;BaseQRankSum=3.801;CI95=0.01549,0.02655;DP=11749;DP4=2222,1998,14,8;Dels=0.00;EL=9;EPP=6.2675;ER=15;FQ=999;FR;FS=2.941;HETAR=9;HOMA=4;HOMR=901;HP=2;HPLen=2;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0515;LEN=8;LRB=0.40373;LRBP=780.64;MQ=56.81;MQ0Fraction=0.0253;MQM=22.167;MQRankSum=-4.809;NF;NR;NS=914;PP;PV4=0.39,1,5.8e-07,1;RA=3093;RL=6;RPP=16.039;RR=18;RUN=1;ReadPosRankSum=-2.827;SAB=0.625;SAF=15;SAP=6.2675;SAR=9;SC=GCTTTAAATTCATCTGGTACT;SRB=0.61623;SRF=1906;SRP=365.95;SRR=1187;TC;TR=1;TU=A;VQSLOD=7.0268;set=Intersection;sumGLbyD=50.23 20 997076 rs11467490 CTG C 15379.78 PASS AA=195;AB=0.59878;ABA=132;ABP=30.896;ABR=197;AC=173;AF=0.14562;AN=1188;BL=7664;BR=7309;BVAR;BaseQRankSum=21.853;DB;DEL;DP=27127;DP4=1801,2002,241,282;Dels=0.13;EL=100;EPP=3.2887;ER=95;FQ=999;FR;FS=6.591;HETAR=77;HOMA=42;HOMR=815;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1284;LEN=2;LRB=0.023709;LRBP=21.287;MQ=61.18;MQ0Fraction=0.0214;MQM=43.041;MQRankSum=6.886;NF;NR;NS=934;PP;PV4=0.61,1.5e-78,1,1;RA=2800;RL=120;RPP=25.56;RR=75;RUN=1;ReadPosRankSum=4.504;SAB=0.62051;SAF=121;SAP=27.609;SAR=74;SC=CAGCTAATTACTGTATTTTTA;SRB=0.49821;SRF=1395;SRP=3.0879;SRR=1405;TC;TR=1;TU=T;VQSLOD=8.9396;set=Intersection;sumGLbyD=16.76 20 1042261 rs10597473 CCCTG C 168658.05 PASS AA=4481;AB=0.29043;ABA=2128;ABP=1147.1;ABR=871;AC=1172;AF=0.97830;AN=1198;BL=169975;BR=194027;BVAR;BaseQRankSum=4.599;DB;DEL;DP=29418;DP4=29,47,1441,2403;Dels=0.84;EL=2358;EPP=29.772;ER=2123;FR;FS=9.122;HETAR=482;HOMA=559;HOMR=30;HP=2;HPLen=3;HR=3;HRun=0;HU=C;INDEL;InbreedingCoeff=0.0470;LEN=4;LRB=0.066077;LRBP=3454.1;MQ=104.58;MQ0=4;MQ0Fraction=0.0014;MQM=58.257;MQRankSum=-3.368;NF;NR;NS=1071;PP;PV4=0.91,6.8e-09,2.8e-05,1;RA=1039;RL=2088;RPP=48.09;RR=2393;RUN=1;ReadPosRankSum=5.288;SAB=0.41442;SAF=1857;SAP=288.09;SAR=2624;SC=CCAAACCCAACCCTGCCTGGC;SRB=0.48893;SRF=508;SRP=4.1159;SRR=531;TC;TR=8;TU=CCTG;VQSLOD=8.5148;dbSNP=120;set=Intersection;sumGLbyD=59.79 20 1046297 rs33956316 C CT,CTT,CTTT 17698 PASS ABR=408;AC=432,79,230;AF=0.39779,0.07274,0.21179;BVAR;BaseQRankSum=-8.413;DB;DP=15649;DP4=147,199,534,436;FR;FS=11.580;HOMA=97;HOMR=457;HP=20;HR=16;HU=T;HaplotypeScore=16.0590;INDEL;INS;InbreedingCoeff=0.6018;KGPilot123;MQ0=19;MQ0Fraction=0.0093;MQRankSum=7.992;NF;NR;NS=767;PP;PV4=6e-05,1,1,1;QD=8.18;RA=1183;RUN=1;ReadPosRankSum=2.684;SB=-6384.08;SC=GGAAAATTTTCTTTTTTTTTT;SRB=0.40913;SRF=484;SRP=87.859;SRR=699;TC;TR=16;TU=T;VQSLOD=8.4941;dbSNP=132;set=Intersection 20 1405740 . T TA 257.28 PASS AF=0.0188;BaseQRankSum=-0.745;DP=3769;Dels=0.00;FS=0.742;HPLen=9;HRun=9;InbreedingCoeff=0.0462;MQ0Fraction=0.0151;MQRankSum=-0.090;ReadPosRankSum=-1.582;VQSLOD=5.6502;set=Intersection;sumGLbyD=6.94 20 1690501 . TC T 27928 PASS AA=108;AB=0.91372;ABA=100;ABP=1726.1;ABR=1059;AC=35;AF=0.02966;AN=1180;BL=593;BR=6973;BVAR;BaseQRankSum=7.567;DEL;DP=10612;Dels=0.01;EL=50;EPP=4.2971;ER=58;FS=0.000;HETAR=378;HOMA=184;HOMR=477;HRun=1;InbreedingCoeff=0.0495;LEN=1;LRB=0.84325;LRBP=11685;MQ0=0;MQ0Fraction=0.0000;MQM=87.361;MQRankSum=4.088;NS=1045;RA=3125;RL=3;RPP=212.2;RR=105;RUN=1;ReadPosRankSum=-13.096;SAB=0.56481;SAF=61;SAP=6.9511;SAR=47;SRB=0.51776;SRF=1618;SRP=11.572;SRR=1507;VQSLOD=3.9824;set=filterInVQSR-2of5;sumGLbyD=4.07 20 1948787 . GTC G,GTCTC 78.70 PASS AC=18,18;AF=0.01466,0.01466;AN=1228;BaseQRankSum=3.894;DP=19030;DP4=1874,1916,21,20;FR;FS=0.767;HP=2;HPLen=1;HR=1;HU=T;HaplotypeScore=16.5619;INDEL;InbreedingCoeff=0.2332;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.080;NF;NR;PP;PV4=0.88,1,0.094,0.47;QD=0.28;ReadPosRankSum=0.822;SB=-172.46;SC=CTCGACCCCTGTCTCTCTCTC;TC;TR=13;TU=CT;VQSLOD=3.7405;set=filterInVQSR-2of5 20 1991285 rs113891396 TAA T,TA,TAAA,TAAAAA,TAAAAAA,TAAAAAAA,TAAAAAAAA 39235.36 PASS AC=5,251,20,39,188,52,79;AF=0.0056,0.2789,0.0222,0.0433,0.2089,0.0578,0.0878;AN=900;BVAR;BaseQRankSum=1.124;DB;DEL;DP=54393;DP4=906,772,824,579;Dels=0.21;FR;FS=37.525;HP=12;HR=12;HRun=12;HU=A;INDEL;INS;InbreedingCoeff=0.6891;MQ=76.81;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-6.593;NF;NR;PP;PV4=0.0087,1,6.3e-19,1;RUN=1;ReadPosRankSum=-2.184;SC=ATCTGCCACTTAAAAAAAAAA;TC;TR=12;TU=A;VQSLOD=9.0007;dbSNP=132;set=Intersection;sumGLbyD=11.45 20 2355911 . TA T 11723 PASS AA=79;AB=0.9393;ABA=57;ABP=1577;ABR=882;AC=38;AF=0.0411;AN=924;BL=644;BR=5536;BVAR;BaseQRankSum=2.434;DEL;DP=9687;Dels=0.00;EL=45;EPP=6.3362;ER=34;FS=3.043;HETAR=321;HOMA=182;HOMR=555;HRun=5;InbreedingCoeff=0.0412;LEN=1;LRB=0.79159;LRBP=8411.9;MQ0=0;MQ0Fraction=0.0000;MQM=70.848;MQRankSum=0.137;NS=1058;RA=3415;RL=3;RPP=149.49;RR=76;RUN=1;ReadPosRankSum=-12.116;SAB=0.44304;SAF=35;SAP=5.2367;SAR=44;SRB=0.43572;SRF=1488;SRP=125.55;SRR=1927;VQSLOD=3.8910;set=filterInVQSR-2of5;sumGLbyD=4.88 20 2512346 . A AC 11046.11 PASS AC=673;AF=0.57034;AN=1180;BaseQRankSum=19.890;DP=2717;FS=26.809;HRun=0;HaplotypeScore=19.0575;InbreedingCoeff=0.3068;MQ=61.07;MQ0=25;MQ0Fraction=0.0092;MQRankSum=2.745;QD=5.80;ReadPosRankSum=3.139;SB=-4564.39;VQSLOD=4.3252;set=VQSR 20 2597210 rs71329387 TAAAG T 32206.62 PASS AA=689;AB=0.5805;ABA=542;ABP=75.724;ABR=750;AC=253;AF=0.20738;BL=29921;BR=30215;BVAR;BaseQRankSum=20.638;DB;DEL;DP=29293;DP4=1750,1070,405,274;Dels=0.18;EL=345;EPP=3.0135;ER=344;FQ=999;FR;FS=1.827;HETAR=225;HOMA=55;HOMR=783;HP=7;HPLen=4;HR=3;HRun=0;HU=A;INDEL;InbreedingCoeff=0.1419;LEN=4;LRB=0.0048889;LRBP=6.1314;MQ=66.96;MQ0=0;MQ0Fraction=0.0000;MQM=42.925;MQRankSum=-7.105;NF;NR;NS=1063;PP;PV4=0.25,1,9e-20,1;RA=4619;RL=345;RPP=3.0135;RR=344;RUN=1;ReadPosRankSum=2.719;SAB=0.53556;SAF=369;SAP=10.577;SAR=320;SC=GAAAGGAAAATAAAGAAGGAG;SRB=0.52414;SRF=2421;SRP=26.389;SRR=2198;TC;TR=3;TU=A;VQSLOD=9.7974;dbSNP=130;set=Intersection;sumGLbyD=33.30 20 2771621 rs11479849 GT G,GTT 1605.60 PASS AA=80;AB=0.79825;ABA=69;ABP=267.24;ABR=273;AC=79,91;AF=0.06551,0.07546;AN=1206;BL=2593;BR=3805;BVAR;BaseQRankSum=7.825;DB;DP=9790;Dels=0.04;EL=37;EPP=3.9875;ER=43;FR;FS=4.751;HETAR=62;HOMA=5;HOMR=958;HP=11;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2646;LEN=1;LRB=0.18943;LRBP=501.57;MQ0=0;MQ0Fraction=0.0000;MQM=52.45;MQRankSum=-0.560;NF;NR;NS=1025;PP;RA=3949;RL=29;RPP=16.148;RR=51;RUN=1;ReadPosRankSum=-2.397;SAB=0.525;SAF=42;SAP=3.4446;SAR=38;SC=TCATTTTAACGTTTTTTTTTT;SRB=0.54368;SRF=2147;SRP=68.46;SRR=1802;TC;TR=11;TU=T;VQSLOD=3.5989;set=filterInVQSR-2of5;sumGLbyD=3.92 20 2891235 . G GT,GTTT 2869.87 PASS AC=236,246;AF=0.2803,0.2922;AN=842;BaseQRankSum=8.979;DP=1067;FS=3.911;HaplotypeScore=20.3595;InbreedingCoeff=0.6511;MQ=44.86;MQ0=114;MQ0Fraction=0.1068;MQRankSum=-2.273;QD=4.00;ReadPosRankSum=-6.601;SB=-991.85;VQSLOD=5.4379;set=VQSR 20 3033550 . TGAG T 2005.90 PASS AA=34;AB=0.51429;ABA=34;ABP=3.1344;ABR=36;AC=22;AF=0.0332;AN=662;BL=1374;BR=1649;BVAR;BaseQRankSum=5.192;DEL;DP=14639;DP4=2271,1492,12,21;Dels=0.02;EL=19;EPP=4.0322;ER=15;FR;FS=16.657;HETAR=17;HOMA=0;HOMR=914;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=-0.0454;LEN=3;LRB=0.090969;LRBP=57.333;MQ=53.99;MQ0Fraction=0.0304;MQM=46.735;MQRankSum=1.938;NF;NR;NS=931;PP;PV4=0.0068,9.4e-05,1,1;RA=2985;RL=11;RPP=12.207;RR=23;RUN=1;ReadPosRankSum=-0.466;SAB=0.41176;SAF=14;SAP=5.3095;SAR=20;SC=CTTGGGAGGCTGAGGTGGGAG;SRB=0.62781;SRF=1874;SRP=426.52;SRR=1111;TC;TR=1;TU=G;VQSLOD=8.9194;set=Intersection;sumGLbyD=24.41 20 3635363 . T TG 999 PASS AA=16;AB=0.61905;ABA=16;ABP=8.1805;ABR=26;AF=0.0141;AF1=0.01726;AN=708;BL=614;BR=523;BVAR;BaseQRankSum=2.337;CI95=0.01106,0.02434;DP=14594;DP4=2128,2038,6,10;Dels=0.00;EL=7;EPP=3.5532;ER=9;FQ=999;FR;FS=5.579;HETAR=8;HOMA=0;HOMR=1055;HP=3;HPLen=3;HR=3;HRun=3;HU=G;INDEL;INS;InbreedingCoeff=0.0633;LEN=1;LRB=0.080035;LRBP=18.826;MQ=100.74;MQ0=0;MQ0Fraction=0.0000;MQM=51.312;MQRankSum=2.569;NF;NR;NS=1063;PP;PV4=0.32,1,1,1;RA=5628;RL=9;RPP=3.5532;RR=7;RUN=1;ReadPosRankSum=-1.941;SAB=0.375;SAF=6;SAP=5.1818;SAR=10;SC=AAGGTTCGCTTGGGTGTGGAG;SRB=0.4984;SRF=2805;SRP=3.1353;SRR=2823;TC;TR=3;TU=G;VQSLOD=9.3275;set=Intersection;sumGLbyD=11.68 20 3873327 rs61519218 A AAG 683.85 PASS AC=25;AF=0.0313;AN=800;BaseQRankSum=4.839;DB;DP=1718;FS=4.265;HRun=0;HaplotypeScore=20.5789;InbreedingCoeff=0.1055;MQ=53.70;MQ0=37;MQ0Fraction=0.0215;MQRankSum=2.468;QD=6.30;ReadPosRankSum=4.254;SB=-403.21;VQSLOD=6.1858;set=VQSR 20 4028835 . GC G 2511.30 PASS AA=66;AB=0.56954;ABA=65;ABP=9.3521;ABR=86;AC=22;AF=0.01836;AN=1198;BL=2303;BR=2463;BVAR;BaseQRankSum=7.621;DEL;DP=22795;DP4=1714,2774,22,37;Dels=0.02;EL=34;EPP=3.1419;ER=32;FQ=999;FR;FS=2.095;HETAR=21;HOMA=0;HOMR=1050;HP=2;HPLen=2;HR=2;HRun=2;HU=C;INDEL;InbreedingCoeff=0.0125;LEN=1;LRB=0.033571;LRBP=14.674;MQ=108.09;MQ0=0;MQ0Fraction=0.0000;MQM=53.318;MQRankSum=5.257;NF;NR;NS=1071;PP;PV4=1,5.4e-13,1,0.075;RA=6185;RL=36;RPP=4.1947;RR=30;RUN=1;ReadPosRankSum=-1.059;SAB=0.45455;SAF=30;SAP=4.1947;SAR=36;SC=TGCTGTCACTGCCTTCTCCTA;SRB=0.42118;SRF=2605;SRP=336.76;SRR=3580;TC;TR=2;TU=C;VQSLOD=10.2409;set=Intersection;sumGLbyD=12.71 20 4039609 rs67812039 G GA 43457 PASS AA=909;AB=0.54639;ABA=572;ABP=26.583;ABR=689;AC=302;AF=0.3455;AN=874;BL=37070;BR=38211;BVAR;BaseQRankSum=20.147;DB;DP=25595;DP4=1483,1374,528,542;Dels=0.00;EL=467;EPP=4.5033;ER=442;FQ=999;FR;FS=5.441;HETAR=243;HOMA=127;HOMR=608;HP=4;HPLen=3;HR=3;HRun=3;HU=A;INDEL;INS;InbreedingCoeff=0.1388;LEN=1;LRB=0.015157;LRBP=40.563;MQ=119.50;MQ0=0;MQ0Fraction=0.0000;MQM=83.197;MQRankSum=1.080;NF;NR;NS=978;PP;PV4=0.16,1,3.6e-12,1;RA=3033;RL=443;RPP=4.274;RR=466;RUN=1;ReadPosRankSum=-1.000;SAB=0.32233;SAF=293;SAP=252.24;SAR=616;SC=TATGTTGGGAGAAATATCAGT;SRB=0.38378;SRF=1164;SRP=358.85;SRR=1869;TC;TR=4;TU=AG;VQSLOD=9.9146;dbSNP=130;set=Intersection;sumGLbyD=16.79 20 4390056 . TC T 49312 PASS AA=91;AB=0.94353;ABA=86;ABP=2605.4;ABR=1437;AC=39;AF=0.03160;AN=1234;BL=6823;BR=731;BVAR;BaseQRankSum=2.727;DEL;DP=13149;Dels=0.00;EL=41;EPP=4.9431;ER=50;FS=4.002;HETAR=465;HOMA=313;HOMR=292;HRun=3;InbreedingCoeff=0.0326;LEN=1;LRB=0.80646;LRBP=10671;MQ0=0;MQ0Fraction=0.0000;MQM=69.824;MQRankSum=-0.903;NS=1073;RA=3078;RL=89;RPP=183.62;RR=2;RUN=1;ReadPosRankSum=-12.526;SAB=0.45055;SAF=41;SAP=4.9431;SAR=50;SRB=0.52567;SRF=1618;SRP=20.622;SRR=1460;VQSLOD=4.3235;set=Intersection;sumGLbyD=3.53 20 4474622 . TA AA,T,TAA,TAAA,TAAAA 94522.28 PASS ABR=114;AC=38,68,16,900;AF=0.03333,0.05965,0.01404,0.78947;AN=1140;BVAR;BaseQRankSum=9.741;DB;DP=16656;Dels=0.00;FR;FS=2.355;HOMA=3;HOMR=936;HP=10;HPLen=10;HR=10;HRun=10;HU=A;INS;InbreedingCoeff=0.4516;MQ0=2;MQ0Fraction=0.0008;MQRankSum=-4.096;NF;NR;NS=980;PP;RA=3766;RUN=1;ReadPosRankSum=2.380;SC=AGAAAAAAATTAAAAAAAAAA;SRB=0.49734;SRF=1873;SRP=3.2409;SRR=1893;TC;TR=10;TU=A;VQSLOD=8.8186;set=Intersection;sumGLbyD=38.79 20 4824911 . AC A 41998.70 PASS AC=1172;AF=0.97342;AN=1204;BaseQRankSum=8.604;DP=3615;FS=9.934;HRun=1;HaplotypeScore=39.6843;InbreedingCoeff=0.0980;MQ=129.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=3.378;QD=11.62;ReadPosRankSum=6.967;SB=-16955.28;VQSLOD=4.2689;set=VQSR 20 4839897 rs35881880 TAA T,TA,TAAA,TAAAAA 3906.80 PASS AC=12,95,137,189;AF=0.01024,0.08106,0.11689,0.16126;AN=1172;BVAR;BaseQRankSum=15.271;DB;DEL;DP=15105;Dels=0.04;FR;FS=43.567;HP=19;HR=13;HRun=13;HU=A;INS;InbreedingCoeff=0.5716;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.569;NF;NR;PP;RUN=1;ReadPosRankSum=-13.794;SC=TGTTAAAAAATAAAAAAAAAA;TC;TR=13;TU=A;VQSLOD=8.1773;set=Intersection;sumGLbyD=3.77 20 5071386 . AT A 45200.27 PASS AC=685;AF=0.7495;AN=914;BaseQRankSum=11.006;DP=2725;FS=8.133;HRun=3;HaplotypeScore=50.5496;InbreedingCoeff=0.2364;MQ=81.40;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.411;QD=18.51;ReadPosRankSum=3.429;SB=-22405.85;VQSLOD=4.2872;set=VQSR 20 5507414 . G GCC 439.08 PASS AC=23;AF=0.01876;AN=1226;BaseQRankSum=3.051;DP=3023;FS=3.636;HRun=1;HaplotypeScore=30.3104;InbreedingCoeff=0.0204;MQ=112.09;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.065;QD=2.85;ReadPosRankSum=-2.709;SB=-302.22;VQSLOD=4.4311;set=VQSR 20 5609676 . GA G,GAA 799.89 PASS AA=42;AB=0.79096;ABA=37;ABP=133.16;ABR=140;AC=43,65;AF=0.03607,0.05453;AF1=0.02826;AN=1192;BL=1360;BR=2334;BVAR;BaseQRankSum=5.069;CI95=0.01242,0.04037;DP=15610;DP4=1548,2441,21,30;Dels=0.02;EL=18;EPP=4.8716;ER=24;FQ=12.1;FR;FS=0.000;HETAR=36;HOMA=1;HOMR=991;HP=13;HPLen=10;HR=10;HRun=10;HU=A;INDEL;INS;InbreedingCoeff=0.2001;LEN=1;LRB=0.26367;LRBP=560.68;MQ=63.29;MQ0Fraction=0.0003;MQM=44.143;MQRankSum=1.755;NF;NR;NS=1028;PP;PV4=0.77,1,0.0087,0.0053;RA=4114;RL=15;RPP=10.455;RR=27;RUN=1;ReadPosRankSum=-2.978;SAB=0.5;SAF=21;SAP=3.0103;SAR=21;SC=AAAAAAGAAAGAAAAAAAAAA;SRB=0.39742;SRF=1635;SRP=379;SRR=2479;TC;TR=11;TU=AAAG;VQSLOD=4.1229;set=filterInVQSR-2of5;sumGLbyD=7.95 20 5736211 rs35303106 CT C,CTT 4384.40 PASS AA=117;AB=0.71499;ABA=116;ABP=166.4;ABR=291;AC=32,145;AF=0.02712,0.12288;AN=1180;BL=5556;BR=4901;BVAR;BaseQRankSum=2.708;DB;DP=9157;Dels=0.01;EL=54;EPP=4.5136;ER=63;FR;FS=2.802;HETAR=79;HOMA=1;HOMR=837;HP=16;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.1903;LEN=1;LRB=0.062637;LRBP=92.1;MQ0Fraction=0.0273;MQM=48.932;MQRankSum=3.654;NF;NR;NS=917;PP;RA=2785;RL=79;RPP=34.209;RR=38;RUN=1;ReadPosRankSum=0.795;SAB=0.5641;SAF=66;SAP=7.1862;SAR=51;SC=TTTTCTTTTTCTTTTTTTTTT;SRB=0.41795;SRF=1164;SRP=165.85;SRR=1621;TC;TR=11;TU=T;VQSLOD=5.0895;set=Intersection;sumGLbyD=4.66 20 5898626 rs34483659 CAAA C,CA,CAA,CAAAAA 1140.16 PASS ABR=34;AC=19,98,56,199;AF=0.0227,0.1172,0.0670,0.2380;AF1=0.08519;BVAR;BaseQRankSum=5.049;CI95=0.03727,0.1273;DB;DEL;DP=5091;DP4=539,408,121,123;FQ=4.43;FR;FS=5.701;HOMA=64;HOMR=156;HP=19;HR=18;HU=A;HaplotypeScore=11.5333;INDEL;InbreedingCoeff=0.7405;MQ0=117;MQ0Fraction=0.0986;MQRankSum=6.290;NF;NR;NS=240;PP;PV4=0.043,1,1,0.0087;QD=1.22;RA=204;RUN=1;ReadPosRankSum=-2.684;SB=-1015.09;SC=ACTAAAAATACAAAAAAAAAA;SRB=0.35294;SRF=72;SRP=41.33;SRR=132;TC;TR=18;TU=A;VQSLOD=4.1696;set=filterInVQSR-2of5 20 5975126 rs10541892 C CAG 504.78 PASS AC=79;AF=0.07004;AN=1128;BaseQRankSum=10.498;DB;DP=2050;FS=38.228;HRun=0;HaplotypeScore=14.1426;InbreedingCoeff=-0.0053;MQ=60.40;MQ0=80;MQ0Fraction=0.0390;MQRankSum=5.098;QD=1.63;ReadPosRankSum=-4.851;SB=-590.69;VQSLOD=4.8517;set=VQSR 20 5992611 . G GT 799.56 PASS AA=39;AB=0.8301;ABA=35;ABP=197.98;ABR=171;AC=13;AF=0.0183;AN=712;BL=1164;BR=1566;BVAR;BaseQRankSum=1.914;DP=9561;Dels=0.01;EL=16;EPP=5.7386;ER=23;FS=0.739;HETAR=32;HOMA=0;HOMR=1024;HRun=9;INS;InbreedingCoeff=0.0339;LEN=1;LRB=0.14725;LRBP=131.55;MQ0=0;MQ0Fraction=0.0000;MQM=97.231;MQRankSum=0.764;NS=1056;RA=5204;RL=16;RPP=5.7386;RR=23;RUN=1;ReadPosRankSum=-1.169;SAB=0.69231;SAF=27;SAP=15.538;SAR=12;SRB=0.56399;SRF=2935;SRP=188.09;SRR=2269;VQSLOD=4.6516;set=Intersection;sumGLbyD=5.96 20 6040983 rs11087710 A AAAAAAGAG,AAAAAGAG,AAAAGAG,AAAAGAGAG,AAAGAG,AAAGAGAG,AAGAG,AAGAGAG,AG,AGAG,AGAGAG 66894.55 PASS ABR=468;AC=80,9,20,136,31,91,33,29,9,3,5;AF=0.0980,0.0110,0.0245,0.1667,0.0380,0.1115,0.0404,0.0355,0.0110,0.0037,0.0061;AN=816;BVAR;BaseQRankSum=-12.470;DB;DP=38726;DP4=426,611,310,472;Dels=0.00;FQ=999;FR;FS=6.635;HOMA=110;HOMR=506;HP=14;HR=15;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.8291;KGPilot123;MQ=54.22;MQ0Fraction=0.0168;MQRankSum=-5.329;NF;NR;NS=861;PP;PV4=0.56,1,6.9e-09,0.31;RA=1828;RUN=1;ReadPosRankSum=-7.857;SC=AAAAAAAAAAAAGAGAGAGAG;SRB=0.62418;SRF=1141;SRP=247.85;SRR=687;TC;TR=15;TU=A;VQSLOD=9.0574;dbSNP=131;set=Intersection;sumGLbyD=36.72 20 6903392 . TC CC,T 999 PASS AF=0.0000;AF1=0.01192;CI95=0.008547,0.01709;DP=10440;DP4=2544,2062,9,11;Dels=0.01;FQ=999;FR;HP=2;HPLen=3;HR=3;HRun=2;HU=T;INDEL;InbreedingCoeff=0.0324;MQ=62.78;MQ0=2;MQ0Fraction=0.0009;NF;NR;PP;PV4=0.38,0.0069,0.36,0.41;QD=8.05;SB=-320.13;SC=TTATTTTCTTTCCAATTTTTA;TC;TR=8;TU=CTTT;set=filterInVQSR-2of5;sumGLbyD=13.22 20 7024548 . G GAT 5041.27 PASS AC=123;AF=0.10336;AN=1190;BaseQRankSum=23.097;DP=3045;FS=7.979;HRun=0;HaplotypeScore=15.6967;InbreedingCoeff=0.1062;MQ=119.29;MQ0=2;MQ0Fraction=0.0007;MQRankSum=-3.725;QD=8.97;ReadPosRankSum=-1.636;SB=-2257.45;VQSLOD=5.9332;set=VQSR 20 7484554 . A AT 5.09 PASS AC=0;AF=0.0000;AN=710;BaseQRankSum=-0.696;DP=1862;FS=2.835;HRun=9;HaplotypeScore=13.5425;InbreedingCoeff=0.0567;MQ=76.92;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.932;ReadPosRankSum=-1.701;VQSLOD=4.3156;set=VQSR 20 7632194 rs77286341 GAA AAA,G 5324 PASS AC=0;AF=0.0000;AN=700;BaseQRankSum=-1.741;DB;DP=1772;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=60.1795;InbreedingCoeff=0.0017;MQ=70.69;MQ0=13;MQ0Fraction=0.0073;MQRankSum=-1.315;NF;NR;PP;ReadPosRankSum=-3.650;SC=GAGAGAGAGAGAAAGGTGTAA;TC;TR=13;TU=AG;set=filterInVQSR-2of5 20 7767508 rs71329674 G GA 17914 PASS AA=415;AB=0.61617;ABA=337;ABP=105.94;ABR=541;AC=141;AF=0.11614;AN=1214;BL=15187;BR=20323;BVAR;BaseQRankSum=-13.946;DB;DP=28222;Dels=0.00;EL=184;EPP=14.569;ER=231;FQ=999;FR;FS=13.296;HETAR=178;HOMA=35;HOMR=822;HP=14;HPLen=9;HR=9;HRun=9;HU=A;INDEL;INS;InbreedingCoeff=0.0714;LEN=1;LRB=0.14464;LRBP=1616.1;MQ=89.69;MQ0=1;MQ0Fraction=0.0003;MQM=51.667;MQRankSum=0.664;NF;NR;NS=1035;PP;RA=3707;RL=171;RPP=30.894;RR=244;RUN=1;ReadPosRankSum=-1.120;SAB=0.45301;SAF=188;SAP=10.969;SAR=227;SC=ATTCTAAAAAGAAAAAAAAAT;SRB=0.38495;SRF=1427;SRP=429.23;SRR=2280;TC;TR=9;TU=A;VQSLOD=9.0748;set=Intersection;sumGLbyD=11.09 20 7920261 . TA T,TAA 802.15 PASS AA=28;AB=0.8;ABA=28;ABP=112.45;ABR=112;AC=22,39;AF=0.01836,0.03255;AN=1198;BL=943;BR=1487;BVAR;BaseQRankSum=2.233;DP=10645;Dels=0.01;EL=11;EPP=5.8022;ER=17;FR;FS=1.691;HETAR=20;HOMA=0;HOMR=1007;HP=10;HPLen=9;HR=9;HRun=9;HU=A;INS;InbreedingCoeff=0.2256;LEN=1;LRB=0.22387;LRBP=267.46;MQ0=0;MQ0Fraction=0.0000;MQM=57.571;MQRankSum=0.940;NF;NR;NS=1027;PP;RA=4776;RL=8;RPP=14.178;RR=20;RUN=1;ReadPosRankSum=-1.567;SAB=0.53571;SAF=15;SAP=3.3205;SAR=13;SC=GTAACTGCTATAAAAAAAAAC;SRB=0.48576;SRF=2320;SRP=11.42;SRR=2456;TC;TR=9;TU=A;VQSLOD=4.0815;set=filterInVQSR-2of5;sumGLbyD=5.37 20 8012465 rs10595338 TATGA T 2104.41 PASS AF=0.03339;BaseQRankSum=10.662;DB;DP=11772;DS;Dels=0.01;FR;FS=7.678;HP=1;HPLen=1;HR=1;HRun=0;HU=A;InbreedingCoeff=0.0266;MQ0Fraction=0.0731;MQRankSum=0.603;NF;NR;PP;ReadPosRankSum=1.276;SC=TGTATGTATGTATGATGTATG;TC;TR=19;TU=ATGT;VQSLOD=4.1376;set=filterInVQSR-2of5;sumGLbyD=6.53 20 8573999 . CGTGT C,CGT,CGTGTGT,TGTGT 45865.96 PASS AC=458,0,731;AF=0.37727,0.00000,0.60214;AN=1214;BVAR;BaseQRankSum=-6.703;DEL;DP=37714;Dels=0.03;FR;FS=11.079;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.7632;LEN=2;MQ0Fraction=0.0026;MQRankSum=-1.394;NF;NR;PP;RUN=1;ReadPosRankSum=-2.102;SC=TGTGTGTGCGCGTGTGTGTGT;TC;TR=18;TU=GT;VQSLOD=6.1435;set=Intersection;sumGLbyD=3.53 20 8610455 rs10571111 TTTTC T 11763.51 PASS AC=190;AF=0.17056;AN=1114;BaseQRankSum=-14.397;DB;DP=2323;FS=2.321;HRun=0;HaplotypeScore=39.8020;InbreedingCoeff=0.2502;MQ=53.39;MQ0=104;MQ0Fraction=0.0448;MQRankSum=3.519;QD=19.07;ReadPosRankSum=4.150;SB=-4067.02;VQSLOD=5.0554;set=VQSR 20 9139079 . ATT A,AT,ATTT,ATTTT,ATTTTT 8777.90 PASS AC=23,140,114,69,113;AF=0.01993,0.12132,0.09879,0.05979,0.09792;AN=1154;BVAR;BaseQRankSum=-0.022;DEL;DP=25109;DP4=502,657,278,313;FR;FS=11.929;HP=16;HR=16;HU=T;HaplotypeScore=20.2361;INDEL;INS;InbreedingCoeff=0.5704;MQ0=16;MQ0Fraction=0.0067;MQRankSum=2.624;NF;NR;PP;PV4=0.14,1,1,1;QD=1.48;RUN=1;ReadPosRankSum=-0.480;SB=-2354.28;SC=CACCTGGCTAATTTTTTTTTT;TC;TR=16;TU=T;VQSLOD=6.9180;set=Intersection 20 9862448 . CT C 49312 PASS AA=60;AB=0.96003;ABA=53;ABP=2440.4;ABR=1273;AC=18;AF=0.01461;AN=1232;BL=3516;BR=140;BVAR;BaseQRankSum=-2.056;DEL;DP=11893;Dels=0.01;EL=35;EPP=6.6294;ER=25;FS=1.787;HETAR=396;HOMA=344;HOMR=334;HRun=1;InbreedingCoeff=0.0379;LEN=1;LRB=0.92341;LRBP=6772.5;MQ0Fraction=0.0006;MQM=54.267;MQRankSum=-0.907;NS=1074;RA=2990;RL=60;RPP=133.3;RR=0;RUN=1;ReadPosRankSum=-10.579;SAB=0.58333;SAF=35;SAP=6.6294;SAR=25;SRB=0.47826;SRF=1430;SRP=15.284;SRR=1560;VQSLOD=3.0237;set=filterInVQSR-2of5;sumGLbyD=2.84 20 9863736 rs73618103 G GT 50570.21 PASS AA=2247;AB=0.48878;ABA=1412;ABP=6.0324;ABR=1350;AC=546;AF=0.44463;AN=1228;BL=86886;BR=95862;BVAR;BaseQRankSum=-23.978;DB;DP=32517;DP4=1125,1133,1017,1048;Dels=0.00;EL=1089;EPP=7.6113;ER=1158;FQ=999;FR;FS=2.529;HETAR=445;HOMA=201;HOMR=393;HP=4;HPLen=4;HR=4;HRun=4;HU=T;INDEL;INS;InbreedingCoeff=0.1393;KGPilot123;LEN=1;LRB=0.049117;LRBP=960.35;MQ=68.10;MQ0=2;MQ0Fraction=0.0006;MQM=50.931;MQRankSum=-1.580;NF;NR;NS=1039;PP;PV4=0.71,1,0.11,1;RA=3139;RL=1089;RPP=7.6113;RR=1158;RUN=1;ReadPosRankSum=0.846;SAB=0.54161;SAF=1217;SAP=36.804;SAR=1030;SC=TGATTGTATGGTTTTGTCCTT;SRB=0.53425;SRF=1677;SRP=34.987;SRR=1462;TC;TR=4;TU=T;VLD;VQSLOD=10.1800;dbSNP=131;set=Intersection;sumGLbyD=18.20 20 10640876 . TA T 42819 PASS AA=86;AB=0.92316;ABA=75;ABP=1521;ABR=901;AC=40;AF=0.0447;AN=894;BL=6265;BR=415;BVAR;BaseQRankSum=-0.850;DEL;DP=8223;Dels=0.00;EL=41;EPP=3.4143;ER=45;FS=3.190;HETAR=336;HOMA=384;HOMR=290;HRun=1;InbreedingCoeff=0.0173;LEN=1;LRB=0.87575;LRBP=11128;MQ0=0;MQ0Fraction=0.0000;MQM=76.163;MQRankSum=1.314;NS=1034;RA=2046;RL=83;RPP=164.61;RR=3;RUN=1;ReadPosRankSum=-12.060;SAB=0.46512;SAF=40;SAP=3.9193;SAR=46;SRB=0.5523;SRF=1130;SRP=51.615;SRR=916;VQSLOD=3.9183;set=filterInVQSR-2of5;sumGLbyD=4.00 20 10926959 . AG A 12239 PASS AA=65;AB=0.92801;ABA=64;ABP=1417.6;ABR=825;AC=24;AF=0.0264;AN=908;BL=616;BR=3782;BVAR;BaseQRankSum=9.990;DEL;DP=10708;Dels=0.01;EL=37;EPP=5.7163;ER=28;FS=1.652;HETAR=275;HOMA=70;HOMR=724;HRun=1;InbreedingCoeff=0.0102;LEN=1;LRB=0.71987;LRBP=4952;MQ0=1;MQ0Fraction=0.0004;MQM=118.82;MQRankSum=1.018;NS=1069;RA=4746;RL=5;RPP=104.07;RR=60;RUN=1;ReadPosRankSum=-12.039;SAB=0.41538;SAF=27;SAP=7.0526;SAR=38;SRB=0.4764;SRF=2261;SRP=25.968;SRR=2485;VQSLOD=2.9713;set=filterInVQSR-2of5;sumGLbyD=4.10 20 11299648 . TG T 49315 PASS AA=62;AB=0.95292;ABA=54;ABP=2046.7;ABR=1093;AC=28;AF=0.0373;AN=750;BL=3126;BR=528;BVAR;BaseQRankSum=-4.929;DEL;DP=10764;Dels=0.01;EL=26;EPP=6.5127;ER=36;FS=3.851;HETAR=366;HOMA=383;HOMR=304;HRun=1;InbreedingCoeff=0.0267;LEN=1;LRB=0.711;LRBP=4014.1;MQ0=1;MQ0Fraction=0.0005;MQM=76.468;MQRankSum=1.327;NS=1070;RA=2588;RL=54;RPP=77.121;RR=8;RUN=1;ReadPosRankSum=-12.507;SAB=0.48387;SAF=30;SAP=3.1504;SAR=32;SRB=0.47643;SRF=1233;SRP=15.499;SRR=1355;VQSLOD=3.8673;set=filterInVQSR-2of5;sumGLbyD=3.00 20 11561096 . CTA C 999 PASS AC=2;AF=0.0029;AF1=0.005602;BaseQRankSum=3.190;CI95=0.004425,0.01106;DP=7521;DP4=1998,1794,2,4;Dels=0.00;FQ=999;FR;FS=5.422;HP=3;HPLen=2;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0056;MQ=113.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.297;NF;NR;PP;PV4=0.43,0.024,1,1;ReadPosRankSum=1.406;SC=CAATAGTATTCTATGTCAGTC;TC;TR=1;TU=T;VQSLOD=8.6243;set=Intersection;sumGLbyD=21.89 20 11723671 . C CA 1096.60 PASS AA=35;AB=0.69565;ABA=35;ABP=41.247;ABR=80;AC=10;AF=0.0141;AN=710;BL=2005;BR=1702;BVAR;BaseQRankSum=-3.427;DP=9819;Dels=0.00;EL=20;EPP=4.5614;ER=15;FR;FS=3.814;HETAR=20;HOMA=0;HOMR=1034;HP=8;HPLen=7;HR=7;HRun=7;HU=A;INS;InbreedingCoeff=0.0323;LEN=1;LRB=0.081737;LRBP=56.79;MQ0=0;MQ0Fraction=0.0000;MQM=81.057;MQRankSum=0.050;NF;NR;NS=1054;PP;RA=5562;RL=22;RPP=8.0357;RR=13;RUN=1;ReadPosRankSum=-2.012;SAB=0.71429;SAF=25;SAP=16.97;SAR=10;SC=ATATTGAAGACAAAAAAACAG;SRB=0.49371;SRF=2746;SRP=4.9233;SRR=2816;TC;TR=7;TU=A;VQSLOD=7.4342;set=Intersection;sumGLbyD=8.30 20 11767787 . CA C 1382.10 PASS AA=24;AB=0.56667;ABA=13;ABP=4.1684;ABR=17;AC=10;AF=0.00810;AN=1234;BL=967;BR=819;BVAR;BaseQRankSum=1.629;DEL;DP=22318;DP4=2190,2491,8,14;Dels=0.01;EL=16;EPP=8.8009;ER=8;FQ=999;FR;FS=2.536;HETAR=6;HOMA=3;HOMR=1051;HP=2;HPLen=1;HR=1;HRun=1;HU=A;INDEL;InbreedingCoeff=0.0823;LEN=1;LRB=0.082867;LRBP=29.642;MQ=65.44;MQ0Fraction=0.0032;MQM=50.583;MQRankSum=0.931;NF;NR;NS=1060;PP;PV4=0.39,0.018,1,0.37;RA=5568;RL=11;RPP=3.3722;RR=13;RUN=1;ReadPosRankSum=-0.694;SAB=0.375;SAF=9;SAP=6.2675;SAR=15;SC=TGAACATGTACAGACTTGGTT;SRB=0.44325;SRF=2468;SRP=158.78;SRR=3100;TC;TR=1;TU=A;VQSLOD=9.9622;set=Intersection;sumGLbyD=15.42 20 12021825 . A AG 1063.30 PASS AA=26;AB=0.53704;ABA=25;ABP=3.6537;ABR=29;AC=12;AF=0.0214;AN=562;BL=1077;BR=815;BVAR;BaseQRankSum=-3.787;DP=22049;DP4=2650,2464,13,12;Dels=0.00;EL=18;EPP=11.362;ER=8;FR;FS=0.735;HETAR=12;HOMA=1;HOMR=1064;HP=1;HR=1;HRun=1;HU=G;INDEL;INS;InbreedingCoeff=0.0876;LEN=1;LRB=0.13848;LRBP=81.794;MQ=102.78;MQ0=0;MQ0Fraction=0.0000;MQM=85.538;MQRankSum=-0.126;NF;NR;NS=1077;PP;PV4=1,1,0.19,0.2;RA=6457;RL=17;RPP=8.3555;RR=9;RUN=1;ReadPosRankSum=-1.941;SAB=0.57692;SAF=15;SAP=4.3466;SAR=11;SC=GTAGTTTAACAGTTTATCAGG;SRB=0.5182;SRF=3346;SRP=21.582;SRR=3111;TC;TR=1;TU=G;VQSLOD=8.0483;set=Intersection;sumGLbyD=13.94 20 12238835 rs113904674 CTCTTCATGGTCT C 1813.44 PASS AA=7;AB=0.73077;ABA=7;ABP=15.037;ABR=19;AC=4;AF=0.0056;AN=712;BL=360;BR=368;BVAR;BaseQRankSum=3.891;DB;DEL;DP=10309;Dels=0.00;EL=4;EPP=3.3205;ER=3;FR;FS=0.000;HETAR=3;HOMA=0;HOMR=1076;HP=1;HPLen=2;HR=2;HRun=0;HU=C;InbreedingCoeff=-0.0381;LEN=12;LRB=0.010989;LRBP=3.2012;MQ0=0;MQ0Fraction=0.0000;MQM=37;MQRankSum=-3.793;NF;NR;NS=1079;PP;RA=6085;RL=4;RPP=3.3205;RR=3;RUN=1;ReadPosRankSum=1.319;SAB=0.42857;SAF=3;SAP=3.3205;SAR=4;SC=CTTAATGCTCCTCTTCATGGT;SRB=0.51257;SRF=3119;SRP=11.364;SRR=2966;TC;TR=6;TU=CCT;VQSLOD=5.7551;set=Intersection;sumGLbyD=69.48 20 12602812 . AT A 12344 PASS AA=47;AB=0.94372;ABA=43;ABP=1309.5;ABR=721;AC=14;AF=0.0196;AN=716;BL=2714;BR=217;BVAR;BaseQRankSum=1.424;DEL;DP=10743;Dels=0.00;EL=24;EPP=3.0565;ER=23;FS=0.629;HETAR=228;HOMA=65;HOMR=769;HRun=1;InbreedingCoeff=0.0233;LEN=1;LRB=0.85193;LRBP=4622.3;MQ0Fraction=0.0000;MQM=99.574;MQRankSum=1.901;NS=1080;RA=4839;RL=46;RPP=96.568;RR=1;RUN=1;ReadPosRankSum=-9.906;SAB=0.53191;SAF=25;SAP=3.4261;SAR=22;SRB=0.51106;SRF=2473;SRP=8.148;SRR=2366;VQSLOD=2.8161;set=filterInVQSR-2of5;sumGLbyD=3.67 20 13600884 . CTG C,CTGTG 1278.10 PASS AA=85;AB=0.77994;ABA=79;ABP=247.38;ABR=280;AC=71,22;AF=0.05907,0.01830;AN=1202;BL=3279;BR=3205;BVAR;BaseQRankSum=8.852;DEL;DP=24185;DP4=1317,931,52,49;Dels=0.03;EL=45;EPP=3.649;ER=40;FQ=999;FR;FS=31.826;HETAR=75;HOMA=4;HOMR=926;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1566;LEN=2;LRB=0.011413;LRBP=4.8442;MQ=65.06;MQ0Fraction=0.0012;MQM=48.671;MQRankSum=-0.511;NF;NR;NS=1005;PP;PV4=0.18,1,0.39,0.27;RA=3342;RL=35;RPP=8.7583;RR=50;RUN=1;ReadPosRankSum=-2.329;SAB=0.43529;SAF=37;SAP=6.1015;SAR=48;SC=TCCCTTTACTCTGTGTGTGTG;SRB=0.59066;SRF=1974;SRP=241.62;SRR=1368;TC;TR=15;TU=GT;VQSLOD=3.8635;set=filterInVQSR-2of5;sumGLbyD=4.23 20 13666265 . T TATAG 556.88 PASS AC=21;AF=0.01959;AN=1072;BaseQRankSum=24.958;DP=2706;FS=2.581;HRun=0;HaplotypeScore=25.9952;InbreedingCoeff=0.1419;MQ=72.43;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.888;QD=4.38;ReadPosRankSum=2.552;SB=-417.04;VQSLOD=7.3380;set=VQSR 20 13861245 rs72422273 C CTCA 2685.46 PASS AC=140;AF=0.11589;AN=1208;BaseQRankSum=24.355;DB;DP=2910;FS=6.808;HRun=0;HaplotypeScore=19.3095;InbreedingCoeff=-0.0991;MQ=78.25;MQ0=22;MQ0Fraction=0.0076;MQRankSum=3.225;QD=3.64;ReadPosRankSum=2.607;SB=-1861.38;VQSLOD=4.1974;set=VQSR 20 13865746 . T TA,TAA 1416.23 PASS AA=63;AB=0.80417;ABA=47;ABP=195.87;ABR=193;AC=122,21;AF=0.10133,0.01744;AN=1204;BL=3673;BR=1145;BVAR;BaseQRankSum=-3.336;DP=10513;Dels=0.00;EL=62;EPP=131.27;ER=1;FR;FS=716.583;HETAR=45;HOMA=1;HOMR=998;HP=2;HR=1;HRun=1;HU=A;INS;InbreedingCoeff=0.0814;LEN=1;LRB=0.5247;LRBP=2883.3;MQ0=0;MQ0Fraction=0.0000;MQM=56.143;MQRankSum=-1.197;NF;NR;NS=1044;PP;RA=4529;RL=62;RPP=131.27;RR=1;RUN=1;ReadPosRankSum=-12.295;SAB=1;SAF=63;SAP=139.81;SAR=0;SC=GGAACATGGATACCCCCCTGC;SRB=0.52462;SRF=2376;SRP=26.853;SRR=2153;TC;TR=1;TU=A;VQSLOD=-4.2308;set=filterInVQSR-2of5;sumGLbyD=4.77 20 13881703 . CTT C 152.85 PASS AC=8;AF=0.0093;AN=862;BaseQRankSum=3.941;DP=2063;FS=0.962;HRun=5;HaplotypeScore=24.0313;InbreedingCoeff=0.0790;MQ=55.05;MQ0=49;MQ0Fraction=0.0238;MQRankSum=-1.418;QD=3.47;ReadPosRankSum=-0.605;SB=-93.04;VQSLOD=5.3874;set=VQSR 20 14033345 . A AT 2718.30 PASS AA=91;AB=0.80899;ABA=85;ABP=372.04;ABR=360;AC=43;AF=0.03895;AN=1104;BL=3916;BR=4753;BVAR;BaseQRankSum=-6.609;DP=8350;Dels=0.02;EL=46;EPP=3.0342;ER=45;FR;FS=0.498;HETAR=70;HOMA=1;HOMR=871;HP=11;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.0952;LEN=1;LRB=0.096551;LRBP=178.49;MQ0=0;MQ0Fraction=0.0000;MQM=54.879;MQRankSum=2.164;NF;NR;NS=942;PP;RA=3717;RL=37;RPP=9.9065;RR=54;RUN=1;ReadPosRankSum=-1.447;SAB=0.48352;SAF=44;SAP=3.2251;SAR=47;SC=TTGCAAACAGATTTTTTTTTT;SRB=0.45252;SRF=1682;SRP=75.807;SRR=2035;TC;TR=11;TU=T;VQSLOD=3.8299;set=filterInVQSR-2of5;sumGLbyD=3.88 20 14260090 rs73619828 A AT 27935 PASS AA=596;AB=0.59484;ABA=487;ABP=96.922;ABR=715;AC=204;AF=0.17000;AN=1200;BL=21718;BR=28458;BVAR;BaseQRankSum=0.756;DB;DP=23629;DP4=1385,1492,287,328;Dels=0.00;EL=299;EPP=3.0249;ER=297;FQ=999;FR;FS=6.187;HETAR=218;HOMA=38;HOMR=788;HP=9;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.0797;LEN=1;LRB=0.13433;LRBP=1969;MQ=100.81;MQ0=0;MQ0Fraction=0.0000;MQM=57.084;MQRankSum=2.224;NF;NR;NS=1044;PP;PV4=0.53,1,1.2e-11,1;RA=4143;RL=238;RPP=55.475;RR=358;RUN=1;ReadPosRankSum=0.198;SAB=0.46812;SAF=279;SAP=8.2714;SAR=317;SC=CCTTAAGTTGATTTTTTTTTC;SRB=0.50374;SRF=2087;SRP=3.514;SRR=2056;TC;TR=9;TU=T;VQSLOD=9.0018;set=Intersection;sumGLbyD=10.82 20 14260558 . AC A 238 PASS AC=1;AF=0.0014;AF1=0.003368;BaseQRankSum=2.868;CI95=0.003106,0.006211;DP=9724;DP4=2075,2329,1,7;Dels=0.00;FQ=106;FR;FS=10.678;HP=1;HPLen=2;HR=2;HRun=1;HU=A;INDEL;InbreedingCoeff=-0.0406;MQ=114.37;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.862;NF;NR;PP;PV4=0.074,0.0096,0.017,1;ReadPosRankSum=-0.042;SC=ATCAGGAATAACTGTGTGACC;TC;TR=2;TU=A;VQSLOD=8.1618;set=Intersection;sumGLbyD=18.65 20 14425481 . GTA G,GTATA 148.85 PASS AC=43,23;AF=0.03473,0.01858;AN=1238;BaseQRankSum=6.289;DP=25167;DP4=1800,2021,38,49;FR;FS=9.416;HP=2;HPLen=1;HR=1;HU=T;HaplotypeScore=17.7453;INDEL;InbreedingCoeff=0.0995;MQ0=21;MQ0Fraction=0.0058;MQRankSum=-0.200;NF;NR;PP;PV4=0.59,1,0.04,0.023;QD=0.35;ReadPosRankSum=-1.689;SB=-367.50;SC=CTGTGTGTGTGTATATATATA;TC;TR=13;TU=AT;VQSLOD=3.5796;set=filterInVQSR-2of5 20 14943522 rs11478299 GA AA,G 1761.24 PASS AA=117;AB=0.68142;ABA=108;ABP=99.919;ABR=231;AC=0;AF=0.0000;AF1=0.04204;AN=712;BL=4931;BR=5802;BVAR;BaseQRankSum=9.118;CI95=0.02876,0.05752;DB;DEL;DP=13717;DP4=1908,1684,59,58;Dels=0.05;EL=60;EPP=3.1773;ER=57;FQ=81.9;FR;HETAR=56;HOMA=1;HOMR=1011;HP=8;HPLen=8;HR=8;HU=A;INDEL;InbreedingCoeff=0.1264;LEN=1;LRB=0.081152;LRBP=156.5;MQ=106.93;MQ0=0;MQ0Fraction=0.0000;MQM=96.855;MQRankSum=1.619;NF;NR;NS=1068;PP;PV4=0.57,1,0.0003,1;QD=7.40;RA=5080;RL=56;RPP=3.4743;RR=61;RUN=1;ReadPosRankSum=0.814;SAB=0.52137;SAF=61;SAP=3.4743;SAR=56;SB=-1122.51;SC=GTTGTTTGGGGAAAAAAAACT;SRB=0.51083;SRF=2595;SRP=8.1825;SRR=2485;TC;TR=8;TU=A;set=filterInVQSR-2of5;sumGLbyD=9.81 20 14974486 . A AG 4101.40 PASS AA=57;AB=0.57143;ABA=51;ABP=8.2839;ABR=68;AC=22;AF=0.01846;AN=1192;BL=2286;BR=2834;BVAR;BaseQRankSum=8.711;DP=20538;DP4=2172,2100,19,13;Dels=0.00;EL=32;EPP=4.877;ER=25;FS=0.517;HETAR=20;HOMA=4;HOMR=1027;HRun=1;INDEL;INS;InbreedingCoeff=0.0677;LEN=1;LRB=0.10703;LRBP=130.37;MQ=126.07;MQ0=0;MQ0Fraction=0.0000;MQM=56.088;MQRankSum=-10.756;NS=1051;PV4=0.38,3.5e-51,7.9e-34,1;RA=5203;RL=26;RPP=3.9627;RR=31;RUN=1;ReadPosRankSum=1.283;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SRB=0.51816;SRF=2696;SRP=17.918;SRR=2507;VQSLOD=8.0072;set=Intersection;sumGLbyD=25.60 20 15111137 . GA G 13533 PASS AA=98;AB=0.84864;ABA=89;ABP=623.8;ABR=499;AC=47;AF=0.03796;AN=1238;BL=5324;BR=856;BVAR;BaseQRankSum=-11.577;DEL;DP=13384;Dels=0.01;EL=53;EPP=4.4284;ER=45;FS=6.099;HETAR=219;HOMA=845;HOMR=18;HRun=1;InbreedingCoeff=-0.0056;LEN=1;LRB=0.72298;LRBP=7017.4;MQ0Fraction=0.0003;MQM=90.449;MQRankSum=1.408;NS=1083;RA=590;RL=87;RPP=130.99;RR=11;RUN=1;ReadPosRankSum=-18.074;SAB=0.55102;SAF=54;SAP=5.2261;SAR=44;SRB=0.52373;SRF=309;SRP=5.8958;SRR=281;VQSLOD=4.1054;set=filterInVQSR-2of5;sumGLbyD=3.06 20 15283028 . A AC,ACACACACACACAC 140844.83 PASS AA=180;AB=0.61442;ABA=123;ABP=39.285;ABR=196;AC=13,817;AF=0.01111,0.69829;AN=1170;BL=4453;BR=11407;BVAR;BaseQRankSum=24.686;DP=6365;Dels=0.00;EL=124;EPP=58.793;ER=56;FR;FS=10.912;HETAR=87;HOMA=48;HOMR=683;HP=1;HR=1;HRun=1;HU=T;INS;InbreedingCoeff=0.2074;LEN=1;LRB=0.43846;LRBP=6624;MQ0Fraction=0.0558;MQM=38.211;MQRankSum=-21.111;NF;NR;NS=818;PP;RA=1732;RL=0;RPP=393.88;RR=180;RUN=1;ReadPosRankSum=-7.620;SAB=0.31111;SAF=56;SAP=58.793;SAR=124;SC=ACACACACACATACACACATA;SRB=0.54042;SRF=936;SRP=27.584;SRR=796;TC;TR=21;TU=AC;VQSLOD=4.7569;set=Intersection;sumGLbyD=18.36 20 15361056 . ATAACT A 4892.81 PASS AA=59;AB=0.63576;ABA=55;ABP=27.184;ABR=96;AC=34;AF=0.0487;AN=698;BL=3164;BR=1999;BVAR;BaseQRankSum=3.391;DEL;DP=7080;Dels=0.03;EL=27;EPP=3.9304;ER=32;FR;FS=4.816;HETAR=35;HOMA=6;HOMR=966;HP=2;HPLen=3;HR=3;HRun=0;HU=A;InbreedingCoeff=0.0785;LEN=5;LRB=0.22564;LRBP=573.84;MQ0=0;MQ0Fraction=0.0000;MQM=70.034;MQRankSum=-8.732;NF;NR;NS=1008;PP;RA=3915;RL=42;RPP=26.013;RR=17;RUN=1;ReadPosRankSum=-0.735;SAB=0.44068;SAF=26;SAP=4.8137;SAR=33;SC=AGATTAGGAAATAACTTAGGG;SRB=0.42682;SRF=1671;SRP=185.12;SRR=2244;TC;TR=3;TU=A;VQSLOD=7.0900;set=Intersection;sumGLbyD=43.38 20 15579507 . AATTAGTC A,TATTAGTC 1936.38 PASS AA=16;AB=0.58974;ABA=16;ABP=5.7386;ABR=23;AC=64;AF=0.05229;AN=1224;BL=699;BR=775;BVAR;BaseQRankSum=-21.390;DEL;DP=21920;DP4=2099,2403,6,6;Dels=0.00;EL=8;EPP=3.0103;ER=8;FR;FS=2.920;HETAR=5;HOMA=0;HOMR=1063;HP=3;HPLen=4;HR=4;HU=A;INDEL;InbreedingCoeff=-0.0143;LEN=7;LRB=0.05156;LRBP=11.519;MQ=129.49;MQ0=0;MQ0Fraction=0.0000;MQM=51.938;MQRankSum=3.331;NF;NR;NS=1068;PP;PV4=1,0.019,1.3e-07,1;RA=5334;RL=5;RPP=7.8961;RR=11;RUN=1;ReadPosRankSum=-16.901;SAB=0.4375;SAF=7;SAP=3.5532;SAR=9;SC=CATACTACAAAATTAGTCATT;SRB=0.41695;SRF=2224;SRP=322.58;SRR=3110;TC;TR=4;TU=A;VQSLOD=3.2237;set=filterInVQSR-2of5;sumGLbyD=43.57 20 15752535 . CT C,GT 3775.20 PASS AA=92;AB=0.78636;ABA=47;ABP=159.71;ABR=173;AC=0;AF=0.0000;AN=608;BL=4955;BR=2380;BVAR;BaseQRankSum=2.910;DEL;DP=3429;Dels=0.04;EL=13;EPP=105.82;ER=79;FR;HETAR=92;HOMA=95;HOMR=544;HP=2;HPLen=2;HR=2;HU=T;InbreedingCoeff=0.0483;LEN=1;LRB=0.35106;LRBP=1966;MQ0Fraction=0.0232;MQM=35.293;MQRankSum=-2.199;NF;NR;NS=732;PP;QD=4.91;RA=1272;RL=81;RPP=118.66;RR=11;RUN=1;ReadPosRankSum=-1.077;SAB=0.021739;SAF=2;SAP=185.79;SAR=90;SB=-59.51;SC=CAAGACCATCCTTGGCTAACA;SRB=0.14623;SRF=186;SRP=1385.8;SRR=1086;TC;TR=2;TU=T;set=filterInVQSR-2of5;sumGLbyD=9.70 20 15883060 rs73619850 A AT 1325.60 PASS AA=38;AB=0.59302;ABA=35;ABP=9.4742;ABR=51;AC=14;AF=0.0156;AN=896;BL=1078;BR=1638;BVAR;BaseQRankSum=-4.526;DB;DP=19854;DP4=1632,1800,15,20;Dels=0.00;EL=18;EPP=3.2389;ER=20;FR;FS=0.000;HETAR=14;HOMA=1;HOMR=1014;HP=1;HPLen=1;HR=1;HRun=1;HU=T;INDEL;INS;InbreedingCoeff=-0.0131;LEN=1;LRB=0.20619;LRBP=253.74;MQ=118.40;MQ0=0;MQ0Fraction=0.0000;MQM=56.526;MQRankSum=0.892;NF;NR;NS=1029;PP;PV4=0.61,1,0.25,0.14;RA=4439;RL=14;RPP=8.7247;RR=24;RUN=1;ReadPosRankSum=-2.061;SAB=0.42105;SAF=16;SAP=5.0675;SAR=22;SC=GGATTGGCAGATAAAAAATGG;SRB=0.46429;SRF=2061;SRP=52.168;SRR=2378;TC;TR=1;TU=T;VQSLOD=9.7576;set=Intersection;sumGLbyD=15.69 20 16073315 rs111824749 GA G,GAA,GAAA 6400.63 PASS AC=138,47,20;AF=0.11577,0.03943,0.01678;AN=1192;BVAR;BaseQRankSum=11.377;DB;DEL;DP=35284;DP4=1695,1547,60,56;Dels=0.08;FR;FS=9.576;HP=11;HPLen=10;HR=10;HRun=10;HU=A;INDEL;INS;InbreedingCoeff=0.2137;MQ=106.87;MQ0=1;MQ0Fraction=0.0003;MQRankSum=0.773;NF;NR;PP;PV4=0.92,1,0.024,0.45;RUN=1;ReadPosRankSum=-2.224;SC=TATTTGAGGAGAAAAAAAAAA;TC;TR=10;TU=A;VQSLOD=9.3264;set=Intersection;sumGLbyD=8.64 20 16122099 . GA G 12914 PASS AA=85;AB=0.85915;ABA=80;ABP=639.4;ABR=488;AC=19;AF=0.01542;AN=1232;BL=805;BR=5457;BVAR;BaseQRankSum=-6.084;DEL;DP=13592;Dels=0.00;EL=45;EPP=3.649;ER=40;FS=0.935;HETAR=218;HOMA=841;HOMR=14;HRun=2;InbreedingCoeff=0.0250;LEN=1;LRB=0.74289;LRBP=7507.5;MQ0=0;MQ0Fraction=0.0000;MQM=103.01;MQRankSum=2.843;NS=1075;RA=541;RL=2;RPP=170.62;RR=83;RUN=1;ReadPosRankSum=-16.222;SAB=0.49412;SAF=42;SAP=3.0358;SAR=43;SRB=0.44917;SRF=243;SRP=15.152;SRR=298;VQSLOD=3.9745;set=filterInVQSR-2of5;sumGLbyD=2.97 20 16828509 . G GT 843.62 PASS AA=30;AB=0.70103;ABA=29;ABP=37.06;ABR=68;AC=10;AF=0.0140;AN=714;BL=1368;BR=1786;BVAR;BaseQRankSum=-4.061;DP=8682;Dels=0.01;EL=14;EPP=3.2998;ER=16;FR;FS=2.681;HETAR=22;HOMA=1;HOMR=1020;HP=8;HPLen=8;HR=8;HRun=8;HU=T;INS;InbreedingCoeff=0.1389;LEN=1;LRB=0.13253;LRBP=123.3;MQ0=0;MQ0Fraction=0.0000;MQM=62.8;MQRankSum=-1.491;NF;NR;NS=1043;PP;RA=4416;RL=11;RPP=7.6428;RR=19;RUN=1;ReadPosRankSum=-1.718;SAB=0.76667;SAF=23;SAP=21.54;SAR=7;SC=CCTTCAAAAGGTTTTTTTTGG;SRB=0.5745;SRF=2537;SRP=215.91;SRR=1879;TC;TR=8;TU=T;VQSLOD=7.6258;set=Intersection;sumGLbyD=10.77 20 17470034 . GC G 46975 PASS AA=57;AB=0.96043;ABA=52;ABP=2422.5;ABR=1262;AC=34;AF=0.02773;AN=1226;BL=418;BR=3446;BVAR;BaseQRankSum=-6.250;DEL;DP=12035;Dels=0.00;EL=22;EPP=9.4485;ER=35;FS=1.350;HETAR=416;HOMA=409;HOMR=244;HRun=1;InbreedingCoeff=0.0083;LEN=1;LRB=0.78364;LRBP=5155.6;MQ0=0;MQ0Fraction=0.0000;MQM=99.509;MQRankSum=2.192;NS=1076;RA=2396;RL=5;RPP=87.164;RR=52;RUN=1;ReadPosRankSum=-15.199;SAB=0.5614;SAF=32;SAP=4.877;SAR=25;SRB=0.52963;SRF=1269;SRP=21.285;SRR=1127;VQSLOD=3.8440;set=filterInVQSR-2of5;sumGLbyD=3.06 20 17471374 . AGCGGC A 850.03 PASS AC=6;AF=0.0085;AF1=0.01301;AN=704;BaseQRankSum=6.259;CI95=0.00885,0.01991;DP=8180;DP4=2215,1878,4,5;Dels=0.01;FQ=131;FS=0.000;HRun=0;INDEL;InbreedingCoeff=0.0009;MQ=104.41;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-5.521;PV4=0.74,0.37,0.0005,1;ReadPosRankSum=2.468;VQSLOD=6.8773;set=Intersection;sumGLbyD=30.85 20 18433202 rs35582929 G GA 2506.90 PASS AA=55;AB=0.5812;ABA=49;ABP=9.7103;ABR=68;AC=20;AF=0.0218;AN=918;BL=2263;BR=2175;BVAR;BaseQRankSum=-6.639;DB;DP=19467;DP4=1845,2365,27,26;Dels=0.00;EL=21;EPP=9.6826;ER=34;FQ=999;FR;FS=5.633;HETAR=16;HOMA=3;HOMR=1045;HP=2;HPLen=3;HR=3;HRun=1;HU=G;INDEL;INS;InbreedingCoeff=0.0700;LEN=1;LRB=0.019829;LRBP=6.7994;MQ=114.03;MQ0=0;MQ0Fraction=0.0000;MQM=83.345;MQRankSum=1.610;NF;NR;NS=1064;PP;PV4=0.33,1,1,1;RA=5380;RL=28;RPP=3.0498;RR=27;RUN=1;ReadPosRankSum=0.873;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TATTTCATGGGAGCATTAAAA;SRB=0.42862;SRF=2306;SRP=241.07;SRR=3074;TC;TR=3;TU=G;VQSLOD=10.0372;dbSNP=126;set=Intersection;sumGLbyD=13.10 20 18551314 rs10659122 CA C,CAA,CAAA,CAAAA,CAAAAA 18810.74 PASS ABR=243;AC=19,169,216,164,188;AF=0.01816,0.16157,0.20650,0.15679,0.17973;BVAR;BaseQRankSum=-5.742;DB;DP=17637;DP4=136,77,560,237;FR;FS=2.693;HOMA=177;HOMR=299;HP=17;HR=17;HU=A;HaplotypeScore=15.5048;INDEL;INS;InbreedingCoeff=0.8901;MQ0=11;MQ0Fraction=0.0069;MQRankSum=1.845;NF;NR;NS=658;PP;PV4=0.08,1,1,1;QD=12.66;RA=673;RUN=1;ReadPosRankSum=0.283;SB=-3514.45;SC=GATTCCATCTCAAAAAAAAAA;SRB=0.63596;SRF=428;SRP=111.06;SRR=245;TC;TR=17;TU=A;VQSLOD=10.6964;dbSNP=130;set=Intersection 20 18785519 . G GTC 415.55 PASS AC=28;AF=0.0400;AN=700;BaseQRankSum=10.889;DP=1929;FS=8.778;HRun=0;HaplotypeScore=27.6448;InbreedingCoeff=0.0510;MQ=61.99;MQ0=36;MQ0Fraction=0.0187;MQRankSum=4.508;QD=3.08;ReadPosRankSum=8.080;SB=-437.03;VQSLOD=4.9313;set=VQSR 20 19149501 . A AG 17.85 PASS AC=1;AF=0.0015;AN=670;BaseQRankSum=0.769;DP=1635;FS=9.858;HRun=0;HaplotypeScore=12.1949;InbreedingCoeff=-0.0381;MQ=102.63;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.200;QD=3.23;ReadPosRankSum=0.292;SB=-7.06;VQSLOD=4.4695;set=VQSR 20 19540281 . AC A 19710 PASS AA=145;AB=0.81843;ABA=134;ABP=652.98;ABR=604;AC=115;AF=0.09583;AN=1200;BL=9637;BR=817;BVAR;BaseQRankSum=-13.669;DEL;DP=10963;Dels=0.01;EL=66;EPP=5.5412;ER=79;FS=1.252;HETAR=305;HOMA=681;HOMR=59;HRun=1;InbreedingCoeff=0.0298;LEN=1;LRB=0.8437;LRBP=16162;MQ0=0;MQ0Fraction=0.0000;MQM=118.51;MQRankSum=-2.194;NS=1046;RA=823;RL=141;RPP=284.09;RR=4;RUN=1;ReadPosRankSum=-20.775;SAB=0.45517;SAF=66;SAP=5.5412;SAR=79;SRB=0.452;SRF=372;SRP=19.477;SRR=451;VQSLOD=3.9584;set=filterInVQSR-2of5;sumGLbyD=3.29 20 20015051 . TGAGGGTGG T 1820.73 PASS AF=0.0112;AF1=0.01638;AN=714;BaseQRankSum=6.652;CI95=0.01106,0.02212;DP=9910;DP4=2812,1912,6,11;Dels=0.01;FQ=999;FR;FS=6.147;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0077;MQ=129.13;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.195;NF;NR;PP;PV4=0.049,1,5.5e-05,0.006;ReadPosRankSum=-1.989;SC=TTGGTGGAGTTGAGGGTGGGA;TC;TR=2;TU=T;VQSLOD=6.5963;set=Intersection;sumGLbyD=33.49 20 20301041 rs35451634 ATATG A 200.42 PASS AC=21;AF=0.0449;AN=468;BaseQRankSum=5.251;DB;DP=579;FS=24.013;HRun=0;HaplotypeScore=27.8977;InbreedingCoeff=0.0113;MQ=78.47;MQ0=26;MQ0Fraction=0.0449;MQRankSum=-5.284;QD=3.06;ReadPosRankSum=1.793;SB=-55.76;VQSLOD=5.0981;set=VQSR 20 20378174 . TC T 245.55 PASS AC=23;AF=0.01879;AN=1224;BaseQRankSum=0.990;DP=3225;FS=10.413;HRun=1;HaplotypeScore=22.6109;InbreedingCoeff=0.0244;MQ=93.70;MQ0=3;MQ0Fraction=0.0009;MQRankSum=-3.349;QD=1.86;ReadPosRankSum=-7.227;SB=-188.62;VQSLOD=4.2553;set=VQSR 20 20809160 rs10571503 TAA AAA,T 3496 PASS AC=0;AF=0.0000;AN=612;BaseQRankSum=1.968;DB;DP=1092;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=26.1253;InbreedingCoeff=0.0603;MQ=68.98;MQ0=1;MQ0Fraction=0.0009;MQRankSum=1.520;NF;NR;PP;ReadPosRankSum=-4.042;SC=TATATATATATAAATTTAAAT;TC;TR=13;TU=AT;set=filterInVQSR-2of5 20 22508765 . CT C 53877.84 PASS AA=187;AB=0.78077;ABA=171;ABP=537.09;ABR=609;AC=1017;AF=0.91787;AN=1108;BL=12690;BR=1718;BVAR;BaseQRankSum=13.773;DEL;DP=7430;Dels=0.02;EL=73;EPP=22.53;ER=114;FR;FS=16.352;HETAR=152;HOMA=9;HOMR=786;HP=8;HR=4;HRun=4;HU=T;InbreedingCoeff=0.3885;LEN=1;LRB=0.76152;LRBP=18147;MQ0=0;MQ0Fraction=0.0000;MQM=46.086;MQRankSum=0.971;NF;NR;NS=947;PP;RA=2868;RL=177;RPP=326.86;RR=10;RUN=1;ReadPosRankSum=9.951;SAB=0.34759;SAF=65;SAP=40.738;SAR=122;SC=AAAAAATTTTCTTTTGAACTG;SRB=0.46269;SRF=1327;SRP=37.684;SRR=1541;TC;TR=4;TU=T;VQSLOD=5.1182;set=Intersection;sumGLbyD=25.15 20 22555082 rs11477526 AT A 11503 PASS AA=530;AB=0.50816;ABA=422;ABP=3.5063;ABR=436;AF=0.1614;AN=700;BL=21453;BR=23313;BVAR;BaseQRankSum=17.562;DB;DEL;DP=25587;DP4=1869,1600,283,201;Dels=0.14;EL=259;EPP=3.6003;ER=271;FQ=999;FR;FS=14.595;HETAR=159;HOMA=41;HOMR=846;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;InbreedingCoeff=0.0995;LEN=1;LRB=0.041549;LRBP=170.83;MQ=95.89;MQ0=0;MQ0Fraction=0.0000;MQM=72.162;MQRankSum=2.564;NF;NR;NS=1046;PP;PV4=0.058,6.6e-129,0.04,1;RA=4303;RL=264;RPP=3.0267;RR=266;RUN=1;ReadPosRankSum=0.176;SAB=0.58679;SAF=311;SAP=37.688;SAR=219;SC=GGGAAAGCTGATTTACTGATT;SRB=0.54892;SRF=2362;SRP=92.453;SRR=1941;TC;TR=3;TU=T;VQSLOD=8.7746;dbSNP=120;set=Intersection;sumGLbyD=15.27 20 22590907 . A AC 4204.88 PASS AA=67;AB=0.592;ABA=51;ABP=12.2;ABR=74;AF=0.0554;AF1=0.0468;AN=560;BL=2277;BR=2389;BVAR;BaseQRankSum=10.968;CI95=0.03759,0.05639;DP=14380;DP4=2514,2018,33,33;Dels=0.00;EL=22;EPP=20.155;ER=45;FQ=999;FR;FS=3.846;HETAR=25;HOMA=4;HOMR=1049;HP=4;HPLen=5;HR=5;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0719;LEN=1;LRB=0.024003;LRBP=8.8481;MQ=110.68;MQ0=0;MQ0Fraction=0.0000;MQM=96.149;MQRankSum=2.668;NF;NR;NS=1078;PP;PV4=0.39,1,0.46,0.36;RA=5468;RL=33;RPP=3.0427;RR=34;RUN=1;ReadPosRankSum=-1.097;SAB=0.50746;SAF=34;SAP=3.0427;SAR=33;SC=TCATATCAAAAACATTACGTT;SRB=0.54389;SRF=2974;SRP=94.508;SRR=2494;TC;TR=5;TU=A;VQSLOD=10.0712;set=Intersection;sumGLbyD=27.69 20 22806326 rs11468890 ATTCCATCAC A 105320.99 PASS AC=567;AF=0.48795;AN=1162;BVAR;BaseQRankSum=32.858;DB;DEL;DP=26278;DP4=727,796,554,587;Dels=0.30;FQ=999;FR;FS=1.923;HP=3;HPLen=3;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.2548;LEN=9;MQ=89.42;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-23.545;NF;NR;PP;PV4=0.7,1,1.3e-167,1;RUN=1;ReadPosRankSum=4.384;SC=GGCTGCTCCCATTCCATCACT;TC;TR=2;TU=T;VQSLOD=8.2594;set=Intersection;sumGLbyD=69.81 20 22999898 rs55966257 CAGGA C 8019.97 PASS AA=23;AB=0.57778;ABA=19;ABP=5.3748;ABR=26;AC=214;AF=0.18838;AN=1136;BL=1143;BR=1040;BVAR;BaseQRankSum=29.294;DB;DEL;DP=8216;Dels=0.02;EL=11;EPP=3.1047;ER=12;FS=14.938;HETAR=14;HOMA=2;HOMR=948;HRun=0;InbreedingCoeff=0.0797;LEN=4;LRB=0.047183;LRBP=13.563;MQ0=0;MQ0Fraction=0.0000;MQM=34.783;MQRankSum=-20.301;NS=964;RA=3637;RL=13;RPP=3.86;RR=10;RUN=1;ReadPosRankSum=-24.607;SAB=0.47826;SAF=11;SAP=3.1047;SAR=12;SRB=0.49024;SRF=1783;SRP=6.02;SRR=1854;VQSLOD=7.9163;set=Intersection;sumGLbyD=9.43 20 23385964 rs57723772 GAA G 8170.95 PASS AC=257;AF=0.20928;AN=1228;BaseQRankSum=32.220;DB;DP=3291;FS=1.688;HRun=3;HaplotypeScore=22.6739;InbreedingCoeff=0.0171;MQ=58.44;MQ0=32;MQ0Fraction=0.0097;MQRankSum=-4.893;QD=6.55;ReadPosRankSum=-35.524;SB=-3631.67;VQSLOD=5.6549;set=VQSR 20 23534530 . TA T 3542.10 PASS AA=45;AB=0.75658;ABA=37;ABP=89.926;ABR=115;AC=35;AF=0.02991;AN=1170;BL=3090;BR=270;BVAR;BaseQRankSum=-6.892;DEL;DP=8108;Dels=0.00;EL=19;EPP=5.3748;ER=26;FS=1.026;HETAR=76;HOMA=896;HOMR=18;HRun=1;InbreedingCoeff=0.0551;LEN=1;LRB=0.83929;LRBP=5142.4;MQ0Fraction=0.0017;MQM=41.578;MQRankSum=0.818;NS=991;RA=203;RL=43;RPP=84.127;RR=2;RUN=1;ReadPosRankSum=-12.923;SAB=0.37778;SAF=17;SAP=8.8491;SAR=28;SRB=0.5665;SRF=115;SRP=10.808;SRR=88;VQSLOD=4.2093;set=Intersection;sumGLbyD=3.49 20 23976810 rs5841018 A ATATTAAT 1782.38 PASS AF=0.1387;AF1=0.01507;BaseQRankSum=3.717;CI95=0.00188,0.03947;DB;DP=1712;DP4=357,376,7,2;Dels=0.00;FQ=31.1;FS=14.489;HPLen=2;HRun=0;INDEL;InbreedingCoeff=0.1123;MQ=49.53;MQ0=2;MQ0Fraction=0.0055;MQRankSum=-4.928;PV4=0.1,1,0.00085,0.016;ReadPosRankSum=-4.456;VQSLOD=5.3140;dbSNP=116;set=Intersection;sumGLbyD=19.98 20 24222100 . CTTTTA C 4219.36 PASS AA=57;AB=0.59434;ABA=43;ABP=11.205;ABR=63;AF=0.01803;AF1=0.01547;AN=1220;BL=2073;BR=2345;BVAR;BaseQRankSum=7.990;CI95=0.0114,0.02137;DEL;DP=17536;DP4=2140,2346,7,12;Dels=0.01;EL=32;EPP=4.877;ER=25;FQ=104;FS=0.614;HETAR=21;HOMA=4;HOMR=1042;HRun=0;INDEL;InbreedingCoeff=0.1941;LEN=5;LRB=0.061566;LRBP=39.374;MQ=73.32;MQ0Fraction=0.0021;MQM=39.614;MQRankSum=-5.728;NS=1067;PV4=0.37,1.1e-39,3.5e-09,1;RA=5527;RL=28;RPP=3.0484;RR=29;RUN=1;ReadPosRankSum=0.214;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SRB=0.49267;SRF=2723;SRP=5.588;SRR=2804;VQSLOD=7.5428;set=Intersection;sumGLbyD=38.08 20 24395018 . AT A 49310 PASS AA=146;AB=0.91198;ABA=130;ABP=2180.5;ABR=1347;AC=50;AF=0.04045;AN=1236;BL=587;BR=9625;BVAR;BaseQRankSum=-4.610;DEL;DP=12793;Dels=0.01;EL=54;EPP=24.487;ER=92;FS=22.108;HETAR=485;HOMA=384;HOMR=210;HRun=2;InbreedingCoeff=0.0374;LEN=1;LRB=0.88504;LRBP=17373;MQ0=0;MQ0Fraction=0.0000;MQM=102.26;MQRankSum=2.256;NS=1080;RA=2377;RL=1;RPP=311.42;RR=145;RUN=1;ReadPosRankSum=-16.347;SAB=0.63699;SAF=93;SAP=26.807;SAR=53;SRB=0.52167;SRF=1240;SRP=12.702;SRR=1137;VQSLOD=3.2421;set=filterInVQSR-2of5;sumGLbyD=3.80 20 24411517 . C CA 246.18 PASS AF=0.01546;AF1=0.01095;BaseQRankSum=7.832;CI95=0.005698,0.01709;DP=7981;DP4=983,2037,7,7;Dels=0.00;FQ=27.9;FS=18.815;HPLen=3;HRun=3;INDEL;InbreedingCoeff=0.0175;MQ=60.28;MQ0Fraction=0.0137;MQRankSum=-7.243;PV4=0.25,1,2.7e-05,1;ReadPosRankSum=-0.143;VQSLOD=4.3701;set=Intersection;sumGLbyD=6.56 20 24421169 . AG A 27480 PASS AA=182;AB=0.8303;ABA=149;ABP=835;ABR=729;AC=89;AF=0.07224;AN=1232;BL=11276;BR=2214;BVAR;BaseQRankSum=-5.447;DEL;DP=11717;Dels=0.01;EL=103;EPP=9.8827;ER=79;FR;FS=15.492;HETAR=343;HOMA=607;HOMR=114;HP=4;HR=1;HRun=1;HU=G;InbreedingCoeff=0.0353;LEN=1;LRB=0.67176;LRBP=13222;MQ0=0;MQ0Fraction=0.0000;MQM=88.324;MQRankSum=2.221;NF;NR;NS=1071;PP;RA=1226;RL=169;RPP=293.37;RR=13;RUN=1;ReadPosRankSum=-19.711;SAB=0.54945;SAF=100;SAP=6.876;SAR=82;SC=CCTTAGCCCCAGAAAACATCT;SRB=0.44535;SRF=546;SRP=34.814;SRR=680;TC;TR=1;TU=G;VQSLOD=4.2669;set=Intersection;sumGLbyD=3.91 20 24765537 rs71841337 ATTT A,AT,ATT,ATTTT,ATTTTT 37852 PASS AC=13,120,527,51,92;AF=0.01102,0.10169,0.44661,0.04322,0.07797;AN=1180;BVAR;BaseQRankSum=8.172;DB;DEL;DP=39116;DP4=200,331,851,1169;FR;FS=2.394;HP=15;HR=15;HU=T;HaplotypeScore=20.8091;INDEL;INS;InbreedingCoeff=0.4815;MQ0=1;MQ0Fraction=0.0003;MQRankSum=4.344;NF;NR;PP;PV4=0.067,1,1,0.1;QD=7.90;RUN=1;ReadPosRankSum=1.798;SB=-8371.96;SC=CTCTGCAACAATTTTTTTTTT;TC;TR=15;TU=T;VQSLOD=9.9679;dbSNP=120;set=Intersection 20 25500689 . A AATTT 84980.72 PASS AC=1005;AF=0.89096;AN=1128;BaseQRankSum=17.400;DP=2324;FS=6.721;HRun=0;HaplotypeScore=25.3376;InbreedingCoeff=0.2148;MQ=75.19;MQ0=1;MQ0Fraction=0.0004;MQRankSum=-8.221;QD=38.28;ReadPosRankSum=4.504;SB=-34833.07;VQSLOD=4.6038;set=VQSR 20 25550373 . GA G 11251.31 PASS AA=246;AB=0.42963;ABA=154;ABP=14.624;ABR=116;AC=566;AF=0.6521;AN=868;BL=5230;BR=11845;BVAR;BaseQRankSum=7.418;DEL;DP=8885;Dels=0.02;EL=99;EPP=23.348;ER=147;FR;FS=50.357;HETAR=150;HOMA=849;HOMR=14;HP=1;HR=2;HRun=1;HU=G;InbreedingCoeff=0.1365;LEN=1;LRB=0.38741;LRBP=5567.9;MQ0=0;MQ0Fraction=0.0000;MQM=97.561;MQRankSum=0.050;NF;NR;NS=1013;PP;RA=269;RL=75;RPP=84.361;RR=171;RUN=1;ReadPosRankSum=-7.128;SAB=0.52846;SAF=130;SAP=4.7404;SAR=116;SC=CACGGAGGCGGAGGAAGCAGC;SRB=0.42379;SRF=114;SRP=16.58;SRR=155;TC;TR=6;TU=AGG;VQSLOD=4.0103;set=filterInVQSR-2of5;sumGLbyD=4.58 20 25903865 . TTC T 7459.23 PASS AC=277;AF=0.23316;AN=1188;BaseQRankSum=31.479;DP=2969;FS=137.723;HRun=0;HaplotypeScore=37.3300;InbreedingCoeff=-0.1755;MQ=53.49;MQ0=50;MQ0Fraction=0.0168;MQRankSum=-25.506;QD=4.70;ReadPosRankSum=-5.913;SB=-1747.98;VQSLOD=5.4731;set=VQSR 20 25934237 . C CCACTT 771.36 PASS AC=37;AF=0.0426;AN=868;BaseQRankSum=16.331;DP=2253;FS=4.545;HRun=0;HaplotypeScore=29.9764;InbreedingCoeff=-0.0685;MQ=48.12;MQ0=87;MQ0Fraction=0.0386;MQRankSum=-12.497;QD=3.37;ReadPosRankSum=-8.428;SB=-297.70;VQSLOD=4.2324;set=VQSR 20 26054751 rs112967123 TATC T 33244 PASS AA=1863;AB=0.79012;ABA=1788;ABP=6231;ABR=6731;AC=227;AF=0.18218;AN=1246;BL=74924;BR=72452;BVAR;BaseQRankSum=32.258;DB;DEL;DP=36404;DS;Dels=0.05;EL=931;EPP=3.0115;ER=932;FR;FS=265.752;HETAR=527;HOMA=2;HOMR=565;HP=1;HR=2;HRun=0;HU=T;InbreedingCoeff=-0.2137;LEN=3;LRB=0.016773;LRBP=93.048;MQ0Fraction=0.0127;MQM=28.797;MQRankSum=-5.329;NF;NR;NS=1094;PP;RA=14604;RL=1014;RPP=34.743;RR=849;RUN=1;ReadPosRankSum=8.394;SAB=0.65486;SAF=1220;SAP=391.07;SAR=643;SC=TCACCATCATTATCATCATTA;SRB=0.56717;SRF=8283;SRP=575.39;SRR=6321;TC;TR=8;TU=ATC;VQSLOD=1.0486;set=filterInVQSR-2of5;sumGLbyD=6.54 20 26075169 . CTTCATT C 34603 PASS AA=311;AB=0.88905;ABA=298;ABP=3534.4;ABR=2388;AC=235;AF=0.18921;AN=1242;BL=17537;BR=5525;BVAR;BaseQRankSum=33.761;DEL;DP=20706;DS;Dels=0.01;EL=206;EPP=74.236;ER=105;FR;FS=94.549;HETAR=596;HOMA=99;HOMR=336;HP=3;HR=2;HRun=0;HU=T;InbreedingCoeff=-0.2083;LEN=6;LRB=0.52086;LRBP=13589;MQ0Fraction=0.0426;MQM=14.524;MQRankSum=-37.199;NF;NR;NS=1038;PP;RA=3600;RL=311;RPP=678.34;RR=0;RUN=1;ReadPosRankSum=-27.333;SAB=0.66238;SAF=206;SAP=74.236;SAR=105;SC=TCACCATCATCTTCATTATCA;SRB=0.55833;SRF=2010;SRP=109.41;SRR=1590;TC;TR=7;TU=ATC;VQSLOD=1.4394;set=filterInVQSR-2of5;sumGLbyD=4.96 20 26120452 . CAG C 7863.19 PASS AA=163;AB=0.70489;ABA=157;ABP=196.99;ABR=375;AC=171;AF=0.1908;AN=896;BL=3455;BR=4877;BVAR;BaseQRankSum=25.536;DEL;DP=7014;Dels=0.10;EL=58;EPP=32.438;ER=105;FS=231.723;HETAR=90;HOMA=5;HOMR=387;HRun=0;InbreedingCoeff=-0.1966;LEN=2;LRB=0.17067;LRBP=530;MQ0Fraction=0.0470;MQM=21.951;MQRankSum=-23.449;NS=482;RA=1117;RL=62;RPP=23.273;RR=101;RUN=1;ReadPosRankSum=1.904;SAB=0.37423;SAF=61;SAP=25.404;SAR=102;SRB=0.41719;SRF=466;SRP=69.544;SRR=651;VQSLOD=-0.9395;set=filterInVQSR-2of5;sumGLbyD=5.06 20 26136208 . A AT 17172.04 PASS AA=252;AB=0.73593;ABA=183;ABP=338.07;ABR=510;AC=381;AF=0.30775;AN=1238;BL=8304;BR=14158;BVAR;BaseQRankSum=41.520;DP=40036;DP4=2448,2564,317,366;Dels=0.00;EL=163;EPP=50.197;ER=89;FQ=999;FS=6.531;HETAR=149;HOMA=52;HOMR=708;HRun=1;INDEL;INS;InbreedingCoeff=-0.3996;LEN=1;LRB=0.26062;LRBP=3315.9;MQ=64.20;MQ0=22;MQ0Fraction=0.0048;MQM=25.706;MQRankSum=-29.318;NS=909;PV4=0.24,1.1e-119,3.2e-281,1;RA=2939;RL=58;RPP=162.39;RR=194;RUN=1;ReadPosRankSum=0.592;SAB=0.24206;SAF=61;SAP=148.64;SAR=191;SRB=0.4852;SRF=1426;SRP=8.6026;SRR=1513;VQSLOD=0.5981;set=filterInVQSR-2of5;sumGLbyD=5.77 20 26185812 . AG A 322.58 PASS AF=0.0342;BaseQRankSum=3.668;DP=3014;Dels=0.01;FR;FS=10.238;HP=8;HPLen=6;HR=6;HRun=6;HU=G;InbreedingCoeff=0.1504;MQ0Fraction=0.0473;MQRankSum=-5.464;NF;NR;PP;ReadPosRankSum=0.536;SC=GGGTGGGTGGAGGGGGGAGGG;TC;TR=6;TU=G;VQSLOD=5.0767;set=Intersection;sumGLbyD=8.46 20 30963468 . AGTTT A 2041.12 PASS AA=38;AB=0.75694;ABA=35;ABP=85.587;ABR=109;AC=34;AF=0.0377;AN=902;BL=1974;BR=668;BVAR;BaseQRankSum=3.060;DEL;DP=22806;DP4=1997,1747,28,36;Dels=0.02;EL=17;EPP=3.9246;ER=21;FR;FS=16.034;HETAR=29;HOMA=1;HOMR=1009;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=0.0752;LEN=4;LRB=0.49432;LRBP=1404.9;MQ=87.17;MQ0Fraction=0.0013;MQM=98.079;MQRankSum=6.021;NF;NR;NS=1039;PP;PV4=0.13,1.5e-07,1,0.051;RA=4052;RL=36;RPP=69.069;RR=2;RUN=1;ReadPosRankSum=-1.847;SAB=0.5;SAF=19;SAP=3.0103;SAR=19;SC=AGAAGTAAGTAGTTTGTTTTT;SRB=0.53776;SRF=2179;SRP=53.19;SRR=1873;TC;TR=9;TU=AAGT;VQSLOD=7.3578;set=Intersection;sumGLbyD=14.03 20 31963212 . AAAAAAAAAAAAG A 727.15 PASS AC=5;AF=0.0080;AN=622;BaseQRankSum=4.037;DP=1480;FS=0.000;HRun=0;HaplotypeScore=43.3793;InbreedingCoeff=0.0350;MQ=51.77;MQ0=59;MQ0Fraction=0.0399;MQRankSum=-1.799;QD=22.72;ReadPosRankSum=3.591;SB=-364.04;VQSLOD=5.3166;set=VQSR 20 31997272 . CT C,CTT,CTTT 1837.10 PASS AA=63;AB=0.77559;ABA=57;ABP=170.57;ABR=197;AC=79,49,30;AF=0.06594,0.04090,0.02504;AN=1198;BL=2372;BR=2640;BVAR;BaseQRankSum=3.277;DP=9050;Dels=0.03;EL=24;EPP=10.766;ER=39;FR;FS=0.303;HETAR=45;HOMA=1;HOMR=981;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2796;LEN=1;LRB=0.053472;LRBP=34.128;MQ0Fraction=0.0000;MQM=50.889;MQRankSum=0.610;NF;NR;NS=1027;PP;RA=3776;RL=30;RPP=3.3205;RR=33;RUN=1;ReadPosRankSum=-0.800;SAB=0.39683;SAF=25;SAP=8.8354;SAR=38;SC=ACCCAACTTCCTTTTTTTTTT;SRB=0.46213;SRF=1745;SRP=50.049;SRR=2031;TC;TR=10;TU=T;VQSLOD=4.1189;set=filterInVQSR-2of5;sumGLbyD=3.66 20 33446974 rs113250263 TAA T,TA,TAAA 17130.16 PASS AC=65,417,184;AF=0.05941,0.38117,0.16819;AN=1094;BVAR;BaseQRankSum=3.400;DB;DEL;DP=22362;DP4=221,247,418,524;Dels=0.33;FR;FS=15.409;HP=15;HR=14;HRun=14;HU=A;INDEL;INS;InbreedingCoeff=0.5215;MQ=61.32;MQ0Fraction=0.0021;MQRankSum=0.481;NF;NR;PP;PV4=0.33,1,1,1;RUN=1;ReadPosRankSum=-0.056;SC=CTCCGTCTCATAAAAAAAAAA;TC;TR=14;TU=A;VQSLOD=8.0974;dbSNP=132;set=Intersection;sumGLbyD=12.78 20 33877149 . C CT 1784.40 PASS AA=58;AB=0.73096;ABA=53;ABP=94.289;ABR=144;AC=65;AF=0.05682;AN=1144;BL=3298;BR=1935;BVAR;BaseQRankSum=-2.066;DP=8074;Dels=0.02;EL=22;EPP=10.348;ER=36;FR;FS=11.452;HETAR=47;HOMA=3;HOMR=754;HP=16;HR=12;HRun=12;HU=T;INS;InbreedingCoeff=0.1178;LEN=1;LRB=0.26046;LRBP=773.91;MQ0Fraction=0.0165;MQM=52.259;MQRankSum=0.734;NF;NR;NS=804;PP;RA=2141;RL=43;RPP=32.363;RR=15;RUN=1;ReadPosRankSum=-1.273;SAB=0.46552;SAF=27;SAP=3.6093;SAR=31;SC=ATTTTCTTTTCTTTTTTTTTT;SRB=0.37553;SRF=804;SRP=291.14;SRR=1337;TC;TR=12;TU=T;VQSLOD=3.1540;set=filterInVQSR-2of5;sumGLbyD=2.84 20 34358698 . A AAAAAAT 583.61 PASS AC=27;AF=0.02542;AN=1062;BaseQRankSum=5.228;DP=1997;FS=3.765;HRun=0;HaplotypeScore=27.7123;InbreedingCoeff=0.0566;MQ=55.50;MQ0=14;MQ0Fraction=0.0070;MQRankSum=-3.961;QD=5.21;ReadPosRankSum=0.862;SB=-399.69;VQSLOD=4.3826;set=VQSR 20 34387589 rs112431805 CT C,CTT 4039.10 PASS AA=121;AB=0.75368;ABA=117;ABP=268.53;ABR=358;AC=84,139;AF=0.07047,0.11661;AN=1192;BL=5557;BR=3901;BVAR;BaseQRankSum=2.693;DB;DP=10157;Dels=0.03;EL=47;EPP=16.093;ER=74;FR;FS=7.639;HETAR=89;HOMA=2;HOMR=913;HP=13;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2097;LEN=1;LRB=0.17509;LRBP=632.63;MQ0Fraction=0.0000;MQM=49.802;MQRankSum=-0.801;NF;NR;NS=1004;PP;RA=3789;RL=77;RPP=22.554;RR=44;RUN=1;ReadPosRankSum=-2.691;SAB=0.3719;SAF=45;SAP=20.256;SAR=76;SC=AAGAAGTGTTCTTTTTTTTTT;SRB=0.40987;SRF=1553;SRP=270.35;SRR=2236;TC;TR=11;TU=T;VQSLOD=4.0473;set=filterInVQSR-2of5;sumGLbyD=4.64 20 34493409 rs73621682 C CAG 62288.93 PASS AA=1069;AB=0.54863;ABA=826;ABP=40.606;ABR=1004;AC=257;AF=0.3640;AN=706;BL=41524;BR=47039;BVAR;BaseQRankSum=-24.248;DB;DP=30195;DP4=1743,1636,614,487;Dels=0.00;EL=582;EPP=21.343;ER=487;FQ=999;FR;FS=5.080;HETAR=298;HOMA=63;HOMR=712;HP=1;HPLen=1;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.1437;LEN=2;LRB=0.062272;LRBP=748.76;MQ=77.99;MQ0=3;MQ0Fraction=0.0015;MQM=54.446;MQRankSum=0.160;NF;NR;NS=1073;PP;PV4=0.016,1,0.01,1;RA=4461;RL=526;RPP=3.5973;RR=543;RUN=1;ReadPosRankSum=-1.716;SAB=0.57343;SAF=613;SAP=53.08;SAR=456;SC=AGGAAGAGATCAGAGCTCCCC;SRB=0.52634;SRF=2348;SRP=29.892;SRR=2113;TC;TR=4;TU=AG;VQSLOD=8.7047;dbSNP=130;set=Intersection;sumGLbyD=49.82 20 35086229 rs112534255 G GAT 6109.24 PASS AA=14;AB=0.71795;ABA=11;ABP=19.101;ABR=28;AC=35;AF=0.0509;AN=688;BL=846;BR=517;BVAR;BaseQRankSum=-7.153;DB;DP=15775;DP4=2064,2212,31,22;Dels=0.00;EL=7;EPP=3.0103;ER=7;FR;FS=0.000;HETAR=10;HOMA=2;HOMR=914;HP=3;HPLen=4;HR=4;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.1170;LEN=2;LRB=0.24138;LRBP=175.46;MQ=54.65;MQ0Fraction=0.0118;MQM=45.643;MQRankSum=1.614;NF;NR;NS=926;PP;PV4=0.17,1,1,1;RA=2867;RL=11;RPP=12.937;RR=3;RUN=1;ReadPosRankSum=-0.520;SAB=0.71429;SAF=10;SAP=8.5941;SAR=4;SC=TTTTAGTAAAGGGGATTTCAC;SRB=0.58249;SRF=1670;SRP=172.46;SRR=1197;TC;TR=4;TU=G;VQSLOD=10.3126;set=Intersection;sumGLbyD=42.13 20 35575895 rs67189278 AGTGT A,AGT,AGTGTGT,TGTGT 43809.26 PASS AC=593,3,481;AF=0.53327,0.00270,0.43255;AN=1112;BVAR;BaseQRankSum=-8.327;DB;DEL;DP=8989;Dels=0.04;FR;FS=9.400;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INS;InbreedingCoeff=0.7735;LEN=2;MQ0Fraction=0.0400;MQRankSum=-2.719;NF;NR;PP;RUN=1;ReadPosRankSum=-9.301;SC=TGTGTGTGTGAGTGTGTGTGT;TC;TR=22;TU=GT;VQSLOD=8.6440;set=Intersection;sumGLbyD=6.01 20 35957317 . CTGACT C,CGACT 4370.96 PASS ABR=81;AC=22,1;AF=0.0321,0.0015;AF1=0.04523;AN=686;BVAR;BaseQRankSum=7.969;CI95=0.0354,0.05752;DEL;DP=16632;DP4=1942,1815,17,21;Dels=0.03;FQ=999;FR;FS=0.531;HOMA=1;HOMR=998;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0587;MQ=83.38;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-7.201;NF;NR;NS=1020;PP;PV4=0.42,0.00017,4.5e-12,1;RA=4620;RUN=1;ReadPosRankSum=-1.007;SC=CCTCTCAGCTCTGACTGAGTC;SRB=0.50043;SRF=2312;SRP=3.0178;SRR=2308;TC;TR=8;TU=ACTG;VQSLOD=9.9778;dbSNP=130;set=Intersection;sumGLbyD=36.45 20 36136198 . GTGTC G 2078.76 PASS AA=35;AB=0.54167;ABA=33;ABP=4.096;ABR=39;AC=17;AF=0.01384;AN=1228;BL=1212;BR=1523;BVAR;BaseQRankSum=6.900;DEL;DP=22483;DP4=1696,2291,9,16;Dels=0.01;EL=9;EPP=20.94;ER=26;FQ=999;FR;FS=3.023;HETAR=13;HOMA=1;HOMR=1061;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1113;LEN=4;LRB=0.11371;LRBP=79.803;MQ=93.98;MQ0=1;MQ0Fraction=0.0003;MQM=83.686;MQRankSum=-1.683;NF;NR;NS=1075;PP;PV4=0.55,1,0.0083,1;RA=5771;RL=19;RPP=3.5687;RR=16;RUN=1;ReadPosRankSum=0.618;SAB=0.37143;SAF=13;SAP=8.0357;SAR=22;SC=TATCATTTTAGTGTCTGTCTG;SRB=0.44966;SRF=2595;SRP=130.03;SRR=3176;TC;TR=11;TU=CTGT;VQSLOD=10.1935;set=Intersection;sumGLbyD=31.66 20 36250522 . CA C 37933 PASS AA=51;AB=0.95582;ABA=44;ABP=1800.5;ABR=952;AC=23;AF=0.01885;AN=1220;BL=691;BR=3464;BVAR;BaseQRankSum=-2.418;DEL;DP=11998;Dels=0.00;EL=18;EPP=12.59;ER=33;FS=2.307;HETAR=348;HOMA=534;HOMR=164;HRun=1;InbreedingCoeff=0.0763;LEN=1;LRB=0.66739;LRBP=4021.7;MQ0=2;MQ0Fraction=0.0006;MQM=53.647;MQRankSum=1.083;NS=1047;RA=1663;RL=2;RPP=97.065;RR=49;RUN=1;ReadPosRankSum=-12.726;SAB=0.68627;SAF=35;SAP=18.381;SAR=16;SRB=0.59651;SRF=992;SRP=137.56;SRR=671;VQSLOD=4.1346;set=filterInVQSR-2of5;sumGLbyD=3.29 20 36285033 rs34715186 AT A 39417 PASS AA=530;AB=0.5406;ABA=447;ABP=16.939;ABR=526;AC=88;AF=0.0950;AN=926;BL=20722;BR=20406;BVAR;BaseQRankSum=15.611;DB;DEL;DP=36713;DP4=2551,2475,236,218;Dels=0.09;EL=241;EPP=12.45;ER=289;FQ=999;FR;FS=1.290;HETAR=141;HOMA=16;HOMR=926;HP=2;HPLen=3;HR=3;HRun=1;HU=A;INDEL;InbreedingCoeff=0.0742;LEN=1;LRB=0.0076833;LRBP=8.2825;MQ=104.81;MQ0=0;MQ0Fraction=0.0000;MQM=84.285;MQRankSum=-0.702;NF;NR;NS=1083;PP;PV4=0.62,1,1,1;RA=6562;RL=263;RPP=3.0759;RR=267;RUN=1;ReadPosRankSum=0.090;SAB=0.55849;SAF=296;SAP=18.76;SAR=234;SC=AAAAACACAAATCAGATCGTG;SRB=0.51707;SRF=3393;SRP=19.614;SRR=3169;TC;TR=3;TU=A;VQSLOD=10.5533;dbSNP=126;set=Intersection;sumGLbyD=14.15 20 36384872 . CTG C 43532.41 PASS AC=1213;AF=0.99589;AN=1218;BaseQRankSum=0.802;DP=3208;FS=9.727;HRun=0;HaplotypeScore=46.6153;InbreedingCoeff=0.1085;MQ=58.37;MQ0=50;MQ0Fraction=0.0156;MQRankSum=-1.672;QD=13.57;ReadPosRankSum=2.063;SB=-18894.12;VQSLOD=4.7353;set=VQSR 20 36542802 . GTA G 31310.15 PASS AA=1481;AB=0.67546;ABA=1378;ABP=1138.4;ABR=2868;AC=437;AF=0.35938;AN=1216;BL=25719;BR=95500;BVAR;BaseQRankSum=9.478;DEL;DP=18068;DS;Dels=0.10;EL=889;EPP=132.34;ER=592;FS=320.726;HETAR=591;HOMA=44;HOMR=378;HRun=0;InbreedingCoeff=-0.4197;LEN=2;LRB=0.57566;LRBP=87231;MQ0Fraction=0.0091;MQM=29.319;MQRankSum=-3.409;NS=1013;RA=4037;RL=3;RPP=3193;RR=1478;RUN=1;ReadPosRankSum=-6.687;SAB=0.40041;SAF=593;SAP=130.61;SAR=888;SRB=0.39014;SRF=1575;SRP=426.21;SRR=2462;VQSLOD=-1.6586;set=filterInVQSR-2of5;sumGLbyD=5.49 20 36985025 . CCA C 4.57 PASS AC=0;AF=0.0000;AN=682;BaseQRankSum=4.199;DP=1504;FS=1.036;HRun=0;HaplotypeScore=18.5241;InbreedingCoeff=0.0460;MQ=57.04;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.774;ReadPosRankSum=-2.105;VQSLOD=6.7455;set=VQSR 20 37139725 . CAG C 250.77 PASS AF=0.0084;AF1=0.0139;BaseQRankSum=4.131;CI95=0.00885,0.01991;DP=7973;DP4=1808,1990,2,7;Dels=0.01;FQ=104;FR;FS=11.160;HP=3;HPLen=2;HR=1;HRun=0;HU=A;INDEL;InbreedingCoeff=-0.0001;MQ=103.71;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.378;NF;NR;PP;PV4=0.18,0.0011,0.041,1;ReadPosRankSum=0.605;SC=AGATGGGGAACAGAGAGCAAG;TC;TR=6;TU=AG;VQSLOD=7.0630;set=Intersection;sumGLbyD=12.13 20 37213224 . G GTA 3230.05 PASS AA=32;AB=0.50769;ABA=32;ABP=3.0437;ABR=33;AC=12;AF=0.0168;AF1=0.02635;AN=714;BL=1271;BR=1743;BVAR;BaseQRankSum=-7.288;CI95=0.02212,0.03319;DP=14304;DP4=2180,2256,13,21;Dels=0.00;EL=20;EPP=7.3532;ER=12;FQ=999;FR;FS=7.863;HETAR=9;HOMA=0;HOMR=1043;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0410;LEN=2;LRB=0.1566;LRBP=163.52;MQ=95.56;MQ0=1;MQ0Fraction=0.0005;MQM=51.562;MQRankSum=0.420;NF;NR;NS=1052;PP;PV4=0.23,1,0.03,0.33;RA=5138;RL=11;RPP=9.7962;RR=21;RUN=1;ReadPosRankSum=-1.122;SAB=0.28125;SAF=9;SAP=16.311;SAR=23;SC=TTTGCATCCAGTAGCACCACT;SRB=0.42293;SRF=2173;SRP=268.11;SRR=2965;TC;TR=1;TU=T;VQSLOD=9.7315;set=Intersection;sumGLbyD=36.69 20 37282014 . ATGG A 2518.52 PASS AF=0.03519;BaseQRankSum=11.994;DP=24592;DP4=415,3804,8,49;DS;Dels=0.01;FQ=999;FR;FS=2.049;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1028;MQ=51.01;MQ0Fraction=0.0139;MQRankSum=-5.912;NF;NR;PP;PV4=0.27,1,0.22,0.015;ReadPosRankSum=1.781;SC=GGTGGTGATGATGGTGGTGGT;TC;TR=17;TU=GGT;VQSLOD=2.1183;set=filterInVQSR-2of5;sumGLbyD=9.05 20 37532218 . GTCCGTCCA ATCCGTCCA,G 76120.88 PASS AC=998;AF=0.92924;AN=1074;BaseQRankSum=-2.877;DP=3087;FR;FS=9.889;HP=2;HPLen=2;HR=1;HRun=0;HU=T;HaplotypeScore=71.6244;InbreedingCoeff=-0.0027;MQ=52.68;MQ0=543;MQ0Fraction=0.1759;MQRankSum=-1.750;NF;NR;PP;QD=24.98;ReadPosRankSum=-0.850;SB=-36635.43;SC=CCGTCCGTCCGTCCGTCCATC;TC;TR=19;TU=CCGT;VQSLOD=5.3068;set=Intersection 20 37712193 . AAG A 2670.33 PASS AA=106;AB=0.62821;ABA=87;ABP=36.418;ABR=147;AC=53;AF=0.0759;AN=698;BL=4672;BR=4303;BVAR;BaseQRankSum=13.696;DEL;DP=15155;DP4=1340,1852,32,52;Dels=0.06;EL=57;EPP=4.3214;ER=49;FR;FS=0.824;HETAR=43;HOMA=7;HOMR=982;HP=1;HPLen=2;HR=2;HRun=0;HU=A;INDEL;InbreedingCoeff=0.0861;LEN=2;LRB=0.041114;LRBP=35.954;MQ=86.12;MQ0=0;MQ0Fraction=0.0000;MQM=54.236;MQRankSum=-5.745;NF;NR;NS=1034;PP;PV4=0.5,7.3e-26,1.1e-10,1;RA=4423;RL=58;RPP=5.0589;RR=48;RUN=1;ReadPosRankSum=2.617;SAB=0.38679;SAF=41;SAP=14.81;SAR=65;SC=GAAAATTCTGAAGAGAGTCAG;SRB=0.43093;SRF=1906;SRP=186.29;SRR=2517;TC;TR=6;TU=AG;VQSLOD=9.8131;set=Intersection;sumGLbyD=14.20 20 37739002 . T TCA 1395.38 PASS AA=16;AB=0.48387;ABA=16;ABP=3.0803;ABR=15;AC=11;AF=0.00950;AN=1158;BL=504;BR=630;BVAR;BaseQRankSum=-3.257;DP=13617;DP4=1660,883,7,5;Dels=0.00;EL=7;EPP=3.5532;ER=9;FR;FS=1.114;HETAR=9;HOMA=0;HOMR=991;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0527;LEN=2;LRB=0.11111;LRBP=33.411;MQ=88.41;MQ0=0;MQ0Fraction=0.0000;MQM=83.75;MQRankSum=1.713;NF;NR;NS=1000;PP;PV4=0.76,1,1,0.5;RA=3257;RL=6;RPP=5.1818;RR=10;RUN=1;ReadPosRankSum=1.190;SAB=0.6875;SAF=11;SAP=7.8961;SAR=5;SC=CCTTTTTTGTTCATTTCTGCA;SRB=0.68806;SRF=2241;SRP=1003.5;SRR=1016;TC;TR=2;TU=T;VQSLOD=10.2220;set=Intersection;sumGLbyD=41.32 20 38122459 . T TG,TGG 1346.40 PASS ABR=339;AC=37,26;AF=0.02989,0.02100;BVAR;BaseQRankSum=10.222;DP=16425;FS=601.551;HOMA=0;HOMR=1008;HaplotypeScore=20.6522;INS;InbreedingCoeff=0.0829;MQ=105.78;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-4.295;NS=1079;QD=0.40;RA=6208;RUN=1;ReadPosRankSum=-14.427;SAB=1;SAR=0;SB=-368.88;SRB=0.34907;SRF=2167;SRP=1231.4;SRR=4041;VQSLOD=-3.3455;set=filterInVQSR-2of5 20 38395256 . TTGAG T 633.19 PASS AF=0.0028;BaseQRankSum=5.667;DP=3839;Dels=0.00;FR;FS=10.238;HP=2;HPLen=3;HR=3;HRun=0;HU=T;InbreedingCoeff=-0.0097;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.276;NF;NR;PP;ReadPosRankSum=-1.016;SC=ATGTGTTTGTTTGAGTATGTT;TC;TR=10;TU=GTTT;VQSLOD=6.4906;set=Intersection;sumGLbyD=10.83 20 38882632 rs72004513 AGTGTGTGTGT A,AGT,AGTGT,AGTGTGT,AGTGTGTGT,AGTGTGTGTGTGT 12304.47 PASS AC=57,24,51,78,89,186;AF=0.04664,0.01964,0.04173,0.06383,0.07283,0.15221;AN=1222;BVAR;BaseQRankSum=3.183;DB;DEL;DP=49261;DP4=144,106,104,101;Dels=0.05;FQ=999;FR;FS=5.209;HP=1;HPLen=2;HR=2;HRun=0;HU=A;INDEL;InbreedingCoeff=0.9090;MQ=87.48;MQ0Fraction=0.0071;MQRankSum=-0.897;NF;NR;PP;PV4=0.16,1,0.19,1;RUN=1;ReadPosRankSum=3.551;SC=TAACTCCTCAAGTGTGTGTGT;TC;TR=47;TU=GT;VQSLOD=9.9069;set=Intersection;sumGLbyD=5.30 20 39345038 . CTGAACCATAATGTG C,CCCATAATGTG 60744.52 PASS AA=23;AB=0.67143;ABA=23;ABP=20.878;ABR=47;AC=232,2;AF=0.19366,0.00167;AN=1198;BL=1607;BR=1843;BVAR;BaseQRankSum=30.955;DEL;DP=31490;DP4=1729,2100,265,278;Dels=0.13;EL=6;EPP=14.434;ER=17;FQ=999;FR;FS=1.767;HETAR=18;HOMA=0;HOMR=1015;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.1991;LEN=14;LRB=0.068406;LRBP=38.066;MQ=104.60;MQ0=0;MQ0Fraction=0.0000;MQM=189.83;MQRankSum=-16.579;NF;NR;NS=1033;PP;PV4=0.12,1,5.5e-137,1;RA=5286;RL=14;RPP=5.3706;RR=9;RUN=1;ReadPosRankSum=4.323;SAB=0.56522;SAF=13;SAP=3.86;SAR=10;SC=TGGGCTGGACCTGAACCATAA;SRB=0.46311;SRF=2448;SRP=65.493;SRR=2838;TC;TR=2;TU=C;VQSLOD=6.2643;dbSNP=130;set=Intersection;sumGLbyD=65.43 20 39418008 . AG A 46796 PASS AA=113;AB=0.9511;ABA=80;ABP=2894.6;ABR=1556;AC=30;AF=0.02412;AN=1244;BL=638;BR=6936;BVAR;BaseQRankSum=7.280;DEL;DP=14307;Dels=0.00;EL=50;EPP=6.2579;ER=63;FR;FS=5.707;HETAR=473;HOMA=361;HOMR=246;HP=3;HR=3;HRun=3;HU=G;InbreedingCoeff=0.0272;LEN=1;LRB=0.83153;LRBP=11375;MQ0=0;MQ0Fraction=0.0000;MQM=62.398;MQRankSum=3.530;NF;NR;NS=1089;PP;RA=3000;RL=3;RPP=223.02;RR=110;RUN=1;ReadPosRankSum=-18.601;SAB=0.58407;SAF=66;SAP=9.9475;SAR=47;SC=ACTGGGGGAAAGGGATTCTAG;SRB=0.494;SRF=1482;SRP=3.9484;SRR=1518;TC;TR=3;TU=G;VQSLOD=4.5834;set=Intersection;sumGLbyD=3.06 20 39876961 . GT G,GTT,GTTT 2302.10 PASS ABR=496;AC=45,51,45;AF=0.03664,0.04153,0.03664;AN=1228;BVAR;BaseQRankSum=4.462;DP=37649;DP4=1457,1975,57,59;Dels=0.02;FR;FS=9.938;HOMA=0;HOMR=978;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.2583;MQ=97.28;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.246;NF;NR;NS=1063;PP;PV4=0.15,1,1.9e-09,0.016;RA=5185;RUN=1;ReadPosRankSum=-4.954;SC=AGTTTCTCCGGTTTTTTTTTT;SRB=0.47464;SRF=2461;SRP=31.978;SRR=2724;TC;TR=10;TU=T;VQSLOD=4.9752;set=Intersection;sumGLbyD=4.39 20 41013333 . TC T 20681 PASS AA=137;AB=0.89211;ABA=134;ABP=1661.6;ABR=1108;AC=68;AF=0.05601;AN=1214;BL=1091;BR=8981;BVAR;BaseQRankSum=1.354;DEL;DP=12998;Dels=0.01;EL=57;EPP=11.395;ER=80;FS=0.758;HETAR=359;HOMA=100;HOMR=610;HRun=1;InbreedingCoeff=0.0104;LEN=1;LRB=0.78336;LRBP=13424;MQ0=1;MQ0Fraction=0.0003;MQM=67.745;MQRankSum=2.563;NS=1072;RA=4447;RL=5;RPP=258.66;RR=132;RUN=1;ReadPosRankSum=-14.092;SAB=0.59124;SAF=81;SAP=12.917;SAR=56;SRB=0.54194;SRF=2410;SRP=70.947;SRR=2037;VQSLOD=3.7531;set=filterInVQSR-2of5;sumGLbyD=4.14 20 41453533 rs112736557 T TA 1734.60 PASS AA=44;AB=0.58025;ABA=34;ABP=7.5409;ABR=47;AC=23;AF=0.0345;AN=666;BL=2061;BR=2408;BVAR;BaseQRankSum=5.768;DB;DP=7437;Dels=0.00;EL=25;EPP=4.787;ER=19;FR;FS=3.680;HETAR=17;HOMA=5;HOMR=975;HP=7;HPLen=6;HR=6;HRun=6;HU=A;INS;InbreedingCoeff=0.1712;LEN=1;LRB=0.077646;LRBP=61.517;MQ0=0;MQ0Fraction=0.0000;MQM=75.614;MQRankSum=-4.976;NF;NR;NS=997;PP;RA=4229;RL=21;RPP=3.2077;RR=23;RUN=1;ReadPosRankSum=-0.039;SAB=0.5;SAF=22;SAP=3.0103;SAR=22;SC=CCTTTCTCCATAAAAAAGCTT;SRB=0.46299;SRF=1958;SRP=53.315;SRR=2271;TC;TR=6;TU=A;VQSLOD=7.8972;set=Intersection;sumGLbyD=13.16 20 41659532 . GC G 40544 PASS AA=42;AB=0.97149;ABA=39;ABP=2644.5;ABR=1329;AC=15;AF=0.0209;AN=716;BL=2531;BR=135;BVAR;BaseQRankSum=-2.537;DEL;DP=12219;Dels=0.00;EL=25;EPP=6.3192;ER=17;FS=2.656;HETAR=374;HOMA=155;HOMR=551;HRun=1;InbreedingCoeff=-0.0270;LEN=1;LRB=0.89872;LRBP=4678.9;MQ0=0;MQ0Fraction=0.0000;MQM=103.31;MQRankSum=2.828;NS=1088;RA=4736;RL=41;RPP=85.733;RR=1;RUN=1;ReadPosRankSum=-9.702;SAB=0.57143;SAF=24;SAP=4.8716;SAR=18;SRB=0.5625;SRF=2664;SRP=163.7;SRR=2072;VQSLOD=4.3267;set=Intersection;sumGLbyD=3.22 20 41687456 . A AT 19682 PASS AA=446;AB=0.61202;ABA=426;ABP=122.69;ABR=672;AC=162;AF=0.13214;AN=1226;BL=15293;BR=20484;BVAR;BaseQRankSum=2.364;DP=29324;DP4=1993,1785,261,252;Dels=0.01;EL=214;EPP=4.5878;ER=232;FQ=999;FR;FS=1.923;HETAR=170;HOMA=7;HOMR=897;HP=11;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.0769;LEN=1;LRB=0.14509;LRBP=1638.5;MQ=91.55;MQ0=0;MQ0Fraction=0.0000;MQM=57.168;MQRankSum=-0.764;NF;NR;NS=1074;PP;PV4=0.45,1,3.5e-08,1;RA=5437;RL=179;RPP=40.714;RR=267;RUN=1;ReadPosRankSum=0.356;SAB=0.51794;SAF=231;SAP=4.2567;SAR=215;SC=AGAAAACCTTATTTTTTTTTC;SRB=0.51094;SRF=2778;SRP=8.666;SRR=2659;TC;TR=9;TU=T;VQSLOD=9.6786;set=Intersection;sumGLbyD=10.93 20 41845580 . GA G 49310 PASS AA=83;AB=0.95258;ABA=69;ABP=2591.6;ABR=1386;AC=46;AF=0.03740;AN=1230;BL=1320;BR=5150;BVAR;BaseQRankSum=-1.121;DEL;DP=13336;Dels=0.00;EL=36;EPP=6.1759;ER=47;FR;FS=0.372;HETAR=442;HOMA=341;HOMR=295;HP=2;HR=3;HRun=1;HU=G;InbreedingCoeff=0.0238;LEN=1;LRB=0.59196;LRBP=4926.2;MQ0=0;MQ0Fraction=0.0000;MQM=89.048;MQRankSum=0.897;NF;NR;NS=1080;PP;RA=3006;RL=5;RPP=142.43;RR=78;RUN=1;ReadPosRankSum=-15.412;SAB=0.55422;SAF=46;SAP=5.1294;SAR=37;SC=CCAGCTGTGGGAGAGAAACAT;SRB=0.47971;SRF=1442;SRP=13.762;SRR=1564;TC;TR=6;TU=AG;VQSLOD=4.4669;set=Intersection;sumGLbyD=3.65 20 42209428 . GC G 13163 PASS AA=89;AB=0.86677;ABA=83;ABP=730.96;ABR=540;AC=39;AF=0.03218;AN=1212;BL=950;BR=5334;BVAR;BaseQRankSum=-10.119;DEL;DP=10692;Dels=0.01;EL=48;EPP=4.2058;ER=41;FS=0.000;HETAR=259;HOMA=727;HOMR=54;HRun=1;InbreedingCoeff=0.0448;LEN=1;LRB=0.69764;LRBP=6644.4;MQ0=0;MQ0Fraction=0.0000;MQM=126.55;MQRankSum=4.223;NS=1040;RA=723;RL=12;RPP=106.09;RR=77;RUN=1;ReadPosRankSum=-17.362;SAB=0.39326;SAF=35;SAP=11.818;SAR=54;SRB=0.37898;SRF=274;SRP=94.99;SRR=449;VQSLOD=3.7157;set=filterInVQSR-2of5;sumGLbyD=3.48 20 42281109 . T TAG 2321.12 PASS AC=181;AF=0.3740;AN=484;BaseQRankSum=8.977;DP=435;FS=17.001;HRun=0;HaplotypeScore=14.6734;InbreedingCoeff=0.2340;MQ=53.88;MQ0=47;MQ0Fraction=0.1080;MQRankSum=0.762;QD=12.41;ReadPosRankSum=3.399;SB=-1299.73;VQSLOD=4.8926;set=VQSR 20 42436117 . TC T 38933 PASS AA=18;AB=0.98435;ABA=17;ABP=2215.9;ABR=1069;AC=15;AF=0.01223;AN=1226;BL=498;BR=428;BVAR;BaseQRankSum=-7.224;DEL;DP=12436;Dels=0.00;EL=1;EPP=33.893;ER=17;FS=2.469;HETAR=303;HOMA=614;HOMR=123;HRun=1;InbreedingCoeff=0.0439;LEN=1;LRB=0.075594;LRBP=14.501;MQ0=0;MQ0Fraction=0.0000;MQM=98.611;MQRankSum=1.086;NS=1075;RA=1656;RL=10;RPP=3.4928;RR=8;RUN=1;ReadPosRankSum=-17.765;SAB=0.5;SAF=9;SAP=3.0103;SAR=9;SRB=0.49879;SRF=826;SRP=3.0313;SRR=830;VQSLOD=4.0821;set=filterInVQSR-2of5;sumGLbyD=3.04 20 42682214 . C A,CAT 3904.51 PASS AA=24;AB=0.6383;ABA=17;ABP=10.818;ABR=30;AC=0;AF=0.0000;AN=636;BL=1119;BR=949;BVAR;BaseQRankSum=1.426;DP=6509;Dels=0.00;EL=9;EPP=6.2675;ER=15;FR;HETAR=12;HOMA=3;HOMR=876;HP=2;HPLen=1;HR=1;HRun=0;HU=A;INS;InbreedingCoeff=0.0006;LEN=2;LRB=0.082205;LRBP=33.356;MQ0Fraction=0.0046;MQM=40.792;MQRankSum=-0.296;NF;NR;NS=891;PP;QD=32.81;RA=2679;RL=15;RPP=6.2675;RR=9;RUN=1;ReadPosRankSum=-1.806;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SB=-924.23;SC=TATACACACACATATATATAC;SRB=0.66293;SRF=1776;SRP=620.76;SRR=903;TC;TR=9;TU=AC;set=filterInVQSR-2of5;sumGLbyD=32.75 20 42973456 . CA C,CAA,CAAA 2675 PASS AA=90;AB=0.79177;ABA=86;ABP=308.39;ABR=327;AC=77,61,39;AF=0.06492,0.05143,0.03288;AN=1186;BL=2983;BR=4446;BVAR;BaseQRankSum=2.422;DP=9416;Dels=0.03;EL=39;EPP=6.4847;ER=51;FR;FS=31.555;HETAR=75;HOMA=1;HOMR=888;HP=11;HR=11;HRun=11;HU=A;INS;InbreedingCoeff=0.2696;LEN=1;LRB=0.19693;LRBP=628.63;MQ0=0;MQ0Fraction=0.0000;MQM=55.567;MQRankSum=1.777;NF;NR;NS=964;PP;RA=3601;RL=37;RPP=9.1869;RR=53;RUN=1;ReadPosRankSum=-4.991;SAB=0.55556;SAF=50;SAP=5.423;SAR=40;SC=TAGTGACTGTCAAAAAAAAAA;SRB=0.60622;SRF=2183;SRP=355.91;SRR=1418;TC;TR=11;TU=A;VQSLOD=1.0763;set=filterInVQSR-2of5;sumGLbyD=4.05 20 43091870 . TC T 2455.60 PASS AA=120;AB=0.10619;ABA=101;ABP=155.22;ABR=12;AC=42;AF=0.03825;AN=1098;BL=573;BR=8744;BVAR;BaseQRankSum=-13.513;DEL;DP=9139;Dels=0.00;EL=64;EPP=4.1684;ER=56;FS=9.856;HETAR=118;HOMA=820;HOMR=0;HRun=1;InbreedingCoeff=0.0833;LEN=1;LRB=0.877;LRBP=15564;MQ0Fraction=0.0017;MQM=45.1;MQRankSum=2.266;NS=938;RA=24;RL=1;RPP=254.97;RR=119;RUN=1;ReadPosRankSum=-15.803;SAB=0.475;SAF=57;SAP=3.6617;SAR=63;SRB=0.54167;SRF=13;SRP=3.3722;SRR=11;VQSLOD=3.9930;set=filterInVQSR-2of5;sumGLbyD=3.09 20 43233648 rs74585029 GA G,GAA 1504.40 PASS AA=113;AB=0.78652;ABA=95;ABP=320.31;ABR=350;AC=41,65;AF=0.03394,0.05381;AF1=0.0115;AN=1208;BL=4677;BR=5548;BVAR;BaseQRankSum=6.744;CI95=0.004274,0.01852;DB;DEL;DP=13996;DP4=1736,1549,15,17;Dels=0.03;EL=69;EPP=15.021;ER=44;FQ=14;FR;FS=12.174;HETAR=119;HOMA=15;HOMR=892;HP=11;HPLen=10;HR=10;HRun=10;HU=A;INDEL;InbreedingCoeff=0.2359;LEN=1;LRB=0.085183;LRBP=164.12;MQ=89.12;MQ0Fraction=0.0000;MQM=69.867;MQRankSum=2.513;NF;NR;NS=1027;PP;PV4=0.59,1,0.065,0.33;RA=3845;RL=46;RPP=11.485;RR=67;RUN=1;ReadPosRankSum=-4.957;SAB=0.33628;SAF=38;SAP=29.318;SAR=75;SC=AAAACAGCCAGAAAAAAAAAA;SRB=0.43667;SRF=1679;SRP=136.95;SRR=2166;TC;TR=10;TU=A;VQSLOD=4.5121;set=Intersection;sumGLbyD=8.22 20 43246548 . AC A,CC 41579.13 PASS AA=382;AB=0.72402;ABA=316;ABP=502.11;ABR=829;AC=1197;AF=0.99254;AN=1206;BL=9889;BR=14293;BVAR;BaseQRankSum=1.373;DEL;DP=10477;DS;Dels=0.05;EL=243;EPP=64.494;ER=139;FS=29.162;HETAR=291;HOMA=85;HOMR=624;HPLen=10;InbreedingCoeff=0.1392;LEN=1;LRB=0.18212;LRBP=1744.6;MQ0Fraction=0.0024;MQM=48.471;MQRankSum=5.726;NS=1001;RA=3138;RL=174;RPP=9.5816;RR=208;RUN=1;ReadPosRankSum=5.755;SAB=0.79843;SAF=305;SAP=298.51;SAR=77;SRB=0.70363;SRF=2208;SRP=1133.2;SRR=930;VQSLOD=5.6318;set=Intersection;sumGLbyD=5.22 20 43258646 . T TT 1107.17 PASS AC=97;AF=0.08420;AN=1152;BaseQRankSum=4.525;DP=2345;FS=19.308;HRun=9;HaplotypeScore=13.6276;InbreedingCoeff=0.1299;MQ=76.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.395;QD=2.67;ReadPosRankSum=-4.696;SB=-899.41;VQSLOD=5.4523;set=VQSR 20 43718299 . ATTACT A 5497.06 PASS AA=56;AB=0.51818;ABA=53;ABP=3.3262;ABR=57;AC=18;AF=0.0251;AF1=0.03729;AN=718;BL=2321;BR=2591;BVAR;BaseQRankSum=11.142;CI95=0.03319,0.04425;DEL;DP=17576;DP4=2460,2692,31,22;Dels=0.02;EL=28;EPP=3.0103;ER=28;FQ=999;FR;FS=9.689;HETAR=15;HOMA=1;HOMR=1068;HP=2;HPLen=2;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0448;LEN=5;LRB=0.054967;LRBP=35.238;MQ=96.55;MQ0=0;MQ0Fraction=0.0000;MQM=50.286;MQRankSum=-5.149;NF;NR;NS=1084;PP;PV4=0.13,1,1.2e-12,1;RA=6745;RL=28;RPP=3.0103;RR=28;RUN=1;ReadPosRankSum=0.828;SAB=0.5;SAF=28;SAP=3.0103;SAR=28;SC=ATGACAGTGGATTACTTTAGT;SRB=0.46835;SRF=3159;SRP=61.709;SRR=3586;TC;TR=2;TU=T;VQSLOD=7.8832;set=Intersection;sumGLbyD=46.60 20 43981749 . A AAAAAAC,AC 20899.71 PASS ABR=192;AC=91,0;AF=0.1285,0.0000;AN=708;BVAR;BaseQRankSum=7.858;DP=23372;DP4=1554,1457,55,42;Dels=0.00;FR;FS=0.000;HOMA=4;HOMR=995;HP=6;HPLen=7;HR=7;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.2109;MQ=95.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-12.081;NF;NR;NS=1051;PP;PV4=0.35,1,8.9e-73,1;RA=5027;RUN=1;ReadPosRankSum=-1.359;SC=TACACTAGCAAAAAAACAAAA;SRB=0.48518;SRF=2439;SRP=12.6;SRR=2588;TC;TR=7;TU=A;VQSLOD=8.0916;set=Intersection;sumGLbyD=54.33 20 43999274 . TCAAA T 2948.85 PASS AA=59;AB=0.59441;ABA=58;ABP=14.08;ABR=85;AC=20;AF=0.0290;AF1=0.04249;AN=690;BL=2277;BR=2436;BVAR;BaseQRankSum=9.320;CI95=0.0354,0.05088;DEL;DP=14599;DP4=2052,2303,21,22;Dels=0.03;EL=32;EPP=3.9304;ER=27;FQ=999;FR;FS=0.000;HETAR=21;HOMA=0;HOMR=1043;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0037;LEN=4;LRB=0.033736;LRBP=14.658;MQ=90.05;MQ0=0;MQ0Fraction=0.0000;MQM=75.339;MQRankSum=-1.294;NF;NR;NS=1064;PP;PV4=0.88,1,0.0026,1;RA=5732;RL=27;RPP=3.9304;RR=32;RUN=1;ReadPosRankSum=-0.915;SAB=0.47458;SAF=28;SAP=3.3415;SAR=31;SC=GGTACACAGCTCAAACAGTCT;SRB=0.4836;SRF=2772;SRP=16.4;SRR=2960;TC;TR=1;TU=C;VQSLOD=9.8086;set=Intersection;sumGLbyD=27.09 20 44098622 . C CG 1092.40 PASS AA=129;AB=0.77301;ABA=74;ABP=214.06;ABR=252;AC=45;AF=0.0455;AN=988;BL=6586;BR=3029;BVAR;BaseQRankSum=2.802;DP=5177;Dels=0.00;EL=122;EPP=225.63;ER=7;FR;FS=355.273;HETAR=66;HOMA=11;HOMR=734;HP=6;HR=4;HRun=4;HU=G;INS;InbreedingCoeff=0.1759;LEN=1;LRB=0.36994;LRBP=2860.4;MQ0=0;MQ0Fraction=0.0000;MQM=52.395;MQRankSum=1.946;NF;NR;NS=811;PP;RA=1981;RL=121;RPP=217.95;RR=8;RUN=1;ReadPosRankSum=-6.413;SAB=0.99225;SAF=128;SAP=274.51;SAR=1;SC=GCGGAAGTGGCGGGGACCCTT;SRB=0.41242;SRF=817;SRP=135;SRR=1164;TC;TR=4;TU=G;VQSLOD=-2.2690;set=filterInVQSR-2of5;sumGLbyD=4.04 20 44327637 . A AG,AGGGGGG 14351.23 PASS AC=9,211;AF=0.0103,0.2409;AN=876;BaseQRankSum=15.517;DP=1704;FS=6.768;HaplotypeScore=31.5906;InbreedingCoeff=0.1538;MQ=54.64;MQ0=4;MQ0Fraction=0.0023;MQRankSum=-12.691;QD=20.83;ReadPosRankSum=-3.583;SB=-6278.99;VQSLOD=5.1556;set=VQSR 20 45202636 . GA G 13269 PASS AA=25;AB=0.96162;ABA=18;ABP=871.09;ABR=451;AC=24;AF=0.02013;AN=1192;BL=567;BR=1728;BVAR;BaseQRankSum=-5.361;DEL;DP=10873;Dels=0.00;EL=10;EPP=5.1818;ER=15;FS=0.928;HETAR=169;HOMA=831;HOMR=45;HRun=1;InbreedingCoeff=0.0999;LEN=1;LRB=0.50588;LRBP=1278.4;MQ0=0;MQ0Fraction=0.0000;MQM=170.56;MQRankSum=0.161;NS=1049;RA=632;RL=2;RPP=41.315;RR=23;RUN=1;ReadPosRankSum=-14.760;SAB=0.68;SAF=17;SAP=10.046;SAR=8;SRB=0.51424;SRF=325;SRP=4.1235;SRR=307;VQSLOD=3.9290;set=filterInVQSR-2of5;sumGLbyD=3.90 20 45417828 . TGAGC T,TGC 4672.90 PASS ABR=317;AC=69,104;AF=0.05712,0.08609;BVAR;BaseQRankSum=18.527;DEL;DP=11835;DS;FS=184.873;HOMA=48;HOMR=575;HaplotypeScore=65.5875;InbreedingCoeff=0.0599;MQ=29.78;MQ0=2988;MQ0Fraction=0.3629;MQRankSum=5.052;NS=713;QD=1.11;RA=1581;RUN=1;ReadPosRankSum=6.574;SB=-2116.87;SRB=0.47502;SRF=751;SRP=11.582;SRR=830;VQSLOD=0.0651;set=filterInVQSR-2of5 20 45525657 rs66759083 TA AA,T 49315 PASS AA=2361;AB=0.45241;ABA=1398;ABP=53.235;ABR=1155;AC=20;AF=0.01701;AN=1176;BL=94913;BR=100886;BVAR;BaseQRankSum=0.740;DB;DEL;DP=30636;DP4=1258,881,1206,999;Dels=0.48;EL=1133;EPP=11.311;ER=1228;FQ=999;FR;FS=7.072;HETAR=503;HOMA=310;HOMR=218;HP=6;HPLen=7;HR=7;HU=T;INDEL;InbreedingCoeff=0.2271;LEN=1;LRB=0.030506;LRBP=398.68;MQ=102.24;MQ0=0;MQ0Fraction=0.0000;MQM=75.359;MQRankSum=0.148;NF;NR;NS=1031;PP;PV4=0.0064,0,4.6e-23,0.47;RA=2042;RL=1183;RPP=3.0333;RR=1178;RUN=1;ReadPosRankSum=-2.999;SAB=0.52139;SAF=1231;SAP=12.392;SAR=1130;SC=AGGATTTTTTTAAAAAGTTTT;SRB=0.55093;SRF=1125;SRP=49.017;SRR=917;TC;TR=7;TU=T;VQSLOD=7.1651;dbSNP=114;set=Intersection;sumGLbyD=18.51 20 45783456 . T TG 2355.68 PASS AA=64;AB=0.78521;ABA=61;ABP=203.67;ABR=223;AC=15;AF=0.0165;AN=910;BL=815;BR=5486;BVAR;BaseQRankSum=8.593;DP=10348;Dels=0.00;EL=48;EPP=37.754;ER=16;FS=77.861;HETAR=56;HOMA=1;HOMR=970;HRun=1;INS;InbreedingCoeff=-0.0549;LEN=1;LRB=0.74131;LRBP=7522.1;MQ0Fraction=0.0122;MQM=44.562;MQRankSum=-1.258;NS=1027;RA=4750;RL=0;RPP=141.98;RR=64;RUN=1;ReadPosRankSum=-7.047;SAB=0.25;SAF=16;SAP=37.754;SAR=48;SRB=0.6;SRF=2850;SRP=415.59;SRR=1900;VQSLOD=1.3146;set=filterInVQSR-2of5;sumGLbyD=6.03 20 46384744 . CT C 17791 PASS AA=51;AB=0.94826;ABA=49;ABP=1655.8;ABR=898;AC=23;AF=0.01867;AN=1232;BL=120;BR=3678;BVAR;BaseQRankSum=-0.185;DEL;DP=13879;Dels=0.00;EL=23;EPP=4.0747;ER=28;FS=2.864;HETAR=262;HOMA=78;HOMR=722;HRun=2;InbreedingCoeff=0.0193;LEN=1;LRB=0.93681;LRBP=7240.9;MQ0=0;MQ0Fraction=0.0000;MQM=66.667;MQRankSum=1.031;NS=1079;RA=5295;RL=0;RPP=113.76;RR=51;RUN=1;ReadPosRankSum=-12.934;SAB=0.54902;SAF=28;SAP=4.0747;SAR=23;SRB=0.54674;SRF=2895;SRP=103.49;SRR=2400;VQSLOD=3.0419;set=filterInVQSR-2of5;sumGLbyD=3.47 20 46517110 . C CT 868.55 PASS AC=15;AF=0.0218;AN=688;BaseQRankSum=8.522;DP=1752;FS=6.570;HRun=0;HaplotypeScore=14.9548;InbreedingCoeff=0.0452;MQ=77.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=3.874;QD=10.98;ReadPosRankSum=-0.733;SB=-396.78;VQSLOD=6.7740;set=VQSR 20 46629361 . TTTCTTTC T,TTTTC 13000.91 PASS AC=188,107;AF=0.2212,0.1259;AN=850;BaseQRankSum=7.214;DP=1846;FS=14.502;HaplotypeScore=40.8481;InbreedingCoeff=0.3210;MQ=50.74;MQ0=79;MQ0Fraction=0.0428;MQRankSum=-6.348;QD=13.59;ReadPosRankSum=3.943;SB=-3581.20;VQSLOD=5.9412;set=VQSR 20 46951099 . G GT 1662.30 PASS AA=55;AB=0.7713;ABA=51;ABP=145.58;ABR=172;AC=47;AF=0.03923;AN=1198;BL=3288;BR=2434;BVAR;BaseQRankSum=-4.014;DP=27423;DP4=1483,1590,58,42;Dels=0.01;EL=21;EPP=9.6826;ER=34;FR;FS=9.565;HETAR=48;HOMA=0;HOMR=913;HP=16;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.0952;LEN=1;LRB=0.14925;LRBP=279.78;MQ=70.36;MQ0Fraction=0.0124;MQM=52.545;MQRankSum=0.717;NF;NR;NS=961;PP;PV4=0.067,1,1,0.17;RA=3035;RL=38;RPP=20.422;RR=17;RUN=1;ReadPosRankSum=-3.014;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TTTGTTTTTTGTTTTTTTTTT;SRB=0.36013;SRF=1093;SRP=518.73;SRR=1942;TC;TR=10;TU=T;VQSLOD=5.4779;set=Intersection;sumGLbyD=3.49 20 47201076 rs58052846 C CT 982.16 PASS AC=50;AF=0.0551;AN=908;BaseQRankSum=12.598;DB;DP=2449;FS=35.648;HRun=0;HaplotypeScore=29.4602;InbreedingCoeff=-0.0542;MQ=63.54;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.196;QD=3.16;ReadPosRankSum=-13.833;SB=-488.19;VQSLOD=6.0429;set=VQSR 20 47965974 rs60011158 G GA 999 PASS AA=21;AB=0.57143;ABA=21;ABP=5.1818;ABR=28;AC=7;AF=0.0101;AF1=0.02061;AN=690;BL=1043;BR=577;BVAR;BaseQRankSum=-3.087;CI95=0.01549,0.02655;DB;DP=14578;DP4=1554,3055,6,17;Dels=0.00;EL=11;EPP=3.1137;ER=10;FQ=999;FR;FS=5.982;HETAR=7;HOMA=0;HOMR=1041;HP=2;HPLen=1;HR=1;HRun=1;HU=A;INDEL;INS;InbreedingCoeff=0.0356;LEN=1;LRB=0.28765;LRBP=294.09;MQ=80.17;MQ0=0;MQ0Fraction=0.0000;MQM=64.19;MQRankSum=2.137;NF;NR;NS=1048;PP;PV4=0.51,1,1,1;RA=5224;RL=16;RPP=15.522;RR=5;RUN=1;ReadPosRankSum=0.236;SAB=0.38095;SAF=8;SAP=5.5954;SAR=13;SC=TTCATGTACAGAGCTGCTGTG;SRB=0.31183;SRF=1629;SRP=1609.6;SRR=3595;TC;TR=4;TU=AG;VQSLOD=9.5466;dbSNP=129;set=Intersection;sumGLbyD=13.83 20 48402974 rs57331436 GA G 27741 PASS AA=401;AB=0.5372;ABA=311;ABP=11.089;ABR=361;AC=84;AF=0.1186;AN=708;BL=16591;BR=14776;BVAR;BaseQRankSum=14.621;DB;DEL;DP=30607;DP4=1928,2310,195,225;Dels=0.11;EL=189;EPP=5.8749;ER=212;FQ=999;FR;FS=15.568;HETAR=110;HOMA=30;HOMR=923;HP=4;HPLen=3;HR=1;HRun=3;HU=A;INDEL;InbreedingCoeff=0.1263;KGPilot123;LEN=1;LRB=0.057863;LRBP=231.06;MQ=106.68;MQ0=0;MQ0Fraction=0.0000;MQM=63.005;MQRankSum=-2.010;NF;NR;NS=1063;PP;PV4=0.72,1,0.001,1;RA=5258;RL=223;RPP=13.976;RR=178;RUN=1;ReadPosRankSum=1.337;SAB=0.37656;SAF=151;SAP=56.084;SAR=250;SC=TGCCCTCAAAGAGAAAAAGGA;SRB=0.38075;SRF=2002;SRP=652.44;SRR=3256;TC;TR=5;TU=AG;VQSLOD=8.7259;dbSNP=132;set=Intersection;sumGLbyD=15.86 20 48519434 rs56747320 TA T,TAA 26754 PASS AC=91,355;AF=0.07738,0.30187;AN=1176;BVAR;BaseQRankSum=-5.499;DB;DEL;DP=24872;DP4=726,883,443,502;Dels=0.04;FR;FS=1.430;HP=12;HR=12;HRun=12;HU=A;INDEL;INS;InbreedingCoeff=0.2576;LEN=1;MQ=71.86;MQ0=1;MQ0Fraction=0.0004;MQRankSum=-0.526;NF;NR;PP;PV4=0.41,1,0.00077,1;RUN=1;ReadPosRankSum=-4.130;SC=CGTCTTAAACTAAAAAAAAAA;TC;TR=12;TU=A;VQSLOD=7.3200;set=Intersection;sumGLbyD=10.43 20 49086519 rs111404890 CA C,CAA 1379.10 PASS AA=43;AB=0.672;ABA=41;ABP=35.131;ABR=84;AC=7,14;AF=0.0100,0.0201;AN=698;BL=1097;BR=2286;BVAR;BaseQRankSum=-2.656;DB;DP=9319;Dels=0.00;EL=22;EPP=3.0608;ER=21;FR;FS=1.147;HETAR=20;HOMA=0;HOMR=1029;HP=11;HPLen=8;HR=8;HRun=8;HU=A;INS;InbreedingCoeff=0.0760;LEN=1;LRB=0.35146;LRBP=910.45;MQ0=0;MQ0Fraction=0.0000;MQM=47.674;MQRankSum=2.682;NF;NR;NS=1049;PP;RA=5237;RL=10;RPP=29.724;RR=33;RUN=1;ReadPosRankSum=-2.367;SAB=0.48837;SAF=21;SAP=3.0608;SAR=22;SC=GTAAAACAAACAAAAAAAATG;SRB=0.48635;SRF=2547;SRP=11.489;SRR=2690;TC;TR=11;TU=AAAC;VQSLOD=7.3084;set=Intersection;sumGLbyD=9.84 20 49101936 . C CT 404.46 PASS AC=40;AF=0.03559;AN=1124;BaseQRankSum=0.750;DP=2162;FS=14.291;HRun=2;HaplotypeScore=30.9513;InbreedingCoeff=-0.0082;MQ=49.78;MQ0=113;MQ0Fraction=0.0523;MQRankSum=-1.289;QD=1.94;ReadPosRankSum=-2.041;SB=-385.48;VQSLOD=4.6365;set=VQSR 20 49681276 . TC T 40042 PASS AA=72;AB=0.93908;ABA=70;ABP=1927.1;ABR=1079;AC=18;AF=0.0196;AN=918;BL=514;BR=4340;BVAR;BaseQRankSum=0.869;DEL;DP=10368;Dels=0.00;EL=33;EPP=4.096;ER=39;FS=17.302;HETAR=389;HOMA=269;HOMR=405;HRun=1;InbreedingCoeff=0.0626;LEN=1;LRB=0.78822;LRBP=6551.6;MQ0=0;MQ0Fraction=0.0000;MQM=123.06;MQRankSum=-1.047;NS=1064;RA=3095;RL=3;RPP=134.38;RR=69;RUN=1;ReadPosRankSum=-10.928;SAB=0.58333;SAF=42;SAP=7.3532;SAR=30;SRB=0.57738;SRF=1787;SRP=163.99;SRR=1308;VQSLOD=2.8517;set=filterInVQSR-2of5;sumGLbyD=3.69 20 49690436 . GT G 473.74 PASS AF=0.0263;AF1=0.02287;BaseQRankSum=3.830;CI95=0.01327,0.03319;DP=7473;DP4=2241,1740,14,12;Dels=0.01;FQ=129;FR;FS=0.000;HP=4;HPLen=4;HR=4;HRun=4;HU=T;INDEL;InbreedingCoeff=0.1310;MQ=51.71;MQ0Fraction=0.0407;MQRankSum=1.792;NF;NR;PP;PV4=0.84,5.7e-10,0.22,1;ReadPosRankSum=0.973;SC=GTAGGACGGGGTTTTACCATG;TC;TR=4;TU=T;VQSLOD=7.4809;set=Intersection;sumGLbyD=10.96 20 49731218 . ATTTTATTTTTTATT A,ATTTTATT 8398.93 PASS AF=0.0656,0.0156;AF1=0.0996;BaseQRankSum=13.996;CI95=0.07743,0.1239;DP=6308;DP4=951,1311,23,35;Dels=0.05;FQ=999;FR;FS=12.503;HP=7;HPLen=4;HR=4;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1892;MQ=57.61;MQ0Fraction=0.0145;MQRankSum=-5.208;NF;NR;PP;PV4=0.79,1,6.3e-06,0.16;ReadPosRankSum=-2.239;SC=TATTTTATTTATTTTATTTTT;TC;TR=11;TU=ATTT;VQSLOD=4.3191;set=Intersection;sumGLbyD=42.27 20 49894989 . TA T 172.25 PASS AF=0.0140;BaseQRankSum=7.220;DP=3882;Dels=0.00;FS=17.217;HPLen=2;HRun=1;InbreedingCoeff=0.0531;MQ0Fraction=0.0214;MQRankSum=-0.661;ReadPosRankSum=-0.592;VQSLOD=3.0905;set=filterInVQSR-2of5;sumGLbyD=6.60 20 50010923 rs66516522 C CT,CTGG 35851 PASS ABR=555;AC=310,11;AF=0.26451,0.00939;BVAR;BaseQRankSum=10.662;DB;DP=8188;FR;FS=34.411;HOMA=261;HOMR=399;HP=5;HR=6;HU=C;HaplotypeScore=45.1715;INS;InbreedingCoeff=0.2090;MQ=72.80;MQ0=0;MQ0Fraction=0.0000;MQRankSum=9.015;NF;NR;NS=831;PP;QD=9.69;RA=1986;RUN=1;ReadPosRankSum=-24.284;SB=-6038.55;SC=TGTCTGTCCCCCCTCAGCACT;SRB=0.45972;SRF=913;SRP=31.001;SRR=1073;TC;TR=6;TU=C;VQSLOD=6.1824;set=Intersection 20 50059710 . C CCA 4175.86 PASS AA=28;AB=0.62963;ABA=20;ABP=10.892;ABR=34;AC=36;AF=0.0738;AN=488;BL=1050;BR=1273;BVAR;BaseQRankSum=3.198;DP=9138;Dels=0.00;EL=10;EPP=7.9737;ER=18;FR;FS=19.190;HETAR=10;HOMA=2;HOMR=1053;HP=6;HPLen=7;HR=7;HRun=0;HU=C;INS;InbreedingCoeff=0.1390;LEN=2;LRB=0.095997;LRBP=49.496;MQ0=0;MQ0Fraction=0.0000;MQM=57.464;MQRankSum=-1.875;NF;NR;NS=1065;PP;RA=5745;RL=12;RPP=4.2511;RR=16;RUN=1;ReadPosRankSum=-2.894;SAB=0.5;SAF=14;SAP=3.0103;SAR=14;SC=GGAGACCCCCCCTTCATCCTA;SRB=0.48129;SRF=2765;SRP=20.482;SRR=2980;TC;TR=7;TU=C;VQSLOD=5.1567;set=Intersection;sumGLbyD=11.49 20 50228709 rs71192536 TG T 20517 PASS AA=924;AB=0.50203;ABA=735;ABP=3.0633;ABR=741;AC=200;AF=0.16502;AN=1212;BL=35460;BR=34197;BVAR;BaseQRankSum=13.810;DB;DEL;DP=32402;DP4=1760,2065,395,449;Dels=0.16;EL=439;EPP=7.9831;ER=485;FQ=999;FR;FS=0.558;HETAR=242;HOMA=63;HOMR=764;HP=5;HPLen=3;HR=3;HRun=3;HU=G;INDEL;InbreedingCoeff=0.1050;LEN=1;LRB=0.018132;LRBP=52.738;MQ=105.83;MQ0=0;MQ0Fraction=0.0000;MQM=75.87;MQRankSum=3.895;NF;NR;NS=1069;PP;PV4=0.7,1.5e-173,1,1;RA=4708;RL=486;RPP=8.4249;RR=438;RUN=1;ReadPosRankSum=1.586;SAB=0.43615;SAF=403;SAP=35.733;SAR=521;SC=GTTTTCCAGGTGGGAAGACCG;SRB=0.44074;SRF=2075;SRP=146.62;SRR=2633;TC;TR=3;TU=G;VQSLOD=10.4820;dbSNP=120;set=Intersection;sumGLbyD=15.35 20 50236115 . AGG A,ACGGG,AG,AGGG 7429.57 PASS AC=192,13,221,183;AF=0.2115,0.0143,0.2434,0.2015;AN=908;BaseQRankSum=1.045;DP=1177;FS=13.479;HaplotypeScore=11.8294;InbreedingCoeff=0.7959;MQ=52.98;MQ0=6;MQ0Fraction=0.0051;MQRankSum=-1.482;QD=7.28;ReadPosRankSum=-2.380;SB=-1229.31;VQSLOD=8.3762;set=VQSR 20 51589568 . TAAAC AAAAC,T 12477.52 PASS AF=0.27949;BaseQRankSum=-28.122;DP=3777;Dels=0.00;FR;FS=31.799;HP=7;HPLen=4;HR=3;HRun=0;HU=A;InbreedingCoeff=-0.1429;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.196;NF;NR;PP;ReadPosRankSum=-16.483;SC=AAATTCAAAATAAACAAACAA;TC;TR=18;TU=AAAC;VQSLOD=3.9201;set=filterInVQSR-2of5;sumGLbyD=52.43 20 51617742 . TGC T,TGCGC 1374.91 PASS AF=0.06000,0.02000;BaseQRankSum=12.051;DP=6231;Dels=0.00;FS=189.609;HPLen=1;HRun=0;InbreedingCoeff=0.0862;MQ0Fraction=0.0180;MQRankSum=-2.959;ReadPosRankSum=-5.090;VQSLOD=-2.8715;set=filterInVQSR-2of5;sumGLbyD=3.97 20 51770354 . AG A 1010.90 PASS AA=26;AB=0.52727;ABA=26;ABP=3.3656;ABR=29;AC=7;AF=0.0097;AF1=0.01637;AN=718;BL=1034;BR=964;BVAR;BaseQRankSum=5.588;CI95=0.01327,0.02212;DEL;DP=16259;DP4=2785,2239,15,10;Dels=0.01;EL=11;EPP=4.3466;ER=15;FQ=999;FR;FS=3.367;HETAR=8;HOMA=0;HOMR=1064;HP=2;HPLen=2;HR=2;HRun=2;HU=G;INDEL;InbreedingCoeff=0.0557;LEN=1;LRB=0.035035;LRBP=8.3357;MQ=90.48;MQ0=0;MQ0Fraction=0.0000;MQM=61.346;MQRankSum=-0.019;NF;NR;NS=1072;PP;PV4=0.69,2.1e-08,0.078,1;RA=6173;RL=13;RPP=3.0103;RR=13;RUN=1;ReadPosRankSum=-0.460;SAB=0.61538;SAF=16;SAP=6.017;SAR=10;SC=GTGGTCCTGCAGGTCAATAAT;SRB=0.56342;SRF=3478;SRP=218.68;SRR=2695;TC;TR=2;TU=G;VQSLOD=10.1601;set=Intersection;sumGLbyD=14.60 20 51848430 . AT A,ATT 999 PASS AA=39;AB=0.83408;ABA=37;ABP=219.19;ABR=186;AC=14,33;AF=0.0153,0.0359;AF1=0.03062;AN=918;BL=1676;BR=1732;BVAR;BaseQRankSum=3.338;CI95=0.02212,0.03982;DP=14886;DP4=1970,1762,22,31;Dels=0.01;EL=18;EPP=3.5114;ER=21;FQ=999;FR;FS=3.004;HETAR=31;HOMA=0;HOMR=1040;HP=10;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.1629;LEN=1;LRB=0.016432;LRBP=5.0085;MQ=80.05;MQ0=0;MQ0Fraction=0.0000;MQM=56.667;MQRankSum=0.325;NF;NR;NS=1071;PP;PV4=0.13,1,0.0095,0.064;RA=5318;RL=21;RPP=3.5114;RR=18;RUN=1;ReadPosRankSum=-0.493;SAB=0.46154;SAF=18;SAP=3.5114;SAR=21;SC=ACAAAACAATATTTTTTTTTC;SRB=0.4968;SRF=2642;SRP=3.4823;SRR=2676;TC;TR=9;TU=T;VQSLOD=5.7417;set=Intersection;sumGLbyD=7.57 20 51897203 . T TG 8427.20 PASS AA=237;AB=0.69846;ABA=215;ABP=246.92;ABR=498;AC=117;AF=0.1662;AN=704;BL=14961;BR=5990;BVAR;BaseQRankSum=22.203;DP=9710;Dels=0.00;EL=83;EPP=49.198;ER=154;FR;FS=9.450;HETAR=123;HOMA=9;HOMR=895;HP=5;HPLen=6;HR=6;HRun=0;HU=T;INS;InbreedingCoeff=-0.0513;LEN=1;LRB=0.42819;LRBP=8344.3;MQ0Fraction=0.0291;MQM=45.861;MQRankSum=-10.426;NF;NR;NS=1027;PP;RA=4919;RL=210;RPP=309.85;RR=27;RUN=1;ReadPosRankSum=-1.843;SAB=0.29536;SAF=70;SAP=89.219;SAR=167;SC=TTTGTTTGTTTTTTGTTGTTG;SRB=0.47794;SRF=2351;SRP=23.798;SRR=2568;TC;TR=23;TU=GTTT;VQSLOD=6.2670;set=Intersection;sumGLbyD=8.99 20 52274070 . AAG A 1400.37 PASS AA=30;AB=0.74227;ABA=25;ABP=52.462;ABR=72;AC=21;AF=0.01756;AN=1196;BL=412;BR=1966;BVAR;BaseQRankSum=6.660;DEL;DP=9362;Dels=0.01;EL=16;EPP=3.2998;ER=14;FS=1.485;HETAR=18;HOMA=2;HOMR=1004;HRun=0;InbreedingCoeff=0.0317;LEN=2;LRB=0.65349;LRBP=2208.2;MQ0Fraction=0.0022;MQM=46.133;MQRankSum=-4.743;NS=1024;RA=3931;RL=2;RPP=51.941;RR=28;RUN=1;ReadPosRankSum=-4.152;SAB=0.4;SAF=12;SAP=5.6161;SAR=18;SRB=0.49784;SRF=1957;SRP=3.1699;SRR=1974;VQSLOD=5.6452;set=Intersection;sumGLbyD=11.11 20 52351501 . TAC T 199.59 PASS AC=22;AF=0.0238;AN=926;BaseQRankSum=7.874;DP=22911;DP4=2146,1691,26,22;FR;FS=2.898;HP=4;HPLen=3;HR=1;HRun=0;HU=A;HaplotypeScore=18.6111;INDEL;InbreedingCoeff=-0.0326;MQ0=2;MQ0Fraction=0.0007;MQRankSum=1.011;NF;NR;PP;PV4=0.88,0.14,0.16,0.24;QD=1.10;ReadPosRankSum=-1.053;SB=-306.09;SC=GACACACAAATACACACACAC;TC;TR=13;TU=AC;VQSLOD=4.0486;set=filterInVQSR-2of5 20 52447173 . CA C 503.89 PASS AC=23;AF=0.01891;AN=1216;BaseQRankSum=0.801;DP=3266;FS=2.606;HRun=2;HaplotypeScore=22.1543;InbreedingCoeff=-0.0097;MQ=118.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.309;QD=2.65;ReadPosRankSum=-7.872;SB=-279.27;VQSLOD=4.1900;set=VQSR 20 52498650 . GT G 24069 PASS AA=74;AB=0.90594;ABA=57;ABP=870.4;ABR=549;AC=28;AF=0.02333;AN=1200;BL=505;BR=4514;BVAR;BaseQRankSum=-3.837;DEL;DP=9798;Dels=0.01;EL=41;EPP=4.8883;ER=33;FS=4.085;HETAR=209;HOMA=663;HOMR=121;HRun=1;InbreedingCoeff=0.0334;LEN=1;LRB=0.79876;LRBP=6956.6;MQ0=2;MQ0Fraction=0.0007;MQM=57.784;MQRankSum=-2.951;NS=995;RA=957;RL=8;RPP=101.72;RR=66;RUN=1;ReadPosRankSum=-14.806;SAB=0.39189;SAF=29;SAP=10.522;SAR=45;SRB=0.39916;SRF=382;SRP=87.53;SRR=575;VQSLOD=3.8710;set=filterInVQSR-2of5;sumGLbyD=2.90 20 52823602 rs11469056 CAAA C,CA,CAA,CAAAA,CAAAAA,CAAAAAA,CAAAAAAA,CAAAAAAAA,CAAAAAAAAA,CAAAAAAAAAA 14515.17 PASS AC=24,83,246,109,83,19,10,16,22,59;AF=0.02128,0.07358,0.21809,0.09663,0.07358,0.01684,0.00887,0.01418,0.01950,0.05230;AN=1128;BVAR;BaseQRankSum=4.150;DB;DEL;DP=28279;FR;FS=2.021;HP=17;HR=17;HU=A;HaplotypeScore=27.8032;INS;InbreedingCoeff=0.7740;MQ=69.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.418;NF;NR;PP;QD=7.90;RUN=1;ReadPosRankSum=-3.864;SB=-3244.40;SC=GGTCCTAAGGCAAAAAAAAAA;TC;TR=17;TU=A;VQSLOD=14.1033;set=Intersection 20 53308906 . CT C,CTT 2276 PASS AA=92;AB=0.84453;ABA=81;ABP=540.17;ABR=440;AC=53,81;AF=0.04351,0.06650;AN=1218;BL=3561;BR=4796;BVAR;BaseQRankSum=3.000;DP=11804;Dels=0.02;EL=48;EPP=3.3879;ER=44;FR;FS=13.197;HETAR=69;HOMA=3;HOMR=993;HP=11;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2297;LEN=1;LRB=0.14778;LRBP=399.32;MQ0=1;MQ0Fraction=0.0003;MQM=56.348;MQRankSum=3.154;NF;NR;NS=1065;PP;RA=5520;RL=39;RPP=7.6365;RR=53;RUN=1;ReadPosRankSum=-2.140;SAB=0.57609;SAF=53;SAP=7.6365;SAR=39;SC=AATCCAAAGTCTTTTTTTTTT;SRB=0.51576;SRF=2847;SRP=14.92;SRR=2673;TC;TR=10;TU=T;VQSLOD=2.4753;set=filterInVQSR-2of5;sumGLbyD=4.42 20 53334602 . T TG,TGG 905.13 PASS ABR=325;AC=44,22;AF=0.03624,0.01812;BVAR;BaseQRankSum=-4.608;DP=15015;FR;FS=494.901;HOMA=0;HOMR=1004;HP=1;HR=1;HU=G;HaplotypeScore=20.5023;INS;InbreedingCoeff=0.0799;MQ=116.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=8.022;NF;NR;NS=1064;PP;QD=0.35;RA=5690;RUN=1;ReadPosRankSum=-14.522;SB=-311.57;SC=AGCCATTGGCTGTTTCACTGA;SRB=0.40738;SRF=2318;SRP=426.97;SRR=3372;TC;TR=1;TU=G;VQSLOD=-2.3042;set=filterInVQSR-2of5 20 53729115 . T TG 15.48 PASS AC=1;AF=0.0015;AN=668;BaseQRankSum=-1.001;DP=1711;FS=9.048;HRun=2;HaplotypeScore=12.4681;InbreedingCoeff=-0.0320;MQ=131.36;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.193;QD=4.57;ReadPosRankSum=0.407;SB=-5.35;VQSLOD=4.8071;set=VQSR 20 53960980 . GC G 588.40 PASS AA=32;AB=0.78632;ABA=25;ABP=86.324;ABR=92;AF=0.0275;AF1=0.01689;AN=690;BL=1047;BR=1108;BVAR;BaseQRankSum=3.049;CI95=0.006637,0.02876;DEL;DP=11389;DP4=1514,1481,16,12;Dels=0.02;EL=27;EPP=35.854;ER=5;FQ=17.6;FS=0.652;HETAR=27;HOMA=3;HOMR=1006;HRun=1;INDEL;InbreedingCoeff=0.0473;LEN=1;LRB=0.028306;LRBP=6.7597;MQ=106.54;MQ0=0;MQ0Fraction=0.0000;MQM=115.53;MQRankSum=1.395;NS=1036;PV4=0.57,0.0057,0.46,0.22;RA=4207;RL=14;RPP=4.096;RR=18;RUN=1;ReadPosRankSum=-5.581;SAB=0.40625;SAF=13;SAP=5.4532;SAR=19;SRB=0.48586;SRF=2044;SRP=10.32;SRR=2163;VQSLOD=6.0155;set=Intersection;sumGLbyD=7.94 20 54033830 . GTATTTTAAAATCA G 2220.86 PASS AF=0.0113;BaseQRankSum=5.506;DP=2577;Dels=0.01;FR;FS=6.533;HP=5;HPLen=4;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0032;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.969;NF;NR;PP;ReadPosRankSum=1.322;SC=TCAATATTTTGTATTTTAAAA;TC;TR=1;TU=T;VQSLOD=5.5145;set=Intersection;sumGLbyD=95.65 20 54375236 . GT G 626.13 PASS AA=40;AB=0.63551;ABA=39;ABP=20.078;ABR=68;AC=18;AF=0.0256;AN=702;BL=1331;BR=1743;BVAR;BaseQRankSum=9.346;DEL;DP=8568;Dels=0.02;EL=26;EPP=10.828;ER=14;FS=0.610;HETAR=21;HOMA=1;HOMR=1035;HRun=1;InbreedingCoeff=-0.0056;LEN=1;LRB=0.13403;LRBP=122.92;MQ0=0;MQ0Fraction=0.0000;MQM=67.125;MQRankSum=-2.537;NS=1058;RA=4870;RL=17;RPP=4.9646;RR=23;RUN=1;ReadPosRankSum=-1.229;SAB=0.525;SAF=21;SAP=3.2274;SAR=19;SRB=0.5271;SRF=2567;SRP=34.087;SRR=2303;VQSLOD=7.9228;set=Intersection;sumGLbyD=10.77 20 54457331 . G GA 1793.40 PASS AA=77;AB=0.66667;ABA=74;ABP=56.573;ABR=148;AC=33;AF=0.02687;AN=1228;BL=3834;BR=1154;BVAR;BaseQRankSum=10.572;DP=10230;Dels=0.00;EL=77;EPP=170.21;ER=0;FS=139.433;HETAR=44;HOMA=1;HOMR=1001;HRun=1;INS;InbreedingCoeff=0.0023;LEN=1;LRB=0.53729;LRBP=3129.8;MQ0Fraction=0.0095;MQM=4.7013;MQRankSum=-8.116;NS=1046;RA=4009;RL=77;RPP=170.21;RR=0;RUN=1;ReadPosRankSum=-6.026;SAB=1;SAF=77;SAP=170.21;SAR=0;SRB=0.57022;SRF=2286;SRP=174.7;SRR=1723;VQSLOD=1.1887;set=filterInVQSR-2of5;sumGLbyD=5.90 20 54469810 . CA C 1697.62 PASS AA=93;AB=0.63855;ABA=90;ABP=44.53;ABR=159;AC=34;AF=0.0374;AF1=0.01719;AN=908;BL=3242;BR=5839;BVAR;BaseQRankSum=10.425;CI95=0.009317,0.02795;DEL;DP=15197;DP4=2134,1896,56,46;Dels=0.03;EL=34;EPP=17.604;ER=59;FQ=16;FR;FS=9.985;HETAR=41;HOMA=1;HOMR=1011;HP=9;HPLen=8;HR=8;HRun=8;HU=A;INDEL;InbreedingCoeff=-0.0472;LEN=1;LRB=0.28598;LRBP=1615.8;MQ=83.37;MQ0=1;MQ0Fraction=0.0004;MQM=64.075;MQRankSum=3.036;NF;NR;NS=1053;PP;PV4=0.76,1,0.31,0.22;RA=5150;RL=28;RPP=34.975;RR=65;RUN=1;ReadPosRankSum=-0.252;SAB=0.5914;SAF=55;SAP=9.7582;SAR=38;SC=ATTGCTAAGACAAAAAAAAGA;SRB=0.50621;SRF=2607;SRP=4.7374;SRR=2543;TC;TR=8;TU=A;VQSLOD=8.3677;set=Intersection;sumGLbyD=9.90 20 54542453 . GTATA G,GTA 5109.66 PASS ABR=112;AC=66,56;AF=0.0682,0.0579;AN=968;BVAR;BaseQRankSum=17.089;DB;DEL;DP=5519;DS;Dels=0.06;FS=99.502;HOMA=15;HOMR=409;HRun=0;InbreedingCoeff=0.1584;MQ0Fraction=0.0178;MQRankSum=-6.854;NS=460;RA=864;RUN=1;ReadPosRankSum=0.855;SRB=0.79282;SRF=685;SRP=646.5;SRR=179;VQSLOD=0.6375;set=filterInVQSR-2of5;sumGLbyD=8.53 20 54629773 . CA C 1799.50 PASS AA=49;AB=0.82707;ABA=46;ABP=250.17;ABR=220;AC=9;AF=0.00746;AN=1206;BL=173;BR=2277;BVAR;BaseQRankSum=5.240;DEL;DP=8557;Dels=0.01;EL=49;EPP=109.41;ER=0;FS=32.359;HETAR=35;HOMA=1;HOMR=325;HRun=1;InbreedingCoeff=0.0892;LEN=1;LRB=0.85878;LRBP=3926.6;MQ0Fraction=0.0602;MQM=32.163;MQRankSum=-3.926;NS=361;RA=1091;RL=0;RPP=109.41;RR=49;RUN=1;ReadPosRankSum=-4.512;SAB=0;SAF=0;SAP=109.41;SAR=49;SRB=0.49404;SRF=539;SRP=3.3467;SRR=552;VQSLOD=1.1233;set=filterInVQSR-2of5;sumGLbyD=3.54 20 54710245 . TA T 999 PASS AF=0.0084;AF1=0.0148;BaseQRankSum=3.954;CI95=0.00885,0.02212;DP=8043;DP4=2000,1849,10,7;Dels=0.01;FQ=999;FR;FS=0.000;HP=9;HPLen=6;HR=3;HRun=6;HU=A;INDEL;InbreedingCoeff=0.1181;MQ=78.51;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.095;NF;NR;PP;PV4=0.63,0.00056,1,1;ReadPosRankSum=-0.448;SC=CAACAAAAAATAAATAAATAA;TC;TR=15;TU=AAAT;VQSLOD=7.8129;set=Intersection;sumGLbyD=19.02 20 54968173 . A AAT,AATAT,AT,ATAT 89535.82 PASS ABR=994;AC=561,278,2,3;AF=0.50179,0.24866,0.00179,0.00268;AN=1118;BVAR;BaseQRankSum=-2.699;DB;DP=27837;DP4=168,177,1045,866;Dels=0.00;FQ=999;FR;FS=12.472;HOMA=71;HOMR=455;HP=3;HPLen=4;HR=4;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.6391;KGPilot123;MQ=80.36;MQ0Fraction=0.0055;MQRankSum=-1.512;NF;NR;NS=913;PP;PV4=0.046,1,1,1;RA=2015;RUN=1;ReadPosRankSum=1.015;SC=GGCCACTTAAAATATATATAT;SRB=0.44864;SRF=904;SRP=49.187;SRR=1111;TC;TR=15;TU=AT;VQSLOD=9.0092;dbSNP=132;set=Intersection;sumGLbyD=42.33 20 55176688 . TA T 421.84 PASS AF=0.01322;AF1=0.01845;BaseQRankSum=5.383;CI95=0.01282,0.02564;DP=10531;DP4=1975,2017,16,14;Dels=0.01;FQ=91.2;FR;FS=7.401;HP=6;HPLen=5;HR=5;HRun=5;HU=A;INDEL;InbreedingCoeff=0.0829;MQ=75.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=-0.471;NF;NR;PP;PV4=0.72,1,1,1;ReadPosRankSum=0.223;SC=CTGCAAAATATAAAAATTAGG;TC;TR=5;TU=A;VQSLOD=6.6000;set=Intersection;sumGLbyD=12.15 20 55664086 . GTT ATT,G,GT,GTTT 5622.44 PASS AC=6,71,136;AF=0.00498,0.05887,0.11277;AN=1206;BVAR;BaseQRankSum=3.173;DB;DEL;DP=40384;DP4=1567,1317,54,29;Dels=0.05;FR;FS=1.949;HP=14;HR=11;HRun=11;HU=T;INDEL;INS;InbreedingCoeff=0.3490;MQ=77.90;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.052;NF;NR;PP;PV4=0.057,1,0.2,1.2e-05;RUN=1;ReadPosRankSum=-13.646;SC=AATTTTATTTGTTTTTTTTTT;TC;TR=11;TU=T;VQSLOD=11.7964;set=Intersection;sumGLbyD=8.09 20 56045006 . TG T 342.15 PASS AC=72;AF=0.0940;AN=766;BaseQRankSum=4.992;DP=1238;FS=1.460;HRun=7;HaplotypeScore=20.2784;InbreedingCoeff=0.1795;MQ=66.42;MQ0=1;MQ0Fraction=0.0008;MQRankSum=-0.937;QD=1.84;ReadPosRankSum=-4.385;SB=-320.83;VQSLOD=5.2383;set=VQSR 20 56158711 . AG A 922.47 PASS AA=18;AB=0.575;ABA=17;ABP=4.9646;ABR=23;AC=2;AF=0.0028;AN=714;BL=953;BR=808;BVAR;BaseQRankSum=3.129;DEL;DP=10462;Dels=0.01;EL=9;EPP=3.0103;ER=9;FR;FS=8.724;HETAR=4;HOMA=0;HOMR=1058;HP=1;HPLen=2;HR=2;HRun=1;HU=A;InbreedingCoeff=0.0262;LEN=1;LRB=0.08234;LRBP=28.936;MQ0=0;MQ0Fraction=0.0000;MQM=55.889;MQRankSum=2.052;NF;NR;NS=1062;PP;RA=6300;RL=9;RPP=3.0103;RR=9;RUN=1;ReadPosRankSum=-0.317;SAB=0.66667;SAF=12;SAP=7.3532;SAR=6;SC=TGGCCTAGCAAGCATCGTGAC;SRB=0.48143;SRF=3033;SRP=21.883;SRR=3267;TC;TR=8;TU=AAGC;VQSLOD=8.3252;set=Intersection;sumGLbyD=13.22 20 56258618 rs113670927 T C,TGC,TGTGC,TGTGTGC 37834.99 PASS ABR=441;AC=11,100,43;AF=0.0123,0.1119,0.0481;AN=894;BVAR;BaseQRankSum=19.514;DB;DP=23173;DP4=541,920,413,579;Dels=0.00;FQ=999;FR;FS=1.238;HOMA=28;HOMR=808;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.2154;MQ=57.25;MQ0Fraction=0.0275;MQRankSum=-6.684;NF;NR;NS=976;PP;PV4=0.023,1,1,1;RA=3294;RUN=1;ReadPosRankSum=11.873;SC=TGCGTGTGTGTGTGTGTGTGT;SRB=0.42441;SRF=1398;SRP=166.5;SRR=1896;TC;TR=30;TU=GT;VQSLOD=6.7457;dbSNP=114;set=Intersection;sumGLbyD=21.27 20 56395857 . T TAGGCAG 6614.22 PASS AA=30;AB=0.63415;ABA=30;ABP=15.827;ABR=52;AC=14;AF=0.0197;AF1=0.03154;AN=710;BL=991;BR=1813;BVAR;BaseQRankSum=-4.589;CI95=0.02434,0.04204;DP=13879;DP4=1543,1833,12,14;Dels=0.00;EL=14;EPP=3.2998;ER=16;FQ=999;FR;FS=1.482;HETAR=11;HOMA=0;HOMR=1051;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0774;LEN=6;LRB=0.29315;LRBP=526.27;MQ=90.42;MQ0=0;MQ0Fraction=0.0000;MQM=39.433;MQRankSum=-7.011;NF;NR;NS=1062;PP;PV4=1,1,3.7e-09,1;RA=5322;RL=9;RPP=13.433;RR=21;RUN=1;ReadPosRankSum=0.679;SAB=0.43333;SAF=13;SAP=4.1684;SAR=17;SC=AAGAGCATCTTAGGCAGAGGC;SRB=0.47294;SRF=2517;SRP=36.853;SRR=2805;TC;TR=2;TU=T;VQSLOD=8.3045;set=Intersection;sumGLbyD=68.22 20 56969289 . GTTTGT G 600.69 PASS AF=0.0056;AF1=0.007726;BaseQRankSum=2.907;CI95=0.004425,0.01327;DP=9643;DP4=1892,1749,6,3;Dels=0.00;FQ=117;FR;FS=16.601;HP=5;HPLen=3;HR=3;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0236;MQ=92.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.134;NF;NR;PP;PV4=0.51,1,0.07,0.3;ReadPosRankSum=0.236;SC=TAAGGACGTTGTTTGTTTTGT;TC;TR=10;TU=GTTT;VQSLOD=5.8458;set=Intersection;sumGLbyD=39.51 20 57187557 . AG A,AGG 1486.69 PASS AA=130;AB=0.55446;ABA=90;ABP=8.2132;ABR=112;AC=56,26;AF=0.0574,0.0266;AN=976;BL=3817;BR=5968;BVAR;BaseQRankSum=5.517;DEL;DP=14174;DP4=925,721,59,48;Dels=0.05;EL=52;EPP=14.302;ER=78;FR;FS=0.917;HETAR=44;HOMA=17;HOMR=864;HP=4;HPLen=4;HR=4;HRun=4;HU=G;INDEL;InbreedingCoeff=0.2856;LEN=1;LRB=0.21983;LRBP=1029.8;MQ=91.56;MQ0=0;MQ0Fraction=0.0000;MQM=63.631;MQRankSum=1.900;NF;NR;NS=925;PP;PV4=0.84,1,1,0.39;RA=2746;RL=44;RPP=32.476;RR=86;RUN=1;ReadPosRankSum=-0.639;SAB=0.44615;SAF=58;SAP=6.2842;SAR=72;SC=TCAGGCCCGCAGGGGTCAGGG;SRB=0.5772;SRF=1585;SRP=145.17;SRR=1161;TC;TR=4;TU=G;VQSLOD=7.7167;set=Intersection;sumGLbyD=14.85 20 57282771 . T TG 506.43 PASS AA=34;AB=0.70312;ABA=19;ABP=25.946;ABR=45;AC=34;AF=0.0373;AN=912;BL=886;BR=1938;BVAR;BaseQRankSum=3.744;DP=4276;Dels=0.00;EL=18;EPP=3.2658;ER=16;FR;FS=0.639;HETAR=17;HOMA=9;HOMR=737;HP=9;HR=8;HRun=8;HU=G;INS;InbreedingCoeff=0.2149;LEN=1;LRB=0.37252;LRBP=853.99;MQ0=0;MQ0Fraction=0.0000;MQM=49.706;MQRankSum=-0.051;NF;NR;NS=763;PP;RA=1822;RL=9;RPP=19.36;RR=25;RUN=1;ReadPosRankSum=-2.111;SAB=0.55882;SAF=19;SAP=4.0322;SAR=15;SC=TCGGGGGGCGTGGGGGGGGTG;SRB=0.51098;SRF=931;SRP=4.9172;SRR=891;TC;TR=8;TU=G;VQSLOD=5.7772;set=Intersection;sumGLbyD=7.95 20 57419740 rs11481507 A AT 82613.57 PASS AA=3850;AB=0.41404;ABA=1786;ABP=198.63;ABR=1262;AC=919;AF=0.75328;AN=1220;BL=140665;BR=151383;BVAR;BaseQRankSum=-27.490;DB;DP=31794;DP4=588,585,1571,1721;Dels=0.00;EL=1924;EPP=3.0126;ER=1926;FQ=999;FR;FS=2.191;HETAR=482;HOMA=454;HOMR=135;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;INS;InbreedingCoeff=0.0861;LEN=1;LRB=0.036699;LRBP=857.15;MQ=123.92;MQ0=0;MQ0Fraction=0.0000;MQM=91.654;MQRankSum=3.016;NF;NR;NS=1071;PP;PV4=0.16,1,0.12,1;RA=1850;RL=1874;RPP=8.8784;RR=1976;RUN=1;ReadPosRankSum=-0.685;SAB=0.47636;SAF=1834;SAP=21.693;SAR=2016;SC=TACACTAGTGATTTAACCCTA;SRB=0.49027;SRF=907;SRP=4.5315;SRR=943;TC;TR=3;TU=T;VQSLOD=9.2768;dbSNP=126;set=Intersection;sumGLbyD=22.78 20 57529209 . TA AA,T 1285.20 PASS AA=52;AB=0.89572;ABA=39;ABP=511.72;ABR=335;AC=0;AF=0.0000;AN=694;BL=1317;BR=3667;BVAR;BaseQRankSum=1.788;DEL;DP=8008;Dels=0.00;EL=30;EPP=5.6829;ER=22;FR;HETAR=151;HOMA=83;HOMR=752;HP=7;HR=7;HU=A;InbreedingCoeff=0.1368;LEN=1;LRB=0.47151;LRBP=2409.1;MQ0=0;MQ0Fraction=0.0000;MQM=58.288;MQRankSum=-0.490;NF;NR;NS=987;PP;QD=2.29;RA=2909;RL=4;RPP=83.856;RR=48;RUN=1;ReadPosRankSum=0.513;SAB=0.46154;SAF=24;SAP=3.6784;SAR=28;SB=-361.38;SC=CATAATTTTTTAAAAAAATAG;SRB=0.46855;SRF=1363;SRP=28.009;SRR=1546;TC;TR=7;TU=A;set=filterInVQSR-2of5;sumGLbyD=5.59 20 57558194 . CT C,CTT,CTTT 6470.30 PASS ABR=451;AC=104,161,177;AF=0.08919,0.13808,0.15180;BVAR;BaseQRankSum=1.172;DP=7985;FR;FS=2.202;HOMA=19;HOMR=778;HP=22;HR=15;HU=T;HaplotypeScore=16.1921;INS;InbreedingCoeff=0.6440;MQ=69.24;MQ0=27;MQ0Fraction=0.0109;MQRankSum=-0.003;NF;NR;NS=943;PP;QD=2.22;RA=2531;RUN=1;ReadPosRankSum=-0.104;SB=-2096.85;SC=GCCTTTTTTTCTTTTTTTTTT;SRB=0.34848;SRF=882;SRP=507.73;SRR=1649;TC;TR=15;TU=T;VQSLOD=6.5151;set=Intersection 20 57693627 . AG A 1991.90 PASS AA=52;AB=0.49462;ABA=47;ABP=3.0336;ABR=46;AC=15;AF=0.01227;AN=1222;BL=1902;BR=1478;BVAR;BaseQRankSum=-6.121;DEL;DP=26459;DP4=2647,2873,16,20;Dels=0.01;EL=25;EPP=3.1773;ER=27;FR;FS=3.135;HETAR=15;HOMA=1;HOMR=1064;HP=2;HPLen=3;HR=3;HRun=2;HU=A;INDEL;InbreedingCoeff=0.0866;LEN=1;LRB=0.12544;LRBP=118.51;MQ=116.26;MQ0=0;MQ0Fraction=0.0000;MQM=114.65;MQRankSum=1.942;NF;NR;NS=1080;PP;PV4=0.74,6.9e-08,1,0.38;RA=6781;RL=33;RPP=11.195;RR=19;RUN=1;ReadPosRankSum=-1.795;SAB=0.5;SAF=26;SAP=3.0103;SAR=26;SC=ATTGGAGGAAAGGCTTTTTCA;SRB=0.46247;SRF=3136;SRP=85.976;SRR=3645;TC;TR=3;TU=A;VQSLOD=8.6672;set=Intersection;sumGLbyD=13.55 20 57716287 . A AT 66.47 PASS AC=6;AF=0.00506;AN=1186;BaseQRankSum=1.369;DP=2744;FS=3.834;HRun=8;HaplotypeScore=11.2046;InbreedingCoeff=0.1196;MQ=73.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-0.086;QD=2.14;ReadPosRankSum=-2.588;SB=-53.80;VQSLOD=4.2080;set=VQSR 20 58121928 rs73625057 T TGG 6649.17 PASS AA=132;AB=0.57854;ABA=110;ABP=16.996;ABR=151;AC=57;AF=0.0617;AN=924;BL=4530;BR=4790;BVAR;BaseQRankSum=-13.456;DB;DP=30353;DP4=2107,2168,61,66;Dels=0.00;EL=67;EPP=3.0761;ER=65;FR;FS=0.708;HETAR=46;HOMA=8;HOMR=1023;HP=3;HPLen=2;HR=2;HRun=2;HU=G;INDEL;INS;InbreedingCoeff=0.1241;LEN=2;LRB=0.027897;LRBP=18.76;MQ=109.61;MQ0=1;MQ0Fraction=0.0004;MQM=79.833;MQRankSum=-0.699;NF;NR;NS=1077;PP;PV4=0.79,1,0.49,0.036;RA=5754;RL=61;RPP=4.6554;RR=71;RUN=1;ReadPosRankSum=-3.309;SAB=0.45455;SAF=60;SAP=5.3792;SAR=72;SC=GATTAGAATGTGGATATCTTT;SRB=0.48836;SRF=2810;SRP=9.7866;SRR=2944;TC;TR=4;TU=GT;VQSLOD=8.5770;set=Intersection;sumGLbyD=27.19 20 58287008 . T TC 23.57 PASS AC=1;AF=0.0015;AN=678;BaseQRankSum=1.500;DP=1783;FS=0.000;HRun=1;HaplotypeScore=13.0585;InbreedingCoeff=0.0243;MQ=98.37;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.259;QD=5.43;ReadPosRankSum=1.115;SB=-40.33;VQSLOD=4.9523;set=VQSR 20 58418087 . TAC T 1908.26 PASS AA=64;AB=0.58667;ABA=62;ABP=12.796;ABR=88;AC=24;AF=0.0337;AN=712;BL=2841;BR=2706;BVAR;BaseQRankSum=12.276;DEL;DP=21427;DP4=2243,2398,22,31;Dels=0.03;EL=29;EPP=4.2318;ER=35;FQ=999;FR;FS=0.961;HETAR=21;HOMA=1;HOMR=1050;HP=2;HPLen=1;HR=1;HRun=0;HU=A;INDEL;InbreedingCoeff=0.0008;LEN=2;LRB=0.024337;LRBP=10.145;MQ=93.02;MQ0=0;MQ0Fraction=0.0000;MQM=51.109;MQRankSum=-3.746;NF;NR;NS=1072;PP;PV4=0.34,1.8e-11,2.3e-08,1;RA=6247;RL=37;RPP=6.4032;RR=27;RUN=1;ReadPosRankSum=0.418;SAB=0.4375;SAF=28;SAP=5.1818;SAR=36;SC=AGCCATAGGATACACAAAATC;SRB=0.47911;SRF=2993;SRP=26.689;SRR=3254;TC;TR=5;TU=AC;VQSLOD=10.5463;set=Intersection;sumGLbyD=12.25 20 58468826 . ACAAG A 999 PASS AF=0.0014;AF1=0.003429;BaseQRankSum=4.082;CI95=0.003106,0.006211;DP=8461;DP4=2500,1817,8,2;Dels=0.01;FQ=999;FR;FS=5.034;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0183;MQ=120.69;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.141;NF;NR;PP;PV4=0.21,1,0.054,1;ReadPosRankSum=2.096;SC=ATCCTGAAACACAAGAAGAAA;TC;TR=5;TU=AC;VQSLOD=7.4928;set=Intersection;sumGLbyD=29.17 20 58731262 . TC T 999 PASS AA=21;AB=0.48649;ABA=19;ABP=3.069;ABR=18;AC=7;AF=0.0101;AF1=0.01493;AN=694;BL=939;BR=848;BVAR;BaseQRankSum=4.205;CI95=0.01106,0.02212;DEL;DP=12598;DP4=1766,1428,11,15;Dels=0.01;EL=13;EPP=5.5954;ER=8;FQ=999;FR;FS=1.796;HETAR=8;HOMA=1;HOMR=1031;HP=7;HPLen=8;HR=8;HRun=2;HU=T;INDEL;InbreedingCoeff=-0.0030;LEN=1;LRB=0.050923;LRBP=13.073;MQ=124.57;MQ0=0;MQ0Fraction=0.0000;MQM=67.905;MQRankSum=1.103;NF;NR;NS=1040;PP;PV4=0.23,1,1,1;RA=4884;RL=10;RPP=3.1137;RR=11;RUN=1;ReadPosRankSum=-0.091;SAB=0.47619;SAF=10;SAP=3.1137;SAR=11;SC=TCATTTTTTTTCCTTGAAACT;SRB=0.58006;SRF=2833;SRP=274.9;SRR=2051;TC;TR=8;TU=T;VQSLOD=10.8783;set=Intersection;sumGLbyD=15.11 20 59181229 rs11476579 CTT C,CT,CTTT,CTTTT 7787.17 PASS AC=19,195,104,91;AF=0.01599,0.16414,0.08754,0.07660;AF1=0.2124;AN=1188;BVAR;BaseQRankSum=6.347;CI95=0.146,0.2743;DB;DEL;DP=26140;DP4=932,880,352,375;Dels=0.13;FQ=85.6;FR;FS=11.914;HP=14;HR=14;HRun=14;HU=T;INDEL;INS;InbreedingCoeff=0.4183;MQ=86.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.469;NF;NR;PP;PV4=0.17,1,1,1;RUN=1;ReadPosRankSum=-1.055;SC=GGTGAGAAAGCTTTTTTTTTT;TC;TR=14;TU=T;VQSLOD=7.4340;dbSNP=120;set=Intersection;sumGLbyD=7.02 20 59213979 rs112141381 G GC 9068 PASS AA=131;AB=0.47115;ABA=110;ABP=4.5136;ABR=98;AF=0.0586;AN=700;BL=5395;BR=5816;BVAR;BaseQRankSum=15.453;DB;DP=23381;DP4=2191,2184,71,49;Dels=0.00;EL=66;EPP=3.0269;ER=65;FR;FS=7.907;HETAR=35;HOMA=5;HOMR=1019;HP=2;HPLen=3;HR=3;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0283;LEN=1;LRB=0.037552;LRBP=37.34;MQ=72.13;MQ0=0;MQ0Fraction=0.0000;MQM=54.496;MQRankSum=0.897;NF;NR;NS=1059;PP;PV4=0.052,1,0.066,1;RA=4976;RL=59;RPP=5.8117;RR=72;RUN=1;ReadPosRankSum=-0.811;SAB=0.58015;SAF=76;SAP=10.32;SAR=55;SC=GATGGACTGGGACAGTGACTC;SRB=0.49457;SRF=2461;SRP=4.2828;SRR=2515;TC;TR=3;TU=G;VQSLOD=9.3917;set=Intersection;sumGLbyD=28.58 20 59252945 . CT C,CTT 557.18 PASS AA=24;AB=0.84868;ABA=23;ABP=163.53;ABR=129;AC=21,29;AF=0.01759,0.02429;BL=1217;BR=1336;BVAR;BaseQRankSum=5.135;DP=9970;Dels=0.01;EL=13;EPP=3.3722;ER=11;FS=2.302;HETAR=21;HOMA=1;HOMR=1012;HRun=9;INS;InbreedingCoeff=0.1549;LEN=1;LRB=0.046612;LRBP=15.055;MQ0=0;MQ0Fraction=0.0000;MQM=67.208;MQRankSum=0.086;NS=1034;RA=4421;RL=11;RPP=3.3722;RR=13;RUN=1;ReadPosRankSum=-1.826;SAB=0.41667;SAF=10;SAP=4.4579;SAR=14;SRB=0.49649;SRF=2195;SRP=3.4823;SRR=2226;VQSLOD=2.8923;set=filterInVQSR-2of5;sumGLbyD=5.47 20 60016966 . CT C 42650 PASS AA=37;AB=0.97834;ABA=31;ABP=2847;ABR=1400;AC=15;AF=0.0163;AN=920;BL=2596;BR=778;BVAR;BaseQRankSum=-0.632;DEL;DP=10967;Dels=0.00;EL=14;EPP=7.7641;ER=23;FS=4.094;HETAR=421;HOMA=256;HOMR=385;HRun=1;InbreedingCoeff=-0.0051;LEN=1;LRB=0.53883;LRBP=2130.2;MQ0=0;MQ0Fraction=0.0000;MQM=120.3;MQRankSum=-0.911;NS=1072;RA=3413;RL=31;RPP=39.691;RR=6;RUN=1;ReadPosRankSum=-12.062;SAB=0.48649;SAF=18;SAP=3.069;SAR=19;SRB=0.47407;SRF=1618;SRP=22.943;SRR=1795;VQSLOD=3.3758;set=filterInVQSR-2of5;sumGLbyD=3.27 20 60188651 . AG A 17624.52 PASS AA=462;AB=0.76548;ABA=409;ABP=1070.7;ABR=1335;AC=403;AF=0.34444;AN=1170;BL=13877;BR=25909;BVAR;BaseQRankSum=6.180;DEL;DP=9900;Dels=0.08;EL=353;EPP=282.84;ER=109;FR;FS=2699.057;HETAR=346;HOMA=26;HOMR=633;HP=3;HR=4;HRun=1;HU=A;InbreedingCoeff=-0.2900;LEN=1;LRB=0.30242;LRBP=7904.3;MQ0Fraction=0.0004;MQM=56.119;MQRankSum=1.644;NF;NR;NS=1005;PP;RA=3521;RL=112;RPP=269.25;RR=350;RUN=1;ReadPosRankSum=2.490;SAB=0.0064935;SAF=3;SAP=980.34;SAR=459;SC=AGGCTTCAAAAGAAAAAAAAA;SRB=0.55978;SRF=1971;SRP=112.32;SRR=1550;TC;TR=4;TU=A;VQSLOD=-34.0667;set=filterInVQSR-2of5;sumGLbyD=7.81 20 60195570 . GTACATACATACA ATACATACATACA,G,GTACATACA 20140 PASS ABR=102;AC=105,2;AF=0.08794,0.00168;AN=1194;BVAR;BaseQRankSum=-28.899;DB;DEL;DP=14347;Dels=0.02;FR;FS=52.125;HOMA=1;HOMR=1006;HP=1;HPLen=1;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0695;MQ0Fraction=0.0007;MQRankSum=1.957;NF;NR;NS=1035;PP;RA=4759;RUN=1;ReadPosRankSum=-22.252;SAB=0.5;SAP=3.0103;SC=TGATAGATTCGTACATACATA;SRB=0.47615;SRF=2266;SRP=26.522;SRR=2493;TC;TR=21;TU=ACAT;VQSLOD=2.7673;set=filterInVQSR-2of5;sumGLbyD=19.14 20 60670601 rs72127450 AT A,ATT 6401.59 PASS AC=177,79;AF=0.16239,0.07248;AF1=0.1602;AN=1090;BVAR;BaseQRankSum=8.618;CI95=0.1106,0.2058;DB;DEL;DP=17508;DP4=1285,1094,313,259;Dels=0.10;FQ=94.1;FR;FS=0.000;HP=12;HR=12;HRun=12;HU=T;INDEL;INS;InbreedingCoeff=0.1076;LEN=1;MQ=64.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.620;NF;NR;PP;PV4=0.78,1,0.012,1;RUN=1;ReadPosRankSum=-1.294;SC=AGCCAGGCACATTTTTTTTTT;TC;TR=12;TU=T;VQSLOD=6.1650;dbSNP=130;set=Intersection;sumGLbyD=5.80 20 60685780 . TC T 1123.58 PASS AC=79;AF=0.07655;AN=1032;BaseQRankSum=14.949;DP=2084;FS=23.521;HRun=1;HaplotypeScore=19.7117;InbreedingCoeff=0.1356;MQ=53.57;MQ0=61;MQ0Fraction=0.0293;MQRankSum=-7.958;QD=4.35;ReadPosRankSum=-13.757;SB=-791.28;VQSLOD=6.3549;set=VQSR 20 60744906 rs113528167 CG C 422.53 PASS AC=48;AF=0.0732;AN=656;BaseQRankSum=17.669;DB;DP=1189;FS=0.356;HRun=1;HaplotypeScore=15.1808;InbreedingCoeff=0.2111;MQ=82.83;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-10.455;QD=2.71;ReadPosRankSum=-16.887;SB=-326.46;VQSLOD=7.1707;set=VQSR 20 60848742 . CGT C,CGTGT 999 PASS AF=0.00980,0.01225;BaseQRankSum=5.597;DP=17065;DP4=1928,2188,17,13;Dels=0.01;FR;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.2094;MQ=115.78;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.281;NF;NR;PP;PV4=0.36,0.4,0.12,0.12;ReadPosRankSum=-1.465;SB=-157.35;SC=TAGACGCTTCCGTGTGTGTGT;TC;TR=11;TU=GT;VQSLOD=1.7100;set=filterInVQSR-2of5;sumGLbyD=16.39 20 61023668 rs57452309 G GAGC 6896.67 PASS AC=115;AF=0.1445;AN=796;BaseQRankSum=12.146;DB;DP=1423;FS=5.070;HRun=0;HaplotypeScore=29.8897;InbreedingCoeff=0.0740;MQ=77.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-9.005;QD=19.16;ReadPosRankSum=-17.440;SB=-3045.82;VQSLOD=4.5788;set=VQSR 20 61180519 . C CA,CT 1774.30 PASS ABR=135;AC=27,15;AF=0.02538,0.01410;BVAR;BaseQRankSum=-2.189;DP=8393;FR;FS=27.692;HOMA=2;HOMR=825;HP=6;HPLen=3;HR=3;HU=T;HaplotypeScore=19.5313;INS;InbreedingCoeff=0.0868;LEN=1;MQ=56.11;MQ0=172;MQ0Fraction=0.0667;MQRankSum=2.605;NF;NR;NS=854;PP;QD=1.99;RA=2868;RUN=1;ReadPosRankSum=-7.324;SB=-385.54;SC=TTCTTTCTTTCTTTCTTTCTT;SRB=0.32741;SRF=939;SRP=745.08;SRR=1929;TC;TR=69;TU=CTTT;VQSLOD=3.4398;set=filterInVQSR-2of5 20 61184281 . AC A 9798.10 PASS AA=24;AB=0.96507;ABA=16;ABP=863.43;ABR=442;AC=4;AF=0.00341;AN=1174;BL=349;BR=1039;BVAR;BaseQRankSum=2.048;DEL;DP=10073;Dels=0.00;EL=11;EPP=3.3722;ER=13;FS=2.097;HETAR=141;HOMA=69;HOMR=829;HRun=1;InbreedingCoeff=0.0697;LEN=1;LRB=0.49712;LRBP=747.85;MQ0=0;MQ0Fraction=0.0000;MQM=98.042;MQRankSum=1.881;NS=1042;RA=3625;RL=5;RPP=20.744;RR=19;RUN=1;ReadPosRankSum=-8.009;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SRB=0.52662;SRF=1909;SRP=25.323;SRR=1716;VQSLOD=1.8117;set=filterInVQSR-2of5;sumGLbyD=5.55 20 62067246 . T TCGA 60869.60 PASS AC=1024;AF=0.88889;AN=1152;BaseQRankSum=17.328;DP=2144;FS=2.378;HRun=0;HaplotypeScore=22.0069;InbreedingCoeff=0.1400;MQ=86.75;MQ0=6;MQ0Fraction=0.0028;MQRankSum=-5.536;QD=29.45;ReadPosRankSum=1.266;SB=-24220.18;VQSLOD=6.4647;set=VQSR 20 62074219 . C CTAT,CTGT 2328 PASS ABR=99;AC=20,6;AF=0.01754,0.00526;BVAR;BaseQRankSum=11.221;DP=9498;DS;FS=4.510;HOMA=15;HOMR=645;HaplotypeScore=82.8868;INS;InbreedingCoeff=0.0880;LEN=3;MQ=29.88;MQ0=1378;MQ0Fraction=0.2286;MQRankSum=-5.309;NS=689;QD=0.77;RA=1679;RUN=1;ReadPosRankSum=-3.510;SAR=1;SB=-93.21;SRB=0.70697;SRF=1187;SRP=627.71;SRR=492;VQSLOD=1.8325;set=filterInVQSR-2of5 20 62304449 . CA C,CAA 6680.17 PASS AC=141,69;AF=0.12567,0.06150;AF1=0.08178;AN=1122;BVAR;BaseQRankSum=9.754;CI95=0.05088,0.1128;DEL;DP=15867;DP4=1252,1289,232,208;Dels=0.10;FQ=52.6;FR;FS=6.576;HP=11;HR=11;HRun=11;HU=A;INDEL;INS;InbreedingCoeff=0.1950;LEN=1;MQ=60.48;MQ0Fraction=0.0004;MQRankSum=-0.049;NF;NR;PP;PV4=0.2,1,1,1;RUN=1;ReadPosRankSum=-2.137;SC=GATTCTGTGTCAAAAAAAAAA;TC;TR=11;TU=A;VQSLOD=7.4714;set=Intersection;sumGLbyD=8.36 20 62804895 rs57769591 CCTT C 1148 PASS AC=8;AF=0.0085;AF1=0.002839;AN=938;BaseQRankSum=4.952;CI95=0.002212,0.006637;DB;DP=8889;DP4=2574,1668,4,8;FQ=12.3;FS=2.289;HPLen=3;HRun=0;HaplotypeScore=29.4184;INDEL;InbreedingCoeff=-0.0270;MQ0=876;MQ0Fraction=0.2674;MQRankSum=-0.641;PV4=0.074,1,1,1;QD=1.03;ReadPosRankSum=0.118;SB=-65.30;VQSLOD=6.4881;dbSNP=126;set=Intersection 20 62907688 . AAT A 6629.57 PASS AC=164;AF=0.13735;AN=1194;BaseQRankSum=27.368;DP=2746;FS=5.985;HRun=0;HaplotypeScore=14.7748;InbreedingCoeff=0.1433;MQ=96.65;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.318;QD=10.81;ReadPosRankSum=0.789;SB=-2662.16;VQSLOD=6.1473;set=VQSR 20 62952465 . G GT 9149.70 PASS AA=156;AB=0.66667;ABA=110;ABP=82.631;ABR=220;AC=8;AF=0.00768;AN=1042;BL=6618;BR=3296;BVAR;BaseQRankSum=-0.466;DP=6244;Dels=0.00;EL=70;EPP=6.5737;ER=86;FS=2.927;HETAR=88;HOMA=34;HOMR=664;HRun=0;INS;InbreedingCoeff=0.0711;LEN=1;LRB=0.33508;LRBP=2420.2;MQ0Fraction=0.0431;MQM=29.506;MQRankSum=-3.251;NS=786;RA=1722;RL=146;RPP=260.47;RR=10;RUN=1;ReadPosRankSum=-2.554;SAB=0.47436;SAF=74;SAP=3.9012;SAR=82;SRB=0.50523;SRF=870;SRP=3.4189;SRR=852;VQSLOD=6.1217;set=Intersection;sumGLbyD=16.58 pysam-0.23.0/tests/tabix_data/vcf/18.vcf000066400000000000000000002723361475062545500177270ustar00rootroot00000000000000##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT DNA_pool_A chr1 1281168 . A G 14 . DP=37;AF1=0.6243;CI95=0.5,1;DP4=4,0,6,0;MQ=15;PV4=1,0.027,1,1 PL:GT:GQ 43,0,4:0/1:6 chr1 1281205 . T C 26 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 58,9,0:1/1:63 chr1 1281206 . G C 25 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 57,9,0:1/1:63 chr1 1922737 . G C 13.2 . DP=21;AF1=1;CI95=1,1;DP4=0,0,0,21;MQ=22 PL:GT:GQ 46,63,0:1/1:99 chr1 21197513 . A G 55.1 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=41 PL:GT:GQ 88,21,0:1/1:84 chr1 21343209 . T C 5.45 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=14 PL:GT:GQ 37,51,0:1/1:99 chr1 22097362 . T C 4.75 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 35,9,0:1/1:63 chr1 22254012 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 22650927 . G A 48.1 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=24 PL:GT:GQ 81,21,0:1/1:84 chr1 23535401 . C T 40.4 . DP=25;AF1=1;CI95=0.5,1;DP4=0,16,0,5;MQ=19;PV4=1,0.2,1,1 PL:GT:GQ 73,13,0:1/1:65 chr1 23543855 . T C 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44 PL:GT:GQ 82,18,0:1/1:90 chr1 24245107 . C G 32 . DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,1,1 PL:GT:GQ 62,0,35:0/1:38 chr1 24274412 . G C 39.5 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=32 PL:GT:GQ 72,12,0:1/1:72 chr1 36529832 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr1 37788090 . A G 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr1 43120440 . C T 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=49;PV4=1,1,1,1 PL:GT:GQ 64,0,31:0/1:34 chr1 43980466 . C T 43 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=19 PL:GT:GQ 76,45,0:1/1:99 chr1 46047795 . T C 29.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=31 PL:GT:GQ 62,18,0:1/1:90 chr1 48860309 . C T 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=46 PL:GT:GQ 141,18,0:1/1:90 chr1 49415599 . T C 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 34,6,0:1/1:49 chr1 51601816 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 51955459 . G C 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr1 68479569 . T G 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 43,6,0:1/1:49 chr1 69032455 . A G 15.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 47,9,0:1/1:63 chr1 71888225 . G T 9.31 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr1 72381528 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr1 82004013 . A G 37.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 70,12,0:1/1:72 chr1 86289622 . C T 18 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 50,9,0:1/1:63 chr1 90267663 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45 PL:GT:GQ 54,9,0:1/1:63 chr1 92699542 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr1 94867317 . G A 26.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 58,6,0:1/1:49 chr1 96428713 . C G 3.98 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=27 PL:GT:GQ 33,6,0:1/1:49 chr1 100466329 . G C 4.85 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=22 PL:GT:GQ 36,18,0:1/1:90 chr1 101909281 . G A 70 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=46;PV4=1,1,0.096,1 PL:GT:GQ 100,0,88:0/1:91 chr1 106216572 . T A 22 . DP=18;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=21 PL:GT:GQ 55,48,0:1/1:99 chr1 107901770 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 40,6,0:1/1:49 chr1 108431179 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=41 PL:GT:GQ 155,24,0:1/1:96 chr1 112005344 . C T 99 . DP=52;AF1=1;CI95=1,1;DP4=7,0,27,0;MQ=44;PV4=1,1,1,1 PL:GT:GQ 196,25,0:1/1:99 chr1 116625452 . C T 36 . DP=44;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,20;MQ=49;PV4=1,2.3e-69,0.42,1 PL:GT:GQ 66,0,179:0/1:69 chr1 118060710 . G T 6.98 . DP=8;AF1=0.4999;CI95=0.5,0.5;DP4=4,0,3,0;MQ=47;PV4=1,0.0071,1,1 PL:GT:GQ 36,0,73:0/1:39 chr1 118198177 . A G 15.9 . DP=23;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 47,6,0:1/1:49 chr1 118586346 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr1 120809555 . G A 20 . DP=8;AF1=0.5;CI95=0.5,0.5;DP4=6,0,2,0;MQ=46;PV4=1,1,1,1 PL:GT:GQ 50,0,106:0/1:53 chr1 130723110 . C A 20.7 . DP=8;AF1=0.5939;CI95=0.5,1;DP4=0,6,0,2;MQ=26;PV4=1,1,1,1 PL:GT:GQ 50,0,5:0/1:7 chr1 133979895 . T C 14.9 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 46,6,0:1/1:49 chr1 134977940 . C T 30 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,1,0.26,1 PL:GT:GQ 60,0,31:0/1:34 chr1 141768589 . G A 18.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=4,0,4,0;MQ=51;PV4=1,2.7e-05,1,1 PL:GT:GQ 48,0,100:0/1:51 chr1 141768590 . G A 22 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=2,0,4,0;MQ=50;PV4=1,0.0033,1,1 PL:GT:GQ 52,0,40:0/1:43 chr1 146506051 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43 PL:GT:GQ 76,9,0:1/1:63 chr1 150997009 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr1 162915612 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 168455400 . A G 4.12 . DP=28;AF1=1;CI95=1,1;DP4=0,0,0,27;MQ=10 PL:GT:GQ 35,81,0:1/1:99 chr1 172784744 . T C 17.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 49,6,0:1/1:49 chr1 183627307 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 185789457 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr1 187081827 . T C 4.77 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=17 PL:GT:GQ 36,30,0:1/1:99 chr1 188468339 . C T 33 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=24 PL:GT:GQ 66,39,0:1/1:99 chr1 188595435 . C T 41.8 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr1 188670561 . G C 3.55 . DP=22;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=18 PL:GT:GQ 34,27,0:1/1:99 chr1 188924877 . G A 6.2 . DP=10;AF1=0.9999;CI95=0.5,1;DP4=2,0,3,0;MQ=21;PV4=1,1,1,0.3 PL:GT:GQ 35,3,0:1/1:41 chr1 190536295 . G A 68 . DP=38;AF1=1;CI95=1,1;DP4=0,0,36,0;MQ=18 PL:GT:GQ 101,108,0:1/1:99 chr1 191129408 . T A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr1 195937816 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr1 198857619 . T C 89 . DP=61;AF1=0.5;CI95=0.5,0.5;DP4=0,38,0,17;MQ=30;PV4=1,0.032,1,1 PL:GT:GQ 119,0,139:0/1:99 chr1 199057483 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 44,6,0:1/1:49 chr1 200133619 . G C 5.83 . DP=49;AF1=1;CI95=0.5,1;DP4=2,0,8,0;MQ=17;PV4=1,0.059,1,0.2 PL:GT:GQ 37,12,0:1/1:72 chr1 200729661 . A T 36 . DP=15;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=27 PL:GT:GQ 69,42,0:1/1:99 chr1 201374519 . T C 69.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39 PL:GT:GQ 102,12,0:1/1:72 chr1 202811668 . G A 20.2 . DP=4;AF1=0.5163;CI95=0.5,1;DP4=0,1,0,3;MQ=24;PV4=1,1,1,1 PL:GT:GQ 50,0,12:0/1:15 chr1 202960650 . C T 16.6 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27 PL:GT:GQ 49,12,0:1/1:72 chr1 205686638 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr1 205949857 . A G 3.14 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=21 PL:GT:GQ 33,15,0:1/1:75 chr1 209806643 . A G 13.2 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=21 PL:GT:GQ 46,24,0:1/1:96 chr1 209871501 . C T 25 . DP=12;AF1=0.5;CI95=0.5,0.5;DP4=5,0,4,0;MQ=41;PV4=1,7.7e-06,1,1 PL:GT:GQ 55,0,84:0/1:58 chr1 211051323 . G A 99 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=49 PL:GT:GQ 176,24,0:1/1:96 chr1 211389716 . C T 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 43,6,0:1/1:49 chr1 211868415 . G A 3.54 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=14 PL:GT:GQ 34,33,0:1/1:99 chr1 211914531 . C T 84.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=46;PV4=1,1,1,1 PL:GT:GQ 116,7,0:1/1:57 chr1 214691313 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr1 215184650 . C T 40.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 72,6,0:1/1:49 chr1 215995258 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr1 217031394 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 217986960 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 76,9,0:1/1:63 chr1 218086681 . A G 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34 PL:GT:GQ 142,27,0:1/1:99 chr1 218546019 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 218632417 . G T 17.1 . DP=19;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=26 PL:GT:GQ 50,21,0:1/1:84 chr1 218833355 . C G 23 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=5,0,2,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 53,0,63:0/1:56 chr1 219303186 . T C 7.79 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=12 PL:GT:GQ 40,75,0:1/1:99 chr1 219517634 . G A 26.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42 PL:GT:GQ 59,12,0:1/1:72 chr1 219590158 . T C 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 33,12,0:1/1:72 chr1 219709853 . A T 99 . DP=124;AF1=0.5;CI95=0.5,0.5;DP4=80,0,41,0;MQ=44;PV4=1,0.26,1,1 PL:GT:GQ 143,0,156:0/1:99 chr1 222457988 . A G 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23 PL:GT:GQ 42,6,0:1/1:49 chr1 222477914 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr1 223010233 . A G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr1 223796360 . G A 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=21 PL:GT:GQ 37,6,0:1/1:49 chr1 224273784 . A T 14.2 . DP=18;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=15 PL:GT:GQ 47,30,0:1/1:99 chr1 224454685 . C T 46.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32 PL:GT:GQ 79,15,0:1/1:75 chr1 224514706 . G C 21 . DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=19 PL:GT:GQ 54,114,0:1/1:99 chr1 224515793 . C T 99 . DP=26;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=45 PL:GT:GQ 211,78,0:1/1:99 chr1 224692969 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 40,6,0:1/1:49 chr1 225607249 . A G 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,1,0,1 PL:GT:GQ 64,0,31:0/1:34 chr1 226923918 . C A 29.1 . DP=52;AF1=1;CI95=0.5,1;DP4=0,2,0,10;MQ=27;PV4=1,1,1,1 PL:GT:GQ 62,18,0:1/1:90 chr1 227125189 . T C 56.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=41 PL:GT:GQ 89,12,0:1/1:72 chr1 227133712 . A T 20.1 . DP=26;AF1=0.5;CI95=0.5,0.5;DP4=11,0,10,0;MQ=23;PV4=1,1,0.48,1 PL:GT:GQ 50,0,39:0/1:42 chr1 227943954 . G C 47 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37 PL:GT:GQ 79,9,0:1/1:63 chr1 227943974 . G A 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34 PL:GT:GQ 66,12,0:1/1:72 chr1 228067480 . A G 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45 PL:GT:GQ 75,15,0:1/1:75 chr1 228067510 . A G 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45 PL:GT:GQ 140,15,0:1/1:75 chr1 228088778 . C T 6.79 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23 PL:GT:GQ 37,6,0:1/1:49 chr1 228117888 . A C 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 45,6,0:1/1:49 chr1 228139641 . T C 44.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 77,12,0:1/1:72 chr1 228577146 . T C 26 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,14;MQ=22;PV4=1,1,1,0.027 PL:GT:GQ 56,0,77:0/1:59 chr1 229001369 . C A 45 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 77,9,0:1/1:63 chr1 229001386 . C T 8.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 39,6,0:1/1:49 chr1 229348080 . T C 18.1 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=40;PV4=1,0.33,0.17,0.33 PL:GT:GQ 48,0,31:0/1:34 chr1 229439710 . C T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=32 PL:GT:GQ 66,12,0:1/1:72 chr1 229655149 . T C 30 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=30 PL:GT:GQ 63,24,0:1/1:96 chr1 229660873 . C G 81 . DP=28;AF1=0.5;CI95=0.5,0.5;DP4=0,20,0,7;MQ=36;PV4=1,1,1,1 PL:GT:GQ 111,0,120:0/1:99 chr2a 3661005 . C G 24 . DP=13;AF1=0.5001;CI95=0.5,0.5;DP4=7,0,4,0;MQ=27;PV4=1,1.1e-05,1,1 PL:GT:GQ 54,0,34:0/1:37 chr2a 4140063 . G A 81 . DP=26;AF1=0.6671;CI95=0.5,1;DP4=18,0,8,0;MQ=24;PV4=1,8.3e-09,1,1 PL:GT:GQ 110,0,3:0/1:5 chr2a 4248440 . T C 20 . DP=28;AF1=0.5;CI95=0.5,0.5;DP4=11,0,7,0;MQ=25;PV4=1,1,0.47,1 PL:GT:GQ 50,0,92:0/1:53 chr2a 4707656 . A G 63 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 95,9,0:1/1:63 chr2a 5194801 . G A 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=24 PL:GT:GQ 38,6,0:1/1:49 chr2a 14111103 . A G 7.84 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=20 PL:GT:GQ 40,21,0:1/1:84 chr2a 17799746 . A G 11.3 . DP=5;AF1=0.5001;CI95=0.5,0.5;DP4=0,3,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 41,0,35:0/1:37 chr2a 24728910 . G A 45.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28 PL:GT:GQ 78,15,0:1/1:75 chr2a 29627939 . G T 5.44 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=27 PL:GT:GQ 36,9,0:1/1:63 chr2a 31373164 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr2a 33935228 . T C 41.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr2a 36311856 . G A 99 . DP=30;AF1=1;CI95=1,1;DP4=0,0,0,29;MQ=44 PL:GT:GQ 213,87,0:1/1:99 chr2a 39281204 . T C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr2a 41087565 . C T 74.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=38 PL:GT:GQ 107,12,0:1/1:72 chr2a 45574768 . C A 11.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=18 PL:GT:GQ 43,9,0:1/1:63 chr2a 55464464 . T C 26.1 . DP=7;AF1=0.9966;CI95=0.5,1;DP4=5,0,2,0;MQ=26;PV4=1,1,1,1 PL:GT:GQ 55,1,0:1/1:23 chr2a 63107673 . T A 70.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34 PL:GT:GQ 103,12,0:1/1:72 chr2a 63141732 . A T 22.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 54,6,0:1/1:49 chr2a 63141910 . G A 3.41 . DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr2a 63141911 . C T 9.55 . DP=16;AF1=0.5031;CI95=0.5,0.5;DP4=0,2,0,3;MQ=33;PV4=1,0.43,1,1 PL:GT:GQ 39,0,19:0/1:22 chr2a 63143543 . C T 28 . DP=18;AF1=1;CI95=1,1;DP4=0,1,0,17;MQ=16;PV4=1,1,1,1 PL:GT:GQ 61,42,0:1/1:99 chr2a 66419805 . G A 3.69 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 34,15,0:1/1:75 chr2a 66563922 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr2a 67719136 . C T 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 71,6,0:1/1:49 chr2a 72781453 . A C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr2a 76733211 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr2a 78190502 . A C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr2a 85021209 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr2a 88554861 . A T 39 . DP=74;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=46;PV4=1,1,1,1 PL:GT:GQ 69,0,92:0/1:72 chr2a 88554877 . A G 92 . DP=90;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,13;MQ=41;PV4=1,0.3,1,1 PL:GT:GQ 122,0,128:0/1:99 chr2a 88824857 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr2a 93546675 . C T 26 . DP=6;AF1=0.5;CI95=0.5,0.5;DP4=4,0,2,0;MQ=46;PV4=1,1,1,1 PL:GT:GQ 56,0,87:0/1:59 chr2a 94788853 . A G 34.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 67,15,0:1/1:75 chr2a 96738146 . T C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr2a 102737384 . A G 12.3 . DP=18;AF1=1;CI95=1,1;DP4=0,0,18,0;MQ=11 PL:GT:GQ 45,54,0:1/1:99 chr2a 103407172 . A G 35 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=19 PL:GT:GQ 68,24,0:1/1:96 chr2a 105774580 . T G 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=30 PL:GT:GQ 135,39,0:1/1:99 chr2a 106376301 . C G 24.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19 PL:GT:GQ 57,18,0:1/1:90 chr2a 106376315 . C T 8.75 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19 PL:GT:GQ 41,18,0:1/1:90 chr2a 112422267 . C T 30 . DP=20;AF1=0.5;CI95=0.5,0.5;DP4=14,0,5,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 60,0,131:0/1:63 chr2b 3049384 . A C 14.9 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 3049385 . G C 14.9 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 3049406 . C G 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=36 PL:GT:GQ 135,18,0:1/1:90 chr2b 4213802 . T C 89.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr2b 5022895 . G A 66 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=49 PL:GT:GQ 99,30,0:1/1:99 chr2b 6037666 . G T 56 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=17 PL:GT:GQ 89,39,0:1/1:99 chr2b 13656952 . G A 19.2 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=21 PL:GT:GQ 52,18,0:1/1:90 chr2b 15026944 . A G 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 37,6,0:1/1:49 chr2b 23362613 . A G 5.64 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 37,15,0:1/1:75 chr2b 45947861 . C G 68 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=50 PL:GT:GQ 101,33,0:1/1:99 chr2b 46597824 . T C 65.6 . DP=39;AF1=0.5939;CI95=0.5,1;DP4=23,0,10,0;MQ=22;PV4=1,0.014,1,1 PL:GT:GQ 95,0,5:0/1:7 chr2b 49665191 . G T 34.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37 PL:GT:GQ 67,21,0:1/1:84 chr2b 61001546 . A G 48 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=26 PL:GT:GQ 81,24,0:1/1:96 chr2b 88502851 . T C 4.77 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=37;PV4=1,1,0.46,1 PL:GT:GQ 33,0,34:0/1:33 chr2b 91675431 . C T 30 . DP=14;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=27 PL:GT:GQ 63,24,0:1/1:96 chr2b 91870148 . T G 67 . DP=14;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=47;PV4=1,1,1,1 PL:GT:GQ 100,31,0:1/1:99 chr2b 97066826 . G A 20.1 . DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=0,6,0,2;MQ=31;PV4=1,1,1,1 PL:GT:GQ 50,0,35:0/1:38 chr2b 97670822 . G A 4.85 . DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=18 PL:GT:GQ 36,18,0:1/1:90 chr2b 102773175 . A G 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 49,9,0:1/1:63 chr2b 109805532 . T C 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=45 PL:GT:GQ 176,24,0:1/1:96 chr2b 110841448 . A G 11.1 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 42,6,0:1/1:49 chr2b 123217025 . T C 31.5 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=37 PL:GT:GQ 64,12,0:1/1:72 chr2b 123263214 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 43,9,0:1/1:63 chr2b 127747292 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=52 PL:GT:GQ 100,9,0:1/1:63 chr2b 130121958 . A G 89.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 122,15,0:1/1:75 chr2b 130253633 . A G 14.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 130692761 . C T 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=51 PL:GT:GQ 82,18,0:1/1:90 chr2b 130743365 . A G 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42 PL:GT:GQ 140,15,0:1/1:75 chr2b 131553874 . A C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37 PL:GT:GQ 43,9,0:1/1:63 chr2b 131716894 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40 PL:GT:GQ 137,24,0:1/1:96 chr2b 131716936 . G A 99 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=36 PL:GT:GQ 173,36,0:1/1:99 chr2b 131716952 . A G 99 . DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,14;MQ=36;PV4=1,1,1,1 PL:GT:GQ 152,0,43:0/1:46 chr2b 133360184 . C T 99 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,20;MQ=32 PL:GT:GQ 163,60,0:1/1:99 chr2b 133644741 . T A 16.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=27 PL:GT:GQ 49,15,0:1/1:75 chr2b 133720595 . T C 41 . DP=15;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=29 PL:GT:GQ 74,36,0:1/1:99 chr2b 133727192 . C T 19.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 52,15,0:1/1:75 chr2b 133727260 . G A 3.56 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18 PL:GT:GQ 34,24,0:1/1:95 chr2b 133800294 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=23 PL:GT:GQ 40,6,0:1/1:49 chr2b 134582754 . A C 56.1 . DP=37;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=36 PL:GT:GQ 89,21,0:1/1:84 chr2b 134582763 . G C 78 . DP=37;AF1=1;CI95=1,1;DP4=0,0,0,36;MQ=34 PL:GT:GQ 111,108,0:1/1:99 chr2b 134809668 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr3 527814 . C G 46 . DP=9;AF1=0.5;CI95=0.5,0.5;DP4=6,0,3,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 76,0,106:0/1:79 chr3 559510 . G A 38 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=10,0,17,0;MQ=28;PV4=1,1,0.014,1 PL:GT:GQ 68,0,111:0/1:71 chr3 879433 . T G 32 . DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 62,0,34:0/1:37 chr3 1809645 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr3 3235812 . C T 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 38,6,0:1/1:49 chr3 3250176 . A G 83 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=32 PL:GT:GQ 116,24,0:1/1:96 chr3 5049073 . T A 99 . DP=25;AF1=0.5;CI95=0.5,0.5;DP4=16,0,9,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 136,0,129:0/1:99 chr3 5142874 . G A 99 . DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=28 PL:GT:GQ 179,114,0:1/1:99 chr3 5554864 . T C 3.54 . DP=7;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,3;MQ=27;PV4=1,1,1,1 PL:GT:GQ 31,0,35:0/1:33 chr3 5749648 . G A 21.2 . DP=26;AF1=0.7303;CI95=0.5,1;DP4=0,7,0,7;MQ=26;PV4=1,0.16,1,0.17 PL:GT:GQ 50,0,2:0/1:3 chr3 16451708 . A T 71.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38 PL:GT:GQ 104,15,0:1/1:75 chr3 23410276 . G A 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 140,15,0:1/1:75 chr3 51368824 . A G 28 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 60,9,0:1/1:63 chr3 53000453 . A G 54 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19 PL:GT:GQ 87,30,0:1/1:99 chr3 53000463 . A G 54 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19 PL:GT:GQ 87,30,0:1/1:99 chr3 59077423 . C T 77.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=33 PL:GT:GQ 110,15,0:1/1:75 chr3 60040501 . T C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 43,9,0:1/1:63 chr3 64203481 . A G 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 66,12,0:1/1:72 chr3 67947441 . C T 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr3 76372631 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 76,9,0:1/1:63 chr3 80611316 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr3 81554381 . G T 17.6 . DP=24;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26 PL:GT:GQ 50,12,0:1/1:72 chr3 87614647 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr3 93900455 . A T 11.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=13 PL:GT:GQ 44,15,0:1/1:75 chr3 96174457 . A G 4.11 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=24 PL:GT:GQ 34,9,0:1/1:63 chr3 96215569 . A C 3.41 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr3 96587998 . A C 7.08 . DP=9;AF1=1;CI95=1,1;DP4=0,0,6,0;MQ=17 PL:GT:GQ 39,18,0:1/1:90 chr3 99711220 . A C 12.8 . DP=11;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 42,2,0:1/1:37 chr3 99789741 . C G 99 . DP=18;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=47 PL:GT:GQ 210,51,0:1/1:99 chr3 103667651 . A C 3.98 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 33,6,0:1/1:49 chr3 104604896 . G C 55 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 87,9,0:1/1:63 chr3 104997217 . G A 33.1 . DP=18;AF1=1;CI95=1,1;DP4=1,0,16,0;MQ=34;PV4=1,3e-10,0.17,0.36 PL:GT:GQ 66,19,0:1/1:76 chr3 106097816 . A G 28 . DP=15;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=26 PL:GT:GQ 61,45,0:1/1:99 chr3 106822259 . G C 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=50 PL:GT:GQ 140,15,0:1/1:75 chr3 109946413 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 44,6,0:1/1:49 chr3 121238963 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr3 126248567 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 45,6,0:1/1:49 chr3 129733836 . A G 6.2 . DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.02,0.31,1 PL:GT:GQ 35,0,28:0/1:30 chr3 131372785 . C T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=34 PL:GT:GQ 76,9,0:1/1:63 chr3 132290987 . C T 22 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=45 PL:GT:GQ 54,9,0:1/1:63 chr3 136054421 . C T 73 . DP=82;AF1=1;CI95=1,1;DP4=0,0,78,0;MQ=28 PL:GT:GQ 106,235,0:1/1:99 chr3 141075246 . G A 30.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41 PL:GT:GQ 62,6,0:1/1:49 chr3 141075262 . T G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41 PL:GT:GQ 73,6,0:1/1:49 chr3 141430649 . G T 81.8 . DP=6;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=41;PV4=1,0.34,1,0.25 PL:GT:GQ 113,6,0:1/1:49 chr3 143617747 . G T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 54,9,0:1/1:63 chr3 163576128 . C T 5.6 . DP=4;AF1=0.7302;CI95=0.5,1;DP4=2,0,2,0;MQ=23;PV4=1,1,1,1 PL:GT:GQ 33,0,2:0/1:3 chr3 163839828 . A G 4.45 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26 PL:GT:GQ 35,12,0:1/1:72 chr3 175839340 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr3 190193258 . G T 3.98 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 33,6,0:1/1:49 chr3 190777007 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr3 190970350 . A G 61 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=37 PL:GT:GQ 94,30,0:1/1:99 chr3 198686408 . G A 36.6 . DP=17;AF1=1;CI95=0.5,1;DP4=0,1,0,16;MQ=25;PV4=1,1,0.026,1 PL:GT:GQ 69,11,0:1/1:66 chr3 199277478 . T C 3.61 . DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=21 PL:GT:GQ 34,18,0:1/1:90 chr3 199780181 . G T 77 . DP=45;AF1=0.5;CI95=0.5,0.5;DP4=0,35,0,10;MQ=33;PV4=1,1,1,1 PL:GT:GQ 107,0,114:0/1:99 chr3 199889335 . A C 9.54 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18 PL:GT:GQ 42,24,0:1/1:96 chr3 200018161 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr4 195475 . A G 13 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 44,6,0:1/1:49 chr4 639141 . C A 14.9 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr4 639152 . C T 15.2 . DP=17;AF1=0.5016;CI95=0.5,0.5;DP4=0,2,0,2;MQ=33;PV4=1,1,1,1 PL:GT:GQ 45,0,22:0/1:25 chr4 986497 . G T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=33 PL:GT:GQ 163,30,0:1/1:99 chr4 986516 . C T 55.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37 PL:GT:GQ 88,21,0:1/1:84 chr4 1207485 . A C 14.9 . DP=22;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 46,6,0:1/1:49 chr4 1323502 . G A 13.2 . DP=13;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=22 PL:GT:GQ 46,33,0:1/1:99 chr4 1613521 . G A 89 . DP=16;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=32 PL:GT:GQ 122,48,0:1/1:99 chr4 1748790 . C T 38 . DP=21;AF1=0.5005;CI95=0.5,0.5;DP4=6,0,8,0;MQ=40;PV4=1,0.09,1,1 PL:GT:GQ 68,0,27:0/1:30 chr4 2255732 . T C 99 . DP=29;AF1=1;CI95=1,1;DP4=0,0,28,0;MQ=31 PL:GT:GQ 186,84,0:1/1:99 chr4 3010159 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr4 3545023 . A G 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=38 PL:GT:GQ 145,27,0:1/1:99 chr4 3586344 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr4 3879337 . A G 16.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 49,12,0:1/1:72 chr4 3940733 . A G 47.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 80,15,0:1/1:75 chr4 4410338 . T C 13.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31 PL:GT:GQ 46,15,0:1/1:75 chr4 4796408 . T C 41 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=17 PL:GT:GQ 74,48,0:1/1:99 chr4 4796414 . A G 11.3 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=17 PL:GT:GQ 44,45,0:1/1:99 chr4 6436959 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr4 9494256 . T C 3.41 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37 PL:GT:GQ 32,6,0:1/1:49 chr4 24881479 . G A 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 46,9,0:1/1:63 chr4 26128644 . A G 23 . DP=18;AF1=0.5006;CI95=0.5,0.5;DP4=8,0,10,0;MQ=22;PV4=1,1,1,1 PL:GT:GQ 53,0,26:0/1:29 chr4 42109100 . G A 17.1 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 49,9,0:1/1:63 chr4 42309652 . C T 68 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr4 46913966 . C T 9.08 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=16 PL:GT:GQ 41,12,0:1/1:72 chr4 50335142 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr4 51658550 . C A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr4 58258023 . T C 26 . DP=5;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,2;MQ=34;PV4=1,1,1,0.05 PL:GT:GQ 56,0,32:0/1:35 chr4 59219112 . C A 42.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50 PL:GT:GQ 75,12,0:1/1:72 chr4 62746067 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr4 67404338 . G T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39 PL:GT:GQ 66,12,0:1/1:72 chr4 73353380 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr4 73946294 . G C 4.77 . DP=51;AF1=0.4999;CI95=0.5,0.5;DP4=0,5,0,3;MQ=40;PV4=1,0.19,0.37,0.11 PL:GT:GQ 33,0,64:0/1:36 chr4 79607484 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr4 82337365 . G C 90 . DP=54;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=28 PL:GT:GQ 123,48,0:1/1:99 chr4 82653801 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 34,9,0:1/1:63 chr4 87130164 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 43,9,0:1/1:63 chr4 87130176 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 43,9,0:1/1:63 chr4 91459729 . C A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr4 96130778 . G C 99 . DP=19;AF1=1;CI95=1,1;DP4=0,0,0,19;MQ=45 PL:GT:GQ 211,57,0:1/1:99 chr4 100709417 . A G 45.1 . DP=16;AF1=0.505;CI95=0.5,0.5;DP4=12,0,4,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 75,0,17:0/1:20 chr4 107276770 . C T 70 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=31;PV4=1,1,1,1 PL:GT:GQ 100,0,97:0/1:98 chr4 115327550 . G C 42 . DP=67;AF1=1;CI95=1,1;DP4=0,1,0,66;MQ=35;PV4=1,3.2e-24,0.13,1 PL:GT:GQ 75,162,0:1/1:99 chr4 136558502 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr4 159572459 . G A 15.1 . DP=126;AF1=0.5;CI95=0.5,0.5;DP4=0,69,0,57;MQ=39;PV4=1,4.1e-96,0.077,1 PL:GT:GQ 45,0,175:0/1:48 chr4 174968484 . G C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 40,6,0:1/1:49 chr4 175030633 . T C 14.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=29 PL:GT:GQ 47,18,0:1/1:90 chr4 183410027 . G T 6.2 . DP=31;AF1=0.5003;CI95=0.5,0.5;DP4=2,0,2,0;MQ=45;PV4=1,0.035,1,0.21 PL:GT:GQ 35,0,28:0/1:30 chr4 190907368 . T C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50 PL:GT:GQ 66,12,0:1/1:72 chr4 192175690 . A G 76.8 . DP=7;AF1=0.95;CI95=0.5,1;DP4=0,3,0,4;MQ=35;PV4=1,1,1,1 PL:GT:GQ 105,0,0:1/1:10 chr4 192673268 . G A 14.2 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=22 PL:GT:GQ 47,27,0:1/1:99 chr4 192943966 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr4 195460104 . C G 23.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=19 PL:GT:GQ 56,24,0:1/1:96 chr4 198277830 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr5 170098 . A G 13 . DP=12;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 44,6,0:1/1:49 chr5 395814 . T C 4.77 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,0.48,1 PL:GT:GQ 33,0,33:0/1:33 chr5 414024 . T A 10.4 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=20 PL:GT:GQ 42,9,0:1/1:63 chr5 496767 . T C 13.9 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr5 805676 . C G 45 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=32 PL:GT:GQ 78,51,0:1/1:99 chr5 1252896 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr5 1418370 . G A 3.65 . DP=8;AF1=0.7301;CI95=0.5,1;DP4=4,0,4,0;MQ=13;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr5 1494911 . G C 62 . DP=9;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=46 PL:GT:GQ 95,24,0:1/1:96 chr5 1494932 . C T 6.98 . DP=8;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=46;PV4=1,0.1,0.077,1 PL:GT:GQ 36,0,31:0/1:33 chr5 1506037 . T C 24.1 . DP=24;AF1=1;CI95=0.5,1;DP4=11,0,13,0;MQ=16;PV4=1,1,1,1 PL:GT:GQ 55,5,0:1/1:46 chr5 1509406 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 73,6,0:1/1:49 chr5 1733649 . A G 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=47 PL:GT:GQ 212,75,0:1/1:99 chr5 1747304 . A G 12.3 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19 PL:GT:GQ 45,36,0:1/1:99 chr5 1747308 . C A 44 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19 PL:GT:GQ 77,36,0:1/1:99 chr5 3519783 . C T 21.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18 PL:GT:GQ 54,24,0:1/1:96 chr5 4101593 . A G 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43 PL:GT:GQ 102,12,0:1/1:72 chr5 7204332 . T A 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=24 PL:GT:GQ 34,6,0:1/1:49 chr5 11510398 . A C 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=51;PV4=1,1,0,1 PL:GT:GQ 64,0,31:0/1:34 chr5 15406720 . T C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 36,6,0:1/1:49 chr5 25152417 . C A 10.9 . DP=28;AF1=0.5718;CI95=0.5,1;DP4=0,2,0,6;MQ=25;PV4=1,1,0.21,1 PL:GT:GQ 40,0,6:0/1:8 chr5 39072637 . A G 35.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=50 PL:GT:GQ 68,15,0:1/1:75 chr5 46022699 . G A 44 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 76,9,0:1/1:63 chr5 55664181 . C G 10.4 . DP=8;AF1=0.9999;CI95=0.5,1;DP4=3,0,5,0;MQ=18;PV4=1,1,1,1 PL:GT:GQ 40,3,0:1/1:41 chr5 56253386 . T C 50.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=36 PL:GT:GQ 83,21,0:1/1:84 chr5 56253447 . C T 42.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=45 PL:GT:GQ 75,12,0:1/1:72 chr5 71950166 . G T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr5 72703090 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 40,6,0:1/1:49 chr5 73570280 . G T 5.45 . DP=41;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=15 PL:GT:GQ 37,123,0:1/1:99 chr5 73701762 . G T 40.8 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 72,6,0:1/1:49 chr5 76956867 . T C 10.2 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 41,6,0:1/1:49 chr5 79097961 . C G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 54,9,0:1/1:63 chr5 87026167 . T C 22 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr5 97680525 . T C 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23 PL:GT:GQ 33,12,0:1/1:72 chr5 100674737 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr5 105389966 . T C 3.52 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=15 PL:GT:GQ 33,9,0:1/1:63 chr5 109998341 . A C 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr5 120629105 . C T 6.79 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 37,6,0:1/1:49 chr5 128383954 . C T 23 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,3.3e-07,1,1 PL:GT:GQ 53,0,98:0/1:56 chr5 133925142 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr5 135375404 . T C 11.8 . DP=6;AF1=1;CI95=0.5,1;DP4=1,0,3,0;MQ=31;PV4=1,0.03,1,1 PL:GT:GQ 42,4,0:1/1:45 chr5 136498281 . T G 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr5 136717285 . A G 82.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 115,12,0:1/1:72 chr5 136910734 . G A 62 . DP=19;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=23;PV4=1,1,1,1 PL:GT:GQ 95,31,0:1/1:99 chr5 141208149 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr5 148056348 . C A 37.1 . DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=38;PV4=1,1,1,1 PL:GT:GQ 66,1,0:1/1:23 chr5 151941534 . G T 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34 PL:GT:GQ 79,12,0:1/1:72 chr5 159967229 . G C 22.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 55,12,0:1/1:72 chr5 174024541 . T G 29.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 59,2,0:1/1:37 chr5 175525290 . A G 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=20 PL:GT:GQ 33,12,0:1/1:72 chr5 175988954 . A C 14.2 . DP=23;AF1=0.5;CI95=0.5,0.5;DP4=0,6,0,4;MQ=47;PV4=1,1,0.2,1 PL:GT:GQ 44,0,76:0/1:47 chr5 176782226 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr5 179132834 . C G 99 . DP=28;AF1=1;CI95=1,1;DP4=0,0,0,28;MQ=41 PL:GT:GQ 207,84,0:1/1:99 chr5 180155809 . G C 3.01 . DP=36;AF1=0.4997;CI95=0.5,0.5;DP4=25,0,9,0;MQ=35;PV4=1,1e-15,1,1 PL:GT:GQ 30,0,121:0/1:33 chr5 181282819 . T G 38.3 . DP=11;AF1=1;CI95=0.5,1;DP4=0,2,0,9;MQ=23;PV4=1,1,1,1 PL:GT:GQ 71,14,0:1/1:70 chr5 182426125 . G C 29 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26 PL:GT:GQ 61,9,0:1/1:63 chr5 182443682 . G A 3.69 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=21 PL:GT:GQ 34,15,0:1/1:75 chr5 183008993 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr5 183312016 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr6_cox_hap1 519146 . G A 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30 PL:GT:GQ 49,9,0:1/1:63 chr6_cox_hap1 687497 . A G 33 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,0.0016,1,1 PL:GT:GQ 63,3,0:1/1:41 chr6_qbl_hap2 120066 . T C 99 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 139,27,0:1/1:99 chr6 277954 . C T 53 . DP=41;AF1=1;CI95=1,1;DP4=4,0,37,0;MQ=19;PV4=1,1,0.3,1 PL:GT:GQ 86,49,0:1/1:99 chr6 593158 . A G 4.61 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 34,6,0:1/1:49 chr6 2865562 . T G 25 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=23 PL:GT:GQ 58,27,0:1/1:99 chr6 3751403 . G A 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32 PL:GT:GQ 75,15,0:1/1:75 chr6 3884989 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr6 4127278 . A T 13.9 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr6 5887783 . C G 99 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34 PL:GT:GQ 142,21,0:1/1:84 chr6 5887811 . C T 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34 PL:GT:GQ 88,21,0:1/1:84 chr6 6937170 . G C 99 . DP=47;AF1=1;CI95=1,1;DP4=0,0,0,47;MQ=28 PL:GT:GQ 157,141,0:1/1:99 chr6 7262317 . C T 13.2 . DP=50;AF1=0.5;CI95=0.5,0.5;DP4=21,0,9,0;MQ=36;PV4=1,4e-05,0.17,0.26 PL:GT:GQ 43,0,158:0/1:46 chr6 7533214 . A G 10.4 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 42,9,0:1/1:63 chr6 20979907 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=38 PL:GT:GQ 76,9,0:1/1:63 chr6 22321632 . A G 41 . DP=5;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=46;PV4=1,0.24,0.19,0.33 PL:GT:GQ 71,0,28:0/1:31 chr6 25352296 . G A 7.8 . DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=0,1,0,3;MQ=38;PV4=1,1,0.16,1 PL:GT:GQ 37,0,28:0/1:30 chr6 26298040 . T A 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=48;PV4=1,1,0.21,0.33 PL:GT:GQ 64,0,31:0/1:34 chr6 33428755 . G A 70 . DP=14;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=32 PL:GT:GQ 103,27,0:1/1:99 chr6 39512099 . G A 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=50 PL:GT:GQ 88,21,0:1/1:84 chr6 39961094 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr6 40452120 . A G 40.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 72,6,0:1/1:49 chr6 43204766 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=51 PL:GT:GQ 176,24,0:1/1:96 chr6 52696512 . C T 70 . DP=76;AF1=0.5;CI95=0.5,0.5;DP4=0,34,0,42;MQ=18;PV4=1,0.11,1,1 PL:GT:GQ 100,0,51:0/1:54 chr6 53785550 . A G 99 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=46 PL:GT:GQ 190,30,0:1/1:99 chr6 53897484 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr6 57038290 . C T 10.2 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 41,6,0:1/1:49 chr6 62925087 . G C 35 . DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,4,0;MQ=36;PV4=1,1,0.2,1 PL:GT:GQ 65,0,25:0/1:28 chr6 62925094 . T C 25.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36 PL:GT:GQ 58,15,0:1/1:75 chr6 70834405 . G A 72.1 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=29 PL:GT:GQ 105,21,0:1/1:84 chr6 71026058 . C T 48.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=42 PL:GT:GQ 81,18,0:1/1:90 chr6 74420752 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 76,9,0:1/1:63 chr6 77498624 . T C 16.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 48,6,0:1/1:49 chr6 80416836 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr6 113611590 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46 PL:GT:GQ 100,9,0:1/1:63 chr6 119308431 . T C 38.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40 PL:GT:GQ 71,12,0:1/1:72 chr6 151758592 . T C 3.07 . DP=17;AF1=0.9966;CI95=0.5,1;DP4=0,8,0,9;MQ=13;PV4=1,1,1,1 PL:GT:GQ 29,1,0:1/1:23 chr6 151759358 . A G 99 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=12,0,15,0;MQ=44;PV4=1,1,1,0.19 PL:GT:GQ 171,0,128:0/1:99 chr6 154741755 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr6 161061053 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52 PL:GT:GQ 40,6,0:1/1:49 chr6 161474189 . C T 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 36,6,0:1/1:49 chr6 164304657 . C T 10.4 . DP=63;AF1=0.5;CI95=0.5,0.5;DP4=0,29,0,19;MQ=22;PV4=1,7.7e-11,1,0.049 PL:GT:GQ 40,0,37:0/1:38 chr6 164703105 . T C 99 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=40 PL:GT:GQ 165,30,0:1/1:99 chr6 167518328 . A G 78 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=27,0,14,0;MQ=33;PV4=1,0.026,0.43,0.056 PL:GT:GQ 108,0,149:0/1:99 chr6 169906323 . G A 41.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr6 171893912 . G A 69.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33 PL:GT:GQ 102,15,0:1/1:75 chr6 173631604 . A G 6.98 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=4,0,3,0;MQ=37;PV4=1,0.069,1,1 PL:GT:GQ 36,0,34:0/1:35 chr7 835856 . C T 27.5 . DP=13;AF1=0.9998;CI95=0.5,1;DP4=4,0,6,0;MQ=23;PV4=1,0.46,1,1 PL:GT:GQ 57,2,0:1/1:37 chr7 1046005 . C T 11.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 43,9,0:1/1:63 chr7 1564339 . C T 71 . DP=66;AF1=0.5;CI95=0.5,0.5;DP4=36,0,24,0;MQ=29;PV4=1,1,0.35,1 PL:GT:GQ 101,0,134:0/1:99 chr7 1806266 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr7 1936013 . G T 7.77 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=17 PL:GT:GQ 39,9,0:1/1:63 chr7 2319532 . C A 4.11 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=14 PL:GT:GQ 34,9,0:1/1:63 chr7 2682121 . C T 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr7 3248116 . T C 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=37;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr7 3624766 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 40,6,0:1/1:49 chr7 5291140 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr7 5314457 . C A 3.56 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18 PL:GT:GQ 34,24,0:1/1:95 chr7 5595072 . T A 79 . DP=13;AF1=0.5;CI95=0.5,0.5;DP4=8,0,5,0;MQ=31;PV4=1,1,1,1 PL:GT:GQ 109,0,57:0/1:60 chr7 5646060 . G C 7.79 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=10 PL:GT:GQ 40,30,0:1/1:99 chr7 6056816 . C G 7.08 . DP=6;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=23;PV4=1,1,1,1 PL:GT:GQ 35,1,0:1/1:23 chr7 6412641 . C T 40 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33 PL:GT:GQ 73,33,0:1/1:99 chr7 6766874 . A G 34.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=43 PL:GT:GQ 67,15,0:1/1:75 chr7 8482729 . C T 5.08 . DP=16;AF1=0.8276;CI95=0.5,1;DP4=3,0,3,0;MQ=22;PV4=1,1,1,0.19 PL:GT:GQ 32,0,1:1/1:5 chr7 9238362 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr7 9687781 . G A 33 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,12;MQ=48;PV4=1,6.5e-38,1,1 PL:GT:GQ 63,0,170:0/1:66 chr7 9752803 . A T 14.2 . DP=17;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18 PL:GT:GQ 47,27,0:1/1:99 chr7 10240910 . T C 45.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 78,12,0:1/1:72 chr7 11046187 . C T 86.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=47 PL:GT:GQ 119,12,0:1/1:72 chr7 11548207 . C G 14.6 . DP=13;AF1=1;CI95=0.5,1;DP4=6,1,0,5;MQ=18;PV4=0.015,1,1,1 PL:GT:GQ 46,7,0:1/1:57 chr7 11580317 . C T 42 . DP=12;AF1=1;CI95=1,1;DP4=0,1,0,10;MQ=22;PV4=1,1,1,1 PL:GT:GQ 75,23,0:1/1:92 chr7 11585384 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr7 13498356 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 73,6,0:1/1:49 chr7 13500887 . G A 15.1 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=22 PL:GT:GQ 48,30,0:1/1:99 chr7 13827079 . C T 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 36,6,0:1/1:49 chr7 14403976 . T G 59 . DP=30;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39 PL:GT:GQ 92,24,0:1/1:96 chr7 14756588 . A G 44 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,5.3e-18,1,1 PL:GT:GQ 74,0,70:0/1:72 chr7 14756619 . T G 44 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,6.4e-10,1,1 PL:GT:GQ 74,0,70:0/1:72 chr7 36734598 . A C 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 42,6,0:1/1:49 chr7 36734599 . A T 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 42,6,0:1/1:49 chr7 36734603 . G C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 40,6,0:1/1:49 chr7 40634921 . A C 55 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=39 PL:GT:GQ 88,39,0:1/1:99 chr7 48271285 . A T 73 . DP=15;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=25 PL:GT:GQ 106,30,0:1/1:99 chr7 56264700 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr7 62326003 . C A 26.1 . DP=35;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28 PL:GT:GQ 59,18,0:1/1:90 chr7 109468934 . T G 5.13 . DP=10;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=39;PV4=1,0.031,1,1 PL:GT:GQ 33,2,0:1/1:37 chr7 110208327 . C G 16.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 48,6,0:1/1:49 chr7 125654934 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=27 PL:GT:GQ 34,9,0:1/1:63 chr7 125770209 . A C 32 . DP=31;AF1=0.5;CI95=0.5,0.5;DP4=11,0,13,0;MQ=34;PV4=1,0.00017,0.16,0.22 PL:GT:GQ 62,0,105:0/1:65 chr7 125770265 . G C 36 . DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,0.0047,0.016,0.035 PL:GT:GQ 66,0,110:0/1:69 chr7 126687042 . A G 21.1 . DP=36;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=22 PL:GT:GQ 54,21,0:1/1:84 chr7 132292897 . G T 99 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=43 PL:GT:GQ 167,21,0:1/1:84 chr7 132334562 . A C 23 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=23 PL:GT:GQ 56,30,0:1/1:99 chr7 132431838 . C T 13.3 . DP=5;AF1=1;CI95=0.5,1;DP4=1,0,4,0;MQ=23;PV4=1,1,1,1 PL:GT:GQ 44,5,0:1/1:46 chr7 136324945 . T C 13.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 46,12,0:1/1:72 chr7 136957634 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr7 141746871 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 40,6,0:1/1:49 chr7 146831870 . C T 4.77 . DP=14;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=37;PV4=1,0.0029,0.28,1 PL:GT:GQ 33,0,28:0/1:30 chr7 147142770 . T C 45 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=31 PL:GT:GQ 77,9,0:1/1:63 chr7 147713906 . C T 4.77 . DP=8;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,4,0;MQ=35;PV4=1,8.9e-06,0.48,0.27 PL:GT:GQ 33,0,29:0/1:31 chr7 148742642 . G A 68 . DP=14;AF1=0.5032;CI95=0.5,0.5;DP4=4,0,10,0;MQ=28;PV4=1,1,1,1 PL:GT:GQ 98,0,19:0/1:22 chr7 148879148 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr7 149484407 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr7 152444478 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 44,6,0:1/1:49 chr7 154106613 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=51 PL:GT:GQ 100,9,0:1/1:63 chr7 154776891 . G T 14.4 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 47,15,0:1/1:75 chr7 155882061 . A C 29 . DP=24;AF1=0.502;CI95=0.5,0.5;DP4=0,1,0,4;MQ=46;PV4=1,0.018,0.15,0.29 PL:GT:GQ 59,0,21:0/1:24 chr7 155956844 . G C 23 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=38;PV4=1,1,0.38,1 PL:GT:GQ 53,0,103:0/1:56 chr7 156277694 . G A 62 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=46 PL:GT:GQ 95,24,0:1/1:96 chr7 156720588 . T C 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr7 156807649 . T C 3.01 . DP=30;AF1=0.4997;CI95=0.5,0.5;DP4=0,4,0,3;MQ=43;PV4=1,0.16,0.15,1 PL:GT:GQ 30,0,72:0/1:33 chr7 157331292 . G T 43.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=34 PL:GT:GQ 76,21,0:1/1:84 chr7 157382957 . T C 33.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 66,12,0:1/1:72 chr8 556382 . A G 37.1 . DP=5;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=31;PV4=1,1,1,1 PL:GT:GQ 66,1,0:1/1:23 chr8 1661673 . T C 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr8 7379751 . C A 6.24 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19 PL:GT:GQ 38,21,0:1/1:84 chr8 8160505 . A T 68.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 101,12,0:1/1:72 chr8 8160508 . C T 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 57,12,0:1/1:72 chr8 16781011 . A G 55.5 . DP=9;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34 PL:GT:GQ 88,12,0:1/1:72 chr8 18716499 . A T 20 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,4,0,2;MQ=29;PV4=1,1,1,1 PL:GT:GQ 50,0,52:0/1:51 chr8 23326483 . A G 60 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47 PL:GT:GQ 92,9,0:1/1:63 chr8 25842819 . T A 12 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 43,6,0:1/1:49 chr8 26300279 . T C 34 . DP=44;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=21 PL:GT:GQ 67,123,0:1/1:99 chr8 29673470 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 73,6,0:1/1:49 chr8 29673473 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 40,6,0:1/1:49 chr8 31685466 . C T 34 . DP=17;AF1=0.5;CI95=0.5,0.5;DP4=10,0,5,0;MQ=28;PV4=1,0.072,1,0.36 PL:GT:GQ 64,0,50:0/1:53 chr8 37378739 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr8 51325952 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr8 59221963 . G A 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr8 62764995 . T G 20 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=32 PL:GT:GQ 52,9,0:1/1:63 chr8 63157426 . C G 41.6 . DP=22;AF1=1;CI95=0.5,1;DP4=0,7,0,15;MQ=19;PV4=1,1,1,0.25 PL:GT:GQ 74,11,0:1/1:66 chr8 68710444 . G A 30 . DP=5;AF1=0.6671;CI95=0.5,1;DP4=3,0,2,0;MQ=32;PV4=1,1,1,1 PL:GT:GQ 59,0,3:0/1:5 chr8 76416560 . G A 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=46 PL:GT:GQ 122,12,0:1/1:72 chr8 81425275 . T G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr8 89842286 . G C 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30 PL:GT:GQ 34,6,0:1/1:49 chr8 100926281 . G A 38 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 70,9,0:1/1:63 chr8 102746002 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr8 107850176 . C T 43.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=45 PL:GT:GQ 76,18,0:1/1:90 chr8 109966441 . T C 27.3 . DP=9;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38 PL:GT:GQ 60,15,0:1/1:75 chr8 118811716 . G T 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=50 PL:GT:GQ 155,18,0:1/1:90 chr8 119440254 . A T 58.5 . DP=5;AF1=0.8277;CI95=0.5,1;DP4=2,0,3,0;MQ=34;PV4=1,1,1,0.14 PL:GT:GQ 87,0,1:1/1:5 chr8 121236024 . G A 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 71,6,0:1/1:49 chr8 125489079 . C T 13 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr8 128502549 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr8 128502551 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr8 130951113 . G A 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=19 PL:GT:GQ 34,6,0:1/1:49 chr8 135307123 . G A 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 36,6,0:1/1:49 chr8 138814155 . C T 57.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 90,18,0:1/1:90 chr8 140566111 . A G 18.1 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=15 PL:GT:GQ 51,36,0:1/1:99 chr8 141586480 . T G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr8 143376712 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr8 150662729 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr8 150741294 . A G 25.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=34 PL:GT:GQ 58,18,0:1/1:90 chr8 150975618 . A G 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr8 151580103 . T C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=20 PL:GT:GQ 36,6,0:1/1:49 chr8 151634410 . G T 48 . DP=17;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,5;MQ=39;PV4=1,0.072,1,1 PL:GT:GQ 78,0,125:0/1:81 chr8 151709267 . G A 91.1 . DP=8;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=40;PV4=1,1,0.28,0.37 PL:GT:GQ 121,0,16:0/1:19 chr8 152636420 . G A 8.75 . DP=3;AF1=0.9966;CI95=0.5,1;DP4=0,1,0,2;MQ=30;PV4=1,1,1,1 PL:GT:GQ 37,1,0:1/1:23 chr8 152706967 . G A 3.01 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=16 PL:GT:GQ 33,30,0:1/1:99 chr8 152786522 . T C 80.1 . DP=16;AF1=0.5102;CI95=0.5,0.5;DP4=0,4,0,12;MQ=31;PV4=1,0.25,1,1 PL:GT:GQ 110,0,14:0/1:17 chr8 152863132 . T G 5.44 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30 PL:GT:GQ 36,9,0:1/1:63 chr9 23235268 . C T 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 43,6,0:1/1:49 chr9 26391176 . T C 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 47,6,0:1/1:49 chr9 26868232 . C G 63 . DP=20;AF1=0.5025;CI95=0.5,0.5;DP4=7,0,13,0;MQ=22;PV4=1,0.2,1,0.44 PL:GT:GQ 93,0,20:0/1:23 chr9 34223668 . C T 22 . DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,7;MQ=27;PV4=1,0.14,0.34,1 PL:GT:GQ 52,0,79:0/1:55 chr9 39696645 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr9 40654130 . T G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr9 41145321 . T G 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 79,12,0:1/1:72 chr9 42273483 . G A 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr9 55633192 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 58705807 . T C 70 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=24 PL:GT:GQ 103,30,0:1/1:99 chr9 61697149 . C G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 63152790 . A C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr9 63703913 . C G 90.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=38 PL:GT:GQ 123,21,0:1/1:84 chr9 65116068 . T C 70 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=49 PL:GT:GQ 103,39,0:1/1:99 chr9 71266598 . C A 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 33,6,0:1/1:49 chr9 73188677 . G T 52 . DP=294;AF1=1;CI95=1,1;DP4=44,0,245,0;MQ=33;PV4=1,0.28,0.0092,1 PL:GT:GQ 85,147,0:1/1:99 chr9 78854179 . G T 22 . DP=97;AF1=0.5;CI95=0.5,0.5;DP4=21,0,12,0;MQ=44;PV4=1,0.02,0.032,0.0033 PL:GT:GQ 52,0,158:0/1:55 chr9 82964679 . A C 13.2 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=36 PL:GT:GQ 45,9,0:1/1:63 chr9 84124545 . G T 57 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=2,0,3,0;MQ=49;PV4=1,1,0.024,1 PL:GT:GQ 87,0,59:0/1:62 chr9 86552862 . C T 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=26 PL:GT:GQ 47,15,0:1/1:75 chr9 87548941 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr9 89021101 . G A 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr9 90447825 . G A 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 40,6,0:1/1:49 chr9 92462035 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 40,6,0:1/1:49 chr9 93077294 . T G 5.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31 PL:GT:GQ 36,9,0:1/1:63 chr9 93998137 . G A 68 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46 PL:GT:GQ 100,9,0:1/1:63 chr9 93998148 . C T 21.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36 PL:GT:GQ 54,15,0:1/1:75 chr9 95028964 . C A 99 . DP=83;AF1=0.5;CI95=0.5,0.5;DP4=0,57,0,26;MQ=32;PV4=1,9.3e-08,1,0.092 PL:GT:GQ 134,0,120:0/1:99 chr9 103829155 . A G 33 . DP=96;AF1=1;CI95=1,1;DP4=0,0,96,0;MQ=16 PL:GT:GQ 66,255,0:1/1:99 chr9 104981331 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 73,6,0:1/1:49 chr9 111070656 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 117395657 . T C 16.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 49,15,0:1/1:75 chr9 117718907 . A G 46.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=29 PL:GT:GQ 79,18,0:1/1:90 chr9 119149161 . T C 3.14 . DP=65;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 33,15,0:1/1:75 chr9 124528802 . G A 78 . DP=23;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=25 PL:GT:GQ 111,39,0:1/1:99 chr9 126707903 . G A 26 . DP=37;AF1=0.5;CI95=0.5,0.5;DP4=0,21,0,8;MQ=46;PV4=1,2.6e-07,0.21,0.42 PL:GT:GQ 56,0,175:0/1:59 chr9 128700686 . C G 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 66,12,0:1/1:72 chr9 129084077 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr9 129116900 . A T 20 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 52,9,0:1/1:63 chr9 130290720 . C G 21.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 53,6,0:1/1:49 chr9 130306057 . C G 71 . DP=14;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=28 PL:GT:GQ 104,42,0:1/1:99 chr9 130528990 . G A 99 . DP=31;AF1=1;CI95=1,1;DP4=0,0,31,0;MQ=27 PL:GT:GQ 174,93,0:1/1:99 chr9 130529002 . A T 7.79 . DP=30;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=15 PL:GT:GQ 40,33,0:1/1:99 chr9 130639996 . A G 8.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 39,6,0:1/1:49 chr9 130704890 . A G 3.27 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=26 PL:GT:GQ 33,12,0:1/1:72 chr9 130708345 . G A 13.3 . DP=11;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=38;PV4=1,0.096,1,1 PL:GT:GQ 42,1,0:1/1:23 chr9 131001601 . T A 3.98 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 33,6,0:1/1:49 chr9 131058539 . T A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 44,6,0:1/1:49 chr9 131808965 . C T 42 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 75,27,0:1/1:99 chr9 132551867 . C T 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 49,9,0:1/1:63 chr9 132685120 . A G 4.75 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 35,9,0:1/1:63 chr9 133175050 . A G 18.1 . DP=30;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=20 PL:GT:GQ 51,51,0:1/1:99 chr9 133584978 . A G 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=45 PL:GT:GQ 212,75,0:1/1:99 chr9 133661895 . A G 99 . DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31 PL:GT:GQ 138,42,0:1/1:99 chr9 133670376 . T C 68 . DP=19;AF1=1;CI95=1,1;DP4=0,1,0,16;MQ=39;PV4=1,1.4e-20,1,1 PL:GT:GQ 101,39,0:1/1:99 chr9 133843777 . T C 99 . DP=9;AF1=0.5129;CI95=0.5,0.5;DP4=1,0,8,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 154,0,13:0/1:16 chr9 134017265 . G C 3.27 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=13 PL:GT:GQ 33,12,0:1/1:72 chr9 134105563 . T C 34.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=39 PL:GT:GQ 67,18,0:1/1:90 chr9 134608906 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr9 134861929 . T A 9.49 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 41,9,0:1/1:63 chr10 796662 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 54,9,0:1/1:63 chr10 1216716 . T A 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr10 1220781 . G A 21 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18 PL:GT:GQ 54,27,0:1/1:99 chr10 1225208 . T C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47 PL:GT:GQ 100,9,0:1/1:63 chr10 1727946 . T C 14.2 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27 PL:GT:GQ 47,21,0:1/1:84 chr10 5986542 . T C 83 . DP=93;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39 PL:GT:GQ 116,30,0:1/1:99 chr10 6436277 . G A 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 36,6,0:1/1:49 chr10 7704114 . C A 35 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=0,2,0,4;MQ=29;PV4=1,0.27,1,0.27 PL:GT:GQ 65,3,0:1/1:41 chr10 10881734 . A G 9.52 . DP=9;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=42;PV4=1,0.0026,0.14,1 PL:GT:GQ 39,0,91:0/1:42 chr10 13099383 . G A 27.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 60,12,0:1/1:72 chr10 15764077 . G C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr10 18091502 . T C 47 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 79,9,0:1/1:63 chr10 19645913 . A T 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 47,6,0:1/1:49 chr10 22845062 . C T 18.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=18 PL:GT:GQ 51,21,0:1/1:84 chr10 28282802 . T C 69 . DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=42 PL:GT:GQ 102,36,0:1/1:99 chr10 28496872 . T G 8.44 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 39,6,0:1/1:49 chr10 32746793 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr10 41437604 . T G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr10 43051239 . C T 6.98 . DP=3;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=40;PV4=1,0.33,0.33,1 PL:GT:GQ 36,0,31:0/1:33 chr10 44455192 . C T 4.41 . DP=6;AF1=0.8276;CI95=0.5,1;DP4=0,3,0,3;MQ=21;PV4=1,1,1,1 PL:GT:GQ 31,0,1:1/1:5 chr10 48387336 . A G 13 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr10 51561705 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr10 51561712 . C G 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 71,6,0:1/1:49 chr10 55617954 . G A 8.44 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 39,6,0:1/1:49 chr10 55718281 . T A 3.41 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr10 55888771 . T C 23.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 56,12,0:1/1:72 chr10 56025569 . C G 34.1 . DP=3;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,2;MQ=39;PV4=1,1,1,1 PL:GT:GQ 64,0,16:0/1:19 chr10 57384943 . G T 84 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=16,0,13,0;MQ=26;PV4=1,0.015,1,1 PL:GT:GQ 114,0,110:0/1:99 chr10 59873077 . T G 49 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=42 PL:GT:GQ 82,24,0:1/1:96 chr10 61329572 . C T 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 47,6,0:1/1:49 chr10 63790636 . T G 32.1 . DP=19;AF1=1;CI95=1,1;DP4=1,0,10,0;MQ=28;PV4=1,0.14,1,1 PL:GT:GQ 65,22,0:1/1:88 chr10 64466048 . C G 18.2 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28 PL:GT:GQ 51,18,0:1/1:90 chr10 65053440 . G T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39 PL:GT:GQ 153,30,0:1/1:99 chr10 65407358 . C G 84.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 117,15,0:1/1:75 chr10 65605291 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr10 66104447 . T C 99 . DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,21;MQ=34;PV4=1,1,0.15,1 PL:GT:GQ 136,0,162:0/1:99 chr10 82160859 . G C 99 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=36 PL:GT:GQ 153,39,0:1/1:99 chr10 82198579 . C T 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr10 87086290 . A G 4.13 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=17 PL:GT:GQ 35,27,0:1/1:99 chr10 89550621 . T G 74 . DP=47;AF1=1;CI95=1,1;DP4=0,0,0,45;MQ=45 PL:GT:GQ 107,135,0:1/1:99 chr10 92325046 . G A 42.3 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 75,15,0:1/1:75 chr10 94488050 . A G 5.46 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,0.16,1,1 PL:GT:GQ 34,0,34:0/1:34 chr10 95024815 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr10 95466306 . G A 53 . DP=7;AF1=0.6671;CI95=0.5,1;DP4=0,4,0,3;MQ=33;PV4=1,1,1,1 PL:GT:GQ 82,0,3:0/1:5 chr10 100256777 . T G 3.83 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23 PL:GT:GQ 34,12,0:1/1:72 chr10 101510485 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr10 101530760 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr10 101879744 . T C 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=44 PL:GT:GQ 54,9,0:1/1:63 chr10 102147276 . G C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33 PL:GT:GQ 43,9,0:1/1:63 chr10 102642248 . T G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr10 107666616 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr10 108319945 . C G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 43,9,0:1/1:63 chr10 109734371 . G A 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr10 112870604 . C T 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=36 PL:GT:GQ 79,12,0:1/1:72 chr10 115304673 . T C 11.3 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr10 119380588 . G A 14.2 . DP=4;AF1=0.502;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.18,0.32,1 PL:GT:GQ 44,0,21:0/1:24 chr10 123063756 . C T 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=23 PL:GT:GQ 46,9,0:1/1:63 chr10 128424770 . T G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 45,6,0:1/1:49 chr10 131229204 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr10 132420570 . G C 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr10 132528066 . C T 99 . DP=19;AF1=1;CI95=1,1;DP4=0,0,19,0;MQ=42 PL:GT:GQ 213,57,0:1/1:99 chr10 132644619 . G A 19.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23 PL:GT:GQ 52,15,0:1/1:75 chr10 132707581 . G C 9.11 . DP=51;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=25;PV4=1,1,1,1 PL:GT:GQ 38,2,0:1/1:37 chr10 133026892 . T C 55.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44 PL:GT:GQ 88,18,0:1/1:90 chr11 768033 . T C 33.5 . DP=4;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 62,0,1:1/1:5 chr11 768042 . T C 33.5 . DP=6;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 62,0,1:1/1:5 chr11 874568 . G C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 66,12,0:1/1:72 chr11 1009210 . T C 4 . DP=70;AF1=0.6241;CI95=0.5,1;DP4=0,3,0,8;MQ=24;PV4=1,1,0.5,1 PL:GT:GQ 31,0,4:0/1:6 chr11 1016692 . C T 27 . DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=22 PL:GT:GQ 60,114,0:1/1:99 chr11 1034477 . A G 66 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 98,9,0:1/1:63 chr11 1074037 . G A 4.13 . DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,5,0;MQ=24;PV4=1,1,0.43,1 PL:GT:GQ 32,0,30:0/1:31 chr11 1556298 . G A 11.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 44,12,0:1/1:72 chr11 1824777 . T C 27 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=28 PL:GT:GQ 60,30,0:1/1:99 chr11 3395801 . C T 22 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr11 3411901 . G A 4.75 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 35,9,0:1/1:63 chr11 3731606 . A C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr11 3783855 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr11 3967636 . A G 4.29 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24 PL:GT:GQ 35,15,0:1/1:75 chr11 4385618 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr11 4424365 . T A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr11 5295586 . C T 3.01 . DP=52;AF1=0.4997;CI95=0.5,0.5;DP4=33,0,10,0;MQ=29;PV4=1,0.0045,0.3,0.17 PL:GT:GQ 30,0,131:0/1:33 chr11 6157144 . C G 45.1 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=35 PL:GT:GQ 78,21,0:1/1:84 chr11 6352044 . C T 18 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31 PL:GT:GQ 50,9,0:1/1:63 chr11 6767356 . T C 9.63 . DP=3;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=29;PV4=1,1,1,1 PL:GT:GQ 38,1,0:1/1:23 chr11 6999404 . G C 21 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37 PL:GT:GQ 53,9,0:1/1:63 chr11 9120930 . C G 17.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr11 9373125 . T C 19.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 51,6,0:1/1:49 chr11 9585101 . C T 67 . DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=45 PL:GT:GQ 100,42,0:1/1:99 chr11 10266192 . A C 14.3 . DP=22;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=27 PL:GT:GQ 47,18,0:1/1:90 chr11 10303263 . T C 8.64 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=18 PL:GT:GQ 41,51,0:1/1:99 chr11 10420170 . T C 35 . DP=17;AF1=1;CI95=1,1;DP4=0,1,0,15;MQ=28;PV4=1,0.12,1,0.4 PL:GT:GQ 68,36,0:1/1:99 chr11 10912169 . G A 99 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=49 PL:GT:GQ 155,18,0:1/1:90 chr11 11315826 . T G 6.29 . DP=27;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=19 PL:GT:GQ 38,18,0:1/1:90 chr11 11603859 . A C 22 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=34;PV4=1,9.5e-13,0.22,1 PL:GT:GQ 52,0,115:0/1:55 chr11 11700034 . C T 33 . DP=11;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=30 PL:GT:GQ 66,27,0:1/1:99 chr11 11822758 . G A 15.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,3;MQ=38;PV4=1,0.18,1,1 PL:GT:GQ 45,0,88:0/1:48 chr11 11976636 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=24 PL:GT:GQ 54,9,0:1/1:63 chr11 14380517 . C G 16.1 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=5,0,5,0;MQ=48;PV4=1,2.1e-05,0.13,1 PL:GT:GQ 46,0,113:0/1:49 chr11 14419212 . A G 91.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38 PL:GT:GQ 124,18,0:1/1:90 chr11 14846792 . A G 55 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=19 PL:GT:GQ 88,33,0:1/1:99 chr11 15494556 . C T 99 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=22,0,14,0;MQ=34;PV4=1,0.0071,1,1 PL:GT:GQ 146,0,159:0/1:99 chr11 16262879 . A C 16.1 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=43;PV4=1,0.061,0.24,0.33 PL:GT:GQ 46,0,28:0/1:31 chr11 21514947 . T C 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=41 PL:GT:GQ 57,12,0:1/1:72 chr11 22532576 . C G 28 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=17 PL:GT:GQ 61,51,0:1/1:99 chr11 23529238 . G T 4.29 . DP=13;AF1=0.5334;CI95=0.5,1;DP4=1,0,3,0;MQ=37;PV4=1,1,0.34,0.21 PL:GT:GQ 32,0,9:0/1:12 chr11 24249554 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr11 24853167 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr11 33353903 . T C 24.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=36 PL:GT:GQ 57,15,0:1/1:75 chr11 35126569 . T C 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 57,12,0:1/1:72 chr11 35132248 . C T 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr11 35155482 . T C 68 . DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=46 PL:GT:GQ 101,66,0:1/1:99 chr11 52494088 . T C 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 140,27,0:1/1:99 chr11 57899943 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr11 62261460 . G T 19.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,5;MQ=27;PV4=1,1.1e-06,1,1 PL:GT:GQ 49,0,58:0/1:51 chr11 67456049 . C T 39.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=19 PL:GT:GQ 72,18,0:1/1:90 chr11 68509708 . C G 3.65 . DP=9;AF1=0.7301;CI95=0.5,1;DP4=0,5,0,4;MQ=17;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr11 70115115 . T A 99 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=49 PL:GT:GQ 140,15,0:1/1:75 chr11 72643951 . T C 70 . DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=39 PL:GT:GQ 103,66,0:1/1:99 chr11 72647930 . G A 36 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=41;PV4=1,1,0.3,1 PL:GT:GQ 66,0,28:0/1:31 chr11 73330148 . C T 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr11 81720893 . A G 5.83 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=19 PL:GT:GQ 37,12,0:1/1:72 chr11 83813797 . A G 23.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 56,12,0:1/1:72 chr11 85949488 . C A 54 . DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=37 PL:GT:GQ 87,42,0:1/1:99 chr11 87634829 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr11 90913093 . A T 35.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 67,6,0:1/1:49 chr11 93793348 . G A 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=31 PL:GT:GQ 139,24,0:1/1:96 chr11 100802294 . T C 16.6 . DP=21;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 49,12,0:1/1:72 chr11 107455449 . C T 8.44 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=26 PL:GT:GQ 39,6,0:1/1:49 chr11 111344355 . A G 69.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43 PL:GT:GQ 102,12,0:1/1:72 chr11 111611115 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr11 113050466 . G C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 36,6,0:1/1:49 chr11 114332544 . T C 3.54 . DP=17;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,5;MQ=37;PV4=1,0.32,0.13,1 PL:GT:GQ 31,0,37:0/1:33 chr11 114332549 . G A 3.54 . DP=17;AF1=0.4998;CI95=0.5,0.5;DP4=0,9,0,8;MQ=36;PV4=1,3.1e-10,0.088,1 PL:GT:GQ 31,0,127:0/1:34 chr11 114843578 . G C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr11 115580279 . A G 99 . DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=48 PL:GT:GQ 190,45,0:1/1:99 chr11 116434328 . G A 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr11 125914161 . A G 20.8 . DP=7;AF1=0.95;CI95=0.5,1;DP4=3,0,4,0;MQ=38;PV4=1,0.074,1,1 PL:GT:GQ 49,0,0:1/1:10 chr11 125917089 . C T 12.3 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,28,0,12;MQ=44;PV4=1,4.7e-25,1,1 PL:GT:GQ 42,0,167:0/1:45 chr11 127194100 . A G 60 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=49 PL:GT:GQ 93,24,0:1/1:96 chr12 70856 . G A 27.5 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 60,12,0:1/1:72 chr12 153693 . T C 52.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=38 PL:GT:GQ 85,15,0:1/1:75 chr12 924547 . C G 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 69,6,0:1/1:49 chr12 1555916 . G A 7.18 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 39,15,0:1/1:75 chr12 1919860 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr12 2283756 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr12 2805983 . G C 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr12 6088203 . T C 72.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=37 PL:GT:GQ 105,15,0:1/1:75 chr12 7099460 . G C 10.8 . DP=6;AF1=0.8277;CI95=0.5,1;DP4=3,0,3,0;MQ=26;PV4=1,0.027,1,1 PL:GT:GQ 39,0,1:1/1:5 chr12 7099464 . G A 13.3 . DP=6;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=28;PV4=1,0.16,1,1 PL:GT:GQ 42,1,0:1/1:23 chr12 7198516 . T G 4.61 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 34,6,0:1/1:49 chr12 23331895 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr12 28209020 . T G 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 47,15,0:1/1:75 chr12 30074073 . C T 32.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 64,6,0:1/1:49 chr12 30563452 . T C 25 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 57,9,0:1/1:63 chr12 30563453 . A G 25 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 57,9,0:1/1:63 chr12 30563464 . C A 78.8 . DP=8;AF1=1;CI95=0.5,1;DP4=0,2,0,5;MQ=34;PV4=1,0.29,1,1 PL:GT:GQ 110,6,0:1/1:49 chr12 31505085 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr12 34041336 . G A 5.46 . DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=36;PV4=1,1,0.48,0.21 PL:GT:GQ 34,0,34:0/1:34 chr12 49003648 . C G 42 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=39 PL:GT:GQ 75,24,0:1/1:96 chr12 51280690 . G A 69 . DP=98;AF1=0.5;CI95=0.5,0.5;DP4=13,0,18,0;MQ=45;PV4=1,1,0.051,1 PL:GT:GQ 99,0,84:0/1:87 chr12 69206633 . T C 17.1 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=17 PL:GT:GQ 50,33,0:1/1:99 chr12 80417253 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr12 86633033 . C T 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=43;PV4=1,1,0.33,1 PL:GT:GQ 64,0,31:0/1:34 chr12 98097274 . C T 47.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31 PL:GT:GQ 80,15,0:1/1:75 chr12 105269319 . C T 19 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26 PL:GT:GQ 51,9,0:1/1:63 chr12 109053425 . G A 9.53 . DP=8;AF1=0.5012;CI95=0.5,0.5;DP4=2,0,6,0;MQ=25;PV4=1,1,0.19,1 PL:GT:GQ 39,0,23:0/1:26 chr12 111904540 . A G 3.41 . DP=65;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 32,6,0:1/1:49 chr12 115038686 . T C 15.2 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27 PL:GT:GQ 48,21,0:1/1:84 chr12 115039419 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 34,9,0:1/1:63 chr12 115103890 . G A 66 . DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=49 PL:GT:GQ 99,114,0:1/1:99 chr12 115833830 . G A 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr12 116361873 . T G 6.34 . DP=5;AF1=0.7302;CI95=0.5,1;DP4=0,2,0,2;MQ=23;PV4=1,1,1,1 PL:GT:GQ 34,0,2:0/1:3 chr12 123583527 . G A 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 46,9,0:1/1:63 chr12 124115330 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 76,9,0:1/1:63 chr12 125062296 . G A 41.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr12 126718106 . A G 8.76 . DP=50;AF1=0.5163;CI95=0.5,1;DP4=2,0,6,0;MQ=26;PV4=1,0.33,0.37,1 PL:GT:GQ 38,0,12:0/1:15 chr12 133348311 . G A 24 . DP=18;AF1=0.5;CI95=0.5,0.5;DP4=14,0,3,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 54,0,118:0/1:57 chr12 134494475 . C T 28 . DP=18;AF1=0.6671;CI95=0.5,1;DP4=8,0,10,0;MQ=18;PV4=1,1,1,1 PL:GT:GQ 57,0,3:0/1:5 chr12 134831761 . C T 41.3 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=27 PL:GT:GQ 74,15,0:1/1:75 chr12 134992770 . A C,T 84 . DP=47;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=29 PL:GT:GQ 117,72,114,0,44,114:1/1:99 chr12 135261117 . G A 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 82,18,0:1/1:90 chr12 135261144 . A G 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 155,18,0:1/1:90 chr12 135460302 . G A 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=40 PL:GT:GQ 198,69,0:1/1:99 chr12 135463758 . A G 83 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=26 PL:GT:GQ 116,48,0:1/1:99 chr12 135523325 . G A 99 . DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=26 PL:GT:GQ 136,66,0:1/1:99 chr12 135782401 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr12 135795472 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr13 18040027 . G C 42 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33 PL:GT:GQ 74,9,0:1/1:63 chr13 19494625 . G T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr13 20121126 . A G 15.1 . DP=36;AF1=0.5;CI95=0.5,0.5;DP4=25,0,9,0;MQ=36;PV4=1,1,0.13,1 PL:GT:GQ 45,0,153:0/1:48 chr13 21536703 . A G 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr13 23160035 . G T 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 33,6,0:1/1:49 chr13 23476554 . C A 6.79 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52 PL:GT:GQ 37,6,0:1/1:49 chr13 26632967 . C G 32 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34 PL:GT:GQ 65,27,0:1/1:99 chr13 26790010 . T C 89.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35 PL:GT:GQ 122,15,0:1/1:75 chr13 36083571 . T C 43 . DP=84;AF1=1;CI95=1,1;DP4=1,0,37,0;MQ=16;PV4=1,1,1,0.3 PL:GT:GQ 76,99,0:1/1:99 chr13 44432419 . C T 3.58 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19 PL:GT:GQ 34,21,0:1/1:84 chr13 46592359 . T C 16.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 48,6,0:1/1:49 chr13 52764657 . A T 3.14 . DP=32;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 33,15,0:1/1:75 chr13 53084193 . C T 9.11 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=29;PV4=1,1,1,1 PL:GT:GQ 38,2,0:1/1:37 chr13 57763228 . C T 45 . DP=555;AF1=1;CI95=1,1;DP4=2,0,21,0;MQ=23;PV4=1,0.00021,1,0.3 PL:GT:GQ 78,45,0:1/1:99 chr13 73857921 . G C 31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 63,9,0:1/1:63 chr13 76718001 . G A 59 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=45;PV4=1,1,0.12,1 PL:GT:GQ 89,0,28:0/1:31 chr13 100912695 . A T 23 . DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,6;MQ=31;PV4=1,0.029,1,0.35 PL:GT:GQ 53,0,103:0/1:56 chr13 101332001 . G C 21 . DP=23;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=21 PL:GT:GQ 54,69,0:1/1:99 chr13 102637334 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr13 102895627 . C T 63 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=48 PL:GT:GQ 96,27,0:1/1:99 chr13 103830322 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr13 112842448 . G A 39 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=27 PL:GT:GQ 72,27,0:1/1:99 chr13 113310291 . C T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 66,12,0:1/1:72 chr13 114775162 . A G 80 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=21 PL:GT:GQ 113,51,0:1/1:99 chr13 115267482 . A G 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr13 116068676 . C T 3.83 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27 PL:GT:GQ 34,12,0:1/1:72 chr13 116455918 . A G 33 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=13,0,15,0;MQ=42;PV4=1,1.8e-20,0.3,1 PL:GT:GQ 63,0,146:0/1:66 chr13 116765012 . G A 30.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 62,6,0:1/1:49 chr13 116779773 . C T 17.1 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=27,0,11,0;MQ=24;PV4=1,4.5e-35,1,1 PL:GT:GQ 47,0,106:0/1:50 chr13 116779791 . C T 57 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=24,0,14,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 87,0,103:0/1:90 chr14 20159250 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr14 23510676 . T C 52 . DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=32 PL:GT:GQ 85,66,0:1/1:99 chr14 24735256 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr14 29525577 . G A 21 . DP=10;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=16 PL:GT:GQ 54,27,0:1/1:99 chr14 36186389 . C T 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20 PL:GT:GQ 37,6,0:1/1:49 chr14 36186394 . A G 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20 PL:GT:GQ 37,6,0:1/1:49 chr14 37440609 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr14 40432807 . A G 18.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=23 PL:GT:GQ 51,12,0:1/1:72 chr14 59466268 . T C 15.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25 PL:GT:GQ 47,9,0:1/1:63 chr14 61368162 . G T 7.18 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=17 PL:GT:GQ 39,15,0:1/1:75 chr14 65152922 . G A 92 . DP=33;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,15;MQ=36;PV4=1,0.059,0.35,1 PL:GT:GQ 122,0,144:0/1:99 chr14 69749148 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25 PL:GT:GQ 40,6,0:1/1:49 chr14 74877658 . C T 45 . DP=48;AF1=1;CI95=1,1;DP4=0,1,0,12;MQ=36;PV4=1,0.02,1,0.39 PL:GT:GQ 78,28,0:1/1:99 chr14 75546678 . C T 19.2 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=17 PL:GT:GQ 52,18,0:1/1:90 chr14 76439185 . T C 67.1 . DP=7;AF1=0.505;CI95=0.5,0.5;DP4=0,1,0,6;MQ=33;PV4=1,1,0.056,0.29 PL:GT:GQ 97,0,17:0/1:20 chr14 77313295 . T A 99 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=48 PL:GT:GQ 191,30,0:1/1:99 chr14 77673422 . G A 11.5 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=24 PL:GT:GQ 44,18,0:1/1:90 chr14 78646125 . T C 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40 PL:GT:GQ 153,24,0:1/1:96 chr14 91702449 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr14 91769842 . G A 63 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47 PL:GT:GQ 95,9,0:1/1:63 chr14 91775899 . C G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr14 91775924 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr14 93482918 . A C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr14 93665819 . C T 75 . DP=7;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,4;MQ=42;PV4=1,1,1,1 PL:GT:GQ 105,0,31:0/1:34 chr14 95422276 . A G 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=45 PL:GT:GQ 88,21,0:1/1:84 chr14 95731986 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr14 96045464 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr14 97172020 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=51 PL:GT:GQ 100,9,0:1/1:63 chr14 100515480 . A G 6.98 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,0.14,0.085,0.33 PL:GT:GQ 36,0,30:0/1:32 chr14 100770214 . A T 8.69 . DP=20;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16 PL:GT:GQ 41,21,0:1/1:84 chr14 101258303 . G A 82 . DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=26 PL:GT:GQ 115,45,0:1/1:99 chr14 101701492 . C G 66 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=49 PL:GT:GQ 99,30,0:1/1:99 chr14 102113772 . T C 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30 PL:GT:GQ 33,6,0:1/1:49 chr14 102751431 . A C 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr14 103708033 . A G 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=27 PL:GT:GQ 141,36,0:1/1:99 chr14 104744582 . G A 3.52 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 33,9,0:1/1:63 chr14 105989100 . C T 3.14 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 33,15,0:1/1:75 chr14 105989162 . C T 3.65 . DP=12;AF1=0.7301;CI95=0.5,1;DP4=0,6,0,6;MQ=15;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr14 106234810 . G A 25.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=39 PL:GT:GQ 58,15,0:1/1:75 chr14 106995572 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr14 107283057 . T C 5.5 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=20 PL:GT:GQ 37,21,0:1/1:84 chr14 107285319 . T C 33 . DP=36;AF1=1;CI95=1,1;DP4=0,0,0,35;MQ=22 PL:GT:GQ 66,105,0:1/1:99 chr14 107640449 . A G 11.8 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36 PL:GT:GQ 44,12,0:1/1:72 chr15 20082092 . T G 18.3 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24 PL:GT:GQ 51,15,0:1/1:75 chr15 22955884 . T C 67 . DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=48 PL:GT:GQ 100,36,0:1/1:99 chr15 22971987 . A G 5.29 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=22 PL:GT:GQ 35,6,0:1/1:49 chr15 23233324 . C A 47 . DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31 PL:GT:GQ 80,42,0:1/1:99 chr15 25175286 . C T 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=42;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr15 25385709 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr15 27372396 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr15 35998093 . C T 9.53 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=17 PL:GT:GQ 42,27,0:1/1:99 chr15 36716538 . C G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr15 36793360 . G T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 76,9,0:1/1:63 chr15 53783097 . A G 10.5 . DP=31;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16 PL:GT:GQ 43,21,0:1/1:84 chr15 54180175 . C T 10.4 . DP=7;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,3,0;MQ=27;PV4=1,1.2e-05,1,1 PL:GT:GQ 40,0,32:0/1:34 chr15 54939306 . C T 99 . DP=34;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,16;MQ=49;PV4=1,1,0.18,1 PL:GT:GQ 172,0,181:0/1:99 chr15 59377916 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr15 59685961 . G C 68 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=36 PL:GT:GQ 101,33,0:1/1:99 chr15 60306384 . A G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr15 60345642 . G C 14.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 46,6,0:1/1:49 chr15 60367387 . G A 13.2 . DP=6;AF1=0.5001;CI95=0.5,0.5;DP4=3,0,3,0;MQ=34;PV4=1,0.098,0.24,1 PL:GT:GQ 43,0,35:0/1:37 chr15 60367446 . C T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr15 61763755 . G A 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45 PL:GT:GQ 100,9,0:1/1:63 chr15 61831362 . C G 11.3 . DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,3;MQ=30;PV4=1,0.00077,0.47,1 PL:GT:GQ 41,0,42:0/1:41 chr15 63978880 . G C 60 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 90,3,0:1/1:41 chr15 64342445 . A G 12.2 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=18 PL:GT:GQ 44,9,0:1/1:63 chr15 65424859 . T C 11.3 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=21 PL:GT:GQ 44,30,0:1/1:99 chr15 65603698 . C T 60 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 92,9,0:1/1:63 chr15 67005078 . G A 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr15 71133512 . G C 22.3 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25 PL:GT:GQ 55,15,0:1/1:75 chr15 72619009 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr15 73272688 . C T 70.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=39 PL:GT:GQ 103,15,0:1/1:75 chr15 73699335 . T A 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=45 PL:GT:GQ 175,27,0:1/1:99 chr15 74513352 . C T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=37 PL:GT:GQ 139,30,0:1/1:99 chr15 75540536 . G A 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr15 75822537 . C A 17.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23 PL:GT:GQ 50,15,0:1/1:75 chr15 78554005 . T C 12 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 43,6,0:1/1:49 chr15 80089369 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=28 PL:GT:GQ 40,6,0:1/1:49 chr15 83089149 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 40,6,0:1/1:49 chr15 86839307 . T C 90.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 123,15,0:1/1:75 chr15 89836258 . T C 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39 PL:GT:GQ 141,24,0:1/1:96 chr15 89837706 . G A 4.13 . DP=8;AF1=0.4998;CI95=0.5,0.5;DP4=0,4,0,4;MQ=30;PV4=1,1,0.25,1 PL:GT:GQ 32,0,59:0/1:35 chr15 89857648 . T C 99 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=8,0,8,0;MQ=40;PV4=1,1,0.3,1 PL:GT:GQ 133,0,130:0/1:99 chr15 89864228 . A C 32 . DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,2,0;MQ=42;PV4=1,1,1,1 PL:GT:GQ 62,0,31:0/1:34 chr15 91261235 . G A 7.8 . DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=44;PV4=1,1,0.32,1 PL:GT:GQ 37,0,30:0/1:32 chr16 256990 . A C 10.4 . DP=16;AF1=0.5008;CI95=0.5,0.5;DP4=4,0,3,0;MQ=23;PV4=1,0.34,1,1 PL:GT:GQ 40,0,25:0/1:28 chr16 260794 . T C 3.01 . DP=19;AF1=0.4999;CI95=0.5,0.5;DP4=13,0,2,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 30,0,32:0/1:31 chr16 419905 . A G 7.9 . DP=5;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=22;PV4=1,1,1,1 PL:GT:GQ 36,1,0:1/1:23 chr16 824086 . T C 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr16 1085063 . C T 52 . DP=12;AF1=0.5;CI95=0.5,0.5;DP4=6,0,6,0;MQ=42;PV4=1,1,0.014,1 PL:GT:GQ 82,0,128:0/1:85 chr16 1221305 . T C 54 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=0,3,0,3;MQ=40;PV4=1,1,1,1 PL:GT:GQ 84,0,60:0/1:63 chr16 1411728 . A G 32.3 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35 PL:GT:GQ 65,15,0:1/1:75 chr16 1443197 . C G 64 . DP=26;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=36 PL:GT:GQ 97,75,0:1/1:99 chr16 1478746 . A T 32 . DP=20;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=28 PL:GT:GQ 65,24,0:1/1:96 chr16 1514438 . A C 45 . DP=49;AF1=1;CI95=1,1;DP4=0,0,48,0;MQ=26 PL:GT:GQ 78,144,0:1/1:99 chr16 1601989 . T C 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=29 PL:GT:GQ 133,39,0:1/1:99 chr16 2043883 . C T 30 . DP=33;AF1=1;CI95=1,1;DP4=0,0,0,33;MQ=14 PL:GT:GQ 63,99,0:1/1:99 chr16 2137470 . A C 39 . DP=38;AF1=0.5016;CI95=0.5,0.5;DP4=4,0,6,0;MQ=34;PV4=1,0.02,1,1 PL:GT:GQ 69,0,22:0/1:25 chr16 2537260 . A G 99 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=40 PL:GT:GQ 177,33,0:1/1:99 chr16 2564737 . T C 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,22;MQ=41 PL:GT:GQ 199,66,0:1/1:99 chr16 2612605 . A T 62.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28 PL:GT:GQ 95,15,0:1/1:75 chr16 2704518 . G A 41 . DP=48;AF1=0.5;CI95=0.5,0.5;DP4=0,17,0,12;MQ=48;PV4=1,1.9e-23,0.24,0.034 PL:GT:GQ 71,0,175:0/1:74 chr16 3274307 . G T 68 . DP=39;AF1=0.5;CI95=0.5,0.5;DP4=0,30,0,8;MQ=37;PV4=1,1,1,1 PL:GT:GQ 98,0,138:0/1:99 chr16 5467292 . G C 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 69,6,0:1/1:49 chr16 10079145 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr16 11483702 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr16 12038227 . A T 23 . DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,22,0,23;MQ=32;PV4=1,4.4e-66,0.47,0.028 PL:GT:GQ 53,0,135:0/1:56 chr16 21336880 . G C 55 . DP=35;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,19;MQ=47;PV4=1,5.6e-21,1,1 PL:GT:GQ 85,0,121:0/1:88 chr16 21980241 . C T 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr16 23275383 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 44,6,0:1/1:49 chr16 27546495 . G T 25 . DP=35;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43 PL:GT:GQ 57,9,0:1/1:63 chr16 27700399 . A T 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=17 PL:GT:GQ 50,12,0:1/1:72 chr16 28021935 . A G 18.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 51,15,0:1/1:75 chr16 29070016 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr16 29478618 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr16 29718140 . C T 46.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 79,15,0:1/1:75 chr16 30700759 . T C 17.1 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=14 PL:GT:GQ 50,42,0:1/1:99 chr16 35139103 . A G 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37 PL:GT:GQ 79,12,0:1/1:72 chr16 35473348 . G A 3.83 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 34,12,0:1/1:72 chr16 36213667 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr16 36705528 . G A 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=32 PL:GT:GQ 47,15,0:1/1:75 chr16 43831353 . C T 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42 PL:GT:GQ 102,12,0:1/1:72 chr16 44715166 . A C 25 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=32 PL:GT:GQ 58,24,0:1/1:96 chr16 44957661 . T C 7.03 . DP=23;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=18 PL:GT:GQ 39,21,0:1/1:84 chr16 44958698 . C T 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=49 PL:GT:GQ 75,15,0:1/1:75 chr16 44959163 . T C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 66,12,0:1/1:72 chr16 45167959 . C T 4.45 . DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=24 PL:GT:GQ 35,12,0:1/1:72 chr16 50254956 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr16 52383122 . A C 46.5 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=42 PL:GT:GQ 79,12,0:1/1:72 chr16 55978159 . C T 10.7 . DP=20;AF1=0.5336;CI95=0.5,1;DP4=2,0,5,0;MQ=35;PV4=1,0.038,1,0.059 PL:GT:GQ 40,0,9:0/1:12 chr16 61358878 . T A 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 47,6,0:1/1:49 chr16 61392487 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 44,6,0:1/1:49 chr16 61621603 . G T 6.59 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=22 PL:GT:GQ 38,12,0:1/1:72 chr16 69120890 . G C 51.3 . DP=36;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42 PL:GT:GQ 84,15,0:1/1:75 chr16 70778219 . A G 21.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=39 PL:GT:GQ 53,6,0:1/1:49 chr16 71899519 . T C 40 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33 PL:GT:GQ 73,33,0:1/1:99 chr16 72079251 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr16 72093003 . G C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr16 72672428 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr16 72864515 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr16 72890560 . G A 47.1 . DP=10;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=49;PV4=1,0.0019,0.0033,1 PL:GT:GQ 77,0,16:0/1:19 chr16 73048929 . A G 6.29 . DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=27;PV4=1,1,1,0.33 PL:GT:GQ 34,1,0:1/1:23 chr16 73177179 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr16 73191468 . C T 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40 PL:GT:GQ 102,12,0:1/1:72 chr16 73367439 . A C 7.41 . DP=36;AF1=1;CI95=0.5,1;DP4=0,2,0,13;MQ=26;PV4=1,1,0.027,1 PL:GT:GQ 37,4,0:1/1:45 chr16 74259316 . C T 89.5 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr16 75271450 . C G 6.99 . DP=15;AF1=0.5015;CI95=0.5,0.5;DP4=0,1,0,3;MQ=44;PV4=1,0.065,0.31,1 PL:GT:GQ 36,0,22:0/1:25 chr16 76199870 . G A 26 . DP=14;AF1=0.5;CI95=0.5,0.5;DP4=8,0,6,0;MQ=47;PV4=1,1.2e-06,0.32,1 PL:GT:GQ 56,0,141:0/1:59 chr16 77723692 . A G 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 122,12,0:1/1:72 chr17 165875 . G A 40.8 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 72,6,0:1/1:49 chr17 1443809 . C G 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr17 1618253 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=39 PL:GT:GQ 54,9,0:1/1:63 chr17 2815309 . T G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr17 3537486 . T G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr17 3734367 . C A 23.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36 PL:GT:GQ 56,12,0:1/1:72 chr17 5634764 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr17 6408090 . C G 3.54 . DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=3,0,2,0;MQ=40;PV4=1,1,0.36,1 PL:GT:GQ 31,0,66:0/1:34 chr17 7089723 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr17 8731503 . G C 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 42,6,0:1/1:49 chr17 9282935 . T C,G 24.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=40 PL:GT:GQ 57,12,61,0,3,61:1/1:72 chr17 17284831 . T C 29 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 61,9,0:1/1:63 chr17 18439515 . G A 4.11 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25 PL:GT:GQ 34,9,0:1/1:63 chr17 18602146 . C T 4.76 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=16 PL:GT:GQ 36,33,0:1/1:99 chr17 19427888 . C T 57 . DP=104;AF1=0.5;CI95=0.5,0.5;DP4=45,0,29,0;MQ=39;PV4=1,2.2e-12,1,1 PL:GT:GQ 87,0,131:0/1:90 chr17 19604159 . T C 9.31 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr17 19610366 . C T 13 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr17 20484706 . C G 51 . DP=35;AF1=0.5001;CI95=0.5,0.5;DP4=0,11,0,21;MQ=21;PV4=1,0.39,0.49,1 PL:GT:GQ 81,0,36:0/1:39 chr17 20555720 . A G 26.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=28 PL:GT:GQ 59,15,0:1/1:75 chr17 24328984 . A C 15.4 . DP=34;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25 PL:GT:GQ 48,15,0:1/1:75 chr17 26237090 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr17 28394766 . C A 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr17 31218277 . A G 3.62 . DP=38;AF1=0.5161;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,0.26,1,1 PL:GT:GQ 31,0,12:0/1:15 chr17 31254021 . C T 15.1 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35 PL:GT:GQ 47,9,0:1/1:63 chr17 32516798 . G A 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 69,6,0:1/1:49 chr17 32600253 . A G 16.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 49,12,0:1/1:72 chr17 34255214 . G C 19.2 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=21 PL:GT:GQ 52,18,0:1/1:90 chr17 34365900 . T C 93.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38 PL:GT:GQ 126,18,0:1/1:90 chr17 35380386 . A T 6.79 . DP=44;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 37,6,0:1/1:49 chr17 41993344 . C T 64 . DP=41;AF1=1;CI95=1,1;DP4=0,0,0,41;MQ=16 PL:GT:GQ 97,123,0:1/1:99 chr17 42128201 . A G 4.13 . DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=0,2,0,2;MQ=52;PV4=1,0.0041,1,1 PL:GT:GQ 32,0,62:0/1:35 chr17 42984490 . C A 56 . DP=33;AF1=0.5001;CI95=0.5,0.5;DP4=6,0,12,0;MQ=42;PV4=1,0.004,1,1 PL:GT:GQ 86,0,34:0/1:37 chr17 43419457 . G A 99 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=45 PL:GT:GQ 185,42,0:1/1:99 chr17 43421225 . A G 65.1 . DP=31;AF1=1;CI95=0.5,1;DP4=0,6,0,17;MQ=43;PV4=1,0.004,1,1 PL:GT:GQ 98,18,0:1/1:90 chr17 45206897 . G A 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47 PL:GT:GQ 54,9,0:1/1:63 chr17 45381302 . T C 18.6 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr17 45530812 . C A 3.54 . DP=6;AF1=0.4998;CI95=0.5,0.5;DP4=0,3,0,2;MQ=40;PV4=1,1,0.37,1 PL:GT:GQ 31,0,58:0/1:34 chr17 50242633 . G A 44 . DP=42;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,13;MQ=32;PV4=1,0.084,0.14,1 PL:GT:GQ 74,0,154:0/1:77 chr17 51275317 . G A 14.9 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 46,6,0:1/1:49 chr17 52325530 . C T 29 . DP=19;AF1=1;CI95=1,1;DP4=0,0,0,18;MQ=24 PL:GT:GQ 62,54,0:1/1:99 chr17 52411748 . T G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr17 53190746 . C G 62.1 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=40 PL:GT:GQ 95,18,0:1/1:90 chr17 58289916 . T C 18.2 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=22 PL:GT:GQ 51,18,0:1/1:90 chr17 59796875 . C T 42 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35 PL:GT:GQ 74,9,0:1/1:63 pysam-0.23.0/tests/tabix_data/vcf/2.vcf000066400000000000000000006560561475062545500176450ustar00rootroot00000000000000##fileformat=VCFv4.0 ##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/combined.phase1.chr20.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false recal_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.recal tranches_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub ts_filter_level=93.0 ignore_filter=null mode=INDEL" ##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR/AFR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN/ASN.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR/AMR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR/EUR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR.admix/AFR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN.admix/ASN.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR.admix/AMR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR.admix/EUR.admix.phase1.chr20.42.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=AFR.admix,AMR.admix,EUR.admix,ASN.admix,AFR,AMR,EUR,ASN printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 masterMerge=false mergeInfoWithMaxAC=true" ##FILTER= ##FILTER== 4 && (MQ0 / (1.0 * DP)) > 0.1"> ##FILTER=10)"> ##FILTER=20.0"> ##FILTER= 7500"> ##FILTER==15"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER==-1.0"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##LeftAlignVariants="analysis_type=LeftAlignVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/ebanks/ALL.chr20.Oxford.20110407.indels.genotypes.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub" ##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/dindel/20110208.chr20.dindel2.ALL.sites.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null select_expressions=[] excludeNonVariants=false excludeFiltered=false discordance= concordance= family_structure= mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_number=0 select_random_fraction=0.0 selectSNPs=false selectIndels=true" ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/broad/shptmp/delangel/calls/chr20/CHB.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CHS.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CLM.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/JPT.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/MXL.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/PUR.phase1.chr20.42.cleaned.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.combined.chr20.vcf, /humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=50 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=8 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=INDEL p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=GENOTYPE_GIVEN_ALLELES output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=4.0 standard_min_confidence_threshold_for_emitting=4.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=true output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[MappingQualityZeroFraction]" ##VariantAnnotator="analysis_type=VariantAnnotator input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[./ALL.chr20.vqsr_2of5_union_sites_for_validation_boosted.vcf] rodToIntervalTrackName=variant BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sampleName=null annotation=[IndelType] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false" ##VariantFiltration="analysis_type=VariantFiltration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/humgen/1kg/processing/pipeline_test_bams/chr22_chunked.hg19.intervals] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/broad/shptmp/rpoplin/ALL.phase1.chr22.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub filterExpression=[MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1, QUAL<30.0, SB>=-1.0, QD<1.0, HRun>=15, HaplotypeScore>20.0] filterName=[HARD_TO_VALIDATE, LowQual, StrandBias, QualByDepth, HomopolymerRun, HaplotypeScore] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false" ##commandline="/share/software/freebayes/bin/freebayes --stdin --min-alternate-count 2 --genotype-combo-step-max 20 --genotype-variant-threshold 4 --no-marginals --pvar 0.0001 --indels --mnps --no-filters --binomial-obs-priors --allele-balance-priors --region 20:0..100000 --vcf /d1/data/1000G/20101123/populations/finalised.phase1/integrated/including454/wg/ALL/Pipeline/none//freebayes/freebayes.20:0-100000.baq.20110328.vcf --fasta-reference /d2/data/references/build_37/human_reference_v37.fa" ##fileDate=2011-03-28 ##filedate=2011-02-08 ##filter="( SNP | MNP ) & ( MQM > 65 | QUAL > 1 ) & ABP < 30 & AB < 0.9 | ( INS | DEL ) & QUAL > 500" ##phasing=none ##platypusOptions={'bamFiles': ['/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06984', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06985', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06986', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06989', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06994', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07000', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07037', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07048', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07051', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07056', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07346', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07347', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07357', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA10847', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA10851', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11829', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11830', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11831', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11832', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11843', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11881', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11892', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11893', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11894', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11918', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11919', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11920', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11930', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11931', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11932', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11933', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11992', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11993', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11994', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11995', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12003', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12004', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12005', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12006', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12043', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12044', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12045', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12046', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12058', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12144', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12154', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12155', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12156', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12234', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12249', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12272', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12273', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12275', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12282', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12283', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12286', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12287', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12340', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12341', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12342', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12347', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12348', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12383', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12399', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12400', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12413', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12414', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12489', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12546', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12716', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12717', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12718', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12748', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12749', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12750', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12751', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12761', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12763', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12775', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12776', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12777', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12778', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12813', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12827', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12828', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12829', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12830', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12842', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12843', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12889', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12890', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18486', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18487', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18488', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18489', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18498', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18499', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18501', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18502', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18504', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18505', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18507', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18508', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18510', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18511', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18516', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18517', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18519', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18520', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18522', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18523', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18526', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18530', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18532', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18533', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18534', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18535', 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'/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18557', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18558', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18559', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18560', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18561', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18562', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18563', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18564', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18565', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18566', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18567', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18570', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18571', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18572', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18573', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18574', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18576', 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G GA 4567.01 PASS AA=20;AB=0.61111;ABA=14;ABP=6.8707;ABR=22;AC=38;AF=0.0544;AN=698;BL=374;BR=1129;BVAR;BaseQRankSum=13.364;DP=15979;DP4=1882,2188,45,37;Dels=0.00;EL=5;EPP=13.868;ER=15;FR;FS=6.503;HETAR=11;HOMA=2;HOMR=985;HP=1;HPLen=2;HR=2;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0157;IndelType=INS.NOVEL_1.Novel_A.;LEN=1;LRB=0.50233;LRBP=826.56;MQ=66.16;MQ0Fraction=0.0110;MQM=70.5;MQRankSum=-3.158;NF;NR;NS=998;PP;PV4=0.15,1,0.42,0.15;RA=3173;RL=1;RPP=38.188;RR=19;RUN=1;ReadPosRankSum=-2.346;SAB=0.7;SAF=14;SAP=9.959;SAR=6;SC=GGGCGTGGTGGTGCATGTAAT;SRB=0.50047;SRF=1588;SRP=3.0165;SRR=1585;TC;TR=9;TU=GGT;VQSLOD=10.0079;set=Intersection;sumGLbyD=23.94 20 573764 . TA T 591.51 PASS AC=91;AF=0.1987;AN=458;BaseQRankSum=0.137;DP=519;FS=3.153;HRun=1;HaplotypeScore=14.0744;InbreedingCoeff=0.1460;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;MQ=48.16;MQ0=26;MQ0Fraction=0.0501;MQRankSum=-1.636;QD=3.63;ReadPosRankSum=-4.140;SB=-408.14;VQSLOD=5.2458;set=VQSR 20 766143 . C CATCTGGTA 5521.70 PASS AA=24;AB=0.5;ABA=18;ABP=3.0103;ABR=18;AC=14;AF=0.0289;AF1=0.02038;AN=484;BL=655;BR=1542;BVAR;BaseQRankSum=3.801;CI95=0.01549,0.02655;DP=11749;DP4=2222,1998,14,8;Dels=0.00;EL=9;EPP=6.2675;ER=15;FQ=999;FR;FS=2.941;HETAR=9;HOMA=4;HOMR=901;HP=2;HPLen=2;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0515;IndelType=INS.NumRepetitions_1.EventLength_8.;LEN=8;LRB=0.40373;LRBP=780.64;MQ=56.81;MQ0Fraction=0.0253;MQM=22.167;MQRankSum=-4.809;NF;NR;NS=914;PP;PV4=0.39,1,5.8e-07,1;RA=3093;RL=6;RPP=16.039;RR=18;RUN=1;ReadPosRankSum=-2.827;SAB=0.625;SAF=15;SAP=6.2675;SAR=9;SC=GCTTTAAATTCATCTGGTACT;SRB=0.61623;SRF=1906;SRP=365.95;SRR=1187;TC;TR=1;TU=A;VQSLOD=7.0268;set=Intersection;sumGLbyD=50.23 20 997076 rs11467490 CTG C 15379.78 PASS AA=195;AB=0.59878;ABA=132;ABP=30.896;ABR=197;AC=173;AF=0.14562;AN=1188;BL=7664;BR=7309;BVAR;BaseQRankSum=21.853;DB;DEL;DP=27127;DP4=1801,2002,241,282;Dels=0.13;EL=100;EPP=3.2887;ER=95;FQ=999;FR;FS=6.591;HETAR=77;HOMA=42;HOMR=815;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1284;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TG.;LEN=2;LRB=0.023709;LRBP=21.287;MQ=61.18;MQ0Fraction=0.0214;MQM=43.041;MQRankSum=6.886;NF;NR;NS=934;PP;PV4=0.61,1.5e-78,1,1;RA=2800;RL=120;RPP=25.56;RR=75;RUN=1;ReadPosRankSum=4.504;SAB=0.62051;SAF=121;SAP=27.609;SAR=74;SC=CAGCTAATTACTGTATTTTTA;SRB=0.49821;SRF=1395;SRP=3.0879;SRR=1405;TC;TR=1;TU=T;VQSLOD=8.9396;set=Intersection;sumGLbyD=16.76 20 1042261 rs10597473 CCCTG C 168658.05 PASS AA=4481;AB=0.29043;ABA=2128;ABP=1147.1;ABR=871;AC=1172;AF=0.97830;AN=1198;BL=169975;BR=194027;BVAR;BaseQRankSum=4.599;DB;DEL;DP=29418;DP4=29,47,1441,2403;Dels=0.84;EL=2358;EPP=29.772;ER=2123;FR;FS=9.122;HETAR=482;HOMA=559;HOMR=30;HP=2;HPLen=3;HR=3;HRun=0;HU=C;INDEL;InbreedingCoeff=0.0470;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.066077;LRBP=3454.1;MQ=104.58;MQ0=4;MQ0Fraction=0.0014;MQM=58.257;MQRankSum=-3.368;NF;NR;NS=1071;PP;PV4=0.91,6.8e-09,2.8e-05,1;RA=1039;RL=2088;RPP=48.09;RR=2393;RUN=1;ReadPosRankSum=5.288;SAB=0.41442;SAF=1857;SAP=288.09;SAR=2624;SC=CCAAACCCAACCCTGCCTGGC;SRB=0.48893;SRF=508;SRP=4.1159;SRR=531;TC;TR=8;TU=CCTG;VQSLOD=8.5148;dbSNP=120;set=Intersection;sumGLbyD=59.79 20 1046297 rs33956316 C CT,CTT,CTTT 17698 PASS ABR=408;AC=432,79,230;AF=0.39779,0.07274,0.21179;BVAR;BaseQRankSum=-8.413;DB;DP=15649;DP4=147,199,534,436;FR;FS=11.580;HOMA=97;HOMR=457;HP=20;HR=16;HU=T;HaplotypeScore=16.0590;INDEL;INS;InbreedingCoeff=0.6018;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ0=19;MQ0Fraction=0.0093;MQRankSum=7.992;NF;NR;NS=767;PP;PV4=6e-05,1,1,1;QD=8.18;RA=1183;RUN=1;ReadPosRankSum=2.684;SB=-6384.08;SC=GGAAAATTTTCTTTTTTTTTT;SRB=0.40913;SRF=484;SRP=87.859;SRR=699;TC;TR=16;TU=T;VQSLOD=8.4941;dbSNP=132;set=Intersection 20 1405740 . T TA 257.28 PASS AF=0.0188;BaseQRankSum=-0.745;DP=3769;Dels=0.00;FS=0.742;HPLen=9;HRun=9;InbreedingCoeff=0.0462;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_A.;MQ0Fraction=0.0151;MQRankSum=-0.090;ReadPosRankSum=-1.582;VQSLOD=5.6502;set=Intersection;sumGLbyD=6.94 20 1690501 . TC T 27928 PASS AA=108;AB=0.91372;ABA=100;ABP=1726.1;ABR=1059;AC=35;AF=0.02966;AN=1180;BL=593;BR=6973;BVAR;BaseQRankSum=7.567;DEL;DP=10612;Dels=0.01;EL=50;EPP=4.2971;ER=58;FS=0.000;HETAR=378;HOMA=184;HOMR=477;HRun=1;InbreedingCoeff=0.0495;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.84325;LRBP=11685;MQ0=0;MQ0Fraction=0.0000;MQM=87.361;MQRankSum=4.088;NS=1045;RA=3125;RL=3;RPP=212.2;RR=105;RUN=1;ReadPosRankSum=-13.096;SAB=0.56481;SAF=61;SAP=6.9511;SAR=47;SRB=0.51776;SRF=1618;SRP=11.572;SRR=1507;VQSLOD=3.9824;set=filterInVQSR-2of5;sumGLbyD=4.07 20 1991285 rs113891396 TAA T,TA,TAAA,TAAAAA,TAAAAAA,TAAAAAAA,TAAAAAAAA 39235.36 PASS AC=5,251,20,39,188,52,79;AF=0.0056,0.2789,0.0222,0.0433,0.2089,0.0578,0.0878;AN=900;BVAR;BaseQRankSum=1.124;DB;DEL;DP=54393;DP4=906,772,824,579;Dels=0.21;FR;FS=37.525;HP=12;HR=12;HRun=12;HU=A;INDEL;INS;InbreedingCoeff=0.6891;IndelType=MULTIALLELIC_INDEL;MQ=76.81;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-6.593;NF;NR;PP;PV4=0.0087,1,6.3e-19,1;RUN=1;ReadPosRankSum=-2.184;SC=ATCTGCCACTTAAAAAAAAAA;TC;TR=12;TU=A;VQSLOD=9.0007;dbSNP=132;set=Intersection;sumGLbyD=11.45 20 2355911 . TA T 11723 PASS AA=79;AB=0.9393;ABA=57;ABP=1577;ABR=882;AC=38;AF=0.0411;AN=924;BL=644;BR=5536;BVAR;BaseQRankSum=2.434;DEL;DP=9687;Dels=0.00;EL=45;EPP=6.3362;ER=34;FS=3.043;HETAR=321;HOMA=182;HOMR=555;HRun=5;InbreedingCoeff=0.0412;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.79159;LRBP=8411.9;MQ0=0;MQ0Fraction=0.0000;MQM=70.848;MQRankSum=0.137;NS=1058;RA=3415;RL=3;RPP=149.49;RR=76;RUN=1;ReadPosRankSum=-12.116;SAB=0.44304;SAF=35;SAP=5.2367;SAR=44;SRB=0.43572;SRF=1488;SRP=125.55;SRR=1927;VQSLOD=3.8910;set=filterInVQSR-2of5;sumGLbyD=4.88 20 2771621 rs11479849 GT G,GTT 1605.60 PASS AA=80;AB=0.79825;ABA=69;ABP=267.24;ABR=273;AC=79,91;AF=0.06551,0.07546;AN=1206;BL=2593;BR=3805;BVAR;BaseQRankSum=7.825;DB;DP=9790;Dels=0.04;EL=37;EPP=3.9875;ER=43;FR;FS=4.751;HETAR=62;HOMA=5;HOMR=958;HP=11;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2646;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.18943;LRBP=501.57;MQ0=0;MQ0Fraction=0.0000;MQM=52.45;MQRankSum=-0.560;NF;NR;NS=1025;PP;RA=3949;RL=29;RPP=16.148;RR=51;RUN=1;ReadPosRankSum=-2.397;SAB=0.525;SAF=42;SAP=3.4446;SAR=38;SC=TCATTTTAACGTTTTTTTTTT;SRB=0.54368;SRF=2147;SRP=68.46;SRR=1802;TC;TR=11;TU=T;VQSLOD=3.5989;set=filterInVQSR-2of5;sumGLbyD=3.92 20 2891235 . G GT,GTTT 2869.87 PASS AC=236,246;AF=0.2803,0.2922;AN=842;BaseQRankSum=8.979;DP=1067;FS=3.911;HaplotypeScore=20.3595;InbreedingCoeff=0.6511;IndelType=MULTIALLELIC_INDEL;MQ=44.86;MQ0=114;MQ0Fraction=0.1068;MQRankSum=-2.273;QD=4.00;ReadPosRankSum=-6.601;SB=-991.85;VQSLOD=5.4379;set=VQSR 20 3033550 . TGAG T 2005.90 PASS AA=34;AB=0.51429;ABA=34;ABP=3.1344;ABR=36;AC=22;AF=0.0332;AN=662;BL=1374;BR=1649;BVAR;BaseQRankSum=5.192;DEL;DP=14639;DP4=2271,1492,12,21;Dels=0.02;EL=19;EPP=4.0322;ER=15;FR;FS=16.657;HETAR=17;HOMA=0;HOMR=914;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=-0.0454;IndelType=DEL.NumRepetitions_1.EventLength_3.;LEN=3;LRB=0.090969;LRBP=57.333;MQ=53.99;MQ0Fraction=0.0304;MQM=46.735;MQRankSum=1.938;NF;NR;NS=931;PP;PV4=0.0068,9.4e-05,1,1;RA=2985;RL=11;RPP=12.207;RR=23;RUN=1;ReadPosRankSum=-0.466;SAB=0.41176;SAF=14;SAP=5.3095;SAR=20;SC=CTTGGGAGGCTGAGGTGGGAG;SRB=0.62781;SRF=1874;SRP=426.52;SRR=1111;TC;TR=1;TU=G;VQSLOD=8.9194;set=Intersection;sumGLbyD=24.41 20 3873327 rs61519218 A AAG 683.85 PASS AC=25;AF=0.0313;AN=800;BaseQRankSum=4.839;DB;DP=1718;FS=4.265;HRun=0;HaplotypeScore=20.5789;InbreedingCoeff=0.1055;IndelType=INS.NOVEL_2.;MQ=53.70;MQ0=37;MQ0Fraction=0.0215;MQRankSum=2.468;QD=6.30;ReadPosRankSum=4.254;SB=-403.21;VQSLOD=6.1858;set=VQSR 20 4028835 . GC G 2511.30 PASS AA=66;AB=0.56954;ABA=65;ABP=9.3521;ABR=86;AC=22;AF=0.01836;AN=1198;BL=2303;BR=2463;BVAR;BaseQRankSum=7.621;DEL;DP=22795;DP4=1714,2774,22,37;Dels=0.02;EL=34;EPP=3.1419;ER=32;FQ=999;FR;FS=2.095;HETAR=21;HOMA=0;HOMR=1050;HP=2;HPLen=2;HR=2;HRun=2;HU=C;INDEL;InbreedingCoeff=0.0125;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.033571;LRBP=14.674;MQ=108.09;MQ0=0;MQ0Fraction=0.0000;MQM=53.318;MQRankSum=5.257;NF;NR;NS=1071;PP;PV4=1,5.4e-13,1,0.075;RA=6185;RL=36;RPP=4.1947;RR=30;RUN=1;ReadPosRankSum=-1.059;SAB=0.45455;SAF=30;SAP=4.1947;SAR=36;SC=TGCTGTCACTGCCTTCTCCTA;SRB=0.42118;SRF=2605;SRP=336.76;SRR=3580;TC;TR=2;TU=C;VQSLOD=10.2409;set=Intersection;sumGLbyD=12.71 20 4039609 rs67812039 G GA 43457 PASS AA=909;AB=0.54639;ABA=572;ABP=26.583;ABR=689;AC=302;AF=0.3455;AN=874;BL=37070;BR=38211;BVAR;BaseQRankSum=20.147;DB;DP=25595;DP4=1483,1374,528,542;Dels=0.00;EL=467;EPP=4.5033;ER=442;FQ=999;FR;FS=5.441;HETAR=243;HOMA=127;HOMR=608;HP=4;HPLen=3;HR=3;HRun=3;HU=A;INDEL;INS;InbreedingCoeff=0.1388;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.015157;LRBP=40.563;MQ=119.50;MQ0=0;MQ0Fraction=0.0000;MQM=83.197;MQRankSum=1.080;NF;NR;NS=978;PP;PV4=0.16,1,3.6e-12,1;RA=3033;RL=443;RPP=4.274;RR=466;RUN=1;ReadPosRankSum=-1.000;SAB=0.32233;SAF=293;SAP=252.24;SAR=616;SC=TATGTTGGGAGAAATATCAGT;SRB=0.38378;SRF=1164;SRP=358.85;SRR=1869;TC;TR=4;TU=AG;VQSLOD=9.9146;dbSNP=130;set=Intersection;sumGLbyD=16.79 20 4390056 . TC T 49312 PASS AA=91;AB=0.94353;ABA=86;ABP=2605.4;ABR=1437;AC=39;AF=0.03160;AN=1234;BL=6823;BR=731;BVAR;BaseQRankSum=2.727;DEL;DP=13149;Dels=0.00;EL=41;EPP=4.9431;ER=50;FS=4.002;HETAR=465;HOMA=313;HOMR=292;HRun=3;InbreedingCoeff=0.0326;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.80646;LRBP=10671;MQ0=0;MQ0Fraction=0.0000;MQM=69.824;MQRankSum=-0.903;NS=1073;RA=3078;RL=89;RPP=183.62;RR=2;RUN=1;ReadPosRankSum=-12.526;SAB=0.45055;SAF=41;SAP=4.9431;SAR=50;SRB=0.52567;SRF=1618;SRP=20.622;SRR=1460;VQSLOD=4.3235;set=Intersection;sumGLbyD=3.53 20 4474622 . TA T,TAA,TAAA,TAAAA 94522.28 PASS ABR=114;AC=38,68,16,900;AF=0.03333,0.05965,0.01404,0.78947;AN=1140;BVAR;BaseQRankSum=9.741;DB;DP=16656;Dels=0.00;FR;FS=2.355;HOMA=3;HOMR=936;HP=10;HPLen=10;HR=10;HRun=10;HU=A;INS;InbreedingCoeff=0.4516;IndelType=MULTIALLELIC_INDEL;MQ0=2;MQ0Fraction=0.0008;MQRankSum=-4.096;NF;NR;NS=980;PP;RA=3766;RUN=1;ReadPosRankSum=2.380;SC=AGAAAAAAATTAAAAAAAAAA;SRB=0.49734;SRF=1873;SRP=3.2409;SRR=1893;TC;TR=10;TU=A;VQSLOD=8.8186;set=Intersection;sumGLbyD=38.79 20 4824911 . AC A 41998.70 PASS AC=1172;AF=0.97342;AN=1204;BaseQRankSum=8.604;DP=3615;FS=9.934;HRun=1;HaplotypeScore=39.6843;InbreedingCoeff=0.0980;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=129.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=3.378;QD=11.62;ReadPosRankSum=6.967;SB=-16955.28;VQSLOD=4.2689;set=VQSR 20 4839897 rs35881880 TAA T,TA,TAAA,TAAAAA 3906.80 PASS AC=12,95,137,189;AF=0.01024,0.08106,0.11689,0.16126;AN=1172;BVAR;BaseQRankSum=15.271;DB;DEL;DP=15105;Dels=0.04;FR;FS=43.567;HP=19;HR=13;HRun=13;HU=A;INS;InbreedingCoeff=0.5716;IndelType=MULTIALLELIC_INDEL;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.569;NF;NR;PP;RUN=1;ReadPosRankSum=-13.794;SC=TGTTAAAAAATAAAAAAAAAA;TC;TR=13;TU=A;VQSLOD=8.1773;set=Intersection;sumGLbyD=3.77 20 5507414 . G GCC 439.08 PASS AC=23;AF=0.01876;AN=1226;BaseQRankSum=3.051;DP=3023;FS=3.636;HRun=1;HaplotypeScore=30.3104;InbreedingCoeff=0.0204;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=112.09;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.065;QD=2.85;ReadPosRankSum=-2.709;SB=-302.22;VQSLOD=4.4311;set=VQSR 20 5609676 . GA G,GAA 799.89 PASS AA=42;AB=0.79096;ABA=37;ABP=133.16;ABR=140;AC=43,65;AF=0.03607,0.05453;AF1=0.02826;AN=1192;BL=1360;BR=2334;BVAR;BaseQRankSum=5.069;CI95=0.01242,0.04037;DP=15610;DP4=1548,2441,21,30;Dels=0.02;EL=18;EPP=4.8716;ER=24;FQ=12.1;FR;FS=0.000;HETAR=36;HOMA=1;HOMR=991;HP=13;HPLen=10;HR=10;HRun=10;HU=A;INDEL;INS;InbreedingCoeff=0.2001;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.26367;LRBP=560.68;MQ=63.29;MQ0Fraction=0.0003;MQM=44.143;MQRankSum=1.755;NF;NR;NS=1028;PP;PV4=0.77,1,0.0087,0.0053;RA=4114;RL=15;RPP=10.455;RR=27;RUN=1;ReadPosRankSum=-2.978;SAB=0.5;SAF=21;SAP=3.0103;SAR=21;SC=AAAAAAGAAAGAAAAAAAAAA;SRB=0.39742;SRF=1635;SRP=379;SRR=2479;TC;TR=11;TU=AAAG;VQSLOD=4.1229;set=filterInVQSR-2of5;sumGLbyD=7.95 20 5736211 rs35303106 CT C,CTT 4384.40 PASS AA=117;AB=0.71499;ABA=116;ABP=166.4;ABR=291;AC=32,145;AF=0.02712,0.12288;AN=1180;BL=5556;BR=4901;BVAR;BaseQRankSum=2.708;DB;DP=9157;Dels=0.01;EL=54;EPP=4.5136;ER=63;FR;FS=2.802;HETAR=79;HOMA=1;HOMR=837;HP=16;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.1903;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.062637;LRBP=92.1;MQ0Fraction=0.0273;MQM=48.932;MQRankSum=3.654;NF;NR;NS=917;PP;RA=2785;RL=79;RPP=34.209;RR=38;RUN=1;ReadPosRankSum=0.795;SAB=0.5641;SAF=66;SAP=7.1862;SAR=51;SC=TTTTCTTTTTCTTTTTTTTTT;SRB=0.41795;SRF=1164;SRP=165.85;SRR=1621;TC;TR=11;TU=T;VQSLOD=5.0895;set=Intersection;sumGLbyD=4.66 20 5898626 rs34483659 CAAA C,CA,CAA,CAAAAA 1140.16 PASS ABR=34;AC=19,98,56,199;AF=0.0227,0.1172,0.0670,0.2380;AF1=0.08519;BVAR;BaseQRankSum=5.049;CI95=0.03727,0.1273;DB;DEL;DP=5091;DP4=539,408,121,123;FQ=4.43;FR;FS=5.701;HOMA=64;HOMR=156;HP=19;HR=18;HU=A;HaplotypeScore=11.5333;INDEL;InbreedingCoeff=0.7405;IndelType=MULTIALLELIC_INDEL;MQ0=117;MQ0Fraction=0.0986;MQRankSum=6.290;NF;NR;NS=240;PP;PV4=0.043,1,1,0.0087;QD=1.22;RA=204;RUN=1;ReadPosRankSum=-2.684;SB=-1015.09;SC=ACTAAAAATACAAAAAAAAAA;SRB=0.35294;SRF=72;SRP=41.33;SRR=132;TC;TR=18;TU=A;VQSLOD=4.1696;set=filterInVQSR-2of5 20 5975126 rs10541892 C CAG 504.78 PASS AC=79;AF=0.07004;AN=1128;BaseQRankSum=10.498;DB;DP=2050;FS=38.228;HRun=0;HaplotypeScore=14.1426;InbreedingCoeff=-0.0053;IndelType=INS.NOVEL_2.;MQ=60.40;MQ0=80;MQ0Fraction=0.0390;MQRankSum=5.098;QD=1.63;ReadPosRankSum=-4.851;SB=-590.69;VQSLOD=4.8517;set=VQSR 20 6040983 rs11087710 A AAAAAAGAG,AAAAAGAG,AAAAGAG,AAAAGAGAG,AAAGAG,AAAGAGAG,AAGAG,AAGAGAG,AG,AGAG,AGAGAG 66894.55 PASS ABR=468;AC=80,9,20,136,31,91,33,29,9,3,5;AF=0.0980,0.0110,0.0245,0.1667,0.0380,0.1115,0.0404,0.0355,0.0110,0.0037,0.0061;AN=816;BVAR;BaseQRankSum=-12.470;DB;DP=38726;DP4=426,611,310,472;Dels=0.00;FQ=999;FR;FS=6.635;HOMA=110;HOMR=506;HP=14;HR=15;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.8291;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ=54.22;MQ0Fraction=0.0168;MQRankSum=-5.329;NF;NR;NS=861;PP;PV4=0.56,1,6.9e-09,0.31;RA=1828;RUN=1;ReadPosRankSum=-7.857;SC=AAAAAAAAAAAAGAGAGAGAG;SRB=0.62418;SRF=1141;SRP=247.85;SRR=687;TC;TR=15;TU=A;VQSLOD=9.0574;dbSNP=131;set=Intersection;sumGLbyD=36.72 20 7024548 . G GAT 5041.27 PASS AC=123;AF=0.10336;AN=1190;BaseQRankSum=23.097;DP=3045;FS=7.979;HRun=0;HaplotypeScore=15.6967;InbreedingCoeff=0.1062;IndelType=INS.NumRepetitions_5.EventLength_2.RepeatExpansion_AT.;MQ=119.29;MQ0=2;MQ0Fraction=0.0007;MQRankSum=-3.725;QD=8.97;ReadPosRankSum=-1.636;SB=-2257.45;VQSLOD=5.9332;set=VQSR 20 7484554 . A AT 5.09 PASS AC=0;AF=0.0000;AN=710;BaseQRankSum=-0.696;DP=1862;FS=2.835;HRun=9;HaplotypeScore=13.5425;InbreedingCoeff=0.0567;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_T.;MQ=76.92;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.932;ReadPosRankSum=-1.701;VQSLOD=4.3156;set=VQSR 20 7632194 rs77286341 GAA AAA,G 5324 PASS AC=0;AF=0.0000;AN=700;BaseQRankSum=-1.741;DB;DP=1772;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=60.1795;InbreedingCoeff=0.0017;IndelType=MIXED;MQ=70.69;MQ0=13;MQ0Fraction=0.0073;MQRankSum=-1.315;NF;NR;PP;ReadPosRankSum=-3.650;SC=GAGAGAGAGAGAAAGGTGTAA;TC;TR=13;TU=AG;set=filterInVQSR-2of5 20 7767508 rs71329674 G GA 17914 PASS AA=415;AB=0.61617;ABA=337;ABP=105.94;ABR=541;AC=141;AF=0.11614;AN=1214;BL=15187;BR=20323;BVAR;BaseQRankSum=-13.946;DB;DP=28222;Dels=0.00;EL=184;EPP=14.569;ER=231;FQ=999;FR;FS=13.296;HETAR=178;HOMA=35;HOMR=822;HP=14;HPLen=9;HR=9;HRun=9;HU=A;INDEL;INS;InbreedingCoeff=0.0714;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.14464;LRBP=1616.1;MQ=89.69;MQ0=1;MQ0Fraction=0.0003;MQM=51.667;MQRankSum=0.664;NF;NR;NS=1035;PP;RA=3707;RL=171;RPP=30.894;RR=244;RUN=1;ReadPosRankSum=-1.120;SAB=0.45301;SAF=188;SAP=10.969;SAR=227;SC=ATTCTAAAAAGAAAAAAAAAT;SRB=0.38495;SRF=1427;SRP=429.23;SRR=2280;TC;TR=9;TU=A;VQSLOD=9.0748;set=Intersection;sumGLbyD=11.09 20 7920261 . TA T,TAA 802.15 PASS AA=28;AB=0.8;ABA=28;ABP=112.45;ABR=112;AC=22,39;AF=0.01836,0.03255;AN=1198;BL=943;BR=1487;BVAR;BaseQRankSum=2.233;DP=10645;Dels=0.01;EL=11;EPP=5.8022;ER=17;FR;FS=1.691;HETAR=20;HOMA=0;HOMR=1007;HP=10;HPLen=9;HR=9;HRun=9;HU=A;INS;InbreedingCoeff=0.2256;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.22387;LRBP=267.46;MQ0=0;MQ0Fraction=0.0000;MQM=57.571;MQRankSum=0.940;NF;NR;NS=1027;PP;RA=4776;RL=8;RPP=14.178;RR=20;RUN=1;ReadPosRankSum=-1.567;SAB=0.53571;SAF=15;SAP=3.3205;SAR=13;SC=GTAACTGCTATAAAAAAAAAC;SRB=0.48576;SRF=2320;SRP=11.42;SRR=2456;TC;TR=9;TU=A;VQSLOD=4.0815;set=filterInVQSR-2of5;sumGLbyD=5.37 20 8012465 rs10595338 TATGA T 2104.41 PASS AF=0.03339;BaseQRankSum=10.662;DB;DP=11772;DS;Dels=0.01;FR;FS=7.678;HP=1;HPLen=1;HR=1;HRun=0;HU=A;InbreedingCoeff=0.0266;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ0Fraction=0.0731;MQRankSum=0.603;NF;NR;PP;ReadPosRankSum=1.276;SC=TGTATGTATGTATGATGTATG;TC;TR=19;TU=ATGT;VQSLOD=4.1376;set=filterInVQSR-2of5;sumGLbyD=6.53 20 8573999 . CGTGT C,CGT,CGTGTGT,TGTGT 45865.96 PASS AC=458,0,731;AF=0.37727,0.00000,0.60214;AN=1214;BVAR;BaseQRankSum=-6.703;DEL;DP=37714;Dels=0.03;FR;FS=11.079;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.7632;IndelType=MIXED;LEN=2;MQ0Fraction=0.0026;MQRankSum=-1.394;NF;NR;PP;RUN=1;ReadPosRankSum=-2.102;SC=TGTGTGTGCGCGTGTGTGTGT;TC;TR=18;TU=GT;VQSLOD=6.1435;set=Intersection;sumGLbyD=3.53 20 8610455 rs10571111 TTTTC T 11763.51 PASS AC=190;AF=0.17056;AN=1114;BaseQRankSum=-14.397;DB;DP=2323;FS=2.321;HRun=0;HaplotypeScore=39.8020;InbreedingCoeff=0.2502;IndelType=DEL.NumRepetitions_2.EventLength_4.;MQ=53.39;MQ0=104;MQ0Fraction=0.0448;MQRankSum=3.519;QD=19.07;ReadPosRankSum=4.150;SB=-4067.02;VQSLOD=5.0554;set=VQSR 20 9139079 . ATT A,AT,ATTT,ATTTT,ATTTTT 8777.90 PASS AC=23,140,114,69,113;AF=0.01993,0.12132,0.09879,0.05979,0.09792;AN=1154;BVAR;BaseQRankSum=-0.022;DEL;DP=25109;DP4=502,657,278,313;FR;FS=11.929;HP=16;HR=16;HU=T;HaplotypeScore=20.2361;INDEL;INS;InbreedingCoeff=0.5704;IndelType=MULTIALLELIC_INDEL;MQ0=16;MQ0Fraction=0.0067;MQRankSum=2.624;NF;NR;PP;PV4=0.14,1,1,1;QD=1.48;RUN=1;ReadPosRankSum=-0.480;SB=-2354.28;SC=CACCTGGCTAATTTTTTTTTT;TC;TR=16;TU=T;VQSLOD=6.9180;set=Intersection 20 9862448 . CT C 49312 PASS AA=60;AB=0.96003;ABA=53;ABP=2440.4;ABR=1273;AC=18;AF=0.01461;AN=1232;BL=3516;BR=140;BVAR;BaseQRankSum=-2.056;DEL;DP=11893;Dels=0.01;EL=35;EPP=6.6294;ER=25;FS=1.787;HETAR=396;HOMA=344;HOMR=334;HRun=1;InbreedingCoeff=0.0379;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.92341;LRBP=6772.5;MQ0Fraction=0.0006;MQM=54.267;MQRankSum=-0.907;NS=1074;RA=2990;RL=60;RPP=133.3;RR=0;RUN=1;ReadPosRankSum=-10.579;SAB=0.58333;SAF=35;SAP=6.6294;SAR=25;SRB=0.47826;SRF=1430;SRP=15.284;SRR=1560;VQSLOD=3.0237;set=filterInVQSR-2of5;sumGLbyD=2.84 20 9863736 rs73618103 G GT 50570.21 PASS AA=2247;AB=0.48878;ABA=1412;ABP=6.0324;ABR=1350;AC=546;AF=0.44463;AN=1228;BL=86886;BR=95862;BVAR;BaseQRankSum=-23.978;DB;DP=32517;DP4=1125,1133,1017,1048;Dels=0.00;EL=1089;EPP=7.6113;ER=1158;FQ=999;FR;FS=2.529;HETAR=445;HOMA=201;HOMR=393;HP=4;HPLen=4;HR=4;HRun=4;HU=T;INDEL;INS;InbreedingCoeff=0.1393;IndelType=INS.NumRepetitions_4.EventLength_1.RepeatExpansion_T.;KGPilot123;LEN=1;LRB=0.049117;LRBP=960.35;MQ=68.10;MQ0=2;MQ0Fraction=0.0006;MQM=50.931;MQRankSum=-1.580;NF;NR;NS=1039;PP;PV4=0.71,1,0.11,1;RA=3139;RL=1089;RPP=7.6113;RR=1158;RUN=1;ReadPosRankSum=0.846;SAB=0.54161;SAF=1217;SAP=36.804;SAR=1030;SC=TGATTGTATGGTTTTGTCCTT;SRB=0.53425;SRF=1677;SRP=34.987;SRR=1462;TC;TR=4;TU=T;VLD;VQSLOD=10.1800;dbSNP=131;set=Intersection;sumGLbyD=18.20 20 10926959 . AG A 12239 PASS AA=65;AB=0.92801;ABA=64;ABP=1417.6;ABR=825;AC=24;AF=0.0264;AN=908;BL=616;BR=3782;BVAR;BaseQRankSum=9.990;DEL;DP=10708;Dels=0.01;EL=37;EPP=5.7163;ER=28;FS=1.652;HETAR=275;HOMA=70;HOMR=724;HRun=1;InbreedingCoeff=0.0102;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.71987;LRBP=4952;MQ0=1;MQ0Fraction=0.0004;MQM=118.82;MQRankSum=1.018;NS=1069;RA=4746;RL=5;RPP=104.07;RR=60;RUN=1;ReadPosRankSum=-12.039;SAB=0.41538;SAF=27;SAP=7.0526;SAR=38;SRB=0.4764;SRF=2261;SRP=25.968;SRR=2485;VQSLOD=2.9713;set=filterInVQSR-2of5;sumGLbyD=4.10 20 11299648 . TG T 49315 PASS AA=62;AB=0.95292;ABA=54;ABP=2046.7;ABR=1093;AC=28;AF=0.0373;AN=750;BL=3126;BR=528;BVAR;BaseQRankSum=-4.929;DEL;DP=10764;Dels=0.01;EL=26;EPP=6.5127;ER=36;FS=3.851;HETAR=366;HOMA=383;HOMR=304;HRun=1;InbreedingCoeff=0.0267;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.711;LRBP=4014.1;MQ0=1;MQ0Fraction=0.0005;MQM=76.468;MQRankSum=1.327;NS=1070;RA=2588;RL=54;RPP=77.121;RR=8;RUN=1;ReadPosRankSum=-12.507;SAB=0.48387;SAF=30;SAP=3.1504;SAR=32;SRB=0.47643;SRF=1233;SRP=15.499;SRR=1355;VQSLOD=3.8673;set=filterInVQSR-2of5;sumGLbyD=3.00 20 11561096 . CTA C 999 PASS AC=2;AF=0.0029;AF1=0.005602;BaseQRankSum=3.190;CI95=0.004425,0.01106;DP=7521;DP4=1998,1794,2,4;Dels=0.00;FQ=999;FR;FS=5.422;HP=3;HPLen=2;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0056;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;MQ=113.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.297;NF;NR;PP;PV4=0.43,0.024,1,1;ReadPosRankSum=1.406;SC=CAATAGTATTCTATGTCAGTC;TC;TR=1;TU=T;VQSLOD=8.6243;set=Intersection;sumGLbyD=21.89 20 11723671 . C CA 1096.60 PASS AA=35;AB=0.69565;ABA=35;ABP=41.247;ABR=80;AC=10;AF=0.0141;AN=710;BL=2005;BR=1702;BVAR;BaseQRankSum=-3.427;DP=9819;Dels=0.00;EL=20;EPP=4.5614;ER=15;FR;FS=3.814;HETAR=20;HOMA=0;HOMR=1034;HP=8;HPLen=7;HR=7;HRun=7;HU=A;INS;InbreedingCoeff=0.0323;IndelType=INS.NumRepetitions_7.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.081737;LRBP=56.79;MQ0=0;MQ0Fraction=0.0000;MQM=81.057;MQRankSum=0.050;NF;NR;NS=1054;PP;RA=5562;RL=22;RPP=8.0357;RR=13;RUN=1;ReadPosRankSum=-2.012;SAB=0.71429;SAF=25;SAP=16.97;SAR=10;SC=ATATTGAAGACAAAAAAACAG;SRB=0.49371;SRF=2746;SRP=4.9233;SRR=2816;TC;TR=7;TU=A;VQSLOD=7.4342;set=Intersection;sumGLbyD=8.30 20 12238835 rs113904674 CTCTTCATGGTCT C 1813.44 PASS AA=7;AB=0.73077;ABA=7;ABP=15.037;ABR=19;AC=4;AF=0.0056;AN=712;BL=360;BR=368;BVAR;BaseQRankSum=3.891;DB;DEL;DP=10309;Dels=0.00;EL=4;EPP=3.3205;ER=3;FR;FS=0.000;HETAR=3;HOMA=0;HOMR=1076;HP=1;HPLen=2;HR=2;HRun=0;HU=C;InbreedingCoeff=-0.0381;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;LEN=12;LRB=0.010989;LRBP=3.2012;MQ0=0;MQ0Fraction=0.0000;MQM=37;MQRankSum=-3.793;NF;NR;NS=1079;PP;RA=6085;RL=4;RPP=3.3205;RR=3;RUN=1;ReadPosRankSum=1.319;SAB=0.42857;SAF=3;SAP=3.3205;SAR=4;SC=CTTAATGCTCCTCTTCATGGT;SRB=0.51257;SRF=3119;SRP=11.364;SRR=2966;TC;TR=6;TU=CCT;VQSLOD=5.7551;set=Intersection;sumGLbyD=69.48 20 12602812 . AT A 12344 PASS AA=47;AB=0.94372;ABA=43;ABP=1309.5;ABR=721;AC=14;AF=0.0196;AN=716;BL=2714;BR=217;BVAR;BaseQRankSum=1.424;DEL;DP=10743;Dels=0.00;EL=24;EPP=3.0565;ER=23;FS=0.629;HETAR=228;HOMA=65;HOMR=769;HRun=1;InbreedingCoeff=0.0233;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.85193;LRBP=4622.3;MQ0Fraction=0.0000;MQM=99.574;MQRankSum=1.901;NS=1080;RA=4839;RL=46;RPP=96.568;RR=1;RUN=1;ReadPosRankSum=-9.906;SAB=0.53191;SAF=25;SAP=3.4261;SAR=22;SRB=0.51106;SRF=2473;SRP=8.148;SRR=2366;VQSLOD=2.8161;set=filterInVQSR-2of5;sumGLbyD=3.67 20 13600884 . CTG C,CTGTG 1278.10 PASS AA=85;AB=0.77994;ABA=79;ABP=247.38;ABR=280;AC=71,22;AF=0.05907,0.01830;AN=1202;BL=3279;BR=3205;BVAR;BaseQRankSum=8.852;DEL;DP=24185;DP4=1317,931,52,49;Dels=0.03;EL=45;EPP=3.649;ER=40;FQ=999;FR;FS=31.826;HETAR=75;HOMA=4;HOMR=926;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1566;IndelType=MULTIALLELIC_INDEL;LEN=2;LRB=0.011413;LRBP=4.8442;MQ=65.06;MQ0Fraction=0.0012;MQM=48.671;MQRankSum=-0.511;NF;NR;NS=1005;PP;PV4=0.18,1,0.39,0.27;RA=3342;RL=35;RPP=8.7583;RR=50;RUN=1;ReadPosRankSum=-2.329;SAB=0.43529;SAF=37;SAP=6.1015;SAR=48;SC=TCCCTTTACTCTGTGTGTGTG;SRB=0.59066;SRF=1974;SRP=241.62;SRR=1368;TC;TR=15;TU=GT;VQSLOD=3.8635;set=filterInVQSR-2of5;sumGLbyD=4.23 20 13666265 . T TATAG 556.88 PASS AC=21;AF=0.01959;AN=1072;BaseQRankSum=24.958;DP=2706;FS=2.581;HRun=0;HaplotypeScore=25.9952;InbreedingCoeff=0.1419;IndelType=INS.NOVEL_4.;MQ=72.43;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.888;QD=4.38;ReadPosRankSum=2.552;SB=-417.04;VQSLOD=7.3380;set=VQSR 20 13861245 rs72422273 C CTCA 2685.46 PASS AC=140;AF=0.11589;AN=1208;BaseQRankSum=24.355;DB;DP=2910;FS=6.808;HRun=0;HaplotypeScore=19.3095;InbreedingCoeff=-0.0991;IndelType=INS.NumRepetitions_1.EventLength_3.;MQ=78.25;MQ0=22;MQ0Fraction=0.0076;MQRankSum=3.225;QD=3.64;ReadPosRankSum=2.607;SB=-1861.38;VQSLOD=4.1974;set=VQSR 20 13865746 . T TA,TAA 1416.23 PASS AA=63;AB=0.80417;ABA=47;ABP=195.87;ABR=193;AC=122,21;AF=0.10133,0.01744;AN=1204;BL=3673;BR=1145;BVAR;BaseQRankSum=-3.336;DP=10513;Dels=0.00;EL=62;EPP=131.27;ER=1;FR;FS=716.583;HETAR=45;HOMA=1;HOMR=998;HP=2;HR=1;HRun=1;HU=A;INS;InbreedingCoeff=0.0814;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.5247;LRBP=2883.3;MQ0=0;MQ0Fraction=0.0000;MQM=56.143;MQRankSum=-1.197;NF;NR;NS=1044;PP;RA=4529;RL=62;RPP=131.27;RR=1;RUN=1;ReadPosRankSum=-12.295;SAB=1;SAF=63;SAP=139.81;SAR=0;SC=GGAACATGGATACCCCCCTGC;SRB=0.52462;SRF=2376;SRP=26.853;SRR=2153;TC;TR=1;TU=A;VQSLOD=-4.2308;set=filterInVQSR-2of5;sumGLbyD=4.77 20 13881703 . CTT C 152.85 PASS AC=8;AF=0.0093;AN=862;BaseQRankSum=3.941;DP=2063;FS=0.962;HRun=5;HaplotypeScore=24.0313;InbreedingCoeff=0.0790;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_T.;MQ=55.05;MQ0=49;MQ0Fraction=0.0238;MQRankSum=-1.418;QD=3.47;ReadPosRankSum=-0.605;SB=-93.04;VQSLOD=5.3874;set=VQSR 20 14260090 rs73619828 A AT 27935 PASS AA=596;AB=0.59484;ABA=487;ABP=96.922;ABR=715;AC=204;AF=0.17000;AN=1200;BL=21718;BR=28458;BVAR;BaseQRankSum=0.756;DB;DP=23629;DP4=1385,1492,287,328;Dels=0.00;EL=299;EPP=3.0249;ER=297;FQ=999;FR;FS=6.187;HETAR=218;HOMA=38;HOMR=788;HP=9;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.0797;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13433;LRBP=1969;MQ=100.81;MQ0=0;MQ0Fraction=0.0000;MQM=57.084;MQRankSum=2.224;NF;NR;NS=1044;PP;PV4=0.53,1,1.2e-11,1;RA=4143;RL=238;RPP=55.475;RR=358;RUN=1;ReadPosRankSum=0.198;SAB=0.46812;SAF=279;SAP=8.2714;SAR=317;SC=CCTTAAGTTGATTTTTTTTTC;SRB=0.50374;SRF=2087;SRP=3.514;SRR=2056;TC;TR=9;TU=T;VQSLOD=9.0018;set=Intersection;sumGLbyD=10.82 20 14260558 . AC A 238 PASS AC=1;AF=0.0014;AF1=0.003368;BaseQRankSum=2.868;CI95=0.003106,0.006211;DP=9724;DP4=2075,2329,1,7;Dels=0.00;FQ=106;FR;FS=10.678;HP=1;HPLen=2;HR=2;HRun=1;HU=A;INDEL;InbreedingCoeff=-0.0406;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=114.37;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.862;NF;NR;PP;PV4=0.074,0.0096,0.017,1;ReadPosRankSum=-0.042;SC=ATCAGGAATAACTGTGTGACC;TC;TR=2;TU=A;VQSLOD=8.1618;set=Intersection;sumGLbyD=18.65 20 14425481 . GTA G,GTATA 148.85 PASS AC=43,23;AF=0.03473,0.01858;AN=1238;BaseQRankSum=6.289;DP=25167;DP4=1800,2021,38,49;FR;FS=9.416;HP=2;HPLen=1;HR=1;HU=T;HaplotypeScore=17.7453;INDEL;InbreedingCoeff=0.0995;IndelType=MULTIALLELIC_INDEL;MQ0=21;MQ0Fraction=0.0058;MQRankSum=-0.200;NF;NR;PP;PV4=0.59,1,0.04,0.023;QD=0.35;ReadPosRankSum=-1.689;SB=-367.50;SC=CTGTGTGTGTGTATATATATA;TC;TR=13;TU=AT;VQSLOD=3.5796;set=filterInVQSR-2of5 20 14943522 rs11478299 GA AA,G 1761.24 PASS AA=117;AB=0.68142;ABA=108;ABP=99.919;ABR=231;AC=0;AF=0.0000;AF1=0.04204;AN=712;BL=4931;BR=5802;BVAR;BaseQRankSum=9.118;CI95=0.02876,0.05752;DB;DEL;DP=13717;DP4=1908,1684,59,58;Dels=0.05;EL=60;EPP=3.1773;ER=57;FQ=81.9;FR;HETAR=56;HOMA=1;HOMR=1011;HP=8;HPLen=8;HR=8;HU=A;INDEL;InbreedingCoeff=0.1264;IndelType=MIXED;LEN=1;LRB=0.081152;LRBP=156.5;MQ=106.93;MQ0=0;MQ0Fraction=0.0000;MQM=96.855;MQRankSum=1.619;NF;NR;NS=1068;PP;PV4=0.57,1,0.0003,1;QD=7.40;RA=5080;RL=56;RPP=3.4743;RR=61;RUN=1;ReadPosRankSum=0.814;SAB=0.52137;SAF=61;SAP=3.4743;SAR=56;SB=-1122.51;SC=GTTGTTTGGGGAAAAAAAACT;SRB=0.51083;SRF=2595;SRP=8.1825;SRR=2485;TC;TR=8;TU=A;set=filterInVQSR-2of5;sumGLbyD=9.81 20 14974486 . A AG 4101.40 PASS AA=57;AB=0.57143;ABA=51;ABP=8.2839;ABR=68;AC=22;AF=0.01846;AN=1192;BL=2286;BR=2834;BVAR;BaseQRankSum=8.711;DP=20538;DP4=2172,2100,19,13;Dels=0.00;EL=32;EPP=4.877;ER=25;FS=0.517;HETAR=20;HOMA=4;HOMR=1027;HRun=1;INDEL;INS;InbreedingCoeff=0.0677;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.10703;LRBP=130.37;MQ=126.07;MQ0=0;MQ0Fraction=0.0000;MQM=56.088;MQRankSum=-10.756;NS=1051;PV4=0.38,3.5e-51,7.9e-34,1;RA=5203;RL=26;RPP=3.9627;RR=31;RUN=1;ReadPosRankSum=1.283;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SRB=0.51816;SRF=2696;SRP=17.918;SRR=2507;VQSLOD=8.0072;set=Intersection;sumGLbyD=25.60 20 15111137 . GA G 13533 PASS AA=98;AB=0.84864;ABA=89;ABP=623.8;ABR=499;AC=47;AF=0.03796;AN=1238;BL=5324;BR=856;BVAR;BaseQRankSum=-11.577;DEL;DP=13384;Dels=0.01;EL=53;EPP=4.4284;ER=45;FS=6.099;HETAR=219;HOMA=845;HOMR=18;HRun=1;InbreedingCoeff=-0.0056;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.72298;LRBP=7017.4;MQ0Fraction=0.0003;MQM=90.449;MQRankSum=1.408;NS=1083;RA=590;RL=87;RPP=130.99;RR=11;RUN=1;ReadPosRankSum=-18.074;SAB=0.55102;SAF=54;SAP=5.2261;SAR=44;SRB=0.52373;SRF=309;SRP=5.8958;SRR=281;VQSLOD=4.1054;set=filterInVQSR-2of5;sumGLbyD=3.06 20 15283028 . A AC,ACACACACACACAC 140844.83 PASS AA=180;AB=0.61442;ABA=123;ABP=39.285;ABR=196;AC=13,817;AF=0.01111,0.69829;AN=1170;BL=4453;BR=11407;BVAR;BaseQRankSum=24.686;DP=6365;Dels=0.00;EL=124;EPP=58.793;ER=56;FR;FS=10.912;HETAR=87;HOMA=48;HOMR=683;HP=1;HR=1;HRun=1;HU=T;INS;InbreedingCoeff=0.2074;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.43846;LRBP=6624;MQ0Fraction=0.0558;MQM=38.211;MQRankSum=-21.111;NF;NR;NS=818;PP;RA=1732;RL=0;RPP=393.88;RR=180;RUN=1;ReadPosRankSum=-7.620;SAB=0.31111;SAF=56;SAP=58.793;SAR=124;SC=ACACACACACATACACACATA;SRB=0.54042;SRF=936;SRP=27.584;SRR=796;TC;TR=21;TU=AC;VQSLOD=4.7569;set=Intersection;sumGLbyD=18.36 20 15361056 . ATAACT A 4892.81 PASS AA=59;AB=0.63576;ABA=55;ABP=27.184;ABR=96;AC=34;AF=0.0487;AN=698;BL=3164;BR=1999;BVAR;BaseQRankSum=3.391;DEL;DP=7080;Dels=0.03;EL=27;EPP=3.9304;ER=32;FR;FS=4.816;HETAR=35;HOMA=6;HOMR=966;HP=2;HPLen=3;HR=3;HRun=0;HU=A;InbreedingCoeff=0.0785;IndelType=DEL.NumRepetitions_1.EventLength_5.;LEN=5;LRB=0.22564;LRBP=573.84;MQ0=0;MQ0Fraction=0.0000;MQM=70.034;MQRankSum=-8.732;NF;NR;NS=1008;PP;RA=3915;RL=42;RPP=26.013;RR=17;RUN=1;ReadPosRankSum=-0.735;SAB=0.44068;SAF=26;SAP=4.8137;SAR=33;SC=AGATTAGGAAATAACTTAGGG;SRB=0.42682;SRF=1671;SRP=185.12;SRR=2244;TC;TR=3;TU=A;VQSLOD=7.0900;set=Intersection;sumGLbyD=43.38 20 15579507 . AATTAGTC A,TATTAGTC 1936.38 PASS AA=16;AB=0.58974;ABA=16;ABP=5.7386;ABR=23;AC=64;AF=0.05229;AN=1224;BL=699;BR=775;BVAR;BaseQRankSum=-21.390;DEL;DP=21920;DP4=2099,2403,6,6;Dels=0.00;EL=8;EPP=3.0103;ER=8;FR;FS=2.920;HETAR=5;HOMA=0;HOMR=1063;HP=3;HPLen=4;HR=4;HU=A;INDEL;InbreedingCoeff=-0.0143;IndelType=MIXED;LEN=7;LRB=0.05156;LRBP=11.519;MQ=129.49;MQ0=0;MQ0Fraction=0.0000;MQM=51.938;MQRankSum=3.331;NF;NR;NS=1068;PP;PV4=1,0.019,1.3e-07,1;RA=5334;RL=5;RPP=7.8961;RR=11;RUN=1;ReadPosRankSum=-16.901;SAB=0.4375;SAF=7;SAP=3.5532;SAR=9;SC=CATACTACAAAATTAGTCATT;SRB=0.41695;SRF=2224;SRP=322.58;SRR=3110;TC;TR=4;TU=A;VQSLOD=3.2237;set=filterInVQSR-2of5;sumGLbyD=43.57 20 15752535 . CT C,GT 3775.20 PASS AA=92;AB=0.78636;ABA=47;ABP=159.71;ABR=173;AC=0;AF=0.0000;AN=608;BL=4955;BR=2380;BVAR;BaseQRankSum=2.910;DEL;DP=3429;Dels=0.04;EL=13;EPP=105.82;ER=79;FR;HETAR=92;HOMA=95;HOMR=544;HP=2;HPLen=2;HR=2;HU=T;InbreedingCoeff=0.0483;IndelType=MIXED;LEN=1;LRB=0.35106;LRBP=1966;MQ0Fraction=0.0232;MQM=35.293;MQRankSum=-2.199;NF;NR;NS=732;PP;QD=4.91;RA=1272;RL=81;RPP=118.66;RR=11;RUN=1;ReadPosRankSum=-1.077;SAB=0.021739;SAF=2;SAP=185.79;SAR=90;SB=-59.51;SC=CAAGACCATCCTTGGCTAACA;SRB=0.14623;SRF=186;SRP=1385.8;SRR=1086;TC;TR=2;TU=T;set=filterInVQSR-2of5;sumGLbyD=9.70 20 15883060 rs73619850 A AT 1325.60 PASS AA=38;AB=0.59302;ABA=35;ABP=9.4742;ABR=51;AC=14;AF=0.0156;AN=896;BL=1078;BR=1638;BVAR;BaseQRankSum=-4.526;DB;DP=19854;DP4=1632,1800,15,20;Dels=0.00;EL=18;EPP=3.2389;ER=20;FR;FS=0.000;HETAR=14;HOMA=1;HOMR=1014;HP=1;HPLen=1;HR=1;HRun=1;HU=T;INDEL;INS;InbreedingCoeff=-0.0131;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.20619;LRBP=253.74;MQ=118.40;MQ0=0;MQ0Fraction=0.0000;MQM=56.526;MQRankSum=0.892;NF;NR;NS=1029;PP;PV4=0.61,1,0.25,0.14;RA=4439;RL=14;RPP=8.7247;RR=24;RUN=1;ReadPosRankSum=-2.061;SAB=0.42105;SAF=16;SAP=5.0675;SAR=22;SC=GGATTGGCAGATAAAAAATGG;SRB=0.46429;SRF=2061;SRP=52.168;SRR=2378;TC;TR=1;TU=T;VQSLOD=9.7576;set=Intersection;sumGLbyD=15.69 20 16122099 . GA G 12914 PASS AA=85;AB=0.85915;ABA=80;ABP=639.4;ABR=488;AC=19;AF=0.01542;AN=1232;BL=805;BR=5457;BVAR;BaseQRankSum=-6.084;DEL;DP=13592;Dels=0.00;EL=45;EPP=3.649;ER=40;FS=0.935;HETAR=218;HOMA=841;HOMR=14;HRun=2;InbreedingCoeff=0.0250;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.74289;LRBP=7507.5;MQ0=0;MQ0Fraction=0.0000;MQM=103.01;MQRankSum=2.843;NS=1075;RA=541;RL=2;RPP=170.62;RR=83;RUN=1;ReadPosRankSum=-16.222;SAB=0.49412;SAF=42;SAP=3.0358;SAR=43;SRB=0.44917;SRF=243;SRP=15.152;SRR=298;VQSLOD=3.9745;set=filterInVQSR-2of5;sumGLbyD=2.97 20 16828509 . G GT 843.62 PASS AA=30;AB=0.70103;ABA=29;ABP=37.06;ABR=68;AC=10;AF=0.0140;AN=714;BL=1368;BR=1786;BVAR;BaseQRankSum=-4.061;DP=8682;Dels=0.01;EL=14;EPP=3.2998;ER=16;FR;FS=2.681;HETAR=22;HOMA=1;HOMR=1020;HP=8;HPLen=8;HR=8;HRun=8;HU=T;INS;InbreedingCoeff=0.1389;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13253;LRBP=123.3;MQ0=0;MQ0Fraction=0.0000;MQM=62.8;MQRankSum=-1.491;NF;NR;NS=1043;PP;RA=4416;RL=11;RPP=7.6428;RR=19;RUN=1;ReadPosRankSum=-1.718;SAB=0.76667;SAF=23;SAP=21.54;SAR=7;SC=CCTTCAAAAGGTTTTTTTTGG;SRB=0.5745;SRF=2537;SRP=215.91;SRR=1879;TC;TR=8;TU=T;VQSLOD=7.6258;set=Intersection;sumGLbyD=10.77 20 17470034 . GC G 46975 PASS AA=57;AB=0.96043;ABA=52;ABP=2422.5;ABR=1262;AC=34;AF=0.02773;AN=1226;BL=418;BR=3446;BVAR;BaseQRankSum=-6.250;DEL;DP=12035;Dels=0.00;EL=22;EPP=9.4485;ER=35;FS=1.350;HETAR=416;HOMA=409;HOMR=244;HRun=1;InbreedingCoeff=0.0083;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.78364;LRBP=5155.6;MQ0=0;MQ0Fraction=0.0000;MQM=99.509;MQRankSum=2.192;NS=1076;RA=2396;RL=5;RPP=87.164;RR=52;RUN=1;ReadPosRankSum=-15.199;SAB=0.5614;SAF=32;SAP=4.877;SAR=25;SRB=0.52963;SRF=1269;SRP=21.285;SRR=1127;VQSLOD=3.8440;set=filterInVQSR-2of5;sumGLbyD=3.06 20 17471374 . AGCGGC A 850.03 PASS AC=6;AF=0.0085;AF1=0.01301;AN=704;BaseQRankSum=6.259;CI95=0.00885,0.01991;DP=8180;DP4=2215,1878,4,5;Dels=0.01;FQ=131;FS=0.000;HRun=0;INDEL;InbreedingCoeff=0.0009;IndelType=DEL.NumRepetitions_1.EventLength_5.;MQ=104.41;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-5.521;PV4=0.74,0.37,0.0005,1;ReadPosRankSum=2.468;VQSLOD=6.8773;set=Intersection;sumGLbyD=30.85 20 18433202 rs35582929 G GA 2506.90 PASS AA=55;AB=0.5812;ABA=49;ABP=9.7103;ABR=68;AC=20;AF=0.0218;AN=918;BL=2263;BR=2175;BVAR;BaseQRankSum=-6.639;DB;DP=19467;DP4=1845,2365,27,26;Dels=0.00;EL=21;EPP=9.6826;ER=34;FQ=999;FR;FS=5.633;HETAR=16;HOMA=3;HOMR=1045;HP=2;HPLen=3;HR=3;HRun=1;HU=G;INDEL;INS;InbreedingCoeff=0.0700;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.019829;LRBP=6.7994;MQ=114.03;MQ0=0;MQ0Fraction=0.0000;MQM=83.345;MQRankSum=1.610;NF;NR;NS=1064;PP;PV4=0.33,1,1,1;RA=5380;RL=28;RPP=3.0498;RR=27;RUN=1;ReadPosRankSum=0.873;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TATTTCATGGGAGCATTAAAA;SRB=0.42862;SRF=2306;SRP=241.07;SRR=3074;TC;TR=3;TU=G;VQSLOD=10.0372;dbSNP=126;set=Intersection;sumGLbyD=13.10 20 18551314 rs10659122 CA C,CAA,CAAA,CAAAA,CAAAAA 18810.74 PASS ABR=243;AC=19,169,216,164,188;AF=0.01816,0.16157,0.20650,0.15679,0.17973;BVAR;BaseQRankSum=-5.742;DB;DP=17637;DP4=136,77,560,237;FR;FS=2.693;HOMA=177;HOMR=299;HP=17;HR=17;HU=A;HaplotypeScore=15.5048;INDEL;INS;InbreedingCoeff=0.8901;IndelType=MULTIALLELIC_INDEL;MQ0=11;MQ0Fraction=0.0069;MQRankSum=1.845;NF;NR;NS=658;PP;PV4=0.08,1,1,1;QD=12.66;RA=673;RUN=1;ReadPosRankSum=0.283;SB=-3514.45;SC=GATTCCATCTCAAAAAAAAAA;SRB=0.63596;SRF=428;SRP=111.06;SRR=245;TC;TR=17;TU=A;VQSLOD=10.6964;dbSNP=130;set=Intersection 20 18785519 . G GTC 415.55 PASS AC=28;AF=0.0400;AN=700;BaseQRankSum=10.889;DP=1929;FS=8.778;HRun=0;HaplotypeScore=27.6448;InbreedingCoeff=0.0510;IndelType=INS.NOVEL_2.;MQ=61.99;MQ0=36;MQ0Fraction=0.0187;MQRankSum=4.508;QD=3.08;ReadPosRankSum=8.080;SB=-437.03;VQSLOD=4.9313;set=VQSR 20 20301041 rs35451634 ATATG A 200.42 PASS AC=21;AF=0.0449;AN=468;BaseQRankSum=5.251;DB;DP=579;FS=24.013;HRun=0;HaplotypeScore=27.8977;InbreedingCoeff=0.0113;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ=78.47;MQ0=26;MQ0Fraction=0.0449;MQRankSum=-5.284;QD=3.06;ReadPosRankSum=1.793;SB=-55.76;VQSLOD=5.0981;set=VQSR 20 20378174 . TC T 245.55 PASS AC=23;AF=0.01879;AN=1224;BaseQRankSum=0.990;DP=3225;FS=10.413;HRun=1;HaplotypeScore=22.6109;InbreedingCoeff=0.0244;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=93.70;MQ0=3;MQ0Fraction=0.0009;MQRankSum=-3.349;QD=1.86;ReadPosRankSum=-7.227;SB=-188.62;VQSLOD=4.2553;set=VQSR 20 20809160 rs10571503 TAA AAA,T 3496 PASS AC=0;AF=0.0000;AN=612;BaseQRankSum=1.968;DB;DP=1092;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=26.1253;InbreedingCoeff=0.0603;IndelType=MIXED;MQ=68.98;MQ0=1;MQ0Fraction=0.0009;MQRankSum=1.520;NF;NR;PP;ReadPosRankSum=-4.042;SC=TATATATATATAAATTTAAAT;TC;TR=13;TU=AT;set=filterInVQSR-2of5 20 22508765 . CT C 53877.84 PASS AA=187;AB=0.78077;ABA=171;ABP=537.09;ABR=609;AC=1017;AF=0.91787;AN=1108;BL=12690;BR=1718;BVAR;BaseQRankSum=13.773;DEL;DP=7430;Dels=0.02;EL=73;EPP=22.53;ER=114;FR;FS=16.352;HETAR=152;HOMA=9;HOMR=786;HP=8;HR=4;HRun=4;HU=T;InbreedingCoeff=0.3885;IndelType=DEL.NumRepetitions_4.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.76152;LRBP=18147;MQ0=0;MQ0Fraction=0.0000;MQM=46.086;MQRankSum=0.971;NF;NR;NS=947;PP;RA=2868;RL=177;RPP=326.86;RR=10;RUN=1;ReadPosRankSum=9.951;SAB=0.34759;SAF=65;SAP=40.738;SAR=122;SC=AAAAAATTTTCTTTTGAACTG;SRB=0.46269;SRF=1327;SRP=37.684;SRR=1541;TC;TR=4;TU=T;VQSLOD=5.1182;set=Intersection;sumGLbyD=25.15 20 22555082 rs11477526 AT A 11503 PASS AA=530;AB=0.50816;ABA=422;ABP=3.5063;ABR=436;AF=0.1614;AN=700;BL=21453;BR=23313;BVAR;BaseQRankSum=17.562;DB;DEL;DP=25587;DP4=1869,1600,283,201;Dels=0.14;EL=259;EPP=3.6003;ER=271;FQ=999;FR;FS=14.595;HETAR=159;HOMA=41;HOMR=846;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;InbreedingCoeff=0.0995;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.041549;LRBP=170.83;MQ=95.89;MQ0=0;MQ0Fraction=0.0000;MQM=72.162;MQRankSum=2.564;NF;NR;NS=1046;PP;PV4=0.058,6.6e-129,0.04,1;RA=4303;RL=264;RPP=3.0267;RR=266;RUN=1;ReadPosRankSum=0.176;SAB=0.58679;SAF=311;SAP=37.688;SAR=219;SC=GGGAAAGCTGATTTACTGATT;SRB=0.54892;SRF=2362;SRP=92.453;SRR=1941;TC;TR=3;TU=T;VQSLOD=8.7746;dbSNP=120;set=Intersection;sumGLbyD=15.27 20 22590907 . A AC 4204.88 PASS AA=67;AB=0.592;ABA=51;ABP=12.2;ABR=74;AF=0.0554;AF1=0.0468;AN=560;BL=2277;BR=2389;BVAR;BaseQRankSum=10.968;CI95=0.03759,0.05639;DP=14380;DP4=2514,2018,33,33;Dels=0.00;EL=22;EPP=20.155;ER=45;FQ=999;FR;FS=3.846;HETAR=25;HOMA=4;HOMR=1049;HP=4;HPLen=5;HR=5;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0719;IndelType=INS.NOVEL_1.Novel_C.;LEN=1;LRB=0.024003;LRBP=8.8481;MQ=110.68;MQ0=0;MQ0Fraction=0.0000;MQM=96.149;MQRankSum=2.668;NF;NR;NS=1078;PP;PV4=0.39,1,0.46,0.36;RA=5468;RL=33;RPP=3.0427;RR=34;RUN=1;ReadPosRankSum=-1.097;SAB=0.50746;SAF=34;SAP=3.0427;SAR=33;SC=TCATATCAAAAACATTACGTT;SRB=0.54389;SRF=2974;SRP=94.508;SRR=2494;TC;TR=5;TU=A;VQSLOD=10.0712;set=Intersection;sumGLbyD=27.69 20 22806326 rs11468890 ATTCCATCAC A 105320.99 PASS AC=567;AF=0.48795;AN=1162;BVAR;BaseQRankSum=32.858;DB;DEL;DP=26278;DP4=727,796,554,587;Dels=0.30;FQ=999;FR;FS=1.923;HP=3;HPLen=3;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.2548;IndelType=DEL.NumRepetitions_2.EventLength_9.;LEN=9;MQ=89.42;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-23.545;NF;NR;PP;PV4=0.7,1,1.3e-167,1;RUN=1;ReadPosRankSum=4.384;SC=GGCTGCTCCCATTCCATCACT;TC;TR=2;TU=T;VQSLOD=8.2594;set=Intersection;sumGLbyD=69.81 20 22999898 rs55966257 CAGGA C 8019.97 PASS AA=23;AB=0.57778;ABA=19;ABP=5.3748;ABR=26;AC=214;AF=0.18838;AN=1136;BL=1143;BR=1040;BVAR;BaseQRankSum=29.294;DB;DEL;DP=8216;Dels=0.02;EL=11;EPP=3.1047;ER=12;FS=14.938;HETAR=14;HOMA=2;HOMR=948;HRun=0;InbreedingCoeff=0.0797;IndelType=DEL.NumRepetitions_1.EventLength_4.;LEN=4;LRB=0.047183;LRBP=13.563;MQ0=0;MQ0Fraction=0.0000;MQM=34.783;MQRankSum=-20.301;NS=964;RA=3637;RL=13;RPP=3.86;RR=10;RUN=1;ReadPosRankSum=-24.607;SAB=0.47826;SAF=11;SAP=3.1047;SAR=12;SRB=0.49024;SRF=1783;SRP=6.02;SRR=1854;VQSLOD=7.9163;set=Intersection;sumGLbyD=9.43 20 23385964 rs57723772 GAA G 8170.95 PASS AC=257;AF=0.20928;AN=1228;BaseQRankSum=32.220;DB;DP=3291;FS=1.688;HRun=3;HaplotypeScore=22.6739;InbreedingCoeff=0.0171;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=58.44;MQ0=32;MQ0Fraction=0.0097;MQRankSum=-4.893;QD=6.55;ReadPosRankSum=-35.524;SB=-3631.67;VQSLOD=5.6549;set=VQSR 20 23534530 . TA T 3542.10 PASS AA=45;AB=0.75658;ABA=37;ABP=89.926;ABR=115;AC=35;AF=0.02991;AN=1170;BL=3090;BR=270;BVAR;BaseQRankSum=-6.892;DEL;DP=8108;Dels=0.00;EL=19;EPP=5.3748;ER=26;FS=1.026;HETAR=76;HOMA=896;HOMR=18;HRun=1;InbreedingCoeff=0.0551;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.83929;LRBP=5142.4;MQ0Fraction=0.0017;MQM=41.578;MQRankSum=0.818;NS=991;RA=203;RL=43;RPP=84.127;RR=2;RUN=1;ReadPosRankSum=-12.923;SAB=0.37778;SAF=17;SAP=8.8491;SAR=28;SRB=0.5665;SRF=115;SRP=10.808;SRR=88;VQSLOD=4.2093;set=Intersection;sumGLbyD=3.49 20 23976810 rs5841018 A ATATTAAT 1782.38 PASS AF=0.1387;AF1=0.01507;BaseQRankSum=3.717;CI95=0.00188,0.03947;DB;DP=1712;DP4=357,376,7,2;Dels=0.00;FQ=31.1;FS=14.489;HPLen=2;HRun=0;INDEL;InbreedingCoeff=0.1123;IndelType=INS.NumRepetitions_1.EventLength_7.;MQ=49.53;MQ0=2;MQ0Fraction=0.0055;MQRankSum=-4.928;PV4=0.1,1,0.00085,0.016;ReadPosRankSum=-4.456;VQSLOD=5.3140;dbSNP=116;set=Intersection;sumGLbyD=19.98 20 24222100 . CTTTTA C 4219.36 PASS AA=57;AB=0.59434;ABA=43;ABP=11.205;ABR=63;AF=0.01803;AF1=0.01547;AN=1220;BL=2073;BR=2345;BVAR;BaseQRankSum=7.990;CI95=0.0114,0.02137;DEL;DP=17536;DP4=2140,2346,7,12;Dels=0.01;EL=32;EPP=4.877;ER=25;FQ=104;FS=0.614;HETAR=21;HOMA=4;HOMR=1042;HRun=0;INDEL;InbreedingCoeff=0.1941;IndelType=DEL.NumRepetitions_2.EventLength_5.;LEN=5;LRB=0.061566;LRBP=39.374;MQ=73.32;MQ0Fraction=0.0021;MQM=39.614;MQRankSum=-5.728;NS=1067;PV4=0.37,1.1e-39,3.5e-09,1;RA=5527;RL=28;RPP=3.0484;RR=29;RUN=1;ReadPosRankSum=0.214;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SRB=0.49267;SRF=2723;SRP=5.588;SRR=2804;VQSLOD=7.5428;set=Intersection;sumGLbyD=38.08 20 24395018 . AT A 49310 PASS AA=146;AB=0.91198;ABA=130;ABP=2180.5;ABR=1347;AC=50;AF=0.04045;AN=1236;BL=587;BR=9625;BVAR;BaseQRankSum=-4.610;DEL;DP=12793;Dels=0.01;EL=54;EPP=24.487;ER=92;FS=22.108;HETAR=485;HOMA=384;HOMR=210;HRun=2;InbreedingCoeff=0.0374;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.88504;LRBP=17373;MQ0=0;MQ0Fraction=0.0000;MQM=102.26;MQRankSum=2.256;NS=1080;RA=2377;RL=1;RPP=311.42;RR=145;RUN=1;ReadPosRankSum=-16.347;SAB=0.63699;SAF=93;SAP=26.807;SAR=53;SRB=0.52167;SRF=1240;SRP=12.702;SRR=1137;VQSLOD=3.2421;set=filterInVQSR-2of5;sumGLbyD=3.80 20 24411517 . C CA 246.18 PASS AF=0.01546;AF1=0.01095;BaseQRankSum=7.832;CI95=0.005698,0.01709;DP=7981;DP4=983,2037,7,7;Dels=0.00;FQ=27.9;FS=18.815;HPLen=3;HRun=3;INDEL;InbreedingCoeff=0.0175;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=60.28;MQ0Fraction=0.0137;MQRankSum=-7.243;PV4=0.25,1,2.7e-05,1;ReadPosRankSum=-0.143;VQSLOD=4.3701;set=Intersection;sumGLbyD=6.56 20 24421169 . AG A 27480 PASS AA=182;AB=0.8303;ABA=149;ABP=835;ABR=729;AC=89;AF=0.07224;AN=1232;BL=11276;BR=2214;BVAR;BaseQRankSum=-5.447;DEL;DP=11717;Dels=0.01;EL=103;EPP=9.8827;ER=79;FR;FS=15.492;HETAR=343;HOMA=607;HOMR=114;HP=4;HR=1;HRun=1;HU=G;InbreedingCoeff=0.0353;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.67176;LRBP=13222;MQ0=0;MQ0Fraction=0.0000;MQM=88.324;MQRankSum=2.221;NF;NR;NS=1071;PP;RA=1226;RL=169;RPP=293.37;RR=13;RUN=1;ReadPosRankSum=-19.711;SAB=0.54945;SAF=100;SAP=6.876;SAR=82;SC=CCTTAGCCCCAGAAAACATCT;SRB=0.44535;SRF=546;SRP=34.814;SRR=680;TC;TR=1;TU=G;VQSLOD=4.2669;set=Intersection;sumGLbyD=3.91 20 24765537 rs71841337 ATTT A,AT,ATT,ATTTT,ATTTTT 37852 PASS AC=13,120,527,51,92;AF=0.01102,0.10169,0.44661,0.04322,0.07797;AN=1180;BVAR;BaseQRankSum=8.172;DB;DEL;DP=39116;DP4=200,331,851,1169;FR;FS=2.394;HP=15;HR=15;HU=T;HaplotypeScore=20.8091;INDEL;INS;InbreedingCoeff=0.4815;IndelType=MULTIALLELIC_INDEL;MQ0=1;MQ0Fraction=0.0003;MQRankSum=4.344;NF;NR;PP;PV4=0.067,1,1,0.1;QD=7.90;RUN=1;ReadPosRankSum=1.798;SB=-8371.96;SC=CTCTGCAACAATTTTTTTTTT;TC;TR=15;TU=T;VQSLOD=9.9679;dbSNP=120;set=Intersection 20 25500689 . A AATTT 84980.72 PASS AC=1005;AF=0.89096;AN=1128;BaseQRankSum=17.400;DP=2324;FS=6.721;HRun=0;HaplotypeScore=25.3376;InbreedingCoeff=0.2148;IndelType=INS.NumRepetitions_1.EventLength_4.;MQ=75.19;MQ0=1;MQ0Fraction=0.0004;MQRankSum=-8.221;QD=38.28;ReadPosRankSum=4.504;SB=-34833.07;VQSLOD=4.6038;set=VQSR 20 25550373 . GA G 11251.31 PASS AA=246;AB=0.42963;ABA=154;ABP=14.624;ABR=116;AC=566;AF=0.6521;AN=868;BL=5230;BR=11845;BVAR;BaseQRankSum=7.418;DEL;DP=8885;Dels=0.02;EL=99;EPP=23.348;ER=147;FR;FS=50.357;HETAR=150;HOMA=849;HOMR=14;HP=1;HR=2;HRun=1;HU=G;InbreedingCoeff=0.1365;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.38741;LRBP=5567.9;MQ0=0;MQ0Fraction=0.0000;MQM=97.561;MQRankSum=0.050;NF;NR;NS=1013;PP;RA=269;RL=75;RPP=84.361;RR=171;RUN=1;ReadPosRankSum=-7.128;SAB=0.52846;SAF=130;SAP=4.7404;SAR=116;SC=CACGGAGGCGGAGGAAGCAGC;SRB=0.42379;SRF=114;SRP=16.58;SRR=155;TC;TR=6;TU=AGG;VQSLOD=4.0103;set=filterInVQSR-2of5;sumGLbyD=4.58 20 25903865 . TTC T 7459.23 PASS AC=277;AF=0.23316;AN=1188;BaseQRankSum=31.479;DP=2969;FS=137.723;HRun=0;HaplotypeScore=37.3300;InbreedingCoeff=-0.1755;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TC.;MQ=53.49;MQ0=50;MQ0Fraction=0.0168;MQRankSum=-25.506;QD=4.70;ReadPosRankSum=-5.913;SB=-1747.98;VQSLOD=5.4731;set=VQSR 20 25934237 . C CCACTT 771.36 PASS AC=37;AF=0.0426;AN=868;BaseQRankSum=16.331;DP=2253;FS=4.545;HRun=0;HaplotypeScore=29.9764;InbreedingCoeff=-0.0685;IndelType=INS.NOVEL_5.;MQ=48.12;MQ0=87;MQ0Fraction=0.0386;MQRankSum=-12.497;QD=3.37;ReadPosRankSum=-8.428;SB=-297.70;VQSLOD=4.2324;set=VQSR 20 26054751 rs112967123 TATC T 33244 PASS AA=1863;AB=0.79012;ABA=1788;ABP=6231;ABR=6731;AC=227;AF=0.18218;AN=1246;BL=74924;BR=72452;BVAR;BaseQRankSum=32.258;DB;DEL;DP=36404;DS;Dels=0.05;EL=931;EPP=3.0115;ER=932;FR;FS=265.752;HETAR=527;HOMA=2;HOMR=565;HP=1;HR=2;HRun=0;HU=T;InbreedingCoeff=-0.2137;IndelType=DEL.NumRepetitions_2.EventLength_3.;LEN=3;LRB=0.016773;LRBP=93.048;MQ0Fraction=0.0127;MQM=28.797;MQRankSum=-5.329;NF;NR;NS=1094;PP;RA=14604;RL=1014;RPP=34.743;RR=849;RUN=1;ReadPosRankSum=8.394;SAB=0.65486;SAF=1220;SAP=391.07;SAR=643;SC=TCACCATCATTATCATCATTA;SRB=0.56717;SRF=8283;SRP=575.39;SRR=6321;TC;TR=8;TU=ATC;VQSLOD=1.0486;set=filterInVQSR-2of5;sumGLbyD=6.54 20 26120452 . CAG C 7863.19 PASS AA=163;AB=0.70489;ABA=157;ABP=196.99;ABR=375;AC=171;AF=0.1908;AN=896;BL=3455;BR=4877;BVAR;BaseQRankSum=25.536;DEL;DP=7014;Dels=0.10;EL=58;EPP=32.438;ER=105;FS=231.723;HETAR=90;HOMA=5;HOMR=387;HRun=0;InbreedingCoeff=-0.1966;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.17067;LRBP=530;MQ0Fraction=0.0470;MQM=21.951;MQRankSum=-23.449;NS=482;RA=1117;RL=62;RPP=23.273;RR=101;RUN=1;ReadPosRankSum=1.904;SAB=0.37423;SAF=61;SAP=25.404;SAR=102;SRB=0.41719;SRF=466;SRP=69.544;SRR=651;VQSLOD=-0.9395;set=filterInVQSR-2of5;sumGLbyD=5.06 20 26185812 . AG A 322.58 PASS AF=0.0342;BaseQRankSum=3.668;DP=3014;Dels=0.01;FR;FS=10.238;HP=8;HPLen=6;HR=6;HRun=6;HU=G;InbreedingCoeff=0.1504;IndelType=DEL.NumRepetitions_6.EventLength_1.RepeatExpansion_G.;MQ0Fraction=0.0473;MQRankSum=-5.464;NF;NR;PP;ReadPosRankSum=0.536;SC=GGGTGGGTGGAGGGGGGAGGG;TC;TR=6;TU=G;VQSLOD=5.0767;set=Intersection;sumGLbyD=8.46 20 30963468 . AGTTT A 2041.12 PASS AA=38;AB=0.75694;ABA=35;ABP=85.587;ABR=109;AC=34;AF=0.0377;AN=902;BL=1974;BR=668;BVAR;BaseQRankSum=3.060;DEL;DP=22806;DP4=1997,1747,28,36;Dels=0.02;EL=17;EPP=3.9246;ER=21;FR;FS=16.034;HETAR=29;HOMA=1;HOMR=1009;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=0.0752;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.49432;LRBP=1404.9;MQ=87.17;MQ0Fraction=0.0013;MQM=98.079;MQRankSum=6.021;NF;NR;NS=1039;PP;PV4=0.13,1.5e-07,1,0.051;RA=4052;RL=36;RPP=69.069;RR=2;RUN=1;ReadPosRankSum=-1.847;SAB=0.5;SAF=19;SAP=3.0103;SAR=19;SC=AGAAGTAAGTAGTTTGTTTTT;SRB=0.53776;SRF=2179;SRP=53.19;SRR=1873;TC;TR=9;TU=AAGT;VQSLOD=7.3578;set=Intersection;sumGLbyD=14.03 20 31963212 . AAAAAAAAAAAAG A 727.15 PASS AC=5;AF=0.0080;AN=622;BaseQRankSum=4.037;DP=1480;FS=0.000;HRun=0;HaplotypeScore=43.3793;InbreedingCoeff=0.0350;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;MQ=51.77;MQ0=59;MQ0Fraction=0.0399;MQRankSum=-1.799;QD=22.72;ReadPosRankSum=3.591;SB=-364.04;VQSLOD=5.3166;set=VQSR 20 31997272 . CT C,CTT,CTTT 1837.10 PASS AA=63;AB=0.77559;ABA=57;ABP=170.57;ABR=197;AC=79,49,30;AF=0.06594,0.04090,0.02504;AN=1198;BL=2372;BR=2640;BVAR;BaseQRankSum=3.277;DP=9050;Dels=0.03;EL=24;EPP=10.766;ER=39;FR;FS=0.303;HETAR=45;HOMA=1;HOMR=981;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2796;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.053472;LRBP=34.128;MQ0Fraction=0.0000;MQM=50.889;MQRankSum=0.610;NF;NR;NS=1027;PP;RA=3776;RL=30;RPP=3.3205;RR=33;RUN=1;ReadPosRankSum=-0.800;SAB=0.39683;SAF=25;SAP=8.8354;SAR=38;SC=ACCCAACTTCCTTTTTTTTTT;SRB=0.46213;SRF=1745;SRP=50.049;SRR=2031;TC;TR=10;TU=T;VQSLOD=4.1189;set=filterInVQSR-2of5;sumGLbyD=3.66 20 33446974 rs113250263 TAA T,TA,TAAA 17130.16 PASS AC=65,417,184;AF=0.05941,0.38117,0.16819;AN=1094;BVAR;BaseQRankSum=3.400;DB;DEL;DP=22362;DP4=221,247,418,524;Dels=0.33;FR;FS=15.409;HP=15;HR=14;HRun=14;HU=A;INDEL;INS;InbreedingCoeff=0.5215;IndelType=MULTIALLELIC_INDEL;MQ=61.32;MQ0Fraction=0.0021;MQRankSum=0.481;NF;NR;PP;PV4=0.33,1,1,1;RUN=1;ReadPosRankSum=-0.056;SC=CTCCGTCTCATAAAAAAAAAA;TC;TR=14;TU=A;VQSLOD=8.0974;dbSNP=132;set=Intersection;sumGLbyD=12.78 20 33877149 . C CT 1784.40 PASS AA=58;AB=0.73096;ABA=53;ABP=94.289;ABR=144;AC=65;AF=0.05682;AN=1144;BL=3298;BR=1935;BVAR;BaseQRankSum=-2.066;DP=8074;Dels=0.02;EL=22;EPP=10.348;ER=36;FR;FS=11.452;HETAR=47;HOMA=3;HOMR=754;HP=16;HR=12;HRun=12;HU=T;INS;InbreedingCoeff=0.1178;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.26046;LRBP=773.91;MQ0Fraction=0.0165;MQM=52.259;MQRankSum=0.734;NF;NR;NS=804;PP;RA=2141;RL=43;RPP=32.363;RR=15;RUN=1;ReadPosRankSum=-1.273;SAB=0.46552;SAF=27;SAP=3.6093;SAR=31;SC=ATTTTCTTTTCTTTTTTTTTT;SRB=0.37553;SRF=804;SRP=291.14;SRR=1337;TC;TR=12;TU=T;VQSLOD=3.1540;set=filterInVQSR-2of5;sumGLbyD=2.84 20 34387589 rs112431805 CT C,CTT 4039.10 PASS AA=121;AB=0.75368;ABA=117;ABP=268.53;ABR=358;AC=84,139;AF=0.07047,0.11661;AN=1192;BL=5557;BR=3901;BVAR;BaseQRankSum=2.693;DB;DP=10157;Dels=0.03;EL=47;EPP=16.093;ER=74;FR;FS=7.639;HETAR=89;HOMA=2;HOMR=913;HP=13;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2097;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.17509;LRBP=632.63;MQ0Fraction=0.0000;MQM=49.802;MQRankSum=-0.801;NF;NR;NS=1004;PP;RA=3789;RL=77;RPP=22.554;RR=44;RUN=1;ReadPosRankSum=-2.691;SAB=0.3719;SAF=45;SAP=20.256;SAR=76;SC=AAGAAGTGTTCTTTTTTTTTT;SRB=0.40987;SRF=1553;SRP=270.35;SRR=2236;TC;TR=11;TU=T;VQSLOD=4.0473;set=filterInVQSR-2of5;sumGLbyD=4.64 20 34493409 rs73621682 C CAG 62288.93 PASS AA=1069;AB=0.54863;ABA=826;ABP=40.606;ABR=1004;AC=257;AF=0.3640;AN=706;BL=41524;BR=47039;BVAR;BaseQRankSum=-24.248;DB;DP=30195;DP4=1743,1636,614,487;Dels=0.00;EL=582;EPP=21.343;ER=487;FQ=999;FR;FS=5.080;HETAR=298;HOMA=63;HOMR=712;HP=1;HPLen=1;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.1437;IndelType=INS.NumRepetitions_2.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.062272;LRBP=748.76;MQ=77.99;MQ0=3;MQ0Fraction=0.0015;MQM=54.446;MQRankSum=0.160;NF;NR;NS=1073;PP;PV4=0.016,1,0.01,1;RA=4461;RL=526;RPP=3.5973;RR=543;RUN=1;ReadPosRankSum=-1.716;SAB=0.57343;SAF=613;SAP=53.08;SAR=456;SC=AGGAAGAGATCAGAGCTCCCC;SRB=0.52634;SRF=2348;SRP=29.892;SRR=2113;TC;TR=4;TU=AG;VQSLOD=8.7047;dbSNP=130;set=Intersection;sumGLbyD=49.82 20 35957317 . CTGACT C,CGACT 4370.96 PASS ABR=81;AC=22,1;AF=0.0321,0.0015;AF1=0.04523;AN=686;BVAR;BaseQRankSum=7.969;CI95=0.0354,0.05752;DEL;DP=16632;DP4=1942,1815,17,21;Dels=0.03;FQ=999;FR;FS=0.531;HOMA=1;HOMR=998;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0587;IndelType=MULTIALLELIC_INDEL;MQ=83.38;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-7.201;NF;NR;NS=1020;PP;PV4=0.42,0.00017,4.5e-12,1;RA=4620;RUN=1;ReadPosRankSum=-1.007;SC=CCTCTCAGCTCTGACTGAGTC;SRB=0.50043;SRF=2312;SRP=3.0178;SRR=2308;TC;TR=8;TU=ACTG;VQSLOD=9.9778;dbSNP=130;set=Intersection;sumGLbyD=36.45 20 36136198 . GTGTC G 2078.76 PASS AA=35;AB=0.54167;ABA=33;ABP=4.096;ABR=39;AC=17;AF=0.01384;AN=1228;BL=1212;BR=1523;BVAR;BaseQRankSum=6.900;DEL;DP=22483;DP4=1696,2291,9,16;Dels=0.01;EL=9;EPP=20.94;ER=26;FQ=999;FR;FS=3.023;HETAR=13;HOMA=1;HOMR=1061;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1113;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.11371;LRBP=79.803;MQ=93.98;MQ0=1;MQ0Fraction=0.0003;MQM=83.686;MQRankSum=-1.683;NF;NR;NS=1075;PP;PV4=0.55,1,0.0083,1;RA=5771;RL=19;RPP=3.5687;RR=16;RUN=1;ReadPosRankSum=0.618;SAB=0.37143;SAF=13;SAP=8.0357;SAR=22;SC=TATCATTTTAGTGTCTGTCTG;SRB=0.44966;SRF=2595;SRP=130.03;SRR=3176;TC;TR=11;TU=CTGT;VQSLOD=10.1935;set=Intersection;sumGLbyD=31.66 20 36250522 . CA C 37933 PASS AA=51;AB=0.95582;ABA=44;ABP=1800.5;ABR=952;AC=23;AF=0.01885;AN=1220;BL=691;BR=3464;BVAR;BaseQRankSum=-2.418;DEL;DP=11998;Dels=0.00;EL=18;EPP=12.59;ER=33;FS=2.307;HETAR=348;HOMA=534;HOMR=164;HRun=1;InbreedingCoeff=0.0763;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.66739;LRBP=4021.7;MQ0=2;MQ0Fraction=0.0006;MQM=53.647;MQRankSum=1.083;NS=1047;RA=1663;RL=2;RPP=97.065;RR=49;RUN=1;ReadPosRankSum=-12.726;SAB=0.68627;SAF=35;SAP=18.381;SAR=16;SRB=0.59651;SRF=992;SRP=137.56;SRR=671;VQSLOD=4.1346;set=filterInVQSR-2of5;sumGLbyD=3.29 20 36285033 rs34715186 AT A 39417 PASS AA=530;AB=0.5406;ABA=447;ABP=16.939;ABR=526;AC=88;AF=0.0950;AN=926;BL=20722;BR=20406;BVAR;BaseQRankSum=15.611;DB;DEL;DP=36713;DP4=2551,2475,236,218;Dels=0.09;EL=241;EPP=12.45;ER=289;FQ=999;FR;FS=1.290;HETAR=141;HOMA=16;HOMR=926;HP=2;HPLen=3;HR=3;HRun=1;HU=A;INDEL;InbreedingCoeff=0.0742;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.0076833;LRBP=8.2825;MQ=104.81;MQ0=0;MQ0Fraction=0.0000;MQM=84.285;MQRankSum=-0.702;NF;NR;NS=1083;PP;PV4=0.62,1,1,1;RA=6562;RL=263;RPP=3.0759;RR=267;RUN=1;ReadPosRankSum=0.090;SAB=0.55849;SAF=296;SAP=18.76;SAR=234;SC=AAAAACACAAATCAGATCGTG;SRB=0.51707;SRF=3393;SRP=19.614;SRR=3169;TC;TR=3;TU=A;VQSLOD=10.5533;dbSNP=126;set=Intersection;sumGLbyD=14.15 20 36384872 . CTG C 43532.41 PASS AC=1213;AF=0.99589;AN=1218;BaseQRankSum=0.802;DP=3208;FS=9.727;HRun=0;HaplotypeScore=46.6153;InbreedingCoeff=0.1085;IndelType=DEL.NumRepetitions_7.EventLength_2.RepeatExpansion_TG.;MQ=58.37;MQ0=50;MQ0Fraction=0.0156;MQRankSum=-1.672;QD=13.57;ReadPosRankSum=2.063;SB=-18894.12;VQSLOD=4.7353;set=VQSR 20 36542802 . GTA G 31310.15 PASS AA=1481;AB=0.67546;ABA=1378;ABP=1138.4;ABR=2868;AC=437;AF=0.35938;AN=1216;BL=25719;BR=95500;BVAR;BaseQRankSum=9.478;DEL;DP=18068;DS;Dels=0.10;EL=889;EPP=132.34;ER=592;FS=320.726;HETAR=591;HOMA=44;HOMR=378;HRun=0;InbreedingCoeff=-0.4197;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;LEN=2;LRB=0.57566;LRBP=87231;MQ0Fraction=0.0091;MQM=29.319;MQRankSum=-3.409;NS=1013;RA=4037;RL=3;RPP=3193;RR=1478;RUN=1;ReadPosRankSum=-6.687;SAB=0.40041;SAF=593;SAP=130.61;SAR=888;SRB=0.39014;SRF=1575;SRP=426.21;SRR=2462;VQSLOD=-1.6586;set=filterInVQSR-2of5;sumGLbyD=5.49 20 36985025 . CCA C 4.57 PASS AC=0;AF=0.0000;AN=682;BaseQRankSum=4.199;DP=1504;FS=1.036;HRun=0;HaplotypeScore=18.5241;InbreedingCoeff=0.0460;IndelType=DEL.NumRepetitions_6.EventLength_2.RepeatExpansion_CA.;MQ=57.04;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.774;ReadPosRankSum=-2.105;VQSLOD=6.7455;set=VQSR 20 37139725 . CAG C 250.77 PASS AF=0.0084;AF1=0.0139;BaseQRankSum=4.131;CI95=0.00885,0.01991;DP=7973;DP4=1808,1990,2,7;Dels=0.01;FQ=104;FR;FS=11.160;HP=3;HPLen=2;HR=1;HRun=0;HU=A;INDEL;InbreedingCoeff=-0.0001;IndelType=DEL.NumRepetitions_3.EventLength_2.RepeatExpansion_AG.;MQ=103.71;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.378;NF;NR;PP;PV4=0.18,0.0011,0.041,1;ReadPosRankSum=0.605;SC=AGATGGGGAACAGAGAGCAAG;TC;TR=6;TU=AG;VQSLOD=7.0630;set=Intersection;sumGLbyD=12.13 20 37213224 . G GTA 3230.05 PASS AA=32;AB=0.50769;ABA=32;ABP=3.0437;ABR=33;AC=12;AF=0.0168;AF1=0.02635;AN=714;BL=1271;BR=1743;BVAR;BaseQRankSum=-7.288;CI95=0.02212,0.03319;DP=14304;DP4=2180,2256,13,21;Dels=0.00;EL=20;EPP=7.3532;ER=12;FQ=999;FR;FS=7.863;HETAR=9;HOMA=0;HOMR=1043;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0410;IndelType=INS.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;LEN=2;LRB=0.1566;LRBP=163.52;MQ=95.56;MQ0=1;MQ0Fraction=0.0005;MQM=51.562;MQRankSum=0.420;NF;NR;NS=1052;PP;PV4=0.23,1,0.03,0.33;RA=5138;RL=11;RPP=9.7962;RR=21;RUN=1;ReadPosRankSum=-1.122;SAB=0.28125;SAF=9;SAP=16.311;SAR=23;SC=TTTGCATCCAGTAGCACCACT;SRB=0.42293;SRF=2173;SRP=268.11;SRR=2965;TC;TR=1;TU=T;VQSLOD=9.7315;set=Intersection;sumGLbyD=36.69 20 37282014 . ATGG A 2518.52 PASS AF=0.03519;BaseQRankSum=11.994;DP=24592;DP4=415,3804,8,49;DS;Dels=0.01;FQ=999;FR;FS=2.049;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1028;IndelType=DEL.NumRepetitions_5.EventLength_3.;MQ=51.01;MQ0Fraction=0.0139;MQRankSum=-5.912;NF;NR;PP;PV4=0.27,1,0.22,0.015;ReadPosRankSum=1.781;SC=GGTGGTGATGATGGTGGTGGT;TC;TR=17;TU=GGT;VQSLOD=2.1183;set=filterInVQSR-2of5;sumGLbyD=9.05 20 37532218 . GTCCGTCCA ATCCGTCCA,G 76120.88 PASS AC=998;AF=0.92924;AN=1074;BaseQRankSum=-2.877;DP=3087;FR;FS=9.889;HP=2;HPLen=2;HR=1;HRun=0;HU=T;HaplotypeScore=71.6244;InbreedingCoeff=-0.0027;IndelType=MIXED;MQ=52.68;MQ0=543;MQ0Fraction=0.1759;MQRankSum=-1.750;NF;NR;PP;QD=24.98;ReadPosRankSum=-0.850;SB=-36635.43;SC=CCGTCCGTCCGTCCGTCCATC;TC;TR=19;TU=CCGT;VQSLOD=5.3068;set=Intersection 20 37712193 . AAG A 2670.33 PASS AA=106;AB=0.62821;ABA=87;ABP=36.418;ABR=147;AC=53;AF=0.0759;AN=698;BL=4672;BR=4303;BVAR;BaseQRankSum=13.696;DEL;DP=15155;DP4=1340,1852,32,52;Dels=0.06;EL=57;EPP=4.3214;ER=49;FR;FS=0.824;HETAR=43;HOMA=7;HOMR=982;HP=1;HPLen=2;HR=2;HRun=0;HU=A;INDEL;InbreedingCoeff=0.0861;IndelType=DEL.NumRepetitions_3.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.041114;LRBP=35.954;MQ=86.12;MQ0=0;MQ0Fraction=0.0000;MQM=54.236;MQRankSum=-5.745;NF;NR;NS=1034;PP;PV4=0.5,7.3e-26,1.1e-10,1;RA=4423;RL=58;RPP=5.0589;RR=48;RUN=1;ReadPosRankSum=2.617;SAB=0.38679;SAF=41;SAP=14.81;SAR=65;SC=GAAAATTCTGAAGAGAGTCAG;SRB=0.43093;SRF=1906;SRP=186.29;SRR=2517;TC;TR=6;TU=AG;VQSLOD=9.8131;set=Intersection;sumGLbyD=14.20 20 37739002 . T TCA 1395.38 PASS AA=16;AB=0.48387;ABA=16;ABP=3.0803;ABR=15;AC=11;AF=0.00950;AN=1158;BL=504;BR=630;BVAR;BaseQRankSum=-3.257;DP=13617;DP4=1660,883,7,5;Dels=0.00;EL=7;EPP=3.5532;ER=9;FR;FS=1.114;HETAR=9;HOMA=0;HOMR=991;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0527;IndelType=INS.NumRepetitions_1.EventLength_2.RepeatExpansion_CA.;LEN=2;LRB=0.11111;LRBP=33.411;MQ=88.41;MQ0=0;MQ0Fraction=0.0000;MQM=83.75;MQRankSum=1.713;NF;NR;NS=1000;PP;PV4=0.76,1,1,0.5;RA=3257;RL=6;RPP=5.1818;RR=10;RUN=1;ReadPosRankSum=1.190;SAB=0.6875;SAF=11;SAP=7.8961;SAR=5;SC=CCTTTTTTGTTCATTTCTGCA;SRB=0.68806;SRF=2241;SRP=1003.5;SRR=1016;TC;TR=2;TU=T;VQSLOD=10.2220;set=Intersection;sumGLbyD=41.32 20 38395256 . TTGAG T 633.19 PASS AF=0.0028;BaseQRankSum=5.667;DP=3839;Dels=0.00;FR;FS=10.238;HP=2;HPLen=3;HR=3;HRun=0;HU=T;InbreedingCoeff=-0.0097;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.276;NF;NR;PP;ReadPosRankSum=-1.016;SC=ATGTGTTTGTTTGAGTATGTT;TC;TR=10;TU=GTTT;VQSLOD=6.4906;set=Intersection;sumGLbyD=10.83 20 39345038 . CTGAACCATAATGTG C,CCCATAATGTG 60744.52 PASS AA=23;AB=0.67143;ABA=23;ABP=20.878;ABR=47;AC=232,2;AF=0.19366,0.00167;AN=1198;BL=1607;BR=1843;BVAR;BaseQRankSum=30.955;DEL;DP=31490;DP4=1729,2100,265,278;Dels=0.13;EL=6;EPP=14.434;ER=17;FQ=999;FR;FS=1.767;HETAR=18;HOMA=0;HOMR=1015;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.1991;IndelType=MULTIALLELIC_INDEL;LEN=14;LRB=0.068406;LRBP=38.066;MQ=104.60;MQ0=0;MQ0Fraction=0.0000;MQM=189.83;MQRankSum=-16.579;NF;NR;NS=1033;PP;PV4=0.12,1,5.5e-137,1;RA=5286;RL=14;RPP=5.3706;RR=9;RUN=1;ReadPosRankSum=4.323;SAB=0.56522;SAF=13;SAP=3.86;SAR=10;SC=TGGGCTGGACCTGAACCATAA;SRB=0.46311;SRF=2448;SRP=65.493;SRR=2838;TC;TR=2;TU=C;VQSLOD=6.2643;dbSNP=130;set=Intersection;sumGLbyD=65.43 20 39418008 . AG A 46796 PASS AA=113;AB=0.9511;ABA=80;ABP=2894.6;ABR=1556;AC=30;AF=0.02412;AN=1244;BL=638;BR=6936;BVAR;BaseQRankSum=7.280;DEL;DP=14307;Dels=0.00;EL=50;EPP=6.2579;ER=63;FR;FS=5.707;HETAR=473;HOMA=361;HOMR=246;HP=3;HR=3;HRun=3;HU=G;InbreedingCoeff=0.0272;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.83153;LRBP=11375;MQ0=0;MQ0Fraction=0.0000;MQM=62.398;MQRankSum=3.530;NF;NR;NS=1089;PP;RA=3000;RL=3;RPP=223.02;RR=110;RUN=1;ReadPosRankSum=-18.601;SAB=0.58407;SAF=66;SAP=9.9475;SAR=47;SC=ACTGGGGGAAAGGGATTCTAG;SRB=0.494;SRF=1482;SRP=3.9484;SRR=1518;TC;TR=3;TU=G;VQSLOD=4.5834;set=Intersection;sumGLbyD=3.06 20 39876961 . GT G,GTT,GTTT 2302.10 PASS ABR=496;AC=45,51,45;AF=0.03664,0.04153,0.03664;AN=1228;BVAR;BaseQRankSum=4.462;DP=37649;DP4=1457,1975,57,59;Dels=0.02;FR;FS=9.938;HOMA=0;HOMR=978;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.2583;IndelType=MULTIALLELIC_INDEL;MQ=97.28;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.246;NF;NR;NS=1063;PP;PV4=0.15,1,1.9e-09,0.016;RA=5185;RUN=1;ReadPosRankSum=-4.954;SC=AGTTTCTCCGGTTTTTTTTTT;SRB=0.47464;SRF=2461;SRP=31.978;SRR=2724;TC;TR=10;TU=T;VQSLOD=4.9752;set=Intersection;sumGLbyD=4.39 20 41013333 . TC T 20681 PASS AA=137;AB=0.89211;ABA=134;ABP=1661.6;ABR=1108;AC=68;AF=0.05601;AN=1214;BL=1091;BR=8981;BVAR;BaseQRankSum=1.354;DEL;DP=12998;Dels=0.01;EL=57;EPP=11.395;ER=80;FS=0.758;HETAR=359;HOMA=100;HOMR=610;HRun=1;InbreedingCoeff=0.0104;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.78336;LRBP=13424;MQ0=1;MQ0Fraction=0.0003;MQM=67.745;MQRankSum=2.563;NS=1072;RA=4447;RL=5;RPP=258.66;RR=132;RUN=1;ReadPosRankSum=-14.092;SAB=0.59124;SAF=81;SAP=12.917;SAR=56;SRB=0.54194;SRF=2410;SRP=70.947;SRR=2037;VQSLOD=3.7531;set=filterInVQSR-2of5;sumGLbyD=4.14 20 41659532 . GC G 40544 PASS AA=42;AB=0.97149;ABA=39;ABP=2644.5;ABR=1329;AC=15;AF=0.0209;AN=716;BL=2531;BR=135;BVAR;BaseQRankSum=-2.537;DEL;DP=12219;Dels=0.00;EL=25;EPP=6.3192;ER=17;FS=2.656;HETAR=374;HOMA=155;HOMR=551;HRun=1;InbreedingCoeff=-0.0270;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.89872;LRBP=4678.9;MQ0=0;MQ0Fraction=0.0000;MQM=103.31;MQRankSum=2.828;NS=1088;RA=4736;RL=41;RPP=85.733;RR=1;RUN=1;ReadPosRankSum=-9.702;SAB=0.57143;SAF=24;SAP=4.8716;SAR=18;SRB=0.5625;SRF=2664;SRP=163.7;SRR=2072;VQSLOD=4.3267;set=Intersection;sumGLbyD=3.22 20 41845580 . GA G 49310 PASS AA=83;AB=0.95258;ABA=69;ABP=2591.6;ABR=1386;AC=46;AF=0.03740;AN=1230;BL=1320;BR=5150;BVAR;BaseQRankSum=-1.121;DEL;DP=13336;Dels=0.00;EL=36;EPP=6.1759;ER=47;FR;FS=0.372;HETAR=442;HOMA=341;HOMR=295;HP=2;HR=3;HRun=1;HU=G;InbreedingCoeff=0.0238;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.59196;LRBP=4926.2;MQ0=0;MQ0Fraction=0.0000;MQM=89.048;MQRankSum=0.897;NF;NR;NS=1080;PP;RA=3006;RL=5;RPP=142.43;RR=78;RUN=1;ReadPosRankSum=-15.412;SAB=0.55422;SAF=46;SAP=5.1294;SAR=37;SC=CCAGCTGTGGGAGAGAAACAT;SRB=0.47971;SRF=1442;SRP=13.762;SRR=1564;TC;TR=6;TU=AG;VQSLOD=4.4669;set=Intersection;sumGLbyD=3.65 20 42209428 . GC G 13163 PASS AA=89;AB=0.86677;ABA=83;ABP=730.96;ABR=540;AC=39;AF=0.03218;AN=1212;BL=950;BR=5334;BVAR;BaseQRankSum=-10.119;DEL;DP=10692;Dels=0.01;EL=48;EPP=4.2058;ER=41;FS=0.000;HETAR=259;HOMA=727;HOMR=54;HRun=1;InbreedingCoeff=0.0448;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.69764;LRBP=6644.4;MQ0=0;MQ0Fraction=0.0000;MQM=126.55;MQRankSum=4.223;NS=1040;RA=723;RL=12;RPP=106.09;RR=77;RUN=1;ReadPosRankSum=-17.362;SAB=0.39326;SAF=35;SAP=11.818;SAR=54;SRB=0.37898;SRF=274;SRP=94.99;SRR=449;VQSLOD=3.7157;set=filterInVQSR-2of5;sumGLbyD=3.48 20 42281109 . T TAG 2321.12 PASS AC=181;AF=0.3740;AN=484;BaseQRankSum=8.977;DP=435;FS=17.001;HRun=0;HaplotypeScore=14.6734;InbreedingCoeff=0.2340;IndelType=INS.NOVEL_2.;MQ=53.88;MQ0=47;MQ0Fraction=0.1080;MQRankSum=0.762;QD=12.41;ReadPosRankSum=3.399;SB=-1299.73;VQSLOD=4.8926;set=VQSR 20 42436117 . TC T 38933 PASS AA=18;AB=0.98435;ABA=17;ABP=2215.9;ABR=1069;AC=15;AF=0.01223;AN=1226;BL=498;BR=428;BVAR;BaseQRankSum=-7.224;DEL;DP=12436;Dels=0.00;EL=1;EPP=33.893;ER=17;FS=2.469;HETAR=303;HOMA=614;HOMR=123;HRun=1;InbreedingCoeff=0.0439;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.075594;LRBP=14.501;MQ0=0;MQ0Fraction=0.0000;MQM=98.611;MQRankSum=1.086;NS=1075;RA=1656;RL=10;RPP=3.4928;RR=8;RUN=1;ReadPosRankSum=-17.765;SAB=0.5;SAF=9;SAP=3.0103;SAR=9;SRB=0.49879;SRF=826;SRP=3.0313;SRR=830;VQSLOD=4.0821;set=filterInVQSR-2of5;sumGLbyD=3.04 20 42682214 . C A,CAT 3904.51 PASS AA=24;AB=0.6383;ABA=17;ABP=10.818;ABR=30;AC=0;AF=0.0000;AN=636;BL=1119;BR=949;BVAR;BaseQRankSum=1.426;DP=6509;Dels=0.00;EL=9;EPP=6.2675;ER=15;FR;HETAR=12;HOMA=3;HOMR=876;HP=2;HPLen=1;HR=1;HRun=0;HU=A;INS;InbreedingCoeff=0.0006;IndelType=MIXED;LEN=2;LRB=0.082205;LRBP=33.356;MQ0Fraction=0.0046;MQM=40.792;MQRankSum=-0.296;NF;NR;NS=891;PP;QD=32.81;RA=2679;RL=15;RPP=6.2675;RR=9;RUN=1;ReadPosRankSum=-1.806;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SB=-924.23;SC=TATACACACACATATATATAC;SRB=0.66293;SRF=1776;SRP=620.76;SRR=903;TC;TR=9;TU=AC;set=filterInVQSR-2of5;sumGLbyD=32.75 20 42973456 . CA C,CAA,CAAA 2675 PASS AA=90;AB=0.79177;ABA=86;ABP=308.39;ABR=327;AC=77,61,39;AF=0.06492,0.05143,0.03288;AN=1186;BL=2983;BR=4446;BVAR;BaseQRankSum=2.422;DP=9416;Dels=0.03;EL=39;EPP=6.4847;ER=51;FR;FS=31.555;HETAR=75;HOMA=1;HOMR=888;HP=11;HR=11;HRun=11;HU=A;INS;InbreedingCoeff=0.2696;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.19693;LRBP=628.63;MQ0=0;MQ0Fraction=0.0000;MQM=55.567;MQRankSum=1.777;NF;NR;NS=964;PP;RA=3601;RL=37;RPP=9.1869;RR=53;RUN=1;ReadPosRankSum=-4.991;SAB=0.55556;SAF=50;SAP=5.423;SAR=40;SC=TAGTGACTGTCAAAAAAAAAA;SRB=0.60622;SRF=2183;SRP=355.91;SRR=1418;TC;TR=11;TU=A;VQSLOD=1.0763;set=filterInVQSR-2of5;sumGLbyD=4.05 20 43091870 . TC T 2455.60 PASS AA=120;AB=0.10619;ABA=101;ABP=155.22;ABR=12;AC=42;AF=0.03825;AN=1098;BL=573;BR=8744;BVAR;BaseQRankSum=-13.513;DEL;DP=9139;Dels=0.00;EL=64;EPP=4.1684;ER=56;FS=9.856;HETAR=118;HOMA=820;HOMR=0;HRun=1;InbreedingCoeff=0.0833;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.877;LRBP=15564;MQ0Fraction=0.0017;MQM=45.1;MQRankSum=2.266;NS=938;RA=24;RL=1;RPP=254.97;RR=119;RUN=1;ReadPosRankSum=-15.803;SAB=0.475;SAF=57;SAP=3.6617;SAR=63;SRB=0.54167;SRF=13;SRP=3.3722;SRR=11;VQSLOD=3.9930;set=filterInVQSR-2of5;sumGLbyD=3.09 20 43233648 rs74585029 GA G,GAA 1504.40 PASS AA=113;AB=0.78652;ABA=95;ABP=320.31;ABR=350;AC=41,65;AF=0.03394,0.05381;AF1=0.0115;AN=1208;BL=4677;BR=5548;BVAR;BaseQRankSum=6.744;CI95=0.004274,0.01852;DB;DEL;DP=13996;DP4=1736,1549,15,17;Dels=0.03;EL=69;EPP=15.021;ER=44;FQ=14;FR;FS=12.174;HETAR=119;HOMA=15;HOMR=892;HP=11;HPLen=10;HR=10;HRun=10;HU=A;INDEL;InbreedingCoeff=0.2359;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.085183;LRBP=164.12;MQ=89.12;MQ0Fraction=0.0000;MQM=69.867;MQRankSum=2.513;NF;NR;NS=1027;PP;PV4=0.59,1,0.065,0.33;RA=3845;RL=46;RPP=11.485;RR=67;RUN=1;ReadPosRankSum=-4.957;SAB=0.33628;SAF=38;SAP=29.318;SAR=75;SC=AAAACAGCCAGAAAAAAAAAA;SRB=0.43667;SRF=1679;SRP=136.95;SRR=2166;TC;TR=10;TU=A;VQSLOD=4.5121;set=Intersection;sumGLbyD=8.22 20 43246548 . AC A,CC 41579.13 PASS AA=382;AB=0.72402;ABA=316;ABP=502.11;ABR=829;AC=1197;AF=0.99254;AN=1206;BL=9889;BR=14293;BVAR;BaseQRankSum=1.373;DEL;DP=10477;DS;Dels=0.05;EL=243;EPP=64.494;ER=139;FS=29.162;HETAR=291;HOMA=85;HOMR=624;HPLen=10;InbreedingCoeff=0.1392;IndelType=MIXED;LEN=1;LRB=0.18212;LRBP=1744.6;MQ0Fraction=0.0024;MQM=48.471;MQRankSum=5.726;NS=1001;RA=3138;RL=174;RPP=9.5816;RR=208;RUN=1;ReadPosRankSum=5.755;SAB=0.79843;SAF=305;SAP=298.51;SAR=77;SRB=0.70363;SRF=2208;SRP=1133.2;SRR=930;VQSLOD=5.6318;set=Intersection;sumGLbyD=5.22 20 43258646 . T TT 1107.17 PASS AC=97;AF=0.08420;AN=1152;BaseQRankSum=4.525;DP=2345;FS=19.308;HRun=9;HaplotypeScore=13.6276;InbreedingCoeff=0.1299;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;MQ=76.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.395;QD=2.67;ReadPosRankSum=-4.696;SB=-899.41;VQSLOD=5.4523;set=VQSR 20 43718299 . ATTACT A 5497.06 PASS AA=56;AB=0.51818;ABA=53;ABP=3.3262;ABR=57;AC=18;AF=0.0251;AF1=0.03729;AN=718;BL=2321;BR=2591;BVAR;BaseQRankSum=11.142;CI95=0.03319,0.04425;DEL;DP=17576;DP4=2460,2692,31,22;Dels=0.02;EL=28;EPP=3.0103;ER=28;FQ=999;FR;FS=9.689;HETAR=15;HOMA=1;HOMR=1068;HP=2;HPLen=2;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0448;IndelType=DEL.NumRepetitions_1.EventLength_5.;LEN=5;LRB=0.054967;LRBP=35.238;MQ=96.55;MQ0=0;MQ0Fraction=0.0000;MQM=50.286;MQRankSum=-5.149;NF;NR;NS=1084;PP;PV4=0.13,1,1.2e-12,1;RA=6745;RL=28;RPP=3.0103;RR=28;RUN=1;ReadPosRankSum=0.828;SAB=0.5;SAF=28;SAP=3.0103;SAR=28;SC=ATGACAGTGGATTACTTTAGT;SRB=0.46835;SRF=3159;SRP=61.709;SRR=3586;TC;TR=2;TU=T;VQSLOD=7.8832;set=Intersection;sumGLbyD=46.60 20 43981749 . A AAAAAAC,AC 20899.71 PASS ABR=192;AC=91,0;AF=0.1285,0.0000;AN=708;BVAR;BaseQRankSum=7.858;DP=23372;DP4=1554,1457,55,42;Dels=0.00;FR;FS=0.000;HOMA=4;HOMR=995;HP=6;HPLen=7;HR=7;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.2109;IndelType=MULTIALLELIC_INDEL;MQ=95.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-12.081;NF;NR;NS=1051;PP;PV4=0.35,1,8.9e-73,1;RA=5027;RUN=1;ReadPosRankSum=-1.359;SC=TACACTAGCAAAAAAACAAAA;SRB=0.48518;SRF=2439;SRP=12.6;SRR=2588;TC;TR=7;TU=A;VQSLOD=8.0916;set=Intersection;sumGLbyD=54.33 20 43999274 . TCAAA T 2948.85 PASS AA=59;AB=0.59441;ABA=58;ABP=14.08;ABR=85;AC=20;AF=0.0290;AF1=0.04249;AN=690;BL=2277;BR=2436;BVAR;BaseQRankSum=9.320;CI95=0.0354,0.05088;DEL;DP=14599;DP4=2052,2303,21,22;Dels=0.03;EL=32;EPP=3.9304;ER=27;FQ=999;FR;FS=0.000;HETAR=21;HOMA=0;HOMR=1043;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0037;IndelType=DEL.NumRepetitions_1.EventLength_4.;LEN=4;LRB=0.033736;LRBP=14.658;MQ=90.05;MQ0=0;MQ0Fraction=0.0000;MQM=75.339;MQRankSum=-1.294;NF;NR;NS=1064;PP;PV4=0.88,1,0.0026,1;RA=5732;RL=27;RPP=3.9304;RR=32;RUN=1;ReadPosRankSum=-0.915;SAB=0.47458;SAF=28;SAP=3.3415;SAR=31;SC=GGTACACAGCTCAAACAGTCT;SRB=0.4836;SRF=2772;SRP=16.4;SRR=2960;TC;TR=1;TU=C;VQSLOD=9.8086;set=Intersection;sumGLbyD=27.09 20 44098622 . C CG 1092.40 PASS AA=129;AB=0.77301;ABA=74;ABP=214.06;ABR=252;AC=45;AF=0.0455;AN=988;BL=6586;BR=3029;BVAR;BaseQRankSum=2.802;DP=5177;Dels=0.00;EL=122;EPP=225.63;ER=7;FR;FS=355.273;HETAR=66;HOMA=11;HOMR=734;HP=6;HR=4;HRun=4;HU=G;INS;InbreedingCoeff=0.1759;IndelType=INS.NumRepetitions_4.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.36994;LRBP=2860.4;MQ0=0;MQ0Fraction=0.0000;MQM=52.395;MQRankSum=1.946;NF;NR;NS=811;PP;RA=1981;RL=121;RPP=217.95;RR=8;RUN=1;ReadPosRankSum=-6.413;SAB=0.99225;SAF=128;SAP=274.51;SAR=1;SC=GCGGAAGTGGCGGGGACCCTT;SRB=0.41242;SRF=817;SRP=135;SRR=1164;TC;TR=4;TU=G;VQSLOD=-2.2690;set=filterInVQSR-2of5;sumGLbyD=4.04 20 44327637 . A AG,AGGGGGG 14351.23 PASS AC=9,211;AF=0.0103,0.2409;AN=876;BaseQRankSum=15.517;DP=1704;FS=6.768;HaplotypeScore=31.5906;InbreedingCoeff=0.1538;IndelType=MULTIALLELIC_INDEL;MQ=54.64;MQ0=4;MQ0Fraction=0.0023;MQRankSum=-12.691;QD=20.83;ReadPosRankSum=-3.583;SB=-6278.99;VQSLOD=5.1556;set=VQSR 20 45202636 . GA G 13269 PASS AA=25;AB=0.96162;ABA=18;ABP=871.09;ABR=451;AC=24;AF=0.02013;AN=1192;BL=567;BR=1728;BVAR;BaseQRankSum=-5.361;DEL;DP=10873;Dels=0.00;EL=10;EPP=5.1818;ER=15;FS=0.928;HETAR=169;HOMA=831;HOMR=45;HRun=1;InbreedingCoeff=0.0999;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.50588;LRBP=1278.4;MQ0=0;MQ0Fraction=0.0000;MQM=170.56;MQRankSum=0.161;NS=1049;RA=632;RL=2;RPP=41.315;RR=23;RUN=1;ReadPosRankSum=-14.760;SAB=0.68;SAF=17;SAP=10.046;SAR=8;SRB=0.51424;SRF=325;SRP=4.1235;SRR=307;VQSLOD=3.9290;set=filterInVQSR-2of5;sumGLbyD=3.90 20 45417828 . TGAGC T,TGC 4672.90 PASS ABR=317;AC=69,104;AF=0.05712,0.08609;BVAR;BaseQRankSum=18.527;DEL;DP=11835;DS;FS=184.873;HOMA=48;HOMR=575;HaplotypeScore=65.5875;InbreedingCoeff=0.0599;IndelType=MULTIALLELIC_INDEL;MQ=29.78;MQ0=2988;MQ0Fraction=0.3629;MQRankSum=5.052;NS=713;QD=1.11;RA=1581;RUN=1;ReadPosRankSum=6.574;SB=-2116.87;SRB=0.47502;SRF=751;SRP=11.582;SRR=830;VQSLOD=0.0651;set=filterInVQSR-2of5 20 45525657 rs66759083 TA AA,T 49315 PASS AA=2361;AB=0.45241;ABA=1398;ABP=53.235;ABR=1155;AC=20;AF=0.01701;AN=1176;BL=94913;BR=100886;BVAR;BaseQRankSum=0.740;DB;DEL;DP=30636;DP4=1258,881,1206,999;Dels=0.48;EL=1133;EPP=11.311;ER=1228;FQ=999;FR;FS=7.072;HETAR=503;HOMA=310;HOMR=218;HP=6;HPLen=7;HR=7;HU=T;INDEL;InbreedingCoeff=0.2271;IndelType=MIXED;LEN=1;LRB=0.030506;LRBP=398.68;MQ=102.24;MQ0=0;MQ0Fraction=0.0000;MQM=75.359;MQRankSum=0.148;NF;NR;NS=1031;PP;PV4=0.0064,0,4.6e-23,0.47;RA=2042;RL=1183;RPP=3.0333;RR=1178;RUN=1;ReadPosRankSum=-2.999;SAB=0.52139;SAF=1231;SAP=12.392;SAR=1130;SC=AGGATTTTTTTAAAAAGTTTT;SRB=0.55093;SRF=1125;SRP=49.017;SRR=917;TC;TR=7;TU=T;VQSLOD=7.1651;dbSNP=114;set=Intersection;sumGLbyD=18.51 20 45783456 . T TG 2355.68 PASS AA=64;AB=0.78521;ABA=61;ABP=203.67;ABR=223;AC=15;AF=0.0165;AN=910;BL=815;BR=5486;BVAR;BaseQRankSum=8.593;DP=10348;Dels=0.00;EL=48;EPP=37.754;ER=16;FS=77.861;HETAR=56;HOMA=1;HOMR=970;HRun=1;INS;InbreedingCoeff=-0.0549;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.74131;LRBP=7522.1;MQ0Fraction=0.0122;MQM=44.562;MQRankSum=-1.258;NS=1027;RA=4750;RL=0;RPP=141.98;RR=64;RUN=1;ReadPosRankSum=-7.047;SAB=0.25;SAF=16;SAP=37.754;SAR=48;SRB=0.6;SRF=2850;SRP=415.59;SRR=1900;VQSLOD=1.3146;set=filterInVQSR-2of5;sumGLbyD=6.03 20 46517110 . C CT 868.55 PASS AC=15;AF=0.0218;AN=688;BaseQRankSum=8.522;DP=1752;FS=6.570;HRun=0;HaplotypeScore=14.9548;InbreedingCoeff=0.0452;IndelType=INS.NOVEL_1.Novel_T.;MQ=77.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=3.874;QD=10.98;ReadPosRankSum=-0.733;SB=-396.78;VQSLOD=6.7740;set=VQSR 20 46629361 . TTTCTTTC T,TTTTC 13000.91 PASS AC=188,107;AF=0.2212,0.1259;AN=850;BaseQRankSum=7.214;DP=1846;FS=14.502;HaplotypeScore=40.8481;InbreedingCoeff=0.3210;IndelType=MULTIALLELIC_INDEL;MQ=50.74;MQ0=79;MQ0Fraction=0.0428;MQRankSum=-6.348;QD=13.59;ReadPosRankSum=3.943;SB=-3581.20;VQSLOD=5.9412;set=VQSR 20 46951099 . G GT 1662.30 PASS AA=55;AB=0.7713;ABA=51;ABP=145.58;ABR=172;AC=47;AF=0.03923;AN=1198;BL=3288;BR=2434;BVAR;BaseQRankSum=-4.014;DP=27423;DP4=1483,1590,58,42;Dels=0.01;EL=21;EPP=9.6826;ER=34;FR;FS=9.565;HETAR=48;HOMA=0;HOMR=913;HP=16;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.0952;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.14925;LRBP=279.78;MQ=70.36;MQ0Fraction=0.0124;MQM=52.545;MQRankSum=0.717;NF;NR;NS=961;PP;PV4=0.067,1,1,0.17;RA=3035;RL=38;RPP=20.422;RR=17;RUN=1;ReadPosRankSum=-3.014;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TTTGTTTTTTGTTTTTTTTTT;SRB=0.36013;SRF=1093;SRP=518.73;SRR=1942;TC;TR=10;TU=T;VQSLOD=5.4779;set=Intersection;sumGLbyD=3.49 20 47201076 rs58052846 C CT 982.16 PASS AC=50;AF=0.0551;AN=908;BaseQRankSum=12.598;DB;DP=2449;FS=35.648;HRun=0;HaplotypeScore=29.4602;InbreedingCoeff=-0.0542;IndelType=INS.NOVEL_1.Novel_T.;MQ=63.54;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.196;QD=3.16;ReadPosRankSum=-13.833;SB=-488.19;VQSLOD=6.0429;set=VQSR 20 47965974 rs60011158 G GA 999 PASS AA=21;AB=0.57143;ABA=21;ABP=5.1818;ABR=28;AC=7;AF=0.0101;AF1=0.02061;AN=690;BL=1043;BR=577;BVAR;BaseQRankSum=-3.087;CI95=0.01549,0.02655;DB;DP=14578;DP4=1554,3055,6,17;Dels=0.00;EL=11;EPP=3.1137;ER=10;FQ=999;FR;FS=5.982;HETAR=7;HOMA=0;HOMR=1041;HP=2;HPLen=1;HR=1;HRun=1;HU=A;INDEL;INS;InbreedingCoeff=0.0356;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.28765;LRBP=294.09;MQ=80.17;MQ0=0;MQ0Fraction=0.0000;MQM=64.19;MQRankSum=2.137;NF;NR;NS=1048;PP;PV4=0.51,1,1,1;RA=5224;RL=16;RPP=15.522;RR=5;RUN=1;ReadPosRankSum=0.236;SAB=0.38095;SAF=8;SAP=5.5954;SAR=13;SC=TTCATGTACAGAGCTGCTGTG;SRB=0.31183;SRF=1629;SRP=1609.6;SRR=3595;TC;TR=4;TU=AG;VQSLOD=9.5466;dbSNP=129;set=Intersection;sumGLbyD=13.83 20 48402974 rs57331436 GA G 27741 PASS AA=401;AB=0.5372;ABA=311;ABP=11.089;ABR=361;AC=84;AF=0.1186;AN=708;BL=16591;BR=14776;BVAR;BaseQRankSum=14.621;DB;DEL;DP=30607;DP4=1928,2310,195,225;Dels=0.11;EL=189;EPP=5.8749;ER=212;FQ=999;FR;FS=15.568;HETAR=110;HOMA=30;HOMR=923;HP=4;HPLen=3;HR=1;HRun=3;HU=A;INDEL;InbreedingCoeff=0.1263;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;KGPilot123;LEN=1;LRB=0.057863;LRBP=231.06;MQ=106.68;MQ0=0;MQ0Fraction=0.0000;MQM=63.005;MQRankSum=-2.010;NF;NR;NS=1063;PP;PV4=0.72,1,0.001,1;RA=5258;RL=223;RPP=13.976;RR=178;RUN=1;ReadPosRankSum=1.337;SAB=0.37656;SAF=151;SAP=56.084;SAR=250;SC=TGCCCTCAAAGAGAAAAAGGA;SRB=0.38075;SRF=2002;SRP=652.44;SRR=3256;TC;TR=5;TU=AG;VQSLOD=8.7259;dbSNP=132;set=Intersection;sumGLbyD=15.86 20 49101936 . C CT 404.46 PASS AC=40;AF=0.03559;AN=1124;BaseQRankSum=0.750;DP=2162;FS=14.291;HRun=2;HaplotypeScore=30.9513;InbreedingCoeff=-0.0082;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_T.;MQ=49.78;MQ0=113;MQ0Fraction=0.0523;MQRankSum=-1.289;QD=1.94;ReadPosRankSum=-2.041;SB=-385.48;VQSLOD=4.6365;set=VQSR 20 49731218 . ATTTTATTTTTTATT A,ATTTTATT 8398.93 PASS AF=0.0656,0.0156;AF1=0.0996;BaseQRankSum=13.996;CI95=0.07743,0.1239;DP=6308;DP4=951,1311,23,35;Dels=0.05;FQ=999;FR;FS=12.503;HP=7;HPLen=4;HR=4;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1892;IndelType=MULTIALLELIC_INDEL;MQ=57.61;MQ0Fraction=0.0145;MQRankSum=-5.208;NF;NR;PP;PV4=0.79,1,6.3e-06,0.16;ReadPosRankSum=-2.239;SC=TATTTTATTTATTTTATTTTT;TC;TR=11;TU=ATTT;VQSLOD=4.3191;set=Intersection;sumGLbyD=42.27 20 49894989 . TA T 172.25 PASS AF=0.0140;BaseQRankSum=7.220;DP=3882;Dels=0.00;FS=17.217;HPLen=2;HRun=1;InbreedingCoeff=0.0531;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;MQ0Fraction=0.0214;MQRankSum=-0.661;ReadPosRankSum=-0.592;VQSLOD=3.0905;set=filterInVQSR-2of5;sumGLbyD=6.60 20 50010923 rs66516522 C CT,CTGG 35851 PASS ABR=555;AC=310,11;AF=0.26451,0.00939;BVAR;BaseQRankSum=10.662;DB;DP=8188;FR;FS=34.411;HOMA=261;HOMR=399;HP=5;HR=6;HU=C;HaplotypeScore=45.1715;INS;InbreedingCoeff=0.2090;IndelType=MULTIALLELIC_INDEL;MQ=72.80;MQ0=0;MQ0Fraction=0.0000;MQRankSum=9.015;NF;NR;NS=831;PP;QD=9.69;RA=1986;RUN=1;ReadPosRankSum=-24.284;SB=-6038.55;SC=TGTCTGTCCCCCCTCAGCACT;SRB=0.45972;SRF=913;SRP=31.001;SRR=1073;TC;TR=6;TU=C;VQSLOD=6.1824;set=Intersection 20 50228709 rs71192536 TG T 20517 PASS AA=924;AB=0.50203;ABA=735;ABP=3.0633;ABR=741;AC=200;AF=0.16502;AN=1212;BL=35460;BR=34197;BVAR;BaseQRankSum=13.810;DB;DEL;DP=32402;DP4=1760,2065,395,449;Dels=0.16;EL=439;EPP=7.9831;ER=485;FQ=999;FR;FS=0.558;HETAR=242;HOMA=63;HOMR=764;HP=5;HPLen=3;HR=3;HRun=3;HU=G;INDEL;InbreedingCoeff=0.1050;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.018132;LRBP=52.738;MQ=105.83;MQ0=0;MQ0Fraction=0.0000;MQM=75.87;MQRankSum=3.895;NF;NR;NS=1069;PP;PV4=0.7,1.5e-173,1,1;RA=4708;RL=486;RPP=8.4249;RR=438;RUN=1;ReadPosRankSum=1.586;SAB=0.43615;SAF=403;SAP=35.733;SAR=521;SC=GTTTTCCAGGTGGGAAGACCG;SRB=0.44074;SRF=2075;SRP=146.62;SRR=2633;TC;TR=3;TU=G;VQSLOD=10.4820;dbSNP=120;set=Intersection;sumGLbyD=15.35 20 50236115 . AGG A,ACGGG,AG,AGGG 7429.57 PASS AC=192,13,221,183;AF=0.2115,0.0143,0.2434,0.2015;AN=908;BaseQRankSum=1.045;DP=1177;FS=13.479;HaplotypeScore=11.8294;InbreedingCoeff=0.7959;IndelType=MULTIALLELIC_INDEL;MQ=52.98;MQ0=6;MQ0Fraction=0.0051;MQRankSum=-1.482;QD=7.28;ReadPosRankSum=-2.380;SB=-1229.31;VQSLOD=8.3762;set=VQSR 20 51589568 . TAAAC AAAAC,T 12477.52 PASS AF=0.27949;BaseQRankSum=-28.122;DP=3777;Dels=0.00;FR;FS=31.799;HP=7;HPLen=4;HR=3;HRun=0;HU=A;InbreedingCoeff=-0.1429;IndelType=MIXED;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.196;NF;NR;PP;ReadPosRankSum=-16.483;SC=AAATTCAAAATAAACAAACAA;TC;TR=18;TU=AAAC;VQSLOD=3.9201;set=filterInVQSR-2of5;sumGLbyD=52.43 20 51617742 . TGC T,TGCGC 1374.91 PASS AF=0.06000,0.02000;BaseQRankSum=12.051;DP=6231;Dels=0.00;FS=189.609;HPLen=1;HRun=0;InbreedingCoeff=0.0862;IndelType=MULTIALLELIC_INDEL;MQ0Fraction=0.0180;MQRankSum=-2.959;ReadPosRankSum=-5.090;VQSLOD=-2.8715;set=filterInVQSR-2of5;sumGLbyD=3.97 20 51770354 . AG A 1010.90 PASS AA=26;AB=0.52727;ABA=26;ABP=3.3656;ABR=29;AC=7;AF=0.0097;AF1=0.01637;AN=718;BL=1034;BR=964;BVAR;BaseQRankSum=5.588;CI95=0.01327,0.02212;DEL;DP=16259;DP4=2785,2239,15,10;Dels=0.01;EL=11;EPP=4.3466;ER=15;FQ=999;FR;FS=3.367;HETAR=8;HOMA=0;HOMR=1064;HP=2;HPLen=2;HR=2;HRun=2;HU=G;INDEL;InbreedingCoeff=0.0557;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.035035;LRBP=8.3357;MQ=90.48;MQ0=0;MQ0Fraction=0.0000;MQM=61.346;MQRankSum=-0.019;NF;NR;NS=1072;PP;PV4=0.69,2.1e-08,0.078,1;RA=6173;RL=13;RPP=3.0103;RR=13;RUN=1;ReadPosRankSum=-0.460;SAB=0.61538;SAF=16;SAP=6.017;SAR=10;SC=GTGGTCCTGCAGGTCAATAAT;SRB=0.56342;SRF=3478;SRP=218.68;SRR=2695;TC;TR=2;TU=G;VQSLOD=10.1601;set=Intersection;sumGLbyD=14.60 20 51848430 . AT A,ATT 999 PASS AA=39;AB=0.83408;ABA=37;ABP=219.19;ABR=186;AC=14,33;AF=0.0153,0.0359;AF1=0.03062;AN=918;BL=1676;BR=1732;BVAR;BaseQRankSum=3.338;CI95=0.02212,0.03982;DP=14886;DP4=1970,1762,22,31;Dels=0.01;EL=18;EPP=3.5114;ER=21;FQ=999;FR;FS=3.004;HETAR=31;HOMA=0;HOMR=1040;HP=10;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.1629;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.016432;LRBP=5.0085;MQ=80.05;MQ0=0;MQ0Fraction=0.0000;MQM=56.667;MQRankSum=0.325;NF;NR;NS=1071;PP;PV4=0.13,1,0.0095,0.064;RA=5318;RL=21;RPP=3.5114;RR=18;RUN=1;ReadPosRankSum=-0.493;SAB=0.46154;SAF=18;SAP=3.5114;SAR=21;SC=ACAAAACAATATTTTTTTTTC;SRB=0.4968;SRF=2642;SRP=3.4823;SRR=2676;TC;TR=9;TU=T;VQSLOD=5.7417;set=Intersection;sumGLbyD=7.57 20 51897203 . T TG 8427.20 PASS AA=237;AB=0.69846;ABA=215;ABP=246.92;ABR=498;AC=117;AF=0.1662;AN=704;BL=14961;BR=5990;BVAR;BaseQRankSum=22.203;DP=9710;Dels=0.00;EL=83;EPP=49.198;ER=154;FR;FS=9.450;HETAR=123;HOMA=9;HOMR=895;HP=5;HPLen=6;HR=6;HRun=0;HU=T;INS;InbreedingCoeff=-0.0513;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.42819;LRBP=8344.3;MQ0Fraction=0.0291;MQM=45.861;MQRankSum=-10.426;NF;NR;NS=1027;PP;RA=4919;RL=210;RPP=309.85;RR=27;RUN=1;ReadPosRankSum=-1.843;SAB=0.29536;SAF=70;SAP=89.219;SAR=167;SC=TTTGTTTGTTTTTTGTTGTTG;SRB=0.47794;SRF=2351;SRP=23.798;SRR=2568;TC;TR=23;TU=GTTT;VQSLOD=6.2670;set=Intersection;sumGLbyD=8.99 20 52274070 . AAG A 1400.37 PASS AA=30;AB=0.74227;ABA=25;ABP=52.462;ABR=72;AC=21;AF=0.01756;AN=1196;BL=412;BR=1966;BVAR;BaseQRankSum=6.660;DEL;DP=9362;Dels=0.01;EL=16;EPP=3.2998;ER=14;FS=1.485;HETAR=18;HOMA=2;HOMR=1004;HRun=0;InbreedingCoeff=0.0317;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.65349;LRBP=2208.2;MQ0Fraction=0.0022;MQM=46.133;MQRankSum=-4.743;NS=1024;RA=3931;RL=2;RPP=51.941;RR=28;RUN=1;ReadPosRankSum=-4.152;SAB=0.4;SAF=12;SAP=5.6161;SAR=18;SRB=0.49784;SRF=1957;SRP=3.1699;SRR=1974;VQSLOD=5.6452;set=Intersection;sumGLbyD=11.11 20 52351501 . TAC T 199.59 PASS AC=22;AF=0.0238;AN=926;BaseQRankSum=7.874;DP=22911;DP4=2146,1691,26,22;FR;FS=2.898;HP=4;HPLen=3;HR=1;HRun=0;HU=A;HaplotypeScore=18.6111;INDEL;InbreedingCoeff=-0.0326;IndelType=DEL.NumRepetitions_6.EventLength_2.RepeatExpansion_AC.;MQ0=2;MQ0Fraction=0.0007;MQRankSum=1.011;NF;NR;PP;PV4=0.88,0.14,0.16,0.24;QD=1.10;ReadPosRankSum=-1.053;SB=-306.09;SC=GACACACAAATACACACACAC;TC;TR=13;TU=AC;VQSLOD=4.0486;set=filterInVQSR-2of5 20 52447173 . CA C 503.89 PASS AC=23;AF=0.01891;AN=1216;BaseQRankSum=0.801;DP=3266;FS=2.606;HRun=2;HaplotypeScore=22.1543;InbreedingCoeff=-0.0097;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_A.;MQ=118.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.309;QD=2.65;ReadPosRankSum=-7.872;SB=-279.27;VQSLOD=4.1900;set=VQSR 20 52498650 . GT G 24069 PASS AA=74;AB=0.90594;ABA=57;ABP=870.4;ABR=549;AC=28;AF=0.02333;AN=1200;BL=505;BR=4514;BVAR;BaseQRankSum=-3.837;DEL;DP=9798;Dels=0.01;EL=41;EPP=4.8883;ER=33;FS=4.085;HETAR=209;HOMA=663;HOMR=121;HRun=1;InbreedingCoeff=0.0334;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.79876;LRBP=6956.6;MQ0=2;MQ0Fraction=0.0007;MQM=57.784;MQRankSum=-2.951;NS=995;RA=957;RL=8;RPP=101.72;RR=66;RUN=1;ReadPosRankSum=-14.806;SAB=0.39189;SAF=29;SAP=10.522;SAR=45;SRB=0.39916;SRF=382;SRP=87.53;SRR=575;VQSLOD=3.8710;set=filterInVQSR-2of5;sumGLbyD=2.90 20 52823602 rs11469056 CAAA C,CA,CAA,CAAAA,CAAAAA,CAAAAAA,CAAAAAAA,CAAAAAAAA,CAAAAAAAAA,CAAAAAAAAAA 14515.17 PASS AC=24,83,246,109,83,19,10,16,22,59;AF=0.02128,0.07358,0.21809,0.09663,0.07358,0.01684,0.00887,0.01418,0.01950,0.05230;AN=1128;BVAR;BaseQRankSum=4.150;DB;DEL;DP=28279;FR;FS=2.021;HP=17;HR=17;HU=A;HaplotypeScore=27.8032;INS;InbreedingCoeff=0.7740;IndelType=MULTIALLELIC_INDEL;MQ=69.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.418;NF;NR;PP;QD=7.90;RUN=1;ReadPosRankSum=-3.864;SB=-3244.40;SC=GGTCCTAAGGCAAAAAAAAAA;TC;TR=17;TU=A;VQSLOD=14.1033;set=Intersection 20 53308906 . CT C,CTT 2276 PASS AA=92;AB=0.84453;ABA=81;ABP=540.17;ABR=440;AC=53,81;AF=0.04351,0.06650;AN=1218;BL=3561;BR=4796;BVAR;BaseQRankSum=3.000;DP=11804;Dels=0.02;EL=48;EPP=3.3879;ER=44;FR;FS=13.197;HETAR=69;HOMA=3;HOMR=993;HP=11;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2297;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.14778;LRBP=399.32;MQ0=1;MQ0Fraction=0.0003;MQM=56.348;MQRankSum=3.154;NF;NR;NS=1065;PP;RA=5520;RL=39;RPP=7.6365;RR=53;RUN=1;ReadPosRankSum=-2.140;SAB=0.57609;SAF=53;SAP=7.6365;SAR=39;SC=AATCCAAAGTCTTTTTTTTTT;SRB=0.51576;SRF=2847;SRP=14.92;SRR=2673;TC;TR=10;TU=T;VQSLOD=2.4753;set=filterInVQSR-2of5;sumGLbyD=4.42 20 53334602 . T TG,TGG 905.13 PASS ABR=325;AC=44,22;AF=0.03624,0.01812;BVAR;BaseQRankSum=-4.608;DP=15015;FR;FS=494.901;HOMA=0;HOMR=1004;HP=1;HR=1;HU=G;HaplotypeScore=20.5023;INS;InbreedingCoeff=0.0799;IndelType=MULTIALLELIC_INDEL;MQ=116.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=8.022;NF;NR;NS=1064;PP;QD=0.35;RA=5690;RUN=1;ReadPosRankSum=-14.522;SB=-311.57;SC=AGCCATTGGCTGTTTCACTGA;SRB=0.40738;SRF=2318;SRP=426.97;SRR=3372;TC;TR=1;TU=G;VQSLOD=-2.3042;set=filterInVQSR-2of5 20 53729115 . T TG 15.48 PASS AC=1;AF=0.0015;AN=668;BaseQRankSum=-1.001;DP=1711;FS=9.048;HRun=2;HaplotypeScore=12.4681;InbreedingCoeff=-0.0320;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;MQ=131.36;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.193;QD=4.57;ReadPosRankSum=0.407;SB=-5.35;VQSLOD=4.8071;set=VQSR 20 54033830 . GTATTTTAAAATCA G 2220.86 PASS AF=0.0113;BaseQRankSum=5.506;DP=2577;Dels=0.01;FR;FS=6.533;HP=5;HPLen=4;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0032;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.969;NF;NR;PP;ReadPosRankSum=1.322;SC=TCAATATTTTGTATTTTAAAA;TC;TR=1;TU=T;VQSLOD=5.5145;set=Intersection;sumGLbyD=95.65 20 54375236 . GT G 626.13 PASS AA=40;AB=0.63551;ABA=39;ABP=20.078;ABR=68;AC=18;AF=0.0256;AN=702;BL=1331;BR=1743;BVAR;BaseQRankSum=9.346;DEL;DP=8568;Dels=0.02;EL=26;EPP=10.828;ER=14;FS=0.610;HETAR=21;HOMA=1;HOMR=1035;HRun=1;InbreedingCoeff=-0.0056;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13403;LRBP=122.92;MQ0=0;MQ0Fraction=0.0000;MQM=67.125;MQRankSum=-2.537;NS=1058;RA=4870;RL=17;RPP=4.9646;RR=23;RUN=1;ReadPosRankSum=-1.229;SAB=0.525;SAF=21;SAP=3.2274;SAR=19;SRB=0.5271;SRF=2567;SRP=34.087;SRR=2303;VQSLOD=7.9228;set=Intersection;sumGLbyD=10.77 20 54457331 . G GA 1793.40 PASS AA=77;AB=0.66667;ABA=74;ABP=56.573;ABR=148;AC=33;AF=0.02687;AN=1228;BL=3834;BR=1154;BVAR;BaseQRankSum=10.572;DP=10230;Dels=0.00;EL=77;EPP=170.21;ER=0;FS=139.433;HETAR=44;HOMA=1;HOMR=1001;HRun=1;INS;InbreedingCoeff=0.0023;IndelType=INS.NOVEL_1.Novel_A.;LEN=1;LRB=0.53729;LRBP=3129.8;MQ0Fraction=0.0095;MQM=4.7013;MQRankSum=-8.116;NS=1046;RA=4009;RL=77;RPP=170.21;RR=0;RUN=1;ReadPosRankSum=-6.026;SAB=1;SAF=77;SAP=170.21;SAR=0;SRB=0.57022;SRF=2286;SRP=174.7;SRR=1723;VQSLOD=1.1887;set=filterInVQSR-2of5;sumGLbyD=5.90 20 54469810 . CA C 1697.62 PASS AA=93;AB=0.63855;ABA=90;ABP=44.53;ABR=159;AC=34;AF=0.0374;AF1=0.01719;AN=908;BL=3242;BR=5839;BVAR;BaseQRankSum=10.425;CI95=0.009317,0.02795;DEL;DP=15197;DP4=2134,1896,56,46;Dels=0.03;EL=34;EPP=17.604;ER=59;FQ=16;FR;FS=9.985;HETAR=41;HOMA=1;HOMR=1011;HP=9;HPLen=8;HR=8;HRun=8;HU=A;INDEL;InbreedingCoeff=-0.0472;IndelType=DEL.NumRepetitions_8.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.28598;LRBP=1615.8;MQ=83.37;MQ0=1;MQ0Fraction=0.0004;MQM=64.075;MQRankSum=3.036;NF;NR;NS=1053;PP;PV4=0.76,1,0.31,0.22;RA=5150;RL=28;RPP=34.975;RR=65;RUN=1;ReadPosRankSum=-0.252;SAB=0.5914;SAF=55;SAP=9.7582;SAR=38;SC=ATTGCTAAGACAAAAAAAAGA;SRB=0.50621;SRF=2607;SRP=4.7374;SRR=2543;TC;TR=8;TU=A;VQSLOD=8.3677;set=Intersection;sumGLbyD=9.90 20 54542453 . GTATA G,GTA 5109.66 PASS ABR=112;AC=66,56;AF=0.0682,0.0579;AN=968;BVAR;BaseQRankSum=17.089;DB;DEL;DP=5519;DS;Dels=0.06;FS=99.502;HOMA=15;HOMR=409;HRun=0;InbreedingCoeff=0.1584;IndelType=MULTIALLELIC_INDEL;MQ0Fraction=0.0178;MQRankSum=-6.854;NS=460;RA=864;RUN=1;ReadPosRankSum=0.855;SRB=0.79282;SRF=685;SRP=646.5;SRR=179;VQSLOD=0.6375;set=filterInVQSR-2of5;sumGLbyD=8.53 20 54629773 . CA C 1799.50 PASS AA=49;AB=0.82707;ABA=46;ABP=250.17;ABR=220;AC=9;AF=0.00746;AN=1206;BL=173;BR=2277;BVAR;BaseQRankSum=5.240;DEL;DP=8557;Dels=0.01;EL=49;EPP=109.41;ER=0;FS=32.359;HETAR=35;HOMA=1;HOMR=325;HRun=1;InbreedingCoeff=0.0892;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.85878;LRBP=3926.6;MQ0Fraction=0.0602;MQM=32.163;MQRankSum=-3.926;NS=361;RA=1091;RL=0;RPP=109.41;RR=49;RUN=1;ReadPosRankSum=-4.512;SAB=0;SAF=0;SAP=109.41;SAR=49;SRB=0.49404;SRF=539;SRP=3.3467;SRR=552;VQSLOD=1.1233;set=filterInVQSR-2of5;sumGLbyD=3.54 20 54710245 . TA T 999 PASS AF=0.0084;AF1=0.0148;BaseQRankSum=3.954;CI95=0.00885,0.02212;DP=8043;DP4=2000,1849,10,7;Dels=0.01;FQ=999;FR;FS=0.000;HP=9;HPLen=6;HR=3;HRun=6;HU=A;INDEL;InbreedingCoeff=0.1181;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=78.51;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.095;NF;NR;PP;PV4=0.63,0.00056,1,1;ReadPosRankSum=-0.448;SC=CAACAAAAAATAAATAAATAA;TC;TR=15;TU=AAAT;VQSLOD=7.8129;set=Intersection;sumGLbyD=19.02 20 54968173 . A AAT,AATAT,AT,ATAT 89535.82 PASS ABR=994;AC=561,278,2,3;AF=0.50179,0.24866,0.00179,0.00268;AN=1118;BVAR;BaseQRankSum=-2.699;DB;DP=27837;DP4=168,177,1045,866;Dels=0.00;FQ=999;FR;FS=12.472;HOMA=71;HOMR=455;HP=3;HPLen=4;HR=4;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.6391;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ=80.36;MQ0Fraction=0.0055;MQRankSum=-1.512;NF;NR;NS=913;PP;PV4=0.046,1,1,1;RA=2015;RUN=1;ReadPosRankSum=1.015;SC=GGCCACTTAAAATATATATAT;SRB=0.44864;SRF=904;SRP=49.187;SRR=1111;TC;TR=15;TU=AT;VQSLOD=9.0092;dbSNP=132;set=Intersection;sumGLbyD=42.33 20 55176688 . TA T 421.84 PASS AF=0.01322;AF1=0.01845;BaseQRankSum=5.383;CI95=0.01282,0.02564;DP=10531;DP4=1975,2017,16,14;Dels=0.01;FQ=91.2;FR;FS=7.401;HP=6;HPLen=5;HR=5;HRun=5;HU=A;INDEL;InbreedingCoeff=0.0829;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_A.;MQ=75.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=-0.471;NF;NR;PP;PV4=0.72,1,1,1;ReadPosRankSum=0.223;SC=CTGCAAAATATAAAAATTAGG;TC;TR=5;TU=A;VQSLOD=6.6000;set=Intersection;sumGLbyD=12.15 20 55664086 . GTT ATT,G,GT,GTTT 5622.44 PASS AC=6,71,136;AF=0.00498,0.05887,0.11277;AN=1206;BVAR;BaseQRankSum=3.173;DB;DEL;DP=40384;DP4=1567,1317,54,29;Dels=0.05;FR;FS=1.949;HP=14;HR=11;HRun=11;HU=T;INDEL;INS;InbreedingCoeff=0.3490;IndelType=MIXED;MQ=77.90;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.052;NF;NR;PP;PV4=0.057,1,0.2,1.2e-05;RUN=1;ReadPosRankSum=-13.646;SC=AATTTTATTTGTTTTTTTTTT;TC;TR=11;TU=T;VQSLOD=11.7964;set=Intersection;sumGLbyD=8.09 20 56045006 . TG T 342.15 PASS AC=72;AF=0.0940;AN=766;BaseQRankSum=4.992;DP=1238;FS=1.460;HRun=7;HaplotypeScore=20.2784;InbreedingCoeff=0.1795;IndelType=DEL.NumRepetitions_7.EventLength_1.RepeatExpansion_G.;MQ=66.42;MQ0=1;MQ0Fraction=0.0008;MQRankSum=-0.937;QD=1.84;ReadPosRankSum=-4.385;SB=-320.83;VQSLOD=5.2383;set=VQSR 20 56158711 . AG A 922.47 PASS AA=18;AB=0.575;ABA=17;ABP=4.9646;ABR=23;AC=2;AF=0.0028;AN=714;BL=953;BR=808;BVAR;BaseQRankSum=3.129;DEL;DP=10462;Dels=0.01;EL=9;EPP=3.0103;ER=9;FR;FS=8.724;HETAR=4;HOMA=0;HOMR=1058;HP=1;HPLen=2;HR=2;HRun=1;HU=A;InbreedingCoeff=0.0262;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.08234;LRBP=28.936;MQ0=0;MQ0Fraction=0.0000;MQM=55.889;MQRankSum=2.052;NF;NR;NS=1062;PP;RA=6300;RL=9;RPP=3.0103;RR=9;RUN=1;ReadPosRankSum=-0.317;SAB=0.66667;SAF=12;SAP=7.3532;SAR=6;SC=TGGCCTAGCAAGCATCGTGAC;SRB=0.48143;SRF=3033;SRP=21.883;SRR=3267;TC;TR=8;TU=AAGC;VQSLOD=8.3252;set=Intersection;sumGLbyD=13.22 20 56258618 rs113670927 T C,TGC,TGTGC,TGTGTGC 37834.99 PASS ABR=441;AC=11,100,43;AF=0.0123,0.1119,0.0481;AN=894;BVAR;BaseQRankSum=19.514;DB;DP=23173;DP4=541,920,413,579;Dels=0.00;FQ=999;FR;FS=1.238;HOMA=28;HOMR=808;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.2154;IndelType=MIXED;MQ=57.25;MQ0Fraction=0.0275;MQRankSum=-6.684;NF;NR;NS=976;PP;PV4=0.023,1,1,1;RA=3294;RUN=1;ReadPosRankSum=11.873;SC=TGCGTGTGTGTGTGTGTGTGT;SRB=0.42441;SRF=1398;SRP=166.5;SRR=1896;TC;TR=30;TU=GT;VQSLOD=6.7457;dbSNP=114;set=Intersection;sumGLbyD=21.27 20 56395857 . T TAGGCAG 6614.22 PASS AA=30;AB=0.63415;ABA=30;ABP=15.827;ABR=52;AC=14;AF=0.0197;AF1=0.03154;AN=710;BL=991;BR=1813;BVAR;BaseQRankSum=-4.589;CI95=0.02434,0.04204;DP=13879;DP4=1543,1833,12,14;Dels=0.00;EL=14;EPP=3.2998;ER=16;FQ=999;FR;FS=1.482;HETAR=11;HOMA=0;HOMR=1051;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0774;IndelType=INS.NumRepetitions_2.EventLength_6.;LEN=6;LRB=0.29315;LRBP=526.27;MQ=90.42;MQ0=0;MQ0Fraction=0.0000;MQM=39.433;MQRankSum=-7.011;NF;NR;NS=1062;PP;PV4=1,1,3.7e-09,1;RA=5322;RL=9;RPP=13.433;RR=21;RUN=1;ReadPosRankSum=0.679;SAB=0.43333;SAF=13;SAP=4.1684;SAR=17;SC=AAGAGCATCTTAGGCAGAGGC;SRB=0.47294;SRF=2517;SRP=36.853;SRR=2805;TC;TR=2;TU=T;VQSLOD=8.3045;set=Intersection;sumGLbyD=68.22 20 56969289 . GTTTGT G 600.69 PASS AF=0.0056;AF1=0.007726;BaseQRankSum=2.907;CI95=0.004425,0.01327;DP=9643;DP4=1892,1749,6,3;Dels=0.00;FQ=117;FR;FS=16.601;HP=5;HPLen=3;HR=3;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0236;IndelType=DEL.NumRepetitions_3.EventLength_5.;MQ=92.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.134;NF;NR;PP;PV4=0.51,1,0.07,0.3;ReadPosRankSum=0.236;SC=TAAGGACGTTGTTTGTTTTGT;TC;TR=10;TU=GTTT;VQSLOD=5.8458;set=Intersection;sumGLbyD=39.51 20 57187557 . AG A,AGG 1486.69 PASS AA=130;AB=0.55446;ABA=90;ABP=8.2132;ABR=112;AC=56,26;AF=0.0574,0.0266;AN=976;BL=3817;BR=5968;BVAR;BaseQRankSum=5.517;DEL;DP=14174;DP4=925,721,59,48;Dels=0.05;EL=52;EPP=14.302;ER=78;FR;FS=0.917;HETAR=44;HOMA=17;HOMR=864;HP=4;HPLen=4;HR=4;HRun=4;HU=G;INDEL;InbreedingCoeff=0.2856;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.21983;LRBP=1029.8;MQ=91.56;MQ0=0;MQ0Fraction=0.0000;MQM=63.631;MQRankSum=1.900;NF;NR;NS=925;PP;PV4=0.84,1,1,0.39;RA=2746;RL=44;RPP=32.476;RR=86;RUN=1;ReadPosRankSum=-0.639;SAB=0.44615;SAF=58;SAP=6.2842;SAR=72;SC=TCAGGCCCGCAGGGGTCAGGG;SRB=0.5772;SRF=1585;SRP=145.17;SRR=1161;TC;TR=4;TU=G;VQSLOD=7.7167;set=Intersection;sumGLbyD=14.85 20 57282771 . T TG 506.43 PASS AA=34;AB=0.70312;ABA=19;ABP=25.946;ABR=45;AC=34;AF=0.0373;AN=912;BL=886;BR=1938;BVAR;BaseQRankSum=3.744;DP=4276;Dels=0.00;EL=18;EPP=3.2658;ER=16;FR;FS=0.639;HETAR=17;HOMA=9;HOMR=737;HP=9;HR=8;HRun=8;HU=G;INS;InbreedingCoeff=0.2149;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.37252;LRBP=853.99;MQ0=0;MQ0Fraction=0.0000;MQM=49.706;MQRankSum=-0.051;NF;NR;NS=763;PP;RA=1822;RL=9;RPP=19.36;RR=25;RUN=1;ReadPosRankSum=-2.111;SAB=0.55882;SAF=19;SAP=4.0322;SAR=15;SC=TCGGGGGGCGTGGGGGGGGTG;SRB=0.51098;SRF=931;SRP=4.9172;SRR=891;TC;TR=8;TU=G;VQSLOD=5.7772;set=Intersection;sumGLbyD=7.95 20 57419740 rs11481507 A AT 82613.57 PASS AA=3850;AB=0.41404;ABA=1786;ABP=198.63;ABR=1262;AC=919;AF=0.75328;AN=1220;BL=140665;BR=151383;BVAR;BaseQRankSum=-27.490;DB;DP=31794;DP4=588,585,1571,1721;Dels=0.00;EL=1924;EPP=3.0126;ER=1926;FQ=999;FR;FS=2.191;HETAR=482;HOMA=454;HOMR=135;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;INS;InbreedingCoeff=0.0861;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.036699;LRBP=857.15;MQ=123.92;MQ0=0;MQ0Fraction=0.0000;MQM=91.654;MQRankSum=3.016;NF;NR;NS=1071;PP;PV4=0.16,1,0.12,1;RA=1850;RL=1874;RPP=8.8784;RR=1976;RUN=1;ReadPosRankSum=-0.685;SAB=0.47636;SAF=1834;SAP=21.693;SAR=2016;SC=TACACTAGTGATTTAACCCTA;SRB=0.49027;SRF=907;SRP=4.5315;SRR=943;TC;TR=3;TU=T;VQSLOD=9.2768;dbSNP=126;set=Intersection;sumGLbyD=22.78 20 57558194 . CT C,CTT,CTTT 6470.30 PASS ABR=451;AC=104,161,177;AF=0.08919,0.13808,0.15180;BVAR;BaseQRankSum=1.172;DP=7985;FR;FS=2.202;HOMA=19;HOMR=778;HP=22;HR=15;HU=T;HaplotypeScore=16.1921;INS;InbreedingCoeff=0.6440;IndelType=MULTIALLELIC_INDEL;MQ=69.24;MQ0=27;MQ0Fraction=0.0109;MQRankSum=-0.003;NF;NR;NS=943;PP;QD=2.22;RA=2531;RUN=1;ReadPosRankSum=-0.104;SB=-2096.85;SC=GCCTTTTTTTCTTTTTTTTTT;SRB=0.34848;SRF=882;SRP=507.73;SRR=1649;TC;TR=15;TU=T;VQSLOD=6.5151;set=Intersection 20 57693627 . AG A 1991.90 PASS AA=52;AB=0.49462;ABA=47;ABP=3.0336;ABR=46;AC=15;AF=0.01227;AN=1222;BL=1902;BR=1478;BVAR;BaseQRankSum=-6.121;DEL;DP=26459;DP4=2647,2873,16,20;Dels=0.01;EL=25;EPP=3.1773;ER=27;FR;FS=3.135;HETAR=15;HOMA=1;HOMR=1064;HP=2;HPLen=3;HR=3;HRun=2;HU=A;INDEL;InbreedingCoeff=0.0866;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.12544;LRBP=118.51;MQ=116.26;MQ0=0;MQ0Fraction=0.0000;MQM=114.65;MQRankSum=1.942;NF;NR;NS=1080;PP;PV4=0.74,6.9e-08,1,0.38;RA=6781;RL=33;RPP=11.195;RR=19;RUN=1;ReadPosRankSum=-1.795;SAB=0.5;SAF=26;SAP=3.0103;SAR=26;SC=ATTGGAGGAAAGGCTTTTTCA;SRB=0.46247;SRF=3136;SRP=85.976;SRR=3645;TC;TR=3;TU=A;VQSLOD=8.6672;set=Intersection;sumGLbyD=13.55 20 57716287 . A AT 66.47 PASS AC=6;AF=0.00506;AN=1186;BaseQRankSum=1.369;DP=2744;FS=3.834;HRun=8;HaplotypeScore=11.2046;InbreedingCoeff=0.1196;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_T.;MQ=73.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-0.086;QD=2.14;ReadPosRankSum=-2.588;SB=-53.80;VQSLOD=4.2080;set=VQSR 20 58121928 rs73625057 T TGG 6649.17 PASS AA=132;AB=0.57854;ABA=110;ABP=16.996;ABR=151;AC=57;AF=0.0617;AN=924;BL=4530;BR=4790;BVAR;BaseQRankSum=-13.456;DB;DP=30353;DP4=2107,2168,61,66;Dels=0.00;EL=67;EPP=3.0761;ER=65;FR;FS=0.708;HETAR=46;HOMA=8;HOMR=1023;HP=3;HPLen=2;HR=2;HRun=2;HU=G;INDEL;INS;InbreedingCoeff=0.1241;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=2;LRB=0.027897;LRBP=18.76;MQ=109.61;MQ0=1;MQ0Fraction=0.0004;MQM=79.833;MQRankSum=-0.699;NF;NR;NS=1077;PP;PV4=0.79,1,0.49,0.036;RA=5754;RL=61;RPP=4.6554;RR=71;RUN=1;ReadPosRankSum=-3.309;SAB=0.45455;SAF=60;SAP=5.3792;SAR=72;SC=GATTAGAATGTGGATATCTTT;SRB=0.48836;SRF=2810;SRP=9.7866;SRR=2944;TC;TR=4;TU=GT;VQSLOD=8.5770;set=Intersection;sumGLbyD=27.19 20 58468826 . ACAAG A 999 PASS AF=0.0014;AF1=0.003429;BaseQRankSum=4.082;CI95=0.003106,0.006211;DP=8461;DP4=2500,1817,8,2;Dels=0.01;FQ=999;FR;FS=5.034;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0183;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ=120.69;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.141;NF;NR;PP;PV4=0.21,1,0.054,1;ReadPosRankSum=2.096;SC=ATCCTGAAACACAAGAAGAAA;TC;TR=5;TU=AC;VQSLOD=7.4928;set=Intersection;sumGLbyD=29.17 20 58731262 . TC T 999 PASS AA=21;AB=0.48649;ABA=19;ABP=3.069;ABR=18;AC=7;AF=0.0101;AF1=0.01493;AN=694;BL=939;BR=848;BVAR;BaseQRankSum=4.205;CI95=0.01106,0.02212;DEL;DP=12598;DP4=1766,1428,11,15;Dels=0.01;EL=13;EPP=5.5954;ER=8;FQ=999;FR;FS=1.796;HETAR=8;HOMA=1;HOMR=1031;HP=7;HPLen=8;HR=8;HRun=2;HU=T;INDEL;InbreedingCoeff=-0.0030;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.050923;LRBP=13.073;MQ=124.57;MQ0=0;MQ0Fraction=0.0000;MQM=67.905;MQRankSum=1.103;NF;NR;NS=1040;PP;PV4=0.23,1,1,1;RA=4884;RL=10;RPP=3.1137;RR=11;RUN=1;ReadPosRankSum=-0.091;SAB=0.47619;SAF=10;SAP=3.1137;SAR=11;SC=TCATTTTTTTTCCTTGAAACT;SRB=0.58006;SRF=2833;SRP=274.9;SRR=2051;TC;TR=8;TU=T;VQSLOD=10.8783;set=Intersection;sumGLbyD=15.11 20 59181229 rs11476579 CTT C,CT,CTTT,CTTTT 7787.17 PASS AC=19,195,104,91;AF=0.01599,0.16414,0.08754,0.07660;AF1=0.2124;AN=1188;BVAR;BaseQRankSum=6.347;CI95=0.146,0.2743;DB;DEL;DP=26140;DP4=932,880,352,375;Dels=0.13;FQ=85.6;FR;FS=11.914;HP=14;HR=14;HRun=14;HU=T;INDEL;INS;InbreedingCoeff=0.4183;IndelType=MULTIALLELIC_INDEL;MQ=86.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.469;NF;NR;PP;PV4=0.17,1,1,1;RUN=1;ReadPosRankSum=-1.055;SC=GGTGAGAAAGCTTTTTTTTTT;TC;TR=14;TU=T;VQSLOD=7.4340;dbSNP=120;set=Intersection;sumGLbyD=7.02 20 59213979 rs112141381 G GC 9068 PASS AA=131;AB=0.47115;ABA=110;ABP=4.5136;ABR=98;AF=0.0586;AN=700;BL=5395;BR=5816;BVAR;BaseQRankSum=15.453;DB;DP=23381;DP4=2191,2184,71,49;Dels=0.00;EL=66;EPP=3.0269;ER=65;FR;FS=7.907;HETAR=35;HOMA=5;HOMR=1019;HP=2;HPLen=3;HR=3;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0283;IndelType=INS.NOVEL_1.Novel_C.;LEN=1;LRB=0.037552;LRBP=37.34;MQ=72.13;MQ0=0;MQ0Fraction=0.0000;MQM=54.496;MQRankSum=0.897;NF;NR;NS=1059;PP;PV4=0.052,1,0.066,1;RA=4976;RL=59;RPP=5.8117;RR=72;RUN=1;ReadPosRankSum=-0.811;SAB=0.58015;SAF=76;SAP=10.32;SAR=55;SC=GATGGACTGGGACAGTGACTC;SRB=0.49457;SRF=2461;SRP=4.2828;SRR=2515;TC;TR=3;TU=G;VQSLOD=9.3917;set=Intersection;sumGLbyD=28.58 20 59252945 . CT C,CTT 557.18 PASS AA=24;AB=0.84868;ABA=23;ABP=163.53;ABR=129;AC=21,29;AF=0.01759,0.02429;BL=1217;BR=1336;BVAR;BaseQRankSum=5.135;DP=9970;Dels=0.01;EL=13;EPP=3.3722;ER=11;FS=2.302;HETAR=21;HOMA=1;HOMR=1012;HRun=9;INS;InbreedingCoeff=0.1549;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.046612;LRBP=15.055;MQ0=0;MQ0Fraction=0.0000;MQM=67.208;MQRankSum=0.086;NS=1034;RA=4421;RL=11;RPP=3.3722;RR=13;RUN=1;ReadPosRankSum=-1.826;SAB=0.41667;SAF=10;SAP=4.4579;SAR=14;SRB=0.49649;SRF=2195;SRP=3.4823;SRR=2226;VQSLOD=2.8923;set=filterInVQSR-2of5;sumGLbyD=5.47 20 60016966 . CT C 42650 PASS AA=37;AB=0.97834;ABA=31;ABP=2847;ABR=1400;AC=15;AF=0.0163;AN=920;BL=2596;BR=778;BVAR;BaseQRankSum=-0.632;DEL;DP=10967;Dels=0.00;EL=14;EPP=7.7641;ER=23;FS=4.094;HETAR=421;HOMA=256;HOMR=385;HRun=1;InbreedingCoeff=-0.0051;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.53883;LRBP=2130.2;MQ0=0;MQ0Fraction=0.0000;MQM=120.3;MQRankSum=-0.911;NS=1072;RA=3413;RL=31;RPP=39.691;RR=6;RUN=1;ReadPosRankSum=-12.062;SAB=0.48649;SAF=18;SAP=3.069;SAR=19;SRB=0.47407;SRF=1618;SRP=22.943;SRR=1795;VQSLOD=3.3758;set=filterInVQSR-2of5;sumGLbyD=3.27 20 60188651 . AG A 17624.52 PASS AA=462;AB=0.76548;ABA=409;ABP=1070.7;ABR=1335;AC=403;AF=0.34444;AN=1170;BL=13877;BR=25909;BVAR;BaseQRankSum=6.180;DEL;DP=9900;Dels=0.08;EL=353;EPP=282.84;ER=109;FR;FS=2699.057;HETAR=346;HOMA=26;HOMR=633;HP=3;HR=4;HRun=1;HU=A;InbreedingCoeff=-0.2900;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.30242;LRBP=7904.3;MQ0Fraction=0.0004;MQM=56.119;MQRankSum=1.644;NF;NR;NS=1005;PP;RA=3521;RL=112;RPP=269.25;RR=350;RUN=1;ReadPosRankSum=2.490;SAB=0.0064935;SAF=3;SAP=980.34;SAR=459;SC=AGGCTTCAAAAGAAAAAAAAA;SRB=0.55978;SRF=1971;SRP=112.32;SRR=1550;TC;TR=4;TU=A;VQSLOD=-34.0667;set=filterInVQSR-2of5;sumGLbyD=7.81 20 60195570 . GTACATACATACA ATACATACATACA,G,GTACATACA 20140 PASS ABR=102;AC=105,2;AF=0.08794,0.00168;AN=1194;BVAR;BaseQRankSum=-28.899;DB;DEL;DP=14347;Dels=0.02;FR;FS=52.125;HOMA=1;HOMR=1006;HP=1;HPLen=1;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0695;IndelType=MIXED;MQ0Fraction=0.0007;MQRankSum=1.957;NF;NR;NS=1035;PP;RA=4759;RUN=1;ReadPosRankSum=-22.252;SAB=0.5;SAP=3.0103;SC=TGATAGATTCGTACATACATA;SRB=0.47615;SRF=2266;SRP=26.522;SRR=2493;TC;TR=21;TU=ACAT;VQSLOD=2.7673;set=filterInVQSR-2of5;sumGLbyD=19.14 20 60670601 rs72127450 AT A,ATT 6401.59 PASS AC=177,79;AF=0.16239,0.07248;AF1=0.1602;AN=1090;BVAR;BaseQRankSum=8.618;CI95=0.1106,0.2058;DB;DEL;DP=17508;DP4=1285,1094,313,259;Dels=0.10;FQ=94.1;FR;FS=0.000;HP=12;HR=12;HRun=12;HU=T;INDEL;INS;InbreedingCoeff=0.1076;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=64.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.620;NF;NR;PP;PV4=0.78,1,0.012,1;RUN=1;ReadPosRankSum=-1.294;SC=AGCCAGGCACATTTTTTTTTT;TC;TR=12;TU=T;VQSLOD=6.1650;dbSNP=130;set=Intersection;sumGLbyD=5.80 20 60685780 . TC T 1123.58 PASS AC=79;AF=0.07655;AN=1032;BaseQRankSum=14.949;DP=2084;FS=23.521;HRun=1;HaplotypeScore=19.7117;InbreedingCoeff=0.1356;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=53.57;MQ0=61;MQ0Fraction=0.0293;MQRankSum=-7.958;QD=4.35;ReadPosRankSum=-13.757;SB=-791.28;VQSLOD=6.3549;set=VQSR 20 60744906 rs113528167 CG C 422.53 PASS AC=48;AF=0.0732;AN=656;BaseQRankSum=17.669;DB;DP=1189;FS=0.356;HRun=1;HaplotypeScore=15.1808;InbreedingCoeff=0.2111;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;MQ=82.83;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-10.455;QD=2.71;ReadPosRankSum=-16.887;SB=-326.46;VQSLOD=7.1707;set=VQSR 20 60848742 . CGT C,CGTGT 999 PASS AF=0.00980,0.01225;BaseQRankSum=5.597;DP=17065;DP4=1928,2188,17,13;Dels=0.01;FR;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.2094;IndelType=MULTIALLELIC_INDEL;MQ=115.78;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.281;NF;NR;PP;PV4=0.36,0.4,0.12,0.12;ReadPosRankSum=-1.465;SB=-157.35;SC=TAGACGCTTCCGTGTGTGTGT;TC;TR=11;TU=GT;VQSLOD=1.7100;set=filterInVQSR-2of5;sumGLbyD=16.39 20 61023668 rs57452309 G GAGC 6896.67 PASS AC=115;AF=0.1445;AN=796;BaseQRankSum=12.146;DB;DP=1423;FS=5.070;HRun=0;HaplotypeScore=29.8897;InbreedingCoeff=0.0740;IndelType=INS.NOVEL_3.;MQ=77.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-9.005;QD=19.16;ReadPosRankSum=-17.440;SB=-3045.82;VQSLOD=4.5788;set=VQSR 20 61180519 . C CA,CT 1774.30 PASS ABR=135;AC=27,15;AF=0.02538,0.01410;BVAR;BaseQRankSum=-2.189;DP=8393;FR;FS=27.692;HOMA=2;HOMR=825;HP=6;HPLen=3;HR=3;HU=T;HaplotypeScore=19.5313;INS;InbreedingCoeff=0.0868;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=56.11;MQ0=172;MQ0Fraction=0.0667;MQRankSum=2.605;NF;NR;NS=854;PP;QD=1.99;RA=2868;RUN=1;ReadPosRankSum=-7.324;SB=-385.54;SC=TTCTTTCTTTCTTTCTTTCTT;SRB=0.32741;SRF=939;SRP=745.08;SRR=1929;TC;TR=69;TU=CTTT;VQSLOD=3.4398;set=filterInVQSR-2of5 20 61184281 . AC A 9798.10 PASS AA=24;AB=0.96507;ABA=16;ABP=863.43;ABR=442;AC=4;AF=0.00341;AN=1174;BL=349;BR=1039;BVAR;BaseQRankSum=2.048;DEL;DP=10073;Dels=0.00;EL=11;EPP=3.3722;ER=13;FS=2.097;HETAR=141;HOMA=69;HOMR=829;HRun=1;InbreedingCoeff=0.0697;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.49712;LRBP=747.85;MQ0=0;MQ0Fraction=0.0000;MQM=98.042;MQRankSum=1.881;NS=1042;RA=3625;RL=5;RPP=20.744;RR=19;RUN=1;ReadPosRankSum=-8.009;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SRB=0.52662;SRF=1909;SRP=25.323;SRR=1716;VQSLOD=1.8117;set=filterInVQSR-2of5;sumGLbyD=5.55 20 62074219 . C CTAT,CTGT 2328 PASS ABR=99;AC=20,6;AF=0.01754,0.00526;BVAR;BaseQRankSum=11.221;DP=9498;DS;FS=4.510;HOMA=15;HOMR=645;HaplotypeScore=82.8868;INS;InbreedingCoeff=0.0880;IndelType=MULTIALLELIC_INDEL;LEN=3;MQ=29.88;MQ0=1378;MQ0Fraction=0.2286;MQRankSum=-5.309;NS=689;QD=0.77;RA=1679;RUN=1;ReadPosRankSum=-3.510;SAR=1;SB=-93.21;SRB=0.70697;SRF=1187;SRP=627.71;SRR=492;VQSLOD=1.8325;set=filterInVQSR-2of5 20 62304449 . CA C,CAA 6680.17 PASS AC=141,69;AF=0.12567,0.06150;AF1=0.08178;AN=1122;BVAR;BaseQRankSum=9.754;CI95=0.05088,0.1128;DEL;DP=15867;DP4=1252,1289,232,208;Dels=0.10;FQ=52.6;FR;FS=6.576;HP=11;HR=11;HRun=11;HU=A;INDEL;INS;InbreedingCoeff=0.1950;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=60.48;MQ0Fraction=0.0004;MQRankSum=-0.049;NF;NR;PP;PV4=0.2,1,1,1;RUN=1;ReadPosRankSum=-2.137;SC=GATTCTGTGTCAAAAAAAAAA;TC;TR=11;TU=A;VQSLOD=7.4714;set=Intersection;sumGLbyD=8.36 20 62804895 rs57769591 CCTT C 1148 PASS AC=8;AF=0.0085;AF1=0.002839;AN=938;BaseQRankSum=4.952;CI95=0.002212,0.006637;DB;DP=8889;DP4=2574,1668,4,8;FQ=12.3;FS=2.289;HPLen=3;HRun=0;HaplotypeScore=29.4184;INDEL;InbreedingCoeff=-0.0270;IndelType=DEL.NumRepetitions_1.EventLength_3.;MQ0=876;MQ0Fraction=0.2674;MQRankSum=-0.641;PV4=0.074,1,1,1;QD=1.03;ReadPosRankSum=0.118;SB=-65.30;VQSLOD=6.4881;dbSNP=126;set=Intersection 20 62907688 . AAT A 6629.57 PASS AC=164;AF=0.13735;AN=1194;BaseQRankSum=27.368;DP=2746;FS=5.985;HRun=0;HaplotypeScore=14.7748;InbreedingCoeff=0.1433;IndelType=DEL.NumRepetitions_2.EventLength_2.RepeatExpansion_AT.;MQ=96.65;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.318;QD=10.81;ReadPosRankSum=0.789;SB=-2662.16;VQSLOD=6.1473;set=VQSR pysam-0.23.0/tests/tabix_data/vcf/20.vcf000066400000000000000000000343421475062545500177110ustar00rootroot00000000000000##fileformat=VCFv4.1 ##INFO= ##INFO= ##INFO= ##INFO= ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO 20 207414 . G A . . PacBio=NoCall;Sqnm=NoCall 20 792106 . C G . . PacBio=Poly;Sqnm=NoCall 20 894031 . G A . . PacBio=Poly;Sqnm=Poly 20 1508892 . A G . . PacBio=Poly;Sqnm=Poly 20 1686745 . G A . . PacBio=Poly;Sqnm=NoCall 20 1818886 . C T . . PacBio=Poly;Sqnm=Poly 20 2062981 . A G . . PacBio=Poly;Sqnm=Poly 20 2773229 . A G . . PacBio=Poly;Sqnm=Poly 20 2817761 . T C . . PacBio=Poly;Sqnm=Poly 20 2994966 . G T . . PacBio=Poly;Sqnm=Poly 20 3126723 . C T . . PacBio=Poly;Sqnm=Poly 20 3523369 . G A . . PacBio=Poly;Sqnm=Poly 20 3635082 . A G . . PacBio=Poly;Sqnm=Poly 20 3714080 . C G . . PacBio=Poly;Sqnm=Poly 20 3905791 . G A . . PacBio=Poly;Sqnm=NoCall 20 3907250 . A G . . PacBio=Poly;Sqnm=Poly 20 4171994 . C T . . PacBio=Poly;Sqnm=Poly 20 4246375 . T C . . PacBio=Poly;Sqnm=NoCall 20 4375206 . C T . . PacBio=Poly;Sqnm=Poly 20 4434727 . A T . . PacBio=NoCall;Sqnm=Mono;Sanger=Mono 20 4495199 . G C . . PacBio=Poly;Sqnm=Poly 20 4835415 . C T . . PacBio=Poly;Sqnm=Poly 20 4915769 . T C . . PacBio=Poly;Sqnm=NoCall 20 4983198 . T C . . PacBio=Poly;Sqnm=Poly 20 5441171 . C T . . PacBio=Poly;Sqnm=NoCall 20 5978029 . T C . . PacBio=Poly;Sqnm=Poly 20 6061317 . C A . . PacBio=Poly;Sqnm=Poly 20 6328925 . C A . . PacBio=Poly;Sqnm=Poly 20 6675461 . C T . . PacBio=Poly;Sqnm=NoCall 20 6976115 . C T . . PacBio=Poly;Sqnm=Poly 20 7013349 . G A . . PacBio=NoCall;Sqnm=NoCall 20 7039302 . C T . . PacBio=Poly;Sqnm=Poly 20 7638704 . C A . . PacBio=Poly;Sqnm=Poly 20 7688381 . G A . . PacBio=Poly;Sqnm=Poly 20 7726350 . G T . . PacBio=Poly;Sqnm=Poly 20 7733957 . C T . . PacBio=Poly;Sqnm=Poly 20 7850516 . T C . . PacBio=Poly;Sqnm=Poly 20 8095059 . G A . . PacBio=NoCall;Sqnm=NoCall 20 8232012 . T A . . PacBio=Poly;Sqnm=Poly 20 8415290 . A C . . PacBio=Poly;Sqnm=Poly 20 8438535 . T C . . PacBio=Poly;Sqnm=NoCall 20 8815233 . G A . . PacBio=Mono;Sqnm=NoCall 20 8953629 . C G . . PacBio=Poly;Sqnm=Poly 20 9237267 . T A . . PacBio=Poly;Sqnm=Poly 20 9744549 . T C . . PacBio=Poly;Sqnm=Poly 20 9780416 . C A . . PacBio=Poly;Sqnm=Poly 20 10252552 . T C . . PacBio=Poly;Sqnm=Poly 20 10314038 . C G . . PacBio=Poly;Sqnm=Poly 20 10757416 . T C . . PacBio=Poly;Sqnm=Poly 20 11087688 . A G . . PacBio=Poly;Sqnm=Poly 20 11094107 . G A . . PacBio=NoCall;Sqnm=NoCall 20 11098680 . G A . . PacBio=Poly;Sqnm=Poly 20 11353163 . G C . . PacBio=Poly;Sqnm=Poly 20 11510559 . A G . . PacBio=Poly;Sqnm=Poly 20 11787224 . C T . . PacBio=Poly;Sqnm=Poly 20 11821024 . T C . . PacBio=Poly;Sqnm=Poly 20 11932295 . A G . . PacBio=Poly;Sqnm=Poly 20 11965311 . G T . . PacBio=Poly;Sqnm=Poly 20 12023599 . C T . . PacBio=Poly;Sqnm=Poly 20 12505523 . G T . . PacBio=Poly;Sqnm=Poly 20 12570054 . A C . . PacBio=NoCall;Sqnm=Poly 20 12667452 . A G . . PacBio=Poly;Sqnm=Poly 20 12678271 . G A . . PacBio=Poly;Sqnm=Mono 20 12704885 . T C . . PacBio=Poly;Sqnm=Poly 20 12733996 . C T . . PacBio=Poly;Sqnm=NoCall 20 12737269 . C T . . PacBio=NoCall;Sqnm=NoCall 20 12788981 . G A . . PacBio=Poly;Sqnm=Poly 20 12828594 . T C . . PacBio=Poly;Sqnm=Poly 20 12999157 . T C . . PacBio=Poly;Sqnm=Poly 20 13083804 . C G . . PacBio=Poly;Sqnm=Poly 20 13197077 . G T . . PacBio=Poly;Sqnm=NoCall 20 13217896 . A G . . PacBio=NoCall;Sqnm=Poly 20 13276778 . G A . . PacBio=Poly;Sqnm=Poly 20 13375116 . G A . . PacBio=Mono;Sqnm=NoCall;NotCalledInValidationSamples 20 13648056 . T C . . PacBio=Poly;Sqnm=Poly 20 13672895 . C T . . PacBio=Poly;Sqnm=Poly 20 14160159 . C G . . PacBio=Poly;Sqnm=Poly 20 14266815 . T A . . PacBio=Poly;Sqnm=Poly 20 14865143 . C T . . PacBio=Poly;Sqnm=Poly 20 14882868 . T G . . PacBio=Poly;Sqnm=Poly 20 15244725 . C A . . PacBio=Poly;Sqnm=Poly 20 15277072 . G A . . PacBio=Poly;Sqnm=Poly 20 15390867 . C T . . PacBio=Poly;Sqnm=Poly 20 15785205 . T C . . PacBio=Poly;Sqnm=Poly 20 15833020 . A G . . PacBio=Poly;Sqnm=Poly 20 15847620 . C T . . PacBio=Poly;Sqnm=Poly 20 15953253 . G A . . PacBio=Poly;Sqnm=NoCall 20 15964434 . G C . . PacBio=NoCall;Sqnm=NoCall 20 16183922 . G A . . PacBio=Poly;Sqnm=Poly 20 16190824 . A G . . PacBio=Poly;Sqnm=Poly 20 16557779 . A G . . PacBio=Poly;Sqnm=Poly 20 16730061 . C T . . PacBio=Poly;Sqnm=Poly 20 16794015 . T C . . PacBio=Poly;Sqnm=Poly 20 17048741 . G A . . PacBio=Poly;Sqnm=Poly 20 17299827 . G A . . PacBio=Poly;Sqnm=Poly 20 17299845 . C T . . PacBio=Poly;Sqnm=Poly 20 17390323 . G A . . PacBio=Poly;Sqnm=Poly 20 17624973 . C G . . PacBio=Poly;Sqnm=Poly 20 17666040 . G A . . PacBio=Poly;Sqnm=Poly 20 17735813 . T C . . PacBio=Poly;Sqnm=Poly 20 17794990 . A G . . PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples 20 17809418 . G A . . PacBio=Poly;Sqnm=Poly 20 17860794 . C T . . PacBio=Mono;Sqnm=NoCall 20 17881936 . A G . . PacBio=Poly;Sqnm=Poly 20 17893097 . C G . . PacBio=NoCall;Sqnm=NoCall 20 18188883 . A G . . PacBio=Poly;Sqnm=Poly 20 18199319 . G A . . PacBio=Poly;Sqnm=Poly 20 18233699 . C T . . PacBio=Poly;Sqnm=Poly 20 18536869 . G A . . PacBio=Poly;Sqnm=Poly 20 18637785 . T C . . PacBio=NoCall;Sqnm=Mono;Sanger=Mono;NotCalledInValidationSamples 20 18763166 . G A . . PacBio=Poly;Sqnm=Poly 20 19102715 . A G . . PacBio=NoCall;Sqnm=NoCall 20 19244609 . C T . . PacBio=Poly;Sqnm=Poly 20 19573719 . C T . . PacBio=Poly;Sqnm=Poly 20 19815613 . A G . . PacBio=NoCall;Sqnm=Poly 20 20511479 . C T . . PacBio=Poly;Sqnm=Poly;Sanger=Poly 20 20639358 . T C . . PacBio=Poly;Sqnm=Poly 20 21278490 . T C . . PacBio=Poly;Sqnm=Poly 20 21297718 . C G . . PacBio=Poly;Sqnm=Poly 20 21418269 . A T . . PacBio=Poly;Sqnm=Poly 20 21560553 . A T . . PacBio=Poly;Sqnm=Poly 20 21618451 . G A . . PacBio=NoCall;Sqnm=NoCall 20 21705723 . C A . . PacBio=Poly;Sqnm=Poly 20 22076189 . A G . . PacBio=Poly;Sqnm=Poly 20 22118677 . T A . . PacBio=Poly;Sqnm=Poly 20 22320721 . C T . . PacBio=Poly;Sqnm=Poly 20 22368918 . C A . . PacBio=Poly;Sqnm=Poly 20 23020003 . A G . . PacBio=Poly;Sqnm=Poly 20 23214163 . G A . . PacBio=Poly;Sqnm=Poly 20 23273877 . T C . . PacBio=Poly;Sqnm=Poly 20 23335790 . C T . . PacBio=Poly;Sqnm=NoCall 20 23790659 . C T . . PacBio=Poly;Sqnm=Poly 20 23830388 . T C . . PacBio=Poly;Sqnm=NoCall 20 23837678 . C G . . PacBio=Poly;Sqnm=Poly 20 23901081 . A C . . PacBio=Poly;Sqnm=Poly 20 23946361 . C T . . PacBio=Poly;Sqnm=Poly 20 23949242 . A G . . PacBio=Poly;Sqnm=Poly 20 24539119 . A G . . PacBio=Poly;Sqnm=Poly 20 24986457 . C T . . PacBio=Poly;Sqnm=Poly 20 25183729 . G A . . PacBio=NoCall;Sqnm=NoCall 20 25277133 . C T . . PacBio=Poly;Sqnm=Poly 20 25292464 . C T . . PacBio=Poly;Sqnm=NoCall 20 25528915 . G C . . PacBio=Poly;Sqnm=Poly 20 25851836 . A G . . PacBio=NoCall;Sqnm=NoCall 20 25970163 . C T . . PacBio=Poly;Sqnm=Poly 20 29920798 . C T . . PacBio=NoCall;Sqnm=NoCall 20 30007713 . T C . . PacBio=Poly;Sqnm=Poly 20 30051768 . T C . . PacBio=Poly;Sqnm=Poly 20 30183598 . T C . . PacBio=Poly;Sqnm=Poly 20 30604408 . G A . . PacBio=NoCall;Sqnm=NoCall 20 30759940 . G T . . PacBio=Poly;Sqnm=Poly 20 30881454 . G T . . PacBio=Poly;Sqnm=Poly 20 31356560 . C T . . PacBio=Poly;Sqnm=Poly 20 31450036 . A G . . PacBio=NoCall;Sqnm=Mono 20 31589920 . A T . . PacBio=Poly;Sqnm=Poly 20 31922121 . C T . . PacBio=NoCall;Sqnm=NoCall 20 32801430 . G C . . PacBio=Poly;Sqnm=Poly 20 32943975 . G T . . PacBio=Mono;Sqnm=Mono 20 33155812 . C A . . PacBio=Poly;Sqnm=Poly 20 34090682 . C T . . PacBio=Poly;Sqnm=Poly 20 34254080 . C T . . PacBio=Mono;Sqnm=NoCall;NotCalledInValidationSamples 20 34312126 . C T . . PacBio=Poly;Sqnm=NoCall 20 34481504 . G A . . PacBio=Poly;Sqnm=Poly 20 34694577 . G A . . PacBio=Poly;Sqnm=Poly 20 35026572 . T C . . PacBio=Poly;Sqnm=Poly 20 35472344 . T G . . PacBio=Poly;Sqnm=Poly 20 35882698 . G A . . PacBio=Poly;Sqnm=NoCall 20 36044719 . G A . . PacBio=Poly;Sqnm=NoCall 20 36047623 . C A . . PacBio=NoCall;Sqnm=NoCall 20 36204890 . C T . . PacBio=Poly;Sqnm=NoCall 20 36469514 . G C . . PacBio=NoCall;Sqnm=Poly 20 36840217 . T C . . PacBio=Poly;Sqnm=Poly 20 37460945 . C T . . PacBio=Mono;Sqnm=Poly 20 37665246 . G A . . PacBio=Poly;Sqnm=NoCall 20 37732397 . A G . . PacBio=Poly;Sqnm=Poly 20 37874645 . G T . . PacBio=Poly;Sqnm=Poly 20 37958191 . T C . . PacBio=Poly;Sqnm=Poly 20 37996273 . C T . . PacBio=Mono;Sqnm=NoCall;NotCalledInValidationSamples 20 38016547 . C T . . PacBio=Poly;Sqnm=Poly 20 38435682 . A G . . PacBio=Poly;Sqnm=Poly 20 38505534 . A T . . PacBio=Poly;Sqnm=Poly 20 38803278 . A G . . PacBio=Poly;Sqnm=Poly 20 38963803 . G C . . PacBio=Poly;Sqnm=Poly 20 38971986 . A G . . PacBio=Poly;Sqnm=Poly 20 39269586 . G A . . PacBio=Poly;Sqnm=Poly 20 39289390 . C A . . PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples 20 39318956 . T A . . PacBio=Poly;Sqnm=Poly 20 39736197 . A G . . PacBio=Poly;Sqnm=Poly 20 40241339 . T C . . PacBio=Poly;Sqnm=Poly 20 41473555 . G A . . PacBio=Poly;Sqnm=Poly 20 41878576 . T G . . PacBio=Poly;Sqnm=Poly 20 42022716 . A G . . PacBio=Poly;Sqnm=Poly 20 42033671 . A C . . PacBio=NoCall;Sqnm=NoCall 20 42270334 . C T . . PacBio=NoCall;Sqnm=NoCall 20 42449590 . C T . . PacBio=Poly;Sqnm=NoCall 20 42521157 . T G . . PacBio=Poly;Sqnm=Poly 20 42624300 . C A . . PacBio=Poly;Sqnm=Poly 20 42984548 . G A . . PacBio=Poly;Sqnm=Poly 20 43200148 . G C . . PacBio=Poly;Sqnm=Poly 20 43425384 . T G . . PacBio=Poly;Sqnm=Poly 20 43521990 . C G . . PacBio=Poly;Sqnm=Poly 20 43565804 . G A . . PacBio=Poly;Sqnm=Poly 20 43591237 . T C . . PacBio=Poly;Sqnm=Poly 20 43805929 . C T . . PacBio=Poly;Sqnm=Poly 20 43866692 . A G . . PacBio=Poly;Sqnm=Poly 20 43902088 . C T . . PacBio=Poly;Sqnm=Poly 20 44478507 . C A . . PacBio=Poly;Sqnm=Poly 20 44768810 . C T . . PacBio=Poly;Sqnm=Poly 20 45151582 . G A . . PacBio=Poly;Sqnm=Poly 20 45414003 . G A . . PacBio=Poly;Sqnm=Poly 20 45776825 . G C . . PacBio=Poly;Sqnm=Poly 20 46454905 . G A . . PacBio=Poly;Sqnm=NoCall 20 46823642 . C T . . PacBio=Poly;Sqnm=Poly 20 47001376 . C T . . PacBio=Poly;Sqnm=Poly 20 47079360 . G C . . PacBio=Poly;Sqnm=NoCall 20 47248953 . G A . . PacBio=Poly;Sqnm=Poly 20 47480655 . C T . . PacBio=Poly;Sqnm=Poly 20 47529099 . T C . . PacBio=Poly;Sqnm=Poly 20 47703355 . A C . . PacBio=Poly;Sqnm=Poly 20 47919541 . A G . . PacBio=Poly;Sqnm=Poly 20 48126120 . A C . . PacBio=Poly;Sqnm=Poly 20 48157380 . G A . . PacBio=Poly;Sqnm=Poly 20 48233077 . C T . . PacBio=Poly;Sqnm=Poly 20 48488571 . G A . . PacBio=Poly;Sqnm=Poly 20 48534468 . G A . . PacBio=Poly;Sqnm=NoCall 20 48631385 . G C . . PacBio=Poly;Sqnm=Poly 20 48654970 . G A . . PacBio=Poly;Sqnm=NoCall 20 48708007 . C T . . PacBio=Poly;Sqnm=Poly 20 48979827 . C A . . PacBio=Poly;Sqnm=Poly 20 49100106 . G A . . PacBio=Poly;Sqnm=Poly 20 49509102 . G A . . PacBio=Poly;Sqnm=Poly 20 49631170 . G A . . PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples 20 50210361 . C T . . PacBio=Poly;Sqnm=Poly 20 50309600 . C A . . PacBio=Poly;Sqnm=Poly 20 50681296 . T C . . PacBio=Poly;Sqnm=Poly 20 50750138 . A G . . PacBio=Poly;Sqnm=Poly 20 51639257 . G A . . PacBio=Mono;Sqnm=Poly 20 51814664 . T C . . PacBio=Poly;Sqnm=Poly 20 51891088 . C T . . PacBio=Poly;Sqnm=Poly 20 52299250 . A G . . PacBio=Poly;Sqnm=Poly 20 52363435 . G A . . PacBio=Poly;Sqnm=NoCall 20 52583941 . C T . . PacBio=Poly;Sqnm=Poly 20 52787584 . C T . . PacBio=Poly;Sqnm=Poly 20 53256945 . G A . . PacBio=Poly;Sqnm=Poly 20 54155398 . A G . . PacBio=Poly;Sqnm=Poly 20 54172374 . G T . . PacBio=Poly;Sqnm=Poly 20 54209446 . A G . . PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;Sanger=Poly 20 54317862 . C T . . PacBio=Poly;Sqnm=Poly 20 54852735 . C T . . PacBio=Poly;Sqnm=NoCall 20 54889864 . G A . . PacBio=Poly;Sqnm=Poly 20 55208711 . G A . . PacBio=Poly;Sqnm=Poly 20 55220477 . G T . . PacBio=Poly;Sqnm=Poly 20 55224856 . G T . . PacBio=NoCall;Sqnm=NoCall 20 55441530 . C T . . PacBio=Poly;Sqnm=NoCall 20 55585710 . C T . . PacBio=Poly;Sqnm=Poly 20 55630163 . C T . . PacBio=Poly;Sqnm=Poly 20 56031994 . A G . . PacBio=Poly;Sqnm=Poly 20 56316071 . T G . . PacBio=Poly;Sqnm=Poly 20 56366198 . C T . . PacBio=Poly;Sqnm=Poly 20 56703987 . G A . . PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;Sanger=Poly 20 56794829 . G C . . PacBio=Poly;Sqnm=Poly 20 56797026 . G A . . PacBio=Poly;Sqnm=Poly 20 56922427 . A G . . PacBio=Poly;Sqnm=Poly 20 57025102 . A T . . PacBio=Poly;Sqnm=Poly 20 57104529 . G A . . PacBio=Poly;Sqnm=Poly 20 57360225 . C T . . PacBio=Poly;Sqnm=Poly 20 57630386 . T A . . PacBio=NoCall;Sqnm=NoCall 20 57754033 . G A . . PacBio=Poly;Sqnm=Poly 20 57956631 . C T . . PacBio=Poly;Sqnm=Poly 20 57997801 . C T . . PacBio=Poly;Sqnm=NoCall 20 58046279 . C G . . PacBio=NoCall;Sqnm=NoCall 20 58186723 . A G . . PacBio=Poly;Sqnm=Poly 20 58214460 . C T . . PacBio=Poly;Sqnm=Poly 20 58317759 . A G . . PacBio=Poly;Sqnm=Poly 20 58491642 . A C . . PacBio=Poly;Sqnm=Poly 20 58560045 . C T . . PacBio=Poly;Sqnm=Poly 20 58629232 . C T . . PacBio=Poly;Sqnm=Poly 20 58805192 . G T . . PacBio=Poly;Sqnm=Poly 20 58869523 . A G . . PacBio=Poly;Sqnm=Poly 20 59337535 . T C . . PacBio=Poly;Sqnm=Poly 20 59441596 . G A . . PacBio=Poly;Sqnm=Poly 20 59445223 . G A . . PacBio=NoCall;Sqnm=NoCall 20 59605846 . C T . . PacBio=Poly;Sqnm=Poly 20 59864395 . G C . . PacBio=Poly;Sqnm=Poly 20 60099821 . G T . . PacBio=Poly;Sqnm=Poly 20 60290551 . A G . . PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;Sanger=Poly 20 60362527 . G C . . PacBio=Poly;Sqnm=Poly 20 60516358 . C T . . PacBio=Poly;Sqnm=Poly 20 60559594 . C T . . PacBio=NoCall;Sqnm=Poly 20 60745115 . G A . . PacBio=Poly;Sqnm=Poly 20 60831300 . G A . . PacBio=Poly;Sqnm=Poly 20 60907675 . G A . . PacBio=Poly;Sqnm=Poly 20 61458191 . G A . . PacBio=Poly;Sqnm=Poly 20 61717607 . C T . . PacBio=Mono;Sqnm=Poly 20 61771154 . G A . . PacBio=Poly;Sqnm=Poly 20 61950497 . G A . . PacBio=Poly;Sqnm=Poly 20 62000091 . C T . . PacBio=Poly;Sqnm=Poly 20 62550780 . C T . . PacBio=NoCall;Sqnm=NoCall 20 62558259 . T C . . PacBio=Poly;Sqnm=Poly 20 62727205 . C T . . PacBio=Poly;Sqnm=Poly pysam-0.23.0/tests/tabix_data/vcf/21.vcf000066400000000000000000000676071475062545500177240ustar00rootroot00000000000000##fileformat=VCFv4.1 ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO 20 207414 . G A 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 792106 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 894031 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 1508892 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 1686745 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 1818886 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 2062981 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 2773229 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 2817761 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 2994966 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 3126723 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 3523369 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 3635082 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 3714080 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 3905791 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 3907250 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 4171994 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 4246375 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 4375206 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 4434727 . A T 0 . Consensus=Mono;PacBio=Mono;Sqnm=Mono;Sanger=Mono;pcr454_ss=NoCall;pcr454_ps=Poly 20 4495199 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 4835415 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 4915769 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall 20 4983198 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 5441171 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 5978029 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 6061317 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Mono;pcr454_ps=Poly 20 6328925 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 6675461 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 6976115 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 7013349 . G A 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 7039302 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 7638704 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 7688381 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 7726350 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 7733957 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 7850516 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 8095059 . G A 0 . Consensus=Mono;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall 20 8232012 . T A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 8415290 . A C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 8438535 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 8815233 . G A 0 . Consensus=Poly;PacBio=Mono;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 8953629 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Mono;pcr454_ps=Poly 20 9237267 . T A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 9744549 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 9780416 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 10252552 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 10314038 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 10757416 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 11087688 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 11094107 . G A 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 11098680 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 11353163 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 11510559 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 11787224 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 11821024 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 11932295 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 11965311 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 12023599 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 12505523 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 12570054 . A C 0 . Consensus=Poly;PacBio=NoCall;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 12667452 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 12678271 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Mono;pcr454_ss=Poly;pcr454_ps=Poly 20 12704885 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 12733996 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 12737269 . C T 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 12788981 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 12828594 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 12999157 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 13083804 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 13197077 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 13217896 . A G 0 . Consensus=Poly;PacBio=NoCall;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 13276778 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 13375116 . G A 0 . Consensus=Mono;PacBio=Mono;Sqnm=NoCall;NotCalledInValidationSamples;pcr454_ss=Mono;pcr454_ps=Mono 20 13648056 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 13672895 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 14160159 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 14266815 . T A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 14865143 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 14882868 . T G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 15244725 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 15277072 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 15390867 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 15785205 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 15833020 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 15847620 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 15953253 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 15964434 . G C 0 . Consensus=NoCall;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall 20 16183922 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 16190824 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 16557779 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 16730061 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 16794015 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 17048741 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 17299827 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 17299845 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 17390323 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 17624973 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 17666040 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 17735813 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 17794990 . A G 0 . Consensus=Mono;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;pcr454_ss=NoCall;pcr454_ps=NoCall 20 17809418 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 17860794 . C T 0 . Consensus=Poly;PacBio=Mono;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 17881936 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 17893097 . C G 0 . Consensus=Mono;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Mono;pcr454_ps=Mono 20 18188883 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 18199319 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 18233699 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 18536869 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 18637785 . T C 0 . Consensus=Mono;PacBio=NoCall;Sqnm=Mono;Sanger=Mono;NotCalledInValidationSamples;pcr454_ss=Mono;pcr454_ps=Mono 20 18763166 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 19102715 . A G 0 . Consensus=Mono;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Mono;pcr454_ps=Mono 20 19244609 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 19573719 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 19815613 . A G 0 . Consensus=Poly;PacBio=NoCall;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 20511479 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;Sanger=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 20639358 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 21278490 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 21297718 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 21418269 . A T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 21560553 . A T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 21618451 . G A 0 . Consensus=NoCall;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall 20 21705723 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 22076189 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 22118677 . T A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 22320721 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 22368918 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 23020003 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 23214163 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 23273877 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 23335790 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Mono 20 23790659 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 23830388 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 23837678 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 23901081 . A C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 23946361 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 23949242 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 24539119 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 24986457 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 25183729 . G A 0 . Consensus=Mono;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Mono;pcr454_ps=Mono 20 25277133 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 25292464 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 25528915 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 25851836 . A G 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 25970163 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 29920798 . C T 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 30007713 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 30051768 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 30183598 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 30604408 . G A 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 30759940 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 30881454 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=Poly 20 31356560 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 31450036 . A G 0 . Consensus=Poly;PacBio=NoCall;Sqnm=Mono;pcr454_ss=Poly;pcr454_ps=Poly 20 31589920 . A T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 31922121 . C T 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 32801430 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 32943975 . G T 0 . Consensus=Mono;PacBio=Mono;Sqnm=Mono;pcr454_ss=NoCall;pcr454_ps=NoCall 20 33155812 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 34090682 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 34254080 . C T 0 . Consensus=Mono;PacBio=Mono;Sqnm=NoCall;NotCalledInValidationSamples;pcr454_ss=Mono;pcr454_ps=Mono 20 34312126 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 34481504 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 34694577 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 35026572 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 35472344 . T G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 35882698 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 36044719 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 36047623 . C A 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 36204890 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 36469514 . G C 0 . Consensus=Poly;PacBio=NoCall;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 36840217 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 37460945 . C T 0 . Consensus=Poly;PacBio=Mono;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 37665246 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 37732397 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 37874645 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 37958191 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 37996273 . C T 0 . Consensus=Mono;PacBio=Mono;Sqnm=NoCall;NotCalledInValidationSamples;pcr454_ss=Mono;pcr454_ps=Mono 20 38016547 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 38435682 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 38505534 . A T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 38803278 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 38963803 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 38971986 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 39269586 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 39289390 . C A 0 . Consensus=Mono;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;pcr454_ss=NoCall;pcr454_ps=NoCall 20 39318956 . T A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=Poly 20 39736197 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 40241339 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 41473555 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 41878576 . T G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 42022716 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 42033671 . A C 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 42270334 . C T 0 . Consensus=NoCall;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall 20 42449590 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 42521157 . T G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 42624300 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 42984548 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 43200148 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 43425384 . T G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 43521990 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 43565804 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 43591237 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 43805929 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 43866692 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 43902088 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 44478507 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 44768810 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 45151582 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 45414003 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Mono;pcr454_ps=Mono 20 45776825 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 46454905 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 46823642 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 47001376 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 47079360 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 47248953 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 47480655 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 47529099 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 47703355 . A C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 47919541 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 48126120 . A C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 48157380 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 48233077 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 48488571 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 48534468 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 48631385 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 48654970 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 48708007 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 48979827 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 49100106 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 49509102 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 49631170 . G A 0 . Consensus=Mono;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;pcr454_ss=Mono;pcr454_ps=Mono 20 50210361 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 50309600 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 50681296 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 50750138 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 51639257 . G A 0 . Consensus=Poly;PacBio=Mono;Sqnm=Poly;pcr454_ss=Mono;pcr454_ps=Mono 20 51814664 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 51891088 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 52299250 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 52363435 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 52583941 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 52787584 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 53256945 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 54155398 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 54172374 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=Poly 20 54209446 . A G 0 . Consensus=Poly;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;Sanger=Poly;pcr454_ss=Mono;pcr454_ps=Mono 20 54317862 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 54852735 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 54889864 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 55208711 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 55220477 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 55224856 . G T 0 . Consensus=NoCall;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall 20 55441530 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 55585710 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 55630163 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 56031994 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 56316071 . T G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 56366198 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 56703987 . G A 0 . Consensus=Poly;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;Sanger=Poly;pcr454_ss=Mono;pcr454_ps=Mono 20 56794829 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 56797026 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 56922427 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 57025102 . A T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 57104529 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 57360225 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 57630386 . T A 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 57754033 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 57956631 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 57997801 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 58046279 . C G 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 58186723 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 58214460 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 58317759 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 58491642 . A C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 58560045 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 58629232 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 58805192 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 58869523 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 59337535 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 59441596 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 59445223 . G A 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 59605846 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 59864395 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 60099821 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 60290551 . A G 0 . Consensus=Poly;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;Sanger=Poly;pcr454_ss=Mono;pcr454_ps=Mono 20 60362527 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 60516358 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 60559594 . C T 0 . Consensus=Poly;PacBio=NoCall;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 60745115 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 60831300 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 60907675 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 61458191 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 61717607 . C T 0 . Consensus=Poly;PacBio=Mono;Sqnm=Poly;pcr454_ss=Mono;pcr454_ps=Mono 20 61771154 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 61950497 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 62000091 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 62550780 . C T 0 . Consensus=NoCall;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall 20 62558259 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 62727205 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly pysam-0.23.0/tests/tabix_data/vcf/22.vcf000066400000000000000000025637421475062545500177300ustar00rootroot00000000000000##fileformat=VCFv4.0 ##FORMAT= ##FilterLiftedVariants="analysis_type=FilterLiftedVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/local/sequence/reference/BWA_ref/hg19/hg19.fasta rodBind=[/local/scratch/xyliu/0.915136538286792.sorted.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub" ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA15029 NA15036 NA15038 NA15056b NA15072 NA15144C NA15213_006 NA15215A NA15216_A2 NA15221b NA15223_6v2 NA15224_4 NA15226A NA15227b NA15236_6 NA15242_005 NA15245v2 NA15268 NA15324_A1 NA15385b NA15386A NA15510_A1 NA15590_4 NA15594_005 NA18500b NA18501 NA18502 NA18503 NA18504 NA18505 NA18506 NA18507 NA18508 NA18515 NA18516 NA18517 NA18521 NA18522 NA18523 NA18524_B1 NA18526_B2 NA18529_B1 NA18532_B1 NA18537_B1 NA18540_B1 NA18542_B1 NA18545_5 NA18547_B1 NA18550_B1 NA18555_A2 NA18561_A3 NA18562_B1 NA18563 NA18564_4 NA18566_3 NA18570_3 NA18571_3 NA18572_3 NA18573_B3 NA18576_4 NA18577_B1 NA18579_B1 NA18582_B1 NA18592_2 NA18593_B1 NA18594_B1 NA18603_B1 NA18605_B1 NA18608_B1 NA18609_B1 NA18611_B1 NA18612_B1 NA18620_3 NA18621_B1 NA18622_B1 NA18623_B1 NA18624 NA18632_3 NA18635_A1 NA18637_2 NA18852 NA18853 NA18854 NA18855 NA18856 NA18857 NA18858 NA18859 NA18860 NA18861 NA18862 NA18863 NA18870 NA18871 NA18872 NA18912 NA18913 NA18914 NA18940_3 NA19092 NA19093 NA19094 NA19098 NA19099 NA19100 NA19101 NA19102 NA19103 NA19116 NA19119b NA19120 NA19127 NA19128 NA19129 NA19130b NA19131 NA19132b NA19137 NA19138 NA19139 NA19140b NA19141 NA19142 NA19143 NA19144 NA19145 NA19152 NA19153 NA19154 NA19159 NA19160 NA19161 NA19171 NA19172 NA19173 NA19192 NA19193 NA19194 NA19200 NA19201 NA19202 NA19203 NA19204 NA19205 NA19206 NA19207 NA19208v2 NA19209 NA19210 NA19211 NA19221 NA19222 NA19223 NA19238 NA19239 NA19240 NA_pos103a NS12911_1 chr1 5911136 . T TGCCATTCCAAAGAGGCACTCA . PASS VC=INDEL;AC=28;AF=0.09;AN=316 GT 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 17054990 . G GA . PASS VC=INDEL;AC=25;AF=0.12;AN=200 GT ./. ./. 0/1 ./. 0/0 ./. ./. ./. ./. 0/0 0/1 ./. ./. 0/0 ./. ./. 0/1 ./. ./. ./. ./. 0/0 0/1 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 ./. ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 ./. ./. ./. ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/1 ./. 0/1 ./. 0/0 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/1 ./. ./. ./. 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 ./. ./. ./. 0/1 ./. ./. 0/0 ./. ./. ./. ./. ./. ./. ./. 0/1 0/1 ./. chr1 17390953 . CT C . PASS VC=INDEL;AC=118;AF=0.37;AN=316 GT 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 chr1 17754916 . CCT C . PASS VC=INDEL;AC=66;AF=0.21;AN=316;refseq.name=NM_018715;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 chr1 18293100 . C CCTC . PASS VC=INDEL;AC=263;AF=0.84;AN=314 GT 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 18823397 . T TTAAT . PASS VC=INDEL;AC=87;AF=0.28;AN=316 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 19215209 . G GAG . PASS VC=INDEL;AC=2;AF=0.01;AN=316;refseq.name=NM_003748;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 19943821 . CACAG C . PASS VC=INDEL;AC=12;AF=0.04;AN=308;refseq.name=NM_001032363;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 20092486 . GAAG G . PASS VC=INDEL;AC=7;AF=0.02;AN=314;refseq.name=NM_181719;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 20977854 . A ATTC . PASS VC=INDEL;AC=152;AF=0.52;AN=292;refseq.name=NM_032409;refseq.positionType=exon GT 0/1 1/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 ./. 0/1 0/1 1/1 0/1 0/1 ./. 0/0 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 ./. 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 ./. ./. 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 ./. 0/0 ./. 0/0 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 ./. 0/1 1/1 1/1 0/0 0/1 0/1 1/1 ./. ./. 0/1 0/0 0/0 0/0 ./. 1/1 0/1 1/1 0/0 ./. 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 chr1 21275058 . CTTTG C . PASS VC=INDEL;AC=30;AF=0.1;AN=296;refseq.name=NM_003760;refseq.positionType=intron GT ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 chr1 22642904 . A AAC . PASS VC=INDEL;AC=255;AF=0.85;AN=300 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 ./. 0/1 0/1 0/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 chr1 22844297 . ATCT A . PASS VC=INDEL;AC=162;AF=0.51;AN=316;refseq.name=NM_001083621;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 chr1 22844299 . CTTC C . PASS VC=INDEL;AC=160;AF=0.51;AN=314;refseq.name=NM_001083621;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 ./. 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 chr1 23162393 . AA A . PASS VC=INDEL;AC=44;AF=0.14;AN=316;refseq.name=NM_004442;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 chr1 23882634 . T TAGGTG . PASS VC=INDEL;AC=24;AF=0.08;AN=284 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/1 0/1 ./. 0/1 0/0 0/0 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 chr1 25799681 . CTCTG C . PASS VC=INDEL;AC=49;AF=0.21;AN=230;refseq.name=NM_018202;refseq.positionType=intron GT 0/1 ./. 1/1 ./. 0/1 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 1/1 0/1 ./. ./. 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 1/1 ./. 1/1 0/0 0/1 1/1 ./. 0/1 ./. 0/1 ./. 0/1 0/1 0/0 1/1 0/1 ./. ./. 0/1 ./. 1/1 0/1 ./. 0/1 1/1 ./. ./. 0/1 ./. 0/1 ./. ./. 1/1 ./. 0/1 ./. 1/1 ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. ./. 0/0 ./. ./. ./. ./. ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 26081170 . CA C . PASS VC=INDEL;AC=17;AF=0.06;AN=308;refseq.name=NM_020379;refseq.positionType=intron GT 0/0 ./. 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 26240086 . GAT G . PASS VC=INDEL;AC=31;AF=0.1;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 chr1 26725650 . A ATGAAG . PASS VC=INDEL;AC=300;AF=0.95;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 chr1 26725655 . G GTGAAG . PASS VC=INDEL;AC=300;AF=0.95;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 chr1 27425097 . CTGG C . PASS VC=INDEL;AC=40;AF=0.16;AN=248;refseq.name=NM_003047;refseq.positionType=terminator GT 1/1 0/1 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/0 0/0 ./. ./. ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. ./. ./. 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 ./. 0/1 ./. 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/1 0/1 ./. ./. 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 chr1 27737240 . A AT . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_006990;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 27744410 . GATCCATG G . PASS VC=INDEL;AC=166;AF=0.56;AN=296;refseq.name=NM_006990;refseq.positionType=intron GT 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 1/1 ./. 0/1 0/0 ./. 0/0 ./. 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 ./. 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 ./. 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 ./. 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 ./. 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 ./. ./. chr1 28156589 . G GGATG . PASS VC=INDEL;AC=127;AF=0.4;AN=314;refseq.name=NM_002713;refseq.positionType=promoter GT 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 ./. 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 chr1 28721777 . TA T . PASS VC=INDEL;AC=287;AF=0.91;AN=316;refseq.name=NM_001048183;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 chr1 28721778 . AA A . PASS VC=INDEL;AC=287;AF=0.91;AN=316;refseq.name=NM_001048183;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 chr1 28907201 . GT G . PASS VC=INDEL;AC=3;AF=0.01;AN=224 GT 0/0 ./. 0/0 0/0 ./. ./. 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 ./. ./. 0/0 ./. ./. 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/1 ./. ./. 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/1 ./. ./. ./. ./. chr1 29223339 . G GTGAG . PASS VC=INDEL;AC=203;AF=0.7;AN=292;refseq.name=NM_004437;refseq.positionType=intron GT 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 ./. 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 ./. 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 ./. 1/1 1/1 0/1 1/1 0/1 ./. 1/1 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 ./. ./. 0/1 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 ./. 0/0 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 1/1 ./. 1/1 0/1 chr1 29223342 . A AGCAA . PASS VC=INDEL;AC=71;AF=0.29;AN=242;refseq.name=NM_004437;refseq.positionType=intron GT 0/1 0/1 1/1 ./. 0/1 0/1 0/1 0/0 ./. 0/0 0/1 ./. 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 ./. 1/1 0/1 ./. ./. 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 ./. 0/1 ./. 0/1 ./. 0/1 0/1 ./. 0/1 0/1 ./. ./. 0/1 ./. ./. ./. ./. 0/1 ./. 0/0 ./. ./. ./. 0/1 0/1 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/0 0/0 ./. 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/1 ./. ./. 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 ./. 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 ./. 0/1 ./. ./. 0/0 chr1 29865521 . G GCTCCGT . PASS VC=INDEL;AC=115;AF=0.36;AN=316 GT 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 chr1 31128790 . C CT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 31135886 . A AG . PASS VC=INDEL;AC=246;AF=0.92;AN=268 GT ./. 1/1 0/1 1/1 0/1 ./. 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. ./. ./. 1/1 ./. 1/1 0/1 0/1 0/1 ./. 1/1 1/1 ./. ./. 0/1 1/1 1/1 ./. 1/1 1/1 ./. 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 ./. 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. chr1 31503645 . AAAAGA A . PASS VC=INDEL;AC=5;AF=0.02;AN=314;refseq.name=NM_001020658;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 31504005 . C CAT . PASS VC=INDEL;AC=84;AF=0.27;AN=316;refseq.name=NM_001020658;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 chr1 31731414 . CCTCT C . PASS VC=INDEL;AC=40;AF=0.13;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 31775152 . A ACTA . PASS VC=INDEL;AC=47;AF=0.15;AN=308;refseq.name=NM_016505;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 31882582 . G GGCCTCA . PASS VC=INDEL;AC=163;AF=0.59;AN=274 GT 1/1 1/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 ./. 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 ./. 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 ./. 0/1 1/1 0/1 0/1 1/1 0/1 ./. 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 ./. 1/1 0/1 1/1 1/1 0/1 ./. ./. ./. 1/1 ./. 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/0 ./. 0/0 1/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 ./. 0/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 ./. 1/1 0/1 ./. 0/1 0/1 0/1 ./. 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/1 0/1 0/1 ./. ./. 0/1 0/1 ./. 0/0 0/1 ./. 0/1 ./. 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 chr1 32010706 . GG G . PASS VC=INDEL;AC=312;AF=1;AN=312 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 32078865 . G GT . PASS VC=INDEL;AC=78;AF=0.25;AN=316 GT 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 chr1 33422344 . G GAA . PASS VC=INDEL;AC=123;AF=0.39;AN=316;refseq.name=NM_153341;refseq.positionType=intron GT 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 chr1 33634618 . TC T . PASS VC=INDEL;AC=238;AF=0.75;AN=316;refseq.name=NM_018207;refseq.positionType=intron GT 0/0 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 chr1 33965999 . CCCAGTTC C . PASS VC=INDEL;AC=203;AF=0.65;AN=314 GT 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 ./. 0/1 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 chr1 34176371 . GAAACATAAG G . PASS VC=INDEL;AC=252;AF=0.95;AN=266;refseq.name=NM_052896;refseq.positionType=intron GT 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 0/1 1/1 ./. ./. ./. 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 ./. 0/1 1/1 ./. 0/1 0/1 1/1 ./. ./. 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 chr1 34931817 . AT A . PASS VC=INDEL;AC=38;AF=0.12;AN=316 GT 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 chr1 35879227 . CAT C . PASS VC=INDEL;AC=31;AF=0.1;AN=316;refseq.name=NM_005095;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 chr1 36429590 . A AG . PASS VC=INDEL;AC=181;AF=0.57;AN=316;refseq.name=NM_024852;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 chr1 36558240 . C CAC . PASS VC=INDEL;AC=11;AF=0.03;AN=316;refseq.name=NM_017825;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 37034721 . ATACT A . PASS VC=INDEL;AC=44;AF=0.16;AN=282 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 ./. ./. ./. 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 chr1 37142202 . AATA A . PASS VC=INDEL;AC=24;AF=0.08;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 37169424 . TA T . PASS VC=INDEL;AC=176;AF=0.56;AN=316 GT 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/0 chr1 37169427 . AA A . PASS VC=INDEL;AC=173;AF=0.56;AN=308 GT 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 ./. 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/0 chr1 37638341 . T TAT . PASS VC=INDEL;AC=11;AF=0.05;AN=222 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/1 ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 ./. ./. ./. 0/0 0/1 ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/0 0/0 0/1 0/0 ./. 0/1 ./. ./. 0/0 ./. ./. ./. ./. 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. ./. ./. 0/0 chr1 38077349 . CTTATCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTA C . PASS VC=INDEL;AC=209;AF=0.77;AN=272;refseq.name=NM_001038633;refseq.positionType=intron GT 0/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 1/1 ./. 1/1 ./. 0/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. ./. 1/1 1/1 ./. 0/1 ./. 1/1 1/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 0/1 1/1 ./. ./. ./. 1/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 ./. 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 ./. 1/1 0/0 0/1 0/0 1/1 1/1 1/1 ./. ./. 0/1 1/1 1/1 1/1 0/0 0/0 0/0 ./. 1/1 0/1 1/1 0/1 chr1 38392549 . AT A . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_005540;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 38664242 . TA T . PASS VC=INDEL;AC=93;AF=0.29;AN=316 GT 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 chr1 38739177 . GTG G . PASS VC=INDEL;AC=32;AF=0.1;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 39288395 . CTTC C . PASS VC=INDEL;AC=36;AF=0.12;AN=306 GT 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 chr1 39615407 . C CGATAT . PASS VC=INDEL;AC=192;AF=0.63;AN=306;refseq.name=NM_012090;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 ./. 0/1 1/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 ./. 0/1 1/1 0/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 0/1 0/1 ./. 0/1 0/0 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 ./. 0/0 1/1 0/1 1/1 1/1 chr1 39615412 . T TGATAT . PASS VC=INDEL;AC=200;AF=0.63;AN=316;refseq.name=NM_012090;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 chr1 39736467 . T TATAT . PASS VC=INDEL;AC=27;AF=0.09;AN=316;refseq.name=NM_012090;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 39936801 . GTG G . PASS VC=INDEL;AC=23;AF=0.07;AN=314;refseq.name=NM_012090;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 40525320 . AACACAAGAAC A . PASS VC=INDEL;AC=21;AF=0.11;AN=196;refseq.name=NM_006367;refseq.positionType=intron GT ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/0 0/1 1/1 1/1 0/1 ./. 1/1 ./. 0/0 1/1 0/0 1/1 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. ./. 0/1 ./. 0/0 ./. ./. ./. 0/0 0/0 ./. ./. 0/0 ./. ./. ./. ./. ./. ./. ./. 0/0 0/0 ./. ./. ./. 0/1 0/1 0/0 ./. ./. ./. ./. ./. 0/0 ./. ./. ./. ./. ./. ./. 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 ./. ./. ./. 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 ./. chr1 40728529 . TA T . PASS VC=INDEL;AC=216;AF=0.68;AN=316;refseq.name=NM_005857;refseq.positionType=intron GT 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 chr1 41281719 . CT C . PASS VC=INDEL;AC=142;AF=0.45;AN=316;refseq.name=NM_004700;refseq.positionType=intron GT 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 chr1 41808814 . CT C . PASS VC=INDEL;AC=32;AF=0.1;AN=308 GT 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 41991662 . CCA C . PASS VC=INDEL;AC=17;AF=0.06;AN=304;refseq.name=NM_024503;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 ./. chr1 42083551 . C CT . PASS VC=INDEL;AC=139;AF=0.44;AN=316;refseq.name=NM_024503;refseq.positionType=intron GT 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/0 1/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 chr1 42531504 . G GATAG . PASS VC=INDEL;AC=199;AF=0.66;AN=302 GT 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 ./. 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 ./. 1/1 1/1 1/1 ./. 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 ./. 0/1 0/1 0/1 0/0 ./. 0/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 chr1 42835720 . C CTTG . PASS VC=INDEL;AC=297;AF=0.94;AN=316 GT 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 42835723 . G GTTG . PASS VC=INDEL;AC=297;AF=0.94;AN=316 GT 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 42880843 . A ACA . PASS VC=INDEL;AC=179;AF=0.57;AN=316;refseq.name=NM_173642;refseq.positionType=exon GT 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/0 0/0 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/1 chr1 44114854 . C CGC . PASS VC=INDEL;AC=107;AF=0.45;AN=238;refseq.name=NM_014663;refseq.positionType=promoter GT 0/0 1/1 1/1 ./. 0/0 ./. ./. 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 ./. 0/1 1/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 ./. ./. 0/0 0/0 ./. 0/1 0/0 0/1 1/1 ./. 1/1 0/1 0/1 0/1 ./. 0/1 0/0 0/1 ./. 0/1 0/1 ./. 0/0 0/0 0/1 0/0 0/0 1/1 ./. 0/0 0/0 0/1 0/1 ./. ./. ./. 0/0 0/0 0/1 0/1 ./. 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 ./. 0/1 ./. 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/0 0/0 0/0 1/1 ./. 0/1 0/1 0/1 ./. ./. ./. 0/1 ./. 0/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 ./. ./. ./. 1/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 ./. ./. 0/1 1/1 0/1 ./. 0/0 0/1 1/1 0/1 0/1 ./. ./. 1/1 0/1 1/1 0/1 0/1 ./. ./. ./. 0/1 ./. 0/0 0/1 chr1 44231607 . CA C . PASS VC=INDEL;AC=216;AF=0.69;AN=314;refseq.name=NM_006279;refseq.positionType=intron GT 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 1/1 ./. 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 chr1 44231608 . AA A . PASS VC=INDEL;AC=215;AF=0.68;AN=314;refseq.name=NM_006279;refseq.positionType=intron GT 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 ./. 0/1 1/1 1/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 chr1 44327106 . GCTGTCAGGACTTGTATAGA G . PASS VC=INDEL;AC=193;AF=0.66;AN=294;refseq.name=NM_006279;refseq.positionType=intron GT 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 ./. 0/0 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 0/1 ./. 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 ./. 1/1 ./. 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 0/1 ./. 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 ./. 0/0 1/1 0/1 0/1 0/1 0/1 ./. 0/1 ./. 1/1 1/1 chr1 44730823 . G GGAGA . PASS VC=INDEL;AC=295;AF=0.96;AN=306;refseq.name=NM_024066;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 ./. 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr1 44881687 . GCAT G . PASS VC=INDEL;AC=29;AF=0.09;AN=314;refseq.name=NM_018150;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 45223909 . GATTAGCTG G . PASS VC=INDEL;AC=167;AF=0.55;AN=306;refseq.name=NM_006845;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 ./. 0/1 ./. 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 ./. ./. 0/1 1/1 1/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 chr1 46900444 . T TGTGGGAATGC . PASS VC=INDEL;AC=2;AF=0.01;AN=296 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 chr1 46900720 . C CTT . PASS VC=INDEL;AC=244;AF=0.79;AN=308 GT 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 ./. 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr1 46900721 . T TTT . PASS VC=INDEL;AC=241;AF=0.79;AN=304 GT 1/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 ./. 1/1 ./. 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr1 47052336 . TGAAA T . PASS VC=INDEL;AC=76;AF=0.24;AN=316;refseq.name=NM_003684;refseq.positionType=intron GT 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 chr1 47167062 . TT T . PASS VC=INDEL;AC=174;AF=0.64;AN=272;refseq.name=NM_014774;refseq.positionType=intron GT ./. 0/1 0/1 0/1 ./. 0/0 0/0 1/1 1/1 0/1 1/1 0/1 ./. ./. 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 1/1 0/1 0/1 0/1 ./. 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 ./. 0/1 1/1 0/1 1/1 1/1 0/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 0/0 0/1 ./. 1/1 1/1 1/1 ./. ./. 0/0 ./. 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 ./. 0/1 1/1 ./. 0/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 ./. 1/1 ./. 1/1 0/1 0/1 1/1 0/1 0/1 0/0 ./. 0/1 ./. 0/1 1/1 0/1 1/1 ./. 1/1 ./. 0/0 chr1 47324578 . CTACTACAAA C . PASS VC=INDEL;AC=150;AF=0.65;AN=232 GT 1/1 ./. ./. ./. ./. 0/1 0/0 0/1 0/0 ./. ./. 1/1 0/1 1/1 0/0 0/1 ./. 0/1 0/1 0/0 0/1 ./. 0/1 0/0 ./. 0/0 1/1 1/1 ./. 0/1 1/1 1/1 ./. 0/1 0/0 0/1 1/1 1/1 ./. 0/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 ./. ./. 0/1 0/1 0/1 ./. 1/1 0/1 0/0 0/1 ./. 0/1 1/1 0/1 ./. 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 ./. 1/1 ./. 0/0 0/1 0/0 ./. 1/1 1/1 1/1 ./. ./. 1/1 ./. ./. 0/0 ./. 0/1 0/1 ./. ./. 1/1 1/1 1/1 0/1 0/1 0/1 1/1 ./. ./. ./. 0/1 ./. 0/1 0/1 0/1 ./. 0/1 chr1 47325281 . CA C . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 47891688 . AT A . PASS VC=INDEL;AC=84;AF=0.29;AN=294 GT 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 1/1 0/0 1/1 ./. 0/0 ./. 0/0 ./. 0/0 1/1 1/1 0/1 0/1 0/1 ./. 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 ./. 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 47931769 . TTCTC T . PASS VC=INDEL;AC=2;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 48000154 . G GTTT . PASS VC=INDEL;AC=11;AF=0.05;AN=232 GT ./. 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/1 ./. 0/0 0/0 ./. ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 ./. ./. ./. 0/0 ./. ./. 0/0 0/0 0/1 0/0 0/1 ./. 0/1 0/1 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 ./. ./. 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. ./. ./. 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 chr1 48146050 . CCTGA C . PASS VC=INDEL;AC=28;AF=0.09;AN=316 GT 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 48520865 . CAGGGTGAGTAGGCCTGGGCAG C . PASS VC=INDEL;AC=4;AF=0.01;AN=316 GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 48520886 . GAG G . PASS VC=INDEL;AC=31;AF=0.14;AN=216 GT ./. 0/0 0/1 0/0 0/0 ./. ./. 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/1 0/0 ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. ./. ./. ./. ./. 0/0 ./. 0/1 0/1 ./. 0/1 0/0 0/1 0/1 0/1 ./. 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 ./. ./. 0/0 ./. ./. ./. 0/0 1/1 0/0 0/1 ./. ./. 0/0 ./. 0/0 0/0 0/1 ./. 0/1 0/1 0/0 ./. ./. ./. chr1 48544917 . G GTGTT . PASS VC=INDEL;AC=43;AF=0.14;AN=314 GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 49109456 . AGAGC A . PASS VC=INDEL;AC=31;AF=0.14;AN=226;refseq.name=NM_032785;refseq.positionType=intron GT 0/0 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 ./. ./. 0/0 0/0 0/1 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/1 0/0 ./. 0/0 0/0 ./. 0/0 0/1 ./. ./. 0/0 0/1 ./. ./. ./. ./. 0/1 0/0 ./. 0/0 ./. 0/0 0/0 0/0 ./. ./. ./. 0/0 ./. 0/0 ./. ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. ./. 0/0 0/0 0/1 ./. ./. ./. 0/1 0/1 0/1 chr1 49124365 . C CGAG . PASS VC=INDEL;AC=93;AF=0.29;AN=316;refseq.name=NM_032785;refseq.positionType=intron GT 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 chr1 49124368 . G GGAG . PASS VC=INDEL;AC=93;AF=0.29;AN=316;refseq.name=NM_032785;refseq.positionType=intron GT 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 chr1 49126514 . C CTG . PASS VC=INDEL;AC=89;AF=0.3;AN=296;refseq.name=NM_032785;refseq.positionType=intron GT 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/1 ./. 0/0 0/0 0/0 1/1 0/1 ./. 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 ./. 0/0 ./. 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/1 ./. 0/0 ./. 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 chr1 50107735 . G GA . PASS VC=INDEL;AC=68;AF=0.22;AN=312 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 ./. 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 chr1 50539498 . T TCT . PASS VC=INDEL;AC=312;AF=0.99;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 50652516 . A AGAA . PASS VC=INDEL;AC=247;AF=0.78;AN=316;refseq.name=NM_021952;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 chr1 51315116 . ACTG A . PASS VC=INDEL;AC=13;AF=0.04;AN=316;refseq.name=NM_007051;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 chr1 52336500 . TAATACA T . PASS VC=INDEL;AC=17;AF=0.07;AN=230;refseq.name=NM_002525;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 ./. 0/1 ./. ./. ./. 0/0 ./. ./. 0/0 ./. ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 ./. ./. ./. 0/1 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/1 0/1 0/1 ./. 0/0 0/0 0/0 ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 ./. 0/0 ./. ./. ./. 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 ./. ./. 0/0 ./. 0/0 0/0 ./. ./. ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. chr1 52798171 . A AT . PASS VC=INDEL;AC=307;AF=0.97;AN=316;refseq.name=NM_004799;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 53554533 . A AT . PASS VC=INDEL;AC=33;AF=0.11;AN=294;refseq.name=NM_006671;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/0 ./. 0/1 ./. 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/0 ./. ./. 0/1 chr1 53986946 . TG T . PASS VC=INDEL;AC=188;AF=0.59;AN=316;refseq.name=NM_147193;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 chr1 54168427 . C CTCTG . PASS VC=INDEL;AC=109;AF=0.35;AN=308;refseq.name=NM_147193;refseq.positionType=intron GT 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 1/1 ./. 1/1 0/0 0/0 ./. 1/1 0/1 0/1 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 chr1 54558546 . T TAGAC . PASS VC=INDEL;AC=66;AF=0.21;AN=316;refseq.name=NM_153035;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 chr1 54558548 . G GACAG . PASS VC=INDEL;AC=66;AF=0.21;AN=316;refseq.name=NM_153035;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 chr1 54619996 . AC A . PASS VC=INDEL;AC=193;AF=0.64;AN=302;refseq.name=NM_201546;refseq.positionType=promoter GT 1/1 0/0 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 ./. 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 ./. 1/1 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 ./. 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 ./. ./. 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 ./. 0/1 0/0 0/1 ./. 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 chr1 54757161 . C CCA . PASS VC=INDEL;AC=186;AF=0.59;AN=314;refseq.name=NM_001009955;refseq.positionType=intron GT 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 ./. 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 chr1 54757166 . C CAC . PASS VC=INDEL;AC=185;AF=0.59;AN=312;refseq.name=NM_001009955;refseq.positionType=intron GT 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 ./. 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 chr1 55566411 . TTAGTC T . PASS VC=INDEL;AC=207;AF=0.66;AN=316;refseq.name=NM_015306;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 chr1 55743440 . C CCT . PASS VC=INDEL;AC=261;AF=0.84;AN=312 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 ./. 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 chr1 55888273 . T TC . PASS VC=INDEL;AC=265;AF=0.88;AN=302 GT 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 0/1 ./. 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 1/1 ./. 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 chr1 55888274 . C CC . PASS VC=INDEL;AC=271;AF=0.89;AN=306 GT 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 ./. 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 chr1 55892282 . T TAGAAAA . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 55998244 . CGCACGCTC C . PASS VC=INDEL;AC=265;AF=0.84;AN=314 GT 1/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 ./. 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 chr1 56495367 . CTGAG C . PASS VC=INDEL;AC=76;AF=0.24;AN=316 GT 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 57353886 . C CTA . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_000562;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 57854490 . AAT A . PASS VC=INDEL;AC=24;AF=0.08;AN=312;refseq.name=NM_021080;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 58391942 . G GAAA . PASS VC=INDEL;AC=10;AF=0.03;AN=314;refseq.name=NM_021080;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 chr1 58413348 . A AG . PASS VC=INDEL;AC=50;AF=0.22;AN=226;refseq.name=NM_021080;refseq.positionType=intron GT 0/0 ./. ./. 0/1 0/0 ./. 0/1 0/1 0/1 1/1 0/0 ./. ./. 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/1 0/0 ./. ./. 0/1 ./. ./. 0/1 0/0 0/0 0/0 ./. ./. ./. 1/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 ./. 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. ./. ./. ./. 0/1 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. ./. 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/1 ./. ./. ./. ./. ./. ./. 0/1 0/1 ./. 0/1 0/0 1/1 0/0 0/1 0/0 0/0 ./. ./. 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/1 1/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 ./. 0/0 0/0 ./. 0/1 ./. 0/1 ./. 1/1 ./. 1/1 chr1 58550673 . CT C . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_021080;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 58629900 . CAGA C . PASS VC=INDEL;AC=15;AF=0.05;AN=316;refseq.name=NM_021080;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 58999156 . AT A . PASS VC=INDEL;AC=151;AF=0.53;AN=286;refseq.name=NM_145243;refseq.positionType=intron GT ./. 1/1 1/1 0/1 0/1 0/0 1/1 ./. 0/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 0/0 1/1 ./. 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/1 0/1 ./. 1/1 0/0 0/0 0/0 0/1 1/1 ./. 1/1 0/1 0/0 0/0 ./. 0/0 0/0 0/1 1/1 0/1 ./. 0/0 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/1 ./. 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 chr1 59009401 . T TT . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_145243;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 59104181 . GA G . PASS VC=INDEL;AC=271;AF=0.89;AN=304 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 chr1 59319761 . AG A . PASS VC=INDEL;AC=195;AF=0.67;AN=290 GT 0/0 0/1 0/0 0/0 ./. 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 ./. 0/0 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 ./. 1/1 0/1 1/1 1/1 1/1 0/1 ./. 0/1 1/1 0/1 ./. 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 ./. 1/1 1/1 ./. 1/1 0/0 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 ./. ./. 1/1 1/1 1/1 1/1 0/1 0/1 0/0 ./. 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 1/1 1/1 1/1 0/1 chr1 59319762 . GG G . PASS VC=INDEL;AC=200;AF=0.68;AN=296 GT 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 ./. 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 ./. 1/1 0/1 0/1 0/1 1/1 ./. 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 0/1 ./. 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 ./. 1/1 ./. 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 1/1 1/1 1/1 0/1 chr1 59630873 . CT C . PASS VC=INDEL;AC=155;AF=0.49;AN=316 GT 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 chr1 59635600 . TAT T . PASS VC=INDEL;AC=287;AF=0.91;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 chr1 60128716 . G GC . PASS VC=INDEL;AC=309;AF=0.98;AN=316;refseq.name=NM_018291;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 60128717 . C CC . PASS VC=INDEL;AC=309;AF=0.98;AN=316;refseq.name=NM_018291;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 60228311 . T TCT . PASS VC=INDEL;AC=250;AF=0.8;AN=314;refseq.name=NM_018291;refseq.positionType=exon GT 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 chr1 60460874 . A ACTA . PASS VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_152377;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 61786308 . ATCTTA A . PASS VC=INDEL;AC=126;AF=0.4;AN=316;refseq.name=NM_005595;refseq.positionType=intron GT 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 chr1 62087979 . T TGACCTACTGTGCT . PASS VC=INDEL;AC=194;AF=0.63;AN=310 GT 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 ./. 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 ./. 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 ./. 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 chr1 62128942 . CTTGCACA C . PASS VC=INDEL;AC=123;AF=0.39;AN=316 GT 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/0 chr1 62940266 . T TG . PASS VC=INDEL;AC=133;AF=0.43;AN=312;refseq.name=NM_033407;refseq.positionType=intron GT 0/0 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 chr1 63331690 . TA T . PASS VC=INDEL;AC=234;AF=0.74;AN=316 GT 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 chr1 63331691 . AA A . PASS VC=INDEL;AC=232;AF=0.74;AN=314 GT 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 ./. 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 chr1 63423181 . T TCAT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 63907866 . A AATGTTT . PASS VC=INDEL;AC=229;AF=0.76;AN=300;refseq.name=NM_014288;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 ./. 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 ./. 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 0/1 0/1 ./. 1/1 ./. 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 ./. 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/1 chr1 63907868 . T TGTTTAT . PASS VC=INDEL;AC=229;AF=0.77;AN=298;refseq.name=NM_014288;refseq.positionType=intron GT ./. 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 ./. ./. 0/1 0/0 1/1 0/1 0/0 0/1 0/0 ./. 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 ./. 1/1 1/1 1/1 0/1 ./. 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 ./. 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr1 63985884 . ATCAT A . PASS VC=INDEL;AC=91;AF=0.31;AN=298;refseq.name=NM_014288;refseq.positionType=intron GT ./. 0/0 0/1 0/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/1 1/1 ./. 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 ./. 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 ./. 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 ./. 0/1 0/1 ./. 0/0 0/0 ./. 0/1 chr1 63987096 . ATG A . PASS VC=INDEL;AC=37;AF=0.18;AN=202;refseq.name=NM_014288;refseq.positionType=intron GT ./. 0/0 0/1 ./. ./. ./. 0/0 0/1 ./. ./. ./. 0/0 ./. 0/1 0/0 0/1 0/0 ./. 0/0 ./. ./. 0/1 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 ./. 0/0 ./. 0/1 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/1 ./. 0/0 0/0 ./. ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/0 ./. 0/1 ./. ./. ./. ./. 0/0 ./. ./. ./. 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. 0/1 0/0 0/1 ./. ./. 0/1 0/0 0/1 ./. ./. 0/1 0/0 0/1 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/1 ./. 0/1 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/1 ./. ./. ./. 0/0 ./. 0/0 0/1 ./. 0/0 0/1 0/0 0/1 ./. ./. 0/0 0/1 ./. 0/1 0/0 0/1 0/1 0/1 0/1 chr1 64264921 . TTGTGTCAT T . PASS VC=INDEL;AC=136;AF=0.46;AN=298;refseq.name=NM_005012;refseq.positionType=intron GT 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 ./. 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 ./. 0/1 ./. 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 ./. ./. 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 chr1 64463351 . GT G . PASS VC=INDEL;AC=244;AF=0.77;AN=316;refseq.name=NM_005012;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 chr1 64627261 . A AAA . PASS VC=INDEL;AC=79;AF=0.25;AN=316;refseq.name=NM_005012;refseq.positionType=intron GT 0/0 1/1 0/1 1/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 65237568 . G GGTTA . PASS VC=INDEL;AC=237;AF=0.75;AN=316;refseq.name=NM_018211;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 chr1 65299673 . T TTAAG . PASS VC=INDEL;AC=10;AF=0.03;AN=314;refseq.name=NM_002227;refseq.positionType=exon GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 65545194 . A AT . PASS VC=INDEL;AC=316;AF=1;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 65545195 . T TT . PASS VC=INDEL;AC=316;AF=1;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 66063617 . ATGT A . PASS VC=INDEL;AC=212;AF=0.67;AN=316;refseq.name=NM_002303;refseq.positionType=intron GT 0/0 0/0 1/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 chr1 66198019 . A ACCATCCA . PASS VC=INDEL;AC=76;AF=0.26;AN=296 GT 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 ./. 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 ./. ./. 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/0 ./. 0/0 ./. ./. 1/1 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 chr1 66460193 . T TC . PASS VC=INDEL;AC=301;AF=0.95;AN=316;refseq.name=NM_001037341;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 66801086 . TGT T . PASS VC=INDEL;AC=19;AF=0.06;AN=316;refseq.name=NM_001037341;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 66952677 . A ATC . PASS VC=INDEL;AC=158;AF=0.65;AN=244 GT 0/1 1/1 1/1 0/0 1/1 ./. ./. 0/1 0/0 0/1 ./. 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 ./. 0/1 1/1 0/1 0/1 0/1 0/1 1/1 ./. 1/1 0/1 0/1 0/1 1/1 ./. 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 ./. 1/1 1/1 ./. 1/1 1/1 0/1 0/1 1/1 0/1 ./. 0/0 0/0 1/1 0/1 1/1 ./. 0/1 0/1 0/1 ./. 0/1 ./. 0/1 ./. ./. 1/1 0/1 ./. ./. 0/1 0/1 0/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 ./. 0/1 0/1 1/1 ./. ./. 0/1 0/1 0/1 1/1 1/1 ./. 0/1 0/0 ./. 0/1 ./. 0/1 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/1 ./. 1/1 0/1 0/1 ./. ./. 0/1 ./. 0/1 ./. 0/1 1/1 1/1 0/1 ./. 0/1 0/1 ./. 0/1 1/1 chr1 67152254 . ATAATTTCACGA A . PASS VC=INDEL;AC=9;AF=0.03;AN=316;refseq.name=NM_032291;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 67206037 . AATTG A . PASS VC=INDEL;AC=50;AF=0.19;AN=268;refseq.name=NM_032291;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/1 ./. 0/0 0/0 0/1 0/1 ./. 0/0 0/1 0/0 0/0 0/1 ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 ./. ./. 0/0 0/1 ./. ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 ./. 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 ./. ./. 0/1 0/0 ./. ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/1 ./. ./. 0/1 0/1 0/1 ./. 0/0 0/1 0/0 ./. 0/1 1/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/1 chr1 67459726 . T TT . PASS VC=INDEL;AC=54;AF=0.18;AN=300 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/1 0/1 0/0 0/1 ./. ./. 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 ./. chr1 68038796 . ACA A . PASS VC=INDEL;AC=21;AF=0.08;AN=264 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/1 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 chr1 68291788 . GC G . PASS VC=INDEL;AC=19;AF=0.06;AN=316;refseq.name=NM_018841;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 chr1 68570194 . CCCT C . PASS VC=INDEL;AC=110;AF=0.35;AN=310;refseq.name=NM_001002292;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 chr1 69008683 . C CA . PASS VC=INDEL;AC=68;AF=0.3;AN=230 GT 0/0 ./. 0/0 ./. 0/0 ./. 0/1 0/0 ./. ./. 0/0 1/1 ./. 1/1 0/0 0/0 0/0 0/1 0/1 ./. 0/1 1/1 ./. ./. 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 1/1 1/1 1/1 0/1 0/0 1/1 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/1 0/1 0/0 ./. ./. ./. 1/1 0/1 1/1 0/0 ./. 1/1 0/1 ./. 0/1 0/0 ./. 0/0 0/1 ./. 0/1 0/0 0/0 ./. 0/1 0/0 ./. ./. 1/1 ./. ./. 0/0 0/0 0/1 0/1 0/1 1/1 ./. 1/1 1/1 ./. 0/1 0/0 1/1 ./. ./. ./. 0/0 ./. 1/1 ./. ./. 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/1 ./. ./. ./. 0/1 0/1 ./. 0/1 0/0 0/0 0/0 0/1 ./. chr1 69398928 . CAAC C . PASS VC=INDEL;AC=66;AF=0.21;AN=316 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 chr1 69424885 . AG A . PASS VC=INDEL;AC=257;AF=0.81;AN=316 GT 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 chr1 69424886 . GG G . PASS VC=INDEL;AC=257;AF=0.81;AN=316 GT 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 chr1 69702172 . T TT . PASS VC=INDEL;AC=186;AF=0.59;AN=316 GT 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 chr1 69947085 . T TT . PASS VC=INDEL;AC=199;AF=0.87;AN=230 GT ./. 1/1 1/1 0/1 0/1 0/0 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 0/1 1/1 0/0 1/1 0/1 ./. ./. ./. 0/0 ./. 1/1 1/1 1/1 1/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 0/1 0/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 ./. ./. 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 0/1 ./. 0/0 ./. ./. 1/1 ./. 1/1 ./. ./. 1/1 0/1 ./. 0/1 ./. 1/1 1/1 ./. 1/1 ./. 0/1 0/0 1/1 ./. 1/1 1/1 0/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 ./. ./. ./. ./. ./. ./. 1/1 1/1 1/1 0/1 1/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. ./. 1/1 1/1 chr1 70116412 . T TAAT . PASS VC=INDEL;AC=236;AF=0.77;AN=308 GT 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 ./. 1/1 1/1 0/1 0/1 chr1 70794740 . AAAAC A . PASS VC=INDEL;AC=49;AF=0.17;AN=288;refseq.name=NM_030816;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 ./. ./. 0/1 ./. 0/0 0/1 0/1 0/0 0/1 ./. ./. ./. 0/0 0/1 ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 ./. 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 70796576 . TTACTT T . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_030816;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 71101845 . TG T . PASS VC=INDEL;AC=38;AF=0.12;AN=310 GT 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 71353307 . AT A . PASS VC=INDEL;AC=88;AF=0.28;AN=310;refseq.name=NM_000957;refseq.positionType=intron GT 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/0 0/0 0/1 ./. 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 ./. 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 ./. 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 chr1 71366228 . AA A . PASS VC=INDEL;AC=123;AF=0.39;AN=314;refseq.name=NM_000957;refseq.positionType=intron GT 1/1 1/1 0/0 1/1 1/1 0/0 1/1 ./. 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 0/0 1/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/1 chr1 71366595 . A AAGTG . PASS VC=INDEL;AC=108;AF=0.34;AN=316;refseq.name=NM_000957;refseq.positionType=intron GT 0/1 0/1 0/0 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 chr1 71366598 . T TGAGT . PASS VC=INDEL;AC=109;AF=0.34;AN=316;refseq.name=NM_000957;refseq.positionType=intron GT 0/1 0/1 0/0 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 chr1 71693491 . TGAG T . PASS VC=INDEL;AC=32;AF=0.1;AN=312 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 71693493 . AGGA A . PASS VC=INDEL;AC=34;AF=0.11;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 72053145 . AG A . PASS VC=INDEL;AC=229;AF=0.72;AN=316;refseq.name=NM_173808;refseq.positionType=intron GT 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 chr1 72321086 . AA A . PASS VC=INDEL;AC=54;AF=0.17;AN=314;refseq.name=NM_173808;refseq.positionType=intron GT 0/1 1/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 chr1 73854019 . T TTTTA . PASS VC=INDEL;AC=181;AF=0.59;AN=308 GT 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 ./. 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 ./. 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 chr1 74227801 . AG A . PASS VC=INDEL;AC=2;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 74404505 . TTT T . PASS VC=INDEL;AC=23;AF=0.07;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 74892891 . AG A . PASS VC=INDEL;AC=75;AF=0.24;AN=316;refseq.name=NM_001112808;refseq.positionType=intron GT 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 74896404 . ACTCAA A . PASS VC=INDEL;AC=26;AF=0.08;AN=316;refseq.name=NM_001112808;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 75049490 . C CT . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_001002912;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 75156563 . GCTT G . PASS VC=INDEL;AC=259;AF=0.82;AN=316 GT 0/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 chr1 75661521 . TTCTT T . PASS VC=INDEL;AC=7;AF=0.02;AN=312 GT 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 76005746 . A AC . PASS VC=INDEL;AC=184;AF=0.58;AN=316;refseq.name=NM_152697;refseq.positionType=intron GT 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 chr1 76054645 . AT A . PASS VC=INDEL;AC=14;AF=0.05;AN=290;refseq.name=NM_152697;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 chr1 76110056 . ATCAT A . PASS VC=INDEL;AC=202;AF=0.7;AN=290 GT 0/0 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 ./. 1/1 ./. 0/1 0/0 0/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 0/0 1/1 0/1 1/1 1/1 ./. 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 ./. 0/0 0/0 0/0 0/1 0/1 ./. 0/1 0/1 1/1 ./. 1/1 1/1 0/0 0/1 0/0 1/1 0/1 ./. 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 ./. 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 ./. 1/1 chr1 76110059 . ATTCA A . PASS VC=INDEL;AC=198;AF=0.68;AN=290 GT ./. 1/1 1/1 0/1 1/1 0/1 0/0 1/1 ./. 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 ./. 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 ./. 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 0/1 0/0 0/0 ./. 0/1 0/1 ./. 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 ./. 0/0 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 ./. 1/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 ./. 1/1 1/1 0/1 0/1 0/1 0/0 1/1 chr1 76603385 . A AA . PASS VC=INDEL;AC=45;AF=0.14;AN=316;refseq.name=NM_152996;refseq.positionType=intron GT 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 76647177 . T TA . PASS VC=INDEL;AC=44;AF=0.15;AN=292;refseq.name=NM_152996;refseq.positionType=intron GT 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/1 0/1 0/0 0/1 ./. ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 ./. 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 chr1 76772246 . TAG T . PASS VC=INDEL;AC=71;AF=0.22;AN=316;refseq.name=NM_152996;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 chr1 77019040 . G GA . PASS VC=INDEL;AC=123;AF=0.39;AN=316;refseq.name=NM_152996;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 chr1 77019568 . TTCTG T . PASS VC=INDEL;AC=72;AF=0.23;AN=316;refseq.name=NM_152996;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 chr1 77147457 . T TG . PASS VC=INDEL;AC=307;AF=0.97;AN=316 GT 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 77154589 . T TA . PASS VC=INDEL;AC=300;AF=0.95;AN=316 GT 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 77350958 . GT G . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_030965;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 77412672 . T TCAAA . PASS VC=INDEL;AC=183;AF=0.58;AN=316;refseq.name=NM_030965;refseq.positionType=intron GT 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 chr1 77412677 . C CAAAC . PASS VC=INDEL;AC=183;AF=0.58;AN=316;refseq.name=NM_030965;refseq.positionType=intron GT 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 chr1 77761353 . ATTCT A . PASS VC=INDEL;AC=87;AF=0.28;AN=310;refseq.name=NM_174858;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 chr1 78436001 . T TCT . PASS VC=INDEL;AC=139;AF=0.45;AN=308;refseq.name=NM_003902;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 ./. 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 ./. 1/1 1/1 ./. 1/1 ./. 0/1 0/0 0/0 0/0 chr1 78477804 . T TAAGAC . PASS VC=INDEL;AC=294;AF=0.93;AN=316;refseq.name=NM_007034;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 78533885 . CAG C . PASS VC=INDEL;AC=126;AF=0.4;AN=316;refseq.name=NM_017655;refseq.positionType=intron GT 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 1/1 chr1 78533886 . AGA A . PASS VC=INDEL;AC=126;AF=0.4;AN=316;refseq.name=NM_017655;refseq.positionType=intron GT 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 1/1 chr1 78752617 . TC T . PASS VC=INDEL;AC=160;AF=0.51;AN=314 GT 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 ./. 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 chr1 79595269 . T TC . PASS VC=INDEL;AC=37;AF=0.12;AN=312 GT 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 chr1 79694557 . CTTGT C . PASS VC=INDEL;AC=173;AF=0.68;AN=254 GT 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 ./. ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 ./. 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 ./. ./. ./. ./. 0/0 0/1 0/1 ./. 0/1 0/1 ./. 0/0 0/1 ./. ./. 0/1 1/1 0/1 0/1 ./. 0/1 0/1 ./. ./. 0/1 ./. 1/1 ./. 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 0/1 1/1 ./. 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 ./. 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 ./. ./. 1/1 0/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 0/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 chr1 80133716 . CA C . PASS VC=INDEL;AC=74;AF=0.27;AN=276 GT 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 ./. 0/0 ./. 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 ./. ./. 0/0 0/0 ./. 0/1 0/0 0/1 1/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/0 0/1 0/1 0/0 0/1 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 ./. 0/1 0/0 0/1 0/1 1/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. ./. 0/1 ./. 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 ./. 0/1 0/1 0/0 1/1 0/1 0/0 0/0 chr1 80193527 . CA C . PASS VC=INDEL;AC=0;AF=0;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 80279810 . T TT . PASS VC=INDEL;AC=69;AF=0.22;AN=314 GT 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 chr1 80415715 . C CATGTCTATTAT . PASS VC=INDEL;AC=197;AF=0.62;AN=316 GT 0/1 0/0 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 chr1 80415717 . T TGTCTATTATAT . PASS VC=INDEL;AC=197;AF=0.62;AN=316 GT 0/1 0/0 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 chr1 80606020 . GTAGGC G . PASS VC=INDEL;AC=282;AF=0.89;AN=316 GT 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 chr1 80684057 . A AA . PASS VC=INDEL;AC=217;AF=0.69;AN=316 GT 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 1/1 1/1 chr1 80857688 . AAATA A . PASS VC=INDEL;AC=97;AF=0.31;AN=316 GT 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 chr1 81007659 . A AC . PASS VC=INDEL;AC=185;AF=0.59;AN=312 GT 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 ./. 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/0 0/0 chr1 81007660 . C CC . PASS VC=INDEL;AC=185;AF=0.59;AN=314 GT 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/0 0/0 chr1 81912884 . C CT . PASS VC=INDEL;AC=15;AF=0.05;AN=298 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 ./. 0/0 0/0 chr1 82042397 . TCTT T . PASS VC=INDEL;AC=5;AF=0.02;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 82264610 . TG T . PASS VC=INDEL;AC=167;AF=0.54;AN=312;refseq.name=NM_012302;refseq.positionType=promoter GT 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 ./. 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 ./. 0/1 0/1 0/0 chr1 82264994 . G GGTAG . PASS VC=INDEL;AC=49;AF=0.16;AN=316;refseq.name=NM_012302;refseq.positionType=promoter GT 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 chr1 82280496 . ATGT A . PASS VC=INDEL;AC=84;AF=0.27;AN=316;refseq.name=NM_012302;refseq.positionType=intron GT 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 82315714 . G GAGTG . PASS VC=INDEL;AC=38;AF=0.12;AN=306;refseq.name=NM_012302;refseq.positionType=intron GT 0/1 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 chr1 82316526 . TT T . PASS VC=INDEL;AC=209;AF=0.67;AN=312;refseq.name=NM_012302;refseq.positionType=intron GT 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 ./. 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 ./. 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 chr1 82329993 . CATAT C . PASS VC=INDEL;AC=305;AF=0.97;AN=316;refseq.name=NM_012302;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 chr1 82710650 . AA A . PASS VC=INDEL;AC=297;AF=0.96;AN=310 GT 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 83144930 . TC T . PASS VC=INDEL;AC=153;AF=0.55;AN=278 GT 1/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 0/0 1/1 0/1 0/0 0/1 ./. 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 ./. ./. 0/1 1/1 0/0 0/1 0/1 0/1 0/1 ./. 1/1 0/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 ./. 0/1 0/1 1/1 1/1 0/1 0/0 0/1 ./. 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 ./. 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 ./. 1/1 0/0 ./. 0/1 0/1 0/0 0/1 ./. 0/0 0/1 1/1 0/1 1/1 ./. 0/0 0/0 ./. 0/1 0/0 ./. 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 1/1 0/0 ./. 0/0 1/1 ./. ./. 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 ./. 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 chr1 83208212 . C CAGAT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 83208213 . A AGATA . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 83581070 . C CCAGA . PASS VC=INDEL;AC=188;AF=0.74;AN=254 GT ./. ./. 1/1 0/1 ./. 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 0/1 ./. ./. ./. 1/1 1/1 ./. 0/0 0/1 0/1 1/1 ./. 0/1 1/1 0/1 0/1 ./. 0/0 1/1 0/1 0/1 ./. ./. 0/1 1/1 ./. 1/1 0/1 0/1 ./. ./. 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 ./. 0/1 0/0 0/1 ./. 0/1 1/1 1/1 1/1 0/1 ./. 1/1 0/1 0/1 ./. ./. ./. 0/1 1/1 ./. 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 0/1 0/1 ./. 1/1 0/1 1/1 ./. ./. 0/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 ./. 1/1 chr1 84127066 . TCT T . PASS VC=INDEL;AC=71;AF=0.22;AN=316 GT 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 chr1 84822658 . TCAATTAAAACTCACAG T . PASS VC=INDEL;AC=45;AF=0.16;AN=286 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 ./. 0/1 1/1 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 ./. 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 ./. 0/1 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 ./. 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 chr1 85570521 . GTTC G . PASS VC=INDEL;AC=166;AF=0.53;AN=316;refseq.name=NM_145172;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 chr1 86565855 . T TCT . PASS VC=INDEL;AC=20;AF=0.06;AN=316;refseq.name=NM_152890;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr1 86714492 . T TA . PASS VC=INDEL;AC=263;AF=0.88;AN=300 GT 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 ./. 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 ./. 1/1 1/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 chr1 86786541 . CAG C . PASS VC=INDEL;AC=7;AF=0.02;AN=316 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 86839425 . TACTT T . PASS VC=INDEL;AC=15;AF=0.05;AN=280;refseq.name=NM_001007022;refseq.positionType=intron GT 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 chr1 87558067 . CACATAC C . PASS VC=INDEL;AC=285;AF=0.97;AN=294;refseq.name=NM_012262;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 0/1 1/1 1/1 chr1 88184554 . T TCA . PASS VC=INDEL;AC=40;AF=0.14;AN=276 GT 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 1/1 ./. 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/1 ./. 0/0 ./. ./. 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/1 0/1 chr1 88351056 . A AGT . PASS VC=INDEL;AC=222;AF=0.7;AN=316 GT 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 chr1 88391828 . C CCTT . PASS VC=INDEL;AC=216;AF=0.7;AN=310 GT 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 ./. 0/1 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 chr1 88391834 . T TCTT . PASS VC=INDEL;AC=219;AF=0.69;AN=316 GT 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 chr1 88423056 . T TA . PASS VC=INDEL;AC=210;AF=0.8;AN=262 GT 1/1 0/0 1/1 ./. 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 ./. ./. ./. 1/1 1/1 ./. 0/1 0/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 0/1 1/1 0/1 0/1 ./. ./. 0/1 0/1 1/1 0/1 0/1 0/1 0/1 ./. ./. ./. 1/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 ./. 1/1 ./. 0/0 0/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/0 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 ./. 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr1 88878932 . TGAAG T . PASS VC=INDEL;AC=222;AF=0.71;AN=314 GT 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 1/1 0/1 0/0 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 ./. 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 88934449 . T TA . PASS VC=INDEL;AC=215;AF=0.71;AN=304 GT 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 ./. 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/0 ./. 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 chr1 89147233 . C CTG . PASS VC=INDEL;AC=270;AF=0.94;AN=288;refseq.name=NM_006256;refseq.positionType=promoter GT 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 ./. ./. 1/1 1/1 0/1 0/1 ./. 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 ./. 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 89147234 . T TGT . PASS VC=INDEL;AC=193;AF=0.91;AN=212;refseq.name=NM_006256;refseq.positionType=promoter GT ./. 1/1 1/1 1/1 ./. ./. 1/1 1/1 ./. 1/1 ./. ./. 1/1 1/1 ./. 1/1 ./. ./. ./. ./. ./. 1/1 1/1 ./. 0/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 ./. ./. ./. 1/1 1/1 ./. 0/1 ./. 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 ./. ./. ./. ./. ./. ./. ./. 1/1 ./. 1/1 ./. ./. ./. 0/1 ./. 1/1 ./. ./. 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. ./. 1/1 1/1 ./. 1/1 0/1 0/1 ./. 0/0 0/1 ./. ./. ./. ./. 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. ./. 1/1 ./. ./. ./. 1/1 chr1 90055475 . TT T . PASS VC=INDEL;AC=35;AF=0.11;AN=316;refseq.name=NM_015350;refseq.positionType=intron GT 0/1 0/0 0/0 1/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 90055577 . TATG T . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_015350;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 90305331 . G GA . PASS VC=INDEL;AC=301;AF=0.95;AN=316;refseq.name=NM_018103;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 91238816 . G GT . PASS VC=INDEL;AC=86;AF=0.29;AN=296 GT 0/0 0/0 ./. 1/1 0/0 0/0 0/1 ./. 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 ./. 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 ./. 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 1/1 ./. 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 ./. 0/0 0/0 1/1 0/1 1/1 1/1 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/0 ./. 0/1 chr1 91308113 . GC G . PASS VC=INDEL;AC=8;AF=0.03;AN=282 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/1 0/1 ./. 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 chr1 91354296 . TT T . PASS VC=INDEL;AC=252;AF=0.83;AN=304 GT 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 ./. 1/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. ./. 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 ./. 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 chr1 91544957 . ACT A . PASS VC=INDEL;AC=99;AF=0.32;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 chr1 91566585 . GTTA G . PASS VC=INDEL;AC=139;AF=0.45;AN=312 GT 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 chr1 92219769 . C CTCCTCAA . PASS VC=INDEL;AC=54;AF=0.17;AN=314;refseq.name=NM_003243;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 chr1 93167519 . C CTG . PASS VC=INDEL;AC=276;AF=1;AN=276;refseq.name=NM_005665;refseq.positionType=intron GT 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 ./. 1/1 ./. 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. ./. 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 93628710 . TACTC T . PASS VC=INDEL;AC=94;AF=0.31;AN=304;refseq.name=NM_016040;refseq.positionType=intron GT 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/1 ./. 0/0 0/1 1/1 0/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/0 ./. 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/1 chr1 93704043 . T TCTAGAAAAATC . PASS VC=INDEL;AC=7;AF=0.02;AN=306;refseq.name=NM_206886;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 94443843 . G GAGAG . PASS VC=INDEL;AC=88;AF=0.3;AN=292 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 ./. 0/0 0/0 0/1 ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 ./. 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/0 ./. 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 ./. 0/0 chr1 94634727 . TGAGT T . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_004815;refseq.positionType=exon GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 95103314 . AGCATCCTAAA A . PASS VC=INDEL;AC=6;AF=0.03;AN=240 GT ./. ./. 0/0 0/0 0/0 ./. ./. 0/1 0/0 ./. 0/0 ./. 0/0 0/0 ./. ./. ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 chr1 95167241 . TTAAC T . PASS VC=INDEL;AC=115;AF=0.36;AN=316 GT 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 1/1 chr1 95167244 . ACTAA A . PASS VC=INDEL;AC=116;AF=0.37;AN=316 GT 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 1/1 chr1 95266356 . A AAAATAAGAATCCA . PASS VC=INDEL;AC=212;AF=0.83;AN=256 GT 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 ./. ./. ./. 0/0 1/1 0/0 0/1 ./. 0/1 0/1 1/1 1/1 1/1 ./. 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 0/1 1/1 0/1 0/0 0/1 1/1 1/1 ./. 1/1 ./. 1/1 0/1 1/1 0/1 1/1 ./. ./. 0/1 ./. 0/1 1/1 0/1 0/1 0/1 ./. 0/1 ./. 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 ./. 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 ./. ./. ./. 0/1 0/1 1/1 ./. 0/1 1/1 0/1 0/1 0/1 1/1 1/1 ./. 0/1 ./. 1/1 ./. ./. ./. chr1 95349846 . G GG . PASS VC=INDEL;AC=195;AF=0.65;AN=302;refseq.name=NM_001114106;refseq.positionType=intron GT 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 ./. 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 ./. 1/1 0/1 ./. 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 1/1 ./. 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 ./. 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 ./. 0/1 0/1 0/1 1/1 1/1 chr1 95638470 . GTAG G . PASS VC=INDEL;AC=9;AF=0.03;AN=306;refseq.name=NM_152487;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 96578762 . CAG C . PASS VC=INDEL;AC=78;AF=0.25;AN=314 GT 1/1 0/0 0/0 0/1 1/1 0/1 0/0 1/1 0/0 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 chr1 97069290 . G GT . PASS VC=INDEL;AC=57;AF=0.18;AN=316 GT 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 97352585 . A AGA . PASS VC=INDEL;AC=167;AF=0.53;AN=316 GT 0/0 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 1/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/0 0/0 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 chr1 97471673 . T TTA . PASS VC=INDEL;AC=39;AF=0.16;AN=238 GT 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/1 0/0 1/1 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 1/1 ./. 0/1 ./. 1/1 0/1 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 ./. ./. 0/1 0/0 0/0 0/1 ./. 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 ./. ./. 0/0 ./. ./. ./. 0/0 0/0 0/0 ./. 0/1 ./. 0/0 ./. 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. ./. ./. ./. 0/0 0/1 ./. ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/1 0/0 0/1 0/0 ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/1 chr1 97654513 . GTTAT G . PASS VC=INDEL;AC=17;AF=0.06;AN=302;refseq.name=NM_000110;refseq.positionType=intron GT ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 97728316 . AATA A . PASS VC=INDEL;AC=15;AF=0.05;AN=316;refseq.name=NM_000110;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 chr1 97862494 . TCCT T . PASS VC=INDEL;AC=47;AF=0.18;AN=256;refseq.name=NM_000110;refseq.positionType=intron GT 0/0 0/1 ./. 0/1 0/0 0/1 ./. 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 ./. 0/1 1/1 0/0 0/0 ./. ./. 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/1 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 ./. 0/1 0/1 ./. ./. 0/1 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 1/1 ./. 0/1 0/1 0/1 ./. 0/1 0/1 0/1 0/0 ./. 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 ./. chr1 97940369 . TAACT T . PASS VC=INDEL;AC=37;AF=0.12;AN=306;refseq.name=NM_000110;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/0 0/1 0/0 ./. ./. 0/1 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr1 98400957 . C CGATAT . PASS VC=INDEL;AC=290;AF=0.92;AN=316 GT 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 99032443 . T TTC . PASS VC=INDEL;AC=230;AF=0.79;AN=292 GT 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 ./. ./. ./. ./. 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 ./. 0/1 1/1 1/1 1/1 ./. 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 ./. 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 ./. 0/0 1/1 chr1 99032444 . T TCT . PASS VC=INDEL;AC=236;AF=0.8;AN=296 GT 0/1 0/1 0/1 1/1 1/1 ./. 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. ./. 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 ./. 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 ./. 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 1/1 0/1 1/1 0/0 1/1 chr1 99662955 . A AAGA . PASS VC=INDEL;AC=146;AF=0.46;AN=316 GT 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 chr1 99714941 . GTTACAG G . PASS VC=INDEL;AC=6;AF=0.02;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 99848725 . AT A . PASS VC=INDEL;AC=50;AF=0.16;AN=316 GT 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 100194878 . C CCT . PASS VC=INDEL;AC=248;AF=0.78;AN=316;refseq.name=NM_001013660;refseq.positionType=intron GT 1/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 1/1 1/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 chr1 100194903 . C CT . PASS VC=INDEL;AC=7;AF=0.02;AN=316;refseq.name=NM_001013660;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 100567908 . C CT . PASS VC=INDEL;AC=43;AF=0.14;AN=300;refseq.name=NM_194292;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. ./. 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 ./. 0/0 0/1 0/1 0/1 0/0 0/0 chr1 100793875 . CACTC C . PASS VC=INDEL;AC=105;AF=0.38;AN=274 GT 0/0 0/1 0/1 ./. 0/1 1/1 0/0 ./. 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/1 0/1 1/1 ./. 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 1/1 1/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 ./. 0/1 0/1 0/0 ./. 0/1 ./. 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/1 0/1 0/1 ./. ./. 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 ./. 0/1 0/1 ./. 0/1 0/1 0/0 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 1/1 ./. 0/1 1/1 0/1 0/0 0/0 ./. 0/0 0/1 ./. 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 ./. 1/1 0/1 ./. ./. 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/1 0/0 chr1 100808351 . TT T . PASS VC=INDEL;AC=27;AF=0.09;AN=294 GT ./. 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 ./. 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 ./. 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 100856872 . T TT . PASS VC=INDEL;AC=79;AF=0.25;AN=316;refseq.name=NM_003672;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 chr1 101093845 . TTCTGTAGTCAC T . PASS VC=INDEL;AC=24;AF=0.08;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 101295925 . CTA C . PASS VC=INDEL;AC=82;AF=0.26;AN=314 GT 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 ./. 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 chr1 101442572 . T TT . PASS VC=INDEL;AC=99;AF=0.31;AN=316;refseq.name=NM_133496;refseq.positionType=exon GT 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 chr1 101482924 . CTGTG C . PASS VC=INDEL;AC=32;AF=0.1;AN=316;refseq.name=NM_001077394;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 101859015 . G GA . PASS VC=INDEL;AC=107;AF=0.34;AN=316 GT 1/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 chr1 102315705 . A ATCTC . PASS VC=INDEL;AC=185;AF=0.59;AN=316;refseq.name=NM_058170;refseq.positionType=intron GT 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/1 chr1 102315708 . T TCTCT . PASS VC=INDEL;AC=185;AF=0.59;AN=316;refseq.name=NM_058170;refseq.positionType=intron GT 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/1 chr1 103391817 . TTA T . PASS VC=INDEL;AC=0;AF=0;AN=244;refseq.name=NM_001854;refseq.positionType=intron GT 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. ./. ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. ./. 0/0 0/0 chr1 103722297 . TGT T . PASS VC=INDEL;AC=32;AF=0.1;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 chr1 104533187 . A AGTT . PASS VC=INDEL;AC=148;AF=0.47;AN=316 GT 0/0 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 chr1 104896267 . GAG G . PASS VC=INDEL;AC=48;AF=0.15;AN=312 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 0/0 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr1 104896390 . ATATT A . PASS VC=INDEL;AC=38;AF=0.14;AN=268 GT 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 ./. ./. 0/0 1/1 0/0 ./. 0/1 1/1 ./. 1/1 0/0 0/0 0/0 ./. 0/0 0/1 ./. 0/0 ./. 0/1 0/0 0/0 1/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/1 0/0 1/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 1/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/1 0/0 chr1 105259435 . CACTAAACGTGCC C . PASS VC=INDEL;AC=6;AF=0.02;AN=250 GT ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. ./. 0/0 ./. ./. 0/0 0/0 ./. ./. 0/1 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 ./. 0/0 chr1 105451424 . A ATCTAGT . PASS VC=INDEL;AC=98;AF=0.31;AN=316 GT 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 chr1 105504523 . C CTTT . PASS VC=INDEL;AC=82;AF=0.29;AN=282 GT ./. 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/1 0/0 ./. 0/1 0/1 0/1 ./. 1/1 0/0 0/1 0/0 ./. 1/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 ./. 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 ./. ./. 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/1 0/1 0/1 0/0 0/1 ./. 0/0 1/1 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/1 ./. 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 1/1 chr1 105837170 . T TAA . PASS VC=INDEL;AC=67;AF=0.24;AN=280 GT 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 ./. 0/0 0/1 1/1 1/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/0 0/1 ./. ./. 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 ./. 0/1 1/1 0/1 1/1 ./. ./. ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/1 ./. 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. ./. 0/0 chr1 105868766 . ATACTT A . PASS VC=INDEL;AC=92;AF=0.34;AN=274 GT ./. 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 ./. 0/0 1/1 0/1 0/0 ./. 1/1 ./. 1/1 0/1 1/1 0/0 ./. ./. ./. 0/0 0/1 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/1 ./. ./. ./. 0/0 0/0 0/0 1/1 0/1 0/1 0/0 ./. 1/1 0/1 ./. 0/1 ./. 1/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 chr1 106762526 . AACT A . PASS VC=INDEL;AC=87;AF=0.28;AN=316 GT 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 chr1 106908645 . AC A . PASS VC=INDEL;AC=25;AF=0.08;AN=316 GT 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 chr1 107217236 . A AGGATCA . PASS VC=INDEL;AC=240;AF=0.79;AN=302 GT 1/1 1/1 ./. 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/0 1/1 ./. 1/1 1/1 ./. 1/1 0/0 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 0/0 0/0 0/0 0/0 1/1 1/1 0/0 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 1/1 ./. 0/0 0/0 0/0 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 1/1 1/1 0/0 1/1 0/0 0/0 0/0 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 ./. 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 107979567 . TT T . PASS VC=INDEL;AC=150;AF=0.55;AN=274;refseq.name=NM_001113226;refseq.positionType=intron GT 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 ./. 1/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 ./. ./. 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 ./. 0/1 0/0 1/1 ./. ./. 0/1 1/1 1/1 1/1 0/0 1/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/0 1/1 ./. 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 ./. 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 1/1 ./. 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 ./. 0/1 0/1 0/0 0/1 ./. 1/1 ./. 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 ./. 0/0 1/1 0/1 ./. 0/1 1/1 0/0 1/1 0/1 0/1 1/1 ./. 0/1 0/1 0/1 ./. 1/1 1/1 0/1 1/1 chr1 108737087 . GG G . PASS VC=INDEL;AC=99;AF=0.32;AN=308;refseq.name=NM_013386;refseq.positionType=intron GT 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 ./. 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 chr1 109186604 . A ATA . PASS VC=INDEL;AC=3;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 109295950 . TA T . PASS VC=INDEL;AC=54;AF=0.17;AN=312;refseq.name=NM_007269;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 chr1 109295955 . TTA T . PASS VC=INDEL;AC=57;AF=0.18;AN=310;refseq.name=NM_007269;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 chr1 109303951 . GTATAG G . PASS VC=INDEL;AC=89;AF=0.28;AN=316;refseq.name=NM_007269;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 chr1 109429108 . G GGAGAAAT . PASS VC=INDEL;AC=33;AF=0.14;AN=234;refseq.name=NM_013296;refseq.positionType=intron GT 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 ./. 0/1 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/1 ./. ./. 0/1 ./. 0/1 0/1 ./. ./. ./. 0/1 ./. 0/1 ./. 0/1 0/1 ./. ./. 0/1 ./. 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. ./. ./. 0/1 ./. 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/1 chr1 109565068 . C CTC . PASS VC=INDEL;AC=304;AF=0.96;AN=316;refseq.name=NM_014969;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 chr1 110418161 . CTTAG C . PASS VC=INDEL;AC=56;AF=0.18;AN=316 GT 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 chr1 110911466 . AT A . PASS VC=INDEL;AC=67;AF=0.22;AN=310;refseq.name=NM_004696;refseq.positionType=intron GT 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 chr1 111820993 . TTAAG T . PASS VC=INDEL;AC=46;AF=0.2;AN=232 GT 0/1 ./. 1/1 ./. 0/0 ./. 0/1 0/1 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/0 0/0 0/1 1/1 ./. 0/1 0/0 0/1 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/0 0/0 0/1 ./. ./. ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 ./. 0/0 0/1 ./. ./. 0/0 0/1 0/1 0/1 0/1 0/0 0/0 ./. ./. 0/1 ./. ./. 0/0 0/1 ./. 0/0 ./. 0/1 ./. 0/0 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/1 ./. 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 ./. ./. ./. 0/0 0/0 0/1 0/0 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/1 ./. ./. ./. chr1 111894729 . C CATG . PASS VC=INDEL;AC=32;AF=0.11;AN=302;refseq.name=NM_181643;refseq.positionType=exon GT 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/1 0/0 chr1 112384059 . G GG . PASS VC=INDEL;AC=111;AF=0.35;AN=314;refseq.name=NM_004980;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 1/1 chr1 112440856 . A ACTTA . PASS VC=INDEL;AC=138;AF=0.44;AN=312;refseq.name=NM_004980;refseq.positionType=intron GT 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/1 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 chr1 112896532 . CTAAC C . PASS VC=INDEL;AC=1;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 112896636 . CA C . PASS VC=INDEL;AC=199;AF=0.64;AN=312 GT 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 ./. 1/1 0/0 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 ./. 1/1 chr1 112896637 . AA A . PASS VC=INDEL;AC=199;AF=0.63;AN=316 GT 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 chr1 113322895 . TTCTA T . PASS VC=INDEL;AC=73;AF=0.3;AN=246 GT 0/0 ./. 0/1 0/0 ./. 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 ./. 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 1/1 0/1 0/0 0/0 0/0 ./. ./. ./. 1/1 0/0 1/1 1/1 0/1 0/1 1/1 ./. ./. ./. 0/0 0/1 1/1 0/0 0/1 ./. ./. 0/0 ./. 0/1 1/1 0/1 0/0 0/1 0/1 ./. 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 ./. 0/0 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 0/1 ./. ./. ./. ./. ./. 0/0 0/1 1/1 ./. 0/0 0/0 0/0 ./. 0/0 0/1 ./. 0/1 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 ./. 0/0 0/0 1/1 0/0 0/1 0/0 0/0 ./. ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 ./. 0/0 ./. 0/0 0/0 chr1 113467083 . CC C . PASS VC=INDEL;AC=1;AF=0;AN=316;refseq.name=NM_003051;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 113635187 . C CTTTG . PASS VC=INDEL;AC=261;AF=0.83;AN=316;refseq.name=NM_014813;refseq.positionType=intron GT 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 chr1 113635190 . T TGTTT . PASS VC=INDEL;AC=261;AF=0.83;AN=316;refseq.name=NM_014813;refseq.positionType=intron GT 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 chr1 113640553 . GA G . PASS VC=INDEL;AC=111;AF=0.35;AN=314;refseq.name=NM_014813;refseq.positionType=intron GT 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 chr1 113640556 . AA A . PASS VC=INDEL;AC=112;AF=0.35;AN=316;refseq.name=NM_014813;refseq.positionType=intron GT 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 chr1 113689905 . GAG G . PASS VC=INDEL;AC=41;AF=0.13;AN=316 GT 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 114240320 . A AA . PASS VC=INDEL;AC=229;AF=0.72;AN=316;refseq.name=NM_006608;refseq.positionType=exon GT 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 114339956 . C CTAAA . PASS VC=INDEL;AC=210;AF=0.78;AN=270;refseq.name=NM_018364;refseq.positionType=intron GT 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. ./. 1/1 0/1 0/0 0/1 1/1 0/0 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/1 ./. 1/1 ./. ./. 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 ./. ./. ./. 0/0 0/1 0/1 ./. ./. 0/0 0/1 0/0 0/1 ./. 0/0 ./. 0/1 0/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 114565357 . CGGAGG C . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 116298599 . A ACTT . PASS VC=INDEL;AC=54;AF=0.17;AN=316;refseq.name=NM_001232;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 chr1 116435014 . ATAACCGA A . PASS VC=INDEL;AC=66;AF=0.26;AN=250 GT 1/1 1/1 ./. 1/1 0/1 0/1 0/1 ./. 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 ./. 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/1 ./. 0/0 0/0 0/1 0/0 1/1 0/0 ./. ./. 0/1 0/0 0/0 0/0 0/1 ./. 1/1 ./. 0/0 0/1 0/1 0/0 0/0 0/1 ./. 1/1 1/1 0/1 0/1 ./. 0/0 1/1 ./. 0/0 1/1 0/1 1/1 ./. 1/1 0/0 ./. 1/1 0/1 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. ./. ./. 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/1 0/0 0/0 ./. 0/1 0/1 chr1 116551982 . T TTAAAGC . PASS VC=INDEL;AC=31;AF=0.1;AN=304;refseq.name=NM_018420;refseq.positionType=intron GT 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 116662025 . T TGA . PASS VC=INDEL;AC=55;AF=0.17;AN=316;refseq.name=NM_152367;refseq.positionType=intron GT 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 chr1 116662028 . G GAG . PASS VC=INDEL;AC=55;AF=0.17;AN=316;refseq.name=NM_152367;refseq.positionType=intron GT 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 chr1 117459931 . AAC A . PASS VC=INDEL;AC=90;AF=0.28;AN=316;refseq.name=NM_020440;refseq.positionType=intron GT 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 117459932 . ACA A . PASS VC=INDEL;AC=90;AF=0.28;AN=316;refseq.name=NM_020440;refseq.positionType=intron GT 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 117592136 . TTG T . PASS VC=INDEL;AC=24;AF=0.08;AN=300 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. chr1 117722836 . C CA . PASS VC=INDEL;AC=36;AF=0.11;AN=316;refseq.name=NM_024626;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 chr1 120034138 . TCTAT T . PASS VC=INDEL;AC=99;AF=0.35;AN=284 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/1 0/0 ./. 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/0 ./. 0/1 0/1 0/1 ./. 0/1 0/1 0/1 ./. 0/1 0/1 0/0 1/1 0/1 1/1 ./. 0/1 0/1 0/1 0/1 0/1 1/1 1/1 ./. 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 ./. ./. 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/0 ./. 0/1 0/0 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/0 ./. 0/1 0/0 0/0 0/1 ./. 1/1 1/1 0/0 0/0 chr1 120185496 . G GGATT . PASS VC=INDEL;AC=264;AF=0.84;AN=314;refseq.name=NM_001080470;refseq.positionType=intron GT 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr1 120280730 . TAA T . PASS VC=INDEL;AC=73;AF=0.23;AN=314;refseq.name=NM_006623;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 chr1 144995277 . AG A . PASS VC=INDEL;AC=41;AF=0.16;AN=258;refseq.name=NM_014644;refseq.positionType=promoter GT 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/1 0/0 ./. 0/1 ./. ./. 0/0 ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 ./. 0/1 0/1 0/1 0/0 ./. ./. ./. 0/0 ./. ./. 0/0 0/1 0/1 ./. 0/1 0/1 0/0 0/0 ./. ./. ./. 0/1 0/0 ./. 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 ./. 0/1 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 chr1 145060382 . A AG . PASS VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_022359;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 146556039 . CCAAC C . PASS VC=INDEL;AC=64;AF=0.21;AN=310 GT 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 ./. ./. 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 chr1 146768690 . TC T . PASS VC=INDEL;AC=289;AF=0.91;AN=316 GT 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 chr1 146979526 . CCT C . PASS VC=INDEL;AC=63;AF=0.2;AN=316 GT 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 chr1 147047674 . AA A . PASS VC=INDEL;AC=101;AF=0.32;AN=314;refseq.name=NM_004326;refseq.positionType=intron GT 0/1 0/1 0/0 1/1 1/1 0/0 1/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 chr1 147108091 . A AC . PASS VC=INDEL;AC=227;AF=0.72;AN=314 GT 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 ./. 1/1 chr1 147392223 . CATGGCTC C . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 147393527 . A AAGAA . PASS VC=INDEL;AC=10;AF=0.05;AN=218 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 ./. ./. 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/1 0/0 ./. 0/0 0/0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0 0/0 ./. 0/0 ./. ./. ./. ./. 0/0 0/1 ./. ./. ./. ./. 0/0 0/0 0/0 0/1 ./. 0/1 ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 chr1 147823728 . A AC . PASS VC=INDEL;AC=2;AF=0.01;AN=266 GT 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 ./. ./. ./. ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 chr1 151094921 . T TA . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 151094936 . CCTTA C . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 151743871 . AA A . PASS VC=INDEL;AC=98;AF=0.32;AN=308;refseq.name=NM_016178;refseq.positionType=terminator GT 1/1 0/1 ./. 0/0 0/1 0/0 1/1 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 ./. 0/1 0/0 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 ./. 0/0 0/1 1/1 1/1 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 1/1 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 chr1 152348228 . TTAT T . PASS VC=INDEL;AC=9;AF=0.03;AN=316 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 152442163 . AAACA A . PASS VC=INDEL;AC=212;AF=0.68;AN=310 GT 0/1 ./. 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 ./. 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 chr1 152572426 . G GT . PASS VC=INDEL;AC=70;AF=0.25;AN=280;refseq.name=NM_178434;refseq.positionType=promoter GT 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 1/1 0/0 0/1 ./. 0/0 ./. 0/1 0/0 0/0 0/0 ./. ./. 0/1 0/1 0/1 0/1 ./. 0/0 0/0 0/0 0/1 0/1 ./. 0/1 ./. 0/0 ./. ./. 0/1 0/1 ./. 1/1 ./. 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/0 ./. 0/1 0/0 0/0 1/1 ./. 1/1 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. 1/1 0/1 0/0 chr1 152797773 . C CC . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_178348;refseq.positionType=promoter GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 153703019 . TGTGTCTCTGCTT T . PASS VC=INDEL;AC=1;AF=0;AN=316;refseq.name=NM_023015;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 154741714 . TAT T . PASS VC=INDEL;AC=1;AF=0;AN=316;refseq.name=NM_002249;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 155303581 . AT A . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 155559888 . C CTTAT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 156565049 . A AAC . PASS VC=INDEL;AC=314;AF=0.99;AN=316;refseq.name=NM_015590;refseq.positionType=exon GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 156572952 . T TGAA . PASS VC=INDEL;AC=39;AF=0.12;AN=312;refseq.name=NM_015590;refseq.positionType=promoter GT 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 156859572 . C CCT . PASS VC=INDEL;AC=219;AF=0.73;AN=300 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 ./. 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 ./. 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 ./. 0/0 ./. 0/1 0/0 0/0 0/0 ./. ./. 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 chr1 156910892 . GCTCGTCTT G . PASS VC=INDEL;AC=39;AF=0.14;AN=270;refseq.name=NM_014784;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/1 0/0 ./. ./. 0/0 0/1 ./. ./. 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. ./. ./. 0/0 0/1 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 ./. ./. 0/0 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/1 ./. ./. 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 chr1 157531425 . CA C . PASS VC=INDEL;AC=16;AF=0.06;AN=260 GT 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 ./. 0/0 ./. 0/0 0/0 ./. ./. 0/1 ./. ./. 0/1 ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/1 ./. 0/0 0/1 ./. 0/1 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 chr1 157807166 . TGTTA T . PASS VC=INDEL;AC=250;AF=0.81;AN=310;refseq.name=NM_005894;refseq.positionType=intron GT 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 chr1 157818429 . AC A . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 157924621 . ATAAG A . PASS VC=INDEL;AC=24;AF=0.08;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 157932325 . T TT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 158154060 . CT C . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_001766;refseq.positionType=exon GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 158684734 . CA C . PASS VC=INDEL;AC=90;AF=0.28;AN=316 GT 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 chr1 158886780 . A AAGAT . PASS VC=INDEL;AC=241;AF=0.76;AN=316 GT 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 chr1 158886783 . A ATAGA . PASS VC=INDEL;AC=240;AF=0.76;AN=314 GT 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 ./. 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 chr1 158984187 . G GAGGC . PASS VC=INDEL;AC=26;AF=0.13;AN=198;refseq.name=NM_005531;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 1/1 1/1 ./. ./. 0/0 0/0 0/0 1/1 0/0 1/1 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 ./. ./. ./. 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 1/1 ./. ./. 0/0 ./. 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 ./. ./. 0/0 ./. ./. ./. 0/0 ./. ./. ./. 1/1 1/1 1/1 ./. 1/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 1/1 1/1 ./. 0/0 ./. 0/0 ./. ./. 0/0 ./. ./. ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. ./. ./. ./. 1/1 1/1 chr1 158984259 . AATT A . PASS VC=INDEL;AC=130;AF=0.49;AN=266;refseq.name=NM_005531;refseq.positionType=intron GT ./. 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 ./. 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 ./. 1/1 1/1 0/1 ./. 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/0 ./. 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 ./. 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 ./. 0/1 ./. 1/1 0/0 0/1 0/1 1/1 0/1 ./. ./. 0/0 0/0 ./. 0/1 1/1 0/1 0/1 1/1 ./. ./. 0/0 0/1 0/0 0/1 1/1 ./. 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 ./. 0/0 0/1 0/0 ./. 0/0 0/1 0/1 ./. 0/1 0/1 ./. ./. ./. ./. ./. 0/1 0/1 1/1 0/1 0/1 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 chr1 159500234 . CT C . PASS VC=INDEL;AC=19;AF=0.06;AN=316 GT 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 159741079 . TGT T . PASS VC=INDEL;AC=163;AF=0.52;AN=314 GT 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 ./. 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 1/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 chr1 160004099 . GATGTAGATAG G . PASS VC=INDEL;AC=3;AF=0.01;AN=314;refseq.name=NM_145167;refseq.positionType=promoter GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 160081222 . TGAAAAG T . PASS VC=INDEL;AC=5;AF=0.02;AN=312 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 160430789 . C CAG . PASS VC=INDEL;AC=51;AF=0.16;AN=314 GT 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 chr1 160464965 . AGTGAATTTTAGA A . PASS VC=INDEL;AC=12;AF=0.06;AN=214;refseq.name=NM_052931;refseq.positionType=intron GT ./. 0/0 0/0 ./. ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 ./. ./. 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/1 ./. 0/0 0/0 ./. 0/1 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 ./. ./. 0/0 ./. ./. 0/0 0/0 ./. ./. ./. ./. 0/1 0/1 0/1 ./. ./. 0/1 ./. 0/0 0/0 ./. ./. ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/1 ./. 0/1 ./. 0/1 chr1 160578541 . C CA . PASS VC=INDEL;AC=277;AF=0.88;AN=316 GT 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 161765879 . T TCTT . PASS VC=INDEL;AC=77;AF=0.25;AN=310;refseq.name=NM_007348;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 ./. 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 ./. 0/1 0/1 1/1 0/1 0/0 0/0 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 chr1 161826110 . TT T . PASS VC=INDEL;AC=0;AF=0;AN=308;refseq.name=NM_007348;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 162354200 . AACAC A . PASS VC=INDEL;AC=32;AF=0.12;AN=262;refseq.name=NM_001085375;refseq.positionType=exon GT 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 1/1 0/0 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 ./. 0/0 0/0 ./. 0/1 ./. 0/0 ./. ./. 0/0 0/1 ./. ./. ./. ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 1/1 chr1 162629796 . C CGTT . PASS VC=INDEL;AC=238;AF=0.75;AN=316;refseq.name=NM_001014796;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 163132415 . TCCTGAACA T . PASS VC=INDEL;AC=7;AF=0.02;AN=314;refseq.name=NM_003617;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 163135904 . C CAGA . PASS VC=INDEL;AC=217;AF=0.84;AN=258;refseq.name=NM_003617;refseq.positionType=intron GT 1/1 1/1 1/1 ./. 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 ./. 0/1 0/0 ./. 0/1 0/0 ./. 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 ./. 1/1 0/1 ./. 0/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. ./. ./. 1/1 1/1 0/1 1/1 0/1 1/1 ./. ./. 0/1 ./. 0/1 ./. 0/1 ./. 1/1 1/1 1/1 0/1 ./. ./. 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 ./. 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 ./. 1/1 chr1 163136054 . T TTC . PASS VC=INDEL;AC=266;AF=0.84;AN=316;refseq.name=NM_003617;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 chr1 163136055 . T TCT . PASS VC=INDEL;AC=265;AF=0.84;AN=314;refseq.name=NM_003617;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 chr1 164351168 . ATTG A . PASS VC=INDEL;AC=261;AF=0.83;AN=316 GT 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 chr1 164448310 . AAAC A . PASS VC=INDEL;AC=236;AF=0.75;AN=316 GT 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr1 164548574 . TT T . PASS VC=INDEL;AC=11;AF=0.04;AN=308;refseq.name=NM_002585;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 chr1 164790567 . C CT . PASS VC=INDEL;AC=164;AF=0.52;AN=314;refseq.name=NM_002585;refseq.positionType=intron GT 1/1 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/0 chr1 165207456 . TAGA T . PASS VC=INDEL;AC=17;AF=0.05;AN=316;refseq.name=NM_177398;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 165218477 . AGAGATTACTCTG A . PASS VC=INDEL;AC=79;AF=0.28;AN=280;refseq.name=NM_177398;refseq.positionType=intron GT 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 ./. 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 1/1 0/1 0/0 0/0 1/1 ./. 1/1 1/1 0/0 0/1 ./. ./. 1/1 0/0 1/1 0/1 0/1 ./. 0/1 1/1 1/1 ./. 0/1 0/1 1/1 ./. 0/0 0/1 ./. 0/1 1/1 0/1 1/1 1/1 ./. 1/1 ./. 0/1 1/1 0/1 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/1 0/1 0/1 0/1 chr1 165261980 . TA T . PASS VC=INDEL;AC=129;AF=0.42;AN=308;refseq.name=NM_177398;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 ./. 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 ./. 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 ./. 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 ./. 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 chr1 165286489 . AA A . PASS VC=INDEL;AC=23;AF=0.07;AN=314;refseq.name=NM_177398;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 165349359 . G GT . PASS VC=INDEL;AC=130;AF=0.42;AN=306 GT 0/1 ./. 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 ./. 0/1 0/1 chr1 165475542 . CT C . PASS VC=INDEL;AC=157;AF=0.5;AN=316 GT 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/0 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 chr1 165627134 . AT A . PASS VC=INDEL;AC=144;AF=0.46;AN=314 GT 0/0 1/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 ./. 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 chr1 165652540 . GTTAA G . PASS VC=INDEL;AC=202;AF=0.66;AN=304;refseq.name=NM_000696;refseq.positionType=intron GT 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 ./. ./. 1/1 0/1 1/1 0/0 ./. 0/1 0/0 0/1 0/0 0/1 ./. 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/0 0/0 0/0 ./. 1/1 chr1 165685796 . GGCACAGAT G . PASS VC=INDEL;AC=155;AF=0.49;AN=314 GT 0/0 0/1 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 ./. 0/1 1/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 chr1 165686450 . TAGG T . PASS VC=INDEL;AC=144;AF=0.46;AN=316 GT 0/1 0/1 1/1 0/1 0/0 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 chr1 165686452 . GGAG G . PASS VC=INDEL;AC=145;AF=0.46;AN=316 GT 1/1 0/1 1/1 0/1 0/0 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 chr1 166083223 . CCAC C . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_001017961;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 166602705 . TTGT T . PASS VC=INDEL;AC=73;AF=0.23;AN=316 GT 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 chr1 166639248 . A AAT . PASS VC=INDEL;AC=289;AF=0.91;AN=316 GT 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 chr1 166708316 . G GTAG . PASS VC=INDEL;AC=102;AF=0.32;AN=316 GT 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 chr1 167512714 . TTCCAAAACCGA T . PASS VC=INDEL;AC=7;AF=0.02;AN=316;refseq.name=NM_003851;refseq.positionType=intron GT 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 167513042 . CA C . PASS VC=INDEL;AC=7;AF=0.02;AN=316;refseq.name=NM_003851;refseq.positionType=intron GT 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 167516739 . T TAA . PASS VC=INDEL;AC=1;AF=0;AN=316;refseq.name=NM_003851;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 167675717 . T TTC . PASS VC=INDEL;AC=22;AF=0.07;AN=296;refseq.name=NM_052862;refseq.positionType=terminator GT 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 ./. 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 167682039 . CCAAA C . PASS VC=INDEL;AC=68;AF=0.22;AN=316 GT 0/0 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 chr1 167682041 . AAACA A . PASS VC=INDEL;AC=68;AF=0.22;AN=316 GT 0/0 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 chr1 167697899 . GTG G . PASS VC=INDEL;AC=50;AF=0.16;AN=316;refseq.name=NM_003953;refseq.positionType=intron GT 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 chr1 167985326 . TG T . PASS VC=INDEL;AC=144;AF=0.49;AN=294;refseq.name=NM_001017977;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 ./. 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/0 1/1 1/1 ./. 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 1/1 1/1 1/1 0/0 1/1 0/1 1/1 ./. ./. 1/1 0/1 0/1 1/1 0/1 ./. 0/1 0/1 0/0 1/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 ./. 1/1 ./. 0/1 1/1 0/1 0/0 ./. 0/1 0/0 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 ./. 0/1 1/1 0/1 chr1 168053859 . ACTCA A . PASS VC=INDEL;AC=11;AF=0.03;AN=316;refseq.name=NM_153832;refseq.positionType=terminator GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 chr1 168133510 . CCTAAC C . PASS VC=INDEL;AC=96;AF=0.3;AN=316 GT 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 chr1 168200152 . GT G . PASS VC=INDEL;AC=135;AF=0.43;AN=316;refseq.name=NM_199344;refseq.positionType=intron GT 1/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 chr1 168423776 . AGC A . PASS VC=INDEL;AC=4;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 169066627 . T TC . PASS VC=INDEL;AC=301;AF=0.95;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 chr1 169066629 . C CC . PASS VC=INDEL;AC=301;AF=0.95;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 chr1 169095586 . T TAT . PASS VC=INDEL;AC=165;AF=0.52;AN=316;refseq.name=NM_001001787;refseq.positionType=intron GT 0/0 1/1 1/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 chr1 169214437 . CA C . PASS VC=INDEL;AC=10;AF=0.03;AN=316;refseq.name=NM_013330;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 169875635 . AG A . PASS VC=INDEL;AC=2;AF=0.01;AN=314 GT 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 170054566 . CAAAT C . PASS VC=INDEL;AC=2;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 170213713 . C CA . PASS VC=INDEL;AC=302;AF=0.96;AN=314 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 chr1 170231599 . C CA . PASS VC=INDEL;AC=178;AF=0.57;AN=314 GT 0/1 0/1 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/1 0/0 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 chr1 170412385 . A AA . PASS VC=INDEL;AC=247;AF=0.79;AN=312 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 ./. 0/0 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 chr1 171564547 . T TT . PASS VC=INDEL;AC=141;AF=0.68;AN=206 GT 1/1 1/1 1/1 ./. 0/1 ./. 1/1 0/1 ./. 0/1 ./. ./. ./. 1/1 1/1 ./. 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 ./. 1/1 ./. 1/1 1/1 ./. ./. ./. 0/1 0/1 ./. ./. ./. 0/1 0/1 ./. 1/1 0/1 ./. 0/1 1/1 ./. 1/1 ./. ./. 0/1 ./. 0/1 ./. ./. ./. ./. 0/1 ./. 1/1 ./. 0/1 1/1 0/1 0/1 1/1 1/1 0/0 ./. ./. ./. ./. ./. 0/1 0/1 1/1 0/1 ./. 0/1 1/1 ./. 0/1 0/1 0/1 ./. 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 ./. 0/0 0/1 ./. 0/1 0/1 1/1 ./. 1/1 1/1 ./. 0/1 1/1 0/1 0/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 ./. ./. ./. ./. 1/1 ./. ./. 0/1 1/1 1/1 ./. 0/1 1/1 ./. ./. 0/1 ./. ./. 0/1 ./. 0/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 0/1 chr1 171668398 . C CATC . PASS VC=INDEL;AC=42;AF=0.13;AN=316 GT 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 171779854 . AAAG A . PASS VC=INDEL;AC=128;AF=0.46;AN=278 GT 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/1 1/1 0/1 ./. 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 ./. 0/1 0/1 ./. ./. ./. 1/1 0/1 ./. 0/1 1/1 0/1 0/1 1/1 0/1 ./. 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 ./. 0/0 0/1 1/1 0/1 1/1 1/1 ./. 1/1 0/1 0/1 1/1 ./. 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 ./. 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/1 ./. 1/1 ./. 0/1 0/1 0/1 0/0 1/1 0/1 ./. 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/1 ./. 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 ./. 0/1 0/1 chr1 171799766 . A ACT . PASS VC=INDEL;AC=48;AF=0.18;AN=268 GT 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/1 ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 ./. 0/1 0/1 0/1 0/1 0/0 0/1 0/0 ./. 0/1 ./. 0/0 0/1 ./. 0/1 0/1 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/0 0/0 ./. 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 ./. 0/0 0/0 0/0 ./. 0/1 ./. 0/1 0/1 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/1 0/0 0/0 chr1 171806532 . C CAT . PASS VC=INDEL;AC=14;AF=0.05;AN=308 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 172312482 . AAG A . PASS VC=INDEL;AC=5;AF=0.02;AN=316;refseq.name=NM_015569;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 172415351 . GA G . PASS VC=INDEL;AC=75;AF=0.24;AN=316;refseq.name=NM_139240;refseq.positionType=intron GT 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 chr1 172620138 . A ACT . PASS VC=INDEL;AC=134;AF=0.42;AN=316 GT 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 chr1 172620139 . C CTC . PASS VC=INDEL;AC=134;AF=0.43;AN=314 GT 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 ./. 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 chr1 173063473 . A ATGTC . PASS VC=INDEL;AC=124;AF=0.62;AN=200 GT 0/0 0/1 0/1 ./. 0/1 ./. ./. 1/1 0/1 0/0 0/1 ./. 0/1 1/1 ./. ./. 0/0 0/1 0/1 ./. 1/1 1/1 0/1 1/1 0/0 1/1 0/0 1/1 ./. 1/1 0/0 1/1 1/1 ./. ./. ./. ./. ./. ./. 1/1 ./. 0/1 ./. 1/1 0/1 1/1 ./. 1/1 ./. 0/1 ./. 0/1 1/1 ./. 1/1 0/1 ./. 0/1 0/1 ./. ./. 0/1 0/1 ./. ./. 0/1 ./. 0/1 ./. ./. 0/1 ./. 1/1 0/1 ./. 1/1 ./. ./. 0/1 ./. 1/1 1/1 ./. 1/1 0/1 ./. ./. 0/0 ./. 0/1 1/1 1/1 ./. 1/1 1/1 0/0 ./. ./. 0/1 0/0 ./. ./. 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 0/1 0/1 ./. ./. 0/1 0/1 0/1 0/0 ./. ./. 0/0 1/1 1/1 1/1 0/0 0/0 ./. 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 ./. ./. 1/1 0/0 ./. 0/1 ./. ./. 1/1 0/0 ./. ./. ./. 1/1 0/1 ./. 0/1 1/1 ./. chr1 173541560 . CAA C . PASS VC=INDEL;AC=233;AF=0.74;AN=316;refseq.name=NM_178527;refseq.positionType=intron GT 0/0 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/0 chr1 173749093 . T TC . PASS VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_014458;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 173755936 . T TGAAG . PASS VC=INDEL;AC=182;AF=0.58;AN=316;refseq.name=NM_014458;refseq.positionType=terminator GT 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 chr1 173870326 . ACTA A . PASS VC=INDEL;AC=235;AF=0.74;AN=316 GT 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 chr1 174411392 . T TTGTAT . PASS VC=INDEL;AC=251;AF=0.8;AN=314;refseq.name=NM_014857;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 chr1 174524160 . T TAT . PASS VC=INDEL;AC=212;AF=0.67;AN=316;refseq.name=NM_014857;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 chr1 175131961 . GA G . PASS VC=INDEL;AC=85;AF=0.28;AN=306 GT 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 ./. 1/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 ./. 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 ./. 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 ./. 0/1 0/1 1/1 ./. 0/1 0/0 0/1 chr1 175299777 . CAT C . PASS VC=INDEL;AC=18;AF=0.06;AN=316;refseq.name=NM_003285;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 chr1 175355790 . GG G . PASS VC=INDEL;AC=199;AF=0.74;AN=270;refseq.name=NM_003285;refseq.positionType=intron GT 1/1 0/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 ./. 0/1 0/1 1/1 0/1 0/1 0/1 ./. ./. 1/1 0/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 0/0 ./. 0/1 0/0 0/0 0/0 ./. ./. 1/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 0/1 1/1 1/1 0/1 ./. 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 ./. 1/1 ./. ./. 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 1/1 1/1 0/1 1/1 ./. ./. 0/0 0/1 ./. 0/1 chr1 175418807 . A AACA . PASS VC=INDEL;AC=118;AF=0.37;AN=316;refseq.name=NM_003285;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 chr1 175420618 . A AG . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_003285;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 175443036 . AGGAGA A . PASS VC=INDEL;AC=1;AF=0;AN=316;refseq.name=NM_003285;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 175472120 . C CTAATCAGGATCTTGACATGTGACACAAGATCCTTGAG . PASS VC=INDEL;AC=14;AF=0.04;AN=316;refseq.name=NM_003285;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 175584762 . CT C . PASS VC=INDEL;AC=45;AF=0.14;AN=314;refseq.name=NM_003285;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 chr1 177236388 . C CG . PASS VC=INDEL;AC=167;AF=0.54;AN=312;refseq.name=NM_021165;refseq.positionType=intron GT 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 ./. 0/1 ./. 0/0 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 chr1 177236389 . G GG . PASS VC=INDEL;AC=166;AF=0.53;AN=316;refseq.name=NM_021165;refseq.positionType=intron GT 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 chr1 177558539 . G GAGA . PASS VC=INDEL;AC=7;AF=0.02;AN=290 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 177558541 . G GAAG . PASS VC=INDEL;AC=10;AF=0.03;AN=296 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 178521563 . TAAGAC T . PASS VC=INDEL;AC=21;AF=0.09;AN=246 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/1 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 ./. 1/1 1/1 ./. ./. 0/0 ./. 0/0 ./. ./. ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/0 0/1 ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/0 ./. ./. ./. 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 1/1 0/0 1/1 0/1 0/0 0/0 chr1 179038241 . GT G . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_014864;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 179293907 . CAA C . PASS VC=INDEL;AC=34;AF=0.11;AN=314;refseq.name=NM_003101;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 chr1 179724329 . G GG . PASS VC=INDEL;AC=307;AF=0.97;AN=316;refseq.name=NM_173509;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 179762445 . GT G . PASS VC=INDEL;AC=85;AF=0.27;AN=316;refseq.name=NM_173509;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 chr1 179762446 . TT T . PASS VC=INDEL;AC=85;AF=0.27;AN=316;refseq.name=NM_173509;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 chr1 179773170 . CTTGTC C . PASS VC=INDEL;AC=77;AF=0.28;AN=274;refseq.name=NM_173509;refseq.positionType=intron GT 1/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 ./. 0/0 0/0 0/0 ./. 0/0 1/1 0/0 1/1 0/0 0/0 1/1 0/0 1/1 0/0 0/1 ./. 0/1 0/0 0/1 0/0 1/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 ./. 1/1 ./. ./. ./. 0/0 0/0 ./. 0/0 0/1 0/1 0/1 ./. 0/1 1/1 1/1 0/0 ./. 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 ./. 0/1 0/1 0/0 0/1 0/1 ./. 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 ./. 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 1/1 0/1 chr1 180108217 . T TTATC . PASS VC=INDEL;AC=229;AF=0.72;AN=316 GT 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 chr1 180722815 . TACTC T . PASS VC=INDEL;AC=4;AF=0.01;AN=316;refseq.name=NM_004736;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 180722816 . ACTCA A . PASS VC=INDEL;AC=5;AF=0.02;AN=316;refseq.name=NM_004736;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 180762626 . CAT C . PASS VC=INDEL;AC=12;AF=0.04;AN=296;refseq.name=NM_004736;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 chr1 180866670 . CCC C . PASS VC=INDEL;AC=73;AF=0.29;AN=256 GT 0/0 0/1 0/1 0/0 ./. 0/0 ./. 0/1 ./. 0/0 ./. 0/1 ./. 0/1 0/0 0/0 0/0 0/1 0/0 0/0 ./. ./. 0/0 ./. 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 1/1 ./. 0/1 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 ./. 0/1 0/1 0/0 0/1 ./. 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/1 ./. 0/1 ./. 0/1 ./. ./. 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/0 ./. ./. ./. 0/1 0/1 0/1 0/1 chr1 180974402 . A AA . PASS VC=INDEL;AC=0;AF=0;AN=298;refseq.name=NM_005819;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 chr1 181233905 . AA A . PASS VC=INDEL;AC=1;AF=0;AN=266 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 ./. ./. ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 chr1 181456872 . CC C . PASS VC=INDEL;AC=2;AF=0.01;AN=300;refseq.name=NM_000721;refseq.positionType=intron GT ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 181610646 . CT C . PASS VC=INDEL;AC=58;AF=0.18;AN=314;refseq.name=NM_000721;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 chr1 182087446 . G GTCT . PASS VC=INDEL;AC=198;AF=0.68;AN=292 GT 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 ./. 1/1 0/1 0/1 0/1 ./. 0/1 ./. ./. 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 ./. 1/1 0/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 0/1 0/1 ./. 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 ./. 0/1 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 1/1 0/1 0/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 ./. 1/1 0/1 1/1 0/0 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 chr1 182739634 . TAAGA T . PASS VC=INDEL;AC=65;AF=0.21;AN=316 GT 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 chr1 182951675 . AGA A . PASS VC=INDEL;AC=78;AF=0.25;AN=316 GT 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/0 chr1 183032447 . C CTAAG . PASS VC=INDEL;AC=125;AF=0.4;AN=316;refseq.name=NM_002293;refseq.positionType=intron GT 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 chr1 183073109 . T TTG . PASS VC=INDEL;AC=125;AF=0.4;AN=316;refseq.name=NM_002293;refseq.positionType=intron GT 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 chr1 183073111 . G GTG . PASS VC=INDEL;AC=125;AF=0.4;AN=316;refseq.name=NM_002293;refseq.positionType=intron GT 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 chr1 183077296 . A AG . PASS VC=INDEL;AC=126;AF=0.4;AN=316;refseq.name=NM_002293;refseq.positionType=intron GT 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 chr1 183097956 . G GTTA . PASS VC=INDEL;AC=127;AF=0.4;AN=314;refseq.name=NM_002293;refseq.positionType=intron GT 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 chr1 183145207 . G GTAG . PASS VC=INDEL;AC=35;AF=0.11;AN=312 GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 chr1 183180446 . GG G . PASS VC=INDEL;AC=54;AF=0.17;AN=316;refseq.name=NM_005562;refseq.positionType=intron GT 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 183330737 . TAA T . PASS VC=INDEL;AC=197;AF=0.63;AN=312;refseq.name=NM_015039;refseq.positionType=intron GT 0/1 1/1 1/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 ./. 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 ./. 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 1/1 chr1 183589923 . A ATCTT . PASS VC=INDEL;AC=117;AF=0.37;AN=314 GT 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 1/1 0/1 0/1 ./. 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/0 chr1 183712910 . AC A . PASS VC=INDEL;AC=131;AF=0.42;AN=312;refseq.name=NM_015149;refseq.positionType=intron GT 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 chr1 183806728 . T TG . PASS VC=INDEL;AC=229;AF=0.85;AN=270;refseq.name=NM_015149;refseq.positionType=intron GT 1/1 ./. 1/1 ./. ./. 0/1 0/1 ./. 1/1 1/1 0/1 1/1 0/1 ./. 1/1 0/1 1/1 1/1 0/1 ./. 0/1 1/1 1/1 0/1 1/1 1/1 ./. ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 ./. 0/1 ./. ./. 0/0 ./. 1/1 1/1 0/0 1/1 ./. 1/1 0/0 1/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 ./. 0/1 1/1 1/1 1/1 0/0 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 ./. 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 183996005 . C CTATTA . PASS VC=INDEL;AC=27;AF=0.09;AN=316;refseq.name=NM_015101;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 184391018 . C CTA . PASS VC=INDEL;AC=68;AF=0.22;AN=312;refseq.name=NM_030806;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 ./. 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 chr1 184561827 . CAGA C . PASS VC=INDEL;AC=47;AF=0.15;AN=316;refseq.name=NM_030806;refseq.positionType=intron GT 0/0 0/1 1/1 0/0 1/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 184577643 . T TC . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_030806;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 185540897 . T TCCAG . PASS VC=INDEL;AC=136;AF=0.48;AN=286 GT 0/0 0/1 0/0 0/1 0/0 ./. 0/1 0/1 0/1 0/1 0/0 0/1 ./. 1/1 ./. 0/1 0/1 0/1 0/0 0/1 ./. 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 ./. 0/0 0/1 0/0 ./. 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/1 ./. 0/0 0/0 0/1 0/1 1/1 1/1 0/1 ./. 0/1 1/1 1/1 1/1 ./. 0/1 1/1 ./. 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 ./. 0/0 0/0 ./. 0/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 chr1 185865550 . C CAT . PASS VC=INDEL;AC=53;AF=0.17;AN=310;refseq.name=NM_031935;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 chr1 186378142 . CAGTT C . PASS VC=INDEL;AC=55;AF=0.21;AN=266;refseq.name=NM_017847;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/1 0/0 ./. 0/1 1/1 0/1 ./. 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/1 ./. 0/0 0/0 0/0 1/1 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/0 1/1 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 ./. ./. 0/0 0/0 0/1 0/1 0/0 1/1 ./. 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 ./. ./. 0/0 0/1 ./. ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 ./. 0/1 0/0 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 chr1 186769215 . T TA . PASS VC=INDEL;AC=45;AF=0.14;AN=316 GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 186933480 . T TTAAT . PASS VC=INDEL;AC=135;AF=0.43;AN=316;refseq.name=NM_024420;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 chr1 187372829 . AGGCTT A . PASS VC=INDEL;AC=34;AF=0.11;AN=304 GT ./. 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 chr1 187372830 . GGCTTG G . PASS VC=INDEL;AC=32;AF=0.1;AN=306 GT 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 chr1 187685847 . CAATT C . PASS VC=INDEL;AC=112;AF=0.36;AN=314 GT 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 ./. 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 chr1 187781028 . C CT . PASS VC=INDEL;AC=278;AF=0.9;AN=310 GT 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 chr1 187815820 . A ACAA . PASS VC=INDEL;AC=21;AF=0.07;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr1 187899550 . AAA A . PASS VC=INDEL;AC=65;AF=0.21;AN=314 GT 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 chr1 188075358 . GTAAG G . PASS VC=INDEL;AC=63;AF=0.2;AN=316 GT 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 chr1 188110355 . C CT . PASS VC=INDEL;AC=222;AF=0.71;AN=312 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 ./. 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 ./. 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 chr1 188372559 . CAAG C . PASS VC=INDEL;AC=230;AF=0.73;AN=314 GT 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 ./. 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 188397016 . C CA . PASS VC=INDEL;AC=9;AF=0.03;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr1 188526820 . C CT . PASS VC=INDEL;AC=262;AF=0.91;AN=288 GT 1/1 1/1 1/1 1/1 ./. 0/1 ./. 1/1 0/1 1/1 ./. 1/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 ./. 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 188533586 . G GTTCT . PASS VC=INDEL;AC=290;AF=0.92;AN=316 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 188628449 . CAACT C . PASS VC=INDEL;AC=100;AF=0.32;AN=314 GT 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 chr1 189027168 . C CTG . PASS VC=INDEL;AC=146;AF=0.69;AN=212 GT 1/1 ./. ./. ./. ./. ./. 0/1 1/1 0/1 0/1 ./. 0/1 ./. 0/1 ./. 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. ./. ./. 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 1/1 ./. ./. 1/1 ./. 1/1 1/1 0/0 1/1 0/0 ./. 1/1 1/1 1/1 1/1 0/1 1/1 0/1 ./. 0/1 1/1 1/1 0/1 0/1 0/1 ./. ./. 1/1 1/1 1/1 0/1 0/1 0/0 ./. 0/1 0/1 ./. ./. 0/1 ./. 1/1 ./. ./. ./. 0/1 0/1 0/1 ./. 1/1 0/1 ./. 0/1 0/1 0/0 0/1 ./. 0/1 ./. 1/1 ./. 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 1/1 1/1 0/1 ./. ./. 1/1 ./. ./. 1/1 0/1 0/0 1/1 0/1 0/1 0/1 ./. ./. ./. ./. ./. 1/1 0/1 ./. ./. ./. ./. 1/1 1/1 ./. ./. 1/1 1/1 1/1 ./. ./. 1/1 ./. ./. ./. chr1 189046798 . C CA . PASS VC=INDEL;AC=86;AF=0.27;AN=316 GT 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 chr1 189087000 . TTA T . PASS VC=INDEL;AC=159;AF=0.53;AN=302 GT 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 ./. 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 ./. 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 ./. 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 ./. 0/0 0/1 ./. 0/0 0/1 1/1 chr1 189190273 . AT A . PASS VC=INDEL;AC=2;AF=0.01;AN=316 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 189547870 . A AAT . PASS VC=INDEL;AC=194;AF=0.79;AN=246 GT 0/1 ./. ./. 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/0 1/1 ./. 0/1 0/1 0/1 1/1 1/1 0/1 ./. ./. 0/1 ./. 0/0 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. ./. 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 ./. ./. ./. 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 ./. 0/1 ./. ./. 0/1 1/1 0/0 ./. 1/1 1/1 ./. ./. ./. 0/0 1/1 ./. ./. 1/1 ./. 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 ./. 0/0 1/1 ./. 0/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 ./. ./. 0/1 ./. 1/1 0/1 1/1 ./. 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 ./. ./. 0/1 1/1 1/1 ./. 0/1 1/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 chr1 189629285 . A ATAACT . PASS VC=INDEL;AC=158;AF=0.59;AN=266 GT 0/1 1/1 0/0 1/1 ./. 0/1 1/1 0/1 0/0 0/0 1/1 0/1 ./. 1/1 ./. 0/1 ./. 0/1 0/1 1/1 0/1 ./. ./. 0/1 0/0 ./. 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 ./. 0/0 0/0 1/1 0/1 ./. 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 ./. 1/1 0/1 0/1 0/0 0/1 ./. 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 ./. ./. 0/1 1/1 1/1 1/1 0/1 ./. 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/1 ./. 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 ./. ./. 0/0 ./. 0/1 ./. 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/0 0/1 1/1 ./. ./. 1/1 1/1 1/1 ./. 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 ./. 0/1 0/1 1/1 1/1 1/1 0/1 0/1 chr1 189867802 . G GC . PASS VC=INDEL;AC=23;AF=0.07;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 chr1 190095126 . CTAACA C . PASS VC=INDEL;AC=143;AF=0.45;AN=316;refseq.name=NM_199051;refseq.positionType=intron GT 0/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 chr1 190095129 . ACATAA A . PASS VC=INDEL;AC=143;AF=0.45;AN=316;refseq.name=NM_199051;refseq.positionType=intron GT 0/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 chr1 190636901 . C CTAA . PASS VC=INDEL;AC=131;AF=0.42;AN=314 GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 chr1 190886420 . AA A . PASS VC=INDEL;AC=76;AF=0.26;AN=292 GT 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 ./. 0/0 0/0 0/1 0/1 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 chr1 191196527 . A AAT . PASS VC=INDEL;AC=191;AF=0.6;AN=316 GT 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 chr1 191340485 . TTAGA T . PASS VC=INDEL;AC=175;AF=0.59;AN=296 GT 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 ./. 0/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 ./. 0/0 ./. 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 ./. 0/1 ./. ./. 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 ./. 0/1 0/0 0/1 0/1 0/1 ./. 0/1 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/1 1/1 0/1 chr1 191464816 . A ATTA . PASS VC=INDEL;AC=213;AF=0.7;AN=306 GT 0/0 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 1/1 0/0 1/1 ./. 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 ./. 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 chr1 191588586 . C CA . PASS VC=INDEL;AC=190;AF=0.61;AN=310 GT 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 ./. 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 1/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/0 ./. 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 chr1 191588587 . A AA . PASS VC=INDEL;AC=186;AF=0.61;AN=304 GT 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 1/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 ./. 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/0 ./. 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 chr1 191752595 . T TCTTT . PASS VC=INDEL;AC=132;AF=0.42;AN=316 GT 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/0 0/0 chr1 192047581 . TT T . PASS VC=INDEL;AC=1;AF=0;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 192460381 . T TT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 192612585 . T TCA . PASS VC=INDEL;AC=80;AF=0.25;AN=316;refseq.name=NM_002927;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 chr1 192726770 . C CT . PASS VC=INDEL;AC=121;AF=0.39;AN=314 GT 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 chr1 193118950 . AGACT A . PASS VC=INDEL;AC=7;AF=0.02;AN=316;refseq.name=NM_024529;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 193158515 . CTG C . PASS VC=INDEL;AC=7;AF=0.02;AN=316;refseq.name=NM_003783;refseq.positionType=promoter GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 193261423 . AAAGTA A . PASS VC=INDEL;AC=7;AF=0.02;AN=316 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 193421510 . A ATCT . PASS VC=INDEL;AC=102;AF=0.33;AN=310 GT 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 1/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 ./. 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 chr1 193482947 . CAA C . PASS VC=INDEL;AC=71;AF=0.22;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 chr1 193569090 . C CG . PASS VC=INDEL;AC=85;AF=0.27;AN=312 GT 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 ./. 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 chr1 193877310 . GG G . PASS VC=INDEL;AC=106;AF=0.34;AN=316 GT 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 193881567 . T TT . PASS VC=INDEL;AC=4;AF=0.01;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 194004698 . TCTT T . PASS VC=INDEL;AC=34;AF=0.11;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 chr1 194047765 . TAT T . PASS VC=INDEL;AC=48;AF=0.2;AN=238 GT ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 ./. 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 ./. 0/1 0/0 0/1 0/0 0/1 ./. 0/0 0/1 0/1 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/1 0/1 0/0 0/1 ./. ./. 0/0 ./. ./. 0/1 0/1 0/0 0/0 ./. ./. ./. 0/0 0/0 0/1 0/0 ./. 0/1 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. ./. ./. 0/0 ./. 0/0 0/1 0/0 0/1 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 ./. ./. 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 ./. 0/1 ./. 1/1 0/1 ./. 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/1 chr1 194160203 . TTAGT T . PASS VC=INDEL;AC=25;AF=0.12;AN=206 GT 0/1 0/0 0/1 0/0 ./. 0/1 0/0 ./. ./. ./. 0/1 ./. 0/0 ./. 0/1 ./. 0/0 0/1 0/1 0/1 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 ./. ./. 0/1 0/0 ./. ./. ./. 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 ./. 0/0 0/0 ./. ./. 0/0 ./. 0/0 ./. ./. ./. ./. 0/1 ./. 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/1 ./. 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/1 ./. ./. 0/0 ./. 0/0 0/0 ./. ./. 0/1 ./. ./. 0/1 0/1 ./. 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/1 chr1 194193740 . A AG . PASS VC=INDEL;AC=316;AF=1;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 194339262 . ATGT A . PASS VC=INDEL;AC=67;AF=0.21;AN=316 GT 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 chr1 194487871 . C CCTAT . PASS VC=INDEL;AC=302;AF=0.97;AN=312 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 194520551 . GG G . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 194563981 . TAAT T . PASS VC=INDEL;AC=169;AF=0.53;AN=316 GT 1/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 chr1 194738670 . T TTT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 194763917 . CATG C . PASS VC=INDEL;AC=267;AF=0.84;AN=316 GT 1/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 chr1 195047681 . GG G . PASS VC=INDEL;AC=29;AF=0.1;AN=278 GT 0/0 0/0 ./. 0/0 0/0 0/0 1/1 1/1 0/0 ./. 0/0 1/1 0/0 0/0 ./. 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 ./. ./. ./. 0/1 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/1 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 ./. 0/1 0/0 0/1 0/0 1/1 1/1 chr1 195637390 . TA T . PASS VC=INDEL;AC=90;AF=0.29;AN=314 GT 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 1/1 1/1 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 1/1 1/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 chr1 195637391 . AA A . PASS VC=INDEL;AC=89;AF=0.28;AN=316 GT 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 1/1 1/1 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 chr1 195877296 . T TAA . PASS VC=INDEL;AC=232;AF=0.73;AN=316 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 chr1 195877297 . A AAA . PASS VC=INDEL;AC=232;AF=0.73;AN=316 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 chr1 195934123 . CCTAT C . PASS VC=INDEL;AC=185;AF=0.59;AN=312 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 ./. 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 ./. 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 chr1 195934125 . TATCT T . PASS VC=INDEL;AC=184;AF=0.59;AN=312 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 ./. 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 ./. 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 chr1 196163677 . TT T . PASS VC=INDEL;AC=284;AF=0.9;AN=316 GT 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 chr1 196344374 . C CA . PASS VC=INDEL;AC=153;AF=0.53;AN=290;refseq.name=NM_198503;refseq.positionType=intron GT 0/0 0/0 0/0 ./. 0/0 ./. 0/0 1/1 1/1 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 ./. 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 ./. 0/1 0/1 0/1 0/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 ./. ./. 0/0 chr1 196448625 . ATG A . PASS VC=INDEL;AC=7;AF=0.03;AN=266;refseq.name=NM_198503;refseq.positionType=intron GT ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 chr1 196448626 . TGTA T . PASS VC=INDEL;AC=8;AF=0.03;AN=302;refseq.name=NM_198503;refseq.positionType=intron GT ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 chr1 197406760 . GAA G . PASS VC=INDEL;AC=78;AF=0.25;AN=312;refseq.name=NM_201253;refseq.positionType=intron GT 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 ./. 0/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 197613756 . ACCT A . PASS VC=INDEL;AC=25;AF=0.08;AN=316;refseq.name=NM_144977;refseq.positionType=intron GT 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 chr1 197690664 . T TG . PASS VC=INDEL;AC=291;AF=0.92;AN=316;refseq.name=NM_144977;refseq.positionType=intron GT 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 chr1 198792990 . T TG . PASS VC=INDEL;AC=131;AF=0.41;AN=316 GT 0/1 0/1 0/0 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 chr1 198940301 . C CCTT . PASS VC=INDEL;AC=258;AF=0.82;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/0 1/1 chr1 198940306 . T TTCT . PASS VC=INDEL;AC=258;AF=0.82;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/0 1/1 chr1 199277515 . AC A . PASS VC=INDEL;AC=36;AF=0.11;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 chr1 200575750 . AAATA A . PASS VC=INDEL;AC=97;AF=0.31;AN=314;refseq.name=NM_014875;refseq.positionType=intron GT 0/0 0/0 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 ./. 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 chr1 201173407 . AA A . PASS VC=INDEL;AC=56;AF=0.18;AN=314 GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/0 chr1 201288249 . TATC T . PASS VC=INDEL;AC=209;AF=0.66;AN=316;refseq.name=NM_000299;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/0 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 chr1 201457641 . AA A . PASS VC=INDEL;AC=55;AF=0.18;AN=310;refseq.name=NM_004078;refseq.positionType=intron GT 1/1 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 1/1 1/1 chr1 201587178 . CA C . PASS VC=INDEL;AC=145;AF=0.47;AN=310 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 ./. 0/1 1/1 ./. 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 chr1 201733889 . G GG . PASS VC=INDEL;AC=46;AF=0.15;AN=316;refseq.name=NM_020443;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 chr1 203792216 . AA A . PASS VC=INDEL;AC=265;AF=0.93;AN=286;refseq.name=NM_014827;refseq.positionType=intron GT 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 0/1 ./. 1/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 1/1 0/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 ./. ./. 1/1 chr1 203829389 . CTCAAC C . PASS VC=INDEL;AC=195;AF=0.62;AN=316;refseq.name=NM_003094;refseq.positionType=promoter GT 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 chr1 203848383 . C CTT . PASS VC=INDEL;AC=275;AF=0.87;AN=316 GT 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 chr1 203848384 . T TTT . PASS VC=INDEL;AC=275;AF=0.87;AN=316 GT 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 chr1 204049028 . T TG . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_005686;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 204452618 . T TGT . PASS VC=INDEL;AC=141;AF=0.47;AN=300;refseq.name=NM_002646;refseq.positionType=intron GT 1/1 0/0 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 ./. 0/0 0/0 0/1 1/1 0/1 0/1 0/1 ./. 1/1 0/1 0/1 1/1 1/1 ./. 1/1 0/1 0/0 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 ./. 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 ./. 1/1 0/1 0/0 0/1 0/0 1/1 1/1 chr1 205036040 . T TG . PASS VC=INDEL;AC=69;AF=0.23;AN=302;refseq.name=NM_005076;refseq.positionType=intron GT 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 ./. 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 ./. 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 ./. 0/0 0/0 0/1 0/1 0/1 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 chr1 205036041 . G GG . PASS VC=INDEL;AC=71;AF=0.23;AN=310;refseq.name=NM_005076;refseq.positionType=intron GT 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 ./. 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 chr1 206303222 . C CAGCCTAGCT . PASS VC=INDEL;AC=105;AF=0.33;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 chr1 206571046 . G GA . PASS VC=INDEL;AC=2;AF=0.01;AN=290;refseq.name=NM_015326;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 ./. chr1 206862605 . G GA . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_004759;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 206955760 . TGTAA T . PASS VC=INDEL;AC=95;AF=0.31;AN=310 GT 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/0 ./. 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 chr1 207260285 . T TCAATTCACAGGAGTATGTGA . PASS VC=INDEL;AC=197;AF=0.62;AN=316;refseq.name=NM_001017365;refseq.positionType=promoter GT 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 chr1 207277350 . CC C . PASS VC=INDEL;AC=201;AF=0.64;AN=316;refseq.name=NM_000715;refseq.positionType=promoter GT 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 chr1 207641329 . TTAAG T . PASS VC=INDEL;AC=13;AF=0.06;AN=216;refseq.name=NM_001006658;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. ./. ./. ./. ./. ./. 0/0 ./. 0/0 0/1 0/0 ./. 0/0 ./. ./. ./. ./. 0/0 ./. 0/1 ./. 0/0 0/0 ./. ./. ./. ./. 0/0 0/0 0/1 ./. ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 1/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 ./. chr1 207824638 . A AATTC . PASS VC=INDEL;AC=153;AF=0.48;AN=316;refseq.name=NM_175710;refseq.positionType=intron GT 0/0 0/1 0/0 1/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 chr1 208201207 . GT G . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_025179;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 208514674 . GTTAC G . PASS VC=INDEL;AC=165;AF=0.53;AN=314 GT 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 ./. 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 chr1 208514676 . TACTT T . PASS VC=INDEL;AC=166;AF=0.53;AN=314 GT 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 ./. 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 chr1 208609280 . GGAAG G . PASS VC=INDEL;AC=55;AF=0.21;AN=256 GT 0/0 ./. 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/1 0/1 1/1 0/1 ./. 0/1 ./. 1/1 0/1 ./. 0/1 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 ./. 1/1 0/0 1/1 0/1 ./. ./. 0/1 1/1 ./. ./. 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 ./. 0/0 0/1 0/0 ./. 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 chr1 208643013 . CA C . PASS VC=INDEL;AC=36;AF=0.12;AN=310 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 208643015 . AA A . PASS VC=INDEL;AC=39;AF=0.12;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 208763800 . C CA . PASS VC=INDEL;AC=175;AF=0.55;AN=316 GT 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 chr1 209124169 . T TA . PASS VC=INDEL;AC=226;AF=0.72;AN=316 GT 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 chr1 209124171 . A AA . PASS VC=INDEL;AC=226;AF=0.72;AN=316 GT 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 chr1 209639686 . A AG . PASS VC=INDEL;AC=203;AF=0.64;AN=316 GT 0/0 0/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/0 1/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 chr1 209662878 . T TG . PASS VC=INDEL;AC=205;AF=0.65;AN=316 GT 0/0 0/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 chr1 209936964 . T TCA . PASS VC=INDEL;AC=184;AF=0.58;AN=316;refseq.name=NM_025228;refseq.positionType=intron GT 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 chr1 210007940 . TCT T . PASS VC=INDEL;AC=190;AF=0.6;AN=316;refseq.name=NM_014388;refseq.positionType=intron GT 1/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/0 0/0 1/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 chr1 210483472 . TG T . PASS VC=INDEL;AC=13;AF=0.04;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 210485101 . A AGGAC . PASS VC=INDEL;AC=232;AF=0.8;AN=290 GT 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 ./. 1/1 0/1 0/1 1/1 1/1 1/1 ./. ./. 0/1 0/1 0/1 0/1 ./. 1/1 0/1 1/1 0/0 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 ./. 0/0 1/1 0/1 0/0 ./. 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 1/1 ./. 0/1 ./. 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. chr1 210713503 . TT T . PASS VC=INDEL;AC=303;AF=0.96;AN=316;refseq.name=NM_018194;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 211710916 . CC C . PASS VC=INDEL;AC=55;AF=0.17;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 chr1 211786200 . TA T . PASS VC=INDEL;AC=147;AF=0.56;AN=264 GT ./. 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 ./. 0/0 1/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 ./. ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 0/0 ./. ./. ./. 0/0 0/0 0/1 0/0 ./. 0/0 0/0 ./. 0/0 ./. 1/1 0/0 0/1 1/1 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. ./. 0/0 ./. 0/1 0/1 ./. ./. 0/0 ./. 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 ./. 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 ./. ./. 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/1 ./. 1/1 0/0 0/0 1/1 ./. 1/1 0/1 chr1 212767202 . TTT T . PASS VC=INDEL;AC=63;AF=0.2;AN=316;refseq.name=NM_001030287;refseq.positionType=intron GT 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 chr1 213150090 . T TGT . PASS VC=INDEL;AC=64;AF=0.21;AN=300;refseq.name=NM_024749;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 ./. 1/1 0/1 0/0 0/1 0/1 0/1 ./. 0/1 0/0 ./. ./. 0/0 chr1 213160084 . A AG . PASS VC=INDEL;AC=129;AF=0.41;AN=312;refseq.name=NM_024749;refseq.positionType=intron GT 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 ./. 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 chr1 213160085 . G GG . PASS VC=INDEL;AC=129;AF=0.41;AN=314;refseq.name=NM_024749;refseq.positionType=intron GT 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 ./. 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 chr1 213393510 . AG A . PASS VC=INDEL;AC=62;AF=0.2;AN=316;refseq.name=NM_012424;refseq.positionType=intron GT 0/1 0/1 0/1 1/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 chr1 213790399 . C CGA . PASS VC=INDEL;AC=2;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 214136369 . CTTC C . PASS VC=INDEL;AC=93;AF=0.29;AN=316 GT 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 chr1 214365999 . C CTG . PASS VC=INDEL;AC=164;AF=0.59;AN=278 GT 1/1 0/1 1/1 0/0 0/1 ./. 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 ./. 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 ./. 0/0 0/1 1/1 0/0 0/0 0/0 ./. 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 ./. 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 ./. 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 ./. 0/1 0/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 ./. 0/1 0/1 ./. ./. ./. 1/1 ./. ./. 1/1 0/1 ./. 1/1 1/1 1/1 0/1 ./. 0/1 0/0 0/1 0/0 ./. 1/1 1/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 ./. 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 ./. 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 chr1 214573392 . G GTTC . PASS VC=INDEL;AC=271;AF=0.86;AN=316;refseq.name=NM_005401;refseq.positionType=intron GT 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 215120715 . AA A . PASS VC=INDEL;AC=36;AF=0.12;AN=312 GT 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 216179286 . T TCAAT . PASS VC=INDEL;AC=30;AF=0.09;AN=316;refseq.name=NM_206933;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr1 216298294 . C CAG . PASS VC=INDEL;AC=113;AF=0.36;AN=316;refseq.name=NM_206933;refseq.positionType=intron GT 0/0 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 chr1 216298296 . G GAG . PASS VC=INDEL;AC=112;AF=0.35;AN=316;refseq.name=NM_206933;refseq.positionType=intron GT 0/0 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 chr1 216454053 . A AACA . PASS VC=INDEL;AC=224;AF=0.71;AN=316;refseq.name=NM_206933;refseq.positionType=intron GT 0/0 1/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 chr1 216780749 . C CC . PASS VC=INDEL;AC=10;AF=0.03;AN=316;refseq.name=NM_206594;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 216835074 . A AGTTT . PASS VC=INDEL;AC=89;AF=0.28;AN=316;refseq.name=NM_206594;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 chr1 217026745 . AA A . PASS VC=INDEL;AC=13;AF=0.04;AN=304;refseq.name=NM_206594;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 chr1 217057204 . G GC . PASS VC=INDEL;AC=231;AF=0.73;AN=316;refseq.name=NM_206594;refseq.positionType=intron GT 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 0/0 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 chr1 217363476 . CTATT C . PASS VC=INDEL;AC=40;AF=0.19;AN=212 GT 0/0 1/1 1/1 0/0 0/1 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/0 ./. 0/0 ./. 0/0 0/1 0/0 1/1 0/0 1/1 1/1 0/0 ./. 1/1 1/1 ./. ./. ./. 0/0 0/0 ./. 1/1 0/0 ./. 0/1 0/0 0/0 ./. 0/1 0/0 ./. ./. ./. ./. ./. ./. ./. 0/0 0/0 ./. 0/0 0/1 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/1 0/0 ./. ./. ./. 0/0 ./. ./. 0/0 0/0 ./. 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 ./. ./. 0/0 ./. ./. ./. ./. ./. ./. ./. chr1 218217904 . C CG . PASS VC=INDEL;AC=130;AF=0.43;AN=302 GT 0/1 0/1 0/1 ./. 1/1 0/1 ./. 0/1 0/0 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 ./. 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 ./. 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. chr1 218473680 . CGAG C . PASS VC=INDEL;AC=16;AF=0.05;AN=316;refseq.name=NM_016052;refseq.positionType=intron GT 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 218574584 . A AT . PASS VC=INDEL;AC=21;AF=0.09;AN=236;refseq.name=NM_003238;refseq.positionType=intron GT 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 ./. ./. 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/1 ./. 0/0 ./. 0/1 0/1 0/1 0/0 ./. 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. ./. ./. 0/1 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 ./. ./. 0/0 0/0 ./. 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/0 ./. 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 218845277 . TTTGT T . PASS VC=INDEL;AC=97;AF=0.31;AN=314 GT 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 ./. 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 chr1 219001503 . T TC . PASS VC=INDEL;AC=176;AF=0.56;AN=316 GT 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 chr1 219293844 . A ACT . PASS VC=INDEL;AC=274;AF=0.89;AN=308 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 ./. 1/1 0/0 1/1 1/1 1/1 1/1 1/1 chr1 219293846 . T TCT . PASS VC=INDEL;AC=199;AF=0.9;AN=222 GT 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 ./. ./. ./. 1/1 1/1 ./. 1/1 1/1 1/1 ./. 0/1 ./. ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. ./. 1/1 ./. ./. ./. 1/1 1/1 ./. 1/1 ./. 1/1 ./. ./. 0/1 0/0 1/1 ./. 1/1 1/1 ./. ./. 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 0/1 ./. 0/1 ./. 1/1 0/1 0/1 1/1 0/1 0/1 ./. 1/1 1/1 0/1 ./. 1/1 1/1 1/1 ./. 1/1 ./. ./. 1/1 1/1 ./. ./. 0/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. ./. ./. 1/1 ./. 1/1 1/1 1/1 ./. 0/1 1/1 ./. 0/1 ./. 1/1 0/1 ./. 0/0 ./. 1/1 ./. 1/1 ./. chr1 219467766 . AAC A . PASS VC=INDEL;AC=102;AF=0.32;AN=314 GT 0/0 1/1 1/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 ./. 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 chr1 219839015 . C CATGG . PASS VC=INDEL;AC=73;AF=0.24;AN=306 GT 1/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 ./. 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 1/1 0/1 chr1 221137225 . T TCTT . PASS VC=INDEL;AC=159;AF=0.61;AN=262 GT 0/0 ./. 0/1 0/1 0/1 ./. 1/1 1/1 ./. 0/1 1/1 1/1 0/1 ./. 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 ./. 0/1 0/1 0/1 0/1 1/1 ./. 0/1 0/1 0/0 0/1 0/1 ./. ./. 0/1 0/0 0/1 0/1 ./. 1/1 0/1 1/1 ./. 0/1 1/1 0/0 0/1 ./. ./. ./. 0/1 ./. 0/1 ./. 0/1 1/1 0/1 0/1 ./. 0/1 0/1 0/0 0/0 ./. 0/1 ./. 0/1 0/1 1/1 0/1 1/1 0/0 1/1 ./. 1/1 1/1 ./. 0/1 0/1 0/0 ./. 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 ./. 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 ./. 1/1 0/1 0/1 0/1 ./. 0/1 0/0 1/1 ./. ./. 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 chr1 221202698 . GA G . PASS VC=INDEL;AC=82;AF=0.26;AN=310 GT 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 ./. 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 chr1 221279126 . CC C . PASS VC=INDEL;AC=0;AF=0;AN=312 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 221315912 . TTCT T . PASS VC=INDEL;AC=94;AF=0.3;AN=312 GT 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 1/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 chr1 222205539 . AATTGACC A . PASS VC=INDEL;AC=90;AF=0.29;AN=310 GT 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 ./. 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 chr1 222493300 . T TGA . PASS VC=INDEL;AC=310;AF=0.98;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 222493301 . G GAG . PASS VC=INDEL;AC=310;AF=0.98;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 222990213 . ATTTG A . PASS VC=INDEL;AC=9;AF=0.04;AN=254 GT 0/1 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. ./. ./. ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 ./. ./. ./. ./. 0/0 0/0 0/1 chr1 223387015 . CTG C . PASS VC=INDEL;AC=6;AF=0.02;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 223657734 . A ATGAG . PASS VC=INDEL;AC=231;AF=0.99;AN=234 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. ./. 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 ./. ./. 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. ./. ./. 1/1 1/1 ./. 1/1 1/1 ./. 1/1 ./. 1/1 1/1 ./. 1/1 ./. ./. 0/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 0/1 ./. 1/1 1/1 1/1 ./. 1/1 ./. ./. 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. ./. 1/1 1/1 1/1 1/1 1/1 chr1 223984835 . G GAA . PASS VC=INDEL;AC=194;AF=0.63;AN=306;refseq.name=NM_001031685;refseq.positionType=intron GT ./. 1/1 0/1 ./. 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 ./. 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 chr1 224264255 . A AG . PASS VC=INDEL;AC=150;AF=0.66;AN=228 GT 0/1 1/1 0/1 0/1 1/1 ./. 0/1 ./. 1/1 1/1 ./. ./. ./. 1/1 ./. 0/1 0/0 ./. ./. 0/1 1/1 0/1 0/1 0/1 ./. 0/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 ./. 0/1 0/1 0/0 1/1 0/0 1/1 1/1 1/1 ./. 1/1 ./. 0/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 ./. 1/1 1/1 0/1 1/1 1/1 ./. 0/1 1/1 0/1 1/1 ./. 1/1 ./. 0/1 1/1 0/0 ./. 1/1 1/1 ./. ./. 1/1 1/1 0/1 ./. 0/0 0/1 0/1 ./. 0/0 1/1 0/1 0/1 1/1 ./. 1/1 ./. ./. 1/1 0/0 0/1 ./. 1/1 0/0 ./. 0/1 0/0 0/1 ./. ./. 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 ./. 0/0 0/1 0/1 1/1 0/1 ./. 0/0 1/1 ./. ./. ./. ./. 1/1 ./. 1/1 0/1 0/1 1/1 0/1 0/1 1/1 ./. 1/1 ./. ./. 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 ./. 0/1 0/1 0/1 ./. ./. chr1 224264346 . TGAG T . PASS VC=INDEL;AC=154;AF=0.63;AN=244 GT 0/1 1/1 0/1 0/1 1/1 ./. ./. 1/1 ./. 1/1 0/0 1/1 1/1 ./. 0/1 ./. 0/1 ./. 1/1 0/1 1/1 0/1 0/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 0/1 0/1 0/0 ./. 0/0 1/1 1/1 1/1 0/1 1/1 ./. 0/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 ./. 1/1 1/1 0/1 1/1 1/1 0/1 0/1 ./. ./. ./. 0/1 ./. 1/1 0/1 ./. 0/0 ./. ./. 1/1 0/1 ./. 1/1 ./. 0/1 ./. 0/0 0/1 0/1 ./. 0/0 1/1 0/1 0/1 ./. 1/1 ./. 0/1 0/1 1/1 0/0 0/1 ./. 1/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 0/1 0/0 1/1 0/1 ./. 0/1 0/1 ./. 0/1 0/1 ./. 0/1 0/0 0/0 1/1 ./. 0/1 1/1 0/1 ./. 0/1 1/1 0/1 ./. 1/1 0/1 0/1 ./. 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 ./. 1/1 0/1 chr1 224833844 . A AAGACGTAAGACAGT . PASS VC=INDEL;AC=215;AF=0.68;AN=314;refseq.name=NM_152495;refseq.positionType=intron GT 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 ./. 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 chr1 225662220 . CT C . PASS VC=INDEL;AC=203;AF=0.66;AN=306 GT 0/1 1/1 0/1 0/1 1/1 0/1 ./. 0/0 ./. 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 ./. 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 ./. 0/0 0/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 chr1 225974486 . T TG . PASS VC=INDEL;AC=187;AF=0.6;AN=310;refseq.name=NM_003133;refseq.positionType=intron GT 0/1 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 ./. 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 ./. 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 chr1 225974487 . G GG . PASS VC=INDEL;AC=189;AF=0.6;AN=314;refseq.name=NM_003133;refseq.positionType=intron GT 0/1 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 ./. 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 chr1 226014266 . ATGG A . PASS VC=INDEL;AC=30;AF=0.1;AN=310;refseq.name=NM_000120;refseq.positionType=intron GT 0/0 0/1 1/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. chr1 226014267 . TGGT T . PASS VC=INDEL;AC=31;AF=0.1;AN=316;refseq.name=NM_000120;refseq.positionType=intron GT 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 226878226 . ACTC A . PASS VC=INDEL;AC=45;AF=0.15;AN=306;refseq.name=NM_002221;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 1/1 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 1/1 ./. 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 chr1 226878233 . CTAC C . PASS VC=INDEL;AC=60;AF=0.21;AN=292;refseq.name=NM_002221;refseq.positionType=intron GT 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 ./. ./. 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 ./. 1/1 ./. ./. 0/0 0/0 0/0 1/1 0/0 0/1 0/1 ./. 0/0 ./. 0/0 0/0 0/1 0/1 0/0 ./. 0/0 ./. 0/1 0/0 chr1 226913049 . GCCA G . PASS VC=INDEL;AC=14;AF=0.05;AN=302;refseq.name=NM_002221;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 226913051 . CACC C . PASS VC=INDEL;AC=6;AF=0.02;AN=280;refseq.name=NM_002221;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 227051261 . G GC . PASS VC=INDEL;AC=21;AF=0.07;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 227252431 . TTTC T . PASS VC=INDEL;AC=21;AF=0.07;AN=316;refseq.name=NM_003607;refseq.positionType=intron GT 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 chr1 227401072 . GC G . PASS VC=INDEL;AC=122;AF=0.39;AN=316;refseq.name=NM_003607;refseq.positionType=intron GT 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 chr1 227560279 . G GTCATAG . PASS VC=INDEL;AC=316;AF=1;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 228479392 . ATG A . PASS VC=INDEL;AC=12;AF=0.04;AN=316;refseq.name=NM_001098623;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 229074693 . TAGAGG T . PASS VC=INDEL;AC=102;AF=0.32;AN=316 GT 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 chr1 229075090 . ATAGCCTG A . PASS VC=INDEL;AC=30;AF=0.11;AN=264 GT 1/1 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 ./. 0/0 ./. 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. chr1 229336842 . CATTT C . PASS VC=INDEL;AC=19;AF=0.06;AN=300 GT ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/1 ./. 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 chr1 229631495 . A AC . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_018230;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 229922597 . CCTT C . PASS VC=INDEL;AC=144;AF=0.46;AN=316 GT 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 chr1 229922599 . TTCT T . PASS VC=INDEL;AC=142;AF=0.45;AN=314 GT 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 chr1 230272407 . GAG G . PASS VC=INDEL;AC=15;AF=0.05;AN=314;refseq.name=NM_004481;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 230625946 . T TGA . PASS VC=INDEL;AC=302;AF=0.96;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 230626726 . CTTTAAGTCCTGT C . PASS VC=INDEL;AC=59;AF=0.19;AN=314 GT 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 chr1 230626728 . TTAAGTCCTGTTT T . PASS VC=INDEL;AC=59;AF=0.19;AN=316 GT 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 chr1 230697057 . ACA A . PASS VC=INDEL;AC=152;AF=0.48;AN=316 GT 0/1 1/1 1/1 0/0 1/1 0/0 1/1 0/0 0/0 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 chr1 230952100 . GG G . PASS VC=INDEL;AC=34;AF=0.11;AN=316 GT 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 chr1 232200072 . CGACT C . PASS VC=INDEL;AC=86;AF=0.28;AN=312 GT 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 ./. 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 chr1 232606995 . GTCTG G . PASS VC=INDEL;AC=54;AF=0.17;AN=316;refseq.name=NM_020808;refseq.positionType=intron GT 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 chr1 232883964 . G GTT . PASS VC=INDEL;AC=279;AF=0.88;AN=316 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 232883965 . T TTT . PASS VC=INDEL;AC=279;AF=0.88;AN=316 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 232944224 . AAGAA A . PASS VC=INDEL;AC=17;AF=0.05;AN=316;refseq.name=NM_019090;refseq.positionType=exon GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 233013835 . C CT . PASS VC=INDEL;AC=38;AF=0.18;AN=214 GT 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/1 ./. ./. 0/1 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/1 1/1 ./. ./. ./. 1/1 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 ./. 0/0 0/0 0/0 0/1 1/1 1/1 0/1 ./. ./. 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/1 0/0 ./. ./. ./. 0/1 ./. 0/1 0/1 ./. ./. ./. 0/0 0/1 ./. 0/1 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/0 0/0 ./. 1/1 0/1 ./. 1/1 0/1 0/0 ./. 0/0 1/1 ./. ./. 0/0 1/1 ./. ./. 0/0 ./. 1/1 ./. 1/1 ./. ./. 0/0 ./. ./. chr1 233013837 . T TT . PASS VC=INDEL;AC=78;AF=0.25;AN=310 GT 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 ./. 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 1/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 chr1 233458691 . ACAC A . PASS VC=INDEL;AC=18;AF=0.06;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 chr1 233593090 . TT T . PASS VC=INDEL;AC=257;AF=0.82;AN=312 GT 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/0 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 chr1 233991847 . T TCA . PASS VC=INDEL;AC=220;AF=0.72;AN=306 GT 1/1 1/1 ./. 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 ./. 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 ./. 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 ./. 0/1 0/1 0/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 chr1 234635298 . G GT . PASS VC=INDEL;AC=205;AF=0.65;AN=316 GT 0/1 0/0 0/0 0/1 0/0 1/1 0/0 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 chr1 234704346 . TCT T . PASS VC=INDEL;AC=36;AF=0.12;AN=312 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 chr1 235770627 . AATTA A . PASS VC=INDEL;AC=56;AF=0.18;AN=316;refseq.name=NM_004485;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 236043714 . ATCCTGTGTTGATTTA A . PASS VC=INDEL;AC=6;AF=0.02;AN=294 GT ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 236043717 . CTGTGTTGATTTATTA C . PASS VC=INDEL;AC=5;AF=0.02;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 236118487 . TT T . PASS VC=INDEL;AC=12;AF=0.04;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 236195380 . GTG G . PASS VC=INDEL;AC=163;AF=0.52;AN=316;refseq.name=NM_002508;refseq.positionType=intron GT 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 chr1 236375505 . T TG . PASS VC=INDEL;AC=130;AF=0.42;AN=310 GT 0/0 ./. 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 chr1 236555148 . T TA . PASS VC=INDEL;AC=3;AF=0.01;AN=316;refseq.name=NM_145861;refseq.positionType=promoter GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 chr1 236723352 . CGACCTCGCTCAGACTCTGTGAGGTGCTGAATAAGCAACA C . PASS VC=INDEL;AC=72;AF=0.23;AN=314;refseq.name=NM_018072;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 chr1 236723354 . ACCTCGCTCAGACTCTGTGAGGTGCTGAATAAGCAACAGA A . PASS VC=INDEL;AC=72;AF=0.23;AN=312;refseq.name=NM_018072;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 chr1 236848307 . A AG . PASS VC=INDEL;AC=62;AF=0.21;AN=300;refseq.name=NM_001103;refseq.positionType=promoter GT 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 ./. ./. 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 ./. 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 chr1 237009685 . TAGC T . PASS VC=INDEL;AC=6;AF=0.02;AN=292;refseq.name=NM_000254;refseq.positionType=intron GT 0/1 0/0 0/0 ./. 0/1 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 237009687 . GCAG G . PASS VC=INDEL;AC=3;AF=0.01;AN=304;refseq.name=NM_000254;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 237055125 . CA C . PASS VC=INDEL;AC=9;AF=0.03;AN=284;refseq.name=NM_000254;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 237277023 . C CA . PASS VC=INDEL;AC=18;AF=0.06;AN=312;refseq.name=NM_001035;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 chr1 237535965 . AA A . PASS VC=INDEL;AC=0;AF=0;AN=280;refseq.name=NM_001035;refseq.positionType=intron GT 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 chr1 237539975 . GCTTGA G . PASS VC=INDEL;AC=3;AF=0.01;AN=316;refseq.name=NM_001035;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 chr1 237649833 . C CTCTT . PASS VC=INDEL;AC=140;AF=0.45;AN=312;refseq.name=NM_001035;refseq.positionType=intron GT 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 ./. 0/0 1/1 0/1 ./. 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 chr1 237649835 . C CTTTC . PASS VC=INDEL;AC=138;AF=0.44;AN=312;refseq.name=NM_001035;refseq.positionType=intron GT 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 1/1 0/1 ./. 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 ./. 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 chr1 237995162 . T TTTGA . PASS VC=INDEL;AC=301;AF=0.96;AN=312;refseq.name=NM_001035;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 238017296 . T TCT . PASS VC=INDEL;AC=80;AF=0.25;AN=316 GT 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 chr1 238125441 . AGA A . PASS VC=INDEL;AC=26;AF=0.08;AN=316 GT 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 238152842 . C CGTAA . PASS VC=INDEL;AC=165;AF=0.52;AN=316 GT 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 chr1 238152845 . A AAGTA . PASS VC=INDEL;AC=166;AF=0.53;AN=316 GT 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 chr1 238257585 . TGAT T . PASS VC=INDEL;AC=159;AF=0.61;AN=262 GT 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 ./. 1/1 0/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 1/1 0/1 ./. 0/0 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 ./. 0/1 ./. 1/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 ./. 0/0 0/1 ./. 0/0 0/0 0/1 ./. 0/1 0/1 0/0 0/0 1/1 ./. 0/1 0/1 ./. 0/1 ./. 0/1 ./. 0/1 0/0 ./. 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 ./. 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 ./. 1/1 0/1 1/1 ./. ./. 0/0 1/1 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 0/1 ./. ./. ./. 0/1 0/1 ./. ./. 0/1 1/1 1/1 chr1 238476744 . A ATCTA . PASS VC=INDEL;AC=283;AF=0.98;AN=290 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 chr1 238497833 . G GAGAA . PASS VC=INDEL;AC=232;AF=0.76;AN=304 GT 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 1/1 1/1 ./. 1/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 ./. 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 ./. 1/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 0/0 ./. ./. 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 chr1 238623394 . C CTTGA . PASS VC=INDEL;AC=178;AF=0.58;AN=308 GT 0/0 1/1 1/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 ./. 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 ./. ./. 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 ./. 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 chr1 238699979 . T TATCT . PASS VC=INDEL;AC=97;AF=0.31;AN=314 GT 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 0/1 0/1 0/0 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 chr1 238921290 . CATTCAT C . PASS VC=INDEL;AC=188;AF=0.59;AN=316 GT 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 chr1 238933453 . C CA . PASS VC=INDEL;AC=26;AF=0.08;AN=314 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 238933454 . A AA . PASS VC=INDEL;AC=25;AF=0.08;AN=314 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 239644576 . C CAA . PASS VC=INDEL;AC=46;AF=0.15;AN=300 GT 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 ./. ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 ./. 1/1 0/0 0/1 0/1 0/0 ./. 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 chr1 240115184 . GAAG G . PASS VC=INDEL;AC=62;AF=0.2;AN=316 GT 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 chr1 240170484 . ATCA A . PASS VC=INDEL;AC=30;AF=0.1;AN=310 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 chr1 240469105 . A ACT . PASS VC=INDEL;AC=44;AF=0.14;AN=308;refseq.name=NM_020066;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 chr1 240556294 . A AG . PASS VC=INDEL;AC=180;AF=0.73;AN=248;refseq.name=NM_020066;refseq.positionType=intron GT ./. 0/1 1/1 ./. 1/1 0/1 1/1 1/1 ./. 0/1 1/1 0/1 1/1 0/1 ./. 0/0 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 ./. ./. ./. 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 ./. 0/1 0/1 0/1 ./. 0/1 1/1 0/0 1/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 ./. 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 ./. 0/0 0/0 0/1 ./. 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 ./. ./. ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 0/1 1/1 0/1 ./. 1/1 1/1 ./. 1/1 0/1 ./. ./. 0/1 ./. 1/1 1/1 0/0 0/1 1/1 1/1 1/1 ./. ./. 1/1 0/1 1/1 ./. ./. ./. ./. 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 ./. 0/1 0/1 0/0 ./. 0/0 0/1 ./. 0/1 1/1 0/1 chr1 240750353 . A AT . PASS VC=INDEL;AC=1;AF=0;AN=208;refseq.name=NM_022469;refseq.positionType=intron GT 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. chr1 241292738 . CGAC C . PASS VC=INDEL;AC=16;AF=0.06;AN=254;refseq.name=NM_002924;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 ./. 0/0 1/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/1 ./. ./. 0/0 ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. ./. 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. ./. ./. 0/0 ./. 0/1 0/1 0/0 0/0 chr1 241342365 . TTCAA T . PASS VC=INDEL;AC=54;AF=0.18;AN=308;refseq.name=NM_002924;refseq.positionType=intron GT 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 ./. 1/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 1/1 ./. 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 chr1 241864983 . A AGTCAAAC . PASS VC=INDEL;AC=235;AF=0.75;AN=314;refseq.name=NM_144625;refseq.positionType=intron GT 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 chr1 241901460 . ACTG A . PASS VC=INDEL;AC=126;AF=0.4;AN=316;refseq.name=NM_144625;refseq.positionType=intron GT 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 1/1 1/1 1/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 chr1 241920499 . TGTAG T . PASS VC=INDEL;AC=5;AF=0.02;AN=316;refseq.name=NM_144625;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 chr1 241920501 . TAGGT T . PASS VC=INDEL;AC=5;AF=0.02;AN=316;refseq.name=NM_144625;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 chr1 242055743 . C CTG . PASS VC=INDEL;AC=47;AF=0.15;AN=314 GT 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 chr1 242257290 . TC T . PASS VC=INDEL;AC=59;AF=0.22;AN=270;refseq.name=NM_152666;refseq.positionType=intron GT 0/1 ./. 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/0 0/1 0/0 0/1 0/0 0/1 ./. ./. ./. 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 ./. ./. 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 ./. 0/0 ./. 0/1 0/1 0/0 ./. 0/1 0/0 ./. 0/0 0/0 0/1 0/0 ./. 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/1 ./. 0/0 1/1 0/1 1/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 ./. 0/1 0/1 0/1 0/0 chr1 242281287 . T TCT . PASS VC=INDEL;AC=296;AF=0.95;AN=312;refseq.name=NM_152666;refseq.positionType=intron GT 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 chr1 242328018 . CATTACACTACTTTT C . PASS VC=INDEL;AC=97;AF=0.4;AN=244;refseq.name=NM_152666;refseq.positionType=intron GT 1/1 0/1 0/1 ./. 1/1 0/0 0/1 0/0 1/1 0/1 ./. 0/0 ./. 0/1 0/0 0/1 0/1 ./. 0/1 0/0 1/1 0/0 0/1 ./. 0/0 0/1 1/1 1/1 0/1 ./. 0/0 0/1 1/1 0/1 1/1 0/0 ./. 0/0 ./. 1/1 0/0 0/1 0/1 0/0 0/1 0/1 ./. ./. ./. 0/1 0/1 ./. 0/0 1/1 0/1 0/1 0/1 0/1 ./. 0/1 ./. 1/1 ./. 0/0 0/0 1/1 0/1 0/1 ./. 1/1 0/1 1/1 0/1 ./. ./. 1/1 0/1 0/1 0/1 ./. ./. 0/0 1/1 0/1 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 ./. ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/0 0/1 0/1 0/1 ./. 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/1 ./. ./. 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 ./. ./. ./. 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 ./. 0/0 0/0 chr1 242602261 . CC C . PASS VC=INDEL;AC=51;AF=0.16;AN=316;refseq.name=NM_152666;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 chr1 243409926 . AAGTT A . PASS VC=INDEL;AC=99;AF=0.32;AN=312;refseq.name=NM_014812;refseq.positionType=intron GT 1/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 chr1 243410210 . G GTAT . PASS VC=INDEL;AC=137;AF=0.43;AN=316;refseq.name=NM_014812;refseq.positionType=intron GT 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 chr1 243435760 . CATT C . PASS VC=INDEL;AC=26;AF=0.1;AN=272;refseq.name=NM_006642;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/1 ./. 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. ./. chr1 244015225 . GTCTG G . PASS VC=INDEL;AC=70;AF=0.22;AN=316 GT 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 chr1 244033256 . GTTGA G . PASS VC=INDEL;AC=18;AF=0.06;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 244186794 . T TT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 244216819 . T TA . PASS VC=INDEL;AC=79;AF=0.25;AN=316;refseq.name=NM_006352;refseq.positionType=exon GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 chr1 244216822 . A AA . PASS VC=INDEL;AC=79;AF=0.25;AN=312;refseq.name=NM_006352;refseq.positionType=exon GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 chr1 244371962 . CAACTGGTCAAC C . PASS VC=INDEL;AC=2;AF=0.01;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 244372739 . C CTA . PASS VC=INDEL;AC=70;AF=0.22;AN=312 GT 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 1/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 1/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 chr1 244517491 . A AG . PASS VC=INDEL;AC=229;AF=0.72;AN=316;refseq.name=NM_001012970;refseq.positionType=intron GT 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 chr1 244552134 . CATTT C . PASS VC=INDEL;AC=41;AF=0.13;AN=314;refseq.name=NM_001012970;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 244794244 . T TAAC . PASS VC=INDEL;AC=2;AF=0.01;AN=316;refseq.name=NM_173807;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 245242885 . A ATT . PASS VC=INDEL;AC=3;AF=0.01;AN=316;refseq.name=NM_032328;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 245242887 . T TTT . PASS VC=INDEL;AC=3;AF=0.01;AN=316;refseq.name=NM_032328;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 245310839 . T TTAAAG . PASS VC=INDEL;AC=156;AF=0.59;AN=266 GT 0/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 ./. 1/1 1/1 1/1 0/0 0/1 0/1 ./. 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 ./. 1/1 0/0 0/0 0/1 ./. 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 ./. ./. 0/0 0/1 0/1 0/0 0/0 ./. 0/1 ./. 0/0 ./. ./. ./. 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/1 1/1 ./. 1/1 1/1 ./. 0/1 0/1 1/1 1/1 0/0 ./. 0/0 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 ./. 1/1 ./. 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 ./. ./. 0/1 ./. 0/1 0/0 0/1 0/0 1/1 0/0 0/1 ./. ./. ./. 0/1 ./. 1/1 1/1 1/1 0/1 0/1 0/1 1/1 ./. 1/1 chr1 245453003 . G GCCAA . PASS VC=INDEL;AC=80;AF=0.26;AN=308;refseq.name=NM_018012;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 ./. 0/0 0/1 ./. 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/0 0/1 chr1 245709104 . A AGTCAAC . PASS VC=INDEL;AC=221;AF=0.7;AN=316;refseq.name=NM_018012;refseq.positionType=intron GT 1/1 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 chr1 245868167 . G GTCTT . PASS VC=INDEL;AC=138;AF=0.44;AN=316 GT 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 chr1 245868172 . T TCTTT . PASS VC=INDEL;AC=137;AF=0.43;AN=316 GT 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 chr1 246124841 . A AAACAGAAG . PASS VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_022743;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 246124843 . A ACAGAAGAA . PASS VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_022743;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 246149511 . C CT . PASS VC=INDEL;AC=69;AF=0.32;AN=214;refseq.name=NM_022743;refseq.positionType=intron GT 1/1 ./. 0/1 0/1 1/1 ./. 0/1 1/1 0/0 ./. ./. 1/1 ./. ./. ./. 0/1 ./. 0/0 ./. ./. 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. ./. ./. 0/1 ./. 1/1 0/1 ./. ./. ./. 1/1 0/1 ./. ./. 1/1 ./. 1/1 0/1 1/1 ./. 0/1 0/1 1/1 ./. 0/1 1/1 0/1 ./. 0/1 0/1 0/0 0/0 0/1 ./. 0/1 1/1 ./. ./. 1/1 ./. 1/1 0/1 ./. 0/1 0/1 ./. 0/1 0/1 0/0 ./. 0/1 ./. 0/0 0/1 ./. 0/1 0/1 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/1 ./. 0/1 0/0 0/0 0/0 ./. ./. ./. 0/1 0/0 0/1 0/1 0/1 0/0 0/0 ./. ./. 0/0 ./. ./. 0/1 ./. chr1 246152615 . GC G . PASS VC=INDEL;AC=164;AF=0.52;AN=316;refseq.name=NM_022743;refseq.positionType=intron GT 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 chr1 247110970 . T TCA . PASS VC=INDEL;AC=157;AF=0.5;AN=316 GT 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 chr1 247340579 . TTTCTT T . PASS VC=INDEL;AC=232;AF=0.74;AN=312 GT 1/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/0 1/1 0/0 0/0 1/1 0/1 0/0 1/1 1/1 ./. 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 1/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 ./. 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr1 247694106 . C CTCCGTGGCCTAAACGGGCAGCCGAGCCCG . PASS VC=INDEL;AC=124;AF=0.62;AN=200;refseq.name=NM_198074;refseq.positionType=exon GT ./. ./. 1/1 1/1 1/1 0/1 ./. 1/1 0/1 ./. 1/1 1/1 0/1 0/1 ./. 0/1 ./. 1/1 ./. 1/1 1/1 ./. 1/1 ./. 0/1 0/1 ./. 0/1 0/1 ./. 0/1 0/1 0/1 ./. 0/1 ./. ./. 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/1 ./. 0/1 0/1 0/1 0/1 ./. 0/1 ./. 0/1 0/1 ./. 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 ./. ./. ./. 0/1 ./. ./. ./. 0/1 0/1 1/1 0/1 ./. 0/1 0/1 0/1 0/1 ./. 0/1 0/1 ./. 1/1 0/1 ./. ./. ./. 1/1 0/1 1/1 ./. ./. 1/1 0/1 1/1 ./. 1/1 1/1 1/1 ./. ./. ./. ./. ./. ./. ./. 0/1 0/1 ./. 0/1 ./. 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/1 ./. 0/1 ./. ./. ./. 0/1 ./. 0/1 ./. ./. 0/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 1/1 ./. chr1 248807991 . TATGA T . PASS VC=INDEL;AC=85;AF=0.34;AN=252 GT 0/0 ./. 0/1 0/1 ./. 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 1/1 0/0 0/1 0/1 ./. ./. 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/0 ./. 0/0 1/1 0/0 ./. 0/1 0/1 ./. ./. 0/0 0/1 0/0 ./. ./. 0/1 ./. 0/1 ./. 0/1 0/1 0/0 1/1 ./. ./. 1/1 0/1 1/1 0/1 0/0 1/1 ./. 0/1 1/1 0/0 ./. ./. 0/1 ./. 0/0 0/1 0/0 0/0 0/1 ./. 0/1 ./. 0/0 ./. 0/1 0/1 1/1 0/1 ./. ./. 0/0 1/1 0/1 0/0 0/1 ./. 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 1/1 ./. 1/1 0/1 0/1 ./. 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 chr1 248809274 . GAACA G . PASS VC=INDEL;AC=79;AF=0.26;AN=304 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. ./. 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 chr1 248809275 . AACAA A . PASS VC=INDEL;AC=79;AF=0.26;AN=306 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 chr1 248809277 . C CAATT . PASS VC=INDEL;AC=9;AF=0.03;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 249122808 . C CAT . PASS VC=INDEL;AC=176;AF=0.58;AN=304;refseq.name=NM_030645;refseq.positionType=promoter GT 0/1 1/1 0/0 0/1 1/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 ./. 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 ./. 0/0 1/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 ./. 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 0/0 1/1 ./. 0/1 1/1 0/0 0/1 1/1 1/1 ./. 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 chr1 249129038 . GCCTCTAACTT G . PASS VC=INDEL;AC=2;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 311906 . TA T . PASS VC=INDEL;AC=148;AF=0.48;AN=308 GT 0/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 ./. 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 ./. 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 chr2 341060 . TC T . PASS VC=INDEL;AC=52;AF=0.17;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 1/1 1/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 chr2 623863 . GTTC G . PASS VC=INDEL;AC=278;AF=0.9;AN=310 GT 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 chr2 623869 . CTTC C . PASS VC=INDEL;AC=283;AF=0.9;AN=314 GT 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 chr2 872231 . G GCC . PASS VC=INDEL;AC=46;AF=0.16;AN=284 GT 1/1 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 ./. 0/1 ./. 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 chr2 872234 . C CCC . PASS VC=INDEL;AC=53;AF=0.21;AN=248 GT 1/1 0/1 0/0 1/1 0/0 1/1 1/1 0/1 ./. 0/0 0/1 0/1 ./. 0/0 0/0 ./. 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/1 ./. ./. ./. 0/0 0/0 ./. ./. ./. 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/1 ./. 0/0 0/0 ./. 0/0 0/0 0/1 ./. 0/1 0/0 ./. 0/1 0/1 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 ./. 0/1 ./. ./. ./. 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/0 ./. 0/0 ./. chr2 1131016 . TTTAGG T . PASS VC=INDEL;AC=189;AF=0.6;AN=316;refseq.name=NM_018968;refseq.positionType=intron GT 0/0 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/0 0/1 chr2 1146399 . T TA . PASS VC=INDEL;AC=280;AF=0.89;AN=316;refseq.name=NM_018968;refseq.positionType=intron GT 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 chr2 1146400 . A AA . PASS VC=INDEL;AC=280;AF=0.89;AN=316;refseq.name=NM_018968;refseq.positionType=intron GT 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 chr2 1184342 . CAACTT C . PASS VC=INDEL;AC=94;AF=0.3;AN=316;refseq.name=NM_018968;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 chr2 1369823 . AGC A . PASS VC=INDEL;AC=243;AF=0.77;AN=316;refseq.name=NM_018968;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 chr2 1371776 . T TTTAA . PASS VC=INDEL;AC=50;AF=0.16;AN=312;refseq.name=NM_018968;refseq.positionType=terminator GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/0 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 ./. 1/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr2 1371779 . A AATTA . PASS VC=INDEL;AC=38;AF=0.13;AN=282;refseq.name=NM_018968;refseq.positionType=terminator GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/1 ./. 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 1/1 0/1 0/1 0/0 ./. ./. 0/0 0/1 0/0 0/0 ./. ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 ./. 0/0 0/0 1/1 0/0 0/1 ./. ./. 1/1 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. chr2 1379755 . A AA . PASS VC=INDEL;AC=5;AF=0.02;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 1789405 . A AT . PASS VC=INDEL;AC=63;AF=0.2;AN=316 GT 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 chr2 2440845 . A AA . PASS VC=INDEL;AC=87;AF=0.32;AN=272 GT ./. 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/1 0/0 0/0 0/0 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 ./. 0/0 0/0 0/0 0/0 0/1 0/1 ./. 1/1 0/1 1/1 ./. 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 ./. ./. ./. 0/1 ./. 0/1 ./. 0/0 ./. 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 ./. 0/1 0/1 0/0 1/1 0/1 ./. 0/1 ./. 0/1 ./. 1/1 1/1 ./. 0/1 ./. 1/1 0/1 0/1 0/1 ./. 0/0 0/1 chr2 2656901 . TG T . PASS VC=INDEL;AC=278;AF=0.9;AN=310 GT 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 chr2 3126017 . G GG . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 3424142 . CGCTGAC C . PASS VC=INDEL;AC=112;AF=0.46;AN=244;refseq.name=NM_016030;refseq.positionType=intron GT 0/1 0/1 ./. 0/0 0/1 ./. 1/1 0/1 0/1 0/0 ./. 1/1 0/0 0/1 ./. ./. 0/1 0/0 0/0 0/1 ./. 0/1 1/1 ./. 0/0 0/1 ./. 1/1 0/1 0/1 0/1 ./. ./. 0/0 0/0 ./. 1/1 1/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 ./. 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 ./. ./. ./. 0/1 0/1 1/1 1/1 ./. 1/1 ./. 0/0 ./. 0/1 0/0 1/1 ./. ./. 1/1 ./. 0/1 0/0 0/1 ./. 0/1 ./. 0/1 1/1 0/1 1/1 0/1 0/1 0/1 ./. 0/1 0/1 0/1 ./. 0/0 0/1 ./. ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 ./. 0/1 1/1 0/1 0/1 ./. 0/0 0/1 ./. ./. 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 1/1 ./. chr2 3658789 . ACAAA A . PASS VC=INDEL;AC=95;AF=0.33;AN=284;refseq.name=NM_024027;refseq.positionType=intron GT 0/1 0/1 0/0 0/1 0/1 0/1 0/1 ./. 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 ./. 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 ./. 0/1 0/0 ./. 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 ./. 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/1 ./. 0/0 ./. 0/0 ./. 0/1 chr2 3749151 . GGAA G . PASS VC=INDEL;AC=163;AF=0.53;AN=310;refseq.name=NM_018436;refseq.positionType=exon GT 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 ./. 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 chr2 3749158 . GAAG G . PASS VC=INDEL;AC=164;AF=0.53;AN=308;refseq.name=NM_018436;refseq.positionType=exon GT 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 1/1 0/1 0/1 ./. 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 ./. 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 chr2 4140967 . G GA . PASS VC=INDEL;AC=125;AF=0.4;AN=312 GT 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 ./. 1/1 1/1 0/1 chr2 4184693 . AGAG A . PASS VC=INDEL;AC=60;AF=0.22;AN=274 GT 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 ./. ./. ./. ./. ./. 0/0 0/1 0/1 0/0 0/1 ./. 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 ./. 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 ./. 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/1 1/1 0/0 0/1 0/1 ./. 0/0 0/0 0/1 0/1 0/1 ./. 0/0 chr2 4296243 . ACCTGGCCTTTT A . PASS VC=INDEL;AC=19;AF=0.06;AN=312 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 chr2 4604536 . ATCTG A . PASS VC=INDEL;AC=82;AF=0.27;AN=308 GT 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 ./. 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 1/1 1/1 1/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 chr2 4607815 . TAT T . PASS VC=INDEL;AC=90;AF=0.28;AN=316 GT 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 1/1 1/1 1/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 chr2 4874174 . CAT C . PASS VC=INDEL;AC=203;AF=0.64;AN=316 GT 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/0 chr2 4933418 . GATC G . PASS VC=INDEL;AC=86;AF=0.28;AN=304 GT 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 ./. 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr2 4987676 . A ACT . PASS VC=INDEL;AC=100;AF=0.32;AN=316 GT 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 chr2 4994909 . G GT . PASS VC=INDEL;AC=122;AF=0.41;AN=294 GT 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 ./. 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 ./. 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/1 0/1 0/1 0/1 ./. 0/0 0/0 0/1 0/1 ./. 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 ./. 0/0 ./. 0/1 ./. 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 ./. 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 chr2 5222830 . CTGTT C . PASS VC=INDEL;AC=127;AF=0.4;AN=314 GT 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 ./. 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 chr2 5418395 . T TAA . PASS VC=INDEL;AC=147;AF=0.47;AN=314 GT 1/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 ./. 0/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 chr2 5821332 . TTCAGTCCCCCTAATGCC T . PASS VC=INDEL;AC=261;AF=0.83;AN=316 GT 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 chr2 5821334 . CAGTCCCCCTAATGCCTC C . PASS VC=INDEL;AC=261;AF=0.83;AN=316 GT 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 chr2 7238500 . A ACTT . PASS VC=INDEL;AC=184;AF=0.58;AN=316 GT 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 chr2 7238505 . T TTCT . PASS VC=INDEL;AC=184;AF=0.58;AN=316 GT 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 chr2 7616680 . C CA . PASS VC=INDEL;AC=196;AF=0.62;AN=314 GT ./. 1/1 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 chr2 10714143 . CAA C . PASS VC=INDEL;AC=143;AF=0.47;AN=306;refseq.name=NM_024894;refseq.positionType=intron GT 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 ./. 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 ./. 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 ./. 0/1 chr2 11163207 . TCA T . PASS VC=INDEL;AC=63;AF=0.2;AN=316 GT 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 1/1 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 11163209 . ACA A . PASS VC=INDEL;AC=63;AF=0.2;AN=316 GT 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 1/1 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 11454443 . TTGTC T . PASS VC=INDEL;AC=85;AF=0.27;AN=310;refseq.name=NM_004850;refseq.positionType=intron GT 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 1/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 ./. 0/1 1/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 chr2 11600452 . TT T . PASS VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_198256;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 11843046 . C CAACT . PASS VC=INDEL;AC=157;AF=0.5;AN=316 GT 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 chr2 11843047 . A AACTA . PASS VC=INDEL;AC=157;AF=0.5;AN=316 GT 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 chr2 12317135 . T TT . PASS VC=INDEL;AC=2;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 12787834 . GT G . PASS VC=INDEL;AC=0;AF=0;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 12877501 . G GA . PASS VC=INDEL;AC=241;AF=0.76;AN=316;refseq.name=NM_021643;refseq.positionType=intron GT 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 chr2 13123234 . A ACTTA . PASS VC=INDEL;AC=273;AF=0.89;AN=308 GT ./. 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 chr2 13297277 . GC G . PASS VC=INDEL;AC=23;AF=0.07;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 13446741 . T TCACT . PASS VC=INDEL;AC=105;AF=0.41;AN=256 GT 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 1/1 ./. ./. 0/1 0/1 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 ./. ./. 0/1 0/0 0/0 ./. 0/0 0/1 1/1 0/1 0/0 0/0 0/0 1/1 ./. 0/1 ./. ./. 0/1 ./. 0/1 0/0 0/1 ./. 1/1 1/1 0/0 0/1 0/1 1/1 ./. 0/1 0/1 ./. ./. 0/1 0/1 0/0 0/1 ./. ./. 0/0 0/0 ./. 0/0 0/1 0/1 ./. 0/0 ./. 0/1 0/1 ./. 0/1 0/1 ./. 0/1 ./. 1/1 0/1 1/1 0/1 ./. 0/1 1/1 1/1 ./. 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 ./. ./. 0/0 0/1 1/1 ./. ./. 0/0 chr2 13637137 . TTGCTG T . PASS VC=INDEL;AC=19;AF=0.06;AN=308 GT 0/0 ./. 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr2 13829513 . T TT . PASS VC=INDEL;AC=91;AF=0.29;AN=314 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 ./. 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 chr2 13967190 . TAGAT T . PASS VC=INDEL;AC=22;AF=0.07;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 chr2 14096044 . AAA A . PASS VC=INDEL;AC=47;AF=0.16;AN=298 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 ./. 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 ./. 1/1 0/0 0/0 chr2 14214846 . C CT . PASS VC=INDEL;AC=40;AF=0.13;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 chr2 14381137 . A ATC . PASS VC=INDEL;AC=0;AF=0;AN=280 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 14428427 . G GC . PASS VC=INDEL;AC=242;AF=0.77;AN=316 GT 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 chr2 14428428 . C CC . PASS VC=INDEL;AC=241;AF=0.77;AN=314 GT 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 chr2 14685393 . C CTTC . PASS VC=INDEL;AC=29;AF=0.09;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 chr2 15208721 . A AC . PASS VC=INDEL;AC=116;AF=0.38;AN=304 GT 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 1/1 ./. 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 1/1 0/1 ./. 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/0 1/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 0/0 0/0 ./. 1/1 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 ./. 1/1 0/1 chr2 15263072 . A AAGGA . PASS VC=INDEL;AC=86;AF=0.33;AN=262 GT 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 ./. 0/0 ./. ./. 0/0 0/0 0/0 ./. 1/1 ./. 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 ./. 0/1 0/0 0/1 1/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/0 0/0 ./. 1/1 0/0 0/0 0/0 ./. ./. 0/1 0/1 0/1 ./. 0/0 ./. 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 ./. 0/0 0/1 0/1 0/1 0/1 0/1 ./. 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 ./. 0/0 1/1 ./. 0/1 0/0 1/1 ./. 0/1 0/1 0/1 ./. 1/1 0/1 1/1 0/1 0/1 ./. ./. 0/1 0/0 0/0 chr2 15744484 . CT C . PASS VC=INDEL;AC=48;AF=0.15;AN=314;refseq.name=NM_004939;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 chr2 15907161 . G GACTG . PASS VC=INDEL;AC=60;AF=0.19;AN=314 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 chr2 16916657 . T TAGAA . PASS VC=INDEL;AC=153;AF=0.51;AN=298 GT 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 chr2 16916659 . G GAAAG . PASS VC=INDEL;AC=145;AF=0.49;AN=294 GT 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. ./. 0/1 ./. 0/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 ./. 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 ./. ./. ./. 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 chr2 17460258 . C CC . PASS VC=INDEL;AC=54;AF=0.17;AN=316 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 chr2 18018674 . TAT T . PASS VC=INDEL;AC=71;AF=0.23;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/0 chr2 18139969 . T TT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 18291829 . TCT T . PASS VC=INDEL;AC=276;AF=0.87;AN=316 GT 0/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 chr2 18382578 . G GC . PASS VC=INDEL;AC=304;AF=0.97;AN=314 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 18386046 . ACAGA A . PASS VC=INDEL;AC=1;AF=0;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 18673070 . CT C . PASS VC=INDEL;AC=0;AF=0;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 18704268 . C CCATGACAAGAACTGCT . PASS VC=INDEL;AC=210;AF=0.66;AN=316 GT 1/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 chr2 18954606 . T TGTA . PASS VC=INDEL;AC=272;AF=0.87;AN=314 GT 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 chr2 19229223 . A AG . PASS VC=INDEL;AC=230;AF=0.82;AN=280 GT 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 ./. 1/1 1/1 0/1 1/1 0/1 1/1 0/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 ./. 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 ./. 0/1 ./. 0/1 0/1 ./. 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 ./. 0/1 1/1 0/1 ./. 1/1 0/1 1/1 0/1 0/1 1/1 0/1 ./. 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 ./. ./. 1/1 chr2 19416083 . CAAT C . PASS VC=INDEL;AC=26;AF=0.08;AN=312 GT 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/1 1/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 19486700 . C CGT . PASS VC=INDEL;AC=200;AF=0.9;AN=222 GT 0/1 ./. ./. ./. 0/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 0/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 ./. ./. ./. 0/1 ./. 1/1 ./. 0/1 ./. 0/1 0/1 0/1 ./. 1/1 ./. ./. ./. ./. 0/1 1/1 ./. ./. 0/1 1/1 1/1 0/1 1/1 ./. 0/1 1/1 0/1 1/1 ./. 0/1 0/1 0/1 0/1 1/1 1/1 1/1 ./. ./. ./. 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 ./. ./. ./. 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. ./. ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. chr2 19792293 . AAA A . PASS VC=INDEL;AC=92;AF=0.29;AN=316 GT 0/1 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 chr2 19850365 . ATA A . PASS VC=INDEL;AC=17;AF=0.06;AN=302 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr2 20061297 . A AATCA . PASS VC=INDEL;AC=10;AF=0.03;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 20902911 . G GC . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_021925;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 21209314 . GTG G . PASS VC=INDEL;AC=13;AF=0.04;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 21319809 . GACAA G . PASS VC=INDEL;AC=64;AF=0.2;AN=316 GT 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 21692599 . AA A . PASS VC=INDEL;AC=78;AF=0.25;AN=314 GT 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 ./. 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 chr2 22508039 . GCCT G . PASS VC=INDEL;AC=70;AF=0.23;AN=300 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 ./. 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 ./. 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 ./. 0/0 0/1 0/1 0/0 0/0 chr2 23055890 . CTT C . PASS VC=INDEL;AC=32;AF=0.1;AN=310 GT 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 chr2 23059421 . CC C . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 23080285 . C CC . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 23252488 . T TGTTT . PASS VC=INDEL;AC=261;AF=0.83;AN=314 GT 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 ./. 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 1/1 1/1 0/0 1/1 0/1 1/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 23656105 . CT C . PASS VC=INDEL;AC=78;AF=0.25;AN=314 GT 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 23929327 . T TAACT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 25136190 . TC T . PASS VC=INDEL;AC=190;AF=0.68;AN=280;refseq.name=NM_004036;refseq.positionType=intron GT 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 1/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 ./. 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/1 ./. 1/1 0/1 1/1 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/0 0/1 ./. 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 ./. ./. ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 0/1 0/1 ./. ./. ./. ./. 0/1 0/1 chr2 25696290 . CA C . PASS VC=INDEL;AC=7;AF=0.02;AN=314;refseq.name=NM_021907;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 chr2 25971939 . A AGTAAA . PASS VC=INDEL;AC=90;AF=0.28;AN=316;refseq.name=NM_018263;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 chr2 26471341 . T TTTC . PASS VC=INDEL;AC=10;AF=0.03;AN=316;refseq.name=NM_000183;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 chr2 26547936 . GAC G . PASS VC=INDEL;AC=69;AF=0.22;AN=308;refseq.name=NM_153835;refseq.positionType=intron GT 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/1 ./. ./. 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr2 26849198 . ACGGTT A . PASS VC=INDEL;AC=85;AF=0.28;AN=308;refseq.name=NM_001029881;refseq.positionType=intron GT 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 1/1 ./. 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 ./. 0/0 0/1 chr2 26849199 . CGGTTC C . PASS VC=INDEL;AC=83;AF=0.27;AN=302;refseq.name=NM_001029881;refseq.positionType=intron GT 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 1/1 0/0 0/1 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 ./. ./. 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 ./. 0/0 0/1 chr2 27134249 . ATA A . PASS VC=INDEL;AC=100;AF=0.32;AN=316;refseq.name=NM_020134;refseq.positionType=intron GT 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/0 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 chr2 27787778 . AAATTAAAATTCTAC A . PASS VC=INDEL;AC=10;AF=0.03;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 28368075 . CACAG C . PASS VC=INDEL;AC=0;AF=0;AN=306;refseq.name=NM_199193;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 28792105 . A AATA . PASS VC=INDEL;AC=100;AF=0.32;AN=308;refseq.name=NM_153021;refseq.positionType=intron GT 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 ./. 1/1 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 ./. 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 ./. 1/1 0/1 chr2 29191749 . GA G . PASS VC=INDEL;AC=87;AF=0.28;AN=316 GT 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 chr2 29191750 . AA A . PASS VC=INDEL;AC=86;AF=0.27;AN=316 GT 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 chr2 29738576 . TA T . PASS VC=INDEL;AC=284;AF=0.9;AN=316;refseq.name=NM_004304;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 29738577 . AA A . PASS VC=INDEL;AC=284;AF=0.9;AN=316;refseq.name=NM_004304;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 30158127 . C CA . PASS VC=INDEL;AC=192;AF=0.61;AN=316 GT 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 1/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/0 chr2 30158129 . A AA . PASS VC=INDEL;AC=192;AF=0.61;AN=316 GT 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 1/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/0 chr2 30645653 . A AAGCTTTTCTAATGAACATCTACAAGACTGTTGTG . PASS VC=INDEL;AC=303;AF=0.96;AN=316 GT 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 chr2 30727159 . C CAGTCTATATGCC . PASS VC=INDEL;AC=189;AF=0.6;AN=316;refseq.name=NM_182551;refseq.positionType=intron GT 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 chr2 30727390 . GTTG G . PASS VC=INDEL;AC=31;AF=0.1;AN=314;refseq.name=NM_182551;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr2 30855218 . CCATGGGA C . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_182551;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 30937800 . GATTTT G . PASS VC=INDEL;AC=14;AF=0.06;AN=244 GT 0/0 ./. ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 ./. ./. ./. 0/0 0/1 0/0 ./. 0/1 0/1 0/1 ./. ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/1 0/0 0/0 0/0 ./. 0/1 ./. ./. 0/1 ./. ./. chr2 31084461 . AATAAAATACAG A . PASS VC=INDEL;AC=36;AF=0.11;AN=316 GT 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 chr2 31249797 . ATATC A . PASS VC=INDEL;AC=34;AF=0.11;AN=316;refseq.name=NM_024572;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr2 31249799 . ATCTA A . PASS VC=INDEL;AC=47;AF=0.16;AN=302;refseq.name=NM_024572;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 1/1 0/0 0/0 ./. 0/0 0/0 0/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 1/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 chr2 31374768 . AGTA A . PASS VC=INDEL;AC=13;AF=0.05;AN=278 GT 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 chr2 31499486 . C CC . PASS VC=INDEL;AC=11;AF=0.03;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 32845664 . A AT . PASS VC=INDEL;AC=138;AF=0.44;AN=316 GT 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/0 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 1/1 chr2 32845666 . T TT . PASS VC=INDEL;AC=138;AF=0.44;AN=316 GT 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/0 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 1/1 chr2 33393523 . AGCAA A . PASS VC=INDEL;AC=10;AF=0.03;AN=308;refseq.name=NM_206943;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 33403610 . ATTG A . PASS VC=INDEL;AC=46;AF=0.15;AN=316;refseq.name=NM_206943;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 chr2 33478311 . TGAGT T . PASS VC=INDEL;AC=2;AF=0.01;AN=314;refseq.name=NM_206943;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 33542959 . TT T . PASS VC=INDEL;AC=258;AF=0.82;AN=316;refseq.name=NM_206943;refseq.positionType=intron GT 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 chr2 33760624 . C CC . PASS VC=INDEL;AC=5;AF=0.02;AN=216;refseq.name=NM_170672;refseq.positionType=intron GT 0/1 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 ./. ./. ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. ./. ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 chr2 33899643 . G GGAG . PASS VC=INDEL;AC=261;AF=0.83;AN=316 GT 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 chr2 34119549 . A AA . PASS VC=INDEL;AC=45;AF=0.14;AN=316 GT 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 chr2 34427438 . A AT . PASS VC=INDEL;AC=175;AF=0.76;AN=230 GT 0/1 0/1 ./. 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 ./. ./. 0/1 1/1 ./. ./. ./. ./. 0/0 0/1 0/1 ./. ./. ./. 0/1 1/1 0/1 0/1 0/1 1/1 ./. 0/1 1/1 ./. 1/1 ./. 1/1 0/1 ./. ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 0/1 0/1 1/1 ./. 1/1 1/1 0/1 0/1 0/1 1/1 ./. 1/1 1/1 ./. 0/1 1/1 ./. 0/1 ./. ./. ./. ./. 1/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 0/1 ./. 1/1 0/1 0/1 1/1 ./. 0/1 1/1 0/1 ./. 0/1 1/1 1/1 0/1 0/0 0/0 0/1 ./. 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 0/0 0/0 0/1 0/1 1/1 0/0 ./. ./. 1/1 1/1 ./. 1/1 0/1 0/1 ./. 1/1 ./. 0/1 0/1 0/1 1/1 ./. ./. 0/1 0/1 ./. 1/1 0/0 1/1 1/1 0/1 chr2 34841691 . TGAAT T . PASS VC=INDEL;AC=165;AF=0.79;AN=210 GT ./. ./. ./. 1/1 ./. ./. ./. 0/1 ./. 1/1 0/1 ./. 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 0/1 ./. ./. ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 ./. 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 ./. ./. 1/1 1/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 0/0 ./. ./. ./. ./. 1/1 ./. 0/1 1/1 ./. 0/1 0/1 0/0 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 0/0 ./. ./. ./. 0/1 ./. ./. 1/1 0/1 ./. ./. 0/1 ./. ./. 0/1 0/1 1/1 ./. 0/1 ./. ./. ./. 0/1 ./. 0/1 0/0 1/1 ./. 0/1 ./. 0/1 0/1 ./. 0/1 0/0 0/1 1/1 1/1 ./. 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 ./. ./. 0/1 1/1 0/1 ./. ./. chr2 35025338 . G GG . PASS VC=INDEL;AC=227;AF=0.72;AN=314 GT 0/1 0/0 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/0 0/0 1/1 1/1 0/1 0/0 1/1 0/1 1/1 ./. 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/0 chr2 35255151 . TCT T . PASS VC=INDEL;AC=29;AF=0.09;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 35667838 . A AGG . PASS VC=INDEL;AC=54;AF=0.21;AN=252 GT 0/0 ./. ./. ./. 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. ./. 0/0 ./. 0/0 0/0 ./. ./. 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 ./. ./. ./. ./. ./. 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/0 ./. 0/1 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/1 0/0 0/1 ./. 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 ./. 0/1 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/1 ./. 0/1 0/1 ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/1 ./. 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr2 35668564 . A AG . PASS VC=INDEL;AC=275;AF=0.87;AN=316 GT 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 chr2 36779604 . C CTT . PASS VC=INDEL;AC=130;AF=0.44;AN=298;refseq.name=NM_001042548;refseq.positionType=exon GT 1/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 ./. 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 ./. 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/1 0/1 ./. 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/0 ./. 0/0 1/1 1/1 1/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 ./. 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 chr2 37233064 . ACT A . PASS VC=INDEL;AC=48;AF=0.16;AN=302;refseq.name=NM_019024;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 ./. 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 ./. 0/0 chr2 37865906 . GA G . PASS VC=INDEL;AC=161;AF=0.51;AN=314 GT 0/0 1/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 ./. 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 chr2 37960289 . A AG . PASS VC=INDEL;AC=1;AF=0;AN=302 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. chr2 38003881 . T TAGA . PASS VC=INDEL;AC=312;AF=0.99;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 38079466 . CAT C . PASS VC=INDEL;AC=93;AF=0.3;AN=308 GT 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 ./. 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 ./. 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 ./. 0/1 0/0 chr2 38476518 . T TCA . PASS VC=INDEL;AC=179;AF=0.57;AN=316 GT 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 chr2 38682923 . T TTTCTCTCT . PASS VC=INDEL;AC=35;AF=0.11;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 chr2 38990657 . C CACTT . PASS VC=INDEL;AC=241;AF=0.76;AN=316 GT 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 chr2 39202671 . TCAC T . PASS VC=INDEL;AC=68;AF=0.22;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 ./. 1/1 1/1 0/1 1/1 1/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 chr2 39848964 . GACTA G . PASS VC=INDEL;AC=92;AF=0.3;AN=304 GT 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 1/1 0/1 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 ./. 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 ./. 0/1 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 1/1 chr2 40095196 . TCTT T . PASS VC=INDEL;AC=22;AF=0.07;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 40207026 . AA A . PASS VC=INDEL;AC=1;AF=0;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr2 40328669 . A ATC . PASS VC=INDEL;AC=182;AF=0.58;AN=316 GT 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 1/1 chr2 40396501 . G GTCAG . PASS VC=INDEL;AC=13;AF=0.04;AN=310;refseq.name=NM_001112802;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 chr2 40446174 . T TCTACCTGCAACCCTTGATTGGCCTC . PASS VC=INDEL;AC=196;AF=0.62;AN=314;refseq.name=NM_001112802;refseq.positionType=intron GT 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 ./. 0/0 1/1 1/1 1/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 chr2 40527545 . T TGC . PASS VC=INDEL;AC=69;AF=0.22;AN=316;refseq.name=NM_001112802;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 chr2 40764424 . TATG T . PASS VC=INDEL;AC=6;AF=0.02;AN=314 GT ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 40840587 . A ATTG . PASS VC=INDEL;AC=15;AF=0.06;AN=242 GT ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/0 ./. ./. ./. ./. 0/0 ./. ./. 0/0 0/1 0/0 0/1 ./. 0/0 ./. 1/1 0/0 ./. 0/1 0/0 0/1 ./. ./. ./. ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. 1/1 0/0 1/1 0/0 0/0 0/1 ./. 0/0 0/1 ./. ./. ./. 0/0 0/0 chr2 41367520 . A AT . PASS VC=INDEL;AC=187;AF=0.6;AN=314 GT 1/1 1/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 chr2 41554849 . TCAGA T . PASS VC=INDEL;AC=231;AF=0.74;AN=314 GT ./. 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 chr2 41554851 . AGACA A . PASS VC=INDEL;AC=233;AF=0.74;AN=316 GT 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 chr2 41628974 . G GA . PASS VC=INDEL;AC=282;AF=0.9;AN=314 GT 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 41628975 . A AA . PASS VC=INDEL;AC=281;AF=0.9;AN=312 GT 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 41838136 . GGC G . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 42604189 . CTTATGGGTTAC C . PASS VC=INDEL;AC=3;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 42773644 . C CC . PASS VC=INDEL;AC=111;AF=0.35;AN=316 GT 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 1/1 chr2 43140881 . TA T . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 43205232 . A AAG . PASS VC=INDEL;AC=287;AF=0.91;AN=316 GT 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 chr2 43324908 . C CA . PASS VC=INDEL;AC=316;AF=1;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 43570900 . TCT T . PASS VC=INDEL;AC=84;AF=0.27;AN=316;refseq.name=NM_022065;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/0 chr2 44397082 . AAGAGTA A . PASS VC=INDEL;AC=39;AF=0.12;AN=316;refseq.name=NM_177968;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr2 44735716 . TAAAC T . PASS VC=INDEL;AC=189;AF=0.6;AN=316;refseq.name=NM_024766;refseq.positionType=intron GT 1/1 0/0 0/0 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 chr2 45472533 . T TATA . PASS VC=INDEL;AC=284;AF=0.92;AN=308 GT 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 ./. 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 chr2 45472535 . T TAAT . PASS VC=INDEL;AC=291;AF=0.92;AN=316 GT 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 chr2 47399270 . TCA T . PASS VC=INDEL;AC=140;AF=0.44;AN=316;refseq.name=NM_001743;refseq.positionType=intron GT 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 chr2 48032874 . ACTAT A . PASS VC=INDEL;AC=254;AF=0.8;AN=316;refseq.name=NM_000179;refseq.positionType=intron GT 0/0 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 chr2 49026643 . A AA . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 49468159 . C CTCTT . PASS VC=INDEL;AC=57;AF=0.18;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr2 49514324 . GAAGAA G . PASS VC=INDEL;AC=179;AF=0.58;AN=310 GT 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 ./. 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 ./. 0/0 0/0 0/0 1/1 0/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 1/1 chr2 49982314 . T TT . PASS VC=INDEL;AC=196;AF=0.64;AN=304 GT 1/1 0/1 1/1 1/1 0/0 ./. 0/0 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 1/1 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 ./. ./. 0/1 0/1 0/0 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 chr2 50152899 . TTTTC T . PASS VC=INDEL;AC=26;AF=0.1;AN=268;refseq.name=NM_004801;refseq.positionType=intron GT ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 0/0 ./. 0/1 ./. 0/0 0/1 0/1 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/1 ./. ./. ./. 0/1 0/0 0/1 ./. 0/0 0/1 0/1 0/0 0/1 ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/0 chr2 50693504 . AAC A . PASS VC=INDEL;AC=193;AF=0.63;AN=306;refseq.name=NM_004801;refseq.positionType=intron GT 0/0 1/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/0 1/1 0/0 0/0 0/1 1/1 1/1 1/1 0/1 ./. 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/0 ./. 1/1 0/1 ./. ./. 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 1/1 0/1 chr2 50703696 . C CTG . PASS VC=INDEL;AC=287;AF=0.91;AN=314;refseq.name=NM_004801;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 50703699 . T TGT . PASS VC=INDEL;AC=285;AF=0.9;AN=316;refseq.name=NM_004801;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 51260591 . T TAT . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_004801;refseq.positionType=promoter GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 51281539 . TT T . PASS VC=INDEL;AC=252;AF=0.8;AN=316 GT 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 chr2 51315220 . A ATT . PASS VC=INDEL;AC=55;AF=0.19;AN=292 GT 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 ./. 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 ./. 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 ./. 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 ./. 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 ./. 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 chr2 51315221 . T TTT . PASS VC=INDEL;AC=56;AF=0.19;AN=300 GT 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 chr2 51355364 . TTT T . PASS VC=INDEL;AC=30;AF=0.1;AN=304 GT 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 chr2 52397945 . A ATGCTATTCCAATATCTCAG . PASS VC=INDEL;AC=33;AF=0.15;AN=214 GT 0/1 ./. 0/0 0/0 0/1 0/0 0/0 0/0 ./. ./. ./. 0/1 ./. ./. ./. 0/1 ./. 0/1 0/1 ./. 0/1 0/1 ./. 0/1 ./. 0/0 0/1 0/0 ./. 0/0 ./. ./. 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 ./. 0/0 0/0 ./. ./. 0/1 0/0 ./. 0/1 ./. ./. 0/1 0/0 0/1 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. ./. 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 ./. ./. ./. 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/1 ./. ./. 0/0 0/0 ./. 0/1 0/0 0/1 0/0 0/1 chr2 52643648 . G GAG . PASS VC=INDEL;AC=140;AF=0.53;AN=266 GT 0/1 ./. 0/0 0/1 0/1 1/1 0/0 0/0 1/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/0 0/1 0/0 0/0 0/1 0/1 0/0 ./. ./. 0/1 0/0 0/1 0/0 0/1 1/1 ./. 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/0 ./. 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 ./. ./. ./. 0/0 ./. 1/1 0/1 0/1 0/0 0/1 ./. 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 ./. 1/1 1/1 0/1 ./. 1/1 1/1 1/1 0/1 0/0 ./. 0/1 0/1 1/1 ./. ./. ./. 0/1 1/1 ./. 1/1 0/1 ./. ./. 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 ./. 0/1 1/1 ./. 0/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 ./. 0/0 1/1 0/0 1/1 0/1 0/0 1/1 chr2 53056176 . G GAG . PASS VC=INDEL;AC=131;AF=0.49;AN=270 GT 1/1 0/0 0/1 ./. ./. 0/0 ./. 1/1 0/1 0/1 0/1 ./. ./. ./. ./. 0/1 1/1 0/1 ./. 0/1 ./. 0/1 ./. 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 ./. 0/0 ./. 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 ./. 1/1 ./. 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/0 ./. 0/1 0/0 ./. 0/0 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 ./. 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 ./. 1/1 chr2 53674036 . AA A . PASS VC=INDEL;AC=106;AF=0.34;AN=310 GT 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 ./. 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 chr2 53737951 . AGGAT A . PASS VC=INDEL;AC=107;AF=0.35;AN=302 GT 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 ./. 0/0 ./. 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 ./. 1/1 1/1 0/1 0/0 ./. 0/1 0/0 0/0 0/0 0/0 1/1 ./. 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 chr2 54573230 . AACA A . PASS VC=INDEL;AC=62;AF=0.2;AN=316;refseq.name=NM_001100396;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 chr2 54726113 . G GA . PASS VC=INDEL;AC=269;AF=0.87;AN=308;refseq.name=NM_003128;refseq.positionType=intron GT 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 ./. 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr2 54726287 . T TGTTA . PASS VC=INDEL;AC=269;AF=0.85;AN=316;refseq.name=NM_003128;refseq.positionType=intron GT 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr2 54783793 . C CTT . PASS VC=INDEL;AC=270;AF=0.85;AN=316;refseq.name=NM_003128;refseq.positionType=intron GT 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr2 55080611 . GCTTT G . PASS VC=INDEL;AC=3;AF=0.01;AN=310 GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 55174675 . AC A . PASS VC=INDEL;AC=6;AF=0.02;AN=306 GT 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. chr2 55208953 . A ATATGAATCACATACAAGCTAAGAAAC . PASS VC=INDEL;AC=211;AF=0.67;AN=316;refseq.name=NM_020532;refseq.positionType=intron GT 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 1/1 0/1 0/0 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 chr2 55208955 . A ATGAATCACATACAAGCTAAGAAACTA . PASS VC=INDEL;AC=211;AF=0.67;AN=316;refseq.name=NM_020532;refseq.positionType=intron GT 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 1/1 0/1 0/0 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 chr2 55284481 . AA A . PASS VC=INDEL;AC=90;AF=0.28;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 chr2 55355370 . CTG C . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 55473492 . AA A . PASS VC=INDEL;AC=27;AF=0.11;AN=236;refseq.name=NM_002453;refseq.positionType=exon GT 0/1 ./. 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/1 ./. 0/1 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/1 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/1 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. ./. 0/1 0/0 0/1 ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. chr2 56088199 . TA T . PASS VC=INDEL;AC=21;AF=0.07;AN=316 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 56603301 . G GT . PASS VC=INDEL;AC=118;AF=0.39;AN=306;refseq.name=NM_001080433;refseq.positionType=intron GT 1/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 ./. 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 ./. 1/1 0/0 0/1 0/1 1/1 ./. 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/0 chr2 57161556 . CCTT C . PASS VC=INDEL;AC=24;AF=0.1;AN=230 GT 0/1 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/1 ./. 0/0 0/0 ./. ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/1 ./. 0/0 0/0 0/1 0/0 ./. ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/0 ./. ./. ./. 0/0 ./. 0/1 0/1 ./. 0/1 ./. 0/1 0/1 ./. ./. ./. 0/1 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/1 ./. 0/0 0/0 ./. 0/0 ./. 0/1 ./. 0/1 0/0 0/0 ./. ./. ./. 0/1 ./. ./. ./. ./. 0/0 chr2 58167700 . AA A . PASS VC=INDEL;AC=220;AF=0.73;AN=300 GT 0/1 1/1 0/1 0/0 1/1 1/1 0/0 1/1 0/0 1/1 ./. 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 ./. 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 ./. 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 ./. 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 0/1 1/1 chr2 58193832 . A ACAA . PASS VC=INDEL;AC=35;AF=0.16;AN=222 GT 0/1 0/1 ./. 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/1 0/0 ./. ./. 0/1 1/1 ./. ./. ./. 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 1/1 ./. 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/1 1/1 0/0 ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 ./. 0/1 ./. ./. 0/0 0/1 ./. 0/0 ./. 0/0 0/0 0/1 0/0 ./. 0/1 ./. ./. 0/0 ./. 0/1 ./. ./. ./. ./. ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/0 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 1/1 0/0 0/1 0/0 ./. 0/1 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/1 ./. 0/0 ./. 0/0 0/0 chr2 58274884 . C CAGG . PASS VC=INDEL;AC=125;AF=0.4;AN=314;refseq.name=NM_006296;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 ./. 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/0 chr2 58274891 . A AGGA . PASS VC=INDEL;AC=123;AF=0.4;AN=308;refseq.name=NM_006296;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/0 ./. 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 ./. 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/0 chr2 58283746 . A ACT . PASS VC=INDEL;AC=268;AF=0.88;AN=304;refseq.name=NM_006296;refseq.positionType=intron GT 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 ./. 1/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 chr2 58283749 . C CTC . PASS VC=INDEL;AC=266;AF=0.86;AN=308;refseq.name=NM_006296;refseq.positionType=intron GT 0/1 1/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 ./. 0/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 ./. 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 chr2 58385305 . T TCTTA . PASS VC=INDEL;AC=79;AF=0.25;AN=316;refseq.name=NM_006296;refseq.positionType=intron GT 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 chr2 58385307 . T TTACT . PASS VC=INDEL;AC=79;AF=0.25;AN=316;refseq.name=NM_006296;refseq.positionType=intron GT 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 pysam-0.23.0/tests/tabix_data/vcf/23.vcf000066400000000000000000004221561475062545500177200ustar00rootroot00000000000000##fileformat=VCFv4.1 ##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/combined.phase1.chr20.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false recal_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.recal tranches_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub ts_filter_level=93.0 ignore_filter=null mode=INDEL" ##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR/AFR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN/ASN.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR/AMR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR/EUR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR.admix/AFR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN.admix/ASN.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR.admix/AMR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR.admix/EUR.admix.phase1.chr20.42.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=AFR.admix,AMR.admix,EUR.admix,ASN.admix,AFR,AMR,EUR,ASN printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 masterMerge=false mergeInfoWithMaxAC=true" ##FILTER= ##FILTER== 4 && (MQ0 / (1.0 * DP)) > 0.1"> ##FILTER=10)"> ##FILTER=20.0"> ##FILTER= 7500"> ##FILTER==15"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER==-1.0"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##LeftAlignVariants="analysis_type=LeftAlignVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/ebanks/ALL.chr20.Oxford.20110407.indels.genotypes.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub" ##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/dindel/20110208.chr20.dindel2.ALL.sites.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null select_expressions=[] excludeNonVariants=false excludeFiltered=false discordance= concordance= family_structure= mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_number=0 select_random_fraction=0.0 selectSNPs=false selectIndels=true" ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/broad/shptmp/delangel/calls/chr20/CHB.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CHS.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CLM.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/JPT.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/MXL.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/PUR.phase1.chr20.42.cleaned.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.combined.chr20.vcf, /humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=50 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=8 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=INDEL p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=GENOTYPE_GIVEN_ALLELES output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=4.0 standard_min_confidence_threshold_for_emitting=4.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=true output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[MappingQualityZeroFraction]" ##VariantAnnotator="analysis_type=VariantAnnotator input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[./ALL.chr20.vqsr_2of5_union_sites_for_validation_boosted.vcf] rodToIntervalTrackName=variant BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sampleName=null annotation=[IndelType] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false" ##VariantFiltration="analysis_type=VariantFiltration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/humgen/1kg/processing/pipeline_test_bams/chr22_chunked.hg19.intervals] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/broad/shptmp/rpoplin/ALL.phase1.chr22.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub filterExpression=[MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1, QUAL<30.0, SB>=-1.0, QD<1.0, HRun>=15, HaplotypeScore>20.0] filterName=[HARD_TO_VALIDATE, LowQual, StrandBias, QualByDepth, HomopolymerRun, HaplotypeScore] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false" ##commandline="/share/software/freebayes/bin/freebayes --stdin --min-alternate-count 2 --genotype-combo-step-max 20 --genotype-variant-threshold 4 --no-marginals --pvar 0.0001 --indels --mnps --no-filters --binomial-obs-priors --allele-balance-priors --region 20:0..100000 --vcf /d1/data/1000G/20101123/populations/finalised.phase1/integrated/including454/wg/ALL/Pipeline/none//freebayes/freebayes.20:0-100000.baq.20110328.vcf --fasta-reference /d2/data/references/build_37/human_reference_v37.fa" ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##fileDate=2011-03-28 ##filedate=2011-02-08 ##filter="( SNP | MNP ) & ( MQM > 65 | QUAL > 1 ) & ABP < 30 & AB < 0.9 | ( INS | DEL ) & QUAL > 500" ##phasing=none ##reference=/lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta ##source=Dindel2 ##source=SelectVariants ##source_20110031.1=/nfs/users/nfs_p/pd3/cvs/vcftools/perl/vcf-annotate -d /nfs/users/nfs_p/pd3/sandbox/hapmap/dbSNP-b132/non-1kg-vld.desc -a /nfs/users/nfs_p/pd3/sandbox/hapmap/dbSNP-b132/non-1kg-vld.tab.gz -c CHROM,FROM,INFO/VLD,INFO/KGPilot123,INFO/dbSNP ##vcfCTools=filter #CHROM POS ID REF ALT QUAL FILTER INFO 20 458502 . G GA 4567.01 PASS AA=20;AB=0.61111;ABA=14;ABP=6.8707;ABR=22;AC=38;AF=0.0544;AN=698;BL=374;BR=1129;BVAR;BaseQRankSum=13.364;DP=15979;DP4=1882,2188,45,37;Dels=0.00;EL=5;EPP=13.868;ER=15;FR;FS=6.503;HETAR=11;HOMA=2;HOMR=985;HP=1;HPLen=2;HR=2;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0157;IndelType=INS.NOVEL_1.Novel_A.;LEN=1;LRB=0.50233;LRBP=826.56;MQ=66.16;MQ0Fraction=0.0110;MQM=70.5;MQRankSum=-3.158;NF;NR;NS=998;PP;PV4=0.15,1,0.42,0.15;RA=3173;RL=1;RPP=38.188;RR=19;RUN=1;ReadPosRankSum=-2.346;SAB=0.7;SAF=14;SAP=9.959;SAR=6;SC=GGGCGTGGTGGTGCATGTAAT;SET_INTEGRATION;SET_WGVQSR;SRB=0.50047;SRF=1588;SRP=3.0165;SRR=1585;TC;TR=9;TU=GGT;VQSLOD=10.0079;set=Intersection;sumGLbyD=23.94 20 573764 . TA T 591.51 PASS AC=91;AF=0.1987;AN=458;BaseQRankSum=0.137;DP=519;FS=3.153;HRun=1;HaplotypeScore=14.0744;InbreedingCoeff=0.1460;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;MQ=48.16;MQ0=26;MQ0Fraction=0.0501;MQRankSum=-1.636;QD=3.63;ReadPosRankSum=-4.140;SB=-408.14;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.2458;set=VQSR 20 766143 . C CATCTGGTA 5521.70 PASS AA=24;AB=0.5;ABA=18;ABP=3.0103;ABR=18;AC=14;AF=0.0289;AF1=0.02038;AN=484;BL=655;BR=1542;BVAR;BaseQRankSum=3.801;CI95=0.01549,0.02655;DP=11749;DP4=2222,1998,14,8;Dels=0.00;EL=9;EPP=6.2675;ER=15;FQ=999;FR;FS=2.941;HETAR=9;HOMA=4;HOMR=901;HP=2;HPLen=2;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0515;IndelType=INS.NumRepetitions_1.EventLength_8.;LEN=8;LRB=0.40373;LRBP=780.64;MQ=56.81;MQ0Fraction=0.0253;MQM=22.167;MQRankSum=-4.809;NF;NR;NS=914;PP;PV4=0.39,1,5.8e-07,1;RA=3093;RL=6;RPP=16.039;RR=18;RUN=1;ReadPosRankSum=-2.827;SAB=0.625;SAF=15;SAP=6.2675;SAR=9;SC=GCTTTAAATTCATCTGGTACT;SET_INTEGRATION;SET_WGVQSR;SRB=0.61623;SRF=1906;SRP=365.95;SRR=1187;TC;TR=1;TU=A;VQSLOD=7.0268;set=Intersection;sumGLbyD=50.23 20 997076 rs11467490 CTG C 15379.78 PASS AA=195;AB=0.59878;ABA=132;ABP=30.896;ABR=197;AC=173;AF=0.14562;AN=1188;BL=7664;BR=7309;BVAR;BaseQRankSum=21.853;DB;DEL;DP=27127;DP4=1801,2002,241,282;Dels=0.13;EL=100;EPP=3.2887;ER=95;FQ=999;FR;FS=6.591;HETAR=77;HOMA=42;HOMR=815;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1284;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TG.;LEN=2;LRB=0.023709;LRBP=21.287;MQ=61.18;MQ0Fraction=0.0214;MQM=43.041;MQRankSum=6.886;NF;NR;NS=934;PP;PV4=0.61,1.5e-78,1,1;RA=2800;RL=120;RPP=25.56;RR=75;RUN=1;ReadPosRankSum=4.504;SAB=0.62051;SAF=121;SAP=27.609;SAR=74;SC=CAGCTAATTACTGTATTTTTA;SET_INTEGRATION;SET_WGVQSR;SRB=0.49821;SRF=1395;SRP=3.0879;SRR=1405;TC;TR=1;TU=T;VQSLOD=8.9396;set=Intersection;sumGLbyD=16.76 20 1042261 rs10597473 CCCTG C 168658.05 PASS AA=4481;AB=0.29043;ABA=2128;ABP=1147.1;ABR=871;AC=1172;AF=0.97830;AN=1198;BL=169975;BR=194027;BVAR;BaseQRankSum=4.599;DB;DEL;DP=29418;DP4=29,47,1441,2403;Dels=0.84;EL=2358;EPP=29.772;ER=2123;FR;FS=9.122;HETAR=482;HOMA=559;HOMR=30;HP=2;HPLen=3;HR=3;HRun=0;HU=C;INDEL;InbreedingCoeff=0.0470;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.066077;LRBP=3454.1;MQ=104.58;MQ0=4;MQ0Fraction=0.0014;MQM=58.257;MQRankSum=-3.368;NF;NR;NS=1071;PP;PV4=0.91,6.8e-09,2.8e-05,1;RA=1039;RL=2088;RPP=48.09;RR=2393;RUN=1;ReadPosRankSum=5.288;SAB=0.41442;SAF=1857;SAP=288.09;SAR=2624;SC=CCAAACCCAACCCTGCCTGGC;SET_INTEGRATION;SET_WGVQSR;SRB=0.48893;SRF=508;SRP=4.1159;SRR=531;TC;TR=8;TU=CCTG;VQSLOD=8.5148;dbSNP=120;set=Intersection;sumGLbyD=59.79 20 1046297 rs33956316 C CT,CTT,CTTT 17698 PASS ABR=408;AC=432,79,230;AF=0.39779,0.07274,0.21179;BVAR;BaseQRankSum=-8.413;DB;DP=15649;DP4=147,199,534,436;FR;FS=11.580;HOMA=97;HOMR=457;HP=20;HR=16;HU=T;HaplotypeScore=16.0590;INDEL;INS;InbreedingCoeff=0.6018;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ0=19;MQ0Fraction=0.0093;MQRankSum=7.992;NF;NR;NS=767;PP;PV4=6e-05,1,1,1;QD=8.18;RA=1183;RUN=1;ReadPosRankSum=2.684;SB=-6384.08;SC=GGAAAATTTTCTTTTTTTTTT;SET_WGVQSR;SRB=0.40913;SRF=484;SRP=87.859;SRR=699;TC;TR=16;TU=T;VQSLOD=8.4941;dbSNP=132;set=Intersection 20 1405740 . T TA 257.28 PASS AF=0.0188;BaseQRankSum=-0.745;DP=3769;Dels=0.00;FS=0.742;HPLen=9;HRun=9;InbreedingCoeff=0.0462;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_A.;MQ0Fraction=0.0151;MQRankSum=-0.090;ReadPosRankSum=-1.582;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.6502;set=Intersection;sumGLbyD=6.94 20 1690501 . TC T 27928 PASS AA=108;AB=0.91372;ABA=100;ABP=1726.1;ABR=1059;AC=35;AF=0.02966;AN=1180;BL=593;BR=6973;BVAR;BaseQRankSum=7.567;DEL;DP=10612;Dels=0.01;EL=50;EPP=4.2971;ER=58;FS=0.000;HETAR=378;HOMA=184;HOMR=477;HRun=1;InbreedingCoeff=0.0495;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.84325;LRBP=11685;MQ0=0;MQ0Fraction=0.0000;MQM=87.361;MQRankSum=4.088;NS=1045;RA=3125;RL=3;RPP=212.2;RR=105;RUN=1;ReadPosRankSum=-13.096;SAB=0.56481;SAF=61;SAP=6.9511;SAR=47;SRB=0.51776;SRF=1618;SRP=11.572;SRR=1507;VQSLOD=3.9824;set=filterInVQSR-2of5;sumGLbyD=4.07 20 1991285 rs113891396 TAA T,TA,TAAA,TAAAAA,TAAAAAA,TAAAAAAA,TAAAAAAAA 39235.36 PASS AC=5,251,20,39,188,52,79;AF=0.0056,0.2789,0.0222,0.0433,0.2089,0.0578,0.0878;AN=900;BVAR;BaseQRankSum=1.124;DB;DEL;DP=54393;DP4=906,772,824,579;Dels=0.21;FR;FS=37.525;HP=12;HR=12;HRun=12;HU=A;INDEL;INS;InbreedingCoeff=0.6891;IndelType=MULTIALLELIC_INDEL;MQ=76.81;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-6.593;NF;NR;PP;PV4=0.0087,1,6.3e-19,1;RUN=1;ReadPosRankSum=-2.184;SC=ATCTGCCACTTAAAAAAAAAA;SET_WGVQSR;TC;TR=12;TU=A;VQSLOD=9.0007;dbSNP=132;set=Intersection;sumGLbyD=11.45 20 2355911 . TA T 11723 PASS AA=79;AB=0.9393;ABA=57;ABP=1577;ABR=882;AC=38;AF=0.0411;AN=924;BL=644;BR=5536;BVAR;BaseQRankSum=2.434;DEL;DP=9687;Dels=0.00;EL=45;EPP=6.3362;ER=34;FS=3.043;HETAR=321;HOMA=182;HOMR=555;HRun=5;InbreedingCoeff=0.0412;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.79159;LRBP=8411.9;MQ0=0;MQ0Fraction=0.0000;MQM=70.848;MQRankSum=0.137;NS=1058;RA=3415;RL=3;RPP=149.49;RR=76;RUN=1;ReadPosRankSum=-12.116;SAB=0.44304;SAF=35;SAP=5.2367;SAR=44;SRB=0.43572;SRF=1488;SRP=125.55;SRR=1927;VQSLOD=3.8910;set=filterInVQSR-2of5;sumGLbyD=4.88 20 2771621 rs11479849 GT G,GTT 1605.60 PASS AA=80;AB=0.79825;ABA=69;ABP=267.24;ABR=273;AC=79,91;AF=0.06551,0.07546;AN=1206;BL=2593;BR=3805;BVAR;BaseQRankSum=7.825;DB;DP=9790;Dels=0.04;EL=37;EPP=3.9875;ER=43;FR;FS=4.751;HETAR=62;HOMA=5;HOMR=958;HP=11;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2646;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.18943;LRBP=501.57;MQ0=0;MQ0Fraction=0.0000;MQM=52.45;MQRankSum=-0.560;NF;NR;NS=1025;PP;RA=3949;RL=29;RPP=16.148;RR=51;RUN=1;ReadPosRankSum=-2.397;SAB=0.525;SAF=42;SAP=3.4446;SAR=38;SC=TCATTTTAACGTTTTTTTTTT;SET_WGVQSR;SRB=0.54368;SRF=2147;SRP=68.46;SRR=1802;TC;TR=11;TU=T;VQSLOD=3.5989;set=filterInVQSR-2of5;sumGLbyD=3.92 20 2891235 . G GT,GTTT 2869.87 PASS AC=236,246;AF=0.2803,0.2922;AN=842;BaseQRankSum=8.979;DP=1067;FS=3.911;HaplotypeScore=20.3595;InbreedingCoeff=0.6511;IndelType=MULTIALLELIC_INDEL;MQ=44.86;MQ0=114;MQ0Fraction=0.1068;MQRankSum=-2.273;QD=4.00;ReadPosRankSum=-6.601;SB=-991.85;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.4379;set=VQSR 20 3033550 . TGAG T 2005.90 PASS AA=34;AB=0.51429;ABA=34;ABP=3.1344;ABR=36;AC=22;AF=0.0332;AN=662;BL=1374;BR=1649;BVAR;BaseQRankSum=5.192;DEL;DP=14639;DP4=2271,1492,12,21;Dels=0.02;EL=19;EPP=4.0322;ER=15;FR;FS=16.657;HETAR=17;HOMA=0;HOMR=914;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=-0.0454;IndelType=DEL.NumRepetitions_1.EventLength_3.;LEN=3;LRB=0.090969;LRBP=57.333;MQ=53.99;MQ0Fraction=0.0304;MQM=46.735;MQRankSum=1.938;NF;NR;NS=931;PP;PV4=0.0068,9.4e-05,1,1;RA=2985;RL=11;RPP=12.207;RR=23;RUN=1;ReadPosRankSum=-0.466;SAB=0.41176;SAF=14;SAP=5.3095;SAR=20;SC=CTTGGGAGGCTGAGGTGGGAG;SET_INTEGRATION;SET_WGVQSR;SRB=0.62781;SRF=1874;SRP=426.52;SRR=1111;TC;TR=1;TU=G;VQSLOD=8.9194;set=Intersection;sumGLbyD=24.41 20 3873327 rs61519218 A AAG 683.85 PASS AC=25;AF=0.0313;AN=800;BaseQRankSum=4.839;DB;DP=1718;FS=4.265;HRun=0;HaplotypeScore=20.5789;InbreedingCoeff=0.1055;IndelType=INS.NOVEL_2.;MQ=53.70;MQ0=37;MQ0Fraction=0.0215;MQRankSum=2.468;QD=6.30;ReadPosRankSum=4.254;SB=-403.21;SET_INTEGRATION;SET_WGVQSR;VQSLOD=6.1858;set=VQSR 20 4028835 . GC G 2511.30 PASS AA=66;AB=0.56954;ABA=65;ABP=9.3521;ABR=86;AC=22;AF=0.01836;AN=1198;BL=2303;BR=2463;BVAR;BaseQRankSum=7.621;DEL;DP=22795;DP4=1714,2774,22,37;Dels=0.02;EL=34;EPP=3.1419;ER=32;FQ=999;FR;FS=2.095;HETAR=21;HOMA=0;HOMR=1050;HP=2;HPLen=2;HR=2;HRun=2;HU=C;INDEL;InbreedingCoeff=0.0125;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.033571;LRBP=14.674;MQ=108.09;MQ0=0;MQ0Fraction=0.0000;MQM=53.318;MQRankSum=5.257;NF;NR;NS=1071;PP;PV4=1,5.4e-13,1,0.075;RA=6185;RL=36;RPP=4.1947;RR=30;RUN=1;ReadPosRankSum=-1.059;SAB=0.45455;SAF=30;SAP=4.1947;SAR=36;SC=TGCTGTCACTGCCTTCTCCTA;SET_INTEGRATION;SET_WGVQSR;SRB=0.42118;SRF=2605;SRP=336.76;SRR=3580;TC;TR=2;TU=C;VQSLOD=10.2409;set=Intersection;sumGLbyD=12.71 20 4039609 rs67812039 G GA 43457 PASS AA=909;AB=0.54639;ABA=572;ABP=26.583;ABR=689;AC=302;AF=0.3455;AN=874;BL=37070;BR=38211;BVAR;BaseQRankSum=20.147;DB;DP=25595;DP4=1483,1374,528,542;Dels=0.00;EL=467;EPP=4.5033;ER=442;FQ=999;FR;FS=5.441;HETAR=243;HOMA=127;HOMR=608;HP=4;HPLen=3;HR=3;HRun=3;HU=A;INDEL;INS;InbreedingCoeff=0.1388;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.015157;LRBP=40.563;MQ=119.50;MQ0=0;MQ0Fraction=0.0000;MQM=83.197;MQRankSum=1.080;NF;NR;NS=978;PP;PV4=0.16,1,3.6e-12,1;RA=3033;RL=443;RPP=4.274;RR=466;RUN=1;ReadPosRankSum=-1.000;SAB=0.32233;SAF=293;SAP=252.24;SAR=616;SC=TATGTTGGGAGAAATATCAGT;SET_INTEGRATION;SET_WGVQSR;SRB=0.38378;SRF=1164;SRP=358.85;SRR=1869;TC;TR=4;TU=AG;VQSLOD=9.9146;dbSNP=130;set=Intersection;sumGLbyD=16.79 20 4390056 . TC T 49312 PASS AA=91;AB=0.94353;ABA=86;ABP=2605.4;ABR=1437;AC=39;AF=0.03160;AN=1234;BL=6823;BR=731;BVAR;BaseQRankSum=2.727;DEL;DP=13149;Dels=0.00;EL=41;EPP=4.9431;ER=50;FS=4.002;HETAR=465;HOMA=313;HOMR=292;HRun=3;InbreedingCoeff=0.0326;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.80646;LRBP=10671;MQ0=0;MQ0Fraction=0.0000;MQM=69.824;MQRankSum=-0.903;NS=1073;RA=3078;RL=89;RPP=183.62;RR=2;RUN=1;ReadPosRankSum=-12.526;SAB=0.45055;SAF=41;SAP=4.9431;SAR=50;SRB=0.52567;SRF=1618;SRP=20.622;SRR=1460;VQSLOD=4.3235;set=Intersection;sumGLbyD=3.53 20 4474622 . TA T,TAA,TAAA,TAAAA 94522.28 PASS ABR=114;AC=38,68,16,900;AF=0.03333,0.05965,0.01404,0.78947;AN=1140;BVAR;BaseQRankSum=9.741;DB;DP=16656;Dels=0.00;FR;FS=2.355;HOMA=3;HOMR=936;HP=10;HPLen=10;HR=10;HRun=10;HU=A;INS;InbreedingCoeff=0.4516;IndelType=MULTIALLELIC_INDEL;MQ0=2;MQ0Fraction=0.0008;MQRankSum=-4.096;NF;NR;NS=980;PP;RA=3766;RUN=1;ReadPosRankSum=2.380;SC=AGAAAAAAATTAAAAAAAAAA;SET_WGVQSR;SRB=0.49734;SRF=1873;SRP=3.2409;SRR=1893;TC;TR=10;TU=A;VQSLOD=8.8186;set=Intersection;sumGLbyD=38.79 20 4824911 . AC A 41998.70 PASS AC=1172;AF=0.97342;AN=1204;BaseQRankSum=8.604;DP=3615;FS=9.934;HRun=1;HaplotypeScore=39.6843;InbreedingCoeff=0.0980;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=129.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=3.378;QD=11.62;ReadPosRankSum=6.967;SB=-16955.28;VQSLOD=4.2689;set=VQSR 20 4839897 rs35881880 TAA T,TA,TAAA,TAAAAA 3906.80 PASS AC=12,95,137,189;AF=0.01024,0.08106,0.11689,0.16126;AN=1172;BVAR;BaseQRankSum=15.271;DB;DEL;DP=15105;Dels=0.04;FR;FS=43.567;HP=19;HR=13;HRun=13;HU=A;INS;InbreedingCoeff=0.5716;IndelType=MULTIALLELIC_INDEL;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.569;NF;NR;PP;RUN=1;ReadPosRankSum=-13.794;SC=TGTTAAAAAATAAAAAAAAAA;TC;TR=13;TU=A;VQSLOD=8.1773;set=Intersection;sumGLbyD=3.77 20 5507414 . G GCC 439.08 PASS AC=23;AF=0.01876;AN=1226;BaseQRankSum=3.051;DP=3023;FS=3.636;HRun=1;HaplotypeScore=30.3104;InbreedingCoeff=0.0204;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=112.09;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.065;QD=2.85;ReadPosRankSum=-2.709;SB=-302.22;VQSLOD=4.4311;set=VQSR 20 5609676 . GA G,GAA 799.89 PASS AA=42;AB=0.79096;ABA=37;ABP=133.16;ABR=140;AC=43,65;AF=0.03607,0.05453;AF1=0.02826;AN=1192;BL=1360;BR=2334;BVAR;BaseQRankSum=5.069;CI95=0.01242,0.04037;DP=15610;DP4=1548,2441,21,30;Dels=0.02;EL=18;EPP=4.8716;ER=24;FQ=12.1;FR;FS=0.000;HETAR=36;HOMA=1;HOMR=991;HP=13;HPLen=10;HR=10;HRun=10;HU=A;INDEL;INS;InbreedingCoeff=0.2001;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.26367;LRBP=560.68;MQ=63.29;MQ0Fraction=0.0003;MQM=44.143;MQRankSum=1.755;NF;NR;NS=1028;PP;PV4=0.77,1,0.0087,0.0053;RA=4114;RL=15;RPP=10.455;RR=27;RUN=1;ReadPosRankSum=-2.978;SAB=0.5;SAF=21;SAP=3.0103;SAR=21;SC=AAAAAAGAAAGAAAAAAAAAA;SET_WGVQSR;SRB=0.39742;SRF=1635;SRP=379;SRR=2479;TC;TR=11;TU=AAAG;VQSLOD=4.1229;set=filterInVQSR-2of5;sumGLbyD=7.95 20 5736211 rs35303106 CT C,CTT 4384.40 PASS AA=117;AB=0.71499;ABA=116;ABP=166.4;ABR=291;AC=32,145;AF=0.02712,0.12288;AN=1180;BL=5556;BR=4901;BVAR;BaseQRankSum=2.708;DB;DP=9157;Dels=0.01;EL=54;EPP=4.5136;ER=63;FR;FS=2.802;HETAR=79;HOMA=1;HOMR=837;HP=16;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.1903;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.062637;LRBP=92.1;MQ0Fraction=0.0273;MQM=48.932;MQRankSum=3.654;NF;NR;NS=917;PP;RA=2785;RL=79;RPP=34.209;RR=38;RUN=1;ReadPosRankSum=0.795;SAB=0.5641;SAF=66;SAP=7.1862;SAR=51;SC=TTTTCTTTTTCTTTTTTTTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.41795;SRF=1164;SRP=165.85;SRR=1621;TC;TR=11;TU=T;VQSLOD=5.0895;set=Intersection;sumGLbyD=4.66 20 5898626 rs34483659 CAAA C,CA,CAA,CAAAAA 1140.16 PASS ABR=34;AC=19,98,56,199;AF=0.0227,0.1172,0.0670,0.2380;AF1=0.08519;BVAR;BaseQRankSum=5.049;CI95=0.03727,0.1273;DB;DEL;DP=5091;DP4=539,408,121,123;FQ=4.43;FR;FS=5.701;HOMA=64;HOMR=156;HP=19;HR=18;HU=A;HaplotypeScore=11.5333;INDEL;InbreedingCoeff=0.7405;IndelType=MULTIALLELIC_INDEL;MQ0=117;MQ0Fraction=0.0986;MQRankSum=6.290;NF;NR;NS=240;PP;PV4=0.043,1,1,0.0087;QD=1.22;RA=204;RUN=1;ReadPosRankSum=-2.684;SB=-1015.09;SC=ACTAAAAATACAAAAAAAAAA;SET_WGVQSR;SRB=0.35294;SRF=72;SRP=41.33;SRR=132;TC;TR=18;TU=A;VQSLOD=4.1696;set=filterInVQSR-2of5 20 5975126 rs10541892 C CAG 504.78 PASS AC=79;AF=0.07004;AN=1128;BaseQRankSum=10.498;DB;DP=2050;FS=38.228;HRun=0;HaplotypeScore=14.1426;InbreedingCoeff=-0.0053;IndelType=INS.NOVEL_2.;MQ=60.40;MQ0=80;MQ0Fraction=0.0390;MQRankSum=5.098;QD=1.63;ReadPosRankSum=-4.851;SB=-590.69;VQSLOD=4.8517;set=VQSR 20 6040983 rs11087710 A AAAAAAGAG,AAAAAGAG,AAAAGAG,AAAAGAGAG,AAAGAG,AAAGAGAG,AAGAG,AAGAGAG,AG,AGAG,AGAGAG 66894.55 PASS ABR=468;AC=80,9,20,136,31,91,33,29,9,3,5;AF=0.0980,0.0110,0.0245,0.1667,0.0380,0.1115,0.0404,0.0355,0.0110,0.0037,0.0061;AN=816;BVAR;BaseQRankSum=-12.470;DB;DP=38726;DP4=426,611,310,472;Dels=0.00;FQ=999;FR;FS=6.635;HOMA=110;HOMR=506;HP=14;HR=15;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.8291;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ=54.22;MQ0Fraction=0.0168;MQRankSum=-5.329;NF;NR;NS=861;PP;PV4=0.56,1,6.9e-09,0.31;RA=1828;RUN=1;ReadPosRankSum=-7.857;SC=AAAAAAAAAAAAGAGAGAGAG;SET_WGVQSR;SRB=0.62418;SRF=1141;SRP=247.85;SRR=687;TC;TR=15;TU=A;VQSLOD=9.0574;dbSNP=131;set=Intersection;sumGLbyD=36.72 20 7024548 . G GAT 5041.27 PASS AC=123;AF=0.10336;AN=1190;BaseQRankSum=23.097;DP=3045;FS=7.979;HRun=0;HaplotypeScore=15.6967;InbreedingCoeff=0.1062;IndelType=INS.NumRepetitions_5.EventLength_2.RepeatExpansion_AT.;MQ=119.29;MQ0=2;MQ0Fraction=0.0007;MQRankSum=-3.725;QD=8.97;ReadPosRankSum=-1.636;SB=-2257.45;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.9332;set=VQSR 20 7484554 . A AT 5.09 PASS AC=0;AF=0.0000;AN=710;BaseQRankSum=-0.696;DP=1862;FS=2.835;HRun=9;HaplotypeScore=13.5425;InbreedingCoeff=0.0567;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_T.;MQ=76.92;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.932;ReadPosRankSum=-1.701;VQSLOD=4.3156;set=VQSR 20 7632194 rs77286341 GAA AAA,G 5324 PASS AC=0;AF=0.0000;AN=700;BaseQRankSum=-1.741;DB;DP=1772;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=60.1795;InbreedingCoeff=0.0017;IndelType=MIXED;MQ=70.69;MQ0=13;MQ0Fraction=0.0073;MQRankSum=-1.315;NF;NR;PP;ReadPosRankSum=-3.650;SC=GAGAGAGAGAGAAAGGTGTAA;TC;TR=13;TU=AG;set=filterInVQSR-2of5 20 7767508 rs71329674 G GA 17914 PASS AA=415;AB=0.61617;ABA=337;ABP=105.94;ABR=541;AC=141;AF=0.11614;AN=1214;BL=15187;BR=20323;BVAR;BaseQRankSum=-13.946;DB;DP=28222;Dels=0.00;EL=184;EPP=14.569;ER=231;FQ=999;FR;FS=13.296;HETAR=178;HOMA=35;HOMR=822;HP=14;HPLen=9;HR=9;HRun=9;HU=A;INDEL;INS;InbreedingCoeff=0.0714;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.14464;LRBP=1616.1;MQ=89.69;MQ0=1;MQ0Fraction=0.0003;MQM=51.667;MQRankSum=0.664;NF;NR;NS=1035;PP;RA=3707;RL=171;RPP=30.894;RR=244;RUN=1;ReadPosRankSum=-1.120;SAB=0.45301;SAF=188;SAP=10.969;SAR=227;SC=ATTCTAAAAAGAAAAAAAAAT;SET_INTEGRATION;SET_WGVQSR;SRB=0.38495;SRF=1427;SRP=429.23;SRR=2280;TC;TR=9;TU=A;VQSLOD=9.0748;set=Intersection;sumGLbyD=11.09 20 7920261 . TA T,TAA 802.15 PASS AA=28;AB=0.8;ABA=28;ABP=112.45;ABR=112;AC=22,39;AF=0.01836,0.03255;AN=1198;BL=943;BR=1487;BVAR;BaseQRankSum=2.233;DP=10645;Dels=0.01;EL=11;EPP=5.8022;ER=17;FR;FS=1.691;HETAR=20;HOMA=0;HOMR=1007;HP=10;HPLen=9;HR=9;HRun=9;HU=A;INS;InbreedingCoeff=0.2256;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.22387;LRBP=267.46;MQ0=0;MQ0Fraction=0.0000;MQM=57.571;MQRankSum=0.940;NF;NR;NS=1027;PP;RA=4776;RL=8;RPP=14.178;RR=20;RUN=1;ReadPosRankSum=-1.567;SAB=0.53571;SAF=15;SAP=3.3205;SAR=13;SC=GTAACTGCTATAAAAAAAAAC;SET_WGVQSR;SRB=0.48576;SRF=2320;SRP=11.42;SRR=2456;TC;TR=9;TU=A;VQSLOD=4.0815;set=filterInVQSR-2of5;sumGLbyD=5.37 20 8012465 rs10595338 TATGA T 2104.41 PASS AF=0.03339;BaseQRankSum=10.662;DB;DP=11772;DS;Dels=0.01;FR;FS=7.678;HP=1;HPLen=1;HR=1;HRun=0;HU=A;InbreedingCoeff=0.0266;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ0Fraction=0.0731;MQRankSum=0.603;NF;NR;PP;ReadPosRankSum=1.276;SC=TGTATGTATGTATGATGTATG;TC;TR=19;TU=ATGT;VQSLOD=4.1376;set=filterInVQSR-2of5;sumGLbyD=6.53 20 8573999 . CGTGT C,CGT,CGTGTGT,TGTGT 45865.96 PASS AC=458,0,731;AF=0.37727,0.00000,0.60214;AN=1214;BVAR;BaseQRankSum=-6.703;DEL;DP=37714;Dels=0.03;FR;FS=11.079;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.7632;IndelType=MIXED;LEN=2;MQ0Fraction=0.0026;MQRankSum=-1.394;NF;NR;PP;RUN=1;ReadPosRankSum=-2.102;SC=TGTGTGTGCGCGTGTGTGTGT;SET_INTEGRATION;SET_WGVQSR;TC;TR=18;TU=GT;VQSLOD=6.1435;set=Intersection;sumGLbyD=3.53 20 8610455 rs10571111 TTTTC T 11763.51 PASS AC=190;AF=0.17056;AN=1114;BaseQRankSum=-14.397;DB;DP=2323;FS=2.321;HRun=0;HaplotypeScore=39.8020;InbreedingCoeff=0.2502;IndelType=DEL.NumRepetitions_2.EventLength_4.;MQ=53.39;MQ0=104;MQ0Fraction=0.0448;MQRankSum=3.519;QD=19.07;ReadPosRankSum=4.150;SB=-4067.02;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.0554;set=VQSR 20 9139079 . ATT A,AT,ATTT,ATTTT,ATTTTT 8777.90 PASS AC=23,140,114,69,113;AF=0.01993,0.12132,0.09879,0.05979,0.09792;AN=1154;BVAR;BaseQRankSum=-0.022;DEL;DP=25109;DP4=502,657,278,313;FR;FS=11.929;HP=16;HR=16;HU=T;HaplotypeScore=20.2361;INDEL;INS;InbreedingCoeff=0.5704;IndelType=MULTIALLELIC_INDEL;MQ0=16;MQ0Fraction=0.0067;MQRankSum=2.624;NF;NR;PP;PV4=0.14,1,1,1;QD=1.48;RUN=1;ReadPosRankSum=-0.480;SB=-2354.28;SC=CACCTGGCTAATTTTTTTTTT;SET_WGVQSR;TC;TR=16;TU=T;VQSLOD=6.9180;set=Intersection 20 9862448 . CT C 49312 PASS AA=60;AB=0.96003;ABA=53;ABP=2440.4;ABR=1273;AC=18;AF=0.01461;AN=1232;BL=3516;BR=140;BVAR;BaseQRankSum=-2.056;DEL;DP=11893;Dels=0.01;EL=35;EPP=6.6294;ER=25;FS=1.787;HETAR=396;HOMA=344;HOMR=334;HRun=1;InbreedingCoeff=0.0379;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.92341;LRBP=6772.5;MQ0Fraction=0.0006;MQM=54.267;MQRankSum=-0.907;NS=1074;RA=2990;RL=60;RPP=133.3;RR=0;RUN=1;ReadPosRankSum=-10.579;SAB=0.58333;SAF=35;SAP=6.6294;SAR=25;SRB=0.47826;SRF=1430;SRP=15.284;SRR=1560;VQSLOD=3.0237;set=filterInVQSR-2of5;sumGLbyD=2.84 20 9863736 rs73618103 G GT 50570.21 PASS AA=2247;AB=0.48878;ABA=1412;ABP=6.0324;ABR=1350;AC=546;AF=0.44463;AN=1228;BL=86886;BR=95862;BVAR;BaseQRankSum=-23.978;DB;DP=32517;DP4=1125,1133,1017,1048;Dels=0.00;EL=1089;EPP=7.6113;ER=1158;FQ=999;FR;FS=2.529;HETAR=445;HOMA=201;HOMR=393;HP=4;HPLen=4;HR=4;HRun=4;HU=T;INDEL;INS;InbreedingCoeff=0.1393;IndelType=INS.NumRepetitions_4.EventLength_1.RepeatExpansion_T.;KGPilot123;LEN=1;LRB=0.049117;LRBP=960.35;MQ=68.10;MQ0=2;MQ0Fraction=0.0006;MQM=50.931;MQRankSum=-1.580;NF;NR;NS=1039;PP;PV4=0.71,1,0.11,1;RA=3139;RL=1089;RPP=7.6113;RR=1158;RUN=1;ReadPosRankSum=0.846;SAB=0.54161;SAF=1217;SAP=36.804;SAR=1030;SC=TGATTGTATGGTTTTGTCCTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.53425;SRF=1677;SRP=34.987;SRR=1462;TC;TR=4;TU=T;VLD;VQSLOD=10.1800;dbSNP=131;set=Intersection;sumGLbyD=18.20 20 10926959 . AG A 12239 PASS AA=65;AB=0.92801;ABA=64;ABP=1417.6;ABR=825;AC=24;AF=0.0264;AN=908;BL=616;BR=3782;BVAR;BaseQRankSum=9.990;DEL;DP=10708;Dels=0.01;EL=37;EPP=5.7163;ER=28;FS=1.652;HETAR=275;HOMA=70;HOMR=724;HRun=1;InbreedingCoeff=0.0102;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.71987;LRBP=4952;MQ0=1;MQ0Fraction=0.0004;MQM=118.82;MQRankSum=1.018;NS=1069;RA=4746;RL=5;RPP=104.07;RR=60;RUN=1;ReadPosRankSum=-12.039;SAB=0.41538;SAF=27;SAP=7.0526;SAR=38;SRB=0.4764;SRF=2261;SRP=25.968;SRR=2485;VQSLOD=2.9713;set=filterInVQSR-2of5;sumGLbyD=4.10 20 11299648 . TG T 49315 PASS AA=62;AB=0.95292;ABA=54;ABP=2046.7;ABR=1093;AC=28;AF=0.0373;AN=750;BL=3126;BR=528;BVAR;BaseQRankSum=-4.929;DEL;DP=10764;Dels=0.01;EL=26;EPP=6.5127;ER=36;FS=3.851;HETAR=366;HOMA=383;HOMR=304;HRun=1;InbreedingCoeff=0.0267;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.711;LRBP=4014.1;MQ0=1;MQ0Fraction=0.0005;MQM=76.468;MQRankSum=1.327;NS=1070;RA=2588;RL=54;RPP=77.121;RR=8;RUN=1;ReadPosRankSum=-12.507;SAB=0.48387;SAF=30;SAP=3.1504;SAR=32;SRB=0.47643;SRF=1233;SRP=15.499;SRR=1355;VQSLOD=3.8673;set=filterInVQSR-2of5;sumGLbyD=3.00 20 11561096 . CTA C 999 PASS AC=2;AF=0.0029;AF1=0.005602;BaseQRankSum=3.190;CI95=0.004425,0.01106;DP=7521;DP4=1998,1794,2,4;Dels=0.00;FQ=999;FR;FS=5.422;HP=3;HPLen=2;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0056;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;MQ=113.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.297;NF;NR;PP;PV4=0.43,0.024,1,1;ReadPosRankSum=1.406;SC=CAATAGTATTCTATGTCAGTC;SET_INTEGRATION;SET_WGVQSR;TC;TR=1;TU=T;VQSLOD=8.6243;set=Intersection;sumGLbyD=21.89 20 11723671 . C CA 1096.60 PASS AA=35;AB=0.69565;ABA=35;ABP=41.247;ABR=80;AC=10;AF=0.0141;AN=710;BL=2005;BR=1702;BVAR;BaseQRankSum=-3.427;DP=9819;Dels=0.00;EL=20;EPP=4.5614;ER=15;FR;FS=3.814;HETAR=20;HOMA=0;HOMR=1034;HP=8;HPLen=7;HR=7;HRun=7;HU=A;INS;InbreedingCoeff=0.0323;IndelType=INS.NumRepetitions_7.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.081737;LRBP=56.79;MQ0=0;MQ0Fraction=0.0000;MQM=81.057;MQRankSum=0.050;NF;NR;NS=1054;PP;RA=5562;RL=22;RPP=8.0357;RR=13;RUN=1;ReadPosRankSum=-2.012;SAB=0.71429;SAF=25;SAP=16.97;SAR=10;SC=ATATTGAAGACAAAAAAACAG;SET_INTEGRATION;SET_WGVQSR;SRB=0.49371;SRF=2746;SRP=4.9233;SRR=2816;TC;TR=7;TU=A;VQSLOD=7.4342;set=Intersection;sumGLbyD=8.30 20 12238835 rs113904674 CTCTTCATGGTCT C 1813.44 PASS AA=7;AB=0.73077;ABA=7;ABP=15.037;ABR=19;AC=4;AF=0.0056;AN=712;BL=360;BR=368;BVAR;BaseQRankSum=3.891;DB;DEL;DP=10309;Dels=0.00;EL=4;EPP=3.3205;ER=3;FR;FS=0.000;HETAR=3;HOMA=0;HOMR=1076;HP=1;HPLen=2;HR=2;HRun=0;HU=C;InbreedingCoeff=-0.0381;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;LEN=12;LRB=0.010989;LRBP=3.2012;MQ0=0;MQ0Fraction=0.0000;MQM=37;MQRankSum=-3.793;NF;NR;NS=1079;PP;RA=6085;RL=4;RPP=3.3205;RR=3;RUN=1;ReadPosRankSum=1.319;SAB=0.42857;SAF=3;SAP=3.3205;SAR=4;SC=CTTAATGCTCCTCTTCATGGT;SET_INTEGRATION;SET_WGVQSR;SRB=0.51257;SRF=3119;SRP=11.364;SRR=2966;TC;TR=6;TU=CCT;VQSLOD=5.7551;set=Intersection;sumGLbyD=69.48 20 12602812 . AT A 12344 PASS AA=47;AB=0.94372;ABA=43;ABP=1309.5;ABR=721;AC=14;AF=0.0196;AN=716;BL=2714;BR=217;BVAR;BaseQRankSum=1.424;DEL;DP=10743;Dels=0.00;EL=24;EPP=3.0565;ER=23;FS=0.629;HETAR=228;HOMA=65;HOMR=769;HRun=1;InbreedingCoeff=0.0233;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.85193;LRBP=4622.3;MQ0Fraction=0.0000;MQM=99.574;MQRankSum=1.901;NS=1080;RA=4839;RL=46;RPP=96.568;RR=1;RUN=1;ReadPosRankSum=-9.906;SAB=0.53191;SAF=25;SAP=3.4261;SAR=22;SRB=0.51106;SRF=2473;SRP=8.148;SRR=2366;VQSLOD=2.8161;set=filterInVQSR-2of5;sumGLbyD=3.67 20 13600884 . CTG C,CTGTG 1278.10 PASS AA=85;AB=0.77994;ABA=79;ABP=247.38;ABR=280;AC=71,22;AF=0.05907,0.01830;AN=1202;BL=3279;BR=3205;BVAR;BaseQRankSum=8.852;DEL;DP=24185;DP4=1317,931,52,49;Dels=0.03;EL=45;EPP=3.649;ER=40;FQ=999;FR;FS=31.826;HETAR=75;HOMA=4;HOMR=926;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1566;IndelType=MULTIALLELIC_INDEL;LEN=2;LRB=0.011413;LRBP=4.8442;MQ=65.06;MQ0Fraction=0.0012;MQM=48.671;MQRankSum=-0.511;NF;NR;NS=1005;PP;PV4=0.18,1,0.39,0.27;RA=3342;RL=35;RPP=8.7583;RR=50;RUN=1;ReadPosRankSum=-2.329;SAB=0.43529;SAF=37;SAP=6.1015;SAR=48;SC=TCCCTTTACTCTGTGTGTGTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.59066;SRF=1974;SRP=241.62;SRR=1368;TC;TR=15;TU=GT;VQSLOD=3.8635;set=filterInVQSR-2of5;sumGLbyD=4.23 20 13666265 . T TATAG 556.88 PASS AC=21;AF=0.01959;AN=1072;BaseQRankSum=24.958;DP=2706;FS=2.581;HRun=0;HaplotypeScore=25.9952;InbreedingCoeff=0.1419;IndelType=INS.NOVEL_4.;MQ=72.43;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.888;QD=4.38;ReadPosRankSum=2.552;SB=-417.04;SET_INTEGRATION;SET_WGVQSR;VQSLOD=7.3380;set=VQSR 20 13861245 rs72422273 C CTCA 2685.46 PASS AC=140;AF=0.11589;AN=1208;BaseQRankSum=24.355;DB;DP=2910;FS=6.808;HRun=0;HaplotypeScore=19.3095;InbreedingCoeff=-0.0991;IndelType=INS.NumRepetitions_1.EventLength_3.;MQ=78.25;MQ0=22;MQ0Fraction=0.0076;MQRankSum=3.225;QD=3.64;ReadPosRankSum=2.607;SB=-1861.38;VQSLOD=4.1974;set=VQSR 20 13865746 . T TA,TAA 1416.23 PASS AA=63;AB=0.80417;ABA=47;ABP=195.87;ABR=193;AC=122,21;AF=0.10133,0.01744;AN=1204;BL=3673;BR=1145;BVAR;BaseQRankSum=-3.336;DP=10513;Dels=0.00;EL=62;EPP=131.27;ER=1;FR;FS=716.583;HETAR=45;HOMA=1;HOMR=998;HP=2;HR=1;HRun=1;HU=A;INS;InbreedingCoeff=0.0814;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.5247;LRBP=2883.3;MQ0=0;MQ0Fraction=0.0000;MQM=56.143;MQRankSum=-1.197;NF;NR;NS=1044;PP;RA=4529;RL=62;RPP=131.27;RR=1;RUN=1;ReadPosRankSum=-12.295;SAB=1;SAF=63;SAP=139.81;SAR=0;SC=GGAACATGGATACCCCCCTGC;SRB=0.52462;SRF=2376;SRP=26.853;SRR=2153;TC;TR=1;TU=A;VQSLOD=-4.2308;set=filterInVQSR-2of5;sumGLbyD=4.77 20 13881703 . CTT C 152.85 PASS AC=8;AF=0.0093;AN=862;BaseQRankSum=3.941;DP=2063;FS=0.962;HRun=5;HaplotypeScore=24.0313;InbreedingCoeff=0.0790;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_T.;MQ=55.05;MQ0=49;MQ0Fraction=0.0238;MQRankSum=-1.418;QD=3.47;ReadPosRankSum=-0.605;SB=-93.04;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.3874;set=VQSR 20 14260090 rs73619828 A AT 27935 PASS AA=596;AB=0.59484;ABA=487;ABP=96.922;ABR=715;AC=204;AF=0.17000;AN=1200;BL=21718;BR=28458;BVAR;BaseQRankSum=0.756;DB;DP=23629;DP4=1385,1492,287,328;Dels=0.00;EL=299;EPP=3.0249;ER=297;FQ=999;FR;FS=6.187;HETAR=218;HOMA=38;HOMR=788;HP=9;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.0797;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13433;LRBP=1969;MQ=100.81;MQ0=0;MQ0Fraction=0.0000;MQM=57.084;MQRankSum=2.224;NF;NR;NS=1044;PP;PV4=0.53,1,1.2e-11,1;RA=4143;RL=238;RPP=55.475;RR=358;RUN=1;ReadPosRankSum=0.198;SAB=0.46812;SAF=279;SAP=8.2714;SAR=317;SC=CCTTAAGTTGATTTTTTTTTC;SET_INTEGRATION;SET_WGVQSR;SRB=0.50374;SRF=2087;SRP=3.514;SRR=2056;TC;TR=9;TU=T;VQSLOD=9.0018;set=Intersection;sumGLbyD=10.82 20 14260558 . AC A 238 PASS AC=1;AF=0.0014;AF1=0.003368;BaseQRankSum=2.868;CI95=0.003106,0.006211;DP=9724;DP4=2075,2329,1,7;Dels=0.00;FQ=106;FR;FS=10.678;HP=1;HPLen=2;HR=2;HRun=1;HU=A;INDEL;InbreedingCoeff=-0.0406;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=114.37;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.862;NF;NR;PP;PV4=0.074,0.0096,0.017,1;ReadPosRankSum=-0.042;SC=ATCAGGAATAACTGTGTGACC;SET_INTEGRATION;SET_WGVQSR;TC;TR=2;TU=A;VQSLOD=8.1618;set=Intersection;sumGLbyD=18.65 20 14425481 . GTA G,GTATA 148.85 PASS AC=43,23;AF=0.03473,0.01858;AN=1238;BaseQRankSum=6.289;DP=25167;DP4=1800,2021,38,49;FR;FS=9.416;HP=2;HPLen=1;HR=1;HU=T;HaplotypeScore=17.7453;INDEL;InbreedingCoeff=0.0995;IndelType=MULTIALLELIC_INDEL;MQ0=21;MQ0Fraction=0.0058;MQRankSum=-0.200;NF;NR;PP;PV4=0.59,1,0.04,0.023;QD=0.35;ReadPosRankSum=-1.689;SB=-367.50;SC=CTGTGTGTGTGTATATATATA;SET_WGVQSR;TC;TR=13;TU=AT;VQSLOD=3.5796;set=filterInVQSR-2of5 20 14943522 rs11478299 GA AA,G 1761.24 PASS AA=117;AB=0.68142;ABA=108;ABP=99.919;ABR=231;AC=0;AF=0.0000;AF1=0.04204;AN=712;BL=4931;BR=5802;BVAR;BaseQRankSum=9.118;CI95=0.02876,0.05752;DB;DEL;DP=13717;DP4=1908,1684,59,58;Dels=0.05;EL=60;EPP=3.1773;ER=57;FQ=81.9;FR;HETAR=56;HOMA=1;HOMR=1011;HP=8;HPLen=8;HR=8;HU=A;INDEL;InbreedingCoeff=0.1264;IndelType=MIXED;LEN=1;LRB=0.081152;LRBP=156.5;MQ=106.93;MQ0=0;MQ0Fraction=0.0000;MQM=96.855;MQRankSum=1.619;NF;NR;NS=1068;PP;PV4=0.57,1,0.0003,1;QD=7.40;RA=5080;RL=56;RPP=3.4743;RR=61;RUN=1;ReadPosRankSum=0.814;SAB=0.52137;SAF=61;SAP=3.4743;SAR=56;SB=-1122.51;SC=GTTGTTTGGGGAAAAAAAACT;SET_WGVQSR;SRB=0.51083;SRF=2595;SRP=8.1825;SRR=2485;TC;TR=8;TU=A;set=filterInVQSR-2of5;sumGLbyD=9.81 20 14974486 . A AG 4101.40 PASS AA=57;AB=0.57143;ABA=51;ABP=8.2839;ABR=68;AC=22;AF=0.01846;AN=1192;BL=2286;BR=2834;BVAR;BaseQRankSum=8.711;DP=20538;DP4=2172,2100,19,13;Dels=0.00;EL=32;EPP=4.877;ER=25;FS=0.517;HETAR=20;HOMA=4;HOMR=1027;HRun=1;INDEL;INS;InbreedingCoeff=0.0677;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.10703;LRBP=130.37;MQ=126.07;MQ0=0;MQ0Fraction=0.0000;MQM=56.088;MQRankSum=-10.756;NS=1051;PV4=0.38,3.5e-51,7.9e-34,1;RA=5203;RL=26;RPP=3.9627;RR=31;RUN=1;ReadPosRankSum=1.283;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SET_INTEGRATION;SET_WGVQSR;SRB=0.51816;SRF=2696;SRP=17.918;SRR=2507;VQSLOD=8.0072;set=Intersection;sumGLbyD=25.60 20 15111137 . GA G 13533 PASS AA=98;AB=0.84864;ABA=89;ABP=623.8;ABR=499;AC=47;AF=0.03796;AN=1238;BL=5324;BR=856;BVAR;BaseQRankSum=-11.577;DEL;DP=13384;Dels=0.01;EL=53;EPP=4.4284;ER=45;FS=6.099;HETAR=219;HOMA=845;HOMR=18;HRun=1;InbreedingCoeff=-0.0056;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.72298;LRBP=7017.4;MQ0Fraction=0.0003;MQM=90.449;MQRankSum=1.408;NS=1083;RA=590;RL=87;RPP=130.99;RR=11;RUN=1;ReadPosRankSum=-18.074;SAB=0.55102;SAF=54;SAP=5.2261;SAR=44;SRB=0.52373;SRF=309;SRP=5.8958;SRR=281;VQSLOD=4.1054;set=filterInVQSR-2of5;sumGLbyD=3.06 20 15283028 . A AC,ACACACACACACAC 140844.83 PASS AA=180;AB=0.61442;ABA=123;ABP=39.285;ABR=196;AC=13,817;AF=0.01111,0.69829;AN=1170;BL=4453;BR=11407;BVAR;BaseQRankSum=24.686;DP=6365;Dels=0.00;EL=124;EPP=58.793;ER=56;FR;FS=10.912;HETAR=87;HOMA=48;HOMR=683;HP=1;HR=1;HRun=1;HU=T;INS;InbreedingCoeff=0.2074;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.43846;LRBP=6624;MQ0Fraction=0.0558;MQM=38.211;MQRankSum=-21.111;NF;NR;NS=818;PP;RA=1732;RL=0;RPP=393.88;RR=180;RUN=1;ReadPosRankSum=-7.620;SAB=0.31111;SAF=56;SAP=58.793;SAR=124;SC=ACACACACACATACACACATA;SRB=0.54042;SRF=936;SRP=27.584;SRR=796;TC;TR=21;TU=AC;VQSLOD=4.7569;set=Intersection;sumGLbyD=18.36 20 15361056 . ATAACT A 4892.81 PASS AA=59;AB=0.63576;ABA=55;ABP=27.184;ABR=96;AC=34;AF=0.0487;AN=698;BL=3164;BR=1999;BVAR;BaseQRankSum=3.391;DEL;DP=7080;Dels=0.03;EL=27;EPP=3.9304;ER=32;FR;FS=4.816;HETAR=35;HOMA=6;HOMR=966;HP=2;HPLen=3;HR=3;HRun=0;HU=A;InbreedingCoeff=0.0785;IndelType=DEL.NumRepetitions_1.EventLength_5.;LEN=5;LRB=0.22564;LRBP=573.84;MQ0=0;MQ0Fraction=0.0000;MQM=70.034;MQRankSum=-8.732;NF;NR;NS=1008;PP;RA=3915;RL=42;RPP=26.013;RR=17;RUN=1;ReadPosRankSum=-0.735;SAB=0.44068;SAF=26;SAP=4.8137;SAR=33;SC=AGATTAGGAAATAACTTAGGG;SET_INTEGRATION;SET_WGVQSR;SRB=0.42682;SRF=1671;SRP=185.12;SRR=2244;TC;TR=3;TU=A;VQSLOD=7.0900;set=Intersection;sumGLbyD=43.38 20 15579507 . AATTAGTC A,TATTAGTC 1936.38 PASS AA=16;AB=0.58974;ABA=16;ABP=5.7386;ABR=23;AC=64;AF=0.05229;AN=1224;BL=699;BR=775;BVAR;BaseQRankSum=-21.390;DEL;DP=21920;DP4=2099,2403,6,6;Dels=0.00;EL=8;EPP=3.0103;ER=8;FR;FS=2.920;HETAR=5;HOMA=0;HOMR=1063;HP=3;HPLen=4;HR=4;HU=A;INDEL;InbreedingCoeff=-0.0143;IndelType=MIXED;LEN=7;LRB=0.05156;LRBP=11.519;MQ=129.49;MQ0=0;MQ0Fraction=0.0000;MQM=51.938;MQRankSum=3.331;NF;NR;NS=1068;PP;PV4=1,0.019,1.3e-07,1;RA=5334;RL=5;RPP=7.8961;RR=11;RUN=1;ReadPosRankSum=-16.901;SAB=0.4375;SAF=7;SAP=3.5532;SAR=9;SC=CATACTACAAAATTAGTCATT;SET_INTEGRATION;SET_WGVQSR;SRB=0.41695;SRF=2224;SRP=322.58;SRR=3110;TC;TR=4;TU=A;VQSLOD=3.2237;set=filterInVQSR-2of5;sumGLbyD=43.57 20 15752535 . CT C,GT 3775.20 PASS AA=92;AB=0.78636;ABA=47;ABP=159.71;ABR=173;AC=0;AF=0.0000;AN=608;BL=4955;BR=2380;BVAR;BaseQRankSum=2.910;DEL;DP=3429;Dels=0.04;EL=13;EPP=105.82;ER=79;FR;HETAR=92;HOMA=95;HOMR=544;HP=2;HPLen=2;HR=2;HU=T;InbreedingCoeff=0.0483;IndelType=MIXED;LEN=1;LRB=0.35106;LRBP=1966;MQ0Fraction=0.0232;MQM=35.293;MQRankSum=-2.199;NF;NR;NS=732;PP;QD=4.91;RA=1272;RL=81;RPP=118.66;RR=11;RUN=1;ReadPosRankSum=-1.077;SAB=0.021739;SAF=2;SAP=185.79;SAR=90;SB=-59.51;SC=CAAGACCATCCTTGGCTAACA;SET_INTEGRATION;SET_WGVQSR;SRB=0.14623;SRF=186;SRP=1385.8;SRR=1086;TC;TR=2;TU=T;set=filterInVQSR-2of5;sumGLbyD=9.70 20 15883060 rs73619850 A AT 1325.60 PASS AA=38;AB=0.59302;ABA=35;ABP=9.4742;ABR=51;AC=14;AF=0.0156;AN=896;BL=1078;BR=1638;BVAR;BaseQRankSum=-4.526;DB;DP=19854;DP4=1632,1800,15,20;Dels=0.00;EL=18;EPP=3.2389;ER=20;FR;FS=0.000;HETAR=14;HOMA=1;HOMR=1014;HP=1;HPLen=1;HR=1;HRun=1;HU=T;INDEL;INS;InbreedingCoeff=-0.0131;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.20619;LRBP=253.74;MQ=118.40;MQ0=0;MQ0Fraction=0.0000;MQM=56.526;MQRankSum=0.892;NF;NR;NS=1029;PP;PV4=0.61,1,0.25,0.14;RA=4439;RL=14;RPP=8.7247;RR=24;RUN=1;ReadPosRankSum=-2.061;SAB=0.42105;SAF=16;SAP=5.0675;SAR=22;SC=GGATTGGCAGATAAAAAATGG;SET_INTEGRATION;SET_WGVQSR;SRB=0.46429;SRF=2061;SRP=52.168;SRR=2378;TC;TR=1;TU=T;VQSLOD=9.7576;set=Intersection;sumGLbyD=15.69 20 16122099 . GA G 12914 PASS AA=85;AB=0.85915;ABA=80;ABP=639.4;ABR=488;AC=19;AF=0.01542;AN=1232;BL=805;BR=5457;BVAR;BaseQRankSum=-6.084;DEL;DP=13592;Dels=0.00;EL=45;EPP=3.649;ER=40;FS=0.935;HETAR=218;HOMA=841;HOMR=14;HRun=2;InbreedingCoeff=0.0250;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.74289;LRBP=7507.5;MQ0=0;MQ0Fraction=0.0000;MQM=103.01;MQRankSum=2.843;NS=1075;RA=541;RL=2;RPP=170.62;RR=83;RUN=1;ReadPosRankSum=-16.222;SAB=0.49412;SAF=42;SAP=3.0358;SAR=43;SRB=0.44917;SRF=243;SRP=15.152;SRR=298;VQSLOD=3.9745;set=filterInVQSR-2of5;sumGLbyD=2.97 20 16828509 . G GT 843.62 PASS AA=30;AB=0.70103;ABA=29;ABP=37.06;ABR=68;AC=10;AF=0.0140;AN=714;BL=1368;BR=1786;BVAR;BaseQRankSum=-4.061;DP=8682;Dels=0.01;EL=14;EPP=3.2998;ER=16;FR;FS=2.681;HETAR=22;HOMA=1;HOMR=1020;HP=8;HPLen=8;HR=8;HRun=8;HU=T;INS;InbreedingCoeff=0.1389;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13253;LRBP=123.3;MQ0=0;MQ0Fraction=0.0000;MQM=62.8;MQRankSum=-1.491;NF;NR;NS=1043;PP;RA=4416;RL=11;RPP=7.6428;RR=19;RUN=1;ReadPosRankSum=-1.718;SAB=0.76667;SAF=23;SAP=21.54;SAR=7;SC=CCTTCAAAAGGTTTTTTTTGG;SET_INTEGRATION;SET_WGVQSR;SRB=0.5745;SRF=2537;SRP=215.91;SRR=1879;TC;TR=8;TU=T;VQSLOD=7.6258;set=Intersection;sumGLbyD=10.77 20 17470034 . GC G 46975 PASS AA=57;AB=0.96043;ABA=52;ABP=2422.5;ABR=1262;AC=34;AF=0.02773;AN=1226;BL=418;BR=3446;BVAR;BaseQRankSum=-6.250;DEL;DP=12035;Dels=0.00;EL=22;EPP=9.4485;ER=35;FS=1.350;HETAR=416;HOMA=409;HOMR=244;HRun=1;InbreedingCoeff=0.0083;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.78364;LRBP=5155.6;MQ0=0;MQ0Fraction=0.0000;MQM=99.509;MQRankSum=2.192;NS=1076;RA=2396;RL=5;RPP=87.164;RR=52;RUN=1;ReadPosRankSum=-15.199;SAB=0.5614;SAF=32;SAP=4.877;SAR=25;SRB=0.52963;SRF=1269;SRP=21.285;SRR=1127;VQSLOD=3.8440;set=filterInVQSR-2of5;sumGLbyD=3.06 20 17471374 . AGCGGC A 850.03 PASS AC=6;AF=0.0085;AF1=0.01301;AN=704;BaseQRankSum=6.259;CI95=0.00885,0.01991;DP=8180;DP4=2215,1878,4,5;Dels=0.01;FQ=131;FS=0.000;HRun=0;INDEL;InbreedingCoeff=0.0009;IndelType=DEL.NumRepetitions_1.EventLength_5.;MQ=104.41;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-5.521;PV4=0.74,0.37,0.0005,1;ReadPosRankSum=2.468;SET_INTEGRATION;SET_WGVQSR;VQSLOD=6.8773;set=Intersection;sumGLbyD=30.85 20 18433202 rs35582929 G GA 2506.90 PASS AA=55;AB=0.5812;ABA=49;ABP=9.7103;ABR=68;AC=20;AF=0.0218;AN=918;BL=2263;BR=2175;BVAR;BaseQRankSum=-6.639;DB;DP=19467;DP4=1845,2365,27,26;Dels=0.00;EL=21;EPP=9.6826;ER=34;FQ=999;FR;FS=5.633;HETAR=16;HOMA=3;HOMR=1045;HP=2;HPLen=3;HR=3;HRun=1;HU=G;INDEL;INS;InbreedingCoeff=0.0700;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.019829;LRBP=6.7994;MQ=114.03;MQ0=0;MQ0Fraction=0.0000;MQM=83.345;MQRankSum=1.610;NF;NR;NS=1064;PP;PV4=0.33,1,1,1;RA=5380;RL=28;RPP=3.0498;RR=27;RUN=1;ReadPosRankSum=0.873;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TATTTCATGGGAGCATTAAAA;SET_INTEGRATION;SET_WGVQSR;SRB=0.42862;SRF=2306;SRP=241.07;SRR=3074;TC;TR=3;TU=G;VQSLOD=10.0372;dbSNP=126;set=Intersection;sumGLbyD=13.10 20 18551314 rs10659122 CA C,CAA,CAAA,CAAAA,CAAAAA 18810.74 PASS ABR=243;AC=19,169,216,164,188;AF=0.01816,0.16157,0.20650,0.15679,0.17973;BVAR;BaseQRankSum=-5.742;DB;DP=17637;DP4=136,77,560,237;FR;FS=2.693;HOMA=177;HOMR=299;HP=17;HR=17;HU=A;HaplotypeScore=15.5048;INDEL;INS;InbreedingCoeff=0.8901;IndelType=MULTIALLELIC_INDEL;MQ0=11;MQ0Fraction=0.0069;MQRankSum=1.845;NF;NR;NS=658;PP;PV4=0.08,1,1,1;QD=12.66;RA=673;RUN=1;ReadPosRankSum=0.283;SB=-3514.45;SC=GATTCCATCTCAAAAAAAAAA;SET_WGVQSR;SRB=0.63596;SRF=428;SRP=111.06;SRR=245;TC;TR=17;TU=A;VQSLOD=10.6964;dbSNP=130;set=Intersection 20 18785519 . G GTC 415.55 PASS AC=28;AF=0.0400;AN=700;BaseQRankSum=10.889;DP=1929;FS=8.778;HRun=0;HaplotypeScore=27.6448;InbreedingCoeff=0.0510;IndelType=INS.NOVEL_2.;MQ=61.99;MQ0=36;MQ0Fraction=0.0187;MQRankSum=4.508;QD=3.08;ReadPosRankSum=8.080;SB=-437.03;SET_INTEGRATION;SET_WGVQSR;VQSLOD=4.9313;set=VQSR 20 20301041 rs35451634 ATATG A 200.42 PASS AC=21;AF=0.0449;AN=468;BaseQRankSum=5.251;DB;DP=579;FS=24.013;HRun=0;HaplotypeScore=27.8977;InbreedingCoeff=0.0113;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ=78.47;MQ0=26;MQ0Fraction=0.0449;MQRankSum=-5.284;QD=3.06;ReadPosRankSum=1.793;SB=-55.76;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.0981;set=VQSR 20 20378174 . TC T 245.55 PASS AC=23;AF=0.01879;AN=1224;BaseQRankSum=0.990;DP=3225;FS=10.413;HRun=1;HaplotypeScore=22.6109;InbreedingCoeff=0.0244;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=93.70;MQ0=3;MQ0Fraction=0.0009;MQRankSum=-3.349;QD=1.86;ReadPosRankSum=-7.227;SB=-188.62;VQSLOD=4.2553;set=VQSR 20 20809160 rs10571503 TAA AAA,T 3496 PASS AC=0;AF=0.0000;AN=612;BaseQRankSum=1.968;DB;DP=1092;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=26.1253;InbreedingCoeff=0.0603;IndelType=MIXED;MQ=68.98;MQ0=1;MQ0Fraction=0.0009;MQRankSum=1.520;NF;NR;PP;ReadPosRankSum=-4.042;SC=TATATATATATAAATTTAAAT;TC;TR=13;TU=AT;set=filterInVQSR-2of5 20 22508765 . CT C 53877.84 PASS AA=187;AB=0.78077;ABA=171;ABP=537.09;ABR=609;AC=1017;AF=0.91787;AN=1108;BL=12690;BR=1718;BVAR;BaseQRankSum=13.773;DEL;DP=7430;Dels=0.02;EL=73;EPP=22.53;ER=114;FR;FS=16.352;HETAR=152;HOMA=9;HOMR=786;HP=8;HR=4;HRun=4;HU=T;InbreedingCoeff=0.3885;IndelType=DEL.NumRepetitions_4.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.76152;LRBP=18147;MQ0=0;MQ0Fraction=0.0000;MQM=46.086;MQRankSum=0.971;NF;NR;NS=947;PP;RA=2868;RL=177;RPP=326.86;RR=10;RUN=1;ReadPosRankSum=9.951;SAB=0.34759;SAF=65;SAP=40.738;SAR=122;SC=AAAAAATTTTCTTTTGAACTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.46269;SRF=1327;SRP=37.684;SRR=1541;TC;TR=4;TU=T;VQSLOD=5.1182;set=Intersection;sumGLbyD=25.15 20 22555082 rs11477526 AT A 11503 PASS AA=530;AB=0.50816;ABA=422;ABP=3.5063;ABR=436;AF=0.1614;AN=700;BL=21453;BR=23313;BVAR;BaseQRankSum=17.562;DB;DEL;DP=25587;DP4=1869,1600,283,201;Dels=0.14;EL=259;EPP=3.6003;ER=271;FQ=999;FR;FS=14.595;HETAR=159;HOMA=41;HOMR=846;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;InbreedingCoeff=0.0995;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.041549;LRBP=170.83;MQ=95.89;MQ0=0;MQ0Fraction=0.0000;MQM=72.162;MQRankSum=2.564;NF;NR;NS=1046;PP;PV4=0.058,6.6e-129,0.04,1;RA=4303;RL=264;RPP=3.0267;RR=266;RUN=1;ReadPosRankSum=0.176;SAB=0.58679;SAF=311;SAP=37.688;SAR=219;SC=GGGAAAGCTGATTTACTGATT;SET_INTEGRATION;SET_WGVQSR;SRB=0.54892;SRF=2362;SRP=92.453;SRR=1941;TC;TR=3;TU=T;VQSLOD=8.7746;dbSNP=120;set=Intersection;sumGLbyD=15.27 20 22590907 . A AC 4204.88 PASS AA=67;AB=0.592;ABA=51;ABP=12.2;ABR=74;AF=0.0554;AF1=0.0468;AN=560;BL=2277;BR=2389;BVAR;BaseQRankSum=10.968;CI95=0.03759,0.05639;DP=14380;DP4=2514,2018,33,33;Dels=0.00;EL=22;EPP=20.155;ER=45;FQ=999;FR;FS=3.846;HETAR=25;HOMA=4;HOMR=1049;HP=4;HPLen=5;HR=5;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0719;IndelType=INS.NOVEL_1.Novel_C.;LEN=1;LRB=0.024003;LRBP=8.8481;MQ=110.68;MQ0=0;MQ0Fraction=0.0000;MQM=96.149;MQRankSum=2.668;NF;NR;NS=1078;PP;PV4=0.39,1,0.46,0.36;RA=5468;RL=33;RPP=3.0427;RR=34;RUN=1;ReadPosRankSum=-1.097;SAB=0.50746;SAF=34;SAP=3.0427;SAR=33;SC=TCATATCAAAAACATTACGTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.54389;SRF=2974;SRP=94.508;SRR=2494;TC;TR=5;TU=A;VQSLOD=10.0712;set=Intersection;sumGLbyD=27.69 20 22806326 rs11468890 ATTCCATCAC A 105320.99 PASS AC=567;AF=0.48795;AN=1162;BVAR;BaseQRankSum=32.858;DB;DEL;DP=26278;DP4=727,796,554,587;Dels=0.30;FQ=999;FR;FS=1.923;HP=3;HPLen=3;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.2548;IndelType=DEL.NumRepetitions_2.EventLength_9.;LEN=9;MQ=89.42;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-23.545;NF;NR;PP;PV4=0.7,1,1.3e-167,1;RUN=1;ReadPosRankSum=4.384;SC=GGCTGCTCCCATTCCATCACT;SET_INTEGRATION;SET_WGVQSR;TC;TR=2;TU=T;VQSLOD=8.2594;set=Intersection;sumGLbyD=69.81 20 22999898 rs55966257 CAGGA C 8019.97 PASS AA=23;AB=0.57778;ABA=19;ABP=5.3748;ABR=26;AC=214;AF=0.18838;AN=1136;BL=1143;BR=1040;BVAR;BaseQRankSum=29.294;DB;DEL;DP=8216;Dels=0.02;EL=11;EPP=3.1047;ER=12;FS=14.938;HETAR=14;HOMA=2;HOMR=948;HRun=0;InbreedingCoeff=0.0797;IndelType=DEL.NumRepetitions_1.EventLength_4.;LEN=4;LRB=0.047183;LRBP=13.563;MQ0=0;MQ0Fraction=0.0000;MQM=34.783;MQRankSum=-20.301;NS=964;RA=3637;RL=13;RPP=3.86;RR=10;RUN=1;ReadPosRankSum=-24.607;SAB=0.47826;SAF=11;SAP=3.1047;SAR=12;SRB=0.49024;SRF=1783;SRP=6.02;SRR=1854;VQSLOD=7.9163;set=Intersection;sumGLbyD=9.43 20 23385964 rs57723772 GAA G 8170.95 PASS AC=257;AF=0.20928;AN=1228;BaseQRankSum=32.220;DB;DP=3291;FS=1.688;HRun=3;HaplotypeScore=22.6739;InbreedingCoeff=0.0171;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=58.44;MQ0=32;MQ0Fraction=0.0097;MQRankSum=-4.893;QD=6.55;ReadPosRankSum=-35.524;SB=-3631.67;VQSLOD=5.6549;set=VQSR 20 23534530 . TA T 3542.10 PASS AA=45;AB=0.75658;ABA=37;ABP=89.926;ABR=115;AC=35;AF=0.02991;AN=1170;BL=3090;BR=270;BVAR;BaseQRankSum=-6.892;DEL;DP=8108;Dels=0.00;EL=19;EPP=5.3748;ER=26;FS=1.026;HETAR=76;HOMA=896;HOMR=18;HRun=1;InbreedingCoeff=0.0551;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.83929;LRBP=5142.4;MQ0Fraction=0.0017;MQM=41.578;MQRankSum=0.818;NS=991;RA=203;RL=43;RPP=84.127;RR=2;RUN=1;ReadPosRankSum=-12.923;SAB=0.37778;SAF=17;SAP=8.8491;SAR=28;SRB=0.5665;SRF=115;SRP=10.808;SRR=88;VQSLOD=4.2093;set=Intersection;sumGLbyD=3.49 20 23976810 rs5841018 A ATATTAAT 1782.38 PASS AF=0.1387;AF1=0.01507;BaseQRankSum=3.717;CI95=0.00188,0.03947;DB;DP=1712;DP4=357,376,7,2;Dels=0.00;FQ=31.1;FS=14.489;HPLen=2;HRun=0;INDEL;InbreedingCoeff=0.1123;IndelType=INS.NumRepetitions_1.EventLength_7.;MQ=49.53;MQ0=2;MQ0Fraction=0.0055;MQRankSum=-4.928;PV4=0.1,1,0.00085,0.016;ReadPosRankSum=-4.456;VQSLOD=5.3140;dbSNP=116;set=Intersection;sumGLbyD=19.98 20 24222100 . CTTTTA C 4219.36 PASS AA=57;AB=0.59434;ABA=43;ABP=11.205;ABR=63;AF=0.01803;AF1=0.01547;AN=1220;BL=2073;BR=2345;BVAR;BaseQRankSum=7.990;CI95=0.0114,0.02137;DEL;DP=17536;DP4=2140,2346,7,12;Dels=0.01;EL=32;EPP=4.877;ER=25;FQ=104;FS=0.614;HETAR=21;HOMA=4;HOMR=1042;HRun=0;INDEL;InbreedingCoeff=0.1941;IndelType=DEL.NumRepetitions_2.EventLength_5.;LEN=5;LRB=0.061566;LRBP=39.374;MQ=73.32;MQ0Fraction=0.0021;MQM=39.614;MQRankSum=-5.728;NS=1067;PV4=0.37,1.1e-39,3.5e-09,1;RA=5527;RL=28;RPP=3.0484;RR=29;RUN=1;ReadPosRankSum=0.214;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SET_INTEGRATION;SET_WGVQSR;SRB=0.49267;SRF=2723;SRP=5.588;SRR=2804;VQSLOD=7.5428;set=Intersection;sumGLbyD=38.08 20 24395018 . AT A 49310 PASS AA=146;AB=0.91198;ABA=130;ABP=2180.5;ABR=1347;AC=50;AF=0.04045;AN=1236;BL=587;BR=9625;BVAR;BaseQRankSum=-4.610;DEL;DP=12793;Dels=0.01;EL=54;EPP=24.487;ER=92;FS=22.108;HETAR=485;HOMA=384;HOMR=210;HRun=2;InbreedingCoeff=0.0374;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.88504;LRBP=17373;MQ0=0;MQ0Fraction=0.0000;MQM=102.26;MQRankSum=2.256;NS=1080;RA=2377;RL=1;RPP=311.42;RR=145;RUN=1;ReadPosRankSum=-16.347;SAB=0.63699;SAF=93;SAP=26.807;SAR=53;SRB=0.52167;SRF=1240;SRP=12.702;SRR=1137;VQSLOD=3.2421;set=filterInVQSR-2of5;sumGLbyD=3.80 20 24411517 . C CA 246.18 PASS AF=0.01546;AF1=0.01095;BaseQRankSum=7.832;CI95=0.005698,0.01709;DP=7981;DP4=983,2037,7,7;Dels=0.00;FQ=27.9;FS=18.815;HPLen=3;HRun=3;INDEL;InbreedingCoeff=0.0175;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=60.28;MQ0Fraction=0.0137;MQRankSum=-7.243;PV4=0.25,1,2.7e-05,1;ReadPosRankSum=-0.143;VQSLOD=4.3701;set=Intersection;sumGLbyD=6.56 20 24421169 . AG A 27480 PASS AA=182;AB=0.8303;ABA=149;ABP=835;ABR=729;AC=89;AF=0.07224;AN=1232;BL=11276;BR=2214;BVAR;BaseQRankSum=-5.447;DEL;DP=11717;Dels=0.01;EL=103;EPP=9.8827;ER=79;FR;FS=15.492;HETAR=343;HOMA=607;HOMR=114;HP=4;HR=1;HRun=1;HU=G;InbreedingCoeff=0.0353;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.67176;LRBP=13222;MQ0=0;MQ0Fraction=0.0000;MQM=88.324;MQRankSum=2.221;NF;NR;NS=1071;PP;RA=1226;RL=169;RPP=293.37;RR=13;RUN=1;ReadPosRankSum=-19.711;SAB=0.54945;SAF=100;SAP=6.876;SAR=82;SC=CCTTAGCCCCAGAAAACATCT;SRB=0.44535;SRF=546;SRP=34.814;SRR=680;TC;TR=1;TU=G;VQSLOD=4.2669;set=Intersection;sumGLbyD=3.91 20 24765537 rs71841337 ATTT A,AT,ATT,ATTTT,ATTTTT 37852 PASS AC=13,120,527,51,92;AF=0.01102,0.10169,0.44661,0.04322,0.07797;AN=1180;BVAR;BaseQRankSum=8.172;DB;DEL;DP=39116;DP4=200,331,851,1169;FR;FS=2.394;HP=15;HR=15;HU=T;HaplotypeScore=20.8091;INDEL;INS;InbreedingCoeff=0.4815;IndelType=MULTIALLELIC_INDEL;MQ0=1;MQ0Fraction=0.0003;MQRankSum=4.344;NF;NR;PP;PV4=0.067,1,1,0.1;QD=7.90;RUN=1;ReadPosRankSum=1.798;SB=-8371.96;SC=CTCTGCAACAATTTTTTTTTT;SET_WGVQSR;TC;TR=15;TU=T;VQSLOD=9.9679;dbSNP=120;set=Intersection 20 25500689 . A AATTT 84980.72 PASS AC=1005;AF=0.89096;AN=1128;BaseQRankSum=17.400;DP=2324;FS=6.721;HRun=0;HaplotypeScore=25.3376;InbreedingCoeff=0.2148;IndelType=INS.NumRepetitions_1.EventLength_4.;MQ=75.19;MQ0=1;MQ0Fraction=0.0004;MQRankSum=-8.221;QD=38.28;ReadPosRankSum=4.504;SB=-34833.07;SET_INTEGRATION;SET_WGVQSR;VQSLOD=4.6038;set=VQSR 20 25550373 . GA G 11251.31 PASS AA=246;AB=0.42963;ABA=154;ABP=14.624;ABR=116;AC=566;AF=0.6521;AN=868;BL=5230;BR=11845;BVAR;BaseQRankSum=7.418;DEL;DP=8885;Dels=0.02;EL=99;EPP=23.348;ER=147;FR;FS=50.357;HETAR=150;HOMA=849;HOMR=14;HP=1;HR=2;HRun=1;HU=G;InbreedingCoeff=0.1365;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.38741;LRBP=5567.9;MQ0=0;MQ0Fraction=0.0000;MQM=97.561;MQRankSum=0.050;NF;NR;NS=1013;PP;RA=269;RL=75;RPP=84.361;RR=171;RUN=1;ReadPosRankSum=-7.128;SAB=0.52846;SAF=130;SAP=4.7404;SAR=116;SC=CACGGAGGCGGAGGAAGCAGC;SRB=0.42379;SRF=114;SRP=16.58;SRR=155;TC;TR=6;TU=AGG;VQSLOD=4.0103;set=filterInVQSR-2of5;sumGLbyD=4.58 20 25903865 . TTC T 7459.23 PASS AC=277;AF=0.23316;AN=1188;BaseQRankSum=31.479;DP=2969;FS=137.723;HRun=0;HaplotypeScore=37.3300;InbreedingCoeff=-0.1755;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TC.;MQ=53.49;MQ0=50;MQ0Fraction=0.0168;MQRankSum=-25.506;QD=4.70;ReadPosRankSum=-5.913;SB=-1747.98;VQSLOD=5.4731;set=VQSR 20 25934237 . C CCACTT 771.36 PASS AC=37;AF=0.0426;AN=868;BaseQRankSum=16.331;DP=2253;FS=4.545;HRun=0;HaplotypeScore=29.9764;InbreedingCoeff=-0.0685;IndelType=INS.NOVEL_5.;MQ=48.12;MQ0=87;MQ0Fraction=0.0386;MQRankSum=-12.497;QD=3.37;ReadPosRankSum=-8.428;SB=-297.70;VQSLOD=4.2324;set=VQSR 20 26054751 rs112967123 TATC T 33244 PASS AA=1863;AB=0.79012;ABA=1788;ABP=6231;ABR=6731;AC=227;AF=0.18218;AN=1246;BL=74924;BR=72452;BVAR;BaseQRankSum=32.258;DB;DEL;DP=36404;DS;Dels=0.05;EL=931;EPP=3.0115;ER=932;FR;FS=265.752;HETAR=527;HOMA=2;HOMR=565;HP=1;HR=2;HRun=0;HU=T;InbreedingCoeff=-0.2137;IndelType=DEL.NumRepetitions_2.EventLength_3.;LEN=3;LRB=0.016773;LRBP=93.048;MQ0Fraction=0.0127;MQM=28.797;MQRankSum=-5.329;NF;NR;NS=1094;PP;RA=14604;RL=1014;RPP=34.743;RR=849;RUN=1;ReadPosRankSum=8.394;SAB=0.65486;SAF=1220;SAP=391.07;SAR=643;SC=TCACCATCATTATCATCATTA;SRB=0.56717;SRF=8283;SRP=575.39;SRR=6321;TC;TR=8;TU=ATC;VQSLOD=1.0486;set=filterInVQSR-2of5;sumGLbyD=6.54 20 26120452 . CAG C 7863.19 PASS AA=163;AB=0.70489;ABA=157;ABP=196.99;ABR=375;AC=171;AF=0.1908;AN=896;BL=3455;BR=4877;BVAR;BaseQRankSum=25.536;DEL;DP=7014;Dels=0.10;EL=58;EPP=32.438;ER=105;FS=231.723;HETAR=90;HOMA=5;HOMR=387;HRun=0;InbreedingCoeff=-0.1966;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.17067;LRBP=530;MQ0Fraction=0.0470;MQM=21.951;MQRankSum=-23.449;NS=482;RA=1117;RL=62;RPP=23.273;RR=101;RUN=1;ReadPosRankSum=1.904;SAB=0.37423;SAF=61;SAP=25.404;SAR=102;SRB=0.41719;SRF=466;SRP=69.544;SRR=651;VQSLOD=-0.9395;set=filterInVQSR-2of5;sumGLbyD=5.06 20 26185812 . AG A 322.58 PASS AF=0.0342;BaseQRankSum=3.668;DP=3014;Dels=0.01;FR;FS=10.238;HP=8;HPLen=6;HR=6;HRun=6;HU=G;InbreedingCoeff=0.1504;IndelType=DEL.NumRepetitions_6.EventLength_1.RepeatExpansion_G.;MQ0Fraction=0.0473;MQRankSum=-5.464;NF;NR;PP;ReadPosRankSum=0.536;SC=GGGTGGGTGGAGGGGGGAGGG;SET_WGVQSR;TC;TR=6;TU=G;VQSLOD=5.0767;set=Intersection;sumGLbyD=8.46 20 30963468 . AGTTT A 2041.12 PASS AA=38;AB=0.75694;ABA=35;ABP=85.587;ABR=109;AC=34;AF=0.0377;AN=902;BL=1974;BR=668;BVAR;BaseQRankSum=3.060;DEL;DP=22806;DP4=1997,1747,28,36;Dels=0.02;EL=17;EPP=3.9246;ER=21;FR;FS=16.034;HETAR=29;HOMA=1;HOMR=1009;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=0.0752;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.49432;LRBP=1404.9;MQ=87.17;MQ0Fraction=0.0013;MQM=98.079;MQRankSum=6.021;NF;NR;NS=1039;PP;PV4=0.13,1.5e-07,1,0.051;RA=4052;RL=36;RPP=69.069;RR=2;RUN=1;ReadPosRankSum=-1.847;SAB=0.5;SAF=19;SAP=3.0103;SAR=19;SC=AGAAGTAAGTAGTTTGTTTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.53776;SRF=2179;SRP=53.19;SRR=1873;TC;TR=9;TU=AAGT;VQSLOD=7.3578;set=Intersection;sumGLbyD=14.03 20 31963212 . AAAAAAAAAAAAG A 727.15 PASS AC=5;AF=0.0080;AN=622;BaseQRankSum=4.037;DP=1480;FS=0.000;HRun=0;HaplotypeScore=43.3793;InbreedingCoeff=0.0350;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;MQ=51.77;MQ0=59;MQ0Fraction=0.0399;MQRankSum=-1.799;QD=22.72;ReadPosRankSum=3.591;SB=-364.04;VQSLOD=5.3166;set=VQSR 20 31997272 . CT C,CTT,CTTT 1837.10 PASS AA=63;AB=0.77559;ABA=57;ABP=170.57;ABR=197;AC=79,49,30;AF=0.06594,0.04090,0.02504;AN=1198;BL=2372;BR=2640;BVAR;BaseQRankSum=3.277;DP=9050;Dels=0.03;EL=24;EPP=10.766;ER=39;FR;FS=0.303;HETAR=45;HOMA=1;HOMR=981;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2796;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.053472;LRBP=34.128;MQ0Fraction=0.0000;MQM=50.889;MQRankSum=0.610;NF;NR;NS=1027;PP;RA=3776;RL=30;RPP=3.3205;RR=33;RUN=1;ReadPosRankSum=-0.800;SAB=0.39683;SAF=25;SAP=8.8354;SAR=38;SC=ACCCAACTTCCTTTTTTTTTT;SET_WGVQSR;SRB=0.46213;SRF=1745;SRP=50.049;SRR=2031;TC;TR=10;TU=T;VQSLOD=4.1189;set=filterInVQSR-2of5;sumGLbyD=3.66 20 33446974 rs113250263 TAA T,TA,TAAA 17130.16 PASS AC=65,417,184;AF=0.05941,0.38117,0.16819;AN=1094;BVAR;BaseQRankSum=3.400;DB;DEL;DP=22362;DP4=221,247,418,524;Dels=0.33;FR;FS=15.409;HP=15;HR=14;HRun=14;HU=A;INDEL;INS;InbreedingCoeff=0.5215;IndelType=MULTIALLELIC_INDEL;MQ=61.32;MQ0Fraction=0.0021;MQRankSum=0.481;NF;NR;PP;PV4=0.33,1,1,1;RUN=1;ReadPosRankSum=-0.056;SC=CTCCGTCTCATAAAAAAAAAA;SET_WGVQSR;TC;TR=14;TU=A;VQSLOD=8.0974;dbSNP=132;set=Intersection;sumGLbyD=12.78 20 33877149 . C CT 1784.40 PASS AA=58;AB=0.73096;ABA=53;ABP=94.289;ABR=144;AC=65;AF=0.05682;AN=1144;BL=3298;BR=1935;BVAR;BaseQRankSum=-2.066;DP=8074;Dels=0.02;EL=22;EPP=10.348;ER=36;FR;FS=11.452;HETAR=47;HOMA=3;HOMR=754;HP=16;HR=12;HRun=12;HU=T;INS;InbreedingCoeff=0.1178;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.26046;LRBP=773.91;MQ0Fraction=0.0165;MQM=52.259;MQRankSum=0.734;NF;NR;NS=804;PP;RA=2141;RL=43;RPP=32.363;RR=15;RUN=1;ReadPosRankSum=-1.273;SAB=0.46552;SAF=27;SAP=3.6093;SAR=31;SC=ATTTTCTTTTCTTTTTTTTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.37553;SRF=804;SRP=291.14;SRR=1337;TC;TR=12;TU=T;VQSLOD=3.1540;set=filterInVQSR-2of5;sumGLbyD=2.84 20 34387589 rs112431805 CT C,CTT 4039.10 PASS AA=121;AB=0.75368;ABA=117;ABP=268.53;ABR=358;AC=84,139;AF=0.07047,0.11661;AN=1192;BL=5557;BR=3901;BVAR;BaseQRankSum=2.693;DB;DP=10157;Dels=0.03;EL=47;EPP=16.093;ER=74;FR;FS=7.639;HETAR=89;HOMA=2;HOMR=913;HP=13;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2097;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.17509;LRBP=632.63;MQ0Fraction=0.0000;MQM=49.802;MQRankSum=-0.801;NF;NR;NS=1004;PP;RA=3789;RL=77;RPP=22.554;RR=44;RUN=1;ReadPosRankSum=-2.691;SAB=0.3719;SAF=45;SAP=20.256;SAR=76;SC=AAGAAGTGTTCTTTTTTTTTT;SET_WGVQSR;SRB=0.40987;SRF=1553;SRP=270.35;SRR=2236;TC;TR=11;TU=T;VQSLOD=4.0473;set=filterInVQSR-2of5;sumGLbyD=4.64 20 34493409 rs73621682 C CAG 62288.93 PASS AA=1069;AB=0.54863;ABA=826;ABP=40.606;ABR=1004;AC=257;AF=0.3640;AN=706;BL=41524;BR=47039;BVAR;BaseQRankSum=-24.248;DB;DP=30195;DP4=1743,1636,614,487;Dels=0.00;EL=582;EPP=21.343;ER=487;FQ=999;FR;FS=5.080;HETAR=298;HOMA=63;HOMR=712;HP=1;HPLen=1;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.1437;IndelType=INS.NumRepetitions_2.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.062272;LRBP=748.76;MQ=77.99;MQ0=3;MQ0Fraction=0.0015;MQM=54.446;MQRankSum=0.160;NF;NR;NS=1073;PP;PV4=0.016,1,0.01,1;RA=4461;RL=526;RPP=3.5973;RR=543;RUN=1;ReadPosRankSum=-1.716;SAB=0.57343;SAF=613;SAP=53.08;SAR=456;SC=AGGAAGAGATCAGAGCTCCCC;SET_INTEGRATION;SET_WGVQSR;SRB=0.52634;SRF=2348;SRP=29.892;SRR=2113;TC;TR=4;TU=AG;VQSLOD=8.7047;dbSNP=130;set=Intersection;sumGLbyD=49.82 20 35957317 . CTGACT C,CGACT 4370.96 PASS ABR=81;AC=22,1;AF=0.0321,0.0015;AF1=0.04523;AN=686;BVAR;BaseQRankSum=7.969;CI95=0.0354,0.05752;DEL;DP=16632;DP4=1942,1815,17,21;Dels=0.03;FQ=999;FR;FS=0.531;HOMA=1;HOMR=998;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0587;IndelType=MULTIALLELIC_INDEL;MQ=83.38;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-7.201;NF;NR;NS=1020;PP;PV4=0.42,0.00017,4.5e-12,1;RA=4620;RUN=1;ReadPosRankSum=-1.007;SC=CCTCTCAGCTCTGACTGAGTC;SET_WGVQSR;SRB=0.50043;SRF=2312;SRP=3.0178;SRR=2308;TC;TR=8;TU=ACTG;VQSLOD=9.9778;dbSNP=130;set=Intersection;sumGLbyD=36.45 20 36136198 . GTGTC G 2078.76 PASS AA=35;AB=0.54167;ABA=33;ABP=4.096;ABR=39;AC=17;AF=0.01384;AN=1228;BL=1212;BR=1523;BVAR;BaseQRankSum=6.900;DEL;DP=22483;DP4=1696,2291,9,16;Dels=0.01;EL=9;EPP=20.94;ER=26;FQ=999;FR;FS=3.023;HETAR=13;HOMA=1;HOMR=1061;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1113;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.11371;LRBP=79.803;MQ=93.98;MQ0=1;MQ0Fraction=0.0003;MQM=83.686;MQRankSum=-1.683;NF;NR;NS=1075;PP;PV4=0.55,1,0.0083,1;RA=5771;RL=19;RPP=3.5687;RR=16;RUN=1;ReadPosRankSum=0.618;SAB=0.37143;SAF=13;SAP=8.0357;SAR=22;SC=TATCATTTTAGTGTCTGTCTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.44966;SRF=2595;SRP=130.03;SRR=3176;TC;TR=11;TU=CTGT;VQSLOD=10.1935;set=Intersection;sumGLbyD=31.66 20 36250522 . CA C 37933 PASS AA=51;AB=0.95582;ABA=44;ABP=1800.5;ABR=952;AC=23;AF=0.01885;AN=1220;BL=691;BR=3464;BVAR;BaseQRankSum=-2.418;DEL;DP=11998;Dels=0.00;EL=18;EPP=12.59;ER=33;FS=2.307;HETAR=348;HOMA=534;HOMR=164;HRun=1;InbreedingCoeff=0.0763;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.66739;LRBP=4021.7;MQ0=2;MQ0Fraction=0.0006;MQM=53.647;MQRankSum=1.083;NS=1047;RA=1663;RL=2;RPP=97.065;RR=49;RUN=1;ReadPosRankSum=-12.726;SAB=0.68627;SAF=35;SAP=18.381;SAR=16;SRB=0.59651;SRF=992;SRP=137.56;SRR=671;VQSLOD=4.1346;set=filterInVQSR-2of5;sumGLbyD=3.29 20 36285033 rs34715186 AT A 39417 PASS AA=530;AB=0.5406;ABA=447;ABP=16.939;ABR=526;AC=88;AF=0.0950;AN=926;BL=20722;BR=20406;BVAR;BaseQRankSum=15.611;DB;DEL;DP=36713;DP4=2551,2475,236,218;Dels=0.09;EL=241;EPP=12.45;ER=289;FQ=999;FR;FS=1.290;HETAR=141;HOMA=16;HOMR=926;HP=2;HPLen=3;HR=3;HRun=1;HU=A;INDEL;InbreedingCoeff=0.0742;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.0076833;LRBP=8.2825;MQ=104.81;MQ0=0;MQ0Fraction=0.0000;MQM=84.285;MQRankSum=-0.702;NF;NR;NS=1083;PP;PV4=0.62,1,1,1;RA=6562;RL=263;RPP=3.0759;RR=267;RUN=1;ReadPosRankSum=0.090;SAB=0.55849;SAF=296;SAP=18.76;SAR=234;SC=AAAAACACAAATCAGATCGTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.51707;SRF=3393;SRP=19.614;SRR=3169;TC;TR=3;TU=A;VQSLOD=10.5533;dbSNP=126;set=Intersection;sumGLbyD=14.15 20 36384872 . CTG C 43532.41 PASS AC=1213;AF=0.99589;AN=1218;BaseQRankSum=0.802;DP=3208;FS=9.727;HRun=0;HaplotypeScore=46.6153;InbreedingCoeff=0.1085;IndelType=DEL.NumRepetitions_7.EventLength_2.RepeatExpansion_TG.;MQ=58.37;MQ0=50;MQ0Fraction=0.0156;MQRankSum=-1.672;QD=13.57;ReadPosRankSum=2.063;SB=-18894.12;VQSLOD=4.7353;set=VQSR 20 36542802 . GTA G 31310.15 PASS AA=1481;AB=0.67546;ABA=1378;ABP=1138.4;ABR=2868;AC=437;AF=0.35938;AN=1216;BL=25719;BR=95500;BVAR;BaseQRankSum=9.478;DEL;DP=18068;DS;Dels=0.10;EL=889;EPP=132.34;ER=592;FS=320.726;HETAR=591;HOMA=44;HOMR=378;HRun=0;InbreedingCoeff=-0.4197;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;LEN=2;LRB=0.57566;LRBP=87231;MQ0Fraction=0.0091;MQM=29.319;MQRankSum=-3.409;NS=1013;RA=4037;RL=3;RPP=3193;RR=1478;RUN=1;ReadPosRankSum=-6.687;SAB=0.40041;SAF=593;SAP=130.61;SAR=888;SRB=0.39014;SRF=1575;SRP=426.21;SRR=2462;VQSLOD=-1.6586;set=filterInVQSR-2of5;sumGLbyD=5.49 20 36985025 . CCA C 4.57 PASS AC=0;AF=0.0000;AN=682;BaseQRankSum=4.199;DP=1504;FS=1.036;HRun=0;HaplotypeScore=18.5241;InbreedingCoeff=0.0460;IndelType=DEL.NumRepetitions_6.EventLength_2.RepeatExpansion_CA.;MQ=57.04;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.774;ReadPosRankSum=-2.105;VQSLOD=6.7455;set=VQSR 20 37139725 . CAG C 250.77 PASS AF=0.0084;AF1=0.0139;BaseQRankSum=4.131;CI95=0.00885,0.01991;DP=7973;DP4=1808,1990,2,7;Dels=0.01;FQ=104;FR;FS=11.160;HP=3;HPLen=2;HR=1;HRun=0;HU=A;INDEL;InbreedingCoeff=-0.0001;IndelType=DEL.NumRepetitions_3.EventLength_2.RepeatExpansion_AG.;MQ=103.71;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.378;NF;NR;PP;PV4=0.18,0.0011,0.041,1;ReadPosRankSum=0.605;SC=AGATGGGGAACAGAGAGCAAG;SET_INTEGRATION;SET_WGVQSR;TC;TR=6;TU=AG;VQSLOD=7.0630;set=Intersection;sumGLbyD=12.13 20 37213224 . G GTA 3230.05 PASS AA=32;AB=0.50769;ABA=32;ABP=3.0437;ABR=33;AC=12;AF=0.0168;AF1=0.02635;AN=714;BL=1271;BR=1743;BVAR;BaseQRankSum=-7.288;CI95=0.02212,0.03319;DP=14304;DP4=2180,2256,13,21;Dels=0.00;EL=20;EPP=7.3532;ER=12;FQ=999;FR;FS=7.863;HETAR=9;HOMA=0;HOMR=1043;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0410;IndelType=INS.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;LEN=2;LRB=0.1566;LRBP=163.52;MQ=95.56;MQ0=1;MQ0Fraction=0.0005;MQM=51.562;MQRankSum=0.420;NF;NR;NS=1052;PP;PV4=0.23,1,0.03,0.33;RA=5138;RL=11;RPP=9.7962;RR=21;RUN=1;ReadPosRankSum=-1.122;SAB=0.28125;SAF=9;SAP=16.311;SAR=23;SC=TTTGCATCCAGTAGCACCACT;SET_INTEGRATION;SET_WGVQSR;SRB=0.42293;SRF=2173;SRP=268.11;SRR=2965;TC;TR=1;TU=T;VQSLOD=9.7315;set=Intersection;sumGLbyD=36.69 20 37282014 . ATGG A 2518.52 PASS AF=0.03519;BaseQRankSum=11.994;DP=24592;DP4=415,3804,8,49;DS;Dels=0.01;FQ=999;FR;FS=2.049;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1028;IndelType=DEL.NumRepetitions_5.EventLength_3.;MQ=51.01;MQ0Fraction=0.0139;MQRankSum=-5.912;NF;NR;PP;PV4=0.27,1,0.22,0.015;ReadPosRankSum=1.781;SC=GGTGGTGATGATGGTGGTGGT;TC;TR=17;TU=GGT;VQSLOD=2.1183;set=filterInVQSR-2of5;sumGLbyD=9.05 20 37532218 . GTCCGTCCA ATCCGTCCA,G 76120.88 PASS AC=998;AF=0.92924;AN=1074;BaseQRankSum=-2.877;DP=3087;FR;FS=9.889;HP=2;HPLen=2;HR=1;HRun=0;HU=T;HaplotypeScore=71.6244;InbreedingCoeff=-0.0027;IndelType=MIXED;MQ=52.68;MQ0=543;MQ0Fraction=0.1759;MQRankSum=-1.750;NF;NR;PP;QD=24.98;ReadPosRankSum=-0.850;SB=-36635.43;SC=CCGTCCGTCCGTCCGTCCATC;TC;TR=19;TU=CCGT;VQSLOD=5.3068;set=Intersection 20 37712193 . AAG A 2670.33 PASS AA=106;AB=0.62821;ABA=87;ABP=36.418;ABR=147;AC=53;AF=0.0759;AN=698;BL=4672;BR=4303;BVAR;BaseQRankSum=13.696;DEL;DP=15155;DP4=1340,1852,32,52;Dels=0.06;EL=57;EPP=4.3214;ER=49;FR;FS=0.824;HETAR=43;HOMA=7;HOMR=982;HP=1;HPLen=2;HR=2;HRun=0;HU=A;INDEL;InbreedingCoeff=0.0861;IndelType=DEL.NumRepetitions_3.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.041114;LRBP=35.954;MQ=86.12;MQ0=0;MQ0Fraction=0.0000;MQM=54.236;MQRankSum=-5.745;NF;NR;NS=1034;PP;PV4=0.5,7.3e-26,1.1e-10,1;RA=4423;RL=58;RPP=5.0589;RR=48;RUN=1;ReadPosRankSum=2.617;SAB=0.38679;SAF=41;SAP=14.81;SAR=65;SC=GAAAATTCTGAAGAGAGTCAG;SET_INTEGRATION;SET_WGVQSR;SRB=0.43093;SRF=1906;SRP=186.29;SRR=2517;TC;TR=6;TU=AG;VQSLOD=9.8131;set=Intersection;sumGLbyD=14.20 20 37739002 . T TCA 1395.38 PASS AA=16;AB=0.48387;ABA=16;ABP=3.0803;ABR=15;AC=11;AF=0.00950;AN=1158;BL=504;BR=630;BVAR;BaseQRankSum=-3.257;DP=13617;DP4=1660,883,7,5;Dels=0.00;EL=7;EPP=3.5532;ER=9;FR;FS=1.114;HETAR=9;HOMA=0;HOMR=991;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0527;IndelType=INS.NumRepetitions_1.EventLength_2.RepeatExpansion_CA.;LEN=2;LRB=0.11111;LRBP=33.411;MQ=88.41;MQ0=0;MQ0Fraction=0.0000;MQM=83.75;MQRankSum=1.713;NF;NR;NS=1000;PP;PV4=0.76,1,1,0.5;RA=3257;RL=6;RPP=5.1818;RR=10;RUN=1;ReadPosRankSum=1.190;SAB=0.6875;SAF=11;SAP=7.8961;SAR=5;SC=CCTTTTTTGTTCATTTCTGCA;SET_INTEGRATION;SET_WGVQSR;SRB=0.68806;SRF=2241;SRP=1003.5;SRR=1016;TC;TR=2;TU=T;VQSLOD=10.2220;set=Intersection;sumGLbyD=41.32 20 38395256 . TTGAG T 633.19 PASS AF=0.0028;BaseQRankSum=5.667;DP=3839;Dels=0.00;FR;FS=10.238;HP=2;HPLen=3;HR=3;HRun=0;HU=T;InbreedingCoeff=-0.0097;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.276;NF;NR;PP;ReadPosRankSum=-1.016;SC=ATGTGTTTGTTTGAGTATGTT;SET_INTEGRATION;SET_WGVQSR;TC;TR=10;TU=GTTT;VQSLOD=6.4906;set=Intersection;sumGLbyD=10.83 20 39345038 . CTGAACCATAATGTG C,CCCATAATGTG 60744.52 PASS AA=23;AB=0.67143;ABA=23;ABP=20.878;ABR=47;AC=232,2;AF=0.19366,0.00167;AN=1198;BL=1607;BR=1843;BVAR;BaseQRankSum=30.955;DEL;DP=31490;DP4=1729,2100,265,278;Dels=0.13;EL=6;EPP=14.434;ER=17;FQ=999;FR;FS=1.767;HETAR=18;HOMA=0;HOMR=1015;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.1991;IndelType=MULTIALLELIC_INDEL;LEN=14;LRB=0.068406;LRBP=38.066;MQ=104.60;MQ0=0;MQ0Fraction=0.0000;MQM=189.83;MQRankSum=-16.579;NF;NR;NS=1033;PP;PV4=0.12,1,5.5e-137,1;RA=5286;RL=14;RPP=5.3706;RR=9;RUN=1;ReadPosRankSum=4.323;SAB=0.56522;SAF=13;SAP=3.86;SAR=10;SC=TGGGCTGGACCTGAACCATAA;SET_WGVQSR;SRB=0.46311;SRF=2448;SRP=65.493;SRR=2838;TC;TR=2;TU=C;VQSLOD=6.2643;dbSNP=130;set=Intersection;sumGLbyD=65.43 20 39418008 . AG A 46796 PASS AA=113;AB=0.9511;ABA=80;ABP=2894.6;ABR=1556;AC=30;AF=0.02412;AN=1244;BL=638;BR=6936;BVAR;BaseQRankSum=7.280;DEL;DP=14307;Dels=0.00;EL=50;EPP=6.2579;ER=63;FR;FS=5.707;HETAR=473;HOMA=361;HOMR=246;HP=3;HR=3;HRun=3;HU=G;InbreedingCoeff=0.0272;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.83153;LRBP=11375;MQ0=0;MQ0Fraction=0.0000;MQM=62.398;MQRankSum=3.530;NF;NR;NS=1089;PP;RA=3000;RL=3;RPP=223.02;RR=110;RUN=1;ReadPosRankSum=-18.601;SAB=0.58407;SAF=66;SAP=9.9475;SAR=47;SC=ACTGGGGGAAAGGGATTCTAG;SRB=0.494;SRF=1482;SRP=3.9484;SRR=1518;TC;TR=3;TU=G;VQSLOD=4.5834;set=Intersection;sumGLbyD=3.06 20 39876961 . GT G,GTT,GTTT 2302.10 PASS ABR=496;AC=45,51,45;AF=0.03664,0.04153,0.03664;AN=1228;BVAR;BaseQRankSum=4.462;DP=37649;DP4=1457,1975,57,59;Dels=0.02;FR;FS=9.938;HOMA=0;HOMR=978;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.2583;IndelType=MULTIALLELIC_INDEL;MQ=97.28;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.246;NF;NR;NS=1063;PP;PV4=0.15,1,1.9e-09,0.016;RA=5185;RUN=1;ReadPosRankSum=-4.954;SC=AGTTTCTCCGGTTTTTTTTTT;SET_WGVQSR;SRB=0.47464;SRF=2461;SRP=31.978;SRR=2724;TC;TR=10;TU=T;VQSLOD=4.9752;set=Intersection;sumGLbyD=4.39 20 41013333 . TC T 20681 PASS AA=137;AB=0.89211;ABA=134;ABP=1661.6;ABR=1108;AC=68;AF=0.05601;AN=1214;BL=1091;BR=8981;BVAR;BaseQRankSum=1.354;DEL;DP=12998;Dels=0.01;EL=57;EPP=11.395;ER=80;FS=0.758;HETAR=359;HOMA=100;HOMR=610;HRun=1;InbreedingCoeff=0.0104;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.78336;LRBP=13424;MQ0=1;MQ0Fraction=0.0003;MQM=67.745;MQRankSum=2.563;NS=1072;RA=4447;RL=5;RPP=258.66;RR=132;RUN=1;ReadPosRankSum=-14.092;SAB=0.59124;SAF=81;SAP=12.917;SAR=56;SRB=0.54194;SRF=2410;SRP=70.947;SRR=2037;VQSLOD=3.7531;set=filterInVQSR-2of5;sumGLbyD=4.14 20 41659532 . GC G 40544 PASS AA=42;AB=0.97149;ABA=39;ABP=2644.5;ABR=1329;AC=15;AF=0.0209;AN=716;BL=2531;BR=135;BVAR;BaseQRankSum=-2.537;DEL;DP=12219;Dels=0.00;EL=25;EPP=6.3192;ER=17;FS=2.656;HETAR=374;HOMA=155;HOMR=551;HRun=1;InbreedingCoeff=-0.0270;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.89872;LRBP=4678.9;MQ0=0;MQ0Fraction=0.0000;MQM=103.31;MQRankSum=2.828;NS=1088;RA=4736;RL=41;RPP=85.733;RR=1;RUN=1;ReadPosRankSum=-9.702;SAB=0.57143;SAF=24;SAP=4.8716;SAR=18;SRB=0.5625;SRF=2664;SRP=163.7;SRR=2072;VQSLOD=4.3267;set=Intersection;sumGLbyD=3.22 20 41845580 . GA G 49310 PASS AA=83;AB=0.95258;ABA=69;ABP=2591.6;ABR=1386;AC=46;AF=0.03740;AN=1230;BL=1320;BR=5150;BVAR;BaseQRankSum=-1.121;DEL;DP=13336;Dels=0.00;EL=36;EPP=6.1759;ER=47;FR;FS=0.372;HETAR=442;HOMA=341;HOMR=295;HP=2;HR=3;HRun=1;HU=G;InbreedingCoeff=0.0238;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.59196;LRBP=4926.2;MQ0=0;MQ0Fraction=0.0000;MQM=89.048;MQRankSum=0.897;NF;NR;NS=1080;PP;RA=3006;RL=5;RPP=142.43;RR=78;RUN=1;ReadPosRankSum=-15.412;SAB=0.55422;SAF=46;SAP=5.1294;SAR=37;SC=CCAGCTGTGGGAGAGAAACAT;SRB=0.47971;SRF=1442;SRP=13.762;SRR=1564;TC;TR=6;TU=AG;VQSLOD=4.4669;set=Intersection;sumGLbyD=3.65 20 42209428 . GC G 13163 PASS AA=89;AB=0.86677;ABA=83;ABP=730.96;ABR=540;AC=39;AF=0.03218;AN=1212;BL=950;BR=5334;BVAR;BaseQRankSum=-10.119;DEL;DP=10692;Dels=0.01;EL=48;EPP=4.2058;ER=41;FS=0.000;HETAR=259;HOMA=727;HOMR=54;HRun=1;InbreedingCoeff=0.0448;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.69764;LRBP=6644.4;MQ0=0;MQ0Fraction=0.0000;MQM=126.55;MQRankSum=4.223;NS=1040;RA=723;RL=12;RPP=106.09;RR=77;RUN=1;ReadPosRankSum=-17.362;SAB=0.39326;SAF=35;SAP=11.818;SAR=54;SRB=0.37898;SRF=274;SRP=94.99;SRR=449;VQSLOD=3.7157;set=filterInVQSR-2of5;sumGLbyD=3.48 20 42281109 . T TAG 2321.12 PASS AC=181;AF=0.3740;AN=484;BaseQRankSum=8.977;DP=435;FS=17.001;HRun=0;HaplotypeScore=14.6734;InbreedingCoeff=0.2340;IndelType=INS.NOVEL_2.;MQ=53.88;MQ0=47;MQ0Fraction=0.1080;MQRankSum=0.762;QD=12.41;ReadPosRankSum=3.399;SB=-1299.73;SET_INTEGRATION;VQSLOD=4.8926;set=VQSR 20 42436117 . TC T 38933 PASS AA=18;AB=0.98435;ABA=17;ABP=2215.9;ABR=1069;AC=15;AF=0.01223;AN=1226;BL=498;BR=428;BVAR;BaseQRankSum=-7.224;DEL;DP=12436;Dels=0.00;EL=1;EPP=33.893;ER=17;FS=2.469;HETAR=303;HOMA=614;HOMR=123;HRun=1;InbreedingCoeff=0.0439;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.075594;LRBP=14.501;MQ0=0;MQ0Fraction=0.0000;MQM=98.611;MQRankSum=1.086;NS=1075;RA=1656;RL=10;RPP=3.4928;RR=8;RUN=1;ReadPosRankSum=-17.765;SAB=0.5;SAF=9;SAP=3.0103;SAR=9;SRB=0.49879;SRF=826;SRP=3.0313;SRR=830;VQSLOD=4.0821;set=filterInVQSR-2of5;sumGLbyD=3.04 20 42682214 . C A,CAT 3904.51 PASS AA=24;AB=0.6383;ABA=17;ABP=10.818;ABR=30;AC=0;AF=0.0000;AN=636;BL=1119;BR=949;BVAR;BaseQRankSum=1.426;DP=6509;Dels=0.00;EL=9;EPP=6.2675;ER=15;FR;HETAR=12;HOMA=3;HOMR=876;HP=2;HPLen=1;HR=1;HRun=0;HU=A;INS;InbreedingCoeff=0.0006;IndelType=MIXED;LEN=2;LRB=0.082205;LRBP=33.356;MQ0Fraction=0.0046;MQM=40.792;MQRankSum=-0.296;NF;NR;NS=891;PP;QD=32.81;RA=2679;RL=15;RPP=6.2675;RR=9;RUN=1;ReadPosRankSum=-1.806;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SB=-924.23;SC=TATACACACACATATATATAC;SET_INTEGRATION;SET_WGVQSR;SRB=0.66293;SRF=1776;SRP=620.76;SRR=903;TC;TR=9;TU=AC;set=filterInVQSR-2of5;sumGLbyD=32.75 20 42973456 . CA C,CAA,CAAA 2675 PASS AA=90;AB=0.79177;ABA=86;ABP=308.39;ABR=327;AC=77,61,39;AF=0.06492,0.05143,0.03288;AN=1186;BL=2983;BR=4446;BVAR;BaseQRankSum=2.422;DP=9416;Dels=0.03;EL=39;EPP=6.4847;ER=51;FR;FS=31.555;HETAR=75;HOMA=1;HOMR=888;HP=11;HR=11;HRun=11;HU=A;INS;InbreedingCoeff=0.2696;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.19693;LRBP=628.63;MQ0=0;MQ0Fraction=0.0000;MQM=55.567;MQRankSum=1.777;NF;NR;NS=964;PP;RA=3601;RL=37;RPP=9.1869;RR=53;RUN=1;ReadPosRankSum=-4.991;SAB=0.55556;SAF=50;SAP=5.423;SAR=40;SC=TAGTGACTGTCAAAAAAAAAA;SET_WGVQSR;SRB=0.60622;SRF=2183;SRP=355.91;SRR=1418;TC;TR=11;TU=A;VQSLOD=1.0763;set=filterInVQSR-2of5;sumGLbyD=4.05 20 43091870 . TC T 2455.60 PASS AA=120;AB=0.10619;ABA=101;ABP=155.22;ABR=12;AC=42;AF=0.03825;AN=1098;BL=573;BR=8744;BVAR;BaseQRankSum=-13.513;DEL;DP=9139;Dels=0.00;EL=64;EPP=4.1684;ER=56;FS=9.856;HETAR=118;HOMA=820;HOMR=0;HRun=1;InbreedingCoeff=0.0833;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.877;LRBP=15564;MQ0Fraction=0.0017;MQM=45.1;MQRankSum=2.266;NS=938;RA=24;RL=1;RPP=254.97;RR=119;RUN=1;ReadPosRankSum=-15.803;SAB=0.475;SAF=57;SAP=3.6617;SAR=63;SRB=0.54167;SRF=13;SRP=3.3722;SRR=11;VQSLOD=3.9930;set=filterInVQSR-2of5;sumGLbyD=3.09 20 43233648 rs74585029 GA G,GAA 1504.40 PASS AA=113;AB=0.78652;ABA=95;ABP=320.31;ABR=350;AC=41,65;AF=0.03394,0.05381;AF1=0.0115;AN=1208;BL=4677;BR=5548;BVAR;BaseQRankSum=6.744;CI95=0.004274,0.01852;DB;DEL;DP=13996;DP4=1736,1549,15,17;Dels=0.03;EL=69;EPP=15.021;ER=44;FQ=14;FR;FS=12.174;HETAR=119;HOMA=15;HOMR=892;HP=11;HPLen=10;HR=10;HRun=10;HU=A;INDEL;InbreedingCoeff=0.2359;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.085183;LRBP=164.12;MQ=89.12;MQ0Fraction=0.0000;MQM=69.867;MQRankSum=2.513;NF;NR;NS=1027;PP;PV4=0.59,1,0.065,0.33;RA=3845;RL=46;RPP=11.485;RR=67;RUN=1;ReadPosRankSum=-4.957;SAB=0.33628;SAF=38;SAP=29.318;SAR=75;SC=AAAACAGCCAGAAAAAAAAAA;SET_INTEGRATION;SET_WGVQSR;SRB=0.43667;SRF=1679;SRP=136.95;SRR=2166;TC;TR=10;TU=A;VQSLOD=4.5121;set=Intersection;sumGLbyD=8.22 20 43246548 . AC A,CC 41579.13 PASS AA=382;AB=0.72402;ABA=316;ABP=502.11;ABR=829;AC=1197;AF=0.99254;AN=1206;BL=9889;BR=14293;BVAR;BaseQRankSum=1.373;DEL;DP=10477;DS;Dels=0.05;EL=243;EPP=64.494;ER=139;FS=29.162;HETAR=291;HOMA=85;HOMR=624;HPLen=10;InbreedingCoeff=0.1392;IndelType=MIXED;LEN=1;LRB=0.18212;LRBP=1744.6;MQ0Fraction=0.0024;MQM=48.471;MQRankSum=5.726;NS=1001;RA=3138;RL=174;RPP=9.5816;RR=208;RUN=1;ReadPosRankSum=5.755;SAB=0.79843;SAF=305;SAP=298.51;SAR=77;SET_INTEGRATION;SET_WGVQSR;SRB=0.70363;SRF=2208;SRP=1133.2;SRR=930;VQSLOD=5.6318;set=Intersection;sumGLbyD=5.22 20 43258646 . T TT 1107.17 PASS AC=97;AF=0.08420;AN=1152;BaseQRankSum=4.525;DP=2345;FS=19.308;HRun=9;HaplotypeScore=13.6276;InbreedingCoeff=0.1299;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;MQ=76.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.395;QD=2.67;ReadPosRankSum=-4.696;SB=-899.41;VQSLOD=5.4523;set=VQSR 20 43718299 . ATTACT A 5497.06 PASS AA=56;AB=0.51818;ABA=53;ABP=3.3262;ABR=57;AC=18;AF=0.0251;AF1=0.03729;AN=718;BL=2321;BR=2591;BVAR;BaseQRankSum=11.142;CI95=0.03319,0.04425;DEL;DP=17576;DP4=2460,2692,31,22;Dels=0.02;EL=28;EPP=3.0103;ER=28;FQ=999;FR;FS=9.689;HETAR=15;HOMA=1;HOMR=1068;HP=2;HPLen=2;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0448;IndelType=DEL.NumRepetitions_1.EventLength_5.;LEN=5;LRB=0.054967;LRBP=35.238;MQ=96.55;MQ0=0;MQ0Fraction=0.0000;MQM=50.286;MQRankSum=-5.149;NF;NR;NS=1084;PP;PV4=0.13,1,1.2e-12,1;RA=6745;RL=28;RPP=3.0103;RR=28;RUN=1;ReadPosRankSum=0.828;SAB=0.5;SAF=28;SAP=3.0103;SAR=28;SC=ATGACAGTGGATTACTTTAGT;SET_INTEGRATION;SET_WGVQSR;SRB=0.46835;SRF=3159;SRP=61.709;SRR=3586;TC;TR=2;TU=T;VQSLOD=7.8832;set=Intersection;sumGLbyD=46.60 20 43981749 . A AAAAAAC,AC 20899.71 PASS ABR=192;AC=91,0;AF=0.1285,0.0000;AN=708;BVAR;BaseQRankSum=7.858;DP=23372;DP4=1554,1457,55,42;Dels=0.00;FR;FS=0.000;HOMA=4;HOMR=995;HP=6;HPLen=7;HR=7;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.2109;IndelType=MULTIALLELIC_INDEL;MQ=95.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-12.081;NF;NR;NS=1051;PP;PV4=0.35,1,8.9e-73,1;RA=5027;RUN=1;ReadPosRankSum=-1.359;SC=TACACTAGCAAAAAAACAAAA;SET_WGVQSR;SRB=0.48518;SRF=2439;SRP=12.6;SRR=2588;TC;TR=7;TU=A;VQSLOD=8.0916;set=Intersection;sumGLbyD=54.33 20 43999274 . TCAAA T 2948.85 PASS AA=59;AB=0.59441;ABA=58;ABP=14.08;ABR=85;AC=20;AF=0.0290;AF1=0.04249;AN=690;BL=2277;BR=2436;BVAR;BaseQRankSum=9.320;CI95=0.0354,0.05088;DEL;DP=14599;DP4=2052,2303,21,22;Dels=0.03;EL=32;EPP=3.9304;ER=27;FQ=999;FR;FS=0.000;HETAR=21;HOMA=0;HOMR=1043;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0037;IndelType=DEL.NumRepetitions_1.EventLength_4.;LEN=4;LRB=0.033736;LRBP=14.658;MQ=90.05;MQ0=0;MQ0Fraction=0.0000;MQM=75.339;MQRankSum=-1.294;NF;NR;NS=1064;PP;PV4=0.88,1,0.0026,1;RA=5732;RL=27;RPP=3.9304;RR=32;RUN=1;ReadPosRankSum=-0.915;SAB=0.47458;SAF=28;SAP=3.3415;SAR=31;SC=GGTACACAGCTCAAACAGTCT;SET_INTEGRATION;SET_WGVQSR;SRB=0.4836;SRF=2772;SRP=16.4;SRR=2960;TC;TR=1;TU=C;VQSLOD=9.8086;set=Intersection;sumGLbyD=27.09 20 44098622 . C CG 1092.40 PASS AA=129;AB=0.77301;ABA=74;ABP=214.06;ABR=252;AC=45;AF=0.0455;AN=988;BL=6586;BR=3029;BVAR;BaseQRankSum=2.802;DP=5177;Dels=0.00;EL=122;EPP=225.63;ER=7;FR;FS=355.273;HETAR=66;HOMA=11;HOMR=734;HP=6;HR=4;HRun=4;HU=G;INS;InbreedingCoeff=0.1759;IndelType=INS.NumRepetitions_4.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.36994;LRBP=2860.4;MQ0=0;MQ0Fraction=0.0000;MQM=52.395;MQRankSum=1.946;NF;NR;NS=811;PP;RA=1981;RL=121;RPP=217.95;RR=8;RUN=1;ReadPosRankSum=-6.413;SAB=0.99225;SAF=128;SAP=274.51;SAR=1;SC=GCGGAAGTGGCGGGGACCCTT;SRB=0.41242;SRF=817;SRP=135;SRR=1164;TC;TR=4;TU=G;VQSLOD=-2.2690;set=filterInVQSR-2of5;sumGLbyD=4.04 20 44327637 . A AG,AGGGGGG 14351.23 PASS AC=9,211;AF=0.0103,0.2409;AN=876;BaseQRankSum=15.517;DP=1704;FS=6.768;HaplotypeScore=31.5906;InbreedingCoeff=0.1538;IndelType=MULTIALLELIC_INDEL;MQ=54.64;MQ0=4;MQ0Fraction=0.0023;MQRankSum=-12.691;QD=20.83;ReadPosRankSum=-3.583;SB=-6278.99;VQSLOD=5.1556;set=VQSR 20 45202636 . GA G 13269 PASS AA=25;AB=0.96162;ABA=18;ABP=871.09;ABR=451;AC=24;AF=0.02013;AN=1192;BL=567;BR=1728;BVAR;BaseQRankSum=-5.361;DEL;DP=10873;Dels=0.00;EL=10;EPP=5.1818;ER=15;FS=0.928;HETAR=169;HOMA=831;HOMR=45;HRun=1;InbreedingCoeff=0.0999;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.50588;LRBP=1278.4;MQ0=0;MQ0Fraction=0.0000;MQM=170.56;MQRankSum=0.161;NS=1049;RA=632;RL=2;RPP=41.315;RR=23;RUN=1;ReadPosRankSum=-14.760;SAB=0.68;SAF=17;SAP=10.046;SAR=8;SRB=0.51424;SRF=325;SRP=4.1235;SRR=307;VQSLOD=3.9290;set=filterInVQSR-2of5;sumGLbyD=3.90 20 45417828 . TGAGC T,TGC 4672.90 PASS ABR=317;AC=69,104;AF=0.05712,0.08609;BVAR;BaseQRankSum=18.527;DEL;DP=11835;DS;FS=184.873;HOMA=48;HOMR=575;HaplotypeScore=65.5875;InbreedingCoeff=0.0599;IndelType=MULTIALLELIC_INDEL;MQ=29.78;MQ0=2988;MQ0Fraction=0.3629;MQRankSum=5.052;NS=713;QD=1.11;RA=1581;RUN=1;ReadPosRankSum=6.574;SB=-2116.87;SRB=0.47502;SRF=751;SRP=11.582;SRR=830;VQSLOD=0.0651;set=filterInVQSR-2of5 20 45525657 rs66759083 TA AA,T 49315 PASS AA=2361;AB=0.45241;ABA=1398;ABP=53.235;ABR=1155;AC=20;AF=0.01701;AN=1176;BL=94913;BR=100886;BVAR;BaseQRankSum=0.740;DB;DEL;DP=30636;DP4=1258,881,1206,999;Dels=0.48;EL=1133;EPP=11.311;ER=1228;FQ=999;FR;FS=7.072;HETAR=503;HOMA=310;HOMR=218;HP=6;HPLen=7;HR=7;HU=T;INDEL;InbreedingCoeff=0.2271;IndelType=MIXED;LEN=1;LRB=0.030506;LRBP=398.68;MQ=102.24;MQ0=0;MQ0Fraction=0.0000;MQM=75.359;MQRankSum=0.148;NF;NR;NS=1031;PP;PV4=0.0064,0,4.6e-23,0.47;RA=2042;RL=1183;RPP=3.0333;RR=1178;RUN=1;ReadPosRankSum=-2.999;SAB=0.52139;SAF=1231;SAP=12.392;SAR=1130;SC=AGGATTTTTTTAAAAAGTTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.55093;SRF=1125;SRP=49.017;SRR=917;TC;TR=7;TU=T;VQSLOD=7.1651;dbSNP=114;set=Intersection;sumGLbyD=18.51 20 45783456 . T TG 2355.68 PASS AA=64;AB=0.78521;ABA=61;ABP=203.67;ABR=223;AC=15;AF=0.0165;AN=910;BL=815;BR=5486;BVAR;BaseQRankSum=8.593;DP=10348;Dels=0.00;EL=48;EPP=37.754;ER=16;FS=77.861;HETAR=56;HOMA=1;HOMR=970;HRun=1;INS;InbreedingCoeff=-0.0549;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.74131;LRBP=7522.1;MQ0Fraction=0.0122;MQM=44.562;MQRankSum=-1.258;NS=1027;RA=4750;RL=0;RPP=141.98;RR=64;RUN=1;ReadPosRankSum=-7.047;SAB=0.25;SAF=16;SAP=37.754;SAR=48;SRB=0.6;SRF=2850;SRP=415.59;SRR=1900;VQSLOD=1.3146;set=filterInVQSR-2of5;sumGLbyD=6.03 20 46517110 . C CT 868.55 PASS AC=15;AF=0.0218;AN=688;BaseQRankSum=8.522;DP=1752;FS=6.570;HRun=0;HaplotypeScore=14.9548;InbreedingCoeff=0.0452;IndelType=INS.NOVEL_1.Novel_T.;MQ=77.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=3.874;QD=10.98;ReadPosRankSum=-0.733;SB=-396.78;SET_INTEGRATION;SET_WGVQSR;VQSLOD=6.7740;set=VQSR 20 46629361 . TTTCTTTC T,TTTTC 13000.91 PASS AC=188,107;AF=0.2212,0.1259;AN=850;BaseQRankSum=7.214;DP=1846;FS=14.502;HaplotypeScore=40.8481;InbreedingCoeff=0.3210;IndelType=MULTIALLELIC_INDEL;MQ=50.74;MQ0=79;MQ0Fraction=0.0428;MQRankSum=-6.348;QD=13.59;ReadPosRankSum=3.943;SB=-3581.20;VQSLOD=5.9412;set=VQSR 20 46951099 . G GT 1662.30 PASS AA=55;AB=0.7713;ABA=51;ABP=145.58;ABR=172;AC=47;AF=0.03923;AN=1198;BL=3288;BR=2434;BVAR;BaseQRankSum=-4.014;DP=27423;DP4=1483,1590,58,42;Dels=0.01;EL=21;EPP=9.6826;ER=34;FR;FS=9.565;HETAR=48;HOMA=0;HOMR=913;HP=16;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.0952;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.14925;LRBP=279.78;MQ=70.36;MQ0Fraction=0.0124;MQM=52.545;MQRankSum=0.717;NF;NR;NS=961;PP;PV4=0.067,1,1,0.17;RA=3035;RL=38;RPP=20.422;RR=17;RUN=1;ReadPosRankSum=-3.014;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TTTGTTTTTTGTTTTTTTTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.36013;SRF=1093;SRP=518.73;SRR=1942;TC;TR=10;TU=T;VQSLOD=5.4779;set=Intersection;sumGLbyD=3.49 20 47201076 rs58052846 C CT 982.16 PASS AC=50;AF=0.0551;AN=908;BaseQRankSum=12.598;DB;DP=2449;FS=35.648;HRun=0;HaplotypeScore=29.4602;InbreedingCoeff=-0.0542;IndelType=INS.NOVEL_1.Novel_T.;MQ=63.54;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.196;QD=3.16;ReadPosRankSum=-13.833;SB=-488.19;VQSLOD=6.0429;set=VQSR 20 47965974 rs60011158 G GA 999 PASS AA=21;AB=0.57143;ABA=21;ABP=5.1818;ABR=28;AC=7;AF=0.0101;AF1=0.02061;AN=690;BL=1043;BR=577;BVAR;BaseQRankSum=-3.087;CI95=0.01549,0.02655;DB;DP=14578;DP4=1554,3055,6,17;Dels=0.00;EL=11;EPP=3.1137;ER=10;FQ=999;FR;FS=5.982;HETAR=7;HOMA=0;HOMR=1041;HP=2;HPLen=1;HR=1;HRun=1;HU=A;INDEL;INS;InbreedingCoeff=0.0356;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.28765;LRBP=294.09;MQ=80.17;MQ0=0;MQ0Fraction=0.0000;MQM=64.19;MQRankSum=2.137;NF;NR;NS=1048;PP;PV4=0.51,1,1,1;RA=5224;RL=16;RPP=15.522;RR=5;RUN=1;ReadPosRankSum=0.236;SAB=0.38095;SAF=8;SAP=5.5954;SAR=13;SC=TTCATGTACAGAGCTGCTGTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.31183;SRF=1629;SRP=1609.6;SRR=3595;TC;TR=4;TU=AG;VQSLOD=9.5466;dbSNP=129;set=Intersection;sumGLbyD=13.83 20 48402974 rs57331436 GA G 27741 PASS AA=401;AB=0.5372;ABA=311;ABP=11.089;ABR=361;AC=84;AF=0.1186;AN=708;BL=16591;BR=14776;BVAR;BaseQRankSum=14.621;DB;DEL;DP=30607;DP4=1928,2310,195,225;Dels=0.11;EL=189;EPP=5.8749;ER=212;FQ=999;FR;FS=15.568;HETAR=110;HOMA=30;HOMR=923;HP=4;HPLen=3;HR=1;HRun=3;HU=A;INDEL;InbreedingCoeff=0.1263;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;KGPilot123;LEN=1;LRB=0.057863;LRBP=231.06;MQ=106.68;MQ0=0;MQ0Fraction=0.0000;MQM=63.005;MQRankSum=-2.010;NF;NR;NS=1063;PP;PV4=0.72,1,0.001,1;RA=5258;RL=223;RPP=13.976;RR=178;RUN=1;ReadPosRankSum=1.337;SAB=0.37656;SAF=151;SAP=56.084;SAR=250;SC=TGCCCTCAAAGAGAAAAAGGA;SET_INTEGRATION;SET_WGVQSR;SRB=0.38075;SRF=2002;SRP=652.44;SRR=3256;TC;TR=5;TU=AG;VQSLOD=8.7259;dbSNP=132;set=Intersection;sumGLbyD=15.86 20 49101936 . C CT 404.46 PASS AC=40;AF=0.03559;AN=1124;BaseQRankSum=0.750;DP=2162;FS=14.291;HRun=2;HaplotypeScore=30.9513;InbreedingCoeff=-0.0082;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_T.;MQ=49.78;MQ0=113;MQ0Fraction=0.0523;MQRankSum=-1.289;QD=1.94;ReadPosRankSum=-2.041;SB=-385.48;VQSLOD=4.6365;set=VQSR 20 49731218 . ATTTTATTTTTTATT A,ATTTTATT 8398.93 PASS AF=0.0656,0.0156;AF1=0.0996;BaseQRankSum=13.996;CI95=0.07743,0.1239;DP=6308;DP4=951,1311,23,35;Dels=0.05;FQ=999;FR;FS=12.503;HP=7;HPLen=4;HR=4;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1892;IndelType=MULTIALLELIC_INDEL;MQ=57.61;MQ0Fraction=0.0145;MQRankSum=-5.208;NF;NR;PP;PV4=0.79,1,6.3e-06,0.16;ReadPosRankSum=-2.239;SC=TATTTTATTTATTTTATTTTT;TC;TR=11;TU=ATTT;VQSLOD=4.3191;set=Intersection;sumGLbyD=42.27 20 49894989 . TA T 172.25 PASS AF=0.0140;BaseQRankSum=7.220;DP=3882;Dels=0.00;FS=17.217;HPLen=2;HRun=1;InbreedingCoeff=0.0531;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;MQ0Fraction=0.0214;MQRankSum=-0.661;ReadPosRankSum=-0.592;SET_INTEGRATION;SET_WGVQSR;VQSLOD=3.0905;set=filterInVQSR-2of5;sumGLbyD=6.60 20 50010923 rs66516522 C CT,CTGG 35851 PASS ABR=555;AC=310,11;AF=0.26451,0.00939;BVAR;BaseQRankSum=10.662;DB;DP=8188;FR;FS=34.411;HOMA=261;HOMR=399;HP=5;HR=6;HU=C;HaplotypeScore=45.1715;INS;InbreedingCoeff=0.2090;IndelType=MULTIALLELIC_INDEL;MQ=72.80;MQ0=0;MQ0Fraction=0.0000;MQRankSum=9.015;NF;NR;NS=831;PP;QD=9.69;RA=1986;RUN=1;ReadPosRankSum=-24.284;SB=-6038.55;SC=TGTCTGTCCCCCCTCAGCACT;SRB=0.45972;SRF=913;SRP=31.001;SRR=1073;TC;TR=6;TU=C;VQSLOD=6.1824;set=Intersection 20 50228709 rs71192536 TG T 20517 PASS AA=924;AB=0.50203;ABA=735;ABP=3.0633;ABR=741;AC=200;AF=0.16502;AN=1212;BL=35460;BR=34197;BVAR;BaseQRankSum=13.810;DB;DEL;DP=32402;DP4=1760,2065,395,449;Dels=0.16;EL=439;EPP=7.9831;ER=485;FQ=999;FR;FS=0.558;HETAR=242;HOMA=63;HOMR=764;HP=5;HPLen=3;HR=3;HRun=3;HU=G;INDEL;InbreedingCoeff=0.1050;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.018132;LRBP=52.738;MQ=105.83;MQ0=0;MQ0Fraction=0.0000;MQM=75.87;MQRankSum=3.895;NF;NR;NS=1069;PP;PV4=0.7,1.5e-173,1,1;RA=4708;RL=486;RPP=8.4249;RR=438;RUN=1;ReadPosRankSum=1.586;SAB=0.43615;SAF=403;SAP=35.733;SAR=521;SC=GTTTTCCAGGTGGGAAGACCG;SET_INTEGRATION;SET_WGVQSR;SRB=0.44074;SRF=2075;SRP=146.62;SRR=2633;TC;TR=3;TU=G;VQSLOD=10.4820;dbSNP=120;set=Intersection;sumGLbyD=15.35 20 50236115 . AGG A,ACGGG,AG,AGGG 7429.57 PASS AC=192,13,221,183;AF=0.2115,0.0143,0.2434,0.2015;AN=908;BaseQRankSum=1.045;DP=1177;FS=13.479;HaplotypeScore=11.8294;InbreedingCoeff=0.7959;IndelType=MULTIALLELIC_INDEL;MQ=52.98;MQ0=6;MQ0Fraction=0.0051;MQRankSum=-1.482;QD=7.28;ReadPosRankSum=-2.380;SB=-1229.31;SET_WGVQSR;VQSLOD=8.3762;set=VQSR 20 51589568 . TAAAC AAAAC,T 12477.52 PASS AF=0.27949;BaseQRankSum=-28.122;DP=3777;Dels=0.00;FR;FS=31.799;HP=7;HPLen=4;HR=3;HRun=0;HU=A;InbreedingCoeff=-0.1429;IndelType=MIXED;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.196;NF;NR;PP;ReadPosRankSum=-16.483;SC=AAATTCAAAATAAACAAACAA;SET_INTEGRATION;SET_WGVQSR;TC;TR=18;TU=AAAC;VQSLOD=3.9201;set=filterInVQSR-2of5;sumGLbyD=52.43 20 51617742 . TGC T,TGCGC 1374.91 PASS AF=0.06000,0.02000;BaseQRankSum=12.051;DP=6231;Dels=0.00;FS=189.609;HPLen=1;HRun=0;InbreedingCoeff=0.0862;IndelType=MULTIALLELIC_INDEL;MQ0Fraction=0.0180;MQRankSum=-2.959;ReadPosRankSum=-5.090;VQSLOD=-2.8715;set=filterInVQSR-2of5;sumGLbyD=3.97 20 51770354 . AG A 1010.90 PASS AA=26;AB=0.52727;ABA=26;ABP=3.3656;ABR=29;AC=7;AF=0.0097;AF1=0.01637;AN=718;BL=1034;BR=964;BVAR;BaseQRankSum=5.588;CI95=0.01327,0.02212;DEL;DP=16259;DP4=2785,2239,15,10;Dels=0.01;EL=11;EPP=4.3466;ER=15;FQ=999;FR;FS=3.367;HETAR=8;HOMA=0;HOMR=1064;HP=2;HPLen=2;HR=2;HRun=2;HU=G;INDEL;InbreedingCoeff=0.0557;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.035035;LRBP=8.3357;MQ=90.48;MQ0=0;MQ0Fraction=0.0000;MQM=61.346;MQRankSum=-0.019;NF;NR;NS=1072;PP;PV4=0.69,2.1e-08,0.078,1;RA=6173;RL=13;RPP=3.0103;RR=13;RUN=1;ReadPosRankSum=-0.460;SAB=0.61538;SAF=16;SAP=6.017;SAR=10;SC=GTGGTCCTGCAGGTCAATAAT;SET_INTEGRATION;SET_WGVQSR;SRB=0.56342;SRF=3478;SRP=218.68;SRR=2695;TC;TR=2;TU=G;VQSLOD=10.1601;set=Intersection;sumGLbyD=14.60 20 51848430 . AT A,ATT 999 PASS AA=39;AB=0.83408;ABA=37;ABP=219.19;ABR=186;AC=14,33;AF=0.0153,0.0359;AF1=0.03062;AN=918;BL=1676;BR=1732;BVAR;BaseQRankSum=3.338;CI95=0.02212,0.03982;DP=14886;DP4=1970,1762,22,31;Dels=0.01;EL=18;EPP=3.5114;ER=21;FQ=999;FR;FS=3.004;HETAR=31;HOMA=0;HOMR=1040;HP=10;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.1629;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.016432;LRBP=5.0085;MQ=80.05;MQ0=0;MQ0Fraction=0.0000;MQM=56.667;MQRankSum=0.325;NF;NR;NS=1071;PP;PV4=0.13,1,0.0095,0.064;RA=5318;RL=21;RPP=3.5114;RR=18;RUN=1;ReadPosRankSum=-0.493;SAB=0.46154;SAF=18;SAP=3.5114;SAR=21;SC=ACAAAACAATATTTTTTTTTC;SET_WGVQSR;SRB=0.4968;SRF=2642;SRP=3.4823;SRR=2676;TC;TR=9;TU=T;VQSLOD=5.7417;set=Intersection;sumGLbyD=7.57 20 51897203 . T TG 8427.20 PASS AA=237;AB=0.69846;ABA=215;ABP=246.92;ABR=498;AC=117;AF=0.1662;AN=704;BL=14961;BR=5990;BVAR;BaseQRankSum=22.203;DP=9710;Dels=0.00;EL=83;EPP=49.198;ER=154;FR;FS=9.450;HETAR=123;HOMA=9;HOMR=895;HP=5;HPLen=6;HR=6;HRun=0;HU=T;INS;InbreedingCoeff=-0.0513;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.42819;LRBP=8344.3;MQ0Fraction=0.0291;MQM=45.861;MQRankSum=-10.426;NF;NR;NS=1027;PP;RA=4919;RL=210;RPP=309.85;RR=27;RUN=1;ReadPosRankSum=-1.843;SAB=0.29536;SAF=70;SAP=89.219;SAR=167;SC=TTTGTTTGTTTTTTGTTGTTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.47794;SRF=2351;SRP=23.798;SRR=2568;TC;TR=23;TU=GTTT;VQSLOD=6.2670;set=Intersection;sumGLbyD=8.99 20 52274070 . AAG A 1400.37 PASS AA=30;AB=0.74227;ABA=25;ABP=52.462;ABR=72;AC=21;AF=0.01756;AN=1196;BL=412;BR=1966;BVAR;BaseQRankSum=6.660;DEL;DP=9362;Dels=0.01;EL=16;EPP=3.2998;ER=14;FS=1.485;HETAR=18;HOMA=2;HOMR=1004;HRun=0;InbreedingCoeff=0.0317;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.65349;LRBP=2208.2;MQ0Fraction=0.0022;MQM=46.133;MQRankSum=-4.743;NS=1024;RA=3931;RL=2;RPP=51.941;RR=28;RUN=1;ReadPosRankSum=-4.152;SAB=0.4;SAF=12;SAP=5.6161;SAR=18;SET_INTEGRATION;SET_WGVQSR;SRB=0.49784;SRF=1957;SRP=3.1699;SRR=1974;VQSLOD=5.6452;set=Intersection;sumGLbyD=11.11 20 52351501 . TAC T 199.59 PASS AC=22;AF=0.0238;AN=926;BaseQRankSum=7.874;DP=22911;DP4=2146,1691,26,22;FR;FS=2.898;HP=4;HPLen=3;HR=1;HRun=0;HU=A;HaplotypeScore=18.6111;INDEL;InbreedingCoeff=-0.0326;IndelType=DEL.NumRepetitions_6.EventLength_2.RepeatExpansion_AC.;MQ0=2;MQ0Fraction=0.0007;MQRankSum=1.011;NF;NR;PP;PV4=0.88,0.14,0.16,0.24;QD=1.10;ReadPosRankSum=-1.053;SB=-306.09;SC=GACACACAAATACACACACAC;SET_INTEGRATION;SET_WGVQSR;TC;TR=13;TU=AC;VQSLOD=4.0486;set=filterInVQSR-2of5 20 52447173 . CA C 503.89 PASS AC=23;AF=0.01891;AN=1216;BaseQRankSum=0.801;DP=3266;FS=2.606;HRun=2;HaplotypeScore=22.1543;InbreedingCoeff=-0.0097;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_A.;MQ=118.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.309;QD=2.65;ReadPosRankSum=-7.872;SB=-279.27;VQSLOD=4.1900;set=VQSR 20 52498650 . GT G 24069 PASS AA=74;AB=0.90594;ABA=57;ABP=870.4;ABR=549;AC=28;AF=0.02333;AN=1200;BL=505;BR=4514;BVAR;BaseQRankSum=-3.837;DEL;DP=9798;Dels=0.01;EL=41;EPP=4.8883;ER=33;FS=4.085;HETAR=209;HOMA=663;HOMR=121;HRun=1;InbreedingCoeff=0.0334;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.79876;LRBP=6956.6;MQ0=2;MQ0Fraction=0.0007;MQM=57.784;MQRankSum=-2.951;NS=995;RA=957;RL=8;RPP=101.72;RR=66;RUN=1;ReadPosRankSum=-14.806;SAB=0.39189;SAF=29;SAP=10.522;SAR=45;SRB=0.39916;SRF=382;SRP=87.53;SRR=575;VQSLOD=3.8710;set=filterInVQSR-2of5;sumGLbyD=2.90 20 52823602 rs11469056 CAAA C,CA,CAA,CAAAA,CAAAAA,CAAAAAA,CAAAAAAA,CAAAAAAAA,CAAAAAAAAA,CAAAAAAAAAA 14515.17 PASS AC=24,83,246,109,83,19,10,16,22,59;AF=0.02128,0.07358,0.21809,0.09663,0.07358,0.01684,0.00887,0.01418,0.01950,0.05230;AN=1128;BVAR;BaseQRankSum=4.150;DB;DEL;DP=28279;FR;FS=2.021;HP=17;HR=17;HU=A;HaplotypeScore=27.8032;INS;InbreedingCoeff=0.7740;IndelType=MULTIALLELIC_INDEL;MQ=69.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.418;NF;NR;PP;QD=7.90;RUN=1;ReadPosRankSum=-3.864;SB=-3244.40;SC=GGTCCTAAGGCAAAAAAAAAA;SET_WGVQSR;TC;TR=17;TU=A;VQSLOD=14.1033;set=Intersection 20 53308906 . CT C,CTT 2276 PASS AA=92;AB=0.84453;ABA=81;ABP=540.17;ABR=440;AC=53,81;AF=0.04351,0.06650;AN=1218;BL=3561;BR=4796;BVAR;BaseQRankSum=3.000;DP=11804;Dels=0.02;EL=48;EPP=3.3879;ER=44;FR;FS=13.197;HETAR=69;HOMA=3;HOMR=993;HP=11;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2297;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.14778;LRBP=399.32;MQ0=1;MQ0Fraction=0.0003;MQM=56.348;MQRankSum=3.154;NF;NR;NS=1065;PP;RA=5520;RL=39;RPP=7.6365;RR=53;RUN=1;ReadPosRankSum=-2.140;SAB=0.57609;SAF=53;SAP=7.6365;SAR=39;SC=AATCCAAAGTCTTTTTTTTTT;SET_WGVQSR;SRB=0.51576;SRF=2847;SRP=14.92;SRR=2673;TC;TR=10;TU=T;VQSLOD=2.4753;set=filterInVQSR-2of5;sumGLbyD=4.42 20 53334602 . T TG,TGG 905.13 PASS ABR=325;AC=44,22;AF=0.03624,0.01812;BVAR;BaseQRankSum=-4.608;DP=15015;FR;FS=494.901;HOMA=0;HOMR=1004;HP=1;HR=1;HU=G;HaplotypeScore=20.5023;INS;InbreedingCoeff=0.0799;IndelType=MULTIALLELIC_INDEL;MQ=116.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=8.022;NF;NR;NS=1064;PP;QD=0.35;RA=5690;RUN=1;ReadPosRankSum=-14.522;SB=-311.57;SC=AGCCATTGGCTGTTTCACTGA;SRB=0.40738;SRF=2318;SRP=426.97;SRR=3372;TC;TR=1;TU=G;VQSLOD=-2.3042;set=filterInVQSR-2of5 20 53729115 . T TG 15.48 PASS AC=1;AF=0.0015;AN=668;BaseQRankSum=-1.001;DP=1711;FS=9.048;HRun=2;HaplotypeScore=12.4681;InbreedingCoeff=-0.0320;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;MQ=131.36;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.193;QD=4.57;ReadPosRankSum=0.407;SB=-5.35;SET_INTEGRATION;SET_WGVQSR;VQSLOD=4.8071;set=VQSR 20 54033830 . GTATTTTAAAATCA G 2220.86 PASS AF=0.0113;BaseQRankSum=5.506;DP=2577;Dels=0.01;FR;FS=6.533;HP=5;HPLen=4;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0032;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.969;NF;NR;PP;ReadPosRankSum=1.322;SC=TCAATATTTTGTATTTTAAAA;SET_INTEGRATION;SET_WGVQSR;TC;TR=1;TU=T;VQSLOD=5.5145;set=Intersection;sumGLbyD=95.65 20 54375236 . GT G 626.13 PASS AA=40;AB=0.63551;ABA=39;ABP=20.078;ABR=68;AC=18;AF=0.0256;AN=702;BL=1331;BR=1743;BVAR;BaseQRankSum=9.346;DEL;DP=8568;Dels=0.02;EL=26;EPP=10.828;ER=14;FS=0.610;HETAR=21;HOMA=1;HOMR=1035;HRun=1;InbreedingCoeff=-0.0056;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13403;LRBP=122.92;MQ0=0;MQ0Fraction=0.0000;MQM=67.125;MQRankSum=-2.537;NS=1058;RA=4870;RL=17;RPP=4.9646;RR=23;RUN=1;ReadPosRankSum=-1.229;SAB=0.525;SAF=21;SAP=3.2274;SAR=19;SET_INTEGRATION;SET_WGVQSR;SRB=0.5271;SRF=2567;SRP=34.087;SRR=2303;VQSLOD=7.9228;set=Intersection;sumGLbyD=10.77 20 54457331 . G GA 1793.40 PASS AA=77;AB=0.66667;ABA=74;ABP=56.573;ABR=148;AC=33;AF=0.02687;AN=1228;BL=3834;BR=1154;BVAR;BaseQRankSum=10.572;DP=10230;Dels=0.00;EL=77;EPP=170.21;ER=0;FS=139.433;HETAR=44;HOMA=1;HOMR=1001;HRun=1;INS;InbreedingCoeff=0.0023;IndelType=INS.NOVEL_1.Novel_A.;LEN=1;LRB=0.53729;LRBP=3129.8;MQ0Fraction=0.0095;MQM=4.7013;MQRankSum=-8.116;NS=1046;RA=4009;RL=77;RPP=170.21;RR=0;RUN=1;ReadPosRankSum=-6.026;SAB=1;SAF=77;SAP=170.21;SAR=0;SRB=0.57022;SRF=2286;SRP=174.7;SRR=1723;VQSLOD=1.1887;set=filterInVQSR-2of5;sumGLbyD=5.90 20 54469810 . CA C 1697.62 PASS AA=93;AB=0.63855;ABA=90;ABP=44.53;ABR=159;AC=34;AF=0.0374;AF1=0.01719;AN=908;BL=3242;BR=5839;BVAR;BaseQRankSum=10.425;CI95=0.009317,0.02795;DEL;DP=15197;DP4=2134,1896,56,46;Dels=0.03;EL=34;EPP=17.604;ER=59;FQ=16;FR;FS=9.985;HETAR=41;HOMA=1;HOMR=1011;HP=9;HPLen=8;HR=8;HRun=8;HU=A;INDEL;InbreedingCoeff=-0.0472;IndelType=DEL.NumRepetitions_8.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.28598;LRBP=1615.8;MQ=83.37;MQ0=1;MQ0Fraction=0.0004;MQM=64.075;MQRankSum=3.036;NF;NR;NS=1053;PP;PV4=0.76,1,0.31,0.22;RA=5150;RL=28;RPP=34.975;RR=65;RUN=1;ReadPosRankSum=-0.252;SAB=0.5914;SAF=55;SAP=9.7582;SAR=38;SC=ATTGCTAAGACAAAAAAAAGA;SET_INTEGRATION;SET_WGVQSR;SRB=0.50621;SRF=2607;SRP=4.7374;SRR=2543;TC;TR=8;TU=A;VQSLOD=8.3677;set=Intersection;sumGLbyD=9.90 20 54542453 . GTATA G,GTA 5109.66 PASS ABR=112;AC=66,56;AF=0.0682,0.0579;AN=968;BVAR;BaseQRankSum=17.089;DB;DEL;DP=5519;DS;Dels=0.06;FS=99.502;HOMA=15;HOMR=409;HRun=0;InbreedingCoeff=0.1584;IndelType=MULTIALLELIC_INDEL;MQ0Fraction=0.0178;MQRankSum=-6.854;NS=460;RA=864;RUN=1;ReadPosRankSum=0.855;SRB=0.79282;SRF=685;SRP=646.5;SRR=179;VQSLOD=0.6375;set=filterInVQSR-2of5;sumGLbyD=8.53 20 54629773 . CA C 1799.50 PASS AA=49;AB=0.82707;ABA=46;ABP=250.17;ABR=220;AC=9;AF=0.00746;AN=1206;BL=173;BR=2277;BVAR;BaseQRankSum=5.240;DEL;DP=8557;Dels=0.01;EL=49;EPP=109.41;ER=0;FS=32.359;HETAR=35;HOMA=1;HOMR=325;HRun=1;InbreedingCoeff=0.0892;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.85878;LRBP=3926.6;MQ0Fraction=0.0602;MQM=32.163;MQRankSum=-3.926;NS=361;RA=1091;RL=0;RPP=109.41;RR=49;RUN=1;ReadPosRankSum=-4.512;SAB=0;SAF=0;SAP=109.41;SAR=49;SRB=0.49404;SRF=539;SRP=3.3467;SRR=552;VQSLOD=1.1233;set=filterInVQSR-2of5;sumGLbyD=3.54 20 54710245 . TA T 999 PASS AF=0.0084;AF1=0.0148;BaseQRankSum=3.954;CI95=0.00885,0.02212;DP=8043;DP4=2000,1849,10,7;Dels=0.01;FQ=999;FR;FS=0.000;HP=9;HPLen=6;HR=3;HRun=6;HU=A;INDEL;InbreedingCoeff=0.1181;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=78.51;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.095;NF;NR;PP;PV4=0.63,0.00056,1,1;ReadPosRankSum=-0.448;SC=CAACAAAAAATAAATAAATAA;SET_INTEGRATION;SET_WGVQSR;TC;TR=15;TU=AAAT;VQSLOD=7.8129;set=Intersection;sumGLbyD=19.02 20 54968173 . A AAT,AATAT,AT,ATAT 89535.82 PASS ABR=994;AC=561,278,2,3;AF=0.50179,0.24866,0.00179,0.00268;AN=1118;BVAR;BaseQRankSum=-2.699;DB;DP=27837;DP4=168,177,1045,866;Dels=0.00;FQ=999;FR;FS=12.472;HOMA=71;HOMR=455;HP=3;HPLen=4;HR=4;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.6391;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ=80.36;MQ0Fraction=0.0055;MQRankSum=-1.512;NF;NR;NS=913;PP;PV4=0.046,1,1,1;RA=2015;RUN=1;ReadPosRankSum=1.015;SC=GGCCACTTAAAATATATATAT;SET_WGVQSR;SRB=0.44864;SRF=904;SRP=49.187;SRR=1111;TC;TR=15;TU=AT;VQSLOD=9.0092;dbSNP=132;set=Intersection;sumGLbyD=42.33 20 55176688 . TA T 421.84 PASS AF=0.01322;AF1=0.01845;BaseQRankSum=5.383;CI95=0.01282,0.02564;DP=10531;DP4=1975,2017,16,14;Dels=0.01;FQ=91.2;FR;FS=7.401;HP=6;HPLen=5;HR=5;HRun=5;HU=A;INDEL;InbreedingCoeff=0.0829;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_A.;MQ=75.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=-0.471;NF;NR;PP;PV4=0.72,1,1,1;ReadPosRankSum=0.223;SC=CTGCAAAATATAAAAATTAGG;SET_INTEGRATION;SET_WGVQSR;TC;TR=5;TU=A;VQSLOD=6.6000;set=Intersection;sumGLbyD=12.15 20 55664086 . GTT ATT,G,GT,GTTT 5622.44 PASS AC=6,71,136;AF=0.00498,0.05887,0.11277;AN=1206;BVAR;BaseQRankSum=3.173;DB;DEL;DP=40384;DP4=1567,1317,54,29;Dels=0.05;FR;FS=1.949;HP=14;HR=11;HRun=11;HU=T;INDEL;INS;InbreedingCoeff=0.3490;IndelType=MIXED;MQ=77.90;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.052;NF;NR;PP;PV4=0.057,1,0.2,1.2e-05;RUN=1;ReadPosRankSum=-13.646;SC=AATTTTATTTGTTTTTTTTTT;SET_INTEGRATION;SET_WGVQSR;TC;TR=11;TU=T;VQSLOD=11.7964;set=Intersection;sumGLbyD=8.09 20 56045006 . TG T 342.15 PASS AC=72;AF=0.0940;AN=766;BaseQRankSum=4.992;DP=1238;FS=1.460;HRun=7;HaplotypeScore=20.2784;InbreedingCoeff=0.1795;IndelType=DEL.NumRepetitions_7.EventLength_1.RepeatExpansion_G.;MQ=66.42;MQ0=1;MQ0Fraction=0.0008;MQRankSum=-0.937;QD=1.84;ReadPosRankSum=-4.385;SB=-320.83;VQSLOD=5.2383;set=VQSR 20 56158711 . AG A 922.47 PASS AA=18;AB=0.575;ABA=17;ABP=4.9646;ABR=23;AC=2;AF=0.0028;AN=714;BL=953;BR=808;BVAR;BaseQRankSum=3.129;DEL;DP=10462;Dels=0.01;EL=9;EPP=3.0103;ER=9;FR;FS=8.724;HETAR=4;HOMA=0;HOMR=1058;HP=1;HPLen=2;HR=2;HRun=1;HU=A;InbreedingCoeff=0.0262;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.08234;LRBP=28.936;MQ0=0;MQ0Fraction=0.0000;MQM=55.889;MQRankSum=2.052;NF;NR;NS=1062;PP;RA=6300;RL=9;RPP=3.0103;RR=9;RUN=1;ReadPosRankSum=-0.317;SAB=0.66667;SAF=12;SAP=7.3532;SAR=6;SC=TGGCCTAGCAAGCATCGTGAC;SET_INTEGRATION;SET_WGVQSR;SRB=0.48143;SRF=3033;SRP=21.883;SRR=3267;TC;TR=8;TU=AAGC;VQSLOD=8.3252;set=Intersection;sumGLbyD=13.22 20 56258618 rs113670927 T C,TGC,TGTGC,TGTGTGC 37834.99 PASS ABR=441;AC=11,100,43;AF=0.0123,0.1119,0.0481;AN=894;BVAR;BaseQRankSum=19.514;DB;DP=23173;DP4=541,920,413,579;Dels=0.00;FQ=999;FR;FS=1.238;HOMA=28;HOMR=808;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.2154;IndelType=MIXED;MQ=57.25;MQ0Fraction=0.0275;MQRankSum=-6.684;NF;NR;NS=976;PP;PV4=0.023,1,1,1;RA=3294;RUN=1;ReadPosRankSum=11.873;SC=TGCGTGTGTGTGTGTGTGTGT;SRB=0.42441;SRF=1398;SRP=166.5;SRR=1896;TC;TR=30;TU=GT;VQSLOD=6.7457;dbSNP=114;set=Intersection;sumGLbyD=21.27 20 56395857 . T TAGGCAG 6614.22 PASS AA=30;AB=0.63415;ABA=30;ABP=15.827;ABR=52;AC=14;AF=0.0197;AF1=0.03154;AN=710;BL=991;BR=1813;BVAR;BaseQRankSum=-4.589;CI95=0.02434,0.04204;DP=13879;DP4=1543,1833,12,14;Dels=0.00;EL=14;EPP=3.2998;ER=16;FQ=999;FR;FS=1.482;HETAR=11;HOMA=0;HOMR=1051;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0774;IndelType=INS.NumRepetitions_2.EventLength_6.;LEN=6;LRB=0.29315;LRBP=526.27;MQ=90.42;MQ0=0;MQ0Fraction=0.0000;MQM=39.433;MQRankSum=-7.011;NF;NR;NS=1062;PP;PV4=1,1,3.7e-09,1;RA=5322;RL=9;RPP=13.433;RR=21;RUN=1;ReadPosRankSum=0.679;SAB=0.43333;SAF=13;SAP=4.1684;SAR=17;SC=AAGAGCATCTTAGGCAGAGGC;SET_INTEGRATION;SET_WGVQSR;SRB=0.47294;SRF=2517;SRP=36.853;SRR=2805;TC;TR=2;TU=T;VQSLOD=8.3045;set=Intersection;sumGLbyD=68.22 20 56969289 . GTTTGT G 600.69 PASS AF=0.0056;AF1=0.007726;BaseQRankSum=2.907;CI95=0.004425,0.01327;DP=9643;DP4=1892,1749,6,3;Dels=0.00;FQ=117;FR;FS=16.601;HP=5;HPLen=3;HR=3;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0236;IndelType=DEL.NumRepetitions_3.EventLength_5.;MQ=92.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.134;NF;NR;PP;PV4=0.51,1,0.07,0.3;ReadPosRankSum=0.236;SC=TAAGGACGTTGTTTGTTTTGT;SET_INTEGRATION;SET_WGVQSR;TC;TR=10;TU=GTTT;VQSLOD=5.8458;set=Intersection;sumGLbyD=39.51 20 57187557 . AG A,AGG 1486.69 PASS AA=130;AB=0.55446;ABA=90;ABP=8.2132;ABR=112;AC=56,26;AF=0.0574,0.0266;AN=976;BL=3817;BR=5968;BVAR;BaseQRankSum=5.517;DEL;DP=14174;DP4=925,721,59,48;Dels=0.05;EL=52;EPP=14.302;ER=78;FR;FS=0.917;HETAR=44;HOMA=17;HOMR=864;HP=4;HPLen=4;HR=4;HRun=4;HU=G;INDEL;InbreedingCoeff=0.2856;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.21983;LRBP=1029.8;MQ=91.56;MQ0=0;MQ0Fraction=0.0000;MQM=63.631;MQRankSum=1.900;NF;NR;NS=925;PP;PV4=0.84,1,1,0.39;RA=2746;RL=44;RPP=32.476;RR=86;RUN=1;ReadPosRankSum=-0.639;SAB=0.44615;SAF=58;SAP=6.2842;SAR=72;SC=TCAGGCCCGCAGGGGTCAGGG;SET_INTEGRATION;SET_WGVQSR;SRB=0.5772;SRF=1585;SRP=145.17;SRR=1161;TC;TR=4;TU=G;VQSLOD=7.7167;set=Intersection;sumGLbyD=14.85 20 57282771 . T TG 506.43 PASS AA=34;AB=0.70312;ABA=19;ABP=25.946;ABR=45;AC=34;AF=0.0373;AN=912;BL=886;BR=1938;BVAR;BaseQRankSum=3.744;DP=4276;Dels=0.00;EL=18;EPP=3.2658;ER=16;FR;FS=0.639;HETAR=17;HOMA=9;HOMR=737;HP=9;HR=8;HRun=8;HU=G;INS;InbreedingCoeff=0.2149;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.37252;LRBP=853.99;MQ0=0;MQ0Fraction=0.0000;MQM=49.706;MQRankSum=-0.051;NF;NR;NS=763;PP;RA=1822;RL=9;RPP=19.36;RR=25;RUN=1;ReadPosRankSum=-2.111;SAB=0.55882;SAF=19;SAP=4.0322;SAR=15;SC=TCGGGGGGCGTGGGGGGGGTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.51098;SRF=931;SRP=4.9172;SRR=891;TC;TR=8;TU=G;VQSLOD=5.7772;set=Intersection;sumGLbyD=7.95 20 57419740 rs11481507 A AT 82613.57 PASS AA=3850;AB=0.41404;ABA=1786;ABP=198.63;ABR=1262;AC=919;AF=0.75328;AN=1220;BL=140665;BR=151383;BVAR;BaseQRankSum=-27.490;DB;DP=31794;DP4=588,585,1571,1721;Dels=0.00;EL=1924;EPP=3.0126;ER=1926;FQ=999;FR;FS=2.191;HETAR=482;HOMA=454;HOMR=135;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;INS;InbreedingCoeff=0.0861;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.036699;LRBP=857.15;MQ=123.92;MQ0=0;MQ0Fraction=0.0000;MQM=91.654;MQRankSum=3.016;NF;NR;NS=1071;PP;PV4=0.16,1,0.12,1;RA=1850;RL=1874;RPP=8.8784;RR=1976;RUN=1;ReadPosRankSum=-0.685;SAB=0.47636;SAF=1834;SAP=21.693;SAR=2016;SC=TACACTAGTGATTTAACCCTA;SET_INTEGRATION;SET_WGVQSR;SRB=0.49027;SRF=907;SRP=4.5315;SRR=943;TC;TR=3;TU=T;VQSLOD=9.2768;dbSNP=126;set=Intersection;sumGLbyD=22.78 20 57558194 . CT C,CTT,CTTT 6470.30 PASS ABR=451;AC=104,161,177;AF=0.08919,0.13808,0.15180;BVAR;BaseQRankSum=1.172;DP=7985;FR;FS=2.202;HOMA=19;HOMR=778;HP=22;HR=15;HU=T;HaplotypeScore=16.1921;INS;InbreedingCoeff=0.6440;IndelType=MULTIALLELIC_INDEL;MQ=69.24;MQ0=27;MQ0Fraction=0.0109;MQRankSum=-0.003;NF;NR;NS=943;PP;QD=2.22;RA=2531;RUN=1;ReadPosRankSum=-0.104;SB=-2096.85;SC=GCCTTTTTTTCTTTTTTTTTT;SET_WGVQSR;SRB=0.34848;SRF=882;SRP=507.73;SRR=1649;TC;TR=15;TU=T;VQSLOD=6.5151;set=Intersection 20 57693627 . AG A 1991.90 PASS AA=52;AB=0.49462;ABA=47;ABP=3.0336;ABR=46;AC=15;AF=0.01227;AN=1222;BL=1902;BR=1478;BVAR;BaseQRankSum=-6.121;DEL;DP=26459;DP4=2647,2873,16,20;Dels=0.01;EL=25;EPP=3.1773;ER=27;FR;FS=3.135;HETAR=15;HOMA=1;HOMR=1064;HP=2;HPLen=3;HR=3;HRun=2;HU=A;INDEL;InbreedingCoeff=0.0866;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.12544;LRBP=118.51;MQ=116.26;MQ0=0;MQ0Fraction=0.0000;MQM=114.65;MQRankSum=1.942;NF;NR;NS=1080;PP;PV4=0.74,6.9e-08,1,0.38;RA=6781;RL=33;RPP=11.195;RR=19;RUN=1;ReadPosRankSum=-1.795;SAB=0.5;SAF=26;SAP=3.0103;SAR=26;SC=ATTGGAGGAAAGGCTTTTTCA;SET_INTEGRATION;SET_WGVQSR;SRB=0.46247;SRF=3136;SRP=85.976;SRR=3645;TC;TR=3;TU=A;VQSLOD=8.6672;set=Intersection;sumGLbyD=13.55 20 57716287 . A AT 66.47 PASS AC=6;AF=0.00506;AN=1186;BaseQRankSum=1.369;DP=2744;FS=3.834;HRun=8;HaplotypeScore=11.2046;InbreedingCoeff=0.1196;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_T.;MQ=73.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-0.086;QD=2.14;ReadPosRankSum=-2.588;SB=-53.80;SET_INTEGRATION;SET_WGVQSR;VQSLOD=4.2080;set=VQSR 20 58121928 rs73625057 T TGG 6649.17 PASS AA=132;AB=0.57854;ABA=110;ABP=16.996;ABR=151;AC=57;AF=0.0617;AN=924;BL=4530;BR=4790;BVAR;BaseQRankSum=-13.456;DB;DP=30353;DP4=2107,2168,61,66;Dels=0.00;EL=67;EPP=3.0761;ER=65;FR;FS=0.708;HETAR=46;HOMA=8;HOMR=1023;HP=3;HPLen=2;HR=2;HRun=2;HU=G;INDEL;INS;InbreedingCoeff=0.1241;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=2;LRB=0.027897;LRBP=18.76;MQ=109.61;MQ0=1;MQ0Fraction=0.0004;MQM=79.833;MQRankSum=-0.699;NF;NR;NS=1077;PP;PV4=0.79,1,0.49,0.036;RA=5754;RL=61;RPP=4.6554;RR=71;RUN=1;ReadPosRankSum=-3.309;SAB=0.45455;SAF=60;SAP=5.3792;SAR=72;SC=GATTAGAATGTGGATATCTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.48836;SRF=2810;SRP=9.7866;SRR=2944;TC;TR=4;TU=GT;VQSLOD=8.5770;set=Intersection;sumGLbyD=27.19 20 58468826 . ACAAG A 999 PASS AF=0.0014;AF1=0.003429;BaseQRankSum=4.082;CI95=0.003106,0.006211;DP=8461;DP4=2500,1817,8,2;Dels=0.01;FQ=999;FR;FS=5.034;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0183;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ=120.69;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.141;NF;NR;PP;PV4=0.21,1,0.054,1;ReadPosRankSum=2.096;SC=ATCCTGAAACACAAGAAGAAA;SET_INTEGRATION;SET_WGVQSR;TC;TR=5;TU=AC;VQSLOD=7.4928;set=Intersection;sumGLbyD=29.17 20 58731262 . TC T 999 PASS AA=21;AB=0.48649;ABA=19;ABP=3.069;ABR=18;AC=7;AF=0.0101;AF1=0.01493;AN=694;BL=939;BR=848;BVAR;BaseQRankSum=4.205;CI95=0.01106,0.02212;DEL;DP=12598;DP4=1766,1428,11,15;Dels=0.01;EL=13;EPP=5.5954;ER=8;FQ=999;FR;FS=1.796;HETAR=8;HOMA=1;HOMR=1031;HP=7;HPLen=8;HR=8;HRun=2;HU=T;INDEL;InbreedingCoeff=-0.0030;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.050923;LRBP=13.073;MQ=124.57;MQ0=0;MQ0Fraction=0.0000;MQM=67.905;MQRankSum=1.103;NF;NR;NS=1040;PP;PV4=0.23,1,1,1;RA=4884;RL=10;RPP=3.1137;RR=11;RUN=1;ReadPosRankSum=-0.091;SAB=0.47619;SAF=10;SAP=3.1137;SAR=11;SC=TCATTTTTTTTCCTTGAAACT;SET_INTEGRATION;SET_WGVQSR;SRB=0.58006;SRF=2833;SRP=274.9;SRR=2051;TC;TR=8;TU=T;VQSLOD=10.8783;set=Intersection;sumGLbyD=15.11 20 59181229 rs11476579 CTT C,CT,CTTT,CTTTT 7787.17 PASS AC=19,195,104,91;AF=0.01599,0.16414,0.08754,0.07660;AF1=0.2124;AN=1188;BVAR;BaseQRankSum=6.347;CI95=0.146,0.2743;DB;DEL;DP=26140;DP4=932,880,352,375;Dels=0.13;FQ=85.6;FR;FS=11.914;HP=14;HR=14;HRun=14;HU=T;INDEL;INS;InbreedingCoeff=0.4183;IndelType=MULTIALLELIC_INDEL;MQ=86.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.469;NF;NR;PP;PV4=0.17,1,1,1;RUN=1;ReadPosRankSum=-1.055;SC=GGTGAGAAAGCTTTTTTTTTT;SET_WGVQSR;TC;TR=14;TU=T;VQSLOD=7.4340;dbSNP=120;set=Intersection;sumGLbyD=7.02 20 59213979 rs112141381 G GC 9068 PASS AA=131;AB=0.47115;ABA=110;ABP=4.5136;ABR=98;AF=0.0586;AN=700;BL=5395;BR=5816;BVAR;BaseQRankSum=15.453;DB;DP=23381;DP4=2191,2184,71,49;Dels=0.00;EL=66;EPP=3.0269;ER=65;FR;FS=7.907;HETAR=35;HOMA=5;HOMR=1019;HP=2;HPLen=3;HR=3;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0283;IndelType=INS.NOVEL_1.Novel_C.;LEN=1;LRB=0.037552;LRBP=37.34;MQ=72.13;MQ0=0;MQ0Fraction=0.0000;MQM=54.496;MQRankSum=0.897;NF;NR;NS=1059;PP;PV4=0.052,1,0.066,1;RA=4976;RL=59;RPP=5.8117;RR=72;RUN=1;ReadPosRankSum=-0.811;SAB=0.58015;SAF=76;SAP=10.32;SAR=55;SC=GATGGACTGGGACAGTGACTC;SET_INTEGRATION;SET_WGVQSR;SRB=0.49457;SRF=2461;SRP=4.2828;SRR=2515;TC;TR=3;TU=G;VQSLOD=9.3917;set=Intersection;sumGLbyD=28.58 20 59252945 . CT C,CTT 557.18 PASS AA=24;AB=0.84868;ABA=23;ABP=163.53;ABR=129;AC=21,29;AF=0.01759,0.02429;BL=1217;BR=1336;BVAR;BaseQRankSum=5.135;DP=9970;Dels=0.01;EL=13;EPP=3.3722;ER=11;FS=2.302;HETAR=21;HOMA=1;HOMR=1012;HRun=9;INS;InbreedingCoeff=0.1549;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.046612;LRBP=15.055;MQ0=0;MQ0Fraction=0.0000;MQM=67.208;MQRankSum=0.086;NS=1034;RA=4421;RL=11;RPP=3.3722;RR=13;RUN=1;ReadPosRankSum=-1.826;SAB=0.41667;SAF=10;SAP=4.4579;SAR=14;SET_WGVQSR;SRB=0.49649;SRF=2195;SRP=3.4823;SRR=2226;VQSLOD=2.8923;set=filterInVQSR-2of5;sumGLbyD=5.47 20 60016966 . CT C 42650 PASS AA=37;AB=0.97834;ABA=31;ABP=2847;ABR=1400;AC=15;AF=0.0163;AN=920;BL=2596;BR=778;BVAR;BaseQRankSum=-0.632;DEL;DP=10967;Dels=0.00;EL=14;EPP=7.7641;ER=23;FS=4.094;HETAR=421;HOMA=256;HOMR=385;HRun=1;InbreedingCoeff=-0.0051;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.53883;LRBP=2130.2;MQ0=0;MQ0Fraction=0.0000;MQM=120.3;MQRankSum=-0.911;NS=1072;RA=3413;RL=31;RPP=39.691;RR=6;RUN=1;ReadPosRankSum=-12.062;SAB=0.48649;SAF=18;SAP=3.069;SAR=19;SRB=0.47407;SRF=1618;SRP=22.943;SRR=1795;VQSLOD=3.3758;set=filterInVQSR-2of5;sumGLbyD=3.27 20 60188651 . AG A 17624.52 PASS AA=462;AB=0.76548;ABA=409;ABP=1070.7;ABR=1335;AC=403;AF=0.34444;AN=1170;BL=13877;BR=25909;BVAR;BaseQRankSum=6.180;DEL;DP=9900;Dels=0.08;EL=353;EPP=282.84;ER=109;FR;FS=2699.057;HETAR=346;HOMA=26;HOMR=633;HP=3;HR=4;HRun=1;HU=A;InbreedingCoeff=-0.2900;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.30242;LRBP=7904.3;MQ0Fraction=0.0004;MQM=56.119;MQRankSum=1.644;NF;NR;NS=1005;PP;RA=3521;RL=112;RPP=269.25;RR=350;RUN=1;ReadPosRankSum=2.490;SAB=0.0064935;SAF=3;SAP=980.34;SAR=459;SC=AGGCTTCAAAAGAAAAAAAAA;SRB=0.55978;SRF=1971;SRP=112.32;SRR=1550;TC;TR=4;TU=A;VQSLOD=-34.0667;set=filterInVQSR-2of5;sumGLbyD=7.81 20 60195570 . GTACATACATACA ATACATACATACA,G,GTACATACA 20140 PASS ABR=102;AC=105,2;AF=0.08794,0.00168;AN=1194;BVAR;BaseQRankSum=-28.899;DB;DEL;DP=14347;Dels=0.02;FR;FS=52.125;HOMA=1;HOMR=1006;HP=1;HPLen=1;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0695;IndelType=MIXED;MQ0Fraction=0.0007;MQRankSum=1.957;NF;NR;NS=1035;PP;RA=4759;RUN=1;ReadPosRankSum=-22.252;SAB=0.5;SAP=3.0103;SC=TGATAGATTCGTACATACATA;SET_INTEGRATION;SRB=0.47615;SRF=2266;SRP=26.522;SRR=2493;TC;TR=21;TU=ACAT;VQSLOD=2.7673;set=filterInVQSR-2of5;sumGLbyD=19.14 20 60670601 rs72127450 AT A,ATT 6401.59 PASS AC=177,79;AF=0.16239,0.07248;AF1=0.1602;AN=1090;BVAR;BaseQRankSum=8.618;CI95=0.1106,0.2058;DB;DEL;DP=17508;DP4=1285,1094,313,259;Dels=0.10;FQ=94.1;FR;FS=0.000;HP=12;HR=12;HRun=12;HU=T;INDEL;INS;InbreedingCoeff=0.1076;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=64.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.620;NF;NR;PP;PV4=0.78,1,0.012,1;RUN=1;ReadPosRankSum=-1.294;SC=AGCCAGGCACATTTTTTTTTT;SET_WGVQSR;TC;TR=12;TU=T;VQSLOD=6.1650;dbSNP=130;set=Intersection;sumGLbyD=5.80 20 60685780 . TC T 1123.58 PASS AC=79;AF=0.07655;AN=1032;BaseQRankSum=14.949;DP=2084;FS=23.521;HRun=1;HaplotypeScore=19.7117;InbreedingCoeff=0.1356;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=53.57;MQ0=61;MQ0Fraction=0.0293;MQRankSum=-7.958;QD=4.35;ReadPosRankSum=-13.757;SB=-791.28;VQSLOD=6.3549;set=VQSR 20 60744906 rs113528167 CG C 422.53 PASS AC=48;AF=0.0732;AN=656;BaseQRankSum=17.669;DB;DP=1189;FS=0.356;HRun=1;HaplotypeScore=15.1808;InbreedingCoeff=0.2111;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;MQ=82.83;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-10.455;QD=2.71;ReadPosRankSum=-16.887;SB=-326.46;VQSLOD=7.1707;set=VQSR 20 60848742 . CGT C,CGTGT 999 PASS AF=0.00980,0.01225;BaseQRankSum=5.597;DP=17065;DP4=1928,2188,17,13;Dels=0.01;FR;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.2094;IndelType=MULTIALLELIC_INDEL;MQ=115.78;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.281;NF;NR;PP;PV4=0.36,0.4,0.12,0.12;ReadPosRankSum=-1.465;SB=-157.35;SC=TAGACGCTTCCGTGTGTGTGT;SET_INTEGRATION;SET_WGVQSR;TC;TR=11;TU=GT;VQSLOD=1.7100;set=filterInVQSR-2of5;sumGLbyD=16.39 20 61023668 rs57452309 G GAGC 6896.67 PASS AC=115;AF=0.1445;AN=796;BaseQRankSum=12.146;DB;DP=1423;FS=5.070;HRun=0;HaplotypeScore=29.8897;InbreedingCoeff=0.0740;IndelType=INS.NOVEL_3.;MQ=77.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-9.005;QD=19.16;ReadPosRankSum=-17.440;SB=-3045.82;VQSLOD=4.5788;set=VQSR 20 61180519 . C CA,CT 1774.30 PASS ABR=135;AC=27,15;AF=0.02538,0.01410;BVAR;BaseQRankSum=-2.189;DP=8393;FR;FS=27.692;HOMA=2;HOMR=825;HP=6;HPLen=3;HR=3;HU=T;HaplotypeScore=19.5313;INS;InbreedingCoeff=0.0868;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=56.11;MQ0=172;MQ0Fraction=0.0667;MQRankSum=2.605;NF;NR;NS=854;PP;QD=1.99;RA=2868;RUN=1;ReadPosRankSum=-7.324;SB=-385.54;SC=TTCTTTCTTTCTTTCTTTCTT;SRB=0.32741;SRF=939;SRP=745.08;SRR=1929;TC;TR=69;TU=CTTT;VQSLOD=3.4398;set=filterInVQSR-2of5 20 61184281 . AC A 9798.10 PASS AA=24;AB=0.96507;ABA=16;ABP=863.43;ABR=442;AC=4;AF=0.00341;AN=1174;BL=349;BR=1039;BVAR;BaseQRankSum=2.048;DEL;DP=10073;Dels=0.00;EL=11;EPP=3.3722;ER=13;FS=2.097;HETAR=141;HOMA=69;HOMR=829;HRun=1;InbreedingCoeff=0.0697;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.49712;LRBP=747.85;MQ0=0;MQ0Fraction=0.0000;MQM=98.042;MQRankSum=1.881;NS=1042;RA=3625;RL=5;RPP=20.744;RR=19;RUN=1;ReadPosRankSum=-8.009;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SRB=0.52662;SRF=1909;SRP=25.323;SRR=1716;VQSLOD=1.8117;set=filterInVQSR-2of5;sumGLbyD=5.55 20 62074219 . C CTAT,CTGT 2328 PASS ABR=99;AC=20,6;AF=0.01754,0.00526;BVAR;BaseQRankSum=11.221;DP=9498;DS;FS=4.510;HOMA=15;HOMR=645;HaplotypeScore=82.8868;INS;InbreedingCoeff=0.0880;IndelType=MULTIALLELIC_INDEL;LEN=3;MQ=29.88;MQ0=1378;MQ0Fraction=0.2286;MQRankSum=-5.309;NS=689;QD=0.77;RA=1679;RUN=1;ReadPosRankSum=-3.510;SAR=1;SB=-93.21;SRB=0.70697;SRF=1187;SRP=627.71;SRR=492;VQSLOD=1.8325;set=filterInVQSR-2of5 20 62304449 . CA C,CAA 6680.17 PASS AC=141,69;AF=0.12567,0.06150;AF1=0.08178;AN=1122;BVAR;BaseQRankSum=9.754;CI95=0.05088,0.1128;DEL;DP=15867;DP4=1252,1289,232,208;Dels=0.10;FQ=52.6;FR;FS=6.576;HP=11;HR=11;HRun=11;HU=A;INDEL;INS;InbreedingCoeff=0.1950;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=60.48;MQ0Fraction=0.0004;MQRankSum=-0.049;NF;NR;PP;PV4=0.2,1,1,1;RUN=1;ReadPosRankSum=-2.137;SC=GATTCTGTGTCAAAAAAAAAA;SET_WGVQSR;TC;TR=11;TU=A;VQSLOD=7.4714;set=Intersection;sumGLbyD=8.36 20 62804895 rs57769591 CCTT C 1148 PASS AC=8;AF=0.0085;AF1=0.002839;AN=938;BaseQRankSum=4.952;CI95=0.002212,0.006637;DB;DP=8889;DP4=2574,1668,4,8;FQ=12.3;FS=2.289;HPLen=3;HRun=0;HaplotypeScore=29.4184;INDEL;InbreedingCoeff=-0.0270;IndelType=DEL.NumRepetitions_1.EventLength_3.;MQ0=876;MQ0Fraction=0.2674;MQRankSum=-0.641;PV4=0.074,1,1,1;QD=1.03;ReadPosRankSum=0.118;SB=-65.30;SET_INTEGRATION;SET_WGVQSR;VQSLOD=6.4881;dbSNP=126;set=Intersection 20 62907688 . AAT A 6629.57 PASS AC=164;AF=0.13735;AN=1194;BaseQRankSum=27.368;DP=2746;FS=5.985;HRun=0;HaplotypeScore=14.7748;InbreedingCoeff=0.1433;IndelType=DEL.NumRepetitions_2.EventLength_2.RepeatExpansion_AT.;MQ=96.65;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.318;QD=10.81;ReadPosRankSum=0.789;SB=-2662.16;SET_INTEGRATION;SET_WGVQSR;VQSLOD=6.1473;set=VQSR pysam-0.23.0/tests/tabix_data/vcf/24.vcf000066400000000000000000001520541475062545500177160ustar00rootroot00000000000000##fileformat=VCFv4.1 ##INFO= ##INFO= ##INFO= ##INFO= ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO 20 256726 . T A . . Sample=HG00097;GT=0/1;PCR_454_AR=739;PCR_454_RR=885 20 256726 . T A . . Sample=HG00099;GT=0/1;PCR_454_AR=723;PCR_454_RR=714 20 256726 . T A . . Sample=HG00106;GT=0/1;PCR_454_AR=1092;PCR_454_RR=1102 20 256726 . T A . . Sample=HG00112;GT=0/1;PCR_454_AR=947;PCR_454_RR=1005 20 256726 . T A . . Sample=HG00104;GT=1/1;PCR_454_AR=1970;PCR_454_RR=52 20 257977 . G C . . Sample=NA19438;GT=0/1;PCR_454_AR=1312;PCR_454_RR=1123 20 330407 . C G . . Sample=HG00134;GT=0/1;PCR_454_AR=1034;PCR_454_RR=1037 20 330407 . C G . . Sample=HG00148;GT=0/1;PCR_454_AR=840;PCR_454_RR=820 20 330407 . C G . . Sample=HG00151;GT=0/1;PCR_454_AR=952;PCR_454_RR=982 20 330407 . C G . . Sample=HG00358;GT=0/1;PCR_454_AR=880;PCR_454_RR=957 20 330407 . C G . . Sample=HG01277;GT=0/1;PCR_454_AR=914;PCR_454_RR=984 20 368826 . G A . . Sample=NA20346;GT=0/1;PCR_454_AR=632;PCR_454_RR=591 20 371957 . G A . . Sample=HG00150;GT=0/1;PCR_454_AR=403;PCR_454_RR=424 20 371957 . G A . . Sample=NA12287;GT=0/1;PCR_454_AR=401;PCR_454_RR=435 20 467031 . T A . . Sample=NA20510;GT=0/0;PCR_454_AR=5;PCR_454_RR=1763 20 741858 . G A . . Sample=NA18634;GT=0/1;PCR_454_AR=1273;PCR_454_RR=1301 20 947853 . C T . . Sample=HG00578;GT=0/0;PCR_454_AR=0;PCR_454_RR=197 20 947853 . C T . . Sample=NA18861;GT=0/1;PCR_454_AR=40;PCR_454_RR=39 20 947853 . C T . . Sample=NA18868;GT=0/1;PCR_454_AR=88;PCR_454_RR=80 20 947853 . C T . . Sample=NA18870;GT=0/1;PCR_454_AR=66;PCR_454_RR=99 20 947853 . C T . . Sample=NA18917;GT=0/1;PCR_454_AR=96;PCR_454_RR=111 20 947908 . C T . . Sample=NA11993;GT=0/1;PCR_454_AR=598;PCR_454_RR=2114 20 947908 . C T . . Sample=NA18501;GT=0/1;PCR_454_AR=392;PCR_454_RR=1687 20 947908 . C T . . Sample=NA18504;GT=0/1;PCR_454_AR=635;PCR_454_RR=2218 20 947908 . C T . . Sample=NA18505;GT=0/1;PCR_454_AR=1312;PCR_454_RR=1429 20 947908 . C T . . Sample=NA18507;GT=0/1;PCR_454_AR=598;PCR_454_RR=2127 20 948715 . T G . . Sample=NA06989;GT=0/0;PCR_454_AR=4;PCR_454_RR=1252 20 1144999 . C T . . Sample=NA18510;GT=0/1;PCR_454_AR=450;PCR_454_RR=447 20 1144999 . C T . . Sample=NA19172;GT=0/1;PCR_454_AR=541;PCR_454_RR=531 20 1285858 . A C . . Sample=NA19311;GT=0/1;PCR_454_AR=1210;PCR_454_RR=1315 20 1285932 . G A . . Sample=HG00097;GT=0/1;PCR_454_AR=868;PCR_454_RR=867 20 1285932 . G A . . Sample=HG00106;GT=0/1;PCR_454_AR=745;PCR_454_RR=680 20 1285932 . G A . . Sample=HG00126;GT=0/1;PCR_454_AR=780;PCR_454_RR=838 20 1285932 . G A . . Sample=HG00134;GT=0/1;PCR_454_AR=978;PCR_454_RR=944 20 1285932 . G A . . Sample=HG00128;GT=1/1;PCR_454_AR=1499;PCR_454_RR=14 20 1286090 . A G . . Sample=HG00235;GT=0/1;PCR_454_AR=1223;PCR_454_RR=1352 20 1286090 . A G . . Sample=HG00351;GT=0/1;PCR_454_AR=799;PCR_454_RR=823 20 1286090 . A G . . Sample=HG01125;GT=0/1;PCR_454_AR=1167;PCR_454_RR=1149 20 1286090 . A G . . Sample=NA19773;GT=0/1;PCR_454_AR=1070;PCR_454_RR=1130 20 1546804 . G A . . Sample=HG00141;GT=0/1;PCR_454_AR=1174;PCR_454_RR=1231 20 1546804 . G A . . Sample=HG00149;GT=0/1;PCR_454_AR=1029;PCR_454_RR=1050 20 1546804 . G A . . Sample=HG00151;GT=0/1;PCR_454_AR=1135;PCR_454_RR=1034 20 1546804 . G A . . Sample=HG00177;GT=0/1;PCR_454_AR=1063;PCR_454_RR=1118 20 1546804 . G A . . Sample=HG00179;GT=0/1;PCR_454_AR=1118;PCR_454_RR=954 20 1551579 . T G . . Sample=NA20515;GT=0/0;PCR_454_AR=5;PCR_454_RR=1812 20 1551579 . T G . . Sample=NA19466;GT=0/1;PCR_454_AR=1011;PCR_454_RR=1042 20 1559334 . C T . . Sample=NA18941;GT=0/0;PCR_454_AR=1;PCR_454_RR=1193 20 1615980 . G A . . Sample=NA19914;GT=0/1;PCR_454_AR=441;PCR_454_RR=492 20 1616047 . C G . . Sample=NA07048;GT=0/1;PCR_454_AR=508;PCR_454_RR=813 20 1629751 . T C . . Sample=HG00156;GT=0/1;PCR_454_AR=285;PCR_454_RR=282 20 1896011 . C T . . Sample=NA18639;GT=0/0;PCR_454_AR=0;PCR_454_RR=29 20 1896011 . C T . . Sample=NA19314;GT=0/0;PCR_454_AR=0;PCR_454_RR=47 20 2291684 . T C . . Sample=NA19036;GT=0/1;PCR_454_AR=873;PCR_454_RR=1025 20 2291684 . T C . . Sample=NA19347;GT=0/1;PCR_454_AR=1116;PCR_454_RR=1217 20 2375127 . G A . . Sample=NA18615;GT=0/1;PCR_454_AR=1016;PCR_454_RR=1016 20 2777844 . T C . . Sample=NA20819;GT=0/1;PCR_454_AR=908;PCR_454_RR=970 20 2844678 . G A . . Sample=HG00360;GT=0/1;PCR_454_AR=1081;PCR_454_RR=1071 20 2944927 . A T . . Sample=NA12347;GT=0/1;PCR_454_AR=704;PCR_454_RR=752 20 2969014 . C G . . Sample=HG00151;GT=0/1;PCR_454_AR=684;PCR_454_RR=809 20 2969014 . C G . . Sample=NA18511;GT=0/1;PCR_454_AR=666;PCR_454_RR=704 20 2969014 . C G . . Sample=NA18523;GT=0/1;PCR_454_AR=767;PCR_454_RR=802 20 2969014 . C G . . Sample=NA18549;GT=0/1;PCR_454_AR=772;PCR_454_RR=838 20 2969014 . C G . . Sample=NA18858;GT=1/1;PCR_454_AR=1313;PCR_454_RR=8 20 3026344 . A C . . Sample=NA18640;GT=0/1;PCR_454_AR=1652;PCR_454_RR=1336 20 3128885 . G A . . Sample=NA19473;GT=0/1;PCR_454_AR=620;PCR_454_RR=669 20 3128950 . G A . . Sample=NA18624;GT=0/1;PCR_454_AR=570;PCR_454_RR=517 20 3128950 . G A . . Sample=NA18953;GT=0/1;PCR_454_AR=685;PCR_454_RR=700 20 3128950 . G A . . Sample=NA18998;GT=0/1;PCR_454_AR=606;PCR_454_RR=638 20 3128950 . G A . . Sample=NA19076;GT=0/1;PCR_454_AR=663;PCR_454_RR=643 20 3128950 . G A . . Sample=NA19088;GT=0/1;PCR_454_AR=492;PCR_454_RR=472 20 3171356 . T C . . Sample=NA12003;GT=0/0;PCR_454_AR=6;PCR_454_RR=1919 20 3171356 . T C . . Sample=NA12872;GT=0/0;PCR_454_AR=6;PCR_454_RR=2324 20 3193990 . G T . . Sample=NA12815;GT=0/0;PCR_454_AR=0;PCR_454_RR=1570 20 3193990 . G T . . Sample=NA18505;GT=0/0;PCR_454_AR=0;PCR_454_RR=1586 20 3204083 . G A . . Sample=HG00104;GT=0/1;PCR_454_AR=1059;PCR_454_RR=982 20 3204083 . G A . . Sample=HG00118;GT=0/1;PCR_454_AR=1190;PCR_454_RR=1178 20 3204083 . G A . . Sample=HG00122;GT=0/1;PCR_454_AR=1156;PCR_454_RR=1277 20 3204083 . G A . . Sample=HG00099;GT=1/1;PCR_454_AR=2171;PCR_454_RR=12 20 3204083 . G A . . Sample=HG00106;GT=1/1;PCR_454_AR=2027;PCR_454_RR=19 20 3214580 . C T . . Sample=HG00097;GT=0/1;PCR_454_AR=852;PCR_454_RR=784 20 3214580 . C T . . Sample=HG00099;GT=0/1;PCR_454_AR=628;PCR_454_RR=682 20 3214580 . C T . . Sample=HG00129;GT=0/1;PCR_454_AR=869;PCR_454_RR=844 20 3214580 . C T . . Sample=HG00130;GT=0/1;PCR_454_AR=651;PCR_454_RR=767 20 3214580 . C T . . Sample=HG00128;GT=1/1;PCR_454_AR=1378;PCR_454_RR=3 20 3214802 . T C . . Sample=NA18526;GT=0/1;PCR_454_AR=969;PCR_454_RR=1018 20 3235915 . T C . . Sample=HG00560;GT=0/1;PCR_454_AR=795;PCR_454_RR=798 20 3235915 . T C . . Sample=HG00566;GT=0/1;PCR_454_AR=688;PCR_454_RR=650 20 3235915 . T C . . Sample=HG00596;GT=0/1;PCR_454_AR=863;PCR_454_RR=935 20 3235915 . T C . . Sample=HG01124;GT=0/1;PCR_454_AR=802;PCR_454_RR=836 20 3235915 . T C . . Sample=NA18487;GT=0/1;PCR_454_AR=942;PCR_454_RR=968 20 3274851 . C T . . Sample=NA19704;GT=0/1;PCR_454_AR=486;PCR_454_RR=479 20 3274851 . C T . . Sample=NA20334;GT=0/1;PCR_454_AR=512;PCR_454_RR=512 20 3274851 . C T . . Sample=NA20336;GT=0/1;PCR_454_AR=510;PCR_454_RR=440 20 3324372 . G C . . Sample=NA19003;GT=0/1;PCR_454_AR=1902;PCR_454_RR=1898 20 3362102 . T G . . Sample=NA06994;GT=0/0;PCR_454_AR=0;PCR_454_RR=526 20 3362102 . T G . . Sample=NA12249;GT=0/0;PCR_454_AR=0;PCR_454_RR=465 20 3515923 . G A . . Sample=HG00122;GT=0/1;PCR_454_AR=237;PCR_454_RR=261 20 3515923 . G A . . Sample=HG00126;GT=0/1;PCR_454_AR=299;PCR_454_RR=293 20 3515923 . G A . . Sample=HG00130;GT=0/1;PCR_454_AR=307;PCR_454_RR=279 20 3515923 . G A . . Sample=HG00128;GT=1/1;PCR_454_AR=633;PCR_454_RR=4 20 3515923 . G A . . Sample=HG00129;GT=1/1;PCR_454_AR=580;PCR_454_RR=2 20 3641233 . G T . . Sample=NA20773;GT=0/0;PCR_454_AR=3;PCR_454_RR=1477 20 3650204 . G A . . Sample=HG00118;GT=0/1;PCR_454_AR=737;PCR_454_RR=771 20 3650204 . G A . . Sample=HG00126;GT=0/1;PCR_454_AR=518;PCR_454_RR=552 20 3650204 . G A . . Sample=HG00141;GT=0/1;PCR_454_AR=643;PCR_454_RR=668 20 3650204 . G A . . Sample=HG00143;GT=0/1;PCR_454_AR=549;PCR_454_RR=613 20 3650204 . G A . . Sample=HG00148;GT=0/1;PCR_454_AR=708;PCR_454_RR=830 20 3652397 . G A . . Sample=NA18635;GT=0/1;PCR_454_AR=1604;PCR_454_RR=1658 20 3672827 . A T . . Sample=HG00130;GT=0/0;PCR_454_AR=0;PCR_454_RR=941 20 3672827 . A T . . Sample=HG00349;GT=0/0;PCR_454_AR=2;PCR_454_RR=943 20 3675119 . G T . . Sample=NA20544;GT=0/1;PCR_454_AR=577;PCR_454_RR=657 20 3687329 . T C . . Sample=NA18532;GT=0/1;PCR_454_AR=702;PCR_454_RR=746 20 3842125 . C G . . Sample=NA12155;GT=0/1;PCR_454_AR=1193;PCR_454_RR=1178 20 4680289 . G A . . Sample=NA18856;GT=0/1;PCR_454_AR=1335;PCR_454_RR=1278 20 4680289 . G A . . Sample=NA19130;GT=0/1;PCR_454_AR=1273;PCR_454_RR=1286 20 4680289 . G A . . Sample=NA19213;GT=0/1;PCR_454_AR=1305;PCR_454_RR=1241 20 4680289 . G A . . Sample=NA19311;GT=0/1;PCR_454_AR=1332;PCR_454_RR=1400 20 4680289 . G A . . Sample=NA19332;GT=0/1;PCR_454_AR=1272;PCR_454_RR=1275 20 4848511 . G A . . Sample=NA19440;GT=0/0;PCR_454_AR=8;PCR_454_RR=2951 20 4848511 . G A . . Sample=NA19448;GT=0/1;PCR_454_AR=1278;PCR_454_RR=1434 20 4848511 . G A . . Sample=NA19461;GT=0/1;PCR_454_AR=1412;PCR_454_RR=1478 20 5099300 . A G . . Sample=NA19138;GT=0/1;PCR_454_AR=511;PCR_454_RR=496 20 5903387 . A C . . Sample=HG00566;GT=0/1;PCR_454_AR=1400;PCR_454_RR=1384 20 5903387 . A C . . Sample=HG01124;GT=0/1;PCR_454_AR=856;PCR_454_RR=1007 20 5903387 . A C . . Sample=HG01125;GT=0/1;PCR_454_AR=891;PCR_454_RR=816 20 5903387 . A C . . Sample=HG01149;GT=0/1;PCR_454_AR=1011;PCR_454_RR=959 20 5903387 . A C . . Sample=HG01278;GT=0/1;PCR_454_AR=1077;PCR_454_RR=1049 20 5923222 . C T . . Sample=HG00592;GT=0/1;PCR_454_AR=968;PCR_454_RR=950 20 5923222 . C T . . Sample=NA18567;GT=0/1;PCR_454_AR=678;PCR_454_RR=728 20 5923222 . C T . . Sample=NA18602;GT=0/1;PCR_454_AR=926;PCR_454_RR=988 20 5923222 . C T . . Sample=NA18624;GT=0/1;PCR_454_AR=991;PCR_454_RR=963 20 5923222 . C T . . Sample=NA18632;GT=0/1;PCR_454_AR=892;PCR_454_RR=906 20 5943955 . G C . . Sample=HG00565;GT=0/1;PCR_454_AR=259;PCR_454_RR=227 20 5943955 . G C . . Sample=HG00566;GT=0/1;PCR_454_AR=245;PCR_454_RR=235 20 5943955 . G C . . Sample=HG00577;GT=0/1;PCR_454_AR=264;PCR_454_RR=305 20 5943955 . G C . . Sample=HG00578;GT=0/1;PCR_454_AR=210;PCR_454_RR=261 20 5943955 . G C . . Sample=HG00593;GT=0/1;PCR_454_AR=261;PCR_454_RR=238 20 6015109 . G A . . Sample=NA20796;GT=0/1;PCR_454_AR=440;PCR_454_RR=500 20 6060150 . C T . . Sample=NA18961;GT=0/1;PCR_454_AR=384;PCR_454_RR=464 20 7967973 . G A . . Sample=NA19371;GT=0/1;PCR_454_AR=281;PCR_454_RR=506 20 7967973 . G A . . Sample=NA19390;GT=0/1;PCR_454_AR=410;PCR_454_RR=538 20 8665657 . G A . . Sample=NA19740;GT=0/1;PCR_454_AR=724;PCR_454_RR=703 20 9453955 . C A . . Sample=NA20314;GT=0/1;PCR_454_AR=1048;PCR_454_RR=1147 20 9520132 . G A . . Sample=HG00143;GT=0/1;PCR_454_AR=472;PCR_454_RR=583 20 9520132 . G A . . Sample=HG01624;GT=0/1;PCR_454_AR=589;PCR_454_RR=589 20 9520132 . G A . . Sample=NA12046;GT=0/1;PCR_454_AR=688;PCR_454_RR=708 20 9520132 . G A . . Sample=NA18517;GT=0/1;PCR_454_AR=566;PCR_454_RR=585 20 9520132 . G A . . Sample=NA18858;GT=0/1;PCR_454_AR=550;PCR_454_RR=561 20 9543621 . C T . . Sample=HG00097;GT=0/1;PCR_454_AR=499;PCR_454_RR=480 20 9543621 . C T . . Sample=HG00104;GT=0/1;PCR_454_AR=524;PCR_454_RR=480 20 9543621 . C T . . Sample=HG00112;GT=0/1;PCR_454_AR=467;PCR_454_RR=406 20 9543621 . C T . . Sample=HG00099;GT=1/1;PCR_454_AR=1321;PCR_454_RR=9 20 9543621 . C T . . Sample=HG00106;GT=1/1;PCR_454_AR=802;PCR_454_RR=6 20 9547022 . G A . . Sample=NA18924;GT=0/1;PCR_454_AR=853;PCR_454_RR=944 20 9560813 . T C . . Sample=NA12761;GT=0/1;PCR_454_AR=692;PCR_454_RR=734 20 10030206 . C T . . Sample=NA19175;GT=0/1;PCR_454_AR=784;PCR_454_RR=759 20 10030206 . C T . . Sample=NA19380;GT=0/1;PCR_454_AR=781;PCR_454_RR=739 20 10030206 . C T . . Sample=NA19446;GT=0/1;PCR_454_AR=533;PCR_454_RR=540 20 13098183 . A C . . Sample=NA19453;GT=0/1;PCR_454_AR=857;PCR_454_RR=1146 20 16253907 . C A . . Sample=NA19087;GT=0/1;PCR_454_AR=868;PCR_454_RR=854 20 16254032 . G A . . Sample=NA19651;GT=0/1;PCR_454_AR=299;PCR_454_RR=263 20 16485159 . T G . . Sample=NA18625;GT=0/1;PCR_454_AR=160;PCR_454_RR=1004 20 17474781 . G A . . Sample=NA18870;GT=0/1;PCR_454_AR=496;PCR_454_RR=536 20 17585255 . C G . . Sample=NA18528;GT=0/1;PCR_454_AR=370;PCR_454_RR=390 20 17923814 . C T . . Sample=HG00104;GT=0/0;PCR_454_AR=1;PCR_454_RR=1854 20 17923814 . C T . . Sample=HG00126;GT=0/0;PCR_454_AR=1;PCR_454_RR=1724 20 17928182 . T G . . Sample=NA18522;GT=0/1;PCR_454_AR=222;PCR_454_RR=1564 20 17931030 . C G . . Sample=NA20508;GT=0/1;PCR_454_AR=495;PCR_454_RR=446 20 17933265 . G A . . Sample=NA19137;GT=0/1;PCR_454_AR=300;PCR_454_RR=315 20 17968811 . C G . . Sample=NA19222;GT=0/1;PCR_454_AR=150;PCR_454_RR=189 20 18123396 . A G . . Sample=NA20507;GT=0/0;PCR_454_AR=5;PCR_454_RR=2239 20 18125941 . T C . . Sample=NA12006;GT=0/0;PCR_454_AR=2;PCR_454_RR=2354 20 18125941 . T C . . Sample=NA12762;GT=0/0;PCR_454_AR=4;PCR_454_RR=1116 20 18374912 . T A . . Sample=NA19189;GT=0/1;PCR_454_AR=896;PCR_454_RR=888 20 18440904 . G C . . Sample=NA19058;GT=0/1;PCR_454_AR=685;PCR_454_RR=881 20 19698200 . C T . . Sample=NA18574;GT=0/1;PCR_454_AR=1012;PCR_454_RR=1086 20 20020489 . T C . . Sample=NA19000;GT=0/1;PCR_454_AR=459;PCR_454_RR=436 20 20028425 . C T . . Sample=NA20787;GT=0/1;PCR_454_AR=687;PCR_454_RR=739 20 20033171 . G A . . Sample=NA19468;GT=0/0;PCR_454_AR=109;PCR_454_RR=1866 20 20051634 . A G . . Sample=NA19711;GT=0/1;PCR_454_AR=659;PCR_454_RR=2324 20 20051634 . A G . . Sample=NA20126;GT=0/1;PCR_454_AR=687;PCR_454_RR=2379 20 20177371 . T C . . Sample=NA19713;GT=0/1;PCR_454_AR=882;PCR_454_RR=785 20 21346240 . C T . . Sample=HG01125;GT=0/1;PCR_454_AR=707;PCR_454_RR=711 20 21346240 . C T . . Sample=NA18489;GT=0/1;PCR_454_AR=670;PCR_454_RR=648 20 21346240 . C T . . Sample=NA18498;GT=0/1;PCR_454_AR=706;PCR_454_RR=667 20 21346240 . C T . . Sample=NA18502;GT=0/1;PCR_454_AR=698;PCR_454_RR=678 20 21346240 . C T . . Sample=NA18505;GT=1/1;PCR_454_AR=1096;PCR_454_RR=2 20 21494183 . C T . . Sample=HG00128;GT=0/1;PCR_454_AR=556;PCR_454_RR=605 20 21494183 . C T . . Sample=HG00151;GT=0/1;PCR_454_AR=465;PCR_454_RR=425 20 21494183 . C T . . Sample=HG00234;GT=0/1;PCR_454_AR=583;PCR_454_RR=487 20 21494183 . C T . . Sample=HG00355;GT=0/1;PCR_454_AR=608;PCR_454_RR=521 20 21494183 . C T . . Sample=HG00362;GT=0/1;PCR_454_AR=518;PCR_454_RR=577 20 21687304 . C T . . Sample=NA19657;GT=0/1;PCR_454_AR=804;PCR_454_RR=862 20 23028428 . C T . . Sample=NA18970;GT=0/1;PCR_454_AR=360;PCR_454_RR=418 20 23028637 . C G . . Sample=NA18517;GT=0/1;PCR_454_AR=358;PCR_454_RR=374 20 23028637 . C G . . Sample=NA19118;GT=0/1;PCR_454_AR=502;PCR_454_RR=432 20 23420987 . G T . . Sample=NA19076;GT=0/0;PCR_454_AR=20;PCR_454_RR=1732 20 23420993 . C G . . Sample=NA19076;GT=0/0;PCR_454_AR=40;PCR_454_RR=3495 20 23424637 . C T . . Sample=HG00126;GT=0/1;PCR_454_AR=766;PCR_454_RR=721 20 23424637 . C T . . Sample=HG00150;GT=0/1;PCR_454_AR=444;PCR_454_RR=435 20 23424637 . C T . . Sample=HG00247;GT=0/1;PCR_454_AR=510;PCR_454_RR=486 20 23424637 . C T . . Sample=HG00565;GT=0/1;PCR_454_AR=684;PCR_454_RR=609 20 23424637 . C T . . Sample=HG00593;GT=0/1;PCR_454_AR=640;PCR_454_RR=676 20 23545657 . A C . . Sample=NA18924;GT=0/1;PCR_454_AR=767;PCR_454_RR=780 20 23548918 . T C . . Sample=NA18501;GT=0/1;PCR_454_AR=1397;PCR_454_RR=1168 20 23548918 . T C . . Sample=NA18502;GT=0/1;PCR_454_AR=1373;PCR_454_RR=1383 20 23548918 . T C . . Sample=NA18856;GT=0/1;PCR_454_AR=1376;PCR_454_RR=1446 20 23548918 . T C . . Sample=NA18907;GT=0/1;PCR_454_AR=1522;PCR_454_RR=1533 20 23548918 . T C . . Sample=NA19036;GT=0/1;PCR_454_AR=1549;PCR_454_RR=1624 20 23667793 . G T . . Sample=NA11994;GT=0/0;PCR_454_AR=135;PCR_454_RR=1637 20 23667793 . G T . . Sample=NA12400;GT=0/1;PCR_454_AR=651;PCR_454_RR=619 20 23667793 . G T . . Sample=NA18527;GT=0/1;PCR_454_AR=816;PCR_454_RR=732 20 23667793 . G T . . Sample=NA18566;GT=0/1;PCR_454_AR=928;PCR_454_RR=2446 20 23667793 . G T . . Sample=NA19064;GT=0/1;PCR_454_AR=892;PCR_454_RR=2346 20 23667834 . A C . . Sample=NA18510;GT=0/0;PCR_454_AR=27;PCR_454_RR=622 20 23667834 . A C . . Sample=NA18858;GT=0/0;PCR_454_AR=32;PCR_454_RR=615 20 23731469 . G T . . Sample=NA20544;GT=0/1;PCR_454_AR=292;PCR_454_RR=376 20 23804690 . A C . . Sample=NA19749;GT=0/1;PCR_454_AR=1141;PCR_454_RR=1145 20 23807156 . G C . . Sample=HG00129;GT=0/0;PCR_454_AR=0;PCR_454_RR=1447 20 23807156 . G C . . Sample=HG00130;GT=0/0;PCR_454_AR=0;PCR_454_RR=1603 20 23860201 . C T . . Sample=NA18553;GT=0/1;PCR_454_AR=722;PCR_454_RR=657 20 23965921 . G A . . Sample=NA18549;GT=0/0;PCR_454_AR=21;PCR_454_RR=582 20 23965921 . G A . . Sample=NA19000;GT=0/0;PCR_454_AR=19;PCR_454_RR=337 20 24523782 . G A . . Sample=NA19921;GT=0/1;PCR_454_AR=933;PCR_454_RR=1005 20 24523986 . C A . . Sample=HG00104;GT=0/1;PCR_454_AR=1056;PCR_454_RR=1346 20 24954343 . G A . . Sample=NA19146;GT=0/1;PCR_454_AR=1208;PCR_454_RR=1132 20 25058490 . T G . . Sample=NA11830;GT=0/0;PCR_454_AR=5;PCR_454_RR=1757 20 25187224 . A G . . Sample=NA19137;GT=0/1;PCR_454_AR=69;PCR_454_RR=566 20 25203611 . T C . . Sample=NA12006;GT=0/1;PCR_454_AR=1326;PCR_454_RR=1209 20 25252066 . A G . . Sample=NA18637;GT=0/1;PCR_454_AR=1208;PCR_454_RR=1230 20 25262768 . G A . . Sample=HG00099;GT=0/1;PCR_454_AR=920;PCR_454_RR=727 20 25262768 . G A . . Sample=HG00106;GT=0/1;PCR_454_AR=733;PCR_454_RR=613 20 25262768 . G A . . Sample=HG00112;GT=0/1;PCR_454_AR=756;PCR_454_RR=723 20 25262768 . G A . . Sample=HG00130;GT=0/1;PCR_454_AR=854;PCR_454_RR=827 20 25262768 . G A . . Sample=HG00152;GT=0/1;PCR_454_AR=798;PCR_454_RR=764 20 25277132 . C T . . Sample=NA18861;GT=0/1;PCR_454_AR=415;PCR_454_RR=446 20 25434162 . C T . . Sample=NA19346;GT=0/1;PCR_454_AR=566;PCR_454_RR=613 20 25434162 . C T . . Sample=NA19395;GT=0/1;PCR_454_AR=504;PCR_454_RR=531 20 25439088 . C T . . Sample=NA19095;GT=0/0;PCR_454_AR=1;PCR_454_RR=1220 20 25439088 . C T . . Sample=NA19923;GT=0/1;PCR_454_AR=575;PCR_454_RR=834 20 25457145 . G A . . Sample=NA12842;GT=0/1;PCR_454_AR=333;PCR_454_RR=438 20 25457559 . G A . . Sample=NA19159;GT=0/1;PCR_454_AR=1225;PCR_454_RR=1285 20 25457665 . C T . . Sample=NA20341;GT=0/1;PCR_454_AR=627;PCR_454_RR=1348 20 25459659 . T C . . Sample=NA18647;GT=0/0;PCR_454_AR=5;PCR_454_RR=2809 20 25459659 . T C . . Sample=NA18748;GT=0/0;PCR_454_AR=5;PCR_454_RR=2184 20 25459659 . T C . . Sample=HG01274;GT=0/1;PCR_454_AR=1246;PCR_454_RR=1375 20 25459659 . T C . . Sample=NA12275;GT=0/1;PCR_454_AR=1183;PCR_454_RR=1148 20 25459659 . T C . . Sample=NA12718;GT=0/1;PCR_454_AR=1017;PCR_454_RR=1225 20 25478961 . G A . . Sample=HG00104;GT=0/0;PCR_454_AR=1;PCR_454_RR=1933 20 25478961 . G A . . Sample=HG00234;GT=0/0;PCR_454_AR=0;PCR_454_RR=1964 20 25478961 . G A . . Sample=HG00364;GT=0/0;PCR_454_AR=2;PCR_454_RR=1909 20 25478961 . G A . . Sample=HG00593;GT=0/0;PCR_454_AR=2;PCR_454_RR=2173 20 25478961 . G A . . Sample=HG01271;GT=0/0;PCR_454_AR=0;PCR_454_RR=2082 20 30407977 . A G . . Sample=NA12287;GT=0/1;PCR_454_AR=1313;PCR_454_RR=1488 20 30432438 . C T . . Sample=NA19352;GT=0/1;PCR_454_AR=1043;PCR_454_RR=964 20 30432438 . C T . . Sample=NA19654;GT=0/1;PCR_454_AR=937;PCR_454_RR=1465 20 30432570 . T C . . Sample=NA18510;GT=0/1;PCR_454_AR=1224;PCR_454_RR=1413 20 30432570 . T C . . Sample=NA18858;GT=0/1;PCR_454_AR=1050;PCR_454_RR=1052 20 30432570 . T C . . Sample=NA18868;GT=0/1;PCR_454_AR=1087;PCR_454_RR=966 20 30432570 . T C . . Sample=NA18871;GT=0/1;PCR_454_AR=1178;PCR_454_RR=1344 20 30432570 . T C . . Sample=NA18522;GT=1/1;PCR_454_AR=1873;PCR_454_RR=7 20 30602754 . C T . . Sample=NA19749;GT=0/1;PCR_454_AR=63;PCR_454_RR=409 20 30729618 . G A . . Sample=NA11994;GT=0/0;PCR_454_AR=0;PCR_454_RR=1866 20 30729618 . G A . . Sample=NA07037;GT=0/1;PCR_454_AR=1373;PCR_454_RR=1435 20 30729618 . G A . . Sample=NA12058;GT=0/1;PCR_454_AR=963;PCR_454_RR=990 20 30729618 . G A . . Sample=NA12144;GT=0/1;PCR_454_AR=1419;PCR_454_RR=1136 20 30729618 . G A . . Sample=NA12282;GT=0/1;PCR_454_AR=1353;PCR_454_RR=1148 20 30789767 . G A . . Sample=HG00350;GT=0/0;PCR_454_AR=36;PCR_454_RR=553 20 30897726 . G A . . Sample=NA20507;GT=0/0;PCR_454_AR=239;PCR_454_RR=2404 20 30918043 . C T . . Sample=NA19707;GT=0/1;PCR_454_AR=1147;PCR_454_RR=1123 20 30918043 . C T . . Sample=NA20775;GT=0/1;PCR_454_AR=1234;PCR_454_RR=1140 20 31021429 . G C . . Sample=NA18870;GT=0/1;PCR_454_AR=747;PCR_454_RR=929 20 31021429 . G C . . Sample=NA19319;GT=0/1;PCR_454_AR=585;PCR_454_RR=657 20 31021429 . G C . . Sample=NA19445;GT=0/1;PCR_454_AR=531;PCR_454_RR=553 20 31021429 . G C . . Sample=NA20127;GT=0/1;PCR_454_AR=661;PCR_454_RR=679 20 31021429 . G C . . Sample=NA20317;GT=0/1;PCR_454_AR=874;PCR_454_RR=917 20 31022764 . C T . . Sample=NA18498;GT=0/1;PCR_454_AR=1455;PCR_454_RR=1259 20 31022764 . C T . . Sample=NA18507;GT=0/1;PCR_454_AR=1020;PCR_454_RR=972 20 31022764 . C T . . Sample=NA18511;GT=0/1;PCR_454_AR=1339;PCR_454_RR=1297 20 31022764 . C T . . Sample=NA18856;GT=0/1;PCR_454_AR=1582;PCR_454_RR=1572 20 31022764 . C T . . Sample=NA18870;GT=0/1;PCR_454_AR=1642;PCR_454_RR=1613 20 31024033 . G A . . Sample=HG01356;GT=0/1;PCR_454_AR=1045;PCR_454_RR=1002 20 31024033 . G A . . Sample=NA18537;GT=0/1;PCR_454_AR=794;PCR_454_RR=788 20 31024033 . G A . . Sample=NA18557;GT=0/1;PCR_454_AR=830;PCR_454_RR=795 20 31024033 . G A . . Sample=NA18558;GT=0/1;PCR_454_AR=833;PCR_454_RR=878 20 31024033 . G A . . Sample=NA18637;GT=1/1;PCR_454_AR=1528;PCR_454_RR=6 20 31040782 . G A . . Sample=HG00097;GT=0/1;PCR_454_AR=978;PCR_454_RR=1231 20 31040782 . G A . . Sample=HG00179;GT=0/1;PCR_454_AR=1054;PCR_454_RR=993 20 31040782 . G A . . Sample=HG01620;GT=0/1;PCR_454_AR=1091;PCR_454_RR=1111 20 31040782 . G A . . Sample=NA12273;GT=0/1;PCR_454_AR=1073;PCR_454_RR=1182 20 31040782 . G A . . Sample=NA12341;GT=0/1;PCR_454_AR=1102;PCR_454_RR=1318 20 31375167 . G A . . Sample=NA18486;GT=0/1;PCR_454_AR=563;PCR_454_RR=523 20 31375167 . G A . . Sample=NA19113;GT=0/1;PCR_454_AR=628;PCR_454_RR=620 20 31388076 . C T . . Sample=NA18504;GT=0/1;PCR_454_AR=809;PCR_454_RR=773 20 31388076 . C T . . Sample=NA18519;GT=0/1;PCR_454_AR=683;PCR_454_RR=752 20 31388076 . C T . . Sample=NA18856;GT=0/1;PCR_454_AR=1012;PCR_454_RR=1073 20 31388076 . C T . . Sample=NA18917;GT=0/1;PCR_454_AR=888;PCR_454_RR=931 20 31388076 . C T . . Sample=NA18522;GT=1/1;PCR_454_AR=1422;PCR_454_RR=2 20 31424592 . C T . . Sample=NA19146;GT=0/1;PCR_454_AR=237;PCR_454_RR=257 20 31434427 . A G . . Sample=NA11995;GT=0/1;PCR_454_AR=325;PCR_454_RR=325 20 31604884 . A G . . Sample=NA12748;GT=0/1;PCR_454_AR=1098;PCR_454_RR=1153 20 31606483 . G C . . Sample=NA18740;GT=0/1;PCR_454_AR=595;PCR_454_RR=964 20 31606907 . G A . . Sample=NA19753;GT=0/0;PCR_454_AR=0;PCR_454_RR=1627 20 31606907 . G A . . Sample=NA19747;GT=0/1;PCR_454_AR=952;PCR_454_RR=884 20 31622899 . A G . . Sample=NA19038;GT=0/1;PCR_454_AR=196;PCR_454_RR=111 20 31626754 . G A . . Sample=NA18579;GT=0/1;PCR_454_AR=941;PCR_454_RR=902 20 31643241 . A C . . Sample=NA18622;GT=0/1;PCR_454_AR=832;PCR_454_RR=877 20 31659074 . G A . . Sample=NA19449;GT=0/1;PCR_454_AR=915;PCR_454_RR=863 20 31672711 . A G . . Sample=NA20754;GT=0/1;PCR_454_AR=762;PCR_454_RR=820 20 31680333 . C T . . Sample=HG00156;GT=0/1;PCR_454_AR=446;PCR_454_RR=438 20 31680333 . C T . . Sample=HG00235;GT=0/1;PCR_454_AR=525;PCR_454_RR=435 20 31680333 . C T . . Sample=HG01125;GT=0/1;PCR_454_AR=433;PCR_454_RR=415 20 31680333 . C T . . Sample=NA12043;GT=0/1;PCR_454_AR=559;PCR_454_RR=477 20 31680333 . C T . . Sample=NA12046;GT=0/1;PCR_454_AR=364;PCR_454_RR=330 20 31695565 . C T . . Sample=NA19054;GT=0/1;PCR_454_AR=988;PCR_454_RR=944 20 31889182 . T C . . Sample=HG01277;GT=0/1;PCR_454_AR=594;PCR_454_RR=639 20 31889182 . T C . . Sample=HG01278;GT=0/1;PCR_454_AR=533;PCR_454_RR=540 20 31889182 . T C . . Sample=HG01623;GT=0/1;PCR_454_AR=703;PCR_454_RR=668 20 31889182 . T C . . Sample=NA18487;GT=0/1;PCR_454_AR=644;PCR_454_RR=647 20 31889182 . T C . . Sample=NA18486;GT=1/1;PCR_454_AR=1419;PCR_454_RR=15 20 31890796 . G A . . Sample=NA18595;GT=0/1;PCR_454_AR=36;PCR_454_RR=49 20 31967485 . T C . . Sample=NA18757;GT=0/0;PCR_454_AR=4;PCR_454_RR=1506 20 32162066 . G C . . Sample=HG00099;GT=0/1;PCR_454_AR=98;PCR_454_RR=92 20 32162066 . G C . . Sample=NA12282;GT=0/1;PCR_454_AR=72;PCR_454_RR=74 20 32162066 . G C . . Sample=NA12342;GT=0/1;PCR_454_AR=105;PCR_454_RR=134 20 32162066 . G C . . Sample=NA12778;GT=0/1;PCR_454_AR=94;PCR_454_RR=122 20 32162066 . G C . . Sample=NA19773;GT=0/1;PCR_454_AR=84;PCR_454_RR=115 20 32295637 . A G . . Sample=NA19204;GT=0/1;PCR_454_AR=1263;PCR_454_RR=1230 20 32298533 . G A . . Sample=HG01125;GT=0/1;PCR_454_AR=1577;PCR_454_RR=1574 20 32298533 . G A . . Sample=NA18510;GT=0/1;PCR_454_AR=1537;PCR_454_RR=1597 20 32298533 . G A . . Sample=NA18520;GT=0/1;PCR_454_AR=1689;PCR_454_RR=1754 20 32298533 . G A . . Sample=NA19099;GT=0/1;PCR_454_AR=1900;PCR_454_RR=1940 20 32298533 . G A . . Sample=NA19129;GT=0/1;PCR_454_AR=1900;PCR_454_RR=1840 20 32336754 . G A . . Sample=HG00358;GT=0/1;PCR_454_AR=1185;PCR_454_RR=1161 20 32336754 . G A . . Sample=HG00565;GT=0/1;PCR_454_AR=1018;PCR_454_RR=958 20 32336754 . G A . . Sample=HG00595;GT=0/1;PCR_454_AR=1201;PCR_454_RR=1222 20 32336754 . G A . . Sample=NA18532;GT=0/1;PCR_454_AR=1204;PCR_454_RR=1235 20 32336754 . G A . . Sample=NA18542;GT=1/1;PCR_454_AR=2997;PCR_454_RR=11 20 32358043 . A T . . Sample=NA18955;GT=0/1;PCR_454_AR=1050;PCR_454_RR=1022 20 32881901 . T C . . Sample=NA19257;GT=0/1;PCR_454_AR=1007;PCR_454_RR=966 20 33328321 . C T . . Sample=NA18487;GT=0/1;PCR_454_AR=637;PCR_454_RR=629 20 33328321 . C T . . Sample=NA18516;GT=0/1;PCR_454_AR=613;PCR_454_RR=605 20 33328321 . C T . . Sample=NA19044;GT=0/1;PCR_454_AR=629;PCR_454_RR=661 20 33328321 . C T . . Sample=NA19102;GT=0/1;PCR_454_AR=680;PCR_454_RR=625 20 33328321 . C T . . Sample=NA19175;GT=0/1;PCR_454_AR=652;PCR_454_RR=703 20 33330691 . C G . . Sample=NA19189;GT=0/1;PCR_454_AR=604;PCR_454_RR=575 20 33433247 . G A . . Sample=NA11919;GT=0/1;PCR_454_AR=196;PCR_454_RR=195 20 33447313 . C T . . Sample=HG01125;GT=0/1;PCR_454_AR=260;PCR_454_RR=285 20 33447313 . C T . . Sample=NA18504;GT=0/1;PCR_454_AR=231;PCR_454_RR=217 20 33447313 . C T . . Sample=NA18517;GT=0/1;PCR_454_AR=298;PCR_454_RR=311 20 33447313 . C T . . Sample=NA18520;GT=0/1;PCR_454_AR=254;PCR_454_RR=256 20 33447313 . C T . . Sample=NA18522;GT=0/1;PCR_454_AR=286;PCR_454_RR=277 20 33517251 . C T . . Sample=HG00126;GT=0/1;PCR_454_AR=685;PCR_454_RR=676 20 33517301 . G A . . Sample=NA20282;GT=0/1;PCR_454_AR=1082;PCR_454_RR=1076 20 33523396 . A C . . Sample=NA18910;GT=0/1;PCR_454_AR=879;PCR_454_RR=933 20 33572880 . C T . . Sample=NA20516;GT=0/1;PCR_454_AR=935;PCR_454_RR=847 20 33575007 . C T . . Sample=NA19118;GT=0/1;PCR_454_AR=793;PCR_454_RR=659 20 33575043 . C T . . Sample=NA19036;GT=0/1;PCR_454_AR=972;PCR_454_RR=919 20 33575043 . C T . . Sample=NA19308;GT=0/1;PCR_454_AR=801;PCR_454_RR=728 20 33575043 . C T . . Sample=NA19434;GT=0/1;PCR_454_AR=825;PCR_454_RR=915 20 33575043 . C T . . Sample=NA19439;GT=0/1;PCR_454_AR=1001;PCR_454_RR=1073 20 33575043 . C T . . Sample=NA19466;GT=0/1;PCR_454_AR=936;PCR_454_RR=931 20 33583330 . A G . . Sample=HG00097;GT=1/1;PCR_454_AR=651;PCR_454_RR=5 20 33583330 . A G . . Sample=HG00099;GT=1/1;PCR_454_AR=326;PCR_454_RR=0 20 33583330 . A G . . Sample=HG00104;GT=1/1;PCR_454_AR=430;PCR_454_RR=2 20 33583330 . A G . . Sample=HG00106;GT=1/1;PCR_454_AR=613;PCR_454_RR=3 20 33583330 . A G . . Sample=HG00112;GT=1/1;PCR_454_AR=632;PCR_454_RR=6 20 33584196 . C T . . Sample=NA12286;GT=0/1;PCR_454_AR=989;PCR_454_RR=1638 20 33584196 . C T . . Sample=NA12750;GT=0/1;PCR_454_AR=886;PCR_454_RR=1206 20 33584196 . C T . . Sample=NA19750;GT=0/1;PCR_454_AR=1179;PCR_454_RR=1155 20 33584196 . C T . . Sample=NA20807;GT=0/1;PCR_454_AR=1089;PCR_454_RR=1724 20 33584196 . C T . . Sample=NA20826;GT=0/1;PCR_454_AR=1373;PCR_454_RR=1259 20 33587399 . G A . . Sample=NA19328;GT=0/1;PCR_454_AR=893;PCR_454_RR=754 20 33711732 . T A . . Sample=NA19347;GT=0/1;PCR_454_AR=887;PCR_454_RR=946 20 33874473 . C A . . Sample=NA18626;GT=0/1;PCR_454_AR=1001;PCR_454_RR=1012 20 33874719 . C T . . Sample=HG00099;GT=0/1;PCR_454_AR=585;PCR_454_RR=542 20 33874719 . C T . . Sample=HG00141;GT=0/1;PCR_454_AR=499;PCR_454_RR=508 20 33874719 . C T . . Sample=HG00142;GT=0/1;PCR_454_AR=541;PCR_454_RR=540 20 33874719 . C T . . Sample=HG00143;GT=0/1;PCR_454_AR=699;PCR_454_RR=604 20 33874719 . C T . . Sample=HG00156;GT=0/1;PCR_454_AR=722;PCR_454_RR=617 20 34092317 . C A . . Sample=HG00128;GT=0/0;PCR_454_AR=0;PCR_454_RR=1205 20 34092317 . C A . . Sample=HG00266;GT=0/0;PCR_454_AR=3;PCR_454_RR=3354 20 34218898 . A G . . Sample=NA12763;GT=0/1;PCR_454_AR=295;PCR_454_RR=291 20 34292440 . T C . . Sample=NA18639;GT=0/1;PCR_454_AR=481;PCR_454_RR=572 20 34317286 . G A . . Sample=NA19204;GT=0/1;PCR_454_AR=665;PCR_454_RR=705 20 34611604 . C T . . Sample=NA11893;GT=0/1;PCR_454_AR=1180;PCR_454_RR=1243 20 35060852 . G A . . Sample=NA12283;GT=0/1;PCR_454_AR=433;PCR_454_RR=444 20 35060852 . G A . . Sample=NA19676;GT=0/1;PCR_454_AR=368;PCR_454_RR=421 20 35068262 . A C . . Sample=NA20759;GT=0/1;PCR_454_AR=1272;PCR_454_RR=1190 20 35075140 . C T . . Sample=NA19444;GT=0/1;PCR_454_AR=1174;PCR_454_RR=605 20 35075140 . C T . . Sample=NA19448;GT=0/1;PCR_454_AR=1574;PCR_454_RR=932 20 35075309 . G A . . Sample=NA18549;GT=0/1;PCR_454_AR=923;PCR_454_RR=1559 20 35075309 . G A . . Sample=NA19391;GT=0/1;PCR_454_AR=1114;PCR_454_RR=1064 20 35075309 . G A . . Sample=NA19397;GT=0/1;PCR_454_AR=1198;PCR_454_RR=1233 20 35176551 . A G . . Sample=NA20289;GT=0/1;PCR_454_AR=532;PCR_454_RR=1682 20 35207263 . G A . . Sample=HG00234;GT=0/1;PCR_454_AR=235;PCR_454_RR=221 20 35219406 . G C . . Sample=HG00105;GT=0/0;PCR_454_AR=57;PCR_454_RR=585 20 35219406 . G C . . Sample=HG00130;GT=0/0;PCR_454_AR=58;PCR_454_RR=574 20 35438474 . G A . . Sample=NA18642;GT=0/1;PCR_454_AR=1030;PCR_454_RR=1093 20 35507540 . G A . . Sample=NA19740;GT=0/1;PCR_454_AR=466;PCR_454_RR=584 20 35539699 . T C . . Sample=NA12717;GT=0/1;PCR_454_AR=336;PCR_454_RR=421 20 35812756 . C T . . Sample=NA19726;GT=0/1;PCR_454_AR=1085;PCR_454_RR=1070 20 35944759 . A C . . Sample=NA11831;GT=0/0;PCR_454_AR=1;PCR_454_RR=1726 20 35944759 . A C . . Sample=NA11832;GT=0/0;PCR_454_AR=3;PCR_454_RR=1809 20 36024598 . C T . . Sample=NA19682;GT=0/1;PCR_454_AR=677;PCR_454_RR=797 20 36024598 . C T . . Sample=NA20528;GT=0/1;PCR_454_AR=691;PCR_454_RR=703 20 36030944 . T C . . Sample=NA18618;GT=0/0;PCR_454_AR=0;PCR_454_RR=985 20 36030944 . T C . . Sample=NA18626;GT=0/0;PCR_454_AR=2;PCR_454_RR=778 20 36030944 . T C . . Sample=NA18916;GT=0/1;PCR_454_AR=454;PCR_454_RR=444 20 36030944 . T C . . Sample=NA19150;GT=0/1;PCR_454_AR=471;PCR_454_RR=509 20 36488331 . A G . . Sample=NA20340;GT=0/1;PCR_454_AR=1388;PCR_454_RR=1472 20 36640610 . C G . . Sample=NA18508;GT=0/1;PCR_454_AR=985;PCR_454_RR=1026 20 36641870 . G A . . Sample=HG00106;GT=0/1;PCR_454_AR=1062;PCR_454_RR=1095 20 36641870 . G A . . Sample=NA11893;GT=0/1;PCR_454_AR=976;PCR_454_RR=1033 20 36641870 . G A . . Sample=NA12399;GT=0/1;PCR_454_AR=971;PCR_454_RR=973 20 36641870 . G A . . Sample=NA12489;GT=0/1;PCR_454_AR=1107;PCR_454_RR=1037 20 36641870 . G A . . Sample=NA12749;GT=0/1;PCR_454_AR=947;PCR_454_RR=885 20 36775155 . A G . . Sample=NA19067;GT=0/1;PCR_454_AR=771;PCR_454_RR=772 20 36775233 . G A . . Sample=NA19352;GT=0/1;PCR_454_AR=732;PCR_454_RR=723 20 36784261 . G A . . Sample=NA19171;GT=0/1;PCR_454_AR=1197;PCR_454_RR=1200 20 36841848 . C T . . Sample=NA19449;GT=0/1;PCR_454_AR=402;PCR_454_RR=394 20 36869075 . G A . . Sample=NA19185;GT=0/1;PCR_454_AR=1430;PCR_454_RR=1382 20 36869206 . C T . . Sample=NA20287;GT=0/1;PCR_454_AR=584;PCR_454_RR=626 20 36979308 . T A . . Sample=NA11894;GT=0/1;PCR_454_AR=973;PCR_454_RR=1087 20 37001736 . C T . . Sample=NA18987;GT=0/1;PCR_454_AR=122;PCR_454_RR=88 20 39798902 . C T . . Sample=NA18994;GT=0/1;PCR_454_AR=1212;PCR_454_RR=1202 20 39981307 . G T . . Sample=NA18595;GT=0/1;PCR_454_AR=1273;PCR_454_RR=1102 20 39981307 . G T . . Sample=NA18622;GT=0/1;PCR_454_AR=635;PCR_454_RR=623 20 39981307 . G T . . Sample=NA18977;GT=0/1;PCR_454_AR=1251;PCR_454_RR=1141 20 39981307 . G T . . Sample=NA18978;GT=0/1;PCR_454_AR=1286;PCR_454_RR=1331 20 39981307 . G T . . Sample=NA18998;GT=0/1;PCR_454_AR=1174;PCR_454_RR=1225 20 39986913 . G A . . Sample=NA20317;GT=0/1;PCR_454_AR=627;PCR_454_RR=535 20 39987386 . G A . . Sample=NA19437;GT=0/1;PCR_454_AR=989;PCR_454_RR=971 20 39992390 . G A . . Sample=NA18636;GT=0/1;PCR_454_AR=925;PCR_454_RR=969 20 39993723 . C T . . Sample=NA18489;GT=0/1;PCR_454_AR=677;PCR_454_RR=819 20 39993723 . C T . . Sample=NA18505;GT=0/1;PCR_454_AR=603;PCR_454_RR=578 20 39993723 . C T . . Sample=NA18517;GT=0/1;PCR_454_AR=791;PCR_454_RR=747 20 39993723 . C T . . Sample=NA19380;GT=0/1;PCR_454_AR=869;PCR_454_RR=972 20 39993790 . G A . . Sample=NA18871;GT=0/1;PCR_454_AR=2297;PCR_454_RR=2512 20 40033848 . A G . . Sample=HG00559;GT=0/0;PCR_454_AR=6;PCR_454_RR=2130 20 40050233 . T G . . Sample=HG01133;GT=0/0;PCR_454_AR=2;PCR_454_RR=1613 20 40050233 . T G . . Sample=NA18502;GT=0/0;PCR_454_AR=4;PCR_454_RR=1967 20 40162202 . T C . . Sample=NA12874;GT=0/1;PCR_454_AR=171;PCR_454_RR=157 20 42143783 . A G . . Sample=NA20334;GT=0/1;PCR_454_AR=1011;PCR_454_RR=632 20 42143783 . A G . . Sample=NA20336;GT=0/1;PCR_454_AR=1556;PCR_454_RR=492 20 42196587 . G A . . Sample=NA19312;GT=0/1;PCR_454_AR=522;PCR_454_RR=486 20 42196587 . G A . . Sample=NA19383;GT=0/1;PCR_454_AR=693;PCR_454_RR=821 20 42333997 . C T . . Sample=NA19058;GT=0/1;PCR_454_AR=994;PCR_454_RR=994 20 42680115 . G A . . Sample=NA18611;GT=0/1;PCR_454_AR=1042;PCR_454_RR=1086 20 42747246 . C T . . Sample=HG00097;GT=0/1;PCR_454_AR=1132;PCR_454_RR=1174 20 42747246 . C T . . Sample=HG00106;GT=0/1;PCR_454_AR=899;PCR_454_RR=983 20 42747246 . C T . . Sample=HG00112;GT=0/1;PCR_454_AR=901;PCR_454_RR=960 20 42747246 . C T . . Sample=HG00135;GT=0/1;PCR_454_AR=677;PCR_454_RR=680 20 42747246 . C T . . Sample=HG00142;GT=0/1;PCR_454_AR=928;PCR_454_RR=956 20 42939738 . C T . . Sample=NA18611;GT=0/1;PCR_454_AR=1131;PCR_454_RR=984 20 43243299 . G C . . Sample=NA18633;GT=0/1;PCR_454_AR=1194;PCR_454_RR=1277 20 43255152 . G A . . Sample=HG00130;GT=0/0;PCR_454_AR=0;PCR_454_RR=2287 20 43255152 . G A . . Sample=HG00234;GT=0/0;PCR_454_AR=1;PCR_454_RR=2172 20 43255152 . G A . . Sample=NA18618;GT=0/0;PCR_454_AR=2;PCR_454_RR=2266 20 43255152 . G A . . Sample=NA18956;GT=0/0;PCR_454_AR=0;PCR_454_RR=2152 20 43255152 . G A . . Sample=NA19083;GT=0/1;PCR_454_AR=986;PCR_454_RR=974 20 43723672 . G A . . Sample=NA18530;GT=0/1;PCR_454_AR=356;PCR_454_RR=401 20 43723672 . G A . . Sample=NA18622;GT=0/1;PCR_454_AR=449;PCR_454_RR=391 20 43739354 . G A . . Sample=NA18504;GT=0/1;PCR_454_AR=455;PCR_454_RR=1477 20 43934213 . G T . . Sample=HG01345;GT=0/1;PCR_454_AR=1327;PCR_454_RR=1169 20 44190750 . T G . . Sample=HG00143;GT=0/1;PCR_454_AR=898;PCR_454_RR=938 20 44190750 . T G . . Sample=NA12340;GT=0/1;PCR_454_AR=882;PCR_454_RR=872 20 44424037 . G A . . Sample=HG00152;GT=0/1;PCR_454_AR=603;PCR_454_RR=593 20 44469565 . C T . . Sample=NA18549;GT=0/1;PCR_454_AR=999;PCR_454_RR=246 20 44485866 . T A . . Sample=NA12890;GT=0/1;PCR_454_AR=536;PCR_454_RR=596 20 44506417 . G A . . Sample=HG00099;GT=0/1;PCR_454_AR=1320;PCR_454_RR=1305 20 44506417 . G A . . Sample=HG00118;GT=0/1;PCR_454_AR=1559;PCR_454_RR=1533 20 44506417 . G A . . Sample=HG00097;GT=1/1;PCR_454_AR=3211;PCR_454_RR=20 20 44506417 . G A . . Sample=HG00112;GT=1/1;PCR_454_AR=2632;PCR_454_RR=20 20 44506417 . G A . . Sample=HG00122;GT=1/1;PCR_454_AR=2875;PCR_454_RR=6 20 44506987 . G C . . Sample=NA19117;GT=0/1;PCR_454_AR=1387;PCR_454_RR=1532 20 44511253 . C T . . Sample=NA20799;GT=0/1;PCR_454_AR=1286;PCR_454_RR=1280 20 44519372 . G A . . Sample=NA19437;GT=0/0;PCR_454_AR=0;PCR_454_RR=2075 20 44519372 . G A . . Sample=NA19917;GT=0/1;PCR_454_AR=1243;PCR_454_RR=1234 20 44576246 . G A . . Sample=NA18912;GT=0/1;PCR_454_AR=458;PCR_454_RR=2154 20 44576246 . G A . . Sample=NA18924;GT=0/1;PCR_454_AR=1131;PCR_454_RR=1078 20 44576246 . G A . . Sample=NA20276;GT=0/1;PCR_454_AR=860;PCR_454_RR=852 20 44576246 . G A . . Sample=NA20289;GT=0/1;PCR_454_AR=492;PCR_454_RR=2174 20 44580998 . T C . . Sample=NA18566;GT=0/1;PCR_454_AR=877;PCR_454_RR=925 20 44680318 . C G . . Sample=HG00592;GT=0/0;PCR_454_AR=0;PCR_454_RR=3602 20 44680318 . C G . . Sample=HG01139;GT=0/0;PCR_454_AR=1;PCR_454_RR=3510 20 44856207 . G A . . Sample=NA11995;GT=0/1;PCR_454_AR=127;PCR_454_RR=17 20 44980779 . G A . . Sample=NA18553;GT=0/1;PCR_454_AR=993;PCR_454_RR=1022 20 45919012 . C T . . Sample=NA19445;GT=0/1;PCR_454_AR=265;PCR_454_RR=525 20 46271051 . C G . . Sample=NA18486;GT=0/1;PCR_454_AR=754;PCR_454_RR=749 20 47262594 . C A . . Sample=NA20291;GT=0/1;PCR_454_AR=1210;PCR_454_RR=1153 20 47558430 . C T . . Sample=NA20296;GT=0/1;PCR_454_AR=699;PCR_454_RR=682 20 47733688 . T C . . Sample=NA18630;GT=0/0;PCR_454_AR=0;PCR_454_RR=806 20 47739668 . G A . . Sample=NA19036;GT=0/0;PCR_454_AR=1;PCR_454_RR=2292 20 47886859 . C T . . Sample=NA18956;GT=0/0;PCR_454_AR=1;PCR_454_RR=2153 20 47990798 . C G . . Sample=HG00105;GT=0/0;PCR_454_AR=0;PCR_454_RR=387 20 47990798 . C G . . Sample=HG00122;GT=0/0;PCR_454_AR=0;PCR_454_RR=534 20 48124475 . C T . . Sample=NA19257;GT=0/1;PCR_454_AR=628;PCR_454_RR=644 20 48273201 . A C . . Sample=NA19914;GT=0/1;PCR_454_AR=338;PCR_454_RR=323 20 48713355 . T C . . Sample=NA12155;GT=0/0;PCR_454_AR=8;PCR_454_RR=1686 20 48713355 . T C . . Sample=NA12815;GT=0/0;PCR_454_AR=10;PCR_454_RR=1607 20 49218698 . C T . . Sample=NA19338;GT=0/1;PCR_454_AR=776;PCR_454_RR=682 20 49218698 . C T . . Sample=NA19457;GT=0/1;PCR_454_AR=803;PCR_454_RR=759 20 49219065 . C T . . Sample=NA18599;GT=0/1;PCR_454_AR=1018;PCR_454_RR=1080 20 49354597 . A G . . Sample=HG00177;GT=0/1;PCR_454_AR=580;PCR_454_RR=617 20 49354597 . A G . . Sample=NA11829;GT=0/1;PCR_454_AR=778;PCR_454_RR=869 20 49354597 . A G . . Sample=NA20510;GT=0/1;PCR_454_AR=518;PCR_454_RR=631 20 49354597 . A G . . Sample=NA20512;GT=0/1;PCR_454_AR=238;PCR_454_RR=333 20 49354597 . A G . . Sample=NA20586;GT=0/1;PCR_454_AR=562;PCR_454_RR=642 20 50048925 . G C . . Sample=NA20507;GT=0/1;PCR_454_AR=774;PCR_454_RR=809 20 50051804 . C T . . Sample=NA19102;GT=0/1;PCR_454_AR=136;PCR_454_RR=155 20 50071136 . C T . . Sample=NA18637;GT=0/1;PCR_454_AR=334;PCR_454_RR=349 20 50140178 . G A . . Sample=NA18924;GT=0/1;PCR_454_AR=540;PCR_454_RR=481 20 50140178 . G A . . Sample=NA19321;GT=0/1;PCR_454_AR=481;PCR_454_RR=652 20 50235576 . G A . . Sample=HG00106;GT=0/1;PCR_454_AR=982;PCR_454_RR=886 20 50235576 . G A . . Sample=HG00122;GT=0/1;PCR_454_AR=838;PCR_454_RR=717 20 50235576 . G A . . Sample=HG00126;GT=0/1;PCR_454_AR=795;PCR_454_RR=769 20 50235576 . G A . . Sample=HG00135;GT=0/1;PCR_454_AR=972;PCR_454_RR=930 20 50235576 . G A . . Sample=HG00148;GT=0/1;PCR_454_AR=933;PCR_454_RR=931 20 50310567 . C T . . Sample=NA19152;GT=0/1;PCR_454_AR=689;PCR_454_RR=773 20 50310567 . C T . . Sample=NA19377;GT=0/1;PCR_454_AR=736;PCR_454_RR=683 20 50406859 . G A . . Sample=NA19921;GT=0/1;PCR_454_AR=1045;PCR_454_RR=930 20 50407501 . A C . . Sample=HG00118;GT=0/1;PCR_454_AR=569;PCR_454_RR=608 20 50407508 . C T . . Sample=NA20534;GT=0/1;PCR_454_AR=753;PCR_454_RR=2120 20 50408613 . A G . . Sample=NA18487;GT=0/1;PCR_454_AR=637;PCR_454_RR=634 20 50408613 . A G . . Sample=NA18502;GT=0/1;PCR_454_AR=561;PCR_454_RR=553 20 50408613 . A G . . Sample=NA18519;GT=0/1;PCR_454_AR=571;PCR_454_RR=554 20 50408613 . A G . . Sample=NA18908;GT=0/1;PCR_454_AR=731;PCR_454_RR=791 20 50408613 . A G . . Sample=NA18909;GT=0/1;PCR_454_AR=683;PCR_454_RR=634 20 50803476 . G A . . Sample=NA19046;GT=0/1;PCR_454_AR=692;PCR_454_RR=685 20 50803476 . G A . . Sample=NA19375;GT=0/1;PCR_454_AR=735;PCR_454_RR=803 20 50803476 . G A . . Sample=NA19376;GT=0/1;PCR_454_AR=892;PCR_454_RR=831 20 51872037 . G A . . Sample=NA18502;GT=0/1;PCR_454_AR=602;PCR_454_RR=654 20 51872037 . G A . . Sample=NA18504;GT=0/1;PCR_454_AR=717;PCR_454_RR=760 20 51872037 . G A . . Sample=NA18507;GT=0/1;PCR_454_AR=790;PCR_454_RR=822 20 51872037 . G A . . Sample=NA18508;GT=0/1;PCR_454_AR=868;PCR_454_RR=914 20 51872037 . G A . . Sample=NA18501;GT=1/1;PCR_454_AR=1687;PCR_454_RR=5 20 52192483 . T C . . Sample=HG00266;GT=0/1;PCR_454_AR=1044;PCR_454_RR=1029 20 52198279 . G A . . Sample=NA19065;GT=0/1;PCR_454_AR=1001;PCR_454_RR=1070 20 52561468 . A G . . Sample=HG00118;GT=0/1;PCR_454_AR=398;PCR_454_RR=501 20 52561468 . A G . . Sample=HG00126;GT=0/1;PCR_454_AR=228;PCR_454_RR=250 20 52561468 . A G . . Sample=HG00130;GT=0/1;PCR_454_AR=472;PCR_454_RR=535 20 52561468 . A G . . Sample=HG00134;GT=0/1;PCR_454_AR=462;PCR_454_RR=543 20 52561468 . A G . . Sample=HG00143;GT=0/1;PCR_454_AR=355;PCR_454_RR=404 20 52779394 . G T . . Sample=NA20540;GT=0/1;PCR_454_AR=470;PCR_454_RR=557 20 53205268 . T C . . Sample=NA19038;GT=0/1;PCR_454_AR=447;PCR_454_RR=421 20 53226967 . G A . . Sample=NA19462;GT=0/1;PCR_454_AR=770;PCR_454_RR=792 20 54961540 . A T . . Sample=HG00106;GT=0/1;PCR_454_AR=457;PCR_454_RR=411 20 54961540 . A T . . Sample=HG00112;GT=0/1;PCR_454_AR=466;PCR_454_RR=483 20 54961540 . A T . . Sample=HG00134;GT=0/1;PCR_454_AR=480;PCR_454_RR=467 20 54961540 . A T . . Sample=HG00143;GT=0/1;PCR_454_AR=522;PCR_454_RR=458 20 54961540 . A T . . Sample=HG00097;GT=1/1;PCR_454_AR=937;PCR_454_RR=4 20 54970682 . C T . . Sample=NA18912;GT=0/1;PCR_454_AR=683;PCR_454_RR=745 20 54970682 . C T . . Sample=NA19171;GT=0/1;PCR_454_AR=819;PCR_454_RR=792 20 55021021 . G A . . Sample=NA19087;GT=0/1;PCR_454_AR=1018;PCR_454_RR=1144 20 55108414 . G A . . Sample=NA20756;GT=1/1;PCR_454_AR=1220;PCR_454_RR=3 20 55206884 . C T . . Sample=NA19726;GT=0/1;PCR_454_AR=806;PCR_454_RR=864 20 55206884 . C T . . Sample=NA19738;GT=0/1;PCR_454_AR=988;PCR_454_RR=1033 20 56087684 . C T . . Sample=NA18599;GT=0/1;PCR_454_AR=1158;PCR_454_RR=1234 20 56089789 . C T . . Sample=HG01277;GT=0/1;PCR_454_AR=737;PCR_454_RR=779 20 56137833 . A G . . Sample=HG00099;GT=0/1;PCR_454_AR=794;PCR_454_RR=777 20 56137833 . A G . . Sample=HG00106;GT=0/1;PCR_454_AR=1272;PCR_454_RR=1196 20 56137833 . A G . . Sample=HG00097;GT=1/1;PCR_454_AR=1763;PCR_454_RR=4 20 56137833 . A G . . Sample=HG00104;GT=1/1;PCR_454_AR=1726;PCR_454_RR=5 20 56137833 . A G . . Sample=HG00112;GT=1/1;PCR_454_AR=1821;PCR_454_RR=3 20 57036354 . C T . . Sample=NA19080;GT=0/1;PCR_454_AR=1722;PCR_454_RR=1581 20 57036538 . C T . . Sample=NA19248;GT=0/1;PCR_454_AR=1224;PCR_454_RR=902 20 57415535 . C T . . Sample=NA19722;GT=0/1;PCR_454_AR=291;PCR_454_RR=1503 20 57415601 . G A . . Sample=NA20296;GT=0/1;PCR_454_AR=1262;PCR_454_RR=350 20 57428947 . G T . . Sample=NA19311;GT=0/1;PCR_454_AR=1304;PCR_454_RR=553 20 57572729 . C T . . Sample=NA19707;GT=0/1;PCR_454_AR=840;PCR_454_RR=1015 20 57576684 . T G . . Sample=NA18747;GT=0/0;PCR_454_AR=3;PCR_454_RR=1578 20 57597952 . C T . . Sample=NA20529;GT=0/1;PCR_454_AR=816;PCR_454_RR=883 20 57768304 . G A . . Sample=NA20818;GT=0/1;PCR_454_AR=710;PCR_454_RR=535 20 57769546 . C T . . Sample=NA18917;GT=0/0;PCR_454_AR=61;PCR_454_RR=810 20 57769738 . A G . . Sample=NA18527;GT=0/1;PCR_454_AR=799;PCR_454_RR=792 20 57769738 . A G . . Sample=NA18530;GT=0/1;PCR_454_AR=558;PCR_454_RR=527 20 57769738 . A G . . Sample=NA18532;GT=0/1;PCR_454_AR=734;PCR_454_RR=719 20 57769738 . A G . . Sample=NA18545;GT=0/1;PCR_454_AR=524;PCR_454_RR=502 20 57769738 . A G . . Sample=NA18593;GT=0/1;PCR_454_AR=809;PCR_454_RR=835 20 58444902 . C T . . Sample=NA19095;GT=0/1;PCR_454_AR=164;PCR_454_RR=144 20 58467100 . C T . . Sample=NA19324;GT=0/1;PCR_454_AR=312;PCR_454_RR=301 20 58560056 . C T . . Sample=HG00593;GT=0/1;PCR_454_AR=1491;PCR_454_RR=1378 20 58560056 . C T . . Sample=NA18553;GT=0/1;PCR_454_AR=1226;PCR_454_RR=1216 20 58564005 . G A . . Sample=NA19355;GT=0/0;PCR_454_AR=0;PCR_454_RR=2602 20 58567458 . A C . . Sample=HG00143;GT=0/0;PCR_454_AR=1;PCR_454_RR=878 20 58567458 . A C . . Sample=HG00149;GT=0/0;PCR_454_AR=0;PCR_454_RR=883 20 58571705 . C T . . Sample=NA19319;GT=0/1;PCR_454_AR=342;PCR_454_RR=265 20 60504808 . C T . . Sample=NA18639;GT=0/1;PCR_454_AR=1079;PCR_454_RR=1027 20 60504808 . C T . . Sample=NA19921;GT=0/1;PCR_454_AR=914;PCR_454_RR=890 20 60701482 . T A . . Sample=NA19651;GT=0/1;PCR_454_AR=540;PCR_454_RR=612 20 60708462 . T C . . Sample=NA18962;GT=0/1;PCR_454_AR=891;PCR_454_RR=784 20 60738559 . G A . . Sample=NA18965;GT=0/1;PCR_454_AR=1072;PCR_454_RR=896 20 60838713 . C T . . Sample=NA20506;GT=0/1;PCR_454_AR=618;PCR_454_RR=642 20 60866830 . A C . . Sample=NA18923;GT=0/0;PCR_454_AR=0;PCR_454_RR=211 20 60868936 . C T . . Sample=NA19119;GT=0/1;PCR_454_AR=1424;PCR_454_RR=1554 20 60878814 . G A . . Sample=NA18638;GT=0/1;PCR_454_AR=223;PCR_454_RR=1299 20 60884465 . G A . . Sample=NA19681;GT=0/1;PCR_454_AR=928;PCR_454_RR=1002 20 60885810 . C T . . Sample=HG00134;GT=0/0;PCR_454_AR=2;PCR_454_RR=2017 20 60885810 . C T . . Sample=HG00350;GT=0/0;PCR_454_AR=4;PCR_454_RR=1963 20 60886712 . T C . . Sample=NA19438;GT=0/1;PCR_454_AR=929;PCR_454_RR=721 20 60891010 . C T . . Sample=NA19700;GT=0/1;PCR_454_AR=334;PCR_454_RR=389 20 60893610 . C T . . Sample=HG00359;GT=0/0;PCR_454_AR=2;PCR_454_RR=2041 20 60893610 . C T . . Sample=NA19758;GT=0/1;PCR_454_AR=1173;PCR_454_RR=1158 20 60893636 . C T . . Sample=NA20520;GT=0/1;PCR_454_AR=847;PCR_454_RR=1197 20 60893636 . C T . . Sample=NA20540;GT=0/1;PCR_454_AR=776;PCR_454_RR=1355 20 60893960 . C T . . Sample=NA19236;GT=0/1;PCR_454_AR=1310;PCR_454_RR=1388 20 60897486 . C T . . Sample=HG00099;GT=0/1;PCR_454_AR=454;PCR_454_RR=403 20 60897486 . C T . . Sample=HG00122;GT=0/1;PCR_454_AR=465;PCR_454_RR=352 20 60897486 . C T . . Sample=HG00097;GT=1/1;PCR_454_AR=849;PCR_454_RR=3 20 60897486 . C T . . Sample=HG00104;GT=1/1;PCR_454_AR=925;PCR_454_RR=4 20 60897486 . C T . . Sample=HG00118;GT=1/1;PCR_454_AR=799;PCR_454_RR=7 20 60907674 . G A . . Sample=HG00104;GT=0/1;PCR_454_AR=279;PCR_454_RR=228 20 60907674 . G A . . Sample=HG00106;GT=0/1;PCR_454_AR=334;PCR_454_RR=295 20 60907674 . G A . . Sample=HG00097;GT=1/1;PCR_454_AR=739;PCR_454_RR=4 20 60907674 . G A . . Sample=HG00099;GT=1/1;PCR_454_AR=395;PCR_454_RR=3 20 60907674 . G A . . Sample=HG00112;GT=1/1;PCR_454_AR=980;PCR_454_RR=6 20 60911433 . A C . . Sample=NA11920;GT=0/1;PCR_454_AR=341;PCR_454_RR=380 20 60911433 . A C . . Sample=NA20278;GT=0/1;PCR_454_AR=398;PCR_454_RR=444 20 60913173 . C T . . Sample=NA18522;GT=0/1;PCR_454_AR=1062;PCR_454_RR=1032 20 60920914 . T C . . Sample=NA18530;GT=0/1;PCR_454_AR=937;PCR_454_RR=877 20 60920914 . T C . . Sample=NA18873;GT=0/1;PCR_454_AR=791;PCR_454_RR=836 20 60920914 . T C . . Sample=NA19038;GT=0/1;PCR_454_AR=895;PCR_454_RR=857 20 60920914 . T C . . Sample=NA19099;GT=0/1;PCR_454_AR=1115;PCR_454_RR=1150 20 60920914 . T C . . Sample=NA19317;GT=0/1;PCR_454_AR=1165;PCR_454_RR=1206 20 60927411 . G A . . Sample=HG00099;GT=0/1;PCR_454_AR=330;PCR_454_RR=345 20 60927411 . G A . . Sample=HG00112;GT=0/1;PCR_454_AR=389;PCR_454_RR=468 20 60927411 . G A . . Sample=HG00118;GT=0/1;PCR_454_AR=1434;PCR_454_RR=538 20 60927411 . G A . . Sample=HG00097;GT=1/1;PCR_454_AR=993;PCR_454_RR=7 20 60927411 . G A . . Sample=HG00104;GT=1/1;PCR_454_AR=837;PCR_454_RR=8 20 60937543 . A G . . Sample=HG00115;GT=0/0;PCR_454_AR=2;PCR_454_RR=3444 20 60963387 . C T . . Sample=NA18992;GT=0/1;PCR_454_AR=689;PCR_454_RR=728 20 60986026 . T C . . Sample=NA18511;GT=0/1;PCR_454_AR=510;PCR_454_RR=522 20 60986026 . T C . . Sample=NA18520;GT=0/1;PCR_454_AR=384;PCR_454_RR=403 20 60986026 . T C . . Sample=NA18861;GT=0/1;PCR_454_AR=372;PCR_454_RR=432 20 60986026 . T C . . Sample=NA18908;GT=0/1;PCR_454_AR=428;PCR_454_RR=386 20 60989186 . G T . . Sample=HG00351;GT=0/0;PCR_454_AR=0;PCR_454_RR=299 20 60989186 . G T . . Sample=HG00099;GT=0/1;PCR_454_AR=1182;PCR_454_RR=966 20 60989186 . G T . . Sample=HG01344;GT=0/1;PCR_454_AR=654;PCR_454_RR=302 20 60989186 . G T . . Sample=NA12045;GT=0/1;PCR_454_AR=504;PCR_454_RR=534 20 60989186 . G T . . Sample=HG00130;GT=1/1;PCR_454_AR=76;PCR_454_RR=2 20 60992370 . C T . . Sample=NA18917;GT=0/1;PCR_454_AR=598;PCR_454_RR=363 20 60992370 . C T . . Sample=NA19453;GT=0/1;PCR_454_AR=541;PCR_454_RR=677 20 61288592 . G A . . Sample=HG01625;GT=0/1;PCR_454_AR=852;PCR_454_RR=871 20 61288592 . G A . . Sample=NA12383;GT=0/1;PCR_454_AR=794;PCR_454_RR=737 20 61288592 . G A . . Sample=NA19780;GT=0/1;PCR_454_AR=1012;PCR_454_RR=880 20 61288592 . G A . . Sample=NA20508;GT=0/1;PCR_454_AR=913;PCR_454_RR=773 20 61512157 . C T . . Sample=NA18933;GT=0/1;PCR_454_AR=1227;PCR_454_RR=1206 20 61512157 . C T . . Sample=NA18934;GT=0/1;PCR_454_AR=1110;PCR_454_RR=1182 20 61512157 . C T . . Sample=NA19771;GT=0/1;PCR_454_AR=1250;PCR_454_RR=1148 20 61512982 . T A . . Sample=NA18559;GT=0/1;PCR_454_AR=1255;PCR_454_RR=1117 20 61513433 . T C . . Sample=NA20810;GT=0/0;PCR_454_AR=1;PCR_454_RR=550 20 61525226 . G A . . Sample=NA19428;GT=0/1;PCR_454_AR=719;PCR_454_RR=719 20 61542496 . G C . . Sample=NA19648;GT=0/1;PCR_454_AR=237;PCR_454_RR=1305 20 61574860 . C T . . Sample=NA19762;GT=0/1;PCR_454_AR=703;PCR_454_RR=488 20 61591950 . T G . . Sample=HG00106;GT=0/0;PCR_454_AR=2;PCR_454_RR=1219 20 61591950 . T G . . Sample=HG00122;GT=0/0;PCR_454_AR=0;PCR_454_RR=1227 20 61833992 . G A . . Sample=NA18489;GT=0/1;PCR_454_AR=738;PCR_454_RR=786 20 61833992 . G A . . Sample=NA19093;GT=0/1;PCR_454_AR=839;PCR_454_RR=739 20 61834856 . G A . . Sample=NA19041;GT=0/1;PCR_454_AR=389;PCR_454_RR=374 20 61834856 . G A . . Sample=NA19095;GT=0/1;PCR_454_AR=383;PCR_454_RR=364 20 61834856 . G A . . Sample=NA19113;GT=0/1;PCR_454_AR=322;PCR_454_RR=325 20 61834856 . G A . . Sample=NA19318;GT=0/1;PCR_454_AR=434;PCR_454_RR=399 20 61834856 . G A . . Sample=NA19334;GT=0/1;PCR_454_AR=380;PCR_454_RR=343 20 61943307 . G C . . Sample=NA19201;GT=0/1;PCR_454_AR=920;PCR_454_RR=890 20 61943346 . G A . . Sample=NA19758;GT=0/1;PCR_454_AR=683;PCR_454_RR=705 20 62187372 . C G . . Sample=NA19117;GT=0/0;PCR_454_AR=0;PCR_454_RR=963 20 62187668 . C T . . Sample=NA12154;GT=0/1;PCR_454_AR=905;PCR_454_RR=664 20 62194106 . C T . . Sample=NA18910;GT=0/1;PCR_454_AR=1083;PCR_454_RR=1040 20 62194106 . C T . . Sample=NA19338;GT=0/1;PCR_454_AR=784;PCR_454_RR=854 20 62194106 . C T . . Sample=NA19346;GT=0/1;PCR_454_AR=757;PCR_454_RR=817 20 62194106 . C T . . Sample=NA19376;GT=0/1;PCR_454_AR=1152;PCR_454_RR=962 20 62194106 . C T . . Sample=NA19439;GT=0/1;PCR_454_AR=1387;PCR_454_RR=1456 20 62194211 . C A . . Sample=HG00156;GT=0/1;PCR_454_AR=1116;PCR_454_RR=536 20 62194211 . C A . . Sample=NA07051;GT=0/1;PCR_454_AR=2089;PCR_454_RR=259 20 62194211 . C A . . Sample=NA12003;GT=0/1;PCR_454_AR=1330;PCR_454_RR=796 20 62194290 . C T . . Sample=NA19346;GT=0/1;PCR_454_AR=1000;PCR_454_RR=751 20 62194290 . C T . . Sample=NA19351;GT=0/1;PCR_454_AR=901;PCR_454_RR=771 20 62198552 . G C . . Sample=NA20542;GT=0/1;PCR_454_AR=1527;PCR_454_RR=1010 20 62198883 . C T . . Sample=NA19346;GT=0/1;PCR_454_AR=1447;PCR_454_RR=1455 20 62198883 . C T . . Sample=NA19351;GT=0/1;PCR_454_AR=903;PCR_454_RR=1401 20 62198883 . C T . . Sample=NA20340;GT=0/1;PCR_454_AR=843;PCR_454_RR=892 20 62198960 . G A . . Sample=NA20534;GT=0/1;PCR_454_AR=1223;PCR_454_RR=864 20 62200240 . G A . . Sample=NA18910;GT=0/1;PCR_454_AR=1221;PCR_454_RR=1347 20 62226984 . G C . . Sample=HG00559;GT=0/0;PCR_454_AR=2;PCR_454_RR=1774 20 62226984 . G C . . Sample=NA12003;GT=0/0;PCR_454_AR=1;PCR_454_RR=1871 20 62250734 . C T . . Sample=NA19473;GT=0/1;PCR_454_AR=607;PCR_454_RR=722 20 62297382 . A T . . Sample=NA11993;GT=0/0;PCR_454_AR=3;PCR_454_RR=2573 20 62297382 . A T . . Sample=NA19117;GT=0/0;PCR_454_AR=5;PCR_454_RR=1753 20 62305427 . G A . . Sample=HG00104;GT=0/0;PCR_454_AR=10;PCR_454_RR=803 20 62305427 . G A . . Sample=HG00122;GT=0/0;PCR_454_AR=28;PCR_454_RR=1300 20 62319912 . G T . . Sample=HG00128;GT=0/0;PCR_454_AR=1;PCR_454_RR=1911 20 62319912 . G T . . Sample=HG00560;GT=0/0;PCR_454_AR=0;PCR_454_RR=2111 20 62324258 . C G . . Sample=NA18562;GT=0/1;PCR_454_AR=1126;PCR_454_RR=1126 20 62324622 . C G . . Sample=NA18574;GT=0/1;PCR_454_AR=1153;PCR_454_RR=1158 20 62325731 . G A . . Sample=NA18548;GT=0/1;PCR_454_AR=779;PCR_454_RR=2199 20 62325821 . G A . . Sample=NA20278;GT=0/1;PCR_454_AR=819;PCR_454_RR=764 20 62325821 . G A . . Sample=NA20507;GT=0/1;PCR_454_AR=1163;PCR_454_RR=1060 20 62326150 . G A . . Sample=NA18870;GT=0/1;PCR_454_AR=1080;PCR_454_RR=892 20 62326234 . C T . . Sample=HG00128;GT=0/0;PCR_454_AR=0;PCR_454_RR=761 20 62326234 . C T . . Sample=HG00179;GT=0/0;PCR_454_AR=1;PCR_454_RR=1158 20 62326811 . G T . . Sample=HG00149;GT=0/0;PCR_454_AR=0;PCR_454_RR=1467 20 62326811 . G T . . Sample=HG00151;GT=0/0;PCR_454_AR=1;PCR_454_RR=1492 20 62407154 . C T . . Sample=NA18987;GT=0/0;PCR_454_AR=181;PCR_454_RR=2041 20 62421536 . C T . . Sample=NA20521;GT=0/1;PCR_454_AR=856;PCR_454_RR=910 20 62421536 . C T . . Sample=NA20543;GT=0/1;PCR_454_AR=865;PCR_454_RR=854 20 62593676 . C T . . Sample=NA20291;GT=0/1;PCR_454_AR=1038;PCR_454_RR=995 20 62594479 . C T . . Sample=NA19746;GT=0/1;PCR_454_AR=349;PCR_454_RR=347 20 62595981 . C T . . Sample=NA19172;GT=0/1;PCR_454_AR=440;PCR_454_RR=415 20 62630426 . C T . . Sample=NA19428;GT=0/1;PCR_454_AR=1246;PCR_454_RR=1277 20 62632542 . C T . . Sample=NA18501;GT=0/1;PCR_454_AR=1203;PCR_454_RR=1150 20 62657404 . C T . . Sample=NA18612;GT=0/1;PCR_454_AR=1480;PCR_454_RR=1071 20 62700725 . G A . . Sample=NA19020;GT=0/1;PCR_454_AR=832;PCR_454_RR=815 20 62700725 . G A . . Sample=NA19036;GT=0/1;PCR_454_AR=1024;PCR_454_RR=966 20 62729481 . C T . . Sample=NA20276;GT=0/1;PCR_454_AR=401;PCR_454_RR=408 20 62899302 . T C . . Sample=HG00104;GT=0/0;PCR_454_AR=10;PCR_454_RR=871 20 62899302 . T C . . Sample=HG00128;GT=0/0;PCR_454_AR=2;PCR_454_RR=950 pysam-0.23.0/tests/tabix_data/vcf/3.vcf000066400000000000000000002545271475062545500176430ustar00rootroot00000000000000##fileformat=VCFv4.0 ##filedate=2010-06-21 ##reference=NCBI36 ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= #CHROM POS ID REF ALT QUAL FILTER INFO 1 1000153 . TCACAC TC 100 PASS AF=0.115095;HP=1;NF=16;NR=13;NS=52;CA=0;DP=615 1 1000906 . CAG CG 48 PASS AF=0.0772696;HP=1;NF=2;NR=9;NS=51;CA=0;DP=281 1 1000950 rs60561655;-/G CGG CG 100 PASS AF=0.447771;HP=5;DB;NF=10;NR=20;NS=50;CA=M;DP=291 1 1010786 rs36095298;-/G,mills,venter AC AGC 100 PASS AF=0.774334;HP=1;DB;NF=21;NR=27;NS=51;CA=0;DP=306 1 1026158 . TG TGGGGGG 100 PASS AF=0.115637;HP=1;NF=5;NR=2;NS=52;CA=0;DP=591 1 1028860 mills,venter ACTCC AC 10 PASS AF=0.0107751;HP=1;NF=5;NR=4;NS=52;CA=0;DP=522 1 1040517 . CA CAA 100 PASS AF=0.0577672;HP=1;NF=7;NR=4;NS=52;CA=0;DP=426 1 1043690 rs5772037;-/G,venter TG TGG 100 PASS AF=0.065857;HP=3;DB;NF=5;NR=8;NS=51;CA=0;DP=427 1 1049375 . TA TACACACCTGAGCACACACACCTGTGCA 100 PASS AF=0.0808078;HP=1;NF=1;NR=1;NS=51;CA=M;DP=643 1 1055459 venter ACC AC 100 PASS AF=0.936429;HP=2;NF=13;NR=24;NS=51;CA=M;DP=342 1 1056251 rs34287831;-/A,venter CT CTT 100 PASS AF=0.725164;HP=1;DB;NF=31;NR=20;NS=52;CA=0;DP=375 1 1057459 rs55853944;-/AG,venter CAGG CG 100 PASS AF=0.525146;HP=1;DB;NF=16;NR=18;NS=51;CA=0;DP=331 1 1057537 rs35574593;-/CC,watson TG TGGG 100 PASS AF=0.591248;HP=1;DB;NF=30;NR=12;NS=50;CA=0;DP=341 1 1058532 rs34990026;-/A GTT GT 100 PASS AF=0.702381;HP=4;DB;NF=29;NR=32;NS=52;CA=0;DP=405 1 1058695 rs56086046;-/GCCTGCCTGCCCGGCC,watson CGCCGCCTGCCTGCCCGG CG 100 PASS AF=0.601284;HP=1;DB;NF=24;NR=23;NS=51;CA=0;DP=365 1 1073880 . AC ACC 13 PASS AF=0.0555821;HP=2;NF=1;NR=6;NS=52;CA=0;DP=457 1 1087270 mills,venter,watson CCCCAC CC 100 PASS AF=0.990156;HP=4;NF=32;NR=27;NS=50;CA=0;DP=339 1 1088683 rs5772039;-/C,venter TCC TC 100 PASS AF=0.957928;HP=9;DB;NF=31;NR=26;NS=49;CA=0;DP=336 1 1093553 . TC TCAC 100 PASS AF=0.962343;HP=5;NF=44;NR=17;NS=51;CA=0;DP=324 1 1111698 rs57346441;-/TG,watson CA CTGA 100 PASS AF=0.0986662;HP=1;DB;NF=8;NR=5;NS=52;CA=0;DP=528 1 1117471 . GT GTT 48 PASS AF=0.04843;HP=6;NF=20;NR=8;NS=52;CA=0;DP=510 1 1118641 . CT CTTAT 38 PASS AF=0.0574453;HP=1;NF=5;NR=1;NS=51;CA=0;DP=424 1 1119225 rs60117456;-/C AC ACC 50 PASS AF=0.0255886;HP=4;DB;NF=8;NR=5;NS=52;CA=0;DP=522 1 1121774 . GCTGTTCAGACCTG GG 100 PASS AF=0.0749767;HP=1;NF=6;NR=6;NS=51;CA=0;DP=508 1 1123178 . AACA AA 14 PASS AF=0.0195065;HP=3;NF=2;NR=3;NS=49;CA=0;DP=329 1 1134362 . GGAG GG 100 PASS AF=0.142028;HP=2;NF=12;NR=17;NS=51;CA=0;DP=407 1 1140087 . TCA TA 19 PASS AF=0.0635822;HP=1;NF=2;NR=5;NS=51;CA=0;DP=446 1 1141951 . CTG CG 100 PASS AF=0.100135;HP=1;NF=7;NR=7;NS=52;CA=0;DP=463 1 1148304 rs34808371;-/GT,venter GCAC GC 100 PASS AF=0.0786699;HP=1;DB;NF=11;NR=18;NS=52;CA=0;DP=687 1 1148425 rs57524763;-/AC AACA AA 100 PASS AF=0.0744913;HP=2;DB;NF=17;NR=8;NS=51;CA=0;DP=647 1 1149524 . GTTTTAT GT 100 PASS AF=0.0475567;HP=4;NF=19;NR=14;NS=50;CA=0;DP=395 1 1150963 . CGCCACAGACACGGGCCACACACTCCACATG CG 100 PASS AF=0.111384;HP=1;NF=46;NR=28;NS=50;CA=0;DP=510 1 1151863 . GT GCT 100 PASS AF=0.126132;HP=1;NF=8;NR=7;NS=52;CA=0;DP=416 1 1153674 rs3831195;-/ACAG GG GGACAG 18 PASS AF=0.0388728;HP=2;DB;NF=3;NR=2;NS=51;CA=0;DP=418 1 1154612 . GT GCT 100 PASS AF=0.0630518;HP=1;NF=7;NR=4;NS=52;CA=0;DP=531 1 1155143 . GCAC GC 100 PASS AF=0.0991605;HP=1;NF=25;NR=23;NS=52;CA=0;DP=540 1 1155183 . CATG CG 100 PASS AF=0.0714383;HP=1;NF=5;NR=8;NS=52;CA=0;DP=527 1 1156953 rs57672822;-/ACCCCGGGA CCCCCGGGAAC CC 59 PASS AF=0.0847102;HP=5;DB;NF=5;NR=8;NS=50;CA=0;DP=312 1 1164370 . AA AACATGCATCCA 100 PASS AF=0.0550752;HP=2;NF=2;NR=1;NS=51;CA=0;DP=481 1 1166826 . AC ACC 11 PASS AF=0.0735648;HP=1;NF=1;NR=10;NS=52;CA=0;DP=379 1 1167781 rs3835300;-/T CTG CG 100 PASS AF=0.0719128;HP=1;DB;NF=3;NR=3;NS=50;CA=0;DP=360 1 1180776 rs35025185;-/T,mills CTT CT 15 PASS AF=0.0182173;HP=3;DB;NF=5;NR=1;NS=52;CA=0;DP=526 1 1184391 . GC GCAC 16 PASS AF=0.0187867;HP=1;NF=2;NR=6;NS=51;CA=M;DP=521 1 1204971 . TGG TG 100 PASS AF=0.0564084;HP=6;NF=11;NR=6;NS=50;CA=0;DP=419 1 1207801 rs35647244;-/GT,watson CC CCAC 100 PASS AF=0.034013;HP=2;DB;NF=9;NR=4;NS=52;CA=0;DP=624 1 1213486 . GTCT GT 100 PASS AF=0.504039;HP=1;NF=9;NR=5;NS=50;CA=M;DP=372 1 1217527 rs3831920;-/CTCA,watson TTGAGT TT 100 PASS AF=0.098042;HP=2;DB;NF=11;NR=14;NS=51;CA=0;DP=444 1 1224625 . AGG AG 40 PASS AF=0.0395551;HP=5;NF=4;NR=4;NS=51;CA=0;DP=406 1 1228918 rs35156558;-/GGA,venter CC CCCTC 100 PASS AF=0.999996;HP=5;DB;NF=24;NR=30;NS=49;CA=0;DP=268 1 1232491 . CTACCTGACCTTC CC 13 PASS AF=0.0510512;HP=1;NF=5;NR=5;NS=52;CA=0;DP=510 1 1236119 . CGGCTCTGGGTCACAGGTG CG 17 PASS AF=0.0581287;HP=2;NF=6;NR=8;NS=49;CA=M;DP=277 1 1245266 rs5772041;-/G,venter TGG TG 100 PASS AF=0.928175;HP=4;DB;NF=39;NR=39;NS=52;CA=0;DP=431 1 1286232 venter,watson GACA GA 100 PASS AF=0.878082;HP=1;NF=31;NR=15;NS=50;CA=0;DP=249 1 1292184 watson TG TGTGTGCAG 100 PASS AF=0.92351;HP=1;NF=36;NR=17;NS=51;CA=0;DP=633 1 1475307 rs35008066;-/G,venter GCC GC 59 PASS AF=0.0854422;HP=2;DB;NF=2;NR=3;NS=52;CA=0;DP=372 1 1476800 rs3835461;-/C AG AGG 100 PASS AF=0.239098;HP=1;DB;NF=13;NR=18;NS=52;CA=0;DP=491 1 1482738 rs34962853;-/AT,watson CATA CA 100 PASS AF=0.1747;HP=1;DB;NF=28;NR=14;NS=51;CA=0;DP=441 1 1483969 rs3835460;-/T,mills CG CAG 100 PASS AF=0.180671;HP=5;DB;NF=6;NR=13;NS=52;CA=0;DP=512 1 1484993 rs35384209;-/CT CA CAGA 100 PASS AF=0.182804;HP=1;DB;NF=9;NR=15;NS=52;CA=0;DP=441 1 1485720 . TC TCGTAC 39 PASS AF=0.0207216;HP=1;NF=1;NR=3;NS=51;CA=0;DP=498 1 1487504 rs35885836;-/AGAA,venter,watson TTTTCT TT 100 PASS AF=0.210263;HP=4;DB;NF=16;NR=20;NS=52;CA=0;DP=574 1 1490348 rs3835459;-/CATGATCCGCCTGCCTT CAAGGCAGGCGGATCATGA CA 59 PASS AF=0.230233;HP=2;DB;NF=5;NR=66;NS=51;CA=M;DP=377 1 1490873 . GT GGGCCCGACGGTGCT 100 PASS AF=0.133846;HP=1;NF=8;NR=3;NS=52;CA=0;DP=572 1 1495811 venter ACC AC 100 PASS AF=0.232263;HP=8;NF=12;NR=29;NS=52;CA=0;DP=481 1 1502734 rs35576478;-/G,venter AC ACC 100 PASS AF=0.221604;HP=4;DB;NF=16;NR=9;NS=51;CA=0;DP=388 1 1507556 . AC ACC 42 PASS AF=0.0176775;HP=1;NF=1;NR=4;NS=51;CA=0;DP=511 1 1508235 . CT CTT 100 PASS AF=0.2555;HP=1;NF=18;NR=15;NS=51;CA=0;DP=535 1 1508689 . CG CGG 100 PASS AF=0.0922424;HP=5;NF=19;NR=17;NS=51;CA=0;DP=568 1 1510533 . TTTTGT TT 100 PASS AF=0.423696;HP=7;NF=37;NR=39;NS=52;CA=0;DP=387 1 1511216 . TA TAATAATAATAAAA 39 PASS AF=0.542394;HP=2;NF=7;NR=3;NS=51;CA=0;DP=331 1 1512041 . CAAAAGTAAA CA 33 PASS AF=0.0333379;HP=4;NF=12;NR=13;NS=52;CA=0;DP=440 1 1514403 . TTTTAT TT 100 PASS AF=0.771875;HP=5;NF=24;NR=58;NS=50;CA=0;DP=243 1 1520133 rs34595829;-/GT,venter GA GACA 100 PASS AF=0.432871;HP=1;DB;NF=24;NR=19;NS=52;CA=0;DP=966 1 1520238 venter,watson TG TGAGACAG 100 PASS AF=0.606404;HP=1;NF=52;NR=36;NS=52;CA=M;DP=847 1 1520271 . CA CAGA 100 PASS AF=0.169509;HP=1;NF=48;NR=39;NS=52;CA=M;DP=736 1 1520357 . CAGAGAGA CA 100 PASS AF=0.218715;HP=1;NF=44;NR=30;NS=52;CA=M;DP=708 1 1520549 . CAGA CA 100 PASS AF=0.257166;HP=1;NF=41;NR=40;NS=52;CA=0;DP=790 1 1520595 . CAGA CA 100 PASS AF=0.107822;HP=1;NF=52;NR=44;NS=52;CA=M;DP=804 1 1520983 . GA GAGAGAGACA 34 PASS AF=0.0372679;HP=1;NF=2;NR=3;NS=52;CA=0;DP=610 1 1521139 . GA GAGACA 100 PASS AF=0.667375;HP=1;NF=10;NR=7;NS=52;CA=M;DP=537 1 1521387 . GAGACA GA 100 PASS AF=0.361313;HP=1;NF=13;NR=34;NS=52;CA=M;DP=598 1 1521833 . GACA GA 100 PASS AF=0.193306;HP=1;NF=23;NR=17;NS=52;CA=0;DP=737 1 1522371 . CC CCCTCAGCTGGACTC 100 PASS AF=0.480499;HP=3;NF=11;NR=12;NS=51;CA=0;DP=535 1 1530305 . AG AGG 15 PASS AF=0.0737746;HP=3;NF=13;NR=4;NS=51;CA=0;DP=569 1 1536491 rs36101309;-/GA ATCT AT 100 PASS AF=0.128408;HP=1;DB;NF=22;NR=14;NS=51;CA=0;DP=621 1 1537805 venter TT TCT 100 PASS AF=0.350404;HP=8;NF=3;NR=18;NS=52;CA=M;DP=419 1 1539301 . CAAAAGA CA 56 PASS AF=0.0156055;HP=4;NF=9;NR=2;NS=51;CA=0;DP=577 1 1549566 venter ATT AT 100 PASS AF=0.505899;HP=3;NF=25;NR=27;NS=52;CA=0;DP=451 1 1554815 . TGG TG 100 PASS AF=0.158582;HP=6;NF=12;NR=6;NS=48;CA=0;DP=271 1 1575329 . GCAAC GC 12 PASS AF=0.0174116;HP=1;NF=27;NR=21;NS=52;CA=0;DP=554 1 1575977 rs35072492;-/A TCC TC 100 PASS AF=0.626664;HP=3;DB;NF=23;NR=50;NS=51;CA=0;DP=361 1 1577203 venter,watson AA AAAACA 100 PASS AF=0.979791;HP=4;NF=59;NR=37;NS=52;CA=0;DP=498 1 1584062 rs5772057;-/T,venter CT CTT 100 PASS AF=0.992883;HP=1;DB;NF=34;NR=22;NS=46;CA=0;DP=291 1 1589954 . TTGT TT 100 PASS AF=0.0452889;HP=8;NF=5;NR=13;NS=51;CA=0;DP=424 1 1611607 venter ATA AA 100 PASS AF=0.528232;HP=1;NF=7;NR=10;NS=50;CA=M;DP=243 1 1615408 venter AC ACGC 100 PASS AF=0.553544;HP=9;NF=16;NR=20;NS=51;CA=M;DP=247 1 1618248 . CTGA CA 100 PASS AF=0.0412633;HP=1;NF=5;NR=2;NS=51;CA=0;DP=789 1 1637509 venter CG CTG 100 PASS AF=0.956642;HP=1;NF=57;NR=41;NS=52;CA=M;DP=533 1 1637828 rs34259364;-/AT,mills CG CATG 100 PASS AF=0.24683;HP=1;DB;NF=5;NR=57;NS=52;CA=0;DP=744 1 1638199 . GA GATGTTAA 100 PASS AF=0.962724;HP=1;NF=22;NR=22;NS=52;CA=0;DP=480 1 1638366 venter AT ATT 100 PASS AF=0.471703;HP=4;NF=50;NR=16;NS=52;CA=0;DP=738 1 1638469 rs34392519;-/AGC,mills GA GAGCA 100 PASS AF=0.428728;HP=1;DB;NF=34;NR=23;NS=52;CA=0;DP=804 1 1639339 rs36127854;-/CT,venter TA TAGA 100 PASS AF=0.27562;HP=1;DB;NF=10;NR=15;NS=52;CA=0;DP=961 1 1639610 . ATTCTC AC 59 PASS AF=0.0697107;HP=2;NF=31;NR=24;NS=52;CA=M;DP=817 1 1640937 venter CG CTCGCTCTGTCACCCAGGCTG 100 PASS AF=0.639983;HP=2;NF=4;NR=3;NS=52;CA=M;DP=638 1 1641995 rs34986248;-/ATT,venter,watson CT CTTAT 100 PASS AF=0.924551;HP=2;DB;NF=33;NR=29;NS=52;CA=0;DP=414 1 1654133 rs34171153;-/ATCG TA TATCGA 100 PASS AF=0.2409;HP=1;DB;NF=10;NR=13;NS=52;CA=0;DP=463 1 1656307 rs35516110;-/GTTT,venter GT GGTTTT 100 PASS AF=0.686901;HP=6;DB;NF=22;NR=20;NS=51;CA=0;DP=293 1 1674207 venter CC CCCTC 100 PASS AF=0.303909;HP=3;NF=26;GC;NR=29;NS=52;CA=0;DP=534 1 1675781 . TCCCTGGGACCGAAGTCGCCCCAC TC 100 PASS AF=0.270579;HP=3;NF=25;NR=24;NS=52;CA=0;DP=473 1 1679986 rs35357728;-/TG,mills,venter,watson AA AACA 100 PASS AF=0.956895;HP=4;DB;NF=60;NR=58;NS=52;CA=0;DP=520 1 1684058 . AAATGA AA 100 PASS AF=0.508762;HP=4;NF=48;NR=55;NS=52;CA=0;DP=471 1 1684177 . TG TGGGGGGGG 100 PASS AF=0.126497;HP=1;NF=5;NR=3;NS=51;CA=0;DP=449 1 1691268 rs35459537;-/AAAAACAAAAAC,mills,venter CAAAACAAAAACAA CA 100 PASS AF=0.305762;HP=4;DB;NF=54;NR=62;NS=51;CA=0;DP=443 1 1697760 mills,venter GAAACA GA 100 PASS AF=0.276545;HP=3;NF=21;NR=43;NS=52;CA=0;DP=564 1 1700966 rs34974144;-/AT,venter TT TTGT 100 PASS AF=0.37365;HP=3;DB;NF=34;NR=30;NS=52;CA=0;DP=445 1 1715347 . TG TGGGGGG 24 PASS AF=0.0415083;HP=1;NF=4;NR=5;NS=52;CA=0;DP=519 1 1717050 rs56070879;-/ACAAAAAA,venter TC TCAAAAAAAC 100 PASS AF=0.90619;HP=1;DB;NF=11;NR=7;NS=52;CA=0;DP=442 1 1729683 . ACT AT 100 PASS AF=0.104273;HP=1;NF=9;NR=11;NS=52;CA=0;DP=587 1 1729941 rs55730045;-/TTTG,watson TTTTGT TT 100 PASS AF=0.270089;HP=5;DB;NF=25;NR=44;NS=52;CA=M;DP=458 1 1733706 rs4012956;-/GT,mills,venter TA TACA 100 PASS AF=0.737658;HP=1;DB;NF=58;NR=26;NS=52;CA=M;DP=547 1 1750193 rs34820549;-/TG,venter TA TACA 100 PASS AF=0.417596;HP=1;DB;NF=42;NR=29;NS=52;CA=0;DP=495 1 1761838 . GCAC GC 17 PASS AF=0.0186129;HP=1;NF=23;NR=23;NS=52;CA=0;DP=566 1 1767123 . TACACACACACACACACACACACACACACACA TA 100 PASS AF=0.205885;HP=1;NF=32;NR=32;NS=52;CA=0;DP=560 1 1767308 . AG ATG 12 PASS AF=0.363076;HP=2;NF=25;NR=12;NS=52;CA=0;DP=611 1 1768358 . ACA AA 11 NoQCALL AF=0.0311546;HP=1;NF=1;NR=4;NS=52;CA=0;DP=502 1 1768592 . AC ACAACAAAATCCCTTTTTC 100 PASS AF=0.0974177;HP=1;NF=2;NR=5;NS=52;CA=0;DP=597 1 1769336 rs34011234;-/TA,venter,watson CT CTAT 100 PASS AF=0.385782;HP=1;DB;NF=21;NR=42;NS=52;CA=0;DP=534 1 1769673 rs56979938;-/A,venter AGA AA 21 PASS AF=0.232442;HP=1;DB;NF=9;NR=3;NS=52;CA=0;DP=465 1 1771291 . TG TGG 100 PASS AF=0.18937;HP=2;NF=5;NR=15;NS=52;CA=0;DP=590 1 1778545 . TA TAAA 100 PASS AF=0.155668;HP=3;NF=5;NR=12;NS=52;CA=0;DP=621 1 1778604 rs34483468;-/AGCC,venter GG GGGCTG 100 PASS AF=0.135521;HP=4;DB;NF=22;NR=28;NS=52;CA=0;DP=629 1 1786587 watson ACCA AA 26 PASS AF=0.0677562;HP=2;NF=15;NR=22;NS=52;CA=M;DP=404 1 1797136 rs59528461;-/C,venter TCC TC 100 PASS AF=0.94689;HP=10;DB;NF=58;NR=57;NS=52;CA=0;DP=531 1 1797791 rs35226472;-/CT,venter CG CGAG 100 PASS AF=0.383219;HP=1;DB;NF=64;NR=38;NS=52;CA=0;DP=673 1 1802225 rs34339560;-/A,mills,venter CAA CA 100 PASS AF=0.973419;HP=2;DB;NF=64;NR=71;NS=52;CA=0;DP=635 1 1802305 . GGAG GG 100 PASS AF=0.273326;HP=2;NF=41;NR=34;NS=52;CA=0;DP=695 1 1806743 . TTAGAT TT 100 PASS AF=0.179706;HP=2;NF=9;NR=6;NS=52;CA=0;DP=377 1 1809681 . AG AGG 21 PASS AF=0.133833;HP=2;NF=7;NR=3;NS=52;CA=0;DP=482 1 1810283 . AC ACC 30 PASS AF=0.0430128;HP=2;NF=4;NR=11;NS=52;CA=0;DP=523 1 1810555 . CTTAAT CT 100 PASS AF=0.0498379;HP=2;NF=9;NR=7;NS=52;CA=0;DP=521 1 1812953 rs34135959;-/TCTC CA CAGAGA 100 PASS AF=0.311555;HP=1;DB;NF=6;NR=8;NS=42;CA=0;DP=242 1 1819911 . CATG CG 100 PASS AF=0.0319085;HP=1;NF=3;NR=6;NS=52;CA=0;DP=765 1 1819947 rs60517384;-/AAGTTGGATATACACACAT CACACACATAAGTTGGATATA CA 100 PASS AF=0.0935091;HP=1;DB;NF=59;NR=69;NS=52;CA=0;DP=854 1 1825723 venter AA AAAATAAATAAATA 100 PASS AF=0.348026;HP=4;NF=9;NR=10;NS=52;CA=0;DP=373 1 1835530 . GTGAGAGTTGTTG GG 100 PASS AF=0.15298;HP=1;NF=12;NR=1;NS=51;CA=0;DP=528 1 1838692 rs5772055;-/AC,mills AA AACA 100 PASS AF=0.0441449;HP=3;DB;NF=2;NR=3;NS=51;CA=0;DP=360 1 1843475 rs3039777;-/ACTG,venter,watson TC TCTGAC 100 PASS AF=0.999998;HP=1;DB;NF=38;NR=39;NS=50;CA=0;DP=422 1 1850674 . AGG AG 100 PASS AF=0.474687;HP=3;NF=7;NR=1;NS=49;CA=0;DP=271 1 1855740 watson GT GTGTAT 100 PASS AF=0.646893;HP=1;NF=42;NR=28;NS=51;CA=0;DP=653 1 1856762 . CACAGG CG 14 PASS AF=0.0324715;HP=1;NF=1;NR=2;NS=50;CA=M;DP=379 1 1857166 . TACA TA 100 PASS AF=0.0531955;HP=1;NF=39;NR=29;NS=52;CA=0;DP=634 1 1859140 mills ACACCAGGTCCACCTCTGGACACAGGTCCACCC AC 100 PASS AF=0.180806;HP=1;NF=26;NR=15;NS=52;CA=0;DP=672 1 1859353 rs35385292;-/TC,venter ACTC AC 100 PASS AF=0.493919;HP=1;DB;NF=26;NR=38;NS=52;CA=M;DP=641 1 1859424 rs34242289;-/CA,venter TCAG TG 100 PASS AF=0.3962;HP=1;DB;NF=40;NR=32;NS=52;CA=M;DP=695 1 1859520 . TCAC TC 100 PASS AF=0.234548;HP=1;NF=26;NR=23;NS=52;CA=0;DP=729 1 1859631 rs35205487;-/GA,venter AC ACTC 100 PASS AF=0.347295;HP=1;DB;NF=15;NR=28;NS=52;CA=0;DP=710 1 1859792 rs34050188;-/AT,watson CG CATG 100 PASS AF=0.715253;HP=1;DB;NF=35;NR=44;NS=52;CA=0;DP=590 1 1864576 . CG CGG 13 PASS AF=0.0158703;HP=1;NF=3;NR=2;NS=51;CA=0;DP=556 1 1867274 rs34832935;-/C TGG TG 100 PASS AF=0.304336;HP=8;DB;NF=38;NR=23;NS=51;CA=0;DP=538 1 1869711 rs56005703;-/ATAT,watson AA AATATA 100 PASS AF=0.652198;HP=3;DB;NF=16;NR=16;NS=51;CA=0;DP=349 1 1870233 . TC TCCCTCCCTTCTTTCCTTCCCTTTCCCTCC 100 PASS AF=0.408049;HP=2;NF=11;NR=9;NS=52;CA=0;DP=814 1 1870305 . CC CCTTTCCCTCCCTTACTCCTTCCTTCCTTC 100 PASS AF=0.121733;HP=4;NF=1;NR=5;NS=52;CA=0;DP=680 1 1870363 . CT CTT 100 PASS AF=0.11398;HP=2;NF=4;NR=6;NS=52;CA=0;DP=680 1 1870863 rs35875775;-/C,venter TT TGT 100 PASS AF=0.744276;HP=2;DB;NF=43;NR=22;NS=52;CA=0;DP=455 1 1873164 . GT GTT 100 PASS AF=0.387355;HP=3;NF=20;NR=18;NS=52;CA=0;DP=523 1 1873889 rs58267869;-/AAGA AA AAAAGA 100 PASS AF=0.252999;HP=5;DB;NF=57;NR=31;NS=52;CA=0;DP=536 1 1874122 rs35595511;-/T TAA TA 100 PASS AF=0.338059;HP=9;DB;NF=38;NR=38;NS=51;CA=0;DP=519 1 1876064 watson AG AGAGTG 100 PASS AF=0.0829624;HP=1;NF=6;NR=5;NS=52;CA=0;DP=465 1 1876204 . AC ACAGC 100 PASS AF=0.256855;HP=1;NF=14;NR=10;NS=52;CA=0;DP=483 1 1876616 . GC GCTGGTGCGCGTC 100 PASS AF=0.0656988;HP=1;NF=5;NR=2;NS=51;CA=0;DP=420 1 1876971 rs3838975;-/G GCC GC 21 PASS AF=0.201137;HP=2;DB;NF=15;NR=6;NS=52;CA=0;DP=439 1 1877704 . CCTGC CC 19 PASS AF=0.0183173;HP=2;NF=7;NR=13;NS=52;CA=0;DP=436 1 1884832 rs34937714;-/T CA CAA 100 PASS AF=0.254902;HP=3;DB;NF=27;NR=6;NS=52;CA=0;DP=449 1 1886549 rs3838974;-/T GG GAG 100 PASS AF=0.153123;HP=4;DB;NF=11;NR=10;NS=52;CA=0;DP=456 1 1889260 rs55954278;-/ATGA GT GTGAAT 100 PASS AF=0.630203;HP=1;DB;NF=12;NR=17;NS=52;CA=0;DP=656 1 1889311 . GTGAAT GT 100 PASS AF=0.167491;HP=1;NF=33;NR=18;NS=52;CA=0;DP=606 1 1889402 rs34520694;-/GTGA AT ATGAGT 100 PASS AF=0.306146;HP=1;DB;NF=24;NR=32;NS=52;CA=0;DP=916 1 1889884 rs56985589;-/G TGC TC 100 PASS AF=0.347999;HP=1;DB;NF=20;NR=28;NS=51;CA=0;DP=537 1 1889966 rs61233860;-/CCT,watson TC TCTCC 100 PASS AF=0.211403;HP=1;DB;NF=12;NR=14;NS=52;CA=0;DP=554 1 1892548 . ACTC AC 21 PASS AF=0.0207771;HP=1;NF=4;NR=3;NS=52;CA=0;DP=750 1 1900826 . AACA AA 100 PASS AF=0.122368;HP=2;NF=13;NR=6;NS=52;CA=M;DP=435 1 1908846 venter CT CTT 100 PASS AF=0.30139;HP=10;NF=11;NR=28;NS=51;CA=0;DP=350 1 1910458 . TGAG TG 15 PASS AF=0.0208928;HP=1;NF=23;NR=12;NS=52;CA=0;DP=514 1 1927207 rs61162553;-/GTTCTCTCTCTCTCTCTCTC,venter CTCTCTCTCTCTCTCTCTCGTT CT 100 PASS AF=0.399955;HP=1;DB;NF=34;NR=47;NS=51;CA=0;DP=427 1 1929307 rs36066718;-/T CAA CA 30 PASS AF=0.114706;HP=10;DB;NF=24;NR=15;NS=52;CA=0;DP=520 1 1933578 . CA CAAAATAAAATA 100 PASS AF=0.562689;HP=4;NF=21;NR=28;NS=52;CA=0;DP=359 1 1947079 rs3831907;-/C CGG CG 100 PASS AF=0.131218;HP=3;DB;NF=4;NR=10;NS=52;CA=0;DP=316 1 1949721 rs35354651;-/G GC GCC 100 PASS AF=0.218024;HP=1;DB;NF=11;NR=5;NS=51;CA=0;DP=306 1 1965555 rs56225932;-/CA,venter TACA TA 100 PASS AF=0.743144;HP=1;DB;NF=50;NR=67;NS=52;CA=0;DP=679 1 1966402 venter,watson GC GCCGCC 100 PASS AF=0.988372;HP=2;NF=36;NR=16;NS=46;CA=0;DP=232 1 1989567 . AC ACC 12 PASS AF=0.0334278;HP=6;NF=10;NR=9;NS=52;CA=0;DP=367 1 1992350 . CA CACCTGGGCGTGTGA 56 PASS AF=0.19029;HP=1;NF=6;NR=3;NS=52;CA=0;DP=412 1 1993852 rs34106910;-/G,venter GCC GC 100 PASS AF=0.178292;HP=2;DB;NF=15;NR=7;NS=51;CA=0;DP=388 1 1996153 . GT GTT 59 PASS AF=0.126167;HP=8;NF=7;NR=14;NS=51;CA=0;DP=436 1 2010531 rs35300904;-/C,venter CA CGA 100 PASS AF=0.2131;HP=1;DB;NF=18;NR=7;NS=52;CA=0;DP=418 1 2019409 rs55716481;-/AGTGACTAAGGTGACCAGG,venter CA CAGGTGACCAGGAGTGACTAA 100 PASS AF=0.901172;HP=1;DB;NF=17;NR=16;NS=52;CA=0;DP=600 1 2019867 rs58602729;-/CT CCTC CC 100 PASS AF=0.15521;HP=3;DB;NF=6;NR=12;NS=52;CA=0;DP=542 1 2019961 mills CGTTTTGTTTTG CG 100 PASS AF=0.239816;HP=1;NF=44;NR=59;NS=52;CA=0;DP=513 1 2027926 . CT CTT 100 PASS AF=0.591615;HP=1;NF=7;NR=4;NS=51;CA=M;DP=262 1 2028042 . CT CTT 100 PASS AF=0.242884;HP=1;NF=28;NR=12;NS=51;CA=M;DP=738 1 2031773 . GA GGGTA 100 PASS AF=0.197429;HP=1;NF=15;NR=7;NS=51;CA=0;DP=405 1 2036771 . AC ACCCC 100 PASS AF=0.173415;HP=3;NF=1;NR=5;NS=52;CA=0;DP=532 1 2040362 venter CT CTT 100 PASS AF=0.61548;HP=3;NF=31;NR=33;NS=52;CA=0;DP=522 1 2042747 . CG CGGGGG 100 PASS AF=0.132985;HP=2;NF=11;NR=6;NS=51;CA=0;DP=880 1 2042976 . GT GTTATT 100 PASS AF=0.225391;HP=2;NF=13;NR=25;NS=51;CA=M;DP=882 1 2045297 . GT GTAGTTATT 36 PASS AF=0.513037;HP=2;NF=5;NR=16;NS=46;CA=M;DP=269 1 2048642 rs56348719;-/A CAG CG 100 PASS AF=0.626672;HP=1;DB;NF=15;NR=37;NS=51;CA=0;DP=337 1 2055895 watson AT AATT 100 PASS AF=0.183323;HP=1;NF=10;NR=14;NS=52;CA=0;DP=511 1 2058884 watson GCCTC GC 100 PASS AF=0.258368;HP=2;NF=23;NR=18;NS=51;CA=0;DP=533 1 2068674 . CTCTAT CT 100 PASS AF=0.0693035;HP=1;NF=7;NR=5;NS=52;CA=0;DP=600 1 2076576 . GTGAT GT 100 PASS AF=0.0691863;HP=1;NF=32;NR=24;NS=52;CA=0;DP=918 1 2076741 . GTGAT GT 49 PASS AF=0.200249;HP=1;NF=13;NR=21;NS=51;CA=0;DP=758 1 2076895 . GTGAT GT 100 PASS AF=0.134423;HP=1;NF=21;NR=19;NS=51;CA=0;DP=658 1 2076954 rs60433546;-/ATG AA AATGA 100 PASS AF=0.310432;HP=2;DB;NF=12;NR=27;NS=52;CA=0;DP=664 1 2079377 rs3835418;-/T CT CTT 100 PASS AF=0.201153;HP=1;DB;NF=13;NR=15;NS=52;CA=0;DP=451 1 2081537 rs56068331;-/GTGT CGTGTG CG 13 PASS AF=0.276967;HP=1;DB;NF=58;NR=66;NS=52;CA=0;DP=516 1 2085600 rs3835419;-/CTGGGCCAACCC GA GACCCCTGGGCCAA 100 PASS AF=0.243746;HP=1;DB;NF=11;NR=6;NS=52;CA=0;DP=535 1 2087974 . GCC GC 15 PASS AF=0.0623565;HP=8;NF=7;NR=14;NS=52;CA=0;DP=325 1 2089182 rs34571180;-/CTC,mills,venter GCCTC GC 100 PASS AF=0.116512;HP=2;DB;NF=9;NR=4;NS=51;CA=0;DP=440 1 2089950 . CG CGGGG 100 PASS AF=0.178382;HP=2;NF=20;NR=7;NS=51;CA=0;DP=444 1 2091793 rs56317708;-/GATA,venter,watson AA AAGATA 100 PASS AF=0.896718;HP=2;DB;NF=37;NR=55;NS=52;CA=0;DP=525 1 2094394 watson TCCACC TC 100 PASS AF=0.191274;HP=2;NF=15;NR=11;NS=52;CA=0;DP=554 1 2099298 . TG TGG 100 PASS AF=0.234547;HP=1;NF=15;NR=4;NS=51;CA=0;DP=434 1 2101678 . AGACG AG 100 PASS AF=0.0220699;HP=1;NF=10;NR=4;NS=51;CA=0;DP=533 1 2104518 rs55672189;-/CGTCTC,venter AG AGTCTCCG 32 PASS AF=0.0318159;HP=1;DB;NF=1;NR=2;NS=51;CA=0;DP=303 1 2110593 rs34825103;-/C TG TGG 100 PASS AF=0.0674605;HP=1;DB;NF=1;NR=4;NS=52;CA=M;DP=336 1 2114205 . TT TTTGT 14 PASS AF=0.0440601;HP=4;NF=24;NR=27;NS=52;CA=0;DP=414 1 2118677 rs35613376;-/T,venter GA GAA 100 PASS AF=0.110597;HP=1;DB;NF=4;NR=6;NS=51;CA=0;DP=395 1 2129208 venter CGTGTGTGTGTGTGTGTGTGTG CG 100 PASS AF=0.312577;HP=1;NF=50;NR=42;NS=51;CA=0;DP=395 1 2136104 rs34745034;-/AC,venter,watson CTGT CT 100 PASS AF=0.148774;HP=1;DB;NF=9;NR=15;NS=51;CA=0;DP=394 1 2147798 . CGG CG 100 PASS AF=0.069257;HP=5;NF=3;NR=7;NS=51;CA=0;DP=433 1 2156467 rs34646035;-/A,venter GG GTG 100 PASS AF=0.0650203;HP=2;DB;NF=3;NR=2;NS=51;CA=0;DP=299 1 2163248 rs34969427;-/CA,venter,watson CT CTGT 59 PASS AF=0.323344;HP=1;DB;NF=36;NR=42;NS=52;CA=0;DP=622 1 2168152 rs34184068;-/C TG TGG 100 PASS AF=0.267631;HP=8;DB;NF=12;NR=25;NS=52;CA=0;DP=462 1 2173905 rs59705675;-/C,venter GCC GC 100 PASS AF=0.519185;HP=4;DB;NF=28;NR=31;NS=52;CA=0;DP=472 1 2178426 . ATCTCT AT 59 PASS AF=0.0153899;HP=1;NF=1;NR=2;NS=52;CA=0;DP=558 1 2180516 . TG TGGG 15 PASS AF=0.10873;HP=1;NF=7;NR=3;NS=52;CA=0;DP=495 1 2193017 rs35691128;-/C,venter TG TGG 100 PASS AF=0.296206;HP=9;DB;NF=9;NR=11;NS=52;CA=0;DP=367 1 2204648 . AGGGG AG 100 PASS AF=0.0847086;HP=8;NF=9;NR=7;NS=52;CA=0;DP=441 1 2211603 . TG TGGGGGGGGGG 100 PASS AF=0.176;HP=1;NF=5;NR=9;NS=52;CA=0;DP=507 1 2211835 rs35471620;-/C,venter CG CGG 100 PASS AF=0.403922;HP=3;DB;NF=20;NR=20;NS=51;CA=0;DP=363 1 2213004 rs35841716;-/G,mills,venter TGG TG 100 PASS AF=0.938006;HP=7;DB;NF=35;NR=9;NS=52;CA=0;DP=297 1 2214726 . GC GCC 100 PASS AF=0.415474;HP=9;NF=18;NR=19;NS=51;CA=0;DP=416 1 2220552 rs35472917;-/C,venter AGG AG 100 PASS AF=0.609848;HP=9;DB;NF=24;NR=22;NS=51;CA=0;DP=385 1 2221276 . GC GCC 23 PASS AF=0.0895016;HP=2;NF=1;NR=11;NS=50;CA=0;DP=396 1 2222657 . AC ACC 16 PASS AF=0.0530452;HP=2;NF=1;NR=3;NS=51;CA=0;DP=404 1 2223900 . CAGGA CA 100 PASS AF=0.105506;HP=1;NF=9;NR=6;NS=52;CA=0;DP=517 1 2232109 . CAGG CG 100 PASS AF=0.220422;HP=1;NF=14;NR=13;NS=51;CA=0;DP=430 1 2233476 rs34394327;-/CGTTT,mills,venter,watson CC CCGTTTC 100 PASS AF=0.982218;HP=3;DB;NF=18;NR=31;NS=52;CA=0;DP=378 1 2238242 rs56200665;-/C,mills GG GCG 100 PASS AF=0.745403;HP=4;DB;NF=37;NR=40;NS=51;CA=0;DP=419 1 2242260 rs34121936;-/C AGG AG 100 PASS AF=0.107749;HP=4;DB;NF=7;NR=6;NS=51;CA=0;DP=427 1 2246276 rs61120130;-/TGC,venter GG GGCTG 100 PASS AF=0.447977;HP=3;DB;NF=13;NR=17;NS=51;CA=0;DP=403 1 2246469 . TT TTCCCTCCCTTCCTTCCTTCCCTCCCT 100 PASS AF=0.0710328;HP=3;NF=8;NR=6;NS=51;CA=B;DP=731 1 2246586 rs59175712;-/CT CC CCTC 100 PASS AF=0.378253;HP=2;DB;NF=33;NR=29;NS=50;CA=0;DP=515 1 2248450 rs61135926;-/CACA AA AACACA 100 PASS AF=0.367115;HP=3;DB;NF=24;NR=19;NS=51;CA=0;DP=445 1 2248486 . CAGA CA 100 PASS AF=0.108968;HP=1;NF=14;NR=11;NS=51;CA=M;DP=382 1 2248806 rs59142249;-/A CA CAA 100 PASS AF=0.0756571;HP=1;DB;NF=4;NR=12;NS=51;CA=0;DP=728 1 2255198 . TGCTGGAAAGAACAG TG 100 PASS AF=0.115149;HP=1;NF=9;NR=12;NS=51;CA=0;DP=470 1 2267148 . ACACACAGA AA 100 PASS AF=0.128331;HP=1;NF=4;NR=6;NS=51;CA=0;DP=681 1 2268675 . TG TGG 10 PASS AF=0.0406249;HP=1;NF=7;NR=3;NS=52;CA=0;DP=508 1 2269958 . GCACGCACACGCAC GC 40 PASS AF=0.0297002;HP=1;NF=6;NR=7;NS=50;CA=0;DP=288 1 2270248 . CCTG CG 100 PASS AF=0.21901;HP=4;NF=14;NR=17;NS=52;CA=0;DP=478 1 2272049 . AGGGGTGGCACGG AG 100 PASS AF=0.0657391;HP=4;NF=20;NR=19;NS=52;CA=0;DP=465 1 2272576 rs35424701;-/T TA TAA 100 PASS AF=0.0794139;HP=1;DB;NF=5;NR=5;NS=51;CA=0;DP=426 1 2273487 . TAA TA 10 PASS AF=0.0158231;HP=10;NF=25;NR=9;NS=51;CA=0;DP=564 1 2282631 rs59328016;-/G AG AGG 100 PASS AF=0.230902;HP=1;DB;NF=1;NR=6;NS=52;CA=M;DP=310 1 2282847 rs34534255;-/AG AC ACTC 100 PASS AF=0.108076;HP=1;DB;NF=5;NR=4;NS=50;CA=0;DP=293 1 2284162 . CA CAA 12 PASS AF=0.0508845;HP=10;NF=7;NR=7;NS=52;CA=0;DP=406 1 2285124 . TAAAAA TA 100 PASS AF=0.226133;HP=8;NF=14;NR=5;NS=52;CA=0;DP=315 1 2288255 rs56670882;-/TACATAGAAAAA,venter,watson CAAAATACATAGAA CA 100 PASS AF=0.154865;HP=4;DB;NF=46;NR=50;NS=51;CA=0;DP=466 1 2291012 venter ATAATT AT 100 PASS AF=0.140631;HP=1;NF=7;NR=9;NS=51;CA=0;DP=365 1 2292525 rs60502597;-/CACAACAAC,venter CA CACAACCACAA 100 PASS AF=0.411828;HP=1;DB;NF=18;NR=3;NS=52;CA=0;DP=515 1 2305015 rs35699260;-/T,venter CAG CG 100 PASS AF=0.283002;HP=1;DB;NF=14;NR=17;NS=51;CA=0;DP=451 1 2310430 . AA AAAGA 100 PASS AF=0.382413;HP=6;NF=20;NR=11;NS=52;CA=0;DP=408 1 2314333 venter CG CGGACGCCAGGCAGAGGACTTCATCCCAGGCTTCAGTGCTCCTG 100 PASS AF=0.736856;HP=2;NF=1;NR=2;NS=52;CA=0;DP=679 1 2319273 rs57204595;-/C ACC AC 100 PASS AF=0.125223;HP=2;DB;NF=7;NR=13;NS=52;CA=0;DP=523 1 2322519 . TCCT TT 100 PASS AF=0.200476;HP=2;NF=2;NR=10;NS=50;CA=0;DP=413 1 2322562 . TCCACCCTCC TC 100 PASS AF=0.3747;HP=2;NF=8;NR=15;NS=51;CA=0;DP=325 1 2322680 . CT CTT 100 PASS AF=0.284453;HP=1;NF=26;NR=24;NS=52;CA=M;DP=388 1 2323804 venter TC TCC 100 PASS AF=0.865363;HP=3;NF=38;NR=47;NS=50;CA=0;DP=438 1 2325452 . CG CGG 39 PASS AF=0.0242463;HP=3;NF=5;NR=8;NS=51;CA=0;DP=547 1 2332518 . GA GAA 100 PASS AF=0.0862532;HP=1;NF=5;NR=13;NS=51;CA=0;DP=414 1 2337697 rs55744642;-/CGACA,venter,watson GG GGGACAG 100 PASS AF=0.867582;HP=3;DB;NF=16;NR=23;NS=51;CA=0;DP=383 1 2338712 rs34210450;-/AGCTTCCC,mills,venter GC GCCCAGCTTC 100 PASS AF=0.431742;HP=3;DB;NF=24;NR=15;NS=52;CA=0;DP=504 1 2341261 . TCC TC 20 PASS AF=0.13716;HP=9;NF=4;NR=20;NS=51;CA=0;DP=258 1 2343280 rs60532031;-/AAAAG,watson GA GAAGAAA 100 PASS AF=0.0544808;HP=2;DB;NF=2;NR=10;NS=49;CA=0;DP=348 1 2343570 venter AA AAAACA 100 PASS AF=0.0882931;HP=6;NF=28;NR=18;NS=52;CA=0;DP=434 1 2344468 . TTTTGT TT 100 PASS AF=0.233529;HP=7;NF=49;NR=55;NS=52;CA=0;DP=493 1 2345597 rs35560781;-/T,venter TAA TA 100 PASS AF=0.501718;HP=6;DB;NF=36;NR=26;NS=52;CA=0;DP=532 1 2352446 . CGTG CG 16 PASS AF=0.0185013;HP=1;NF=10;NR=25;NS=52;CA=0;DP=432 1 2352629 rs35263617;-/CA,venter CG CGTG 100 PASS AF=0.4693;HP=1;DB;NF=44;NR=38;NS=51;CA=0;DP=539 1 2355283 rs35314501;-/G TC TCC 100 PASS AF=0.408524;HP=4;DB;NF=21;NR=18;NS=52;CA=0;DP=436 1 2356275 rs34090130;-/G,mills AGG AG 100 PASS AF=0.172214;HP=6;DB;NF=16;NR=9;NS=51;CA=0;DP=415 1 2356753 rs58056215;-/TGGAGGC TGGCTGGAG TG 100 PASS AF=0.178356;HP=2;DB;NF=43;NR=59;NS=51;CA=0;DP=429 1 2357119 . TGG TG 100 PASS AF=0.179635;HP=6;NF=12;NR=18;NS=52;CA=0;DP=495 1 2357323 . TCCCT TT 100 PASS AF=0.0931072;HP=3;NF=8;NR=9;NS=52;CA=0;DP=484 1 2357636 . CTCCACCTTT CT 100 PASS AF=0.252701;HP=1;NF=11;NR=9;NS=47;CA=M;DP=266 1 2358758 . CAA CA 26 PASS AF=0.0241071;HP=3;NF=1;NR=3;NS=51;CA=0;DP=486 1 2360543 rs34299371;-/G,venter GCC GC 100 PASS AF=0.460241;HP=7;DB;NF=18;NR=28;NS=51;CA=0;DP=403 1 2365835 rs35499456;-/A GT GTT 100 PASS AF=0.299753;HP=3;DB;NF=19;NR=20;NS=52;CA=0;DP=431 1 2370798 . AAACCA AA 100 PASS AF=0.315002;HP=4;NF=56;NR=52;NS=52;CA=0;DP=505 1 2379981 rs35697743;-/C,venter TGC TC 100 PASS AF=0.0396508;HP=1;DB;NF=1;NR=5;NS=50;CA=0;DP=425 1 2383170 rs35931789;-/T,venter CC CAC 100 PASS AF=0.441832;HP=7;DB;NF=24;NR=21;NS=52;CA=0;DP=453 1 2383775 . ACC AC 19 PASS AF=0.0298335;HP=5;NF=6;NR=2;NS=52;CA=0;DP=442 1 2388741 watson GCCTTCCTCAC GC 100 PASS AF=0.134128;HP=2;NF=6;NR=9;NS=47;CA=0;DP=257 1 2394261 rs34886292;-/T,venter CA CAA 100 PASS AF=0.640008;HP=1;DB;NF=28;NR=33;NS=51;CA=0;DP=459 1 2395694 venter AGG AG 100 PASS AF=0.518622;HP=3;NF=29;NR=23;NS=50;CA=0;DP=387 1 2406522 rs35886782;-/CTCTGGACGCT,venter,watson TG TGCTCTCTGGACG 100 PASS AF=0.531691;HP=1;DB;NF=12;NR=19;NS=51;CA=0;DP=452 1 2429911 rs3831090;-/AT,mills TT TTAT 100 PASS AF=0.138967;HP=3;DB;NF=24;NR=13;NS=52;CA=0;DP=328 1 2458287 . CGTG CG 100 PASS AF=0.0696687;HP=1;NF=38;NR=32;NS=52;CA=0;DP=613 1 2458465 . AGTG AG 31 PASS AF=0.0212179;HP=1;NF=18;NR=32;NS=51;CA=0;DP=600 1 2460527 . TG TGCGGCCCATCTCAG 51 PASS AF=0.164756;HP=1;NF=1;NR=4;NS=51;CA=0;DP=496 1 2477778 . AC ACCC 100 PASS AF=0.157812;HP=2;NF=2;NR=11;NS=51;CA=0;DP=389 1 2501833 rs34000217;-/ATT AA AAATA 100 PASS AF=0.437274;HP=5;DB;NF=19;NR=23;NS=51;CA=0;DP=337 1 2503512 rs59345997;-/CAAA AAAACA AA 100 PASS AF=0.46764;HP=4;DB;NF=44;NR=29;NS=52;CA=0;DP=456 1 2506681 . TG TGGG 46 PASS AF=0.310909;HP=9;NF=14;NR=8;NS=51;CA=0;DP=273 1 2513520 rs5772070;-/G,mills CGG CG 100 PASS AF=0.652792;HP=8;DB;NF=8;NR=34;NS=51;CA=0;DP=275 1 2517761 . TGC TC 100 PASS AF=0.0839269;HP=1;NF=3;NR=6;NS=50;CA=0;DP=359 1 2520201 rs34705971;-/C,venter AG AGG 100 PASS AF=0.612406;HP=1;DB;NF=42;NR=46;NS=52;CA=0;DP=518 1 2521983 . TCAAACAAACAAAC TC 100 PASS AF=0.365407;HP=1;NF=35;NR=29;NS=52;CA=0;DP=501 1 2522019 . CT CTGTT 100 PASS AF=0.523695;HP=1;NF=28;NR=12;NS=52;CA=0;DP=410 1 2522313 rs34791736;-/A,venter CT CTT 100 PASS AF=0.621139;HP=1;DB;NF=47;NR=24;NS=52;CA=0;DP=472 1 2524952 rs35090174;-/CT ACTC AC 100 PASS AF=0.224915;HP=1;DB;NF=19;NR=15;NS=51;CA=0;DP=517 1 2529806 . CATA CA 100 PASS AF=0.236462;HP=1;NF=22;NR=13;NS=51;CA=0;DP=625 1 2529841 . CACATA CA 100 PASS AF=0.190786;HP=1;NF=20;NR=19;NS=51;CA=0;DP=663 1 2530205 rs61132608;-/CATATA,watson CA CACATATA 100 PASS AF=0.547698;HP=1;DB;NF=20;NR=28;NS=52;CA=0;DP=660 1 2543402 rs5772073;-/GAG,mills TAGGA TA 100 PASS AF=0.24689;HP=1;DB;NF=12;NR=31;NS=52;CA=0;DP=543 1 2547236 rs58240187;-/AGA,venter,watson GG GGAAG 100 PASS AF=0.531939;HP=2;DB;NF=25;NR=25;NS=52;CA=0;DP=444 1 2551119 rs35955733;-/CCC,venter,watson GCCCC GC 100 PASS AF=0.606107;HP=9;DB;NF=24;NR=35;NS=52;CA=0;DP=492 1 2551885 rs36036408;-/AC,venter CGTG CG 100 PASS AF=0.356574;HP=1;DB;NF=39;NR=38;NS=52;CA=0;DP=803 1 2552076 . CGTG CG 100 PASS AF=0.066645;HP=1;NF=25;NR=15;NS=51;CA=0;DP=782 1 2552384 . CTGT CT 12 PASS AF=0.0121638;HP=1;NF=13;NR=25;NS=52;CA=0;DP=612 1 2556252 . ACACTC AC 59 PASS AF=0.143579;HP=1;NF=12;NR=9;NS=49;CA=0;DP=331 1 2578474 . CCACACCCCCAG CG 100 PASS AF=0.930867;HP=3;NF=16;NR=12;NS=51;CA=M;DP=281 1 2688911 rs34425096;-/TC,venter TTCT TT 100 PASS AF=0.26327;HP=5;DB;NF=17;NR=12;NS=52;CA=0;DP=451 1 2691366 rs36213670;-/CTCTGGGCCA,mills,venter GCTCTGGGCCAC GC 39 PASS AF=0.191253;HP=1;DB;NF=21;NR=36;NS=52;CA=0;DP=344 1 2691723 rs57511628;-/ACCCCAGGAGATCCCTGC TA TACCCCAGGAGATCCCTGCA 100 PASS AF=0.332823;HP=1;DB;NF=6;NR=7;NS=52;CA=0;DP=453 1 2703254 . CA CAA 100 PASS AF=0.111948;HP=3;NF=8;NR=13;NS=51;CA=0;DP=502 1 2703885 . AC ACC 100 PASS AF=0.0959517;HP=6;NF=24;NR=11;NS=51;CA=0;DP=531 1 2725125 rs34936518;-/C,venter GCT GT 100 PASS AF=0.375093;HP=1;DB;NF=33;NR=32;NS=52;CA=0;DP=621 1 2725735 . AACACA AA 24 PASS AF=0.0139746;HP=2;NF=16;NR=4;NS=51;CA=0;DP=639 1 2726135 rs34620269;-/CA GCAC GC 100 PASS AF=0.0410325;HP=1;DB;NF=28;NR=22;NS=52;CA=0;DP=626 1 2726213 . GC GCAC 13 PASS AF=0.0257105;HP=1;NF=8;NR=9;NS=52;CA=0;DP=552 1 2746483 . AC ACC 40 PASS AF=0.0544668;HP=1;NF=4;NR=12;NS=51;CA=0;DP=544 1 2747281 . TG TGAGAG 100 PASS AF=0.152256;HP=1;NF=11;NR=8;NS=52;CA=0;DP=855 1 2754002 rs36202379;-/CTGCTTGT,mills,watson ATTGTCTGCT AT 100 PASS AF=0.260861;HP=2;DB;NF=32;NR=35;NS=52;CA=0;DP=496 1 2755160 rs34916159;-/A TA TAA 100 PASS AF=0.532865;HP=7;DB;NF=10;NR=34;NS=52;CA=0;DP=533 1 2755983 . GCC GC 100 PASS AF=0.106339;HP=3;NF=18;NR=26;NS=52;CA=M;DP=700 1 2765711 . AA AAGGAAGGA 100 PASS AF=0.686149;HP=2;NF=11;NR=8;NS=50;CA=0;DP=364 1 2765863 . AG AGG 100 PASS AF=0.999885;HP=1;NF=14;NR=36;NS=49;CA=0;DP=364 1 2765952 . AG AGG 100 PASS AF=0.0789769;HP=1;NF=29;NR=29;NS=51;CA=B;DP=851 1 2779479 . TTTTCTTCTCTTTCT TT 100 PASS AF=0.712577;HP=4;NF=29;NR=22;NS=50;CA=0;DP=322 1 2794338 rs34131736;-/T CTG CG 100 PASS AF=0.089184;HP=1;DB;NF=7;NR=4;NS=51;CA=0;DP=440 1 2801123 . TCCTCCCCACCCTGAC TC 48 PASS AF=0.0412327;HP=2;NF=13;NR=18;NS=51;CA=0;DP=343 1 2803308 watson CATG CG 100 PASS AF=0.160766;HP=1;NF=23;NR=20;NS=52;CA=0;DP=816 1 2805468 rs56260225;-/ACAA AAAACA AA 100 PASS AF=0.859977;HP=4;DB;NF=62;NR=35;NS=51;CA=0;DP=433 1 2806441 rs34966309;-/G CG CGG 100 PASS AF=0.211987;HP=4;DB;NF=20;NR=11;NS=52;CA=0;DP=441 1 2810388 . GCC GC 100 PASS AF=0.11183;HP=2;NF=8;NR=5;NS=51;CA=0;DP=431 1 2822166 . TACATGCACACA TA 100 PASS AF=0.150719;HP=1;NF=43;NR=52;NS=52;CA=0;DP=844 1 2822270 rs59677991;-/GC GGCG GG 18 NoQCALL AF=0.0194725;HP=2;DB;NF=15;NR=5;NS=52;CA=0;DP=806 1 2822473 . CACACAC CC 100 PASS AF=0.138944;HP=1;NF=6;NR=7;NS=52;CA=0;DP=951 1 2827616 . CAAGC CC 52 PASS AF=0.132317;HP=2;NF=8;NR=4;NS=51;CA=0;DP=300 1 2828576 . CG CTG 100 PASS AF=0.168378;HP=1;NF=8;NR=2;NS=52;CA=0;DP=325 1 2829365 rs35758696;-/A TAA TA 100 PASS AF=0.216995;HP=6;DB;NF=20;NR=20;NS=51;CA=0;DP=531 1 2833106 . TG TGTTGGG 100 PASS AF=0.237115;HP=1;NF=11;NR=4;NS=52;CA=0;DP=336 1 2834384 . AC ACC 32 PASS AF=0.0617917;HP=1;NF=3;NR=5;NS=52;CA=0;DP=592 1 2835704 rs35824541;-/G AGG AG 100 PASS AF=0.188967;HP=3;DB;NF=15;NR=11;NS=52;CA=0;DP=691 1 2836635 rs56691957;-/AT CATG CG 100 PASS AF=0.126742;HP=1;DB;NF=8;NR=13;NS=52;CA=0;DP=611 1 2851063 . ATGTGTGTCT AT 100 PASS AF=0.224053;HP=1;NF=34;NR=32;NS=52;CA=0;DP=798 1 2859183 rs34869376;-/CT ACTC AC 100 PASS AF=0.228335;HP=1;DB;NF=11;NR=14;NS=52;CA=0;DP=446 1 2859269 rs34009406;-/C AC ACC 100 PASS AF=0.168197;HP=2;DB;NF=8;NR=14;NS=52;CA=0;DP=460 1 2862455 rs34488344;-/T GT GTT 100 PASS AF=0.140555;HP=10;DB;NF=25;NR=16;NS=52;CA=0;DP=484 1 2866073 . AC ACC 56 PASS AF=0.0758065;HP=1;NF=2;NR=11;NS=51;CA=0;DP=513 1 2871504 . TA TACTAA 100 PASS AF=0.128765;HP=1;NF=11;NR=12;NS=52;CA=0;DP=676 1 2871601 rs60410855;-/TCCA CC CCCATC 100 PASS AF=0.11635;HP=3;DB;NF=19;NR=14;NS=52;CA=0;DP=682 1 2874709 . GT GTT 100 PASS AF=0.138394;HP=9;NF=8;NR=12;NS=51;CA=0;DP=534 1 2876814 rs5772089;-/A,mills,venter GG GAG 100 PASS AF=0.999994;HP=10;DB;NF=39;NR=42;NS=50;CA=0;DP=343 1 2877421 rs35085736;-/C,venter GC GCC 100 PASS AF=0.582204;HP=6;DB;NF=29;NR=37;NS=50;CA=0;DP=426 1 2881114 . GG GTG 100 PASS AF=0.586283;HP=5;NF=16;NR=5;NS=47;CA=M;DP=256 1 2883970 . GG GCG 16 PASS AF=0.516075;HP=4;NF=6;NR=2;NS=51;CA=M;DP=332 1 2885504 . TCC TC 29 PASS AF=0.140908;HP=9;NF=12;NR=8;NS=51;CA=0;DP=353 1 2886983 . AG AGG 50 PASS AF=0.0436199;HP=3;NF=7;NR=2;NS=50;CA=0;DP=401 1 2887864 rs57379840;-/T,venter CG CTG 100 PASS AF=0.770236;HP=2;DB;NF=41;NR=25;NS=51;CA=0;DP=375 1 2892284 . CAT CT 100 PASS AF=0.0885935;HP=1;NF=23;NR=17;NS=52;CA=0;DP=685 1 2892433 venter AT ATCCATCCTCCATCCT 100 PASS AF=0.814532;HP=1;NF=13;NR=12;NS=52;CA=0;DP=620 1 2892472 . CCCATC CC 100 PASS AF=0.181828;HP=3;NF=50;NR=61;NS=52;CA=0;DP=633 1 2899352 . CTA CA 100 PASS AF=0.0433393;HP=1;NF=5;NR=2;NS=51;CA=0;DP=512 1 2902379 . TAGA TA 40 PASS AF=0.0165292;HP=1;NF=3;NR=2;NS=51;CA=0;DP=476 1 2903930 rs36097640;-/A TAA TA 12 PASS AF=0.0522384;HP=8;DB;NF=13;NR=15;NS=51;CA=0;DP=535 1 2907194 rs35693840;-/G AG AGG 100 PASS AF=0.136995;HP=5;DB;NF=14;NR=8;NS=52;CA=0;DP=516 1 2916313 . AC ACC 40 PASS AF=0.0606632;HP=1;NF=1;NR=13;NS=52;CA=0;DP=529 1 2923107 . GA GGGGGGAA 35 PASS AF=0.311458;HP=1;NF=1;NR=2;NS=50;CA=0;DP=285 1 2923994 . AAGGA AA 100 PASS AF=0.136914;HP=3;NF=4;NR=16;NS=52;CA=0;DP=475 1 2926544 rs58065168;-/G TG TGG 100 PASS AF=0.231871;HP=7;DB;NF=23;NR=13;NS=51;CA=0;DP=445 1 2927774 . GTCT GT 100 PASS AF=0.039848;HP=1;NF=24;NR=39;NS=52;CA=0;DP=466 1 2928267 rs4013154;-/TCT CAGAA CA 100 PASS AF=0.176094;HP=1;DB;NF=10;GC;NR=20;NS=52;CA=0;DP=390 1 2931584 . GTGGTGTTTTCATT GT 100 PASS AF=0.171247;HP=1;NF=23;NR=10;NS=52;CA=0;DP=486 1 2932462 . GT GTGAT 56 PASS AF=0.766604;HP=1;NF=33;NR=13;NS=52;CA=M;DP=790 1 2932531 . GT GTGGTGAT 56 PASS AF=0.365205;HP=1;NF=19;NR=4;NS=52;CA=M;DP=738 1 2938240 rs57953122;-/AAGCC AC ACCAAGC 100 PASS AF=0.229942;HP=2;DB;NF=5;NR=7;NS=52;CA=0;DP=387 1 2939820 rs35035410;-/C,venter GCC GC 100 PASS AF=0.270114;HP=6;DB;NF=15;NR=21;NS=52;CA=0;DP=477 1 2940602 . GA GAA 100 PASS AF=0.245189;HP=10;NF=31;NR=30;NS=52;CA=0;DP=516 1 2941986 . ACCC AC 100 PASS AF=0.242307;HP=10;NF=20;NR=20;NS=52;CA=0;DP=471 1 2943041 rs34450334;-/G,mills CGG CG 100 PASS AF=0.212427;HP=8;DB;NF=13;NR=12;NS=52;CA=0;DP=523 1 2943605 rs5772091;-/C,mills GC GCC 100 PASS AF=0.155328;HP=1;DB;NF=7;NR=7;NS=52;CA=0;DP=349 1 2946559 . TT TTGT 100 PASS AF=0.174249;HP=3;NF=13;NR=14;NS=52;CA=0;DP=596 1 2948391 . TT TTTTTCT 100 PASS AF=0.137955;HP=5;NF=19;NR=16;NS=52;CA=0;DP=557 1 2949076 rs33910396;-/G,mills CG CGG 100 PASS AF=0.102902;HP=1;DB;NF=3;NR=8;NS=52;CA=0;DP=413 1 2950056 . TC TCAAACAAAC 100 PASS AF=0.133966;HP=1;NF=9;NR=9;NS=51;CA=0;DP=587 1 2950689 rs60031908;-/A CAA CA 100 PASS AF=0.200188;HP=8;DB;NF=20;NR=25;NS=51;CA=0;DP=517 1 2958314 . CC CCCATC 100 PASS AF=0.190271;HP=3;NF=39;NR=18;NS=52;CA=M;DP=454 1 2961502 rs60708459;-/T AT ATT 100 PASS AF=0.219472;HP=3;DB;NF=14;NR=16;NS=52;CA=0;DP=460 1 2968615 . AG AGG 100 PASS AF=0.288912;HP=2;NF=11;NR=13;NS=51;CA=0;DP=324 1 2982005 . GT GGGTT 100 PASS AF=0.189932;HP=5;NF=6;NR=5;NS=52;CA=0;DP=460 1 2984462 rs34471979;-/C,venter TCC TC 100 PASS AF=0.423837;HP=2;DB;NF=20;NR=27;NS=51;CA=0;DP=459 1 2985828 rs5772093;-/TTCGGGG,mills,venter,watson CT CTTCGGGGT 100 PASS AF=0.888966;HP=1;DB;NF=22;NR=15;NS=49;CA=0;DP=372 1 2987353 . AGTG AG 39 PASS AF=0.0534166;HP=1;NF=13;NR=12;NS=51;CA=0;DP=341 1 2990018 . TC TGC 51 PASS AF=0.347647;HP=1;NF=9;NR=5;NS=52;CA=0;DP=328 1 2992552 rs55740340;-/TTGT,mills,venter,watson CT CTGTTT 100 PASS AF=0.633228;HP=1;DB;NF=31;NR=31;NS=52;CA=0;DP=471 1 2994869 . TT TTTAT 48 PASS AF=0.246512;HP=4;NF=8;NR=15;NS=49;CA=0;DP=238 1 2996339 rs60239912;-/TCATTCAT CT CTCATTCATT 100 PASS AF=0.288255;HP=1;DB;NF=27;NR=24;NS=52;CA=0;DP=550 1 2996940 . TG TGGG 52 PASS AF=0.252534;HP=1;NF=5;NR=3;NS=51;CA=0;DP=485 1 2997430 rs58914207;-/TC TTCT TT 17 PASS AF=0.0239916;HP=3;DB;NF=1;NR=3;NS=51;CA=0;DP=533 1 2998548 rs3067411;-/GC,mills,watson TT TGCT 100 PASS AF=0.513959;HP=2;DB;NF=16;NR=33;NS=51;CA=0;DP=457 1 2998746 rs33948447;-/CTGAGGGTAT,mills,watson CCTGAGGGTATC CC 100 PASS AF=0.567187;HP=2;DB;NF=32;NR=26;NS=51;CA=0;DP=446 1 2998922 rs3067390;-/CA,mills,watson CTGT CT 100 PASS AF=0.344398;HP=1;DB;NF=25;NR=25;NS=52;CA=0;DP=544 1 3001309 . TCTTCC TC 100 PASS AF=0.122521;HP=1;NF=13;NR=16;NS=51;CA=0;DP=463 1 3003643 rs34727240;-/A CA CAA 100 PASS AF=0.30407;HP=4;DB;NF=23;NR=14;NS=51;CA=0;DP=462 1 3003980 . ATTCT AT 100 PASS AF=0.0770408;HP=2;NF=12;NR=8;NS=51;CA=0;DP=436 1 3015507 rs36215320;-/AATAAT,mills AAATAATA AA 100 PASS AF=0.341849;HP=4;DB;NF=19;NR=21;NS=52;CA=M;DP=287 1 3020627 . GC GCGCGCAC 45 PASS AF=0.0864166;HP=1;NF=3;NR=4;NS=52;CA=0;DP=675 1 3020729 . GCAC GC 100 PASS AF=0.270815;HP=1;NF=26;NR=22;NS=52;CA=0;DP=511 1 3020780 . GCAC GC 100 PASS AF=0.0529136;HP=1;NF=14;NR=13;NS=52;CA=0;DP=580 1 3020851 rs36140038;-/G,venter CC CGC 100 PASS AF=0.0570603;HP=2;DB;NF=7;NR=8;NS=52;CA=0;DP=580 1 3020930 . GCAC GC 100 PASS AF=0.0608239;HP=1;NF=21;NR=20;NS=52;CA=0;DP=662 1 3020996 . ACT AT 100 PASS AF=0.0376658;HP=1;NF=4;NR=2;NS=52;CA=0;DP=646 1 3021049 rs58793198;-/CA AA AACA 100 PASS AF=0.0822964;HP=2;DB;NF=19;NR=18;NS=52;CA=0;DP=756 1 3024532 . TGTGTGCG TG 100 PASS AF=0.0453628;HP=1;NF=12;NR=35;NS=51;CA=0;DP=585 1 3035092 venter,watson CTCCCACCATGCTACTGGAGACCAT CT 100 PASS AF=0.175148;HP=1;NF=41;NR=54;NS=51;CA=0;DP=464 1 3035605 rs56967751;-/TG,venter,watson AG AGTG 100 PASS AF=0.387697;HP=1;DB;NF=30;NR=25;NS=51;CA=0;DP=671 1 3035812 . CGTG CG 100 PASS AF=0.051827;HP=1;NF=28;NR=20;NS=51;CA=0;DP=643 1 3035887 . ATGT AT 50 PASS AF=0.0421027;HP=1;NF=24;NR=34;NS=52;CA=0;DP=556 1 3036291 rs36033160;-/CCG CT CCCGT 100 PASS AF=0.0605711;HP=1;DB;NF=3;NR=5;NS=51;CA=0;DP=428 1 3037949 rs34840011;-/A,venter TA TAA 100 PASS AF=0.096326;HP=8;DB;NF=5;NR=6;NS=52;CA=0;DP=462 1 3046082 rs35271327;-/T AT ATT 19 PASS AF=0.0473995;HP=7;DB;NF=9;NR=8;NS=52;CA=0;DP=430 1 3049499 . ACC AC 27 PASS AF=0.0269129;HP=3;NF=3;NR=1;NS=51;CA=0;DP=373 1 3053337 . TGG TG 100 PASS AF=0.205181;HP=7;NF=15;NR=19;NS=52;CA=0;DP=424 1 3058772 . TCATCC TC 100 PASS AF=0.716787;HP=1;NF=61;NR=51;NS=52;CA=0;DP=435 1 3069377 . CATGGT CT 100 PASS AF=0.42044;HP=1;NF=3;NR=14;NS=48;CA=M;DP=257 1 3076481 rs35945121;-/T,mills ATT AT 100 PASS AF=0.33892;HP=10;DB;NF=9;NR=38;NS=52;CA=0;DP=438 1 3079028 . TA TCA 100 PASS AF=0.0528803;HP=1;NF=5;NR=3;NS=51;CA=0;DP=475 1 3084256 watson AGTTTAGATACTG AG 100 PASS AF=0.123981;HP=1;NF=18;NR=14;NS=52;CA=0;DP=554 1 3087172 rs34468831;-/A GAA GA 100 PASS AF=0.0618762;HP=3;DB;NF=2;NR=5;NS=50;CA=0;DP=475 1 3087517 . CACACGCAGTCTTA CA 100 PASS AF=0.637316;HP=1;NF=41;NR=37;NS=52;CA=0;DP=973 1 3087777 . TA TACA 100 PASS AF=0.377666;HP=1;NF=43;NR=55;NS=52;CA=M;DP=966 1 3087871 . CACGGTCTTA CA 100 PASS AF=0.589214;HP=1;NF=16;NR=14;NS=51;CA=0;DP=710 1 3087938 . AG AGTCTTACACAAGCGG 100 PASS AF=0.469462;HP=1;NF=28;NR=29;NS=52;CA=M;DP=816 1 3088154 . GG GCAG 100 PASS AF=0.0511127;HP=2;NF=11;NR=10;NS=52;CA=M;DP=894 1 3088232 rs35125658;-/TT GG GCAG 100 PASS AF=0.0967781;HP=2;DB;NF=3;NR=24;NS=51;CA=M;DP=938 1 3088301 . CT CTTGCACACGCAGTTT 47 PASS AF=0.0188781;HP=2;NF=5;NR=2;NS=51;CA=M;DP=684 1 3105704 rs35372326;-/G,mills CGG CG 100 PASS AF=0.0956114;HP=2;DB;NF=6;NR=4;NS=52;CA=0;DP=378 1 3107408 rs5772098;-/G,mills AG AGG 100 PASS AF=0.107417;HP=5;DB;NF=19;NR=15;NS=52;CA=0;DP=504 1 3107714 rs34461209;-/G,venter TG TGG 100 PASS AF=0.61875;HP=3;DB;NF=21;NR=28;NS=52;CA=0;DP=454 1 3108534 rs59512254;-/GA GGAG GG 100 PASS AF=0.184609;HP=2;DB;NF=17;NR=11;NS=52;CA=0;DP=510 1 3121064 . TG TGAG 59 PASS AF=0.0221492;HP=1;NF=7;NR=3;NS=52;CA=0;DP=555 1 3131583 rs57750843;-/A GAA GA 100 PASS AF=0.166149;HP=9;DB;NF=21;NR=20;NS=52;CA=0;DP=490 1 3131742 . GT GGGGGGGGGTT 27 PASS AF=0.243052;HP=3;NF=2;NR=1;NS=49;CA=0;DP=394 1 3135855 rs34340862;-/TAA,mills CT CTAAT 100 PASS AF=0.183257;HP=1;DB;NF=11;NR=9;NS=51;CA=0;DP=520 1 3146366 . GGAG GG 100 PASS AF=0.040688;HP=4;NF=13;NR=14;NS=51;CA=0;DP=434 1 3152159 . AT ATT 100 PASS AF=0.0396994;HP=4;NF=8;NR=9;NS=52;CA=0;DP=489 1 3157729 venter,watson AG AGGGGTGAGGTG 100 PASS AF=0.830079;HP=4;NF=30;NR=23;NS=51;CA=0;DP=548 1 3158807 . AGG AG 100 PASS AF=0.705976;HP=6;NF=35;NR=30;NS=52;CA=0;DP=371 1 3158885 . CATG CG 100 PASS AF=0.09216;HP=1;NF=6;NR=6;NS=51;CA=0;DP=375 1 3163280 . CAAAATA CA 100 PASS AF=0.148526;HP=4;NF=13;NR=1;NS=49;CA=M;DP=326 1 3164018 rs5772100;-/A,mills,venter TAA TA 100 PASS AF=0.999998;HP=3;DB;NF=67;NR=69;NS=52;CA=0;DP=511 1 3174387 . CAGG CG 17 PASS AF=0.0141709;HP=1;NF=1;NR=2;NS=51;CA=0;DP=428 1 3176024 . GACAGTCCCAGAGGAGCA GA 44 PASS AF=0.0444872;HP=1;NF=3;NR=10;NS=52;CA=M;DP=480 1 3177102 . AG AGAGGAGGACAGTCGGGGAGGACAGTCCCGG 100 PASS AF=0.346135;HP=1;NF=8;NR=13;NS=52;CA=0;DP=550 1 3179862 rs35987870;-/GTGG ATGTGT AT 100 PASS AF=0.0762534;HP=1;DB;NF=17;NR=17;NS=51;CA=0;DP=618 1 3183094 rs33953525;-/GGTGCCGTGAACAGAGCCAGCGAGG,mills AG AGGTGCCGTGAACAGAGCCAGCGAGGG 100 PASS AF=0.665581;HP=2;DB;NF=15;NR=15;NS=52;CA=0;DP=424 1 3183166 rs35451643;-/C,venter TCC TC 100 PASS AF=0.123295;HP=4;DB;NF=12;NR=6;NS=52;CA=0;DP=460 1 3184208 rs59663829;-/GCACACACAA TA TGCACACACAAA 100 PASS AF=0.152939;HP=1;DB;NF=4;NR=4;NS=52;CA=0;DP=733 1 3186299 . ACC AC 100 PASS AF=0.951135;HP=8;NF=16;NR=14;NS=51;CA=0;DP=311 1 3202609 . TG TGGGGGGG 11 PASS AF=0.122471;HP=1;NF=3;NR=3;NS=52;CA=0;DP=479 1 3292566 . TC TCGGGGTGCCC 12 PASS AF=0.209628;HP=1;NF=22;NR=17;NS=51;CA=0;DP=462 1 3292669 . AAGA AA 100 PASS AF=0.312194;HP=8;NF=13;NR=14;NS=51;CA=0;DP=483 1 3293018 rs35846516;-/A,venter GAA GA 100 PASS AF=0.791047;HP=9;DB;NF=59;NR=44;NS=51;CA=0;DP=507 1 3293422 rs34150215;-/A,mills,venter TA TAA 100 PASS AF=0.418316;HP=7;DB;NF=27;NR=18;NS=52;CA=0;DP=481 1 3307979 rs35082175;-/A,venter CAT CT 100 PASS AF=0.379363;HP=1;DB;NF=36;NR=25;NS=52;CA=0;DP=659 1 3308056 . CATA CA 100 PASS AF=0.0313721;HP=1;NF=4;NR=5;NS=52;CA=0;DP=699 1 3308306 rs34659426;-/AA CAAA CA 100 PASS AF=0.238591;HP=3;DB;NF=23;NR=22;NS=52;CA=0;DP=732 1 3308692 . GC GCC 100 PASS AF=0.610676;HP=6;NF=23;NR=26;NS=52;CA=0;DP=447 1 3309461 . ACCCTCCTCTGAGTCTTCCTCCCCTTCCCGTGC AC 100 PASS AF=0.218197;HP=3;NF=28;NR=41;NS=51;CA=0;DP=430 1 3313004 . ATT AT 18 PASS AF=0.117282;HP=10;NF=22;NR=12;NS=51;CA=0;DP=407 1 3315219 rs35154920;-/GT CG CGTG 100 PASS AF=0.407055;HP=1;DB;NF=23;NR=17;NS=52;CA=0;DP=498 1 3315279 rs34306698;-/AT CG CATG 100 PASS AF=0.27165;HP=1;DB;NF=18;NR=10;NS=51;CA=0;DP=460 1 3315552 rs61650876;-/ATGT CATGTG CG 100 PASS AF=0.074251;HP=1;DB;NF=10;NR=7;NS=52;CA=0;DP=612 1 3315608 . CGTG CG 44 PASS AF=0.0200264;HP=1;NF=15;NR=25;NS=52;CA=0;DP=622 1 3316180 rs34769314;-/GTGA TGTGAG TG 100 PASS AF=0.13026;HP=1;DB;NF=29;NR=21;NS=52;CA=0;DP=930 1 3316258 rs57503175;-/TGTATGTGCGTGTGTGTGGTGTG GG GGTGTGTGGTGTGTGTATGTGCGTG 100 PASS AF=0.277124;HP=3;DB;NF=3;NR=11;NS=52;CA=0;DP=898 1 3316338 rs34133894;-/GT GGTG GG 100 PASS AF=0.121606;HP=2;DB;NF=18;NR=27;NS=52;CA=0;DP=901 1 3316408 . TGG TG 100 PASS AF=0.153074;HP=7;NF=23;NR=10;NS=52;CA=0;DP=898 1 3316476 rs60842130;-/GTG TGTGG TG 43 PASS AF=0.0151943;HP=1;DB;NF=4;NR=1;NS=52;CA=0;DP=732 1 3317481 rs34240659;-/AT CATA CA 100 PASS AF=0.127605;HP=1;DB;NF=14;NR=8;NS=52;CA=0;DP=538 1 3319964 . ACC AC 100 PASS AF=0.0511239;HP=5;NF=12;NR=4;NS=52;CA=0;DP=505 1 3327173 rs56093721;-/A,venter TAA TA 100 PASS AF=0.89527;HP=9;DB;NF=37;NR=68;NS=52;CA=0;DP=540 1 3328302 . AG AGGGGGG 53 PASS AF=0.124625;HP=2;NF=13;NR=2;NS=52;CA=0;DP=585 1 3335208 . CGG CG 100 PASS AF=0.0438559;HP=2;NF=3;NR=3;NS=52;CA=0;DP=448 1 3335551 rs34869178;-/T CTC CC 100 PASS AF=0.0947355;HP=1;DB;NF=4;NR=8;NS=52;CA=0;DP=487 1 3342021 rs34485545;-/A TA TAA 100 PASS AF=0.154806;HP=9;DB;NF=25;NR=23;NS=52;CA=0;DP=444 1 3347098 venter CG CAG 100 PASS AF=0.931731;HP=1;NF=49;NR=54;NS=52;CA=0;DP=497 1 3348129 rs55866341;-/G,venter CG CGG 100 PASS AF=0.883294;HP=1;DB;NF=55;NR=55;NS=52;CA=0;DP=521 1 3352897 . AA ACA 46 PASS AF=0.0385898;HP=6;NF=2;NR=6;NS=51;CA=0;DP=407 1 3353821 rs34792713;-/T AT ATT 36 PASS AF=0.0290672;HP=1;DB;NF=3;NR=3;NS=52;CA=0;DP=428 1 3356271 . TTCCT TT 15 PASS AF=0.00990969;HP=3;NF=1;NR=1;NS=52;CA=0;DP=537 1 3356391 rs4018597;-/TA TT TTAT 100 PASS AF=0.0517593;HP=2;DB;NF=13;NR=11;NS=52;CA=0;DP=475 1 3356436 rs5772104;-/GT CGTG CG 100 PASS AF=0.82813;HP=1;DB;NF=59;NR=53;NS=51;CA=0;DP=449 1 3356871 . CATG CG 26 PASS AF=0.0193592;HP=1;NF=1;NR=3;NS=51;CA=0;DP=430 1 3359412 rs34037774;-/G,venter TGG TG 59 PASS AF=0.0301496;HP=2;DB;NF=4;NR=5;NS=52;CA=0;DP=451 1 3370575 rs35597752;-/TG,venter,watson CTGT CT 100 PASS AF=0.760154;HP=1;DB;NF=43;NR=36;NS=52;CA=0;DP=405 1 3372018 rs34109718;-/G,venter CGG CG 100 PASS AF=0.891318;HP=3;DB;NF=46;NR=36;NS=51;CA=0;DP=349 1 3383745 rs57207202;-/C AC ACC 100 PASS AF=0.182529;HP=4;DB;NF=9;NR=7;NS=47;CA=D;DP=229 1 3384084 rs5772105;-/G,mills,venter CG CGG 100 PASS AF=0.937697;HP=2;DB;NF=49;NR=47;NS=50;CA=0;DP=457 1 3385833 rs5772106;-/CC,mills,venter,watson ACCC AC 100 PASS AF=0.778535;HP=5;DB;NF=33;NR=14;NS=51;CA=0;DP=418 1 3387275 rs56102150;-/TC,venter CC CCTC 100 PASS AF=0.999995;HP=4;DB;NF=16;NR=36;NS=50;CA=0;DP=364 1 3388739 rs58188396;-/GGGGGGCGGGTAGCC GG GGGGGGGCGGGTAGCCG 40 PASS AF=0.263678;HP=7;DB;NF=3;NR=2;NS=48;CA=0;DP=326 1 3393157 . AAAAAATA AA 100 PASS AF=0.0549314;HP=6;NF=23;NR=18;NS=51;CA=0;DP=468 1 3393524 . GGTGTG GG 23 PASS AF=0.017751;HP=2;NF=1;NR=19;NS=49;CA=0;DP=266 1 3409800 . AAGA AA 100 PASS AF=0.0431791;HP=3;NF=1;NR=8;NS=51;CA=0;DP=643 1 3410131 rs58666986;-/GTGT ATGTGT AT 100 PASS AF=0.0433727;HP=1;DB;NF=7;NR=13;NS=52;CA=0;DP=603 1 3411485 rs60864742;-/ACACCGGTAGCAAGGCA,mills ACACCGGTAGCAAGGCACC AC 100 PASS AF=0.0858716;HP=1;DB;NF=8;NR=17;NS=52;CA=0;DP=523 1 3417374 . GCACACGCCCCCACCC GC 20 PASS AF=0.0294079;HP=1;NF=4;NR=3;NS=50;CA=0;DP=447 1 3429498 rs56204236;-/G CG CGG 100 PASS AF=0.596026;HP=10;DB;NF=6;NR=7;NS=51;CA=0;DP=322 1 3435396 . CACAGA CA 100 PASS AF=0.0433621;HP=1;NF=2;NR=6;NS=52;CA=0;DP=457 1 3442767 rs36106109;-/G CG CGG 100 PASS AF=0.112939;HP=5;DB;NF=5;NR=6;NS=50;CA=0;DP=369 1 3451064 rs36030995;-/C GC GCC 100 PASS AF=0.385449;HP=5;DB;NF=22;NR=12;NS=50;CA=0;DP=388 1 3456931 rs35289361;-/G AG AGG 100 PASS AF=0.0676076;HP=4;DB;NF=11;NR=9;NS=52;CA=0;DP=554 1 3467274 watson GGGCTG GG 100 PASS AF=0.132596;HP=3;NF=16;NR=12;NS=51;CA=0;DP=428 1 3475422 rs61428836;-/G TG TGG 100 PASS AF=0.0480433;HP=3;DB;NF=6;NR=10;NS=52;CA=0;DP=468 1 3482055 . CA CGTCTTATA 100 PASS AF=0.593516;HP=1;NF=10;NR=11;NS=49;CA=M;DP=256 1 3482413 mills,watson TCTCC TC 100 PASS AF=0.414589;HP=1;NF=24;NR=32;NS=51;CA=0;DP=496 1 3485140 venter,watson CCAAC CC 100 PASS AF=0.714294;HP=2;NF=21;NR=32;NS=52;CA=0;DP=460 1 3486991 rs35452084;-/G,venter AGG AG 100 PASS AF=0.744909;HP=4;DB;NF=15;NR=35;NS=50;CA=0;DP=363 1 3492812 . CGTG CG 14 PASS AF=0.0148914;HP=1;NF=22;NR=26;NS=51;CA=0;DP=585 1 3494290 . AC ACAGGACCGGCC 100 PASS AF=0.117184;HP=1;NF=2;NR=22;NS=52;CA=0;DP=464 1 3496820 rs34860893;-/C,mills,venter ACC AC 100 PASS AF=0.924032;HP=7;DB;NF=33;NR=48;NS=52;CA=0;DP=386 1 3504928 rs36094767;-/C,venter TC TCC 100 PASS AF=0.786142;HP=4;DB;NF=23;NR=43;NS=51;CA=0;DP=405 1 3511572 rs3072238;-/TCAC,venter ACACTC AC 100 PASS AF=0.160871;HP=1;DB;NF=22;NR=22;NS=52;CA=0;DP=824 1 3511789 rs59801836;-/CTCA,watson ACACTC AC 100 PASS AF=0.620819;HP=1;DB;NF=54;NR=52;NS=52;CA=0;DP=740 1 3511919 . TACA TA 100 PASS AF=0.049568;HP=1;NF=20;NR=22;NS=52;CA=0;DP=729 1 3511980 rs57128321;-/ACTC,venter,watson AC ACACTC 100 PASS AF=0.937206;HP=1;DB;NF=63;NR=38;NS=52;CA=0;DP=712 1 3512089 rs61705210;-/TCACAC,venter,watson AACTCACA AA 100 PASS AF=0.658764;HP=3;DB;NF=65;NR=52;NS=52;CA=0;DP=808 1 3516936 rs60239345;-/CA,venter CG CCAG 100 PASS AF=0.999997;HP=1;DB;NF=52;NR=26;NS=52;CA=0;DP=391 1 3519155 rs35740208;-/G,venter AGG AG 100 PASS AF=0.108418;HP=3;DB;NF=7;NR=11;NS=51;CA=0;DP=505 1 3523781 rs56339243;-/GGCTCC,venter,watson AC ACCGGCTC 100 PASS AF=0.603986;HP=3;DB;NF=20;NR=23;NS=52;CA=0;DP=449 1 3526023 . GGCACTTCCCGCCCCCGTCACCCCTGCCGCCATG GG 100 PASS AF=0.227609;HP=2;NF=10;NR=15;NS=52;CA=0;DP=454 1 3526486 rs35020651;-/C,venter TC TCC 100 PASS AF=0.389171;HP=3;DB;NF=32;NR=20;NS=52;CA=0;DP=470 1 3530060 . TGG TG 100 PASS AF=0.033793;HP=3;NF=6;NR=1;NS=52;CA=0;DP=540 1 3531966 rs3838971;-/C TG TGG 100 PASS AF=0.155382;HP=6;DB;NF=14;NR=11;NS=49;CA=0;DP=292 1 3534095 rs35816205;-/A,mills,venter TAA TA 100 PASS AF=0.160054;HP=3;DB;NF=9;NR=10;NS=52;CA=0;DP=455 1 3535035 rs58849058;-/TCTGGGAGCTCCTCCCCCT,venter,watson GTTCTGGGAGCTCCTCCCCCT GT 100 PASS AF=0.609724;HP=2;DB;NF=50;NR=48;NS=52;CA=0;DP=487 1 3535985 . CCAAAC CC 100 PASS AF=0.116123;HP=2;NF=10;NR=13;NS=51;CA=0;DP=553 1 3536124 rs55905548;-/GGCG,venter,watson CCGGGC CC 100 PASS AF=0.45742;HP=3;DB;NF=28;NR=31;NS=51;CA=0;DP=499 1 3543853 . TC TCC 100 PASS AF=0.156605;HP=6;NF=12;NR=13;NS=52;CA=0;DP=527 1 3549495 . AC ACCCCC 34 PASS AF=0.0959154;HP=1;NF=1;NR=3;NS=52;CA=0;DP=496 1 3553372 rs34514629;-/C,venter GCA GA 100 PASS AF=0.652107;HP=1;DB;NF=45;NR=47;NS=52;CA=0;DP=551 1 3556485 rs3831025;-/CAGCCTGC,venter,watson AGCAGGCTGC AC 100 PASS AF=0.38103;HP=1;DB;NF=13;NR=9;NS=49;CA=0;DP=292 1 3556883 . CA CATA 14 PASS AF=0.0221011;HP=1;NF=9;NR=13;NS=50;CA=0;DP=436 1 3563429 . CG CGGGGG 56 PASS AF=0.17049;HP=2;NF=3;NR=7;NS=52;CA=0;DP=586 1 3564334 rs3034639;-/GT,mills GA GACA 100 PASS AF=0.227635;HP=1;DB;NF=10;NR=13;NS=50;CA=0;DP=364 1 3564964 rs5772113;-/G TGG TG 100 PASS AF=0.220888;HP=2;DB;NF=11;NR=18;NS=50;CA=0;DP=408 1 3565238 venter GGTCTCCTACAGTCATATTTTGGGGTGACGTATTCTAG GG 100 PASS AF=0.145422;HP=2;NF=1;NR=10;NS=52;CA=M;DP=323 1 3566253 rs57149403;-/GTCCAGC AC ACGTCCAGC 100 PASS AF=0.0476733;HP=1;DB;NF=3;NR=3;NS=52;CA=0;DP=363 1 3567114 . ATG AG 100 PASS AF=0.0358982;HP=1;NF=3;NR=5;NS=52;CA=0;DP=555 1 3568146 rs3034606;-/TA GTAT GT 100 PASS AF=0.533957;HP=1;DB;NF=12;NR=29;NS=51;CA=0;DP=247 1 3570893 rs34305694;-/C TCC TC 100 PASS AF=0.0467251;HP=2;DB;NF=5;NR=3;NS=52;CA=0;DP=443 1 3574939 . CG CGTGTGTG 23 PASS AF=0.401022;HP=1;NF=46;NR=32;NS=52;CA=0;DP=481 1 3586002 . ACTC AC 100 PASS AF=0.157197;HP=1;NF=17;NR=24;NS=52;CA=0;DP=691 1 3586231 rs61542341;-/GTCTCT CTCTCTGT CT 12 PASS AF=0.0310208;HP=1;DB;NF=1;NR=11;NS=52;CA=M;DP=400 1 3586281 . CTTT CT 21 PASS AF=0.115475;HP=3;NF=1;NR=3;NS=51;CA=M;DP=469 1 3589610 rs57492244;-/G TGG TG 100 PASS AF=0.0691843;HP=7;DB;NF=11;NR=8;NS=51;CA=0;DP=527 1 3593995 rs57765962;-/AT,watson AATG AG 100 PASS AF=0.127015;HP=2;DB;NF=10;NR=8;NS=52;CA=0;DP=423 1 3603570 . GCGGGGCCCACCTCGCACCCGCGGCCCACGTCGCACCC GC 100 PASS AF=0.0758905;HP=1;NF=8;NR=12;NS=51;CA=0;DP=414 1 3606881 rs5772119;-/A,venter TAG TG 100 PASS AF=0.333638;HP=1;DB;NF=12;NR=36;NS=51;CA=0;DP=522 1 3618309 rs3841787;-/TG,watson CATG CG 100 PASS AF=0.219932;HP=1;DB;NF=14;NR=14;NS=50;CA=0;DP=449 1 3619353 venter GCCCCTGCC GC 100 PASS AF=0.290838;HP=4;NF=18;NR=8;NS=51;CA=0;DP=322 1 3629994 rs35939665;-/CTGC,mills,venter,watson TCTGCC TC 100 PASS AF=0.953969;HP=1;DB;NF=43;NR=31;NS=51;CA=0;DP=364 1 3630547 rs35380007;-/A,venter TA TAA 100 PASS AF=0.373122;HP=2;DB;NF=20;NR=12;NS=51;CA=0;DP=293 1 3632819 rs61728692;-/CGGA GT GCGGAT 100 PASS AF=0.63605;HP=1;DB;NF=18;NR=3;NS=48;CA=0;DP=238 1 3632891 . GGATTG GG 46 PASS AF=0.024415;HP=2;NF=4;NR=2;NS=49;CA=0;DP=381 1 3633325 . CG CGATGGATGGGTGG 100 PASS AF=0.870192;HP=1;NF=3;NR=4;NS=52;CA=0;DP=751 1 3635416 rs3034587;-/CTCTCT,mills,venter AA AAGAGAGA 100 PASS AF=0.707697;HP=3;DB;NF=37;NR=27;NS=52;CA=0;DP=538 1 3643833 . AC ACCC 25 PASS AF=0.0664372;HP=1;NF=3;NR=3;NS=51;CA=0;DP=511 1 3648954 rs3216059;-/G AG AGG 100 PASS AF=0.42719;HP=4;DB;NF=35;NR=35;NS=51;CA=0;DP=551 1 3660684 . GA GCA 100 PASS AF=0.136632;HP=1;NF=2;NR=10;NS=49;CA=0;DP=480 1 3663009 rs35440871;-/AA CAAG CG 100 PASS AF=0.2595;HP=2;DB;NF=19;NR=14;NS=51;CA=0;DP=498 1 3665663 rs60798590;-/TATTTAAAAAT,watson CA CAATTATTTAAAA 33 PASS AF=0.0338921;HP=2;DB;NF=8;NR=3;NS=51;CA=0;DP=388 1 3665995 . TTTGAAACT TT 33 PASS AF=0.00986571;HP=4;NF=1;NR=3;NS=52;CA=0;DP=507 1 3668078 . AGG AG 100 PASS AF=0.341281;HP=8;NF=21;NR=29;NS=52;CA=0;DP=467 1 3677245 rs36002367;-/AG AAGA AA 100 PASS AF=0.137474;HP=3;DB;NF=6;NR=10;NS=52;CA=0;DP=521 1 3680208 . TG TGG 10 PASS AF=0.0239017;HP=1;NF=7;NR=5;NS=51;CA=0;DP=448 1 3681294 venter CC CGCAC 100 PASS AF=0.200075;HP=8;NF=7;NR=2;NS=50;CA=0;DP=245 1 3682989 rs35616712;-/C TCC TC 100 PASS AF=0.0813904;HP=3;DB;NF=9;NR=3;NS=51;CA=0;DP=447 1 3684305 venter CG CGG 100 PASS AF=0.0596707;HP=3;NF=4;NR=6;NS=51;CA=0;DP=416 1 3686623 rs35661250;-/AG CA CAGA 100 PASS AF=0.0609898;HP=1;DB;NF=5;NR=6;NS=52;CA=0;DP=626 1 3691009 rs35756038;-/A,venter CAA CA 100 PASS AF=0.444393;HP=2;DB;NF=24;NR=32;NS=52;CA=0;DP=562 1 3696676 . CCTG CG 100 PASS AF=0.102585;HP=4;NF=7;NR=6;NS=52;CA=0;DP=502 1 3697316 rs34679063;-/C,venter GC GCC 100 PASS AF=0.8246;HP=1;DB;NF=51;NR=32;NS=52;CA=0;DP=438 1 3704105 . TT TTAATTTTTATATTAACCGTGTTAATAT 100 PASS AF=0.377269;HP=2;NF=17;NR=26;NS=52;CA=0;DP=476 1 3708451 watson TG TGGAGG 43 PASS AF=0.0406373;HP=2;NF=3;NR=4;NS=52;CA=0;DP=587 1 3710853 rs35447451;-/G,venter AG AGG 100 PASS AF=0.272856;HP=4;DB;NF=25;NR=31;NS=52;CA=0;DP=507 1 3711553 rs36007194;-/T AT ATT 100 PASS AF=0.093968;HP=10;DB;NF=11;NR=13;NS=52;CA=0;DP=515 1 3712668 rs35364504;-/GA,venter GGAG GG 100 PASS AF=0.369523;HP=5;DB;NF=18;NR=34;NS=51;CA=0;DP=320 1 3713867 venter TTTTATTTAT TT 100 PASS AF=0.301438;HP=5;NF=21;NR=36;NS=49;CA=0;DP=294 1 3714365 rs58666367;-/CTCAT,venter,watson GA GATCTCA 100 PASS AF=0.431722;HP=1;DB;NF=24;NR=17;NS=52;CA=0;DP=484 1 3721514 rs3838969;-/A,venter CG CTG 100 PASS AF=0.472733;HP=2;DB;NF=27;NR=26;NS=52;CA=0;DP=461 1 3726918 rs34085838;-/G CG CGG 100 PASS AF=0.242958;HP=1;DB;NF=17;NR=14;NS=52;CA=0;DP=479 1 3728638 rs61301856;-/GA,venter,watson TGAG TG 100 PASS AF=0.446341;HP=1;DB;NF=54;NR=33;NS=52;CA=0;DP=666 1 3729131 rs56900717;-/A TT TAT 100 PASS AF=0.489357;HP=2;DB;NF=33;NR=22;NS=52;CA=0;DP=466 1 3733293 rs5772126;-/G,venter TG TGG 100 PASS AF=0.701257;HP=2;DB;NF=17;NR=26;NS=51;CA=0;DP=451 1 3733413 . CA CAA 100 PASS AF=0.107016;HP=5;NF=12;NR=16;NS=52;CA=0;DP=523 1 3735276 venter TA TAAA 100 PASS AF=0.491527;HP=1;NF=29;NR=33;NS=52;CA=0;DP=477 1 3737219 rs61056063;-/A AGA AA 11 PASS AF=0.205567;HP=1;DB;NF=13;NR=6;NS=51;CA=0;DP=431 1 3740075 rs35801288;-/C ACA AA 100 PASS AF=0.438207;HP=1;DB;NF=35;NR=12;NS=52;CA=0;DP=395 1 3741588 rs34966926;-/T,venter GT GTT 100 PASS AF=0.212825;HP=10;DB;NF=21;NR=22;NS=51;CA=0;DP=541 1 3748510 mills TTTTTTAT TT 53 PASS AF=0.0323102;HP=7;NF=21;NR=15;NS=51;CA=0;DP=420 1 3759325 . CG CGGCCAAGGAG 100 PASS AF=0.391954;HP=2;NF=19;NR=18;NS=52;CA=0;DP=465 1 3759824 . CG CGGG 22 PASS AF=0.0355289;HP=5;NF=4;NR=8;NS=52;CA=0;DP=591 1 3760224 rs61309375;-/A,venter CAG CG 100 PASS AF=0.303624;HP=1;DB;NF=27;NR=13;NS=51;CA=0;DP=447 1 3773150 . CTT CT 12 NoQCALL AF=0.0786801;HP=2;NF=1;NR=9;NS=52;CA=0;DP=540 1 3774838 . GT GTT 11 PASS AF=0.0109686;HP=1;NF=2;NR=1;NS=52;CA=0;DP=492 1 3774974 venter CG CTG 100 PASS AF=0.552417;HP=1;NF=26;NR=38;NS=52;CA=0;DP=559 1 3776839 . TGG TG 100 PASS AF=0.0926011;HP=3;NF=5;NR=5;NS=52;CA=0;DP=441 1 3780438 venter CT CTTT 100 PASS AF=0.113197;HP=2;NF=10;NR=13;NS=52;CA=0;DP=654 1 3780687 rs34664006;-/G TGT TT 50 PASS AF=0.0614825;HP=1;DB;NF=4;NR=8;NS=50;CA=M;DP=299 1 3784253 venter ACTGTGCCGGCTTTCTATTC AC 100 PASS AF=0.0567473;HP=1;NF=81;NR=75;NS=52;CA=0;DP=627 1 3786092 . TACTCA TA 100 PASS AF=0.0330531;HP=1;NF=1;NR=6;NS=52;CA=0;DP=497 1 3788460 rs35600694;-/ATA,watson CA CAATA 100 PASS AF=0.42686;HP=1;DB;NF=20;NR=17;NS=51;CA=0;DP=533 1 3788666 rs34172576;-/T,venter GT GTT 100 PASS AF=0.481873;HP=1;DB;NF=26;NR=12;NS=52;CA=0;DP=409 1 3804956 rs60302317;-/CAACA AACAACA AA 46 PASS AF=0.0866272;HP=2;DB;NF=6;NR=2;NS=52;CA=M;DP=556 1 3805210 rs58663935;-/AAAG CA CAAAGA 100 PASS AF=0.0920558;HP=3;DB;NF=9;NR=2;NS=52;CA=0;DP=523 1 3805480 . GAA GA 55 PASS AF=0.0675729;HP=8;NF=13;NR=11;NS=52;CA=0;DP=539 1 3805914 . CCAGACACTGGCACCCCCCTTC CC 100 PASS AF=0.0288464;HP=2;NF=5;NR=4;NS=52;CA=0;DP=613 1 3806447 rs35704040;-/C,mills GCC GC 100 PASS AF=0.0700176;HP=6;DB;NF=4;NR=8;NS=52;CA=0;DP=350 1 3807398 rs35759189;-/G,venter AGG AG 100 PASS AF=0.324114;HP=3;DB;NF=21;NR=8;NS=50;CA=0;DP=355 1 3808303 venter GT GTTCTTTTCTTT 100 PASS AF=0.475205;HP=2;NF=19;NR=9;NS=52;CA=0;DP=264 1 3809301 . TACA TA 100 PASS AF=0.028676;HP=1;NF=26;NR=22;NS=52;CA=0;DP=553 1 3813066 rs34938659;-/T ATT AT 100 PASS AF=0.131264;HP=2;DB;NF=8;NR=6;NS=52;CA=0;DP=521 1 3814885 . TCACACACACACACACAC TC 34 PASS AF=0.149965;HP=1;NF=6;NR=2;NS=52;CA=M;DP=644 1 3818483 . AC ACC 29 PASS AF=0.0676027;HP=3;NF=1;NR=7;NS=50;CA=0;DP=412 1 3820456 . TGG TG 12 PASS AF=0.0215117;HP=4;NF=5;NR=1;NS=51;CA=0;DP=417 1 3824944 . GCTC GC 100 PASS AF=0.174164;HP=1;NF=9;NR=17;NS=50;CA=0;DP=277 1 3825911 . CG CGGGGGG 100 PASS AF=0.29134;HP=2;NF=24;NR=12;NS=52;CA=0;DP=514 1 3827024 . TTCCCT TT 16 PASS AF=0.0318298;HP=2;NF=34;NR=70;NS=51;CA=M;DP=394 1 3827604 . TG TGG 40 PASS AF=0.0159039;HP=1;NF=2;NR=5;NS=52;CA=0;DP=571 1 3833062 watson TC TCCACC 100 PASS AF=0.312659;HP=2;NF=17;NR=16;NS=52;CA=0;DP=463 1 3833266 venter,watson AT ATCAGT 100 PASS AF=0.497122;HP=1;NF=10;NR=19;NS=51;CA=0;DP=412 1 3833395 . CTATCTT CT 24 PASS AF=0.0218407;HP=1;NF=7;NR=3;NS=50;CA=0;DP=400 1 3833485 . GTCTAT GT 100 PASS AF=0.417779;HP=1;NF=11;NR=12;NS=50;CA=0;DP=323 1 3833578 watson TTATCT TT 100 PASS AF=0.329625;HP=2;NF=27;NR=26;NS=51;CA=0;DP=388 1 3833880 watson CA CATCTA 100 PASS AF=0.347946;HP=1;NF=11;NR=13;NS=52;CA=0;DP=458 1 3906706 . TGG TG 100 PASS AF=0.149111;HP=3;NF=11;NR=9;NS=52;CA=0;DP=498 1 3907565 rs34088401;-/C,mills TCC TC 100 PASS AF=0.191109;HP=6;DB;NF=11;NR=14;NS=51;CA=0;DP=478 1 3909253 . AC ACC 100 PASS AF=0.0974891;HP=2;NF=10;NR=9;NS=52;CA=0;DP=591 1 3909917 rs35302885;-/T,venter CTT CT 100 PASS AF=0.766256;HP=7;DB;NF=45;NR=61;NS=52;CA=0;DP=605 1 3916501 rs55698528;-/A,venter GA GAA 100 PASS AF=0.624637;HP=1;DB;NF=37;NR=28;NS=52;CA=0;DP=488 1 3920626 rs59758170;-/TAAATAAATA AATAAATAAATA AA 100 PASS AF=0.276985;HP=3;DB;NF=6;NR=6;NS=50;CA=M;DP=308 1 3923069 . TCG TG 100 PASS AF=0.224119;HP=1;NF=23;NR=7;NS=52;CA=0;DP=488 1 3925431 rs34400281;-/T,venter CTT CT 100 PASS AF=0.372459;HP=2;DB;NF=14;NR=10;NS=51;CA=0;DP=500 1 3933527 . ATTCCCCACAGTGTCTATGGGGACTCTAGCACGGTCAGGGACCCT AT 100 PASS AF=0.0367516;HP=2;NF=29;NR=33;NS=51;CA=0;DP=622 1 3934862 venter GCAC GC 100 PASS AF=0.565308;HP=1;NF=47;NR=42;NS=51;CA=0;DP=648 1 3935044 . TCAC TC 40 PASS AF=0.0156518;HP=1;NF=25;NR=8;NS=52;CA=0;DP=717 1 3937578 rs56700097;-/A,venter TG TAG 100 PASS AF=0.540707;HP=1;DB;NF=40;NR=17;NS=52;CA=0;DP=392 1 3938627 rs58820377;-/ATAG TTAGAT TT 100 PASS AF=0.0846429;HP=2;DB;NF=10;NR=11;NS=52;CA=0;DP=489 1 3945777 . CAGA CA 100 PASS AF=0.442957;HP=1;NF=49;NR=35;NS=52;CA=M;DP=511 1 3967107 venter GAGAA GA 100 PASS AF=0.226936;HP=1;NF=10;NR=15;NS=52;CA=0;DP=543 1 3971955 rs56102422;-/T AT ATT 100 PASS AF=0.275646;HP=10;DB;NF=12;NR=15;NS=52;CA=0;DP=477 1 3973109 rs56883229;-/T,venter ATT AT 100 PASS AF=0.374332;HP=8;DB;NF=7;NR=38;NS=52;CA=0;DP=398 1 3974590 . ATT AT 100 PASS AF=0.373956;HP=8;NF=19;NR=19;NS=51;CA=0;DP=352 1 3976220 . TTCCAGCTGTTGGACTGGCAAACAGT TT 100 PASS AF=0.155908;HP=3;NF=51;NR=67;NS=52;CA=0;DP=702 1 3983232 . GC GCC 100 PASS AF=0.153929;HP=3;NF=2;NR=12;NS=51;CA=0;DP=479 1 3989673 rs34117538;-/T CTT CT 100 PASS AF=0.138005;HP=7;DB;NF=10;NR=16;NS=52;CA=0;DP=480 1 3991472 . GT GTT 41 PASS AF=0.0921994;HP=10;NF=23;NR=19;NS=52;CA=0;DP=490 1 3995340 . GAATA GA 100 PASS AF=0.126804;HP=2;NF=18;NR=25;NS=51;CA=0;DP=456 1 3995701 rs35842317;-/A GA GAA 100 PASS AF=0.287765;HP=3;DB;NF=16;NR=28;NS=52;CA=0;DP=515 1 3998289 rs34690250;-/C AT ATT 31 PASS AF=0.0505667;HP=1;DB;NF=5;NR=6;NS=50;CA=0;DP=373 1 3998556 rs35439065;-/C,venter AC ACC 100 PASS AF=0.152989;HP=1;DB;NF=17;NR=4;NS=52;CA=0;DP=565 1 4003805 . CCCTTC CC 100 PASS AF=0.497734;HP=3;NF=13;NR=9;NS=52;CA=M;DP=357 1 4004467 . TA TAA 100 PASS AF=0.178845;HP=10;NF=39;NR=12;NS=52;CA=0;DP=482 1 4005161 . AAGA AA 10 PASS AF=0.109604;HP=8;NF=5;NR=3;NS=52;CA=0;DP=418 1 4009724 . GGAGAGGGAGAAG GG 100 PASS AF=0.0443217;HP=4;NF=7;NR=9;NS=51;CA=0;DP=347 1 4010638 rs59300943;-/T CT CTT 100 PASS AF=0.238748;HP=5;DB;NF=17;NR=13;NS=52;CA=0;DP=424 1 4018608 . GGGAG GG 14 PASS AF=0.0210215;HP=3;NF=11;NR=22;NS=52;CA=0;DP=439 1 4020045 rs60135555;-/AAA,venter TA TAAAA 55 PASS AF=0.669408;HP=9;DB;NF=19;NR=3;NS=52;CA=0;DP=315 1 4021381 . CTGGGAAC CC 26 PASS AF=0.0682584;HP=1;NF=1;NR=7;NS=52;CA=0;DP=500 1 4022270 . TG TCG 59 PASS AF=0.0269606;HP=6;NF=2;NR=3;NS=52;CA=0;DP=522 1 4022431 rs58149124;-/CC,watson TC TCCC 100 PASS AF=0.833755;HP=1;DB;NF=29;NR=41;NS=52;CA=0;DP=574 1 4024133 rs56013829;-/GTCA,venter ACAGTC AC 100 PASS AF=0.444062;HP=1;DB;NF=29;NR=25;NS=52;CA=0;DP=599 1 4024168 rs56372495;-/AC,venter TCAC TC 100 PASS AF=0.370935;HP=1;DB;NF=14;NR=39;NS=52;CA=0;DP=645 1 4024408 rs55816119;-/TT,watson TC TCAC 100 PASS AF=0.479654;HP=1;DB;NF=17;NR=29;NS=52;CA=0;DP=726 1 4024524 . ACTC AC 100 PASS AF=0.220192;HP=1;NF=11;NR=5;NS=52;CA=0;DP=721 1 4024673 . TT TTCACT 100 PASS AF=0.173855;HP=2;NF=11;NR=13;NS=52;CA=0;DP=887 1 4024704 . TCAG TG 100 PASS AF=0.0291681;HP=1;NF=6;NR=1;NS=52;CA=0;DP=750 1 4024735 venter TC TCAC 100 PASS AF=0.247468;HP=1;NF=19;NR=5;NS=52;CA=0;DP=775 1 4024928 . CTCAGT CT 100 PASS AF=0.0974879;HP=1;NF=11;NR=7;NS=52;CA=0;DP=919 1 4025065 . TCAC TC 100 PASS AF=0.273013;HP=1;NF=7;NR=12;NS=52;CA=0;DP=714 1 4025127 . ACTC AC 100 PASS AF=0.380734;HP=1;NF=17;NR=20;NS=52;CA=M;DP=574 1 4025165 . TC TCACTCAC 100 PASS AF=0.0820414;HP=1;NF=1;NR=9;NS=52;CA=M;DP=574 1 4025232 watson TC TCAC 100 PASS AF=0.631924;HP=1;NF=15;NR=11;NS=52;CA=M;DP=459 1 4025339 . TTCACT TT 53 PASS AF=0.159738;HP=2;NF=17;NR=14;NS=51;CA=0;DP=609 1 4025399 . CA CATA 100 PASS AF=0.0862676;HP=1;NF=4;NR=7;NS=52;CA=0;DP=506 1 4025472 . CA CATTTA 39 PASS AF=0.0270865;HP=1;NF=2;NR=1;NS=52;CA=0;DP=538 1 4025543 venter,watson TC TCAC 100 PASS AF=0.26036;HP=1;NF=9;NR=12;NS=52;CA=0;DP=482 1 4025589 . AC ACTC 53 PASS AF=0.0696821;HP=1;NF=1;NR=1;NS=52;CA=0;DP=575 1 4025678 watson TACTCA TA 100 PASS AF=0.299176;HP=1;NF=14;NR=7;NS=52;CA=0;DP=549 1 4025718 . CATT CT 100 PASS AF=0.0815807;HP=1;NF=8;NR=6;NS=52;CA=0;DP=570 1 4025810 watson TC TCAC 100 PASS AF=0.240222;HP=1;NF=8;NR=8;NS=52;CA=0;DP=442 1 4025920 . ACTCACACTC AC 15 PASS AF=0.0440807;HP=1;NF=5;NR=6;NS=52;CA=0;DP=439 1 4025988 . ATCACT AT 100 PASS AF=0.115745;HP=1;NF=7;NR=3;NS=52;CA=M;DP=409 1 4026021 . ATTCGC AC 19 PASS AF=0.0230633;HP=2;NF=4;NR=4;NS=52;CA=0;DP=408 1 4026091 . ACAGTC AC 100 PASS AF=0.239672;HP=1;NF=10;NR=12;NS=52;CA=0;DP=418 1 4026188 . GTCACTCGTT GT 100 PASS AF=0.0942528;HP=1;NF=17;NR=15;NS=51;CA=M;DP=704 1 4026243 . AC ACTCACTC 100 PASS AF=0.0701669;HP=1;NF=8;NR=2;NS=52;CA=0;DP=852 1 4026341 . AC ACTC 100 PASS AF=0.180464;HP=1;NF=7;NR=12;NS=52;CA=0;DP=797 1 4026433 . AC ACTCACAGTC 100 PASS AF=0.0755971;HP=1;NF=10;NR=4;NS=52;CA=0;DP=727 1 4026489 . CCACTC CC 100 PASS AF=0.152175;HP=2;NF=20;NR=14;NS=52;CA=0;DP=896 1 4026521 . AT ACT 18 PASS AF=0.0348752;HP=1;NF=8;NR=8;NS=52;CA=0;DP=896 1 4026676 . ACACTC AC 100 PASS AF=0.345964;HP=1;NF=25;NR=27;NS=52;CA=0;DP=805 1 4026745 . ACTC AC 100 PASS AF=0.277096;HP=1;NF=6;NR=11;NS=52;CA=0;DP=625 1 4026831 . AC ACTC 100 PASS AF=0.158736;HP=1;NF=13;NR=9;NS=52;CA=0;DP=585 1 4026904 . TACTCA TA 59 PASS AF=0.094457;HP=1;NF=7;NR=4;NS=52;CA=0;DP=594 1 4026996 . TT TTCACT 100 PASS AF=0.0816069;HP=2;NF=19;NR=16;NS=52;CA=0;DP=668 1 4027100 watson GT GTCACT 100 PASS AF=0.51624;HP=1;NF=22;NR=20;NS=52;CA=0;DP=958 1 4027153 . AC ACTCACACTC 100 PASS AF=0.221157;HP=1;NF=11;NR=7;NS=52;CA=0;DP=694 1 4027249 . ACACTCGCTCAGTC AC 100 PASS AF=0.191741;HP=1;NF=20;NR=16;NS=52;CA=0;DP=528 1 4027301 . TCAC TC 100 PASS AF=0.21653;HP=1;NF=6;NR=9;NS=52;CA=0;DP=511 1 4027378 . TT TTCACT 100 PASS AF=0.23813;HP=2;NF=19;NR=16;NS=52;CA=0;DP=565 1 4027440 . TT TTCACT 100 PASS AF=0.351897;HP=2;NF=28;NR=13;NS=52;CA=0;DP=736 1 4031776 venter,watson GC GCTGCTCC 100 PASS AF=0.57914;HP=1;NF=17;NR=13;NS=52;CA=0;DP=475 1 4046995 rs60127181;-/ATG,watson GC GGATC 100 PASS AF=0.863384;HP=1;DB;NF=37;NR=32;NS=51;CA=0;DP=427 1 4053051 . AC AACC 10 PASS AF=0.0731381;HP=1;NF=2;NR=3;NS=52;CA=0;DP=453 1 4056743 rs57501900;-/T,venter ATT AT 100 PASS AF=0.863012;HP=6;DB;NF=63;NR=45;NS=52;CA=0;DP=485 1 4078234 venter,watson CTGCCTGTGTGAGCAAGAT CT 100 PASS AF=0.308447;HP=1;NF=26;NR=18;NS=52;CA=0;DP=484 1 4080449 rs35774756;-/T GTT GT 100 PASS AF=0.285891;HP=2;DB;NF=20;NR=24;NS=51;CA=0;DP=526 1 4082493 rs35701497;-/G CGG CG 100 PASS AF=0.277913;HP=4;DB;NF=14;NR=16;NS=52;CA=0;DP=416 1 4086137 . CA CTA 100 PASS AF=0.0260425;HP=1;NF=4;NR=2;NS=52;CA=0;DP=569 1 4088196 . TTCT TT 100 PASS AF=0.0658972;HP=3;NF=67;NR=77;NS=51;CA=B;DP=647 1 4091673 rs56198003;-/TTA GTTAT GT 100 PASS AF=0.0274099;HP=2;DB;NF=4;NR=7;NS=52;CA=0;DP=489 1 4093407 rs35442233;-/G,venter TGG TG 100 PASS AF=0.056726;HP=4;DB;NF=4;NR=5;NS=51;CA=0;DP=432 1 4097902 rs5772141;-/ATT,mills,venter,watson CA CATTA 100 PASS AF=0.999995;HP=1;DB;NF=38;NR=34;NS=52;CA=0;DP=432 1 4106716 . AC ACACACACACACGC 100 PASS AF=0.316911;HP=1;NF=1;NR=1;NS=52;CA=0;DP=601 1 4114274 rs60603556;-/CAT,watson AATCA AA 100 PASS AF=0.135224;HP=3;DB;NF=17;NR=9;NS=51;CA=0;DP=587 1 4114592 rs56285575;-/ACA,venter AAACA AA 100 PASS AF=0.254759;HP=3;DB;NF=21;NR=18;NS=52;CA=0;DP=554 1 4114812 . TTAT TT 33 PASS AF=0.14738;HP=3;NF=5;NR=4;NS=52;CA=0;DP=411 1 4114996 . AA AATTATTA 11 PASS AF=0.228122;HP=2;NF=26;NR=29;NS=49;CA=0;DP=276 1 4120825 . GAA GA 43 PASS AF=0.147904;HP=2;NF=11;NR=17;NS=51;CA=0;DP=328 1 4121802 . ATGT AT 11 PASS AF=0.0113836;HP=1;NF=24;NR=16;NS=52;CA=0;DP=570 1 4131826 . ATTGTTT AT 100 PASS AF=0.999996;HP=2;NF=38;NR=35;NS=52;CA=0;DP=456 1 4134659 rs35271731;-/G TG TGG 100 PASS AF=0.417516;HP=5;DB;NF=21;NR=19;NS=52;CA=0;DP=429 1 4139315 rs35859581;-/T,venter GT GTT 100 PASS AF=0.371694;HP=2;DB;NF=12;NR=16;NS=52;CA=0;DP=444 1 4144542 . CAA CA 100 PASS AF=0.0915309;HP=2;NF=7;NR=8;NS=52;CA=M;DP=461 1 4149378 rs35644791;-/CCT,venter,watson AC ACCTC 100 PASS AF=0.955034;HP=2;DB;NF=35;NR=24;NS=52;CA=0;DP=461 1 4150078 . ATC AC 100 PASS AF=0.0248618;HP=1;NF=3;NR=1;NS=52;CA=0;DP=489 1 4158176 rs61115653;-/A CA CAA 100 PASS AF=0.109858;HP=9;DB;NF=9;NR=8;NS=52;CA=0;DP=480 1 4158371 rs35550030;-/G AGA AA 100 PASS AF=0.282272;HP=1;DB;NF=22;NR=13;NS=52;CA=0;DP=508 1 4160853 . AG AGTG 100 PASS AF=0.883963;HP=1;NF=52;NR=40;NS=52;CA=0;DP=475 1 4163479 rs35439066;-/T,venter ATT AT 100 PASS AF=0.421487;HP=7;DB;NF=35;NR=40;NS=52;CA=0;DP=580 1 4165518 rs5772143;-/A,mills CAT CT 100 PASS AF=0.0997002;HP=1;DB;NF=8;NR=9;NS=52;CA=0;DP=569 1 4168412 . TG TGG 100 PASS AF=0.0597927;HP=5;NF=7;NR=5;NS=50;CA=0;DP=411 1 4174019 . CCTTTC CC 100 PASS AF=0.223832;HP=2;NF=5;NR=11;NS=51;CA=M;DP=369 1 4176371 rs5772145;-/GGGCT,mills,venter,watson GG GGGGCTG 100 PASS AF=0.965127;HP=4;DB;NF=37;NR=39;NS=51;CA=0;DP=577 1 4180359 rs35134459;-/T,venter CG CTG 100 PASS AF=0.994644;HP=2;DB;NF=70;NR=40;NS=52;CA=0;DP=510 1 4198168 . GCCATTTACATCCCACC GC 100 PASS AF=0.0947023;HP=2;NF=47;NR=53;NS=52;CA=0;DP=625 1 4203370 . TCAC TC 22 PASS AF=0.151126;HP=1;NF=40;NR=22;NS=51;CA=0;DP=481 1 4224147 . ATGT AT 100 PASS AF=0.459042;HP=1;NF=45;NR=57;NS=52;CA=0;DP=508 1 4236168 venter,watson GT GTCCTGTT 100 PASS AF=0.465028;HP=1;NF=21;NR=21;NS=51;CA=0;DP=473 1 4238553 . TAG TG 100 PASS AF=0.0884036;HP=1;NF=3;NR=3;NS=52;CA=0;DP=313 1 4243904 . TG TGGGGG 28 PASS AF=0.177328;HP=1;NF=6;NR=9;NS=52;CA=0;DP=598 1 4252300 . AATTTA AA 27 PASS AF=0.0160294;HP=2;NF=16;NR=12;NS=52;CA=0;DP=550 1 4256051 . CC CCTCAC 100 PASS AF=0.423907;HP=2;NF=10;NR=6;NS=52;CA=M;DP=450 1 4256251 rs56817136;-/AATCCATC TC TCATCAATCC 27 PASS AF=0.483921;HP=1;DB;NF=24;NR=28;NS=52;CA=M;DP=501 1 4256338 rs59859709;-/CCAT CCCATC CC 100 PASS AF=0.420087;HP=3;DB;NF=47;NR=73;NS=52;CA=0;DP=510 1 4258560 rs35749795;-/G,venter TGG TG 100 PASS AF=0.563751;HP=3;DB;NF=30;NR=43;NS=52;CA=0;DP=533 1 4270968 rs5772150;-/A,mills,venter TAA TA 100 PASS AF=0.863858;HP=2;DB;NF=66;NR=65;NS=52;CA=0;DP=554 1 4272781 rs34523387;-/CA,venter,watson TCAC TC 100 PASS AF=0.221206;HP=1;DB;NF=55;NR=32;NS=52;CA=0;DP=555 1 4276688 rs56762609;-/A CA CAA 25 PASS AF=0.0168189;HP=4;DB;NF=5;NR=7;NS=52;CA=0;DP=567 1 4278344 rs33957131;-/A,mills TAT TT 100 PASS AF=0.260307;HP=1;DB;NF=13;NR=14;NS=52;CA=M;DP=390 1 4280264 rs35972891;-/G,venter TG TGG 100 PASS AF=0.36321;HP=6;DB;NF=16;NR=21;NS=52;CA=0;DP=487 1 4280920 rs3058085;-/AGA,mills,venter,watson AT ATCTT 100 PASS AF=0.75024;HP=1;DB;NF=34;NR=50;NS=52;CA=0;DP=518 1 4281851 rs59086076;-/TTGT CTGTTT CT 100 PASS AF=0.15371;HP=1;DB;NF=12;NR=13;NS=52;CA=0;DP=454 1 4287207 rs3986843;-/CCT CA CAGGA 100 PASS AF=0.100002;HP=1;DB;NF=8;NR=1;NS=52;CA=0;DP=451 1 4289708 . GTGTTAG GG 37 PASS AF=0.0904846;HP=1;NF=3;NR=9;NS=52;CA=0;DP=447 1 4291813 . CGC CC 41 PASS AF=0.05598;HP=1;NF=1;NR=9;NS=52;CA=0;DP=504 1 4291856 rs33950418;-/C,mills ACA AA 53 PASS AF=0.0424203;HP=1;DB;NF=2;NR=10;NS=52;CA=M;DP=504 1 4292024 rs33982329;-/CA,mills CG CATG 100 PASS AF=0.0974178;HP=1;DB;NF=14;NR=14;NS=52;CA=0;DP=697 1 4296830 . CTT CT 100 PASS AF=0.101792;HP=2;NF=15;NR=4;NS=52;CA=0;DP=805 1 4298115 rs34054009;-/G,venter AG AGG 100 PASS AF=0.314255;HP=2;DB;NF=25;NR=10;NS=52;CA=0;DP=565 1 4310246 rs35999105;-/A TA TAA 100 PASS AF=0.229765;HP=5;DB;NF=23;NR=13;NS=52;CA=0;DP=488 1 4310305 venter GA GAA 39 PASS AF=0.078696;HP=9;NF=15;NR=5;NS=52;CA=0;DP=455 1 4312461 . GAAAGAAA GA 24 PASS AF=0.0372797;HP=3;NF=23;NR=6;NS=52;CA=M;DP=401 1 4313453 . GG GTG 23 PASS AF=0.026167;HP=2;NF=2;NR=5;NS=52;CA=0;DP=614 1 4315016 rs34078493;-/T,venter CT CTT 100 PASS AF=0.459017;HP=1;DB;NF=25;NR=37;NS=52;CA=0;DP=493 1 4316236 rs35864764;-/TC ATCT AT 100 PASS AF=0.164629;HP=1;DB;NF=18;NR=15;NS=52;CA=0;DP=434 1 4317119 rs35907112;-/AG AAGA AA 100 PASS AF=0.210583;HP=3;DB;NF=19;NR=13;NS=52;CA=0;DP=652 1 4319781 rs34098980;-/AAAAA,mills,venter CC CAAAAAC 100 PASS AF=0.451406;HP=2;DB;NF=9;NR=1;NS=52;CA=0;DP=605 1 4323411 . GT GTT 41 PASS AF=0.0448346;HP=6;NF=4;NR=5;NS=52;CA=0;DP=498 1 4326343 . CG CGGGGGGGGGGG 100 PASS AF=0.212625;HP=2;NF=5;NR=11;NS=52;CA=0;DP=475 1 4329138 . GTGAT GT 47 PASS AF=0.0168095;HP=1;NF=35;NR=37;NS=52;CA=0;DP=675 1 4329500 venter ATGGTGATGGT AT 100 PASS AF=0.0491;HP=1;NF=35;NR=49;NS=52;CA=0;DP=718 1 4333035 . CCACTC CC 100 PASS AF=0.0536691;HP=2;NF=18;NR=17;NS=52;CA=0;DP=614 1 4333090 . CCCATC CC 100 PASS AF=0.896174;HP=3;NF=52;NR=56;NS=52;CA=0;DP=564 1 4333868 rs34013096;-/CCAT AC ACCATC 100 PASS AF=0.411752;HP=2;DB;NF=63;NR=59;NS=52;CA=0;DP=556 1 4352929 . TAA TA 100 PASS AF=0.0606075;HP=5;NF=10;NR=5;NS=51;CA=0;DP=422 1 4360308 . CAA CA 100 PASS AF=0.160821;HP=3;NF=12;NR=13;NS=52;CA=0;DP=502 1 4360675 rs55750624;-/A GAA GA 100 PASS AF=0.209252;HP=2;DB;NF=18;NR=10;NS=52;CA=0;DP=456 1 4362123 rs57250327;-/AAATT TA TAATTAA 100 PASS AF=0.202867;HP=2;DB;NF=23;NR=24;NS=52;CA=0;DP=404 1 4372014 rs34773421;-/A,venter TAA TA 100 PASS AF=0.507594;HP=2;DB;NF=43;NR=31;NS=52;CA=0;DP=496 1 4373092 . CATTTA CA 100 PASS AF=0.155807;HP=1;NF=19;NR=10;NS=52;CA=0;DP=440 1 4375952 . TCT TT 100 PASS AF=0.0215948;HP=1;NF=3;NR=2;NS=52;CA=0;DP=530 1 4376164 rs57973702;-/TG,venter CG CGTG 100 PASS AF=0.555727;HP=1;DB;NF=33;NR=60;NS=52;CA=0;DP=552 1 4382255 . GT GTT 100 PASS AF=0.134524;HP=8;NF=12;NR=14;NS=52;CA=0;DP=445 1 4382929 . CG CGCCGTGCCCTGCTCAG 100 PASS AF=0.293977;HP=1;NF=3;NR=1;NS=52;CA=0;DP=423 1 4386769 rs34696074;-/G TGG TG 100 PASS AF=0.524405;HP=3;DB;NF=43;NR=31;NS=51;CA=0;DP=586 1 4386900 rs35831569;-/GTGA,watson TG TGTGAG 100 PASS AF=0.786341;HP=1;DB;NF=49;NR=47;NS=52;CA=0;DP=728 1 4387089 rs35106948;-/GA,venter,watson TGAG TG 100 PASS AF=0.76407;HP=1;DB;NF=42;NR=48;NS=52;CA=0;DP=730 1 4398343 rs56075652;-/AGCTAG,mills,venter,watson GGAGCTAG GG 100 PASS AF=0.850798;HP=2;DB;NF=51;NR=52;NS=52;CA=0;DP=535 1 4403445 . ATC AC 100 PASS AF=0.0257077;HP=1;NF=3;NR=3;NS=52;CA=0;DP=579 1 4413424 . GGAAG GG 100 PASS AF=0.0911622;HP=2;NF=13;NR=11;NS=52;CA=0;DP=539 1 4415363 rs35655214;-/A,mills,venter CAA CA 100 PASS AF=0.279808;HP=10;DB;NF=16;NR=13;NS=52;CA=0;DP=623 1 4419729 rs34301403;-/T,venter CT CTT 100 PASS AF=0.276688;HP=3;DB;NF=23;NR=17;NS=52;CA=0;DP=491 1 4429935 . ACC AC 100 PASS AF=0.121066;HP=2;NF=8;NR=7;NS=52;CA=0;DP=509 1 4432975 rs35185885;-/TTAT,venter TT TTTTAT 100 PASS AF=0.370788;HP=4;DB;NF=7;NR=50;NS=51;CA=0;DP=329 1 4433724 . AC ACC 100 PASS AF=0.191535;HP=2;NF=16;NR=17;NS=52;CA=0;DP=609 1 4434361 . GA GATGATATTGAAA 100 PASS AF=0.175787;HP=1;NF=8;NR=5;NS=52;CA=0;DP=496 1 4439328 rs55695069;-/TGTG,watson TGTGAG TG 100 PASS AF=0.115075;HP=1;DB;NF=13;NR=10;NS=51;CA=0;DP=510 1 4444447 . GC GCC 100 PASS AF=0.126735;HP=1;NF=8;NR=6;NS=52;CA=0;DP=442 1 4444562 watson TTCG TG 100 PASS AF=0.167206;HP=3;NF=13;NR=9;NS=52;CA=0;DP=477 1 4448379 rs55971665;-/A,venter GAA GA 100 PASS AF=0.999997;HP=5;DB;NF=29;NR=34;NS=51;CA=0;DP=398 1 4456774 rs34368344;-/CTCA,watson TCTCAC TC 100 PASS AF=0.4985;HP=1;DB;NF=46;NR=35;NS=52;CA=0;DP=679 1 4456823 . TT TTTTCTCTCT 100 PASS AF=0.281015;HP=3;NF=18;NR=7;NS=52;CA=0;DP=566 1 4460399 . CAGA CA 17 PASS AF=0.0162627;HP=1;NF=4;NR=1;NS=52;CA=0;DP=437 1 4461064 . TG TGGG 100 PASS AF=0.136493;HP=8;NF=11;NR=12;NS=52;CA=0;DP=516 1 4461120 . GAGTCA GA 100 PASS AF=0.106497;HP=1;NF=4;NR=10;NS=52;CA=0;DP=513 1 4462914 rs35786528;-/T,venter GTT GT 100 PASS AF=0.636288;HP=9;DB;NF=46;NR=44;NS=52;CA=0;DP=457 1 4464201 rs35933446;-/G AGC AC 100 PASS AF=0.0422945;HP=1;DB;NF=3;NR=5;NS=52;CA=0;DP=559 1 4465553 rs33984734;-/C,mills,venter GCC GC 100 PASS AF=0.832437;HP=3;DB;NF=43;NR=36;NS=52;CA=0;DP=507 1 4465878 rs55781312;-/GAACA,watson TACAGAA TA 100 PASS AF=0.547352;HP=1;DB;NF=48;NR=55;NS=52;CA=0;DP=612 1 4466414 rs34356738;-/T,venter AT ATT 100 PASS AF=0.0343632;HP=4;DB;NF=5;NR=2;NS=52;CA=0;DP=523 1 4468803 . CT CTTTTCTTTTCTTT 100 PASS AF=0.185641;HP=2;NF=2;NR=1;NS=51;CA=0;DP=271 1 4469024 . TT TTGTGT 26 PASS AF=0.65093;HP=2;NF=51;NR=54;NS=51;CA=0;DP=465 1 4470162 rs34280110;-/T,venter CT CTT 100 PASS AF=0.19103;HP=3;DB;NF=13;NR=16;NS=52;CA=0;DP=581 1 4472390 rs35540877;-/AAG TAAGA TA 100 PASS AF=0.0513799;HP=2;DB;NF=4;NR=3;NS=52;CA=0;DP=531 1 4481812 rs34806922;-/A,venter GAA GA 100 PASS AF=0.0356083;HP=3;DB;NF=4;NR=4;NS=52;CA=0;DP=576 1 4482705 . CA CATCTA 100 PASS AF=0.203301;HP=1;NF=34;NR=52;NS=50;CA=M;DP=382 1 4482808 . CTA CA 16 PASS AF=0.0550307;HP=1;NF=1;NR=1;NS=51;CA=M;DP=356 1 4482848 rs5772166;-/TCTCTCTC,mills ATCTCTCTCT AT 100 PASS AF=0.561639;HP=1;DB;NF=52;NR=17;NS=51;CA=M;DP=311 1 4484471 rs3059158;-/CT,mills,watson AG ACTG 100 PASS AF=0.497825;HP=1;DB;NF=31;NR=34;NS=52;CA=0;DP=538 1 4486660 rs34976033;-/CCCT,mills,venter,watson GCTCCC GC 100 PASS AF=0.593551;HP=1;DB;NF=42;NR=55;NS=52;CA=0;DP=566 1 4486840 rs35808993;-/A,venter GAT GT 100 PASS AF=0.0446408;HP=1;DB;NF=4;NR=4;NS=52;CA=0;DP=539 1 4495865 watson TGACCT TT 100 PASS AF=0.477912;HP=1;NF=15;NR=22;NS=52;CA=0;DP=386 1 4498895 . TAAACTCA TA 100 PASS AF=0.365307;HP=3;NF=30;NR=28;NS=52;CA=0;DP=561 1 4499763 . TT TTTTAGTTTAGTTTAGTTTAGTTTAGT 15 PASS AF=0.437504;HP=4;NF=5;NR=8;NS=51;CA=0;DP=440 1 4500994 rs57293099;-/A,venter GG GAG 19 PASS AF=0.533167;HP=5;DB;NF=26;NR=15;NS=51;CA=0;DP=466 1 4501978 rs34937816;-/T,mills,venter GT GTT 100 PASS AF=0.677682;HP=1;DB;NF=47;NR=42;NS=52;CA=0;DP=475 1 4504724 venter,watson TAGACA TA 100 PASS AF=0.381777;HP=1;NF=34;NR=33;NS=52;CA=0;DP=728 1 4504861 venter TACAGAGAGAGACAGAGAGA TA 100 PASS AF=0.208225;HP=1;NF=42;NR=31;NS=52;CA=0;DP=820 1 4506249 rs56013880;-/T,mills,venter GC GTC 100 PASS AF=0.652109;HP=2;DB;NF=41;NR=48;NS=52;CA=0;DP=522 1 4506287 venter TAG TG 100 PASS AF=0.348604;HP=1;NF=23;NR=27;NS=52;CA=0;DP=534 1 4510123 rs35963445;-/C,venter TC TCC 100 PASS AF=0.750939;HP=6;DB;NF=32;NR=50;NS=52;CA=0;DP=488 1 4511427 rs34235356;-/T,venter AT ATT 100 PASS AF=0.559297;HP=8;DB;NF=40;NR=27;NS=52;CA=0;DP=549 1 4512561 rs57315980;-/GAG TGGAG TG 100 PASS AF=0.0276885;HP=2;DB;NF=7;NR=4;NS=52;CA=0;DP=581 1 4512788 rs56318426;-/GGATAGTGTG TC TGTGTGGGATAC 100 PASS AF=0.145759;HP=1;DB;NF=7;NR=6;NS=52;CA=0;DP=570 1 4513234 rs5772168;-/ATCA,venter,watson TA TATCAA 100 PASS AF=0.761132;HP=1;DB;NF=45;NR=38;NS=52;CA=0;DP=478 1 4513552 rs34248962;-/G,venter CTC CC 100 PASS AF=0.397344;HP=1;DB;NF=19;NR=21;NS=52;CA=0;DP=502 1 4518079 . CTTTATGTCAAC CC 31 PASS AF=0.0537494;HP=3;NF=13;NR=6;NS=52;CA=0;DP=567 1 4519870 . CATAA CA 100 PASS AF=0.156873;HP=1;NF=25;NR=19;NS=52;CA=0;DP=518 1 4520552 venter,watson ATATT AT 100 PASS AF=0.0454741;HP=1;NF=13;NR=21;NS=52;CA=0;DP=523 1 4524683 rs60936673;-/A,venter GAC GC 100 PASS AF=0.0433734;HP=1;DB;NF=5;NR=1;NS=51;CA=0;DP=407 1 4531795 . CG CGAGCAGATAG 100 PASS AF=0.0529244;HP=1;NF=2;NR=3;NS=52;CA=0;DP=598 1 4533811 rs61232512;-/TCCCTCCTGGACAGCCAGG,watson TCCTCCTGGACAGCCAGGTCC TC 100 PASS AF=0.455665;HP=2;DB;NF=9;NR=12;NS=52;CA=0;DP=455 1 4535415 rs34971058;-/C,mills,venter GC GCC 100 PASS AF=0.872856;HP=1;DB;NF=71;NR=50;NS=52;CA=0;DP=585 1 4540778 rs5772169;-/T,mills CTG CG 100 PASS AF=0.129616;HP=1;DB;NF=9;NR=6;NS=52;CA=0;DP=518 1 4541031 . TT TTTTCT 100 PASS AF=0.0665496;HP=6;NF=18;NR=24;NS=51;CA=0;DP=371 1 4541492 rs5772170;-/G,mills,venter TG TGG 100 PASS AF=0.912727;HP=3;DB;NF=57;NR=39;NS=52;CA=0;DP=454 1 4542962 . CC CCTCTCTCTCTC 100 PASS AF=0.767807;HP=2;NF=57;NR=35;NS=52;CA=0;DP=481 1 4544333 rs3059964;-/CT,venter ACTC AC 100 PASS AF=0.941425;HP=1;DB;NF=54;NR=73;NS=52;CA=0;DP=591 1 4547027 rs34146010;-/C ACC AC 100 PASS AF=0.974502;HP=2;DB;NF=55;NR=74;NS=52;CA=0;DP=535 1 4547927 rs34056554;-/T,venter ATT AT 100 PASS AF=0.867021;HP=3;DB;NF=7;NR=12;NS=51;CA=0;DP=398 1 4551259 rs34018288;-/TG,venter,watson CT CTGT 100 PASS AF=0.964821;HP=1;DB;NF=25;NR=27;NS=52;CA=0;DP=445 1 4552887 . GT GTCT 100 PASS AF=0.155774;HP=1;NF=6;NR=7;NS=52;CA=0;DP=507 1 4556585 rs3833958;-/GGGCT,venter GA GAGCCCA 100 PASS AF=0.248571;HP=1;DB;NF=9;NR=9;NS=52;CA=0;DP=416 1 4558195 rs58248788;-/T,venter ATT AT 100 PASS AF=0.949748;HP=4;DB;NF=38;NR=18;NS=51;CA=0;DP=446 1 4558625 . AGA AA 100 PASS AF=0.105248;HP=1;NF=12;NR=4;NS=52;CA=0;DP=526 1 4570630 . GT GGGTTT 14 PASS AF=0.0570941;HP=1;NF=4;NR=2;NS=52;CA=0;DP=480 1 4574298 . GC GAC 41 PASS AF=0.0333335;HP=2;NF=1;NR=4;NS=52;CA=0;DP=497 1 4574507 . TT TTCCTCTAATGCT 100 PASS AF=0.406213;HP=2;NF=13;NR=8;NS=52;CA=0;DP=437 1 4577694 rs33988719;-/G,mills,venter TG TGG 100 PASS AF=0.999997;HP=1;DB;NF=52;NR=28;NS=52;CA=0;DP=381 1 4578235 . TAT TT 26 PASS AF=0.292482;HP=1;NF=8;NR=14;NS=51;CA=0;DP=330 1 4580634 . ATAAAATA AA 100 PASS AF=0.328083;HP=1;NF=11;NR=4;NS=51;CA=M;DP=372 1 4581760 . CTT CT 100 PASS AF=0.0551414;HP=2;NF=4;NR=7;NS=52;CA=0;DP=578 1 4583153 rs35427335;-/CA,venter,watson GCAC GC 100 PASS AF=0.0310016;HP=1;DB;NF=3;NR=4;NS=52;CA=0;DP=483 1 4586257 rs34899280;-/T GTC GC 100 PASS AF=0.311452;HP=1;DB;NF=16;NR=8;NS=51;CA=0;DP=441 1 4589959 venter,watson GG GGGCCTG 100 PASS AF=0.0494854;HP=3;NF=3;NR=4;NS=52;CA=0;DP=469 1 4590830 rs34057361;-/GCAAAGC,mills,venter,watson TGCAAAGCG TG 100 PASS AF=0.739178;HP=1;DB;NF=42;NR=52;NS=50;CA=0;DP=465 1 4595540 rs56784481;-/T TCT TT 53 PASS AF=0.154234;HP=1;DB;NF=7;NR=21;NS=52;CA=0;DP=439 1 4596270 . AC ACGCTGAGGCTGCAGCACCCCTCGTGGAGC 100 PASS AF=0.171201;HP=1;NF=6;NR=1;NS=52;CA=0;DP=498 1 4600396 rs36042545;-/AT,venter CATA CA 100 PASS AF=0.185579;HP=1;DB;NF=24;NR=23;NS=52;CA=0;DP=357 1 4603645 rs60786353;-/C,venter AC ACC 100 PASS AF=0.999998;HP=1;DB;NF=76;NR=57;NS=52;CA=0;DP=571 1 4607282 . GTGAT GT 100 PASS AF=0.287968;HP=1;NF=38;NR=26;NS=52;CA=0;DP=810 1 4607435 . GTGAT GT 100 PASS AF=0.347474;HP=1;NF=39;NR=53;NS=52;CA=0;DP=674 1 4611309 . CGTGTG CG 100 PASS AF=0.311775;HP=1;NF=38;NR=31;NS=52;CA=0;DP=486 1 4621966 rs35610947;-/GT TTGT TT 100 PASS AF=0.252136;HP=3;DB;NF=41;NR=42;NS=52;CA=0;DP=612 1 4623256 rs59174221;-/CTCCAGAAAGCAC GGAAAGCACCTCCAG GG 100 PASS AF=0.248792;HP=2;DB;NF=24;NR=28;NS=52;CA=0;DP=458 1 4623618 rs60584333;-/GTGTCGGGAGCAGAGACTG,venter GC GCTGGTGTCGGGAGCAGAGAC 100 PASS AF=0.624955;HP=1;DB;NF=8;NR=16;NS=51;CA=0;DP=518 1 4628242 rs56871532;-/TG,venter,watson CTGT CT 100 PASS AF=0.630417;HP=1;DB;NF=46;NR=41;NS=52;CA=0;DP=605 1 4631325 watson GAGGACATA GA 100 PASS AF=0.0694082;HP=1;NF=14;NR=10;NS=51;CA=0;DP=388 1 4633949 . TCC TC 100 PASS AF=0.223776;HP=7;NF=13;NR=4;NS=51;CA=0;DP=492 1 4637510 . TAAA TA 18 PASS AF=0.0428857;HP=9;NF=13;NR=6;NS=52;CA=0;DP=456 1 4639728 . GGTGTGTGTGTGTGTG GG 56 PASS AF=0.223403;HP=3;NF=39;NR=66;NS=51;CA=0;DP=466 1 4645583 rs59275910;-/G,venter AG AGG 100 PASS AF=0.999998;HP=1;DB;NF=41;NR=59;NS=51;CA=0;DP=416 1 4649824 . CTT CT 100 PASS AF=0.0615007;HP=2;NF=3;NR=3;NS=52;CA=0;DP=371 1 4653490 . GAG GG 19 PASS AF=0.016501;HP=1;NF=1;NR=2;NS=52;CA=0;DP=448 1 4654099 rs3086606;-/GTCTGCA,mills CC CCAGTCTGC 100 PASS AF=0.299705;HP=2;DB;NF=11;NR=10;NS=52;CA=0;DP=440 1 4655877 rs58828516;-/G TG TGG 100 PASS AF=0.083803;HP=6;DB;NF=13;NR=14;NS=52;CA=0;DP=553 1 4656096 rs34592768;-/G,mills TGG TG 100 PASS AF=0.0586852;HP=2;DB;NF=6;NR=4;NS=52;CA=0;DP=486 1 4656943 . GGTGTG GG 53 PASS AF=0.0156574;HP=2;NF=15;NR=18;NS=52;CA=0;DP=804 1 4668803 . CTT CT 39 PASS AF=0.0748695;HP=8;NF=8;NR=6;NS=52;CA=0;DP=401 1 4670089 rs34058244;-/AC,venter GA GACA 100 PASS AF=0.471432;HP=1;DB;NF=47;NR=39;NS=52;CA=0;DP=789 1 4670383 rs35737766;-/TCAC,watson ACACTC AC 100 PASS AF=0.331554;HP=1;DB;NF=20;NR=35;NS=52;CA=0;DP=609 1 4676654 . AGATG AG 10 PASS AF=0.011049;HP=1;NF=15;NR=18;NS=52;CA=0;DP=617 1 4684590 . TCCTGCACCTGCTGTGCCCCTGGCTCCCAGCACC TC 100 PASS AF=0.0368566;HP=2;NF=13;NR=7;NS=52;CA=0;DP=543 1 4689505 . TC TCTGTCCTCTCTCCTAGCTCTGGTGCCCTGAGATGC 100 PASS AF=0.355136;HP=1;NF=2;NR=3;NS=52;CA=0;DP=597 1 4693342 rs3835539;-/TTCA CC CCATTC 100 PASS AF=0.307703;HP=2;DB;NF=60;NR=61;NS=52;CA=0;DP=594 1 4695582 venter TGTGAGG TG 100 PASS AF=0.630317;HP=1;NF=17;NR=29;NS=52;CA=0;DP=408 1 4700273 . GCCT GT 51 PASS AF=0.154012;HP=2;NF=3;NR=3;NS=52;CA=0;DP=402 1 4700727 rs34897087;-/A,venter CG CGG 13 PASS AF=0.0702045;HP=8;DB;NF=22;NR=6;NS=51;CA=M;DP=305 1 4702014 rs34592315;-/AA,venter TAAA TA 100 PASS AF=0.183045;HP=3;DB;NF=9;NR=20;NS=52;CA=0;DP=551 1 4702135 . GCC GC 100 PASS AF=0.132917;HP=5;NF=18;NR=10;NS=52;CA=0;DP=561 1 4702842 rs3835540;-/GAC TGACG TG 100 PASS AF=0.333162;HP=1;DB;NF=25;NR=19;NS=52;CA=0;DP=517 1 4703849 rs35422518;-/TCTCCAGGC,mills,venter,watson AGCTCTCCAGG AG 100 PASS AF=0.461699;HP=1;DB;NF=52;NR=39;NS=52;CA=0;DP=558 1 4704242 . ATT AT 100 PASS AF=0.124811;HP=6;NF=16;NR=12;NS=52;CA=0;DP=518 1 4704545 . GCACAC GC 43 PASS AF=0.374122;HP=1;NF=68;NR=46;NS=52;CA=0;DP=586 1 4709952 rs55677440;-/GT TT TTGT 100 PASS AF=0.111566;HP=3;DB;NF=37;NR=55;NS=52;CA=0;DP=757 1 4712998 rs35177072;-/CTC,mills,venter,watson TCTCC TC 100 PASS AF=0.409205;HP=1;DB;NF=23;NR=30;NS=52;CA=0;DP=527 1 4714785 rs3835541;-/A,venter CAA CA 100 PASS AF=0.207747;HP=2;DB;NF=12;NR=9;NS=52;CA=0;DP=525 1 4715739 . GT GTT 100 PASS AF=0.0593871;HP=1;NF=4;NR=4;NS=52;CA=0;DP=486 1 4717874 rs33969697;-/C,mills,venter TCA TA 100 PASS AF=0.644689;HP=1;DB;NF=37;NR=47;NS=52;CA=0;DP=521 1 4720164 rs5772181;-/GA,mills,venter,watson TG TGAG 100 PASS AF=0.660601;HP=1;DB;NF=60;NR=61;NS=52;CA=0;DP=723 1 4725394 venter AG AGAGAGACATGAGTGAAGAAGG 100 PASS AF=0.486541;HP=1;NF=34;NR=40;NS=52;CA=0;DP=600 1 4726136 rs35816653;-/T,venter CT CTT 100 PASS AF=0.325542;HP=7;DB;NF=25;NR=33;NS=52;CA=0;DP=561 1 4728249 rs35594902;-/TGTT CT CTGTTT 100 PASS AF=0.236832;HP=1;DB;NF=16;NR=16;NS=52;CA=0;DP=595 1 4730619 rs56688128;-/AAGGC,venter,watson ACAAGGC AC 100 PASS AF=0.197783;HP=1;DB;NF=14;NR=10;NS=52;CA=0;DP=450 1 4738491 . ATCTCTCTCTCTCTCTCTCTCT AT 100 PASS AF=0.109332;HP=1;NF=34;NR=36;NS=52;CA=0;DP=556 1 4743143 rs34960969;-/T,venter ATT AT 100 PASS AF=0.443382;HP=2;DB;NF=27;NR=29;NS=51;CA=0;DP=521 1 4750482 . AC ACC 44 PASS AF=0.0773717;HP=1;NF=1;NR=10;NS=52;CA=0;DP=532 1 4751808 . CC CTC 100 PASS AF=0.287743;HP=6;NF=22;NR=19;NS=52;CA=0;DP=549 1 4753639 rs56735073;-/G AG AGG 100 PASS AF=0.354197;HP=6;DB;NF=26;NR=25;NS=52;CA=0;DP=499 1 4756338 . TGG TG 100 PASS AF=0.145276;HP=6;NF=12;NR=22;NS=52;CA=0;DP=505 1 4756654 . CTGT CT 100 PASS AF=0.0253358;HP=1;NF=2;NR=3;NS=52;CA=0;DP=502 1 4768227 rs34482713;-/A,venter CAC CC 100 PASS AF=0.624286;HP=1;DB;NF=16;NR=29;NS=52;CA=0;DP=382 1 4769408 rs3030792;-/CA,venter TC TCAC 100 PASS AF=0.564397;HP=1;DB;NF=37;NR=45;NS=51;CA=0;DP=550 1 4771107 rs59952959;-/TTATCGGTGGTTT ATTATCGGTGGTTTC AC 100 PASS AF=0.43732;HP=2;DB;NF=24;NR=26;NS=52;CA=0;DP=437 1 4771150 . AGGCAGAGGATTTAGGGGGCAGTGAAACTA AA 100 PASS AF=0.365014;HP=2;NF=25;NR=17;NS=51;CA=0;DP=446 1 4773228 . AACA AA 100 PASS AF=0.358433;HP=4;NF=49;NR=37;NS=51;CA=0;DP=403 1 4779293 rs35799766;-/A,venter GAA GA 100 PASS AF=0.620558;HP=4;DB;NF=40;NR=44;NS=52;CA=0;DP=539 1 4783405 . TACGTATATACATATACA TA 100 PASS AF=0.346752;HP=1;NF=20;NR=40;NS=52;CA=0;DP=331 1 4784171 . TA TAAGA 100 PASS AF=0.058761;HP=2;NF=4;NR=4;NS=52;CA=0;DP=522 1 4787548 rs35350740;-/CA,mills AACA AA 100 PASS AF=0.294238;HP=3;DB;NF=43;NR=40;NS=52;CA=0;DP=565 1 4790642 rs5772184;-/T,venter ATT AT 100 PASS AF=0.360239;HP=10;DB;NF=23;NR=25;NS=52;CA=0;DP=544 1 4794867 . AATA AA 59 PASS AF=0.0541594;HP=2;NF=6;NR=24;NS=52;CA=0;DP=316 1 4794934 . CT CTCTCTTT 21 PASS AF=0.322809;HP=1;NF=7;NR=9;NS=50;CA=M;DP=241 1 4800829 rs35005833;-/C,venter TC TCC 100 PASS AF=0.404199;HP=5;DB;NF=48;NR=15;NS=52;CA=0;DP=479 1 4806476 . GC GCC 100 PASS AF=0.0973173;HP=6;NF=8;NR=8;NS=52;CA=M;DP=398 1 4808450 rs34573971;-/A,venter GAA GA 100 PASS AF=0.332411;HP=9;DB;NF=26;NR=22;NS=52;CA=0;DP=474 1 4809140 rs60726929;-/TCCA,venter,watson TC TCATCC 100 PASS AF=0.348085;HP=1;DB;NF=49;NR=32;NS=52;CA=0;DP=579 1 4810276 rs3030822;-/TAGT,watson ATAGTT AT 100 PASS AF=0.242205;HP=1;DB;NF=27;NR=13;NS=52;CA=0;DP=582 1 4831434 . TA TACCACACACACA 100 PASS AF=0.49717;HP=1;NF=18;NR=17;NS=52;CA=0;DP=675 1 4831567 rs34042090;-/CA CCAC CC 100 PASS AF=0.535527;HP=4;DB;NF=52;NR=45;NS=52;CA=0;DP=738 1 4833596 rs35226825;-/T AT ATT 100 PASS AF=0.237481;HP=5;DB;NF=19;NR=19;NS=52;CA=0;DP=498 1 4839967 . TCCTGCCAGCCGGGGGC TC 100 PASS AF=0.0394386;HP=2;NF=5;NR=2;NS=52;CA=0;DP=565 1 4840948 rs59349393;-/AAACCACATCCCTTGAACT GACTAAACCACATCCCTTGAA GA 100 PASS AF=0.144437;HP=1;DB;NF=16;NR=17;NS=52;CA=0;DP=578 1 4846284 rs36118323;-/T,venter CT CTT 100 PASS AF=0.130437;HP=7;DB;NF=12;NR=15;NS=52;CA=0;DP=415 1 4855247 venter GA GACACA 100 PASS AF=0.301971;HP=1;NF=19;NR=3;NS=52;CA=0;DP=635 1 4864897 venter AT ATT 100 PASS AF=0.215684;HP=6;NF=17;NR=20;NS=52;CA=0;DP=450 1 4865373 rs34273857;-/A,venter CA CAA 100 PASS AF=0.169967;HP=6;DB;NF=17;NR=15;NS=52;CA=0;DP=533 pysam-0.23.0/tests/tabix_data/vcf/4.vcf000066400000000000000000012320201475062545500176250ustar00rootroot00000000000000##fileformat=VCFv4.1 ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##fileDate=20110524 ##reference=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz ##source=EricBanksValidationQC;fromGoncaloAbecasisValidationSelection #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00127 HG00128 HG00136 HG00137 HG00138 HG00139 HG00152 HG00156 HG00234 HG00235 HG00237 HG00242 HG00244 HG00262 HG01055 HG01079 NA19138 NA18974 NA18523 NA12717 NA19209 NA18577 NA18973 NA18943 NA12873 NA18623 NA18622 NA18948 NA19171 NA19204 NA06994 NA18563 NA18547 NA18861 NA18608 NA12282 NA12751 NA18959 NA19331 NA19453 NA20537 NA12046 NA20515 NA20516 NA20521 NA20524 NA20528 NA20759 NA20768 NA20769 NA20774 NA20775 NA20783 NA20787 NA20790 NA20800 NA20819 NA20812 NA20505 NA20530 NA20540 NA20538 NA20581 NA20815 NA20544 NA20810 NA20807 NA20816 NA20504 NA20753 NA20502 NA12342 NA19150 NA19468 NA20336 NA19395 NA19257 NA19360 NA19700 NA18867 NA20317 NA18968 NA19107 HG00111 HG00108 NA19077 NA19684 NA18511 NA12044 NA19382 NA19457 NA18933 NA18923 NA18965 HG00141 NA20341 NA18740 HG00537 HG00346 HG01173 HG00702 HG00313 HG00150 NA18612 HG00339 NA12273 HG00250 NA18593 NA18621 HG00478 HG00251 HG01070 NA19160 NA18995 NA10851 NA18976 NA18603 NA19200 HG01204 HG01191 HG01101 HG00146 HG00306 NA18985 HG00160 HG00635 HG00372 HG00357 HG00634 NA18541 NA18950 NA19759 HG00351 HG00257 HG00118 HG00336 HG00448 HG01354 NA18609 HG00428 HG00326 NA11894 NA18956 HG00173 HG00117 NA11893 HG01251 HG01441 HG01437 HG00182 HG00330 HG01060 HG00329 NA18960 NA18856 NA07346 NA18871 NA19057 NA18868 NA18636 NA12830 NA19007 NA18910 NA18874 NA19056 NA19064 NA19066 NA18487 NA18642 NA19236 NA07056 NA18637 NA19235 NA19309 NA19311 NA19334 NA19346 NA19347 NA19372 NA19376 NA19383 NA19384 NA19394 NA19428 NA19430 NA19451 NA19466 NA19313 NA19321 NA19324 NA19332 HG00479 HG00608 NA18573 HG00375 NA19248 NA19093 HG01170 HG00534 HG01171 HG01522 NA18624 HG00683 HG01521 NA19005 NA20412 NA18971 HG00446 NA12748 HG00530 HG00690 HG01356 HG01516 NA20532 HG00344 HG00328 NA18542 HG00254 HG00321 HG00577 HG00656 HG00342 HG00524 HG00650 HG00557 HG00319 HG00457 HG00125 HG00578 HG00543 HG00638 HG00171 HG00699 HG00595 HG00187 HG00704 HG00533 HG00596 HG00268 HG01083 HG00651 HG01133 HG00671 HG00327 HG01148 HG00246 HG00672 HG00556 HG00436 HG00554 NA18633 NA20344 NA11993 NA07037 NA11930 HG01366 HG01389 HG00620 NA19740 HG00190 HG00419 NA18535 HG01495 NA18592 HG01497 HG00174 HG01140 NA12287 HG00689 HG01550 HG00334 HG01375 HG00637 NA18507 HG01113 NA18550 NA19129 HG01551 HG01462 HG00331 NA12413 HG01456 HG01360 HG00708 HG01350 HG00684 NA19099 HG00284 NA12399 NA12286 NA12777 HG00277 HG00266 NA19985 HG00353 HG01102 NA07347 NA07051 NA19900 NA18984 NA07048 HG00640 HG01066 NA12812 HG01174 HG01188 NA19390 NA19436 NA19439 NA19440 NA19463 NA19470 NA19471 NA19472 NA19676 NA19660 NA19661 NA19663 NA19722 NA19725 NA19728 NA19729 NA19731 NA19749 NA19755 NA19756 NA19758 NA19770 NA19773 NA19777 NA19780 NA19783 NA20525 NA20589 NA20765 NA20802 NA20804 NA18544 NA18602 NA18546 NA18610 NA18957 NA18615 NA18616 NA19010 NA18638 NA18639 NA18627 NA19072 NA18630 NA19074 NA19080 NA19081 NA19083 NA19085 NA19088 NA20287 NA19835 NA20276 NA19818 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C T 100 PASS SEQUENOM.AC=3;SRC=2-OF-7-ONLY;PQ=19 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1577285 . G A 4 HIGH_NO_CALL_RATE SEQUENOM.AC=0;SRC=VQSR-ONLY;PQ=57 GT . . . 0/0 0/0 . 0/0 . . . 0/0 0/0 . 0/0 . . 0/0 0/0 . . . 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 . 0/0 . 0/0 . 0/0 0/0 . . 0/0 . . . 0/0 . 0/0 . . . 0/0 . . . . . . 0/0 . 0/0 . 0/0 0/0 . 0/0 . . . 0/0 . . . . . 0/0 0/0 . . . . 0/0 0/0 . 0/0 . . 0/0 0/0 . . . . . 0/0 . 0/0 . . . 0/0 0/0 0/0 0/0 . . 0/0 0/0 . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 . . . 0/0 0/0 0/0 0/0 0/0 . . . 0/0 0/0 . 0/0 0/0 . . . 0/0 . . 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 . . . . . 0/0 . 0/0 . 0/0 . . . 0/0 0/0 0/0 0/0 . . . . 0/0 . . . . . . . . 0/0 . . . 0/0 . . . . . . . . . . . . 0/0 . . 0/0 0/0 . 0/0 . . 0/0 . 0/0 . 0/0 . . 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 . . . 0/0 . . . 0/0 0/0 . . 0/0 0/0 0/0 . 0/0 . . 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 . . . . . 0/0 0/0 0/0 0/0 . 0/0 . . 0/0 0/0 . . . 0/0 . 0/0 . . . 0/0 . 0/0 0/0 . . 0/0 . 0/0 0/0 . . 0/0 . . . . . . 0/0 . 0/0 0/0 . 0/0 . . . 0/0 . . . 0/0 . 0/0 0/0 . . . . 0/0 0/0 0/0 . . . . 0/0 0/0 . . . . . . 0/0 0/0 . . . . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 . . . . 0/0 0/0 0/0 . 0/0 . 0/0 . 0/0 0/0 . 0/0 . 0/0 . 0/0 . 0/0 . . . . . 0/0 0/0 0/0 . . 0/0 0/0 20 1577845 . 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G A 9 NOT_DESIGNED BCM.AC=4;SRC=VQSR+2-OF-7 20 2280790 rs214779 T A 57436 NOT_DESIGNED BCM.AC=758;DB;SRC=VQSR+2-OF-7 20 2843004 rs118020362 T C 131 PASS BCM.AC=4;DB;SEQUENOM.AC=4;SRC=VQSR+INTERSECTION;PQ=57 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 2854191 . C T 78 POSSIBLE_PROBE_FAILURE BCM.AC=25;SEQUENOM.AC=0;SRC=VQSR+2-OF-7;PQ=60 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 2999522 . 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T G 86 NOT_TYPED;PQ10 BCM.AC=493;SRC=VQSR-ONLY;PQ=0 20 25751184 . G C 100 NOT_TYPED;PQ10 BCM.AC=180;SRC=2-OF-7-ONLY;PQ=0 20 25766473 . T A 124 NOT_TYPED;PQ10 SRC=VQSR+2-OF-7;PQ=0 20 25789517 . A T 40 NOT_TYPED;PQ10 BCM.AC=319;SRC=VQSR+2-OF-7;PQ=0 20 25794555 . G A 18 NOT_TYPED;PQ10 BCM.AC=181;SRC=VQSR-ONLY;PQ=0 20 25922316 . T C 26 PASS BCM.AC=1;SEQUENOM.AC=0;SRC=VQSR+2-OF-7;PQ=18 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 25999667 . 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G A 26 NOT_TYPED;PQ10 BCM.AC=354;SRC=VQSR-ONLY;PQ=0 20 26057903 . G A 100 NOT_TYPED;PQ10 SRC=2-OF-7-ONLY;PQ=0 20 26071009 . 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0/0 0/0 0/0 0/0 0/0 20 29574811 rs73620522 G A 16281 HIGH_NO_CALL_RATE DB;SEQUENOM.AC=24;SRC=VQSR-ONLY;PQ=15 GT 0/1 1/1 1/1 . 1/1 1/1 0/1 1/1 1/1 . 1/1 1/1 . . 0/0 . . 1/1 . 1/1 1/1 . 1/1 1/1 0/1 1/1 . . 1/1 0/0 . 1/1 1/1 1/1 1/1 1/1 . 1/1 1/1 . 1/1 . . 1/1 . . . . 1/1 1/1 . . . . . . . . . . . 1/1 1/1 1/1 1/1 1/1 . 1/1 1/1 . . . . . 1/1 . 1/1 . 0/1 . . . 0/1 . 1/1 . 1/1 . 1/1 1/1 0/1 1/1 . . 1/1 . 1/1 . . . 1/1 1/1 . . 1/1 . . . 1/1 1/1 1/1 . 1/1 1/1 . 1/1 1/1 . 1/1 1/1 . 1/1 1/1 . 1/1 . 0/1 1/1 1/1 . 1/1 . . 1/1 1/1 . 1/1 1/1 1/1 1/1 1/1 . 1/1 1/1 . . 1/1 . 1/1 1/1 . . . . . 1/1 . 1/1 1/1 . 1/1 1/1 . 1/1 1/1 . 1/1 1/1 . 1/1 . . 1/1 1/1 . 1/1 . . 1/1 . . . 0/0 . 1/1 1/1 . . . . 1/1 1/1 . 1/1 1/1 . 1/1 . . . 1/1 . 1/1 1/1 . 1/1 . . . 1/1 1/1 1/1 1/1 . 1/1 . 1/1 . . . . . . . 1/1 . . . . . . . . . . 1/1 1/1 1/1 1/1 1/1 1/1 . . . . . 1/1 1/1 1/1 . 1/1 . . . . . . . 1/1 1/1 1/1 1/1 1/1 . 1/1 . . . . . . 1/1 1/1 1/1 . 1/1 0/0 . . . . . 1/1 1/1 1/1 1/1 1/1 . . 1/1 . 1/1 . 0/1 1/1 1/1 . 1/1 1/1 1/1 . . . . 1/1 . . . . . . . . . . . 1/1 1/1 . . 1/1 1/1 . 1/1 . 0/0 . . . . . . . 0/0 . . . . 1/1 . 1/1 1/1 1/1 1/1 1/1 1/1 . 1/1 . . . . 1/1 1/1 1/1 1/1 0/0 . . . 1/1 . . 1/1 . 1/1 1/1 1/1 1/1 1/1 . 1/1 1/1 . 1/1 . 1/1 . . 1/1 1/1 1/1 0/0 20 29598472 rs73612735 T G 10639 NOT_TYPED;PQ10 DB;SRC=VQSR-ONLY;PQ=0 20 29632410 . T C 5.11 NOT_TYPED;PQ10 SRC=2-OF-7-ONLY;PQ=0 20 29642272 rs77298479 T A 100 NOT_TYPED;PQ10 DB;SRC=2-OF-7-ONLY;PQ=9 20 29827087 rs62641496 G C 100 NOT_DESIGNED DB;SRC=2-OF-7-ONLY 20 30120025 . C G 1113 POSSIBLE_PROBE_FAILURE;PQ10 BCM.AC=9;SEQUENOM.AC=0;SRC=VQSR+2-OF-7;PQ=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 30595334 rs62206358 C A 62 PASS BCM.AC=3;DB;SEQUENOM.AC=1;SRC=VQSR+2-OF-7;PQ=20 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 30616314 . 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T C 5 NOT_DESIGNED SRC=VQSR-ONLY 20 41137712 rs230167 C T 24 NOT_DESIGNED DB;SRC=VQSR+2-OF-7 20 41311175 . 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T C 198 NOT_DESIGNED BCM.AC=9;SRC=VQSR+2-OF-7 20 54313664 rs112885916 A T 98 PASS BCM.AC=10;DB;SEQUENOM.AC=0;SRC=VQSR+2-OF-7;PQ=57 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 54424603 . T C 116 PQ10 BCM.AC=8;SEQUENOM.AC=0;SRC=VQSR+2-OF-7;PQ=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 54542220 . C T 33 NOT_DESIGNED SRC=VQSR-ONLY 20 54628591 . G A 87 POLYMORPHIC_SAMPLES_FAILED;PQ10 BCM.AC=2;SEQUENOM.AC=4;SRC=VQSR+2-OF-7;PQ=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 54793377 . C T 8 HIGH_NO_CALL_RATE BCM.AC=1;SEQUENOM.AC=0;SRC=VQSR-ONLY;PQ=60 GT . . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . 0/0 0/0 0/0 . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0/0 0/0 . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 55067830 . 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T A 100 PASS SEQUENOM.AC=0;SRC=2-OF-7-ONLY;PQ=11 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 62724959 . G T 10 NOT_DESIGNED SRC=VQSR-ONLY 20 62888718 . T C 57 POLYMORPHIC_SAMPLES_FAILED BCM.AC=1;SEQUENOM.AC=0;SRC=VQSR+2-OF-7;PQ=60 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 62918298 . G A 33 NOT_DESIGNED SRC=VQSR+2-OF-7 20 62961477 . T C 17 AMBIGUOUS_SEQUENOM_CALLS;PQ10 SEQUENOM.AC=0;SRC=VQSR+2-OF-7;PQ=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 pysam-0.23.0/tests/tabix_data/vcf/5.vcf000066400000000000000000004070371475062545500176410ustar00rootroot00000000000000##fileformat=VCFv4.0 ##fileDate=2011-07-18 ##source=Platypus_Version_0.1 ##platypusOptions={'bamFiles': ['/data/lindah/illumina_projects/rimmer_indels/AllData.bam'], 'labels': None, 'refFile': '/ib/groups/bsg/scratch/rimmer/Genomes/human_g1k_v37_ebv.fa', 'maxHaplotypes': 256, 'maxSize': 250, 'parseNCBI': 0, 'ploidy': 2, 'bufferSize': 1000000, 'nCPU': 1, 'minFlank': 3, 'minPosterior': 5, 'logFileName': 'log.txt', 'regions': ['20'], 'processRegionSize': 30000000, 'maxVariants': 8, 'maxReads': 5000000, 'genIndels': 1, 'minReads': 2, 'dataType': 'population', 'minMapQual': 20, 'rlen': 150, 'nInd': 1, 'getVariantsFromBAMs': 1, 'genSNPs': 1, 'strandFilter': 0, 'verbosity': 2, 'sourceFile': None, 'callOnlyIndels': 0, 'output': 'test.vcf', 'minBaseQual': 20} ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AllData.bam 20 67500 . T TTGGTATCTAG . PASS FR=0.5;HP=2;NF=6;NR=2;PP=100.0;SC=CCTGATTTCCTTGGTATTAAA;TC=20;TR=8 GT:GL:GQ 0/1:-198.02,-21.47,-166.02:100 20 69506 . G GAC,GACACAC . PASS FR=0.5,0.5;HP=1;NF=1,3;NR=1,0;PP=44.0,72.0;SC=TGGACACGTGGACACACACAC;TC=20;TR=2,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 70484 . CTCTT C . PASS FR=0.5;HP=2;NF=13;NR=3;PP=100.0;SC=GTCTATGTCTCTCTTTCTCTT;TC=31;TR=16 GT:GL:GQ 0/1:-189.04,-24.53,-147.47:100 20 72104 . TA T . PASS FR=0.5;HP=4;NF=9;NR=10;PP=100.0;SC=TTTAAGTCTGTAAAACCATAC;TC=39;TR=19 GT:GL:GQ 0/1:-173.69,-34.04,-169.85:100 20 74729 . G GT . PASS FR=0.5;HP=9;NF=4;NR=4;PP=100.0;SC=AAGTTTTTTGGTTTTTTTTTA;TC=29;TR=8 GT:GL:GQ 0/1:-83.86,-25.71,-59.16:100 20 117309 . G GCAGGATTTCAT . PASS FR=0.5;HP=1;NF=4;NR=4;PP=100.0;SC=CAGGATTTCTGCAGGATTTCA;TC=25;TR=8 GT:GL:GQ 0/1:-259.57,-46.67,-146.18:100 20 119645 . G GT . PASS FR=1.0;HP=5;NF=6;NR=5;PP=100.0;SC=TTGTTTGTTTGTTGTTGTTGT;TC=16;TR=11 GT:GL:GQ 1/1:-157.48,-18.84,-7.1:77 20 120122 . A AAG . PASS FR=1.0;HP=6;NF=10;NR=8;PP=100.0;SC=ATAAAGAAAAAAATTTTAAAA;TC=27;TR=18 GT:GL:GQ 1/1:-266.98,-24.1,-5.49:100 20 120750 . C CAATT . PASS FR=1.0;HP=6;NF=10;NR=10;PP=100.0;SC=TTTTATAAAACAATTGAGACT;TC=21;TR=20 GT:GL:GQ 1/1:-319.22,-18.71,-2.07:100 20 122806 . T TTA . PASS FR=0.5;HP=2;NF=8;NR=7;PP=100.0;SC=CAGAAAAGAATTATATATATA;TC=29;TR=15 GT:GL:GQ 0/1:-181.3,-19.86,-96.14:100 20 126155 . GCAAA G . PASS FR=0.5;HP=1;NF=5;NR=5;PP=100.0;SC=GCAATGTGCGGCAAACAAAGG;TC=32;TR=10 GT:GL:GQ 0/1:-122.73,-27.0,-209.16:100 20 126310 . ACC A . PASS FR=0.5;HP=5;NF=3;NR=8;PP=100.0;SC=GATGGCTCCTACCCCCGTTTC;TC=26;TR=11 GT:GL:GQ 0/1:-153.97,-42.91,-110.82:100 20 131505 . CTCT C . PASS FR=1.0;HP=2;NF=11;NR=11;PP=100.0;SC=TACTTGTGATCTCTTGTCTTT;TC=24;TR=22 GT:GL:GQ 1/1:-487.46,-251.24,-235.3:100 20 131948 . C CCA . PASS FR=1.0;HP=1;NF=2;NR=11;PP=100.0;SC=TTATCTTACACCACACACACA;TC=27;TR=13 GT:GL:GQ 1/1:-201.6,-36.32,-23.94:100 20 135116 . T TTTGCATTCACAGGAAGACTATAAATA . PASS FR=1.0;HP=2;NF=2;NR=1;PP=100.0;SC=TCTAGAGAAGTGCTCTCCAAT;TC=15;TR=3 GT:GL:GQ 1/1:-603.73,-461.77,-448.12:100 20 135119 . TC T . PASS FR=1.0;HP=2;NF=2;NR=2;PP=100.0;SC=AGAGAAGTGCTCTCCAATAGA;TC=21;TR=4 GT:GL:GQ 1/1:-603.73,-576.89,-572.06:100 20 137518 . GTA G . PASS FR=0.5005;HP=2;NF=5;NR=5;PP=100.0;SC=GTGTGTGTGTGTATATATATA;TC=21;TR=10 GT:GL:GQ 1/0:-210.61,-46.97,-32.7:29 20 138178 . GC G . PASS FR=1.0;HP=3;NF=21;NR=5;PP=100.0;SC=CTTCTGGAAAGCCTGGCCATG;TC=29;TR=26 GT:GL:GQ 1/1:-267.55,-29.21,-9.21:100 20 138570 . ATATGTGTGTG ATG,A . PASS FR=0.5,0.5;HP=2;NF=6,2;NR=9,2;PP=100.0,10.0;SC=TCAAATATATATATGTGTGTG;TC=28;TR=15,4 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:65 20 140396 . TTTG T . PASS FR=1.0;HP=2;NF=15;NR=4;PP=100.0;SC=AGGTTTTTGCTTTGTTGTTGT;TC=34;TR=19 GT:GL:GQ 1/1:-246.82,-30.67,-15.42:100 20 144832 . C CT . PASS FR=1.0;HP=3;NF=12;NR=22;PP=100.0;SC=TCCTAAAACTCTTGTAATATC;TC=35;TR=34 GT:GL:GQ 1/1:-541.89,-322.78,-299.72:100 20 144884 . CCTT C . PASS FR=1.0;HP=1;NF=9;NR=16;PP=100.0;SC=TGTAATGACACCTTCTTTTTC;TC=29;TR=25 GT:GL:GQ 1/1:-590.4,-430.25,-411.02:100 20 145257 . G GC . PASS FR=1.0;HP=2;NF=11;NR=8;PP=100.0;SC=ATGGTGGCAGGGCCTGTAATC;TC=21;TR=19 GT:GL:GQ 1/1:-258.74,-106.61,-91.83:100 20 153298 . T TTC . PASS FR=1.0;HP=2;NF=13;NR=17;PP=100.0;SC=CAGGATTTCTTTGTTTTAAGA;TC=34;TR=30 GT:GL:GQ 1/1:-447.58,-228.67,-205.19:100 20 160111 . A AT . PASS FR=1.0;HP=10;NF=8;NR=9;PP=100.0;SC=GAGCTCTTGAATTTTTTTTTT;TC=25;TR=17 GT:GL:GQ 1/1:-115.49,-38.32,-28.08:85 20 163607 . A AAT . PASS FR=1.0;HP=2;NF=12;NR=14;PP=100.0;SC=ACATTAAATGATTCAAATGAT;TC=31;TR=26 GT:GL:GQ 1/1:-308.34,-35.98,-14.5:100 20 163741 . T TACACAC . PASS FR=0.5243;HP=1;NF=13;NR=6;PP=100.0;SC=GAACCCTCTGTACACACACAC;TC=28;TR=19 GT:GL:GQ 0/1:-416.01,-75.48,-55.48:13 20 164279 . G GAAAAC . PASS FR=0.5;HP=8;NF=1;NR=1;PP=100.0;SC=GAAAAGAAAAGAAAAGAAAAC;TC=34;TR=2 GT:GL:GQ 0/1:-492.01,-428.61,-448.28:100 20 164284 . G GAAAAC,C . PASS FR=0.5,0.5;HP=8;NF=5,10;NR=11,9;PP=100.0,100.0;SC=GAAAAGAAAAGAAAACTCATC;TC=33;TR=16,19 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 176386 . CGTGTGT C . PASS FR=1.0;HP=2;NF=3;NR=2;PP=100.0;SC=TAATCCCATTCGTGTGTGTGT;TC=25;TR=5 GT:GL:GQ 1/1:-176.18,-68.1,-61.92:77 20 179735 . TTAAAA T . PASS FR=0.5;HP=1;NF=4;NR=4;PP=100.0;SC=ACCTTTGATCTTAAAATAAAA;TC=27;TR=8 GT:GL:GQ 0/1:-142.0,-61.37,-164.64:100 20 218255 . A AG . PASS FR=0.5;HP=1;NF=5;NR=3;PP=100.0;SC=TGCTCACTGCAATAAAAAGAA;TC=17;TR=8 GT:GL:GQ 0/1:-99.61,-20.66,-85.67:100 20 222539 . C CA . PASS FR=0.5;HP=2;NF=1;NR=9;PP=100.0;SC=TACCCAGCTACTTCTCTTAAG;TC=31;TR=10 GT:GL:GQ 0/1:-113.51,-40.72,-197.06:100 20 230058 . CAT C . PASS FR=0.5;HP=1;NF=6;NR=2;PP=100.0;SC=GACTCCATCTCATAAAAAAAA;TC=33;TR=8 GT:GL:GQ 0/1:-215.64,-148.07,-177.0:100 20 236459 . G GAT . PASS FR=0.5001;HP=2;NF=1;NR=1;PP=100.0;SC=TTGGAATACAGATATATATAT;TC=14;TR=2 GT:GL:GQ 0/1:-82.0,-46.74,-54.25:35 20 237649 . CAGAT C . PASS FR=0.5;HP=2;NF=1;NR=1;PP=79.0;SC=AGATAGATGACAGATAGATAG;TC=23;TR=2 GT:GL:GQ 0/1:-209.52,-180.44,-254.54:100 20 237816 . A AT . PASS FR=0.5;HP=4;NF=4;NR=7;PP=100.0;SC=CATTTTCATCATTTTAATAAC;TC=32;TR=11 GT:GL:GQ 0/1:-124.3,-28.61,-145.84:100 20 243223 . C CT . PASS FR=0.5;HP=1;NF=12;NR=4;PP=100.0;SC=ATCTGTGTGACTGTGATCAAA;TC=33;TR=16 GT:GL:GQ 0/1:-191.55,-34.68,-144.05:100 20 246483 . T TTAAA . PASS FR=0.5;HP=1;NF=3;NR=4;PP=100.0;SC=AGACTCCATCTTAAATAAATA;TC=25;TR=7 GT:GL:GQ 0/1:-110.34,-17.05,-40.1:100 20 251373 . ACTT A . PASS FR=0.5;HP=2;NF=1;NR=4;PP=100.0;SC=TTGCTCCAGCACTTCTTCTGG;TC=19;TR=5 GT:GL:GQ 0/1:-99.2,-52.91,-150.48:100 20 271135 . G GC . PASS FR=1.0;HP=2;NF=3;NR=4;PP=100.0;SC=AAGACCGAGGGCGACCTCGAG;TC=16;TR=7 GT:GL:GQ 1/1:-163.65,-94.48,-85.08:78 20 286648 . TAAATA T . PASS FR=0.5;HP=6;NF=5;NR=5;PP=100.0;SC=TCTAAATAAATAAATAAAAGG;TC=22;TR=10 GT:GL:GQ 0/1:-240.51,-100.72,-176.05:100 20 299585 . AC A . PASS FR=1.0;HP=2;NF=4;NR=7;PP=21.0;SC=ACAGGGAGAGACCTTGTCGAA;TC=14;TR=11 GT:GL:GQ 1/1:-152.36,-140.91,-138.05:46 20 334317 . TC T . PASS FR=1.0;HP=6;NF=9;NR=8;PP=100.0;SC=CCTGGATCCTTCCCCCCTTCT;TC=24;TR=17 GT:GL:GQ 1/1:-177.37,-48.79,-33.34:100 20 337392 . ACC A . PASS FR=0.5;HP=6;NF=5;NR=1;PP=100.0;SC=CCTTGTTACCACCCCTCCCTG;TC=19;TR=6 GT:GL:GQ 0/1:-91.61,-45.67,-115.7:100 20 340044 . GCAC G . PASS FR=0.5;HP=1;NF=2;NR=5;PP=100.0;SC=ATGAAGGCTGGCACCACCAGT;TC=22;TR=7 GT:GL:GQ 0/1:-122.54,-28.81,-115.11:100 20 343323 . A ATG . PASS FR=0.5;HP=2;NF=8;NR=4;PP=100.0;SC=GATAAACAGGATGTCCACCAG;TC=23;TR=12 GT:GL:GQ 0/1:-150.99,-48.03,-125.5:100 20 346702 . AGCCTCCCAAAGGAG A . PASS FR=0.5;HP=1;NF=4;NR=3;PP=100.0;SC=CACCCACCTCAGCCTCCCAAA;TC=17;TR=7 GT:GL:GQ 0/1:-191.1,-120.01,-173.49:100 20 347858 . A AAAACAAAC . PASS FR=0.5;HP=4;NF=2;NR=1;PP=100.0;SC=TCCGTCTCCAAAAACAAACAA;TC=22;TR=3 GT:GL:GQ 0/1:-270.04,-201.07,-226.88:100 20 347878 . A AAAAC . PASS FR=0.5;HP=3;NF=2;NR=1;PP=100.0;SC=AAAAAACAAAACAAACAAACA;TC=22;TR=3 GT:GL:GQ 0/1:-258.23,-262.98,-327.72:100 20 348365 . G GT . PASS FR=0.5;HP=2;NF=5;NR=4;PP=100.0;SC=ACGGCCCATGGGATCGAATAG;TC=19;TR=9 GT:GL:GQ 0/1:-127.12,-35.07,-72.46:100 20 349321 . ACT A . PASS FR=0.5;HP=3;NF=10;NR=3;PP=100.0;SC=CCAGGCCTCCACTCTCTGCTG;TC=20;TR=13 GT:GL:GQ 0/1:-183.61,-95.19,-129.48:100 20 355549 . A AC . PASS FR=1.0;HP=10;NF=12;NR=9;PP=100.0;SC=AACAACAACAAAAAAAAAAAC;TC=24;TR=21 GT:GL:GQ 1/1:-171.74,-97.15,-84.12:100 20 356670 . T TCAAA . PASS FR=0.5;HP=3;NF=4;NR=2;PP=100.0;SC=AGACACTGCCTCAAAAAAACA;TC=16;TR=6 GT:GL:GQ 0/1:-204.44,-131.78,-155.8:100 20 356675 . A AAAAC . PASS FR=1.0;HP=6;NF=2;NR=3;PP=100.0;SC=CTGCCTCAAAAAAACAAACAA;TC=17;TR=5 GT:GL:GQ 1/1:-201.68,-85.68,-76.1:85 20 358147 . CA C . PASS FR=1.0;HP=4;NF=10;NR=5;PP=100.0;SC=TGGGATTTGACAAACCCAGCT;TC=18;TR=15 GT:GL:GQ 1/1:-150.87,-32.16,-20.25:100 20 360927 . TAA T . PASS FR=1.0;HP=7;NF=4;NR=7;PP=100.0;SC=ATGTGCTTTATAAAAAAGGGG;TC=18;TR=11 GT:GL:GQ 1/1:-185.94,-114.38,-104.3:84 20 380790 . C CT . PASS FR=1.0;HP=3;NF=16;NR=12;PP=100.0;SC=CACCACACCCCGACCCTAATT;TC=32;TR=28 GT:GL:GQ 1/1:-323.67,-24.71,-1.84:100 20 385989 . T TA . PASS FR=0.5;HP=7;NF=7;NR=4;PP=100.0;SC=AGATTTTTTTTAAAAAACTCT;TC=29;TR=11 GT:GL:GQ 0/1:-131.67,-23.75,-80.28:100 20 386575 . GTTCT G . PASS FR=0.5;HP=3;NF=2;NR=3;PP=100.0;SC=TGATAAGAATGTTCTTTCTTT;TC=24;TR=5 GT:GL:GQ 0/1:-109.28,-29.71,-86.14:100 20 387657 . G GA . PASS FR=1.0;HP=8;NF=13;NR=19;PP=100.0;SC=ATGCTGAGAAGAAAAAATGAA;TC=38;TR=32 GT:GL:GQ 1/1:-284.64,-52.81,-28.53:100 20 396023 . A AAAAC . PASS FR=1.0;HP=4;NF=9;NR=9;PP=100.0;SC=AAAAAAAACAAAAACAAACAA;TC=25;TR=18 GT:GL:GQ 1/1:-279.26,-33.44,-17.73:100 20 403158 . GA G . PASS FR=0.5;HP=2;NF=4;NR=7;PP=89.0;SC=ATCTATGAAGGAAGGACAGCA;TC=20;TR=11 GT:GL:GQ 0/1:-137.87,-107.23,-160.58:100 20 405057 . A AC . PASS FR=0.5;HP=2;NF=5;NR=4;PP=100.0;SC=AAACACATACACAGACCTCCT;TC=25;TR=9 GT:GL:GQ 0/1:-136.78,-33.82,-124.47:100 20 421805 . T TCCA . PASS FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=AGAACACATTTCCAACTAAAC;TC=29;TR=6 GT:GL:GQ 0/1:-108.14,-30.52,-185.93:100 20 425206 . GTTTT G . PASS FR=0.5;HP=7;NF=2;NR=7;PP=100.0;SC=TTGTTTGTTTGTTTTGTTTTT;TC=25;TR=9 GT:GL:GQ 0/1:-158.57,-21.01,-100.22:100 20 430158 . GA G . PASS FR=0.5;HP=3;NF=2;NR=4;PP=100.0;SC=AGAGTCGCTTGAAACCCAGGA;TC=16;TR=6 GT:GL:GQ 0/1:-74.97,-35.93,-74.51:100 20 434939 . G GA . PASS FR=0.5;HP=10;NF=6;NR=2;PP=100.0;SC=AAGAAAAAAGGAAAAAAAAAA;TC=22;TR=8 GT:GL:GQ 0/1:-99.4,-65.02,-85.64:92 20 436981 . TTTCATCCA T . PASS FR=0.5;HP=2;NF=1;NR=2;PP=100.0;SC=AGGTGTGTCCTTTCATCCATT;TC=27;TR=3 GT:GL:GQ 0/1:-88.19,-26.08,-154.96:100 20 525046 . G GT . PASS FR=0.5;HP=10;NF=5;NR=8;PP=100.0;SC=AAAATACAGTGTTTTTTTTTC;TC=33;TR=13 GT:GL:GQ 0/1:-160.44,-103.25,-141.37:100 20 538639 . C CA . PASS FR=1.0;HP=9;NF=14;NR=9;PP=100.0;SC=ACCACCACAACAAAAAAACCC;TC=36;TR=23 GT:GL:GQ 1/1:-261.69,-66.02,-42.16:100 20 539756 . G GT . PASS FR=0.5;HP=1;NF=6;NR=2;PP=100.0;SC=AATGTGAGCAGTCTAGGTAAA;TC=24;TR=8 GT:GL:GQ 0/1:-130.62,-70.51,-165.77:100 20 540198 . T TG . PASS FR=1.0;HP=1;NF=9;NR=16;PP=100.0;SC=AGAGTCGCTGTTATTAAAACC;TC=26;TR=25 GT:GL:GQ 1/1:-262.05,-37.69,-19.11:100 20 545849 . A AT . PASS FR=1.0;HP=9;NF=6;NR=13;PP=100.0;SC=CTCTGGACTGATTTTTTTTTA;TC=24;TR=19 GT:GL:GQ 1/1:-225.47,-140.74,-126.39:100 20 555243 . C CT . PASS FR=0.5;HP=1;NF=3;NR=4;PP=100.0;SC=TTGGGGCCTCCTGGGTCCCAG;TC=23;TR=7 GT:GL:GQ 0/1:-124.01,-59.66,-144.99:100 20 559298 . TACAC T . PASS FR=0.5081;HP=1;NF=1;NR=1;PP=100.0;SC=GGCACACATGTACACACACAC;TC=20;TR=2 GT:GL:GQ 0/1:-95.31,-59.31,-62.75:17 20 570945 . A AACAC . PASS FR=1.0;HP=1;NF=7;NR=2;PP=100.0;SC=AGAAGGCAATAACACACACAC;TC=28;TR=9 GT:GL:GQ 1/1:-281.44,-73.27,-58.53:100 20 576287 . T TTTA . PASS FR=1.0;HP=3;NF=2;NR=9;PP=100.0;SC=CTGGAAAAGTTTTATTATTAT;TC=26;TR=11 GT:GL:GQ 1/1:-188.46,-27.21,-14.74:100 20 593205 . AG A . PASS FR=0.5;HP=6;NF=2;NR=2;PP=100.0;SC=GGGAGTGCGGAGGGGACTCCT;TC=14;TR=4 GT:GL:GQ 0/1:-90.79,-21.16,-46.9:100 20 635817 . C CAGAAAAAAA . PASS FR=1.0;HP=1;NF=6;NR=7;PP=100.0;SC=GAGACTCTCTCAGAAAAAAAA;TC=23;TR=13 GT:GL:GQ 1/1:-318.1,-28.61,-13.35:100 20 666340 . AAATAATAATAAT AAATAAT,A . PASS FR=0.5,0.5;HP=2;NF=1,2;NR=3,3;PP=100.0,100.0;SC=ATACAAATACAAATAATAATA;TC=16;TR=4,5 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 671463 . AGTGT A . PASS FR=1.0;HP=1;NF=6;NR=2;PP=100.0;SC=CATGCATGCAAGTGTGTGTGT;TC=25;TR=8 GT:GL:GQ 1/1:-248.41,-147.67,-140.04:63 20 675799 . G GTA . PASS FR=0.5;HP=2;NF=7;NR=3;PP=100.0;SC=TAATGAACATGTATATATACA;TC=20;TR=10 GT:GL:GQ 0/1:-154.12,-35.67,-66.33:100 20 704073 . CTCT C . PASS FR=0.5;HP=3;NF=3;NR=3;PP=100.0;SC=CTTCATTCTTCTCTTTTCTTT;TC=20;TR=6 GT:GL:GQ 0/1:-159.89,-91.96,-171.96:100 20 704111 . C CTTTCT . PASS FR=0.5;HP=4;NF=2;NR=3;PP=100.0;SC=TTCCTCCTCTCTTTGTCTAGT;TC=20;TR=5 GT:GL:GQ 0/1:-189.74,-115.92,-237.08:100 20 714136 . TA T . PASS FR=1.0;HP=2;NF=12;NR=13;PP=100.0;SC=CTGTGGTTGTTAACTGTAGTC;TC=30;TR=25 GT:GL:GQ 1/1:-253.68,-26.24,-6.67:100 20 715254 . G GGT,GGTGTGT . PASS FR=0.5,0.5;HP=1;NF=3,4;NR=0,1;PP=57.0,100.0;SC=ATAGTTTATAGGTGTGTGTGT;TC=23;TR=3,5 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 715847 . C CA . PASS FR=1.0;HP=7;NF=10;NR=6;PP=100.0;SC=GGCTCCGTCTCAAAAAAATAA;TC=26;TR=16 GT:GL:GQ 1/1:-157.25,-40.0,-26.17:100 20 718268 . A AAATAAT . PASS FR=0.5;HP=3;NF=1;NR=1;PP=81.0;SC=AAAAAATACAAAATAATAATA;TC=15;TR=2 GT:GL:GQ 0/1:-64.86,-29.69,-87.73:100 20 724447 . A AG . PASS FR=0.5;HP=2;NF=12;NR=9;PP=100.0;SC=GGGTGTTGTGAGACTGATTGA;TC=42;TR=21 GT:GL:GQ 0/1:-229.53,-40.83,-188.06:100 20 726275 . CAGA C . PASS FR=0.5;HP=3;NF=10;NR=10;PP=100.0;SC=ACATATATAACAGAAGGAGAG;TC=41;TR=20 GT:GL:GQ 0/1:-286.26,-52.94,-197.08:100 20 728851 . CT C . PASS FR=0.5;HP=1;NF=5;NR=1;PP=21.0;SC=GATCACACCACTGCAGTCCAG;TC=22;TR=6 GT:GL:GQ 0/1:-200.76,-185.85,-212.48:67 20 732117 . CTTTATTTTAT C . PASS FR=0.9998;HP=4;NF=1;NR=1;PP=80.0;SC=TCAGGTATGTCTTTATTTTAT;TC=14;TR=2 GT:GL:GQ 1/1:-96.6,-68.07,-66.69:34 20 739616 . CGTGTGTGT C . PASS FR=1.0;HP=1;NF=4;NR=4;PP=100.0;SC=TAAAAGTGCTCGTGTGTGTGT;TC=20;TR=8 GT:GL:GQ 1/1:-222.59,-24.43,-16.81:63 20 744662 . A ACAGGTCAAT . PASS FR=0.5;HP=1;NF=3;NR=4;PP=100.0;SC=AAAGGACAAGACAGATCCCTG;TC=16;TR=7 GT:GL:GQ 0/1:-105.45,-32.23,-150.03:100 20 746855 . A AG . PASS FR=1.0;HP=1;NF=9;NR=5;PP=100.0;SC=CTGGGATTACAGTGTGAGCCA;TC=22;TR=14 GT:GL:GQ 1/1:-242.45,-177.27,-167.62:80 20 747680 . A ATAG . PASS FR=0.5;HP=1;NF=3;NR=3;PP=100.0;SC=CTTGTTGGTAATAGCAAGTTA;TC=17;TR=6 GT:GL:GQ 0/1:-177.8,-96.72,-120.09:100 20 755106 . C CA . PASS FR=1.0;HP=3;NF=7;NR=15;PP=100.0;SC=GCTGAGAGGTCAAACCACAAA;TC=27;TR=22 GT:GL:GQ 1/1:-255.81,-41.84,-23.33:100 20 757564 . T TG . PASS FR=0.5;HP=3;NF=3;NR=1;PP=78.0;SC=GGTGGAGCCATGGGTGTCAAA;TC=10;TR=4 GT:GL:GQ 0/1:-67.44,-38.36,-58.29:89 20 757919 . A AC . PASS FR=0.5;HP=9;NF=3;NR=9;PP=100.0;SC=AAAAAACAAAAAAAAAACACC;TC=27;TR=12 GT:GL:GQ 0/1:-172.2,-112.42,-144.61:100 20 762893 . G GA . PASS FR=1.0;HP=6;NF=8;NR=9;PP=100.0;SC=TCTTGGGGGGGAAAAAATGGG;TC=24;TR=17 GT:GL:GQ 1/1:-215.19,-64.36,-48.0:100 20 782496 . CAAATAAAT C . PASS FR=0.5;HP=3;NF=2;NR=1;PP=100.0;SC=GACTCTGCCTCAAATAAATAA;TC=17;TR=3 GT:GL:GQ 0/1:-87.5,-27.65,-92.5:100 20 786252 . AAG A . PASS FR=1.0;HP=5;NF=4;NR=13;PP=100.0;SC=TTAATTAAAAAAGATATTGCA;TC=19;TR=17 GT:GL:GQ 1/1:-216.25,-31.31,-17.45:100 20 786764 . T TA . PASS FR=1.0;HP=3;NF=17;NR=12;PP=100.0;SC=ACTATATATATAATATATTTT;TC=33;TR=29 GT:GL:GQ 1/1:-388.27,-147.23,-125.36:100 20 787870 . T TTTTATTTATTTATTTATTTA . PASS FR=1.0;HP=3;NF=2;NR=1;PP=100.0;SC=ATATCAAGCATTTTATTTATT;TC=19;TR=3 GT:GL:GQ 1/1:-317.88,-65.36,-53.59:99 20 787893 . T TATTTATTTA . PASS FR=0.5;HP=4;NF=1;NR=1;PP=100.0;SC=TTTATTTATTTTTGAGATGGA;TC=20;TR=2 GT:GL:GQ 0/1:-356.98,-227.18,-263.76:5 20 789767 . T TA . PASS FR=1.0;HP=10;NF=8;NR=5;PP=100.0;SC=CAAAGCCAATTAAAAAAAAAA;TC=29;TR=13 GT:GL:GQ 1/1:-124.57,-44.47,-30.25:100 20 795148 . T TTTTA . PASS FR=1.0;HP=4;NF=9;NR=1;PP=100.0;SC=ATAAGTTTATTTTTATTTATT;TC=16;TR=10 GT:GL:GQ 1/1:-136.44,-12.46,-4.83:63 20 797336 . GA G . PASS FR=1.0;HP=10;NF=18;NR=11;PP=100.0;SC=CCATTTATGTGAAAAAAAAAA;TC=35;TR=29 GT:GL:GQ 1/1:-156.82,-42.02,-20.72:100 20 801157 . T TTTC . PASS FR=1.0;HP=6;NF=1;NR=6;PP=100.0;SC=CTTCTCTTTCTTTTTTTCTTT;TC=13;TR=7 GT:GL:GQ 1/1:-142.57,-41.24,-32.92:92 20 825082 . TGCCCAGGTC T . PASS FR=0.5;HP=1;NF=5;NR=1;PP=100.0;SC=CTGCTCAGGTTGCCCAGGTCG;TC=8;TR=6 GT:GL:GQ 1/0:-180.72,-60.67,-71.61:61 20 833239 . ACT A . PASS FR=0.5;HP=1;NF=3;NR=5;PP=100.0;SC=GGAGAAATAGACTCTCTCTCT;TC=21;TR=8 GT:GL:GQ 0/1:-96.13,-31.34,-89.12:100 20 835500 . TTGTG T . PASS FR=1.0;HP=2;NF=8;NR=2;PP=100.0;SC=GTGTTTGTGTTTGTGTGTGTG;TC=29;TR=10 GT:GL:GQ 1/1:-258.26,-62.01,-52.79:77 20 855678 . TC T . PASS FR=0.5;HP=2;NF=3;NR=5;PP=100.0;SC=TCTTTTTCTTTCTTTTTTTTC;TC=28;TR=8 GT:GL:GQ 0/1:-124.38,-62.93,-124.85:100 20 860945 . A AG . PASS FR=0.5;HP=6;NF=2;NR=6;PP=100.0;SC=GTATATTAAGAGGGGGTGAAA;TC=23;TR=8 GT:GL:GQ 0/1:-96.52,-33.16,-85.46:100 20 863148 . C CTAT . PASS FR=0.5;HP=2;NF=3;NR=12;PP=100.0;SC=CCAGAGAAGGCTATTGCTCTC;TC=37;TR=15 GT:GL:GQ 0/1:-223.19,-48.7,-208.9:100 20 899789 . CTCTT C . PASS FR=0.5;HP=3;NF=1;NR=3;PP=100.0;SC=TTTCCTTCTTCTCTTTCTTTC;TC=21;TR=4 GT:GL:GQ 0/1:-62.34,-23.94,-85.48:100 20 900698 . T TC . PASS FR=1.0;HP=4;NF=11;NR=5;PP=100.0;SC=AGGAAGGCAGTCCCCTTTCCT;TC=29;TR=16 GT:GL:GQ 1/1:-292.54,-113.13,-95.49:100 20 902060 . T TG,G . PASS FR=0.5,0.5;HP=5;NF=2,7;NR=2,4;PP=100.0,100.0;SC=TTGACTGCCCTCCTCCACTTT;TC=19;TR=4,11 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 909945 . TTATGG TTGG,T . PASS FR=0.5,0.5;HP=2;NF=10,8;NR=5,5;PP=100.0,100.0;SC=TTAGTTTAGTTTATGGTATCC;TC=32;TR=15,13 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 913303 . A AT . PASS FR=1.0;HP=10;NF=9;NR=4;PP=100.0;SC=AGATTTAAAGATTTTTTTTTT;TC=21;TR=13 GT:GL:GQ 1/1:-227.97,-180.37,-171.35:75 20 922916 . A AT . PASS FR=1.0;HP=6;NF=2;NR=1;PP=27.0;SC=TTATTTATTTATTTATTTTTT;TC=7;TR=3 GT:GL:GQ 1/1:-68.71,-54.63,-52.11:41 20 933970 . GTTAT G . PASS FR=1.0;HP=4;NF=5;NR=5;PP=100.0;SC=CAGGCTAATTGTTATTTATTT;TC=24;TR=10 GT:GL:GQ 1/1:-169.08,-10.86,-0.46:87 20 934153 . A AT . PASS FR=1.0;HP=7;NF=4;NR=5;PP=100.0;SC=ATTTTTTTGTATTTTTTAATA;TC=11;TR=9 GT:GL:GQ 1/1:-123.08,-66.05,-59.03:57 20 945474 . CAT C . PASS FR=1.0;HP=2;NF=2;NR=6;PP=100.0;SC=CACACACACACATATATATAT;TC=31;TR=8 GT:GL:GQ 1/1:-229.9,-58.37,-41.73:100 20 954102 . A ATTGT . PASS FR=0.5;HP=6;NF=4;NR=1;PP=100.0;SC=TGTTTGTTTTATTGTTTGTTT;TC=30;TR=5 GT:GL:GQ 0/1:-77.28,-28.19,-134.91:100 20 972071 . A AT . PASS FR=0.5;HP=8;NF=7;NR=5;PP=100.0;SC=ATTAAAAAAGATTTTTTTTGT;TC=27;TR=12 GT:GL:GQ 0/1:-76.99,-19.47,-57.49:100 20 995685 . CAAAT C . PASS FR=1.0;HP=3;NF=3;NR=2;PP=100.0;SC=AACTCTATCTCAAATAAATAA;TC=15;TR=5 GT:GL:GQ 1/1:-96.06,-12.82,-6.68:77 20 1000562 . TTTCA T . PASS FR=0.5;HP=2;NF=10;NR=1;PP=100.0;SC=TCACCCTTTCTTTCATTCACT;TC=23;TR=11 GT:GL:GQ 0/1:-127.76,-31.92,-110.25:100 20 1005659 . CTCAG C . PASS FR=1.0;HP=3;NF=15;NR=6;PP=100.0;SC=AACAAACAAACTCAGTCTGTC;TC=34;TR=21 GT:GL:GQ 1/1:-379.32,-49.71,-26.34:100 20 1018266 . CAAT C . PASS FR=1.0;HP=4;NF=10;NR=7;PP=100.0;SC=GAAGTAACAACAATAATAATA;TC=26;TR=17 GT:GL:GQ 1/1:-307.78,-61.51,-42.82:100 20 1023817 . C CCCT . PASS FR=1.0;HP=3;NF=7;NR=3;PP=100.0;SC=CAGTGCCCACCCCTCCTCTCC;TC=22;TR=10 GT:GL:GQ 1/1:-230.45,-50.55,-37.14:100 20 1024121 . A AT . PASS FR=1.0;HP=6;NF=5;NR=3;PP=100.0;SC=CGGGTCAGGCATTTTTTATCA;TC=16;TR=8 GT:GL:GQ 1/1:-95.55,-28.09,-20.26:65 20 1042261 . CCCTG C . PASS FR=1.0;HP=2;NF=10;NR=10;PP=100.0;SC=CCAAACCCAACCCTGCCTGGC;TC=25;TR=20 GT:GL:GQ 1/1:-365.29,-133.94,-117.57:100 20 1050585 . AT A . PASS FR=1.0;HP=10;NF=9;NR=15;PP=100.0;SC=TTCTAATTCCATTTTTTTTTT;TC=33;TR=24 GT:GL:GQ 1/1:-288.37,-205.98,-189.27:100 20 1059991 . G GAATT . PASS FR=1.0;HP=2;NF=10;NR=6;PP=100.0;SC=AACATTTGTTGAATTAATTAA;TC=25;TR=16 GT:GL:GQ 1/1:-290.89,-32.75,-16.81:100 20 1072882 . CAG C . PASS FR=0.5;HP=6;NF=5;NR=6;PP=100.0;SC=ATCAGAAAAACAGAGACCACA;TC=23;TR=11 GT:GL:GQ 0/1:-124.42,-26.5,-135.46:100 20 1084744 . TG T . PASS FR=1.0;HP=5;NF=9;NR=12;PP=100.0;SC=ACCATAAATGTGGGGCTACTG;TC=23;TR=21 GT:GL:GQ 1/1:-326.86,-192.89,-179.07:100 20 1100621 . TAG T . PASS FR=0.5;HP=4;NF=6;NR=3;PP=100.0;SC=GCTTCTCAAATAGAGTCTTAA;TC=23;TR=9 GT:GL:GQ 0/1:-166.5,-71.13,-124.84:100 20 1105206 . C CAT . PASS FR=1.0;HP=1;NF=15;NR=11;PP=100.0;SC=AATTTATCCACGTGTACCAGA;TC=32;TR=26 GT:GL:GQ 1/1:-427.57,-192.92,-171.28:100 20 1114638 . C CTCTT . PASS FR=1.0;HP=4;NF=9;NR=17;PP=100.0;SC=TGTGTCCTCTCTTTGTATTTG;TC=34;TR=26 GT:GL:GQ 1/1:-420.88,-72.2,-49.92:100 20 1118278 . GAA G . PASS FR=1.0;HP=5;NF=13;NR=8;PP=100.0;SC=AGAAAAGGGAGAAAAGGAGGC;TC=24;TR=21 GT:GL:GQ 1/1:-206.9,-16.17,-0.92:100 20 1127807 . TCATCATCATCATCAC T . PASS FR=0.5;HP=1;NF=2;NR=3;PP=100.0;SC=ATCATCATCATCATCATCATC;TC=18;TR=5 GT:GL:GQ 1/0:-246.11,-143.41,-171.3:100 20 1133620 . GC G . PASS FR=1.0;HP=3;NF=17;NR=8;PP=100.0;SC=TAAGGACCAAGCCCTGTTTAT;TC=28;TR=25 GT:GL:GQ 1/1:-266.52,-52.99,-34.3:100 20 1162839 . AG A . PASS FR=0.5;HP=10;NF=1;NR=6;PP=100.0;SC=GGGGTGGGGGAGGGGGTAGAA;TC=27;TR=7 GT:GL:GQ 0/1:-154.34,-117.72,-158.43:100 20 1165265 . TACAC T . PASS FR=1.0;HP=1;NF=2;NR=1;PP=100.0;SC=CACACGCGCGTACACACACAC;TC=13;TR=3 GT:GL:GQ 1/1:-65.7,-24.93,-20.64:52 20 1168799 . T TAC . PASS FR=0.5;HP=3;NF=1;NR=3;PP=100.0;SC=ATATATATAATACACACACAC;TC=33;TR=4 GT:GL:GQ 0/1:-146.28,-74.63,-149.77:100 20 1194678 . A AT . PASS FR=1.0;HP=8;NF=13;NR=12;PP=100.0;SC=TACAAGATTAATTTTTTTTGT;TC=37;TR=25 GT:GL:GQ 1/1:-428.37,-300.25,-279.55:89 20 1195705 . AAAG A . PASS FR=1.0;HP=2;NF=10;NR=12;PP=100.0;SC=AGAGATGGCCAAAGAAGACAT;TC=27;TR=22 GT:GL:GQ 1/1:-481.8,-237.54,-219.64:100 20 1200593 . GA G . PASS FR=0.5;HP=5;NF=7;NR=5;PP=100.0;SC=TTTTTTAAAAGATCAACAAAA;TC=31;TR=12 GT:GL:GQ 0/1:-291.7,-258.36,-302.47:100 20 1202056 . C CT . PASS FR=0.5;HP=6;NF=2;NR=1;PP=73.0;SC=TTCTTTCTTTCTTTCTTTCTT;TC=17;TR=3 GT:GL:GQ 0/1:-78.02,-50.24,-96.3:100 20 1217230 . C CT . PASS FR=0.5;HP=3;NF=6;NR=7;PP=100.0;SC=TGAATCTGAACTTTCTCTATT;TC=29;TR=13 GT:GL:GQ 0/1:-136.34,-37.11,-139.78:100 20 1238533 . TATC T . PASS FR=0.5;HP=1;NF=6;NR=8;PP=100.0;SC=ATTCCCTTATTATCCTTTTAA;TC=32;TR=14 GT:GL:GQ 0/1:-203.0,-27.66,-145.09:100 20 1258183 . GTGTC G . PASS FR=0.5;HP=2;NF=9;NR=7;PP=100.0;SC=CTGTGCATGTGTGTCTGTGTG;TC=40;TR=16 GT:GL:GQ 0/1:-393.66,-270.04,-334.02:100 20 1258199 . C CTG . PASS FR=1.0;HP=2;NF=10;NR=8;PP=100.0;SC=GTGTGTGTATCTGTGTGTGTG;TC=39;TR=18 GT:GL:GQ 1/1:-443.43,-273.82,-255.93:100 20 1258268 . C CTG . PASS FR=1.0;HP=1;NF=14;NR=7;PP=100.0;SC=GTATGTGTGCCTGTGTGTGTG;TC=36;TR=21 GT:GL:GQ 1/1:-385.28,-210.98,-205.13:73 20 1258437 . GTGTGCCTGTGTGTGTC G . PASS FR=0.5;HP=2;NF=3;NR=4;PP=100.0;SC=GCCTGTGTATGTGTGCCTGTG;TC=40;TR=7 GT:GL:GQ 0/1:-300.85,-170.75,-363.46:100 20 1258704 . C CTGTT . PASS FR=0.5;HP=2;NF=6;NR=3;PP=100.0;SC=GTGTGTGTGTCTGTGTGTGTA;TC=34;TR=9 GT:GL:GQ 0/1:-182.12,-58.28,-233.67:100 20 1270442 . CA C . PASS FR=1.0;HP=2;NF=5;NR=12;PP=100.0;SC=CACTGCACTCCAAGCCTAGGT;TC=17;TR=17 GT:GL:GQ 1/1:-162.61,-26.2,-14.46:98 20 1272295 . CTCTGT C . PASS FR=1.0;HP=1;NF=13;NR=7;PP=100.0;SC=CCAAGTTCTGCTCTGTTGATT;TC=25;TR=20 GT:GL:GQ 1/1:-389.78,-103.27,-85.17:100 20 1272815 . C CATAG . PASS FR=1.0;HP=2;NF=11;NR=10;PP=100.0;SC=TAGTCTAAGGCATAGCATCCT;TC=27;TR=21 GT:GL:GQ 1/1:-368.78,-50.48,-32.46:100 20 1291149 . GCAA G . PASS FR=0.5;HP=1;NF=2;NR=3;PP=100.0;SC=CCTGGATACAGCAACAACAGT;TC=25;TR=5 GT:GL:GQ 0/1:-151.35,-93.7,-185.23:100 20 1292033 . C CTTGT . PASS FR=0.5;HP=2;NF=7;NR=5;PP=100.0;SC=CTTACATTTGCTTGTTTGATA;TC=29;TR=12 GT:GL:GQ 0/1:-444.32,-314.49,-337.3:100 20 1292718 . GT G . PASS FR=1.0;HP=8;NF=9;NR=3;PP=100.0;SC=TAATTTTTTAGTTTTTTTTGT;TC=17;TR=12 GT:GL:GQ 1/1:-140.26,-85.11,-76.3:73 20 1292776 . T TA . PASS FR=1.0;HP=1;NF=14;NR=10;PP=100.0;SC=CTCCTGGACTTAGTGATCCTC;TC=25;TR=24 GT:GL:GQ 1/1:-310.19,-119.02,-102.21:100 20 1303648 . A AG . PASS FR=0.5;HP=4;NF=6;NR=2;PP=100.0;SC=GGCAACACTCACCCGGCTGAG;TC=19;TR=8 GT:GL:GQ 0/1:-115.57,-32.83,-76.0:100 20 1312294 . A AT . PASS FR=1.0;HP=7;NF=5;NR=6;PP=100.0;SC=CACCTGGCTAATTTTTTTATT;TC=17;TR=11 GT:GL:GQ 1/1:-196.82,-109.27,-98.21:93 20 1318554 . TCCCACAGAGAAGTCC T . PASS FR=1.0;HP=3;NF=5;NR=4;PP=100.0;SC=ACCTAAGCATTCCCACAGAGA;TC=12;TR=9 GT:GL:GQ 1/1:-228.16,-15.45,-7.14:62 20 1322791 . G GCACACA,GCACACACA . PASS FR=0.5,0.5;HP=1;NF=3,3;NR=0,4;PP=43.0,100.0;SC=GAGAACAAATGCACACACACA;TC=18;TR=3,7 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 1333430 . C CT . PASS FR=1.0;HP=2;NF=18;NR=9;PP=100.0;SC=ATGAAGGTGACTTCTCAGGTG;TC=32;TR=27 GT:GL:GQ 1/1:-276.34,-27.55,-7.09:100 20 1342649 . AT A . PASS FR=1.0;HP=6;NF=17;NR=10;PP=100.0;SC=AGTGTATGAGATTTTTTGTTA;TC=29;TR=27 GT:GL:GQ 1/1:-209.72,-24.22,-4.14:100 20 1349439 . C CCCT . PASS FR=0.5;HP=4;NF=2;NR=6;PP=100.0;SC=CCCACATTCCCCCTCCTCTGA;TC=22;TR=8 GT:GL:GQ 0/1:-157.47,-56.31,-133.86:100 20 1358694 . C CAGTTTGGGCACTAACACCTACTT . PASS FR=0.5;HP=1;NF=4;NR=1;PP=100.0;SC=CTATACGGGTCAGTTTGGGCA;TC=19;TR=5 GT:GL:GQ 0/1:-272.45,-105.91,-212.24:100 20 1364390 . G GA . PASS FR=1.0;HP=2;NF=9;NR=6;PP=100.0;SC=GATCAAGTGGGAGATCACTTG;TC=25;TR=15 GT:GL:GQ 1/1:-334.68,-154.31,-139.66:100 20 1369478 . CG C . PASS FR=0.5;HP=2;NF=7;NR=4;PP=100.0;SC=TAAAAACCAACGAGGCTCCAC;TC=23;TR=11 GT:GL:GQ 0/1:-184.87,-113.86,-180.77:100 20 1372404 . GA G . PASS FR=1.0;HP=7;NF=8;NR=5;PP=100.0;SC=GAGGGAGTGGGAAAAAAAGAG;TC=17;TR=13 GT:GL:GQ 1/1:-147.21,-77.38,-68.31:75 20 1379453 . C CTG . PASS FR=1.0;HP=2;NF=4;NR=11;PP=100.0;SC=TGCCAGGACTCTCCTCGCTGT;TC=19;TR=15 GT:GL:GQ 1/1:-192.19,-47.83,-35.2:100 20 1381135 . AG A . PASS FR=0.5;HP=2;NF=3;NR=5;PP=100.0;SC=CTTGAGGACAAGGCATTATAG;TC=26;TR=8 GT:GL:GQ 0/1:-99.07,-46.56,-212.4:100 20 1386382 . AGAG A . PASS FR=0.5;HP=3;NF=7;NR=1;PP=100.0;SC=ACTAATTAAAAGAGAACCCTG;TC=26;TR=8 GT:GL:GQ 0/1:-184.22,-117.09,-276.56:100 20 1389225 . CGTGTGT C . PASS FR=1.0;HP=1;NF=1;NR=1;PP=100.0;SC=TATGAAGACTCGTGTGTGTGT;TC=12;TR=2 GT:GL:GQ 1/1:-80.8,-37.12,-33.18:48 20 1392633 . AT A . PASS FR=0.5;HP=9;NF=8;NR=5;PP=100.0;SC=AAGCCAACACATTTTTTTTTC;TC=29;TR=13 GT:GL:GQ 0/1:-142.17,-103.31,-156.4:100 20 1399660 . A AAAAAC . PASS FR=0.5;HP=2;NF=1;NR=7;PP=100.0;SC=TGTTTATGTTAGAAACAAAAC;TC=28;TR=8 GT:GL:GQ 0/1:-237.24,-123.87,-245.2:100 20 1401887 . T TC . PASS FR=0.5;HP=6;NF=3;NR=5;PP=100.0;SC=TGACTTTTTTTCTCCCTGAGA;TC=26;TR=8 GT:GL:GQ 0/1:-140.81,-26.64,-103.7:100 20 1403888 . G GT . PASS FR=0.5;HP=1;NF=3;NR=5;PP=100.0;SC=CAGAGAGGGCGTAAGATTGGA;TC=18;TR=8 GT:GL:GQ 0/1:-134.33,-94.6,-144.84:100 20 1411174 . G GT . PASS FR=1.0;HP=1;NF=14;NR=18;PP=100.0;SC=TTCCAACAGTGACAAGGGTTT;TC=34;TR=32 GT:GL:GQ 1/1:-370.91,-42.86,-18.85:100 20 1411544 . TG T . PASS FR=0.5;HP=4;NF=7;NR=2;PP=36.0;SC=ATTTATAAAATGTTTTTGTTG;TC=28;TR=9 GT:GL:GQ 0/1:-275.92,-257.59,-310.84:82 20 1420200 . CT C . PASS FR=1.0;HP=2;NF=13;NR=7;PP=100.0;SC=AAGATGGAACCTTAAGTTCAA;TC=24;TR=20 GT:GL:GQ 1/1:-229.24,-45.08,-29.19:100 20 1421627 . GC G . PASS FR=1.0;HP=4;NF=12;NR=6;PP=100.0;SC=GGAGCCCAACGCCCATTTAAA;TC=24;TR=18 GT:GL:GQ 1/1:-219.35,-32.03,-15.65:100 20 1428402 . A ATCTAT . PASS FR=0.5;HP=2;NF=6;NR=3;PP=100.0;SC=AATAGCTGATATCAGTTAAGG;TC=30;TR=9 GT:GL:GQ 0/1:-414.87,-348.43,-419.1:100 20 1428454 . TC T . PASS FR=0.5;HP=2;NF=11;NR=7;PP=100.0;SC=TTACACCGACTCTGTGCAGGT;TC=37;TR=18 GT:GL:GQ 0/1:-456.05,-415.06,-465.1:100 20 1448428 . AC A . PASS FR=1.0;HP=2;NF=12;NR=6;PP=100.0;SC=ACGGTAAACAACCTTCCCGCG;TC=21;TR=18 GT:GL:GQ 1/1:-289.43,-190.83,-179.1:98 20 1450561 . A AAATAAT . PASS FR=1.0;HP=8;NF=6;NR=4;PP=100.0;SC=CTGTCTCAAAAAAAAATAATA;TC=23;TR=10 GT:GL:GQ 1/1:-324.02,-170.06,-160.02:94 20 1454025 . GCACACACGCA G . PASS FR=1.0;HP=1;NF=5;NR=3;PP=100.0;SC=ACGCACACATGCACACACGCA;TC=23;TR=8 GT:GL:GQ 1/1:-298.98,-49.31,-43.52:72 20 1455718 . AC A . PASS FR=0.5;HP=8;NF=5;NR=3;PP=100.0;SC=TGGTGGTAGCACCCCCCCAGG;TC=26;TR=8 GT:GL:GQ 0/1:-122.23,-68.33,-113.23:100 20 1466298 . C CCA . PASS FR=0.5;HP=1;NF=3;NR=2;PP=100.0;SC=CACACACACACCACACACACA;TC=25;TR=5 GT:GL:GQ 0/1:-174.97,-31.68,-40.82:42 20 1470727 . TG T . PASS FR=1.0;HP=4;NF=9;NR=10;PP=100.0;SC=CAACAATCATTGGGGAATATT;TC=24;TR=19 GT:GL:GQ 1/1:-243.08,-66.7,-50.7:100 20 1473489 . ATAATT A . PASS FR=0.5;HP=2;NF=13;NR=9;PP=100.0;SC=TTACTTACAAATAATTTTATT;TC=35;TR=22 GT:GL:GQ 0/1:-297.03,-26.79,-121.41:100 20 1475430 . C CTCT . PASS FR=0.5;HP=3;NF=5;NR=7;PP=100.0;SC=CTCATTTCTTCTCTTTTCATT;TC=31;TR=12 GT:GL:GQ 0/1:-179.5,-26.21,-143.42:100 20 1477952 . AGTCTACACGT A . PASS FR=0.5;HP=1;NF=1;NR=2;PP=100.0;SC=TTGTCTTTTCAGTCTACACGT;TC=26;TR=3 GT:GL:GQ 0/1:-132.31,-83.49,-272.8:100 20 1485444 . TGAGAGAGA T . PASS FR=0.5;HP=2;NF=1;NR=2;PP=100.0;SC=TGTGTGTGTGTGAGAGAGAGA;TC=17;TR=3 GT:GL:GQ 1/0:-294.27,-239.82,-244.87:100 20 1498426 . G GA . PASS FR=1.0;HP=6;NF=18;NR=13;PP=100.0;SC=TACAACGGAAGAAAAGCCTAA;TC=33;TR=31 GT:GL:GQ 1/1:-335.62,-79.86,-57.15:100 20 1499276 . TGAGA T . PASS FR=0.5;HP=2;NF=4;NR=2;PP=100.0;SC=TCAAAGTGAATGAGAGAGAGG;TC=23;TR=6 GT:GL:GQ 0/1:-190.39,-128.87,-245.46:100 20 1500650 . A AG . PASS FR=1.0;HP=1;NF=9;NR=8;PP=100.0;SC=AAGGAGCAGCAGTTCTGAGAG;TC=19;TR=17 GT:GL:GQ 1/1:-187.24,-32.97,-19.25:100 20 1510246 . CA C . PASS FR=1.0;HP=10;NF=15;NR=6;PP=100.0;SC=AACTCTGTCTCAAAAAAAAAA;TC=29;TR=21 GT:GL:GQ 1/1:-113.89,-25.37,-8.27:100 20 1510966 . C CTA . PASS FR=1.0;HP=2;NF=10;NR=3;PP=100.0;SC=TTTTATCTCTCTGTGTCATTT;TC=21;TR=13 GT:GL:GQ 1/1:-215.34,-14.55,0.0:100 20 1512623 . TTGTC T . PASS FR=0.5;HP=1;NF=2;NR=7;PP=100.0;SC=ACTCCATAGATTGTCTGGGTA;TC=27;TR=9 GT:GL:GQ 0/1:-204.17,-64.36,-220.46:100 20 1516154 . A AAG . PASS FR=0.5;HP=1;NF=9;NR=1;PP=100.0;SC=GTTTTATAAGAAGAGAGAGAG;TC=28;TR=10 GT:GL:GQ 0/1:-197.81,-103.51,-159.44:100 20 1524117 . G GTGA . PASS FR=1.0;HP=2;NF=12;NR=14;PP=100.0;SC=TGGGATCAGGGTATTCCCTTC;TC=27;TR=26 GT:GL:GQ 1/1:-368.49,-35.51,-15.43:100 20 1525024 . CT C . PASS FR=0.5;HP=7;NF=3;NR=3;PP=96.0;SC=CCTTCTTTGTCTTTTTTGATC;TC=18;TR=6 GT:GL:GQ 0/1:-53.12,-20.94,-98.55:100 20 1525853 . G GT . PASS FR=0.5;HP=5;NF=7;NR=4;PP=100.0;SC=CCTGAAGTGTGTTTTCCAACT;TC=29;TR=11 GT:GL:GQ 0/1:-133.05,-52.13,-148.67:100 20 1597255 . TG T . PASS FR=0.5;HP=2;NF=13;NR=3;PP=100.0;SC=GTAAAAGTACTGGAAGAAAAG;TC=39;TR=16 GT:GL:GQ 0/1:-269.31,-182.14,-334.79:100 20 1627288 . ATTTGT A . PASS FR=0.5;HP=3;NF=4;NR=2;PP=100.0;SC=ACTTTTTTTCATTTGTTTTGT;TC=20;TR=6 GT:GL:GQ 0/1:-133.15,-70.66,-175.26:100 20 1629280 . T TAATAAAATAA . PASS FR=0.5;HP=3;NF=1;NR=4;PP=100.0;SC=ACTTAAAGTATAATAAAATAA;TC=18;TR=5 GT:GL:GQ 0/1:-155.63,-27.66,-95.67:100 20 1648829 . CTTTCTTTTTCTTTTCT C . PASS FR=0.5;HP=6;NF=1;NR=1;PP=74.0;SC=TTCTTTCTTTCTTTCTTTTTC;TC=20;TR=2 GT:GL:GQ 0/1:-191.4,-160.88,-232.59:100 20 1653387 . T TTTG . PASS FR=0.5;HP=2;NF=2;NR=7;PP=100.0;SC=CGGCCAATCATTTGTTGTTGT;TC=25;TR=9 GT:GL:GQ 0/1:-189.9,-54.75,-106.65:100 20 1656519 . GT G . PASS FR=0.5;HP=9;NF=4;NR=5;PP=100.0;SC=GAGCTGCACTGTTTTTTTTCT;TC=20;TR=9 GT:GL:GQ 0/1:-62.34,-19.97,-47.7:100 20 1658890 . ACT A . PASS FR=0.5;HP=2;NF=6;NR=2;PP=100.0;SC=CATGTGATACACTGTGGGCCC;TC=27;TR=8 GT:GL:GQ 0/1:-198.65,-163.08,-324.51:100 20 1660493 . AT A . PASS FR=0.5;HP=1;NF=6;NR=5;PP=100.0;SC=CATTTGGGAGATGCTATTACC;TC=31;TR=11 GT:GL:GQ 0/1:-160.86,-59.8,-177.36:100 20 1661355 . TG T . PASS FR=0.5;HP=1;NF=6;NR=7;PP=100.0;SC=GAAAAACACATGATTATCCAT;TC=34;TR=13 GT:GL:GQ 0/1:-171.31,-99.84,-269.81:100 20 1661478 . G GT . PASS FR=0.5;HP=9;NF=7;NR=5;PP=100.0;SC=ATACTTTCTTGTTTTTTTGGC;TC=35;TR=12 GT:GL:GQ 0/1:-150.06,-61.16,-108.32:100 20 1661816 . C CA . PASS FR=0.5;HP=1;NF=1;NR=6;PP=100.0;SC=AATTTGCAATCATACAGAAAG;TC=24;TR=7 GT:GL:GQ 0/1:-96.53,-29.07,-136.56:100 20 1662592 . GATATAACTA G . PASS FR=0.5;HP=1;NF=4;NR=5;PP=100.0;SC=TATGGATATGGATATAACTAA;TC=23;TR=9 GT:GL:GQ 0/1:-238.09,-62.84,-220.35:100 20 1665050 . A ATG . PASS FR=0.5;HP=2;NF=6;NR=6;PP=100.0;SC=ATACACACATATATATATGTA;TC=34;TR=12 GT:GL:GQ 0/1:-151.91,-67.61,-244.28:100 20 1667770 . TG T . PASS FR=0.5;HP=6;NF=5;NR=5;PP=100.0;SC=AGGGTTATGATGGGGGGAGAA;TC=29;TR=10 GT:GL:GQ 0/1:-75.51,-17.52,-115.09:100 20 1674714 . A AT . PASS FR=1.0;HP=6;NF=12;NR=9;PP=100.0;SC=AAGGAGAATCATTTTTTCTTA;TC=26;TR=21 GT:GL:GQ 1/1:-198.16,-29.36,-11.98:100 20 1679689 . TACACAC TACACACACAC,T . PASS FR=0.5,0.5;HP=3;NF=2,1;NR=0,1;PP=100.0,100.0;SC=TTAGATGCCCTACACACACAC;TC=23;TR=2,2 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 1680048 . G GA . PASS FR=0.5;HP=9;NF=4;NR=9;PP=100.0;SC=GAAAACAACAGAAAAAAAACT;TC=30;TR=13 GT:GL:GQ 0/1:-157.3,-90.19,-130.66:100 20 1680109 . GA G . PASS FR=0.5;HP=4;NF=9;NR=8;PP=100.0;SC=AACAGCAAGAGAAATTATAAA;TC=32;TR=17 GT:GL:GQ 0/1:-210.03,-97.05,-217.17:100 20 1682621 . A AT . PASS FR=1.0;HP=3;NF=18;NR=11;PP=100.0;SC=AATATATCATATTACACAGTG;TC=31;TR=29 GT:GL:GQ 1/1:-304.45,-32.07,-10.59:100 20 1683112 . T TC . PASS FR=1.0;HP=2;NF=6;NR=11;PP=100.0;SC=CAAACCCTCTTCCTATACCAC;TC=23;TR=17 GT:GL:GQ 1/1:-265.19,-181.47,-172.55:74 20 1683153 . CA C . PASS FR=0.5;HP=2;NF=5;NR=7;PP=100.0;SC=GCAGCAGCTGCAAGAAGTCTC;TC=22;TR=12 GT:GL:GQ 0/1:-291.99,-237.27,-279.09:100 20 1683250 . ATAGCTCTACCAGT A . PASS FR=0.5;HP=1;NF=5;NR=4;PP=100.0;SC=AGTTCGAATCATAGCTCTACC;TC=22;TR=9 GT:GL:GQ 0/1:-267.9,-88.45,-154.18:100 20 1683813 . C CT . PASS FR=0.5;HP=6;NF=12;NR=13;PP=100.0;SC=AAGAGAATGTCTTTTTAAAAT;TC=53;TR=25 GT:GL:GQ 0/1:-327.36,-122.23,-224.07:100 20 1683959 . C CA . PASS FR=0.5;HP=8;NF=4;NR=9;PP=100.0;SC=TCAACAATGACAAAAAAAGCA;TC=24;TR=13 GT:GL:GQ 0/1:-130.55,-27.62,-42.34:66 20 1684576 . A AATGTATAATAC . PASS FR=0.5;HP=2;NF=5;NR=4;PP=96.0;SC=ATACTGTTTAAATATTTCCTG;TC=24;TR=9 GT:GL:GQ 0/1:-370.23,-353.25,-494.05:100 20 1688002 . AAAAC A . PASS FR=1.0;HP=3;NF=4;NR=6;PP=100.0;SC=ACTCCCTCTCAAAACAAACAA;TC=22;TR=10 GT:GL:GQ 1/1:-132.2,-18.69,-9.78:74 20 1690549 . CCT C . PASS FR=0.5;HP=3;NF=6;NR=6;PP=100.0;SC=GAAATCTTCCCCTGTCTGTGA;TC=32;TR=12 GT:GL:GQ 0/1:-184.81,-148.16,-332.53:100 20 1694183 . CT C . PASS FR=0.5;HP=3;NF=8;NR=5;PP=100.0;SC=TATACAAAGACTTTATAACCA;TC=29;TR=13 GT:GL:GQ 0/1:-144.04,-44.56,-141.78:100 20 1699510 . T TCCCA . PASS FR=0.5;HP=3;NF=10;NR=2;PP=100.0;SC=AATGTCTCATTCCCACATCCT;TC=19;TR=12 GT:GL:GQ 0/1:-164.23,-17.54,-74.37:100 20 1701571 . TTAAAATAAAA T . PASS FR=0.5;HP=4;NF=5;NR=2;PP=100.0;SC=CATCTCAAAATTAAAATAAAA;TC=21;TR=7 GT:GL:GQ 0/1:-177.13,-95.66,-194.53:100 20 1716144 . A AGTGT . PASS FR=0.5;HP=8;NF=3;NR=4;PP=100.0;SC=GGTTTTTTTTAGTGTGTGTGT;TC=23;TR=7 GT:GL:GQ 0/1:-151.21,-52.44,-109.8:100 20 1719870 . TG T . PASS FR=0.5;HP=1;NF=3;NR=11;PP=100.0;SC=ATCAAACCTCTGTGGGAGAGA;TC=27;TR=14 GT:GL:GQ 0/1:-146.54,-22.92,-111.48:100 20 1721789 . GT G . PASS FR=0.5;HP=9;NF=6;NR=4;PP=100.0;SC=GCACTTGGGAGTTTTTTTTTC;TC=23;TR=10 GT:GL:GQ 0/1:-60.27,-22.43,-60.17:100 20 1722316 . CCTTT C . PASS FR=1.0;HP=2;NF=2;NR=1;PP=100.0;SC=TTTCTCTCTTCCTTTCTTTCT;TC=7;TR=3 GT:GL:GQ 1/1:-85.7,-30.24,-25.46:57 20 1727042 . T TA . PASS FR=1.0;HP=2;NF=10;NR=8;PP=100.0;SC=AATTAAATTATATAGAGGAAG;TC=20;TR=18 GT:GL:GQ 1/1:-223.19,-104.73,-92.26:100 20 1728298 . G GT . PASS FR=1.0;HP=4;NF=11;NR=14;PP=100.0;SC=AAGAACAGAGGTTTTAAGCAT;TC=28;TR=25 GT:GL:GQ 1/1:-297.24,-94.99,-75.97:100 20 1730788 . T TGATA . PASS FR=1.0;HP=3;NF=3;NR=6;PP=100.0;SC=AGATGATAAATGATAGATAGA;TC=36;TR=9 GT:GL:GQ 1/1:-190.89,-23.51,-13.12:87 20 1731625 . CA C . PASS FR=1.0;HP=9;NF=5;NR=8;PP=100.0;SC=GACTCCATCTCAAAAAAAAAG;TC=23;TR=13 GT:GL:GQ 1/1:-93.68,-29.69,-18.4:95 20 1734082 . AAAAAT A . PASS FR=0.5;HP=4;NF=6;NR=3;PP=100.0;SC=CAATAGCTATAAAAATAAAAT;TC=38;TR=9 GT:GL:GQ 0/1:-124.98,-23.78,-220.83:100 20 1738324 . T TC . PASS FR=1.0;HP=3;NF=7;NR=10;PP=100.0;SC=ACACTCCTTTTCCTTCATGAT;TC=22;TR=17 GT:GL:GQ 1/1:-213.69,-47.59,-33.85:100 20 1738519 . A AG . PASS FR=1.0;HP=1;NF=13;NR=11;PP=100.0;SC=CTGTCAAACTAGCCTCTGGCT;TC=29;TR=24 GT:GL:GQ 1/1:-269.52,-42.45,-23.17:100 20 1741051 . T TAA . PASS FR=1.0;HP=1;NF=12;NR=12;PP=100.0;SC=TAAATATATATGACTATTTTT;TC=35;TR=24 GT:GL:GQ 1/1:-395.96,-52.09,-26.1:100 20 1745352 . A ACAATAATCACATCAAAGAT . PASS FR=1.0;HP=2;NF=4;NR=8;PP=100.0;SC=CAAGACCATTACACTAATCAC;TC=17;TR=12 GT:GL:GQ 1/1:-425.27,-43.37,-23.58:100 20 1746606 . GTA G . PASS FR=1.0;HP=2;NF=1;NR=4;PP=100.0;SC=ATATATATGTGTATATATATA;TC=9;TR=5 GT:GL:GQ 1/1:-98.72,-49.48,-45.34:50 20 1768362 . G GAA . PASS FR=1.0;HP=2;NF=7;NR=14;PP=100.0;SC=TAGAGTGATGGAAGAGACTGG;TC=27;TR=21 GT:GL:GQ 1/1:-269.69,-41.32,-23.11:100 20 1778684 . A AGTGCTT . PASS FR=0.5;HP=2;NF=1;NR=1;PP=83.0;SC=ATTGCCCTCCATTGGAGGCTG;TC=14;TR=2 GT:GL:GQ 1/0:-256.33,-220.54,-244.27:69 20 1833292 . TA T . PASS FR=0.5;HP=3;NF=5;NR=5;PP=100.0;SC=ATATTATGTATAATCTCAATT;TC=25;TR=10 GT:GL:GQ 0/1:-147.42,-89.75,-210.06:100 20 1848829 . CTTTTCT C . PASS FR=1.0;HP=8;NF=6;NR=15;PP=100.0;SC=CTTTTCTTTTCTTTTCTTTTC;TC=25;TR=21 GT:GL:GQ 1/1:-409.42,-172.01,-156.56:100 20 1848853 . CTT C . PASS FR=0.5;HP=4;NF=3;NR=4;PP=100.0;SC=CTTTCTTTCTCTTTCTTTCTT;TC=26;TR=7 GT:GL:GQ 0/1:-469.4,-397.68,-416.1:83 20 1848877 . C CTT . PASS FR=0.9999;HP=4;NF=2;NR=1;PP=100.0;SC=TTCTTTCTTTCTCTTTCTTTC;TC=26;TR=3 GT:GL:GQ 1/1:-373.17,-284.63,-280.27:37 20 1852149 . CCA C . PASS FR=0.5;HP=1;NF=4;NR=1;PP=100.0;SC=CACCCCCTCTCCACACACACA;TC=23;TR=5 GT:GL:GQ 0/1:-139.51,-90.17,-161.53:100 20 1855569 . AACACAC A . PASS FR=1.0;HP=1;NF=7;NR=3;PP=100.0;SC=GTCACTCTACAACACACACAC;TC=14;TR=10 GT:GL:GQ 1/1:-159.46,-18.21,-11.49:84 20 1857852 . TC T . PASS FR=1.0;HP=6;NF=4;NR=19;PP=100.0;SC=CCCGTGTCCATCCCCCCTGTA;TC=58;TR=23 GT:GL:GQ 1/1:-667.45,-637.23,-632.11:63 20 1857976 . G GT . PASS FR=1.0;HP=5;NF=12;NR=1;PP=100.0;SC=GCTTTGTTTTGTCAGTTGTTT;TC=22;TR=13 GT:GL:GQ 1/1:-196.6,-28.45,-14.03:100 20 1872437 . AT A . PASS FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=TCCCTGGCTAATTCCCCCCAC;TC=23;TR=6 GT:GL:GQ 0/1:-111.11,-55.77,-134.66:100 20 1890990 . CTT C . PASS FR=1.0;HP=5;NF=11;NR=12;PP=100.0;SC=TGTTTCATTACTTTTTAACTT;TC=24;TR=23 GT:GL:GQ 1/1:-245.45,-38.39,-20.54:100 20 1895466 . T TATAG . PASS FR=1.0;HP=1;NF=11;NR=5;PP=100.0;SC=AGATTAGAATTAGCCCAGCTC;TC=24;TR=16 GT:GL:GQ 1/1:-500.31,-454.72,-448.18:79 20 1895484 . ACT A . PASS FR=1.0;HP=1;NF=14;NR=4;PP=52.0;SC=CTCAGATGTGACTCTTCCAGA;TC=23;TR=18 GT:GL:GQ 1/1:-454.69,-436.37,-433.13:53 20 1912065 . AC A . PASS FR=0.5;HP=2;NF=7;NR=8;PP=100.0;SC=TGCCTTCATCACTGTTCCCAT;TC=25;TR=15 GT:GL:GQ 0/1:-166.95,-40.53,-113.76:100 20 1930288 . TAAG T . PASS FR=0.5;HP=2;NF=9;NR=4;PP=100.0;SC=TATAAGTTGTTAAGAAGAAAA;TC=31;TR=13 GT:GL:GQ 0/1:-196.67,-58.02,-140.92:100 20 1940722 . GTT G . PASS FR=0.5;HP=2;NF=6;NR=7;PP=100.0;SC=AAAAACCCAGGTTATATATAC;TC=25;TR=13 GT:GL:GQ 0/1:-178.3,-32.72,-93.72:100 20 1940980 . G GA . PASS FR=0.5;HP=3;NF=5;NR=3;PP=100.0;SC=AACTACTCAGGGGCTGAGATG;TC=20;TR=8 GT:GL:GQ 0/1:-91.81,-43.36,-126.02:100 20 1941170 . A AC . PASS FR=0.5;HP=1;NF=10;NR=2;PP=100.0;SC=ATACCTGTATAGAAAAAAAGT;TC=31;TR=12 GT:GL:GQ 0/1:-250.35,-208.27,-291.77:100 20 1943171 . T TG . PASS FR=0.5;HP=7;NF=1;NR=1;PP=56.0;SC=AGGGGAAGCCTGGGGGGGTTG;TC=19;TR=2 GT:GL:GQ 0/1:-65.38,-41.58,-85.08:100 20 1949783 . C CT . PASS FR=0.5;HP=10;NF=3;NR=4;PP=100.0;SC=GTGCTGAGCCCTTTTTTTTTT;TC=26;TR=7 GT:GL:GQ 0/1:-82.34,-46.95,-63.27:73 20 1959266 . A ATG . PASS FR=0.5;HP=2;NF=3;NR=4;PP=100.0;SC=CAACCTGAATATGTGTGTGTG;TC=24;TR=7 GT:GL:GQ 0/1:-140.42,-42.47,-66.02:100 20 1967894 . GATGA G . PASS FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=TTGAGTGATTGATGAATGAAT;TC=24;TR=6 GT:GL:GQ 0/1:-113.7,-41.87,-83.28:100 20 1977448 . A ACACACACACG . PASS FR=0.5;HP=1;NF=1;NR=1;PP=100.0;SC=ACACACACACATAGAAGGCCA;TC=32;TR=2 GT:GL:GQ 0/1:-253.96,-71.96,-163.76:100 20 1996777 . CT C . PASS FR=0.5;HP=2;NF=4;NR=7;PP=100.0;SC=GTGTTTTAGGCTGTTATTTCA;TC=21;TR=11 GT:GL:GQ 0/1:-127.06,-33.79,-125.68:100 20 1997708 . CAT C . PASS FR=0.5;HP=2;NF=5;NR=4;PP=100.0;SC=CACACACACACATACAAAATA;TC=31;TR=9 GT:GL:GQ 0/1:-145.15,-85.85,-245.36:100 20 2004765 . T TG . PASS FR=0.5;HP=1;NF=2;NR=2;PP=76.0;SC=AGGATTTTTCTATCAGTCCAC;TC=12;TR=4 GT:GL:GQ 0/1:-54.31,-25.7,-84.4:100 20 2034931 . G GTTC . PASS FR=0.5;HP=2;NF=6;NR=4;PP=100.0;SC=AGATAGGTAAGTTCTTCCCCA;TC=24;TR=10 GT:GL:GQ 0/1:-162.21,-52.77,-146.87:100 20 2035677 . AACACAC AAC,A . PASS FR=0.5,0.5;HP=2;NF=2,3;NR=0,2;PP=39.0,100.0;SC=TTTTATAATAAACACACACAC;TC=29;TR=2,5 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:88 20 2050099 . AATTG A . PASS FR=0.5;HP=2;NF=10;NR=5;PP=100.0;SC=TCTTATTCTTAATTGATCTAA;TC=35;TR=15 GT:GL:GQ 0/1:-259.54,-91.86,-224.89:100 20 2052246 . AC A . PASS FR=0.5;HP=1;NF=3;NR=6;PP=100.0;SC=GGTCCCAGCTACTCAGGAGGC;TC=19;TR=9 GT:GL:GQ 0/1:-113.96,-44.77,-115.57:100 20 2053863 . C CA . PASS FR=0.5;HP=9;NF=3;NR=4;PP=96.0;SC=ACTAAAAATACAAAAAAAATA;TC=16;TR=7 GT:GL:GQ 0/1:-46.07,-13.04,-34.97:98 20 2054845 . AAAGAGGAAAAAG A . PASS FR=0.5;HP=4;NF=7;NR=1;PP=100.0;SC=AAAAGAGGAAAAAGAGGAAAA;TC=27;TR=8 GT:GL:GQ 0/1:-251.05,-86.54,-294.87:100 20 2055452 . AAAGG A . PASS FR=0.5;HP=4;NF=4;NR=4;PP=100.0;SC=AAGAAAAGAAAAAGGAAGGAA;TC=27;TR=8 GT:GL:GQ 0/1:-227.92,-152.39,-281.38:100 20 2077127 . AAC A . PASS FR=0.5;HP=3;NF=1;NR=3;PP=97.0;SC=TCTCTACTAAAACACACACAC;TC=17;TR=4 GT:GL:GQ 0/1:-57.31,-24.65,-94.33:100 20 2078747 . CCT C . PASS FR=0.5;HP=3;NF=3;NR=2;PP=100.0;SC=AGAAAATTCCCCTGTGGCCCT;TC=15;TR=5 GT:GL:GQ 0/1:-78.54,-32.73,-103.05:100 20 2120509 . AAAGGT A . PASS FR=0.5;HP=2;NF=8;NR=1;PP=100.0;SC=CTGAAATGAGAAAGGTAAGGA;TC=19;TR=9 GT:GL:GQ 0/1:-189.27,-90.48,-174.84:100 20 2122413 . CT C . PASS FR=0.5;HP=4;NF=3;NR=8;PP=100.0;SC=GTAACCTACCCTTTTCCACCT;TC=23;TR=11 GT:GL:GQ 0/1:-132.75,-34.8,-69.03:100 20 2126052 . T TCTATGTGA . PASS FR=0.5;HP=2;NF=3;NR=1;PP=100.0;SC=CATTTCCGTTTCTATGTGACC;TC=22;TR=4 GT:GL:GQ 0/1:-179.74,-76.1,-178.95:100 20 2131707 . T TGG . PASS FR=0.5;HP=2;NF=7;NR=1;PP=100.0;SC=CCCTGTTGCCTGACCTGAGCC;TC=20;TR=8 GT:GL:GQ 0/1:-145.56,-92.76,-163.87:100 20 2153043 . C CTTTATTTA . PASS FR=0.5;HP=3;NF=1;NR=2;PP=100.0;SC=GGTGACATCACTTTATTTATT;TC=21;TR=3 GT:GL:GQ 0/1:-97.11,-28.78,-48.32:87 20 2155932 . C CAT . PASS FR=0.5;HP=7;NF=4;NR=3;PP=100.0;SC=AATTAAAAAACATATATATAT;TC=32;TR=7 GT:GL:GQ 0/1:-176.17,-66.01,-150.43:100 20 2160585 . AT A . PASS FR=0.5;HP=7;NF=9;NR=11;PP=100.0;SC=GTTTTTAAATATTTTTTAATT;TC=41;TR=20 GT:GL:GQ 0/1:-237.9,-137.73,-264.06:100 20 2162113 . A ATT . PASS FR=0.5;HP=1;NF=2;NR=4;PP=100.0;SC=TATCAGGAATAATTTTTTTTT;TC=25;TR=6 GT:GL:GQ 0/1:-145.37,-128.61,-213.61:100 20 2165761 . GTTAT G . PASS FR=0.5;HP=3;NF=4;NR=1;PP=100.0;SC=CTAATAACCTGTTATTTATTT;TC=28;TR=5 GT:GL:GQ 0/1:-79.63,-28.99,-73.78:100 20 2171122 . CAAACA C . PASS FR=0.5;HP=4;NF=4;NR=1;PP=100.0;SC=AACAAACAGACAAACAAAACA;TC=18;TR=5 GT:GL:GQ 0/1:-113.12,-57.95,-91.54:100 20 2171346 . TA T . PASS FR=0.5;HP=8;NF=4;NR=5;PP=100.0;SC=AATTTTTTTTTAAAATCCTTA;TC=20;TR=9 GT:GL:GQ 0/1:-174.43,-122.88,-194.49:100 20 2171402 . T TA . PASS FR=0.5;HP=2;NF=3;NR=1;PP=92.0;SC=TGATTGATCCTAACTTAATGA;TC=23;TR=4 GT:GL:GQ 0/1:-112.12,-79.99,-224.63:100 20 2198337 . AAG A . PASS FR=0.5;HP=2;NF=17;NR=3;PP=100.0;SC=CAACCAAAGAAAGAATGGGAG;TC=38;TR=20 GT:GL:GQ 0/1:-234.35,-51.22,-161.95:100 20 2199055 . G GCCACACACTTCTAAA . PASS FR=0.5;HP=2;NF=2;NR=5;PP=100.0;SC=AGGGGGAAGTGCCATCAGATG;TC=20;TR=7 GT:GL:GQ 0/1:-318.25,-129.11,-238.35:100 20 2199168 . T TG . PASS FR=0.5;HP=9;NF=3;NR=6;PP=100.0;SC=TGAGATTTGGTGGGGGGGACA;TC=37;TR=9 GT:GL:GQ 0/1:-144.44,-70.03,-129.92:100 20 2209336 . A AGTG . PASS FR=0.5;HP=1;NF=4;NR=1;PP=100.0;SC=GCTGGAGTGCAGTGGTACAAT;TC=18;TR=5 GT:GL:GQ 0/1:-105.48,-46.83,-99.81:100 20 2215492 . T TA . PASS FR=1.0;HP=1;NF=17;NR=16;PP=100.0;SC=TGGATGAACGTATTTATTTAA;TC=37;TR=33 GT:GL:GQ 1/1:-589.49,-315.53,-293.02:100 20 2215506 . G GT . PASS FR=1.0;HP=3;NF=18;NR=13;PP=100.0;SC=TATTTAACCAGTTTCTCTTGA;TC=36;TR=31 GT:GL:GQ 1/1:-602.79,-346.63,-325.98:100 20 2216792 . CAG C . PASS FR=0.5;HP=1;NF=6;NR=7;PP=100.0;SC=TGCGTTCATGCAGTTTATGGG;TC=25;TR=13 GT:GL:GQ 0/1:-181.42,-37.01,-108.03:100 20 2217535 . CCT C . PASS FR=0.5;HP=1;NF=6;NR=6;PP=100.0;SC=CATTGCATCACCTGCCTCTGA;TC=32;TR=12 GT:GL:GQ 0/1:-224.94,-75.19,-157.78:100 20 2218702 . CA C . PASS FR=0.5;HP=1;NF=3;NR=5;PP=100.0;SC=AATCACGACTCATTGTAGCCT;TC=18;TR=8 GT:GL:GQ 0/1:-111.7,-55.95,-90.25:100 20 2221607 . TTTTCTTTCTTTCTTTTTCC T . PASS FR=0.5;HP=4;NF=4;NR=2;PP=100.0;SC=AAAGTTTTCTTTTTCTTTCTT;TC=29;TR=6 GT:GL:GQ 0/1:-196.61,-29.28,-142.76:100 20 2241427 . AAAAC A . PASS FR=1.0;HP=4;NF=4;NR=3;PP=100.0;SC=CTTGTCTCTAAAAACAAACAA;TC=19;TR=7 GT:GL:GQ 1/1:-166.73,-37.97,-27.83:84 20 2263098 . TG T . PASS FR=1.0;HP=4;NF=5;NR=5;PP=100.0;SC=TGACGGATGGTGGAGTGAGAA;TC=12;TR=10 GT:GL:GQ 1/1:-115.83,-17.15,-8.29:71 20 2278675 . A ATGAATGGCACT . PASS FR=1.0;HP=4;NF=8;NR=9;PP=100.0;SC=ACTCTGAAAAATGGTCACAGA;TC=18;TR=17 GT:GL:GQ 1/1:-567.99,-218.0,-199.44:100 20 2280081 . C CT . PASS FR=1.0;HP=3;NF=15;NR=9;PP=100.0;SC=TAACTTCATGCGGCTCCACCC;TC=30;TR=24 GT:GL:GQ 1/1:-287.69,-60.5,-41.43:100 20 2280751 . TA T . PASS FR=1.0;HP=10;NF=11;NR=3;PP=100.0;SC=AGACTCCATTTAAAAAAAAAA;TC=22;TR=14 GT:GL:GQ 1/1:-139.24,-88.42,-77.92:88 20 2280882 . A AAAAG . PASS FR=1.0;HP=6;NF=2;NR=2;PP=100.0;SC=AAGAAAGAAAAAAAGAAAGAA;TC=21;TR=4 GT:GL:GQ 1/1:-160.24,-78.2,-70.5:63 20 2285898 . AGTCACTG A . PASS FR=1.0;HP=1;NF=9;NR=3;PP=100.0;SC=CCAAGTCTCTAGTCACTGGTT;TC=19;TR=12 GT:GL:GQ 1/1:-272.68,-30.42,-16.26:99 20 2287002 . TAAG T . PASS FR=1.0;HP=2;NF=12;NR=8;PP=100.0;SC=GAAAAATCTCTAAGAAGGCTC;TC=24;TR=20 GT:GL:GQ 1/1:-245.61,-20.38,-4.14:100 20 2294297 . A ACT . PASS FR=1.0;HP=2;NF=5;NR=3;PP=100.0;SC=AATCACACACACTCTCTCTCT;TC=24;TR=8 GT:GL:GQ 1/1:-199.54,-41.84,-28.04:100 20 2297084 . AT A . PASS FR=1.0;HP=2;NF=10;NR=7;PP=100.0;SC=GGTGGCACGCATTAACACCAG;TC=18;TR=17 GT:GL:GQ 1/1:-184.14,-27.34,-14.78:100 20 2297605 . CT C . PASS FR=0.5;HP=3;NF=4;NR=6;PP=100.0;SC=CAATCATGGCCTTTGGCTTCC;TC=24;TR=10 GT:GL:GQ 0/1:-137.24,-29.13,-84.17:100 20 2298589 . C CAT,T . PASS FR=0.5,0.5;HP=1;NF=5,2;NR=2,3;PP=100.0,100.0;SC=ATATATATATCATATATATAT;TC=23;TR=7,5 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 2316853 . G GC . PASS FR=1.0;HP=4;NF=3;NR=6;PP=100.0;SC=TCACCCTGTAGCCCCTGTGCC;TC=15;TR=9 GT:GL:GQ 1/1:-147.72,-38.92,-28.94:83 20 2318317 . GATCACACC G . PASS FR=1.0;HP=2;NF=8;NR=8;PP=100.0;SC=AGTGAGCCGAGATCACACCAC;TC=22;TR=16 GT:GL:GQ 1/1:-356.42,-104.52,-90.96:100 20 2318716 . AG A . PASS FR=1.0;HP=3;NF=13;NR=4;PP=100.0;SC=CACTCAGAGCAGGGCACCGAT;TC=26;TR=17 GT:GL:GQ 1/1:-256.21,-181.8,-170.54:94 20 2323655 . A AT . PASS FR=1.0;HP=8;NF=11;NR=9;PP=100.0;SC=AGGAAAAAAAAACACTGATGT;TC=31;TR=20 GT:GL:GQ 1/1:-290.56,-28.0,-5.91:100 20 2326944 . G GA . PASS FR=1.0;HP=5;NF=6;NR=12;PP=100.0;SC=AGATACAGAGGAAAAATGAAG;TC=25;TR=18 GT:GL:GQ 1/1:-204.47,-32.24,-15.14:100 20 2329825 . T TC . PASS FR=1.0;HP=1;NF=16;NR=4;PP=100.0;SC=ATATGGGTTGTCTTTGAGACT;TC=22;TR=20 GT:GL:GQ 1/1:-212.37,-32.28,-17.55:100 20 2334719 . CTAT C . PASS FR=1.0;HP=3;NF=14;NR=16;PP=100.0;SC=TTCCCAGGTTCTATTATGTAG;TC=36;TR=30 GT:GL:GQ 1/1:-368.57,-33.34,-9.9:100 20 2335944 . C CTG . PASS FR=1.0;HP=4;NF=10;NR=19;PP=100.0;SC=GCTGAGAAAACTATATCCAAA;TC=34;TR=29 GT:GL:GQ 1/1:-370.96,-31.85,-8.29:100 20 2340299 . TTGTC T . PASS FR=1.0;HP=2;NF=10;NR=15;PP=100.0;SC=ATCCTGTAGGTTGTCTGTTTA;TC=27;TR=25 GT:GL:GQ 1/1:-327.39,-42.17,-22.8:100 20 2342117 . T TG . PASS FR=1.0;HP=5;NF=14;NR=14;PP=100.0;SC=TGCTTATTTTTTCCACTTAAT;TC=32;TR=28 GT:GL:GQ 1/1:-450.6,-326.69,-308.08:100 20 2344369 . TAAG T . PASS FR=1.0;HP=2;NF=13;NR=10;PP=100.0;SC=TGAGAGGTGGTAAGAAGAAGA;TC=36;TR=23 GT:GL:GQ 1/1:-351.7,-76.99,-56.29:100 20 2344451 . G GAGGA . PASS FR=1.0;HP=2;NF=12;NR=3;PP=100.0;SC=ACACCCAACAGAGGAAGGTTA;TC=20;TR=15 GT:GL:GQ 1/1:-372.02,-158.89,-145.61:100 20 2344539 . T TTTTGTTTG . PASS FR=1.0;HP=3;NF=8;NR=4;PP=100.0;SC=ACTACCCCAGTTTTGTTTGTT;TC=23;TR=12 GT:GL:GQ 1/1:-243.77,-36.7,-24.92:99 20 2345269 . TCCTGGC T . PASS FR=1.0;HP=2;NF=7;NR=13;PP=100.0;SC=ATCGAGACCATCCTGGCTAAC;TC=21;TR=20 GT:GL:GQ 1/1:-260.12,-24.22,-9.67:100 20 2346660 . T TAATAAATAAATAAATA . PASS FR=1.0;HP=3;NF=3;NR=4;PP=100.0;SC=CAATTCCTTATAATAAATAAA;TC=13;TR=7 GT:GL:GQ 1/1:-305.93,-18.69,-7.6:93 20 2352930 . AC A . PASS FR=1.0;HP=2;NF=10;NR=8;PP=100.0;SC=TTTCAGGCCTACCTCTCAAGC;TC=21;TR=18 GT:GL:GQ 1/1:-216.23,-90.38,-78.46:100 20 2362643 . C CTG . PASS FR=1.0;HP=3;NF=11;NR=8;PP=100.0;SC=AAGAACTTGTCTTAGATGCTG;TC=21;TR=19 GT:GL:GQ 1/1:-259.19,-87.0,-72.75:100 20 2379170 . TC T . PASS FR=0.5;HP=4;NF=1;NR=3;PP=99.0;SC=AGCTTGGGCTTCCCCACAATA;TC=23;TR=4 GT:GL:GQ 0/1:-84.89,-51.93,-137.5:100 20 2401510 . ATGT A . PASS FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=CATTATATGGATGTACACAGT;TC=23;TR=6 GT:GL:GQ 0/1:-138.83,-80.65,-217.86:100 20 2406090 . AACT A . PASS FR=0.5;HP=3;NF=8;NR=7;PP=100.0;SC=GTTGCCACAAAACTTCAATTT;TC=36;TR=15 GT:GL:GQ 0/1:-277.31,-158.31,-369.27:100 20 2407722 . A AT . PASS FR=0.5;HP=9;NF=4;NR=11;PP=100.0;SC=AATTGCTATAATTTTTTTTTC;TC=38;TR=15 GT:GL:GQ 0/1:-112.13,-34.3,-69.71:100 20 2409340 . C CAATA . PASS FR=0.5;HP=2;NF=4;NR=3;PP=100.0;SC=CATAATAAATCAATCAATAAA;TC=22;TR=7 GT:GL:GQ 0/1:-189.45,-43.56,-132.72:100 20 2409613 . G GCA . PASS FR=0.5;HP=1;NF=6;NR=4;PP=57.0;SC=GGGATTATAGGCACAACACCA;TC=25;TR=10 GT:GL:GQ 0/1:-231.71,-206.44,-319.84:100 20 2411731 . CAG C . PASS FR=0.5;HP=1;NF=1;NR=2;PP=36.0;SC=GTGGATGAGCCAGAGAGAAGT;TC=13;TR=3 GT:GL:GQ 0/1:-55.56,-36.89,-120.4:84 20 2414786 . G GA . PASS FR=1.0;HP=8;NF=8;NR=10;PP=100.0;SC=GAAGCTTTCAGAAAAAAACCC;TC=23;TR=18 GT:GL:GQ 1/1:-173.45,-78.53,-65.46:100 20 2418166 . GTGTT G . PASS FR=0.5;HP=1;NF=1;NR=4;PP=100.0;SC=CACCTGGCTAGTGTTTGTTTG;TC=21;TR=5 GT:GL:GQ 0/1:-134.79,-72.62,-117.78:100 20 2425523 . A ATTTATTTTATTTTAT . PASS FR=0.5;HP=7;NF=3;NR=2;PP=100.0;SC=ATTTTATTTTATTTATTTTAT;TC=23;TR=5 GT:GL:GQ 0/1:-149.61,-12.23,-46.02:100 20 2425934 . T TA . PASS FR=0.5;HP=8;NF=8;NR=4;PP=67.0;SC=TTAATCAATTTAAAAAAAATG;TC=25;TR=12 GT:GL:GQ 0/1:-160.28,-133.72,-162.95:100 20 2430943 . ATGTG A . PASS FR=0.5;HP=1;NF=1;NR=1;PP=100.0;SC=GTGCGTGTGCATGTGTGTGTG;TC=29;TR=2 GT:GL:GQ 0/1:-164.1,-78.49,-99.2:92 20 2433931 . TC T . PASS FR=0.5;HP=5;NF=1;NR=1;PP=26.0;SC=CCCTGGAAGCTCCCCTTTGTG;TC=10;TR=2 GT:GL:GQ 0/1:-34.79,-18.58,-53.81:73 20 2436455 . A AAAAAAG,AAAAAG . PASS FR=0.5,0.5;HP=9;NF=3,3;NR=1,4;PP=50.0,100.0;SC=CTACCAAAAAAAAAAGAAAAG;TC=25;TR=4,7 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 2436835 . A AC . PASS FR=0.5;HP=1;NF=7;NR=8;PP=100.0;SC=ACAATGATGTACATTTTTCAG;TC=37;TR=15 GT:GL:GQ 0/1:-177.52,-36.56,-198.23:100 20 2448573 . CCT C . PASS FR=0.5;HP=2;NF=6;NR=5;PP=100.0;SC=CCCATGCCACCCTGTTTTAGC;TC=34;TR=11 GT:GL:GQ 0/1:-159.22,-114.6,-320.68:100 20 2450954 . CA C . PASS FR=0.5;HP=2;NF=1;NR=4;PP=100.0;SC=CAAACTTCCGCAAGTCTGAGC;TC=22;TR=5 GT:GL:GQ 0/1:-106.22,-51.15,-126.38:100 20 2452700 . TAAAAAAGAA T . PASS FR=0.5;HP=6;NF=4;NR=5;PP=100.0;SC=TTTCTTGGATTAAAAAAGAAA;TC=32;TR=9 GT:GL:GQ 0/1:-216.2,-29.76,-153.35:100 20 2458350 . G GA . PASS FR=0.5;HP=3;NF=4;NR=6;PP=100.0;SC=CAAGGTGGGAGAATTGCTTGA;TC=27;TR=10 GT:GL:GQ 0/1:-156.97,-38.22,-122.55:100 20 2477736 . A AT . PASS FR=0.5;HP=10;NF=4;NR=3;PP=100.0;SC=AAAAAAAAAAATTTTACCATC;TC=23;TR=7 GT:GL:GQ 0/1:-89.51,-39.15,-127.81:100 20 2498012 . GTA G . PASS FR=0.5;HP=2;NF=3;NR=6;PP=100.0;SC=GTATATGTGTGTATATATATA;TC=22;TR=9 GT:GL:GQ 0/1:-140.02,-17.32,-103.73:100 20 2516178 . GA G . PASS FR=0.5;HP=8;NF=3;NR=5;PP=100.0;SC=GTTTAATTGGGAAAAAAAATA;TC=17;TR=8 GT:GL:GQ 0/1:-52.67,-14.95,-45.28:100 20 2520604 . T TAGCA . PASS FR=0.5;HP=4;NF=4;NR=3;PP=100.0;SC=CTCCCGCAAATAGCACACAAG;TC=20;TR=7 GT:GL:GQ 0/1:-194.0,-75.16,-105.67:100 20 2522684 . G GA . PASS FR=0.5;HP=7;NF=5;NR=6;PP=83.0;SC=TTTCTTATTTGAAAAAAACTT;TC=31;TR=11 GT:GL:GQ 0/1:-153.71,-123.52,-187.08:100 20 2523586 . T TA . PASS FR=1.0;HP=4;NF=11;NR=6;PP=100.0;SC=TTTTTCTTTTTAAAACAAAAT;TC=23;TR=17 GT:GL:GQ 1/1:-179.22,-18.0,-3.45:100 20 2526468 . GAAGA G . PASS FR=0.5001;HP=2;NF=2;NR=4;PP=100.0;SC=AGAGGAAGAGGAAGAAAGAAA;TC=25;TR=6 GT:GL:GQ 0/1:-210.76,-128.72,-136.62:37 20 2526552 . A AAG . PASS FR=0.5;HP=6;NF=5;NR=8;PP=100.0;SC=GAAAGAAAGAAAAAAAGAAAG;TC=30;TR=13 GT:GL:GQ 0/1:-215.19,-78.8,-144.35:100 20 2527129 . G GTTGGGCATAAGCTGTAGATC . PASS FR=0.5;HP=2;NF=3;NR=1;PP=100.0;SC=AACCTGCAGAGTTGGGCATAA;TC=18;TR=4 GT:GL:GQ 0/1:-243.57,-136.91,-199.82:100 20 2534184 . T TGTTTTGTGTGAC . PASS FR=0.5;HP=1;NF=5;NR=9;PP=100.0;SC=GATACAGGTCTGTTTTTGTCT;TC=31;TR=14 GT:GL:GQ 0/1:-444.44,-61.75,-181.17:100 20 2546156 . TGG T . PASS FR=0.5;HP=3;NF=4;NR=12;PP=100.0;SC=CCCAAAGTGCTGGGATTACAG;TC=31;TR=16 GT:GL:GQ 0/1:-172.01,-63.37,-146.93:100 20 2568176 . G GT . PASS FR=1.0;HP=10;NF=12;NR=9;PP=100.0;SC=ATTTGGGAATGTTTTTTTTTA;TC=27;TR=21 GT:GL:GQ 1/1:-116.08,-18.72,-6.68:100 20 2577356 . A AAT . PASS FR=0.5;HP=6;NF=1;NR=2;PP=100.0;SC=ATCAGAAAAAAATATATATGT;TC=26;TR=3 GT:GL:GQ 0/1:-199.48,-88.19,-98.9:49 20 2579040 . C CTTTATTTA . PASS FR=0.5;HP=3;NF=1;NR=2;PP=100.0;SC=CTTGCCTCTACTTTATTTATT;TC=16;TR=3 GT:GL:GQ 0/1:-103.59,-10.59,-52.57:100 20 2586119 . GGA G . PASS FR=0.5;HP=1;NF=2;NR=1;PP=30.0;SC=GCATGTGCATGGAGAGAGAGA;TC=23;TR=3 GT:GL:GQ 0/1:-35.49,-18.23,-170.44:77 20 2594696 . A AT . PASS FR=0.5;HP=8;NF=2;NR=7;PP=100.0;SC=TTTCTGTCACATTTTTTTTCG;TC=24;TR=9 GT:GL:GQ 0/1:-70.9,-30.05,-77.99:100 20 2597210 . TAAAG T . PASS FR=0.5;HP=7;NF=2;NR=2;PP=100.0;SC=GAAAGGAAAATAAAGAAGGAG;TC=20;TR=4 GT:GL:GQ 0/1:-85.33,-27.89,-144.98:100 20 2611781 . A ATATCT . PASS FR=0.5;HP=1;NF=8;NR=8;PP=100.0;SC=ATTATAATTAATATAACAAAC;TC=31;TR=16 GT:GL:GQ 0/1:-408.96,-183.07,-309.58:100 20 2613623 . T TTTG . PASS FR=0.5;HP=3;NF=2;NR=2;PP=100.0;SC=CTTCCATGGGTTTGTTGTTGT;TC=18;TR=4 GT:GL:GQ 0/1:-165.53,-112.66,-139.53:100 20 2613971 . TA T . PASS FR=0.5;HP=4;NF=4;NR=7;PP=100.0;SC=CTTGGACACATAAACAGCCCT;TC=27;TR=11 GT:GL:GQ 0/1:-121.36,-29.89,-140.29:100 20 2614405 . T TGGGTAGG . PASS FR=0.5;HP=3;NF=2;NR=2;PP=52.0;SC=ACTACAGAACTGGGTAGGGGA;TC=30;TR=4 GT:GL:GQ 0/1:-185.89,-156.26,-363.71:100 20 2616002 . C CT . PASS FR=0.5;HP=4;NF=5;NR=5;PP=100.0;SC=ACCTCCACCTCCCCCTCTCAG;TC=22;TR=10 GT:GL:GQ 0/1:-182.46,-117.29,-171.16:100 20 2617861 . C CCT . PASS FR=0.5;HP=2;NF=2;NR=5;PP=100.0;SC=ATGGTGAACCCGTCTCTACTA;TC=17;TR=7 GT:GL:GQ 0/1:-111.22,-36.32,-97.76:100 20 2625967 . TGAG T . PASS FR=0.5;HP=1;NF=2;NR=3;PP=100.0;SC=CTGAGTAGGCTGAGGAGGAGG;TC=15;TR=5 GT:GL:GQ 0/1:-133.1,-85.47,-137.74:100 20 2627766 . TTTTATTTA T . PASS FR=0.5;HP=3;NF=1;NR=1;PP=86.0;SC=ACTGAATTTATTTTATTTATT;TC=19;TR=2 GT:GL:GQ 0/1:-102.46,-70.95,-132.69:100 20 2630436 . T TACC . PASS FR=0.5;HP=2;NF=6;NR=5;PP=100.0;SC=ACATGCCAGGTACACCATTGT;TC=23;TR=11 GT:GL:GQ 0/1:-159.47,-31.83,-143.4:100 20 2634285 . CTG C . PASS FR=0.5;HP=1;NF=3;NR=15;PP=100.0;SC=CTTGTGGGCACTGTAGTGACA;TC=29;TR=18 GT:GL:GQ 0/1:-229.42,-26.07,-86.72:100 20 2641823 . C CTG . PASS FR=0.5;HP=5;NF=2;NR=2;PP=100.0;SC=ATTGCATTTTCTGTGTGTGTG;TC=21;TR=4 GT:GL:GQ 0/1:-96.78,-48.19,-99.13:100 20 2643833 . G GAAATGCAAT . PASS FR=0.5;HP=4;NF=9;NR=2;PP=100.0;SC=TGGTATTCCAGAAATGCAATG;TC=31;TR=11 GT:GL:GQ 0/1:-379.88,-109.48,-180.95:100 20 2650007 . T TACACACACACACACACAC . PASS FR=1.0;HP=1;NF=3;NR=1;PP=100.0;SC=ACCCTTTTCTTACACACACAC;TC=19;TR=4 GT:GL:GQ 1/1:-231.82,-84.82,-75.66:76 20 2650235 . C CT . PASS FR=1.0;HP=9;NF=12;NR=9;PP=100.0;SC=TTTATTGGGCCTTTTTTTTTG;TC=28;TR=21 GT:GL:GQ 1/1:-325.44,-296.08,-289.77:79 20 2656886 . AT A . PASS FR=1.0;HP=6;NF=17;NR=6;PP=100.0;SC=ATAAATAATAATTTTTTAAAA;TC=29;TR=23 GT:GL:GQ 1/1:-339.94,-246.4,-231.12:100 20 2663020 . G GGAA . PASS FR=1.0;HP=1;NF=8;NR=7;PP=100.0;SC=AAGAGGAAGAGGAAGAAGACA;TC=28;TR=15 GT:GL:GQ 1/1:-408.26,-206.61,-189.41:100 20 2665268 . TA T . PASS FR=1.0;HP=8;NF=2;NR=1;PP=43.0;SC=TATGCAGCCATAAAAAAATGA;TC=4;TR=3 GT:GL:GQ 1/1:-20.74,-4.04,-1.38:43 20 2665956 . AG A . PASS FR=1.0;HP=1;NF=9;NR=5;PP=100.0;SC=CCCAGGCTATAGTGCAGTGGC;TC=16;TR=14 GT:GL:GQ 1/1:-156.94,-33.67,-23.62:84 20 2666401 . TA T . PASS FR=0.5;HP=2;NF=8;NR=7;PP=100.0;SC=ACTTTTCTATTAAGAAACGCA;TC=38;TR=15 GT:GL:GQ 0/1:-158.74,-28.32,-160.06:100 20 2668149 . A ATG . PASS FR=0.5;HP=2;NF=1;NR=2;PP=100.0;SC=ATATATATATATGTGTGTGTG;TC=17;TR=3 GT:GL:GQ 0/1:-54.4,-18.57,-68.0:100 20 2671350 . GTA G . PASS FR=1.0;HP=2;NF=8;NR=5;PP=100.0;SC=ATATATATGTGTATATATATA;TC=23;TR=13 GT:GL:GQ 1/1:-348.62,-348.37,-348.16:60 20 2676135 . C CAG . PASS FR=0.5;HP=1;NF=6;NR=2;PP=100.0;SC=TGCTGGGATGCAGAGGGCTTC;TC=17;TR=8 GT:GL:GQ 0/1:-189.45,-108.27,-131.01:100 20 2678198 . A AAAAG . PASS FR=1.0;HP=10;NF=1;NR=2;PP=100.0;SC=CTCAAAAAAAAAAAGAAAGAA;TC=16;TR=3 GT:GL:GQ 1/1:-113.89,-62.27,-58.08:51 20 2691794 . AAAT A . PASS FR=1.0;HP=3;NF=2;NR=4;PP=100.0;SC=ACCCTGTCTAAAATAATAATA;TC=12;TR=6 GT:GL:GQ 1/1:-83.97,-10.76,-5.22:69 20 2713483 . C CAG . PASS FR=0.5;HP=2;NF=7;NR=1;PP=100.0;SC=TTTTTTGAGACGGAATTATAA;TC=28;TR=8 GT:GL:GQ 0/1:-114.91,-36.16,-205.08:100 20 2717474 . A ACAAAGGTCTC . PASS FR=1.0;HP=2;NF=9;NR=5;PP=100.0;SC=AGTCATAAGGACAAAGGACCC;TC=17;TR=14 GT:GL:GQ 1/1:-343.26,-32.05,-17.5:94 20 2724519 . AG A . PASS FR=0.5;HP=3;NF=6;NR=7;PP=100.0;SC=CCAGATATTTAGGGTGTCCAT;TC=28;TR=13 GT:GL:GQ 0/1:-149.48,-35.03,-149.61:100 20 2734607 . C CCCCCTTGGTTTTGAAACTTT . PASS FR=1.0;HP=4;NF=2;NR=4;PP=100.0;SC=TCTGTGGGCACCCCCTTGGGC;TC=12;TR=6 GT:GL:GQ 1/1:-301.3,-108.37,-98.31:100 20 2742852 . C CCAGCAATCCTCAGT . PASS FR=0.5;HP=1;NF=1;NR=5;PP=100.0;SC=CTCAATAGCACCTGAGGATGA;TC=16;TR=6 GT:GL:GQ 0/1:-233.59,-35.77,-130.91:100 20 2766949 . C CT . PASS FR=1.0;HP=10;NF=5;NR=10;PP=100.0;SC=ACTTCATTCCCTTTTTTTTTT;TC=28;TR=15 GT:GL:GQ 1/1:-134.68,-37.76,-21.4:100 20 2782855 . AC A . PASS FR=1.0;HP=4;NF=3;NR=8;PP=100.0;SC=AATCACTTGTACCCCGGGGGC;TC=25;TR=11 GT:GL:GQ 1/1:-262.64,-187.36,-174.92:100 20 2789088 . AC A . PASS FR=1.0;HP=9;NF=1;NR=4;PP=100.0;SC=CAAAAAAAAAACCAAAAAACA;TC=13;TR=5 GT:GL:GQ 1/1:-119.81,-36.46,-27.82:89 20 2796485 . C CCTTTT . PASS FR=0.5;HP=4;NF=1;NR=4;PP=100.0;SC=CATCAGGCCCCCTTTTCTCCT;TC=18;TR=5 GT:GL:GQ 0/1:-128.25,-42.55,-123.81:100 20 2797764 . AG A . PASS FR=1.0;HP=3;NF=1;NR=4;PP=100.0;SC=CTGCCTTGGCAGGGCCCAGAC;TC=14;TR=5 GT:GL:GQ 1/1:-134.46,-67.08,-59.42:63 20 2834884 . T TAC . PASS FR=0.5;HP=1;NF=2;NR=1;PP=100.0;SC=ACCCCGTCTCTACACACACAC;TC=22;TR=3 GT:GL:GQ 0/1:-64.62,-28.32,-80.82:100 20 2849974 . AT A . PASS FR=0.5;HP=10;NF=4;NR=6;PP=99.0;SC=TTGGTTTGCAATTTTTTTTTT;TC=36;TR=10 GT:GL:GQ 0/1:-66.95,-34.01,-107.66:100 20 2850721 . ACT A . PASS FR=0.5;HP=1;NF=4;NR=4;PP=100.0;SC=CCAGTGAAAGACTCTTGGGGT;TC=17;TR=8 GT:GL:GQ 0/1:-88.06,-17.99,-74.67:100 20 2858849 . GT G . PASS FR=0.5;HP=8;NF=1;NR=5;PP=52.0;SC=GACAGCTGTAGTTTTTTTTAA;TC=15;TR=6 GT:GL:GQ 0/1:-33.96,-11.94,-50.39:98 20 2867547 . AT A . PASS FR=0.5;HP=6;NF=5;NR=6;PP=100.0;SC=AAATAAAAAAATGTAGTATCT;TC=32;TR=11 GT:GL:GQ 0/1:-115.49,-28.1,-161.94:100 20 2880787 . C CCT . PASS FR=0.5;HP=1;NF=4;NR=5;PP=100.0;SC=GAAAAATCTGCCTCCTTTTTT;TC=27;TR=9 GT:GL:GQ 0/1:-140.77,-68.5,-172.28:100 20 2890657 . C CAT . PASS FR=0.5003;HP=1;NF=2;NR=1;PP=100.0;SC=TATCATATATCATATATAATC;TC=5;TR=3 GT:GL:GQ 0/1:-44.82,-3.47,-10.33:32 20 2890805 . CAT C . PASS FR=0.5017;HP=1;NF=1;NR=6;PP=100.0;SC=TACTATACGTCATATATAATA;TC=9;TR=7 GT:GL:GQ 0/1:-87.98,-14.06,-19.03:24 20 2894312 . CTTATT C . PASS FR=0.5;HP=4;NF=3;NR=5;PP=100.0;SC=GTGCTGTGTTCTTATTTTATC;TC=22;TR=8 GT:GL:GQ 0/1:-141.94,-29.98,-159.98:100 20 2896142 . T TTATC . PASS FR=1.0;HP=2;NF=9;NR=10;PP=100.0;SC=TAAGAGTTCTTTATTCTGATA;TC=30;TR=19 GT:GL:GQ 1/1:-399.17,-94.52,-74.73:100 20 2912364 . T TTG . PASS FR=0.5004;HP=1;NF=1;NR=1;PP=75.0;SC=GGGTCTTGGCTTGTGTGTGTG;TC=20;TR=2 GT:GL:GQ 0/1:-121.99,-92.59,-99.11:31 20 2926228 . GGTGTGTGT G . PASS FR=0.5;HP=1;NF=1;NR=9;PP=100.0;SC=ATAATTGGCAGGTGTGTGTGT;TC=27;TR=10 GT:GL:GQ 0/1:-233.62,-33.54,-77.33:100 20 2937307 . AAAATAAAT A . PASS FR=0.5;HP=4;NF=3;NR=3;PP=100.0;SC=TCAGTAAATAAAAATAAATAA;TC=17;TR=6 GT:GL:GQ 0/1:-165.86,-12.93,-101.78:100 20 2950624 . T TAATA,TAATAAATAAATA . PASS FR=0.5,0.5;HP=5;NF=5,2;NR=2,2;PP=100.0,100.0;SC=TCTAAATAAATAATAAATAAA;TC=24;TR=7,4 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 2966530 . CTTGTTTGT CTTGT,C . PASS FR=0.5,0.5;HP=2;NF=1,1;NR=2,1;PP=100.0,27.0;SC=CAGCTGTCTCCTTGTTTGTTT;TC=22;TR=3,2 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:80 20 2973326 . T TTTAGGGTTTTTC . PASS FR=0.5;HP=4;NF=1;NR=5;PP=100.0;SC=CATATCCAAATATTACGATTC;TC=15;TR=6 GT:GL:GQ 0/0:-275.74,-159.4,-213.4:3 20 2977781 . CATAT C . PASS FR=0.5;HP=5;NF=3;NR=6;PP=100.0;SC=TGTGAGAAAACATATGTGGGA;TC=26;TR=9 GT:GL:GQ 0/1:-131.98,-30.22,-206.04:100 20 2979576 . T TTATTA . PASS FR=0.5;HP=2;NF=2;NR=5;PP=100.0;SC=TATTTATAATTTATTATATAT;TC=21;TR=7 GT:GL:GQ 0/1:-148.89,-17.32,-97.42:100 20 2982245 . CT C . PASS FR=0.5;HP=3;NF=8;NR=4;PP=100.0;SC=CTGTGGAAATCTTATGTGAAG;TC=27;TR=12 GT:GL:GQ 0/1:-126.56,-21.8,-132.46:100 20 2982823 . CA C . PASS FR=1.0;HP=7;NF=10;NR=9;PP=100.0;SC=TTCCATCTGACAAAAAATTGG;TC=21;TR=19 GT:GL:GQ 1/1:-196.74,-95.2,-82.42:100 20 2989926 . AT A . PASS FR=0.5;HP=10;NF=2;NR=5;PP=29.0;SC=GAGTTGTGTGATTTTTTTTTT;TC=36;TR=7 GT:GL:GQ 0/1:-66.0,-49.11,-118.97:76 20 3005541 . TC T . PASS FR=0.5;HP=5;NF=7;NR=7;PP=100.0;SC=AGCAGTTTTTTCTGTAAGAGC;TC=32;TR=14 GT:GL:GQ 0/1:-167.85,-53.03,-186.47:100 20 3007694 . A AGGT . PASS FR=0.5;HP=3;NF=4;NR=5;PP=100.0;SC=CCAGGGCCTGAGGTGGGAGCA;TC=22;TR=9 GT:GL:GQ 0/1:-162.22,-42.91,-117.4:100 20 3012419 . C CTGTT . PASS FR=0.5;HP=2;NF=5;NR=3;PP=100.0;SC=CCTCCTTACTCTGTGTGTTTT;TC=26;TR=8 GT:GL:GQ 0/1:-154.4,-24.26,-143.38:100 20 3022136 . GAATT G . PASS FR=0.5;HP=7;NF=8;NR=1;PP=100.0;SC=AAAAGAAAAAGAATTAATTAA;TC=20;TR=9 GT:GL:GQ 1/0:-190.17,-78.0,-90.9:100 20 3039218 . GT G . PASS FR=1.0;HP=5;NF=12;NR=13;PP=100.0;SC=TGTTGTTGTTGTTTGTTTGTT;TC=29;TR=25 GT:GL:GQ 1/1:-226.7,-48.88,-31.11:100 20 3042034 . T TA . PASS FR=1.0;HP=10;NF=5;NR=14;PP=100.0;SC=AAGACACTGATAAAAAAAAAT;TC=25;TR=19 GT:GL:GQ 1/1:-125.74,-31.3,-15.65:100 20 3047853 . A ATTCCCCCATT . PASS FR=0.5;HP=2;NF=6;NR=1;PP=100.0;SC=ACTCCCTCTCATTCCCCCATT;TC=20;TR=7 GT:GL:GQ 0/1:-258.31,-36.83,-99.91:100 20 3050529 . A AT . PASS FR=0.5;HP=10;NF=4;NR=1;PP=23.0;SC=GCAAAAAAAAAAATTTTTATT;TC=22;TR=5 GT:GL:GQ 0/1:-257.11,-262.46,-292.84:73 20 3050531 . A ATTT,T . PASS FR=0.5,0.5;HP=10;NF=3,13;NR=0,6;PP=97.0,100.0;SC=AAAAAAAAAAATTTTTATTTT;TC=22;TR=3,19 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 3051123 . A AT . PASS FR=0.5;HP=6;NF=2;NR=1;PP=69.0;SC=TCAAGAAAAAAATATATATAT;TC=17;TR=3 GT:GL:GQ 0/1:-107.95,-81.12,-160.4:100 20 3058938 . C CTT . PASS FR=1.0;HP=2;NF=19;NR=9;PP=100.0;SC=ACTGGATACTCTGAACTCCTA;TC=30;TR=28 GT:GL:GQ 1/1:-404.4,-115.7,-94.26:100 20 3060201 . C CAAT . PASS FR=0.5;HP=4;NF=13;NR=9;PP=100.0;SC=ACAAAGTCAACAATAATTCAT;TC=44;TR=22 GT:GL:GQ 0/1:-325.42,-43.13,-189.79:100 20 3062903 . T TC . PASS FR=0.5;HP=3;NF=1;NR=5;PP=94.0;SC=TCCAGGCCTTTCCCTCTCTGC;TC=19;TR=6 GT:GL:GQ 0/1:-95.35,-62.58,-147.62:100 20 3072606 . A AAGG . PASS FR=1.0;HP=5;NF=4;NR=4;PP=100.0;SC=CCAAGTAAAAAAGGGCGGGGG;TC=22;TR=8 GT:GL:GQ 1/1:-220.94,-78.12,-65.62:100 20 3126086 . CCT TCT,C . PASS FR=0.5,0.5;HP=7;NF=1,1;NR=3,1;PP=8.0,36.0;SC=GCCTTTTTTTCCTTTTTTTTT;TC=19;TR=4,2 GT:GL:GQ 2/1:-1.0,-1.0,-1.0:42 20 3159346 . C CA . PASS FR=1.0;HP=2;NF=3;NR=12;PP=100.0;SC=GCTGGGACTACGGCATTTACT;TC=15;TR=15 GT:GL:GQ 1/1:-149.15,-11.32,-0.92:87 20 3161722 . C CAGAT,CAGATAGAT . PASS FR=0.5,0.5;HP=2;NF=2,1;NR=2,2;PP=35.0,42.0;SC=GATAGATAGACAGATAGATAG;TC=18;TR=4,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:99 20 3161783 . CTA C . PASS FR=1.0;HP=2;NF=9;NR=7;PP=100.0;SC=TTTTATATATCTATATATATA;TC=25;TR=16 GT:GL:GQ 1/1:-263.89,-139.12,-127.54:97 20 3162560 . CAT C . PASS FR=0.5369;HP=2;NF=1;NR=3;PP=100.0;SC=CACACACACACATGGTCCATG;TC=6;TR=4 GT:GL:GQ 0/1:-84.99,-50.52,-52.5:11 20 3169476 . T TTTG . PASS FR=0.5;HP=3;NF=5;NR=9;PP=100.0;SC=AATGTTTACTTTTAATAAACT;TC=35;TR=14 GT:GL:GQ 0/1:-273.66,-64.07,-202.46:100 20 3169541 . A AT . PASS FR=0.5;HP=7;NF=5;NR=9;PP=100.0;SC=AGGATCATAGATTTTTTTCCT;TC=23;TR=14 GT:GL:GQ 0/1:-204.2,-123.3,-145.94:100 20 3172618 . GACAC G . PASS FR=0.7893;HP=1;NF=3;NR=1;PP=100.0;SC=TTGCTCCCCTGACACACACAC;TC=16;TR=4 GT:GL:GQ 1/1:-154.29,-100.95,-101.25:3 20 3172771 . C CAT . PASS FR=1.0;HP=1;NF=13;NR=6;PP=100.0;SC=CCGAGACACACGAGTGGTAAT;TC=24;TR=19 GT:GL:GQ 1/1:-267.07,-44.87,-28.98:100 20 3177159 . T TA . PASS FR=1.0;HP=5;NF=6;NR=3;PP=87.0;SC=CTGTCTCCACTAAAAATACAA;TC=15;TR=9 GT:GL:GQ 1/1:-169.92,-142.98,-139.57:56 20 3177517 . C CAT . PASS FR=1.0;HP=2;NF=15;NR=10;PP=100.0;SC=TAATAAATAACGTTACTGGAT;TC=26;TR=25 GT:GL:GQ 1/1:-294.64,-37.59,-18.88:100 20 3188342 . A AAACAACAACAACAAC . PASS FR=0.5;HP=3;NF=2;NR=2;PP=100.0;SC=CTCCATCTCAAAACAACAACA;TC=17;TR=4 GT:GL:GQ 0/1:-131.35,-46.51,-82.74:100 20 3192138 . T TTTTGTTTGTTTG . PASS FR=0.5;HP=3;NF=3;NR=1;PP=99.0;SC=TTTTGTTTTGTTTTGTTTGTT;TC=17;TR=4 GT:GL:GQ 0/1:-79.23,-33.31,-124.52:100 20 3192798 . C CAG . PASS FR=0.5;HP=2;NF=2;NR=6;PP=100.0;SC=GCCTGGGTGACAGAGAGAGAG;TC=20;TR=8 GT:GL:GQ 0/1:-108.84,-41.85,-123.5:100 20 3198551 . G GTT . PASS FR=0.5;HP=2;NF=1;NR=2;PP=63.0;SC=AGTTTTTGTGGGTTTTTTTTT;TC=22;TR=3 GT:GL:GQ 0/1:-111.88,-112.41,-193.71:91 20 3202220 . GTGGC G . PASS FR=0.5;HP=2;NF=2;NR=5;PP=100.0;SC=TGTCCCGGGTGTGGCTGGCGA;TC=19;TR=7 GT:GL:GQ 0/1:-150.53,-63.82,-136.14:100 20 3276659 . CT C . PASS FR=1.0;HP=3;NF=5;NR=6;PP=100.0;SC=ACATCGGGAACTTTCGGTTTC;TC=16;TR=11 GT:GL:GQ 1/1:-135.26,-24.21,-14.73:79 20 3290980 . A AAAAG . PASS FR=0.9998;HP=4;NF=1;NR=1;PP=30.0;SC=AAGAGAAAGAAAAAGAAAGAA;TC=7;TR=2 GT:GL:GQ 1/1:-37.89,-18.65,-17.26:34 20 3313547 . G GGTGT . PASS FR=1.0;HP=1;NF=1;NR=3;PP=100.0;SC=GTGTGCGTGTGGTGTGTGTGT;TC=20;TR=4 GT:GL:GQ 1/1:-194.22,-148.74,-144.19:56 20 3314333 . G GT . PASS FR=1.0;HP=10;NF=9;NR=9;PP=100.0;SC=CTTATTAAAGGTTTTTTTTTT;TC=34;TR=18 GT:GL:GQ 1/1:-126.24,-28.85,-19.8:75 20 3317061 . G GT . PASS FR=1.0;HP=10;NF=5;NR=7;PP=100.0;SC=GTTTTGTTCAGTTTTTTTTTT;TC=20;TR=12 GT:GL:GQ 1/1:-81.13,-22.72,-13.12:80 20 3318622 . TATAAAATATATAATAC T . PASS FR=0.5;HP=2;NF=3;NR=5;PP=100.0;SC=ATATATAATATATAAAATATA;TC=21;TR=8 GT:GL:GQ 1/0:-309.41,-50.93,-55.49:45 20 3320964 . AGTTT A . PASS FR=1.0;HP=1;NF=6;NR=12;PP=100.0;SC=AATCATACCTAGTTTGTACTA;TC=22;TR=18 GT:GL:GQ 1/1:-403.07,-167.86,-153.33:100 20 3320971 . A AC . PASS FR=1.0;HP=1;NF=6;NR=13;PP=100.0;SC=CCTAGTTTGTACTATAAAAAA;TC=19;TR=19 GT:GL:GQ 1/1:-403.07,-261.66,-248.63:100 20 3323678 . AT A . PASS FR=1.0;HP=5;NF=3;NR=1;PP=100.0;SC=TCTGATGATTATTTCTATTGC;TC=28;TR=4 GT:GL:GQ 1/1:-575.25,-570.95,-570.67:100 20 3323683 . T TAAA . PASS FR=1.0;HP=1;NF=13;NR=11;PP=100.0;SC=TGATTATTTCTATTGCTGTGC;TC=29;TR=24 GT:GL:GQ 1/1:-597.36,-560.99,-550.34:86 20 3323709 . T TA . PASS FR=1.0;HP=2;NF=16;NR=21;PP=100.0;SC=CATGTTCATTTGTTAGGTCCC;TC=38;TR=37 GT:GL:GQ 1/1:-694.83,-570.91,-558.14:100 20 3325237 . TACACACAC T . PASS FR=1.0;HP=2;NF=4;NR=2;PP=100.0;SC=TACACACACATACACACACAC;TC=33;TR=6 GT:GL:GQ 1/1:-276.44,-185.04,-177.42:63 20 3332481 . TTTTA T . PASS FR=1.0;HP=3;NF=7;NR=10;PP=100.0;SC=GTTTGTGTTATTTTATTTATT;TC=28;TR=17 GT:GL:GQ 1/1:-276.75,-43.8,-27.83:100 20 3333166 . TCA T . PASS FR=1.0;HP=1;NF=9;NR=10;PP=100.0;SC=TGGCTGTCATTCACATTCCAG;TC=22;TR=19 GT:GL:GQ 1/1:-222.99,-23.7,-9.78:100 20 3333493 . T TTA . PASS FR=1.0;HP=2;NF=6;NR=7;PP=100.0;SC=TTCAAAATATTTATATATATA;TC=27;TR=13 GT:GL:GQ 1/1:-272.96,-96.81,-86.7:65 20 3336192 . G GC . PASS FR=1.0;HP=2;NF=5;NR=10;PP=100.0;SC=CTGCACTCCAGCCTGGGTGAC;TC=18;TR=15 GT:GL:GQ 1/1:-163.64,-31.05,-19.12:100 20 3338276 . G GCTTAT . PASS FR=1.0;HP=1;NF=8;NR=10;PP=100.0;SC=CACCCATCCAGCTTTATCTTT;TC=23;TR=18 GT:GL:GQ 1/1:-329.33,-26.75,-8.74:100 20 3345587 . C CT . PASS FR=1.0;HP=6;NF=1;NR=10;PP=100.0;SC=CCTTCTTTTCCTTTTTTCTTT;TC=27;TR=11 GT:GL:GQ 1/1:-267.74,-155.91,-141.96:100 20 3346020 . TTTTATTTA T . PASS FR=1.0;HP=3;NF=7;NR=6;PP=100.0;SC=TTTGATAACATTTTATTTATT;TC=29;TR=13 GT:GL:GQ 1/1:-347.46,-36.68,-23.65:100 20 3349612 . T TA . PASS FR=1.0;HP=2;NF=8;NR=3;PP=100.0;SC=ACCCCATTTCTCTAAAAATAC;TC=11;TR=11 GT:GL:GQ 1/1:-135.85,-60.43,-52.97:61 20 3377965 . G GTTTTGTT . PASS FR=1.0;HP=8;NF=3;NR=2;PP=100.0;SC=TTTTTGTTTTGTTTTGTTTTT;TC=16;TR=5 GT:GL:GQ 1/1:-157.49,-62.9,-56.59:79 20 3378366 . TG T . PASS FR=1.0;HP=10;NF=6;NR=4;PP=100.0;SC=AGATTTTTTTTGGGGGGGGGG;TC=22;TR=10 GT:GL:GQ 1/1:-84.99,-30.32,-19.67:66 20 3382249 . T TA . PASS FR=1.0;HP=2;NF=7;NR=9;PP=100.0;SC=AATTATTATCTTTCATTCAAT;TC=19;TR=16 GT:GL:GQ 1/1:-178.1,-44.13,-31.76:100 20 3382515 . TC T . PASS FR=1.0;HP=6;NF=2;NR=10;PP=100.0;SC=TGGGGAGGGCTCCCCCGCCCC;TC=19;TR=12 GT:GL:GQ 1/1:-132.42,-42.62,-32.12:88 20 3398847 . T TAC . PASS FR=0.5;HP=2;NF=2;NR=1;PP=82.0;SC=AATAACAACATACACACACAC;TC=26;TR=3 GT:GL:GQ 0/1:-87.09,-56.01,-103.69:100 20 3418279 . TACACACACAC T . PASS FR=0.5;HP=3;NF=2;NR=1;PP=100.0;SC=CACACGAGGGTACACACACAC;TC=17;TR=3 GT:GL:GQ 0/1:-117.7,-66.19,-77.13:50 20 3419562 . TACAC T . PASS FR=0.5;HP=2;NF=2;NR=2;PP=100.0;SC=TCAAAATACATACACACACAC;TC=29;TR=4 GT:GL:GQ 0/1:-141.17,-79.46,-166.16:100 20 3426771 . T TC . PASS FR=1.0;HP=1;NF=13;NR=10;PP=100.0;SC=TTGCAGAAACTGACAAAATAG;TC=25;TR=23 GT:GL:GQ 1/1:-297.92,-207.29,-192.68:100 20 3439128 . AT A . PASS FR=1.0;HP=4;NF=4;NR=3;PP=100.0;SC=TGTCTCAAAAATATATATATA;TC=13;TR=7 GT:GL:GQ 1/1:-127.06,-48.08,-43.43:57 20 3439712 . CATTTATTTATTT CATTTATTT,C . PASS FR=0.5,0.5;HP=1;NF=2,5;NR=1,1;PP=100.0,100.0;SC=AACATAAAATCATTTATTTAT;TC=23;TR=3,6 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 3441674 . G GA . PASS FR=0.5;HP=7;NF=13;NR=3;PP=100.0;SC=TTCTTATTAGGAAAAAAACCA;TC=23;TR=16 GT:GL:GQ 0/1:-122.74,-20.86,-35.93:68 20 3456629 . CA C . PASS FR=0.5;HP=8;NF=3;NR=5;PP=100.0;SC=TCCTCACTACCAAAAAAAAGA;TC=22;TR=8 GT:GL:GQ 0/1:-62.73,-25.03,-67.91:100 20 3462307 . A ATTC . PASS FR=0.5;HP=2;NF=7;NR=2;PP=100.0;SC=TAAATTTTTAATTAAGTTTTC;TC=17;TR=9 GT:GL:GQ 0/1:-213.54,-117.72,-169.88:100 20 3465413 . G GTTA . PASS FR=0.5;HP=3;NF=4;NR=7;PP=100.0;SC=TATATTTCCAGTTTAGGTCTC;TC=32;TR=11 GT:GL:GQ 0/1:-171.48,-39.39,-198.21:100 20 3465556 . AATT A . PASS FR=0.5;HP=3;NF=3;NR=3;PP=100.0;SC=TGGATTTTAAAATTATTATTA;TC=23;TR=6 GT:GL:GQ 0/1:-128.2,-26.49,-64.94:100 20 3467027 . TTTTCC T . PASS FR=0.5;HP=3;NF=3;NR=10;PP=100.0;SC=GTTGTTTTTCTTTTCCTTTTT;TC=35;TR=13 GT:GL:GQ 0/1:-205.57,-36.22,-212.27:100 20 3468732 . AT A . PASS FR=0.5;HP=1;NF=7;NR=3;PP=100.0;SC=GTTGGCTAACATGTTCCCTGC;TC=24;TR=10 GT:GL:GQ 0/1:-129.57,-23.07,-107.21:100 20 3472426 . T TA . PASS FR=0.5;HP=1;NF=4;NR=5;PP=100.0;SC=CCCCAAAACTTATCTAAGTAT;TC=30;TR=9 GT:GL:GQ 0/1:-164.9,-36.91,-163.8:100 20 3473769 . TTGTGTGTGTG TTGTGTGTG,T . PASS FR=0.5,0.5;HP=2;NF=3,2;NR=1,0;PP=100.0,100.0;SC=GTACGTTTGTTTGTGTGTGTG;TC=10;TR=4,2 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 3489906 . C CAG . PASS FR=0.5;HP=3;NF=7;NR=5;PP=100.0;SC=TGTAATGAGTCAAATATTGAA;TC=30;TR=12 GT:GL:GQ 0/1:-218.47,-143.39,-285.84:100 20 3495915 . T TG . PASS FR=0.5;HP=1;NF=8;NR=2;PP=100.0;SC=GTGTTACCATTCTAGAGATGA;TC=24;TR=10 GT:GL:GQ 0/1:-170.31,-150.44,-250.52:100 20 3509359 . CTAAAA C . PASS FR=0.5;HP=1;NF=7;NR=9;PP=100.0;SC=CCCCTTGAACCTAAAATAAAA;TC=36;TR=16 GT:GL:GQ 0/1:-259.32,-75.45,-201.38:100 20 3516100 . GA G . PASS FR=0.5;HP=2;NF=4;NR=5;PP=100.0;SC=AACATTACTTGATAACCTTTC;TC=24;TR=9 GT:GL:GQ 0/1:-89.87,-17.09,-134.48:100 20 3517232 . T TA . PASS FR=0.5;HP=4;NF=5;NR=10;PP=100.0;SC=TTTATTCATTTAAAAGCAACA;TC=33;TR=15 GT:GL:GQ 0/1:-148.46,-23.56,-134.17:100 20 3518135 . TTG T . PASS FR=0.5;HP=1;NF=2;NR=7;PP=100.0;SC=TATTTTTTTCTTGTTTTTTTT;TC=24;TR=9 GT:GL:GQ 0/1:-164.48,-76.63,-118.93:100 20 3520111 . TGAGAAACAGAAA T . PASS FR=0.5;HP=1;NF=6;NR=4;PP=100.0;SC=GTCAAATACTTGAGAAACAGA;TC=30;TR=10 GT:GL:GQ 0/1:-291.42,-56.72,-205.51:100 20 3533082 . C CTA . PASS FR=0.5;HP=6;NF=5;NR=7;PP=100.0;SC=CCAGATGTCCCCCCCAGTTAA;TC=28;TR=12 GT:GL:GQ 0/1:-172.54,-164.36,-281.23:100 20 3536203 . CA C . PASS FR=0.5;HP=5;NF=5;NR=1;PP=100.0;SC=TGGTAGACCACAAAACAAAAT;TC=20;TR=6 GT:GL:GQ 0/1:-93.07,-22.5,-78.34:100 20 3549166 . A AT . PASS FR=0.5;HP=7;NF=6;NR=5;PP=100.0;SC=ACTCAAAAAAAATATATTTCA;TC=27;TR=11 GT:GL:GQ 0/1:-132.66,-26.81,-119.92:100 20 3550790 . AT A . PASS FR=0.5;HP=10;NF=9;NR=3;PP=100.0;SC=AATTGTCTCAATTTTTTTTTT;TC=36;TR=12 GT:GL:GQ 0/1:-95.8,-54.46,-109.39:100 20 3554405 . TTTTA T . PASS FR=0.5;HP=3;NF=5;NR=3;PP=100.0;SC=TTTTATTTTATTTTATTTATT;TC=28;TR=8 GT:GL:GQ 0/1:-169.52,-76.02,-126.65:100 20 3557342 . G GTCTATCTATCTATCTATCTA,GTCTGTCTGTCTATCTA . PASS FR=0.5,0.5;HP=2;NF=0,1;NR=2,1;PP=100.0,100.0;SC=CTGTCTGTCTGTCTATCTATC;TC=14;TR=2,2 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 3577359 . AACTTT A . PASS FR=0.5;HP=3;NF=8;NR=4;PP=100.0;SC=GTTCTCTTAAAACTTTACTTT;TC=28;TR=12 GT:GL:GQ 0/1:-187.21,-26.31,-190.0:100 20 3587084 . A ACT . PASS FR=0.5;HP=2;NF=5;NR=2;PP=100.0;SC=TTCTCTCTTCACTGTTTCCTG;TC=27;TR=7 GT:GL:GQ 0/1:-175.39,-93.87,-225.08:100 20 3587106 . TGTG T . PASS FR=0.5;HP=1;NF=4;NR=3;PP=100.0;SC=ATGTGGGACTTGTGGTGCCAC;TC=26;TR=7 GT:GL:GQ 0/1:-197.29,-142.58,-281.02:100 20 3597598 . AT A . PASS FR=0.5;HP=5;NF=5;NR=7;PP=29.0;SC=CAAGGATCGCATTTTTATCCC;TC=39;TR=12 GT:GL:GQ 0/1:-225.54,-208.64,-370.51:76 20 3599489 . G GGTT . PASS FR=0.5;HP=1;NF=6;NR=4;PP=100.0;SC=TGGTGGTGGTGGTTTTGTTTC;TC=28;TR=10 GT:GL:GQ 0/1:-173.69,-38.78,-110.57:100 20 3601166 . T TAC . PASS FR=0.5;HP=1;NF=1;NR=5;PP=100.0;SC=GTACTGGGATTAGGCGTGAGC;TC=23;TR=6 GT:GL:GQ 0/1:-99.56,-38.65,-114.14:100 20 3607044 . TAAAAA T . PASS FR=0.5;HP=5;NF=6;NR=1;PP=100.0;SC=TTTTCTCTCTTAAAAAGAAAA;TC=23;TR=7 GT:GL:GQ 0/1:-96.17,-24.47,-167.72:100 20 3608928 . A AAG . PASS FR=0.5;HP=2;NF=6;NR=2;PP=100.0;SC=GAAAACTAGAAAGAAACTTCT;TC=32;TR=8 GT:GL:GQ 0/1:-96.19,-24.02,-201.47:100 20 3610589 . G GT . PASS FR=0.5;HP=7;NF=7;NR=8;PP=100.0;SC=ATCATTCTGAGTTTTTTTATT;TC=36;TR=15 GT:GL:GQ 0/1:-148.28,-61.67,-123.51:100 20 3612124 . A AC . PASS FR=0.5;HP=1;NF=5;NR=1;PP=100.0;SC=GTCTGTTGAGACTGTGTCCTA;TC=17;TR=6 GT:GL:GQ 0/1:-86.01,-27.19,-97.39:100 20 3627840 . C CA . PASS FR=0.5;HP=6;NF=4;NR=7;PP=100.0;SC=CTCAACTGTGCAAAAAACAAA;TC=27;TR=11 GT:GL:GQ 0/1:-99.01,-25.59,-91.79:100 20 3627925 . A ATTAAC . PASS FR=0.5;HP=2;NF=2;NR=9;PP=100.0;SC=AGTCAGATGAATTGTTTTCAT;TC=29;TR=11 GT:GL:GQ 0/1:-210.42,-38.37,-176.36:100 20 3635158 . A AT . PASS FR=0.5;HP=2;NF=8;NR=5;PP=100.0;SC=CAAGAAAGCCATAGACCGGAA;TC=23;TR=13 GT:GL:GQ 0/1:-191.76,-111.36,-148.51:100 20 3642221 . TTC T . PASS FR=1.0;HP=2;NF=12;NR=3;PP=100.0;SC=TCGCCACCATTTCTCCAGAAC;TC=20;TR=15 GT:GL:GQ 1/1:-312.08,-172.82,-161.67:43 20 3643129 . TC T . PASS FR=1.0;HP=9;NF=4;NR=4;PP=100.0;SC=CGGGGTGGTATCCCCCCCCCA;TC=20;TR=8 GT:GL:GQ 1/1:-89.01,-45.99,-37.4:71 20 3645120 . AAAAC A . PASS FR=1.0;HP=5;NF=1;NR=4;PP=100.0;SC=TTTTTTTTAAAAAACAAACAA;TC=18;TR=5 GT:GL:GQ 1/1:-88.2,-13.8,-7.58:77 20 3650540 . A ACACCACC . PASS FR=1.0;HP=1;NF=3;NR=4;PP=100.0;SC=CCAGGCTCTGACAGCAGCCTG;TC=12;TR=7 GT:GL:GQ 1/1:-183.63,-21.64,-13.12:68 20 3664603 . AG A . PASS FR=1.0;HP=6;NF=3;NR=9;PP=100.0;SC=TTCTGTAGACAGGGGGGTCTC;TC=16;TR=12 GT:GL:GQ 1/1:-110.02,-26.49,-16.31:85 20 3667748 . C CG . PASS FR=1.0;HP=2;NF=12;NR=5;PP=100.0;SC=AAAGTTCACCCGCCCCCAACT;TC=24;TR=17 GT:GL:GQ 1/1:-221.42,-44.79,-28.21:100 20 3677095 . T TGCTG . PASS FR=1.0;HP=1;NF=4;NR=13;PP=100.0;SC=GGAGGCCTTCTGCTGGCTGGA;TC=22;TR=17 GT:GL:GQ 1/1:-297.16,-58.83,-44.05:100 20 3685444 . A AT . PASS FR=1.0;HP=7;NF=6;NR=4;PP=100.0;SC=TTGTTTTTTAATTTTTTTGTA;TC=15;TR=10 GT:GL:GQ 1/1:-93.4,-15.67,-6.68:75 20 3699376 . AAAAT A . PASS FR=1.0;HP=5;NF=4;NR=2;PP=100.0;SC=CAAAAAATAAAAAATAAATAA;TC=21;TR=6 GT:GL:GQ 1/1:-124.16,-19.34,-11.28:66 20 3700024 . TTTAC T . PASS FR=0.5;HP=2;NF=3;NR=4;PP=100.0;SC=TATTTATTTATTTACTTACTT;TC=22;TR=7 GT:GL:GQ 0/1:-142.54,-24.82,-34.29:44 20 3702676 . C CT . PASS FR=1.0;HP=9;NF=9;NR=6;PP=100.0;SC=ATATGTTGAACTTTTTTTTTA;TC=20;TR=15 GT:GL:GQ 1/1:-102.25,-23.87,-11.51:100 20 3703373 . GAATA G . PASS FR=1.0;HP=3;NF=3;NR=4;PP=100.0;SC=TATACATGGAGAATAAATAAA;TC=24;TR=7 GT:GL:GQ 1/1:-129.84,-26.73,-19.11:63 20 3705235 . G GGAAA . PASS FR=1.0;HP=3;NF=3;NR=2;PP=100.0;SC=AAGAAAGAAAGGAAAGAAATA;TC=24;TR=5 GT:GL:GQ 1/1:-319.51,-157.83,-145.36:98 20 3717704 . AAAATAAATAAATAAAT AAAATAAATAAAT,A . PASS FR=0.5,0.5;HP=4;NF=1,0;NR=1,2;PP=100.0,55.0;SC=CTCTGCCTCAAAAATAAATAA;TC=12;TR=2,2 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 3719488 . AGT A . PASS FR=0.5;HP=2;NF=4;NR=6;PP=100.0;SC=TCTGTGAGTGAGTGTGTGTGT;TC=28;TR=10 GT:GL:GQ 0/1:-149.53,-25.54,-102.21:100 20 3736407 . CCCCCAGCCCAGTGG C . PASS FR=0.5;HP=4;NF=3;NR=1;PP=100.0;SC=AGCTGATCGACCCCCAGCCCA;TC=22;TR=4 GT:GL:GQ 0/1:-177.03,-114.74,-207.47:100 20 3740620 . GCA G . PASS FR=1.0;HP=1;NF=4;NR=6;PP=100.0;SC=ACTCACACATGCACACACACA;TC=17;TR=10 GT:GL:GQ 1/1:-154.32,-36.11,-25.75:86 20 3751453 . G GT . PASS FR=1.0;HP=6;NF=1;NR=1;PP=100.0;SC=CAAACACACGGTTTTTTGTTT;TC=25;TR=2 GT:GL:GQ 1/1:-234.3,-199.49,-191.92:62 20 3752464 . A AACAC,AACACAC . PASS FR=0.5,0.5;HP=3;NF=4,3;NR=3,3;PP=100.0,100.0;SC=AAAAAGAGAAAACACACACAC;TC=29;TR=7,6 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 3755004 . G GACA . PASS FR=1.0;HP=2;NF=1;NR=7;PP=100.0;SC=GACAGAGTGAGACATCTCATA;TC=13;TR=8 GT:GL:GQ 1/1:-134.63,-25.28,-17.61:63 20 3768789 . A AAAAG . PASS FR=0.5;HP=8;NF=4;NR=3;PP=100.0;SC=ATCTCAAAAAAAAAGAAAGAA;TC=28;TR=7 GT:GL:GQ 0/1:-141.47,-38.74,-119.72:100 20 3770324 . T TAATAATA . PASS FR=0.5;HP=8;NF=1;NR=2;PP=29.0;SC=GGCCAAAAAATAATAATAAAT;TC=11;TR=3 GT:GL:GQ 0/1:-67.44,-43.02,-52.14:42 20 3774219 . AATTTT A . PASS FR=0.5;HP=1;NF=2;NR=3;PP=100.0;SC=GGTTTTAGAGAATTTTATTTT;TC=20;TR=5 GT:GL:GQ 0/1:-126.4,-91.22,-154.58:100 20 3775162 . GTT G . PASS FR=0.5;HP=10;NF=3;NR=6;PP=100.0;SC=TCTCGGGGCAGTTTTTTTTTT;TC=26;TR=9 GT:GL:GQ 0/1:-103.9,-68.26,-117.09:100 20 3776005 . C CA . PASS FR=0.5;HP=8;NF=1;NR=4;PP=23.0;SC=GACTCCATCCCAAAAAAAACA;TC=14;TR=5 GT:GL:GQ 0/1:-145.51,-129.15,-148.62:73 20 3776021 . AAAC A . PASS FR=0.5;HP=3;NF=3;NR=1;PP=100.0;SC=AAACAAAACAAAACAAAAAGA;TC=21;TR=4 GT:GL:GQ 0/1:-163.41,-119.44,-232.96:100 20 3780857 . T TGGACTGGAGACCTGGTGCTAG . PASS FR=0.5;HP=6;NF=4;NR=1;PP=100.0;SC=TACTCCCCCCTGGACTGGGGG;TC=10;TR=5 GT:GL:GQ 0/1:-153.98,-19.16,-34.72:70 20 3786892 . C CT . PASS FR=1.0;HP=4;NF=10;NR=2;PP=100.0;SC=CTTGTCCCTTCTTCTCCCAAT;TC=16;TR=12 GT:GL:GQ 1/1:-171.33,-64.44,-53.38:92 20 3787614 . CAT C . PASS FR=1.0;HP=2;NF=11;NR=13;PP=100.0;SC=AGTGCACACACATGTCAGGCA;TC=30;TR=24 GT:GL:GQ 1/1:-451.43,-312.17,-297.5:100 20 3789927 . C CCCG . PASS FR=1.0;HP=2;NF=2;NR=10;PP=100.0;SC=AGTTACCACGCGCTCTCTTTC;TC=17;TR=12 GT:GL:GQ 1/1:-241.99,-120.76,-110.7:78 20 3790246 . ATATAT A . PASS FR=1.0;HP=8;NF=5;NR=2;PP=92.0;SC=TCAAAAAAAAATATATATATA;TC=14;TR=7 GT:GL:GQ 1/1:-198.37,-176.0,-172.1:52 20 3795480 . AGGCGTGAGCCACCGCGCCC A . PASS FR=0.5;HP=2;NF=2;NR=2;PP=100.0;SC=CTGGGATTACAGGCGTGAGCC;TC=12;TR=4 GT:GL:GQ 0/1:-109.14,-46.17,-99.46:100 20 3824585 . TTTTAC T . PASS FR=1.0;HP=3;NF=18;NR=4;PP=100.0;SC=AGATGATTTATTTTACTTTAT;TC=28;TR=22 GT:GL:GQ 1/1:-337.35,-36.39,-16.32:100 20 3843259 . A AT . PASS FR=0.5;HP=10;NF=3;NR=7;PP=100.0;SC=AGTTTTCCAAATTTTTTTTTT;TC=31;TR=10 GT:GL:GQ 0/1:-80.23,-37.02,-73.45:100 20 3859483 . TCACACACACA TCA,T . PASS FR=0.5,0.5;HP=1;NF=1,2;NR=1,1;PP=100.0,85.0;SC=TGAGACTCTGTCACACACACA;TC=21;TR=2,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 3860757 . AAAAC A . PASS FR=0.5;HP=4;NF=5;NR=2;PP=100.0;SC=GTCTCTACTAAAAACAAACAA;TC=18;TR=7 GT:GL:GQ 0/1:-108.81,-21.22,-75.5:100 20 3860858 . GC G . PASS FR=0.5;HP=1;NF=5;NR=1;PP=100.0;SC=AACCCAGGAGGCGGAGCTTGT;TC=16;TR=6 GT:GL:GQ 0/1:-84.65,-31.03,-99.29:100 20 3865910 . A AGGC . PASS FR=0.5;HP=3;NF=8;NR=4;PP=100.0;SC=TCTGTCACCCAGGCTCAAGTT;TC=27;TR=12 GT:GL:GQ 0/1:-249.42,-106.14,-180.19:100 20 3873092 . TTTTA T . PASS FR=1.0;HP=5;NF=6;NR=8;PP=100.0;SC=ACTAAATCTTTTTTATTTATT;TC=25;TR=14 GT:GL:GQ 1/1:-225.87,-50.85,-37.99:100 20 3879882 . AGT A . PASS FR=1.0;HP=1;NF=4;NR=4;PP=100.0;SC=GCAGTGATGTAGTGTAGGCTC;TC=17;TR=8 GT:GL:GQ 1/1:-213.63,-128.83,-121.45:61 20 3882311 . TTTTG T . PASS FR=1.0;HP=3;NF=15;NR=11;PP=100.0;SC=AAGTCAGTACTTTTGTTTATT;TC=29;TR=26 GT:GL:GQ 1/1:-341.87,-21.25,-0.46:100 20 3883619 . GACACACACACACACAC G . PASS FR=0.5013;HP=2;NF=4;NR=1;PP=100.0;SC=GATGTGTATAGACACACACAC;TC=14;TR=5 GT:GL:GQ 0/1:-204.43,-28.1,-33.39:25 20 3885810 . GACTGCACC G . PASS FR=1.0;HP=1;NF=4;NR=7;PP=100.0;SC=CATCGCTTGTGACTGCACCAC;TC=19;TR=11 GT:GL:GQ 1/1:-301.58,-43.69,-32.0:95 20 3899973 . T TTGA . PASS FR=1.0;HP=3;NF=18;NR=6;PP=100.0;SC=AGAAAAACCCTTGAACATTCC;TC=30;TR=24 GT:GL:GQ 1/1:-376.13,-29.44,-7.6:100 20 3900864 . T TA . PASS FR=1.0;HP=10;NF=11;NR=11;PP=100.0;SC=AAGTTAACCTTAAAAAAAAAA;TC=30;TR=22 GT:GL:GQ 1/1:-160.94,-53.86,-35.6:100 20 3929292 . G GA . PASS FR=1.0;HP=1;NF=16;NR=6;PP=100.0;SC=TACATACCAGGATAACTGTTG;TC=29;TR=22 GT:GL:GQ 1/1:-330.17,-190.24,-173.09:100 20 3930806 . T TGACTGG . PASS FR=1.0;HP=2;NF=7;NR=14;PP=100.0;SC=CCTTGTATAGTGATGAATGTG;TC=26;TR=21 GT:GL:GQ 1/1:-450.24,-61.65,-40.95:100 20 3945171 . A AT . PASS FR=1.0;HP=10;NF=7;NR=12;PP=100.0;SC=TTTTCAAGTAATTTTTTTTTT;TC=29;TR=19 GT:GL:GQ 1/1:-126.38,-32.45,-22.97:79 20 3956227 . C CA . PASS FR=1.0;HP=5;NF=12;NR=13;PP=100.0;SC=ATTGTGTTCTCAAAAAGATAT;TC=28;TR=25 GT:GL:GQ 1/1:-249.31,-33.1,-13.35:100 20 3965697 . AACC A . PASS FR=1.0;HP=1;NF=9;NR=9;PP=100.0;SC=GAACAACAACAACCACAACAA;TC=26;TR=18 GT:GL:GQ 1/1:-461.94,-340.35,-326.48:100 20 3971557 . G GTTCCATGATAACAT . PASS FR=1.0;HP=2;NF=12;NR=8;PP=100.0;SC=ATTTGGCACAGTTCCATGATA;TC=27;TR=20 GT:GL:GQ 1/1:-553.38,-41.98,-23.08:100 20 3990695 . CACAAACAA C . PASS FR=1.0;HP=1;NF=6;NR=4;PP=100.0;SC=GAGACCCTGTCACAAACAAAC;TC=23;TR=10 GT:GL:GQ 1/1:-176.37,-39.86,-31.94:65 20 3995386 . GCACACA G . PASS FR=1.0;HP=2;NF=1;NR=1;PP=100.0;SC=ACTTGAATGCGCACACACACA;TC=18;TR=2 GT:GL:GQ 1/1:-95.82,-46.66,-41.67:61 20 4008931 . C CTCTT . PASS FR=1.0;HP=2;NF=1;NR=4;PP=100.0;SC=TCTCATCTCTCTGTCTTTCTC;TC=9;TR=5 GT:GL:GQ 1/1:-127.43,-46.42,-40.22:77 20 4021562 . C CGA . PASS FR=1.0;HP=2;NF=8;NR=2;PP=100.0;SC=GAAGAGAAAGCGAGAGAGAGA;TC=21;TR=10 GT:GL:GQ 1/1:-216.37,-85.41,-73.73:98 20 4025709 . TGA T . PASS FR=1.0;HP=2;NF=12;NR=9;PP=100.0;SC=AAATACATAATGAGAGAGAGA;TC=26;TR=21 GT:GL:GQ 1/1:-247.4,-21.57,-4.6:100 20 4035810 . T TGTTTGTATTACA . PASS FR=1.0;HP=2;NF=10;NR=4;PP=100.0;SC=TAGCTGGGCATGGTGGCGGGT;TC=15;TR=14 GT:GL:GQ 1/1:-361.94,-174.62,-163.57:92 20 4042278 . A AT . PASS FR=1.0;HP=2;NF=7;NR=15;PP=100.0;SC=AAACACATAAATCTCTCTCTC;TC=29;TR=22 GT:GL:GQ 1/1:-269.48,-66.17,-47.18:100 20 4044153 . C CA . PASS FR=1.0;HP=6;NF=8;NR=10;PP=100.0;SC=GCCCCAGGGACGGGGGGCTGG;TC=21;TR=18 GT:GL:GQ 1/1:-167.11,-27.75,-13.35:100 20 4048870 . AGAGTTATCTTGCCTGAG A . PASS FR=0.5;HP=4;NF=9;NR=5;PP=100.0;SC=CACGTGCCCCAGAGTTATCTT;TC=24;TR=14 GT:GL:GQ 1/0:-626.63,-331.02,-449.96:74 20 4050067 . A AT . PASS FR=1.0;HP=8;NF=14;NR=11;PP=100.0;SC=TAAGTTTTAAATTTTTTTTGT;TC=36;TR=25 GT:GL:GQ 1/1:-400.71,-316.84,-301.94:100 20 4052527 . A AT . PASS FR=1.0;HP=1;NF=15;NR=9;PP=100.0;SC=CTAAGCATGAAGTGGTCTCAG;TC=27;TR=24 GT:GL:GQ 1/1:-335.51,-240.21,-229.69:88 20 4057207 . G GT . PASS FR=1.0;HP=3;NF=17;NR=11;PP=100.0;SC=TAGATTATTTGGTTTTTTTTT;TC=40;TR=28 GT:GL:GQ 1/1:-398.27,-278.49,-261.61:100 20 4057861 . T TTTCC . PASS FR=1.0;HP=4;NF=8;NR=13;PP=100.0;SC=CTGATGATTTTTATGTTTTCT;TC=33;TR=21 GT:GL:GQ 1/1:-430.04,-131.81,-113.85:100 20 4058335 . T TATTA . PASS FR=1.0;HP=2;NF=14;NR=5;PP=100.0;SC=TTAATATGTTTATTATACATA;TC=19;TR=19 GT:GL:GQ 1/1:-424.99,-369.88,-364.34:69 20 4060198 . CTCTT C . PASS FR=0.5;HP=3;NF=8;NR=6;PP=100.0;SC=TTCTATTGTTCTCTTTGTTTT;TC=37;TR=14 GT:GL:GQ 0/1:-273.47,-128.98,-306.0:100 20 4060592 . C CTTTA . PASS FR=0.5;HP=3;NF=4;NR=8;PP=100.0;SC=ATAATTTTTGCTTTATTTATT;TC=31;TR=12 GT:GL:GQ 0/1:-163.9,-38.86,-129.26:100 20 4070170 . GTA G . PASS FR=0.5;HP=2;NF=3;NR=2;PP=100.0;SC=GTGTGTGTGTGTATATATATA;TC=25;TR=5 GT:GL:GQ 0/1:-276.88,-237.9,-267.79:100 20 4070252 . A ATGTATATATG . PASS FR=1.0;HP=2;NF=3;NR=1;PP=100.0;SC=GTGTGTATATATGTATATATG;TC=16;TR=4 GT:GL:GQ 1/1:-231.61,-30.38,-18.61:81 20 4070382 . ATATGTGTGTGTG A . PASS FR=1.0;HP=2;NF=1;NR=2;PP=100.0;SC=ATGTGTATATATATGTGTGTG;TC=25;TR=3 GT:GL:GQ 1/1:-347.8,-231.66,-223.35:51 20 4070396 . GTGTGTGTGTGTGTATATATATATATA G . PASS FR=0.5;HP=2;NF=4;NR=4;PP=100.0;SC=GTGTGTGTGTGTGTGTGTGTG;TC=18;TR=8 GT:GL:GQ 1/0:-384.34,-235.32,-225.8:62 20 4071341 . CA C . PASS FR=0.5026;HP=9;NF=5;NR=5;PP=100.0;SC=CTGATTATGGCAAAAAAAAAC;TC=20;TR=10 GT:GL:GQ 0/1:-155.5,-119.13,-123.71:22 20 4071895 . G GT . PASS FR=0.5;HP=8;NF=3;NR=3;PP=72.0;SC=TGGGACCTTTGTTTTTGCAAA;TC=22;TR=6 GT:GL:GQ 0/1:-127.95,-100.32,-170.75:100 20 4074739 . G GA . PASS FR=0.5;HP=9;NF=2;NR=4;PP=75.0;SC=ACTACATCTCGAAAAAAAAAG;TC=16;TR=6 GT:GL:GQ 0/1:-104.75,-76.46,-99.49:100 20 4077346 . ATATTAT A . PASS FR=0.5;HP=1;NF=2;NR=2;PP=100.0;SC=TATGAGGACAATATTATTATT;TC=23;TR=4 GT:GL:GQ 0/1:-62.56,-10.62,-98.18:100 20 4092195 . G GTCAGCCAGAGAGGCTC . PASS FR=1.0;HP=1;NF=7;NR=5;PP=100.0;SC=AGGTAAGACAGTCAGCCAGAG;TC=21;TR=12 GT:GL:GQ 1/1:-408.88,-45.59,-29.88:100 20 4092421 . A AT . PASS FR=0.5;HP=4;NF=5;NR=6;PP=100.0;SC=CTGGCAGCAGATTTTCCCTTA;TC=31;TR=11 GT:GL:GQ 0/1:-137.54,-52.61,-154.29:100 20 4095639 . T TATAC . PASS FR=0.5;HP=2;NF=3;NR=6;PP=100.0;SC=TATATATATATACACACACAT;TC=30;TR=9 GT:GL:GQ 0/1:-239.61,-67.33,-166.02:100 20 4096614 . T TG . PASS FR=0.5;HP=1;NF=3;NR=8;PP=100.0;SC=TTTGATGGCTTGTGAAGCCCA;TC=42;TR=11 GT:GL:GQ 0/1:-166.13,-48.49,-243.23:100 20 4099234 . C CTCT . PASS FR=1.0;HP=1;NF=2;NR=7;PP=100.0;SC=CTTCTTCTTCCTCTTCTTCCT;TC=17;TR=9 GT:GL:GQ 1/1:-213.81,-121.18,-113.85:91 20 4106279 . C CA . PASS FR=1.0;HP=4;NF=9;NR=14;PP=100.0;SC=ATGATCCACCCCCTTGGCCTC;TC=27;TR=23 GT:GL:GQ 1/1:-261.7,-33.57,-14.72:100 20 4106498 . AC A . PASS FR=0.5;HP=3;NF=4;NR=6;PP=100.0;SC=ACCCGCCACCACGTCAAGCTA;TC=17;TR=10 GT:GL:GQ 0/1:-151.03,-63.2,-86.55:100 20 4107003 . T TCTAA . PASS FR=0.5;HP=2;NF=4;NR=9;PP=100.0;SC=TGGAGGTAACTCTAGGACATA;TC=28;TR=13 GT:GL:GQ 0/1:-216.14,-60.6,-196.15:100 20 4108348 . A AC . PASS FR=1.0;HP=3;NF=9;NR=6;PP=100.0;SC=TTCTATGGAAAAGAGCAGTCA;TC=22;TR=15 GT:GL:GQ 1/1:-263.65,-164.58,-152.76:96 20 4111438 . CA C . PASS FR=1.0;HP=2;NF=13;NR=9;PP=100.0;SC=GGTGATCACACAGGGGCATGG;TC=27;TR=22 GT:GL:GQ 1/1:-393.14,-310.63,-301.96:68 20 4111530 . T TG . PASS FR=1.0;HP=1;NF=13;NR=14;PP=100.0;SC=CATCAAAACTTGCAGAAGTAT;TC=30;TR=27 GT:GL:GQ 1/1:-576.34,-531.28,-526.81:55 20 4112367 . TA T . PASS FR=0.5;HP=2;NF=7;NR=2;PP=100.0;SC=AGACTTTAGTTAATAATAATA;TC=25;TR=9 GT:GL:GQ 0/1:-105.53,-48.17,-185.05:100 20 4124037 . TACAC TAC,T . PASS FR=0.5,0.5;HP=2;NF=0,1;NR=6,6;PP=100.0,100.0;SC=TGTATGTGTATACACACACAC;TC=29;TR=6,7 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 4165244 . C CAG . PASS FR=0.5;HP=3;NF=9;NR=7;PP=100.0;SC=TAAAACTCAACAGTTATATTT;TC=28;TR=16 GT:GL:GQ 0/1:-164.36,-34.34,-133.84:100 20 4189405 . A AGTGTTCT . PASS FR=1.0;HP=1;NF=8;NR=19;PP=100.0;SC=TGATCACAGAAGTGTTGAATG;TC=31;TR=27 GT:GL:GQ 1/1:-510.65,-52.94,-31.94:100 20 4193006 . T TA . PASS FR=1.0;HP=9;NF=5;NR=11;PP=100.0;SC=TGTGTTTGATTAAAAAAAAAT;TC=25;TR=16 GT:GL:GQ 1/1:-189.06,-113.86,-103.2:89 20 4204545 . CAACAGGTTT C . PASS FR=0.5;HP=3;NF=5;NR=5;PP=100.0;SC=TTTCAATTTACAACAGGTTTA;TC=29;TR=10 GT:GL:GQ 0/1:-264.93,-66.16,-208.86:100 20 4210072 . T TA . PASS FR=0.5;HP=5;NF=7;NR=3;PP=100.0;SC=GGAAGGAAGATGGGGGCGAGT;TC=33;TR=10 GT:GL:GQ 0/1:-169.78,-122.55,-232.56:100 20 4211685 . T TTTTCTTTC . PASS FR=1.0;HP=4;NF=3;NR=1;PP=100.0;SC=CTTTCTTTCTTTTTCTTTCTT;TC=17;TR=4 GT:GL:GQ 1/1:-163.69,-62.85,-59.76:50 20 4222606 . TG T,AG . PASS FR=0.5,0.5;HP=2;NF=14,3;NR=8,0;PP=72.0,7.0;SC=CAGCACAGCCTGATGGCTCTG;TC=29;TR=22,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:41 20 4223993 . CG C . PASS FR=1.0;HP=4;NF=10;NR=1;PP=100.0;SC=CTGGGCTCCTCGGGGCATCCG;TC=14;TR=11 GT:GL:GQ 1/1:-180.73,-119.68,-111.91:64 20 4255571 . TGAAA T . PASS FR=1.0;HP=1;NF=5;NR=4;PP=100.0;SC=AGGTATGCTCTGAAAGGAAGA;TC=15;TR=9 GT:GL:GQ 1/1:-155.75,-66.2,-58.38:79 20 4260218 . C CA . PASS FR=0.5;HP=3;NF=1;NR=9;PP=100.0;SC=CTGGTCTCCCCAGCATCTAGT;TC=27;TR=10 GT:GL:GQ 0/1:-138.73,-38.26,-150.01:100 20 4280077 . G GTGA . PASS FR=0.5;HP=1;NF=2;NR=4;PP=100.0;SC=GATGTCTTTGGTGATGATGAT;TC=23;TR=6 GT:GL:GQ 0/1:-118.58,-26.45,-67.22:100 20 4300671 . G GT . PASS FR=1.0;HP=9;NF=9;NR=7;PP=100.0;SC=TATTTTTTAAGTTTTTTTTTC;TC=22;TR=16 GT:GL:GQ 1/1:-112.49,-30.96,-17.5:100 20 4305010 . C CCTGT . PASS FR=1.0;HP=1;NF=9;NR=14;PP=100.0;SC=AGGTTTGGCTCCTGTCTGACA;TC=27;TR=23 GT:GL:GQ 1/1:-478.98,-124.12,-105.32:100 20 4306264 . GT G . PASS FR=0.5;HP=3;NF=7;NR=4;PP=100.0;SC=ACAATATAAGGTTTACTTCAA;TC=24;TR=11 GT:GL:GQ 0/1:-115.0,-27.63,-111.62:100 20 4310291 . T TC . PASS FR=1.0;HP=1;NF=20;NR=9;PP=100.0;SC=CTCCTACGTGTCATGCCAGCT;TC=32;TR=29 GT:GL:GQ 1/1:-333.81,-66.33,-44.4:100 20 4310977 . GC G . PASS FR=0.5;HP=1;NF=14;NR=6;PP=100.0;SC=CCTGAAACTGGCGTAATTTAT;TC=41;TR=20 GT:GL:GQ 0/1:-231.9,-39.91,-159.66:100 20 4321071 . A AG . PASS FR=0.5;HP=5;NF=3;NR=2;PP=100.0;SC=AAGTCAAATCAGGGGGAGGAA;TC=19;TR=5 GT:GL:GQ 0/1:-50.11,-15.88,-71.26:100 20 4322091 . CA C . PASS FR=0.5;HP=1;NF=11;NR=7;PP=100.0;SC=GCCGTGTGTCCAGCCAAAACT;TC=33;TR=18 GT:GL:GQ 0/1:-210.17,-46.06,-156.61:100 20 4329185 . TC T . PASS FR=0.5;HP=1;NF=8;NR=2;PP=100.0;SC=AATTCTAGGTTCTTTCTCTCA;TC=28;TR=10 GT:GL:GQ 0/1:-148.46,-71.81,-182.2:100 20 4330761 . GGTGTGTGT G . PASS FR=1.0;HP=3;NF=1;NR=3;PP=100.0;SC=TAATTCATGGGGTGTGTGTGT;TC=30;TR=4 GT:GL:GQ 1/1:-224.07,-44.24,-35.58:72 20 4332044 . TG T . PASS FR=1.0;HP=6;NF=5;NR=2;PP=57.0;SC=TTTGTTTTTTTGTTTTTTTTT;TC=24;TR=7 GT:GL:GQ 1/1:-226.96,-113.86,-100.61:42 20 4343821 . TA T . PASS FR=0.5;HP=8;NF=5;NR=8;PP=100.0;SC=CATTTTTTTTTAAAATTTTTG;TC=35;TR=13 GT:GL:GQ 1/0:-274.8,-111.87,-90.41:100 20 4349378 . A AT . PASS FR=0.5;HP=3;NF=11;NR=7;PP=100.0;SC=TTTTGAAGGCATTTCCAGGGT;TC=27;TR=18 GT:GL:GQ 0/1:-181.47,-28.52,-69.89:100 20 4366637 . AAAAC A . PASS FR=1.0;HP=3;NF=8;NR=10;PP=100.0;SC=AAAACAAAACAAAACAAACAA;TC=29;TR=18 GT:GL:GQ 1/1:-255.42,-38.69,-23.59:100 20 4378952 . A AAAC . PASS FR=1.0;HP=2;NF=5;NR=8;PP=100.0;SC=CAAAACAAACAAACAACAACA;TC=26;TR=13 GT:GL:GQ 1/1:-242.03,-34.58,-19.38:100 20 4380979 . CACAT C . PASS FR=1.0;HP=2;NF=6;NR=6;PP=100.0;SC=CACACACACACACATACAAGC;TC=29;TR=12 GT:GL:GQ 1/1:-310.99,-41.83,-21.18:100 20 4381267 . T TGTGTATTGTGGA . PASS FR=1.0;HP=2;NF=4;NR=9;PP=100.0;SC=GACAGCCTCCTTCAACAAAAA;TC=23;TR=13 GT:GL:GQ 1/1:-573.3,-462.6,-447.82:96 20 4381268 . TC T . PASS FR=1.0;HP=1;NF=4;NR=9;PP=100.0;SC=ACAGCCTCCTTCAACAAAAAA;TC=27;TR=13 GT:GL:GQ 1/1:-573.3,-567.48,-566.42:96 20 4384878 . TAGAC T . PASS FR=0.5;HP=4;NF=7;NR=6;PP=100.0;SC=ATGGAAGAAATAGACAGAGAG;TC=32;TR=13 GT:GL:GQ 0/1:-215.18,-58.15,-186.03:100 20 4390996 . ACT A . PASS FR=0.5;HP=1;NF=5;NR=4;PP=100.0;SC=AACACTCGAGACTCTCCAGCT;TC=25;TR=9 GT:GL:GQ 0/1:-160.6,-43.63,-115.25:100 20 4392384 . T TTG . PASS FR=0.5;HP=1;NF=2;NR=1;PP=100.0;SC=GGGAATATAGTTGTGTGTGTG;TC=26;TR=3 GT:GL:GQ 0/1:-141.31,-92.22,-156.97:100 20 4403198 . CGT CGTGT,C . PASS FR=0.5,0.5;HP=2;NF=3,3;NR=2,0;PP=100.0,91.0;SC=TGTGTGTGTGCGTGTGTGTGT;TC=16;TR=5,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 4418283 . TCC T . PASS FR=1.0;HP=5;NF=9;NR=17;PP=100.0;SC=TGAAAAATGCTCCCCAGGTTT;TC=26;TR=26 GT:GL:GQ 1/1:-235.22,-17.92,0.0:100 20 4422138 . A AAGAGGCAAGGCTTCCCCACATGCTCAGAATGG,G . PASS FR=0.5,0.5;HP=1;NF=2,3;NR=0,5;PP=100.0,87.0;SC=CTACAGAAAGATGATGGAGGT;TC=14;TR=2,8 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:23 20 4422142 . T TG . PASS FR=1.0;HP=2;NF=8;NR=6;PP=100.0;SC=AGAAAGATGATGGAGGTACTA;TC=19;TR=14 GT:GL:GQ 1/1:-319.37,-289.62,-286.77:23 20 4427312 . A AGCTTCTAT . PASS FR=0.5;HP=2;NF=1;NR=1;PP=100.0;SC=TGTATAATAGAGTCCAGAGTC;TC=11;TR=2 GT:GL:GQ 1/0:-513.43,-441.06,-437.62:42 20 4431651 . TA T . PASS FR=0.5;HP=5;NF=9;NR=13;PP=100.0;SC=TCTAGACCCTTAAAAATAACA;TC=34;TR=22 GT:GL:GQ 0/1:-196.04,-30.01,-107.67:100 20 4438168 . T TTACACAAATGTAACCTATGTAACAA . PASS FR=0.5;HP=1;NF=2;NR=3;PP=100.0;SC=CCTGCACATGTACCCTTGAAC;TC=16;TR=5 GT:GL:GQ 0/1:-418.07,-256.53,-367.22:100 20 4439599 . GT G . PASS FR=0.5;HP=2;NF=11;NR=12;PP=100.0;SC=TGTGGGGAGAGTTAGCAAGAG;TC=36;TR=23 GT:GL:GQ 0/1:-329.81,-228.22,-300.4:100 20 4442338 . CTTTATTTTATTTTAT CTTTATTTTAT,C . PASS FR=0.5,0.5;HP=3;NF=2,1;NR=0,3;PP=100.0,100.0;SC=AAGTATCTAACTTTATTTTAT;TC=21;TR=2,4 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 4445547 . T TAA . PASS FR=1.0;HP=1;NF=18;NR=22;PP=100.0;SC=TGTTTCCAGTTGTTATACTTT;TC=39;TR=40 GT:GL:GQ 1/1:-459.22,-244.89,-221.84:100 20 4452980 . TACAC T . PASS FR=1.0;HP=2;NF=1;NR=2;PP=100.0;SC=TTAATTCTTATACACACACAC;TC=21;TR=3 GT:GL:GQ 1/1:-75.87,-32.41,-30.31:43 20 4460649 . G GA . PASS FR=0.5;HP=9;NF=5;NR=8;PP=100.0;SC=TTTCCTCGGAGAAAAAAAACA;TC=39;TR=13 GT:GL:GQ 0/1:-191.57,-119.31,-159.65:100 20 4462152 . GGTCAATGTTATAAACTTTGC G . PASS FR=0.5;HP=2;NF=6;NR=5;PP=100.0;SC=CTACTTCTTGGGTCAATGTTA;TC=18;TR=11 GT:GL:GQ 1/0:-501.72,-174.1,-171.31:67 20 4462516 . T TTC . PASS FR=0.5;HP=1;NF=16;NR=1;PP=100.0;SC=GGGTTTAAAGTTCTCTAATGA;TC=41;TR=17 GT:GL:GQ 0/1:-181.56,-38.08,-223.18:100 20 4462799 . C CTT . PASS FR=0.5;HP=1;NF=1;NR=1;PP=100.0;SC=TCTTCTTCGTCCTTTTTTTTT;TC=36;TR=2 GT:GL:GQ 0/1:-520.7,-504.74,-499.84:81 20 4465737 . TG T . PASS FR=1.0;HP=2;NF=9;NR=18;PP=100.0;SC=CTCCTTGACATGGACTGAGAA;TC=27;TR=27 GT:GL:GQ 1/1:-258.03,-34.15,-15.14:100 20 4468340 . TA T . PASS FR=0.5;HP=10;NF=5;NR=2;PP=57.0;SC=ATATATATATTAAAAAAAAAA;TC=21;TR=7 GT:GL:GQ 0/1:-41.89,-18.73,-52.45:100 20 4469569 . C CT . PASS FR=0.5;HP=4;NF=3;NR=6;PP=100.0;SC=CAAGTAAAGACTTTTGATTGT;TC=23;TR=9 GT:GL:GQ 0/1:-113.7,-24.95,-84.55:100 20 4474613 . GA G . PASS FR=0.5;HP=8;NF=4;NR=6;PP=100.0;SC=ATTAGGAACAGAAAAAAATTA;TC=37;TR=10 GT:GL:GQ 0/1:-311.99,-245.02,-353.92:100 20 4474629 . A AAAT . PASS FR=0.5;HP=9;NF=11;NR=5;PP=100.0;SC=AATTAAAAAAAAAATATACAC;TC=32;TR=16 GT:GL:GQ 0/1:-322.36,-111.27,-187.62:100 20 4475883 . AT A . PASS FR=0.5;HP=5;NF=1;NR=3;PP=100.0;SC=AAATATATATATTTTAATATA;TC=14;TR=4 GT:GL:GQ 0/1:-74.26,-40.07,-92.44:100 20 4481373 . A AG . PASS FR=1.0;HP=1;NF=5;NR=6;PP=100.0;SC=TCTTTTTTCAAGTTTTTAGCT;TC=13;TR=11 GT:GL:GQ 1/1:-84.43,-9.42,-0.46:74 20 4484587 . T TA . PASS FR=0.5;HP=9;NF=4;NR=9;PP=100.0;SC=TCTCTGATTTTAAAAAAAAAG;TC=46;TR=13 GT:GL:GQ 0/1:-163.36,-92.55,-141.98:100 20 4487527 . TG T . PASS FR=0.5006;HP=5;NF=8;NR=7;PP=100.0;SC=TACTAGGGGCTGGGGGCAGGG;TC=34;TR=15 GT:GL:GQ 0/1:-421.09,-350.88,-356.92:29 20 4492336 . C CA . PASS FR=1.0;HP=1;NF=11;NR=14;PP=100.0;SC=ACATTCTTGCCACCTTTGGTA;TC=27;TR=25 GT:GL:GQ 1/1:-281.59,-90.33,-72.03:100 20 4493592 . C CG . PASS FR=1.0;HP=2;NF=20;NR=17;PP=100.0;SC=GCATTTTGGACATCTCACCCT;TC=39;TR=37 GT:GL:GQ 1/1:-454.89,-182.56,-157.87:100 20 4497462 . TTA T . PASS FR=0.5;HP=2;NF=2;NR=2;PP=88.0;SC=TAAATCAACTTTATATATATA;TC=14;TR=4 GT:GL:GQ 1/0:-149.41,-117.69,-112.45:46 20 4500613 . G GC . PASS FR=1.0;HP=2;NF=12;NR=13;PP=100.0;SC=ATGCCCAAGGGTGTCCCAGAG;TC=29;TR=25 GT:GL:GQ 1/1:-293.02,-49.83,-29.64:100 20 4502874 . CT C . PASS FR=1.0;HP=4;NF=11;NR=7;PP=100.0;SC=TACAGCCCTTCTTGGGAGCCC;TC=24;TR=18 GT:GL:GQ 1/1:-204.97,-36.44,-20.43:100 20 4512447 . AAAACAAAC AAAAC,A . PASS FR=0.5,0.5;HP=3;NF=3,4;NR=0,1;PP=100.0,100.0;SC=ACTCCATCTCAAAACAAACAA;TC=20;TR=3,5 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 4519983 . GA G . PASS FR=0.5;HP=3;NF=7;NR=13;PP=100.0;SC=TCCAAACTAAGACAGGTATTA;TC=36;TR=20 GT:GL:GQ 0/1:-201.76,-27.24,-148.43:100 20 4524299 . AGTGTGT A . PASS FR=0.5;HP=3;NF=2;NR=1;PP=100.0;SC=TCTGTGCTTTAGTGTGTGTGT;TC=28;TR=3 GT:GL:GQ 0/1:-144.55,-75.64,-138.78:100 20 4530940 . CTT C . PASS FR=0.5002;HP=6;NF=2;NR=9;PP=80.0;SC=TTCTTTCTTTCTTTCTCTCTC;TC=25;TR=11 GT:GL:GQ 0/1:-323.77,-294.9,-301.87:33 20 4541935 . A AGAG . PASS FR=0.5;HP=2;NF=8;NR=4;PP=100.0;SC=GTGGCAGATTAGAGGAGACAT;TC=32;TR=12 GT:GL:GQ 0/1:-211.5,-48.19,-198.54:100 20 4547067 . G GA . PASS FR=0.5116;HP=10;NF=5;NR=1;PP=100.0;SC=TATAGAGAGAGAAAAAAAAAC;TC=18;TR=6 GT:GL:GQ 0/1:-156.12,-119.31,-122.4:16 20 4553580 . GT G . PASS FR=0.5;HP=10;NF=1;NR=1;PP=71.0;SC=TTTTGTTTTTGTTTTTGTTTT;TC=17;TR=2 GT:GL:GQ 1/0:-197.42,-152.57,-154.01:100 20 4553925 . T TC . PASS FR=1.0;HP=1;NF=7;NR=5;PP=100.0;SC=CGGCCCCTCTTCACTTTTAAG;TC=16;TR=12 GT:GL:GQ 1/1:-135.25,-18.29,-7.82:87 20 4560578 . C CCTTA . PASS FR=1.0;HP=1;NF=11;NR=12;PP=100.0;SC=ATGTTATATACCTTTTAGAGA;TC=32;TR=23 GT:GL:GQ 1/1:-416.23,-42.65,-19.11:100 20 4566007 . G GC . PASS FR=0.5;HP=1;NF=9;NR=3;PP=100.0;SC=AGCTGGGGCTGACTCATCTGA;TC=27;TR=12 GT:GL:GQ 0/1:-150.18,-87.47,-213.89:100 20 4572622 . T TA . PASS FR=0.5;HP=1;NF=5;NR=4;PP=100.0;SC=AAAGGGGTGCTAGGAATTCCA;TC=21;TR=9 GT:GL:GQ 0/1:-105.47,-33.77,-107.56:100 20 4580659 . ATTG A . PASS FR=0.5;HP=3;NF=9;NR=11;PP=100.0;SC=AATAATTTATATTGTTATTAT;TC=41;TR=20 GT:GL:GQ 0/1:-343.69,-136.17,-313.1:100 20 4580822 . AAC A . PASS FR=0.5;HP=1;NF=7;NR=7;PP=100.0;SC=TATCTTACATAACAGTGTATC;TC=27;TR=14 GT:GL:GQ 0/1:-159.59,-31.47,-183.78:100 20 4589159 . TAC T . PASS FR=0.5;HP=1;NF=5;NR=5;PP=100.0;SC=CACACACACGTACACACACAC;TC=25;TR=10 GT:GL:GQ 0/1:-134.67,-33.29,-88.29:100 20 4590266 . T TCTGGCC . PASS FR=0.5;HP=3;NF=3;NR=4;PP=100.0;SC=GCTGGCAGCCTCTGGCCCTGG;TC=20;TR=7 GT:GL:GQ 0/1:-180.62,-56.12,-103.3:100 20 4613873 . T TATA . PASS FR=0.5;HP=3;NF=6;NR=2;PP=100.0;SC=CTCTTTCTTTTATAATAATAA;TC=26;TR=8 GT:GL:GQ 0/1:-121.23,-16.51,-65.45:100 20 4616453 . G GAGTAGA . PASS FR=0.5;HP=3;NF=5;NR=7;PP=100.0;SC=CACAGAGTAGGGGTTCAATAA;TC=22;TR=12 GT:GL:GQ 0/1:-211.56,-25.38,-113.94:100 20 4617264 . G GAGAA . PASS FR=0.5;HP=2;NF=3;NR=1;PP=100.0;SC=GAAAGCAAGAGAGAAAGAAGA;TC=22;TR=4 GT:GL:GQ 0/1:-126.22,-46.88,-138.67:100 20 4617272 . AG A . PASS FR=0.5;HP=1;NF=1;NR=3;PP=20.0;SC=GAGAGAAAGAAGAGAAGAGAA;TC=22;TR=4 GT:GL:GQ 0/1:-134.04,-119.35,-223.11:66 20 4617303 . G GAGGA . PASS FR=0.5;HP=2;NF=2;NR=3;PP=100.0;SC=GGGAGGGAGAGAGGAAGGAAG;TC=19;TR=5 GT:GL:GQ 0/1:-154.78,-90.63,-135.29:100 20 4655424 . G GA . PASS FR=0.5;HP=8;NF=13;NR=4;PP=100.0;SC=GTTCTTTAGAGAAAAAAAGAT;TC=30;TR=17 GT:GL:GQ 0/1:-186.33,-114.25,-152.75:100 20 4668235 . AT A . PASS FR=0.5;HP=10;NF=12;NR=5;PP=100.0;SC=TAGGAAATAGATTTTTTTTTT;TC=33;TR=17 GT:GL:GQ 0/1:-91.71,-31.87,-60.05:100 20 4673330 . C CTTT . PASS FR=0.5;HP=5;NF=6;NR=8;PP=100.0;SC=TGAAGAAAATCTTTTCTTCCT;TC=24;TR=14 GT:GL:GQ 0/1:-183.35,-23.94,-71.42:100 20 4684173 . TG T . PASS FR=0.5;HP=1;NF=5;NR=1;PP=100.0;SC=CAGGCACAGTTGCTCACGCCT;TC=17;TR=6 GT:GL:GQ 0/1:-81.87,-25.35,-94.89:100 20 4691383 . CA C . PASS FR=1.0;HP=2;NF=14;NR=12;PP=100.0;SC=TGGGGTCATCCAAGCATGGCT;TC=29;TR=26 GT:GL:GQ 1/1:-259.65,-39.57,-19.54:100 20 4692075 . C CA . PASS FR=0.5;HP=9;NF=5;NR=3;PP=95.0;SC=AGTAATTGGACAAAAAAAACA;TC=26;TR=8 GT:GL:GQ 0/1:-67.83,-34.9,-96.78:100 20 4704696 . A ATG . PASS FR=0.5;HP=2;NF=5;NR=3;PP=100.0;SC=ATATGTATATATGTGTGTGTA;TC=30;TR=8 GT:GL:GQ 0/1:-168.25,-105.64,-257.19:100 20 4706654 . GTGCCATCA G . PASS FR=1.0;HP=2;NF=7;NR=4;PP=100.0;SC=TTACAGGTGTGTGCCATCATG;TC=17;TR=11 GT:GL:GQ 1/1:-236.92,-30.58,-21.39:67 20 4727159 . C CATTTTATTTT . PASS FR=1.0;HP=1;NF=2;NR=4;PP=100.0;SC=ATAGCATTTGCATTTTATTTT;TC=27;TR=6 GT:GL:GQ 1/1:-510.26,-402.24,-397.15:63 20 4735780 . T TTTCTTTCTTTCTTTCTTTCTTTCTTTC,C . PASS FR=0.5,0.5;HP=3;NF=0,5;NR=3,16;PP=100.0,100.0;SC=CCTTTCTTTCTTTTCTTTCTT;TC=27;TR=3,21 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 4737530 . T TA . PASS FR=1.0;HP=1;NF=11;NR=14;PP=100.0;SC=TTAAATGTATTGAGGCTCATT;TC=26;TR=25 GT:GL:GQ 1/1:-245.38,-21.97,-3.97:100 20 4737701 . T TTGA . PASS FR=1.0;HP=1;NF=12;NR=7;PP=100.0;SC=ACTTTCTGTCTTGACCTGTCT;TC=19;TR=19 GT:GL:GQ 1/1:-227.02,-18.69,-5.52:100 20 4741155 . G GGA . PASS FR=1.0;HP=1;NF=5;NR=11;PP=100.0;SC=AACACACCAGGTGTGTCAAAA;TC=22;TR=16 GT:GL:GQ 1/1:-218.41,-31.08,-15.98:100 20 4743693 . G GTTAA . PASS FR=1.0;HP=2;NF=6;NR=7;PP=100.0;SC=AGCCCAGGAGGTTAAGTCTGC;TC=16;TR=13 GT:GL:GQ 1/1:-225.23,-59.89,-50.88:75 20 4743774 . A AAAATAAAT . PASS FR=1.0;HP=5;NF=4;NR=3;PP=100.0;SC=AAAAGGAGAAAAAATAAATAA;TC=16;TR=7 GT:GL:GQ 1/1:-319.93,-209.77,-203.54:78 20 4748739 . A ACTAT . PASS FR=1.0;HP=1;NF=12;NR=7;PP=100.0;SC=TCTTTCACCAACTATTTTCAC;TC=23;TR=19 GT:GL:GQ 1/1:-501.66,-334.66,-319.16:100 20 4761877 . T TG . PASS FR=0.5;HP=8;NF=1;NR=4;PP=100.0;SC=ACAGATATTTTGGGGGGGGCA;TC=23;TR=5 GT:GL:GQ 0/1:-97.23,-58.4,-90.76:100 20 4768475 . A AAGGGACT . PASS FR=1.0;HP=2;NF=7;NR=8;PP=100.0;SC=CAGGGGTCCAAAGGCACCTTA;TC=23;TR=15 GT:GL:GQ 1/1:-372.13,-36.56,-17.94:100 20 4783543 . CATAT C . PASS FR=0.5;HP=2;NF=1;NR=2;PP=100.0;SC=TATATATATACATATATATAT;TC=23;TR=3 GT:GL:GQ 0/1:-115.71,-29.18,-62.14:100 20 4794428 . CGT C . PASS FR=0.5;HP=3;NF=3;NR=2;PP=100.0;SC=CAGTGTGTGGCGTGTGTGTGT;TC=28;TR=5 GT:GL:GQ 0/1:-119.46,-68.74,-106.78:100 20 4796034 . TACC T . PASS FR=0.5;HP=1;NF=7;NR=5;PP=100.0;SC=TATCTGAGGCTACCACCACCC;TC=27;TR=12 GT:GL:GQ 0/1:-222.6,-98.55,-189.77:100 20 4802486 . G GCC . PASS FR=0.5;HP=2;NF=5;NR=4;PP=100.0;SC=GACTGCCACAGCCTAGGCATC;TC=24;TR=9 GT:GL:GQ 0/1:-135.36,-38.11,-126.44:100 20 4803072 . CT C . PASS FR=0.5;HP=1;NF=1;NR=5;PP=100.0;SC=GTGCACGCAGCTGTTGAGAGG;TC=15;TR=6 GT:GL:GQ 0/1:-82.81,-37.85,-91.55:100 20 4823348 . AT A . PASS FR=1.0;HP=8;NF=17;NR=7;PP=100.0;SC=AATATTTTCCATTTTTTTTGA;TC=32;TR=24 GT:GL:GQ 1/1:-298.64,-180.3,-160.97:100 20 4850186 . GAC G . PASS FR=0.5;HP=1;NF=3;NR=2;PP=49.0;SC=ATCTCCAAATGACACACACAC;TC=34;TR=5 GT:GL:GQ 0/1:-186.75,-165.14,-349.63:96 20 4880132 . AGCTCAATGCCTTCTGC A . PASS FR=1.0;HP=1;NF=3;NR=4;PP=100.0;SC=CAAACGGCGCAGCTCAATGCC;TC=17;TR=7 GT:GL:GQ 1/1:-255.52,-55.88,-53.61:44 20 4883735 . G GGA . PASS FR=1.0;HP=1;NF=13;NR=18;PP=100.0;SC=GGTGAAAAGAGTAATTCTAAA;TC=34;TR=31 GT:GL:GQ 1/1:-361.9,-346.05,-342.67:97 20 4886527 . GA G . PASS FR=0.5;HP=3;NF=5;NR=6;PP=100.0;SC=ACTCTACTGAGAAGAACAGAT;TC=19;TR=11 GT:GL:GQ 0/1:-166.67,-86.72,-123.24:100 20 4892485 . AATTT A . PASS FR=0.5;HP=1;NF=2;NR=7;PP=100.0;SC=TTTATTTATGAATTTATTTAT;TC=34;TR=9 GT:GL:GQ 0/1:-148.07,-23.75,-121.86:100 20 4922648 . CTAAACTAACT C . PASS FR=0.5;HP=5;NF=1;NR=10;PP=100.0;SC=TCTATATTTTCTAAACTAACT;TC=33;TR=11 GT:GL:GQ 0/1:-284.06,-37.14,-228.78:100 20 4942899 . C CA . PASS FR=0.5;HP=7;NF=4;NR=3;PP=100.0;SC=ACCCCCGCCCCAAAAAAACAG;TC=28;TR=7 GT:GL:GQ 0/1:-99.42,-46.78,-95.55:100 20 4947451 . G GTTTGA . PASS FR=0.5;HP=4;NF=4;NR=4;PP=100.0;SC=ACTTTTGATAGTTTTACACAC;TC=18;TR=8 GT:GL:GQ 0/1:-283.81,-185.62,-217.52:100 20 4947582 . TG T . PASS FR=0.5;HP=4;NF=9;NR=4;PP=100.0;SC=GATTACATGATGGGGAGCAGG;TC=22;TR=13 GT:GL:GQ 0/1:-139.84,-55.72,-119.49:100 20 4947775 . T TA . PASS FR=0.5;HP=6;NF=8;NR=4;PP=100.0;SC=GAAATCTAAATAAACACAGGG;TC=24;TR=12 GT:GL:GQ 0/1:-128.76,-21.0,-91.02:100 20 4949766 . CTT C . PASS FR=0.5;HP=3;NF=8;NR=4;PP=100.0;SC=GAGTTTCCCTCTTGTTACCCA;TC=25;TR=12 GT:GL:GQ 0/1:-147.72,-32.95,-112.56:100 20 4954109 . G GGACTT . PASS FR=0.5;HP=2;NF=4;NR=8;PP=100.0;SC=ATGGCTGGAAGGACTTAACTA;TC=30;TR=12 GT:GL:GQ 0/1:-203.74,-23.32,-169.48:100 20 4965192 . C CT . PASS FR=0.5;HP=2;NF=5;NR=3;PP=100.0;SC=GAGCAAGACTCTGTCTCAAAA;TC=26;TR=8 GT:GL:GQ 0/1:-134.47,-59.87,-111.38:100 20 4969015 . AG A . PASS FR=1.0;HP=8;NF=4;NR=5;PP=100.0;SC=TGGGAAACCGAGGGGGGGCCA;TC=12;TR=9 GT:GL:GQ 1/1:-67.79,-12.99,-5.52:61 20 4970270 . C CTTAATAT . PASS FR=0.5;HP=1;NF=4;NR=1;PP=100.0;SC=TGCAGTGAGCCATGATCTTGC;TC=22;TR=5 GT:GL:GQ 0/1:-247.44,-164.56,-281.24:100 20 4972366 . TCA TCACACA,T . PASS FR=0.5,0.5;HP=2;NF=1,0;NR=1,2;PP=100.0,49.0;SC=AGACTCCGTTTCACACACACA;TC=15;TR=2,2 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:97 20 4979252 . ATGAGG A . PASS FR=0.5;HP=1;NF=5;NR=2;PP=100.0;SC=AAATGAATTAATGAGGTGAGG;TC=24;TR=7 GT:GL:GQ 0/1:-146.48,-63.04,-172.38:100 20 4985646 . A AAAAT . PASS FR=0.5;HP=4;NF=2;NR=1;PP=100.0;SC=CTCCGTCTCAAAAATAAATAA;TC=22;TR=3 GT:GL:GQ 0/1:-69.57,-20.73,-73.7:100 20 4987193 . T TTTTA . PASS FR=1.0;HP=3;NF=5;NR=7;PP=100.0;SC=GTAAAAGCCATTTTATTTATT;TC=33;TR=12 GT:GL:GQ 1/1:-198.93,-19.38,-8.29:93 20 5003823 . C CA . PASS FR=1.0;HP=2;NF=2;NR=1;PP=69.0;SC=CTCAGCCTCCCAGTAGCTGGG;TC=5;TR=3 GT:GL:GQ 1/1:-35.46,-12.52,-9.15:55 20 5006924 . GTATATATATGTGTA G . PASS FR=0.5;HP=2;NF=3;NR=1;PP=100.0;SC=ATGTATATATGTATATATATG;TC=17;TR=4 GT:GL:GQ 0/1:-102.23,-17.74,-69.04:100 20 5019857 . C CT . PASS FR=1.0;HP=1;NF=5;NR=1;PP=100.0;SC=CACCCCTGCACTCCAGCCTGG;TC=10;TR=6 GT:GL:GQ 1/1:-78.84,-38.79,-34.59:51 20 5021323 . T TC . PASS FR=1.0;HP=10;NF=8;NR=5;PP=100.0;SC=CTTTTTTTTTTTCAATGGCAA;TC=18;TR=13 GT:GL:GQ 1/1:-164.3,-19.64,-6.44:82 20 5021471 . G GA . PASS FR=1.0;HP=1;NF=11;NR=14;PP=100.0;SC=ACATAATGCTGGTTAAAGAGG;TC=33;TR=25 GT:GL:GQ 1/1:-406.51,-306.39,-293.23:100 20 5033824 . G GTATA . PASS FR=1.0;HP=8;NF=6;NR=6;PP=100.0;SC=CCAAAAAAAAGTATATATATA;TC=19;TR=12 GT:GL:GQ 1/1:-293.31,-92.78,-80.65:100 20 5034013 . GGCAT G . PASS FR=1.0;HP=1;NF=8;NR=10;PP=100.0;SC=ATGACAGCCAGGCATGGGGGC;TC=24;TR=18 GT:GL:GQ 1/1:-275.61,-34.13,-17.26:100 20 5044461 . A AAATTTTTAT . PASS FR=1.0;HP=4;NF=13;NR=12;PP=100.0;SC=GTTAACTTGGAAAAATTTCTA;TC=29;TR=25 GT:GL:GQ 1/1:-660.59,-158.53,-137.22:100 20 5058110 . G GGGGGCT . PASS FR=1.0;HP=2;NF=6;NR=6;PP=100.0;SC=CAACATTTTGGGAGGTGGGTG;TC=14;TR=12 GT:GL:GQ 1/1:-206.1,-87.92,-82.33:69 20 5062840 . AAAG A . PASS FR=1.0;HP=4;NF=12;NR=4;PP=100.0;SC=AATTTTTTAAAAAGAAGAAGA;TC=21;TR=16 GT:GL:GQ 1/1:-217.23,-55.74,-43.97:99 20 5079870 . AAATAAATAAATCAATC A . PASS FR=0.5;HP=2;NF=4;NR=6;PP=100.0;SC=ATAAATAAATAAATAAATAAA;TC=24;TR=10 GT:GL:GQ 1/0:-419.18,-202.82,-208.38:27 20 5094493 . T TA . PASS FR=1.0;HP=1;NF=7;NR=16;PP=100.0;SC=AAAATGAACTTACTACTGGAC;TC=26;TR=23 GT:GL:GQ 1/1:-300.98,-148.38,-131.87:100 20 5097837 . AC A . PASS FR=1.0;HP=1;NF=15;NR=5;PP=100.0;SC=TAAAGGTTATACGCCTAACTT;TC=25;TR=20 GT:GL:GQ 1/1:-243.65,-32.97,-15.65:100 20 5100990 . AAG A . PASS FR=1.0;HP=1;NF=10;NR=6;PP=100.0;SC=TTGCAGCCTGAAGAGAGTACA;TC=18;TR=16 GT:GL:GQ 1/1:-198.64,-18.46,-5.29:100 20 5105482 . C CATTTTAGG . PASS FR=1.0;HP=2;NF=6;NR=11;PP=100.0;SC=GTTCAGACCACATGTTATCCA;TC=22;TR=17 GT:GL:GQ 1/1:-471.45,-181.5,-164.38:100 20 5118209 . A AT . PASS FR=0.5;HP=8;NF=3;NR=2;PP=100.0;SC=TTTAAGTCTTATTTTTTCAAA;TC=16;TR=5 GT:GL:GQ 0/1:-55.51,-21.15,-68.35:100 20 5145860 . A AC . PASS FR=0.5;HP=5;NF=6;NR=2;PP=100.0;SC=TTTTTTGGAAACCCCCGTATT;TC=29;TR=8 GT:GL:GQ 0/1:-81.29,-28.9,-130.37:100 20 5150896 . G GC . PASS FR=0.5;HP=3;NF=2;NR=5;PP=100.0;SC=ACCTCGCTGTGCCCAGAGGAG;TC=17;TR=7 GT:GL:GQ 0/1:-79.22,-17.13,-53.13:100 20 5156258 . CCT C . PASS FR=0.5093;HP=2;NF=6;NR=6;PP=100.0;SC=ATGGTGAAACCCTGTCTCTAC;TC=16;TR=12 GT:GL:GQ 0/1:-101.9,-26.13,-29.44:17 20 5156432 . AAAAC A . PASS FR=0.5;HP=3;NF=5;NR=3;PP=100.0;SC=ACTCCATCTCAAAACAAACAA;TC=23;TR=8 GT:GL:GQ 0/1:-98.71,-15.69,-97.38:100 20 5173014 . C CA . PASS FR=1.0;HP=2;NF=8;NR=13;PP=100.0;SC=GAAGGGGGGTCTAGGAAGCCG;TC=22;TR=21 GT:GL:GQ 1/1:-250.84,-61.97,-47.15:100 20 5178081 . C CCT . PASS FR=0.5;HP=1;NF=5;NR=6;PP=100.0;SC=AGAGGTCAGCCGTGTCTGCCC;TC=22;TR=11 GT:GL:GQ 0/1:-193.35,-72.27,-102.13:100 20 5181165 . C CA . PASS FR=0.5;HP=8;NF=1;NR=6;PP=91.0;SC=TTAGACACAACAAAAAAGAGA;TC=22;TR=7 GT:GL:GQ 0/1:-61.45,-29.38,-90.08:100 20 5187401 . A AC . PASS FR=0.5;HP=6;NF=4;NR=3;PP=100.0;SC=TTTTCATGTCACCCCCGAGGT;TC=17;TR=7 GT:GL:GQ 0/1:-139.03,-104.99,-121.15:73 20 5187831 . G GAATC . PASS FR=0.5;HP=5;NF=5;NR=3;PP=100.0;SC=TGAAAGGAAAGAAGCATGTTT;TC=22;TR=8 GT:GL:GQ 0/1:-144.73,-26.29,-132.63:100 20 5192127 . A AATT . PASS FR=0.5;HP=3;NF=2;NR=7;PP=100.0;SC=AATGTGTTAAAATTATATAAG;TC=32;TR=9 GT:GL:GQ 0/1:-228.5,-119.37,-283.27:100 20 5212592 . TA T . PASS FR=1.0;HP=9;NF=20;NR=10;PP=100.0;SC=CCTGCCATATTAAAAAAAAAC;TC=39;TR=30 GT:GL:GQ 1/1:-191.03,-64.37,-41.93:100 20 5223122 . TA T . PASS FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=GAATAAGACCTAGTATTTGCT;TC=11;TR=6 GT:GL:GQ 0/1:-63.8,-25.4,-69.29:100 20 5234499 . AAC A . PASS FR=0.5;HP=1;NF=1;NR=1;PP=25.0;SC=GTGCCTTCACAACACACACAC;TC=26;TR=2 GT:GL:GQ 0/1:-75.14,-59.09,-216.84:72 20 5236854 . A AATTAT . PASS FR=1.0;HP=1;NF=17;NR=9;PP=100.0;SC=AAAAGACATGAATTATCATTA;TC=29;TR=26 GT:GL:GQ 1/1:-427.74,-26.55,-5.07:100 20 5240296 . CT C . PASS FR=0.5;HP=1;NF=7;NR=6;PP=100.0;SC=AATTGATACACTACAATGGCC;TC=39;TR=13 GT:GL:GQ 0/1:-220.75,-129.27,-297.86:100 20 5242946 . A AC . PASS FR=0.5;HP=3;NF=6;NR=5;PP=100.0;SC=AGCTGGAACCACTGTTGTGGA;TC=22;TR=11 GT:GL:GQ 0/1:-141.29,-37.29,-109.65:100 20 5246342 . GC G . PASS FR=0.5;HP=7;NF=6;NR=8;PP=100.0;SC=AACCGAGACAGCCCCCCCTTT;TC=21;TR=14 GT:GL:GQ 0/1:-107.74,-25.34,-35.96:49 20 5247531 . T TTGCAGTAGAGAAACTCCC . PASS FR=0.5;HP=1;NF=3;NR=5;PP=100.0;SC=TTGCAGGTTATTGCAGTAGAG;TC=31;TR=8 GT:GL:GQ 0/1:-296.8,-101.13,-189.63:100 20 5251109 . ACTCTCTCTCTCTCTCTCT A . PASS FR=0.5;HP=1;NF=3;NR=2;PP=37.0;SC=CATCCAGTGTACTCTCTCTCT;TC=27;TR=5 GT:GL:GQ 0/1:-322.05,-299.54,-356.33:100 20 5251154 . G GTGTA . PASS FR=0.5;HP=2;NF=1;NR=4;PP=100.0;SC=CTCTGTGTGTGTGTATGTGTG;TC=19;TR=5 GT:GL:GQ 0/1:-297.98,-257.24,-280.47:100 20 5256228 . GAAAAAC G . PASS FR=0.5;HP=5;NF=8;NR=3;PP=100.0;SC=CAAATGTTTTGAAAAACAAAA;TC=29;TR=11 GT:GL:GQ 0/1:-159.47,-21.9,-134.38:100 20 5256836 . CT C . PASS FR=0.5;HP=10;NF=4;NR=7;PP=58.0;SC=TCTCAACTCACTTTTTTTTTT;TC=23;TR=11 GT:GL:GQ 0/1:-145.3,-121.72,-154.45:100 20 5260631 . G GA . PASS FR=0.5;HP=9;NF=6;NR=2;PP=100.0;SC=TTTAATGAAGGAAAAAAAAAT;TC=25;TR=8 GT:GL:GQ 0/1:-133.97,-86.93,-109.55:100 20 5261161 . ACT A . PASS FR=0.5;HP=2;NF=9;NR=8;PP=100.0;SC=CTTGAATGAAACTTATCTAAC;TC=33;TR=17 GT:GL:GQ 0/1:-246.04,-189.54,-319.81:100 20 5275657 . CAAAATAACTATTACAAATAACA C . PASS FR=0.5;HP=6;NF=2;NR=1;PP=100.0;SC=TCAAACATAACAAAATAACTA;TC=27;TR=3 GT:GL:GQ 0/1:-135.83,-52.75,-276.31:100 20 5277471 . C CCTT . PASS FR=0.5;HP=1;NF=11;NR=5;PP=100.0;SC=GTATCCATGTCCTAGGGTACA;TC=27;TR=16 GT:GL:GQ 0/1:-278.16,-87.4,-130.16:100 20 5278336 . TA T . PASS FR=0.5;HP=4;NF=3;NR=6;PP=100.0;SC=TTGAACTCTTTAAAAGTTTGA;TC=24;TR=9 GT:GL:GQ 0/1:-132.29,-83.79,-178.99:100 20 5280465 . TTG T . PASS FR=0.5;HP=4;NF=6;NR=8;PP=100.0;SC=GATGGGGTTTTTGGCCATGTT;TC=30;TR=14 GT:GL:GQ 0/1:-161.14,-49.68,-168.09:100 20 5280839 . T TATA . PASS FR=0.5;HP=1;NF=9;NR=3;PP=100.0;SC=ACCACAAATGTATAATACAAA;TC=30;TR=12 GT:GL:GQ 0/1:-228.47,-89.38,-201.59:100 20 5285786 . T TG . PASS FR=0.5;HP=1;NF=3;NR=2;PP=21.0;SC=GGCTAATCAGTTCACTCTAAG;TC=24;TR=5 GT:GL:GQ 0/1:-80.46,-64.62,-184.45:71 20 5289619 . GA G . PASS FR=0.5;HP=1;NF=9;NR=5;PP=100.0;SC=GAAGATCTAGGATGAAGCTGG;TC=22;TR=14 GT:GL:GQ 0/1:-219.59,-148.82,-190.02:100 20 5291220 . TGATCA T . PASS FR=0.5;HP=2;NF=6;NR=6;PP=100.0;SC=GTTTAGAACCTGATCAGAGAA;TC=27;TR=12 GT:GL:GQ 0/1:-284.71,-179.16,-294.64:100 20 5291304 . G GACTTATGGGGAGCTGGGGTATAAATACCCCAGCTCCCTCCT . PASS FR=0.5;HP=1;NF=1;NR=1;PP=100.0;SC=CCTCATCAATGACCTCCCACC;TC=8;TR=2 GT:GL:GQ 0/1:-488.84,-441.13,-506.41:71 20 5293792 . ATG A . PASS FR=0.5;HP=3;NF=6;NR=12;PP=100.0;SC=TACAATTATTATGTGTCAATT;TC=42;TR=18 GT:GL:GQ 0/1:-201.09,-30.39,-231.82:100 20 5303337 . CAGCT C . PASS FR=0.5;HP=2;NF=7;NR=7;PP=100.0;SC=AAATGTCACACAGCTAGCTGG;TC=32;TR=14 GT:GL:GQ 0/1:-273.85,-111.21,-258.62:100 20 5313928 . TA T . PASS FR=0.5;HP=10;NF=9;NR=8;PP=100.0;SC=ATACAGTTGATAAAAAAAAAC;TC=39;TR=17 GT:GL:GQ 0/1:-100.8,-36.94,-107.23:100 20 5316589 . GT G . PASS FR=1.0;HP=2;NF=7;NR=11;PP=100.0;SC=GAATATCTGGGTAAAATTTAA;TC=22;TR=18 GT:GL:GQ 1/1:-227.4,-66.98,-52.55:100 20 5320851 . AT A . PASS FR=0.5;HP=6;NF=5;NR=10;PP=100.0;SC=ATCTCAATAGATTTTTTAAAA;TC=39;TR=15 GT:GL:GQ 0/1:-177.77,-103.88,-250.39:100 20 5323468 . GA G . PASS FR=0.5;HP=10;NF=2;NR=4;PP=85.0;SC=GGCAACAAAAGAAAAAATAGA;TC=23;TR=6 GT:GL:GQ 0/1:-61.27,-31.53,-121.44:100 20 5326511 . G GT . PASS FR=0.5;HP=9;NF=11;NR=2;PP=100.0;SC=TTGATTCAAAGTTTTTTTTTA;TC=29;TR=13 GT:GL:GQ 0/1:-178.07,-139.61,-153.82:64 20 5326660 . T TA . PASS FR=0.5;HP=8;NF=4;NR=6;PP=100.0;SC=CTTTATCCTTTAAAAAAAATC;TC=26;TR=10 GT:GL:GQ 0/1:-181.43,-128.15,-159.02:100 20 5328799 . CA C . PASS FR=1.0;HP=4;NF=10;NR=6;PP=100.0;SC=AACCACCTTCCAAAATGTGGA;TC=20;TR=16 GT:GL:GQ 1/1:-179.33,-21.23,-7.37:100 20 5351875 . T TACACACAC . PASS FR=0.5;HP=6;NF=1;NR=1;PP=38.0;SC=ATCTTAAAAATACACACACAC;TC=12;TR=2 GT:GL:GQ 0/1:-48.31,-20.86,-63.23:100 20 5354510 . G GGC . PASS FR=0.5;HP=1;NF=5;NR=5;PP=100.0;SC=CCTCCTCCCTGCAGAGCTCCT;TC=28;TR=10 GT:GL:GQ 0/1:-148.18,-38.3,-173.54:100 20 5373349 . A AATTT . PASS FR=0.5;HP=6;NF=1;NR=2;PP=96.0;SC=CTAATTTTTTAATTTTTTTTT;TC=20;TR=3 GT:GL:GQ 0/1:-100.6,-64.12,-96.6:100 20 5390447 . C CA . PASS FR=0.5;HP=6;NF=4;NR=5;PP=100.0;SC=CATTAGCATACAAAAACCATC;TC=26;TR=9 GT:GL:GQ 0/1:-88.65,-28.46,-120.44:100 20 5408475 . AAAAC A . PASS FR=0.5;HP=4;NF=4;NR=5;PP=100.0;SC=CTCTGTCTCAAAAACAAACAA;TC=29;TR=9 GT:GL:GQ 0/1:-128.94,-29.02,-144.52:100 20 5410361 . G GA . PASS FR=1.0;HP=9;NF=6;NR=7;PP=100.0;SC=CTGGGTTGGGGAAAAAAAAAG;TC=25;TR=13 GT:GL:GQ 1/1:-119.78,-34.18,-19.33:100 20 5419440 . CTCCCTGTG C . PASS FR=0.5;HP=3;NF=1;NR=4;PP=100.0;SC=TGTTGTTCCCCTCCCTGTGTC;TC=19;TR=5 GT:GL:GQ 0/1:-128.97,-30.52,-125.82:100 20 5432204 . A AG . PASS FR=0.5;HP=8;NF=2;NR=3;PP=100.0;SC=AAAGAAAGAGAAAAAAAAAGG;TC=19;TR=5 GT:GL:GQ 0/1:-83.51,-76.05,-116.49:100 20 5432394 . G GT . PASS FR=1.0;HP=5;NF=9;NR=14;PP=100.0;SC=TTCCTCAATTGAAAAATCTTA;TC=26;TR=23 GT:GL:GQ 1/1:-328.05,-211.91,-196.14:100 20 5435136 . GAGAAAA G . PASS FR=0.5;HP=3;NF=3;NR=6;PP=44.0;SC=AAAAAAAGGGGAGAAAAAGAA;TC=24;TR=9 GT:GL:GQ 0/1:-190.59,-169.15,-271.82:96 20 5435153 . A ATTT . PASS FR=0.5;HP=8;NF=4;NR=10;PP=100.0;SC=AGAAAAAAAAATTTTAATGTT;TC=22;TR=14 GT:GL:GQ 0/1:-325.96,-275.2,-333.88:100 20 5435908 . G GTTAAT . PASS FR=0.5;HP=2;NF=5;NR=2;PP=100.0;SC=ACCAGGCCCAGTTATTTTTTG;TC=16;TR=7 GT:GL:GQ 0/1:-176.12,-112.78,-176.63:100 20 5443418 . A ACAGGGGCAC . PASS FR=0.5;HP=4;NF=3;NR=1;PP=100.0;SC=GCTTTGTCCCACAGCCTGATG;TC=15;TR=4 GT:GL:GQ 0/1:-94.87,-42.4,-160.11:100 20 5443724 . C CT . PASS FR=0.5;HP=3;NF=6;NR=4;PP=38.0;SC=GTTACCTTTCCCCTGAGATGC;TC=20;TR=10 GT:GL:GQ 0/1:-163.73,-143.91,-199.73:89 20 5452897 . G GA . PASS FR=0.5;HP=10;NF=2;NR=2;PP=26.0;SC=TCAGTCAGAAGAAAAAAAATT;TC=15;TR=4 GT:GL:GQ 0/1:-34.37,-17.3,-53.75:77 20 5460271 . C CA . PASS FR=0.5;HP=10;NF=2;NR=2;PP=67.0;SC=ACCCCTGTCTCAAAAAAAAAA;TC=21;TR=4 GT:GL:GQ 0/1:-56.83,-30.33,-56.83:100 20 5473577 . A AGT . PASS FR=0.5;HP=2;NF=2;NR=8;PP=100.0;SC=AACTGAGCAGAGTTCCTTTTT;TC=29;TR=10 GT:GL:GQ 0/1:-165.26,-86.94,-217.65:100 20 5475853 . CTTATTTAT CTTATTTATTTAT,C . PASS FR=0.5,0.5;HP=4;NF=1,1;NR=2,2;PP=100.0,100.0;SC=GAAGGCTCTTCTTATTTATTT;TC=18;TR=3,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 5485434 . C CT . PASS FR=0.5001;HP=10;NF=4;NR=1;PP=63.0;SC=TTTTTATCTTCTTTTTTTTCC;TC=9;TR=5 GT:GL:GQ 0/1:-37.99,-12.58,-20.26:36 20 5518456 . C CG . PASS FR=0.5;HP=7;NF=7;NR=6;PP=100.0;SC=GTGACAAATGCGGGGGGTCTT;TC=27;TR=13 GT:GL:GQ 0/1:-115.32,-28.55,-76.08:100 20 5546352 . A AAG . PASS FR=1.0;HP=1;NF=13;NR=12;PP=100.0;SC=AAGTAGTCACAAGCTGTGATT;TC=26;TR=25 GT:GL:GQ 1/1:-322.1,-20.79,0.0:100 20 5596481 . TTATG T . PASS FR=1.0;HP=2;NF=4;NR=4;PP=100.0;SC=TGCTACTGGTTTATGTATGTA;TC=20;TR=8 GT:GL:GQ 1/1:-167.17,-32.77,-22.47:86 20 5596891 . ATGTGTGTG A . PASS FR=1.0;HP=2;NF=3;NR=4;PP=100.0;SC=AATTTGGGGTATGTGTGTGTG;TC=23;TR=7 GT:GL:GQ 1/1:-241.36,-45.12,-34.38:90 20 5600458 . A AG . PASS FR=1.0;HP=2;NF=3;NR=3;PP=100.0;SC=TCTTGACCTGAGTGATACACC;TC=16;TR=6 GT:GL:GQ 1/1:-146.08,-65.05,-55.59:79 20 5613790 . GA G . PASS FR=1.0;HP=4;NF=11;NR=9;PP=100.0;SC=CATGATTTCTGAAAACAAGCT;TC=26;TR=20 GT:GL:GQ 1/1:-222.44,-43.9,-26.57:100 20 5624959 . C CCTCCTTACCCT . PASS FR=0.5;HP=1;NF=1;NR=1;PP=100.0;SC=AACTTGTCCACCTCCATTACC;TC=28;TR=2 GT:GL:GQ 0/1:-225.26,-176.16,-303.27:100 20 5627592 . AT A . PASS FR=0.5;HP=6;NF=4;NR=3;PP=100.0;SC=TCTCAAAAAAATAATAAAGTT;TC=19;TR=7 GT:GL:GQ 0/1:-112.89,-28.55,-78.51:100 20 5629324 . T TTAC . PASS FR=0.5;HP=1;NF=3;NR=3;PP=100.0;SC=ATTATTACTATTATTATTATT;TC=26;TR=6 GT:GL:GQ 1/0:-227.05,-75.82,-72.8:100 20 5635153 . TGGAATATGAAAGAG T . PASS FR=1.0;HP=2;NF=7;NR=11;PP=100.0;SC=CAAGCCTGTTTGGAATATGAA;TC=27;TR=18 GT:GL:GQ 1/1:-490.0,-56.65,-38.89:100 20 5635246 . T TTGTGTG,TTGTGTGTG . PASS FR=0.5,0.5;HP=1;NF=2,0;NR=2,3;PP=100.0,100.0;SC=AAAATGAATATTGTGTGTGTG;TC=22;TR=4,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 5644716 . GTCTCTCTCTCTC G . PASS FR=1.0;HP=1;NF=1;NR=6;PP=100.0;SC=ATGAGACCTCGTCTCTCTCTC;TC=22;TR=7 GT:GL:GQ 1/1:-261.18,-61.24,-58.02:52 20 5654462 . C CGTGTGTGTGTGTGT . PASS FR=0.5;HP=1;NF=3;NR=1;PP=100.0;SC=TATACATATACGTGTGTGTGT;TC=16;TR=4 GT:GL:GQ 0/1:-129.11,-28.26,-136.2:100 20 5654661 . AAAAAAATTTTTTTTGCTT A . PASS FR=0.5;HP=6;NF=7;NR=3;PP=100.0;SC=ATTTTTTGCCAAAAAAATTTT;TC=21;TR=10 GT:GL:GQ 0/1:-264.68,-158.41,-268.38:100 20 5655925 . ACG A . PASS FR=0.5047;HP=2;NF=4;NR=3;PP=100.0;SC=TTGCATGCGCACGCGCGCACA;TC=34;TR=7 GT:GL:GQ 0/1:-234.34,-106.46,-110.43:20 20 5674501 . T TTTTG . PASS FR=0.5;HP=4;NF=2;NR=2;PP=100.0;SC=AGATTTAGATTTTTGTTTGTT;TC=22;TR=4 GT:GL:GQ 0/1:-64.3,-21.33,-64.69:100 20 5691054 . A AC . PASS FR=0.5;HP=6;NF=4;NR=5;PP=100.0;SC=GTATAGTGAGACCCCCCATCT;TC=18;TR=9 GT:GL:GQ 0/1:-137.75,-89.82,-120.86:100 20 5696589 . AAAG A . PASS FR=0.5;HP=2;NF=3;NR=9;PP=100.0;SC=AGAAAACCATAAAGAAGAGAA;TC=35;TR=12 GT:GL:GQ 0/1:-142.07,-32.31,-238.04:100 20 5706639 . T TA . PASS FR=0.5;HP=9;NF=5;NR=2;PP=98.0;SC=TTGTCTCAATTAAAAAAAAAT;TC=31;TR=7 GT:GL:GQ 0/1:-60.75,-27.2,-75.24:100 20 5707109 . A ATTTTTCCC . PASS FR=0.5;HP=7;NF=2;NR=2;PP=100.0;SC=TGCCCAGCTGATTTTTTTAAA;TC=15;TR=4 GT:GL:GQ 0/1:-95.63,-40.43,-104.52:100 20 5740635 . T TAC,TACAC . PASS FR=0.5,0.5;HP=2;NF=3,1;NR=7,4;PP=100.0,100.0;SC=TGTATTTTTATACACACACAC;TC=23;TR=10,5 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 5747768 . ATTTTC ATTTTCTTTTC,A . PASS FR=0.5,0.5;HP=4;NF=1,4;NR=1,1;PP=100.0,100.0;SC=CTCCATTCACATTTTCTTTTC;TC=17;TR=2,5 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 5754003 . A AT . PASS FR=0.5;HP=9;NF=6;NR=4;PP=100.0;SC=AGAGAGTGGAATTTTTTTTTG;TC=33;TR=10 GT:GL:GQ 0/1:-69.42,-30.04,-87.94:100 20 5762289 . A AT . PASS FR=0.5;HP=8;NF=2;NR=3;PP=95.0;SC=CTGCCCAGCTATTTTTTTGTA;TC=13;TR=5 GT:GL:GQ 0/1:-43.82,-10.94,-28.53:79 20 5767540 . AGATCATTT A . PASS FR=1.0;HP=2;NF=5;NR=6;PP=100.0;SC=TTCTCAAGCCAGATCATTTGA;TC=16;TR=11 GT:GL:GQ 1/1:-333.85,-224.08,-215.75:69 20 5768941 . AGTT A . PASS FR=0.5;HP=1;NF=4;NR=9;PP=100.0;SC=TATATTCAGTAGTTGTTGTTT;TC=21;TR=13 GT:GL:GQ 0/1:-159.07,-13.83,-29.97:73 20 5771896 . CAAATAAATA C . PASS FR=1.0;HP=3;NF=11;NR=5;PP=100.0;SC=AAAATCTTAGCAAATAAATAA;TC=26;TR=16 GT:GL:GQ 1/1:-433.86,-58.29,-43.98:62 20 5778212 . AAAG A . PASS FR=1.0;HP=5;NF=6;NR=12;PP=100.0;SC=CCATCTCAAAAAAGAAGAAGA;TC=23;TR=18 GT:GL:GQ 1/1:-251.53,-37.12,-21.87:100 20 5781503 . GCGTA G . PASS FR=1.0;HP=1;NF=9;NR=6;PP=100.0;SC=GTGTGTGTGTGCGTATGTCTA;TC=23;TR=15 GT:GL:GQ 1/1:-450.31,-256.77,-243.2:93 20 5788895 . C CAGCCTGGGTGACAG . PASS FR=1.0;HP=1;NF=3;NR=6;PP=100.0;SC=CACTGCACTCCAGCAAGACTC;TC=11;TR=9 GT:GL:GQ 1/1:-304.26,-23.03,-12.43:73 20 5798352 . CTGGCATTA C . PASS FR=0.5;HP=1;NF=1;NR=3;PP=100.0;SC=CTGGCTGTGCCTGGCATTATG;TC=29;TR=4 GT:GL:GQ 1/0:-390.33,-302.72,-305.99:100 20 5798359 . T TGC . PASS FR=0.5;HP=1;NF=6;NR=6;PP=100.0;SC=TGCCTGGCATTATGACTTAGT;TC=26;TR=12 GT:GL:GQ 0/1:-390.33,-366.98,-362.46:100 20 5807781 . T TG . PASS FR=1.0;HP=3;NF=7;NR=3;PP=100.0;SC=TGAGTGGGCGTGGCACCCACA;TC=10;TR=10 GT:GL:GQ 1/1:-98.15,-11.06,-4.14:57 20 5808542 . C CT . PASS FR=1.0;HP=3;NF=16;NR=16;PP=100.0;SC=ATCATTCACTCTTGTGGGTAG;TC=33;TR=32 GT:GL:GQ 1/1:-408.08,-203.57,-182.32:100 20 5808967 . T TGTGTAGTAG . PASS FR=1.0;HP=2;NF=7;NR=18;PP=100.0;SC=CTTAGAACAGTGTGATAGGTC;TC=28;TR=25 GT:GL:GQ 1/1:-678.96,-93.79,-70.92:100 20 5809144 . TTGA T . PASS FR=1.0;HP=1;NF=10;NR=16;PP=100.0;SC=GAGTCATTTCTTGATGACTCC;TC=34;TR=26 GT:GL:GQ 1/1:-408.43,-70.02,-46.73:100 20 5809747 . CCTGGGCTCA C . PASS FR=1.0;HP=1;NF=13;NR=15;PP=100.0;SC=GGTCTCAACTCCTGGGCTCAA;TC=33;TR=28 GT:GL:GQ 1/1:-583.71,-71.8,-56.82:48 20 5810527 . G GA . PASS FR=1.0;HP=9;NF=9;NR=9;PP=100.0;SC=TCTTCTTTAGGAAAAAAAAAC;TC=26;TR=18 GT:GL:GQ 1/1:-296.92,-216.99,-203.12:100 20 5820132 . A AAGATAGAT,AAGATAGATAGAT . PASS FR=0.5,0.5;HP=2;NF=4,2;NR=2,6;PP=100.0,100.0;SC=ATTAGATAGAAAGATAGATAG;TC=36;TR=6,8 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 5822610 . A AAAG . PASS FR=0.5;HP=2;NF=4;NR=6;PP=100.0;SC=GACTATGGAGAAAGAGAACAT;TC=30;TR=10 GT:GL:GQ 0/1:-160.25,-33.5,-176.54:100 20 5830758 . C CAATAATAAT . PASS FR=1.0;HP=2;NF=2;NR=2;PP=100.0;SC=GACCCCGTCTCAATAATAATA;TC=8;TR=4 GT:GL:GQ 1/1:-112.77,-19.78,-14.93:60 20 5848219 . C CAAAAT . PASS FR=1.0;HP=7;NF=10;NR=13;PP=100.0;SC=ATTAAACACTCAAAAAAATAA;TC=29;TR=23 GT:GL:GQ 1/1:-431.75,-125.0,-103.09:100 20 5848530 . A AAT . PASS FR=1.0;HP=1;NF=13;NR=10;PP=100.0;SC=ATATATATAGAATATATATAT;TC=33;TR=23 GT:GL:GQ 1/1:-409.72,-328.74,-317.3:96 20 5850230 . A AT . PASS FR=1.0;HP=6;NF=1;NR=1;PP=100.0;SC=TAATTTTTGCATTTTTTGTTT;TC=22;TR=2 GT:GL:GQ 1/1:-134.01,-105.23,-98.33:86 20 5854908 . A AATTTTATTTT . PASS FR=1.0;HP=3;NF=3;NR=7;PP=100.0;SC=CATATACTTTAATTTTATTTT;TC=28;TR=10 GT:GL:GQ 1/1:-352.01,-27.1,-12.2:100 20 5856355 . CTAAA C . PASS FR=1.0;HP=4;NF=2;NR=2;PP=100.0;SC=GACCCTATTTCTAAATAAATA;TC=15;TR=4 GT:GL:GQ 1/1:-57.0,-6.23,-2.76:42 20 5860647 . TGAG T . PASS FR=1.0;HP=4;NF=8;NR=6;PP=100.0;SC=AGAAAGAAAATGAGGAGCGAA;TC=18;TR=14 GT:GL:GQ 1/1:-182.28,-15.91,-4.13:99 20 5879792 . CAA C . PASS FR=1.0;HP=10;NF=14;NR=15;PP=100.0;SC=ACAATAACATCAAAAAAAAAA;TC=39;TR=29 GT:GL:GQ 1/1:-170.66,-28.34,-5.76:100 20 5898748 . GAA G . PASS FR=1.0;HP=2;NF=5;NR=5;PP=100.0;SC=AGCCAAGATTGAACTCCATTG;TC=13;TR=10 GT:GL:GQ 1/1:-132.95,-97.25,-91.93:66 20 5900669 . G GC . PASS FR=0.5;HP=1;NF=4;NR=2;PP=100.0;SC=CATGACAGATGCATTTCCCTG;TC=15;TR=6 GT:GL:GQ 0/1:-72.42,-12.46,-72.17:100 20 5911588 . TCA T . PASS FR=0.5;HP=2;NF=6;NR=1;PP=100.0;SC=CTGGCAAATCTCACACACACA;TC=19;TR=7 GT:GL:GQ 0/1:-115.11,-26.04,-76.51:100 20 5923828 . CAGAGAGAATACATGCTTA C . PASS FR=0.5;HP=1;NF=3;NR=5;PP=100.0;SC=TGTATTCTTCCAGAGAGAATA;TC=22;TR=8 GT:GL:GQ 0/1:-297.99,-115.43,-361.46:100 20 5928403 . T TA . PASS FR=0.5;HP=2;NF=3;NR=2;PP=100.0;SC=ACCTAGGTGCTTTGAAACACT;TC=18;TR=5 GT:GL:GQ 0/1:-52.7,-18.59,-121.61:100 20 5930573 . A AG . PASS FR=0.5;HP=3;NF=4;NR=4;PP=100.0;SC=ACAGGTGATTAGGGTGTGGAG;TC=26;TR=8 GT:GL:GQ 0/1:-121.38,-46.04,-144.61:100 20 5932104 . C CT . PASS FR=0.5;HP=2;NF=5;NR=6;PP=100.0;SC=TCTTTATTTACTTGTATACTT;TC=20;TR=11 GT:GL:GQ 0/1:-138.34,-48.83,-107.16:100 20 5934084 . GGTGT GGT,G . PASS FR=0.5,0.5;HP=3;NF=1,2;NR=3,2;PP=100.0,100.0;SC=TCTCATGAGGGGTGTGTGTGT;TC=32;TR=4,4 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 5938650 . A AT . PASS FR=0.5;HP=3;NF=3;NR=6;PP=100.0;SC=TTTTCCTTAAATTTCTTTTTT;TC=36;TR=9 GT:GL:GQ 0/1:-182.01,-137.8,-289.15:100 20 5939638 . G GT . PASS FR=0.5;HP=7;NF=8;NR=7;PP=100.0;SC=ATTAGTGTCTGTTTTTTACCT;TC=37;TR=15 GT:GL:GQ 0/1:-244.24,-166.31,-240.23:100 20 5946414 . TTTTACTTCTTAGAGTATGC T . PASS FR=0.5;HP=3;NF=2;NR=4;PP=100.0;SC=TAAGTGCTGGTTTTACTTCTT;TC=34;TR=6 GT:GL:GQ 0/1:-213.07,-102.23,-466.92:100 20 5948421 . CATT C . PASS FR=0.5;HP=1;NF=6;NR=8;PP=100.0;SC=CTAGTTGAGTCATTGTAGGGA;TC=25;TR=14 GT:GL:GQ 0/1:-180.5,-26.28,-114.93:100 20 5958367 . TATA T . PASS FR=0.5;HP=2;NF=1;NR=12;PP=100.0;SC=TAAATCAGGATATAATAATAC;TC=28;TR=13 GT:GL:GQ 0/1:-168.03,-21.02,-138.69:100 20 5958971 . AT A . PASS FR=0.5;HP=8;NF=7;NR=10;PP=100.0;SC=ATTTGTGATCATTTTTTTTAA;TC=36;TR=17 GT:GL:GQ 0/1:-190.15,-122.85,-187.1:100 20 5972522 . TC T . PASS FR=0.5;HP=2;NF=3;NR=8;PP=100.0;SC=AGTTTTCATCTCTTCAGCTTC;TC=35;TR=11 GT:GL:GQ 0/1:-138.05,-67.95,-261.75:100 20 5974701 . T TTTTG . PASS FR=0.5;HP=6;NF=12;NR=8;PP=100.0;SC=TTAGCTTGATTTTTTTCAGCT;TC=40;TR=20 GT:GL:GQ 0/1:-282.01,-46.13,-199.33:100 20 5979818 . CTA C . PASS FR=0.5;HP=1;NF=4;NR=2;PP=100.0;SC=CACACACACACTATATAGAGT;TC=23;TR=6 GT:GL:GQ 0/1:-148.54,-97.12,-217.3:100 20 5979861 . T TAG . PASS FR=0.5;HP=1;NF=1;NR=6;PP=100.0;SC=GTATATATACTAGTGTGTATA;TC=23;TR=7 GT:GL:GQ 0/1:-206.33,-148.87,-246.11:100 20 5979921 . ATATATATTATATATAC A . PASS FR=0.5;HP=2;NF=2;NR=3;PP=100.0;SC=TCTATAAAGTATATATATTAT;TC=15;TR=5 GT:GL:GQ 0/1:-143.6,-52.22,-114.36:100 20 5980041 . CTATA C . PASS FR=0.5;HP=1;NF=6;NR=4;PP=100.0;SC=TATATATACACTATATATAGT;TC=35;TR=10 GT:GL:GQ 0/1:-130.29,-26.74,-240.87:100 20 5982833 . CTT C . PASS FR=0.5;HP=5;NF=2;NR=5;PP=100.0;SC=GCAATGCACTCTTTTGCTTAC;TC=22;TR=7 GT:GL:GQ 0/1:-154.07,-87.47,-142.2:100 20 5984269 . CTT C . PASS FR=0.5;HP=5;NF=6;NR=7;PP=100.0;SC=AATCCTTTCTCTTTTCACGTT;TC=31;TR=13 GT:GL:GQ 0/1:-161.92,-47.17,-162.99:100 20 5986173 . A ATAATT . PASS FR=0.5;HP=3;NF=9;NR=5;PP=100.0;SC=AAAATTTAAAATAAAAACTAT;TC=31;TR=14 GT:GL:GQ 0/1:-275.95,-89.41,-205.85:100 20 5997120 . T TGTGTGA . PASS FR=0.5;HP=2;NF=2;NR=2;PP=100.0;SC=TGTGTGTGTGTGAGTTTTCTT;TC=20;TR=4 GT:GL:GQ 0/1:-128.89,-41.21,-139.69:100 20 5999929 . G GTTA . PASS FR=0.5;HP=5;NF=7;NR=6;PP=100.0;SC=CTTTTGACCAGTTTTTAAGTT;TC=34;TR=13 GT:GL:GQ 0/1:-145.72,-26.46,-192.55:100 20 6013970 . C CG . PASS FR=0.5;HP=4;NF=4;NR=1;PP=100.0;SC=TTAGTAGAGACGGGGTTTCAC;TC=18;TR=5 GT:GL:GQ 0/1:-76.07,-30.4,-70.18:100 20 6019907 . TTGTGTGTGTGTGTGTG T . PASS FR=0.5;HP=2;NF=1;NR=1;PP=100.0;SC=GCAGTTTTGTTTGTGTGTGTG;TC=27;TR=2 GT:GL:GQ 0/1:-146.39,-89.3,-170.65:100 20 6052252 . CT C . PASS FR=1.0;HP=2;NF=5;NR=9;PP=100.0;SC=ATCCCCAGCCCTTCCTGGCTT;TC=21;TR=14 GT:GL:GQ 1/1:-166.42,-15.59,-2.3:100 20 6054897 . T TG . PASS FR=1.0;HP=3;NF=4;NR=7;PP=100.0;SC=TGGGCAAGGCTGGGAAGGAAG;TC=16;TR=11 GT:GL:GQ 1/1:-170.6,-33.42,-22.33:90 20 6056042 . T TA . PASS FR=1.0;HP=2;NF=8;NR=17;PP=100.0;SC=ACATCAAGTATATACGGTACA;TC=29;TR=25 GT:GL:GQ 1/1:-301.61,-48.56,-28.73:100 20 6163149 . CATTT C . PASS FR=1.0;HP=1;NF=11;NR=10;PP=100.0;SC=AACCTCTGAGCATTTATTTCA;TC=24;TR=21 GT:GL:GQ 1/1:-265.47,-16.86,-0.92:100 20 6169158 . C CT . PASS FR=1.0;HP=1;NF=11;NR=21;PP=100.0;SC=AATTGCAAGACCTTAAGAACC;TC=38;TR=32 GT:GL:GQ 1/1:-377.27,-55.22,-28.98:100 20 6186522 . G GC . PASS FR=1.0;HP=6;NF=10;NR=10;PP=100.0;SC=TAAAAAATGTGTTTTTAATCA;TC=21;TR=20 GT:GL:GQ 1/1:-309.42,-177.87,-163.8:100 20 6186628 . C CA . PASS FR=0.5;HP=3;NF=5;NR=12;PP=100.0;SC=TTCATCACCTCAAACATTTAT;TC=33;TR=17 GT:GL:GQ 0/1:-173.72,-30.0,-131.16:100 20 6189872 . C CCTT . PASS FR=0.5;HP=1;NF=1;NR=10;PP=100.0;SC=CTTCCTCCCTCCTTTCCCTCT;TC=26;TR=11 GT:GL:GQ 0/1:-217.8,-111.28,-184.18:100 20 6190124 . C CTT . PASS FR=0.5;HP=2;NF=2;NR=4;PP=92.0;SC=TCCTGCCTCTCTCTTTCCTCC;TC=16;TR=6 GT:GL:GQ 0/1:-129.79,-96.5,-151.55:100 20 6190921 . A AT . PASS FR=0.5;HP=2;NF=5;NR=4;PP=100.0;SC=CCATAAGTACATTAAAAAAAA;TC=24;TR=9 GT:GL:GQ 0/1:-121.19,-85.53,-104.7:86 20 6202427 . C CT . PASS FR=1.0;HP=6;NF=6;NR=13;PP=100.0;SC=GAAATCCTTTCTTTCCCCCTA;TC=20;TR=19 GT:GL:GQ 1/1:-165.74,-14.09,-0.92:100 20 6211244 . GT G . PASS FR=0.5;HP=10;NF=5;NR=6;PP=100.0;SC=TTGATTTCCAGTTTTTTTTTT;TC=33;TR=11 GT:GL:GQ 0/1:-97.67,-63.78,-117.4:100 20 6217057 . T TA . PASS FR=0.5;HP=2;NF=4;NR=7;PP=100.0;SC=TCTCTACAACTAACCATCAAC;TC=33;TR=11 GT:GL:GQ 0/1:-151.16,-56.84,-189.09:100 20 6227811 . TTTTTCTTTTC T . PASS FR=0.5;HP=6;NF=3;NR=2;PP=100.0;SC=TATACTGCTTTTTTTCTTTTC;TC=28;TR=5 GT:GL:GQ 0/1:-171.28,-80.47,-279.48:100 20 6228139 . TA T . PASS FR=0.5;HP=8;NF=6;NR=7;PP=100.0;SC=ACTGGTTGTTTAAAAAAAACA;TC=27;TR=13 GT:GL:GQ 0/1:-101.53,-37.68,-71.46:100 20 6229361 . G GTA . PASS FR=0.5;HP=2;NF=7;NR=5;PP=100.0;SC=TGCTTTTGAAGTATACCTTTA;TC=28;TR=12 GT:GL:GQ 0/1:-168.24,-128.05,-263.48:100 20 6232719 . T TA . PASS FR=1.0;HP=4;NF=10;NR=14;PP=100.0;SC=CGTACCTCAATAAGTACTGTT;TC=26;TR=24 GT:GL:GQ 1/1:-246.13,-19.86,-1.84:100 20 6235756 . T TA . PASS FR=0.5;HP=10;NF=4;NR=2;PP=51.0;SC=ATATAAAAGTTAAAAAAAAAA;TC=22;TR=6 GT:GL:GQ 0/1:-59.89,-37.16,-67.02:100 20 6242610 . GCAGACC G . PASS FR=0.5;HP=1;NF=7;NR=3;PP=100.0;SC=ACTGGGAGAGGCAGACCCACC;TC=27;TR=10 GT:GL:GQ 0/1:-180.6,-46.65,-174.85:100 20 6245977 . A AT . PASS FR=0.5;HP=6;NF=7;NR=5;PP=100.0;SC=CTTAGTTTTCATTTTTTAGCA;TC=29;TR=12 GT:GL:GQ 0/1:-149.75,-66.4,-136.45:100 20 6258987 . CT C . PASS FR=0.5;HP=6;NF=4;NR=10;PP=100.0;SC=GTATGTTCTTCTTTTGTCCCC;TC=34;TR=14 GT:GL:GQ 0/1:-185.84,-121.45,-268.81:100 20 6272029 . T TA . PASS FR=0.5;HP=3;NF=4;NR=9;PP=100.0;SC=TAATAGCTGGTAAACCCAACC;TC=39;TR=13 GT:GL:GQ 0/1:-151.49,-56.11,-226.05:100 20 6293812 . G GA . PASS FR=1.0;HP=7;NF=15;NR=12;PP=100.0;SC=GGAAAAGAAAGAAAAGAAAAA;TC=35;TR=27 GT:GL:GQ 1/1:-393.29,-260.24,-242.04:100 20 6296458 . T TA . PASS FR=1.0;HP=8;NF=5;NR=17;PP=100.0;SC=GAAAGCACAATTTTTTTTTCT;TC=39;TR=22 GT:GL:GQ 1/1:-284.36,-128.48,-104.71:100 20 6304002 . A ATG . PASS FR=1.0;HP=2;NF=6;NR=5;PP=100.0;SC=ATATATATATATATGTGTGTG;TC=30;TR=11 GT:GL:GQ 1/1:-328.64,-256.07,-245.8:100 20 6307745 . GTA G . PASS FR=1.0;HP=3;NF=4;NR=7;PP=100.0;SC=TATATATGTTGTATATATATA;TC=16;TR=11 GT:GL:GQ 1/1:-114.94,-15.25,-6.19:75 20 6307849 . TATATATATGGTATATATATC T . PASS FR=0.5034;HP=1;NF=2;NR=2;PP=100.0;SC=ATATATGGTGTATATATATGG;TC=11;TR=4 GT:GL:GQ 0/1:-108.24,-70.67,-74.96:21 20 6307908 . TG T . PASS FR=0.5;HP=2;NF=3;NR=4;PP=100.0;SC=ATATCATATATGGTGTATATA;TC=21;TR=7 GT:GL:GQ 0/1:-127.13,-92.55,-148.07:100 20 6308166 . G GTA,GTATA . PASS FR=0.5,0.5;HP=2;NF=2,1;NR=0,3;PP=86.0,100.0;SC=GTGTGTGTGTGTATATATATA;TC=16;TR=2,4 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 6308279 . G GTA . PASS FR=1.0;HP=2;NF=5;NR=4;PP=100.0;SC=TATATATGGTGTATATATATA;TC=12;TR=9 GT:GL:GQ 1/1:-129.24,-92.18,-87.75:54 20 6308322 . GTGTGTGTATATATATATATATATA G . PASS FR=1.0;HP=2;NF=1;NR=2;PP=88.0;SC=ATGTATGTGTGTGTGTGTATA;TC=16;TR=3 GT:GL:GQ 1/1:-227.62,-141.11,-132.99:40 20 6319701 . G GGT . PASS FR=0.5;HP=1;NF=1;NR=5;PP=100.0;SC=GAGTCTATGTGGTGTGTGTGT;TC=19;TR=6 GT:GL:GQ 0/1:-99.44,-38.84,-115.36:100 20 6345189 . G GT . PASS FR=0.5;HP=8;NF=8;NR=3;PP=100.0;SC=ATTGTTTTCAGTTTTTTTTCT;TC=31;TR=11 GT:GL:GQ 0/1:-92.31,-34.03,-73.88:100 20 6346428 . C CTCTGTATG . PASS FR=0.5;HP=4;NF=5;NR=1;PP=45.0;SC=TATTCTCTATCTTTAATTTAA;TC=31;TR=6 GT:GL:GQ 0/1:-234.84,-191.03,-405.18:86 20 6349738 . TAC T . PASS FR=0.5;HP=1;NF=2;NR=1;PP=86.0;SC=GACACATACGTACACACACAC;TC=15;TR=3 GT:GL:GQ 0/1:-95.85,-65.71,-99.67:100 20 6364214 . ACTCTT A . PASS FR=0.5;HP=3;NF=5;NR=10;PP=100.0;SC=TCTTTACAAAACTCTTCTAGA;TC=36;TR=15 GT:GL:GQ 0/1:-210.3,-34.68,-236.21:100 20 6373382 . TCTACCTAC T . PASS FR=1.0;HP=1;NF=9;NR=8;PP=100.0;SC=ATTTCCTCTATCTACCTACCT;TC=38;TR=17 GT:GL:GQ 1/1:-510.97,-41.39,-20.72:100 20 6384835 . TACACACAC TAC,T . PASS FR=0.5,0.5;HP=2;NF=2,2;NR=7,1;PP=100.0,51.0;SC=GGATGACACATACACACACAC;TC=32;TR=9,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 6390974 . TAA T . PASS FR=1.0;HP=3;NF=19;NR=16;PP=100.0;SC=CTGCCTACCTTAAACACATAA;TC=42;TR=35 GT:GL:GQ 1/1:-376.88,-34.87,-5.52:100 20 6401100 . A AT . PASS FR=1.0;HP=9;NF=15;NR=9;PP=100.0;SC=TTCAAAAAGCATTTTTTTTTG;TC=34;TR=24 GT:GL:GQ 1/1:-148.27,-28.49,-8.51:100 20 6406758 . C CT . PASS FR=1.0;HP=7;NF=4;NR=16;PP=100.0;SC=TCTCTCCCCTCTTTTTTCTCC;TC=31;TR=20 GT:GL:GQ 1/1:-235.73,-83.65,-66.42:100 20 6410888 . CAGGGCTTGGCCCTGGAGT C . PASS FR=0.5;HP=1;NF=2;NR=4;PP=100.0;SC=TTCTCCACTCCAGGGCTTGGC;TC=24;TR=6 GT:GL:GQ 0/1:-188.53,-25.15,-199.92:100 20 6426272 . T TCTC,TTTC . PASS FR=0.5,0.5;HP=1;NF=11,6;NR=5,5;PP=100.0,100.0;SC=TTAAAAATTATCTCATTTCCT;TC=28;TR=16,11 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 6428681 . CA C . PASS FR=0.5009;HP=2;NF=4;NR=5;PP=100.0;SC=GGTGGGCCACCAACAGTGTCT;TC=20;TR=9 GT:GL:GQ 0/1:-312.7,-243.18,-248.77:27 20 6430456 . A AT . PASS FR=0.5;HP=10;NF=10;NR=6;PP=100.0;SC=TAATATTTAAATTTTTTTTTT;TC=35;TR=16 GT:GL:GQ 0/1:-143.54,-83.39,-119.6:100 20 6438083 . TA T . PASS FR=0.5;HP=7;NF=2;NR=8;PP=100.0;SC=AACAGATATATAAAAAATGCT;TC=21;TR=10 GT:GL:GQ 0/1:-86.86,-14.54,-78.87:100 20 6441903 . C CT . PASS FR=0.5;HP=9;NF=10;NR=11;PP=100.0;SC=AAATTAAATACTTTTTTTTTA;TC=43;TR=21 GT:GL:GQ 0/1:-221.48,-121.14,-137.31:73 20 6443155 . TTA T . PASS FR=0.5005;HP=5;NF=2;NR=2;PP=100.0;SC=AAACAGTTTTTTATATATATA;TC=14;TR=4 GT:GL:GQ 0/1:-162.1,-119.94,-126.23:30 20 6443546 . G GTA . PASS FR=0.5;HP=2;NF=1;NR=2;PP=100.0;SC=ATATATATGTGTATATATATA;TC=14;TR=3 GT:GL:GQ 0/1:-156.72,-103.24,-116.61:61 20 6447485 . C CA . PASS FR=0.5;HP=3;NF=4;NR=13;PP=100.0;SC=TTTTGAATTTCAAATATTTTC;TC=38;TR=17 GT:GL:GQ 0/1:-255.09,-105.01,-200.26:100 20 6448179 . TAATAA T . PASS FR=0.5;HP=5;NF=3;NR=4;PP=100.0;SC=TATCTCGAAATAATAAAATAA;TC=36;TR=7 GT:GL:GQ 0/1:-185.97,-96.1,-256.82:100 20 6456952 . ATT AT,A . PASS FR=0.5,0.5;HP=10;NF=7,8;NR=4,5;PP=100.0,100.0;SC=CAATGATGTCATTTTTTTTTT;TC=27;TR=11,13 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 6458185 . GA G . PASS FR=0.5;HP=10;NF=11;NR=4;PP=100.0;SC=AAATAAAAATGAAAAAAAAAA;TC=48;TR=15 GT:GL:GQ 0/1:-255.96,-202.85,-273.91:100 20 6459292 . G GA . PASS FR=0.5;HP=10;NF=2;NR=6;PP=49.0;SC=TATCCTATCAGAAAAAAAAAC;TC=30;TR=8 GT:GL:GQ 0/1:-83.74,-61.52,-111.1:99 20 6473904 . TAGGTGAAATTTTCTTTTCTGTTTTTTTAA T . PASS FR=0.5;HP=1;NF=2;NR=1;PP=100.0;SC=TCCCTAATTCTAGGTGAAATT;TC=25;TR=3 GT:GL:GQ 0/1:-202.85,-99.33,-502.66:100 20 6481086 . T TTGTC . PASS FR=1.0;HP=2;NF=7;NR=5;PP=100.0;SC=TTGTTCCTCTTTGTCAGAGCA;TC=21;TR=12 GT:GL:GQ 1/1:-268.34,-19.84,-4.6:100 20 6488178 . CTTG C . PASS FR=1.0;HP=2;NF=13;NR=13;PP=100.0;SC=AAGCTACTTGCTTGTTGTTGA;TC=32;TR=26 GT:GL:GQ 1/1:-335.98,-26.27,-4.81:100 20 6520175 . C CTT . PASS FR=1.0;HP=3;NF=12;NR=17;PP=100.0;SC=TTACTTAAGACTTTCTATTGA;TC=35;TR=29 GT:GL:GQ 1/1:-362.42,-32.47,-7.59:100 20 6524976 . GACTAC G . PASS FR=1.0;HP=2;NF=12;NR=13;PP=100.0;SC=CTATGAAATTGACTACACTAC;TC=32;TR=25 GT:GL:GQ 1/1:-403.49,-65.81,-45.47:100 20 6531643 . GT G . PASS FR=1.0;HP=4;NF=17;NR=11;PP=100.0;SC=CAGATAAAGTGTTTAATTCAT;TC=31;TR=28 GT:GL:GQ 1/1:-281.56,-58.08,-38.11:100 20 6544912 . CAGAT CAGATAGATAGATAGAT,C . PASS FR=0.5,0.5;HP=1;NF=1,1;NR=4,1;PP=100.0,100.0;SC=TATTCACTGCCAGATAGATAG;TC=24;TR=5,2 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 6548435 . A AAGAG . PASS FR=1.0;HP=2;NF=5;NR=8;PP=100.0;SC=GAGAAACAGAAAGAGAGAGAG;TC=33;TR=13 GT:GL:GQ 1/1:-316.58,-47.12,-29.98:100 20 6549783 . C CTT . PASS FR=1.0;HP=9;NF=3;NR=10;PP=100.0;SC=TGGTCCAGGCCTTTTTTTTTG;TC=24;TR=13 GT:GL:GQ 1/1:-145.52,-61.65,-53.62:66 20 6553955 . TTATA T . PASS FR=1.0;HP=3;NF=12;NR=6;PP=100.0;SC=ATTTTACATTTTATATATATA;TC=30;TR=18 GT:GL:GQ 1/1:-272.92,-35.6,-20.34:100 20 6563467 . CTAGGTAGGTAGG C . PASS FR=1.0;HP=1;NF=3;NR=6;PP=100.0;SC=ACATGCATTCCTAGGTAGGTA;TC=22;TR=9 GT:GL:GQ 1/1:-367.98,-150.14,-139.95:85 20 6565618 . CGTGT C . PASS FR=1.0;HP=2;NF=4;NR=3;PP=100.0;SC=TGTGTGTGTTCGTGTGTGTGT;TC=19;TR=7 GT:GL:GQ 1/1:-220.73,-126.68,-119.85:85 20 6565651 . G GTA . PASS FR=0.5286;HP=2;NF=3;NR=2;PP=100.0;SC=GTGTATATGTGTATATATATA;TC=16;TR=5 GT:GL:GQ 0/1:-258.66,-193.34,-195.57:12 20 6585232 . C CT . PASS FR=1.0;HP=2;NF=15;NR=16;PP=100.0;SC=ACAAACCCATCTCCTAAAATC;TC=33;TR=31 GT:GL:GQ 1/1:-314.24,-29.76,-6.91:100 20 6590623 . C CCTGCTT . PASS FR=1.0;HP=1;NF=17;NR=14;PP=100.0;SC=AGAGTTATCTCCTGCTGTCAT;TC=32;TR=31 GT:GL:GQ 1/1:-527.33,-38.07,-14.51:100 20 6603635 . C CA . PASS FR=1.0;HP=4;NF=12;NR=8;PP=100.0;SC=TTAGTCAAGCCAAAATCACAT;TC=27;TR=20 GT:GL:GQ 1/1:-325.58,-214.53,-199.34:100 20 6609608 . CTT C . PASS FR=1.0;HP=3;NF=10;NR=9;PP=100.0;SC=TGTTTTGATGCTTTCTGGCTT;TC=27;TR=19 GT:GL:GQ 1/1:-576.75,-576.47,-576.51:100 20 6609611 . T TGGAGGAGGA . PASS FR=1.0;HP=2;NF=9;NR=9;PP=100.0;SC=TTTGATGCTTTCTGGCTTGGA;TC=23;TR=18 GT:GL:GQ 1/1:-576.75,-311.9,-294.35:100 20 6644452 . C CTGTAG . PASS FR=1.0;HP=1;NF=14;NR=16;PP=100.0;SC=ATAAAAGGCACTGTAGCATAG;TC=35;TR=30 GT:GL:GQ 1/1:-563.91,-35.77,-9.44:100 20 6647434 . A ATC . PASS FR=1.0;HP=2;NF=4;NR=14;PP=100.0;SC=GGATACTGAGATTCTAAGTAG;TC=21;TR=18 GT:GL:GQ 1/1:-241.28,-23.07,-7.83:100 20 6655343 . T TG . PASS FR=1.0;HP=6;NF=6;NR=9;PP=100.0;SC=AGTCTAAAGATTTTTTTCTGG;TC=18;TR=15 GT:GL:GQ 1/1:-141.83,-27.31,-14.91:95 20 6655876 . GTATATA GTA,G . PASS FR=0.5,0.5;HP=1;NF=8,2;NR=11,1;PP=100.0,58.0;SC=TACATATATAGTATATATATA;TC=31;TR=19,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 6664331 . C CTG . PASS FR=1.0;HP=5;NF=5;NR=10;PP=100.0;SC=GGTTTAAAAACTGTGTGTGTG;TC=30;TR=15 GT:GL:GQ 1/1:-232.49,-35.13,-29.16:74 20 6668238 . CT C . PASS FR=1.0;HP=10;NF=7;NR=15;PP=100.0;SC=ACTGGAGAAACTTTTTTTTTT;TC=30;TR=22 GT:GL:GQ 1/1:-332.94,-279.88,-269.29:89 20 6677392 . CTGTGTG C . PASS FR=0.5;HP=2;NF=1;NR=6;PP=100.0;SC=GTGTGTGGCCCTGTGTGTGTG;TC=24;TR=7 GT:GL:GQ 0/1:-156.67,-56.12,-128.5:100 20 6687137 . CAT C . PASS FR=1.0;HP=2;NF=12;NR=13;PP=100.0;SC=ATAAGATCCACATGAGACAAT;TC=26;TR=25 GT:GL:GQ 1/1:-279.85,-22.16,-4.14:100 20 6690400 . T TG . PASS FR=1.0;HP=2;NF=22;NR=8;PP=100.0;SC=TTAATACATTTGTATGCCCTG;TC=31;TR=30 GT:GL:GQ 1/1:-315.1,-40.57,-19.1:100 20 6694813 . GAA G . PASS FR=1.0;HP=6;NF=5;NR=4;PP=100.0;SC=AAGAAAGAAAGAAAGAGAAAG;TC=13;TR=9 GT:GL:GQ 1/1:-119.78,-18.28,-9.43:64 20 6717401 . G GA . PASS FR=1.0;HP=10;NF=14;NR=6;PP=100.0;SC=CTCTCTTAAGGAAAAAAAAAA;TC=27;TR=20 GT:GL:GQ 1/1:-134.21,-33.86,-20.0:100 20 6723994 . A AAC . PASS FR=1.0;HP=4;NF=10;NR=3;PP=100.0;SC=CACATACAAAAACACACACAC;TC=23;TR=13 GT:GL:GQ 1/1:-174.48,-22.71,-13.76:74 20 6746236 . C CTTAT . PASS FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=CTGGAGACTACTTATTTATTT;TC=23;TR=6 GT:GL:GQ 0/1:-115.46,-26.87,-109.86:100 20 6759758 . A AAT . PASS FR=0.5;HP=2;NF=2;NR=3;PP=100.0;SC=TAAATACATAAATATATATAT;TC=21;TR=5 GT:GL:GQ 0/1:-98.2,-23.97,-51.3:100 20 6765134 . A AACAC . PASS FR=0.5;HP=1;NF=2;NR=5;PP=100.0;SC=TTGAGAATCTAACACACACAC;TC=25;TR=7 GT:GL:GQ 0/1:-145.56,-56.64,-151.12:100 pysam-0.23.0/tests/tabix_data/vcf/6.vcf000066400000000000000000015366501475062545500176470ustar00rootroot00000000000000##fileformat=VCFv4.1 ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##fileDate=20110531 ##reference=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz ##source=EricBanksValidationQC;fromGertonLunterValidationSelection #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00127 HG00128 HG00136 HG00137 HG00138 HG00139 HG00152 HG00156 HG00234 HG00235 HG00237 HG00242 HG00244 HG00262 HG01055 HG01079 NA19138 NA18974 NA18523 NA12717 NA19209 NA18577 NA18973 NA18943 NA12873 NA18623 NA18622 NA18948 NA19171 NA19204 NA06994 NA18563 NA18547 NA18861 NA18608 NA18995 NA10851 NA18976 NA18603 NA19200 HG01204 HG01191 HG01101 HG00146 HG00306 NA18985 HG00160 HG00635 HG00372 HG00357 HG00634 NA18541 NA18950 NA19759 HG00351 HG00257 HG00118 HG00336 HG00448 HG01354 NA18609 HG00428 HG00326 NA11894 NA18956 HG00173 HG00117 NA11893 HG01251 HG01441 HG01437 HG00182 HG00330 HG01060 HG00329 NA18960 NA18856 NA07346 NA18871 NA19057 NA18868 NA18636 NA12830 NA19007 NA18910 NA18874 NA19056 NA19064 NA19066 NA18487 NA18642 NA19236 NA07056 NA18637 NA19235 NA19309 NA19311 NA19334 NA19346 NA19347 NA19372 NA19376 NA19383 NA19384 NA19394 NA19428 NA19430 NA19451 NA19466 NA19313 NA19321 NA19324 NA19332 NA19390 NA19436 NA19439 NA19440 NA19463 NA19470 NA19471 NA19472 NA19676 NA19660 NA19661 NA19663 NA19722 NA19725 NA19728 NA19729 NA19731 NA19749 NA19755 NA19756 NA19758 NA19770 NA19773 NA19777 NA19780 NA19783 NA20525 NA20589 NA20765 NA20802 NA20804 NA18544 NA18602 NA18546 NA18610 NA18957 NA18615 NA18616 NA19010 NA18638 NA18639 NA18627 NA19072 NA18630 NA19074 NA19080 NA19081 NA19083 NA19085 NA19088 NA20287 NA19835 NA20276 NA19818 NA20278 NA20282 NA20342 NA20296 NA20314 NA20346 NA19712 NA19198 NA19108 NA18934 NA18916 NA18907 NA18917 NA06989 NA12058 NA12341 NA12546 NA12489 HG01197 NA18983 NA11843 NA11892 NA12749 NA12282 NA12751 NA18959 NA19331 NA19453 NA20537 NA12046 NA20515 NA20516 NA20521 NA20524 NA20528 NA20759 NA20768 NA20769 NA20774 NA20775 NA20783 NA20787 NA20790 NA20800 NA20819 NA20812 NA20505 NA20530 NA20540 NA20538 NA20581 NA20815 NA20544 NA20810 NA20807 NA20816 NA20504 NA20753 NA20502 NA12342 NA19150 NA19468 NA20336 NA19395 NA19257 NA19360 NA19700 NA18867 NA20317 NA18968 NA19107 HG00111 HG00108 NA19077 NA19684 NA18511 NA12044 NA19382 NA19457 NA18933 NA18923 NA18965 HG00141 NA20341 NA18740 HG00537 HG00346 HG01173 HG00702 HG00313 HG00150 NA18612 HG00339 NA12273 HG00250 NA18593 NA18621 HG00478 HG00251 HG01070 NA19160 HG00479 HG00608 NA18573 HG00375 NA19248 NA19093 HG01170 HG00534 HG01171 HG01522 NA18624 HG00683 HG01521 NA19005 NA20412 NA18971 HG00446 NA12748 HG00530 HG00690 HG01356 HG01516 NA20532 HG00344 HG00328 NA18542 HG00254 HG00321 HG00577 HG00656 HG00342 HG00524 HG00650 HG00557 HG00319 HG00457 HG00125 HG00578 HG00543 HG00638 HG00171 HG00699 HG00595 HG00187 HG00704 HG00533 HG00596 HG00268 HG01083 HG00651 HG01133 HG00671 HG00327 HG01148 HG00246 HG00672 HG00556 HG00436 HG00554 NA18633 NA20344 NA11993 NA07037 NA11930 HG01366 HG01389 HG00620 NA19740 HG00190 HG00419 NA18535 HG01495 NA18592 HG01497 HG00174 HG01140 NA12287 HG00689 HG01550 HG00334 HG01375 HG00637 NA18507 HG01113 NA18550 NA19129 HG01551 HG01462 HG00331 NA12413 HG01456 HG01360 HG00708 HG01350 HG00684 NA19099 HG00284 NA12399 NA12286 NA12777 HG00277 HG00266 NA19985 HG00353 HG01102 NA07347 NA07051 NA19900 NA18984 NA07048 HG00640 HG01066 NA12812 HG01174 HG01188 20 669442 . TG T 99 PASS SEQUENCING.AC=101;CallSetAC=116,128,155,72,71;CallSetAC2=2,2,2,2,2;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=7;HU=G;IH=1;TR=7;TU=G;Set=SAMTOOLS;SEQUENOM.AC=54 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 676148 . A AC 99 PASS SEQUENCING.AC=3;CallSetAC=0,0,3,0,0;CallSetAC2=0,0,1,0,0;Groups=DINDEL;HR=3;HU=A;IH=0;TR=6;TU=AAG;Set=DINDEL;SEQUENOM.AC=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 719486 . 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AAAAT A 99 PASS SEQUENCING.AC=8;CallSetAC=10,9,10,7,8;CallSetAC2=1,1,1,1,1;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=5;HU=A;IH=0;TR=5;TU=A;Set=BC;SEQUENOM.AC=6 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 3203741 . 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C CT 99 PASS SEQUENCING.AC=6;CallSetAC=14,3,9,6,7;CallSetAC2=1,0,0,0,0;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=6;HU=T;IH=1;TR=6;TU=T;Set=OX;SEQUENOM.AC=1 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 8233352 . TACTC T 99 PASS SEQUENCING.AC=146;CallSetAC=167,156,155,119,140;CallSetAC2=1,1,0,0,1;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=2;HU=T;IH=0;TR=2;TU=T;Set=SAMTOOLS;SEQUENOM.AC=56 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 20 8504000 . 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GGGA G 99 PASS SEQUENCING.AC=2;CallSetAC=0,3,5,3,3;CallSetAC2=0,1,1,1,1;Groups=BI,DINDEL,OX,SAMTOOLS;HR=4;HU=G;IH=0;TR=7;TU=AGG;Set=DINDEL;SEQUENOM.AC=3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 13128894 . 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TA T 99 PASS SEQUENCING.AC=7;CallSetAC=0,0,7,0,0;CallSetAC2=0,0,1,0,0;Groups=DINDEL;HR=2;HU=A;IH=0;TR=2;TU=A;Set=DINDEL;SEQUENOM.AC=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 13960028 . TC T 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=8;CallSetAC=10,0,0,0,0;CallSetAC2=1,0,0,0,0;Groups=BC;HR=3;HU=T;IH=0;TR=3;TU=T;Set=BC;SEQUENOM.AC=188 GT 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 . 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 . . 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 . 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 20 14159734 . 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TG T 99 PASS SEQUENCING.AC=50;CallSetAC=58,58,56,47,53;CallSetAC2=2,2,2,1,2;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=2;HU=T;IH=0;TR=7;TU=GTT;Set=BC;SEQUENOM.AC=34 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 15703503 . TG T 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=9;CallSetAC=11,0,0,0,0;CallSetAC2=1,0,0,0,0;Groups=BC;HR=4;HU=T;IH=0;TR=4;TU=T;Set=BC;SEQUENOM.AC=87 GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 . 0/0 0/0 0/1 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/1 0/0 0/1 0/0 . 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 . 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 15871330 . AG A 99 PASS SEQUENCING.AC=1;CallSetAC=2,2,2,2,2;CallSetAC2=0,0,1,0,0;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=3;HU=A;IH=0;TR=3;TU=A;Set=BC;SEQUENOM.AC=1 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16016504 . TA T 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=17;CallSetAC=4,36,0,18,0;CallSetAC2=0,1,0,0,0;Groups=BC,BI,OX;HR=1;HU=A;IH=0;TR=1;TU=A;Set=OX;SEQUENOM.AC=578 GT 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 . 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 20 16192114 . AT A 99 INCORRECT_SEQUENOM_CALLS SEQUENCING.AC=45;CallSetAC=52,49,48,42,48;CallSetAC2=3,2,3,2,3;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=3;HU=A;IH=0;TR=4;TU=CT;Set=BC;SEQUENOM.AC=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16259934 . 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TA T 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=18;CallSetAC=0,0,0,19,0;CallSetAC2=0,0,0,1,0;Groups=OX;HR=2;HU=T;IH=0;TR=2;TU=T;Set=OX;SEQUENOM.AC=682 GT 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 . 0/1 . 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 20 17473782 . 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CA C 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=13;CallSetAC=12,49,0,14,0;CallSetAC2=1,0,0,0,0;Groups=BC,BI,OX;HR=2;HU=C;IH=0;TR=2;TU=C;Set=OX;SEQUENOM.AC=432 GT 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 1/1 0/0 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/0 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 . 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 1/1 . 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 20 21968507 . AC A 99 PASS SEQUENCING.AC=10;CallSetAC=0,12,10,12,7;CallSetAC2=0,1,0,0,0;Groups=BI,DINDEL,OX,SAMTOOLS;HR=5;HU=C;IH=0;TR=5;TU=C;Set=DINDEL;SEQUENOM.AC=7 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 22434333 . 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TATC T 99 PASS SEQUENCING.AC=12;CallSetAC=14,15,18,11,14;CallSetAC2=1,1,0,0,1;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=1;HU=A;IH=0;TR=4;TU=AT;Set=OX;SEQUENOM.AC=6 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23200197 . ATT A 99 PASS SEQUENCING.AC=1;CallSetAC=0,0,0,0,1;CallSetAC2=0,0,0,0,1;Groups=SAMTOOLS;HR=4;HU=T;IH=0;TR=4;TU=T;Set=SAMTOOLS;SEQUENOM.AC=1 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23293728 . 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CATA C 99 PASS SEQUENCING.AC=1;CallSetAC=0,1,2,1,1;CallSetAC2=0,1,2,1,1;Groups=BI,DINDEL,OX,SAMTOOLS;HR=1;HU=A;IH=0;TR=7;TU=AAT;Set=SAMTOOLS;SEQUENOM.AC=1 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 25905250 . GT G 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=56;CallSetAC=0,58,57,0,0;CallSetAC2=0,1,1,0,0;Groups=BI,DINDEL;HR=6;HU=T;IH=1;TR=6;TU=T;Set=DINDEL;SEQUENOM.AC=764 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 . 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 20 29589873 . 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CAT C 99 PASS SEQUENCING.AC=8;CallSetAC=8,13,12,9,10;CallSetAC2=0,1,1,0,0;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=1;HU=A;IH=0;TR=5;TU=AC;Set=SAMTOOLS;SEQUENOM.AC=7 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37678954 . 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AAG A 99 PASS SEQUENCING.AC=44;CallSetAC=52,57,44,21,47;CallSetAC2=1,1,2,1,1;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=2;HU=A;IH=0;TR=6;TU=AG;Set=SAMTOOLS;SEQUENOM.AC=29 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37836124 . AAAT A 99 PASS SEQUENCING.AC=3;CallSetAC=4,4,6,3,3;CallSetAC2=1,1,1,0,0;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=4;HU=A;IH=0;TR=4;TU=A;Set=BC;SEQUENOM.AC=3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37954797 . A AGT 99 PASS SEQUENCING.AC=110;CallSetAC=126,0,0,0,0;CallSetAC2=1,0,0,0,0;Groups=BC;HR=1;HU=T;IH=0;TR=5;TU=AT;Set=BC;SEQUENOM.AC=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37962643 . T TAA 99 PASS SEQUENCING.AC=370;CallSetAC=395,424,394,367,423;CallSetAC2=4,4,4,3,3;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=2;HU=A;IH=0;TR=4;TU=AT;Set=DINDEL;SEQUENOM.AC=178 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/0 1/1 1/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 . 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 20 38336199 . TA T 99 PASS SEQUENCING.AC=1;CallSetAC=0,2,4,2,2;CallSetAC2=0,1,1,1,1;Groups=BI,DINDEL,OX,SAMTOOLS;HR=2;HU=T;IH=0;TR=2;TU=T;Set=SAMTOOLS;SEQUENOM.AC=1 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 38495835 . T TA 99 AMBIGUOUS_SEQUENOM_CALLS SEQUENCING.AC=147;CallSetAC=0,0,0,153,0;CallSetAC2=0,0,0,1,0;Groups=OX;HR=3;HU=A;IH=0;TR=4;TU=AT;Set=OX;SEQUENOM.AC=14 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 38696054 . GAAGA G 99 PASS SEQUENCING.AC=2;CallSetAC=0,3,5,3,3;CallSetAC2=0,1,1,1,1;Groups=BI,DINDEL,OX,SAMTOOLS;HR=2;HU=A;IH=0;TR=6;TU=AAG;Set=SAMTOOLS;SEQUENOM.AC=3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 38784318 . CCTT C 99 PASS SEQUENCING.AC=17;CallSetAC=20,19,19,15,17;CallSetAC2=2,1,1,1,1;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=2;HU=C;IH=0;TR=7;TU=CTT;Set=SAMTOOLS;SEQUENOM.AC=7 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 39042026 . 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AG A 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=24;CallSetAC=3,51,0,25,0;CallSetAC2=0,2,0,1,0;Groups=BC,BI,OX;HR=2;HU=A;IH=0;TR=4;TU=GT;Set=OX;SEQUENOM.AC=688 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 . 1/1 . 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/0 0/0 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 . 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 20 39607037 . 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AC A 99 PASS SEQUENCING.AC=1;CallSetAC=0,1,14,1,1;CallSetAC2=0,0,2,0,0;Groups=BI,DINDEL,OX,SAMTOOLS;HR=3;HU=A;IH=0;TR=3;TU=A;Set=OX;SEQUENOM.AC=1 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 51838824 . GA G 99 PASS SEQUENCING.AC=1;CallSetAC=2,0,0,0,0;CallSetAC2=1,0,0,0,0;Groups=BC;HR=3;HU=G;IH=0;TR=4;TU=AC;Set=BC;SEQUENOM.AC=4 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 51961394 . 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GT G 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=8;CallSetAC=4,15,0,0,0;CallSetAC2=0,1,0,0,0;Groups=BC,BI;HR=1;HU=T;IH=0;TR=1;TU=T;Set=BC;SEQUENOM.AC=172 GT 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 20 55264363 . AG A 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=12;CallSetAC=7,0,0,19,0;CallSetAC2=1,0,0,0,0;Groups=BC,OX;HR=1;HU=G;IH=0;TR=5;TU=AG;Set=OX;SEQUENOM.AC=530 GT 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/0 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 1/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 . 1/1 . 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 20 55608811 . 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##reference=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz ##source=EricBanksValidationQC;fromGoncaloAbecasisValidationSelection #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00127 HG00128 HG00136 HG00137 HG00138 HG00139 HG00152 HG00156 HG00234 HG00235 HG00237 HG00242 HG00244 HG00262 HG01055 HG01079 NA19138 NA18974 NA18523 NA12717 NA19209 NA18577 NA18973 NA18943 NA12873 NA18623 NA18622 NA18948 NA19171 NA19204 NA06994 NA18563 NA18547 NA18861 NA18608 NA12282 NA12751 NA18959 NA19331 NA19453 NA20537 NA12046 NA20515 NA20516 NA20521 NA20524 NA20528 NA20759 NA20768 NA20769 NA20774 NA20775 NA20783 NA20787 NA20790 NA20800 NA20819 NA20812 NA20505 NA20530 NA20540 NA20538 NA20581 NA20815 NA20544 NA20810 NA20807 NA20816 NA20504 NA20753 NA20502 NA12342 NA19150 NA19468 NA20336 NA19395 NA19257 NA19360 NA19700 NA18867 NA20317 NA18968 NA19107 HG00111 HG00108 NA19077 NA19684 NA18511 NA12044 NA19382 NA19457 NA18933 NA18923 NA18965 HG00141 NA20341 NA18740 HG00537 HG00346 HG01173 HG00702 HG00313 HG00150 NA18612 HG00339 NA12273 HG00250 NA18593 NA18621 HG00478 HG00251 HG01070 NA19160 NA18995 NA10851 NA18976 NA18603 NA19200 HG01204 HG01191 HG01101 HG00146 HG00306 NA18985 HG00160 HG00635 HG00372 HG00357 HG00634 NA18541 NA18950 NA19759 HG00351 HG00257 HG00118 HG00336 HG00448 HG01354 NA18609 HG00428 HG00326 NA11894 NA18956 HG00173 HG00117 NA11893 HG01251 HG01441 HG01437 HG00182 HG00330 HG01060 HG00329 NA18960 NA18856 NA07346 NA18871 NA19057 NA18868 NA18636 NA12830 NA19007 NA18910 NA18874 NA19056 NA19064 NA19066 NA18487 NA18642 NA19236 NA07056 NA18637 NA19235 NA19309 NA19311 NA19334 NA19346 NA19347 NA19372 NA19376 NA19383 NA19384 NA19394 NA19428 NA19430 NA19451 NA19466 NA19313 NA19321 NA19324 NA19332 HG00479 HG00608 NA18573 HG00375 NA19248 NA19093 HG01170 HG00534 HG01171 HG01522 NA18624 HG00683 HG01521 NA19005 NA20412 NA18971 HG00446 NA12748 HG00530 HG00690 HG01356 HG01516 NA20532 HG00344 HG00328 NA18542 HG00254 HG00321 HG00577 HG00656 HG00342 HG00524 HG00650 HG00557 HG00319 HG00457 HG00125 HG00578 HG00543 HG00638 HG00171 HG00699 HG00595 HG00187 HG00704 HG00533 HG00596 HG00268 HG01083 HG00651 HG01133 HG00671 HG00327 HG01148 HG00246 HG00672 HG00556 HG00436 HG00554 NA18633 NA20344 NA11993 NA07037 NA11930 HG01366 HG01389 HG00620 NA19740 HG00190 HG00419 NA18535 HG01495 NA18592 HG01497 HG00174 HG01140 NA12287 HG00689 HG01550 HG00334 HG01375 HG00637 NA18507 HG01113 NA18550 NA19129 HG01551 HG01462 HG00331 NA12413 HG01456 HG01360 HG00708 HG01350 HG00684 NA19099 HG00284 NA12399 NA12286 NA12777 HG00277 HG00266 NA19985 HG00353 HG01102 NA07347 NA07051 NA19900 NA18984 NA07048 HG00640 HG01066 NA12812 HG01174 HG01188 NA19390 NA19436 NA19439 NA19440 NA19463 NA19470 NA19471 NA19472 NA19676 NA19660 NA19661 NA19663 NA19722 NA19725 NA19728 NA19729 NA19731 NA19749 NA19755 NA19756 NA19758 NA19770 NA19773 NA19777 NA19780 NA19783 NA20525 NA20589 NA20765 NA20802 NA20804 NA18544 NA18602 NA18546 NA18610 NA18957 NA18615 NA18616 NA19010 NA18638 NA18639 NA18627 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G T 10 NOT_DESIGNED SRC=VQSR-ONLY 20 62888718 . T C 57 POLYMORPHIC_SAMPLES_FAILED BCM.AC=1;SEQUENOM.AC=0;SRC=VQSR+2-OF-7 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 62918298 . G A 33 NOT_DESIGNED SRC=VQSR+2-OF-7 20 62961477 . T C 17 AMBIGUOUS_SEQUENOM_CALLS SEQUENOM.AC=0;SRC=VQSR+2-OF-7 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 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##ValidationMetrics_PolymorphicPassingRecords="195 (75%)" ##ValidationMetrics_RecordsPassingFilters="258 (87%)" ##ValidationMetrics_RecordsProcessed=296 ##ValidationMetrics_SamplesAssayed=383 ##VariantValidationAssessor="analysis_type=VariantValidationAssessor input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[rawData/plink.renamed.sorted.fixed.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub maxHardy=20.0 maxNoCall=0.05 maxHomVar=1.1" ##source=PLINK #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00127 HG00128 HG00136 HG00137 HG00138 HG00139 HG00152 HG00156 HG00234 HG00235 HG00237 HG00242 HG00244 HG00262 HG01055 HG01079 NA19138 NA18974 NA18523 NA12717 NA19209 NA18577 NA18973 NA18943 NA12873 NA18623 NA18622 NA18948 NA19171 NA19204 NA06994 NA18563 NA18547 NA18861 NA18608 NA18995 NA10851 NA18976 NA18603 NA19200 HG01204 HG01191 HG01101 HG00146 HG00306 NA18985 HG00160 HG00635 HG00372 HG00357 HG00634 NA18541 NA18950 NA19759 HG00351 HG00257 HG00118 HG00336 HG00448 HG01354 NA18609 HG00428 HG00326 NA11894 NA18956 HG00173 HG00117 NA11893 HG01251 HG01441 HG01437 HG00182 HG00330 HG01060 HG00329 NA18960 NA18856 NA07346 NA18871 NA19057 NA18868 NA18636 NA12830 NA19007 NA18910 NA18874 NA19056 NA19064 NA19066 NA18487 NA18642 NA19236 NA07056 NA18637 NA19235 NA19309 NA19311 NA19334 NA19346 NA19347 NA19372 NA19376 NA19383 NA19384 NA19394 NA19428 NA19430 NA19451 NA19466 NA19313 NA19321 NA19324 NA19332 NA19390 NA19436 NA19439 NA19440 NA19463 NA19470 NA19471 NA19472 NA19676 NA19660 NA19661 NA19663 NA19722 NA19725 NA19728 NA19729 NA19731 NA19749 NA19755 NA19756 NA19758 NA19770 NA19773 NA19777 NA19780 NA19783 NA20525 NA20589 NA20765 NA20802 NA20804 NA18544 NA18602 NA18546 NA18610 NA18957 NA18615 NA18616 NA19010 NA18638 NA18639 NA18627 NA19072 NA18630 NA19074 NA19080 NA19081 NA19083 NA19085 NA19088 NA20287 NA19835 NA20276 NA19818 NA20278 NA20282 NA20342 NA20296 NA20314 NA20346 NA19712 NA19198 NA19108 NA18934 NA18916 NA18907 NA18917 NA06989 NA12058 NA12341 NA12546 NA12489 HG01197 NA18983 NA11843 NA11892 NA12749 NA12282 NA12751 NA18959 NA19331 NA19453 NA20537 NA12046 NA20515 NA20516 NA20521 NA20524 NA20528 NA20759 NA20768 NA20769 NA20774 NA20775 NA20783 NA20787 NA20790 NA20800 NA20819 NA20812 NA20505 NA20530 NA20540 NA20538 NA20581 NA20815 NA20544 NA20810 NA20807 NA20816 NA20504 NA20753 NA20502 NA12342 NA19150 NA19468 NA20336 NA19395 NA19257 NA19360 NA19700 NA18867 NA20317 NA18968 NA19107 HG00111 HG00108 NA19077 NA19684 NA18511 NA12044 NA19382 NA19457 NA18933 NA18923 NA18965 HG00141 NA20341 NA18740 HG00537 HG00346 HG01173 HG00702 HG00313 HG00150 NA18612 HG00339 NA12273 HG00250 NA18593 NA18621 HG00478 HG00251 HG01070 NA19160 HG00479 HG00608 NA18573 HG00375 NA19248 NA19093 HG01170 HG00534 HG01171 HG01522 NA18624 HG00683 HG01521 NA19005 NA20412 NA18971 HG00446 NA12748 HG00530 HG00690 HG01356 HG01516 NA20532 HG00344 HG00328 NA18542 HG00254 HG00321 HG00577 HG00656 HG00342 HG00524 HG00650 HG00557 HG00319 HG00457 HG00125 HG00578 HG00543 HG00638 HG00171 HG00699 HG00595 HG00187 HG00704 HG00533 HG00596 HG00268 HG01083 HG00651 HG01133 HG00671 HG00327 HG01148 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A AC . 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A AAGAT . 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CT C . 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C CT . 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AGCC A . 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A AG . 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T TC . 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AT A . 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C CAA . 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T TC . 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GTC G . 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A AT . 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ATC A . 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A AGT . 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C CA . 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C CA . 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T TG . 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A AG . 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TATTA T . PASS AC=0;AN=762;HW=0.00;HetPct=0.0;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 61531765 . AG A . PASS AC=0;AN=766;HW=0.00;HetPct=0.0;HomRefPct=100.0;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 pysam-0.23.0/tests/tabix_data/vcf/9.vcf000066400000000000000000002723361475062545500176470ustar00rootroot00000000000000##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT DNA_pool_A chr1 1281168 . A G 14 . DP=37;AF1=0.6243;CI95=0.5,1;DP4=4,0,6,0;MQ=15;PV4=1,0.027,1,1 PL:GT:GQ 43,0,4:0/1:6 chr1 1281205 . T C 26 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 58,9,0:1/1:63 chr1 1281206 . G C 25 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 57,9,0:1/1:63 chr1 1922737 . G C 13.2 . DP=21;AF1=1;CI95=1,1;DP4=0,0,0,21;MQ=22 PL:GT:GQ 46,63,0:1/1:99 chr1 21197513 . A G 55.1 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=41 PL:GT:GQ 88,21,0:1/1:84 chr1 21343209 . T C 5.45 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=14 PL:GT:GQ 37,51,0:1/1:99 chr1 22097362 . T C 4.75 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 35,9,0:1/1:63 chr1 22254012 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 22650927 . G A 48.1 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=24 PL:GT:GQ 81,21,0:1/1:84 chr1 23535401 . C T 40.4 . DP=25;AF1=1;CI95=0.5,1;DP4=0,16,0,5;MQ=19;PV4=1,0.2,1,1 PL:GT:GQ 73,13,0:1/1:65 chr1 23543855 . T C 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44 PL:GT:GQ 82,18,0:1/1:90 chr1 24245107 . C G 32 . DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,1,1 PL:GT:GQ 62,0,35:0/1:38 chr1 24274412 . G C 39.5 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=32 PL:GT:GQ 72,12,0:1/1:72 chr1 36529832 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr1 37788090 . A G 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr1 43120440 . C T 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=49;PV4=1,1,1,1 PL:GT:GQ 64,0,31:0/1:34 chr1 43980466 . C T 43 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=19 PL:GT:GQ 76,45,0:1/1:99 chr1 46047795 . T C 29.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=31 PL:GT:GQ 62,18,0:1/1:90 chr1 48860309 . C T 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=46 PL:GT:GQ 141,18,0:1/1:90 chr1 49415599 . T C 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 34,6,0:1/1:49 chr1 51601816 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 51955459 . G C 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr1 68479569 . T G 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 43,6,0:1/1:49 chr1 69032455 . A G 15.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 47,9,0:1/1:63 chr1 71888225 . G T 9.31 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr1 72381528 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr1 82004013 . A G 37.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 70,12,0:1/1:72 chr1 86289622 . C T 18 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 50,9,0:1/1:63 chr1 90267663 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45 PL:GT:GQ 54,9,0:1/1:63 chr1 92699542 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr1 94867317 . G A 26.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 58,6,0:1/1:49 chr1 96428713 . C G 3.98 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=27 PL:GT:GQ 33,6,0:1/1:49 chr1 100466329 . G C 4.85 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=22 PL:GT:GQ 36,18,0:1/1:90 chr1 101909281 . G A 70 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=46;PV4=1,1,0.096,1 PL:GT:GQ 100,0,88:0/1:91 chr1 106216572 . T A 22 . DP=18;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=21 PL:GT:GQ 55,48,0:1/1:99 chr1 107901770 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 40,6,0:1/1:49 chr1 108431179 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=41 PL:GT:GQ 155,24,0:1/1:96 chr1 112005344 . C T 99 . DP=52;AF1=1;CI95=1,1;DP4=7,0,27,0;MQ=44;PV4=1,1,1,1 PL:GT:GQ 196,25,0:1/1:99 chr1 116625452 . C T 36 . DP=44;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,20;MQ=49;PV4=1,2.3e-69,0.42,1 PL:GT:GQ 66,0,179:0/1:69 chr1 118060710 . G T 6.98 . DP=8;AF1=0.4999;CI95=0.5,0.5;DP4=4,0,3,0;MQ=47;PV4=1,0.0071,1,1 PL:GT:GQ 36,0,73:0/1:39 chr1 118198177 . A G 15.9 . DP=23;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 47,6,0:1/1:49 chr1 118586346 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr1 120809555 . G A 20 . DP=8;AF1=0.5;CI95=0.5,0.5;DP4=6,0,2,0;MQ=46;PV4=1,1,1,1 PL:GT:GQ 50,0,106:0/1:53 chr1 130723110 . C A 20.7 . DP=8;AF1=0.5939;CI95=0.5,1;DP4=0,6,0,2;MQ=26;PV4=1,1,1,1 PL:GT:GQ 50,0,5:0/1:7 chr1 133979895 . T C 14.9 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 46,6,0:1/1:49 chr1 134977940 . C T 30 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,1,0.26,1 PL:GT:GQ 60,0,31:0/1:34 chr1 141768589 . G A 18.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=4,0,4,0;MQ=51;PV4=1,2.7e-05,1,1 PL:GT:GQ 48,0,100:0/1:51 chr1 141768590 . G A 22 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=2,0,4,0;MQ=50;PV4=1,0.0033,1,1 PL:GT:GQ 52,0,40:0/1:43 chr1 146506051 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43 PL:GT:GQ 76,9,0:1/1:63 chr1 150997009 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr1 162915612 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 168455400 . A G 4.12 . DP=28;AF1=1;CI95=1,1;DP4=0,0,0,27;MQ=10 PL:GT:GQ 35,81,0:1/1:99 chr1 172784744 . T C 17.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 49,6,0:1/1:49 chr1 183627307 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 185789457 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr1 187081827 . T C 4.77 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=17 PL:GT:GQ 36,30,0:1/1:99 chr1 188468339 . C T 33 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=24 PL:GT:GQ 66,39,0:1/1:99 chr1 188595435 . C T 41.8 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr1 188670561 . G C 3.55 . DP=22;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=18 PL:GT:GQ 34,27,0:1/1:99 chr1 188924877 . G A 6.2 . DP=10;AF1=0.9999;CI95=0.5,1;DP4=2,0,3,0;MQ=21;PV4=1,1,1,0.3 PL:GT:GQ 35,3,0:1/1:41 chr1 190536295 . G A 68 . DP=38;AF1=1;CI95=1,1;DP4=0,0,36,0;MQ=18 PL:GT:GQ 101,108,0:1/1:99 chr1 191129408 . T A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr1 195937816 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr1 198857619 . T C 89 . DP=61;AF1=0.5;CI95=0.5,0.5;DP4=0,38,0,17;MQ=30;PV4=1,0.032,1,1 PL:GT:GQ 119,0,139:0/1:99 chr1 199057483 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 44,6,0:1/1:49 chr1 200133619 . G C 5.83 . DP=49;AF1=1;CI95=0.5,1;DP4=2,0,8,0;MQ=17;PV4=1,0.059,1,0.2 PL:GT:GQ 37,12,0:1/1:72 chr1 200729661 . A T 36 . DP=15;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=27 PL:GT:GQ 69,42,0:1/1:99 chr1 201374519 . T C 69.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39 PL:GT:GQ 102,12,0:1/1:72 chr1 202811668 . G A 20.2 . DP=4;AF1=0.5163;CI95=0.5,1;DP4=0,1,0,3;MQ=24;PV4=1,1,1,1 PL:GT:GQ 50,0,12:0/1:15 chr1 202960650 . C T 16.6 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27 PL:GT:GQ 49,12,0:1/1:72 chr1 205686638 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr1 205949857 . A G 3.14 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=21 PL:GT:GQ 33,15,0:1/1:75 chr1 209806643 . A G 13.2 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=21 PL:GT:GQ 46,24,0:1/1:96 chr1 209871501 . C T 25 . DP=12;AF1=0.5;CI95=0.5,0.5;DP4=5,0,4,0;MQ=41;PV4=1,7.7e-06,1,1 PL:GT:GQ 55,0,84:0/1:58 chr1 211051323 . G A 99 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=49 PL:GT:GQ 176,24,0:1/1:96 chr1 211389716 . C T 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 43,6,0:1/1:49 chr1 211868415 . G A 3.54 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=14 PL:GT:GQ 34,33,0:1/1:99 chr1 211914531 . C T 84.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=46;PV4=1,1,1,1 PL:GT:GQ 116,7,0:1/1:57 chr1 214691313 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr1 215184650 . C T 40.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 72,6,0:1/1:49 chr1 215995258 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr1 217031394 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 217986960 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 76,9,0:1/1:63 chr1 218086681 . A G 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34 PL:GT:GQ 142,27,0:1/1:99 chr1 218546019 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 218632417 . G T 17.1 . DP=19;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=26 PL:GT:GQ 50,21,0:1/1:84 chr1 218833355 . C G 23 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=5,0,2,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 53,0,63:0/1:56 chr1 219303186 . T C 7.79 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=12 PL:GT:GQ 40,75,0:1/1:99 chr1 219517634 . G A 26.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42 PL:GT:GQ 59,12,0:1/1:72 chr1 219590158 . T C 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 33,12,0:1/1:72 chr1 219709853 . A T 99 . DP=124;AF1=0.5;CI95=0.5,0.5;DP4=80,0,41,0;MQ=44;PV4=1,0.26,1,1 PL:GT:GQ 143,0,156:0/1:99 chr1 222457988 . A G 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23 PL:GT:GQ 42,6,0:1/1:49 chr1 222477914 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr1 223010233 . A G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr1 223796360 . G A 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=21 PL:GT:GQ 37,6,0:1/1:49 chr1 224273784 . A T 14.2 . DP=18;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=15 PL:GT:GQ 47,30,0:1/1:99 chr1 224454685 . C T 46.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32 PL:GT:GQ 79,15,0:1/1:75 chr1 224514706 . G C 21 . DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=19 PL:GT:GQ 54,114,0:1/1:99 chr1 224515793 . C T 99 . DP=26;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=45 PL:GT:GQ 211,78,0:1/1:99 chr1 224692969 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 40,6,0:1/1:49 chr1 225607249 . A G 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,1,0,1 PL:GT:GQ 64,0,31:0/1:34 chr1 226923918 . C A 29.1 . DP=52;AF1=1;CI95=0.5,1;DP4=0,2,0,10;MQ=27;PV4=1,1,1,1 PL:GT:GQ 62,18,0:1/1:90 chr1 227125189 . T C 56.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=41 PL:GT:GQ 89,12,0:1/1:72 chr1 227133712 . A T 20.1 . DP=26;AF1=0.5;CI95=0.5,0.5;DP4=11,0,10,0;MQ=23;PV4=1,1,0.48,1 PL:GT:GQ 50,0,39:0/1:42 chr1 227943954 . G C 47 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37 PL:GT:GQ 79,9,0:1/1:63 chr1 227943974 . G A 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34 PL:GT:GQ 66,12,0:1/1:72 chr1 228067480 . A G 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45 PL:GT:GQ 75,15,0:1/1:75 chr1 228067510 . A G 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45 PL:GT:GQ 140,15,0:1/1:75 chr1 228088778 . C T 6.79 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23 PL:GT:GQ 37,6,0:1/1:49 chr1 228117888 . A C 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 45,6,0:1/1:49 chr1 228139641 . T C 44.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 77,12,0:1/1:72 chr1 228577146 . T C 26 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,14;MQ=22;PV4=1,1,1,0.027 PL:GT:GQ 56,0,77:0/1:59 chr1 229001369 . C A 45 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 77,9,0:1/1:63 chr1 229001386 . C T 8.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 39,6,0:1/1:49 chr1 229348080 . T C 18.1 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=40;PV4=1,0.33,0.17,0.33 PL:GT:GQ 48,0,31:0/1:34 chr1 229439710 . C T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=32 PL:GT:GQ 66,12,0:1/1:72 chr1 229655149 . T C 30 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=30 PL:GT:GQ 63,24,0:1/1:96 chr1 229660873 . C G 81 . DP=28;AF1=0.5;CI95=0.5,0.5;DP4=0,20,0,7;MQ=36;PV4=1,1,1,1 PL:GT:GQ 111,0,120:0/1:99 chr2a 3661005 . C G 24 . DP=13;AF1=0.5001;CI95=0.5,0.5;DP4=7,0,4,0;MQ=27;PV4=1,1.1e-05,1,1 PL:GT:GQ 54,0,34:0/1:37 chr2a 4140063 . G A 81 . DP=26;AF1=0.6671;CI95=0.5,1;DP4=18,0,8,0;MQ=24;PV4=1,8.3e-09,1,1 PL:GT:GQ 110,0,3:0/1:5 chr2a 4248440 . T C 20 . DP=28;AF1=0.5;CI95=0.5,0.5;DP4=11,0,7,0;MQ=25;PV4=1,1,0.47,1 PL:GT:GQ 50,0,92:0/1:53 chr2a 4707656 . A G 63 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 95,9,0:1/1:63 chr2a 5194801 . G A 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=24 PL:GT:GQ 38,6,0:1/1:49 chr2a 14111103 . A G 7.84 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=20 PL:GT:GQ 40,21,0:1/1:84 chr2a 17799746 . A G 11.3 . DP=5;AF1=0.5001;CI95=0.5,0.5;DP4=0,3,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 41,0,35:0/1:37 chr2a 24728910 . G A 45.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28 PL:GT:GQ 78,15,0:1/1:75 chr2a 29627939 . G T 5.44 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=27 PL:GT:GQ 36,9,0:1/1:63 chr2a 31373164 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr2a 33935228 . T C 41.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr2a 36311856 . G A 99 . DP=30;AF1=1;CI95=1,1;DP4=0,0,0,29;MQ=44 PL:GT:GQ 213,87,0:1/1:99 chr2a 39281204 . T C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr2a 41087565 . C T 74.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=38 PL:GT:GQ 107,12,0:1/1:72 chr2a 45574768 . C A 11.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=18 PL:GT:GQ 43,9,0:1/1:63 chr2a 55464464 . T C 26.1 . DP=7;AF1=0.9966;CI95=0.5,1;DP4=5,0,2,0;MQ=26;PV4=1,1,1,1 PL:GT:GQ 55,1,0:1/1:23 chr2a 63107673 . T A 70.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34 PL:GT:GQ 103,12,0:1/1:72 chr2a 63141732 . A T 22.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 54,6,0:1/1:49 chr2a 63141910 . G A 3.41 . DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr2a 63141911 . C T 9.55 . DP=16;AF1=0.5031;CI95=0.5,0.5;DP4=0,2,0,3;MQ=33;PV4=1,0.43,1,1 PL:GT:GQ 39,0,19:0/1:22 chr2a 63143543 . C T 28 . DP=18;AF1=1;CI95=1,1;DP4=0,1,0,17;MQ=16;PV4=1,1,1,1 PL:GT:GQ 61,42,0:1/1:99 chr2a 66419805 . G A 3.69 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 34,15,0:1/1:75 chr2a 66563922 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr2a 67719136 . C T 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 71,6,0:1/1:49 chr2a 72781453 . A C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr2a 76733211 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr2a 78190502 . A C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr2a 85021209 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr2a 88554861 . A T 39 . DP=74;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=46;PV4=1,1,1,1 PL:GT:GQ 69,0,92:0/1:72 chr2a 88554877 . A G 92 . DP=90;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,13;MQ=41;PV4=1,0.3,1,1 PL:GT:GQ 122,0,128:0/1:99 chr2a 88824857 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr2a 93546675 . C T 26 . DP=6;AF1=0.5;CI95=0.5,0.5;DP4=4,0,2,0;MQ=46;PV4=1,1,1,1 PL:GT:GQ 56,0,87:0/1:59 chr2a 94788853 . A G 34.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 67,15,0:1/1:75 chr2a 96738146 . T C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr2a 102737384 . A G 12.3 . DP=18;AF1=1;CI95=1,1;DP4=0,0,18,0;MQ=11 PL:GT:GQ 45,54,0:1/1:99 chr2a 103407172 . A G 35 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=19 PL:GT:GQ 68,24,0:1/1:96 chr2a 105774580 . T G 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=30 PL:GT:GQ 135,39,0:1/1:99 chr2a 106376301 . C G 24.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19 PL:GT:GQ 57,18,0:1/1:90 chr2a 106376315 . C T 8.75 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19 PL:GT:GQ 41,18,0:1/1:90 chr2a 112422267 . C T 30 . DP=20;AF1=0.5;CI95=0.5,0.5;DP4=14,0,5,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 60,0,131:0/1:63 chr2b 3049384 . A C 14.9 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 3049385 . G C 14.9 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 3049406 . C G 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=36 PL:GT:GQ 135,18,0:1/1:90 chr2b 4213802 . T C 89.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr2b 5022895 . G A 66 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=49 PL:GT:GQ 99,30,0:1/1:99 chr2b 6037666 . G T 56 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=17 PL:GT:GQ 89,39,0:1/1:99 chr2b 13656952 . G A 19.2 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=21 PL:GT:GQ 52,18,0:1/1:90 chr2b 15026944 . A G 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 37,6,0:1/1:49 chr2b 23362613 . A G 5.64 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 37,15,0:1/1:75 chr2b 45947861 . C G 68 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=50 PL:GT:GQ 101,33,0:1/1:99 chr2b 46597824 . T C 65.6 . DP=39;AF1=0.5939;CI95=0.5,1;DP4=23,0,10,0;MQ=22;PV4=1,0.014,1,1 PL:GT:GQ 95,0,5:0/1:7 chr2b 49665191 . G T 34.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37 PL:GT:GQ 67,21,0:1/1:84 chr2b 61001546 . A G 48 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=26 PL:GT:GQ 81,24,0:1/1:96 chr2b 88502851 . T C 4.77 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=37;PV4=1,1,0.46,1 PL:GT:GQ 33,0,34:0/1:33 chr2b 91675431 . C T 30 . DP=14;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=27 PL:GT:GQ 63,24,0:1/1:96 chr2b 91870148 . T G 67 . DP=14;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=47;PV4=1,1,1,1 PL:GT:GQ 100,31,0:1/1:99 chr2b 97066826 . G A 20.1 . DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=0,6,0,2;MQ=31;PV4=1,1,1,1 PL:GT:GQ 50,0,35:0/1:38 chr2b 97670822 . G A 4.85 . DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=18 PL:GT:GQ 36,18,0:1/1:90 chr2b 102773175 . A G 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 49,9,0:1/1:63 chr2b 109805532 . T C 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=45 PL:GT:GQ 176,24,0:1/1:96 chr2b 110841448 . A G 11.1 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 42,6,0:1/1:49 chr2b 123217025 . T C 31.5 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=37 PL:GT:GQ 64,12,0:1/1:72 chr2b 123263214 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 43,9,0:1/1:63 chr2b 127747292 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=52 PL:GT:GQ 100,9,0:1/1:63 chr2b 130121958 . A G 89.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 122,15,0:1/1:75 chr2b 130253633 . A G 14.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 130692761 . C T 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=51 PL:GT:GQ 82,18,0:1/1:90 chr2b 130743365 . A G 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42 PL:GT:GQ 140,15,0:1/1:75 chr2b 131553874 . A C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37 PL:GT:GQ 43,9,0:1/1:63 chr2b 131716894 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40 PL:GT:GQ 137,24,0:1/1:96 chr2b 131716936 . G A 99 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=36 PL:GT:GQ 173,36,0:1/1:99 chr2b 131716952 . A G 99 . DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,14;MQ=36;PV4=1,1,1,1 PL:GT:GQ 152,0,43:0/1:46 chr2b 133360184 . C T 99 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,20;MQ=32 PL:GT:GQ 163,60,0:1/1:99 chr2b 133644741 . T A 16.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=27 PL:GT:GQ 49,15,0:1/1:75 chr2b 133720595 . T C 41 . DP=15;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=29 PL:GT:GQ 74,36,0:1/1:99 chr2b 133727192 . C T 19.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 52,15,0:1/1:75 chr2b 133727260 . G A 3.56 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18 PL:GT:GQ 34,24,0:1/1:95 chr2b 133800294 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=23 PL:GT:GQ 40,6,0:1/1:49 chr2b 134582754 . A C 56.1 . DP=37;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=36 PL:GT:GQ 89,21,0:1/1:84 chr2b 134582763 . G C 78 . DP=37;AF1=1;CI95=1,1;DP4=0,0,0,36;MQ=34 PL:GT:GQ 111,108,0:1/1:99 chr2b 134809668 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr3 527814 . C G 46 . DP=9;AF1=0.5;CI95=0.5,0.5;DP4=6,0,3,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 76,0,106:0/1:79 chr3 559510 . G A 38 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=10,0,17,0;MQ=28;PV4=1,1,0.014,1 PL:GT:GQ 68,0,111:0/1:71 chr3 879433 . T G 32 . DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 62,0,34:0/1:37 chr3 1809645 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr3 3235812 . C T 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 38,6,0:1/1:49 chr3 3250176 . A G 83 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=32 PL:GT:GQ 116,24,0:1/1:96 chr3 5049073 . T A 99 . DP=25;AF1=0.5;CI95=0.5,0.5;DP4=16,0,9,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 136,0,129:0/1:99 chr3 5142874 . G A 99 . DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=28 PL:GT:GQ 179,114,0:1/1:99 chr3 5554864 . T C 3.54 . DP=7;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,3;MQ=27;PV4=1,1,1,1 PL:GT:GQ 31,0,35:0/1:33 chr3 5749648 . G A 21.2 . DP=26;AF1=0.7303;CI95=0.5,1;DP4=0,7,0,7;MQ=26;PV4=1,0.16,1,0.17 PL:GT:GQ 50,0,2:0/1:3 chr3 16451708 . A T 71.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38 PL:GT:GQ 104,15,0:1/1:75 chr3 23410276 . G A 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 140,15,0:1/1:75 chr3 51368824 . A G 28 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 60,9,0:1/1:63 chr3 53000453 . A G 54 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19 PL:GT:GQ 87,30,0:1/1:99 chr3 53000463 . A G 54 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19 PL:GT:GQ 87,30,0:1/1:99 chr3 59077423 . C T 77.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=33 PL:GT:GQ 110,15,0:1/1:75 chr3 60040501 . T C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 43,9,0:1/1:63 chr3 64203481 . A G 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 66,12,0:1/1:72 chr3 67947441 . C T 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr3 76372631 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 76,9,0:1/1:63 chr3 80611316 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr3 81554381 . G T 17.6 . DP=24;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26 PL:GT:GQ 50,12,0:1/1:72 chr3 87614647 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr3 93900455 . A T 11.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=13 PL:GT:GQ 44,15,0:1/1:75 chr3 96174457 . A G 4.11 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=24 PL:GT:GQ 34,9,0:1/1:63 chr3 96215569 . A C 3.41 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr3 96587998 . A C 7.08 . DP=9;AF1=1;CI95=1,1;DP4=0,0,6,0;MQ=17 PL:GT:GQ 39,18,0:1/1:90 chr3 99711220 . A C 12.8 . DP=11;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 42,2,0:1/1:37 chr3 99789741 . C G 99 . DP=18;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=47 PL:GT:GQ 210,51,0:1/1:99 chr3 103667651 . A C 3.98 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 33,6,0:1/1:49 chr3 104604896 . G C 55 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 87,9,0:1/1:63 chr3 104997217 . G A 33.1 . DP=18;AF1=1;CI95=1,1;DP4=1,0,16,0;MQ=34;PV4=1,3e-10,0.17,0.36 PL:GT:GQ 66,19,0:1/1:76 chr3 106097816 . A G 28 . DP=15;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=26 PL:GT:GQ 61,45,0:1/1:99 chr3 106822259 . G C 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=50 PL:GT:GQ 140,15,0:1/1:75 chr3 109946413 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 44,6,0:1/1:49 chr3 121238963 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr3 126248567 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 45,6,0:1/1:49 chr3 129733836 . A G 6.2 . DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.02,0.31,1 PL:GT:GQ 35,0,28:0/1:30 chr3 131372785 . C T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=34 PL:GT:GQ 76,9,0:1/1:63 chr3 132290987 . C T 22 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=45 PL:GT:GQ 54,9,0:1/1:63 chr3 136054421 . C T 73 . DP=82;AF1=1;CI95=1,1;DP4=0,0,78,0;MQ=28 PL:GT:GQ 106,235,0:1/1:99 chr3 141075246 . G A 30.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41 PL:GT:GQ 62,6,0:1/1:49 chr3 141075262 . T G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41 PL:GT:GQ 73,6,0:1/1:49 chr3 141430649 . G T 81.8 . DP=6;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=41;PV4=1,0.34,1,0.25 PL:GT:GQ 113,6,0:1/1:49 chr3 143617747 . G T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 54,9,0:1/1:63 chr3 163576128 . C T 5.6 . DP=4;AF1=0.7302;CI95=0.5,1;DP4=2,0,2,0;MQ=23;PV4=1,1,1,1 PL:GT:GQ 33,0,2:0/1:3 chr3 163839828 . A G 4.45 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26 PL:GT:GQ 35,12,0:1/1:72 chr3 175839340 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr3 190193258 . G T 3.98 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 33,6,0:1/1:49 chr3 190777007 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr3 190970350 . A G 61 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=37 PL:GT:GQ 94,30,0:1/1:99 chr3 198686408 . G A 36.6 . DP=17;AF1=1;CI95=0.5,1;DP4=0,1,0,16;MQ=25;PV4=1,1,0.026,1 PL:GT:GQ 69,11,0:1/1:66 chr3 199277478 . T C 3.61 . DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=21 PL:GT:GQ 34,18,0:1/1:90 chr3 199780181 . G T 77 . DP=45;AF1=0.5;CI95=0.5,0.5;DP4=0,35,0,10;MQ=33;PV4=1,1,1,1 PL:GT:GQ 107,0,114:0/1:99 chr3 199889335 . A C 9.54 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18 PL:GT:GQ 42,24,0:1/1:96 chr3 200018161 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr4 195475 . A G 13 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 44,6,0:1/1:49 chr4 639141 . C A 14.9 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr4 639152 . C T 15.2 . DP=17;AF1=0.5016;CI95=0.5,0.5;DP4=0,2,0,2;MQ=33;PV4=1,1,1,1 PL:GT:GQ 45,0,22:0/1:25 chr4 986497 . G T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=33 PL:GT:GQ 163,30,0:1/1:99 chr4 986516 . C T 55.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37 PL:GT:GQ 88,21,0:1/1:84 chr4 1207485 . A C 14.9 . DP=22;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 46,6,0:1/1:49 chr4 1323502 . G A 13.2 . DP=13;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=22 PL:GT:GQ 46,33,0:1/1:99 chr4 1613521 . G A 89 . DP=16;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=32 PL:GT:GQ 122,48,0:1/1:99 chr4 1748790 . C T 38 . DP=21;AF1=0.5005;CI95=0.5,0.5;DP4=6,0,8,0;MQ=40;PV4=1,0.09,1,1 PL:GT:GQ 68,0,27:0/1:30 chr4 2255732 . T C 99 . DP=29;AF1=1;CI95=1,1;DP4=0,0,28,0;MQ=31 PL:GT:GQ 186,84,0:1/1:99 chr4 3010159 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr4 3545023 . A G 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=38 PL:GT:GQ 145,27,0:1/1:99 chr4 3586344 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr4 3879337 . A G 16.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 49,12,0:1/1:72 chr4 3940733 . A G 47.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 80,15,0:1/1:75 chr4 4410338 . T C 13.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31 PL:GT:GQ 46,15,0:1/1:75 chr4 4796408 . T C 41 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=17 PL:GT:GQ 74,48,0:1/1:99 chr4 4796414 . A G 11.3 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=17 PL:GT:GQ 44,45,0:1/1:99 chr4 6436959 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr4 9494256 . T C 3.41 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37 PL:GT:GQ 32,6,0:1/1:49 chr4 24881479 . G A 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 46,9,0:1/1:63 chr4 26128644 . A G 23 . DP=18;AF1=0.5006;CI95=0.5,0.5;DP4=8,0,10,0;MQ=22;PV4=1,1,1,1 PL:GT:GQ 53,0,26:0/1:29 chr4 42109100 . G A 17.1 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 49,9,0:1/1:63 chr4 42309652 . C T 68 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr4 46913966 . C T 9.08 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=16 PL:GT:GQ 41,12,0:1/1:72 chr4 50335142 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr4 51658550 . C A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr4 58258023 . T C 26 . DP=5;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,2;MQ=34;PV4=1,1,1,0.05 PL:GT:GQ 56,0,32:0/1:35 chr4 59219112 . C A 42.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50 PL:GT:GQ 75,12,0:1/1:72 chr4 62746067 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr4 67404338 . G T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39 PL:GT:GQ 66,12,0:1/1:72 chr4 73353380 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr4 73946294 . G C 4.77 . DP=51;AF1=0.4999;CI95=0.5,0.5;DP4=0,5,0,3;MQ=40;PV4=1,0.19,0.37,0.11 PL:GT:GQ 33,0,64:0/1:36 chr4 79607484 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr4 82337365 . G C 90 . DP=54;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=28 PL:GT:GQ 123,48,0:1/1:99 chr4 82653801 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 34,9,0:1/1:63 chr4 87130164 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 43,9,0:1/1:63 chr4 87130176 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 43,9,0:1/1:63 chr4 91459729 . C A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr4 96130778 . G C 99 . DP=19;AF1=1;CI95=1,1;DP4=0,0,0,19;MQ=45 PL:GT:GQ 211,57,0:1/1:99 chr4 100709417 . A G 45.1 . DP=16;AF1=0.505;CI95=0.5,0.5;DP4=12,0,4,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 75,0,17:0/1:20 chr4 107276770 . C T 70 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=31;PV4=1,1,1,1 PL:GT:GQ 100,0,97:0/1:98 chr4 115327550 . G C 42 . DP=67;AF1=1;CI95=1,1;DP4=0,1,0,66;MQ=35;PV4=1,3.2e-24,0.13,1 PL:GT:GQ 75,162,0:1/1:99 chr4 136558502 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr4 159572459 . G A 15.1 . DP=126;AF1=0.5;CI95=0.5,0.5;DP4=0,69,0,57;MQ=39;PV4=1,4.1e-96,0.077,1 PL:GT:GQ 45,0,175:0/1:48 chr4 174968484 . G C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 40,6,0:1/1:49 chr4 175030633 . T C 14.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=29 PL:GT:GQ 47,18,0:1/1:90 chr4 183410027 . G T 6.2 . DP=31;AF1=0.5003;CI95=0.5,0.5;DP4=2,0,2,0;MQ=45;PV4=1,0.035,1,0.21 PL:GT:GQ 35,0,28:0/1:30 chr4 190907368 . T C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50 PL:GT:GQ 66,12,0:1/1:72 chr4 192175690 . A G 76.8 . DP=7;AF1=0.95;CI95=0.5,1;DP4=0,3,0,4;MQ=35;PV4=1,1,1,1 PL:GT:GQ 105,0,0:1/1:10 chr4 192673268 . G A 14.2 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=22 PL:GT:GQ 47,27,0:1/1:99 chr4 192943966 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr4 195460104 . C G 23.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=19 PL:GT:GQ 56,24,0:1/1:96 chr4 198277830 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr5 170098 . A G 13 . DP=12;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 44,6,0:1/1:49 chr5 395814 . T C 4.77 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,0.48,1 PL:GT:GQ 33,0,33:0/1:33 chr5 414024 . T A 10.4 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=20 PL:GT:GQ 42,9,0:1/1:63 chr5 496767 . T C 13.9 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr5 805676 . C G 45 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=32 PL:GT:GQ 78,51,0:1/1:99 chr5 1252896 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr5 1418370 . G A 3.65 . DP=8;AF1=0.7301;CI95=0.5,1;DP4=4,0,4,0;MQ=13;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr5 1494911 . G C 62 . DP=9;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=46 PL:GT:GQ 95,24,0:1/1:96 chr5 1494932 . C T 6.98 . DP=8;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=46;PV4=1,0.1,0.077,1 PL:GT:GQ 36,0,31:0/1:33 chr5 1506037 . T C 24.1 . DP=24;AF1=1;CI95=0.5,1;DP4=11,0,13,0;MQ=16;PV4=1,1,1,1 PL:GT:GQ 55,5,0:1/1:46 chr5 1509406 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 73,6,0:1/1:49 chr5 1733649 . A G 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=47 PL:GT:GQ 212,75,0:1/1:99 chr5 1747304 . A G 12.3 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19 PL:GT:GQ 45,36,0:1/1:99 chr5 1747308 . C A 44 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19 PL:GT:GQ 77,36,0:1/1:99 chr5 3519783 . C T 21.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18 PL:GT:GQ 54,24,0:1/1:96 chr5 4101593 . A G 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43 PL:GT:GQ 102,12,0:1/1:72 chr5 7204332 . T A 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=24 PL:GT:GQ 34,6,0:1/1:49 chr5 11510398 . A C 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=51;PV4=1,1,0,1 PL:GT:GQ 64,0,31:0/1:34 chr5 15406720 . T C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 36,6,0:1/1:49 chr5 25152417 . C A 10.9 . DP=28;AF1=0.5718;CI95=0.5,1;DP4=0,2,0,6;MQ=25;PV4=1,1,0.21,1 PL:GT:GQ 40,0,6:0/1:8 chr5 39072637 . A G 35.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=50 PL:GT:GQ 68,15,0:1/1:75 chr5 46022699 . G A 44 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 76,9,0:1/1:63 chr5 55664181 . C G 10.4 . DP=8;AF1=0.9999;CI95=0.5,1;DP4=3,0,5,0;MQ=18;PV4=1,1,1,1 PL:GT:GQ 40,3,0:1/1:41 chr5 56253386 . T C 50.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=36 PL:GT:GQ 83,21,0:1/1:84 chr5 56253447 . C T 42.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=45 PL:GT:GQ 75,12,0:1/1:72 chr5 71950166 . G T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr5 72703090 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 40,6,0:1/1:49 chr5 73570280 . G T 5.45 . DP=41;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=15 PL:GT:GQ 37,123,0:1/1:99 chr5 73701762 . G T 40.8 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 72,6,0:1/1:49 chr5 76956867 . T C 10.2 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 41,6,0:1/1:49 chr5 79097961 . C G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 54,9,0:1/1:63 chr5 87026167 . T C 22 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr5 97680525 . T C 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23 PL:GT:GQ 33,12,0:1/1:72 chr5 100674737 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr5 105389966 . T C 3.52 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=15 PL:GT:GQ 33,9,0:1/1:63 chr5 109998341 . A C 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr5 120629105 . C T 6.79 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 37,6,0:1/1:49 chr5 128383954 . C T 23 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,3.3e-07,1,1 PL:GT:GQ 53,0,98:0/1:56 chr5 133925142 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr5 135375404 . T C 11.8 . DP=6;AF1=1;CI95=0.5,1;DP4=1,0,3,0;MQ=31;PV4=1,0.03,1,1 PL:GT:GQ 42,4,0:1/1:45 chr5 136498281 . T G 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr5 136717285 . A G 82.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 115,12,0:1/1:72 chr5 136910734 . G A 62 . DP=19;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=23;PV4=1,1,1,1 PL:GT:GQ 95,31,0:1/1:99 chr5 141208149 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr5 148056348 . C A 37.1 . DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=38;PV4=1,1,1,1 PL:GT:GQ 66,1,0:1/1:23 chr5 151941534 . G T 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34 PL:GT:GQ 79,12,0:1/1:72 chr5 159967229 . G C 22.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 55,12,0:1/1:72 chr5 174024541 . T G 29.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 59,2,0:1/1:37 chr5 175525290 . A G 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=20 PL:GT:GQ 33,12,0:1/1:72 chr5 175988954 . A C 14.2 . DP=23;AF1=0.5;CI95=0.5,0.5;DP4=0,6,0,4;MQ=47;PV4=1,1,0.2,1 PL:GT:GQ 44,0,76:0/1:47 chr5 176782226 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr5 179132834 . C G 99 . DP=28;AF1=1;CI95=1,1;DP4=0,0,0,28;MQ=41 PL:GT:GQ 207,84,0:1/1:99 chr5 180155809 . G C 3.01 . DP=36;AF1=0.4997;CI95=0.5,0.5;DP4=25,0,9,0;MQ=35;PV4=1,1e-15,1,1 PL:GT:GQ 30,0,121:0/1:33 chr5 181282819 . T G 38.3 . DP=11;AF1=1;CI95=0.5,1;DP4=0,2,0,9;MQ=23;PV4=1,1,1,1 PL:GT:GQ 71,14,0:1/1:70 chr5 182426125 . G C 29 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26 PL:GT:GQ 61,9,0:1/1:63 chr5 182443682 . G A 3.69 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=21 PL:GT:GQ 34,15,0:1/1:75 chr5 183008993 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr5 183312016 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr6_cox_hap1 519146 . G A 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30 PL:GT:GQ 49,9,0:1/1:63 chr6_cox_hap1 687497 . A G 33 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,0.0016,1,1 PL:GT:GQ 63,3,0:1/1:41 chr6_qbl_hap2 120066 . T C 99 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 139,27,0:1/1:99 chr6 277954 . C T 53 . DP=41;AF1=1;CI95=1,1;DP4=4,0,37,0;MQ=19;PV4=1,1,0.3,1 PL:GT:GQ 86,49,0:1/1:99 chr6 593158 . A G 4.61 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 34,6,0:1/1:49 chr6 2865562 . T G 25 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=23 PL:GT:GQ 58,27,0:1/1:99 chr6 3751403 . G A 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32 PL:GT:GQ 75,15,0:1/1:75 chr6 3884989 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr6 4127278 . A T 13.9 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr6 5887783 . C G 99 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34 PL:GT:GQ 142,21,0:1/1:84 chr6 5887811 . C T 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34 PL:GT:GQ 88,21,0:1/1:84 chr6 6937170 . G C 99 . DP=47;AF1=1;CI95=1,1;DP4=0,0,0,47;MQ=28 PL:GT:GQ 157,141,0:1/1:99 chr6 7262317 . C T 13.2 . DP=50;AF1=0.5;CI95=0.5,0.5;DP4=21,0,9,0;MQ=36;PV4=1,4e-05,0.17,0.26 PL:GT:GQ 43,0,158:0/1:46 chr6 7533214 . A G 10.4 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 42,9,0:1/1:63 chr6 20979907 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=38 PL:GT:GQ 76,9,0:1/1:63 chr6 22321632 . A G 41 . DP=5;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=46;PV4=1,0.24,0.19,0.33 PL:GT:GQ 71,0,28:0/1:31 chr6 25352296 . G A 7.8 . DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=0,1,0,3;MQ=38;PV4=1,1,0.16,1 PL:GT:GQ 37,0,28:0/1:30 chr6 26298040 . T A 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=48;PV4=1,1,0.21,0.33 PL:GT:GQ 64,0,31:0/1:34 chr6 33428755 . G A 70 . DP=14;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=32 PL:GT:GQ 103,27,0:1/1:99 chr6 39512099 . G A 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=50 PL:GT:GQ 88,21,0:1/1:84 chr6 39961094 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr6 40452120 . A G 40.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 72,6,0:1/1:49 chr6 43204766 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=51 PL:GT:GQ 176,24,0:1/1:96 chr6 52696512 . C T 70 . DP=76;AF1=0.5;CI95=0.5,0.5;DP4=0,34,0,42;MQ=18;PV4=1,0.11,1,1 PL:GT:GQ 100,0,51:0/1:54 chr6 53785550 . A G 99 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=46 PL:GT:GQ 190,30,0:1/1:99 chr6 53897484 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr6 57038290 . C T 10.2 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 41,6,0:1/1:49 chr6 62925087 . G C 35 . DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,4,0;MQ=36;PV4=1,1,0.2,1 PL:GT:GQ 65,0,25:0/1:28 chr6 62925094 . T C 25.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36 PL:GT:GQ 58,15,0:1/1:75 chr6 70834405 . G A 72.1 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=29 PL:GT:GQ 105,21,0:1/1:84 chr6 71026058 . C T 48.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=42 PL:GT:GQ 81,18,0:1/1:90 chr6 74420752 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 76,9,0:1/1:63 chr6 77498624 . T C 16.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 48,6,0:1/1:49 chr6 80416836 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr6 113611590 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46 PL:GT:GQ 100,9,0:1/1:63 chr6 119308431 . T C 38.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40 PL:GT:GQ 71,12,0:1/1:72 chr6 151758592 . T C 3.07 . DP=17;AF1=0.9966;CI95=0.5,1;DP4=0,8,0,9;MQ=13;PV4=1,1,1,1 PL:GT:GQ 29,1,0:1/1:23 chr6 151759358 . A G 99 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=12,0,15,0;MQ=44;PV4=1,1,1,0.19 PL:GT:GQ 171,0,128:0/1:99 chr6 154741755 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr6 161061053 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52 PL:GT:GQ 40,6,0:1/1:49 chr6 161474189 . C T 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 36,6,0:1/1:49 chr6 164304657 . C T 10.4 . DP=63;AF1=0.5;CI95=0.5,0.5;DP4=0,29,0,19;MQ=22;PV4=1,7.7e-11,1,0.049 PL:GT:GQ 40,0,37:0/1:38 chr6 164703105 . T C 99 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=40 PL:GT:GQ 165,30,0:1/1:99 chr6 167518328 . A G 78 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=27,0,14,0;MQ=33;PV4=1,0.026,0.43,0.056 PL:GT:GQ 108,0,149:0/1:99 chr6 169906323 . G A 41.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr6 171893912 . G A 69.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33 PL:GT:GQ 102,15,0:1/1:75 chr6 173631604 . A G 6.98 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=4,0,3,0;MQ=37;PV4=1,0.069,1,1 PL:GT:GQ 36,0,34:0/1:35 chr7 835856 . C T 27.5 . DP=13;AF1=0.9998;CI95=0.5,1;DP4=4,0,6,0;MQ=23;PV4=1,0.46,1,1 PL:GT:GQ 57,2,0:1/1:37 chr7 1046005 . C T 11.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 43,9,0:1/1:63 chr7 1564339 . C T 71 . DP=66;AF1=0.5;CI95=0.5,0.5;DP4=36,0,24,0;MQ=29;PV4=1,1,0.35,1 PL:GT:GQ 101,0,134:0/1:99 chr7 1806266 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr7 1936013 . G T 7.77 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=17 PL:GT:GQ 39,9,0:1/1:63 chr7 2319532 . C A 4.11 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=14 PL:GT:GQ 34,9,0:1/1:63 chr7 2682121 . C T 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr7 3248116 . T C 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=37;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr7 3624766 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 40,6,0:1/1:49 chr7 5291140 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr7 5314457 . C A 3.56 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18 PL:GT:GQ 34,24,0:1/1:95 chr7 5595072 . T A 79 . DP=13;AF1=0.5;CI95=0.5,0.5;DP4=8,0,5,0;MQ=31;PV4=1,1,1,1 PL:GT:GQ 109,0,57:0/1:60 chr7 5646060 . G C 7.79 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=10 PL:GT:GQ 40,30,0:1/1:99 chr7 6056816 . C G 7.08 . DP=6;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=23;PV4=1,1,1,1 PL:GT:GQ 35,1,0:1/1:23 chr7 6412641 . C T 40 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33 PL:GT:GQ 73,33,0:1/1:99 chr7 6766874 . A G 34.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=43 PL:GT:GQ 67,15,0:1/1:75 chr7 8482729 . C T 5.08 . DP=16;AF1=0.8276;CI95=0.5,1;DP4=3,0,3,0;MQ=22;PV4=1,1,1,0.19 PL:GT:GQ 32,0,1:1/1:5 chr7 9238362 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr7 9687781 . G A 33 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,12;MQ=48;PV4=1,6.5e-38,1,1 PL:GT:GQ 63,0,170:0/1:66 chr7 9752803 . A T 14.2 . DP=17;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18 PL:GT:GQ 47,27,0:1/1:99 chr7 10240910 . T C 45.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 78,12,0:1/1:72 chr7 11046187 . C T 86.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=47 PL:GT:GQ 119,12,0:1/1:72 chr7 11548207 . C G 14.6 . DP=13;AF1=1;CI95=0.5,1;DP4=6,1,0,5;MQ=18;PV4=0.015,1,1,1 PL:GT:GQ 46,7,0:1/1:57 chr7 11580317 . C T 42 . DP=12;AF1=1;CI95=1,1;DP4=0,1,0,10;MQ=22;PV4=1,1,1,1 PL:GT:GQ 75,23,0:1/1:92 chr7 11585384 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr7 13498356 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 73,6,0:1/1:49 chr7 13500887 . G A 15.1 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=22 PL:GT:GQ 48,30,0:1/1:99 chr7 13827079 . C T 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 36,6,0:1/1:49 chr7 14403976 . T G 59 . DP=30;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39 PL:GT:GQ 92,24,0:1/1:96 chr7 14756588 . A G 44 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,5.3e-18,1,1 PL:GT:GQ 74,0,70:0/1:72 chr7 14756619 . T G 44 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,6.4e-10,1,1 PL:GT:GQ 74,0,70:0/1:72 chr7 36734598 . A C 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 42,6,0:1/1:49 chr7 36734599 . A T 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 42,6,0:1/1:49 chr7 36734603 . G C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 40,6,0:1/1:49 chr7 40634921 . A C 55 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=39 PL:GT:GQ 88,39,0:1/1:99 chr7 48271285 . A T 73 . DP=15;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=25 PL:GT:GQ 106,30,0:1/1:99 chr7 56264700 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr7 62326003 . C A 26.1 . DP=35;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28 PL:GT:GQ 59,18,0:1/1:90 chr7 109468934 . T G 5.13 . DP=10;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=39;PV4=1,0.031,1,1 PL:GT:GQ 33,2,0:1/1:37 chr7 110208327 . C G 16.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 48,6,0:1/1:49 chr7 125654934 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=27 PL:GT:GQ 34,9,0:1/1:63 chr7 125770209 . A C 32 . DP=31;AF1=0.5;CI95=0.5,0.5;DP4=11,0,13,0;MQ=34;PV4=1,0.00017,0.16,0.22 PL:GT:GQ 62,0,105:0/1:65 chr7 125770265 . G C 36 . DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,0.0047,0.016,0.035 PL:GT:GQ 66,0,110:0/1:69 chr7 126687042 . A G 21.1 . DP=36;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=22 PL:GT:GQ 54,21,0:1/1:84 chr7 132292897 . G T 99 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=43 PL:GT:GQ 167,21,0:1/1:84 chr7 132334562 . A C 23 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=23 PL:GT:GQ 56,30,0:1/1:99 chr7 132431838 . C T 13.3 . DP=5;AF1=1;CI95=0.5,1;DP4=1,0,4,0;MQ=23;PV4=1,1,1,1 PL:GT:GQ 44,5,0:1/1:46 chr7 136324945 . T C 13.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 46,12,0:1/1:72 chr7 136957634 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr7 141746871 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 40,6,0:1/1:49 chr7 146831870 . C T 4.77 . DP=14;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=37;PV4=1,0.0029,0.28,1 PL:GT:GQ 33,0,28:0/1:30 chr7 147142770 . T C 45 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=31 PL:GT:GQ 77,9,0:1/1:63 chr7 147713906 . C T 4.77 . DP=8;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,4,0;MQ=35;PV4=1,8.9e-06,0.48,0.27 PL:GT:GQ 33,0,29:0/1:31 chr7 148742642 . G A 68 . DP=14;AF1=0.5032;CI95=0.5,0.5;DP4=4,0,10,0;MQ=28;PV4=1,1,1,1 PL:GT:GQ 98,0,19:0/1:22 chr7 148879148 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr7 149484407 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr7 152444478 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 44,6,0:1/1:49 chr7 154106613 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=51 PL:GT:GQ 100,9,0:1/1:63 chr7 154776891 . G T 14.4 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 47,15,0:1/1:75 chr7 155882061 . A C 29 . DP=24;AF1=0.502;CI95=0.5,0.5;DP4=0,1,0,4;MQ=46;PV4=1,0.018,0.15,0.29 PL:GT:GQ 59,0,21:0/1:24 chr7 155956844 . G C 23 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=38;PV4=1,1,0.38,1 PL:GT:GQ 53,0,103:0/1:56 chr7 156277694 . G A 62 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=46 PL:GT:GQ 95,24,0:1/1:96 chr7 156720588 . T C 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr7 156807649 . T C 3.01 . DP=30;AF1=0.4997;CI95=0.5,0.5;DP4=0,4,0,3;MQ=43;PV4=1,0.16,0.15,1 PL:GT:GQ 30,0,72:0/1:33 chr7 157331292 . G T 43.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=34 PL:GT:GQ 76,21,0:1/1:84 chr7 157382957 . T C 33.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 66,12,0:1/1:72 chr8 556382 . A G 37.1 . DP=5;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=31;PV4=1,1,1,1 PL:GT:GQ 66,1,0:1/1:23 chr8 1661673 . T C 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr8 7379751 . C A 6.24 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19 PL:GT:GQ 38,21,0:1/1:84 chr8 8160505 . A T 68.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 101,12,0:1/1:72 chr8 8160508 . C T 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 57,12,0:1/1:72 chr8 16781011 . A G 55.5 . DP=9;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34 PL:GT:GQ 88,12,0:1/1:72 chr8 18716499 . A T 20 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,4,0,2;MQ=29;PV4=1,1,1,1 PL:GT:GQ 50,0,52:0/1:51 chr8 23326483 . A G 60 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47 PL:GT:GQ 92,9,0:1/1:63 chr8 25842819 . T A 12 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 43,6,0:1/1:49 chr8 26300279 . T C 34 . DP=44;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=21 PL:GT:GQ 67,123,0:1/1:99 chr8 29673470 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 73,6,0:1/1:49 chr8 29673473 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 40,6,0:1/1:49 chr8 31685466 . C T 34 . DP=17;AF1=0.5;CI95=0.5,0.5;DP4=10,0,5,0;MQ=28;PV4=1,0.072,1,0.36 PL:GT:GQ 64,0,50:0/1:53 chr8 37378739 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr8 51325952 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr8 59221963 . G A 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr8 62764995 . T G 20 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=32 PL:GT:GQ 52,9,0:1/1:63 chr8 63157426 . C G 41.6 . DP=22;AF1=1;CI95=0.5,1;DP4=0,7,0,15;MQ=19;PV4=1,1,1,0.25 PL:GT:GQ 74,11,0:1/1:66 chr8 68710444 . G A 30 . DP=5;AF1=0.6671;CI95=0.5,1;DP4=3,0,2,0;MQ=32;PV4=1,1,1,1 PL:GT:GQ 59,0,3:0/1:5 chr8 76416560 . G A 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=46 PL:GT:GQ 122,12,0:1/1:72 chr8 81425275 . T G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr8 89842286 . G C 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30 PL:GT:GQ 34,6,0:1/1:49 chr8 100926281 . G A 38 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 70,9,0:1/1:63 chr8 102746002 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr8 107850176 . C T 43.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=45 PL:GT:GQ 76,18,0:1/1:90 chr8 109966441 . T C 27.3 . DP=9;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38 PL:GT:GQ 60,15,0:1/1:75 chr8 118811716 . G T 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=50 PL:GT:GQ 155,18,0:1/1:90 chr8 119440254 . A T 58.5 . DP=5;AF1=0.8277;CI95=0.5,1;DP4=2,0,3,0;MQ=34;PV4=1,1,1,0.14 PL:GT:GQ 87,0,1:1/1:5 chr8 121236024 . G A 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 71,6,0:1/1:49 chr8 125489079 . C T 13 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr8 128502549 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr8 128502551 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr8 130951113 . G A 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=19 PL:GT:GQ 34,6,0:1/1:49 chr8 135307123 . G A 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 36,6,0:1/1:49 chr8 138814155 . C T 57.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 90,18,0:1/1:90 chr8 140566111 . A G 18.1 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=15 PL:GT:GQ 51,36,0:1/1:99 chr8 141586480 . T G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr8 143376712 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr8 150662729 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr8 150741294 . A G 25.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=34 PL:GT:GQ 58,18,0:1/1:90 chr8 150975618 . A G 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr8 151580103 . T C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=20 PL:GT:GQ 36,6,0:1/1:49 chr8 151634410 . G T 48 . DP=17;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,5;MQ=39;PV4=1,0.072,1,1 PL:GT:GQ 78,0,125:0/1:81 chr8 151709267 . G A 91.1 . DP=8;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=40;PV4=1,1,0.28,0.37 PL:GT:GQ 121,0,16:0/1:19 chr8 152636420 . G A 8.75 . DP=3;AF1=0.9966;CI95=0.5,1;DP4=0,1,0,2;MQ=30;PV4=1,1,1,1 PL:GT:GQ 37,1,0:1/1:23 chr8 152706967 . G A 3.01 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=16 PL:GT:GQ 33,30,0:1/1:99 chr8 152786522 . T C 80.1 . DP=16;AF1=0.5102;CI95=0.5,0.5;DP4=0,4,0,12;MQ=31;PV4=1,0.25,1,1 PL:GT:GQ 110,0,14:0/1:17 chr8 152863132 . T G 5.44 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30 PL:GT:GQ 36,9,0:1/1:63 chr9 23235268 . C T 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 43,6,0:1/1:49 chr9 26391176 . T C 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 47,6,0:1/1:49 chr9 26868232 . C G 63 . DP=20;AF1=0.5025;CI95=0.5,0.5;DP4=7,0,13,0;MQ=22;PV4=1,0.2,1,0.44 PL:GT:GQ 93,0,20:0/1:23 chr9 34223668 . C T 22 . DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,7;MQ=27;PV4=1,0.14,0.34,1 PL:GT:GQ 52,0,79:0/1:55 chr9 39696645 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr9 40654130 . T G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr9 41145321 . T G 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 79,12,0:1/1:72 chr9 42273483 . G A 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr9 55633192 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 58705807 . T C 70 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=24 PL:GT:GQ 103,30,0:1/1:99 chr9 61697149 . C G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 63152790 . A C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr9 63703913 . C G 90.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=38 PL:GT:GQ 123,21,0:1/1:84 chr9 65116068 . T C 70 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=49 PL:GT:GQ 103,39,0:1/1:99 chr9 71266598 . C A 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 33,6,0:1/1:49 chr9 73188677 . G T 52 . DP=294;AF1=1;CI95=1,1;DP4=44,0,245,0;MQ=33;PV4=1,0.28,0.0092,1 PL:GT:GQ 85,147,0:1/1:99 chr9 78854179 . G T 22 . DP=97;AF1=0.5;CI95=0.5,0.5;DP4=21,0,12,0;MQ=44;PV4=1,0.02,0.032,0.0033 PL:GT:GQ 52,0,158:0/1:55 chr9 82964679 . A C 13.2 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=36 PL:GT:GQ 45,9,0:1/1:63 chr9 84124545 . G T 57 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=2,0,3,0;MQ=49;PV4=1,1,0.024,1 PL:GT:GQ 87,0,59:0/1:62 chr9 86552862 . C T 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=26 PL:GT:GQ 47,15,0:1/1:75 chr9 87548941 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr9 89021101 . G A 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr9 90447825 . G A 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 40,6,0:1/1:49 chr9 92462035 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 40,6,0:1/1:49 chr9 93077294 . T G 5.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31 PL:GT:GQ 36,9,0:1/1:63 chr9 93998137 . G A 68 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46 PL:GT:GQ 100,9,0:1/1:63 chr9 93998148 . C T 21.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36 PL:GT:GQ 54,15,0:1/1:75 chr9 95028964 . C A 99 . DP=83;AF1=0.5;CI95=0.5,0.5;DP4=0,57,0,26;MQ=32;PV4=1,9.3e-08,1,0.092 PL:GT:GQ 134,0,120:0/1:99 chr9 103829155 . A G 33 . DP=96;AF1=1;CI95=1,1;DP4=0,0,96,0;MQ=16 PL:GT:GQ 66,255,0:1/1:99 chr9 104981331 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 73,6,0:1/1:49 chr9 111070656 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 117395657 . T C 16.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 49,15,0:1/1:75 chr9 117718907 . A G 46.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=29 PL:GT:GQ 79,18,0:1/1:90 chr9 119149161 . T C 3.14 . DP=65;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 33,15,0:1/1:75 chr9 124528802 . G A 78 . DP=23;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=25 PL:GT:GQ 111,39,0:1/1:99 chr9 126707903 . G A 26 . DP=37;AF1=0.5;CI95=0.5,0.5;DP4=0,21,0,8;MQ=46;PV4=1,2.6e-07,0.21,0.42 PL:GT:GQ 56,0,175:0/1:59 chr9 128700686 . C G 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 66,12,0:1/1:72 chr9 129084077 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr9 129116900 . A T 20 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 52,9,0:1/1:63 chr9 130290720 . C G 21.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 53,6,0:1/1:49 chr9 130306057 . C G 71 . DP=14;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=28 PL:GT:GQ 104,42,0:1/1:99 chr9 130528990 . G A 99 . DP=31;AF1=1;CI95=1,1;DP4=0,0,31,0;MQ=27 PL:GT:GQ 174,93,0:1/1:99 chr9 130529002 . A T 7.79 . DP=30;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=15 PL:GT:GQ 40,33,0:1/1:99 chr9 130639996 . A G 8.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 39,6,0:1/1:49 chr9 130704890 . A G 3.27 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=26 PL:GT:GQ 33,12,0:1/1:72 chr9 130708345 . G A 13.3 . DP=11;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=38;PV4=1,0.096,1,1 PL:GT:GQ 42,1,0:1/1:23 chr9 131001601 . T A 3.98 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 33,6,0:1/1:49 chr9 131058539 . T A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 44,6,0:1/1:49 chr9 131808965 . C T 42 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 75,27,0:1/1:99 chr9 132551867 . C T 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 49,9,0:1/1:63 chr9 132685120 . A G 4.75 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 35,9,0:1/1:63 chr9 133175050 . A G 18.1 . DP=30;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=20 PL:GT:GQ 51,51,0:1/1:99 chr9 133584978 . A G 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=45 PL:GT:GQ 212,75,0:1/1:99 chr9 133661895 . A G 99 . DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31 PL:GT:GQ 138,42,0:1/1:99 chr9 133670376 . T C 68 . DP=19;AF1=1;CI95=1,1;DP4=0,1,0,16;MQ=39;PV4=1,1.4e-20,1,1 PL:GT:GQ 101,39,0:1/1:99 chr9 133843777 . T C 99 . DP=9;AF1=0.5129;CI95=0.5,0.5;DP4=1,0,8,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 154,0,13:0/1:16 chr9 134017265 . G C 3.27 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=13 PL:GT:GQ 33,12,0:1/1:72 chr9 134105563 . T C 34.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=39 PL:GT:GQ 67,18,0:1/1:90 chr9 134608906 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr9 134861929 . T A 9.49 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 41,9,0:1/1:63 chr10 796662 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 54,9,0:1/1:63 chr10 1216716 . T A 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr10 1220781 . G A 21 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18 PL:GT:GQ 54,27,0:1/1:99 chr10 1225208 . T C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47 PL:GT:GQ 100,9,0:1/1:63 chr10 1727946 . T C 14.2 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27 PL:GT:GQ 47,21,0:1/1:84 chr10 5986542 . T C 83 . DP=93;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39 PL:GT:GQ 116,30,0:1/1:99 chr10 6436277 . G A 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 36,6,0:1/1:49 chr10 7704114 . C A 35 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=0,2,0,4;MQ=29;PV4=1,0.27,1,0.27 PL:GT:GQ 65,3,0:1/1:41 chr10 10881734 . A G 9.52 . DP=9;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=42;PV4=1,0.0026,0.14,1 PL:GT:GQ 39,0,91:0/1:42 chr10 13099383 . G A 27.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 60,12,0:1/1:72 chr10 15764077 . G C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr10 18091502 . T C 47 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 79,9,0:1/1:63 chr10 19645913 . A T 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 47,6,0:1/1:49 chr10 22845062 . C T 18.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=18 PL:GT:GQ 51,21,0:1/1:84 chr10 28282802 . T C 69 . DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=42 PL:GT:GQ 102,36,0:1/1:99 chr10 28496872 . T G 8.44 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 39,6,0:1/1:49 chr10 32746793 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr10 41437604 . T G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr10 43051239 . C T 6.98 . DP=3;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=40;PV4=1,0.33,0.33,1 PL:GT:GQ 36,0,31:0/1:33 chr10 44455192 . C T 4.41 . DP=6;AF1=0.8276;CI95=0.5,1;DP4=0,3,0,3;MQ=21;PV4=1,1,1,1 PL:GT:GQ 31,0,1:1/1:5 chr10 48387336 . A G 13 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr10 51561705 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr10 51561712 . C G 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 71,6,0:1/1:49 chr10 55617954 . G A 8.44 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 39,6,0:1/1:49 chr10 55718281 . T A 3.41 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr10 55888771 . T C 23.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 56,12,0:1/1:72 chr10 56025569 . C G 34.1 . DP=3;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,2;MQ=39;PV4=1,1,1,1 PL:GT:GQ 64,0,16:0/1:19 chr10 57384943 . G T 84 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=16,0,13,0;MQ=26;PV4=1,0.015,1,1 PL:GT:GQ 114,0,110:0/1:99 chr10 59873077 . T G 49 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=42 PL:GT:GQ 82,24,0:1/1:96 chr10 61329572 . C T 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 47,6,0:1/1:49 chr10 63790636 . T G 32.1 . DP=19;AF1=1;CI95=1,1;DP4=1,0,10,0;MQ=28;PV4=1,0.14,1,1 PL:GT:GQ 65,22,0:1/1:88 chr10 64466048 . C G 18.2 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28 PL:GT:GQ 51,18,0:1/1:90 chr10 65053440 . G T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39 PL:GT:GQ 153,30,0:1/1:99 chr10 65407358 . C G 84.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 117,15,0:1/1:75 chr10 65605291 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr10 66104447 . T C 99 . DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,21;MQ=34;PV4=1,1,0.15,1 PL:GT:GQ 136,0,162:0/1:99 chr10 82160859 . G C 99 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=36 PL:GT:GQ 153,39,0:1/1:99 chr10 82198579 . C T 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr10 87086290 . A G 4.13 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=17 PL:GT:GQ 35,27,0:1/1:99 chr10 89550621 . T G 74 . DP=47;AF1=1;CI95=1,1;DP4=0,0,0,45;MQ=45 PL:GT:GQ 107,135,0:1/1:99 chr10 92325046 . G A 42.3 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 75,15,0:1/1:75 chr10 94488050 . A G 5.46 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,0.16,1,1 PL:GT:GQ 34,0,34:0/1:34 chr10 95024815 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr10 95466306 . G A 53 . DP=7;AF1=0.6671;CI95=0.5,1;DP4=0,4,0,3;MQ=33;PV4=1,1,1,1 PL:GT:GQ 82,0,3:0/1:5 chr10 100256777 . T G 3.83 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23 PL:GT:GQ 34,12,0:1/1:72 chr10 101510485 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr10 101530760 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr10 101879744 . T C 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=44 PL:GT:GQ 54,9,0:1/1:63 chr10 102147276 . G C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33 PL:GT:GQ 43,9,0:1/1:63 chr10 102642248 . T G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr10 107666616 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr10 108319945 . C G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 43,9,0:1/1:63 chr10 109734371 . G A 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr10 112870604 . C T 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=36 PL:GT:GQ 79,12,0:1/1:72 chr10 115304673 . T C 11.3 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr10 119380588 . G A 14.2 . DP=4;AF1=0.502;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.18,0.32,1 PL:GT:GQ 44,0,21:0/1:24 chr10 123063756 . C T 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=23 PL:GT:GQ 46,9,0:1/1:63 chr10 128424770 . T G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 45,6,0:1/1:49 chr10 131229204 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr10 132420570 . G C 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr10 132528066 . C T 99 . DP=19;AF1=1;CI95=1,1;DP4=0,0,19,0;MQ=42 PL:GT:GQ 213,57,0:1/1:99 chr10 132644619 . G A 19.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23 PL:GT:GQ 52,15,0:1/1:75 chr10 132707581 . G C 9.11 . DP=51;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=25;PV4=1,1,1,1 PL:GT:GQ 38,2,0:1/1:37 chr10 133026892 . T C 55.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44 PL:GT:GQ 88,18,0:1/1:90 chr11 768033 . T C 33.5 . DP=4;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 62,0,1:1/1:5 chr11 768042 . T C 33.5 . DP=6;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 62,0,1:1/1:5 chr11 874568 . G C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 66,12,0:1/1:72 chr11 1009210 . T C 4 . DP=70;AF1=0.6241;CI95=0.5,1;DP4=0,3,0,8;MQ=24;PV4=1,1,0.5,1 PL:GT:GQ 31,0,4:0/1:6 chr11 1016692 . C T 27 . DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=22 PL:GT:GQ 60,114,0:1/1:99 chr11 1034477 . A G 66 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 98,9,0:1/1:63 chr11 1074037 . G A 4.13 . DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,5,0;MQ=24;PV4=1,1,0.43,1 PL:GT:GQ 32,0,30:0/1:31 chr11 1556298 . G A 11.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 44,12,0:1/1:72 chr11 1824777 . T C 27 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=28 PL:GT:GQ 60,30,0:1/1:99 chr11 3395801 . C T 22 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr11 3411901 . G A 4.75 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 35,9,0:1/1:63 chr11 3731606 . A C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr11 3783855 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr11 3967636 . A G 4.29 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24 PL:GT:GQ 35,15,0:1/1:75 chr11 4385618 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr11 4424365 . T A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr11 5295586 . C T 3.01 . DP=52;AF1=0.4997;CI95=0.5,0.5;DP4=33,0,10,0;MQ=29;PV4=1,0.0045,0.3,0.17 PL:GT:GQ 30,0,131:0/1:33 chr11 6157144 . C G 45.1 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=35 PL:GT:GQ 78,21,0:1/1:84 chr11 6352044 . C T 18 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31 PL:GT:GQ 50,9,0:1/1:63 chr11 6767356 . T C 9.63 . DP=3;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=29;PV4=1,1,1,1 PL:GT:GQ 38,1,0:1/1:23 chr11 6999404 . G C 21 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37 PL:GT:GQ 53,9,0:1/1:63 chr11 9120930 . C G 17.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr11 9373125 . T C 19.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 51,6,0:1/1:49 chr11 9585101 . C T 67 . DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=45 PL:GT:GQ 100,42,0:1/1:99 chr11 10266192 . A C 14.3 . DP=22;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=27 PL:GT:GQ 47,18,0:1/1:90 chr11 10303263 . T C 8.64 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=18 PL:GT:GQ 41,51,0:1/1:99 chr11 10420170 . T C 35 . DP=17;AF1=1;CI95=1,1;DP4=0,1,0,15;MQ=28;PV4=1,0.12,1,0.4 PL:GT:GQ 68,36,0:1/1:99 chr11 10912169 . G A 99 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=49 PL:GT:GQ 155,18,0:1/1:90 chr11 11315826 . T G 6.29 . DP=27;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=19 PL:GT:GQ 38,18,0:1/1:90 chr11 11603859 . A C 22 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=34;PV4=1,9.5e-13,0.22,1 PL:GT:GQ 52,0,115:0/1:55 chr11 11700034 . C T 33 . DP=11;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=30 PL:GT:GQ 66,27,0:1/1:99 chr11 11822758 . G A 15.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,3;MQ=38;PV4=1,0.18,1,1 PL:GT:GQ 45,0,88:0/1:48 chr11 11976636 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=24 PL:GT:GQ 54,9,0:1/1:63 chr11 14380517 . C G 16.1 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=5,0,5,0;MQ=48;PV4=1,2.1e-05,0.13,1 PL:GT:GQ 46,0,113:0/1:49 chr11 14419212 . A G 91.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38 PL:GT:GQ 124,18,0:1/1:90 chr11 14846792 . A G 55 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=19 PL:GT:GQ 88,33,0:1/1:99 chr11 15494556 . C T 99 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=22,0,14,0;MQ=34;PV4=1,0.0071,1,1 PL:GT:GQ 146,0,159:0/1:99 chr11 16262879 . A C 16.1 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=43;PV4=1,0.061,0.24,0.33 PL:GT:GQ 46,0,28:0/1:31 chr11 21514947 . T C 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=41 PL:GT:GQ 57,12,0:1/1:72 chr11 22532576 . C G 28 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=17 PL:GT:GQ 61,51,0:1/1:99 chr11 23529238 . G T 4.29 . DP=13;AF1=0.5334;CI95=0.5,1;DP4=1,0,3,0;MQ=37;PV4=1,1,0.34,0.21 PL:GT:GQ 32,0,9:0/1:12 chr11 24249554 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr11 24853167 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr11 33353903 . T C 24.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=36 PL:GT:GQ 57,15,0:1/1:75 chr11 35126569 . T C 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 57,12,0:1/1:72 chr11 35132248 . C T 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr11 35155482 . T C 68 . DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=46 PL:GT:GQ 101,66,0:1/1:99 chr11 52494088 . T C 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 140,27,0:1/1:99 chr11 57899943 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr11 62261460 . G T 19.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,5;MQ=27;PV4=1,1.1e-06,1,1 PL:GT:GQ 49,0,58:0/1:51 chr11 67456049 . C T 39.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=19 PL:GT:GQ 72,18,0:1/1:90 chr11 68509708 . C G 3.65 . DP=9;AF1=0.7301;CI95=0.5,1;DP4=0,5,0,4;MQ=17;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr11 70115115 . T A 99 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=49 PL:GT:GQ 140,15,0:1/1:75 chr11 72643951 . T C 70 . DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=39 PL:GT:GQ 103,66,0:1/1:99 chr11 72647930 . G A 36 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=41;PV4=1,1,0.3,1 PL:GT:GQ 66,0,28:0/1:31 chr11 73330148 . C T 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr11 81720893 . A G 5.83 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=19 PL:GT:GQ 37,12,0:1/1:72 chr11 83813797 . A G 23.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 56,12,0:1/1:72 chr11 85949488 . C A 54 . DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=37 PL:GT:GQ 87,42,0:1/1:99 chr11 87634829 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr11 90913093 . A T 35.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 67,6,0:1/1:49 chr11 93793348 . G A 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=31 PL:GT:GQ 139,24,0:1/1:96 chr11 100802294 . T C 16.6 . DP=21;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 49,12,0:1/1:72 chr11 107455449 . C T 8.44 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=26 PL:GT:GQ 39,6,0:1/1:49 chr11 111344355 . A G 69.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43 PL:GT:GQ 102,12,0:1/1:72 chr11 111611115 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr11 113050466 . G C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 36,6,0:1/1:49 chr11 114332544 . T C 3.54 . DP=17;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,5;MQ=37;PV4=1,0.32,0.13,1 PL:GT:GQ 31,0,37:0/1:33 chr11 114332549 . G A 3.54 . DP=17;AF1=0.4998;CI95=0.5,0.5;DP4=0,9,0,8;MQ=36;PV4=1,3.1e-10,0.088,1 PL:GT:GQ 31,0,127:0/1:34 chr11 114843578 . G C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr11 115580279 . A G 99 . DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=48 PL:GT:GQ 190,45,0:1/1:99 chr11 116434328 . G A 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr11 125914161 . A G 20.8 . DP=7;AF1=0.95;CI95=0.5,1;DP4=3,0,4,0;MQ=38;PV4=1,0.074,1,1 PL:GT:GQ 49,0,0:1/1:10 chr11 125917089 . C T 12.3 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,28,0,12;MQ=44;PV4=1,4.7e-25,1,1 PL:GT:GQ 42,0,167:0/1:45 chr11 127194100 . A G 60 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=49 PL:GT:GQ 93,24,0:1/1:96 chr12 70856 . G A 27.5 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 60,12,0:1/1:72 chr12 153693 . T C 52.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=38 PL:GT:GQ 85,15,0:1/1:75 chr12 924547 . C G 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 69,6,0:1/1:49 chr12 1555916 . G A 7.18 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 39,15,0:1/1:75 chr12 1919860 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr12 2283756 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr12 2805983 . G C 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr12 6088203 . T C 72.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=37 PL:GT:GQ 105,15,0:1/1:75 chr12 7099460 . G C 10.8 . DP=6;AF1=0.8277;CI95=0.5,1;DP4=3,0,3,0;MQ=26;PV4=1,0.027,1,1 PL:GT:GQ 39,0,1:1/1:5 chr12 7099464 . G A 13.3 . DP=6;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=28;PV4=1,0.16,1,1 PL:GT:GQ 42,1,0:1/1:23 chr12 7198516 . T G 4.61 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 34,6,0:1/1:49 chr12 23331895 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr12 28209020 . T G 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 47,15,0:1/1:75 chr12 30074073 . C T 32.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 64,6,0:1/1:49 chr12 30563452 . T C 25 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 57,9,0:1/1:63 chr12 30563453 . A G 25 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 57,9,0:1/1:63 chr12 30563464 . C A 78.8 . DP=8;AF1=1;CI95=0.5,1;DP4=0,2,0,5;MQ=34;PV4=1,0.29,1,1 PL:GT:GQ 110,6,0:1/1:49 chr12 31505085 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr12 34041336 . G A 5.46 . DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=36;PV4=1,1,0.48,0.21 PL:GT:GQ 34,0,34:0/1:34 chr12 49003648 . C G 42 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=39 PL:GT:GQ 75,24,0:1/1:96 chr12 51280690 . G A 69 . DP=98;AF1=0.5;CI95=0.5,0.5;DP4=13,0,18,0;MQ=45;PV4=1,1,0.051,1 PL:GT:GQ 99,0,84:0/1:87 chr12 69206633 . T C 17.1 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=17 PL:GT:GQ 50,33,0:1/1:99 chr12 80417253 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr12 86633033 . C T 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=43;PV4=1,1,0.33,1 PL:GT:GQ 64,0,31:0/1:34 chr12 98097274 . C T 47.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31 PL:GT:GQ 80,15,0:1/1:75 chr12 105269319 . C T 19 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26 PL:GT:GQ 51,9,0:1/1:63 chr12 109053425 . G A 9.53 . DP=8;AF1=0.5012;CI95=0.5,0.5;DP4=2,0,6,0;MQ=25;PV4=1,1,0.19,1 PL:GT:GQ 39,0,23:0/1:26 chr12 111904540 . A G 3.41 . DP=65;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 32,6,0:1/1:49 chr12 115038686 . T C 15.2 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27 PL:GT:GQ 48,21,0:1/1:84 chr12 115039419 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 34,9,0:1/1:63 chr12 115103890 . G A 66 . DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=49 PL:GT:GQ 99,114,0:1/1:99 chr12 115833830 . G A 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr12 116361873 . T G 6.34 . DP=5;AF1=0.7302;CI95=0.5,1;DP4=0,2,0,2;MQ=23;PV4=1,1,1,1 PL:GT:GQ 34,0,2:0/1:3 chr12 123583527 . G A 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 46,9,0:1/1:63 chr12 124115330 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 76,9,0:1/1:63 chr12 125062296 . G A 41.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr12 126718106 . A G 8.76 . DP=50;AF1=0.5163;CI95=0.5,1;DP4=2,0,6,0;MQ=26;PV4=1,0.33,0.37,1 PL:GT:GQ 38,0,12:0/1:15 chr12 133348311 . G A 24 . DP=18;AF1=0.5;CI95=0.5,0.5;DP4=14,0,3,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 54,0,118:0/1:57 chr12 134494475 . C T 28 . DP=18;AF1=0.6671;CI95=0.5,1;DP4=8,0,10,0;MQ=18;PV4=1,1,1,1 PL:GT:GQ 57,0,3:0/1:5 chr12 134831761 . C T 41.3 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=27 PL:GT:GQ 74,15,0:1/1:75 chr12 134992770 . A C,T 84 . DP=47;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=29 PL:GT:GQ 117,72,114,0,44,114:1/1:99 chr12 135261117 . G A 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 82,18,0:1/1:90 chr12 135261144 . A G 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 155,18,0:1/1:90 chr12 135460302 . G A 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=40 PL:GT:GQ 198,69,0:1/1:99 chr12 135463758 . A G 83 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=26 PL:GT:GQ 116,48,0:1/1:99 chr12 135523325 . G A 99 . DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=26 PL:GT:GQ 136,66,0:1/1:99 chr12 135782401 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr12 135795472 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr13 18040027 . G C 42 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33 PL:GT:GQ 74,9,0:1/1:63 chr13 19494625 . G T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr13 20121126 . A G 15.1 . DP=36;AF1=0.5;CI95=0.5,0.5;DP4=25,0,9,0;MQ=36;PV4=1,1,0.13,1 PL:GT:GQ 45,0,153:0/1:48 chr13 21536703 . A G 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr13 23160035 . G T 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 33,6,0:1/1:49 chr13 23476554 . C A 6.79 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52 PL:GT:GQ 37,6,0:1/1:49 chr13 26632967 . C G 32 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34 PL:GT:GQ 65,27,0:1/1:99 chr13 26790010 . T C 89.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35 PL:GT:GQ 122,15,0:1/1:75 chr13 36083571 . T C 43 . DP=84;AF1=1;CI95=1,1;DP4=1,0,37,0;MQ=16;PV4=1,1,1,0.3 PL:GT:GQ 76,99,0:1/1:99 chr13 44432419 . C T 3.58 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19 PL:GT:GQ 34,21,0:1/1:84 chr13 46592359 . T C 16.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 48,6,0:1/1:49 chr13 52764657 . A T 3.14 . DP=32;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 33,15,0:1/1:75 chr13 53084193 . C T 9.11 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=29;PV4=1,1,1,1 PL:GT:GQ 38,2,0:1/1:37 chr13 57763228 . C T 45 . DP=555;AF1=1;CI95=1,1;DP4=2,0,21,0;MQ=23;PV4=1,0.00021,1,0.3 PL:GT:GQ 78,45,0:1/1:99 chr13 73857921 . G C 31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 63,9,0:1/1:63 chr13 76718001 . G A 59 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=45;PV4=1,1,0.12,1 PL:GT:GQ 89,0,28:0/1:31 chr13 100912695 . A T 23 . DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,6;MQ=31;PV4=1,0.029,1,0.35 PL:GT:GQ 53,0,103:0/1:56 chr13 101332001 . G C 21 . DP=23;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=21 PL:GT:GQ 54,69,0:1/1:99 chr13 102637334 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr13 102895627 . C T 63 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=48 PL:GT:GQ 96,27,0:1/1:99 chr13 103830322 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr13 112842448 . G A 39 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=27 PL:GT:GQ 72,27,0:1/1:99 chr13 113310291 . C T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 66,12,0:1/1:72 chr13 114775162 . A G 80 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=21 PL:GT:GQ 113,51,0:1/1:99 chr13 115267482 . A G 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr13 116068676 . C T 3.83 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27 PL:GT:GQ 34,12,0:1/1:72 chr13 116455918 . A G 33 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=13,0,15,0;MQ=42;PV4=1,1.8e-20,0.3,1 PL:GT:GQ 63,0,146:0/1:66 chr13 116765012 . G A 30.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 62,6,0:1/1:49 chr13 116779773 . C T 17.1 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=27,0,11,0;MQ=24;PV4=1,4.5e-35,1,1 PL:GT:GQ 47,0,106:0/1:50 chr13 116779791 . C T 57 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=24,0,14,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 87,0,103:0/1:90 chr14 20159250 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr14 23510676 . T C 52 . DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=32 PL:GT:GQ 85,66,0:1/1:99 chr14 24735256 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr14 29525577 . G A 21 . DP=10;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=16 PL:GT:GQ 54,27,0:1/1:99 chr14 36186389 . C T 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20 PL:GT:GQ 37,6,0:1/1:49 chr14 36186394 . A G 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20 PL:GT:GQ 37,6,0:1/1:49 chr14 37440609 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr14 40432807 . A G 18.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=23 PL:GT:GQ 51,12,0:1/1:72 chr14 59466268 . T C 15.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25 PL:GT:GQ 47,9,0:1/1:63 chr14 61368162 . G T 7.18 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=17 PL:GT:GQ 39,15,0:1/1:75 chr14 65152922 . G A 92 . DP=33;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,15;MQ=36;PV4=1,0.059,0.35,1 PL:GT:GQ 122,0,144:0/1:99 chr14 69749148 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25 PL:GT:GQ 40,6,0:1/1:49 chr14 74877658 . C T 45 . DP=48;AF1=1;CI95=1,1;DP4=0,1,0,12;MQ=36;PV4=1,0.02,1,0.39 PL:GT:GQ 78,28,0:1/1:99 chr14 75546678 . C T 19.2 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=17 PL:GT:GQ 52,18,0:1/1:90 chr14 76439185 . T C 67.1 . DP=7;AF1=0.505;CI95=0.5,0.5;DP4=0,1,0,6;MQ=33;PV4=1,1,0.056,0.29 PL:GT:GQ 97,0,17:0/1:20 chr14 77313295 . T A 99 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=48 PL:GT:GQ 191,30,0:1/1:99 chr14 77673422 . G A 11.5 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=24 PL:GT:GQ 44,18,0:1/1:90 chr14 78646125 . T C 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40 PL:GT:GQ 153,24,0:1/1:96 chr14 91702449 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr14 91769842 . G A 63 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47 PL:GT:GQ 95,9,0:1/1:63 chr14 91775899 . C G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr14 91775924 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr14 93482918 . A C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr14 93665819 . C T 75 . DP=7;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,4;MQ=42;PV4=1,1,1,1 PL:GT:GQ 105,0,31:0/1:34 chr14 95422276 . A G 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=45 PL:GT:GQ 88,21,0:1/1:84 chr14 95731986 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr14 96045464 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr14 97172020 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=51 PL:GT:GQ 100,9,0:1/1:63 chr14 100515480 . A G 6.98 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,0.14,0.085,0.33 PL:GT:GQ 36,0,30:0/1:32 chr14 100770214 . A T 8.69 . DP=20;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16 PL:GT:GQ 41,21,0:1/1:84 chr14 101258303 . G A 82 . DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=26 PL:GT:GQ 115,45,0:1/1:99 chr14 101701492 . C G 66 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=49 PL:GT:GQ 99,30,0:1/1:99 chr14 102113772 . T C 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30 PL:GT:GQ 33,6,0:1/1:49 chr14 102751431 . A C 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr14 103708033 . A G 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=27 PL:GT:GQ 141,36,0:1/1:99 chr14 104744582 . G A 3.52 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 33,9,0:1/1:63 chr14 105989100 . C T 3.14 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 33,15,0:1/1:75 chr14 105989162 . C T 3.65 . DP=12;AF1=0.7301;CI95=0.5,1;DP4=0,6,0,6;MQ=15;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr14 106234810 . G A 25.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=39 PL:GT:GQ 58,15,0:1/1:75 chr14 106995572 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr14 107283057 . T C 5.5 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=20 PL:GT:GQ 37,21,0:1/1:84 chr14 107285319 . T C 33 . DP=36;AF1=1;CI95=1,1;DP4=0,0,0,35;MQ=22 PL:GT:GQ 66,105,0:1/1:99 chr14 107640449 . A G 11.8 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36 PL:GT:GQ 44,12,0:1/1:72 chr15 20082092 . T G 18.3 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24 PL:GT:GQ 51,15,0:1/1:75 chr15 22955884 . T C 67 . DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=48 PL:GT:GQ 100,36,0:1/1:99 chr15 22971987 . A G 5.29 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=22 PL:GT:GQ 35,6,0:1/1:49 chr15 23233324 . C A 47 . DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31 PL:GT:GQ 80,42,0:1/1:99 chr15 25175286 . C T 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=42;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr15 25385709 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr15 27372396 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr15 35998093 . C T 9.53 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=17 PL:GT:GQ 42,27,0:1/1:99 chr15 36716538 . C G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr15 36793360 . G T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 76,9,0:1/1:63 chr15 53783097 . A G 10.5 . DP=31;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16 PL:GT:GQ 43,21,0:1/1:84 chr15 54180175 . C T 10.4 . DP=7;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,3,0;MQ=27;PV4=1,1.2e-05,1,1 PL:GT:GQ 40,0,32:0/1:34 chr15 54939306 . C T 99 . DP=34;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,16;MQ=49;PV4=1,1,0.18,1 PL:GT:GQ 172,0,181:0/1:99 chr15 59377916 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr15 59685961 . G C 68 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=36 PL:GT:GQ 101,33,0:1/1:99 chr15 60306384 . A G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr15 60345642 . G C 14.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 46,6,0:1/1:49 chr15 60367387 . G A 13.2 . DP=6;AF1=0.5001;CI95=0.5,0.5;DP4=3,0,3,0;MQ=34;PV4=1,0.098,0.24,1 PL:GT:GQ 43,0,35:0/1:37 chr15 60367446 . C T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr15 61763755 . G A 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45 PL:GT:GQ 100,9,0:1/1:63 chr15 61831362 . C G 11.3 . DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,3;MQ=30;PV4=1,0.00077,0.47,1 PL:GT:GQ 41,0,42:0/1:41 chr15 63978880 . G C 60 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 90,3,0:1/1:41 chr15 64342445 . A G 12.2 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=18 PL:GT:GQ 44,9,0:1/1:63 chr15 65424859 . T C 11.3 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=21 PL:GT:GQ 44,30,0:1/1:99 chr15 65603698 . C T 60 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 92,9,0:1/1:63 chr15 67005078 . G A 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr15 71133512 . G C 22.3 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25 PL:GT:GQ 55,15,0:1/1:75 chr15 72619009 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr15 73272688 . C T 70.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=39 PL:GT:GQ 103,15,0:1/1:75 chr15 73699335 . T A 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=45 PL:GT:GQ 175,27,0:1/1:99 chr15 74513352 . C T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=37 PL:GT:GQ 139,30,0:1/1:99 chr15 75540536 . G A 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr15 75822537 . C A 17.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23 PL:GT:GQ 50,15,0:1/1:75 chr15 78554005 . T C 12 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 43,6,0:1/1:49 chr15 80089369 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=28 PL:GT:GQ 40,6,0:1/1:49 chr15 83089149 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 40,6,0:1/1:49 chr15 86839307 . T C 90.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 123,15,0:1/1:75 chr15 89836258 . T C 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39 PL:GT:GQ 141,24,0:1/1:96 chr15 89837706 . G A 4.13 . DP=8;AF1=0.4998;CI95=0.5,0.5;DP4=0,4,0,4;MQ=30;PV4=1,1,0.25,1 PL:GT:GQ 32,0,59:0/1:35 chr15 89857648 . T C 99 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=8,0,8,0;MQ=40;PV4=1,1,0.3,1 PL:GT:GQ 133,0,130:0/1:99 chr15 89864228 . A C 32 . DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,2,0;MQ=42;PV4=1,1,1,1 PL:GT:GQ 62,0,31:0/1:34 chr15 91261235 . G A 7.8 . DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=44;PV4=1,1,0.32,1 PL:GT:GQ 37,0,30:0/1:32 chr16 256990 . A C 10.4 . DP=16;AF1=0.5008;CI95=0.5,0.5;DP4=4,0,3,0;MQ=23;PV4=1,0.34,1,1 PL:GT:GQ 40,0,25:0/1:28 chr16 260794 . T C 3.01 . DP=19;AF1=0.4999;CI95=0.5,0.5;DP4=13,0,2,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 30,0,32:0/1:31 chr16 419905 . A G 7.9 . DP=5;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=22;PV4=1,1,1,1 PL:GT:GQ 36,1,0:1/1:23 chr16 824086 . T C 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr16 1085063 . C T 52 . DP=12;AF1=0.5;CI95=0.5,0.5;DP4=6,0,6,0;MQ=42;PV4=1,1,0.014,1 PL:GT:GQ 82,0,128:0/1:85 chr16 1221305 . T C 54 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=0,3,0,3;MQ=40;PV4=1,1,1,1 PL:GT:GQ 84,0,60:0/1:63 chr16 1411728 . A G 32.3 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35 PL:GT:GQ 65,15,0:1/1:75 chr16 1443197 . C G 64 . DP=26;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=36 PL:GT:GQ 97,75,0:1/1:99 chr16 1478746 . A T 32 . DP=20;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=28 PL:GT:GQ 65,24,0:1/1:96 chr16 1514438 . A C 45 . DP=49;AF1=1;CI95=1,1;DP4=0,0,48,0;MQ=26 PL:GT:GQ 78,144,0:1/1:99 chr16 1601989 . T C 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=29 PL:GT:GQ 133,39,0:1/1:99 chr16 2043883 . C T 30 . DP=33;AF1=1;CI95=1,1;DP4=0,0,0,33;MQ=14 PL:GT:GQ 63,99,0:1/1:99 chr16 2137470 . A C 39 . DP=38;AF1=0.5016;CI95=0.5,0.5;DP4=4,0,6,0;MQ=34;PV4=1,0.02,1,1 PL:GT:GQ 69,0,22:0/1:25 chr16 2537260 . A G 99 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=40 PL:GT:GQ 177,33,0:1/1:99 chr16 2564737 . T C 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,22;MQ=41 PL:GT:GQ 199,66,0:1/1:99 chr16 2612605 . A T 62.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28 PL:GT:GQ 95,15,0:1/1:75 chr16 2704518 . G A 41 . DP=48;AF1=0.5;CI95=0.5,0.5;DP4=0,17,0,12;MQ=48;PV4=1,1.9e-23,0.24,0.034 PL:GT:GQ 71,0,175:0/1:74 chr16 3274307 . G T 68 . DP=39;AF1=0.5;CI95=0.5,0.5;DP4=0,30,0,8;MQ=37;PV4=1,1,1,1 PL:GT:GQ 98,0,138:0/1:99 chr16 5467292 . G C 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 69,6,0:1/1:49 chr16 10079145 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr16 11483702 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr16 12038227 . A T 23 . DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,22,0,23;MQ=32;PV4=1,4.4e-66,0.47,0.028 PL:GT:GQ 53,0,135:0/1:56 chr16 21336880 . G C 55 . DP=35;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,19;MQ=47;PV4=1,5.6e-21,1,1 PL:GT:GQ 85,0,121:0/1:88 chr16 21980241 . C T 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr16 23275383 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 44,6,0:1/1:49 chr16 27546495 . G T 25 . DP=35;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43 PL:GT:GQ 57,9,0:1/1:63 chr16 27700399 . A T 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=17 PL:GT:GQ 50,12,0:1/1:72 chr16 28021935 . A G 18.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 51,15,0:1/1:75 chr16 29070016 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr16 29478618 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr16 29718140 . C T 46.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 79,15,0:1/1:75 chr16 30700759 . T C 17.1 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=14 PL:GT:GQ 50,42,0:1/1:99 chr16 35139103 . A G 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37 PL:GT:GQ 79,12,0:1/1:72 chr16 35473348 . G A 3.83 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 34,12,0:1/1:72 chr16 36213667 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr16 36705528 . G A 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=32 PL:GT:GQ 47,15,0:1/1:75 chr16 43831353 . C T 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42 PL:GT:GQ 102,12,0:1/1:72 chr16 44715166 . A C 25 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=32 PL:GT:GQ 58,24,0:1/1:96 chr16 44957661 . T C 7.03 . DP=23;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=18 PL:GT:GQ 39,21,0:1/1:84 chr16 44958698 . C T 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=49 PL:GT:GQ 75,15,0:1/1:75 chr16 44959163 . T C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 66,12,0:1/1:72 chr16 45167959 . C T 4.45 . DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=24 PL:GT:GQ 35,12,0:1/1:72 chr16 50254956 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr16 52383122 . A C 46.5 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=42 PL:GT:GQ 79,12,0:1/1:72 chr16 55978159 . C T 10.7 . DP=20;AF1=0.5336;CI95=0.5,1;DP4=2,0,5,0;MQ=35;PV4=1,0.038,1,0.059 PL:GT:GQ 40,0,9:0/1:12 chr16 61358878 . T A 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 47,6,0:1/1:49 chr16 61392487 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 44,6,0:1/1:49 chr16 61621603 . G T 6.59 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=22 PL:GT:GQ 38,12,0:1/1:72 chr16 69120890 . G C 51.3 . DP=36;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42 PL:GT:GQ 84,15,0:1/1:75 chr16 70778219 . A G 21.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=39 PL:GT:GQ 53,6,0:1/1:49 chr16 71899519 . T C 40 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33 PL:GT:GQ 73,33,0:1/1:99 chr16 72079251 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr16 72093003 . G C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr16 72672428 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr16 72864515 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr16 72890560 . G A 47.1 . DP=10;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=49;PV4=1,0.0019,0.0033,1 PL:GT:GQ 77,0,16:0/1:19 chr16 73048929 . A G 6.29 . DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=27;PV4=1,1,1,0.33 PL:GT:GQ 34,1,0:1/1:23 chr16 73177179 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr16 73191468 . C T 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40 PL:GT:GQ 102,12,0:1/1:72 chr16 73367439 . A C 7.41 . DP=36;AF1=1;CI95=0.5,1;DP4=0,2,0,13;MQ=26;PV4=1,1,0.027,1 PL:GT:GQ 37,4,0:1/1:45 chr16 74259316 . C T 89.5 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr16 75271450 . C G 6.99 . DP=15;AF1=0.5015;CI95=0.5,0.5;DP4=0,1,0,3;MQ=44;PV4=1,0.065,0.31,1 PL:GT:GQ 36,0,22:0/1:25 chr16 76199870 . G A 26 . DP=14;AF1=0.5;CI95=0.5,0.5;DP4=8,0,6,0;MQ=47;PV4=1,1.2e-06,0.32,1 PL:GT:GQ 56,0,141:0/1:59 chr16 77723692 . A G 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 122,12,0:1/1:72 chr17 165875 . G A 40.8 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 72,6,0:1/1:49 chr17 1443809 . C G 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr17 1618253 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=39 PL:GT:GQ 54,9,0:1/1:63 chr17 2815309 . T G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr17 3537486 . T G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr17 3734367 . C A 23.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36 PL:GT:GQ 56,12,0:1/1:72 chr17 5634764 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr17 6408090 . C G 3.54 . DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=3,0,2,0;MQ=40;PV4=1,1,0.36,1 PL:GT:GQ 31,0,66:0/1:34 chr17 7089723 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr17 8731503 . G C 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 42,6,0:1/1:49 chr17 9282935 . T C,G 24.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=40 PL:GT:GQ 57,12,61,0,3,61:1/1:72 chr17 17284831 . T C 29 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 61,9,0:1/1:63 chr17 18439515 . G A 4.11 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25 PL:GT:GQ 34,9,0:1/1:63 chr17 18602146 . C T 4.76 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=16 PL:GT:GQ 36,33,0:1/1:99 chr17 19427888 . C T 57 . DP=104;AF1=0.5;CI95=0.5,0.5;DP4=45,0,29,0;MQ=39;PV4=1,2.2e-12,1,1 PL:GT:GQ 87,0,131:0/1:90 chr17 19604159 . T C 9.31 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr17 19610366 . C T 13 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr17 20484706 . C G 51 . DP=35;AF1=0.5001;CI95=0.5,0.5;DP4=0,11,0,21;MQ=21;PV4=1,0.39,0.49,1 PL:GT:GQ 81,0,36:0/1:39 chr17 20555720 . A G 26.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=28 PL:GT:GQ 59,15,0:1/1:75 chr17 24328984 . A C 15.4 . DP=34;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25 PL:GT:GQ 48,15,0:1/1:75 chr17 26237090 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr17 28394766 . C A 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr17 31218277 . A G 3.62 . DP=38;AF1=0.5161;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,0.26,1,1 PL:GT:GQ 31,0,12:0/1:15 chr17 31254021 . C T 15.1 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35 PL:GT:GQ 47,9,0:1/1:63 chr17 32516798 . G A 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 69,6,0:1/1:49 chr17 32600253 . A G 16.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 49,12,0:1/1:72 chr17 34255214 . G C 19.2 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=21 PL:GT:GQ 52,18,0:1/1:90 chr17 34365900 . T C 93.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38 PL:GT:GQ 126,18,0:1/1:90 chr17 35380386 . A T 6.79 . DP=44;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 37,6,0:1/1:49 chr17 41993344 . C T 64 . DP=41;AF1=1;CI95=1,1;DP4=0,0,0,41;MQ=16 PL:GT:GQ 97,123,0:1/1:99 chr17 42128201 . A G 4.13 . DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=0,2,0,2;MQ=52;PV4=1,0.0041,1,1 PL:GT:GQ 32,0,62:0/1:35 chr17 42984490 . C A 56 . DP=33;AF1=0.5001;CI95=0.5,0.5;DP4=6,0,12,0;MQ=42;PV4=1,0.004,1,1 PL:GT:GQ 86,0,34:0/1:37 chr17 43419457 . G A 99 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=45 PL:GT:GQ 185,42,0:1/1:99 chr17 43421225 . A G 65.1 . DP=31;AF1=1;CI95=0.5,1;DP4=0,6,0,17;MQ=43;PV4=1,0.004,1,1 PL:GT:GQ 98,18,0:1/1:90 chr17 45206897 . G A 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47 PL:GT:GQ 54,9,0:1/1:63 chr17 45381302 . T C 18.6 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr17 45530812 . C A 3.54 . DP=6;AF1=0.4998;CI95=0.5,0.5;DP4=0,3,0,2;MQ=40;PV4=1,1,0.37,1 PL:GT:GQ 31,0,58:0/1:34 chr17 50242633 . G A 44 . DP=42;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,13;MQ=32;PV4=1,0.084,0.14,1 PL:GT:GQ 74,0,154:0/1:77 chr17 51275317 . G A 14.9 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 46,6,0:1/1:49 chr17 52325530 . C T 29 . DP=19;AF1=1;CI95=1,1;DP4=0,0,0,18;MQ=24 PL:GT:GQ 62,54,0:1/1:99 chr17 52411748 . T G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr17 53190746 . C G 62.1 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=40 PL:GT:GQ 95,18,0:1/1:90 chr17 58289916 . T C 18.2 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=22 PL:GT:GQ 51,18,0:1/1:90 chr17 59796875 . C T 42 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35 PL:GT:GQ 74,9,0:1/1:63 pysam-0.23.0/tests/tabix_data/vcf/README.txt000066400000000000000000000005221475062545500204570ustar00rootroot00000000000000Edits that were necessary to parse these files: 23.vcf: change ##INFO= to ##INFO= similar changes in 16.vcf and 2.vcf 13.vcf Flag should not have a value. pysam-0.23.0/tests/tabix_data/vcf/issue85.vcf000066400000000000000000000046511475062545500207750ustar00rootroot00000000000000##fileformat=VCFv4.1 ##samtoolsVersion=0.1.18 (r982:295) ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= pysam-0.23.0/tests/tabix_data/vcf/vcf_v42.vcf000066400000000000000000000032411475062545500207330ustar00rootroot00000000000000##fileformat=VCFv4.2 ##fileDate=20090805 ##source=myImputationProgramV3.1 ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta ##contig= ##phasing=partial ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 pysam-0.23.0/tests/tabix_test.py000066400000000000000000001177711475062545500166420ustar00rootroot00000000000000#!/usr/bin/env python '''unit testing code for pysam. Execute in the :file:`tests` directory as it requires the Makefile and data files located there. ''' import os import shutil import gzip import pysam import unittest import glob import re from TestUtils import checkBinaryEqual, checkGZBinaryEqual, check_url, \ load_and_convert, make_data_files, TABIX_DATADIR, get_temp_filename def setUpModule(): make_data_files(TABIX_DATADIR) def myzip_open(infile, mode="r"): '''open compressed file and decode.''' def _convert(f): for l in f: yield l.decode("ascii") if mode == "r": return _convert(gzip.open(infile, "r")) def splitToBytes(s): '''split string and return list of bytes.''' return [x.encode("ascii") for x in s.split("\t")] class TestIndexing(unittest.TestCase): filename = os.path.join(TABIX_DATADIR, "example.gtf.gz") filename_idx = os.path.join(TABIX_DATADIR, "example.gtf.gz.tbi") def setUp(self): self.tmpfilename = get_temp_filename(suffix="gtf.gz") shutil.copyfile(self.filename, self.tmpfilename) def test_indexing_with_preset_works(self): '''test indexing via preset.''' pysam.tabix_index(self.tmpfilename, preset="gff") self.assertTrue(checkGZBinaryEqual( self.tmpfilename + ".tbi", self.filename_idx)) def test_indexing_to_custom_location_works(self): '''test indexing a file with a non-default location.''' index_path = get_temp_filename(suffix='custom.tbi') pysam.tabix_index(self.tmpfilename, preset="gff", index=index_path, force=True) self.assertTrue(checkGZBinaryEqual(index_path, self.filename_idx)) os.unlink(index_path) def test_indexing_with_explict_columns_works(self): '''test indexing via preset.''' pysam.tabix_index(self.tmpfilename, seq_col=0, start_col=3, end_col=4, line_skip=0, zerobased=False) self.assertTrue(checkGZBinaryEqual( self.tmpfilename + ".tbi", self.filename_idx)) def test_indexing_with_lineskipping_works(self): '''test indexing via preset and lineskip.''' pysam.tabix_index(self.tmpfilename, seq_col=0, start_col=3, end_col=4, line_skip=1, zerobased=False) self.assertFalse(checkGZBinaryEqual( self.tmpfilename + ".tbi", self.filename_idx)) def tearDown(self): os.unlink(self.tmpfilename) if os.path.exists(self.tmpfilename + ".tbi"): os.unlink(self.tmpfilename + ".tbi") class TestCompression(unittest.TestCase): filename = os.path.join(TABIX_DATADIR, "example.gtf.gz") filename_idx = os.path.join(TABIX_DATADIR, "example.gtf.gz.tbi") preset = "gff" def setUp(self): self.tmpfilename = get_temp_filename(suffix="gtf") with gzip.open(self.filename, "rb") as infile, \ open(self.tmpfilename, "wb") as outfile: outfile.write(infile.read()) def testCompression(self): '''see also issue 106''' pysam.tabix_compress(self.tmpfilename, self.tmpfilename + ".gz") checkBinaryEqual(self.tmpfilename, self.tmpfilename + ".gz") def testIndexPresetUncompressed(self): '''test indexing via preset.''' pysam.tabix_index(self.tmpfilename, preset=self.preset) # check if uncompressed file has been removed self.assertEqual(os.path.exists(self.tmpfilename), False) checkBinaryEqual(self.tmpfilename + ".gz", self.filename) checkBinaryEqual(self.tmpfilename + ".gz.tbi", self.filename_idx) def testIndexPresetCompressed(self): '''test indexing via preset.''' pysam.tabix_compress(self.tmpfilename, self.tmpfilename + ".gz") pysam.tabix_index(self.tmpfilename + ".gz", preset=self.preset) checkBinaryEqual(self.tmpfilename + ".gz", self.filename) checkBinaryEqual(self.tmpfilename + ".gz.tbi", self.filename_idx) def tearDown(self): if os.path.exists(self.tmpfilename): os.unlink(self.tmpfilename) if os.path.exists(self.tmpfilename + ".gz"): os.unlink(self.tmpfilename + ".gz") if os.path.exists(self.tmpfilename + ".gz.tbi"): os.unlink(self.tmpfilename + ".gz.tbi") class TestCompressionSam(TestCompression): filename = os.path.join(TABIX_DATADIR, "example.sam.gz") filename_index = os.path.join(TABIX_DATADIR, "example.sam.gz.tbi") preset = "sam" class TestCompressionBed(TestCompression): filename = os.path.join(TABIX_DATADIR, "example.bed.gz") filename_index = os.path.join(TABIX_DATADIR, "example.bed.gz.tbi") preset = "bed" class TestCompressionVCF(TestCompression): filename = os.path.join(TABIX_DATADIR, "example.vcf.gz") filename_index = os.path.join(TABIX_DATADIR, "example.vcf.gz.tbi") preset = "vcf" class IterationTest(unittest.TestCase): with_comments = False def setUp(self): lines = [] with gzip.open(self.filename, "rb") as inf: for line in inf: line = line.decode('ascii') if line.startswith("#"): if not self.with_comments: continue lines.append(line) # creates index of contig, start, end, adds content without newline. self.compare = [ (x[0][0], int(x[0][3]), int(x[0][4]), x[1]) for x in [(y.split("\t"), y[:-1]) for y in lines if not y.startswith("#")]] self.comments = [x[:-1] for x in lines if x.startswith("#")] def getSubset(self, contig=None, start=None, end=None): if contig is None: # all lines subset = [x[3] for x in self.compare] else: if start is not None and end is None: # until end of contig subset = [x[3] for x in self.compare if x[0] == contig and x[2] > start] elif start is None and end is not None: # from start of contig subset = [x[3] for x in self.compare if x[0] == contig and x[1] <= end] elif start is None and end is None: subset = [x[3] for x in self.compare if x[0] == contig] else: # all within interval subset = [x[3] for x in self.compare if x[0] == contig and min(x[2], end) - max(x[1], start) > 0] if self.with_comments: subset.extend(self.comments) return subset def checkPairwise(self, result, ref): '''check pairwise results. ''' result.sort() ref.sort() a = set(result) b = set(ref) self.assertEqual( len(result), len(ref), "unexpected number of results: " "result=%i, expected ref=%i, differences are %s: %s" % (len(result), len(ref), a.difference(b), b.difference(a))) for x, d in enumerate(list(zip(result, ref))): self.assertEqual( d[0], d[1], "unexpected results in pair %i:\n'%s', expected\n'%s'" % (x, d[0], d[1])) class TestGZFile(IterationTest): filename = os.path.join(TABIX_DATADIR, "example.gtf.gz") with_comments = True def setUp(self): super().setUp() self.gzfile = pysam.GZIterator(self.filename) def testAll(self): result = list(self.gzfile) ref = self.getSubset() self.checkPairwise(result, ref) class TestIterationWithoutComments(IterationTest): '''test iterating with TabixFile.fetch() when there are no comments in the file.''' filename = os.path.join(TABIX_DATADIR, "example.gtf.gz") def setUp(self): super().setUp() self.tabix = pysam.TabixFile(self.filename) def tearDown(self): self.tabix.close() def testRegionStrings(self): """test if access with various region strings works""" self.assertEqual(218, len(list( self.tabix.fetch("chr1")))) self.assertEqual(218, len(list( self.tabix.fetch("chr1", 1000)))) self.assertEqual(218, len(list( self.tabix.fetch("chr1", end=1000000)))) self.assertEqual(218, len(list( self.tabix.fetch("chr1", 1000, 1000000)))) def testAll(self): result = list(self.tabix.fetch()) ref = self.getSubset() self.checkPairwise(result, ref) def testPerContig(self): for contig in ("chr1", "chr2", "chr1", "chr2"): result = list(self.tabix.fetch(contig)) ref = self.getSubset(contig) self.checkPairwise(result, ref) def testPerContigToEnd(self): end = None for contig in ("chr1", "chr2", "chr1", "chr2"): for start in range(0, 200000, 1000): result = list(self.tabix.fetch(contig, start, end)) ref = self.getSubset(contig, start, end) self.checkPairwise(result, ref) def testPerContigFromStart(self): start = None for contig in ("chr1", "chr2", "chr1", "chr2"): for end in range(0, 200000, 1000): result = list(self.tabix.fetch(contig, start, end)) ref = self.getSubset(contig, start, end) self.checkPairwise(result, ref) def testPerContig2(self): start, end = None, None for contig in ("chr1", "chr2", "chr1", "chr2"): result = list(self.tabix.fetch(contig, start, end)) ref = self.getSubset(contig, start, end) self.checkPairwise(result, ref) def testPerInterval(self): start, end = None, None for contig in ("chr1", "chr2", "chr1", "chr2"): for start in range(0, 200000, 2000): for end in range(start, start + 2000, 500): result = list(self.tabix.fetch(contig, start, end)) ref = self.getSubset(contig, start, end) self.checkPairwise(result, ref) def testInvalidIntervals(self): # invalid intervals (start > end) self.assertRaises(ValueError, self.tabix.fetch, "chr1", 0, -10) self.assertRaises(ValueError, self.tabix.fetch, "chr1", 200, 0) # out of range intervals self.assertRaises(ValueError, self.tabix.fetch, "chr1", -10, 200) self.assertRaises(ValueError, self.tabix.fetch, "chr1", -10, -20) # unknown chromosome self.assertRaises(ValueError, self.tabix.fetch, "chrUn") # out of range access # to be implemented # self.assertRaises(IndexError, self.tabix.fetch, "chr1", 1000000, 2000000) # raise no error for empty intervals self.tabix.fetch("chr1", 100, 100) def testGetContigs(self): self.assertEqual(sorted(self.tabix.contigs), ["chr1", "chr2"]) # check that contigs is read-only self.assertRaises( AttributeError, setattr, self.tabix, "contigs", ["chr1", "chr2"]) def testHeader(self): ref = [] with gzip.open(self.filename) as inf: for x in inf: x = x.decode("ascii") if not x.startswith("#"): break ref.append(x[:-1]) header = list(self.tabix.header) self.assertEqual(ref, header) def testReopening(self): '''test repeated opening of the same file.''' def func1(): # opens any tabix file with pysam.TabixFile(self.filename) as inf: pass for i in range(1000): func1() class TestIterationWithComments(TestIterationWithoutComments): '''test iterating with TabixFile.fetch() when there are comments in the file. Tests will create plenty of warnings on stderr. ''' filename = os.path.join(TABIX_DATADIR, "example_comments.gtf.gz") class TestIterators(unittest.TestCase): filename = os.path.join(TABIX_DATADIR, "example.gtf.gz") iterator = pysam.tabix_generic_iterator parser = pysam.asTuple is_compressed = False def setUp(self): self.tabix = pysam.TabixFile(self.filename) self.compare = load_and_convert(self.filename) self.tmpfilename_uncompressed = 'tmp_TestIterators' with gzip.open(self.filename, "rb") as infile, \ open(self.tmpfilename_uncompressed, "wb") as outfile: outfile.write(infile.read()) def tearDown(self): self.tabix.close() os.unlink(self.tmpfilename_uncompressed) def open(self): if self.is_compressed: infile = gzip.open(self.filename) else: infile = open(self.tmpfilename_uncompressed) return infile def testIteration(self): with self.open() as infile: for x, r in enumerate(self.iterator(infile, self.parser())): self.assertEqual(self.compare[x], list(r)) self.assertEqual(len(self.compare[x]), len(r)) # test indexing for c in range(0, len(r)): self.assertEqual(self.compare[x][c], r[c]) # test slicing access for c in range(0, len(r) - 1): for cc in range(c + 1, len(r)): self.assertEqual(self.compare[x][c:cc], r[c:cc]) def testClosedFile(self): '''test for error when iterating from closed file.''' infile = self.open() infile.close() # iterating from a closed file should raise a value error self.assertRaises(ValueError, self.iterator, infile, self.parser()) def testClosedFileIteration(self): '''test for error when iterating from file that has been closed''' infile = self.open() i = self.iterator(infile, self.parser()) x = next(i) infile.close() # Not implemented # self.assertRaises(ValueError, i.next) class TestIteratorsGenericCompressed(TestIterators): is_compressed = True class TestIteratorsFileCompressed(TestIterators): iterator = pysam.tabix_file_iterator is_compressed = True class TestIteratorsFileUncompressed(TestIterators): iterator = pysam.tabix_file_iterator is_compressed = False class TestIterationMalformattedGTFFiles(unittest.TestCase): '''test reading from malformatted gtf files.''' iterator = pysam.tabix_generic_iterator parser = pysam.asGTF def testGTFTooManyFields(self): with gzip.open(os.path.join( TABIX_DATADIR, "gtf_toomany_fields.gtf.gz")) as infile: iterator = self.iterator( infile, parser=self.parser()) self.assertRaises(ValueError, iterator.__next__) def testGTFTooFewFields(self): with gzip.open(os.path.join( TABIX_DATADIR, "gtf_toofew_fields.gtf.gz")) as infile: iterator = self.iterator( infile, parser=self.parser()) self.assertRaises(ValueError, iterator.__next__) class TestBed(unittest.TestCase): filename = os.path.join(TABIX_DATADIR, "example.bed.gz") def setUp(self): self.tabix = pysam.TabixFile(self.filename) self.compare = load_and_convert(self.filename) def tearDown(self): self.tabix.close() def testRead(self): for x, r in enumerate(self.tabix.fetch(parser=pysam.asBed())): c = self.compare[x] self.assertEqual(len(c), len(r)) self.assertEqual(c, str(r).split("\t")) self.assertEqual(c[0], r.contig) self.assertEqual(int(c[1]), r.start) self.assertEqual(int(c[2]), r.end) # Needs lambda so that the property getter isn't called too soon self.assertRaises(KeyError, lambda: r.name) self.assertRaises(KeyError, lambda: r.score) self.assertEqual(list(c), list(r)) self.assertEqual("\t".join(map(str, c)), str(r)) def testWrite(self): for x, r in enumerate(self.tabix.fetch(parser=pysam.asBed())): c = self.compare[x] self.assertEqual(c, str(r).split("\t")) self.assertEqual(list(c), list(r)) r.contig = "test" self.assertEqual("test", r.contig) self.assertEqual("test", r[0]) r.start += 1 self.assertEqual(int(c[1]) + 1, r.start) self.assertEqual(str(int(c[1]) + 1), r[1]) r.end += 1 self.assertEqual(int(c[2]) + 1, r.end) self.assertEqual(str(int(c[2]) + 1), r[2]) with self.assertRaises(IndexError): r.name = "test" with self.assertRaises(IndexError): r.score = 1 class TestVCF(unittest.TestCase): filename = os.path.join(TABIX_DATADIR, "example.vcf40") def setUp(self): self.tmpfilename = get_temp_filename(suffix="vcf") shutil.copyfile(self.filename, self.tmpfilename) pysam.tabix_index(self.tmpfilename, preset="vcf") def tearDown(self): os.unlink(self.tmpfilename + ".gz") if os.path.exists(self.tmpfilename + ".gz.tbi"): os.unlink(self.tmpfilename + ".gz.tbi") class TestUnicode(unittest.TestCase): '''test reading from a file with non-ascii characters.''' filename = os.path.join(TABIX_DATADIR, "example_unicode.vcf") def setUp(self): self.tmpfilename = get_temp_filename(suffix="vcf") shutil.copyfile(self.filename, self.tmpfilename) pysam.tabix_index(self.tmpfilename, preset="vcf") def tearDown(self): os.unlink(self.tmpfilename + ".gz") if os.path.exists(self.tmpfilename + ".gz.tbi"): os.unlink(self.tmpfilename + ".gz.tbi") def testFromTabix(self): # use ascii encoding - should raise error with pysam.TabixFile( self.tmpfilename + ".gz", encoding="ascii") as t: results = list(t.fetch(parser=pysam.asVCF())) self.assertRaises(UnicodeDecodeError, getattr, results[1], "id") with pysam.TabixFile( self.tmpfilename + ".gz", encoding="utf-8") as t: results = list(t.fetch(parser=pysam.asVCF())) self.assertEqual(getattr(results[1], "id"), u"Rene\xe9") def testFromVCF(self): self.vcf = pysam.VCF() self.assertRaises( UnicodeDecodeError, self.vcf.connect, self.tmpfilename + ".gz", "ascii") self.vcf.connect(self.tmpfilename + ".gz", encoding="utf-8") v = self.vcf.getsamples()[0] class TestVCFFromTabix(TestVCF): columns = ("contig", "pos", "id", "ref", "alt", "qual", "filter", "info", "format") def setUp(self): super().setUp() self.tabix = pysam.TabixFile(self.tmpfilename + ".gz") self.compare = load_and_convert(self.filename) def tearDown(self): self.tabix.close() super().tearDown() def testRead(self): ncolumns = len(self.columns) for x, r in enumerate(self.tabix.fetch(parser=pysam.asVCF())): c = self.compare[x] for y, field in enumerate(self.columns): # it is ok to have a missing format column if y == 8 and y == len(c): continue if field == "pos": self.assertEqual(int(c[y]) - 1, getattr(r, field)) self.assertEqual(int(c[y]) - 1, r.pos) else: self.assertEqual(c[y], getattr(r, field), "mismatch in field %s: %s != %s" % (field, c[y], getattr(r, field))) if len(c) == 8: self.assertEqual(0, len(r)) else: self.assertEqual(len(c), len(r) + ncolumns) for y in range(len(c) - ncolumns): self.assertEqual(c[ncolumns + y], r[y]) self.assertEqual("\t".join(map(str, c)), str(r)) def testWrite(self): ncolumns = len(self.columns) for x, r in enumerate(self.tabix.fetch(parser=pysam.asVCF())): c = self.compare[x] # check unmodified string cmp_string = str(r) ref_string = "\t".join([x for x in c]) self.assertEqual(ref_string, cmp_string) # set fields and compare field-wise for y, field in enumerate(self.columns): # it is ok to have a missing format column if y == 8 and y == len(c): continue if field == "pos": rpos = getattr(r, field) self.assertEqual(int(c[y]) - 1, rpos) self.assertEqual(int(c[y]) - 1, r.pos) # increment pos by 1 setattr(r, field, rpos + 1) self.assertEqual(getattr(r, field), rpos + 1) c[y] = str(int(c[y]) + 1) else: setattr(r, field, "test_%i" % y) c[y] = "test_%i" % y self.assertEqual(c[y], getattr(r, field), "mismatch in field %s: %s != %s" % (field, c[y], getattr(r, field))) if len(c) == 8: self.assertEqual(0, len(r)) else: self.assertEqual(len(c), len(r) + ncolumns) for y in range(len(c) - ncolumns): c[ncolumns + y] = "test_%i" % y r[y] = "test_%i" % y self.assertEqual(c[ncolumns + y], r[y]) class TestVCFFromVCF(TestVCF): columns = ("chrom", "pos", "id", "ref", "alt", "qual", "filter", "info", "format") # tests failing while parsing fail_on_parsing = ( (5, "Flag fields should not have a value"), (9, "aouao"), (12, "Error BAD_NUMBER_OF_PARAMETERS"), (13, "aoeu"), (18, "Error BAD_NUMBER_OF_PARAMETERS"), (24, "Error HEADING_NOT_SEPARATED_BY_TABS")) # tests failing on opening fail_on_opening = ((24, "Error HEADING_NOT_SEPARATED_BY_TABS"), ) fail_on_samples = [] check_samples = False coordinate_offset = 1 # value returned for missing values missing_value = "." missing_quality = -1 def setUp(self): super().setUp() self.vcf = pysam.VCF() self.compare = load_and_convert(self.filename, encode=False) def tearDown(self): super().tearDown() self.vcf.close() def open_vcf(self, fn): return self.vcf.connect(fn) def get_failure_stage(self): fn = os.path.basename(self.filename) for x, msg in self.fail_on_opening: if "{}.vcf".format(x) == fn: return "opening" for x, msg in self.fail_on_parsing: if "{}.vcf".format(x) == fn: return "parsing" for x, msg in self.fail_on_samples: if "{}.vcf".format(x) == fn: return "samples" return None def testConnecting(self): if self.get_failure_stage() == "opening": self.assertRaises(ValueError, self.open_vcf, self.tmpfilename + ".gz") else: self.open_vcf(self.tmpfilename + ".gz") def get_iterator(self): with open(self.filename) as f: fn = os.path.basename(self.filename) return list(self.vcf.parse(f)) def get_field_value(self, record, field): return record[field] def sample2value(self, r, v): return r, v def alt2value(self, r, v): if r == ".": return [], v else: return r.split(","), list(v) def filter2value(self, r, v): if r == "PASS": return [], v elif r == ".": return [], v else: return r.split(";"), v def testParsing(self): if self.get_failure_stage() in ("opening", "parsing"): return itr = self.get_iterator() if itr is None: return fn = os.path.basename(self.filename) check_samples = self.check_samples for vcf_code, msg in self.fail_on_samples: if "%i.vcf" % vcf_code == fn: check_samples = False for x, r in enumerate(itr): c = self.compare[x] for y, field in enumerate(self.columns): # it is ok to have a missing format column if y == 8 and y == len(c): continue val = self.get_field_value(r, field) if field == "pos": self.assertEqual(int(c[y]) - self.coordinate_offset, val) elif field == "alt" or field == "alts": cc, vv = self.alt2value(c[y], val) if cc != vv: # import pdb; pdb.set_trace() pass self.assertEqual( cc, vv, "mismatch in field %s: expected %s, got %s" % (field, cc, vv)) elif field == "filter": cc, vv = self.filter2value(c[y], val) self.assertEqual( cc, vv, "mismatch in field %s: expected %s, got %s" % (field, cc, vv)) elif field == "info": # tests for info field not implemented pass elif field == "qual" and c[y] == ".": self.assertEqual( self.missing_quality, val, "mismatch in field %s: expected %s, got %s" % (field, c[y], val)) elif field == "format": # format field converted to list self.assertEqual( c[y].split(":"), list(val), "mismatch in field %s: expected %s, got %s" % (field, c[y], val)) elif type(val) in (int, float): if c[y] == ".": self.assertEqual( None, val, "mismatch in field %s: expected %s, got %s" % (field, c[y], val)) else: self.assertAlmostEqual( float(c[y]), float(val), 2, "mismatch in field %s: expected %s, got %s" % (field, c[y], val)) else: if c[y] == ".": ref_val = self.missing_value else: ref_val = c[y] self.assertEqual( ref_val, val, "mismatch in field %s: expected %s(%s), got %s(%s)" % (field, ref_val, type(ref_val), val, type(val))) # parse samples if check_samples: if len(c) == 8: for x, s in enumerate(r.samples): self.assertEqual( [], r.samples[s].values(), "mismatch in sample {}: " "expected [], got {}, src={}, line={}".format( s, r.samples[s].values(), r.samples[s].items(), r)) else: for x, s in enumerate(r.samples): ref, comp = self.sample2value( c[9 + x], r.samples[s]) self.compare_samples(ref, comp, s, r) def compare_samples(self, ref, comp, s, r): if ref != comp: # check if GT not at start, not VCF conform and # not supported by cbcf.pyx k = r.format.keys() if "GT" in k and k[0] != "GT": return # perform an element-wise checto work around rounding differences for a, b in zip(re.split("[:,;]", ref), re.split("[:,;]", comp)): is_float = True try: a = float(a) b = float(b) except ValueError: is_float = False if is_float: self.assertAlmostEqual( a, b, 2, "mismatch in sample {}: " "expected {}, got {}, src={}, line={}" .format( s, ref, comp, r.samples[s].items(), r)) else: self.assertEqual( a, b, "mismatch in sample {}: " "expected {}, got {}, src={}, line={}" .format( s, ref, comp, r.samples[s].items(), r)) ############################################################################ # create a test class for each example vcf file. # Two samples are created - # 1. Testing pysam/tabix access # 2. Testing the VCF class vcf_files = glob.glob(os.path.join(TABIX_DATADIR, "vcf", "*.vcf")) for vcf_file in vcf_files: n = "VCFFromTabixTest_%s" % os.path.basename(vcf_file[:-4]) globals()[n] = type(n, (TestVCFFromTabix,), dict(filename=vcf_file,)) n = "VCFFromVCFTest_%s" % os.path.basename(vcf_file[:-4]) globals()[n] = type(n, (TestVCFFromVCF,), dict(filename=vcf_file,)) class TestVCFFromVariantFile(TestVCFFromVCF): columns = ("chrom", "pos", "id", "ref", "alts", "qual", "filter", "info", "format") fail_on_parsing = [ (24, 'Could not parse the "#CHROM.." line'), ("issue85", "empty VCF"), ] fail_on_opening = [ (24, 'Could not parse the "#CHROM.." line'), ("issue85", "empty VCF"), ] coordinate_offset = 0 check_samples = True fail_on_samples = [ (9, "PL field not defined. Expected to be scalar, but is array"), (12, "PL field not defined. Expected to be scalar, but is array"), (18, "PL field not defined. Expected to be scalar, but is array"), ] # value returned for missing values missing_value = None missing_quality = None vcf = None def filter2value(self, r, v): if r == "PASS": return ["PASS"], list(v) elif r == ".": return [], list(v) else: return r.split(";"), list(v) def alt2value(self, r, v): if r == ".": return None, v else: return r.split(","), list(v) def sample2value(self, r, smp): def convert_field(f): if f is None: return "." elif isinstance(f, tuple): return ",".join(map(convert_field, f)) else: return str(f) v = smp.values() if 'GT' in smp: alleles = [ str(a) if a is not None else '.' for a in smp.allele_indices] v[0] = '/|'[smp.phased].join(alleles) comp = ":".join(map(convert_field, v)) if comp.endswith(":."): comp = comp[:-2] return r, comp def setUp(self): TestVCF.setUp(self) self.compare = load_and_convert(self.filename, encode=False) def tearDown(self): if self.vcf: self.vcf.close() self.vcf = None TestVCF.tearDown(self) def get_iterator(self): self.vcf = pysam.VariantFile(self.filename) return self.vcf.fetch() def get_field_value(self, record, field): return getattr(record, field) def open_vcf(self, fn): with pysam.VariantFile(fn) as inf: pass for vcf_file in vcf_files: p = os.path.basename(vcf_file[:-4]) n = "TestVCFFromVariantFile_%s" % p globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,)) class TestRemoteFileHTTP(unittest.TestCase): url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz" region = "chr1:1-1000" local = os.path.join(TABIX_DATADIR, "example.gtf.gz") def setUp(self): if not getattr(pysam.config, "HAVE_LIBCURL", 0) or not check_url(self.url): self.remote_file = None else: self.remote_file = pysam.TabixFile(self.url, "r") self.local_file = pysam.TabixFile(self.local, "r") def tearDown(self): if self.remote_file is None: return self.remote_file.close() self.local_file.close() def testFetchAll(self): if self.remote_file is None: return remote_result = list(self.remote_file.fetch()) local_result = list(self.local_file.fetch()) self.assertEqual(len(remote_result), len(local_result)) for x, y in zip(remote_result, local_result): self.assertEqual(x, y) def testHeader(self): if self.remote_file is None: return self.assertEqual(list(self.local_file.header), []) class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP): url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz" region = "chr1:1-1000" local = os.path.join(TABIX_DATADIR, "example_comments.gtf.gz") def setUp(self): if not getattr(pysam.config, "HAVE_LIBCURL", 0) or not check_url(self.url): self.remote_file = None else: self.remote_file = pysam.TabixFile(self.url, "r") self.local_file = pysam.TabixFile(self.local, "r") def testHeader(self): if self.remote_file is None: return self.assertEqual(list(self.local_file.header), ["# comment at start"]) self.assertEqual(list(self.local_file.header), self.remote_file.header) class TestIndexArgument(unittest.TestCase): filename_src = os.path.join(TABIX_DATADIR, "example.vcf.gz") filename_dst = "tmp_example.vcf.gz" index_src = os.path.join(TABIX_DATADIR, "example.vcf.gz.tbi") index_dst = "tmp_index_example.vcf.gz.tbi" index_dst_dat = "tmp_index_example.vcf.gz.tbi.dat" preset = "vcf" def testFetchAll(self): shutil.copyfile(self.filename_src, self.filename_dst) shutil.copyfile(self.index_src, self.index_dst) with pysam.TabixFile( self.filename_src, "r", index=self.index_src) as same_basename_file: same_basename_results = list(same_basename_file.fetch()) with pysam.TabixFile( self.filename_dst, "r", index=self.index_dst) as diff_index_file: diff_index_result = list(diff_index_file.fetch()) self.assertEqual(len(same_basename_results), len(diff_index_result)) for x, y in zip(same_basename_results, diff_index_result): self.assertEqual(x, y) os.unlink(self.filename_dst) os.unlink(self.index_dst) def testLoadIndexWithoutTbiExtension(self): shutil.copyfile(self.filename_src, self.filename_dst) shutil.copyfile(self.index_src, self.index_dst_dat) with pysam.TabixFile( self.filename_src, "r", index=self.index_src) as same_basename_file: same_basename_results = list(same_basename_file.fetch()) with pysam.TabixFile( self.filename_dst, "r", index=self.index_dst_dat) as diff_index_file: diff_index_result = list(diff_index_file.fetch()) self.assertEqual(len(same_basename_results), len(diff_index_result)) for x, y in zip(same_basename_results, diff_index_result): self.assertEqual(x, y) os.unlink(self.filename_dst) os.unlink(self.index_dst_dat) def _TestMultipleIteratorsHelper(filename, multiple_iterators): '''open file within scope, return iterator.''' tabix = pysam.TabixFile(filename) iterator = tabix.fetch(parser=pysam.asGTF(), multiple_iterators=multiple_iterators) tabix.close() return iterator class TestBackwardsCompatibility(unittest.TestCase): """check if error is raised if a tabix file from an old version is accessed from pysam""" def check(self, filename, raises=None): with pysam.TabixFile(filename) as tf: ref = load_and_convert(filename) if raises is None: self.assertEqual(len(list(tf.fetch())), len(ref)) else: self.assertRaises(raises, tf.fetch) def testVCF0v23(self): self.check(os.path.join(TABIX_DATADIR, "example_0v23.vcf.gz"), ValueError) def testBED0v23(self): self.check(os.path.join(TABIX_DATADIR, "example_0v23.bed.gz"), ValueError) def testVCF0v26(self): self.check(os.path.join(TABIX_DATADIR, "example_0v26.vcf.gz"), ValueError) def testBED0v26(self): self.check(os.path.join(TABIX_DATADIR, "example_0v26.bed.gz"), ValueError) def testVCF(self): self.check(os.path.join(TABIX_DATADIR, "example.vcf.gz")) def testBED(self): self.check(os.path.join(TABIX_DATADIR, "example.bed.gz")) def testEmpty(self): self.check(os.path.join(TABIX_DATADIR, "empty.bed.gz")) class TestMultipleIterators(unittest.TestCase): filename = os.path.join(TABIX_DATADIR, "example.gtf.gz") def testJoinedIterators(self): # two iterators working on the same file with pysam.TabixFile(self.filename) as tabix: a = next(tabix.fetch(parser=pysam.asGTF())) b = next(tabix.fetch(parser=pysam.asGTF())) # the first two lines differ only by the feature field self.assertEqual(a.feature, "UTR") self.assertEqual(b.feature, "exon") self.assertEqual(re.sub("UTR", "", str(a)), re.sub("exon", "", str(b))) def testDisjointIterators(self): # two iterators working on the same file with pysam.TabixFile(self.filename) as tabix: a = next(tabix.fetch(parser=pysam.asGTF(), multiple_iterators=True)) b = next(tabix.fetch(parser=pysam.asGTF(), multiple_iterators=True)) # both iterators are at top of file self.assertEqual(str(a), str(b)) def testScope(self): # technically it does not really test if the scope is correct i = _TestMultipleIteratorsHelper(self.filename, multiple_iterators=True) self.assertTrue(next(i)) i = _TestMultipleIteratorsHelper(self.filename, multiple_iterators=False) self.assertRaises(IOError, i.__next__) def testDoubleFetch(self): with pysam.TabixFile(self.filename) as f: for a, b in zip(f.fetch(multiple_iterators=True), f.fetch(multiple_iterators=True)): self.assertEqual(str(a), str(b)) class TestContextManager(unittest.TestCase): filename = os.path.join(TABIX_DATADIR, "example.gtf.gz") def testManager(self): with pysam.TabixFile(self.filename) as tabixfile: tabixfile.fetch() self.assertEqual(tabixfile.closed, True) class TestMultithreadTabixFile(unittest.TestCase): filename = os.path.join(TABIX_DATADIR, "example.gtf.gz") def testMultithreadEqualsSinglethread(self): with pysam.TabixFile(self.filename) as tabixfile: single = [r for r in tabixfile.fetch()] with pysam.TabixFile(self.filename, threads=2) as tabixfile: multi = [r for r in tabixfile.fetch()] for r1, r2 in zip(single, multi): assert str(r1) == str(r2) if __name__ == "__main__": unittest.main() pysam-0.23.0/tests/tabixproxies_test.py000066400000000000000000000313271475062545500202440ustar00rootroot00000000000000import unittest import pysam import os import re import copy import gzip from TestUtils import load_and_convert, make_data_files, TABIX_DATADIR def setUpModule(): make_data_files(TABIX_DATADIR) class TestBED(unittest.TestCase): filename = os.path.join(TABIX_DATADIR, "fivecolumns.bed.gz") def setUp(self): self.tabix = pysam.TabixFile(self.filename) def tearDown(self): self.tabix.close() def testAssignmentToTargetList(self): for row in self.tabix.fetch(parser=pysam.asTuple()): # Test that *others gets the right columns... contig, start, end, *others = row self.assertEqual(3 + len(others), len(row)) # ...and that a TupleProxy can be assigned from more than once contig, *others = row self.assertEqual(1 + len(others), len(row)) class TestParser(unittest.TestCase): filename = os.path.join(TABIX_DATADIR, "example.gtf.gz") def setUp(self): self.tabix = pysam.TabixFile(self.filename) self.compare = load_and_convert(self.filename) def tearDown(self): self.tabix.close() def testRead(self): for x, r in enumerate(self.tabix.fetch(parser=pysam.asTuple())): c = self.compare[x] self.assertEqual(c, list(r)) self.assertEqual(len(c), len(r)) # test indexing for y in range(0, len(r)): self.assertEqual(c[y], r[y]) # test slicing access for y in range(0, len(r) - 1): for cc in range(y + 1, len(r)): self.assertEqual(c[y:cc], r[y:cc]) self.assertEqual("\t".join(map(str, c)), str(r)) def testAssignmentToTargetList(self): for x, r in enumerate(self.tabix.fetch(parser=pysam.asTuple())): col1, col2, *others, colN = r self.assertEqual(2 + len(others) + 1, len(r)) def testWrite(self): for x, r in enumerate(self.tabix.fetch(parser=pysam.asTuple())): self.assertEqual(self.compare[x], list(r)) c = list(r) for y in range(len(r)): r[y] = "test_%05i" % y c[y] = "test_%05i" % y self.assertEqual([x for x in c], list(r)) self.assertEqual("\t".join(c), str(r)) # check second assignment for y in range(len(r)): r[y] = "test_%05i" % y self.assertEqual([x for x in c], list(r)) self.assertEqual("\t".join(c), str(r)) def testUnset(self): for x, r in enumerate(self.tabix.fetch(parser=pysam.asTuple())): self.assertEqual(self.compare[x], list(r)) c = list(r) e = list(r) for y in range(len(r)): r[y] = None c[y] = None e[y] = "" self.assertEqual(c, list(r)) self.assertEqual("\t".join(e), str(r)) def testIteratorCompressed(self): '''test iteration from compressed file.''' with gzip.open(self.filename) as infile: for x, r in enumerate(pysam.tabix_iterator( infile, pysam.asTuple())): self.assertEqual(self.compare[x], list(r)) self.assertEqual(len(self.compare[x]), len(r)) # test indexing for c in range(0, len(r)): self.assertEqual(self.compare[x][c], r[c]) # test slicing access for c in range(0, len(r) - 1): for cc in range(c + 1, len(r)): self.assertEqual(self.compare[x][c:cc], r[c:cc]) def testIteratorUncompressed(self): '''test iteration from uncompressed file.''' tmpfilename = 'tmp_testIteratorUncompressed' with gzip.open(self.filename, "rb") as infile, \ open(tmpfilename, "wb") as outfile: outfile.write(infile.read()) with open(tmpfilename) as infile: for x, r in enumerate(pysam.tabix_iterator( infile, pysam.asTuple())): self.assertEqual(self.compare[x], list(r)) self.assertEqual(len(self.compare[x]), len(r)) # test indexing for c in range(0, len(r)): self.assertEqual(self.compare[x][c], r[c]) # test slicing access for c in range(0, len(r) - 1): for cc in range(c + 1, len(r)): self.assertEqual(self.compare[x][c:cc], r[c:cc]) os.unlink(tmpfilename) def testCopy(self): a = next(self.tabix.fetch(parser=pysam.asTuple())) b = copy.copy(a) self.assertEqual(a, b) a = next(self.tabix.fetch(parser=pysam.asGTF())) b = copy.copy(a) self.assertEqual(a, b) class TestGTF(TestParser): parser = pysam.asGTF def build_attribute_string(self, d): """build attribute string from dictionary d""" s = "; ".join(["{} \"{}\"".format(x, y) for (x, y) in d.items()]) + ";" # remove quotes around numeric values s = re.sub(r'"(\d+)"', r'\1', s) return s def testRead(self): for x, r in enumerate(self.tabix.fetch(parser=self.parser())): c = self.compare[x] self.assertEqual(len(c), len(r)) self.assertEqual(list(c), list(r)) self.assertEqual(c, str(r).split("\t")) self.assertTrue(r.gene_id.startswith("ENSG")) if r.feature != 'gene': self.assertTrue(r.transcript_id.startswith("ENST")) self.assertEqual(c[0], r.contig) self.assertEqual("\t".join(map(str, c)), str(r)) def test_setting_fields(self): r = next(self.tabix.fetch(parser=self.parser())) r.contig = r.contig + "_test_contig" r.source = r.source + "_test_source" r.feature = r.feature + "_test_feature" r.start += 10 r.end += 10 r.score = 20 r.strand = "+" r.frame = 0 r.attributes = 'gene_id "0001";' r.transcript_id = "0002" sr = str(r) self.assertTrue("_test_contig" in sr) self.assertTrue("_test_source" in sr) self.assertTrue("_test_feature" in sr) self.assertTrue("gene_id \"0001\"" in sr) self.assertTrue("transcript_id \"0002\"" in sr) def test_setAttribute_makes_changes(self): r = next(self.tabix.fetch(parser=self.parser())) r.setAttribute("transcript_id", "abcd") sr = str(r) self.assertEqual(r.transcript_id, "abcd") self.assertTrue("transcript_id \"abcd\"" in sr) def test_added_attribute_is_output(self): r = next(self.tabix.fetch(parser=self.parser())) r.new_int_attribute = 12 self.assertTrue("new_int_attribute 12" in str(r).split("\t")[8]) r.new_float_attribute = 12.0 self.assertTrue("new_float_attribute 12.0" in str(r).split("\t")[8]) r.new_text_attribute = "abc" self.assertTrue("new_text_attribute \"abc\"" in str(r).split("\t")[8]) def test_setting_start_is_one_based(self): r = next(self.tabix.fetch(parser=self.parser())) r.start = 1800 self.assertEqual(r.start, 1800) self.assertEqual(str(r).split("\t")[3], "1801") def test_setting_end_is_one_based(self): r = next(self.tabix.fetch(parser=self.parser())) r.end = 2100 self.assertEqual(r.end, 2100) self.assertEqual(str(r).split("\t")[4], "2100") def test_setting_frame_to_none_produces_dot(self): r = next(self.tabix.fetch(parser=self.parser())) r.frame = None self.assertEqual(str(r).split("\t")[7], ".") r.frame = 2 self.assertEqual(str(r).split("\t")[7], "2") r = next(self.tabix.fetch(parser=self.parser())) r.frame = "." self.assertEqual(r.frame, None) self.assertEqual(str(r).split("\t")[7], ".") def test_setting_source_to_none_produces_dot(self): r = next(self.tabix.fetch(parser=self.parser())) r.source = None self.assertEqual(str(r).split("\t")[1], ".") r.source = "source" self.assertEqual(str(r).split("\t")[1], "source") r = next(self.tabix.fetch(parser=self.parser())) r.source = "." self.assertEqual(r.source, None) self.assertEqual(str(r).split("\t")[1], ".") def test_setting_feature_to_none_produces_dot(self): r = next(self.tabix.fetch(parser=self.parser())) r.feature = None self.assertEqual(str(r).split("\t")[2], ".") r.feature = "feature" self.assertEqual(str(r).split("\t")[2], "feature") r = next(self.tabix.fetch(parser=self.parser())) r.feature = "." self.assertEqual(r.feature, None) self.assertEqual(str(r).split("\t")[2], ".") def test_setting_strand_to_none_produces_dot(self): r = next(self.tabix.fetch(parser=self.parser())) r.strand = None self.assertEqual(str(r).split("\t")[6], ".") r.strand = "-" self.assertEqual(str(r).split("\t")[6], "-") r = next(self.tabix.fetch(parser=self.parser())) r.strand = "." self.assertEqual(r.strand, None) self.assertEqual(str(r).split("\t")[6], ".") def test_setting_score_to_none_produces_dot(self): r = next(self.tabix.fetch(parser=self.parser())) r.score = None self.assertEqual(str(r).split("\t")[5], ".") r.score = 12.0 self.assertEqual(str(r).split("\t")[5], "12.0") r.score = -12.0 self.assertEqual(str(r).split("\t")[5], "-12.0") r = next(self.tabix.fetch(parser=self.parser())) r.score = "." self.assertEqual(r.score, None) self.assertEqual(str(r).split("\t")[5], ".") r.score = 12 self.assertEqual(str(r).split("\t")[5], "12") r.score = -12 self.assertEqual(str(r).split("\t")[5], "-12") def test_asdict_contains_attributes(self): r = next(self.tabix.fetch(parser=self.parser())) d = r.to_dict() c = self.compare[0] s = self.build_attribute_string(d) self.assertEqual(s, c[8]) def test_asdict_can_be_modified(self): r = next(self.tabix.fetch(parser=self.parser())) d = r.to_dict() d["gene_id"] = "new_gene_id" self.assertTrue("gene_id \"new_gene_id\"", str(r)) class TestGFF3(TestGTF): parser = pysam.asGFF3 filename = os.path.join(TABIX_DATADIR, "example.gff3.gz") def build_attribute_string(self, d): """build attribute string from dictionary d""" s = ";".join(["{}={}".format(x, y) for (x, y) in d.items()]) + ";" return s def build_attribute_string(self, d): """build attribute string from dictionary d""" s = ";".join(["{}={}".format(x, y) for (x, y) in d.items()]) + ";" return s def testRead(self): for x, r in enumerate(self.tabix.fetch(parser=self.parser())): c = self.compare[x] self.assertEqual(len(c), len(r)) self.assertEqual(list(c), list(r)) self.assertEqual(c, str(r).split("\t")) self.assertEqual(c[0], r.contig) self.assertEqual("\t".join(map(str, c)), str(r)) self.assertTrue(r.ID.startswith("MI00")) def test_setting_fields(self): for r in self.tabix.fetch(parser=self.parser()): r.contig = r.contig + "_test_contig" r.source = "test_source" r.feature = "test_feature" r.start += 10 r.end += 10 r.score = 20 r.strand = "+" r.frame = 0 r.ID = "test" sr = str(r) self.assertTrue("test_contig" in sr) self.assertTrue("test_source" in sr) self.assertTrue("test_feature" in sr) self.assertTrue("ID=test" in sr) def test_setAttribute_makes_changes(self): r = next(self.tabix.fetch(parser=self.parser())) r.setAttribute("transcript_id", "abcd") sr = str(r) self.assertEqual(r.transcript_id, "abcd") self.assertTrue("transcript_id=abcd" in sr) def test_added_attribute_is_output(self): r = next(self.tabix.fetch(parser=self.parser())) r.new_int_attribute = 12 self.assertTrue("new_int_attribute=12" in str(r).split("\t")[8]) r.new_float_attribute = 12.0 self.assertTrue("new_float_attribute=12.0" in str(r).split("\t")[8]) r.new_text_attribute = "abc" self.assertTrue("new_text_attribute=abc" in str(r).split("\t")[8]) if __name__ == "__main__": unittest.main() pysam-0.23.0/tests/test_samtools_python.py000066400000000000000000000036321475062545500207630ustar00rootroot00000000000000import pysam import os from TestUtils import make_data_files, BAM_DATADIR def setUpModule(): make_data_files(BAM_DATADIR) def test_idxstats_parse_split_lines(): bam_filename = os.path.join(BAM_DATADIR, "ex2.bam") # Test pysam 0.8.X style output, which returns a list of lines lines = pysam.idxstats(bam_filename, split_lines=True) for line in lines: _seqname, _seqlen, nmapped, _nunmapped = line.split() def test_bedcov_split_lines(): bam_filename = os.path.join(BAM_DATADIR, "ex1.bam") bed_filename = os.path.join(BAM_DATADIR, "ex1.bed") # Test pysam 0.8.X style output, which returns a list of lines lines = pysam.bedcov(bed_filename, bam_filename, split_lines=True) for line in lines: fields = line.split('\t') assert len(fields) in [4, 5], \ ("bedcov should give tab delimited output with 4 or 5 fields. " "Split line (%s) gives %d fields." % (fields, len(fields))) def test_idxstats_parse(): bam_filename = os.path.join(BAM_DATADIR, "ex2.bam") # Test pysam 0.9.X style output, which returns a string that needs to be split by \n idxstats_string = pysam.idxstats(bam_filename, split_lines=False) lines = idxstats_string.splitlines() for line in lines: splt = line.split("\t") _seqname, _seqlen, nmapped, _nunmapped = splt def test_bedcov(): bam_filename = os.path.join(BAM_DATADIR, "ex1.bam") bed_filename = os.path.join(BAM_DATADIR, "ex1.bed") # Test pysam 0.9.X style output, which returns a string that needs to be split by \n bedcov_string = pysam.bedcov(bed_filename, bam_filename, split_lines=False) lines = bedcov_string.splitlines() for line in lines: fields = line.split('\t') assert len(fields) in [4, 5], \ ("bedcov should give tab delimited output with 4 or 5 fields. " "Split line (%s) gives %d fields." % (fields, len(fields))) pysam-0.23.0/tests/typechecking_test.py000066400000000000000000000071161475062545500201770ustar00rootroot00000000000000import inspect import os import pytest import re from typing import TYPE_CHECKING import pysam import pysam.samtools import pysam.bcftools from TestUtils import BAM_DATADIR, make_data_files try: import mypy.api except ImportError: pytest.skip('mypy API not available', allow_module_level=True) PREAMBLE = """ import re from typing import TYPE_CHECKING import pysam import pysam.samtools import pysam.bcftools def typecheck(check_locals = True): pass """ MYPY_OPTIONS = ['--no-incremental', '--no-error-summary', '--follow-imports', 'silent'] def typecheck(check_locals: bool = True): myframe = inspect.currentframe() if not myframe: pytest.skip('current stack frame not available') caller = myframe.f_back if not caller: pytest.skip('caller stack frame not available') code = inspect.getsource(caller) stdout, stderr, status = mypy.api.run(MYPY_OPTIONS + ['--command', PREAMBLE + code]) assert status == 0, f'mypy failed:\n{stdout}{stderr}' types = {} for line in stdout.splitlines(): m = re.search(r'note: *(\w+): ([\w.]*)', line) if m: types[m.group(1)] = m.group(2) def _plain(s): s = re.sub(r"", r'\1', s) s = re.sub(r'builtins\.', '', s) return s if check_locals: for var, vartype in types.items(): assert _plain(vartype) == _plain(repr(type(caller.f_locals[var]))), f'Incorrect type for {var!r}' return types def setUpModule(): make_data_files(BAM_DATADIR) @pytest.fixture def aln(): header = pysam.AlignmentHeader.from_references(['chr1', 'chr2'], [50000, 20000]) a = pysam.AlignedSegment(header) a.query_name = 'read_one' a.flag = pysam.FPAIRED | pysam.FREAD1 a.reference_id = 0 a.reference_start = 1000 a.mapping_quality = 20 a.next_reference_id = 1 a.next_reference_start = 5000 a.template_length = 0 a.cigartuples = ((pysam.CMATCH, 6), (pysam.CINS, 4), (pysam.CMATCH, 2)) a.query_sequence = 'ATGCATGCATGC' a.query_qualities = pysam.qualitystring_to_array('abcdefghijkl') return a @pytest.fixture def sam_fname(): return os.path.join(BAM_DATADIR, 'ex3.sam') @pytest.fixture def bam_fname(): return os.path.join(BAM_DATADIR, 'ex1.bam') def test_AlignedSegment_is_mapped(aln: pysam.AlignedSegment) -> None: rmap = aln.is_mapped mmap = aln.mate_is_mapped rfwd = aln.is_forward mfwd = aln.mate_is_forward if TYPE_CHECKING: reveal_locals() types = typecheck() def test_AlignmentHeader_get_reference_length(sam_fname: str) -> None: inf = pysam.AlignmentFile(sam_fname) n1 = inf.get_reference_length('chr1') hdr = inf.header n2 = hdr.get_reference_length('chr1') if TYPE_CHECKING: reveal_locals() types = typecheck() def test_pileup_iterator_column(bam_fname: str) -> None: inf = pysam.AlignmentFile(bam_fname) pu = inf.pileup('chr1') for p in pu: pid = p.reference_id ppos = p.reference_pos if TYPE_CHECKING: reveal_locals() types = typecheck(check_locals=False) assert re.search(r'\.IteratorColumn(|All|AllRefs|Region)$', types['pu']) assert types['p'].endswith('PileupColumn') assert types['pid'] == 'builtins.int' assert types['ppos'] == 'builtins.int' def test_samtools_subcommands() -> None: p1_samtools_faidx = pysam.samtools.faidx p2_faidx = pysam.faidx p3_view = pysam.view p4_bcftools_view = pysam.bcftools.view if TYPE_CHECKING: reveal_locals() types = typecheck() for var, vartype in types.items(): assert vartype.endswith('PysamDispatcher'), f'{var!r} is not a dispatcher' pysam-0.23.0/win32/000077500000000000000000000000001475062545500137045ustar00rootroot00000000000000pysam-0.23.0/win32/getopt.c000066400000000000000000001211141475062545500153520ustar00rootroot00000000000000/* Getopt for GNU. NOTE: getopt is now part of the C library, so if you don't know what "Keep this file name-space clean" means, talk to drepper@gnu.org before changing it! Copyright (C) 1987,88,89,90,91,92,93,94,95,96,98,99,2000,2001 Free Software Foundation, Inc. This file is part of the GNU C Library. The GNU C Library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. The GNU C Library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with the GNU C Library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. */ /* This tells Alpha OSF/1 not to define a getopt prototype in . Ditto for AIX 3.2 and . */ #ifndef _NO_PROTO # define _NO_PROTO #endif #ifdef HAVE_CONFIG_H # include #endif #if !defined __STDC__ || !__STDC__ /* This is a separate conditional since some stdc systems reject `defined (const)'. */ # ifndef const # define const # endif #endif #include /* Comment out all this code if we are using the GNU C Library, and are not actually compiling the library itself. This code is part of the GNU C Library, but also included in many other GNU distributions. Compiling and linking in this code is a waste when using the GNU C library (especially if it is a shared library). Rather than having every GNU program understand `configure --with-gnu-libc' and omit the object files, it is simpler to just do this in the source for each such file. */ #define GETOPT_INTERFACE_VERSION 2 #if !defined _LIBC && defined __GLIBC__ && __GLIBC__ >= 2 # include # if _GNU_GETOPT_INTERFACE_VERSION == GETOPT_INTERFACE_VERSION # define ELIDE_CODE # endif #endif #ifndef ELIDE_CODE /* This needs to come after some library #include to get __GNU_LIBRARY__ defined. */ #ifdef __GNU_LIBRARY__ /* Don't include stdlib.h for non-GNU C libraries because some of them contain conflicting prototypes for getopt. */ # include # include #endif /* GNU C library. */ #ifdef VMS # include # if HAVE_STRING_H - 0 # include # endif #endif #ifndef _ /* This is for other GNU distributions with internationalized messages. */ # if (HAVE_LIBINTL_H && ENABLE_NLS) || defined _LIBC # include # ifndef _ # define _(msgid) gettext (msgid) # endif # else # define _(msgid) (msgid) # endif # if defined _LIBC && defined USE_IN_LIBIO # include # endif #endif /* This version of `getopt' appears to the caller like standard Unix `getopt' but it behaves differently for the user, since it allows the user to intersperse the options with the other arguments. As `getopt' works, it permutes the elements of ARGV so that, when it is done, all the options precede everything else. Thus all application programs are extended to handle flexible argument order. Setting the environment variable POSIXLY_CORRECT disables permutation. Then the behavior is completely standard. GNU application programs can use a third alternative mode in which they can distinguish the relative order of options and other arguments. */ #include "getopt.h" /* For communication from `getopt' to the caller. When `getopt' finds an option that takes an argument, the argument value is returned here. Also, when `ordering' is RETURN_IN_ORDER, each non-option ARGV-element is returned here. */ char *optarg; /* Index in ARGV of the next element to be scanned. This is used for communication to and from the caller and for communication between successive calls to `getopt'. On entry to `getopt', zero means this is the first call; initialize. When `getopt' returns -1, this is the index of the first of the non-option elements that the caller should itself scan. Otherwise, `optind' communicates from one call to the next how much of ARGV has been scanned so far. */ /* 1003.2 says this must be 1 before any call. */ int optind = 1; /* Formerly, initialization of getopt depended on optind==0, which causes problems with re-calling getopt as programs generally don't know that. */ int __getopt_initialized; /* The next char to be scanned in the option-element in which the last option character we returned was found. This allows us to pick up the scan where we left off. If this is zero, or a null string, it means resume the scan by advancing to the next ARGV-element. */ static char *nextchar; /* Callers store zero here to inhibit the error message for unrecognized options. */ int opterr = 1; /* Set to an option character which was unrecognized. This must be initialized on some systems to avoid linking in the system's own getopt implementation. */ int optopt = '?'; /* Describe how to deal with options that follow non-option ARGV-elements. If the caller did not specify anything, the default is REQUIRE_ORDER if the environment variable POSIXLY_CORRECT is defined, PERMUTE otherwise. REQUIRE_ORDER means don't recognize them as options; stop option processing when the first non-option is seen. This is what Unix does. This mode of operation is selected by either setting the environment variable POSIXLY_CORRECT, or using `+' as the first character of the list of option characters. PERMUTE is the default. We permute the contents of ARGV as we scan, so that eventually all the non-options are at the end. This allows options to be given in any order, even with programs that were not written to expect this. RETURN_IN_ORDER is an option available to programs that were written to expect options and other ARGV-elements in any order and that care about the ordering of the two. We describe each non-option ARGV-element as if it were the argument of an option with character code 1. Using `-' as the first character of the list of option characters selects this mode of operation. The special argument `--' forces an end of option-scanning regardless of the value of `ordering'. In the case of RETURN_IN_ORDER, only `--' can cause `getopt' to return -1 with `optind' != ARGC. */ static enum { REQUIRE_ORDER, PERMUTE, RETURN_IN_ORDER } ordering; /* Value of POSIXLY_CORRECT environment variable. */ static char *posixly_correct; #ifdef __GNU_LIBRARY__ /* We want to avoid inclusion of string.h with non-GNU libraries because there are many ways it can cause trouble. On some systems, it contains special magic macros that don't work in GCC. */ # include # define my_index strchr #else /* # if HAVE_STRING_H || WIN32 /* Pete Wilson mod 7/28/02 * / # include # else # include # endif */ /* Avoid depending on library functions or files whose names are inconsistent. */ #ifndef getenv extern char *getenv (); #endif static char * my_index (str, chr) const char *str; int chr; { while (*str) { if (*str == chr) return (char *) str; str++; } return 0; } /* If using GCC, we can safely declare strlen this way. If not using GCC, it is ok not to declare it. */ #ifdef __GNUC__ /* Note that Motorola Delta 68k R3V7 comes with GCC but not stddef.h. That was relevant to code that was here before. */ # if (!defined __STDC__ || !__STDC__) && !defined strlen /* gcc with -traditional declares the built-in strlen to return int, and has done so at least since version 2.4.5. -- rms. */ extern int strlen (const char *); # endif /* not __STDC__ */ #endif /* __GNUC__ */ #endif /* not __GNU_LIBRARY__ */ /* Handle permutation of arguments. */ /* Describe the part of ARGV that contains non-options that have been skipped. `first_nonopt' is the index in ARGV of the first of them; `last_nonopt' is the index after the last of them. */ static int first_nonopt; static int last_nonopt; #ifdef _LIBC /* Stored original parameters. XXX This is no good solution. We should rather copy the args so that we can compare them later. But we must not use malloc(3). */ extern int __libc_argc; extern char **__libc_argv; /* Bash 2.0 gives us an environment variable containing flags indicating ARGV elements that should not be considered arguments. */ # ifdef USE_NONOPTION_FLAGS /* Defined in getopt_init.c */ extern char *__getopt_nonoption_flags; static int nonoption_flags_max_len; static int nonoption_flags_len; # endif # ifdef USE_NONOPTION_FLAGS # define SWAP_FLAGS(ch1, ch2) \ if (nonoption_flags_len > 0) \ { \ char __tmp = __getopt_nonoption_flags[ch1]; \ __getopt_nonoption_flags[ch1] = __getopt_nonoption_flags[ch2]; \ __getopt_nonoption_flags[ch2] = __tmp; \ } # else # define SWAP_FLAGS(ch1, ch2) # endif #else /* !_LIBC */ # define SWAP_FLAGS(ch1, ch2) #endif /* _LIBC */ /* Exchange two adjacent subsequences of ARGV. One subsequence is elements [first_nonopt,last_nonopt) which contains all the non-options that have been skipped so far. The other is elements [last_nonopt,optind), which contains all the options processed since those non-options were skipped. `first_nonopt' and `last_nonopt' are relocated so that they describe the new indices of the non-options in ARGV after they are moved. */ #if defined __STDC__ && __STDC__ static void exchange (char **); #endif static void exchange (argv) char **argv; { int bottom = first_nonopt; int middle = last_nonopt; int top = optind; char *tem; /* Exchange the shorter segment with the far end of the longer segment. That puts the shorter segment into the right place. It leaves the longer segment in the right place overall, but it consists of two parts that need to be swapped next. */ #if defined _LIBC && defined USE_NONOPTION_FLAGS /* First make sure the handling of the `__getopt_nonoption_flags' string can work normally. Our top argument must be in the range of the string. */ if (nonoption_flags_len > 0 && top >= nonoption_flags_max_len) { /* We must extend the array. The user plays games with us and presents new arguments. */ char *new_str = malloc (top + 1); if (new_str == NULL) nonoption_flags_len = nonoption_flags_max_len = 0; else { memset (__mempcpy (new_str, __getopt_nonoption_flags, nonoption_flags_max_len), '\0', top + 1 - nonoption_flags_max_len); nonoption_flags_max_len = top + 1; __getopt_nonoption_flags = new_str; } } #endif while (top > middle && middle > bottom) { if (top - middle > middle - bottom) { /* Bottom segment is the short one. */ int len = middle - bottom; register int i; /* Swap it with the top part of the top segment. */ for (i = 0; i < len; i++) { tem = argv[bottom + i]; argv[bottom + i] = argv[top - (middle - bottom) + i]; argv[top - (middle - bottom) + i] = tem; SWAP_FLAGS (bottom + i, top - (middle - bottom) + i); } /* Exclude the moved bottom segment from further swapping. */ top -= len; } else { /* Top segment is the short one. */ int len = top - middle; register int i; /* Swap it with the bottom part of the bottom segment. */ for (i = 0; i < len; i++) { tem = argv[bottom + i]; argv[bottom + i] = argv[middle + i]; argv[middle + i] = tem; SWAP_FLAGS (bottom + i, middle + i); } /* Exclude the moved top segment from further swapping. */ bottom += len; } } /* Update records for the slots the non-options now occupy. */ first_nonopt += (optind - last_nonopt); last_nonopt = optind; } /* Initialize the internal data when the first call is made. */ #if defined __STDC__ && __STDC__ static const char *_getopt_initialize (int, char *const *, const char *); #endif static const char * _getopt_initialize (argc, argv, optstring) int argc; char *const *argv; const char *optstring; { /* Start processing options with ARGV-element 1 (since ARGV-element 0 is the program name); the sequence of previously skipped non-option ARGV-elements is empty. */ first_nonopt = last_nonopt = optind; nextchar = NULL; posixly_correct = getenv ("POSIXLY_CORRECT"); /* Determine how to handle the ordering of options and nonoptions. */ if (optstring[0] == '-') { ordering = RETURN_IN_ORDER; ++optstring; } else if (optstring[0] == '+') { ordering = REQUIRE_ORDER; ++optstring; } else if (posixly_correct != NULL) ordering = REQUIRE_ORDER; else ordering = PERMUTE; #if defined _LIBC && defined USE_NONOPTION_FLAGS if (posixly_correct == NULL && argc == __libc_argc && argv == __libc_argv) { if (nonoption_flags_max_len == 0) { if (__getopt_nonoption_flags == NULL || __getopt_nonoption_flags[0] == '\0') nonoption_flags_max_len = -1; else { const char *orig_str = __getopt_nonoption_flags; int len = nonoption_flags_max_len = strlen (orig_str); if (nonoption_flags_max_len < argc) nonoption_flags_max_len = argc; __getopt_nonoption_flags = (char *) malloc (nonoption_flags_max_len); if (__getopt_nonoption_flags == NULL) nonoption_flags_max_len = -1; else memset (__mempcpy (__getopt_nonoption_flags, orig_str, len), '\0', nonoption_flags_max_len - len); } } nonoption_flags_len = nonoption_flags_max_len; } else nonoption_flags_len = 0; #endif return optstring; } /* Scan elements of ARGV (whose length is ARGC) for option characters given in OPTSTRING. If an element of ARGV starts with '-', and is not exactly "-" or "--", then it is an option element. The characters of this element (aside from the initial '-') are option characters. If `getopt' is called repeatedly, it returns successively each of the option characters from each of the option elements. If `getopt' finds another option character, it returns that character, updating `optind' and `nextchar' so that the next call to `getopt' can resume the scan with the following option character or ARGV-element. If there are no more option characters, `getopt' returns -1. Then `optind' is the index in ARGV of the first ARGV-element that is not an option. (The ARGV-elements have been permuted so that those that are not options now come last.) OPTSTRING is a string containing the legitimate option characters. If an option character is seen that is not listed in OPTSTRING, return '?' after printing an error message. If you set `opterr' to zero, the error message is suppressed but we still return '?'. If a char in OPTSTRING is followed by a colon, that means it wants an arg, so the following text in the same ARGV-element, or the text of the following ARGV-element, is returned in `optarg'. Two colons mean an option that wants an optional arg; if there is text in the current ARGV-element, it is returned in `optarg', otherwise `optarg' is set to zero. If OPTSTRING starts with `-' or `+', it requests different methods of handling the non-option ARGV-elements. See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above. Long-named options begin with `--' instead of `-'. Their names may be abbreviated as long as the abbreviation is unique or is an exact match for some defined option. If they have an argument, it follows the option name in the same ARGV-element, separated from the option name by a `=', or else the in next ARGV-element. When `getopt' finds a long-named option, it returns 0 if that option's `flag' field is nonzero, the value of the option's `val' field if the `flag' field is zero. The elements of ARGV aren't really const, because we permute them. But we pretend they're const in the prototype to be compatible with other systems. LONGOPTS is a vector of `struct option' terminated by an element containing a name which is zero. LONGIND returns the index in LONGOPT of the long-named option found. It is only valid when a long-named option has been found by the most recent call. If LONG_ONLY is nonzero, '-' as well as '--' can introduce long-named options. */ int _getopt_internal (argc, argv, optstring, longopts, longind, long_only) int argc; char *const *argv; const char *optstring; const struct option *longopts; int *longind; int long_only; { int print_errors = opterr; if (optstring[0] == ':') print_errors = 0; if (argc < 1) return -1; optarg = NULL; if (optind == 0 || !__getopt_initialized) { if (optind == 0) optind = 1; /* Don't scan ARGV[0], the program name. */ optstring = _getopt_initialize (argc, argv, optstring); __getopt_initialized = 1; } /* Test whether ARGV[optind] points to a non-option argument. Either it does not have option syntax, or there is an environment flag from the shell indicating it is not an option. The later information is only used when the used in the GNU libc. */ #if defined _LIBC && defined USE_NONOPTION_FLAGS # define NONOPTION_P (argv[optind][0] != '-' || argv[optind][1] == '\0' \ || (optind < nonoption_flags_len \ && __getopt_nonoption_flags[optind] == '1')) #else # define NONOPTION_P (argv[optind][0] != '-' || argv[optind][1] == '\0') #endif if (nextchar == NULL || *nextchar == '\0') { /* Advance to the next ARGV-element. */ /* Give FIRST_NONOPT and LAST_NONOPT rational values if OPTIND has been moved back by the user (who may also have changed the arguments). */ if (last_nonopt > optind) last_nonopt = optind; if (first_nonopt > optind) first_nonopt = optind; if (ordering == PERMUTE) { /* If we have just processed some options following some non-options, exchange them so that the options come first. */ if (first_nonopt != last_nonopt && last_nonopt != optind) exchange ((char **) argv); else if (last_nonopt != optind) first_nonopt = optind; /* Skip any additional non-options and extend the range of non-options previously skipped. */ while (optind < argc && NONOPTION_P) optind++; last_nonopt = optind; } /* The special ARGV-element `--' means premature end of options. Skip it like a null option, then exchange with previous non-options as if it were an option, then skip everything else like a non-option. */ if (optind != argc && !strcmp (argv[optind], "--")) { optind++; if (first_nonopt != last_nonopt && last_nonopt != optind) exchange ((char **) argv); else if (first_nonopt == last_nonopt) first_nonopt = optind; last_nonopt = argc; optind = argc; } /* If we have done all the ARGV-elements, stop the scan and back over any non-options that we skipped and permuted. */ if (optind == argc) { /* Set the next-arg-index to point at the non-options that we previously skipped, so the caller will digest them. */ if (first_nonopt != last_nonopt) optind = first_nonopt; return -1; } /* If we have come to a non-option and did not permute it, either stop the scan or describe it to the caller and pass it by. */ if (NONOPTION_P) { if (ordering == REQUIRE_ORDER) return -1; optarg = argv[optind++]; return 1; } /* We have found another option-ARGV-element. Skip the initial punctuation. */ nextchar = (argv[optind] + 1 + (longopts != NULL && argv[optind][1] == '-')); } /* Decode the current option-ARGV-element. */ /* Check whether the ARGV-element is a long option. If long_only and the ARGV-element has the form "-f", where f is a valid short option, don't consider it an abbreviated form of a long option that starts with f. Otherwise there would be no way to give the -f short option. On the other hand, if there's a long option "fubar" and the ARGV-element is "-fu", do consider that an abbreviation of the long option, just like "--fu", and not "-f" with arg "u". This distinction seems to be the most useful approach. */ if (longopts != NULL && (argv[optind][1] == '-' || (long_only && (argv[optind][2] || !my_index (optstring, argv[optind][1]))))) { char *nameend; const struct option *p; const struct option *pfound = NULL; int exact = 0; int ambig = 0; int indfound = -1; int option_index; for (nameend = nextchar; *nameend && *nameend != '='; nameend++) /* Do nothing. */ ; /* Test all long options for either exact match or abbreviated matches. */ for (p = longopts, option_index = 0; p->name; p++, option_index++) if (!strncmp (p->name, nextchar, nameend - nextchar)) { if ((unsigned int) (nameend - nextchar) == (unsigned int) strlen (p->name)) { /* Exact match found. */ pfound = p; indfound = option_index; exact = 1; break; } else if (pfound == NULL) { /* First nonexact match found. */ pfound = p; indfound = option_index; } else if (long_only || pfound->has_arg != p->has_arg || pfound->flag != p->flag || pfound->val != p->val) /* Second or later nonexact match found. */ ambig = 1; } if (ambig && !exact) { if (print_errors) { #if defined _LIBC && defined USE_IN_LIBIO char *buf; __asprintf (&buf, _("%s: option `%s' is ambiguous\n"), argv[0], argv[optind]); if (_IO_fwide (stderr, 0) > 0) __fwprintf (stderr, L"%s", buf); else fputs (buf, stderr); free (buf); #else fprintf (stderr, _("%s: option `%s' is ambiguous\n"), argv[0], argv[optind]); #endif } nextchar += strlen (nextchar); optind++; optopt = 0; return '?'; } if (pfound != NULL) { option_index = indfound; optind++; if (*nameend) { /* Don't test has_arg with >, because some C compilers don't allow it to be used on enums. */ if (pfound->has_arg) optarg = nameend + 1; else { if (print_errors) { #if defined _LIBC && defined USE_IN_LIBIO char *buf; #endif if (argv[optind - 1][1] == '-') { /* --option */ #if defined _LIBC && defined USE_IN_LIBIO __asprintf (&buf, _("\ %s: option `--%s' doesn't allow an argument\n"), argv[0], pfound->name); #else fprintf (stderr, _("\ %s: option `--%s' doesn't allow an argument\n"), argv[0], pfound->name); #endif } else { /* +option or -option */ #if defined _LIBC && defined USE_IN_LIBIO __asprintf (&buf, _("\ %s: option `%c%s' doesn't allow an argument\n"), argv[0], argv[optind - 1][0], pfound->name); #else fprintf (stderr, _("\ %s: option `%c%s' doesn't allow an argument\n"), argv[0], argv[optind - 1][0], pfound->name); #endif } #if defined _LIBC && defined USE_IN_LIBIO if (_IO_fwide (stderr, 0) > 0) __fwprintf (stderr, L"%s", buf); else fputs (buf, stderr); free (buf); #endif } nextchar += strlen (nextchar); optopt = pfound->val; return '?'; } } else if (pfound->has_arg == 1) { if (optind < argc) optarg = argv[optind++]; else { if (print_errors) { #if defined _LIBC && defined USE_IN_LIBIO char *buf; __asprintf (&buf, _("%s: option `%s' requires an argument\n"), argv[0], argv[optind - 1]); if (_IO_fwide (stderr, 0) > 0) __fwprintf (stderr, L"%s", buf); else fputs (buf, stderr); free (buf); #else fprintf (stderr, _("%s: option `%s' requires an argument\n"), argv[0], argv[optind - 1]); #endif } nextchar += strlen (nextchar); optopt = pfound->val; return optstring[0] == ':' ? ':' : '?'; } } nextchar += strlen (nextchar); if (longind != NULL) *longind = option_index; if (pfound->flag) { *(pfound->flag) = pfound->val; return 0; } return pfound->val; } /* Can't find it as a long option. If this is not getopt_long_only, or the option starts with '--' or is not a valid short option, then it's an error. Otherwise interpret it as a short option. */ if (!long_only || argv[optind][1] == '-' || my_index (optstring, *nextchar) == NULL) { if (print_errors) { #if defined _LIBC && defined USE_IN_LIBIO char *buf; #endif if (argv[optind][1] == '-') { /* --option */ #if defined _LIBC && defined USE_IN_LIBIO __asprintf (&buf, _("%s: unrecognized option `--%s'\n"), argv[0], nextchar); #else fprintf (stderr, _("%s: unrecognized option `--%s'\n"), argv[0], nextchar); #endif } else { /* +option or -option */ #if defined _LIBC && defined USE_IN_LIBIO __asprintf (&buf, _("%s: unrecognized option `%c%s'\n"), argv[0], argv[optind][0], nextchar); #else fprintf (stderr, _("%s: unrecognized option `%c%s'\n"), argv[0], argv[optind][0], nextchar); #endif } #if defined _LIBC && defined USE_IN_LIBIO if (_IO_fwide (stderr, 0) > 0) __fwprintf (stderr, L"%s", buf); else fputs (buf, stderr); free (buf); #endif } nextchar = (char *) ""; optind++; optopt = 0; return '?'; } } /* Look at and handle the next short option-character. */ { char c = *nextchar++; char *temp = my_index (optstring, c); /* Increment `optind' when we start to process its last character. */ if (*nextchar == '\0') ++optind; if (temp == NULL || c == ':') { if (print_errors) { #if defined _LIBC && defined USE_IN_LIBIO char *buf; #endif if (posixly_correct) { /* 1003.2 specifies the format of this message. */ #if defined _LIBC && defined USE_IN_LIBIO __asprintf (&buf, _("%s: illegal option -- %c\n"), argv[0], c); #else fprintf (stderr, _("%s: illegal option -- %c\n"), argv[0], c); #endif } else { #if defined _LIBC && defined USE_IN_LIBIO __asprintf (&buf, _("%s: invalid option -- %c\n"), argv[0], c); #else fprintf (stderr, _("%s: invalid option -- %c\n"), argv[0], c); #endif } #if defined _LIBC && defined USE_IN_LIBIO if (_IO_fwide (stderr, 0) > 0) __fwprintf (stderr, L"%s", buf); else fputs (buf, stderr); free (buf); #endif } optopt = c; return '?'; } /* Convenience. Treat POSIX -W foo same as long option --foo */ if (temp[0] == 'W' && temp[1] == ';') { char *nameend; const struct option *p; const struct option *pfound = NULL; int exact = 0; int ambig = 0; int indfound = 0; int option_index; /* This is an option that requires an argument. */ if (*nextchar != '\0') { optarg = nextchar; /* If we end this ARGV-element by taking the rest as an arg, we must advance to the next element now. */ optind++; } else if (optind == argc) { if (print_errors) { /* 1003.2 specifies the format of this message. */ #if defined _LIBC && defined USE_IN_LIBIO char *buf; __asprintf (&buf, _("%s: option requires an argument -- %c\n"), argv[0], c); if (_IO_fwide (stderr, 0) > 0) __fwprintf (stderr, L"%s", buf); else fputs (buf, stderr); free (buf); #else fprintf (stderr, _("%s: option requires an argument -- %c\n"), argv[0], c); #endif } optopt = c; if (optstring[0] == ':') c = ':'; else c = '?'; return c; } else /* We already incremented `optind' once; increment it again when taking next ARGV-elt as argument. */ optarg = argv[optind++]; /* optarg is now the argument, see if it's in the table of longopts. */ for (nextchar = nameend = optarg; *nameend && *nameend != '='; nameend++) /* Do nothing. */ ; /* Test all long options for either exact match or abbreviated matches. */ for (p = longopts, option_index = 0; p->name; p++, option_index++) if (!strncmp (p->name, nextchar, nameend - nextchar)) { if ((unsigned int) (nameend - nextchar) == strlen (p->name)) { /* Exact match found. */ pfound = p; indfound = option_index; exact = 1; break; } else if (pfound == NULL) { /* First nonexact match found. */ pfound = p; indfound = option_index; } else /* Second or later nonexact match found. */ ambig = 1; } if (ambig && !exact) { if (print_errors) { #if defined _LIBC && defined USE_IN_LIBIO char *buf; __asprintf (&buf, _("%s: option `-W %s' is ambiguous\n"), argv[0], argv[optind]); if (_IO_fwide (stderr, 0) > 0) __fwprintf (stderr, L"%s", buf); else fputs (buf, stderr); free (buf); #else fprintf (stderr, _("%s: option `-W %s' is ambiguous\n"), argv[0], argv[optind]); #endif } nextchar += strlen (nextchar); optind++; return '?'; } if (pfound != NULL) { option_index = indfound; if (*nameend) { /* Don't test has_arg with >, because some C compilers don't allow it to be used on enums. */ if (pfound->has_arg) optarg = nameend + 1; else { if (print_errors) { #if defined _LIBC && defined USE_IN_LIBIO char *buf; __asprintf (&buf, _("\ %s: option `-W %s' doesn't allow an argument\n"), argv[0], pfound->name); if (_IO_fwide (stderr, 0) > 0) __fwprintf (stderr, L"%s", buf); else fputs (buf, stderr); free (buf); #else fprintf (stderr, _("\ %s: option `-W %s' doesn't allow an argument\n"), argv[0], pfound->name); #endif } nextchar += strlen (nextchar); return '?'; } } else if (pfound->has_arg == 1) { if (optind < argc) optarg = argv[optind++]; else { if (print_errors) { #if defined _LIBC && defined USE_IN_LIBIO char *buf; __asprintf (&buf, _("\ %s: option `%s' requires an argument\n"), argv[0], argv[optind - 1]); if (_IO_fwide (stderr, 0) > 0) __fwprintf (stderr, L"%s", buf); else fputs (buf, stderr); free (buf); #else fprintf (stderr, _("%s: option `%s' requires an argument\n"), argv[0], argv[optind - 1]); #endif } nextchar += strlen (nextchar); return optstring[0] == ':' ? ':' : '?'; } } nextchar += strlen (nextchar); if (longind != NULL) *longind = option_index; if (pfound->flag) { *(pfound->flag) = pfound->val; return 0; } return pfound->val; } nextchar = NULL; return 'W'; /* Let the application handle it. */ } if (temp[1] == ':') { if (temp[2] == ':') { /* This is an option that accepts an argument optionally. */ if (*nextchar != '\0') { optarg = nextchar; optind++; } else optarg = NULL; nextchar = NULL; } else { /* This is an option that requires an argument. */ if (*nextchar != '\0') { optarg = nextchar; /* If we end this ARGV-element by taking the rest as an arg, we must advance to the next element now. */ optind++; } else if (optind == argc) { if (print_errors) { /* 1003.2 specifies the format of this message. */ #if defined _LIBC && defined USE_IN_LIBIO char *buf; __asprintf (&buf, _("%s: option requires an argument -- %c\n"), argv[0], c); if (_IO_fwide (stderr, 0) > 0) __fwprintf (stderr, L"%s", buf); else fputs (buf, stderr); free (buf); #else fprintf (stderr, _("%s: option requires an argument -- %c\n"), argv[0], c); #endif } optopt = c; if (optstring[0] == ':') c = ':'; else c = '?'; } else /* We already incremented `optind' once; increment it again when taking next ARGV-elt as argument. */ optarg = argv[optind++]; nextchar = NULL; } } return c; } } int getopt (argc, argv, optstring) int argc; char *const *argv; const char *optstring; { return _getopt_internal (argc, argv, optstring, (const struct option *) 0, (int *) 0, 0); } #endif /* Not ELIDE_CODE. */ /* Compile with -DTEST to make an executable for use in testing the above definition of `getopt'. */ /* #define TEST */ /* Pete Wilson mod 7/28/02 */ #ifdef TEST #ifndef exit /* Pete Wilson mod 7/28/02 */ int exit(int); /* Pete Wilson mod 7/28/02 */ #endif /* Pete Wilson mod 7/28/02 */ int main (argc, argv) int argc; char **argv; { int c; int digit_optind = 0; while (1) { int this_option_optind = optind ? optind : 1; c = getopt (argc, argv, "abc:d:0123456789"); if (c == -1) break; switch (c) { case '0': case '1': case '2': case '3': case '4': case '5': case '6': case '7': case '8': case '9': if (digit_optind != 0 && digit_optind != this_option_optind) printf ("digits occur in two different argv-elements.\n"); digit_optind = this_option_optind; printf ("option %c\n", c); break; case 'a': printf ("option a\n"); break; case 'b': printf ("option b\n"); break; case 'c': printf ("option c with value `%s'\n", optarg); break; case '?': break; default: printf ("?? getopt returned character code 0%o ??\n", c); } } if (optind < argc) { printf ("non-option ARGV-elements: "); while (optind < argc) printf ("%s ", argv[optind++]); printf ("\n"); } exit (0); } #endif /* TEST */ pysam-0.23.0/win32/getopt.h000066400000000000000000000152761475062545500153720ustar00rootroot00000000000000/* getopt.h */ /* Declarations for getopt. Copyright (C) 1989-1994, 1996-1999, 2001 Free Software Foundation, Inc. This file is part of the GNU C Library. The GNU C Library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. The GNU C Library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with the GNU C Library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. */ #ifndef _GETOPT_H #ifndef __need_getopt # define _GETOPT_H 1 #endif /* If __GNU_LIBRARY__ is not already defined, either we are being used standalone, or this is the first header included in the source file. If we are being used with glibc, we need to include , but that does not exist if we are standalone. So: if __GNU_LIBRARY__ is not defined, include , which will pull in for us if it's from glibc. (Why ctype.h? It's guaranteed to exist and it doesn't flood the namespace with stuff the way some other headers do.) */ #if !defined __GNU_LIBRARY__ # include #endif #ifdef __cplusplus extern "C" { #endif /* For communication from `getopt' to the caller. When `getopt' finds an option that takes an argument, the argument value is returned here. Also, when `ordering' is RETURN_IN_ORDER, each non-option ARGV-element is returned here. */ extern char *optarg; /* Index in ARGV of the next element to be scanned. This is used for communication to and from the caller and for communication between successive calls to `getopt'. On entry to `getopt', zero means this is the first call; initialize. When `getopt' returns -1, this is the index of the first of the non-option elements that the caller should itself scan. Otherwise, `optind' communicates from one call to the next how much of ARGV has been scanned so far. */ extern int optind; /* Callers store zero here to inhibit the error message `getopt' prints for unrecognized options. */ extern int opterr; /* Set to an option character which was unrecognized. */ extern int optopt; #ifndef __need_getopt /* Describe the long-named options requested by the application. The LONG_OPTIONS argument to getopt_long or getopt_long_only is a vector of `struct option' terminated by an element containing a name which is zero. The field `has_arg' is: no_argument (or 0) if the option does not take an argument, required_argument (or 1) if the option requires an argument, optional_argument (or 2) if the option takes an optional argument. If the field `flag' is not NULL, it points to a variable that is set to the value given in the field `val' when the option is found, but left unchanged if the option is not found. To have a long-named option do something other than set an `int' to a compiled-in constant, such as set a value from `optarg', set the option's `flag' field to zero and its `val' field to a nonzero value (the equivalent single-letter option character, if there is one). For long options that have a zero `flag' field, `getopt' returns the contents of the `val' field. */ struct option { # if (defined __STDC__ && __STDC__) || defined __cplusplus const char *name; # else char *name; # endif /* has_arg can't be an enum because some compilers complain about type mismatches in all the code that assumes it is an int. */ int has_arg; int *flag; int val; }; /* Names for the values of the `has_arg' field of `struct option'. */ # define no_argument 0 # define required_argument 1 # define optional_argument 2 #endif /* need getopt */ /* Get definitions and prototypes for functions to process the arguments in ARGV (ARGC of them, minus the program name) for options given in OPTS. Return the option character from OPTS just read. Return -1 when there are no more options. For unrecognized options, or options missing arguments, `optopt' is set to the option letter, and '?' is returned. The OPTS string is a list of characters which are recognized option letters, optionally followed by colons, specifying that that letter takes an argument, to be placed in `optarg'. If a letter in OPTS is followed by two colons, its argument is optional. This behavior is specific to the GNU `getopt'. The argument `--' causes premature termination of argument scanning, explicitly telling `getopt' that there are no more options. If OPTS begins with `--', then non-option arguments are treated as arguments to the option '\0'. This behavior is specific to the GNU `getopt'. */ #if (defined __STDC__ && __STDC__) || defined __cplusplus # ifdef __GNU_LIBRARY__ /* Many other libraries have conflicting prototypes for getopt, with differences in the consts, in stdlib.h. To avoid compilation errors, only prototype getopt for the GNU C library. */ extern int getopt (int ___argc, char *const *___argv, const char *__shortopts); # else /* not __GNU_LIBRARY__ */ extern int getopt (); # endif /* __GNU_LIBRARY__ */ # ifndef __need_getopt extern int getopt_long (int ___argc, char *const *___argv, const char *__shortopts, const struct option *__longopts, int *__longind); extern int getopt_long_only (int ___argc, char *const *___argv, const char *__shortopts, const struct option *__longopts, int *__longind); /* Internal only. Users should not call this directly. */ extern int _getopt_internal (int ___argc, char *const *___argv, const char *__shortopts, const struct option *__longopts, int *__longind, int __long_only); # endif #else /* not __STDC__ */ extern int getopt (); # ifndef __need_getopt extern int getopt_long (); extern int getopt_long_only (); extern int _getopt_internal (); # endif #endif /* __STDC__ */ #ifdef __cplusplus } #endif /* Make sure we later can get all the definitions and declarations. */ #undef __need_getopt #endif /* getopt.h */ pysam-0.23.0/win32/stdint.h000066400000000000000000000650101475062545500153640ustar00rootroot00000000000000/* A portable stdint.h **************************************************************************** * BSD License: **************************************************************************** * * Copyright (c) 2005-2007 Paul Hsieh * All rights reserved. * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * 3. The name of the author may not be used to endorse or promote products * derived from this software without specific prior written permission. * * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. * **************************************************************************** * * Version 0.1.11 * * The ANSI C standard committee, for the C99 standard, specified the * inclusion of a new standard include file called stdint.h. This is * a very useful and long desired include file which contains several * very precise definitions for integer scalar types that is * critically important for making portable several classes of * applications including cryptography, hashing, variable length * integer libraries and so on. But for most developers its likely * useful just for programming sanity. * * The problem is that most compiler vendors have decided not to * implement the C99 standard, and the next C++ language standard * (which has a lot more mindshare these days) will be a long time in * coming and its unknown whether or not it will include stdint.h or * how much adoption it will have. Either way, it will be a long time * before all compilers come with a stdint.h and it also does nothing * for the extremely large number of compilers available today which * do not include this file, or anything comparable to it. * * So that's what this file is all about. Its an attempt to build a * single universal include file that works on as many platforms as * possible to deliver what stdint.h is supposed to. A few things * that should be noted about this file: * * 1) It is not guaranteed to be portable and/or present an identical * interface on all platforms. The extreme variability of the * ANSI C standard makes this an impossibility right from the * very get go. Its really only meant to be useful for the vast * majority of platforms that possess the capability of * implementing usefully and precisely defined, standard sized * integer scalars. Systems which are not intrinsically 2s * complement may produce invalid constants. * * 2) There is an unavoidable use of non-reserved symbols. * * 3) Other standard include files are invoked. * * 4) This file may come in conflict with future platforms that do * include stdint.h. The hope is that one or the other can be * used with no real difference. * * 5) In the current verison, if your platform can't represent * int32_t, int16_t and int8_t, it just dumps out with a compiler * error. * * 6) 64 bit integers may or may not be defined. Test for their * presence with the test: #ifdef INT64_MAX or #ifdef UINT64_MAX. * Note that this is different from the C99 specification which * requires the existence of 64 bit support in the compiler. If * this is not defined for your platform, yet it is capable of * dealing with 64 bits then it is because this file has not yet * been extended to cover all of your system's capabilities. * * 7) (u)intptr_t may or may not be defined. Test for its presence * with the test: #ifdef PTRDIFF_MAX. If this is not defined * for your platform, then it is because this file has not yet * been extended to cover all of your system's capabilities, not * because its optional. * * 8) The following might not been defined even if your platform is * capable of defining it: * * WCHAR_MIN * WCHAR_MAX * (u)int64_t * PTRDIFF_MIN * PTRDIFF_MAX * (u)intptr_t * * 9) The following have not been defined: * * WINT_MIN * WINT_MAX * * 10) The criteria for defining (u)int_least(*)_t isn't clear, * except for systems which don't have a type that precisely * defined 8, 16, or 32 bit types (which this include file does * not support anyways). Default definitions have been given. * * 11) The criteria for defining (u)int_fast(*)_t isn't something I * would trust to any particular compiler vendor or the ANSI C * committee. It is well known that "compatible systems" are * commonly created that have very different performance * characteristics from the systems they are compatible with, * especially those whose vendors make both the compiler and the * system. Default definitions have been given, but its strongly * recommended that users never use these definitions for any * reason (they do *NOT* deliver any serious guarantee of * improved performance -- not in this file, nor any vendor's * stdint.h). * * 12) The following macros: * * PRINTF_INTMAX_MODIFIER * PRINTF_INT64_MODIFIER * PRINTF_INT32_MODIFIER * PRINTF_INT16_MODIFIER * PRINTF_LEAST64_MODIFIER * PRINTF_LEAST32_MODIFIER * PRINTF_LEAST16_MODIFIER * PRINTF_INTPTR_MODIFIER * * are strings which have been defined as the modifiers required * for the "d", "u" and "x" printf formats to correctly output * (u)intmax_t, (u)int64_t, (u)int32_t, (u)int16_t, (u)least64_t, * (u)least32_t, (u)least16_t and (u)intptr_t types respectively. * PRINTF_INTPTR_MODIFIER is not defined for some systems which * provide their own stdint.h. PRINTF_INT64_MODIFIER is not * defined if INT64_MAX is not defined. These are an extension * beyond what C99 specifies must be in stdint.h. * * In addition, the following macros are defined: * * PRINTF_INTMAX_HEX_WIDTH * PRINTF_INT64_HEX_WIDTH * PRINTF_INT32_HEX_WIDTH * PRINTF_INT16_HEX_WIDTH * PRINTF_INT8_HEX_WIDTH * PRINTF_INTMAX_DEC_WIDTH * PRINTF_INT64_DEC_WIDTH * PRINTF_INT32_DEC_WIDTH * PRINTF_INT16_DEC_WIDTH * PRINTF_INT8_DEC_WIDTH * * Which specifies the maximum number of characters required to * print the number of that type in either hexadecimal or decimal. * These are an extension beyond what C99 specifies must be in * stdint.h. * * Compilers tested (all with 0 warnings at their highest respective * settings): Borland Turbo C 2.0, WATCOM C/C++ 11.0 (16 bits and 32 * bits), Microsoft Visual C++ 6.0 (32 bit), Microsoft Visual Studio * .net (VC7), Intel C++ 4.0, GNU gcc v3.3.3 * * This file should be considered a work in progress. Suggestions for * improvements, especially those which increase coverage are strongly * encouraged. * * Acknowledgements * * The following people have made significant contributions to the * development and testing of this file: * * Chris Howie * John Steele Scott * Dave Thorup * */ #include #include #include /* * For gcc with _STDINT_H, fill in the PRINTF_INT*_MODIFIER macros, and * do nothing else. On the Mac OS X version of gcc this is _STDINT_H_. */ #if ((defined(__STDC__) && __STDC__ && __STDC_VERSION__ >= 199901L) || (defined (__WATCOMC__) && (defined (_STDINT_H_INCLUDED) || __WATCOMC__ >= 1250)) || (defined(__GNUC__) && (defined(_STDINT_H) || defined(_STDINT_H_)) )) && !defined (_PSTDINT_H_INCLUDED) #include #define _PSTDINT_H_INCLUDED # ifndef PRINTF_INT64_MODIFIER # define PRINTF_INT64_MODIFIER "ll" # endif # ifndef PRINTF_INT32_MODIFIER # define PRINTF_INT32_MODIFIER "l" # endif # ifndef PRINTF_INT16_MODIFIER # define PRINTF_INT16_MODIFIER "h" # endif # ifndef PRINTF_INTMAX_MODIFIER # define PRINTF_INTMAX_MODIFIER PRINTF_INT64_MODIFIER # endif # ifndef PRINTF_INT64_HEX_WIDTH # define PRINTF_INT64_HEX_WIDTH "16" # endif # ifndef PRINTF_INT32_HEX_WIDTH # define PRINTF_INT32_HEX_WIDTH "8" # endif # ifndef PRINTF_INT16_HEX_WIDTH # define PRINTF_INT16_HEX_WIDTH "4" # endif # ifndef PRINTF_INT8_HEX_WIDTH # define PRINTF_INT8_HEX_WIDTH "2" # endif # ifndef PRINTF_INT64_DEC_WIDTH # define PRINTF_INT64_DEC_WIDTH "20" # endif # ifndef PRINTF_INT32_DEC_WIDTH # define PRINTF_INT32_DEC_WIDTH "10" # endif # ifndef PRINTF_INT16_DEC_WIDTH # define PRINTF_INT16_DEC_WIDTH "5" # endif # ifndef PRINTF_INT8_DEC_WIDTH # define PRINTF_INT8_DEC_WIDTH "3" # endif # ifndef PRINTF_INTMAX_HEX_WIDTH # define PRINTF_INTMAX_HEX_WIDTH PRINTF_INT64_HEX_WIDTH # endif # ifndef PRINTF_INTMAX_DEC_WIDTH # define PRINTF_INTMAX_DEC_WIDTH PRINTF_INT64_DEC_WIDTH # endif /* * Something really weird is going on with Open Watcom. Just pull some of * these duplicated definitions from Open Watcom's stdint.h file for now. */ # if defined (__WATCOMC__) && __WATCOMC__ >= 1250 # if !defined (INT64_C) # define INT64_C(x) (x + (INT64_MAX - INT64_MAX)) # endif # if !defined (UINT64_C) # define UINT64_C(x) (x + (UINT64_MAX - UINT64_MAX)) # endif # if !defined (INT32_C) # define INT32_C(x) (x + (INT32_MAX - INT32_MAX)) # endif # if !defined (UINT32_C) # define UINT32_C(x) (x + (UINT32_MAX - UINT32_MAX)) # endif # if !defined (INT16_C) # define INT16_C(x) (x) # endif # if !defined (UINT16_C) # define UINT16_C(x) (x) # endif # if !defined (INT8_C) # define INT8_C(x) (x) # endif # if !defined (UINT8_C) # define UINT8_C(x) (x) # endif # if !defined (UINT64_MAX) # define UINT64_MAX 18446744073709551615ULL # endif # if !defined (INT64_MAX) # define INT64_MAX 9223372036854775807LL # endif # if !defined (UINT32_MAX) # define UINT32_MAX 4294967295UL # endif # if !defined (INT32_MAX) # define INT32_MAX 2147483647L # endif # if !defined (INTMAX_MAX) # define INTMAX_MAX INT64_MAX # endif # if !defined (INTMAX_MIN) # define INTMAX_MIN INT64_MIN # endif # endif #endif #ifndef _PSTDINT_H_INCLUDED #define _PSTDINT_H_INCLUDED #ifndef SIZE_MAX # define SIZE_MAX (~(size_t)0) #endif /* * Deduce the type assignments from limits.h under the assumption that * integer sizes in bits are powers of 2, and follow the ANSI * definitions. */ #ifndef UINT8_MAX # define UINT8_MAX 0xff #endif #ifndef uint8_t # if (UCHAR_MAX == UINT8_MAX) || defined (S_SPLINT_S) typedef unsigned char uint8_t; # define UINT8_C(v) ((uint8_t) v) # else # error "Platform not supported" # endif #endif #ifndef INT8_MAX # define INT8_MAX 0x7f #endif #ifndef INT8_MIN # define INT8_MIN INT8_C(0x80) #endif #ifndef int8_t # if (SCHAR_MAX == INT8_MAX) || defined (S_SPLINT_S) typedef signed char int8_t; # define INT8_C(v) ((int8_t) v) # else # error "Platform not supported" # endif #endif #ifndef UINT16_MAX # define UINT16_MAX 0xffff #endif #ifndef uint16_t #if (UINT_MAX == UINT16_MAX) || defined (S_SPLINT_S) typedef unsigned int uint16_t; # ifndef PRINTF_INT16_MODIFIER # define PRINTF_INT16_MODIFIER "" # endif # define UINT16_C(v) ((uint16_t) (v)) #elif (USHRT_MAX == UINT16_MAX) typedef unsigned short uint16_t; # define UINT16_C(v) ((uint16_t) (v)) # ifndef PRINTF_INT16_MODIFIER # define PRINTF_INT16_MODIFIER "h" # endif #else #error "Platform not supported" #endif #endif #ifndef INT16_MAX # define INT16_MAX 0x7fff #endif #ifndef INT16_MIN # define INT16_MIN INT16_C(0x8000) #endif #ifndef int16_t #if (INT_MAX == INT16_MAX) || defined (S_SPLINT_S) typedef signed int int16_t; # define INT16_C(v) ((int16_t) (v)) # ifndef PRINTF_INT16_MODIFIER # define PRINTF_INT16_MODIFIER "" # endif #elif (SHRT_MAX == INT16_MAX) typedef signed short int16_t; # define INT16_C(v) ((int16_t) (v)) # ifndef PRINTF_INT16_MODIFIER # define PRINTF_INT16_MODIFIER "h" # endif #else #error "Platform not supported" #endif #endif #ifndef UINT32_MAX # define UINT32_MAX (0xffffffffUL) #endif #ifndef uint32_t #if (ULONG_MAX == UINT32_MAX) || defined (S_SPLINT_S) typedef unsigned long uint32_t; # define UINT32_C(v) v ## UL # ifndef PRINTF_INT32_MODIFIER # define PRINTF_INT32_MODIFIER "l" # endif #elif (UINT_MAX == UINT32_MAX) typedef unsigned int uint32_t; # ifndef PRINTF_INT32_MODIFIER # define PRINTF_INT32_MODIFIER "" # endif # define UINT32_C(v) v ## U #elif (USHRT_MAX == UINT32_MAX) typedef unsigned short uint32_t; # define UINT32_C(v) ((unsigned short) (v)) # ifndef PRINTF_INT32_MODIFIER # define PRINTF_INT32_MODIFIER "" # endif #else #error "Platform not supported" #endif #endif #ifndef INT32_MAX # define INT32_MAX (0x7fffffffL) #endif #ifndef INT32_MIN # define INT32_MIN INT32_C(0x80000000) #endif #ifndef int32_t #if (LONG_MAX == INT32_MAX) || defined (S_SPLINT_S) typedef signed long int32_t; # define INT32_C(v) v ## L # ifndef PRINTF_INT32_MODIFIER # define PRINTF_INT32_MODIFIER "l" # endif #elif (INT_MAX == INT32_MAX) typedef signed int int32_t; # define INT32_C(v) v # ifndef PRINTF_INT32_MODIFIER # define PRINTF_INT32_MODIFIER "" # endif #elif (SHRT_MAX == INT32_MAX) typedef signed short int32_t; # define INT32_C(v) ((short) (v)) # ifndef PRINTF_INT32_MODIFIER # define PRINTF_INT32_MODIFIER "" # endif #else #error "Platform not supported" #endif #endif /* * The macro stdint_int64_defined is temporarily used to record * whether or not 64 integer support is available. It must be * defined for any 64 integer extensions for new platforms that are * added. */ #undef stdint_int64_defined #if (defined(__STDC__) && defined(__STDC_VERSION__)) || defined (S_SPLINT_S) # if (__STDC__ && __STDC_VERSION >= 199901L) || defined (S_SPLINT_S) # define stdint_int64_defined typedef long long int64_t; typedef unsigned long long uint64_t; # define UINT64_C(v) v ## ULL # define INT64_C(v) v ## LL # ifndef PRINTF_INT64_MODIFIER # define PRINTF_INT64_MODIFIER "ll" # endif # endif #endif #if !defined (stdint_int64_defined) # if defined(__GNUC__) # define stdint_int64_defined __extension__ typedef long long int64_t; __extension__ typedef unsigned long long uint64_t; # define UINT64_C(v) v ## ULL # define INT64_C(v) v ## LL # ifndef PRINTF_INT64_MODIFIER # define PRINTF_INT64_MODIFIER "ll" # endif # elif defined(__MWERKS__) || defined (__SUNPRO_C) || defined (__SUNPRO_CC) || defined (__APPLE_CC__) || defined (_LONG_LONG) || defined (_CRAYC) || defined (S_SPLINT_S) # define stdint_int64_defined typedef long long int64_t; typedef unsigned long long uint64_t; # define UINT64_C(v) v ## ULL # define INT64_C(v) v ## LL # ifndef PRINTF_INT64_MODIFIER # define PRINTF_INT64_MODIFIER "ll" # endif # elif (defined(__WATCOMC__) && defined(__WATCOM_INT64__)) || (defined(_MSC_VER) && _INTEGRAL_MAX_BITS >= 64) || (defined (__BORLANDC__) && __BORLANDC__ > 0x460) || defined (__alpha) || defined (__DECC) # define stdint_int64_defined typedef __int64 int64_t; typedef unsigned __int64 uint64_t; # define UINT64_C(v) v ## UI64 # define INT64_C(v) v ## I64 # ifndef PRINTF_INT64_MODIFIER # define PRINTF_INT64_MODIFIER "I64" # endif # endif #endif #if !defined (LONG_LONG_MAX) && defined (INT64_C) # define LONG_LONG_MAX INT64_C (9223372036854775807) #endif #ifndef ULONG_LONG_MAX # define ULONG_LONG_MAX UINT64_C (18446744073709551615) #endif #if !defined (INT64_MAX) && defined (INT64_C) # define INT64_MAX INT64_C (9223372036854775807) #endif #if !defined (INT64_MIN) && defined (INT64_C) # define INT64_MIN INT64_C (-9223372036854775808) #endif #if !defined (UINT64_MAX) && defined (INT64_C) # define UINT64_MAX UINT64_C (18446744073709551615) #endif /* * Width of hexadecimal for number field. */ #ifndef PRINTF_INT64_HEX_WIDTH # define PRINTF_INT64_HEX_WIDTH "16" #endif #ifndef PRINTF_INT32_HEX_WIDTH # define PRINTF_INT32_HEX_WIDTH "8" #endif #ifndef PRINTF_INT16_HEX_WIDTH # define PRINTF_INT16_HEX_WIDTH "4" #endif #ifndef PRINTF_INT8_HEX_WIDTH # define PRINTF_INT8_HEX_WIDTH "2" #endif #ifndef PRINTF_INT64_DEC_WIDTH # define PRINTF_INT64_DEC_WIDTH "20" #endif #ifndef PRINTF_INT32_DEC_WIDTH # define PRINTF_INT32_DEC_WIDTH "10" #endif #ifndef PRINTF_INT16_DEC_WIDTH # define PRINTF_INT16_DEC_WIDTH "5" #endif #ifndef PRINTF_INT8_DEC_WIDTH # define PRINTF_INT8_DEC_WIDTH "3" #endif /* * Ok, lets not worry about 128 bit integers for now. Moore's law says * we don't need to worry about that until about 2040 at which point * we'll have bigger things to worry about. */ #ifdef stdint_int64_defined typedef int64_t intmax_t; typedef uint64_t uintmax_t; # define INTMAX_MAX INT64_MAX # define INTMAX_MIN INT64_MIN # define UINTMAX_MAX UINT64_MAX # define UINTMAX_C(v) UINT64_C(v) # define INTMAX_C(v) INT64_C(v) # ifndef PRINTF_INTMAX_MODIFIER # define PRINTF_INTMAX_MODIFIER PRINTF_INT64_MODIFIER # endif # ifndef PRINTF_INTMAX_HEX_WIDTH # define PRINTF_INTMAX_HEX_WIDTH PRINTF_INT64_HEX_WIDTH # endif # ifndef PRINTF_INTMAX_DEC_WIDTH # define PRINTF_INTMAX_DEC_WIDTH PRINTF_INT64_DEC_WIDTH # endif #else typedef int32_t intmax_t; typedef uint32_t uintmax_t; # define INTMAX_MAX INT32_MAX # define UINTMAX_MAX UINT32_MAX # define UINTMAX_C(v) UINT32_C(v) # define INTMAX_C(v) INT32_C(v) # ifndef PRINTF_INTMAX_MODIFIER # define PRINTF_INTMAX_MODIFIER PRINTF_INT32_MODIFIER # endif # ifndef PRINTF_INTMAX_HEX_WIDTH # define PRINTF_INTMAX_HEX_WIDTH PRINTF_INT32_HEX_WIDTH # endif # ifndef PRINTF_INTMAX_DEC_WIDTH # define PRINTF_INTMAX_DEC_WIDTH PRINTF_INT32_DEC_WIDTH # endif #endif /* * Because this file currently only supports platforms which have * precise powers of 2 as bit sizes for the default integers, the * least definitions are all trivial. Its possible that a future * version of this file could have different definitions. */ #ifndef stdint_least_defined typedef int8_t int_least8_t; typedef uint8_t uint_least8_t; typedef int16_t int_least16_t; typedef uint16_t uint_least16_t; typedef int32_t int_least32_t; typedef uint32_t uint_least32_t; # define PRINTF_LEAST32_MODIFIER PRINTF_INT32_MODIFIER # define PRINTF_LEAST16_MODIFIER PRINTF_INT16_MODIFIER # define UINT_LEAST8_MAX UINT8_MAX # define INT_LEAST8_MAX INT8_MAX # define UINT_LEAST16_MAX UINT16_MAX # define INT_LEAST16_MAX INT16_MAX # define UINT_LEAST32_MAX UINT32_MAX # define INT_LEAST32_MAX INT32_MAX # define INT_LEAST8_MIN INT8_MIN # define INT_LEAST16_MIN INT16_MIN # define INT_LEAST32_MIN INT32_MIN # ifdef stdint_int64_defined typedef int64_t int_least64_t; typedef uint64_t uint_least64_t; # define PRINTF_LEAST64_MODIFIER PRINTF_INT64_MODIFIER # define UINT_LEAST64_MAX UINT64_MAX # define INT_LEAST64_MAX INT64_MAX # define INT_LEAST64_MIN INT64_MIN # endif #endif #undef stdint_least_defined /* * The ANSI C committee pretending to know or specify anything about * performance is the epitome of misguided arrogance. The mandate of * this file is to *ONLY* ever support that absolute minimum * definition of the fast integer types, for compatibility purposes. * No extensions, and no attempt to suggest what may or may not be a * faster integer type will ever be made in this file. Developers are * warned to stay away from these types when using this or any other * stdint.h. */ typedef int_least8_t int_fast8_t; typedef uint_least8_t uint_fast8_t; typedef int_least16_t int_fast16_t; typedef uint_least16_t uint_fast16_t; typedef int_least32_t int_fast32_t; typedef uint_least32_t uint_fast32_t; #define UINT_FAST8_MAX UINT_LEAST8_MAX #define INT_FAST8_MAX INT_LEAST8_MAX #define UINT_FAST16_MAX UINT_LEAST16_MAX #define INT_FAST16_MAX INT_LEAST16_MAX #define UINT_FAST32_MAX UINT_LEAST32_MAX #define INT_FAST32_MAX INT_LEAST32_MAX #define INT_FAST8_MIN INT_LEAST8_MIN #define INT_FAST16_MIN INT_LEAST16_MIN #define INT_FAST32_MIN INT_LEAST32_MIN #ifdef stdint_int64_defined typedef int_least64_t int_fast64_t; typedef uint_least64_t uint_fast64_t; # define UINT_FAST64_MAX UINT_LEAST64_MAX # define INT_FAST64_MAX INT_LEAST64_MAX # define INT_FAST64_MIN INT_LEAST64_MIN #endif #undef stdint_int64_defined /* * Whatever piecemeal, per compiler thing we can do about the wchar_t * type limits. */ #if defined(__WATCOMC__) || defined(_MSC_VER) || defined (__GNUC__) # include # ifndef WCHAR_MIN # define WCHAR_MIN 0 # endif # ifndef WCHAR_MAX # define WCHAR_MAX ((wchar_t)-1) # endif #endif /* * Whatever piecemeal, per compiler/platform thing we can do about the * (u)intptr_t types and limits. */ #if defined (_MSC_VER) && defined (_UINTPTR_T_DEFINED) # define STDINT_H_UINTPTR_T_DEFINED #endif #ifndef STDINT_H_UINTPTR_T_DEFINED # if defined (__alpha__) || defined (__ia64__) || defined (__x86_64__) || defined (_WIN64) # define stdint_intptr_bits 64 # elif defined (__WATCOMC__) || defined (__TURBOC__) # if defined(__TINY__) || defined(__SMALL__) || defined(__MEDIUM__) # define stdint_intptr_bits 16 # else # define stdint_intptr_bits 32 # endif # elif defined (__i386__) || defined (_WIN32) || defined (WIN32) # define stdint_intptr_bits 32 # elif defined (__INTEL_COMPILER) /* TODO -- what will Intel do about x86-64? */ # endif # ifdef stdint_intptr_bits # define stdint_intptr_glue3_i(a,b,c) a##b##c # define stdint_intptr_glue3(a,b,c) stdint_intptr_glue3_i(a,b,c) # ifndef PRINTF_INTPTR_MODIFIER # define PRINTF_INTPTR_MODIFIER stdint_intptr_glue3(PRINTF_INT,stdint_intptr_bits,_MODIFIER) # endif # ifndef PTRDIFF_MAX # define PTRDIFF_MAX stdint_intptr_glue3(INT,stdint_intptr_bits,_MAX) # endif # ifndef PTRDIFF_MIN # define PTRDIFF_MIN stdint_intptr_glue3(INT,stdint_intptr_bits,_MIN) # endif # ifndef UINTPTR_MAX # define UINTPTR_MAX stdint_intptr_glue3(UINT,stdint_intptr_bits,_MAX) # endif # ifndef INTPTR_MAX # define INTPTR_MAX stdint_intptr_glue3(INT,stdint_intptr_bits,_MAX) # endif # ifndef INTPTR_MIN # define INTPTR_MIN stdint_intptr_glue3(INT,stdint_intptr_bits,_MIN) # endif # ifndef INTPTR_C # define INTPTR_C(x) stdint_intptr_glue3(INT,stdint_intptr_bits,_C)(x) # endif # ifndef UINTPTR_C # define UINTPTR_C(x) stdint_intptr_glue3(UINT,stdint_intptr_bits,_C)(x) # endif typedef stdint_intptr_glue3(uint,stdint_intptr_bits,_t) uintptr_t; typedef stdint_intptr_glue3( int,stdint_intptr_bits,_t) intptr_t; # else /* TODO -- This following is likely wrong for some platforms, and does nothing for the definition of uintptr_t. */ typedef ptrdiff_t intptr_t; # endif # define STDINT_H_UINTPTR_T_DEFINED #endif /* * Assumes sig_atomic_t is signed and we have a 2s complement machine. */ #ifndef SIG_ATOMIC_MAX # define SIG_ATOMIC_MAX ((((sig_atomic_t) 1) << (sizeof (sig_atomic_t)*CHAR_BIT-1)) - 1) #endif #endif #if defined (__TEST_PSTDINT_FOR_CORRECTNESS) /* * Please compile with the maximum warning settings to make sure macros are not * defined more than once. */ #include #include #include #define glue3_aux(x,y,z) x ## y ## z #define glue3(x,y,z) glue3_aux(x,y,z) #define DECLU(bits) glue3(uint,bits,_t) glue3(u,bits,=) glue3(UINT,bits,_C) (0); #define DECLI(bits) glue3(int,bits,_t) glue3(i,bits,=) glue3(INT,bits,_C) (0); #define DECL(us,bits) glue3(DECL,us,) (bits) #define TESTUMAX(bits) glue3(u,bits,=) glue3(~,u,bits); if (glue3(UINT,bits,_MAX) glue3(!=,u,bits)) printf ("Something wrong with UINT%d_MAX\n", bits) int main () { DECL(I,8) DECL(U,8) DECL(I,16) DECL(U,16) DECL(I,32) DECL(U,32) #ifdef INT64_MAX DECL(I,64) DECL(U,64) #endif intmax_t imax = INTMAX_C(0); uintmax_t umax = UINTMAX_C(0); char str0[256], str1[256]; sprintf (str0, "%d %x\n", 0, ~0); sprintf (str1, "%d %x\n", i8, ~0); if (0 != strcmp (str0, str1)) printf ("Something wrong with i8 : %s\n", str1); sprintf (str1, "%u %x\n", u8, ~0); if (0 != strcmp (str0, str1)) printf ("Something wrong with u8 : %s\n", str1); sprintf (str1, "%d %x\n", i16, ~0); if (0 != strcmp (str0, str1)) printf ("Something wrong with i16 : %s\n", str1); sprintf (str1, "%u %x\n", u16, ~0); if (0 != strcmp (str0, str1)) printf ("Something wrong with u16 : %s\n", str1); sprintf (str1, "%" PRINTF_INT32_MODIFIER "d %x\n", i32, ~0); if (0 != strcmp (str0, str1)) printf ("Something wrong with i32 : %s\n", str1); sprintf (str1, "%" PRINTF_INT32_MODIFIER "u %x\n", u32, ~0); if (0 != strcmp (str0, str1)) printf ("Something wrong with u32 : %s\n", str1); #ifdef INT64_MAX sprintf (str1, "%" PRINTF_INT64_MODIFIER "d %x\n", i64, ~0); if (0 != strcmp (str0, str1)) printf ("Something wrong with i64 : %s\n", str1); #endif sprintf (str1, "%" PRINTF_INTMAX_MODIFIER "d %x\n", imax, ~0); if (0 != strcmp (str0, str1)) printf ("Something wrong with imax : %s\n", str1); sprintf (str1, "%" PRINTF_INTMAX_MODIFIER "u %x\n", umax, ~0); if (0 != strcmp (str0, str1)) printf ("Something wrong with umax : %s\n", str1); TESTUMAX(8); TESTUMAX(16); TESTUMAX(32); #ifdef INT64_MAX TESTUMAX(64); #endif return EXIT_SUCCESS; } #endif pysam-0.23.0/win32/unistd.h000066400000000000000000000007671475062545500153750ustar00rootroot00000000000000#ifndef _UNISTD_H #define _UNISTD_H 1 /* This file intended to serve as a drop-in replacement for * * unistd.h on Windows * * Please add functionality as neeeded * */ #include #include #include /* getopt from: http://www.pwilson.net/sample.html. */ #define srandom srand #define random rand /* const W_OK = 2; const R_OK = 4; */ #define access _access #define ftruncate _chsize #define ssize_t int #endif /* unistd.h */